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 composition-based statistics:
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|254780406|ref|YP_003064819.1| putative ribosomal large
subunit pseudouridine synthase B [Candidatus Liberibacter asiaticus
str. psy62]
         (354 letters)

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

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



>gi|254780406|ref|YP_003064819.1| putative ribosomal large subunit pseudouridine synthase B
           [Candidatus Liberibacter asiaticus str. psy62]
 gi|254040083|gb|ACT56879.1| putative ribosomal large subunit pseudouridine synthase B
           [Candidatus Liberibacter asiaticus str. psy62]
          Length = 354

 Score =  260 bits (664), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 354/354 (100%), Positives = 354/354 (100%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI
Sbjct: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG
Sbjct: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD
Sbjct: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI
Sbjct: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK
Sbjct: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK
Sbjct: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354


>gi|220929165|ref|YP_002506074.1| pseudouridine synthase [Clostridium cellulolyticum H10]
 gi|219999493|gb|ACL76094.1| pseudouridine synthase [Clostridium cellulolyticum H10]
          Length = 235

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 82/230 (35%), Positives = 121/230 (52%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R+ K IA AG+ASRR  E MI Q RV VN  +++     V + D + VDG P++  E 
Sbjct: 3   GIRLQKFIAHAGVASRRTAEEMIKQGRVAVNNTVVQDMGFTVSNDDFVTVDGKPVKIEEE 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + HKP+G V+T  D  GR TV D +     R+  VGRLD +T GL+LLTNDG    
Sbjct: 63  KVYIMLHKPVGYVSTSQDQFGRPTVVDLVKDAGKRLYPVGRLDYDTSGLILLTNDGDFTY 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  +VY     G  +++++   + G+ I+       +  +  ++G N  V + 
Sbjct: 123 RLTHPKHEINKVYEAVISGFPEKNEIKSFESGLKIENYQTSPAEFVVLEKQGINTLVRIT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGKNR+++K+ E    KV  L RI  GP  L  L  G  R +S + L+
Sbjct: 183 IHEGKNRQVRKMCEAIGHKVLTLKRIQIGPIALDNLPVGKWRHLSLRELK 232


>gi|260574583|ref|ZP_05842586.1| RNA-binding S4 domain protein [Rhodobacter sp. SW2]
 gi|259023000|gb|EEW26293.1| RNA-binding S4 domain protein [Rhodobacter sp. SW2]
          Length = 358

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 141/341 (41%), Positives = 187/341 (54%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++KV++RAGIASRRE ERMI   +V VNG ++   A+NV + D I VDG P+   
Sbjct: 15  PEGDRIAKVLSRAGIASRREAERMIELGQVAVNGKVITSPALNVTAKDRITVDGKPVAAP 74

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E  RLWLY+KP GLVT+ +D  GR T++D +P    RV++VGRLD+N+EGLLLLTNDG L
Sbjct: 75  EPARLWLYYKPEGLVTSDNDEKGRETIYDQMPEDLPRVMAVGRLDLNSEGLLLLTNDGEL 134

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            R LELPST WLR YRVR  G      L  L+ GI ++G  +  M V +D  +G+NAW+T
Sbjct: 135 KRRLELPSTGWLRKYRVRIKGNPTDPDLEPLRAGITVEGERFQPMLVVIDRIQGANAWLT 194

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           VGLREGKNREI++     N  VNRLIRISYGPF+LG L  G   EV  K+LR+QLG    
Sbjct: 195 VGLREGKNREIRRAMFALNLTVNRLIRISYGPFRLGDLQPGEVAEVRGKVLRDQLGFDPR 254

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
            E +    +   + +          +          K S      + +  +A     +  
Sbjct: 255 AEDEELSTSGKPAPKKPATRTLAPRTPAKPGAKPGAKPSRGVAKPAAEAPVARAKPVKPG 314

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                   G  S     +  R E  + +P  P +R      
Sbjct: 315 PGWAKAQPGGKSGPGPKATSRNEGAKPAPRSPGRRPPAGPR 355


>gi|326202112|ref|ZP_08191982.1| pseudouridine synthase [Clostridium papyrosolvens DSM 2782]
 gi|325987907|gb|EGD48733.1| pseudouridine synthase [Clostridium papyrosolvens DSM 2782]
          Length = 235

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 81/229 (35%), Positives = 118/229 (51%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A AG+ASRR+ E MI Q RV VN +++E     V   D + VDG P+   E  
Sbjct: 4   IRLQKYLAHAGVASRRKAEEMIKQGRVAVNNVIIENMGATVTCNDVVTVDGKPVTTEEAK 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP+G V+T  D  GR  V D +     R+  VGRLD +T GL+LLTNDG     
Sbjct: 64  VYIMLNKPVGYVSTSKDQFGRPAVIDLVKDAGKRLYPVGRLDYDTSGLILLTNDGDFTYR 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  +VY     G  D++++   + G+ I        +  +  +KG N  V + +
Sbjct: 124 LTHPKHEVNKVYEAVISGFPDKNEITRFETGLKIDDYQTSPAEFEVLNKKGINTLVRITI 183

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EGKNR+++K+ E    KV  L RI  GP  L  L  G  R +S   ++
Sbjct: 184 HEGKNRQVRKMCEAIGHKVLTLKRIQIGPIALENLPEGKWRHLSDNEVK 232


>gi|163867551|ref|YP_001608750.1| ribosomal large subunit pseudouridine synthase B [Bartonella
           tribocorum CIP 105476]
 gi|161017197|emb|CAK00755.1| ribosomal large subunit pseudouridine synthase B [Bartonella
           tribocorum CIP 105476]
          Length = 466

 Score =  216 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 164/377 (43%), Positives = 217/377 (57%), Gaps = 29/377 (7%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + EN   +R++K +ARAG+ASRR+ E MI   RV VNG ++   A NV  +D I+VDG P
Sbjct: 1   MNENNESERIAKRLARAGVASRRDAEMMIVAGRVSVNGTVVTTPAFNVSRSDVIKVDGKP 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L   ERTRLWLYHKP GLVTT+ DP+GR TVF +LP    RV+SVGRLDINTEGLLLLTN
Sbjct: 61  LSPIERTRLWLYHKPAGLVTTNRDPEGRPTVFSHLPKGMPRVVSVGRLDINTEGLLLLTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGGLARVLELP T W+R YRVR HG+V Q  L+ LK GI I GI YG ++ +++ ++G+N
Sbjct: 121 DGGLARVLELPVTGWVRKYRVRAHGRVKQSALDNLKNGIAINGIFYGSIEASIEREQGAN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            W+++ LREGKNREIK V       VNRLIR+SYGPF L  L  G+ +E+  ++LR+QLG
Sbjct: 181 IWLSIALREGKNREIKNVLGALGLSVNRLIRVSYGPFHLSDLKEGAVQELKGRMLRDQLG 240

Query: 247 PHLLEEAQVNLDAPIYSS------------------------ETLVRDRPNIISEVPDDF 282
             L+ +A  + DAPI                            +  R      ++   + 
Sbjct: 241 ERLIMQANADFDAPILKPFSNSPVIAEKQSQKDVSVANDGWVFSSERVIRRRSNDGSVEH 300

Query: 283 TRMKKNSSQKNGLSKQKKLATPVHR---RNLASNVWMAKGIHSSFLSDSGQ--REENHRR 337
            R +  +     ++K K       R   R+  +NVWMA G              E++H  
Sbjct: 301 DRARLRAKSHENMNKGKSEEGKAERFLPRSRRANVWMAPGARPQSARRKPSYNEEKSHDH 360

Query: 338 SPSFPSKRSLRRTSAKK 354
                 K+S  R   K+
Sbjct: 361 KGDTADKKSFYRGKEKR 377


>gi|49473909|ref|YP_031951.1| hypothetical protein BQ02470 [Bartonella quintana str. Toulouse]
 gi|49239412|emb|CAF25750.1| hypothetical protein BQ02470 [Bartonella quintana str. Toulouse]
          Length = 467

 Score =  215 bits (548), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 173/377 (45%), Positives = 216/377 (57%), Gaps = 30/377 (7%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + EN   +R++K +ARAGIASRR+ E MI   R+ +N  ++   A NV  +D I+VDG P
Sbjct: 1   MNENSKGERIAKRLARAGIASRRDAEMMIIAGRIVINDTVVTTPAFNVTRSDVIKVDGKP 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L   ERTRLWLYHKP GLVTTH DP+GR TVF+NLP    RV+SVGRLDINTEGLLLLTN
Sbjct: 61  LSPIERTRLWLYHKPAGLVTTHRDPEGRPTVFNNLPKGMPRVLSVGRLDINTEGLLLLTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGGLARVLELP T W+R YRVR HG+V Q  L+ LK GI I+GI YG ++ +++ ++GSN
Sbjct: 121 DGGLARVLELPLTGWVRKYRVRAHGRVKQSALDNLKNGIAIEGIFYGSIEASIEREQGSN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            W++V LREGKNREIK V       VNRLIR+SYGPFQL  L  G+ RE+  ++LR+QLG
Sbjct: 181 IWLSVALREGKNREIKNVLGALGLSVNRLIRVSYGPFQLSDLEEGAVRELKGRMLRDQLG 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNI----------------------ISEVPDDFTR 284
             L+ +A  N DAPI  S +                                       R
Sbjct: 241 ERLIMQANANFDAPILKSFSNSVVVAEKQNHKDLAITNDGWIFSSIGDVQRRRRGGFSER 300

Query: 285 MKKNSSQKNGL---SKQKKLATPVHR---RNLASNVWMAKGIHSSFLSDSG--QREENHR 336
            +   S K G     ++K       R   R+  SNVWMA G              +  H 
Sbjct: 301 SRARLSTKPGEKFMRQEKSEGGKAERFLPRSRRSNVWMAPGARPQSTRKKSFYSEDTPHD 360

Query: 337 RSPSFPSKRSLRRTSAK 353
              +   KRSL R   K
Sbjct: 361 YKSNLAGKRSLHRGKEK 377


>gi|240849922|ref|YP_002971311.1| ribosomal large subunit pseudouridine synthase B [Bartonella
           grahamii as4aup]
 gi|240267045|gb|ACS50633.1| ribosomal large subunit pseudouridine synthase B [Bartonella
           grahamii as4aup]
          Length = 466

 Score =  214 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 164/376 (43%), Positives = 217/376 (57%), Gaps = 29/376 (7%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + EN   +R++K +ARAG+ASRR+ E MI   R+ VNG ++   A NV  +D I+VDG P
Sbjct: 1   MNENNESERIAKRLARAGVASRRDAEMMIVAGRISVNGTVVTTPAFNVSRSDVIKVDGKP 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L   ERTRLWLYHKP GLVTT+ DP+GR TVF NLP    RV+SVGRLDINTEGLLLLTN
Sbjct: 61  LPPIERTRLWLYHKPAGLVTTNRDPEGRPTVFSNLPKGMPRVLSVGRLDINTEGLLLLTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGGLARVLELP T W+R YRVR HG+V +  L+ LK GI I GI YG ++ +++ ++GSN
Sbjct: 121 DGGLARVLELPVTGWVRKYRVRAHGRVKKSALDNLKNGIAINGIFYGSIEASIEREQGSN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            W++V LREGKNREIK V       VNRLIR+SYGPF L  L  G+ +E+  ++LR+QLG
Sbjct: 181 IWLSVALREGKNREIKNVLGALGLSVNRLIRVSYGPFHLSDLEEGAVQELKGRMLRDQLG 240

Query: 247 PHLLEEAQVNLDAPIYSS------------------------ETLVRDRPNIISEVPDDF 282
             L+ +A  + DAPI                            +  R       +   + 
Sbjct: 241 ERLIMQANADFDAPILKPFSNSAVVAEKQSQKDLSVANDGWVFSSERAIRRRPRDGSVEH 300

Query: 283 TRMKKNSSQKNGLSKQKKLATPVHR---RNLASNVWMAKGIHSSFLSDSG--QREENHRR 337
           +R + ++     + K+K       R   R+  +NVWMA G              E++H  
Sbjct: 301 SRARLSTKSHENVKKEKSEEGKAERFLPRSRRANVWMAPGARPQSTRRKPSYSEEKSHDH 360

Query: 338 SPSFPSKRSLRRTSAK 353
                 ++S  R   K
Sbjct: 361 KSDLDGRKSFHRGKEK 376


>gi|125973211|ref|YP_001037121.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           thermocellum ATCC 27405]
 gi|256003686|ref|ZP_05428674.1| pseudouridine synthase [Clostridium thermocellum DSM 2360]
 gi|281417410|ref|ZP_06248430.1| pseudouridine synthase [Clostridium thermocellum JW20]
 gi|125713436|gb|ABN51928.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           thermocellum ATCC 27405]
 gi|255992247|gb|EEU02341.1| pseudouridine synthase [Clostridium thermocellum DSM 2360]
 gi|281408812|gb|EFB39070.1| pseudouridine synthase [Clostridium thermocellum JW20]
 gi|316940559|gb|ADU74593.1| pseudouridine synthase [Clostridium thermocellum DSM 1313]
          Length = 239

 Score =  213 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 82/234 (35%), Positives = 119/234 (50%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R+ K +A  G+ASRR+ E +I+Q RVKVNG  + +    V   D +EVDG  ++  +
Sbjct: 2   KEMRLQKYLAECGVASRRKAEELISQGRVKVNGETVTQMGKKVSQNDVVEVDGKLVKMEK 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R      +KP+G +++  D  GR TV D +  I  R+  VGRLD +T GLLLLTNDG  A
Sbjct: 62  RKVYIALNKPVGYISSVKDQFGRKTVMDLVKDIKERIFPVGRLDYDTSGLLLLTNDGDFA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P  +  +VY     G   +D +   K G+ I           +    G    V +
Sbjct: 122 YRLTHPKHEIKKVYEADLLGVPSKDDIMRFKNGLWIDDYFTSPADFEILKSDGKTTKVRI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EGKNR+++K+       V RL RIS G   LG L  GS R ++++ +   L
Sbjct: 182 TIHEGKNRQVRKMCNKIGCPVIRLKRISIGEVSLGDLKEGSWRNLTEREINSFL 235


>gi|49475072|ref|YP_033113.1| hypothetical protein BH02610 [Bartonella henselae str. Houston-1]
 gi|49237877|emb|CAF27073.1| hypothetical protein BH02610 [Bartonella henselae str. Houston-1]
          Length = 465

 Score =  212 bits (539), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 176/378 (46%), Positives = 218/378 (57%), Gaps = 30/378 (7%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + EN   +R++K +ARAGIASRR+ E MI   R+ VNG ++   A+NV  +D I+VDG P
Sbjct: 1   MNENSESERIAKRLARAGIASRRDAEMMILAGRIVVNGTVVTTPALNVTRSDVIKVDGKP 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L   ERTRLWLYHKP GLVTTH DP+GR TVF NLP    RV+SVGRLDINTEGLLLLTN
Sbjct: 61  LSPIERTRLWLYHKPAGLVTTHRDPEGRPTVFSNLPKEMPRVLSVGRLDINTEGLLLLTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGGLARVLELP T W+R YRVR HG+V Q  L+ LK GI I GI YG ++ +++ ++GSN
Sbjct: 121 DGGLARVLELPLTGWVRKYRVRAHGRVKQSALDNLKNGIAIDGIFYGSIEASIEREQGSN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            W++V LREGKNREIK +       VNRLIRISYGPFQL  L  G+ RE+  ++LR+QLG
Sbjct: 181 IWLSVALREGKNREIKNILGALGLSVNRLIRISYGPFQLSDLEEGAVREIKGRMLRDQLG 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVR-------------DRPNIISEVPDDFTRMKKNSSQKN 293
             L+ +A  + DAPI    +                     IS    D  R ++ SS + 
Sbjct: 241 ERLIMQANADFDAPILKPFSNTAVVAEKRSHKDLTVANDGWISSHGGDLRRRQRKSSAER 300

Query: 294 GL------------SKQKKLATPVHR---RNLASNVWMAKGIHSSFLSDSGQREEN--HR 336
           G              K+K     + R   R+  SNVWMA G             E   H 
Sbjct: 301 GRTRLSTKLDKKFMGKEKSEEGKIERFLPRSRHSNVWMAPGARPQSAHRKSFYSEGIHHA 360

Query: 337 RSPSFPSKRSLRRTSAKK 354
                   RS  R    K
Sbjct: 361 HKSDLSVNRSFHRAKQSK 378


>gi|56697819|ref|YP_168190.1| RNA pseudouridylate synthase family protein [Ruegeria pomeroyi
           DSS-3]
 gi|56679556|gb|AAV96222.1| RNA pseudouridylate synthase family protein [Ruegeria pomeroyi
           DSS-3]
          Length = 387

 Score =  212 bits (539), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 145/349 (41%), Positives = 196/349 (56%), Gaps = 1/349 (0%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +       +R++K+++RAG+ASRRE ERMI   RV VNG +++  A+NV   D + VDG 
Sbjct: 1   MSNTPPPGERIAKILSRAGVASRREAERMIEAGRVAVNGKVIDSPALNVTERDRVTVDGA 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL  AE  RLWLYHKP GLVTT  D  GR T+FD+LP    RV+SVGRLD+N+EGLLLLT
Sbjct: 61  PLADAEPARLWLYHKPSGLVTTARDEKGRKTIFDDLPEDMPRVMSVGRLDLNSEGLLLLT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG + R LELPST WLR YRVR  G    +    L++G+VI+G  +  M V++D Q+G+
Sbjct: 121 NDGAVKRQLELPSTGWLRRYRVRIKGTPKDEDFAPLRQGLVIEGERFQPMIVSIDRQQGA 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           NAW+TVGLREGKNREI++  E   + VNRLIRISYGPFQLGTL  G   EV +++LR+QL
Sbjct: 181 NAWLTVGLREGKNREIRRAIEDIGFIVNRLIRISYGPFQLGTLAPGKVEEVRRRVLRDQL 240

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G    ++      A            P           R    ++ ++  + + +   P 
Sbjct: 241 GLDGEDQPTDERPARPERKRKPGASAPATPRGGTTAKARPGGAAAGRSDAASKPRSGAPA 300

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             R+         G      S    +      + +        R S  +
Sbjct: 301 KSRSGDPAK-QRSGAPPRTRSGDPVKARTDGPARARADGPGKPRGSGPR 348


>gi|77462817|ref|YP_352321.1| pseudouridine synthase [Rhodobacter sphaeroides 2.4.1]
 gi|77387235|gb|ABA78420.1| Pseudouridine synthase, (predicted) [Rhodobacter sphaeroides 2.4.1]
          Length = 508

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 144/347 (41%), Positives = 193/347 (55%), Gaps = 2/347 (0%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + ++   +R++KV++RAGIASRR+ ERMI   R+ VNG  ++  A+NV   D I VDG P
Sbjct: 1   MTDSKDGERIAKVLSRAGIASRRDAERMIELGRIAVNGRTIDSPALNVGPKDRITVDGQP 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L   E  RLWLY+KP GLVT+ SD  GR TVFD+LP    RV+SVGRLD+N+EGLLLLTN
Sbjct: 61  LAPPEPARLWLYYKPEGLVTSASDEKGRETVFDHLPEGMPRVMSVGRLDLNSEGLLLLTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L R LELPST WLR YRVR  G      L  L+KGI ++G  +  M V+LD  +G+N
Sbjct: 121 DGELKRRLELPSTGWLRKYRVRVKGNPTDADLEPLRKGITVEGESFQPMTVSLDRVQGAN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           AW+TVGLREGKNREI++        VNRLIR+SYGPF+L  L  G   EV  KILR+QLG
Sbjct: 181 AWLTVGLREGKNREIRRAMSALGLTVNRLIRVSYGPFRLNELEPGMVEEVRPKILRDQLG 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                + +                R    +             ++  G ++ ++ A P  
Sbjct: 241 LDPHADGEARPARGRKPEGAARPARSEGAAR--PARAEGGARPARAEGAARSERTARPPR 298

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                      +G  S   +   +    H  +    + +   R++ K
Sbjct: 299 GAAAEGPARAGRGAGSEGAAGPAKGRSPHGAARRAGAPKDSARSAGK 345


>gi|319408053|emb|CBI81707.1| Pseudouridine synthase [Bartonella schoenbuchensis R1]
          Length = 486

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 165/375 (44%), Positives = 219/375 (58%), Gaps = 23/375 (6%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           ++K  + EN   +R++K +ARAG+ASRR+ E MI   RV VNG ++     NVM +D I 
Sbjct: 29  QNKKKIDENSESERIAKRLARAGVASRRDAEMMIIAGRVVVNGAVVTTPVFNVMRSDVIT 88

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +DG  L   ERTRLWLYHKP G VTT+ DP+GR TVFDNLP    RV+SVGRLDINTEGL
Sbjct: 89  IDGKSLPPMERTRLWLYHKPAGFVTTNRDPEGRPTVFDNLPKEMPRVLSVGRLDINTEGL 148

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDGGLAR+LELP T W+R YRVR HG++ Q KL+ LK GI I+G+ YG ++ +++ 
Sbjct: 149 LLLTNDGGLARILELPITGWVRKYRVRAHGKIKQSKLDSLKNGIAIKGVFYGSIEASIER 208

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++G+N W++V LREGKNREIK V       VNRLIRISYGPFQL  L  G+ RE+  ++L
Sbjct: 209 EQGANIWLSVALREGKNREIKNVLGALGLSVNRLIRISYGPFQLADLDKGAVRELKGRVL 268

Query: 242 REQLGPHLLEEAQVNLD-----APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           R+QLG  L+ +A  + D         S  ++ +     +    DD    + N ++    S
Sbjct: 269 RDQLGERLIAQANADFDSPILKPFSNSVVSVKKQNSKKLFVAGDDEVVSRVNGTRHEKQS 328

Query: 297 K--QKKLATPVHR--------------RNLASNVWMAKGIHSSFLSDS--GQREENHRRS 338
              + + A    +              R+  SNVWMA G                 H RS
Sbjct: 329 GFCEGRRARLNTKSDEQSMGKTKNLSLRSRHSNVWMAPGARPQVERKKFCYNEGSYHNRS 388

Query: 339 PSFPSKRSLRRTSAK 353
             +  K+   R   K
Sbjct: 389 SDYVGKKFSGREKEK 403


>gi|259416443|ref|ZP_05740363.1| pseudouridine synthase, Rsu [Silicibacter sp. TrichCH4B]
 gi|259347882|gb|EEW59659.1| pseudouridine synthase, Rsu [Silicibacter sp. TrichCH4B]
          Length = 410

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 144/346 (41%), Positives = 196/346 (56%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
            +    R++KV++RAG+ASRRE ERMI + RV VNG +++  A+NV  +D I VDG PL 
Sbjct: 57  PSAEGDRIAKVLSRAGVASRREAERMITEGRVAVNGAVIDSPALNVTGSDRIVVDGTPLP 116

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           +AE  RLWLY+KP GLVTT+SD  GR T+FD LP    RV++VGRLD+N+EGLLLLTNDG
Sbjct: 117 EAEAPRLWLYYKPTGLVTTNSDEKGRRTIFDELPEDLPRVMTVGRLDLNSEGLLLLTNDG 176

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           G+ R LELPST WLR YRVR +G+    + ++L+KG+VI G  +  M V LD Q+G+NAW
Sbjct: 177 GVKRQLELPSTGWLRRYRVRINGRPQDHEFDVLRKGVVIDGERFQPMTVNLDRQQGANAW 236

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +T+GLREGKNREI++  E   + VNRL+RISYGPFQLGTL  G   E+  +++R+QLG  
Sbjct: 237 LTIGLREGKNREIRRAMEEVGYPVNRLLRISYGPFQLGTLKEGEVEELRPRVVRDQLGLA 296

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
             E        P               ++         K  S   G  K           
Sbjct: 297 APEGDGEAKKKPTRPGRGPRNPGGTPGAQPTGKGGSAPKGRSIGKGAGKGSGKPFEGKTF 356

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +  ++         S     G +  +   +         +     +
Sbjct: 357 SGKASAGKPGAGKPSGTKSFGSKPASGAGARKTGGPSGGKSAPGAR 402


>gi|260767790|ref|ZP_05876725.1| ribosomal large subunit pseudouridine synthase F [Vibrio furnissii
           CIP 102972]
 gi|260617299|gb|EEX42483.1| ribosomal large subunit pseudouridine synthase F [Vibrio furnissii
           CIP 102972]
          Length = 347

 Score =  208 bits (530), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 70/344 (20%), Positives = 131/344 (38%), Gaps = 10/344 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
              T +R++K I+  G  SRRE +++I Q RV +NG L       V   D + +D  PLR
Sbjct: 2   STPTEKRLNKYISETGFCSRREADKLIEQGRVTINGQLP-EMGTKVSDDDEVCIDDKPLR 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             E+      +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG
Sbjct: 61  SKEKPVYIALNKPTGITCTTERDV--PGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y VR    +  D +  +  G+ I        +VT    + +   
Sbjct: 119 DIVNKILRAGNNHEKEYVVRVDKAITADFIKQMSSGVRILDTVTLPCKVT----QETKFS 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E   ++V +L R+      L  +  G  R +++  + E L   
Sbjct: 175 FRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLTEAEVAEILAMC 234

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNI--ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                           + + +        S   +  ++ ++N     G +  +    P  
Sbjct: 235 EASSGTEEASRVDSQGQRIRKATDAKLFDSREENQPSKARRNPKTFRGHNADEFRHAPNS 294

Query: 307 RRN-LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           ++    S    +    +           +H   P+   K +  R
Sbjct: 295 KKGKTRSERPDSSRADNRADRKPKSTGFHHSGKPASAGKPAAAR 338


>gi|315179378|gb|ADT86292.1| pseudouridine synthase family 1 protein [Vibrio furnissii NCTC
           11218]
          Length = 347

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 70/344 (20%), Positives = 131/344 (38%), Gaps = 10/344 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
              T +R++K I+  G  SRRE +++I Q RV +NG L       V   D + +D  PLR
Sbjct: 2   STPTEKRLNKYISETGFCSRREADKLIEQGRVTINGQLP-EMGTKVSDDDEVCIDDKPLR 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             E+      +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG
Sbjct: 61  SKEKPVYIALNKPTGITCTTERDV--PGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y VR    +  D +  +  G+ I        +VT    + +   
Sbjct: 119 DIVNKILRAGNNHEKEYVVRVDKAITADFIKQMSSGVRILDTVTLPCKVT----QETKFS 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E   ++V +L R+      L  +  G  R +++  + E L   
Sbjct: 175 FRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLTEAEVAEILAMC 234

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNI--ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                           + + +        S   +  ++ ++N     G +  +    P  
Sbjct: 235 EASSGTEEASRVDSQGQRIRKATDAKLFDSREENQPSKARRNPKTFRGHNADEFRHAPNS 294

Query: 307 RRN-LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           ++    S    +    +           +H   P+   K +  R
Sbjct: 295 KKGKTRSERPDSSRADNRTDRKPKSTGFHHSGKPASAGKPAAAR 338


>gi|221638684|ref|YP_002524946.1| Pseudouridine synthase [Rhodobacter sphaeroides KD131]
 gi|221159465|gb|ACM00445.1| Pseudouridine synthase [Rhodobacter sphaeroides KD131]
          Length = 491

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 141/349 (40%), Positives = 186/349 (53%), Gaps = 1/349 (0%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + ++   +R++KV++RAGIASRR+ ERMI   R+ VNG  ++  A+NV   D I VDG P
Sbjct: 1   MTDSKDGERIAKVLSRAGIASRRDAERMIELGRIAVNGRTIDSPALNVGPKDRITVDGQP 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L   E  RLWLY+KP GLVT+ SD  GR TVFD+LP    RV+SVGRLD+N+EGLLLLTN
Sbjct: 61  LAPPEPARLWLYYKPEGLVTSASDEKGRETVFDHLPEGMPRVMSVGRLDLNSEGLLLLTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L R LELPST WLR YRVR  G      L  L+KGI ++G  +  M V+LD  +G+N
Sbjct: 121 DGELKRRLELPSTGWLRKYRVRVKGNPTDADLEPLRKGITVEGESFQPMTVSLDRVQGAN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           AW+TVGLREGKNREI++        VNRLIR+SYGPF+L  L  G   EV  KILR+QLG
Sbjct: 181 AWLTVGLREGKNREIRRAMSALGLTVNRLIRVSYGPFRLNELEPGMVEEVRPKILRDQLG 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS-KQKKLATPV 305
                + +                R    +         +     ++      +    P 
Sbjct: 241 LDPHADGEARPAKGRKPEGAARPARSESAARRARAEGGARSEKPARSPRGAAAEGPTRPA 300

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                  +    +G      +      ++  R          R   A +
Sbjct: 301 RGAGSEGSAGATRGRSPQGAAPKAGAPKDGARFAGKGPAEGARPARASR 349


>gi|163745924|ref|ZP_02153283.1| RNA pseudouridylate synthase family protein, putative [Oceanibulbus
           indolifex HEL-45]
 gi|161380669|gb|EDQ05079.1| RNA pseudouridylate synthase family protein, putative [Oceanibulbus
           indolifex HEL-45]
          Length = 354

 Score =  208 bits (528), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 138/340 (40%), Positives = 186/340 (54%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           ++ +         R++KV++RAG+ASRRE ERMI   RV+VNG  ++  A+NV   D I 
Sbjct: 13  QNTDTDASTSKGDRIAKVLSRAGVASRREAERMIEAGRVRVNGEQIDSPALNVTPEDKIT 72

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           VD  P+   E  R+WLYHKP GLVTT  D  GR T+FD+LP    RV+++GRLD+N+EGL
Sbjct: 73  VDNTPVGAPEPPRMWLYHKPAGLVTTARDEKGRETIFDDLPEDMPRVMTIGRLDLNSEGL 132

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDGG+ R LELPST WLR YR R +G+   + L  L++GI ++G  +  M VTLD 
Sbjct: 133 LLLTNDGGVKRKLELPSTGWLRRYRARVNGRPTDEMLEPLRRGITVEGENFLPMDVTLDR 192

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           Q+G+NAW+T+GLREG+NREI++  E     VNRLIR SYGPFQLG L  G   E+ +KI+
Sbjct: 193 QQGANAWLTIGLREGRNREIRRAMEAVGLTVNRLIRTSYGPFQLGELKTGEVEELRRKIV 252

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+QLG  L +     +  P        R                +    +        K 
Sbjct: 253 RDQLGLELEDPTGTAVKKPTAVRRPPRRKPGGFGGAGQPGMPVQRGEDDEPPPRRGGGKA 312

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF 341
                 +  A       G      +      +   R P  
Sbjct: 313 KNAPRGKAAAGRTADKPGARPGSRTGGKPAGKPGSRGPKP 352


>gi|303242311|ref|ZP_07328797.1| pseudouridine synthase [Acetivibrio cellulolyticus CD2]
 gi|302590150|gb|EFL59912.1| pseudouridine synthase [Acetivibrio cellulolyticus CD2]
          Length = 237

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 80/230 (34%), Positives = 122/230 (53%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R+ K IA  G+ASRR+ E +I Q  VKVNGI++    + V S+D +EV+G  ++   
Sbjct: 2   EMTRLQKYIADCGVASRRKAEELIQQGSVKVNGIVVSEMGIKVSSSDRVEVNGSVIKPES 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +    L +KP G VTT  D   R TV D L  +  RV  VGRLD  T GLL+LTNDG   
Sbjct: 62  KKVYILLNKPSGYVTTVKDQFRRPTVIDLLKGVDERVFPVGRLDYETTGLLVLTNDGDFT 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P  +  + Y+    G   +D+++  + G+ I+       ++ + + K     + V
Sbjct: 122 HKMTHPRHEIEKTYQATIAGTPTKDEIHSFESGLEIEDYVTSPAKLKIISTKERTCVIEV 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + EG+NR+++K+ E     V  L RIS G   LG L  GS RE+++  +
Sbjct: 182 TIHEGRNRQVRKMCEAIGHPVLALKRISLGKVTLGNLPEGSWRELTRDEV 231


>gi|126732069|ref|ZP_01747871.1| RNA pseudouridylate synthase family protein [Sagittula stellata
           E-37]
 gi|126707358|gb|EBA06422.1| RNA pseudouridylate synthase family protein [Sagittula stellata
           E-37]
          Length = 341

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 149/342 (43%), Positives = 186/342 (54%), Gaps = 3/342 (0%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +  +     R++KVIARAG ASRRE ERMIA+ RV VNG +++  A+NV   D I VD  
Sbjct: 1   MDNKTPPGDRIAKVIARAGRASRREAERMIAEGRVAVNGTVIDSPALNVTDKDRITVDDT 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL   E  RLWLYHK  GLVTT  D  GR T++D+LP    RV+SVGRLD+N+EGLLLLT
Sbjct: 61  PLDGPEEARLWLYHKSTGLVTTTKDEQGRPTIYDDLPDDLPRVMSVGRLDLNSEGLLLLT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDGGL R LELPST WLR YRVR +G+     L  L+ G+ + G  +  M V+LD Q+G+
Sbjct: 121 NDGGLKRRLELPSTGWLRRYRVRINGRPTDPMLQPLRDGLTVDGQTFQPMIVSLDRQQGA 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           NAW+TVGLREGKNREI++        VNRLIRISYGPFQLG +  G  +EV +KILR+QL
Sbjct: 181 NAWLTVGLREGKNREIRRAMADLGLSVNRLIRISYGPFQLGQMKPGEVQEVRRKILRDQL 240

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ--KNGLSKQKKLAT 303
           G  L  E +              + R    S  P                   K      
Sbjct: 241 GLGLDAEPEAEAKPKPGLQPRTRKSRAAPTSAKPVPARSGAGGGKSVTGGPARKSTSPGA 300

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
               ++       A          +  R       PS P + 
Sbjct: 301 KPAGKSGPKPGGRAGPAKGKPTRSAPSRP-GAGHGPSKPRRG 341


>gi|257877013|ref|ZP_05656666.1| pseudouridine synthase [Enterococcus casseliflavus EC20]
 gi|257811179|gb|EEV39999.1| pseudouridine synthase [Enterococcus casseliflavus EC20]
          Length = 257

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 63/247 (25%), Positives = 107/247 (43%), Gaps = 4/247 (1%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDG 64
           ++ E   P R+ K +A  G  SR+EV+++I +  V VNG +++     V  T D +  +G
Sbjct: 11  VLYERKKPMRLDKFLADMGYGSRKEVKQLIKKGLVTVNGQVIKSDKAQVQETQDTVCFEG 70

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P+    +    L      +  T    +       +  +    +  VGRLD +TEG LL+
Sbjct: 71  EPIAYQSQFYYLLNKPAGVISATVDSYEETVLDLFSEEAFREDLFPVGRLDKDTEGFLLI 130

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDGGLA  L  P     + Y  +  G +  +   +  KGI + G      ++ +     
Sbjct: 131 TNDGGLAHQLLSPKKHVEKEYYAQVEGIMTAEDQKIFAKGIKLDGEWTLPAELQILNVDE 190

Query: 185 S--NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
               + + + L EGK  ++K++      +V  L RI  G   L   L  G  RE++ + L
Sbjct: 191 DEMRSEIKLILHEGKFHQVKRMVHAVGKEVVYLKRIRMGGLSLPDDLALGEYRELTSEEL 250

Query: 242 REQLGPH 248
            +     
Sbjct: 251 AKLQERR 257


>gi|260776566|ref|ZP_05885461.1| ribosomal large subunit pseudouridine synthase F [Vibrio
           coralliilyticus ATCC BAA-450]
 gi|260607789|gb|EEX34054.1| ribosomal large subunit pseudouridine synthase F [Vibrio
           coralliilyticus ATCC BAA-450]
          Length = 344

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 67/345 (19%), Positives = 120/345 (34%), Gaps = 12/345 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +R++K I+  G  SRRE +R+I Q RV +NG +       V+  D + VD  P+  
Sbjct: 2   SQDAKRLNKFISETGFCSRREADRLIEQGRVTINGKVP-EMGTKVLPGDDVCVDDKPISA 60

Query: 70  AERT-RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                     +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG
Sbjct: 61  VTDKPVYIALNKPTGITCTTERDI--PGNIVDFIGHKKRIFPIGRLDKPSDGLIFLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y VR    + +  +  +  G+ I        +V     K +   
Sbjct: 119 DIVNKILRAGNNHEKEYVVRVDKPITEQFIKKMSSGVDILDTTTLPCKV----SKETKFS 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L   
Sbjct: 175 FRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGQWRYLSDDEIGEILAMC 234

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
                  +        +   R+          D     + S  +    ++          
Sbjct: 235 ESSSGTEDASK----VDARGRNIRKATDAKLFDSREENQESKARRNQKQRTFKGKNAEEF 290

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             A N    +G  S   S     +      P             +
Sbjct: 291 RHAPNSKKGRGGKSDSKSKPSTNKGKSVYKPKSDKPAQRPSNKPR 335


>gi|325568269|ref|ZP_08144636.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           casseliflavus ATCC 12755]
 gi|325158038|gb|EGC70191.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           casseliflavus ATCC 12755]
          Length = 250

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 63/240 (26%), Positives = 108/240 (45%), Gaps = 4/240 (1%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDG 64
           ++ E   P R+ K +A  G  SR+EV+++I +  V VNG +++     V+ T D +  +G
Sbjct: 4   VLYERKKPMRLDKFLADMGYGSRKEVKQLIKKGLVTVNGQVIKSDKAQVLETQDTVCFEG 63

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P+    +    L      +  T    +       +  +    +  VGRLD +TEG LL+
Sbjct: 64  EPIVYQSQFYYLLNKPAGVISATVDSYEETVLDLFSEEAFREDLFPVGRLDKDTEGFLLI 123

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--Q 182
           TNDGGLA  L  P     + Y  +  G +  +      KGI + G      ++ +    +
Sbjct: 124 TNDGGLAHQLLSPKKHVEKEYYAQVEGIMTAEDQKTFAKGIKLDGEWTLPAELQILNVDE 183

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
             + + + + L EGK  ++K++      +V  L RI  G   L   L  G  RE++ + L
Sbjct: 184 DETRSEIKLILHEGKFHQVKRMVHAVGKEVVYLKRIRMGGLSLPDDLALGEYRELTPEEL 243


>gi|307320038|ref|ZP_07599459.1| RNA-binding S4 domain protein [Sinorhizobium meliloti AK83]
 gi|306894253|gb|EFN25018.1| RNA-binding S4 domain protein [Sinorhizobium meliloti AK83]
          Length = 573

 Score =  207 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 179/372 (48%), Positives = 233/372 (62%), Gaps = 28/372 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             PQR+SK+++RAG+ASRR+VERMI + RV +NG++L+   VN    D IEVDG P+R  
Sbjct: 44  DEPQRISKILSRAGVASRRDVERMIMEGRVSLNGVVLDTPVVNATLADRIEVDGHPIRGI 103

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ERTRLWLYHKP GLVTT++DP+GR TVF+NLP    RV+SVGRLDINTEGLLLLTNDGGL
Sbjct: 104 ERTRLWLYHKPGGLVTTNADPEGRPTVFENLPEELPRVLSVGRLDINTEGLLLLTNDGGL 163

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           ARVLELPST WLR YRVR HG++DQ+ L+ LK+GI + G+ YG ++ TLD  +GSN W+T
Sbjct: 164 ARVLELPSTGWLRRYRVRAHGEIDQEALDRLKEGIAVDGVLYGAIEATLDRVQGSNVWIT 223

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           +GLREGKNREIK V       VNRLIRISYGPFQLG L  G  +E+  + LREQLGP L+
Sbjct: 224 MGLREGKNREIKNVLGALGLDVNRLIRISYGPFQLGELPIGQVQEIRGRTLREQLGPRLI 283

Query: 251 EEAQVNLDAP-----------------------IYSSETLVRDRPNIISEVPDDFTRMKK 287
            +++ N DAP                           E     R   ++ +       + 
Sbjct: 284 ADSKANFDAPIYNDQPAAAEPEAEPADHDKAEWGSKREKAEDKRERALARLDTRRDDGRP 343

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR-----EENHRRSPSFP 342
           +   ++    +++ A P  RRN +SNVWMA G   +              +  RR+P+  
Sbjct: 344 SERGRSRGKPEERPARPPVRRNRSSNVWMAPGARPTVEKKPKAAEDDLSPKGARRAPAEG 403

Query: 343 SKRSLRRTSAKK 354
            +R   + +A K
Sbjct: 404 KRRDRPKDAAAK 415



 Score = 37.5 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 18/131 (13%), Positives = 27/131 (20%), Gaps = 12/131 (9%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           E   K   + L P     A           +   +                 +  +   G
Sbjct: 381 EKKPKAAEDDLSPKGARRAPAEGKRRDRPKDAAAKAGGFDAERQGKAGKSAGRKDAAGAG 440

Query: 295 LSKQKKL------------ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
             ++++               P  R N    V  A    SS       R        SF 
Sbjct: 441 GFERRRPLESAERKSRDHGDRPPRRPNGERAVRPADDRTSSEGRKESARPPRGDGKKSFA 500

Query: 343 SKRSLRRTSAK 353
             R       K
Sbjct: 501 GDRPRASAGGK 511


>gi|15964554|ref|NP_384907.1| hypothetical protein SMc00904 [Sinorhizobium meliloti 1021]
 gi|307314744|ref|ZP_07594340.1| RNA-binding S4 domain protein [Sinorhizobium meliloti BL225C]
 gi|15073732|emb|CAC45373.1| Hypothetical protein SMc00904 [Sinorhizobium meliloti 1021]
 gi|306898968|gb|EFN29614.1| RNA-binding S4 domain protein [Sinorhizobium meliloti BL225C]
          Length = 573

 Score =  207 bits (526), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 179/372 (48%), Positives = 233/372 (62%), Gaps = 28/372 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             PQR+SK+++RAG+ASRR+VERMI + RV +NG++L+   VN    D IEVDG P+R  
Sbjct: 44  DEPQRISKILSRAGVASRRDVERMIMEGRVSLNGVVLDTPVVNATLADRIEVDGHPIRGI 103

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ERTRLWLYHKP GLVTT++DP+GR TVF+NLP    RV+SVGRLDINTEGLLLLTNDGGL
Sbjct: 104 ERTRLWLYHKPGGLVTTNADPEGRPTVFENLPEELPRVLSVGRLDINTEGLLLLTNDGGL 163

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           ARVLELPST WLR YRVR HG++DQ+ L+ LK+GI + G+ YG ++ TLD  +GSN W+T
Sbjct: 164 ARVLELPSTGWLRRYRVRAHGEIDQEALDRLKEGIAVDGVLYGAIEATLDRVQGSNVWIT 223

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           +GLREGKNREIK V       VNRLIRISYGPFQLG L  G  +E+  + LREQLGP L+
Sbjct: 224 MGLREGKNREIKNVLGALGLDVNRLIRISYGPFQLGELPIGQVQEIRGRTLREQLGPRLI 283

Query: 251 EEAQVNLDAP-----------------------IYSSETLVRDRPNIISEVPDDFTRMKK 287
            +++ N DAP                           E     R   ++ +       + 
Sbjct: 284 ADSKANFDAPIYNDQPAAAEPEAEPADHGKAEWGSKREKAEDKRERALARLDTRRDDGRP 343

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR-----EENHRRSPSFP 342
           +   ++    +++ A P  RRN +SNVWMA G   +              +  RR+P+  
Sbjct: 344 SERGRSRGKPEERPARPPVRRNRSSNVWMAPGARPTVEKKPKAAEDDLSPKGARRAPAEG 403

Query: 343 SKRSLRRTSAKK 354
            +R   + +A K
Sbjct: 404 KRRDRPKDAAAK 415



 Score = 37.5 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 18/131 (13%), Positives = 27/131 (20%), Gaps = 12/131 (9%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           E   K   + L P     A           +   +                 +  +   G
Sbjct: 381 EKKPKAAEDDLSPKGARRAPAEGKRRDRPKDAAAKAGGFDAERQGKAGKSAGRKDAAGAG 440

Query: 295 LSKQKKL------------ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
             ++++               P  R N    V  A    SS       R        SF 
Sbjct: 441 GFERRRPLESAERKSRDHGDRPPRRPNGERAVRPADDRTSSEGRKESARPPRGDGKKSFA 500

Query: 343 SKRSLRRTSAK 353
             R       K
Sbjct: 501 GDRPRASAGGK 511


>gi|159045330|ref|YP_001534124.1| RNA pseudouridine synthase [Dinoroseobacter shibae DFL 12]
 gi|157913090|gb|ABV94523.1| RNA pseudouridine synthase [Dinoroseobacter shibae DFL 12]
          Length = 322

 Score =  206 bits (525), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 138/319 (43%), Positives = 173/319 (54%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
                  R++KV+ARAGIASRRE ER+IA+ RV VNG  ++  A+NV   D I  DG P+
Sbjct: 4   NTTPPGDRIAKVLARAGIASRREAERLIAEGRVAVNGKTVDSPALNVTEADKITFDGTPI 63

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            + E  RLW YHKP+GLVTT  D  GR TVFD LP+   RV+SVGRLD+N+EGLLLLTND
Sbjct: 64  AEPEPPRLWRYHKPVGLVTTAKDEKGRETVFDALPADLPRVMSVGRLDLNSEGLLLLTND 123

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G + R LELP+T WLR YRVR  G   +D L  L+ GI ++G  +  M+  LD  +G+NA
Sbjct: 124 GEIKRRLELPTTGWLRRYRVRVKGAPTEDDLAPLRAGIEVEGERFKPMEARLDRLQGANA 183

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+T+GLREG+NREI++        VNRLIRISYGPF+LG L  G   E+  +ILREQLG 
Sbjct: 184 WLTLGLREGRNREIRRAMGALGLVVNRLIRISYGPFRLGELKPGEVEEIKGRILREQLGL 243

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              E       A                                K G     K       
Sbjct: 244 ESPEPPVGTAQARPKRGPGRKPGATPGGKPTGKPSRAPNARPGAKPGGKPGAKPDPKPGA 303

Query: 308 RNLASNVWMAKGIHSSFLS 326
           R  ++              
Sbjct: 304 RAGSARRKAPARPRPERGR 322


>gi|86140014|ref|ZP_01058578.1| RNA pseudouridylate synthase family protein [Roseobacter sp.
           MED193]
 gi|85823264|gb|EAQ43475.1| RNA pseudouridylate synthase family protein [Roseobacter sp.
           MED193]
          Length = 394

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 146/345 (42%), Positives = 198/345 (57%), Gaps = 3/345 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++KV++RAG+ASRRE ERMIA+ RVKVNG  ++  A+NV   D I VDG PL +AE 
Sbjct: 40  GDRIAKVLSRAGVASRREAERMIAEGRVKVNGTKIDSPALNVTERDRIIVDGKPLPQAEA 99

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            RLWLY+KP GLVT++SD  GR T+FD LP    RV++VGRLD+N+EGLLLLTNDGG+ R
Sbjct: 100 PRLWLYNKPTGLVTSNSDEKGRRTIFDELPEDLPRVMTVGRLDLNSEGLLLLTNDGGIKR 159

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            LELPST WLR YRVR +G+   +    L+KG+VI+G  +  M V LD Q+G+NAW+T+G
Sbjct: 160 RLELPSTGWLRRYRVRINGRPKDEDFEPLRKGMVIEGERFQPMTVALDRQQGANAWLTIG 219

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           LREGKNREI++  E   + VNRL+R+SYGPFQLG+L  G   E+  +++R+QLG    + 
Sbjct: 220 LREGKNREIRRALEDIGFNVNRLLRLSYGPFQLGSLKLGEVEELRPRVVRDQLGLEAEDM 279

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
            +     P          +            +    +  K       + A     R    
Sbjct: 280 EETPAARPTRGRPGAKPGQKPSGKPGSKTAPKSGGMTFGKPKGKPTGRPADESTGRPTGK 339

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR---SLRRTSAKK 354
           +     G  S           N +   S  + R      R ++ K
Sbjct: 340 SSGKPGGKPSGKPGTRSAGSFNDKPGGSGAASRNGKPGPRGASSK 384


>gi|170744111|ref|YP_001772766.1| RNA-binding S4 domain-containing protein [Methylobacterium sp.
           4-46]
 gi|168198385|gb|ACA20332.1| RNA-binding S4 domain protein [Methylobacterium sp. 4-46]
          Length = 609

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 146/341 (42%), Positives = 189/341 (55%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            E   P+R++KV+ARAG+ASRR+ E MI + RV +NG  L   AV V   D I VDG PL
Sbjct: 34  SETAEPERIAKVMARAGVASRRDAEAMILEGRVSLNGETLTTPAVTVGPGDRIVVDGEPL 93

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              ERTRLW++HKP G+VTT  DP+GR TVFD LP    RV+++GRLDINTEGLLLLTND
Sbjct: 94  PVRERTRLWIFHKPRGVVTTARDPEGRQTVFDILPEDLPRVVAIGRLDINTEGLLLLTND 153

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GGLA+V+  P T WLR YRVR +G VDQ  L+ L+ G+ I G+ YG ++ ++D Q+G N 
Sbjct: 154 GGLAKVIAHPETGWLRRYRVRAYGDVDQAALDRLRGGVTIDGMEYGPVEASIDRQQGDNV 213

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+T+GLREGKNRE+K++ E     VNRLIR+S+GPFQLG L  G   EV  K+L+EQLG 
Sbjct: 214 WLTLGLREGKNREVKRILEHLGLSVNRLIRLSFGPFQLGDLEVGLVEEVRTKVLKEQLGR 273

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            L E+A V+  +P+                        +     +      +        
Sbjct: 274 SLAEQAGVDFTSPVREPIAPFGSPKPPAPAAGRTGAPGRDRPRGERPDRSARPDRGERLD 333

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           R               F           R           R
Sbjct: 334 RGERPARPGRDPARPQFARPPAPGARPERDRKPATGPALRR 374


>gi|257866937|ref|ZP_05646590.1| pseudouridine synthase [Enterococcus casseliflavus EC30]
 gi|257873270|ref|ZP_05652923.1| pseudouridine synthase [Enterococcus casseliflavus EC10]
 gi|257800993|gb|EEV29923.1| pseudouridine synthase [Enterococcus casseliflavus EC30]
 gi|257807434|gb|EEV36256.1| pseudouridine synthase [Enterococcus casseliflavus EC10]
          Length = 257

 Score =  206 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 62/240 (25%), Positives = 108/240 (45%), Gaps = 4/240 (1%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDG 64
           ++ E   P R+ K +A  G  SR+EV+++I +  V VNG +++     V  T D +  +G
Sbjct: 11  VLYERKKPMRLDKFLADMGYGSRKEVKQLIKKGLVTVNGQVIKSDKAQVQETQDTVCFEG 70

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P+    +    L      +  T    +       +  +    +  VGRLD +TEG LL+
Sbjct: 71  EPIAYQSQFYYLLNKPAGVISATVDSYEETVLDLFSEEAFREDLFPVGRLDKDTEGFLLI 130

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--Q 182
           TNDGGLA  L  P     + Y  +  G +  +   +  KGI + G      ++ +    +
Sbjct: 131 TNDGGLAHQLLSPKKHVEKEYYAQVEGIMTAEDQKIFAKGIKLDGEWTLPAELQILNVDE 190

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           +   + + + L EGK  ++K++      +V  L RI  G   L   L  G  RE++ + +
Sbjct: 191 EEMRSEIKLILHEGKFHQVKRMVHAVGKEVVYLKRIRMGGLSLPDDLALGEYRELTSEEM 250


>gi|27262400|gb|AAN87481.1| Ribosomal large subunit pseudouridine synthase B [Heliobacillus
           mobilis]
          Length = 253

 Score =  205 bits (522), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 89/255 (34%), Positives = 138/255 (54%), Gaps = 4/255 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DH 59
           MK+   V    T +R+ KV+A  G+ASRRE E  I   RV+VNG ++    + V    D 
Sbjct: 1   MKE---VLSTTTAERLQKVLAAHGLASRREAEDWIRAGRVQVNGTVVTELGLRVEEGKDV 57

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           I+VDG PL   ER + +L +KP G VTT  DP+GR TV D L  + +R+  VGRLD +TE
Sbjct: 58  IQVDGKPLTVRERHQYFLLYKPRGFVTTRKDPEGRPTVIDLLKDVPARIYPVGRLDQDTE 117

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLLTNDG LA  L  P     + Y  R  G V    +    +G++++       +V +
Sbjct: 118 GLLLLTNDGELAYRLTHPKYGVEKTYHARMRGNVPDPVIKAFAEGVMLEDGLTAPAKVKV 177

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             ++G   W+ + + EG+NR+++++ +   + V  L R+S+GP  +  L  G+ R +  +
Sbjct: 178 LDREGGATWIELTIHEGRNRQVRRMGDAVGYPVVHLTRVSFGPLTISGLKPGAYRPLKPQ 237

Query: 240 ILREQLGPHLLEEAQ 254
            +R        +  +
Sbjct: 238 EVRALQRAAECKADR 252


>gi|39996504|ref|NP_952455.1| ribosomal large subunit pseudouridine synthase B [Geobacter
           sulfurreducens PCA]
 gi|39983385|gb|AAR34778.1| ribosomal large subunit pseudouridine synthase B [Geobacter
           sulfurreducens PCA]
 gi|298505521|gb|ADI84244.1| 23S rRNA pseudouridine 2605 synthase [Geobacter sulfurreducens
           KN400]
          Length = 247

 Score =  205 bits (522), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 88/234 (37%), Positives = 132/234 (56%), Gaps = 1/234 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++++AG+ASRRE ER I + RV VNG ++           D I VDG P+R AE+
Sbjct: 3   ERLQKLLSQAGVASRREAERFITEGRVAVNGTVVTELGSKADPERDRITVDGQPVRPAEK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP+G +TT  DP+GR  V D L  +  RV  VGRLD NTEGLLLLTNDG  A 
Sbjct: 63  KVYLILNKPVGYMTTLRDPEGRPIVTDLLKGLDVRVFPVGRLDYNTEGLLLLTNDGAWAN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + Y VR  G V ++++  L  G+ +        +V + +Q  +N W+++ 
Sbjct: 123 RLAHPRHEVDKEYLVRVRGAVAKEQIRRLATGVELDDGPTAPAKVEVSSQSDNNTWLSIV 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + EG+ R+++++ E  +  V RL R+ YG   LG L  G  R +S   +    G
Sbjct: 183 IHEGRYRQVRRMCEAVSLSVVRLRRVRYGAVSLGDLKPGEYRPLSPTEVAALAG 236


>gi|212638876|ref|YP_002315396.1| Pseudouridine synthase [Anoxybacillus flavithermus WK1]
 gi|212560356|gb|ACJ33411.1| Pseudouridine synthase [Anoxybacillus flavithermus WK1]
          Length = 255

 Score =  205 bits (522), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 78/246 (31%), Positives = 126/246 (51%), Gaps = 3/246 (1%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            +  E    +R+ KVIA AG+ASRR+ E++I + +VKVNG ++    V V   D IEVDG
Sbjct: 3   KLYSEVNEMERLQKVIAHAGVASRRKAEQLIVEGKVKVNGKVVTELGVKVSPQDRIEVDG 62

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
           +PL + E     LY     + +   +  GR  V D    +  R+  +GRLD +T GLLLL
Sbjct: 63  IPLEREEPVYYLLYKPRGVISSVKDE-KGRKVVTDFFKHVNKRIYPIGRLDYDTSGLLLL 121

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG  A +L  P  +  +VY  +  G   ++K+  L+KG++++       +  + +   
Sbjct: 122 TNDGEFANILMHPRYEIEKVYIAKVKGIPAREKVKQLEKGVMLEDGVTAPAKAKVLSIDK 181

Query: 185 SNAW--VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
                 V + + EG+NR+++++FE     V +L R  Y    L  L  G  RE+S   ++
Sbjct: 182 RKQTAIVELRIHEGRNRQVRRMFEAIGHPVLKLKRERYAFLDLKGLNPGDYRELSPHEVK 241

Query: 243 EQLGPH 248
           +     
Sbjct: 242 QLRALA 247


>gi|121601745|ref|YP_989462.1| RNA pseudouridine synthase [Bartonella bacilliformis KC583]
 gi|120613922|gb|ABM44523.1| RNA pseudouridine synthase [Bartonella bacilliformis KC583]
          Length = 499

 Score =  205 bits (522), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 170/378 (44%), Positives = 225/378 (59%), Gaps = 25/378 (6%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +++  V  N   +R++K +ARAGIASRR+ E MI   R+ VNG ++    +NV+ +DHI 
Sbjct: 33  QNEEDVYTNCDSERIAKRLARAGIASRRDAEMMIIAGRIAVNGTVVTTPVLNVIPSDHIT 92

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           VD +P+   ERTRLWLYHKP GLVTT+ DP+GR TVFDNLP    RV+SVGRLDINTEGL
Sbjct: 93  VDEIPIPPIERTRLWLYHKPSGLVTTNRDPEGRPTVFDNLPKEMPRVVSVGRLDINTEGL 152

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDGGLARVLELP T W+R YRVR HG++ Q +L+ LK GI I GI YG +  ++D 
Sbjct: 153 LLLTNDGGLARVLELPLTGWVRKYRVRAHGKIKQSELDKLKNGIAIDGIFYGSIDASIDR 212

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++GSN W++V LREGKNREIK         VNRLIR+SYGPFQL  L  G+ RE+  + L
Sbjct: 213 EQGSNVWLSVALREGKNREIKNFLGALGLSVNRLIRVSYGPFQLSDLEEGAVRELKGRTL 272

Query: 242 REQLGPHLLEEAQVNLDAPIYSSET-----LVRDRPNIISEVPDDFTRMKKNSSQK---- 292
           R+QLG  L+ +A  N DAPI    +     + +     +S+  D++     +  Q+    
Sbjct: 273 RDQLGERLIMQANANFDAPILKPFSNSAVVVKQQSNKKLSQANDEWISSSGHHKQRNKKD 332

Query: 293 ------NGLSKQKKLATPVHRRNL--------ASNVWMAKGIHSSFLSDSG--QREENHR 336
                      +K    P+ +R           SNVWMA G              E+N  
Sbjct: 333 GFIEHNRAQLSKKPNEQPIEQRKTERFSSRSRRSNVWMASGARPQITRKRPYYGEEDNQD 392

Query: 337 RSPSFPSKRSLRRTSAKK 354
           RS  F  ++ L +   K+
Sbjct: 393 RSRVFAGEKFLYKNKEKQ 410


>gi|323491918|ref|ZP_08097088.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio brasiliensis
           LMG 20546]
 gi|323313839|gb|EGA66933.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio brasiliensis
           LMG 20546]
          Length = 342

 Score =  205 bits (521), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 69/345 (20%), Positives = 128/345 (37%), Gaps = 12/345 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
              T +R++K I+  G  SRRE +R+I Q RV +NG +       V S D + VD  P+ 
Sbjct: 2   SQDTGKRLNKFISETGFCSRREADRLIEQGRVTINGKIP-EMGTKVQSGDDVRVDDKPIA 60

Query: 69  K-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             +++      +KP G+  T            +      R+  +GRLD  ++GL+ LTND
Sbjct: 61  AASDKPIYIALNKPTGITCTTERDI--PGNIVDFVGHKKRIFPIGRLDKPSDGLIFLTND 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +        + Y VR    +  D +  +  G+ I        +V    +K +  
Sbjct: 119 GDIVNKILRAGNNHEKEYVVRVDKPISDDFIKKMSSGVNILDTVTLPCKV----EKETKY 174

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E   ++V +L R+      L  +  G  R ++   + E L  
Sbjct: 175 SFRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGQWRYLTDAEVAEILAM 234

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNI----ISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                            + + R           E  +   R  +      G +  +    
Sbjct: 235 CEDSSGTEEASKMDAKGKRIRRATDAKLFDSREENQESKARRNQKQRTFKGRNADEFRHA 294

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           P  ++   S+         +      +   +    P+ P   +L 
Sbjct: 295 PNSKKGRNSDKQSEPKGKPAKGKTFYKPASDKAPRPAKPKGGTLS 339


>gi|84394472|ref|ZP_00993186.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio splendidus
           12B01]
 gi|84374913|gb|EAP91846.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio splendidus
           12B01]
          Length = 364

 Score =  205 bits (521), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 69/359 (19%), Positives = 135/359 (37%), Gaps = 19/359 (5%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + +    +R++K I+  G  SRRE +++I   RV +NG +       V+  D +E+D  P
Sbjct: 1   MSQESQAKRLNKYISETGFCSRREADKLIDAGRVTINGKIP-EMGTKVLPGDDVEIDNKP 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +R  E+      +KP G+  T            +      R+  +GRLD  ++GL+ LTN
Sbjct: 60  VRSKEKPIYIALNKPTGITCTTERDI--PGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTN 117

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG +   +        + Y VR    +  + L  +  G+ I        +V    +K + 
Sbjct: 118 DGDIVNKILRAGNNHEKEYVVRVDKPITTEFLKQMGAGVHILDTVTLPCKV----EKETK 173

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               + L +G NR+I+++ E   ++V +L R+      L  +  G  R +S + + E L 
Sbjct: 174 FSFRITLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSDEEITEILA 233

Query: 247 PH-------LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
                       +          +++  + D             + +  +    G +  +
Sbjct: 234 MCEGSVSTEDASKMNAKGQRIRKATDAKLFDSREENQTSTARRNQNENRTRTYRGNNADE 293

Query: 300 KLATPVHRRNLASNVWMAKG-----IHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               P  +R   S+   + G       +S    S     +  R+ +  +    R     
Sbjct: 294 FRHAPNSKRGRNSSNGESGGNTENWKSNSRSERSNSDRNSSDRTRTDRNNNDRRSGKPA 352


>gi|254474349|ref|ZP_05087735.1| pseudouridine synthase, Rsu:RNA-binding S4:Pseudouridine synthase
           [Ruegeria sp. R11]
 gi|214028592|gb|EEB69427.1| pseudouridine synthase, Rsu:RNA-binding S4:Pseudouridine synthase
           [Ruegeria sp. R11]
          Length = 414

 Score =  205 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 145/346 (41%), Positives = 193/346 (55%), Gaps = 1/346 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
                  R++KV++RAG+ASRRE ERMIA  RV+VNG +++  A+NV+   D I VDG  
Sbjct: 39  SSGPDGDRIAKVLSRAGLASRREAERMIADGRVEVNGKVIDSPALNVVVGKDRIVVDGKQ 98

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           + + E  RLWLYHKP GLVTT SD   R T+FD+LP    RV++VGRLD+N+EGLLLLTN
Sbjct: 99  VEEPEPPRLWLYHKPAGLVTTTSDELDRKTIFDDLPEDLPRVMTVGRLDLNSEGLLLLTN 158

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGG+ R LELPST WLR YRVR +G+        L+KG+VI+G  +  M VTLD Q+G+N
Sbjct: 159 DGGIKRQLELPSTGWLRRYRVRINGRPQDSDFEPLRKGLVIEGEKFQPMIVTLDRQQGAN 218

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           AW+TVGLREGKNREI++  E   + VNRL+R+SYGPFQLG L  G   E+  +++R+QLG
Sbjct: 219 AWLTVGLREGKNREIRRAMEDIGFSVNRLLRLSYGPFQLGQLKPGEVEELRPRVVRDQLG 278

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
               EE Q +   P      +             D     +  + + G       A    
Sbjct: 279 LAAPEEEQDSPKRPGTRQRPMRGKPGTRPGSGQSDRGTDSRAGAGRTGRPGSAPNAKGTG 338

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           +                     G R  +     S P   +     +
Sbjct: 339 KGTGKPLSKAGGKSMGKPTGRPGARSSDKAAGNSGPKGNARPSGKS 384


>gi|319406590|emb|CBI80232.1| Pseudouridine synthase [Bartonella sp. 1-1C]
          Length = 493

 Score =  205 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 167/381 (43%), Positives = 213/381 (55%), Gaps = 29/381 (7%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           ++  V E    +R++K +ARAG+ASRR+ E MI   R+ VNG ++   A NV  +D I V
Sbjct: 31  NEKRVSEKSESERIAKRLARAGLASRRDAEMMIVAGRIVVNGTVVTTPAFNVSRSDVIMV 90

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG PL   ERTRLWLY+KPIG VTT+ DP GR TVFDNLP    RV+SVGRLDINTEGLL
Sbjct: 91  DGKPLPPIERTRLWLYYKPIGFVTTNRDPQGRPTVFDNLPKGMPRVLSVGRLDINTEGLL 150

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTNDGGLARVLELP T W+R YRVR HG+V Q  L  LK GI + GI YG ++ +++ +
Sbjct: 151 LLTNDGGLARVLELPLTGWVRKYRVRAHGKVKQSALQDLKNGIAVNGIFYGSIEASIERE 210

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +GSN W++V LREGKNREIK V       VNRLIR+SYGPFQL  L  G+ RE+  ++LR
Sbjct: 211 QGSNVWLSVALREGKNREIKNVLGALGLSVNRLIRVSYGPFQLSDLKEGAVRELKGRMLR 270

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRD-------------------------RPNIISE 277
           +QLG  L+ +A  + DAPI    +                                    
Sbjct: 271 DQLGERLIVQANADFDAPILKPFSNSAVVAKQNITKSSVIEDSWIVSSKENLLYGRKSRF 330

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHR--RNLASNVWMAKGIHSSFLSDSGQREENH 335
           +     R+ K    K       K         R+  SNVWMA G            + ++
Sbjct: 331 LGHSQVRLSKKIDTKLRAKDHNKGGKEERAFLRSRCSNVWMAPGACPQIARKKSSSDADN 390

Query: 336 --RRSPSFPSKRSLRRTSAKK 354
              R  ++  KRS  R   K+
Sbjct: 391 HYDRKSNWVGKRSTDRGKEKR 411


>gi|319403673|emb|CBI77258.1| Pseudouridine synthase [Bartonella rochalimae ATCC BAA-1498]
          Length = 492

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 170/382 (44%), Positives = 219/382 (57%), Gaps = 29/382 (7%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +++  V E    +R++K +ARAG+ASRR+ E MIA  R+ VNG ++   A NV  +D I 
Sbjct: 29  RNEKRVSEKSESERIAKRLARAGLASRRDAEMMIAAGRIVVNGAVVTTPAFNVTRSDVIM 88

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           VDG PL   ERTRLWLY+KPIG VTT+ DP GR TVFDNLP    RV+SVGRLDINTEGL
Sbjct: 89  VDGKPLPPIERTRLWLYYKPIGFVTTNRDPQGRPTVFDNLPKGMPRVLSVGRLDINTEGL 148

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDGGLARVLELP T W+R YRVR HG+V Q  L  LK GI + GI YG ++ +++ 
Sbjct: 149 LLLTNDGGLARVLELPLTGWVRKYRVRAHGKVKQSALQDLKNGIAVNGIFYGSIEASIER 208

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++GSN W++V LREGKNREIK V       VNRLIR+SYGPFQL  L  G+ RE+  ++L
Sbjct: 209 EQGSNVWLSVALREGKNREIKNVLGALGLSVNRLIRVSYGPFQLSDLKEGAVRELKGRML 268

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD--------------------- 280
           R+QLG  L+ +A  + DAPI    +            P                      
Sbjct: 269 RDQLGERLIMQANADFDAPILKPFSNSAVSEKQNITKPPVIKDNWIVSSKENLSYGKKSR 328

Query: 281 ----DFTRMKKNSSQKNGLSKQKKLATPVHR--RNLASNVWMAKGIHSSFLSDSGQREEN 334
                  R+ K   +K    +Q K         R+  SNVWMA G     +      + +
Sbjct: 329 FLGHSQVRLSKKIDEKLRGKEQNKGGKEERAFLRSRCSNVWMAPGACPKIVRKKSYSDTD 388

Query: 335 H--RRSPSFPSKRSLRRTSAKK 354
           +   R  ++  KRS  R   K+
Sbjct: 389 NYYDRKSNWVGKRSTDRGKEKR 410


>gi|304393184|ref|ZP_07375112.1| ribosomal large subunit pseudouridine synthase B [Ahrensia sp.
           R2A130]
 gi|303294191|gb|EFL88563.1| ribosomal large subunit pseudouridine synthase B [Ahrensia sp.
           R2A130]
          Length = 344

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 150/332 (45%), Positives = 201/332 (60%), Gaps = 2/332 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           ++    +R++K +ARAG+ SRR+ ER I   RVKVNG LL   A  V   D IEVD   L
Sbjct: 13  EKPADAERIAKRMARAGLCSRRDAERWIEAGRVKVNGKLLTTPAHTVTPRDRIEVDDKLL 72

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              ERTRLWL +K  GLVTT+ DP+GR+T+F+ LP    RV+SVGRLDINTEGLLLLTND
Sbjct: 73  GGPERTRLWLLNKRSGLVTTNKDPEGRTTIFERLPDDLPRVLSVGRLDINTEGLLLLTND 132

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GGLARVLELP+T WLR YRVR HGQ  Q++L+ L  GI + G+ YG ++  L+ Q+G+N 
Sbjct: 133 GGLARVLELPTTGWLRRYRVRAHGQTTQEELDKLADGIAVDGVLYGAIEAELERQQGTNV 192

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+T  +REGKNRE+K V      +VNRLIRISYGPFQLG L +G  +EV  ++LR+QLG 
Sbjct: 193 WLTFAMREGKNREVKNVLSALGLEVNRLIRISYGPFQLGDLASGEVQEVRGRMLRQQLGA 252

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK--KNSSQKNGLSKQKKLATPV 305
            L+  +  + DAP+ ++          I +   +       + +     L+ QK    P 
Sbjct: 253 KLISASGADFDAPLAATAPKNNPVGEKIEKARPNKRGTNTPRKADPLERLTTQKPTQKPG 312

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
            + +            +   +  G R  + RR
Sbjct: 313 TKPSDGRGRGAKDKSSNKPGNKQGGRGADRRR 344


>gi|126461709|ref|YP_001042823.1| RNA-binding S4 domain-containing protein [Rhodobacter sphaeroides
           ATCC 17029]
 gi|126103373|gb|ABN76051.1| RNA-binding S4 domain protein [Rhodobacter sphaeroides ATCC 17029]
          Length = 489

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 140/345 (40%), Positives = 181/345 (52%), Gaps = 1/345 (0%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + ++   +R++KV++RAGIASRR+ ERMI   R+ VNG  ++  A+NV   D I VDG P
Sbjct: 1   MTDSKDGERIAKVLSRAGIASRRDAERMIELGRIAVNGRTIDSPALNVGPKDRITVDGQP 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L   E  RLWLY+KP GLVT+ SD  GR TVFD+LP    RV+SVGRLD+N+EGLLLLTN
Sbjct: 61  LAPPEPARLWLYYKPEGLVTSASDEKGRETVFDHLPEGMPRVMSVGRLDLNSEGLLLLTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L R LELPST WLR YRVR  G      L  L+KGI ++G  +  M V+LD  +G+N
Sbjct: 121 DGELKRRLELPSTGWLRKYRVRVKGNPTDADLEPLRKGITVEGESFQPMTVSLDRVQGAN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           AW+TVGLREGKNREI++        VNRLIR+SYGPF+L  L  G   EV  KILR+QLG
Sbjct: 181 AWLTVGLREGKNREIRRAMSALGLTVNRLIRVSYGPFRLNELEPGMVEEVRPKILRDQLG 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                + +               +                                +   
Sbjct: 241 LDPHADGEARPARGRKPEGAARAEGAARSERTARPPRGAAAEGPT-RPARAAGSEGSAGA 299

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
            R  +      K       +    +       P+  +     R S
Sbjct: 300 TRGRSPQGAAPKAGAPKDGARFAGKGPAEGARPARSAATDPARAS 344



 Score = 39.8 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 13/108 (12%), Positives = 26/108 (24%), Gaps = 3/108 (2%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R   G      A  +                   +  P   +R     +     + + + 
Sbjct: 303 RSPQGAAPKAGAPKDGARFAGKGPAEGARPARSAATDPARASRPASTETTGRTRTAEGRG 362

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                 R+  +    A      F S S +      R P+  +  +  R
Sbjct: 363 KPAAAGRSGKTEAADAPRA---FRSRSAEAPAKGPRGPAKAAGPARSR 407


>gi|254711457|ref|ZP_05173268.1| hypothetical protein BpinB_14632 [Brucella pinnipedialis B2/94]
          Length = 611

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 166/348 (47%), Positives = 222/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 99  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 158

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 159 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 218

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 219 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 278

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 279 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 338

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 398

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G+      ++ +      + P   +K
Sbjct: 399 REEKTEKVEPRRRGNANVWMAPGVRPKGEKEAAKPARVEHQQPHRSAK 446



 Score = 37.1 bits (84), Expect = 3.7,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 452 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 511

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 512 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 562


>gi|294853220|ref|ZP_06793892.1| ribosomal large subunit pseudouridine synthase B [Brucella sp. NVSL
           07-0026]
 gi|294818875|gb|EFG35875.1| ribosomal large subunit pseudouridine synthase B [Brucella sp. NVSL
           07-0026]
          Length = 611

 Score =  204 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 164/348 (47%), Positives = 220/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MI   R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 99  EEETSERIAKRLARAGIASRREAETMIVAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 158

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 159 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 218

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+R+LELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 219 GLSRILELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 278

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 279 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 338

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 398

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 399 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 446



 Score = 37.1 bits (84), Expect = 3.7,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 452 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 511

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 512 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 562


>gi|306840967|ref|ZP_07473708.1| conserved hypothetical protein [Brucella sp. BO2]
 gi|306289024|gb|EFM60289.1| conserved hypothetical protein [Brucella sp. BO2]
          Length = 614

 Score =  204 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 166/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 99  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 158

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 159 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 218

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 219 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 278

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 279 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 338

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGEPPQEGERRRAPREREWISSTGERRRG 398

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 399 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 446



 Score = 36.3 bits (82), Expect = 6.6,   Method: Composition-based stats.
 Identities = 10/116 (8%), Positives = 23/116 (19%), Gaps = 4/116 (3%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +          +               +          D    ++   +  G  K+++  
Sbjct: 450 DLQMRPRRYSDEERGGEEGGERRYKRPEGRFEREGGRPDNREKREKYEKHEGAGKERRPG 509

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK----RSLRRTSAKK 354
                    +     +     F      +    R    F       RS  R S  +
Sbjct: 510 KRERAELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 565


>gi|256014991|ref|YP_003105000.1| RNA pseudouridylate synthase family protein [Brucella microti CCM
           4915]
 gi|255997651|gb|ACU49338.1| RNA pseudouridylate synthase family protein [Brucella microti CCM
           4915]
          Length = 611

 Score =  204 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 165/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I V+G PLR
Sbjct: 99  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVNGKPLR 158

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 159 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 218

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 219 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 278

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 279 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 338

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 398

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 399 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 446



 Score = 37.1 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 452 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 511

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 512 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 562


>gi|146278267|ref|YP_001168426.1| RNA-binding S4 domain-containing protein [Rhodobacter sphaeroides
           ATCC 17025]
 gi|145556508|gb|ABP71121.1| RNA-binding S4 domain protein [Rhodobacter sphaeroides ATCC 17025]
          Length = 466

 Score =  204 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 150/402 (37%), Positives = 191/402 (47%), Gaps = 54/402 (13%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + ++   +R++KV++RAG+ASRR+ ERMI   RV VNG  ++  A+NV   D I VDG P
Sbjct: 1   MTDSTDGERIAKVLSRAGVASRRDAERMIELGRVAVNGRTIDSPALNVGPKDRITVDGQP 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L   +  RLWLY+KP GLVT+ +D  GR TVFD+LP    RV+SVGRLD+N+EGLLLLTN
Sbjct: 61  LAPPQPARLWLYYKPEGLVTSAADEKGRETVFDHLPEDLPRVMSVGRLDLNSEGLLLLTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L R LELPST WLR YRVR  G      L  L+KGI ++G  +  M VTLD  +G+N
Sbjct: 121 DGELKRRLELPSTGWLRKYRVRVKGNPTDPDLEPLRKGITVEGERFQPMTVTLDRVQGAN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           AW+TVGLREGKNREI++        VNRLIRISYGPF+L  L  G   EV  K+LR+QLG
Sbjct: 181 AWLTVGLREGKNREIRRAMSAIGLTVNRLIRISYGPFRLNELQPGMVEEVRPKVLRDQLG 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEV--------PDDFTRMKKNSSQKNGLSKQ 298
               EE      A             +             PD+     K + +  G    
Sbjct: 241 LDPREEDGRPPKAARPPRGAGAASGRSHPGARPSGSKPLPPDEARGGSKGAPRGRGAGAA 300

Query: 299 KKLATPVHRR----------------------------------------------NLAS 312
            K A P  RR                                                  
Sbjct: 301 PKSAGPARRRDALPDAAIDARPSGPRARPAAGAAKAPSGRAFGGARPTSSRPTGTPAGTP 360

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                             R       P+    R   +++  K
Sbjct: 361 AATGPAKAGGRRPPGPAPRGTGPGTGPASGGPRQGPKSAPAK 402



 Score = 35.9 bits (81), Expect = 8.5,   Method: Composition-based stats.
 Identities = 8/88 (9%), Positives = 17/88 (19%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P            P  +            +               K+  +K  +   P 
Sbjct: 351 RPTGTPAGTPAATGPAKAGGRRPPGPAPRGTGPGTGPASGGPRQGPKSAPAKAPRRTGPD 410

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREE 333
             R   +    A+    +  +      E
Sbjct: 411 EGRGGPAGAGSARTGKPAASAPRKPPSE 438


>gi|332557705|ref|ZP_08412027.1| RNA-binding S4 domain-containing protein [Rhodobacter sphaeroides
           WS8N]
 gi|332275417|gb|EGJ20732.1| RNA-binding S4 domain-containing protein [Rhodobacter sphaeroides
           WS8N]
          Length = 385

 Score =  204 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 143/328 (43%), Positives = 181/328 (55%), Gaps = 1/328 (0%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + ++   +R++KV++RAGIASRR+ ERMI   R+ VNG  ++  A+NV   D I VDG P
Sbjct: 1   MTDSKDGERIAKVLSRAGIASRRDAERMIELGRIAVNGRTIDSPALNVGPKDRITVDGQP 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L   E  RLWLY+KP GLVT+ SD  GR TVFD+LP    RV+SVGRLD+N+EGLLLLTN
Sbjct: 61  LAPPEPARLWLYYKPEGLVTSASDEKGRETVFDHLPEGMPRVMSVGRLDLNSEGLLLLTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L R LELPST WLR YRVR  G      L  L+KGI ++G  +  M V+LD  +G+N
Sbjct: 121 DGELKRRLELPSTGWLRKYRVRVKGNPTDADLEPLRKGITVEGESFQPMTVSLDRVQGAN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           AW+TVGLREGKNREI++        VNRLIR+SYGPF+L  L  G   EV  KILR+QLG
Sbjct: 181 AWLTVGLREGKNREIRRAMSALGLTVNRLIRVSYGPFRLNELEPGMVEEVRPKILRDQLG 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ-KKLATPV 305
                + +               +                     + G     +  A P 
Sbjct: 241 LDPHADGEARPARGRKPEGAARAEGAARSERAARPPRGAAAEGPARAGRGAGSEGAAGPA 300

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREE 333
             R+       A     S  S      E
Sbjct: 301 KGRSPHGAAPRAGAPKDSARSAGKGAAE 328


>gi|302036776|ref|YP_003797098.1| 23S rRNA pseudouridylate synthase B [Candidatus Nitrospira
           defluvii]
 gi|190343191|gb|ACE75579.1| ribosomal large subunit pseudouridine synthase B [Candidatus
           Nitrospira defluvii]
 gi|300604840|emb|CBK41172.1| 23S rRNA pseudouridylate synthase B (modular protein) [Candidatus
           Nitrospira defluvii]
          Length = 420

 Score =  203 bits (517), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 97/351 (27%), Positives = 163/351 (46%), Gaps = 10/351 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+IA  G+ASRR+ E +I   RV +NG +++     V    DH++VDG  LR A+ 
Sbjct: 3   VRLQKLIAGTGLASRRKAEELITSGRVTINGSVVKELGTKVDPARDHVKVDGKHLRAAQP 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP  +++T  DP+GR TV D L  +  RV  VGRLD ++EGL+LLTN G LA+
Sbjct: 63  YVYLILNKPKNVMSTLDDPEGRPTVKDLLHGVTVRVFPVGRLDFDSEGLMLLTNHGDLAQ 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y ++  G +D  K+  L++G+ ++       +V   ++  SN+W+ V 
Sbjct: 123 ALLHPRYHVPKTYLIKVKGVLDDAKIEALERGVKLEDGFTAPAKVKKVSRAESNSWLEVT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI---LREQLGPHL 249
           + EG+  ++K++ E     V +L+R+  GP  LG L     R ++ +    LRE +   +
Sbjct: 183 IHEGRKHQVKRMVEAVGHSVIKLVRVRMGPLLLGDLAPREYRFLTDREANRLRELVEDRV 242

Query: 250 LEEAQVNLDAPIYSSE-TLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
               +  LDA    +      +        P+   R  K+   + G   Q+ LA     R
Sbjct: 243 ARAERPELDASGKPTRWMPPTEPAPPRPPKPERSGRGPKSQRSERGPRSQRSLAGSKPSR 302

Query: 309 NLASNVWMAKGIHSSFLSDSG-----QREENHRRSPSFPSKRSLRRTSAKK 354
           +   N        + F   +      + +       +     S    S +K
Sbjct: 303 SGRGNTRRPMSPGAKFRRPAKGVGFQRTQAGPIPQGADRGPGSRPTGSDQK 353


>gi|161620283|ref|YP_001594169.1| hypothetical protein BCAN_B0204 [Brucella canis ATCC 23365]
 gi|161337094|gb|ABX63398.1| conserved hypothetical protein [Brucella canis ATCC 23365]
          Length = 611

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 166/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 99  EEETSERIAKRLARAGIASRREAETMIATGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 158

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 159 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 218

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 219 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 278

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 279 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 338

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 398

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 399 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 446



 Score = 37.1 bits (84), Expect = 3.7,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 452 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 511

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 512 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 562


>gi|222151389|ref|YP_002560545.1| ribosomal large subunit pseudouridine synthase B [Macrococcus
           caseolyticus JCSC5402]
 gi|222120514|dbj|BAH17849.1| ribosomal large subunit pseudouridine synthase B [Macrococcus
           caseolyticus JCSC5402]
          Length = 245

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 71/245 (28%), Positives = 125/245 (51%), Gaps = 3/245 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N   +R+ KVIA++G+ SRR+ E +I + +V VNG  +      V  +D IEV+G+PL  
Sbjct: 2   NEQLERLQKVIAKSGVTSRRKAEVLITEGKVTVNGQTVTELGTKVKPSDIIEVEGIPLEN 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E+  +  +     + +   +   +            R+  VGRLD +T GLLLLTNDG 
Sbjct: 62  PEKIYILFHKPTGVITSVSDEKGRKVVTDYFPGLNL-RIFPVGRLDYDTSGLLLLTNDGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNA 187
            A  +  P  +  + Y  +  G + ++++  L+KGI+++         +V    ++ +  
Sbjct: 121 FANQMTHPKYKMKKKYVAKLKGFLLREQVKQLEKGIMLEDGKTAPALVKVKSQDKEKNTT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V + + EG+NR+++++F  F  +V +L RI YGP  L  L AG  RE++   ++     
Sbjct: 181 LVEITIYEGRNRQVRRMFAHFGHEVVKLSRIEYGPLTLKGLNAGDARELTPHEVKTLRNM 240

Query: 248 HLLEE 252
            L + 
Sbjct: 241 ALNKS 245


>gi|237816712|ref|ZP_04595704.1| conserved hypothetical protein [Brucella abortus str. 2308 A]
 gi|254691364|ref|ZP_05154618.1| hypothetical protein Babob68_14690 [Brucella abortus bv. 6 str.
           870]
 gi|254731879|ref|ZP_05190457.1| hypothetical protein Babob42_11997 [Brucella abortus bv. 4 str.
           292]
 gi|237787525|gb|EEP61741.1| conserved hypothetical protein [Brucella abortus str. 2308 A]
          Length = 611

 Score =  203 bits (516), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 166/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 99  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 158

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 159 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 218

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 219 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 278

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 279 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 338

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 398

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 399 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 446



 Score = 37.1 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 452 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 511

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 512 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 562


>gi|256158081|ref|ZP_05455999.1| hypothetical protein BcetM4_04490 [Brucella ceti M490/95/1]
          Length = 611

 Score =  203 bits (516), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 165/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 99  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 158

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           +  RTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 159 QTARTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 218

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 219 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 278

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 279 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 338

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRTPREREWISSTGERRRG 398

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G+      ++ +      + P   +K
Sbjct: 399 REEKTEKVEPRRRGNANVWMAPGVRPKGEKEAAKPARVEHQQPHRSAK 446



 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 452 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 511

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 512 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 562


>gi|256111893|ref|ZP_05452849.1| hypothetical protein Bmelb3E_04410 [Brucella melitensis bv. 3 str.
           Ether]
          Length = 611

 Score =  203 bits (516), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 165/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 99  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 158

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 159 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 218

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V + +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 219 GLSRVLELPSTGWLRRYRVRAHGKVTRQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 278

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 279 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 338

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 398

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 399 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 446



 Score = 35.9 bits (81), Expect = 9.9,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 452 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 511

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 512 ELRNAEGQTTERGKGGSEGCKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 562


>gi|221090247|ref|YP_002519390.1| RNA pseudouridylate synthase family protein [Brucella suis 1330]
 gi|54112368|gb|AAV28863.1| RNA pseudouridylate synthase family protein [Brucella suis 1330]
          Length = 598

 Score =  203 bits (515), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 166/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 86  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 145

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 146 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 205

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 206 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 265

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 266 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 325

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 326 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 385

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 386 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 433



 Score = 37.1 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 439 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 498

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 499 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 549


>gi|148558125|ref|YP_001257253.1| RNA pseudouridylate synthase family protein [Brucella ovis ATCC
           25840]
 gi|148369410|gb|ABQ62282.1| RNA pseudouridylate synthase family protein [Brucella ovis ATCC
           25840]
          Length = 598

 Score =  203 bits (515), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 165/348 (47%), Positives = 220/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 86  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 145

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ER RLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 146 QTERNRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 205

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 206 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 265

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 266 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 325

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 326 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 385

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 386 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 433



 Score = 37.1 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 439 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 498

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 499 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 549


>gi|304406989|ref|ZP_07388643.1| pseudouridine synthase [Paenibacillus curdlanolyticus YK9]
 gi|304343976|gb|EFM09816.1| pseudouridine synthase [Paenibacillus curdlanolyticus YK9]
          Length = 445

 Score =  203 bits (515), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 96/356 (26%), Positives = 153/356 (42%), Gaps = 15/356 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
             +R+ K++A+AGIASRR+ E +I   +V+VNG+ +           D I V G P+  +
Sbjct: 3   KLERLQKILAQAGIASRRKCEELIISGQVEVNGVPVTTLGAKADPEEDVITVGGKPI-VS 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E     + +KP G++T+ SDP GR  V D L  I  RV  +GRLD +TEGLLLLTNDG  
Sbjct: 62  ENKLYIMLNKPKGVITSASDPQGRKVVSDFLTGIKQRVYPIGRLDYDTEGLLLLTNDGEF 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAW 188
           A +L  P     + Y     G    DKL+ L+KGI ++       +V     + S   + 
Sbjct: 122 ANLLTHPKHHVPKTYWATVKGVPHGDKLDKLRKGIELEDGMTSPAEVEYQDIEPSDKEST 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + + + EG+NR+++++F+     V RL R+ +G   L  L  G  R +    ++E L   
Sbjct: 182 IRITIYEGRNRQVRRMFDAIGHPVIRLKRVKFGELGLQNLKRGGWRPLKPHEVQELLQEA 241

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
              E + +       +             +     +   N  ++ G    +K        
Sbjct: 242 AKAEGKSSYVPSGKPATKPEWKPKPKPKHLTASGDKNHSNGQKEGGSETGRKPFRSKQAS 301

Query: 309 NLASNVWMAKGIHSSF-----------LSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           N A+     KG  S              +    +      S +    RS  +  AK
Sbjct: 302 NAAATTGSRKGKRSRQSYAESVLGAAAATQGKGKPSAGVSSSTRAGSRSAGKGPAK 357


>gi|227820997|ref|YP_002824967.1| pseudouridylate synthase, subunit B protein [Sinorhizobium fredii
           NGR234]
 gi|227339996|gb|ACP24214.1| pseudouridylate synthase, subunit B protein [Sinorhizobium fredii
           NGR234]
          Length = 607

 Score =  203 bits (515), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 177/369 (47%), Positives = 228/369 (61%), Gaps = 29/369 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             PQR+SK+++RAG+ASRR++ERMI + RVK+NG++LE   VN    D IEVDG P+R  
Sbjct: 44  DEPQRISKILSRAGVASRRDIERMIMEGRVKLNGVVLETPVVNATLADQIEVDGHPIRGI 103

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ERTRLWLY+KP GLVTT+SDP+GR TVFDNLP    RV+SVGRLDINTEGLLLLTNDGGL
Sbjct: 104 ERTRLWLYYKPAGLVTTNSDPEGRPTVFDNLPDELPRVLSVGRLDINTEGLLLLTNDGGL 163

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           AR LELPST WLR YRVR HG++DQ+ L+ LK+GI + G+ YG ++ TLD  +GSN W+T
Sbjct: 164 ARALELPSTGWLRRYRVRAHGEIDQEALDRLKEGIAVDGVLYGAIEATLDRVQGSNVWIT 223

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           +GLREGKNREIK V       VNRLIRISYGPFQLG L  G  +E+  + LR+QLGP L+
Sbjct: 224 MGLREGKNREIKNVLGALGLDVNRLIRISYGPFQLGELPEGHVQEIRGRTLRDQLGPRLI 283

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK------------- 297
            E++ N DAP+Y+ +    +R       P+          +     +             
Sbjct: 284 AESKANFDAPLYNDQPAAPEREAHNEVAPEWGKERSARREKPEDKRERALARLDTQRDDS 343

Query: 298 -------------QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
                        + + A P  +R+  +NVWMA G            EE+    P+   +
Sbjct: 344 RSRDRRERPREKFEDRPARPPAKRSRTANVWMAPGARPVAEKKPKGAEEDTSPKPA---R 400

Query: 345 RSLRRTSAK 353
           R     + K
Sbjct: 401 RERPEGAPK 409



 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 11/110 (10%), Positives = 21/110 (19%), Gaps = 3/110 (2%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                   + + D    S+   VR +        +          +      +       
Sbjct: 445 RAPRPPVKRADEDGDWISASEPVRRKDEARDGGFERRRPFDSGERKSRDHGDRPPRREGS 504

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR---SLRRTSA 352
            R         A    +        R ++ R        R      R  A
Sbjct: 505 ERPRGERPARAAGDSRAFSEKPRTSRSKDDRPQGREGGDRPFGDRPRGKA 554



 Score = 37.5 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 28/111 (25%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           +K+  R + G      A+ + D     ++   R        V          S+ +    
Sbjct: 410 TKRYGRTKDGAATKTSAKFDPDRKARPAKADARPDRAPRPPVKRADEDGDWISASEPVRR 469

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
           K +       RR    +       H          E      P+  +  S 
Sbjct: 470 KDEARDGGFERRRPFDSGERKSRDHGDRPPRREGSERPRGERPARAAGDSR 520


>gi|225628667|ref|ZP_03786701.1| conserved hypothetical protein [Brucella ceti str. Cudo]
 gi|225616513|gb|EEH13561.1| conserved hypothetical protein [Brucella ceti str. Cudo]
          Length = 611

 Score =  203 bits (515), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 165/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 99  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 158

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           +  RTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 159 QTARTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 218

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 219 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 278

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 279 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 338

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 398

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G+      ++ +      + P   +K
Sbjct: 399 REEKTEKVEPRRRGNANVWMAPGVRPKGEKETAKPARVEHQQPHRSAK 446



 Score = 37.5 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 452 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 511

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 512 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 562


>gi|256043125|ref|ZP_05446067.1| hypothetical protein Bmelb1R_01497 [Brucella melitensis bv. 1 str.
           Rev.1]
          Length = 611

 Score =  202 bits (514), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 165/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 99  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 158

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 159 QKERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 218

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V + +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 219 GLSRVLELPSTGWLRRYRVRAHGKVTRQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 278

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 279 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 338

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 398

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 399 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 446



 Score = 37.5 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 452 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 511

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 512 ELRNAEGQTTERGKGGSEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 562


>gi|99081768|ref|YP_613922.1| pseudouridine synthase, Rsu [Ruegeria sp. TM1040]
 gi|99038048|gb|ABF64660.1| Pseudouridine synthase Rsu [Ruegeria sp. TM1040]
          Length = 422

 Score =  202 bits (514), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 141/342 (41%), Positives = 193/342 (56%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
            +    R++KV++RAG+ASRRE ERMIA+ RV VNG +++  A+NV + D I VDG PL 
Sbjct: 57  PSQDGDRIAKVLSRAGVASRREAERMIAEGRVAVNGKVIDSPALNVTNLDRIVVDGNPLP 116

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           +AE  RLWLY+KP GLVTT SD  GR T+FD LP    RV++VGRLD+N+EGLLLLTNDG
Sbjct: 117 EAEAPRLWLYYKPNGLVTTTSDEKGRKTIFDALPEDLPRVMTVGRLDLNSEGLLLLTNDG 176

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           G+ R LELPST WLR YRVR +G+    + ++L+KG+VI G  +  M ++LD Q+G+NAW
Sbjct: 177 GVKRQLELPSTGWLRRYRVRINGRPQDHEFDVLRKGVVIDGERFQPMTISLDRQQGANAW 236

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +T+GLREGKNREI++  E   + VNRL+RISYGPFQLGTL  G   E+  +++R+QLG  
Sbjct: 237 LTIGLREGKNREIRRAMEEVGYPVNRLLRISYGPFQLGTLKEGEVEELRPRVVRDQLGLA 296

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
             E        P                +                    +         +
Sbjct: 297 APEGDGEAKKKPTRPGRGPRNPGAKTAGKGIGAPNARPTGKGAVKAPEGRVFSGKTFSGK 356

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                              SG +    ++     ++ S +  
Sbjct: 357 TTGKTAGKPAAHKGQGGKPSGPKSFGTKQGGGSGARGSGKPN 398


>gi|320157132|ref|YP_004189511.1| ribosomal large subunit pseudouridine synthase F [Vibrio vulnificus
           MO6-24/O]
 gi|319932444|gb|ADV87308.1| ribosomal large subunit pseudouridine synthase F [Vibrio vulnificus
           MO6-24/O]
          Length = 347

 Score =  202 bits (514), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 66/340 (19%), Positives = 119/340 (35%), Gaps = 11/340 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RV +NG         V+  D + VDG P+   E+  
Sbjct: 8   RLNKYISETGFCSRREADKLIEQGRVTINGKQP-EMGTKVLPGDDVCVDGKPVAAKEKPV 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCTTERNI--PGNIVDFIGHKKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + +  +  G+ I        +VT    + +     + L 
Sbjct: 125 LRAGNHHEKEYVVRVDKPITPEFIKAMSSGVNILDTVTLPCKVT----QETKFSFRIVLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E   ++V +L R+      L  +  G  R ++   + E L         
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLTDDEVTEILAMCEGSVGT 240

Query: 255 VNLDAPIYSSETLVRDRPNI----ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
                       + +           E      R  +      G +  +    P  ++  
Sbjct: 241 EEASRVDAKGRRIRKATDAKLFDSREENQTSTARRNQKQRTFKGNNADEFRHAPNSKKAQ 300

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                              Q  +  R      +K   R  
Sbjct: 301 QRKQQDGDKPRFEKTKRPEQAGKAKRYDNPNAAKPVKRTG 340


>gi|163844393|ref|YP_001622048.1| hypothetical protein BSUIS_B0209 [Brucella suis ATCC 23445]
 gi|163675116|gb|ABY39226.1| conserved hypothetical protein [Brucella suis ATCC 23445]
          Length = 598

 Score =  202 bits (513), Expect = 7e-50,   Method: Composition-based stats.
 Identities = 164/348 (47%), Positives = 219/348 (62%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 86  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 145

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVG LDINTEGLLLLTNDG
Sbjct: 146 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGHLDINTEGLLLLTNDG 205

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  + +N W
Sbjct: 206 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQDANVW 265

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 266 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 325

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 326 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 385

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 386 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 433



 Score = 37.1 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 439 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 498

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 499 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 549


>gi|54309880|ref|YP_130900.1| putative 16S rRNA uridine-516 pseudouridylate synthase
           [Photobacterium profundum SS9]
 gi|46914319|emb|CAG21098.1| putative 16S rRNA uridine-516 pseudouridylate synthase
           [Photobacterium profundum SS9]
          Length = 372

 Score =  202 bits (513), Expect = 7e-50,   Method: Composition-based stats.
 Identities = 71/362 (19%), Positives = 129/362 (35%), Gaps = 19/362 (5%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K+ +     P R++K I+  G  SRRE +++I Q RV +NG         VM  D + V
Sbjct: 8   NKDQLDPQNKPVRLNKFISDTGYCSRREADKLIDQGRVTINGTQP-EMGTKVMPDDEVLV 66

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           D  PLR  ER      +KP G+  T            +      R+  +GRLD  ++GL+
Sbjct: 67  DDKPLRAKERPIYIALNKPTGVTCTTERHV--KDNIVDFIGHRKRIFPIGRLDKPSDGLI 124

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
            LTNDG +   +        + Y VR   Q+  + L  +  G+ I              +
Sbjct: 125 FLTNDGDIVNKILRAGNSHEKEYVVRVSHQITPEFLEKMASGVEILDTVTLPC----IVK 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           K ++    + L +G NR+I+++ E   + V +L R+      +  L  G  R ++   + 
Sbjct: 181 KETDYSFRITLTQGLNRQIRRMCEALGYDVYKLRRVRIMNITIDGLPNGKWRYLTDAEIA 240

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNI------------ISEVPDDFTRMKKNSS 290
           E                     + + +                   E           + 
Sbjct: 241 EINTLISQSSGTEEASKVDAEGQAIAKATDAKLFDSRQQAAEERQRERERGMRDATYKTF 300

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
           +  G   + +  T    ++  S    A+   S        +    + +    + R  + +
Sbjct: 301 KAKGEFTRTRRNTDRDDKSTDSRNGSARHGDSRPSQSRDHQSFRDQSARDSQAPRGNKPS 360

Query: 351 SA 352
           S 
Sbjct: 361 SG 362


>gi|126739258|ref|ZP_01754952.1| RNA pseudouridylate synthase family protein [Roseobacter sp.
           SK209-2-6]
 gi|126719875|gb|EBA16583.1| RNA pseudouridylate synthase family protein [Roseobacter sp.
           SK209-2-6]
          Length = 377

 Score =  201 bits (512), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 144/320 (45%), Positives = 193/320 (60%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +  +     T  R++KV++RAG+ASRRE ERMIA+ R+ VNG +++  A+NV   + I V
Sbjct: 58  NDKVDHPPSTGDRIAKVLSRAGVASRREAERMIAEGRISVNGTVIDSPALNVTGQERILV 117

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG PL +AE  RLWLYHKP GLVTT+ D  GR T+FD+LP    RV++VGRLD+N+EGLL
Sbjct: 118 DGAPLPQAEAPRLWLYHKPSGLVTTNRDEKGRKTIFDDLPETLPRVMTVGRLDLNSEGLL 177

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTNDGG+ R LELPST WLR YRVR +G+  ++    L+KG+VI G  +  M V LD Q
Sbjct: 178 LLTNDGGIKRKLELPSTGWLRRYRVRINGRPKEEDFAPLRKGLVIDGERFQPMIVDLDRQ 237

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +G+NAW+TVGLREGKNREI++  E   + VNRL+R+SYGPFQLG L  G   E+  ++LR
Sbjct: 238 QGANAWLTVGLREGKNREIRRAMEDIGYNVNRLLRVSYGPFQLGDLKPGEVEELRPRVLR 297

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +QLG     E          S         +          R K  +S+ +     K   
Sbjct: 298 DQLGLEAETEESTPKPRAQRSRGPAPSKGKSDAVRAGAKPGRGKPLASRNSSEGAAKAGG 357

Query: 303 TPVHRRNLASNVWMAKGIHS 322
            P   ++      + K    
Sbjct: 358 KPRQGQSRKKPSPIGKNPRR 377


>gi|269965448|ref|ZP_06179567.1| pseudouridine synthase family 1 protein [Vibrio alginolyticus 40B]
 gi|269829927|gb|EEZ84157.1| pseudouridine synthase family 1 protein [Vibrio alginolyticus 40B]
          Length = 385

 Score =  201 bits (512), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 76/344 (22%), Positives = 127/344 (36%), Gaps = 20/344 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +R+I Q RV +NG         V+  D + VDG P+   E+  
Sbjct: 8   RLNKFISETGFCSRREADRLIEQGRVTINGNKP-EMGTKVLPGDDVCVDGKPVAAKEKPI 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCTTERDV--PGNIVDFIGHQKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + L  +  G+ I        +VT    K +     + L 
Sbjct: 125 LRAGNSHEKEYVVRVDKPITGEFLKQMSSGVKILDTVTLPCKVT----KETKFSFRIVLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL----L 250
           +G NR+I+++ E   ++V +L R+      L  +  G  R +S + + E L         
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSDEEVAEILAMCEGSVGT 240

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           EEA           +       +   E  D   R  + +    G +  +    P  ++  
Sbjct: 241 EEASKTDSGGRNIRKATDAKLFDSREENQDSTARRNQKTRTFRGNNADEFRHAPNSKKGQ 300

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                           D G R            +RS  +    K
Sbjct: 301 Q---------KRRQRDDEGGRPAKEHYKAKPQGERSRPQGEHGK 335


>gi|83859466|ref|ZP_00952987.1| RNA pseudouridylate synthase family protein [Oceanicaulis
           alexandrii HTCC2633]
 gi|83852913|gb|EAP90766.1| RNA pseudouridylate synthase family protein [Oceanicaulis
           alexandrii HTCC2633]
          Length = 354

 Score =  201 bits (512), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 144/345 (41%), Positives = 195/345 (56%), Gaps = 3/345 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E    +R++KV+A AGIASRRE ER+I + RV VNG +L   A  VM+ D + VDG  + 
Sbjct: 12  EEEGGERIAKVLAHAGIASRREAERLIEKGRVSVNGEILRTPAFKVMAGDDVRVDGESIG 71

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           +   TR+W YHKP+GL+TTHSDP GR TVF  LP    RVISVGRLD+N+EGLLLLTNDG
Sbjct: 72  QRPPTRVWRYHKPVGLLTTHSDPQGRDTVFQTLPQDMGRVISVGRLDLNSEGLLLLTNDG 131

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LARVLELPST W R YRVR +G      L  L+ G V+ G+ YG ++VT+D + G+N W
Sbjct: 132 ELARVLELPSTGWTRRYRVRAYGNASDKALAELENGTVVDGVVYGPVEVTVDRRTGANVW 191

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +TVG++EGKNRE++KV +     VNRL+R++YGPFQLG+L  G   E    +LR+QLG  
Sbjct: 192 LTVGIKEGKNREVRKVLQSVGLTVNRLMRVAYGPFQLGSLKRGEISESKLSVLRDQLGKL 251

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
              +       P+   ET   D     ++      R  + S  K           P   +
Sbjct: 252 YPLDTD---GLPLKPGETAKPDTRTGTAKAKPKANRPHQKSGGKPRAGLDADSIMPAGGK 308

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +  +  W      ++    S +R +           +S      +
Sbjct: 309 SKTAKGWAKAKPKANEKPKSSKRSDPKGSGGKASKGKSDADRRRR 353


>gi|326791357|ref|YP_004309178.1| pseudouridine synthase Rsu [Clostridium lentocellum DSM 5427]
 gi|326542121|gb|ADZ83980.1| pseudouridine synthase Rsu [Clostridium lentocellum DSM 5427]
          Length = 240

 Score =  201 bits (512), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 81/239 (33%), Positives = 133/239 (55%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A  GIASRR+ E +I + +V VNG +++     V   D +  +   ++  E+ 
Sbjct: 1   MRLQKYLASCGIASRRKCEELILEGKVSVNGQIIQTLGTQVEEDDEVYYNHKRVQLEEKH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP G VTT  D   R+TV D +  + +R+  VGRLD NT GLLLLT+DG L   
Sbjct: 61  VYYMLNKPAGYVTTVQDEKQRATVLDLMKGVKTRIFPVGRLDYNTSGLLLLTSDGALTYG 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     + Y V+  G+V +  L++L+KG++I        +V +  Q   + W+ + +
Sbjct: 121 LTHPKHHVNKTYEVKLSGKVTERSLDMLRKGVMIDHRKTYPAEVEVVKQNAKHTWLKITI 180

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
            EG+NR+I+K+ E   + V +L R+S G  QLG+L  G  R ++K+ +       ++EE
Sbjct: 181 HEGRNRQIRKMCEAVGYPVVQLKRLSVGSIQLGSLKVGEYRALTKEEVDYLKSIAIIEE 239


>gi|254466733|ref|ZP_05080144.1| RNA pseudouridine synthase family protein [Rhodobacterales
           bacterium Y4I]
 gi|206687641|gb|EDZ48123.1| RNA pseudouridine synthase family protein [Rhodobacterales
           bacterium Y4I]
          Length = 355

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 140/331 (42%), Positives = 191/331 (57%), Gaps = 9/331 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++KV++RAG+ASRRE ERMIA+ RV VNG  ++  A+NV + D I +DG PL +A
Sbjct: 34  PEGDRIAKVLSRAGVASRREAERMIAEGRVSVNGKKIDSPALNVTARDRISIDGQPLPEA 93

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E  R+WLY+KPIGLVT++SD  GR T+FD LP    RV++VGRLD+N+EGLLLLTNDGG+
Sbjct: 94  EGPRMWLYYKPIGLVTSNSDEKGRKTIFDELPEDMPRVMTVGRLDLNSEGLLLLTNDGGI 153

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            R LELP+T WLR YRVR +G+   +    L+KG+VI+G  +  M V+LD Q+G+NAW+T
Sbjct: 154 KRKLELPATGWLRRYRVRINGRPKDEDFAPLRKGLVIEGERFQPMTVSLDRQQGANAWLT 213

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           VGLREGKNREI++  E   + VNRL+R+SYGPFQLG L  G   E+  +++R+QLG    
Sbjct: 214 VGLREGKNREIRRAMEDIGFSVNRLLRVSYGPFQLGNLKPGEVEELRPRVVRDQLGLAEE 273

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           EE            +   +       +                   KQ            
Sbjct: 274 EEIPAARPTRARGGKPAGKPMGKPAGKPMGKPAGKPAGKQAAQPSGKQGNPGRTA----- 328

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSF 341
                 A     +     G  +    ++P  
Sbjct: 329 ----GKAPPARGTRPDQRGGGKRPAGKNPRR 355


>gi|323498587|ref|ZP_08103579.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio sinaloensis
           DSM 21326]
 gi|323316285|gb|EGA69304.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio sinaloensis
           DSM 21326]
          Length = 344

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 72/350 (20%), Positives = 130/350 (37%), Gaps = 16/350 (4%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
              + +R++K I+  G  SRRE +R+I Q RV +NG +       V+  D + VD  P+ 
Sbjct: 2   SQDSAKRLNKFISETGFCSRREADRLIEQGRVTINGRVP-EMGTKVLPGDDVRVDDKPIS 60

Query: 69  KAERT-RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            A         +KP G+  T            +      R+  +GRLD  ++GL+ LTND
Sbjct: 61  AATDKPVYIALNKPTGITCTTERDI--PGNIVDFVGHKKRIFPIGRLDKPSDGLIFLTND 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +        + Y VR    V  D +N +  G+ I         VT +T+     
Sbjct: 119 GDIVNKILRAGNNHEKEYVVRVDKPVSDDFINKMSSGVNILDTVTLPCTVTRETK----F 174

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E   ++V +L R+      L  +  G  R ++   + E L  
Sbjct: 175 SFRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGQWRYLTDAEVAEILAM 234

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNI----ISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                            + + +           E  +   R  +      G +  +    
Sbjct: 235 CEDSSGTEEASKVDGKGKRIRKATDAKLYDSREENQNSTARRNQKQRTFKGRNADEFRHA 294

Query: 304 PVHRRNLASNV--WMAKGIHSSFLS--DSGQREENHRRSPSFPSKRSLRR 349
           P  ++   +      AKG  +   +       + +    P      SL++
Sbjct: 295 PNSKKGRNNGGKHGEAKGKPNKGKTFFKPNSEQSSRPSKPKSGGTLSLKK 344


>gi|256059561|ref|ZP_05449760.1| RNA pseudouridylate synthase family protein [Brucella neotomae
           5K33]
 gi|261323529|ref|ZP_05962726.1| RNA-binding S4 domain-containing protein [Brucella neotomae 5K33]
 gi|261299509|gb|EEY03006.1| RNA-binding S4 domain-containing protein [Brucella neotomae 5K33]
          Length = 581

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 166/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 69  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 128

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 129 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 188

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 189 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 248

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 249 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 308

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 369 REEKAEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 416



 Score = 36.7 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 422 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 481

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 482 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 532


>gi|37679122|ref|NP_933731.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio vulnificus
           YJ016]
 gi|37197864|dbj|BAC93702.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio vulnificus
           YJ016]
          Length = 347

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 66/341 (19%), Positives = 125/341 (36%), Gaps = 14/341 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RV +NG         V+  D + VDG P+   E+  
Sbjct: 8   RLNKYISETGFCSRREADKLIEQGRVTINGKQP-EMGTKVLPGDDVCVDGKPVAAKEKPV 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCTTERNI--PGNIVDFIGHKKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + +  +  G+ I        +VT    + +     + L 
Sbjct: 125 LRAGNHHEKEYVVRVDKPITPEFIKAMSSGVNILDTVTLPCKVT----QETKFSFRIVLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E   ++V +L R+      L  +  G  R ++   + E L         
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLTDDEVTEILAMCEGSVGT 240

Query: 255 VNLDAPIYSSETLVRDRPNI----ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR-- 308
                       + +           E      R  +      G +  +    P  ++  
Sbjct: 241 EEASRVDAKGRRIRKATDAKLFDSREENQTSTARRNQKQRTFKGNNADEFRHAPNSKKAQ 300

Query: 309 -NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                +    +         +G+ +     + + P KR+  
Sbjct: 301 QRKQQDGDKPRFEKPKRQEQAGKAKRYDNPNAAKPVKRTGG 341


>gi|148981998|ref|ZP_01816586.1| pseudouridine synthase family 1 protein [Vibrionales bacterium
           SWAT-3]
 gi|145960686|gb|EDK26030.1| pseudouridine synthase family 1 protein [Vibrionales bacterium
           SWAT-3]
          Length = 381

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 70/362 (19%), Positives = 133/362 (36%), Gaps = 23/362 (6%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + +    +R++K I+  G  SRRE +++I   RV +NG +       VM  D +E+D  P
Sbjct: 1   MSQESQAKRLNKYISETGFCSRREADKLIDAGRVTINGKIP-EMGTKVMPGDDVEIDNKP 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +R  E+      +KP G+  T            +      R+  +GRLD  ++GL+ LTN
Sbjct: 60  VRSKEKPIYIALNKPTGITCTTERDI--PGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTN 117

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG +   +        + Y VR    +  + L  +  G+ I        +V    +K + 
Sbjct: 118 DGDIVNKILRAGNNHEKEYVVRVDKPITGEFLQKMAAGVPILDTVTLPCKV----EKETK 173

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               + L +G NR+I+++ E   ++V +L R+      L  +  G  R +S++ + E L 
Sbjct: 174 FSFRITLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSEEEIAEILA 233

Query: 247 PH-------LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
                       +          +++  + D               +  +    G +  +
Sbjct: 234 MCEGSVSTEDASKINAKGQRIRKATDAKLFDSREENQASTARRNPKENRTRTYRGNNADE 293

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFL---------SDSGQREENHRRSPSFPSKRSLRRT 350
               P  +R   S+    KG                 S    ++  R+ +       R  
Sbjct: 294 FRHAPNSKRGRNSSNGENKGQSKGNTENWKSNSRSERSNSDNKSSDRNRAGRGNADHRGG 353

Query: 351 SA 352
             
Sbjct: 354 KP 355


>gi|27363727|ref|NP_759255.1| ribosomal large subunit pseudouridine synthase F [Vibrio vulnificus
           CMCP6]
 gi|27359843|gb|AAO08782.1| Ribosomal large subunit pseudouridine synthase F [Vibrio vulnificus
           CMCP6]
          Length = 347

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 66/341 (19%), Positives = 125/341 (36%), Gaps = 14/341 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RV +NG         V+  D + VDG P+   E+  
Sbjct: 8   RLNKYISETGFCSRREADKLIEQGRVTINGKQP-EMGTKVLPGDDVCVDGKPVAAKEKPV 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCTTERDI--PGNIVDFIGHKKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + +  +  G+ I        +VT    + +     + L 
Sbjct: 125 LRAGNHHEKEYVVRVDKPITPEFIKAMSSGVNILDTVTLPCKVT----QETKFSFRIVLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E   ++V +L R+      L  +  G  R ++   + E L         
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLTDDEVTEILAMCEGSVGT 240

Query: 255 VNLDAPIYSSETLVRDRPNI----ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR-- 308
                       + +           E      R  +      G +  +    P  ++  
Sbjct: 241 EEASRVDAKGRRIRKATDAKLFDSREENQTSTARRNQKQRTFKGNNADEFRHAPNSKKAQ 300

Query: 309 -NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                +    +         +G+ +     + + P KR+  
Sbjct: 301 QRKQQDGDKPRFEKPKRQEQAGKAKRYDNPNAAKPVKRTGG 341


>gi|189425784|ref|YP_001952961.1| pseudouridine synthase [Geobacter lovleyi SZ]
 gi|189422043|gb|ACD96441.1| pseudouridine synthase [Geobacter lovleyi SZ]
          Length = 274

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 96/268 (35%), Positives = 138/268 (51%), Gaps = 1/268 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K+I+ AGI SRR  E MI   RV VNG ++           D I +DG P++ AE 
Sbjct: 3   ERLQKIISAAGITSRRAAEEMILAGRVTVNGQVVTELGSKADPAKDLIALDGQPVKPAET 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L HKP G VT+  DP GR  V + +  +  R+  VGRLD N+EGLLLLTNDG  A 
Sbjct: 63  FYYVLLHKPAGYVTSLKDPQGRQLVTELVKDVGERLFPVGRLDYNSEGLLLLTNDGAWAN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  Q  + Y VR  G++D  ++  L  G+ ++    G   V L     SN W++V 
Sbjct: 123 RLMHPRHQVDKEYHVRVRGKIDPQQIKKLADGVELEDGPTGATTVRLLKNDQSNDWLSVT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           +REG+NR+++++       V RL RI YG   LG L  G  R +S++  +    P  +++
Sbjct: 183 IREGRNRQVRRMCAAVGLFVVRLRRIRYGNLTLGGLQPGEYRLLSREEAQALDAPPPVKQ 242

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPD 280
            +  + AP+ SS T     P        
Sbjct: 243 REQRMAAPVKSSTTPQSQTPGKRPPRRK 270


>gi|227513314|ref|ZP_03943363.1| pseudouridylate synthase [Lactobacillus buchneri ATCC 11577]
 gi|227083515|gb|EEI18827.1| pseudouridylate synthase [Lactobacillus buchneri ATCC 11577]
          Length = 241

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 80/241 (33%), Positives = 121/241 (50%), Gaps = 1/241 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +R+ KV+A AG+ASRR+ E++I +  VKVNG +++     V  +D +EVD VP+ K   
Sbjct: 2   SERLQKVMAHAGVASRRKAEKLIVEGHVKVNGKVVKELGTKVTESDEVEVDEVPISKEVP 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               LY     ++T  +D   R TV D L  +  R+  VGRLD +T GLLLLTNDG L  
Sbjct: 62  VYYLLYKPRG-VITAVTDDKHRKTVIDLLSEVTERIYPVGRLDYDTSGLLLLTNDGDLDN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + Y  +  G +  D +  L+ GI I G      + T+     ++  V++ 
Sbjct: 121 HLTHPKYEVDKTYVAKVKGTITNDDMKKLRTGIHIDGRKTASAKATIIRNNNNSTIVSLT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           + EG+N ++KK+F      V +L R SYG   L  L  G  R +    + E        +
Sbjct: 181 IHEGRNHQVKKMFLALGHPVEKLSRQSYGFLNLDGLQPGDYRRLKPHEVEELKKMSQDRK 240

Query: 253 A 253
            
Sbjct: 241 R 241


>gi|220926361|ref|YP_002501663.1| RNA-binding S4 domain-containing protein [Methylobacterium nodulans
           ORS 2060]
 gi|219950968|gb|ACL61360.1| RNA-binding S4 domain protein [Methylobacterium nodulans ORS 2060]
          Length = 576

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 190/334 (56%), Gaps = 1/334 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KVIARAGIASRR+ E MI + RV +NG  L   AVNV   D I VDG PL   ERTR
Sbjct: 36  RIAKVIARAGIASRRDAEAMILEGRVTLNGETLTSPAVNVGPNDRITVDGEPLPVRERTR 95

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LW++HKP G+VTT  DP+GR TVF+ LP    RV++VGRLDINTEGLLLLTNDGGLA+V+
Sbjct: 96  LWIFHKPRGVVTTARDPEGRQTVFEILPEDLPRVVAVGRLDINTEGLLLLTNDGGLAKVI 155

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P T WLR YRVR +G +DQ +L+ L+ G+ I G+ YG ++ ++D Q+G N W+T+GLR
Sbjct: 156 AHPETGWLRRYRVRAYGDIDQAQLDRLRDGVTIDGMEYGPIEASIDRQQGDNVWLTLGLR 215

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           EGKNRE+K++ E     VNRLIR+S+GPFQLG L  G   EV  K+L+EQLG  L E+A 
Sbjct: 216 EGKNREVKRILEHLGLSVNRLIRLSFGPFQLGDLEVGLVEEVRTKVLKEQLGTALAEQAG 275

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
           V+  +P+                        +     +    ++             +  
Sbjct: 276 VDFTSPVREPIAPFGSPKGARKTAAATAQAPQGRGEGRPARGERPAWGERPMWGERPARG 335

Query: 315 WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                    F    G      R           R
Sbjct: 336 GRDP-ARPQFGRAPGPGTRPERSRTPEAGPAPRR 368


>gi|297249906|ref|ZP_06933607.1| ribosomal large subunit pseudouridine synthase B [Brucella abortus
           bv. 5 str. B3196]
 gi|297173775|gb|EFH33139.1| ribosomal large subunit pseudouridine synthase B [Brucella abortus
           bv. 5 str. B3196]
          Length = 598

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 166/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 86  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 145

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 146 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 205

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 206 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 265

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 266 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 325

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 326 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 385

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 386 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 433



 Score = 36.7 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 439 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 498

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 499 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 549


>gi|89072747|ref|ZP_01159312.1| putative 16S rRNA uridine-516 pseudouridylate synthase
           [Photobacterium sp. SKA34]
 gi|89051567|gb|EAR57021.1| putative 16S rRNA uridine-516 pseudouridylate synthase
           [Photobacterium sp. SKA34]
          Length = 357

 Score =  201 bits (510), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 79/351 (22%), Positives = 134/351 (38%), Gaps = 14/351 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M      Q++    R++K I+  G  SRRE +++I Q RV +NG       V VM  D +
Sbjct: 1   MSQNPTEQQSPKGVRLNKFISDTGYCSRREADKLIDQGRVTINGQKP-EMGVRVMDNDDV 59

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            +D  PLR  ER      +KP G+  T       + V         R+  +GRLD  ++G
Sbjct: 60  LIDDKPLRSKERPIYIALNKPTGITCTTERHIEGNIVDFI--GHRKRIFPIGRLDKPSDG 117

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+ LTNDG +   +        + Y VR    +  + L  +  G+ I        +VT  
Sbjct: 118 LIFLTNDGDIVNKILRAGNSHEKEYVVRVDKVITPEFLEKMASGVEILDTVTLPCKVT-- 175

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             K +N    + L +G NR+I+++ E   ++V +L R+      +  L  G  R ++   
Sbjct: 176 --KETNFSFRIVLTQGLNRQIRRMCEALGYEVYKLRRVRIMNITIDGLPNGKWRYLTDDE 233

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN------- 293
           + E                       + +     + +      R +K + +K        
Sbjct: 234 IGEINRLIAQSSGTEEASKVDAEGRKIAKATDAKLYDHRQQEARNEKRAQEKAFKTYSGT 293

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           G   ++      +RRN  S     +       +    R  +    PSF  K
Sbjct: 294 GEFTRRPGGQRQNRRNEESGESRQQRSQGRNDNRRPARTSDRDSKPSFGGK 344


>gi|154251100|ref|YP_001411924.1| RNA-binding S4 domain-containing protein [Parvibaculum
           lavamentivorans DS-1]
 gi|154155050|gb|ABS62267.1| RNA-binding S4 domain protein [Parvibaculum lavamentivorans DS-1]
          Length = 327

 Score =  201 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 188/318 (59%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +     R++KVIARAGI SRRE E++I + RV V+G +L+  A+NV   + I VDG  L 
Sbjct: 10  DTPAGDRIAKVIARAGICSRREAEKLIEEGRVTVDGKVLKSPALNVTGRETIIVDGKALP 69

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             E T+LW YHKP GLVTT  DP+GR+TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 70  AQEPTKLWRYHKPAGLVTTAKDPEGRTTVFEKLPDDIPRVVSVGRLDINTEGLLLLTNDG 129

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LAR+LELP+T W R YRVR  G++ Q  L+ LK GI ++G+ YG ++ T+D  +GSN W
Sbjct: 130 ELARLLELPATGWTRRYRVRAWGRITQADLDKLKNGITVEGVRYGPIEATIDKVQGSNVW 189

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +T+GL+EGKNRE+K+V       VNRLIR+S+GPFQ+G L  G  ++V  ++L +QLG H
Sbjct: 190 LTLGLKEGKNREVKRVLAELGLSVNRLIRLSFGPFQIGDLEPGDIKQVPNRVLMDQLGAH 249

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
             + A   +     ++                   +      +      + KL T   ++
Sbjct: 250 AEQFAPAEVRPSKGAATGSTGKWTGGKPVGRKAGDKPPAKPERTKPGGTKPKLKTFREKK 309

Query: 309 NLASNVWMAKGIHSSFLS 326
              +    A         
Sbjct: 310 ADTAGKRKAPNADRRRRP 327


>gi|254230555|ref|ZP_04923923.1| conserved hypothetical protein, putative [Vibrio sp. Ex25]
 gi|262394965|ref|YP_003286819.1| ribosomal large subunit pseudouridine synthase F [Vibrio sp. Ex25]
 gi|151936927|gb|EDN55817.1| conserved hypothetical protein, putative [Vibrio sp. Ex25]
 gi|262338559|gb|ACY52354.1| ribosomal large subunit pseudouridine synthase F [Vibrio sp. Ex25]
          Length = 385

 Score =  201 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 72/344 (20%), Positives = 122/344 (35%), Gaps = 20/344 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +R+I Q RV +NG         V+  D + VDG P+   E+  
Sbjct: 8   RLNKFISETGFCSRREADRLIEQGRVTINGNKP-EMGTKVLPGDDVCVDGKPVAAKEKPI 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCTTERDV--PGNIVDFIGHKKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + L  +  G+ I        +VT    K +     + L 
Sbjct: 125 LRAGNSHEKEYVVRVDKPITGEFLKQMSSGVKILDTVTLPCKVT----KETKFSFRIVLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E   ++V +L R+      L  +  G  R ++   + E L         
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLTDDEVAEILAMCDGSVGT 240

Query: 255 VNLDAPIYSSETLVRDRPNI----ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
                       + +           E  D  +R  +      G +       P  ++  
Sbjct: 241 EEASRVDSKGRNIRKATDAKLYDSREENQDSVSRRNQKPRTYRGNNADDFRHAPNSKKGQ 300

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                           D G R            +RS  +    K
Sbjct: 301 Q---------KRRQRDDEGGRPAKEHYKAKPQGERSRPQGEHGK 335


>gi|269961576|ref|ZP_06175938.1| Ribosomal large subunit pseudouridine synthase F [Vibrio harveyi
           1DA3]
 gi|269833617|gb|EEZ87714.1| Ribosomal large subunit pseudouridine synthase F [Vibrio harveyi
           1DA3]
          Length = 384

 Score =  201 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 68/343 (19%), Positives = 124/343 (36%), Gaps = 11/343 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +R+I Q RV +NG         V+  D + VDG P+   E+  
Sbjct: 8   RLNKYISETGFCSRREADRLIEQGRVTINGQQP-EMGTKVLPGDDVCVDGNPVAAKEKPI 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCTTERDI--PGNIVDFIGHKKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + L  +  G+ I        +V    +K +     + L 
Sbjct: 125 LRAGNNHEKEYVVRVDKPITGEFLKQMSSGVKILDTVTLPCKV----EKETKFSFRIVLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L         
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSDDEVAEILAMCEGSVGT 240

Query: 255 VNLDAPIYSSETLVRDRPNI----ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
                       + +           E      R  + +    G +  +    P  ++  
Sbjct: 241 EEASKTDSRGRNIRKATDAKLYDSREENQGSTARRNQKTRTFRGNNADEFRHAPNSKKGQ 300

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                  +G   +      + +    R      K   +  ++ 
Sbjct: 301 QRRQRDDEGGRPAKEHYKAKPQGERSRPQGEHGKSHRKPDASS 343


>gi|254719940|ref|ZP_05181751.1| RNA pseudouridylate synthase family protein [Brucella sp. 83/13]
 gi|265984948|ref|ZP_06097683.1| RNA-binding S4 domain-containing protein [Brucella sp. 83/13]
 gi|264663540|gb|EEZ33801.1| RNA-binding S4 domain-containing protein [Brucella sp. 83/13]
          Length = 577

 Score =  201 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 166/348 (47%), Positives = 220/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 69  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 128

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 129 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 188

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 189 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 248

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 249 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 308

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGEPPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P    K
Sbjct: 369 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSVK 416



 Score = 37.1 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 14/111 (12%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    + +   +            R       PD+  + +K+          K+   
Sbjct: 422 QMRPRRYSDEERGGEEGGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 481

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 482 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 532


>gi|224541350|ref|ZP_03681889.1| hypothetical protein CATMIT_00510 [Catenibacterium mitsuokai DSM
           15897]
 gi|224525684|gb|EEF94789.1| hypothetical protein CATMIT_00510 [Catenibacterium mitsuokai DSM
           15897]
          Length = 247

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 76/230 (33%), Positives = 118/230 (51%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA++G  SRR+ E +I Q +V VNG ++      V   D I V+G  + K ++ 
Sbjct: 3   ERLQKVIAQSGYTSRRKAEELIQQGKVTVNGEVVTVLGTKVTKKDTICVNGKLINKEDKV 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     + T   +   R+ V D       RV  VGRLD +T G L +TNDG  A +
Sbjct: 63  YYLFYKPEKCVCTMSDE-HDRTCVADYFADSNERVYPVGRLDYDTTGALFMTNDGEFANL 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVTV 191
           +  PS+   +VY V   G + + + N L+KGI ++G+     ++ +  + ++     + +
Sbjct: 122 IMHPSSHLEKVYEVSVKGLLTKAEKNQLEKGIYLEGVKTLPCEIAITGNDEEHGTTMLLI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            L EGKNR+IKK+FE     V RL RI  GP  L  L  G+ R +    +
Sbjct: 182 RLVEGKNRQIKKMFEEVGHPVKRLRRIMIGPIDLKGLTPGTYRRLKPHEV 231


>gi|90961915|ref|YP_535831.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           salivarius UCC118]
 gi|301299322|ref|ZP_07205607.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           salivarius ACS-116-V-Col5a]
 gi|90821109|gb|ABD99748.1| Ribosomal large subunit pseudouridine synthase B [Lactobacillus
           salivarius UCC118]
 gi|300214638|gb|ADJ79054.1| Pseudouridine synthase [Lactobacillus salivarius CECT 5713]
 gi|300853062|gb|EFK80661.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           salivarius ACS-116-V-Col5a]
          Length = 242

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 83/240 (34%), Positives = 132/240 (55%), Gaps = 2/240 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR  E++I + RV VNG+++      V S D I VDG  L+K E+ 
Sbjct: 3   ERLQKVMANAGVASRRASEKLIQEGRVMVNGVVVTELGTKVESDDSISVDGKLLKKDEKK 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G+++   D  GR  V D L  +  R+  VGRLD +T GLL+LTNDG  A  
Sbjct: 63  VYYLLYKPRGVISAAKDNKGREVVTDYLKDVPERLYPVGRLDYDTSGLLILTNDGDFANQ 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  + Y  +  G +  D +  L+ G+VI G      +  + ++    + + V++
Sbjct: 123 MMHPRYKVDKTYVAKVEGLITPDSIKKLRNGVVIDGKPTSRARAKILSRDAKKNTSIVSL 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+  ++KK+F+    KV +L R +YG   L  L +G  RE+S   +RE L     +
Sbjct: 183 TIHEGRYHQVKKMFDAVGHKVQKLSRTTYGTLTLDGLTSGEYRELSHNEVRELLKLINNK 242


>gi|91228934|ref|ZP_01262832.1| pseudouridine synthase family 1 protein [Vibrio alginolyticus
           12G01]
 gi|91187517|gb|EAS73851.1| pseudouridine synthase family 1 protein [Vibrio alginolyticus
           12G01]
          Length = 385

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 76/344 (22%), Positives = 127/344 (36%), Gaps = 20/344 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +R+I Q RV +NG         V+  D + VDG P+   E+  
Sbjct: 8   RLNKFISETGFCSRREADRLIEQGRVTINGNKP-EMGTKVLPGDDVCVDGKPVAAKEKPI 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCTTERDV--PGNIVDFIGHQKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + L  +  G+ I        +VT    K +     + L 
Sbjct: 125 LRAGNSHEKEYVVRVDKPITVEFLKQMSSGVKILDTVTLPCKVT----KETKFSFRIVLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL----L 250
           +G NR+I+++ E   ++V +L R+      L  +  G  R +S + + E L         
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSDEEVAEILAMCEGSVGT 240

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           EEA           +       +   E  D   R  + +    G +  +    P  ++  
Sbjct: 241 EEASKTDSRGRNIRKATDAKLFDSREENQDSTARRNQKTRTFRGNNADQFRHAPNSKKGQ 300

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                           D G R            +RS  +    K
Sbjct: 301 Q---------KRRQCDDEGGRPAKEHYKAKPQGERSRPQGEHGK 335


>gi|256029912|ref|ZP_05443526.1| RNA pseudouridylate synthase family protein [Brucella pinnipedialis
           M292/94/1]
 gi|261319066|ref|ZP_05958263.1| RNA-binding S4 domain-containing protein [Brucella pinnipedialis
           B2/94]
 gi|265986930|ref|ZP_06099487.1| RNA-binding S4 domain-containing protein [Brucella pinnipedialis
           M292/94/1]
 gi|261298289|gb|EEY01786.1| RNA-binding S4 domain-containing protein [Brucella pinnipedialis
           B2/94]
 gi|264659127|gb|EEZ29388.1| RNA-binding S4 domain-containing protein [Brucella pinnipedialis
           M292/94/1]
          Length = 581

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 166/348 (47%), Positives = 222/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 69  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 128

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 129 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 188

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 189 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 248

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 249 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 308

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G+      ++ +      + P   +K
Sbjct: 369 REEKTEKVEPRRRGNANVWMAPGVRPKGEKEAAKPARVEHQQPHRSAK 416



 Score = 36.7 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 422 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 481

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 482 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 532


>gi|254712060|ref|ZP_05173871.1| RNA pseudouridylate synthase family protein [Brucella ceti
           M644/93/1]
 gi|254715130|ref|ZP_05176941.1| RNA pseudouridylate synthase family protein [Brucella ceti
           M13/05/1]
 gi|261216838|ref|ZP_05931119.1| RNA-binding S4 domain-containing protein [Brucella ceti M13/05/1]
 gi|260921927|gb|EEX88495.1| RNA-binding S4 domain-containing protein [Brucella ceti M13/05/1]
          Length = 581

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 166/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 69  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 128

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 129 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 188

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 189 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 248

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 249 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 308

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 369 REEKTEKVEPRRRSNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 416



 Score = 36.7 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 422 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 481

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 482 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 532


>gi|254706249|ref|ZP_05168077.1| RNA pseudouridylate synthase family protein [Brucella pinnipedialis
           M163/99/10]
          Length = 581

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 166/348 (47%), Positives = 222/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 69  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 128

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 129 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 188

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 189 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 248

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 249 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 308

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G+      ++ +      + P   +K
Sbjct: 369 REEKTEKVEPRRRGNANVWMAPGVRPKGEKEAAKPARVEHQQPHRSAK 416



 Score = 36.7 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 422 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 481

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 482 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 532


>gi|295399019|ref|ZP_06809001.1| pseudouridine synthase [Geobacillus thermoglucosidasius C56-YS93]
 gi|312110375|ref|YP_003988691.1| pseudouridine synthase [Geobacillus sp. Y4.1MC1]
 gi|294978485|gb|EFG54081.1| pseudouridine synthase [Geobacillus thermoglucosidasius C56-YS93]
 gi|311215476|gb|ADP74080.1| pseudouridine synthase [Geobacillus sp. Y4.1MC1]
          Length = 243

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 81/237 (34%), Positives = 128/237 (54%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIARAGIASRR+ E++I Q +VKVNG ++    V V   D +EVDG+P+ K E  
Sbjct: 2   ERLQKVIARAGIASRRKAEQLILQGKVKVNGKIVTELGVKVGPRDKVEVDGIPVEKEEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     ++++  D  GR  V D    I  R+  VGRLD +T G+LLLTNDG  A +
Sbjct: 62  YYLFYKPRG-VISSVKDDKGRKVVTDFFKDIDKRIYPVGRLDYDTSGILLLTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           L  P  +  +VY  +      +++L  L+KGI+++       +V L    ++   A + +
Sbjct: 121 LMHPRYEIEKVYIAKVKKIPTREQLKQLEKGIMLEDGMTAPAKVKLLSHDKQKQTAIIEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + EG+NR+++++FE     V +L R  Y    L  L  G  RE++   +++     
Sbjct: 181 RIHEGRNRQVRRMFEAIGCNVMKLKRERYAFLDLKGLNPGEYRELTPHEVKQLRALA 237


>gi|239827574|ref|YP_002950198.1| pseudouridine synthase [Geobacillus sp. WCH70]
 gi|239807867|gb|ACS24932.1| pseudouridine synthase [Geobacillus sp. WCH70]
          Length = 243

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 77/237 (32%), Positives = 129/237 (54%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGIASRR+ E++I Q +VKVNG ++    V V   D +EVDG+P+ + E  
Sbjct: 2   ERLQKVIAHAGIASRRKAEQLILQGKVKVNGKVVTELGVKVGPQDKVEVDGIPVEREEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     ++++  D  GR  V D    +  R+  +GRLD +T G+LLLTNDG  A +
Sbjct: 62  YYLFYKPRG-VISSVKDDKGRKVVTDFFKDVDKRIYPIGRLDYDTSGILLLTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           L  P  +  +VY  +  G   +++L  L++GI+++       +V L    ++   A + +
Sbjct: 121 LMHPRYEIEKVYIAKVKGIPTREQLKQLERGIMLEDGMTAPAKVKLLSHNKQKQTAIIEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + EG+NR+++++FE    KV +L R  Y    L  L  G  R+++   +++     
Sbjct: 181 RIHEGRNRQVRRMFEAIGCKVMKLKRERYAFLDLKGLNPGEYRKLTPHEVKQLRALA 237


>gi|295112967|emb|CBL31604.1| ribosomal large subunit pseudouridine synthase B [Enterococcus sp.
           7L76]
          Length = 238

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 80/237 (33%), Positives = 121/237 (51%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA AG+ SRR+ E +I + RVKVNG +++     V   D +EVDGVP+ + E  
Sbjct: 2   ERLQKAIAHAGVTSRRKAEELIVKGRVKVNGQVVKELGTQVSKQDTVEVDGVPIYQEEYG 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     +++  SD  GR  V D    +  R+  VGRLD +T GLLLLTNDG  ++ 
Sbjct: 62  YYLFYKPKG-VISAVSDDKGRKVVTDYFTDVTERIYPVGRLDYDTSGLLLLTNDGSFSQK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTV 191
           L  P  +  +VY  +  G   +  L  L KGI I G         + +       + V +
Sbjct: 121 LTHPKHEVDKVYVAKIKGVPTKRDLLPLAKGIRIDGKRTAPANFQILSADIKTGSSVVEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + EG+N ++KK+F+   + V +L R  YG   L  L  G  R+++KK + + L   
Sbjct: 181 TIHEGRNHQVKKMFQAVGFPVQKLKRERYGELTLQGLRPGQYRDLTKKEISQLLNQA 237


>gi|163803577|ref|ZP_02197444.1| pseudouridine synthase family 1 protein [Vibrio sp. AND4]
 gi|159172619|gb|EDP57476.1| pseudouridine synthase family 1 protein [Vibrio sp. AND4]
          Length = 383

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 68/331 (20%), Positives = 120/331 (36%), Gaps = 12/331 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +R+I Q RV +NG         V   D + VDG P+   E+  
Sbjct: 8   RLNKFISETGFCSRREADRLIEQGRVTINGQQP-EMGTKVQPGDDVCVDGNPVAAKEKPI 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCTTERDI--PGNIVDFIGHKKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + L  +  G+ I        +V    +K +     + L 
Sbjct: 125 LRAGNNHEKEYVVRVDKPITGEFLKQMSSGVKILDTVTLPCKV----EKETKFSFRIVLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L         
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSDNEVSEILAMCEGSVGT 240

Query: 255 VNLDAPIYSSETLVRDRPNI----ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
                       + +           E  D   R  + +    G +  +    P  ++  
Sbjct: 241 EEASKRDAKGRNIRKATDAKLYDSRDENQDSTARRNQTARTFRGNNADEFRHAPNSKKGQ 300

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSF 341
                  +G   +       + +  R     
Sbjct: 301 QRRQRDNEGGRPASDHYR-AKPQGERSKSHG 330


>gi|297580866|ref|ZP_06942791.1| pseudouridine synthase family 1 protein [Vibrio cholerae RC385]
 gi|297534692|gb|EFH73528.1| pseudouridine synthase family 1 protein [Vibrio cholerae RC385]
          Length = 340

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 76/349 (21%), Positives = 138/349 (39%), Gaps = 21/349 (6%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           + + +     R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG
Sbjct: 11  DYMSQPTEK-RLNKFISETGYCSRREADKLIEQGRVTLNGLQPEV-GSKVTEQDEVCIDG 68

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PLR  ER      +KP G+  T            +      R+  +GRLD  ++GL+ L
Sbjct: 69  KPLRSKERPIYIALNKPTGITCTTERDV--PGNIVDFIGHHKRIFPIGRLDKPSDGLIFL 126

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG +   +        + Y VR    +  + +  +  G+ I        +VT    + 
Sbjct: 127 TNDGDIVNKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVT----QE 182

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +     + L +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E 
Sbjct: 183 TQYSFRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEI 242

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNI--ISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           L                 S +T+ R        S   +  ++ ++N    +G + Q+   
Sbjct: 243 LAMCEDSSGTEEASRVAQSGDTIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRH 302

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
            P  ++                 S S       + +P      SLR++ 
Sbjct: 303 APNSKK-----------AQRRPSSPSSNTASGSKPTPRTGGTLSLRKSK 340


>gi|156973557|ref|YP_001444464.1| pseudouridylate synthase [Vibrio harveyi ATCC BAA-1116]
 gi|156525151|gb|ABU70237.1| hypothetical protein VIBHAR_01258 [Vibrio harveyi ATCC BAA-1116]
          Length = 384

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 68/343 (19%), Positives = 124/343 (36%), Gaps = 11/343 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +R+I Q RV +NG         V+  D + VDG P+   E+  
Sbjct: 8   RLNKYISETGFCSRREADRLIEQGRVTINGQQP-EMGTKVLPGDDVCVDGSPVAAKEKPI 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCTTERDI--PGNIVDFIGHKKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + L  +  G+ I        +V    +K +     + L 
Sbjct: 125 LRAGNNHEKEYVVRVDKPITGEFLKQMSSGVKILDTVTLPCKV----EKETKFSFRIVLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L         
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSDDEVAEILAMCEGSVGT 240

Query: 255 VNLDAPIYSSETLVRDRPNI----ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
                       + +           E      R  + +    G +  +    P  ++  
Sbjct: 241 EEASKTDSRGRNIRKATDAKLYDSREENQGSTARRNQKTRTFLGNNADEFRHAPNSKKGQ 300

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                  +G   +      + +    R      K   +  ++ 
Sbjct: 301 QRRQRDDEGGRPAKEHYKAKPQGERSRPQGEHGKSQRKPDASS 343


>gi|15642221|ref|NP_231854.1| pseudouridine synthase family 1 protein [Vibrio cholerae O1 biovar
           El Tor str. N16961]
 gi|121586284|ref|ZP_01676074.1| pseudouridine synthase family 1 protein [Vibrio cholerae 2740-80]
 gi|121726558|ref|ZP_01679807.1| pseudouridine synthase family 1 protein [Vibrio cholerae V52]
 gi|147674574|ref|YP_001217740.1| pseudouridine synthase family 1 protein [Vibrio cholerae O395]
 gi|153817102|ref|ZP_01969769.1| pseudouridine synthase family 1 protein [Vibrio cholerae NCTC 8457]
 gi|153820868|ref|ZP_01973535.1| pseudouridine synthase family 1 protein [Vibrio cholerae B33]
 gi|153825357|ref|ZP_01978024.1| pseudouridine synthase family 1 protein [Vibrio cholerae MZO-2]
 gi|227082347|ref|YP_002810898.1| pseudouridine synthase family 1 protein [Vibrio cholerae M66-2]
 gi|254849353|ref|ZP_05238703.1| pseudouridine synthase family 1 protein [Vibrio cholerae MO10]
 gi|298500401|ref|ZP_07010206.1| pseudouridine synthase family 1 protein [Vibrio cholerae MAK 757]
 gi|9656781|gb|AAF95367.1| pseudouridine synthase family 1 protein [Vibrio cholerae O1 biovar
           El Tor str. N16961]
 gi|121549550|gb|EAX59576.1| pseudouridine synthase family 1 protein [Vibrio cholerae 2740-80]
 gi|121631011|gb|EAX63390.1| pseudouridine synthase family 1 protein [Vibrio cholerae V52]
 gi|126512370|gb|EAZ74964.1| pseudouridine synthase family 1 protein [Vibrio cholerae NCTC 8457]
 gi|126521660|gb|EAZ78883.1| pseudouridine synthase family 1 protein [Vibrio cholerae B33]
 gi|146316457|gb|ABQ20996.1| pseudouridine synthase family 1 protein [Vibrio cholerae O395]
 gi|149741041|gb|EDM55110.1| pseudouridine synthase family 1 protein [Vibrio cholerae MZO-2]
 gi|227010235|gb|ACP06447.1| pseudouridine synthase family 1 protein [Vibrio cholerae M66-2]
 gi|227014119|gb|ACP10329.1| pseudouridine synthase family 1 protein [Vibrio cholerae O395]
 gi|254845058|gb|EET23472.1| pseudouridine synthase family 1 protein [Vibrio cholerae MO10]
 gi|297541094|gb|EFH77148.1| pseudouridine synthase family 1 protein [Vibrio cholerae MAK 757]
          Length = 340

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 77/345 (22%), Positives = 137/345 (39%), Gaps = 20/345 (5%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
              T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR
Sbjct: 14  SQPTEKRLNKFISETGYCSRREADKLIEQGRVTLNGLQPEV-GSKVTEQDEVCIDGKPLR 72

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ER      +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG
Sbjct: 73  SKERPIYIALNKPTGITCTTERDV--PGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTNDG 130

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y VR    +  + +  +  G+ I        +VT    + +   
Sbjct: 131 DIVNKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVT----QETQYS 186

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L   
Sbjct: 187 FRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILAMC 246

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNI--ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                         S +T+ R        S   +  ++ ++N    +G + Q+    P  
Sbjct: 247 EDSSGTEEASRVAQSGDTIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNS 306

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
           ++                 S S       + +P      SLR++ 
Sbjct: 307 KK-----------AQRRPSSPSSNTASGSKPTPRTGGTLSLRKSK 340


>gi|153213785|ref|ZP_01948993.1| pseudouridine synthase family 1 protein [Vibrio cholerae 1587]
 gi|124115709|gb|EAY34529.1| pseudouridine synthase family 1 protein [Vibrio cholerae 1587]
          Length = 340

 Score =  200 bits (509), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 77/345 (22%), Positives = 136/345 (39%), Gaps = 20/345 (5%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
              T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR
Sbjct: 14  SQPTEKRLNKFISETGYCSRREADKLIEQGRVTLNGLQPEV-GSKVTEQDEVCIDGKPLR 72

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ER      +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG
Sbjct: 73  SKERPIYIALNKPTGITCTTERDV--PGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTNDG 130

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y VR    +  + +  +  G+ I        +VT    + +   
Sbjct: 131 DIVNKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVT----QETQYS 186

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L   
Sbjct: 187 FRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSDTEVSEILAMC 246

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNI--ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                         S +T+ R        S   +  ++ ++N    +G + Q+    P  
Sbjct: 247 EDSSGTEEASRVAQSGDTIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNS 306

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
           ++                 S S       + +P      SLR++ 
Sbjct: 307 KK-----------AQRRPSSPSSNTASGSKPTPRTGGTLSLRKSK 340


>gi|225686060|ref|YP_002734032.1| hypothetical protein BMEA_B0205 [Brucella melitensis ATCC 23457]
 gi|225642165|gb|ACO02078.1| conserved hypothetical protein [Brucella melitensis ATCC 23457]
          Length = 598

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 165/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 86  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 145

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 146 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 205

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V + +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 206 GLSRVLELPSTGWLRRYRVRAHGKVTRQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 265

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 266 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 325

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 326 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 385

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 386 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 433



 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 439 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 498

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 499 ELRNAEGQTTERGKGGSEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 549


>gi|227890935|ref|ZP_04008740.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           salivarius ATCC 11741]
 gi|227867344|gb|EEJ74765.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           salivarius ATCC 11741]
          Length = 242

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 83/240 (34%), Positives = 132/240 (55%), Gaps = 2/240 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR  E++I + RV VNG+++      V S D I VDG  L+K E+ 
Sbjct: 3   ERLQKVMANAGVASRRASEKLIQEGRVMVNGVVVTELGTKVESDDSISVDGKLLKKDEKK 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G+++   D  GR  V D L  +  R+  VGRLD +T GLL+LTNDG  A  
Sbjct: 63  VYYLLYKPRGVISAAKDNKGREVVTDYLKDVPERLYPVGRLDYDTSGLLILTNDGDFANQ 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  + Y  +  G +  D +  L+ G+VI G      +  + ++    + + V++
Sbjct: 123 MMHPRYKVDKTYVAKVEGLITPDSIKKLRNGVVIDGKPTSRARAKIISRDAKKNTSIVSL 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+  ++KK+F+    KV +L R +YG   L  L +G  RE+S   +RE L     +
Sbjct: 183 TIHEGRYHQVKKMFDAVGHKVQKLSRTTYGTLTLDGLTSGEYRELSHNEVRELLKLINNK 242


>gi|328473478|gb|EGF44326.1| pseudouridine synthase family 1 protein [Vibrio parahaemolyticus
           10329]
          Length = 371

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 67/343 (19%), Positives = 123/343 (35%), Gaps = 13/343 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRR  +++I + RV +NG         V+  D + VDG P+   E+  
Sbjct: 8   RLNKFISETGFCSRRAADKLIEEGRVTINGKQP-EMGTKVLPGDDVCVDGKPVASKEKPI 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCTTERDI--PGNIVDFIGHKKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + L  +  G+ I        +VT    K +     + L 
Sbjct: 125 LRAGNNHEKEYVVRVDKPITDEFLKQMSSGVRILDTVTLPCKVT----KETKFSFRIVLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL----L 250
           +G NR+I+++ E   ++V +L R+      L  +  G  R ++   + E L         
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLTDDEVAEILAMCDGSVGT 240

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           EEA           +       +   E      R  + +    G +  +    P  ++  
Sbjct: 241 EEASKTDSRGRNIRKATDAKLFDSREENQGSTARRNQKTRTFRGNNADEFRHAPNSKKGQ 300

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                               + +  R  P    +    +   +
Sbjct: 301 QKRRQRDDENSRPAKEHYKAKPQGERAKP--QGEHGRPQNKPQ 341


>gi|254699496|ref|ZP_05161324.1| RNA pseudouridylate synthase family protein [Brucella suis bv. 5
           str. 513]
 gi|261749951|ref|ZP_05993660.1| RNA-binding S4 domain-containing protein [Brucella suis bv. 5 str.
           513]
 gi|261739704|gb|EEY27630.1| RNA-binding S4 domain-containing protein [Brucella suis bv. 5 str.
           513]
          Length = 581

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 166/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 69  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 128

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 129 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 188

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 189 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 248

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 249 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 308

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 369 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 416



 Score = 36.7 bits (83), Expect = 6.1,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 422 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 481

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 482 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 532


>gi|227524458|ref|ZP_03954507.1| pseudouridylate synthase [Lactobacillus hilgardii ATCC 8290]
 gi|227088377|gb|EEI23689.1| pseudouridylate synthase [Lactobacillus hilgardii ATCC 8290]
          Length = 241

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 80/241 (33%), Positives = 121/241 (50%), Gaps = 1/241 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +R+ KV+A AG+ASRR+ E++I +  VKVNG +++     V  +D +EVD VP+ K   
Sbjct: 2   SERLQKVMAHAGVASRRKAEKLIVEGHVKVNGKVVKELGTKVTESDEVEVDEVPISKEVP 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               LY     ++T  +D   R TV D L  +  R+  VGRLD +T GLLLLTNDG L  
Sbjct: 62  VYYLLYKPRG-VITAVTDDKHRKTVIDLLSEVTERIYPVGRLDYDTSGLLLLTNDGDLDN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + Y  +  G +  D +  L+ GI I G      + T+     ++  V++ 
Sbjct: 121 HLTHPKYEVDKTYVAKVKGTITNDDMKRLRTGIHIDGRKTASAKATVIRNNNNSTIVSLT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           + EG+N ++KK+F      V +L R SYG   L  L  G  R +    + E        +
Sbjct: 181 IHEGRNHQVKKMFLALGHPVEKLSRQSYGFLNLDGLQPGDYRRLKPHEVEELKKMSQDRK 240

Query: 253 A 253
            
Sbjct: 241 R 241


>gi|254286468|ref|ZP_04961425.1| pseudouridine synthase family 1 protein [Vibrio cholerae AM-19226]
 gi|150423417|gb|EDN15361.1| pseudouridine synthase family 1 protein [Vibrio cholerae AM-19226]
          Length = 340

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 73/334 (21%), Positives = 130/334 (38%), Gaps = 9/334 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
              T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR
Sbjct: 14  SQPTEKRLNKFISETGYCSRREADKLIEQGRVTLNGLQPEV-GSKVTEQDEVCIDGKPLR 72

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ER      +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG
Sbjct: 73  SKERPIYIALNKPTGITCTTERDV--PGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTNDG 130

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y VR    +  + +  +  G+ I        +VT    + +   
Sbjct: 131 DIVNKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVT----QETQYS 186

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L   
Sbjct: 187 FRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILAMC 246

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNI--ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                         S +T+ R        S   +  ++ ++N    +G + Q+    P  
Sbjct: 247 EDSSGTEEASRVAQSGDTIKRATDAKLFDSRETNKESKARRNPKTYHGKNAQEFRHAPNS 306

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
           ++        +    S              R   
Sbjct: 307 KKAQRRPSSTSSNTASGSKPTPRTGGTLSLRKSK 340


>gi|254225784|ref|ZP_04919389.1| pseudouridine synthase family 1 protein [Vibrio cholerae V51]
 gi|125621690|gb|EAZ50019.1| pseudouridine synthase family 1 protein [Vibrio cholerae V51]
          Length = 340

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 77/345 (22%), Positives = 137/345 (39%), Gaps = 20/345 (5%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
              T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR
Sbjct: 14  SQPTEKRLNKFISETGYCSRREADKLIEQGRVTLNGLQPEV-GSKVTDQDEVCIDGKPLR 72

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ER      +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG
Sbjct: 73  SKERPIYIALNKPTGITCTTERDV--PGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTNDG 130

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y VR    +  + +  +  G+ I        +VT    + +   
Sbjct: 131 DIVNKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVT----QETQYS 186

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L   
Sbjct: 187 FRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILAMC 246

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNI--ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                         S +T+ R        S   +  ++ ++N    +G + Q+    P  
Sbjct: 247 EDSSGTEEASRVAQSGDTIKRATDAKLFDSRETNKESKARRNPKTYHGKNAQEFRHAPNS 306

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
           ++                 S S       + +P      SLR++ 
Sbjct: 307 KK-----------AQRRPSSPSSNTASGSKPTPRTGGTLSLRKSK 340


>gi|319898380|ref|YP_004158473.1| Pseudouridine synthase [Bartonella clarridgeiae 73]
 gi|319402344|emb|CBI75883.1| Pseudouridine synthase [Bartonella clarridgeiae 73]
          Length = 496

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 163/382 (42%), Positives = 211/382 (55%), Gaps = 29/382 (7%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           + +  + E    +R++K +ARAG+ASRR+ E MI   R+ VNG ++     NV  +D I 
Sbjct: 29  QSEKKMSEKSESERIAKRLARAGVASRRDAEMMIFAGRIVVNGAIIATPVFNVTRSDVIT 88

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           VDG PL   ERTRLWLYHKP+G VTT+ DP GR TVFDNLP    RV+SVGRLD+NTEGL
Sbjct: 89  VDGKPLPPIERTRLWLYHKPVGFVTTNRDPQGRPTVFDNLPKDMPRVLSVGRLDMNTEGL 148

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDGGLARVLELP T W+R YRVR HG+V Q  L  LK GI + GI YG ++ +++ 
Sbjct: 149 LLLTNDGGLARVLELPLTGWVRKYRVRAHGKVKQSALQDLKNGIAVNGIFYGSIEASIER 208

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++GSN W++V LREGKNREIK V       VNRLIR+SYGPFQL  L  G+ RE+  ++L
Sbjct: 209 EQGSNVWLSVALREGKNREIKNVLGALGLSVNRLIRVSYGPFQLSDLKEGAVRELKGRML 268

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM----------KKNSSQ 291
           R+QLG  L+ +A  + +API    +         S  P                +    +
Sbjct: 269 RDQLGERLILQANADFNAPIIKPFSNSAVIEKQNSTKPPVMKNSWIVSRKESILRGKKGR 328

Query: 292 KNGLS--------------KQKKLATPVHR---RNLASNVWMAKGIHSSFLSDSGQREEN 334
             G S              K +  +    R   R+  SNVWMA G              +
Sbjct: 329 FPGHSQVRLSKKFDEKLRVKDQNKSGKEERVFLRSRCSNVWMAPGACPQIARKKPSSVAD 388

Query: 335 HRRSPSFP--SKRSLRRTSAKK 354
           +          KR   R   K+
Sbjct: 389 NHYGRKINWVGKRFTDRGKEKR 410


>gi|315122182|ref|YP_004062671.1| putative ribosomal large subunit pseudouridine synthase B
           [Candidatus Liberibacter solanacearum CLso-ZC1]
 gi|313495584|gb|ADR52183.1| putative ribosomal large subunit pseudouridine synthase B
           [Candidatus Liberibacter solanacearum CLso-ZC1]
          Length = 393

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 240/333 (72%), Positives = 281/333 (84%), Gaps = 1/333 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +KD  IV E+  P+RVSKVIARAGIASRREVERMI Q+RVKVNG+ LERAAVNV+STD I
Sbjct: 8   LKDGQIVPEDLMPERVSKVIARAGIASRREVERMITQKRVKVNGVCLERAAVNVISTDCI 67

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           EVD VPLRKAERTRLWLYHKP+GLVTTHSDP GRSTVFDN+PSI SRV+SVGRLDINTEG
Sbjct: 68  EVDDVPLRKAERTRLWLYHKPVGLVTTHSDPTGRSTVFDNVPSIVSRVVSVGRLDINTEG 127

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLLLTNDGGLAR+LELPSTQWLRVYRVR +GQ+DQ+KL+LLK+GIVI+GI Y  MQVT+D
Sbjct: 128 LLLLTNDGGLARILELPSTQWLRVYRVRAYGQIDQEKLDLLKEGIVIKGIHYRGMQVTID 187

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +QKG+N W+TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG LL G TREV+KK+
Sbjct: 188 SQKGANVWLTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGELLEGDTREVAKKV 247

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           LREQLG +LL+EA+VNL+  +YSSET +RD   +  +  D      K  S+ +G +K+K 
Sbjct: 248 LREQLGANLLKEARVNLEGLVYSSETPIRDHSKMKVKSDDISKTKNKK-SKVHGFNKKKH 306

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREE 333
           +  P+ RRN +SNVWMA+GIHSS   +    ++
Sbjct: 307 VDFPIQRRNRSSNVWMAQGIHSSLPYEKQGEKD 339


>gi|315172332|gb|EFU16349.1| conserved hypothetical protein [Enterococcus faecalis TX1346]
          Length = 238

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 80/237 (33%), Positives = 121/237 (51%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA AG+ SRR+ E +I + RVKVNG +++     V   D +EVDGVP+ + E  
Sbjct: 2   ERLQKAIAHAGVTSRRKAEELIVKGRVKVNGQVVKELGTQVSKQDTVEVDGVPIYQEEYG 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     +++  SD  GR  V D    +  R+  VGRLD +T GLLLLTNDG  ++ 
Sbjct: 62  YYLFYKPRG-VISAVSDDKGRKVVTDYFTDVTERIYPVGRLDYDTSGLLLLTNDGSFSQK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTV 191
           L  P  +  +VY  +  G   +  L  L KGI I G         + +       + V +
Sbjct: 121 LTHPKHEVDKVYVAKIKGVPTKRDLLPLVKGIRIDGKRTAPANFQILSADIKTGSSVVEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + EG+N ++KK+F+   + V +L R  YG   L  L  G  R+++KK + + L   
Sbjct: 181 TIHEGRNHQVKKMFQAVGFPVQKLKRERYGELTLQGLRPGQYRDLTKKEISQLLNQA 237


>gi|20807779|ref|NP_622950.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Thermoanaerobacter tengcongensis MB4]
 gi|254478705|ref|ZP_05092076.1| conserved hypothetical protein, putative [Carboxydibrachium
           pacificum DSM 12653]
 gi|20516335|gb|AAM24554.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           Pseudouridylate synthase [Thermoanaerobacter
           tengcongensis MB4]
 gi|214035392|gb|EEB76095.1| conserved hypothetical protein, putative [Carboxydibrachium
           pacificum DSM 12653]
          Length = 236

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 77/230 (33%), Positives = 123/230 (53%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  GIASRR+ E  I Q RVKVNG +++     +    D IE D   +R+ E+
Sbjct: 2   VRLQKYLAECGIASRRKCEEYILQGRVKVNGKVVKELGTKIDPDVDIIEFDDKIVRREEK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G +T+  DP GR TV  +L  +  R+  VGRLD +T GLLLLTNDG LA 
Sbjct: 62  KVYIMLYKPAGYITSVKDPFGRPTV-LDLVKVKERIYPVGRLDFDTSGLLLLTNDGELAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +L  P  + ++ Y  +  G   ++++   + G++I G      ++ +   K   + V + 
Sbjct: 121 ILMHPKHEIVKTYVAKIKGIPTKEEMERFENGLIIDGRKTAKAKIRILNVKNGTSVVEIQ 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EG+NR++KK+ +     V  L R   G  +L  L  G  R +++  +R
Sbjct: 181 IHEGRNRQVKKMCKAIGHPVIALKRTKIGELELKGLKPGEWRYLTEDEIR 230


>gi|227518731|ref|ZP_03948780.1| pseudouridylate synthase [Enterococcus faecalis TX0104]
 gi|227553340|ref|ZP_03983389.1| pseudouridylate synthase [Enterococcus faecalis HH22]
 gi|229545844|ref|ZP_04434569.1| pseudouridylate synthase [Enterococcus faecalis TX1322]
 gi|229550036|ref|ZP_04438761.1| pseudouridylate synthase [Enterococcus faecalis ATCC 29200]
 gi|255972817|ref|ZP_05423403.1| pseudouridine synthase [Enterococcus faecalis T1]
 gi|255975873|ref|ZP_05426459.1| pseudouridine synthase [Enterococcus faecalis T2]
 gi|256619043|ref|ZP_05475889.1| pseudouridine synthase [Enterococcus faecalis ATCC 4200]
 gi|256762469|ref|ZP_05503049.1| pseudouridine synthase [Enterococcus faecalis T3]
 gi|256853105|ref|ZP_05558475.1| pseudouridine synthase [Enterococcus faecalis T8]
 gi|256958960|ref|ZP_05563131.1| pseudouridine synthase [Enterococcus faecalis DS5]
 gi|256961947|ref|ZP_05566118.1| pseudouridine synthase [Enterococcus faecalis Merz96]
 gi|256965145|ref|ZP_05569316.1| pseudouridine synthase [Enterococcus faecalis HIP11704]
 gi|257078991|ref|ZP_05573352.1| pseudouridine synthase [Enterococcus faecalis JH1]
 gi|257082570|ref|ZP_05576931.1| pseudouridine synthase [Enterococcus faecalis E1Sol]
 gi|257085203|ref|ZP_05579564.1| pseudouridine synthase [Enterococcus faecalis Fly1]
 gi|257086764|ref|ZP_05581125.1| pseudouridine synthase [Enterococcus faecalis D6]
 gi|257089865|ref|ZP_05584226.1| pseudouridine synthase [Enterococcus faecalis CH188]
 gi|257416073|ref|ZP_05593067.1| pseudouridine synthase [Enterococcus faecalis AR01/DG]
 gi|257419276|ref|ZP_05596270.1| pseudouridine synthase [Enterococcus faecalis T11]
 gi|257422639|ref|ZP_05599629.1| pseudouridine synthase [Enterococcus faecalis X98]
 gi|293383015|ref|ZP_06628933.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecalis R712]
 gi|293389496|ref|ZP_06633953.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecalis S613]
 gi|294781343|ref|ZP_06746686.1| pseudouridylate synthase [Enterococcus faecalis PC1.1]
 gi|300860430|ref|ZP_07106517.1| pseudouridine synthase B, ribosomal large subunit [Enterococcus
           faecalis TUSoD Ef11]
 gi|307271038|ref|ZP_07552321.1| hypothetical protein HMPREF9498_03124 [Enterococcus faecalis
           TX4248]
 gi|307273245|ref|ZP_07554491.1| hypothetical protein HMPREF9514_02011 [Enterococcus faecalis
           TX0855]
 gi|307278094|ref|ZP_07559178.1| hypothetical protein HMPREF9515_00429 [Enterococcus faecalis
           TX0860]
 gi|307289085|ref|ZP_07569041.1| hypothetical protein HMPREF9505_02455 [Enterococcus faecalis
           TX0109]
 gi|307292016|ref|ZP_07571885.1| hypothetical protein HMPREF9509_02313 [Enterococcus faecalis
           TX0411]
 gi|312900740|ref|ZP_07760037.1| conserved hypothetical protein [Enterococcus faecalis TX0470]
 gi|312903287|ref|ZP_07762467.1| conserved hypothetical protein [Enterococcus faecalis TX0635]
 gi|312907514|ref|ZP_07766505.1| conserved hypothetical protein [Enterococcus faecalis DAPTO 512]
 gi|312910132|ref|ZP_07768979.1| conserved hypothetical protein [Enterococcus faecalis DAPTO 516]
 gi|312951473|ref|ZP_07770369.1| conserved hypothetical protein [Enterococcus faecalis TX0102]
 gi|227073812|gb|EEI11775.1| pseudouridylate synthase [Enterococcus faecalis TX0104]
 gi|227177527|gb|EEI58499.1| pseudouridylate synthase [Enterococcus faecalis HH22]
 gi|229304842|gb|EEN70838.1| pseudouridylate synthase [Enterococcus faecalis ATCC 29200]
 gi|229309043|gb|EEN75030.1| pseudouridylate synthase [Enterococcus faecalis TX1322]
 gi|255963835|gb|EET96311.1| pseudouridine synthase [Enterococcus faecalis T1]
 gi|255968745|gb|EET99367.1| pseudouridine synthase [Enterococcus faecalis T2]
 gi|256598570|gb|EEU17746.1| pseudouridine synthase [Enterococcus faecalis ATCC 4200]
 gi|256683720|gb|EEU23415.1| pseudouridine synthase [Enterococcus faecalis T3]
 gi|256711564|gb|EEU26602.1| pseudouridine synthase [Enterococcus faecalis T8]
 gi|256949456|gb|EEU66088.1| pseudouridine synthase [Enterococcus faecalis DS5]
 gi|256952443|gb|EEU69075.1| pseudouridine synthase [Enterococcus faecalis Merz96]
 gi|256955641|gb|EEU72273.1| pseudouridine synthase [Enterococcus faecalis HIP11704]
 gi|256987021|gb|EEU74323.1| pseudouridine synthase [Enterococcus faecalis JH1]
 gi|256990600|gb|EEU77902.1| pseudouridine synthase [Enterococcus faecalis E1Sol]
 gi|256993233|gb|EEU80535.1| pseudouridine synthase [Enterococcus faecalis Fly1]
 gi|256994794|gb|EEU82096.1| pseudouridine synthase [Enterococcus faecalis D6]
 gi|256998677|gb|EEU85197.1| pseudouridine synthase [Enterococcus faecalis CH188]
 gi|257157901|gb|EEU87861.1| pseudouridine synthase [Enterococcus faecalis ARO1/DG]
 gi|257161104|gb|EEU91064.1| pseudouridine synthase [Enterococcus faecalis T11]
 gi|257164463|gb|EEU94423.1| pseudouridine synthase [Enterococcus faecalis X98]
 gi|291079680|gb|EFE17044.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecalis R712]
 gi|291081113|gb|EFE18076.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecalis S613]
 gi|294451573|gb|EFG20032.1| pseudouridylate synthase [Enterococcus faecalis PC1.1]
 gi|300849469|gb|EFK77219.1| pseudouridine synthase B, ribosomal large subunit [Enterococcus
           faecalis TUSoD Ef11]
 gi|306497014|gb|EFM66562.1| hypothetical protein HMPREF9509_02313 [Enterococcus faecalis
           TX0411]
 gi|306499794|gb|EFM69155.1| hypothetical protein HMPREF9505_02455 [Enterococcus faecalis
           TX0109]
 gi|306505491|gb|EFM74677.1| hypothetical protein HMPREF9515_00429 [Enterococcus faecalis
           TX0860]
 gi|306510230|gb|EFM79254.1| hypothetical protein HMPREF9514_02011 [Enterococcus faecalis
           TX0855]
 gi|306512536|gb|EFM81185.1| hypothetical protein HMPREF9498_03124 [Enterococcus faecalis
           TX4248]
 gi|310626542|gb|EFQ09825.1| conserved hypothetical protein [Enterococcus faecalis DAPTO 512]
 gi|310630439|gb|EFQ13722.1| conserved hypothetical protein [Enterococcus faecalis TX0102]
 gi|310633163|gb|EFQ16446.1| conserved hypothetical protein [Enterococcus faecalis TX0635]
 gi|311289405|gb|EFQ67961.1| conserved hypothetical protein [Enterococcus faecalis DAPTO 516]
 gi|311292221|gb|EFQ70777.1| conserved hypothetical protein [Enterococcus faecalis TX0470]
 gi|315027286|gb|EFT39218.1| conserved hypothetical protein [Enterococcus faecalis TX2137]
 gi|315029405|gb|EFT41337.1| conserved hypothetical protein [Enterococcus faecalis TX4000]
 gi|315033949|gb|EFT45881.1| conserved hypothetical protein [Enterococcus faecalis TX0017]
 gi|315036958|gb|EFT48890.1| conserved hypothetical protein [Enterococcus faecalis TX0027]
 gi|315144437|gb|EFT88453.1| conserved hypothetical protein [Enterococcus faecalis TX2141]
 gi|315147244|gb|EFT91260.1| conserved hypothetical protein [Enterococcus faecalis TX4244]
 gi|315150557|gb|EFT94573.1| conserved hypothetical protein [Enterococcus faecalis TX0012]
 gi|315152504|gb|EFT96520.1| conserved hypothetical protein [Enterococcus faecalis TX0031]
 gi|315155782|gb|EFT99798.1| conserved hypothetical protein [Enterococcus faecalis TX0043]
 gi|315158051|gb|EFU02068.1| conserved hypothetical protein [Enterococcus faecalis TX0312]
 gi|315160465|gb|EFU04482.1| conserved hypothetical protein [Enterococcus faecalis TX0645]
 gi|315163994|gb|EFU08011.1| conserved hypothetical protein [Enterococcus faecalis TX1302]
 gi|315169055|gb|EFU13072.1| conserved hypothetical protein [Enterococcus faecalis TX1341]
 gi|315169707|gb|EFU13724.1| conserved hypothetical protein [Enterococcus faecalis TX1342]
 gi|315575887|gb|EFU88078.1| conserved hypothetical protein [Enterococcus faecalis TX0309B]
 gi|315577727|gb|EFU89918.1| conserved hypothetical protein [Enterococcus faecalis TX0630]
 gi|315580539|gb|EFU92730.1| conserved hypothetical protein [Enterococcus faecalis TX0309A]
 gi|323480703|gb|ADX80142.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecalis 62]
 gi|327535112|gb|AEA93946.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecalis OG1RF]
          Length = 238

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 80/237 (33%), Positives = 121/237 (51%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA AG+ SRR+ E +I + RVKVNG +++     V   D +EVDGVP+ + E  
Sbjct: 2   ERLQKAIAHAGVTSRRKAEELIVKGRVKVNGQVVKELGTQVSKQDTVEVDGVPIYQEEYG 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     +++  SD  GR  V D    +  R+  VGRLD +T GLLLLTNDG  ++ 
Sbjct: 62  YYLFYKPRG-VISAVSDDKGRKVVTDYFTDVTERIYPVGRLDYDTSGLLLLTNDGSFSQK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTV 191
           L  P  +  +VY  +  G   +  L  L KGI I G         + +       + V +
Sbjct: 121 LTHPKHEVDKVYVAKIKGVPTKRDLLPLAKGIRIDGKRTAPANFQILSADIKTGSSVVEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + EG+N ++KK+F+   + V +L R  YG   L  L  G  R+++KK + + L   
Sbjct: 181 TIHEGRNHQVKKMFQAVGFPVQKLKRERYGELTLQGLRPGQYRDLTKKEISQLLNQA 237


>gi|153829940|ref|ZP_01982607.1| pseudouridine synthase family 1 protein [Vibrio cholerae 623-39]
 gi|148874575|gb|EDL72710.1| pseudouridine synthase family 1 protein [Vibrio cholerae 623-39]
          Length = 340

 Score =  200 bits (507), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 73/334 (21%), Positives = 130/334 (38%), Gaps = 9/334 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
              T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR
Sbjct: 14  SQPTEKRLNKFISETGYCSRREADKLIEQGRVTLNGLQPEV-GSKVTEQDEVCIDGKPLR 72

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ER      +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG
Sbjct: 73  SKERPIYIALNKPTGITCTTERDV--PGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTNDG 130

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y VR    +  + +  +  G+ I        +VT    + +   
Sbjct: 131 DIVNKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVT----QETQYS 186

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L   
Sbjct: 187 FRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILAMC 246

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNI--ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                         S +T+ R        S   +  ++ ++N    +G + Q+    P  
Sbjct: 247 EDSSGTEEASRVAQSGDTIKRATDAKLFDSRESNKESKARRNPKTYHGKNAQEFRHAPNS 306

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
           ++        +    S              R   
Sbjct: 307 KKAQRRPSSTSSNTASGSKPTPRTGGTLSLRKSK 340


>gi|90410657|ref|ZP_01218672.1| putative 16S rRNA uridine-516 pseudouridylate synthase
           [Photobacterium profundum 3TCK]
 gi|90328288|gb|EAS44586.1| putative 16S rRNA uridine-516 pseudouridylate synthase
           [Photobacterium profundum 3TCK]
          Length = 367

 Score =  200 bits (507), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 71/357 (19%), Positives = 127/357 (35%), Gaps = 19/357 (5%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K+ +     P R++K I+  G  SRRE +++I Q RV +NG         VM  D + V
Sbjct: 8   NKDQLDTQNKPVRLNKFISDTGYCSRREADKLIDQGRVTINGTQP-EMGTKVMPDDEVLV 66

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           D  PLR  ER      +KP G+  T            +      R+  +GRLD  ++GL+
Sbjct: 67  DDKPLRAKERPIYIALNKPTGVTCTTERHV--KDNIVDFIGHRKRIFPIGRLDKPSDGLI 124

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
            LTNDG +   +        + Y VR   Q+  + L  +  G+ I         V    +
Sbjct: 125 FLTNDGDIVNKILRAGNSHEKEYVVRVDHQITPEFLEKMASGVEILDTVTLPCTV----K 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           K ++    + L +G NR+I+++ E   + V +L R+      +  L  G  R ++   + 
Sbjct: 181 KETDYSFRITLTQGLNRQIRRMCEALGYDVYKLRRVRIMNITIDGLPNGKWRYLTDAEIS 240

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNI------------ISEVPDDFTRMKKNSS 290
           E                     + + +                   E           + 
Sbjct: 241 EINTLISQSSGTEEASKVDAEGQAISKATDAKLFDSRQQAAEERQRERERGMRDATYKTF 300

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
           +  G   + +  T    +  ++     +   S     S  +     ++P      S 
Sbjct: 301 KAKGEFTRTRRTTERDDKTGSARNGDNRPSQSRDRQSSRDQSTRDSQAPHGNKPSSG 357


>gi|62317153|ref|YP_223006.1| RNA pseudouridylate synthase family protein [Brucella abortus bv. 1
           str. 9-941]
 gi|83269136|ref|YP_418427.1| high mobility group protein HMG-I-like protein [Brucella melitensis
           biovar Abortus 2308]
 gi|254695336|ref|ZP_05157164.1| high mobility group proteins HMG-I and HMG-Y:pseudouridine
           synthase, Rsu:RNA-binding S4:pseudouridine synthase
           [Brucella abortus bv. 3 str. Tulya]
 gi|254698432|ref|ZP_05160260.1| high mobility group proteins HMG-I and HMG-Y:pseudouridine
           synthase, Rsu:RNA-binding S4:pseudouridine synthase
           [Brucella abortus bv. 2 str. 86/8/59]
 gi|256256549|ref|ZP_05462085.1| high mobility group proteins HMG-I and HMG-Y:pseudouridine
           synthase, Rsu:RNA-binding S4:pseudouridine synthase
           [Brucella abortus bv. 9 str. C68]
 gi|260544386|ref|ZP_05820207.1| RNA pseudouridylate synthase [Brucella abortus NCTC 8038]
 gi|260756976|ref|ZP_05869324.1| RNA-binding S4 domain-containing protein [Brucella abortus bv. 6
           str. 870]
 gi|260759650|ref|ZP_05871998.1| RNA-binding S4 domain-containing protein [Brucella abortus bv. 4
           str. 292]
 gi|260762893|ref|ZP_05875225.1| RNA-binding S4 domain-containing protein [Brucella abortus bv. 2
           str. 86/8/59]
 gi|260882787|ref|ZP_05894401.1| RNA-binding S4 domain-containing protein [Brucella abortus bv. 9
           str. C68]
 gi|261215707|ref|ZP_05929988.1| RNA-binding S4 domain-containing protein [Brucella abortus bv. 3
           str. Tulya]
 gi|62197346|gb|AAX75645.1| RNA pseudouridylate synthase family protein [Brucella abortus bv. 1
           str. 9-941]
 gi|82939410|emb|CAJ12364.1| High mobility group proteins HMG-I and HMG-Y:Pseudouridine
           synthase, Rsu:RNA-binding S4:Pseudouridine synthase
           [Brucella melitensis biovar Abortus 2308]
 gi|260097657|gb|EEW81531.1| RNA pseudouridylate synthase [Brucella abortus NCTC 8038]
 gi|260669968|gb|EEX56908.1| RNA-binding S4 domain-containing protein [Brucella abortus bv. 4
           str. 292]
 gi|260673314|gb|EEX60135.1| RNA-binding S4 domain-containing protein [Brucella abortus bv. 2
           str. 86/8/59]
 gi|260677084|gb|EEX63905.1| RNA-binding S4 domain-containing protein [Brucella abortus bv. 6
           str. 870]
 gi|260872315|gb|EEX79384.1| RNA-binding S4 domain-containing protein [Brucella abortus bv. 9
           str. C68]
 gi|260917314|gb|EEX84175.1| RNA-binding S4 domain-containing protein [Brucella abortus bv. 3
           str. Tulya]
          Length = 581

 Score =  200 bits (507), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 166/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 69  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 128

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 129 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 188

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 189 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 248

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 249 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 308

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 369 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 416



 Score = 36.7 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 422 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 481

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 482 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 532


>gi|265993341|ref|ZP_06105898.1| RNA-binding S4 domain-containing protein [Brucella melitensis bv. 3
           str. Ether]
 gi|262764211|gb|EEZ10243.1| RNA-binding S4 domain-containing protein [Brucella melitensis bv. 3
           str. Ether]
          Length = 581

 Score =  200 bits (507), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 165/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 69  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 128

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 129 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 188

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V + +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 189 GLSRVLELPSTGWLRRYRVRAHGKVTRQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 248

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 249 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 308

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 369 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 416


>gi|254702620|ref|ZP_05164448.1| hypothetical protein Bsuib36_01462 [Brucella suis bv. 3 str. 686]
          Length = 581

 Score =  200 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 166/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 69  EEETSERIAKRLARAGIASRREAETMIATGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 128

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 129 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 188

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 189 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 248

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 249 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 308

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 369 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 416



 Score = 36.7 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 422 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 481

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 482 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 532


>gi|256252964|ref|ZP_05458500.1| RNA pseudouridylate synthase family protein [Brucella ceti B1/94]
 gi|261220057|ref|ZP_05934338.1| RNA-binding S4 domain-containing protein [Brucella ceti B1/94]
 gi|265996596|ref|ZP_06109153.1| RNA-binding S4 domain-containing protein [Brucella ceti M490/95/1]
 gi|260918641|gb|EEX85294.1| RNA-binding S4 domain-containing protein [Brucella ceti B1/94]
 gi|262550893|gb|EEZ07054.1| RNA-binding S4 domain-containing protein [Brucella ceti M490/95/1]
          Length = 581

 Score =  200 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 165/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 69  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 128

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           +  RTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 129 QTARTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 188

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 189 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 248

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 249 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 308

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRTPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G+      ++ +      + P   +K
Sbjct: 369 REEKTEKVEPRRRGNANVWMAPGVRPKGEKEAAKPARVEHQQPHRSAK 416



 Score = 36.7 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 422 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 481

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 482 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 532


>gi|183179476|ref|ZP_02957687.1| pseudouridine synthase family 1 protein [Vibrio cholerae MZO-3]
 gi|183012887|gb|EDT88187.1| pseudouridine synthase family 1 protein [Vibrio cholerae MZO-3]
          Length = 340

 Score =  200 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 73/334 (21%), Positives = 130/334 (38%), Gaps = 9/334 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
              T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR
Sbjct: 14  SQPTEKRLNKFISETGYCSRREADKLIEQGRVTLNGLQPEV-GSKVTEQDEVCIDGKPLR 72

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ER      +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG
Sbjct: 73  SKERPIYIALNKPTGITCTTERDV--PGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTNDG 130

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y VR    +  + +  +  G+ I        +VT    + +   
Sbjct: 131 DIVNKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVT----QETQYS 186

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L   
Sbjct: 187 FRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILAMC 246

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNI--ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                         S +T+ R        S   +  ++ ++N    +G + Q+    P  
Sbjct: 247 EDSSGTEEASRVAQSGDTIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNS 306

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
           ++        +    S              R   
Sbjct: 307 KKAQRRPSSTSSNTASGSKPTPRTGGTLSLRKSK 340


>gi|328545045|ref|YP_004305154.1| RNA pseudouridylate synthase family protein [polymorphum gilvum
           SL003B-26A1]
 gi|326414786|gb|ADZ71849.1| RNA pseudouridylate synthase family protein [Polymorphum gilvum
           SL003B-26A1]
          Length = 562

 Score =  200 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 158/350 (45%), Positives = 204/350 (58%), Gaps = 8/350 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +R++KV+ARAG+ SRR+ E  I   RV VNG +LE  A+ V   D I VDG PL + E
Sbjct: 85  DGERIAKVMARAGLCSRRDAEAWILAGRVAVNGKILESPALTVTYDDEIVVDGQPLPQKE 144

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RTRLWLYHKP GLVTT  DP+GR TVFD+LP    RV++VGRLDINTEGLLLLTNDGGLA
Sbjct: 145 RTRLWLYHKPRGLVTTARDPEGRPTVFDSLPKDLPRVLAVGRLDINTEGLLLLTNDGGLA 204

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           RVLELP+T WLR YRVR +G+++Q +L+ L  GI I GI YG ++  LD Q+G N W+TV
Sbjct: 205 RVLELPATGWLRRYRVRAYGKIEQSQLDSLADGIAIDGILYGTIEAVLDKQQGDNVWLTV 264

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
           GLREGKNRE+K+V E     VNRLIR+S+GPFQL  L  G  RE+  ++LR+QLG  L E
Sbjct: 265 GLREGKNREVKRVLEHLGLSVNRLIRLSFGPFQLADLGEGEVREIRGRVLRDQLGDKLAE 324

Query: 252 EAQVNLDAP-----IYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
            A  + +AP             ++         +  +  +  ++ + G  +      P  
Sbjct: 325 AAGADFEAPVLTQAEPDKPLKKKENIQKSRAGGEWMSAREGAAATRTGGRRSASDEAPER 384

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF---PSKRSLRRTSAK 353
           RR  A N    +            R +       F      R   R   +
Sbjct: 385 RRKGAGNPPETRRPSGKSQDRPQDRPQKVSPRSRFRLTSEPRPRSRAPER 434


>gi|261252238|ref|ZP_05944811.1| ribosomal large subunit pseudouridine synthase F [Vibrio orientalis
           CIP 102891]
 gi|260935629|gb|EEX91618.1| ribosomal large subunit pseudouridine synthase F [Vibrio orientalis
           CIP 102891]
          Length = 344

 Score =  200 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 71/335 (21%), Positives = 121/335 (36%), Gaps = 13/335 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT- 73
           R++K I+  G  SRRE +R+I Q RV +NG +       V   D + VD  P+  A    
Sbjct: 8   RLNKFISETGFCSRREADRLIEQGRVTINGQVP-EMGTKVQLGDDVRVDDKPIAAATDKP 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG +   
Sbjct: 67  VYIALNKPTGITCTTERDI--PGNIVDFVGHKKRIFPIGRLDKPSDGLIFLTNDGDIVNK 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y VR    +  D +  +  G+ I         VT    K +     + L
Sbjct: 125 ILRAGNSHEKEYVVRVDKPISDDFIKKMSSGVNILDTITLPCTVT----KETKYSFRIVL 180

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
            +G NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L        
Sbjct: 181 TQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGQWRYLSDSEVTEILAMCEDSSG 240

Query: 254 QVNLDAPIYSSETLVRDRPNI----ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                      + + R           E  +   R  +      G +  +    P  ++ 
Sbjct: 241 TEEASKMDNKGKRIRRATDAKLFDSREENQESKARRNQKQRTFKGRNADEFRHAPNSKKG 300

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHR-RSPSFPS 343
              +         S    S  +  +   + PS P 
Sbjct: 301 RHGDKQSEFKGKPSGKGKSFHKPASDNGQRPSKPK 335


>gi|319405144|emb|CBI78750.1| Pseudouridine synthase [Bartonella sp. AR 15-3]
          Length = 459

 Score =  200 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 167/377 (44%), Positives = 214/377 (56%), Gaps = 29/377 (7%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + E    +R++K +ARAG+ASRR+ E MIA  R+ VNG ++     NV  +D I VD   
Sbjct: 1   MSEKSESERIAKRLARAGLASRRDAEMMIAAGRIVVNGAVVTTPVFNVTRSDVITVDNKS 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L   ERTRLWLY+KP G +TT+ DP GR TVFDNLP    RV+SVGRLDINTEGLLLLTN
Sbjct: 61  LPPIERTRLWLYYKPTGFITTNRDPQGRPTVFDNLPKDMPRVLSVGRLDINTEGLLLLTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGGLARVLELP T W+R YRVR HG+V Q  L  LK GI + GI YG ++ +++  +GSN
Sbjct: 121 DGGLARVLELPLTGWVRKYRVRAHGKVKQSALQDLKNGIAVNGIFYGSIEASIERDQGSN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            W++V LREGKNREIK V       VNRLIR+SYGPFQL  L  G+ RE+  ++LREQLG
Sbjct: 181 VWLSVALREGKNREIKNVLGALGLSVNRLIRVSYGPFQLSDLKEGAVRELKGRVLREQLG 240

Query: 247 PHLLEEAQVNLDAP--------------IYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
             L+ +A  N DAP                +   +++D   I S+    + + +K S   
Sbjct: 241 ERLILQANANFDAPILKPFSNSTVVEKQNSTKAPVIKDSWIISSKESLLYGKKRKFSGHS 300

Query: 293 NG----------LSKQKKLATPVHR---RNLASNVWMAKGIHSSFLSDSGQREEN--HRR 337
                         K +       R   R+  SNVWMA G              N  H R
Sbjct: 301 QAQLSKKIDEKLRGKDQNKGGKEERAFLRSRCSNVWMAPGACPQITRKKSSSNANNHHDR 360

Query: 338 SPSFPSKRSLRRTSAKK 354
             ++  K+S  R   K+
Sbjct: 361 KSNWIDKKSTDRGKEKR 377


>gi|260772257|ref|ZP_05881173.1| ribosomal large subunit pseudouridine synthase F [Vibrio
           metschnikovii CIP 69.14]
 gi|260611396|gb|EEX36599.1| ribosomal large subunit pseudouridine synthase F [Vibrio
           metschnikovii CIP 69.14]
          Length = 332

 Score =  200 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 64/324 (19%), Positives = 122/324 (37%), Gaps = 9/324 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RV +NG L       V   D + +DG P+   E+  
Sbjct: 8   RLNKYISETGFCSRREADKLIEQGRVTINGQLPP-MGSKVTEHDQVCIDGKPVGYKEKPI 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCTTERDV--PGNIVDFIGHNKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR +  +  + +  +  G+ I        +V     + +     + L 
Sbjct: 125 LRAGNNHEKEYVVRVNKPISAEFIRQMSAGVNILDTVTLPCKVV----QETQYSFRIILT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E   ++V +L R+      L  +  G  R ++   + E L       + 
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGQWRYLTDAEVNEILAMCESSVST 240

Query: 255 VNLDAPIYSSETLVRDRPNI--ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
                   S + + +        S +    T  +       G    +    P  ++    
Sbjct: 241 EEASKTDSSGKQIRKATDAKLFDSRLAQSKTTSETPHKTYQGRQAHEFRHAPNSKKGREQ 300

Query: 313 NVWMAKGIHSSFLSDSGQREENHR 336
                    +   + S +R    +
Sbjct: 301 RQQHGDVKRNDNTARSARRNPTRK 324


>gi|227510307|ref|ZP_03940356.1| pseudouridylate synthase [Lactobacillus brevis subsp. gravesensis
           ATCC 27305]
 gi|227189959|gb|EEI70026.1| pseudouridylate synthase [Lactobacillus brevis subsp. gravesensis
           ATCC 27305]
          Length = 241

 Score =  200 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 80/241 (33%), Positives = 120/241 (49%), Gaps = 1/241 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +R+ KV+A AG+ASRR+ E++I +  VKVNG ++      V  +D +EVD VP+ K   
Sbjct: 2   SERLQKVMAHAGVASRRKAEKLIVEGHVKVNGKVVRELGTKVTESDEVEVDEVPISKEVP 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               LY     ++T  +D   R TV D L  +  R+  VGRLD +T GLLLLTNDG L  
Sbjct: 62  VYYLLYKPRG-VITAVTDDKHRKTVIDLLSEVTERIYPVGRLDYDTSGLLLLTNDGDLDN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + Y  +  G +  D +  L+ GI I G      + T+     ++  V++ 
Sbjct: 121 HLTHPKYEVDKTYVAKVKGTITNDDMKKLRTGIHIDGRKTASAKATVIRNNNNSTIVSLT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           + EG+N ++KK+F      V +L R SYG   L  L  G  R +    + E        +
Sbjct: 181 IHEGRNHQVKKMFLALGHPVEKLSRQSYGFLNLDGLQPGDYRRLKPHEVEELKKMSQDRK 240

Query: 253 A 253
            
Sbjct: 241 R 241


>gi|307274982|ref|ZP_07556145.1| hypothetical protein HMPREF9521_00595 [Enterococcus faecalis
           TX2134]
 gi|306508430|gb|EFM77537.1| hypothetical protein HMPREF9521_00595 [Enterococcus faecalis
           TX2134]
          Length = 238

 Score =  200 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 80/237 (33%), Positives = 122/237 (51%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA AG+ SRR+ E +I + RVKVNG +++     V   D +EVDGVP+ + E  
Sbjct: 2   ERLQKAIAHAGVTSRRKAEELIVKGRVKVNGQVVKELGTQVSKQDTVEVDGVPIYQEEYG 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     +++  SD  GR  V D    +  R+  VGRLD +T GLLLLTNDG  ++ 
Sbjct: 62  YYLFYKPRG-VISAVSDDKGRKVVTDYFTDVTERIYPVGRLDYDTSGLLLLTNDGSFSQK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTV 191
           L  P  +  +VY  +  G   + +L  L KGI I G         + +       + V +
Sbjct: 121 LTHPKHEVDKVYVAKIKGVPTKRELLPLAKGIRIDGKRTAPANFQILSADIKTGSSVVEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + EG+N ++KK+F+   + V +L R  YG   L  L  G  R+++KK + + L   
Sbjct: 181 TIHEGRNHQVKKMFQAVGFPVQKLKRERYGELTLQGLRPGQYRDLTKKEISQLLNQA 237


>gi|260568472|ref|ZP_05838941.1| RNA pseudouridylate synthase [Brucella suis bv. 4 str. 40]
 gi|260155137|gb|EEW90218.1| RNA pseudouridylate synthase [Brucella suis bv. 4 str. 40]
          Length = 581

 Score =  199 bits (506), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 166/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 69  EEETSERIAKRLARAGIASRREAETMIATGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 128

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 129 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 188

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 189 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 248

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 249 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 308

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 369 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 416



 Score = 36.7 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 422 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 481

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 482 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 532


>gi|90579322|ref|ZP_01235132.1| putative 16S rRNA uridine-516 pseudouridylate synthase [Vibrio
           angustum S14]
 gi|90440155|gb|EAS65336.1| putative 16S rRNA uridine-516 pseudouridylate synthase [Vibrio
           angustum S14]
          Length = 375

 Score =  199 bits (506), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 76/365 (20%), Positives = 135/365 (36%), Gaps = 22/365 (6%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M      Q++    R++K I+  G  SRRE +++I Q RV +NG       V VM  D +
Sbjct: 1   MSQNPTEQQSPKGVRLNKFISDTGYCSRREADKLIDQGRVTINGQKP-EMGVRVMDNDDV 59

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            +D  PLR  ER      +KP G+  T       + V         R+  +GRLD  ++G
Sbjct: 60  LIDDKPLRSKERPIYIALNKPTGITCTTERHIEGNIVDFI--GHRKRIFPIGRLDKPSDG 117

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+ LTNDG +   +        + Y VR    +  + L  +  G+ I        +VT  
Sbjct: 118 LIFLTNDGDIVNKILRAGNSHEKEYVVRVDKVITPEFLEKMASGVEILDTVTLPCKVT-- 175

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             K +N    + L +G NR+I+++ E   ++V +L R+      +  L  G  R ++   
Sbjct: 176 --KETNFSFRIVLTQGLNRQIRRMCEALGYEVYKLRRVRIMNITIDGLPNGKWRYLTDDE 233

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS----------- 289
           + E                       + +     + +      R +K +           
Sbjct: 234 IGEINRLIAQSSGTEEASKVDAEGRKIAKATDAKLYDHRQQEARNEKRAQEKAFKTYSGT 293

Query: 290 ----SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
                +  G  + ++       R         +  +    +D   +  N  R P+  S R
Sbjct: 294 GEFTRRPGGQRQNRRNEEGGESRQQRGQGRNDRNSNGRNSNDRNGQGRNDNRRPARTSDR 353

Query: 346 SLRRT 350
             + +
Sbjct: 354 DSKPS 358


>gi|260166986|ref|ZP_05753797.1| RNA pseudouridylate synthase family protein [Brucella sp. F5/99]
 gi|261756373|ref|ZP_06000082.1| RNA pseudouridylate synthase [Brucella sp. F5/99]
 gi|261736357|gb|EEY24353.1| RNA pseudouridylate synthase [Brucella sp. F5/99]
          Length = 581

 Score =  199 bits (505), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 165/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 69  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 128

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           +  RTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 129 QTARTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 188

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 189 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 248

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 249 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 308

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G+      ++ +      + P   +K
Sbjct: 369 REEKTEKVEPRRRGNANVWMAPGVRPKGEKETAKPARVEHQQPHRSAK 416



 Score = 36.7 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 422 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 481

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 482 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 532


>gi|260564347|ref|ZP_05834832.1| RNA pseudouridylate synthase [Brucella melitensis bv. 1 str. 16M]
 gi|265989557|ref|ZP_06102114.1| RNA-binding S4 domain-containing protein [Brucella melitensis bv. 1
           str. Rev.1]
 gi|260151990|gb|EEW87083.1| RNA pseudouridylate synthase [Brucella melitensis bv. 1 str. 16M]
 gi|263000226|gb|EEZ12916.1| RNA-binding S4 domain-containing protein [Brucella melitensis bv. 1
           str. Rev.1]
          Length = 581

 Score =  199 bits (505), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 165/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 69  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 128

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 129 QKERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 188

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V + +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 189 GLSRVLELPSTGWLRRYRVRAHGKVTRQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 248

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 249 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 308

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 369 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 416



 Score = 37.1 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 422 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 481

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 482 ELRNAEGQTTERGKGGSEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 532


>gi|28897524|ref|NP_797129.1| pseudouridine synthase family 1 protein [Vibrio parahaemolyticus
           RIMD 2210633]
 gi|260879260|ref|ZP_05891615.1| ribosomal large subunit pseudouridine synthase F [Vibrio
           parahaemolyticus AN-5034]
 gi|260897564|ref|ZP_05906060.1| ribosomal large subunit pseudouridine synthase F [Vibrio
           parahaemolyticus Peru-466]
 gi|260903534|ref|ZP_05911929.1| ribosomal large subunit pseudouridine synthase F [Vibrio
           parahaemolyticus AQ4037]
 gi|28805736|dbj|BAC59013.1| pseudouridine synthase family 1 protein [Vibrio parahaemolyticus
           RIMD 2210633]
 gi|308086349|gb|EFO36044.1| ribosomal large subunit pseudouridine synthase F [Vibrio
           parahaemolyticus Peru-466]
 gi|308089664|gb|EFO39359.1| ribosomal large subunit pseudouridine synthase F [Vibrio
           parahaemolyticus AN-5034]
 gi|308110853|gb|EFO48393.1| ribosomal large subunit pseudouridine synthase F [Vibrio
           parahaemolyticus AQ4037]
          Length = 371

 Score =  199 bits (505), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 66/343 (19%), Positives = 122/343 (35%), Gaps = 13/343 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRR  +++I + RV +NG         V+  D + VDG P+   E+  
Sbjct: 8   RLNKFISETGFCSRRAADKLIEEGRVTINGKQP-EMGTKVLPGDDVCVDGKPVASKEKPI 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCTTERDI--PGNIVDFIGHKKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + L  +  G+ I        +VT    K +     + L 
Sbjct: 125 LRAGNNHEKEYVVRVDKPITDEFLKQMSSGVRILDTVTLPCKVT----KETKFSFRIVLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL----L 250
           +G NR+I+++ E   ++V +L R+      L  +  G  R ++   + E L         
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLTDDEVAEILAMCDGSVGT 240

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           EEA           +       +   E      R  + +    G +  +    P  ++  
Sbjct: 241 EEASKTDSRGRNIRKATDAKLFDSREENQGSTARRNQKTRTFRGNNADEFRHAPNSKKGQ 300

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                               + +     P    +    +   +
Sbjct: 301 QKRRQRDDESSRPAKEHYKAKTQGEHAKP--QGEHGRPQNKPQ 341


>gi|262192131|ref|ZP_06050292.1| ribosomal large subunit pseudouridine synthase F [Vibrio cholerae
           CT 5369-93]
 gi|262031980|gb|EEY50557.1| ribosomal large subunit pseudouridine synthase F [Vibrio cholerae
           CT 5369-93]
          Length = 328

 Score =  199 bits (505), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 78/345 (22%), Positives = 136/345 (39%), Gaps = 20/345 (5%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
              T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR
Sbjct: 2   SQPTEKRLNKFISETGYCSRREADKLIEQGRVTLNGLQPEV-GSKVTEQDEVCIDGKPLR 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ER      +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG
Sbjct: 61  SKERPIYIALNKPTGITCTTERDV--PGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y VR    +  + +  +  G+ I        +VT    + +   
Sbjct: 119 DIVNKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVT----QETQYS 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L   
Sbjct: 175 FRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSDAEVSEILAMC 234

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNI--ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                         S +T+ R        S   +  ++ ++N    +G + Q+    P  
Sbjct: 235 EDSSGTEEASRVAQSGDTIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNS 294

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
           ++                 S S       R +P      SLR++ 
Sbjct: 295 KK-----------AQRRPSSPSSNTASGSRPTPRTGGTLSLRKSK 328


>gi|253576375|ref|ZP_04853705.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
 gi|251844268|gb|EES72286.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
          Length = 256

 Score =  199 bits (505), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 73/253 (28%), Positives = 118/253 (46%), Gaps = 4/253 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
            N   +R+ K++A AG+ASRR+ E +I   +V+VNG  +         + D I V+G P+
Sbjct: 5   TNANMERLQKILAAAGVASRRKCEELILSGKVQVNGETVTTLGTKADPSVDVITVEGKPI 64

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              ++  L        + +          V D L  I  RV  VGRLD +TEGLLLLTND
Sbjct: 65  GAEKKLYLMFNKPKGVITSASDPQGR-KIVTDYLKGIKERVYPVGRLDYDTEGLLLLTND 123

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGS 185
           G  A +L  P     + Y     G      L+ LK+G++++       +V       +  
Sbjct: 124 GEFAHLLTHPKHHVPKTYLATVKGVPHGTALDKLKQGVMLEDGMTAPAEVEYYDIDPEEK 183

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            A +++ + EG+NR+++++F+  +  V RL RIS+G   LG L  G  R ++K+ +    
Sbjct: 184 YATISITIHEGRNRQVRRMFDAISHPVTRLKRISFGDLVLGNLKRGLYRHLTKEEVDSLY 243

Query: 246 GPHLLEEAQVNLD 258
                        
Sbjct: 244 KLARTTTPPTPKR 256


>gi|265999201|ref|ZP_05465351.2| RNA pseudouridylate synthase [Brucella melitensis bv. 2 str. 63/9]
 gi|263092640|gb|EEZ16861.1| RNA pseudouridylate synthase [Brucella melitensis bv. 2 str. 63/9]
 gi|326410384|gb|ADZ67448.1| RNA-binding S4 domain-containing protein [Brucella melitensis M28]
 gi|326553677|gb|ADZ88316.1| RNA-binding S4 domain-containing protein [Brucella melitensis
           M5-90]
          Length = 581

 Score =  199 bits (505), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 165/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 69  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 128

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 129 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 188

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V + +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 189 GLSRVLELPSTGWLRRYRVRAHGKVTRQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 248

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 249 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 308

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 369 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 416



 Score = 37.1 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 422 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 481

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 482 ELRNAEGQTTERGKGGSEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 532


>gi|167756635|ref|ZP_02428762.1| hypothetical protein CLORAM_02172 [Clostridium ramosum DSM 1402]
 gi|237733923|ref|ZP_04564404.1| ribosomal large subunit pseudouridine synthase B [Mollicutes
           bacterium D7]
 gi|167702810|gb|EDS17389.1| hypothetical protein CLORAM_02172 [Clostridium ramosum DSM 1402]
 gi|229383004|gb|EEO33095.1| ribosomal large subunit pseudouridine synthase B [Coprobacillus sp.
           D7]
          Length = 241

 Score =  199 bits (505), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 69/241 (28%), Positives = 119/241 (49%), Gaps = 3/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I Q +V+VNG ++      V   D I V+G PL    + 
Sbjct: 2   ERLQKAIAASGYTSRRKAEDLIVQGKVEVNGKVVTELGTKVKQGDLITVEGKPLVGENKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     + T   +   R  + D    +  R+  VGRLD +T GL++++NDG  A +
Sbjct: 62  YYVFYKPKGCVCTLDDE-FDRPIITDYFTEVKERIYPVGRLDFDTTGLIIMSNDGEFANM 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW--VTV 191
           +  P +   ++Y V   G +    LN L+KG+ ++G+     ++ +  +   +    + +
Sbjct: 121 IMHPRSHLEKIYEVSIKGLITGPTLNKLEKGVYLEGVKTLPCKIKVVDKDTEHKTTMLKI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L EGKNR++KK+FE     V RL R+S G   L  L  G  R +  + +++       +
Sbjct: 181 KLVEGKNRQVKKMFESVGHPVKRLHRVSIGGINLKGLTPGRYRILKPQEVKDLKKLVNTD 240

Query: 252 E 252
           +
Sbjct: 241 K 241


>gi|254509192|ref|ZP_05121290.1| ribosomal large subunit pseudouridine synthase F [Vibrio
           parahaemolyticus 16]
 gi|219547897|gb|EED24924.1| ribosomal large subunit pseudouridine synthase F [Vibrio
           parahaemolyticus 16]
          Length = 345

 Score =  198 bits (504), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 69/345 (20%), Positives = 119/345 (34%), Gaps = 17/345 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT- 73
           R++K I+  G  SRRE +R+I Q RV +NG +       VM  D + VD  P+       
Sbjct: 8   RLNKFISETGFCSRREADRLIEQGRVTINGQVP-EMGTKVMPGDDVRVDDKPINAVTDKP 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG +   
Sbjct: 67  VYIALNKPTGITCTTERDI--PGNIVDFVGHKKRIFPIGRLDKPSDGLIFLTNDGDIVNK 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y VR    +  D +  +  G+ I        +VT    K +     + L
Sbjct: 125 ILRAGNNHEKEYVVRVDKPISDDFIKKMSSGVNILDTITLPCKVT----KETKFSFRIVL 180

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
            +G NR+I+++ E   ++V +L R+      L  +  G  R ++   + E L        
Sbjct: 181 TQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGQWRYLTDAEVAEILAMCEGSSN 240

Query: 254 QVNLDAPIYSSETLVRDRPNI----ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                      + + +           E  D   R  +      G +  +    P  ++ 
Sbjct: 241 TEEASKIDAKGKRIRKATDAKLFDSREENQDSTARRNQKQRTFKGRNADEFRHAPNSKKG 300

Query: 310 LASNVWMAKGIHSSFL-----SDSGQREENHRRSPSFPSKRSLRR 349
             S                               P      SL++
Sbjct: 301 RHSGKQSEFKGKPGGNKGKTFHKPASENSQRPSKPKRGGTLSLKK 345


>gi|229507701|ref|ZP_04397206.1| ribosomal large subunit pseudouridine synthase F [Vibrio cholerae
           BX 330286]
 gi|229512104|ref|ZP_04401583.1| ribosomal large subunit pseudouridine synthase F [Vibrio cholerae
           B33]
 gi|229519239|ref|ZP_04408682.1| ribosomal large subunit pseudouridine synthase F [Vibrio cholerae
           RC9]
 gi|229528772|ref|ZP_04418162.1| ribosomal large subunit pseudouridine synthase F [Vibrio cholerae
           12129(1)]
 gi|229607205|ref|YP_002877853.1| ribosomal large subunit pseudouridine synthase F [Vibrio cholerae
           MJ-1236]
 gi|255747078|ref|ZP_05421023.1| ribosomal large subunit pseudouridine synthase F [Vibrio cholera
           CIRS 101]
 gi|262161377|ref|ZP_06030487.1| ribosomal large subunit pseudouridine synthase F [Vibrio cholerae
           INDRE 91/1]
 gi|262167753|ref|ZP_06035455.1| ribosomal large subunit pseudouridine synthase F [Vibrio cholerae
           RC27]
 gi|229332546|gb|EEN98032.1| ribosomal large subunit pseudouridine synthase F [Vibrio cholerae
           12129(1)]
 gi|229343928|gb|EEO08903.1| ribosomal large subunit pseudouridine synthase F [Vibrio cholerae
           RC9]
 gi|229352069|gb|EEO17010.1| ribosomal large subunit pseudouridine synthase F [Vibrio cholerae
           B33]
 gi|229355206|gb|EEO20127.1| ribosomal large subunit pseudouridine synthase F [Vibrio cholerae
           BX 330286]
 gi|229369860|gb|ACQ60283.1| ribosomal large subunit pseudouridine synthase F [Vibrio cholerae
           MJ-1236]
 gi|255735480|gb|EET90880.1| ribosomal large subunit pseudouridine synthase F [Vibrio cholera
           CIRS 101]
 gi|262023818|gb|EEY42517.1| ribosomal large subunit pseudouridine synthase F [Vibrio cholerae
           RC27]
 gi|262028688|gb|EEY47342.1| ribosomal large subunit pseudouridine synthase F [Vibrio cholerae
           INDRE 91/1]
          Length = 328

 Score =  198 bits (504), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 77/345 (22%), Positives = 137/345 (39%), Gaps = 20/345 (5%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
              T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR
Sbjct: 2   SQPTEKRLNKFISETGYCSRREADKLIEQGRVTLNGLQPEV-GSKVTEQDEVCIDGKPLR 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ER      +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG
Sbjct: 61  SKERPIYIALNKPTGITCTTERDV--PGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y VR    +  + +  +  G+ I        +VT    + +   
Sbjct: 119 DIVNKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVT----QETQYS 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L   
Sbjct: 175 FRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILAMC 234

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNI--ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                         S +T+ R        S   +  ++ ++N    +G + Q+    P  
Sbjct: 235 EDSSGTEEASRVAQSGDTIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNS 294

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
           ++                 S S       + +P      SLR++ 
Sbjct: 295 KK-----------AQRRPSSPSSNTASGSKPTPRTGGTLSLRKSK 328


>gi|220931567|ref|YP_002508475.1| ribosomal large subunit pseudouridine synthase B [Halothermothrix
           orenii H 168]
 gi|219992877|gb|ACL69480.1| ribosomal large subunit pseudouridine synthase B [Halothermothrix
           orenii H 168]
          Length = 237

 Score =  198 bits (504), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 72/231 (31%), Positives = 119/231 (51%), Gaps = 2/231 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +A AG+ASRR+ E++I Q RVKVNG ++      +    D +EVDG  + K + 
Sbjct: 2   ERLQKYMAHAGVASRRKSEKIITQGRVKVNGKIVTELGTKIDPDKDIVEVDGRVISKEKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + +         TV   +  +  R+  VGRLD +T GLL+LTNDG L  
Sbjct: 62  VYILLNKPVGYITSVSDPHGR-KTVTGLIKGVSQRIYPVGRLDYDTSGLLILTNDGELTY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           VL  PS    + YRV   G    + L  L+ G+ ++       +V+   +K  N    + 
Sbjct: 121 VLTHPSHMVEKTYRVEVKGFPSDEVLKKLETGVKLKDGLTAPARVSAVKRKEKNTIFNLT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + EG+NR+++++ +   + V  L RI++GP  L  L  G  R +++K ++ 
Sbjct: 181 IHEGRNRQVRRMCDKIGFPVVNLKRIAFGPLNLKGLKTGQYRFLTEKEVKA 231


>gi|328957343|ref|YP_004374729.1| ribosomal large subunit pseudouridine synthase B [Carnobacterium
           sp. 17-4]
 gi|328673667|gb|AEB29713.1| ribosomal large subunit pseudouridine synthase B [Carnobacterium
           sp. 17-4]
          Length = 251

 Score =  198 bits (504), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 88/252 (34%), Positives = 138/252 (54%), Gaps = 3/252 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + E    +R+ KV+A AG+ASRR+ E +I++  VKVNG +++   + + ++D +EVDGVP
Sbjct: 1   MYEGEIMERLQKVLAHAGVASRRKSEELISKGHVKVNGKVVKEMGIQIGNSDVVEVDGVP 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +   E    +L +KP  ++T  SD  GR  V D   +I  R+  VGRLD +T G L+LTN
Sbjct: 61  I-YREEPVYFLLNKPRNMITAVSDDKGRPVVTDLFTNIEQRIYPVGRLDYDTTGALMLTN 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L+++L  P  Q  + Y  +  G VD+  LN L+KGIVI+G      +  + +   + 
Sbjct: 120 DGELSQLLMHPKYQIDKTYVAKVKGLVDRKALNKLEKGIVIEGKKTAPAKAKILSADRAK 179

Query: 187 --AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
               V + + EG+NR++K +F+     V +L R SYG   L  L  G  RE+    + + 
Sbjct: 180 DITMVELTIHEGRNRQVKNMFQAIGHPVEKLKRESYGTLTLDGLQTGEWRELKTFEIYQL 239

Query: 245 LGPHLLEEAQVN 256
                 EE +  
Sbjct: 240 RNSATQEENKTK 251


>gi|312884985|ref|ZP_07744674.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio
           caribbenthicus ATCC BAA-2122]
 gi|309367317|gb|EFP94880.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio
           caribbenthicus ATCC BAA-2122]
          Length = 342

 Score =  198 bits (504), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 68/326 (20%), Positives = 120/326 (36%), Gaps = 17/326 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RV +N  +       VM  D + +DG PL + E+T 
Sbjct: 8   RLNKYISETGFCSRREADKLIEQGRVSINDSVP-EMGTKVMPDDKVCIDGKPLSQKEKTI 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T            +      R+  +GRLD  ++GL+LLTNDG +   +
Sbjct: 67  YIALNKPTGITCTTERDV--PGNIVDFIGHKKRIFPIGRLDKPSDGLILLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    + +  ++ +  G+ I        +V     + +     + L 
Sbjct: 125 LRAGNNHEKEYVVRVDKPITKKFVDQMSSGVEILDTKTLPCKVI----QETKFSFRITLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L         
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGQWRYLSDHEVTEILSMCESSSNT 240

Query: 255 VNLDAPIYS----SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN- 309
                                 +   E      R  +      G +  +    P  ++  
Sbjct: 241 EEASQRDAKGTQIKSATDAKLFDSREENKASTARRNQKQRTFKGRNADEFRHAPNSKKRH 300

Query: 310 -----LASNVWMAKGIHSSFLSDSGQ 330
                  +N    K   S   S    
Sbjct: 301 HGNKLDKNNTARPKNDKSFSKSKPTA 326


>gi|229522171|ref|ZP_04411588.1| ribosomal large subunit pseudouridine synthase F [Vibrio cholerae
           TM 11079-80]
 gi|229341096|gb|EEO06101.1| ribosomal large subunit pseudouridine synthase F [Vibrio cholerae
           TM 11079-80]
          Length = 328

 Score =  198 bits (504), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 77/345 (22%), Positives = 136/345 (39%), Gaps = 20/345 (5%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
              T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR
Sbjct: 2   SQPTEKRLNKFISETGYCSRREADKLIEQGRVTLNGLQPEV-GSKVTEQDEVCIDGKPLR 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ER      +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG
Sbjct: 61  SKERPIYIALNKPTGITCTTERDV--PGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y VR    +  + +  +  G+ I        +VT    + +   
Sbjct: 119 DIVNKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVT----QETQYS 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L   
Sbjct: 175 FRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSDAEVSEILAMC 234

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNI--ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                         S +T+ R        S   +  ++ ++N    +G + Q+    P  
Sbjct: 235 EDSSGTEEASRVAQSGDTIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNS 294

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
           ++                 S S       + +P      SLR++ 
Sbjct: 295 KK-----------AQRRPSSPSSNTASGSKPTPRTGGTLSLRKSK 328


>gi|306845522|ref|ZP_07478091.1| conserved hypothetical protein [Brucella sp. BO1]
 gi|306273843|gb|EFM55670.1| conserved hypothetical protein [Brucella sp. BO1]
          Length = 567

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 166/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 53  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 112

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 113 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 172

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 173 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 232

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 233 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 292

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 293 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 352

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 353 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 400


>gi|306838529|ref|ZP_07471367.1| conserved hypothetical protein [Brucella sp. NF 2653]
 gi|306406396|gb|EFM62637.1| conserved hypothetical protein [Brucella sp. NF 2653]
          Length = 561

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 166/348 (47%), Positives = 220/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 53  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 112

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 113 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 172

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 173 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 232

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 233 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 292

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 293 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGEPPQEGERRRAPREREWISSTGERRRG 352

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P    K
Sbjct: 353 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSVK 400



 Score = 36.7 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 14/111 (12%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    + +   +            R       PD+  + +K+          K+   
Sbjct: 406 QMRPRRYSDEERGGEEGGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 465

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 466 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 516


>gi|152996949|ref|YP_001341784.1| 23S rRNA pseudouridine synthase F [Marinomonas sp. MWYL1]
 gi|150837873|gb|ABR71849.1| pseudouridine synthase [Marinomonas sp. MWYL1]
          Length = 355

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 70/354 (19%), Positives = 127/354 (35%), Gaps = 15/354 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N +  R++K I+ +GI SRR+ +R I Q  V +NG         V++ D + V+G  +  
Sbjct: 3   NASSTRLNKYISESGICSRRDADRFIEQGNVFINGKRASV-GDQVVAGDTVRVNGQIIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +            +    +          +  S   R+  +GRLD +++GL+ LTN+G 
Sbjct: 62  QDADDFVFIVLNKPVGIVSTTESSEKNNIVDFVSHGVRIFPIGRLDKDSQGLIFLTNNGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  +  D +  L  G+ I G       VT    K S    
Sbjct: 122 LVNKVLRAGNNHEKEYLVTVNKPITDDFIAGLAGGVPILGTMTKKCPVT----KVSPTVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++ K L   L    
Sbjct: 178 NITLVQGLNRQIRRMCEYFGYEVVKLERTRIMNVSLKGIPVGEWRDLTPKELSVLLKSIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRP----------NIISEVPDDFTRMKKNSSQKNGLSKQK 299
              ++ +  A    +      R              +               K+   K  
Sbjct: 238 DSSSEASAPAKKSRNAPRKNTRTDGSSKPKVSSKPKAPSKPMGAAKGNTKHPKDDARKPA 297

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              +   R    S      G         G   + + +  +   + S  R S +
Sbjct: 298 GSKSKDRRPFGDSKKPAGNGAGKRPTGKPGGSPKGNGKPTTNGKRPSAGRGSQR 351


>gi|261319705|ref|ZP_05958902.1| RNA-binding S4 domain-containing protein [Brucella ceti M644/93/1]
 gi|261292395|gb|EEX95891.1| RNA-binding S4 domain-containing protein [Brucella ceti M644/93/1]
          Length = 565

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 166/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 53  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 112

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 113 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 172

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 173 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 232

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 233 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 292

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 293 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 352

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 353 REEKTEKVEPRRRSNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 400



 Score = 36.3 bits (82), Expect = 7.0,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 406 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 465

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 466 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 516


>gi|296133130|ref|YP_003640377.1| pseudouridine synthase [Thermincola sp. JR]
 gi|296031708|gb|ADG82476.1| pseudouridine synthase [Thermincola potens JR]
          Length = 244

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 82/231 (35%), Positives = 130/231 (56%), Gaps = 1/231 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
             QR+ K +A AG+ASRR+ E +IA  +VKVNG ++      V  + D +EV G+ +   
Sbjct: 2   ERQRLQKFMAHAGVASRRKCEELIAAGKVKVNGKVVTEMGYTVDPSVDRVEVAGLGIIVH 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E+    L +KP G++++ SD  GR TV D + +  +R+  VGRLD +TEGL+LLTNDG L
Sbjct: 62  EKKEYILLYKPAGVLSSASDDRGRKTVVDLIKNAKTRLYPVGRLDYDTEGLILLTNDGRL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             +L  P  +  + YR    G   +DKL  L+ GI+++       +V +  Q   N  V 
Sbjct: 122 TNLLIHPRYKVDKTYRAVVQGIPGEDKLAALRNGIMLEDGPTYPARVKMLKQINGNGLVE 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + EG+NR+++++F+     V +L R  +G  +LG L  G  R +S   +
Sbjct: 182 ITIHEGRNRQVRRMFDAIGHPVLKLKRTRFGFLELGNLQPGQYRALSAAEV 232


>gi|222056371|ref|YP_002538733.1| pseudouridine synthase [Geobacter sp. FRC-32]
 gi|221565660|gb|ACM21632.1| pseudouridine synthase [Geobacter sp. FRC-32]
          Length = 240

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 91/234 (38%), Positives = 133/234 (56%), Gaps = 1/234 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ K++++AGIASRRE E++I   RV VNG ++          +D I +DG P+R+  R
Sbjct: 3   ERLQKILSQAGIASRREAEKIITAGRVAVNGQVVTELGSKADAESDRITLDGKPIRQESR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R  L +KP+G +TT  DP+GR  V D L  +  RV  VGRLD NTEGLLLLTNDG LA 
Sbjct: 63  KRYLLLYKPVGYMTTMKDPEGRPIVTDLLKDVKERVYPVGRLDYNTEGLLLLTNDGALAN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS +  + Y VR  GQ    +L  L+ G+ ++       QV+L  +   N W+++ 
Sbjct: 123 RLAHPSHEVDKGYLVRIRGQASPSQLKHLQMGVDLEDGMTAPAQVSLVRESDHNCWISIT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + EG+ R+++++ E     V RL R  YG  ++G L  G  RE+S   +     
Sbjct: 183 IHEGRYRQVRRMCEAVGLTVVRLKRSRYGFLEIGELKPGQYRELSSTEVERLQQ 236


>gi|229513867|ref|ZP_04403329.1| ribosomal large subunit pseudouridine synthase F [Vibrio cholerae
           TMA 21]
 gi|229349048|gb|EEO14005.1| ribosomal large subunit pseudouridine synthase F [Vibrio cholerae
           TMA 21]
          Length = 328

 Score =  198 bits (502), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 77/345 (22%), Positives = 137/345 (39%), Gaps = 20/345 (5%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
              T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR
Sbjct: 2   SQPTEKRLNKFISETGYCSRREADKLIEQGRVTLNGLQPEV-GSKVTDQDEVCIDGKPLR 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ER      +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG
Sbjct: 61  SKERPIYIALNKPTGITCTTERDV--PGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y VR    +  + +  +  G+ I        +VT    + +   
Sbjct: 119 DIVNKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVT----QETQYS 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L   
Sbjct: 175 FRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILAMC 234

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNI--ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                         S +T+ R        S   +  ++ ++N    +G + Q+    P  
Sbjct: 235 EDSSGTEEASRVAQSGDTIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNS 294

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
           ++                 S S       + +P      SLR++ 
Sbjct: 295 KK-----------AQRRPSSPSSNTASGSKPTPRTGGTLSLRKSK 328


>gi|149192366|ref|ZP_01870569.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio shilonii AK1]
 gi|148833805|gb|EDL50839.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio shilonii AK1]
          Length = 342

 Score =  198 bits (502), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 69/342 (20%), Positives = 135/342 (39%), Gaps = 9/342 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +      +R++K I+  G  SRRE +++I QQRV +NG +       V+S D++E+DG P
Sbjct: 1   MPNAAEGKRLNKYISETGFCSRREADKLIEQQRVTINGKIP-EMGTKVLSGDNVEIDGKP 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +R  E+      +KP G+  T            +      R+  +GRLD  ++GL+ LTN
Sbjct: 60  VRSKEKPVYIALNKPTGITCTTERDV--PGNIVDFVGHHKRIFPIGRLDKPSDGLIFLTN 117

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG +   +        + Y VR    V +D L  +  G+ I        +V    ++ + 
Sbjct: 118 DGDIVNKILRAGNNHEKEYVVRVDKPVTRDFLKKMGSGVAILDTVTLPCRV----EQETK 173

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               + L +G NR+I+++ E   ++V +L R+      +  +  G  R ++ + + E   
Sbjct: 174 FSFRITLTQGLNRQIRRMCEALGFEVLKLRRVRIMNISIDGIPNGKWRYLTDQEVAEIHR 233

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                 +             + +     + +   +  R  +     +G    +   +P  
Sbjct: 234 LCEGSVSTEEASRKDAKGRHITKATDAKLHDARAEAKR--EKMKTFSGHGADEFRRSPNK 291

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
            +        +    +       ++    +   S PSK   R
Sbjct: 292 NKRHKQEQGRSDKARNHHGKTQNRKPVAAKPDSSKPSKPRTR 333


>gi|169351006|ref|ZP_02867944.1| hypothetical protein CLOSPI_01783 [Clostridium spiroforme DSM 1552]
 gi|169292068|gb|EDS74201.1| hypothetical protein CLOSPI_01783 [Clostridium spiroforme DSM 1552]
          Length = 241

 Score =  198 bits (502), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 70/241 (29%), Positives = 121/241 (50%), Gaps = 3/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA +G  SRR+ E +I Q +V+VNG ++      V   D + V+G P+    + 
Sbjct: 2   ERLQKVIAASGYTSRRKAEDLIVQGKVEVNGQVVRELGTKVKKGDIVTVEGKPIVGENKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     + T   +   R  V D    +  R+  VGRLD +T GL++++NDG  A +
Sbjct: 62  YYVFYKPKGCVCTLDDE-FDRPIVTDYFTDVKERIYPVGRLDFDTTGLIIMSNDGEFANM 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW--VTV 191
           +  P +   ++Y V   G ++   LN L+KGI ++G+     ++ +  +   +    + +
Sbjct: 121 IMHPRSHLEKIYEVSVKGLINGQTLNKLEKGIYLEGVKTLPCKIKVVNKDIEHKTTMLKI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L EGKNR++KK+FE     V RL R+S G   L  L  G  R +  + +++       +
Sbjct: 181 KLVEGKNRQVKKMFESVGHPVKRLHRVSIGCVNLKGLTPGKYRILKPQEVKDLKKLVNGK 240

Query: 252 E 252
           +
Sbjct: 241 K 241


>gi|51892921|ref|YP_075612.1| ribosomal large subunit pseudouridine synthase B [Symbiobacterium
           thermophilum IAM 14863]
 gi|51856610|dbj|BAD40768.1| ribosomal large subunit pseudouridine synthase B [Symbiobacterium
           thermophilum IAM 14863]
          Length = 254

 Score =  198 bits (502), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 89/238 (37%), Positives = 129/238 (54%), Gaps = 3/238 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV+ARAG+ASRR  E +I   RV VNG ++ +    V+   D IEVDG PL   E 
Sbjct: 3   ERLQKVMARAGVASRRHCEALIQAGRVTVNGQVVTQLGTKVVPGKDVIEVDGRPLGTPET 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G V+T  DP GR  V D L      RV  VGRLD +TEGLLLLTNDG LA
Sbjct: 63  KVYVMLNKPKGYVSTLYDPQGRPKVIDLLGDEVAQRVYPVGRLDFDTEGLLLLTNDGDLA 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA-WVT 190
             L  PS    + Y V+  G     KL  L++GI ++       +V +   +  N+  ++
Sbjct: 123 HGLMHPSRMVKKTYIVKVRGVPGPAKLRALQEGIELEDGPTAPAEVKMLDVRPPNSATLS 182

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           V + EG+NR+++++F     +V  L R + GP +LG L  G  R ++ + + +     
Sbjct: 183 VRIHEGRNRQVRRMFAALGHEVIHLRRTTLGPLKLGDLSVGEWRYLTDQEVADLYRAA 240


>gi|331701399|ref|YP_004398358.1| pseudouridine synthase Rsu [Lactobacillus buchneri NRRL B-30929]
 gi|329128742|gb|AEB73295.1| pseudouridine synthase Rsu [Lactobacillus buchneri NRRL B-30929]
          Length = 242

 Score =  198 bits (502), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 81/234 (34%), Positives = 119/234 (50%), Gaps = 1/234 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E +IA+  VKVNG +++     V   D ++VD VP+ K    
Sbjct: 4   ERLQKVIAHAGVASRRKAEELIAKGHVKVNGEVVKELGTKVTPNDEVKVDEVPISKEAPV 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     ++T  +D   R TV D L  +  R+  VGRLD +T GLLLLTNDG L   
Sbjct: 64  YYLLYKPRG-VITAVTDDKHRKTVVDILEEVPERIYPVGRLDYDTSGLLLLTNDGDLDNK 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  + Y  +  G V  D L  L+ G+VI+       +  L      ++ V + +
Sbjct: 123 LTHPKYEVEKTYVAKVKGIVTNDDLKHLRTGVVIEHRKTAKAKTKLIRTNKDSSIVQLTI 182

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            EG+N ++K +FE   + V +L R +YG   L  L  G  R +    + E    
Sbjct: 183 HEGRNHQVKNMFEKIGYPVEKLSRETYGFLTLKGLQPGDYRPLKPHEVEELKEL 236


>gi|312143709|ref|YP_003995155.1| pseudouridine synthase [Halanaerobium sp. 'sapolanicus']
 gi|311904360|gb|ADQ14801.1| pseudouridine synthase [Halanaerobium sp. 'sapolanicus']
          Length = 236

 Score =  198 bits (502), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 69/230 (30%), Positives = 119/230 (51%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV+A AG+ASRR+ E +IA+ RVKVNG ++      V    D IEVDG  + K ++
Sbjct: 2   ERLQKVMAHAGVASRRKSEEIIAEGRVKVNGEIVTEMGFKVDPKKDEIEVDGEVIAKEKK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L+     + T     + ++   D +P +  RV   GRLD ++ GLL+LTNDG L  
Sbjct: 62  VYLLLHKPEGYITTVSDPKERQTV-MDLIPDLKQRVYPAGRLDYDSSGLLILTNDGDLCY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + Y VR  G +  +  N  ++G+VI G      ++       +     + 
Sbjct: 121 KLTHPKKEVDKRYWVRAKGTIFAEDFNKFEEGMVIDGRKTAPAKIANINYLDNYTEFEIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EG+NR+++++     + V +L R ++    L  L  G  R ++++ ++
Sbjct: 181 IHEGRNRQVRRMCRIAGFSVVKLKRTAFAFLSLDGLAEGEYRYLNEEEIK 230


>gi|261753204|ref|ZP_05996913.1| RNA-binding S4 domain-containing protein [Brucella suis bv. 3 str.
           686]
 gi|261742957|gb|EEY30883.1| RNA-binding S4 domain-containing protein [Brucella suis bv. 3 str.
           686]
          Length = 565

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 166/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 53  EEETSERIAKRLARAGIASRREAETMIATGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 112

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 113 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 172

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 173 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 232

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 233 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 292

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 293 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 352

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 353 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 400



 Score = 36.3 bits (82), Expect = 7.1,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 406 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 465

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 466 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 516


>gi|163737477|ref|ZP_02144894.1| Pseudouridine synthase, Rsu [Phaeobacter gallaeciensis BS107]
 gi|161389003|gb|EDQ13355.1| Pseudouridine synthase, Rsu [Phaeobacter gallaeciensis BS107]
          Length = 447

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 145/348 (41%), Positives = 196/348 (56%), Gaps = 3/348 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
           +     R++KV++RAG+ASRRE ERMIA+ RV VNG +++  A+NV+   D I VDG P+
Sbjct: 47  DGPEGDRIAKVLSRAGVASRREAERMIAEGRVAVNGKVIDSPALNVVLGKDRIVVDGNPM 106

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +  E  RLW+YHKP GLVTT +D   R T+FD LP    RV++VGRLD+N+EGLLLLTND
Sbjct: 107 QDPEPPRLWMYHKPSGLVTTTNDELDRRTIFDALPEDMPRVMTVGRLDLNSEGLLLLTND 166

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GG+ R LELPST WLR YRVR +G+        L++G+VI+G  +  M V LD Q+G+NA
Sbjct: 167 GGIKRQLELPSTGWLRRYRVRINGRPKDTDFEPLRQGLVIEGERFQPMTVALDRQQGANA 226

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+T+GLREGKNREI++  E   + VNRL+R+SYGPFQLG L  G   E+  +++R+QLG 
Sbjct: 227 WLTIGLREGKNREIRRAIEDIGFTVNRLLRLSYGPFQLGNLKPGEVEELRPRVVRDQLGL 286

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD--DFTRMKKNSSQKNGLSKQKKLATPV 305
              E  +                        PD     +     S K             
Sbjct: 287 AAPETEEDEKPKRPVRQRPGAGKPGTKPGAKPDFKSGGKPGGKPSGKPSGRSFGSADRSS 346

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            +    S    A      F S     +    +S   P+ R+  RTS +
Sbjct: 347 EKPGDRSGARPAGKPGGKFASKGKPSDRFAGKSEGKPTGRTADRTSDR 394


>gi|182679330|ref|YP_001833476.1| RNA-binding S4 domain-containing protein [Beijerinckia indica
           subsp. indica ATCC 9039]
 gi|182635213|gb|ACB95987.1| RNA-binding S4 domain protein [Beijerinckia indica subsp. indica
           ATCC 9039]
          Length = 528

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 148/340 (43%), Positives = 195/340 (57%), Gaps = 3/340 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           ++   PQR++KV+ARAG+ SRR+ E  IA+ RV VNG +L +  V+V   D I VDG  L
Sbjct: 84  KDAQEPQRIAKVMARAGLCSRRDAEAWIAEGRVSVNGTVLTQPGVSVSDEDVILVDGEKL 143

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLL 124
                TRL+L+HKP GLVTT+ DP+GR TVFD L      +   +S+GRLDINTEGLLLL
Sbjct: 144 AARGHTRLFLFHKPRGLVTTNHDPEGRPTVFDYLHERHPDMPRVLSIGRLDINTEGLLLL 203

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDGGL+R+LELP+T W+R YRVR  G  DQ  L+ L++GI I GI Y  M+VT D ++G
Sbjct: 204 TNDGGLSRLLELPTTGWVRRYRVRAKGTTDQAVLDQLRQGITIDGIHYAGMEVTFDREQG 263

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +N+W+T+ LREGKNRE+K+V E    +VNRLIR+S+GPFQLG L  G   EV  ++LR+Q
Sbjct: 264 ANSWLTLSLREGKNREVKRVLEQIGLEVNRLIRLSFGPFQLGDLPEGDVTEVRTRVLRDQ 323

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           LGP L   A V+       +           +             S         +  T 
Sbjct: 324 LGPSLAAAAGVDWTRHDEDAAEPAAPERARKTPSKTRTEGKSVTKSHGAAPRPSSRTFTK 383

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
              R        AK    S    S  R E+  R  +   +
Sbjct: 384 DKPREDEHPARTAKPAPRSRKHISLLRAEDENRKGAPRKR 423


>gi|255533735|ref|YP_003094107.1| pseudouridine synthase [Pedobacter heparinus DSM 2366]
 gi|255346719|gb|ACU06045.1| pseudouridine synthase [Pedobacter heparinus DSM 2366]
          Length = 348

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 69/344 (20%), Positives = 131/344 (38%), Gaps = 10/344 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           + +  R++K I+ +G+ SRR  +R I Q  V +NG   +     V   D + V+G  +  
Sbjct: 2   SDSTTRLNKYISESGLCSRRAADRYIEQGNVYINGKKAKV-GDKVFFGDIVTVNGQTIDP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E     L      +  T +   G      +  +   RV  +GRLD +++GL+ LTN+G 
Sbjct: 61  KEVENSVLIAYNKPVGITSTTEAGVKGNIVDHVNHSERVFPIGRLDKDSQGLIFLTNNGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  +    +  + KG+ + G+     +V     K S    
Sbjct: 121 LVNKILRAGNNHEKEYVVTVNKPLTDQFITGMAKGVPVLGVMTKKCKVV----KESPLIF 176

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F ++V +L R+      L  +  G  RE++ + L        
Sbjct: 177 KITLIQGLNRQIRRMCEYFGYEVTKLERVRIMNIPLKGIPLGEWRELTPEELTGIFNMVA 236

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
              A+ +      S +       + +  V    +  +    +  G +          RR 
Sbjct: 237 KSSAEADATPKRVSKKPKTPKEEDFLENVTPGRSSGRNAKPKSKGKAAPA-----SVRRE 291

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                   K    +  +               PSKR ++ T  +
Sbjct: 292 DRPAGGKGKSGPKTSAAFKTTGAAGDWNKSGGPSKRPVKPTKGR 335


>gi|257869547|ref|ZP_05649200.1| pseudouridine synthase [Enterococcus gallinarum EG2]
 gi|257803711|gb|EEV32533.1| pseudouridine synthase [Enterococcus gallinarum EG2]
          Length = 238

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 79/232 (34%), Positives = 123/232 (53%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E +I   RV VNG +++   V V + D +EVDGVP+ +    
Sbjct: 2   ERLQKVIAHAGITSRRKAEELIVAGRVSVNGQIVKELGVQVSAKDRVEVDGVPIEQESPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     +++  +D   R  V D    +  R+  +GRLD +T GLLLLTNDG L++ 
Sbjct: 62  YYMLYKPRG-VISAVTDDKKRKVVLDFFTEVPERLYPIGRLDYDTSGLLLLTNDGDLSQK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVTV 191
           L  P  +  +VY  +  G  D+ +L  L +GI I+G      +  + +   +   + V +
Sbjct: 121 LMHPKHEVDKVYVAKVKGIADKKQLLPLSRGIRIEGKKTAPARFEILSTDAATQTSIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + EG+N ++K + +     V +L R  YG   L  L  G  RE++KK + E
Sbjct: 181 TIHEGRNHQVKNMLKAVGLPVQKLKREMYGSLTLAGLRPGEYRELTKKEVNE 232


>gi|302392426|ref|YP_003828246.1| ribosomal large subunit pseudouridine synthase B [Acetohalobium
           arabaticum DSM 5501]
 gi|302204503|gb|ADL13181.1| ribosomal large subunit pseudouridine synthase B [Acetohalobium
           arabaticum DSM 5501]
          Length = 244

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 74/231 (32%), Positives = 117/231 (50%), Gaps = 2/231 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV+++AG+ASRR+ E +I   RV+VNG ++      V    D I+VDG  +++ + 
Sbjct: 2   ERLQKVMSQAGVASRRKSEDIITAGRVEVNGEVVTELGTKVDPEQDTIKVDGQQIKREKL 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L      + T     +   TV D +  +   V  VGRLD +TEGLLLLTNDG L  
Sbjct: 62  VYLLLNKPQGYITTVDDPHNR-RTVIDLIQDVSQAVHPVGRLDKDTEGLLLLTNDGDLTY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS    + Y     G  +Q K+  L+KGI ++       +  L  +    A V++ 
Sbjct: 121 ALTHPSHGIDKTYMATVKGVPNQSKIEALEKGIKLKDGWTAPAEAKLVAELAERAVVSLT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + EG+  ++K++ +     V  L RI +GP  L  L  G  R ++   ++E
Sbjct: 181 IHEGRKHQVKRMLKSVGHPVEELKRIKFGPLDLTGLSPGEYRHLTNSEIKE 231


>gi|294501116|ref|YP_003564816.1| pseudouridine synthase [Bacillus megaterium QM B1551]
 gi|295706463|ref|YP_003599538.1| pseudouridine synthase [Bacillus megaterium DSM 319]
 gi|294351053|gb|ADE71382.1| pseudouridine synthase [Bacillus megaterium QM B1551]
 gi|294804122|gb|ADF41188.1| pseudouridine synthase [Bacillus megaterium DSM 319]
          Length = 241

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 81/238 (34%), Positives = 126/238 (52%), Gaps = 3/238 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E +I Q RVKVNG ++      V   D IEVD VP+      
Sbjct: 2   ERLQKVIAHAGVASRRKAEELIGQGRVKVNGKVVRELGTKVGPNDKIEVDEVPVESEAPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     +++  +D  GR TV D  P +  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 62  YFMLYKPRG-VISAANDDKGRKTVVDFFPHVEERIYPIGRLDYDTSGLLLLTNDGEFANQ 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW--VTV 191
           L  P  +  +VY  +  G   ++K+  L++G++++       +  + +   S     V +
Sbjct: 121 LMHPKFEVDKVYVAKIKGIPSREKIRQLQRGVMLEDGKTAPARAKVLSIDKSKQTAIVEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + EGKNR+++++F+     V +L R  YGP  L  L AG  RE++   +++      
Sbjct: 181 TIHEGKNRQVRRMFDAIGHSVLKLKRERYGPLDLRGLNAGEARELTAHEVKQLYSMSQ 238


>gi|262166303|ref|ZP_06034040.1| ribosomal large subunit pseudouridine synthase F [Vibrio mimicus
           VM223]
 gi|262026019|gb|EEY44687.1| ribosomal large subunit pseudouridine synthase F [Vibrio mimicus
           VM223]
          Length = 332

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 77/339 (22%), Positives = 137/339 (40%), Gaps = 16/339 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RV +NG   E     V   D + +DG PLR  ER  
Sbjct: 8   RLNKFISETGFCSRREADKLIEQGRVTLNGAQPEV-GSKVTEQDEVCIDGKPLRSKERPI 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCTTERDV--PGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + +  +  G+ I        +VT    + +     + L 
Sbjct: 125 LRAGNNHEKEYVVRVDKPITPEFIRQMASGVNILDTVTLPCKVT----QETQYSFRIVLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L         
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVNEILAMCEDSSGT 240

Query: 255 VNLDAPIYSSETLVRDRPNI--ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
                   S +++ R        S   +  ++ ++N    +G + Q+    P  ++    
Sbjct: 241 EEASRVAQSGDSIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNSKKAQR- 299

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                    SS  + S   +   R +P      SLR++ 
Sbjct: 300 ------HPKSSPSNSSTASKPASRPTPRTGGTLSLRKSK 332


>gi|261211343|ref|ZP_05925631.1| ribosomal large subunit pseudouridine synthase F [Vibrio sp. RC341]
 gi|260839298|gb|EEX65924.1| ribosomal large subunit pseudouridine synthase F [Vibrio sp. RC341]
          Length = 332

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 77/339 (22%), Positives = 137/339 (40%), Gaps = 16/339 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RV +NG   E     V   D + +DG PLR  ER  
Sbjct: 8   RLNKFISETGFCSRREADKLIEQGRVTLNGAQPEV-GSKVTEQDEVCIDGKPLRSKERPI 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCTTERDV--PGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + +  +  G+ I        +VT    + +     + L 
Sbjct: 125 LRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVT----QETQYSFRIVLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + + L         
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVNDILAMCEDSSGT 240

Query: 255 VNLDAPIYSSETLVRDRPNI--ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
                   S +T+ R        S   +  ++ ++N    +G + Q+    P  ++    
Sbjct: 241 EEASRVAQSGDTIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNSKKAQRR 300

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                    +S  S S   +   R +P      SLR++ 
Sbjct: 301 PT-------NSSSSSSTASKPAQRATPRTGGTLSLRKSK 332


>gi|189022412|ref|YP_001932153.1| RNA pseudouridylate synthase family protein [Brucella abortus S19]
 gi|189020986|gb|ACD73707.1| RNA pseudouridylate synthase family protein [Brucella abortus S19]
          Length = 565

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 166/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 53  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 112

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 113 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 172

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 173 GLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 232

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 233 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 292

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 293 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 352

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 353 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 400



 Score = 35.9 bits (81), Expect = 8.4,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 406 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 465

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 466 ELRNAEGQTTERGKGGFEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 516


>gi|307267525|ref|ZP_07549006.1| pseudouridine synthase [Thermoanaerobacter wiegelii Rt8.B1]
 gi|326391079|ref|ZP_08212626.1| pseudouridine synthase [Thermoanaerobacter ethanolicus JW 200]
 gi|306917457|gb|EFN47750.1| pseudouridine synthase [Thermoanaerobacter wiegelii Rt8.B1]
 gi|325992864|gb|EGD51309.1| pseudouridine synthase [Thermoanaerobacter ethanolicus JW 200]
          Length = 236

 Score =  197 bits (500), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 76/230 (33%), Positives = 122/230 (53%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +A  GIASRR+ E  I Q RVKVNG +++   V +    D IE D   +R+ ++
Sbjct: 2   ERLQKYLAECGIASRRKCEEYILQGRVKVNGKVVKELGVKINPDVDIIEFDDKIVRREKK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G +T+  D  GR TV  +L  +  R+  VGRLD +T GLLLLTNDG +A 
Sbjct: 62  KVYIMLNKPTGYITSVKDQFGRPTVM-DLVKVKERIYPVGRLDYDTSGLLLLTNDGEIAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +L  P  + ++ Y  +  G   Q++L   + G++I        ++ +   K   + V + 
Sbjct: 121 ILMHPRHEIVKTYIAKIKGIPTQEELERFRNGLLIGDYLTSKAEIEILAVKNGTSVVEIK 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGKNR+++++ E     V  L R   G   L  L  G  R +++K + 
Sbjct: 181 IHEGKNRQVRRMCEAIGHPVISLTRTKIGELSLEGLKPGEWRYLTQKEID 230


>gi|323705338|ref|ZP_08116913.1| pseudouridine synthase [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323535240|gb|EGB25016.1| pseudouridine synthase [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 235

 Score =  197 bits (500), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 80/230 (34%), Positives = 122/230 (53%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +A  GIASRR+ E++I   +VKVNG  +    V V    D +E +G  + K  +
Sbjct: 2   ERLQKYLAECGIASRRKCEQLILDGKVKVNGETVRELGVKVDPNKDVVEYNGKVVTKVNK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP+G +TT  D   R +V  +L SI  RV  +GRLD +T GLLLLTNDG LA 
Sbjct: 62  NIYIMLNKPVGYITTVKDQFDRPSVI-DLVSIDDRVYPIGRLDYDTSGLLLLTNDGDLAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VY  +  G  D+ KL++ + G+ I        ++ +      N+ V + 
Sbjct: 121 KLMHPRHNINKVYIAQIKGVPDKMKLDMFRNGLRIDNYKTAKAEIDILKVTNGNSTVKIA 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EG+NR+I+K+ E     V +L R+  G   +G L  G  R +SK  + 
Sbjct: 181 IHEGRNRQIRKMCELIGHPVLKLKRVKIGNLDIGNLKTGQWRYLSKDEVE 230


>gi|167037554|ref|YP_001665132.1| pseudouridine synthase [Thermoanaerobacter pseudethanolicus ATCC
           33223]
 gi|167040216|ref|YP_001663201.1| pseudouridine synthase [Thermoanaerobacter sp. X514]
 gi|300914300|ref|ZP_07131616.1| pseudouridine synthase [Thermoanaerobacter sp. X561]
 gi|307724464|ref|YP_003904215.1| pseudouridine synthase [Thermoanaerobacter sp. X513]
 gi|320115969|ref|YP_004186128.1| pseudouridine synthase [Thermoanaerobacter brockii subsp. finnii
           Ako-1]
 gi|166854456|gb|ABY92865.1| pseudouridine synthase [Thermoanaerobacter sp. X514]
 gi|166856388|gb|ABY94796.1| pseudouridine synthase [Thermoanaerobacter pseudethanolicus ATCC
           33223]
 gi|300889235|gb|EFK84381.1| pseudouridine synthase [Thermoanaerobacter sp. X561]
 gi|307581525|gb|ADN54924.1| pseudouridine synthase [Thermoanaerobacter sp. X513]
 gi|319929060|gb|ADV79745.1| pseudouridine synthase [Thermoanaerobacter brockii subsp. finnii
           Ako-1]
          Length = 236

 Score =  197 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 76/230 (33%), Positives = 122/230 (53%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +A  GIASRR+ E  I Q RVKVNG +++   V +    D IE D   +R+ ++
Sbjct: 2   ERLQKYLAECGIASRRKCEEYILQGRVKVNGKVVKELGVKINPDVDIIEFDDKIVRREKK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G +T+  D  GR TV  +L  +  R+  VGRLD +T GLLLLTNDG +A 
Sbjct: 62  KVYIMLNKPTGYITSVKDQFGRPTVM-DLVKVKERIYPVGRLDYDTSGLLLLTNDGEIAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +L  P  + ++ Y  +  G   Q++L   + G++I        ++ +   K   + V + 
Sbjct: 121 ILMHPRHEIVKTYIAKIKGIPTQEELERFRNGLLIGDYLTSKAEIEILAVKNGTSVVEIK 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGKNR+++++ E     V  L R   G   L  L  G  R +++K + 
Sbjct: 181 IHEGKNRQVRRMCEAIGHPVISLTRTKIGDLSLEGLKPGKWRYLTQKEID 230


>gi|262170804|ref|ZP_06038482.1| ribosomal large subunit pseudouridine synthase F [Vibrio mimicus
           MB-451]
 gi|261891880|gb|EEY37866.1| ribosomal large subunit pseudouridine synthase F [Vibrio mimicus
           MB-451]
          Length = 332

 Score =  197 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 77/339 (22%), Positives = 138/339 (40%), Gaps = 16/339 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RV +NG   E     V   D + +DG PLR  ER  
Sbjct: 8   RLNKFISETGFCSRREADKLIEQGRVTLNGAQPEV-GSKVTEQDEVCIDGKPLRSKERPI 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T            +  S   R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCTTERDV--PGNIVDFISHHKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + +  +  G+ I        +VT    + +     + L 
Sbjct: 125 LRAGNNHEKEYVVRVDKPITPEFIRQMASGVNILDTVTLPCKVT----QETQYSFRIVLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L         
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVNEILAMCEDSSGT 240

Query: 255 VNLDAPIYSSETLVRDRPNI--ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
                   S +++ R        +   +  ++ ++N    +G + Q+    P  ++    
Sbjct: 241 EEASRVAQSGDSIKRATDAKLFDNREANKESKARRNPKTYHGKNAQEFRHAPNSKKAQR- 299

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                    SS  + S   +   R +P      SLR++ 
Sbjct: 300 ------HPKSSPSNSSTASKPASRPTPRTGGTLSLRKSK 332


>gi|196248745|ref|ZP_03147445.1| pseudouridine synthase [Geobacillus sp. G11MC16]
 gi|196211621|gb|EDY06380.1| pseudouridine synthase [Geobacillus sp. G11MC16]
          Length = 243

 Score =  197 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 83/231 (35%), Positives = 125/231 (54%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIARAGIASRR+ E MI Q RVKVNG ++    V V   D +EVDG+P+ + E  
Sbjct: 2   ERLQKVIARAGIASRRKAEEMILQGRVKVNGRVVTELGVKVGPRDDVEVDGIPVEREEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     + +   +  GR  V D    I  R+  +GRLD +T GLLLLTNDG  A +
Sbjct: 62  YYLLYKPRGVISSVKDE-KGRKVVTDFFKDIHQRIYPIGRLDYDTSGLLLLTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW--VTV 191
           L  P  +  +VY  +  G   +++L  L+KG++++       +V L +         V +
Sbjct: 121 LMHPRYEIEKVYVAKVKGIPTREQLKQLEKGVLLEDGITAPAKVKLLSADRKKRTAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EG+NR+++++FE    +V +L R  Y    L  L  G  RE+S   ++
Sbjct: 181 SIHEGRNRQVRRMFEAIGCEVLKLKRERYAFLDLKGLRPGEYRELSPHEVK 231


>gi|258621029|ref|ZP_05716063.1| Ribosomal large subunit pseudouridine synthase F [Vibrio mimicus
           VM573]
 gi|258586417|gb|EEW11132.1| Ribosomal large subunit pseudouridine synthase F [Vibrio mimicus
           VM573]
          Length = 332

 Score =  197 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 77/339 (22%), Positives = 137/339 (40%), Gaps = 16/339 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RV +NG   E     V   D + +DG PLR  ER  
Sbjct: 8   RLNKFISETGFCSRREADKLIEQGRVTLNGAQPEV-GSKVTEQDEVCIDGKPLRSKERPI 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCTTERDV--PGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + +  +  G+ I        +VT    + +     + L 
Sbjct: 125 LRAGNNHEKEYVVRVDKPITPEFIRQMASGVNILDTVTLPCKVT----QETQYSFRIVLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L         
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVNEILAMCEDSSGT 240

Query: 255 VNLDAPIYSSETLVRDRPNI--ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
                   S +++ R        S   +  ++ ++N    +G + Q+    P  ++    
Sbjct: 241 EEASRVAQSGDSIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNSKKAQR- 299

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                    SS  + S   +   R +P      SLR++ 
Sbjct: 300 ------HPKSSPSNSSTASKPAPRPTPRTGGTLSLRKSK 332


>gi|326797290|ref|YP_004315110.1| pseudouridine synthase Rsu [Marinomonas mediterranea MMB-1]
 gi|326548054|gb|ADZ93274.1| pseudouridine synthase Rsu [Marinomonas mediterranea MMB-1]
          Length = 355

 Score =  196 bits (499), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 67/353 (18%), Positives = 127/353 (35%), Gaps = 16/353 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T  R++K I+ +G+ SRRE +R I Q  V +NG         V   D ++V+G  +   E
Sbjct: 5   TSIRINKYISESGLCSRREADRFIDQGSVFINGKRAGT-GDQVSPGDLVKVNGQIIEPQE 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L        +    +          +     +R+  +GRLD +++GL+ LTN+G L 
Sbjct: 64  AEDLIFIALNKPVGIVSTTESSEPANIVSFVKHGARIFPIGRLDKDSQGLIFLTNNGDLV 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +   +    + Y V  +  + Q  ++ +  G+ I G      +V     K S     +
Sbjct: 124 NKILRAANNHEKEYLVTVNKPITQAFIDGMSGGVPILGQVTKKCKVV----KESTYVFNI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ E F ++V RL RI      L  L  G  R++++K L+  +      
Sbjct: 180 TLVQGLNRQIRRMAEHFGYEVTRLERIRIMNVSLKGLALGDWRDLTQKELQTLVKLTEDS 239

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           +            +                       ++       +          +  
Sbjct: 240 DTTNPPAKNPRKPKPQGNRHSGNRESGNRRSDTRDGKNNGGARRGGRPSAPGKGKPGSSK 299

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSP----------SFPSKRSLRRTSAKK 354
            +            S     + N + +P            P+ RS  + + K+
Sbjct: 300 PSNSKPGSSRP-GSSKPPHSKGNGKPAPKGKTGTGGKGRAPAGRSAPKPAGKR 351


>gi|170746519|ref|YP_001752779.1| RNA-binding S4 domain-containing protein [Methylobacterium
           radiotolerans JCM 2831]
 gi|170653041|gb|ACB22096.1| RNA-binding S4 domain protein [Methylobacterium radiotolerans JCM
           2831]
          Length = 601

 Score =  196 bits (499), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 147/341 (43%), Positives = 201/341 (58%), Gaps = 2/341 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E    +R++K +ARAGIASRR+ E MI   RV VNG  L   A NV   D I +DG P+ 
Sbjct: 81  ETPPGERIAKAMARAGIASRRDAETMIVAGRVSVNGETLTSPARNVTENDRILIDGEPMP 140

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ER+RLW++HKP G+VTT  DP+GR TVFD LP    RV++VGRLDINTEGLLLLTNDG
Sbjct: 141 SRERSRLWIFHKPRGVVTTARDPEGRQTVFDVLPEDLPRVVAVGRLDINTEGLLLLTNDG 200

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GLA+V+  P T WLR YRVR HG  DQ +L+ L KG+ I G+ YG ++ TLD  +G N W
Sbjct: 201 GLAKVIAHPDTGWLRRYRVRAHGDTDQAQLDRLAKGVTIDGMEYGPVEATLDRVQGDNVW 260

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +T+GLREGKNRE+K++ E     VNRLIR+S+GPFQLG L  G   EV  ++L++QLG  
Sbjct: 261 LTLGLREGKNREVKRILEHLGLSVNRLIRLSFGPFQLGDLEVGLVEEVRTRVLKDQLGKS 320

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
           L E+A V+ D+P+               +         + ++ +   + +          
Sbjct: 321 LAEQAGVDFDSPVREPIAPFGGTRPADRDAKSAQPAPARRNAARPAPAPRVSTGGAGP-- 378

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
              S+ W  +       +   +R  + R + +  ++R   R
Sbjct: 379 GPRSSTWRDEDAAKPRGTRVPRRGADPRTAQAAAAERGRER 419



 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 17/140 (12%), Positives = 33/140 (23%), Gaps = 7/140 (5%)

Query: 217 RISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIIS 276
           R   G  +     AG  R V +++      P  + + +                 P    
Sbjct: 417 RERVGSIR-----AGERRVVVERLSATPAEPAPVAKPKRRFADRGAPERQERPAGPRNER 471

Query: 277 EVPDDFTRMKKNSSQKNGLSK-QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENH 335
              +   R    S       +  ++      RR         +G         G +    
Sbjct: 472 RGDERPRRETARSDAPRDERRFDERGGKSGGRRERTFEAGPTEGTSRKPGGFRGSKPAGA 531

Query: 336 RRSPSFPSKR-SLRRTSAKK 354
              P+F   +    R    +
Sbjct: 532 GGKPAFGGPKTGAPRPGGSR 551


>gi|117619273|ref|YP_856164.1| 23S rRNA pseudouridine synthase F [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
 gi|117560680|gb|ABK37628.1| ribosomal large subunit pseudouridine synthase F [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
          Length = 344

 Score =  196 bits (499), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 70/344 (20%), Positives = 131/344 (38%), Gaps = 5/344 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K I+ +GI SRRE +R I Q  V +NG         V + D ++V+G  +   
Sbjct: 4   DESMRLNKYISESGICSRREADRFIEQGNVFINGKRAGV-GDQVFAGDLVKVNGQVIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L        +    +   G      +  +  +R+  +GRLD +++GL+ LTN G L
Sbjct: 63  EADSLVFIVLNKPVGIVSTTEAGEKDNIVDFVNHSTRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V  + +  +  G+ I G      +V    +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPVTDEFIRGMGAGVPILGAVTKKCKV----KKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L RI      L  L  G  R+++   L E       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGFEVTKLERIRIMNVSLKGLPVGEWRDLTDDELIELFKLIED 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
             ++V       ++           ++        K      + +  +  +  P    + 
Sbjct: 239 SSSEVKPAKGGQAAAGQGGKPKASAAQAGKPAPGKKPRRDDDHEIGGRPNVPGPSAFESK 298

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +     A G   +    +G+   N    P+    R+ +    KK
Sbjct: 299 SPAGKGAAGKGGAAKGSAGKGAPNKGAKPAAGKPRAGQGGRQKK 342


>gi|69248060|ref|ZP_00604605.1| Pseudouridine synthase, Rsu [Enterococcus faecium DO]
 gi|257877984|ref|ZP_05657637.1| pseudouridine synthase [Enterococcus faecium 1,230,933]
 gi|257881230|ref|ZP_05660883.1| pseudouridine synthase [Enterococcus faecium 1,231,502]
 gi|257884895|ref|ZP_05664548.1| pseudouridine synthase [Enterococcus faecium 1,231,501]
 gi|257889817|ref|ZP_05669470.1| pseudouridine synthase [Enterococcus faecium 1,231,410]
 gi|257892245|ref|ZP_05671898.1| pseudouridine synthase [Enterococcus faecium 1,231,408]
 gi|258616531|ref|ZP_05714301.1| ribosomal large subunit pseudouridine synthase B, putative
           [Enterococcus faecium DO]
 gi|260559035|ref|ZP_05831221.1| pseudouridine synthase [Enterococcus faecium C68]
 gi|261207569|ref|ZP_05922254.1| pseudouridine synthase [Enterococcus faecium TC 6]
 gi|289565081|ref|ZP_06445534.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium D344SRF]
 gi|293556726|ref|ZP_06675289.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1039]
 gi|293563384|ref|ZP_06677833.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1162]
 gi|293568042|ref|ZP_06679380.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1071]
 gi|294614860|ref|ZP_06694755.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1636]
 gi|294618690|ref|ZP_06698224.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1679]
 gi|294622981|ref|ZP_06701871.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium U0317]
 gi|314939485|ref|ZP_07846719.1| conserved hypothetical protein [Enterococcus faecium TX0133a04]
 gi|314941116|ref|ZP_07848014.1| conserved hypothetical protein [Enterococcus faecium TX0133C]
 gi|314948728|ref|ZP_07852100.1| conserved hypothetical protein [Enterococcus faecium TX0082]
 gi|314951701|ref|ZP_07854744.1| conserved hypothetical protein [Enterococcus faecium TX0133A]
 gi|314993952|ref|ZP_07859279.1| conserved hypothetical protein [Enterococcus faecium TX0133B]
 gi|314997516|ref|ZP_07862461.1| conserved hypothetical protein [Enterococcus faecium TX0133a01]
 gi|68194579|gb|EAN09070.1| Pseudouridine synthase, Rsu [Enterococcus faecium DO]
 gi|257812212|gb|EEV40970.1| pseudouridine synthase [Enterococcus faecium 1,230,933]
 gi|257816888|gb|EEV44216.1| pseudouridine synthase [Enterococcus faecium 1,231,502]
 gi|257820733|gb|EEV47881.1| pseudouridine synthase [Enterococcus faecium 1,231,501]
 gi|257826177|gb|EEV52803.1| pseudouridine synthase [Enterococcus faecium 1,231,410]
 gi|257828624|gb|EEV55231.1| pseudouridine synthase [Enterococcus faecium 1,231,408]
 gi|260074792|gb|EEW63108.1| pseudouridine synthase [Enterococcus faecium C68]
 gi|260077952|gb|EEW65658.1| pseudouridine synthase [Enterococcus faecium TC 6]
 gi|289163088|gb|EFD10935.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium D344SRF]
 gi|291589263|gb|EFF21073.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1071]
 gi|291592322|gb|EFF23936.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1636]
 gi|291595073|gb|EFF26416.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1679]
 gi|291597609|gb|EFF28770.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium U0317]
 gi|291601058|gb|EFF31347.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1039]
 gi|291604645|gb|EFF34130.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1162]
 gi|313588427|gb|EFR67272.1| conserved hypothetical protein [Enterococcus faecium TX0133a01]
 gi|313591554|gb|EFR70399.1| conserved hypothetical protein [Enterococcus faecium TX0133B]
 gi|313596165|gb|EFR75010.1| conserved hypothetical protein [Enterococcus faecium TX0133A]
 gi|313600117|gb|EFR78960.1| conserved hypothetical protein [Enterococcus faecium TX0133C]
 gi|313641287|gb|EFS05867.1| conserved hypothetical protein [Enterococcus faecium TX0133a04]
 gi|313644794|gb|EFS09374.1| conserved hypothetical protein [Enterococcus faecium TX0082]
          Length = 238

 Score =  196 bits (499), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 82/236 (34%), Positives = 122/236 (51%), Gaps = 3/236 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E  I   RVKVNG ++    + V   D +EVD VP+ + E  
Sbjct: 2   ERLQKVIAHAGITSRRKAEEFILAGRVKVNGQVVRELGIKVGKHDTVEVDEVPIYQEEYG 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     +++  +D  GR  V D LP +  R+  VGRLD +T G+LLLTNDG  A+ 
Sbjct: 62  YYLLYKPKG-VISAVADDKGRKVVTDLLPMVKERIYPVGRLDYDTSGILLLTNDGDFAQR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           L  P  +  +VY  +  G   +  L  L KGI I+G      +  + +     +++ V +
Sbjct: 121 LTHPKHEVDKVYVAKVKGIATKSMLAPLTKGIKIEGRKTSPAKFQILSVDPKTNHSIVEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + EG+N ++K + +     V +L R  YG   L  L  G  RE++KK +   L  
Sbjct: 181 TIHEGRNHQVKNMLQAVGLPVQKLKREKYGDLTLQGLRPGDYRELNKKEVSSLLNH 236


>gi|256752042|ref|ZP_05492910.1| pseudouridine synthase [Thermoanaerobacter ethanolicus CCSD1]
 gi|256749052|gb|EEU62088.1| pseudouridine synthase [Thermoanaerobacter ethanolicus CCSD1]
          Length = 236

 Score =  196 bits (499), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 76/230 (33%), Positives = 122/230 (53%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +A  GIASRR+ E  I Q RVKVNG +++   V +    D IE D   +R+ ++
Sbjct: 2   ERLQKYLAECGIASRRKCEEYILQGRVKVNGKVVKELGVKINPDVDIIEFDDKIVRREKK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G +T+  D  GR TV  +L  +  R+  VGRLD +T GLLLLTNDG +A 
Sbjct: 62  KVYIILNKPTGYITSVKDQFGRPTVM-DLVKVKERIYPVGRLDYDTSGLLLLTNDGEIAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +L  P  + ++ Y  +  G   Q++L   + G++I        ++ +   K   + V + 
Sbjct: 121 ILMHPRHEIVKTYIAKIKGIPTQEELERFRNGLLIGDYLTSKAEIEILAVKNGTSVVEIK 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGKNR+++++ E     V  L R   G   L  L  G  R +++K + 
Sbjct: 181 IHEGKNRQVRRMCEAIGHPVISLTRTKIGDLSLEGLKPGKWRYLTQKEID 230


>gi|150395641|ref|YP_001326108.1| pseudouridine synthase [Sinorhizobium medicae WSM419]
 gi|150027156|gb|ABR59273.1| pseudouridine synthase [Sinorhizobium medicae WSM419]
          Length = 576

 Score =  196 bits (499), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 180/371 (48%), Positives = 236/371 (63%), Gaps = 29/371 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             PQR+SK+++RAG+ASRR+VERMI + RV +NG++L+   VN    D IEVDG P+R  
Sbjct: 45  EQPQRISKILSRAGVASRRDVERMIMEGRVSLNGLVLDTPVVNATLADRIEVDGHPIRGI 104

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ERTRLWLYHKP GLVTT++DP+GR TVF+NLP    RV+S+GRLDINTEGLLLLTNDGGL
Sbjct: 105 ERTRLWLYHKPGGLVTTNADPEGRPTVFENLPEDLPRVLSIGRLDINTEGLLLLTNDGGL 164

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           ARVLELPST WLR YRVR HG++DQ  L+ LK+GI ++G+ YG ++ TLD  +GSN W+T
Sbjct: 165 ARVLELPSTGWLRRYRVRAHGEIDQAALDRLKEGIAVEGVLYGAIEATLDRVQGSNVWIT 224

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           +GLREGKNREIK V       VNRLIRISYGPFQLG L  G  +E+  + LREQLGP L+
Sbjct: 225 MGLREGKNREIKNVLGALGLDVNRLIRISYGPFQLGELPIGQVQEIRGRTLREQLGPRLI 284

Query: 251 EEAQVNLDAPIYSSETLVR------------------------DRPNIISEVPDDFTRMK 286
            +A+ N DAPIY+ ++                            R   ++ +       +
Sbjct: 285 ADAKANFDAPIYNDQSTAAEPEAEPVADHGKAEWGSKREKAGDKRERALARLDTRRDDGR 344

Query: 287 KNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR-----EENHRRSPSF 341
            N   ++    +++ A P  RRN +SNVWMA G   +              ++ RR+P+ 
Sbjct: 345 PNDRGRSRGKAEERPARPPLRRNRSSNVWMAPGARPTVEKKPKAAEDELSPKSTRRAPAD 404

Query: 342 PSKRSLRRTSA 352
             +R   +  A
Sbjct: 405 VKRRDRAKDPA 415



 Score = 36.3 bits (82), Expect = 6.4,   Method: Composition-based stats.
 Identities = 15/122 (12%), Positives = 26/122 (21%), Gaps = 3/122 (2%)

Query: 235 EVSKKILREQ---LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           E+S K  R     +      +      A  +  E   +   +   +        ++    
Sbjct: 392 ELSPKSTRRAPADVKRRDRAKDPATAKAAGFDEERKGKAGKSAGRKDAAGGFERRRPLEG 451

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
               S+      P       +    A    SS       R         F   R      
Sbjct: 452 AERKSRDHGDRPPRRPEGERAARDPADDRASSGGRKETARPPRGDGKKRFADDRPRANAG 511

Query: 352 AK 353
            K
Sbjct: 512 GK 513


>gi|109897967|ref|YP_661222.1| pseudouridine synthase, Rsu [Pseudoalteromonas atlantica T6c]
 gi|109700248|gb|ABG40168.1| ribosomal large subunit pseudouridine synthase F [Pseudoalteromonas
           atlantica T6c]
          Length = 317

 Score =  196 bits (499), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 79/353 (22%), Positives = 143/353 (40%), Gaps = 41/353 (11%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M   N      +  R++K I+ +G  SRRE +++I  QRV +NG++       V+S D +
Sbjct: 1   MNTSNTSNTTVSSIRLNKFISDSGFCSRREADKLIDSQRVTINGVIP-ELGTKVLSGDEV 59

Query: 61  EVDGVPLRK----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            VDG  ++             YHKP+G+  T       + +         R+  +GRLD 
Sbjct: 60  RVDGNLIKASAENKSDRVYLAYHKPVGITCTTERHVKGNIIDAI--GHPERIFPIGRLDK 117

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
            +EGL+ LT+DG +   +        + Y V     + +  ++ +  G+ I         
Sbjct: 118 PSEGLIFLTSDGDIVNKILRAENAHDKEYIVTVDRPLTERFIHAMGAGVPILDTVTKPCT 177

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           VT+     S     + L +G NR+I+++ E+  + V +L R      +L  L  G  R +
Sbjct: 178 VTMQ----SKFVFRIILTQGLNRQIRRMCEYLGYGVTKLKRSRIMSIRLAGLKVGQWRNL 233

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           +   +RE              DA   S++T ++    I + V D               +
Sbjct: 234 TPDEMREI------------SDAVEGSTKTALKTDQKIAANVTDKNA----------PKT 271

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           +  + +   H R + S V  AK           +R+  +  +P+ PS+    +
Sbjct: 272 EPTRSSKRSHHRGIKSQVGEAKHG--------SRRQATNNTAPATPSRGRKPK 316


>gi|307941691|ref|ZP_07657046.1| ribosomal large subunit pseudouridine synthase B [Roseibium sp.
           TrichSKD4]
 gi|307775299|gb|EFO34505.1| ribosomal large subunit pseudouridine synthase B [Roseibium sp.
           TrichSKD4]
          Length = 380

 Score =  196 bits (499), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 154/321 (47%), Positives = 196/321 (61%), Gaps = 1/321 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
              F  +R++KV+ARAG+ SRRE E  IA  RV+VNG  L+  A+ V + D + VDG PL
Sbjct: 10  SSAFEGERIAKVMARAGLCSRREAETWIAAGRVEVNGKKLDTPAITVGAKDKVLVDGNPL 69

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              ERTRLWLYHKP GLVTT+ DP+GR TVFD LP    RV++VGRLDINTEGLLLLTND
Sbjct: 70  PTRERTRLWLYHKPRGLVTTNKDPEGRKTVFDRLPKDLPRVLTVGRLDINTEGLLLLTND 129

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GGLARVLELP+T WLR YRVR  G+V Q  L+ L  G+ I G+ YG ++ +LD ++G N 
Sbjct: 130 GGLARVLELPATGWLRRYRVRAFGKVTQADLDTLADGVAIDGVLYGGIEASLDKEQGDNV 189

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+TVGLREGKNRE+K+V E     VNRLIR+S+GPFQL  +  G  RE+  ++LR+QLG 
Sbjct: 190 WLTVGLREGKNREVKRVLEHLGLSVNRLIRLSFGPFQLQDIAEGEVREIRGRVLRDQLGD 249

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            L EEA  + DAPI  ++    ++P     V       +                 P  R
Sbjct: 250 KLAEEAGADFDAPI-LNQPKQDEQPKKKKSVGQKGGGSEARWMSSRDGEAAVNRKKPGTR 308

Query: 308 RNLASNVWMAKGIHSSFLSDS 328
              A +    +          
Sbjct: 309 DKGAKSYRDQQRPSRDQRPSR 329


>gi|227551154|ref|ZP_03981203.1| pseudouridylate synthase [Enterococcus faecium TX1330]
 gi|257896222|ref|ZP_05675875.1| pseudouridine synthase [Enterococcus faecium Com12]
 gi|257898859|ref|ZP_05678512.1| pseudouridine synthase [Enterococcus faecium Com15]
 gi|293379537|ref|ZP_06625679.1| pseudouridylate synthase [Enterococcus faecium PC4.1]
 gi|227179716|gb|EEI60688.1| pseudouridylate synthase [Enterococcus faecium TX1330]
 gi|257832787|gb|EEV59208.1| pseudouridine synthase [Enterococcus faecium Com12]
 gi|257836771|gb|EEV61845.1| pseudouridine synthase [Enterococcus faecium Com15]
 gi|292641846|gb|EFF60014.1| pseudouridylate synthase [Enterococcus faecium PC4.1]
          Length = 238

 Score =  196 bits (499), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 82/236 (34%), Positives = 122/236 (51%), Gaps = 3/236 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E  I   RVKVNG ++    + V   D +EVD VP+ + E  
Sbjct: 2   ERLQKVIAHAGITSRRKAEEFILAGRVKVNGQVVRELGIKVGKHDTVEVDEVPIYQEEYG 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     +++  +D  GR  V D LP +  R+  VGRLD +T G+LLLTNDG  A+ 
Sbjct: 62  YYLLYKPKG-VISAVADDKGRKVVTDLLPMVKERIYPVGRLDYDTSGILLLTNDGDFAQR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           L  P  +  +VY  +  G   +  L  L KGI I+G      +  + +     +++ V +
Sbjct: 121 LTHPKHEVDKVYVAKVKGIATKSMLAPLAKGIKIEGRKTSPAKFQILSVDPKTNHSIVEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + EG+N ++K + +     V +L R  YG   L  L  G  RE++KK +   L  
Sbjct: 181 TIHEGRNHQVKNMLQAVGLPVQKLKREKYGDLTLQGLRPGDYRELNKKEVSSLLNH 236


>gi|260432945|ref|ZP_05786916.1| ribosomal large subunit pseudouridine synthase B [Silicibacter
           lacuscaerulensis ITI-1157]
 gi|260416773|gb|EEX10032.1| ribosomal large subunit pseudouridine synthase B [Silicibacter
           lacuscaerulensis ITI-1157]
          Length = 291

 Score =  196 bits (499), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 137/270 (50%), Positives = 178/270 (65%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +        R++KV+ARAGIASRRE ERMI   RV VNG  ++  A+NV  +D I VDG 
Sbjct: 22  MSNTPPPGDRIAKVLARAGIASRREAERMIEAGRVTVNGKTIDSPALNVTPSDRITVDGK 81

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P+ + E  RLWLYHKP GLVTT+ D  GR T+FDNLP    RV+SVGRLD+N+EGLLLLT
Sbjct: 82  PVAEPEPARLWLYHKPTGLVTTNRDEKGRPTIFDNLPEDMPRVMSVGRLDLNSEGLLLLT 141

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG + R LELPST WLR YRVR +G+   +    L++G+VI+G  +  M VTLD Q+G+
Sbjct: 142 NDGTIKRKLELPSTGWLRKYRVRINGRPKDEDFAPLRQGLVIEGERFQPMTVTLDRQQGA 201

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           NAW+T+GLREGKNREI++  E   + VNRL+R+SYGPFQLG L  G   E+ +++LR+QL
Sbjct: 202 NAWLTIGLREGKNREIRRAIEDIGFTVNRLLRVSYGPFQLGNLKPGEVEEIRRRVLRDQL 261

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNII 275
           G    ++                  R +  
Sbjct: 262 GLGPEDKPTPAKRPARPQRSRKPAGRKSRG 291


>gi|17989384|ref|NP_542017.1| tRNA pseudouridine synthase A [Brucella melitensis bv. 1 str. 16M]
 gi|17985257|gb|AAL54281.1| tRNA pseudouridine synthase a [Brucella melitensis bv. 1 str. 16M]
          Length = 565

 Score =  196 bits (498), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 165/348 (47%), Positives = 221/348 (63%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PLR
Sbjct: 53  EEETSERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLR 112

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV+SVGRLDINTEGLLLLTNDG
Sbjct: 113 QKERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPPEMPRVLSVGRLDINTEGLLLLTNDG 172

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V + +L+ LK GI + G+ YG ++  L+  +G+N W
Sbjct: 173 GLSRVLELPSTGWLRRYRVRAHGKVTRQQLDELKNGIAVDGVFYGSVEAELERVQGANVW 232

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+QLG  
Sbjct: 233 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRDQLGDK 292

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK------------NSSQKNGLS 296
           L+EE+  + DAP+ +  +    +     E+ +     +             +S+ +    
Sbjct: 293 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 352

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +++K      RR   +NVWMA G       ++ +      + P   +K
Sbjct: 353 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAK 400



 Score = 36.7 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q+ P    E +   +            R       PD+  + +K+          K+   
Sbjct: 406 QMRPRRFSEEERGGEESGERRYKRPEGRFEREGGRPDNREKYEKHEGAGKERRPGKRERA 465

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      +      G         G      R   +    RS  R S  +
Sbjct: 466 ELRNAEGQTTERGKGGSEGRKPGKPGGPRSEGRFGGADRDTRSGPRGSGPR 516


>gi|119468781|ref|ZP_01611833.1| putative ribosomal RNA pseudouridine synthase [Alteromonadales
           bacterium TW-7]
 gi|119447837|gb|EAW29103.1| putative ribosomal RNA pseudouridine synthase [Alteromonadales
           bacterium TW-7]
          Length = 338

 Score =  196 bits (498), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 69/327 (21%), Positives = 136/327 (41%), Gaps = 10/327 (3%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + +    +R++K I+  G  SRRE ++ I Q RV VNG       V V +TD + VDG P
Sbjct: 15  LSDMTELKRLNKFISETGFCSRREADKYIEQGRVSVNGN-APEMGVKVAATDVVLVDGKP 73

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L+   +     Y+KP+G+  T       + V     +   R+  +GRLD  +EGL+ LTN
Sbjct: 74  LKTPPKRVYIAYNKPVGITCTTERKIQSNIVKAV--NYPDRIFPIGRLDRPSEGLIFLTN 131

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G +   +        + Y V     +++  ++ +  GI I        +VT    + + 
Sbjct: 132 EGDIVNKILRAGNNHEKEYVVTVDKPLNRQFVSKMANGIPILDTVTKKCKVT----QTAP 187

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               + L +G NR+I+++ E+  ++V  L R       L  L  G  R +S   + +   
Sbjct: 188 KEFKIILTQGLNRQIRRMCEYLGYEVVTLKRTRIMNVTLKGLKVGQWRHLSDVEMAQI-- 245

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              + ++    +  + +++ + ++               +    ++    K  +   P  
Sbjct: 246 NDSIADSGKTQEHSLDTNKQVDKNAVISPKRDFQGENPRRNKQKERGDEQKNNRTNAPYQ 305

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREE 333
           +R+  + V   K   ++  S +     
Sbjct: 306 KRST-TYVGKPKTAKANSASSNKAGAR 331


>gi|293570237|ref|ZP_06681306.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E980]
 gi|291609644|gb|EFF38905.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E980]
          Length = 238

 Score =  196 bits (498), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 82/236 (34%), Positives = 122/236 (51%), Gaps = 3/236 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E  I   RVKVNG ++    + V   D +EVD VP+ + E  
Sbjct: 2   ERLQKVIAHAGITSRRKAEEFILAGRVKVNGQVVRELGIKVGKQDTVEVDEVPIYQEEYG 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     +++  +D  GR  V D LP +  R+  VGRLD +T G+LLLTNDG  A+ 
Sbjct: 62  YYLLYKPKG-VISAVADDKGRKVVTDLLPMVKERIYPVGRLDYDTSGILLLTNDGDFAQR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           L  P  +  +VY  +  G   +  L  L KGI I+G      +  + +     +++ V +
Sbjct: 121 LTHPKHEVDKVYVAKVKGIATKSMLAPLAKGIKIEGRKTSPAKFQILSVDPKTNHSIVEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + EG+N ++K + +     V +L R  YG   L  L  G  RE++KK +   L  
Sbjct: 181 TIHEGRNHQVKNMLQAVGLPVQKLKREKYGDLTLQGLRPGDYRELNKKEVSSLLNH 236


>gi|322420558|ref|YP_004199781.1| pseudouridine synthase [Geobacter sp. M18]
 gi|320126945|gb|ADW14505.1| pseudouridine synthase [Geobacter sp. M18]
          Length = 262

 Score =  196 bits (498), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 86/260 (33%), Positives = 134/260 (51%), Gaps = 1/260 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++++AGIASRRE E +IA+ RV VNG ++           D I VDG P+  AE+
Sbjct: 3   ERLQKILSQAGIASRRESETIIAEGRVAVNGTVVTELGTKADPDTDTITVDGKPITIAEQ 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP+G +TT  DP+GR  V D L  I  RV  +GRLD NTEGLLLLTNDG LA 
Sbjct: 63  RVYLLLYKPVGYMTTMKDPEGRPIVSDLLKGISERVYPIGRLDYNTEGLLLLTNDGALAN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS +  + Y VR  G V   ++  L +G+ ++       +V   ++  +N+W+++ 
Sbjct: 123 TLMHPSHEVDKGYLVRVSGHVSPAQIQELSEGVKLEDGMTAPAKVLPVSESENNSWISIT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           + EG+ R+++++ E     V RL R  Y    +G +  G  R ++   + +     +   
Sbjct: 183 IHEGRYRQVRRMCEAVGLNVVRLKRSRYDFLVIGEMKPGDFRHLTADEVAKLRRKTVPSG 242

Query: 253 AQVNLDAPIYSSETLVRDRP 272
                      +      R 
Sbjct: 243 TGRGPRKTGVVARRKTAPRR 262


>gi|125624024|ref|YP_001032507.1| pseudouridylate synthase [Lactococcus lactis subsp. cremoris
           MG1363]
 gi|124492832|emb|CAL97787.1| pseudouridylate synthase [Lactococcus lactis subsp. cremoris
           MG1363]
          Length = 257

 Score =  196 bits (498), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 73/252 (28%), Positives = 124/252 (49%), Gaps = 3/252 (1%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           ++           R++K +A AG+ASRR+ E +I   +V VN + +      V + D +E
Sbjct: 7   QNNKPYLTKVKKMRINKYLAHAGVASRRKAEELILAGKVTVNNVPMTNLGYQVSTGDVVE 66

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           V+GV +   E     L      + +   D   ++   D +P +  R+  VGRLD +T GL
Sbjct: 67  VNGVAVYNEEPVYYLLNKPRGYISSVSDDKGRQTV-MDLMPQVKERIYPVGRLDWDTSGL 125

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDG    ++  PS    +VY  +  GQ +++ L  L  G+ I+G      +  +  
Sbjct: 126 LLLTNDGEFTNMMTHPSHGVDKVYVAKVEGQANKENLRPLTLGMTIEGKKVSPARYEIIK 185

Query: 182 QK--GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           Q+   +++ V++ + EG+N ++KK+F      V +L RI YG   L  L  G  R +SKK
Sbjct: 186 QEKTKNHSIVSLTIHEGQNHQVKKMFAAAGLPVQKLSRIQYGTLTLDGLPTGQFRRLSKK 245

Query: 240 ILREQLGPHLLE 251
            + + +     +
Sbjct: 246 EVSQLINAAQGK 257


>gi|257876560|ref|ZP_05656213.1| pseudouridine synthase [Enterococcus casseliflavus EC20]
 gi|257810726|gb|EEV39546.1| pseudouridine synthase [Enterococcus casseliflavus EC20]
          Length = 240

 Score =  196 bits (497), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 82/234 (35%), Positives = 127/234 (54%), Gaps = 3/234 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +R+ KVIA AGI SRR+ E +I + RV+VNG +++   V V S D +EVDGVP+ + +
Sbjct: 2   KMERLQKVIAHAGITSRRKAEGLITEGRVRVNGQVIKELGVQVSSKDVVEVDGVPIEQEQ 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                 Y     +++  +D   R  V D    +  RV  VGRLD +T GLLLLTNDG L+
Sbjct: 62  HVYYLFYKPRG-VISAVTDDKKRKVVLDYFAEVPERVYPVGRLDYDTSGLLLLTNDGELS 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWV 189
           + L  P  +  +VY  +  G  D+ +L  L KGI I+G      +  + +   +   + V
Sbjct: 121 QTLMHPKHEVDKVYVAKVKGIADKKQLLPLTKGIRIEGRKTAPARFEILSTDQTTQSSIV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + + EG+N ++K + +     V +L R +YGP  L  L  G  RE++KK + +
Sbjct: 181 QLTIHEGRNHQVKNMLKAVGLPVQKLKRENYGPLDLKGLRPGEYRELTKKEVSQ 234


>gi|134299005|ref|YP_001112501.1| pseudouridine synthase [Desulfotomaculum reducens MI-1]
 gi|134051705|gb|ABO49676.1| ribosomal large subunit pseudouridine synthase B [Desulfotomaculum
           reducens MI-1]
          Length = 309

 Score =  196 bits (497), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 92/281 (32%), Positives = 143/281 (50%), Gaps = 1/281 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++A+AG+ASRR  E +I   +VKVNG  +    + V  T D IEV G PL   E+
Sbjct: 3   ERLQKILAKAGVASRRHSEELIISGQVKVNGKTVTEMGLKVDPTKDKIEVKGKPLPPLEK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G VTT SD   R TV D L  +  RV  VGRLD ++EGLLLLTNDG L +
Sbjct: 63  KVYLLMNKPRGYVTTLSDERDRKTVVDLLKGVEQRVYPVGRLDYDSEGLLLLTNDGELTQ 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + Y  +  G  + ++L  + KG+V++        V L     + A + + 
Sbjct: 123 ALTHPKHKVKKTYLAKVDGIPETEELKAMAKGLVLEDGPTAPADVRLAGTGDNRALLEIS 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           + EG+NR+++++ E   +KV RL R   G  +LG+L +G  R ++KK LRE      L++
Sbjct: 183 IHEGRNRQVRRMCEHIGYKVLRLRRTRIGTLELGSLKSGEVRALTKKELRELASLVGLKQ 242

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
              ++       +        +         +    S++  
Sbjct: 243 NYNDMQLTTEVQKKKPSPCGRVGRIKGKVSEQKSNRSAKSK 283


>gi|300024100|ref|YP_003756711.1| RNA-binding S4 domain protein [Hyphomicrobium denitrificans ATCC
           51888]
 gi|299525921|gb|ADJ24390.1| RNA-binding S4 domain protein [Hyphomicrobium denitrificans ATCC
           51888]
          Length = 302

 Score =  196 bits (497), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 127/274 (46%), Positives = 166/274 (60%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             N  +    P R++K +ARAG+ SRRE ER IA  RV VNG LL+  A  V   D + V
Sbjct: 27  TSNTAETRDGPMRIAKAMARAGLCSRREAERWIADGRVSVNGKLLKTPACEVGPKDKVIV 86

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG PL  A   +LW YHKP G+VTTHSDP GR TVF+ LP    RVIS+GRLD NTEGLL
Sbjct: 87  DGKPLPAASTPQLWRYHKPKGVVTTHSDPQGRPTVFEKLPPEMPRVISIGRLDFNTEGLL 146

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLT DG LAR  ELP+  W+R YRVR  G+V    L  LK G+ I G+ YG ++ ++DT 
Sbjct: 147 LLTTDGALARHFELPANGWVRRYRVRAKGRVTPADLAKLKDGVEIDGVSYGPIEASVDTV 206

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +G+N+W+++ +REGKNRE++ V  +    VNRLIR+S+GPFQL  L  G+   V +++L 
Sbjct: 207 QGANSWLSISIREGKNREVRNVLAYLGLTVNRLIRVSFGPFQLLDLAPGAVEAVRRRVLV 266

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIIS 276
            QLGP       ++                +   
Sbjct: 267 AQLGPKAAASLGLSESQEERKERHARGKAASGSR 300


>gi|154491797|ref|ZP_02031423.1| hypothetical protein PARMER_01414 [Parabacteroides merdae ATCC
           43184]
 gi|154088038|gb|EDN87083.1| hypothetical protein PARMER_01414 [Parabacteroides merdae ATCC
           43184]
          Length = 249

 Score =  196 bits (497), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 58/241 (24%), Positives = 115/241 (47%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           MK K ++ +   P R++K ++ AG+ SRRE +  I +  V+VNG ++      +   D +
Sbjct: 1   MKYKEVLADPNEPIRLNKFLSNAGVCSRREADEFIQEGVVQVNGQIVTELGTKITRQDTV 60

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                P++   +  + L      + T+    +  + +     +   R+  VGRLD NT G
Sbjct: 61  LFKDQPVQIESKVYIVLNKPKNCVTTSDDPQERLTVMDLVKNACQERIYPVGRLDRNTTG 120

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  PS +  ++Y V     V  + +  +  G+ ++        ++  
Sbjct: 121 VLLLTNDGDLASKLTHPSFKKKKIYHVWLDKNVSIEDMEKIANGLELEDGEIHADAISYA 180

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++    + V + +  G+NR ++++FE   + V +L R+ +       L  G  R ++++ 
Sbjct: 181 SED-DKSQVGIEIHSGRNRIVRRIFESLGYHVVKLDRVYFAGLTKKNLGRGKWRYLNERE 239

Query: 241 L 241
           +
Sbjct: 240 V 240


>gi|167629967|ref|YP_001680466.1| pseudouridine synthase [Heliobacterium modesticaldum Ice1]
 gi|167592707|gb|ABZ84455.1| pseudouridine synthase [Heliobacterium modesticaldum Ice1]
          Length = 333

 Score =  196 bits (497), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 96/331 (29%), Positives = 146/331 (44%), Gaps = 5/331 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLR 68
           +    R+ K++A  G+ASRRE E MI   RV++NG ++    V V  + D IEVDG  L+
Sbjct: 2   DSQTVRLQKLLAAHGVASRREAEAMIRAGRVRINGTVVREQGVRVDGARDVIEVDGRILK 61

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + E    +  +KP G+VTT  DP GR TV   L  +  RV  VGRLD +TEGLLLLTNDG
Sbjct: 62  RREAPLYYALYKPRGVVTTCKDPQGRQTVIGLLSGVNERVYPVGRLDRDTEGLLLLTNDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     + YR R  G V    L  L +G+ ++       QV L  ++G   W
Sbjct: 122 QLAFRLTHPRFGVEKTYRARLRGDVSAGALKALAEGVQLEDGVTAPAQVRLLRREGDATW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + + + EG+ R+I+++ +     V  L RI++GP  LG L  G  R ++   LR      
Sbjct: 182 IEIKIHEGRKRQIRRMGDAIGHPVIDLERIAFGPITLGKLKPGEVRPLTSAELRALKSAA 241

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR----MKKNSSQKNGLSKQKKLATP 304
            ++EA  +       +    R                         ++       +  + 
Sbjct: 242 GMKEATAHGRDERRQTARPSRTAATAKVASAHKDAGKGVFKGLKGLREASNGGDGRGKSA 301

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENH 335
             +R  +      +G +            + 
Sbjct: 302 SGKRFDSGVHGKCQGKNDGGPWSRPAGPRSR 332


>gi|257887727|ref|ZP_05667380.1| pseudouridine synthase [Enterococcus faecium 1,141,733]
 gi|257823781|gb|EEV50713.1| pseudouridine synthase [Enterococcus faecium 1,141,733]
          Length = 238

 Score =  196 bits (497), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 82/236 (34%), Positives = 122/236 (51%), Gaps = 3/236 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E  I   RVKVNG ++    + V   D +EVD VP+ + E  
Sbjct: 2   ERLQKVIAHAGITSRRKAEEFILAGRVKVNGQVIRELGIKVGKHDTVEVDEVPIYQEEYG 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     +++  +D  GR  V D LP +  R+  VGRLD +T G+LLLTNDG  A+ 
Sbjct: 62  YYLLYKPKG-VISAVADDKGRKVVTDLLPMVKERIYPVGRLDYDTSGILLLTNDGDFAQR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           L  P  +  +VY  +  G   +  L  L KGI I+G      +  + +     +++ V +
Sbjct: 121 LTHPKHEVDKVYVAKVKGIATKSMLAPLAKGIKIEGRKTSPAKFQILSVDPKTNHSIVEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + EG+N ++K + +     V +L R  YG   L  L  G  RE++KK +   L  
Sbjct: 181 TIHEGRNHQVKNMLQAVGLPVQKLKREKYGDLTLQGLRPGDYRELNKKEVSSLLNH 236


>gi|330446629|ref|ZP_08310281.1| 23S rRNA pseudouridine 2604 synthase [Photobacterium leiognathi
           subsp. mandapamensis svers.1.1.]
 gi|328490820|dbj|GAA04778.1| 23S rRNA pseudouridine 2604 synthase [Photobacterium leiognathi
           subsp. mandapamensis svers.1.1.]
          Length = 378

 Score =  196 bits (497), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 75/356 (21%), Positives = 136/356 (38%), Gaps = 10/356 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M      Q++    R++K I+  G  SRRE +++I Q RV +NG       V V  +D +
Sbjct: 1   MSQNPTQQQSPQGVRLNKFISDTGYCSRREADKLIDQGRVTINGKKP-EMGVRVTDSDDV 59

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            +D  PLR  ER      +KP G+  T       + V         R+  +GRLD  ++G
Sbjct: 60  LIDDKPLRSKERPIYIALNKPTGITCTTERHIEGNIVDFI--GHRKRIFPIGRLDKPSDG 117

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+ LTNDG +   +        + Y VR    +  + L  +  G+ I        +VT  
Sbjct: 118 LIFLTNDGDIVNKILRAGNSHEKEYVVRVDKVITPEFLEKMASGVEILDTVTLPCKVT-- 175

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             K +N    + L +G NR+I+++ E   ++V +L R+      +  L  G  R ++   
Sbjct: 176 --KETNFSFRIVLTQGLNRQIRRMCEALGYEVYKLRRVRIMNITIDGLPNGKWRYLTDDE 233

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL---SK 297
           + E                       + +     + +      R +K + +K        
Sbjct: 234 IAEIHRLISQSSGTEEASKVDGEGRKIEKATDAKLYDHRQQEARNEKRAQEKKFKTYSGT 293

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            +    P  +R    N    +G       +   R + + +  +   +   RR  ++
Sbjct: 294 GEFTRRPGGQRQNRRNEEGGEGRQQRGQRNGQGRNDRNSQDRNGNERNDNRRQDSR 349


>gi|257867652|ref|ZP_05647305.1| pseudouridine synthase [Enterococcus casseliflavus EC30]
 gi|257873981|ref|ZP_05653634.1| pseudouridine synthase [Enterococcus casseliflavus EC10]
 gi|257801735|gb|EEV30638.1| pseudouridine synthase [Enterococcus casseliflavus EC30]
 gi|257808145|gb|EEV36967.1| pseudouridine synthase [Enterococcus casseliflavus EC10]
          Length = 240

 Score =  196 bits (497), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 82/234 (35%), Positives = 128/234 (54%), Gaps = 3/234 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +R+ KVIA AGI SRR+ E +I + RV+VNG +++   V V S D +EVDGVP+ + +
Sbjct: 2   KMERLQKVIAHAGITSRRKAEGLITEGRVRVNGQVIKELGVQVSSKDVVEVDGVPIEQEQ 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                 Y     +++  +D   R  V D    +  RV  VGRLD +T GLLLLTNDG L+
Sbjct: 62  HVYYLFYKPRG-VISAVTDDKKRKVVLDYFAEVPERVYPVGRLDYDTSGLLLLTNDGELS 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWV 189
           + L  P  +  +VY  +  G  D+ +L  L KGI I+G      +  + +   +  ++ V
Sbjct: 121 QTLMHPKHEVDKVYVAKVKGIADKKQLLPLTKGIRIEGRKTAPARFEILSTDQTAQSSIV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + + EG+N ++K + +     V +L R +YGP  L  L  G  RE++KK + +
Sbjct: 181 QLTIHEGRNHQVKNMLKAVGLPVQKLKRENYGPLDLKGLRPGEYRELTKKEVSQ 234


>gi|262404561|ref|ZP_06081116.1| ribosomal large subunit pseudouridine synthase F [Vibrio sp. RC586]
 gi|262349593|gb|EEY98731.1| ribosomal large subunit pseudouridine synthase F [Vibrio sp. RC586]
          Length = 332

 Score =  196 bits (497), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 74/339 (21%), Positives = 134/339 (39%), Gaps = 16/339 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RV +NG   E     V   D + +DG PLR  ER  
Sbjct: 8   RLNKFISETGFCSRREADKLIEQGRVTLNGAQPEV-GSKVTEQDEVCIDGKPLRSKERPI 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T       + V             +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCTTERDVQGNIVDFIGHHKRI--FPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + +  +  G+ I        +VT    + +     + L 
Sbjct: 125 LRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVT----QETQYSFRIVLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L         
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVNEILAMCEDSSGT 240

Query: 255 VNLDAPIYSSETLVRDRPNI--ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
                   S +++ R        S   +  ++ ++N    +G + Q+    P  ++    
Sbjct: 241 EEASRVAQSGDSIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNSKKAQRR 300

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
               +    ++            R +P      SLR++ 
Sbjct: 301 PTSSSSNSSTASKPTP-------RPTPRTGGTLSLRKSK 332


>gi|332686546|ref|YP_004456320.1| ribosomal large subunit pseudouridine synthase B [Melissococcus
           plutonius ATCC 35311]
 gi|332370555|dbj|BAK21511.1| ribosomal large subunit pseudouridine synthase B [Melissococcus
           plutonius ATCC 35311]
          Length = 236

 Score =  195 bits (496), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 76/235 (32%), Positives = 114/235 (48%), Gaps = 3/235 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KV+A AGIASRR+ E++I + RVKVNG ++      V   D IEVD VP+ +     
Sbjct: 3   RLQKVLAHAGIASRRKAEQIILEGRVKVNGEIINELGRQVSKQDKIEVDNVPIYQEAPVY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
              Y     + +   D   ++     L S   RV  VGRLD +T GLL++TNDG L + L
Sbjct: 63  YLFYKPRGIITSVSDDKKRKTVADYFLHSN-ERVYPVGRLDYDTTGLLIVTNDGSLTQQL 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTVG 192
             PS +  +VY  +  G   +  L  L KGI I+G         + +       + V + 
Sbjct: 122 THPSHEIDKVYVAKVKGIALRKTLLPLTKGIKIKGRKTAPANFQILSVDTKKQTSLVQLT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           + EG+N ++K + +   + V +L R   G   L  L  G  R ++KK +   L  
Sbjct: 182 IHEGRNHQVKDMLDTVGYPVQKLKRERIGDLTLEGLHPGEYRRLTKKEIHALLNH 236


>gi|188997597|ref|YP_001931848.1| RNA-binding S4 domain protein [Sulfurihydrogenibium sp. YO3AOP1]
 gi|188932664|gb|ACD67294.1| RNA-binding S4 domain protein [Sulfurihydrogenibium sp. YO3AOP1]
          Length = 244

 Score =  195 bits (496), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 55/244 (22%), Positives = 104/244 (42%), Gaps = 5/244 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K ++  G  SR +V+++I +  VKVN  +++  + ++    D +E++   +   E 
Sbjct: 1   MRLDKFLSNQGFGSRSQVQKLIKKGFVKVNDEIVKDPSYHIDPMKDKVELEDEEILYKEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  +         +   I S++  VGRLDI+TEGLL+LT DG    
Sbjct: 61  HYFMLNKPAGYITATEDEEYPTVLDLFSDLPIASKLFPVGRLDIDTEGLLILTTDGQFGH 120

Query: 133 VLELPSTQWLRVYRVRFH---GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            L  P     + Y          +D  +       +  +       +V +       + +
Sbjct: 121 RLSHPKWNIEKEYYAIVEGDISNIDFSESENKGIYLKKEKYQTKPFKVKVLNTSKDKSEI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
            + L EGK   +K++ +   + V  L RI  G  +L   LL G  RE+++K +++     
Sbjct: 181 LITLTEGKYHIVKRIMQELGYPVLYLKRIRIGNLKLDEDLLPGEFRELTEKEIKDLKKLI 240

Query: 249 LLEE 252
            + +
Sbjct: 241 KMND 244


>gi|78045168|ref|YP_360757.1| ribosomal large subunit pseudouridine synthase B [Carboxydothermus
           hydrogenoformans Z-2901]
 gi|77997283|gb|ABB16182.1| ribosomal large subunit pseudouridine synthase B [Carboxydothermus
           hydrogenoformans Z-2901]
          Length = 241

 Score =  195 bits (496), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 70/228 (30%), Positives = 119/228 (52%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K +ARAG+A+RR+ E++I   RVKVNG +++     V   D +EVDG  ++  +  
Sbjct: 2   ERLQKYLARAGVAARRDAEQLILAGRVKVNGKVVKELGFKVSDRDVVEVDGRIVKPEKLV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +Y     + T        + +      +  RV  VGRLD+NTEGLL+LTNDG LA  
Sbjct: 62  YILMYKPAGYITTVDDPFGRPTVLSLLAGKVKERVFPVGRLDMNTEGLLILTNDGDLAMA 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  Q  + Y     G  ++ KL  L++G++++       +V     +G N+W+ + +
Sbjct: 122 LTHPKHQVPKTYLALVRGTPNRAKLKELERGVLLEDGYTAPAKVNFKKPEGKNSWIEITI 181

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            EG+ R+++++F+     V +LIR          L  GS R ++   +
Sbjct: 182 HEGRKRQVRRMFKKIGHPVLKLIRTRIAFLTGYGLKKGSFRYLTPAEV 229


>gi|163783757|ref|ZP_02178743.1| hypothetical protein HG1285_01633 [Hydrogenivirga sp. 128-5-R1-1]
 gi|159881003|gb|EDP74521.1| hypothetical protein HG1285_01633 [Hydrogenivirga sp. 128-5-R1-1]
          Length = 244

 Score =  195 bits (496), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 72/231 (31%), Positives = 119/231 (51%), Gaps = 1/231 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+++ ++  G+ SRR+ +++I + RVKVNG ++    V +    D +EVDG  ++   +
Sbjct: 3   VRLNRYLSMCGVTSRRKADKLIEEGRVKVNGEVVRDLGVKIDPEVDRVEVDGKEVKPPRK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      L        G+ T+ + +  +  RV  VGRLD NTEGLLLLTNDG LA 
Sbjct: 63  IYIILNKPCCYLTQLGKSQSGKKTIEELIKDVPERVFPVGRLDYNTEGLLLLTNDGELAN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  +VY     G+V ++ L  +K G  ++        V +   +G N  + + 
Sbjct: 123 RVLHPRYKLPKVYLALVKGKVSKNTLRKMKHGAELEDGFAKPDDVRIVRYEGDNTLLEIV 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
             EG+   +K+    F   V +L RI+ G  +LG L  G  RE+S++ LR+
Sbjct: 183 FHEGRKHIVKRFLASFGHPVIKLKRIALGTLKLGKLPPGKWRELSQRELRQ 233


>gi|292558985|gb|ADE31986.1| Pseudouridine synthase, Rsu [Streptococcus suis GZ1]
          Length = 245

 Score =  195 bits (496), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 83/245 (33%), Positives = 134/245 (54%), Gaps = 3/245 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V VNG ++      + S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELGTVIKSGDKVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVVDLLPTVKERIYPVGRLDWDTSGVLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +G+VI G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGVANKEVLRPLTRGVVIDGKKTKPAVYEIIKVDPVKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE    +V++L R  +G   L  L  G  R+++KK + +     LL 
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGNLDLTGLRPGEYRKLNKKDISKLHTWPLLS 239

Query: 252 EAQVN 256
           + + N
Sbjct: 240 QLKNN 244


>gi|228990582|ref|ZP_04150547.1| Pseudouridine synthase [Bacillus pseudomycoides DSM 12442]
 gi|228996683|ref|ZP_04156320.1| Pseudouridine synthase [Bacillus mycoides Rock3-17]
 gi|229004333|ref|ZP_04162121.1| Pseudouridine synthase [Bacillus mycoides Rock1-4]
 gi|228756916|gb|EEM06173.1| Pseudouridine synthase [Bacillus mycoides Rock1-4]
 gi|228763002|gb|EEM11912.1| Pseudouridine synthase [Bacillus mycoides Rock3-17]
 gi|228769108|gb|EEM17706.1| Pseudouridine synthase [Bacillus pseudomycoides DSM 12442]
          Length = 244

 Score =  195 bits (496), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 80/244 (32%), Positives = 130/244 (53%), Gaps = 3/244 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +R+ KVIA+AGIASRR+ E +I Q +VKVNG ++      V   D +EV+ +PL K E
Sbjct: 2   EMERLQKVIAQAGIASRRKAEELIQQGKVKVNGKVVTELGTKVTPQDKVEVNNIPLEKEE 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                LY     + +   D  GR  V D  P I  R+  +GRLD +T G+LL+TNDG  A
Sbjct: 62  PIYFLLYKPTGVISSVS-DDKGRKVVTDFFPEITQRLFPIGRLDYDTSGVLLMTNDGDFA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWV 189
            +L  P  +  + Y  +  G +  +K+ +L+KG+V++       +V + +       A V
Sbjct: 121 NILMHPKYKVEKTYVAKVKGPLTGEKIRMLEKGVVLEDGKTAPARVKILSWDKRKEMAIV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + + EG+NR+++++FE    KV +L R  Y   ++G+L  G  RE+S   +++      
Sbjct: 181 QLTIHEGRNRQVRRMFEALGCKVMKLKRERYAFLEVGSLRPGDARELSPHEVKQLRALAS 240

Query: 250 LEEA 253
            +  
Sbjct: 241 TKPR 244


>gi|56420818|ref|YP_148136.1| ribosomal large subunit pseudouridine synthase B [Geobacillus
           kaustophilus HTA426]
 gi|261417880|ref|YP_003251562.1| pseudouridine synthase [Geobacillus sp. Y412MC61]
 gi|297529548|ref|YP_003670823.1| pseudouridine synthase [Geobacillus sp. C56-T3]
 gi|319767308|ref|YP_004132809.1| pseudouridine synthase [Geobacillus sp. Y412MC52]
 gi|56380660|dbj|BAD76568.1| ribosomal large subunit pseudouridine synthaseB (pseudouridylate
           synthase) (uracil hydrolyase) [Geobacillus kaustophilus
           HTA426]
 gi|261374337|gb|ACX77080.1| pseudouridine synthase [Geobacillus sp. Y412MC61]
 gi|297252800|gb|ADI26246.1| pseudouridine synthase [Geobacillus sp. C56-T3]
 gi|317112174|gb|ADU94666.1| pseudouridine synthase [Geobacillus sp. Y412MC52]
          Length = 243

 Score =  195 bits (496), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 82/231 (35%), Positives = 128/231 (55%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIARAGIASRR+ E +I Q RVKVNG +++   V V   D +EVDG+P+ + E  
Sbjct: 2   ERLQKVIARAGIASRRKAEELILQGRVKVNGRVVKELGVKVGPRDDVEVDGIPIEREEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     ++++  D  GR  V D    +  R+  +GRLD +T GLLLLTNDG  A +
Sbjct: 62  YYLLYKPRG-VISSVKDDRGRKVVTDFFKDLDKRIYPIGRLDYDTSGLLLLTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           L  P  +  +VY  +  G    ++L  L++G+ ++       +V L    +K   A V +
Sbjct: 121 LMHPRYEIEKVYIAKVKGIPTHEQLKRLEQGVQLEDGMTAPAKVKLLSADRKKGTAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EG+NR+++++FE    +V +L R  Y    L  L  G  RE++   ++
Sbjct: 181 RIHEGRNRQVRRMFEAIGCEVLKLKRERYAFLDLKGLRPGEYRELTPHEVK 231


>gi|323703049|ref|ZP_08114704.1| pseudouridine synthase [Desulfotomaculum nigrificans DSM 574]
 gi|323531943|gb|EGB21827.1| pseudouridine synthase [Desulfotomaculum nigrificans DSM 574]
          Length = 238

 Score =  195 bits (496), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 89/230 (38%), Positives = 127/230 (55%), Gaps = 1/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ KV+ARAGIASRR  E +I   +VKVNG  +      V +  D IEV+G P+  ++ 
Sbjct: 3   ERLQKVLARAGIASRRRCEELIVAGKVKVNGKAVTALGTKVDAAKDKIEVNGQPVTASQP 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +KP G VTT  D  GR TV D L  I  RV  VGRLD ++EGLLLLTNDG L  
Sbjct: 63  KVYFMLNKPRGYVTTLHDERGRKTVIDLLEGIEQRVYPVGRLDYDSEGLLLLTNDGELTN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + Y VR  G  +  KL  + +G+V+        QV L   + + A + + 
Sbjct: 123 ALTHPKHKVPKTYLVRVEGVPEPAKLKAMARGLVLADGPTAPAQVRLAGVRDNRALLEIT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EG+NR+++++ E     V RL RI  GP  L  L  G  R +++  L+
Sbjct: 183 IHEGRNRQVRRMCEHIGHPVLRLKRIRVGPLVLEGLKPGQFRPLTEVELK 232


>gi|148264550|ref|YP_001231256.1| pseudouridine synthase [Geobacter uraniireducens Rf4]
 gi|146398050|gb|ABQ26683.1| ribosomal large subunit pseudouridine synthase B [Geobacter
           uraniireducens Rf4]
          Length = 239

 Score =  195 bits (496), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 89/230 (38%), Positives = 127/230 (55%), Gaps = 1/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ K++++AGIASRRE ER+I   RV VNG ++           D I VDG P+R    
Sbjct: 3   ERLQKILSQAGIASRREAERIITDGRVAVNGQVVTELGTKADAEKDRITVDGRPIRVEAN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP+G +TT  DP+GR  V D L  I  RV  VGRLD NTEGLLLLTNDG LA 
Sbjct: 63  KLYVLLYKPVGYMTTMKDPEGRPIVTDLLKGIKERVYPVGRLDYNTEGLLLLTNDGALAN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS +  + Y VR  G+V   +L  L  G+ ++        V+L  +   N W+++ 
Sbjct: 123 RLAHPSHEVDKGYLVRVRGKVTPAQLKHLAVGVDLEDGRTAPAVVSLVRESEQNCWISIT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EG+ R+++++ E     V RL R  YG  ++G L  G  R ++   + 
Sbjct: 183 IHEGRYRQVRRMCEAVGLTVVRLKRSRYGFLEIGELKPGEYRLLTPAEVE 232


>gi|319651400|ref|ZP_08005529.1| pseudouridine synthase [Bacillus sp. 2_A_57_CT2]
 gi|317396931|gb|EFV77640.1| pseudouridine synthase [Bacillus sp. 2_A_57_CT2]
          Length = 241

 Score =  195 bits (495), Expect = 9e-48,   Method: Composition-based stats.
 Identities = 81/241 (33%), Positives = 131/241 (54%), Gaps = 3/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG ASRR+ E ++A+ RVKVNG  ++   V V  +D IEVDG+P+ + E  
Sbjct: 2   ERLQKVIAHAGFASRRKAEELMAEGRVKVNGKTVKELGVKVSPSDRIEVDGIPVEREEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     +++  SD  GR  V D    I  R+  VGRLD +T G+L+LTNDG  A +
Sbjct: 62  YFLLYKPRG-VISAVSDDKGRKVVTDFFEGIKQRIYPVGRLDYDTSGILILTNDGEFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW--VTV 191
           L  PS +  +VY  +  G   ++ +  L++G+V++       +  L +         V +
Sbjct: 121 LMHPSNEIEKVYVAKIKGIPSKEGMRSLQRGVVLEDGKTAPAKTKLLSMDKKKQTAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE     V +L R  YG   L  L AG  RE++   +++     + +
Sbjct: 181 SIHEGRNRQVRRMFEAIGHPVLKLKRERYGYLTLQGLSAGDARELTAHEVKQLRALAMKK 240

Query: 252 E 252
           +
Sbjct: 241 K 241


>gi|163791509|ref|ZP_02185915.1| RluB [Carnobacterium sp. AT7]
 gi|159873232|gb|EDP67330.1| RluB [Carnobacterium sp. AT7]
          Length = 244

 Score =  195 bits (495), Expect = 9e-48,   Method: Composition-based stats.
 Identities = 86/242 (35%), Positives = 137/242 (56%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR+ E +I++  VKVNG +++   + + ++D +EVDGVP+   E  
Sbjct: 2   ERLQKVLAHAGVASRRKSEELISKGHVKVNGKVVKEMGIQIGNSDVVEVDGVPI-YREEP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP  ++T  SD  GR  V D  P+I  R+  VGRLD +T G L+LTNDG L+++
Sbjct: 61  VYFLLNKPRNMITAVSDDKGRPVVTDLFPNIEQRIYPVGRLDYDTTGALMLTNDGELSQL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTV 191
           L  P  Q  + Y  +  G VD+  LN L+KG+V++G      +  + +   +     V +
Sbjct: 121 LMHPKYQINKTYVAKVKGLVDRKALNKLEKGVVVEGKKTAPAKAKILSADRAKDITMVEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR++K +F+     V +L R SYG   L  L  G  RE+    + +     + E
Sbjct: 181 TIHEGRNRQVKNMFQAIGHPVEKLKRESYGTLNLDGLQTGEWRELKTFEIYQLRNSAIQE 240

Query: 252 EA 253
           E 
Sbjct: 241 ET 242


>gi|319892477|ref|YP_004149352.1| Ribosomal large subunit pseudouridine synthase B [Staphylococcus
           pseudintermedius HKU10-03]
 gi|317162173|gb|ADV05716.1| Ribosomal large subunit pseudouridine synthase B [Staphylococcus
           pseudintermedius HKU10-03]
 gi|323464420|gb|ADX76573.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           pseudintermedius ED99]
          Length = 248

 Score =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 73/247 (29%), Positives = 133/247 (53%), Gaps = 3/247 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +R+ K IA +G  SRR+ E +I + +V+VNG  +      V  +D + V+G+PL +
Sbjct: 2   SQQLERLQKRIANSGYTSRRKAETLIEEGKVQVNGKTVTELGTKVRPSDEVTVEGIPLEQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ++  +  Y     ++T+ SD  GR  V D    + +R+  VGRLD +T GLLLLTNDG 
Sbjct: 62  EDKLYILFYKP-AQVITSVSDDRGRKVVTDYFDDLVTRIYPVGRLDYDTSGLLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNA 187
              ++  P  +  + Y  +  G + ++++  L+KGI ++       +V +    ++ + +
Sbjct: 121 FTNLMTHPRYKIPKTYVAKIEGYILREQVKQLEKGIQLEDGLTQPAKVKVKKQNKEKNTS 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V + + EG+NR+++++FE F + V +L R+S+GP  L  L AG  R +S   ++     
Sbjct: 181 LVEITITEGRNRQVRRMFEHFGFSVQKLSRVSFGPLTLKGLGAGEGRVLSPHEVKSLRHL 240

Query: 248 HLLEEAQ 254
               + Q
Sbjct: 241 AENGQQQ 247


>gi|197119460|ref|YP_002139887.1| 23S rRNA pseudouridine 2605 synthase [Geobacter bemidjiensis Bem]
 gi|197088820|gb|ACH40091.1| 23S rRNA pseudouridine 2605 synthase [Geobacter bemidjiensis Bem]
          Length = 266

 Score =  195 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 84/267 (31%), Positives = 135/267 (50%), Gaps = 4/267 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++++AG+ASRRE E +IA  RV VNG ++           D I +DG P+   E+
Sbjct: 3   ERLQKILSQAGVASRRESEGIIAAGRVAVNGTVVTELGTKADPDTDTITLDGKPITIEEK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP+G +TT  DP+GR  V D L  +  RV  +GRLD NTEGLLLLTNDG LA 
Sbjct: 63  RVYILLYKPVGYMTTMKDPEGRPIVSDLLNGVKERVYPIGRLDYNTEGLLLLTNDGALAN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS +  + Y VR  GQV   ++  L +G+ ++       +V   ++  +N+W+++ 
Sbjct: 123 SLMHPSHEVDKGYLVRVSGQVSPLQIKKLSEGVKLEDGMTAPAKVLPVSESENNSWISIT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           + EG+ R+++++ E     V RL R  Y   ++G +  G  R ++ + +      +    
Sbjct: 183 IHEGRYRQVRRMCEAVGLNVVRLKRARYDFLEIGDMKPGEYRHLAPEEV---TRLNRKMA 239

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVP 279
                  P  +     R          
Sbjct: 240 PVGTGRGPRKTGVVARRGSTGTGRRTR 266


>gi|300070794|gb|ADJ60194.1| ribosomal large subunit pseudouridine synthase B [Lactococcus
           lactis subsp. cremoris NZ9000]
          Length = 239

 Score =  195 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 73/240 (30%), Positives = 122/240 (50%), Gaps = 3/240 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K +A AG+ASRR+ E +I   +V VN + +      V + D +EV+GV +   E  
Sbjct: 1   MRINKYLAHAGVASRRKAEELILAGKVTVNNVPMTNLGYQVSTGDVVEVNGVAVYNEEPV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      + +   D   ++   D +P +  R+  VGRLD +T GLLLLTNDG    +
Sbjct: 61  YYLLNKPRGYISSVSDDKGRQTV-MDLMPQVKERIYPVGRLDWDTSGLLLLTNDGEFTNM 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  PS    +VY  +  GQ +++ L  L  G+ I+G      +  +  Q+   +++ V++
Sbjct: 120 MTHPSHGVDKVYVAKVEGQANKENLRPLTLGMTIEGKKVSPARYEIIKQEKTKNHSIVSL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+F      V +L RI YG   L  L  G  R +SKK + + +     +
Sbjct: 180 TIHEGQNHQVKKMFAAAGLPVQKLSRIQYGTLTLDGLPTGQFRRLSKKEVSQLINAAQGK 239


>gi|86148705|ref|ZP_01066982.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio sp. MED222]
 gi|85833498|gb|EAQ51679.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio sp. MED222]
          Length = 379

 Score =  195 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 71/372 (19%), Positives = 137/372 (36%), Gaps = 31/372 (8%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + +    +R++K I+  G  SRRE +++I   RV +NG +       V+  D +E+D  P
Sbjct: 1   MSQESQAKRLNKYISETGFCSRREADKLIDAGRVTINGKIP-EMGTKVLPGDDVEIDNKP 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +R  E+      +KP G+  T            +      R+  +GRLD  ++GL+ LTN
Sbjct: 60  VRSREKPIYIALNKPTGITCTTERDI--PGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTN 117

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG +   +        + Y VR    +  + L  +  G+ I        +V    +K + 
Sbjct: 118 DGDIVNKILRAGNNHEKEYVVRVDKPITTEFLKQMGAGVHILDTVTLPCKV----EKETK 173

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               + L +G NR+I+++ E   ++V +L R+      L  +  G  R +S + + E L 
Sbjct: 174 FSFRITLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSDEEITEILA 233

Query: 247 PH-------LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
                       +          +++  + D             + +  +    G +  +
Sbjct: 234 MCEGSVSTEDASKMNAKGQRIRKATDAKLFDSREENQTSTARRNQNENRTRTYRGNNADE 293

Query: 300 KLATPVHRRNLASNVWMAKGIH-----------------SSFLSDSGQREENHRRSPSFP 342
               P  +R   S+   + G                    +    +    +N+ R    P
Sbjct: 294 FRHAPNSKRGRNSSNGESGGGGNTENWKSNSRSERSNSDKNRSDRNRTDRDNNERRSGKP 353

Query: 343 SKRSLRRTSAKK 354
           + RS       K
Sbjct: 354 TNRSPDSNRPNK 365


>gi|315658229|ref|ZP_07911101.1| pseudouridine synthase RluB [Staphylococcus lugdunensis M23590]
 gi|315496558|gb|EFU84881.1| pseudouridine synthase RluB [Staphylococcus lugdunensis M23590]
          Length = 247

 Score =  195 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 72/238 (30%), Positives = 128/238 (53%), Gaps = 3/238 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +  +   +R+ K IA +G  SRR+ E +I + +VKVNG ++      V  +D +EV+G+ 
Sbjct: 1   MIMSKELERLQKRIANSGYTSRRKAETLITEGKVKVNGEVVTELGTKVKPSDQVEVEGIK 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +   E     L+HKP  ++T+ SD  GR+ V D    + +R+  VGRLD +T G+LLLTN
Sbjct: 61  ME-QEDKIYILFHKPAQVITSVSDDHGRTVVTDYFKDLDTRIYPVGRLDYDTSGVLLLTN 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKG 184
           DG    ++  P     + Y  +  G + ++++  L+ GI ++         ++    +  
Sbjct: 120 DGEFTNLMTHPRYHIPKTYVAKLKGYLMREEVKTLEAGIELEDGLTQPATVKIKRQDKDK 179

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +   V + + EG+NR+++++FE F   VN+L RI +G   L  L AG  R ++   ++
Sbjct: 180 NTTLVEITISEGRNRQVRRMFEHFGHSVNKLTRIQFGSLNLKGLNAGEGRVLTPHEVK 237


>gi|218708762|ref|YP_002416383.1| ribosomal large subunit pseudouridine synthase F [Vibrio splendidus
           LGP32]
 gi|218321781|emb|CAV17738.1| Ribosomal large subunit pseudouridine synthase F [Vibrio splendidus
           LGP32]
          Length = 379

 Score =  195 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 71/372 (19%), Positives = 137/372 (36%), Gaps = 31/372 (8%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + +    +R++K I+  G  SRRE +++I   RV +NG +       V+  D +E+D  P
Sbjct: 1   MSQESQAKRLNKYISETGFCSRREADKLIDAGRVTINGKIP-EMGTKVLPGDDVEIDNKP 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +R  E+      +KP G+  T            +      R+  +GRLD  ++GL+ LTN
Sbjct: 60  VRSREKPIYIALNKPTGITCTTERDI--PGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTN 117

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG +   +        + Y VR    +  + L  +  G+ I        +V    +K + 
Sbjct: 118 DGDIVNKILRAGNNHEKEYVVRVDKPITTEFLKQMGAGVHILDTVTLPCKV----EKETK 173

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               + L +G NR+I+++ E   ++V +L R+      L  +  G  R +S + + E L 
Sbjct: 174 FSFRITLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSDEEITEILA 233

Query: 247 PH-------LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
                       +          +++  + D             + +  +    G +  +
Sbjct: 234 MCEGSVSTEDASKMNAKGQRIRKATDAKLFDSREENQTSTARRNQNENRARTYRGNNADE 293

Query: 300 KLATPVHRRNLASNVWMAKGIH-----------------SSFLSDSGQREENHRRSPSFP 342
               P  +R   S+   + G                    +    +    +N+ R    P
Sbjct: 294 FRHAPNSKRGRNSSNGESSGGGNTENWKSNSRSERSNSDKNRSDRNRTDRDNNERRSGKP 353

Query: 343 SKRSLRRTSAKK 354
           + RS       K
Sbjct: 354 TNRSQDSNRPNK 365


>gi|327484742|gb|AEA79149.1| Ribosomal large subunit pseudouridine synthase F LSU Psi2604
           [Vibrio cholerae LMA3894-4]
          Length = 328

 Score =  195 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 73/334 (21%), Positives = 129/334 (38%), Gaps = 9/334 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
              T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR
Sbjct: 2   SQPTEKRLNKFISETGYCSRREADKLIEQGRVTINGLQPEV-GSKVTEQDEVCIDGKPLR 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ER      +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG
Sbjct: 61  SKERPIYIALNKPTGITCTTERDV--PGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y VR    +  + +  +  G+ I        +VT    + +   
Sbjct: 119 DIVNKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVT----QETQYS 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L   
Sbjct: 175 FRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSDAEVSEILAMC 234

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNI--ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                         S +T+ R        S   +  ++ ++N    +G + Q+    P  
Sbjct: 235 EDSSGTEEASRVAQSGDTIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNS 294

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
           ++        +    S              R   
Sbjct: 295 KKAQRRPSSSSSNTASGSKPTPRTGGTLSLRKSK 328


>gi|295099584|emb|CBK88673.1| ribosomal large subunit pseudouridine synthase B [Eubacterium
           cylindroides T2-87]
          Length = 241

 Score =  194 bits (493), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 70/232 (30%), Positives = 114/232 (49%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIAR+GI SRR+ E +I + +V VNG L       V   D IEVDG  L   ++ 
Sbjct: 2   ERLQKVIARSGICSRRKAEELILEGKVYVNGELCTTLGTKVSGNDEIEVDGKLLELEDKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +      + +++ D D R+ +      I  RV +VGRLD +T G+LLLTNDG     
Sbjct: 62  YYVINKTKGCICSSNDDRDRRTVLDYL--DIPQRVYTVGRLDYDTSGVLLLTNDGDFCNQ 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P     + Y V   G + QD + LL+KG+      +   +V + +           +
Sbjct: 120 MIHPRYHLPKTYVVNLQGTLTQDDIRLLRKGLKTNIGDFQPAKVKIISNDVTRDRTIFEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + EGKN ++K + E    +V +L R+ +G  ++  L  G  R +    +++
Sbjct: 180 TIMEGKNHQVKNMMEALGHQVRKLHRVRFGSIEVNDLKPGEYRRLKPYEVKQ 231


>gi|239833548|ref|ZP_04681876.1| conserved hypothetical protein [Ochrobactrum intermedium LMG 3301]
 gi|239821611|gb|EEQ93180.1| conserved hypothetical protein [Ochrobactrum intermedium LMG 3301]
          Length = 562

 Score =  194 bits (493), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 165/353 (46%), Positives = 214/353 (60%), Gaps = 12/353 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           +N   +    +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VD
Sbjct: 52  RNAEAQEDASERIAKRMARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVD 111

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G PL++ ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP+   RV+SVGRLDINTEGLLL
Sbjct: 112 GKPLKQTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPAEMPRVLSVGRLDINTEGLLL 171

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDGGL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++  L+  +
Sbjct: 172 LTNDGGLSRVLELPSTGWLRRYRVRAHGKVTQQQLDELKNGIAVDGVFYGSVEAELERVQ 231

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           G+N W+++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  + LR+
Sbjct: 232 GANVWISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRTLRD 291

Query: 244 QLGPHLLEEAQVNLDAP------------IYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           QLG  L+EE+  + DAP                E                  R   +S  
Sbjct: 292 QLGDKLIEESGADFDAPVLNEFSNAAVQGRTRREMEEGQPEQDGETRRAPREREWISSRP 351

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +    ++ K      RR   +NVWMA G        + +      + P   +K
Sbjct: 352 ERRRGREDKTEKVEPRRRGNANVWMAPGARPKGEKAAAKPPRVEHQVPHRSAK 404



 Score = 36.3 bits (82), Expect = 8.2,   Method: Composition-based stats.
 Identities = 13/96 (13%), Positives = 18/96 (18%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
               +          R RP           R +     +      K+    +        
Sbjct: 432 NKRPEGRFDKDSRPQRPRPEGNRSEEGRPERREPREDGRKERRPGKRERAELRDAEGRVG 491

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                G         G      R S S    RS  R
Sbjct: 492 ERGKGGFEGRKSGKPGAPRGEGRFSASDRDTRSGPR 527



 Score = 35.9 bits (81), Expect = 8.4,   Method: Composition-based stats.
 Identities = 9/113 (7%), Positives = 29/113 (25%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R       +            +    V  +    S       +M+   + +    +++  
Sbjct: 368 RRGNANVWMAPGARPKGEKAAAKPPRVEHQVPHRSAKFSGDLQMRPRRAGEEEQGREEGG 427

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               ++R        ++        +  +     RR P    ++  R    ++
Sbjct: 428 ERRYNKRPEGRFDKDSRPQRPRPEGNRSEEGRPERREPREDGRKERRPGKRER 480


>gi|258627383|ref|ZP_05722167.1| Ribosomal large subunit pseudouridine synthase F [Vibrio mimicus
           VM603]
 gi|258580421|gb|EEW05386.1| Ribosomal large subunit pseudouridine synthase F [Vibrio mimicus
           VM603]
          Length = 332

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 75/339 (22%), Positives = 137/339 (40%), Gaps = 16/339 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR  ER  
Sbjct: 8   RLNKFISETGFCSRREADKLIEQGRVTLNGVQPEV-GSKVTEQDEVCIDGKPLRSKERPI 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCTTERDV--PGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + +  +  G+ I        +VT    + +     + L 
Sbjct: 125 LRAGNNHEKEYVVRVDKPITPEFIRQMASGVNILDTVTLPCKVT----QETQYSFRIVLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L         
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVNEILAMCEDSSGT 240

Query: 255 VNLDAPIYSSETLVRDRPNI--ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
                   S +++ R        +   +  ++ ++N    +G + Q+       ++    
Sbjct: 241 EEASRVAQSGDSIKRATDAKLFDNREANKESKARRNPKTYHGKNAQEFRHALNSKKAQR- 299

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                    SS  + S   +   R +P      SLR++ 
Sbjct: 300 ------HPKSSPSNSSTASKPASRPTPRTGGTLSLRKSK 332


>gi|255528344|ref|ZP_05395151.1| pseudouridine synthase [Clostridium carboxidivorans P7]
 gi|296188339|ref|ZP_06856731.1| pseudouridine synthase [Clostridium carboxidivorans P7]
 gi|255507968|gb|EET84401.1| pseudouridine synthase [Clostridium carboxidivorans P7]
 gi|296047465|gb|EFG86907.1| pseudouridine synthase [Clostridium carboxidivorans P7]
          Length = 258

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 61/255 (23%), Positives = 103/255 (40%), Gaps = 5/255 (1%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K    EN    R++K I+  GI SRRE + +I ++RV +NGI        V STD +++
Sbjct: 4   NKINHNENSDSMRINKFISEKGICSRREADTLIQEKRVTINGITA-ELGSRVKSTDEVKL 62

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG  L + E+           +    +          +  +   R+  +GRLD ++EGL+
Sbjct: 63  DGKLLTEKEKDDKVYIALNKPVGIICTTEKKIKNNIVDFVNYPKRIFHIGRLDKDSEGLI 122

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
            LTNDG +   +        + Y V     +    L  +  G+ I        +V     
Sbjct: 123 FLTNDGDIVNKILRAGNNHEKEYIVTVDKCITNSFLKEMASGVSILNTVTKPCKVY---- 178

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           K  +    + L +G NR+I+++ E   + V +L RI      L  +  G  R +S   L+
Sbjct: 179 KEGSHIFRIILTQGLNRQIRRMCEALGYNVLKLKRIRIMNVTLKDIPVGKWRYLSPSELK 238

Query: 243 EQLGPHLLEEAQVNL 257
                          
Sbjct: 239 TINKLTSTSIKTEEA 253


>gi|315640594|ref|ZP_07895700.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           italicus DSM 15952]
 gi|315483622|gb|EFU74112.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           italicus DSM 15952]
          Length = 236

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 78/233 (33%), Positives = 114/233 (48%), Gaps = 3/233 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KVIA+AGI SRR+ E  I   RVKVNG+++      V S D IEVD VP+ +     
Sbjct: 3   RLQKVIAQAGITSRRKAEVYILDGRVKVNGVVVNELGTKVSSKDTIEVDNVPISQEGSVY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
              Y     +++  SD   R  V D    +  R+  +GRLD NT GLLLLTNDG  +++L
Sbjct: 63  YLFYKPRG-VISAVSDDKKRKVVTDFFTEVSERIYPIGRLDYNTSGLLLLTNDGEFSQLL 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTVG 192
             P  +  + Y  +  G      L  L +G+  +G  Y   +  + +       + V + 
Sbjct: 122 THPKNEIEKKYVAKVKGVALPHALKPLTRGLKYKGEKYAPAKYDILSTDTRAETSIVQLT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + EGKN ++K + E     V +L R  YG   LG L  G  R + KK + +  
Sbjct: 182 IHEGKNHQVKNMLEAVGLPVQKLKREQYGNLTLGNLKPGEYRPLLKKEINQFF 234


>gi|146319353|ref|YP_001199065.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Streptococcus suis 05ZYH33]
 gi|146321558|ref|YP_001201269.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Streptococcus suis 98HAH33]
 gi|253752382|ref|YP_003025523.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           suis SC84]
 gi|253754208|ref|YP_003027349.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           suis P1/7]
 gi|253756142|ref|YP_003029282.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           suis BM407]
 gi|145690159|gb|ABP90665.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           Pseudouridylate synthase [Streptococcus suis 05ZYH33]
 gi|145692364|gb|ABP92869.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           Pseudouridylate synthase [Streptococcus suis 98HAH33]
 gi|251816671|emb|CAZ52312.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           suis SC84]
 gi|251818606|emb|CAZ56440.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           suis BM407]
 gi|251820454|emb|CAR47153.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           suis P1/7]
 gi|319758787|gb|ADV70729.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Streptococcus suis JS14]
          Length = 243

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 80/244 (32%), Positives = 132/244 (54%), Gaps = 3/244 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V VNG ++      + S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELGTVIKSGDKVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVVDLLPTVKERIYPVGRLDWDTSGVLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +G+VI G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGVANKEVLRPLTRGVVIDGKKTKPAVYEIIKVDPVKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE    +V++L R  +G   L  L  G  R+++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGNLDLTGLRPGEYRKLNKKDISKLHTLAVTK 239

Query: 252 EAQV 255
             + 
Sbjct: 240 PVKK 243


>gi|254453766|ref|ZP_05067203.1| ribosomal large subunit pseudouridine synthase [Octadecabacter
           antarcticus 238]
 gi|198268172|gb|EDY92442.1| ribosomal large subunit pseudouridine synthase [Octadecabacter
           antarcticus 238]
          Length = 328

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 140/308 (45%), Positives = 187/308 (60%), Gaps = 1/308 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++KV+ARAG+ASRRE E++I   RV VNG  +   A+NV   D I VDG PL + E 
Sbjct: 22  GDRIAKVLARAGVASRREAEKIIEAGRVTVNGKTILTPALNVTDKDRIVVDGKPLAEPEP 81

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R+WLY+KPIGLVT+  D  GR TVFD LP    RV+SVGRLDIN+EGLLLLTNDG L R
Sbjct: 82  PRIWLYYKPIGLVTSERDEKGRETVFDTLPDDMPRVVSVGRLDINSEGLLLLTNDGELKR 141

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +ELPST WLR YRVR +G + + KL+ L+ GI I G+ Y  ++V  D Q+G+NAW+T+G
Sbjct: 142 KMELPSTGWLRRYRVRINGSLSEAKLDELRAGIQIDGVHYAPVEVKFDRQQGANAWLTMG 201

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           LREGKNREI+K+ E     VNRL+RISYGPFQLGTL  G   EV ++I+R+Q+G     +
Sbjct: 202 LREGKNREIRKLMEAMGVVVNRLLRISYGPFQLGTLKPGKVEEVKQRIVRDQMGLRETPK 261

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
             +   A         +      ++   D  +   +   K      ++ + P    +   
Sbjct: 262 PTMVGKAAEKGKRPPPKRGTAASAKRFTDPEKRN-SDPTKRNTGAVERNSGPTSGHSAGR 320

Query: 313 NVWMAKGI 320
           +       
Sbjct: 321 SAGKPPRK 328


>gi|223934211|ref|ZP_03626147.1| pseudouridine synthase [Streptococcus suis 89/1591]
 gi|302024332|ref|ZP_07249543.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           suis 05HAS68]
 gi|330833322|ref|YP_004402147.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           suis ST3]
 gi|223897127|gb|EEF63552.1| pseudouridine synthase [Streptococcus suis 89/1591]
 gi|329307545|gb|AEB81961.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           suis ST3]
          Length = 243

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 80/244 (32%), Positives = 132/244 (54%), Gaps = 3/244 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V VNG ++      + S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELGTVIKSGDKVEVEGKPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVVDLLPTVKERIYPVGRLDWDTSGVLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +G+VI G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGVANKEVLRPLTRGVVIDGKKTKPAVYEIIKVDPVKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE    +V++L R  +G   L  L  G  R+++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGNLDLTGLRPGEYRKLNKKDISKLHTLAVTK 239

Query: 252 EAQV 255
             + 
Sbjct: 240 PVKK 243


>gi|254502639|ref|ZP_05114790.1| conserved hypothetical protein, putative [Labrenzia alexandrii
           DFL-11]
 gi|222438710|gb|EEE45389.1| conserved hypothetical protein, putative [Labrenzia alexandrii
           DFL-11]
          Length = 498

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 156/349 (44%), Positives = 211/349 (60%), Gaps = 2/349 (0%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
            + +  + +R++KV+ARAG+ SRRE E  +   RV+VNG +L   AV V S D + VDG 
Sbjct: 51  TIPDTASGERIAKVMARAGLCSRREAETWVMDGRVEVNGKVLTTPAVTVTSNDKVLVDGE 110

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL   ERTRLWLYHKP GLVTT+ DP+GR TVFD LP    RV++VGRLDINTEGLLLLT
Sbjct: 111 PLPMRERTRLWLYHKPRGLVTTNKDPEGRPTVFDRLPDDLPRVLTVGRLDINTEGLLLLT 170

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDGGLARVLELP+T WLR YRVR  G++ Q +L+ L  G+ I G+ YG ++ TLD ++G 
Sbjct: 171 NDGGLARVLELPATGWLRRYRVRAFGKITQAELDTLNDGVAIDGVLYGAIEATLDKEQGG 230

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           N W+TVGLREGKNRE+K+V E     VNRLIR+SYGPFQL  L  G  RE+  ++LR+QL
Sbjct: 231 NVWMTVGLREGKNREVKRVLEHLGMSVNRLIRLSYGPFQLMDLAEGDVREIRGRVLRDQL 290

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G  L EEA  + DAPI+       ++           +  +K   Q   L+ ++  +   
Sbjct: 291 GDALAEEAGADFDAPIFHMPKQEEEKKRPGPRGGSRDSSSEKG--QGKWLTAREGKSATD 348

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            ++   S+    K           ++     +       R  +  + ++
Sbjct: 349 RKKAARSDDGGPKQGKRRNEGPRREKVSPRSKFRMTSEPRFRKDYNEER 397


>gi|253699802|ref|YP_003020991.1| pseudouridine synthase [Geobacter sp. M21]
 gi|251774652|gb|ACT17233.1| pseudouridine synthase [Geobacter sp. M21]
          Length = 266

 Score =  194 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 84/267 (31%), Positives = 135/267 (50%), Gaps = 4/267 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++++AG+ASRRE E +IA  RV VNG ++           D I +DG P+   E+
Sbjct: 3   ERLQKILSQAGVASRRESEGIIAAGRVAVNGTVVTELGTKADPDTDTITLDGKPITIEEK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP+G +TT  DP+GR  V D L  +  RV  +GRLD NTEGLLLLTNDG LA 
Sbjct: 63  RVYILLYKPVGYMTTMKDPEGRPIVSDLLKGVKERVYPIGRLDYNTEGLLLLTNDGALAN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS +  + Y VR  GQV   ++  L +G+ ++       +V   ++  +N+W+++ 
Sbjct: 123 SLMHPSHEVDKGYLVRVSGQVSPLQIKKLSEGVKLEDGMTAPAKVLPMSESENNSWISIT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           + EG+ R+++++ E     V RL R  Y   ++G +  G  R ++ + +      +    
Sbjct: 183 IHEGRYRQVRRMCEAVGLNVVRLKRARYDFLEIGDMKPGEYRHLAPEEV---TRLNRKMA 239

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVP 279
                  P  +     R          
Sbjct: 240 PVGTGRGPRKTGVVARRGSTGPGRRTR 266


>gi|12724251|gb|AAK05373.1|AE006360_2 pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403]
          Length = 257

 Score =  194 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 72/250 (28%), Positives = 121/250 (48%), Gaps = 3/250 (1%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +            R++K +A AG+ASRR+ E +I   +V VN + +      V + D +E
Sbjct: 7   QKNKPYLTKVKKMRINKYLAHAGVASRRKAEELILAGKVTVNNVPMTNLGYQVSTGDIVE 66

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           V+GV +   E     L      + +   D   ++   D +P +  R+  VGRLD +T GL
Sbjct: 67  VNGVAVYNEEPVYYLLNKPRGYISSVSDDKGRQTV-MDLMPQVKERIYPVGRLDWDTSGL 125

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDG    ++  P     +VY  +  GQ +++ L  L  G+ I+G      +  +  
Sbjct: 126 LLLTNDGEFTNMMTHPRHGVDKVYVAKVEGQANKENLRPLTLGMTIEGKKVSPARYEIIK 185

Query: 182 QK--GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           Q+   +++ V++ + EG+N ++KK+F      V +L RI YG   L  L  G  R +SKK
Sbjct: 186 QEKTKNHSIVSLTIHEGQNHQVKKMFAAAGLPVQKLSRIQYGSLTLDGLPTGQFRRLSKK 245

Query: 240 ILREQLGPHL 249
            + + +    
Sbjct: 246 EVSQLINAAQ 255


>gi|152974996|ref|YP_001374513.1| pseudouridine synthase [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152023748|gb|ABS21518.1| pseudouridine synthase [Bacillus cytotoxicus NVH 391-98]
          Length = 242

 Score =  194 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 76/242 (31%), Positives = 129/242 (53%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG ++      V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVTELGTKVTPQDKVEVNHIPLEKEEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     + +   D  GR  V D    I  R+  +GRLD +T G+LL+TNDG  A +
Sbjct: 62  YFLLYKPTGVISSVS-DDKGRKVVTDFFQDIPQRLFPIGRLDYDTSGVLLMTNDGDFANI 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTV 191
           L  P  +  + Y  +  G +  +K+ +L+KG++++       +V + +       + V +
Sbjct: 121 LMHPKYKVEKTYVAKVKGPLTGEKIRMLEKGVILEDGKTSPARVKIISWDKRKEMSIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE    KV +L R  Y   ++G+L  G  RE++   +++       +
Sbjct: 181 TIHEGRNRQVRRMFEAIGCKVMKLKRERYAFLEVGSLRPGDARELTPHEVKQLRALASTK 240

Query: 252 EA 253
             
Sbjct: 241 PR 242


>gi|325571145|ref|ZP_08146717.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           casseliflavus ATCC 12755]
 gi|325156230|gb|EGC68416.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           casseliflavus ATCC 12755]
          Length = 240

 Score =  194 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 83/234 (35%), Positives = 127/234 (54%), Gaps = 3/234 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +R+ KVIA AGI SRR+ E +I + RV+VNG +++   V V S D +EVDGVP+ +  
Sbjct: 2   KMERLQKVIAHAGITSRRKAEGLITEGRVRVNGQVIKELGVQVGSKDVVEVDGVPIEQEP 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                 Y     +++  +D   R  V D    +  RV  VGRLD +T GLLLLTNDG L+
Sbjct: 62  HVYYLFYKPRG-VISAVTDDKKRKVVLDYFAEVPERVYPVGRLDYDTSGLLLLTNDGELS 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWV 189
           + L  P  +  +VY  +  G  D+ +L  L KGI I+G      +  + +   +  ++ V
Sbjct: 121 QTLMHPKHEVEKVYVAKVKGIADKKQLLPLTKGIRIEGRKTAPARFEILSTDQTAQSSIV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + + EG+N ++K + +     V +L R +YGP  L  L  G  RE+SKK + +
Sbjct: 181 QLTIHEGRNHQVKNMLKAVGLPVQKLKRENYGPLDLKGLRPGEYRELSKKEVSQ 234


>gi|218282361|ref|ZP_03488643.1| hypothetical protein EUBIFOR_01225 [Eubacterium biforme DSM 3989]
 gi|218216647|gb|EEC90185.1| hypothetical protein EUBIFOR_01225 [Eubacterium biforme DSM 3989]
          Length = 242

 Score =  194 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 69/243 (28%), Positives = 115/243 (47%), Gaps = 4/243 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGI SRR+ E +I   +VKVNG + +     V   D IEV+G  + K E+ 
Sbjct: 2   ERLQKVIAQAGICSRRKAEELILDGKVKVNGEICDVLGTKVSKQDIIEVNGNMISKEEKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +      L T+  D   ++ +         R+ SVGRLD +T G+LLLTNDG     
Sbjct: 62  YYIMNKPKGCLCTSSDDKGRKTVLDY--MPKNERIFSVGRLDYDTSGVLLLTNDGEFCNH 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P     + Y V   G + +D +  L+KG+  +   Y   +V +  +    +     +
Sbjct: 120 MIHPRYHLEKTYVVNLQGILSEDDIKQLRKGLKTKTEKYQPAKVFVLQKDLTRNRTQFEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EGKN ++K +      +V RL R+ +    +  L AG  R +    +++     +  
Sbjct: 180 TISEGKNHQVKNMMLALGHEVRRLHRVKFAFLDVKDLRAGEYRRLKPYEIKQLNRLAMEG 239

Query: 252 EAQ 254
           E +
Sbjct: 240 ENK 242


>gi|312868359|ref|ZP_07728559.1| pseudouridine synthase B, ribosomal large subunit [Streptococcus
           parasanguinis F0405]
 gi|322390066|ref|ZP_08063601.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           parasanguinis ATCC 903]
 gi|311096104|gb|EFQ54348.1| pseudouridine synthase B, ribosomal large subunit [Streptococcus
           parasanguinis F0405]
 gi|321143193|gb|EFX38636.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           parasanguinis ATCC 903]
          Length = 243

 Score =  194 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 77/244 (31%), Positives = 129/244 (52%), Gaps = 3/244 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + + D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATIIKTGDQVEVEGTPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR+TV D L  +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRTTVVDLLSQVPERIYPVGRLDWDTSGVLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGIANKENLRPLTRGVTIDGKKTKPATYEILKVDVEKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE     V++L R  +G   +  L  G  R ++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFEAVGLLVDKLSRTQFGNLDVSGLRPGEYRRLNKKEISQLHNLAVTK 239

Query: 252 EAQV 255
             + 
Sbjct: 240 SKKA 243


>gi|116333418|ref|YP_794945.1| 16S rRNA uridine-516 pseudouridylate synthase related enzyme
           [Lactobacillus brevis ATCC 367]
 gi|116098765|gb|ABJ63914.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           brevis ATCC 367]
          Length = 240

 Score =  194 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 85/240 (35%), Positives = 124/240 (51%), Gaps = 3/240 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR+ E++I   RVKVNG  +      V   D I VDGVP+      
Sbjct: 2   ERLQKVLAHAGVASRRQSEKLIMSGRVKVNGAAVTELGTKVGVHDQILVDGVPISSEAPI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + LY     +V+T +D  GR TV D + ++  RV  VGRLD +T GLLLLTNDG LA  
Sbjct: 62  YIMLYKPRG-VVSTANDDKGRKTVVDLVENVSQRVYPVGRLDYDTSGLLLLTNDGELANR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  R  G    D +  L++GI + G  Y   +  + +       A +++
Sbjct: 121 LTHPRYEVEKTYIARVTGVPTNDAMKQLRQGITVDGETYAPAKSKVLSAADDRKTAIISL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EGKN ++KK+       V +L R  YG   L  L AG  R++  + ++E      L 
Sbjct: 181 TIHEGKNHQVKKMLAAVGCPVEKLKREQYGFLTLKGLNAGEARQLKPEEVKELRRLTHLA 240


>gi|86605480|ref|YP_474243.1| RNA pseudouridine synthase family protein [Synechococcus sp.
           JA-3-3Ab]
 gi|86554022|gb|ABC98980.1| RNA pseudouridine synthase family protein [Synechococcus sp.
           JA-3-3Ab]
          Length = 272

 Score =  194 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 79/269 (29%), Positives = 125/269 (46%), Gaps = 12/269 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK- 69
           TPQR+ K++A+ G+ASRR+VE  I   R++VNG ++           D +EVDG  +   
Sbjct: 3   TPQRLQKLLAQQGLASRRQVEAWILAGRIRVNGKVVTELGFKADPERDRVEVDGRVIPFG 62

Query: 70  -AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTN 126
              R  L L+     L T       ++ +    P    ++    VGRLD ++ G LLLTN
Sbjct: 63  DPARYVLLLHKPLGVLSTCKDPWGRKTVLDLLPPPWNRQIRLYPVGRLDADSSGALLLTN 122

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT----- 181
           DG L   L  P     ++YRV+  G+  +  L   + G+ ++G      +V         
Sbjct: 123 DGDLTLKLTHPRYHLPKIYRVQVQGRPSRATLQQWRDGVNLEGYTTLPAEVEFCPAPNFG 182

Query: 182 --QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             Q  +++W+ V L EG+NR+I++V E     V RL R + GP  LG L AG  R +  +
Sbjct: 183 YRQDANSSWLRVVLFEGRNRQIRRVAEQLGHPVLRLHREAIGPLHLGNLKAGQFRLLEPQ 242

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLV 268
            ++  L P    ++     +    S    
Sbjct: 243 EVQALLAPLAGTDSLALFRSASLHSFRPS 271


>gi|326406814|gb|ADZ63885.1| ribosomal large subunit pseudouridine synthase B [Lactococcus
           lactis subsp. lactis CV56]
          Length = 257

 Score =  193 bits (491), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 72/250 (28%), Positives = 121/250 (48%), Gaps = 3/250 (1%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +            R++K +A AG+ASRR+ E +I   +V VN + +      V + D +E
Sbjct: 7   QKNKPYLTKVKKMRINKYLAHAGVASRRKAEELILAGKVTVNNVPMTNLGYQVSTGDIVE 66

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           V+GV +   E     L      + +   D   ++   D +P +  R+  VGRLD +T GL
Sbjct: 67  VNGVAVYNEEPVYYLLNKPRGYISSVSDDKGRQTV-MDLMPQVKERIYPVGRLDWDTSGL 125

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDG    ++  P     +VY  +  GQ +++ L  L  G+ I+G      +  +  
Sbjct: 126 LLLTNDGEFTNMMTHPRHGVDKVYVAKVEGQANKENLRPLTLGMTIEGKKVSPARYEIIK 185

Query: 182 QK--GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           Q+   +++ V++ + EG+N ++KK+F      V +L RI YG   L  L  G  R +SKK
Sbjct: 186 QEKTKNHSIVSLTIHEGQNHQVKKMFAAAGLPVQKLSRIQYGTLTLDGLPTGQFRRLSKK 245

Query: 240 ILREQLGPHL 249
            + + +    
Sbjct: 246 EVSQLINAAQ 255


>gi|261406009|ref|YP_003242250.1| pseudouridine synthase [Paenibacillus sp. Y412MC10]
 gi|329929803|ref|ZP_08283479.1| pseudouridine synthase B, ribosomal large subunit [Paenibacillus
           sp. HGF5]
 gi|261282472|gb|ACX64443.1| pseudouridine synthase [Paenibacillus sp. Y412MC10]
 gi|328935781|gb|EGG32242.1| pseudouridine synthase B, ribosomal large subunit [Paenibacillus
           sp. HGF5]
          Length = 251

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 81/237 (34%), Positives = 130/237 (54%), Gaps = 4/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K++A+AG+ASRR+ E +I + +V+VNG  +           D I V G P++  E+
Sbjct: 2   ERLQKIMAQAGVASRRKCEELILEGKVQVNGETVTELGTKADPAQDIITVSGKPIK-NEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G++T+ SDP+GR  V D L  I  RV  +GRLD +TEGLLLLTNDG  A 
Sbjct: 61  KVYVMLNKPKGVITSASDPEGRKIVSDYLKGIKERVYPIGRLDYDTEGLLLLTNDGEFAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
           +L  P     + Y     G     +L+ L++GI+++       +V        N  + ++
Sbjct: 121 LLSHPKYHVPKTYLATVKGVPHGTELDKLRQGIMLEDGMTSPAEVEYKDVDPDNKQSVIS 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           + + EG+NR+++++FE  +  V RL RISYG   L  L  G  R ++   + + L  
Sbjct: 181 ITIHEGRNRQVRRMFEAISHPVLRLKRISYGDLLLQNLKRGLYRHLTADEINQLLQM 237


>gi|30024033|ref|NP_267431.2| pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403]
          Length = 239

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 72/238 (30%), Positives = 120/238 (50%), Gaps = 3/238 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K +A AG+ASRR+ E +I   +V VN + +      V + D +EV+GV +   E  
Sbjct: 1   MRINKYLAHAGVASRRKAEELILAGKVTVNNVPMTNLGYQVSTGDIVEVNGVAVYNEEPV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      + +   D   ++   D +P +  R+  VGRLD +T GLLLLTNDG    +
Sbjct: 61  YYLLNKPRGYISSVSDDKGRQTV-MDLMPQVKERIYPVGRLDWDTSGLLLLTNDGEFTNM 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P     +VY  +  GQ +++ L  L  G+ I+G      +  +  Q+   +++ V++
Sbjct: 120 MTHPRHGVDKVYVAKVEGQANKENLRPLTLGMTIEGKKVSPARYEIIKQEKTKNHSIVSL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + EG+N ++KK+F      V +L RI YG   L  L  G  R +SKK + + +    
Sbjct: 180 TIHEGQNHQVKKMFAAAGLPVQKLSRIQYGSLTLDGLPTGQFRRLSKKEVSQLINAAQ 237


>gi|225174838|ref|ZP_03728835.1| pseudouridine synthase [Dethiobacter alkaliphilus AHT 1]
 gi|225169478|gb|EEG78275.1| pseudouridine synthase [Dethiobacter alkaliphilus AHT 1]
          Length = 242

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 79/240 (32%), Positives = 123/240 (51%), Gaps = 1/240 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K ++ AG+ SRR  E++I   RV VNG  +    V V    D +EVDG  ++  + 
Sbjct: 3   IRLQKFLSMAGVCSRRAGEKLIESGRVTVNGSRVTAMGVTVDPENDVVEVDGRRVKVQQN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP+G VTT  D  GR TV + +  I +RV  VGRLD++T GLLLLTNDG LA 
Sbjct: 63  NEYILLYKPVGYVTTLKDEFGRPTVKELVADIKTRVYPVGRLDLDTSGLLLLTNDGELAN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS    + Y  + H    ++ L +L KG+ +        +V L       + V++ 
Sbjct: 123 QLTHPSFGVEKEYLAKVHDTPKKEALEILAKGVRLDDGMTAPAKVQLVKSGRLTSVVSLI 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           ++EG+NR+++++ E     V  L R+ +GP  L  L  G  R +  + + +       + 
Sbjct: 183 IKEGRNRQVRRMLEAVGHPVVSLKRVRFGPLTLSGLQEGRWRRLEPREIEQLRRAAGAKR 242


>gi|293375505|ref|ZP_06621784.1| pseudouridylate synthase [Turicibacter sanguinis PC909]
 gi|325844949|ref|ZP_08168314.1| pseudouridine synthase B, ribosomal large subunit [Turicibacter sp.
           HGF1]
 gi|292645905|gb|EFF63936.1| pseudouridylate synthase [Turicibacter sanguinis PC909]
 gi|325488999|gb|EGC91388.1| pseudouridine synthase B, ribosomal large subunit [Turicibacter sp.
           HGF1]
          Length = 255

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 76/254 (29%), Positives = 123/254 (48%), Gaps = 2/254 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E++I   +V VN  ++      V   + IEV+GVPL++ ++ 
Sbjct: 2   ERLQKVIAQAGIASRRKAEQLILDGKVTVNDKVVRELGTKVTGKEKIEVEGVPLQREKKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L+     + T   +   R+ +      +  RV  VGRLD +T G+LL+TNDG  A  
Sbjct: 62  YYVLHKPRGYVSTVSDELGRRTVLDFFADRVSERVYPVGRLDYDTSGVLLMTNDGEFANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTV 191
           +  PS +  +VY  R  G V  + L    KGI I G        TL +    N  + V +
Sbjct: 122 MMHPSGEIDKVYLARVKGIVLPENLKPFGKGIEIDGYKTKPASATLVSVDKKNQSSLVRL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+  ++KK+F+   + V +L R  +G   +  L AG  R ++   ++  L      
Sbjct: 182 TIHEGRYHQVKKMFDAIGFPVKKLRREQFGTIDVQGLAAGEFRPLTPHEVKTLLTAANST 241

Query: 252 EAQVNLDAPIYSSE 265
           + +  L        
Sbjct: 242 QVKKKLKFNKMRQF 255


>gi|295398585|ref|ZP_06808617.1| ribosomal large subunit pseudouridine synthase B [Aerococcus
           viridans ATCC 11563]
 gi|294973186|gb|EFG48981.1| ribosomal large subunit pseudouridine synthase B [Aerococcus
           viridans ATCC 11563]
          Length = 240

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 83/240 (34%), Positives = 122/240 (50%), Gaps = 3/240 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRRE E++IA  RVKVNG ++      V + D IEVD VP+ K E  
Sbjct: 2   ERLQKVMAHAGVASRRESEKLIAAGRVKVNGEVVRELGYKVSNNDRIEVDQVPIYKEEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     +++   D   R  V D  P I  R+  VGRLD NT GLLLLTNDG  A  
Sbjct: 62  YYVFYKPIG-VISAVKDDKDRKVVTDFFPGIEQRIYPVGRLDYNTSGLLLLTNDGEFANT 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           L  P  +  +VY  +  G +  ++   L++G+ I G+     Q  +    +      + +
Sbjct: 121 LMHPRYEINKVYVAKVEGVITGEERKQLERGVEIDGVKTAPAQAKILSVDKDKKTTIIEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++K+ E     V +L R  YG   L  L  G +R + K  + E L     +
Sbjct: 181 VIHEGRNRQVRKMLEAVGHPVTKLKRERYGFLDLKGLKPGDSRTLLKHEIEELLANAKKK 240


>gi|314933670|ref|ZP_07841035.1| pseudouridine synthase RluB [Staphylococcus caprae C87]
 gi|313653820|gb|EFS17577.1| pseudouridine synthase RluB [Staphylococcus caprae C87]
          Length = 245

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 70/241 (29%), Positives = 130/241 (53%), Gaps = 3/241 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +R+ K IA +G  SRR+ E +I + +VKVNG ++      V  +D +EV+G+ + +
Sbjct: 2   SKELERLQKRIANSGYTSRRKAETLITEGKVKVNGQVVTELGTKVSHSDTVEVEGIKIEQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ++  +  Y     ++T+ SD  GR  V D    I +R+  VGRLD +T G+LLLTNDG 
Sbjct: 62  EDKMYILFYKPT-QVITSVSDDLGRKVVTDYFEDIETRIYPVGRLDYDTSGVLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNA 187
              ++  P     + Y  +  G + ++++  L++GI ++         ++    ++ +  
Sbjct: 121 FTNLMTHPRYHIKKKYVAKLKGYLMREQVKELEQGIELEDGFTQPAQVKIKRQDKEKNTT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V + + EG+NR+++++FE+F  +VN+L RI +GP  L  L AG  R ++   ++     
Sbjct: 181 LVEITISEGRNRQVRRMFEYFGHEVNKLTRIQFGPLDLKGLNAGEGRVLTPHEVKTLRHL 240

Query: 248 H 248
            
Sbjct: 241 A 241


>gi|319946464|ref|ZP_08020701.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           australis ATCC 700641]
 gi|319747432|gb|EFV99688.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           australis ATCC 700641]
          Length = 242

 Score =  193 bits (490), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 79/240 (32%), Positives = 128/240 (53%), Gaps = 3/240 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTVNGKVVRELATTIKSGDKVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRPTVIDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGLANKENLRPLTRGVTIDGKKTKPATYEILKVDPEKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE     V++L R  +G   +  L  G  R ++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFEAVGLLVDKLSRTQFGNLDVSGLRPGEYRRLNKKEISQLHTLAVTK 239


>gi|116512118|ref|YP_809334.1| ribosomal large subunit pseudouridine synthase B [Lactococcus
           lactis subsp. cremoris SK11]
 gi|116107772|gb|ABJ72912.1| ribosomal large subunit pseudouridine synthase B [Lactococcus
           lactis subsp. cremoris SK11]
          Length = 239

 Score =  193 bits (490), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 73/240 (30%), Positives = 122/240 (50%), Gaps = 3/240 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K +A AG+ASRR+ E +I   +V VN + +      V + D +EV+GV +   E  
Sbjct: 1   MRINKYLAHAGVASRRKAEELILAGKVTVNNVPMTNLGYQVSTGDVVEVNGVAVYNEEPV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      + +   D   ++   D +P +  R+  VGRLD +T GLLLLTNDG    +
Sbjct: 61  YYLLNKPRGYISSVRDDKGRQTV-MDLMPQVKERIYPVGRLDWDTSGLLLLTNDGEFTNM 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  PS    +VY  +  GQ +++ L  L  G+ I+G      +  +  Q+   +++ V++
Sbjct: 120 MTHPSHGVDKVYVAKVEGQANKENLRPLTLGMTIEGKKVSPARYEIIKQEKTKNHSIVSL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+F      V +L RI YG   L  L  G  R +SKK + + +     +
Sbjct: 180 TIHEGQNHQVKKMFAAAGLPVQKLSRIQYGTLTLDGLPTGQFRRLSKKEVSQLINAAQGK 239


>gi|218896501|ref|YP_002444912.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           G9842]
 gi|228900151|ref|ZP_04064384.1| Pseudouridine synthase [Bacillus thuringiensis IBL 4222]
 gi|228907203|ref|ZP_04071064.1| Pseudouridine synthase [Bacillus thuringiensis IBL 200]
 gi|228938683|ref|ZP_04101288.1| Pseudouridine synthase [Bacillus thuringiensis serovar berliner
           ATCC 10792]
 gi|228964544|ref|ZP_04125654.1| Pseudouridine synthase [Bacillus thuringiensis serovar sotto str.
           T04001]
 gi|228971565|ref|ZP_04132189.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228978176|ref|ZP_04138554.1| Pseudouridine synthase [Bacillus thuringiensis Bt407]
 gi|218545922|gb|ACK98316.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           G9842]
 gi|228781648|gb|EEM29848.1| Pseudouridine synthase [Bacillus thuringiensis Bt407]
 gi|228788224|gb|EEM36179.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228795144|gb|EEM42640.1| Pseudouridine synthase [Bacillus thuringiensis serovar sotto str.
           T04001]
 gi|228821059|gb|EEM67079.1| Pseudouridine synthase [Bacillus thuringiensis serovar berliner
           ATCC 10792]
 gi|228852424|gb|EEM97217.1| Pseudouridine synthase [Bacillus thuringiensis IBL 200]
 gi|228859557|gb|EEN03984.1| Pseudouridine synthase [Bacillus thuringiensis IBL 4222]
 gi|326939191|gb|AEA15087.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           thuringiensis serovar chinensis CT-43]
          Length = 242

 Score =  193 bits (490), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 74/242 (30%), Positives = 127/242 (52%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     + +   D        D  P I  R+  +GRLD +T G+LL+TNDG  A +
Sbjct: 62  YFLLYKPTGVISSVSDDKGRSVVT-DFFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANI 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++        V + +       A V +
Sbjct: 121 LMHPKYKVEKTYVAKIKGPLTGEKIRMLERGVALEDGKTAPAHVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++   +++       +
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELTPHEVKQLRALASTK 240

Query: 252 EA 253
             
Sbjct: 241 PR 242


>gi|322385923|ref|ZP_08059564.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           cristatus ATCC 51100]
 gi|321270038|gb|EFX52957.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           cristatus ATCC 51100]
          Length = 273

 Score =  193 bits (490), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 83/245 (33%), Positives = 130/245 (53%), Gaps = 3/245 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E     R++K IA AGIASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+ 
Sbjct: 26  ERTISMRINKYIAHAGIASRRKAEELIKQGLVTVNGQVVRELATTIKSGDRVEVEGQPI- 84

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             E    +L +KP G++++ +D  GR TV D LP +  R+  VGRLD +T G L+LTNDG
Sbjct: 85  YNEEKVYYLLNKPRGVISSVTDDKGRKTVVDLLPQVKERIYPVGRLDWDTSGALILTNDG 144

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSN 186
                +  P  +  +VY  R  G  +++ L  L +G+VI+G         +       + 
Sbjct: 145 DFTDEMIHPRNEIDKVYVARVKGVANKEVLRPLTRGLVIEGKKTKPAVYEILKVDPVKNR 204

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + V + + EG+N ++KK+FE     V++L R  +G   L  L  G  R +SKK + +   
Sbjct: 205 SVVQLTIHEGRNHQVKKMFEAVGLPVDKLSRTQFGHLDLTGLKPGEARRLSKKEVSQLHN 264

Query: 247 PHLLE 251
             + +
Sbjct: 265 LAVTK 269


>gi|296875977|ref|ZP_06900036.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           parasanguinis ATCC 15912]
 gi|296433052|gb|EFH18840.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           parasanguinis ATCC 15912]
          Length = 243

 Score =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 77/244 (31%), Positives = 129/244 (52%), Gaps = 3/244 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + + D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATIIKTGDQVEVEGTPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR+TV D L  +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRTTVVDLLSQVPERIYPVGRLDWDTSGVLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGIANKENLRPLTRGVTIDGKKTKPATYEILKVDVEKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE     V++L R  +G   +  L  G  R ++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFEAVGLLVDKLSRTQFGNLDVSGLRPGEYRRLNKKEISQLHNLAVTK 239

Query: 252 EAQV 255
             + 
Sbjct: 240 SKKS 243


>gi|314936380|ref|ZP_07843727.1| pseudouridylate synthase [Staphylococcus hominis subsp. hominis
           C80]
 gi|313654999|gb|EFS18744.1| pseudouridylate synthase [Staphylococcus hominis subsp. hominis
           C80]
          Length = 245

 Score =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 74/235 (31%), Positives = 133/235 (56%), Gaps = 3/235 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N   +R+ K IA +G  SRR+ E +I + +VKVNG ++      V S+D +EV+G+ + +
Sbjct: 2   NKDLERLQKRIANSGYTSRRKAETLITEGKVKVNGQVVTELGTKVKSSDTVEVEGIKIEQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ++  +  Y     ++T+ SD  GR+ V D   ++ +R+  VGRLD +T GLLLLTNDG 
Sbjct: 62  EDKIYILFYKPT-QVITSVSDDRGRTVVTDYFKNLEARIYPVGRLDYDTSGLLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNA 187
              ++  P     + Y  +  G + ++++  L++GI ++       QV +    ++ +  
Sbjct: 121 FTNLMTHPRYHIQKKYVAKLKGYLMREEVKALEQGIELEDGFTQPAQVKIKNQNKEKNTT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V + + EG+NR+++++FE FN  V++LIRI +G   L  L AG  R ++   ++
Sbjct: 181 LVEITISEGRNRQVRRMFEHFNHTVDKLIRIEFGNLNLKGLNAGEGRVLTPHEVK 235


>gi|262283235|ref|ZP_06061002.1| ribosomal large subunit pseudouridine synthase B [Streptococcus sp.
           2_1_36FAA]
 gi|262261487|gb|EEY80186.1| ribosomal large subunit pseudouridine synthase B [Streptococcus sp.
           2_1_36FAA]
          Length = 242

 Score =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 78/243 (32%), Positives = 131/243 (53%), Gaps = 3/243 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V +NG ++   A  V + D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTINGQVVRELATLVKTGDKVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ +D  GR TV D LP +  R+  VGRLD +T GLL+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVTDDKGRKTVVDLLPQVKERIYPVGRLDWDTSGLLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGIANKENLLPLTRGVEIDGKKTKPAVYEIIKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+F+    +V++L R  +G   L  L  G +R ++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFQAVGLEVDKLSRTRFGHLDLTGLRPGESRRLNKKEISQLHNLAITK 239

Query: 252 EAQ 254
             +
Sbjct: 240 AGK 242


>gi|110632789|ref|YP_672997.1| pseudouridine synthase, Rsu [Mesorhizobium sp. BNC1]
 gi|110283773|gb|ABG61832.1| Pseudouridine synthase, Rsu [Chelativorans sp. BNC1]
          Length = 466

 Score =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 158/353 (44%), Positives = 206/353 (58%), Gaps = 1/353 (0%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           KD+         +R++K +ARAG+ASRR+ E MI   RVKVNG +L   A NV  +D IE
Sbjct: 37  KDEIREDGRTDGERIAKRLARAGLASRRDAEAMIEAGRVKVNGRVLSSPAFNVRPSDRIE 96

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           VD  PL  AERTRL+L+HKP G+VTT  DP+GR T+FD LP    R+I+VGRLDINTEGL
Sbjct: 97  VDDEPLPAAERTRLFLFHKPAGVVTTTRDPEGRRTIFDTLPEGLPRLITVGRLDINTEGL 156

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           +LLTNDGGLAR LELPST WLR YRVR HG+VD   L  L+KGI + G+ YG +  +LD 
Sbjct: 157 ILLTNDGGLARALELPSTGWLRRYRVRVHGKVDPKALAELEKGIAVDGVFYGAITASLDR 216

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           Q+GSNAW+T+GLREGKNRE+K V      +V RLIR+SYGPFQLG L  G+  EV  + L
Sbjct: 217 QQGSNAWLTLGLREGKNREVKNVLGALGLEVTRLIRVSYGPFQLGDLPEGAVLEVKGRTL 276

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+QLG  L+E+A  + +API         R        +      +  +      K    
Sbjct: 277 RDQLGERLIEQAGADFEAPIAIPFANKPVRAERRKPEEEKRKTGLEE-NAGRQERKPANR 335

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                 ++  +   +       F        +   + P   SK +    S ++
Sbjct: 336 RKSREEKHEEARDRLQTKRPDDFKGKGSAAHKGKDQRPPRISKTARPEKSGQE 388



 Score = 47.5 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 23/132 (17%), Positives = 36/132 (27%), Gaps = 17/132 (12%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE   +  R++L     ++ +    A     +                  RM  +S    
Sbjct: 339 REEKHEEARDRLQTKRPDDFKGKGSAAHKGKDQRPPRISKTARPEKSGQERMSGDSKA-- 396

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHS-----------SFLSDSGQREENHRRSPSFP 342
               +     PV RR+ ASNVWMA G                            R+    
Sbjct: 397 ----EGPTRAPVERRSRASNVWMAPGARPVGKKRAEEASKDAEKKPRAGRPATGRAERRD 452

Query: 343 SKRSLRRTSAKK 354
             R  R    ++
Sbjct: 453 GDRPTRPGKGRR 464


>gi|15606629|ref|NP_214009.1| hypothetical protein aq_1464 [Aquifex aeolicus VF5]
 gi|3915445|sp|O67444|Y1464_AQUAE RecName: Full=Uncharacterized RNA pseudouridine synthase aq_1464;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|2983856|gb|AAC07410.1| hypothetical protein aq_1464 [Aquifex aeolicus VF5]
          Length = 249

 Score =  193 bits (489), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 84/234 (35%), Positives = 126/234 (53%), Gaps = 1/234 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R++K ++ AG+ASRR+ E++I + RVKVNG ++    V V    D +EVDG P++   +
Sbjct: 4   VRINKFLSEAGVASRRKAEKLILEGRVKVNGEVVRSLGVKVNPEVDIVEVDGKPVKPQRK 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      L      PDGR T+ + +  I  RV  VGRLD NTEGLL+LTNDG LA 
Sbjct: 64  RYIILNKPCCYLTQLGRSPDGRKTIEELIKDIPERVFPVGRLDYNTEGLLILTNDGELAN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  +VY     G+VDQ  L  +K+GI ++        + +   +G N  + + 
Sbjct: 124 RILHPRYKLPKVYLALVEGKVDQKTLKRMKQGIELEDGFAKPDNIRIVRYEGKNTLLEIT 183

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
             EG+   +K+    F  KV RL RI+ GP +LG L  G  RE+++  L +   
Sbjct: 184 FHEGRKHLVKRFLGAFGHKVKRLKRIAIGPIKLGKLSPGKWRELNQGELAQLFK 237


>gi|94499453|ref|ZP_01305990.1| Hypothetical protein yjbC [Oceanobacter sp. RED65]
 gi|94428207|gb|EAT13180.1| Hypothetical protein yjbC [Oceanobacter sp. RED65]
          Length = 376

 Score =  193 bits (489), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 69/348 (19%), Positives = 128/348 (36%), Gaps = 10/348 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N +  R++K I+ +GI SRRE +R I Q  V +NG   E     V   D ++V+G  +  
Sbjct: 3   NDSTTRLNKYISESGICSRREADRYIEQGNVYINGKRAEV-GDRVAPGDTVKVNGQIIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E            +    +                +R+  +GRLD +++GL+ LTN+G 
Sbjct: 62  QEPEDFVFIALNKPVGIVSTTESSERNNIVRFVGHSTRIFPIGRLDKDSQGLIFLTNNGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  +  + +  +  G+ I G      +V    +K S    
Sbjct: 122 LVNKILRAGNDHEKEYLVEVNKPIRDNFIEGMANGVPILGTMTKKCKV----KKESPTVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L EG NR+I+++ E+F + V  L R+      L  L  G  R++++K L        
Sbjct: 178 RITLVEGLNRQIRRMCEYFGYDVVALERVRIMNVDLKGLATGDWRDLTQKELNGIFDAIK 237

Query: 250 LEEAQVNLDAPIYSSETLVR-----DRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
              ++                    ++P   +       +  K+  ++ G  K KK +  
Sbjct: 238 DSSSEAPAGRKTTQKRGGKPGGSGQNKPGNKTNSKKPAAKASKSGPKRGGPHKAKKTSGN 297

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            + ++             S    +G +          PS +       
Sbjct: 298 PNTKHPPKPPGGKPSGKPSPKGKAGGKPSGKPMKGGKPSPKGKAGGKP 345


>gi|156740189|ref|YP_001430318.1| pseudouridine synthase [Roseiflexus castenholzii DSM 13941]
 gi|156231517|gb|ABU56300.1| pseudouridine synthase [Roseiflexus castenholzii DSM 13941]
          Length = 556

 Score =  193 bits (489), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 101/363 (27%), Positives = 155/363 (42%), Gaps = 27/363 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV+A AGIASRR+ E  IA  RV VNG ++      V    D I VDG P+ K   
Sbjct: 4   ERLQKVLASAGIASRRDCEEYIAAGRVMVNGKVVRIPGTRVDPEHDEILVDGKPIGKIHH 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + HKP G+V+T  DP GR TV  +L ++  R+  VGRLD ++EGLLLLT+DG L +
Sbjct: 64  RTYVMLHKPAGVVSTTDDPHGRPTV-VDLVNLPQRLFPVGRLDYDSEGLLLLTDDGELTQ 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS Q  + Y+V  +     + L   + G+ + G+      V L  +    AWV V 
Sbjct: 123 KLTHPSYQVEKEYQVLLNDAPSPNALRAWRTGVELDGVKTAPAWVELIERTPEGAWVRVI 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L EG+ R+I++V     ++V RLIR+  GP  LG L +G+ R ++ + +           
Sbjct: 183 LHEGRKRQIREVARLLGYEVRRLIRVREGPLALGDLPSGTWRFLTDEEVDMLREHAERNA 242

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ--------------------- 291
           A  + + P    +  ++          +   R+ +   +                     
Sbjct: 243 AVADAERPRRREQDEMKAVGGRRLRRINPSARLLQKGEKVTETTLPELDEAIGSEKGIPS 302

Query: 292 ----KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
                  +  ++                   G  S   +D G    + RR       R  
Sbjct: 303 IGEEGRKVRDKEAPHRNASPARDFRRDDRGSGFRSDRRNDRGSGPRDFRRDDRGNGPRDF 362

Query: 348 RRT 350
           RR 
Sbjct: 363 RRD 365


>gi|138895852|ref|YP_001126305.1| pseudouridylate synthase [Geobacillus thermodenitrificans NG80-2]
 gi|134267365|gb|ABO67560.1| Pseudouridylate synthase [Geobacillus thermodenitrificans NG80-2]
          Length = 243

 Score =  193 bits (489), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 82/231 (35%), Positives = 124/231 (53%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIARAGIASRR+ E MI Q RVKVNG ++    V V   D +EVDG+P+ + E  
Sbjct: 2   ERLQKVIARAGIASRRKAEEMILQGRVKVNGRVVTELGVKVGPRDDVEVDGIPVEREEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     + +   +  GR  V D    I  R+  +GRLD +T GLLLLTNDG  A +
Sbjct: 62  YYLLYKPRGVISSVKDE-KGRKVVTDFFKDIHQRIYPIGRLDYDTSGLLLLTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA--WVTV 191
           L  P  +  +VY  +  G   +++L   +KG++++       +V L +         V +
Sbjct: 121 LMHPRYEIEKVYVAKVKGIPTREQLKQPEKGVLLEDGITAPAKVKLLSADRKKRAAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EG+NR+++++FE    +V +L R  Y    L  L  G  RE+S   ++
Sbjct: 181 SIHEGRNRQVRRMFEAIGCEVLKLKRERYAFLDLKGLRPGEYRELSPHEVK 231


>gi|90419975|ref|ZP_01227884.1| pseudouridine synthase, rRNA [Aurantimonas manganoxydans SI85-9A1]
 gi|90336016|gb|EAS49764.1| pseudouridine synthase, rRNA [Aurantimonas manganoxydans SI85-9A1]
          Length = 497

 Score =  193 bits (489), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 153/354 (43%), Positives = 208/354 (58%), Gaps = 13/354 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K +ARAGIASRR+ E MIA  RVK+NG +L+  AV V ++D IE+D  PL   ERT
Sbjct: 69  MRIAKRLARAGIASRRDAEGMIADGRVKLNGKVLDTPAVVVTASDRIEIDNAPLPAIERT 128

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWL+HK  G VTT+ DP+GR T+FD LPS   RV++VGRLDINTEGLLLLTNDGGLAR+
Sbjct: 129 RLWLFHKAAGTVTTNRDPEGRPTIFDRLPSDMPRVLTVGRLDINTEGLLLLTNDGGLARI 188

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP+T WLR YRVR HG + Q +L+ L++GI I G+ YG ++ T+D ++GSN W+T+GL
Sbjct: 189 LELPATGWLRRYRVRAHGAITQARLDELRQGIAIDGVFYGAIEATMDREQGSNVWLTLGL 248

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNRE+KKV      +VNRLIR+S+GPFQLG L  GS +E+  ++LR+QLG  L+EE+
Sbjct: 249 REGKNREVKKVLAHLGLEVNRLIRLSFGPFQLGDLKEGSVQEIKGRMLRDQLGERLIEES 308

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPD-----------DFTRMKKNSSQKNGLSKQKKLA 302
             + DAP+    +                            +  + + +++ L +    A
Sbjct: 309 GADFDAPVAKPFSNRPVEAERTERPKKADEWISASETAPNKKRVREAKREDALGRLDTRA 368

Query: 303 TPVHR--RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               R  R                        +         S       + K+
Sbjct: 369 GRPERNDRGDRKPYGERPAKRFEGPKKPYGDRDAAGGRDDAASPPKRPIDAPKR 422


>gi|289550733|ref|YP_003471637.1| Ribosomal large subunit pseudouridine synthase B [Staphylococcus
           lugdunensis HKU09-01]
 gi|289180265|gb|ADC87510.1| Ribosomal large subunit pseudouridine synthase B [Staphylococcus
           lugdunensis HKU09-01]
          Length = 245

 Score =  193 bits (489), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 72/235 (30%), Positives = 127/235 (54%), Gaps = 3/235 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +R+ K IA +G  SRR+ E +I + +VKVNG ++      V  +D +EV+G+ +  
Sbjct: 2   SKELERLQKRIANSGYTSRRKAETLITEGKVKVNGEVVTELGTKVKPSDQVEVEGIKME- 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E     L+HKP  ++T+ SD  GR+ V D    + +R+  VGRLD +T G+LLLTNDG 
Sbjct: 61  QEDKIYILFHKPAQVITSVSDDRGRTVVTDYFKDLDTRIYPVGRLDYDTSGVLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNA 187
              ++  P     + Y  +  G + ++++  L+ GI ++         ++    +  +  
Sbjct: 121 FTNLMTHPRYHIPKTYVAKLKGYLMREEVKALEAGIELEDGLTQPATVKIKRQDKDKNTT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V + + EG+NR+++++FE F   VN+L RI +G   L  L AG  R ++   ++
Sbjct: 181 LVEITISEGRNRQVRRMFEHFGHSVNKLTRIQFGSLNLKGLNAGEGRVLTPHEVK 235


>gi|118590702|ref|ZP_01548103.1| pseudouridylate synthase, subunit B protein [Stappia aggregata IAM
           12614]
 gi|118436678|gb|EAV43318.1| pseudouridylate synthase, subunit B protein [Stappia aggregata IAM
           12614]
          Length = 520

 Score =  193 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 158/347 (45%), Positives = 209/347 (60%), Gaps = 2/347 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N   +R++KV+AR G+ SRRE E  I   RV++NG LL   AV V   D + VDG PL  
Sbjct: 99  NDRGERIAKVMARVGLCSRREAEVWIENGRVELNGKLLTTPAVTVTPDDKVVVDGQPLPM 158

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV++VGRLDINTEGLLLLTNDGG
Sbjct: 159 RERTRLWLYHKPRGLVTTNKDPEGRPTVFERLPDDLPRVLTVGRLDINTEGLLLLTNDGG 218

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LARVLELP+T WLR YRVR  G+V Q  L+ LK GI I+G+ YG ++ TLD ++G+N W+
Sbjct: 219 LARVLELPATGWLRRYRVRAFGKVTQPDLDTLKDGIAIEGVLYGAIEATLDKEQGNNVWM 278

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           TVGLREGKNRE+K+V E     VNRLIR+SYGPFQL  L  G  RE+  ++LR+QLG  L
Sbjct: 279 TVGLREGKNREVKRVLEHLGLAVNRLIRLSYGPFQLMDLPEGDVREIRGRVLRDQLGDAL 338

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
            EEA  + DAPI+ +     ++    ++         +    ++G  +         R  
Sbjct: 339 AEEAGADFDAPIFHAPKPEAEKKPAGAKRGGSRDGGNREGRDRDGGGRDGGGRDGGKREG 398

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRS--PSFPSKRSLRRTSAKK 354
                  A+   S        + E + +       + +  R+ +  +
Sbjct: 399 GQGRWMTAREGRSETDRKRAAKNERNEQREERKKGAGKGPRKNAGPR 445


>gi|121535833|ref|ZP_01667633.1| pseudouridine synthase [Thermosinus carboxydivorans Nor1]
 gi|121305605|gb|EAX46547.1| pseudouridine synthase [Thermosinus carboxydivorans Nor1]
          Length = 241

 Score =  193 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 83/240 (34%), Positives = 121/240 (50%), Gaps = 4/240 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAE 71
           P+R+ K++++AGIASRR  E++I   RV VNG ++      V    D + VDG P+   E
Sbjct: 2   PERLQKILSQAGIASRRAAEKLILDGRVAVNGKIITELGAKVDWPRDRVTVDGKPIAA-E 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                L +KP G++T+  DP GR TV D L  +  RV  VGRLD NTEGLLLLTNDG L 
Sbjct: 61  APVYILLNKPKGVITSLKDPRGRKTVIDLLKDVPERVYPVGRLDYNTEGLLLLTNDGDLT 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA--WV 189
             L  PS +  + Y  +  G  ++++L+ L+ GI +         V L           V
Sbjct: 121 HALTHPSHEIKKTYVSKIAGLPNEEQLDRLRAGIKLSDGMTSPAAVRLLDFDPVKQVAVV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + + EG+NR+++++FE     V  L R  Y    L  L  G  R ++   +        
Sbjct: 181 EITIHEGRNRQVRRMFEAIGHPVKSLKRTKYAFLTLTGLKRGEYRRLTPDEVASLKKLAQ 240


>gi|153010359|ref|YP_001371573.1| RNA-binding S4 domain-containing protein [Ochrobactrum anthropi
           ATCC 49188]
 gi|151562247|gb|ABS15744.1| RNA-binding S4 domain protein [Ochrobactrum anthropi ATCC 49188]
          Length = 576

 Score =  193 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 168/347 (48%), Positives = 225/347 (64%), Gaps = 11/347 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PL+
Sbjct: 53  QEDTGERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLK 112

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP+   RV+SVGRLDINTEGLLLLTNDG
Sbjct: 113 QTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPAEMPRVLSVGRLDINTEGLLLLTNDG 172

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++ TL+ ++G+N W
Sbjct: 173 GLSRVLELPSTGWLRRYRVRAHGKVTQVQLDELKNGIAVDGVFYGSIEATLEREQGANVW 232

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  +ILR+QLG  
Sbjct: 233 ISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRILRDQLGDK 292

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK-----------NSSQKNGLSK 297
           L+E++  + DAP+ +  +    +     +V D+    ++           +S Q+     
Sbjct: 293 LIEDSGADFDAPVLNEFSNAAVQGRTRRDVEDEGEEGERRRGPREREWISSSPQRRRGRD 352

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
            K       RR   +NVWMA G      + + +     R+ P   +K
Sbjct: 353 DKGAEKVEPRRRGNANVWMAPGARPKGENAAAKPARVERQVPHRSAK 399



 Score = 40.5 bits (93), Expect = 0.39,   Method: Composition-based stats.
 Identities = 14/137 (10%), Positives = 32/137 (23%), Gaps = 8/137 (5%)

Query: 226 GTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
           G L     R   ++  R++ G     +            +    +        P+   + 
Sbjct: 402 GDLQMRPRRAGDEEQGRDEGGERRYNKRPEGRFDKDARPQRPRPEGNRSEEGRPERREQR 461

Query: 286 KKNSSQKNGLSKQKKLATPVHRRN--------LASNVWMAKGIHSSFLSDSGQREENHRR 337
           +    ++    +++        R                  G        +  R+     
Sbjct: 462 EDGRKERRPGKRERAELRDAEGRTVEHGKGGFEGRKTGKPGGPRGEGRFGASDRDTRSGP 521

Query: 338 SPSFPSKRSLRRTSAKK 354
             S P  +S R     K
Sbjct: 522 RSSGPGNKSRRFDDGSK 538



 Score = 39.4 bits (90), Expect = 0.80,   Method: Composition-based stats.
 Identities = 9/113 (7%), Positives = 26/113 (23%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R       +            +    V  +    S       +M+   +      + +  
Sbjct: 363 RRGNANVWMAPGARPKGENAAAKPARVERQVPHRSAKFSGDLQMRPRRAGDEEQGRDEGG 422

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               ++R        A+        +  +     RR      ++  R    ++
Sbjct: 423 ERRYNKRPEGRFDKDARPQRPRPEGNRSEEGRPERREQREDGRKERRPGKRER 475


>gi|228476152|ref|ZP_04060860.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           hominis SK119]
 gi|228269975|gb|EEK11455.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           hominis SK119]
          Length = 245

 Score =  193 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 74/235 (31%), Positives = 132/235 (56%), Gaps = 3/235 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N   +R+ K IA +G  SRR+ E +I + +VKVNG ++      V S+D +EV+G+ + +
Sbjct: 2   NKDLERLQKRIANSGYTSRRKAETLITEGKVKVNGQVVTELGTKVKSSDTVEVEGIKIEQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ++  +  Y     ++T+ SD  GR+ V D    + +R+  VGRLD +T GLLLLTNDG 
Sbjct: 62  EDKIYILFYKPT-QVITSVSDDRGRTVVTDYFKDLEARIYPVGRLDYDTSGLLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNA 187
              ++  P     + Y  +  G + ++++  L++GI ++       QV +    ++ +  
Sbjct: 121 FTNLMTHPRYHIQKKYVAKLKGYLMREEVKSLEQGIELEDGFTQPAQVKIKNQNKEKNTT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V + + EG+NR+++++FE FN  V++LIRI +G   L  L AG  R ++   ++
Sbjct: 181 LVEITISEGRNRQVRRMFEHFNHTVDKLIRIEFGNLNLKGLNAGEGRVLTPHEVK 235


>gi|229074764|ref|ZP_04207783.1| Pseudouridine synthase [Bacillus cereus Rock4-18]
 gi|229096063|ref|ZP_04227037.1| Pseudouridine synthase [Bacillus cereus Rock3-29]
 gi|229102175|ref|ZP_04232885.1| Pseudouridine synthase [Bacillus cereus Rock3-28]
 gi|229115019|ref|ZP_04244430.1| Pseudouridine synthase [Bacillus cereus Rock1-3]
 gi|228668435|gb|EEL23866.1| Pseudouridine synthase [Bacillus cereus Rock1-3]
 gi|228681245|gb|EEL35412.1| Pseudouridine synthase [Bacillus cereus Rock3-28]
 gi|228687355|gb|EEL41259.1| Pseudouridine synthase [Bacillus cereus Rock3-29]
 gi|228708362|gb|EEL60516.1| Pseudouridine synthase [Bacillus cereus Rock4-18]
          Length = 242

 Score =  193 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 75/242 (30%), Positives = 127/242 (52%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     + +   D        D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 62  YFLLYKPTGVISSVSDDKGRNVVT-DFFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++        V + +       A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGEKIRMLERGVTLEDGKTAPANVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++   +++       +
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELTPHEVKQLRALASTK 240

Query: 252 EA 253
             
Sbjct: 241 PR 242


>gi|311030759|ref|ZP_07708849.1| pseudouridine synthase [Bacillus sp. m3-13]
          Length = 242

 Score =  193 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 76/242 (31%), Positives = 128/242 (52%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGIASRR+ E +I + +V+VN  +++   V V   D IEV+G+P+ + +  
Sbjct: 2   ERLQKVIAHAGIASRRKAEELIKEGKVRVNDKVVKELGVKVNPNDKIEVEGIPVEREKPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     + +   D  GR    D  P I  R+  VGRLD +T GLLL+TNDG  A V
Sbjct: 62  YFLLYKPRGVISSVS-DDKGRKVATDFFPYIEERIYPVGRLDYDTSGLLLMTNDGEFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           L  P+++  +VY  +  G   ++ +  L++GI ++       ++ L    +  + +   +
Sbjct: 121 LMHPASEVEKVYVAKLKGIPSREAIKSLERGIKLEDGKTAPARIKLLSMERTKNTSIFEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE     V +L R  YG   L  L AG  RE++   +++        
Sbjct: 181 SIHEGRNRQVRRMFEAIGHPVMKLKRERYGFLNLHGLSAGEARELTPHEVKQLRVMATKP 240

Query: 252 EA 253
           + 
Sbjct: 241 KK 242


>gi|158320609|ref|YP_001513116.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
 gi|158140808|gb|ABW19120.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
          Length = 234

 Score =  193 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 75/229 (32%), Positives = 113/229 (49%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ASRR+ E +I+  RVKVNG ++      V    D I VD   +   ER
Sbjct: 1   MRLQKFLAANGVASRRKSEELISSGRVKVNGNIITEMGYKVDLDIDKISVDNKDIILQER 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G VT             +L  +  R+  VGRLD NT GLL+LTNDG L  
Sbjct: 61  KVYILLNKPTGYVT-TVSEQFNRKKVTDLVDVPYRIFPVGRLDYNTSGLLILTNDGELTY 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  +VY  +  G   ++ L   + G+ I+       ++ +  +   +  V V 
Sbjct: 120 KLTHPKFKVEKVYIAKVKGIPTKEALEAFENGLKIEDYITAPAKIKILKEINQHTLVEVR 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +REGKNR+++K+ E     V  L RI+ G   LG L  G+ R  +++ +
Sbjct: 180 IREGKNRQVRKMCEAIGHPVVELKRIAMGRIHLGNLDVGNWRYFTEREI 228


>gi|311693777|gb|ADP96650.1| pseudouridine synthase family 1 protein [marine bacterium HP15]
          Length = 312

 Score =  192 bits (488), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 60/308 (19%), Positives = 113/308 (36%), Gaps = 5/308 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++K I+ +G+ SRRE +R I Q  V +NG         V+  D ++V+G  +     
Sbjct: 6   STRLNKYISESGMCSRREADRYIEQGNVYINGKRATV-GDQVLPGDTVKVNGQVIEPRAE 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L        +    +                 R+  +GRLD +++GL+ +T++G L  
Sbjct: 65  EDLVFIALNKPVGIVSTTDSAEKHNIQRFVGHSERIFPIGRLDKDSQGLIFMTSNGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V     V ++ +  +  G+ I G      +V+ +    S     + 
Sbjct: 125 KILRAGNNHEKEYLVTVDKPVTREFVEGMANGVPILGTMTKKCKVSRE----SRFVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E+F ++V +L RI      L  L  G  R++S+K L           
Sbjct: 181 LVQGLNRQIRRMCEYFGYEVTKLERIRIMNVSLKGLAVGQWRDLSEKELAGLFDAIRDSS 240

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
           ++    A   + +             P   +   K    +    K K             
Sbjct: 241 SEAPPGAGKPAKKKSGTKAKPKPDRKPGSASTPGKPGGARRPGPKGKPAPGKKPASGKRP 300

Query: 313 NVWMAKGI 320
                +  
Sbjct: 301 KGGKPRQK 308


>gi|296131694|ref|YP_003638941.1| pseudouridine synthase [Thermincola sp. JR]
 gi|296030272|gb|ADG81040.1| pseudouridine synthase [Thermincola potens JR]
          Length = 244

 Score =  192 bits (488), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 68/235 (28%), Positives = 115/235 (48%), Gaps = 4/235 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
               QR+ KV+A  G+ +R+E +++I +++V+VNG L +   ++V    D I V+G P+ 
Sbjct: 3   EKERQRLDKVLAHMGLGTRKEAKKLIKERKVEVNGELAQDPGLHVRPGQDRIVVNGEPVE 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             +   L L      L  T  +         +          VGRLD +TEGLLLLTNDG
Sbjct: 63  YRQFVYLMLNKPQGVLSATGDESGQVVVDLLSPNYQSFHPFPVGRLDKDTEGLLLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNA 187
            LA  L  P     + Y     G V Q+ + + ++G+++          + +  + G  +
Sbjct: 123 HLAHRLLSPKKHVPKTYYATVSGTVTQEDVEMFRQGVILDDGYRTLPGCLKIL-RSGPES 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            V + + EGK  ++K++F+    KV  L RI+ GP  L   L  G  RE++++ +
Sbjct: 182 EVELTIYEGKYHQVKRMFQAVGKKVTYLKRIAMGPLTLDNTLKPGEYRELTEEEI 236


>gi|218264461|ref|ZP_03478294.1| hypothetical protein PRABACTJOHN_03990 [Parabacteroides johnsonii
           DSM 18315]
 gi|218221954|gb|EEC94604.1| hypothetical protein PRABACTJOHN_03990 [Parabacteroides johnsonii
           DSM 18315]
          Length = 249

 Score =  192 bits (488), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 56/241 (23%), Positives = 112/241 (46%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           MK K ++ +   P R++K ++ AG+ SRRE +  I    V+VN  ++      +   D +
Sbjct: 1   MKYKEVLADPNEPIRLNKFLSNAGVCSRREADEFIQAGVVQVNDQVVTELGTKITRQDKV 60

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 ++   +  + L      + T+    +  + +     +   R+  VGRLD NT G
Sbjct: 61  LFKDQQVQIESKVYIVLNKPKNCVTTSDDPQERLTVMDLVKNACQERIYPVGRLDRNTTG 120

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  PS +  ++Y V     V  + +  +  G+ ++        ++  
Sbjct: 121 VLLLTNDGDLASKLTHPSFKKKKIYHVWLDKNVSIEDMEKIANGLELEDGEIHADAISYA 180

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++    + V + +  G+NR ++++FE   + V +L R+ +       L  G  R ++++ 
Sbjct: 181 SED-DKSQVGIEIHSGRNRIVRRIFESLGYHVVKLDRVYFAGLTKKNLGRGKWRYLNERE 239

Query: 241 L 241
           +
Sbjct: 240 V 240


>gi|118580486|ref|YP_901736.1| pseudouridine synthase [Pelobacter propionicus DSM 2379]
 gi|118503196|gb|ABK99678.1| ribosomal large subunit pseudouridine synthase B [Pelobacter
           propionicus DSM 2379]
          Length = 271

 Score =  192 bits (488), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 96/268 (35%), Positives = 138/268 (51%), Gaps = 1/268 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K+I++AGIASRR  E MI   RV VNG+++         T D I VDG P++ A +
Sbjct: 3   ERLQKLISQAGIASRRAAEEMILAGRVTVNGLVVTELGSKADPTVDSIAVDGRPVKPASQ 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G +TT  DP+GR  V D LP I  RV  VGRLD NTEGLLLLTNDG  A 
Sbjct: 63  HLYILLNKPAGFMTTLDDPEGRQVVTDLLPEIKERVYPVGRLDYNTEGLLLLTNDGDWAN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + Y VR  G+V Q +++ LK G+ + G      QV L      N W+++ 
Sbjct: 123 KLMHPRHEIEKEYHVRVRGKVHQSQIDQLKNGVDLDGRPTAPAQVRLIKDGEQNDWLSIT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           + EG+NR+++++ E  +  V RL R+ YG  ++  L  G  R +++   R  L P     
Sbjct: 183 IHEGRNRQVRRMCEAVSLSVVRLKRVRYGALEMRGLKPGQHRLLTEAEARALLTPGAGLR 242

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPD 280
           +          +            + P 
Sbjct: 243 SAEAPREKRARNAGQPPRETRGRGKKPT 270


>gi|260893153|ref|YP_003239250.1| pseudouridine synthase [Ammonifex degensii KC4]
 gi|260865294|gb|ACX52400.1| pseudouridine synthase [Ammonifex degensii KC4]
          Length = 251

 Score =  192 bits (488), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 97/247 (39%), Positives = 140/247 (56%), Gaps = 1/247 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV+ARAGIASRR+ E +I   RVKVNG ++++  V V    D IEVDG P++  ER
Sbjct: 4   ERLQKVLARAGIASRRKAEELIVAGRVKVNGQVVDKLGVKVDPERDSIEVDGKPVKLPER 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP G+VTT  DP GR  V D L  I  RV  VGRLD ++EGLLLLTNDG LA 
Sbjct: 64  LVYLAFHKPRGVVTTLHDPQGRPKVADFLKGIKERVFPVGRLDYDSEGLLLLTNDGELAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V   G+V ++KLNLL++GI ++       +V +  +      + + 
Sbjct: 124 RLLHPRFHVPKTYLVWVKGEVGKEKLNLLRRGIKLEDGPTLPAEVRVLRRARGETVLQLT 183

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           +REG+ R+I+++ +    +V RL R++ GP +LG L  G  R ++ + +        L E
Sbjct: 184 IREGRKRQIRRMLKALGCEVLRLKRVAVGPVRLGPLRPGEYRHLTPREVDSLRKAAGLVE 243

Query: 253 AQVNLDA 259
                  
Sbjct: 244 VTKKEFR 250


>gi|229084572|ref|ZP_04216842.1| Pseudouridine synthase [Bacillus cereus Rock3-44]
 gi|228698722|gb|EEL51437.1| Pseudouridine synthase [Bacillus cereus Rock3-44]
          Length = 242

 Score =  192 bits (488), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 80/242 (33%), Positives = 129/242 (53%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG ++      V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKVVTELGTKVTPQDKVEVNNIPLEKEEPI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     + +   D  GR  V D  P I  R+  +GRLD +T G+LL+TNDG  A +
Sbjct: 62  YFLLYKPTGVISSVS-DDKGRKVVTDFFPEIRQRLFPIGRLDYDTSGVLLMTNDGDFANI 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTV 191
           L  P  +  + Y  +  G +  +K+ +L+KG+V++       +V + +       A V +
Sbjct: 121 LMHPKYKVEKTYVAKVKGPLTGEKIRMLEKGVVLEDGKTAPARVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE    KV +L R  Y   + G+L  G  RE+S   +++       +
Sbjct: 181 TIHEGRNRQVRRMFEALGCKVMKLKRERYAFLEAGSLRPGDARELSPHEVKQLRALASTK 240

Query: 252 EA 253
             
Sbjct: 241 PR 242


>gi|229524219|ref|ZP_04413624.1| ribosomal large subunit pseudouridine synthase F [Vibrio cholerae
           bv. albensis VL426]
 gi|229337800|gb|EEO02817.1| ribosomal large subunit pseudouridine synthase F [Vibrio cholerae
           bv. albensis VL426]
          Length = 328

 Score =  192 bits (488), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 73/334 (21%), Positives = 130/334 (38%), Gaps = 9/334 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
              T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR
Sbjct: 2   SQPTEKRLNKFISETGYCSRREADKLIEQGRVTLNGLQPEV-GSKVTDQDEVCIDGKPLR 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ER      +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG
Sbjct: 61  SKERPIYIALNKPTGITCTTERDV--PGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y VR    +  + +  +  G+ I        +VT    + +   
Sbjct: 119 DIVNKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVT----QETQYS 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L   
Sbjct: 175 FRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILAMC 234

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNI--ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                         S +T+ R        S   +  ++ ++N    +G + Q+    P  
Sbjct: 235 EDSSGTEEASRVAQSGDTIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNS 294

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
           ++        +    S              R   
Sbjct: 295 KKAQRRPSSPSSNTTSGSKPTPRTGGTLSLRKSK 328


>gi|242373794|ref|ZP_04819368.1| pseudouridylate synthase [Staphylococcus epidermidis M23864:W1]
 gi|242348531|gb|EES40133.1| pseudouridylate synthase [Staphylococcus epidermidis M23864:W1]
          Length = 245

 Score =  192 bits (488), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 72/241 (29%), Positives = 131/241 (54%), Gaps = 3/241 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +R+ K IA +G  SRR+ E +I + +V VNG ++      V ++D +EV+G+ + +
Sbjct: 2   SKEQERLQKRIANSGYTSRRKAETLITEGKVSVNGQVVTELGTKVSNSDTVEVEGIKIEQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ++  +  Y     ++T+ SD  GR+ V D    I +R+  VGRLD +T G+LLLTNDG 
Sbjct: 62  EDKMYILFYKPT-QVITSVSDDRGRTVVTDYFDDIETRIYPVGRLDYDTSGILLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNA 187
              ++  P     + Y  +  G + ++++  L+KGI ++       QV +    ++ +  
Sbjct: 121 FTNLMTHPRYHIKKKYVAKLKGYLMREEVKELEKGIQLEDGFTQPAQVKIKKQDKEKNTT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V + + EG+NR+++++FE F  +VN+L RI +GP  L  L AG  R ++   ++     
Sbjct: 181 LVEITISEGRNRQVRRMFEHFGHQVNKLTRIQFGPLDLKGLNAGEGRVLTPHEVKTLRHL 240

Query: 248 H 248
            
Sbjct: 241 A 241


>gi|281491795|ref|YP_003353775.1| ribosomal large subunit pseudouridine synthase B [Lactococcus
           lactis subsp. lactis KF147]
 gi|281375509|gb|ADA65019.1| Ribosomal large subunit pseudouridine synthase B [Lactococcus
           lactis subsp. lactis KF147]
          Length = 257

 Score =  192 bits (488), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 72/250 (28%), Positives = 121/250 (48%), Gaps = 3/250 (1%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +            R++K +A AG+ASRR+ E +I   +V VN + +      V + D +E
Sbjct: 7   QKNKPYLTKVKKMRINKYLAHAGVASRRKAEELILAGKVTVNNVSMTNLGYQVSTGDIVE 66

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           V+GV +   E     L      + +   D   ++   D +P +  R+  VGRLD +T GL
Sbjct: 67  VNGVAVYNEEPVYYLLNKPRGYISSVSDDKGRQTV-MDLMPQVKERIYPVGRLDWDTSGL 125

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDG    ++  P     +VY  +  GQ +++ L  L  G+ I+G      +  +  
Sbjct: 126 LLLTNDGEFTNMMTHPRHGVDKVYVAKVEGQANKENLRPLTLGMTIEGKKVSPARYEIIK 185

Query: 182 QK--GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           Q+   +++ V++ + EG+N ++KK+F      V +L RI YG   L  L  G  R +SKK
Sbjct: 186 QEKTKNHSIVSLTIHEGQNHQVKKMFAAAGLPVQKLSRIQYGTLTLDGLPTGQFRRLSKK 245

Query: 240 ILREQLGPHL 249
            + + +    
Sbjct: 246 EVSQLINAAQ 255


>gi|150390402|ref|YP_001320451.1| pseudouridine synthase [Alkaliphilus metalliredigens QYMF]
 gi|149950264|gb|ABR48792.1| pseudouridine synthase [Alkaliphilus metalliredigens QYMF]
          Length = 234

 Score =  192 bits (488), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 81/229 (35%), Positives = 119/229 (51%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K IA  G+ASRR+ E +I Q  V VN  ++      +    DH++V G  ++  E 
Sbjct: 1   MRLQKYIANCGVASRRKSETLIQQGLVTVNDKVVTEMGFKLDVVEDHVKVRGKLIKPTEE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G VTT SD   R TV  +L  +  R+  VGRLD +T G LLLTNDG L  
Sbjct: 61  MIYILLNKPTGFVTTVSDQFDRKTV-TDLVGVSERIFPVGRLDYHTSGFLLLTNDGNLTF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  +VY  +  G+    KL+L +KG+ I+       ++++         V + 
Sbjct: 120 KLTHPKFKVSKVYIAKVKGKPSSSKLSLFEKGLEIEDYVTAPAKISIIKILPHEVIVKIT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           LREGKNR+++K+ +     V  L R S G  QLG L  G  R +++K +
Sbjct: 180 LREGKNRQVRKMCDAIGHPVVELNRESMGDLQLGDLEIGKWRHLTQKEI 228


>gi|149181685|ref|ZP_01860178.1| RluB [Bacillus sp. SG-1]
 gi|148850663|gb|EDL64820.1| RluB [Bacillus sp. SG-1]
          Length = 243

 Score =  192 bits (488), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 81/237 (34%), Positives = 127/237 (53%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E +I + +VKVNG   +     V  TD IEV+G+ + +  + 
Sbjct: 2   ERLQKVIAHAGVASRRKAEELILEGKVKVNGKTEKELGTKVSGTDKIEVNGIQIERENKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     +++  +D   R  V D  P I  R+  VGRLD +T GL+LLTNDG  A +
Sbjct: 62  YYLLYKPRG-VISAVTDDKDRKVVTDFFPYIQERIYPVGRLDYDTSGLILLTNDGEFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVTV 191
           L  P     + Y  R  G   + KL  L+KGI+++       +V +    +K   + V +
Sbjct: 121 LTHPRYNIDKTYVARLKGIPPKFKLKELEKGIMLEDGKTAPAKVKVLKIEKKQDKSIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + EGKNR++K++FE   ++V +L R  +    L  L AG +RE+S   +++     
Sbjct: 181 TIHEGKNRQVKRMFEAIGYQVQKLKRERFAFLDLHGLNAGESRELSPHEVKQLRALA 237


>gi|126650120|ref|ZP_01722353.1| RluB [Bacillus sp. B14905]
 gi|126593292|gb|EAZ87254.1| RluB [Bacillus sp. B14905]
          Length = 243

 Score =  192 bits (488), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 81/237 (34%), Positives = 124/237 (52%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGIASRR+ E++I + +VKVNG ++      V ++D IEV+GV L K ++ 
Sbjct: 2   ERLQKVIAYAGIASRRKAEQLILEGKVKVNGKVIRELGTKVSNSDTIEVEGVKLEKEDKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     +     D  GR TV D    I  R+  VGRLD +T GLLLLTNDG  + +
Sbjct: 62  YFLLYKPRGTISAVT-DDKGRKTVTDLFHHIPQRIFPVGRLDYDTSGLLLLTNDGEFSYM 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           L  P  +  + Y  R  G    + L  L++GI ++       +  +T   +K   A   +
Sbjct: 121 LTHPKFKIDKTYIARVKGIPTIEGLKKLQRGIKLEDGKTAPAKVSMTSFDEKAGKAICEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + EG+NR+++++FE     V +L R  +    L  L  G  RE+SK  +++     
Sbjct: 181 TIHEGRNRQVRRMFEAIGTPVVKLKRERFAFLDLFGLAPGEFRELSKHEVKQLRVLA 237


>gi|296449151|ref|ZP_06890938.1| ribosomal small subunit pseudouridine synthase A [Clostridium
           difficile NAP08]
 gi|296880870|ref|ZP_06904818.1| ribosomal small subunit pseudouridine synthase A [Clostridium
           difficile NAP07]
 gi|296261970|gb|EFH08778.1| ribosomal small subunit pseudouridine synthase A [Clostridium
           difficile NAP08]
 gi|296428157|gb|EFH14056.1| ribosomal small subunit pseudouridine synthase A [Clostridium
           difficile NAP07]
          Length = 240

 Score =  192 bits (488), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 105/234 (44%), Gaps = 4/234 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA 70
             QR+ K+++  G  SR E+++   Q  V VNG  +      V    D I  +G  +   
Sbjct: 3   KKQRIDKILSNLGYGSRSEIKKYCKQGSVVVNGSEVSNPGTQVDTENDEILFNGEEVIYR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L +      +  T    D       +L  +      VGRLD +TEGLL+LTNDG L
Sbjct: 63  EYIYLMMNKPDGYVSATTDKYDPTVLDLIDLSYLAFEPFPVGRLDKDTEGLLVLTNDGKL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWV 189
           +  +  P     + Y  +  G V ++ +    +G+V+         Q+ +  +    + +
Sbjct: 123 SHRVLSPKKHVPKTYYAKIDGVVTEEDVEAFLEGVVLDDGYKTMPSQLNIL-KSDDESEI 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R+S G  +L   L  G  RE++ + ++
Sbjct: 182 ELTIHEGKFHQVKRMFESVGKKVVYLKRLSMGNLKLDESLELGEYRELTDEEIK 235


>gi|289548362|ref|YP_003473350.1| pseudouridine synthase [Thermocrinis albus DSM 14484]
 gi|289181979|gb|ADC89223.1| pseudouridine synthase [Thermocrinis albus DSM 14484]
          Length = 247

 Score =  192 bits (488), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 73/231 (31%), Positives = 117/231 (50%), Gaps = 1/231 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R++K ++  G+ SRR+ +++I + RVKVNG+++      +    D +EVDG  L+   +
Sbjct: 8   VRLNKYLSMCGVTSRRKADQLIKEGRVKVNGLVVRELGYKIDPHRDTVEVDGKVLKPPRK 67

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + LY     L         +  + + L  I  RV   GRLD N EGLL+LTNDG LA 
Sbjct: 68  RYIALYKPCCYLTAIGRGVGDKKPLDELLKGIPERVFPAGRLDYNAEGLLILTNDGELAN 127

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  +VY+V   G+V+Q  L  + +G  +         V     +G N W+ + 
Sbjct: 128 RILHPRYKLPKVYKVLVRGKVEQATLKRMLEGAQLLDGFAKPQDVKFLRYEGENTWLQIT 187

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
              G+   +K+    F  KV RLIRI+ GP +LG L  G  R+++ + + E
Sbjct: 188 FTIGRKHIVKRYCAHFGHKVLRLIRIAIGPIRLGKLSPGKWRDLTLQEVTE 238


>gi|229160522|ref|ZP_04288517.1| Pseudouridine synthase [Bacillus cereus R309803]
 gi|228622932|gb|EEK79763.1| Pseudouridine synthase [Bacillus cereus R309803]
          Length = 242

 Score =  192 bits (487), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 75/242 (30%), Positives = 128/242 (52%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     + +   D        D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 62  YFLLYKPTGVISSVSDDKGRSVVT-DFFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++       +V + +       A V +
Sbjct: 121 LMHPKYKVEKTYVAKVKGPLTGEKIRMLERGVALEDGKTAPARVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++   +++       +
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELTPHEVKQLRALASTK 240

Query: 252 EA 253
             
Sbjct: 241 PR 242


>gi|42780671|ref|NP_977918.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           ATCC 10987]
 gi|47569145|ref|ZP_00239833.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           G9241]
 gi|206978260|ref|ZP_03239138.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           H3081.97]
 gi|217959048|ref|YP_002337596.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           AH187]
 gi|222095202|ref|YP_002529262.1| ribosomal large subunit pseudouridine synthase b [Bacillus cereus
           Q1]
 gi|228984651|ref|ZP_04144824.1| Pseudouridine synthase [Bacillus thuringiensis serovar tochigiensis
           BGSC 4Y1]
 gi|229138265|ref|ZP_04266860.1| Pseudouridine synthase [Bacillus cereus BDRD-ST26]
 gi|229155139|ref|ZP_04283251.1| Pseudouridine synthase [Bacillus cereus ATCC 4342]
 gi|229195772|ref|ZP_04322532.1| Pseudouridine synthase [Bacillus cereus m1293]
 gi|300117500|ref|ZP_07055290.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           SJ1]
 gi|301053111|ref|YP_003791322.1| pseudouridylate synthase [Bacillus anthracis CI]
 gi|42736591|gb|AAS40526.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           ATCC 10987]
 gi|47554216|gb|EAL12579.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           G9241]
 gi|206743509|gb|EDZ54938.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           H3081.97]
 gi|217066494|gb|ACJ80744.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           AH187]
 gi|221239260|gb|ACM11970.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           Q1]
 gi|228587669|gb|EEK45727.1| Pseudouridine synthase [Bacillus cereus m1293]
 gi|228628266|gb|EEK84981.1| Pseudouridine synthase [Bacillus cereus ATCC 4342]
 gi|228645157|gb|EEL01394.1| Pseudouridine synthase [Bacillus cereus BDRD-ST26]
 gi|228775045|gb|EEM23438.1| Pseudouridine synthase [Bacillus thuringiensis serovar tochigiensis
           BGSC 4Y1]
 gi|298725335|gb|EFI65987.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           SJ1]
 gi|300375280|gb|ADK04184.1| pseudouridylate synthase [Bacillus cereus biovar anthracis str. CI]
 gi|324325588|gb|ADY20848.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           thuringiensis serovar finitimus YBT-020]
          Length = 242

 Score =  192 bits (487), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 75/242 (30%), Positives = 129/242 (53%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     + +   D        D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 62  YFLLYKPTGVISSVSDDKGRSVVT-DFFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G++++       +V + +       A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGEKIRMLERGVMLEDGKTAPARVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++   +++       +
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELTPHEVKQLRALASTK 240

Query: 252 EA 253
             
Sbjct: 241 PR 242


>gi|168487318|ref|ZP_02711826.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CDC1087-00]
 gi|183569796|gb|EDT90324.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CDC1087-00]
          Length = 240

 Score =  192 bits (487), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 80/241 (33%), Positives = 132/241 (54%), Gaps = 3/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVTDDKGRKTVVDLLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  ++D L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGVANKDNLRPLTRGLEIDGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLHPGESRRLNKKEISQLHTMAVTK 239

Query: 252 E 252
           +
Sbjct: 240 K 240


>gi|83313225|ref|YP_423489.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthase [Magnetospirillum magneticum
           AMB-1]
 gi|82948066|dbj|BAE52930.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthase [Magnetospirillum magneticum
           AMB-1]
          Length = 348

 Score =  192 bits (487), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 151/305 (49%), Positives = 194/305 (63%), Gaps = 2/305 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           Q     +R++K +ARAG+ SRRE ER I   RV VNG  L   A  V   D + VDG+PL
Sbjct: 46  QTKSEGERIAKRLARAGLCSRREAERWIEDGRVTVNGHRLSSPACVVGPGDIVIVDGIPL 105

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            + E+TRLW YHKP GLVTTH DP+GR TVFD+LP    RVISVGRLD+N+EGLLLLTND
Sbjct: 106 SEPEKTRLWRYHKPAGLVTTHKDPEGRPTVFDHLPEGMPRVISVGRLDLNSEGLLLLTND 165

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LAR LELPS  WLR YRVR HG+V +D L  L+ GI I G+ YG +  TLD ++G+NA
Sbjct: 166 GELARKLELPSNAWLRRYRVRVHGEVSEDALARLENGITIDGMAYGPISATLDRRQGANA 225

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W++V LREGKNREI++V E+  W V+RLIR+SYGPFQLGTL  G+  EV+ K+LREQ+G 
Sbjct: 226 WLSVSLREGKNREIRRVMEYLGWPVSRLIRVSYGPFQLGTLEEGAADEVAGKVLREQMGE 285

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              +           + E     R    +         +  S++K+   + ++   P   
Sbjct: 286 --GKAVLKPKAETKSAGEREKEQRVAAKARKQKLAEDKRAASAKKDKPYEARQAGKPDAH 343

Query: 308 RNLAS 312
           R  +S
Sbjct: 344 RRRSS 348


>gi|312864688|ref|ZP_07724919.1| pseudouridine synthase B, ribosomal large subunit [Streptococcus
           downei F0415]
 gi|311099815|gb|EFQ58028.1| pseudouridine synthase B, ribosomal large subunit [Streptococcus
           downei F0415]
          Length = 241

 Score =  192 bits (487), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 80/242 (33%), Positives = 129/242 (53%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V +NG ++   A  V + D +EV G P+   E  
Sbjct: 1   MRINKYIAHAGLASRRKAEELIKQGLVTINGQVVTELATTVKNGDRVEVSGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVLDLLPDVKERIYPVGRLDWDTTGVLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G   G  +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARLKGLATKENLRPLTRGVVIDGKKTGPARYKIIKVEPDKNRSLVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++K +F+     V++L R  +G   L  L  G +R +SKK + +     + +
Sbjct: 180 TIHEGRNHQVKNMFQAVGLLVDKLSRTQFGTLNLRGLQPGESRRLSKKEVSQLHNAAVTK 239

Query: 252 EA 253
             
Sbjct: 240 HQ 241


>gi|329115789|ref|ZP_08244506.1| pseudouridine synthase B, ribosomal large subunit [Streptococcus
           parauberis NCFD 2020]
 gi|326906194|gb|EGE53108.1| pseudouridine synthase B, ribosomal large subunit [Streptococcus
           parauberis NCFD 2020]
          Length = 241

 Score =  192 bits (487), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 83/237 (35%), Positives = 128/237 (54%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V +NG ++   A  V S D +E++G P+   E  
Sbjct: 1   MRINKFIAHAGVASRRKAEELIKQGLVTINGQVVTELATTVKSGDQVEIEGSPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T GLLLLTNDG    +
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVIDLLPQVKERIYPVGRLDWDTSGLLLLTNDGDFTDM 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P  +  +VY  R  G   +D L  L +G+VI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKDNLRPLTRGVVIDGKKTKPARYNIIRVEADKNRSIVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK + +     
Sbjct: 180 TIHEGRNHQVKKMFESVGLIVDKLSRTQFGTLDLTGLRPGEARRLNKKEISQLHNAA 236


>gi|30019620|ref|NP_831251.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           ATCC 14579]
 gi|49477247|ref|YP_035689.1| pseudouridylate synthase [Bacillus thuringiensis serovar konkukian
           str. 97-27]
 gi|118477028|ref|YP_894179.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           thuringiensis str. Al Hakam]
 gi|196036830|ref|ZP_03104219.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           W]
 gi|196039034|ref|ZP_03106341.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           NVH0597-99]
 gi|196047636|ref|ZP_03114843.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           03BB108]
 gi|206968047|ref|ZP_03229003.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           AH1134]
 gi|218232708|ref|YP_002366253.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           B4264]
 gi|218902682|ref|YP_002450516.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           AH820]
 gi|225863435|ref|YP_002748813.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           03BB102]
 gi|228914146|ref|ZP_04077764.1| Pseudouridine synthase [Bacillus thuringiensis serovar pulsiensis
           BGSC 4CC1]
 gi|228920281|ref|ZP_04083629.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228926603|ref|ZP_04089672.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228932858|ref|ZP_04095725.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228945172|ref|ZP_04107528.1| Pseudouridine synthase [Bacillus thuringiensis serovar monterrey
           BGSC 4AJ1]
 gi|228951948|ref|ZP_04114046.1| Pseudouridine synthase [Bacillus thuringiensis serovar kurstaki
           str. T03a001]
 gi|228957847|ref|ZP_04119587.1| Pseudouridine synthase [Bacillus thuringiensis serovar pakistani
           str. T13001]
 gi|229043313|ref|ZP_04191033.1| Pseudouridine synthase [Bacillus cereus AH676]
 gi|229069124|ref|ZP_04202416.1| Pseudouridine synthase [Bacillus cereus F65185]
 gi|229078754|ref|ZP_04211308.1| Pseudouridine synthase [Bacillus cereus Rock4-2]
 gi|229090533|ref|ZP_04221769.1| Pseudouridine synthase [Bacillus cereus Rock3-42]
 gi|229109026|ref|ZP_04238627.1| Pseudouridine synthase [Bacillus cereus Rock1-15]
 gi|229121114|ref|ZP_04250351.1| Pseudouridine synthase [Bacillus cereus 95/8201]
 gi|229126886|ref|ZP_04255898.1| Pseudouridine synthase [Bacillus cereus BDRD-Cer4]
 gi|229144171|ref|ZP_04272585.1| Pseudouridine synthase [Bacillus cereus BDRD-ST24]
 gi|229149770|ref|ZP_04278000.1| Pseudouridine synthase [Bacillus cereus m1550]
 gi|229177979|ref|ZP_04305351.1| Pseudouridine synthase [Bacillus cereus 172560W]
 gi|229183767|ref|ZP_04310984.1| Pseudouridine synthase [Bacillus cereus BGSC 6E1]
 gi|229189653|ref|ZP_04316668.1| Pseudouridine synthase [Bacillus cereus ATCC 10876]
 gi|254721252|ref|ZP_05183042.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A1055]
 gi|296502142|ref|YP_003663842.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           thuringiensis BMB171]
 gi|29895164|gb|AAP08452.1| Ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           ATCC 14579]
 gi|49328803|gb|AAT59449.1| pseudouridylate synthase [Bacillus thuringiensis serovar konkukian
           str. 97-27]
 gi|118416253|gb|ABK84672.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           thuringiensis str. Al Hakam]
 gi|195990559|gb|EDX54538.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           W]
 gi|196021550|gb|EDX60250.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           03BB108]
 gi|196030179|gb|EDX68779.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           NVH0597-99]
 gi|206736967|gb|EDZ54114.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           AH1134]
 gi|218160665|gb|ACK60657.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           B4264]
 gi|218539452|gb|ACK91850.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           AH820]
 gi|225790880|gb|ACO31097.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           03BB102]
 gi|228593917|gb|EEK51721.1| Pseudouridine synthase [Bacillus cereus ATCC 10876]
 gi|228599616|gb|EEK57219.1| Pseudouridine synthase [Bacillus cereus BGSC 6E1]
 gi|228605467|gb|EEK62916.1| Pseudouridine synthase [Bacillus cereus 172560W]
 gi|228633801|gb|EEK90400.1| Pseudouridine synthase [Bacillus cereus m1550]
 gi|228639179|gb|EEK95595.1| Pseudouridine synthase [Bacillus cereus BDRD-ST24]
 gi|228656826|gb|EEL12652.1| Pseudouridine synthase [Bacillus cereus BDRD-Cer4]
 gi|228662233|gb|EEL17836.1| Pseudouridine synthase [Bacillus cereus 95/8201]
 gi|228674495|gb|EEL29738.1| Pseudouridine synthase [Bacillus cereus Rock1-15]
 gi|228692800|gb|EEL46523.1| Pseudouridine synthase [Bacillus cereus Rock3-42]
 gi|228704627|gb|EEL57059.1| Pseudouridine synthase [Bacillus cereus Rock4-2]
 gi|228714069|gb|EEL65952.1| Pseudouridine synthase [Bacillus cereus F65185]
 gi|228726027|gb|EEL77264.1| Pseudouridine synthase [Bacillus cereus AH676]
 gi|228801763|gb|EEM48640.1| Pseudouridine synthase [Bacillus thuringiensis serovar pakistani
           str. T13001]
 gi|228807871|gb|EEM54392.1| Pseudouridine synthase [Bacillus thuringiensis serovar kurstaki
           str. T03a001]
 gi|228814407|gb|EEM60672.1| Pseudouridine synthase [Bacillus thuringiensis serovar monterrey
           BGSC 4AJ1]
 gi|228826779|gb|EEM72546.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228832979|gb|EEM78547.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228839480|gb|EEM84773.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228845479|gb|EEM90512.1| Pseudouridine synthase [Bacillus thuringiensis serovar pulsiensis
           BGSC 4CC1]
 gi|296323194|gb|ADH06122.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           thuringiensis BMB171]
          Length = 242

 Score =  192 bits (487), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 75/242 (30%), Positives = 128/242 (52%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     + +   D        D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 62  YFLLYKPTGVISSVSDDKGRSVVT-DFFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++       +V + +       A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGEKIRMLERGVTLEDGKTAPARVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++   +++       +
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELTPHEVKQLRALASTK 240

Query: 252 EA 253
             
Sbjct: 241 PR 242


>gi|319936458|ref|ZP_08010874.1| pseudouridine synthase [Coprobacillus sp. 29_1]
 gi|319808573|gb|EFW05125.1| pseudouridine synthase [Coprobacillus sp. 29_1]
          Length = 247

 Score =  192 bits (487), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 71/247 (28%), Positives = 119/247 (48%), Gaps = 3/247 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +IA  RVKVNG ++      V   D I +D   L+   + 
Sbjct: 2   ERLQKAIAASGYTSRRKAEDLIAAGRVKVNGEVISELGFKVKKGDMIMIDDKALKGENKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     + +   +    + +    P +  R+  VGRLD +T G+LL++NDG  A +
Sbjct: 62  YYVFYKPKGCICSLSDELGRSTVIDYF-PEVEERIYPVGRLDYDTTGVLLMSNDGEFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  PS+   +VY V   G V  + L+ L+KG+ ++G      ++ +  +        + +
Sbjct: 121 MMHPSSHLEKVYEVSVSGLVQGETLHKLEKGVYLEGTKTLPCKIKVTHKDVEHKTTILMI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L EGKNR++KK+FE    KV RL R+  G   L  L  G  R +  + ++E     + +
Sbjct: 181 KLVEGKNRQVKKMFEAMGHKVKRLHRLQVGTINLKGLTPGHYRLLKPQEVKELKTMAMAK 240

Query: 252 EAQVNLD 258
           +      
Sbjct: 241 KTSGKKR 247


>gi|223043161|ref|ZP_03613208.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           capitis SK14]
 gi|222443372|gb|EEE49470.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           capitis SK14]
          Length = 245

 Score =  192 bits (487), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 70/241 (29%), Positives = 130/241 (53%), Gaps = 3/241 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +R+ K IA +G  SRR+ E +I + +VKVNG ++      V  +D +EV+G+ + +
Sbjct: 2   SKELERLQKRIANSGYTSRRKAETLITEGKVKVNGQVVTELGTKVSHSDTVEVEGIKIEQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ++  +  Y     ++T+ SD  GR  V D    I +R+  VGRLD +T G+LLLTNDG 
Sbjct: 62  EDKMYILFYKPT-QVITSVSDDRGRKVVTDYFEDIETRIYPVGRLDYDTSGVLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNA 187
              ++  P     + Y  +  G + ++++  L++GI ++         ++    ++ +  
Sbjct: 121 FTNLMTHPRYHIKKKYVAKLKGYLMREQVKELEQGIELEDGFTQPAQVKIKRQDKEKNTT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V + + EG+NR+++++FE+F  +VN+L RI +GP  L  L AG  R ++   ++     
Sbjct: 181 LVEITISEGRNRQVRRMFEYFGHEVNKLTRIQFGPLDLKGLNAGEGRVLTPHEVKTLRHL 240

Query: 248 H 248
            
Sbjct: 241 A 241


>gi|163740839|ref|ZP_02148232.1| RNA pseudouridylate synthase family protein [Phaeobacter
           gallaeciensis 2.10]
 gi|161385830|gb|EDQ10206.1| RNA pseudouridylate synthase family protein [Phaeobacter
           gallaeciensis 2.10]
          Length = 447

 Score =  192 bits (487), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 141/348 (40%), Positives = 194/348 (55%), Gaps = 3/348 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
           +     R++KV++RAG+ASRRE ERMIA+ RV VNG +++  A+NV+   D I VDG  +
Sbjct: 47  DGPEGDRIAKVLSRAGVASRREAERMIAEGRVAVNGKVIDSPALNVVLGKDRIVVDGNQM 106

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +  E  RLW+YHKP GLVTT +D   R T+FD LP    RV++VGRLD+N+EGLLLLTND
Sbjct: 107 QDPEPPRLWMYHKPSGLVTTTNDELDRRTIFDELPEDMPRVMTVGRLDLNSEGLLLLTND 166

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GG+ R LELPST WLR YRVR +G+        L++G+VI+G  +  M V LD Q+G+NA
Sbjct: 167 GGIKRQLELPSTGWLRRYRVRINGRPKDTDFEPLRQGLVIEGERFQPMTVALDRQQGANA 226

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+T+GLREGKNREI++  E   + VNRL+R+SYGPFQLG L  G   E+  +++R+QLG 
Sbjct: 227 WLTIGLREGKNREIRRAIEDIGFTVNRLLRLSYGPFQLGNLKPGEVEELRSRVVRDQLGL 286

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD--DFTRMKKNSSQKNGLSKQKKLATPV 305
              E  +                        PD    ++       K             
Sbjct: 287 TAPETEEDEKPKRPVRQRPGAGKPGPKPGAKPDFKSGSKPGGKPGGKPSGRSFGSSDRSS 346

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            +    S    A      F       +    ++   P+ R+  RTS +
Sbjct: 347 EKPGDRSGARPAGKPGGKFAGKGKPSDRFAGKAEGKPTGRTADRTSDR 394


>gi|297544608|ref|YP_003676910.1| pseudouridine synthase [Thermoanaerobacter mathranii subsp.
           mathranii str. A3]
 gi|296842383|gb|ADH60899.1| pseudouridine synthase [Thermoanaerobacter mathranii subsp.
           mathranii str. A3]
          Length = 236

 Score =  192 bits (487), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 77/230 (33%), Positives = 121/230 (52%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  GIASRR+ E  I Q RVKVNG  ++   V +    D IE D   +R+ ++
Sbjct: 2   VRLQKYLAECGIASRRKCEEYILQGRVKVNGKEVKELGVKINPDVDIIEFDDKIVRREKK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G +T+  D  GR TV  +L  +  R+  VGRLD +T GLLLLTNDG +A 
Sbjct: 62  KVYIMLNKPTGYITSVKDQFGRPTVM-DLVKVKERIYPVGRLDYDTSGLLLLTNDGEIAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +L  P  +  + Y  +  G   +++L   + G++I+       ++ + T K   + V + 
Sbjct: 121 ILMHPRHEIAKTYIAKIKGIPTEEELERFRNGLLIEDYVTSKAEIKVLTVKKGTSVVEIK 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGKNR+++K+ E     V  L+R   G   L  L  G  R ++ K + 
Sbjct: 181 IHEGKNRQVRKMCEAIGHPVISLMRTKIGELSLEGLKPGEWRYLTNKEID 230


>gi|319937384|ref|ZP_08011791.1| pseudouridine synthase [Coprobacillus sp. 29_1]
 gi|319807750|gb|EFW04343.1| pseudouridine synthase [Coprobacillus sp. 29_1]
          Length = 234

 Score =  192 bits (487), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 104/231 (45%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K++A +G  +R+EV+  I +  V VNG + E+  + V   TD + V+G  +   E 
Sbjct: 1   MRLDKLLAHSGFGTRKEVKDFIKKGIVTVNGEIAEKDKMQVDPQTDEVCVNGEVITYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      + +   D    + V          +  VGRLD++TEGLLL++NDG LA 
Sbjct: 61  VYYMLNKPAGYV-SATEDNLYPTVVDLIDDYYRDDLFPVGRLDVDTEGLLLISNDGVLAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VY  + +G V    +     GI I        ++ + +   + + + V 
Sbjct: 120 QLLSPKKHCPKVYYAKINGIVTNQDVEAFFNGITIDDYQCQSAELKILSTSATTSEIEVT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           + EGK  ++KK+F     +V  L RI      L   L  G  R ++ + L 
Sbjct: 180 IYEGKFHQVKKMFIAVGKEVTYLKRIRMKDLCLDNSLQLGEYRHLTDEELD 230


>gi|59712175|ref|YP_204951.1| 23S rRNA pseudouridine synthase [Vibrio fischeri ES114]
 gi|197334855|ref|YP_002156383.1| ribosomal large subunit pseudouridine synthase F [Vibrio fischeri
           MJ11]
 gi|59480276|gb|AAW86063.1| 23S rRNA pseudouridine synthase [Vibrio fischeri ES114]
 gi|197316345|gb|ACH65792.1| ribosomal large subunit pseudouridine synthase F [Vibrio fischeri
           MJ11]
          Length = 314

 Score =  192 bits (487), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 68/321 (21%), Positives = 127/321 (39%), Gaps = 10/321 (3%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +        R++K I+  G  SRRE +++I QQR+ +NG +       V   D + VDG 
Sbjct: 1   MTSPEPKLTRLNKFISDTGYCSRREADKLIDQQRITINGKIP-EMGTKVADGDEVLVDGK 59

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL++ +      ++KP+G+  T       + V     +   R+  +GRLD  ++GL+ LT
Sbjct: 60  PLKEKQDRIYIAFNKPVGITCTTERHVEGNIVDYI--NHEQRIFPIGRLDKPSDGLIFLT 117

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +   +        + Y VR    +  + L  +  G+ I        ++    ++ S
Sbjct: 118 NDGDIVNKILRAGNAHEKEYVVRVDKPITDEFLQKMAAGVPILDTVTLPCKI----KQES 173

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++ E+ +++V +L R+      LG L +G  R +S+  + +  
Sbjct: 174 RFVFRITLTQGLNRQIRRMCEYLDYEVFKLKRVRIMNIDLGKLASGEWRYLSQAEMDQLN 233

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT---RMKKNSSQKNGLSKQKKLA 302
           G              +   +  VR      S          +  +    K G   +    
Sbjct: 234 GMIGTSSKTEEASRKVKEIDGKVRVLKKASSGRNHHSNNTFKENRREKAKEGRFSKSAPK 293

Query: 303 TPVHRRNLASNVWMAKGIHSS 323
               R+         K     
Sbjct: 294 RKNDRKEQGKPQSEIKVWRPK 314


>gi|288905991|ref|YP_003431213.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           gallolyticus UCN34]
 gi|306832010|ref|ZP_07465165.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325978958|ref|YP_004288674.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
 gi|288732717|emb|CBI14291.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           gallolyticus UCN34]
 gi|304425936|gb|EFM29053.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325178886|emb|CBZ48930.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
          Length = 241

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 81/242 (33%), Positives = 132/242 (54%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I +  V +NG ++   A  V S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKKGLVTINGKVVTELATTVKSGDVVEVEGSPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV D LP++  R+  VGRLD +T GLL+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDEKGRKTVVDLLPNVTERIYPVGRLDWDTTGLLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIVKVDPEKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE     V++L R  +G   L  L  G +R ++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTQFGTLDLAGLRPGESRRLNKKEISQLHNLAVNK 239

Query: 252 EA 253
           + 
Sbjct: 240 QK 241


>gi|289578329|ref|YP_003476956.1| pseudouridine synthase [Thermoanaerobacter italicus Ab9]
 gi|289528042|gb|ADD02394.1| pseudouridine synthase [Thermoanaerobacter italicus Ab9]
          Length = 236

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 76/230 (33%), Positives = 120/230 (52%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  GIASRR+ E  I Q RVKVNG  ++   V +    D IE D   +R+ ++
Sbjct: 2   VRLQKYLAECGIASRRKCEEYILQGRVKVNGKEVKELGVKINPDVDIIEFDDKIVRREKK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G +T+  D  GR TV  +L  +  R+  VGRLD +T GLLLLTNDG +A 
Sbjct: 62  KVYIMLNKPTGYITSVKDQFGRPTVM-DLVKVKERIYPVGRLDYDTSGLLLLTNDGEIAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +L  P  + ++ Y  +  G   Q++L   + G++I        ++ +   K   + V + 
Sbjct: 121 ILMHPRHEIVKTYIAKIKGIPTQEELERFRNGLLIGDYLTSKAEIEILAVKNGTSVVEIK 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGKNR+++++ E     V  L R   G   L  L  G  R +++K + 
Sbjct: 181 IHEGKNRQVRRMCEAIGHPVISLTRTKIGDLSLEGLKPGKWRYLTQKEID 230


>gi|229822888|ref|ZP_04448958.1| hypothetical protein GCWU000282_00178 [Catonella morbi ATCC 51271]
 gi|229787701|gb|EEP23815.1| hypothetical protein GCWU000282_00178 [Catonella morbi ATCC 51271]
          Length = 290

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 96/288 (33%), Positives = 135/288 (46%), Gaps = 6/288 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KV+A AGIASRR+ E +I + RV VNG  +      V S D IEVDGVP+   E  R
Sbjct: 3   RLQKVMAHAGIASRRKCESLITEGRVSVNGQTVRELGTQVSSKDRIEVDGVPI-YREEPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             L +KP  +++  SD   R  + D +  I  R+  VGRLD +T GLLLLTNDG  A  L
Sbjct: 62  YILINKPRHVISAVSDDKNRQVILDYIQGIEERIYPVGRLDYDTTGLLLLTNDGAFANQL 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW--VTVG 192
             P  Q  +VY  +  G   +  L  L+ GIV+ G      +  L +Q   N    V + 
Sbjct: 122 MHPRHQIDKVYVAKVKGIPSEKSLARLEAGIVLDGKKTAKAKAQLLSQNLDNQTAIVELT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI---LREQLGPHL 249
           +REG N ++K++FE     VN+L R  Y    LG LL G  RE++      L++      
Sbjct: 182 IREGWNHQVKRMFEAVGHPVNKLKRERYAFLTLGKLLPGEWRELTAHEVNKLKQMSQSEG 241

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
               +     P          +P+  S       + +K  S+      
Sbjct: 242 QAGQEARKAKPKRIMGRPTGQKPSRKSSASSSARKARKGQSKPKPARN 289


>gi|224025133|ref|ZP_03643499.1| hypothetical protein BACCOPRO_01867 [Bacteroides coprophilus DSM
           18228]
 gi|224018369|gb|EEF76367.1| hypothetical protein BACCOPRO_01867 [Bacteroides coprophilus DSM
           18228]
          Length = 253

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 62/241 (25%), Positives = 111/241 (46%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K+I+ +   P R++K +A AG+ SRRE +  I    V VNG ++      V  TD +
Sbjct: 5   IEYKDILTDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKVKRTDEV 64

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P+    +  + L      + T+    + ++ +     +   R+  VGRLD NT G
Sbjct: 65  KFHDQPVNIERKVYVLLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTTG 124

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     V +  L+ + +GI +             
Sbjct: 125 VLLLTNDGDLASKLTHPKFLKKKIYHVYCDKNVTKADLDQIVQGITLDDGEIH-ADAVSY 183

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 + V + +  GKNR ++++FE   ++V +L R+ +       L  G  R +++  
Sbjct: 184 ASDTDKSQVGIEIHSGKNRIVRRIFESLGYRVIKLDRVYFAGLTKKGLRRGDWRYLTEME 243

Query: 241 L 241
           +
Sbjct: 244 V 244


>gi|255099545|ref|ZP_05328522.1| putative RNA pseudouridine synthase [Clostridium difficile
           QCD-63q42]
          Length = 240

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 105/234 (44%), Gaps = 4/234 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA 70
             QR+ K+++  G  SR E+++   Q  V VNG  +      V    D I  +G  +   
Sbjct: 3   KKQRIDKILSNLGYGSRSEIKKYCKQGSVVVNGSEVSNPGTQVDTENDEILFNGEEVIYR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L +      +  T    D       +L  +      VGRLD +TEGLL+LTNDG L
Sbjct: 63  EYIYLMMNKPAGYISATTDKYDPTVLDLIDLSYLVFEPFPVGRLDKDTEGLLVLTNDGKL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWV 189
           +  +  P     + Y  +  G V ++ +    +G+V+         Q+ +  +    + +
Sbjct: 123 SHRVLSPKKHVPKTYYAKIDGVVTEEDVEAFLEGVVLDDGYKTMPSQLNIL-KSDDESEI 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R+S G  +L   L  G  RE++ + ++
Sbjct: 182 ELTIHEGKFHQVKRMFESVGKKVVYLKRLSMGNLKLDESLELGEYRELTDEEVK 235


>gi|332532521|ref|ZP_08408398.1| putative ribosomal RNA pseudouridine synthase [Pseudoalteromonas
           haloplanktis ANT/505]
 gi|332037942|gb|EGI74390.1| putative ribosomal RNA pseudouridine synthase [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 358

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 73/351 (20%), Positives = 134/351 (38%), Gaps = 14/351 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K+   +      +R++K I+  G  SRRE ++ I Q RV VNG       V V +TD +
Sbjct: 9   LKNYYAISAMTELKRLNKFISETGFCSRREADKYIEQGRVSVNGYSP-EMGVKVAATDVV 67

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            VDG PL+   +     Y+KP+G+  T       + +     +  +R+  +GRLD  +EG
Sbjct: 68  LVDGKPLKATPKRVYIAYNKPVGITCTTESKIQSNIIRAV--NYPTRIFPIGRLDRPSEG 125

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+ LTN+G +   +        + Y V     +++  +  +  G+ I        +VT  
Sbjct: 126 LIFLTNEGDIVNKILRAGNNHEKEYVVTVDKPLNRQFVTKMANGVPILDTVTKKCKVT-- 183

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             + +     + L +G NR+I+++ E+  ++V  L R       L  L  G  R +S   
Sbjct: 184 --QTAPKEFKIVLTQGLNRQIRRMCEYLGYEVVTLKRTRIMNVTLKGLKVGQWRHLSDTE 241

Query: 241 -------LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
                  + +                    S    RD         +   +  + S+++N
Sbjct: 242 MAQINDSISDSGKTQEHSLDANKQSENNTPSAPKKRDFQGENPRRFNKGEQSGERSTERN 301

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
                 +      R+N  S     K   +        +E    +S     +
Sbjct: 302 SSRNSDRSNANGERKNERSKAPYQKRSTTYVGKPKSIKENKSSQSKPSSGR 352


>gi|302389711|ref|YP_003825532.1| ribosomal large subunit pseudouridine synthase B
           [Thermosediminibacter oceani DSM 16646]
 gi|302200339|gb|ADL07909.1| ribosomal large subunit pseudouridine synthase B
           [Thermosediminibacter oceani DSM 16646]
          Length = 237

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 77/230 (33%), Positives = 118/230 (51%), Gaps = 1/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A AGIASRR  E++I + RV+VNG  +    V V    D + VDG   R   +
Sbjct: 3   IRLQKFLAMAGIASRRACEKLILEGRVQVNGKTVRELGVKVDPALDEVRVDGNVCRLNNK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G++TT  DP GR TV D L  +  RV  VGRLD +TEGLL+LTNDG L+ 
Sbjct: 63  PIYILMNKPKGILTTVKDPFGRPTVIDLLKGVRERVFPVGRLDKDTEGLLILTNDGELSY 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + Y  +  G  D+     L++GIV++       +V +         + + 
Sbjct: 123 RLTHPKHEIEKTYVAKVVGTPDESDFIRLRRGIVLEDGRTAPAKVRILKAGRDFTVLEII 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EG+ R+++++ +     V  L R   G   L  L  G  R +++  ++
Sbjct: 183 IHEGRKRQVRRMCKAIGHPVISLKRTRIGKLNLRGLAPGCWRYMTEAEIK 232


>gi|169827290|ref|YP_001697448.1| ribosomal large subunit pseudouridine synthase B [Lysinibacillus
           sphaericus C3-41]
 gi|168991778|gb|ACA39318.1| Ribosomal large subunit pseudouridine synthase B [Lysinibacillus
           sphaericus C3-41]
          Length = 243

 Score =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 80/237 (33%), Positives = 124/237 (52%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E++I + +VKVNGI++      V ++D IEV+GV L K ++ 
Sbjct: 2   ERLQKVIAYAGVASRRKAEQLIVEGKVKVNGIVVRELGTKVSNSDTIEVEGVKLEKEDKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     +     D  GR TV D    I  R+  VGRLD +T GLLLLTNDG  + +
Sbjct: 62  YFLLYKPRGTISAVT-DDKGRKTVTDLFHHIPQRIFPVGRLDYDTSGLLLLTNDGEFSYM 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           L  P  +  + Y  R  G    + L  L++GI ++       +  +T   +    A   +
Sbjct: 121 LTHPKFKIDKTYIARVKGIPTIEGLKKLQRGIKLEDGKTAPAKVSMTSFDENAGKAICEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + EG+NR+++++FE     V +L R  +    L  L  G  RE+SK  +++     
Sbjct: 181 TIHEGRNRQVRRMFEAIGTPVVKLKRERFAFLDLYGLAPGEFRELSKHEVKQLRVLA 237


>gi|256827115|ref|YP_003151074.1| pseudouridine synthase family protein [Cryptobacterium curtum DSM
           15641]
 gi|256583258|gb|ACU94392.1| pseudouridine synthase family protein [Cryptobacterium curtum DSM
           15641]
          Length = 296

 Score =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 70/231 (30%), Positives = 106/231 (45%), Gaps = 2/231 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK-A 70
           P R+ K +ARAG+ASRR  ER+I+  RV VNGI++      V    D + VDG  +   A
Sbjct: 49  PLRLQKFLARAGVASRRGSERLISAGRVAVNGIVITELGTKVDPLVDEVCVDGAIVTWGA 108

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               L L      + T       R          +  +  +GRLD +T GLLL + DG L
Sbjct: 109 PAVTLALNKPAGIITTMKDLRGRRCVADIMPTEQYPGLFPIGRLDQDTTGLLLFSTDGNL 168

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  PS    +VYR    G + Q  L  L  GI++        +V++      ++ + 
Sbjct: 169 GNALLHPSHGVSKVYRATIEGSIGQAALEQLASGILLDDGMTAPARVSVVQAGKKHSVIE 228

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + L EG+  ++K++ +     V +L R S+GP  L  L  G+ R +    L
Sbjct: 229 LELHEGRKHQVKRMCQAVGHPVVKLHRASFGPIDLAGLATGAYRRLEGAEL 279


>gi|229166414|ref|ZP_04294170.1| Pseudouridine synthase [Bacillus cereus AH621]
 gi|228616988|gb|EEK74057.1| Pseudouridine synthase [Bacillus cereus AH621]
          Length = 242

 Score =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 75/242 (30%), Positives = 127/242 (52%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     + +   D        D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 62  YFLLYKPTGVISSVSDDKGRNVVT-DFFPEIRQRLFPIGRLDYDTSGVLLMTNDGEFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++       Q  + +       A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGEKIRMLERGVALEDGKTAPAQAKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++   +++       +
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELTPHEVKQLRALASTK 240

Query: 252 EA 253
             
Sbjct: 241 PR 242


>gi|145299656|ref|YP_001142497.1| 23S rRNA pseudouridine synthase F [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|142852428|gb|ABO90749.1| ribosomal large subunit pseudouridine synthase F [Aeromonas
           salmonicida subsp. salmonicida A449]
          Length = 344

 Score =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 71/344 (20%), Positives = 126/344 (36%), Gaps = 5/344 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K I+ +GI SRRE +R I Q +V +NG         V + D ++V+G  +   
Sbjct: 4   NESMRLNKYISESGICSRREADRFIEQGQVFINGKRA-GIGDQVFAGDLVKVNGQVIEAR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L        +    +   G      +  +  +RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EADSLVFIVLNKPVGIVSTTEAGEKDNIVDFVNHSTRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V  D +  +  G+ I G      +V    +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPVTDDFIKGMGAGVPILGAVTKKCKV----KKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L RI      L  L  G  R+++   L E       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGFEVTKLERIRIMNVSLKGLPVGEWRDLTDDELIELFKLIED 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
             ++V                    +       R   +           +          
Sbjct: 239 SSSEVKPAKGDKPKVAKAAVAQTGKAAQGKKPRRDDDHEIGGRPNVSGPEAFEKKIPVGK 298

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +      G  ++    +G+   N  R P+    R+ +    KK
Sbjct: 299 GAVGKGGAGKAAAGKGSAGKGASNKGRKPAAAKPRAGQSGRQKK 342


>gi|15895126|ref|NP_348475.1| pseudouridylate synthase [Clostridium acetobutylicum ATCC 824]
 gi|15024828|gb|AAK79815.1|AE007694_1 Predicted pseudouridylate synthase [Clostridium acetobutylicum ATCC
           824]
 gi|325509265|gb|ADZ20901.1| pseudouridylate synthase [Clostridium acetobutylicum EA 2018]
          Length = 236

 Score =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 79/230 (34%), Positives = 124/230 (53%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ K +A  G+ASRR+ E+MI   RVKVNG ++      V    D IE+D   ++  ++
Sbjct: 3   ERLQKYMAECGVASRRKCEKMIQDGRVKVNGTIVTELGFKVDYKKDTIELDNKEIKLEDK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G +T  SD  GR TV D L     RV  VGRLD NT GLL++TNDG +  
Sbjct: 63  KVYAILNKPKGYLTAASDYRGRKTVIDLLNF-KERVFPVGRLDFNTTGLLIVTNDGEIFN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y     G+     L+ L+KGI I G    + +V++ +  G N+ + + 
Sbjct: 122 RIMHPRQNVNKCYLATVKGKPQFKHLDALRKGIDIGGYITKEAEVSVVSFDGKNSILKIV 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGK R+++++     + V  L RIS G  +LG L  G+ R ++K+ + 
Sbjct: 182 IHEGKKRQVRRMCAAVGFPVEELKRISIGNIKLGDLKEGNVRMLNKEEIE 231


>gi|255305403|ref|ZP_05349575.1| putative RNA pseudouridine synthase [Clostridium difficile ATCC
           43255]
          Length = 240

 Score =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 105/234 (44%), Gaps = 4/234 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA 70
             QR+ K+++  G  SR E+++   Q  V VNG  +      V    D I  +G  +   
Sbjct: 3   KKQRIDKILSNLGYGSRSEIKKYCKQGSVVVNGSEVSNPGTQVDTENDEILFNGEEVIYR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L +      +  T    D       +L  +      VGRLD +TEGLL+LTNDG L
Sbjct: 63  EYIYLMMNKPDGYISATTDKYDPTVLDLIDLSYLAFEPFPVGRLDKDTEGLLVLTNDGKL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWV 189
           +  +  P     + Y  +  G V ++ +    +G+V+         Q+ +  +    + +
Sbjct: 123 SHRVLSPKKHVSKTYYAKIDGVVTEEDVEAFLEGVVLDDGYKTMPSQLNIL-KSDDESEI 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R+S G  +L   L  G  RE++ + ++
Sbjct: 182 ELTIHEGKFHQVKRMFESVGKKVVYLKRLSMGNLKLDESLELGEYRELTDEEVK 235


>gi|322391362|ref|ZP_08064832.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           peroris ATCC 700780]
 gi|321145788|gb|EFX41179.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           peroris ATCC 700780]
          Length = 240

 Score =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 81/237 (34%), Positives = 129/237 (54%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVTDDKGRKTVVDLLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  D+D L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGIADKDNLRPLTRGVEIDGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK + +     
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGESRRLNKKEISQLHTMA 236


>gi|156933739|ref|YP_001437655.1| 23S rRNA pseudouridylate synthase B [Cronobacter sakazakii ATCC
           BAA-894]
 gi|156531993|gb|ABU76819.1| hypothetical protein ESA_01565 [Cronobacter sakazakii ATCC BAA-894]
          Length = 361

 Score =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 94/348 (27%), Positives = 139/348 (39%), Gaps = 16/348 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E MI   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIEAMIEAGRVSVDGKIATLGDRVEVTPALKIRIDGHLISVKE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T        +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SVEQICRVLAYYKPEGELCTRSDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD  K+  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSQEVEREYAVRVFGQVDDAKVRELARGVQLEDGPAAFKTIRFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E +G     E    +                 +          ++ +  + G +   + A
Sbjct: 242 ELVGL--EPETSSKVAVEKDRRRMKANQIRRAVKRHSQTAGASRQGAPARQGQAGAARPA 299

Query: 303 TPVHR----RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
                    R+  S    +        + SG         P+    R+
Sbjct: 300 GSARAAENTRSGNSTSRASGNARPGGNARSGGARATGNGRPASSGGRA 347


>gi|313884122|ref|ZP_07817888.1| pseudouridine synthase B, ribosomal large subunit [Eremococcus
           coleocola ACS-139-V-Col8]
 gi|312620569|gb|EFR31992.1| pseudouridine synthase B, ribosomal large subunit [Eremococcus
           coleocola ACS-139-V-Col8]
          Length = 236

 Score =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 86/236 (36%), Positives = 126/236 (53%), Gaps = 3/236 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AGIASRR+ E +I+Q RV VNG  +      V  +D IEVD VP+   E  
Sbjct: 2   ERLQKVMAHAGIASRRKCEEIISQGRVTVNGQTVTELGFKVKQSDKIEVDQVPI-YLEEP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP  +++  SD  GR  V D    I  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 61  RYFLFYKPRNVISAVSDDKGRPVVLDYFKHIDQRIYPIGRLDFDTTGLLLLTNDGEFANQ 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           L  P  Q  +VY  +    +D++ L  L++GI+I G      +  +     +   + V +
Sbjct: 121 LMHPRYQVDKVYVAKLDKILDKEALRKLERGIIIDGKKTSKARAKVLDTNLEKKMSVVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + EG N ++KK+FE     V +L R  +GP  LG +  G  RE+    + E    
Sbjct: 181 TIHEGWNHQVKKMFEAVGAHVVKLKREKFGPLNLGKMQPGEYRELLPNEVTELKNL 236


>gi|89070784|ref|ZP_01158037.1| RNA pseudouridylate synthase family protein [Oceanicola granulosus
           HTCC2516]
 gi|89043626|gb|EAR49833.1| RNA pseudouridylate synthase family protein [Oceanicola granulosus
           HTCC2516]
          Length = 279

 Score =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 143/279 (51%), Positives = 177/279 (63%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + +    +R++K+++R G+ASRRE ERMI   RV VNG L++  A+NV ++D I VDG P
Sbjct: 1   MSDEHAGERIAKILSRRGVASRREAERMIEAGRVSVNGRLIDSPALNVTTSDRILVDGKP 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +   E  RLWLYHKP GLVTT  D  GR TVF  LP    RV+SVGRLDI +EGLLLLTN
Sbjct: 61  VAAPEPPRLWLYHKPAGLVTTERDEKGRPTVFGALPEEMPRVMSVGRLDIASEGLLLLTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG + R LELP+T WLR YRVR HG V+  KL  L++GI ++G+ Y  M VT D Q+G+N
Sbjct: 121 DGEIKRRLELPATGWLRRYRVRSHGYVEDAKLEPLRRGISVEGVRYQPMSVTFDRQQGAN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           AW+TV LREGKNREI++  E    KVNRLIRISYGPFQLG L AG   EV  K+LR+QLG
Sbjct: 181 AWMTVALREGKNREIRRAMEAIGIKVNRLIRISYGPFQLGNLAAGEVEEVRPKVLRDQLG 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
                + Q    A     +      P             
Sbjct: 241 LDARPKPQRRRAAGRDDGDAARPRGPARPGPTGPRKPPR 279


>gi|332307043|ref|YP_004434894.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
 gi|332174372|gb|AEE23626.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
          Length = 305

 Score =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 60/311 (19%), Positives = 114/311 (36%), Gaps = 11/311 (3%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           N      +  R++K I+ +G  SRRE +++I   RV +NG++       V+  D + VDG
Sbjct: 2   NTSNTTSSSIRLNKFISDSGFCSRREADKLIDSNRVTINGVIP-ELGTKVLPGDEVRVDG 60

Query: 65  VPLRK----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
             ++             YHKP+G+  T       + +         R+  +GRLD  +EG
Sbjct: 61  NLVKASAENKSDRVYLAYHKPVGITCTTERHVKGNIIDAI--GHRERIFPIGRLDKPSEG 118

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+ LT+DG +   +        + Y V     + +  +  +  G+ I         VT+ 
Sbjct: 119 LIFLTSDGDIVNKILRAENAHDKEYIVTVDRPLTERFIQAMAAGVPILDTVTKPCTVTMQ 178

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
               S     + L +G NR+I+++ E+  + V +L R      +L  L  G  R ++   
Sbjct: 179 ----SKFVFRIILTQGLNRQIRRMCEYLGYGVTKLKRSRIMSIRLAGLKVGQWRNLTPDE 234

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           + E                    +    +   ++     +   +  +   +         
Sbjct: 235 MHEINSAVAGSTKTAEDAKHKTDTAVPDKRTNHVAKRSGNRGLKSDRGPERSQVRKHSTS 294

Query: 301 LATPVHRRNLA 311
             T   R    
Sbjct: 295 AKTSSRRAPKR 305


>gi|114569169|ref|YP_755849.1| pseudouridine synthase, Rsu [Maricaulis maris MCS10]
 gi|114339631|gb|ABI64911.1| Pseudouridine synthase, Rsu [Maricaulis maris MCS10]
          Length = 372

 Score =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 139/352 (39%), Positives = 191/352 (54%), Gaps = 10/352 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T +R++K +ARAG+ASRREVERMI   RVKV+G  L+  A  V  ++HIEVDG  +   
Sbjct: 6   DTSERIAKFLARAGVASRREVERMIEGGRVKVDGKTLDTPAFKVTGSEHIEVDGKRIEPP 65

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             T+LW YHKP GLVTTH+DP+GR TVFD +P    RVIS+GRLD+ +EGLLLLTNDG L
Sbjct: 66  AATKLWRYHKPDGLVTTHADPEGRETVFDAIPKDIGRVISIGRLDLTSEGLLLLTNDGAL 125

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           AR LELPST W R YR R  G + +  L +L+ G+ ++GI YG M+V ++ + GSN W+ 
Sbjct: 126 ARALELPSTGWTRRYRARAFGSISESALKILRAGVTVEGIKYGPMEVEVERETGSNIWLE 185

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           VG+REGKNRE++K  +    +VNRLIRI+YGPFQLG L  G  + V  ++L +Q G  + 
Sbjct: 186 VGIREGKNREVRKALDAVGLRVNRLIRIAYGPFQLGQLEKGEIKSVPSRVLHDQCGHLID 245

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ--------KKLA 302
                   A           R            R      Q     ++         +  
Sbjct: 246 MGDTPTGQAIAKPRPANRAARKPGQKPDGKPGQRAMGGPGQPGLPKREVDDSLIEDARKG 305

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            P+  ++  +          +    +G+       S S   +    RT   +
Sbjct: 306 RPLDAKSTRARRGKD--GKPTAKPAAGRAAPRATTSRSETPRPDTPRTGGPR 355


>gi|212690763|ref|ZP_03298891.1| hypothetical protein BACDOR_00250 [Bacteroides dorei DSM 17855]
 gi|212666640|gb|EEB27212.1| hypothetical protein BACDOR_00250 [Bacteroides dorei DSM 17855]
          Length = 243

 Score =  191 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 61/235 (25%), Positives = 111/235 (47%), Gaps = 1/235 (0%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + +   P R++K +A AGI SRRE +  I    V VNG ++      +  TD ++    P
Sbjct: 1   MTDPNEPIRLNKFLANAGICSRREADEFITAGVVSVNGEVVTELGTKIKRTDEVKFHDEP 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +    +T + L      + T+    + ++ +     +   R+  VGRLD NT G+LLLTN
Sbjct: 61  VSIERKTYILLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTTGVLLLTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  P     ++Y V     V +  L+ +  G+ +         ++  ++    
Sbjct: 121 DGDLASKLTHPKYLKKKIYHVYCDKNVTKADLDQIAAGVTLDDGEIHADAISYASET-DK 179

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++ +
Sbjct: 180 SQVGIEIHSGKNRIVRRIFESLGYKVIKLDRVYFAGLTKKGLRRGDWRYLTEQEV 234


>gi|322387120|ref|ZP_08060731.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           infantis ATCC 700779]
 gi|321142107|gb|EFX37601.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           infantis ATCC 700779]
          Length = 241

 Score =  191 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 79/237 (33%), Positives = 129/237 (54%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVTDDKGRKTVVDLLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGIANKENLRPLTRGLEIDGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK + +     
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGESRRLNKKEISQLHTMA 236


>gi|83944513|ref|ZP_00956965.1| RNA pseudouridylate synthase family protein [Sulfitobacter sp.
           EE-36]
 gi|83844619|gb|EAP82504.1| RNA pseudouridylate synthase family protein [Sulfitobacter sp.
           EE-36]
          Length = 335

 Score =  191 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 140/321 (43%), Positives = 187/321 (58%), Gaps = 2/321 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++KV++RAGIASRRE ERMI   RV+VNG  ++  A+NV  +D I VDG P+ + E 
Sbjct: 17  GDRIAKVLSRAGIASRREAERMIEAGRVRVNGAQIDSPALNVTPSDAITVDGKPVGEPEP 76

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R+WL+HKP GLVTT+ D  GR T+FD+LP    RV+S+GRLD+N+EGLLLLTNDG + R
Sbjct: 77  PRVWLFHKPTGLVTTNRDEKGRGTIFDDLPEDMPRVMSIGRLDLNSEGLLLLTNDGEVKR 136

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            LELPS  WLR YRVR +G+   D L  L+KGI + G  +  M VTLD Q+G+NAW+TVG
Sbjct: 137 RLELPSNGWLRRYRVRVNGRPTDDMLEPLRKGITVDGEDFQPMTVTLDRQQGANAWLTVG 196

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           LREGKNREI++  E  N  VNRLIR SYGPFQLG L  G   E+ +K++R+QLG   + +
Sbjct: 197 LREGKNREIRRAMEAVNLSVNRLIRTSYGPFQLGELKTGEVEELKRKVVRDQLGL-EIAD 255

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
                     +     + R              +       G +   K   P + ++  +
Sbjct: 256 TTGTAIKKKPARIIKRKARKPGEPGPGRPGLPKEPGDKTATGKTIPGKP-KPGYGKSKPA 314

Query: 313 NVWMAKGIHSSFLSDSGQREE 333
                             R+ 
Sbjct: 315 RPASDPAPRKFGTRVKSTRKP 335


>gi|319938699|ref|ZP_08013063.1| pseudouridine synthase [Streptococcus anginosus 1_2_62CV]
 gi|319811749|gb|EFW08015.1| pseudouridine synthase [Streptococcus anginosus 1_2_62CV]
          Length = 241

 Score =  191 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 81/242 (33%), Positives = 129/242 (53%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q  V VNG ++   A  + S D +EV G P+   E  
Sbjct: 1   MRINKYIAHAGIASRRKAEELIKQGLVTVNGQVVRELATTIKSGDRVEVSGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVTDDKGRPTVVDLLPNVTERIYPVGRLDWDTSGALILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  D++ L  L KG+ + G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGVADKEVLRPLTKGVEVDGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE    +V++L R  +G   L  L  G  R ++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTQFGHLNLTGLRPGEARRLNKKEVSQLHNLAVTK 239

Query: 252 EA 253
           + 
Sbjct: 240 KK 241


>gi|157149683|ref|YP_001450946.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           gordonii str. Challis substr. CH1]
 gi|157074477|gb|ABV09160.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           gordonii str. Challis substr. CH1]
          Length = 242

 Score =  191 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 78/243 (32%), Positives = 131/243 (53%), Gaps = 3/243 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V +NG ++   A  V + D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTINGQVVRELATLVKTGDKVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ +D  GR TV D LP +  R+  VGRLD +T GLL+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVTDDKGRKTVVDLLPQVKERIYPVGRLDWDTSGLLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGIANKENLRPLTRGVEINGKKTKPAVYEIIKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+F+    +V++L R  +G   L  L  G +R ++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFQAVGLEVDKLSRTRFGHLDLTGLRPGESRRLNKKEISQLHNLAITK 239

Query: 252 EAQ 254
             +
Sbjct: 240 AGK 242


>gi|52143877|ref|YP_082953.1| pseudouridylate synthase [Bacillus cereus E33L]
 gi|51977346|gb|AAU18896.1| pseudouridylate synthase [Bacillus cereus E33L]
          Length = 242

 Score =  191 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 75/242 (30%), Positives = 129/242 (53%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVAPQDKVEVNNIPLEKEEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     + +   D        D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 62  YFLLYKPTGVISSVSDDKGRSVVT-DFFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G++++       +V + +       A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGEKIRMLERGVMLEDGKTAPARVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++   +++       +
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELTPHEVKQLRALASTK 240

Query: 252 EA 253
             
Sbjct: 241 PR 242


>gi|83955333|ref|ZP_00963988.1| RNA pseudouridylate synthase family protein [Sulfitobacter sp.
           NAS-14.1]
 gi|83840326|gb|EAP79500.1| RNA pseudouridylate synthase family protein [Sulfitobacter sp.
           NAS-14.1]
          Length = 335

 Score =  191 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 140/321 (43%), Positives = 187/321 (58%), Gaps = 2/321 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++KV++RAGIASRRE ERMI   RV+VNG  ++  A+NV  +D I VDG P+ + E 
Sbjct: 17  GDRIAKVLSRAGIASRREAERMIEAGRVRVNGAQIDSPALNVTPSDAITVDGKPVGEPEP 76

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R+WL+HKP GLVTT+ D  GR T+FD+LP    RV+S+GRLD+N+EGLLLLTNDG + R
Sbjct: 77  PRVWLFHKPTGLVTTNRDEKGRGTIFDDLPEDMPRVMSIGRLDLNSEGLLLLTNDGEVKR 136

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            LELPS  WLR YRVR +G+   D L  L+KGI + G  +  M VTLD Q+G+NAW+TVG
Sbjct: 137 RLELPSNGWLRRYRVRVNGRPTDDMLEPLRKGITVDGEDFQPMTVTLDRQQGANAWLTVG 196

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           LREGKNREI++  E  N  VNRLIR SYGPFQLG L  G   E+ +K++R+QLG   + +
Sbjct: 197 LREGKNREIRRAMEAVNLSVNRLIRTSYGPFQLGELKTGEVEELKRKVVRDQLGL-EIAD 255

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
                     +     + R              +       G +   K   P + ++  +
Sbjct: 256 TTGTAVKKKPARIIKRKARKPGEPGPGRPGLPKEPGDKTATGKTIPGKP-KPGYGKSKPA 314

Query: 313 NVWMAKGIHSSFLSDSGQREE 333
                             R+ 
Sbjct: 315 RPASDPAPRKFGTRVKSTRKP 335


>gi|239636840|ref|ZP_04677839.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           warneri L37603]
 gi|239597514|gb|EEQ80012.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           warneri L37603]
          Length = 246

 Score =  191 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 77/241 (31%), Positives = 130/241 (53%), Gaps = 3/241 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +R+ K IA +G  SRR+ E +I   +VKVNG ++      V ++D +EV+G+ L  
Sbjct: 2   SKELERLQKRIASSGYTSRRKAETLITDGKVKVNGHVVTELGTKVSNSDTVEVEGIKLE- 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E     L++KP  ++T+ SD  GR  V D    I +R+  VGRLD +T GLLLLTNDG 
Sbjct: 61  QEDKIYILFNKPAQVITSVSDDRGRKVVTDYFKDIETRIYPVGRLDYDTSGLLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNA 187
              ++  P     + Y  +  G + ++++  L+KGI ++       QV +    +  +  
Sbjct: 121 FTNLMTHPRYHIKKKYVAKLKGYLMREEVKALEKGIELEDGFTQPAQVKVKNQDKDKNTT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V + + EG+NR+++++FE F  +V++L RI +GP  L  L AG  R ++   ++     
Sbjct: 181 LVEITISEGRNRQVRRMFEHFGHQVSKLTRIQFGPLDLKGLNAGEGRVLTPHEVKTIRHL 240

Query: 248 H 248
            
Sbjct: 241 A 241


>gi|229029250|ref|ZP_04185341.1| Pseudouridine synthase [Bacillus cereus AH1271]
 gi|229172210|ref|ZP_04299774.1| Pseudouridine synthase [Bacillus cereus MM3]
 gi|228611198|gb|EEK68456.1| Pseudouridine synthase [Bacillus cereus MM3]
 gi|228732063|gb|EEL82954.1| Pseudouridine synthase [Bacillus cereus AH1271]
          Length = 242

 Score =  191 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 77/242 (31%), Positives = 129/242 (53%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     + +   D        D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 62  YFLLYKPTGVISSVSDDKGRSVVT-DFFPEIRQRLFPIGRLDYDTSGVLLMTNDGEFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++       QV +    ++   A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGEKIRMLERGVALEDGKTAPAQVKIISWDKRKETAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE+S   +++       +
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELSPHEVKQLRALASTK 240

Query: 252 EA 253
             
Sbjct: 241 PR 242


>gi|255526472|ref|ZP_05393383.1| pseudouridine synthase [Clostridium carboxidivorans P7]
 gi|296184845|ref|ZP_06853256.1| pseudouridine synthase [Clostridium carboxidivorans P7]
 gi|255509854|gb|EET86183.1| pseudouridine synthase [Clostridium carboxidivorans P7]
 gi|296050627|gb|EFG90050.1| pseudouridine synthase [Clostridium carboxidivorans P7]
          Length = 238

 Score =  191 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 109/232 (46%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAER 72
           +R+ K+++  G  +R+E++ ++ Q  V+++  +++ + + +   D  I V G  +   + 
Sbjct: 2   ERLDKILSNLGYGTRKEIKALVKQGLVEIDNEVVKDSGMKIDPDDKEIRVSGEMVNYRQN 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  T  + D       +      +   VGRLD +T GLLLLTNDG L  
Sbjct: 62  IYLIMNKPNGVVSATFDNYDETVVDLLDPEHQAFKPFPVGRLDKDTVGLLLLTNDGELNH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     ++Y       VDQ+ +   K GI +         ++ +     + + V V
Sbjct: 122 RLISPKWHVDKIYYAEIDKPVDQNDVEKFKIGITLDDGYKCLPGKLKILESDENGSKVEV 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            ++EGK  ++K++F   +  V  L RI +GP +L   L  G  RE+S+  ++
Sbjct: 182 TIQEGKFHQVKRMFNALDKNVVYLKRIKFGPMELDLDLEEGEYRELSEDEIK 233


>gi|198277516|ref|ZP_03210047.1| hypothetical protein BACPLE_03738 [Bacteroides plebeius DSM 17135]
 gi|198270014|gb|EDY94284.1| hypothetical protein BACPLE_03738 [Bacteroides plebeius DSM 17135]
          Length = 253

 Score =  191 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 111/241 (46%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K ++ +   P R++K +A AGI SRRE +  I    V VNG ++      V  +D +
Sbjct: 5   IEYKELLTDPDEPIRLNKFLANAGICSRREADEFITAGVVSVNGEIVTELGTKVKRSDEV 64

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P+    +  + L      + T+    + ++ +     +   R+  VGRLD NT G
Sbjct: 65  KFHDQPVNIERKVYVLLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTTG 124

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     V +  L+ + +GI +             
Sbjct: 125 VLLLTNDGDLASKLTHPKFLKKKIYHVYCDKNVTKADLDQIVQGITLDDGEIH-ADAISY 183

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 + V + +  GKNR ++++FE   ++V +L R+ +       L  G  R ++++ 
Sbjct: 184 ASDTDKSQVGIEIHSGKNRIVRRIFESLGYRVIKLDRVYFAGLTKKGLRRGDWRYLTEQE 243

Query: 241 L 241
           +
Sbjct: 244 V 244


>gi|254441794|ref|ZP_05055287.1| conserved hypothetical protein, putative [Octadecabacter
           antarcticus 307]
 gi|198251872|gb|EDY76187.1| conserved hypothetical protein, putative [Octadecabacter
           antarcticus 307]
          Length = 308

 Score =  191 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 141/297 (47%), Positives = 187/297 (62%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           N + ++    R++KV+ARAG+ASRRE E++I   RV VNG  +   A+NV   D I VDG
Sbjct: 12  NAIAKSVPGDRIAKVLARAGVASRRESEKIIEAGRVTVNGKTILTPALNVTDKDRIVVDG 71

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL + E  R+WLY+KPIGLVT+  D  GR TVFD LP    RV+SVGRLDIN+EGLLLL
Sbjct: 72  KPLAEPEPPRIWLYYKPIGLVTSERDEKGRETVFDTLPDDMPRVVSVGRLDINSEGLLLL 131

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG L R +ELPST WLR YRVR +G + + KL+ L+ GI I G+ Y  ++V  D Q+G
Sbjct: 132 TNDGELKRKMELPSTGWLRRYRVRINGSLSEAKLDELRAGIQIDGVHYAPVEVKFDRQQG 191

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +NAW+T+GLREGKNREI+K+ E     VNRL+RISYGPFQLGTL  G   EV ++I+R+Q
Sbjct: 192 ANAWLTMGLREGKNREIRKLMEAMGVAVNRLLRISYGPFQLGTLKPGKVEEVKQRIVRDQ 251

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +G     +  +    P        +      ++   D  +     +  N   K  + 
Sbjct: 252 MGLRETPKPTMVRKGPEKGKRPPPKRGTAASAKRHTDPAKRNSGPTSGNSAGKPPRR 308


>gi|27468095|ref|NP_764732.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           epidermidis ATCC 12228]
 gi|57866960|ref|YP_188633.1| pseudouridine synthase RluB [Staphylococcus epidermidis RP62A]
 gi|251810910|ref|ZP_04825383.1| pseudouridylate synthase [Staphylococcus epidermidis BCM-HMP0060]
 gi|293366546|ref|ZP_06613223.1| pseudouridine synthase RluB [Staphylococcus epidermidis
           M23864:W2(grey)]
 gi|27315641|gb|AAO04776.1|AE016748_10 ribosomal large subunit pseudouridine synthase B [Staphylococcus
           epidermidis ATCC 12228]
 gi|57637618|gb|AAW54406.1| pseudouridine synthase RluB [Staphylococcus epidermidis RP62A]
 gi|251805590|gb|EES58247.1| pseudouridylate synthase [Staphylococcus epidermidis BCM-HMP0060]
 gi|291319315|gb|EFE59684.1| pseudouridine synthase RluB [Staphylococcus epidermidis
           M23864:W2(grey)]
 gi|329725404|gb|EGG61887.1| pseudouridine synthase B, ribosomal large subunit [Staphylococcus
           epidermidis VCU144]
 gi|329735190|gb|EGG71482.1| pseudouridine synthase B, ribosomal large subunit [Staphylococcus
           epidermidis VCU045]
          Length = 245

 Score =  191 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 76/235 (32%), Positives = 131/235 (55%), Gaps = 3/235 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +R+ K IA +G  SRR+ E +I + RVKVNG  +      VM +D +EVDG+ + +
Sbjct: 2   SKEQERLQKRIANSGYTSRRKAEVLITEGRVKVNGQTVTELGSKVMPSDLVEVDGIKIEQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ++  +  Y     ++T+ SD  GR  V D    + SR+  VGRLD +T G+LLLTNDG 
Sbjct: 62  EDKIYILFYKPT-QVITSVSDDRGRRVVTDYFDDLESRIYPVGRLDYDTSGVLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNA 187
              ++  P     + Y  +  G + ++++  L+KGI ++       QV +    ++ +  
Sbjct: 121 FTNLMTHPRYHIKKKYVAKLKGYLMREEIKQLEKGIELEDGYTQPAQVKIKKQDKEKNTT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V + + EG+NR+++++FE+F  +VN+L RI +GP  L  L AG  R ++   ++
Sbjct: 181 LVEITISEGRNRQVRRMFEYFGHQVNKLTRIQFGPIDLKGLNAGEGRVLTPHEVK 235


>gi|320547375|ref|ZP_08041664.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           equinus ATCC 9812]
 gi|320447971|gb|EFW88725.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           equinus ATCC 9812]
          Length = 241

 Score =  191 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 83/242 (34%), Positives = 133/242 (54%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I +  V +NG ++   A  V S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGIASRRKAEELIKKGLVSINGKVVTELATTVKSGDIVEVEGTPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV D LP++  R+  VGRLD +T GLL+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVVDLLPNVTERIYPVGRLDWDTTGLLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIIKVDPEKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE     V++L R ++G   L  L  G +R +SKK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTNFGTLDLSGLRPGESRRLSKKEISQLHNLAVNK 239

Query: 252 EA 253
           + 
Sbjct: 240 QK 241


>gi|242242766|ref|ZP_04797211.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
 gi|242233902|gb|EES36214.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
          Length = 245

 Score =  191 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 76/241 (31%), Positives = 133/241 (55%), Gaps = 3/241 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +R+ K IA++G  SRR+ E +I + RVKVNG  +      VM +D +EVDG+ + +
Sbjct: 2   SKEQERLQKRIAKSGYTSRRKAEVLITEGRVKVNGQTVTELGSKVMPSDLVEVDGIKIEQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ++  +  Y     ++T+ SD  GR  V D    + SR+  VGRLD +T G+LLLTNDG 
Sbjct: 62  EDKIYILFYKPT-QVITSVSDDRGRRVVTDYFDDLESRIYPVGRLDYDTSGVLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNA 187
              ++  P     + Y  +  G + ++++  L+KGI ++       QV +    ++ +  
Sbjct: 121 FTNLMTHPRYHIKKKYIAKLKGYLMREEIKQLEKGIELEDGYTQPAQVKIKKQDKEKNTT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V + + EG+NR+++++FE+F  +VN+L+RI +GP  L  L AG  R ++   ++     
Sbjct: 181 LVEITISEGRNRQVRRMFEYFGHQVNKLVRIQFGPIDLKGLNAGEGRVLTPHEVKTLRHL 240

Query: 248 H 248
            
Sbjct: 241 A 241


>gi|52786201|ref|YP_092030.1| RluB [Bacillus licheniformis ATCC 14580]
 gi|163119522|ref|YP_079621.2| pseudouridine synthase [Bacillus licheniformis ATCC 14580]
 gi|319645211|ref|ZP_07999444.1| pseudouridine synthase [Bacillus sp. BT1B_CT2]
 gi|52348703|gb|AAU41337.1| RluB [Bacillus licheniformis ATCC 14580]
 gi|145903029|gb|AAU23983.2| pseudouridine synthase [Bacillus licheniformis ATCC 14580]
 gi|317393020|gb|EFV73814.1| pseudouridine synthase [Bacillus sp. BT1B_CT2]
          Length = 244

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 79/239 (33%), Positives = 121/239 (50%), Gaps = 3/239 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGIASRR+ E +I + RV VNG  +    V V S+D IEV+GV L   E  
Sbjct: 2   ERLQKVIAHAGIASRRKAEELIKEGRVTVNGKTVRELGVKVSSSDRIEVNGVQLESEEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     +++   D  GR  V D    +  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 62  YFLLYKPRG-VISAVKDDKGRKVVTDFFTEVEERIYPIGRLDYDTSGLLLLTNDGDFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVTV 191
           L  P  +  + Y  +  G   ++ L  L++G+ ++       +V L    +K   + V +
Sbjct: 121 LMHPKYEINKTYVAKLKGIPLKENLKKLERGVRLEDGKTAPAKVKLLSLDKKKQTSIVQI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
            + EG+NR+++++FE    +V +L R  Y    L  L  G  RE++   ++        
Sbjct: 181 TIHEGRNRQVRRMFEAIGHEVLKLKREEYAFLNLAGLKTGEKRELTPHEVKRLRALAEH 239


>gi|229058206|ref|ZP_04196594.1| Pseudouridine synthase [Bacillus cereus AH603]
 gi|228720070|gb|EEL71654.1| Pseudouridine synthase [Bacillus cereus AH603]
          Length = 242

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 77/242 (31%), Positives = 128/242 (52%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     + +   D        D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 62  YFLLYKPTGVISSVSDDKGRNVVT-DFFPEIRQRLFPIGRLDYDTSGVLLMTNDGEFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTV 191
           L  P  +  + Y  +  G +  DK+ +L++G+ ++       QV + +       A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGDKIRMLERGVALEDGKTAPAQVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++   +++       +
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVMKLKRERYAFLEVGSLRPGDARELTPHEVKQLRALASTK 240

Query: 252 EA 253
             
Sbjct: 241 PR 242


>gi|229010875|ref|ZP_04168072.1| Pseudouridine synthase [Bacillus mycoides DSM 2048]
 gi|228750549|gb|EEM00378.1| Pseudouridine synthase [Bacillus mycoides DSM 2048]
          Length = 242

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 75/242 (30%), Positives = 127/242 (52%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     + +   D        D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 62  YFLLYKPTGVISSVSDDKGRNVVT-DFFPEIRQRLFPIGRLDYDTSGVLLMTNDGEFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++       Q  + +       A V +
Sbjct: 121 LMHPRYKIEKTYVAKIKGPLTGEKIRMLERGVALEDGKTAPAQAKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++   +++       +
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVMKLKRERYAFLEVGSLRPGDARELTPHEVKQLRALASTK 240

Query: 252 EA 253
             
Sbjct: 241 PR 242


>gi|315223141|ref|ZP_07865009.1| conserved hypothetical protein [Streptococcus anginosus F0211]
 gi|315187830|gb|EFU21577.1| conserved hypothetical protein [Streptococcus anginosus F0211]
          Length = 241

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 80/242 (33%), Positives = 129/242 (53%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA +GIASRR+ E +I Q  V VNG ++   A  + S D +EV G P+   E  
Sbjct: 1   MRINKYIAHSGIASRRKAEELIKQGLVTVNGQVVRELATTIKSGDRVEVSGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVTDDKGRPTVVDLLPNVTERIYPVGRLDWDTSGALILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  D++ L  L KG+ + G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGVADKEVLRPLTKGVEVDGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE    +V++L R  +G   L  L  G  R ++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTQFGHLNLTGLRPGEARRLNKKEVSQLHNLAVTK 239

Query: 252 EA 253
           + 
Sbjct: 240 KK 241


>gi|304440267|ref|ZP_07400157.1| ribosomal large subunit pseudouridine synthase B [Peptoniphilus
           duerdenii ATCC BAA-1640]
 gi|304371316|gb|EFM24932.1| ribosomal large subunit pseudouridine synthase B [Peptoniphilus
           duerdenii ATCC BAA-1640]
          Length = 234

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 83/231 (35%), Positives = 124/231 (53%), Gaps = 2/231 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A AG+ASRR  E +I   RVKVNG ++      V    D +  D   L+    
Sbjct: 1   MRLQKYLAHAGVASRRTSEELILNGRVKVNGEVVTELGYKVDPLKDKVYFDDKKLKLVRE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KPIG+V+T  D   R TV  +L     R+  +GRLDI+T GLL+LTNDG LA 
Sbjct: 61  YTYVMINKPIGIVSTAKDEKNRKTV-VDLVPNDERIYPIGRLDIDTTGLLILTNDGELAN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  +VY     G   +  L+ L+ GI I G      ++ +     S++ V V 
Sbjct: 120 KLMHPRKEIDKVYIATVEGTPSKSGLDKLRNGITIDGYKLSKSEIKILKSYESDSIVRVT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + EG+NR++KK+FE     V +L RIS+GP +L  L  G+ R ++ + ++E
Sbjct: 180 IHEGRNRQVKKMFERIGNPVKKLKRISFGPIELANLEIGAYRYLTNEEIKE 230


>gi|163939386|ref|YP_001644270.1| pseudouridine synthase [Bacillus weihenstephanensis KBAB4]
 gi|229132378|ref|ZP_04261232.1| Pseudouridine synthase [Bacillus cereus BDRD-ST196]
 gi|163861583|gb|ABY42642.1| pseudouridine synthase [Bacillus weihenstephanensis KBAB4]
 gi|228651084|gb|EEL07065.1| Pseudouridine synthase [Bacillus cereus BDRD-ST196]
          Length = 242

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 75/242 (30%), Positives = 127/242 (52%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     + +   D        D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 62  YFLLYKPTGVISSVSDDKGRNVVT-DFFPEIRQRLFPIGRLDYDTSGVLLMTNDGEFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++       Q  + +       A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGEKIRMLERGVALEDGKTAPAQAKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++   +++       +
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVMKLKRERYAFLEVGSLRPGDARELTPHEVKQLRALASTK 240

Query: 252 EA 253
             
Sbjct: 241 PR 242


>gi|77362345|ref|YP_341919.1| putative ribosomal RNA pseudouridine synthase [Pseudoalteromonas
           haloplanktis TAC125]
 gi|76877256|emb|CAI89473.1| putative ribosomal RNA pseudouridine synthase [Pseudoalteromonas
           haloplanktis TAC125]
          Length = 327

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 71/323 (21%), Positives = 134/323 (41%), Gaps = 14/323 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE ++ I   RV VNGI      V V STD + VDG  L+   +  
Sbjct: 6   RLNKFISDTGFCSRREADKYIEDGRVTVNGIRP-EMGVKVSSTDVVLVDGKTLKAIPKRV 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
              Y+KP+G+  T       + V     +   R+  +GRLD  +EGL+ LTN+G +   +
Sbjct: 65  YIAYNKPVGITCTTERKIQSNIVKAV--NYPDRIFPIGRLDRPSEGLIFLTNEGDIVNKI 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y V     +++  +  +  G+ I        +VT    +      T+ L 
Sbjct: 123 LRAGNNHEKEYVVTVDKPLNRQFVAKMGNGVPILDTITKKCKVTQTGAQQ----FTIILT 178

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI-------LREQLGP 247
           +G NR+I+++ E+  ++V  L R+      L  L  G  R ++++        + +    
Sbjct: 179 QGLNRQIRRMCEYLGYEVVTLKRVRIMNVTLKGLKVGQWRHLTEQEMAIINNSISDSGKT 238

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                          S + + + +     +        K+ +  +    ++K+ +   ++
Sbjct: 239 QEHSVYDEANALQQQSPQAVAKPQKTSDKKRDFQGENPKRFNQGERTEERKKERSKTPYQ 298

Query: 308 RNLASNVWMAKGIHSSFLSDSGQ 330
           +   + V   K I ++  SDS  
Sbjct: 299 KRSTTYVGKPKSIKANKSSDSKG 321


>gi|56963596|ref|YP_175327.1| ribosomal large subunit pseudouridine synthase B [Bacillus clausii
           KSM-K16]
 gi|56909839|dbj|BAD64366.1| ribosomal large subunit pseudouridine synthase B [Bacillus clausii
           KSM-K16]
          Length = 242

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 75/243 (30%), Positives = 121/243 (49%), Gaps = 5/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ KVIA+AG+ASRR+ E  I + RVKVNG  +      V    D +EVDGVPL K E 
Sbjct: 2   ERLQKVIAKAGVASRRKAEEYIVEGRVKVNGETVTELGTKVNPSKDAVEVDGVPLDKEEP 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               LY     + T++ +   +            R+  +GRLD +T GLLLLTNDG  A 
Sbjct: 62  VYHLLYKPTGVVSTSNDEKGRKVVTDFI--ESEQRIYPIGRLDYDTSGLLLLTNDGEFAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW--VT 190
           +L  P  +  + Y  +  G  ++ ++  L+ GIV++       +  + +         V 
Sbjct: 120 LLMHPRYKIEKEYIAKVKGIPERKRIKELETGIVLEDGKTAPAKAKVLSIDKKKQTAIVR 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + + EGKNR+++++FE     V +L R  YG   LG L  G +R +    +++     + 
Sbjct: 180 LIIHEGKNRQVRRMFEAIGHPVVKLKRERYGFLTLGHLHPGESRPLKPIEVKQLKELAVT 239

Query: 251 EEA 253
           + +
Sbjct: 240 KPS 242


>gi|323351021|ref|ZP_08086678.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis VMC66]
 gi|322122745|gb|EFX94454.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis VMC66]
 gi|324991310|gb|EGC23243.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK353]
 gi|325696344|gb|EGD38235.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK160]
 gi|327474540|gb|EGF19945.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK408]
 gi|332362256|gb|EGJ40056.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK1056]
          Length = 242

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 83/240 (34%), Positives = 133/240 (55%), Gaps = 3/240 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q +V +NG ++   A NV S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGIASRRKAEELIRQGKVSINGQVVRELATNVKSGDRVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVVDLLPQVKERIYPVGRLDWDTSGILILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +GI I+G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTKPAVYEIIKVDPAKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+F+    +V++L R  +G   L  L  G  R++SKK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLSKKEVSQLHTLAVTK 239


>gi|284032996|ref|YP_003382927.1| pseudouridine synthase [Kribbella flavida DSM 17836]
 gi|283812289|gb|ADB34128.1| pseudouridine synthase [Kribbella flavida DSM 17836]
          Length = 244

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 79/242 (32%), Positives = 117/242 (48%), Gaps = 1/242 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
                 R+ K +A+AG+ASRR  E +I Q RV+V+G ++      V      I VDG  +
Sbjct: 2   TEEDGIRLQKALAQAGVASRRNAELLIEQGRVEVDGAVVTEFGTRVDPAVSVIRVDGERI 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                    + +KP G+VTT SDP GR  + D +     R+  +GRLD +TEGLLLLTN 
Sbjct: 62  PPVTAHVYLVLNKPRGVVTTMSDPQGRPCIADYVQERPERLFHIGRLDTDTEGLLLLTNH 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G  A  L  PS +  + Y     G V    L  L  G+ ++        V + ++     
Sbjct: 122 GEFAHRLAHPSYEVSKTYVAEVDGNVKPIVLRRLLDGVELEDGFAQADTVKVMSEIKGRT 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + + L EG+NR ++++F+     V RL R + GP + G L  G  RE+  K L + L  
Sbjct: 182 LIQITLHEGRNRIVRRMFDAVGHPVKRLTRTAIGPVRRGNLHTGELRELDPKELGQLLDL 241

Query: 248 HL 249
             
Sbjct: 242 VN 243


>gi|293364213|ref|ZP_06610939.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           oralis ATCC 35037]
 gi|306824561|ref|ZP_07457907.1| ribosomal large subunit pseudouridine synthase B [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
 gi|307702434|ref|ZP_07639390.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           oralis ATCC 35037]
 gi|291317059|gb|EFE57486.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           oralis ATCC 35037]
 gi|304433348|gb|EFM36318.1| ribosomal large subunit pseudouridine synthase B [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
 gi|307624016|gb|EFO02997.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           oralis ATCC 35037]
          Length = 240

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 79/241 (32%), Positives = 132/241 (54%), Gaps = 3/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + + D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKAGDKVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVTDDKGRKTVVDLLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  ++D L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGVANKDNLRPLTRGLEIDGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGESRRLNKKEISQLHTMAVTK 239

Query: 252 E 252
           +
Sbjct: 240 K 240


>gi|251781834|ref|YP_002996136.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
 gi|242390463|dbj|BAH80922.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
 gi|323126647|gb|ADX23944.1| hypothetical protein SDE12394_02010 [Streptococcus dysgalactiae
           subsp. equisimilis ATCC 12394]
          Length = 240

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 80/241 (33%), Positives = 131/241 (54%), Gaps = 3/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V +NG ++   A  V S D +E++G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTLNGQIITDLATTVKSGDVVEIEGSPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDT 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIIRVEADKNRSIVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE     V++L R  +G  +L  L  G +R ++KK + +       +
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTRFGTLELTGLRPGESRRLNKKEISQLHNLANTK 239

Query: 252 E 252
           +
Sbjct: 240 K 240


>gi|325687113|gb|EGD29136.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK72]
          Length = 242

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 82/240 (34%), Positives = 133/240 (55%), Gaps = 3/240 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q +V +NG ++   A NV S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGIASRRKAEELIRQGKVSINGQVVRELATNVKSGDCVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV + LP +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVVELLPQVKERIYPVGRLDWDTSGILILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +GI I+G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTKPAVYEIIKVDPAKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+F+    +V++L R  +G   L  L  G  R++SKK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLSKKEVSQLHTLAVTK 239


>gi|306834130|ref|ZP_07467250.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           bovis ATCC 700338]
 gi|304423703|gb|EFM26849.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           bovis ATCC 700338]
          Length = 241

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 82/242 (33%), Positives = 133/242 (54%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I +  V +NG ++   A  V + D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGIASRRKAEDLIKRGLVTINGKVVTELATTVKAGDVVEVEGTPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV D LP++  R+  VGRLD +T GLL+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVVDLLPNVTERIYPVGRLDWDTTGLLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGLATKENLRPLTRGVVIDGKKTKPARYNIIKVDPEKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE     V++L R ++G   L  L  G +R +SKK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTNFGTLDLSGLRPGESRRLSKKEISQLHNLAVNK 239

Query: 252 EA 253
           + 
Sbjct: 240 QK 241


>gi|89053708|ref|YP_509159.1| pseudouridine synthase, Rsu [Jannaschia sp. CCS1]
 gi|88863257|gb|ABD54134.1| Pseudouridine synthase Rsu [Jannaschia sp. CCS1]
          Length = 296

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 136/278 (48%), Positives = 176/278 (63%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +R++K ++RAG+ASRRE ERMI   RV VNG ++E  A+NV   D IEVD  PL + E
Sbjct: 3   DGERIAKRLSRAGVASRREAERMIEAGRVSVNGAVIESPALNVTDADVIEVDNAPLPEIE 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R R+W+YHKP GLVT+++D  GR TVFD LP    RV+SVGRLD+N+EGLLLLTNDGG+ 
Sbjct: 63  RPRVWMYHKPTGLVTSNADEKGRETVFDKLPDSLPRVMSVGRLDMNSEGLLLLTNDGGVK 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           R LELPST WLR YRVR  G    +    L++GIV +G  +  M+V+LD  +G+NAW+TV
Sbjct: 123 RKLELPSTGWLRKYRVRMKGAPKDEDFAPLRRGIVAEGERFQPMEVSLDRVQGANAWITV 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
           GLREGKNREI++      ++VNRLIR+SYGPF+LG L  G   EV  ++LR+QLG     
Sbjct: 183 GLREGKNREIRRAMAELGFEVNRLIRVSYGPFRLGELKPGEVEEVRPRVLRDQLGLEAAT 242

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
           E      A         +      S            +
Sbjct: 243 EGHAEPKAKPAFKGKRRKAPDARKSGERLAPRGKPSGA 280


>gi|331265750|ref|YP_004325380.1| ribosomal small subunit pseudouridine synthase A, 16S rRNA
           pseudouridylate synthase and related pseudouridylate
           synthases [Streptococcus oralis Uo5]
 gi|326682422|emb|CBZ00039.1| ribosomal small subunit pseudouridine synthase A, 16S rRNA
           pseudouridylate synthase and related pseudouridylate
           synthases [Streptococcus oralis Uo5]
          Length = 240

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 80/241 (33%), Positives = 131/241 (54%), Gaps = 3/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVTDDKGRKTVVDLLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  ++D L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYIARVKGVANKDNLRPLTRGLEIDGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE    +V++L R  +G   L  L  G  R ++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGEARRLNKKEISQLHTMAVTK 239

Query: 252 E 252
           +
Sbjct: 240 K 240


>gi|197106628|ref|YP_002132005.1| pseudouridine synthase, Rsu [Phenylobacterium zucineum HLK1]
 gi|196480048|gb|ACG79576.1| pseudouridine synthase, Rsu [Phenylobacterium zucineum HLK1]
          Length = 521

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 144/349 (41%), Positives = 203/349 (58%), Gaps = 7/349 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +R++K++AR+G+ SRR+VER+IA+ RV +NG +L   AV V   D + VDG  + + E 
Sbjct: 150 GERIAKLLARSGVGSRRDVERLIAEGRVAINGQVLTTPAVKVEPGDILTVDGAVVGEPEP 209

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R++ YHKP+GLVTTH DP GR TVF+ LP    R+ISVGRLD+N+EGLLLLTNDGGLAR
Sbjct: 210 VRVFRYHKPVGLVTTHKDPQGRPTVFEALPEGLPRLISVGRLDLNSEGLLLLTNDGGLAR 269

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----KGSNAW 188
            LELP+T  +R YR R HG++ Q++L+ LK GI ++G+ YG ++  LD      +G+N W
Sbjct: 270 ALELPATGVVRRYRARAHGRITQERLDTLKDGITVEGVRYGAIEARLDKAKEGHQGANLW 329

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +TV L+EGKNRE+++V E    KVNRLIR+SYGPF LGTL  G   EV  +++REQL  H
Sbjct: 330 LTVTLQEGKNREVRRVLEALGLKVNRLIRLSYGPFALGTLDVGEIEEVGPRVIREQLEGH 389

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ---KNGLSKQKKLATPV 305
           +  E     D P Y S      R    S   +      +  ++   K G +K K  A P 
Sbjct: 390 IPPENMPKGDRPQYRSPARKSRRAQAESRQAELVPPRPEAPAKKAYKAGWAKPKAKAKPH 449

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +    +     +                 +R+ S        +   ++
Sbjct: 450 AKTAGKAAKAKLQAKIEGKTIGPRHEPAAGKRTASQGKPPGRPKGGPQR 498


>gi|15901702|ref|NP_346306.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae TIGR4]
 gi|15903731|ref|NP_359281.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae R6]
 gi|111657282|ref|ZP_01408047.1| hypothetical protein SpneT_02001499 [Streptococcus pneumoniae
           TIGR4]
 gi|116515785|ref|YP_817104.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae D39]
 gi|148984326|ref|ZP_01817621.1| hypothetical protein CGSSp3BS71_03857 [Streptococcus pneumoniae
           SP3-BS71]
 gi|148989667|ref|ZP_01820999.1| hypothetical protein CGSSp6BS73_00460 [Streptococcus pneumoniae
           SP6-BS73]
 gi|148993332|ref|ZP_01822872.1| hypothetical protein CGSSp9BS68_07037 [Streptococcus pneumoniae
           SP9-BS68]
 gi|148998738|ref|ZP_01826176.1| hypothetical protein CGSSp11BS70_11759 [Streptococcus pneumoniae
           SP11-BS70]
 gi|149003915|ref|ZP_01828729.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae SP14-BS69]
 gi|149006471|ref|ZP_01830170.1| segregation and condensation protein B [Streptococcus pneumoniae
           SP18-BS74]
 gi|149011261|ref|ZP_01832508.1| segregation and condensation protein B [Streptococcus pneumoniae
           SP19-BS75]
 gi|149024998|ref|ZP_01836378.1| hypothetical protein CGSSp23BS72_10018 [Streptococcus pneumoniae
           SP23-BS72]
 gi|168483406|ref|ZP_02708358.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CDC1873-00]
 gi|168489848|ref|ZP_02714047.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae SP195]
 gi|168491811|ref|ZP_02715954.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CDC0288-04]
 gi|168494210|ref|ZP_02718353.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CDC3059-06]
 gi|168574937|ref|ZP_02720900.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae MLV-016]
 gi|169833469|ref|YP_001695240.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae Hungary19A-6]
 gi|182684817|ref|YP_001836564.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CGSP14]
 gi|194398119|ref|YP_002038463.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae G54]
 gi|221232609|ref|YP_002511763.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae ATCC 700669]
 gi|225855307|ref|YP_002736819.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae JJA]
 gi|225859636|ref|YP_002741146.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae 70585]
 gi|225861667|ref|YP_002743176.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae Taiwan19F-14]
 gi|237651140|ref|ZP_04525392.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CCRI 1974]
 gi|237820920|ref|ZP_04596765.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CCRI 1974M2]
 gi|270292159|ref|ZP_06198374.1| ribosomal large subunit pseudouridine synthase B [Streptococcus sp.
           M143]
 gi|289167211|ref|YP_003445478.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           mitis B6]
 gi|298230346|ref|ZP_06964027.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae str. Canada MDR_19F]
 gi|298254732|ref|ZP_06978318.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae str. Canada MDR_19A]
 gi|298503601|ref|YP_003725541.1| pseudouridylate synthase [Streptococcus pneumoniae TCH8431/19A]
 gi|303254617|ref|ZP_07340719.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae BS455]
 gi|303258820|ref|ZP_07344800.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae SP-BS293]
 gi|303261983|ref|ZP_07347929.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae SP14-BS292]
 gi|303263846|ref|ZP_07349768.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae BS397]
 gi|303265619|ref|ZP_07351518.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae BS457]
 gi|303269887|ref|ZP_07355630.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae BS458]
 gi|307068487|ref|YP_003877453.1| 16S rRNA uridine-516 pseudouridylate synthase-like pseudouridylate
           synthase [Streptococcus pneumoniae AP200]
 gi|307128069|ref|YP_003880100.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae 670-6B]
 gi|307705578|ref|ZP_07642430.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           mitis SK597]
 gi|307707612|ref|ZP_07644093.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           mitis NCTC 12261]
 gi|322377639|ref|ZP_08052129.1| ribosomal large subunit pseudouridine synthase B [Streptococcus sp.
           M334]
 gi|14973377|gb|AAK75946.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae TIGR4]
 gi|15459364|gb|AAL00492.1| Ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae R6]
 gi|116076361|gb|ABJ54081.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae D39]
 gi|147755432|gb|EDK62481.1| hypothetical protein CGSSp11BS70_11759 [Streptococcus pneumoniae
           SP11-BS70]
 gi|147758055|gb|EDK65060.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae SP14-BS69]
 gi|147761769|gb|EDK68732.1| segregation and condensation protein B [Streptococcus pneumoniae
           SP18-BS74]
 gi|147764251|gb|EDK71182.1| segregation and condensation protein B [Streptococcus pneumoniae
           SP19-BS75]
 gi|147923615|gb|EDK74728.1| hypothetical protein CGSSp3BS71_03857 [Streptococcus pneumoniae
           SP3-BS71]
 gi|147924984|gb|EDK76066.1| hypothetical protein CGSSp6BS73_00460 [Streptococcus pneumoniae
           SP6-BS73]
 gi|147928099|gb|EDK79118.1| hypothetical protein CGSSp9BS68_07037 [Streptococcus pneumoniae
           SP9-BS68]
 gi|147929491|gb|EDK80486.1| hypothetical protein CGSSp23BS72_10018 [Streptococcus pneumoniae
           SP23-BS72]
 gi|168995971|gb|ACA36583.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae Hungary19A-6]
 gi|172043185|gb|EDT51231.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CDC1873-00]
 gi|182630151|gb|ACB91099.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CGSP14]
 gi|183571751|gb|EDT92279.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae SP195]
 gi|183573862|gb|EDT94390.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CDC0288-04]
 gi|183575773|gb|EDT96301.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CDC3059-06]
 gi|183578730|gb|EDT99258.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae MLV-016]
 gi|194357786|gb|ACF56234.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae G54]
 gi|220675071|emb|CAR69649.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae ATCC 700669]
 gi|225720104|gb|ACO15958.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae 70585]
 gi|225723654|gb|ACO19507.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae JJA]
 gi|225728206|gb|ACO24057.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae Taiwan19F-14]
 gi|270279687|gb|EFA25529.1| ribosomal large subunit pseudouridine synthase B [Streptococcus sp.
           M143]
 gi|288906776|emb|CBJ21610.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           mitis B6]
 gi|298239196|gb|ADI70327.1| pseudouridylate synthase [Streptococcus pneumoniae TCH8431/19A]
 gi|301794836|emb|CBW37292.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae INV104]
 gi|301800653|emb|CBW33297.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae OXC141]
 gi|301802565|emb|CBW35326.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae INV200]
 gi|302598329|gb|EFL65373.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae BS455]
 gi|302637066|gb|EFL67555.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae SP14-BS292]
 gi|302640321|gb|EFL70776.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae SP-BS293]
 gi|302640590|gb|EFL70994.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae BS458]
 gi|302644746|gb|EFL74994.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae BS457]
 gi|302646884|gb|EFL77109.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae BS397]
 gi|306410024|gb|ADM85451.1| 16S rRNA uridine-516 pseudouridylate synthase-like pseudouridylate
           synthase [Streptococcus pneumoniae AP200]
 gi|306485131|gb|ADM92000.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae 670-6B]
 gi|307616325|gb|EFN95517.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           mitis NCTC 12261]
 gi|307620855|gb|EFN99939.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           mitis SK597]
 gi|321281404|gb|EFX58414.1| ribosomal large subunit pseudouridine synthase B [Streptococcus sp.
           M334]
 gi|327390035|gb|EGE88380.1| hypothetical protein SPAR5_1727 [Streptococcus pneumoniae GA04375]
 gi|332072212|gb|EGI82697.1| hypothetical protein SPAR148_1785 [Streptococcus pneumoniae
           GA17545]
 gi|332072697|gb|EGI83180.1| hypothetical protein SPAR50_1869 [Streptococcus pneumoniae GA17570]
 gi|332073025|gb|EGI83505.1| hypothetical protein SPAR68_1901 [Streptococcus pneumoniae GA41301]
 gi|332199894|gb|EGJ13969.1| hypothetical protein SPAR69_1806 [Streptococcus pneumoniae GA41317]
 gi|332200429|gb|EGJ14502.1| hypothetical protein SPAR93_1907 [Streptococcus pneumoniae GA47368]
 gi|332201284|gb|EGJ15355.1| hypothetical protein SPAR120_1791 [Streptococcus pneumoniae
           GA47901]
          Length = 240

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 80/241 (33%), Positives = 132/241 (54%), Gaps = 3/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVTDDKGRKTVVDLLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  ++D L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGVANKDNLRPLTRGLEIDGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGESRRLNKKEISQLHTMAVTK 239

Query: 252 E 252
           +
Sbjct: 240 K 240


>gi|315611769|ref|ZP_07886691.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis ATCC 49296]
 gi|322375935|ref|ZP_08050446.1| ribosomal large subunit pseudouridine synthase B [Streptococcus sp.
           C300]
 gi|315316184|gb|EFU64214.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis ATCC 49296]
 gi|321279203|gb|EFX56245.1| ribosomal large subunit pseudouridine synthase B [Streptococcus sp.
           C300]
          Length = 240

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 79/241 (32%), Positives = 132/241 (54%), Gaps = 3/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVTDDKGRKTVVDLLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGVANKENLRPLTRGLEIDGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGESRRLNKKEISQLHTMAVTK 239

Query: 252 E 252
           +
Sbjct: 240 K 240


>gi|307710771|ref|ZP_07647199.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           mitis SK321]
 gi|307617377|gb|EFN96549.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           mitis SK321]
          Length = 240

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 80/241 (33%), Positives = 132/241 (54%), Gaps = 3/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVTDDKGRKTVVDLLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  ++D L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGVANKDNLRPLTRGLDIDGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGESRRLNKKEISQLHTMAVTK 239

Query: 252 E 252
           +
Sbjct: 240 K 240


>gi|309807638|ref|ZP_07701581.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LactinV 01V1-a]
 gi|312875457|ref|ZP_07735460.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LEAF 2053A-b]
 gi|325911995|ref|ZP_08174397.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners UPII 143-D]
 gi|325912892|ref|ZP_08175270.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners UPII 60-B]
 gi|329921334|ref|ZP_08277772.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners SPIN 1401G]
 gi|308169119|gb|EFO71194.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LactinV 01V1-a]
 gi|311088968|gb|EFQ47409.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LEAF 2053A-b]
 gi|325476180|gb|EGC79344.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners UPII 143-D]
 gi|325477885|gb|EGC81019.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners UPII 60-B]
 gi|328934626|gb|EGG31130.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners SPIN 1401G]
          Length = 239

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 80/229 (34%), Positives = 117/229 (51%), Gaps = 3/229 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KVIA AGIASRR+ E +I   +V VNG L+      V   D IEV+GVP+ K +   
Sbjct: 4   RLQKVIAEAGIASRRKAEILITSGQVTVNGNLVTTLGTKVDDNDKIEVNGVPIHKEQLHT 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             LY     + T   D  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  L
Sbjct: 64  YLLYKPRNVVSTVS-DNKGRKTVTDFFKDLPYRLYPVGRLDYDTSGLLLMTNDGELANRL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVG 192
             P  +  +VY  +  G +   ++  LK G+ I G      +V +     +     V + 
Sbjct: 123 MHPKNEIEKVYVAKISGFLTASEIYDLKHGVTIDGRKTAPAKVKIIKTDKNRNIQLVQLT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EG   ++K +F+  N  V +L R  Y    L +L++G  RE++ + +
Sbjct: 183 IHEGHYHQVKNMFKAVNHLVEKLSRERYAFLTLKSLISGEYRELTHEEI 231


>gi|209966844|ref|YP_002299759.1| RNA pseudouridine synthase, putative [Rhodospirillum centenum SW]
 gi|209960310|gb|ACJ00947.1| RNA pseudouridine synthase, putative [Rhodospirillum centenum SW]
          Length = 551

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 140/346 (40%), Positives = 194/346 (56%), Gaps = 2/346 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           ++   +R+SK ++RAG+ SRR+ ER IA+ RV VNG +L+  AV V   D I VDG P+ 
Sbjct: 26  DDQGGERISKRLSRAGLCSRRDAERWIAEGRVSVNGRVLDTPAVTVRPGDRIVVDGQPVP 85

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + E TR+W YHKP GLVTT  D  GR TVFDNLP    RV+SVGRLD+ +EGLLLLTNDG
Sbjct: 86  EPEPTRVWRYHKPDGLVTTARDEKGRPTVFDNLPPELPRVVSVGRLDLTSEGLLLLTNDG 145

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LAR LELP T WLR YRVR HG  D+ ++  L +GI+I+GI YG ++  +D   G+N W
Sbjct: 146 ALARHLELPVTGWLRRYRVRVHGAPDEAQIAKLAQGIIIEGIEYGPIETVVDRSVGANTW 205

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +TV LREG+NRE+++V E     V+RLIR++YGPFQLG L  G   EV +++LR+QL   
Sbjct: 206 LTVSLREGRNREVRRVMEHLGLPVSRLIRVAYGPFQLGKLEPGQVEEVPRRVLRDQLPGF 265

Query: 249 LLEEAQVNLDAPIYSSETLVR--DRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              E     D    +    +R    P    +           +  +    +++    P  
Sbjct: 266 FAAEDAAAADGRPAAGPVRMRYDRLPRAARDAAPPSATKGGRAPAREAGGQEQARRGPRA 325

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           + +  S     + +         +R     R     + R+  R   
Sbjct: 326 KPSARSAREAVQRLLGDSRPPERERPARRPRPEERAALRAEGRGEG 371


>gi|254486476|ref|ZP_05099681.1| ribosomal large subunit pseudouridine synthase B [Roseobacter sp.
           GAI101]
 gi|214043345|gb|EEB83983.1| ribosomal large subunit pseudouridine synthase B [Roseobacter sp.
           GAI101]
          Length = 336

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 136/325 (41%), Positives = 186/325 (57%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            +     R++KV++RAG+ASRRE ERMI   RV+VNG+ ++  A+NV + D+I VDG P+
Sbjct: 12  TDTPPGDRIAKVLSRAGLASRREAERMIEAGRVRVNGVQIDSPALNVTAADNITVDGKPV 71

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              E  R+WLYHKP GLVTT+ D  GR T+FD+LP    RV+S+GRLD+N+EGLLLLTND
Sbjct: 72  GDPEPPRMWLYHKPTGLVTTNRDEKGRGTIFDDLPEDMPRVMSIGRLDLNSEGLLLLTND 131

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G + R LELPS  WLR YRVR +G+   + L  L++GI + G  +  M VTLD Q+G+NA
Sbjct: 132 GDVKRKLELPSNGWLRRYRVRVNGRPSDEVLEPLRRGITVDGEEFQPMTVTLDRQQGANA 191

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+TVGLREGKNREI++  E  N  VNRLIR SYGPFQLG L  G   E+ +K++R+QLG 
Sbjct: 192 WLTVGLREGKNREIRRAMEAVNLSVNRLIRTSYGPFQLGELKPGEVEELKRKVVRDQLGI 251

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            + +     +             +P           +     +    +   K        
Sbjct: 252 EIEDNTGTAVKKKPSHIVKRKPRKPGAPGPGRPGLPKEPGEKTATGKVIPGKPKPGYGKS 311

Query: 308 RNLASNVWMAKGIHSSFLSDSGQRE 332
           +                   S ++ 
Sbjct: 312 KAPRPPSDAPGPRKFGTRVKSTRKP 336


>gi|19879252|gb|AAK38326.1| hypothetical pseudouridine synthase [Flavobacterium johnsoniae
           UW101]
          Length = 304

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 64/274 (23%), Positives = 117/274 (42%), Gaps = 11/274 (4%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           ++EN    R++K I   G  SRRE +++I + RV +NG         V S D I +DG  
Sbjct: 1   MEENLK--RLNKFIGETGYCSRREADKLIEEGRVTINGA-AAEMGTKVSSDDEIRIDGKL 57

Query: 67  L-RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +  K E+     ++KP+G+  T +     + V     +   R+  +GRLD  +EGL+ +T
Sbjct: 58  IVEKHEKLVYLAFNKPVGIECTTNLEVKNNIVDYI--NYPKRIFPIGRLDKASEGLIFMT 115

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +   +        + Y V  +  + +  +  +  G+ I        +     ++ S
Sbjct: 116 NDGDIVNKILRARNNHEKEYTVTVNKPITERFIQRMGNGVPILDTVTKKCK----VEQIS 171

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++ E+  ++V  L RI      L  +  G  R+++   ++E  
Sbjct: 172 KYTFKIILTQGLNRQIRRMSEYLGYEVTALKRIRIINISL-DVPVGRYRDLTDAEIKELN 230

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVP 279
                         P  ++ T  R    I    P
Sbjct: 231 KLIEPSSKTEEASLPKAAAPTPSRRSTFISKNDP 264


>gi|296332020|ref|ZP_06874484.1| putative 16S pseudouridylate synthase [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305675585|ref|YP_003867257.1| putative 16S pseudouridylate synthase [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|296150791|gb|EFG91676.1| putative 16S pseudouridylate synthase [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305413829|gb|ADM38948.1| putative 16S pseudouridylate synthase [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 239

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 103/238 (43%), Gaps = 3/238 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A +G  SR+EV+ ++    V V+G   +    +V      + V G P+   + 
Sbjct: 1   MRLDKLLANSGYGSRKEVKAVVKAGAVMVDGKPAKDVKAHVDPDTQEVTVYGEPVDYRKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      L  T                +       GRLD +TEG LLLTNDG LA 
Sbjct: 61  IYLMMNKPQGVLSATEDSRQQTVIDLLTPEEMRFEPFPAGRLDKDTEGFLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V    Q+  + ++ L+ G+ I+G       +  +      N  V +
Sbjct: 121 RLLSPKKHVPKTYEVHLKSQISPEDISDLETGVYIEGGYKTKPAKAEIKANDNGNTVVYL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
            + EGK  ++K++ +    +V  L R+S GP  L   L  G  RE++++ L+    P 
Sbjct: 181 TITEGKFHQVKQMAKAVGNEVIYLKRLSMGPVSLDPALAPGEYRELTEEELKRLNEPQ 238


>gi|260583963|ref|ZP_05851711.1| ribosomal large subunit pseudouridine synthase B [Granulicatella
           elegans ATCC 700633]
 gi|260158589|gb|EEW93657.1| ribosomal large subunit pseudouridine synthase B [Granulicatella
           elegans ATCC 700633]
          Length = 241

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 78/240 (32%), Positives = 123/240 (51%), Gaps = 3/240 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AGIASRR+ E  I + RVKVNG ++      V  +D IEVDG+P+   E  
Sbjct: 2   ERLQKVMAHAGIASRRKCEAFIEEGRVKVNGTVVRELGYKVSQSDKIEVDGIPI-YKEEP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++++KP  ++++ +D  GR+ + D    I  RV  VGRLD +T GL+LLTNDG  A +
Sbjct: 61  VYFMFYKPKSVLSSVTDDRGRTVISDYFKDIPQRVYPVGRLDYDTTGLILLTNDGEFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW--VTV 191
           +  P     + Y  +  G      +  L++GI I G         + +         V++
Sbjct: 121 MTHPKHHVEKKYIAKVKGVPTPRHMRQLERGIWIDGKKTSKAVARILSVDTEKNTGIVSL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG N ++KK+FE     V +L R  +G   L  L  G  RE+    +++ +     E
Sbjct: 181 TIHEGWNHQVKKMFEAVELPVQKLKREEFGFLTLENLRPGDYRELRAFEVQKLVRLAKNE 240


>gi|229916174|ref|YP_002884820.1| pseudouridine synthase [Exiguobacterium sp. AT1b]
 gi|229467603|gb|ACQ69375.1| pseudouridine synthase [Exiguobacterium sp. AT1b]
          Length = 252

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 72/241 (29%), Positives = 115/241 (47%), Gaps = 5/241 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AG+ASRR+ E MI   RV+VNG ++      V     IEVDGV + + E  
Sbjct: 2   ERLQKVIAQAGVASRRKAEEMILDGRVRVNGKVVRELGTKVGPKSEIEVDGVKIEQEEHV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     + T   D   +     +L    +RV  VGRLD NT GL++LTNDG  + +
Sbjct: 62  YYLLYKPSGYVSTVDDDKGRKVI--TDLVPPGARVFPVGRLDYNTTGLIILTNDGEFSNM 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY---GDMQVTLDTQKGSNAWVT 190
           +  P  +  + Y  +         +  L+ G+ +          +++    QK + A + 
Sbjct: 120 MTHPKYKIQKRYVAKVKNIPSYLAIKQLESGVELDDGFKTGSAKVKMKSVDQKKNTAILE 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + + EG NR+I+++ E    +V +L R  +G   L  L  G  RE+S K + +       
Sbjct: 180 IVISEGHNRQIRRMVEAIGSEVIKLKREQFGFLTLDGLNTGDWRELSHKEISKLRELANP 239

Query: 251 E 251
            
Sbjct: 240 T 240


>gi|306830112|ref|ZP_07463296.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           mitis ATCC 6249]
 gi|304427638|gb|EFM30734.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           mitis ATCC 6249]
          Length = 240

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 76/241 (31%), Positives = 130/241 (53%), Gaps = 3/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + + D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKAGDKVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ +D  GR TV D L ++  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVTDDKGRKTVVDLLSNVKERIYPVGRLDWDTSGVLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  +++ L    +G+ I+G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGVANKENLRPFTRGVEIEGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE    +V++L R  +G   L  L  G  R ++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGEARRLNKKEISQLHTMAVTK 239

Query: 252 E 252
           +
Sbjct: 240 K 240


>gi|125718577|ref|YP_001035710.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK36]
 gi|125498494|gb|ABN45160.1| Ribosomal large subunit pseudouridine synthase B, putative
           [Streptococcus sanguinis SK36]
 gi|325695058|gb|EGD36961.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK150]
 gi|328946852|gb|EGG40989.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK1087]
 gi|332367409|gb|EGJ45142.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK1059]
          Length = 242

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 82/240 (34%), Positives = 133/240 (55%), Gaps = 3/240 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q +V +NG ++   A NV S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGIASRRKAEELIRQGKVSINGQVVRELATNVKSGDRVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV + LP +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVVELLPQVKERIYPVGRLDWDTSGILILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +GI I+G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTKPAVYEIIKVDPAKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+F+    +V++L R  +G   L  L  G  R++SKK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLSKKEVSQLHTLAVTK 239


>gi|148543988|ref|YP_001271358.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           reuteri DSM 20016]
 gi|184153383|ref|YP_001841724.1| putative pseudouridylate synthase [Lactobacillus reuteri JCM 1112]
 gi|227364901|ref|ZP_03848946.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           reuteri MM2-3]
 gi|325682474|ref|ZP_08161991.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           reuteri MM4-1A]
 gi|148531022|gb|ABQ83021.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           reuteri DSM 20016]
 gi|183224727|dbj|BAG25244.1| putative pseudouridylate synthase [Lactobacillus reuteri JCM 1112]
 gi|227070048|gb|EEI08426.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           reuteri MM2-3]
 gi|324978313|gb|EGC15263.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           reuteri MM4-1A]
          Length = 238

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 74/232 (31%), Positives = 115/232 (49%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K +A AG+ASRR  E++I Q +V VNG ++      V   D I V+GVP+   +  
Sbjct: 2   ERLQKAMAEAGVASRRASEKLILQGKVAVNGKIVTELGTKVGVHDEIVVNGVPIHHEQHV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              L      + + H D   R+ V       I  R+  VGRLD +T G+LLLTNDG LA 
Sbjct: 62  YYLLNKPRGVISSAHDDKGRRTVVDIIHDADIDERIYPVGRLDYDTTGILLLTNDGTLAN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            L  P  +  + Y  +  G V  D+L  L+ G++I G      +  L     +   + V 
Sbjct: 122 KLMHPKYEVEKTYVAKVEGIVKNDELKQLRLGVIIDGRKTKPAKSKLLNVDRAKKTSLVQ 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + + EG+N ++K +F+     V +L R +YGP  L  L  G  R +  + ++
Sbjct: 182 LTIHEGRNHQVKNMFKAVGHPVTKLHRETYGPLNLYGLQPGEFRALKPEEVQ 233


>gi|315646387|ref|ZP_07899505.1| pseudouridine synthase [Paenibacillus vortex V453]
 gi|315278030|gb|EFU41350.1| pseudouridine synthase [Paenibacillus vortex V453]
          Length = 251

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 81/251 (32%), Positives = 132/251 (52%), Gaps = 4/251 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K++A+AG+ASRR+ E +I + +V+VNG  +           D I V G P++  E+
Sbjct: 2   ERLQKIMAQAGVASRRKCEELILEGKVQVNGETVTELGTKADPAQDMITVSGKPIK-HEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G++T+ SDP+GR  V D L  I  RV  +GRLD +TEGLLLLTNDG  A 
Sbjct: 61  KVYVMLNKPKGVITSASDPEGRKIVSDYLKGIKERVYPIGRLDYDTEGLLLLTNDGEFAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
           +L  P     + Y     G     +L+ L++GI+++       +V        N  + ++
Sbjct: 121 LLSHPKYHVPKTYLATVKGVPHGTELDKLRQGIMLEDGMTSPAEVEYKDVDPDNKQSVIS 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + + EG+NR+++++FE  +  V RL RISYG   L  L  G  R ++   + + +     
Sbjct: 181 ITIHEGRNRQVRRMFEAISHPVLRLKRISYGDLLLQNLKRGLYRHLTADEINQLMQMAKA 240

Query: 251 EEAQVNLDAPI 261
            +   N     
Sbjct: 241 AKPGGNPKKKR 251


>gi|227515180|ref|ZP_03945229.1| pseudouridylate synthase [Lactobacillus fermentum ATCC 14931]
 gi|227086512|gb|EEI21824.1| pseudouridylate synthase [Lactobacillus fermentum ATCC 14931]
          Length = 241

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 74/237 (31%), Positives = 113/237 (47%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR  E +I   +VKVNG ++      V   D + V+G P+ + +  
Sbjct: 4   ERLQKVIAHAGVASRRAAEGLILAGKVKVNGQVVTELGTKVDGNDEVMVNGEPVEQEQHE 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLAR 132
              L      + + H D   ++ V              VGRLD +T GLL++TNDG LA 
Sbjct: 64  YYLLDKPRGVISSAHDDKGRKTVVDILKNEGVQTRVYPVGRLDYDTTGLLVMTNDGELAN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVT 190
            L  P  +  +VY  +  G V  D++ LL++G+ I G      +  L    Q+   + V 
Sbjct: 124 RLMHPRFEVDKVYIAKVKGLVSNDEMRLLREGVKIDGKKSQPARTKLLEANQRQKTSVVK 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           + + EG   ++KK+ E     V +L R SYGP  L  L  G  R++    +R     
Sbjct: 184 LTIHEGHYHQVKKMMEAVGHPVLKLHRESYGPLTLAGLNPGQFRKLKVDEVRALRKL 240


>gi|184155350|ref|YP_001843690.1| pseudouridine synthase [Lactobacillus fermentum IFO 3956]
 gi|260662137|ref|ZP_05863033.1| pseudouridine synthase [Lactobacillus fermentum 28-3-CHN]
 gi|183226694|dbj|BAG27210.1| pseudouridine synthase [Lactobacillus fermentum IFO 3956]
 gi|260553520|gb|EEX26412.1| pseudouridine synthase [Lactobacillus fermentum 28-3-CHN]
          Length = 241

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 74/237 (31%), Positives = 113/237 (47%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR  E +I   +VKVNG ++      V   D + V+G P+ + +  
Sbjct: 4   ERLQKVIAHAGVASRRAAEGLILAGKVKVNGQVVTELGTKVDGNDEVMVNGEPVEQEQHE 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLAR 132
              L      + + H D   ++ V              VGRLD +T GLL++TNDG LA 
Sbjct: 64  YYLLDKPRGVISSAHDDKGRKTVVDILKNEGVQTRVYPVGRLDYDTTGLLVMTNDGELAN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVT 190
            L  P  +  +VY  +  G V  D++ LL++G+ I G      +  L    Q+   + V 
Sbjct: 124 RLMHPRFEVDKVYIAKVKGLVSNDEMRLLREGVKIDGKKSQPARTKLLEANQRQKTSVVK 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           + + EG   ++KK+ E     V +L R SYGP  L  L  G  R++    +R     
Sbjct: 184 LTIHEGHYHQVKKMMEAVGHPVLKLHRESYGPLTLAGLNPGQFRKLKVDEVRALRKL 240


>gi|327490097|gb|EGF21885.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK1058]
          Length = 242

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 83/240 (34%), Positives = 134/240 (55%), Gaps = 3/240 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q +V +NG ++   A+NV S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGIASRRKAEELIKQGKVSINGQVVRELAINVKSGDRVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVVDLLPQVKERIYPVGRLDWDTSGILILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +GI I+G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTQPAVYEIIKVDPAKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+F+    +V++L R  +G   L  L  G  R++SKK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLSKKEVSQLHTLAVTK 239


>gi|324993667|gb|EGC25586.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK405]
 gi|324995021|gb|EGC26934.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK678]
 gi|327462936|gb|EGF09257.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK1]
          Length = 242

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 81/240 (33%), Positives = 133/240 (55%), Gaps = 3/240 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q +V +NG ++   A NV S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGIASRRKAEELIRQGKVSINGQVVRELATNVKSGDRVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV + LP +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVVELLPQVKERIYPVGRLDWDTSGILILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +GI I+G         +       + + + +
Sbjct: 120 MIHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTKPAVYEIIKVDPAKNRSVIQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+F+    +V++L R  +G   L  L  G  R++SKK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLSKKEVSQLHTLAVTK 239


>gi|325111054|ref|YP_004272122.1| pseudouridine synthase Rsu [Planctomyces brasiliensis DSM 5305]
 gi|324971322|gb|ADY62100.1| pseudouridine synthase Rsu [Planctomyces brasiliensis DSM 5305]
          Length = 368

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 97/340 (28%), Positives = 155/340 (45%), Gaps = 2/340 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPL 67
           E  T  R+ K +A AG+ SRR+ E +I   RV V+G+ +E   +NV      +E DG  L
Sbjct: 25  ETPTEFRLQKFLASAGLGSRRQCEELIRTGRVTVDGLPVENPGINVNPLKQVVEYDGERL 84

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +  ER + ++ +KP G++ T+ DP GR+ V D       R+  VGRLD ++EGLL++TND
Sbjct: 85  KP-ERLKYFVLNKPKGVLCTNHDPAGRTRVIDLFAKERVRLFPVGRLDEDSEGLLIVTND 143

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P  +  R YRV+  G    +KL  L+ GI  +   +  +      ++G +A
Sbjct: 144 GDLANQLAHPRYRIYRTYRVQVAGFPTNEKLQQLRDGIFFREGKFQVISAKFAGKQGKSA 203

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           ++ + L +G NREI+++F     KV  L RI++GP +LG    G  RE+++  L E    
Sbjct: 204 FLEIVLGQGHNREIRRLFARIGHKVMSLQRIAFGPIRLGKQKVGQYRELTRNELEELRSI 263

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               +           S      R +  +              +  G  +       + R
Sbjct: 264 LERNKKTPPKGPRSGGSGNSSPKRGSKGAPKGRRKPEGSGRKPEMAGSEEATPQKKRIRR 323

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            N +  V  + G      S    R       P+   K++ 
Sbjct: 324 PNNSPTVGASGGKSGGRPSGGKSRSGYGSSKPAAGKKKTK 363


>gi|325690957|gb|EGD32957.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK115]
          Length = 242

 Score =  190 bits (481), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 83/240 (34%), Positives = 133/240 (55%), Gaps = 3/240 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q +V +NG ++   A NV S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGIASRRKAEELIRQGKVSINGQVVRELATNVKSGDRVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVVDLLPQVKERIYPVGRLDWDTSGILILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +GI I+G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTQPAVYEIIKVDPAKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+F+    +V++L R  +G   L  L  G  R++SKK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLSKKEVSQLHTLAVTK 239


>gi|330685968|gb|EGG97591.1| pseudouridine synthase B, ribosomal large subunit [Staphylococcus
           epidermidis VCU121]
          Length = 246

 Score =  190 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 76/241 (31%), Positives = 130/241 (53%), Gaps = 3/241 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +R+ K IA +G  SRR+ E +I   +VKVNG ++      V ++D +EV+G+ L  
Sbjct: 2   SKELERLQKRIASSGYTSRRKAETLITDGKVKVNGQVVTELGTKVSNSDTVEVEGIKLE- 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E     L++KP  ++T+ SD  GR  V D    I +R+  VGRLD +T GLLLLTNDG 
Sbjct: 61  QEDKIYILFNKPAQVITSVSDDRGRKVVTDYFKDIETRIYPVGRLDYDTSGLLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNA 187
              ++  P     + Y  +  G + ++++  L+KGI ++       QV +    +  +  
Sbjct: 121 FTNLMTHPRYHIKKKYVAKLKGYLMREEVKALEKGIELEDGFTQPAQVKVKNQDKDKNTT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V + + EG+NR+++++FE F  +V++L RI +GP  +  L AG  R ++   ++     
Sbjct: 181 LVEITISEGRNRQVRRMFEHFGHQVSKLTRIQFGPLDIKGLNAGEGRVLTPHEVKTIRHL 240

Query: 248 H 248
            
Sbjct: 241 A 241


>gi|162452113|ref|YP_001614480.1| pseudouridine synthase [Sorangium cellulosum 'So ce 56']
 gi|161162695|emb|CAN94000.1| Pseudouridine synthase [Sorangium cellulosum 'So ce 56']
          Length = 399

 Score =  190 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 93/342 (27%), Positives = 145/342 (42%), Gaps = 8/342 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K+IARAG+ASRR  E +I   RV+VNG ++    +      D IEVDG  L  +E 
Sbjct: 3   ERLQKIIARAGVASRRASEELILAGRVRVNGRVVTELGLKADRQKDRIEVDGKRL-VSEA 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 HKP  +V+T  DP+GR TV D++    +R+  VGRLD  T G+LL+TNDG  A 
Sbjct: 62  PVYVALHKPRNVVSTLRDPEGRPTVADHVRGTGARLYPVGRLDFATSGILLMTNDGDFAN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y ++  G +  D L   ++GI ++       +  L   +G   W+ V 
Sbjct: 122 ALLHPRGGVPKTYVLKVQGVMSDDDLTPWREGIRLEDGVTLPAEARLLRHEGDKTWLEVT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           LREG+N++I+++ E   W V RL R ++       L  G  R ++   L      H+ E 
Sbjct: 182 LREGRNQQIRRMGEATGWPVMRLARTTFAGVSSEGLRPGEWRALTVDEL-----LHIREA 236

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
             V                 +  +               +       +   P   R  + 
Sbjct: 237 FGVPKRIRGAVMGASSGPVDHRRTASSARSGAKASPRPTQEAAGAAARSRGPAQPRVRSR 296

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               A        +    R      +PS P++    RT+  +
Sbjct: 297 ANADAPSAPGQGPAGRTARSR-TDAAPSTPARSPAGRTARSR 337


>gi|116629543|ref|YP_814715.1| 16S rRNA uridine-516 pseudouridylate synthase related enzyme
           [Lactobacillus gasseri ATCC 33323]
 gi|116095125|gb|ABJ60277.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           gasseri ATCC 33323]
          Length = 245

 Score =  190 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 77/238 (32%), Positives = 127/238 (53%), Gaps = 3/238 (1%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +++E+   +R+ KVIA+AG+ASRR+ E+MI+  +V VNG  +      V  +D IEV+GV
Sbjct: 1   MMKESKMAERLQKVIAQAGVASRRKAEKMISAGQVTVNGKKITELGTKVEPSDKIEVNGV 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P+ K        Y     ++++  D  GR TV D    +  R+  VGRLD +T GLLL+T
Sbjct: 61  PIEKETLHTYLFYKPRG-VISSVKDDKGRKTVVDFFEDVPYRLYPVGRLDYDTSGLLLMT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQK 183
           NDG LA  L  P  +  +VY  +  G +  + +  L  G+ I G      ++ +    +K
Sbjct: 120 NDGELANKLMHPRNEVPKVYVAKIKGLLSPEDIRSLTHGVRIDGRKSAPAKLKILKTDEK 179

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +   V + + EG   ++K++FE  +  V +L R  Y    L +L +G  RE++ + +
Sbjct: 180 KNTQIVQLTIHEGHYHQVKRMFEAVHHFVEKLSREKYAFLTLKSLTSGEYRELTHEEV 237


>gi|259500661|ref|ZP_05743563.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           iners DSM 13335]
 gi|302191350|ref|ZP_07267604.1| 16S rRNA uridine-516 pseudouridylate synthase related enzyme
           [Lactobacillus iners AB-1]
 gi|312871408|ref|ZP_07731503.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LEAF 3008A-a]
 gi|315653504|ref|ZP_07906425.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           iners ATCC 55195]
 gi|259168045|gb|EEW52540.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           iners DSM 13335]
 gi|311093061|gb|EFQ51410.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LEAF 3008A-a]
 gi|315489195|gb|EFU78836.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           iners ATCC 55195]
          Length = 239

 Score =  190 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 80/229 (34%), Positives = 118/229 (51%), Gaps = 3/229 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KVIA AGIASRR+ E +I   +V VNG L+      V   D IEV+GVP+ K +   
Sbjct: 4   RLQKVIAEAGIASRRKAEILITSGQVTVNGNLVTTLGTKVDDNDKIEVNGVPIHKEQLHT 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             LY     + T   D  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  L
Sbjct: 64  YLLYKPRNVVSTVS-DNKGRKTVTDFFKDLPYRLYPVGRLDYDTSGLLLMTNDGELANRL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVG 192
             P  +  +VY  +  G +   ++  LK G+ I G      +V +     +     V + 
Sbjct: 123 MHPKNEIEKVYVAKISGFLTASEIYDLKHGVTIDGRKTAPAKVKIIKTDKNRNIQLVQLT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EG   ++K +F+  N  V++L R  Y    L +L++G  RE++ + +
Sbjct: 183 IHEGHYHQVKNMFKAVNHLVDKLSRERYAFLTLKSLISGEYRELTHEEI 231


>gi|225378037|ref|ZP_03755258.1| hypothetical protein ROSEINA2194_03697 [Roseburia inulinivorans DSM
           16841]
 gi|225210038|gb|EEG92392.1| hypothetical protein ROSEINA2194_03697 [Roseburia inulinivorans DSM
           16841]
          Length = 261

 Score =  190 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 64/239 (26%), Positives = 113/239 (47%), Gaps = 5/239 (2%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDG 64
           I +      R+ K +   G+ +R EV++++  +++ VNG ++ +    V    D I   G
Sbjct: 17  IEKGKNELMRLDKFLTEMGLGTRSEVKKILKTKQITVNGEIVTKPETKVAPENDQISYKG 76

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P+   E      Y     + T   D   ++ +     ++ S +  VGRLDI+TEGLLL+
Sbjct: 77  EPVTYCEYEYYLFYKPAGCV-TATEDQLHKTVMDYLTDTVRSDLFPVGRLDIDTEGLLLI 135

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQK 183
           TNDG LA  L  P+    + Y     G V +  +N  + G+ I         ++ +  + 
Sbjct: 136 TNDGALAHDLLSPAKHVEKTYYAVIDGVVTEKDVNSFENGVDIGEEKLTKPGKLRIL-KS 194

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
              + + + + EG+  ++K++FE    KV  L RIS GP QL   L  G  R ++++ +
Sbjct: 195 EPESEIELTITEGRFHQVKRMFEAVGKKVLYLKRISMGPLQLTDDLKPGEYRPLTEEEI 253


>gi|327462027|gb|EGF08356.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK1057]
          Length = 242

 Score =  190 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 81/240 (33%), Positives = 133/240 (55%), Gaps = 3/240 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q +V +NG ++   A NV S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGIASRRKAEELIRQGKVSINGQVVCELATNVKSGDRVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV + LP +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVVELLPQVKERIYPVGRLDWDTSGILILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +GI I+G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTKPAVYEIIKVDPAKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+F+    +V++L R  +G   L  L  G  R+++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLNKKEVSQLHTLAVTK 239


>gi|28378541|ref|NP_785433.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|254556755|ref|YP_003063172.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
 gi|300767486|ref|ZP_07077398.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|308180698|ref|YP_003924826.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
 gi|28271377|emb|CAD64282.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|254045682|gb|ACT62475.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
 gi|300495305|gb|EFK30461.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|308046189|gb|ADN98732.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
          Length = 238

 Score =  190 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 81/237 (34%), Positives = 114/237 (48%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AGIASRR+ E +I    VKVNG  +    V V  +DH+EVDGVPL   +  
Sbjct: 3   ERLQKVMAEAGIASRRKSEVLITSGHVKVNGKTVTTLGVKVEPSDHVEVDGVPLNAEKLV 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     + T   D  GR TV D    +  R+  VGRLD +T GLL++TNDG LA  
Sbjct: 63  YYLFYKPRGVVTTV-HDEKGRKTVLDFFEDVPERIYPVGRLDYDTSGLLIMTNDGALANR 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           L  P  +  + Y  +  G      L  L+ G+ I G      +  L       +NA V +
Sbjct: 122 LTHPKYEVKKTYLAKVEGVPTNADLKQLRLGVEIDGRKTAPAKSNLLDSDHKKNNALVQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + EG N ++KK+       V +L R  YG   L +L  G  R++    + +  G  
Sbjct: 182 TIHEGHNHQVKKMLAAVGHPVTKLKRERYGVLDLQSLQPGEYRKLKPIEISKLKGER 238


>gi|309804173|ref|ZP_07698251.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LactinV 11V1-d]
 gi|308163756|gb|EFO66025.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LactinV 11V1-d]
          Length = 239

 Score =  190 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 80/229 (34%), Positives = 116/229 (50%), Gaps = 3/229 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KVIA AGIASRR  E +I   +V VNG L+      V   D IEV+GVP+ K +   
Sbjct: 4   RLQKVIAEAGIASRRNAEILITSGQVTVNGNLVTTLGTKVDDNDKIEVNGVPIHKEQLHT 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             LY     + T   D  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  L
Sbjct: 64  YLLYKPRNVVSTVS-DNKGRKTVTDFFKDLPYRLYPVGRLDYDTSGLLLMTNDGELANRL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVG 192
             P  +  +VY  +  G +   ++  LK G+ I G      +V +     +     V + 
Sbjct: 123 MHPKNEIEKVYVAKISGFLTASEIYDLKHGVTIDGRKTAPAKVKIIKTDKNRNIQLVQLT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EG   ++K +F+  N  V +L R  Y    L +L++G  RE++ + +
Sbjct: 183 IHEGHYHQVKNMFKAVNHLVEKLSRERYAFLTLKSLISGEYRELTHEEI 231


>gi|171780251|ref|ZP_02921155.1| hypothetical protein STRINF_02039 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171281599|gb|EDT47034.1| hypothetical protein STRINF_02039 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 241

 Score =  190 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 82/242 (33%), Positives = 133/242 (54%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I +  V +NG ++   A  V + D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGIASRRKAEDLIKRGLVTINGKVVTELATTVKAGDVVEVEGTPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV D LP++  R+  VGRLD +T GLL+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVVDLLPNVTERIYPVGRLDWDTTGLLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGLATKENLRPLTRGVVIDGKKTKPARYNIIKVDPEKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE     V++L R ++G   L  L  G +R +SKK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFELVGLLVDKLSRTNFGTLDLSGLRPGESRRLSKKEISQLHNLAVNK 239

Query: 252 EA 253
           + 
Sbjct: 240 QK 241


>gi|227544893|ref|ZP_03974942.1| pseudouridylate synthase [Lactobacillus reuteri CF48-3A]
 gi|300910080|ref|ZP_07127540.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           reuteri SD2112]
 gi|227185105|gb|EEI65176.1| pseudouridylate synthase [Lactobacillus reuteri CF48-3A]
 gi|300892728|gb|EFK86088.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           reuteri SD2112]
          Length = 238

 Score =  190 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 74/232 (31%), Positives = 115/232 (49%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K +A AG+ASRR  E++I Q +V VNG ++      V   D I V+GVP+   +  
Sbjct: 2   ERLQKAMAEAGVASRRASEKLILQGKVAVNGKIVTELGTKVGVHDEIVVNGVPIHHEQHV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              L      + + H D   R+ V       I  R+  VGRLD +T G+LLLTNDG LA 
Sbjct: 62  YYLLNKPRGVISSAHDDKGRRTVVDIIHDAEIDERIYPVGRLDYDTTGILLLTNDGALAN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            +  P  +  + Y  +  G V  D+L  L+ G+VI G      +  L     +   + V 
Sbjct: 122 KMMHPKYEVEKTYVAKVEGIVKNDELKQLRLGVVIDGRKTKPAKSKLLNVDRAKKTSLVQ 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + + EG+N ++K +F+     V +L R +YGP  L  L  G  R +  + ++
Sbjct: 182 LTIHEGRNHQVKNMFKAVGHPVTKLHRETYGPLNLYGLQPGEFRALKPEEVQ 233


>gi|85705167|ref|ZP_01036267.1| RNA pseudouridylate synthase family protein [Roseovarius sp. 217]
 gi|85670489|gb|EAQ25350.1| RNA pseudouridylate synthase family protein [Roseovarius sp. 217]
          Length = 269

 Score =  189 bits (480), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 140/265 (52%), Positives = 175/265 (66%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           + +  +    +R++KVIARAGIASRRE ER+I   RV VNG  + RAA+NV   D + VD
Sbjct: 5   RRMNTKTPEGERIAKVIARAGIASRREAERLIEAGRVTVNGQKVLRAALNVTPADKVVVD 64

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G  L   E  RLWLYHKP GLVTT  D  GRST++D+LP    RV+SVGRLD+N+EGLLL
Sbjct: 65  GRALDAPEPARLWLYHKPTGLVTTTRDEQGRSTIYDDLPEDMPRVMSVGRLDLNSEGLLL 124

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG L R LELPST WLR YRVR +G+        L+KG+V+ G  +  M VTLD Q+
Sbjct: 125 LTNDGELKRKLELPSTGWLRRYRVRVNGRPTDGTFEPLRKGLVVDGEAFQPMMVTLDRQQ 184

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           G+NAW+TV +REGKNREI++  E     VNRLIR+SYGPFQLG L  G+  E+  ++LR+
Sbjct: 185 GANAWITVSIREGKNREIRRAMEAVGLVVNRLIRLSYGPFQLGQLKPGAVEEIRPRVLRD 244

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLV 268
           QLG     EA+    A         
Sbjct: 245 QLGMKEEPEAEQPKPARPKPQRRRR 269


>gi|49184399|ref|YP_027651.1| RNA pseudouridine [Bacillus anthracis str. Sterne]
 gi|165872651|ref|ZP_02217281.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0488]
 gi|167634452|ref|ZP_02392773.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0442]
 gi|167641611|ref|ZP_02399857.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0193]
 gi|170689224|ref|ZP_02880420.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0465]
 gi|170706366|ref|ZP_02896827.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0389]
 gi|177651473|ref|ZP_02934262.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0174]
 gi|190568102|ref|ZP_03021012.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis Tsiankovskii-I]
 gi|227815681|ref|YP_002815690.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. CDC 684]
 gi|229602768|ref|YP_002865978.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0248]
 gi|254682364|ref|ZP_05146225.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. CNEVA-9066]
 gi|254733779|ref|ZP_05191493.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. Western North America USA6153]
 gi|254740530|ref|ZP_05198221.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. Kruger B]
 gi|254753919|ref|ZP_05205954.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. Vollum]
 gi|254759015|ref|ZP_05211042.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. Australia 94]
 gi|270000599|ref|YP_003329038.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. Ames]
 gi|291612213|ref|YP_003541027.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. 'Ames Ancestor']
 gi|49178326|gb|AAT53702.1| RNA pseudouridine [Bacillus anthracis str. Sterne]
 gi|164711595|gb|EDR17142.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0488]
 gi|167510404|gb|EDR85804.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0193]
 gi|167530340|gb|EDR93066.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0442]
 gi|170128900|gb|EDS97766.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0389]
 gi|170666779|gb|EDT17546.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0465]
 gi|172082751|gb|EDT67814.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0174]
 gi|190560836|gb|EDV14811.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis Tsiankovskii-I]
 gi|224552864|gb|ACN55073.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. 'Ames Ancestor']
 gi|227004794|gb|ACP14537.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. CDC 684]
 gi|229267176|gb|ACQ48813.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0248]
 gi|269850258|gb|ACZ49988.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. Ames]
          Length = 242

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 75/241 (31%), Positives = 127/241 (52%), Gaps = 3/241 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E   
Sbjct: 3   RLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEEPVY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             LY     + +   D        D  P I  R+  +GRLD +T G+LL+TNDG  A VL
Sbjct: 63  FLLYKPTGVISSVSDDKGRSVVT-DFFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANVL 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVG 192
             P  +  + Y  +  G +  +K+ +L++G+ ++       +V + +       A V + 
Sbjct: 122 MHPRYKVEKTYVAKIKGPLTGEKIRMLERGVTLEDGKTAPARVKIISWDKRKEMAIVQLT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++   +++       + 
Sbjct: 182 IHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELTPHEVKQLRALASTKP 241

Query: 253 A 253
            
Sbjct: 242 R 242


>gi|144897623|emb|CAM74487.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Magnetospirillum
           gryphiswaldense MSR-1]
          Length = 287

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 138/278 (49%), Positives = 184/278 (66%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           + + E    +R++K +ARAGI SRR+ E++I  ++V VNG++LE  A  V   D I VDG
Sbjct: 10  DTLPETEEKERIAKRLARAGICSRRDAEKLITSRKVAVNGVVLESPAFLVGPGDRIVVDG 69

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             + +AE+ R+W YHKP GLVTTH DP GR+TVF+ LP+   RVISVGRLD+N+EGLLLL
Sbjct: 70  QLVPEAEKARVWRYHKPAGLVTTHRDPQGRATVFEKLPATMPRVISVGRLDLNSEGLLLL 129

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG LAR LELP+  W+R YRVR HG ++ + L  L+KG+ I G+ YG ++  LD QKG
Sbjct: 130 TNDGELARSLELPAAGWVRRYRVRVHGTIEPESLVPLEKGLTIDGVKYGPIKAILDRQKG 189

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           SNAW+T+ L+EGKNREI++V E   W V+RLIR+SYGPFQLG+L  G   EV  KI++EQ
Sbjct: 190 SNAWLTISLKEGKNREIRRVMEHLGWPVSRLIRVSYGPFQLGSLEEGGVEEVPGKIVKEQ 249

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDF 282
           LG      A+ + +          +      S      
Sbjct: 250 LGQGGGNWAKADTEDRPRPPSNHKKPHAGKASHENRRR 287


>gi|299535393|ref|ZP_07048715.1| putative RNA pseudouridine synthase ytzF [Lysinibacillus fusiformis
           ZC1]
 gi|298729154|gb|EFI69707.1| putative RNA pseudouridine synthase ytzF [Lysinibacillus fusiformis
           ZC1]
          Length = 237

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 67/238 (28%), Positives = 110/238 (46%), Gaps = 4/238 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-VDGVPLRKAER 72
            R+ K++A  G  SR+EV++++ Q+ V V+G  ++ AA++V     I  V G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKQLLKQKAVTVDGAYVKDAALHVDPEQQIVSVFGERVVYTEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +   P  +  T    D              +   VGRLD +TEGLLLLTNDG LA 
Sbjct: 61  VYFIMNKPPGVISATEDLRDETVIDLLEPLHQHFQPFPVGRLDKDTEGLLLLTNDGHLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY  +  G V ++       GI +         ++ +  +    + + +
Sbjct: 121 NLLSPKKHVPKVYYAQIEGVVTEEDAEKFANGIELDDGYVTKPGKLVIL-KSAQQSEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
            ++EGK  ++K++FE    +V  L RIS G  +L   L  G  RE++ + L +    H
Sbjct: 180 TIQEGKFHQVKRMFEAVGKRVTYLKRISMGSLKLDENLALGEYRELTAEELNDLQNNH 237


>gi|149200863|ref|ZP_01877838.1| RNA pseudouridylate synthase family protein [Roseovarius sp.
           TM1035]
 gi|149145196|gb|EDM33222.1| RNA pseudouridylate synthase family protein [Roseovarius sp.
           TM1035]
          Length = 268

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 139/268 (51%), Positives = 178/268 (66%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M +K   ++    +R++KVIARAGIASRRE ER+I + RV VNG  + RAA+NV   D +
Sbjct: 1   MNNKTPEKKPPEGERIAKVIARAGIASRREAERLIEEGRVTVNGQKVLRAALNVTPADKV 60

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            V+G  L  AE  RLWLYHKP GLVTT  D  GR T++D+LP    RV+SVGRLD+N+EG
Sbjct: 61  VVNGRALEAAEPARLWLYHKPTGLVTTTRDEKGRRTIYDDLPEDMPRVMSVGRLDLNSEG 120

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLLLTNDG L R LELPST WLR YRVR +G+        L+KG+V+ G  +  M V+LD
Sbjct: 121 LLLLTNDGELKRKLELPSTGWLRRYRVRVNGRPTDASFEPLRKGLVVDGEAFQPMIVSLD 180

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            Q+G+NAW+TV +REGKNREI++  E     VNRLIR+SYGPFQLG L  G+  E+  ++
Sbjct: 181 RQQGANAWITVAIREGKNREIRRAMEAVGLVVNRLIRLSYGPFQLGQLKPGAVEEIRPRV 240

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLV 268
           +R+QLG     EA+    A         
Sbjct: 241 MRDQLGMPQEPEAEPAKPARPKPQRRRR 268


>gi|194467810|ref|ZP_03073796.1| pseudouridine synthase [Lactobacillus reuteri 100-23]
 gi|194452663|gb|EDX41561.1| pseudouridine synthase [Lactobacillus reuteri 100-23]
          Length = 238

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 75/232 (32%), Positives = 115/232 (49%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K +A AG+ASRR  E++I Q +V VNG ++      V   D I V+GVP+   +  
Sbjct: 2   ERLQKAMAEAGVASRRASEKLILQGKVAVNGKIVTELGTKVGVHDEIVVNGVPIHHEQHV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              L      + + H D   R+ V       I  R+  VGRLD +T G+LLLTNDG LA 
Sbjct: 62  YYLLNKPRGVISSAHDDKGRRTVVDIIHDADIDERIYPVGRLDYDTTGILLLTNDGALAN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            L  P  +  + Y  +  G V  D+L  L+ G+VI G      +  L     +   + V 
Sbjct: 122 KLMHPKYEVEKTYVAKVEGIVKNDELKQLRLGVVIDGRKTKPAKSKLLNVDRAKKTSLVQ 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + + EG+N ++K +F+     V +L R +YGP  L  L  G  R +  + ++
Sbjct: 182 LTIHEGRNHQVKNMFKAVGHPVTKLHRETYGPLNLYGLQPGEFRALKPEEVQ 233


>gi|319400836|gb|EFV89055.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           epidermidis FRI909]
          Length = 245

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 76/241 (31%), Positives = 132/241 (54%), Gaps = 3/241 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +R+ K IA++G  SRR+ E +I + RVKVNG  +      VM +D +EVDG+ + +
Sbjct: 2   SKEKERLQKRIAKSGYTSRRKAEVLITEGRVKVNGQTVTELGSKVMPSDLVEVDGIKIEQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ++  +  Y     ++T+ SD  GR  V D    + SR+  VGRLD +T G+LLLTNDG 
Sbjct: 62  EDKIYILFYKPT-QVITSVSDDRGRRVVTDYFDDLESRIYPVGRLDYDTSGVLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNA 187
              ++  P     + Y  +  G + ++++  L+KGI ++       QV +    ++ +  
Sbjct: 121 FTNLMTHPRYHIKKKYVAKLKGYLMREEIKQLEKGIELEDGYTQPAQVKIKKQDKEKNTT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V + + EG+NR+++++FE+F  +VN+L RI +GP  L  L AG  R ++   ++     
Sbjct: 181 LVEITISEGRNRQVRRMFEYFGHQVNKLARIQFGPIDLKGLNAGEGRVLTPHEVKTLRHL 240

Query: 248 H 248
            
Sbjct: 241 A 241


>gi|241764490|ref|ZP_04762511.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
 gi|241366074|gb|EER60671.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
          Length = 504

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 80/358 (22%), Positives = 137/358 (38%), Gaps = 17/358 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          V   D ++V+
Sbjct: 147 KRVLLPQVETPKLHKVLAQAGLGSRLEMEQLILEGRISVNNEPA-HIGQRVQFGDQVKVN 205

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+R          +  +     +V+     +  +           +  SVGRLD+NTE
Sbjct: 206 GKPIRYRIDPPPARVIAYHKPVGEVVSHDDPQNRPTVFRKLPRLQQGKWQSVGRLDLNTE 265

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL T+ G LA  L  P     R Y VR  G +  ++   L  G+ +         +  
Sbjct: 266 GLLLFTSSGELANKLMHPRFGLEREYAVRVLGALSNEEKQQLLDGVRLDDGMAAFGSIED 325

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +GSN W  V + EG+NRE++++ E     V+RLIRI YG   L   L  G+  E+ +
Sbjct: 326 GGGEGSNCWYRVTISEGRNREVRRMLEAVGHAVSRLIRIRYGAMVLPRGLKRGAWLELGE 385

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             +R  +                        +     +    +  R    +      +  
Sbjct: 386 GDIRALMQAAGAGRPDA---------AGPRTEAEGGAARGNRERGRGSVRAGDGRKRTGG 436

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSF--LSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              +     +  A     A G           G++ +  + S  +    SL R    +
Sbjct: 437 ANGSMGSGGQGRAPRRSDAPGARGGNAERPRGGEQPDPMKTSVGYIGADSLSRHRQDQ 494


>gi|50913682|ref|YP_059654.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS10394]
 gi|50902756|gb|AAT86471.1| Ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS10394]
          Length = 248

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 78/249 (31%), Positives = 125/249 (50%), Gaps = 3/249 (1%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +++      R++K IA AGIASRR+ E +I Q  V +NG ++   A  V S D +E++G 
Sbjct: 1   MLKRKKNIMRINKYIAHAGIASRRKAEELIKQGLVTLNGQVITDLATTVKSGDVVEIEGS 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P+   E+    L      + +   D  GR TV D LP +  R+  VGRLD +T G+L+LT
Sbjct: 61  PIYNEEKVYYLLNKPRGAISSVS-DDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--K 183
           NDG     +  P  +  +VY  R  G   ++ L  L +GIVI G      +  +      
Sbjct: 120 NDGDFTDTMIHPRNEIDKVYLARVKGIATKENLRPLTRGIVIDGKKTKPARYNIVHVEAD 179

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + + V + + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK + +
Sbjct: 180 KNRSIVELTIHEGRNHQVKKMFESVGLLVDKLSRTRFGTVDLKGLRPGEARRLNKKEISQ 239

Query: 244 QLGPHLLEE 252
                  ++
Sbjct: 240 LHNLANTKK 248


>gi|309805712|ref|ZP_07699752.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LactinV 09V1-c]
 gi|309809248|ref|ZP_07703117.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners SPIN 2503V10-D]
 gi|312872332|ref|ZP_07732402.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LEAF 2062A-h1]
 gi|312873963|ref|ZP_07733999.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LEAF 2052A-d]
 gi|308164965|gb|EFO67208.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LactinV 09V1-c]
 gi|308170361|gb|EFO72385.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners SPIN 2503V10-D]
 gi|311090512|gb|EFQ48920.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LEAF 2052A-d]
 gi|311092155|gb|EFQ50529.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LEAF 2062A-h1]
          Length = 239

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 80/229 (34%), Positives = 117/229 (51%), Gaps = 3/229 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KVIA AGIASRR+ E +I   +V VNG L+      V   D IEV+GVP+ K +   
Sbjct: 4   RLQKVIAEAGIASRRKAEILITSGQVTVNGNLVTTLGTKVDDNDKIEVNGVPIHKEQLHT 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             LY     + T   D  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  L
Sbjct: 64  YLLYKPRNVVSTVS-DNKGRKTVTDFFKDLPYRLYPVGRLDYDTSGLLLMTNDGELANRL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVG 192
             P  +  +VY  +  G +   ++  LK G+ I G      +V +     +     V + 
Sbjct: 123 MHPKNEIEKVYVAKIRGFLTASEIYDLKHGVTIDGRKTAPAKVKIIKTDKNRNIQLVQLT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EG   ++K +F+  N  V +L R  Y    L +L++G  RE++ + +
Sbjct: 183 IHEGHYHQVKNMFKAVNHLVEKLSRERYAFLTLKSLISGEYRELTHEEI 231


>gi|291538915|emb|CBL12026.1| ribosomal small subunit pseudouridine synthase A [Roseburia
           intestinalis XB6B4]
          Length = 235

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 68/237 (28%), Positives = 112/237 (47%), Gaps = 5/237 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K++   G  SR EV++ I    V VNG ++++    V    D +   G PL   E 
Sbjct: 1   MRLDKLLTELGTGSRSEVKKYIRSGLVTVNGEVVKKPEQKVDEKNDTVCFRGNPLTYTEY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +     + T   D   R+ +     +    +  VGRLDI+TEGLLL+TNDG LA 
Sbjct: 61  EYYLFHKPAGCV-TATEDNLHRTVMDYLTDTARHDLFPVGRLDIDTEGLLLITNDGALAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P+    +VY  +  G+V ++ +NL + G+ I +        + +    G N+ + +
Sbjct: 120 DLLSPAKHVSKVYYAKIDGRVTEEDVNLFENGVDIGEEKPAKPALLEVLH-SGDNSEIRL 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
            + EG+  ++K++FE    KV  L R+  G   L   L  G  R +++K L+E    
Sbjct: 179 TITEGRFHQVKRMFEAVGKKVTYLKRVEMGSLVLPDELAPGEYRPLTEKELQELRRH 235


>gi|209695446|ref|YP_002263375.1| ribosomal large subunit pseudouridine synthase F [Aliivibrio
           salmonicida LFI1238]
 gi|208009398|emb|CAQ79672.1| ribosomal large subunit pseudouridine synthase F [Aliivibrio
           salmonicida LFI1238]
          Length = 314

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 69/321 (21%), Positives = 129/321 (40%), Gaps = 15/321 (4%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +        R++K I+  G  SRRE +++I QQR+ +NG +       V   D + VDG 
Sbjct: 1   MTSPEPKLTRLNKYISDTGYCSRREADKLIDQQRITINGNVP-EMGTKVAEGDDVLVDGK 59

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL+  +      ++KP+G+  T       + +     +   R+  +GRLD  ++GL+ LT
Sbjct: 60  PLKAKQERIYIAFNKPVGITCTSERHVEGNIIDYI--NHEQRIFPIGRLDKPSDGLIFLT 117

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG +   +        + Y VR    +  D L  +  G+ I        QV    ++ S
Sbjct: 118 SDGDIVNKILRAGNAHEKEYVVRVDKPITDDFLAQMAAGVPILDTVTLPCQV----KQES 173

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++ E+ +++V +L R+      LGTL +G  R ++   + +  
Sbjct: 174 RFVFRITLTQGLNRQIRRMCEYLDYEVFKLKRVRIMNIDLGTLASGEWRYLTASEMEQIN 233

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD-------FTRMKKNSSQKNGLSKQ 298
                          +   +  +R      S              R +           Q
Sbjct: 234 NMIGTSSKTEEASRKVKEVDGKIRTIKKASSGRNHHSNNTFSQKRREESKDRGFGKSYSQ 293

Query: 299 KKLATPVHRRNLAS-NVWMAK 318
           ++       +  ++  VW AK
Sbjct: 294 RRDEGKDQDKPQSTIKVWRAK 314


>gi|219847277|ref|YP_002461710.1| pseudouridine synthase [Chloroflexus aggregans DSM 9485]
 gi|219541536|gb|ACL23274.1| pseudouridine synthase [Chloroflexus aggregans DSM 9485]
          Length = 567

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 95/350 (27%), Positives = 158/350 (45%), Gaps = 9/350 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA 70
           +P+R+ KV+A AGIASRR+ E +IA  RV VNG ++      V    D + VDG PLR  
Sbjct: 2   SPERLQKVLASAGIASRRDCEELIAAGRVTVNGRVVTVPGTRVDLEHDEVLVDGQPLRMP 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            +    + HKP G+V+T  DP GR TV  +L  + +RV  VGRLD+++EGL+LLT+DG L
Sbjct: 62  AKRTYIMLHKPAGVVSTAEDPHGRPTV-VDLVDVPARVFPVGRLDLDSEGLILLTDDGEL 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS +  + YRV     +  D L   + G++++G       V L        WV 
Sbjct: 121 AYALTHPSFEVEKEYRVLLDRALTPDALRSWRNGVLLEGEMTAPAWVELLETTPEGVWVR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + LREG+ R+I+ V +   ++V RL+R+  GP QLG L   + R ++ + +        +
Sbjct: 181 IVLREGRKRQIRAVAKLLGYEVRRLVRVREGPLQLGDLPPRAWRHLTDEEVAALRAHVSV 240

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR--- 307
             +  ++                            +++   +   S + +      R   
Sbjct: 241 RRSLADVPTRSTDVVKSRALDEKPHRAGDSAPVTRQRSEHSERRSSDRSRREQRDERVTE 300

Query: 308 ----RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                   +    A         ++G+       + +  + R  + +  +
Sbjct: 301 GPTWGETDARAGRAPRGRQDSRGEAGRGAWGETDARAGRAPRGRQDSRGE 350


>gi|126697974|ref|YP_001086871.1| putative RNA pseudouridine synthase [Clostridium difficile 630]
 gi|115249411|emb|CAJ67226.1| Ribosomal small subunit pseudouridine synthase A [Clostridium
           difficile]
          Length = 240

 Score =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 105/234 (44%), Gaps = 4/234 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA 70
             QR+ K+++  G  SR E+++   Q  V VNG  +      V    D I  +G  +   
Sbjct: 3   KKQRIDKILSNLGYGSRSEIKKYCKQGSVVVNGSEVSNPGTQVDTENDEILFNGEEVIYR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L +      +  T    D       +L  +      VGRLD +TEGLL+LTNDG L
Sbjct: 63  EYIYLMMNKPDGYISATTDKYDPTVLDLIDLSYLAFEPFPVGRLDKDTEGLLVLTNDGKL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWV 189
           +  +  P     + Y  +  G V ++ +    +G+V+         Q+ +  +    + +
Sbjct: 123 SHRVLSPKKHVPKTYYAKIDGVVTEEDVEAFLEGVVLDDRYKTMPSQLNIL-KSDDESEI 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R+S G  +L   L  G  RE++ + ++
Sbjct: 182 ELTIHEGKFHQVKRMFESVGKKVVYLKRLSMGNLKLDESLELGEYRELTDEEVK 235


>gi|84515287|ref|ZP_01002649.1| RNA pseudouridylate synthase family protein [Loktanella
           vestfoldensis SKA53]
 gi|84510570|gb|EAQ07025.1| RNA pseudouridylate synthase family protein [Loktanella
           vestfoldensis SKA53]
          Length = 272

 Score =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 135/271 (49%), Positives = 173/271 (63%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +  +     R++KV++RAG+ASRR+ ERMI + RV VNG ++   A+NV   D I VDG 
Sbjct: 1   MSNDTPQGDRIAKVLSRAGVASRRDAERMITEGRVSVNGKVITSPALNVTDADRIVVDGK 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +R  E  R+WLYHKP GLVTT  D   R TVF +LP    RV+SVGRLD+N+EGLLLLT
Sbjct: 61  AMRAPEAPRIWLYHKPAGLVTTERDEKDRPTVFASLPEDMPRVMSVGRLDLNSEGLLLLT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDGG+ R LELPST WLR YRVR +G V + +L  L+ GI + GI Y  M VT D Q+G+
Sbjct: 121 NDGGVKRRLELPSTGWLRRYRVRINGSVSEARLEQLRAGITVDGIRYQPMIVTFDRQQGA 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           NAW+TV LREGKNREI++  E     VNRLIR+SYGPFQLG L AG+  EV  +++R+QL
Sbjct: 181 NAWLTVSLREGKNREIRRAMEAIGVTVNRLIRVSYGPFQLGNLEAGAVEEVKGRVVRDQL 240

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIIS 276
           G    +  + +                    
Sbjct: 241 GLSDKDLGKDSAKPTRVRKPVNRPVTGKKRQ 271


>gi|307709770|ref|ZP_07646221.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           mitis SK564]
 gi|307619472|gb|EFN98597.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           mitis SK564]
          Length = 240

 Score =  189 bits (479), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 81/241 (33%), Positives = 132/241 (54%), Gaps = 3/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVTDDKGRKTVVDLLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  ++D L  L +G+ I G         +       + A V +
Sbjct: 120 MIHPRNEIDKVYVARVKGVANKDNLRPLTRGLEIDGKKTKPAVYEILKVDPVKNRAVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGESRRLNKKEISQLHTMAVTK 239

Query: 252 E 252
           +
Sbjct: 240 K 240


>gi|332523615|ref|ZP_08399867.1| pseudouridine synthase B, ribosomal large subunit [Streptococcus
           porcinus str. Jelinkova 176]
 gi|332314879|gb|EGJ27864.1| pseudouridine synthase B, ribosomal large subunit [Streptococcus
           porcinus str. Jelinkova 176]
          Length = 240

 Score =  189 bits (479), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 82/237 (34%), Positives = 127/237 (53%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V +NG ++   A  V S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTLNGQVITDLATIVKSGDVVEVEGSPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T GLL+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVIDLLPQVKERIYPVGRLDWDTSGLLILTNDGDFTDK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIIRVEADKNRSIVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK + +     
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTRFGTLDLTGLRPGEARRLNKKEVSQLHNAA 236


>gi|225857461|ref|YP_002738972.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae P1031]
 gi|225725990|gb|ACO21842.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae P1031]
          Length = 240

 Score =  189 bits (479), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 80/241 (33%), Positives = 132/241 (54%), Gaps = 3/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVTDDKGRKTVVDLLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  ++D L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGVANKDNLRPLTRGLEIDGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK + +     + +
Sbjct: 180 IIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGESRRLNKKEISQLHTMAVTK 239

Query: 252 E 252
           +
Sbjct: 240 K 240


>gi|217967848|ref|YP_002353354.1| pseudouridine synthase [Dictyoglomus turgidum DSM 6724]
 gi|217336947|gb|ACK42740.1| pseudouridine synthase [Dictyoglomus turgidum DSM 6724]
          Length = 241

 Score =  189 bits (479), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 122/232 (52%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K I+R+G+ SRR+ E +I + RVKVNG ++    V +    D +EVD   ++  ++
Sbjct: 3   ERLQKFISRSGVTSRRKAEELILEGRVKVNGKVIRTLGVKIDPEKDVVEVDNKIIKPEKK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + LY     L + +     R+        + SRV  VGRLD ++EGLLL TNDG +A 
Sbjct: 63  LYIALYKPVGYLSSLYDPFGRRTIKDLLKDKLSSRVYPVGRLDFDSEGLLLCTNDGEIAN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVT 190
            +  P  +  ++Y V  +G   +++L   ++G++++       +  +  +      + + 
Sbjct: 123 FVIHPRYKIPKIYEVLVNGIPKEEELKKFREGVILEEGKTLPAEFEVVWKNSKTKRSLLK 182

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           V L +G  R+I+++   F ++V +L RI  G  +LG L  G  R ++ + ++
Sbjct: 183 VVLYQGWKRQIRRMLALFGYEVLKLKRIQIGEIRLGNLKPGEFRFLNDEEIK 234


>gi|163758412|ref|ZP_02165500.1| putative ribosomal large subunit pseudouridine synthase B [Hoeflea
           phototrophica DFL-43]
 gi|162284701|gb|EDQ34984.1| putative ribosomal large subunit pseudouridine synthase B [Hoeflea
           phototrophica DFL-43]
          Length = 520

 Score =  189 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 159/352 (45%), Positives = 208/352 (59%), Gaps = 9/352 (2%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           Q +    R++K++AR G+ASRR+VERM+A+ R++VNG LL+  AV V  +D IEVDG  +
Sbjct: 35  QASAESGRIAKILARVGVASRRDVERMVAEGRIRVNGKLLDSPAVVVSLSDRIEVDGEEV 94

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              ERTRLW+YHKP GLVTT+ DP+GR TVF+ LP    RV+S+GRLDINTEGLLLLTND
Sbjct: 95  AGIERTRLWIYHKPAGLVTTNRDPEGRRTVFETLPKHLPRVLSIGRLDINTEGLLLLTND 154

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GGLAR LELP T WLR YRVR +G +DQ++L+ LK GI + G+ YG ++ TLD ++G N 
Sbjct: 155 GGLARTLELPETGWLRRYRVRAYGDIDQNRLDTLKDGIAVDGVLYGAIEATLDRKQGHNV 214

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+T+GLREGKNREIK V       VNRLIRIS+GPFQLG +  G   E+  + LREQLG 
Sbjct: 215 WITMGLREGKNREIKNVLSALGLDVNRLIRISFGPFQLGDVREGDVVEIKSRTLREQLGV 274

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR--------MKKNSSQKNGLSKQK 299
            L+EE+  N DAP+  S    +                        +  +       +  
Sbjct: 275 RLIEESGANFDAPLNDSAPASKKEAKPSPAAKPAQREWISSSEKVERARARFDTKPGRPD 334

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS-FPSKRSLRRT 350
           +   P  RR+            SS    S  R        +  P  +  +R 
Sbjct: 335 RDGKPGERRSEWGPGKERGERKSSGDKASRPRSGGPEGKRNEEPGAKPAKRG 386



 Score = 37.5 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 11/111 (9%), Positives = 22/111 (19%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R            V             +         P   TR       +      +  
Sbjct: 392 RASNVWMAPGARPVADADKPEGGRGGAKSGHKKADADPRAETRRGSFPKGRAKPRPDRDE 451

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                RR+       A G  +   S     + + +       K   +  ++
Sbjct: 452 NDGRPRRDGDRPFGKAPGKPAGKPSGKFAGKPSGKPDGKPGGKPVRKPDAS 502


>gi|139474355|ref|YP_001129071.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes str. Manfredo]
 gi|134272602|emb|CAM30869.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes str. Manfredo]
          Length = 240

 Score =  189 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 78/241 (32%), Positives = 122/241 (50%), Gaps = 3/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q  V +NG ++   A  V S D +E++G P+   E+ 
Sbjct: 1   MRINKYIAHAGIASRRKAEELIKQGLVTLNGQVITDLATTVKSGDVVEIEGSPIYNEEKV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      + +   D  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 61  YYLLNKPRGAISSVS-DDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDT 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +GIVI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGIVIDGKKTKPARYNIVRVEADKNRSIVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK + +       +
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTRFGTVNLKGLRPGEARRLNKKEISQLHNLANTK 239

Query: 252 E 252
           +
Sbjct: 240 K 240


>gi|210622938|ref|ZP_03293443.1| hypothetical protein CLOHIR_01391 [Clostridium hiranonis DSM 13275]
 gi|210153904|gb|EEA84910.1| hypothetical protein CLOHIR_01391 [Clostridium hiranonis DSM 13275]
          Length = 238

 Score =  189 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 74/231 (32%), Positives = 120/231 (51%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R++K IA  G+ASRR+ E +I   RV +NG L+   +  V  T D +EVDGVP+ + E+
Sbjct: 1   MRINKYIASCGVASRRKAEELIISGRVTINGELITELSTTVDETKDIVEVDGVPINQEEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G +TT  D   R +V D L  +  RV  VGRLD  T GLL+LTNDG L  
Sbjct: 61  KVYILLNKPEGYITTVKDQFDRPSVLDILKDVDERVYPVGRLDYETSGLLILTNDGDLTY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVT 190
            L  P  +  + Y    +G +  ++    + G+ I+       ++ +    ++ + +   
Sbjct: 121 KLTHPKHEVEKTYLAMVNGIITPEEKRRFENGLQIEDYTTAKAKLKIVKVNEEKNYSVCK 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + EG+NR+++K+ +  N  V  L RI  G   +  L  G  R ++ + +
Sbjct: 181 ITIHEGRNRQVRKMCKAINHPVRNLRRIQMGRINIRGLEVGEYRNLTDEEV 231


>gi|15674518|ref|NP_268692.1| hypothetical protein SPy_0369 [Streptococcus pyogenes M1 GAS]
 gi|13621621|gb|AAK33413.1| putative hypothetical protein [Streptococcus pyogenes M1 GAS]
          Length = 240

 Score =  189 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 79/241 (32%), Positives = 122/241 (50%), Gaps = 3/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q  V +NG ++   A  V S D +E++G P+   E+ 
Sbjct: 1   MRINKYIAHAGIASRRKAEELIKQGLVTLNGQVITDLATTVKSGDVVEIEGSPIYNEEKV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      + +   D  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 61  YYLLNKPRGAISSVS-DDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDT 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +GIVI G      +  +       S + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGIVIDGKKTKPARYNIVRVEADKSRSIVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK + +       +
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTRFGTVDLKGLRPGEARRLNKKEISQLHNLANTK 239

Query: 252 E 252
           +
Sbjct: 240 K 240


>gi|73662568|ref|YP_301349.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           saprophyticus subsp. saprophyticus ATCC 15305]
 gi|72495083|dbj|BAE18404.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           saprophyticus subsp. saprophyticus ATCC 15305]
          Length = 245

 Score =  189 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 74/235 (31%), Positives = 128/235 (54%), Gaps = 3/235 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N   +R+ K IA +G  SRR+ E +I + +VKVNG +       V  +D IEV+G+ L +
Sbjct: 2   NKDTERLQKRIANSGYTSRRKAETLITEGKVKVNGTVETELGTKVKPSDSIEVEGIKLEQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ++  +  Y     ++T+ SD  GR  V D    I +R+  VGRLD +T GLLLLTNDG 
Sbjct: 62  EDKLYILFYKP-AQVITSVSDDRGRKVVTDYFKQIKTRIYPVGRLDYDTSGLLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNA 187
              ++  P  +  + Y V+  G + ++++  L++G+ ++         +V    +  +  
Sbjct: 121 FTNLMTHPRYKIKKKYVVKLKGYLMREEVKSLEQGVQLEDGVTQPAIIKVKNQDKDKNTT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V + + EG+NR+++++FE F  +V +L RI +GP  L  L AG  R ++   ++
Sbjct: 181 LVEITITEGRNRQVRRMFEHFGHQVTKLQRIEFGPLNLKGLNAGEGRVLTPHEVK 235


>gi|149909594|ref|ZP_01898247.1| ribosomal large subunit pseudouridine synthase F [Moritella sp.
           PE36]
 gi|149807298|gb|EDM67251.1| ribosomal large subunit pseudouridine synthase F [Moritella sp.
           PE36]
          Length = 407

 Score =  189 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 61/291 (20%), Positives = 112/291 (38%), Gaps = 7/291 (2%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + Q++    R++K I+  G  SRRE +R+I Q RV +NG +       V   D + V+G 
Sbjct: 1   MTQQDIKLTRLNKYISDTGYCSRREADRLIEQGRVTINGKIP-EMGTKVSDGDMVSVNGR 59

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P+++ ++      +KP G+  T       + +  +L    +R+  +GRLD  +EGL+ LT
Sbjct: 60  PVKEKQKRIYIALNKPAGITCTTERHIHGNVI--DLIDYSTRIFPIGRLDKPSEGLIFLT 117

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +   +        + Y V+    V    L  + +G+ I        +VT +     
Sbjct: 118 NDGDIVNKILRAGNAHEKEYIVKVDSTVTDKFLTGMARGVPILDTVTKPCKVTRE----G 173

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G N++I+++ E F ++V  L R       +  L  G  R ++   + E  
Sbjct: 174 RFEFKIILTQGLNQQIRRMCEHFGFQVKSLTRTRIMNIDIKGLATGQWRLLTDNEMAEIN 233

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
                  +             +                R            
Sbjct: 234 AMVEGSSSTEEASDYGQVKPKVKGQHSKRGVNSAARQKRFGYGDYAATPGQ 284


>gi|327470426|gb|EGF15882.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK330]
          Length = 242

 Score =  189 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 81/240 (33%), Positives = 133/240 (55%), Gaps = 3/240 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q +V +NG ++   A N+ S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGIASRRKAEELIRQGKVSINGQVVRELATNIKSGDRVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV + LP +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVVELLPQVKERIYPVGRLDWDTSGILILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +GI I+G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTKPAVYEIIKVDPAKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+F+    +V++L R  +G   L  L  G  R++SKK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLSKKEVSQLHTLAVTK 239


>gi|322411180|gb|EFY02088.1| hypothetical protein SDD27957_02020 [Streptococcus dysgalactiae
           subsp. dysgalactiae ATCC 27957]
          Length = 240

 Score =  189 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 81/241 (33%), Positives = 132/241 (54%), Gaps = 3/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V +NG ++  +A  V S D +E++G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTLNGQVITDSATTVKSGDVVEIEGSPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV D LP +  R+  VGRLD NT G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVLDLLPQVKERIYPVGRLDWNTSGVLILTNDGDFTDT 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIIRVEADKNRSIVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE     V++L R  +G  +L  L  G +R ++KK + +       +
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTRFGTLELTGLRPGESRRLNKKEISQLHNLANTK 239

Query: 252 E 252
           +
Sbjct: 240 K 240


>gi|254509889|ref|ZP_05121956.1| ribosomal large subunit pseudouridine synthase [Rhodobacteraceae
           bacterium KLH11]
 gi|221533600|gb|EEE36588.1| ribosomal large subunit pseudouridine synthase [Rhodobacteraceae
           bacterium KLH11]
          Length = 298

 Score =  189 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 137/273 (50%), Positives = 176/273 (64%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           + +        R++KV+ARAGIASRRE ERMI   RV VNG  +   A+NV   D I VD
Sbjct: 26  RGMSNTPPPGDRIAKVLARAGIASRREAERMIEAGRVAVNGKPINSPALNVTGKDKITVD 85

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G P+ + E +RLWLYHKP GLVTT  D  GR+T+FD LP    RV+SVGRLD+N+EGLLL
Sbjct: 86  GKPVSEPEPSRLWLYHKPPGLVTTARDEKGRTTIFDKLPENMPRVMSVGRLDLNSEGLLL 145

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDGG+ R LELPST WLR YRVR +G+   +    L+KG+VI G  +  M VTLD Q+
Sbjct: 146 LTNDGGIKRKLELPSTGWLRKYRVRVNGRPRDEDFAPLRKGLVIDGERFQPMTVTLDRQQ 205

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           G+NAW+T+GLREGKNREI++  E   + VNRL+R+SYGPFQLG L  G   E+ ++++R+
Sbjct: 206 GANAWLTIGLREGKNREIRRAIEDIGYVVNRLLRVSYGPFQLGDLKPGEVEEIRRRVMRD 265

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIIS 276
           QLG     + +     P                
Sbjct: 266 QLGLDAEGDGKAPAKRPARPQRKRPAIGKKPRK 298


>gi|291536218|emb|CBL09330.1| ribosomal small subunit pseudouridine synthase A [Roseburia
           intestinalis M50/1]
          Length = 235

 Score =  189 bits (479), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 68/237 (28%), Positives = 112/237 (47%), Gaps = 5/237 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K++   G  SR EV++ I    V VNG ++++    V    D +   G PL   E 
Sbjct: 1   MRLDKLLTELGTGSRSEVKKYIRSGLVTVNGEVVKKPEQKVDEKNDTVCFRGNPLTYTEY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +     + T   D   R+ +     +    +  VGRLDI+TEGLLL+TNDG LA 
Sbjct: 61  EYYLFHKPAGCV-TATEDNLHRTVMDYLTDTARHDLFPVGRLDIDTEGLLLITNDGALAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P+    +VY  +  G+V ++ +NL K G+ I +        + +    G N+ + +
Sbjct: 120 DLLSPAKHVSKVYYAKIDGRVTEEDVNLFKNGVDIGEEKPAKPALLEVLH-SGDNSEIRL 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
            + EG+  ++K++FE    KV  L R+  G   L   L  G  R ++++ L+E    
Sbjct: 179 TITEGRFHQVKRMFEAVGKKVTYLKRVEMGSLVLPDELAPGEYRPLTEEELQELRRH 235


>gi|302875017|ref|YP_003843650.1| pseudouridine synthase [Clostridium cellulovorans 743B]
 gi|307690365|ref|ZP_07632811.1| pseudouridine synthase [Clostridium cellulovorans 743B]
 gi|302577874|gb|ADL51886.1| pseudouridine synthase [Clostridium cellulovorans 743B]
          Length = 235

 Score =  188 bits (478), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 69/230 (30%), Positives = 120/230 (52%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K +A+ G+ASRR+ E +I Q +V VN  ++      V    D I+V+ V +    +
Sbjct: 2   ERLQKYMAKCGVASRRKCEELILQGKVSVNNTIITELGYKVEEENDIIKVNNVIIYPEAQ 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP+  +++  D  GR  V  +L  +  R+  +GRLD ++ GLLLLTNDG +  
Sbjct: 62  KVYIALNKPVKYISSVKDEKGRKNVI-DLIDVKERIYPIGRLDYDSSGLLLLTNDGDIYN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS +  + Y V  +G    +++  L+ GI I G      +V ++    + A + + 
Sbjct: 121 NLMHPSKEVYKTYLVTVNGIPTIEEIKKLETGIDIGGYITAPAKVKIEKLDYNKASLKIQ 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGKNR+I+K+ +     V  L RI+ G  +L  +  G  R ++K+ + 
Sbjct: 181 IYEGKNRQIRKMCDSIGHSVIALKRIAIGDIKLKDIPQGKYRFLTKEEID 230


>gi|78222432|ref|YP_384179.1| ribosomal large subunit pseudouridine synthase B [Geobacter
           metallireducens GS-15]
 gi|78193687|gb|ABB31454.1| ribosomal large subunit pseudouridine synthase B [Geobacter
           metallireducens GS-15]
          Length = 258

 Score =  188 bits (478), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 89/255 (34%), Positives = 136/255 (53%), Gaps = 1/255 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++++AGIASRRE ERMI   RV VNG  +        S+ D I VDG P+   E+
Sbjct: 3   ERLQKILSQAGIASRREAERMITDGRVAVNGKPVIELGAKADSSRDAITVDGKPVTVDEK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP+G VTT  DP+GR  V + L  +  RV  VGRLD NTEGLLLLTNDG  A 
Sbjct: 63  RVYILLNKPVGYVTTLKDPEGRPIVTELLKGLGVRVFPVGRLDYNTEGLLLLTNDGEWAN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + Y VR  G V ++++  L++GI ++       +V++  Q  +N WV++ 
Sbjct: 123 RLAHPRHEVDKEYLVRVRGTVAREQITRLEQGIELEDGKAAPARVSVTKQSDNNTWVSIT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           + EG+ R+++++ E  +  V RL R+ YG   +G L  G+ R ++   +       +   
Sbjct: 183 IHEGRYRQVRRMCEAVSLSVVRLRRVRYGALSMGDLKIGAYRHLTSGEVAALSDGKIGAR 242

Query: 253 AQVNLDAPIYSSETL 267
                     +    
Sbjct: 243 GGAPRRRGPSAPPRK 257


>gi|22537733|ref|NP_688584.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae 2603V/R]
 gi|76787925|ref|YP_330211.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae A909]
 gi|76799444|ref|ZP_00781590.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae 18RS21]
 gi|77406891|ref|ZP_00783916.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae H36B]
 gi|77409463|ref|ZP_00786156.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae COH1]
 gi|77412369|ref|ZP_00788680.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae CJB111]
 gi|22534623|gb|AAN00457.1|AE014264_12 ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae 2603V/R]
 gi|76562982|gb|ABA45566.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae A909]
 gi|76585200|gb|EAO61812.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae 18RS21]
 gi|77161589|gb|EAO72589.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae CJB111]
 gi|77171930|gb|EAO75106.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae COH1]
 gi|77174500|gb|EAO77344.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae H36B]
 gi|319745532|gb|EFV97834.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae ATCC 13813]
          Length = 240

 Score =  188 bits (478), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 82/241 (34%), Positives = 130/241 (53%), Gaps = 3/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q  V +NG ++   A  V + D +E++G P+   E  
Sbjct: 1   MRINKYIAHAGIASRRKAEELIKQGMVTINGQVVNELATQVKAGDLVEIEGSPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T GLL+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVIDLLPQVKERIYPVGRLDWDTTGLLILTNDGDFTDK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      + T+       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYTIIKVDHEKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFEQVGLLVDKLSRTQFGTLDLTGLRPGEARRLNKKEISQLHNAAINK 239

Query: 252 E 252
            
Sbjct: 240 S 240


>gi|224283102|ref|ZP_03646424.1| pseudouridine synthase [Bifidobacterium bifidum NCIMB 41171]
 gi|310287470|ref|YP_003938728.1| Ribosomal large subunit pseudouridine synthase B [Bifidobacterium
           bifidum S17]
 gi|311064385|ref|YP_003971110.1| ribosomal large subunit pseudouridine synthase B [Bifidobacterium
           bifidum PRL2010]
 gi|313140251|ref|ZP_07802444.1| ribosomal large subunit pseudouridine synthase B [Bifidobacterium
           bifidum NCIMB 41171]
 gi|309251406|gb|ADO53154.1| Ribosomal large subunit pseudouridine synthase B [Bifidobacterium
           bifidum S17]
 gi|310866704|gb|ADP36073.1| RluB Ribosomal large subunit pseudouridine synthase B
           [Bifidobacterium bifidum PRL2010]
 gi|313132761|gb|EFR50378.1| ribosomal large subunit pseudouridine synthase B [Bifidobacterium
           bifidum NCIMB 41171]
          Length = 258

 Score =  188 bits (478), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 72/237 (30%), Positives = 118/237 (49%), Gaps = 2/237 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
             N    R+ K++A+AG  SRR+ E+MI   RV+V+G L+      V     HI VDG  
Sbjct: 14  DNNNEGIRLQKILAQAGFGSRRKCEQMITDGRVEVDGELVTELGTRVDPKKQHIRVDGSR 73

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +           +KP  +++   DP GR T+ D +   + RV  +GRLD ++EGL+L+TN
Sbjct: 74  VHLNPNHVTLALNKPKKVLSAMDDPKGRYTLADIIGDKYERVFHMGRLDYDSEGLILMTN 133

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
           DG L++ +  P  +  + Y     G++  +    L  +G+ +           +      
Sbjct: 134 DGELSQHVMHPKYEVEKTYIATIDGKIGGNVCRRLVTQGVQLDDGLVKLDHCAIIDANRD 193

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
              V V L  GKNR ++++F    + V RL+R   GP +LG L +G+ R +S+  +R
Sbjct: 194 QTIVKVVLHSGKNRIVRRIFGAIGYPVRRLVRTQIGPIKLGDLKSGTYRVLSQVEVR 250


>gi|300361572|ref|ZP_07057749.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           gasseri JV-V03]
 gi|300354191|gb|EFJ70062.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           gasseri JV-V03]
          Length = 244

 Score =  188 bits (478), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 73/237 (30%), Positives = 122/237 (51%), Gaps = 3/237 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           ++E+   +R+ KVIA+AG+ASRR+ E+MI   +V VNG  +      V  +D IEV+GVP
Sbjct: 1   MKESKMAERLQKVIAQAGVASRRKAEKMITAGQVTVNGKRITELGTKVEPSDKIEVNGVP 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           + K        Y     + +   D   ++ V      +  R+  VGRLD +T GLLL+TN
Sbjct: 61  IEKETLHTYLFYKPRGVISSVKDDKGRKTVVDYF-EDVPYRLYPVGRLDYDTSGLLLMTN 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKG 184
           DG LA  L  P  +  +VY  +  G +  + ++ L  G+ I G      ++ +    +K 
Sbjct: 120 DGELANKLMHPRNEVPKVYVAKIKGLLSPEDIHSLTHGVRIDGRKSAPAKLKILKTDEKK 179

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +   V + + EG   ++K++FE  +  V +L R  Y    L +L +G  RE++ + +
Sbjct: 180 NTQIVQLTIHEGHYHQVKRMFEAVHHFVEKLSREKYAFLTLKSLTSGEYRELTHEEV 236


>gi|169829656|ref|YP_001699814.1| putative RNA pseudouridine synthase ytzF [Lysinibacillus sphaericus
           C3-41]
 gi|168994144|gb|ACA41684.1| Hypothetical RNA pseudouridine synthase ytzF [Lysinibacillus
           sphaericus C3-41]
          Length = 237

 Score =  188 bits (478), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 108/232 (46%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++ Q+ V V+G  ++ AA++V      + V G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKQLLKQKAVTVDGASVKDAAMHVDPEQQNVSVYGERVIYTEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +   P  +  T    D              +   VGRLD +TEGLL+LTNDG LA 
Sbjct: 61  VYFMMNKPPGVISATEDLRDETVIDLLEPVDQHFQPFPVGRLDKDTEGLLVLTNDGILAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY     G V ++ +     G+ +         ++ +  +    + + +
Sbjct: 121 NLLSPKKHVPKVYYAHIEGVVTEEDVEKFANGVELDDGYMTKPGKLVIL-KSAPQSEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            ++EGK  ++K++FE    +V  L RIS G  +L   L  G  RE++ + L 
Sbjct: 180 TIQEGKFHQVKRMFEAVGKRVTYLKRISMGNLKLDDQLELGEYRELTVEELD 231


>gi|164687721|ref|ZP_02211749.1| hypothetical protein CLOBAR_01363 [Clostridium bartlettii DSM
           16795]
 gi|164603495|gb|EDQ96960.1| hypothetical protein CLOBAR_01363 [Clostridium bartlettii DSM
           16795]
          Length = 258

 Score =  188 bits (478), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 63/235 (26%), Positives = 106/235 (45%), Gaps = 4/235 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRK 69
              QR+ K+++  G  SR E+++      VKVNG ++    V V    D I  DG  +  
Sbjct: 19  SKKQRIDKILSNLGYGSRSELKKFCKNGLVKVNGKVINNPGVQVDVENDEIIFDGEKVTY 78

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   L L      +  T    D       +   +      VGRLD +TEGLL+LTNDG 
Sbjct: 79  KEFIYLMLNKPDGYISATFDKRDPIVLDLIDKEDLVFEPFPVGRLDKDTEGLLVLTNDGQ 138

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAW 188
           LA  +  P     + Y  +  G V ++ +    KG+ +         ++ +  +    + 
Sbjct: 139 LAHRVLSPKKHVPKTYYAKIEGIVTEEDIKAFAKGVTLDDGYETMPAELIIL-KSDEISE 197

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + + + EGK  ++K++FE  + KV  L R+S G  +L   L  G  RE++ + ++
Sbjct: 198 IELTIHEGKFHQVKRMFESVDKKVIYLKRLSMGKLKLDENLALGEYRELTDEEVK 252


>gi|309807073|ref|ZP_07701052.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LactinV 03V1-b]
 gi|308166503|gb|EFO68703.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LactinV 03V1-b]
          Length = 239

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 80/229 (34%), Positives = 117/229 (51%), Gaps = 3/229 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KVIA AGIASRR+ E +I   +V VNG L+      V   D IEV+GVP+ K +   
Sbjct: 4   RLQKVIAEAGIASRRKAEILITSGQVTVNGDLVTTLGTKVDDNDKIEVNGVPIHKEQLHT 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             LY     + T   D  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  L
Sbjct: 64  YLLYKPRNVVSTVS-DNKGRKTVTDFFKDLPYRLYPVGRLDYDTSGLLLMTNDGELANRL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVG 192
             P  +  +VY  +  G +   ++  LK G+ I G      +V +     +     V + 
Sbjct: 123 MHPKNEIEKVYVAKIRGFLTASEIYDLKHGVTIDGRKTAPAKVKIIKTDKNRNIQLVQLT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EG   ++K +F+  N  V +L R  Y    L +L++G  RE++ + +
Sbjct: 183 IHEGHYHQVKNMFKAVNHLVEKLSRERYAFLTLKSLISGEYRELTHEEI 231


>gi|222152585|ref|YP_002561760.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           uberis 0140J]
 gi|222113396|emb|CAR41051.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           uberis 0140J]
          Length = 240

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 83/237 (35%), Positives = 128/237 (54%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V +NG ++   A  V S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTLNGQVVSDLATTVKSGDTVEVEGSPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T GLL+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVIDLLPQVKERIYPVGRLDWDTSGLLILTNDGDFTDK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P  +  +VY  R  G   +D L  L +G+VI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKDNLRPLTRGVVIDGKKTKPARYNIIRVEADKNRSIVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + EG+N ++KK+FE     V++L R  +G   L  L  G +R ++KK + +     
Sbjct: 180 TIHEGRNHQVKKMFESVGLIVDKLSRTRFGTLDLTGLRPGESRRLNKKEISQLHNAA 236


>gi|149377823|ref|ZP_01895554.1| 23S rRNA pseudouridine synthase [Marinobacter algicola DG893]
 gi|149357881|gb|EDM46372.1| 23S rRNA pseudouridine synthase [Marinobacter algicola DG893]
          Length = 318

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 65/318 (20%), Positives = 118/318 (37%), Gaps = 5/318 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++K I+ +G+ SRRE +R I    V +NG   +     V+  D + V+G  +   + 
Sbjct: 6   STRLNKYISESGMCSRREADRYIENGNVAINGKAAQV-GDQVLPGDKVTVNGQLIEPRDE 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L        +    +          N      R+  +GRLD +++GL+ LT++G L  
Sbjct: 65  EDLIFIALNKPVGVVSTTDPAERRNIVNHVGHGERIFPIGRLDKDSQGLIFLTSNGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  V  + +  +  G+ I G      +V    +K S     + 
Sbjct: 125 KILRAGNNHEKEYLVTVNKPVTTEFVQGMSAGVPILGTVTKRCKV----EKVSRFVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ EFF ++V +L R+      L  L  G  R++  K L           
Sbjct: 181 LVQGLNRQIRRMCEFFGYEVTKLERVRIMNISLKGLSVGEWRDLGPKELAGLFDMIRDSS 240

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
           ++V+ D    + +  V+         P         + Q     K         R    S
Sbjct: 241 SEVSPDNRSETKKPAVKRPSKKPGASPSGPRGKGAKTGQPGRPGKPTGKHGKPSRPGKPS 300

Query: 313 NVWMAKGIHSSFLSDSGQ 330
                  +     S   +
Sbjct: 301 KRGKPGKLRKPRQSSVKR 318


>gi|332358327|gb|EGJ36153.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK355]
          Length = 242

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 80/240 (33%), Positives = 133/240 (55%), Gaps = 3/240 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q +V +NG ++   A NV S D +E++G P+   E  
Sbjct: 1   MRINKYIAHAGIASRRKAEELIRQGKVSINGQVVRELATNVKSGDRVEIEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV + LP +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVVELLPQVKERIYPVGRLDWDTSGILILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +GI I+G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTKPAVYEIIKVDPAKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+F+    +V++L R  +G   L  L  G  R+++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLNKKEVSQLHTLAVTK 239


>gi|21909805|ref|NP_664073.1| putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes MGAS315]
 gi|28896502|ref|NP_802852.1| hypothetical protein SPs1590 [Streptococcus pyogenes SSI-1]
 gi|21903991|gb|AAM78876.1| putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes MGAS315]
 gi|28811756|dbj|BAC64685.1| putative hypothetical protein [Streptococcus pyogenes SSI-1]
          Length = 240

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 78/241 (32%), Positives = 122/241 (50%), Gaps = 3/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q  V +NG ++   A  V S D +E++G P+   E+ 
Sbjct: 1   MRINKYIAHAGIASRRKAEELIKQGLVTLNGQVITDLATTVKSGDVVEIEGSPIYNEEKV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      + +   D  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 61  YYLLNKPRGAISSVS-DDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDT 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +GIVI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGIVIDGKKTKPARYNIVRVEADKNRSIVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK + +       +
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTRFGTVDLKGLRPGEARRLNKKEISQLHNLANTK 239

Query: 252 E 252
           +
Sbjct: 240 K 240


>gi|23099754|ref|NP_693220.1| 16S pseudouridine synthase [Oceanobacillus iheyensis HTE831]
 gi|22777984|dbj|BAC14255.1| 16S pseudouridine synthase [Oceanobacillus iheyensis HTE831]
          Length = 237

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 60/232 (25%), Positives = 113/232 (48%), Gaps = 5/232 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G+ SR+EV++++  +R+ VN ++++ + ++V    D I VD   +   + 
Sbjct: 2   MRLDKLLSNMGVGSRKEVKQLLKSKRITVNEVIVKDSGMHVDPEYDQIFVDDQLISYQKH 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L ++  P  +  T  + D       +          VGRLD +TEGLLL+TNDG LA 
Sbjct: 62  IYLMMHKPPGVVSATVDNRDRTVIDLLSADEKKFEPFPVGRLDKDTEGLLLITNDGELAH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY     G+  ++ +   ++G+ ++        ++ +  ++  +  V V
Sbjct: 122 RLTSPKKHVEKVYIAHISGEFPENIVEQFQEGLTLEDGYQTKPAKLEILNKQ--SKEVKV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            + EGK  +IK++F     KV  L R+     QL   L  G  R +++  L+
Sbjct: 180 TITEGKYHQIKRMFIAVGCKVTYLKRVQMANLQLDDSLPIGDFRPLTEDELQ 231


>gi|152977062|ref|YP_001376579.1| pseudouridine synthase [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152025814|gb|ABS23584.1| pseudouridine synthase [Bacillus cytotoxicus NVH 391-98]
          Length = 242

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 103/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    V+++G  ++ A  +V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVRIDGKPVKDAKFHVNIEKQEVTIYGEVVEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L ++     +  T  D                    VGRLDI+TEGLLLLTNDG L  
Sbjct: 61  VYLMMHKPQGVISATEDDHHETVVDLLEFEDAIFNPFPVGRLDIDTEGLLLLTNDGKLTH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G V +  +    KG+V+         ++T+       + + +
Sbjct: 121 QLLSPKKHVPKKYYAHIEGVVTEKDVEDFAKGVVLDDGYETKPGELTILNSD-DISEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++FE    KV  L R+  GP  L   L  G  RE++ + + 
Sbjct: 180 VITEGKFHQVKRMFEAVGKKVVYLKRVEMGPLTLDEELELGQYRELTDEEVE 231


>gi|306827950|ref|ZP_07461217.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes ATCC 10782]
 gi|304429869|gb|EFM32911.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes ATCC 10782]
          Length = 240

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 77/241 (31%), Positives = 121/241 (50%), Gaps = 3/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q  V +NG ++   A  V   D +E++G P+   E+ 
Sbjct: 1   MRINKYIAHAGIASRRKAEELIKQGLVTLNGQVITDLATTVKLGDVVEIEGSPIYNEEKV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      + +   D  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 61  YYLLNKPRGAISSVS-DDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDT 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +GIVI G      +  +       + + V +
Sbjct: 120 MTHPRNEIDKVYLARVKGIATKENLRPLTRGIVIDGKKTKPARYNIVRVEADKNRSIVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK + +       +
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTRFGTVDLKGLRPGEARRLNKKEISQLHNLANTK 239

Query: 252 E 252
           +
Sbjct: 240 K 240


>gi|258511697|ref|YP_003185131.1| pseudouridine synthase [Alicyclobacillus acidocaldarius subsp.
           acidocaldarius DSM 446]
 gi|257478423|gb|ACV58742.1| pseudouridine synthase [Alicyclobacillus acidocaldarius subsp.
           acidocaldarius DSM 446]
          Length = 273

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 92/276 (33%), Positives = 140/276 (50%), Gaps = 8/276 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV+A AG+ASRR+ E +I   RV V+G ++ +    V  +   I VDGVP+   E+
Sbjct: 2   ERLQKVLAHAGVASRRKCEELILAGRVSVDGEIVTQLGAKVDPSRQRIAVDGVPIEL-EQ 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + + +KP+  ++T SDP GR TV   LP I  RV  VGRLD +T GLLL TNDG L +
Sbjct: 61  PVVLVLNKPVAYLSTVSDPLGRRTVMQLLPPIRERVYPVGRLDYDTSGLLLFTNDGELTQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ---KGSNAWV 189
            L  PS +  +VYRV   G VD++    L +G+ ++       +V +  Q   +   A V
Sbjct: 121 RLLHPSREIEKVYRVSVRGIVDRETRRALMEGVELEDGVTAPAKVEVLRQADREDGVAVV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + + EG+NR+++++FE     V RL RI++GP  LG L  G  R ++++     +  + 
Sbjct: 181 HLAIHEGRNRQVRRMFERLGLPVLRLKRIAFGPVSLGHLKTGEWRALTQEEW---VALYQ 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
                         S    R      S       R 
Sbjct: 238 AAGMTPPPYRRPTISREPARKGAARASARDHGSRRG 273


>gi|238786255|ref|ZP_04630200.1| Ribosomal large subunit pseudouridine synthase F [Yersinia
           bercovieri ATCC 43970]
 gi|238712846|gb|EEQ04913.1| Ribosomal large subunit pseudouridine synthase F [Yersinia
           bercovieri ATCC 43970]
          Length = 290

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 61/293 (20%), Positives = 116/293 (39%), Gaps = 5/293 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRR+ +R I Q  V +NG       V V + D ++V+G  +  
Sbjct: 3   TNSSIRLNKYISESGICSRRDADRYIEQGNVFINGKRATV-GVQVSAGDVVKVNGQIIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L L      +    +  DG      +  +   RV  +GRLD +++GL+LLTN G 
Sbjct: 62  RNEEDLILIALNKPVGVISTTEDGEQNNIVDFVNHSKRVFPIGRLDKDSQGLILLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  V  + +  L  G+ + G      +V  +    +    
Sbjct: 122 LVNKILRAGNDHEKEYVVTVNKPVTDEFILGLGAGVPMLGTVTKKCKVKRE----ATFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ + F ++V +L R+      L  L  G  R++++  L E      
Sbjct: 178 RITLVQGLNRQIRRMCKHFGYEVTKLERVRIMNISLKGLPQGEWRDLTEDELIELFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
              +               +       +  +       +  +     ++KK  
Sbjct: 238 NSSSDEKPVKKAPVKAVEAKRVSISGPKKTEKPDGNAASRKRFAQPGRKKKGR 290


>gi|323485703|ref|ZP_08091040.1| pseudouridine synthase [Clostridium symbiosum WAL-14163]
 gi|323400966|gb|EGA93327.1| pseudouridine synthase [Clostridium symbiosum WAL-14163]
          Length = 244

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 69/246 (28%), Positives = 114/246 (46%), Gaps = 6/246 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           MK+ N   +     R++K ++ AGI SRRE +R+I   +V V+G       + V ++  I
Sbjct: 1   MKNMNDNAKTDNGIRLNKYLSEAGICSRREADRLIEDGKVTVDGRTA-SMGMKVFTSQEI 59

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            V+G  +   ER  L   +KP G+V T SD D    + +       R+  VGRLD ++EG
Sbjct: 60  TVNGKRVEGKERPVLLAVNKPRGIVCTTSDKDRAENIVEFFKY-PVRIYPVGRLDKDSEG 118

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLL+TN G L   +        + Y V     V +  +  ++ G+ I G      +  + 
Sbjct: 119 LLLMTNQGDLVNRILRGRYGHEKEYLVTVDRPVTEAFIRQMRNGVEILGTRTKPCEAEI- 177

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                    ++ L +G NR+I+++ E   ++V  L R+     +LG L  G  RE++   
Sbjct: 178 ---TGERSFSIILTQGLNRQIRRMCEALGYQVKTLKRVRIMNVKLGNLKTGQYRELTPAE 234

Query: 241 LREQLG 246
             E   
Sbjct: 235 WEELQR 240


>gi|222147689|ref|YP_002548646.1| ribosomal large subunit pseudouridine synthase B [Agrobacterium
           vitis S4]
 gi|221734677|gb|ACM35640.1| ribosomal large subunit pseudouridine synthase B [Agrobacterium
           vitis S4]
          Length = 704

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 169/349 (48%), Positives = 216/349 (61%), Gaps = 2/349 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           ++   P+R+SK++ARAGIASRR+VERMI + RV VNG +L+   +N    D IEVDG P+
Sbjct: 77  EDTLKPERISKLLARAGIASRRDVERMIMEGRVAVNGKVLDSPVLNATLADRIEVDGEPI 136

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R  ERTRLWLYHKP GLVTT+SDP+GR TVFDNLP    RV+S+GRLDINTEGLLLLTND
Sbjct: 137 RGIERTRLWLYHKPSGLVTTNSDPEGRPTVFDNLPEELPRVMSIGRLDINTEGLLLLTND 196

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GGLARVLELP+T WLR YRVR +G++DQ KL+ LK GI + G+ YG +   LD  +G N 
Sbjct: 197 GGLARVLELPTTGWLRRYRVRAYGEIDQAKLDTLKDGIAVDGVLYGAIDAVLDRSQGHNV 256

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+T+GLREGKNREIK V      +VNRLIRISYGPFQLG L     +EV  ++LR+QLGP
Sbjct: 257 WITMGLREGKNREIKNVLGALGLEVNRLIRISYGPFQLGDLPESQVQEVRGRMLRDQLGP 316

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            L+EE++ N DAP+YS+     +                K  ++               +
Sbjct: 317 RLIEESKANFDAPLYSNAPAEEEDAPAPKAKAKAEEGNWKKDTRPAKPRGFDNREDAREK 376

Query: 308 --RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               L +    AK    S     G+     + +       + R    K+
Sbjct: 377 ALSRLDTRRDGAKPAFGSKPGFGGKPGFKGKPAAGRDGDDAARDGKPKR 425


>gi|259046873|ref|ZP_05737274.1| ribosomal large subunit pseudouridine synthase B [Granulicatella
           adiacens ATCC 49175]
 gi|259036496|gb|EEW37751.1| ribosomal large subunit pseudouridine synthase B [Granulicatella
           adiacens ATCC 49175]
          Length = 241

 Score =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 79/241 (32%), Positives = 127/241 (52%), Gaps = 3/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR+ E  I + RVKVNG ++      V + D IEVDG+P+   E  
Sbjct: 2   ERLQKVMAHAGVASRRKCEAFIQEGRVKVNGEVVRELGFKVGANDKIEVDGIPI-YKEEP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++++KP G++++ SD  GR+ V D    +  RV  VGRLD +T GLLLLTNDG  + +
Sbjct: 61  VYFMFYKPKGVLSSASDDKGRTVVTDYFKDVEQRVYPVGRLDYDTTGLLLLTNDGEFSNL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW--VTV 191
           +  P     + Y  +  G     ++  L++GIV+ G    +    + +         V +
Sbjct: 121 MTHPKHHVEKKYIAKVKGIPTPRQMRQLERGIVLDGKKTSNAIAQILSVDTDKGTGIVAL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG N ++K++FE     V +L R  +G   L  L  G  RE+    +++     L E
Sbjct: 181 TIHEGWNHQVKRMFEAVELPVMKLKREEFGFLTLENLRPGDYRELRSFEVQKLRKLALDE 240

Query: 252 E 252
           +
Sbjct: 241 K 241


>gi|77414368|ref|ZP_00790523.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae 515]
 gi|77159558|gb|EAO70714.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae 515]
          Length = 240

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 81/241 (33%), Positives = 129/241 (53%), Gaps = 3/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q  V +NG ++   A  V + D +E++G P+   E  
Sbjct: 1   MRINKYIAHAGIASRRKAEELIKQGMVTINGQVVNELATKVKAGDLVEIEGSPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T GLL+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVIDLLPQVKERIYPVGRLDWDTTGLLILTNDGDFTDK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIIKVDHEKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFEQVGLLVDKLSRTQFGTLDLTGLRPGEARRLNKKEISQLHNAAINK 239

Query: 252 E 252
            
Sbjct: 240 S 240


>gi|126667221|ref|ZP_01738195.1| 23S rRNA pseudouridine synthase [Marinobacter sp. ELB17]
 gi|126628377|gb|EAZ99000.1| 23S rRNA pseudouridine synthase [Marinobacter sp. ELB17]
          Length = 317

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 62/323 (19%), Positives = 117/323 (36%), Gaps = 7/323 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
              +  R++K I+ +GI SRRE +R I Q  V++NG         V+ TD + V+G  + 
Sbjct: 2   TQSSSTRLNKYISESGICSRREADRYIEQGNVRINGKRASV-GDQVLPTDTVMVNGQIIE 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                          +    +                 R+  +GRLD +++GL+ +T++G
Sbjct: 61  PRAEEDQVFIALNKPVGIVSTTDSAERDNIQRFVGHTVRIFPIGRLDKDSQGLIFMTSNG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   +        + Y V     + +  ++ +  G+ I G      +V     + S   
Sbjct: 121 DLVNKILRAGNNHEKEYLVTVDKPITKTFIDGMAGGVPILGTVTKKCRV----SQESRFV 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E F + V RL R       LG L  G  R+++ K L   +   
Sbjct: 177 FRIVLVQGLNRQIRRMAEHFGFDVTRLERQRIMNISLGNLPVGQWRDLTSKEL--AVLMD 234

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
            + ++  +  A         +       +      R    +  + G     +       R
Sbjct: 235 SIRDSSSDAPAAPQKPAGKTKPANAPAQKRESHKPRAGNKTPPRPGAKSAGQPGGRPDNR 294

Query: 309 NLASNVWMAKGIHSSFLSDSGQR 331
             +      K         S +R
Sbjct: 295 PGSKPAARPKSKPKKQRQRSTKR 317


>gi|25011682|ref|NP_736077.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae NEM316]
 gi|24413222|emb|CAD47301.1| Unknown [Streptococcus agalactiae NEM316]
          Length = 240

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 81/241 (33%), Positives = 129/241 (53%), Gaps = 3/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q  V +NG ++   A  V + D +E++G P+   E  
Sbjct: 1   MRINKYIAHAGIASRRKAEELIKQGMVTINGQVVNELATKVKAGDLVEIEGSPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T GLL+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVIDLLPQVKERIYPVGRLDWDTTGLLILTNDGDFTDK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARIKGIATKENLRPLTRGVVIDGKKTKPARYNIIKVDHEKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFEQVGLLVDKLSRTQFGTLDLTGLRPGEARRLNKKEISQLHNAAINK 239

Query: 252 E 252
            
Sbjct: 240 S 240


>gi|254460191|ref|ZP_05073607.1| ribosomal large subunit pseudouridine synthase [Rhodobacterales
           bacterium HTCC2083]
 gi|206676780|gb|EDZ41267.1| ribosomal large subunit pseudouridine synthase [Rhodobacteraceae
           bacterium HTCC2083]
          Length = 310

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 139/309 (44%), Positives = 190/309 (61%), Gaps = 1/309 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            E     R++KV+ARAG+ASRRE ERMI   R+ V+G +++  A+NV+ T  I VDG P+
Sbjct: 3   TETPKGDRIAKVLARAGVASRREAERMIDAGRISVDGKIIDSPALNVLPTARISVDGKPM 62

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              E  R+W+YHKP GLVTT SD  GR T+FD+LP    RV+SVGRLD+N+EGLLLLTND
Sbjct: 63  AAPEPPRVWMYHKPTGLVTTDSDEKGRKTIFDDLPEDMPRVMSVGRLDLNSEGLLLLTND 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GGL R LELPST WLR YRVR +G+  ++    L+KG+ +QG  +  M V++D Q+G+NA
Sbjct: 123 GGLKRKLELPSTGWLRKYRVRINGRPTEETFEPLRKGLNLQGEHFQPMLVSIDRQQGANA 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+TVG+REGKNREI++  E     VNRLIR+SYGPFQLG L      E+ ++ L++QLG 
Sbjct: 183 WLTVGIREGKNREIRRAMEAIQLNVNRLIRVSYGPFQLGNLKTSGVEEIRRRALKDQLGL 242

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              E+ +V    P  +              +P    R +   S  + +++ K    P  +
Sbjct: 243 S-DEDLEVPGAKPKPTQRGKNSVTRGKRPPLPKGPLRGRDRFSDSDPMARPKSSGKPKSK 301

Query: 308 RNLASNVWM 316
                    
Sbjct: 302 PANKPRPKR 310


>gi|255525211|ref|ZP_05392153.1| pseudouridine synthase [Clostridium carboxidivorans P7]
 gi|255511074|gb|EET87372.1| pseudouridine synthase [Clostridium carboxidivorans P7]
          Length = 234

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 75/231 (32%), Positives = 120/231 (51%), Gaps = 2/231 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +A  GIASRR+ E +I Q RVKVNG ++    V +    D + +DG  ++K + 
Sbjct: 3   ERLQKYMAACGIASRRKCEEIILQARVKVNGKIVNELGVKIDEEKDLVTLDGKLIKKEKN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP G V+T  D  GR T   +L  +  R+  +GRLD +T GL+LLTNDG +  
Sbjct: 63  KVYIALNKPKGYVSTVKDERGRKT-ILDLVDVTERIYPIGRLDYDTSGLILLTNDGDIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  ++Y     G   ++ +   + GI I G      +  +  +      V + 
Sbjct: 122 KIIHPKQEKNKIYIALIKGIPTENDIKKFEIGINIDGYVTAPAKFKIIKKFKDYCEVEII 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + EG+NR+I+K+ +F N +V  L RI  G  +LG L  G  R +S K ++ 
Sbjct: 182 IHEGRNRQIRKMCDFINHQVLELKRIQIGDIKLGNLPLGKWRYLSNKEVKN 232


>gi|188589639|ref|YP_001920921.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum E3 str. Alaska E43]
 gi|188499920|gb|ACD53056.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum E3 str. Alaska E43]
          Length = 236

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 75/229 (32%), Positives = 120/229 (52%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K +A  G+ASRR+ E MI    VKVNG+++      V    D +E  G  ++K E 
Sbjct: 3   ERLQKYMASCGLASRRKCEEMILSGEVKVNGVVVTELGTRVNPVEDKVEYKGCLIKKEEN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G +T+  D  GR TV  +L  +  R+  +GRLD ++ G++LLTNDG +  
Sbjct: 63  KVYIILNKPEGYITSAKDEKGRKTV-LDLVKVNERIYPIGRLDYDSSGIILLTNDGDIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + Y     G+V +  ++   KGI I G       + + + +   + V V 
Sbjct: 122 KIIHPREELNKKYIAVVKGEVSKKDIDTFNKGIDIGGYVTAPASLEVLSYENGKSTVEVC 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGKNR+I+K+    N +V  L R+S G  QL  L  G  RE++ + L
Sbjct: 182 IHEGKNRQIRKMCTAINHEVLSLNRVSIGEIQLKYLKKGEWRELTTEEL 230


>gi|218289586|ref|ZP_03493806.1| pseudouridine synthase [Alicyclobacillus acidocaldarius LAA1]
 gi|218240236|gb|EED07419.1| pseudouridine synthase [Alicyclobacillus acidocaldarius LAA1]
          Length = 273

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 92/276 (33%), Positives = 140/276 (50%), Gaps = 8/276 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV+A AG+ASRR+ E +I   RV V+G ++ +    V  +   I VDGVP+   E+
Sbjct: 2   ERLQKVLAHAGVASRRKCEELILAGRVSVDGEIVTQLGAKVDPSRQRIAVDGVPIEL-EQ 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + + +KP+  ++T SDP GR TV   LP I  RV  VGRLD +T GLLL TNDG L +
Sbjct: 61  PVVLVLNKPVAYLSTVSDPLGRRTVMQLLPPIRERVYPVGRLDYDTSGLLLFTNDGELTQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ---KGSNAWV 189
            L  PS +  +VYRV   G VD++    L +G+ ++       +V +  Q   +   A V
Sbjct: 121 RLLHPSREIEKVYRVSVRGIVDRETRRALMEGVELEDGVTAPAKVEVLRQADREDGVAVV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + + EG+NR+++++FE     V RL RI++GP  LG L  G  R ++++     +  + 
Sbjct: 181 HLAIHEGRNRQVRRMFERLGLPVLRLKRIAFGPVSLGHLKTGEWRALTQEEW---VALYQ 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
                         S    R      S       R 
Sbjct: 238 AAGMTPPPYRRPTISREPERKGAARASARDHGSRRG 273


>gi|119386847|ref|YP_917902.1| RNA-binding S4 domain-containing protein [Paracoccus denitrificans
           PD1222]
 gi|119377442|gb|ABL72206.1| RNA-binding S4 domain protein [Paracoccus denitrificans PD1222]
          Length = 457

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 146/354 (41%), Positives = 203/354 (57%), Gaps = 11/354 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
            N    R++KV+ARAG+ASRRE ERMI + RV VNG  ++  A++V   D I VDG PL 
Sbjct: 10  PNPQADRIAKVMARAGVASRREAERMILEGRVTVNGKKIDSPALDVTPADRIRVDGKPLE 69

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + + TRLWLY+KP+GLVT++SD  GR TVFD LP    RV++VGRLD+N+EGLLLLTNDG
Sbjct: 70  EPQETRLWLYYKPLGLVTSNSDEKGRQTVFDALPRDLPRVMTVGRLDLNSEGLLLLTNDG 129

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L R LELP+T WLR YRVR +GQ +      L++G+ I G  +  M++ LD+Q+G+NAW
Sbjct: 130 ELKRRLELPTTGWLRRYRVRVNGQPNDLTFAPLRRGVTIDGEEFAPMEINLDSQQGANAW 189

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +TVG+REG+NREI++        VNRLIRI YGPF+L  L     REV +K+LR+QLG  
Sbjct: 190 LTVGIREGRNREIRRAMAHVGLIVNRLIRIGYGPFKLTGLEENEVREVKRKVLRDQLGGL 249

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR----MKKNSSQKNGLSKQKKLATP 304
           L  E +    +          +      +  D+  R     +++  +K    +++    P
Sbjct: 250 LTGETEEKPRSFRERGAAKPAEGDARPRKPRDEGGRKPFARREDGDRKPFARREEGDRKP 309

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP-----SFPSKRSLRRTSAK 353
             RR          G           + E+  R P         K ++R  + K
Sbjct: 310 FARREDGER--KPFGKRPDGGRKPFAKREDGERKPFARREDRDGKPAVRDGARK 361


>gi|86607697|ref|YP_476459.1| RNA pseudouridine synthase family protein [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86556239|gb|ABD01196.1| RNA pseudouridine synthase family protein [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 274

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 82/272 (30%), Positives = 122/272 (44%), Gaps = 13/272 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
            PQR+ K++A+ G+ASRR+VE  I   RV+VNG ++           D IEV+G  +  A
Sbjct: 3   EPQRLQKLLAQQGLASRRQVEAWILAGRVRVNGKVVTELGSKADPERDCIEVNGQVIPLA 62

Query: 71  ERT---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLT 125
           +      L L+     L T       ++ +    PS   +     VGRLD ++ G LLLT
Sbjct: 63  KDPARYVLLLHKPVGVLSTCADPWGRKTVLDLLPPSWKRQTRLYPVGRLDADSSGALLLT 122

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------ 179
           NDG L   L  P     + YRV+  G   Q  L   + G+ ++G      +V        
Sbjct: 123 NDGDLTLKLTHPRYHLPKTYRVQVQGHPSQATLQHWRDGVDLEGYTTLPAEVEFCPAPDF 182

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              +  + +W+ V L EG+NR+I++V E     V  L R + GP  LG L AG  R++  
Sbjct: 183 RQREHPNCSWLRVVLFEGRNRQIRRVAERLGHPVLSLHREAIGPLGLGNLKAGQFRQLDP 242

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRD 270
             L+  L P     +  +L           RD
Sbjct: 243 HELQALLAPLTGHSSSSSLGKRPLRPPARSRD 274


>gi|24380085|ref|NP_722040.1| putative pseudouridylate synthase B, large subunit [Streptococcus
           mutans UA159]
 gi|24378080|gb|AAN59346.1|AE015000_4 putative pseudouridylate synthase B, large subunit [Streptococcus
           mutans UA159]
          Length = 240

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 85/240 (35%), Positives = 130/240 (54%), Gaps = 3/240 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V +NG ++   A  V S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTLNGQMVTELATTVKSGDRVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++  D  GR TV D LP +  R+  VGRLD +T GLL+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVRDDKGRQTVVDLLPEVKERIYPVGRLDWDTSGLLILTNDGDFTDK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           +  P  +  +VY  R  G   +D L  L KGIVI G      +  +    ++ + + V +
Sbjct: 120 MLHPRHEIDKVYVARVKGLASKDNLRPLTKGIVIDGKKTQPARYRIVKTDREKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK + +     + E
Sbjct: 180 TIHEGRNHQVKKMFEAVGLMVDKLSRTRFGTLDLSGLNPGEARRLNKKEISQLYNAAVNE 239


>gi|284048580|ref|YP_003398919.1| pseudouridine synthase [Acidaminococcus fermentans DSM 20731]
 gi|283952801|gb|ADB47604.1| pseudouridine synthase [Acidaminococcus fermentans DSM 20731]
          Length = 244

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 87/234 (37%), Positives = 129/234 (55%), Gaps = 2/234 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T +R+ KV+A AG+ASRRE E++I   RV+VNG  +      V   D I VDG  L +
Sbjct: 2   EQTKERLQKVMAAAGVASRRECEKIILAGRVQVNGKPVTELGTRVGKADRITVDGKALHR 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                 +L +KP G+VTT  DP GR TV D +  +  R+  VGRLD  TEGLLL+TNDG 
Sbjct: 62  KSARHTYLLYKPGGVVTTMKDPQGRRTVADLMAGLHQRLYPVGRLDYLTEGLLLMTNDGE 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--A 187
           LA+ L  PS    + Y V  HG+V ++KL++L+ G+ ++        V +          
Sbjct: 122 LAQHLTHPSHHVDKTYEVEVHGRVPEEKLDVLRLGVPLEDGLTAPAVVYVKKWDPEKNLT 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             TV + EG+NR+++++ +F  + V  L RI  G   L  +  G  RE++ + +
Sbjct: 182 RFTVTIHEGRNRQVRRMCDFIGFPVKSLKRIQVGTLTLEGMKKGEFRELTPEEV 235


>gi|199598710|ref|ZP_03212124.1| 16S rRNA uridine-516 pseudouridylate synthase related enzyme
           [Lactobacillus rhamnosus HN001]
 gi|229552173|ref|ZP_04440898.1| pseudouridylate synthase [Lactobacillus rhamnosus LMS2-1]
 gi|258508377|ref|YP_003171128.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           rhamnosus GG]
 gi|258539588|ref|YP_003174087.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           rhamnosus Lc 705]
 gi|199590398|gb|EDY98490.1| 16S rRNA uridine-516 pseudouridylate synthase related enzyme
           [Lactobacillus rhamnosus HN001]
 gi|229314475|gb|EEN80448.1| pseudouridylate synthase [Lactobacillus rhamnosus LMS2-1]
 gi|257148304|emb|CAR87277.1| Ribosomal large subunit pseudouridine synthase B [Lactobacillus
           rhamnosus GG]
 gi|257151264|emb|CAR90236.1| Ribosomal large subunit pseudouridine synthase B [Lactobacillus
           rhamnosus Lc 705]
 gi|259649691|dbj|BAI41853.1| pseudouridylate synthase [Lactobacillus rhamnosus GG]
          Length = 248

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 82/247 (33%), Positives = 124/247 (50%), Gaps = 3/247 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R+ KVIA AGIASRR  E +IA   VKVNG +     + +   D +EVDGVP+  
Sbjct: 2   TTKNERLQKVIANAGIASRRHAETLIASGHVKVNGHVTTEMGIKIGPHDTVEVDGVPI-G 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E  R +L++KP G+++   D  GR  V D    +  R+  VGRLD +T GLL++TNDG 
Sbjct: 61  KEAKRYFLFYKPRGVISAVEDNKGRKVVTDYFEDVQERLYPVGRLDYDTSGLLVMTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW- 188
           LA  L  P     + Y  +  G  ++  L  LK G+ I G      +V + +   +    
Sbjct: 121 LANHLMHPRYALEKKYVAKVEGIPNRPALAPLKTGVSIDGKMTAPAKVEILSTDKAKKTA 180

Query: 189 -VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V + + +G N ++KK+F+   + V +L R +YG   L  L  G  R +  + L +    
Sbjct: 181 IVALTIHQGMNHQVKKMFKAVGFPVIKLSREAYGNLTLAGLQPGEHRPIKPQELHDLRQL 240

Query: 248 HLLEEAQ 254
              +E  
Sbjct: 241 TGEQEEA 247


>gi|228476518|ref|ZP_04061208.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           salivarius SK126]
 gi|228251939|gb|EEK10985.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           salivarius SK126]
          Length = 241

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 79/240 (32%), Positives = 129/240 (53%), Gaps = 3/240 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I + RV +NG  +   A  V + D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKEGRVTLNGKTVTELATIVKNGDIVEVNGSPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD   R TV D +P +  R+  VGRLD +T GLL+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDEKNRKTVIDLMPHVKERIYPVGRLDWDTTGLLILTNDGDFTDK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIIKVDHEKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE     V++L R  +G   L  L  G +R ++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTRFGTLDLTGLRPGESRRLNKKEISQLHNAAVNK 239


>gi|304316801|ref|YP_003851946.1| pseudouridine synthase [Thermoanaerobacterium thermosaccharolyticum
           DSM 571]
 gi|302778303|gb|ADL68862.1| pseudouridine synthase [Thermoanaerobacterium thermosaccharolyticum
           DSM 571]
          Length = 235

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 73/230 (31%), Positives = 123/230 (53%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +A   IASRR+ E++I   ++KVNG +++   + +    D +E DG  + K + 
Sbjct: 2   ERLQKYLAECSIASRRKCEQLILDGKIKVNGTVIKNLGIKIDPDKDIVEYDGRVVAKVQH 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G +TT  D  GR +V D +     R+  VGRLD +T GLLLLTNDG +A 
Sbjct: 62  NIYIMLNKPTGFITTVKDQFGRPSVLDIIKI-KDRIYPVGRLDCDTSGLLLLTNDGDIAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  +VY  +  G  D   L+  + G+++        ++ +  +  ++A V + 
Sbjct: 121 KLMHPKHEIDKVYIAKIRGIPDDKDLDRFRNGLLLDNRLTAKAKIEILKKINNDALVKIV 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EG+NR+I+++ E     V  L RI  G  +LG L  G  R +S + ++
Sbjct: 181 IHEGRNRQIRRMCELIGHPVMTLKRIKIGDLELGNLKVGQWRYLSGEEVQ 230


>gi|282880895|ref|ZP_06289588.1| pseudouridylate synthase [Prevotella timonensis CRIS 5C-B1]
 gi|281305277|gb|EFA97344.1| pseudouridylate synthase [Prevotella timonensis CRIS 5C-B1]
          Length = 253

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 63/246 (25%), Positives = 109/246 (44%), Gaps = 5/246 (2%)

Query: 1   MKDKNIVQEN----FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           MK +    E       P R++K +A AG+ SRRE +  I    VKVNG ++      V+ 
Sbjct: 1   MKKRIEYNEEHIDPTVPVRLNKYLANAGVCSRREADEFIQAGVVKVNGEVVTELGTKVLR 60

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           +D +     P+   ++  + L      + T+      ++ +     +   R+  VGRLD 
Sbjct: 61  SDEVVFHDQPVSLEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKNACPERIYPVGRLDR 120

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NT G+LL TNDG LA  L  P     +VY V     V    +  + +GI ++        
Sbjct: 121 NTTGVLLFTNDGDLASKLTHPKFLKKKVYHVFLDKNVTAHDMQQIAEGIELEDGEIHADA 180

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           +    +   N  V + +  GKNR ++++FE   ++V +L R+ +       L  G  R +
Sbjct: 181 IEYTNETEKNQ-VGIEIHSGKNRIVRRIFESLGYRVIKLDRVQFAGLTKKNLRRGDWRYL 239

Query: 237 SKKILR 242
           + + + 
Sbjct: 240 TAQEVD 245


>gi|260598145|ref|YP_003210716.1| 23S rRNA pseudouridylate synthase B [Cronobacter turicensis z3032]
 gi|260217322|emb|CBA31307.1| Ribosomal large subunit pseudouridine synthase B [Cronobacter
           turicensis z3032]
          Length = 364

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 91/350 (26%), Positives = 139/350 (39%), Gaps = 12/350 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E MI   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIEAMIEAGRVSVDGKIATLGDRVEVTPALKIRIDGHLISVKE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T        +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SVEQICRVLAYYKPEGELCTRSDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD +K+  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSQEVEREYAVRVFGQVDDNKVRELARGVQLEDGPAAFKTIRFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E +G      ++V ++                +          ++ S  + G  +     
Sbjct: 242 ELVGLPPETASKVAVEKDRRRM--KANQIRRAVKRHSQTAGGPRQGSPARQGQGQAGAAR 299

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                R   +         +S  +  G          +   + +      
Sbjct: 300 PAGSARPAENTRAGNNTSRASGNARPGGNPRASGARATGSGRPNSGSGRP 349


>gi|315123457|ref|YP_004065463.1| putative ribosomal RNA pseudouridine synthase [Pseudoalteromonas
           sp. SM9913]
 gi|315017217|gb|ADT70554.1| putative ribosomal RNA pseudouridine synthase [Pseudoalteromonas
           sp. SM9913]
          Length = 329

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 74/325 (22%), Positives = 134/325 (41%), Gaps = 17/325 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE ++ I Q RV VNG L     V V  +D + VDG  L+   +  
Sbjct: 6   RLNKFISETGFCSRREADKYIEQGRVTVNGELP-EMGVKVAQSDVVLVDGKQLKAPPKRV 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
              Y+KP+G+  T       + V     +   R+  +GRLD  +EGL+ LTN+G +   +
Sbjct: 65  YIAYNKPVGITCTTERKIQSNIVKAV--NYPERIFPIGRLDRPSEGLIFLTNEGDIVNKI 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y V     +++  +N +  GI I        +VT    +      ++ L 
Sbjct: 123 LRAGNNHEKEYVVTVDKPLNRQFVNKMANGIPILDTVTKKCKVTQTGAQQ----FSIILT 178

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI---LREQLGPHLLE 251
           +G NR+I+++ E+  ++V  L R+      L  L  G  R +S      + + +      
Sbjct: 179 QGLNRQIRRMCEYLGYEVVTLKRVRIMNVTLKGLKVGQWRHLSDAEMAVINDSIADSGKT 238

Query: 252 EAQV---NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
           +      + +   Y+ +       +            ++N+ ++   +K+    TP  +R
Sbjct: 239 QEHSLYDDTEQRKYTEQDKNSGAKSAHKRDFQGGKLRRENNDEQQKHAKKNSRNTPYQKR 298

Query: 309 N----LASNVWMAKGIHSSFLSDSG 329
           +      SN   A     +    SG
Sbjct: 299 STTYVGKSNTHKANTATGNKTRSSG 323


>gi|13476819|ref|NP_108388.1| hypothetical protein mlr8253 [Mesorhizobium loti MAFF303099]
 gi|14027580|dbj|BAB53849.1| mlr8253 [Mesorhizobium loti MAFF303099]
          Length = 546

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 151/347 (43%), Positives = 204/347 (58%), Gaps = 9/347 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
                +R++K +ARAG+ASRR+ E +IA  RVKVNG  L   A NVM  D I +DG+ + 
Sbjct: 93  TEEAGERIAKRLARAGLASRRDAEELIAAGRVKVNGRALTSPAFNVMPGDIIHLDGMEIP 152

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ERTRL+L+HKP G+VTT+ DP+GR TVFD LP+   R++++GRLDINTEGLLLLTNDG
Sbjct: 153 PIERTRLFLFHKPAGVVTTNRDPEGRKTVFDVLPAELPRLMTIGRLDINTEGLLLLTNDG 212

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+RVLELP+T WLR YRVR HG+V++  L  L++GI + G+ YG ++ +LD ++GSNAW
Sbjct: 213 GLSRVLELPATGWLRRYRVRVHGKVEESALAGLREGIAVDGVFYGAIEASLDREQGSNAW 272

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +T+GLREGKNRE+K +       V RLIRISYGPFQL  L  G   E+  ++LR+QLG  
Sbjct: 273 LTIGLREGKNREVKNILGALGLDVTRLIRISYGPFQLEDLPEGHVLEIKGRVLRDQLGER 332

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
           L+EE+  N DA I    +        +          ++    ++G  +       +  R
Sbjct: 333 LVEESGANFDAEIAKPFS-----NKPVRRTEVREPEPERPKFTRDGERRPIGEGGLIKNR 387

Query: 309 NLASNVWMAKGIHSSFLSDSGQREEN----HRRSPSFPSKRSLRRTS 351
                         S   D G+R E         P         R S
Sbjct: 388 KRREGSRDEALGKLSTSPDRGERPEKSFGERGPRPERGGFGDKPRGS 434


>gi|312862494|ref|ZP_07722736.1| pseudouridine synthase B, ribosomal large subunit [Streptococcus
           vestibularis F0396]
 gi|322517477|ref|ZP_08070350.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           vestibularis ATCC 49124]
 gi|311101899|gb|EFQ60100.1| pseudouridine synthase B, ribosomal large subunit [Streptococcus
           vestibularis F0396]
 gi|322123959|gb|EFX95518.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           vestibularis ATCC 49124]
          Length = 241

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 79/240 (32%), Positives = 129/240 (53%), Gaps = 3/240 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I + RV +NG  +   A  V S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKEGRVTLNGKTVTELATIVKSGDIVEVNGSPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD   R TV D +P +  R+  VGRLD +T GLL+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDEKNRKTVIDLMPHVKERIYPVGRLDWDTTGLLILTNDGDFTDK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+V+ G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLIRGVVLDGKKTQPARYNIIKVDHEKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE     V++L R  +G   L  L  G +R ++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTRFGTLDLTGLRPGESRRLNKKEISQLHNVAVNK 239


>gi|65318840|ref|ZP_00391799.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Bacillus anthracis str.
           A2012]
          Length = 242

 Score =  188 bits (476), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 75/241 (31%), Positives = 127/241 (52%), Gaps = 3/241 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E   
Sbjct: 3   RLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEEPVY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             LY     + +   D        D  P I  R+  +GRLD +T G+LL+TNDG  A VL
Sbjct: 63  FLLYKPTGVISSVSDDKGRSVVT-DFSPEITQRLFPIGRLDYDTSGVLLMTNDGDFANVL 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVG 192
             P  +  + Y  +  G +  +K+ +L++G+ ++       +V + +       A V + 
Sbjct: 122 MHPRYKVEKTYVAKIKGPLTGEKIRMLERGVTLEDGKTAPARVKIISWDKRKEMAIVQLT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++   +++       + 
Sbjct: 182 IHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELTPHEVKQLRALASTKP 241

Query: 253 A 253
            
Sbjct: 242 R 242


>gi|238924043|ref|YP_002937559.1| 16S pseudouridylate synthase [Eubacterium rectale ATCC 33656]
 gi|238875718|gb|ACR75425.1| 16S pseudouridylate synthase [Eubacterium rectale ATCC 33656]
          Length = 250

 Score =  188 bits (476), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 64/237 (27%), Positives = 116/237 (48%), Gaps = 5/237 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGV 65
           V+ N    R+ K ++  G+ +R EV+++I   ++ +NG +  +    V +  D + V+G 
Sbjct: 5   VERNINMIRLDKFLSEMGLGTRSEVKKLIKTGQIAINGTVAAKPETKVDTDADEVSVNGR 64

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            ++               + +   D    + +     ++   +  VGRLDI+TEGLLL+T
Sbjct: 65  IVKYQRYEYYLFNKPSGCV-SATCDNVHDTVMDYITDAVHDDLFPVGRLDIDTEGLLLIT 123

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG 184
           NDG L+  L  PS    + Y  R  G+V  D +   K+GI I +       ++ +  + G
Sbjct: 124 NDGALSHELLSPSKHVAKTYYARIDGEVTLDDIIRFKEGIDIGEEKPTKPAEL-VIKKSG 182

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
           S + + + + EGK  ++K++FE    +V  L RIS GP +L   L  G+ R +++  
Sbjct: 183 SVSEIELTITEGKFHQVKRMFEALGKRVIYLKRISMGPLKLPDDLKTGTYRALTQAE 239


>gi|168700584|ref|ZP_02732861.1| ribosomal large subunit pseudouridine synthase B [Gemmata
           obscuriglobus UQM 2246]
          Length = 271

 Score =  188 bits (476), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 86/271 (31%), Positives = 132/271 (48%), Gaps = 2/271 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAER 72
           +R++K +A AG+ SRR  +++I+  RVKVNG+ +    + +  +   I VD  P+R  E+
Sbjct: 2   ERLNKYLAHAGVGSRRHCDKLISAGRVKVNGVKVTELGLKIDPSAHQIAVDDQPVRA-EK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              W  +KP+G + T+ DP GR    D LP +  RV +VGRLD  ++GLLL+TNDG LA+
Sbjct: 61  LVYWAVNKPVGHLCTNHDPAGRPRAVDLLPHVEQRVYTVGRLDEGSDGLLLMTNDGDLAQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     ++Y V   G+   D L  L  G+ +               +G+  WV V 
Sbjct: 121 GLTHPRYGVPKMYFVLVAGRPTDDDLQKLMDGVWLSDGKVRAKSAKRIKAQGNGTWVRVV 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L EGKNREI+++   F  KV RL R++ GP +L  L  G  R +S + L+          
Sbjct: 181 LTEGKNREIRRMLAKFGHKVMRLKRVAIGPVKLDKLPKGKARRISDEELKALKAFVTRAR 240

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
            ++       +       +         D  
Sbjct: 241 QKITAARLKAADGGRKTSQDAPKRPRKTDGA 271


>gi|71910124|ref|YP_281674.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS5005]
 gi|71852906|gb|AAZ50929.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS5005]
          Length = 248

 Score =  188 bits (476), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 79/249 (31%), Positives = 125/249 (50%), Gaps = 3/249 (1%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +++      R++K IA AGIASRR+ E +I Q  V +NG ++   A  V S D +E++G 
Sbjct: 1   MLKRKKNIMRINKYIAHAGIASRRKAEELIKQGLVTLNGQVITDLATTVKSGDVVEIEGS 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P+   E+    L      + +   D  GR TV D LP +  R+  VGRLD +T G+L+LT
Sbjct: 61  PIYNEEKVYYLLNKPRGAISSVS-DDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--K 183
           NDG     +  P  +  +VY  R  G   ++ L  L +GIVI G      +  +      
Sbjct: 120 NDGDFTDTMIHPRNEIDKVYLARVKGIATKENLRPLTRGIVIDGKKTKPARYNIVRVEAD 179

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            S + V + + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK + +
Sbjct: 180 KSRSIVELTIHEGRNHQVKKMFESVGLLVDKLSRTRFGTVDLKGLRPGEARRLNKKEISQ 239

Query: 244 QLGPHLLEE 252
                  ++
Sbjct: 240 LHNLANTKK 248


>gi|83590199|ref|YP_430208.1| ribosomal large subunit pseudouridine synthase B [Moorella
           thermoacetica ATCC 39073]
 gi|83573113|gb|ABC19665.1| ribosomal large subunit pseudouridine synthase B [Moorella
           thermoacetica ATCC 39073]
          Length = 240

 Score =  188 bits (476), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 85/240 (35%), Positives = 120/240 (50%), Gaps = 1/240 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A AG+ASRR  E +I   RV+VNG +++   V V    D + VDG P+   ER
Sbjct: 1   MRLQKYLALAGVASRRRAEDLIRAGRVRVNGRVIKVMGVQVEPGQDKVTVDGQPVTGPER 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L  KP G VTT SDP GR  V D +  I +R+  VGRLD  TEGLLLLTNDG L  
Sbjct: 61  KYYLLLFKPAGYVTTVSDPRGRPKVTDLVHGIPARLYPVGRLDYATEGLLLLTNDGELTL 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y     G  D + +  L+ G+ ++       +V L      +A + + 
Sbjct: 121 RLTHPRYGVTKTYLALVRGIPDANTIQHLRCGVKLEDGPTAPARVNLCRAGKDSALLELT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           LREG+NRE++++       V RL RI      L  L  G+ R ++   +        L++
Sbjct: 181 LREGRNREVRRMLAAVGHPVLRLRRIRLAFLTLRGLKPGTYRHLTPHEVERLYRLVGLKK 240


>gi|126651298|ref|ZP_01723505.1| pseudouridylate synthase (ribosomal small subunit pseudouridine
           synthase A) [Bacillus sp. B14905]
 gi|126591827|gb|EAZ85910.1| pseudouridylate synthase (ribosomal small subunit pseudouridine
           synthase A) [Bacillus sp. B14905]
          Length = 237

 Score =  188 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 109/231 (47%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++ Q+ V V+G  ++ AA++V      + V G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKQLLKQKAVTVDGASVKDAAMHVDPEQQNVSVYGERVVYTEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +   P  +  T    D              +   VGRLD +TEGLL+LTNDG LA 
Sbjct: 61  VYFMMNKPPGVISATEDLRDETVIDLLEPLDQHFQPFPVGRLDKDTEGLLVLTNDGILAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY     G V ++ +    +G+ +         ++ +  +    + + +
Sbjct: 121 KLLSPKKHVPKVYYAHIEGVVTEEDVEKFAEGVELDDGYMTKPGKLVIL-KSAPQSEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            ++EGK  ++K++FE    +V  L RIS G  +L   L  G  RE++ + L
Sbjct: 180 TIQEGKFHQVKRMFESVGKRVTYLKRISMGNLKLDDHLALGEYRELTAEEL 230


>gi|295687634|ref|YP_003591327.1| RNA-binding S4 domain-containing protein [Caulobacter segnis ATCC
           21756]
 gi|295429537|gb|ADG08709.1| RNA-binding S4 domain protein [Caulobacter segnis ATCC 21756]
          Length = 426

 Score =  188 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 138/346 (39%), Positives = 189/346 (54%), Gaps = 7/346 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +RV+K +ARAG+ASRREVER+I   RV +NG +L   A+ V   D + VDG  + + E 
Sbjct: 25  GERVAKALARAGVASRREVERLIEAGRVAINGKVLTTPAIKVKPGDFLTVDGQLVAEREP 84

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR++ YHKP GL+TTH+DP GR TVF  LP    R+ISVGRLD+N+EGLLLLTNDG L+R
Sbjct: 85  TRIFRYHKPTGLMTTHNDPKGRPTVFQTLPKDLPRLISVGRLDLNSEGLLLLTNDGELSR 144

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----QKGSNA 187
            LE PS  W+R YR R  G   Q KL+ LK G+ I+G+ YG ++  LD        G N 
Sbjct: 145 ALETPSNAWVRRYRARAFGDTTQAKLDTLKDGVTIEGVKYGSIEARLDKAHDKAGGGKNI 204

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+TV L EGKNRE++KV E    KVNRLIR+SYGPF LG L AG   EV  +++RE L  
Sbjct: 205 WITVSLSEGKNREVRKVLESVGLKVNRLIRMSYGPFALGALAAGQIEEVGPRVIRELLEG 264

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            +  E     D P ++       +        D   R    + +    +  +K   PV++
Sbjct: 265 VVPPENMPTGDRPKFAGI-ANPVKAPGTDGGGDLQRRGVPRADRDLKPAAPEKPEKPVYK 323

Query: 308 RNLASNVWM-AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
              A      +    +   +   +       +     ++ + R   
Sbjct: 324 AGWAKPKKKVSPHAPAKGAAKPKRAPAKSLETKFIDDRKPVARGKP 369


>gi|164688313|ref|ZP_02212341.1| hypothetical protein CLOBAR_01958 [Clostridium bartlettii DSM
           16795]
 gi|164602726|gb|EDQ96191.1| hypothetical protein CLOBAR_01958 [Clostridium bartlettii DSM
           16795]
          Length = 237

 Score =  188 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 70/232 (30%), Positives = 122/232 (52%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R++K IA  G+ASRR+ E +I   RV VN  ++   +  V    D ++VD   +++  +
Sbjct: 1   MRINKYIALCGVASRRKAEELILAGRVTVNDEVMTELSYKVDEENDIVKVDDKLIKEENK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G +TT  D   R +V D +  I  RV  +GRLD  T GLLLLTNDG L  
Sbjct: 61  LVYILLNKPEGYITTVKDQFDRPSVLDLVSDIKERVYPIGRLDYETSGLLLLTNDGDLTY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVT 190
            L  P  +  + Y  R  G++ ++++   K G+ I+       ++ +    ++  ++ + 
Sbjct: 121 KLTHPKHEVDKTYVARVKGKLTKEEIERFKTGLKIEDYTTAPAKLKVIKYDEQRDSSLLE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + + EGKNR+++K+ +  N  V RL R + G  ++G    G  R +++  ++
Sbjct: 181 IKIHEGKNRQVRKMCKAINHPVLRLRRSAMGKIKIGDCEIGKYRYLTEDEIK 232


>gi|312793758|ref|YP_004026681.1| pseudouridine synthase [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|312180898|gb|ADQ41068.1| pseudouridine synthase [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 240

 Score =  188 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 74/230 (32%), Positives = 118/230 (51%), Gaps = 2/230 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
              R+ K +A+ GIASRR+ E +I Q RVKVNG  + +    V    D +EVDG  +   
Sbjct: 3   ELVRLQKYMAQCGIASRRKCEEIILQGRVKVNGKTVNQLGFKVDPEKDVVEVDGKRITLQ 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGG 129
            +    + +KP G++++  D  GR TV D +    +     VGRLD +T GL+LLTNDG 
Sbjct: 63  MQKVYIMLNKPFGVISSAKDEKGRKTVVDLVKDKVNVRVFPVGRLDFDTTGLILLTNDGE 122

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P     + Y     G   ++++   +KG++I G      +  +      NA V
Sbjct: 123 FAYKVTHPKHDIEKTYIALIRGIPSKEEIERFEKGLLIDGKMTAPAKFKILKLINGNALV 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+NR+I+K+ +    +V +L R++ G  QLG L  G    + K+
Sbjct: 183 EIKIHEGRNRQIRKMCDQIGHEVLKLKRVAIGKLQLGKLKEGEFVFLDKE 232


>gi|253578001|ref|ZP_04855273.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251850319|gb|EES78277.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 323

 Score =  188 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 75/329 (22%), Positives = 132/329 (40%), Gaps = 9/329 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K   +      R++K ++ AGI SRRE +RMI + R+ VNG   E     V   D I
Sbjct: 1   MYKKLYNRTMDEKIRINKYLSEAGICSRREADRMIEEGRITVNGKKAES-GQKVSLEDEI 59

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
             D +P+ K E+  L L++KP G+V +       +TV D L         VGRLD  ++G
Sbjct: 60  CADNIPVHKNEKKVLLLFNKPRGIVCSTKQQFDETTVTDYLDYPLRV-YPVGRLDKESQG 118

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLLLTN+G L   +        + Y V  +  VD++ +  + KG+ +        +V   
Sbjct: 119 LLLLTNEGDLVNKIMRAGNYHEKEYFVTVNKPVDREFVRRMSKGVPVLDTVTRPCRVV-- 176

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             +       + L +G NR+I+++  +  ++V +L RI      L  +  G  RE++ + 
Sbjct: 177 --QTGECSFRIILTQGLNRQIRRMCRYLGYEVQKLKRIRIMNLTLDGIREGEYREITAQE 234

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT---RMKKNSSQKNGLSK 297
             E         ++  +     +  +         ++                ++  +  
Sbjct: 235 WEELNHLLESSTSETVIRTGEQNGNSSDHANERAGAKAGQGSKGVLPAGYRDHKQQRVRS 294

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLS 326
             + A+    RN   +            S
Sbjct: 295 DVRRASGSGERNRHCSGKQPNRKRRVRGS 323


>gi|83591991|ref|YP_425743.1| pseudouridine synthase, Rsu [Rhodospirillum rubrum ATCC 11170]
 gi|83574905|gb|ABC21456.1| Pseudouridine synthase, Rsu [Rhodospirillum rubrum ATCC 11170]
          Length = 293

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 136/290 (46%), Positives = 183/290 (63%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +R++KVIARAGI SRR+ E++I + RV +NG  +E  A  V ++D + VDG PL   E
Sbjct: 4   DSERIAKVIARAGICSRRDAEKLIVEGRVTLNGRKVETPATLVAASDTVTVDGKPLPALE 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             RLW Y+KPIGLVT+H D  GR TVF+ LP+   RVISVGRLD+N+EGLLLLTNDG LA
Sbjct: 64  PARLWRYNKPIGLVTSHRDEQGRPTVFERLPATLPRVISVGRLDLNSEGLLLLTNDGELA 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           R LE PS  WLR YRVR HG  D  KL  L+KG+ ++G+ YG ++V L+ Q+G+NAW++V
Sbjct: 124 RRLEHPSQGWLRRYRVRVHGAPDPVKLAALEKGVTVEGVAYGSIRVALERQQGANAWLSV 183

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            LREGKNREI++V E     V+RLIR++YGPFQLG L  G+  E+  KI+REQLG     
Sbjct: 184 SLREGKNREIRRVMEHLGLPVSRLIRVAYGPFQLGQLEEGTVDEIPGKIMREQLGKDAPP 243

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
             +        +       +  +      +  R+ + +       K +  
Sbjct: 244 PPRRAEAKAKGNKGAAPPPKGTLSLPESSNTGRVARIARATRRAHKPEPS 293


>gi|310658498|ref|YP_003936219.1| ribosomal small subunit pseudouridine synthase a [Clostridium
           sticklandii DSM 519]
 gi|308825276|emb|CBH21314.1| Ribosomal small subunit pseudouridine synthase A [Clostridium
           sticklandii]
          Length = 243

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 58/238 (24%), Positives = 105/238 (44%), Gaps = 3/238 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           ++      R+ K +A  G+ SR E++R I  +RV VNG+ +    + +   D I  D   
Sbjct: 1   MKAQVEKMRIDKYLANMGVGSRSEIKRYIKNKRVMVNGVYITDNGLIINLDDDIIFDEEK 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +   +   + +      +  T            +   +   +   GRLD +TEG LLLTN
Sbjct: 61  ISYRKFVYIMMNKPQGVISATEDKYQNTVLDLLDPSYLHFDLFPAGRLDKDTEGFLLLTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGS 185
           DG LA  +  P     + Y V   G +  + ++     I+I         ++ +      
Sbjct: 121 DGKLAHNMLSPKKHVEKKYYVEVIGHLVNEDIDAFSGNIIIDDGYECMPAKLEILDSN-D 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            +   V ++EGK  +IK++FE    +V  L R++ GP +L   L  G  RE++++ ++
Sbjct: 180 ISKAYVTIKEGKFHQIKRMFEAIGKEVTYLKRLTMGPLKLDENLELGEYRELTEQEMQ 237


>gi|255656021|ref|ZP_05401430.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile QCD-23m63]
 gi|296450550|ref|ZP_06892304.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           difficile NAP08]
 gi|296879328|ref|ZP_06903323.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           difficile NAP07]
 gi|296260625|gb|EFH07466.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           difficile NAP08]
 gi|296429871|gb|EFH15723.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           difficile NAP07]
          Length = 238

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 71/232 (30%), Positives = 120/232 (51%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R++K IA  GIASRR+ E +I + R+KVNG +++    NV    D +E D   ++ +E 
Sbjct: 1   MRINKYIASCGIASRRKAEEIILEGRIKVNGSIVKELFFNVDEEKDIVEFDNKKVKPSEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G +TT  D   R +V D L  +  RV  +GRLD  T GLL+LTNDG L  
Sbjct: 61  YIYIVLNKPEGYITTVKDQFNRPSVIDILKDVKERVYPIGRLDYETSGLLILTNDGDLTY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVT 190
            L  P  +  + Y     G +  D++   + G+ I+       ++ +  + ++ + +   
Sbjct: 121 KLTHPKHEIDKTYVASVKGIISGDEIRKFETGLKIEDYTTAPAKIKVTKENKEKNYSVCE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + + EG+NR+++K+ +  N  V  L RIS G   L     G  R +++  ++
Sbjct: 181 ITIHEGRNRQVRKMCKAINHPVLNLRRISVGKIVLKDTKVGEYRYLTEDEIK 232


>gi|319651915|ref|ZP_08006038.1| pseudouridine synthase [Bacillus sp. 2_A_57_CT2]
 gi|317396407|gb|EFV77122.1| pseudouridine synthase [Bacillus sp. 2_A_57_CT2]
          Length = 239

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 63/236 (26%), Positives = 108/236 (45%), Gaps = 4/236 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A  G  SR++V++++    V VN   ++     V    D + ++G  +   E 
Sbjct: 1   MRIDKMLANLGYGSRKDVKKLLKDGAVTVNDEKVKDPKHQVDPEQDAVIINGEKVEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +   P  +  T             +  +      VGRLD +TEGLLLLTNDG LA 
Sbjct: 61  IYLMMNKPPGVISATEDSQFETVVDLLEMRDLVFSPFPVGRLDKDTEGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y      +V  D +   KKG+++         ++ +  + G  + + +
Sbjct: 121 RLLSPKKHVPKTYFAVIDREVTADDVAAFKKGVILDDGYETKPGELEIL-KSGITSDIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
            + EGK  ++K++FE    +V  L RIS GP +L   L  G  RE++ + L + + 
Sbjct: 180 TITEGKFHQVKRMFEAVGKRVIYLKRISMGPLELDKTLELGEYRELTDEELDKLMN 235


>gi|84686243|ref|ZP_01014138.1| RNA pseudouridylate synthase family protein [Maritimibacter
           alkaliphilus HTCC2654]
 gi|84665770|gb|EAQ12245.1| RNA pseudouridylate synthase family protein [Rhodobacterales
           bacterium HTCC2654]
          Length = 293

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 140/266 (52%), Positives = 177/266 (66%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +  +     R++KV++RAG+ASRRE ERMI   RV VNG +++  A+NV   D I VDG 
Sbjct: 28  MTDKTPPGDRIAKVLSRAGVASRREAERMIEAGRVSVNGKVIDSPALNVTPRDKITVDGT 87

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            + K E  RLWLYHKP GLVTT  D  GR TVFD LP    RV+SVGRLD+N+EGLLLLT
Sbjct: 88  LVEKPEAPRLWLYHKPTGLVTTERDEKGRETVFDKLPEDMPRVMSVGRLDLNSEGLLLLT 147

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDGG+ R LELPST W+R YRVR +G+ ++  L  L+KGI + G  +  M VTLD Q+G+
Sbjct: 148 NDGGIKRKLELPSTGWVRKYRVRVNGKPEEAVLEKLRKGITVDGEAFQGMSVTLDRQQGA 207

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           NAW+T+GLREGKNREI++  E     VNRLIRISYGPF+LG L AG+  EV  ++LR+QL
Sbjct: 208 NAWLTIGLREGKNREIRRAMEAVGLTVNRLIRISYGPFRLGELKAGAVEEVKGRVLRDQL 267

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDR 271
           G    ++                R R
Sbjct: 268 GLEAPKDPTGTAKKTPVRRRKPTRKR 293


>gi|221319479|ref|ZP_03600773.1| RluB [Bacillus subtilis subsp. subtilis str. JH642]
 gi|221323755|ref|ZP_03605049.1| RluB [Bacillus subtilis subsp. subtilis str. SMY]
 gi|255767501|ref|NP_390197.2| pseudouridine synthase [Bacillus subtilis subsp. subtilis str. 168]
 gi|321311788|ref|YP_004204075.1| pseudouridine synthase [Bacillus subtilis BSn5]
 gi|251757325|sp|P35159|RLUB_BACSU RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|225185129|emb|CAB14248.2| pseudouridine synthase [Bacillus subtilis subsp. subtilis str. 168]
 gi|291484745|dbj|BAI85820.1| pseudouridine synthase [Bacillus subtilis subsp. natto BEST195]
 gi|320018062|gb|ADV93048.1| pseudouridine synthase [Bacillus subtilis BSn5]
          Length = 244

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 75/243 (30%), Positives = 124/243 (51%), Gaps = 3/243 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E +I + +VKVNG ++    V V  +D IEV+G+ + + E  
Sbjct: 2   ERLQKVIAHAGVASRRKAEELIKEGKVKVNGKVVTELGVKVTGSDQIEVNGLKVEREEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     +++   D  GR  V D   +I  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 62  YFLLYKPRG-VISAAQDDKGRKVVTDFFKNIPQRIYPIGRLDYDTSGLLLLTNDGEFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVTV 191
           L  P  +  + Y  +  G   ++ L  L++GI ++       +  L    +K   + + +
Sbjct: 121 LMHPKYEIDKTYVAKVKGIPPKELLRKLERGIRLEEGKTAPAKAKLLSLDKKKQTSIIQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE    +V +L R  Y    L  L  G  RE++   ++         
Sbjct: 181 TIHEGRNRQVRRMFEAIGHEVIKLKREEYAFLNLRGLHTGDARELTPHEVKRLRALADHG 240

Query: 252 EAQ 254
           +  
Sbjct: 241 KNA 243


>gi|19745526|ref|NP_606662.1| hypothetical protein spyM18_0418 [Streptococcus pyogenes MGAS8232]
 gi|71902965|ref|YP_279768.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS6180]
 gi|94987940|ref|YP_596041.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS9429]
 gi|94989814|ref|YP_597914.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS10270]
 gi|94993700|ref|YP_601798.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS10750]
 gi|19747645|gb|AAL97161.1| putative hypothetical protein [Streptococcus pyogenes MGAS8232]
 gi|71802060|gb|AAX71413.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS6180]
 gi|94541448|gb|ABF31497.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS9429]
 gi|94543322|gb|ABF33370.1| Ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS10270]
 gi|94547208|gb|ABF37254.1| Ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS10750]
          Length = 248

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 78/249 (31%), Positives = 125/249 (50%), Gaps = 3/249 (1%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +++      R++K IA AGIASRR+ E +I Q  V +NG ++   A  V S D +E++G 
Sbjct: 1   MLKRKKNIMRINKYIAHAGIASRRKAEELIKQGLVTLNGQVITDLATTVKSGDVVEIEGS 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P+   E+    L      + +   D  GR TV D LP +  R+  VGRLD +T G+L+LT
Sbjct: 61  PIYNEEKVYYLLNKPRGAISSVS-DDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--K 183
           NDG     +  P  +  +VY  R  G   ++ L  L +GIVI G      +  +      
Sbjct: 120 NDGDFTDTMIHPRNEIDKVYLARVKGIATKENLRPLTRGIVIDGKKTKPARYNIVRVEAD 179

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + + V + + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK + +
Sbjct: 180 KNRSIVELTIHEGRNHQVKKMFESVGLLVDKLSRTRFGTVDLKGLRPGEARRLNKKEISQ 239

Query: 244 QLGPHLLEE 252
                  ++
Sbjct: 240 LHNLANTKK 248


>gi|163797848|ref|ZP_02191793.1| Pseudouridine synthase, Rsu [alpha proteobacterium BAL199]
 gi|159176892|gb|EDP61459.1| Pseudouridine synthase, Rsu [alpha proteobacterium BAL199]
          Length = 387

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 147/348 (42%), Positives = 204/348 (58%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + +E+   +R+SK +ARAG+ SRR+ ER IA+ RVKV+G++L   AVNV     I VD  
Sbjct: 1   MFEESRGSERISKRLARAGLCSRRDAERWIAEGRVKVDGVMLTSPAVNVDDDSVILVDEK 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL + E  RLW YHKP GLVT++ DP+GRSTVFD LP    RV++VGRLDI++EGLLLLT
Sbjct: 61  PLPEIEPPRLWRYHKPDGLVTSNRDPEGRSTVFDRLPKDLPRVVTVGRLDIDSEGLLLLT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDGGLAR LELPST W+R YRVR  G +D+ KL+ LKKG+ I+G+ YG ++VT+D    +
Sbjct: 121 NDGGLARYLELPSTGWVRRYRVRVFGPLDEAKLDNLKKGVRIEGVEYGPIEVTIDKATRT 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           N+W+TV LREGKNREI++V E     V+RLIR +YGPFQLG +  G   E+ +++L++QL
Sbjct: 181 NSWLTVALREGKNREIRRVMEHVGLTVSRLIRTTYGPFQLGEVPPGGVEEIKRRVLKDQL 240

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G    +++      P  +       RP  +           ++    +G   Q+  A  V
Sbjct: 241 GLAKGDDSGHAKAKPERTGTQPPGRRPGTLRLRSKPTDIEVESDRPSSGGRVQRTRADMV 300

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                +  V        S  S   +   +          +S      K
Sbjct: 301 KSAPRSGTVEKVSLKSGSSKSAGSRSATSKPVVSKTGWAKSSAAKPGK 348


>gi|322373877|ref|ZP_08048412.1| ribosomal large subunit pseudouridine synthase B [Streptococcus sp.
           C150]
 gi|321277249|gb|EFX54319.1| ribosomal large subunit pseudouridine synthase B [Streptococcus sp.
           C150]
          Length = 241

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 79/240 (32%), Positives = 129/240 (53%), Gaps = 3/240 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I + RV +NG  +   A  V + D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKEGRVTLNGKTVTELATIVKNGDTVEVNGSPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD   R TV D +P +  R+  VGRLD +T GLL+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDEKDRKTVIDLMPHVKERIYPVGRLDWDTTGLLILTNDGDFTDK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIVKVDHEKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE     V++L R  +G   L  L  G +R ++KK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTRFGTLDLTGLRPGESRRLNKKEISQLHNAAVNK 239


>gi|251779623|ref|ZP_04822543.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum E1 str. 'BoNT E Beluga']
 gi|243083938|gb|EES49828.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum E1 str. 'BoNT E Beluga']
          Length = 236

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 75/229 (32%), Positives = 120/229 (52%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K +A  G+ASRR+ E +I    VKVNG+++      V    D +E  G  ++K E 
Sbjct: 3   ERLQKYMASCGLASRRKCEEIILSGEVKVNGVVVTELGTRVNPVEDKVEYKGCLIKKEEN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G +T+  D  GR TV  +L  +  R+  +GRLD ++ GL+LLTNDG +  
Sbjct: 63  KVYIILNKPEGYITSAKDEKGRKTV-LDLVKVNERIYPIGRLDYDSSGLILLTNDGDIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + Y     G+V +  ++   KGI I G       + + + +   + V V 
Sbjct: 122 KIIHPREELNKKYIAVVKGEVSKKDIDAFNKGIDIGGYVTAPASLEVLSYENGKSTVEVC 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGKNR+I+K+    N +V  L R+S G  QL  L  G  RE++ + L
Sbjct: 182 IHEGKNRQIRKMCTAINHEVLSLNRVSIGEIQLKYLKKGEWRELTAEEL 230


>gi|310828101|ref|YP_003960458.1| pseudouridine synthase [Eubacterium limosum KIST612]
 gi|308739835|gb|ADO37495.1| pseudouridine synthase [Eubacterium limosum KIST612]
          Length = 241

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 70/243 (28%), Positives = 114/243 (46%), Gaps = 8/243 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A+ G+ASRR+ E MIA  RV VNG  +    + V    D + VDG  + + ++
Sbjct: 1   MRLQKYMAQCGVASRRKSEEMIAAGRVCVNGEAVLTPGLQVDPEADTVTVDGKTIAEDKK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + T+      ++ +      I  R+ +VGRLD +TEGLL+LTNDG L  
Sbjct: 61  IYVLLNKPKGVVSTSADRHADQTVMDRL--PIKERLFTVGRLDKDTEGLLILTNDGDLTF 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNA 187
            L  PS ++ ++Y     G     +L L  +G+ I+             V +     S A
Sbjct: 119 RLTHPSHEFNKIYEGLVKGIPSAGELRLFAEGVQIEDDDHTLHTTAPASVQVLKTYRSTA 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + + + EG+ R+I+K+       V  L R + G   L  L AG  R ++++ +R   G 
Sbjct: 179 LLEMTIHEGRKRQIRKMCAAIGHPVIHLKRTAIGSITLKGLKAGEWRYLTEEEIRYLRGE 238

Query: 248 HLL 250
              
Sbjct: 239 KDD 241


>gi|253680889|ref|ZP_04861692.1| RNA pseudouridine synthase family protein [Clostridium botulinum D
           str. 1873]
 gi|253562738|gb|EES92184.1| RNA pseudouridine synthase family protein [Clostridium botulinum D
           str. 1873]
          Length = 238

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 55/232 (23%), Positives = 108/232 (46%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K+++  G  SR+E++ ++ +  ++++G +++   + V      I+V G  +   + 
Sbjct: 2   ERLDKILSNLGYGSRKEIKALVKKGEIEIDGKIIKDNGIKVDPNKSTIKVSGEEINYRKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  T  + D       +          VGRLD +TEG LL+TNDG L  
Sbjct: 62  IYLMMNKPAGVVSATFDNYDETVIDLLDYEYTVFDPFPVGRLDKDTEGFLLITNDGDLNH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     ++Y       VD+  +   +KGIV+         ++ + +   + + V +
Sbjct: 122 RLTSPKWHVDKIYYAEIDKIVDEKDIRAFEKGIVLDDGYKCLPAKLEILSADENGSEVNI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            ++EGK  ++K++FE    KV  L R+  G   L   L  G  RE+++  ++
Sbjct: 182 TIQEGKFHQVKRMFEAREKKVIYLKRLQMGNLVLDESLNEGEYRELTEDEIK 233


>gi|217966542|ref|YP_002352048.1| RNA-binding S4 domain protein [Dictyoglomus turgidum DSM 6724]
 gi|217335641|gb|ACK41434.1| RNA-binding S4 domain protein [Dictyoglomus turgidum DSM 6724]
          Length = 243

 Score =  187 bits (474), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 58/233 (24%), Positives = 100/233 (42%), Gaps = 5/233 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G  SR+EV+++I    V VN   +E  + ++    D +E++G  +   E 
Sbjct: 1   MRLDKFLVNQGFGSRKEVQKLIKAGIVYVNNFPVEDPSFHINPEKDVVEIEGQEIEYKEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T+ +             I S++  VGRLD++TEGLL++T+DG LA 
Sbjct: 61  YYFMLNKPKGYITATYDENYPTVMDLFASEPIVSKLFPVGRLDVDTEGLLIITSDGVLAH 120

Query: 133 VLELPSTQWLRVYRVRFH---GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            L  P     + Y V        +D  K       +  +       +V +       + +
Sbjct: 121 RLSHPKWNVEKEYFVIVEGDISDIDFSKYEKEGMYLKKEKYKTKPFKVKVLKTSFEESEL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + + EGK   +KK+      +V  L R+  GP  L   L  G  RE++K+ +
Sbjct: 181 LITITEGKYHIVKKIMYAVGHEVKYLKRVRIGPLILDEDLEVGEYRELTKEEI 233


>gi|317051704|ref|YP_004112820.1| pseudouridine synthase [Desulfurispirillum indicum S5]
 gi|316946788|gb|ADU66264.1| pseudouridine synthase [Desulfurispirillum indicum S5]
          Length = 251

 Score =  187 bits (474), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 82/243 (33%), Positives = 121/243 (49%), Gaps = 5/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A+AG+ASRR+ E  I Q RV VNG ++           D + VDG  ++    
Sbjct: 3   MRLQKILAQAGVASRRKAEEYIRQGRVMVNGKVVTELGTQADPDEDFVAVDGKRIQIFHN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + HKP G +T+ SD   R  V D LP+I   +I VGRLD +T GLLLLTNDG LA 
Sbjct: 63  HAYIILHKPTGYITSRSDDKERPVVMDLLPNIREPLIPVGRLDWDTSGLLLLTNDGDLAY 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG----SNAW 188
           VL  P+    + Y VR    +  + + + +KGI+++       +V            N W
Sbjct: 123 VLTHPAFHVAKTYLVRLDKPMTAEHMQVFEKGILLEDGKTKPARVRRVNTGKQTATPNLW 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             V + EG+NR+I+K+FE   + V +L R+S G   LG +  G  R      +       
Sbjct: 183 YEVTITEGRNRQIRKMFEALKYDVRKLKRVSLGEILLGGVGVGKYRRAEAWEIEYFEKLK 242

Query: 249 LLE 251
             +
Sbjct: 243 REK 245


>gi|315038194|ref|YP_004031762.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           amylovorus GRL 1112]
 gi|325956646|ref|YP_004292058.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           acidophilus 30SC]
 gi|312276327|gb|ADQ58967.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           amylovorus GRL 1112]
 gi|325333211|gb|ADZ07119.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           acidophilus 30SC]
 gi|327183471|gb|AEA31918.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           amylovorus GRL 1118]
          Length = 238

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 70/236 (29%), Positives = 118/236 (50%), Gaps = 3/236 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+IA AGIASRR+ E+MI   RVKV+G ++ +    V +  +I VD  P+ +    
Sbjct: 3   ERLQKIIAEAGIASRRKAEKMITAGRVKVDGKVITKLGTKVDTFSNITVDDEPIERESLH 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     + T   D D ++ V      +  R+  VGRLD +T GLLL+TNDG LA +
Sbjct: 63  TYLFYKPRGVVSTASDDKDRKTVVDYF-EDVPYRLYPVGRLDYDTSGLLLMTNDGKLANL 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           L  P  +  +VY  +  G +  +++  L  G+ +        +V +    ++     V +
Sbjct: 122 LMHPRNEVSKVYVAKIKGILTPEEIKTLTHGVKLDDFKAAPAKVKVLKTDKRKDTQIVQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + EG   ++K++F+     V +L R  Y    L +L +G  RE+SK  + + +  
Sbjct: 182 TIHEGHYHQVKRMFKAVGHLVEKLSREKYAFLTLDSLTSGQYRELSKNEVDKLMRL 237


>gi|150016762|ref|YP_001309016.1| pseudouridine synthase [Clostridium beijerinckii NCIMB 8052]
 gi|149903227|gb|ABR34060.1| pseudouridine synthase [Clostridium beijerinckii NCIMB 8052]
          Length = 236

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 73/230 (31%), Positives = 122/230 (53%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K +A  G+ASRR+ E +I   +VKVNG+++    + V    D IE DG  ++K E 
Sbjct: 3   ERLQKYLANCGVASRRKCEELIISGKVKVNGVIVNEVGIKVDPLKDMIEYDGKEIKKKED 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G +++  D  GR T+ D +     R+  +GRLD ++ GLLLLTNDG +  
Sbjct: 63  KVYIMLNKPEGYISSVKDEKGRDTILDIVKVN-ERIYPIGRLDYDSSGLLLLTNDGEIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  + ++ Y     G++        + GI I G      ++ + +     + + +G
Sbjct: 122 KIIHPRVEIIKRYVAVVKGEITDKDKMKFEIGIDIGGYITAPAELKVISYDKGVSTIEIG 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGKNR+I+K+    +  V  L RIS G  +LG L  G  R+++K+ L 
Sbjct: 182 IHEGKNRQIRKMCAAIHHDVLSLKRISIGEIKLGYLKRGEYRKLNKEELD 231


>gi|332359120|gb|EGJ36941.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK49]
          Length = 242

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 81/240 (33%), Positives = 132/240 (55%), Gaps = 3/240 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q +V +NG ++   A NV S D +EV+  P+   E  
Sbjct: 1   MRINKYIAHAGIASRRKAEELIRQGKVSINGQVVRELATNVKSGDRVEVEDQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDEKGRKTVVDLLPQVKERIYPVGRLDWDTSGILILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +GI I+G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTKPAVYEIIKVDPAKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+F+    +V++L R  +G   L  +  G  R++SKK + +     + +
Sbjct: 180 TIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTDIKPGEYRKLSKKEVSQLHTLAVTK 239


>gi|126727512|ref|ZP_01743346.1| RNA pseudouridylate synthase family protein [Rhodobacterales
           bacterium HTCC2150]
 gi|126703292|gb|EBA02391.1| RNA pseudouridylate synthase family protein [Rhodobacterales
           bacterium HTCC2150]
          Length = 259

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 142/259 (54%), Positives = 175/259 (67%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +        R++KV++RAGIASRRE ERMI   RV VNG ++   A+NV   D I+VDG 
Sbjct: 1   MTDTPEKGDRIAKVLSRAGIASRREAERMIEAGRVSVNGKVIPSPALNVTPKDKIKVDGK 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +  AE  RLWLYHKP+GLVTT  D  GR TVFDNLP    RV+SVGRLDIN+EGLLLLT
Sbjct: 61  EVGDAEPARLWLYHKPVGLVTTERDEKGRDTVFDNLPDGLPRVMSVGRLDINSEGLLLLT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDGGL R LELPST WLR YRVR +G V +D L  L+KG+VI G  +  M +++D Q+GS
Sbjct: 121 NDGGLKRKLELPSTGWLRKYRVRVNGIVIEDHLTPLRKGLVIDGEKFQPMNISVDRQQGS 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           NAW+TVG+REGKNREI++ FE     VNRLIR+SYGPFQL  L A    E+  ++LR+QL
Sbjct: 181 NAWLTVGIREGKNREIRRAFETIFLPVNRLIRVSYGPFQLNDLRADEVEEIKGRVLRDQL 240

Query: 246 GPHLLEEAQVNLDAPIYSS 264
           G       + +        
Sbjct: 241 GLTPETATKKSKKIVKRRR 259


>gi|332185277|ref|ZP_08387026.1| hypothetical protein SUS17_350 [Sphingomonas sp. S17]
 gi|332015001|gb|EGI57057.1| hypothetical protein SUS17_350 [Sphingomonas sp. S17]
          Length = 420

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 124/343 (36%), Positives = 179/343 (52%), Gaps = 3/343 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K++ARAG+ASRREVERMIA+ R+ +NG  ++  A  + S D + VDG P+   E TR
Sbjct: 6   RIAKLLARAGVASRREVERMIAEGRIALNGTTIDTPATLLSSLDGVTVDGNPVDAPEPTR 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L+LY+KP GL+ T  DP GR T++D LP    R++ VGRLD+NTEGLLLLT DGG  R L
Sbjct: 66  LFLYNKPNGLLVTERDPKGRPTIYDRLPEGLPRLMPVGRLDLNTEGLLLLTTDGGFKRQL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELP+T   R YR R +G + Q +L  L  GI I GI YG +   L+ + G+N W+ + LR
Sbjct: 126 ELPATGVERTYRARAYGDITQAQLEELIHGIEIDGIRYGQIDANLERRTGANVWIELTLR 185

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK---ILREQLGPHLLE 251
           EGKNRE+++V E+   +V+RLIR+ YGPF LG L  G   EV        R+ L   +  
Sbjct: 186 EGKNREVRRVLEYLGLQVSRLIRLRYGPFVLGDLPVGEIGEVKGAAIVEFRKTLLGGIPA 245

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           +A        + +                D          ++   ++        +R  A
Sbjct: 246 DAVRPSPRAGFRTPPTRAKTDRPDRPAAQDRRPSDGRDRPQSDAKRRAAGPGGDRQRPAA 305

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                +        +D+  R     RS     +       +++
Sbjct: 306 PRTARSTDRGERPSADAQFRPSGGERSRPTGKRAPRSGDRSER 348


>gi|218281417|ref|ZP_03487881.1| hypothetical protein EUBIFOR_00446 [Eubacterium biforme DSM 3989]
 gi|218217429|gb|EEC90967.1| hypothetical protein EUBIFOR_00446 [Eubacterium biforme DSM 3989]
          Length = 227

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 108/233 (46%), Gaps = 6/233 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++  G  +R +V+++I    V +N   +++A  NV   D + VD  P+   E  
Sbjct: 1   MRLDKYLSHMGFGTRNDVKKLIKNGWVTINDETIKKADYNVKEDDKVFVDDEPVSYVEFE 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      +  T        TV + + S    +  VGRLD++TEGLLL++NDG L   
Sbjct: 61  YYILNKPQGYVSATE--DMLYPTVMELIQSQRHDLYPVGRLDVDTEGLLLISNDGKLTHE 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V F G + ++ ++   + +  +       ++ +     +     + +
Sbjct: 119 VLSPKKHVDKKYYVEFDGTLPENAVDFFNQPMEFEEFTSAPSKLEILDTNKA----YLTI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            EGK  ++K++FE  N  V  L RI +GP +L  L  G  R ++++ L    G
Sbjct: 175 HEGKFHQVKRMFEKANCTVTYLQRIEFGPLKLNDLPLGEFRALTQEELDALKG 227


>gi|296332250|ref|ZP_06874712.1| pseudouridine synthase [Bacillus subtilis subsp. spizizenii ATCC
           6633]
 gi|305674952|ref|YP_003866624.1| pseudouridine synthase [Bacillus subtilis subsp. spizizenii str.
           W23]
 gi|296150564|gb|EFG91451.1| pseudouridine synthase [Bacillus subtilis subsp. spizizenii ATCC
           6633]
 gi|305413196|gb|ADM38315.1| pseudouridine synthase [Bacillus subtilis subsp. spizizenii str.
           W23]
          Length = 244

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 74/243 (30%), Positives = 123/243 (50%), Gaps = 3/243 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E +I + +VKVNG ++    V V  +D IEV+G+ + + E  
Sbjct: 2   ERLQKVIAHAGVASRRKAEELIKEGKVKVNGKVVTELGVKVTGSDQIEVNGLKVEREEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     +++   D  GR  V D    +  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 62  YFLLYKPRG-VISAAQDDKGRKVVTDFFKEVPQRIYPIGRLDYDTSGLLLLTNDGEFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVTV 191
           L  P  +  + Y  +  G   ++ L  L++GI ++       +  L    +K   + + +
Sbjct: 121 LMHPKYEIDKTYVAKVKGIPPKELLRKLERGIRLEEGKTAPAKAKLLSLDKKKQTSIIQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE    +V +L R  Y    L  L  G  RE++   ++         
Sbjct: 181 TIHEGRNRQVRRMFEAIGHEVIKLKREEYAFLNLRGLHTGDARELTPHEVKRLRALADHG 240

Query: 252 EAQ 254
           +  
Sbjct: 241 KNA 243


>gi|88857390|ref|ZP_01132033.1| putative ribosomal RNA pseudouridine synthase [Pseudoalteromonas
           tunicata D2]
 gi|88820587|gb|EAR30399.1| putative ribosomal RNA pseudouridine synthase [Pseudoalteromonas
           tunicata D2]
          Length = 285

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 68/278 (24%), Positives = 120/278 (43%), Gaps = 11/278 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K I+  G  SRRE ++ IA  RV +NG + E     V  +D +E+DG PL+  
Sbjct: 2   SESTRLNKYISDTGFCSRREADKYIADGRVTLNGKIPEV-GTKVTDSDVVEIDGKPLKAK 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            +     Y+KP+G+  T       + +     +   R+  +GRLD  +EGL+ LTN+G +
Sbjct: 61  PKAVFIAYNKPVGVTCTTELNIRSNIISAI--NHPERIFPIGRLDRPSEGLIFLTNEGDI 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +    +  +  G+ I G      +VT    + S+    
Sbjct: 119 VNKILRAGNNHEKEYLVTVDKAISPQFIKKMGAGVPILGTVTKQCKVT----QVSSHGFN 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL----REQLG 246
           + L +G NR+I+++ EF  ++V  L R+      L  L +G  R ++ K +    R   G
Sbjct: 175 IVLTQGLNRQIRRMCEFLGYEVVTLKRVRIMNIDLTGLRSGQWRNLTDKEMAIINRSIEG 234

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
               EE  V+ +      + + +        +     R
Sbjct: 235 SGKTEELSVDPNKNKNFKKPVKKQFDEPEQTMKTQAVR 272


>gi|28211988|ref|NP_782932.1| putative ribosomal small subunit pseudouridine synthase A
           [Clostridium tetani E88]
 gi|28204431|gb|AAO36869.1| putative ribosomal small subunit pseudouridine synthase A
           [Clostridium tetani E88]
          Length = 238

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 65/236 (27%), Positives = 112/236 (47%), Gaps = 3/236 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++A  G  SR+EV+++I    V+VNG  ++  ++N+    D I V    +   + 
Sbjct: 2   ERIDKILANMGYGSRKEVKKLIKNNLVEVNGEKVKDPSINIDPEKDKILVGDKVVNYRKF 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      +  T  + D                  VGRLD +T GLLL+TNDG L  
Sbjct: 62  IYIMMNKPEGVVSATFDNYDETVIDLLEEEYQVFNPFPVGRLDKDTVGLLLITNDGELNH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P  +  +VY    + +V++  +   + GIVI  G      ++ +     + A V V
Sbjct: 122 KLISPKWKVDKVYYAEINKEVNEKDIEAFQNGIVISDGYKCMPGKLEIIKSDENGAEVYV 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
            ++EGK  ++K++FE  + KV  L R+ +G   L   L  G  RE++++ L   L 
Sbjct: 182 TIQEGKFHQVKRMFEALDKKVVYLKRVKFGNINLDETLEEGEYRELTEEELENILE 237


>gi|191638365|ref|YP_001987531.1| Pseudouridine synthase [Lactobacillus casei BL23]
 gi|190712667|emb|CAQ66673.1| Pseudouridine synthase [Lactobacillus casei BL23]
 gi|327382393|gb|AEA53869.1| Ribosomal large subunit pseudouridine synthase B [Lactobacillus
           casei LC2W]
 gi|327385594|gb|AEA57068.1| Ribosomal large subunit pseudouridine synthase B [Lactobacillus
           casei BD-II]
          Length = 247

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 81/247 (32%), Positives = 126/247 (51%), Gaps = 3/247 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R+ K+IA AGIASRR  E +IA   VKVNG +     + +   D +EVDGVP+  
Sbjct: 2   TTKTERLQKIIANAGIASRRHAETLIATGHVKVNGQIETEMGIKIGPHDEVEVDGVPI-G 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E  R +L++KP G+++   D  GR  V D    I  R+  VGRLD +T GLL++TNDG 
Sbjct: 61  KEAKRYFLFYKPRGVISAVQDNKGRDVVTDYFKDITERLYPVGRLDYDTSGLLVMTNDGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW- 188
           LA  L  P     + Y  +  G  ++  L  LK G+ + G      +V + +   +    
Sbjct: 121 LANHLMHPRYALEKKYVAKVQGVPNRPALAPLKTGVEVDGKMTAPAKVDIISTDKAKKTA 180

Query: 189 -VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V++ + +G N ++KK+F+   + V +L R +YG   L  L  G  R +  + L+     
Sbjct: 181 IVSLTIHQGMNHQVKKMFKAVGFPVLKLSREAYGNLTLVGLQPGEHRPIKPQELQALRKL 240

Query: 248 HLLEEAQ 254
               E++
Sbjct: 241 AGESESK 247


>gi|116494858|ref|YP_806592.1| 16S rRNA uridine-516 pseudouridylate synthase related enzyme
           [Lactobacillus casei ATCC 334]
 gi|227535145|ref|ZP_03965194.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           ATCC 25302]
 gi|116105008|gb|ABJ70150.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           casei ATCC 334]
 gi|227187190|gb|EEI67257.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           ATCC 25302]
          Length = 247

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 81/247 (32%), Positives = 125/247 (50%), Gaps = 3/247 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R+ K+IA AGIASRR  E +IA   VKVNG +     + +   D +EVDGVP+  
Sbjct: 2   TTKTERLQKIIANAGIASRRHAETLIATGHVKVNGQIETEMGIKIGPHDEVEVDGVPI-G 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E  R +L++KP G+++   D  GR  V D    I  R+  VGRLD +T GLL++TNDG 
Sbjct: 61  KEAKRYFLFYKPRGVISAVQDNKGRDVVTDYFKDITERLYPVGRLDYDTSGLLVMTNDGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW- 188
           LA  L  P     + Y  +  G  ++  L  LK G+ + G      +V + +   +    
Sbjct: 121 LANHLMHPRYALEKKYVAKVQGVPNRPALAPLKTGVEVDGKMTAPAKVDIISTDKAKKTA 180

Query: 189 -VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V++ + +G N ++KK+F+   + V +L R +YG   L  L  G  R +  + L+     
Sbjct: 181 IVSLTIHQGMNHQVKKMFKAVGFPVLKLSREAYGNLTLVGLQPGEHRPIKPQELQALRKL 240

Query: 248 HLLEEAQ 254
               E +
Sbjct: 241 AGESENK 247


>gi|327403362|ref|YP_004344200.1| ribosomal large subunit pseudouridine synthase B [Fluviicola
           taffensis DSM 16823]
 gi|327318870|gb|AEA43362.1| ribosomal large subunit pseudouridine synthase B [Fluviicola
           taffensis DSM 16823]
          Length = 339

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 107/232 (46%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N    R++K ++ AG+ SRRE + +I    V VNG ++      +   D I+ DG  +  
Sbjct: 101 NEDAVRLNKYLSNAGVCSRREADVLIQTGVVSVNGEVITEMGYKIKPGDKIQYDGETINA 160

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             +  + L      + T       ++ +   + +   R+  VGRLD +T GLLL TNDG 
Sbjct: 161 ETKRYVLLNKPKGFITTMDDPLGRKTVMGLVIKACKERIYPVGRLDRDTTGLLLFTNDGD 220

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +A+ L  P  +  ++Y V     V  + L  L  GI ++       +        S+  V
Sbjct: 221 MAKKLTHPRYEATKIYHVEVDKPVQSEHLEQLMSGIELEDGTIKADKAEYVKDGKSSREV 280

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V +  GKNR ++++FE   ++V +L R+ +       L  G  R +++K +
Sbjct: 281 GVEIHSGKNRIVRRMFEKLGYEVVKLDRVQFASLTKKDLPRGYYRHLTEKEV 332


>gi|257413346|ref|ZP_04742734.2| ribosomal small subunit pseudouridine synthase A [Roseburia
           intestinalis L1-82]
 gi|257203834|gb|EEV02119.1| ribosomal small subunit pseudouridine synthase A [Roseburia
           intestinalis L1-82]
          Length = 239

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 67/237 (28%), Positives = 112/237 (47%), Gaps = 5/237 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K++   G  SR EV++ I    V VNG ++++    V    D +   G PL   E 
Sbjct: 5   MRLDKLLTELGTGSRSEVKKYIRSGLVTVNGEVVKKPEQRVDEKNDTVCFRGNPLTYTEY 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +     + T   D   R+ +     +    +  VGRLDI+TEGLLL+TNDG LA 
Sbjct: 65  EYYLFHKPAGCV-TATEDNLHRTVMDYLTDTARHDLFPVGRLDIDTEGLLLITNDGALAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P+    +VY  +  G+V ++ +NL + G+ I +        + +    G N+ + +
Sbjct: 124 DLLSPAKHVSKVYYAKIDGRVTEEDVNLFENGVDIGEEKPAKPALLEVLH-SGDNSEIRL 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
            + EG+  ++K++FE    KV  L R+  G   L   L  G  R ++++ L+E    
Sbjct: 183 TITEGRFHQVKRMFEAVGKKVTYLKRVEMGSLVLPDELAPGEYRPLTEEELQELRRH 239


>gi|239631549|ref|ZP_04674580.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           paracasei subsp. paracasei 8700:2]
 gi|301066420|ref|YP_003788443.1| 16S rRNA uridine-516 pseudouridylate synthase-like protein
           [Lactobacillus casei str. Zhang]
 gi|239526014|gb|EEQ65015.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           paracasei subsp. paracasei 8700:2]
 gi|300438827|gb|ADK18593.1| 16S rRNA uridine-516 pseudouridylate synthase related enzyme
           [Lactobacillus casei str. Zhang]
          Length = 247

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 81/247 (32%), Positives = 126/247 (51%), Gaps = 3/247 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R+ K+IA AGIASRR  E +IA   VKVNG +     + +   D +EVDGVP+  
Sbjct: 2   TTKTERLQKIIANAGIASRRHAETLIATGHVKVNGQIETEMGIKIGPHDEVEVDGVPI-G 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E  R +L++KP G+++   D  GR  V D    I  R+  VGRLD +T GLL++TNDG 
Sbjct: 61  KEAKRYFLFYKPRGVISAVQDNKGRDVVTDYFKDIAERLYPVGRLDYDTSGLLVMTNDGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW- 188
           LA  L  P     + Y  +  G  ++  L  LK G+ + G      +V + +   +    
Sbjct: 121 LANHLMHPRYALEKKYVAKVQGVPNRPALAPLKTGVEVDGKMTAPAKVDIISTDKAKKTA 180

Query: 189 -VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V++ + +G N ++KK+F+   + V +L R +YG   L  L  G  R +  + L+     
Sbjct: 181 IVSLTIHQGMNHQVKKMFKAVGFPVLKLSREAYGNLTLVGLQPGEHRPIKPQELQALRKL 240

Query: 248 HLLEEAQ 254
               E++
Sbjct: 241 AGESESK 247


>gi|110679275|ref|YP_682282.1| RNA pseudouridylate synthase family protein, putative [Roseobacter
           denitrificans OCh 114]
 gi|109455391|gb|ABG31596.1| RNA pseudouridylate synthase family protein, putative [Roseobacter
           denitrificans OCh 114]
          Length = 285

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 137/279 (49%), Positives = 173/279 (62%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
                R++KV++RAG+ASRRE ERMI   RVKVNG  +   A+NV ++D I VDG  +  
Sbjct: 6   TPQGDRIAKVLSRAGVASRREAERMIEAGRVKVNGKPISSPALNVQASDKITVDGKDVSP 65

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E  RLWLYHKP GLVTT +D  GR T++  LP+   RV+SVGRLDIN+EGLLLLTNDG 
Sbjct: 66  PEPARLWLYHKPTGLVTTDNDEKGRETIYSALPADLPRVMSVGRLDINSEGLLLLTNDGS 125

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           + R LELP+T WLR YRVR +G+     L  L++GI  +G  +  MQVTLD Q+G+NAW+
Sbjct: 126 IKRRLELPTTGWLRRYRVRVNGRPTDATLEPLRRGISSEGENFQPMQVTLDRQQGANAWL 185

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           T+GLREGKNREI++        VNRLIRISYGPFQLG L +G+  EV +K+LR+QLG   
Sbjct: 186 TMGLREGKNREIRRALAELGLTVNRLIRISYGPFQLGELKSGAVEEVRRKVLRDQLGLEE 245

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
                                R    +         K  
Sbjct: 246 DAGTDPAKRLEAGRKRGPPIRRTRATAGAKPARYAKKPR 284


>gi|168179079|ref|ZP_02613743.1| RNA pseudouridine synthase family protein [Clostridium botulinum
           NCTC 2916]
 gi|226950699|ref|YP_002805790.1| RNA pseudouridine synthase family protein [Clostridium botulinum A2
           str. Kyoto]
 gi|182669965|gb|EDT81941.1| RNA pseudouridine synthase family protein [Clostridium botulinum
           NCTC 2916]
 gi|226843144|gb|ACO85810.1| RNA pseudouridine synthase family protein [Clostridium botulinum A2
           str. Kyoto]
          Length = 238

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 107/231 (46%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++A  G  +R+EV+ +I + +V V+G +++   + +    + I V G  L   + 
Sbjct: 2   ERLDKILANLGYGTRKEVKALIKKGQVDVDGEVVKDNGMQIDPEKNKIFVFGKELVYKKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  T  + D                  VGRLD NT GLLL TNDG L  
Sbjct: 62  IYLMMNKPQGVVSATFDNYDETVIDLLEDEDRIFEPFPVGRLDKNTVGLLLFTNDGELNH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     ++Y  + + +V  + +   KKGI++         ++ +       + V V
Sbjct: 122 RLISPKWHVDKIYYAKINKKVTDEDIKKFKKGIILDDGYECFPAKLEIIKSFNEESEVRV 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++FE  + KV  L R  +GP +L   L  G  RE++ + +
Sbjct: 182 TIHEGKFHQVKRMFESVDKKVIYLKREEFGPLKLDESLEEGQYRELTDEEI 232


>gi|149914092|ref|ZP_01902624.1| RNA pseudouridylate synthase family protein [Roseobacter sp.
           AzwK-3b]
 gi|149812376|gb|EDM72207.1| RNA pseudouridylate synthase family protein [Roseobacter sp.
           AzwK-3b]
          Length = 263

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 145/263 (55%), Positives = 177/263 (67%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + +      R++KVIARAG+ASRRE ERMI   RV VNG  ++RAA+NV   D I VDG 
Sbjct: 1   MTENTHKGDRIAKVIARAGLASRREAERMIEAGRVTVNGKKIDRAALNVTDKDRIAVDGR 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            LR  E  RLWLYHKP GLVTT+ D  GR T+FD LP    RV+SVGRLDIN+EGLLLLT
Sbjct: 61  DLRAPEPQRLWLYHKPTGLVTTNKDEQGRPTIFDELPEDLPRVMSVGRLDINSEGLLLLT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDGGL R LELPST WLR YRVR +G+   D    L++G+VI G  +  M VTLD Q+G+
Sbjct: 121 NDGGLKRKLELPSTGWLRRYRVRVNGRPTDDTFAPLRQGLVIDGEKFQPMIVTLDRQQGA 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           NAWVTVG+REG+NRE+++  E     VNRLIR+SYGPFQLGTL  G+  E+  +ILR+QL
Sbjct: 181 NAWVTVGIREGRNREVRRAMEAVGLSVNRLIRVSYGPFQLGTLKPGAVEEIRPRILRDQL 240

Query: 246 GPHLLEEAQVNLDAPIYSSETLV 268
           G    E  +         +    
Sbjct: 241 GETSEEAPKKPGKPAPKRTRRRS 263


>gi|313888050|ref|ZP_07821728.1| pseudouridine synthase B, ribosomal large subunit [Peptoniphilus
           harei ACS-146-V-Sch2b]
 gi|312846005|gb|EFR33388.1| pseudouridine synthase B, ribosomal large subunit [Peptoniphilus
           harei ACS-146-V-Sch2b]
          Length = 235

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 77/236 (32%), Positives = 126/236 (53%), Gaps = 2/236 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G ASRR+ E  I +  VKVN  ++      +    D + +DG  L    +
Sbjct: 1   MRLQKYMAHCGAASRRKCEEFIQEGLVKVNDKVVTELGTKIDPNVDRVYLDGKRLTLEGK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KPIG+VT+ SD   R TV  +L     RV  VGRLDI+T GL+ LTNDG LA 
Sbjct: 61  KVYMILNKPIGVVTSASDEKDRPTV-TDLVPDDYRVYPVGRLDIDTTGLVFLTNDGQLAN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           ++  P  +  + Y V   G  +  +L++L++G+ I+ +      V +      ++ + + 
Sbjct: 120 IMMHPRYKIGKKYIVTVDGTPNARELSILREGLDIRDLKTSPANVRILKSFKQDSILEIE 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + EG+N ++K++F++   KV +L RIS G  QL  L  G+ R +S+K ++   G  
Sbjct: 180 IFEGQNHQVKRMFDYIGHKVKKLKRISIGEIQLLDLEPGNYRYLSEKEVKYLKGLK 235


>gi|290579936|ref|YP_003484328.1| putative pseudouridylate synthase B large subunit [Streptococcus
           mutans NN2025]
 gi|254996835|dbj|BAH87436.1| putative pseudouridylate synthase B large subunit [Streptococcus
           mutans NN2025]
          Length = 240

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 85/240 (35%), Positives = 131/240 (54%), Gaps = 3/240 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V +NG ++   A  V S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTLNGQMVTELATTVKSGDRVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++  D  GR TV D LP +  R+  VGRLD +T GLL+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVRDDKGRQTVVDLLPEVKERIYPVGRLDWDTSGLLILTNDGDFTDK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           +  P  +  +VY  R  G   +D L  L KGIVI G      +  +    ++ + + V +
Sbjct: 120 MLHPRHEIDKVYVARVKGLASKDNLRPLTKGIVIDGKKTQPARYRIVKTDREKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE     V++L R  +G   L  L +G  R ++KK + +     + E
Sbjct: 180 TIHEGRNHQVKKMFEAVGLMVDKLSRTRFGTLDLSGLNSGEARRLNKKEISQLYNAAVNE 239


>gi|16124485|ref|NP_419049.1| S4 domain-containing protein [Caulobacter crescentus CB15]
 gi|221233169|ref|YP_002515605.1| ribosomal large subunit pseudouridine synthase B [Caulobacter
           crescentus NA1000]
 gi|13421359|gb|AAK22217.1| S4 domain protein [Caulobacter crescentus CB15]
 gi|220962341|gb|ACL93697.1| ribosomal large subunit pseudouridine synthase B [Caulobacter
           crescentus NA1000]
          Length = 421

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 147/361 (40%), Positives = 193/361 (53%), Gaps = 21/361 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +RV+K +ARAG+ASRREVER+I   RV +NG +L   AV V   D + VDG  + + E 
Sbjct: 34  GERVAKALARAGVASRREVERLIEAGRVAINGKVLTTPAVKVAPGDFLTVDGQLVAEREP 93

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR++ YHKP GL+TTH+DP GR TVF  LP    R+ISVGRLD+N+EGLLLLTNDG L+R
Sbjct: 94  TRIFRYHKPTGLMTTHNDPKGRPTVFGALPKDLPRLISVGRLDLNSEGLLLLTNDGELSR 153

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----QKGSNA 187
            LE PS  W+R YR R  G   Q KL+ LK G+ I+G+ YG ++  LD        G N 
Sbjct: 154 ALETPSNAWVRRYRARAFGDTTQAKLDKLKDGVTIEGVTYGAIEAKLDKAHEKAGGGKNV 213

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+TV L EGKNRE++KV E    KVNRLIR+SYGPF LGTL AG   EV  +++RE L  
Sbjct: 214 WITVSLSEGKNREVRKVLESIGLKVNRLIRLSYGPFALGTLAAGQIEEVGPRVIRELLEG 273

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            +  E     D P ++       +        +   R    + +   L   +K   PV++
Sbjct: 274 VVSPENMPTGDRPKFAGI-ANPTKAPGTEGGGELQRRGAPRADRAVILDTPEKPEKPVYK 332

Query: 308 RNLASNVWMAK--GIHSSFLSDSGQREENHRR-------------SPSFPSKRSLRRTSA 352
              A     A   G          +     +R              P+   K +  R  A
Sbjct: 333 PGWAKPKKKASPHGPPKGAGKGPAKGPAKAKRPAKSIESKFIDIGKPAARGKPAAPRPGA 392

Query: 353 K 353
           K
Sbjct: 393 K 393


>gi|87120132|ref|ZP_01076028.1| putative pseudouridine synthase [Marinomonas sp. MED121]
 gi|86164834|gb|EAQ66103.1| putative pseudouridine synthase [Marinomonas sp. MED121]
          Length = 376

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 66/344 (19%), Positives = 125/344 (36%), Gaps = 7/344 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T  R++K I+ +G+ SRRE +R I Q  V +N    E     V   D + V+G  +   E
Sbjct: 5   TSTRLNKYISESGMCSRREADRFIEQGNVFINKKRAEV-GDQVNPGDVVRVNGAKIEPPE 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L        +    +          +  +  SR+  +GRLD +++GL+ LT++G L 
Sbjct: 64  AEDLVFIALNKPVGIVSTTEMEEPDNMVSFVNHSSRIFPIGRLDKDSQGLIFLTSNGDLV 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     + +D +N +  G+ + G      +V     + +     +
Sbjct: 124 NKILRAGNNHEKEYVVTVDKPLTEDAINTMASGVPMLGTKTKKCKVV----QEAPNVFRI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP--HL 249
            L +G NR+I+++ EF  ++V  L R+      L  L  G  R++++K + E      H 
Sbjct: 180 FLVQGLNRQIRRMCEFCGYQVTELERVRIMNISLKGLPVGDWRDLTEKEMTELSKMIEHS 239

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
             E           +++  R      S+        +K  SQ +  + + K         
Sbjct: 240 SSEDTSKQKPAPAKAKSKGRSNSKSFSKSKAQAAESRKEKSQSSKPASKGKSDGRSRPGE 299

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             +     K       +   +           P      +    
Sbjct: 300 GKNESGRGKNEGGRGKAPLNRSRSGEGGKGGSPKGNGANKGRPA 343


>gi|188583517|ref|YP_001926962.1| RNA-binding S4 domain protein [Methylobacterium populi BJ001]
 gi|179347015|gb|ACB82427.1| RNA-binding S4 domain protein [Methylobacterium populi BJ001]
          Length = 577

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 148/344 (43%), Positives = 196/344 (56%), Gaps = 1/344 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R++K IARAGIASRR+ E MI   RV +NG +L   A+NV  +D I +DG PL   
Sbjct: 23  PEGERIAKAIARAGIASRRDAEAMIEAGRVSLNGKILTSPAINVTESDRIAIDGEPLPAR 82

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ERTRLWL HKP G+VTT  DP+GR TVFD LP    RV+++GRLDINTEGLLLLTNDGGL
Sbjct: 83  ERTRLWLLHKPRGVVTTARDPEGRQTVFDGLPDDLPRVVAIGRLDINTEGLLLLTNDGGL 142

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A+V+  P T WLR YRVR  G + Q  L+ LKKG+ + G+ YG ++ TLD  +G N W+T
Sbjct: 143 AKVIAHPDTGWLRRYRVRAFGDITQADLDRLKKGVTVDGMEYGPVEATLDRVQGDNLWLT 202

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           +GLREGKNRE+K++ E     VNRLIR+S+GPFQLG L  G   E+  K+L+EQLG  L 
Sbjct: 203 LGLREGKNREVKRILEHLGLSVNRLIRLSFGPFQLGDLEVGLVEEIRTKVLKEQLGKSLA 262

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           E+A V+ ++P+  +                           + G   + +       R  
Sbjct: 263 EQAGVDFESPVREAIAPFGSPKKAARAAQSPRAEAPAGRGGRQGAHDEGRSEPRSGARGG 322

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           A+          +      +  +    SP+        R  A K
Sbjct: 323 AAGRPPRDPARPAAPRAGARPAQRA-PSPTVWRADDETRPRASK 365



 Score = 35.9 bits (81), Expect = 8.4,   Method: Composition-based stats.
 Identities = 10/128 (7%), Positives = 27/128 (21%), Gaps = 7/128 (5%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R+   +  RE                           R        +   R +    ++ 
Sbjct: 436 RQERPERSREDRPRRDAPAGDARPRRREAGEGAAPERRGPPRERRFEGEGRPEGRPPRER 495

Query: 294 GLSKQKK-LATPVHRRNLASNVWM------AKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
              + ++       RR  ++           +    +   +   R      +P     R 
Sbjct: 496 SEGRPQRDRGEGAPRRERSAEAGAPERRGPPRDRPRAAEGERPARSPRGADAPERGGFRK 555

Query: 347 LRRTSAKK 354
                 ++
Sbjct: 556 GPGGRLRR 563


>gi|238852693|ref|ZP_04643103.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           gasseri 202-4]
 gi|282852074|ref|ZP_06261432.1| pseudouridylate synthase [Lactobacillus gasseri 224-1]
 gi|311110814|ref|ZP_07712211.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           gasseri MV-22]
 gi|238834839|gb|EEQ27066.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           gasseri 202-4]
 gi|282556834|gb|EFB62438.1| pseudouridylate synthase [Lactobacillus gasseri 224-1]
 gi|311065968|gb|EFQ46308.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           gasseri MV-22]
          Length = 239

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 76/230 (33%), Positives = 122/230 (53%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AG+ASRR+ E+MI+  +V VNG  +      V  +D IEV+GVP+ K    
Sbjct: 3   ERLQKVIAQAGVASRRKAEKMISAGQVTVNGKKITELGTKVEPSDKIEVNGVPIEKETLH 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     ++++  D  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  
Sbjct: 63  TYLFYKPRG-VISSVKDDKGRKTVVDFFEDVPYRLYPVGRLDYDTSGLLLMTNDGELANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           L  P  +  +VY  +  G +  + +  L  G+ I G      ++ +    +K +   V +
Sbjct: 122 LMHPRNEVPKVYVAKIKGLLSPEDIRSLTHGVRIDGRKSAPAKLKILKTDEKKNTQIVQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + EG   ++K++FE  +  V +L R  Y    L +L +G  RE++ + +
Sbjct: 182 TIHEGHYHQVKRMFEAVHHFVEKLSREKYAFLTLKSLTSGEYRELTHEEV 231


>gi|42519012|ref|NP_964942.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           johnsonii NCC 533]
 gi|41583299|gb|AAS08908.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           johnsonii NCC 533]
          Length = 239

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 76/230 (33%), Positives = 120/230 (52%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AG+ASRR+ E+MI+  +V VNG  +      V  +D IEV+GVP+ K    
Sbjct: 3   ERLQKVIAQAGVASRRKAEKMISAGQVTVNGKKVTELGTKVEPSDKIEVNGVPIEKEALH 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     + +   D  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  
Sbjct: 63  TYLFYKPRGVISSVS-DDKGRKTVVDFFEDVPYRLYPVGRLDYDTSGLLLMTNDGELANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           L  P  +  +VY  +  G +  +++  L  G+ I G      ++ +    +K     V +
Sbjct: 122 LMHPRNEVPKVYVAKIKGILSPEEIRSLTHGVRIDGRKSAPAKLKILKTDEKKKTQIVQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + EG   ++K++FE  +  V +L R  Y    L +L +G  RE++ + +
Sbjct: 182 TIHEGHYHQVKRMFEAVHHFVEKLAREKYAFLTLKSLNSGEYRELTNEEV 231


>gi|322807584|emb|CBZ05159.1| ribosomal small subunit pseudouridine synthase A [Clostridium
           botulinum H04402 065]
          Length = 238

 Score =  186 bits (472), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 108/231 (46%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++A  G  +R+EV+ +I + +V V+G +++   + +    + I V G  L   + 
Sbjct: 2   ERLDKILANLGYGTRKEVKALIKKGQVDVDGEVVKDNGMQIDPEKNKIFVFGKELVYKKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  T  + D                  VGRLD NT GLLLLTNDG L  
Sbjct: 62  IYLMMNKPQGVVSATFDNYDETVVDLLEDEDRIFEPFPVGRLDKNTVGLLLLTNDGELNH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     ++Y  + + +V  + +   KKGI++         ++ +       + V V
Sbjct: 122 RLISPKWHVDKIYYAKINKKVTDEDIKKFKKGIILDDGYECFPAKLEIIKSFNEESEVRV 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++FE  + KV  L R  +GP +L   L  G  RE++ + +
Sbjct: 182 TIHEGKFHQVKRMFESVDKKVIYLKREEFGPLKLDESLEEGQYRELTDEEI 232


>gi|311068833|ref|YP_003973756.1| RluB protein [Bacillus atrophaeus 1942]
 gi|310869350|gb|ADP32825.1| RluB [Bacillus atrophaeus 1942]
          Length = 244

 Score =  186 bits (472), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 73/243 (30%), Positives = 122/243 (50%), Gaps = 3/243 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E +I + +VKVNG ++    V V  +D IEV+G+ + + E  
Sbjct: 2   ERLQKVIAHAGVASRRKAEELIKEGKVKVNGKIITELGVKVTGSDQIEVNGMKIEREEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     +++   D  GR  V D    I  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 62  YFLLYKPRG-VISAADDDKGRKVVTDFFKEIPQRIYPIGRLDYDTSGLLLLTNDGDFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTV 191
           L  P  Q  + Y  +  G   ++ +  L++G+ ++       +  L +       + + +
Sbjct: 121 LMHPKYQIDKTYVAKVKGIPSKELVRKLERGVQLEEGKTAPAKAKLLSLDKRKQTSIIQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE    +V +L R  Y    L  L  G  RE++   ++         
Sbjct: 181 TIHEGRNRQVRRMFEAIGHEVLKLKREEYAFLDLRGLHTGDARELTPHEVKRLRALAEHG 240

Query: 252 EAQ 254
           +  
Sbjct: 241 KNA 243


>gi|260425745|ref|ZP_05779725.1| ribosomal large subunit pseudouridine synthase B [Citreicella sp.
           SE45]
 gi|260423685|gb|EEX16935.1| ribosomal large subunit pseudouridine synthase B [Citreicella sp.
           SE45]
          Length = 316

 Score =  186 bits (472), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 135/266 (50%), Positives = 175/266 (65%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
                R++KV+ARAG+ASRRE E+MI   RV VNG ++ RAA+NV   D + VDG P+  
Sbjct: 51  TPAGDRIAKVLARAGVASRREAEKMIEMGRVAVNGEIITRAALNVTDKDKVTVDGKPVDA 110

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E  R+WLYHKP GLVTT  D  GR T++D+LP    RV+SVGRLD+N+EGLLLLTNDG 
Sbjct: 111 PEDPRIWLYHKPAGLVTTTKDEQGRPTIYDDLPEELPRVMSVGRLDLNSEGLLLLTNDGS 170

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           + R LELPST WLR YRVR +G+   D L  L+ GIV+ G  +  M+VTLD Q+G+NAW+
Sbjct: 171 IKRRLELPSTGWLRKYRVRVNGKPSDDMLAPLRAGIVVDGQAFQPMEVTLDRQQGANAWL 230

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           T+GLREGKNREI++        VNRLIR+SYGPFQLG L  G  +EV  +++R+QLG   
Sbjct: 231 TIGLREGKNREIRRAMTDIGLTVNRLIRVSYGPFQLGQLKQGEVQEVRSRVVRDQLGLEG 290

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNII 275
            +  +         +    +  P   
Sbjct: 291 AKSNRPQPTRRRKPAPDGAKQSPKRR 316


>gi|313890897|ref|ZP_07824521.1| pseudouridine synthase B, ribosomal large subunit [Streptococcus
           pseudoporcinus SPIN 20026]
 gi|313120795|gb|EFR43910.1| pseudouridine synthase B, ribosomal large subunit [Streptococcus
           pseudoporcinus SPIN 20026]
          Length = 240

 Score =  186 bits (472), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 81/237 (34%), Positives = 128/237 (54%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V +NG ++   A  V S+D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTLNGQVITDLATLVKSSDVVEVEGSPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T GLL+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRKTVIDLLPQVKERIYPVGRLDWDTSGLLILTNDGDFTDK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIIRVEADKNRSIVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + EG++ ++KK+FE     V++L R  +G   L  L  G  R ++KK + +     
Sbjct: 180 TIHEGRHHQVKKMFESVGLLVDKLSRTRFGTLDLTGLRPGEARRLNKKEVSQLHNAA 236


>gi|312277674|gb|ADQ62331.1| Pseudouridine synthase [Streptococcus thermophilus ND03]
          Length = 255

 Score =  186 bits (472), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 81/251 (32%), Positives = 131/251 (52%), Gaps = 3/251 (1%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            K+  +      R++K IA AG+ASRR+ E +I + RV +NG  +   A  V + D +EV
Sbjct: 4   RKDTAEAVEKRMRINKYIAHAGVASRRKAEELIKEGRVTLNGKTVMELATIVKNGDIVEV 63

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           +G P+   E    +L +KP G++++ SD   R TV D +P +  R+  VGRLD +T GLL
Sbjct: 64  NGSPI-YNEEKVYYLLNKPRGVISSVSDEKNRKTVIDLMPHVKERIYPVGRLDWDTTGLL 122

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           +LTNDG     +  P  +  +VY  R  G   ++ L  L +G+VI G         +   
Sbjct: 123 ILTNDGDFTDKMIHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTQPAHYNIIKV 182

Query: 183 K--GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
               + + V + + EG+N ++KK+FE     V++L R  +G   L  L  G +R +SKK 
Sbjct: 183 DHEKNRSVVELTIHEGRNHQVKKMFESVGLIVDKLSRTRFGTLDLTGLRPGESRRLSKKE 242

Query: 241 LREQLGPHLLE 251
           + +     + +
Sbjct: 243 ISQLHNIAVNK 253


>gi|168183575|ref|ZP_02618239.1| RNA pseudouridine synthase family protein [Clostridium botulinum
           Bf]
 gi|237796714|ref|YP_002864266.1| RNA pseudouridine synthase family protein [Clostridium botulinum
           Ba4 str. 657]
 gi|182673348|gb|EDT85309.1| RNA pseudouridine synthase family protein [Clostridium botulinum
           Bf]
 gi|229261203|gb|ACQ52236.1| RNA pseudouridine synthase family protein [Clostridium botulinum
           Ba4 str. 657]
          Length = 238

 Score =  186 bits (472), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 108/231 (46%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++A  G  +R+EV+ +I + +V V+G +++   + +    + I V G  L   + 
Sbjct: 2   ERLDKILANLGYGTRKEVKALIKKGQVDVDGEVVKDNGMQIDPEKNKIFVFGKELVYKKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  T  + D                  VGRLD NT GLLLLTNDG L  
Sbjct: 62  IYLIMNKPQGVVSATFDNYDETVVDLLEDEDRIFEPFPVGRLDKNTVGLLLLTNDGELNH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     ++Y  + + +V  + +   KKGI++         ++ +       + V V
Sbjct: 122 RLISPKWHVDKIYYAKINKKVTDEDIKKFKKGIILDDGYECFPAKLEIIKSFNEESEVRV 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++FE  + KV  L R  +GP +L   L  G  RE++ + +
Sbjct: 182 TIHEGKFHQVKRMFESVDKKVIYLKREEFGPLKLDESLEEGQYRELTDEEI 232


>gi|172058280|ref|YP_001814740.1| pseudouridine synthase [Exiguobacterium sibiricum 255-15]
 gi|171990801|gb|ACB61723.1| pseudouridine synthase [Exiguobacterium sibiricum 255-15]
          Length = 239

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 55/231 (23%), Positives = 105/231 (45%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV++++    ++V+G ++     +V      + + G P+   + 
Sbjct: 1   MRLDKLLSNMGAGSRKEVKQLLKSGAIQVDGEIVYDPKQHVDTENQQVLLYGEPVTYQKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +   P  +  T    D            + +   VGRLD +TEGLLLLTNDG    
Sbjct: 61  IYLMMNKPPGVISATEDKRDQTVIDLLFDDVTYFKPFPVGRLDKDTEGLLLLTNDGSFNH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY     G + ++ +  + +G+ ++        ++ +       + + +
Sbjct: 121 ALMSPKKHVEKVYYAEVIGTLTEEDVEEVAEGVTLEDGYKTKPGKLIILEATDETSTLEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++K++      +V  L R+S G   L  TL AG  RE+++  L
Sbjct: 181 TITEGKFHQVKRMMLALGKEVTYLKRLSIGQLPLDPTLEAGEYRELTRGEL 231


>gi|325274077|ref|ZP_08140221.1| RNA-binding S4 domain-containing protein [Pseudomonas sp. TJI-51]
 gi|324100788|gb|EGB98490.1| RNA-binding S4 domain-containing protein [Pseudomonas sp. TJI-51]
          Length = 355

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 86/344 (25%), Positives = 145/344 (42%), Gaps = 9/344 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            + +++ KV+AR G+ SRR+VE  I+Q R+KVNG +       V   D I VDG  +++ 
Sbjct: 14  PSGEKLQKVLARIGVGSRRDVEAWISQGRIKVNG-VAATLGQRVDLHDAIAVDGKLIKRE 72

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E     R  +        + T        +           R I++GRLDINT GLLL T
Sbjct: 73  EAAEATRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLDINTTGLLLFT 132

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-KG 184
            DG LA  L  PS +  R Y VR  G+VD + +  LK G++++        +      +G
Sbjct: 133 TDGELANRLMHPSYEMDREYAVRVRGEVDDEMIERLKAGVMLEDGPAKFTDIQKAPGGEG 192

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
            N W    + EG+NRE+++++E     V+RL R+ +GP  L   L  G  RE+S+  + +
Sbjct: 193 FNHWYHCVVMEGRNREVRRLWESQGMVVSRLKRVRFGPVFLNSDLPMGRWREMSQGEI-D 251

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            L   +  +        + + + + R +      +           + +   + ++    
Sbjct: 252 ILAAEVGLQPVALPALNLKAKDKMERLQRKSSRPLGRGERVRNLRPAHEGAAAGERPARQ 311

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
           P        N   A     S +     + E  + +     K   
Sbjct: 312 PREEAPRKGNRGSAVAERPSEMRKRPAKPEGDKPAGRGRGKPRG 355


>gi|319790172|ref|YP_004151805.1| pseudouridine synthase [Thermovibrio ammonificans HB-1]
 gi|317114674|gb|ADU97164.1| pseudouridine synthase [Thermovibrio ammonificans HB-1]
          Length = 238

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 66/239 (27%), Positives = 116/239 (48%), Gaps = 2/239 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K++A  G  +R +V+R+I +  V+VNG +++  +  V    D + VDG P+   E 
Sbjct: 1   MRLDKLLAEGGFGTRSQVKRLIKKGHVEVNGEVVKDPSFQVDPLKDEVTVDGEPVYYEEE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L      + +   D              F ++  VGRLD + EGLLL+T DG LA 
Sbjct: 61  YYLVLNKPAGYVTS-TKDRQMTVMELVADIPRFDKLFPVGRLDKDAEGLLLMTTDGELAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + Y V+  G++ ++ +  L++GI ++       +V +       +   + 
Sbjct: 120 RLTHPKWKVPKTYVVKVEGRLTEEAVEPLRRGIELKDFKAKPAEVRILRSSEEESEAEIT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
           + EGK  ++K++F      V  L R+++GP +LG L  G  R ++++ LR       LE
Sbjct: 180 ITEGKFHQVKRMFAAIGHPVKELKRVAFGPLKLGELPTGEYRHLTEEELRALRKAVKLE 238


>gi|153939754|ref|YP_001392619.1| RNA pseudouridine synthase family protein [Clostridium botulinum F
           str. Langeland]
 gi|170754583|ref|YP_001782897.1| RNA pseudouridine synthase family protein [Clostridium botulinum B1
           str. Okra]
 gi|152935650|gb|ABS41148.1| RNA pseudouridine synthase family protein [Clostridium botulinum F
           str. Langeland]
 gi|169119795|gb|ACA43631.1| RNA pseudouridine synthase family protein [Clostridium botulinum B1
           str. Okra]
 gi|295320605|gb|ADG00983.1| RNA pseudouridine synthase family protein [Clostridium botulinum F
           str. 230613]
          Length = 238

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 108/231 (46%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++A  G  +R+EV+ +I + +V V+G +++   + +    + I V G  L   + 
Sbjct: 2   ERLDKILANLGYGTRKEVKALIKKGQVDVDGEVVKDNGMQIDPEKNKIFVFGKELVYKKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  T  + D                  VGRLD NT GLLLLTNDG L  
Sbjct: 62  IYLMMNKPQGVVSATFDNYDETVIDLLEDEDRIFEPFPVGRLDKNTVGLLLLTNDGELNH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     ++Y  + + +V  + +   KKGI++         ++ +       + V V
Sbjct: 122 RLISPKWHVDKIYYAKINKKVTDEDIKKFKKGIILDDGYECFPAKLEIIKSFNEESEVRV 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++FE  + KV  L R  +GP +L   L  G  RE++ + +
Sbjct: 182 TIHEGKFHQVKRMFESVDKKVIYLKREEFGPLKLDESLEEGEYRELTDEEI 232


>gi|148381218|ref|YP_001255759.1| RNA pseudouridine synthase family protein [Clostridium botulinum A
           str. ATCC 3502]
 gi|153932230|ref|YP_001385593.1| RNA pseudouridine synthase family protein [Clostridium botulinum A
           str. ATCC 19397]
 gi|153934698|ref|YP_001388999.1| RNA pseudouridine synthase family protein [Clostridium botulinum A
           str. Hall]
 gi|148290702|emb|CAL84832.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum A str. ATCC 3502]
 gi|152928274|gb|ABS33774.1| RNA pseudouridine synthase family protein [Clostridium botulinum A
           str. ATCC 19397]
 gi|152930612|gb|ABS36111.1| RNA pseudouridine synthase family protein [Clostridium botulinum A
           str. Hall]
          Length = 238

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 108/231 (46%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++A  G  +R+EV+ +I + +V V+G +++   + +    + I V G  L   + 
Sbjct: 2   ERLDKILANLGYGTRKEVKALIKKGQVDVDGEVVKDNGMQIDPEKNKIFVFGKELVYKKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  T  + D                  VGRLD NT GLLLLTNDG L  
Sbjct: 62  IYLMMNKPQGVVSATFDNYDETVIDLLEDEDRIFEPFPVGRLDKNTVGLLLLTNDGELNH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     ++Y  + + +V  + +   KKGI++         ++ +       + V V
Sbjct: 122 RLISPKWHVDKIYYAKINKKVTDEDIKKFKKGIILDDGYECFPAKLEIIKSFNEESEVRV 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++FE  + KV  L R  +GP +L   L  G  RE++ + +
Sbjct: 182 TIHEGKFHQVKRMFESVDKKVIYLKREEFGPLKLDESLEEGQYRELTDEEI 232


>gi|46201216|ref|ZP_00208014.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Magnetospirillum
           magnetotacticum MS-1]
          Length = 294

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 149/293 (50%), Positives = 185/293 (63%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
                +R++K +ARAG+ SRRE ER I   RV VNG  L+  A  V   D I VDG PL 
Sbjct: 2   TEEKGERIAKRLARAGLCSRREAERWIEMGRVSVNGKTLDSPACVVGPGDIILVDGTPLS 61

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + E+TRLW YHKP GLVTTH DP+GR TVFD+LP    RVISVGRLD+N+EGLLLLTNDG
Sbjct: 62  EPEKTRLWRYHKPAGLVTTHKDPEGRPTVFDHLPEGMPRVISVGRLDLNSEGLLLLTNDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LAR LELPS  WLR YRVR HG+V +D L  L+ GI I G+ YG +  TLD ++G+NAW
Sbjct: 122 ELARKLELPSNAWLRRYRVRVHGEVSEDALARLENGITIDGMAYGPISATLDRRQGANAW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           ++V LREGKNREI++V EF  W V+RLIR+SYGPFQLGTL  G+  EV+ K+LREQ+G  
Sbjct: 182 LSVSLREGKNREIRRVMEFLGWPVSRLIRVSYGPFQLGTLEEGAADEVAGKVLREQMGEG 241

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
                    +      E   R       +   D          K+   +++  
Sbjct: 242 KAVLKPRPENKSAGEREKEQRVAAKARKQKLADDKHAASAKKAKSDAHRRRSS 294


>gi|226310436|ref|YP_002770330.1| pseudouridine synthase [Brevibacillus brevis NBRC 100599]
 gi|226093384|dbj|BAH41826.1| pseudouridine synthase [Brevibacillus brevis NBRC 100599]
          Length = 228

 Score =  186 bits (471), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 66/230 (28%), Positives = 112/230 (48%), Gaps = 7/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+  GI SRRE +++I  +RV +NG L       V S D + +DG PL   ++ 
Sbjct: 1   MRINKFISETGICSRREADKLIESKRVTINGQLA-ELGSTVASGDDVRIDGQPLGVKKKD 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T            +  +   R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCTTELHV--KGNIIDFVNHPERIFPIGRLDKDSQGLILLTNDGDIVNK 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V     +  + L+ +  G+ I G      +VT    K S+    + L
Sbjct: 118 ILRAENNHDKEYIVTVDKPITANFLHGMANGVRILGTTTKPCKVT----KVSDRVFNIVL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            +G NR+I+++ + F ++V +L RI      LG L  G  R ++ K L +
Sbjct: 174 TQGLNRQIRRMCQAFGYQVRKLERIRIMNIALGNLKLGQWRNLTAKELTD 223


>gi|23465315|ref|NP_695918.1| ribosomal large subunit pseudouridine synthase B [Bifidobacterium
           longum NCC2705]
 gi|189439325|ref|YP_001954406.1| 16S rRNA uridine-516 pseudouridylate synthase [Bifidobacterium
           longum DJO10A]
 gi|227547249|ref|ZP_03977298.1| ribosomal large subunit pseudouridine synthase B [Bifidobacterium
           longum subsp. infantis ATCC 55813]
 gi|239621483|ref|ZP_04664514.1| ribosomal large subunit pseudouridine synthase B [Bifidobacterium
           longum subsp. infantis CCUG 52486]
 gi|296454186|ref|YP_003661329.1| pseudouridine synthase [Bifidobacterium longum subsp. longum
           JDM301]
 gi|312132697|ref|YP_004000036.1| rsua [Bifidobacterium longum subsp. longum BBMN68]
 gi|317483248|ref|ZP_07942243.1| RNA pseudouridylate synthase [Bifidobacterium sp. 12_1_47BFAA]
 gi|322689199|ref|YP_004208933.1| pseudouridine synthase [Bifidobacterium longum subsp. infantis
           157F]
 gi|322691265|ref|YP_004220835.1| pseudouridine synthase [Bifidobacterium longum subsp. longum JCM
           1217]
 gi|23325954|gb|AAN24554.1| ribosomal large subunit pseudouridine synthase B [Bifidobacterium
           longum NCC2705]
 gi|189427760|gb|ACD97908.1| 16S rRNA uridine-516 pseudouridylate synthase [Bifidobacterium
           longum DJO10A]
 gi|227212208|gb|EEI80104.1| ribosomal large subunit pseudouridine synthase B [Bifidobacterium
           longum subsp. infantis ATCC 55813]
 gi|239515944|gb|EEQ55811.1| ribosomal large subunit pseudouridine synthase B [Bifidobacterium
           longum subsp. infantis CCUG 52486]
 gi|291516882|emb|CBK70498.1| pseudouridine synthase family [Bifidobacterium longum subsp. longum
           F8]
 gi|296183617|gb|ADH00499.1| pseudouridine synthase [Bifidobacterium longum subsp. longum
           JDM301]
 gi|311773655|gb|ADQ03143.1| RsuA [Bifidobacterium longum subsp. longum BBMN68]
 gi|316915317|gb|EFV36744.1| RNA pseudouridylate synthase [Bifidobacterium sp. 12_1_47BFAA]
 gi|320456121|dbj|BAJ66743.1| pseudouridine synthase [Bifidobacterium longum subsp. longum JCM
           1217]
 gi|320460535|dbj|BAJ71155.1| pseudouridine synthase [Bifidobacterium longum subsp. infantis
           157F]
          Length = 256

 Score =  186 bits (471), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 117/237 (49%), Gaps = 2/237 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVP 66
           Q++    R+ K++A+AG  SRR+ E MI + RV+V+G L+      V      + VDG  
Sbjct: 12  QDDSNSIRLQKLLAQAGFGSRRKCEDMITEGRVEVDGELVTELGTRVDPHKQQVRVDGSR 71

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +R          +KP  +++   DP GR T+ D +   + R+  +GRLD ++EGL+L+TN
Sbjct: 72  VRVNPNHVTLALNKPRKVLSAMDDPKGRYTLRDIVGDKYERIFHMGRLDYDSEGLILMTN 131

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L++ +  P  +  + Y     G++       L    + +           +      
Sbjct: 132 DGELSQHVMHPKYEVEKTYVATLEGKISGTVCRRLVTTGVQLDDGWIKLDHCAIIDSSRD 191

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +  V V L  GKNR ++++F    + V RL+R   GP +LG L  GS R +S+  +R
Sbjct: 192 HTMVKVVLHSGKNRIVRRIFGSIGFPVKRLVRTQIGPIKLGDLKPGSYRVLSQTEVR 248


>gi|213692048|ref|YP_002322634.1| pseudouridine synthase [Bifidobacterium longum subsp. infantis ATCC
           15697]
 gi|213523509|gb|ACJ52256.1| pseudouridine synthase [Bifidobacterium longum subsp. infantis ATCC
           15697]
 gi|320458160|dbj|BAJ68781.1| pseudouridine synthase [Bifidobacterium longum subsp. infantis ATCC
           15697]
          Length = 256

 Score =  186 bits (471), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 116/237 (48%), Gaps = 2/237 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVP 66
           Q++    R+ K++A+AG  SRR+ E MI + RV+V+G L+      V      + VDG  
Sbjct: 12  QDDSNSIRLQKLLAQAGFGSRRKCEDMITEGRVEVDGELVTELGTRVDPHKQQVRVDGSR 71

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +R          +KP  +++   DP GR T+ D +   + R+  +GRLD ++EGL+L+TN
Sbjct: 72  VRVNPNHVTLALNKPRKVLSAMDDPKGRYTLRDIVGDKYERIFHMGRLDYDSEGLILMTN 131

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L++ +  P  +  + Y     G++       L    + +           +      
Sbjct: 132 DGELSQHVMHPKYEVEKTYVATLEGKISGTVCRRLVTTGVQLDDGWIKLDHCAIIDASRD 191

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
              V V L  GKNR ++++F    + V RL+R   GP +LG L  GS R +S+  +R
Sbjct: 192 YTMVKVVLHSGKNRIVRRIFGSIGFPVKRLVRTQIGPIKLGDLKPGSYRVLSQTEVR 248


>gi|281421747|ref|ZP_06252746.1| ribosomal large subunit pseudouridine synthase B [Prevotella copri
           DSM 18205]
 gi|281404242|gb|EFB34922.1| ribosomal large subunit pseudouridine synthase B [Prevotella copri
           DSM 18205]
          Length = 253

 Score =  186 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 63/246 (25%), Positives = 111/246 (45%), Gaps = 5/246 (2%)

Query: 1   MKDKNIVQENF----TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           MK +   +E       P R++K +A AG+ SRRE +  I    V VNG ++      ++ 
Sbjct: 1   MKKRIEYKEENIDPTEPLRLNKFLANAGVCSRREADEFIQAGLVTVNGEVVTELGTKILR 60

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           TD ++    P+   ++  + L      + T+      ++ +         R+  VGRLD 
Sbjct: 61  TDEVKFHDAPVTLEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKDVCPERIYPVGRLDR 120

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NT G+LLLTNDG LA  L  P     +VY V     +    ++ +++GI ++        
Sbjct: 121 NTTGVLLLTNDGDLASKLTHPKFLKKKVYHVHLDKNLTAHDMDQIREGITLEDGEIK-AD 179

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                     A V + +  GKNR ++++FE   ++V +L R+ +       L  G  R +
Sbjct: 180 AVEYADDRDKAQVGIEIHSGKNRIVRRIFESLGYRVTKLDRVQFAGLTKKNLRRGDWRFL 239

Query: 237 SKKILR 242
           ++K + 
Sbjct: 240 TEKEVD 245


>gi|70726424|ref|YP_253338.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           haemolyticus JCSC1435]
 gi|68447148|dbj|BAE04732.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           haemolyticus JCSC1435]
          Length = 245

 Score =  186 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 70/235 (29%), Positives = 127/235 (54%), Gaps = 3/235 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +R+ K IA +G  SRR+ E +I + +VKVNG  +      V S+D +EV+G+ + +
Sbjct: 2   SKELERLQKRIANSGYTSRRKAETLITEGKVKVNGQTVTELGTKVKSSDTVEVEGIKIEQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ++  +  Y     ++T+ SD  GR+ V D    + +R+  VGRLD +T GLLLLTNDG 
Sbjct: 62  EDKMYILFYKPT-QVITSVSDDRGRTVVTDYFKDLETRIYPVGRLDYDTSGLLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNA 187
              ++  P     + Y  +  G + ++++  L+ GI ++         +V    +  +  
Sbjct: 121 FTNLMTHPRYHIQKKYVAKLKGYLMREEVKALENGIELEDGFTQPAQVKVKKQDKDKNIT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V + + EG+NR+++++FE F  +V++L RI +G   L  L AG  R ++   ++
Sbjct: 181 LVEITISEGRNRQVRRMFEHFGHQVDKLTRIEFGNLNLKGLNAGEGRVLTPHEVK 235


>gi|254517670|ref|ZP_05129726.1| pseudouridine synthase [Clostridium sp. 7_2_43FAA]
 gi|226911419|gb|EEH96620.1| pseudouridine synthase [Clostridium sp. 7_2_43FAA]
          Length = 238

 Score =  186 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 112/231 (48%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV++  G  +R+E+++++ +  ++VNG +++   + +    D I V+G  +   + 
Sbjct: 2   ERLDKVLSNLGYGTRKEIKQVVRKGLIEVNGEIVKDNGMQIDPEVDKILVNGEEIFYRKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  T  + D        +         VGRLD +T GLLLLTNDG L  
Sbjct: 62  IYLMMNKPDGVVSATFDNRDETVIDLLEIEHQVFEPFPVGRLDKDTVGLLLLTNDGELNH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P  +  +VY  +   +V +  +   K GI +       + ++ +     S + V +
Sbjct: 122 RLISPKWKVDKVYYAKIDKKVTEADIKKFKNGITLDDGYTCKEAKLEILESSDSGSEVMI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            ++EGK  ++K++FE  +  V  L R+ +G  QL   L  G  RE++++ +
Sbjct: 182 TIQEGKFHQVKRMFEAVDKSVVYLKRVEFGTLQLDEDLEEGEYRELTEEEV 232


>gi|89901090|ref|YP_523561.1| pseudouridine synthase Rsu [Rhodoferax ferrireducens T118]
 gi|89345827|gb|ABD70030.1| ribosomal large subunit pseudouridine synthase B [Rhodoferax
           ferrireducens T118]
          Length = 466

 Score =  186 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 81/359 (22%), Positives = 137/359 (38%), Gaps = 11/359 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          +   DH++V+
Sbjct: 87  KRVLAPLAETPKLHKVLAQAGMGSRLEMEQLIMEGRITVNNEPA-HIGQRIQFGDHVKVN 145

Query: 64  GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+R          +  +     +VT     +  +           +  SVGRLD+NTE
Sbjct: 146 GKPIRFRIDAPPARVIAYHKPVGEVVTHDDPQNRPTVFRRLPKLFQGKWQSVGRLDLNTE 205

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL T+ G LA  L  P     R Y VR  G +++D+   L  G+ +         +  
Sbjct: 206 GLLLFTSSGELANNLMHPRFGLEREYAVRVLGALNKDEKQRLLDGVKLDDGVAQFGSIEA 265

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E+ +
Sbjct: 266 GGGEGANCWYRVTIAEGRNREVRRMFEAVGHAVSRLIRIRYGAMMLPRGLKRGAWMELDE 325

Query: 239 KILR---EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
             ++   +  GP                            S       R     +  NG 
Sbjct: 326 SDIKSLMQAAGPRSSSAQGNEAGEGGVDVSRREGAEQGPGSRNRRRGARGNGVRNTGNGQ 385

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ--REENHRRSPSFPSKRSLRRTSA 352
                   P      +     ++              + +  + +  +    S  R   
Sbjct: 386 RNATVGGAPKSGAGFSQGSGQSRKKQGQTGDRQAGASQPDPMKTAFGYIGADSFTRQRQ 444


>gi|291524779|emb|CBK90366.1| ribosomal small subunit pseudouridine synthase A [Eubacterium
           rectale DSM 17629]
          Length = 240

 Score =  186 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 63/230 (27%), Positives = 114/230 (49%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K ++  G+ +R EV+++I   ++ +NG +  +    V +  D + V+G  ++    
Sbjct: 2   IRLDKFLSEMGLGTRSEVKKLIKTGQIAINGTVAAKPETKVDTDADEVSVNGRIVKYQRY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                      + +  SD    + +     ++   +  VGRLDI+TEGLLL+TNDG L+ 
Sbjct: 62  EYYLFNKPSGCV-SATSDNVHDTVMDYITDAVHDDLFPVGRLDIDTEGLLLITNDGALSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  PS    + Y  R  G+V  D +   K+GI I +       ++ +  + GS + + +
Sbjct: 121 ELLSPSKHVAKTYYARIDGEVTWDDIIRFKEGIDIGEERPTKPAEL-VIKKSGSVSEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
            + EGK  ++K++FE    +V  L RIS GP +L   L  G+ R +++  
Sbjct: 180 TITEGKFHQVKRMFEALGKRVIYLKRISMGPLKLPDDLKTGTYRALTQAE 229


>gi|228993454|ref|ZP_04153364.1| Pseudouridine synthase [Bacillus pseudomycoides DSM 12442]
 gi|228999492|ref|ZP_04159070.1| Pseudouridine synthase [Bacillus mycoides Rock3-17]
 gi|229007048|ref|ZP_04164675.1| Pseudouridine synthase [Bacillus mycoides Rock1-4]
 gi|228754197|gb|EEM03615.1| Pseudouridine synthase [Bacillus mycoides Rock1-4]
 gi|228760203|gb|EEM09171.1| Pseudouridine synthase [Bacillus mycoides Rock3-17]
 gi|228766276|gb|EEM14920.1| Pseudouridine synthase [Bacillus pseudomycoides DSM 12442]
          Length = 244

 Score =  186 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 104/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++GI ++ A  +V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGISVKDAKFHVNVEEQEVTIHGEIVEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L ++     +  T  D          L         VGRLDI+TEG LLLTNDG L  
Sbjct: 61  VYLMMHKPQGVISATEDDNHETVVDLLELEDAIFDPFPVGRLDIDTEGFLLLTNDGKLTH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G V +  +    KG+++         ++T+  +    + + +
Sbjct: 121 QLLSPKKHVPKKYYAHVAGVVTEKDVEEFAKGVILDDGYETKPGELTIL-KSDDVSEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 180 VITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 231


>gi|167038569|ref|YP_001666147.1| pseudouridine synthase [Thermoanaerobacter pseudethanolicus ATCC
           33223]
 gi|307266602|ref|ZP_07548133.1| pseudouridine synthase [Thermoanaerobacter wiegelii Rt8.B1]
 gi|320116965|ref|YP_004187124.1| pseudouridine synthase [Thermoanaerobacter brockii subsp. finnii
           Ako-1]
 gi|166857403|gb|ABY95811.1| pseudouridine synthase [Thermoanaerobacter pseudethanolicus ATCC
           33223]
 gi|306918399|gb|EFN48642.1| pseudouridine synthase [Thermoanaerobacter wiegelii Rt8.B1]
 gi|319930056|gb|ADV80741.1| pseudouridine synthase [Thermoanaerobacter brockii subsp. finnii
           Ako-1]
          Length = 241

 Score =  186 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 66/231 (28%), Positives = 109/231 (47%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K+++  GI +R+EV++ I +  V VNG  ++ A + V   +D I  DG  +   E 
Sbjct: 4   MRIDKLLSNIGIGTRKEVKKFIKEGLVLVNGNTVKDAGLIVDTESDEILFDGEKINYKEF 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      +  T+ + +                  VGRLD +TEGLLL+TNDG LA 
Sbjct: 64  IYIMINKPKGVISATYDEVEKTVIDLLPQELKARNPFPVGRLDKDTEGLLLITNDGDLAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P    ++ Y     G V++  +    +GI+++         + +       + V V
Sbjct: 124 QLLSPKKNVIKKYYAEILGFVNESDIKAFNEGIILEDGYKTLPANLEILFSSSDVSKVYV 183

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            +REGK  +IK++FE    KV  L R++ G   L   L  G  RE+S++ L
Sbjct: 184 YIREGKYHQIKRMFESVGKKVIYLKRLAMGSLTLDENLKPGEWRELSEEEL 234


>gi|157692817|ref|YP_001487279.1| pseudouridylate synthase [Bacillus pumilus SAFR-032]
 gi|157681575|gb|ABV62719.1| pseudouridylate synthase [Bacillus pumilus SAFR-032]
          Length = 281

 Score =  186 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 74/250 (29%), Positives = 121/250 (48%), Gaps = 3/250 (1%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            K + +     +R+ KVIA AG+ASRR+ E +I + RV VNG  +    V V S+D IEV
Sbjct: 28  SKIVHEVKDKMERLQKVIAHAGVASRRKAEELIKEGRVTVNGQTVTELGVKVGSSDKIEV 87

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           +G+ L + E     LY     +++   D  GR  V D    +  R+  +GRLD +T GL+
Sbjct: 88  NGLKLEREEPVYFMLYKPRG-VISAAEDDKGRKVVTDFFDDVPQRLYPIGRLDYDTSGLI 146

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L+TNDG  A  L  P  +  + Y  +  G   ++ L  L+KGI++        +  + + 
Sbjct: 147 LITNDGEFAHKLMHPKYEIDKTYAAKLKGIPSKELLRKLEKGIMLDHKKTAPARAKMLSI 206

Query: 183 KGSNAW--VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                   V + + EG+NR+++++FE     V +L R  Y    +  +  G  RE+S   
Sbjct: 207 DKRKQTCIVQLTIHEGRNRQVRRMFEAIGHDVLKLKREHYAFLHIEGMRPGDRRELSPHE 266

Query: 241 LREQLGPHLL 250
           ++        
Sbjct: 267 VKRLRAIADH 276


>gi|55820359|ref|YP_138801.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           thermophilus LMG 18311]
 gi|55822249|ref|YP_140690.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           thermophilus CNRZ1066]
 gi|116627195|ref|YP_819814.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           thermophilus LMD-9]
 gi|55736344|gb|AAV59986.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           thermophilus LMG 18311]
 gi|55738234|gb|AAV61875.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           thermophilus CNRZ1066]
 gi|116100472|gb|ABJ65618.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           thermophilus LMD-9]
          Length = 255

 Score =  186 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 80/251 (31%), Positives = 131/251 (52%), Gaps = 3/251 (1%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            K+  +      R++K IA AG+ASRR+ E +I + RV +NG  +   A  V + D +EV
Sbjct: 4   RKDTAEAVEKRMRINKYIAHAGVASRRKAEELIKEGRVTLNGKTVMELATIVKNGDIVEV 63

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           +G P+   E    +L +KP G++++ SD   R TV D +P +  R+  VGRLD +T GLL
Sbjct: 64  NGSPI-YNEEKVYYLLNKPRGVISSVSDEKNRKTVIDLMPHVKERIYPVGRLDWDTTGLL 122

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           +LTNDG     +  P  +  +VY  R  G   ++ L  L +G+VI G         +   
Sbjct: 123 ILTNDGDFTDKMIHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTQPAHYNIIKV 182

Query: 183 K--GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
               + + V + + EG+N ++KK+FE     V++L R  +G   L  L  G +R ++KK 
Sbjct: 183 DHEKNRSVVELTIHEGRNHQVKKMFESVGLIVDKLSRTRFGTLDLTGLRPGESRRLNKKE 242

Query: 241 LREQLGPHLLE 251
           + +     + +
Sbjct: 243 ISQLHNIAVNK 253


>gi|187776810|ref|ZP_02993283.1| hypothetical protein CLOSPO_00326 [Clostridium sporogenes ATCC
           15579]
 gi|187775469|gb|EDU39271.1| hypothetical protein CLOSPO_00326 [Clostridium sporogenes ATCC
           15579]
          Length = 238

 Score =  185 bits (470), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 108/231 (46%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++A  G  +R+EV+ +I + +V V+G +++   + +    + I V G  L   + 
Sbjct: 2   ERLDKILANLGYGTRKEVKALIKKGQVDVDGEVVKDNGMQIDPEKNKIFVFGKELVYKKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  T  + D                  VGRLD NT GLLLLTNDG L  
Sbjct: 62  IYLMMNKPQGVVSATFDNYDETIVDLLEDEDRIFEPFPVGRLDKNTVGLLLLTNDGELNH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     ++Y  + + +V  + +   KKGIV+         ++ +       + V V
Sbjct: 122 RLISPKWHVDKIYYAKINKKVTDEDIEKFKKGIVLDDGYECFPAKLEIIKSFNEESEVRV 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++FE  + KV  L R  +GP +L   L  G  RE++ + +
Sbjct: 182 TIHEGKFHQVKRMFESVDKKVIYLKREEFGPLKLDESLEEGQYRELTDEEI 232


>gi|167648594|ref|YP_001686257.1| RNA-binding S4 domain-containing protein [Caulobacter sp. K31]
 gi|167351024|gb|ABZ73759.1| RNA-binding S4 domain protein [Caulobacter sp. K31]
          Length = 501

 Score =  185 bits (470), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 136/353 (38%), Positives = 189/353 (53%), Gaps = 7/353 (1%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            ++    RV+K++ARAG+ASRR VER+I   RV +NG +L   A+ V   D + VDG  +
Sbjct: 18  DDDGEGARVAKMLARAGVASRRAVERLIEDGRVALNGEVLTTPAIKVRPGDILTVDGKMI 77

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            + E TR++ YHKP GL+TTH+DP  R TVF  LP    R+ISVGRLD+N+EGLLLLTND
Sbjct: 78  DEPEATRVFRYHKPSGLMTTHNDPKQRPTVFQALPRDLPRLISVGRLDLNSEGLLLLTND 137

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---- 183
           G L+R LE+P   W+R YR R  G   Q KL+ LK G  ++G+ YG ++  LD  +    
Sbjct: 138 GALSRALEMPQNAWVRRYRARAFGDTTQAKLDKLKDGCTVEGVRYGPIEARLDKAQEKAG 197

Query: 184 -GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            G N W+T+ L EGKNRE+++V E    KVNRLIR+SYGPF LGTLL G   EV  +++R
Sbjct: 198 GGKNIWITLTLSEGKNREVRRVLESIGLKVNRLIRLSYGPFALGTLLPGQVEEVGPRVIR 257

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E L   + EE     D P +        +    +   D   R    +++   +S      
Sbjct: 258 ELLEGIVAEENMPKGDKPQF-IGVADPLKAVGTAGGGDMQRRGVPRTNKLTQVSIITPEE 316

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR-RTSAKK 354
                + +    W       + +     R             + L  R +A K
Sbjct: 317 PVEEEKFVRKPGWAKPKKKPAIVGREPVRTAKKSIESKMIGPKPLSYRDAAAK 369



 Score = 36.3 bits (82), Expect = 7.0,   Method: Composition-based stats.
 Identities = 16/111 (14%), Positives = 22/111 (19%), Gaps = 5/111 (4%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ-----KK 300
            P   ++          S   L   R N    + +   R            K        
Sbjct: 390 KPARPDKPAGQPSGGHTSKPKLGALRANGYKPLTEGPARSAGKPGGARPGGKPSTVKAAG 449

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
              P     + S   MAK          G      +     P   S  R  
Sbjct: 450 AGKPGEPGKVWSKPGMAKSAGPRPDGPKGPPRAGGKPGGPRPGGSSAPRGK 500


>gi|330719107|ref|ZP_08313707.1| 16S rRNA uridine-516 pseudouridylate synthase [Leuconostoc fallax
           KCTC 3537]
          Length = 252

 Score =  185 bits (470), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 86/237 (36%), Positives = 131/237 (55%), Gaps = 2/237 (0%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + E    +R+ KVIA+AG+ASRR  E +I + RV VNG  ++     V  +D + VDGVP
Sbjct: 1   MSEIQNEERLQKVIAQAGLASRRGAEALIVEGRVSVNGQQVKELGTKVRRSDTVAVDGVP 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +   ER   +L +KP G+VTT  D  GR+TV D L  +  RV  VGRLD +T G LLLTN
Sbjct: 61  IEGRERLVYYLLNKPRGVVTTTQDEKGRATVLDILDDVSQRVYPVGRLDYDTTGALLLTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKG 184
           DG +A  L  P ++  +VY  +  G   ++ L  LKKG++I+G      +V+++   +  
Sbjct: 121 DGTIANELMHPKSKVDKVYIAKVKGMATENDLLPLKKGVMIEGHKTQPARVSVESVDKTK 180

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             + V + + EGKN ++K +     + V +L R  Y    L  L  G  R+++   +
Sbjct: 181 KTSMVKLIIHEGKNHQVKNMLAKVGFPVEKLKREQYAFLDLVGLQPGEYRKLTNAEV 237


>gi|154484655|ref|ZP_02027103.1| hypothetical protein EUBVEN_02372 [Eubacterium ventriosum ATCC
           27560]
 gi|149734503|gb|EDM50420.1| hypothetical protein EUBVEN_02372 [Eubacterium ventriosum ATCC
           27560]
          Length = 245

 Score =  185 bits (470), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 70/249 (28%), Positives = 112/249 (44%), Gaps = 10/249 (4%)

Query: 1   MKDKNIVQEN---FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M+    ++E        R++K ++ AG  SRRE +R++ Q  VKVNG         V   
Sbjct: 1   MEQNIRLKEKKSADEQIRLNKFLSDAGYCSRREADRLVEQGVVKVNGKTA-VMGQKVTIN 59

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           D I V G  + + E   L   +KP+G+  T    +       +  +   RV  +GRLD N
Sbjct: 60  DSIMVKGKNISREEEQILIALNKPVGIECTTDLNN--PDNIVDFINFDKRVYPIGRLDKN 117

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           ++GL+LLTNDG +   +   S    + Y V     V  D +  +  G+ I        +V
Sbjct: 118 SQGLILLTNDGSIVNNILKGSNYHEKEYVVTVDKPVTDDFIKKMSTGVRILDQVTRPCKV 177

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           T    K       + L +G NR+I+++     + V +L RI     +LG L  G  R+V+
Sbjct: 178 T----KVKKHVFNIVLTQGLNRQIRRMCGELGYNVQKLKRIRIMNIELGNLPVGQYRKVT 233

Query: 238 KKILREQLG 246
              L+E + 
Sbjct: 234 DSELKELMR 242


>gi|168186069|ref|ZP_02620704.1| RNA pseudouridine synthase family protein [Clostridium botulinum C
           str. Eklund]
 gi|169295997|gb|EDS78130.1| RNA pseudouridine synthase family protein [Clostridium botulinum C
           str. Eklund]
          Length = 238

 Score =  185 bits (470), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 56/232 (24%), Positives = 111/232 (47%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV++  G  SR+E++ ++ +  ++++G +++   + V      I+V+G  +   + 
Sbjct: 2   ERLDKVLSNLGYGSRKEIKALVKKGEIEIDGKVIKDNGLKVDPNKSIIKVNGEKINYRKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      +  T  + D       +          VGRLD +TEGLL++TNDG L  
Sbjct: 62  IYIMMNKPAGVVSATFDNYDETVIDLLDYEYTVFDPFPVGRLDKDTEGLLIITNDGELNH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     ++Y      +VD+  +   +KGI +         ++ + +   + + V V
Sbjct: 122 RLTSPKWHVDKIYYAEIDKRVDEKDVEKFEKGITLDDGYKCLPAKLEILSADENGSEVNV 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            ++EGK  ++K++FE  + KV  L R+  G   L   L  G  RE+++K + 
Sbjct: 182 IIQEGKFHQVKRMFEARDKKVVYLKRLKMGNISLDNELEEGEYRELTEKEIE 233


>gi|262382422|ref|ZP_06075559.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           2_1_33B]
 gi|262295300|gb|EEY83231.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           2_1_33B]
          Length = 334

 Score =  185 bits (470), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 57/241 (23%), Positives = 113/241 (46%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K K ++ +   P R++K ++ AG+ SRRE +  I +  VKVN +++      +   D +
Sbjct: 86  IKYKEVLADPNEPIRLNKFLSNAGVCSRREADEFIQKGAVKVNDVVVTELGTKITRQDVV 145

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
             +  P++   +  + L      + T+    +  + +     +   R+  VGRLD NT G
Sbjct: 146 TFNEKPVQIESKVYIVLNKPKNCVTTSDDPQERLTVMDLVKNACQERIYPVGRLDRNTTG 205

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  PS +  ++Y V     V  + +  +  G+ ++            
Sbjct: 206 VLLLTNDGDLASKLTHPSFKKKKIYHVWLDKNVAIEDMEKIANGLELEDGEIH-ADAISY 264

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             +   + V + +  G+NR ++++FE   + V +L R+ +       L  G  R ++++ 
Sbjct: 265 ASEDDKSQVGIEIHSGRNRIVRRIFESLGYHVTKLDRVYFAGLTKKNLGRGKWRYLNERE 324

Query: 241 L 241
           +
Sbjct: 325 V 325


>gi|227889866|ref|ZP_04007671.1| pseudouridylate synthase [Lactobacillus johnsonii ATCC 33200]
 gi|227849730|gb|EEJ59816.1| pseudouridylate synthase [Lactobacillus johnsonii ATCC 33200]
          Length = 244

 Score =  185 bits (470), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 77/237 (32%), Positives = 122/237 (51%), Gaps = 3/237 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           ++ +   +R+ KVIA+AGIASRR+ E+MI   +V VNG  +      V  +D IEV+GVP
Sbjct: 1   MRVSKMAERLQKVIAQAGIASRRKAEKMITAGQVTVNGKKVTELGTKVEPSDKIEVNGVP 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           + K        Y     + +   D  GR TV D    +  R+  VGRLD +T GLLL+TN
Sbjct: 61  IEKEALHTYLFYKPRGVISSVS-DDKGRKTVVDFFEDVPYRLYPVGRLDYDTSGLLLMTN 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKG 184
           DG LA  L  P  +  +VY  +  G +  +++  L  G+ I G      ++ +    +K 
Sbjct: 120 DGELANKLMHPRNEVPKVYVAKIKGILSPEEIRSLTHGVRIDGRKSAPAKLKILKTDEKK 179

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
               V + + EG   ++K++FE  +  V +L R  Y    L +L +G  RE++ + +
Sbjct: 180 KTQIVQLTIHEGHYHQVKRMFEAVHHFVEKLAREKYAFLTLKSLNSGEYRELTNEEV 236


>gi|312622236|ref|YP_004023849.1| pseudouridine synthase [Caldicellulosiruptor kronotskyensis 2002]
 gi|312202703|gb|ADQ46030.1| pseudouridine synthase [Caldicellulosiruptor kronotskyensis 2002]
          Length = 240

 Score =  185 bits (470), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 75/228 (32%), Positives = 118/228 (51%), Gaps = 2/228 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A+ G+ASRR+ E +I Q RVKVNG L+ +    V    D +EVDG  +    +
Sbjct: 5   VRLQKFMAQCGVASRRKCEEIILQGRVKVNGELVNQLGFKVDPEKDVVEVDGKRISPQMQ 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G++++  D  GR TV D +    +     VGRLD +T GL+LLTNDG  A
Sbjct: 65  KVYIMLNKPFGVISSAKDEKGRKTVVDLVKDKVNVRVFPVGRLDFDTTGLILLTNDGEFA 124

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P     + Y     G   + ++   +KG++I G      +  +      NA V +
Sbjct: 125 YKVTHPKHDIEKTYIALIKGIPSKKEIERFEKGLLIDGKMTAPAKFKILKLINGNALVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG+NR+I+K+ +    KV +L RI+ G  QLG L  G    + ++
Sbjct: 185 KIHEGRNRQIRKMCDQIGHKVLKLKRIAIGKLQLGKLKEGEFVFLDRE 232


>gi|210623378|ref|ZP_03293775.1| hypothetical protein CLOHIR_01725 [Clostridium hiranonis DSM 13275]
 gi|210153639|gb|EEA84645.1| hypothetical protein CLOHIR_01725 [Clostridium hiranonis DSM 13275]
          Length = 241

 Score =  185 bits (470), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 62/234 (26%), Positives = 107/234 (45%), Gaps = 4/234 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
             QRV KV++  G  SR E+++   Q  V VNG  +    + V +  D I  +G  +   
Sbjct: 3   KKQRVDKVLSNLGYGSRAELKKFCKQGLVFVNGKAVSNPGLQVDTDIDEIVFNGEKINYR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L +      +  T    D       +   +      VGRLD +TEGLL+LTNDG L
Sbjct: 63  EFIYLMMNKPDGYISATFDKHDPIVLDLIDDEYLVFEPFPVGRLDKDTEGLLVLTNDGQL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWV 189
           A  +  P     + Y  +  G+V ++ +   K+G+V+         ++ +  +    + +
Sbjct: 123 AHRVLSPKKHVPKTYYAKIDGKVTEEDIEAFKQGVVLDDGYETMPSELVIL-KSDDISEI 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            + + EGK  ++K++FE     V  L R+S G  +L   L  G  RE++ + ++
Sbjct: 182 ELTIHEGKFHQVKRMFESVGKTVVYLKRLSMGALKLDETLELGEYRELTDEEVK 235


>gi|206900740|ref|YP_002251175.1| ribosomal large subunit pseudouridine synthase B [Dictyoglomus
           thermophilum H-6-12]
 gi|206739843|gb|ACI18901.1| ribosomal large subunit pseudouridine synthase B [Dictyoglomus
           thermophilum H-6-12]
          Length = 241

 Score =  185 bits (470), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 68/232 (29%), Positives = 120/232 (51%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K IA+AG+ SRR+ E++I + RVKVNG ++    V +    D +E+D   ++  ++
Sbjct: 3   ERLQKFIAKAGVTSRRKAEKLILEGRVKVNGEVIRTLGVKIDPEKDIVEIDNKIVKPDKK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + LY     + + +     R+        +  RV  VGRLD ++EGLLL TNDG +A 
Sbjct: 63  IYIALYKPVGYISSLYDPFGRRTIKDLLRDKVPFRVYPVGRLDFDSEGLLLCTNDGEIAN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
           VL  P  +  +VY V   G   +++L  L++G++++          +  +      + + 
Sbjct: 123 VLIHPRYKIPKVYEVLIDGIPKEEELKKLREGVILEEGRTLPAGFEIIWENRRKNISLLK 182

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + L +G  R+I+++   FN+KV  L R+  G  +LG L  G  R +    +R
Sbjct: 183 ITLYQGWKRQIRRMLALFNYKVLNLKRVQIGKIKLGDLKPGEIRFLRDDEIR 234


>gi|269925805|ref|YP_003322428.1| pseudouridine synthase [Thermobaculum terrenum ATCC BAA-798]
 gi|269789465|gb|ACZ41606.1| pseudouridine synthase [Thermobaculum terrenum ATCC BAA-798]
          Length = 253

 Score =  185 bits (470), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 85/243 (34%), Positives = 129/243 (53%), Gaps = 4/243 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+ K++A+ G+ASRR  ERMIA+ RV VNG ++          D I VDG  +R+ 
Sbjct: 2   NEPIRLHKLLAQMGVASRRAAERMIAEGRVSVNGRIVNTPGAMASPEDEIRVDGKLVRQQ 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            + R  L +KP G+++T  D  GR TV D L    +RV  VGRLD ++EGL+LLTNDG L
Sbjct: 62  PKMRYILLNKPAGVLSTAKDERGRKTVIDLL-GQSNRVYPVGRLDKDSEGLMLLTNDGEL 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A+ +  P     + Y V   G      L  L +G+ ++      +   + ++    + + 
Sbjct: 121 AQRITHPRYGVHKQYMVEVEGYFSDRSLQDLLQGVELEDGFSKPLDAKIISRSRDKSKLL 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI---LREQLGP 247
           + + EG+ R++++      +KV RL R++ GP  LG L  G  RE+S +    LR QLG 
Sbjct: 181 ITMGEGRKRQVRRTLAALGYKVKRLTRVALGPLSLGNLKPGEYRELSDQEAKWLRSQLGL 240

Query: 248 HLL 250
              
Sbjct: 241 TPE 243


>gi|228903228|ref|ZP_04067361.1| Pseudouridine synthase [Bacillus thuringiensis IBL 4222]
 gi|228967810|ref|ZP_04128824.1| Pseudouridine synthase [Bacillus thuringiensis serovar sotto str.
           T04001]
 gi|228791860|gb|EEM39448.1| Pseudouridine synthase [Bacillus thuringiensis serovar sotto str.
           T04001]
 gi|228856402|gb|EEN00929.1| Pseudouridine synthase [Bacillus thuringiensis IBL 4222]
          Length = 242

 Score =  185 bits (469), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 105/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G  ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L ++     +  T  D          L         VGRLDI+TEG LL+TNDG L+ 
Sbjct: 61  VYLMMHKPQGVISATEDDNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKLSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G V ++ +    KG+++          +T+  +    + + +
Sbjct: 121 QLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGTLTIL-KSDDISEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 180 VITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 231


>gi|163733415|ref|ZP_02140858.1| RNA pseudouridylate synthase family protein, putative [Roseobacter
           litoralis Och 149]
 gi|161393203|gb|EDQ17529.1| RNA pseudouridylate synthase family protein, putative [Roseobacter
           litoralis Och 149]
          Length = 285

 Score =  185 bits (469), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 141/284 (49%), Positives = 178/284 (62%), Gaps = 2/284 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           +      R++KV++RAG+ASRRE ERMI   RVKVNG  +   A+NV  TD I VDG  +
Sbjct: 4   EPTPQGDRIAKVLSRAGVASRREAERMIEAGRVKVNGQHISSPALNVQGTDKITVDGKEV 63

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              E  RLWLYHKP GLVTT +D  GR T++  LP    RV+SVGRLDIN+EGLLLLTND
Sbjct: 64  SPPEPARLWLYHKPTGLVTTDNDEKGRETIYSALPEDMPRVMSVGRLDINSEGLLLLTND 123

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GG+ R LELP+T WLR YRVR +G+     L+ L++GI  +G  +  MQ+TLD Q+G+NA
Sbjct: 124 GGVKRRLELPTTGWLRRYRVRINGRPTDATLDPLRRGISSEGENFQPMQITLDRQQGANA 183

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+TVGLREGKNREI++     +  VNRLIRISYGPFQLG L  G+  EV +KILR+QLG 
Sbjct: 184 WLTVGLREGKNREIRRALAELDLSVNRLIRISYGPFQLGELKPGAVEEVRRKILRDQLGL 243

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
               E                 +     +  P    +  K   +
Sbjct: 244 EGEVEESAPKHPDAGK--KRGPNVNRTRTAAPGKSFKHTKKPRK 285


>gi|325292073|ref|YP_004277937.1| ribosomal large subunit pseudouridine synthase B [Agrobacterium sp.
           H13-3]
 gi|325059926|gb|ADY63617.1| ribosomal large subunit pseudouridine synthase B [Agrobacterium sp.
           H13-3]
          Length = 658

 Score =  185 bits (469), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 169/343 (49%), Positives = 217/343 (63%), Gaps = 3/343 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P+R+SK++ARAG+ASRR++ERMI + RV +NG+ L+   +N   +D IEVDG+P+R A
Sbjct: 50  TKPERISKIMARAGVASRRDIERMIMEGRVSLNGVKLDTPVMNATLSDKIEVDGMPIRGA 109

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ERTRLWLYHKP GLVTT+SDP+GR TVFDNLP    RV+S+GRLDINTEGLLLLTNDGGL
Sbjct: 110 ERTRLWLYHKPAGLVTTNSDPEGRPTVFDNLPGELPRVLSIGRLDINTEGLLLLTNDGGL 169

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +RVLELP+T WLR YRVR HG+VDQ  L+ LK+GI + G+ YG +  TLD  +G N W+T
Sbjct: 170 SRVLELPTTGWLRRYRVRAHGEVDQAALDKLKEGIAVDGVLYGAIDATLDRTQGHNVWIT 229

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           +GLREGKNREIK V      +VNRLIRISYGPFQLG L  G   EV  ++LR+QLGP L+
Sbjct: 230 MGLREGKNREIKNVLGALGLEVNRLIRISYGPFQLGDLPEGKVLEVRGRMLRDQLGPRLI 289

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           E++  N DAPIY +     +  N     P         S    G  +  + A     R  
Sbjct: 290 EQSGANFDAPIYDAPVADDEEENTPKRAP---RSEWAKSDAPEGKPRFDRAAGKPEDRRE 346

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            +   +            G +      + +   +    R  A+
Sbjct: 347 KALGRLDTKRGDKPAGKFGGKPAGKFGAKTRGEEDGEERRPAR 389



 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 9/102 (8%), Positives = 23/102 (22%), Gaps = 2/102 (1%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR--R 308
                      +  +               + +   + +  +    ++     P     R
Sbjct: 515 ARGGKPFGDRPFRDKPREEGDRPRSDRPRGEKSFGDRTARGEKPFGERPFRDKPREDGDR 574

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                 +  K   +      G R  + + S   P +R  R  
Sbjct: 575 PRGDRPFGDKPRGAKSGGKPGGRPASGKPSFGKPGERGERSG 616


>gi|290475237|ref|YP_003468123.1| Ribosomal large subunit pseudouridine synthase F [Xenorhabdus
           bovienii SS-2004]
 gi|289174556|emb|CBJ81350.1| Ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Xenorhabdus bovienii SS-2004]
          Length = 290

 Score =  185 bits (469), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 63/291 (21%), Positives = 119/291 (40%), Gaps = 6/291 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +   + 
Sbjct: 6   SIRLNKYISESGICSRRDADRYIEQGNVFINGKRAAV-GDQVFAGDIVKVNGQLIEPRDE 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L      +    +  D       +  +   RV  +GRLD +++GL+ LTN G L  
Sbjct: 65  EDLVLIALNKPVGIITTMEDSERDNISDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  V  + +  +  G+ + G      +V    QK ++    + 
Sbjct: 125 KILRAGNNHEKEYVVTVNKPVTDEFIQGMSAGVPMLGTVTKKCKV----QKEASFVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ + F ++V RL R       L  L  G  R+++   L E     +   
Sbjct: 181 LVQGLNRQIRRMCKHFGYEVTRLERTRIMNVNLKGLPQGEWRDLTDDELIELFKL-IENS 239

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           +     A    ++ +   +         + +     S ++   S +KK   
Sbjct: 240 SSEEKSAKKAQTKHVTAKKTGFNEPKNAEKSDGNSASRKRFTQSGRKKKGR 290


>gi|84501543|ref|ZP_00999715.1| RNA pseudouridylate synthase family protein [Oceanicola batsensis
           HTCC2597]
 gi|84390164|gb|EAQ02723.1| RNA pseudouridylate synthase family protein [Oceanicola batsensis
           HTCC2597]
          Length = 331

 Score =  185 bits (469), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 143/325 (44%), Positives = 190/325 (58%), Gaps = 2/325 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           ++     R++KV+ARAG+ASRRE ERMIA+ R+ V+G +++  A+NV +   IEVDG PL
Sbjct: 6   EKPPAGDRIAKVLARAGVASRREAERMIAEGRISVDGTVIDSPALNVTARARIEVDGRPL 65

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              E  RLWLYHKP GLVTTH D  GR T+FD+LP    RV+SVGRLD+N+EGLLLLTND
Sbjct: 66  DAPEPARLWLYHKPPGLVTTHKDDQGRPTIFDDLPEDMPRVMSVGRLDLNSEGLLLLTND 125

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GG+ R LELPST WLR YRVR  G      L  L++G+V+    +  MQVTLD Q+G+NA
Sbjct: 126 GGIKRRLELPSTGWLRRYRVRVKGTPTDATLAPLREGVVVDREIFQPMQVTLDRQQGANA 185

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+TVGLREGKNREI++  E     VNRLIRISYGPFQLG L  G+  EV ++++R+QLG 
Sbjct: 186 WLTVGLREGKNREIRRAMESIGLSVNRLIRISYGPFQLGPLAPGAVEEVRRRVMRDQLGL 245

Query: 248 HLLEEAQVNLDAPIY--SSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
              E              +    + R  + +      +   +        +  +    P 
Sbjct: 246 DDAEADAPRPKRSRAGQRTGPETKTRDKVRARTGGKTSGGGRTPDAPVPEAPWETRPKPR 305

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQ 330
            +         A+           +
Sbjct: 306 GKPPGPDGSGKARPRPHVTRRRRKK 330


>gi|310816564|ref|YP_003964528.1| ribosomal large subunit pseudouridine synthase B
           [Ketogulonicigenium vulgare Y25]
 gi|308755299|gb|ADO43228.1| ribosomal large subunit pseudouridine synthase B
           [Ketogulonicigenium vulgare Y25]
          Length = 649

 Score =  185 bits (469), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 155/343 (45%), Positives = 199/343 (58%), Gaps = 7/343 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++KV+ARAGIASRR+VERMI   RV VNG ++   AVNV   D + VDG P+  AE
Sbjct: 18  TGERIAKVLARAGIASRRDVERMILDGRVSVNGKVINSPAVNVADRDRVSVDGQPVAAAE 77

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             RLWLYHKP GLVTT+ D  GR TVFD LP    RV++VGRLD+ +EGLLLLTNDG + 
Sbjct: 78  PPRLWLYHKPSGLVTTNKDELGRETVFDALPEDLPRVMTVGRLDLTSEGLLLLTNDGEVK 137

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           R LELP+T WLR YRVR +G+V + +L+ L+ GI +  I Y  M V LD Q+G+NAW+T+
Sbjct: 138 RKLELPATGWLRRYRVRVNGEVTEPELDKLRAGITVDDIEYQPMDVELDRQQGANAWLTI 197

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
           GLREGKNREI++V E   + VNRLIRISYGPFQLG L AG  +EV +K+LR+QLG     
Sbjct: 198 GLREGKNREIRRVMEALGFVVNRLIRISYGPFQLGALEAGEVQEVRRKVLRDQLGLDQDA 257

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
                    I + + +           P      K +  + +   +      P       
Sbjct: 258 PDLQRSRRIIRNEKIVDETPKRGRPAKPGFKPGAKPSGDRPSYGDRPSFGDKPR------ 311

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                 +G   SF       ++     PSF  K    R    K
Sbjct: 312 -FGDKPRGDRPSFGDKPRFGDKPRGDRPSFGDKPRGDRPYGDK 353



 Score = 37.1 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 10/106 (9%), Positives = 18/106 (16%), Gaps = 1/106 (0%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
                 G       +               D+P       D     +    +  G     
Sbjct: 545 EGDAPRGERKSFGDKPRFGDKPRGDRPSFGDKPRGDRPYGDKPRGDRPYGDKPRGDR-PS 603

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
               P    +        +G   S         +   R P     +
Sbjct: 604 FGDKPRSFGDKPRFGDKPRGDRPSGDRRPSGAPQGGNRRPPRRDDK 649


>gi|295426293|ref|ZP_06818953.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           amylolyticus DSM 11664]
 gi|295064032|gb|EFG54980.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           amylolyticus DSM 11664]
          Length = 239

 Score =  185 bits (469), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 81/231 (35%), Positives = 123/231 (53%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGIASRR+ E+MI   RV+V+G L+ +    V +   I VD  P+ +    
Sbjct: 4   ERLQKVIAEAGIASRRKAEKMIVAGRVRVDGKLVTKLGTKVDTFSTITVDDEPIERESLH 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     +V+T  D  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA +
Sbjct: 64  TYLFYKPRG-VVSTAHDDKGRKTVVDYFDDLPYRLYPVGRLDYDTSGLLLMTNDGKLANL 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           L  P  +  +VY  +  G ++ D++  LKKG+ + G      +V +    QK +N  V +
Sbjct: 123 LMHPKNEVPKVYVAKIEGILEPDQIMTLKKGVKVDGRKCAPAKVKILKTNQKKNNQIVQL 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EG   E+K++F+     V +L R  Y    L  L  G  RE++++ + 
Sbjct: 183 TIHEGHYHEVKRMFKAVGHPVEKLSRERYAFLDLHALTYGQYRELTREEVD 233


>gi|229019939|ref|ZP_04176733.1| Pseudouridine synthase [Bacillus cereus AH1273]
 gi|229026174|ref|ZP_04182538.1| Pseudouridine synthase [Bacillus cereus AH1272]
 gi|228735102|gb|EEL85733.1| Pseudouridine synthase [Bacillus cereus AH1272]
 gi|228741357|gb|EEL91563.1| Pseudouridine synthase [Bacillus cereus AH1273]
          Length = 242

 Score =  185 bits (469), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 59/232 (25%), Positives = 103/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G  ++    +V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGHGSRKEVKKLLKDGVVKIDGTPVKDPKFHVNVEEQEVMIHGEVVEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L ++     +  T  D          L         VGRLDI+TEG LL+TNDG L  
Sbjct: 61  VYLMMHKPQGVISATEDDNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKLTH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G V ++ +    KG++++         +T+  +    + + +
Sbjct: 121 QLLSPKKHVPKKYYAHVSGVVTEEDVKEFAKGVILEDGYETKPGDLTIL-KSDDISEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 180 VITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 231


>gi|227879091|ref|ZP_03996980.1| pseudouridylate synthase [Lactobacillus crispatus JV-V01]
 gi|256843080|ref|ZP_05548568.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           crispatus 125-2-CHN]
 gi|256850268|ref|ZP_05555697.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           crispatus MV-1A-US]
 gi|262046340|ref|ZP_06019302.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           crispatus MV-3A-US]
 gi|293379763|ref|ZP_06625895.1| pseudouridine synthase [Lactobacillus crispatus 214-1]
 gi|295692876|ref|YP_003601486.1| pseudouridine synthase [Lactobacillus crispatus ST1]
 gi|312977265|ref|ZP_07789013.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           crispatus CTV-05]
 gi|227861332|gb|EEJ68962.1| pseudouridylate synthase [Lactobacillus crispatus JV-V01]
 gi|256614500|gb|EEU19701.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           crispatus 125-2-CHN]
 gi|256712905|gb|EEU27897.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           crispatus MV-1A-US]
 gi|260573211|gb|EEX29769.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           crispatus MV-3A-US]
 gi|290923672|gb|EFE00543.1| pseudouridine synthase [Lactobacillus crispatus 214-1]
 gi|295030982|emb|CBL50461.1| Pseudouridine synthase [Lactobacillus crispatus ST1]
 gi|310895696|gb|EFQ44762.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           crispatus CTV-05]
          Length = 238

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 71/236 (30%), Positives = 117/236 (49%), Gaps = 3/236 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGIASRR+ E+MI   RVKV+G ++ +    V +  +I VD  P+ +    
Sbjct: 3   ERLQKVIAEAGIASRRKAEKMIVAGRVKVDGHVVTKLGTKVDTFSNITVDDEPIERESLH 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     + T   D   ++ V      +  R+  VGRLD +T GLLL+TNDG LA +
Sbjct: 63  TYLFYKPRGVVSTAEDDRGRKTVVDYF-EDLPYRLYPVGRLDYDTSGLLLMTNDGKLANL 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           L  P  +  +VY  +  G +  D++  L +G+ +        +V +           V +
Sbjct: 122 LMHPKNEVAKVYVAKIKGILTPDEIKTLTQGVKLDHFKAAPAKVKVLKTDHKKDTQIVQI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + EG   ++K++F+     V++L R  Y    L +L +G  RE+SK  + + +  
Sbjct: 182 TIHEGHYHQVKRMFKAVGHLVDKLAREKYAFLTLDSLTSGQYRELSKHEVDKLMQL 237


>gi|126699667|ref|YP_001088564.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile 630]
 gi|255101182|ref|ZP_05330159.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile QCD-63q42]
 gi|255307056|ref|ZP_05351227.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile ATCC 43255]
 gi|115251104|emb|CAJ68935.1| Ribosomal large subunit pseudouridine synthase B [Clostridium
           difficile]
          Length = 238

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 70/232 (30%), Positives = 120/232 (51%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R++K IA  GIASRR+ E +I   R+KVNG +++  + N+    D +E D   ++ +E 
Sbjct: 1   MRINKYIASCGIASRRKAEEIILGGRIKVNGSVVKELSFNIDEEKDIVEFDNKKVKPSEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G +TT  D   R +V D L  +  RV  +GRLD  T GLL+LTNDG L  
Sbjct: 61  YIYIVLNKPEGYITTVKDQFNRPSVIDILKDVRERVYPIGRLDYETSGLLILTNDGDLTY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVT 190
            L  P  +  + Y     G +  D++   + G+ I+       ++ +  + ++ + +   
Sbjct: 121 KLTHPKHEIDKTYVASVKGIISDDEIRQFETGLKIEDYTTAPAKIRVTKENKEKNYSVCE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + + EG+NR+++K+ +  N  V  L RIS G   L     G  R +++  ++
Sbjct: 181 ITIHEGRNRQVRKMCKAINHPVLNLRRISVGKIVLKDTKVGEYRYLTEDEIK 232


>gi|83952774|ref|ZP_00961504.1| RNA pseudouridylate synthase family protein [Roseovarius
           nubinhibens ISM]
 gi|83835909|gb|EAP75208.1| RNA pseudouridylate synthase family protein [Roseovarius
           nubinhibens ISM]
          Length = 268

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 139/268 (51%), Positives = 175/268 (65%), Gaps = 1/268 (0%)

Query: 7   VQENFTP-QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + E   P  R++KVIARAG+ASRRE ERM+   RV VNG  ++  A+NV  +D I VDG 
Sbjct: 1   MSETPPPGDRIAKVIARAGLASRREAERMVEAGRVTVNGRKIDSPALNVTPSDKITVDGR 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            L   E  RLWLYHKP GLVTT  D  GR T+FD LP    RV+SVGRLD+N+EGLLLLT
Sbjct: 61  ALATPEPPRLWLYHKPTGLVTTTRDEQGRDTIFDKLPEDLPRVMSVGRLDLNSEGLLLLT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDGG+ R LELPST WLR YRVR +G+ +      L+KG+ ++G  +  MQVTLD Q+G+
Sbjct: 121 NDGGIKRRLELPSTGWLRRYRVRVNGRPNDATFEPLRKGVTLEGERFQPMQVTLDRQQGA 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           NAW+TV +REGKNREI++  E     VNRLIR+SYGPFQLG L +G   E+  +++REQL
Sbjct: 181 NAWITVAIREGKNREIRRAMESVGLSVNRLIRVSYGPFQLGQLKSGEVEEIRPRVMREQL 240

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPN 273
           G    E  +              + R  
Sbjct: 241 GLTEEEAGRTPGPQAKAKPRGKPQRRRK 268


>gi|119945902|ref|YP_943582.1| pseudouridine synthase [Psychromonas ingrahamii 37]
 gi|119864506|gb|ABM03983.1| ribosomal large subunit pseudouridine synthase F [Psychromonas
           ingrahamii 37]
          Length = 318

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 69/286 (24%), Positives = 115/286 (40%), Gaps = 12/286 (4%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           NIV  N    R++K I+ +G  SRRE +++I Q RVK+NG +       V   D + VDG
Sbjct: 15  NIVDNNSE-IRLNKFISDSGFCSRREADKLIEQNRVKINGDIP-ELGTKVQLGDLVLVDG 72

Query: 65  VPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
             +  + +        +Y+KPIG+  T       + +         R+  +GRLD  +EG
Sbjct: 73  KRINASAQDKLDRIYIVYNKPIGITCTTERHIHGNIINAI--GHKKRIFPIGRLDKPSEG 130

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+ LT+DG +   +        + Y V     + +  +  +++G+ I        +VT+D
Sbjct: 131 LIFLTSDGDIVNKILRAENAHDKEYLVTVDKPLSERFVERMQRGVPILDTITKPCKVTVD 190

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
               S     + L +G NR+I+++ E   ++V +L R       LG L  G  R ++   
Sbjct: 191 ----SRFIFRIVLTQGLNRQIRRMCEHLGYEVLKLKRTRIMKVGLGNLKPGQWRNLTNIE 246

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
           L E               A   S                      K
Sbjct: 247 LAEINQAVSSSSKTATDPAKPVSKAPQSEAIKKSTGANNSHQPAKK 292


>gi|229169439|ref|ZP_04297147.1| Pseudouridine synthase [Bacillus cereus AH621]
 gi|228614044|gb|EEK71161.1| Pseudouridine synthase [Bacillus cereus AH621]
          Length = 248

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 60/237 (25%), Positives = 107/237 (45%), Gaps = 4/237 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPL 67
           +     R+ K++A  G  SR+EV++++    VK++G+ ++ A  +V      + + G  +
Sbjct: 2   KKVKNMRLDKLLANMGHGSRKEVKKLLKDGVVKIDGVPVKDAKFHVNVEEQEVMIHGEVV 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              E   L ++     +  T  D          L         VGRLDI+TEG LL+TND
Sbjct: 62  EYKEFVYLMMHKPQGVISATEDDNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITND 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSN 186
           G L   L  P     + Y     G V ++ +    KG++++        ++T+  +    
Sbjct: 122 GKLTHQLLSPKKHVPKKYYAHISGVVTEEDVIEFAKGVILEDGYETKPGELTIL-KSDDI 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + + + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 181 SEIELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLMLDEELELGQYRELTDEEVE 237


>gi|251796373|ref|YP_003011104.1| pseudouridine synthase [Paenibacillus sp. JDR-2]
 gi|247543999|gb|ACT01018.1| pseudouridine synthase [Paenibacillus sp. JDR-2]
          Length = 250

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 82/243 (33%), Positives = 128/243 (52%), Gaps = 4/243 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K++A+AG+ASRR+ E +I    V+VNG  +    V     TD I V+G P+R +E+
Sbjct: 5   ERLQKILAQAGVASRRKCEELILAGAVEVNGEKVTTLGVKADPATDEITVNGKPIR-SEK 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G++T+  DP GR  V D LP I  RV  VGRLD +TEGLLLLTNDG  A 
Sbjct: 64  KIYLMLNKPKGVITSAKDPQGRKVVADFLPGIRERVYPVGRLDYDTEGLLLLTNDGEFAN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
           +L  PS    + Y     G      L+ LKKG++++       +V           + + 
Sbjct: 124 LLTHPSHHVPKTYYATVKGVPHGSLLDQLKKGVMLEDGLTAPAEVEYQDIDEEKNMSTIR 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + + EG+NR+++++F+     V +L R+ +G   L TL  G  R ++   ++E       
Sbjct: 184 ITIYEGRNRQVRRMFDAIKHPVLKLRRVKFGELGLRTLARGQFRHLTPVEVKELRDQARK 243

Query: 251 EEA 253
              
Sbjct: 244 THK 246


>gi|118444164|ref|YP_878165.1| ribosomal large subunit pseudouridine synthase B [Clostridium novyi
           NT]
 gi|118134620|gb|ABK61664.1| ribosomal large subunit pseudouridine synthase B [Clostridium novyi
           NT]
          Length = 236

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 66/230 (28%), Positives = 110/230 (47%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K +A  G+ASRR+ E +I   RVKVNG ++      V    D + VD   +   E+
Sbjct: 3   ERLQKYMASCGVASRRKCEEIIISNRVKVNGTIVNELGFKVDPSKDKVYVDSKLIFLEEK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP G V+T  D   R T+  +L  +  R+  +GRLD NT GLLL+TNDG +  
Sbjct: 63  KVYIALNKPEGYVSTVKDERNRKTIM-DLVEVEERIFPIGRLDYNTSGLLLMTNDGDIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  +VY     G    ++++    G+ I           +  +    + V + 
Sbjct: 122 KIIHPRKEIDKVYIAIIKGVPSDEEIHKFCNGLDIGDYITSKANFEVIDKLEDKSKVRIT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGKNR+++++ +     V  L RIS G   L  L     R +++  ++
Sbjct: 182 IHEGKNRQVRRMCDKIGHPVIALKRISVGKISLNNLKRSQWRYLNESEIK 231


>gi|30022777|ref|NP_834408.1| ribosomal small subunit pseudouridine synthase A [Bacillus cereus
           ATCC 14579]
 gi|206969480|ref|ZP_03230434.1| RNA pseudouridine synthase family protein [Bacillus cereus AH1134]
 gi|218233459|ref|YP_002369504.1| RNA pseudouridine synthase family protein [Bacillus cereus B4264]
 gi|228923463|ref|ZP_04086748.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228954985|ref|ZP_04117002.1| Pseudouridine synthase [Bacillus thuringiensis serovar kurstaki
           str. T03a001]
 gi|228960980|ref|ZP_04122610.1| Pseudouridine synthase [Bacillus thuringiensis serovar pakistani
           str. T13001]
 gi|229048415|ref|ZP_04193982.1| Pseudouridine synthase [Bacillus cereus AH676]
 gi|229072210|ref|ZP_04205418.1| Pseudouridine synthase [Bacillus cereus F65185]
 gi|229081964|ref|ZP_04214455.1| Pseudouridine synthase [Bacillus cereus Rock4-2]
 gi|229129987|ref|ZP_04258951.1| Pseudouridine synthase [Bacillus cereus BDRD-Cer4]
 gi|229147277|ref|ZP_04275628.1| Pseudouridine synthase [Bacillus cereus BDRD-ST24]
 gi|229152907|ref|ZP_04281089.1| Pseudouridine synthase [Bacillus cereus m1550]
 gi|229181024|ref|ZP_04308359.1| Pseudouridine synthase [Bacillus cereus 172560W]
 gi|229192993|ref|ZP_04319949.1| Pseudouridine synthase [Bacillus cereus ATCC 10876]
 gi|296505173|ref|YP_003666873.1| ribosomal small subunit pseudouridine synthase A [Bacillus
           thuringiensis BMB171]
 gi|29898336|gb|AAP11609.1| Ribosomal small subunit pseudouridine synthase A [Bacillus cereus
           ATCC 14579]
 gi|206735168|gb|EDZ52336.1| RNA pseudouridine synthase family protein [Bacillus cereus AH1134]
 gi|218161416|gb|ACK61408.1| RNA pseudouridine synthase family protein [Bacillus cereus B4264]
 gi|228590440|gb|EEK48303.1| Pseudouridine synthase [Bacillus cereus ATCC 10876]
 gi|228602581|gb|EEK60067.1| Pseudouridine synthase [Bacillus cereus 172560W]
 gi|228630520|gb|EEK87167.1| Pseudouridine synthase [Bacillus cereus m1550]
 gi|228636178|gb|EEK92657.1| Pseudouridine synthase [Bacillus cereus BDRD-ST24]
 gi|228653431|gb|EEL09305.1| Pseudouridine synthase [Bacillus cereus BDRD-Cer4]
 gi|228701341|gb|EEL53836.1| Pseudouridine synthase [Bacillus cereus Rock4-2]
 gi|228710948|gb|EEL62915.1| Pseudouridine synthase [Bacillus cereus F65185]
 gi|228722930|gb|EEL74308.1| Pseudouridine synthase [Bacillus cereus AH676]
 gi|228798697|gb|EEM45680.1| Pseudouridine synthase [Bacillus thuringiensis serovar pakistani
           str. T13001]
 gi|228804712|gb|EEM51314.1| Pseudouridine synthase [Bacillus thuringiensis serovar kurstaki
           str. T03a001]
 gi|228836189|gb|EEM81545.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|296326225|gb|ADH09153.1| ribosomal small subunit pseudouridine synthase A [Bacillus
           thuringiensis BMB171]
          Length = 242

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 105/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G  ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L ++     +  T  D          L         VGRLDI+TEG LL+TNDG L+ 
Sbjct: 61  VYLMMHKPQGVISATEDDNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKLSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G V ++ +    KG+++          +T+  +    + + +
Sbjct: 121 QLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 180 VITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 231


>gi|329667453|gb|AEB93401.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           johnsonii DPC 6026]
          Length = 239

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 75/230 (32%), Positives = 119/230 (51%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AG+ASRR+ E+MI+  +V VNG  +      V  +D IEV+GVP+ K    
Sbjct: 3   ERLQKVIAQAGVASRRKAEKMISAGQVTVNGKKVTELGTKVEPSDKIEVNGVPIEKEALH 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                     + +   D  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  
Sbjct: 63  TYLFCKPRGVISSVS-DDKGRKTVVDFFEDVPYRLYPVGRLDYDTSGLLLMTNDGELANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           L  P  +  +VY  +  G +  +++  L  G+ I G      ++ +    +K     V +
Sbjct: 122 LMHPRNEVPKVYVAKIKGILSPEEIRSLTHGVRIDGRKSAPAKLKILKTDEKKKTQIVQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + EG   ++K++FE  +  V +L R  Y    L +L +G  RE++ + +
Sbjct: 182 TIHEGHYHQVKRMFEAVHHFVEKLAREKYAFLTLKSLNSGEYRELTNEEV 231


>gi|294678028|ref|YP_003578643.1| ribosomal large subunit pseudouridine synthase B [Rhodobacter
           capsulatus SB 1003]
 gi|294476848|gb|ADE86236.1| ribosomal large subunit pseudouridine synthase B [Rhodobacter
           capsulatus SB 1003]
          Length = 594

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 136/344 (39%), Positives = 193/344 (56%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T +R++KVIAR+G+ASRR+ E+MI   RV VNG  ++  A++V   D + +DG P+   
Sbjct: 15  DTAERIAKVIARSGVASRRDAEKMILAGRVTVNGKKVDSPALDVKPADKVAIDGKPIDAP 74

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TRLWLY+KP+GLVTT  D  GR T+FD +P    RV++VGRLD+N+EGLLLLTNDGGL
Sbjct: 75  QETRLWLYYKPLGLVTTEKDEQGRRTIFDEMPEEMPRVLNVGRLDLNSEGLLLLTNDGGL 134

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            R LELP T WLR YRVR +G+   +  + L++GI I G  +  M+V+LD Q+G+NAW+T
Sbjct: 135 KRRLELPETGWLRKYRVRVNGRPTTETFDPLRRGITIDGEDFQPMEVSLDRQQGANAWLT 194

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           VG+REGKNREI++        VNRLIR+SYGPF+L  +  G+  EV +K+LR+QLG  LL
Sbjct: 195 VGIREGKNREIRRAMGEVGMTVNRLIRVSYGPFRLNDMEPGAVVEVKRKMLRDQLGDRLL 254

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
              +                R         +  +         G    +K  +   + + 
Sbjct: 255 LGVEDGKPPRSERMAPKPGARRPRPEGGEGEERKGFGRQRDFAGAEGDRKPKSFGMKSHR 314

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                               R E+  R P  P     +  + ++
Sbjct: 315 EEGERKPFARREDGERKPYARREDGDRKPYAPRDGEKKPYARRE 358


>gi|172056824|ref|YP_001813284.1| pseudouridine synthase [Exiguobacterium sibiricum 255-15]
 gi|171989345|gb|ACB60267.1| pseudouridine synthase [Exiguobacterium sibiricum 255-15]
          Length = 231

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 56/229 (24%), Positives = 112/229 (48%), Gaps = 7/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+  G  SRR  +++I   RV +NG +       V  TD +E+DG PL+     
Sbjct: 1   MRINKFISETGYCSRRAADKLIDAGRVTINGNVA-ELGSQVEKTDAVEIDGQPLQPKPDL 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP+G+  T       + +  +  +  +R+  +GRLD +++GL++LTNDG +   
Sbjct: 60  EYLILNKPVGITCTTERDIEGNII--DFVNHPNRIFPIGRLDKDSDGLIILTNDGDIVNR 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V     + +  +  +  G+ I G    +       ++  +    + L
Sbjct: 118 ILRAENNHDKEYIVTVDAPITETFIEGMAGGVDILGTTTKEC----VVEQLESRTFRIVL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ + F ++V RL R+     +LG L  G  R++++  ++
Sbjct: 174 TQGLNRQIRRMCKEFGYRVKRLQRVRIMNIELGDLPIGEWRDLTESEMK 222


>gi|302333165|gb|ADL23358.1| ribosomal large subunit pseudouridine synthase B, RluB
           [Staphylococcus aureus subsp. aureus JKD6159]
          Length = 245

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 78/243 (32%), Positives = 129/243 (53%), Gaps = 3/243 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R+ K IA +G  SRR+ E +I++ +VKVNG  +      V  +D IEV+G+ +  
Sbjct: 2   TKELERLQKRIANSGYTSRRKAETLISEGKVKVNGTTVTELGTKVKPSDTIEVEGIKIEL 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E     L+HKP  ++T+ SD  GR+ V D    I +R+  VGRLD +T GLLLLTNDG 
Sbjct: 62  -EDKIYILFHKPTQVITSVSDDRGRTVVTDYFKDIDARIYPVGRLDYDTSGLLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNA 187
              ++  P  Q  + Y  +  G + ++++  L+KGI ++       +  V    +  +  
Sbjct: 121 FTNLMTHPRYQIKKKYVAKLKGYLMREEVKALEKGIELEDGMTQPAEVKVKKQDKDKNTT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V + + EG+NR+++++FE F  +V +L RI YGP  +  L AG  R ++   ++     
Sbjct: 181 LVEITITEGRNRQVRRMFEHFGHQVTKLSRIEYGPLNVVGLNAGEGRVLTPHEVKVMRHL 240

Query: 248 HLL 250
              
Sbjct: 241 AEH 243


>gi|332799305|ref|YP_004460804.1| pseudouridine synthase Rsu [Tepidanaerobacter sp. Re1]
 gi|332697040|gb|AEE91497.1| pseudouridine synthase Rsu [Tepidanaerobacter sp. Re1]
          Length = 237

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 73/235 (31%), Positives = 119/235 (50%), Gaps = 1/235 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +++AG+ SRR  E +I Q +V VNG  +++    V   TD I+V+G        
Sbjct: 3   MRLQKYLSQAGVDSRRACEDIILQGKVSVNGKTIKKLGTKVNPETDIIKVNGKVCSLKYD 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G++TT  DP GR TV D LP    RV  VGRLD  TEGLL+LTNDG +  
Sbjct: 63  FIYILINKPKGILTTVKDPLGRPTVLDLLPEFCERVFPVGRLDKETEGLLILTNDGEVTY 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  + ++ Y     G V  +K+  L+KGI+++       +  +     ++  + + 
Sbjct: 123 KLTHPKYKVIKTYVAHVRGIVGNNKIKSLEKGIILEDGVTAPAKANILKVLRNSTIIKLE 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           + EG+ R+++++ +     +  L R   G   +  L  G  R +S++ +    G 
Sbjct: 183 IHEGRKRQVRRMCDSIGHPIIELKRTQIGDISIKGLKPGEWRLLSQREIDYIKGL 237


>gi|298346749|ref|YP_003719436.1| pseudouridylate synthase [Mobiluncus curtisii ATCC 43063]
 gi|304389546|ref|ZP_07371509.1| ribosomal large subunit pseudouridine synthase B [Mobiluncus
           curtisii subsp. curtisii ATCC 35241]
 gi|298236810|gb|ADI67942.1| pseudouridylate synthase [Mobiluncus curtisii ATCC 43063]
 gi|304327356|gb|EFL94591.1| ribosomal large subunit pseudouridine synthase B [Mobiluncus
           curtisii subsp. curtisii ATCC 35241]
          Length = 278

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 77/240 (32%), Positives = 121/240 (50%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           +    P+R+ KV++RAG+ASRR  E +IA+ RV++NG  +    V V+ TD I VDG  +
Sbjct: 36  ESTSEPERLQKVLSRAGVASRRASEDLIARGRVQINGETVREMGVKVLPTDRITVDGQRI 95

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                 ++W +HKP+G V++    D R  + D +  +  RV +VGRLD  T GLLLLTN+
Sbjct: 96  HTDTVLQVWAFHKPVGTVSSMQPEDDRPCIGDWVTKLPERVYNVGRLDAATAGLLLLTNN 155

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  +  PS +  + Y     GQV      +L++G+ ++       +  L   +  ++
Sbjct: 156 GELANRIMHPSYEVPKTYVAVVQGQVKMGLGKVLRRGVELEDGKVKVDKFKLIEVRRGSS 215

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V + L  GKNR ++++       V+ L R       L  L  G  R +  K L      
Sbjct: 216 IVQLTLHSGKNRVVRRLLSAVGHPVSALTRTGIANLTLDGLKEGQFRLLHGKELAALQEM 275


>gi|237795222|ref|YP_002862774.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum Ba4 str. 657]
 gi|229261861|gb|ACQ52894.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum Ba4 str. 657]
          Length = 236

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 71/230 (30%), Positives = 120/230 (52%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +A  G+ASRR+ E +I + RV+VNGI ++     ++S  D I+VDG  +   E 
Sbjct: 3   ERLQKYMASCGVASRRKCEDIILEGRVEVNGIKIKELGTKIISGEDIIKVDGNIIEPEEN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G V T  D   R T   +L  +  R+  +GRLD++T G+++LTNDG +  
Sbjct: 63  KIYILLNKPKGYVCTAKDEKDRKT-ILDLVKVKERIYPIGRLDMDTSGIIILTNDGEIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  + ++ Y+ +  G + +D + L KKGI I         + +       + + + 
Sbjct: 122 KIIHPKFEKIKTYKAKVKGTIKKDHIELFKKGIDIGDYITAPATLEILKISKDTSEIIIK 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGKNR+++++ +     V  L RIS G      L  G  R ++KK + 
Sbjct: 182 IHEGKNRQVRRMCKSIGHAVIDLDRISIGNITKNDLKLGEWRYLTKKEID 231


>gi|229105336|ref|ZP_04235984.1| Pseudouridine synthase [Bacillus cereus Rock3-28]
 gi|228678093|gb|EEL32322.1| Pseudouridine synthase [Bacillus cereus Rock3-28]
          Length = 242

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 105/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G  ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L+     +  T  D          L         VGRLDI+TEG LL+TNDG L+ 
Sbjct: 61  VYLMLHKPQGVISATEDDNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKLSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G V ++ +    KG+++          +T+  +    + + +
Sbjct: 121 QLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 180 VITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGEYRELTDEEVE 231


>gi|312127407|ref|YP_003992281.1| pseudouridine synthase [Caldicellulosiruptor hydrothermalis 108]
 gi|311777426|gb|ADQ06912.1| pseudouridine synthase [Caldicellulosiruptor hydrothermalis 108]
          Length = 240

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 74/230 (32%), Positives = 118/230 (51%), Gaps = 2/230 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
              R+ K +A+ G+ASRR+ E +I Q RVKVNG L+ +    V    D +EVDG  +   
Sbjct: 3   ELVRLQKFMAQCGVASRRKCEEIILQGRVKVNGKLVNQLGFKVDPEKDVVEVDGKRISLQ 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGG 129
            +    + +KP G++++  D  GR TV D +    +     VGRLD +T GL+LLTNDG 
Sbjct: 63  RQKVYIMLNKPFGVISSAKDEKGRKTVVDLVKDKVNVRVFPVGRLDFDTTGLILLTNDGE 122

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P     + Y     G   ++++   +KG++I G      +  +      NA V
Sbjct: 123 FAYKVTHPKHDIEKTYIALIKGIPSKEEIERFEKGLLIDGKMTAPAKFKILKLINGNALV 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+NR+I+K+ +    KV +L R++ G  QLG L  G    + + 
Sbjct: 183 EIKIHEGRNRQIRKMCDQIGHKVLKLKRVAIGKLQLGKLKEGKFVFLDRD 232


>gi|283783292|ref|YP_003374046.1| pseudouridylate synthase [Gardnerella vaginalis 409-05]
 gi|283441908|gb|ADB14374.1| pseudouridylate synthase [Gardnerella vaginalis 409-05]
          Length = 284

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 120/237 (50%), Gaps = 2/237 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
            ++    R+ K++A AG  SRR+ E +I   RV+V+  L+      V      + VDG  
Sbjct: 40  SDDNNAIRLQKLLAEAGFGSRRKCEEIILDGRVEVDDELVTTLGTRVDPKRQKVRVDGSR 99

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           ++   +      HKP  +++   DP GR T+ D +   + R+  +GRLD ++EGL+L+TN
Sbjct: 100 VKFNTKLVTLALHKPKRVLSAMDDPKGRFTLRDIVGDKYERIFHMGRLDYDSEGLILMTN 159

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
           DG L++ +  P  +  + Y     G+++      L  +G+ ++       +  +  Q   
Sbjct: 160 DGELSQHVMHPKYEVEKTYIATVEGKINGMVCRRLVSQGVNLEDGWIKLDRCAIIDQNHD 219

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
              V + L  GKNR ++++F    + V RL+R   GP +LG L AGS R +S+  +R
Sbjct: 220 TTMVKIVLHSGKNRIVRRIFGAVGFPVKRLVRTQIGPIKLGDLKAGSYRVLSQTEVR 276


>gi|52140796|ref|YP_086033.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus
           E33L]
 gi|229198871|ref|ZP_04325562.1| Pseudouridine synthase [Bacillus cereus m1293]
 gi|51974265|gb|AAU15815.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus
           E33L]
 gi|228584574|gb|EEK42701.1| Pseudouridine synthase [Bacillus cereus m1293]
          Length = 242

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 106/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++GI ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGIPVKDAKVHVNVEEQEVMIHGEVVEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L ++     +  T  D          L         VGRLDI+TEG LL+TNDG L+ 
Sbjct: 61  VYLMMHKPQGVISATEDDNHETVIDLLELEDAIFNPFPVGRLDIDTEGFLLITNDGKLSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G V ++ +    KG+++          +T+  +    + + +
Sbjct: 121 QLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 180 VITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 231


>gi|88855489|ref|ZP_01130153.1| RNA pseudouridine synthase [marine actinobacterium PHSC20C1]
 gi|88815396|gb|EAR25254.1| RNA pseudouridine synthase [marine actinobacterium PHSC20C1]
          Length = 257

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 85/257 (33%), Positives = 131/257 (50%), Gaps = 2/257 (0%)

Query: 1   MKDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M + N     N   +R+ KV+A AG+ASRR  E +I Q RV VNG ++E A   V+ TD 
Sbjct: 1   MNNANGESPSNPEGERLQKVMAAAGVASRRVCEDLIYQGRVAVNGEVVEAAGRRVLPTDR 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           + VD V ++     +  + +KP+G+V++ +D  GR  + +       R+ +VGRLD NT 
Sbjct: 61  VTVDDVAIQLDTTKQYVMLNKPVGVVSSMADESGRPDLREFTRDYDERLFNVGRLDANTS 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LTNDG LA +L  PS    + Y  +  G V    +  L KGI +        +   
Sbjct: 121 GLLILTNDGELAHILAHPSFGVSKTYIAKVEGIVSAQTIAKLTKGIELDDGPIVADKARA 180

Query: 180 DTQ-KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
             +  G+   V + L  G+N  ++++ +     V  L+R  +GP  LG+L  G TR+++K
Sbjct: 181 LGRASGNETMVEITLHSGRNHIVRRMLDAVGHPVIDLVRRQFGPLTLGSLPVGRTRDLTK 240

Query: 239 KILREQLGPHLLEEAQV 255
             L   L      E Q 
Sbjct: 241 AELGAVLTIARNAEEQS 257


>gi|253732136|ref|ZP_04866301.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus USA300_TCH959]
 gi|253724091|gb|EES92820.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus USA300_TCH959]
          Length = 245

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 78/243 (32%), Positives = 129/243 (53%), Gaps = 3/243 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R+ K IA +G  SRR+ E +I++ +VKVNG  +      V  +D IEV+G+ +  
Sbjct: 2   TKELERLQKRIANSGYTSRRKAETLISEGKVKVNGTTVTELGTKVKPSDTIEVEGIKIEL 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E     L+HKP  ++T+ SD  GR+ V D    I +R+  VGRLD +T GLLLLTNDG 
Sbjct: 62  -EDKIYILFHKPTQVITSVSDDRGRTVVTDYFKDIEARIYPVGRLDYDTSGLLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNA 187
              ++  P  Q  + Y  +  G + ++++  L+KGI ++       +  V    +  +  
Sbjct: 121 FTNLMTHPRYQIKKKYVAKLKGYIMREEVKALEKGIELEDGMTQPAEVKVKKQDKDKNTT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V + + EG+NR+++++FE F  +V +L RI YGP  +  L AG  R ++   ++     
Sbjct: 181 LVEITITEGRNRQVRRMFEHFGHQVTKLSRIEYGPLNVVGLNAGEGRVLTPHEVKVMRHL 240

Query: 248 HLL 250
              
Sbjct: 241 AEH 243


>gi|15924483|ref|NP_372017.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus Mu50]
 gi|15927074|ref|NP_374607.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus N315]
 gi|21283176|ref|NP_646264.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus MW2]
 gi|49483743|ref|YP_040967.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus MRSA252]
 gi|49486331|ref|YP_043552.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus MSSA476]
 gi|57650449|ref|YP_186378.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus COL]
 gi|82751087|ref|YP_416828.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus RF122]
 gi|87160582|ref|YP_494139.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus USA300_FPR3757]
 gi|88195298|ref|YP_500102.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus NCTC 8325]
 gi|148267977|ref|YP_001246920.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus JH9]
 gi|150394042|ref|YP_001316717.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus JH1]
 gi|151221613|ref|YP_001332435.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus str. Newman]
 gi|156979812|ref|YP_001442071.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus Mu3]
 gi|161509722|ref|YP_001575381.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus USA300_TCH1516]
 gi|221140086|ref|ZP_03564579.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus str. JKD6009]
 gi|253314861|ref|ZP_04838074.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus str. CF-Marseille]
 gi|253733259|ref|ZP_04867424.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus TCH130]
 gi|255006279|ref|ZP_05144880.2| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus Mu50-omega]
 gi|257425616|ref|ZP_05602040.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus 55/2053]
 gi|257428277|ref|ZP_05604675.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus 65-1322]
 gi|257430914|ref|ZP_05607294.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus 68-397]
 gi|257433603|ref|ZP_05609961.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus E1410]
 gi|257436516|ref|ZP_05612560.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus M876]
 gi|257793570|ref|ZP_05642549.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9781]
 gi|258407188|ref|ZP_05680336.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9763]
 gi|258437324|ref|ZP_05689308.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9299]
 gi|258443529|ref|ZP_05691868.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A8115]
 gi|258446736|ref|ZP_05694890.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A6300]
 gi|258448651|ref|ZP_05696763.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A6224]
 gi|258451151|ref|ZP_05699186.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A5948]
 gi|258454267|ref|ZP_05702237.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A5937]
 gi|262049080|ref|ZP_06021957.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus D30]
 gi|262053234|ref|ZP_06025385.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus 930918-3]
 gi|269203120|ref|YP_003282389.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus ED98]
 gi|282892992|ref|ZP_06301226.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A8117]
 gi|282904073|ref|ZP_06311961.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus C160]
 gi|282905900|ref|ZP_06313755.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus Btn1260]
 gi|282908810|ref|ZP_06316628.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus WW2703/97]
 gi|282911129|ref|ZP_06318931.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus WBG10049]
 gi|282914298|ref|ZP_06322084.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus M899]
 gi|282916759|ref|ZP_06324517.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus D139]
 gi|282919267|ref|ZP_06327002.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus C427]
 gi|282924592|ref|ZP_06332260.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus C101]
 gi|282924742|ref|ZP_06332409.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9765]
 gi|282928963|ref|ZP_06336550.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A10102]
 gi|283958255|ref|ZP_06375706.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           A017934/97]
 gi|284024553|ref|ZP_06378951.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus 132]
 gi|293503375|ref|ZP_06667222.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus 58-424]
 gi|293510390|ref|ZP_06669096.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus M809]
 gi|293530929|ref|ZP_06671611.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           M1015]
 gi|294848523|ref|ZP_06789269.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9754]
 gi|295406613|ref|ZP_06816418.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A8819]
 gi|295428069|ref|ZP_06820701.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus EMRSA16]
 gi|296276357|ref|ZP_06858864.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus MR1]
 gi|297207787|ref|ZP_06924222.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus ATCC
           51811]
 gi|297245803|ref|ZP_06929668.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A8796]
 gi|297590963|ref|ZP_06949601.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus MN8]
 gi|300911868|ref|ZP_07129311.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TCH70]
 gi|304380920|ref|ZP_07363580.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus ATCC
           BAA-39]
 gi|13701292|dbj|BAB42586.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus N315]
 gi|14247264|dbj|BAB57655.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus Mu50]
 gi|21204616|dbj|BAB95312.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus MW2]
 gi|49241872|emb|CAG40565.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus MRSA252]
 gi|49244774|emb|CAG43210.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus MSSA476]
 gi|57284635|gb|AAW36729.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus COL]
 gi|82656618|emb|CAI81043.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus RF122]
 gi|87126556|gb|ABD21070.1| ribosomal large subunit pseudouridine synthase B, RluB
           [Staphylococcus aureus subsp. aureus USA300_FPR3757]
 gi|87202856|gb|ABD30666.1| ribosomal large subunit pseudouridine synthase B, putative
           [Staphylococcus aureus subsp. aureus NCTC 8325]
 gi|147741046|gb|ABQ49344.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus JH9]
 gi|149946494|gb|ABR52430.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus JH1]
 gi|150374413|dbj|BAF67673.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus str. Newman]
 gi|156721947|dbj|BAF78364.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus Mu3]
 gi|160368531|gb|ABX29502.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|253728799|gb|EES97528.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus TCH130]
 gi|257271310|gb|EEV03456.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus 55/2053]
 gi|257275118|gb|EEV06605.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus 65-1322]
 gi|257278344|gb|EEV08980.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus 68-397]
 gi|257281696|gb|EEV11833.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus E1410]
 gi|257283867|gb|EEV13990.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus M876]
 gi|257787542|gb|EEV25882.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9781]
 gi|257841215|gb|EEV65661.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9763]
 gi|257848529|gb|EEV72517.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9299]
 gi|257850935|gb|EEV74878.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A8115]
 gi|257854311|gb|EEV77260.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A6300]
 gi|257857929|gb|EEV80818.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A6224]
 gi|257861206|gb|EEV84019.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A5948]
 gi|257863546|gb|EEV86304.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A5937]
 gi|259158873|gb|EEW43966.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus 930918-3]
 gi|259162749|gb|EEW47314.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus D30]
 gi|262075410|gb|ACY11383.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus ED98]
 gi|269940985|emb|CBI49369.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus TW20]
 gi|282313427|gb|EFB43822.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus C101]
 gi|282317077|gb|EFB47451.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus C427]
 gi|282319246|gb|EFB49598.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus D139]
 gi|282321479|gb|EFB51804.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus M899]
 gi|282324824|gb|EFB55134.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus WBG10049]
 gi|282327074|gb|EFB57369.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus WW2703/97]
 gi|282331192|gb|EFB60706.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus Btn1260]
 gi|282589370|gb|EFB94461.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A10102]
 gi|282592749|gb|EFB97755.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9765]
 gi|282595691|gb|EFC00655.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus C160]
 gi|282764310|gb|EFC04436.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A8117]
 gi|283470772|emb|CAQ49983.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus ST398]
 gi|283790404|gb|EFC29221.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           A017934/97]
 gi|285817174|gb|ADC37661.1| Ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus 04-02981]
 gi|290920197|gb|EFD97263.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           M1015]
 gi|291095041|gb|EFE25306.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus 58-424]
 gi|291466754|gb|EFF09274.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus M809]
 gi|294824549|gb|EFG40972.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9754]
 gi|294968360|gb|EFG44384.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A8819]
 gi|295128427|gb|EFG58061.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus EMRSA16]
 gi|296887804|gb|EFH26702.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus ATCC
           51811]
 gi|297177454|gb|EFH36706.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A8796]
 gi|297575849|gb|EFH94565.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus MN8]
 gi|300886114|gb|EFK81316.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TCH70]
 gi|302751325|gb|ADL65502.1| ribosomal large subunit pseudouridine synthase B, RluB
           [Staphylococcus aureus subsp. aureus str. JKD6008]
 gi|304340647|gb|EFM06581.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus ATCC
           BAA-39]
 gi|312438039|gb|ADQ77110.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TCH60]
 gi|312829882|emb|CBX34724.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Staphylococcus aureus subsp. aureus ECT-R 2]
 gi|315129766|gb|EFT85756.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           CGS03]
 gi|315195390|gb|EFU25777.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           CGS00]
 gi|315198816|gb|EFU29144.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           CGS01]
 gi|320140623|gb|EFW32477.1| hypothetical protein HMPREF9528_01247 [Staphylococcus aureus subsp.
           aureus MRSA131]
 gi|320144159|gb|EFW35928.1| hypothetical protein HMPREF9529_00596 [Staphylococcus aureus subsp.
           aureus MRSA177]
 gi|323441527|gb|EGA99178.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus O46]
 gi|329314171|gb|AEB88584.1| Pseudouridine synthase [Staphylococcus aureus subsp. aureus T0131]
 gi|329725278|gb|EGG61765.1| pseudouridine synthase B, ribosomal large subunit [Staphylococcus
           aureus subsp. aureus 21189]
 gi|329727675|gb|EGG64131.1| pseudouridine synthase B, ribosomal large subunit [Staphylococcus
           aureus subsp. aureus 21172]
 gi|329730831|gb|EGG67209.1| pseudouridine synthase B, ribosomal large subunit [Staphylococcus
           aureus subsp. aureus 21193]
          Length = 245

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 78/243 (32%), Positives = 129/243 (53%), Gaps = 3/243 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R+ K IA +G  SRR+ E +I++ +VKVNG  +      V  +D IEV+G+ +  
Sbjct: 2   TKELERLQKRIANSGYTSRRKAETLISEGKVKVNGTTVTELGTKVKPSDTIEVEGIKIEL 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E     L+HKP  ++T+ SD  GR+ V D    I +R+  VGRLD +T GLLLLTNDG 
Sbjct: 62  -EDKIYILFHKPTQVITSVSDDRGRTVVTDYFKDIEARIYPVGRLDYDTSGLLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNA 187
              ++  P  Q  + Y  +  G + ++++  L+KGI ++       +  V    +  +  
Sbjct: 121 FTNLMTHPRYQIKKKYVAKLKGYLMREEVKALEKGIELEDGMTQPAEVKVKKQDKDKNTT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V + + EG+NR+++++FE F  +V +L RI YGP  +  L AG  R ++   ++     
Sbjct: 181 LVEITITEGRNRQVRRMFEHFGHQVTKLSRIEYGPLNVVGLNAGEGRVLTPHEVKVMRHL 240

Query: 248 HLL 250
              
Sbjct: 241 AEH 243


>gi|313204302|ref|YP_004042959.1| ribosomal large subunit pseudouridine synthase f [Paludibacter
           propionicigenes WB4]
 gi|312443618|gb|ADQ79974.1| ribosomal large subunit pseudouridine synthase F [Paludibacter
           propionicigenes WB4]
          Length = 320

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 65/335 (19%), Positives = 122/335 (36%), Gaps = 16/335 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K I+ +G+ SRRE ++ I Q  V +NG         V   D + ++G  +   
Sbjct: 2   TEKIRLNKFISDSGVCSRREADKYIEQGHVFINGRRATV-GAQVSKHDKVTLNGNLIEAK 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E T          +    +   G      +      R+  +GRLD  ++GL+ LTN+G +
Sbjct: 61  EGTDFAFIAFNKPVGIISTTEIGVKDSIIDYIGYHERIFPIGRLDKESQGLIFLTNNGDI 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +     +  + Y V  +  +  + +  +  G+ I G       V     K S     
Sbjct: 121 VNKILRAGNKHEKEYLVTVNKPITDEFILKMGNGVPILGEMTKKCSVI----KESVFSFR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E+F ++V +L RI      L  +  G  R++  + + E +     
Sbjct: 177 IVLIQGLNRQIRRMCEYFEYEVVKLERIRIMNIGLKGIPLGEWRQLEAEEMNEIMMAIKD 236

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
             +     +    S+   ++      + P   ++  K     N   K K+L         
Sbjct: 237 SSSTAKPKSNGGESKIQHQEPRRKTMDRPMSGSKPSKTDRTSNPNPKSKELRG------- 289

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
                 A                   R+   P KR
Sbjct: 290 ----GYAGQAGKKTNPSRSASNAKGNRTSGKPGKR 320


>gi|291528900|emb|CBK94486.1| ribosomal small subunit pseudouridine synthase A [Eubacterium
           rectale M104/1]
          Length = 240

 Score =  184 bits (467), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 63/230 (27%), Positives = 114/230 (49%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K ++  G+ +R EV+++I   ++ +NG +  +    V +  D + V+G  ++    
Sbjct: 2   IRLDKFLSEMGLGTRSEVKKLIKTGQIAINGTVAAKPETKVDTDADEVSVNGRIVKYQRY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                      + +  SD    + +     ++   +  VGRLDI+TEGLLL+TNDG L+ 
Sbjct: 62  EYYLFNKPSGCV-SATSDNVHDTVMDYITDAVHDDLFPVGRLDIDTEGLLLITNDGALSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  PS    + Y  R  G+V  D +   K+GI I +       ++ +  + GS + + +
Sbjct: 121 ELLSPSKHVAKTYYARIDGEVTLDDIIRFKEGIDIGEERPTKPAEL-VIKKSGSVSEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
            + EGK  ++K++FE    +V  L RIS GP +L   L  G+ R +++  
Sbjct: 180 TITEGKFHQVKRMFEALGKRVIYLKRISMGPLKLPDDLKTGTYRALTQAE 229


>gi|114765382|ref|ZP_01444497.1| RNA pseudouridylate synthase family protein [Pelagibaca bermudensis
           HTCC2601]
 gi|114542225|gb|EAU45255.1| RNA pseudouridylate synthase family protein [Roseovarius sp.
           HTCC2601]
          Length = 283

 Score =  184 bits (467), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 136/267 (50%), Positives = 171/267 (64%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            +     R++KV++RAGIASRRE ERMI + RV VNG  +   A+NV   D I VDG PL
Sbjct: 16  TDTPPGDRIAKVLSRAGIASRREAERMIEEGRVTVNGETIASPALNVTDKDRITVDGKPL 75

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              E  R+W+YHKP GLVTT  D  GR T+FD LP    RV++VGRLD+N+EGLLLLTND
Sbjct: 76  EAPEAPRMWMYHKPAGLVTTTKDEQGRETIFDKLPEDLPRVMTVGRLDLNSEGLLLLTND 135

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GG+ R LELPST WLR YRVR +G+  ++ L  L+ GI + G  +  MQV LD Q+GSNA
Sbjct: 136 GGIKRKLELPSTGWLRRYRVRVNGKPTEEMLKPLRDGITVDGQTFQPMQVELDRQQGSNA 195

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+TVGLREGKNREI++        VNRLIRISYGPFQLG +  G   E+  +I+R+QLG 
Sbjct: 196 WLTVGLREGKNREIRRAMSDIGLTVNRLIRISYGPFQLGQMKVGEVVELRGRIVRDQLGL 255

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNI 274
              +  +              + R   
Sbjct: 256 EGAKTTRPEPSRRRKPRPIPDKSRRTR 282


>gi|298694777|gb|ADI97999.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus ED133]
          Length = 245

 Score =  184 bits (467), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 78/243 (32%), Positives = 129/243 (53%), Gaps = 3/243 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R+ K IA +G  SRR+ E +I++ +VKVNG  +      V  +D IEV+G+ +  
Sbjct: 2   TKELERLQKRIANSGYTSRRKAETLISEGKVKVNGTTVTELGTKVKPSDTIEVEGIKIEL 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E     L+HKP  ++T+ SD  GR+ V D    I +R+  VGRLD +T GLLLLTNDG 
Sbjct: 62  -EDKIYILFHKPTQVITSVSDDRGRTVVTDYFKDIDARIYPVGRLDYDTSGLLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNA 187
              ++  P  Q  + Y  +  G + ++++  L+KGI ++       +  V    +  +  
Sbjct: 121 FTNLMTHPRYQIKKKYVAKLKGYLMREEVKALEKGIELEDGMTQPAEVKVKKQDKDKNTT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V + + EG+NR+++++FE F  +V +L RI YGP  +  L AG  R ++   ++     
Sbjct: 181 LVEITITEGRNRQVRRMFEHFGHQVTKLSRIDYGPLNVVGLNAGEGRVLTPHEVKVMRHL 240

Query: 248 HLL 250
              
Sbjct: 241 AEH 243


>gi|300173429|ref|YP_003772595.1| ribosomal large subunit pseudouridine synthase B [Leuconostoc
           gasicomitatum LMG 18811]
 gi|299887808|emb|CBL91776.1| ribosomal large subunit pseudouridine synthase B [Leuconostoc
           gasicomitatum LMG 18811]
          Length = 249

 Score =  184 bits (467), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 90/235 (38%), Positives = 136/235 (57%), Gaps = 2/235 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   QR+ K+IA+AG+ASRR  E +IA+ RV+VNG  +    + V   DH+EVDG P+  
Sbjct: 2   SEEAQRLQKIIAQAGLASRRGAEELIAKGRVQVNGQTITELGMKVEPNDHVEVDGSPIEG 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E+   +L +KP G+VTT++D  GR TV D L  +  RV  +GRLD +T G+LLLTNDG 
Sbjct: 62  REKLVYYLLNKPRGVVTTNNDEKGRQTVIDLLGDVSQRVYPIGRLDYDTTGVLLLTNDGV 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--A 187
           +A  L  P ++  +VY  +  G    +KL  LK G+VI+G      +VT++        +
Sbjct: 122 VANQLMHPKSRVDKVYVAKVEGIATDEKLAPLKHGVVIKGRKTAPARVTIERVDKDKKTS 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V V + EG+N +IK + +  +  V +L R  Y  F L  L +G  R+++   +R
Sbjct: 182 MVRVIIHEGRNHQIKNMLQKVHLPVVKLTREQYAFFDLIGLQSGEYRKLTGAEVR 236


>gi|268319598|ref|YP_003293254.1| hypothetical protein FI9785_1123 [Lactobacillus johnsonii FI9785]
 gi|262397973|emb|CAX66987.1| conserved hypothetical protein [Lactobacillus johnsonii FI9785]
          Length = 239

 Score =  184 bits (467), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 76/230 (33%), Positives = 119/230 (51%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AG+ASRR+ E+MI+  +V VNG  +      V   D IEV+GVP+ K    
Sbjct: 3   ERLQKVIAQAGVASRRKAEKMISAGQVTVNGKKVTELGTKVEPRDKIEVNGVPIEKEALH 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     + +   D  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  
Sbjct: 63  TYLFYKPRGVISSVS-DDKGRKTVVDFFEDVPYRLYPVGRLDYDTSGLLLMTNDGELANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           L  P  +  +VY  +  G +  +++  L  G+ I G      ++ +    +K     V +
Sbjct: 122 LMHPRNEVPKVYVAKIKGILSTEEIRSLTHGVRIDGRKSAPAKLKILKTDEKKKTQIVQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + EG   ++K++FE  +  V +L R  Y    L +L +G  RE++ + +
Sbjct: 182 TIHEGHYHQVKRMFEAVHHFVEKLAREKYAFLTLKSLNSGEYRELTNEEV 231


>gi|187933805|ref|YP_001885871.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum B str. Eklund 17B]
 gi|187721958|gb|ACD23179.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum B str. Eklund 17B]
          Length = 236

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 75/230 (32%), Positives = 119/230 (51%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K +A  G+ASRR+ E +I    VKVNG+++      V    D +E  G  + K E 
Sbjct: 3   ERLQKYMASCGVASRRKCEEIILNGEVKVNGVVITELGTRVNPVEDKVEYKGSLITKEEN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G +T+  D  GR TV  +L  +  R+  +GRLD ++ GL+LLTNDG +  
Sbjct: 63  KVYIILNKPEGYITSAKDEKGRKTV-LDLVKVNERIYPIGRLDYDSSGLILLTNDGDVYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + Y     G+V +  +++  KGI I G       + + +     + V V 
Sbjct: 122 KIIHPREELNKKYIAVVKGKVSKKDIDIFNKGIDIGGYITAPASLEVLSYANEKSTVEVC 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGKNR+I+K+    N +V  L R+S G  QL  L  G  RE++ + L 
Sbjct: 182 IHEGKNRQIRKMCTAINHEVLSLNRVSIGEIQLKYLKKGEWRELTTEELD 231


>gi|182419893|ref|ZP_02951131.1| RNA pseudouridine synthase family protein [Clostridium butyricum
           5521]
 gi|237667549|ref|ZP_04527533.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           butyricum E4 str. BoNT E BL5262]
 gi|182376262|gb|EDT73846.1| RNA pseudouridine synthase family protein [Clostridium butyricum
           5521]
 gi|237655897|gb|EEP53453.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           butyricum E4 str. BoNT E BL5262]
          Length = 238

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 75/232 (32%), Positives = 118/232 (50%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K +A  GIASRR+ E +I   +VKVNG ++E     V    D +E DG  + K ER
Sbjct: 3   ERLQKYMASCGIASRRKCEELILLGKVKVNGNIIEELGFKVNPLKDIVEYDGRVITKEER 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP  ++T+  D   R TV D +     R+  +GRLD ++ GL+LLTNDG L  
Sbjct: 63  KVYIMLNKPEDVITSVKDEKDRKTVIDIVKVN-ERIFPIGRLDYDSSGLILLTNDGELYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            +  P  +  + Y     G+V  D     + GI I G      ++ +         + + 
Sbjct: 122 KIIHPRVELDKKYVAVVKGEVSLDDKEKFESGIDIGGYITAPAKLKMLEYSHRKDLSTIE 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           V + EGKNR+I+K+    N +V  L R+S G  +LG L  G  R ++ + ++
Sbjct: 182 VCIHEGKNRQIRKMCSAINHEVISLKRVSIGNIRLGQLKKGEYRYLNDEEMK 233


>gi|307244534|ref|ZP_07526639.1| pseudouridylate synthase [Peptostreptococcus stomatis DSM 17678]
 gi|306492061|gb|EFM64109.1| pseudouridylate synthase [Peptostreptococcus stomatis DSM 17678]
          Length = 244

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 106/237 (44%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  +R E+++M  Q  V VNG  +++   ++    D + ++G  +R  E 
Sbjct: 1   MRLDKMLSNLGYGTRSEIKKMCRQGMVTVNGQEVKKPDHHIDPDQDQVCLNGQAVRYREY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  T+   D       +   +      VGRLD +TEGLL++TNDG L+ 
Sbjct: 61  IYLMMNKPAGCVSATYDKYDQTVIDLIDPEYLAFEPFPVGRLDKDTEGLLVITNDGQLSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGS-----N 186
            +  P     ++Y      +V    +    KG+ I         ++ +     +     +
Sbjct: 121 RVLSPKKHVPKIYYAEIDHEVLARDIEAFSKGVYIGDDYTTKPAKLEVIKSFEAEDGAIH 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           + + V + EGK  ++K++FE     V  L RI  G  +L   L  G  RE++++ + 
Sbjct: 181 SEIYVTISEGKFHQVKRMFEAVGKSVLYLKRIQMGGLKLDESLGLGEYRELTEEEID 237


>gi|194016715|ref|ZP_03055328.1| ribosomal large subunit pseudouridine synthase B [Bacillus pumilus
           ATCC 7061]
 gi|194011321|gb|EDW20890.1| ribosomal large subunit pseudouridine synthase B [Bacillus pumilus
           ATCC 7061]
          Length = 290

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 73/250 (29%), Positives = 122/250 (48%), Gaps = 3/250 (1%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            K + +     +R+ KVIA AG+ASRR+ E +I + RV VNG  +    V V S+D IEV
Sbjct: 37  SKIVHEVKDKMERLQKVIAHAGVASRRKAEELIKEGRVTVNGQTVTELGVKVGSSDKIEV 96

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           +G+ L + E     LY     +++   D  GR  V D    +  R+  +GRLD +T GL+
Sbjct: 97  NGLKLEREEPVYFMLYKPRG-VISAAEDDKGRKVVTDFFDDVPQRLYPIGRLDYDTSGLI 155

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L+TNDG  A  L  P  +  + Y  +  G   ++ L  L+KGI++        +  + + 
Sbjct: 156 LITNDGEFAHKLMHPKYEIDKTYAAKLKGIPSKELLRKLEKGIMLDHKKTARARAKMLSI 215

Query: 183 KGSN--AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 + V + + EG+NR+++++FE     V +L R  Y    +  +  G  RE++   
Sbjct: 216 DKRKQTSIVQLTIHEGRNRQVRRMFEAIGHDVLKLKREQYAFLHIEGMRPGDRRELTPHE 275

Query: 241 LREQLGPHLL 250
           ++        
Sbjct: 276 VKRLRAIADH 285


>gi|154247023|ref|YP_001417981.1| RNA-binding S4 domain-containing protein [Xanthobacter
           autotrophicus Py2]
 gi|154161108|gb|ABS68324.1| RNA-binding S4 domain protein [Xanthobacter autotrophicus Py2]
          Length = 620

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 153/376 (40%), Positives = 209/376 (55%), Gaps = 34/376 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +R++KV+ARAG+ SRRE+E  I   RV VNG +L   AV V + D I VDG PL + E
Sbjct: 28  EAERIAKVVARAGLGSRREIEEWIEAGRVAVNGEVLTTPAVTVTAEDAITVDGAPLPERE 87

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RTRL++YHKP G+VTT+ DP+GR+T+F+ LP    R++SVGRLD+N+EGLLLLTNDGGLA
Sbjct: 88  RTRLFIYHKPRGVVTTNRDPEGRTTLFEILPQGLPRLVSVGRLDLNSEGLLLLTNDGGLA 147

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           RVLELP T WLR YRVR +G+V+Q +L+ L KGI + G+ YG ++  LD  +G+NAW+TV
Sbjct: 148 RVLELPETGWLRRYRVRANGEVNQAQLDSLLKGITVDGVEYGPIEAELDRVQGANAWITV 207

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            LREGKNREI+ VF     +VNRLIR+SYGPFQLG +  G   EV  ++LR+Q+G  L  
Sbjct: 208 SLREGKNREIRNVFGALGLQVNRLIRVSYGPFQLGDVPEGGIEEVRTRVLRDQIGNDLAA 267

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK------------ 299
            A  +    +   E         +          +K  + K    + +            
Sbjct: 268 AAGADFTGLLVERELEEAPPRVALRPAGKRQAAAEKGGTLKAPARRSRQDEDFDAPVEDV 327

Query: 300 -KLATPVHRRNLA---------------------SNVWMAKGIHSSFLSDSGQREENHRR 337
            + A P  RR ++                       V   K    +  + +G R    + 
Sbjct: 328 IRPAGPRTRRRMSDENAVESRGSVADRKGRTVKVERVVAPKADAPTRGARTGARPGARKS 387

Query: 338 SPSFPSKRSLRRTSAK 353
                  R  RR  A+
Sbjct: 388 DRDEAGARPFRRGPAE 403



 Score = 37.9 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 9/101 (8%), Positives = 22/101 (21%), Gaps = 4/101 (3%)

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
           D P           P    +           +  +      ++   P    +       A
Sbjct: 445 DRPRRPRPETADGAPRRGRDERPQQGERPFRTRSERPDRTSEQEGRPARGGSRPYGDKPA 504

Query: 318 KGIHSSFLSDSGQREE----NHRRSPSFPSKRSLRRTSAKK 354
                +    +G        +     ++  K +  R S  +
Sbjct: 505 GRARPTGDRPAGAGRAYGEKSEGSGRAYGDKPARSRPSGDR 545


>gi|163942437|ref|YP_001647321.1| pseudouridine synthase [Bacillus weihenstephanensis KBAB4]
 gi|229013913|ref|ZP_04171040.1| Pseudouridine synthase [Bacillus mycoides DSM 2048]
 gi|229135547|ref|ZP_04264331.1| Pseudouridine synthase [Bacillus cereus BDRD-ST196]
 gi|163864634|gb|ABY45693.1| pseudouridine synthase [Bacillus weihenstephanensis KBAB4]
 gi|228647927|gb|EEL03978.1| Pseudouridine synthase [Bacillus cereus BDRD-ST196]
 gi|228747383|gb|EEL97259.1| Pseudouridine synthase [Bacillus mycoides DSM 2048]
          Length = 242

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 60/232 (25%), Positives = 105/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G  ++ A  +V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGHGSRKEVKKLLKDGVVKIDGTPVKDAKFHVNVEEQEVMIHGEVVEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L ++     +  T  D          L         VGRLDI+TEG LL+TNDG L  
Sbjct: 61  VYLMMHKPQGVISATEDDNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKLTH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G V ++ +    KG++++        ++T+  +    + + +
Sbjct: 121 QLLSPKKHVPKKYYAHISGVVTEEDVIEFAKGVILEDGYETKPGELTIL-KSDDISEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 180 VITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLMLDEELELGQYRELTDEEVE 231


>gi|325287412|ref|YP_004263202.1| pseudouridine synthase Rsu [Cellulophaga lytica DSM 7489]
 gi|324322866|gb|ADY30331.1| pseudouridine synthase Rsu [Cellulophaga lytica DSM 7489]
          Length = 245

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 61/246 (24%), Positives = 111/246 (45%), Gaps = 8/246 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL- 67
           +     R++K ++  G  SRR  +++I Q RV +NG +       ++ TD + VDG  + 
Sbjct: 2   KEIQATRINKYLSEVGYCSRRAADKLIDQGRVTINGKIP-EMGTKIIPTDEVRVDGELIS 60

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              E      ++KP+G+V T      +  + D +     R+  +GRLD  +EGL+ LTND
Sbjct: 61  ESKEDFVYLAFNKPVGIVCTTDTRVEKDNIIDYINYPK-RIFPIGRLDKPSEGLIFLTND 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +        + Y V+    +  D ++ +  GI I        +     +K S  
Sbjct: 120 GDIVNKILRARNHHEKEYIVKVDNIITDDFVHQMSNGIPILDTITRKCK----VEKLSKY 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+  + V +L R+      L  +  G+ RE +K+ L+E    
Sbjct: 176 EFRIILTQGLNRQIRRMTEYLGYNVVKLKRVRIMNISL-DMPVGTYREFTKEELKEINRL 234

Query: 248 HLLEEA 253
                 
Sbjct: 235 VSTSAK 240


>gi|229076216|ref|ZP_04209183.1| Pseudouridine synthase [Bacillus cereus Rock4-18]
 gi|229099186|ref|ZP_04230119.1| Pseudouridine synthase [Bacillus cereus Rock3-29]
 gi|229118198|ref|ZP_04247556.1| Pseudouridine synthase [Bacillus cereus Rock1-3]
 gi|228665245|gb|EEL20729.1| Pseudouridine synthase [Bacillus cereus Rock1-3]
 gi|228684239|gb|EEL38184.1| Pseudouridine synthase [Bacillus cereus Rock3-29]
 gi|228706865|gb|EEL59071.1| Pseudouridine synthase [Bacillus cereus Rock4-18]
          Length = 242

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 105/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G  ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L+     +  T  D          L         VGRLDI+TEG LL+TNDG L+ 
Sbjct: 61  VYLMLHKPQGVISATEDDNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKLSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G V ++ +    KG+++          +T+  +    + + +
Sbjct: 121 QLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDVSEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 180 VITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGEYRELTDEEVE 231


>gi|188586260|ref|YP_001917805.1| pseudouridine synthase [Natranaerobius thermophilus JW/NM-WN-LF]
 gi|179350947|gb|ACB85217.1| pseudouridine synthase [Natranaerobius thermophilus JW/NM-WN-LF]
          Length = 238

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 81/241 (33%), Positives = 122/241 (50%), Gaps = 4/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K ++RAGIASRR+ E +I Q RV VNG ++ R    +    D ++VDG P+ + E 
Sbjct: 1   MRLQKFMSRAGIASRRKSEELIQQGRVTVNGQVITRLGTKINPDTDTVKVDGEPITQEES 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP   +T+  DP GR TV  +L  +  RV  VGRLD ++ GL+LLTNDG LA 
Sbjct: 61  NVYIMLNKPKDYITSKDDPQGRKTVM-DLIQVKERVYPVGRLDYDSRGLVLLTNDGELAN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V+      QDKL+ L  GI ++        V +      N  + + 
Sbjct: 120 RLMHPKYNIPKTYMVKVDKLPLQDKLDNLVNGIYLEEGLCKADHVEIL--DTKNNILKII 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L EG+ R+I+++      +V  L R S G   L  L  G+ R+++K  +        L +
Sbjct: 178 LSEGRKRQIRRMLASLGIEVKDLKRDSLGTLTLKDLSEGNYRKLTKDEIDNIKKLAGLTD 237

Query: 253 A 253
            
Sbjct: 238 N 238


>gi|168180387|ref|ZP_02615051.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum NCTC 2916]
 gi|168184870|ref|ZP_02619534.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum Bf]
 gi|226949054|ref|YP_002804145.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum A2 str. Kyoto]
 gi|182668845|gb|EDT80823.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum NCTC 2916]
 gi|182672066|gb|EDT84027.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum Bf]
 gi|226841110|gb|ACO83776.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum A2 str. Kyoto]
          Length = 236

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 71/230 (30%), Positives = 120/230 (52%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +A  G+ASRR+ E +I + RV+VNGI ++     ++S  D I+VDG  +   E 
Sbjct: 3   ERLQKYMASCGVASRRKCEDIILEGRVEVNGIRIKELGTKIISGEDIIKVDGNIIEPEEN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G V T  D   R T   +L  +  R+  +GRLD++T G+++LTNDG +  
Sbjct: 63  KIYILLNKPKGYVCTAKDEKDRKT-ILDLVKVKERIYPIGRLDMDTSGIIILTNDGEIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  + ++ Y+ +  G + +D + L KKGI I         + +       + + + 
Sbjct: 122 KIIHPKFEKIKTYKAKVKGTIKKDHIELFKKGIDIGDYITAPATLEILKISKDTSEIIIK 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGKNR+++++ +     V  L RIS G      L  G  R ++KK + 
Sbjct: 182 IHEGKNRQVRRMCKSIGHAVIDLDRISIGNITKNDLKLGEWRYLTKKEID 231


>gi|116618395|ref|YP_818766.1| ribosomal large subunit pseudouridine synthase B [Leuconostoc
           mesenteroides subsp. mesenteroides ATCC 8293]
 gi|116097242|gb|ABJ62393.1| ribosomal large subunit pseudouridine synthase B [Leuconostoc
           mesenteroides subsp. mesenteroides ATCC 8293]
          Length = 249

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 82/235 (34%), Positives = 132/235 (56%), Gaps = 2/235 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   QR+ K+IA+AG+ASRR  E +I   RV+VNG  +      V + D ++VDG P+  
Sbjct: 2   SEEAQRLQKIIAQAGLASRRGAEELIINGRVQVNGQTVTELGTKVTANDKVQVDGAPIEG 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E+   +L +KP G+VTT+ D  GR TV D L  +  RV  VGRLD +T G+LLLTNDG 
Sbjct: 62  REKLVYYLLNKPRGVVTTNDDEKGRRTVLDILEDVDQRVYPVGRLDYDTTGVLLLTNDGV 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--A 187
           +A  L  P T+  + Y  +  G   ++KL  LK+G+V++G      +V+++  + +   +
Sbjct: 122 VANQLMHPKTKVDKTYVAKVEGIATEEKLAPLKRGVVLKGRKTAPARVSIERIEPTKRTS 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V + + EG+N ++K +       V +L R  Y  F +  L  G  R+++   ++
Sbjct: 182 MVRLTIHEGRNHQVKNMLAKVGLPVQKLKREQYAFFDVTGLQPGEYRKLTSVEIK 236


>gi|324328601|gb|ADY23861.1| RNA pseudouridine synthase family protein [Bacillus thuringiensis
           serovar finitimus YBT-020]
          Length = 242

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 107/232 (46%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++GI ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGISVKDAKVHVNVEEQEVMIHGEVVEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L ++     +  T  D          L         VGRLDI+TEG LL+TNDG L+ 
Sbjct: 61  VYLMMHKPQGVISATEDDNHETVIDLLELEDAIFNPFPVGRLDIDTEGFLLITNDGKLSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G V ++ +    KG+++          +T+  +    + + +
Sbjct: 121 QLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++FE    KV  L RI  GP  L   L  G  RE++ + + 
Sbjct: 180 VITEGKFHQVKRMFEAVGKKVVYLKRIEMGPLVLDEELELGQYRELTDEEVE 231


>gi|121533339|ref|ZP_01665167.1| pseudouridine synthase [Thermosinus carboxydivorans Nor1]
 gi|121307898|gb|EAX48812.1| pseudouridine synthase [Thermosinus carboxydivorans Nor1]
          Length = 245

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 72/233 (30%), Positives = 104/233 (44%), Gaps = 4/233 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
             QR+ KV+A  G  SRRE+++M+  +RV VNG ++    ++V    D IEVDG P+   
Sbjct: 5   ERQRLDKVLAHLGYGSRREIKKMVKAERVIVNGAVVRDPELHVFPWQDRIEVDGEPIHYR 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L +      L  T                       VGRLD +TEGLLLLTNDG L
Sbjct: 65  EYIYLMMNKPQGVLSATEDAAGKVVVDLLRPEHKAFAPFPVGRLDKDTEGLLLLTNDGQL 124

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y  R  G V  +     + GI +         ++T+    G  + V
Sbjct: 125 AHRLLAPKKHVPKRYYARVKGVVTDEDKGAFQAGITLDDGYRTLPAELTILHA-GPVSEV 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + + EGK  ++K++F      V  L R++ G   L   L  G  RE++   L
Sbjct: 184 ELVIYEGKFHQVKRMFAARGKTVTYLKRLAMGALVLDEKLAPGEYRELTADEL 236


>gi|290968712|ref|ZP_06560250.1| pseudouridylate synthase [Megasphaera genomosp. type_1 str. 28L]
 gi|290781365|gb|EFD93955.1| pseudouridylate synthase [Megasphaera genomosp. type_1 str. 28L]
          Length = 238

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 72/233 (30%), Positives = 115/233 (49%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV++  G+ASRR  E+MI   RV+VNG+++      V    D I VDG  L    +
Sbjct: 2   ERLQKVMSNCGVASRRASEQMILDGRVRVNGVIVRELGTKVKPEQDIILVDGRRLEIQPK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                      + T   +  GR TV D    I  R+ ++GRLD NTEGLLL+TNDG LA 
Sbjct: 62  HYYLFNKPKGVITTCSDE-QGRPTVLDYFKRIKDRIYAIGRLDQNTEGLLLMTNDGELAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
           +L  P     + Y V+  G +    L  L  G+++         V             + 
Sbjct: 121 ILMHPGHMVDKTYEVKIKGHIADAVLQQLADGVLLSDGMTAPADVYYVGYDTHTGITSLE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + + EGKNR+++++ E F ++V+ L R+ Y    L  +  G+ R ++++ + E
Sbjct: 181 ITIHEGKNRQVRRMMEHFGYQVHNLRRVQYAFLTLSGVKRGAYRALTREEVME 233


>gi|81428635|ref|YP_395635.1| pseudouridylate synthase, 16SrRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
 gi|78610277|emb|CAI55326.1| Pseudouridylate synthase, 16SrRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
          Length = 256

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 81/251 (32%), Positives = 131/251 (52%), Gaps = 4/251 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAER 72
           +R+ KVIA AG+ASRR+ E +IA   V +NG +++   + V ST  HIEVDGVPL   E+
Sbjct: 2   ERLQKVIANAGVASRRKAETLIATGHVTLNGKVVKEMGIKVDSTSAHIEVDGVPLT-REK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +  +KP  +++  +D   R  V + L  I  RV  +GRLD +T GLLLLTNDG  A 
Sbjct: 61  KVYYALYKPRQVISAVTDDKKRRVVTEYLEDIQERVYPIGRLDYDTSGLLLLTNDGDFAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVT 190
           ++  P  +  + Y  +  G    + L  L+KGI+++       +V + +     + A ++
Sbjct: 121 MMMHPKYKVDKTYVAKVSGLPTAEMLRQLRKGIMLEKRKTAPAKVKIISTDRRKNTAILS 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + + EG N ++K +       V++L R +YG   L  L++G  R +    + E      L
Sbjct: 181 ITIHEGMNHQVKNMLAAVGLPVSKLKRETYGFLTLDGLVSGEYRALKPIEVAEFKKIAEL 240

Query: 251 EEAQVNLDAPI 261
            E   + + P 
Sbjct: 241 NEKPKHKNRPK 251


>gi|229163701|ref|ZP_04291648.1| Pseudouridine synthase [Bacillus cereus R309803]
 gi|228619763|gb|EEK76642.1| Pseudouridine synthase [Bacillus cereus R309803]
          Length = 242

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 105/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G  ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L ++     +  T  D          L         VGRLDI+TEG LL+TNDG L+ 
Sbjct: 61  VYLMMHKPQGVISATEDDNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKLSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G V ++ +    KG+++          +T+  +    + + +
Sbjct: 121 QLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGVLTIL-KSDDISEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 180 VITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 231


>gi|332981538|ref|YP_004462979.1| pseudouridine synthase [Mahella australiensis 50-1 BON]
 gi|332699216|gb|AEE96157.1| pseudouridine synthase [Mahella australiensis 50-1 BON]
          Length = 244

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 107/238 (44%), Gaps = 2/238 (0%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGV 65
           +  +    R+ K +A+ G+ASRR+ E +I    V VNG +++   + +    D + V G 
Sbjct: 1   MANSGDLIRLHKYMAQCGVASRRKSEELIKSGAVSVNGHVVKDMGILIDPQKDEVRVYGR 60

Query: 66  PLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            +R   +   + +      + T        + +     +   R+  VGRLD +T GL+LL
Sbjct: 61  IIRLKSDMIYIAVNKPRGYVSTVKDQFGRPTVLDLVPVADEYRLYPVGRLDYDTTGLILL 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG L   L  P  +  ++Y     G  D   +   + G+V++G         L     
Sbjct: 121 TNDGDLTYRLTHPKHEIEKIYVAGLRGIPDNQDIFRFEHGLVLEGRLTAPAGFELIKADQ 180

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
             + V + LREG+NR+I+K+ +     V  L R + G  +L  L  G  R ++ K + 
Sbjct: 181 RLSVVKITLREGRNRQIRKMCDMIGHPVIWLRREAIGEVELCGLQPGQWRYLTPKEIE 238


>gi|85057763|ref|YP_456679.1| 16S rRNA pseudouridylate synthase [Aster yellows witches'-broom
           phytoplasma AYWB]
 gi|84789868|gb|ABC65600.1| 16S rRNA pseudouridylate synthase [Aster yellows witches'-broom
           phytoplasma AYWB]
          Length = 245

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 116/233 (49%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ KV+A A +ASRR+ E +I ++R+KVNG ++      V S+D I +D  P+ KA  +
Sbjct: 2   QRLQKVLAYANVASRRKAEILILEKRIKVNGKIISELGTKVSSSDIITLDDKPITKATYS 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      L T     +  + +     +   R+  +GRLD NT GLLL+TNDG L + 
Sbjct: 62  YFLLNKPNGFLSTAKDKKNRPTVLDLIEEASIQRLYPIGRLDFNTTGLLLITNDGDLTQK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----KGSNAWV 189
           L  PS    + Y V+ +  + +  L+   KGI+I        +     +       + W+
Sbjct: 122 LTHPSFCIPKEYHVKINACLQKKDLSTFCKGIIIDKKYLAVCKEIDILKISYMPKPSTWL 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + + EGKNR+++K+ +   ++V +L R  Y    +  L  G+ R +    ++
Sbjct: 182 KLVITEGKNRQVRKMMQALGYQVLKLKRYRYSFLTIENLTIGAYRPLKIHEIK 234


>gi|303229867|ref|ZP_07316643.1| pseudouridine synthase B, ribosomal large subunit [Veillonella
           atypica ACS-134-V-Col7a]
 gi|303232045|ref|ZP_07318748.1| pseudouridine synthase B, ribosomal large subunit [Veillonella
           atypica ACS-049-V-Sch6]
 gi|302513151|gb|EFL55190.1| pseudouridine synthase B, ribosomal large subunit [Veillonella
           atypica ACS-049-V-Sch6]
 gi|302515423|gb|EFL57389.1| pseudouridine synthase B, ribosomal large subunit [Veillonella
           atypica ACS-134-V-Col7a]
          Length = 241

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 119/237 (50%), Gaps = 4/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K IA  G+ASRR+ E +IA  +V+VNG  +    V V    D + VDG  L   + 
Sbjct: 2   ERLQKFIASCGVASRRKAEELIASGKVRVNGRKVTELGVKVDPMKDKVMVDGQLLAVEKP 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      + +        +   D + +   R+  +GRLD++TEGLLLLTNDG LA+
Sbjct: 62  VYYLMNKPKGVITSVTDPQGRETV-MDYIKNEKRRIYPIGRLDLHTEGLLLLTNDGELAQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            L  PS    + Y VR  G+V+   L ++  G+ ++        +        N    V 
Sbjct: 121 NLTHPSKGVEKTYEVRIKGRVNDTDLQVIADGVPLEDGVTAPATLVDLGFDDHNGVHEVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           + + EG+NR+++++FE F ++++ L RI+YG   L  +  G  R+++++ +      
Sbjct: 181 ITIHEGRNRQVRRMFEHFGYRIHNLKRIAYGGLTLSGVKRGGVRQLTQREVSALKAL 237


>gi|302871660|ref|YP_003840296.1| pseudouridine synthase [Caldicellulosiruptor obsidiansis OB47]
 gi|302574519|gb|ADL42310.1| pseudouridine synthase [Caldicellulosiruptor obsidiansis OB47]
          Length = 236

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 74/228 (32%), Positives = 118/228 (51%), Gaps = 2/228 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A+ G+ASRR+ E +I Q RVKVNG  + +    +    D +EVDG  +     
Sbjct: 1   MRLQKFMAQCGVASRRKCEEIIQQGRVKVNGKTVNQLGFKIDPEKDIVEVDGERISLQSH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G++++  D  GR TV D +    +     VGRLD +T GL+LLTNDG  A
Sbjct: 61  KVYIMLNKPFGVISSAKDEKGRKTVVDLVKDKVNVRVFPVGRLDFDTTGLILLTNDGEFA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P     + Y     G   ++++   +KG++I G      +  +  Q   NA V +
Sbjct: 121 YKVTHPKHDIEKTYIALIKGIPSKEEIERFEKGLLIDGKMTAPAKFKVLKQINGNAMVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG+NR+I+K+ +    KV +L RI+ G  QLG L  G    + ++
Sbjct: 181 KIHEGRNRQIRKMCDMIGHKVLKLKRIAIGKLQLGKLKEGEFVFLDRE 228


>gi|120556720|ref|YP_961071.1| 23S rRNA pseudouridine synthase F [Marinobacter aquaeolei VT8]
 gi|120326569|gb|ABM20884.1| ribosomal large subunit pseudouridine synthase F [Marinobacter
           aquaeolei VT8]
          Length = 332

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 67/335 (20%), Positives = 125/335 (37%), Gaps = 5/335 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N T  R++K I+ +G+ SRR+ +R I Q  V +NG   +     V+  D ++V+G  +  
Sbjct: 3   NRTSTRLNKYISESGMCSRRDADRFIEQGNVHINGRRAQV-GDQVLPGDVVKVNGQVVEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   L        +    +                 R+  +GRLD +++GL+ LT++G 
Sbjct: 62  RDEEDLVFIALNKPVGIVSTTDSAEKDNIQRFVGHSERIFPIGRLDKDSQGLIFLTSNGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     V ++ +  +  G+ I G      +V    +K S    
Sbjct: 122 LVNKILRAGNNHEKEYLVTVDKPVTREFVEGMSNGVPILGTMTKRCKV----EKVSRFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F ++V RL R+      L  L  G+ R++++K L        
Sbjct: 178 RITLVQGLNRQIRRMAEYFGYEVARLERVRIMNVSLQGLPVGAWRDLTEKELAVLFDAIR 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
              ++    A     +     R               K   +      +K   +   +R 
Sbjct: 238 DSSSEATEPAGSKPRKKPAGARGARPGPGGKPARAGAKAGGKSPAGKGRKGPGSGPGKRP 297

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
                   K       S     +    R PS   +
Sbjct: 298 SGKPGGGPKPGGRGPGSKGKPSKPGKPRKPSIKKR 332


>gi|302874254|ref|YP_003842887.1| pseudouridine synthase [Clostridium cellulovorans 743B]
 gi|307689482|ref|ZP_07631928.1| pseudouridine synthase [Clostridium cellulovorans 743B]
 gi|302577111|gb|ADL51123.1| pseudouridine synthase [Clostridium cellulovorans 743B]
          Length = 241

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 68/231 (29%), Positives = 109/231 (47%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV+A  G  +R+EV+ ++ +  V++NG+  + + V V +  D I+V+G  +   + 
Sbjct: 2   ERLDKVLANLGYGTRKEVKVLVKKGAVEINGVQAKNSDVKVDTNEDIIKVNGETINYRKF 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  T  + D       +          VGRLD +T GLLLLTNDG L  
Sbjct: 62  IYLMMNKPAGVVSATFDNYDETVIDLLDPEEQIFEPFPVGRLDKDTVGLLLLTNDGELNH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY       VD   +   +KGIV+         ++ +       + V V
Sbjct: 122 KLISPKYHVDKVYYAEIDKPVDDKDVKCFEKGIVLDDGYKTMPGKLEILKATEHGSEVYV 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            ++EGK  ++K++FE    KV  L RIS+G   L   L  G  RE+S+  L
Sbjct: 182 TIQEGKFHQVKRMFESLGKKVVFLKRISFGGIILDEDLEEGQYREISEDEL 232


>gi|226312000|ref|YP_002771894.1| ribosomal large subunit pseudouridine synthase B [Brevibacillus
           brevis NBRC 100599]
 gi|226094948|dbj|BAH43390.1| probable ribosomal large subunit pseudouridine synthase B
           [Brevibacillus brevis NBRC 100599]
          Length = 249

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 79/232 (34%), Positives = 116/232 (50%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ KV+A AG+ASRR  E +IAQ +V+VNG ++    + V    D I V+G  ++  + 
Sbjct: 2   ERLQKVLAHAGVASRRHCEELIAQGKVQVNGQVVREQGIKVDPLKDKIVVNGQQVKLEQH 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L LY     + +          V D L  I  RV  VGRLD +T GLLLLTNDG LA 
Sbjct: 62  VYLLLYKPTGVITSVTDPQGR-RVVIDLLKGIQERVYPVGRLDYDTSGLLLLTNDGELAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVT 190
            L  PS +  +VYR    G    +K+  L  GI ++       Q  L   + S   A V 
Sbjct: 121 RLAHPSYEIDKVYRAWVKGIPSPEKVRKLATGIRLEDGMTSPGQSKLLKAESSSQRALVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + + EG+NR+++++ E     V  L RI  G   L  L  G  R+++ + + 
Sbjct: 181 LTIHEGRNRQVRRMCEAIGHPVLTLERIRLGFLTLDGLKPGEFRKLTHEEVE 232


>gi|148379772|ref|YP_001254313.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum A str. ATCC 3502]
 gi|153931029|ref|YP_001384070.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum A str. ATCC 19397]
 gi|153937131|ref|YP_001387610.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum A str. Hall]
 gi|148289256|emb|CAL83352.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum A str. ATCC 3502]
 gi|152927073|gb|ABS32573.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum A str. ATCC 19397]
 gi|152933045|gb|ABS38544.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum A str. Hall]
          Length = 236

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 70/230 (30%), Positives = 119/230 (51%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +A  G+ASRR+ E +I + RV+VNGI ++     ++S  D I+VDG  +   E 
Sbjct: 3   ERLQKYMASCGVASRRKCEDIILEGRVEVNGIKIKELGTKIISGKDIIKVDGNIIEPEEN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G V T  D   R T   +L  +  R+  +GRLD++T G+++LTNDG +  
Sbjct: 63  KIYILLNKPKGYVCTAKDEKDRKT-ILDLVKVKERIYPIGRLDMDTSGIIILTNDGEIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  + ++ Y+ +  G + +D + L KKGI I         + +       + + + 
Sbjct: 122 KIIHPKFEKIKTYKAKVKGTIKKDHIELFKKGIDIGDYLTAPATLEILKINKDTSEIIIK 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGKNR+++++ +     V  L RIS G      L  G  R ++ K + 
Sbjct: 182 IHEGKNRQVRRMCKSIGHAVIDLDRISIGNITKSDLKLGEWRYLTNKEID 231


>gi|218899863|ref|YP_002448274.1| RNA pseudouridine synthase family protein [Bacillus cereus G9842]
 gi|228910563|ref|ZP_04074377.1| Pseudouridine synthase [Bacillus thuringiensis IBL 200]
 gi|228941890|ref|ZP_04104435.1| Pseudouridine synthase [Bacillus thuringiensis serovar berliner
           ATCC 10792]
 gi|228974817|ref|ZP_04135381.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228981409|ref|ZP_04141709.1| Pseudouridine synthase [Bacillus thuringiensis Bt407]
 gi|218544778|gb|ACK97172.1| RNA pseudouridine synthase family protein [Bacillus cereus G9842]
 gi|228778609|gb|EEM26876.1| Pseudouridine synthase [Bacillus thuringiensis Bt407]
 gi|228784915|gb|EEM32930.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228817795|gb|EEM63875.1| Pseudouridine synthase [Bacillus thuringiensis serovar berliner
           ATCC 10792]
 gi|228849127|gb|EEM93967.1| Pseudouridine synthase [Bacillus thuringiensis IBL 200]
 gi|326942491|gb|AEA18387.1| ribosomal small subunit pseudouridine synthase A [Bacillus
           thuringiensis serovar chinensis CT-43]
          Length = 242

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 105/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G  ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L ++     +  T  D          L         VGRLDI+TEG LL+TNDG L+ 
Sbjct: 61  VYLMMHKPQGVISATEDDNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKLSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G V ++ +    KG+++          +T+  +    + + +
Sbjct: 121 QLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 180 VITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 231


>gi|294084708|ref|YP_003551466.1| pseudouridine synthase [Candidatus Puniceispirillum marinum
           IMCC1322]
 gi|292664281|gb|ADE39382.1| Pseudouridine synthase, Rsu [Candidatus Puniceispirillum marinum
           IMCC1322]
          Length = 312

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 131/315 (41%), Positives = 184/315 (58%), Gaps = 6/315 (1%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            +   + +    +R++K IARAG+ SRRE E  I + RVKVNG ++    +NV  TD I 
Sbjct: 4   NETFTLDKKSDSERIAKRIARAGVCSRREAEARINEGRVKVNGKVITSPVLNVSDTDRIN 63

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           VDG  L   E  +LW Y+KP GLV +  D   R T+FD+LP+   RV++VGRLDI++EGL
Sbjct: 64  VDGQALPHREPAKLWRYYKPRGLVVSDRDEKDRETIFDHLPASLPRVMTVGRLDIDSEGL 123

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDG LAR LELP+T W R YRVR  G V++  L  L+KGI I G+ YG +   LD 
Sbjct: 124 LLLTNDGDLARHLELPATGWSRKYRVRVQGHVNEAALAPLEKGITIDGVRYGRIVANLDR 183

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           Q  SNAW+TV +REGKNRE++++ E    KV+RLIR+SYGPFQLG +  G   ++  ++L
Sbjct: 184 QMQSNAWLTVAIREGKNREVRRIMEHLGHKVSRLIRVSYGPFQLGDMSDGDVEQIRARVL 243

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            +QLG    E+          +++  +R +P++       +     +S Q +   K    
Sbjct: 244 SDQLGLTDPEDDG------HATAKPRLRAKPSMKRSGGGRYKGKTSSSQQDDKRGKDAHN 297

Query: 302 ATPVHRRNLASNVWM 316
             P  R     +   
Sbjct: 298 RGPSSRHKTGQSGRR 312


>gi|261337756|ref|ZP_05965640.1| ribosomal large subunit pseudouridine synthase B [Bifidobacterium
           gallicum DSM 20093]
 gi|270277210|gb|EFA23064.1| ribosomal large subunit pseudouridine synthase B [Bifidobacterium
           gallicum DSM 20093]
          Length = 258

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 74/235 (31%), Positives = 118/235 (50%), Gaps = 2/235 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           N    R+ K++A+AG  SRR+ E MI   RV+V+G L+      V      + VDG  +R
Sbjct: 16  NNEGIRLQKILAQAGFGSRRKCEEMILDGRVEVDGELVTELGSRVDPKRQEVRVDGSRIR 75

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              R      +KP  +++T  DP GR T+ D +   + R+  +GRLD ++EGL+L+TNDG
Sbjct: 76  LNNRHVTLALNKPKRVLSTMDDPKGRYTLRDIVGDKYERIFHMGRLDYDSEGLILMTNDG 135

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNA 187
            L++ +  P  +  + Y V   G +  +    L +  + +        Q ++        
Sbjct: 136 ELSQHVMHPRYEVAKTYVVTLDGHLSGNVCRRLVRTGVQLDDGWIKLDQCSIIDANRETT 195

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V V L  GKNR ++++F    + V RL+R   GP +LG L  GS R +S   +R
Sbjct: 196 IVKVVLHSGKNRIVRRIFGAIGFPVRRLVRTQIGPIKLGDLKPGSYRVLSDAEVR 250


>gi|206889194|ref|YP_002248392.1| ribosomal large subunit pseudouridine synthase B
           [Thermodesulfovibrio yellowstonii DSM 11347]
 gi|206741132|gb|ACI20189.1| ribosomal large subunit pseudouridine synthase B
           [Thermodesulfovibrio yellowstonii DSM 11347]
          Length = 237

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 87/229 (37%), Positives = 132/229 (57%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+++  GIASRR  E +I + RV VNG +           D+I+VDG  L K E  
Sbjct: 3   ERLQKILSDYGIASRRHAEELIKEGRVTVNGQIAVIGQKADPEKDYIKVDGKLLIKPEPK 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + ++KP  ++T   DP GR T+ D +  I  R+  VGRLD ++EGLLLLTNDG LA  
Sbjct: 63  VYYAFYKPRKVITALLDPQGRPTIRDFIKGIKFRIYPVGRLDFDSEGLLLLTNDGELAYK 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  PS+Q  + Y V+  G V+ + +  L+KGI I+G     + V L  +  +N+W+ + L
Sbjct: 123 VMHPSSQIEKTYMVKVDGIVEPETIEKLRKGIKIEGKLAVPVSVHLVKKLKANSWIKITL 182

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EG+ R+I+K+ E     V RLIRI+    +LG L  G  R ++K+ + 
Sbjct: 183 HEGRKRQIRKMLERVGHPVIRLIRIAIDGVKLGDLKPGQLRPLTKEEIE 231


>gi|256847151|ref|ZP_05552597.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           coleohominis 101-4-CHN]
 gi|256715815|gb|EEU30790.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           coleohominis 101-4-CHN]
          Length = 240

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 71/238 (29%), Positives = 114/238 (47%), Gaps = 4/238 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR  E++IA   V VNG ++      V  +D + VDGVP+++    
Sbjct: 2   ERLQKVMAEAGVASRRASEKLIAAGHVAVNGQVVTELGTKVTKSDQVTVDGVPIKREPLK 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLAR 132
              L      + T H D   R+ V              VGRLD +T G+LLLTNDG LA 
Sbjct: 62  YYLLNKPRGVVSTAHDDKGRRTVVDILKDDDVEERVYPVGRLDYDTTGILLLTNDGALAN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            L  P  +  + Y  +  G +    L  L++G+++ G    + +  L     +   + V 
Sbjct: 122 KLMHPKFEVEKTYIAKVKGVLSNHDLQKLRQGVIVDGRKTREAKSKLLEVADNRQSSRVR 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGP 247
           + + EG   ++K++ +     V +L R SYGP  L  L + G  RE+    +++    
Sbjct: 182 LTIHEGHYHQVKRMLKAVGHPVIKLHRESYGPLNLYGLASGGQWRELKPNEVKQLKNL 239


>gi|88802487|ref|ZP_01118014.1| putative pseudouridine synthase [Polaribacter irgensii 23-P]
 gi|88781345|gb|EAR12523.1| putative pseudouridine synthase [Polaribacter irgensii 23-P]
          Length = 296

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 64/298 (21%), Positives = 122/298 (40%), Gaps = 7/298 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N     ++K I+ +G+ SRRE E+ I + R+ +NG    +    V   D ++ DG  +  
Sbjct: 5   NQQSINLNKYISSSGVCSRREAEKFIKEGRITINGK-ATQLGNRVGKKDVVKFDGRLVEP 63

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
              T     +KP+G+V+T  + +          +   R+  +GRLD  +EGL+ LTNDG 
Sbjct: 64  KNVTLYIALNKPVGIVSTTDERE--PHNIVKHVNYPERLFPIGRLDKPSEGLIFLTNDGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +        + Y V     +  D +  +  GI I G      +V    +K S+   
Sbjct: 122 IVNKILRAGNNHEKEYFVSVDKSITNDFITSMGNGIPILGTMTKRCKV----EKVSDKIF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+ +++V +L R       LG L +G  RE++++ +++      
Sbjct: 178 KIVLTQGLNRQIRRMCEYLDYEVTKLKRTRIMNVDLGYLQSGDWRELTEEEMKDINKMIA 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                    +     +     R    ++   +        S           +    R
Sbjct: 238 TSSKTEEASSIEEKPKQARPKRNKAPTKNDFNKKSASFRKSSPKSKRSNTSFSAKKKR 295


>gi|323695091|ref|ZP_08109233.1| pseudouridine synthase [Clostridium symbiosum WAL-14673]
 gi|323500846|gb|EGB16766.1| pseudouridine synthase [Clostridium symbiosum WAL-14673]
          Length = 241

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 68/243 (27%), Positives = 113/243 (46%), Gaps = 9/243 (3%)

Query: 7   VQENFT---PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           + +N       R++K ++ AGI SRRE +R+I   +V V+G       + V ++  I V+
Sbjct: 1   MNDNAKTDNGIRLNKYLSEAGICSRREADRLIEDGKVTVDGRTA-SMGMKVFTSQEITVN 59

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G  +   ER  L   +KP G+V T SD D    + + L     R+  VGRLD ++EGLLL
Sbjct: 60  GKRVEGKERPVLLAVNKPRGIVCTTSDKDRAENIVEFLKY-PVRIYPVGRLDKDSEGLLL 118

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           +TN G L   +        + Y V     V +  +  ++ G+ I G      +  +    
Sbjct: 119 MTNQGDLVNRILRGRYGHEKEYLVTVDRPVTEAFIRQMRNGVEILGTRTKPCEAEI---- 174

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
                 ++ L +G NR+I+++ E   ++V  L R+     +LG L  G  RE++     E
Sbjct: 175 TGKRSFSIILTQGLNRQIRRMCEALGYQVKTLKRVRIMNVKLGNLKTGQYRELTPAEWEE 234

Query: 244 QLG 246
              
Sbjct: 235 LQR 237


>gi|229817643|ref|ZP_04447925.1| hypothetical protein BIFANG_02913 [Bifidobacterium angulatum DSM
           20098]
 gi|229785432|gb|EEP21546.1| hypothetical protein BIFANG_02913 [Bifidobacterium angulatum DSM
           20098]
          Length = 257

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 72/241 (29%), Positives = 120/241 (49%), Gaps = 2/241 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEV 62
           +     N    R+ K++A+AG  SRR+ E+MI   RV+V+G L+      V  T   I V
Sbjct: 9   RKAHDNNQEGIRLQKLLAQAGFGSRRKCEQMITDGRVEVDGELVTELGTRVDPTHQQIRV 68

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG  +R + +      +KP  +++   DP GR T+ D +   + R+  +GRLD ++EGL+
Sbjct: 69  DGSRVRISNKHITLALNKPRKVLSAMDDPKGRYTLRDIVGDKYERIFHMGRLDYDSEGLI 128

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDT 181
           L+TNDG L++ +  P  +  + Y     G++       L    + +        +  +  
Sbjct: 129 LMTNDGELSQHVMHPKYEVEKTYIATLEGRISGTVCRRLVTTGVQLDDGWIKLDRCAIID 188

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                  V V L  GKNR ++++F    + V RL+R   GP +LG L +GS R +S+  +
Sbjct: 189 ATHDTTIVKVVLHSGKNRIVRRIFGSIGFPVKRLVRTQIGPIKLGDLKSGSYRVLSQTEV 248

Query: 242 R 242
           R
Sbjct: 249 R 249


>gi|197122579|ref|YP_002134530.1| pseudouridine synthase [Anaeromyxobacter sp. K]
 gi|196172428|gb|ACG73401.1| pseudouridine synthase [Anaeromyxobacter sp. K]
          Length = 329

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 88/321 (27%), Positives = 132/321 (41%), Gaps = 6/321 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +A AGIASRR+ E +I+  RV+VN   +      V    D + VDG  + + E+
Sbjct: 4   ERLQKFLAGAGIASRRKAEALISAGRVRVNQRTVTELGTKVDPGRDLVTVDGALVSQPEQ 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP G VTT SDP GR T  + L  +  R   VGRLD + EG LLLT+DG LA 
Sbjct: 64  RSYYLLYKPSGCVTTASDPQGRPTAMEYLRGVPGRPFPVGRLDYDAEGALLLTDDGELAN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     RVY V+  G    + L  +K G+ ++      ++V +      N W+ V 
Sbjct: 124 RLAHPRYGHQRVYLVKVKGDPPAEALERMKAGVRLEDGPARALEVAVHEHADRNVWIRVV 183

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           + EG+   +K++ E    +V RL R  +G   +G L  G  R +  + +R       LE 
Sbjct: 184 VGEGRFHLVKRLCEAVGLQVQRLFRPEFGGIGVGGLRPGKFRRLEPEEVRALRQRVGLES 243

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
                   +       R                      + G  + +  A    R     
Sbjct: 244 GTPARGPSVRELPKAARRHG-----HGPPAAPGAVPPPAEPGADEVEPRARGASRGGPRP 298

Query: 313 NVWMAKGIHSSFLSDSGQREE 333
               A        +    R  
Sbjct: 299 AGPRATAPGPGGRASRPSRPS 319


>gi|153939039|ref|YP_001391068.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum F str. Langeland]
 gi|152934935|gb|ABS40433.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum F str. Langeland]
 gi|295319117|gb|ADF99494.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum F str. 230613]
          Length = 236

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 73/230 (31%), Positives = 121/230 (52%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +A  G+ASRR+ E +I + RV+VNGI ++     ++S  D I+VDG  +   E 
Sbjct: 3   ERLQKYMASCGVASRRKCEDIILEGRVEVNGIKIKELGTKIISGKDIIKVDGNIIEPEEN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G V T  D  GR T   +L  I  R+  +GRLD++T G+++LTNDG +  
Sbjct: 63  KIYILLNKPKGYVCTAKDEKGRKT-ILDLVKIKERIYPIGRLDMDTSGIIILTNDGEIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  + ++ Y+ +  G + +D + L KKGI I         + +       + + + 
Sbjct: 122 KIIHPKFEKIKTYKAKVKGTIKKDHIELFKKGIDIGDYITAPATLEILKINKDTSEIIIK 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGKNR+++++ +     V  L RIS G      L  G  R ++KK + 
Sbjct: 182 IHEGKNRQVRRMCKSIGHAVIDLDRISIGNITKSDLKLGEWRYLTKKEID 231


>gi|15888032|ref|NP_353713.1| ribosomal large subunit pseudouridine synthase B [Agrobacterium
           tumefaciens str. C58]
 gi|15155650|gb|AAK86498.1| ribosomal large subunit pseudouridine synthase B [Agrobacterium
           tumefaciens str. C58]
          Length = 669

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 176/343 (51%), Positives = 221/343 (64%), Gaps = 7/343 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P+R+SK++ARAG+ASRR+VERMI + RV +NG+LL+   VN   +D IEVDG+P+R AE
Sbjct: 55  KPERISKIMARAGVASRRDVERMIMEGRVSLNGVLLDTPVVNATLSDKIEVDGMPIRGAE 114

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RTRLWLYHKP GLVTT+SDP+GR TVFDNLP    RV+S+GRLDINTEGLLLLTNDGGL+
Sbjct: 115 RTRLWLYHKPAGLVTTNSDPEGRPTVFDNLPGELPRVLSIGRLDINTEGLLLLTNDGGLS 174

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           RVLELP+T WLR YRVR HG+VDQ  L+ LK GI + G+ YG +  TLD  +G N W+T+
Sbjct: 175 RVLELPTTGWLRRYRVRAHGEVDQAALDKLKDGIAVDGVLYGAIDATLDRTQGHNVWITM 234

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
           GLREGKNREIK V      +VNRLIRISYGPFQLG L  G   EV  ++LR+QLGP L+E
Sbjct: 235 GLREGKNREIKNVLGALGLEVNRLIRISYGPFQLGDLPEGKVLEVRGRMLRDQLGPRLIE 294

Query: 252 EAQVNLDAPIYSSE-------TLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           EA  N DAPIY++           R +         +     + ++ K    ++K L   
Sbjct: 295 EAGANFDAPIYNTSVDDEEEAPAKRAKSEWAKSDAPEGKPRFEKAAGKPEDRREKALGRL 354

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
             +R+              F       +E   R P  P+  S 
Sbjct: 355 DTKRSDKPAGKFGAKPAGKFGGKGRNDDEGDDRRPRPPAGTSR 397



 Score = 37.5 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 12/105 (11%), Positives = 22/105 (20%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P   ++   +        E   R R +          R  +     +    + K     
Sbjct: 524 RPARGDKPFGDRPFRDRPREDGDRPRSDRPRGEKSFGDRTARGEKPFSERPFRDKPREEG 583

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
            R                     G R  + + S     +R  R  
Sbjct: 584 DRPGSDRPRGDRPFGDKPRGGKPGGRPASGKPSFGKSGERGERSG 628



 Score = 35.9 bits (81), Expect = 8.6,   Method: Composition-based stats.
 Identities = 15/110 (13%), Positives = 23/110 (20%), Gaps = 1/110 (0%)

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
            G       +   D P        R R +      D   R  K+   +     +     P
Sbjct: 477 FGDRGGRGGKPFGDRPSGDRPFRDRPREDGDRPRGDRPARGTKSFGDRPARGDKPFGDRP 536

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              R         +          G R     +  S    R   R    +
Sbjct: 537 FRDRPREDGD-RPRSDRPRGEKSFGDRTARGEKPFSERPFRDKPREEGDR 585


>gi|326390305|ref|ZP_08211864.1| pseudouridine synthase [Thermoanaerobacter ethanolicus JW 200]
 gi|325993582|gb|EGD52015.1| pseudouridine synthase [Thermoanaerobacter ethanolicus JW 200]
          Length = 241

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 66/231 (28%), Positives = 108/231 (46%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K+++  GI +R+EV++ I +  V VNG  ++ A + V   +D I  DG  +   E 
Sbjct: 4   MRIDKLLSNIGIGTRKEVKKFIKEGLVLVNGNTVKDAGLIVDTESDEILFDGEKINYKEF 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      +  T+ + +                  VGRLD +TEGLLL+TNDG LA 
Sbjct: 64  IYIMINKPKGVISATYDEVEKTVIDLLPQELKARNPFPVGRLDKDTEGLLLITNDGDLAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P    ++ Y     G V++  +    +GI+++         + +       + V V
Sbjct: 124 QLLSPKKNVIKKYYAEILGFVNESDIKAFNEGIILEDGYKTLPANLEILFSSSDVSKVYV 183

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            +REGK  +IK++FE    KV  L R++     L   L  G  RE+S+K L
Sbjct: 184 YIREGKYHQIKRMFESVGKKVIYLKRLAMDNLTLDENLKPGEWRELSEKEL 234


>gi|170288482|ref|YP_001738720.1| pseudouridine synthase [Thermotoga sp. RQ2]
 gi|170175985|gb|ACB09037.1| pseudouridine synthase [Thermotoga sp. RQ2]
          Length = 239

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 61/245 (24%), Positives = 113/245 (46%), Gaps = 7/245 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++ +G+ +R+EV+++I Q RV VNG ++      V+  D + +DG  +R  ++ 
Sbjct: 1   MRLDRYLSNSGVGTRKEVKKLIKQGRVTVNGRVVLDPGHPVLENDAVALDGEVVRFHKKV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +  Y     + +T       S            +  VGRLD + EGLL++TNDG  A  
Sbjct: 61  YILFYKPSGYVTSTKDP---HSETIMEFLPPLKGIFPVGRLDKDAEGLLIITNDGDFAHR 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V+  G+V +DK+  LK G+ ++   +   +     +K SN  + + +
Sbjct: 118 VISPKWSVEKEYIVKVEGEVTEDKIEKLKNGVTLRDGFFAKAKCV---EKLSNDTLKIVI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHLLEE 252
            EGK  +IK++      K   L R   G   L   +  G  R +S++ +++       +E
Sbjct: 175 TEGKYHQIKRMTAAVGLKTVHLKRTRIGGLVLPDDMKPGEYRFLSEEEVKKVFEREDQKE 234

Query: 253 AQVNL 257
                
Sbjct: 235 DTPRF 239


>gi|170760151|ref|YP_001788590.1| RNA pseudouridine synthase family protein [Clostridium botulinum A3
           str. Loch Maree]
 gi|169407140|gb|ACA55551.1| RNA pseudouridine synthase family protein [Clostridium botulinum A3
           str. Loch Maree]
          Length = 238

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 108/231 (46%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++A  G  +R+EV+ +I + +V V+G +++   + +    + I V G  L   + 
Sbjct: 2   ERLDKILANLGYGTRKEVKALIKKGQVDVDGEVVKDNGMQIDPEKNKIFVFGKELVYKKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  T  + D                  VGRLD NT GLLLLTNDG L  
Sbjct: 62  IYLIMNKPQGVVSATFDNYDETVVDLLEDEDRIFEPFPVGRLDKNTVGLLLLTNDGELNH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     ++Y  + + +V  + +   KKGI++         ++ +       + V V
Sbjct: 122 RLISPKWHVDKIYYAKINKKVTDEDIKKFKKGIILDDGYECFPAKLEIIKSFNEESEVRV 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++FE  + KV  L R  +GP +L   L  G  RE++ + +
Sbjct: 182 TIHEGKFHQVKRMFESVDKKVIYLKREEFGPLKLDESLEEGQCRELTDEEI 232


>gi|293379060|ref|ZP_06625213.1| pseudouridylate synthase [Enterococcus faecium PC4.1]
 gi|292642339|gb|EFF60496.1| pseudouridylate synthase [Enterococcus faecium PC4.1]
          Length = 239

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 59/238 (24%), Positives = 104/238 (43%), Gaps = 5/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ SR+EV+ +I +  ++VNG +++     V    D +   G  +   + 
Sbjct: 1   MRLDKFLADMGLGSRKEVKGLIKKGTIEVNGQVVKSDKTQVNEFEDTVTYLGEIIAYQKD 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T  + D               +  VGRLD +TEGLL+LTNDG  A 
Sbjct: 61  FYYILHKPAGVISATQDNHDQTVIDLLKDQDYREDLFPVGRLDKDTEGLLILTNDGIFAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKG--SNAWV 189
            L  P     + Y     G + ++ + L  +G++I         ++ +D        + +
Sbjct: 121 QLLSPKKHVEKEYLAEVSGIMTEEDIRLFAEGLIIDGDEQTLPAKLQIDQVDQESETSII 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
            + L EGK  ++K++ +    +V  L RI  G F L   L  G  R ++K+ L +   
Sbjct: 181 RLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGNFWLPKDLNKGQYRPMTKEELEQVRE 238


>gi|258423147|ref|ZP_05686040.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9635]
 gi|257846597|gb|EEV70618.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9635]
          Length = 245

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 78/243 (32%), Positives = 129/243 (53%), Gaps = 3/243 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R+ K IA +G  SRR+ E +I++ +VKVNG  +      V  +D IEV+G+ +  
Sbjct: 2   TKELERLQKRIANSGYTSRRKAETLISEGKVKVNGTTVTELGTKVKPSDTIEVEGIKIE- 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E     L+HKP  ++T+ SD  GR+ V D    I +R+  VGRLD +T GLLLLTNDG 
Sbjct: 61  QEDKIYILFHKPTQVITSVSDDRGRTVVTDYFKDIDARIYPVGRLDYDTSGLLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNA 187
              ++  P  Q  + Y  +  G + ++++  L+KGI ++         +V    +  +  
Sbjct: 121 FTNLMTHPRYQIKKKYVAKLKGYLMREEVKALEKGIELEDGLTQPADVKVKKQDKDKNTT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V + + EG+NR+++++FE F  +V +L RI YGP  +  L AG  R ++   ++     
Sbjct: 181 LVEITITEGRNRQVRRMFEHFGHQVTKLSRIEYGPLNVVGLNAGEGRVLTPHEVKVMRHL 240

Query: 248 HLL 250
              
Sbjct: 241 AEH 243


>gi|170761840|ref|YP_001787134.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum A3 str. Loch Maree]
 gi|169408829|gb|ACA57240.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum A3 str. Loch Maree]
          Length = 236

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 72/230 (31%), Positives = 121/230 (52%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +A  G+ASRR+ E +I + RV+VNGI ++     ++S  D I+VDG  +   E 
Sbjct: 3   ERLQKYMASCGVASRRKCEDIILEGRVEVNGIKIKELGTKIISGKDIIKVDGNIIEPEEN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G V T  D  GR T   +L  +  R+  +GRLD++T G+++LTNDG +  
Sbjct: 63  KIYILLNKPKGYVCTAKDEKGRKT-ILDLVKVKERIYPIGRLDMDTSGIIILTNDGEIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  + ++ Y+ +  G + +D + L KKGI I         + +       + + + 
Sbjct: 122 KIIHPKFEKIKTYKAKVKGTIKKDHIELFKKGIDIGDYITAPATLEILKINKDTSEIIIK 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGKNR+++++ +     V  L RIS G      L  G  R ++KK + 
Sbjct: 182 IHEGKNRQVRRMCKSIGHAVIDLDRISIGNITKSDLKLGEWRYLTKKEID 231


>gi|315656791|ref|ZP_07909678.1| ribosomal large subunit pseudouridine synthase B [Mobiluncus
           curtisii subsp. holmesii ATCC 35242]
 gi|315492746|gb|EFU82350.1| ribosomal large subunit pseudouridine synthase B [Mobiluncus
           curtisii subsp. holmesii ATCC 35242]
          Length = 278

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 77/238 (32%), Positives = 120/238 (50%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
              P+R+ KV++RAG+ASRR  E +IA+ RV++NG  +    V V+ TD I VDG  +  
Sbjct: 38  TSEPERLQKVLSRAGVASRRASEDLIARGRVQINGETVREMGVKVLPTDRITVDGQRIHT 97

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               ++W +HKP+G V++    D R  + D +  +  RV +VGRLD  T GLLLLTN+G 
Sbjct: 98  DTVLQVWAFHKPVGTVSSMQPEDDRPCIGDWVTKLPERVYNVGRLDAATAGLLLLTNNGE 157

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  +  PS +  + Y     GQV      +L++G+ ++       +  L   +  ++ V
Sbjct: 158 LANRIMHPSYEVPKTYVAVVQGQVKMGLGKVLRRGVELEDGKVKVDKFKLIEVRRGSSIV 217

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + L  GKNR ++++       V+ L R       L  L  G  R +  K L      
Sbjct: 218 QLTLHSGKNRVVRRLLSAVGHPVSALTRTGIANLTLDGLKEGQFRLLHGKELAALQEM 275


>gi|317128531|ref|YP_004094813.1| pseudouridine synthase [Bacillus cellulosilyticus DSM 2522]
 gi|315473479|gb|ADU30082.1| pseudouridine synthase [Bacillus cellulosilyticus DSM 2522]
          Length = 242

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 68/238 (28%), Positives = 115/238 (48%), Gaps = 5/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ KVIA+AG+ SRR+ E++I + +V VNG  +      V    D + V+GVPL K E 
Sbjct: 5   ERLQKVIAQAGVTSRRKAEQLILEGKVIVNGNKVTELGTKVDLQHDEVIVEGVPLEKEEP 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               LY     + +   +   +                +GRLD +T GL+LLTNDG  A 
Sbjct: 65  IYFLLYKPTGVISSVDDEKGRKVVTDFIPTDKRI--FPIGRLDYDTSGLILLTNDGDFAN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVT 190
           +L  P  +  + Y  +  G   ++ +  L+KGI ++       +V +    +K   + + 
Sbjct: 123 LLMHPKHEIYKTYIAKVEGVPLREDIKKLEKGIHLEDGRTAPAKVKVSRSDKKKGTSIIE 182

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + + EG+NR+++++FE     V +L R +YG   L  L AG  RE+    ++      
Sbjct: 183 ISIHEGRNRQVRRMFEAIGHPVMKLKRENYGFLNLKGLNAGDFRELKPHEVKRLRELA 240


>gi|238855198|ref|ZP_04645517.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii 269-3]
 gi|260664561|ref|ZP_05865413.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii SJ-7A-US]
 gi|282932508|ref|ZP_06337933.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii 208-1]
 gi|313471973|ref|ZP_07812465.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii 1153]
 gi|238832090|gb|EEQ24408.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii 269-3]
 gi|239529095|gb|EEQ68096.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii 1153]
 gi|260561626|gb|EEX27598.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii SJ-7A-US]
 gi|281303457|gb|EFA95634.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii 208-1]
          Length = 237

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 78/230 (33%), Positives = 128/230 (55%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+IA+AGIASRR+ E++I + RV VNG ++      V S+  IEVDG+P++K  + 
Sbjct: 3   ERLQKLIAQAGIASRRKAEKLITEGRVAVNGKIVTELGTKVESSASIEVDGLPIQKESKH 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     ++++  D  GR TV D       R+  VGRLD +T GLLL+TNDG LA  
Sbjct: 63  TYLLYKPRG-VISSVKDDKGRKTVLDFFEESPYRLYPVGRLDYDTSGLLLITNDGELANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           L  P     +VY  +  G +  ++++ LK G+ I G      +V +    ++   + V +
Sbjct: 122 LMHPRHMVDKVYVAKIKGFLTPEEIHSLKHGVRIDGKKSAPAKVKIISTNREKGTSIVQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + EG   ++K++F+     V++L R  Y    L +L AG  RE++++ +
Sbjct: 182 TIHEGHYHQVKRMFKAVGHLVDKLSRERYAFLTLKSLTAGKYRELTREEV 231


>gi|309389185|gb|ADO77065.1| ribosomal large subunit pseudouridine synthase B [Halanaerobium
           praevalens DSM 2228]
          Length = 236

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 64/236 (27%), Positives = 117/236 (49%), Gaps = 2/236 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAER 72
           +R+ KV+A AG+ASRR+ E +IA+ RVKVNG ++      +      + VDG  + + ++
Sbjct: 2   ERLQKVMAHAGVASRRKSEEIIAEGRVKVNGQVITEMGYKIDPAQAEVMVDGQVISEEKK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + T     +   TV D +P +  R+   GRLD ++ GLL++TNDG L  
Sbjct: 62  VYILLNKPEGYITTVSDPENR-PTVMDLIPDLNQRLYPAGRLDFDSSGLLIMTNDGDLTY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + YRV   G+++++     + G+VI G      +++    KG      + 
Sbjct: 121 KLTHPKKEVDKKYRVLIQGKLEEEDFEKFEAGMVIDGQETAPAEISNVDYKGEQTEFDIV 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + EG+NR+++++ +   + V  L RI +    L  +  G  R +++  +       
Sbjct: 181 IHEGRNRQVRRMAKIAGFSVISLKRIGFAFLTLTGVEEGKFRYLTEAEVENLKKLA 236


>gi|257063679|ref|YP_003143351.1| ribosomal large subunit pseudouridine synthase B [Slackia
           heliotrinireducens DSM 20476]
 gi|256791332|gb|ACV22002.1| ribosomal large subunit pseudouridine synthase B [Slackia
           heliotrinireducens DSM 20476]
          Length = 249

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 67/237 (28%), Positives = 107/237 (45%), Gaps = 2/237 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
           +E   P RV K +ARAG+ASRR  E ++   RV VNG ++      V    D + VDG  
Sbjct: 5   EERIVPMRVQKFLARAGVASRRRSEDLMTAGRVCVNGEVVTELGAKVDPRVDTVTVDGRE 64

Query: 67  LRKAERTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +R  +    + L      + T                  +  +  VGRLD +T GLLL +
Sbjct: 65  VRLTDGPVTIMLNKPCGFITTMSDPYGRACVAELVPSDDYPGLFPVGRLDTDTSGLLLFS 124

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG L   L  P     + Y     G++  + L  L+ G+ +         VTL ++   
Sbjct: 125 TDGELGNSLLHPRHHVDKTYEACVQGRISDEALQTLRDGVELDDGVTSPAAVTLVSRSKE 184

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + +T+ + EG+ R+++++ +     V  L R  +GP  LG L  GS RE++K  + 
Sbjct: 185 KSRITLVIHEGRTRQVRRMCQKVGHPVLELHRAQFGPLTLGDLPEGSWRELTKAEVE 241


>gi|91205136|ref|YP_537491.1| ribosomal large subunit pseudouridine synthase [Rickettsia bellii
           RML369-C]
 gi|157827531|ref|YP_001496595.1| ribosomal large subunit pseudouridine synthase [Rickettsia bellii
           OSU 85-389]
 gi|122425930|sp|Q1RJR2|Y321_RICBR RecName: Full=Uncharacterized RNA pseudouridine synthase RBE_0321;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|91068680|gb|ABE04402.1| Ribosomal large subunit pseudouridine synthase [Rickettsia bellii
           RML369-C]
 gi|157802835|gb|ABV79558.1| Ribosomal large subunit pseudouridine synthase [Rickettsia bellii
           OSU 85-389]
          Length = 229

 Score =  183 bits (465), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 110/226 (48%), Positives = 154/226 (68%), Gaps = 2/226 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR++K+I+ AGI SRR+ E++I   +VKVNGI++   A NV + + +EV G  +  ++++
Sbjct: 2   QRLAKLISNAGICSRRDAEKLILDGQVKVNGIIVTSPATNVDTDNQVEVSGSLITSSQKS 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW+Y+KP+GL+TTH DP  R TVF+ L +   RVIS+GRLD+N+EGLLLLTN+G LAR 
Sbjct: 62  RLWIYYKPVGLITTHKDPLSRKTVFEQL-TGLPRVISIGRLDLNSEGLLLLTNNGDLARQ 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
            ELPS++  RVY VR +G  D    +   K + I GI Y    + L  +  +N+W+ V L
Sbjct: 121 FELPSSKLKRVYHVRAYGNPDPLLKSN-YKNLEIDGIFYNPQSIKLLRKNSTNSWLEVIL 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            EGKNREI+++FE F  KVN+LIR  YG F+L  L     REV+KK
Sbjct: 180 FEGKNREIRRIFEHFGLKVNKLIRTEYGDFKLDNLKPNEYREVTKK 225


>gi|293572005|ref|ZP_06683018.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E980]
 gi|291607929|gb|EFF37238.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E980]
          Length = 239

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 59/238 (24%), Positives = 105/238 (44%), Gaps = 5/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ SR+EV+ +I +  ++VNG +++     V    D +   G  +   + 
Sbjct: 1   MRLDKFLADMGLGSRKEVKGLIKKGTIEVNGQVVKSDKAQVNEFEDTVTYLGEIIAYQKD 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T  + D               +  VGRLD +TEGLL+LTNDG  A 
Sbjct: 61  FYYILHKPAGVISATQDNHDQTVIDLLEDQDYREDLFPVGRLDKDTEGLLILTNDGVFAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKG--SNAWV 189
            L  P     + Y    +G + ++ + L  +G++I         ++ +D        + +
Sbjct: 121 QLLSPKKHVEKEYLAEVNGIMTEEDIRLFAEGLIIDGDEQTLPAKLQIDQVDQESETSII 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
            + L EGK  ++K++ +    +V  L RI  G F L   L  G  R ++K+ L +   
Sbjct: 181 RLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGNFCLPKDLNRGQYRPMTKEELEQVRE 238


>gi|297584469|ref|YP_003700249.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
 gi|297142926|gb|ADH99683.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
          Length = 239

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 75/240 (31%), Positives = 122/240 (50%), Gaps = 5/240 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ K+IA+AGI SRR+ E++I + RV VNG  ++         TD I VDGVPL+K E 
Sbjct: 2   ERLQKLIAQAGITSRRKAEKLIEEGRVYVNGNQVKEVGAKADLQTDEISVDGVPLQKEEP 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               LY     + +   D   ++ +  +L     RV  VGRLD +T GL++LTNDG  A 
Sbjct: 62  VYYLLYKPSGVISSAGDDKGRKTVI--DLVPGEFRVFPVGRLDFDTSGLIVLTNDGEFAN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVT 190
           +L  P  +  + Y  +  G   ++ L  L +GIV++       +  +    ++   A V 
Sbjct: 120 LLMHPKYRIHKTYIAKVKGLPLREDLKKLDRGIVLEDGKTAPAKTKVIKTDKRKGTAVVE 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + + EG+NR+++++F+   + V +L R  YG   L  L AG  RE+    ++        
Sbjct: 180 ITIHEGRNRQVRRMFDAIGFPVMKLKRERYGILDLKGLNAGDWRELKPHEVKTLREIAEK 239


>gi|261880058|ref|ZP_06006485.1| ribosomal large subunit pseudouridine synthase B [Prevotella
           bergensis DSM 17361]
 gi|270333299|gb|EFA44085.1| ribosomal large subunit pseudouridine synthase B [Prevotella
           bergensis DSM 17361]
          Length = 253

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 63/246 (25%), Positives = 114/246 (46%), Gaps = 5/246 (2%)

Query: 1   MKDKNIVQEN----FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           MK +   +E+      P R++K +A AGI SRRE +  I    V VNG ++      V+ 
Sbjct: 1   MKKRIEYKEDHIDPNEPLRLNKFLANAGICSRREADEFIQAGVVTVNGEVVTELGTKVLR 60

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           +D ++    P+   ++  + L      + T+      ++ +     +   R+  VGRLD 
Sbjct: 61  SDEVKFRDQPVTLEKKVYVLLNKPKNYVTTSDDPQQRKTVMDLVKDACPERIYPVGRLDR 120

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NT G+LLLTNDG +A  L  P     +VY V     +  + L  + +GI ++        
Sbjct: 121 NTTGVLLLTNDGDMASKLTHPKFLKKKVYHVFLDKNIGVEDLQKIAEGIELEDGEIHADA 180

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V    +    + V + +  G+NR ++++FE   ++V RL R+ +       L  G  R +
Sbjct: 181 VEYANEN-DKSQVGIEIHSGRNRIVRRIFEALGYRVVRLDRVLFAGLTKKNLRRGDWRFL 239

Query: 237 SKKILR 242
           +++ + 
Sbjct: 240 TEQEVD 245


>gi|260591212|ref|ZP_05856670.1| ribosomal large subunit pseudouridine synthase B [Prevotella
           veroralis F0319]
 gi|260537077|gb|EEX19694.1| ribosomal large subunit pseudouridine synthase B [Prevotella
           veroralis F0319]
          Length = 253

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 64/246 (26%), Positives = 111/246 (45%), Gaps = 5/246 (2%)

Query: 1   MKDKNIVQENF----TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           MK +   +E       P R++K +A AG+ SRRE +  I    V VNG +++     V+ 
Sbjct: 1   MKKRIEYKEENFDPNEPIRLNKYLANAGVCSRREADEFILSGAVTVNGEVVKELGSKVLR 60

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           TD +     P+   ++  + L      + T+      ++ +     +   R+  VGRLD 
Sbjct: 61  TDVVLFQDKPVSLEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKGACPERIYPVGRLDR 120

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NT G+LLLTNDG LA  L  P     +VY V     V  + L  +  GI ++        
Sbjct: 121 NTTGVLLLTNDGDLASKLTHPKFLKKKVYHVFLDKPVTANDLQKISDGIELEDGEIKADA 180

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           +   +       V + +  GKNR ++++FE   ++V +L R+ +       +  G  R +
Sbjct: 181 IEYASPDDL-TQVGIEIHSGKNRIVRRIFESLGYRVVKLDRVQFAGLTKKNVRRGDWRFL 239

Query: 237 SKKILR 242
           ++K + 
Sbjct: 240 TEKEVD 245


>gi|293400568|ref|ZP_06644713.1| ribosomal small subunit pseudouridine synthase A
           [Erysipelotrichaceae bacterium 5_2_54FAA]
 gi|291305594|gb|EFE46838.1| ribosomal small subunit pseudouridine synthase A
           [Erysipelotrichaceae bacterium 5_2_54FAA]
          Length = 232

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 112/229 (48%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++ AG+ +R+EV+++I ++ V+VNG L+ +  ++V   D +++DG  +      
Sbjct: 1   MRLDKYLSHAGVGTRKEVKQLIRKKHVRVNGELVVKDDMHVEEDDLVQLDGEHIYYEPFV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L      ++    D +  + +      +      VGRLD++TEGL+L++NDG LA  
Sbjct: 61  YLMLNKPSG-VICATQDSEHETVLDCFDVMLPKGCFPVGRLDMDTEGLVLISNDGKLAHH 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     + Y V     +D+  +  L  G +I           L+    ++ +  +  
Sbjct: 120 LLSPKHHVRKTYYVEHQLCLDETAIKTLCNGSIILDEKTVLC-AALEVINETSCFFHIE- 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EG+  +IK++F     +V  L R++ GP +L   L  G  R ++++ L
Sbjct: 178 -EGRYHQIKRMFSAVGNEVLYLKRVAMGPLRLDDHLEVGEWRALTQEEL 225


>gi|170756858|ref|YP_001781361.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum B1 str. Okra]
 gi|169122070|gb|ACA45906.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum B1 str. Okra]
 gi|322806051|emb|CBZ03618.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum H04402 065]
          Length = 236

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 71/230 (30%), Positives = 120/230 (52%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +A  G+ASRR+ E +I + RV+VNGI ++     ++S  D I+VDG  +   E 
Sbjct: 3   ERLQKYMASCGVASRRKCEDIILEGRVEVNGIKIKELGTKIISGKDIIKVDGNIIEPEEN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G V T  D  GR T   +L  +  R+  +GRLD++T G+++LTNDG +  
Sbjct: 63  KIYILLNKPKGYVCTAKDEKGRKT-ILDLVKVKERIYPIGRLDMDTSGIIILTNDGEIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  + ++ Y+ +  G + +D + L KKGI I         + +       + + + 
Sbjct: 122 KIIHPKFEKIKTYKAKVKGTIKKDHIELFKKGIDIGDYLTAPATLEILKINKDTSEIIIK 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGKNR+++++ +     V  L RIS G      L  G  R ++ K + 
Sbjct: 182 IHEGKNRQVRRMCKSIGHAVIDLDRISIGNITKSDLKLGEWRYLTNKEID 231


>gi|255035028|ref|YP_003085649.1| pseudouridine synthase [Dyadobacter fermentans DSM 18053]
 gi|254947784|gb|ACT92484.1| pseudouridine synthase [Dyadobacter fermentans DSM 18053]
          Length = 248

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 59/232 (25%), Positives = 109/232 (46%), Gaps = 7/232 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R++K I+  G  SRRE ++++ Q RV +NG           ++D + VDG PL+  +
Sbjct: 2   EPVRINKFISETGFCSRREADKLVEQGRVMLNGRKA-VLGDKATTSDDVRVDGKPLKAKK 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                 ++KP+G+  T       + +         R+  +GRLD  +EGL+ LT+DG + 
Sbjct: 61  AGVYIAFNKPVGITCTTERHIKGNIIDYI--RHKERIFPIGRLDKPSEGLIFLTSDGDIV 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V  +  +  + +  +  G+ I G+           +K S+   T+
Sbjct: 119 NKILRAGNNHEKEYVVTVNKPITPEFIQKMSSGVPILGVVTKKC----FVRKDSSYVFTI 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            L +G NR+I+++ EF  + V +L R+      L  L  G  R+++   ++E
Sbjct: 175 ILTQGLNRQIRRMCEFLGYNVTKLKRVRIMNVTLKDLPVGKWRDLTAAEMQE 226


>gi|308174106|ref|YP_003920811.1| pseudouridine synthase [Bacillus amyloliquefaciens DSM 7]
 gi|307606970|emb|CBI43341.1| pseudouridine synthase [Bacillus amyloliquefaciens DSM 7]
 gi|328552765|gb|AEB23257.1| pseudouridine synthase [Bacillus amyloliquefaciens TA208]
 gi|328912437|gb|AEB64033.1| pseudouridine synthase [Bacillus amyloliquefaciens LL3]
          Length = 244

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 72/243 (29%), Positives = 122/243 (50%), Gaps = 3/243 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E +I + +VKVNG ++    V V  +D IEV+G+ + + E  
Sbjct: 2   ERLQKVIAHAGVASRRKAEELIKEGKVKVNGKVITELGVKVTGSDQIEVNGLKVEREEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     +++   D  GR  V D    +  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 62  YFLLYKPRG-VISAADDDKGRKVVTDFFKEVPQRIYPIGRLDYDTSGLLLLTNDGEFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD--MQVTLDTQKGSNAWVTV 191
           L  P  +  + Y  +  G   ++ L  L++GI ++         ++    ++   + + +
Sbjct: 121 LMHPKYEIDKTYVAKVKGIPSKELLRKLERGIQLEEGKTAPARAKMLSLDKRKQTSIIQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE     V +L R  Y    L  L  G  RE++   ++         
Sbjct: 181 TIHEGRNRQVRRMFEAIGHDVLKLKREEYAFLDLRGLHTGDARELTPHEVKRLRALADHG 240

Query: 252 EAQ 254
           +  
Sbjct: 241 KNA 243


>gi|317057433|ref|YP_004105900.1| pseudouridine synthase [Ruminococcus albus 7]
 gi|315449702|gb|ADU23266.1| pseudouridine synthase [Ruminococcus albus 7]
          Length = 244

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 83/234 (35%), Positives = 120/234 (51%), Gaps = 2/234 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R+ K+I+ +G  SRR+ E  IA  +V VNG         +   D I VDG+ + +  
Sbjct: 2   EKVRIQKIISESGFCSRRKAEEFIAAGKVTVNGRPCTLGDKALPGKDLIVVDGIKIDQPR 61

Query: 72  RT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +      + HKP G VTT +D   R  V D L  +  RV  VGRLD N+EGLLLLTNDG 
Sbjct: 62  KRTLYYIMLHKPRGYVTTMNDELDRKCVTDLLTGLPERVYPVGRLDKNSEGLLLLTNDGA 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  PS    + YRV     ++ ++L  L  G+ I G    +  VT+  ++     +
Sbjct: 122 FANDIMHPSKHVNKTYRVTVRPDINDEQLVKLASGVEIDGRMTSECSVTVLDKQPGRVVL 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + + EG+NR+I+K+ E    +V RL R + GP +LG L  G  RE+    LR 
Sbjct: 182 QMTIHEGRNRQIRKMCEAVGLEVARLKRTAIGPLRLGMLKPGEYRELKPDELRA 235


>gi|229062392|ref|ZP_04199708.1| Pseudouridine synthase [Bacillus cereus AH603]
 gi|228716863|gb|EEL68550.1| Pseudouridine synthase [Bacillus cereus AH603]
          Length = 242

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 60/232 (25%), Positives = 105/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G  ++ A  +V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGHGSRKEVKKLLKDGVVKIDGTPVKDAKFHVNIEEQEVMIHGEVVEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L ++     +  T  D          L         VGRLDI+TEG LL+TNDG L  
Sbjct: 61  VYLMMHKPQGVISATEDDNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKLTH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G V ++ +    KG++++        ++T+  +    + + +
Sbjct: 121 QLLSPKKHVPKKYYAHISGVVTEEDVKEFSKGVILEDGYETKPGELTIL-KSDDISEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 180 VITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLMLDQELELGQYRELTDEEVE 231


>gi|254563182|ref|YP_003070277.1| hypothetical protein METDI4845 [Methylobacterium extorquens DM4]
 gi|254270460|emb|CAX26460.1| conserved hypothetical protein; putative pseudouridine
           synthase-like domain [Methylobacterium extorquens DM4]
          Length = 669

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 148/361 (40%), Positives = 203/361 (56%), Gaps = 21/361 (5%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R++K IARAGIASRR+ E +I   RV +NG +L   A+NV  +D I VD  PL  
Sbjct: 18  TPEGERIAKAIARAGIASRRDAEALIEAGRVTLNGKVLTSPAINVTDSDRITVDDEPLPA 77

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ERTRLWL HKP G+VTT  DP+GR TVFD LP    RV+++GRLDINTEGLLLLTNDGG
Sbjct: 78  RERTRLWLLHKPRGVVTTARDPEGRPTVFDGLPEELPRVVAIGRLDINTEGLLLLTNDGG 137

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA+V+  P T WLR YRVR  G V Q  L+ LKKG+ + G+ YG ++ TLD  +G N W+
Sbjct: 138 LAKVIAHPDTGWLRRYRVRAFGDVTQPDLDKLKKGLTVDGMEYGPIEATLDRAQGDNVWL 197

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           T+GLREGKNRE+K++ E     VNRLIR+S+GPFQLG L  G   E+  K+L++QLG +L
Sbjct: 198 TLGLREGKNREVKRILEHLGLSVNRLIRLSFGPFQLGDLEVGLVEEIRTKVLKDQLGKNL 257

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
            E+A V+ ++P+  +                      +  ++  G S+ +  +       
Sbjct: 258 AEQAGVDFESPVRETIAPFGSPKKATRATQAAPAGRGRQGARDEGASEARSGSRGGAAGR 317

Query: 310 LASN---------------------VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
              +                     VW A        S   +R  + + + +  ++R   
Sbjct: 318 PPRDPARPAAPRAGARPAPRPPSPTVWRADEETRPRASKVPRRGMDPKTARAEAAERGRE 377

Query: 349 R 349
           R
Sbjct: 378 R 378



 Score = 44.0 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 10/114 (8%), Positives = 25/114 (21%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           ++      +L E                    N            +    Q      + +
Sbjct: 382 IQAAGERRVLVERLQPSPEKPAPEPHRRVRFRNEEERSAPRDRAREDRPRQDRPGQDRPR 441

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              P       +     +     F   +   +   RR  +  +  + RR   ++
Sbjct: 442 EDRPRSEGPRENRARDERPGRDEFRRGAPAGDARPRRREAGEAAPAERRGPPRE 495



 Score = 42.9 bits (99), Expect = 0.081,   Method: Composition-based stats.
 Identities = 13/112 (11%), Positives = 26/112 (23%), Gaps = 1/112 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R  L   L    +     P         +  +   +   +    +    Q      + + 
Sbjct: 388 RRVLVERLQPSPEKPAPEPHRRVRFRNEEERSAPRDRAREDRPRQDRPGQDRPREDRPRS 447

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSD-SGQREENHRRSPSFPSKRSLRRTSA 352
             P   R         +    +   D   +R E    +P+        R S 
Sbjct: 448 EGPRENRARDERPGRDEFRRGAPAGDARPRRREAGEAAPAERRGPPRERPSD 499



 Score = 42.1 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 23/112 (20%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R +      +    +            R+          D  R    +       ++   
Sbjct: 424 RAREDRPRQDRPGQDRPREDRPRSEGPRENRARDERPGRDEFRRGAPAGDARPRRREAGE 483

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           A P  RR                    G+ + +         + + RR    
Sbjct: 484 AAPAERRGPPRERPSDFEGRPPRERSEGRPQRDFHGDSRERGEGAPRRERPS 535



 Score = 40.2 bits (92), Expect = 0.47,   Method: Composition-based stats.
 Identities = 13/123 (10%), Positives = 32/123 (26%), Gaps = 1/123 (0%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
            TR  + K+ R  + P                +     +R  ++  +     +      +
Sbjct: 349 ETRPRASKVPRRGMDPKTARAEAAERGRERVGAIQAAGERRVLVERLQPSPEKPAPEPHR 408

Query: 292 KNGLSKQKKLATPVHR-RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
           +     +++ + P  R R                     +    +R     P +   RR 
Sbjct: 409 RVRFRNEEERSAPRDRAREDRPRQDRPGQDRPREDRPRSEGPRENRARDERPGRDEFRRG 468

Query: 351 SAK 353
           +  
Sbjct: 469 APA 471



 Score = 39.8 bits (91), Expect = 0.60,   Method: Composition-based stats.
 Identities = 13/125 (10%), Positives = 31/125 (24%), Gaps = 6/125 (4%)

Query: 234 REVSKKILREQLGPHLLEEAQV-----NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
           R +  K  R +      E              +   +                    +++
Sbjct: 360 RGMDPKTARAEAAERGRERVGAIQAAGERRVLVERLQPSPEKPAPEPHRRVRFRNEEERS 419

Query: 289 SSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           + +      + +   P   R             +    +   R+E  R +P+    R  R
Sbjct: 420 APRDRAREDRPRQDRPGQDRPREDRPRSEGPRENRARDERPGRDEFRRGAPA-GDARPRR 478

Query: 349 RTSAK 353
           R + +
Sbjct: 479 REAGE 483


>gi|255264455|ref|ZP_05343797.1| ribosomal large subunit pseudouridine synthase B [Thalassiobium sp.
           R2A62]
 gi|255106790|gb|EET49464.1| ribosomal large subunit pseudouridine synthase B [Thalassiobium sp.
           R2A62]
          Length = 267

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 135/261 (51%), Positives = 178/261 (68%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
               T QR++KV+ARAG+ASRRE ERMI   RV+VN  L+E  A+NV+ +D I VDG  +
Sbjct: 7   NTGPTGQRIAKVLARAGVASRREAERMIEAGRVRVNSKLIESPALNVVPSDRISVDGKLI 66

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              E TR+WL+HKP GL+T+  D +GR TVFD LP    RV+SVGRLD+N+EGLL+LTND
Sbjct: 67  GDPEPTRMWLFHKPQGLITSERDEEGRETVFDVLPPEMPRVLSVGRLDLNSEGLLVLTND 126

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G + R LELPST WLR YRVR  G + + KL+ L++GI ++G+ Y  M VT D Q+G+NA
Sbjct: 127 GEVKRKLELPSTGWLRRYRVRIKGSLSEAKLDELREGITVEGVHYQPMDVTFDRQQGANA 186

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+T+G+REGKNREI++  E     VNRLIRISYGPFQLG + AG   E+  +++R+QLG 
Sbjct: 187 WLTIGIREGKNREIRRTMEALGVTVNRLIRISYGPFQLGNIKAGEVEELKSRVVRDQLGL 246

Query: 248 HLLEEAQVNLDAPIYSSETLV 268
               + +           T  
Sbjct: 247 DPRPKPERTRKTGAKGKNTRK 267


>gi|89099642|ref|ZP_01172516.1| 16S pseudouridylate synthase [Bacillus sp. NRRL B-14911]
 gi|89085585|gb|EAR64712.1| 16S pseudouridylate synthase [Bacillus sp. NRRL B-14911]
          Length = 239

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 65/236 (27%), Positives = 113/236 (47%), Gaps = 4/236 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ KV+A  G  SR+EV++++    V VN   ++ A  +V    D I ++G  +   E 
Sbjct: 1   MRIDKVLANLGYGSRKEVKKLLKDGSVTVNDEKIKDAKQHVDPEKDLIRINGETVEYREF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +   P  +  T  + D           +      VGRLD +TEGLLL+TNDG LA 
Sbjct: 61  IYLMMNKPPGVISATEDNRDETVIDLLEAEDLIFEPFPVGRLDKDTEGLLLITNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y      +V ++ +   +KG+++         ++ +  + G  + + +
Sbjct: 121 RLLSPKKHVPKTYFAVIDQEVTEEDVTAFRKGVILDDGYATKPGELNIL-KSGERSDIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
            + EGK  ++K++FE    KV  L R+S GP +L   L  G  RE++++ L+  + 
Sbjct: 180 TITEGKFHQVKRMFEAVGKKVVYLQRLSMGPLRLDETLELGEYRELTEEELQSLME 235


>gi|331270360|ref|YP_004396852.1| pseudouridine synthase [Clostridium botulinum BKT015925]
 gi|329126910|gb|AEB76855.1| pseudouridine synthase [Clostridium botulinum BKT015925]
          Length = 240

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 55/232 (23%), Positives = 109/232 (46%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K+++  G  SR+E++ ++ +  ++++G  ++   V V      I+V G  +   + 
Sbjct: 4   ERLDKILSNLGYGSRKEIKVLVKKGEIEIDGEKIKDNGVKVDPNKSIIKVSGEEINYRKY 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  T  + D       +          VGRLD +TEG LL+TNDG L  
Sbjct: 64  IYLMMNKPAGVVSATFDNYDETVIDLLDYEYTVFDPFPVGRLDKDTEGFLLITNDGDLNH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     ++Y       VD+  +   +KGI+++        ++ + +   + + V +
Sbjct: 124 RLTSPKWHVDKIYYAEIDKIVDEKDIKAFEKGIMLEDGYRCLPAKLRVLSADENGSEVNI 183

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            ++EGK  ++K++FE  + KV  L R+  G   L   L  G  RE+++  ++
Sbjct: 184 TIQEGKFHQVKRMFEARDKKVIYLKRLQMGNLVLDESLSEGEYRELTEDEVK 235


>gi|255657972|ref|ZP_05403381.1| ribosomal large subunit pseudouridine synthase B [Mitsuokella
           multacida DSM 20544]
 gi|260850173|gb|EEX70180.1| ribosomal large subunit pseudouridine synthase B [Mitsuokella
           multacida DSM 20544]
          Length = 250

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 78/246 (31%), Positives = 128/246 (52%), Gaps = 7/246 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
           +R+ K+I++AGIASRR  E+MI + RV+V+G ++      V    H I VDG  +   E+
Sbjct: 5   ERLQKIISQAGIASRRAAEKMILEGRVRVDGQVVRELGTKVDPAAHTILVDGKKIAGEEQ 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G ++T  D  GR TV D LP +  RV  VGRLD NTEGLLL+TNDG L  
Sbjct: 65  HVYLLLNKPKGYLSTAKDDRGRRTVLDLLPEVRERVYPVGRLDNNTEGLLLITNDGALMN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-- 190
            L  P  +  + Y     G++ ++KL +L+ G++++       +V+L  ++     V   
Sbjct: 125 GLLHPRFEVEKTYHAGVTGKLTEEKLQMLRDGLLLEDGMTAPAKVSLLPEREPGERVRGL 184

Query: 191 ----VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               + + EG+NR+++++F      V  L R+ +    L  +  G  R ++++ +     
Sbjct: 185 TRAAITIHEGRNRQVRRMFAAVGCDVKSLKRVRFAGLTLKGVARGQHRALTEEEVSSLYR 244

Query: 247 PHLLEE 252
                 
Sbjct: 245 LAGCTR 250


>gi|304436412|ref|ZP_07396387.1| ribosomal large subunit pseudouridine synthase B [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
 gi|304370576|gb|EFM24226.1| ribosomal large subunit pseudouridine synthase B [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
          Length = 292

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 83/291 (28%), Positives = 138/291 (47%), Gaps = 6/291 (2%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRL 75
            K+++ AG+ASRR  E +I   RV V+G+ +         +   I VDG P++ +E    
Sbjct: 2   QKILSHAGVASRRAAEALIRDGRVTVDGVPVTMLGSKYDPSFHEIAVDGTPVQGSEEKLY 61

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L HKP G ++T  D  GR TV D LP    R+  VGRLD +TEGLL++TNDG + + L 
Sbjct: 62  ILLHKPRGCLSTAHDDRGRRTVLDLLPHFPVRLYPVGRLDADTEGLLIITNDGAMTQGLL 121

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
            P  +  +VY     G V +DKL+ L++GI++        Q+++  ++G    V   + E
Sbjct: 122 HPRFEIDKVYHAEVTGTVTEDKLSKLRRGILLDDGKTAPAQLSILRREGGRTLVETIIHE 181

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG-----PHLL 250
           G+NR+++++F     +V RL R+ +    L  L  G+ R ++   + E            
Sbjct: 182 GRNRQVRRMFAAVGCRVQRLRRVRFAMLTLDGLPCGAFRHLTLDEIHELQKIAGGIHSEE 241

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
              +    +      +    R    +   D   R + +   K  L + K+ 
Sbjct: 242 GSRRRRRTSGDDGGGSGGGTRRERNAARKDAARRPQDDDHGKRPLQRDKRR 292


>gi|269215383|ref|ZP_06159237.1| ribosomal large subunit pseudouridine synthase B [Slackia exigua
           ATCC 700122]
 gi|269130870|gb|EEZ61945.1| ribosomal large subunit pseudouridine synthase B [Slackia exigua
           ATCC 700122]
          Length = 256

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 62/239 (25%), Positives = 102/239 (42%), Gaps = 2/239 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE 71
           P RV K +ARAG+ASRR  E ++   RV VNG ++      V    D + VDG  +  ++
Sbjct: 17  PMRVQKFLARAGVASRRGSENLMTTGRVSVNGRVVTELGSRVDPRCDVVRVDGHVVHLSD 76

Query: 72  -RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             T L L      + T                  +  +  +GRLD +T G+LL + DG L
Sbjct: 77  GSTTLMLNKPAGYITTMSDPFGRACVAELVPIDAYPGLFPIGRLDADTTGILLFSTDGEL 136

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + Y+    G V +++L  L+ G+ ++       +  L       + + 
Sbjct: 137 GNGLLHPRKHVDKTYQALVEGSVSEEELERLRSGVELEDGMTAPAEARLTCVSEDESRLD 196

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           + + EG+ R+++++       V  L R  +GP  LG L  GS R +S   +        
Sbjct: 197 ITIHEGRKRQVRRMCATVGHPVVTLHRSRFGPLVLGDLPEGSWRMLSGSEVAALHAAAR 255


>gi|167462334|ref|ZP_02327423.1| pseudouridylate synthase [Paenibacillus larvae subsp. larvae
           BRL-230010]
 gi|322381784|ref|ZP_08055738.1| pseudouridine synthase-like protein [Paenibacillus larvae subsp.
           larvae B-3650]
 gi|321154172|gb|EFX46494.1| pseudouridine synthase-like protein [Paenibacillus larvae subsp.
           larvae B-3650]
          Length = 249

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 71/248 (28%), Positives = 115/248 (46%), Gaps = 4/248 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV+A AG+ASRR+ E +I   RV+VN  ++    V V    D I+VDG  ++  E+
Sbjct: 3   ERLQKVLAAAGVASRRKCEEIILAGRVEVNDKVVSTLGVKVNPHQDVIKVDGRAIQNQEK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +        + +          V D L  I  RV  VGRLD +TEGLL+LTNDG  A 
Sbjct: 63  IYILFNKPKGVITSVSDPEGR-RVVGDFLKGIKERVYPVGRLDYDTEGLLILTNDGEFAN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
           ++  P     + Y     G      L  L++G+ ++       +V           + ++
Sbjct: 122 MVTHPRHHVSKTYHATVKGVPHGSVLEKLREGVKLEDGMTAPAEVEYHDIDPDKKQSVIS 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + + EGKNR+++++FE   + V RL R+ +G   L  L  G  R + K+ ++  L     
Sbjct: 182 ITIYEGKNRQVRRMFEAVGYPVTRLKRVKFGSIPLVGLPRGKFRRMRKEEVQALLNEASQ 241

Query: 251 EEAQVNLD 258
                   
Sbjct: 242 SHKVQKGQ 249


>gi|146296765|ref|YP_001180536.1| pseudouridine synthase [Caldicellulosiruptor saccharolyticus DSM
           8903]
 gi|145410341|gb|ABP67345.1| ribosomal large subunit pseudouridine synthase B
           [Caldicellulosiruptor saccharolyticus DSM 8903]
          Length = 237

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 69/235 (29%), Positives = 115/235 (48%), Gaps = 2/235 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ASRR+ E +I Q RVKVNG  +      V    D + VDG  L   ++
Sbjct: 2   VRLQKFMADCGVASRRKCEEIILQGRVKVNGRTITELGFKVDPQKDKVLVDGKKLVPVQK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G++++  D  GR TV D +          VGRLD +T GL+LLTNDG  A
Sbjct: 62  KIYIMLNKPFGVISSAKDEKGRKTVVDLVKDKVDVRVFPVGRLDFDTTGLILLTNDGEFA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P     + Y     G   ++++   KKG+ I G      +  +       + V +
Sbjct: 122 YKVTHPKHDIEKTYIALIEGVPTKEEIEQFKKGLFIDGKLTSPAKFRILKVFKGMSLVEI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            + EG+NR+++K+ +    +V +L R++ G  +LG L  G    + + ++ +   
Sbjct: 182 KIHEGRNRQVRKMCDAIGHRVLKLKRVAIGKLKLGKLKEGEFVFLDENMVNKVFE 236


>gi|229013752|ref|ZP_04170880.1| RNA pseudouridine synthase [Bacillus mycoides DSM 2048]
 gi|228747421|gb|EEL97296.1| RNA pseudouridine synthase [Bacillus mycoides DSM 2048]
          Length = 229

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 63/230 (27%), Positives = 111/230 (48%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVTINGEICTHGAI-VSDGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T ++    + +         R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAAEHIEDNIIDYI--DYPERIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT   Q    +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVTRVNQ----STFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++   F + V +L R+     +L  L AG  R+++ K L 
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELNELEAGKWRDITPKELE 223


>gi|323342117|ref|ZP_08082350.1| pseudouridylate synthase [Erysipelothrix rhusiopathiae ATCC 19414]
 gi|322464542|gb|EFY09735.1| pseudouridylate synthase [Erysipelothrix rhusiopathiae ATCC 19414]
          Length = 246

 Score =  183 bits (464), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 77/240 (32%), Positives = 124/240 (51%), Gaps = 3/240 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA +G  SRR+ E +I + +VKVNGI +    + V + D + V+G+ +   E+ 
Sbjct: 7   IRLQKFIAMSGYCSRRKAEVLINEGKVKVNGIKVTEQGLKVSTEDRVMVNGILINVEEKK 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP G+V++ +D D       +L     RV  VGRLD  T G L+LTNDG  A  
Sbjct: 67  VYYILNKPRGIVSSAND-DKDRESVVDLVPNDIRVFPVGRLDRETTGALILTNDGDFAYY 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P     ++YRV   G++  +  N LK+GI I+G+ Y  ++++             ++
Sbjct: 126 MTHPKFDLSKIYRVSVRGRLSYEVTNSLKEGITIEGVEYKGVEISRVKYDAAKDKTQFSI 185

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L EGKNR+I+K+F  F   V +L R   G   +  L  G  RE+    +++ L     E
Sbjct: 186 TLHEGKNRQIRKIFAHFGLPVLKLHRYQIGYLDIDELKIGQYRELKPFEVKKLLLTAKGE 245


>gi|212715827|ref|ZP_03323955.1| hypothetical protein BIFCAT_00728 [Bifidobacterium catenulatum DSM
           16992]
 gi|212661194|gb|EEB21769.1| hypothetical protein BIFCAT_00728 [Bifidobacterium catenulatum DSM
           16992]
          Length = 257

 Score =  183 bits (464), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 68/235 (28%), Positives = 117/235 (49%), Gaps = 2/235 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           +    R+ K++A+AG  SRR+ E +I + RV+++G L+      V      + VDG  +R
Sbjct: 15  DNEGIRLQKLLAQAGFGSRRKCEEIITEGRVEIDGELVTELGTRVDPKHQEVRVDGSRVR 74

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                     +KP  +++   DP GR T+ D +   + R+  +GRLD ++EGL+L+TNDG
Sbjct: 75  VNPNHVTLALNKPKRVLSAMEDPKGRYTLSDIVGDKYDRIFHMGRLDYDSEGLILMTNDG 134

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNA 187
            L++ +  P  +  + Y     G++       L    + +        +  +      N 
Sbjct: 135 ELSQHVMHPKYEVEKTYIATLEGRISGQVCRRLVTTGVQLDDGWIKLDRCAILDASRDNT 194

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V V L  GKNR ++++F    + V RL+R   GP +LG L +GS R +S+  +R
Sbjct: 195 LVKVVLHSGKNRIVRRIFGSIGFPVRRLVRTQIGPIKLGDLKSGSYRVLSQTEVR 249


>gi|282882075|ref|ZP_06290716.1| ribosomal large subunit pseudouridine synthase B [Peptoniphilus
           lacrimalis 315-B]
 gi|300814964|ref|ZP_07095192.1| putative pseudouridine synthase B, ribosomal large subunit
           [Peptoniphilus sp. oral taxon 836 str. F0141]
 gi|281298105|gb|EFA90560.1| ribosomal large subunit pseudouridine synthase B [Peptoniphilus
           lacrimalis 315-B]
 gi|300510934|gb|EFK38206.1| putative pseudouridine synthase B, ribosomal large subunit
           [Peptoniphilus sp. oral taxon 836 str. F0141]
          Length = 235

 Score =  183 bits (464), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 75/230 (32%), Positives = 123/230 (53%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A AG ASRR+ E +I + RVKVN  ++    + V    D + +DG  L     
Sbjct: 1   MRLQKFMAHAGAASRRKSEELIKEGRVKVNNNIVTEMGLEVDPNKDRVYLDGKRLNLENE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KPIG+VTT    +       +L     RV  VGRLDI+T GL+LLTNDG LA 
Sbjct: 61  NIYIILNKPIGVVTTS-SDEKGRINVVDLVDETKRVYPVGRLDIDTTGLVLLTNDGTLAN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +L  P     + Y     G+ +  +LNLL+ G+ ++ +     +V +      ++ + + 
Sbjct: 120 ILMHPKNNIYKTYIATVEGKPNARELNLLRNGLSLRDLKTSKAKVKILKNFDKDSIIEIS 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGKN ++K++F +   +V +L RIS G  +LG L  G+ R ++ + ++
Sbjct: 180 IHEGKNHQVKRMFSYIGHEVKKLKRISIGKIELGNLEIGNYRYLNNEEVK 229


>gi|229032362|ref|ZP_04188334.1| Pseudouridine synthase [Bacillus cereus AH1271]
 gi|228728970|gb|EEL79974.1| Pseudouridine synthase [Bacillus cereus AH1271]
          Length = 242

 Score =  183 bits (464), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 105/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G  ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L ++     +  T  D          L         VGRLDI+TEG LL+TNDG L+ 
Sbjct: 61  VYLMMHKPQGVISATEDDNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKLSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G V ++ +    KG+++          +T+  +    + + +
Sbjct: 121 QLLSPKKHVPKKYYAHIAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDEISEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++FE    KV  L R   GP  L   L  G  RE+S + + 
Sbjct: 180 VITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDAELELGEYRELSDEEVE 231


>gi|295095390|emb|CBK84480.1| ribosomal large subunit pseudouridine synthase F [Enterobacter
           cloacae subsp. cloacae NCTC 9394]
          Length = 290

 Score =  183 bits (464), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 62/292 (21%), Positives = 117/292 (40%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K I+ +GI SRRE +R I Q  V +NG         V+  D ++V+G  +   
Sbjct: 4   TQSTRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVVPGDVVKVNGQVIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L        +    +  DG      +  +  SR+  +GRLD +++GL+ LTN G L
Sbjct: 63  DAEDLVFIALNKPVGIVSTTEDGERDNIVDFVNHSSRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + +  +  G+ I G      +V    +K +     
Sbjct: 123 VNKILRAGNDHEKEYIVTVNKPVTDEFIRGMGAGVPILGTVTKKCKV----RKEAPFAFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L E       
Sbjct: 179 ITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIELFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++    A        ++       +  +       N  +     ++KK  
Sbjct: 239 SSSEAKPKAKAKPKTQAIKRPVVKAPQAEEKGRGKPGNGKRFTQPGRKKKGR 290


>gi|251796174|ref|YP_003010905.1| pseudouridine synthase [Paenibacillus sp. JDR-2]
 gi|247543800|gb|ACT00819.1| pseudouridine synthase [Paenibacillus sp. JDR-2]
          Length = 249

 Score =  183 bits (464), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 63/247 (25%), Positives = 106/247 (42%), Gaps = 7/247 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
              R+ K+++  G  +R E+++++ Q +V V G +++ +   V    D +  DG  +   
Sbjct: 3   KKMRIDKLLSHTGYGTRSEIKKLVKQGKVTVAGKVVKDSGQLVDPELDEVAFDGELVLYR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L +   P  +  T    +                  VGRLD +T GLLLLTNDG L
Sbjct: 63  EVIYLMMNKPPGVISATEDRRERTVIDLLEQEDQLMDPFPVGRLDKDTVGLLLLTNDGQL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQK----GS 185
           A  L  P     + Y     G V ++     K G+ +          + +  +     G 
Sbjct: 123 AHELLSPRKHVPKTYEAVVQGDVGEEDQEQFKAGVTLDDGYVTMPSDLKILKKDSGEGGV 182

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            + +++ + EGK  ++K++FE    KV  L RIS GP +L   L  G+ RE++ + L   
Sbjct: 183 TSVISLTIMEGKFHQVKRMFEAVGKKVVFLKRISMGPLELDADLEEGTYRELTDEELALL 242

Query: 245 LGPHLLE 251
                 E
Sbjct: 243 RAHRATE 249


>gi|310765941|gb|ADP10891.1| 23S rRNA pseudouridine synthase F [Erwinia sp. Ejp617]
          Length = 292

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 62/292 (21%), Positives = 114/292 (39%), Gaps = 5/292 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++K I  +GI SRR+ +R I Q  V +NG         V + D ++V+G  +     
Sbjct: 6   SIRLNKYIGESGICSRRDADRYIEQGNVFINGKRASV-GDRVFAGDVVKVNGQLIEPRNE 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +    +  +G      +  +   RV  +GRLD +++GL+ LTN G L  
Sbjct: 65  DDLVVIALNKPVGIISTTEEGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  V ++ +  L  G+ + G      +V     K S     + 
Sbjct: 125 KILRAGNDHEKEYLVTVNKPVTEEFIRGLGAGVPMLGTVTKKCKV----NKESTFVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E F ++V++L R       L  L  G  R+++   L E         
Sbjct: 181 LVQGLNRQIRRMSEHFGYEVSKLERTRIMNISLKGLPPGEWRDLTDDELIELFKLIENSS 240

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           ++           T  +      ++     T     + +K      +K    
Sbjct: 241 SEDGTAKKAKPKATTAKKPAASGAKGGAKVTGNANAAPRKRFAQPGRKKKGR 292


>gi|148273158|ref|YP_001222719.1| putative pseudouridine synthase [Clavibacter michiganensis subsp.
           michiganensis NCPPB 382]
 gi|147831088|emb|CAN02033.1| putative pseudouridine synthase [Clavibacter michiganensis subsp.
           michiganensis NCPPB 382]
          Length = 286

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 78/273 (28%), Positives = 125/273 (45%), Gaps = 1/273 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
            E     R+ KV+A AG+ASRR  E MIA  RV VNG ++      +    D + VD   
Sbjct: 14  DEPVQGVRLQKVMAAAGVASRRVCEDMIAAGRVTVNGEVVTEPGRRIDPDVDEVAVDDQA 73

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           ++     R  + +KP+G+ ++  D  GR  + +       R+ +VGRLD  T GLL+LTN
Sbjct: 74  VQLDTSKRYLMLNKPVGIYSSLRDERGRPDLREFTEEFEERLFNVGRLDAETSGLLILTN 133

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA VL  PS   L+ Y  +  G+V    +  L +G+ ++       +  + +  G  
Sbjct: 134 DGDLAHVLAHPSFGVLKTYIAKVTGRVTPQTIQRLTQGVDLEDGPIQADRARILSGGGDQ 193

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
             V + L  G+NR ++++ +     V  L+R  +GP  LG+L  G  R+++   L + L 
Sbjct: 194 TLVEITLHSGRNRIVRRMLDEVGHPVEELVRRQFGPLHLGSLGVGRVRDLTSDELGQLLT 253

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVP 279
                 AQ     P  +             +  
Sbjct: 254 ISREARAQAGPATPQGAGAAAEAQGDVDREDGE 286


>gi|332830030|gb|EGK02658.1| hypothetical protein HMPREF9455_00908 [Dysgonomonas gadei ATCC
           BAA-286]
          Length = 342

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 72/343 (20%), Positives = 143/343 (41%), Gaps = 10/343 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +G  SRRE +R I + RV +NG   +   + V+    ++V+G  +       
Sbjct: 4   RLNKYISNSGFCSRREADRFIEEGRVTINGKRAQV-GMRVLPGQKVKVNGELIVNKIEPV 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
              ++KP+G+V+T    +  + +         R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 63  YIAFNKPVGIVSTTDPQERDNIINFI--RHEQRIFPIGRLDKDSQGLILLTNDGDIVNKI 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y V+ +  + +D L  + +G+ I        ++     + +     + L 
Sbjct: 121 LRAGNNHKKDYLVKVNRPITKDFLTRMAQGVPILDRVTRRCEIV----EINPYMFRISLI 176

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR---EQLGPHLLE 251
           +G NR+I+++ E+F+++V +L RI     +LG L  G+ R ++   L    + L      
Sbjct: 177 QGLNRQIRRMCEYFDYEVLKLERIQIMNIKLGDLGQGNWRNLTPTELEGLFDMLENSEKT 236

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           +         ++      D      +        KK+ + K G +  K   T     +  
Sbjct: 237 QMSKAPSNKAFNKALEEFDIKTDYRKASIAAKYGKKDKTDKPGSTNSKSSNTAAPSSDEN 296

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +    K            +++     P    K   +  S KK
Sbjct: 297 EHKAKPKRKGKPASGLRVGKQKVAANKPKGGPKPKAKNQSKKK 339


>gi|158320760|ref|YP_001513267.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
 gi|158140959|gb|ABW19271.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
          Length = 228

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 62/229 (27%), Positives = 111/229 (48%), Gaps = 7/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+  GI SRRE ++ I  +RV +NGI+      +V   D + VD  P+ +  + 
Sbjct: 1   MRINKYISETGICSRREADQWIIDKRVTINGIVA-ELGSDVSPGDAVFVDHKPIGQKRKP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T            +      R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCTTEKHV--KGNIVDFVHHKERIFPIGRLDKDSQGLILLTNDGDIVNK 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V  +  +  + +  +  G+ I G      +VT    K ++    + L
Sbjct: 118 ILRAENNHEKEYIVTVNKPITPEFIKGMSSGVKILGTKTKPCKVT----KINDTVFRIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ + F +KV +L RI     +L  L  G  R+++K+ L 
Sbjct: 174 TQGLNRQIRRMCQVFGYKVVKLQRIRIMNVKLKGLEIGQWRDLTKEELE 222


>gi|297205889|ref|ZP_06923284.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii JV-V16]
 gi|297149015|gb|EFH29313.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii JV-V16]
          Length = 237

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 78/230 (33%), Positives = 127/230 (55%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+IA+AGIASRR+ E+MI + RV VNG ++      V  + +IEVDG+P++K  + 
Sbjct: 3   ERLQKLIAQAGIASRRKAEKMITEGRVAVNGRIVTELGTKVEPSANIEVDGLPIQKESKH 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     ++++  D  GR TV D       R+  VGRLD +T GLLL+TNDG LA  
Sbjct: 63  TYLLYKPRG-VISSVKDDKGRKTVLDFFEESPYRLYPVGRLDYDTSGLLLITNDGELANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           L  P     +VY  +  G +  +++  LK G+ I G      +V +    ++   + V +
Sbjct: 122 LMHPRHMVDKVYVAKIKGFLTPEEIYSLKHGVRIDGKKSAPAKVKIISTNREKGTSIVQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + EG   ++K++F+     V++L R  Y    L +L AG  RE++++ +
Sbjct: 182 TIHEGHYHQVKRMFKAVGHLVDKLSRERYAFLTLKSLTAGKYRELTREEV 231


>gi|281412320|ref|YP_003346399.1| pseudouridine synthase [Thermotoga naphthophila RKU-10]
 gi|281373423|gb|ADA66985.1| pseudouridine synthase [Thermotoga naphthophila RKU-10]
          Length = 239

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 55/243 (22%), Positives = 111/243 (45%), Gaps = 7/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++ +G+ +R+EV+++I Q RV VNG ++     +V   D + +DG  +    + 
Sbjct: 1   MRLDRYLSNSGVGTRKEVKKLIKQGRVTVNGRVVLDPGHSVSENDVVVLDGETVNFHRKV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +  +     + +T       S            +  VGRLD + EGLL++TNDG  A  
Sbjct: 61  YILFHKPSGYVTSTKDP---HSETIMEFLPPLKGIFPVGRLDKDAEGLLIITNDGDFAHR 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V+  G++ +DK+  LK G+ ++   +   +     +K SN  + + +
Sbjct: 118 VTSPKWSVEKEYIVKVEGEITEDKIEKLKNGVTLRDGFFAKAKCV---EKLSNDTLKIVI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHLLEE 252
            EG+  ++K++      +   L R   G   L   +  G  R +S++ +++       +E
Sbjct: 175 TEGRYHQVKRMTAAVGLRTVHLKRTRIGELVLPDDMKPGEYRFLSEEEVKKVFEGENKKE 234

Query: 253 AQV 255
              
Sbjct: 235 NTP 237


>gi|42783894|ref|NP_981141.1| RNA pseudouridylate synthase family protein [Bacillus cereus ATCC
           10987]
 gi|49478734|ref|YP_038752.1| pseudouridylate synthase (ribosomal small subunit pseudouridine
           synthase A) [Bacillus thuringiensis serovar konkukian
           str. 97-27]
 gi|206977314|ref|ZP_03238211.1| RNA pseudouridine synthase family protein [Bacillus cereus
           H3081.97]
 gi|217962194|ref|YP_002340764.1| RNA pseudouridine synthase family protein [Bacillus cereus AH187]
 gi|228987961|ref|ZP_04148067.1| Pseudouridine synthase [Bacillus thuringiensis serovar tochigiensis
           BGSC 4Y1]
 gi|229141441|ref|ZP_04269978.1| Pseudouridine synthase [Bacillus cereus BDRD-ST26]
 gi|229158317|ref|ZP_04286384.1| Pseudouridine synthase [Bacillus cereus ATCC 4342]
 gi|42739824|gb|AAS43749.1| RNA pseudouridylate synthase family protein [Bacillus cereus ATCC
           10987]
 gi|49330290|gb|AAT60936.1| pseudouridylate synthase (ribosomal small subunit pseudouridine
           synthase A) [Bacillus thuringiensis serovar konkukian
           str. 97-27]
 gi|206744465|gb|EDZ55875.1| RNA pseudouridine synthase family protein [Bacillus cereus
           H3081.97]
 gi|217065826|gb|ACJ80076.1| RNA pseudouridine synthase family protein [Bacillus cereus AH187]
 gi|228625275|gb|EEK82035.1| Pseudouridine synthase [Bacillus cereus ATCC 4342]
 gi|228642004|gb|EEK98298.1| Pseudouridine synthase [Bacillus cereus BDRD-ST26]
 gi|228771765|gb|EEM20225.1| Pseudouridine synthase [Bacillus thuringiensis serovar tochigiensis
           BGSC 4Y1]
          Length = 242

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 106/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++GI ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGISVKDAKVHVNVEEQEVMIHGEVVEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L ++     +  T  D          L         VGRLDI+TEG LL+TNDG L+ 
Sbjct: 61  VYLMMHKPQGVISATEDDNHETVIDLLELEDAIFNPFPVGRLDIDTEGFLLITNDGKLSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G V ++ +    KG+++          +T+  +    + + +
Sbjct: 121 QLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 180 VITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 231


>gi|254494897|ref|ZP_01052309.2| ribosomal large subunit pseudouridine synthase B [Polaribacter sp.
           MED152]
 gi|213690479|gb|EAQ41737.2| ribosomal large subunit pseudouridine synthase B [Polaribacter sp.
           MED152]
          Length = 302

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 66/299 (22%), Positives = 125/299 (41%), Gaps = 7/299 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N     ++K I+ +GI SRRE E+ I + RV +NG    +    V   D +++DG  ++ 
Sbjct: 11  NQKSTNLNKYISSSGICSRREAEKFIKEGRVTLNGK-ATQLGNRVTKKDVVKLDGRVVKP 69

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + T     +KP+G+V+T    +          +   R+  +GRLD  +EGL+ LTNDG 
Sbjct: 70  KDVTIYIALNKPVGIVSTTDGRE--PNNIVKHINYPERLFPIGRLDKPSEGLIFLTNDGD 127

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +        + Y V  +  + +D +  +  GI I G            +K ++   
Sbjct: 128 IVNKILRAGNNHEKEYFVTVNKSITEDFIEKMGNGIPILGTVTQKC----LVEKVNDKIF 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+ +++V +L R      +LG L  G  RE++++ + E      
Sbjct: 184 KIILTQGLNRQIRRMCEYLDYEVTKLKRTRIMNVELGYLQTGDWRELTEEEMNEINKMIS 243

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
                          +     +    ++   +        S      K    ++   RR
Sbjct: 244 TSSKTEEASKIKEKPKAKKPKKKLAPTKNDFNRKSASFRKSSPKNKRKNTSFSSKRKRR 302


>gi|168205142|ref|ZP_02631147.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           E str. JGS1987]
 gi|169347063|ref|ZP_02866005.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           C str. JGS1495]
 gi|169296746|gb|EDS78875.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           C str. JGS1495]
 gi|170663342|gb|EDT16025.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           E str. JGS1987]
          Length = 301

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 63/250 (25%), Positives = 111/250 (44%), Gaps = 7/250 (2%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            E     R++K I+  G  SRRE +++I Q RVK++G+      + V +   + +DG PL
Sbjct: 57  NEIRDEVRLNKYISETGFCSRREADKLIEQGRVKIDGVKATT-GMKVSNGQSVSIDGKPL 115

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +          +KP+G+  T            +  +   R+  +GRLD +++GL+ +TND
Sbjct: 116 KVENELVYIALNKPVGITCTTESKI--KGNIVDFINHEKRIFPIGRLDKDSQGLIFMTND 173

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +        + Y V  +  +  + +  +  G+ I G            +K S  
Sbjct: 174 GDIVNKILRAGNNHEKEYIVTVNKPITDEFIKGMSNGVPILGTVTKKC----LVKKESKN 229

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+F ++V +L RI      LG L  GS R ++KK L E    
Sbjct: 230 SFRIILTQGLNRQIRRMCEYFGYEVKKLERIRIMNVSLGNLKMGSWRYLTKKELAEINRL 289

Query: 248 HLLEEAQVNL 257
                     
Sbjct: 290 TENSSKTEEA 299


>gi|123442126|ref|YP_001006108.1| 23S rRNA pseudouridine synthase F [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|122089087|emb|CAL11923.1| conserved hypothetical protein [Yersinia enterocolitica subsp.
           enterocolitica 8081]
          Length = 290

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 59/293 (20%), Positives = 114/293 (38%), Gaps = 6/293 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +  
Sbjct: 3   TNSSIRLNKYISESGICSRRDADRYIEQGNVFINGKRATV-GEQVYAGDVVKVNGQLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ++  L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G 
Sbjct: 62  RDQNDLVLIALNKPVGIICTTEDGEGDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  +  + +  L  G+ + G      +V    +K +    
Sbjct: 122 LVNKILRAGNDHEKEYVVTVNKPLTDEFILGLGAGVPMLGTVTKKCKV----RKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           ++ L +G NR+I+++ ++F ++V +L R       L  L  G  R++    L E      
Sbjct: 178 SITLVQGLNRQIRRMCKYFGYEVTKLERTRIMNINLKGLPIGEWRDLRDDELIELFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRP-NIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
              +         +   + +    +                       K+K  
Sbjct: 238 NSSSDEKPQKKPKAKPVVAKKPAISRSKPAEKSEANSAGRKRFTQPGRKKKGR 290


>gi|295399574|ref|ZP_06809556.1| pseudouridine synthase [Geobacillus thermoglucosidasius C56-YS93]
 gi|312109871|ref|YP_003988187.1| pseudouridine synthase [Geobacillus sp. Y4.1MC1]
 gi|294979040|gb|EFG54636.1| pseudouridine synthase [Geobacillus thermoglucosidasius C56-YS93]
 gi|311214972|gb|ADP73576.1| pseudouridine synthase [Geobacillus sp. Y4.1MC1]
          Length = 240

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 108/231 (46%), Gaps = 4/231 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K++A  G  +R+EV++++    VK++G++++     V      + V G  +   E  
Sbjct: 4   RIDKMLANMGFGTRKEVKKLLKSGVVKIDGMIVKDPKTQVNPSEQVVTVRGEEVEYKEFI 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L +   P  +  T    +                  VGRLD +TEGLLLLTNDG LA  
Sbjct: 64  YLMMNKPPGVISATEDMAEETVIDLLEEEDRVFAPFPVGRLDKDTEGLLLLTNDGQLAHQ 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVG 192
           L  P     + Y     G+V ++ +   + GIV+         ++ +  + G  + V V 
Sbjct: 124 LLSPKKHVPKTYFAVIDGEVTEEDIESFRHGIVLDDGYKTKPAELIIL-KSGLRSDVEVT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + EGK  +IK++F     +V  L RI  GP  L  +L  G  RE+++K ++
Sbjct: 183 ITEGKFHQIKRMFRALGKRVVYLKRIQMGPLALDPSLEVGEYRELTEKEVK 233


>gi|325289798|ref|YP_004265979.1| ribosomal large subunit pseudouridine synthase B [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324965199|gb|ADY55978.1| ribosomal large subunit pseudouridine synthase B [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 270

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 90/247 (36%), Positives = 140/247 (56%), Gaps = 5/247 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +   + +EN    R+ K IA +G+ASRR  E M+ + RVKVNG+++    + V  TD IE
Sbjct: 13  EKDQVNEENQIRMRLQKAIALSGLASRRRAEEMMTEGRVKVNGVVVTELGMKVCGTDTIE 72

Query: 62  VDGV-----PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           VDG       ++  E    ++ +KP+G++T+  DP GR TV D L  +  RV  VGRLD 
Sbjct: 73  VDGKTVQSLEVKGKENKVYYMLNKPVGVITSLRDPQGRKTVRDLLGDVKERVYPVGRLDY 132

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +T G+LLLTNDG LA  L  P     ++YRV+   ++    +  L+KG++++       +
Sbjct: 133 DTSGILLLTNDGDLAYRLTHPKFGVSKIYRVQTGSRIPPKSIEQLEKGLLLEDGWTAPAK 192

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V    Q  ++  V + + EG+NR+I+++FE   + V RL R S+GP   G L  G  R +
Sbjct: 193 VHRLPQGQNDHIVEITIHEGRNRQIRRMFERIGYPVQRLHRKSFGPLFTGELAPGGHRRL 252

Query: 237 SKKILRE 243
           S+K +R 
Sbjct: 253 SQKEIRA 259


>gi|332977338|gb|EGK14123.1| ribosomal large subunit pseudouridine synthase B [Desmospora sp.
           8437]
          Length = 236

 Score =  183 bits (463), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 72/235 (30%), Positives = 112/235 (47%), Gaps = 2/235 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV+ARAG+ASRR+ E  I   +V+VNG  + +    V    D IEV+G  +R  ++
Sbjct: 2   ERLQKVMARAGVASRRKSEEWILSGKVRVNGKTVTQLGTRVDPERDRIEVEGRLIRPEQK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                Y     + +          V D    +  RV  VGRLD +TEGLLLLTNDG L  
Sbjct: 62  RYFLFYKPKGVITSLSDPDGR-PVVTDWFREVEERVYPVGRLDYDTEGLLLLTNDGELTH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  +VY+    G   +  L  L+ G+ +        +V +       A + + 
Sbjct: 121 GLAHPRHEVDKVYQATVKGIPAKKSLRRLETGVKLTDGWTAPAKVRMLRSGKEQACLELT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           + EG+NR+++++ E     V  L+R+      L  L  G  RE+SK+ +R     
Sbjct: 181 IHEGRNRQVRRMCEAVGHPVVHLVRVQLAFLTLSGLQPGEYRELSKEEIRRLKEL 235


>gi|313123424|ref|YP_004033683.1| pseudouridine synthase [Lactobacillus delbrueckii subsp. bulgaricus
           ND02]
 gi|312279987|gb|ADQ60706.1| Pseudouridine synthase [Lactobacillus delbrueckii subsp. bulgaricus
           ND02]
          Length = 241

 Score =  183 bits (463), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 99/231 (42%), Gaps = 4/231 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR +V  +I   +V VNG +   A   V     + V+G  +   +   
Sbjct: 3   RLDKFLANMKVGSRSQVHEIIKAGQVTVNGKVCRSAKQKVKEDAEVLVNGQAVIYQQYHY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             L      L  T                 + ++  VGRLD +T GLLLLTNDG LA  L
Sbjct: 63  FLLNKPAGVLSATEDSRQKTVLDLLKDQDSYQKIAPVGRLDKDTTGLLLLTNDGQLAHQL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGD--MQVTLDTQKGSNAWVTV 191
             P     + Y     G  D++    +  G+ ++         +++    +    + + +
Sbjct: 123 LAPEYHVPKPYYALLAGVADEETAKAIAAGLTLKDGTELKPGQLKILRQDKDQEQSEIEI 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            + EGK  ++K++F     KV +L R+S GP  L   L  GS R ++++ L
Sbjct: 183 TITEGKYHQVKRMFASQGMKVLKLKRLSMGPLTLPADLAPGSYRPLTEEEL 233


>gi|297529009|ref|YP_003670284.1| pseudouridine synthase [Geobacillus sp. C56-T3]
 gi|297252261|gb|ADI25707.1| pseudouridine synthase [Geobacillus sp. C56-T3]
          Length = 248

 Score =  183 bits (463), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 62/244 (25%), Positives = 105/244 (43%), Gaps = 4/244 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A  G  +R+EV++++    VKV+G  +  A   V      + V G  +      
Sbjct: 4   RIDKLLAHMGYGTRKEVKKLLKSGAVKVDGAPVRDAKTKVRPDEQIVTVWGETVEYKPFI 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L +      +  T    +     F            VGRLD +TEGLLLLTNDG LA  
Sbjct: 64  YLMMNKPSGVVSATEDAVEETVVDFLEEEDRAFSPFPVGRLDKDTEGLLLLTNDGQLAHQ 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVG 192
           L  P     + Y     G+V +  +   ++G+V+         ++ +  + G  + V V 
Sbjct: 124 LLSPKKHVPKTYFAVVDGEVTEADVAAFQRGVVLDDGYETKPAKLVVL-KSGLRSDVEVT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLLE 251
           + EGK  ++K++F+    +V  L RI  GP  L   L  G  RE++ + +          
Sbjct: 183 ITEGKFHQVKRMFQAVGKRVVYLKRIQMGPLALDPDLAVGEYRELTDEEVDMLKQYRPET 242

Query: 252 EAQV 255
           + + 
Sbjct: 243 DEKK 246


>gi|90020429|ref|YP_526256.1| ribosomal large subunit pseudouridine synthase F [Saccharophagus
           degradans 2-40]
 gi|89950029|gb|ABD80044.1| ribosomal large subunit pseudouridine synthase F [Saccharophagus
           degradans 2-40]
          Length = 324

 Score =  183 bits (463), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 74/332 (22%), Positives = 129/332 (38%), Gaps = 15/332 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK- 69
            +  R++K I+ +G  SRRE +++IA  RVK+NG+L       V S D + VD  PLR  
Sbjct: 4   DSAVRLNKFISDSGHCSRREADKLIASDRVKINGLLP-ELGAVVESGDVVTVDDQPLRAS 62

Query: 70  ---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                      Y+KP G+  T       + V             +GRLD  +EGL+LLT+
Sbjct: 63  AADKTDRIYIAYNKPFGITCTTDQTVKGNIVDAIDHDERI--FPIGRLDKPSEGLILLTS 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG +   +        + Y V  +  +  +    + +G+ I G      +V +       
Sbjct: 121 DGDIVNKILRAENAHDKEYIVTVNKNLAPNFAEKMSRGLPILGTITKPCKVRVI----GK 176

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               + L +G NR+I+++ ++  + V +L+R      +LG L  G  R ++K  L     
Sbjct: 177 TTFKIILTQGLNRQIRRMCDYLGYDVKQLVRTRIMNIELGKLKPGQWRRLTKVELDLLTK 236

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                       A   SS +    +P +         + +     K+G  K K       
Sbjct: 237 ATSQSSKTAIKGANAKSSASPTATKPRVAKPK----VKKEPKDLDKHGRPKNKSTGVKRG 292

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRS 338
            ++         G   +   ++G+      R 
Sbjct: 293 AKSKNLTTGGRTGNKGAGRGNAGRPTAPRGRK 324


>gi|15895934|ref|NP_349283.1| pseudouridylate synthase [Clostridium acetobutylicum ATCC 824]
 gi|15025707|gb|AAK80623.1|AE007765_5 Predicted pseudouridylate synthase [Clostridium acetobutylicum ATCC
           824]
 gi|325510086|gb|ADZ21722.1| pseudouridylate synthase [Clostridium acetobutylicum EA 2018]
          Length = 242

 Score =  183 bits (463), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 106/233 (45%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K+I+  G  SR++V+++I   RVKV+G +++     +      I V+G  +   + 
Sbjct: 2   ERLDKIISNMGYGSRKDVKKIIKDGRVKVDGEVVKDNNKQLDPQKSKIIVNGEEISYKKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  T  D D        +         +GRLD +T GLL LTNDG    
Sbjct: 62  IYLMMNKPDGVISATSDDYDKTVIDLLEVEDQVFEPFPIGRLDKDTVGLLFLTNDGDFNH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY  +    V  + +   K+GIV+         ++ +       + V V
Sbjct: 122 RLISPKWHVDKVYYAKIDKDVTSEDVVAFKEGIVLDDGYKCMSAKLEVLNNSKEGSEVKV 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
            +REGK  ++K++FE    KV  L RIS+   +L   L  G  RE+++  ++ 
Sbjct: 182 TVREGKYHQVKRMFEAQGKKVVYLKRISFAGIKLDENLEEGEYRELTEDEMKA 234


>gi|294786929|ref|ZP_06752183.1| ribosomal large subunit pseudouridine synthase B [Parascardovia
           denticolens F0305]
 gi|315226566|ref|ZP_07868354.1| ribosomal large subunit pseudouridine synthase B [Parascardovia
           denticolens DSM 10105]
 gi|294485762|gb|EFG33396.1| ribosomal large subunit pseudouridine synthase B [Parascardovia
           denticolens F0305]
 gi|315120698|gb|EFT83830.1| ribosomal large subunit pseudouridine synthase B [Parascardovia
           denticolens DSM 10105]
          Length = 257

 Score =  183 bits (463), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 73/236 (30%), Positives = 122/236 (51%), Gaps = 2/236 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVP 66
           +++    R+ KV+A+AG  SRR+ E MI   RV+V+G L+    V V      I VDG  
Sbjct: 13  EDSQEGVRLQKVLAQAGFGSRRKCETMITDGRVEVDGDLVTELGVRVDPLHQEIRVDGSR 72

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +  + R      +KP  +++T  DP GR T+ D +   + R+  +GRLD +TEGL+L+T+
Sbjct: 73  IHISNRHVTLALNKPRKVLSTMDDPKGRWTLRDIVGDRYERIFHMGRLDYDTEGLILMTD 132

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG LA+ +  P  +  + Y     G +     + L +  + +        Q ++  Q   
Sbjct: 133 DGELAQHVMHPKYEVDKTYIATVEGHIGGSVCHRLVRTGVQLDDGWIKLDQCSIIDQNRD 192

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + V V +  G+NR +++VF    + V +LIR   GP +LG L +GS R ++   +
Sbjct: 193 RSVVKVVIHSGRNRIVRRVFGAIGFPVVKLIRTQIGPIKLGELKSGSYRVLTGAEV 248


>gi|187779593|ref|ZP_02996066.1| hypothetical protein CLOSPO_03189 [Clostridium sporogenes ATCC
           15579]
 gi|187773218|gb|EDU37020.1| hypothetical protein CLOSPO_03189 [Clostridium sporogenes ATCC
           15579]
          Length = 236

 Score =  183 bits (463), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 72/230 (31%), Positives = 123/230 (53%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +A  G+ASRR+ E +I + RV+VNGI ++     ++S  D I+VDG  ++  E 
Sbjct: 3   ERLQKYMASCGVASRRKCEDIILEGRVEVNGIKIKEVGTKIISGKDIIKVDGNIIKPEEN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G + T  D  GR T   +L  +  R+  +GRLD++T G+++LTNDG +  
Sbjct: 63  KIYILLNKPKGYLCTAKDEKGRKT-ILDLVKVKERIYPIGRLDMDTSGIIILTNDGEIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  + ++ Y+ +  G + +D + L KKGI I         + +       + + + 
Sbjct: 122 KIIHPKFEKIKTYKAKVKGTMKKDHIELFKKGIDIGDYITAPAALEIFKTNKDTSEIIIK 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGKNR+++++ +     V  L RIS G    G L  G  R ++KK + 
Sbjct: 182 IHEGKNRQVRRMCKSIGHPVIDLDRISIGNISKGDLKLGEWRYLTKKEID 231


>gi|288818760|ref|YP_003433108.1| pseudouridine synthase [Hydrogenobacter thermophilus TK-6]
 gi|288788160|dbj|BAI69907.1| pseudouridine synthase [Hydrogenobacter thermophilus TK-6]
 gi|308752347|gb|ADO45830.1| pseudouridine synthase [Hydrogenobacter thermophilus TK-6]
          Length = 253

 Score =  183 bits (463), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 68/236 (28%), Positives = 118/236 (50%), Gaps = 1/236 (0%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGV 65
           ++      R+++ I+  G+ASRR+ +++I + +VKVNGI ++     V    D +EV+G 
Sbjct: 1   MERGEVLVRLNRFISMCGVASRRKADKLIKEGKVKVNGITIKEMGYRVDPQKDVVEVEGR 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            ++      + L      L +     DG+ ++ + + +I  RV   GRLD N EGLL+LT
Sbjct: 61  VIKAPRYRYVILNKPCCYLSSLAEGKDGKKSIKELIKNIPERVYPAGRLDYNAEGLLVLT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  +  P  +  + Y V   G+V+   L  + KG  ++       +V +   +  
Sbjct: 121 NDGELANRIMHPRYKLKKTYLVWVEGRVNPKTLKEMAKGAHLEDGFARPDKVRIVKMQKD 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +  + V   EG+   +K+    F  KV  L R + GP +LG L  G  R+++ + L
Sbjct: 181 STLLEVVFHEGRKHIVKRFMAKFGHKVKALKRTAIGPIKLGKLPPGKWRDLTAEEL 236


>gi|165869849|ref|ZP_02214507.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0488]
 gi|167633985|ref|ZP_02392308.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0442]
 gi|167637988|ref|ZP_02396266.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0193]
 gi|170685858|ref|ZP_02877081.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0465]
 gi|170705568|ref|ZP_02896032.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0389]
 gi|177651245|ref|ZP_02934076.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0174]
 gi|190568332|ref|ZP_03021240.1| RNA pseudouridine synthase family protein [Bacillus anthracis
           Tsiankovskii-I]
 gi|196033247|ref|ZP_03100660.1| RNA pseudouridine synthase family protein [Bacillus cereus W]
 gi|196040819|ref|ZP_03108117.1| RNA pseudouridine synthase family protein [Bacillus cereus
           NVH0597-99]
 gi|196043991|ref|ZP_03111228.1| RNA pseudouridine synthase family protein [Bacillus cereus 03BB108]
 gi|225866694|ref|YP_002752072.1| RNA pseudouridine synthase family protein [Bacillus cereus 03BB102]
 gi|228917358|ref|ZP_04080911.1| Pseudouridine synthase [Bacillus thuringiensis serovar pulsiensis
           BGSC 4CC1]
 gi|228929759|ref|ZP_04092776.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228936016|ref|ZP_04098826.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228948455|ref|ZP_04110737.1| Pseudouridine synthase [Bacillus thuringiensis serovar monterrey
           BGSC 4AJ1]
 gi|229186962|ref|ZP_04314116.1| Pseudouridine synthase [Bacillus cereus BGSC 6E1]
 gi|229600897|ref|YP_002868983.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0248]
 gi|254687515|ref|ZP_05151371.1| ribosomal small subunit pseudouridine synthase A [Bacillus
           anthracis str. CNEVA-9066]
 gi|254725079|ref|ZP_05186862.1| ribosomal small subunit pseudouridine synthase A [Bacillus
           anthracis str. A1055]
 gi|254736817|ref|ZP_05194523.1| ribosomal small subunit pseudouridine synthase A [Bacillus
           anthracis str. Western North America USA6153]
 gi|254741853|ref|ZP_05199540.1| ribosomal small subunit pseudouridine synthase A [Bacillus
           anthracis str. Kruger B]
 gi|254754548|ref|ZP_05206583.1| ribosomal small subunit pseudouridine synthase A [Bacillus
           anthracis str. Vollum]
 gi|254757380|ref|ZP_05209407.1| ribosomal small subunit pseudouridine synthase A [Bacillus
           anthracis str. Australia 94]
 gi|270000608|ref|YP_003329047.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           Ames]
 gi|291612224|ref|YP_003541038.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           'Ames Ancestor']
 gi|301056214|ref|YP_003794425.1| RNA pseudouridylate synthase [Bacillus anthracis CI]
 gi|164714678|gb|EDR20197.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0488]
 gi|167513805|gb|EDR89173.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0193]
 gi|167530786|gb|EDR93488.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0442]
 gi|170129693|gb|EDS98556.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0389]
 gi|170670322|gb|EDT21062.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0465]
 gi|172083071|gb|EDT68133.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0174]
 gi|190560588|gb|EDV14565.1| RNA pseudouridine synthase family protein [Bacillus anthracis
           Tsiankovskii-I]
 gi|195994676|gb|EDX58631.1| RNA pseudouridine synthase family protein [Bacillus cereus W]
 gi|196025327|gb|EDX63997.1| RNA pseudouridine synthase family protein [Bacillus cereus 03BB108]
 gi|196028273|gb|EDX66882.1| RNA pseudouridine synthase family protein [Bacillus cereus
           NVH0597-99]
 gi|224552861|gb|ACN55070.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           'Ames Ancestor']
 gi|225786978|gb|ACO27195.1| RNA pseudouridine synthase family protein [Bacillus cereus 03BB102]
 gi|228596516|gb|EEK54182.1| Pseudouridine synthase [Bacillus cereus BGSC 6E1]
 gi|228811214|gb|EEM57553.1| Pseudouridine synthase [Bacillus thuringiensis serovar monterrey
           BGSC 4AJ1]
 gi|228823784|gb|EEM69606.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228829938|gb|EEM75558.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228842285|gb|EEM87380.1| Pseudouridine synthase [Bacillus thuringiensis serovar pulsiensis
           BGSC 4CC1]
 gi|229265305|gb|ACQ46942.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0248]
 gi|269850291|gb|ACZ49996.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           Ames]
 gi|300378383|gb|ADK07287.1| RNA pseudouridylate synthase [Bacillus cereus biovar anthracis str.
           CI]
          Length = 242

 Score =  183 bits (463), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 106/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++GI ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGISVKDAKVHVNVEEQEVMIHGEVVEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L ++     +  T  D          L         VGRLDI+TEG LL+TNDG L+ 
Sbjct: 61  VYLMMHKPQGVISATEDDNHETVIDLLELEDAIFNPFPVGRLDIDTEGFLLITNDGKLSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G V ++ +    KG+++          +T+  +    + + +
Sbjct: 121 QLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 180 VITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 231


>gi|314936152|ref|ZP_07843499.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           hominis subsp. hominis C80]
 gi|313654771|gb|EFS18516.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           hominis subsp. hominis C80]
          Length = 228

 Score =  183 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 99/231 (42%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K ++  G+ +R EV++++ +  VKVN  + +     V    D I VDG  +     
Sbjct: 1   MRLDKFLSNMGVGTRTEVKQLLKKNSVKVNDKVEKSPKSQVDPEQDEITVDGKIIEYINH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + +   D   ++ +          +  VGRLD +TEGLLL+TNDG    
Sbjct: 61  VYIMLNKPKGYV-SATYDDINQTVIDLIADYCHLDLFPVGRLDKDTEGLLLITNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS    + Y+V     +  + +   K GI +        Q+       S     V 
Sbjct: 120 NLMSPSKHVSKTYKVTSKYPIKNEDIIAFKNGIELSDGKVKPAQLEKLDHNVS----LVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + EGK  ++K++F   + +V  L R+      L   L +G  R ++ + L+
Sbjct: 176 IYEGKYHQVKRMFHSIDNEVLELKRLKIANLTLDENLKSGEYRLLTSEELK 226


>gi|77918905|ref|YP_356720.1| ribosomal large subunit pseudouridine synthase B [Pelobacter
           carbinolicus DSM 2380]
 gi|77544988|gb|ABA88550.1| ribosomal large subunit pseudouridine synthase B [Pelobacter
           carbinolicus DSM 2380]
          Length = 236

 Score =  183 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 93/228 (40%), Positives = 129/228 (56%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ K+IA AG+ SRR  E  IA  RV VNG + E  A      D I VD  PL +AE  
Sbjct: 3   QRLQKLIAAAGLTSRRRAEEWIANGRVTVNGRVAELGAQADPDKDRILVDNRPLPQAEEP 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L HKP+G VT+  DP GR  V D L    +R+  VGRLD+NTEGLLLLTNDG LA  
Sbjct: 63  VCVLLHKPVGYVTSRRDPQGRPVVTDLLGKFRARLFPVGRLDLNTEGLLLLTNDGDLAWR 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  PS +  + Y VR  G +  +    L++G++++       +V    Q GS+ W+ + +
Sbjct: 123 LSHPSHEVCKTYLVRVQGSLSCEARRQLQEGVLLEEGVTAPAKVARVRQAGSHTWMELSI 182

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            EG+NR+++++ E     V+RL RI Y    LG L  G  R++S+  +
Sbjct: 183 HEGRNRQVRRMCEAVGCPVSRLKRIRYAFLDLGDLRPGQHRQLSRNEV 230


>gi|197334991|ref|YP_002155841.1| ribosomal large subunit pseudouridine synthase B [Vibrio fischeri
           MJ11]
 gi|197316481|gb|ACH65928.1| ribosomal large subunit pseudouridine synthase B [Vibrio fischeri
           MJ11]
          Length = 354

 Score =  183 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 90/353 (25%), Positives = 144/353 (40%), Gaps = 12/353 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG+ SRRE+E MI   RV V+G   +           I +DG  +   E 
Sbjct: 2   SEKLQKVLARAGLGSRRELETMIQAGRVSVDGQRAKLGDRLENVDAKIRIDGHVVSVKES 61

Query: 73  TRLWL-----YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           T +       +     L T H     R+          SR +SVGRLD NT GLLL T D
Sbjct: 62  TDVICRVLAYHKPEGELCTRHDPEGRRTVFDRLPKIRDSRWVSVGRLDANTAGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y  R  G++++  +  L  G+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRKVEREYMCRVFGEINEKMIRNLVTGVKLEDGEARFEDVMYAGGEGMNH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI---LRE 243
              V + EG+NRE++++++     V+RL R+ YG   L   L  G   E+  K    LRE
Sbjct: 182 TFYVVINEGRNREVRRLWDSQGVTVSRLKRVRYGDIFLEKALPRGGWMELELKEVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +     +E+ +++D            +     +  D+ +  ++N+         KK   
Sbjct: 242 MVELPPEKESLLDVDKESRKRAKSKTQKIRRAVKRYDERSTEERNTPAGRRGRNNKKPVG 301

Query: 304 ---PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              P  +R   +      G   S        ++  R   S   K    +   +
Sbjct: 302 SSLPSAKRGSNNGDSKPSGKPQSKGKKPAAGQKPVRSKFSPNGKAPKSKPRQR 354


>gi|299541884|ref|ZP_07052207.1| ribosomal large subunit pseudouridine synthase F [Lysinibacillus
           fusiformis ZC1]
 gi|298725622|gb|EFI66263.1| ribosomal large subunit pseudouridine synthase F [Lysinibacillus
           fusiformis ZC1]
          Length = 233

 Score =  183 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 61/227 (26%), Positives = 108/227 (47%), Gaps = 7/227 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K ++  GI SRR  ++ IA+ +V +NG +       V + D + VDG  ++K ++ 
Sbjct: 1   MRINKYLSETGIISRRGADKWIAEGKVTINGEVATV-GSQVEAGDIVCVDGKEVKKEQQL 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+ +T       + V  +  +   R+  +GRLD  +EGLLLLTNDG +   
Sbjct: 60  VYIALNKPVGITSTTERHIKGNVV--DFVNHPLRIFHIGRLDKESEGLLLLTNDGDIVNK 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V+    +    +  +  G+ I         V    +K S     + L
Sbjct: 118 ILRAENHHEKEYIVQVDKPITAQFIQKMGAGVDILDTTTLPCHV----EKISEKVFKIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +G NR+I+++     + V RL RI     +LG L  G  R++++K 
Sbjct: 174 EQGLNRQIRRMCSALGYSVKRLQRIRIMNIKLGNLKVGQWRDLTEKE 220


>gi|138896374|ref|YP_001126827.1| ribosomal small subunit pseudouridine synthase A [Geobacillus
           thermodenitrificans NG80-2]
 gi|196250000|ref|ZP_03148695.1| pseudouridine synthase [Geobacillus sp. G11MC16]
 gi|134267887|gb|ABO68082.1| Ribosomal small subunit pseudouridine synthase A [Geobacillus
           thermodenitrificans NG80-2]
 gi|196210514|gb|EDY05278.1| pseudouridine synthase [Geobacillus sp. G11MC16]
          Length = 248

 Score =  183 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 104/231 (45%), Gaps = 4/231 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A  G  +R+EV++++    VKV+G  +      V      + V G  +   +  
Sbjct: 4   RIDKLLAHMGYGTRKEVKKLLKSGLVKVDGAAVYDPKTKVRPDEQTVTVWGETVEYKQFI 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L +   P  +  T    +                  VGRLD +TEGLLLLTNDG LA  
Sbjct: 64  YLMMNKPPGVISATEDAVEETVVDLLEEEDRLFDPFPVGRLDKDTEGLLLLTNDGQLAHQ 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVG 192
           L  P     + Y     G+V +D +   ++G+V+         ++ +  + G  + V V 
Sbjct: 124 LLAPKKHVPKTYFAVIDGEVTEDDVEAFRRGVVLDDGYETKPAELVVL-KSGLRSDVEVT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + EGK  ++K++F+    +V  L R+  GP  L   L  G  RE++ + + 
Sbjct: 183 ITEGKFHQVKRMFQAVGKRVVYLKRVQMGPLSLDPNLAVGEYRELTDEEVE 233


>gi|15614139|ref|NP_242442.1| pseudouridylate synthase [Bacillus halodurans C-125]
 gi|10174193|dbj|BAB05295.1| pseudouridylate synthase [Bacillus halodurans C-125]
          Length = 242

 Score =  183 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 75/243 (30%), Positives = 125/243 (51%), Gaps = 5/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KVIA+AGIASRR+ E++I + +VKVNG +++   + V    D IEV+GVP+ K E 
Sbjct: 2   ERLQKVIAQAGIASRRKAEQLILEGKVKVNGQVVKELGIKVNPNQDDIEVEGVPVEKEEP 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               LY     + +   D   +         I  RV  VGRLD +T GLLLLTNDG  A 
Sbjct: 62  VYFLLYKPTGVISSVKDDKGRKVVTDFL--EIEQRVYPVGRLDYDTSGLLLLTNDGEFAN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW--VT 190
           +L  P  +  +VY  +  G   +D+L LL +G+ ++       +V + +         V 
Sbjct: 120 LLMHPRHKIEKVYVAKVKGIPTRDQLKLLARGVKLEDGPTAPAKVKMLSVDRRKQTAIVK 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + + EG+NR+++++FE    +V +L R  +    L  +  G  R +    ++      + 
Sbjct: 180 LTIHEGRNRQVRRMFETIGCEVMKLKREQFAFLDLSGMNPGDVRPLKPIEVKHLRELAVT 239

Query: 251 EEA 253
           +++
Sbjct: 240 KKS 242


>gi|104773810|ref|YP_618790.1| pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|116513816|ref|YP_812722.1| 16S rRNA uridine-516 pseudouridylate synthase related
           pseudouridylate synthase [Lactobacillus delbrueckii
           subsp. bulgaricus ATCC BAA-365]
 gi|103422891|emb|CAI97553.1| Pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|116093131|gb|ABJ58284.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC BAA-365]
 gi|325125474|gb|ADY84804.1| Ribosomal large subunit pseudouridine synthase B [Lactobacillus
           delbrueckii subsp. bulgaricus 2038]
          Length = 241

 Score =  183 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 99/231 (42%), Gaps = 4/231 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR +V  +I   +V VNG +   A   V     + V+G  +   +   
Sbjct: 3   RLDKFLANMKVGSRSQVHEIIKAGQVTVNGKVCRSAKQKVKEDAEVLVNGQAVVYQQYHY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             L      L  T                 + ++  VGRLD +T GLLLLTNDG LA  L
Sbjct: 63  FLLNKPAGVLSATEDSRQKTVLDLLKDQDRYQKIAPVGRLDKDTTGLLLLTNDGQLAHQL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGS--NAWVTV 191
             P     + Y     G  D++    +  G+ ++        Q+ +  Q      + + +
Sbjct: 123 LAPEYHVPKTYYALLAGVADEETAKAIAAGLTLKDGTELKPGQLNILRQDKDQEQSEIEI 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            + EGK  ++K++F     KV +L R+S GP  L   L  GS R ++++ L
Sbjct: 183 TITEGKYHQVKRMFASQGMKVLKLKRLSMGPLTLPADLAPGSYRPLTEEEL 233


>gi|300811357|ref|ZP_07091854.1| pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
 gi|300497721|gb|EFK32746.1| pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
          Length = 241

 Score =  183 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 99/231 (42%), Gaps = 4/231 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR +V  +I   +V VNG +   A   V     + V+G  +   +   
Sbjct: 3   RLDKFLANMKVGSRSQVHEIIKAGQVTVNGKVCRSAKQKVKEDAEVLVNGQAVVYQQYHY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             L      L  T                 + ++  VGRLD +T GLLLLTNDG LA  L
Sbjct: 63  FLLNKPAGVLSATEDSRQKTVLDLLKDQDRYQKIAPVGRLDKDTTGLLLLTNDGQLAHQL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGS--NAWVTV 191
             P     + Y     G  D++    +  G+ ++        Q+ +  Q      + + +
Sbjct: 123 LAPEYHVPKTYYALLAGVADEETAKAIAAGLTLKDGTELKPGQLKILRQDKDQEQSEIEI 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            + EGK  ++K++F     KV +L R+S GP  L   L  GS R ++++ L
Sbjct: 183 TITEGKYHQVKRMFASQGMKVLKLKRLSMGPLTLPADLAPGSYRPLTEEEL 233


>gi|253998637|ref|YP_003050700.1| pseudouridine synthase [Methylovorus sp. SIP3-4]
 gi|313200711|ref|YP_004039369.1| pseudouridine synthase [Methylovorus sp. MP688]
 gi|253985316|gb|ACT50173.1| pseudouridine synthase [Methylovorus sp. SIP3-4]
 gi|312440027|gb|ADQ84133.1| pseudouridine synthase [Methylovorus sp. MP688]
          Length = 362

 Score =  183 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 80/339 (23%), Positives = 133/339 (39%), Gaps = 6/339 (1%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
             +  PQR+ K++A AG+ SRRE+E +I   R+ +NG + E  A  V   D +  D  P+
Sbjct: 23  DPDAVPQRLHKLLALAGLGSRREMEELILSGRITINGKVAEVGAAVV-PGDVVRFDSRPV 81

Query: 68  RKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                      L  +     +V+        +          ++ I++GRLDINT GLL+
Sbjct: 82  HLPFEAELAQVLIYHKPEGEIVSQDDPEKRATVFDKLPRVRGAKWIAIGRLDINTSGLLI 141

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T  G LA     P  +  R Y VR  G++ + ++  L +GI ++        +     +
Sbjct: 142 FTTSGELANRFMHPRYEVEREYAVRIFGELTEGEMLQLTQGIELEDGPASFDSIRPQGGE 201

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           G+N W  V LREG+NRE++++F+ F   V+RL+R+ +GP  L   L  G    +  K + 
Sbjct: 202 GANHWYQVILREGRNREVRRLFDAFQKPVSRLMRVRFGPVNLPPRLKRGQMLNLDPKEVL 261

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             L    L   +  L       +          +         +   +        +  A
Sbjct: 262 GLLEWAGLPLPKAPLRQRTAREKEKAGQVFTPKARRAAPEREPRAEGTTGRPAYGARPDA 321

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF 341
                    S     K   S  +           R P+ 
Sbjct: 322 AGRADGRKTSTSPARKPAQSRRIRQDADIPAPRSRRPAT 360


>gi|225352118|ref|ZP_03743141.1| hypothetical protein BIFPSEUDO_03733 [Bifidobacterium
           pseudocatenulatum DSM 20438]
 gi|225157365|gb|EEG70704.1| hypothetical protein BIFPSEUDO_03733 [Bifidobacterium
           pseudocatenulatum DSM 20438]
          Length = 257

 Score =  183 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 67/235 (28%), Positives = 117/235 (49%), Gaps = 2/235 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           +    R+ K++A+AG  SRR+ E +I + RV+++G L+      V      + VDG  +R
Sbjct: 15  DNEGIRLQKLLAQAGFGSRRKCEEIITEGRVEIDGELVTELGTRVDPKHQEVRVDGSRVR 74

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                     +KP  +++   DP GR T+ D +   + R+  +GRLD ++EGL+L+TNDG
Sbjct: 75  VNPNHVTLALNKPKRVLSAMEDPKGRYTLSDIVGDKYDRIFHMGRLDYDSEGLILMTNDG 134

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNA 187
            L++ +  P  +  + Y     G++       L    + +        +  +      + 
Sbjct: 135 ELSQHVMHPKYEVEKTYIATLEGRISGQVCRRLVTTGVQLDDGWIKLDRCAILDASRDST 194

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V V L  GKNR ++++F    + V RL+R   GP +LG L +GS R +S+  +R
Sbjct: 195 LVKVVLHSGKNRIVRRIFGSIGFPVKRLVRTQIGPIKLGDLKSGSYRVLSQTEVR 249


>gi|296448607|ref|ZP_06890477.1| RNA-binding S4 domain protein [Methylosinus trichosporium OB3b]
 gi|296253879|gb|EFH01036.1| RNA-binding S4 domain protein [Methylosinus trichosporium OB3b]
          Length = 405

 Score =  183 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 157/348 (45%), Positives = 206/348 (59%), Gaps = 5/348 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           + F   R++KV+ARAG  SRR+ E  IA+ RV VNG +L+  A NV   D IEVDG PL 
Sbjct: 36  KAFEGDRIAKVMARAGACSRRDAEIWIAEGRVAVNGAVLDSPAFNVREGDRIEVDGAPLA 95

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLT 125
           + E TRL+L+HKP GLVT+  DP+GR TVF  L        R++SVGRLDINTEGLLLLT
Sbjct: 96  EREPTRLFLFHKPEGLVTSAKDPEGRDTVFGFLEERHPDLPRLVSVGRLDINTEGLLLLT 155

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDGGLAR LELP+T W R YRVR HG++DQ +L+ L+KG+ +  + Y  ++  LD  +G+
Sbjct: 156 NDGGLARTLELPATGWTRRYRVRAHGEIDQARLDELRKGVTVDDVDYAPIEARLDRVQGA 215

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           N W+T+ LREGKNREIK+V E     VNRLIRIS+GPFQLG L  G+  EV  KILREQL
Sbjct: 216 NVWITMALREGKNREIKRVLEHLGLGVNRLIRISFGPFQLGELAEGAVEEVKLKILREQL 275

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G  L E A V+  +P    ET   +            TR +K+ S      ++ +     
Sbjct: 276 GKGLAELAGVDFSSPRR--ETAEPEHVIEEERRQHAKTRARKHVSTLRAEVEESRGKKAP 333

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R   S     KG   +  +    R      +P   ++ + R  + +
Sbjct: 334 RARIERSATADRKGRAVAVETIKPVRRRLEEEAPPLATRNARRFQAER 381


>gi|121607089|ref|YP_994896.1| pseudouridine synthase [Verminephrobacter eiseniae EF01-2]
 gi|121551729|gb|ABM55878.1| ribosomal large subunit pseudouridine synthase B [Verminephrobacter
           eiseniae EF01-2]
          Length = 520

 Score =  183 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 79/356 (22%), Positives = 137/356 (38%), Gaps = 16/356 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          +   D ++V+
Sbjct: 161 KRVLLPQVETPKLHKVLAQAGLGSRLEMEQLILEGRISVNNEPA-HIGQRIQFGDQVKVN 219

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+R          +  +     +V+     +  +        +  +  SVGRLD+NTE
Sbjct: 220 GKPIRYRIDPPPARVIAYHKPVGEVVSHDDPHNRPTVFRRLPRLVQGKWQSVGRLDLNTE 279

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLLT+ G LA  L  P     R Y VR  G +  ++   L  G+ +         +  
Sbjct: 280 GLLLLTSSGELANQLMHPRFGLEREYAVRVLGALSNEEKQKLLDGVRLDDGIASFGTIED 339

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V + EG+NRE++++ E     V+RLIRI YG   L   L  G+  E+ +
Sbjct: 340 GGGEGANCWYRVTIAEGRNREVRRMLEAVGHAVSRLIRIRYGAMVLPRGLKRGTWLELDE 399

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           + +R       L +A       + +                       +      G +  
Sbjct: 400 RDIR------ALAQAAGARAPALSTRTPTDARAGKQRERSGPPMGNGPRRGRSPQGPAAG 453

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +   P                       +  + +  + S  +    SL R    K
Sbjct: 454 ARAQNPRRDGGGQGVGAGGNHAGP----RAAAQPDPMQTSVGYIGGDSLSRLRQSK 505


>gi|291542267|emb|CBL15377.1| ribosomal large subunit pseudouridine synthase B [Ruminococcus
           bromii L2-63]
          Length = 249

 Score =  183 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 77/242 (31%), Positives = 125/242 (51%), Gaps = 3/242 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
              P R+ K IA+ GIASRR+ E +I    VKVNG         V+ TD + V G  +  
Sbjct: 3   KIEPIRLQKFIAQCGIASRRKAEELILGGHVKVNGKTA-ILGDKVLPTDKVFVRGKRIVV 61

Query: 70  AE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            +    R  + +KP G +TT +D  GR  V   + ++  RV  +GRLD ++EG+L+ TND
Sbjct: 62  PKGGNYRYIMLNKPRGFITTMNDERGRKCVAQLVENVGERVYPIGRLDKDSEGMLVFTND 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G  A  +  P     ++YRV     +D+D+L  L+ G+ + G       V +  ++    
Sbjct: 122 GDFANKVMHPKNNVYKIYRVTVRPSIDEDQLVKLETGVELDGRKTAPAYVHVIHKEQGRV 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + + L EGKNREI+++ E    +V RL R   G  ++G L  G  R+++++ +++ L  
Sbjct: 182 VLEMILHEGKNREIRRMCEAVGLEVARLKRTQIGGVKMGMLKQGDWRDLTEQEVKKLLAN 241

Query: 248 HL 249
             
Sbjct: 242 PF 243


>gi|157693404|ref|YP_001487866.1| pseudouridylate synthase [Bacillus pumilus SAFR-032]
 gi|157682162|gb|ABV63306.1| pseudouridylate synthase [Bacillus pumilus SAFR-032]
          Length = 238

 Score =  183 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 104/232 (44%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K++A +G  SR++V++++  + V VNG L ++   +V    D + V G  +   E 
Sbjct: 1   MRLDKLLASSGFGSRKDVKKLVKARAVTVNGELAKQVKDHVDPSNDEVLVHGERVEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  T    D           I      VGRLD +T GLLLLTNDG LA 
Sbjct: 61  IYLMMNKPDGVISATEDVRDETVVDLLEPEDIAREPFPVGRLDKDTVGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V     +    +N L++G++I         +V +D  +  +  + +
Sbjct: 121 QLLSPKKHVPKTYEVHLKYPLGDQDINRLEEGVIILDDYRTKPAKVEVDANESEDTRIRL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K + +    +V  L R S G   L   L  G  RE++ + L 
Sbjct: 181 TITEGKYHQVKLMAQAVGNEVIFLKRRSMGSLSLDEDLAPGEYRELTDEELD 232


>gi|256851006|ref|ZP_05556395.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii 27-2-CHN]
 gi|260661218|ref|ZP_05862132.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii 115-3-CHN]
 gi|282932041|ref|ZP_06337499.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii 208-1]
 gi|256616068|gb|EEU21256.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii 27-2-CHN]
 gi|260548155|gb|EEX24131.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii 115-3-CHN]
 gi|281303808|gb|EFA95952.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii 208-1]
          Length = 237

 Score =  183 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 77/230 (33%), Positives = 128/230 (55%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+IA+AG+ASRR+ E+MI + RV VNG ++      V  + +IEVDG+P++K  + 
Sbjct: 3   ERLQKLIAQAGVASRRKAEKMITEGRVAVNGRIVTELGTKVEPSANIEVDGLPIQKESKH 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     ++++  D  GR TV D       R+  VGRLD +T GLLL+TNDG LA  
Sbjct: 63  TYLLYKPRG-VISSVKDDKGRKTVLDFFEESPYRLYPVGRLDYDTSGLLLITNDGELANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           L  P     +VY  +  G +  ++++ LK G+ I G      +V +    ++   + V +
Sbjct: 122 LMHPRHMVDKVYVAKIKGFLTPEEIHSLKHGVRIDGKKSAPAKVKIISTNREKGTSIVQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + EG   ++K++F+     V++L R  Y    L +L AG  RE++++ +
Sbjct: 182 TIHEGHYHQVKRMFKAVGHLVDKLSRERYAFLTLKSLTAGKYRELTREEV 231


>gi|254473658|ref|ZP_05087054.1| pseudouridylate synthase, subunit B protein [Pseudovibrio sp.
           JE062]
 gi|211957370|gb|EEA92574.1| pseudouridylate synthase, subunit B protein [Pseudovibrio sp.
           JE062]
          Length = 681

 Score =  183 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 159/356 (44%), Positives = 212/356 (59%), Gaps = 7/356 (1%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K K       T +R++K +ARAG+ SRRE E  I   RV VNG +L+  A  V   D + 
Sbjct: 25  KKKQEETVTVTGERIAKAMARAGLCSRREAETWIEAGRVSVNGNVLDTPAFTVTQKDKVY 84

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           VDG PL   ERTRLWL+HKP G VTT+ DP+GR TVFD LP    RV++VGRLDINTEGL
Sbjct: 85  VDGKPLPTRERTRLWLFHKPRGTVTTNKDPEGRKTVFDILPKDMPRVVTVGRLDINTEGL 144

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDGGL+RV+ELP+T WLR YRVR  G+V Q++L+ LK G+ I G+ YG ++ TLDT
Sbjct: 145 LLLTNDGGLSRVIELPATGWLRRYRVRAFGKVTQEQLDALKDGVAIDGVLYGAIEATLDT 204

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +KG N W+T+GLREGKNRE+K++ E  +  VNRLIRIS+GPFQLG L  G  +E+  ++L
Sbjct: 205 EKGDNVWLTIGLREGKNREVKRILEHLDLSVNRLIRISFGPFQLGDLGEGELQEIRGRVL 264

Query: 242 REQLGPHLLEEAQVNLDAP-IYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           R+QLG  L+ EA ++ DAP I   +     +  +  +            S K+  +   K
Sbjct: 265 RDQLGERLVSEADLDFDAPIINQMDARTSKKAEMKKKKKSSGGAGGGWISAKDAAAVLAK 324

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL--RRTSAKK 354
                 R          +G   +   D  +        P+F  ++S   R    +K
Sbjct: 325 HNKKPMRHGEDKRDGDGEGSERNPFGDRKR----VGVKPTFGDRKSFGDRDGGERK 376


>gi|39938724|ref|NP_950490.1| 16S rRNA pseudouridylate synthase [Onion yellows phytoplasma OY-M]
 gi|39721833|dbj|BAD04323.1| 16S rRNA pseudouridylate synthase [Onion yellows phytoplasma OY-M]
          Length = 245

 Score =  183 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 67/233 (28%), Positives = 115/233 (49%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ KV+A A +ASRR+ E +I ++R+KVNG ++      V S+D I +D  P+ K   +
Sbjct: 2   QRLQKVLAYANVASRRKAEILILEKRIKVNGKIISELGTKVSSSDIITLDDKPITKTTYS 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      L T   +    + +     +   R+  +GRLD NT GLLL+TNDG L + 
Sbjct: 62  YFLLNKPNGFLSTAKDNKKRPTVLDLIEEANIQRLYPIGRLDFNTTGLLLITNDGDLTQK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----GSNAWV 189
           L  PS    + Y V+ +  + +  L   +KGI+I        +     +       + W+
Sbjct: 122 LTHPSFCIPKEYHVKINACLQKKDLATFRKGIIIDKNYLAFCKEIDILKSSYKPKPSTWL 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + + EGKNR+++K+ +   ++V +L R  Y    +  L  G+ R +    ++
Sbjct: 182 KLVITEGKNRQVRKMMQSLGYQVLKLKRYRYSFLTIENLTIGAYRPLKIHEIK 234


>gi|212638279|ref|YP_002314799.1| RNA pseudouridine synthase [Anoxybacillus flavithermus WK1]
 gi|212559759|gb|ACJ32814.1| RNA pseudouridine synthase [Anoxybacillus flavithermus WK1]
          Length = 240

 Score =  183 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 107/230 (46%), Gaps = 4/230 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A  G  +R+EV++++    VKV+G +++ A  +V      + V G  +      
Sbjct: 3   RIDKLLANMGYGTRKEVKKLLKAGVVKVDGTIIKDAKTHVDPKAQVVTVWGEEVEYKPFI 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L +      +  T    +                  VGRLD +TEGLLLLTNDG LA  
Sbjct: 63  YLMMNKPKGVISATEDAVEETVVDLLEEEDRIFDPFPVGRLDKDTEGLLLLTNDGQLAHQ 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVG 192
           L  P     ++Y     G+V +D +   ++G+V+         ++ +  + G  + V + 
Sbjct: 123 LLSPKKHVPKIYEAIIDGEVTEDDVVAFQRGVVLDDGYETKPAELVVI-RTGLRSDVRIT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + EGK  +IK++F+    +V  L RI  GP  L   L  G  RE++ + +
Sbjct: 182 ITEGKFHQIKRMFQAVGKRVIYLKRIQMGPIPLDETLELGEYRELTDEEI 231


>gi|229175424|ref|ZP_04302937.1| Pseudouridine synthase [Bacillus cereus MM3]
 gi|228608032|gb|EEK65341.1| Pseudouridine synthase [Bacillus cereus MM3]
          Length = 242

 Score =  182 bits (462), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 105/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G  ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L+     +  T  D          L         VGRLDI+TEG LL+TNDG L+ 
Sbjct: 61  IYLMLHKPQGVISATEDDNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKLSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G V ++ +    KG+++          +T+  +    + + +
Sbjct: 121 QLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDEISEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++FE    KV  L R   GP  L   L  G  RE+S + + 
Sbjct: 180 VITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELSDEEVE 231


>gi|258543615|ref|YP_003189048.1| tRNA/rRNA pseudouridine synthase [Acetobacter pasteurianus IFO
           3283-01]
 gi|256634693|dbj|BAI00669.1| tRNA/rRNA pseudouridine synthase [Acetobacter pasteurianus IFO
           3283-01]
 gi|256637749|dbj|BAI03718.1| tRNA/rRNA pseudouridine synthase [Acetobacter pasteurianus IFO
           3283-03]
 gi|256640803|dbj|BAI06765.1| tRNA/rRNA pseudouridine synthase [Acetobacter pasteurianus IFO
           3283-07]
 gi|256643858|dbj|BAI09813.1| tRNA/rRNA pseudouridine synthase [Acetobacter pasteurianus IFO
           3283-22]
 gi|256646913|dbj|BAI12861.1| tRNA/rRNA pseudouridine synthase [Acetobacter pasteurianus IFO
           3283-26]
 gi|256649966|dbj|BAI15907.1| tRNA/rRNA pseudouridine synthase [Acetobacter pasteurianus IFO
           3283-32]
 gi|256652956|dbj|BAI18890.1| tRNA/rRNA pseudouridine synthase [Acetobacter pasteurianus IFO
           3283-01-42C]
 gi|256656010|dbj|BAI21937.1| tRNA/rRNA pseudouridine synthase [Acetobacter pasteurianus IFO
           3283-12]
          Length = 258

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 135/258 (52%), Positives = 174/258 (67%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + +    +R++K +AR+G+ASRR+ ERMI + R+++NG  +   A  V + D ++VDG P
Sbjct: 1   MTQETRGERIAKWLARSGVASRRDAERMIEENRIRLNGQPVTHPATFVTNGDIVQVDGEP 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +   ERTRLW YHKP GLVTTH DP+GR TVF +LP    RVISVGRLD+N+EGLLLLTN
Sbjct: 61  VSAPERTRLWRYHKPDGLVTTHKDPEGRPTVFASLPEGMPRVISVGRLDLNSEGLLLLTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LAR LELPS  WLR YRVR  G VD+++L  L +G V  G+ YG +   LD++KG N
Sbjct: 121 DGELARRLELPSNGWLRRYRVRVFGVVDEERLASLAQGCVFDGVRYGPIHAVLDSRKGDN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           AW+TV L+EGKNREI+KV    N  V+RLIR SYGPFQLGTL      EVS ++LR+QL 
Sbjct: 181 AWLTVSLKEGKNREIRKVMAGMNLHVSRLIRTSYGPFQLGTLQRRELEEVSPRVLRDQLP 240

Query: 247 PHLLEEAQVNLDAPIYSS 264
               +           + 
Sbjct: 241 KATEKAPPARRAPAKQAD 258


>gi|118479700|ref|YP_896851.1| pseudouridylate synthase [Bacillus thuringiensis str. Al Hakam]
 gi|196044919|ref|ZP_03112153.1| RNA pseudouridine synthase family protein [Bacillus cereus 03BB108]
 gi|225866524|ref|YP_002751902.1| RNA pseudouridine synthase family protein [Bacillus cereus 03BB102]
 gi|229186804|ref|ZP_04313959.1| RNA pseudouridine synthase [Bacillus cereus BGSC 6E1]
 gi|118418925|gb|ABK87344.1| pseudouridylate synthase [Bacillus thuringiensis str. Al Hakam]
 gi|196024407|gb|EDX63080.1| RNA pseudouridine synthase family protein [Bacillus cereus 03BB108]
 gi|225789275|gb|ACO29492.1| RNA pseudouridine synthase family protein [Bacillus cereus 03BB102]
 gi|228596541|gb|EEK54206.1| RNA pseudouridine synthase [Bacillus cereus BGSC 6E1]
          Length = 229

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 110/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEANSCSRRETDRLIKAGRVAINGEICTH-GALVNEGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D    + +     +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAADHIDDNIIEYI--NYPERIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFMNEMSSGVKIKDGMTKPCKVTRV----DQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>gi|59711645|ref|YP_204421.1| 23S rRNA pseudouridylate synthase [Vibrio fischeri ES114]
 gi|59479746|gb|AAW85533.1| 23S rRNA pseudouridylate synthase [Vibrio fischeri ES114]
          Length = 354

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 90/353 (25%), Positives = 144/353 (40%), Gaps = 12/353 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG+ SRRE+E MI   RV V+G   +           I +DG  +   E 
Sbjct: 2   SEKLQKVLARAGLGSRRELETMIQAGRVSVDGQRAKLGDRLENVDAKIRIDGHVVSVKES 61

Query: 73  TRLWL-----YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           T +       +     L T H     R+          SR +SVGRLD NT GLLL T D
Sbjct: 62  TDVICRVLAYHKPEGELCTRHDPEGRRTVFDRLPKIRDSRWVSVGRLDANTAGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y  R  G++++  +  L  G+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRKVEREYMCRVFGEINEKMIRNLVTGVKLEDGEARFEDVMYAGGEGMNH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI---LRE 243
              V + EG+NRE++++++     V+RL R+ YG   L   L  G   E+  K    LRE
Sbjct: 182 TFYVVINEGRNREVRRLWDSQGVTVSRLKRVRYGDIFLEKALPRGGWMELELKEVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +     +E+ +++D            +     +  D+ +  ++N+         KK   
Sbjct: 242 MVELPPEKESLLDVDKESRKRAKSKTQKIRRAVKRYDERSTEERNTPAGRRGRNNKKPVG 301

Query: 304 ---PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              P  +R   +      G   S        ++  R   S   K    +   +
Sbjct: 302 SSLPSAKRGSNNGDSQPSGKPQSKGKKPAAGQKPVRSKFSPNGKAPKSKPRQR 354


>gi|229087263|ref|ZP_04219407.1| Pseudouridine synthase [Bacillus cereus Rock3-44]
 gi|228696053|gb|EEL48894.1| Pseudouridine synthase [Bacillus cereus Rock3-44]
          Length = 242

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 103/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G  ++ A  +V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKFHVNVEEQEVMIHGEIVEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L ++     +  T  D          L         VGRLDI+TEG LLLTNDG LA 
Sbjct: 61  VYLMMHKPQGVISATEDDNHETVVDLLELEDAIFDPFPVGRLDIDTEGFLLLTNDGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G V +  +    KG+++          +T+  +    + + +
Sbjct: 121 QLLSPKKHVPKKYYAHVAGIVTEKDVEEFAKGVILDDGYETKPGALTIL-KSDDVSEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 180 VITEGKFHQVKRMFEAVEKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 231


>gi|254975638|ref|ZP_05272110.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile QCD-66c26]
 gi|255093025|ref|ZP_05322503.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile CIP 107932]
 gi|255314767|ref|ZP_05356350.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile QCD-76w55]
 gi|255517442|ref|ZP_05385118.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile QCD-97b34]
 gi|255650552|ref|ZP_05397454.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile QCD-37x79]
 gi|260683650|ref|YP_003214935.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile CD196]
 gi|260687310|ref|YP_003218444.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile R20291]
 gi|306520500|ref|ZP_07406847.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile QCD-32g58]
 gi|260209813|emb|CBA63664.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile CD196]
 gi|260213327|emb|CBE04906.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile R20291]
          Length = 238

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 70/232 (30%), Positives = 120/232 (51%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R++K IA  GIASRR+ E +I   R+KVNG +++  + N+    D +E D   ++ +E 
Sbjct: 1   MRINKYIASCGIASRRKSEEIILGGRIKVNGSVVKELSFNIDEEKDIVEFDNKKVKPSEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G +TT  D   R +V D L  +  RV  +GRLD  T GLL+LTNDG L  
Sbjct: 61  YIYIVLNKPEGYITTVKDQFNRPSVIDILKDVRERVYPIGRLDYETSGLLILTNDGDLTY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVT 190
            L  P  +  + Y     G +  D++   + G+ I+       ++ +  + ++ + +   
Sbjct: 121 KLTHPKHEIDKTYVASVKGIISDDEIRQFETGLKIEDYTTAPAKIRVTKENKEKNYSVCE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + + EG+NR+++K+ +  N  V  L RIS G   L     G  R +++  ++
Sbjct: 181 ITIHEGRNRQVRKMCKAINHPVLNLRRISVGKIVLKDTKVGEYRYLTEDEIK 232


>gi|229093645|ref|ZP_04224745.1| RNA pseudouridine synthase [Bacillus cereus Rock3-42]
 gi|228689732|gb|EEL43539.1| RNA pseudouridine synthase [Bacillus cereus Rock3-42]
          Length = 229

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 109/234 (46%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEANSCSRRETDRLIKAGRVAINGEICTH-GALVNEGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T ++    + +     +   R+  VGRLD  +EGL+ LTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAAEHIEGNIIDYI--NYPERIFPVGRLDKASEGLIFLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFMNEMSSGVKIKDGMTKPCKVTRV----DQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>gi|325295032|ref|YP_004281546.1| pseudouridine synthase Rsu [Desulfurobacterium thermolithotrophum
           DSM 11699]
 gi|325065480|gb|ADY73487.1| pseudouridine synthase Rsu [Desulfurobacterium thermolithotrophum
           DSM 11699]
          Length = 238

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 72/231 (31%), Positives = 118/231 (51%), Gaps = 2/231 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K++A +G  +R +V+R+I +  V VNG  ++  + NV    D + VDG  +   + 
Sbjct: 1   MRLDKLLADSGFGTRSQVKRLIKKGFVTVNGETIKDPSFNVDPQKDEVLVDGELVEYEKD 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L+     + +   D              F R+  VGRLD + EGLLL+TNDG LA 
Sbjct: 61  YYLILHKPQGYITS-TKDRQMTVMELIADIPRFERLFPVGRLDKDAEGLLLITNDGELAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  +VY V   G+++++ L  LKKGI ++       +V +   + S +   + 
Sbjct: 120 RLTHPKWKVPKVYFVVVEGKLNEENLEPLKKGIELKDFRAKPAKVRILKAEESESEAEIE 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + EGK  ++K++FE     V  L RI +G  +LG L  G  R ++K+ L+E
Sbjct: 180 ITEGKYHQVKRMFEKIGHPVKYLRRIQFGNLKLGNLPVGEYRFLTKEELKE 230


>gi|114327123|ref|YP_744280.1| ribosomal large subunit pseudouridine synthase B [Granulibacter
           bethesdensis CGDNIH1]
 gi|114315297|gb|ABI61357.1| ribosomal large subunit pseudouridine synthase B [Granulibacter
           bethesdensis CGDNIH1]
          Length = 251

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 129/245 (52%), Positives = 171/245 (69%), Gaps = 2/245 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+D +        +R++K +ARAG+ASRR+ E+++   RV++N  ++   A  V S D +
Sbjct: 6   MEDAD--SGTPRGERIAKWLARAGVASRRDAEKLVEDGRVRLNNQVVTHPATFVGSGDLV 63

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            V+G  +   +RTRLW YHK  G++TTH DP GR TVF+ LPS   RV+SVGRLD+N+EG
Sbjct: 64  TVNGALVEAPDRTRLWRYHKTDGVMTTHRDPQGRPTVFEKLPSSMPRVVSVGRLDLNSEG 123

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLLLTNDG LAR LELP T W+R YRVR HG V Q  L+ L +G+ ++G+ YG ++  LD
Sbjct: 124 LLLLTNDGMLARRLELPQTGWIRRYRVRVHGDVTQAMLDSLARGVTVEGVRYGSIEAGLD 183

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           + KGSN+W+TV L+EGKNREI+KV       V RLIRI+YGPFQLG L  G   EV+ K+
Sbjct: 184 SSKGSNSWLTVSLKEGKNREIRKVMRHIGLHVTRLIRIAYGPFQLGQLGKGEVEEVTGKV 243

Query: 241 LREQL 245
           LREQL
Sbjct: 244 LREQL 248


>gi|315655295|ref|ZP_07908195.1| ribosomal large subunit pseudouridine synthase B [Mobiluncus
           curtisii ATCC 51333]
 gi|315490235|gb|EFU79860.1| ribosomal large subunit pseudouridine synthase B [Mobiluncus
           curtisii ATCC 51333]
          Length = 278

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 77/238 (32%), Positives = 120/238 (50%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
              P+R+ KV++RAG+ASRR  E +IA+ RV++NG  +    V V+ TD I VDG  +  
Sbjct: 38  TSEPERLQKVLSRAGVASRRASEDLIARGRVQINGETVREMGVKVLPTDRITVDGQRIHT 97

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               ++W +HKP+G V++    D R  + D +  +  RV +VGRLD  T GLLLLTN+G 
Sbjct: 98  DTVLQVWAFHKPVGTVSSMQPEDDRPCIGDWVTKLPERVYNVGRLDAATAGLLLLTNNGE 157

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  +  PS +  + Y     GQV      +L++G+ ++       +  L   +  ++ V
Sbjct: 158 LANRIMHPSYEVPKTYVAVVQGQVKMGLGKVLRRGVELEDGKVKVDKFKLIEVRRGSSIV 217

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + L  GKNR ++++       V+ L R       L  L  G  R +  K L      
Sbjct: 218 QLTLHSGKNRVVRRLLSAVGHPVSALTRTGIANLTLDGLKEGQFRLLHGKELAALQEM 275


>gi|224476606|ref|YP_002634212.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           carnosus subsp. carnosus TM300]
 gi|222421213|emb|CAL28027.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           carnosus subsp. carnosus TM300]
          Length = 245

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 71/242 (29%), Positives = 130/242 (53%), Gaps = 4/242 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +R+ K IA +G  SRR+ E +I + +VKVNG  +      V  +D++EV+GV L +
Sbjct: 2   SKELERLQKRIANSGYTSRRKAETLIVEGKVKVNGETVTELGTKVKPSDNVEVEGVKLEQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ++  +  Y     ++T+ SD  GR+ V D    + +R+  VGRLD +T GLLLLTNDG 
Sbjct: 62  EDKLYILFYKP-AQVITSVSDDRGRTVVTDYFDDLETRIYPVGRLDYDTSGLLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNA 187
              ++  P  +  + Y  +  G + +D++  L+KGI ++       +V +    ++ +  
Sbjct: 121 FTNLMTHPRYKIKKKYVAKLKGYLMRDEVKALEKGIQLEDGKTHPAEVKIKNQNKEKNTT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP-FQLGTLLAGSTREVSKKILREQLG 246
            V + + EG+NR+++++FE F  +V++L R+       L  L AG  R ++   +++   
Sbjct: 181 VVEITISEGRNRQVRRMFEHFGHEVSKLSRVELADFLTLKGLNAGEGRVLTPHEVKKLRN 240

Query: 247 PH 248
             
Sbjct: 241 LA 242


>gi|110803415|ref|YP_699574.1| ribosomal large subunit pseudouridine synthase f [Clostridium
           perfringens SM101]
 gi|110683916|gb|ABG87286.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           SM101]
          Length = 298

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 65/260 (25%), Positives = 115/260 (44%), Gaps = 10/260 (3%)

Query: 1   MKDKNIVQENFT---PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           +K+  IV          R++K I+  G  SRRE +++I Q RVK++G+      + V   
Sbjct: 44  VKNTIIVSNKNEIRDEVRLNKYISETGFCSRREADKLIEQGRVKIDGVKATT-GMKVSKG 102

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
             + +DG PL+        + +KP+G+  T            +  +   R+  +GRLD +
Sbjct: 103 QSVFIDGKPLKVENELVYIVLNKPVGITCTTESKI--KGNIVDFINHEKRIFPIGRLDKD 160

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           ++GL+ +TNDG +   +        + Y V  +  +  + +  +  G+ I G        
Sbjct: 161 SQGLIFMTNDGDIVNKILRAGNNHEKEYIVTVNKPITDEFIKGMSNGVPILGTVTKKC-- 218

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +K S     + L +G NR+I+++ E+F ++V +L RI      LG L  GS R ++
Sbjct: 219 --LVKKESKNSFRIILTQGLNRQIRRMCEYFGYEVKKLERIRIMNVSLGNLKIGSWRYLT 276

Query: 238 KKILREQLGPHLLEEAQVNL 257
           KK L E              
Sbjct: 277 KKELAEINRLTENSSKTEEA 296


>gi|325679067|ref|ZP_08158661.1| pseudouridylate synthase [Ruminococcus albus 8]
 gi|324109191|gb|EGC03413.1| pseudouridylate synthase [Ruminococcus albus 8]
          Length = 244

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 84/234 (35%), Positives = 124/234 (52%), Gaps = 2/234 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R+ K+IA +G  SRR+ E  IA  +V VNG  +      +   D I VDG+ + + +
Sbjct: 2   EKIRIQKIIAESGFCSRRKAEEFIAAGKVTVNGRKVTLGDKALPGKDLIVVDGIKIDQPK 61

Query: 72  RT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +      + HKP G VTT +D   R  V D L  +  RV  VGRLD ++EGLLLLTNDGG
Sbjct: 62  KRNLYYIMLHKPRGYVTTMNDELNRKCVTDLLDGVPERVYPVGRLDKDSEGLLLLTNDGG 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  PS    + YRV     ++ ++L  L  G+ I G    +  V +  ++ +   +
Sbjct: 122 FANDIMHPSRHVAKTYRVTVRPDINDEQLVKLASGVEIDGRMTAECSVVVLDKQPNRVVL 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + + EG+NR+I+K+ E    +V RL R + GP +LG L AG  RE+    LR 
Sbjct: 182 QMTIHEGRNRQIRKMCEAVGLEVARLKRTAVGPLRLGMLKAGEWRELKPDELRA 235


>gi|227893487|ref|ZP_04011292.1| pseudouridylate synthase [Lactobacillus ultunensis DSM 16047]
 gi|227864712|gb|EEJ72133.1| pseudouridylate synthase [Lactobacillus ultunensis DSM 16047]
          Length = 238

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 72/236 (30%), Positives = 117/236 (49%), Gaps = 3/236 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGIASRR+ E+MI   RVKV+G ++ +    V +  +I VD  P+ +    
Sbjct: 3   ERLQKVIAEAGIASRRKAEKMITAGRVKVDGKVITKLGTKVDTFSNITVDDEPIERESLH 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     + T   D   R+ V      I  R+  VGRLD +T GLLL+TNDG LA +
Sbjct: 63  TYLFYKPRGVVSTASDDKGRRTVVDYF-EDIPYRLYPVGRLDYDTSGLLLMTNDGKLANL 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           L  P  +  +VY  +  G +  +++  L  G+ +        +V +    ++     V +
Sbjct: 122 LMHPRNEVQKVYVAKIKGILTPEEIEGLTHGVKLDRFKAAPAKVKILKTDKRKDTQIVQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + EG   ++K++F+     V +L R  Y    L +L +G  RE+SK  + + +  
Sbjct: 182 TIHEGHYHQVKRMFKAVGHLVEKLSREKYAFLTLDSLTSGQYRELSKNEVDKLMRL 237


>gi|261345329|ref|ZP_05972973.1| ribosomal large subunit pseudouridine synthase F [Providencia
           rustigianii DSM 4541]
 gi|282566663|gb|EFB72198.1| ribosomal large subunit pseudouridine synthase F [Providencia
           rustigianii DSM 4541]
          Length = 291

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 65/300 (21%), Positives = 120/300 (40%), Gaps = 10/300 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  +  R++K I+ +GI SRRE +R I Q  V +NG         V + D ++V+G  + 
Sbjct: 2   EINSSTRLNKYISESGICSRREADRYIEQGNVFINGKRA-GIGDQVSAGDIVKVNGQLIE 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             +   L L      +    +   G      +  +   R+  +GRLD +++GL+ LTN G
Sbjct: 61  PRDEDDLVLIALNKPVGIVSTTESGEKGNIVDYVNHSKRIFPIGRLDKDSQGLIFLTNHG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   +        + Y V  +  V  + +  +  G+ I G      +V    +K +   
Sbjct: 121 DLVNKILRAGNDHEKEYVVTVNKPVTDEFIQGMASGVPILGTMTKKCKV----KKEAPFV 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E F ++V +L R+     +L  +  G  R+++   L E     
Sbjct: 177 FRITLVQGLNRQIRRMTEHFGYEVTKLERVRIMNVKLTGIPVGEWRDLTDDELIELFNLI 236

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
              E+ V             + R           T  K  ++ +    K  +      +R
Sbjct: 237 EKSESDVKPKK-----AAKPQARNTGSKTAGKQGTSSKPKANAEPPKKKFTQPGRKKKKR 291


>gi|167772309|ref|ZP_02444362.1| hypothetical protein ANACOL_03686 [Anaerotruncus colihominis DSM
           17241]
 gi|167665412|gb|EDS09542.1| hypothetical protein ANACOL_03686 [Anaerotruncus colihominis DSM
           17241]
          Length = 259

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 84/257 (32%), Positives = 131/257 (50%), Gaps = 5/257 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DH 59
           MK ++I+ +     R+ KV++  G+ SRR+ E  IAQ RV VNG   +     V    D 
Sbjct: 1   MKTEDIMAK-VNGIRIQKVLSENGVMSRRKAEEAIAQGRVTVNGHPAQ-PGNPVDPARDV 58

Query: 60  IEVDGVPLRKAERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           I +DGV ++  ++      + HKP G VTT SD  GR  V D +    + V  VGRLD N
Sbjct: 59  IAIDGVRVQLRKKKQNVYIMLHKPRGFVTTTSDELGRRCVTDLVKDAPAHVYPVGRLDRN 118

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           +EGLLLLTNDG  A ++  PS    + YRV     V  ++   +  G+++ G       V
Sbjct: 119 SEGLLLLTNDGAFANLVMHPSNHISKTYRVTVRPDVSDEQAAKMSAGVMLDGRMTLPATV 178

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +  ++     + + ++EG+NR+++++ E    +V RL R S GP +LG L  G  RE+ 
Sbjct: 179 LVLEKQDGRVVLQITIQEGRNRQVRRMCEAVGLEVARLKRTSVGPLKLGMLQPGQWRELR 238

Query: 238 KKILREQLGPHLLEEAQ 254
              +         ++A 
Sbjct: 239 PGEVAALRNAASKKQAG 255


>gi|114566930|ref|YP_754084.1| ribosomal large subunit pseudouridine synthaseB [Syntrophomonas
           wolfei subsp. wolfei str. Goettingen]
 gi|114337865|gb|ABI68713.1| ribosomal large subunit pseudouridine synthase B [Syntrophomonas
           wolfei subsp. wolfei str. Goettingen]
          Length = 239

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 63/240 (26%), Positives = 113/240 (47%), Gaps = 1/240 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K +A +GI+SRR+ ER+I Q +VKVN   +   A  +   D +E  G  + + ++ 
Sbjct: 1   MRLAKYLAESGISSRRQAERLITQGKVKVNDKTITELAFTLKPGDRVEFAGKIIEQTDKI 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L+     + +            D L ++ +RV  VGRLD +TEGLLLL+NDG  + +
Sbjct: 61  YLLLHKPAGYISSLADPQGRPRV-IDLLSAVNTRVFPVGRLDYDTEGLLLLSNDGEFSNL 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y     G V  D +  L++G+ ++       +V L + K   + + + +
Sbjct: 120 MTHPRYLIPKKYEAWVQGLVKPDTIRQLEQGVALEDGITAPARVRLLSSKKGQSLLELEI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
            EGK R+IK++      +V +L R +     L  +  G  R ++   +   +        
Sbjct: 180 HEGKKRQIKRMCLAVGHRVTKLKRTALAFLTLEGVPRGQFRFLTASEVESLIMLARQSGK 239


>gi|289178586|gb|ADC85832.1| Ribosomal large subunit pseudouridine synthase B [Bifidobacterium
           animalis subsp. lactis BB-12]
          Length = 266

 Score =  182 bits (461), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 119/242 (49%), Gaps = 2/242 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEV 62
           +   + +    R+ K++A+AG  SRR+ E MI   RV+V+G L+      V      + V
Sbjct: 18  RKQYENDGDGIRLQKLLAQAGFGSRRKCEEMITDGRVEVDGELVTELGTRVDPKRQQVRV 77

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG  +R   R      +KP  +++T  DP GR T+ D +   + R+  +GRLD ++EGL+
Sbjct: 78  DGSRIRLNPRHITLALNKPRKVLSTMDDPKGRYTLRDIVGDKYERIFHMGRLDYDSEGLI 137

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDT 181
           L+TNDG L++ +  P  +  + Y     G +       L +  + +          ++  
Sbjct: 138 LMTNDGELSQHVMHPKYEVEKTYIATLEGHMSGTVCRRLVRTGVQLDDGWIKLDHCSIID 197

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                  V V L  G+NR ++++F    + V RL+R   GP +LG + +GS R +S+  +
Sbjct: 198 SNRDQTIVKVVLHSGRNRIVRRIFGAIGFPVKRLVRTQIGPIKLGDIKSGSYRVLSQDEV 257

Query: 242 RE 243
           R 
Sbjct: 258 RA 259


>gi|160893004|ref|ZP_02073792.1| hypothetical protein CLOL250_00542 [Clostridium sp. L2-50]
 gi|156865087|gb|EDO58518.1| hypothetical protein CLOL250_00542 [Clostridium sp. L2-50]
          Length = 239

 Score =  182 bits (461), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 59/235 (25%), Positives = 101/235 (42%), Gaps = 5/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A   I SR +V++ I +  + VNGI+ +     +    D I  +G  +   + 
Sbjct: 1   MRIDKFLANQDIGSRSQVKQYIKKGMISVNGIVCKSPEQKIDENADQISYNGKVIGYQKH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T+ +                 +  VGRLDI+TEGLLL+T+DG L+ 
Sbjct: 61  HYYMLNKPSGCVSATNDNLHITVLDLLKASVPVKNLFPVGRLDIDTEGLLLITDDGELSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGS--NAWV 189
            L  PS    + Y  R  G   ++ +   K+G+ I          + +     +   + +
Sbjct: 121 NLLSPSKHVAKTYFARIDGLATEEHIKAFKEGLDIGDDKPTKPGTLVIKNTDLNTQTSEI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
            + + EG+  ++K+ FE    KV  L R+S G   L   L  G  RE++   L+ 
Sbjct: 181 LLTITEGRYHQVKRSFEALGMKVTYLKRLSMGSLTLDEALAPGEFRELTDIELQA 235


>gi|308272550|emb|CBX29154.1| Ribosomal large subunit pseudouridine synthase F [uncultured
           Desulfobacterium sp.]
          Length = 235

 Score =  182 bits (461), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 72/235 (30%), Positives = 117/235 (49%), Gaps = 7/235 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAE 71
             R+ K ++ AG  SRR+ E+ I    VKVNG+++      V    D +EVDG  +   +
Sbjct: 4   GMRLQKYLSAAGFCSRRKGEKFILSGLVKVNGVVISELGTKVDPAKDVVEVDGNKIEAKD 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                  +KP G +TT S    R  +  +L +I  R+  VGRLD ++ GLLLLTNDG L 
Sbjct: 64  DLIYIALNKPKGYITTCSRQRDRIVL--DLVNIPQRIYPVGRLDKDSTGLLLLTNDGRLH 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
            VL  PS    + Y V     +  + L+ +K+G  + G      +++  + +       +
Sbjct: 122 NVLSHPSFDHEKEYEVSLKWPIADEALDKMKEGFFLMGSKTRPAEISRISPEK----FHI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            L+EG+NR+I+++ +    +V  L RI     +LG L  G+ R ++ K  +  L 
Sbjct: 178 TLKEGRNRQIRRMVDKVGNRVLELKRIRISDVKLGNLKEGAWRYLTDKEKKALLK 232


>gi|308069544|ref|YP_003871149.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) [Paenibacillus polymyxa E681]
 gi|305858823|gb|ADM70611.1| Ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) [Paenibacillus polymyxa E681]
          Length = 252

 Score =  182 bits (461), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 73/252 (28%), Positives = 120/252 (47%), Gaps = 4/252 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++A+AG+ASRR+ E +I    V+VNG+++           D I V G P++  ++
Sbjct: 2   ERLQKILAQAGVASRRKCEELIQAGSVEVNGVIVTELGTKADPDQDMITVKGRPIKTEKK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      + +          V D L  +  RV  VGRLD +TEGLLLLTNDG  A 
Sbjct: 62  IYLMMNKPKGVITSASDPEGR-KIVSDYLKGVKERVYPVGRLDYDTEGLLLLTNDGEFAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVT 190
           +L  P     + Y     G     +L+ LKKGIV++       +         G  + + 
Sbjct: 121 LLTHPKHHVPKTYVATVKGVPHGTELDKLKKGIVLEDGITAPAEVEYKDVDPNGKESVIQ 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + + EG+NR+++++FE  +  V RL RI++G   L  L  G TR ++K  +   +     
Sbjct: 181 ITIYEGRNRQVRRMFEAISHPVIRLKRIAFGDLLLQNLKRGLTRPLTKDEINRLIQLAKS 240

Query: 251 EEAQVNLDAPIY 262
           +  +        
Sbjct: 241 DNTKKKRTGRGS 252


>gi|28211002|ref|NP_781946.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           tetani E88]
 gi|28203441|gb|AAO35883.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           tetani E88]
          Length = 234

 Score =  182 bits (461), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 77/232 (33%), Positives = 124/232 (53%), Gaps = 2/232 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +A  G+ SRR+ E +I   RVKVNG  ++   V V    D + +D   ++K E 
Sbjct: 2   ERLQKYMASCGVDSRRKCEDIILNGRVKVNGESIKELGVKVDPEKDIVTIDNRIIKKEEN 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            +    +KP G +++  D  GR T   +L  +  R+  +GRLD +T GL+LLTNDG    
Sbjct: 62  KKYIALNKPTGYISSVKDDKGRKT-ILDLIDVKERIYPIGRLDYDTSGLILLTNDGDFYN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  +VY     G  +  +L   KKG+VI        ++ + + K +NA V + 
Sbjct: 121 KVIHPREEKEKVYVATIKGIPNSSELQDFKKGLVIDDYLTSPSKIKIISVKNNNAEVIIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG+NR+++K+ E  N  V +L RIS G   LG L  GS R +++K + + 
Sbjct: 181 IMEGRNRQVRKMCEKINHPVIKLKRISVGHVGLGDLPIGSWRYLTQKEIDKF 232


>gi|228948275|ref|ZP_04110558.1| RNA pseudouridine synthase [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228811262|gb|EEM57600.1| RNA pseudouridine synthase [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
          Length = 229

 Score =  182 bits (461), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 110/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ ++ A   SRRE +R+I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYLSEANSCSRRETDRLIKAGRVAINGEICTH-GALVNEGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T ++    + +     +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAAEHIEGNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGITKPCKVTRV----DKSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>gi|226309632|ref|YP_002769526.1| pseudouridine synthase [Brevibacillus brevis NBRC 100599]
 gi|226092580|dbj|BAH41022.1| pseudouridine synthase [Brevibacillus brevis NBRC 100599]
          Length = 239

 Score =  182 bits (461), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 70/232 (30%), Positives = 116/232 (50%), Gaps = 4/232 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKA 70
             +R+ KV+A   I +R+EV+ ++ Q+ + V+G++     ++V      I VDG PL   
Sbjct: 2   KRERLDKVLANMAIGTRKEVKALVKQRLIVVDGVVATDPGMHVIAEEQEILVDGEPLNFK 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + L   P  +V+   D    + V         +V  VGRLDI+TEGLLLLTNDG L
Sbjct: 62  RWVYVLLNKPPG-VVSATEDNVHETVVDLLPYEWAIKVHPVGRLDIDTEGLLLLTNDGHL 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  L  P  +  + Y  R  G+V +  +    KG+ ++       ++ +    G  + + 
Sbjct: 121 SHSLLSPKKKVDKEYFARIEGRVTERHVQEFAKGVELEDFTTLPAKLEII-SSGETSEIR 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           V + EGK  ++K++F  F+  V  L RI  GP  L  +L  G  RE++++ L
Sbjct: 180 VTIMEGKFHQVKRMFAAFDLHVVYLQRIRMGPLHLDPSLAPGEYRELTEEEL 231


>gi|149277497|ref|ZP_01883638.1| 23S rRNA pseudouridine synthase [Pedobacter sp. BAL39]
 gi|149231730|gb|EDM37108.1| 23S rRNA pseudouridine synthase [Pedobacter sp. BAL39]
          Length = 329

 Score =  182 bits (461), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 67/319 (21%), Positives = 123/319 (38%), Gaps = 8/319 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +G+ SRR  +R I Q  V +NG   +     V   D + V+G  +   E   
Sbjct: 7   RLNKYISESGLCSRRAADRYIEQGNVYINGKKAKV-GDKVFFGDLVMVNGQTIEPKEVEH 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             L      +  T +   G      +  +   RV  +GRLD +++GL+ LTN+G L   +
Sbjct: 66  SVLIAYNKPVGITSTTEAGVKGNIVDHVNHSERVFPIGRLDKDSQGLIFLTNNGDLVNKI 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y V  +  + +  +  + KG+ I GI     +VT    K S     + L 
Sbjct: 126 LRAGNNHEKEYLVTVNKPLTEQFITNMSKGVPILGIMTKKCKVT----KESPFVFKITLI 181

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E F ++V +L R       L  +  G  RE++ +   +         + 
Sbjct: 182 QGLNRQIRRMCEHFGFEVTKLERTRIMNIGLKGIPLGEWRELTAEEQTDIYNMVAKSSSL 241

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
               AP  S++   ++               +   ++ +   K +           AS  
Sbjct: 242 EAASAPKKSAKKPEQELTEKPVAR---KKNSRPAGAKPSAAGKARPERKSGPASRGASAS 298

Query: 315 WMAKGIHSSFLSDSGQREE 333
                  S+  S    +  
Sbjct: 299 AAPDWNKSNGPSRRPVKPS 317


>gi|58337261|ref|YP_193846.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           acidophilus NCFM]
 gi|227903846|ref|ZP_04021651.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           acidophilus ATCC 4796]
 gi|58254578|gb|AAV42815.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           acidophilus NCFM]
 gi|227868733|gb|EEJ76154.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           acidophilus ATCC 4796]
          Length = 238

 Score =  182 bits (461), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 72/236 (30%), Positives = 116/236 (49%), Gaps = 3/236 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGIASRR+ E+MI   RVKV+G ++ +    V +  +I VD  P+ +    
Sbjct: 3   ERLQKVIAEAGIASRRKAEKMITAGRVKVDGQVVTKLGTKVDTFSNITVDDEPIERESLH 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     + T   D   ++ V      I  RV  +GRLD +T GLLL+TNDG LA +
Sbjct: 63  TYIFYKPRGVVSTADDDKGRKTVVDYF-EDIPYRVYPIGRLDYDTSGLLLMTNDGELANL 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW--VTV 191
           L  P  +  +VY  +  G +  +++  L KG+ +        +V +           V +
Sbjct: 122 LMHPRNEVSKVYVAKIKGILTPEEIKSLTKGVKLGRFKSAPAKVKVLKTDKRKNTQIVQI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + EG   ++K++F+     V +L R  Y    L +L +G  RE+SK  + + +  
Sbjct: 182 TIHEGHYHQVKRMFKAVGHLVEKLSREKYAFLTLDSLTSGQYRELSKNEVDKLMKL 237


>gi|297243477|ref|ZP_06927409.1| 16S rRNA uridine-516 pseudouridylate synthase [Gardnerella
           vaginalis AMD]
 gi|298252770|ref|ZP_06976564.1| 16S rRNA uridine-516 pseudouridylate synthase [Gardnerella
           vaginalis 5-1]
 gi|296888522|gb|EFH27262.1| 16S rRNA uridine-516 pseudouridylate synthase [Gardnerella
           vaginalis AMD]
 gi|297533134|gb|EFH72018.1| 16S rRNA uridine-516 pseudouridylate synthase [Gardnerella
           vaginalis 5-1]
          Length = 257

 Score =  182 bits (461), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 120/237 (50%), Gaps = 2/237 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
            ++    R+ K++A AG  SRR+ E +I   RV+V+  L+      V      + VDG  
Sbjct: 13  SDDNNAIRLQKLLAEAGFGSRRKCEEIILDGRVEVDDELVTTLGTRVDPKRQKVRVDGSR 72

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           ++   +      HKP  +++   DP GR T+ D +   + R+  +GRLD ++EGL+L+TN
Sbjct: 73  VKFNTKLVTLALHKPKRVLSAMDDPKGRFTLRDIVGDKYERIFHMGRLDYDSEGLILMTN 132

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
           DG L++ +  P  +  + Y     G+++      L  +G+ ++       +  +  Q   
Sbjct: 133 DGELSQHVMHPKYEVEKTYIATVEGKINGMVCRRLVSQGVNLEDGWIKLDRCAIIDQNHD 192

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
              V V L  GKNR ++++F    + V RL+R   GP +LG L AGS R +S+  +R
Sbjct: 193 TTMVKVVLHSGKNRIVRRIFGAVGYPVKRLVRTQIGPIKLGDLKAGSYRVLSQTEVR 249


>gi|288958822|ref|YP_003449163.1| ribosomal large subunit pseudouridine synthase B [Azospirillum sp.
           B510]
 gi|288911130|dbj|BAI72619.1| ribosomal large subunit pseudouridine synthase B [Azospirillum sp.
           B510]
          Length = 401

 Score =  182 bits (461), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 137/343 (39%), Positives = 187/343 (54%), Gaps = 3/343 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K +ARAG+ SRR+ ER IA+ RV VN  +L   A  V   D ++VDG  + + E  
Sbjct: 22  ERIAKRLARAGLCSRRDAERWIAEGRVAVNSRVLGSPACVVRPGDIVQVDGKVIPEPEPA 81

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW YHKP GLVTT  D  GR TVFD LP    RV+S+GRLD+ TEGLLLLTNDG LAR 
Sbjct: 82  RLWRYHKPSGLVTTARDEKGRETVFDRLPDDLPRVVSIGRLDLTTEGLLLLTNDGELARF 141

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP+T W R YRVR  G+VD+ +L  L+KG  I+G+ YG ++  LD  +G NAW+TV L
Sbjct: 142 LELPATGWTRRYRVRVFGEVDEKQLAALEKGPTIEGVKYGPIEAVLDRIQGRNAWLTVSL 201

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           +EGKNREI+KV E    +VNRLIR++YGPFQLG L  G+  EV K+++REQ+ P      
Sbjct: 202 KEGKNREIRKVMESLGLQVNRLIRVAYGPFQLGKLEEGAVEEVPKRVVREQIAPFFGTPE 261

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
                          R    + +              +  G ++  +      R   ++ 
Sbjct: 262 GAEPAESGTKQRAKARAEAAVKTAPAKAPGAKASTGPRSAGKTEAAEAKAGPKRVPRSAT 321

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSP---SFPSKRSLRRTSAK 353
                    +  +   +R     R+       S + +R     
Sbjct: 322 KRHEAEAARTEEAKPARRGGASGRATLTLGGASAKPVRSGKPA 364


>gi|229099009|ref|ZP_04229944.1| RNA pseudouridine synthase [Bacillus cereus Rock3-29]
 gi|229118040|ref|ZP_04247400.1| RNA pseudouridine synthase [Bacillus cereus Rock1-3]
 gi|228665489|gb|EEL20971.1| RNA pseudouridine synthase [Bacillus cereus Rock1-3]
 gi|228684507|gb|EEL38450.1| RNA pseudouridine synthase [Bacillus cereus Rock3-29]
          Length = 240

 Score =  181 bits (460), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 62/237 (26%), Positives = 109/237 (45%), Gaps = 8/237 (3%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + E     ++++ I+ A   SRRE +R+I   RV +NG +       V   D + +DG  
Sbjct: 5   IYEKEQNMKINQYISEAKSCSRRETDRLIKAGRVAINGEICTH-GALVSDDDVVTIDGQV 63

Query: 67  LRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           + K E+      +HKP+G+  T +D    + +     +   R+  VGRLD  +EGL+LLT
Sbjct: 64  IAKEEKEKVYIAFHKPVGITCTAADHIEDNIIDYI--NYPERIFPVGRLDKASEGLILLT 121

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +A  +     +  + Y V          ++ +  G+ I+       +VT       
Sbjct: 122 NDGAIANQILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVTRV----G 177

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +   + L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L 
Sbjct: 178 QSTFRIVLTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELHELEVGKWRSVTAEELE 234


>gi|18311295|ref|NP_563229.1| hypothetical protein CPE2313 [Clostridium perfringens str. 13]
 gi|18145978|dbj|BAB82019.1| conserved hypothetical protein [Clostridium perfringens str. 13]
          Length = 301

 Score =  181 bits (460), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 63/250 (25%), Positives = 111/250 (44%), Gaps = 7/250 (2%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            E     R++K I+  G  SRRE +++I Q RVK++G+      + V +   + +DG  L
Sbjct: 57  NEIRDEVRLNKYISETGFCSRREADKLIEQGRVKIDGVKATT-GMKVSNGQSVSIDGKSL 115

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +          +KP+G+  T       + V     +   R+  +GRLD +++GL+ +TND
Sbjct: 116 KVENELVYIALNKPVGITCTTESKIKGNIVDFI--NHEKRIFPIGRLDKDSQGLIFMTND 173

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +        + Y V  +  +  + +  +  G+ I G            +K S  
Sbjct: 174 GDIVNKILRAGNNHEKEYIVTVNKPITDEFIKGMSNGVPILGTVTKKC----LVKKESKN 229

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+F ++V +L RI      LG L  GS R ++KK L E    
Sbjct: 230 SFRIILTQGLNRQIRRMCEYFGYEVKKLERIRIMNVSLGNLKMGSWRYLTKKELAEINRL 289

Query: 248 HLLEEAQVNL 257
                     
Sbjct: 290 TENSSKTEEA 299


>gi|225848372|ref|YP_002728535.1| ribosomal large subunit pseudouridine synthase B
           [Sulfurihydrogenibium azorense Az-Fu1]
 gi|225643927|gb|ACN98977.1| ribosomal large subunit pseudouridine synthase B
           [Sulfurihydrogenibium azorense Az-Fu1]
          Length = 247

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 72/242 (29%), Positives = 129/242 (53%), Gaps = 4/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R++K IA++GI SRR+ + +I + +VKVNG  ++   + +    D +EV+G  ++  E+
Sbjct: 2   ERLNKYIAKSGICSRRKADELILEGKVKVNGKTVKNLGLKIDPKKDVVEVEGKIVKPTEK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRS---TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                 +KP+G ++            T F N   I  ++  VGRLD N+EGLL+LTNDG 
Sbjct: 62  KIYLAIYKPVGYLSAVGKDRFGRKTLTDFLNELKIPYKLFPVGRLDYNSEGLLILTNDGE 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P  +  +VY+V+  G+V Q+ L  +++G +++   +   ++ +  ++    W+
Sbjct: 122 FANKVAHPRNEIKKVYKVKVAGEVSQETLKKMEEGTILEDGFFKPDKIKMLKREEDGTWL 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            V +  GK R I++  + F  +V RLIR+  G   +G L     R +S+K +R  L    
Sbjct: 182 LVEIHSGKKRIIRRFMDSFGHRVKRLIRVKIGSIDIGNLKPFDYRYLSEKEIRSILDEKR 241

Query: 250 LE 251
             
Sbjct: 242 DS 243


>gi|323141768|ref|ZP_08076638.1| pseudouridylate synthase [Phascolarctobacterium sp. YIT 12067]
 gi|322413757|gb|EFY04606.1| pseudouridylate synthase [Phascolarctobacterium sp. YIT 12067]
          Length = 241

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 78/238 (32%), Positives = 122/238 (51%), Gaps = 4/238 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
           +R+ K++A AG+ASRRE E++I   RV+VNG ++        +    I VDG P+ +  +
Sbjct: 3   ERLQKILAAAGVASRREAEKIITAGRVRVNGKVVTELGCKFDADKVRISVDGKPIAQEAK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                Y     + T     +   ++ D + ++  RV  VGRLD NTEGLLLLTNDG LA+
Sbjct: 63  AYYMFYKPRGVVTTMSDPQNR-RSIADFVQNLPERVFPVGRLDFNTEGLLLLTNDGALAQ 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            L  PS +  + Y V+  G V Q+KL+ L+ G+ ++        V L             
Sbjct: 122 ALMHPSHEVNKTYFVKVPGIVPQEKLDQLRLGVKLEDGPTAPAIVNLRDYDHERGFTLFD 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + + EG+NR+I+++ +   + V  L RI  GP QL  L  G  R +S++ L +     
Sbjct: 182 ITIHEGRNRQIRRMCDAIGFPVRDLKRIKLGPLQLQNLGRGKFRSLSEQELSQLRKAA 239


>gi|221310234|ref|ZP_03592081.1| pseudouridine synthase [Bacillus subtilis subsp. subtilis str. 168]
          Length = 245

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 77/239 (32%), Positives = 125/239 (52%), Gaps = 3/239 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++   I+ E    +R+ KVIA AG+ASRR+ E +I + +VKVNG ++    V V  +D I
Sbjct: 5   VEKSKIILEVKDMERLQKVIAHAGVASRRKAEELIKEGKVKVNGKVVTELGVKVTGSDQI 64

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           EV+G+ + + E     LY     +++   D  GR  V D   +I  R+  +GRLD +T G
Sbjct: 65  EVNGLKVEREEPVYFLLYKPRG-VISAAQDDKGRKVVTDFFKNIPQRIYPIGRLDYDTSG 123

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL- 179
           LLLLTNDG  A  L  P  +  + Y  +  G   ++ L  L++GI ++       +  L 
Sbjct: 124 LLLLTNDGEFANKLMHPKYEIDKTYVAKVKGIPPKELLRKLERGIRLEEGKTAPAKAKLL 183

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              +K   + + + + EG+NR+++++FE    +V +L R  Y    L  L  G  RE+ 
Sbjct: 184 SLDKKKQTSIIQLTIHEGRNRQVRRMFEAIGHEVIKLKREEYAFLNLRGLHTGDARELR 242


>gi|168186328|ref|ZP_02620963.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum C str. Eklund]
 gi|169295670|gb|EDS77803.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum C str. Eklund]
          Length = 236

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 65/230 (28%), Positives = 108/230 (46%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K +A  G+ASRR+ E +I   RV+VNG ++      V    D + VD   +   E+
Sbjct: 3   ERLQKYMASCGVASRRKCEEIITSNRVQVNGTVVNELGFKVDPSKDKVYVDSKLIFLEEK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP G V+T  D   R T+  +L  +  R+  +GRLD NT GLLL+TNDG +  
Sbjct: 63  NVYIALNKPEGYVSTVKDERDRKTIM-DLVEVEERIFPIGRLDYNTSGLLLMTNDGDVYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  +VY     G    + +     G+ I           +     + + V + 
Sbjct: 122 KIIHPRKEIDKVYIAIIKGIPSNEAIRKFCNGLDIGDYITSKANFEVIDTSENKSKVKIT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGKNR+++++ +     V  L RIS G   L  L     R +++  ++
Sbjct: 182 IHEGKNRQVRRMCDKIGHPVIALKRISVGKISLNYLKRSEWRYLNESEIK 231


>gi|168210383|ref|ZP_02636008.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           B str. ATCC 3626]
 gi|170711586|gb|EDT23768.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           B str. ATCC 3626]
          Length = 298

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 66/260 (25%), Positives = 115/260 (44%), Gaps = 10/260 (3%)

Query: 1   MKDKNIVQENFT---PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           +K+  IV          R++K I+  G  SRRE +++I Q RVK++G+      + V   
Sbjct: 44  VKNTIIVSNKNEIRDKVRLNKYISETGFCSRREADKLIEQGRVKIDGLKATT-GMKVSKG 102

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
             + +DG PL+          +KP+G+  T       + V     +   R+  +GRLD +
Sbjct: 103 QSVSIDGKPLKVENELVYIALNKPVGITCTTESKIKGNIVDFI--NHEKRIFPIGRLDKD 160

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           ++GL+ +TNDG +   +        + Y V  +  +  + +  +  G+ I G        
Sbjct: 161 SQGLIFMTNDGDIVNKILRAGNNHEKEYIVTVNKPITHEFIKGMSNGVPILGTVTKKC-- 218

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +K S     + L +G NR+I+++ E+F ++V +L RI      LG L  GS R ++
Sbjct: 219 --LVKKESKNSFRIILTQGLNRQIRRMCEYFGYEVKKLERIRIMNVSLGNLKMGSWRYLT 276

Query: 238 KKILREQLGPHLLEEAQVNL 257
           KK L E              
Sbjct: 277 KKELAEINRLTENSSKTEEA 296


>gi|170781661|ref|YP_001709993.1| putative RNA pseudouridine synthase [Clavibacter michiganensis
           subsp. sepedonicus]
 gi|169156229|emb|CAQ01371.1| putative RNA pseudouridine synthase [Clavibacter michiganensis
           subsp. sepedonicus]
          Length = 291

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 78/273 (28%), Positives = 124/273 (45%), Gaps = 1/273 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
            E     R+ KV+A AG+ASRR  E MIA  RV VNG  +      +    D + VD   
Sbjct: 19  DEPVAGVRLQKVMAAAGVASRRVCEDMIAAGRVTVNGETVTEPGRRIDPDVDEVAVDDQA 78

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           ++     R  + +KP+G+ ++  D  GR  + +       R+ +VGRLD  T GLL+LTN
Sbjct: 79  VQLDTSKRYLMLNKPVGIYSSLRDERGRPDLREFTEEFEERLFNVGRLDAETSGLLILTN 138

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA VL  PS   L+ Y  +  G+V    +  L +G+ ++       +  + +  G  
Sbjct: 139 DGDLAHVLAHPSFGVLKTYIAKVTGRVTPQTIQRLTQGVDLEDGPIQADRARILSGGGDQ 198

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
             V + L  G+NR ++++ +     V  L+R  +GP  LG+L  G  R+++   L + L 
Sbjct: 199 TLVEITLHSGRNRIVRRMLDEVGHPVEELVRRQFGPLHLGSLGVGRVRDLTSDELGQLLT 258

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVP 279
                 AQ     P  +             +  
Sbjct: 259 ISREARAQAGPANPQGAGAAAEAQGDVDREDGE 291


>gi|290580875|ref|YP_003485267.1| putative 16S pseudouridylate synthase [Streptococcus mutans NN2025]
 gi|254997774|dbj|BAH88375.1| putative 16S pseudouridylate synthase [Streptococcus mutans NN2025]
          Length = 238

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 104/229 (45%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++ +AG  SR +V++ I  Q+V+V+G L      NV  +   I V G  L  +  
Sbjct: 1   MRLDKLLGQAGFGSRGQVKKFIRSQQVRVDGELARTGNQNVDPSLQTITVSGKQLSYSPH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                +      +  VGRLD +TEGL+L+TN+G L  
Sbjct: 61  VYYILNKPAGLVSVVRDQHYQTVIDLIAVVDRREGLYPVGRLDRDTEGLVLITNNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V  +G +  D +     GI  + G      ++ + +     +   +
Sbjct: 121 RLLHPKYHVDKTYYVEVNGDLGIDAIAFFDNGIAFLDGTVCKSAKLQIISSSSEVSRAYI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + EGK  ++KK+F  +  KV  L RIS+GPF+LG L  G  RE++ + 
Sbjct: 181 TITEGKFHQVKKMFLAYGVKVTYLKRISFGPFELGDLSVGEYRELTAEE 229


>gi|218905935|ref|YP_002453769.1| RNA pseudouridine synthase family protein [Bacillus cereus AH820]
 gi|218539238|gb|ACK91636.1| RNA pseudouridine synthase family protein [Bacillus cereus AH820]
          Length = 242

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 107/232 (46%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++GI ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGISVKDAKVHVNVEEQEVMIHGEVVEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L ++     +  T  D          L         VGRLDI+TEG LL+TNDG L+ 
Sbjct: 61  VYLMMHKPQGVISATEDDNHETVIDLLELEDAIFNPFPVGRLDIDTEGFLLITNDGKLSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G V ++ +    KG+++          +T+ ++    + + +
Sbjct: 121 QLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTI-SKSDDISEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 180 VITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 231


>gi|310658781|ref|YP_003936502.1| rlub [Clostridium sticklandii DSM 519]
 gi|308825559|emb|CBH21597.1| RluB [Clostridium sticklandii]
          Length = 235

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 77/229 (33%), Positives = 118/229 (51%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA  GIASRR+ E MI + RV++N  ++   +  V   D +++DG  + K E  
Sbjct: 1   MRINKFIASCGIASRRKAEEMIQEGRVRINDSVVSDLSTKVSEIDIVKIDGKIISKVEEK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KPIG V+T  D  GR +V D       R+  VGRLD ++ GLLL+TNDG L   
Sbjct: 61  YYYMLNKPIGYVSTAKDQFGRPSVVDFF-DKKQRIYPVGRLDYDSRGLLLMTNDGDLTYA 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     ++Y V     +   ++   K GI I G      ++T       N    V +
Sbjct: 120 LTHPKYHIEKIYEVIVSSTLSNSEIEKFKSGIDIGGYVTAKSRITFI----GNTSYEVII 175

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +EGKNR+I+K+F      V  L R+S G  +L  L  G+ R++  + + 
Sbjct: 176 KEGKNRQIRKMFSALGKDVLDLKRVSIGKLKLMDLKEGTYRKLINEEVE 224


>gi|293400699|ref|ZP_06644844.1| ribosomal large subunit pseudouridine synthase B
           [Erysipelotrichaceae bacterium 5_2_54FAA]
 gi|291305725|gb|EFE46969.1| ribosomal large subunit pseudouridine synthase B
           [Erysipelotrichaceae bacterium 5_2_54FAA]
          Length = 245

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 73/245 (29%), Positives = 120/245 (48%), Gaps = 5/245 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E MIAQ RV VNG ++      V   D +EVDG P+ K  + 
Sbjct: 2   ERLQKVIAQAGIASRRKAEEMIAQGRVCVNGDIITEMGYKVKRGDVVEVDGNPIEKENKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +      + T++ +     T   +L     R+ +VGRLD +T G+LLLTNDG  A  
Sbjct: 62  YFLMNKPKKTMCTSNDE--FDRTTVIDLIPCKERIFTVGRLDYDTSGVLLLTNDGEFANE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQK--GSNAWVT 190
           +  P     +VY +  +G +  +++  +KKGIV+         ++ L  +    +     
Sbjct: 120 IIHPRYHIPKVYNLTINGILTPEEMIQIKKGIVLDDGKKTLPAKLKLTEKDVTKNQCSFD 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + + EG+NR+IK++ E   ++V RL R      +   L  G  R +    + +       
Sbjct: 180 LTIYEGRNRQIKRMMEALGYEVRRLHRKELAFLKCSDLRQGEYRILKPFEVAQLRSLATK 239

Query: 251 EEAQV 255
            + + 
Sbjct: 240 GKMKS 244


>gi|229543960|ref|ZP_04433019.1| pseudouridine synthase [Bacillus coagulans 36D1]
 gi|229325099|gb|EEN90775.1| pseudouridine synthase [Bacillus coagulans 36D1]
          Length = 245

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 80/237 (33%), Positives = 128/237 (54%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AG+ SRR+ E++I + +VKVNG  +      V  +D IEV+G+PL + E+ 
Sbjct: 2   ERLQKVIAQAGVTSRRKAEQLILEGKVKVNGETVRTLGTKVSQSDKIEVEGIPLEREEKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     +++  SD  GR TV D      +RV  VGRLD +T GLL++TNDG  A +
Sbjct: 62  YYLFYKPRG-VISAVSDDKGRKTVSDYFRDAGARVYPVGRLDYDTSGLLVVTNDGEFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           L  P  +  + Y  R  G   + +L  L+KGI ++       +  L    ++   A V +
Sbjct: 121 LMHPRFEIDKTYIARLSGIPSRQELKQLEKGIRLKDGMTAPARAKLLSMDKRKKKAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + EG+NR+++++FE   + V +L R +YG   L  L AG  RE++   ++      
Sbjct: 181 TIHEGRNRQVRRMFEHLGYPVEKLRREAYGMLTLKGLNAGEKRELTPHEVKTLRSLA 237


>gi|261418151|ref|YP_003251833.1| pseudouridine synthase [Geobacillus sp. Y412MC61]
 gi|319767889|ref|YP_004133390.1| pseudouridine synthase [Geobacillus sp. Y412MC52]
 gi|261374608|gb|ACX77351.1| pseudouridine synthase [Geobacillus sp. Y412MC61]
 gi|317112755|gb|ADU95247.1| pseudouridine synthase [Geobacillus sp. Y412MC52]
          Length = 248

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 61/244 (25%), Positives = 104/244 (42%), Gaps = 4/244 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A  G  +R+EV++++    VKV+G  +  A   V      + V G  +      
Sbjct: 4   RIDKLLAHMGYGTRKEVKKLLKSGAVKVDGAPVRDAKTKVRPDEQIVTVWGETVEYKPFI 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L +      +  T    +                  VGRLD +TEGLLLLTNDG LA  
Sbjct: 64  YLMMNKPSGVVSATEDAVEETVVDLLEEEDRAFCPFPVGRLDKDTEGLLLLTNDGQLAHQ 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVG 192
           L  P     + Y     G+V +  +   ++G+V+         ++ +  + G  + V V 
Sbjct: 124 LLSPKKHVPKTYFAVVGGEVTEADVAAFQRGVVLDDGYETKPAKLVVL-KSGLRSDVEVT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLLE 251
           + EGK  ++K++F+    +V  L RI  GP  L   L  G  RE++ + +          
Sbjct: 183 ITEGKFHQVKRMFQAVGKRVVYLKRIQMGPLALDPDLAVGEYRELTDEEVDMLKQYRPET 242

Query: 252 EAQV 255
           + + 
Sbjct: 243 DEKK 246


>gi|183601655|ref|ZP_02963025.1| ribosomal large subunit pseudouridine synthase B [Bifidobacterium
           animalis subsp. lactis HN019]
 gi|219683811|ref|YP_002470194.1| pseudouridine synthase [Bifidobacterium animalis subsp. lactis
           AD011]
 gi|241190846|ref|YP_002968240.1| 16S rRNA uridine-516 pseudo uridylate synthase [Bifidobacterium
           animalis subsp. lactis Bl-04]
 gi|241196252|ref|YP_002969807.1| 16S rRNA uridine-516 pseudo uridylate synthase [Bifidobacterium
           animalis subsp. lactis DSM 10140]
 gi|183219261|gb|EDT89902.1| ribosomal large subunit pseudouridine synthase B [Bifidobacterium
           animalis subsp. lactis HN019]
 gi|219621461|gb|ACL29618.1| pseudouridine synthase [Bifidobacterium animalis subsp. lactis
           AD011]
 gi|240249238|gb|ACS46178.1| 16S rRNA uridine-516 pseudo uridylate synthase [Bifidobacterium
           animalis subsp. lactis Bl-04]
 gi|240250806|gb|ACS47745.1| 16S rRNA uridine-516 pseudo uridylate synthase [Bifidobacterium
           animalis subsp. lactis DSM 10140]
 gi|295793835|gb|ADG33370.1| 16S rRNA uridine-516 pseudo uridylate synthase [Bifidobacterium
           animalis subsp. lactis V9]
          Length = 257

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 119/242 (49%), Gaps = 2/242 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEV 62
           +   + +    R+ K++A+AG  SRR+ E MI   RV+V+G L+      V      + V
Sbjct: 9   RKQYENDGDGIRLQKLLAQAGFGSRRKCEEMITDGRVEVDGELVTELGTRVDPKRQQVRV 68

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG  +R   R      +KP  +++T  DP GR T+ D +   + R+  +GRLD ++EGL+
Sbjct: 69  DGSRIRLNPRHITLALNKPRKVLSTMDDPKGRYTLRDIVGDKYERIFHMGRLDYDSEGLI 128

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDT 181
           L+TNDG L++ +  P  +  + Y     G +       L +  + +          ++  
Sbjct: 129 LMTNDGELSQHVMHPKYEVEKTYIATLEGHMSGTVCRRLVRTGVQLDDGWIKLDHCSIID 188

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                  V V L  G+NR ++++F    + V RL+R   GP +LG + +GS R +S+  +
Sbjct: 189 SNRDQTIVKVVLHSGRNRIVRRIFGAIGFPVKRLVRTQIGPIKLGDIKSGSYRVLSQDEV 248

Query: 242 RE 243
           R 
Sbjct: 249 RA 250


>gi|89890360|ref|ZP_01201870.1| RNA pseudouridine synthase, Rsu [Flavobacteria bacterium BBFL7]
 gi|89517275|gb|EAS19932.1| RNA  pseudouridine synthase, Rsu [Flavobacteria bacterium BBFL7]
          Length = 253

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 60/245 (24%), Positives = 111/245 (45%), Gaps = 7/245 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + EN    R++K ++  G  SRR  +R+I QQRV +NG +       V   D++ VDG P
Sbjct: 1   MSEN-KGIRINKYLSEQGFCSRRAADRLIEQQRVTINGTVP-EMGTKVQPNDNVAVDGEP 58

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           + K +   +++       +   +D            +  +R+  +GRLD  +EGL+ LTN
Sbjct: 59  ISKKKEKPVYIAFHKPTGIVCTTDTRVEPDNIIEYINYPTRIFPIGRLDKMSEGLIFLTN 118

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG +   +        + Y V     +D   ++ +  GI I        +     ++   
Sbjct: 119 DGDIVNKILRSRNNHGKEYIVTVDHSIDDRFISRMASGIPILDTVTKKCE----VEQIGR 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               + L +G NR+I+++ E+ N++V +L RI     +L  +  G+ R+++K+ L E   
Sbjct: 175 KTFRIVLTQGLNRQIRRMCEYLNYRVTKLKRIRIMNVEL-DIPKGTYRDLTKEELDEIYR 233

Query: 247 PHLLE 251
                
Sbjct: 234 LTAES 238


>gi|312135342|ref|YP_004002680.1| pseudouridine synthase [Caldicellulosiruptor owensensis OL]
 gi|311775393|gb|ADQ04880.1| pseudouridine synthase [Caldicellulosiruptor owensensis OL]
          Length = 236

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 73/228 (32%), Positives = 118/228 (51%), Gaps = 2/228 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A+ GIASRR+ E +I Q RVKVNG  + +    V    D +E+DG  +    +
Sbjct: 1   MRLQKFMAQCGIASRRKCEEIILQGRVKVNGKTVNQLGFKVDPEKDVVEIDGKRISLQRQ 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G++++  D  GR TV D +    +     VGRLD +T GL+LLTNDG  A
Sbjct: 61  KVYIMLNKPFGVISSAKDEKGRKTVVDLVREKVNVRVFPVGRLDFDTTGLILLTNDGEFA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P     + Y     G   + ++ + ++G++I G      +  +      NA V +
Sbjct: 121 YKVTHPKHDIEKTYIALVKGIPSKKEIEMFERGLLIDGKMTAPAKFKILKLINGNALVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG+NR+I+K+ +    KV +L RI+ G  QLG L  G    + ++
Sbjct: 181 KIHEGRNRQIRKMCDMIGHKVLKLKRIAIGKLQLGKLKEGEFVFLDRE 228


>gi|65322075|ref|ZP_00395034.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Bacillus anthracis str.
           A2012]
 gi|118479842|ref|YP_896993.1| ribosomal small subunit pseudouridine synthase A [Bacillus
           thuringiensis str. Al Hakam]
 gi|118419067|gb|ABK87486.1| ribosomal small subunit pseudouridine synthase A [Bacillus
           thuringiensis str. Al Hakam]
          Length = 245

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 62/234 (26%), Positives = 106/234 (45%), Gaps = 4/234 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA 70
              R+ K++A  G  SR+EV++++    VK++GI ++ A V+V      + + G  +   
Sbjct: 2   KNVRLDKLLANMGYGSRKEVKKLLKDGVVKIDGISVKDAKVHVNVEEQEVMIHGEVVEYK 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L ++     +  T  D          L         VGRLDI+TEG LL+TNDG L
Sbjct: 62  EFVYLMMHKPQGVISATEDDNHETVIDLLELEDAIFNPFPVGRLDIDTEGFLLITNDGKL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWV 189
           +  L  P     + Y     G V ++ +    KG+++          +T+  +    + +
Sbjct: 122 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 181 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 234


>gi|126735086|ref|ZP_01750832.1| RNA pseudouridylate synthase family protein [Roseobacter sp. CCS2]
 gi|126715641|gb|EBA12506.1| RNA pseudouridylate synthase family protein [Roseobacter sp. CCS2]
          Length = 267

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 133/257 (51%), Positives = 169/257 (65%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++KV++RAGIASRRE ERMI   RV VNG  +   A+NV + D I VDG  + + E 
Sbjct: 9   GDRIAKVLSRAGIASRREAERMIEDGRVSVNGKTITSPALNVTADDRIVVDGKQVGEPEP 68

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R+WLYHKP GLVTT  D   R TVF +LP    RV+SVGRLD+N+EGLLLLTNDG + R
Sbjct: 69  PRIWLYHKPAGLVTTERDEKDRPTVFASLPETMPRVMSVGRLDLNSEGLLLLTNDGEVKR 128

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            LELPST WLR YRVR +G V + KL+ L++GI ++GI Y  M VT D Q+G+NAW+TV 
Sbjct: 129 KLELPSTGWLRRYRVRINGSVSEAKLDELREGITVEGIQYQPMVVTFDRQQGANAWLTVS 188

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           LREGKNREI++        VNRLIR+SYGPFQL  L  G   E+ ++++R+QLG      
Sbjct: 189 LREGKNREIRRAMGEIGVTVNRLIRVSYGPFQLAALKQGEVEELKQRVVRDQLGISGKPT 248

Query: 253 AQVNLDAPIYSSETLVR 269
            +         +    R
Sbjct: 249 PKRVRKPVNRPTRGKKR 265


>gi|329113791|ref|ZP_08242562.1| Putative RNA pseudouridine synthase [Acetobacter pomorum DM001]
 gi|326696801|gb|EGE48471.1| Putative RNA pseudouridine synthase [Acetobacter pomorum DM001]
          Length = 258

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 136/258 (52%), Positives = 175/258 (67%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + +    +R++K +AR+G+ASRR+ ERMI + R+++NG  +   A  V + D ++VDG P
Sbjct: 1   MTQETRGERIAKWLARSGVASRRDAERMIEENRIRLNGQPVTHPATFVTNGDIVQVDGEP 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +   ERTRLW YHKP GLVTTH DP+GR TVF +LP    RVISVGRLD+N+EGLLLLTN
Sbjct: 61  VSAPERTRLWRYHKPDGLVTTHKDPEGRPTVFASLPEGMPRVISVGRLDLNSEGLLLLTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LAR LELPS  WLR YRVR  G VD+++L  L +G V  G+ YG +   LD++KG N
Sbjct: 121 DGELARRLELPSNGWLRRYRVRVFGVVDEERLASLAQGSVFDGVRYGPIHAVLDSRKGDN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           AW+TV L+EGKNREI+KV    N  V+RLIR SYGPFQLGTLL     EVS ++LR+QL 
Sbjct: 181 AWLTVSLKEGKNREIRKVMAGMNLHVSRLIRTSYGPFQLGTLLRRELEEVSPRVLRDQLP 240

Query: 247 PHLLEEAQVNLDAPIYSS 264
               +           + 
Sbjct: 241 KATEKTPTTQRAPAKQAD 258


>gi|289423805|ref|ZP_06425600.1| ribosomal large subunit pseudouridine synthase B
           [Peptostreptococcus anaerobius 653-L]
 gi|289155844|gb|EFD04514.1| ribosomal large subunit pseudouridine synthase B
           [Peptostreptococcus anaerobius 653-L]
          Length = 238

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 116/233 (49%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA-E 71
            R++K IA +G+ASRR+ E +I + R++VN  +++  +  V    D +  D  P+    E
Sbjct: 1   MRINKFIAASGVASRRKAETLILEGRIRVNNKVIKELSYQVDEDLDQVTFDNKPISVKDE 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +    + +KP G +T+  D   R +V D    I  R+  VGRLD  T GLLL+TNDG L 
Sbjct: 61  KLVYIMLNKPEGYITSVKDQFDRPSVSDLTSDIKERIYPVGRLDYETSGLLLMTNDGDLT 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWV 189
             +  P  +  + Y     G V Q++    + G+ I+        + +       + +  
Sbjct: 121 YKITHPKHEMNKTYIASVRGIVTQEEKYAFENGLKIEDYTTAKANLKILKTDTNKNYSVC 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V + EGKNR+++K+F+  N     L R+  G   +G L  G  R+++K+ + 
Sbjct: 181 KVTIHEGKNRQVRKMFQAINHPTMNLKRVQVGKINIGDLELGKYRKLTKEEIE 233


>gi|227550282|ref|ZP_03980331.1| pseudouridylate synthase [Enterococcus faecium TX1330]
 gi|257889008|ref|ZP_05668661.1| pseudouridine synthase [Enterococcus faecium 1,141,733]
 gi|257897603|ref|ZP_05677256.1| pseudouridine synthase [Enterococcus faecium Com12]
 gi|227180583|gb|EEI61555.1| pseudouridylate synthase [Enterococcus faecium TX1330]
 gi|257825071|gb|EEV51994.1| pseudouridine synthase [Enterococcus faecium 1,141,733]
 gi|257834168|gb|EEV60589.1| pseudouridine synthase [Enterococcus faecium Com12]
          Length = 255

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 61/254 (24%), Positives = 109/254 (42%), Gaps = 8/254 (3%)

Query: 1   MKDKNIVQ---ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS- 56
           M  K+ +    +     R+ K +A  G+ SR+EV+ +I +  ++VNG +++     V   
Sbjct: 1   MNGKSRINALLKWGKRMRLDKFLADMGLGSRKEVKGLIKKGTIEVNGQVVKSDKTQVNEF 60

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            D +   G  +   +     L+     +  T  + D               +  VGRLD 
Sbjct: 61  EDTVTYLGEIIAYQKDFYYILHKPAGVISATQDNHDQTVIDLLKDQDYREDLFPVGRLDK 120

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDM 175
           +TEGLL+LTNDG  A  L  P     + Y     G + ++ + L  +G++I         
Sbjct: 121 DTEGLLILTNDGIFAHQLLSPKKHVEKEYLAEVSGIMTEEDIRLFAEGLIIDGDEQTLPA 180

Query: 176 QVTLDTQKG--SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGS 232
           ++ +D        + + + L EGK  ++K++ +    +V  L RI  G F L   L  G 
Sbjct: 181 KLQIDQVDQESETSIIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGNFWLPKDLNKGQ 240

Query: 233 TREVSKKILREQLG 246
            R ++K+ L +   
Sbjct: 241 YRPMTKEELEQVRE 254


>gi|95931320|ref|ZP_01314035.1| Pseudouridine synthase, Rsu [Desulfuromonas acetoxidans DSM 684]
 gi|95132621|gb|EAT14305.1| Pseudouridine synthase, Rsu [Desulfuromonas acetoxidans DSM 684]
          Length = 242

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 87/231 (37%), Positives = 134/231 (58%), Gaps = 2/231 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K+IA+AG+ASRR+ E+ +   RV+VNG  +         + D IEVDG  L +AE+
Sbjct: 5   ERLQKLIAQAGLASRRQAEQWLKDGRVRVNGRSVT-LGDKADPSVDRIEVDGKALPRAEQ 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP+G VTT  DP GR T+   L  I  RV  VGRLD+N+EGLLLLTNDG L +
Sbjct: 64  KLYLLLNKPLGYVTTLKDPQGRPTIRRFLKGIPQRVYPVGRLDVNSEGLLLLTNDGALTQ 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  Q  + YRV+ +G++       L++G+ ++        V        N+W  + 
Sbjct: 124 HLLHPRHQVSKTYRVKVNGRISPQACRQLEQGVELEDGVTAPAVVRNVHHSPRNSWFDLE 183

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           +REG+NR+++++     ++V+ L RI  G  +LGTL  G  R ++ K +++
Sbjct: 184 IREGRNRQVRRMCRGVGFEVSALKRIRIGSLELGTLAKGQCRSLTSKEIQD 234


>gi|239828089|ref|YP_002950713.1| pseudouridine synthase [Geobacillus sp. WCH70]
 gi|239808382|gb|ACS25447.1| pseudouridine synthase [Geobacillus sp. WCH70]
          Length = 240

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 108/231 (46%), Gaps = 4/231 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A  G  +R+EV++++    VK++G++++     V  T   + V G  +   E  
Sbjct: 4   RIDKMLANMGYGTRKEVKKLLKSGVVKIDGVVVKDPKTQVNPTEQVVTVRGKEVEYKEFI 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L +   P  +  T    +                  VGRLD +TEGLLLLTNDG LA  
Sbjct: 64  YLMMNKPPGVVSATEDVVEETVVDLLEEEDRVFSPFPVGRLDKDTEGLLLLTNDGQLAHQ 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVG 192
           L  P     + Y     G+V ++ +   ++GIV+         ++ +  + G  + V V 
Sbjct: 124 LLSPKKHVPKTYFAVIDGEVTEEDIASFRRGIVLDDGYETKPAELVVL-KSGLRSDVEVT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + EGK  ++K++F     +V  L RI  GP  L  +L  G  RE++ + + 
Sbjct: 183 ITEGKFHQVKRMFRAIGKRVIYLKRIQMGPLVLDPSLDLGEYRELTDEEVE 233


>gi|301056058|ref|YP_003794269.1| pseudouridylate synthase [Bacillus anthracis CI]
 gi|300378227|gb|ADK07131.1| pseudouridylate synthase [Bacillus cereus biovar anthracis str. CI]
          Length = 229

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 62/234 (26%), Positives = 110/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEANSCSRRETDRLIKAGRVAINGEICTH-GALVNEGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T ++    + +     +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAAEHIEGNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVTRV----DQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>gi|311069499|ref|YP_003974422.1| putative 16S pseudouridylate synthase [Bacillus atrophaeus 1942]
 gi|310870016|gb|ADP33491.1| putative 16S pseudouridylate synthase [Bacillus atrophaeus 1942]
          Length = 239

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 102/231 (44%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K++A +GI SR+EV++++    V ++G   +    +V      + V G P+   E 
Sbjct: 1   MRLDKLLANSGIGSRKEVKKIVKAGAVSIDGKQAKDVKTHVDPSEHEVTVYGEPIEYREF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      L  T                +       GRLD +T GLLLLTNDG LA 
Sbjct: 61  IYLMMNKPQGVLSATEDSRQKTVIDLLAPDDMRFEPFPAGRLDKDTVGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V     + ++ +  L+ G+ I+G       +V        +  + +
Sbjct: 121 RLLSPKKHVPKTYEVHLRSGLSEEDIANLESGVFIEGGYKTKPAKVETIANSEEHTEIRL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++K++ +    +V  L R+S G   L  +L  G  RE++++ L
Sbjct: 181 TITEGKYHQVKQMAKAVENEVIFLKRLSMGSLLLDPSLEPGEYRELTEEEL 231


>gi|169830079|ref|YP_001700237.1| ribosomal large subunit pseudouridine synthase F [Lysinibacillus
           sphaericus C3-41]
 gi|168994567|gb|ACA42107.1| Ribosomal large subunit pseudouridine synthase F [Lysinibacillus
           sphaericus C3-41]
          Length = 233

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 108/234 (46%), Gaps = 7/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K ++  GI SRR  ++ IA+ +V +NG         V   D + +DG  ++K ++ 
Sbjct: 1   MRINKYLSETGIISRRGADKWIAEGKVTINGEPATV-GSQVQDGDIVCIDGKEVKKEQQL 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+ +T       + V  +  +   R+  +GRLD  +EGLLLLTNDG +   
Sbjct: 60  VYIALNKPVGITSTTERHIKGNVV--DFVNHPLRIFHIGRLDKESEGLLLLTNDGDIVNK 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V+    + +  +N +  G+ I              +K S+    + L
Sbjct: 118 ILRAENHHEKEYIVQVDKPITEQFINKMSAGVDILDTTTLPC----YVEKISDKVFKIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            +G NR+I+++     + V RL RI     +LG L  G  R+++ K   E    
Sbjct: 174 EQGLNRQIRRMCSALGYSVKRLQRIRIMNIKLGNLKVGQWRDLTDKEQTELFKL 227


>gi|157148091|ref|YP_001455410.1| 23S rRNA pseudouridine synthase F [Citrobacter koseri ATCC BAA-895]
 gi|157085296|gb|ABV14974.1| hypothetical protein CKO_03898 [Citrobacter koseri ATCC BAA-895]
          Length = 291

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 62/301 (20%), Positives = 116/301 (38%), Gaps = 13/301 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         VM  D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFINGKRAT-IGDQVMPGDVVKVNGRLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L        +    +  D       +  +   R+  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVFIALNKPVGIVSTTEDSERDNIVDFVNHSKRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V  D +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPVTDDFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  L  G  R+++   L         
Sbjct: 179 ITLIQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLSGLPPGEWRDLTDDELIALFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
             ++    +   +       +            +++K + +    S  K+  +P  ++  
Sbjct: 239 SSSEAKPTSKAKAKPKTAGIKRP--------VVKIEKTNEKARPASNGKRFTSPGRKKKG 290

Query: 311 A 311
            
Sbjct: 291 R 291


>gi|171742924|ref|ZP_02918731.1| hypothetical protein BIFDEN_02041 [Bifidobacterium dentium ATCC
           27678]
 gi|283456055|ref|YP_003360619.1| RNA pseudouridylate synthase [Bifidobacterium dentium Bd1]
 gi|171278538|gb|EDT46199.1| hypothetical protein BIFDEN_02041 [Bifidobacterium dentium ATCC
           27678]
 gi|283102689|gb|ADB09795.1| RNA pseudouridylate synthase [Bifidobacterium dentium Bd1]
          Length = 257

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 67/237 (28%), Positives = 116/237 (48%), Gaps = 2/237 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
             N    R+ K++A+AG  SRR+ E +I   RV+++G L+      V      + VDG  
Sbjct: 13  DNNNEGIRLQKLLAQAGFGSRRKCEEIITDGRVEIDGELITELGTRVDPKHQEVRVDGSR 72

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +R          +KP  +++   DP GR T+ D +   + R+  +GRLD ++EGL+L+TN
Sbjct: 73  VRVNPNHVTLALNKPKRVLSAMDDPKGRYTLRDIVGDKYERIFHMGRLDYDSEGLILMTN 132

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L++ +  P  +  + Y     G++       L    + +        +  +      
Sbjct: 133 DGELSQHIMHPKYEVEKTYIATLDGRISGTVCRRLVTTGVQLDDGWIKLDRCAILDSSRD 192

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +  V V L  GKNR ++++F    + V RL+R   GP +LG L +G+ R +S+  +R
Sbjct: 193 STLVKVVLHSGKNRIVRRIFGSIGFPVRRLVRTQIGPIKLGDLKSGTYRVLSQVEVR 249


>gi|306822735|ref|ZP_07456113.1| ribosomal large subunit pseudouridine synthase B [Bifidobacterium
           dentium ATCC 27679]
 gi|309801018|ref|ZP_07695150.1| pseudouridylate synthase [Bifidobacterium dentium JCVIHMP022]
 gi|304554280|gb|EFM42189.1| ribosomal large subunit pseudouridine synthase B [Bifidobacterium
           dentium ATCC 27679]
 gi|308222554|gb|EFO78834.1| pseudouridylate synthase [Bifidobacterium dentium JCVIHMP022]
          Length = 257

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 67/237 (28%), Positives = 116/237 (48%), Gaps = 2/237 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
             N    R+ K++A+AG  SRR+ E +I   RV+++G L+      V      + VDG  
Sbjct: 13  DNNNEGIRLQKLLAQAGFGSRRKCEEIITDGRVEIDGELITELGTRVDPKHQEVRVDGSR 72

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +R          +KP  +++   DP GR T+ D +   + R+  +GRLD ++EGL+L+TN
Sbjct: 73  VRVNPNHVTLALNKPKRVLSAMDDPKGRYTLRDIVGDKYERIFHMGRLDYDSEGLILMTN 132

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L++ +  P  +  + Y     G++       L    + +        +  +      
Sbjct: 133 DGELSQHVMHPKYEVEKTYIATLDGRISGTVCRRLVTTGVQLDDGWIKLDRCAILDSSRD 192

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +  V V L  GKNR ++++F    + V RL+R   GP +LG L +G+ R +S+  +R
Sbjct: 193 STLVKVVLHSGKNRIVRRIFGSIGFPVRRLVRTQIGPIKLGDLKSGTYRVLSQVEVR 249


>gi|227498494|ref|ZP_03928640.1| pseudouridine synthase [Acidaminococcus sp. D21]
 gi|226903952|gb|EEH89870.1| pseudouridine synthase [Acidaminococcus sp. D21]
          Length = 246

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 83/230 (36%), Positives = 127/230 (55%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K++A +G+ASRRE E++I Q RV VNG  +      V  TD I +DG PLR  ER 
Sbjct: 7   ERLQKMMAASGVASRRECEKIILQGRVTVNGKPVIELGTKVSPTDRILIDGRPLR-KERH 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L +KP  ++TT  DP GR TV + +     RV  VGRLD  TEGLL++TNDG LA+ 
Sbjct: 66  RYFLLNKPPAVMTTMKDPRGRRTVAELMDKERERVYPVGRLDFMTEGLLIMTNDGALAQG 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTV 191
           +  PS    + Y V   G V+++KL+ L+ GI +          +V     +   +   V
Sbjct: 126 MTHPSYHINKTYEVVVDGHVEEEKLDKLRTGIRLCDGMTAPALVEVKRYDSRRDQSIFEV 185

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + EG+NR+++++ E   + V +L R       L  +  G+ RE++   +
Sbjct: 186 TIHEGRNRQVRRMCEAIGYPVRKLKRTQVAFLSLQGVKKGAYRELTDDEV 235


>gi|310642601|ref|YP_003947359.1| pseudouridine synthase [Paenibacillus polymyxa SC2]
 gi|309247551|gb|ADO57118.1| Pseudouridine synthase [Paenibacillus polymyxa SC2]
          Length = 252

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 73/252 (28%), Positives = 119/252 (47%), Gaps = 4/252 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++A+AG+ASRR+ E +I    V+VNG+ +           D I V G P++  ++
Sbjct: 2   ERLQKILAQAGVASRRKCEELIQAGSVEVNGVTVTELGTKADPDQDMITVKGRPIKTEKK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      + +          V D L  +  RV  VGRLD +TEGLLLLTNDG  A 
Sbjct: 62  IYLMMNKPKGVITSASDPEGR-KIVSDYLKGVKERVYPVGRLDYDTEGLLLLTNDGEFAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVT 190
           +L  P     + Y     G     +L+ LKKGIV++       +         G  + + 
Sbjct: 121 LLTHPKHHVPKTYVATVKGVPHGTELDKLKKGIVLEDGITAPAEVEYKDVDPDGKESVIQ 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + + EG+NR+++++FE  +  V RL RI++G   L  L  G TR ++K  +   +     
Sbjct: 181 ITIYEGRNRQVRRMFEAISHPVIRLKRIAFGDLLLQNLKRGLTRPLTKDEINRLIQLAKS 240

Query: 251 EEAQVNLDAPIY 262
           +  +        
Sbjct: 241 DNTKKKRTGRGS 252


>gi|169831357|ref|YP_001717339.1| pseudouridine synthase [Candidatus Desulforudis audaxviator MP104C]
 gi|169638201|gb|ACA59707.1| pseudouridine synthase [Candidatus Desulforudis audaxviator MP104C]
          Length = 238

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 75/239 (31%), Positives = 111/239 (46%), Gaps = 2/239 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A AGIASRR  E +I   RV+VNG ++      V S+ D +EVDG  +R   +
Sbjct: 1   MRLQKYLAEAGIASRRASEELILAGRVRVNGEVVRELGTTVDSSRDRVEVDGQKIRPEPK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + LY     + T       R    D +     RV  VGRLD ++EGLLLLTNDG LA 
Sbjct: 61  IYVLLYKPRGYVTTARDPQGRRKVT-DLVAGAGGRVFPVGRLDYDSEGLLLLTNDGELAY 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V          L  + +G+ +         V L  + G  A V + 
Sbjct: 120 RLTHPRFHVPKTYHVVLDRSPGPAALRAIARGVELDDGLTAPAGVRLVRRDGREALVEMT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
           + EG+ R++++++    ++V RL R+     +LG L  G  R +    +RE      L 
Sbjct: 180 IHEGRKRQVRRMWAALGFEVQRLKRVRMAGLELGGLEPGRWRHLRTTEVRELRKLVRLP 238


>gi|161507454|ref|YP_001577408.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           helveticus DPC 4571]
 gi|260101634|ref|ZP_05751871.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           helveticus DSM 20075]
 gi|160348443|gb|ABX27117.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           helveticus DPC 4571]
 gi|260084567|gb|EEW68687.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           helveticus DSM 20075]
          Length = 238

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 70/236 (29%), Positives = 117/236 (49%), Gaps = 3/236 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGIASRR+ E+MI   RVKV+G ++ +    V +  +I VD  P+ +    
Sbjct: 3   ERLQKVIAEAGIASRRKAEKMIVAGRVKVDGKVVTKLGTKVETFSNITVDDEPIERESLH 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     + T   D   ++ V      +  R+  VGRLD +T GLLL+TNDG LA +
Sbjct: 63  TYLFYKPRGVVSTADDDKGRKTVVDYF-EDVPYRLYPVGRLDYDTSGLLLMTNDGKLANL 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           L  P  +  +VY  +  G +  D++  L  G+ +        +V +    ++     + +
Sbjct: 122 LMHPRNEVSKVYVAKIKGILTPDEIKTLTTGVKLDRFKAAPAKVKILKTDKRKDTQIIQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + EG   ++K++F+     V +L R  Y    L +L +G  RE+SK  + + +  
Sbjct: 182 TIHEGHYHQVKRMFKAVGHLVEKLSREKYAFLTLDSLTSGQYRELSKHEVDKLMRL 237


>gi|218532076|ref|YP_002422892.1| RNA-binding S4 domain protein [Methylobacterium chloromethanicum
           CM4]
 gi|218524379|gb|ACK84964.1| RNA-binding S4 domain protein [Methylobacterium chloromethanicum
           CM4]
          Length = 674

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 143/336 (42%), Positives = 194/336 (57%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R++K IARAGIASRR+ E +I   RV +NG +L   A+NV  +D I VD  PL   
Sbjct: 19  PEGERIAKAIARAGIASRRDAEALIEAGRVTLNGKVLTSPAINVTDSDRITVDDEPLPAR 78

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ERTRLWL HKP G+VTT  DP+GR TVFD LP    RV+++GRLDINTEGLLLLTNDGGL
Sbjct: 79  ERTRLWLLHKPRGVVTTARDPEGRPTVFDGLPEELPRVVAIGRLDINTEGLLLLTNDGGL 138

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A+V+  P T WLR YRVR  G V Q  L+ LKKG+ + G+ YG ++ TLD  +G N W+T
Sbjct: 139 AKVIAHPDTGWLRRYRVRAFGDVTQPDLDKLKKGLTVDGMEYGPIEATLDRAQGDNVWLT 198

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           +GLREGKNRE+K++ E     VNRLIR+S+GPFQLG L  G   E+  K+L++QLG +L 
Sbjct: 199 LGLREGKNREVKRILEHLGLSVNRLIRLSFGPFQLGDLEVGLVEEIRTKVLKDQLGKNLA 258

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           E+A V+ ++P+  +                      +  ++  G S+ +  +        
Sbjct: 259 EQAGVDFESPVRETIAPFGSPKKATRATQAAPAGRGRQGARDEGASEPRSGSRGGSAGRP 318

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
             +        +              R+      R+
Sbjct: 319 PRDPARPAAPRAGARPAPRPPSPTVWRADEETRPRA 354



 Score = 43.2 bits (100), Expect = 0.056,   Method: Composition-based stats.
 Identities = 16/116 (13%), Positives = 31/116 (26%), Gaps = 2/116 (1%)

Query: 239 KILREQLGPHLLEEAQVN-LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           ++L E+L P   + A          + E     R     + P      +    +      
Sbjct: 389 RVLVERLQPSPEKPAPEPHRRVRFRNEEERSAPRDRAREDRPRQDRPGQDRPREDRPRDD 448

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSD-SGQREENHRRSPSFPSKRSLRRTSA 352
           + +   P   R         +    +   D   +R E    +P+        R S 
Sbjct: 449 RPRSEGPRENRARDERPGRDEFRRGAPAGDARPRRREAGEAAPAERRGPPRERPSD 504



 Score = 39.0 bits (89), Expect = 1.00,   Method: Composition-based stats.
 Identities = 12/120 (10%), Positives = 23/120 (19%), Gaps = 3/120 (2%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R +  K  R        E       A                           +N  +++
Sbjct: 360 RGMDPKTARAAAAERGRERVGAIQAAGERRVLVERLQPSPEKPAPEPHRRVRFRNEEERS 419

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               + +   P   R                     +    +R     P +   RR +  
Sbjct: 420 APRDRAREDRPRQDRPGQDRPRED---RPRDDRPRSEGPRENRARDERPGRDEFRRGAPA 476


>gi|154686561|ref|YP_001421722.1| RluB [Bacillus amyloliquefaciens FZB42]
 gi|154352412|gb|ABS74491.1| RluB [Bacillus amyloliquefaciens FZB42]
          Length = 244

 Score =  181 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 74/243 (30%), Positives = 121/243 (49%), Gaps = 3/243 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E +I + +VKVNG ++    V V  +D IEV+G+ + + E  
Sbjct: 2   ERLQKVIAHAGVASRRKAEELIKEGKVKVNGKVITELGVKVTGSDQIEVNGLKVEREEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     +++   D  GR  V D    +  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 62  YFLLYKPRG-VISAADDDKGRKVVTDFFKEVPQRIYPIGRLDYDTSGLLLLTNDGEFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTV 191
           L  P  +  + Y  +  G   ++ L  L++GI ++       +  L +       + + +
Sbjct: 121 LMHPKYEIDKTYVAKVKGIPSKELLRKLERGIQLEEGKTAPARAKLLSLDKRKQTSIIQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE     V +L R  Y    L  L  G  RE+S   ++         
Sbjct: 181 TIHEGRNRQVRRMFEAIGHDVLKLKREEYAFLDLRGLRTGDARELSPHEVKRLRALAEHG 240

Query: 252 EAQ 254
           +  
Sbjct: 241 KNA 243


>gi|320355051|ref|YP_004196390.1| ribosomal large subunit pseudouridine synthase B [Desulfobulbus
           propionicus DSM 2032]
 gi|320123553|gb|ADW19099.1| ribosomal large subunit pseudouridine synthase B [Desulfobulbus
           propionicus DSM 2032]
          Length = 247

 Score =  181 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 76/230 (33%), Positives = 118/230 (51%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++A+AGIASRR+ E++I + R+++NG ++           D I  DG PL   E+
Sbjct: 3   ERLQKILAKAGIASRRKAEQLILEGRIRINGHVVTGMGSKADPNRDTITCDGHPLVFEEK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + T          V D L  I  R+  VGRLD++TEG LL+TNDG L  
Sbjct: 63  IYVLLNKPAGYVTTLSDPQGR-PMVSDLLADIPLRLFPVGRLDLDTEGALLMTNDGELGN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + Y     G    DKL  L+ GI I G+      V L  +      V + 
Sbjct: 122 AILHPRYEVNKTYEAEVSGSPSVDKLKRLESGIEIDGVMTRPAVVRLLRRHKGTTLVEIT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGK R+++K+F+  N +V  L R +YG  +LG+L  G  R +++  L+
Sbjct: 182 IHEGKKRQVRKMFQAINHRVLHLRRTAYGNLRLGSLPLGKYRVLNQNDLK 231


>gi|220917363|ref|YP_002492667.1| pseudouridine synthase [Anaeromyxobacter dehalogenans 2CP-1]
 gi|219955217|gb|ACL65601.1| pseudouridine synthase [Anaeromyxobacter dehalogenans 2CP-1]
          Length = 324

 Score =  181 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 88/321 (27%), Positives = 136/321 (42%), Gaps = 1/321 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +A AGIASRR+ E +I+  RV+VN   +      V    D + VDG  + + E+
Sbjct: 4   ERLQKFLAGAGIASRRKAEALISAGRVRVNQRTVTELGTKVDPGRDLVTVDGALVSQPEQ 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP G VTT SDP GR T  + L  +  R   VGRLD + EG LLLT+DG LA 
Sbjct: 64  RSYYLLYKPSGCVTTASDPQGRPTAMEYLRGVPGRPFPVGRLDYDAEGALLLTDDGELAN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     RVY V+  G    + L  +K G+ ++      ++V +      N W+ V 
Sbjct: 124 RLAHPRYGHQRVYLVKVKGDPPAEALERMKAGVRLEDGPARALEVAVHEHADRNVWIRVV 183

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           + EG+   +K++ E    +V RL R  +G   +G L  G  R +  + +R       LE 
Sbjct: 184 VGEGRFHLVKRLCEAVGLQVQRLFRPEFGGIGVGGLRPGRFRRLEPEEVRALRQRVGLES 243

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
                   +       R   +     P       +  + + G   +              
Sbjct: 244 GTPARGPSVRELPKAARRHGHGPPAAPGAAPPPAEPDADEVGPRARGASRAGPRAAAPGP 303

Query: 313 NVWMAKGIHSSFLSDSGQREE 333
               ++    S    +G R  
Sbjct: 304 GGRASRPSRPSRPGRAGTRRR 324


>gi|196034318|ref|ZP_03101727.1| RNA pseudouridine synthase family protein [Bacillus cereus W]
 gi|218905776|ref|YP_002453610.1| RNA pseudouridine synthase family protein [Bacillus cereus AH820]
 gi|228917189|ref|ZP_04080746.1| RNA pseudouridine synthase [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228929598|ref|ZP_04092616.1| RNA pseudouridine synthase [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|229124116|ref|ZP_04253308.1| RNA pseudouridine synthase [Bacillus cereus 95/8201]
 gi|254724523|ref|ZP_05186306.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A1055]
 gi|195992860|gb|EDX56819.1| RNA pseudouridine synthase family protein [Bacillus cereus W]
 gi|218539434|gb|ACK91832.1| RNA pseudouridine synthase family protein [Bacillus cereus AH820]
 gi|228659418|gb|EEL15066.1| RNA pseudouridine synthase [Bacillus cereus 95/8201]
 gi|228829985|gb|EEM75604.1| RNA pseudouridine synthase [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228842390|gb|EEM87481.1| RNA pseudouridine synthase [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
          Length = 229

 Score =  181 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 62/234 (26%), Positives = 110/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEANSCSRRETDRLIKAGRVAINGEICTH-GALVNEGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T ++    + +     +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAAEHIEGNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGITKPCKVTRV----DKSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>gi|49478685|ref|YP_038599.1| pseudouridylate synthase [Bacillus thuringiensis serovar konkukian
           str. 97-27]
 gi|228935861|ref|ZP_04098671.1| RNA pseudouridine synthase [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|49330241|gb|AAT60887.1| pseudouridylate synthase [Bacillus thuringiensis serovar konkukian
           str. 97-27]
 gi|228823629|gb|EEM69451.1| RNA pseudouridine synthase [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
          Length = 229

 Score =  181 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 62/234 (26%), Positives = 110/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTH-GALVNEGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T ++    + +     +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAAEHIEGNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFMNEMSSGVKIKDGMTKPCKVTRV----DQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRERIMNIELNDLEVGKWRDITTEELELLIG 227


>gi|148546656|ref|YP_001266758.1| RNA-binding S4 domain-containing protein [Pseudomonas putida F1]
 gi|148510714|gb|ABQ77574.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           putida F1]
 gi|313497712|gb|ADR59078.1| RNA-binding S4 domain-containing protein [Pseudomonas putida
           BIRD-1]
          Length = 355

 Score =  181 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 83/347 (23%), Positives = 144/347 (41%), Gaps = 12/347 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            + +++ KV+AR G+ SRR+VE  I+Q R+KVNG+        V   D I VDG  +++ 
Sbjct: 14  PSGEKLQKVLARIGVGSRRDVEAWISQGRIKVNGVEAT-LGQRVDLHDAIAVDGKLIKRE 72

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E     R  +        + T        +           R I++GRLDINT GLLL T
Sbjct: 73  EAAEATRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLDINTTGLLLFT 132

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-KG 184
            DG LA  L  PS +  R Y VR  G+VD + +  LK G++++        +      +G
Sbjct: 133 TDGELANRLMHPSYEMDREYAVRVRGEVDDEMIERLKAGVMLEDGPAKFTDIQKAPGGEG 192

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
            N W    + EG+NRE+++++E     V+RL R+ +GP  L   L  G  RE+++  + +
Sbjct: 193 FNHWYHCVVMEGRNREVRRLWESQGMVVSRLKRVRFGPVFLNSDLPMGRWREMTQGEI-D 251

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            L   +  +        + + + + R +      +           + +   + ++    
Sbjct: 252 ILAAEVGLQPVALPAMKLKAKDKMERLQRKSTRPLGRGERVRNLRPAHEGAATGERPARQ 311

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
           P                  S +     + +  + +      R   R 
Sbjct: 312 PREEAPRKPTRGSTVAERPSEMRKRPGKPDGDKPA---GRGRGKPRG 355


>gi|323489657|ref|ZP_08094884.1| pseudouridine synthase [Planococcus donghaensis MPA1U2]
 gi|323396788|gb|EGA89607.1| pseudouridine synthase [Planococcus donghaensis MPA1U2]
          Length = 243

 Score =  181 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 81/231 (35%), Positives = 130/231 (56%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR+ E++I   +V+VNG  ++   V V ++D IEV+GV L   E+ 
Sbjct: 2   ERLQKVLAHAGVASRRKSEQLILDGKVRVNGKTIKELGVKVSNSDKIEVEGVQLE-KEQK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L +KP G+++  SD   R  V D    I  R+  VGRLD +T GLL++TNDG  A +
Sbjct: 61  VYHLLYKPRGVISAVSDDKNRKVVTDFFEGIEKRIYPVGRLDYDTSGLLIMTNDGEFANM 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           L  P  +  + Y  R  G  ++D L  L++GI ++       +V L +       A V +
Sbjct: 121 LTHPKFEIDKTYVARLKGIPEKDDLRKLERGIKLEDGMTAPAKVKLLSGDKKTGKAIVQI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EG+NR+++++FE   + V +L R  +    L  L AG +RE+S   ++
Sbjct: 181 TIHEGRNRQVRRMFEAIGYPVQKLSREQFAFLTLHGLNAGESRELSAHEVK 231


>gi|310639571|ref|YP_003944329.1| tRNA pseudouridine synthase a [Paenibacillus polymyxa SC2]
 gi|309244521|gb|ADO54088.1| tRNA pseudouridine synthase A [Paenibacillus polymyxa SC2]
          Length = 233

 Score =  181 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 62/234 (26%), Positives = 108/234 (46%), Gaps = 7/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+  G  SRRE ++++   RV +NG +           D + V+G PLR     
Sbjct: 1   MRINKFISETGFCSRREADKLVESGRVTINGEVA-VLGSQAEEGDDVRVNGKPLRDKSDH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+ +T            +      R+  +GRLD ++EGL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITSTTESHI--RGNIVDFVGHPQRIFPIGRLDKDSEGLILLTNDGDIVNK 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     V    +  +  G+ I G      +VT      S     + L
Sbjct: 118 ILRAEGKHEKEYIVTVDRPVTPSFVQGMSSGVKILGHRTLPCEVTRV----SEYVFRIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            EGKNR+I+++   F ++V +L R+     +LG+L  G+ R++++   +E    
Sbjct: 174 TEGKNRQIRRMCAAFGYEVKKLQRLRIMNIRLGSLQKGAWRDLTEAEKQELGQM 227


>gi|268593179|ref|ZP_06127400.1| ribosomal large subunit pseudouridine synthase F [Providencia
           rettgeri DSM 1131]
 gi|291311225|gb|EFE51678.1| ribosomal large subunit pseudouridine synthase F [Providencia
           rettgeri DSM 1131]
          Length = 289

 Score =  181 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 65/293 (22%), Positives = 117/293 (39%), Gaps = 5/293 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +  +  R++K I+ +GI SRRE +R I Q  V +NG         V S D ++V+G  + 
Sbjct: 2   DTRSSTRLNKYISESGICSRREADRYIEQGNVFINGKRA-GIGDQVFSGDVVKVNGQLIE 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 L L      +    +   G      +  +  +R+  +GRLD +++GL+ LTN G
Sbjct: 61  PRNEEDLVLIALNKPVGIVSTTESGEKDNIVDYVNHSTRIFPIGRLDKDSQGLIFLTNHG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   +        + Y V  +  V  + +  +  G+ I G      +V    +K +   
Sbjct: 121 DLVNKILRAGNSHEKEYLVTVNKPVTDEFIRGMGAGVPILGTMTKKCKV----KKEAPFV 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E F ++V +L R+     +L  +  G  R+++   L E     
Sbjct: 177 FRITLVQGLNRQIRRMCEHFGFEVTKLERVRIMNVRLTGIPVGEWRDLTDDELIELFDMM 236

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
              E+ +       S      +        P   T             K+KK 
Sbjct: 237 EKSESDIKPKKAQKSVSANKGNTKQASPSKPKVKTENPTRKKFTQPGRKKKKR 289


>gi|167034997|ref|YP_001670228.1| RNA-binding S4 domain-containing protein [Pseudomonas putida GB-1]
 gi|166861485|gb|ABY99892.1| RNA-binding S4 domain protein [Pseudomonas putida GB-1]
          Length = 355

 Score =  181 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 84/347 (24%), Positives = 145/347 (41%), Gaps = 12/347 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            + +++ KV+AR G+ SRR+VE  I+Q R+KVNG+        V   D I VDG  +++ 
Sbjct: 14  PSGEKLQKVLARIGVGSRRDVEAWISQGRIKVNGVEAT-LGQRVDLHDAIAVDGKLIKRE 72

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E     R  +        + T        +           R I++GRLDINT GLLL T
Sbjct: 73  EAAEATRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLDINTTGLLLFT 132

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-KG 184
            DG LA  L  PS +  R Y VR  G+VD + +  LK G++++        +      +G
Sbjct: 133 TDGELANRLMHPSYEMDREYAVRVRGEVDDEMIERLKAGVMLEDGPAKFTDIQKAPGGEG 192

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
            N W    + EG+NRE+++++E     V+RL R+ +GP  L   L  G  RE+++  + +
Sbjct: 193 FNHWYHCVVMEGRNREVRRLWESQGMVVSRLKRVRFGPVFLNSDLPMGRWREMTQGEI-D 251

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            L   +  +        + + + + R +      +           + +   + ++    
Sbjct: 252 ILAAEVGLQPVALPAMKLKAKDKMERLQRKSTRPLGRGERVRNLRPAHEGAATGERPARQ 311

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
           P       +          S +     + E  + +      R   R 
Sbjct: 312 PREEAPRKNTRGSTVAERPSEMRKRPAKPEGDKPA---GRGRGKPRG 355


>gi|56421368|ref|YP_148686.1| 16S pseudouridylate synthase [Geobacillus kaustophilus HTA426]
 gi|56381210|dbj|BAD77118.1| 16S pseudouridylate synthase [Geobacillus kaustophilus HTA426]
          Length = 248

 Score =  181 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 102/230 (44%), Gaps = 4/230 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A  G  +R+EV++++    VKV+G  +  A   V      + V G  +      
Sbjct: 4   RIDKLLAHMGYGTRKEVKKLLKSGAVKVDGAPVRDAKTKVRPDEQIVTVWGETVEYKPFI 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L +      +  T    +                  VGRLD +TEGLLLLTNDG LA  
Sbjct: 64  YLMMNKPSGVVSATEDAVEETVVDLLEEEDRAFSPFPVGRLDKDTEGLLLLTNDGQLAHQ 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVG 192
           L  P     + Y     G+V +  +   ++G+V+         ++ +  + G  + V V 
Sbjct: 124 LLSPKKHVPKTYFAVVDGEVTEADVAAFQRGVVLDDGYETKPAKLVVL-KSGLRSDVEVT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F+    +V  L RI  GP  L   L  G  RE++ + +
Sbjct: 183 ITEGKFHQVKRMFQAVGKRVVYLKRIQMGPLPLDPDLAVGEYRELTDEEV 232


>gi|326803723|ref|YP_004321541.1| pseudouridine synthase B, ribosomal large subunit [Aerococcus
           urinae ACS-120-V-Col10a]
 gi|326650759|gb|AEA00942.1| pseudouridine synthase B, ribosomal large subunit [Aerococcus
           urinae ACS-120-V-Col10a]
          Length = 240

 Score =  181 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 83/231 (35%), Positives = 124/231 (53%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E++I   RV+VNG ++      V   D +EVD VP+   E  
Sbjct: 2   ERLQKVIAHAGVASRRDAEKLILAGRVRVNGQVVTELGTKVTKKDLVEVDQVPI-YKEEP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G++++ +D  GR  V D    I  R+  +GRLD +T G+LLLTNDG  A +
Sbjct: 61  VYYLFNKPDGVISSVADDKGRKVVVDYFKEIPQRIYPIGRLDYHTTGVLLLTNDGEFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           L  P  +  +VY  +  G    D L  L++G+VI G      +  +   K    NA V +
Sbjct: 121 LMHPRYEIDKVYVAKVKGYPSPDALKRLEEGLVIDGQKTAKARARIRKNKAAKENATVEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EG+NR+++K+ E     V RL R  YG      L  G  R + K  + 
Sbjct: 181 TIHEGRNRQVRKMLEAVGHPVKRLNRERYGFLTTEGLGVGEYRPLLKAEVE 231


>gi|229152747|ref|ZP_04280931.1| RNA pseudouridine synthase [Bacillus cereus m1550]
 gi|228630725|gb|EEK87370.1| RNA pseudouridine synthase [Bacillus cereus m1550]
          Length = 229

 Score =  181 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 62/234 (26%), Positives = 110/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTH-GALVSDGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D    + +     +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAADHIEDNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVTRV----DQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRERIMNIELNDLQVGKWRDITGEELELLIG 227


>gi|168216722|ref|ZP_02642347.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           NCTC 8239]
 gi|182381245|gb|EDT78724.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           NCTC 8239]
          Length = 298

 Score =  181 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 65/260 (25%), Positives = 114/260 (43%), Gaps = 10/260 (3%)

Query: 1   MKDKNIVQENFT---PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           +K+  IV          R++K I+  G  SRRE +++I Q RVK++G+      + V   
Sbjct: 44  VKNTIIVSNKNEIRDKVRLNKYISETGFCSRREADKLIEQGRVKIDGLKATT-GMKVSKG 102

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
             + +DG PL+          +KP+G+  T            +  +   R+  +GRLD +
Sbjct: 103 QSVSIDGKPLKVENELVYIALNKPVGITCTTESKI--KGNIVDFINHEKRIFPIGRLDKD 160

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           ++GL+ +TNDG +   +        + Y V  +  +  + +  +  G+ I G        
Sbjct: 161 SQGLIFMTNDGDIVNKILRAGNNHEKEYIVTVNKPITHEFIKGMSNGVPILGTVTKKC-- 218

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +K S     + L +G NR+I+++ E+F ++V +L RI      LG L  GS R ++
Sbjct: 219 --LVKKESKNSFRIILTQGLNRQIRRMCEYFGYEVKKLERIRIMNVSLGNLKIGSWRYLT 276

Query: 238 KKILREQLGPHLLEEAQVNL 257
           KK L E              
Sbjct: 277 KKELAEINRLTENSSKTEEA 296


>gi|293376750|ref|ZP_06622972.1| pseudouridylate synthase [Turicibacter sanguinis PC909]
 gi|325845685|ref|ZP_08168968.1| ribosomal large subunit pseudouridine synthase F [Turicibacter sp.
           HGF1]
 gi|292644616|gb|EFF62704.1| pseudouridylate synthase [Turicibacter sanguinis PC909]
 gi|325488286|gb|EGC90712.1| ribosomal large subunit pseudouridine synthase F [Turicibacter sp.
           HGF1]
          Length = 235

 Score =  181 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 67/227 (29%), Positives = 113/227 (49%), Gaps = 7/227 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ +G ASRR  +++IA+ RVKVNG + +     V   D + V+G  +R A   
Sbjct: 1   MRLNKFISDSGKASRRGADKLIAEGRVKVNGRIAK-IGDQVKPGDEVMVNGNIIRLARNH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T            +L +   RV ++GRLD +++GL+LLTNDG +   
Sbjct: 60  VYLALNKPVGITCTTEKGV--KGNIVDLVNHPLRVFNIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V     +  + +  + KG+ I G      +VT    + S     + L
Sbjct: 118 ILRAENNHEKEYIVSVDKPITPEFIEKMSKGVRILGQKTLPCKVT----QISKYEFNIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +G NR+I+++ E   ++V RL R+      LG L  G  R+++KK 
Sbjct: 174 TQGLNRQIRRMCEVLGYEVYRLQRVRIMNITLGNLPVGQWRDLTKKE 220


>gi|196042136|ref|ZP_03109420.1| RNA pseudouridine synthase family protein [Bacillus cereus
           NVH0597-99]
 gi|196027072|gb|EDX65695.1| RNA pseudouridine synthase family protein [Bacillus cereus
           NVH0597-99]
          Length = 229

 Score =  181 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 108/234 (46%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE + +I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEANSCSRRETDHLIKAGRVAINGEICTH-GALVNEGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T ++    + +     +   R+  VGRLD  +EGL+ LTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAAEHIEGNIIDYI--NYPERIFPVGRLDKASEGLIFLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVTRV----DQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>gi|294790885|ref|ZP_06756043.1| ribosomal large subunit pseudouridine synthase B [Scardovia
           inopinata F0304]
 gi|294458782|gb|EFG27135.1| ribosomal large subunit pseudouridine synthase B [Scardovia
           inopinata F0304]
          Length = 257

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 76/236 (32%), Positives = 122/236 (51%), Gaps = 2/236 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVP 66
           QE+    R+ KV+A+AG  SRR+ E MI   RV+V+G L+    V V      I VDG  
Sbjct: 13  QESHDGVRLQKVLAQAGFGSRRKCEVMITDGRVEVDGELVTELGVRVDPQHQEIRVDGSR 72

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +  + +      +KP  +++T  DP GR T+ D +   + R+  +GRLD +TEGL+L+T+
Sbjct: 73  IHLSNKHITLALNKPRKVLSTMDDPKGRWTLRDIVGDRYERIFHMGRLDYDTEGLILMTD 132

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG LA+ +  P  +  + Y     G +     + L +  + +        Q ++ TQ   
Sbjct: 133 DGELAQHVMHPKYEIEKTYIATVEGHIGGGVCHRLVRTGVQLDDGWIKLDQCSIITQNRE 192

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + + V L  G+NR ++++F    + V RLIR   GP  LG L +GS R +S   +
Sbjct: 193 RSVLKVVLHSGRNRIVRRIFGSIGFPVTRLIRTQIGPISLGELKSGSYRILSTHEV 248


>gi|257900337|ref|ZP_05679990.1| pseudouridine synthase [Enterococcus faecium Com15]
 gi|257838249|gb|EEV63323.1| pseudouridine synthase [Enterococcus faecium Com15]
          Length = 255

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 61/254 (24%), Positives = 109/254 (42%), Gaps = 8/254 (3%)

Query: 1   MKDKNIVQ---ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS- 56
           M  K+ +    +     R+ K +A  G+ SR+EV+ +I +  ++VNG +++     V   
Sbjct: 1   MNGKSRINALLKWGKRMRLDKFLADMGLGSRKEVKGLIKKGTIEVNGQVVKSDKAQVNEF 60

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            D +   G  +   +     L+     +  T  + D               +  VGRLD 
Sbjct: 61  EDTVTYLGEIIAYQKDFYYILHKPAGVISATQDNHDQTVIDLLEDQDYREDLFPVGRLDK 120

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDM 175
           +TEGLL+LTNDG  A  L  P     + Y     G + ++ + L  +G++I         
Sbjct: 121 DTEGLLILTNDGVFAHQLLSPKKHVEKEYLAEVSGIMTEEDIRLFAEGLIIDGDEQTLPA 180

Query: 176 QVTLDTQKG--SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGS 232
           ++ +D        + + + L EGK  ++K++ +    +V  L RI  G F L   L  G 
Sbjct: 181 KLQIDQVDQESETSIIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGNFCLPKDLNRGQ 240

Query: 233 TREVSKKILREQLG 246
            R ++K+ L +   
Sbjct: 241 YRPMTKEELEQVRE 254


>gi|163853261|ref|YP_001641304.1| RNA-binding S4 domain-containing protein [Methylobacterium
           extorquens PA1]
 gi|163664866|gb|ABY32233.1| RNA-binding S4 domain protein [Methylobacterium extorquens PA1]
          Length = 669

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 143/336 (42%), Positives = 193/336 (57%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R++K IARAGIASRR+ E +I   RV +NG +L   A+NV   D I VD  PL   
Sbjct: 19  PEGERIAKAIARAGIASRRDAEALIEAGRVTLNGKVLTSPAINVTDADRITVDDEPLPAR 78

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ERTRLWL HKP G+VTT  DP+GR TVFD LP    RV+++GRLDINTEGLLLLTNDGGL
Sbjct: 79  ERTRLWLLHKPRGVVTTARDPEGRPTVFDGLPEELPRVVAIGRLDINTEGLLLLTNDGGL 138

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A+V+  P T WLR YRVR  G V Q  L+ LKKG+ + G+ YG ++ TLD  +G N W+T
Sbjct: 139 AKVIAHPDTGWLRRYRVRAFGDVTQPDLDKLKKGLTVDGMEYGPIEATLDRAQGDNVWLT 198

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           +GLREGKNRE+K++ E     VNRLIR+S+GPFQLG L  G   E+  K+L++QLG +L 
Sbjct: 199 LGLREGKNREVKRILEHLGLSVNRLIRLSFGPFQLGDLEVGLVEEIRTKVLKDQLGKNLA 258

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           E+A V+ ++P+  +                      +  ++  G S+ +  +        
Sbjct: 259 EQAGVDFESPVRETIAPFGSPKKATRATQAAPAGRGRQGARDEGASEARSGSRGGSAGRP 318

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
             +        +              R+      R+
Sbjct: 319 PRDPARPAAPRAGARPAPRPPSPTVWRADEETRPRA 354



 Score = 43.6 bits (101), Expect = 0.041,   Method: Composition-based stats.
 Identities = 10/114 (8%), Positives = 25/114 (21%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           ++      +L E                    N            +    Q      + +
Sbjct: 382 IQAAGERRVLVERLQPSPEKPAPEPHRRVRFRNEEERSAPRDRAREDRPRQDRPGQDRPR 441

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              P       +     +     F   +   +   RR  +  +  + RR   ++
Sbjct: 442 EDRPRSEGPRENRARDERPGRDEFRRGAPAGDARPRRREAGEAAPAERRGPPRE 495



 Score = 42.9 bits (99), Expect = 0.084,   Method: Composition-based stats.
 Identities = 13/112 (11%), Positives = 26/112 (23%), Gaps = 1/112 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R  L   L    +     P         +  +   +   +    +    Q      + + 
Sbjct: 388 RRVLVERLQPSPEKPAPEPHRRVRFRNEEERSAPRDRAREDRPRQDRPGQDRPREDRPRS 447

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSD-SGQREENHRRSPSFPSKRSLRRTSA 352
             P   R         +    +   D   +R E    +P+        R S 
Sbjct: 448 EGPRENRARDERPGRDEFRRGAPAGDARPRRREAGEAAPAERRGPPRERPSD 499



 Score = 42.1 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 23/112 (20%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R +      +    +            R+          D  R    +       ++   
Sbjct: 424 RAREDRPRQDRPGQDRPREDRPRSEGPRENRARDERPGRDEFRRGAPAGDARPRRREAGE 483

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           A P  RR                    G+ + +         + + RR    
Sbjct: 484 AAPAERRGPPRERPSDFEGRPPRERSEGRPQRDFHGDSRERGEGAPRRERPS 535



 Score = 38.2 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 14/123 (11%), Positives = 33/123 (26%), Gaps = 1/123 (0%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
            TR  + K+ R  + P     A          +     +R  ++  +     +      +
Sbjct: 349 ETRPRASKVPRRGMDPKTARAAAAERGRERVGAIQAAGERRVLVERLQPSPEKPAPEPHR 408

Query: 292 KNGLSKQKKLATPVHR-RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
           +     +++ + P  R R                     +    +R     P +   RR 
Sbjct: 409 RVRFRNEEERSAPRDRAREDRPRQDRPGQDRPREDRPRSEGPRENRARDERPGRDEFRRG 468

Query: 351 SAK 353
           +  
Sbjct: 469 APA 471


>gi|23099278|ref|NP_692744.1| ribosomal large subunit pseudouridylate synthase [Oceanobacillus
           iheyensis HTE831]
 gi|22777507|dbj|BAC13779.1| ribosomal large subunit pseudouridylate synthase [Oceanobacillus
           iheyensis HTE831]
          Length = 244

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 81/243 (33%), Positives = 126/243 (51%), Gaps = 3/243 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R+ KVIA++G+ SRR+ E+MI   +VKVNG  ++   V V + D I VDGVPL K
Sbjct: 2   TNNGERLQKVIAQSGVTSRRKAEQMILDGKVKVNGETVQEMGVKVTANDEIVVDGVPLEK 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                  LY     ++++  D  GR  V D   ++  R+  +GRLD +T G+LLLTNDG 
Sbjct: 62  ETPVYFLLYKPRG-VISSVKDDKGRKVVTDYFEAVEQRIFPIGRLDYDTSGVLLLTNDGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNA 187
            A +L  P  +  +VY  +  G  ++ +L LL+KGI         +QV L     +   +
Sbjct: 121 FANLLMHPRHEIDKVYIAKVRGIPNKKELALLQKGIRSDKDVLKAVQVKLLSTDHQKKTS 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + + L EGKNR+++++ E   + V +L R  Y    L  L AG  R ++ K + +    
Sbjct: 181 IIELTLHEGKNRQVRRMLEELGYPVMKLKRERYDFIGLEGLNAGEYRSLTPKEVNQLRAQ 240

Query: 248 HLL 250
              
Sbjct: 241 AQK 243


>gi|182625540|ref|ZP_02953311.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           D str. JGS1721]
 gi|177909228|gb|EDT71693.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           D str. JGS1721]
          Length = 298

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 66/260 (25%), Positives = 115/260 (44%), Gaps = 10/260 (3%)

Query: 1   MKDKNIVQENFT---PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           +K+  IV          R++K I+  G  SRRE +++I Q RVK++G+      + V   
Sbjct: 44  VKNTIIVSNKNEIRDEVRLNKYISETGFCSRREADKLIEQGRVKIDGLKATT-GMKVSKG 102

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
             + +DG PL+          +KP+G+  T       + V     +   R+  +GRLD +
Sbjct: 103 QSVSIDGKPLKVENELVYIALNKPVGITCTTESKIKGNIVDFI--NHEKRIFPIGRLDKD 160

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           ++GL+ +TNDG +   +        + Y V  +  +  + +  +  G+ I G        
Sbjct: 161 SQGLIFMTNDGDIVNKILRAGNNHEKEYIVTVNKPITDEFIKGMSNGVPILGTVTKKC-- 218

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +K S     + L +G NR+I+++ E+F ++V +L RI      LG L  GS R ++
Sbjct: 219 --LVKKESKNSFRIILTQGLNRQIRRMCEYFGYEVKKLERIRIMNVSLGNLKMGSWRYLT 276

Query: 238 KKILREQLGPHLLEEAQVNL 257
           KK L E              
Sbjct: 277 KKELAEINRLTENSSKTEEA 296


>gi|240140668|ref|YP_002965148.1| hypothetical protein MexAM1_META1p4234 [Methylobacterium extorquens
           AM1]
 gi|240010645|gb|ACS41871.1| conserved hypothetical protein with putative pseudouridine
           synthase-like domain [Methylobacterium extorquens AM1]
          Length = 669

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 143/337 (42%), Positives = 194/337 (57%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R++K IARAGIASRR+ E +I   RV +NG +L   A+NV  +D I VD  PL  
Sbjct: 18  TPEGERIAKAIARAGIASRRDAEALIEAGRVTLNGKVLTSPAINVTDSDRITVDDEPLPA 77

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ERTRLWL HKP G+VTT  DP+GR TVFD LP    RV+++GRLDINTEGLLLLTNDGG
Sbjct: 78  RERTRLWLLHKPRGVVTTARDPEGRPTVFDGLPEELPRVVAIGRLDINTEGLLLLTNDGG 137

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA+V+  P T WLR YRVR  G V Q  L+ LKKG+ + G+ YG ++ TLD  +G N W+
Sbjct: 138 LAKVIAHPDTGWLRRYRVRAFGDVTQPDLDKLKKGLTVDGMEYGPIEATLDRAQGDNVWL 197

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           T+GLREGKNRE+K++ E     VNRLIR+S+GPFQLG L  G   E+  K+L++QLG +L
Sbjct: 198 TLGLREGKNREVKRILEHLGLSVNRLIRLSFGPFQLGDLEVGLVEEIRTKVLKDQLGKNL 257

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
            E+A V+ ++P+  +                      +  ++  G S+ +  +       
Sbjct: 258 AEQAGVDFESPVRETIAPFGSPKKATRAAQAAPAGRGRQGARDEGASEARSGSRGGAAGR 317

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
              +        +              R+      R+
Sbjct: 318 PPRDPARPAAPRAGARPAPRPPSPTVWRADEETRPRA 354



 Score = 44.0 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 10/114 (8%), Positives = 25/114 (21%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           ++      +L E                    N            +    Q      + +
Sbjct: 382 IQAAGERRVLVERLQPSPEKPAPEPHRRVRFRNEEERSAPRDRAREDRPRQDRPGQDRPR 441

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              P       +     +     F   +   +   RR  +  +  + RR   ++
Sbjct: 442 DDRPRSEGPRENRARDERPGRDEFRRGAPAGDARPRRREAGEAAPAERRGPPRE 495



 Score = 42.9 bits (99), Expect = 0.069,   Method: Composition-based stats.
 Identities = 13/112 (11%), Positives = 26/112 (23%), Gaps = 1/112 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R  L   L    +     P         +  +   +   +    +    Q      + + 
Sbjct: 388 RRVLVERLQPSPEKPAPEPHRRVRFRNEEERSAPRDRAREDRPRQDRPGQDRPRDDRPRS 447

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSD-SGQREENHRRSPSFPSKRSLRRTSA 352
             P   R         +    +   D   +R E    +P+        R S 
Sbjct: 448 EGPRENRARDERPGRDEFRRGAPAGDARPRRREAGEAAPAERRGPPRERPSD 499



 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 23/112 (20%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R +      +    +            R+          D  R    +       ++   
Sbjct: 424 RAREDRPRQDRPGQDRPRDDRPRSEGPRENRARDERPGRDEFRRGAPAGDARPRRREAGE 483

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           A P  RR                    G+ + +         + + RR    
Sbjct: 484 AAPAERRGPPRERPSDFEGRPPRERSEGRPQRDFHGDSRERGEGAPRRERPS 535



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 14/123 (11%), Positives = 33/123 (26%), Gaps = 1/123 (0%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
            TR  + K+ R  + P     A          +     +R  ++  +     +      +
Sbjct: 349 ETRPRASKVPRRGMDPKTARAAAAERGRERVGAIQAAGERRVLVERLQPSPEKPAPEPHR 408

Query: 292 KNGLSKQKKLATPVHR-RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
           +     +++ + P  R R                     +    +R     P +   RR 
Sbjct: 409 RVRFRNEEERSAPRDRAREDRPRQDRPGQDRPRDDRPRSEGPRENRARDERPGRDEFRRG 468

Query: 351 SAK 353
           +  
Sbjct: 469 APA 471


>gi|121308590|dbj|BAF43685.1| hypothetical protein [Vibrio fischeri]
          Length = 354

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 90/353 (25%), Positives = 145/353 (41%), Gaps = 12/353 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG+ SRRE+E MI   RV V+G   +           I +DG  +   E 
Sbjct: 2   SEKLQKVLARAGLGSRRELETMIQAGRVSVDGQRAKLGDRLENVDAKIRIDGHVVSVKES 61

Query: 73  TRLWL-----YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           T +       +     L T H     R+          SR +SVGRLD NT GLLL T D
Sbjct: 62  TDVICRVLAYHKPEGELCTRHDPEGRRTVFDRLPKIRDSRWVSVGRLDANTAGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y  R  G++++  +  L  G+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRKVEREYMCRVFGEINEKMIRNLVSGVKLEDGEARFEDVMYAGGEGMNH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI---LRE 243
              V + EG+NRE++++++     V+RL R+ YG   L   L  G   E+  K    LRE
Sbjct: 182 TFYVVINEGRNREVRRLWDSQGVTVSRLKRVRYGDIFLEKALPRGGWMELELKEVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +     +E+ +++D            +     +  D+ +  ++N+         KK   
Sbjct: 242 MVELPAEKESLLDVDKESRKRAKSKTQKIRRAVKRYDERSTEERNTPAGRRGRSNKKPVG 301

Query: 304 ---PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              P  +R   +    + G   S        ++  R   S   K    +   +
Sbjct: 302 SSLPSAKRGSNNGESQSSGKPQSKGKKPVAGQKPVRSKFSPNGKAPKSKPRQR 354


>gi|326692499|ref|ZP_08229504.1| ribosomal large subunit pseudouridine synthase B [Leuconostoc
           argentinum KCTC 3773]
          Length = 249

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 90/235 (38%), Positives = 136/235 (57%), Gaps = 2/235 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   QR+ KVIA+AG+ASRR  E +I Q RV+VNG  ++   + VM  D ++VDG P+  
Sbjct: 2   SEEAQRLQKVIAQAGLASRRGAEELITQGRVQVNGETVKTLGIKVMPHDTVQVDGAPIEG 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E+   +L +KP G+VTT+SD  GR TV D L  +  RV  VGRLD +T G+LLLTNDG 
Sbjct: 62  REKLVYYLMNKPRGVVTTNSDDKGRQTVLDVLEDVPQRVYPVGRLDYDTTGVLLLTNDGV 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--A 187
           +A  L  P ++  +VY  +  G    +KL  LK+G+VIQG      +V+++        +
Sbjct: 122 IANQLMHPKSRVDKVYMAKVEGIATDEKLAPLKRGVVIQGRKTAPARVSVERVDKDKKTS 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V V + EG+N ++K + +     V +L R  Y  F L  L +G  R+++   ++
Sbjct: 182 MVRVIIHEGRNHQVKNMLQKVGLPVAKLTREQYAFFDLTGLQSGEYRKLTSAEVK 236


>gi|120437125|ref|YP_862811.1| ribosomal large subunit pseudouridine synthase F [Gramella forsetii
           KT0803]
 gi|117579275|emb|CAL67744.1| ribosomal large subunit pseudouridine synthase F [Gramella forsetii
           KT0803]
          Length = 266

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 59/270 (21%), Positives = 113/270 (41%), Gaps = 10/270 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL---R 68
              R++K +++ G  SRR  +++I Q R+ +N  +       V   D ++VDG P+    
Sbjct: 3   EEVRINKYLSQLGYCSRRAADKLIDQGRITINDKVP-EMGTKVTPGDLVKVDGKPVSKEE 61

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             E      ++KP+G+V T      +  + D +     R+  +GRLD  +EGL+ LTNDG
Sbjct: 62  LKEPNVYIAFNKPVGIVCTTDTRVEKDNIIDYINYPK-RIFPIGRLDKPSEGLIFLTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y V  +  V  + L  +  G+ I      + +     +K  +  
Sbjct: 121 DIVNKILRARNNHEKEYVVSVNKPVSSEFLKKMSAGVPILDTVTRECE----IEKLGHHT 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ EF +++V  L RI      L  +  G  R+++ + L+      
Sbjct: 177 FRIVLTQGLNRQIRRMCEFLDYQVTSLKRIRIMNVSL-DIPVGEWRDLTSEELKTINNLT 235

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEV 278
                         + +  +R         
Sbjct: 236 DESTKTEEGSLTSTAKKANLRTGKRPRKPK 265


>gi|51595406|ref|YP_069597.1| 23S rRNA pseudouridine synthase F [Yersinia pseudotuberculosis IP
           32953]
 gi|170025288|ref|YP_001721793.1| 23S rRNA pseudouridine synthase F [Yersinia pseudotuberculosis
           YPIII]
 gi|186894432|ref|YP_001871544.1| 23S rRNA pseudouridine synthase F [Yersinia pseudotuberculosis
           PB1/+]
 gi|51588688|emb|CAH20298.1| conserved hypothetical protein [Yersinia pseudotuberculosis IP
           32953]
 gi|169751822|gb|ACA69340.1| pseudouridine synthase [Yersinia pseudotuberculosis YPIII]
 gi|186697458|gb|ACC88087.1| pseudouridine synthase [Yersinia pseudotuberculosis PB1/+]
          Length = 290

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 58/299 (19%), Positives = 112/299 (37%), Gaps = 11/299 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +  
Sbjct: 3   TNSSIRLNKYISESGICSRRDGDRYIEQGNVFINGKRATV-GDQVFAGDVVKVNGQIIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   L             +  +G      +  +   RV  +GRLD +++GL+ LTN G 
Sbjct: 62  RDEEDLVFIALNKPAGIITTMEEGERDNISDFVNHSKRVFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  V  + +  +  G+ I G      +V    QK +    
Sbjct: 122 LVNKILRAGNNHEKEYVVTVNKPVTDEFIQGMSAGVPILGTVTKKCKV----QKEAPLVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ + F ++V +L R       L  L  G  R+++   L        
Sbjct: 178 RITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNISLKGLPLGEWRDLTDDELLTLFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
              ++        + +                  + +K+        +  +       R
Sbjct: 238 NSSSE------EKTVKKAPPKPVAAKRPGIQGQKKAEKSDDNTASRKRFTQPGRKKKGR 290


>gi|296129772|ref|YP_003637022.1| pseudouridine synthase [Cellulomonas flavigena DSM 20109]
 gi|296021587|gb|ADG74823.1| pseudouridine synthase [Cellulomonas flavigena DSM 20109]
          Length = 306

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 124/233 (53%), Gaps = 1/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
           +    R+ KV+A AG+ SRR  E +IA  RV V G ++    V V   T  I +DG+ ++
Sbjct: 65  DPEGVRLQKVLASAGLGSRRACEELIAAGRVTVAGQVVTELGVRVDPRTAVIHLDGMRVQ 124

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                     +KP+G+V+T  DP+GR ++   + +   R+  VGRLD ++EGLLLLTNDG
Sbjct: 125 LDSSVVTLALNKPVGVVSTMHDPEGRPSLAQYVANREERLFHVGRLDADSEGLLLLTNDG 184

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS    + Y V   G+V       LK+G+ ++       +  +       + 
Sbjct: 185 ELANRLAHPSHGVPKTYLVEVQGRVRDALGKQLKEGVELEDGTVRVDEFKVVQVASHASL 244

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L EG+NR ++++F+     V+RL+R   GP +LG L  G TR +SK  +
Sbjct: 245 VEVVLHEGRNRVVRRLFDEVGHPVDRLVRTRIGPIRLGDLRPGRTRVLSKTEV 297


>gi|160890592|ref|ZP_02071595.1| hypothetical protein BACUNI_03037 [Bacteroides uniformis ATCC 8492]
 gi|156859591|gb|EDO53022.1| hypothetical protein BACUNI_03037 [Bacteroides uniformis ATCC 8492]
          Length = 242

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 58/233 (24%), Positives = 101/233 (43%), Gaps = 1/233 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +   P R++K +A AG+ SRRE +  I    V VNG ++      +   D ++     + 
Sbjct: 2   DPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRGDEVKFHDQTVS 61

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              +  + L      + T+      R+ +     +   R+  VGRLD NT G+LLLTNDG
Sbjct: 62  IERKIYVLLNKPKDTVTTSDDPQARRTVMDLVKGACDERIYPVGRLDRNTTGVLLLTNDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     ++Y V     + +  +  +  GI +             T       
Sbjct: 122 DLASKLTHPKYLKKKIYHVHLDKNLTKADMEQIAAGIQLDDGEIH-ADAISYTDDFKKDD 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++ +
Sbjct: 181 VGIEIHSGKNRIVRRIFESLGYKVMKLDRVYFAGLTKKGLRRGEWRYLTEQEV 233


>gi|15643034|ref|NP_228077.1| 16S pseudouridylate synthase [Thermotoga maritima MSB8]
 gi|4980760|gb|AAD35352.1|AE001708_20 16S pseudouridylate synthase [Thermotoga maritima MSB8]
          Length = 239

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 61/243 (25%), Positives = 113/243 (46%), Gaps = 7/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++ +G+ +R+EV+++I Q RV VNG ++      V+  D + +DG  +R  ++ 
Sbjct: 1   MRLDRYLSNSGVGTRKEVKKLIKQGRVTVNGRVVLDPGHPVLENDAVALDGEVVRFHKKV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +  Y     + +T       S            +  VGRLD + EGLL++TNDG  A  
Sbjct: 61  YILFYKPSGYVTSTKDP---HSETIMEFLPPLKGIFPVGRLDKDAEGLLIITNDGDFAHR 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V+  G+V +DK+  LK G+ ++   +   +     +K SN  + + +
Sbjct: 118 VISPKWSVEKEYIVKVEGEVTEDKIEKLKNGVTLRDGFFAKAKRV---EKLSNDTLKIVI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHLLEE 252
            EGK  +IK++      K   L R   G   L   +  G  R +S++ +++       +E
Sbjct: 175 TEGKYHQIKRMTAAVGLKTVHLKRTRIGGLVLPDDMKPGEYRFLSEEEVKKVFEREDQKE 234

Query: 253 AQV 255
              
Sbjct: 235 DTP 237


>gi|228903068|ref|ZP_04067205.1| RNA pseudouridine synthase [Bacillus thuringiensis IBL 4222]
 gi|228856554|gb|EEN01077.1| RNA pseudouridine synthase [Bacillus thuringiensis IBL 4222]
          Length = 229

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 106/230 (46%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTH-GALVSDGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D    + +         R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAADHIEDNIIDYI--HYPERIFPVGRLDKASEGLILLTNDGTIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVTRV----DQSTFRII 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L 
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTSEELD 223


>gi|56750544|ref|YP_171245.1| ribosomal large subunit pseudouridine synthase B [Synechococcus
           elongatus PCC 6301]
 gi|81299819|ref|YP_400027.1| ribosomal large subunit pseudouridine synthase B [Synechococcus
           elongatus PCC 7942]
 gi|56685503|dbj|BAD78725.1| probable ribosomal large subunit pseudouridine synthase B
           [Synechococcus elongatus PCC 6301]
 gi|81168700|gb|ABB57040.1| ribosomal large subunit pseudouridine synthase B [Synechococcus
           elongatus PCC 7942]
          Length = 243

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 69/239 (28%), Positives = 109/239 (45%), Gaps = 3/239 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
           +R+ K++++ G+ASRR+ E+ I Q RV +NG + E      +  D I +DG  LR     
Sbjct: 3   ERLQKILSQLGVASRRQAEQWIQQGRVTINGRVAEIGQQADLKRDRIHLDGKRLRPKHRP 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L+     + T       R+ +    P     +  VGRLD ++ GLLLL NDG L
Sbjct: 63  EARYLLLHKPVGVVSTCRDPQRRRTVIDLVDPEFRPGLHPVGRLDTDSSGLLLLCNDGEL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P     + YRV   G      L   + G+ +         V +   +  +  + 
Sbjct: 123 TYQISHPRFHIEKTYRVWVEGHPPASVLEHWRSGVWLDDYQTLPAGVRILHDRAESTLLE 182

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           V L EG+NR+I++V E     V RL R++ GP +LG+L  G  R ++   +        
Sbjct: 183 VILHEGRNRQIRRVAEQLGHPVLRLTRVAIGPLRLGSLQPGEYRSLTAAEVYRLRQLAQ 241


>gi|311114733|ref|YP_003985954.1| ribosomal large subunit pseudouridine synthase B [Gardnerella
           vaginalis ATCC 14019]
 gi|310946227|gb|ADP38931.1| ribosomal large subunit pseudouridine synthase B [Gardnerella
           vaginalis ATCC 14019]
          Length = 257

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 72/237 (30%), Positives = 121/237 (51%), Gaps = 2/237 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVP 66
           QE+    R+ K++A AG  SRR+ E +I   RV+V+  L+      V      I VDG  
Sbjct: 13  QESKNAVRLQKLLAEAGFGSRRKCEEIILDGRVEVDDELVTTLGTRVDPSKQKIRVDGSR 72

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           ++   +      +KP  +++   DP GR T+ D +   + R+  +GRLD ++EGL+L+TN
Sbjct: 73  VKFNHKLVTLALNKPKRVLSAMDDPKGRFTLRDIVGDKYERIFHMGRLDYDSEGLILMTN 132

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
           DG L++ +  P  +  + Y     G+++      L  +G+ ++       +  +  Q   
Sbjct: 133 DGELSQHVMHPKYEVEKTYIATVEGKINGMVCRRLVSQGVNLEDGWIKLDRCAIIDQNHD 192

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
              V V L  GKNR ++++F    + V RL+R   GP +LG L AGS R +S+  +R
Sbjct: 193 ATIVKVVLHSGKNRIVRRIFGAVGYPVKRLVRTQIGPIKLGDLKAGSYRVLSQTEVR 249


>gi|229032197|ref|ZP_04188170.1| RNA pseudouridine synthase [Bacillus cereus AH1271]
 gi|228728977|gb|EEL79980.1| RNA pseudouridine synthase [Bacillus cereus AH1271]
          Length = 229

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 106/230 (46%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE + +I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDCLIKAGRVAINGEICTH-GALVSDGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D    + +     +   R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAADHIEDNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGAIAH 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVTRV----DQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L 
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELDNLEVGKWRSVTSEELE 223


>gi|253573324|ref|ZP_04850667.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
 gi|251846852|gb|EES74857.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
          Length = 257

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 63/244 (25%), Positives = 112/244 (45%), Gaps = 8/244 (3%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGV 65
           + +    QR+ K++   G  +R E+++ + Q RV +NG++++ + +      D +E+DG 
Sbjct: 1   MSKGKKTQRLDKILGHLGYGTRSEIKKYVKQGRVTINGVVVKDSGIQCNPDVDVVELDGE 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +   E   L L+  P  +  T    +        +         VGRLD +TEGLLLLT
Sbjct: 61  QIFYREFVYLMLHKPPGVISATEDMREKTVIDLLPVDFQVFSPFPVGRLDKDTEGLLLLT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKG 184
           NDG LA  L  P     + Y     G V  ++    ++G+ +         ++ +     
Sbjct: 121 NDGQLAHDLLSPRKHVPKTYEAVVLGHVGDEEAARFREGVELDDGYVTLPAELKVLEHGI 180

Query: 185 S-----NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSK 238
                  + V + + EGK  ++K++FE    +V  L R+S GP  L   L  G+ RE+++
Sbjct: 181 DADGTRISRVQLTISEGKFHQVKRMFEAVGSRVIYLKRLSMGPLVLDESLPLGAFRELTE 240

Query: 239 KILR 242
             L+
Sbjct: 241 SELQ 244


>gi|212710610|ref|ZP_03318738.1| hypothetical protein PROVALCAL_01676 [Providencia alcalifaciens DSM
           30120]
 gi|212686691|gb|EEB46219.1| hypothetical protein PROVALCAL_01676 [Providencia alcalifaciens DSM
           30120]
          Length = 292

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 65/300 (21%), Positives = 119/300 (39%), Gaps = 9/300 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  +  R++K I+ +GI SRRE +R I Q  V +NG         V + D ++V+G  + 
Sbjct: 2   EINSTTRLNKYISESGICSRREADRYIEQGHVFINGKRA-GIGDQVSAGDVVKVNGQLIE 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 L L      +    +   G      +  +  +R+  +GRLD +++GL+ LTN G
Sbjct: 61  PRNEEDLVLIALNKPVGIVSTTESGEKDNIVDYVNHSTRIFPIGRLDKDSQGLIFLTNHG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   +        + Y V  +  V  + +  +  G+ I G      +V    +K +   
Sbjct: 121 DLVNKILRAGNDHEKEYIVTVNKPVTDEFIRGMGAGVPILGTMTKKCKV----KKEAPFV 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E F ++V +L R+     +L  +  G  R+++   L E     
Sbjct: 177 FRITLVQGLNRQIRRMTEHFGYEVTKLERVRIMNVRLTGIPVGEWRDLTDDELIELFNLI 236

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
              E+ V        +        N  S         K   + +    K  +      +R
Sbjct: 237 EKSESDVKP----KKAAKPQARASNNKSSGKQGSGSQKPKVNAEPPKKKFTQPGRKKKKR 292


>gi|206559870|ref|YP_002230634.1| RNA pseudouridylate synthase family protein [Burkholderia
           cenocepacia J2315]
 gi|198035911|emb|CAR51803.1| RNA pseudouridylate synthase family protein [Burkholderia
           cenocepacia J2315]
          Length = 583

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 82/351 (23%), Positives = 144/351 (41%), Gaps = 6/351 (1%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 172 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRI 230

Query: 63  DGVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           +G P+++         L  +     +V+        S      P   ++ ++VGRLD NT
Sbjct: 231 NGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNT 290

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLL+LT  G LA     P     R Y VR  G++ +     L  G+ ++      +++ 
Sbjct: 291 EGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELAEGMRQKLLHGVELEDGPANFLRIR 350

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
               +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ 
Sbjct: 351 DGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELD 410

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
              +R+ +    L+           +  T  R    + + +          +  +    +
Sbjct: 411 DAQVRKLMATVGLKAPSEEKGKRGGAGPTERRQPDPMQTSMGFIGREPVLTTHGQLDQPR 470

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           +             S         S + + +G   + +R        R+  
Sbjct: 471 RGGGRRGAPGLPGLSGYGSLPVAPSGYGNRTGGGRDGNRMGGGRDGNRAGG 521


>gi|315641868|ref|ZP_07896860.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           italicus DSM 15952]
 gi|315482436|gb|EFU72976.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           italicus DSM 15952]
          Length = 272

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 103/251 (41%), Gaps = 5/251 (1%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEV 62
           K  V       R+ K +A   + SR+EV++ I + +V VNG +       +    D I  
Sbjct: 14  KFFVLTRRKTMRLDKFLATMQLGSRKEVKQFIKKGKVTVNGEITRSDKAQINEYEDQISF 73

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           +G  ++  +     L      +  T  + D               +  VGRLD +TEGLL
Sbjct: 74  EGEVIQYQKDYYYLLNKPAGVISATVDNYDETVMDLLVDEDFREDLFPVGRLDKDTEGLL 133

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT 181
           +LTNDG LA  L  P     + Y     G +  + + L  +G++I  G      ++T+ +
Sbjct: 134 VLTNDGQLAHRLLSPKKHVEKEYHATVAGVMTAEDVALFSEGLMIDQGEQCLPAKLTILS 193

Query: 182 QKGS--NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSK 238
              S   + +++ L EGK  ++K++      +V  L RI  G   L   L  G  R ++ 
Sbjct: 194 VDESAQTSQISLILHEGKFHQVKRMVAAVGKEVVYLKRIRMGQLTLDESLALGEYRALTA 253

Query: 239 KILREQLGPHL 249
             +        
Sbjct: 254 LEVEALQQNPF 264


>gi|300728331|ref|ZP_07061696.1| pseudouridine synthase B, ribosomal large subunit [Prevotella
           bryantii B14]
 gi|299774396|gb|EFI71023.1| pseudouridine synthase B, ribosomal large subunit [Prevotella
           bryantii B14]
          Length = 431

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 104/234 (44%), Gaps = 1/234 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +   P R++K +A AG+ SRRE +  I    + VNG ++      VM TD ++     + 
Sbjct: 191 DPNEPIRLNKYLANAGVCSRREADEFIQAGVITVNGEVVTELGTKVMRTDEVKFHDQNVS 250

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ++  + L      + T+      ++ +     +   R+  VGRLD N  G+LLLTNDG
Sbjct: 251 LEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKDACPERIYPVGRLDRNPTGVLLLTNDG 310

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     +VY V     V    L  +  GI ++        +    +      
Sbjct: 311 DLASKLTHPKFLKKKVYHVYLDKPVAAHDLQQIADGITLEDGEIHADAIEYADEHDKKQ- 369

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           V + +  GKNR ++++FE   ++V +L R+ +       L  G  R +S+K + 
Sbjct: 370 VGIEIHSGKNRIVRRIFEALGYRVTKLDRVQFAGLTKKNLRRGDWRFLSEKEVD 423


>gi|148269796|ref|YP_001244256.1| pseudouridine synthase [Thermotoga petrophila RKU-1]
 gi|147735340|gb|ABQ46680.1| ribosomal small subunit pseudouridine synthase A [Thermotoga
           petrophila RKU-1]
          Length = 239

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 57/243 (23%), Positives = 111/243 (45%), Gaps = 7/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++ +G+ +R+EV+++I Q RV VNG ++     +V   D + +DG  +    + 
Sbjct: 1   MRLDRYLSNSGVGTRKEVKKLIKQGRVTVNGRVVLDPGHSVSENDVVVLDGETVNFHRKV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +  +     + +T       S            +  VGRLD + EGLL++T+DG  A  
Sbjct: 61  YILFHKPSGYVTSTKDP---HSETIMEFLPPLKGIFPVGRLDKDAEGLLIITSDGDFAHR 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V+  G+V +DK+  LK G+ ++   +   +     +K SN  + + +
Sbjct: 118 VISPKWSVEKEYIVKVEGEVTEDKIEKLKNGVTLRDGFFAKAKCV---EKLSNDTLKIVI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHLLEE 252
            EGK  +IK++      +   L R   G   L   +  G  R +S++ +++       +E
Sbjct: 175 TEGKYHQIKRMTVAVGLRTVHLKRTRIGRLVLPEDMKPGEYRFLSEEEVKKVFEREDQKE 234

Query: 253 AQV 255
              
Sbjct: 235 DTP 237


>gi|170769533|ref|ZP_02903986.1| ribosomal large subunit pseudouridine synthase F [Escherichia
           albertii TW07627]
 gi|170121590|gb|EDS90521.1| ribosomal large subunit pseudouridine synthase F [Escherichia
           albertii TW07627]
          Length = 290

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 65/292 (22%), Positives = 117/292 (40%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVNPGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPVTDEFVTGMAAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L E       
Sbjct: 179 ITLVQGLNRQIRRMCEYFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIELFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             +     A      T ++     + +  +  +R   N  +     ++KK  
Sbjct: 239 SSSGTKPKAKAKPKTTGIKRPVVKMEKTAEKGSRPASNGKRFTSPGRKKKGR 290


>gi|52081501|ref|YP_080292.1| putative pseudouridine synthase YtzF [Bacillus licheniformis ATCC
           14580]
 gi|52786879|ref|YP_092708.1| hypothetical protein BLi03154 [Bacillus licheniformis ATCC 14580]
 gi|319647410|ref|ZP_08001631.1| pseudouridine synthase [Bacillus sp. BT1B_CT2]
 gi|52004712|gb|AAU24654.1| putative Pseudouridine synthase YtzF [Bacillus licheniformis ATCC
           14580]
 gi|52349381|gb|AAU42015.1| putative protein [Bacillus licheniformis ATCC 14580]
 gi|317390456|gb|EFV71262.1| pseudouridine synthase [Bacillus sp. BT1B_CT2]
          Length = 240

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 70/231 (30%), Positives = 109/231 (47%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++ +G  SR+EV++M+    V+VN  L++ A  +V    D I V G P+   E 
Sbjct: 1   MRLDKLLSNSGYGSRKEVKKMLKNGAVRVNDQLVKDAKKHVDPESDDITVYGAPVMYREF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      L  T            +   +      VGRLD +TEGLLLLTNDG LA 
Sbjct: 61  IYLMMNKPQGVLSATEDSRQETVVDLLDPELLRFEPFPVGRLDKDTEGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V  +  +DQ  L+ L+KG+ I +G      + +L   +     + +
Sbjct: 121 QLLSPKKHVPKTYEVHVNKPIDQAALDQLEKGVDIGEGYVTKPAEASLLASENGVERLLL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++K++ +     V  L R+  G   L   LL G  RE+S+  L
Sbjct: 181 TITEGKFHQVKRMLKAVGHDVIYLKRLKMGDVDLDEELLPGEYRELSEHEL 231


>gi|160895210|ref|ZP_02075982.1| hypothetical protein CLOL250_02769 [Clostridium sp. L2-50]
 gi|156863089|gb|EDO56520.1| hypothetical protein CLOL250_02769 [Clostridium sp. L2-50]
          Length = 272

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 74/277 (26%), Positives = 122/277 (44%), Gaps = 7/277 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K ++ AGI SRR  +  I + R+ +NG         + + D + VDG P+RK E
Sbjct: 3   EGIRINKYLSEAGICSRRAADEYILKGRITINGKPA-EMGQKIEANDRVMVDGKPVRKRE 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            T +  Y+KP+GL  T S          +      R+  VGRLD +++GLLLLTNDG L+
Sbjct: 62  ETVILAYNKPLGLTCTAS--HDDPDNIFDHIKYPIRLQYVGRLDKDSQGLLLLTNDGDLS 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             ++       + YRVR +  +  + L  +  G+ I        ++     K  N    +
Sbjct: 120 NSIQKSVNNHEKEYRVRVNKPITDEFLTQMAAGVPILDTVTKKCRLY----KIDNYSFKI 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + +G NR+I+++ E+F +KV  L R+     +LG L  G  R ++K+   E       +
Sbjct: 176 IITQGLNRQIRRMCEYFGYKVVNLKRLRVINIRLGNLRPGEYRHLTKEEETELRRLVERK 235

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
           E                ++       V        KN
Sbjct: 236 EEVKTKREEAQPDNKNEQNVVGNKRYVSWKRETGSKN 272


>gi|110800779|ref|YP_697003.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           ATCC 13124]
 gi|168213224|ref|ZP_02638849.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           CPE str. F4969]
 gi|110675426|gb|ABG84413.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           ATCC 13124]
 gi|170715223|gb|EDT27405.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           CPE str. F4969]
          Length = 298

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 66/260 (25%), Positives = 115/260 (44%), Gaps = 10/260 (3%)

Query: 1   MKDKNIVQENFT---PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           +K+  IV          R++K I+  G  SRRE +++I Q RVK++G+      + V   
Sbjct: 44  VKNTIIVSNKNEIRDKVRLNKYISETGFCSRREADKLIEQGRVKIDGLKATT-GMKVSKG 102

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
             + +DG PL+          +KP+G+  T       + V     +   R+  +GRLD +
Sbjct: 103 QSVSIDGKPLKVENELVYIALNKPVGITCTTESKIKGNIVDFI--NHEKRIFPIGRLDKD 160

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           ++GL+ +TNDG +   +        + Y V  +  +  + +  +  G+ I G        
Sbjct: 161 SQGLIFMTNDGDIVNKILRAGNNHEKEYIVTVNKSITDEFIKGMSNGVPILGTVTKKC-- 218

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +K S     + L +G NR+I+++ E+F ++V +L RI      LG L  GS R ++
Sbjct: 219 --LVKKESKNSFRIILTQGLNRQIRRMCEYFGYEVKKLERIRIMNVSLGNLKIGSWRYLT 276

Query: 238 KKILREQLGPHLLEEAQVNL 257
           KK L E              
Sbjct: 277 KKELAEINRLTENSSKTEEA 296


>gi|146298001|ref|YP_001192592.1| pseudouridine synthase [Flavobacterium johnsoniae UW101]
 gi|146152419|gb|ABQ03273.1| ribosomal large subunit pseudouridine synthase F [Flavobacterium
           johnsoniae UW101]
          Length = 272

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 65/281 (23%), Positives = 118/281 (41%), Gaps = 11/281 (3%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           ++EN    R++K I   G  SRRE +++I + RV +NG         V S D I +DG  
Sbjct: 1   MEENLK--RLNKFIGETGYCSRREADKLIEEGRVTINGA-AAEMGTKVSSDDEIRIDGKL 57

Query: 67  L-RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +  K E+     ++KP+G+  T +     + V     +   R+  +GRLD  +EGL+ +T
Sbjct: 58  IVEKHEKLVYLAFNKPVGIECTTNLEVKNNIVDYI--NYPKRIFPIGRLDKASEGLIFMT 115

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +   +        + Y V  +  + +  +  +  G+ I        +     ++ S
Sbjct: 116 NDGDIVNKILRARNNHEKEYTVTVNKPITERFIQRMGNGVPILDTVTKKCK----VEQIS 171

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++ E+  ++V  L RI      L  +  G  R+++   ++E  
Sbjct: 172 KYTFKIILTQGLNRQIRRMSEYLGYEVTALKRIRIINISL-DVPVGRYRDLTDAEIKELN 230

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
                         P  ++ T  R    I    P    R  
Sbjct: 231 KLIEPSSKTEEASLPKAAAPTPSRRSTFISKNDPRFRKRGN 271


>gi|194017854|ref|ZP_03056463.1| RNA pseudouridine synthase family protein [Bacillus pumilus ATCC
           7061]
 gi|194010506|gb|EDW20079.1| RNA pseudouridine synthase family protein [Bacillus pumilus ATCC
           7061]
          Length = 238

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 60/232 (25%), Positives = 102/232 (43%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K++A +G  SR++V++++  + V VNG L ++   +V    D + V G  +   E 
Sbjct: 1   MRLDKLLASSGFGSRKDVKKLVKARAVTVNGELAKQVKDHVDPSNDEVLVHGERVEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  T    D           I      VGRLD +T GLLLLTNDG LA 
Sbjct: 61  IYLMMNKPDGVISATEDLRDETVVDLLEPEDIAREPFPVGRLDKDTVGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V     +    +  L++  +++        +V +D  +  +  + +
Sbjct: 121 QLLSPKKHVPKTYEVHLKYPLGDQDIKRLEEGVVILDDYRTKPAKVEVDANESEDTRIRL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K + +    +V  L R S G   L   L  G  RE++ + L 
Sbjct: 181 TITEGKYHQVKLMAQAVGNEVIFLKRRSMGAVSLDEDLAPGEYRELTDEELD 232


>gi|262276079|ref|ZP_06053888.1| ribosomal large subunit pseudouridine synthase B [Grimontia
           hollisae CIP 101886]
 gi|262219887|gb|EEY71203.1| ribosomal large subunit pseudouridine synthase B [Grimontia
           hollisae CIP 101886]
          Length = 331

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 83/331 (25%), Positives = 134/331 (40%), Gaps = 9/331 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
            +++ KV+ARAG+ SRRE+E MI   RV VNG++ +           I VDG  +     
Sbjct: 2   SEKLQKVLARAGLGSRREIESMIQAGRVSVNGVVAKLGDRLEDLNAAIRVDGHHVSVSAS 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L        L T       R+          +R ++VGRLD NT GLLL T D
Sbjct: 62  SEQVCRVLAYNKPEGELCTRSDPEGRRTVFDRLPRLNGARWVAVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G+V++  +  L +G+ ++        V     +G+N 
Sbjct: 122 GELANRLMHPSRQVQREYMVRVFGEVNEQMVKNLVRGVELEDGEARFEDVVYAGGEGANH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+    L++   
Sbjct: 182 TFYVVITEGRNREVRRLWETQGVTVSRLKRVRYGDIYLSKELPRGGWMEL---ELKDVNY 238

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              + E +   +  I       + R   I      +    ++   +   +++        
Sbjct: 239 LREMVELRPESETLINPEAKKRKSRVQKIRRAVRRYEERVESGETRKPRNRRGGQPAGNR 298

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
            R                 S+  ++   +R 
Sbjct: 299 TRVGGGRSGKPGASRPGQSSNRQKKSGGNRN 329


>gi|170017037|ref|YP_001727956.1| 16S rRNA uridine-516 pseudouridylate synthase [Leuconostoc citreum
           KM20]
 gi|169803894|gb|ACA82512.1| 16S rRNA uridine-516 pseudouridylate synthase [Leuconostoc citreum
           KM20]
          Length = 249

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 88/235 (37%), Positives = 132/235 (56%), Gaps = 2/235 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +    R+ KV+A+AG+ASRR  E MI + RVKVNG  +    V V   D +EVDG P+  
Sbjct: 2   SEEEMRLQKVVAQAGLASRRGAETMITEGRVKVNGETVTTLGVKVGIHDTVEVDGAPIEG 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E+   +L +KP G+VTT SD  GR TV D L  I  RV  VGRLD +T G LLLTNDG 
Sbjct: 62  REKLVYYLLNKPRGVVTTTSDEKGRKTVLDLLEDIDQRVYPVGRLDYDTTGALLLTNDGT 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--A 187
           +A  L  P ++  ++Y  +  G    +KL  LK+G++I+G      +VT++        +
Sbjct: 122 IANQLMHPKSRVDKIYLAKVSGIATVEKLAPLKQGVIIKGRKTAPARVTIERVDKDKKTS 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V + + EG+N ++K + +     V++L R  Y  F L  L +G  R+++   ++
Sbjct: 182 MVRIIIHEGRNHQVKDMLQKVGLPVDKLTREQYAFFDLIGLQSGEYRKLTGVEVK 236


>gi|329946750|ref|ZP_08294162.1| pseudouridylate synthase [Actinomyces sp. oral taxon 170 str.
           F0386]
 gi|328526561|gb|EGF53574.1| pseudouridylate synthase [Actinomyces sp. oral taxon 170 str.
           F0386]
          Length = 324

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 79/246 (32%), Positives = 114/246 (46%), Gaps = 10/246 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDG-VPLRK 69
           + QR+ KV+A AG+ASRR  E++IA  RV V+GI +    V V   T  I VDG   L  
Sbjct: 76  SGQRLQKVLAHAGVASRRACEQLIADGRVSVDGITVTEPGVRVDPLTQEIRVDGSRILTN 135

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--------ISVGRLDINTEGL 121
            E   L L+     + T        +     L  +            + VGRLD  TEGL
Sbjct: 136 PELITLMLHKPAGVVTTMEDPEGRPTVAQYGLDYLAEHPELPDSLRLVHVGRLDTETEGL 195

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLL+NDG L+  L  PS +  + Y     GQV+      L++GI ++       +VT+  
Sbjct: 196 LLLSNDGELSHRLMHPSFEIAKTYVAIVEGQVEPWVPRKLRRGIALEDGETRADRVTVKD 255

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                + V + L  GKNR ++++ +     V RL R   GP +LG L  G TR +S + +
Sbjct: 256 SGPRGSIVEITLHSGKNRIVRRMLDAVGHPVTRLARTRLGPLRLGNLRPGETRPLSGEEI 315

Query: 242 REQLGP 247
                 
Sbjct: 316 AALQRE 321


>gi|157825866|ref|YP_001493586.1| ribosomal large subunit pseudouridine synthase [Rickettsia akari
           str. Hartford]
 gi|157799824|gb|ABV75078.1| Ribosomal large subunit pseudouridine synthase [Rickettsia akari
           str. Hartford]
          Length = 229

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 113/230 (49%), Positives = 156/230 (67%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR++K+I+ AGI SRR+ E++IA+ +VKV+GI +   A NV  ++ IEV G+ +   ++ 
Sbjct: 2   QRLAKIISNAGICSRRDAEKLIAEGQVKVDGITILSPATNVDISNKIEVSGILINNIQKP 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW+Y+KP+GL+TTH DP  R TVF+ L     RVIS+GRLD+N+EGLLLLTN G LAR 
Sbjct: 62  RLWIYYKPVGLITTHKDPLSRKTVFEQLTG-LPRVISIGRLDLNSEGLLLLTNSGDLARQ 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
            ELPS +  RVY VR +G+ D    +   K + I GI Y    + L  Q  SN+W  V L
Sbjct: 121 FELPSNRLKRVYHVRAYGKSDILLKSD-YKNLEIDGIFYNPHSIKLLKQNKSNSWFEVVL 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            EGKNREI+++FE+F  KV++LIRI YG F +  L  G+ +E++ KIL E
Sbjct: 180 FEGKNREIRRIFEYFGLKVHKLIRIQYGSFTIDNLKPGAYKEINNKILAE 229


>gi|303232224|ref|ZP_07318923.1| pseudouridylate synthase [Atopobium vaginae PB189-T1-4]
 gi|302481634|gb|EFL44695.1| pseudouridylate synthase [Atopobium vaginae PB189-T1-4]
          Length = 375

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 70/304 (23%), Positives = 119/304 (39%), Gaps = 26/304 (8%)

Query: 3   DKNIVQENFTP----QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-ST 57
           D++I+  N        R+ + +AR G+ASRR  E++I+  RV VNG++ +     V  + 
Sbjct: 64  DEDIMAGNLPSSTFTMRLQRYLARCGVASRRGAEKLISAGRVTVNGVVQDVLGSKVDCAH 123

Query: 58  DHIEVDGVP-LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           D + VDG P +   E T L L      L T                  +  + +VGRLD 
Sbjct: 124 DVVCVDGTPCVLGDEHTYLILNKPQGVLTTMSDPFGHPCVAALVPKDTYPGLFAVGRLDG 183

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +T GLLL + DG +   L  PS    + Y     G + +     L+ GI++         
Sbjct: 184 DTTGLLLFSTDGNMGNRLLHPSHHVWKTYVCLLQGSLTRAAQKQLEAGIMLDDGPCAPSH 243

Query: 177 VTLDTQKGSNAWV-------------------TVGLREGKNREIKKVFEFFNWKVNRLIR 217
           +T      +   +                   ++ +REG+  ++K++F+     V RL R
Sbjct: 244 ITRLAPTDALCTLAPQCHILDGIPSARGYTICSISIREGRYHQVKRMFDAVGCPVVRLHR 303

Query: 218 ISYGPFQLGT-LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIIS 276
             +GP  LG  L  G+ R  +   +   +      +   N    + +       R     
Sbjct: 304 AQFGPLSLGDALPFGAWRMCTPAEVDALMRTVSSSDGIANAQTNVQTKAHTSALRYTQHG 363

Query: 277 EVPD 280
             P+
Sbjct: 364 ATPN 367


>gi|291166791|gb|EFE28837.1| ribosomal large subunit pseudouridine synthase B [Filifactor alocis
           ATCC 35896]
          Length = 242

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 71/230 (30%), Positives = 113/230 (49%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+++ IA  GI+SRR+ +++I + RV VNG  +    + V    D ++VDG  +     
Sbjct: 1   MRINQYIAHCGISSRRKADQLIEEGRVFVNGKKVTSPGMQVEEGNDMVKVDGKIISSEVN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +KP+  ++     D        L     R+  VGRLD  + GLLLLTNDG LA 
Sbjct: 61  KVYYMLNKPLRYIS-AVSDDRGRNTVLELFRTKERIYPVGRLDYLSTGLLLLTNDGELAN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V+  G   ++     +KG+ + G      ++    ++       V 
Sbjct: 120 RLIHPRYHLEKTYFVQVKGDAPENLKERFQKGMFLDGYKTKPAELEFLGKRDGIIKYKVT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           LREG+NR+I+K+FE    KV  L RIS G   +G L  G  R ++ K ++
Sbjct: 180 LREGRNRQIRKMFEAARLKVVSLKRISMGDLYIGNLKEGEYRALTSKEVQ 229


>gi|320547064|ref|ZP_08041362.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           equinus ATCC 9812]
 gi|320448301|gb|EFW89046.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           equinus ATCC 9812]
          Length = 242

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 104/233 (44%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +  AG+ SR EV++++ +++V VNG L       +    D I   G  L   + 
Sbjct: 1   MRLDKFLVEAGVGSRTEVKQLLKKKQVLVNGKLETSPKTQIDEKLDKIVCQGQNLSYEKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  D         +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYMLNKPKGVISATEDDHHKTVLDLLDKTAWDKEVFPVGRLDIDTHGLLLLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVT 190
            +  P     ++Y  +  G +  + +     GI ++       Q+ +    +K + + V 
Sbjct: 121 AMLSPKKHVDKLYCAKVAGIMTDEDVKAFADGIELKDFTCQPAQLNIINADEKSNTSLVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           + ++EGK  ++K++      +V  L R+S GP +L   L  G  R +S   L 
Sbjct: 181 IVIKEGKFHQVKRMVLACGKEVTDLQRLSMGPLRLDDELALGEWRRLSPAELE 233


>gi|228967648|ref|ZP_04128669.1| RNA pseudouridine synthase [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228792024|gb|EEM39605.1| RNA pseudouridine synthase [Bacillus thuringiensis serovar sotto
           str. T04001]
          Length = 229

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 107/230 (46%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTH-GALVSDGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D    + +     +   R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAADHIEDNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGTIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVTRV----DQSTFRII 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L 
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTSEELD 223


>gi|69244107|ref|ZP_00602643.1| Pseudouridine synthase, Rsu [Enterococcus faecium DO]
 gi|258614116|ref|ZP_05711886.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecium DO]
 gi|293557176|ref|ZP_06675728.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1039]
 gi|293563963|ref|ZP_06678370.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1162]
 gi|293568184|ref|ZP_06679518.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1071]
 gi|294614323|ref|ZP_06694240.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1636]
 gi|294619970|ref|ZP_06699342.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1679]
 gi|294622171|ref|ZP_06701239.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium U0317]
 gi|314940301|ref|ZP_07847468.1| conserved hypothetical protein [Enterococcus faecium TX0133a04]
 gi|314941863|ref|ZP_07848734.1| conserved hypothetical protein [Enterococcus faecium TX0133C]
 gi|314949516|ref|ZP_07852851.1| conserved hypothetical protein [Enterococcus faecium TX0082]
 gi|314952902|ref|ZP_07855870.1| conserved hypothetical protein [Enterococcus faecium TX0133A]
 gi|314994523|ref|ZP_07859796.1| conserved hypothetical protein [Enterococcus faecium TX0133B]
 gi|314995270|ref|ZP_07860382.1| conserved hypothetical protein [Enterococcus faecium TX0133a01]
 gi|68196564|gb|EAN10990.1| Pseudouridine synthase, Rsu [Enterococcus faecium DO]
 gi|291589084|gb|EFF20898.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1071]
 gi|291592795|gb|EFF24387.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1636]
 gi|291593800|gb|EFF25302.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1679]
 gi|291598298|gb|EFF29389.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium U0317]
 gi|291600677|gb|EFF30977.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1039]
 gi|291604053|gb|EFF33580.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1162]
 gi|313590526|gb|EFR69371.1| conserved hypothetical protein [Enterococcus faecium TX0133a01]
 gi|313591101|gb|EFR69946.1| conserved hypothetical protein [Enterococcus faecium TX0133B]
 gi|313595024|gb|EFR73869.1| conserved hypothetical protein [Enterococcus faecium TX0133A]
 gi|313599347|gb|EFR78192.1| conserved hypothetical protein [Enterococcus faecium TX0133C]
 gi|313640477|gb|EFS05057.1| conserved hypothetical protein [Enterococcus faecium TX0133a04]
 gi|313644130|gb|EFS08710.1| conserved hypothetical protein [Enterococcus faecium TX0082]
          Length = 239

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 59/238 (24%), Positives = 104/238 (43%), Gaps = 5/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ SR+EV+ +I +  ++VNG +++     V    D +   G  +   + 
Sbjct: 1   MRLDKFLADMGLGSRKEVKGLIKKGTIEVNGQVVKSDKAQVNEFEDAVTYLGEIITYQKD 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T  + D               +  VGRLD +TEGLL+LTNDG  A 
Sbjct: 61  FYYILHKPAGVISATQDNHDQTVIDLLEDQDYREDLFPVGRLDKDTEGLLILTNDGVFAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKG--SNAWV 189
            L  P     + Y     G + ++ + L  +G++I         ++ +D        + +
Sbjct: 121 QLLSPKKHVEKEYLAEVSGIMTEEDIRLFAEGLIIDGDEQTLPAKLQIDQVDQETETSII 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
            + L EGK  ++K++ +    +V  L RI  G F L   L  G  R ++K+ L +   
Sbjct: 181 RLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGKFWLPKDLNKGQYRPMTKEELEQVRE 238


>gi|153950805|ref|YP_001401950.1| 23S rRNA pseudouridine synthase F [Yersinia pseudotuberculosis IP
           31758]
 gi|152962300|gb|ABS49761.1| RNA pseudouridine synthase family protein [Yersinia
           pseudotuberculosis IP 31758]
          Length = 290

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 58/293 (19%), Positives = 111/293 (37%), Gaps = 5/293 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +  
Sbjct: 3   TNSSIRLNKYISESGICSRRDGDRYIEQGNVFINGKRATV-GDQVFAGDVVKVNGQIIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   L             +  +G      +  +   RV  +GRLD +++GL+ LTN G 
Sbjct: 62  RDEEDLVFIALNKPAGIITTMEEGERDNISDFVNHSKRVFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  V  + +  +  G+ I G      +V    QK +    
Sbjct: 122 LVNKILRAGNNHEKEYVVTVNKPVTDEFIQGMSAGVPILGTVTKKCKV----QKEAPLVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ + F ++V +L R       L  L  G  R+++   L        
Sbjct: 178 RITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNISLKGLPLGEWRDLTDDELLTLFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
              ++              +       +  +       +        ++KK  
Sbjct: 238 NSSSEEKTVKKAPPKPVAAKRPGIQGQKKAEKSDDNTASRKHFTQPGRKKKGR 290


>gi|182419423|ref|ZP_02950675.1| RNA pseudouridine synthase family protein [Clostridium butyricum
           5521]
 gi|237666914|ref|ZP_04526899.1| RNA pseudouridine synthase family protein [Clostridium butyricum E4
           str. BoNT E BL5262]
 gi|182376754|gb|EDT74326.1| RNA pseudouridine synthase family protein [Clostridium butyricum
           5521]
 gi|237658113|gb|EEP55668.1| RNA pseudouridine synthase family protein [Clostridium butyricum E4
           str. BoNT E BL5262]
          Length = 238

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 110/231 (47%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KVI+  G  SR++V+  + +  ++V+G++++   ++V      I+++G  +   + 
Sbjct: 2   ERLDKVISNLGYGSRKDVKAFVKKGLIEVDGVIVKDNGLSVDPEKSVIKINGEEVFYRKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  TH + D        +         VGRLD +T GLLLLTNDG L  
Sbjct: 62  IYLMMNKPAGVISATHDNRDETVIDLLYVDHQVFEPFPVGRLDKDTVGLLLLTNDGELNH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY  +   +VD+  +   K GI +       + ++ + +     + + V
Sbjct: 122 RLISPKWHVDKVYYAKIDKKVDEKDIQAFKSGITLDDGYKCMEAKLEIISASEEGSEIRV 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            ++EGK  ++K++FE    KV  L R  +G   L   L  G  RE+S + L
Sbjct: 182 TIQEGKFHQVKRMFEAVGKKVEYLKREEFGGLSLDTDLEEGEYRELSDEEL 232


>gi|134295571|ref|YP_001119306.1| ribosomal large subunit pseudouridine synthase B [Burkholderia
           vietnamiensis G4]
 gi|134138728|gb|ABO54471.1| ribosomal large subunit pseudouridine synthase B [Burkholderia
           vietnamiensis G4]
          Length = 563

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 82/348 (23%), Positives = 144/348 (41%), Gaps = 7/348 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 173 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRI 231

Query: 63  DGVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           +G P+++         L  +     +V+        S      P   ++ ++VGRLD NT
Sbjct: 232 NGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNT 291

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++ 
Sbjct: 292 EGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEGMRQKLLHGVELDDGPANFLRIR 351

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
               +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ 
Sbjct: 352 DGGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPIPLPRGLKRGRWEELD 411

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +  +R+ +    L+             +   R    + + +          +  +    +
Sbjct: 412 EAQVRKLMATVGLKAPSEEKGKRAGGQQE-RRQPDPMQTSMGFISREPVLTTHGQLDQPR 470

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
           +             S         S + + SG R+ +  R+      +
Sbjct: 471 RGGGRRGAPGLPGLSGYGSLPVAPSGYGNRSGGRDVDGNRASYGAGPK 518


>gi|315149408|gb|EFT93424.1| conserved hypothetical protein [Enterococcus faecalis TX0012]
          Length = 257

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 64/248 (25%), Positives = 109/248 (43%), Gaps = 5/248 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           I + G  L   +     L+     +  T    D             + +  VGRLD +TE
Sbjct: 61  IALMGEILTYQKFFYYMLHKPQGVISATEDQRDETVIDLLTDQDYRADLFPVGRLDKDTE 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVT 178
           GLLLLTNDG LA  L  P     + Y     G V  +   L  +G  +  G      ++ 
Sbjct: 121 GLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEMVKPSRLV 180

Query: 179 L--DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTRE 235
           +    ++   + V + ++EGK  ++K++       V  L R+  G   L   L  G  R 
Sbjct: 181 IETINEEEGTSVVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEYRP 240

Query: 236 VSKKILRE 243
           +++  L++
Sbjct: 241 LTEDELQQ 248


>gi|308066931|ref|YP_003868536.1| ribosomal large subunit pseudouridine synthase F [Paenibacillus
           polymyxa E681]
 gi|305856210|gb|ADM67998.1| Ribosomal large subunit pseudouridine synthase F [Paenibacillus
           polymyxa E681]
          Length = 233

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 62/227 (27%), Positives = 108/227 (47%), Gaps = 7/227 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+  G  SRRE ++++   RV +NG +           D + V+G PLR+    
Sbjct: 1   MRINKFISETGFCSRREADKLVESGRVTINGEVA-VLGSQAEEGDDVRVNGKPLREKSDH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+ +T       + V  +      R+  +GRLD ++EGL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITSTTESHIRGNVV--DFVGHPQRIFPIGRLDKDSEGLILLTNDGDIVNK 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     V    +  +  G+ I G      +VT      S     + L
Sbjct: 118 ILRAEGKHEKEYIVTVDRPVIPSFVQGMSSGVKILGQRTLPCEVTRV----SEYVFRIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            EGKNR+I+++   F ++V +L R+     +LG+L  G+ R +++  
Sbjct: 174 TEGKNRQIRRMCAAFGYEVKKLQRLRIMNIRLGSLQKGAWRNLTEAE 220


>gi|238791770|ref|ZP_04635407.1| Ribosomal large subunit pseudouridine synthase F [Yersinia
           intermedia ATCC 29909]
 gi|238728874|gb|EEQ20391.1| Ribosomal large subunit pseudouridine synthase F [Yersinia
           intermedia ATCC 29909]
          Length = 290

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 62/299 (20%), Positives = 115/299 (38%), Gaps = 11/299 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I  +GI SRR+ +R I Q  V +NG         V S D ++V+G  +  
Sbjct: 3   TNSSTRLNKYIGESGICSRRDADRYIEQGHVFINGKRAAV-GDQVYSGDVVKVNGQLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L L      +    +  +G S    +  +   RV  +GRLD +++GL+ LTN G 
Sbjct: 62  RNENDLVLIALNKPVGIISTTEEGESDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  V ++ +  L  G+ + G      +V     K +    
Sbjct: 122 LVNKILRAGNDHEKEYLVTVNKPVTEEFILGLGAGVPMMGTVTKKCKV----SKVATFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ + F ++V +L R       L  L  G  R+++   L E      
Sbjct: 178 NITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNVTLKGLPMGEWRDLTDDELIELFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
              +           + +            +   + +K+ S      +  +       R
Sbjct: 238 NSSSD------EKPVKKVQAKSVADKKPRVNGVKKPEKSDSNSAPRKRFAQPGRKKKGR 290


>gi|152981088|ref|YP_001354188.1| ribosomal large subunit pseudouridine synthase B [Janthinobacterium
           sp. Marseille]
 gi|151281165|gb|ABR89575.1| ribosomal large subunit pseudouridine synthase B [Janthinobacterium
           sp. Marseille]
          Length = 546

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 85/352 (24%), Positives = 143/352 (40%), Gaps = 17/352 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           +  +  +    ++ KV+A AG+ SRR++E +I   RV VNG         ++ TD + ++
Sbjct: 174 RRDLTADDDAPKLHKVLAEAGLGSRRDMEELIIAGRVSVNGEPA-HIGQRILPTDQVRIN 232

Query: 64  GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G  ++    K     L  +     +V+T+      S          ++ ++VGRLD NTE
Sbjct: 233 GKLIQRKVSKKPPRVLVYHKPAGEIVSTNDPEGRPSVFDRLPTMKAAKWLAVGRLDFNTE 292

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL T  G LA  L  P     R Y VR  G++++     L  G+ ++       ++  
Sbjct: 293 GLLLFTTSGDLANRLMHPRYGIDREYAVRTLGELEEGMRQKLLAGVELEDGLAQFSKIAD 352

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G N W  V + EG+NRE++++FE     V+RLIR  YG   L   L  G   E+ +
Sbjct: 353 GGGEGVNKWYRVTIGEGRNREVRRMFEAIGLTVSRLIRTRYGLLTLPKNLKRGRWEEMEE 412

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             +R+ L           LD     +    + R      V  +      N   +     Q
Sbjct: 413 HAVRDLLAL-------SGLDKNTGEAGPANKGRAAGGDRVNGNRAPRVDNGLGQPRSPSQ 465

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
            +       R+         G  +       ++ +  + S  FP     RR+
Sbjct: 466 WQNTGTGQGRSQ----GQNPGKPNRQGQQRSRQPDPLQTSLGFPGMGQPRRS 513


>gi|299821620|ref|ZP_07053508.1| ribosomal large subunit pseudouridine synthase B [Listeria grayi
           DSM 20601]
 gi|299817285|gb|EFI84521.1| ribosomal large subunit pseudouridine synthase B [Listeria grayi
           DSM 20601]
          Length = 243

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 75/231 (32%), Positives = 119/231 (51%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA +G+ SRR+ E++IA  RV VNG ++      V   D IEV+G+ L K E  
Sbjct: 2   ERLQKVIANSGVTSRRKAEQLIAAGRVTVNGEVVRELGTKVSPNDRIEVEGIELTKEEHR 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     +     D   ++     +  I  R+  VGRLD  T GLLL+TNDG  A  
Sbjct: 62  YFLFYKPRGVVSAVTDDKGRKTVADYFV-DIPERLYPVGRLDYETSGLLLMTNDGDFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVTV 191
           L  P  +  + Y  R  G   +++L  L++G+VI G      +V L    +    A + +
Sbjct: 121 LMHPKHEVEKQYIARVKGIPTKEQLRRLERGVVIDGRKTAPAKVKLRSADKAKEKAIIEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EG+NR+++K+FE   + V +L+R +Y    +  + AG  RE+S   ++
Sbjct: 181 TIHEGRNRQVRKMFESIGFPVQKLMREAYAFLNVAGMNAGERRELSHHEVK 231


>gi|228469771|ref|ZP_04054729.1| ribosomal large subunit pseudouridine synthase B [Porphyromonas
           uenonis 60-3]
 gi|228308610|gb|EEK17361.1| ribosomal large subunit pseudouridine synthase B [Porphyromonas
           uenonis 60-3]
          Length = 472

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 66/270 (24%), Positives = 120/270 (44%), Gaps = 1/270 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E   P R++K ++ +G+ SRR  ++ IA  RVKVNG ++      V+ TD + VD  P+ 
Sbjct: 201 EAGEPIRLNKFLSNSGLCSRRTADQYIAAGRVKVNGAVVSELGSQVLPTDQVMVDDKPVT 260

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              +  + L      + T       R+ +     +   R+  +GRLD NT G+LLLTNDG
Sbjct: 261 LEAKVYVLLNKPKNCVTTLTDPEGRRTVMDLVHNACTERIYPIGRLDRNTTGILLLTNDG 320

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P+ +  ++Y V    +V  + + ++  G  ++        ++  T + ++  
Sbjct: 321 DLAVRLMHPAFRKKKIYEVALDKEVTVEHMQMIAHGFELEDGEIHADAISYITGQ-THDK 379

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           V + +  G+NR ++++FE   ++V  L R+ Y       L  G  R ++ + +R      
Sbjct: 380 VGIEIHSGRNRIVRRIFEHLGYRVVHLDRVYYAGLTKKDLPRGRWRYLTPEEVRYLRMGI 439

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEV 278
             +E            +          SE 
Sbjct: 440 KEQEDNGVAPTTKVYHKHQETPDHPFSSEE 469


>gi|119716723|ref|YP_923688.1| ribosomal large subunit pseudouridine synthase B [Nocardioides sp.
           JS614]
 gi|119537384|gb|ABL82001.1| ribosomal large subunit pseudouridine synthase B [Nocardioides sp.
           JS614]
          Length = 251

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 77/250 (30%), Positives = 129/250 (51%), Gaps = 1/250 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDH 59
           M    I  ++    R+ K++A++G+ASRR+ E ++ +  V V+G ++ R    V   T  
Sbjct: 1   MTTPGIESDDDGLVRLQKLLAQSGVASRRKCEELMLEGHVVVDGEVVTRLGTKVDPRTAV 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           I VDG  L         + +KP G+V+T SDP+GR T+ D +     R+  VGRLD +T 
Sbjct: 61  IRVDGKRLPPVSEKVYLVLNKPRGVVSTMSDPEGRRTLSDLVADRPERLFHVGRLDTDTS 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLLTNDG  A  +  PS +  + Y     G+V +  +  L +G+ +        +  +
Sbjct: 121 GLLLLTNDGDFAHRMAHPSYEVDKTYVAEVEGEVYRRTIKQLLEGVTLDDGPVTVSKARI 180

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                + + V + + EG+NR ++++ +     V RL R + GP  LG L +G  R+++++
Sbjct: 181 VEATAAKSIVELVIHEGRNRIVRRLLDQVGHPVRRLTRTAIGPVSLGRLPSGELRDLTRQ 240

Query: 240 ILREQLGPHL 249
            L E L    
Sbjct: 241 ELGELLDTAQ 250


>gi|291086679|ref|ZP_06356433.2| ribosomal large subunit pseudouridine synthase F [Citrobacter
           youngae ATCC 29220]
 gi|291067434|gb|EFE05543.1| ribosomal large subunit pseudouridine synthase F [Citrobacter
           youngae ATCC 29220]
          Length = 318

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 63/293 (21%), Positives = 112/293 (38%), Gaps = 5/293 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 31  DSSIRLNKYISESGICSRREADRFIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGRLIEPR 89

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L        +    +  D       +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 90  EAEDLVFIALNKPVGIVSTTEDSERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 149

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  D +  +  G+ I G            +K +     
Sbjct: 150 VNKILRAGNDHEKEYLVTVDKPITDDFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 205

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V RL R       L  L  G  R+++   L E       
Sbjct: 206 ITLIQGLNRQIRRMCEHFGYEVTRLERTRIMNVGLSGLPLGEWRDLTDDELIELFKLIEN 265

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
             ++    A        ++     I +  +        + ++     +KK   
Sbjct: 266 SSSEAKPKAKAKPKTAGIKRPVVKIEKSAEKEKSRPAANGKRFTSPGRKKKGR 318


>gi|149370621|ref|ZP_01890310.1| ribosomal large subunit pseudouridine synthase F [unidentified
           eubacterium SCB49]
 gi|149356172|gb|EDM44729.1| ribosomal large subunit pseudouridine synthase F [unidentified
           eubacterium SCB49]
          Length = 291

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 61/281 (21%), Positives = 120/281 (42%), Gaps = 5/281 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +  +    R++K I+ +G  SRR+ +++I + +V +NG  +       M  D I V+G  
Sbjct: 1   MANHPNSTRLNKAISDSGYCSRRQADKLIEEGKVTLNGNPV-SLGDRAMPDDVIHVEGNL 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           + +       + +KP+G+  T       + V         R+  VGRLD  +EGLLL+TN
Sbjct: 60  ITENNNLVYIILNKPVGITCTTDLRVEGNVVDYI--DHKERIFHVGRLDKPSEGLLLMTN 117

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG +   +        + Y V+    +  + +  +  GI ++ +     +  +  ++ S 
Sbjct: 118 DGDIVNKILRAGNSHEKEYFVKVDRPITTEFIRRMGNGIPLEELETTTKKCFV--EQVSR 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               + L +G NR+I+++ E+ +++V  L R      +LG L  G  R+++K+ L+    
Sbjct: 176 FVFRIILVQGLNRQIRRMCEYLDYEVMELKRERIMNIELGDLPYGEWRDLTKEELQGLKD 235

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
                E    +D              N      +   R  +
Sbjct: 236 AVAKSENDSFIDREEKRKAAPKTGDANRNRPRNEAPKRESR 276


>gi|24379111|ref|NP_721066.1| putative 16S pseudouridylate synthase [Streptococcus mutans UA159]
 gi|24377013|gb|AAN58372.1|AE014907_9 putative 16S pseudouridylate synthase [Streptococcus mutans UA159]
          Length = 238

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 62/229 (27%), Positives = 101/229 (44%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++ +AG  SR +V++ I  Q+V+V+  L      NV      I V G  L  +  
Sbjct: 1   MRLGKLLGQAGFGSRGQVKKFIRSQQVRVDDELARTGNQNVDPNLQTITVSGKQLSYSPH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                +      +  VG LD +TEGL+L+TN+G L  
Sbjct: 61  VYYILNKPAGLVSVVRDQHYQTVIDLIAVVDRREGLYPVGCLDRDTEGLVLITNNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V  +G +  D +     GI  + G      ++ + +     +   +
Sbjct: 121 RLLHPKYHVDKTYYVEVNGDLGIDAIAFFDNGIAFLDGTVCKPAKLQIISSSSEVSRAYI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + EGK  ++KK+F  +  KV  L RIS+GPF+LG L  G  RE++ + 
Sbjct: 181 TITEGKFHQVKKMFLAYGVKVTYLKRISFGPFELGDLPVGEYRELTAEE 229


>gi|218899705|ref|YP_002448116.1| RNA pseudouridine synthase family protein [Bacillus cereus G9842]
 gi|218542895|gb|ACK95289.1| RNA pseudouridine synthase family protein [Bacillus cereus G9842]
          Length = 229

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 107/230 (46%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTH-GALVSDGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T ++    + +     +   R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAAEHIEDNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGTIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVTRV----DQSTFRII 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L 
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTSEELD 223


>gi|260641988|ref|ZP_05859178.1| ribosomal large subunit pseudouridine synthase B [Bacteroides
           finegoldii DSM 17565]
 gi|260624005|gb|EEX46876.1| ribosomal large subunit pseudouridine synthase B [Bacteroides
           finegoldii DSM 17565]
          Length = 253

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 60/241 (24%), Positives = 108/241 (44%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +  +D +
Sbjct: 5   IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVV 64

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P+    +  + L      + T+    + R+ +     +   R+  VGRLD NT G
Sbjct: 65  KFHEEPVSIERKVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTTG 124

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     + +  ++ +  GI ++            
Sbjct: 125 VLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADMDQIAAGIQLEDGEIH-ADAISY 183

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           T       V + +  GKNR ++++FE   +KV +L R+ +       L  G  R +++  
Sbjct: 184 TDDFKKDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLTEAE 243

Query: 241 L 241
           +
Sbjct: 244 V 244


>gi|124267190|ref|YP_001021194.1| ribosomal large subunit pseudouridine synthase B [Methylibium
           petroleiphilum PM1]
 gi|124259965|gb|ABM94959.1| ribosomal large subunit pseudouridine synthase B [Methylibium
           petroleiphilum PM1]
          Length = 686

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 91/356 (25%), Positives = 144/356 (40%), Gaps = 9/356 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            K +++      ++ KV+A++GI SRR++E+ I   +V VN  +     + +   D I V
Sbjct: 224 TKRVLRPEPEAPKLHKVLAQSGIGSRRDMEQFILDGKVTVNDEVAHV-GMRISYGDRIAV 282

Query: 63  DGVP----LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           DG P    ++      L  +     +VT +      +           +  SVGRLDINT
Sbjct: 283 DGKPVRLRIQPGPARLLAYHKPTGEVVTLNDPEGRPTVFRRLPRLQQGKWQSVGRLDINT 342

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLLL TN G LA  L  P     R Y VR  G +++++   L +G+ I G   G   + 
Sbjct: 343 EGLLLFTNSGELANQLMHPRFGVEREYAVRVLGSLNEEQRAKLLEGVEIDGQTAGFKSIE 402

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
               +G+N W  V + EG+NRE++K+F+     V+RLIRI YG   L   L  G   E+ 
Sbjct: 403 EGGGEGANRWYRVVITEGRNREVRKLFDKVGLAVSRLIRIRYGTVVLPRGLKRGVWVELD 462

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK---KNSSQKNG 294
            + LR                    +     + R N  +  P+   R        +Q  G
Sbjct: 463 DQDLRAIRQLASGNRGAAAQSESRDAQGNREQRRNNGRNGKPERNARGPQQGGARAQGQG 522

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
             ++     P   R   +           F       E+   R  +   +R   + 
Sbjct: 523 GGERGPRREPRESRFGEAAPDTDGAGEEDFGRIPNPLEQTFDRRFAKGPRRGAAQG 578


>gi|332999092|gb|EGK18679.1| ribosomal large subunit pseudouridine synthase F [Shigella flexneri
           K-218]
          Length = 291

 Score =  179 bits (455), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 60/290 (20%), Positives = 114/290 (39%), Gaps = 5/290 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDIVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R ++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRYLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
             ++    A        ++     + +  +   R   N  +     ++++
Sbjct: 239 SSSEAKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKRR 288


>gi|134301050|ref|YP_001114546.1| pseudouridine synthase [Desulfotomaculum reducens MI-1]
 gi|134053750|gb|ABO51721.1| ribosomal small subunit pseudouridine synthase A [Desulfotomaculum
           reducens MI-1]
          Length = 249

 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 65/238 (27%), Positives = 110/238 (46%), Gaps = 5/238 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGV 65
           + EN    R+ +++   G+ +R+E++++I  ++V VNG L     +++    DHIEV G 
Sbjct: 1   MAEN-EKLRLDRLLNHMGLGTRKEIKKLIKAKQVMVNGELAMDPGLHIFPQRDHIEVQGE 59

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +   E   L L      L  T    D       +          VGRLD +TEGLLLLT
Sbjct: 60  VIEYREYIYLMLNKPQDVLSATEDASDKVVIDLLDPTYHSFNPFPVGRLDKDTEGLLLLT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKG 184
           N+G LA  L  P     + Y     G V ++ +    +G+ +         Q+ +  +  
Sbjct: 120 NNGKLAHQLLSPKKHVPKTYYALVQGLVTEEDVAAFARGVELDDGYRTLPGQLKII-RSA 178

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
             + + + + EGK  ++K++FE    +V  L R+S GP  L   L  G  RE++ + +
Sbjct: 179 PQSEIELTIYEGKYHQVKRMFEAVGKRVIYLKRLSMGPLVLDNNLKPGEYRELTDEEI 236


>gi|293394546|ref|ZP_06638842.1| ribosomal large subunit pseudouridine synthase F [Serratia
           odorifera DSM 4582]
 gi|291423011|gb|EFE96244.1| ribosomal large subunit pseudouridine synthase F [Serratia
           odorifera DSM 4582]
          Length = 289

 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 59/289 (20%), Positives = 108/289 (37%), Gaps = 5/289 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++K I+ +GI SRR+ +R I Q  V +NG  +      V   D ++V+G  +     
Sbjct: 6   SIRLNKYISESGICSRRDADRYIEQGNVFINGKRVA-LGDRVFPGDVVKVNGQLIEPRNE 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L        +    +  DG      +  +  +R+  +GRLD +++GL+ LTN G L  
Sbjct: 65  DNLIFIALNKPVGVVSTTEDGEKDNIVDFVNHSTRIFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  V  + ++ L  G+ + G            +K +     + 
Sbjct: 125 KILRAGNDHEKEYLVTVNKPVTDEFIHGLGAGVPMLGTV----TKKCKVKKVAPFVFRIV 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E F ++V +L R       L  L  G  R+++   L E         
Sbjct: 181 LVQGLNRQIRRMCEHFGYEVTKLERTRIMNVGLAGLPLGEWRDLTDDELVELFKLIEDSS 240

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           ++         +        N                       K+K  
Sbjct: 241 SEAKPAKKAKPAVKKPASSGNGQRTADKPSGNPAARKRFTQPGRKKKGR 289


>gi|71281709|ref|YP_267665.1| RNA pseudouridine synthase family protein [Colwellia
           psychrerythraea 34H]
 gi|71147449|gb|AAZ27922.1| RNA pseudouridine synthase family protein [Colwellia
           psychrerythraea 34H]
          Length = 314

 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 62/291 (21%), Positives = 122/291 (41%), Gaps = 11/291 (3%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             + +  +  P+R++K I+ +G  SRR  ++MI   RV +N  +       V++ D ++V
Sbjct: 2   SSDKLTTSTPPKRLNKYISDSGFCSRRSADKMIEANRVTINDKVP-ELGTKVLAGDVVKV 60

Query: 63  DGVPLRK----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           DG  +              Y+KPIG+  T       + +         R+  +GRLD  +
Sbjct: 61  DGYDIAPISDDKSDRIYIAYNKPIGITCTTEKHVRGNIIDAI--GHKKRIFPIGRLDKPS 118

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGL+ LT+DG +   +        + Y V     + +  +  + +G+ I G         
Sbjct: 119 EGLIFLTSDGDIVNKILRAENAHDKEYIVTVDKPISERFIERMSRGVPILGTITKPC--- 175

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              Q  S    T+ L +G NR+I+++ E+ +++V +L R      +LG L  G  RE++ 
Sbjct: 176 -IVQVKSRFEFTIILTQGLNRQIRRMCEYLDYEVLKLKRSRIMKVELGDLTPGQWRELTI 234

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
             + E               A    + + + D   + + + +   + +  +
Sbjct: 235 TEMAEINQAVEGSSKTAINTAQPKQTTSSMNDLEELSASLNNADNKSESKT 285


>gi|16131848|ref|NP_418446.1| 23S rRNA U2604 pseudouridine synthase [Escherichia coli str. K-12
           substr. MG1655]
 gi|89110743|ref|AP_004523.1| 23S rRNA pseudouridine synthase [Escherichia coli str. K-12 substr.
           W3110]
 gi|170083479|ref|YP_001732799.1| 23S rRNA pseudouridine synthase [Escherichia coli str. K-12 substr.
           DH10B]
 gi|194437171|ref|ZP_03069269.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           101-1]
 gi|238903075|ref|YP_002928871.1| 23S rRNA pseudouridine synthase [Escherichia coli BW2952]
 gi|253775354|ref|YP_003038185.1| 23S rRNA pseudouridine synthase F [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254037014|ref|ZP_04871091.1| ribosomal large subunit pseudouridine synthase F [Escherichia sp.
           1_1_43]
 gi|254163958|ref|YP_003047066.1| 23S rRNA pseudouridine synthase F [Escherichia coli B str. REL606]
 gi|256024891|ref|ZP_05438756.1| 23S rRNA pseudouridine synthase F [Escherichia sp. 4_1_40B]
 gi|300929753|ref|ZP_07145207.1| conserved hypothetical protein [Escherichia coli MS 187-1]
 gi|300946586|ref|ZP_07160846.1| conserved hypothetical protein [Escherichia coli MS 116-1]
 gi|300957575|ref|ZP_07169780.1| hypothetical protein HMPREF9547_03329 [Escherichia coli MS 175-1]
 gi|301019105|ref|ZP_07183310.1| conserved hypothetical protein [Escherichia coli MS 196-1]
 gi|301645001|ref|ZP_07244966.1| conserved hypothetical protein [Escherichia coli MS 146-1]
 gi|418534|sp|P32684|RLUF_ECOLI RecName: Full=Ribosomal large subunit pseudouridine synthase F;
           AltName: Full=rRNA pseudouridylate synthase F; AltName:
           Full=rRNA-uridine isomerase F
 gi|228312012|pdb|3DH3|A Chain A, Crystal Structure Of Rluf In Complex With A 22 Nucleotide
           Rna Substrate
 gi|228312014|pdb|3DH3|B Chain B, Crystal Structure Of Rluf In Complex With A 22 Nucleotide
           Rna Substrate
 gi|228312016|pdb|3DH3|C Chain C, Crystal Structure Of Rluf In Complex With A 22 Nucleotide
           Rna Substrate
 gi|228312018|pdb|3DH3|D Chain D, Crystal Structure Of Rluf In Complex With A 22 Nucleotide
           Rna Substrate
 gi|396357|gb|AAC43116.1| ORF_o290a [Escherichia coli str. K-12 substr. MG1655]
 gi|1790453|gb|AAC76992.1| 23S rRNA U2604 pseudouridine synthase [Escherichia coli str. K-12
           substr. MG1655]
 gi|85676774|dbj|BAE78024.1| 23S rRNA pseudouridine synthase [Escherichia coli str. K12 substr.
           W3110]
 gi|169891314|gb|ACB05021.1| 23S rRNA pseudouridine synthase [Escherichia coli str. K-12 substr.
           DH10B]
 gi|194423727|gb|EDX39716.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           101-1]
 gi|226840120|gb|EEH72122.1| ribosomal large subunit pseudouridine synthase F [Escherichia sp.
           1_1_43]
 gi|238859759|gb|ACR61757.1| 23S rRNA pseudouridine synthase [Escherichia coli BW2952]
 gi|242379552|emb|CAQ34371.1| 23S rRNA pseudouridine 2604 synthase [Escherichia coli BL21(DE3)]
 gi|253326398|gb|ACT31000.1| pseudouridine synthase [Escherichia coli 'BL21-Gold(DE3)pLysS AG']
 gi|253975859|gb|ACT41530.1| 23S rRNA pseudouridine synthase [Escherichia coli B str. REL606]
 gi|253980015|gb|ACT45685.1| 23S rRNA pseudouridine synthase [Escherichia coli BL21(DE3)]
 gi|260451153|gb|ACX41575.1| pseudouridine synthase [Escherichia coli DH1]
 gi|299882399|gb|EFI90610.1| conserved hypothetical protein [Escherichia coli MS 196-1]
 gi|300315689|gb|EFJ65473.1| hypothetical protein HMPREF9547_03329 [Escherichia coli MS 175-1]
 gi|300453742|gb|EFK17362.1| conserved hypothetical protein [Escherichia coli MS 116-1]
 gi|300462326|gb|EFK25819.1| conserved hypothetical protein [Escherichia coli MS 187-1]
 gi|301076689|gb|EFK91495.1| conserved hypothetical protein [Escherichia coli MS 146-1]
 gi|309704434|emb|CBJ03783.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           ETEC H10407]
 gi|315138575|dbj|BAJ45734.1| 23S rRNA pseudouridine synthase F [Escherichia coli DH1]
 gi|323935584|gb|EGB31911.1| RNA pseudouridylate synthase [Escherichia coli E1520]
 gi|323940200|gb|EGB36393.1| RNA pseudouridylate synthase [Escherichia coli E482]
 gi|323960493|gb|EGB56124.1| RNA pseudouridylate synthase [Escherichia coli H489]
          Length = 290

 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 63/292 (21%), Positives = 117/292 (40%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     + ++ +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++V   A        ++     + +  +   R   N  +     ++KK  
Sbjct: 239 SSSEVKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 290


>gi|309775550|ref|ZP_07670550.1| pseudouridine synthase RluB [Erysipelotrichaceae bacterium 3_1_53]
 gi|308916644|gb|EFP62384.1| pseudouridine synthase RluB [Erysipelotrichaceae bacterium 3_1_53]
          Length = 245

 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 67/244 (27%), Positives = 116/244 (47%), Gaps = 5/244 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E +I++ RV VNG  +      V   D IEVDG P+ K ++ 
Sbjct: 2   ERLQKVIAAAGITSRRKAEVLISEGRVAVNGKTVTELGYKVKRGDLIEVDGKPIAKEDKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +      + T+  +   ++    +L     R+ +VGRLD +T GL++LTNDG  A  
Sbjct: 62  YFLMNKPKRTMCTSEDEFGRQTV--VDLIDCEQRIFTVGRLDYDTSGLIILTNDGDFANE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQ--KGSNAWVT 190
           +  P     +VY +  +G +  + +  +K GIV+         +  +  +  + +     
Sbjct: 120 IIHPRYHIPKVYNLTINGILTSEDMKKIKSGIVLDDGIKTLPAKYRITEKDPQKNQCSFD 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + + EG+NR+IK++ E   ++V RL R          L  G  R +    +++       
Sbjct: 180 LTIVEGRNRQIKRMMEALGYEVRRLHRSKLAFLHCSDLRQGEYRVLKPFEVKQLRSLAQK 239

Query: 251 EEAQ 254
            E +
Sbjct: 240 GEMK 243


>gi|258515325|ref|YP_003191547.1| pseudouridine synthase [Desulfotomaculum acetoxidans DSM 771]
 gi|257779030|gb|ACV62924.1| pseudouridine synthase [Desulfotomaculum acetoxidans DSM 771]
          Length = 264

 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 89/235 (37%), Positives = 126/235 (53%), Gaps = 1/235 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
           N   +R+ KV+ARAGIASRR+ E +IA+  VKVNG L++   + V    D I V G  + 
Sbjct: 8   NVQKERLQKVMARAGIASRRKCEELIAEGVVKVNGRLVKEQGIKVDPQKDRIMVQGKIIN 67

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + E     L +KP G VTT  DP+GR T+ D L +I  RV  VGRLD ++EGLLL+TNDG
Sbjct: 68  RLEDKIYLLMYKPRGYVTTLHDPEGRKTIVDLLKNIKERVFPVGRLDYDSEGLLLVTNDG 127

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P  +  + Y V   G      L  + KG+ ++       QV L       + 
Sbjct: 128 ELANALTHPRHEVKKTYLVTVAGIPLPKSLEQMSKGLELEDGMTAPTQVALVELLEDRSL 187

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + + + EGKNR ++++ E     V RL RI  G   +  +  G  R ++ K +RE
Sbjct: 188 LEITVHEGKNRLVRRMCEKIGHPVLRLKRIKLGTLSIKGVKPGQYRLLNTKEIRE 242


>gi|332752067|gb|EGJ82460.1| ribosomal large subunit pseudouridine synthase F [Shigella flexneri
           4343-70]
          Length = 290

 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 62/292 (21%), Positives = 114/292 (39%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDIVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R ++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRYLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++    A        ++     + +  +   R   N  +     ++KK  
Sbjct: 239 SSSEAKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 290


>gi|157163487|ref|YP_001460805.1| 23S rRNA pseudouridine synthase F [Escherichia coli HS]
 gi|300916198|ref|ZP_07132950.1| conserved hypothetical protein [Escherichia coli MS 115-1]
 gi|157069167|gb|ABV08422.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           HS]
 gi|300416478|gb|EFJ99788.1| conserved hypothetical protein [Escherichia coli MS 115-1]
          Length = 290

 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 63/292 (21%), Positives = 116/292 (39%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++V   A        ++     + +  +   R   N  +     ++KK  
Sbjct: 239 SSSEVKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 290


>gi|332799735|ref|YP_004461234.1| pseudouridine synthase Rsu [Tepidanaerobacter sp. Re1]
 gi|332697470|gb|AEE91927.1| pseudouridine synthase Rsu [Tepidanaerobacter sp. Re1]
          Length = 242

 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 55/236 (23%), Positives = 115/236 (48%), Gaps = 2/236 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
           ++  P R+ K++A  G  SR++V+++I   +V +NG+++  A   V  + D I V G  +
Sbjct: 2   KSQKPARIDKILASCGYGSRKDVKKLIKSGQVSINGVIINDAGTLVNPSLDEIIVAGECI 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   + +      + +T+ D +              ++  VGRLD + EGL+ LT+D
Sbjct: 62  FYEDNVYIMMNKPQDVVSSTYDDFETTVIDLLEGEYFHRKLFPVGRLDKDAEGLIFLTDD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +A  L  P  +  + Y V  +G++++  +     G+ ++       ++ +  +  + +
Sbjct: 122 GKMAHRLLSPKNRVPKTYYVEVYGRLNESDVKAFAAGMELEDFTALPAELDILEKNNNIS 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
              V + EGK  +IK++ +    +V  L R+  GP +L   L  G  R+++K+ + 
Sbjct: 182 SAYVTIYEGKFHQIKRMMKARGKEVTYLKRLFLGPLRLDEELEPGMWRKLTKEEVD 237


>gi|254518907|ref|ZP_05130963.1| pseudouridine synthase [Clostridium sp. 7_2_43FAA]
 gi|226912656|gb|EEH97857.1| pseudouridine synthase [Clostridium sp. 7_2_43FAA]
          Length = 242

 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 67/235 (28%), Positives = 118/235 (50%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K +AR G+ASRR+ E +I   +VK+N  ++    V +    D +  +G  +   E 
Sbjct: 3   ERLQKYMARCGVASRRKCEEIILSSKVKINDKVVNELGVKIDPYKDKVFYNGKRILPEEN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G +T+  D  GR T   +L  +  R+  +GRLD ++ GL+LLTNDG +  
Sbjct: 63  KLYIMLNKPEGYITSVKDEKGRKT-ILDLVKVNERIYPIGRLDYDSSGLILLTNDGDIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS------N 186
            +  P  +  + Y     G    +++   + GI I G    + ++ L  ++        N
Sbjct: 122 KIIHPRVEVEKKYIALCKGVFSDEEIKKFENGIDIGGYITANAKIKLIDKEKDKKTNTVN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + V + + EGKNR+I+K+      +V  L R++ G  +LG L  G  R +++  L
Sbjct: 182 SLVEIIIHEGKNRQIRKMCSALGHEVITLKRVAVGDIKLGYLKRGEWRNLTEDEL 236


>gi|315617385|gb|EFU97991.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           3431]
          Length = 290

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 63/292 (21%), Positives = 117/292 (40%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGGRDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     + ++ +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++V   A        ++     + +  +   R   N  +     ++KK  
Sbjct: 239 SSSEVKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 290


>gi|324112367|gb|EGC06345.1| RNA pseudouridylate synthase [Escherichia fergusonii B253]
          Length = 290

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 63/292 (21%), Positives = 116/292 (39%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSIRLNKYISESGICSRREADRFIEQGNVFINGKRAT-IGDQVKPGDVVKVNGRLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKSVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++V   A        ++     + +  +   R   N  +     ++KK  
Sbjct: 239 STSEVKPKAKAKPKTAGIKRPVVKMEKTSEKGGRPASNGKRFTSPGRKKKGR 290


>gi|254517600|ref|ZP_05129656.1| ribosomal large subunit pseudouridine synthase f [Clostridium sp.
           7_2_43FAA]
 gi|226911349|gb|EEH96550.1| ribosomal large subunit pseudouridine synthase f [Clostridium sp.
           7_2_43FAA]
          Length = 258

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 64/265 (24%), Positives = 110/265 (41%), Gaps = 14/265 (5%)

Query: 1   MKDKN-------IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN 53
           MK KN       I  +     R++K I+  G  SRRE +++I   RV V+GI        
Sbjct: 1   MKQKNNEDKFVIIHNDRGPEIRLNKFISETGFCSRREADKLIENGRVTVDGIKA-VMGTK 59

Query: 54  VMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
           V  +  ++VDG  ++K +       +KP+G+  T            +  +   R+  +GR
Sbjct: 60  VKESADVKVDGKSIKKVDELVYIALNKPVGITCTTEKKV--KGNIVDFVNHKKRIFPIGR 117

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LD +++GL+LLTNDG +   +        + Y V     +D+  +  +  G+ I G    
Sbjct: 118 LDKDSQGLILLTNDGDVVNKILRAGNNHEKEYIVTVDKPIDEKFIKSMSSGVKILGTITK 177

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                    K +     + L +G NR+I+++ E   + V +L RI      +  L  G  
Sbjct: 178 KC----IVTKENKNTFRIILTQGMNRQIRRMCEALGYNVVKLNRIRIMNINIERLKIGEW 233

Query: 234 REVSKKILREQLGPHLLEEAQVNLD 258
           R ++ K L+               D
Sbjct: 234 RNLTSKELKGLNNLISNSGKTKEFD 258


>gi|15615835|ref|NP_244139.1| 16S pseudouridylate synthase [Bacillus halodurans C-125]
 gi|10175896|dbj|BAB06992.1| 16S pseudouridylate synthase [Bacillus halodurans C-125]
          Length = 238

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 56/231 (24%), Positives = 97/231 (41%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
            R+ K +A  G  SR++V++++    V+V G  ++  + +V      I V G  +     
Sbjct: 1   MRIDKFLANMGFGSRKDVKKLLKTGAVRVQGQPIKDPSTHVEPESESITVYGEEVEYKPY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  T                       VGRLD +T GLLL+TNDG    
Sbjct: 61  VYLMMNKPKGVICATEDLEHETVIDLLGEEERHYEPSPVGRLDKDTVGLLLITNDGKFNH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + YR    G V ++ +     G+V+          + +  + G+ + + +
Sbjct: 121 WLMSPKHHVPKTYRALVEGHVTEEDVGAFSHGVVLDDGYVTKPATLHIL-EAGARSHIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            L EGK  ++K++F+    +V  L RI  G   L   L  G  RE++K+ +
Sbjct: 180 ILTEGKFHQVKRMFQAVGKRVLELERIKIGNLLLDPELARGEYRELTKEEI 230


>gi|332530537|ref|ZP_08406476.1| pseudouridine synthase [Hylemonella gracilis ATCC 19624]
 gi|332040012|gb|EGI76399.1| pseudouridine synthase [Hylemonella gracilis ATCC 19624]
          Length = 444

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 83/358 (23%), Positives = 134/358 (37%), Gaps = 25/358 (6%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
             K ++Q      ++ KV+A+AG+ SR E+E++I + R+ VN          +   D I+
Sbjct: 71  PSKRVLQPQAETPKLHKVLAQAGMGSRLEMEQLIMEGRISVNNEPA-HIGQRIQFGDQIK 129

Query: 62  VDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           V+G P+R          +  +     +VT     +  +           +  SVGRLD+N
Sbjct: 130 VNGKPIRFRIAPPPARVIAYHKPVGEVVTHDDPQNRPTVFRRLPKLPQGKWQSVGRLDLN 189

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLLL TN G LA  L  P     R Y  R  G +  ++   L  G+ +         +
Sbjct: 190 TEGLLLFTNSGDLANRLMHPRFGLEREYAARVLGALSNEEKQRLLDGVPLDDTKAQFGSI 249

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                +GSN W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E+
Sbjct: 250 EEGGGEGSNLWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMVLPRGLRRGAWMEL 309

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
             + +R  +                                          + +     +
Sbjct: 310 DDRDIRALMQAAGGSVESSE-------------------PGGGTSSRGRPGSGNAGGFKN 350

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              + A    +   A     A G         G + +  + S  +    S  R    K
Sbjct: 351 GNGRPAGAQRQGGAAGKSGKAAGKSGRGAGGQGAQPDPMKTSQGYIGHDSFIRQRQDK 408


>gi|297617939|ref|YP_003703098.1| pseudouridine synthase [Syntrophothermus lipocalidus DSM 12680]
 gi|297145776|gb|ADI02533.1| pseudouridine synthase [Syntrophothermus lipocalidus DSM 12680]
          Length = 249

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 71/238 (29%), Positives = 115/238 (48%), Gaps = 2/238 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+++ +A AGI SRR+ E +I   RVKVNG ++      +    D +E+DG  L + E  
Sbjct: 11  RLARYLAAAGITSRRKAETLIQAGRVKVNGRVVRELGFVINEEKDQVELDGWLLHREEPV 70

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L       + T +D  GR TV D L  +  RV  VGRLD +TEGLLLL+NDG    +
Sbjct: 71  YILLNKPSG-YLCTLADTHGRPTVVDLLRGVTQRVYPVGRLDYDTEGLLLLSNDGDFTHL 129

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  +VY     G V +  +  L+ G++I  +     +V +  ++     + + +
Sbjct: 130 MTHPRFEIEKVYEAWVQGMVSRKAIERLRAGVIIDAVKTAPAKVRVLAKRKDRTLMEIRI 189

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            EG+ R++KK+       V  L R  +G   L  L  G  R ++K  +         +
Sbjct: 190 HEGRKRQVKKMCASVGHPVVALKRTRFGDLTLDGLRPGEFRYLTKDEVEYLQNLAKGQ 247


>gi|237703577|ref|ZP_04534058.1| 23S rRNA pseudouridine synthase F [Escherichia sp. 3_2_53FAA]
 gi|226901489|gb|EEH87748.1| 23S rRNA pseudouridine synthase F [Escherichia sp. 3_2_53FAA]
          Length = 290

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 62/292 (21%), Positives = 114/292 (39%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD + +GL+ LTN G L
Sbjct: 63  ESEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDFQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++    A        ++     + +  +   R   N  +     ++KK  
Sbjct: 239 SSSEAKPKAKAKPKTVGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 290


>gi|209558865|ref|YP_002285337.1| Putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes NZ131]
 gi|209540066|gb|ACI60642.1| Putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes NZ131]
          Length = 240

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 75/241 (31%), Positives = 117/241 (48%), Gaps = 3/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q  V +NG ++   A  V S D +E++G P+   E+ 
Sbjct: 1   MRINKYIAHAGIASRRKAEELIKQGLVTLNGQVIMDLATTVKSGDVVEIEGSPIYNEEKV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      + +   D  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 61  YYLLNKPRGAISSVS-DDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDT 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P  +  +V          +  L  L +GIVI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVIWRVSKVLQRKKNLRPLTRGIVIDGKKTKPARYNIVRVEADKNRSIVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+N ++KK+FE     V++L R   G   L  L  G  R ++KK + +       +
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTRLGTVDLKGLRPGEARRLNKKEISQLHNLANTK 239

Query: 252 E 252
           +
Sbjct: 240 K 240


>gi|227529187|ref|ZP_03959236.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           vaginalis ATCC 49540]
 gi|227350912|gb|EEJ41203.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           vaginalis ATCC 49540]
          Length = 240

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 74/232 (31%), Positives = 115/232 (49%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR  E++IA   V+VNG  +    + V   D + VDGVPL +    
Sbjct: 2   ERLQKVMAEAGVASRRASEKLIASGHVQVNGKTVTEMGIKVSEHDEVVVDGVPLHREAHV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
              L      + + H D   R+ V          RV  VGRLD +T G+LLLTNDG LA 
Sbjct: 62  YYLLNKPRSVITSAHDDKGRRTVVDILKEEGVAERVYPVGRLDYDTTGILLLTNDGELAN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVT 190
            L  P  +  + Y  +  G V+ + L  L+ G+ + G      +  L         + V 
Sbjct: 122 RLMHPKFEVEKTYIAKVRGIVNNNDLKQLRIGVEVNGRLTKKAKSRLIETDHKKQTSLVK 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + + EG+  ++K +F+  +  V +L R +YGP  L  L +G  RE+ +  ++
Sbjct: 182 LTIHEGRYHQVKLMFDAIHHPVIKLHRETYGPLDLNGLQSGEFRELKQDEVK 233


>gi|218551308|ref|YP_002385100.1| 23S rRNA pseudouridine synthase F [Escherichia fergusonii ATCC
           35469]
 gi|218358850|emb|CAQ91507.1| 23S rRNA pseudouridine synthase [Escherichia fergusonii ATCC 35469]
 gi|325499580|gb|EGC97439.1| 23S rRNA pseudouridine synthase F [Escherichia fergusonii ECD227]
          Length = 290

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 63/292 (21%), Positives = 116/292 (39%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSIRLNKYISESGICSRREADRFIEQGNVFINGKRAT-IGDQVKPGDVVKVNGRLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++V   A        ++     + +  +   R   N  +     ++KK  
Sbjct: 239 STSEVKPKAKAKPKTAGIKRPVVKMEKTSEKGGRPASNGKRFTSPGRKKKGR 290


>gi|119478215|ref|ZP_01618271.1| putative pseudouridine synthase [marine gamma proteobacterium
           HTCC2143]
 gi|119448724|gb|EAW29968.1| putative pseudouridine synthase [marine gamma proteobacterium
           HTCC2143]
          Length = 307

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 65/311 (20%), Positives = 120/311 (38%), Gaps = 8/311 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T  R++K I+ +GI SRRE +R + +  V +NG   +     V + D ++V+G  +   +
Sbjct: 5   TTTRLNKYISESGICSRREADRFVEKGSVFINGKRAKV-GDQVSAGDTVKVNGQIIDPRD 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             RL L      +    +          +  +   R+  +GRLD +++GL+ LTN+G L 
Sbjct: 64  EERLVLIALNKPVGVVCTTEGSEKNNIVDYVNHGERIFPIGRLDKDSQGLIFLTNNGDLV 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +     +  + Y V     +    +  + KG+ I G      ++     K +     +
Sbjct: 124 NKILRAGNRHEKEYLVTVDKPITDTFIRDMAKGVPILGEVTRKCKIV----KETPTLFRI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ + F + + RL R+      +  L  G  R+ S+  L   L      
Sbjct: 180 TLVQGLNRQIRRMCDHFGYDIVRLERVRIMNVSMKGLGVGEWRDFSQNELAGILESTADS 239

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           ++     AP    +           E P      +K S      +K    +     R   
Sbjct: 240 QSAA---APSKKRKPAKTGDRPWYPEKPKSAYSSRKKSPSGTPKAKNGGASGDKPSRPPK 296

Query: 312 SNVWMAKGIHS 322
           S V        
Sbjct: 297 SGVAGRTKKRR 307


>gi|325684334|gb|EGD26503.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 241

 Score =  179 bits (453), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 99/231 (42%), Gaps = 4/231 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR +V  +I   +V VNG +   A   V     + V+G  +   +   
Sbjct: 3   RLDKFLANMKVGSRSQVHEIIKAGQVTVNGKVCRSAKQKVKEDAEVLVNGQAVIYQQYHY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             L      L  T                 + ++  VGRLD +T GLLLLTNDG LA  L
Sbjct: 63  FLLNKPAGVLSATEDSRQKTVLDLLKDQDRYQKIAPVGRLDKDTTGLLLLTNDGQLAHQL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGD--MQVTLDTQKGSNAWVTV 191
             P     + Y     G  D++    +  G+ ++         +++    +    + + +
Sbjct: 123 LAPEYHVPKTYYALLAGVADEETAKAIAAGLTLKDGTELKPGQLKILRQDKDQEQSEIEI 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            + EGK  ++K++F     KV +L R+S GP  L   L  GS R ++++ +
Sbjct: 183 TITEGKYHQVKRMFASQGMKVLKLKRLSMGPLTLPADLALGSYRPLTEEEM 233


>gi|167635583|ref|ZP_02393895.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0442]
 gi|170688259|ref|ZP_02879469.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0465]
 gi|254686959|ref|ZP_05150817.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           CNEVA-9066]
 gi|254741694|ref|ZP_05199381.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           Kruger B]
 gi|167529003|gb|EDR91758.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0442]
 gi|170667765|gb|EDT18518.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0465]
          Length = 229

 Score =  179 bits (453), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 62/234 (26%), Positives = 110/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEANSCSRRETDRLIKAGRVAINGEICTH-GALVNEGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T ++    + +     +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAAEHIEGNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKSFTDWFINEMSSGVKIKDGITKPCKVTRV----DKSTCRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>gi|303242956|ref|ZP_07329414.1| pseudouridine synthase [Acetivibrio cellulolyticus CD2]
 gi|302589505|gb|EFL59295.1| pseudouridine synthase [Acetivibrio cellulolyticus CD2]
          Length = 250

 Score =  179 bits (453), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 64/233 (27%), Positives = 113/233 (48%), Gaps = 4/233 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
             QRV ++++  G  +RRE+++++    VKV+G +++ + ++V   T  IE+ G  L   
Sbjct: 3   ETQRVDRILSNFGFGTRREIKQLVKNGEVKVDGEVIKDSGMHVDPKTSKIEISGQVLNYR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   + +      +  T  +                    VGRLDI+TEGLLL+TNDG L
Sbjct: 63  QFIYVMMNKPAGVISATFDNRHETVVDILPEEYKCFDPFPVGRLDIDTEGLLLMTNDGQL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y     G+V    + + ++GI++         ++ +  ++G ++ V
Sbjct: 123 AHELLSPRKHVPKKYFAYIEGEVSAGDVKMFEEGILLDDGYKTLPAELHIL-EQGESSSV 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            V + EGK  ++K++FE    KV  L RI+ G   L   L  G  RE+++  L
Sbjct: 182 EVIIFEGKFHQVKRMFEAVGKKVKYLKRITMGNLVLDEALATGECRELTENEL 234


>gi|228475940|ref|ZP_04060649.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           hominis SK119]
 gi|228270011|gb|EEK11485.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           hominis SK119]
          Length = 228

 Score =  179 bits (453), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 99/231 (42%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K ++  G+ +R EV++++ +  VKVN  + +     V    D I VDG  +     
Sbjct: 1   MRLDKFLSNMGVGTRTEVKQLLKKNSVKVNDKVEKSPKSQVDPEQDEITVDGKIIEYINH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + +   D   ++ +          +  VGRLD +TEGLLL+TNDG    
Sbjct: 61  VYIMLNKPKGYV-SATYDDINQTVIDLIADYRHLDLFPVGRLDKDTEGLLLITNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS    + Y+V     +  + +   K GI +        Q+       S     V 
Sbjct: 120 NLMSPSKHVSKTYKVTSKYPIKNEDIIAFKNGIELSDGKVKPAQLEKLDHNVS----LVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + EGK  ++K++F   + +V  L R+      L   L +G  R ++ + L+
Sbjct: 176 IYEGKYHQVKRMFHSIDNEVLELKRLKISNLTLDENLKSGEYRLLTSEELK 226


>gi|319951787|ref|YP_004163054.1| ribosomal large subunit pseudouridine synthase f [Cellulophaga
           algicola DSM 14237]
 gi|319420447|gb|ADV47556.1| ribosomal large subunit pseudouridine synthase F [Cellulophaga
           algicola DSM 14237]
          Length = 243

 Score =  179 bits (453), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 56/248 (22%), Positives = 106/248 (42%), Gaps = 6/248 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
            + TP R++K ++  G  SRR  +++I Q RV +NG +       + + D I VDG  + 
Sbjct: 2   SDTTPTRINKYLSEVGYCSRRAADKLIDQGRVTINGKVP-EMGTKITAADEIRVDGELIG 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           K +    +L       +   +D         +  +   R+  +GRLD  +EGL+ LT+DG
Sbjct: 61  KPKGKHTYLAFNKPVGIVCTTDTGVEKDNIIDFINYPKRIFPIGRLDKPSEGLIFLTDDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y V  +  ++ D L  +  G+ I        +V           
Sbjct: 121 DIVNKILRARNNHEKEYIVSVNKPINSDFLRQMSSGVPILDTVTRPCKVERI----DKYT 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            ++ L +G NR+I+++ +   ++V RL R+     +L  L  G  R++++  L E     
Sbjct: 177 FSIILTQGLNRQIRRMCDHLEYRVKRLQRVRIMNVEL-DLEVGKYRDLTEAELSEINRLV 235

Query: 249 LLEEAQVN 256
                  +
Sbjct: 236 EASAKTHD 243


>gi|167464456|ref|ZP_02329545.1| pseudouridine synthase [Paenibacillus larvae subsp. larvae
           BRL-230010]
          Length = 250

 Score =  179 bits (453), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 116/242 (47%), Gaps = 7/242 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
              R+ K+++  G  +R E++++     V VNG +++ +   V    D+IEV+G  +   
Sbjct: 3   ETLRLDKMLSHLGYGTRSELKKLAKNGGVTVNGKVVKDSGWKVYPDEDYIEVNGEQVIFR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   + L      +  T    D       +       V  VGRLD +TEGLLLLTNDG L
Sbjct: 63  EHVYVLLNKPAGVISATEDMRDRTVVDLLDDHIRVFGVFPVGRLDKDTEGLLLLTNDGKL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLD----TQKGS 185
           A  L  P     + Y  R +G V ++ + +  +G+V+         Q+ +      ++  
Sbjct: 123 AHNLLSPRKHVPKTYYARVNGDVTEEDVRIFSEGVVLDDGYMTMPAQLVVLDSGNPEEEK 182

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            A + + + EGK  ++K++FE  + KV  L RIS G  +L  +L  G++RE++ K L   
Sbjct: 183 PAEIELTIHEGKFHQVKRMFEAVHKKVVYLKRISMGSLKLDPSLSPGASRELTAKELEAL 242

Query: 245 LG 246
            G
Sbjct: 243 QG 244


>gi|126663357|ref|ZP_01734355.1| ribosomal large subunit pseudouridine synthase F [Flavobacteria
           bacterium BAL38]
 gi|126625015|gb|EAZ95705.1| ribosomal large subunit pseudouridine synthase F [Flavobacteria
           bacterium BAL38]
          Length = 262

 Score =  179 bits (453), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 58/272 (21%), Positives = 114/272 (41%), Gaps = 11/272 (4%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           ++EN T  R++K ++  G  SRRE +R+I Q RV +NG +       V  +D + V+G  
Sbjct: 1   MEENAT--RINKFLSETGFCSRREADRLIEQGRVTINGKVP-EMGTKVTPSDEVRVNGKL 57

Query: 67  LRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +++  E+     ++KP G+  T +          +  +   R+  +GRLD  +EGL+ +T
Sbjct: 58  IQERTEKPIYLAFNKPAGIECTTNL--DVRDNIIDFINYPERIFPIGRLDKASEGLIFMT 115

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +   +        + Y V  +  +    ++ +  GI I        +     ++ S
Sbjct: 116 NDGDIVNKILRARNNHEKEYIVTVNHPITDRFIDRMANGIPILETITKKCK----VEQIS 171

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++ E+ +++V  L R       L  +  G  R ++   + E  
Sbjct: 172 KFVFRIILTQGLNRQIRRMCEYLDYEVTALKRTRIINISL-DVAEGKYRNLTDAEVAELN 230

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISE 277
                         P    +   +      + 
Sbjct: 231 KLIEPSSKTEEASLPSNKGKFTGKRNYGERNR 262


>gi|20806585|ref|NP_621756.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Thermoanaerobacter tengcongensis MB4]
 gi|254478969|ref|ZP_05092328.1| conserved hypothetical protein, putative [Carboxydibrachium
           pacificum DSM 12653]
 gi|20515028|gb|AAM23360.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           Pseudouridylate synthase [Thermoanaerobacter
           tengcongensis MB4]
 gi|214035085|gb|EEB75800.1| conserved hypothetical protein, putative [Carboxydibrachium
           pacificum DSM 12653]
          Length = 240

 Score =  179 bits (453), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 110/231 (47%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K+++  GI +R+EV++ I    V+VNG ++   +  V    D +  DG  +   E 
Sbjct: 4   MRLDKLLSNMGIGTRKEVKKYIKDGLVEVNGEIVLDPSKTVDTEKDEVLFDGEKVEYKEF 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      +  TH   +              +V  VGRLD +TEGLL++TNDG LA 
Sbjct: 64  IYVMMNKPQGVISATHDKSEETVIDLLPEEIALRKVFPVGRLDKDTEGLLIITNDGELAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P  + ++ Y     G++ +      K+G++++        Q+ +  +    + V V
Sbjct: 124 KLLSPKKKVVKKYYAEVLGKITEKDAEKFKEGVILEDGYRTMPSQLEII-ESSDISKVYV 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            L EGK  ++K++FE    KV  L R+  G  QL   L  G  RE++++ +
Sbjct: 183 YLTEGKYHQVKRMFEAIGKKVLYLKRLCMGKLQLDENLEPGEWRELTEEEV 233


>gi|193063125|ref|ZP_03044217.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           E22]
 gi|193067850|ref|ZP_03048816.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           E110019]
 gi|194426901|ref|ZP_03059454.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           B171]
 gi|260846816|ref|YP_003224594.1| 23S rRNA pseudouridine synthase [Escherichia coli O103:H2 str.
           12009]
 gi|192931384|gb|EDV83986.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           E22]
 gi|192958825|gb|EDV89262.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           E110019]
 gi|194415237|gb|EDX31506.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           B171]
 gi|257761963|dbj|BAI33460.1| 23S rRNA pseudouridine synthase [Escherichia coli O103:H2 str.
           12009]
 gi|323161320|gb|EFZ47228.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           E128010]
          Length = 290

 Score =  179 bits (453), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 61/292 (20%), Positives = 114/292 (39%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++             ++     + +  +   R   N  +     ++KK  
Sbjct: 239 SSSEAKPKVKAKPKTAGIKRPLVKMEKTSEKGGRPASNGKRFTSPGRKKKGR 290


>gi|328952678|ref|YP_004370012.1| pseudouridine synthase Rsu [Desulfobacca acetoxidans DSM 11109]
 gi|328453002|gb|AEB08831.1| pseudouridine synthase Rsu [Desulfobacca acetoxidans DSM 11109]
          Length = 242

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 83/240 (34%), Positives = 122/240 (50%), Gaps = 1/240 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA 70
           T +R+ K +ARAG+ASRR+ E +I   RV V+G ++      +      + VDG  +   
Sbjct: 2   TKERLQKYLARAGVASRRQGEELIRAGRVSVDGRIVTTLGQLIDSEKAEVMVDGRKVLPP 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              R  + +KP G VTT +DP GR  V D LP    R+  VGRLD +  GLLLLTNDG L
Sbjct: 62  PHCRTIVLNKPYGCVTTMADPQGRRKVIDLLPDQEERLYPVGRLDYDATGLLLLTNDGEL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P  +  + YR    GQ        L++GI + G      QV L       + + 
Sbjct: 122 AHRLMHPRYKVAKTYRATVAGQFSPAARRRLREGITLDGRLTIPEQVRLVKTSSERSVLE 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + +REG+   +K++       V +L RI+YGP +LG L  G+ RE++++ +R        
Sbjct: 182 LTIREGRYHLVKRLCAAVGCPVLKLKRIAYGPLRLGRLALGTWRELTQEEVRRLKEAVNC 241


>gi|323340736|ref|ZP_08080988.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           ruminis ATCC 25644]
 gi|323091859|gb|EFZ34479.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           ruminis ATCC 25644]
          Length = 261

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 81/259 (31%), Positives = 137/259 (52%), Gaps = 6/259 (2%)

Query: 1   MKD---KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           MK+   KN  +++    R+ K +A AG+ASRR  E++I + RVKVNG++++     V   
Sbjct: 1   MKNCTRKNNKEDHMAEVRLQKAMADAGVASRRASEKLILEGRVKVNGVVVKELGTKVKGD 60

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           D IEV+G  + +      +L++KP G+++   D  GR  V D      +R+  +GRLD +
Sbjct: 61  DAIEVNGTLIERERNKVYYLFYKPRGVISAVKDDKGRRVVTDYFEGEKNRIYPIGRLDYD 120

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY---GD 174
           T G+LLLTNDG LA +L  P  +  + Y  +  G V  D L  L+KG+ ++   Y     
Sbjct: 121 TSGILLLTNDGELANLLMHPRYKVDKTYVAKVEGLVQSDDLKRLRKGVKMKDGHYSARAK 180

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +V    +  +++ V++ + EG+N ++K +FE     V +L R +Y    L  L++G  R
Sbjct: 181 AKVISSDRAKNHSIVSLTIHEGRNHQVKNMFEAIGHPVMKLKRETYDFLTLKGLVSGQYR 240

Query: 235 EVSKKILREQLGPHLLEEA 253
           E+S + ++           
Sbjct: 241 ELSNEEVKTLYENARKNSK 259


>gi|323975348|gb|EGB70451.1| RNA pseudouridylate synthase [Escherichia coli TW10509]
          Length = 290

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 63/292 (21%), Positives = 116/292 (39%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++V   A        ++     + +  +   R   N  +     ++KK  
Sbjct: 239 STSEVKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 290


>gi|206901970|ref|YP_002251612.1| ribosomal small subunit pseudouridine synthase A [Dictyoglomus
           thermophilum H-6-12]
 gi|206741073|gb|ACI20131.1| ribosomal small subunit pseudouridine synthase A [Dictyoglomus
           thermophilum H-6-12]
          Length = 242

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 55/226 (24%), Positives = 96/226 (42%), Gaps = 5/226 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G  SR+EV+++I    V VN + ++  + ++    D +E++G  +   E 
Sbjct: 1   MRLDKFLVNQGFGSRKEVQKLIKAGIVYVNDVPVKDPSFHIDPNTDVVEIEGQEVEYKEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T+ +         +   I +++  +GRLDI+TEGLL++T+DG LA 
Sbjct: 61  YYFMLNKPKGYITATYDENYPTVMDLFSAEPIVNKLFPIGRLDIDTEGLLIITSDGVLAH 120

Query: 133 VLELPSTQWLRVYRVRFH---GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            L  P     + Y V        +D  K       +          +V +       + +
Sbjct: 121 RLSHPKWNVEKEYFVIVEGDVSDIDFSKYEKEGIYLKKDKYKTKPFKVNVLKTSFEESEL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
            + + EGK   IKK+    + +V  L R+  GP  L   L  G  R
Sbjct: 181 LITITEGKYHIIKKIMYALDHEVKYLKRVRIGPLTLDEDLDVGEYR 226


>gi|49187441|ref|YP_030693.1| RNA pseudouridylate synthase [Bacillus anthracis str. Sterne]
 gi|65321917|ref|ZP_00394876.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Bacillus anthracis str.
           A2012]
 gi|165871506|ref|ZP_02216153.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0488]
 gi|167641580|ref|ZP_02399827.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0193]
 gi|170708716|ref|ZP_02899154.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0389]
 gi|177653142|ref|ZP_02935429.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0174]
 gi|190566866|ref|ZP_03019782.1| RNA pseudouridine synthase family protein [Bacillus anthracis
           Tsiankovskii-I]
 gi|227817333|ref|YP_002817342.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           CDC 684]
 gi|229602926|ref|YP_002868829.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0248]
 gi|254736656|ref|ZP_05194362.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           Western North America USA6153]
 gi|254754709|ref|ZP_05206744.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           Vollum]
 gi|254757541|ref|ZP_05209568.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           Australia 94]
 gi|270000607|ref|YP_003329046.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           Ames]
 gi|291612223|ref|YP_003541037.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           'Ames Ancestor']
 gi|49181368|gb|AAT56744.1| RNA pseudouridylate synthase [Bacillus anthracis str. Sterne]
 gi|164712803|gb|EDR18333.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0488]
 gi|167510465|gb|EDR85864.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0193]
 gi|170126396|gb|EDS95285.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0389]
 gi|172081666|gb|EDT66737.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0174]
 gi|190561857|gb|EDV15826.1| RNA pseudouridine synthase family protein [Bacillus anthracis
           Tsiankovskii-I]
 gi|224552862|gb|ACN55071.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           'Ames Ancestor']
 gi|227003424|gb|ACP13167.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           CDC 684]
 gi|229267334|gb|ACQ48971.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0248]
 gi|269850265|gb|ACZ49990.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           Ames]
          Length = 229

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 62/234 (26%), Positives = 110/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEANSCSRRETDRLIKAGRVAINGEICTH-GALVNEGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T ++    + +     +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAAEHIEGNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGITKPCKVTRV----DKSTCRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>gi|241889716|ref|ZP_04777014.1| ribosomal large subunit pseudouridine synthase B [Gemella
           haemolysans ATCC 10379]
 gi|241863338|gb|EER67722.1| ribosomal large subunit pseudouridine synthase B [Gemella
           haemolysans ATCC 10379]
          Length = 243

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 72/242 (29%), Positives = 129/242 (53%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+IA +G  SRR+ E++I   +V VNG +++   V    +D I V+GV L   E  
Sbjct: 3   ERLQKLIAASGYTSRRKAEQLILDGKVSVNGEVVKELGVKAEPSDIIIVEGVRL-LKENK 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP  ++T+ SD   R+ V D   ++  RV+ VGRLD +T G L+++NDG    +
Sbjct: 62  RYYLFYKPEKVITSMSDEKDRTCVKDFFENVNERVVPVGRLDYDTSGALIMSNDGEFINL 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  + Y  + +G+++ + L +L+ G+ I        +V +   K    N  V +
Sbjct: 122 ITHPKHKIKKTYVAKINGKLEDNHLRILRNGVRIDNYKTAKAEVNVVKNKNKSGNTLVRL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EGKNR+++++FE   ++V +L R S     L  L  G  R ++   ++  +      
Sbjct: 182 TIHEGKNRQVRRMFEALGYEVIKLKRESIEDLTLEGLKKGEYRPLTIHEVKRLINKAKNG 241

Query: 252 EA 253
           E 
Sbjct: 242 EK 243


>gi|322384180|ref|ZP_08057890.1| 16S pseudouridylate synthase-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321151072|gb|EFX44389.1| 16S pseudouridylate synthase-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 256

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 69/239 (28%), Positives = 116/239 (48%), Gaps = 7/239 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K+++  G  +R E++++     V VNG +++ +   V    D+IEV+G  +   E  
Sbjct: 12  RLDKMLSHLGYGTRSELKKLAKNGGVTVNGKVVKDSGWKVYPDEDYIEVNGEQVIFREHV 71

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L      +  T    D       +       V  VGRLD +TEGLLLLTNDG LA  
Sbjct: 72  YVLLNKPAGVISATEDMRDRTVVDLLDDHIRVFGVFPVGRLDKDTEGLLLLTNDGKLAHN 131

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLD----TQKGSNAW 188
           L  P     + Y  R +G V ++ + +  +G+V+         Q+ +      ++   A 
Sbjct: 132 LLSPRKHVPKTYYARVNGDVTEEDVRIFSEGVVLDDGYMTMPAQLVVLDSGNPEEEKPAE 191

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           + + + EGK  ++K++FE  + KV  L RIS G  +L  +L  G++RE++ K L    G
Sbjct: 192 IELTIHEGKFHQVKRMFEAVHKKVVYLKRISMGSLKLDPSLSPGASRELTAKELEALQG 250


>gi|288556014|ref|YP_003427949.1| pseudouridylate synthase [Bacillus pseudofirmus OF4]
 gi|288547174|gb|ADC51057.1| pseudouridylate synthase [Bacillus pseudofirmus OF4]
          Length = 242

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 73/243 (30%), Positives = 119/243 (48%), Gaps = 5/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KVIA+AGI SRR+ E MI + +VKVNG ++    V V    D IEV+GVP+ K E 
Sbjct: 2   ERLQKVIAQAGITSRRKAETMITEGKVKVNGQVVRELGVKVNPNKDEIEVEGVPIDKEEP 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +Y     + +   +   +         I  RV  +GRLD +T GL+LLTNDG  A 
Sbjct: 62  VYYLMYKPQGVISSVKDEKGRKVVTDFL--EIEQRVFPIGRLDYDTSGLILLTNDGEFAN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW--VT 190
            L  P  +  +VY  +  G   ++ L  L+ G+V++       +V L +         V 
Sbjct: 120 QLMHPKFKIDKVYVAKVKGIPARESLKKLQHGVVLEDGKTAPAKVKLVSMDKKKQTAIVQ 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + + EG+NR+++++FE     V +L R  Y    L ++  G  R +    ++      + 
Sbjct: 180 LTIHEGRNRQVRRMFEAIGHPVMKLKREQYSFLNLRSMNPGDVRPLKPIEVKHLRELAVT 239

Query: 251 EEA 253
           + +
Sbjct: 240 KPS 242


>gi|333030055|ref|ZP_08458116.1| pseudouridine synthase Rsu [Bacteroides coprosuis DSM 18011]
 gi|332740652|gb|EGJ71134.1| pseudouridine synthase Rsu [Bacteroides coprosuis DSM 18011]
          Length = 321

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 67/325 (20%), Positives = 132/325 (40%), Gaps = 7/325 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +G  SRRE +++I   +VKVNG         V     + V+G  +       
Sbjct: 4   RLNKYISNSGYCSRREADKLIEAGQVKVNGKKA-SIGDRVYPKQKVTVNGELIVNDIEPV 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
              ++KP+G+V+T    +  + V     S   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 63  YIAFNKPVGIVSTTDPNEKANIVKYI--SHEQRIFPIGRLDKDSQGLILLTNDGDIVNKI 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   +VY V+    +  + +  +K G+ I        +V    +K +     + L 
Sbjct: 121 LRAGNNHKKVYIVQVDKPITDEFIEKMKTGVPILDRVTRKCEV----EKINPYTFKIELI 176

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++  +F+++V +L R      +L  L  GS R+++   L             
Sbjct: 177 QGLNRQIRRMCAYFDYEVLKLERTQIMNIELEGLGLGSWRDLNPGELEVLFDMLEDSNKH 236

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
           V+      S++++ +    +  +     + +   +       K++  A      +     
Sbjct: 237 VDDKGRSVSNKSINKQLELLDIQTDFRKSGLNAKNRAATKNRKRQSPAQASSGTSSFKPK 296

Query: 315 WMAKGIHSSFLSDSGQREENHRRSP 339
               G        S       R   
Sbjct: 297 KTGSGPRIGKQKASKVSHRGSRNKR 321


>gi|291544370|emb|CBL17479.1| ribosomal large subunit pseudouridine synthase B [Ruminococcus sp.
           18P13]
          Length = 242

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 87/234 (37%), Positives = 125/234 (53%), Gaps = 3/234 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--RK 69
              R+ K+IA +G  SRR+ E  IA  +VK NG  ++       S D I V+G  +   K
Sbjct: 2   EKTRIQKIIADSGYCSRRKAESFIAAGQVKCNGRPVK-LGDKAGSRDLITVNGERIAIPK 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ++    + +KP G VTT SD   R  V D L  +  RV  VGRLD N+EGLLLLTNDG 
Sbjct: 61  KKQKLYLMLNKPRGYVTTMSDELDRRCVMDLLEDVPERVYPVGRLDRNSEGLLLLTNDGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  PS    + YRV     +   +L  L +G+ I G       V + T++     +
Sbjct: 121 FANSIMHPSRHVSKTYRVTVRPDITDQQLVQLSEGVEIDGKPTLPATVNVLTKEPGRVVL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + +REG+NR+I+++ E    +V RL RIS GP +LG L  G+ RE++ + LR 
Sbjct: 181 LITIREGRNRQIRRMCEAVGLEVARLRRISIGPLKLGMLKPGTYRELTAEELRA 234


>gi|260858132|ref|YP_003232023.1| 23S rRNA pseudouridine synthase [Escherichia coli O26:H11 str.
           11368]
 gi|260870735|ref|YP_003237137.1| 23S rRNA pseudouridine synthase [Escherichia coli O111:H- str.
           11128]
 gi|257756781|dbj|BAI28283.1| 23S rRNA pseudouridine synthase [Escherichia coli O26:H11 str.
           11368]
 gi|257767091|dbj|BAI38586.1| 23S rRNA pseudouridine synthase [Escherichia coli O111:H- str.
           11128]
 gi|323155588|gb|EFZ41764.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           EPECa14]
 gi|323174457|gb|EFZ60082.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           LT-68]
 gi|323177584|gb|EFZ63169.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           1180]
          Length = 290

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 63/292 (21%), Positives = 116/292 (39%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDIVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++V   A        ++     + +  +   R   N  +     ++KK  
Sbjct: 239 SSSEVKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 290


>gi|125625272|ref|YP_001033755.1| ribosomal small subunit pseudouridine synthase A [Lactococcus
           lactis subsp. cremoris MG1363]
 gi|124494080|emb|CAL99081.1| ribosomal small subunit pseudouridine synthase A [Lactococcus
           lactis subsp. cremoris MG1363]
          Length = 328

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 63/242 (26%), Positives = 102/242 (42%), Gaps = 9/242 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRK 69
               R+ K +A +G+ SR EV+ ++ + RV V G +       V      +  DG  L  
Sbjct: 84  NKGMRLDKFLAESGLGSRSEVKVLLKKGRVTVAGEIQRDGRFQVDKNSRQVAFDGQILDY 143

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E     L      +  T  +         +       +  VGRLD NTEGLL+LTNDG 
Sbjct: 144 QEYYYYLLNKPQGVVSATKDNVFKTVVQLLSEKDFRKDIFPVGRLDKNTEGLLILTNDGA 203

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT------Q 182
           L   L  P     + Y  R  G+V  + +N   +G+ ++ G      ++ ++       Q
Sbjct: 204 LGHDLTQPKKHVEKEYFARIDGKVTDEIINKFAEGLTLKNGEKARPGELFVEKTYKGDSQ 263

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            G  + + V + EGK  ++K++FE     V  L RI  G   L   L  G+ R ++ + +
Sbjct: 264 SGWVSEIRVIIHEGKFHQVKRMFEAVEMYVLYLKRIRMGNLALDSDLALGAYRPLTIEEI 323

Query: 242 RE 243
             
Sbjct: 324 EN 325


>gi|15804615|ref|NP_290656.1| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H7 EDL933]
 gi|15834259|ref|NP_313032.1| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H7 str.
           Sakai]
 gi|168750850|ref|ZP_02775872.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4113]
 gi|168755170|ref|ZP_02780177.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4401]
 gi|168760865|ref|ZP_02785872.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4501]
 gi|168766260|ref|ZP_02791267.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4486]
 gi|168774357|ref|ZP_02799364.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4196]
 gi|168780412|ref|ZP_02805419.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4076]
 gi|168784615|ref|ZP_02809622.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC869]
 gi|168798338|ref|ZP_02823345.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC508]
 gi|195935788|ref|ZP_03081170.1| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H7 str.
           EC4024]
 gi|208808749|ref|ZP_03251086.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4206]
 gi|208811969|ref|ZP_03253298.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4045]
 gi|208821132|ref|ZP_03261452.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4042]
 gi|209400390|ref|YP_002273541.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4115]
 gi|209921498|ref|YP_002295582.1| 23S rRNA pseudouridine synthase F [Escherichia coli SE11]
 gi|217325648|ref|ZP_03441732.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. TW14588]
 gi|254796022|ref|YP_003080859.1| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H7 str.
           TW14359]
 gi|261223462|ref|ZP_05937743.1| 23S rRNA pseudouridine synthase [Escherichia coli O157:H7 str.
           FRIK2000]
 gi|261256997|ref|ZP_05949530.1| 23S rRNA pseudouridine synthase [Escherichia coli O157:H7 str.
           FRIK966]
 gi|291285439|ref|YP_003502257.1| Ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O55:H7 str. CB9615]
 gi|293417527|ref|ZP_06660149.1| 23S rRNA pseudouridine synthase F [Escherichia coli B185]
 gi|331655840|ref|ZP_08356828.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli M718]
 gi|34098615|sp|Q8X4L9|RLUF_ECO57 RecName: Full=Ribosomal large subunit pseudouridine synthase F;
           AltName: Full=rRNA pseudouridylate synthase F; AltName:
           Full=rRNA-uridine isomerase F
 gi|12518965|gb|AAG59221.1|AE005635_1 orf, hypothetical protein [Escherichia coli O157:H7 str. EDL933]
 gi|13364481|dbj|BAB38428.1| hypothetical protein [Escherichia coli O157:H7 str. Sakai]
 gi|187769953|gb|EDU33797.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4196]
 gi|188015005|gb|EDU53127.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4113]
 gi|189001699|gb|EDU70685.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4076]
 gi|189357499|gb|EDU75918.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4401]
 gi|189364343|gb|EDU82762.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4486]
 gi|189368503|gb|EDU86919.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4501]
 gi|189374896|gb|EDU93312.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC869]
 gi|189379218|gb|EDU97634.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC508]
 gi|208728550|gb|EDZ78151.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4206]
 gi|208733246|gb|EDZ81933.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4045]
 gi|208741255|gb|EDZ88937.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4042]
 gi|209161790|gb|ACI39223.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4115]
 gi|209751528|gb|ACI74071.1| hypothetical protein ECs5005 [Escherichia coli]
 gi|209751530|gb|ACI74072.1| hypothetical protein ECs5005 [Escherichia coli]
 gi|209751532|gb|ACI74073.1| hypothetical protein ECs5005 [Escherichia coli]
 gi|209751534|gb|ACI74074.1| hypothetical protein ECs5005 [Escherichia coli]
 gi|209751536|gb|ACI74075.1| hypothetical protein ECs5005 [Escherichia coli]
 gi|209914757|dbj|BAG79831.1| putative pseudouridine synthase [Escherichia coli SE11]
 gi|217321869|gb|EEC30293.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. TW14588]
 gi|254595422|gb|ACT74783.1| 23S rRNA pseudouridine synthase [Escherichia coli O157:H7 str.
           TW14359]
 gi|290765312|gb|ADD59273.1| Ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O55:H7 str. CB9615]
 gi|291430245|gb|EFF03243.1| 23S rRNA pseudouridine synthase F [Escherichia coli B185]
 gi|320190877|gb|EFW65527.1| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H7 str.
           EC1212]
 gi|320638776|gb|EFX08422.1| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H7 str.
           G5101]
 gi|320644144|gb|EFX13209.1| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H- str.
           493-89]
 gi|320649463|gb|EFX17987.1| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H- str. H
           2687]
 gi|320654859|gb|EFX22820.1| 23S rRNA pseudouridine synthase F [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320660707|gb|EFX28164.1| 23S rRNA pseudouridine synthase F [Escherichia coli O55:H7 str.
           USDA 5905]
 gi|320665636|gb|EFX32673.1| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H7 str.
           LSU-61]
 gi|324017076|gb|EGB86295.1| hypothetical protein HMPREF9542_04288 [Escherichia coli MS 117-3]
 gi|326340567|gb|EGD64365.1| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H7 str.
           1125]
 gi|326342524|gb|EGD66299.1| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H7 str.
           1044]
 gi|331046194|gb|EGI18284.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli M718]
          Length = 290

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 62/292 (21%), Positives = 115/292 (39%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++    A        ++     + +  +   R   N  +     ++KK  
Sbjct: 239 SSSEAKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 290


>gi|157156860|ref|YP_001465515.1| 23S rRNA pseudouridine synthase F [Escherichia coli E24377A]
 gi|170021980|ref|YP_001726934.1| 23S rRNA pseudouridine synthase F [Escherichia coli ATCC 8739]
 gi|188492339|ref|ZP_02999609.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           53638]
 gi|191167475|ref|ZP_03029289.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           B7A]
 gi|218556572|ref|YP_002389486.1| 23S rRNA pseudouridine synthase F [Escherichia coli IAI1]
 gi|218697724|ref|YP_002405391.1| 23S rRNA pseudouridine synthase F [Escherichia coli 55989]
 gi|293476325|ref|ZP_06664733.1| 23S rRNA pseudouridine synthase F [Escherichia coli B088]
 gi|300817929|ref|ZP_07098142.1| conserved hypothetical protein [Escherichia coli MS 107-1]
 gi|300823552|ref|ZP_07103680.1| conserved hypothetical protein [Escherichia coli MS 119-7]
 gi|300924275|ref|ZP_07140255.1| hypothetical protein HMPREF9548_02431 [Escherichia coli MS 182-1]
 gi|301330618|ref|ZP_07223223.1| conserved hypothetical protein [Escherichia coli MS 78-1]
 gi|307312141|ref|ZP_07591778.1| pseudouridine synthase [Escherichia coli W]
 gi|309795820|ref|ZP_07690234.1| conserved hypothetical protein [Escherichia coli MS 145-7]
 gi|312974192|ref|ZP_07788363.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           1827-70]
 gi|331670876|ref|ZP_08371710.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli TA271]
 gi|331680144|ref|ZP_08380803.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli H591]
 gi|157078890|gb|ABV18598.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           E24377A]
 gi|169756908|gb|ACA79607.1| pseudouridine synthase [Escherichia coli ATCC 8739]
 gi|188487538|gb|EDU62641.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           53638]
 gi|190902517|gb|EDV62252.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           B7A]
 gi|218354456|emb|CAV01282.1| 23S rRNA pseudouridine synthase [Escherichia coli 55989]
 gi|218363341|emb|CAR00994.1| 23S rRNA pseudouridine synthase [Escherichia coli IAI1]
 gi|291320778|gb|EFE60220.1| 23S rRNA pseudouridine synthase F [Escherichia coli B088]
 gi|300419503|gb|EFK02814.1| hypothetical protein HMPREF9548_02431 [Escherichia coli MS 182-1]
 gi|300523884|gb|EFK44953.1| conserved hypothetical protein [Escherichia coli MS 119-7]
 gi|300529339|gb|EFK50401.1| conserved hypothetical protein [Escherichia coli MS 107-1]
 gi|300843430|gb|EFK71190.1| conserved hypothetical protein [Escherichia coli MS 78-1]
 gi|306907948|gb|EFN38449.1| pseudouridine synthase [Escherichia coli W]
 gi|308120481|gb|EFO57743.1| conserved hypothetical protein [Escherichia coli MS 145-7]
 gi|310331726|gb|EFP98982.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           1827-70]
 gi|315063343|gb|ADT77670.1| 23S rRNA pseudouridine synthase [Escherichia coli W]
 gi|320200854|gb|EFW75440.1| 23S rRNA pseudouridine synthase F [Escherichia coli EC4100B]
 gi|323182119|gb|EFZ67529.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           1357]
 gi|323380593|gb|ADX52861.1| pseudouridine synthase [Escherichia coli KO11]
 gi|323946150|gb|EGB42184.1| RNA pseudouridylate synthase [Escherichia coli H120]
 gi|324118589|gb|EGC12481.1| RNA pseudouridylate synthase [Escherichia coli E1167]
 gi|331061790|gb|EGI33715.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli TA271]
 gi|331071607|gb|EGI42943.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli H591]
          Length = 290

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 61/292 (20%), Positives = 114/292 (39%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++             ++     + +  +   R   N  +     ++KK  
Sbjct: 239 SSSEAKPKVKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 290


>gi|315166874|gb|EFU10891.1| conserved hypothetical protein [Enterococcus faecalis TX1341]
          Length = 257

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 63/248 (25%), Positives = 109/248 (43%), Gaps = 5/248 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           I + G  L   +     L+     +  T    +             + +  VGRLD +TE
Sbjct: 61  IALMGEILTYQKFFYYMLHKPQGVISATEDQRNETVIDLLTDQDYRADLFPVGRLDKDTE 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVT 178
           GLLLLTNDG LA  L  P     + Y     G V  +   L  +G  +  G      ++ 
Sbjct: 121 GLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEMVKPSRLV 180

Query: 179 L--DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTRE 235
           +    ++   + V + ++EGK  ++K++       V  L R+  G   L   L  G  R 
Sbjct: 181 IETINEEEGTSVVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEYRP 240

Query: 236 VSKKILRE 243
           +++  L++
Sbjct: 241 LTEAELQQ 248


>gi|311032169|ref|ZP_07710259.1| pseudouridine synthase F (ribosomal large subunit) [Bacillus sp.
           m3-13]
          Length = 235

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 67/242 (27%), Positives = 117/242 (48%), Gaps = 7/242 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ +G+ASRR  +++I + +VK+NG + +     V   D + V+G  +R A   
Sbjct: 1   MRINKFISDSGVASRRGADKLIEEGKVKINGKVAQIGGQ-VNPGDEVLVNGQIIRIARDN 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KPIG+ +T            +L +   R+  +GRLD  +EGL+LLTNDG +   
Sbjct: 60  VYIALNKPIGITSTTEKKV--KGNIIDLVNHPLRLSHIGRLDKESEGLILLTNDGDIINE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y V     +  D +  + +G+ I G      +V    ++ S     + L
Sbjct: 118 ILRPENKHEKEYIVSVDKPITPDFVKQMSEGVKILGTKTLPCEV----EQLSKFDFKIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
            +G NR+I+++     ++V RL R      +LG L  G  R++SKK  R+       E  
Sbjct: 174 TQGLNRQIRRMCAELGYEVLRLQRTRIMNIELGNLPMGQWRDLSKKEKRQLFAELNYEPK 233

Query: 254 QV 255
           + 
Sbjct: 234 EW 235


>gi|172060471|ref|YP_001808123.1| RNA-binding S4 domain-containing protein [Burkholderia ambifaria
           MC40-6]
 gi|171992988|gb|ACB63907.1| RNA-binding S4 domain protein [Burkholderia ambifaria MC40-6]
          Length = 572

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 83/357 (23%), Positives = 143/357 (40%), Gaps = 6/357 (1%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 176 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRI 234

Query: 63  DGVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           +G P+++         L  +     +V+        S      P   ++ ++VGRLD NT
Sbjct: 235 NGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNT 294

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++ 
Sbjct: 295 EGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEGMRQKLLHGVELDDGPANFLRIR 354

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
               +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ 
Sbjct: 355 DGGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPIPLPRGLKRGRWEELD 414

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +  +R+ +    L+           S     R    + + +          +  +    +
Sbjct: 415 EAQVRKLMATVGLKAPSEEKGKRGGSGPAERRQPDPMQTSMGFISREPVLTTHGQLDQPR 474

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +             S         S   + SG   +      S+ +       +  K
Sbjct: 475 RGGGRRGGPGLPGLSGYGSLPVSPSGHGNRSGGGRDVDGNRASYGAGPKREGGAGAK 531


>gi|229546498|ref|ZP_04435223.1| pseudouridylate synthase [Enterococcus faecalis TX1322]
 gi|307277044|ref|ZP_07558150.1| hypothetical protein HMPREF9521_02651 [Enterococcus faecalis
           TX2134]
 gi|307289941|ref|ZP_07569870.1| hypothetical protein HMPREF9509_00254 [Enterococcus faecalis
           TX0411]
 gi|312904312|ref|ZP_07763474.1| conserved hypothetical protein [Enterococcus faecalis TX0635]
 gi|229308398|gb|EEN74385.1| pseudouridylate synthase [Enterococcus faecalis TX1322]
 gi|306499007|gb|EFM68496.1| hypothetical protein HMPREF9509_00254 [Enterococcus faecalis
           TX0411]
 gi|306506288|gb|EFM75452.1| hypothetical protein HMPREF9521_02651 [Enterococcus faecalis
           TX2134]
 gi|310632408|gb|EFQ15691.1| conserved hypothetical protein [Enterococcus faecalis TX0635]
 gi|315030592|gb|EFT42524.1| conserved hypothetical protein [Enterococcus faecalis TX4000]
 gi|315159713|gb|EFU03730.1| conserved hypothetical protein [Enterococcus faecalis TX0312]
 gi|315162686|gb|EFU06703.1| conserved hypothetical protein [Enterococcus faecalis TX0645]
 gi|315578753|gb|EFU90944.1| conserved hypothetical protein [Enterococcus faecalis TX0630]
          Length = 257

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 64/248 (25%), Positives = 109/248 (43%), Gaps = 5/248 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           I + G  L   +     L+     +  T    D             + +  VGRLD +TE
Sbjct: 61  IALMGEILTYQKFFYYMLHKPQGVISATEDQRDETVIDLLTDQDYRADLFPVGRLDKDTE 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVT 178
           GLLLLTNDG LA  L  P     + Y     G V  +   L  +G  +  G      ++ 
Sbjct: 121 GLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTVEDCQLFAQGFALKDGEMVKPSRLV 180

Query: 179 L--DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTRE 235
           +    ++   + V + ++EGK  ++K++       V  L R+  G   L   L  G  R 
Sbjct: 181 IETINEEEGTSVVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEYRP 240

Query: 236 VSKKILRE 243
           +++  L++
Sbjct: 241 LTEAELQQ 248


>gi|160881056|ref|YP_001560024.1| pseudouridine synthase [Clostridium phytofermentans ISDg]
 gi|160429722|gb|ABX43285.1| pseudouridine synthase [Clostridium phytofermentans ISDg]
          Length = 477

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 73/357 (20%), Positives = 136/357 (38%), Gaps = 13/357 (3%)

Query: 3   DKNIVQENFTPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
            K       T +   R++K ++ +GI SRRE +  IA+  V ++G +       V+    
Sbjct: 5   TKRSFDTEETGEKAVRINKYLSESGICSRREADTRIAKGEVTIDGEVA-VMGSKVLPGQK 63

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           + +    + + E+  L  +HKP G+V T    +       +      R+  +GRLD ++E
Sbjct: 64  VVLGKKEVSREEKMVLIAFHKPKGIVCTTEKRE--PDNIIDYIKYSQRIYPIGRLDKDSE 121

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GL+ LTN+G +   +        + Y V  +  +    L  +  G+ I         +  
Sbjct: 122 GLIFLTNNGDIVNKILRAGNHHEKEYIVTVNKPITAAFLKGMAGGVPILDTVTKPCTLEA 181

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                      + L +G NR+I+++ E F++KV +L+RI      LG L  G  R ++ K
Sbjct: 182 I----DKVTFRIILTQGLNRQIRRMCEHFDYKVTKLVRIRIMNVNLGRLKVGGYRNLTDK 237

Query: 240 IL---REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            L   +EQ+     E   +  D         V +             R  K+        
Sbjct: 238 ELEGIKEQIELSNNEALNLEPDDEFPIERVNVANIAKTHGNNVATGKRRTKDKYFAEKKD 297

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            +K+     ++  +       K   + F S +           SF   +   + S++
Sbjct: 298 DKKRSDATRNKAEVNKFASKNKSEGNKFGSKNSSEGNKFGSKNSFEGNKFGSKNSSE 354


>gi|115351432|ref|YP_773271.1| pseudouridine synthase, Rsu [Burkholderia ambifaria AMMD]
 gi|115281420|gb|ABI86937.1| ribosomal large subunit pseudouridine synthase B [Burkholderia
           ambifaria AMMD]
          Length = 572

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 83/357 (23%), Positives = 143/357 (40%), Gaps = 6/357 (1%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 176 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRI 234

Query: 63  DGVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           +G P+++         L  +     +V+        S      P   ++ ++VGRLD NT
Sbjct: 235 NGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNT 294

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++ 
Sbjct: 295 EGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEGMRQKLLHGVELDDGPANFLRIR 354

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
               +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ 
Sbjct: 355 DGGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPIPLPRGLKRGRWEELD 414

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +  +R+ +    L+           S     R    + + +          +  +    +
Sbjct: 415 EAQVRKLMATVGLKAPSEEKGKRGGSGPAERRQPDPMQTSMGFISREPVLTTHGQLDQPR 474

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +             S         S   + SG   +      S+ +       +  K
Sbjct: 475 RGGGRRGGPGLPGLSGYGSLPVSPSGHGNRSGGGRDVDGNRASYGAGPKREGGAGAK 531


>gi|323965683|gb|EGB61135.1| RNA pseudouridylate synthase [Escherichia coli M863]
 gi|327250364|gb|EGE62077.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           STEC_7v]
          Length = 290

 Score =  178 bits (452), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 63/292 (21%), Positives = 115/292 (39%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPVTDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++    A        ++     + +  +   R   N  +     ++KK  
Sbjct: 239 SSSEAKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 290


>gi|296533931|ref|ZP_06896455.1| ribosomal large subunit pseudouridine synthase B [Roseomonas
           cervicalis ATCC 49957]
 gi|296265748|gb|EFH11849.1| ribosomal large subunit pseudouridine synthase B [Roseomonas
           cervicalis ATCC 49957]
          Length = 267

 Score =  178 bits (452), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 127/247 (51%), Positives = 174/247 (70%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           Q+    +R++K +ARAGIASRR+ E++IA+ +V VNG +L+  A  V   D + V G  +
Sbjct: 5   QDGPKGERIAKWLARAGIASRRDAEKLIAEGQVAVNGRVLDGPASFVQPGDSVTVSGKKV 64

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            + ERTRL+ YHKP GLVTTH DP+GR TVF+ LP+   R++SVGRLD+N+EGLLLLTND
Sbjct: 65  GEPERTRLFRYHKPPGLVTTHKDPEGRRTVFEELPAGLPRLVSVGRLDLNSEGLLLLTND 124

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L+R LELP  QW+R YR R HG+VD+  L  L  G+ ++G+ YG +Q  LD+++G+NA
Sbjct: 125 GALSRKLELPDNQWIRRYRARVHGRVDERALAALAHGVTVEGVAYGPIQAGLDSRQGTNA 184

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+TV L EGKNRE+++V +     V RLIRI+YGPF L  L  G+  E++ K+LREQLG 
Sbjct: 185 WLTVSLSEGKNREVRRVLQHLGLTVTRLIRIAYGPFALADLPRGAVEEINAKVLREQLGL 244

Query: 248 HLLEEAQ 254
                 +
Sbjct: 245 DAPPRIK 251


>gi|296100644|ref|YP_003610790.1| 23S rRNA pseudouridine synthase F [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
 gi|295055103|gb|ADF59841.1| 23S rRNA pseudouridine synthase F [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
          Length = 289

 Score =  178 bits (452), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 61/291 (20%), Positives = 112/291 (38%), Gaps = 5/291 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K I+ +GI SRRE +R I Q  V +NG         VM  D ++V+G  +   
Sbjct: 4   TQSIRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVMPGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L        +    +  DG      +  +  SR+  +GRLD +++GL+ LTN G L
Sbjct: 63  DAEDLVFIALNKPVGIVSTTEDGERDNIVDFVNHSSRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYIVTVNKPVTDEFIRGMGAGVPILGTV----TKKCKVKKEAPFAFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L E       
Sbjct: 179 ITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIELFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
             ++    A        ++       +  +                K+K  
Sbjct: 239 SSSEAKPKAKAKPKTQAIKRPVVKAPQSEEKGRGKPAGKRFTQPGRKKKGR 289


>gi|227517632|ref|ZP_03947681.1| pseudouridylate synthase [Enterococcus faecalis TX0104]
 gi|227554784|ref|ZP_03984831.1| pseudouridylate synthase [Enterococcus faecalis HH22]
 gi|293384990|ref|ZP_06630824.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis R712]
 gi|293389260|ref|ZP_06633722.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis S613]
 gi|307270257|ref|ZP_07551569.1| hypothetical protein HMPREF9498_02370 [Enterococcus faecalis
           TX4248]
 gi|307272482|ref|ZP_07553735.1| hypothetical protein HMPREF9514_01246 [Enterococcus faecalis
           TX0855]
 gi|307278240|ref|ZP_07559319.1| hypothetical protein HMPREF9515_00573 [Enterococcus faecalis
           TX0860]
 gi|307289637|ref|ZP_07569581.1| hypothetical protein HMPREF9505_02998 [Enterococcus faecalis
           TX0109]
 gi|312900258|ref|ZP_07759570.1| conserved hypothetical protein [Enterococcus faecalis TX0470]
 gi|312905979|ref|ZP_07764992.1| conserved hypothetical protein [Enterococcus faecalis DAPTO 512]
 gi|312909325|ref|ZP_07768181.1| conserved hypothetical protein [Enterococcus faecalis DAPTO 516]
 gi|227074938|gb|EEI12901.1| pseudouridylate synthase [Enterococcus faecalis TX0104]
 gi|227176083|gb|EEI57055.1| pseudouridylate synthase [Enterococcus faecalis HH22]
 gi|291077668|gb|EFE15032.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis R712]
 gi|291081424|gb|EFE18387.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis S613]
 gi|306499451|gb|EFM68824.1| hypothetical protein HMPREF9505_02998 [Enterococcus faecalis
           TX0109]
 gi|306504991|gb|EFM74182.1| hypothetical protein HMPREF9515_00573 [Enterococcus faecalis
           TX0860]
 gi|306510767|gb|EFM79784.1| hypothetical protein HMPREF9514_01246 [Enterococcus faecalis
           TX0855]
 gi|306513400|gb|EFM82020.1| hypothetical protein HMPREF9498_02370 [Enterococcus faecalis
           TX4248]
 gi|310627974|gb|EFQ11257.1| conserved hypothetical protein [Enterococcus faecalis DAPTO 512]
 gi|311290349|gb|EFQ68905.1| conserved hypothetical protein [Enterococcus faecalis DAPTO 516]
 gi|311292619|gb|EFQ71175.1| conserved hypothetical protein [Enterococcus faecalis TX0470]
 gi|315031424|gb|EFT43356.1| conserved hypothetical protein [Enterococcus faecalis TX0017]
 gi|315034401|gb|EFT46333.1| conserved hypothetical protein [Enterococcus faecalis TX0027]
 gi|315164553|gb|EFU08570.1| conserved hypothetical protein [Enterococcus faecalis TX1302]
 gi|315575298|gb|EFU87489.1| conserved hypothetical protein [Enterococcus faecalis TX0309B]
 gi|315581464|gb|EFU93655.1| conserved hypothetical protein [Enterococcus faecalis TX0309A]
          Length = 257

 Score =  178 bits (452), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 64/248 (25%), Positives = 109/248 (43%), Gaps = 5/248 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           I + G  L   +     L+     +  T    D             + +  VGRLD +TE
Sbjct: 61  IALMGEILTYQKFFYYMLHKPQGVISATEDQRDETVIDLLTDQDYRADLFPVGRLDKDTE 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVT 178
           GLLLLTNDG LA  L  P     + Y     G V  +   L  +G  +  G      ++ 
Sbjct: 121 GLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEMVKPSRLV 180

Query: 179 L--DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTRE 235
           +    ++   + V + ++EGK  ++K++       V  L R+  G   L   L  G  R 
Sbjct: 181 IETINEEEGTSVVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEYRP 240

Query: 236 VSKKILRE 243
           +++  L++
Sbjct: 241 LTEAELQQ 248


>gi|228910375|ref|ZP_04074190.1| RNA pseudouridine synthase [Bacillus thuringiensis IBL 200]
 gi|228849141|gb|EEM93980.1| RNA pseudouridine synthase [Bacillus thuringiensis IBL 200]
          Length = 229

 Score =  178 bits (452), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 107/230 (46%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTH-GALVSDGDRVTIDGQVIVKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D    + +     +   R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAADHIENNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGTIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVTRI----DQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L 
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTSEELD 223


>gi|160915013|ref|ZP_02077226.1| hypothetical protein EUBDOL_01020 [Eubacterium dolichum DSM 3991]
 gi|158432812|gb|EDP11101.1| hypothetical protein EUBDOL_01020 [Eubacterium dolichum DSM 3991]
          Length = 244

 Score =  178 bits (452), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 68/238 (28%), Positives = 112/238 (47%), Gaps = 5/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AGIASRR+ E +I Q RV VNG L+      V   D I VDG  + K  + 
Sbjct: 2   ERLQKVMAAAGIASRRKCEELIVQGRVSVNGQLVSELGYKVKKGDQIAVDGKMIEKEGKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +      + T++ +   ++ +   L     R+ +VGRLD +T G+LLLTNDG  A  
Sbjct: 62  YYLMNKPKKSMCTSNDEFGRKTVIE--LVEGTERIFTVGRLDYDTSGVLLLTNDGDFANE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQK--GSNAWVT 190
           +  P     +VY +  +G +  + +  LK GIV+         +  +  +    +     
Sbjct: 120 IIHPRYHLPKVYNLTINGILKPEDMRKLKNGIVLDDGYKTMPAKFKITEKDLKKNQCSFD 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + + EG+NR+IK++ E   ++V RL R          L  G  R +    +++     
Sbjct: 180 LTIYEGRNRQIKRMMEALGYEVRRLHRKQIAFLGCSDLRQGEYRTLKPFEVKKLRTLA 237


>gi|149197232|ref|ZP_01874284.1| hypothetical protein LNTAR_12521 [Lentisphaera araneosa HTCC2155]
 gi|149139778|gb|EDM28179.1| hypothetical protein LNTAR_12521 [Lentisphaera araneosa HTCC2155]
          Length = 297

 Score =  178 bits (452), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 65/302 (21%), Positives = 111/302 (36%), Gaps = 6/302 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ +G  SRRE +R+I + RV +NG   +     V   D +EVDG  ++   + 
Sbjct: 1   MRLNKFISDSGFCSRREADRLIEEGRVLINGRRCKT-GQQVEDKDFVEVDGQRIKAKRQK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                        T +          +  +   ++  +GRLD  + GL+ +TNDG +   
Sbjct: 60  ERVYLAFNKPEGITCTTEGSVKGNIVDFINYPEKIFPIGRLDKFSNGLIFMTNDGDIVNK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V     V  + L  +  GI I        +VT    K S     + L
Sbjct: 120 ILRAGNAHEKEYVVTIDRPVTDEFLRKMSNGIPILDTVTKKCKVT----KVSKNTFRIIL 175

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
            +G NR+I+++ E+   +V  L R       LG L  G+ R ++ K + E          
Sbjct: 176 TQGLNRQIRRMCEYLACRVLSLQRTRIMKVDLGKLKPGTWRHLNPKEMAEINQMIESSSN 235

Query: 254 QVNLDAPIYSSETLV-RDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
                             RP     +       KK+S ++ G +  +        R    
Sbjct: 236 TQEASKDSNKQGRRSLPKRPVARQNMKTSSQSHKKSSPKRRGQTSGRPSKQNSKSRPQRK 295

Query: 313 NV 314
             
Sbjct: 296 RR 297


>gi|315146884|gb|EFT90900.1| conserved hypothetical protein [Enterococcus faecalis TX4244]
          Length = 257

 Score =  178 bits (452), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 63/248 (25%), Positives = 109/248 (43%), Gaps = 5/248 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           I + G  L   +     L+     +  T    D             + +  VGRLD +TE
Sbjct: 61  IALMGEILTYQKFFYYMLHKPQGVISATEDQRDETVIDLLTDQDYRADLFPVGRLDKDTE 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVT 178
           GLLLLTNDG LA  L  P     + Y     G V  +   L  +G  ++        ++ 
Sbjct: 121 GLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEIVKPSRLV 180

Query: 179 L--DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTRE 235
           +    ++   + V + ++EGK  ++K++       V  L R+  G   L   L  G  R 
Sbjct: 181 IETINEEEGTSVVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEYRP 240

Query: 236 VSKKILRE 243
           +++  L++
Sbjct: 241 LTEAELQQ 248


>gi|323439505|gb|EGA97226.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus O11]
          Length = 245

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 76/243 (31%), Positives = 127/243 (52%), Gaps = 3/243 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R+ K IA +G  SRR+ E +I++ + KVNG  +      V  +D IEV+G+ +  
Sbjct: 2   TKELERLQKRIANSGYTSRRKAETLISEGKAKVNGTTVTELGTKVKPSDTIEVEGIKIEL 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E     L+HKP  ++T+ SD  GR+ V D    I +R+  VGRLD +T GLLLLTNDG 
Sbjct: 62  -EDKIYILFHKPTQVITSVSDDRGRTVVTDYFKDIEARIYPVGRLDYDTSGLLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNA 187
              ++  P  Q  + Y  +  G + ++++  L+KGI ++       +  V    +  +  
Sbjct: 121 FTNLMTHPRYQIKKKYVAKLKGYLMREEVKALEKGIELEDGMTQPAEVKVKKQDKDKNTT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V + + EG+NR+++++ E F  +V +L RI YGP  +  L AG  R ++   ++     
Sbjct: 181 LVEITITEGRNRQVRRMLEHFGHQVTKLSRIEYGPLNVVGLNAGEGRVLTPHEVKVMRHL 240

Query: 248 HLL 250
              
Sbjct: 241 AEH 243


>gi|256019605|ref|ZP_05433470.1| 23S rRNA pseudouridine synthase F [Shigella sp. D9]
 gi|332280733|ref|ZP_08393146.1| 23S rRNA pseudouridine synthase F [Shigella sp. D9]
 gi|332103085|gb|EGJ06431.1| 23S rRNA pseudouridine synthase F [Shigella sp. D9]
          Length = 290

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 61/292 (20%), Positives = 114/292 (39%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDIVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++             ++     + +  +   R   N  +     ++KK  
Sbjct: 239 SSSEAKPKVKAKPKTAGIKRPLVKMEKTSEKGGRPASNGKRFTSPGRKKKGR 290


>gi|218707643|ref|YP_002415162.1| 23S rRNA pseudouridine synthase F [Escherichia coli UMN026]
 gi|293402661|ref|ZP_06646758.1| 23S rRNA pseudouridine synthase F [Escherichia coli FVEC1412]
 gi|298378190|ref|ZP_06988074.1| 23S rRNA pseudouridine synthase F [Escherichia coli FVEC1302]
 gi|300899867|ref|ZP_07118079.1| conserved hypothetical protein [Escherichia coli MS 198-1]
 gi|218434740|emb|CAR15672.1| 23S rRNA pseudouridine synthase [Escherichia coli UMN026]
 gi|291429576|gb|EFF02590.1| 23S rRNA pseudouridine synthase F [Escherichia coli FVEC1412]
 gi|298280524|gb|EFI22025.1| 23S rRNA pseudouridine synthase F [Escherichia coli FVEC1302]
 gi|300356569|gb|EFJ72439.1| conserved hypothetical protein [Escherichia coli MS 198-1]
          Length = 290

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 62/292 (21%), Positives = 116/292 (39%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEYFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++    A        ++     + +  +   R   N  +     ++KK  
Sbjct: 239 SSSEAKPKAKAKPKTVGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 290


>gi|167040440|ref|YP_001663425.1| pseudouridine synthase [Thermoanaerobacter sp. X514]
 gi|300913725|ref|ZP_07131042.1| pseudouridine synthase [Thermoanaerobacter sp. X561]
 gi|307723259|ref|YP_003903010.1| pseudouridine synthase [Thermoanaerobacter sp. X513]
 gi|166854680|gb|ABY93089.1| pseudouridine synthase [Thermoanaerobacter sp. X514]
 gi|300890410|gb|EFK85555.1| pseudouridine synthase [Thermoanaerobacter sp. X561]
 gi|307580320|gb|ADN53719.1| pseudouridine synthase [Thermoanaerobacter sp. X513]
          Length = 240

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 67/231 (29%), Positives = 110/231 (47%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K+++  GI +R+EV++ I +  V VNG  ++ A + +   TD I  DG  +   E 
Sbjct: 4   MRIDKLLSNIGIGTRKEVKKFIKEGLVLVNGNTVKDAGLIINTETDEILFDGKKIYYKEF 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      +  T+   +                  VGRLD +TEGLLL+TNDG LA 
Sbjct: 64  IYIMMNKPEGVISATYDPIEKTVIDLLPQELKARNPFPVGRLDKDTEGLLLITNDGDLAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P    ++ Y  +  G V++  +    +GIV++         + + +     + V V
Sbjct: 124 KLLSPKKNVIKKYYAKILGFVNESDIKAFNEGIVLEDGYKTLPANLEILSSSDV-SKVYV 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            +REGK  +IK++FE    KV  L R++ G   L   L  G  RE+S++ L
Sbjct: 183 YIREGKYHQIKRMFESVGKKVIYLKRLAMGNLTLDENLKPGEWRELSEEEL 233


>gi|315924794|ref|ZP_07921011.1| ribosomal large subunit pseudouridine synthase B [Pseudoramibacter
           alactolyticus ATCC 23263]
 gi|315621693|gb|EFV01657.1| ribosomal large subunit pseudouridine synthase B [Pseudoramibacter
           alactolyticus ATCC 23263]
          Length = 246

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 75/248 (30%), Positives = 115/248 (46%), Gaps = 9/248 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A+ G+ASRR  E MIA  RV VNG +++   V V   D + VDG  +    + 
Sbjct: 1   MRLQKYMAQCGVASRRGSEAMIADGRVMVNGSVVDTPGVQVTPGDVVFVDGKLIAPERKV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L      + T+      R     +L +   R+ ++GRLD +TEGLL+LTNDG L   
Sbjct: 61  YLLLNKPRGVVTTSEDVHAERRI--LDLVAAEVRLYAIGRLDKDTEGLLILTNDGDLTFR 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-------QGICYGDMQVTLDTQKGSN 186
           L  PS    +VY     GQ+    L  L++G+VI       +       +VT+  +K  +
Sbjct: 119 LTHPSYHLDKVYEAVVKGQLTAPALAALREGVVIPLDDAGTKTYRTQPAEVTVLRRKRGS 178

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
             +++ L EGK R+I+K+     + V  L R + G     TL  G  R +    + +   
Sbjct: 179 TRLSITLCEGKKRQIRKMCAAVGYPVVALRRTAIGDIADDTLKPGEWRRLRPDEVAKLRR 238

Query: 247 PHLLEEAQ 254
               E   
Sbjct: 239 AVQGEGDA 246


>gi|228923295|ref|ZP_04086583.1| RNA pseudouridine synthase [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228836249|gb|EEM81602.1| RNA pseudouridine synthase [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 229

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 109/230 (47%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTH-GTLVSDGDRVTIDGKVIVKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G++ T +D    + +     +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGIICTAADHIEDNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVTRV----DQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L 
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTAEELE 223


>gi|295135656|ref|YP_003586332.1| ribosomal large subunit pseudouridine synthase F [Zunongwangia
           profunda SM-A87]
 gi|294983671|gb|ADF54136.1| ribosomal large subunit pseudouridine synthase F [Zunongwangia
           profunda SM-A87]
          Length = 278

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 59/279 (21%), Positives = 118/279 (42%), Gaps = 12/279 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL----RKA 70
           R++K ++ AG  SRR  +++I Q RV +NG ++      +   D ++VDG  +    ++ 
Sbjct: 8   RINKFLSEAGYCSRRAADKLIDQGRVTING-VVPEMGTKIAPGDEVKVDGELIATEEKEK 66

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               +        + TT +  +  + +     +   R+  +GRLD  +EGL+ LT+DG +
Sbjct: 67  PNVYIAFNKPIGIVCTTDTKREKNNIIDYI--NYPERIFPIGRLDKPSEGLIFLTSDGDI 124

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V+ +  +  D +  + KGI I      +       ++       
Sbjct: 125 VNKILRARNNHEKEYIVKVNKPLQPDFVKKMSKGIPILDTVTREC----FVEQTGENEFR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E+  + V +L RI      L  +  G  R ++K  L+E       
Sbjct: 181 IILTQGLNRQIRRMCEYLGYAVTKLKRIRIMNVPL-DIPVGKWRHLTKAELKEIDRLVNT 239

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
                       +++  +     I  + P+   R +K S
Sbjct: 240 SSKTEEASQLSENNDNKIAKPKGIKPKNPNKHKRPRKKS 278


>gi|229019771|ref|ZP_04176574.1| RNA pseudouridine synthase [Bacillus cereus AH1273]
 gi|229025998|ref|ZP_04182382.1| RNA pseudouridine synthase [Bacillus cereus AH1272]
 gi|228735279|gb|EEL85890.1| RNA pseudouridine synthase [Bacillus cereus AH1272]
 gi|228741496|gb|EEL91693.1| RNA pseudouridine synthase [Bacillus cereus AH1273]
          Length = 229

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 63/230 (27%), Positives = 110/230 (47%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +     V V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVCINGEMCTH-GVLVSDGDVVMIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D    + +         R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAADHIEDNIIDYI--HYPERIFPVGRLDKASEGLILLTNDGGIAH 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVTRV----DQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++   F + V +L R+     +L  L +G  R+++ + L 
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELNGLESGKWRDITAEELE 223


>gi|42783720|ref|NP_980967.1| RNA pseudouridylate synthase family protein [Bacillus cereus ATCC
           10987]
 gi|42739650|gb|AAS43575.1| RNA pseudouridylate synthase family protein [Bacillus cereus ATCC
           10987]
          Length = 229

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 107/230 (46%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  L K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAI-VNDGDVVTIDGQVLAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D    + +     +   R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAADHIEDNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVTRV----DQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++   F + V +L R      +L  L  G  R ++   L 
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRERIMNIELDDLEVGKWRNITDGELE 223


>gi|258591956|emb|CBE68261.1| Uncharacterized RNA pseudouridine synthase aq_1464 (RNA-uridine
           isomerase) (RNA pseudouridylate synthase) [NC10
           bacterium 'Dutch sediment']
          Length = 282

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 80/258 (31%), Positives = 122/258 (47%), Gaps = 2/258 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ + +ARAG+ SRR  E++I   RV+VNG +  +    V    D +  D  P+  ++ 
Sbjct: 25  ERLQRYLARAGLGSRRSCEQLILDGRVRVNGRIASQLGTKVSPGLDTVTCDHKPVTSSQS 84

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLA 131
               + HKP G++T+ SDP GR  + D LP         VGRLD  TEGL+LLTNDG LA
Sbjct: 85  LHYLILHKPAGVLTSLSDPRGRPVIGDLLPPRGLPRLFPVGRLDYQTEGLVLLTNDGVLA 144

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  PS +  + Y  +  G    D L  LK G+V +G         +      +AW+ +
Sbjct: 145 HGLMHPSFEVEKEYLAKVRGCPTPDDLARLKAGVVSEGEKLWATHAAIVKPGIGSAWLKL 204

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + +G+  EI+++ +     V RL RI  GP  LG L  G  R+++   L +     L  
Sbjct: 205 IVHQGRYHEIRRMCDAIGHPVLRLQRIRVGPIVLGKLPKGCWRQLTPAELADIRRACLNA 264

Query: 252 EAQVNLDAPIYSSETLVR 269
             +  +            
Sbjct: 265 ARRQTVGRRTARRPESEG 282


>gi|332670389|ref|YP_004453397.1| pseudouridine synthase [Cellulomonas fimi ATCC 484]
 gi|332339427|gb|AEE46010.1| pseudouridine synthase [Cellulomonas fimi ATCC 484]
          Length = 248

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 117/233 (50%), Gaps = 1/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
           +    R+ KV+A AG+ SRR  E +IA  RV V+G  +    V V   T  I VDG+ ++
Sbjct: 7   DPDGVRLQKVLASAGLGSRRACEELIATGRVTVDGSTVRELGVRVDPLTAVIHVDGMRVQ 66

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                     +KP G+V+T  DP+GR +V   +     R+  VGRLD  TEGLLLLTNDG
Sbjct: 67  LDSSVVTLALNKPKGVVSTMHDPEGRPSVAQFVADRSERLFHVGRLDSETEGLLLLTNDG 126

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS    + Y     G+V       L +G+ ++       +  +       + 
Sbjct: 127 ELANRLSHPSHGVAKTYLAHVEGRVAGSLAGRLARGVELEDGVVTVDRFQVVQTTPQASL 186

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L EG+NR ++++ E     V RL+R   GP +LG L  G TR +SK  +
Sbjct: 187 VEVVLHEGRNRVVRRLLEEVGHPVTRLVRTQIGPIRLGDLKPGRTRVLSKTEV 239


>gi|254480346|ref|ZP_05093594.1| conserved hypothetical protein, putative [marine gamma
           proteobacterium HTCC2148]
 gi|214039908|gb|EEB80567.1| conserved hypothetical protein, putative [marine gamma
           proteobacterium HTCC2148]
          Length = 313

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 73/341 (21%), Positives = 130/341 (38%), Gaps = 34/341 (9%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL- 67
           +     R++K I+ +G  SRRE +++IA  RVK+NG         V S D + VDG  + 
Sbjct: 2   DPNNSIRLNKFISESGHCSRREADKLIASNRVKINGTRP-ELGTKVESGDVVTVDGQEIM 60

Query: 68  ---RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                        Y+KP+G+  T       + V             +GRLD  +EGL+LL
Sbjct: 61  GSAPGKSDRVYIAYNKPVGITCTTERSVQGNIVDAIDHHQRI--FPIGRLDKPSEGLILL 118

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T+DG +   +        + Y V  +  + +     +  GI I        +V++  +  
Sbjct: 119 TSDGDIVNKILRAENAHEKEYLVTVNKSIGKGFSEKMAGGIPILNTVTKPCKVSVVRRN- 177

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
                 + L EG NR+I+++ EF +++V +L+R+      LG L  G  R ++++ + + 
Sbjct: 178 ---VFKIILTEGLNRQIRRMCEFLDYEVTQLVRLRIMNVHLGKLKVGQWRNLTEQEMAQL 234

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
                                             P   ++      +     K       
Sbjct: 235 NIAISGS-----------------------TGSPPKKSSQSAAKKRKPQHRLKGTGSDAK 271

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
             R++  S    +K   S   S    R+   R+SP+   +R
Sbjct: 272 PARKSTKSRHSSSKNKDSGSDSRRSARKPGSRKSPTSSKRR 312


>gi|26250800|ref|NP_756840.1| 23S rRNA pseudouridine synthase F [Escherichia coli CFT073]
 gi|91213543|ref|YP_543529.1| 23S rRNA pseudouridine synthase F [Escherichia coli UTI89]
 gi|117626291|ref|YP_859614.1| 23S rRNA pseudouridine synthase F [Escherichia coli APEC O1]
 gi|191171992|ref|ZP_03033537.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           F11]
 gi|215489360|ref|YP_002331791.1| 23S rRNA pseudouridine synthase F [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218561092|ref|YP_002394005.1| 23S rRNA pseudouridine synthase F [Escherichia coli S88]
 gi|218692307|ref|YP_002400519.1| 23S rRNA pseudouridine synthase F [Escherichia coli ED1a]
 gi|227886973|ref|ZP_04004778.1| RluF protein [Escherichia coli 83972]
 gi|300980609|ref|ZP_07175103.1| hypothetical protein HMPREF9553_01625 [Escherichia coli MS 200-1]
 gi|300992903|ref|ZP_07180085.1| conserved hypothetical protein [Escherichia coli MS 45-1]
 gi|306815865|ref|ZP_07450010.1| 23S rRNA pseudouridine synthase F [Escherichia coli NC101]
 gi|312965319|ref|ZP_07779552.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           2362-75]
 gi|34098551|sp|Q8FB47|RLUF_ECOL6 RecName: Full=Ribosomal large subunit pseudouridine synthase F;
           AltName: Full=rRNA pseudouridylate synthase F; AltName:
           Full=rRNA-uridine isomerase F
 gi|26111231|gb|AAN83414.1|AE016770_214 Hypothetical protein yjbC [Escherichia coli CFT073]
 gi|91075117|gb|ABE09998.1| putative 23S rRNA pseudouridine synthase subunit yjbC [Escherichia
           coli UTI89]
 gi|115515415|gb|ABJ03490.1| conserved hypothetical protein [Escherichia coli APEC O1]
 gi|190907757|gb|EDV67351.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           F11]
 gi|215267432|emb|CAS11885.1| 23S rRNA pseudouridine synthase [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218367861|emb|CAR05656.1| 23S rRNA pseudouridine synthase [Escherichia coli S88]
 gi|218429871|emb|CAR10842.2| 23S rRNA pseudouridine synthase [Escherichia coli ED1a]
 gi|222035737|emb|CAP78482.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           LF82]
 gi|227836114|gb|EEJ46580.1| RluF protein [Escherichia coli 83972]
 gi|294492958|gb|ADE91714.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           IHE3034]
 gi|300307733|gb|EFJ62253.1| hypothetical protein HMPREF9553_01625 [Escherichia coli MS 200-1]
 gi|300406779|gb|EFJ90317.1| conserved hypothetical protein [Escherichia coli MS 45-1]
 gi|305850840|gb|EFM51296.1| 23S rRNA pseudouridine synthase F [Escherichia coli NC101]
 gi|307556168|gb|ADN48943.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           ABU 83972]
 gi|307629071|gb|ADN73375.1| 23S rRNA pseudouridine synthase F [Escherichia coli UM146]
 gi|312289993|gb|EFR17880.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           2362-75]
 gi|312948600|gb|ADR29427.1| 23S rRNA pseudouridine synthase F [Escherichia coli O83:H1 str. NRG
           857C]
 gi|315287806|gb|EFU47208.1| conserved hypothetical protein [Escherichia coli MS 110-3]
 gi|315291492|gb|EFU50852.1| conserved hypothetical protein [Escherichia coli MS 153-1]
 gi|320193592|gb|EFW68228.1| 23S rRNA pseudouridine synthase F [Escherichia coli WV_060327]
 gi|323950434|gb|EGB46315.1| RNA pseudouridylate synthase [Escherichia coli H252]
 gi|323954517|gb|EGB50301.1| RNA pseudouridylate synthase [Escherichia coli H263]
 gi|324014259|gb|EGB83478.1| hypothetical protein HMPREF9533_01657 [Escherichia coli MS 60-1]
          Length = 290

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 62/292 (21%), Positives = 115/292 (39%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  ESEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++    A        ++     + +  +   R   N  +     ++KK  
Sbjct: 239 SSSEAKPKAKAKPKTVGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 290


>gi|327480926|gb|AEA84236.1| pseudouridine synthase [Pseudomonas stutzeri DSM 4166]
          Length = 375

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 97/363 (26%), Positives = 152/363 (41%), Gaps = 27/363 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+AR GIASRR+VE+ I + RVKVNG +       V S D I VDG  L++ E 
Sbjct: 14  GEKLQKVLARLGIASRRDVEKWIVEGRVKVNGAVAT-LGQRVDSHDAIAVDGRLLKREET 72

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R  L        + T +      +           R I++GRLDINT GLLL T D
Sbjct: 73  SQVVRRVLIYNKPDGEICTRNDPEGRPTVFDRLPRPKEGRWINIGRLDINTTGLLLFTTD 132

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSN 186
           G LA  L  PS +  R Y VR  G+VD + +  LK G++++        +      +G N
Sbjct: 133 GELANRLMHPSYEMDREYAVRVRGEVDDEMIERLKTGVMLEDGPARFTDIQEAPGGEGFN 192

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL---- 241
            W    + EG+NRE+++++E     V+RL R+ +GP  +   L  G  RE+S+  +    
Sbjct: 193 HWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFMTSDLPMGRWREMSQAEVDILS 252

Query: 242 ---------------REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
                          + +     ++               ++R        V D     +
Sbjct: 253 EEVGLKPIALPSMKAKTKEKIDRMQRKVAKPLGRGERRSRVLRPAHEADMPVADKPRAAR 312

Query: 287 KNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
            + S++      K   TPV  R   +     +       S   ++     + P F  +RS
Sbjct: 313 DDKSERKPRGSDKPRGTPVAERPGDTRKGGKRHEGGGRSSGPARKPAGEGQRPGFGRERS 372

Query: 347 LRR 349
            R 
Sbjct: 373 KRP 375


>gi|206601589|gb|EDZ38072.1| Pseudouridine synthase, Rsu [Leptospirillum sp. Group II '5-way
           CG']
          Length = 583

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 98/345 (28%), Positives = 160/345 (46%), Gaps = 12/345 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K++A  G+ASRR  E MI    VKVNGI++      V   TD + VDG  +     
Sbjct: 18  IRLQKLLAHRGLASRRNAEEMIRGGLVKVNGIVVTVPGTKVHPETDRVTVDGKNVPVEPE 77

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L+L++KP G+V+T  DPDG++T+ D  P I + +I VGRLDI +EG+LLLTN+G LA+
Sbjct: 78  PFLFLFYKPKGVVSTLHDPDGKTTLKDFFPRI-NPLIHVGRLDIQSEGVLLLTNNGDLAQ 136

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
            +  P  +  R Y V+  G V  + L+ L+   + + G     +++  +    +N+W  +
Sbjct: 137 RILHPRYEIPRTYLVKVQGVVTPEHLDRLRSGKVRLDGRPVQPLELEQERLTETNSWYRI 196

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L EG+NRE++++F+  ++ V +L RI++G   L  L  G  R V+ + +   L      
Sbjct: 197 TLTEGRNREVRRLFDALHYFVLKLTRIAFGNLDLTGLEPGEYRLVTPEEIDLLL-----S 251

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
            A+      I   E   R      +  PD   R  ++       +    +       +  
Sbjct: 252 GARWKRKEAIPPPERSPRKPNFAAASSPDFRRRSVRSRPTFPDRAFSGPVDGNQEEDHFP 311

Query: 312 SNVWMAKGIHSSFLSDSGQREEN----HRRSPSFPSKRSLRRTSA 352
                         S  G R ++    H R P    K+      +
Sbjct: 312 RQARQGYSSRPDTRSRGGTRSDSEMFFHDRPPHRSDKKQESGGPS 356


>gi|295110375|emb|CBL24328.1| ribosomal large subunit pseudouridine synthase F [Ruminococcus
           obeum A2-162]
          Length = 310

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 75/314 (23%), Positives = 137/314 (43%), Gaps = 9/314 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           DK +  E+    R++K ++ AG+ SRR+ +R+    RV VNG  +      +     I +
Sbjct: 2   DKKMKSEDQNTIRINKYLSSAGVCSRRDADRLTEAGRVTVNGKKIGT-GERIPVDAVICL 60

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG P+ K ER  L L++KP G+V +       +TV + +    +R+  VGRLD ++EGLL
Sbjct: 61  DGKPVEKEEREVLLLFYKPRGIVCSTKKQRRETTVTEYIDY-PTRIYPVGRLDKDSEGLL 119

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L+TN G L   +        + Y+V    +V  + +  ++ G+ I G         +  +
Sbjct: 120 LMTNQGELVNRIMRAGNYHEKEYQVTVDHEVTDEFVRHMQTGVPILGTVTRPC---IVRK 176

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK--- 239
            G N+  T+ L +G NR+I+++ E+  + V  L R+      L  L  G+ RE+ +    
Sbjct: 177 TGRNS-FTIVLTQGLNRQIRRMCEYHGYHVRTLKRVRIMNLTLDGLKCGAYREIRRDEWS 235

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
            L+E +     E           S         +            ++   ++ G+ +  
Sbjct: 236 ELKELIRNSSSETITETGGHHGNSRSNPNERTGSEAERGGKGILSGRQRDHEQQGVRRAV 295

Query: 300 KLATPVHRRNLASN 313
           +      + N   +
Sbjct: 296 QRTGADRKNNRNRS 309


>gi|170682433|ref|YP_001746411.1| 23S rRNA pseudouridine synthase F [Escherichia coli SMS-3-5]
 gi|218702664|ref|YP_002410293.1| 23S rRNA pseudouridine synthase F [Escherichia coli IAI39]
 gi|300939713|ref|ZP_07154358.1| conserved hypothetical protein [Escherichia coli MS 21-1]
 gi|331660590|ref|ZP_08361522.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli TA206]
 gi|170520151|gb|ACB18329.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           SMS-3-5]
 gi|218372650|emb|CAR20525.1| 23S rRNA pseudouridine synthase [Escherichia coli IAI39]
 gi|284924116|emb|CBG37215.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           042]
 gi|300455410|gb|EFK18903.1| conserved hypothetical protein [Escherichia coli MS 21-1]
 gi|315300783|gb|EFU60008.1| conserved hypothetical protein [Escherichia coli MS 16-3]
 gi|323190114|gb|EFZ75392.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           RN587/1]
 gi|331051632|gb|EGI23671.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli TA206]
          Length = 290

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 62/292 (21%), Positives = 115/292 (39%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++    A        ++     + +  +   R   N  +     ++KK  
Sbjct: 239 SSSEAKPKAKAKPKTVGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 290


>gi|332298353|ref|YP_004440275.1| pseudouridine synthase Rsu [Treponema brennaborense DSM 12168]
 gi|332181456|gb|AEE17144.1| pseudouridine synthase Rsu [Treponema brennaborense DSM 12168]
          Length = 257

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 70/243 (28%), Positives = 108/243 (44%), Gaps = 5/243 (2%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           Q      R+   +A  G+ASRR  E  IA  RV VNG ++      V+  D + VDG  +
Sbjct: 18  QSQPESLRLQVYLAHCGVASRRSCETYIADGRVSVNGTVVTVPGTKVLPDDTVCVDGKRV 77

Query: 68  RKAERTRL-WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
              E  R   L      + +   +   ++      P    R+ +VGRLD+ + GL+L TN
Sbjct: 78  TLEETKRYVLLNKPAGFVCSLSDEKGRQTAASLLEPHYSERLYNVGRLDMFSAGLVLFTN 137

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  A  +  PS++  + Y V     V         KGI +  + Y            ++
Sbjct: 138 DGEFAARVSHPSSEMEKEYVVDTSLPVPPALAEKFVKGIRVDNVFYRCKSAERL----NS 193

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
             + + L EGKNREI++VFE FN  V +L+RI  G   +  L  G  R+++   + + L 
Sbjct: 194 RRMRIVLIEGKNREIRRVFEAFNIGVKQLVRIRIGNLNIQGLGPGEFRDLTAAEVADILA 253

Query: 247 PHL 249
              
Sbjct: 254 LCR 256


>gi|67459255|ref|YP_246879.1| ribosomal large subunit pseudouridine synthase [Rickettsia felis
           URRWXCal2]
 gi|75536313|sp|Q4UL59|Y544_RICFE RecName: Full=Uncharacterized RNA pseudouridine synthase RF_0863;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|67004788|gb|AAY61714.1| Ribosomal large subunit pseudouridine synthase [Rickettsia felis
           URRWXCal2]
          Length = 229

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 112/229 (48%), Positives = 157/229 (68%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR++K+I+ AGI SRR+ E++I + +VKV+GI +   A NV  ++ IEV G+ + ++++ 
Sbjct: 2   QRLAKIISNAGICSRRDAEKLILEGQVKVDGITILSPATNVDISNQIEVSGILINQSQKP 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW+Y+KP+GL+TTH DP  R TVF+ L +   RVIS+GRLD+N+EGLLLLTN G LAR 
Sbjct: 62  RLWIYYKPVGLITTHKDPLSRKTVFEQL-TGLPRVISIGRLDLNSEGLLLLTNSGDLARQ 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
            ELPS +  RVY VR +G+ D    +   K + I GI Y    + L  Q  SN+W  V L
Sbjct: 121 FELPSNRLKRVYHVRAYGKSDILLKSD-YKNLEIDGIFYNPHSIKLFKQNKSNSWFEVVL 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EGKNREI+++FE+F  KVN+LIRI YG F +  L  G+ +E++ KIL 
Sbjct: 180 FEGKNREIRRIFEYFGLKVNKLIRIQYGSFTIDNLKPGAYKEINNKILE 228


>gi|221314557|ref|ZP_03596362.1| pseudouridine synthase [Bacillus subtilis subsp. subtilis str. NCIB
           3610]
          Length = 229

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 75/226 (33%), Positives = 120/226 (53%), Gaps = 3/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E +I + +VKVNG ++    V V  +D IEV+G+ + + E  
Sbjct: 2   ERLQKVIAHAGVASRRKAEELIKEGKVKVNGKVVTELGVKVTGSDQIEVNGLKVEREEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     +++   D  GR  V D   +I  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 62  YFLLYKPRG-VISAAQDDKGRKVVTDFFKNIPQRIYPIGRLDYDTSGLLLLTNDGEFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVTV 191
           L  P  +  + Y  +  G   ++ L  L++GI ++       +  L    +K   + + +
Sbjct: 121 LMHPKYEIDKTYVAKVKGIPPKELLRKLERGIRLEEGKTAPAKAKLLSLDKKKQTSIIQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++++FE    +V +L R  Y    L  L  G  RE+ 
Sbjct: 181 TIHEGRNRQVRRMFEAIGHEVIKLKREEYAFLNLRGLHTGDARELR 226


>gi|18311246|ref|NP_563180.1| 16S pseudouridylate synthase [Clostridium perfringens str. 13]
 gi|110800371|ref|YP_696936.1| 16S pseudouridylate synthase [Clostridium perfringens ATCC 13124]
 gi|168205092|ref|ZP_02631097.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           E str. JGS1987]
 gi|168216772|ref|ZP_02642397.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           NCTC 8239]
 gi|182625568|ref|ZP_02953339.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           D str. JGS1721]
 gi|18145929|dbj|BAB81970.1| 16S pseudouridylate synthase [Clostridium perfringens str. 13]
 gi|110675018|gb|ABG84005.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           ATCC 13124]
 gi|170663292|gb|EDT15975.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           E str. JGS1987]
 gi|177909256|gb|EDT71721.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           D str. JGS1721]
 gi|182381141|gb|EDT78620.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           NCTC 8239]
          Length = 239

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 56/231 (24%), Positives = 105/231 (45%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV++  G  +R+E+++++ +  V VN   ++ + + +    D I ++G  +   + 
Sbjct: 2   ERLDKVLSNLGYGTRKEIKQVVKKGFVTVNDEKVKDSGLQIDPEKDTIVINGEKVEYKKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  T+   D        +         VGRLD +T GLLLLTNDG L  
Sbjct: 62  IYLMMNKPAGVISATYDKRDETVIDLLYMEDQVFEPFPVGRLDKDTVGLLLLTNDGDLNH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY    +  + +  +   + G+ +         ++ +      ++ V V
Sbjct: 122 KLISPKYHVDKVYYAEINAPITEKDIKAFENGVTLDDGYKCMSAKLKVIENLEDSSRVEV 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            ++EGK  ++K++FE    KV  L R S+G   L   L  G  +E+S+  L
Sbjct: 182 TVQEGKYHQVKRMFEARGKKVVYLKRTSFGNLPLDESLEEGEYKELSESEL 232


>gi|258404933|ref|YP_003197675.1| pseudouridine synthase [Desulfohalobium retbaense DSM 5692]
 gi|257797160|gb|ACV68097.1| pseudouridine synthase [Desulfohalobium retbaense DSM 5692]
          Length = 274

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 80/239 (33%), Positives = 120/239 (50%), Gaps = 8/239 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R++K +A+AG+ SRR+ +  IA  RV+VNG L+ +  V V    D + VDG  +  
Sbjct: 27  PESCRLNKFLAQAGVCSRRKADTYIAAGRVQVNGSLVTQLGVQVHPGQDEVRVDGRVVEL 86

Query: 70  AERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLL 123
            E         L HKP+ +VTT  DP GR TV D L   +   R+  VGRLD  +EGLLL
Sbjct: 87  PEAQSAGHDYILLHKPVQVVTTAKDPQGRRTVLDLLPSQTFTRRIFPVGRLDFMSEGLLL 146

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQ 182
           LT+DG LA  L  P     +VY V     V ++ +  +  G+ + +G     + V     
Sbjct: 147 LTSDGELANRLTHPRWHVEKVYEVTLREAVTEEHMRQMSSGMRLSEGEQLAPVDVQRRKT 206

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
               + + + L +G NR+I+++       + RL RI  GP +LG L  G  R ++   +
Sbjct: 207 AADTSSLELTLHQGVNRQIRRMCRDLGLTILRLKRIRQGPVRLGKLPQGHWRHLTATEI 265


>gi|24115303|ref|NP_709813.1| 23S rRNA pseudouridine synthase F [Shigella flexneri 2a str. 301]
 gi|30064697|ref|NP_838868.1| 23S rRNA pseudouridine synthase F [Shigella flexneri 2a str. 2457T]
 gi|74314515|ref|YP_312934.1| 23S rRNA pseudouridine synthase F [Shigella sonnei Ss046]
 gi|82546365|ref|YP_410312.1| 23S rRNA pseudouridine synthase F [Shigella boydii Sb227]
 gi|110807871|ref|YP_691391.1| 23S rRNA pseudouridine synthase F [Shigella flexneri 5 str. 8401]
 gi|187733719|ref|YP_001882708.1| 23S rRNA pseudouridine synthase F [Shigella boydii CDC 3083-94]
 gi|194432289|ref|ZP_03064577.1| ribosomal large subunit pseudouridine synthase F [Shigella
           dysenteriae 1012]
 gi|34098456|sp|Q83IR6|RLUF_SHIFL RecName: Full=Ribosomal large subunit pseudouridine synthase F;
           AltName: Full=rRNA pseudouridylate synthase F; AltName:
           Full=rRNA-uridine isomerase F
 gi|24054601|gb|AAN45520.1| orf, conserved hypothetical protein [Shigella flexneri 2a str. 301]
 gi|30042957|gb|AAP18679.1| hypothetical protein S3635 [Shigella flexneri 2a str. 2457T]
 gi|73857992|gb|AAZ90699.1| conserved hypothetical protein [Shigella sonnei Ss046]
 gi|81247776|gb|ABB68484.1| conserved hypothetical protein [Shigella boydii Sb227]
 gi|110617419|gb|ABF06086.1| conserved hypothetical protein [Shigella flexneri 5 str. 8401]
 gi|187430711|gb|ACD09985.1| ribosomal large subunit pseudouridine synthase F [Shigella boydii
           CDC 3083-94]
 gi|194419492|gb|EDX35573.1| ribosomal large subunit pseudouridine synthase F [Shigella
           dysenteriae 1012]
 gi|281603406|gb|ADA76390.1| Ribosomal large subunit pseudouridine synthase F [Shigella flexneri
           2002017]
 gi|313648678|gb|EFS13118.1| ribosomal large subunit pseudouridine synthase F [Shigella flexneri
           2a str. 2457T]
 gi|320187140|gb|EFW61842.1| 23S rRNA pseudouridine synthase F [Shigella flexneri CDC 796-83]
 gi|332083850|gb|EGI89067.1| ribosomal large subunit pseudouridine synthase F [Shigella boydii
           5216-82]
 gi|332084289|gb|EGI89492.1| ribosomal large subunit pseudouridine synthase F [Shigella
           dysenteriae 155-74]
 gi|332087766|gb|EGI92892.1| ribosomal large subunit pseudouridine synthase F [Shigella boydii
           3594-74]
 gi|332752238|gb|EGJ82630.1| ribosomal large subunit pseudouridine synthase F [Shigella flexneri
           K-671]
 gi|332753238|gb|EGJ83619.1| ribosomal large subunit pseudouridine synthase F [Shigella flexneri
           2747-71]
 gi|332764829|gb|EGJ95058.1| 23S rRNA pseudouridine synthase [Shigella flexneri 2930-71]
 gi|332998087|gb|EGK17691.1| ribosomal large subunit pseudouridine synthase F [Shigella flexneri
           VA-6]
 gi|332999015|gb|EGK18604.1| ribosomal large subunit pseudouridine synthase F [Shigella flexneri
           K-272]
 gi|333014244|gb|EGK33600.1| ribosomal large subunit pseudouridine synthase F [Shigella flexneri
           K-304]
 gi|333014452|gb|EGK33803.1| ribosomal large subunit pseudouridine synthase F [Shigella flexneri
           K-227]
          Length = 290

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 62/292 (21%), Positives = 115/292 (39%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDIVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++    A        ++     + +  +   R   N  +     ++KK  
Sbjct: 239 SSSEAKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 290


>gi|320179014|gb|EFW53973.1| 23S rRNA pseudouridine synthase F [Shigella boydii ATCC 9905]
          Length = 290

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 62/292 (21%), Positives = 115/292 (39%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDIVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRVGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++    A        ++     + +  +   R   N  +     ++KK  
Sbjct: 239 SSSEAKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 290


>gi|327438231|dbj|BAK14596.1| 16S rRNA uridine-516 pseudouridylate synthase [Solibacillus
           silvestris StLB046]
          Length = 234

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 112/234 (47%), Gaps = 7/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K +A  GI SRR  ++ +   RVK+NG++       V + D + VDG P+++ E  
Sbjct: 1   MRINKFLAETGIVSRRGADKWVEDGRVKINGVVATN-GSQVETGDEVLVDGKPVKRQEEL 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP+G+ +T       + V  +  +   R+  +GRLD ++EGLLLLTNDG +   
Sbjct: 60  VYIVLNKPVGITSTTEKQIEGNVV--DFVNHRLRIFHIGRLDKDSEGLLLLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V+    +    ++ +  G+ I        +V    +K S+    + L
Sbjct: 118 ILRAENHHEKEYVVQVDKPITDQFIHDMSSGVEILDTTTLPCRV----EKVSSKVFKIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            +G NR+I+++     + V RL RI      +G L  G  R+++ K   E    
Sbjct: 174 EQGLNRQIRRMCSALGYSVQRLQRIRIMNIHIGNLKVGQWRDLTDKERNELFQL 227


>gi|317133055|ref|YP_004092369.1| pseudouridine synthase [Ethanoligenens harbinense YUAN-3]
 gi|315471034|gb|ADU27638.1| pseudouridine synthase [Ethanoligenens harbinense YUAN-3]
          Length = 243

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 76/240 (31%), Positives = 120/240 (50%), Gaps = 3/240 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
           +    R+ K ++  G  SRR+ E  I   RV+VNG        +V    D + VDG  + 
Sbjct: 2   SAKEMRLQKYLSECGETSRRKAEIWITAGRVQVNGRPAR-LGQSVHPSKDLVTVDGRAVA 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            +        +KP G VTT  D   R  V D L  + +RV  +GRLD ++EGLLLLT+DG
Sbjct: 61  PSP-KVYIALNKPRGYVTTLHDELDRRCVTDLLKGVETRVYPIGRLDRDSEGLLLLTDDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             A  L  P     ++Y V    +V ++++  L+ GI + G      +VT+       + 
Sbjct: 120 AFANALTHPRHHVPKIYHVSVRPRVTEEQVARLQNGIELDGRMTAPAKVTVLRSGSDRSV 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + + L EG+NR+I+++ E    +V RL R++ G  +LG L +G  RE++ K +R      
Sbjct: 180 LELVLYEGRNRQIRRMCEALGLEVARLSRVAVGTVKLGGLRSGQWRELTDKEVRALERAA 239


>gi|205374450|ref|ZP_03227246.1| pseudouridylate synthase (ribosomal small subunit pseudouridine
           synthase A) [Bacillus coahuilensis m4-4]
          Length = 236

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 101/233 (43%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV+ ++    V VNG   +    +V  + D + V G  +   E 
Sbjct: 1   MRIDKLLANMGYGSRKEVKSLLKSGNVVVNGTGCKDGKQHVNPSQDEVFVHGEKVVYREF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  T    D                  VGRLD +TEGLL++TNDG L+ 
Sbjct: 61  IYLLMNKPQGVISATEDLRDETVIDLLEPDHRVFNPFPVGRLDKDTEGLLIITNDGQLSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G V ++ +    +G+ +          + +    G  + + +
Sbjct: 121 QLLSPKKHVPKTYYAEVKGVVTEEDVAAFSEGVTLDDGYHTKPGDLVIL-SSGEMSEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
            + EGK  ++K++FE    KV  L RI  GP  L   L  G  RE+S++ + +
Sbjct: 180 TITEGKFHQVKRMFESVGKKVVYLQRIKMGPILLDENLELGEYRELSQEEIDQ 232


>gi|157803631|ref|YP_001492180.1| repair protein [Rickettsia canadensis str. McKiel]
 gi|157784894|gb|ABV73395.1| predicted repair protein [Rickettsia canadensis str. McKiel]
          Length = 229

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 110/229 (48%), Positives = 157/229 (68%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR++KVI+ +G+ SRR+ E++IA+ +VKV+GI +   A NV  ++ IEV G+ + ++++ 
Sbjct: 2   QRLAKVISNSGVCSRRDAEKLIAEGQVKVDGITILAPATNVDISNQIEVSGILINQSQKP 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW+Y+KP+GL+TTH DP  R TVF++L +   RVIS+GRLD+N+EGLLLLTN G LAR 
Sbjct: 62  RLWIYYKPVGLITTHKDPLSRKTVFEDL-TSLPRVISIGRLDLNSEGLLLLTNSGDLARQ 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
            ELPS +  RVY VR +G  D    +   K + I GI Y    + L     +NAW  + L
Sbjct: 121 FELPSNKLKRVYHVRAYGNPDILLKSE-YKNLEIDGILYNPYSIKLLRGNNTNAWFEIVL 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EGKNREI+++FE+F  KVN+LIR+ YG F +G L  G  +E++ KIL 
Sbjct: 180 FEGKNREIRRIFEYFGLKVNKLIRVQYGSFTIGNLKPGDYKEINNKILE 228


>gi|269978223|ref|ZP_06185173.1| ribosomal large subunit pseudouridine synthase B [Mobiluncus
           mulieris 28-1]
 gi|306818599|ref|ZP_07452322.1| ribosomal large subunit pseudouridine synthase B [Mobiluncus
           mulieris ATCC 35239]
 gi|269933732|gb|EEZ90316.1| ribosomal large subunit pseudouridine synthase B [Mobiluncus
           mulieris 28-1]
 gi|304648772|gb|EFM46074.1| ribosomal large subunit pseudouridine synthase B [Mobiluncus
           mulieris ATCC 35239]
          Length = 278

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 70/231 (30%), Positives = 118/231 (51%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+ K++++AG+ASRR  E +I + RV+V+G  +    + V+ +  I V+G  +   
Sbjct: 39  EEPVRLQKLLSQAGVASRRASEDLIKRGRVQVDGETVTEMGLKVLPSARITVNGQRIHTD 98

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++W ++KP+G V+T    D R  + D    +  RV  VGRLD+ T GL+LLTN+G L
Sbjct: 99  AALQVWAFNKPVGTVSTMQPEDDRPCLGDWATKLPQRVFHVGRLDVATSGLILLTNNGDL 158

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P  +  + Y     GQV      +L++G+ ++          L   +  ++ V 
Sbjct: 159 ANRLVHPRYEVPKTYVAMVQGQVKPGLGKVLRRGVELEDGVTKVDTFKLVEVRRGSSIVQ 218

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + L  GKNR ++++       V+ L R + G  +LG L  G  R ++   L
Sbjct: 219 LTLHSGKNRVVRRLLSEVGHPVSALTRTAIGTLRLGDLKEGHFRLLTGSDL 269


>gi|255012441|ref|ZP_05284567.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           2_1_7]
          Length = 495

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 57/241 (23%), Positives = 116/241 (48%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K K ++ +   P R++K ++ AG+ SRRE +  I +  VKVN +++      +   D +
Sbjct: 247 IKYKEVLADPNEPIRLNKFLSNAGVCSRREADEFIQKGAVKVNDVVVTELGTKITRQDVV 306

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
             +  P++   +  + L      + T+    +  + +     +   R+  VGRLD NT G
Sbjct: 307 TFNEKPVQIESKVYIVLNKPKNCVTTSDDPQERLTVMDLVKNACQERIYPVGRLDRNTTG 366

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  PS +  ++Y V     V  + +  +  G+ ++        ++  
Sbjct: 367 VLLLTNDGDLASKLTHPSFKKKKIYHVWLDKNVAIEDMEKIANGLELEDGEIHADAISYA 426

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++    + V + +  G+NR ++++FE   + V +L R+ +       L  G  R ++++ 
Sbjct: 427 SED-DKSQVGIEIHSGRNRIVRRIFESLGYHVTKLDRVYFAGLTKKNLGRGKWRYLNERE 485

Query: 241 L 241
           +
Sbjct: 486 V 486


>gi|110802628|ref|YP_699525.1| 16S pseudouridylate synthase [Clostridium perfringens SM101]
 gi|110683129|gb|ABG86499.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           SM101]
          Length = 239

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 56/231 (24%), Positives = 105/231 (45%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV++  G  +R+E+++++ +  V VN   ++ + + +    D I ++G  +   + 
Sbjct: 2   ERLDKVLSNLGYGTRKEIKQVVKKGFVTVNDEKVKDSGLQIDPEKDTIVINGEKVEYKKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  T+   D        +         VGRLD +T GLLLLTNDG L  
Sbjct: 62  IYLMMNKPAGVISATYDKRDETVIDLLYMEDQVFEPFPVGRLDKDTVGLLLLTNDGDLNH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY    +  + +  +   + G+ +         ++ +      ++ V V
Sbjct: 122 KLISPKYHVDKVYYAEINAPITEKDIKAFENGVTLDDGYKCMSAKLKVIENLEDSSRVEV 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            ++EGK  ++K++FE    KV  L R S+G   L   L  G  +E+S+  L
Sbjct: 182 TVQEGKYHQVKRMFEARGKKVIYLKRTSFGNLPLDESLEEGEYKELSESEL 232


>gi|15598375|ref|NP_251869.1| hypothetical protein PA3179 [Pseudomonas aeruginosa PAO1]
 gi|107102709|ref|ZP_01366627.1| hypothetical protein PaerPA_01003775 [Pseudomonas aeruginosa PACS2]
 gi|116051168|ref|YP_790001.1| hypothetical protein PA14_23110 [Pseudomonas aeruginosa UCBPP-PA14]
 gi|218890629|ref|YP_002439493.1| putative pseudouridine synthase [Pseudomonas aeruginosa LESB58]
 gi|254236141|ref|ZP_04929464.1| conserved hypothetical protein [Pseudomonas aeruginosa C3719]
 gi|254241866|ref|ZP_04935188.1| conserved hypothetical protein [Pseudomonas aeruginosa 2192]
 gi|296388337|ref|ZP_06877812.1| putative pseudouridine synthase [Pseudomonas aeruginosa PAb1]
 gi|34098721|sp|Q9HZ55|RLUB_PSEAE RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|9949297|gb|AAG06567.1|AE004742_3 conserved hypothetical protein [Pseudomonas aeruginosa PAO1]
 gi|115586389|gb|ABJ12404.1| putative pseudouridine synthase [Pseudomonas aeruginosa UCBPP-PA14]
 gi|126168072|gb|EAZ53583.1| conserved hypothetical protein [Pseudomonas aeruginosa C3719]
 gi|126195244|gb|EAZ59307.1| conserved hypothetical protein [Pseudomonas aeruginosa 2192]
 gi|218770852|emb|CAW26617.1| putative pseudouridine synthase [Pseudomonas aeruginosa LESB58]
          Length = 386

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 89/360 (24%), Positives = 145/360 (40%), Gaps = 19/360 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+AR G+ SRR+VE  IA+ RV VNG +       V S D I VDG  +R+ E 
Sbjct: 13  GEKLQKVLARLGVGSRRDVEVWIAEGRVNVNGSVA-SLGQRVDSHDAITVDGHLIRREEA 71

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R  L        + T        +           R I+VGRLDINT GLLL T D
Sbjct: 72  AESVRRVLIYNKPEGEVCTRDDPEGRPTIFDRLPRLRTGRWINVGRLDINTTGLLLFTTD 131

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSN 186
           G LA  L  PS +  R Y VR  G+V ++ +  L  G++++        +      +G N
Sbjct: 132 GELANRLMHPSYEMDREYAVRVRGEVTEEMIERLLNGVMLEDGPAKFSDIQQAPGGEGFN 191

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR--- 242
            W    + EG+NRE+++++E     V+RL R+ +GP  L   L  G  RE+ ++ +    
Sbjct: 192 HWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLTSELTMGRYREMDQREIDILS 251

Query: 243 --------EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
                      G       +        +      +RP    +        +  + +   
Sbjct: 252 EEVGLKPVALPGMTTKAREKAERQQRKQARPLARSERPEAGRKRAPRREDGENAARRAPA 311

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               +       R+       +A+    S       +  + R + +   K + R+   K+
Sbjct: 312 SRPARGPQPSAERKGREQGTPVAERPRESNRKPRPSKPRDERPASAPGDKPAARKPQVKR 371


>gi|306833833|ref|ZP_07466958.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           bovis ATCC 700338]
 gi|304424027|gb|EFM27168.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           bovis ATCC 700338]
          Length = 242

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 101/232 (43%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +  AGI SR EV++++ +++V VNG +       +    D I   G  L   + 
Sbjct: 1   MRLDKFLVEAGIGSRTEVKQLLKKKQVLVNGKVEISPKTQIDEKADQIRCQGQTLSYEKY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  +         +  +       VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYMLNKPKGVISATEDNHHKTVLDLLDKTAWDKETFPVGRLDIDTHGLLLLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVT 190
            +  P     + YR +  G +    +     GI ++       Q+ +     +   + V 
Sbjct: 121 AMLSPKKHVDKTYRAKVAGLMTTTDVAAFANGIDLKDFTCQPAQLVILEINEAERTSVVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + ++EGK  +IK++ +    KV  L R+S GP QL   L  G  R ++   L
Sbjct: 181 ITIKEGKFHQIKRMVQACGKKVTDLQRLSMGPLQLDKQLALGEWRRLTDDEL 232


>gi|269797888|ref|YP_003311788.1| pseudouridine synthase [Veillonella parvula DSM 2008]
 gi|269094517|gb|ACZ24508.1| pseudouridine synthase [Veillonella parvula DSM 2008]
          Length = 242

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 67/237 (28%), Positives = 119/237 (50%), Gaps = 4/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K IA  GIASRR+ E +I + +V+VNG  +    V +    D ++V+G  L + + 
Sbjct: 2   ERLQKYIASCGIASRRKAEELITEGKVQVNGRKVTELGVKINPQKDKVKVNGQLLAQEKP 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      + +        + +         R+  +GRLD+ TEGLLLLTNDG  A+
Sbjct: 62  VYYLLNKPKGVITSVSDPQGRETVLDYIKNETK-RIYPIGRLDLYTEGLLLLTNDGEFAQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            L  PS    + Y VR  G+V  D L ++  G+ ++        +        N    V 
Sbjct: 121 NLTHPSKGVEKTYEVRIKGRVRDDDLQIIANGVELEDGITAPATIVDLGFDDHNGVHEVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           + + EG+NR+++++FE F ++++ L RI+Y    LG +  G++R+++ + ++     
Sbjct: 181 ITIHEGRNRQVRRMFEHFGYRIHNLKRIAYAGLTLGGVKRGASRQLTIREVKALKAL 237


>gi|320160581|ref|YP_004173805.1| pseudouridine synthase [Anaerolinea thermophila UNI-1]
 gi|319994434|dbj|BAJ63205.1| pseudouridine synthase [Anaerolinea thermophila UNI-1]
          Length = 245

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 77/231 (33%), Positives = 114/231 (49%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +RV K++ARAG  SRR  E +I   RVK+NG            + D I VDG  +     
Sbjct: 4   ERVQKILARAGYGSRRACEELILAGRVKINGQTA-VLGSKADPSRDQILVDGQKIPLQPP 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + HKP G+++             +L  +   + SVGRLD  +EGL+LLTNDG LA 
Sbjct: 63  PVYIMLHKPQGVLSDVEVHKDPRPTVRDLVPVEGHLFSVGRLDYESEGLILLTNDGELAN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + YRV    + D+ +L   + G+V++        QV ++   G  AW+ V
Sbjct: 123 RLTHPRYGHEKEYRVLVGTRPDERQLEAWRHGVVLEDGYRTAPAQVRVEGVAGKGAWLRV 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            LREG+ R+I+++       V R+IRI  G   LG L  G  R ++ + +R
Sbjct: 183 ILREGRKRQIREMGRLTGLPVLRIIRIRIGSLLLGDLKPGEWRYLTPQEVR 233


>gi|52140956|ref|YP_085874.1| tRNA pseudouridine synthase A [Bacillus cereus E33L]
 gi|51974425|gb|AAU15975.1| tRNA pseudouridine synthase A [Bacillus cereus E33L]
          Length = 229

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 110/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGKICTH-GALVNEGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T ++    + +     +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAAEHIEGNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYIVTVDKPFTDWFIDEMSGGVKIKDGMTKPCKVTRV----DQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVKKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>gi|147677969|ref|YP_001212184.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthase [Pelotomaculum
           thermopropionicum SI]
 gi|146274066|dbj|BAF59815.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthase [Pelotomaculum
           thermopropionicum SI]
          Length = 252

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 83/236 (35%), Positives = 125/236 (52%), Gaps = 1/236 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV+ARAG+ASRR  ER+IA   VKVNG ++      V    D I+V    +    R
Sbjct: 14  ERLQKVMARAGVASRRHCERLIAAGAVKVNGKVVTEVGCKVDPARDKIQVGNRTISLFPR 73

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G VTT SD  GR  V D L  +  RV  VGRLD ++EGLLLLTNDG L  
Sbjct: 74  RYYILLYKPRGYVTTLSDEKGRKKVTDLLKGVAGRVYPVGRLDYDSEGLLLLTNDGELTY 133

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + Y V   G   ++KL  +  G++++       +V L  ++G N  + + 
Sbjct: 134 ALTHPKHRVPKTYVVSVKGLPGREKLEKMAGGLMLEDGPTAPARVRLIGRRGKNVLLEIT 193

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + EG+NR+I+++ +     V RL R   G   +G L  G  R ++++ +++     
Sbjct: 194 ISEGRNRQIRRMCDSIGHPVVRLKRTKLGSLSIGNLRPGQYRHLTREEIKKLKEDA 249


>gi|227875336|ref|ZP_03993478.1| possible pseudouridine synthase [Mobiluncus mulieris ATCC 35243]
 gi|307700863|ref|ZP_07637888.1| putative pseudouridine synthase B, ribosomal large subunit
           [Mobiluncus mulieris FB024-16]
 gi|227844241|gb|EEJ54408.1| possible pseudouridine synthase [Mobiluncus mulieris ATCC 35243]
 gi|307613858|gb|EFN93102.1| putative pseudouridine synthase B, ribosomal large subunit
           [Mobiluncus mulieris FB024-16]
          Length = 278

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 70/231 (30%), Positives = 118/231 (51%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+ K++++AG+ASRR  E +I + RV+V+G  +    + V+ +  I V+G  +   
Sbjct: 39  EEPVRLQKLLSQAGVASRRASEDLIKRGRVQVDGETVTEMGLKVLPSARITVNGQRIHTD 98

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++W ++KP+G V+T    D R  + D    +  RV  VGRLD+ T GL+LLTN+G L
Sbjct: 99  AALQVWAFNKPVGTVSTMQPEDDRPCLGDWATKLPQRVFHVGRLDVATAGLILLTNNGDL 158

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P  +  + Y     GQV      +L++G+ ++          L   +  ++ V 
Sbjct: 159 ANRLVHPRYEVPKTYVAMVQGQVKPGLGKVLRRGVELEDGVTKVDTFKLVEVRRGSSIVQ 218

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + L  GKNR ++++       V+ L R + G  +LG L  G  R ++   L
Sbjct: 219 LTLHSGKNRVVRRLLSEVGHPVSALTRTAIGTLRLGDLKEGHFRLLTGSDL 269


>gi|229163541|ref|ZP_04291491.1| RNA pseudouridine synthase [Bacillus cereus R309803]
 gi|228619923|gb|EEK76799.1| RNA pseudouridine synthase [Bacillus cereus R309803]
          Length = 229

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 106/230 (46%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTH-GALVSDGDVVTIDGQIIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D    + +     +   R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAADHIEDNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +   + I+       QVT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSGVVKIKDGMTKQCQVTRV----DQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L 
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELDNLEVGKWRNVTSEELE 223


>gi|317495282|ref|ZP_07953652.1| RNA pseudouridylate synthase [Gemella moribillum M424]
 gi|316914704|gb|EFV36180.1| RNA pseudouridylate synthase [Gemella moribillum M424]
          Length = 243

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 64/237 (27%), Positives = 121/237 (51%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+IA +G  SRR+ E++I + +V VNG ++++  V    +D I V+G+ L K  + 
Sbjct: 3   ERLQKLIAASGYTSRRKAEQLILEGKVSVNGEVIKQLGVKAEPSDVIIVEGLRLLKENKK 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     + +   +   R  V D   ++  RV+ VGRLD +T G L+++NDG    +
Sbjct: 63  YYLFYKPEKVITSMSDE-KDRVCVKDFFEAVNERVVPVGRLDYDTSGALIMSNDGEFINL 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  + Y  + +G++++  L +L+ G+ I        +V +   K    N  V +
Sbjct: 122 ITHPKHKIKKTYVAKINGKLEEHHLKILRSGVRIDNYKTSPAEVNIVKNKNKSGNTLVRL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + EGKNR+++++FE   ++V +L R S     L  L  G  R ++   ++  +   
Sbjct: 182 TIHEGKNRQVRRMFEALGYEVMKLKRESIEDLTLDGLRKGEYRILTIHEVKRLINKA 238


>gi|302389211|ref|YP_003825032.1| ribosomal small subunit pseudouridine synthase A
           [Thermosediminibacter oceani DSM 16646]
 gi|302199839|gb|ADL07409.1| ribosomal small subunit pseudouridine synthase A
           [Thermosediminibacter oceani DSM 16646]
          Length = 243

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 65/234 (27%), Positives = 113/234 (48%), Gaps = 3/234 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
              +R+ KV++ AG  SR++V+++I +  V+VNG ++  A   V    D I V G  L  
Sbjct: 3   EKTERLDKVLSMAGYGSRKDVKKIIKRGEVEVNGRVVTDAGTPVAPAVDSISVSGELLIF 62

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   + +      +  TH   +               +  VGRLD + EGLLLLT+DG 
Sbjct: 63  KEHIYIMMNKPQGVISATHDRRETTVIDLLEDEFSHRNLFPVGRLDKDAEGLLLLTDDGQ 122

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  P  +  +VY V   G++ ++ +   K+G+ +        ++ +      ++ +
Sbjct: 123 LAHRLLSPRKKVEKVYYVEVKGRLVEEDVKAFKEGVFLGDYRALPAKLEILEAGEVSSAL 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            V + EGK  +IK++ +    +V  L R+S GP +L   L  G  RE++ + +R
Sbjct: 183 -VTIYEGKFHQIKRMMKARGKEVTYLKRLSMGPLKLDENLEPGEWRELTDEEIR 235


>gi|157964674|ref|YP_001499498.1| ribosomal large subunit pseudouridine synthase [Rickettsia
           massiliae MTU5]
 gi|157844450|gb|ABV84951.1| Ribosomal large subunit pseudouridine synthase [Rickettsia
           massiliae MTU5]
          Length = 229

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 109/228 (47%), Positives = 150/228 (65%), Gaps = 2/228 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K+I+ AG+ SRR+ E++I + +VKV+GI +   A NV  ++ IEV G  +    + R
Sbjct: 3   RLAKIISNAGVCSRRDAEKLIVEGQVKVDGITILSPATNVDISNQIEVSGTLINNIHKPR 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LW+Y+KP+GL+TTH DP  R TVF+ L      VIS+GRLD+N+EGLLLLTN G LAR  
Sbjct: 63  LWIYYKPVGLITTHKDPLSRKTVFEQLTG-LPHVISIGRLDLNSEGLLLLTNSGDLARQF 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPS++  RVY VR +G+ D    +   K + I GI Y    + L  Q  SN+W  V L 
Sbjct: 122 ELPSSRLKRVYHVRAYGKSDILLKSH-YKNLEIDGIFYNPHSIKLLKQNKSNSWFEVVLF 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           EGKNREI+++FE+F  KVN+LIRI YG F +  L  G  +E++ KIL 
Sbjct: 181 EGKNREIRRIFEYFGLKVNKLIRIQYGSFTIDNLKPGDYKEINNKILE 228


>gi|323488402|ref|ZP_08093649.1| pseudouridine synthase [Planococcus donghaensis MPA1U2]
 gi|323397909|gb|EGA90708.1| pseudouridine synthase [Planococcus donghaensis MPA1U2]
          Length = 237

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 102/231 (44%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K ++  G  SR+EV+ ++  + V+VNG ++    V+V   TD + V G  +   E 
Sbjct: 1   MRLDKYLSNMGHGSRKEVKVLLKSKAVEVNGEIVRDPKVHVNEHTDLVSVGGEAVTYTEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  T    D                  VGRLD +TEG LLLTNDG LA 
Sbjct: 61  IYLLMNKPQGVISATEDKYDKTVIDLLGKDEQHFEPFPVGRLDKDTEGFLLLTNDGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G V ++     KKG+V+          + +       + + +
Sbjct: 121 ELLSPKKHVDKTYFAHVEGVVTEEDTEAFKKGVVLDDGYETKPASLNILD-SAVVSKIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++K++FE    +V  L R+S GP  L   L  G  R ++++ +
Sbjct: 180 TITEGKFHQVKRMFESVGKRVVYLKRLSMGPLSLDPELELGEYRHLTEEEM 230


>gi|256752686|ref|ZP_05493537.1| pseudouridine synthase [Thermoanaerobacter ethanolicus CCSD1]
 gi|256748448|gb|EEU61501.1| pseudouridine synthase [Thermoanaerobacter ethanolicus CCSD1]
          Length = 240

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 67/231 (29%), Positives = 110/231 (47%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K+++  GI +R+EV++ I +  V VNG  ++ A + +   TD I  DG  +   E 
Sbjct: 4   MRIDKLLSNIGIGTRKEVKKFIKEGLVLVNGNTVKDAGLIINTETDEILFDGKKIYYKEF 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      +  T+   +                  VGRLD +TEGLLL+TNDG LA 
Sbjct: 64  IYIMMNKPKGVISATYDPIEKTVIDLLPQELKARNPFPVGRLDKDTEGLLLITNDGDLAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P    ++ Y  +  G V++  +    +GIV++         + + +     + V V
Sbjct: 124 KLLSPKKNVIKKYYAKILGFVNESDIKAFNEGIVLEDGYKTLPANLEILSSSDV-SKVYV 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            +REGK  +IK++FE    KV  L R++ G   L   L  G  RE+S++ L
Sbjct: 183 YIREGKYHQIKRMFESVGKKVIYLKRLAMGNLTLDENLKPGEWRELSEEEL 233


>gi|148260478|ref|YP_001234605.1| RNA-binding S4 domain-containing protein [Acidiphilium cryptum
           JF-5]
 gi|326403671|ref|YP_004283753.1| ribosomal large subunit pseudouridine synthase B [Acidiphilium
           multivorum AIU301]
 gi|146402159|gb|ABQ30686.1| RNA-binding S4 domain protein [Acidiphilium cryptum JF-5]
 gi|325050533|dbj|BAJ80871.1| ribosomal large subunit pseudouridine synthase B [Acidiphilium
           multivorum AIU301]
          Length = 247

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 132/238 (55%), Positives = 168/238 (70%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           +     +R++K +ARAG+ASRR+ ERMI   RV +NG  +   A  V + D I +DG P+
Sbjct: 5   ESGERGERIAKYLARAGVASRRDAERMIESGRVALNGTKVLHPATFVAAGDIILIDGSPV 64

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            +  RTRLW YHK  GL+TTH DP+GR T+F+ +P    RV+SVGRLD+N+EGLLLLTND
Sbjct: 65  GEPSRTRLWRYHKRAGLLTTHRDPEGRPTIFERMPPELPRVVSVGRLDLNSEGLLLLTND 124

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LAR LELP+T WLR YRVR HG VD  +L  LK GIV+ G+ YG +   +D+ KGSN+
Sbjct: 125 GALARQLELPTTGWLRRYRVRVHGTVDPARLAALKGGIVVDGVRYGPISAEIDSTKGSNS 184

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           W+ VGL EGKNREI+KV      +  RLIRI+YGPFQLG L  G+  EV+ K+LREQL
Sbjct: 185 WLAVGLNEGKNREIRKVMAALGLETTRLIRIAYGPFQLGNLPRGAVAEVNPKVLREQL 242


>gi|30022627|ref|NP_834258.1| tRNA pseudouridine synthase A [Bacillus cereus ATCC 14579]
 gi|229112015|ref|ZP_04241558.1| RNA pseudouridine synthase [Bacillus cereus Rock1-15]
 gi|229129835|ref|ZP_04258801.1| RNA pseudouridine synthase [Bacillus cereus BDRD-Cer4]
 gi|229147110|ref|ZP_04275469.1| RNA pseudouridine synthase [Bacillus cereus BDRD-ST24]
 gi|29898185|gb|AAP11459.1| tRNA pseudouridine synthase A [Bacillus cereus ATCC 14579]
 gi|228636359|gb|EEK92830.1| RNA pseudouridine synthase [Bacillus cereus BDRD-ST24]
 gi|228653526|gb|EEL09398.1| RNA pseudouridine synthase [Bacillus cereus BDRD-Cer4]
 gi|228671338|gb|EEL26639.1| RNA pseudouridine synthase [Bacillus cereus Rock1-15]
          Length = 229

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 110/230 (47%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A + SRRE +R+I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKLCSRRETDRLIKAGRVAINGEICTH-GALVSDGDRVTIDGQVIVKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D    + +     +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAADHIEDNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ + +G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSRGVKIKDGMTKPCKVTRV----DQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L 
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTAEELE 223


>gi|262091774|gb|ACY25362.1| pseudouridine synthase family [uncultured actinobacterium]
          Length = 237

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 75/229 (32%), Positives = 115/229 (50%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R++K+IA AGI SRR  + +I   RV VNGI++           D + VDG  + +   
Sbjct: 4   MRLNKIIADAGITSRRGADELIEDGRVAVNGIIVREMGSKFDPEMDKVMVDGETITRTLT 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 HKP G+++T  DP+GR ++ D +     R+  VGRLD ++EGL+LLTNDG L  
Sbjct: 64  KSYLALHKPKGVLSTMFDPEGRPSLDDFIDLRKERLFHVGRLDKDSEGLILLTNDGDLTF 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               PS    + Y + F G +      +L KG+ ++          L  ++ S  W+ V 
Sbjct: 124 RATHPSFGLEKTYIIEFDGILPTGVDKVLLKGVELEDGMGR----VLTFKQLSPKWIEVS 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EG+   I+++ E     V RLIR  +GP  LG    G  R+++   L
Sbjct: 180 IHEGRYHIIRRLMEAVGVNVLRLIRTKFGPISLGDTPEGRWRDLNDGEL 228


>gi|134095614|ref|YP_001100689.1| putative pseudouridine synthase (Uracil hydrolyase) [Herminiimonas
           arsenicoxydans]
 gi|133739517|emb|CAL62568.1| Pseudouridine synthase [Herminiimonas arsenicoxydans]
          Length = 538

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 84/354 (23%), Positives = 148/354 (41%), Gaps = 17/354 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           +  +  +    ++ KV+A AG+ SRR++E +I   RV VNG         ++  D + ++
Sbjct: 167 RRDLTADDDAPKLHKVLAEAGLGSRRDMEELIIAGRVSVNGEPA-HIGQRILPADQVRIN 225

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G  +++         L  +     +V+T+      S          ++ ++VGRLD NTE
Sbjct: 226 GKLIQRKVSNKPPRVLVYHKPAGEIVSTNDPEGRPSVFERLPTMKAAKWLAVGRLDFNTE 285

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL T  G LA  L  P     R Y VR  G++++     L  G+ ++       ++  
Sbjct: 286 GLLLFTTSGDLANRLMHPRYGIDREYAVRTLGELEEGMRQKLLAGVELEDGLAQFSKIAD 345

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G N W  V + EG+NRE++++FE     V+RLIR  YG   L   L  G   E+ +
Sbjct: 346 GGGEGVNKWYRVTIGEGRNREVRRMFEAIGLTVSRLIRTRYGTLTLPKNLKRGRWEEMEE 405

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             +R+ L    LE+  V+      +  +    +    +   D+   + ++ SQ   L  Q
Sbjct: 406 HAVRDLLAMSGLEKKSVDGAPKGRN--SPADRQNGNRAPRVDNGMGLPRSPSQWGNLGGQ 463

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            +                  G          ++ +  + S  FP     RR++ 
Sbjct: 464 GRPQG---------QNGKPAGGRQGQGQPRSRQPDPLQTSLGFPGMGQPRRSNG 508


>gi|293407757|ref|ZP_06651597.1| 23S rRNA pseudouridine synthase F [Escherichia coli B354]
 gi|301021535|ref|ZP_07185540.1| conserved hypothetical protein [Escherichia coli MS 69-1]
 gi|331665691|ref|ZP_08366585.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli TA143]
 gi|331675512|ref|ZP_08376260.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli TA280]
 gi|331685769|ref|ZP_08386350.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli H299]
 gi|291472008|gb|EFF14490.1| 23S rRNA pseudouridine synthase F [Escherichia coli B354]
 gi|300398018|gb|EFJ81556.1| conserved hypothetical protein [Escherichia coli MS 69-1]
 gi|331056742|gb|EGI28736.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli TA143]
 gi|331067286|gb|EGI38693.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli TA280]
 gi|331076966|gb|EGI48183.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli H299]
          Length = 290

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 61/292 (20%), Positives = 114/292 (39%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++             ++     + +  +   R   N  +     ++KK  
Sbjct: 239 SSSEAKPKTKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 290


>gi|331006652|ref|ZP_08329935.1| ribosomal large subunit pseudouridine synthase F [gamma
           proteobacterium IMCC1989]
 gi|330419541|gb|EGG93924.1| ribosomal large subunit pseudouridine synthase F [gamma
           proteobacterium IMCC1989]
          Length = 289

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 60/285 (21%), Positives = 107/285 (37%), Gaps = 15/285 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK- 69
               R++K I+ +G  SRRE +++I    V VNG             D + V+G  ++  
Sbjct: 2   TDGIRLNKFISDSGYCSRREADKLIEDDLVLVNGQPPT-LGTRCHPGDVVYVEGKRIKSR 60

Query: 70  -----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                        Y+KP  +  T       + +         R+  +GRLD  +EGL+LL
Sbjct: 61  ANAGSQADREYIAYNKPTHITCTTEADVVGNIISAV--GYKKRIFPIGRLDKMSEGLILL 118

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T+DG +   +        + Y V     +    +  +  G+ I G      ++ +     
Sbjct: 119 TSDGDIVNKILRAENAHDKEYLVTVDKPITDKFIEKMGNGVPILGTKTLPCKINMQ---- 174

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
                 + L EG NR+I+++ E+F ++V +L R+      LG L  G  R+++   L + 
Sbjct: 175 GEFMFKIILTEGLNRQIRRMCEYFGYEVTKLKRVRIMNITLGNLKPGEWRKLTANQLTDI 234

Query: 245 LG--PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
                H   +A       I         +   I        R  +
Sbjct: 235 NNAIEHSSGDAAPKGAKLIRRKPKKPSQQERAIKSKTPKVVRTPR 279


>gi|260463253|ref|ZP_05811454.1| RNA-binding S4 domain protein [Mesorhizobium opportunistum WSM2075]
 gi|259030843|gb|EEW32118.1| RNA-binding S4 domain protein [Mesorhizobium opportunistum WSM2075]
          Length = 607

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 145/336 (43%), Positives = 199/336 (59%), Gaps = 1/336 (0%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           ++K +ARAG+ASRR+ E +IA  RVKVNG +L   A NVM  D I +DG+ +   ERTRL
Sbjct: 163 IAKRLARAGLASRRDAEDLIAAGRVKVNGRVLASPAFNVMPGDIIHLDGMEIPPIERTRL 222

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           +L+HKP G+VTT+ DP+GR TVFD LP+   R++++GRLDINTEGLLLLTNDGGL+RVLE
Sbjct: 223 FLFHKPAGVVTTNRDPEGRKTVFDVLPAELPRLMTIGRLDINTEGLLLLTNDGGLSRVLE 282

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
           LP+T WLR YRVR HG+V++  L  L++GI + G+ YG ++ +LD ++GSNAW+T+GLRE
Sbjct: 283 LPATGWLRRYRVRVHGKVEESALAGLREGIAVDGVFYGAIEASLDREQGSNAWLTIGLRE 342

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQV 255
           GKNRE+K +       V RLIRISYGPFQL  L  G   E+  ++LR+QLG  L+EE+  
Sbjct: 343 GKNREVKNILGALGLDVTRLIRISYGPFQLEDLPEGHVLEIKGRVLRDQLGERLVEESGA 402

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW 315
           N DA I    +    R     +   +  ++ +    +                +    + 
Sbjct: 403 NFDAEISKPFSNKPVRRTEPRQEEAERPKIMREGDHRPIGEGGLIKNRKRREGSRDEALG 462

Query: 316 MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                            E   R P         R +
Sbjct: 463 KLSTSPDRGERPEKSFGERGPR-PERGGFGDKPRGN 497



 Score = 36.7 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 13/120 (10%), Positives = 23/120 (19%), Gaps = 4/120 (3%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           E      RE  GP      + +              R            R      ++  
Sbjct: 26  EGKPYEKRE--GPRKPYAPRGDRPVAAEGERKPYEKREGPRKPYAPRGDRPMSAEGERKP 83

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDS--GQREENHRRSPSFPSKRSLRRTSA 352
             K++    P   R          G           G R +               + ++
Sbjct: 84  YEKREGPRKPYAPRGDRPAASAEGGERRFDRPKRDFGDRPKRDFNDRPKRDFGDRPQGAS 143


>gi|50954353|ref|YP_061641.1| RNA pseudouridine synthase [Leifsonia xyli subsp. xyli str. CTCB07]
 gi|50950835|gb|AAT88536.1| RNA pseudouridine synthase [Leifsonia xyli subsp. xyli str. CTCB07]
          Length = 260

 Score =  178 bits (450), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 82/251 (32%), Positives = 125/251 (49%), Gaps = 2/251 (0%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGV 65
           +      +R+ KV+A AG+ASRR  E +IA  RV VNG ++      V    DH+ VDG 
Sbjct: 1   MSAEPQGERLQKVMAAAGVASRRVSEELIAAGRVSVNGTVVTELGRRVDPVVDHVAVDGA 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            ++     R  + +KP+G+V++  D  GR  +   +     R+ +VGRLD  T GLL+LT
Sbjct: 61  AVQLDTTLRYVMLNKPVGVVSSLRDEQGRPDLSRFVADYEERLFNVGRLDAETSGLLILT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-G 184
           NDG LA VL  P     + Y  R  G V    +  L +G+ ++       +  L     G
Sbjct: 121 NDGELAHVLAHPRFGVTKTYIARVRGAVTPQTIGRLTRGVELEDGPIAADRAKLLQSDPG 180

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
             + V V L  G+NR ++++       V  L+R  +GP  LGTL AG+ R+++K  L   
Sbjct: 181 GGSLVEVTLHSGRNRIVRRMLAEVGHPVVELVRRQFGPLHLGTLKAGALRDLTKAELGSL 240

Query: 245 LGPHLLEEAQV 255
           L     + +Q 
Sbjct: 241 LTISREDGSQA 251


>gi|325103401|ref|YP_004273055.1| ribosomal large subunit pseudouridine synthase F [Pedobacter
           saltans DSM 12145]
 gi|324972249|gb|ADY51233.1| ribosomal large subunit pseudouridine synthase F [Pedobacter
           saltans DSM 12145]
          Length = 298

 Score =  178 bits (450), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 61/274 (22%), Positives = 113/274 (41%), Gaps = 10/274 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---E 71
           R++K I+ +GI SRRE +R+I + RV +NG   +     V + D + VD   L+     E
Sbjct: 12  RLNKAISDSGICSRREADRLIEEGRVTINGKTAKV-GDRVSAFDEVIVDDRRLKLNKTGE 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R     ++KP G+V T       + +     +   R+  +GRLD  +EGL+ LT+DG + 
Sbjct: 71  RPVYIAFNKPRGIVCTTEPDVKDNIIDYI--NFPKRIFPIGRLDKPSEGLIFLTSDGNIV 128

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     +  + +  + KG+ I        QV     K       +
Sbjct: 129 NKILRAGNNHEKEYIVTVDKPITDEFIKGMMKGVPILDTVTKKCQVF----KEGELVFRI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G  R+++K+ E+F + V +L R       L  L  G+ R ++ + L+  +      
Sbjct: 185 ILTQGLYRQVRKMCEYFGYHVTKLKRTRIMNISLAKLPLGTWRYLTPEELQGIMDMVDSS 244

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
                        +   +   +   ++ +     
Sbjct: 245 SGTEEASFENTEFKKEQKHIRSKPQDLKNKKRDE 278


>gi|330996052|ref|ZP_08319946.1| pseudouridylate synthase [Paraprevotella xylaniphila YIT 11841]
 gi|329574049|gb|EGG55627.1| pseudouridylate synthase [Paraprevotella xylaniphila YIT 11841]
          Length = 253

 Score =  178 bits (450), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 56/241 (23%), Positives = 108/241 (44%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K +  +   P R++K +A AG+ SRRE +  I    V VNG ++      V  +D +
Sbjct: 5   IEYKELNVDPDAPIRLNKFLANAGVCSRREADEFITAGVVSVNGTVVTELGTKVKRSDEV 64

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P+    +  + L      + T+    + ++ +         R+  VGRLD NT G
Sbjct: 65  KFHEQPVSIERKVYVLLNKPKDYVTTSDDPQNRKTVMDLVKNVCRERIYPVGRLDRNTTG 124

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LL TNDG LA  L  P     ++Y V     V    +  + +GI ++        +   
Sbjct: 125 VLLFTNDGELASKLTHPKFLKKKIYHVTTDKNVTAADMRQIAEGITLEDGEIKADAIEYA 184

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +       + + +  GKNR ++++FE   ++V +L R+ +       +  G  R ++++ 
Sbjct: 185 SPTDKKQ-IGIEIHSGKNRIVRRIFEALGYRVVKLDRVLFAGLTKKNVRRGDWRFLTEQE 243

Query: 241 L 241
           +
Sbjct: 244 V 244


>gi|218231008|ref|YP_002369348.1| RNA pseudouridine synthase family protein [Bacillus cereus B4264]
 gi|218158965|gb|ACK58957.1| RNA pseudouridine synthase family protein [Bacillus cereus B4264]
          Length = 229

 Score =  178 bits (450), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 109/230 (47%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTH-GALVSDGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D    + +     +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAADHIEDNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ + +G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSRGVKIKDGMTKPCKVTRV----DQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L 
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTAEELE 223


>gi|260587929|ref|ZP_05853842.1| ribosomal large subunit pseudouridine synthase B [Blautia hansenii
           DSM 20583]
 gi|331084524|ref|ZP_08333625.1| hypothetical protein HMPREF0992_02549 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|260541456|gb|EEX22025.1| ribosomal large subunit pseudouridine synthase B [Blautia hansenii
           DSM 20583]
 gi|330401232|gb|EGG80823.1| hypothetical protein HMPREF0992_02549 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 271

 Score =  178 bits (450), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 71/278 (25%), Positives = 129/278 (46%), Gaps = 7/278 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K ++ AG+ SRRE +R+I ++RV V+G       + V     I+VDG  +++ E+ 
Sbjct: 1   MRLNKYLSDAGVCSRREADRLIEEKRVLVDGKPA-VQGMQVEDFQEIKVDGKAIKREEKK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L ++HKP G+  T +    ++ +     +   RV   GRLD ++EGLLLLTN G L   
Sbjct: 60  VLLVFHKPKGIECTANPNVKKNVISYI--NYPIRVYYAGRLDKDSEGLLLLTNQGELVNQ 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +    +   + Y V     V ++ L  +++G+ + G      +V    +K S     + L
Sbjct: 118 IMKAGSYHEKEYLVTVDKPVTEEFLQSMREGVPVLGTITRKCKV----EKESEKVFRITL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
            +G NR+I+++  +  ++V +L RI     +LG L  GS RE +K+ L E       +  
Sbjct: 174 TQGLNRQIRRMCNYLGYEVVKLKRIRIMNIELGNLPIGSYREATKEELDELKRQISEKAE 233

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           +          + +                R + + + 
Sbjct: 234 KRQETDFHKGKKPVKNAGKYRNPSKVRKQKRQEASRNG 271


>gi|313897459|ref|ZP_07831002.1| pseudouridine synthase B, ribosomal large subunit [Clostridium sp.
           HGF2]
 gi|312957829|gb|EFR39454.1| pseudouridine synthase B, ribosomal large subunit [Clostridium sp.
           HGF2]
          Length = 245

 Score =  178 bits (450), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 65/244 (26%), Positives = 114/244 (46%), Gaps = 5/244 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E +I++ RV VNG  +      V   D IEVDG  + K ++ 
Sbjct: 2   ERLQKVIAAAGITSRRKAEVLISEGRVAVNGETITELGYKVKRGDLIEVDGKAIEKEDKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +      + T+  +   ++    +L     R+ +VGRLD +T G+++LTNDG  A  
Sbjct: 62  YFLMNKPKRTMCTSDDEFGRQTV--VDLVDCRQRIFTVGRLDYDTSGVIILTNDGDFANE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQK--GSNAWVT 190
           +  P     +VY +  +G +  + +  +K GIV+         +  +  +    +     
Sbjct: 120 IIHPRYHIPKVYNLTINGILTPEDMKKIKAGIVLDDGIKTLPAKYRMTEKDTEKNQCSFD 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + + EG+NR+IK++ E   ++V RL R          L  G  R +    +++       
Sbjct: 180 LTIVEGRNRQIKRMMEALGYEVRRLHRSRLAFLHCSDLRQGEYRVLKPFEVKQLRSLAQK 239

Query: 251 EEAQ 254
            E +
Sbjct: 240 GEMK 243


>gi|262091731|gb|ACY25320.1| ribosomal large subunit pseudouridine synthase B [uncultured
           actinobacterium]
          Length = 240

 Score =  178 bits (450), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 70/236 (29%), Positives = 116/236 (49%), Gaps = 10/236 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
              +R+ KV+A+ G  SRR  E +IA  RV VNG +       V    D +E+DG P+  
Sbjct: 3   DEGERLQKVLAQRGWGSRRACEEIIADGRVTVNGEVA-VLGRRVNVDVDRVEIDGAPVGV 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                 +L +KP+ +++T  D   R TV D +P+       VGRLD ++EGLLL+TNDG 
Sbjct: 62  RPDLVYYLLNKPVDVISTAIDTHDRETVVDFVPADPRV-YPVGRLDGDSEGLLLITNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFH---GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           L   +  P     + Y V+       V    ++ L+ GI ++       +V+   +    
Sbjct: 121 LTNRITHPKYGLEKEYLVQVDVSSADVSDVAIHRLRNGIELEDGVTAPAEVSRLQEG--- 177

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
             + + + EGKNR+I+++ +   + V RL+R   GP     L  G  R +++  ++
Sbjct: 178 -VLRMVIHEGKNRQIRRMCDAVGYPVIRLVRTRIGPIMDKKLAPGQWRNLTQAEVK 232


>gi|94263642|ref|ZP_01287451.1| Pseudouridine synthase, Rsu [delta proteobacterium MLMS-1]
 gi|93455947|gb|EAT06102.1| Pseudouridine synthase, Rsu [delta proteobacterium MLMS-1]
          Length = 240

 Score =  178 bits (450), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 86/231 (37%), Positives = 120/231 (51%), Gaps = 1/231 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
           TP+R+ KV+ARAG+ SRR  E  IA  RV V+G  +    + V      I  DG PLR  
Sbjct: 2   TPERLQKVLARAGVGSRRRAEEFIAAGRVTVDGRRVTEMGLRVDPEKQAITFDGRPLRLP 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E     L +KP G VTT +DP GR  V   L     R+  VGRLD +TEG LLLTNDG L
Sbjct: 62  ENKVTVLLNKPAGYVTTMADPQGRPMVGSLLKEPGLRLFPVGRLDFDTEGALLLTNDGDL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS +  R Y+    G      L  L++GI ++G       V    ++G    + 
Sbjct: 122 AHRLLHPSFEIKRTYQATVEGTPGAQALRALRQGIELEGRRTHPAMVKTLRRRGEQTVLE 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + EG+ R+++K+       V  L R++YG  +LG L  GS R ++ + +
Sbjct: 182 IIIHEGRKRQVRKMLAAVGHPVLHLKRVAYGDLRLGRLPLGSYRRLNHEDI 232


>gi|319784272|ref|YP_004143748.1| RNA-binding S4 domain protein [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
 gi|317170160|gb|ADV13698.1| RNA-binding S4 domain protein [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
          Length = 670

 Score =  178 bits (450), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 142/338 (42%), Positives = 198/338 (58%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           ++K +ARAG+ASRR+ E +IA  RVKVNG  L   A NVM  D I +DG+ +   ERTRL
Sbjct: 224 IAKRLARAGLASRRDAEELIAAGRVKVNGRALTSPAFNVMPDDIIHLDGMEIPPIERTRL 283

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           +L+HKP G+VTT+ DP+GR TVFD LP+   R++++GRLDINTEGLLLLTNDGGL+RVLE
Sbjct: 284 FLFHKPAGVVTTNRDPEGRKTVFDVLPAELPRLMTIGRLDINTEGLLLLTNDGGLSRVLE 343

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
           LP+T WLR YRVR HG+V++  L  L++GI + G+ YG ++ TLD ++G+NAW+T+GLRE
Sbjct: 344 LPATGWLRRYRVRVHGKVEESALAGLREGIAVDGVFYGAIEATLDREQGTNAWLTIGLRE 403

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQV 255
           GKNRE++ +       V RLIRISYGPFQL  L  G   E+  ++LR+QLG  L+EE+  
Sbjct: 404 GKNREVRNILGSLGLDVTRLIRISYGPFQLDDLAEGHVLEIKGRVLRDQLGERLVEESGA 463

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW 315
           N DA +    +    R   + E   +  +  ++  ++                +    + 
Sbjct: 464 NFDADVTKPFSNKPVRRTEVREPEPERPKFTRDGERRPIGEGGLIKNRKRREGSRDEALG 523

Query: 316 MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                       S                R       +
Sbjct: 524 KLSTSPDRNAEKSFGERAPRPERSFGDKPRGNFGDKPR 561


>gi|311281430|ref|YP_003943661.1| pseudouridine synthase [Enterobacter cloacae SCF1]
 gi|308750625|gb|ADO50377.1| pseudouridine synthase [Enterobacter cloacae SCF1]
          Length = 292

 Score =  178 bits (450), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 61/294 (20%), Positives = 114/294 (38%), Gaps = 5/294 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   TQSTRLNKYISESGICSRREADRFIEQGNVFINGKRAT-IGDQVAPGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L        +    +  DG      +  +  SR+  +GRLD +++GL+ LTN G L
Sbjct: 63  DAEDLVFIALNKPVGIVSTTEDGERNNIVDFVNHSSRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYVVTVNKPVTDEFIRAMGAGVPILGTV----TKKCKVKKEAPFAFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L E       
Sbjct: 179 ITLIQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLAGIPPGEWRDLTDDELIELFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
             ++    A           +    +   +      + +++K   S  +K    
Sbjct: 239 SSSEAKPKAKAKPKTAAGAVKKPAGNGGKNMAKTPAEMANRKRFTSPGRKKKGR 292


>gi|298374690|ref|ZP_06984648.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           3_1_19]
 gi|298269058|gb|EFI10713.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           3_1_19]
          Length = 495

 Score =  178 bits (450), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 57/241 (23%), Positives = 116/241 (48%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K K ++ +   P R++K ++ AG+ SRRE +  I +  VKVN +++      +   D +
Sbjct: 247 IKYKEVLADPNEPIRLNKFLSNAGVCSRREADEFIQKGAVKVNDVVVTELGTKITRQDVV 306

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
             +  P++   +  + L      + T+    +  + +     +   R+  VGRLD NT G
Sbjct: 307 TFNEKPVQIESKVYIVLNKPKNCVTTSDDPQERLTVMDLVKNACQERIYPVGRLDRNTTG 366

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  PS +  ++Y V     V  + +  +  G+ ++        ++  
Sbjct: 367 VLLLTNDGDLASKLTHPSFKKKKIYHVWLDKNVAIEDMEKIANGLELEDGEIHADAISYA 426

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++    + V + +  G+NR ++++FE   + V +L R+ +       L  G  R ++++ 
Sbjct: 427 SED-DKSQVGIEIHSGRNRIVRRIFESLGYHVTKLDRVYFAGLTKKNLGRGKWRYLNERE 485

Query: 241 L 241
           +
Sbjct: 486 V 486


>gi|150010293|ref|YP_001305036.1| ribosomal large subunit pseudouridine synthase B [Parabacteroides
           distasonis ATCC 8503]
 gi|256839144|ref|ZP_05544654.1| ribosomal large subunit pseudouridine synthase B [Parabacteroides
           sp. D13]
 gi|149938717|gb|ABR45414.1| ribosomal large subunit pseudouridine synthase B [Parabacteroides
           distasonis ATCC 8503]
 gi|256740063|gb|EEU53387.1| ribosomal large subunit pseudouridine synthase B [Parabacteroides
           sp. D13]
          Length = 495

 Score =  178 bits (450), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 57/241 (23%), Positives = 116/241 (48%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K K ++ +   P R++K ++ AG+ SRRE +  I +  VKVN +++      +   D +
Sbjct: 247 IKYKEVLADPNEPIRLNKFLSNAGVCSRREADEFIQKGAVKVNDVVVTELGTKITRQDVV 306

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
             +  P++   +  + L      + T+    +  + +     +   R+  VGRLD NT G
Sbjct: 307 TFNEKPVQIESKVYIVLNKPKNCVTTSDDPQERLTVMDLVKNACQERIYPVGRLDRNTTG 366

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  PS +  ++Y V     V  + +  +  G+ ++        ++  
Sbjct: 367 VLLLTNDGDLASKLTHPSFKKKKIYHVWLDKNVAIEDMEKIANGLELEDGEIHADAISYA 426

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++    + V + +  G+NR ++++FE   + V +L R+ +       L  G  R ++++ 
Sbjct: 427 SED-DKSQVGIEIHSGRNRIVRRIFESLGYHVTKLDRVYFAGLTKKNLGRGKWRYLNERE 485

Query: 241 L 241
           +
Sbjct: 486 V 486


>gi|315170764|gb|EFU14781.1| conserved hypothetical protein [Enterococcus faecalis TX1342]
          Length = 257

 Score =  178 bits (450), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 63/248 (25%), Positives = 109/248 (43%), Gaps = 5/248 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGNVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           I + G  L   +     L+     +  T    D             + +  VGRLD +TE
Sbjct: 61  IALMGEILTYQKFFYYMLHKPQGVISATEDQRDETVIDLLTDQDYRADLFPVGRLDKDTE 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVT 178
           GLLLLTNDG LA  L  P     + Y     G V  +   L  +G  ++        ++ 
Sbjct: 121 GLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEIVKPSRLV 180

Query: 179 L--DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTRE 235
           +    ++   + V + ++EGK  ++K++       V  L R+  G   L   L  G  R 
Sbjct: 181 IETINEEEGTSVVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGGYRP 240

Query: 236 VSKKILRE 243
           +++  L++
Sbjct: 241 LTEAELQQ 248


>gi|110644361|ref|YP_672091.1| 23S rRNA pseudouridine synthase F [Escherichia coli 536]
 gi|110345953|gb|ABG72190.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           536]
          Length = 290

 Score =  178 bits (450), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 63/292 (21%), Positives = 116/292 (39%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  ESEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P     + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRPGNDHEKEYLVTVDKPITDEFIRGMGPGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++    A        ++     + +  +   R   N  +     ++KK  
Sbjct: 239 SSSEAKPKAKAKPKTVGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 290


>gi|311745139|ref|ZP_07718924.1| RNA pseudouridine synthase family protein [Algoriphagus sp. PR1]
 gi|126577657|gb|EAZ81877.1| RNA pseudouridine synthase family protein [Algoriphagus sp. PR1]
          Length = 243

 Score =  178 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 57/249 (22%), Positives = 109/249 (43%), Gaps = 8/249 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL- 67
           E     R++K ++  G  SRRE ++++   R+ +NG +       VM  D + VDG P+ 
Sbjct: 2   EEKQGIRINKYLSEVGFCSRREGDKLLEAGRITLNGKIP-EIGTKVMPKDVVCVDGKPVG 60

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +  +      ++KP+G+V+T            +      R+  +GRLD ++EGL+ LT++
Sbjct: 61  KPIQDHVYIAFNKPVGIVSTTDT-KAEKNNMIDYIGHQQRIFPIGRLDKDSEGLIFLTSE 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +        + Y V     +    +  +  GI I        +     +K S  
Sbjct: 120 GDIVNKILRSKNNHEKEYIVTVDKPITDRFIQKMGAGIPILDTVTDPCK----VEKISKV 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+  ++V +L RI      L  +  G  R+++   L+E    
Sbjct: 176 KFRIILTQGLNRQIRRMCEYLGYEVRQLKRIRIMNVHL-DIPVGKWRDLTASELKELNDL 234

Query: 248 HLLEEAQVN 256
                  V+
Sbjct: 235 VSESSKTVD 243


>gi|86356481|ref|YP_468373.1| pseudouridylate synthase, subunit B protein [Rhizobium etli CFN 42]
 gi|86280583|gb|ABC89646.1| pseudouridylate synthase, subunit B protein [Rhizobium etli CFN 42]
          Length = 628

 Score =  178 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 168/340 (49%), Positives = 214/340 (62%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
                +R+SKV+ARAG+ASRR++ERMI + RV +NG +L+   VNV   D IEVDGVP+R
Sbjct: 47  SEAKAERISKVMARAGVASRRDIERMIMEGRVTLNGKVLDTPVVNVTLADRIEVDGVPIR 106

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ERTRLWLYHKP GLVTT++DP+GR TVFDNLP    RV+S+GRLDINTEGLLLLTNDG
Sbjct: 107 GIERTRLWLYHKPAGLVTTNADPEGRPTVFDNLPEELPRVMSIGRLDINTEGLLLLTNDG 166

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GLAR LELP+T WLR YRVR HG++DQ+ L+ LK GI + G+ YG ++ TLD  +GSN W
Sbjct: 167 GLARALELPATGWLRRYRVRAHGEIDQEALDKLKDGIAVDGVLYGSIEATLDRTQGSNVW 226

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +T+GLREGKNREIK V       VNRLIRISYGPFQLG L  G   EV  + LR+QLGP 
Sbjct: 227 ITMGLREGKNREIKNVLGALGLDVNRLIRISYGPFQLGDLPEGHVVEVRGRTLRDQLGPR 286

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
           L+EEA+ N DAPIY++  +  +     +         +    ++  LS+           
Sbjct: 287 LIEEAKANFDAPIYNAPAVAAEEETEAAAPEKRERPRRDEDKRERALSRLDTKRDDRRGA 346

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
               +     G          Q     R +  + +  +  
Sbjct: 347 GRRDDDRRDGGRKDDDKPKRSQPPGQRRSANVWMAPGARP 386



 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 18/120 (15%), Positives = 31/120 (25%), Gaps = 6/120 (5%)

Query: 233 TREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
            RE   + +R    P   +E +       +S +    DRP+       D  R  +     
Sbjct: 430 VREEDGEWIRSSEQPRRKDEDE------GFSRKRSFGDRPSRGERPFGDKPRGDRRPRAD 483

Query: 293 NGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                +   A+    R+         G   S        +    R P        R   +
Sbjct: 484 GDERPRAARASAGEGRSERPRGDRPFGDRPSRGDRPFGDKPRGDRRPREEGDERPRAARS 543



 Score = 39.4 bits (90), Expect = 0.82,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 21/112 (18%), Gaps = 3/112 (2%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
             G       +   D P               +          +    +   + +     
Sbjct: 508 PFGDRPSRGDRPFGDKPRGDRRPREEGDERPRAARSFAGEGRSERPRGERSFAGKSAGGK 567

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR---SPSFPSKRSLRRTSA 352
           P   +          G   SF      +  + R     P+    R   R   
Sbjct: 568 PSSDKPRGKGFGAKPGGSKSFSGKPKGKPGSDRPGGDRPAGGLSRGGARGKG 619



 Score = 39.4 bits (90), Expect = 0.91,   Method: Composition-based stats.
 Identities = 10/102 (9%), Positives = 25/102 (24%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            + EE    + +          +  +      D  +R ++    K    ++ +       
Sbjct: 429 RVREEDGEWIRSSEQPRRKDEDEGFSRKRSFGDRPSRGERPFGDKPRGDRRPRADGDERP 488

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           R   ++    +          G R     R      +   R 
Sbjct: 489 RAARASAGEGRSERPRGDRPFGDRPSRGDRPFGDKPRGDRRP 530



 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 8/109 (7%), Positives = 25/109 (22%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           ++        A  +       +            + P      + +    +     ++  
Sbjct: 472 DKPRGDRRPRADGDERPRAARASAGEGRSERPRGDRPFGDRPSRGDRPFGDKPRGDRRPR 531

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                R  A+  +  +G       +     ++    PS    R     +
Sbjct: 532 EEGDERPRAARSFAGEGRSERPRGERSFAGKSAGGKPSSDKPRGKGFGA 580


>gi|195978740|ref|YP_002123984.1| ribosomal large subunit pseudouridine synthase B RluB
           [Streptococcus equi subsp. zooepidemicus MGCS10565]
 gi|195975445|gb|ACG62971.1| ribosomal large subunit pseudouridine synthase B RluB
           [Streptococcus equi subsp. zooepidemicus MGCS10565]
          Length = 266

 Score =  178 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 80/237 (33%), Positives = 128/237 (54%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I +  V +NG ++   A  V S D +E++G P+   E  
Sbjct: 27  MRINKYIAHAGVASRRKAEELIKRGLVTLNGQVVTDLATTVKSGDLVEIEGSPI-YNEEK 85

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T GLL+LTNDG     
Sbjct: 86  VYYLLNKPRGVISSVSDDKGRQTVIDLLPQVKERIYPVGRLDWDTSGLLILTNDGDFTDK 145

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P  +  +VY  R  G V ++ L  L +G+VI G      +  +       + + V +
Sbjct: 146 MIHPRNEIDKVYLARVKGVVTKESLRPLTRGVVIDGKKTKPARYRIIRVEPDKNRSIVEL 205

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + EG++ ++KK+FE     V++L R  +G   +  L  G  R +SKK + +     
Sbjct: 206 TIHEGRHHQVKKMFEAVGHLVDKLSRTQFGSLDVRGLKPGEARRLSKKEVSQLHHLA 262


>gi|94267153|ref|ZP_01290785.1| Pseudouridine synthase, Rsu [delta proteobacterium MLMS-1]
 gi|93452121|gb|EAT02795.1| Pseudouridine synthase, Rsu [delta proteobacterium MLMS-1]
          Length = 240

 Score =  178 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 86/231 (37%), Positives = 120/231 (51%), Gaps = 1/231 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
           TP+R+ KV+ARAG+ SRR  E  IA  RV V+G  +    + V      I  DG PLR  
Sbjct: 2   TPERLQKVLARAGVGSRRRAEEFIAAGRVTVDGRRVTEMGLRVDPEKQAITFDGRPLRFP 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E     L +KP G VTT +DP GR  V   L     R+  VGRLD +TEG LLLTNDG L
Sbjct: 62  ENKVTVLLNKPAGYVTTMADPQGRPMVGSLLKEPGLRLFPVGRLDFDTEGALLLTNDGDL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS +  R Y+    G      L  L++GI ++G       V    ++G    + 
Sbjct: 122 AHRLLHPSFEIKRTYQATVEGTPGAQALRALRQGIELEGRRTHPAMVKTLRRRGEQTVLE 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + EG+ R+++K+       V  L R++YG  +LG L  GS R ++ + +
Sbjct: 182 IIIHEGRKRQVRKMLAAVGHPVLHLKRVAYGDLRLGRLPLGSYRRLNHEDI 232


>gi|329769599|ref|ZP_08261003.1| hypothetical protein HMPREF0433_00767 [Gemella sanguinis M325]
 gi|328838354|gb|EGF87963.1| hypothetical protein HMPREF0433_00767 [Gemella sanguinis M325]
          Length = 243

 Score =  178 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 75/242 (30%), Positives = 128/242 (52%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+IA +G  SRR+ E++I   +V VNG ++ +  V    +D I V+GV L   E  
Sbjct: 3   ERLQKLIAASGYTSRRKAEQLILDGKVTVNGTVVNQLGVKAEPSDIIIVEGVRL-LKENK 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP  ++T+ SD   R+ V D   S+  RV+ VGRLD +T G L+++NDG    +
Sbjct: 62  RYYLFYKPEKVITSMSDEKDRTCVKDFFESVNERVVPVGRLDYDTSGALIMSNDGEFINL 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  + Y  +  G++D   L +L+ G+ I        +V +   K   SN  V +
Sbjct: 122 ITHPRHKIKKTYVAKISGKLDDRHLKILRSGVRIDNYKTAPAEVNIVKNKNKSSNTLVRL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EGKNR+I+++FE   ++V +L R +     L  L  G  R ++   ++  +      
Sbjct: 182 TIHEGKNRQIRRMFETLGYEVLKLKREAIEDLTLEGLKKGEYRVLTIHEVKRLINKANNG 241

Query: 252 EA 253
           E 
Sbjct: 242 EK 243


>gi|260685750|ref|YP_003216883.1| pseudouridine synthase [Clostridium difficile R20291]
 gi|260211766|emb|CBE02116.1| pseudouridine synthase [Clostridium difficile R20291]
          Length = 258

 Score =  178 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 61/252 (24%), Positives = 105/252 (41%), Gaps = 22/252 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA 70
             QR+ K+++  G  SR E+++   Q  V VNG  +      V    D I  +G  +   
Sbjct: 3   KKQRIDKILSNLGYGSRSEIKKYCKQGSVVVNGSEVSNPGTQVDTENDEILFNGEEVIYR 62

Query: 71  ERTRLWL------------------YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
           E   L +                        +  T    D       +L  +      VG
Sbjct: 63  EYIYLIMQNSVKQEPCDFSHGRFRMNKPDGYISATTDKYDPTVLDLIDLSYLAFEPFPVG 122

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-C 171
           RLD +TEGLL+LTNDG L+  +  P     + Y  +  G V ++ +    +G+V+     
Sbjct: 123 RLDKDTEGLLVLTNDGKLSHRVLSPKKHVPKTYYAKIDGVVTEEDVEAFLEGVVLDDGYK 182

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLA 230
               Q+ +  +    + + + + EGK  ++K++FE    KV  L R+S G  +L   L  
Sbjct: 183 TMPSQLNIL-KSDDESEIELTIHEGKFHQVKRMFESVGKKVVYLKRLSMGNLKLDESLEL 241

Query: 231 GSTREVSKKILR 242
           G  RE++ + ++
Sbjct: 242 GEYRELTDEEVK 253


>gi|257870825|ref|ZP_05650478.1| pseudouridine synthase [Enterococcus gallinarum EG2]
 gi|257804989|gb|EEV33811.1| pseudouridine synthase [Enterococcus gallinarum EG2]
          Length = 241

 Score =  178 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 64/241 (26%), Positives = 106/241 (43%), Gaps = 5/241 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G  SR+EV++ I +  V VNG  ++     V    D +   G  +R  + 
Sbjct: 1   MRLDKFLADMGYGSRKEVKQAIKKGVVAVNGQQVKSDKFQVAEQEDQVSFAGELVRYQKD 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +++  +DP+               +  VGRLD +TEGLLL+TNDG LA 
Sbjct: 61  FYYLLNKPAG-VISATTDPEKTVLDLFAAEDYRRDLFPVGRLDKDTEGLLLITNDGQLAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVT 190
            L  P     + Y     G + ++  +   +GI + G      Q+T+    ++   + +T
Sbjct: 120 RLLSPKKHVEKEYYAEVRGIMTEEDRHQFLQGIELDGETLMPAQLTILKVDEQAETSTIT 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHL 249
           + L EGK  ++K++ +    +V  L R   G  QL   L  G  R V++K L +      
Sbjct: 180 LILHEGKFHQVKRMVQAVGKEVTYLKRTRMGGLQLPKDLALGEYRSVTEKELAQLSAEPA 239

Query: 250 L 250
            
Sbjct: 240 E 240


>gi|410137|gb|AAA67493.1| ORFX13 [Bacillus subtilis subsp. subtilis str. 168]
          Length = 229

 Score =  178 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 74/226 (32%), Positives = 119/226 (52%), Gaps = 3/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASR + E +I + +VKVNG ++    V V  +D IEV+G+ + + E  
Sbjct: 2   ERLQKVIAHAGVASRSKAEELIKEGKVKVNGKVVTELGVKVTGSDQIEVNGLKVEREEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     +++   D  GR  V D   +I  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 62  YFLLYKPRG-VISAAQDDKGRKVVTDFFKNIPQRIYPIGRLDYDTSGLLLLTNDGEFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVTV 191
           L  P  +  + Y  +  G   ++ L  L++GI ++       +  L    +K   + + +
Sbjct: 121 LMHPKYEIDKTYVAKVKGIPPKELLRKLERGIRLEEGKTAPAKAKLLSLDKKKQTSIIQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++++FE    +V +L R  Y    L  L  G  RE+ 
Sbjct: 181 TIHEGRNRQVRRMFEAIGHEVIKLKREEYAFLNLRGLHTGDARELR 226


>gi|282848924|ref|ZP_06258314.1| pseudouridylate synthase [Veillonella parvula ATCC 17745]
 gi|294793632|ref|ZP_06758769.1| pseudouridylate synthase [Veillonella sp. 3_1_44]
 gi|282581429|gb|EFB86822.1| pseudouridylate synthase [Veillonella parvula ATCC 17745]
 gi|294455202|gb|EFG23574.1| pseudouridylate synthase [Veillonella sp. 3_1_44]
          Length = 242

 Score =  178 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 68/237 (28%), Positives = 120/237 (50%), Gaps = 4/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K IA  GIASRR+ E +I + +V+VNG  +    V +    D ++V+G  L + + 
Sbjct: 2   ERLQKYIASCGIASRRKAEELITEGKVQVNGRKVTELGVKINPQKDKVKVNGQLLAQEKP 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      + +        + +         R+  +GRLD+ TEGLLLLTNDG LA+
Sbjct: 62  VYYLLNKPKGVITSVSDPQGRETVLDYIKNETK-RIYPIGRLDLYTEGLLLLTNDGELAQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            L  PS    + Y VR  G+V  D L ++  G+ ++        +        N    V 
Sbjct: 121 NLTHPSKGIEKTYEVRIKGRVRDDDLQIIANGVELEDGITAPATIVDLGFDDHNGVHEVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           + + EG+NR+++++FE F ++++ L RI+Y    LG +  G++R+++ + ++     
Sbjct: 181 ITIHEGRNRQVRRMFEHFGYRIHNLKRIAYAGLTLGGVKRGASRQLTIREVKALKAL 237


>gi|299143841|ref|ZP_07036921.1| ribosomal large subunit pseudouridine synthase B [Peptoniphilus sp.
           oral taxon 386 str. F0131]
 gi|298518326|gb|EFI42065.1| ribosomal large subunit pseudouridine synthase B [Peptoniphilus sp.
           oral taxon 386 str. F0131]
          Length = 235

 Score =  178 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 72/229 (31%), Positives = 123/229 (53%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A +G ASRR+ E  I   RVKVNG ++      V    D + +D   L+  + 
Sbjct: 1   MRLQKYMAHSGAASRRKSEEYILDGRVKVNGKIVTELGYVVDENKDKVYLDDKRLKIIKE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP+G+V+T  D   R TV  +L    +R+  +GRLDI+T GL++LT+DG +  
Sbjct: 61  NTYIALNKPMGIVSTVKDEKDRKTV-VDLIDGSTRLYPIGRLDIDTTGLIILTDDGAITN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + Y     G+  + +L++++KGI +    +   +V +     +++ + V 
Sbjct: 120 KLTHPKNEINKTYIATVEGKPTKTELDMIRKGIKVGAEKFSPAKVKILKSFEADSIIEVI 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGKN E+K +F+  N  V +L RIS G  +LG L  G+ R +++  +
Sbjct: 180 IHEGKNHEVKLMFDKINHPVKKLKRISIGDIELGDLEIGNFRYLTEDEI 228


>gi|308174693|ref|YP_003921398.1| 16S pseudouridylate synthase [Bacillus amyloliquefaciens DSM 7]
 gi|307607557|emb|CBI43928.1| putative 16S pseudouridylate synthase [Bacillus amyloliquefaciens
           DSM 7]
 gi|328913028|gb|AEB64624.1| putative 16S pseudouridylate synthase [Bacillus amyloliquefaciens
           LL3]
          Length = 240

 Score =  178 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 100/231 (43%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A +G  SR++V++++    V ++G   +   ++V      I V G P    E 
Sbjct: 2   MRLDKLLANSGFGSRKDVKKIVKAGAVMIDGEPAKDVKIHVDPDKQDITVYGEPAEYREF 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      L  T                        GRLD +TEG LLLTNDG LA 
Sbjct: 62  IYVMMNKPQGVLSATEDSRQQTVVDLLTPEEQRFEPFPAGRLDKDTEGFLLLTNDGQLAH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y VR    +  + +  L++G+VI+G        V   T+      + +
Sbjct: 122 RLLSPKKHVPKTYEVRLTSPLSPEDIIDLERGVVIEGGYKTKPAAVKTITESPDETVIHL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++K + +    +V  L R+S G   L   L  G  RE++++ L
Sbjct: 182 TITEGKYHQVKLMAKAVGNEVAYLKRLSMGAVSLDPELKPGEFRELTEEEL 232


>gi|292670796|ref|ZP_06604222.1| RNA pseudouridine synthase [Selenomonas noxia ATCC 43541]
 gi|292647417|gb|EFF65389.1| RNA pseudouridine synthase [Selenomonas noxia ATCC 43541]
          Length = 296

 Score =  178 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 79/294 (26%), Positives = 135/294 (45%), Gaps = 6/294 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K+++ AG+ASRR  E +I   RV V+G+ +             I VD  P+   E+
Sbjct: 3   ERLQKILSNAGVASRRAAEDLIRAGRVAVDGVAVTELGRKFDPANHTITVDSKPIHSDEK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G ++T  D  GR TV D LP   +R+  VGRLD +TEG+LL+TNDG + +
Sbjct: 63  RFYILLNKPRGYLSTARDDRGRKTVLDLLPDFPARLYPVGRLDADTEGVLLITNDGAITQ 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  +VY     G V +  L  L++GI+++       ++ +         V   
Sbjct: 123 GLLHPRFEIDKVYHAEVAGPVTEGGLTRLRRGILLEDGMTASAKLRILRADKGYTVVETI 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           + EG+NR+++++F     +V  L R+ +    L  L  GS R +++  + E      +  
Sbjct: 183 IHEGRNRQVRRMFAAIGCRVCALRRVRFAMLTLRGLSCGSFRHLTRDEIHELRIIAGVMS 242

Query: 253 AQVNLDAPIYS-----SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           ++ +            S      R    +   D   R + +   K  L + K+ 
Sbjct: 243 SEEDCRRGCRPSGHDGSGRSRGMRRARPAPREDAACRPQDDDHGKRPLQRHKRR 296


>gi|168213173|ref|ZP_02638798.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           CPE str. F4969]
 gi|170715238|gb|EDT27420.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           CPE str. F4969]
          Length = 239

 Score =  178 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 56/231 (24%), Positives = 106/231 (45%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV++  G  +R+E+++++ +  V VN   ++ + + +    D I ++G  +   + 
Sbjct: 2   ERLDKVLSNLGYGTRKEIKQVVKKGFVTVNDEKVKDSGLQIDPEKDTIVINGEKVEYKKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  T+   D        +        +VGRLD +T GLLLLTNDG L  
Sbjct: 62  IYLMMNKPAGVISATYDKRDETVIDLLYMEDQVFEPFTVGRLDKDTVGLLLLTNDGDLNH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY    +  + +  +   + G+ +         ++ +      ++ V V
Sbjct: 122 KLISPKYHVDKVYYAEINAPITEKDIKAFENGVTLDDGYKCMSAKLKVIENLEDSSRVEV 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            ++EGK  ++K++FE    KV  L R S+G   L   L  G  +E+S+  L
Sbjct: 182 TVQEGKYHQVKRMFEARGKKVVYLKRTSFGNLPLDESLEEGEYKELSESEL 232


>gi|228987800|ref|ZP_04147909.1| RNA pseudouridine synthase [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228771848|gb|EEM20305.1| RNA pseudouridine synthase [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
          Length = 229

 Score =  178 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 107/230 (46%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTH-GALVSDGDRVTIDGQVIVKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D    + +     +   R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAADHIEDNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVTRV----DQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L 
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELNELEVGKWRSVTAEELE 223


>gi|227357716|ref|ZP_03842065.1| ribosomal small subunit pseudouridine synthase A [Proteus mirabilis
           ATCC 29906]
 gi|227162045|gb|EEI47059.1| ribosomal small subunit pseudouridine synthase A [Proteus mirabilis
           ATCC 29906]
          Length = 244

 Score =  178 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 54/238 (22%), Positives = 102/238 (42%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +    V ++G +++  A  +     +  DG  L +    
Sbjct: 11  MRLDKFLSQQLGISRNLVARELRAGLVTIDGEMVKTGATKITPEQEVAYDGNVLTQILGP 70

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KPIG V +  DP   + ++     +  ++ + GRLDI+T GL+LLT++G  +  
Sbjct: 71  RYFMLNKPIGYVCSTDDPVNPTILYFIDEPLAHKLHAAGRLDIDTTGLVLLTDNGQWSHR 130

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +  D     K G+ + G         + +     +   V +
Sbjct: 131 ITAPKHHCEKTYVVTLEQPIATDVAEKFKTGVQLNGEKELTKPATLEVI----TPTEVKL 186

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
            + EGK  ++K++F      V  L R   G   L   L  G  R ++++ +     P 
Sbjct: 187 TISEGKYHQVKRMFAAVGNHVVALHRERIGDITLDDALAPGEYRPLTEEEINSIHLPK 244


>gi|197284712|ref|YP_002150584.1| 16S rRNA pseudouridylate synthase A [Proteus mirabilis HI4320]
 gi|194682199|emb|CAR41885.1| ribosomal small subunit pseudouridine synthase A [Proteus mirabilis
           HI4320]
          Length = 234

 Score =  178 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 54/238 (22%), Positives = 102/238 (42%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +    V ++G +++  A  +     +  DG  L +    
Sbjct: 1   MRLDKFLSQQLGISRNLVARELRAGLVTIDGEMVKTGATKITPEQEVAYDGNVLTQILGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KPIG V +  DP   + ++     +  ++ + GRLDI+T GL+LLT++G  +  
Sbjct: 61  RYFMLNKPIGYVCSTDDPVNPTILYFIDEPLAHKLHAAGRLDIDTTGLVLLTDNGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +  D     K G+ + G         + +     +   V +
Sbjct: 121 ITAPKHHCEKTYVVTLEQPIATDVAEKFKTGVQLNGEKELTKPATLEVI----TPTEVKL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
            + EGK  ++K++F      V  L R   G   L   L  G  R ++++ +     P 
Sbjct: 177 TISEGKYHQVKRMFAAVGNHVVALHRERIGDITLDDALAPGEYRPLTEEEINSIHLPK 234


>gi|172057049|ref|YP_001813509.1| RNA-binding S4 domain-containing protein [Exiguobacterium sibiricum
           255-15]
 gi|171989570|gb|ACB60492.1| RNA-binding S4 domain protein [Exiguobacterium sibiricum 255-15]
          Length = 253

 Score =  178 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 81/254 (31%), Positives = 125/254 (49%), Gaps = 5/254 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+IA+AG+ASRR+ E +I + RVKVNG ++      V     +EVDGV L + E  
Sbjct: 2   ERLQKIIAQAGVASRRKAEELITEGRVKVNGKVITELGTKVGGRAEVEVDGVKLEREEHV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     + T   D   ++    +L     RV  VGRLD NT GLLLLTNDG  + +
Sbjct: 62  YYMLYKPTGVVSTVEDDKGRKTV--VDLVPPGHRVFPVGRLDYNTSGLLLLTNDGEFSNL 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDM--QVTLDTQKGSNAWVT 190
           L  P  +  + Y V+  G  D   +  L+KG+V+  G   G    ++    +K + A + 
Sbjct: 120 LLHPKYKVPKRYIVKIKGVPDYYHVKGLEKGVVLPDGFKTGKARVEMRDIDKKKNTAILE 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + + EG NR+++++ E    +V +L R  +G   L  L +G  RE+SKK + +       
Sbjct: 180 MVIYEGHNRQVRQMVETLGAEVIKLKREQFGFLTLAGLTSGDWRELSKKEVNQLRELADP 239

Query: 251 EEAQVNLDAPIYSS 264
             A           
Sbjct: 240 VAAPTKRRKNTKKR 253


>gi|294791771|ref|ZP_06756919.1| pseudouridylate synthase [Veillonella sp. 6_1_27]
 gi|294457001|gb|EFG25363.1| pseudouridylate synthase [Veillonella sp. 6_1_27]
          Length = 242

 Score =  178 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 68/237 (28%), Positives = 120/237 (50%), Gaps = 4/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K IA  GIASRR+ E +I + +V+VNG  +    V +    D ++V+G  L + + 
Sbjct: 2   ERLQKYIASCGIASRRKAEELITEGKVQVNGRKVTELGVKINPQKDKVKVNGQLLAQEKP 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      + +        + +         R+  +GRLD+ TEGLLLLTNDG LA+
Sbjct: 62  VYYLLNKPKGVITSVSDPQGRETVLDYIKNETK-RIYPIGRLDLYTEGLLLLTNDGELAQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            L  PS    + Y VR  G+V  D L ++  G+ ++        +        N    V 
Sbjct: 121 NLTHPSKGVEKTYEVRIKGRVRDDDLQIIANGVELEDGITAPATIVDLGFDDHNGVHEVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           + + EG+NR+++++FE F ++++ L RI+Y    LG +  G++R+++ + ++     
Sbjct: 181 ITIHEGRNRQVRRMFEHFGYRIHNLKRIAYAGLTLGGVKRGASRQLTIREVKALKAL 237


>gi|188995083|ref|YP_001929335.1| ribosomal large subunit pseudouridine synthase B [Porphyromonas
           gingivalis ATCC 33277]
 gi|188594763|dbj|BAG33738.1| ribosomal large subunit pseudouridine synthase B [Porphyromonas
           gingivalis ATCC 33277]
          Length = 439

 Score =  178 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 53/241 (21%), Positives = 111/241 (46%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K + ++ +   P R++K ++ AG+ SRRE + +I +  + VNG ++      +   D +
Sbjct: 191 VKYREVLADPNEPIRLNKFLSNAGVCSRREADLLIEKGEITVNGEVVTELGRRITRQDEV 250

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 +    +  + L      + T+       + +     +   R+  VGRLD NT G
Sbjct: 251 IYKDKRVEIESKVYVLLNKPKNCVTTSDDPECRTTVMDIVRYACPERIYPVGRLDRNTTG 310

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LL+TNDG LA  L  PS +  ++Y V  +  V  + +  +  G+ +             
Sbjct: 311 VLLITNDGDLASKLTHPSFKKKKIYHVWLNKDVSIEDMQKIADGVELDDGEIH-ADAISY 369

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            ++   + V + +  G+NR ++++FE   ++V +L R+ +       L  G  R ++++ 
Sbjct: 370 VKEDDLSQVGIEIHSGRNRIVRRLFEHLGYRVVKLDRVYFAGLTKKNLPRGKWRYLNEQE 429

Query: 241 L 241
           +
Sbjct: 430 V 430


>gi|330830315|ref|YP_004393267.1| Pseudouridine synthase [Aeromonas veronii B565]
 gi|328805451|gb|AEB50650.1| Pseudouridine synthase [Aeromonas veronii B565]
          Length = 230

 Score =  178 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 108/231 (46%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +      +R    ++I Q  V V+GI++++ A ++     IE DGV L   +R 
Sbjct: 1   MRLDKFLCDCSDLTRSLAGKLIRQGEVMVDGIVVKQPAFHINEQSQIEFDGVLLTLEQRN 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V ++ DPD  +  F        ++  VGRLD++T GL+L+T+DG  +  
Sbjct: 61  RYFMLHKPEGYVCSNEDPDHPTVFFLMDEPAMGKLHVVGRLDLDTTGLVLVTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--CYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y V     V  D + L  +G+ ++         Q+ +           +
Sbjct: 121 ITSPRHECAKTYHVWLADPVSPDAIALFAEGVYLRNETDKTRPAQLEIL----GECEARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R   G   L   L  G  RE++ + +
Sbjct: 177 TIHEGKYHQVKRMFASIGNKVVGLHRERVGGLTLDDELAPGEYRELTAEEI 227


>gi|312869081|ref|ZP_07729255.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           oris PB013-T2-3]
 gi|311095327|gb|EFQ53597.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           oris PB013-T2-3]
          Length = 238

 Score =  178 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 109/237 (45%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR  E++IA   V+VNG  +      V + D IEVDG+PL + ++ 
Sbjct: 2   ERLQKVMAEAGVASRRASEKLIATGHVQVNGQTVTTLGTKVTAKDKIEVDGIPLHREKQV 61

Query: 74  RLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              L      + +                  I  R+  VGRLD +T GLLLLTNDG LA 
Sbjct: 62  YYLLNKPRGVISSAHDEKGRRTVVDILREDEIEERIYPVGRLDYDTTGLLLLTNDGTLAN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVT 190
            +  P     + Y  +  G +  D L  L+ G+ + G      +  L    ++   + V 
Sbjct: 122 KMMHPKFAVDKTYVAKVKGLISNDDLKQLRTGVKVDGRRTKPAKTRLKGTDREKKTSIVQ 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           + + EG   ++K++       V +L R SYG   L  +  G  RE+  + ++     
Sbjct: 182 LTIHEGHYHQVKRMLAAVGHPVIKLHRESYGFLNLQGVQPGDYRELRPEEVKRLNRL 238


>gi|328554622|gb|AEB25114.1| 16S pseudouridylate synthase [Bacillus amyloliquefaciens TA208]
          Length = 239

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 100/231 (43%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A +G  SR++V++++    V ++G   +   ++V      I V G P    E 
Sbjct: 1   MRLDKLLANSGFGSRKDVKKIVKAGAVMIDGEPAKDVKIHVDPDKQDITVYGEPAEYREF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      L  T                        GRLD +TEG LLLTNDG LA 
Sbjct: 61  IYVMMNKPQGVLSATEDSRQQTVVDLLTPEEQRFEPFPAGRLDKDTEGFLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y VR    +  + +  L++G+VI+G        V   T+      + +
Sbjct: 121 RLLSPKKHVPKTYEVRLTSPLSPEDIIDLERGVVIEGGYKTKPAAVKTITESPDETVIHL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++K + +    +V  L R+S G   L   L  G  RE++++ L
Sbjct: 181 TITEGKYHQVKLMAKAVGNEVAYLKRLSMGAVSLDPELKPGEFRELTEEEL 231


>gi|308234451|ref|ZP_07665188.1| ribosomal large subunit pseudouridine synthase B [Atopobium vaginae
           DSM 15829]
 gi|328944298|ref|ZP_08241762.1| RNA pseudouridine synthase [Atopobium vaginae DSM 15829]
 gi|327491217|gb|EGF22992.1| RNA pseudouridine synthase [Atopobium vaginae DSM 15829]
          Length = 285

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 68/253 (26%), Positives = 112/253 (44%), Gaps = 22/253 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE 71
             R+ + +ARAG+ASRR  E++I+  RV VNG  +      VM   DH+ VDG       
Sbjct: 24  TMRLQRFLARAGVASRRGSEKLISAGRVCVNGKQVRVLGTKVMPQYDHVTVDGKEYVLGN 83

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGL 130
                L +KP  ++TT SDP G   V   +P         VGRLD +T G+LL T +G +
Sbjct: 84  DHVYLLLNKPSQVLTTMSDPFGFPCVASLVPCDDYPGLFPVGRLDSDTTGVLLFTTNGNM 143

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV- 189
              L  PS    + Y     G++   ++  L +GI+++        +   TQ      + 
Sbjct: 144 GNRLLHPSHHVWKTYVALIEGKLTSSQMQKLSQGIMLEDGMTSPCFIRTITQDEPCTHLD 203

Query: 190 ------------------TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA- 230
                              + + EG+N ++K++ +     V +L R  +GP  L   +  
Sbjct: 204 KNHSLFDDMRLNAASSLCELKIHEGRNHQVKRMLQEIGHPVIKLHRFQFGPLCLNAQIPL 263

Query: 231 GSTREVSKKILRE 243
           GS R  +++ + +
Sbjct: 264 GSWRMCTQQEIHD 276


>gi|171059554|ref|YP_001791903.1| pseudouridine synthase [Leptothrix cholodnii SP-6]
 gi|170776999|gb|ACB35138.1| pseudouridine synthase [Leptothrix cholodnii SP-6]
          Length = 736

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 86/370 (23%), Positives = 143/370 (38%), Gaps = 20/370 (5%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K +++      ++ KV+A+AG+ SRR++E++I + +V VNG +     + +   D I++ 
Sbjct: 280 KRVLRPEPEAPKLHKVLAQAGVGSRRDMEQLIQEGQVSVNGEVA-HIGMRIAQGDQIKIA 338

Query: 64  GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P++          L  +     +VT H      +           + +SVGRLDINTE
Sbjct: 339 GRPIKVRIAPPPARVLAYHKPVGEVVTHHDPEGRPTVFRRLPRLPVGKWLSVGRLDINTE 398

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL TN G LA  L  P     R Y VR  G +D+     L +G+ I+G       +  
Sbjct: 399 GLLLFTNSGELANQLMHPRFGVEREYAVRVLGSLDEAARARLLEGVEIEGQRAMFKSIDD 458

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G N W  V + EG+NRE++++F+     V+RLIRI Y    L   L  G   E+  
Sbjct: 459 GGGEGINHWYRVVITEGRNREVRRLFDAVGLTVSRLIRIRYATVVLPRGLKRGVWVELDD 518

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEV--------------PDDFTR 284
             +R+         A+                 P    +                     
Sbjct: 519 NDVRQIRQIANGPRAERGEREERGPRADRAERGPRDGQQPGRGAGKGKGGGQGQGQGPQM 578

Query: 285 MKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
            +   +   G   Q++   PV +       +  +G      +      E     P+    
Sbjct: 579 SQGGQNAPGGRGNQQRGNKPVGKGGQGGQGFERRGPDGRPGAPRSGGAEWRDERPARDGN 638

Query: 345 RSLRRTSAKK 354
            S      ++
Sbjct: 639 VSREPPRERE 648


>gi|329889977|ref|ZP_08268320.1| hypothetical protein BDIM_16710 [Brevundimonas diminuta ATCC 11568]
 gi|328845278|gb|EGF94842.1| hypothetical protein BDIM_16710 [Brevundimonas diminuta ATCC 11568]
          Length = 513

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 138/353 (39%), Positives = 188/353 (53%), Gaps = 9/353 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R++K +ARAGIASRREVER+I   +V VNG +L   AV V   D I VDG P+  A
Sbjct: 78  ERTERIAKAMARAGIASRREVERLIGLGKVAVNGRILATPAVLVTRDDKITVDGKPIGAA 137

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+W YHKP GL+T+H+DP GR TVFD LPS   RVISVGRLD+ TEGLLLLTNDG L
Sbjct: 138 QATRVWRYHKPAGLITSHNDPAGRPTVFDALPSGLPRVISVGRLDLATEGLLLLTNDGEL 197

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--------Q 182
           +R LELP T  +R YR R  G++ Q++L+ LK G+V+ G+ YG ++ T+D         +
Sbjct: 198 SRALELPETALVRQYRARARGRITQEQLDKLKDGVVVDGVRYGPVEATIDKAKEKTEGEK 257

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
             +N W++V + EGKNRE++KV E     VNRLIR++YGPFQLGTL  GS  EV  +++R
Sbjct: 258 SSANLWLSVSITEGKNREVRKVLESIGLTVNRLIRLAYGPFQLGTLPVGSVEEVGPRVIR 317

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E L  H+  E     +     +    R     I            +       + +    
Sbjct: 318 EMLAEHIRPENLPTGNTVATPTPIPGRRTGTPIVRGKSGSAMSDPSRKPSRVRAAETAAE 377

Query: 303 TPVH-RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                 +      W               R        +    R  R  + ++
Sbjct: 378 DGAEFGKPARKEGWAKAKPKFEHKKTFKPRARPGDDEGTEGGDRPRRPFTPRE 430


>gi|257880467|ref|ZP_05660120.1| pseudouridine synthase [Enterococcus faecium 1,230,933]
 gi|257883279|ref|ZP_05662932.1| pseudouridine synthase [Enterococcus faecium 1,231,502]
 gi|257886356|ref|ZP_05666009.1| pseudouridine synthase [Enterococcus faecium 1,231,501]
 gi|257891502|ref|ZP_05671155.1| pseudouridine synthase [Enterococcus faecium 1,231,410]
 gi|257894555|ref|ZP_05674208.1| pseudouridine synthase [Enterococcus faecium 1,231,408]
 gi|260562466|ref|ZP_05832976.1| pseudouridine synthase [Enterococcus faecium C68]
 gi|261207204|ref|ZP_05921893.1| pseudouridine synthase [Enterococcus faecium TC 6]
 gi|289566697|ref|ZP_06447113.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecium D344SRF]
 gi|257814695|gb|EEV43453.1| pseudouridine synthase [Enterococcus faecium 1,230,933]
 gi|257818937|gb|EEV46265.1| pseudouridine synthase [Enterococcus faecium 1,231,502]
 gi|257822212|gb|EEV49342.1| pseudouridine synthase [Enterococcus faecium 1,231,501]
 gi|257827862|gb|EEV54488.1| pseudouridine synthase [Enterococcus faecium 1,231,410]
 gi|257830934|gb|EEV57541.1| pseudouridine synthase [Enterococcus faecium 1,231,408]
 gi|260073151|gb|EEW61496.1| pseudouridine synthase [Enterococcus faecium C68]
 gi|260078832|gb|EEW66534.1| pseudouridine synthase [Enterococcus faecium TC 6]
 gi|289161514|gb|EFD09398.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecium D344SRF]
          Length = 245

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 59/240 (24%), Positives = 104/240 (43%), Gaps = 5/240 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
              R+ K +A  G+ SR+EV+ +I +  ++VNG +++     V    D +   G  +   
Sbjct: 5   KRMRLDKFLADMGLGSRKEVKGLIKKGTIEVNGQVVKSDKAQVNEFEDAVTYLGEIITYQ 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +     L+     +  T  + D               +  VGRLD +TEGLL+LTNDG  
Sbjct: 65  KDFYYILHKPAGVISATQDNHDQTVIDLLEDQDYREDLFPVGRLDKDTEGLLILTNDGVF 124

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKG--SNA 187
           A  L  P     + Y     G + ++ + L  +G++I         ++ +D        +
Sbjct: 125 AHQLLSPKKHVEKEYLAEVSGIMTEEDIRLFAEGLIIDGDEQTLPAKLQIDQVDQETETS 184

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
            + + L EGK  ++K++ +    +V  L RI  G F L   L  G  R ++K+ L +   
Sbjct: 185 IIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGKFWLPKDLNKGQYRPMTKEELEQVRE 244


>gi|237807721|ref|YP_002892161.1| RNA-binding S4 domain-containing protein [Tolumonas auensis DSM
           9187]
 gi|237499982|gb|ACQ92575.1| RNA-binding S4 domain protein [Tolumonas auensis DSM 9187]
          Length = 348

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 92/348 (26%), Positives = 144/348 (41%), Gaps = 13/348 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG+ SRRE+E +I++ RV VNG +       V + D I VDG  +     
Sbjct: 2   SEKLQKVLARAGVGSRREMETVISEGRVSVNGKVAT-LGDRVEAKDVIRVDGHQISVPTL 60

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  +     + T H      +          SR ++VGRLD+NT GLLL T D
Sbjct: 61  NDVICRVLAYHKPEGEVCTRHDPEGRPTVFDRLPRIKDSRWVAVGRLDVNTSGLLLFTTD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V +  L  L+ G+ ++       ++T    +G N 
Sbjct: 121 GELANRLMHPSHEVEREYAVRVFGEVTEGMLQKLRHGVQLEDGPAKFDKITAGGGEGLNQ 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSK---KILRE 243
           W  V L EG+NRE+++++E    +V+RL+RI YG  +L   L  G   E+       LR+
Sbjct: 181 WFNVTLCEGRNREVRRLWESLEVQVSRLMRIRYGDIKLDKTLPRGGWAELELPQVNYLRK 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDF---TRMKKNSSQKNGLSKQKK 300
            +     + ++V       S           +    +            +      K  +
Sbjct: 241 MVSLLPEDRSKVFGVEDRRSEFKQAAQIRRAVRRHRERTVLQGEEVAGEAPAMPRPKVPR 300

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
            A PV R       W               R   + R     + ++ R
Sbjct: 301 AAPPVKRERDDEVSWENARKRLRDGEPRKARPNANNRQRITRAGKTGR 348


>gi|104782896|ref|YP_609394.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           entomophila L48]
 gi|95111883|emb|CAK16607.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           entomophila L48]
          Length = 353

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 93/357 (26%), Positives = 150/357 (42%), Gaps = 14/357 (3%)

Query: 1   MKDKNIVQENFTP---QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M DK++  +  TP   +++ KV+AR G+ SRR+VE  I Q R+KVNG+      + V   
Sbjct: 1   MSDKDLQDQQPTPPSGEKLQKVLARIGVGSRRDVEAWIGQGRIKVNGVEAT-LGLRVDLH 59

Query: 58  DHIEVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
           D I VDG  +++ E     R  +        + T        +           R I++G
Sbjct: 60  DAITVDGKLIKRVEAAEATRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIG 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RLDINT GLLL T DG LA  L  PS +  R Y VR  G+VD D ++ LK G++++    
Sbjct: 120 RLDINTTGLLLFTTDGELANRLMHPSYEMDREYAVRVRGEVDDDMVDRLKAGVMLEDGPA 179

Query: 173 GDMQVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
               +      +G N W    + EG+NRE+++++E     V+RL R+ +GP  L   L  
Sbjct: 180 KFTDIQKAPGGEGFNHWYHCVVMEGRNREVRRLWESQGVVVSRLKRVRFGPVFLNSDLPM 239

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G  RE+S+  +        L+   +         +     R +       +  R  + + 
Sbjct: 240 GRWREMSQGEIDILAAEVGLQPVALPEMKLKAKDKLERLQRKSTRPLGRGERVRTLRPAQ 299

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
           +  G    +       R++             S +     R E  + +     K   
Sbjct: 300 EGQGERPARPAREEAPRKSGR---GSTVAERPSEMRKRPARPEGDKPAGRGRGKPRG 353


>gi|317129994|ref|YP_004096276.1| pseudouridine synthase [Bacillus cellulosilyticus DSM 2522]
 gi|315474942|gb|ADU31545.1| pseudouridine synthase [Bacillus cellulosilyticus DSM 2522]
          Length = 237

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 100/231 (43%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++ +  V VN  L++     +    DHIEV G  +     
Sbjct: 1   MRIDKLLSNTGFGSRKEVKGLLKKGGVTVNSELIKDGKRQIDPSEDHIEVFGEVIEYKPF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  T    D                  VGRLD +T G +LLTNDG LA 
Sbjct: 61  IYLMMNKPKGVISATEDVTDKTVVDLLATEHALYDPFPVGRLDKDTTGFMLLTNDGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P  +  + YRV     +       L  G+ +         ++T       N  + +
Sbjct: 121 QLTSPKKKVDKTYRVHIDAPLTSADEASLIAGVELDDGYITKPAKLTY---GNDNTVIFL 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++K++F+    KV  L R + GP +L  +LL G  RE++ + +
Sbjct: 178 TITEGKFHQVKRMFQALGRKVINLKRETIGPLKLDPSLLLGEYRELTDEEV 228


>gi|313887215|ref|ZP_07820911.1| pseudouridylate synthase [Porphyromonas asaccharolytica
           PR426713P-I]
 gi|312923444|gb|EFR34257.1| pseudouridylate synthase [Porphyromonas asaccharolytica
           PR426713P-I]
          Length = 470

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 66/270 (24%), Positives = 120/270 (44%), Gaps = 1/270 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E   P R++K ++ +G+ SRR  ++ IA  RVKVNG ++      V+ TD + VD  P+ 
Sbjct: 199 EAGEPIRLNKFLSNSGLCSRRMADQYIAAGRVKVNGAVISELGSQVLPTDQVMVDDKPVS 258

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              +  + L      + T       R+ +     +   R+  +GRLD NT G+LLLTNDG
Sbjct: 259 LEAKVYVLLNKPKNCVTTLTDPEGRRTVMDLVHNACTERIYPIGRLDRNTTGILLLTNDG 318

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P+ +  ++Y V    +V  + + ++  G  ++        ++  T + ++  
Sbjct: 319 DLAVRLMHPAFRKKKIYEVALDKEVTVEHMQMIAHGFELEDGEIHADAISYITGQ-THDK 377

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           V + +  G+NR ++++FE   ++V  L R+ Y       L  G  R ++ + +R      
Sbjct: 378 VGIEIHSGRNRIVRRIFEHLGYRVVHLDRVYYAGLTKKDLPRGRWRYLTPEEVRYLRMGV 437

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEV 278
             +E            +          SE 
Sbjct: 438 KEQEDNGVAPTTKVYHKHQETPDHPFASEE 467


>gi|238795690|ref|ZP_04639204.1| Ribosomal large subunit pseudouridine synthase F [Yersinia
           mollaretii ATCC 43969]
 gi|238720416|gb|EEQ12218.1| Ribosomal large subunit pseudouridine synthase F [Yersinia
           mollaretii ATCC 43969]
          Length = 290

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 65/302 (21%), Positives = 121/302 (40%), Gaps = 14/302 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRR+ +R I Q  V +NG       V V   D ++V+G  +  
Sbjct: 3   TNSSIRLNKYISESGICSRRDADRYIEQGNVFINGKRAAV-GVQVFPGDVVKVNGQTIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L L      +    +  DG      +  +   RV  +GRLD +++GL+LLTN G 
Sbjct: 62  RNEEDLVLIALNKPVGVISTTEDGEQNNIVDFVNHSKRVFPIGRLDKDSQGLILLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  V  + +  L  G+ + G            +K S    
Sbjct: 122 LVNKILRAGNDHEKEYVVTVNKPVTDEFILGLGAGVPMLGTV----TKKCKVKKESTFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ + F ++V +L R+      L  L  G  R++++  L E      
Sbjct: 178 RITLVQGLNRQIRRMTKHFGYEVTKLERVRIMNISLKGLPQGEWRDLTEDELIELFKL-- 235

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                  ++      +   +     +       +  KK     +  + +K+ A P  ++ 
Sbjct: 236 -------IENSSSDEKPAKKAPVKRVEAKRVSISGPKKAEKPDSNAAARKRFAQPGRKKK 288

Query: 310 LA 311
             
Sbjct: 289 GR 290


>gi|239947675|ref|ZP_04699428.1| pseudouridine synthase, Rsu [Rickettsia endosymbiont of Ixodes
           scapularis]
 gi|239921951|gb|EER21975.1| pseudouridine synthase, Rsu [Rickettsia endosymbiont of Ixodes
           scapularis]
          Length = 229

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 113/228 (49%), Positives = 157/228 (68%), Gaps = 2/228 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K+I+ AGI SRR+ E++IA+ +VKV+GI +   A NV  ++ IEV G+ + +++  R
Sbjct: 3   RLAKIISNAGICSRRDAEKLIAEGQVKVDGITILSPATNVDISNQIEVSGILINQSQTPR 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LW+Y+KP+GL+TTH DP  R TVF+  P+   RVIS+GRLD+N+EGLLLLTN G LAR  
Sbjct: 63  LWIYYKPVGLITTHKDPLSRKTVFEQ-PTGLPRVISIGRLDLNSEGLLLLTNSGDLARQF 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPS++  RVY VR +G+ D    +   K + I GI Y    + L  Q  SN+W  V L 
Sbjct: 122 ELPSSRLKRVYHVRAYGKSDILLKSN-YKNLEIDGIFYNPHSIKLLKQNKSNSWFEVVLF 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           EGKNREI+++FE+F  KVN+LIRI YG F +G L  G  +E++ KIL 
Sbjct: 181 EGKNREIRRIFEYFGLKVNKLIRIQYGSFTIGNLKPGDYKEINNKILE 228


>gi|238019398|ref|ZP_04599824.1| hypothetical protein VEIDISOL_01262 [Veillonella dispar ATCC 17748]
 gi|237864097|gb|EEP65387.1| hypothetical protein VEIDISOL_01262 [Veillonella dispar ATCC 17748]
          Length = 242

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 67/242 (27%), Positives = 125/242 (51%), Gaps = 4/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K IA  G+ASRR+ E +I + +V+VNG  +    V +    D ++V+G  L + + 
Sbjct: 2   ERLQKFIASCGVASRRKAEELITEGKVQVNGRKVTELGVKIDPQKDKVKVNGQLLAQEKP 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      + +        + + D + +   R+  +GRLD+ TEGLLLLTNDG LA+
Sbjct: 62  VYYLLNKPKGVITSVSDPQGRETVL-DYIKNESKRIYPIGRLDLYTEGLLLLTNDGELAQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            L  PS    + Y VR  G+V  + L ++  G+ ++        +        N    V 
Sbjct: 121 NLTHPSKGVEKTYEVRIKGRVRDEDLQVIANGVKLEDGMTAPATIVDLGFDDHNGVHEVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + + EG+NR+++++FE F ++++ L RI+Y    LG +  G++R+++ + ++        
Sbjct: 181 ITIHEGRNRQVRRMFEHFGYRIHNLKRIAYAGLTLGGVKRGASRQLTIREVKALKALGTD 240

Query: 251 EE 252
           ++
Sbjct: 241 KK 242


>gi|302383495|ref|YP_003819318.1| pseudouridine synthase [Brevundimonas subvibrioides ATCC 15264]
 gi|302194123|gb|ADL01695.1| pseudouridine synthase [Brevundimonas subvibrioides ATCC 15264]
          Length = 511

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 139/354 (39%), Positives = 188/354 (53%), Gaps = 12/354 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E    +R++K +ARAGIASRREVER+I   +V VNG +L+  A  V   D I VDG P+ 
Sbjct: 94  EPKRSERIAKAMARAGIASRREVERLIGLGKVAVNGRILDTPATLVTRDDVITVDGKPIA 153

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            A+ TR+W Y+KP+GL+T+H+DP GR TVFD LPS   RVISVGRLDINTEGLLLLTNDG
Sbjct: 154 AAQATRVWRYNKPVGLLTSHNDPQGRPTVFDALPSGLPRVISVGRLDINTEGLLLLTNDG 213

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT------- 181
            L+R LELP T  +R YR R  G+V Q  L+ LK G+ + G+ YG ++ ++D        
Sbjct: 214 ELSRALELPETALVRQYRARARGRVTQADLDKLKDGVTVDGVRYGPVEASIDKATTKEDG 273

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + +N W++V + EGKNRE++KV E     VNRLIR++YGPFQLGTL  GS  EV  +++
Sbjct: 274 SQAANLWISVQIAEGKNREVRKVLESVGLTVNRLIRLAYGPFQLGTLAVGSVEEVGPRVI 333

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNII-----SEVPDDFTRMKKNSSQKNGLS 296
           RE LG H+  +     +     +    R                D +R            
Sbjct: 334 RELLGEHIRPDNLPQGNTVETPAPIPGRRTGAPKVTGTSGSAMSDPSRKPSRVRAAATAQ 393

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
            +         +        A               E    +   P++    R 
Sbjct: 394 VEGAERANRPPKKAGWAKAAAPNPRGPSTKKPWAPREGAAPTGDRPARVFKPRD 447


>gi|52841677|ref|YP_095476.1| pseudouridine synthase [Legionella pneumophila subsp. pneumophila
           str. Philadelphia 1]
 gi|52628788|gb|AAU27529.1| pseudouridine synthase [Legionella pneumophila subsp. pneumophila
           str. Philadelphia 1]
          Length = 248

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 79/240 (32%), Positives = 124/240 (51%), Gaps = 7/240 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--- 68
           + +R+ K++++AG+ SRRE+ER I    V+VNG   +    +   +D I V G  +    
Sbjct: 2   SSERLQKILSQAGLGSRREMERWIDNGWVQVNGKPAK-LGDSAGPSDKISVKGKLIPNPL 60

Query: 69  --KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
             K     L  +     + + H     ++   +       R + VGRLD+NT GLL+ TN
Sbjct: 61  KSKQNIRVLLYHKPVGEVSSRHDPKFEKTVFDNLPHLRQGRWVQVGRLDLNTSGLLIFTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G LA  L  P     R Y VR HGQV Q+ LN L KG+++        ++     +G+N
Sbjct: 121 NGELANQLMHPKYGLEREYAVRVHGQVSQESLNNLLKGVMLDDGLAKFTKIQFRGGEGTN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
           +W  V L EG+NRE+++++E    +V+RLIRI YG   +   L  G   E++ K + E L
Sbjct: 181 SWYHVTLNEGRNREVRRLWESQGVEVSRLIRIRYGMLTMPRFLSRGQFYELTPKEVTEFL 240


>gi|195952397|ref|YP_002120687.1| pseudouridine synthase [Hydrogenobaculum sp. Y04AAS1]
 gi|195932009|gb|ACG56709.1| pseudouridine synthase [Hydrogenobaculum sp. Y04AAS1]
          Length = 239

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 64/230 (27%), Positives = 115/230 (50%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+++ ++ AG+ SRR+ +  I +  VKVN  +++     +    D +E  G  ++  + 
Sbjct: 1   MRLNRFLSLAGVCSRRKADEYIEKGYVKVNNNIVKELGTTINPDEDIVEFRGRIVKAQK- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP   +T+  + + + T+ + +  +  RV   GRLD N EGLL+LTNDG LA 
Sbjct: 60  PVYIILNKPCCYLTSLGEKEEKPTIRELIKDVGVRVYPAGRLDYNVEGLLILTNDGELAN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  +VY     G++D + L  +K+G+ ++        + L  +  + A + + 
Sbjct: 120 RIIHPRYKLPKVYIATIKGEIDDETLEKMKRGVRLEDGFVKPDSLKLLKRFKNGANIEIT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
             EGKN  +K+ F  F   V  LIR + GP  LG L  G  R +    ++
Sbjct: 180 FHEGKNHLVKRFFLAFKKPVKHLIRTAIGPISLGNLPKGKWRHLKPAEIK 229


>gi|288905607|ref|YP_003430829.1| ribosomal small subunit pseudouridine synthase [Streptococcus
           gallolyticus UCN34]
 gi|288732333|emb|CBI13903.1| ribosomal small subunit pseudouridine synthase [Streptococcus
           gallolyticus UCN34]
          Length = 242

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 101/232 (43%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +  AGI SR EV++++ +++V VNG +       +    D I   G  L   + 
Sbjct: 1   MRLDKFLVEAGIGSRTEVKQLLKKKQVLVNGKVEISPKTQIDEKADRISCQGQTLSYEKY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  +         +  +       VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYMLNKPKGVISATEDNHHKTVLDLLDKIAWDKEAFPVGRLDIDTHGLLLLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVT 190
            +  P     + YR +  G +    +     GI ++       Q+ +     +   + V 
Sbjct: 121 AMLSPKKHVDKTYRAKVAGLMTTADVAAFANGIDLKDFTCQPAQLVILETNEAERTSVVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + ++EGK  ++K++ +    KV  L R+S GP QL   L  G  R ++   L
Sbjct: 181 ITIKEGKFHQVKRMVQACGKKVTDLQRLSMGPLQLDKQLALGEWRRLTDDEL 232


>gi|229820641|ref|YP_002882167.1| pseudouridine synthase [Beutenbergia cavernae DSM 12333]
 gi|229566554|gb|ACQ80405.1| pseudouridine synthase [Beutenbergia cavernae DSM 12333]
          Length = 245

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 81/236 (34%), Positives = 118/236 (50%), Gaps = 1/236 (0%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGV 65
           +       R+ KV+A AG+ SRR  E +I+  RV V+G ++      V  T   I VDG+
Sbjct: 1   MSAPAEGVRLQKVLAGAGLGSRRACEDLISAGRVSVDGEVVRELGTRVDPTAAVIHVDGL 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            L+          +KP G+ +T  D  GR  + + +     R+  VGRLD +TEGLLLLT
Sbjct: 61  RLQLDPGVVTLALNKPRGVHSTMHDDRGRPALAELVADRPERLFHVGRLDADTEGLLLLT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  PS +  + Y  R  G+V +     LK GI +        + T+  Q   
Sbjct: 121 NDGELAHRLAHPSYEVPKTYVARVTGRVARGLGRRLKDGIELDDGPARVDRFTILEQGPD 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +A V + L EG+NR ++++ +     V RL R   GP  LG L  G+TR +  + L
Sbjct: 181 SAVVELVLHEGRNRIVRRLLDAAGHPVQRLTRTRVGPVLLGQLRPGATRVIDGEEL 236


>gi|237728101|ref|ZP_04558582.1| 23S rRNA pseudouridine synthase F [Citrobacter sp. 30_2]
 gi|226910112|gb|EEH96030.1| 23S rRNA pseudouridine synthase F [Citrobacter sp. 30_2]
          Length = 291

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 63/293 (21%), Positives = 113/293 (38%), Gaps = 5/293 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         VM  D ++V+G  +   
Sbjct: 4   DSSIRLNKYISESGICSRREADRFIEQGNVFLNGKRAT-IGDQVMPGDVVKVNGRLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L        +    +  D       +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVFIALNKPVGIVSTTEDSERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V  D +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPVTDDFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  L  G  R+++   L +       
Sbjct: 179 ITLIQGLNRQIRRMCEHFGYEVTKLERTRIMNVGLSGLPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
             ++    A        ++     I +  +        + ++     +KK   
Sbjct: 239 SSSEAKPKAKAKPKTAGIKRPVVKIEKSAEKEKSRPAANGKRFTSPGRKKKGR 291


>gi|107022570|ref|YP_620897.1| pseudouridine synthase, Rsu [Burkholderia cenocepacia AU 1054]
 gi|116689519|ref|YP_835142.1| pseudouridine synthase, Rsu [Burkholderia cenocepacia HI2424]
 gi|105892759|gb|ABF75924.1| ribosomal large subunit pseudouridine synthase B [Burkholderia
           cenocepacia AU 1054]
 gi|116647608|gb|ABK08249.1| ribosomal large subunit pseudouridine synthase B [Burkholderia
           cenocepacia HI2424]
          Length = 586

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 82/352 (23%), Positives = 145/352 (41%), Gaps = 7/352 (1%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 174 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRI 232

Query: 63  DGVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           +G P+++         L  +     +V+        S      P   ++ ++VGRLD NT
Sbjct: 233 NGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNT 292

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++ 
Sbjct: 293 EGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELAEGMRQKLLHGVELDDGPANFLRIR 352

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
               +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ 
Sbjct: 353 DGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELD 412

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIIS-EVPDDFTRMKKNSSQKNGLS 296
              +R+ +    L+           ++    R +P+ +   +          +  +    
Sbjct: 413 DAQVRKLMATVGLKAPSEEKGKRGGAAGPTERRQPDPMQTSMGFISREPVLTTHGQLDQP 472

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           ++             S         S + + +G   + +R        R+  
Sbjct: 473 RRGGGRRGGPGLPGLSGYGSLPVAPSGYGNRAGGGRDGNRTGGGRDGNRAGG 524


>gi|225012273|ref|ZP_03702710.1| pseudouridine synthase [Flavobacteria bacterium MS024-2A]
 gi|225003828|gb|EEG41801.1| pseudouridine synthase [Flavobacteria bacterium MS024-2A]
          Length = 244

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 59/248 (23%), Positives = 112/248 (45%), Gaps = 6/248 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +QE     R++K ++  G  SRR  +R+I + RV++NG+ +      V   D IEVDGV 
Sbjct: 1   MQEQTEGIRLNKYLSEIGHCSRRAADRLIEEGRVQINGVQV-IMGQKVTPLDRIEVDGVL 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +   +   +++       +   +D         +  +  +R+  +GRLD  +EGL+LLTN
Sbjct: 60  VEDLQERNVYIAFNKPIGIVCTTDTRVEKDNIIDYINYPTRIFPIGRLDKPSEGLILLTN 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG +   +        + Y V  +  V  + +  +  GI I              ++   
Sbjct: 120 DGDIVNKILRARNNHEKEYIVTVNKPVTTEFVEKMANGIPILDTITRKC----VVEQIHK 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               + L +G NR+I+++ E+ +++V +L RI     +L  +  G  R+++KK + E   
Sbjct: 176 NQFRIILTQGLNRQIRRMCEYLDYRVVKLKRIRIMNIEL-NVGVGKYRDLTKKEMVELQN 234

Query: 247 PHLLEEAQ 254
                +  
Sbjct: 235 LIADSDKH 242


>gi|332878090|ref|ZP_08445820.1| pseudouridylate synthase [Capnocytophaga sp. oral taxon 329 str.
           F0087]
 gi|332684052|gb|EGJ56919.1| pseudouridylate synthase [Capnocytophaga sp. oral taxon 329 str.
           F0087]
          Length = 253

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 58/241 (24%), Positives = 108/241 (44%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K +  +   P R++K +A AG+ SRRE +  I    V VNG ++      V  TD +
Sbjct: 5   IEYKELNVDPDAPIRLNKFLANAGVCSRREADEFITAGVVSVNGTVVTELGTKVKRTDEV 64

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P+    +  + L      + T+    + ++ +         R+  VGRLD NT G
Sbjct: 65  KFHEQPVSIERKVYVLLNKPKDYVTTSDDPQNRKTVMDLVKNVCRERIYPVGRLDRNTTG 124

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LL TNDG LA  L  P     ++Y V     V    +  + +GI ++        +   
Sbjct: 125 VLLFTNDGELASKLTHPKFLKKKIYHVTTDKNVTAADMRQIAEGITLEDGEIRADAIDYA 184

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +       V + +  GKNR ++++FE   ++V +L R+ +       +  G  R ++++ 
Sbjct: 185 SPTDKKQ-VGIEIHSGKNRIVRRIFEALGYRVVKLDRVLFAGLTKKNVRRGDWRFLTEQE 243

Query: 241 L 241
           +
Sbjct: 244 V 244


>gi|171779942|ref|ZP_02920846.1| hypothetical protein STRINF_01729 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171281290|gb|EDT46725.1| hypothetical protein STRINF_01729 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 242

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 60/232 (25%), Positives = 104/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +  AGI SR +V++++ +++V VNG +       +    D I   G  L   + 
Sbjct: 1   MRLDKFLVGAGIGSRNDVKQLLKKKQVTVNGEIETSPKTQIDEKIDKIVCQGENLSYEKY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  +         +  +    V  VGRLDI+T GLL LTN+G LA 
Sbjct: 61  VYYMLNKPKGVISATEDNHHKTVLDLLDKTAWDKEVFPVGRLDIDTHGLLFLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVT 190
            +  P     ++YR +  G +  + +    KGI ++       Q+ +     +   + V 
Sbjct: 121 AMLSPKKHVDKLYRAKVAGIMTAEDVEHFAKGIELKDFTCQPAQLEILEIDEAAKTSLVA 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + ++EGK  ++K++      +V  L R+S GP QL   L  G  R ++ + L
Sbjct: 181 ITIKEGKFHQVKRMVLACGKEVTDLERLSMGPLQLDENLSLGEWRRLTAEEL 232


>gi|322392605|ref|ZP_08066065.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           peroris ATCC 700780]
 gi|321144597|gb|EFX39998.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           peroris ATCC 700780]
          Length = 240

 Score =  177 bits (448), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 65/237 (27%), Positives = 102/237 (43%), Gaps = 4/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +    + SR EV+  +   RV VNG   + A + +   TD I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNFLKAGRVTVNGKKEKSAKLQIDEETDEICFDGKKLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T +          +  +    V  VGRLDI+T GLLLLTNDG LA 
Sbjct: 61  VYYMMNKPQGVISATENPKHKTVLDLMDDYACAKEVFPVGRLDIDTHGLLLLTNDGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVT 190
            L  P     + Y  +  G +  + +    KGI ++       ++ L     + + + V 
Sbjct: 121 ALLSPKRHVDKTYMAQVKGIMTDEDIETFAKGIPLKDFTCQPAKLELVSIDTEENKSLVR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           V + EGK  ++K++  +   +V  L R++ G   L   L  G  R +SK+ L   L 
Sbjct: 181 VTIAEGKFHQVKRMVAYCGKEVVDLQRVTMGTLTLDEELKRGEWRRLSKEELEGLLE 237


>gi|228477053|ref|ZP_04061691.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus salivarius SK126]
 gi|228251072|gb|EEK10243.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus salivarius SK126]
          Length = 243

 Score =  177 bits (448), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 57/234 (24%), Positives = 105/234 (44%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+  + +++V VNG +       +    D I   G  L     
Sbjct: 1   MRLDKFLVDCGVGSRSQVKTFLKKKQVAVNGQVETSPKTQIDENQDQIAFQGQVLTHETF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T            +  +   +V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPQGVISATEDARHKTVLDLLDDTARHKQVFPVGRLDIDTHGLLLLTNNGDLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVT 190
            +  P     ++Y+ +  G ++Q+ +   +KGI ++       ++ + +   +   + V 
Sbjct: 121 AMLSPKKHVDKIYQAKVDGIMNQEDILAFEKGIELKDYTCQPAKLEIISVDRATGTSLVQ 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           + + EGK  ++K++      +V  L R+S GP  L   L  G+ R ++++ L  
Sbjct: 181 ITIAEGKFHQVKRMVAACGKEVTELQRLSMGPLSLPNDLEVGAWRRLTEEELEA 234


>gi|315025675|gb|EFT37607.1| conserved hypothetical protein [Enterococcus faecalis TX2137]
 gi|315173996|gb|EFU18013.1| conserved hypothetical protein [Enterococcus faecalis TX1346]
          Length = 257

 Score =  177 bits (448), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 64/248 (25%), Positives = 109/248 (43%), Gaps = 5/248 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           I + G  L   +     L+     +  T    D             + +  VGRLD +TE
Sbjct: 61  IALMGEILTYQKFFYYMLHKPQGVISATEDQRDETVIDLLTDQDYRADLFPVGRLDKDTE 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVT 178
           GLLLLTNDG LA  L  P     + Y     G V  +   L  +G  +  G      ++ 
Sbjct: 121 GLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEMVKPSRLV 180

Query: 179 L--DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTRE 235
           +    ++   + V + ++EGK  ++K++       V  L R+  G   L   L  G  R 
Sbjct: 181 IETINEEEGTSVVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGGYRP 240

Query: 236 VSKKILRE 243
           +++  L++
Sbjct: 241 LTEAELQQ 248


>gi|168211270|ref|ZP_02636895.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           B str. ATCC 3626]
 gi|169347003|ref|ZP_02865945.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           C str. JGS1495]
 gi|169296686|gb|EDS78815.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           C str. JGS1495]
 gi|170710722|gb|EDT22904.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           B str. ATCC 3626]
          Length = 239

 Score =  177 bits (448), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 105/231 (45%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV++  G  +R+E+++++ +  V VN   ++ + + +    D I ++G  +   + 
Sbjct: 2   ERLDKVLSNLGYGTRKEIKQVVKKGFVTVNDEKVKDSGLQIDPEKDTIVINGEKVEYKKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  T+   D        +         VGRLD +T GLLLLTNDG L  
Sbjct: 62  IYLMMNKPAGVISATYDKRDETVIDLLYMEDQVFEPFPVGRLDKDTVGLLLLTNDGDLNH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY    +  + +  +   + G+ +         ++ +      +A V V
Sbjct: 122 KLISPKYHVDKVYYAEINAPITEKDIKAFENGVTLDDGYKCMSAKLKVIENLEDSARVEV 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            ++EGK  ++K++FE    KV  L R S+G   L   L  G  +E+S+  L
Sbjct: 182 TVQEGKYHQVKRMFEARGKKVVYLKRTSFGNLPLDESLEEGEYKELSESEL 232


>gi|118444952|ref|YP_878908.1| RNA pseudouridylate synthase family protein [Clostridium novyi NT]
 gi|118135408|gb|ABK62452.1| RNA pseudouridylate synthase family protein [Clostridium novyi NT]
          Length = 238

 Score =  177 bits (448), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 55/224 (24%), Positives = 102/224 (45%), Gaps = 3/224 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV++  G  SR+E++  + +  ++V+G +++   + V      I+V+G  +   + 
Sbjct: 2   ERLDKVLSNLGYGSRKEIKAFVKKGEIEVDGKVVKDNGIKVDPNKSIIKVNGEEINYRKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      +  T  + D       +          VGRLD +TEGLLL+TNDG L  
Sbjct: 62  IYIMMNKPAGVVSATFDNYDETVIDLLDYEYTVFDPFPVGRLDKDTEGLLLITNDGELNH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y       VD+  +   KKGI +         ++ + +   + + V +
Sbjct: 122 RLTSPKWHVDKTYYAEIDKMVDEKDVEKFKKGITLDDGYKCLPAKLEILSSDENGSEVNI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
            ++EGK  ++K++FE     V  L R++ G   L   L  G+ R
Sbjct: 182 TIQEGKFHQVKRMFEARGKNVVYLKRLTMGNISLDEELDEGTYR 225


>gi|329766937|ref|ZP_08258465.1| hypothetical protein HMPREF0428_00162 [Gemella haemolysans M341]
 gi|328837662|gb|EGF87287.1| hypothetical protein HMPREF0428_00162 [Gemella haemolysans M341]
          Length = 243

 Score =  177 bits (448), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 72/242 (29%), Positives = 128/242 (52%), Gaps = 3/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+IA +G  SRR+ E++I   +V VNG +++   V    +D I V+GV L   E  
Sbjct: 3   ERLQKLIAASGYTSRRKAEQLILDGKVSVNGEVVKELGVKAEPSDIIIVEGVRL-LKENK 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP  ++T+ SD   R+ V D    +  RV+ VGRLD +T G L+++NDG    +
Sbjct: 62  RYYLFYKPEKVITSMSDEKDRTCVKDFFEDVNERVVPVGRLDYDTSGALIMSNDGEFINL 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  + Y  + +G+++ + L +L+ G+ I        +V +   K    N  V +
Sbjct: 122 ITHPKHKIRKTYVAKINGKLEDNHLRILRNGVRIDNYKTAKAEVNIVKNKNKSGNTLVRL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EGKNR+++++FE   ++V +L R S     L  L  G  R ++   ++  +      
Sbjct: 182 TIHEGKNRQVRRMFEALGYEVMKLKRESIEDLTLEGLKKGEYRTLTIHEVKRLINKAKNG 241

Query: 252 EA 253
           E 
Sbjct: 242 EK 243


>gi|229548610|ref|ZP_04437335.1| pseudouridylate synthase [Enterococcus faecalis ATCC 29200]
 gi|312953045|ref|ZP_07771898.1| conserved hypothetical protein [Enterococcus faecalis TX0102]
 gi|229306241|gb|EEN72237.1| pseudouridylate synthase [Enterococcus faecalis ATCC 29200]
 gi|310629074|gb|EFQ12357.1| conserved hypothetical protein [Enterococcus faecalis TX0102]
 gi|315144498|gb|EFT88514.1| conserved hypothetical protein [Enterococcus faecalis TX2141]
 gi|315153886|gb|EFT97902.1| conserved hypothetical protein [Enterococcus faecalis TX0031]
 gi|315156684|gb|EFU00701.1| conserved hypothetical protein [Enterococcus faecalis TX0043]
 gi|327534254|gb|AEA93088.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis OG1RF]
          Length = 257

 Score =  177 bits (448), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 63/248 (25%), Positives = 109/248 (43%), Gaps = 5/248 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           I + G  L   +     L+     +  T    D             + +  VGRLD +TE
Sbjct: 61  IALMGEILTYQKFFYYMLHKPQGVISATEDQRDETVIDLLTDQDYRADLFPVGRLDKDTE 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVT 178
           GLLLLTNDG LA  L  P     + Y     G V  +   L  +G  ++        ++ 
Sbjct: 121 GLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEIVKPSRLV 180

Query: 179 L--DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTRE 235
           +    ++   + V + ++EGK  ++K++       V  L R+  G   L   L  G  R 
Sbjct: 181 IETINEEEGTSVVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGGYRP 240

Query: 236 VSKKILRE 243
           +++  L++
Sbjct: 241 LTEAELQQ 248


>gi|187934882|ref|YP_001884642.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum B str. Eklund 17B]
 gi|187723035|gb|ACD24256.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum B str. Eklund 17B]
          Length = 238

 Score =  177 bits (448), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 109/231 (47%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K+I+  G  SR+E + +  +  ++V+G +++ ++V +      ++++G  +   + 
Sbjct: 2   ERLDKIISNLGYGSRKEAKVLARKGLIEVDGKIIKDSSVTIDPEKSIVKINGEEIFYRKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  TH   D        L         VGRLD +T GLLLLTNDG    
Sbjct: 62  IYLMMNKPTGVISATHDSKDETVIDLLELDHQIFNPFPVGRLDKDTVGLLLLTNDGEFNH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            +  P     +VY  +   +V++      KKG+V+       + ++ + +     + V +
Sbjct: 122 RMISPKWHVDKVYYAKIDKEVNEKDQQAFKKGVVLDDGYKCLEAKLDIISASPEGSEVRI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            ++EGK  ++K++FE  + KV  L R  +G   L   L  G  RE+S + L
Sbjct: 182 TIQEGKYHQVKRMFEACDKKVVYLKREEFGGLILDENLEEGEYRELSDEEL 232


>gi|78066108|ref|YP_368877.1| ribosomal large subunit pseudouridine synthase B [Burkholderia sp.
           383]
 gi|77966853|gb|ABB08233.1| ribosomal large subunit pseudouridine synthase B [Burkholderia sp.
           383]
          Length = 588

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 81/355 (22%), Positives = 141/355 (39%), Gaps = 6/355 (1%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 175 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRI 233

Query: 63  DGVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           +G P+++         L  +     +V+        S      P   ++ ++VGRLD NT
Sbjct: 234 NGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNT 293

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++ 
Sbjct: 294 EGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELAEGMRQKLLHGVELDDGPANFLRIR 353

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
               +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ 
Sbjct: 354 DGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELD 413

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
              +R+ +    L+           + +   R    + + +          +  +    +
Sbjct: 414 DTQVRKLMATVGLKAPSEEKGKRGGTGQAERRQPDPMQTSMGFIGREPVLTAHGQLDQPR 473

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           +             S         S F + +G   + +R                
Sbjct: 474 RGSGRRGGPGLPGLSGYGSLPVAPSGFGNRAGGGRDGNRAGGGGRDGNRAGGGRG 528


>gi|160931609|ref|ZP_02079004.1| hypothetical protein CLOLEP_00441 [Clostridium leptum DSM 753]
 gi|156869480|gb|EDO62852.1| hypothetical protein CLOLEP_00441 [Clostridium leptum DSM 753]
          Length = 242

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 80/234 (34%), Positives = 129/234 (55%), Gaps = 2/234 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
                R+ K++A  G+ASRR+ E +I Q +VKVNG + +     V   TDH+ V G  + 
Sbjct: 2   QDQKIRLQKMLADCGVASRRKAEELIQQGKVKVNGHVAQ-IGDKVNPKTDHVTVAGRRIV 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            + +    + HKP G V+T SD  GR  V + +  I +RV  VGRLD ++EGLLL+TNDG
Sbjct: 61  ASRQYYYIMLHKPRGYVSTMSDEMGRKCVAELVKDIPARVYPVGRLDRDSEGLLLMTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             A ++  PS    + YRV     + +++L L+  G+ I G+        + +++     
Sbjct: 121 EFANLIMHPSKHVPKTYRVTVRPDISEEQLALMNVGMEIDGVRTAPADAWVISREPGRVV 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + + LREG+NR+I+K+ E    +V RL R++ G  +LG L  G  R ++   ++
Sbjct: 181 LEIILREGRNRQIRKMCEQLGVEVARLKRVAVGQVKLGMLQPGKWRNLTLDEVK 234


>gi|148358978|ref|YP_001250185.1| pseudouridine synthase [Legionella pneumophila str. Corby]
 gi|296107027|ref|YP_003618727.1| ribosomal large subunit pseudouridine synthase B [Legionella
           pneumophila 2300/99 Alcoy]
 gi|148280751|gb|ABQ54839.1| pseudouridine synthase [Legionella pneumophila str. Corby]
 gi|295648928|gb|ADG24775.1| ribosomal large subunit pseudouridine synthase B [Legionella
           pneumophila 2300/99 Alcoy]
          Length = 248

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 79/240 (32%), Positives = 124/240 (51%), Gaps = 7/240 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--- 68
           + +R+ K++++AG+ SRRE+ER I    V+VNG   +    +   +D I V G  +    
Sbjct: 2   SSERLQKILSQAGLGSRREMERWIDNGWVQVNGKPAK-LGDSAGPSDKISVKGKLIPNPL 60

Query: 69  --KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
             K     L  +     + + H     ++   +       R + VGRLD+NT GLL+ TN
Sbjct: 61  KGKQNIRVLLYHKPVGEVSSRHDPKFEKTVFDNLPHLRQGRWVQVGRLDLNTSGLLIFTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G LA  L  P     R Y VR HGQV Q+ LN L KG+++        ++     +G+N
Sbjct: 121 NGELANQLMHPKYGLEREYAVRVHGQVSQESLNNLLKGVMLDDGLAKFTKIQFRGGEGTN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
           +W  V L EG+NRE+++++E    +V+RLIRI YG   +   L  G   E++ K + E L
Sbjct: 181 SWYHVTLNEGRNREVRRLWESQGVEVSRLIRIRYGMLTMPRFLSRGQFYELTPKEVTEFL 240


>gi|82779348|ref|YP_405697.1| 23S rRNA pseudouridine synthase F [Shigella dysenteriae Sd197]
 gi|309784076|ref|ZP_07678718.1| ribosomal large subunit pseudouridine synthase F [Shigella
           dysenteriae 1617]
 gi|81243496|gb|ABB64206.1| conserved hypothetical protein [Shigella dysenteriae Sd197]
 gi|308928069|gb|EFP73534.1| ribosomal large subunit pseudouridine synthase F [Shigella
           dysenteriae 1617]
          Length = 290

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 61/292 (20%), Positives = 114/292 (39%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLNGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++    A        ++     + +  +       N  +     ++KK  
Sbjct: 239 SSSEAKPKAKAKPKTAGIKRPVVKMEKTAEKGGCPASNGKRFTSPGRKKKGR 290


>gi|332161503|ref|YP_004298080.1| 23S rRNA pseudouridine synthase F [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|325665733|gb|ADZ42377.1| 23S rRNA pseudouridine synthase F [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
          Length = 290

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 61/293 (20%), Positives = 117/293 (39%), Gaps = 5/293 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRR+ +R + Q  V +NG         V   D ++V+G  +  
Sbjct: 3   TNSSIRLNKYISESGICSRRDADRYVEQGNVFINGKRAAV-GDQVYVGDVVKVNGQLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + + L L      +    +  DG S    +  +   RV  +GRLD +++GL+ LTN G 
Sbjct: 62  RDESDLILIALNKPVGIISTTEDGESDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  V  + +  L  G+ + G      +V    +K +    
Sbjct: 122 LVNKILRAGNDHEKEYVVTVNKPVTDEFILGLGAGVPMLGTVTKKCKV----RKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           ++ L +G NR+I+++ + F ++V +L R       L  L  G  R++    L E      
Sbjct: 178 SITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNVNLKGLPIGEWRDLRDDELIELFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
              +         +   + +      S+  +          +     ++KK  
Sbjct: 238 NSSSDEKPQKKPKAKPVVAKKPAISRSKPAEKSETNSAGRKRFTQPGRKKKGR 290


>gi|229198700|ref|ZP_04325399.1| RNA pseudouridine synthase [Bacillus cereus m1293]
 gi|228584776|gb|EEK42895.1| RNA pseudouridine synthase [Bacillus cereus m1293]
          Length = 229

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 109/230 (47%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + ++G  + K E+ 
Sbjct: 1   MKINQYISEANSCSRRETDRLIKAGRVAINGEICTHGAI-VSDDDVVTINGRVIVKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D    + +     +   R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAADHIEDNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVTRV----DQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L 
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELNELEVGKWRSVTAEELE 223


>gi|327405122|ref|YP_004345960.1| ribosomal large subunit pseudouridine synthase F [Fluviicola
           taffensis DSM 16823]
 gi|327320630|gb|AEA45122.1| ribosomal large subunit pseudouridine synthase F [Fluviicola
           taffensis DSM 16823]
          Length = 305

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 54/308 (17%), Positives = 117/308 (37%), Gaps = 5/308 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K I+ +G  SRRE ++ I Q  V +NG+  +     V   D + V+G  L++  
Sbjct: 3   ESIRLNKFISDSGYCSRREADKYIEQGSVFINGVRAK-IGTQVTRRDKVVVNGHTLQQKS 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +              T +   G      +      R+  +GRLD +++GL+ LT++G + 
Sbjct: 62  QEEEIYIALNKPPGVTSTTEKGVVDNIVDYVGHPQRIFPIGRLDKDSQGLIFLTSNGDIV 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +     +  + Y V     +  D +  +  G+ I G+           ++ S+    +
Sbjct: 122 NKILRAGNEHQKEYLVTVDKPITPDFIAKMATGVPILGVVTKKC----IVEQISSNVFKI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ E+F + V +L R      +L  +  G  RE+++  +R         
Sbjct: 178 VLIQGLNRQIRRMCEYFQYNVTKLERTRIMNIELKGIPLGEWRELTESEMRILNDMLKDS 237

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           +++ +  +   S+            +        K  + +      +             
Sbjct: 238 KSETDRVSQKASAVGQKPKSKPTPPKKKPIVAAKKTGTQKPRSFGSKPGTGGKSASSRGK 297

Query: 312 SNVWMAKG 319
            +    + 
Sbjct: 298 KSTSRGRR 305


>gi|268610237|ref|ZP_06143964.1| pseudouridine synthase [Ruminococcus flavefaciens FD-1]
          Length = 247

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 84/248 (33%), Positives = 130/248 (52%), Gaps = 3/248 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + +     R+ K+IA +G+ SRR+ E +I++ RVK+NG  ++         D I +DG  
Sbjct: 1   MGDKVEKIRIQKMIADSGVCSRRKAEELISRGRVKLNGHPVK-LGDKCGYKDIITIDGER 59

Query: 67  --LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             + K +  R  + +KP G VTT SD   R  V D L  +  RV  VGRLD N+EGLLL 
Sbjct: 60  LYIPKKKSFRYIIMNKPRGYVTTVSDELDRRCVMDLLDDVEDRVYPVGRLDRNSEGLLLF 119

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG  A  +  PS    + YRV     +  ++L  L +G+ I G       V +  ++ 
Sbjct: 120 TNDGEFANSIMHPSRHISKTYRVTVRPDISDEQLIQLSEGVEIDGKRTLPATVIVKDKQP 179

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
               + + ++EG+NR+I+K+ E    +V RL R S GP +LG L  G+ R+++ + LR  
Sbjct: 180 GRVVLLMTIKEGRNRQIRKMCEAVGLEVARLRRTSIGPIKLGMLKPGTYRDLTAEELRAI 239

Query: 245 LGPHLLEE 252
                 E+
Sbjct: 240 RNAIGKEK 247


>gi|168821347|ref|ZP_02833347.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|238913060|ref|ZP_04656897.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Tennessee str. CDC07-0191]
 gi|205342140|gb|EDZ28904.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|320088621|emb|CBY98379.1| pseudouridylate synthase [Salmonella enterica subsp. enterica
           serovar Weltevreden str. 2007-60-3289-1]
          Length = 289

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 62/292 (21%), Positives = 116/292 (39%), Gaps = 5/292 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R++K I+ +GI SRRE +R I Q  V +NG         V++ D ++V+G  +  
Sbjct: 3   TDTSIRLNKYISESGICSRREADRFIEQGNVFINGKRAA-IGDQVVAGDVVKVNGRLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   L L      +    +  DG      +  +   R+  +GRLD +++GL+ LTN G 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRIFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     +  + +  +  G+ I G            +K +    
Sbjct: 122 LVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +      
Sbjct: 178 RITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
              ++    A      T ++     I +  +            +   K+K  
Sbjct: 238 RSSSEAKPKAKAKPKTTGIKRPVVAIEKSNEKARPASSGKRFTSPGRKKKGR 289


>gi|313674669|ref|YP_004052665.1| ribosomal large subunit pseudouridine synthase f [Marivirga
           tractuosa DSM 4126]
 gi|312941367|gb|ADR20557.1| ribosomal large subunit pseudouridine synthase F [Marivirga
           tractuosa DSM 4126]
          Length = 243

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 54/247 (21%), Positives = 105/247 (42%), Gaps = 6/247 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +R++K ++ AG  SRR  +++I +  V +NG +       V   D + V G  + +
Sbjct: 2   DTQLKRINKFLSEAGYCSRRNADKLIEEGAVTINGKIP-EMGTKVGPDDEVRVKGELITE 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                ++L       +   +D         +  +   R+  +GRLD  +EGL+LLTNDG 
Sbjct: 61  PNSNFVYLAFNKPRGIVCTTDTRREKDNIIDYINYPERIFPIGRLDKYSEGLILLTNDGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +        + Y V  +  +  D +  +  G+ I              ++   +  
Sbjct: 121 IVNKILRARNNHEKEYIVHLNKPIKGDFIQKMGDGVPILDTVTKKC----FVEQIGKSSF 176

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F++KV  L RI     +L T   G  R ++   L+E      
Sbjct: 177 KIILTQGLNRQIRRMCEYFDYKVAGLKRIRIMNVKLDT-EKGKWRHLTPNELKEIQELVS 235

Query: 250 LEEAQVN 256
             +   +
Sbjct: 236 HSDKTHD 242


>gi|295100099|emb|CBK89188.1| ribosomal small subunit pseudouridine synthase A [Eubacterium
           cylindroides T2-87]
          Length = 230

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 104/229 (45%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++  G  +R +V+ +I    V + G  +++A   V     + VD  P+   +  
Sbjct: 1   MRLDKFLSHMGYGTRNKVKNIIKNGWVTIEGKTIKKADHQVKEDQIVYVDDTPVSYIQYE 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      +  T  +     T+ + +PSI   +  VGRLDI+TEGLLL+ NDG L   
Sbjct: 61  YYILNKPSGYVSATEDN--VHPTIMELIPSIRKDLYPVGRLDIDTEGLLLVCNDGQLTHD 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     + Y V F G + ++ + +  + + +         + +     +     + +
Sbjct: 119 LLSPKKHVQKKYYVEFEGTLPENAVEIFNQPMDLDDFIAKPSTLEILDTNKA----YLTI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EGK  ++K++F+    +V  L R+S+GP +L  L  G  R +S   + 
Sbjct: 175 SEGKFHQVKRMFQKIGCEVTYLQRVSFGPLELKNLEIGQARALSPDEIE 223


>gi|205354985|ref|YP_002228786.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205274766|emb|CAR39823.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|326630136|gb|EGE36479.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
          Length = 289

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 62/292 (21%), Positives = 116/292 (39%), Gaps = 5/292 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R++K I+ +GI SRRE +R I Q  V +NG         V++ D ++V+G  +  
Sbjct: 3   TDTSIRLNKYISESGICSRREADRFIEQGNVFINGKRAA-IGDQVVAGDVVKVNGRLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   L L      +    +  DG      +  +   R+  +GRLD +++GL+ LTN G 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRIFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     +  + +  +  G+ I G            +K +    
Sbjct: 122 LVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVSILGTV----TKKCKVKKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +      
Sbjct: 178 RITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
              ++    A      T ++     I +  +            +   K+K  
Sbjct: 238 RSSSEAKPKAKAKPKTTGIKRPVIAIEKSNEKARPASSGKRFTSPGRKKKGR 289


>gi|91788475|ref|YP_549427.1| ribosomal large subunit pseudouridine synthase B [Polaromonas sp.
           JS666]
 gi|91697700|gb|ABE44529.1| ribosomal large subunit pseudouridine synthase B [Polaromonas sp.
           JS666]
          Length = 544

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 80/356 (22%), Positives = 140/356 (39%), Gaps = 8/356 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          +   D ++V+
Sbjct: 87  KRVLSPQPETPKLHKVLAQAGLGSRLEMEQLILEGRISVNAEPA-HIGQRIQFGDTVKVN 145

Query: 64  GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+R          +  +     +VT     +  +           +  SVGRLD+NTE
Sbjct: 146 GKPIRVRIDPPPPRVIAYHKPSGEVVTHDDPQNRPTVFRRLPKLFQGKWQSVGRLDLNTE 205

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLLT+ G LA  L  P     R Y VR  G +  ++   L +G+ +         +  
Sbjct: 206 GLLLLTSSGELANKLMHPRFGLEREYAVRVLGALSNEEKKRLLEGVTLDDGVAQFSSIEA 265

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E+ +
Sbjct: 266 GGGEGANCWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMLLPRGLKRGAFVELDE 325

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           + +          E++ +          +  D        P    R  + S    G    
Sbjct: 326 RDIWALTNAVTRSESRADPRGAPKHPGHVRGDEGGEFR--PGRGPRRNERSRGDRGRLPA 383

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +       +   ++           +  +      +RR       +     S  +
Sbjct: 384 PESGQADDFQPADADAEQEPNELQPPMHRTDSAPRGNRRRGGKGRGQGGNPGSPPR 439


>gi|262045577|ref|ZP_06018597.1| ribosomal large subunit pseudouridine synthase F [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
 gi|259037074|gb|EEW38325.1| ribosomal large subunit pseudouridine synthase F [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
          Length = 291

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 60/301 (19%), Positives = 114/301 (37%), Gaps = 13/301 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSTRLNKYISESGICSRREADRFIEQGNVFINGKRAT-IGDQVKPGDLVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   R+  +GRLD +++GL+ LTN G L
Sbjct: 63  EADDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPVTDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLTGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
             ++                       +     +M+ ++ +       K+   P  ++  
Sbjct: 239 SSSEAK--------PKARPKAKAATPGIKRPVVKMENSNDKGRPAGNGKRFTQPGRKKKG 290

Query: 311 A 311
            
Sbjct: 291 R 291


>gi|332162312|ref|YP_004298889.1| 16S rRNA pseudouridylate synthase A [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|325666542|gb|ADZ43186.1| 16S rRNA pseudouridylate synthase A [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330859689|emb|CBX70026.1| ribosomal small subunit pseudouridine synthase A [Yersinia
           enterocolitica W22703]
          Length = 235

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 55/238 (23%), Positives = 108/238 (45%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    
Sbjct: 1   MRLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQTVGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +  D       G+ +          Q+ +   +     V +
Sbjct: 121 ITSPRHHCEKTYLVTLEQPIADDTAQQFTDGVQLHNEKSLTKPAQLEVIEPQ----LVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
            + EG+  ++K++F     +V  L R   G  +L   L  G  R ++ + +     PH
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVLELHRERIGDIKLDDDLAPGEYRPLTPEEIASVGAPH 234


>gi|88860840|ref|ZP_01135476.1| putative ribosomal RNA pseudouridylate synthase [Pseudoalteromonas
           tunicata D2]
 gi|88817053|gb|EAR26872.1| putative ribosomal RNA pseudouridylate synthase [Pseudoalteromonas
           tunicata D2]
          Length = 229

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 67/231 (29%), Positives = 110/231 (47%), Gaps = 7/231 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K IA AG+ SRR+  R+I Q  V VNG + +     V + D I V+   L   
Sbjct: 2   NDGIRLAKYIANAGLCSRRQASRLIDQGLVTVNGGIADHICF-VGTDDVITVNDELLVYQ 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                +L++KP+G+ +     D  S +   L     R+  +GRLD ++ GL++LTNDG L
Sbjct: 61  TEQVYYLFNKPVGIDSRLLPNDSASLIH--LLPSEIRIYPIGRLDKDSYGLMILTNDGEL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P     + YRV     +D +  N + +GI + G       V     + +     
Sbjct: 119 YHQMNHPDHHQEKEYRVSVERPIDANFCNKMAQGIPVDGQLTQPCSVW----QTAENEFH 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + L +G NR+I+K+ +   +KV  L RI      +G L AG  + ++K  +
Sbjct: 175 IVLTQGLNRQIRKMAKHCGYKVVDLERIRIANLAIGDLSAGEFKTLTKADI 225


>gi|296112011|ref|YP_003622393.1| pseudouridylate synthase [Leuconostoc kimchii IMSNU 11154]
 gi|295833543|gb|ADG41424.1| pseudouridylate synthase [Leuconostoc kimchii IMSNU 11154]
          Length = 249

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 91/235 (38%), Positives = 133/235 (56%), Gaps = 2/235 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   QRV KVIA+AG+ASRR  E +I + RV+VNG  +    V V  TD + VD +PL  
Sbjct: 2   SEEAQRVQKVIAQAGLASRRGAEELIIKGRVQVNGQTITALGVKVEPTDTVTVDSIPLEG 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E+   +L +KP G+VTT++D  GR TV D L  +  RV  +GRLD +T G+LLLTNDG 
Sbjct: 62  REKLVYYLLNKPRGVVTTNNDEKGRRTVLDILSDVNERVYPIGRLDYDTTGVLLLTNDGV 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--A 187
           +A  L  P ++  +VY  +  G    DKL  LK G+VI+G      +VT++        +
Sbjct: 122 IANQLMHPKSRVDKVYIAKVAGIATDDKLAPLKHGVVIKGRKTAPARVTIERIDKDKKTS 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V V L EG+N ++K + +     V +L R  Y  F L  L +G  R+++   ++
Sbjct: 182 MVRVILHEGRNHQVKNMLQKVGLPVEKLTREQYAFFDLTGLQSGEYRKLTSPEIK 236


>gi|304315594|ref|YP_003850739.1| RNA-binding S4 domain protein [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302777096|gb|ADL67655.1| RNA-binding S4 domain protein [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 241

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 104/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K+++  G  +R+EV+  I +  V VNG  +    + +    D I  +   +   + 
Sbjct: 4   MRIDKLLSNTGFGTRKEVKGFIKEGLVTVNGRTVNDPGLIIETDKDDIIFNDEKIFYRKY 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      +  T+   +              +V   GRLD +TEGLLLLTNDG LA 
Sbjct: 64  IYIMMNKPRGVISATYDPSEKTVLDLLPDDIKARKVFPAGRLDKDTEGLLLLTNDGILAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G +D+D ++L   GIV+          + +    GS + V V
Sbjct: 124 KLLSPKKHVYKKYYAEISGFIDEDDISLFSNGIVLDDGYKTMPAYLEII-SSGSISKVYV 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            ++EGK  +IK++FE    KV  L R+S G   L   L  G  RE++   L+
Sbjct: 183 SIKEGKYHQIKRMFESLGSKVIYLKRLSMGYLNLDENLKEGEWRELTDNELK 234


>gi|219870596|ref|YP_002474971.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           parasuis SH0165]
 gi|219690800|gb|ACL32023.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           parasuis SH0165]
          Length = 230

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 102/229 (44%), Gaps = 3/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + +   +V VNG++ + +A  +   D I  DG PL   +  
Sbjct: 1   MRLDKFIAENTGLTRSQASKALRAGQVTVNGVVEKNSATKISEQDEICFDGEPLAWVDEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ +KP   V +H D D  +        + +++   GRLD +T GL+LLT+DG  +  
Sbjct: 61  QYFMLYKPQNCVCSHDDGDYPTVFQFFDYPLTTKLHCAGRLDADTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+        +GI+++G         L+     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEDFYATQFAEGILLRGEKTATKPAQLEILDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     KV  L R   G   L   L  G  R +++  +
Sbjct: 179 SEGRYHQVKRMFAALGNKVVALHRWRIGDVVLDENLAEGEFRALTEDEI 227


>gi|90021367|ref|YP_527194.1| ribosomal large subunit pseudouridine synthase B [Saccharophagus
           degradans 2-40]
 gi|89950967|gb|ABD80982.1| ribosomal large subunit pseudouridine synthase B [Saccharophagus
           degradans 2-40]
          Length = 398

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 96/359 (26%), Positives = 150/359 (41%), Gaps = 14/359 (3%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
                +   +++ KV+ARAG  SRRE+ER I + RVKVNG++       V  +D I+VD 
Sbjct: 2   KTTDSSPQDEKLQKVLARAGQGSRREMERAITEGRVKVNGVVAT-LGDRVTESDKIQVDD 60

Query: 65  VPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
             +R  +        +        + + +      +   +       R ISVGRLD NT 
Sbjct: 61  QYIRVKKGEADTTRVILYNKPEGQICSRNDPEGRPTVYDNLPRLKSGRWISVGRLDFNTS 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL TNDG LA  L  PS+   R Y VR  G+VD D L  L+ G++++        +  
Sbjct: 121 GLLLFTNDGELAHKLMHPSSNIDREYLVRVQGEVDGDMLQRLRDGVLLEDGLAKFTDIVP 180

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
             Q+GSN W    + EGKNRE+++++E    +V+RL R+ YG   +   +  G   E+  
Sbjct: 181 GAQEGSNRWFYCVVMEGKNREVRRLWESQECRVSRLKRVRYGNIFIPSNVRVGQWIELED 240

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           K L+E      +        A +       R R     E P      + N+   +  S+ 
Sbjct: 241 KELKELCQTADIPVPDRKFSAGLQDFRDRQRRRL----ESPGSKRSSRPNTKVPDARSRP 296

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF---PSKRSLRRTSAKK 354
                        +    A     +  S       +  R P      SK++  R   ++
Sbjct: 297 SSAHFDPEVTVGKAATPNAPKARMNTRSAPNFDNGSDTRQPKPRQQASKKTNSRNKDRR 355


>gi|257458228|ref|ZP_05623378.1| ribosomal large subunit pseudouridine synthase B [Treponema
           vincentii ATCC 35580]
 gi|257444338|gb|EEV19431.1| ribosomal large subunit pseudouridine synthase B [Treponema
           vincentii ATCC 35580]
          Length = 252

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 84/256 (32%), Positives = 129/256 (50%), Gaps = 6/256 (2%)

Query: 1   MKDKNIVQENFTPQ-RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N   ++  P+ R+   +A AG+ASRR  E++I + RV VNG ++      V + D 
Sbjct: 1   MRGNNHFSQSSKPEMRLQVYLAHAGVASRRACEKIIEEGRVSVNGTVVTGMGSKVCAGDT 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINT 118
           +  DG P+    R    L +KP G V T SD  GR T  D L      R+ ++GRLD+ +
Sbjct: 61  VLFDGKPVHPEARKCYVLLNKPAGFVCTLSDEKGRPTAADLLKEAYSERLYNIGRLDMFS 120

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            G +L TNDG  A  +E PS Q  + Y +        + L   ++GI + GI Y      
Sbjct: 121 SGAILFTNDGDFAAKIEHPSAQIEKEYVIETTQDFPPELLTRFERGIRVDGIFYKCRSAA 180

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
                 +   + + L EGKNREI++V + FN  + RL+R+  G  +LGTL AG  R+++ 
Sbjct: 181 AV----NRRKLRIVLVEGKNREIRRVLDSFNCTIKRLVRVRIGNLELGTLKAGEFRDLTV 236

Query: 239 KILREQLGPHLLEEAQ 254
           +  +  LG     +  
Sbjct: 237 QERQALLGLAAQNDNS 252


>gi|261341580|ref|ZP_05969438.1| ribosomal large subunit pseudouridine synthase F [Enterobacter
           cancerogenus ATCC 35316]
 gi|288316382|gb|EFC55320.1| ribosomal large subunit pseudouridine synthase F [Enterobacter
           cancerogenus ATCC 35316]
          Length = 290

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 61/292 (20%), Positives = 112/292 (38%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K I+ +GI SRRE +R I Q  V +NG         V+  D ++V+G  +   
Sbjct: 4   TQSTRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVVPGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L        +    +  DG      +  +  SR+  +GRLD +++GL+ LTN G L
Sbjct: 63  DAEDLVFIALNKPVGIVSTTEDGERDNIVDFVNHSSRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYIVTVNKPVTDEFIRGMGAGVPILGTV----TKKCKVKKEAPFAFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F + V +L R       L  +  G  R+++   L E       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYDVTKLERTRIMNVSLSGIPLGEWRDLTDDELIELFRLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++    A        ++          +       N  +     ++KK  
Sbjct: 239 SSSEAKPKAKAKPKTQAIKRPVVKAPPAEEKGRGKPANGKRFAQPGRKKKGR 290


>gi|210633114|ref|ZP_03297681.1| hypothetical protein COLSTE_01590 [Collinsella stercoris DSM 13279]
 gi|210159268|gb|EEA90239.1| hypothetical protein COLSTE_01590 [Collinsella stercoris DSM 13279]
          Length = 282

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 81/261 (31%), Positives = 120/261 (45%), Gaps = 13/261 (4%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
            E   P R+ + +ARAG+ASRR  E +++  RV VNG +       V    D + VDGVP
Sbjct: 22  DERVVPMRLQRFLARAGVASRRGSEALMSAGRVSVNGEVKTELGTKVDPAIDQVAVDGVP 81

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLT 125
           +         + +KP G++TT SDP GR  V D +P         VGRLD++T GLLL T
Sbjct: 82  VVLGVGAAYLMLNKPAGVLTTMSDPHGRPCVADIMPVRSYPGLFPVGRLDMDTTGLLLFT 141

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
            DG L   L  PS    + Y     G   +  L  L++GIV+        +  L  ++  
Sbjct: 142 TDGDLGHALLHPSRHVWKTYVAVVDGVCREGDLEPLRRGIVLDDGPCQPARCALRDERDV 201

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                         V + +REG+  ++K++       V RL R+ +GP +L  L  GS R
Sbjct: 202 RDIAPRGLRAGTTAVRIEIREGRKNQVKRMLSKIGHPVLRLHRLRFGPLELNDLPCGSWR 261

Query: 235 EVSKKILREQLGPHLLEEAQV 255
           E++   +        +EE   
Sbjct: 262 ELTPTEVAALQSTPAVEEISA 282


>gi|167856142|ref|ZP_02478882.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           parasuis 29755]
 gi|167852738|gb|EDS24012.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           parasuis 29755]
          Length = 230

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 103/229 (44%), Gaps = 3/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + +   +V VNG++ + +A  +   D I  DG PL   +  
Sbjct: 1   MRLDKFIAENTGLTRSQASKALRAGQVTVNGVVEKNSATKISEQDEICFDGEPLAWVDEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ +KP   V +H D D  +        + +++   GRLD +T GL+LLT+DG  +  
Sbjct: 61  QYFMLYKPQNCVCSHDDGDYPTVFQFFDYPLTTKLHCAGRLDADTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+        +GI+++G        TL+     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEDFYATQFAEGILLRGEKTLTKPATLEILDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EG+  ++K++F     KV  L R   G   L   L  G  R +++  +
Sbjct: 179 SEGRYHQVKRMFAALGNKVVALHRWRIGNVVLDETLAEGEFRALTEDEV 227


>gi|209694708|ref|YP_002262636.1| ribosomal large subunit pseudouridine synthase B (rRNA
           pseudouridylate synthase B) [Aliivibrio salmonicida
           LFI1238]
 gi|208008659|emb|CAQ78844.1| ribosomal large subunit pseudouridine synthase B (rRNA
           pseudouridylate synthase B) [Aliivibrio salmonicida
           LFI1238]
          Length = 354

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 92/353 (26%), Positives = 148/353 (41%), Gaps = 14/353 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG+ SRRE+E MI   RV ++G   +           I +DG  +   E 
Sbjct: 2   SEKLQKVLARAGLGSRRELETMIQAGRVSIDGQKAKLGDRLENVDARIRIDGHVVSVKES 61

Query: 73  TRLWL-----YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           T +       +     L T H     R+          SR +SVGRLD NT GLLL T D
Sbjct: 62  TDVICRVLAYHKPEGELCTRHDPEGRRTVFDRLPKIKDSRWVSVGRLDANTAGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y  R  G ++   +  L  G+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRKVEREYMCRIFGDINDKMVKNLVTGVKLEDGEARFEDVMYAGGEGMNH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI---LRE 243
              V + EG+NRE++++++     V+RL R+ YG   L   L  G   E+  K    LR+
Sbjct: 182 TFYVVINEGRNREVRRLWDSQGVTVSRLKRVRYGDIFLEKALPRGGWMELELKEVNYLRD 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +     +E+ +++D            +     +  D+ T   +N++        KK   
Sbjct: 242 MVELPHEKESLLDVDKESRKRAKSKSQKIRRAVKRHDERTTEDRNTAGGRRGRNNKKPVG 301

Query: 304 ---PVHRRNLA--SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
              P  ++  +  S     KG      S +G +    + SP+  + +S  R  
Sbjct: 302 GSLPTAKKPTSIESAKPAGKGKPKGKPSANGAKPIRTKFSPNGKAPKSAPRQR 354


>gi|198242968|ref|YP_002218105.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|207859366|ref|YP_002246017.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|197937484|gb|ACH74817.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Dublin str.
           CT_02021853]
 gi|206711169|emb|CAR35544.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|326625901|gb|EGE32246.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Dublin str. 3246]
          Length = 289

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 62/292 (21%), Positives = 116/292 (39%), Gaps = 5/292 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R++K I+ +GI SRRE +R I Q  V +NG         V++ D ++V+G  +  
Sbjct: 3   TDTSIRLNKYISESGICSRREADRFIEQGNVFINGKRAA-IGDQVVAGDVVKVNGRLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   L L      +    +  DG      +  +   R+  +GRLD +++GL+ LTN G 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRIFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     +  + +  +  G+ I G            +K +    
Sbjct: 122 LVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +      
Sbjct: 178 RITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
              ++    A      T ++     I +  +            +   K+K  
Sbjct: 238 RSSSEAKPKAKAKPKTTGIKRPVIAIEKSNEKARPASSGKRFTSPGRKKKGR 289


>gi|330866214|gb|EGH00923.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. aesculi str. 0893_23]
          Length = 408

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 91/354 (25%), Positives = 140/354 (39%), Gaps = 15/354 (4%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG         V   D I
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDAT-LGQRVDLHDAI 62

Query: 61  EVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            VDG  +++ E     R  +        + T        +           R I++GRLD
Sbjct: 63  SVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           INT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++       
Sbjct: 123 INTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPARFT 182

Query: 176 QVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE+S+  + + L   +  +          + + + R +      +           +   
Sbjct: 243 REMSQYEV-DILAAEVGLQPVAQPQMNAKTKDKMERLQRQPSRPLGKGERVRTLRPAAGA 301

Query: 294 GLSKQKKLATP-----VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
             +  +    P        R    +                +       S   P
Sbjct: 302 PATGDRAPRQPQITGSERDRPRGGDSTQRPSPRKDSGKPGSRAPRPADNSRGTP 355



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 17/91 (18%), Positives = 24/91 (26%), Gaps = 2/91 (2%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
            E             +  +D     S  P      +     +      K+ A P  +R  
Sbjct: 317 SERDRPRGGDSTQRPSPRKDSGKPGSRAPRPADNSRGTPVAERPSEMNKRPAKPGPKRVG 376

Query: 311 AS--NVWMAKGIHSSFLSDSGQREENHRRSP 339
               N     G      + SGQR    RR P
Sbjct: 377 IKLVNDDAPSGKRRGPPAGSGQRPGFGRRKP 407


>gi|324328441|gb|ADY23701.1| RNA pseudouridine synthase family protein [Bacillus thuringiensis
           serovar finitimus YBT-020]
          Length = 229

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 62/234 (26%), Positives = 109/234 (46%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE + +I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDSLIKAGRVAINGEICTH-GALVNEGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D    + +     +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAADHIEGNIIDYI--NYPGRIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVTRV----DQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRVFGFTVKKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>gi|307130686|ref|YP_003882702.1| 16S rRNA pseudouridylate 516 synthase [Dickeya dadantii 3937]
 gi|306528215|gb|ADM98145.1| 16S rRNA pseudouridylate 516 synthase [Dickeya dadantii 3937]
          Length = 232

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 104/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  QRV VNG +++  A  ++    +  DG  L +    
Sbjct: 1   MRLDKFLSQQLGISRALVARELRAQRVTVNGEVIKSGAFKLLPEHEVAFDGNVLEQQNGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+LLT+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTILYFIDEPVAHKLHAAGRLDIDTSGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +  D  +  + G+ + G              ++ S   V +
Sbjct: 121 ITSPKHHCEKTYLVTLEQPLAPDTADNFQAGVQLHGEKNLTRPAT----LEQISEHQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L  G  R ++ + +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVALHRERIGAITLDDALEPGEYRPLTPEEV 227


>gi|152987584|ref|YP_001347332.1| hypothetical protein PSPA7_1951 [Pseudomonas aeruginosa PA7]
 gi|150962742|gb|ABR84767.1| conserved hypothetical protein [Pseudomonas aeruginosa PA7]
          Length = 386

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 89/360 (24%), Positives = 143/360 (39%), Gaps = 19/360 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+AR G+ SRR+VE  IA+ RV VNG +       V S D I VDG  +R+ E 
Sbjct: 13  GEKLQKVLARLGVGSRRDVEVWIAEGRVNVNGSVA-SLGQRVDSHDAITVDGHLIRREEA 71

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R  L        + T        +           R I+VGRLDINT GLLL T D
Sbjct: 72  AENVRRVLIYNKPEGEVCTRDDPEGRPTIFDRLPRLRTGRWINVGRLDINTTGLLLFTTD 131

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSN 186
           G LA  L  PS +  R Y VR  G+V ++ +  L  G++++        +      +G N
Sbjct: 132 GELANRLMHPSYEMDREYAVRVRGEVSEEMIERLLDGVMLEDGPAKFSDIQQAPGGEGFN 191

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR--- 242
            W    + EG+NRE+++++E     V+RL R+ +GP  L   L  G  RE+ ++ +    
Sbjct: 192 HWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLTSELTMGRYREMDQREIDILS 251

Query: 243 --------EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
                      G       +        +      +RP    +             +   
Sbjct: 252 EEVGLKPVALPGMTTKAREKAERQQRKQARPLARSERPEAGRKRAPRREDGDNAGRRTPA 311

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               +       R+       +A+    S       +  + R + +   K + R+   K+
Sbjct: 312 SRSSRGPQPGAERKGREQGTPVAERPRESNRKPRPSKPRDERPAGAPGDKPAARKPQVKR 371


>gi|93005736|ref|YP_580173.1| 23S rRNA pseudouridine synthase F [Psychrobacter cryohalolentis K5]
 gi|92393414|gb|ABE74689.1| ribosomal large subunit pseudouridine synthase F [Psychrobacter
           cryohalolentis K5]
          Length = 328

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 67/336 (19%), Positives = 122/336 (36%), Gaps = 10/336 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N +  R++K I+ +GI SRR+ +R I Q  V +NG         V++ D ++V+G  +  
Sbjct: 3   NASSTRLNKYISESGICSRRDADRFIEQGNVYLNGKRAAV-GDQVVAGDTVKVNGQLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E            +    +          +      R+  +GRLD +++GL+ LT++G 
Sbjct: 62  KEADDFVFIVLNKPVGIVSTTESSEKNNIVDFVRHSVRIFPIGRLDKDSQGLIFLTSNGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  +    +  L  G+ + G       VT    K +    
Sbjct: 122 LVNKVLRAGNNHEKEYLVTVNKPLTDSVIEGLAGGVPMLGKMTKKCPVT----KVAPNVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E F ++V +L R       L     G  R+++ K L   +    
Sbjct: 178 NITLVQGLNRQIRRMCEHFGYEVVKLERTRIMNVSLKGTPVGDWRDLTPKEL--SVLLKS 235

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
           +E++      P   S    R  P          +     +++ N    +     P   + 
Sbjct: 236 VEDSSSQDSKPAKKSRNAPRKNPRTDDSSKAKSSSKTAGAAKGNKKHSKDGARKPAGSKG 295

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
                W                    R S    SKR
Sbjct: 296 KD---WRPFSDGKKSGGKGKPATNGKRPSKGRGSKR 328


>gi|271500910|ref|YP_003333935.1| pseudouridine synthase [Dickeya dadantii Ech586]
 gi|270344465|gb|ACZ77230.1| pseudouridine synthase [Dickeya dadantii Ech586]
          Length = 232

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 55/232 (23%), Positives = 103/232 (44%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  + R +  QRV VNG +++  A  ++    +  DG  L +    
Sbjct: 1   MRLDKFLSQQLGISRSLIVRELRAQRVTVNGEVVKSGAFKLLPEHEVAFDGNVLEQQNGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+LLT+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTILYFIDEPVAHKLHAAGRLDIDTSGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +  D     + G+ +           + +     S   V +
Sbjct: 121 ITSPKHHCEKTYLVTLEQPLAADTAEKFQAGVQLHNEKNLTRPATLEVL----SEHQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            + EG+  ++K++F      V  L R   G   L   L  G  R ++++ + 
Sbjct: 177 TITEGRYHQVKRMFAAIGNHVVALHRERIGAITLDDTLEPGEYRPLTQEEVD 228


>gi|157144864|ref|YP_001452183.1| 16S rRNA pseudouridylate synthase A [Citrobacter koseri ATCC
           BAA-895]
 gi|157082069|gb|ABV11747.1| hypothetical protein CKO_00593 [Citrobacter koseri ATCC BAA-895]
          Length = 245

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 61/244 (25%), Positives = 107/244 (43%), Gaps = 7/244 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M D  I+       R+ K IA+    SR    R I   RV V+G ++  AA  ++   ++
Sbjct: 1   MPDFRIITGKIKLMRLDKFIAQQLGVSRAIAGREIRSNRVTVDGEIIRNAAFKLLPEHNV 60

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           E DG  L +    R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T G
Sbjct: 61  EYDGNTLVQQNGPRYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTG 120

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVT 178
           L+L+T+DG  +  +  P     + Y V     V  D      KG+ +           + 
Sbjct: 121 LVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVAADTAEQFAKGVQLHNEKDLTKPAVLE 180

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
           +     +   V + + EG+  ++K++F      V  L R   G   L   L  G  R ++
Sbjct: 181 VI----TPTQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGAIVLDDDLEPGEYRPLT 236

Query: 238 KKIL 241
           ++ +
Sbjct: 237 EEEI 240


>gi|256848777|ref|ZP_05554211.1| 16s pseudouridylate synthase [Lactobacillus crispatus MV-1A-US]
 gi|256714316|gb|EEU29303.1| 16s pseudouridylate synthase [Lactobacillus crispatus MV-1A-US]
          Length = 236

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 62/234 (26%), Positives = 102/234 (43%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV ++I +  V VNG  ++     +   D + V+G  +   +  
Sbjct: 1   MRIDKYLANMNVGSRKEVHQLIKKGVVAVNGKTVKTLKEKINENDVVTVNGEEIAYQKYH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      L  T            +    +  ++ VGRLD +T GLLLLTNDG L   
Sbjct: 61  YFLLNKPKGVLSATEDRSQKTVISLLDPQDRYQGIVPVGRLDKDTTGLLLLTNDGQLNHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN--AWVT 190
           L  P+    +VYR    G  D++       G+++  G      ++ +  Q   N  + + 
Sbjct: 121 LVAPNKHVAKVYRAEIAGVADEETAKAFASGMMLGDGTKLKPAKLKILKQDRENATSEIE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           + + EGK  +IK++F     KV  L R+S G   L   L  G   E+S   ++ 
Sbjct: 181 IEISEGKYHQIKRMFGAVGMKVTALDRLSMGNLHLQSDLKRGKYVELSLDEIKN 234


>gi|83590579|ref|YP_430588.1| ribosomal small subunit pseudouridine synthase A [Moorella
           thermoacetica ATCC 39073]
 gi|83573493|gb|ABC20045.1| ribosomal small subunit pseudouridine synthase A [Moorella
           thermoacetica ATCC 39073]
          Length = 243

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 70/233 (30%), Positives = 117/233 (50%), Gaps = 4/233 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
             QR+ +V+A  G  +R+ ++++I ++RV+VNG   E   ++V+   D+IEV+G PL   
Sbjct: 5   ERQRLDRVLAHMGFGTRKMIKKLIKEKRVQVNGRPAEDPGLHVIPGRDYIEVNGEPLVYE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      L  T                       VGRLD + EGLLLLTNDG L
Sbjct: 65  EYIYLMLNKPQGVLSATEDRYAKVVVDLLPPRYRAFHPFPVGRLDKDAEGLLLLTNDGEL 124

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWV 189
           A  L  P     ++Y     G V +  +   ++GI++         ++T+  + G+ + V
Sbjct: 125 AHRLLSPKKHVSKMYYAVVDGIVTETDVEAFRQGIILNDGYRTMPGELTIL-RSGTESEV 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + + EGK  ++K++FE  + +V  L RI+ GP +L   L  G  RE++++ +
Sbjct: 184 ELTIYEGKYHQVKRMFEAVSKRVLYLKRIAMGPLRLDELLRPGEYRELTEEEI 236


>gi|219669430|ref|YP_002459865.1| pseudouridine synthase [Desulfitobacterium hafniense DCB-2]
 gi|219539690|gb|ACL21429.1| pseudouridine synthase [Desulfitobacterium hafniense DCB-2]
          Length = 255

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 91/246 (36%), Positives = 139/246 (56%), Gaps = 4/246 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M   N        +R+ KV+A+AGIASRR  E +I Q RVKVNG ++      V+STD I
Sbjct: 1   MNRNNERGRPRQEERLQKVLAQAGIASRRHAEEIILQGRVKVNGEVIRTLGTKVVSTDRI 60

Query: 61  EVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
            VDG  L         +L HKP G +T+ +DP GR TV + +P I  RV  VGRLD +T 
Sbjct: 61  VVDGRLLSIPQNDYAYYLLHKPTGYITSVTDPQGRKTVMELMPKIPRRVYPVGRLDYDTS 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLLTNDG LA  L  PS    + YRV    ++ +  L  L+KG++++       ++  
Sbjct: 121 GLLLLTNDGDLAHRLMHPSYGVEKTYRVEVGEKIPEQALKRLEKGVLLEDGKTAPARIRE 180

Query: 180 DTQKGSNA--WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
            + KG  +     + + EG+NR+++++F+   + ++ L R+ +GP +L  +L  G+ R +
Sbjct: 181 VSPKGRGSLPTYEITIHEGRNRQVRRMFKAVGFPLSTLKRLRFGPLELDPSLAPGAFRTL 240

Query: 237 SKKILR 242
           SK  ++
Sbjct: 241 SKTEIQ 246


>gi|331649882|ref|ZP_08350959.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli M605]
 gi|281181089|dbj|BAI57419.1| putative pseudouridine synthase [Escherichia coli SE15]
 gi|330908342|gb|EGH36861.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           AA86]
 gi|331041262|gb|EGI13415.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli M605]
          Length = 290

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 63/292 (21%), Positives = 116/292 (39%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V S D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKSGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++    A        ++     + +  +   R   N  +     ++KK  
Sbjct: 239 SSSEAKPKAKAKPKTVGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 290


>gi|225867942|ref|YP_002743890.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           equi subsp. zooepidemicus]
 gi|225871142|ref|YP_002747089.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           equi subsp. equi 4047]
 gi|225700546|emb|CAW95028.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           equi subsp. equi 4047]
 gi|225701218|emb|CAW98156.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           equi subsp. zooepidemicus]
          Length = 240

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 81/237 (34%), Positives = 129/237 (54%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I +  V +NG ++   A  V S D +EV+G+P+   E  
Sbjct: 1   MRINKYIAHAGLASRRKAEELIKRGLVTLNGQVITDLATTVKSGDLVEVEGIPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T GLL+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVSDDKGRQTVIDLLPQVKERIYPVGRLDWDTSGLLILTNDGDFTDK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P  +  +VY  R  G V ++ L  L +G+VI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGVVTKESLRPLTRGVVIDGKKTKPARYRIIRVEPDKNRSIVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + EG++ ++KK+FE     V++L R  +G   +  L  G  R +SKK + +     
Sbjct: 180 TIHEGRHHQVKKMFEVVGHLVDKLSRTQFGSLDVRGLKPGEARRLSKKEVSQLHHLA 236


>gi|85859158|ref|YP_461360.1| RNA pseudouridylate synthase S4 domain-containing protein
           [Syntrophus aciditrophicus SB]
 gi|85722249|gb|ABC77192.1| RNA pseudouridylate synthase S4 domain [Syntrophus aciditrophicus
           SB]
          Length = 251

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 84/249 (33%), Positives = 136/249 (54%), Gaps = 1/249 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ K++AR+G+ASRR+ E MI + RV VN  ++           D I VDG  +   E 
Sbjct: 3   ERLQKILARSGVASRRKAEEMIREGRVSVNSEIVRELGSKADIERDEIRVDGKLICAEET 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G VT  SDP  R  V   LP +  R+  VGRLD ++EGLLLLTNDGG A+
Sbjct: 63  KVYVMLNKPRGYVTALSDPQKRPLVIHLLPELGVRLFPVGRLDYDSEGLLLLTNDGGFAQ 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            ++ P  +  + YRV+  G+++  + N L+KG+ ++   +   +V L+     ++W+T+ 
Sbjct: 123 RVQHPRYRISKTYRVKISGRLNAAEFNRLQKGLELEDGKFAPDEVALEEINPKSSWLTMK 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           + EG+NR I++ FE    +V RLIR +     LG L  G  R +    +++ L P     
Sbjct: 183 ISEGRNRVIRRAFEQLGHEVLRLIRTAVADLHLGNLREGDYRLLKGWEVQQLLTPRKRSG 242

Query: 253 AQVNLDAPI 261
           +++  +   
Sbjct: 243 SKILPEKEK 251


>gi|229169278|ref|ZP_04296989.1| RNA pseudouridine synthase [Bacillus cereus AH621]
 gi|228614173|gb|EEK71287.1| RNA pseudouridine synthase [Bacillus cereus AH621]
          Length = 229

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 109/230 (47%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   R  +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRACINGEVCTH-GALVNEGDIVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D    + +     +   R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAADHIEDNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++++  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKSFTDWFIDMMSSGVKIKDGMTKPCKVTRV----DQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++   F + V +L R+     +L  L AG  R+++ K L 
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELNELEAGKWRDITPKELE 223


>gi|222085015|ref|YP_002543544.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
 gi|221722463|gb|ACM25619.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
          Length = 680

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 173/367 (47%), Positives = 227/367 (61%), Gaps = 26/367 (7%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +R+SKV+ARAG+ASRR++ERMI   RV++NG+LL+   VNV   D IEVDG+P+R 
Sbjct: 48  DGKAERISKVMARAGVASRRDIERMIMDGRVRLNGVLLDSPVVNVTLADKIEVDGMPIRG 107

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ERTRLWLYHKP GLVTT++DP+GR TVFDNLP    RV+S+GRLDINTEGLLLLTNDGG
Sbjct: 108 IERTRLWLYHKPAGLVTTNADPEGRPTVFDNLPEELPRVMSIGRLDINTEGLLLLTNDGG 167

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LARVLELP+T WLR YRVR HG++DQD L+ LK+GI + G+ YG ++ TLD  +GSN W+
Sbjct: 168 LARVLELPTTGWLRRYRVRAHGEIDQDALDKLKEGIAVDGVLYGSIEATLDRTQGSNVWI 227

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           T+GLREGKNREIK V      +VNRLIRISYGPFQLG L  G   EV  + LR+QLGP L
Sbjct: 228 TMGLREGKNREIKNVLGALGLEVNRLIRISYGPFQLGDLPEGRVLEVRGRTLRDQLGPRL 287

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK---------- 299
           +E+A+ N DAP+Y++     +                +   ++    +++          
Sbjct: 288 VEDAKANFDAPLYNASAPAGEDEAEAKPERAAKEERPRRDRERPEDKRERALGRLDTKRD 347

Query: 300 ----------------KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
                           +   P       +NVWMA G        + +  +N R +     
Sbjct: 348 DRRDEGRREGGHKEDDRPKRPPLGARRNANVWMAPGARPLGEKAAAKAAKNTRTAAKRGE 407

Query: 344 KRSLRRT 350
               +R+
Sbjct: 408 PERPQRS 414



 Score = 39.8 bits (91), Expect = 0.63,   Method: Composition-based stats.
 Identities = 14/108 (12%), Positives = 22/108 (20%), Gaps = 3/108 (2%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK---NGLSKQKKLA 302
            P   +  +         SE    DRP       D     K    +         +    
Sbjct: 506 RPEGSDRPRAKSFQGEARSERPRGDRPFGDKPRGDRPYGDKPRGDRPYGDKPRGDRAFSD 565

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
            P   R   +         S       +R    R     P +    + 
Sbjct: 566 RPTGDRRPRAEGDERPRARSFDGEQRSERPRGDRPFGDRPPRGDRPQG 613


>gi|223985880|ref|ZP_03635918.1| hypothetical protein HOLDEFILI_03224 [Holdemania filiformis DSM
           12042]
 gi|223962146|gb|EEF66620.1| hypothetical protein HOLDEFILI_03224 [Holdemania filiformis DSM
           12042]
          Length = 244

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 72/239 (30%), Positives = 122/239 (51%), Gaps = 4/239 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K+IA +G+ SRR+ E  I Q RVKV+G ++    V       IEVDG  +   E   
Sbjct: 3   RLQKIIAASGLTSRRKAEEWILQGRVKVDGQVVTELGVKPRKGALIEVDGKAI-AREDKV 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP  ++ T +D   R TV D +  +  RV  VGRLD +T G+L++TNDG  A  +
Sbjct: 62  YYVMNKPKKVLCTLNDEHDRRTVVDLMMDVPQRVFPVGRLDYDTTGVLIMTNDGEFANEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQK--GSNAWVTV 191
             P     +VY V  +G +  +++  L++G+V+         ++ +  +          +
Sbjct: 122 IHPRYHIAKVYEVTINGILKTEEIKQLEQGVVLDDGIKTLPAKLWVTNKDFAHEQTMFEL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
            ++EG+NR+IK++ E F ++V RL R S GP  +  L  G  R +    +++       
Sbjct: 182 TIQEGRNRQIKRMLEVFGYEVRRLHRRSLGPITVRGLNPGEYRLMKPFEVKQLRRLANE 240


>gi|170732823|ref|YP_001764770.1| RNA-binding S4 domain-containing protein [Burkholderia cenocepacia
           MC0-3]
 gi|169816065|gb|ACA90648.1| RNA-binding S4 domain protein [Burkholderia cenocepacia MC0-3]
          Length = 586

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 82/352 (23%), Positives = 145/352 (41%), Gaps = 7/352 (1%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 174 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRI 232

Query: 63  DGVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           +G P+++         L  +     +V+        S      P   ++ ++VGRLD NT
Sbjct: 233 NGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNT 292

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++ 
Sbjct: 293 EGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELAEGMRQKLLHGVELDDGPANFLRIR 352

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
               +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ 
Sbjct: 353 DGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELD 412

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIIS-EVPDDFTRMKKNSSQKNGLS 296
              +R+ +    L+           ++    R +P+ +   +          +  +    
Sbjct: 413 DAQVRKLMATVGLKAPSEEKGKRGGAAGPTERRQPDPMQTSMGFISREPVLTTHGQLDQP 472

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           ++             S         S + + +G   + +R        R+  
Sbjct: 473 RRGGGRRGGPGLPGLSGYGSLPVAPSGYGNRAGGGRDGNRTGGGRDGNRAGG 524


>gi|332666758|ref|YP_004449546.1| pseudouridine synthase Rsu [Haliscomenobacter hydrossis DSM 1100]
 gi|332335572|gb|AEE52673.1| pseudouridine synthase Rsu [Haliscomenobacter hydrossis DSM 1100]
          Length = 239

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 64/227 (28%), Positives = 103/227 (45%), Gaps = 7/227 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
               ++K I+  GI SRRE ++ I   RV +NG++  +    V S D + +DG PLR   
Sbjct: 2   DSISLNKYISETGICSRREADKFIEAGRVSLNGVVATK-GNRVASGDTVLLDGKPLRSNP 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +     +HKP GL  T    D   T      +   R+  +GRLD ++EGL+ LTNDG + 
Sbjct: 61  KRIYLAFHKPKGLTCTTDLRD--RTNVIAYINHPQRIFPIGRLDKDSEGLIFLTNDGDIV 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V        D +  +  GI I G            ++   +   +
Sbjct: 119 NKILRSRNGHEKEYIVVVDKPFAPDFIRRMSNGIPILGTTTKKC----VVEQKGQSTFRI 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            L +G NR+I+++ E+  ++V +L RI     +L  L  G  R  S+
Sbjct: 175 ILTQGLNRQIRRMCEYMGYEVKKLKRIRIMSIKLDDLAPGKWRYFSE 221


>gi|332300498|ref|YP_004442419.1| pseudouridine synthase Rsu [Porphyromonas asaccharolytica DSM
           20707]
 gi|332177561|gb|AEE13251.1| pseudouridine synthase Rsu [Porphyromonas asaccharolytica DSM
           20707]
          Length = 470

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 65/270 (24%), Positives = 119/270 (44%), Gaps = 1/270 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E   P R++K ++ +G+ SRR  ++ IA  RVKVNG ++      V+ TD + VD   + 
Sbjct: 199 EAGEPIRLNKFLSNSGLCSRRMADQYIAAGRVKVNGAVISELGSQVLPTDQVMVDDKLVS 258

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              +  + L      + T       R+ +     +   R+  +GRLD NT G+LLLTNDG
Sbjct: 259 LEAKVYVLLNKPKNCVTTLTDPEGRRTVMDLVHNACTERIYPIGRLDRNTTGILLLTNDG 318

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P+ +  ++Y V    +V  + + ++  G  ++        ++  T + ++  
Sbjct: 319 DLAVRLMHPAFRKKKIYEVALDKEVTVEHMQMIAHGFELEDGEIHADAISYITGQ-THDK 377

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           V + +  G+NR ++++FE   ++V  L R+ Y       L  G  R ++ + +R      
Sbjct: 378 VGIEIHSGRNRIVRRIFEHLGYRVVHLDRVYYAGLTKKDLPRGRWRYLTPEEVRYLRMGV 437

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEV 278
             +E            +          SE 
Sbjct: 438 KEQEDNGVAPTTKVYHKHQETPDHPFASEE 467


>gi|317491810|ref|ZP_07950245.1| RNA pseudouridylate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316920244|gb|EFV41568.1| RNA pseudouridylate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 293

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 57/296 (19%), Positives = 113/296 (38%), Gaps = 5/296 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +  
Sbjct: 3   TNSSTRLNKYISESGICSRRDADRYIEQGHVFINGKRA-GIGDQVFAGDVVKVNGQLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   L L      +    +  +G      +  +  +RV  +GRLD +++G++ LTN G 
Sbjct: 62  RDADDLVLIALNKPVGIVSTTENGEKDNIVDYVNHSTRVFPIGRLDKDSQGIIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  V  + +  +  G+ I G            +K +    
Sbjct: 122 LVNKILRAGNDHEKEYLVTVNKPVTDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E F ++V +L R       L  L  G  R+++   L E      
Sbjct: 178 RITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLSGLPLGEWRDLTDDELIELFKAIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
              ++                +                ++S +   ++  +     
Sbjct: 238 DSSSEAKPTKKAKPKAKPAAAKSPPNKGAKPAGKSSSADASSRKRFTQPGRKKKGR 293


>gi|197247683|ref|YP_002149101.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197211386|gb|ACH48783.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Agona str. SL483]
          Length = 289

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 62/292 (21%), Positives = 116/292 (39%), Gaps = 5/292 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R++K I+ +GI SRRE +R I Q  V +NG         V++ D ++V+G  +  
Sbjct: 3   TDTSTRLNKYISESGICSRREADRFIEQGNVFINGKRAA-IGDQVVAGDVVKVNGRLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   L L      +    +  DG      +  +   R+  +GRLD +++GL+ LTN G 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRIFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     +  + +  +  G+ I G            +K +    
Sbjct: 122 LVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +      
Sbjct: 178 RITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
              ++    A      T ++     I +  +            +   K+K  
Sbjct: 238 HSSSEAKPKAKAKPKTTGIKRPVVAIEKSNEKARPASSGKRFTSPGRKKKGR 289


>gi|16762895|ref|NP_458512.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. CT18]
 gi|29144382|ref|NP_807724.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|213420596|ref|ZP_03353662.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
 gi|213581144|ref|ZP_03362970.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-0664]
 gi|213647413|ref|ZP_03377466.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. J185]
 gi|213855503|ref|ZP_03383743.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
 gi|289827405|ref|ZP_06546017.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
 gi|34098634|sp|Q8Z1V3|RLUF_SALTI RecName: Full=Ribosomal large subunit pseudouridine synthase F;
           AltName: Full=rRNA pseudouridylate synthase F; AltName:
           Full=rRNA-uridine isomerase F
 gi|25324020|pir||AE1012 probable pseudouridine synthase STY4410 [imported] - Salmonella
           enterica subsp. enterica serovar Typhi (strain CT18)
 gi|16505202|emb|CAD09198.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Typhi]
 gi|29140020|gb|AAO71584.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
          Length = 289

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 61/292 (20%), Positives = 115/292 (39%), Gaps = 5/292 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R++K I+ +GI SRRE +R I Q  V +NG         V++ D ++V+G  +  
Sbjct: 3   TDTSTRLNKYISESGICSRREADRFIEQGNVFINGKRAA-IGDQVVAGDVVKVNGRLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   L L      +    +  DG      +  +   R+  +GRLD +++GL+ LTN G 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRIFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     +  + +  +  G+ I G            +K +    
Sbjct: 122 LVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +      
Sbjct: 178 RITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
              ++    A        ++     I +  +            +   K+K  
Sbjct: 238 GSSSEAKPKAKAKPKTAGIKRPVVAIEKSNEKARPASSGKRFTSPGRKKKGR 289


>gi|206969528|ref|ZP_03230482.1| RNA pseudouridine synthase family protein [Bacillus cereus AH1134]
 gi|229072053|ref|ZP_04205262.1| RNA pseudouridine synthase [Bacillus cereus F65185]
 gi|229081804|ref|ZP_04214296.1| RNA pseudouridine synthase [Bacillus cereus Rock4-2]
 gi|229180870|ref|ZP_04308205.1| RNA pseudouridine synthase [Bacillus cereus 172560W]
 gi|229192751|ref|ZP_04319709.1| RNA pseudouridine synthase [Bacillus cereus ATCC 10876]
 gi|206735216|gb|EDZ52384.1| RNA pseudouridine synthase family protein [Bacillus cereus AH1134]
 gi|228590590|gb|EEK48451.1| RNA pseudouridine synthase [Bacillus cereus ATCC 10876]
 gi|228602427|gb|EEK59913.1| RNA pseudouridine synthase [Bacillus cereus 172560W]
 gi|228701392|gb|EEL53886.1| RNA pseudouridine synthase [Bacillus cereus Rock4-2]
 gi|228710987|gb|EEL62953.1| RNA pseudouridine synthase [Bacillus cereus F65185]
          Length = 229

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 108/230 (46%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTH-GELVSDGDVVTIDGQVIVKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D    + +     +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAADHIEDNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT        +   + 
Sbjct: 118 RILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVTRV----DQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L 
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTAEELE 223


>gi|253681692|ref|ZP_04862489.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum D str. 1873]
 gi|253561404|gb|EES90856.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum D str. 1873]
          Length = 236

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 71/229 (31%), Positives = 111/229 (48%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K +A  G+ASRR+ E +I Q RVKVNG ++      V    D + VD V +   E+
Sbjct: 3   ERLQKYMAACGVASRRKCEEIILQDRVKVNGEIVNELGFKVDPAKDRVHVDSVLISLEEK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP G V+T  D  GR T+ D +     R+  +GRLD NT GL++LTNDG +  
Sbjct: 63  KVYIALNKPEGYVSTVKDERGRKTILDIVKVN-ERIFPIGRLDYNTSGLIILTNDGDVYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  +VY     G    D++     G+ I G         +  +      V + 
Sbjct: 122 KIIHPREEIDKVYIAVIKGVPSNDEIKNFCNGVDIGGYVTSKANFEIIEKLDDKCKVKIV 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGKNR+++++ E     V  L R+S G   L T+  G  R ++   +
Sbjct: 182 IHEGKNRQVRRMCEKIGHPVIALKRVSVGKISLSTIKRGEWRYLNDSEV 230


>gi|301308375|ref|ZP_07214329.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           20_3]
 gi|300833845|gb|EFK64461.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           20_3]
          Length = 495

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 57/241 (23%), Positives = 116/241 (48%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K K ++ +   P R++K ++ AG+ SRRE +  I +  VKVN +++      +   D +
Sbjct: 247 IKYKEVLADPNEPIRLNKFLSNAGVCSRREADEFIQKGAVKVNDVVVTELGTKITRQDVV 306

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
             +  P++   +  + L      + T+    +  + +     +   R+  VGRLD NT G
Sbjct: 307 TFNEKPVQIESKVYIVLNKPKNCVTTSDDPQERLTVMDLVKNACQERIYPVGRLDRNTTG 366

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  PS +  ++Y V     V  + +  +  G+ ++        ++  
Sbjct: 367 VLLLTNDGDLASKLTHPSFKKKKIYHVWLDKNVAIEDMEKIANGLELEDGEIHADAISYA 426

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++    + V + +  G+NR ++++FE   + V +L R+ +       L  G  R ++++ 
Sbjct: 427 SED-DKSQVGIEIHSGRNRIVRRIFESLGYHVTKLDRVYFAGLTKKNLGRGKWRYLNERE 485

Query: 241 L 241
           +
Sbjct: 486 V 486


>gi|322386947|ref|ZP_08060571.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           cristatus ATCC 51100]
 gi|321269229|gb|EFX52165.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           cristatus ATCC 51100]
          Length = 242

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 111/233 (47%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +  +G+ SR +V++++ + +V VNG  +  A   +   +D I VDG  L   + 
Sbjct: 1   MRLDKFLVESGLGSRSQVKQLLKKGQVWVNGAAVTSAKTQINERSDQIVVDGQTLVYEKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  D         +  +    V  VGRLD++T GLLLLTN+G L+ 
Sbjct: 61  VYYLLNKPKGVISATEDDRHKTVLDLLDDTARQKEVFPVGRLDVDTHGLLLLTNNGQLSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVT 190
            +  P     +VY+ +  G +DQ  +    +GI ++       Q+ +  +      + V 
Sbjct: 121 AMLSPKRHVAKVYQAQVAGLMDQADVERFAQGIELKDFTCQPAQLEILERDEGAKTSLVR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + L EGK  ++K++      +V  L R+S GP QL  +L  G  R ++++ ++
Sbjct: 181 ITLSEGKFHQVKRMVLACGKEVTDLQRLSMGPLQLDPSLELGQWRRLTEEEMQ 233


>gi|331269561|ref|YP_004396053.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum BKT015925]
 gi|329126111|gb|AEB76056.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum BKT015925]
          Length = 237

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 72/230 (31%), Positives = 113/230 (49%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +A  G+ASRR+ E +I+Q RVKVN  ++      V    D + VD V +   E+
Sbjct: 4   ERLQKYMAACGVASRRKCEEIISQDRVKVNCEIVNELGFKVDPEIDKVYVDSVLITLEEQ 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP G V+T  D  GR T+ D +     R+  +GRLD NT GL+LLTNDG +  
Sbjct: 64  KVYIALNKPEGYVSTVKDERGRKTILDIVKVN-ERIFPIGRLDYNTSGLILLTNDGDVYN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  +VY     G    D++     GI I G         +  +      V + 
Sbjct: 123 KIIHPREEIDKVYIAVIKGIPSHDEIKNFCNGIDIGGYVTSKASFEILEKLNDKCKVKII 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGKNR+++++ E     V  L R+S G   L T+  G  R +++  ++
Sbjct: 183 IHEGKNRQVRRMCEKIGHPVIALKRVSVGKISLNTIKRGEWRYLNESEIK 232


>gi|313207477|ref|YP_004046654.1| ribosomal large subunit pseudouridine synthase f [Riemerella
           anatipestifer DSM 15868]
 gi|312446793|gb|ADQ83148.1| ribosomal large subunit pseudouridine synthase F [Riemerella
           anatipestifer DSM 15868]
 gi|315023377|gb|EFT36387.1| pseudouridine synthase, Rsu [Riemerella anatipestifer RA-YM]
 gi|325335063|gb|ADZ11337.1| 16S rRNA uridine-516 pseudouridylate synthase related
           pseudouridylate synthase [Riemerella anatipestifer
           RA-GD]
          Length = 241

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 59/232 (25%), Positives = 110/232 (47%), Gaps = 8/232 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-RKA 70
              R++K ++  G  SRRE ++++ Q R+ +NG +       V + D I+VDG  +    
Sbjct: 3   EKVRINKYLSEVGFCSRREADKILEQGRITINGKIP-ELGTKVSAEDEIKVDGKLITEPK 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E      ++KP+G+V T      ++ + D +     R+  +GRLD  +EGL+LLT+DG +
Sbjct: 62  EENVYIAFNKPVGIVCTTDTKREKNNIIDYIKYPK-RIFPIGRLDKPSEGLILLTSDGDI 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y VR    +    L  ++ G+ I G      +     ++       
Sbjct: 121 VNKILRARNNHEKEYIVRVDKPITNKFLEQMRAGVPILGTVTRKCE----VEQLDKMQFR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + L +G NR+I+++ E+  ++V +L RI      L  L  G  RE++   ++
Sbjct: 177 IVLTQGLNRQIRRMCEYLGYEVKKLKRIRIMNIHL-DLPIGKWRELTPNEMK 227


>gi|332521591|ref|ZP_08398044.1| pseudouridine synthase [Lacinutrix algicola 5H-3-7-4]
 gi|332042680|gb|EGI78880.1| pseudouridine synthase [Lacinutrix algicola 5H-3-7-4]
          Length = 261

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 60/269 (22%), Positives = 114/269 (42%), Gaps = 10/269 (3%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           ++E  T  R++K ++ AG  SRRE +R+I   RV +NG +       V   D +EVDG  
Sbjct: 1   MEEKLT--RLNKYLSEAGYCSRREADRLIDAGRVTINGTVP-ELGTKVGENDVVEVDGKS 57

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           + + +   ++L       +   +D         +      R+  +GRLD  +EGL+ LT+
Sbjct: 58  ITERKTDFVYLAFNKPVGIVCTTDTRVEKDNIIDFIKYPKRIFPIGRLDKPSEGLIFLTD 117

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKG 184
           DG +   +   S    + Y V     + Q  +  +  GI ++               +K 
Sbjct: 118 DGDIVNKILRASNNHEKEYIVTVDKPISQTFIKRMAGGIYLEDLDKTTKKCT----VRKI 173

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            +   ++ L +G NR+I+++ E+  ++V  L R+     +L  +  G  RE + + L+  
Sbjct: 174 DSQTFSIILTQGLNRQIRRMCEYLTYEVTSLKRVRIMNIKL-DVPIGEYREFTAEELKTL 232

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPN 273
                  +   +   P      + R + N
Sbjct: 233 NMLLEDSDKNYSETTPAKKVHKINRRKTN 261


>gi|229105177|ref|ZP_04235826.1| RNA pseudouridine synthase [Bacillus cereus Rock3-28]
 gi|228678103|gb|EEL32331.1| RNA pseudouridine synthase [Bacillus cereus Rock3-28]
          Length = 229

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 107/230 (46%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV ++G +       V   D I +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAIDGEICTH-GALVSDGDVITIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D    + +     +   R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAADHIEDNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVTRV----GQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L 
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELHELEVGKWRSVTAEELE 223


>gi|295692648|ref|YP_003601258.1| pseudouridine synthase [Lactobacillus crispatus ST1]
 gi|295030754|emb|CBL50233.1| Pseudouridine synthase [Lactobacillus crispatus ST1]
          Length = 236

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 62/234 (26%), Positives = 104/234 (44%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV ++I +  V VNG  ++     +   D + V+G  +   +  
Sbjct: 1   MRIDKYLANMNVGSRKEVHQLIKKGVVAVNGKTVKTLKEKINENDVVTVNGEEIAYQKYH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +      L  T            +L   +  ++ VGRLD +T GLLLLTNDG L   
Sbjct: 61  YFLVNKPKGVLSATEDRNQKTVISLLDLQDQYQGIVPVGRLDKDTTGLLLLTNDGQLNHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN--AWVT 190
           L  P+    +VYR +  G  D++       G+++  G      ++ +  Q   N  + + 
Sbjct: 121 LLAPNKHVAKVYRAQIAGVADEETAKAFASGMMLGDGTKLKPAKLKILKQDRENATSEIE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           + + EGK  +IK++F     KV  L R+S G   L   L  G   E+S   ++ 
Sbjct: 181 IEISEGKYYQIKRMFGAVGMKVTALDRLSMGNLHLPSDLKRGKYVELSLDEIKN 234


>gi|145298479|ref|YP_001141320.1| 16S rRNA uridine-516 pseudouridylate synthase [Aeromonas
           salmonicida subsp. salmonicida A449]
 gi|142851251|gb|ABO89572.1| 16S rRNA uridine-516 pseudouridylate synthase [Aeromonas
           salmonicida subsp. salmonicida A449]
          Length = 230

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 62/234 (26%), Positives = 111/234 (47%), Gaps = 7/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +      +R    ++I Q  V V+GI++++ A ++     +E DGV L   +R 
Sbjct: 1   MRLDKFLCDCSDLTRSLAGKLIRQGEVTVDGIVVKQPAFHINEQSQVEFDGVMLTLDQRN 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V ++ DPD  +  F        ++  VGRLD++T GL+L+T+DG  +  
Sbjct: 61  RYFMLHKPEGYVCSNEDPDHPTVFFLMDEPAMGKLHVVGRLDLDTTGLVLVTDDGKWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y V     V QD ++L   G+ ++         Q+ +     +     +
Sbjct: 121 ITSPRHECAKTYHVWLADPVHQDAISLFADGVFLRNETEKTRPAQLEIL----AECEARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
            + EGK  ++K++F     KV  L R   G   L   L  G  RE++ + + + 
Sbjct: 177 TIHEGKYHQVKRMFASIGNKVVGLHREQIGTLALDEALAPGEYRELTAEEIAQF 230


>gi|291531258|emb|CBK96843.1| ribosomal large subunit pseudouridine synthase B [Eubacterium
           siraeum 70/3]
          Length = 251

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 118/233 (50%), Gaps = 3/233 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPL-RK 69
              R+ K+IA +G  SRR+ E  I Q  VKVNG  +           D + V+G  +   
Sbjct: 2   EKVRLQKIIADSGYCSRRKAEEYIEQGCVKVNGRPV-SLGDKADPKNDIVTVNGEKIASL 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             + R    +KP G VTT +D  GR  V D L  I  RV  VGRLD ++EGLL+LTNDG 
Sbjct: 61  GTQLRYIKLYKPRGYVTTMADTHGRKIVTDLLDDIDERVYPVGRLDKDSEGLLILTNDGA 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  +  PS    + YRV   G+V  DKL  L  G+ I         V +  ++ +   +
Sbjct: 121 LANAVMHPSRHIKKRYRVTVRGEVTDDKLTTLASGVKIDTGVTLPCTVAVLAEEENRTVL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
              + EGKNR+I+K+ E    ++ RL R + G  +LG L  G   +++ + L+
Sbjct: 181 EFTIAEGKNRQIRKMCEAVKLQIVRLKRNAVGNIKLGMLKPGEWADLTAEELK 233


>gi|315607439|ref|ZP_07882435.1| ribosomal large subunit pseudouridine synthase B [Prevotella buccae
           ATCC 33574]
 gi|315250871|gb|EFU30864.1| ribosomal large subunit pseudouridine synthase B [Prevotella buccae
           ATCC 33574]
          Length = 492

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 64/245 (26%), Positives = 111/245 (45%), Gaps = 5/245 (2%)

Query: 1   MKDKNIVQENF----TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           MK +    E       P R++K +A AG+ SRRE +  I    V VNG ++      V+ 
Sbjct: 240 MKKRIEYSEENIDPNEPIRLNKYLANAGVCSRREADEFIQAGVVTVNGEVVTELGTKVLR 299

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           TD ++    P+   ++  + L      + T+      ++ +     +   R+  VGRLD 
Sbjct: 300 TDEVKFHDNPVSLEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKDACPERIYPVGRLDR 359

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NT G+LLLTNDG +A  L  P     +VY V     V    L  + +G+ ++        
Sbjct: 360 NTTGVLLLTNDGDMASKLTHPKFLKKKVYHVHLDKNVTAHDLEQIAQGVTLEDGEIHADA 419

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V    +    + V + +  GKNR ++++FE   ++V +L R+ +       L  G  R +
Sbjct: 420 VEYADEH-DKSQVGIEIHSGKNRIVRRIFESLGYRVTKLDRVQFAGLTKKNLRRGDWRFL 478

Query: 237 SKKIL 241
           ++K +
Sbjct: 479 TEKEV 483


>gi|317054344|ref|YP_004118369.1| pseudouridine synthase [Pantoea sp. At-9b]
 gi|316952339|gb|ADU71813.1| pseudouridine synthase [Pantoea sp. At-9b]
          Length = 290

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 58/293 (19%), Positives = 115/293 (39%), Gaps = 5/293 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +  
Sbjct: 3   TNSSTRLNKYISESGICSRRDADRYIEQGNVFINGKRASV-GAQVFAGDEVKVNGQLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   L L      +    +  +G      +  +   RV  +GRLD +++GL+ LTN G 
Sbjct: 62  RDEEDLVLIALNKPVGIITTMEEGERDNISDFVNHSKRVFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     +  + +  +  G+ + G            +K S    
Sbjct: 122 LVNKILRAGNNHEKEYVVTVDKPITDEFITGMGAGVPMLGTV----TKKCKVKKESTFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ + F ++V +L R       L  L  G  R+++   L E      
Sbjct: 178 RITLVQGLNRQIRRMTKHFGYEVTKLERTRIMNVNLKGLPLGEWRDLTDDELIELFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
              ++        +  T  +      ++  +       +  +     ++KK  
Sbjct: 238 NSSSEDKPAKKGQAKTTPAKKPAASGAKTSEKPNANPASRKRFTQPGRKKKGR 290


>gi|71735145|ref|YP_275686.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. phaseolicola 1448A]
 gi|289650389|ref|ZP_06481732.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. aesculi str. 2250]
 gi|71555698|gb|AAZ34909.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. phaseolicola 1448A]
 gi|331012316|gb|EGH92372.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. tabaci ATCC 11528]
          Length = 408

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 91/354 (25%), Positives = 140/354 (39%), Gaps = 15/354 (4%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG         V   D I
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDAT-LGQRVDLHDAI 62

Query: 61  EVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            VDG  +++ E     R  +        + T        +           R I++GRLD
Sbjct: 63  SVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           INT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++       
Sbjct: 123 INTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPARFT 182

Query: 176 QVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE+S+  + + L   +  +          + + + R +      +           +   
Sbjct: 243 REMSQYEV-DILAAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVRTLRPAAGA 301

Query: 294 GLSKQKKLATP-----VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
             +  +    P        R    +                +       S   P
Sbjct: 302 PATGDRAPRQPQITGSERDRPRGGDSTQRPSPRKDSGKPGSRAPRPADNSRGTP 355


>gi|161505323|ref|YP_001572435.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160866670|gb|ABX23293.1| hypothetical protein SARI_03464 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 309

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 63/302 (20%), Positives = 118/302 (39%), Gaps = 13/302 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R++K I+ +GI SRRE +R I Q  V +NG         V++ D ++V+G  +  
Sbjct: 21  TDTSIRLNKYISESGICSRREADRFIEQGNVFINGKRAA-IGDQVVAGDVVKVNGRLIEP 79

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   L L      +    +  DG      +  +   R+  VGRLD +++GL+ LTN G 
Sbjct: 80  READDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRIFPVGRLDKDSQGLIFLTNHGD 139

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     V  + +  +  G+ I G            +K +    
Sbjct: 140 LVNKILRAGNDHEKEYLVTVDKPVTDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVF 195

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E F + V +L R       L  +  G  R+++   L +      
Sbjct: 196 RITLVQGLNRQIRRMCEHFGYDVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIE 255

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
              ++                     + +      ++K++ +    S  K+  +P  ++ 
Sbjct: 256 RSSSEAK--------TKTKATPKPKTAGIKRPVVAIEKSNEKARPASSGKRFTSPGRKKK 307

Query: 310 LA 311
             
Sbjct: 308 GR 309


>gi|62182642|ref|YP_219059.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|62130275|gb|AAX67978.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|322717140|gb|EFZ08711.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
          Length = 289

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 62/292 (21%), Positives = 116/292 (39%), Gaps = 5/292 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R++K I+ +GI SRRE +R I Q  V +NG         V++ D ++V+G  +  
Sbjct: 3   TDTSIRLNKYISESGICSRREADRFIEQGNVFINGKRAA-IGDQVVAGDVVKVNGRLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   L L      +    +  DG      +  +   R+  +GRLD +++GL+ LTN G 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRIFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     +  + +  +  G+ I G            +K +    
Sbjct: 122 LVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +      
Sbjct: 178 RITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
              ++    A      T ++     I +  +            +   K+K  
Sbjct: 238 RSSSEAKPKAKAKPKTTGIKRPVVAIEKSNEKARPTSSGKRFTSPGRKKKGR 289


>gi|228941730|ref|ZP_04104277.1| RNA pseudouridine synthase [Bacillus thuringiensis serovar berliner
           ATCC 10792]
 gi|228974654|ref|ZP_04135220.1| RNA pseudouridine synthase [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228981248|ref|ZP_04141548.1| RNA pseudouridine synthase [Bacillus thuringiensis Bt407]
 gi|228778448|gb|EEM26715.1| RNA pseudouridine synthase [Bacillus thuringiensis Bt407]
 gi|228785057|gb|EEM33070.1| RNA pseudouridine synthase [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228817942|gb|EEM64020.1| RNA pseudouridine synthase [Bacillus thuringiensis serovar berliner
           ATCC 10792]
 gi|326942335|gb|AEA18231.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 229

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 107/230 (46%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTH-GALVSDGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D    + +     +   R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAADHIEDNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVTRV----DQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++   F + V +L R+     +L  L  G  R ++ + L 
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELGVGKWRNIATEELE 223


>gi|288924576|ref|ZP_06418513.1| ribosomal large subunit pseudouridine synthase B [Prevotella buccae
           D17]
 gi|288338363|gb|EFC76712.1| ribosomal large subunit pseudouridine synthase B [Prevotella buccae
           D17]
          Length = 492

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 64/245 (26%), Positives = 111/245 (45%), Gaps = 5/245 (2%)

Query: 1   MKDKNIVQENF----TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           MK +    E       P R++K +A AG+ SRRE +  I    V VNG ++      V+ 
Sbjct: 240 MKKRIEYSEENIDPNEPIRLNKYLANAGVCSRREADEFIQAGVVTVNGEVVTELGTKVLR 299

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           TD ++    P+   ++  + L      + T+      ++ +     +   R+  VGRLD 
Sbjct: 300 TDEVKFHDNPVSLEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKDACPERIYPVGRLDR 359

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NT G+LLLTNDG +A  L  P     +VY V     V    L  + +G+ ++        
Sbjct: 360 NTTGVLLLTNDGDMASKLTHPKFLKKKVYHVHLDKNVTAHDLEQIAQGVTLEDGEIHADA 419

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V    +    + V + +  GKNR ++++FE   ++V +L R+ +       L  G  R +
Sbjct: 420 VEYADEH-DKSQVGIEIHSGKNRIVRRIFESLGYRVTKLDRVQFAGLTKKNLRRGDWRFL 478

Query: 237 SKKIL 241
           ++K +
Sbjct: 479 TEKEV 483


>gi|188996649|ref|YP_001930900.1| pseudouridine synthase [Sulfurihydrogenibium sp. YO3AOP1]
 gi|188931716|gb|ACD66346.1| pseudouridine synthase [Sulfurihydrogenibium sp. YO3AOP1]
          Length = 244

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 68/242 (28%), Positives = 121/242 (50%), Gaps = 4/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R++K IA++GI SRR+ + +I + +VKVNG +++     +    D +EV+G  ++  E+
Sbjct: 3   VRLNKYIAQSGICSRRKADELIKEGKVKVNGEIIKDLGAKINPEKDIVEVEGNIIKPVEK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGG 129
                 +KP+G ++             +L    +I   +  VGRLD N+EGLL+LTNDG 
Sbjct: 63  KIYIKIYKPVGYLSAVGKDKFGRKTLTDLLKELNIKENLFPVGRLDYNSEGLLILTNDGE 122

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P  +  +VY V    +VD++ LN +KKG +++   +   +V +      + W+
Sbjct: 123 FANKIAHPKHKIKKVYHVEVVPKVDEETLNQMKKGAILEDGFFKPDKVEILKHTKDSTWL 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
              +  GK R +++    FN KV RL+R+      +  L     + ++ K +R       
Sbjct: 183 LFEIHSGKKRILRRYVSKFNHKVKRLVRVKIDSISIENLKPHQFKHLTDKEVRSIYERDS 242

Query: 250 LE 251
            E
Sbjct: 243 AE 244


>gi|327462777|gb|EGF09099.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1057]
          Length = 242

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 103/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++++ +  V VNG   +     +  T D I V G  L   + 
Sbjct: 1   MRLDKFLAENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDETADEIIVSGQRLTYEKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  D         +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPQGVISATEDDHHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            +  P     ++YR +  G ++Q  +     GI ++        + +         + V 
Sbjct: 121 AMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKDFTCQPAHLKILELDEEKEASLVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + L EGK  ++K++      +V  L R++ GP QL + L  G  R +++  +
Sbjct: 181 ITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDSALALGEWRRLTEAEI 232


>gi|283787307|ref|YP_003367172.1| ribosomal large subunit pseudouridine synthase F [Citrobacter
           rodentium ICC168]
 gi|282950761|emb|CBG90437.1| ribosomal large subunit pseudouridine synthase F [Citrobacter
           rodentium ICC168]
          Length = 291

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 62/299 (20%), Positives = 112/299 (37%), Gaps = 13/299 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++K I+ +GI SRRE +R I Q  V +NG         VM  D ++V+G  +   E 
Sbjct: 6   SIRLNKYISESGICSRREADRFIEQGNVFINGKRAA-IGDQVMPGDVVKVNGRLIEPREA 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L        +    +  D       +  +   RV  +GRLD +++GL+ LTN G L  
Sbjct: 65  EELVFIALNKPVGIVSTTEDSERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V     +  + +  +  G+ I G            +K +     + 
Sbjct: 125 KILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E+F ++V +L R       L  L  G  R+++   L           
Sbjct: 181 LIQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLAGLPPGEWRDLTDDELITLFKLIENSS 240

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           ++    A                 + P       K   +    +  K+  +P  ++   
Sbjct: 241 SEAKPKAKAKPKT--------AGIKRPVVKIEKPKEKEKARPAANGKRFTSPGRKKKGR 291


>gi|330889215|gb|EGH21876.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. mori str. 301020]
          Length = 396

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 90/355 (25%), Positives = 142/355 (40%), Gaps = 10/355 (2%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG         V   D I
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDAT-LGQRVDLHDAI 62

Query: 61  EVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            VDG  +++ E     R  +        + T        +           R I++GRLD
Sbjct: 63  SVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           INT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++       
Sbjct: 123 INTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPARFT 182

Query: 176 QVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE+S+  + + L   +  +          + + + R +      +           +   
Sbjct: 243 REMSQYEV-DILAAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVRTLRPAAGA 301

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
             +  +    P    +                     +  +    P+  + R   
Sbjct: 302 PATGDRAPRQPQITGSERDRPRGGDSTQRPSPRKDSGKPGSRAPRPAETNSRGTP 356


>gi|332993044|gb|AEF03099.1| RNA pseudouridine synthase family protein [Alteromonas sp. SN2]
          Length = 246

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 62/247 (25%), Positives = 110/247 (44%), Gaps = 11/247 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
            +R++K I+  G+ SRRE +++I Q RV +N  L       V   D ++VDG  ++    
Sbjct: 6   TKRLNKYISDTGLCSRREADKLIEQNRVTINDKLP-ELGTKVAQGDKVKVDGKLVKAVAE 64

Query: 70  -AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   +Y+KPIG+  T       + +         R+  VGRLD  +EGL++LT+DG
Sbjct: 65  DKSDRIYLVYNKPIGITCTTERHVKGNIIDAI--KHKQRIFPVGRLDKPSEGLIILTSDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y V  +  + +  +  + KG+ I G      +V           
Sbjct: 123 DIVNKILRAENSHDKEYEVTVNQPISERFVQKMAKGVPILGTVTKPCKVNA----RGKFQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            ++ L +G NR+I+++ EF  ++V +L R      +LG L  G  R +++K L +     
Sbjct: 179 FSIILTQGLNRQIRRMCEFLGYEVTKLKRTRIMHLELGNLKPGQWRNLTEKELNQLNNAV 238

Query: 249 LLEEAQV 255
                  
Sbjct: 239 QQSSKTA 245


>gi|305664746|ref|YP_003861033.1| pseudouridine synthase, Rsu [Maribacter sp. HTCC2170]
 gi|88707868|gb|EAR00107.1| pseudouridine synthase, Rsu [Maribacter sp. HTCC2170]
          Length = 245

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 59/251 (23%), Positives = 111/251 (44%), Gaps = 8/251 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-R 68
                R++K ++  G  SRR  +++I Q RV +NG +       ++S D + VDG  +  
Sbjct: 2   TQKETRINKYLSEVGYCSRRAADKLIDQGRVTINGKVP-EMGTKIISGDEVRVDGELISE 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             E+     ++KPIG+V T      +  + D +     R+  +GRLD  ++GL+ LTNDG
Sbjct: 61  PKEKPVYLAFNKPIGIVCTTDTRVEKDNIIDFINYPK-RIFPIGRLDKPSQGLIFLTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y V     +++  L+ +  G+ I        ++T    + +   
Sbjct: 120 DIVNKILRARNHHEKEYLVTVDKPINKKFLDQMASGVPILDTVTRKCEIT----EVNKYQ 175

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E+  + V +L RI     +L  +  G  R ++   L+E     
Sbjct: 176 FKIILTQGLNRQIRRMCEYLGYNVKKLKRIRIMNVKL-DMPIGKWRNLTNSELQEINRLV 234

Query: 249 LLEEAQVNLDA 259
                  N   
Sbjct: 235 SGSSKTHNKIK 245


>gi|313893433|ref|ZP_07827005.1| pseudouridine synthase B, ribosomal large subunit [Veillonella sp.
           oral taxon 158 str. F0412]
 gi|313442074|gb|EFR60494.1| pseudouridine synthase B, ribosomal large subunit [Veillonella sp.
           oral taxon 158 str. F0412]
          Length = 242

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 125/242 (51%), Gaps = 4/242 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K IA  GIASRR+ E +I + +V+VNG  +    V +    D ++V+G  L + + 
Sbjct: 2   ERLQKYIASCGIASRRKAEELITEGKVQVNGRKVTELGVKINPQKDKVKVNGQLLAQEKP 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      + +        + + D + +   R+  VGRLD+ TEGLLLLTNDG LA+
Sbjct: 62  VYYLLNKPKGVITSVSDPQGRETVL-DYIKNESKRIYPVGRLDLYTEGLLLLTNDGELAQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            L  PS    + Y VR  G+V  + L ++  G+ ++        +        N    V 
Sbjct: 121 NLTHPSKGVEKTYEVRIKGRVRDEDLQVIANGVKLEDGMTAPATIVDLGFDDHNGVHEVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + + EG+NR+++++FE F ++++ L RI+Y    LG +  G++R+++ + ++        
Sbjct: 181 ITIHEGRNRQVRRMFEHFGYRIHNLKRIAYAGLTLGGVKRGASRQLTIREVKALKALETG 240

Query: 251 EE 252
           ++
Sbjct: 241 KK 242


>gi|228954820|ref|ZP_04116840.1| RNA pseudouridine synthase [Bacillus thuringiensis serovar kurstaki
           str. T03a001]
 gi|228804809|gb|EEM51408.1| RNA pseudouridine synthase [Bacillus thuringiensis serovar kurstaki
           str. T03a001]
          Length = 229

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 63/230 (27%), Positives = 108/230 (46%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTH-GELVSDGDVVTIDGQVIVKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D    + +     +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAADHIEDNIIDYI--NYPERIFPVGRLDKVSEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT        +   + 
Sbjct: 118 RILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVTRV----DQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L 
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTAEELE 223


>gi|123441748|ref|YP_001005732.1| 16S rRNA pseudouridylate synthase A [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|122088709|emb|CAL11514.1| ribosomal small subunit pseudouridine synthase A [Yersinia
           enterocolitica subsp. enterocolitica 8081]
          Length = 235

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 55/238 (23%), Positives = 108/238 (45%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    
Sbjct: 1   MRLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQTVGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +  D       G+ +          Q+ +   +     V +
Sbjct: 121 ITSPRHHCEKTYLVTLEQPIADDTAQQFTDGVQLHNEKSLTKPAQLEVIEPQ----LVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
            + EG+  ++K++F     +V  L R   G  +L   L  G  R ++ + +     PH
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVLELHRERIGAIKLDDDLAPGEYRPLTPEEIASVGAPH 234


>gi|16801498|ref|NP_471766.1| hypothetical protein lin2436 [Listeria innocua Clip11262]
 gi|16414958|emb|CAC97663.1| lin2436 [Listeria innocua Clip11262]
          Length = 233

 Score =  176 bits (445), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 99/231 (42%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D + V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQVTVHGTPVIYQEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T  +               +    VGRLD +TEGLL++TNDG LA 
Sbjct: 61  VYFMLHKPQNVVSATEDNLSETVIDLLEQEDTLTNPFPVGRLDKDTEGLLIITNDGTLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y  +  G V  + +     G+ +          + + T       + V
Sbjct: 121 NLLSPKKHIDKTYYAKIDGDVTAEDVEAFSAGVTLDDGYTCKPAHLEIITPN----EIKV 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            ++EGK  ++K++F      V+ L RIS G  QL   L  G  R +++  L
Sbjct: 177 TIQEGKFHQVKRMFAARGKTVSYLKRISMGNLQLDDSLELGEYRPLTENEL 227


>gi|116492846|ref|YP_804581.1| ribosomal large subunit pseudouridine synthase B [Pediococcus
           pentosaceus ATCC 25745]
 gi|116102996|gb|ABJ68139.1| ribosomal large subunit pseudouridine synthase B [Pediococcus
           pentosaceus ATCC 25745]
          Length = 241

 Score =  176 bits (445), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 72/232 (31%), Positives = 119/232 (51%), Gaps = 3/232 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +R+ KV+A AG+ASRR+ E++I +  V+VNG ++++    V + D IEVDGVPL++ +
Sbjct: 2   EEERLQKVMAEAGVASRRKSEKLITEGHVRVNGKVIKQLGTKVTAHDKIEVDGVPLQREK 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                L      + +   D   R TV D  P +  R+  VGRLD +T G +L+TNDG LA
Sbjct: 62  MVYFLLNKPRGVITSVS-DDKKRKTVMDFFPDVVERIYPVGRLDYDTSGAVLMTNDGTLA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWV 189
             L  P  ++ + Y  +  G V+   L  L+ G+VI        +  L     +   + V
Sbjct: 121 NGLTHPKFKFEKTYTAKVKGIVNSLDLKKLENGLVIDHKKTAKAKAHLISTDDEKKTSIV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++ + EG+N ++K +F      V +L R SY    +  + +G  R +    +
Sbjct: 181 SLTIHEGRNHQVKNMFMAVGHPVQKLRRDSYSFLNIDGVQSGKWRALKVNEI 232


>gi|310641380|ref|YP_003946138.1| ribosomal small subunit pseudouridine synthase a [Paenibacillus
           polymyxa SC2]
 gi|309246330|gb|ADO55897.1| Ribosomal small subunit pseudouridine synthase A [Paenibacillus
           polymyxa SC2]
          Length = 260

 Score =  176 bits (445), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 65/240 (27%), Positives = 111/240 (46%), Gaps = 10/240 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
             QR+ K++   G  SR ++++ + Q  + VNG  ++ + + V    D IEV+G  +   
Sbjct: 7   QTQRLDKILTHMGYGSRSDIKKQVKQGMITVNGRTIKDSGLQVHPYQDQIEVNGELVVFR 66

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   + L+  P  +  T    +       +          VGRLD +TEGLLLLTNDG L
Sbjct: 67  EFIYIMLHKPPGVISATEDTRERTVLDLLSAEERHFEPFPVGRLDKDTEGLLLLTNDGKL 126

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSN--- 186
           A  L  P     + Y     G V ++ +     G+ +         Q+T+   +  +   
Sbjct: 127 AHELLSPRRHVPKTYEATVSGHVTEEDILQFTAGVELDDGYVTLPAQLTILRHEQPHQAD 186

Query: 187 ----AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
               +++++ + EGK  ++K++FE    KV  L R + GP +L   L  GS RE++ + L
Sbjct: 187 GEVTSYISLVIHEGKFHQVKRMFEAIGKKVTYLKRTAMGPLKLDDQLPLGSYRELTSEEL 246


>gi|226327594|ref|ZP_03803112.1| hypothetical protein PROPEN_01465 [Proteus penneri ATCC 35198]
 gi|225204120|gb|EEG86474.1| hypothetical protein PROPEN_01465 [Proteus penneri ATCC 35198]
          Length = 303

 Score =  176 bits (445), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 57/293 (19%), Positives = 119/293 (40%), Gaps = 5/293 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++K I+ +GI SRRE +R I Q  V +NG         V + D ++V+G  +   + 
Sbjct: 16  STRLNKYISESGICSRREADRYIEQGLVLINGKRA-SIGDQVFAGDEVKVNGRLIEAQDN 74

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + L L      +    +  DG      +  +  +R+  +GRLD +++GL+ LTN G L  
Sbjct: 75  SELVLIALNKPVGIVSTTDDGEKDNIVDYVNHSTRIFPIGRLDKDSQGLIFLTNHGDLVN 134

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  +  + ++ +  G+ I G            +K +     + 
Sbjct: 135 KILRAGNDHEKEYLVTVNKPITDEFIHGMGAGVPIMGQK----TKKCKVKKEAPMVFRIT 190

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E+F ++V +L R+      L  L  G  R+++   L +         
Sbjct: 191 LVQGLNRQIRRMCEYFGYEVTKLERVRIMNVSLSGLPVGEWRDLTDDELIKLFDAIEKST 250

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           ++    A     +  +      +          +  ++ +   ++  +     
Sbjct: 251 SEAPPKAKQNKPKKQISSNAKALGIHIPQTKTKETENNSRKRFAQPGRKKKKR 303


>gi|158520075|ref|YP_001527945.1| pseudouridine synthase [Desulfococcus oleovorans Hxd3]
 gi|158508901|gb|ABW65868.1| pseudouridine synthase [Desulfococcus oleovorans Hxd3]
          Length = 241

 Score =  176 bits (445), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 73/233 (31%), Positives = 113/233 (48%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K ++ AG+ SRR  E  IA+ RV VNG ++      V    D +  DG  +  AE 
Sbjct: 10  IRLQKFLSGAGVCSRRRAEVYIAEGRVAVNGQVVTELGTKVDPESDDVMFDGHRVTLAES 69

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP G VT+       + +   L ++  RV  VGRLD  + GLLL+T+DGGL +
Sbjct: 70  HVYIALNKPPGYVTSCLQKQETTVME--LVAVDQRVFPVGRLDKPSCGLLLMTSDGGLHQ 127

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS    + Y V     V    L+ +++G+VI G      +V       S+    + 
Sbjct: 128 RLSHPSFDHEKEYDVACDRPVSDADLDAMRRGMVITGRKTRPAKVKRL----SDRRFLII 183

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           L+EG+NR+I+++ E    +V  L RI      LG L  G  R ++++  +  L
Sbjct: 184 LQEGRNRQIRRMAEMLGNRVVLLRRIRIAHIHLGDLAEGRWRYLTEEEKKALL 236


>gi|291558038|emb|CBL35155.1| ribosomal large subunit pseudouridine synthase B [Eubacterium
           siraeum V10Sc8a]
          Length = 251

 Score =  176 bits (445), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 119/233 (51%), Gaps = 3/233 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
              R+ K+IA +G  SRR+ E  I Q  VKVNG  +           D + V+G  +  +
Sbjct: 2   EKVRLQKIIADSGYCSRRKAEEYIEQGCVKVNGRPV-SLGDKADPKNDIVTVNGEKIASS 60

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             + R    +KP G VTT +D  GR  V D L  I  RV  VGRLD ++EGLL+LTNDG 
Sbjct: 61  GTQLRYIKLYKPRGYVTTMADTHGRKIVTDLLDDIDERVYPVGRLDKDSEGLLILTNDGA 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  +  PS    + YRV   G+V  DKL  L  G+ I         V +  ++ +   +
Sbjct: 121 LANAVMHPSRHIKKRYRVTVRGEVTDDKLTTLASGVKIDTGVTLPCTVAVLAEEENRTVL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
              + EGKNR+I+K+ E    ++ RL R + G  +LG L  G   +++ + L+
Sbjct: 181 EFTIAEGKNRQIRKMCEAVKLQIVRLKRNAVGNIKLGMLKPGEWADLTAEELK 233


>gi|260778847|ref|ZP_05887739.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           coralliilyticus ATCC BAA-450]
 gi|260605011|gb|EEX31306.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           coralliilyticus ATCC BAA-450]
          Length = 233

 Score =  176 bits (445), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 52/230 (22%), Positives = 99/230 (43%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  A+R+E  ++I    V VN I+ +  AV V     +E  G  ++K    
Sbjct: 1   MRLDKYLCDALGATRKEATKIIKSGDVTVNDIVQKSGAVKVTDDCIVEWQGREIQKPGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+     + +     +  +            +   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLFKPDGFVCSHEDGFNQ-TAFMLLDEVKMEDLHFAGRLDVDTTGLVLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     ++ D +   ++GI ++      +   L+        V + +
Sbjct: 120 ITSPKHKCEKTYRVWLVDPIEADYVAQFEQGIELRNEKAATLPAKLEIVDEEEKEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            EGK  ++K++F     KV  L R   G   L   L  G  R ++++ + 
Sbjct: 180 TEGKYHQVKRMFAALGNKVEHLHRERIGNIVLDDELEPGEYRYLTQEEIE 229


>gi|114773340|ref|ZP_01450544.1| RNA pseudouridylate synthase family protein [alpha proteobacterium
           HTCC2255]
 gi|114546274|gb|EAU49185.1| RNA pseudouridylate synthase family protein [alpha proteobacterium
           HTCC2255]
          Length = 239

 Score =  176 bits (445), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 126/238 (52%), Positives = 167/238 (70%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +  PQR++K +ARAG+ASRRE+ERMIA  ++ +NG  L+  AV V + D I V+G  +  
Sbjct: 2   SDEPQRIAKYLARAGVASRREIERMIAIGQINLNGKTLDTPAVKVTNKDIILVNGKQIGD 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           AE+ R W Y+KP GL+TT  D  GR T++D  P    RV++VGRLDIN+EGLLLLTNDGG
Sbjct: 62  AEKVRFWRYYKPTGLITTDRDEKGRDTIYDYFPENMPRVMTVGRLDINSEGLLLLTNDGG 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L R LELP+T WLR YRVR +G   ++ +  L+ GIVI    +  M++ LD Q+GSNAW+
Sbjct: 122 LKRKLELPATGWLRKYRVRVNGNPTEEMVAPLRNGIVIDRERFKGMEIRLDRQQGSNAWL 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           TVGLREGKNREI++  E+   +VNRLIR SYGPF+L  L  G   E+  K +++QLG 
Sbjct: 182 TVGLREGKNREIRRAMEYVGLRVNRLIRTSYGPFKLDDLKPGDVEEIKAKTIKDQLGL 239


>gi|54294518|ref|YP_126933.1| hypothetical protein lpl1594 [Legionella pneumophila str. Lens]
 gi|53754350|emb|CAH15834.1| hypothetical protein lpl1594 [Legionella pneumophila str. Lens]
 gi|307610150|emb|CBW99696.1| hypothetical protein LPW_14641 [Legionella pneumophila 130b]
          Length = 248

 Score =  176 bits (445), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 79/240 (32%), Positives = 124/240 (51%), Gaps = 7/240 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--- 68
           + +R+ K++++AG+ SRRE+ER I    V+VNG   +    +   +D I V G  +    
Sbjct: 2   SSERLQKILSQAGLGSRREMERWIDNGWVQVNGKPAK-LGDSAGPSDKISVKGKLIPNPL 60

Query: 69  --KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
             K     L  +     + + H     ++   +       R + VGRLD+NT GLL+ TN
Sbjct: 61  KGKQNIRVLLYHKPVGEVSSRHDPKFEKTVFDNLPHLRQGRWVQVGRLDLNTSGLLIFTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G LA  L  P     R Y VR HGQV Q+ LN L KG+++        ++     +G+N
Sbjct: 121 NGELANQLMHPKYGLEREYAVRVHGQVSQEALNNLLKGVMLDDGLAKFTKIQFRGGEGTN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
           +W  V L EG+NRE+++++E    +V+RLIRI YG   +   L  G   E++ K + E L
Sbjct: 181 SWYHVTLNEGRNREVRRLWESQGVEVSRLIRIRYGMLAMPRFLSRGQFYELTPKEVTEFL 240


>gi|125718847|ref|YP_001035980.1| 16S rRNA uridine-516 pseudouridylate synthase [Streptococcus
           sanguinis SK36]
 gi|125498764|gb|ABN45430.1| 16S rRNA uridine-516 pseudouridylate synthase, putative
           [Streptococcus sanguinis SK36]
          Length = 242

 Score =  176 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 103/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++++ +  V VNG   +     +  T D I V G  L   + 
Sbjct: 1   MRLDKFLAENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDETADEIIVSGQRLTYEKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  D         +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPQGVISATEDDQHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            +  P     + YR +  G + Q  +     GI ++       Q+ +     +   + V 
Sbjct: 121 AMLSPKKHVEKTYRAQVAGLMKQADVERFAAGIELKDFTCQPAQLKILELDEAKETSLVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + L EGK  ++K++      +V  L R++ GP QL   L  G  R ++++ +
Sbjct: 181 ITLAEGKFHQVKRMVAACGKEVTDLQRLAMGPLQLDPALALGEWRRLTEEEI 232


>gi|222110298|ref|YP_002552562.1| pseudouridine synthase [Acidovorax ebreus TPSY]
 gi|221729742|gb|ACM32562.1| pseudouridine synthase [Acidovorax ebreus TPSY]
          Length = 435

 Score =  176 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 80/338 (23%), Positives = 135/338 (39%), Gaps = 8/338 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          V   D I+V+
Sbjct: 101 KRVLLPQPETPKLHKVLAQAGMGSRLEMEQLILEGRISVNNEPA-HIGQRVQFGDQIKVN 159

Query: 64  GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+R          +  +     +VT     +  +           +  SVGRLD+NTE
Sbjct: 160 GKPIRFRIAPPPVRVIAYHKPVGEVVTHDDPQNRPTVFRKLPRLQQGKWQSVGRLDLNTE 219

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL T+ G LA  L  P     R Y  R  G +  ++   L +G+ ++        V  
Sbjct: 220 GLLLFTSSGELANKLMHPRFGLEREYAARVLGALSTEEKQRLLEGVPLEDGMASFGSVED 279

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E+ +
Sbjct: 280 GGGEGANCWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMMLPRGLKRGAWLELDE 339

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           + +R  +             A   S +     + +  S  P   +   ++ +        
Sbjct: 340 RDIRALMQAAGATLDG--GGARPTSGQGRGGRKGDRRSAGPGKASGSGRDKTGGRAGRSP 397

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR 336
              A P   +     +             +       R
Sbjct: 398 SPNAQPDPMKTSLGYIGADSFSRHRQQQRNNGPRRGGR 435


>gi|218674407|ref|ZP_03524076.1| putative ribosomal large subunit pseudouridine synthase B
           [Rhizobium etli GR56]
          Length = 277

 Score =  176 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 147/230 (63%), Positives = 176/230 (76%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R+SKV+ARAG+ASRR++ERMI + RV +NG +L+   VNV   D IEVDGVP+R 
Sbjct: 48  EAKAERISKVMARAGVASRRDIERMIMEGRVTLNGRVLDTPVVNVTLADRIEVDGVPIRG 107

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ERTRLWLYHKP GLVTT++DP+GR TVFDNLP    RV+S+GRLDINTEGLLLLTNDGG
Sbjct: 108 IERTRLWLYHKPAGLVTTNADPEGRPTVFDNLPEELPRVMSIGRLDINTEGLLLLTNDGG 167

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LAR LELP+T WLR YRVR HG++DQ+ L+ LK GI + G+ YG ++ TLD  +GSN W+
Sbjct: 168 LARALELPATGWLRRYRVRAHGEIDQEALDKLKDGIAVDGVLYGSIEATLDRTQGSNVWI 227

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           T+GLREGKNREIK V       VNRLIRISYGPFQLG L  G   EV  +
Sbjct: 228 TMGLREGKNREIKNVLGALGLDVNRLIRISYGPFQLGDLPEGHVIEVRGR 277


>gi|323144920|ref|ZP_08079483.1| pseudouridine synthase B, ribosomal large subunit [Succinatimonas
           hippei YIT 12066]
 gi|322415318|gb|EFY06089.1| pseudouridine synthase B, ribosomal large subunit [Succinatimonas
           hippei YIT 12066]
          Length = 340

 Score =  176 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 92/342 (26%), Positives = 150/342 (43%), Gaps = 13/342 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL----- 67
            +++ KV+AR G+ SRRE++ +IA  RV+VNG +       V     +++DG  +     
Sbjct: 2   SEKLQKVLARQGLGSRRELDALIAAGRVEVNGKVAAV-GDRVEGPLTVKIDGKVVLTPLS 60

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            K +   L  Y     + T     D  +           R I VGRLD+NT GLLL T D
Sbjct: 61  EKPKCRVLMYYKPEGEVTTYKDPEDRPTVFDHLPRPDGGRWIYVGRLDLNTSGLLLFTTD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  RVY  R +G+V   ++  LK+G++++       +V     +G N 
Sbjct: 121 GELANALMHPSKEIERVYAARIYGEVTDKQIAALKQGVMLEDGKASFDKVVFVGGEGRNQ 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI---LRE 243
           W  V L+EG+NRE+++++E    +V+RLIRI Y    L   L AG  RE++      LR 
Sbjct: 181 WYHVSLKEGRNREVRRLWEAVGLQVSRLIRIRYAGVDLDNKLRAGKYRELTLSEINNLRA 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +G   LE +++   +    S               +     +K  +  +   ++ +   
Sbjct: 241 AVGLKALESSEIARTSLASMSNDKKHALEKFAKHKANIKAAGRKALNASHNPFRKGRADD 300

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
                  + +     G        S  R++N R +  F    
Sbjct: 301 KDRNPYGSRSGKYVYG---DAKRSSYGRKDNGRFAKRFSKND 339


>gi|325686573|gb|EGD28599.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK72]
          Length = 242

 Score =  176 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 104/233 (44%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++++ +  V VNG   +     +  T D I V G  L   + 
Sbjct: 1   MRLDKFLAENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDETADEIIVSGQRLTYEKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  D         +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPQGVISATEDDHHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVT 190
            +  P     ++YR +  G ++Q  +     GI ++        + +    ++  ++ V 
Sbjct: 121 AMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKDFTCQPAHLKILELDEEKEDSLVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + L EGK  ++K++      +V  L R++ GP QL   L  G  R ++   L 
Sbjct: 181 ITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDFALALGEWRRLTTDELE 233


>gi|257080911|ref|ZP_05575272.1| pseudouridine synthase [Enterococcus faecalis E1Sol]
 gi|257415240|ref|ZP_05592234.1| pseudouridine synthase [Enterococcus faecalis AR01/DG]
 gi|256988941|gb|EEU76243.1| pseudouridine synthase [Enterococcus faecalis E1Sol]
 gi|257157068|gb|EEU87028.1| pseudouridine synthase [Enterococcus faecalis ARO1/DG]
          Length = 244

 Score =  176 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 62/235 (26%), Positives = 104/235 (44%), Gaps = 5/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD I + G  L   + 
Sbjct: 1   MRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQIALMGEILTYQKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T    D               +  VGRLD +TEGLLLLTNDG LA 
Sbjct: 61  FYYMLHKPQGVISATEDQRDETVIDLLTDQDYRVDLFPVGRLDKDTEGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTL--DTQKGSNAWV 189
            L  P     + Y     G V  +   L  +G  +  G      ++ +    ++   + V
Sbjct: 121 QLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEMVKPSRLVIETINEEEGTSVV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
            + ++EGK  ++K++       V  L R+  G   L   L  G  R +++  L++
Sbjct: 181 RLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEYRPLTEAELQQ 235


>gi|256854470|ref|ZP_05559834.1| pseudouridine synthase [Enterococcus faecalis T8]
 gi|257089099|ref|ZP_05583460.1| pseudouridine synthase [Enterococcus faecalis CH188]
 gi|256710030|gb|EEU25074.1| pseudouridine synthase [Enterococcus faecalis T8]
 gi|256997911|gb|EEU84431.1| pseudouridine synthase [Enterococcus faecalis CH188]
 gi|323479852|gb|ADX79291.1| S4 domain pseudouridine synthase family protein [Enterococcus
           faecalis 62]
          Length = 244

 Score =  176 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 62/235 (26%), Positives = 105/235 (44%), Gaps = 5/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD I + G  L   + 
Sbjct: 1   MRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQIALMGEILTYQKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T    D             + +  VGRLD +TEGLLLLTNDG LA 
Sbjct: 61  FYYMLHKPQGVISATEDQRDETVIDLLTDQDYRADLFPVGRLDKDTEGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTL--DTQKGSNAWV 189
            L  P     + Y     G V  +   L  +G  +  G      ++ +    ++   + V
Sbjct: 121 QLLSPKKHVDKEYLAEVEGLVTVEDCQLFAQGFALKDGEMVKPSRLVIETINEEEGTSVV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
            + ++EGK  ++K++       V  L R+  G   L   L  G  R +++  L++
Sbjct: 181 RLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEYRPLTEAELQQ 235


>gi|71065415|ref|YP_264142.1| 23S rRNA pseudouridine synthase F [Psychrobacter arcticus 273-4]
 gi|71038400|gb|AAZ18708.1| ribosomal large subunit pseudouridine synthase F [Psychrobacter
           arcticus 273-4]
          Length = 332

 Score =  176 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 71/337 (21%), Positives = 128/337 (37%), Gaps = 19/337 (5%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N +  R++K I+ +GI SRR+ +R I Q  V +NG         V++ D ++V+G  +  
Sbjct: 3   NASSTRLNKYISESGICSRRDADRFIEQGNVYLNGKRAAV-GDQVVAGDTVKVNGQLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E            +    +          +      R+  +GRLD +++GL+ LTN+G 
Sbjct: 62  KEADDFVFIVLNKPVGIVSTTESSEKNNIVDFVRHSVRIFPIGRLDKDSQGLIFLTNNGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  +    +  L  G+ + G       VT    K +    
Sbjct: 122 LVNKVLRAGNNHEKDYVVTVNKPITDSFIEGLAGGVPMLGKMTKKCPVT----KVAPNVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E F ++V +L R       L     G  R+++ + L   L    
Sbjct: 178 NITLVQGLNRQIRRMCEHFGYEVVKLERTRIMNVSLKGTPVGDWRDLTPQELSVLL---- 233

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
               +   D+   SS    + R         D +   K SS+  G +K          R 
Sbjct: 234 ----KSIEDSSSESSTPAKKSRNTPRKNARTDTSEKPKVSSKPKGAAKGNAKHPKDGARK 289

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
            A +          +   S  ++   +  P+   KR 
Sbjct: 290 PAGSKGK------DWRPFSDGKKSGGKGKPATNGKRP 320


>gi|152976935|ref|YP_001376452.1| pseudouridine synthase [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152025687|gb|ABS23457.1| pseudouridine synthase [Bacillus cytotoxicus NVH 391-98]
          Length = 229

 Score =  176 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 111/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            ++++ I+ A   SRRE +R+I   RV +N  +     V V   D + VDG  + K E+ 
Sbjct: 1   MKINQFISEALSCSRRETDRLIKAGRVAMNDKVCTH-GVLVKPDDVVTVDGKVIEKEEKE 59

Query: 74  R-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +    +HKP+G+  T +     + +     +   R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAAKHIEGNIIAYI--NYPERIFPVGRLDKASEGLILLTNDGKIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V          ++ +  G+ I+       +VT       ++   + 
Sbjct: 118 QILHGDHGHEKEYVVTVDKSFTDGFIHGMSCGVKIKDGMTKPCKVTRV----DDSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +LG L  G  R ++ + L+E  G
Sbjct: 174 LTQGMNRQIRRMSRAFGYTVTKLKRVRIMNIKLGELEVGKWRYLTDEELQELRG 227


>gi|331092461|ref|ZP_08341285.1| hypothetical protein HMPREF9477_01928 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330401201|gb|EGG80793.1| hypothetical protein HMPREF9477_01928 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 243

 Score =  176 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 65/245 (26%), Positives = 112/245 (45%), Gaps = 7/245 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
                R++K ++ AG+ SRRE +R+I   +V V+G   E   + V     I+V    + K
Sbjct: 2   KEELIRLNKFLSEAGVCSRREADRLIEAGKVFVDGRRAET-GMRVSPAQEIKVGKKVIHK 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L   +KP G+V T    +  + +           I  GRLD ++EGLLL+TN+G 
Sbjct: 61  GNEMVLLAVNKPAGIVCTEEKKEKHNIIRFLNYPTRITYI--GRLDKDSEGLLLMTNNGD 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +     +  + Y+V  +  V ++ +  + +G+ I        +V            
Sbjct: 119 IINKMMRAGNRHEKEYKVTVNKPVTREFIEKMGQGVPILDTVTRPCKVKAI----GKYKF 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F +KV RL R+     QLG+L  G  REV+   +RE      
Sbjct: 175 NIVLTQGLNRQIRRMCEYFGYKVTRLERVRVMNIQLGSLKPGEYREVTDDEIRELYELIK 234

Query: 250 LEEAQ 254
               +
Sbjct: 235 DSSNE 239


>gi|167587342|ref|ZP_02379730.1| pseudouridine synthase [Burkholderia ubonensis Bu]
          Length = 389

 Score =  176 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 77/320 (24%), Positives = 131/320 (40%), Gaps = 6/320 (1%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 66  NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRI 124

Query: 63  DGVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           +G P+++         L  +     +V+        S      P   ++ ++VGRLD NT
Sbjct: 125 NGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNT 184

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++ 
Sbjct: 185 EGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEGNRQKLLHGVELDDGPANFLRIR 244

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
               +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ 
Sbjct: 245 DGGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPIPLPRGLKRGRWEELD 304

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
              +R+ +    L+             +   R    + + +          +       +
Sbjct: 305 DAQVRKLMATVGLKAPSEEKGKRGSGGQAERRQPDPMQTSMGFIGREPVLTTHGNLEQPR 364

Query: 298 QKKLATPVHRRNLASNVWMA 317
           +             S     
Sbjct: 365 RGPRRGAAGGFAGPSGFGGG 384


>gi|84394229|ref|ZP_00992957.1| pseudouridine synthase family 1 protein [Vibrio splendidus 12B01]
 gi|218709944|ref|YP_002417565.1| ribosomal large subunit pseudouridine synthase B [Vibrio splendidus
           LGP32]
 gi|84375143|gb|EAP92062.1| pseudouridine synthase family 1 protein [Vibrio splendidus 12B01]
 gi|218322963|emb|CAV19140.1| Ribosomal large subunit pseudouridine synthase B [Vibrio splendidus
           LGP32]
          Length = 342

 Score =  176 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 91/343 (26%), Positives = 149/343 (43%), Gaps = 8/343 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E +I   RV VNG + +           I +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRRELEGLIKSGRVSVNGQVAKLGERLEDENSVIRIDGHTITGKAS 61

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  Y     L T H     R+          SR ISVGRLD NT GLLL T D
Sbjct: 62  EEVVCRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G+V + K+  + +G+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRQVEREYLVRVFGEVTEQKVKNVTRGVQLEDGMARFEDVVYAGGEGMNH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G  +E+  + +   L 
Sbjct: 182 TFYVAINEGRNREVRRLWESQETTVSRLKRVRYGDIYLDKKLPRGGWKELDLQEV-NYLR 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
             +  + +      +  + T  +   +   ++     R ++ ++   G S Q K   P  
Sbjct: 241 ELVELQPEKETLLDLDPANTSRKRERSRSQKIRRAVKRHEERANAPKGRSNQTKRKKPAT 300

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           R     +   +    ++    + ++ + +   P+ P+K   R+
Sbjct: 301 RGTTTPDSGRSAPA-TNGKPQATKKPKLNNGRPAKPAKPRSRK 342


>gi|298245869|ref|ZP_06969675.1| pseudouridine synthase [Ktedonobacter racemifer DSM 44963]
 gi|297553350|gb|EFH87215.1| pseudouridine synthase [Ktedonobacter racemifer DSM 44963]
          Length = 277

 Score =  176 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 77/247 (31%), Positives = 127/247 (51%), Gaps = 8/247 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
            +    +R+++ +A AG+ASRR  E +IAQ RV+VNG ++      ++   D I VDG  
Sbjct: 31  NQEAQGERLARFLAHAGVASRRHAEELIAQGRVRVNGTIITAQGTRILPGQDRIVVDGKE 90

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLL 124
           ++        L HKP G V+T SDP+GR+TV D LP      R+  VGRLD +T GLLLL
Sbjct: 91  IQAKAPHAYLLLHKPAGYVSTVSDPEGRATVLDLLPPELRSLRLYPVGRLDRDTSGLLLL 150

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICY---GDMQVTL 179
           TNDG  A+ L  P  +  + Y V+  G   +  L  L+ G+        +      +   
Sbjct: 151 TNDGAFAQHLTHPRYEKEKHYEVQVKGIPTERTLQALRDGVTFTEDDGKHYTSSPARTRK 210

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            +    ++W+T+ + EG+ R+++++ +  +  V +L R+  G   L  +  G  R ++  
Sbjct: 211 LSSTEQSSWLTLTIHEGRKRQVRRMLQAVDHPVLQLRRVGLGSLTLRGVTPGKWRHLTPA 270

Query: 240 ILREQLG 246
            ++  L 
Sbjct: 271 EVQTLLA 277


>gi|168239322|ref|ZP_02664380.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|168466867|ref|ZP_02700715.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|194442736|ref|YP_002043438.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194735254|ref|YP_002117092.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|204927294|ref|ZP_03218496.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|194401399|gb|ACF61621.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Newport str. SL254]
 gi|194710756|gb|ACF89977.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           CVM19633]
 gi|195630602|gb|EDX49214.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|197287935|gb|EDY27323.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|204323959|gb|EDZ09154.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
          Length = 289

 Score =  176 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 62/292 (21%), Positives = 116/292 (39%), Gaps = 5/292 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R++K I+ +GI SRRE +R I Q  V +NG         V++ D ++V+G  +  
Sbjct: 3   TDTSTRLNKYISESGICSRREADRFIEQGNVFINGKRAA-IGDQVVAGDVVKVNGRLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   L L      +    +  DG      +  +   R+  +GRLD +++GL+ LTN G 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRIFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     +  + +  +  G+ I G            +K +    
Sbjct: 122 LVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +      
Sbjct: 178 RITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
              ++    A      T ++     I +  +            +   K+K  
Sbjct: 238 RSSSEAKPKAKAKPKTTGIKRPVVAIEKSNEKARPASSGKRFTSPGRKKKGR 289


>gi|116748130|ref|YP_844817.1| pseudouridine synthase [Syntrophobacter fumaroxidans MPOB]
 gi|116697194|gb|ABK16382.1| ribosomal large subunit pseudouridine synthase B [Syntrophobacter
           fumaroxidans MPOB]
          Length = 250

 Score =  176 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 92/249 (36%), Positives = 131/249 (52%), Gaps = 1/249 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
           T  R+ KV+A+AGIASRR  E +I Q RV VNGI++    V V    D I VD V +   
Sbjct: 2   TKVRLQKVLAQAGIASRRGAEEVIRQGRVVVNGIVVTELGVKVDPHADRITVDRVTIAMV 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E     L  KP   VTT  DP GR TVFD +P   +R+  VGRLD + EGLLLLTNDG L
Sbjct: 62  ESRVYLLLFKPRCCVTTARDPQGRKTVFDFVPDAGARLFPVGRLDFDAEGLLLLTNDGLL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L+ P     + Y V   G      L+ L+ G++++       +VT+      +  + 
Sbjct: 122 ANRLQHPRYGVTKTYEVAAMGHPTPAALDRLRTGVMLEEGMTAPAEVTVIGSSPRSTRLR 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+IK++ E     V  + R+++GP +LG+L  G +R +    +        L
Sbjct: 182 IVLHQGWNRQIKRMGEAVGHPVLSIKRVAFGPLKLGSLKPGGSRHLKSGEVELLYKLVHL 241

Query: 251 EEAQVNLDA 259
           ++ Q N D 
Sbjct: 242 DKEQRNADG 250


>gi|318606383|emb|CBY27881.1| ribosomal small subunit pseudouridine synthase A [Yersinia
           enterocolitica subsp. palearctica Y11]
          Length = 235

 Score =  176 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 55/238 (23%), Positives = 108/238 (45%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    
Sbjct: 1   MRLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQTVGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +  D       G+ +          Q+ +   +     V +
Sbjct: 121 ITSPRHHCEKTYLVTLEQPIADDTAQQFTDGVQLHNEKSLTKPAQLEVIEPQ----LVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
            + EG+  ++K++F     +V  L R   G  +L   L  G  R ++ + +     PH
Sbjct: 177 TISEGRYHQVKRMFAAAGNRVLELHRERIGDIKLDDDLAPGEYRPLTPEEIASVGAPH 234


>gi|255971130|ref|ZP_05421716.1| pseudouridine synthase [Enterococcus faecalis T1]
 gi|255973742|ref|ZP_05424328.1| pseudouridine synthase [Enterococcus faecalis T2]
 gi|256761441|ref|ZP_05502021.1| pseudouridine synthase [Enterococcus faecalis T3]
 gi|256957465|ref|ZP_05561636.1| pseudouridine synthase [Enterococcus faecalis DS5]
 gi|256959802|ref|ZP_05563973.1| pseudouridine synthase [Enterococcus faecalis Merz96]
 gi|256964546|ref|ZP_05568717.1| pseudouridine synthase [Enterococcus faecalis HIP11704]
 gi|257077544|ref|ZP_05571905.1| pseudouridine synthase [Enterococcus faecalis JH1]
 gi|257418285|ref|ZP_05595279.1| pseudouridine synthase [Enterococcus faecalis T11]
 gi|294780454|ref|ZP_06745819.1| pseudouridylate synthase [Enterococcus faecalis PC1.1]
 gi|255962148|gb|EET94624.1| pseudouridine synthase [Enterococcus faecalis T1]
 gi|255966614|gb|EET97236.1| pseudouridine synthase [Enterococcus faecalis T2]
 gi|256682692|gb|EEU22387.1| pseudouridine synthase [Enterococcus faecalis T3]
 gi|256947961|gb|EEU64593.1| pseudouridine synthase [Enterococcus faecalis DS5]
 gi|256950298|gb|EEU66930.1| pseudouridine synthase [Enterococcus faecalis Merz96]
 gi|256955042|gb|EEU71674.1| pseudouridine synthase [Enterococcus faecalis HIP11704]
 gi|256985574|gb|EEU72876.1| pseudouridine synthase [Enterococcus faecalis JH1]
 gi|257160113|gb|EEU90073.1| pseudouridine synthase [Enterococcus faecalis T11]
 gi|294452453|gb|EFG20890.1| pseudouridylate synthase [Enterococcus faecalis PC1.1]
 gi|295114108|emb|CBL32745.1| ribosomal small subunit pseudouridine synthase A [Enterococcus sp.
           7L76]
          Length = 244

 Score =  176 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 62/235 (26%), Positives = 105/235 (44%), Gaps = 5/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD I + G  L   + 
Sbjct: 1   MRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQIALMGEILTYQKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T    D             + +  VGRLD +TEGLLLLTNDG LA 
Sbjct: 61  FYYMLHKPQGVISATEDQRDETVIDLLTDQDYRADLFPVGRLDKDTEGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTL--DTQKGSNAWV 189
            L  P     + Y     G V  +   L  +G  +  G      ++ +    ++   + V
Sbjct: 121 QLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEMVKPSRLVIETINEEEGTSVV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
            + ++EGK  ++K++       V  L R+  G   L   L  G  R +++  L++
Sbjct: 181 RLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEYRPLTEAELQQ 235


>gi|237736761|ref|ZP_04567242.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           mortiferum ATCC 9817]
 gi|229420623|gb|EEO35670.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           mortiferum ATCC 9817]
          Length = 236

 Score =  176 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 72/232 (31%), Positives = 129/232 (55%), Gaps = 3/232 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-A 70
              R++K +A  G+ SRRE++++I + +++VNG ++  A V V   D IEV G  + K  
Sbjct: 2   EEIRINKYLASLGVGSRREIDKLIEEGKIRVNGEVI-SAGVKVTDKDIIEVKGKKISKDI 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E+   ++ +KP+ ++++  D  GR TV D +     R+  +GRLD NT GL+LLTNDG L
Sbjct: 61  EKKVYYMLNKPLEVLSSAKDDRGRKTVVDIVKC-KERIFPIGRLDYNTTGLILLTNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P ++  + Y V+  G++    +  L+ G+ ++        V L +++   + + 
Sbjct: 120 FNRVIHPRSEVYKEYYVKVLGEIKDSSIKKLEDGVELEDGITLPAYVKLISRERGKSELM 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           V +REG+NR+++++ E  N  V  L R   G   LG L  G  RE+++  ++
Sbjct: 180 VSIREGRNRQVRRMLEAVNTPVLVLRRERIGKLSLGKLKVGEYRELTESEVK 231


>gi|152972885|ref|YP_001338031.1| 23S rRNA pseudouridine synthase F [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|238892493|ref|YP_002917227.1| 23S rRNA pseudouridine synthase F [Klebsiella pneumoniae
           NTUH-K2044]
 gi|288937681|ref|YP_003441740.1| pseudouridine synthase [Klebsiella variicola At-22]
 gi|150957734|gb|ABR79764.1| pseudouridine synthase [Klebsiella pneumoniae subsp. pneumoniae MGH
           78578]
 gi|238544809|dbj|BAH61160.1| pseudouridine synthase [Klebsiella pneumoniae subsp. pneumoniae
           NTUH-K2044]
 gi|288892390|gb|ADC60708.1| pseudouridine synthase [Klebsiella variicola At-22]
          Length = 291

 Score =  176 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 60/301 (19%), Positives = 114/301 (37%), Gaps = 13/301 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSTRLNKYISESGICSRREADRFIEQGNVFINGKRAT-IGDQVKPGDLVKVNGRLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   R+  +GRLD +++GL+ LTN G L
Sbjct: 63  EADDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPVTDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLTGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
             ++                       +     +M+ ++ +       K+   P  ++  
Sbjct: 239 SSSEAK--------PKARPKAKAATPGIKRPVVKMENSNDKGRPAGNGKRFTQPGRKKKG 290

Query: 311 A 311
            
Sbjct: 291 R 291


>gi|315633718|ref|ZP_07889008.1| ribosomal small subunit pseudouridine synthase A [Aggregatibacter
           segnis ATCC 33393]
 gi|315477760|gb|EFU68502.1| ribosomal small subunit pseudouridine synthase A [Aggregatibacter
           segnis ATCC 33393]
          Length = 234

 Score =  176 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 105/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R +  +++ Q  V +NG + +  A  V   D I  DG  L   E  
Sbjct: 1   MRLDKFLAETTGLTRSQAAKVLRQSAVTINGKIEKSGAAKVSPDDEIYYDGERLTWVENG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +  + HKP G + +H D D  +        + + + S GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYIMLHKPQGYICSHEDGDHPTIYQFFDYPLSTCLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P   + + Y V     V+ +      +GI+++G        ++ +      +  V +
Sbjct: 121 ITSPKHHYPKTYLVTLADPVEANYAQACAEGILLRGEKEPTKPAELEIL----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            + EG+  ++K++F     KV  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAALGNKVVGLHRWKIGNLVLDDDLGEGEFRPLTEEEI 227


>gi|229135383|ref|ZP_04264172.1| RNA pseudouridine synthase [Bacillus cereus BDRD-ST196]
 gi|228648079|gb|EEL04125.1| RNA pseudouridine synthase [Bacillus cereus BDRD-ST196]
          Length = 229

 Score =  176 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 108/230 (46%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   R  +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRACINGEVCTH-GALVNEGDIVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T ++    + +         R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAAEHIEDNIIDYI--DYPERIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT   Q    +   + 
Sbjct: 118 QILHGDHEHEKEYVVAVDKPFTDWFIDEMSSGVKIKDGMTKPCKVTRVNQ----STFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++   F + V +L R+     +L  L AG  R+++ K L 
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELNELEAGKWRDITPKELE 223


>gi|257083600|ref|ZP_05577961.1| pseudouridine synthase [Enterococcus faecalis Fly1]
 gi|256991630|gb|EEU78932.1| pseudouridine synthase [Enterococcus faecalis Fly1]
          Length = 244

 Score =  175 bits (444), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 61/235 (25%), Positives = 105/235 (44%), Gaps = 5/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD I + G  L   + 
Sbjct: 1   MRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQIALMGEILTYQKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T    D             + +  VGRLD +TEGLLLLTNDG LA 
Sbjct: 61  FYYMLHKPQGVISATEDQRDETVIDLLTDQDYRADLFPVGRLDKDTEGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTL--DTQKGSNAWV 189
            L  P     + Y     G V  +   L  +G  ++        ++ +    ++   + V
Sbjct: 121 QLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEVVKPSRLVIETINEEEGTSVV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
            + ++EGK  ++K++       V  L R+  G   L   L  G  R +++  L++
Sbjct: 181 RLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEYRPLTEAELQQ 235


>gi|171317089|ref|ZP_02906292.1| RNA-binding S4 domain protein [Burkholderia ambifaria MEX-5]
 gi|171097723|gb|EDT42550.1| RNA-binding S4 domain protein [Burkholderia ambifaria MEX-5]
          Length = 427

 Score =  175 bits (444), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 81/349 (23%), Positives = 140/349 (40%), Gaps = 7/349 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 31  NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRI 89

Query: 63  DGVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           +G P+++         L  +     +V+        S      P   ++ ++VGRLD NT
Sbjct: 90  NGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNT 149

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++ 
Sbjct: 150 EGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEGMRQKLLHGVELDDGPANFLRIR 209

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
               +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ 
Sbjct: 210 DGGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPIPLPRGLKRGRWEELD 269

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +  +R+ +    L+           S     R    + + +          +  +    +
Sbjct: 270 EAQVRKLMATVGLKAPSEEKGKRGGSGPAERRQPDPMQTSMGFISREPVLTTHGQLDQPR 329

Query: 298 QKKLATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKR 345
           +             S                 G R+ +  R+      +
Sbjct: 330 RGGGRRGGPGLPGLSGYGSLPVSPSGHGNRSGGGRDVDGNRASYGAGPK 378


>gi|300778899|ref|ZP_07088757.1| ribosomal large subunit pseudouridine synthase F [Chryseobacterium
           gleum ATCC 35910]
 gi|300504409|gb|EFK35549.1| ribosomal large subunit pseudouridine synthase F [Chryseobacterium
           gleum ATCC 35910]
          Length = 240

 Score =  175 bits (444), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 111/231 (48%), Gaps = 8/231 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-RKA 70
              R++K ++  G  SRR  ++++ + R+K+NG +       V   D +EVDG P+    
Sbjct: 2   EKTRINKYLSEVGYCSRRAADKLLEEGRIKINGKIP-ELGTKVSDEDLVEVDGKPIREPQ 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E+    +++KP+G+V T      ++ + D +     R+  +GRLD  +EGL+LLT+DG +
Sbjct: 61  EKPVYIVFNKPVGIVCTTDTKREKNNIVDYINHPK-RIFPIGRLDKPSEGLILLTSDGDI 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y VR    +    L  ++ G+ I        +     +K       
Sbjct: 120 VNKILRARNNHEKEYLVRVDKPITPKFLEKMRNGVPILDTITRKCK----VEKIDEMNFR 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + L +G NR+I+++ E+  ++V +L RI     +L  L  G  R+++   L
Sbjct: 176 IILTQGLNRQIRRMCEYLGYEVKKLKRIRIMNIKL-DLPVGKWRDLTDDEL 225


>gi|153813747|ref|ZP_01966415.1| hypothetical protein RUMOBE_04181 [Ruminococcus obeum ATCC 29174]
 gi|149830167|gb|EDM85260.1| hypothetical protein RUMOBE_04181 [Ruminococcus obeum ATCC 29174]
          Length = 315

 Score =  175 bits (444), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 71/320 (22%), Positives = 131/320 (40%), Gaps = 10/320 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M +K I  +  T  R++K ++ AG+ SRRE +++    RV V G  +      + +   +
Sbjct: 1   MDEKRITTD-QTTIRINKYLSAAGVCSRREADQLTDAGRVTVAGKEIGT-GERIPADAEV 58

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            +DG P++   R  L L++KP G+V +       +TV + L     RV  VGRLD ++EG
Sbjct: 59  FLDGRPVKAETRQVLLLFYKPRGIVCSTKKQRQETTVTEFLDY-PVRVYPVGRLDKDSEG 117

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLLLTN G L   +        + Y V    ++ +  +  +  G+ I G           
Sbjct: 118 LLLLTNQGDLVNRIMRAGNYHEKEYEVTVDKKITETFIRKMSSGVPILGTVTRPCT---V 174

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + G  +  ++ L +G NR+I+++ E+  + V  L RI      L  L  G  RE+    
Sbjct: 175 YKTGDKS-FSIILTQGLNRQIRRMCEYLGYHVCTLKRIRIMNLTLDGLKCGEYREICGDE 233

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT---RMKKNSSQKNGLSK 297
            ++         ++  +       +   R      +E           +    ++  + +
Sbjct: 234 WKKLNELIRDSSSETVIRTGGQHGKISGRTNKRTGAEAERSGKGILSGRPGDHEQQRVRR 293

Query: 298 QKKLATPVHRRNLASNVWMA 317
             +      +RN   +    
Sbjct: 294 TVRSTGKNGKRNRNRSGRQP 313


>gi|170700025|ref|ZP_02891050.1| RNA-binding S4 domain protein [Burkholderia ambifaria IOP40-10]
 gi|170135084|gb|EDT03387.1| RNA-binding S4 domain protein [Burkholderia ambifaria IOP40-10]
          Length = 427

 Score =  175 bits (444), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 81/349 (23%), Positives = 140/349 (40%), Gaps = 7/349 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 31  NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRI 89

Query: 63  DGVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           +G P+++         L  +     +V+        S      P   ++ ++VGRLD NT
Sbjct: 90  NGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNT 149

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++ 
Sbjct: 150 EGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEGMRQKLLHGVELDDGPANFLRIR 209

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
               +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ 
Sbjct: 210 DGGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPIPLPRGLKRGRWEELD 269

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +  +R+ +    L+           S     R    + + +          +  +    +
Sbjct: 270 EAQVRKLMATVGLKAPSEEKGKRGGSGPAERRQPDPMQTSMGFISREPVLTTHGQLDQPR 329

Query: 298 QKKLATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKR 345
           +             S                 G R+ +  R+      +
Sbjct: 330 RGGGRRGGPGLPGLSGYGSLPVSPSGHGNRSGGGRDVDGNRASYGAGPK 378


>gi|51473726|ref|YP_067483.1| pseudouridine synthase [Rickettsia typhi str. Wilmington]
 gi|81390049|sp|Q68WJ1|Y532_RICTY RecName: Full=Uncharacterized RNA pseudouridine synthase RT0532;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|51460038|gb|AAU04001.1| Pseudouridine synthase [Rickettsia typhi str. Wilmington]
          Length = 242

 Score =  175 bits (444), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 106/231 (45%), Positives = 151/231 (65%), Gaps = 2/231 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K+I+ AG+ SRR  E++I   +VK++GI +   A NV  ++ IEV G  +   ++ R
Sbjct: 3   RLAKIISNAGVCSRRNAEKLIVGGKVKIDGITILSPATNVDISNQIEVSGRLINNIQKPR 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LW+Y+KPIGL+TTH DP  R TVF+ L     RVIS+GRLD+N+EGLLLLTN G LA   
Sbjct: 63  LWIYYKPIGLITTHKDPLSRKTVFEQLIG-LPRVISIGRLDLNSEGLLLLTNSGDLAHQF 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           E+PS++  RVY VR +G  +    N     + I GI Y    + L  Q  +N+W  V L 
Sbjct: 122 EMPSSKLKRVYNVRAYGNANFLLKNN-YNNLKIDGIFYNPYSIKLLRQNKNNSWFEVVLF 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           EGKNREI+++FE+F  KVN+LIR+ YG  ++G L  G  +E+S KIL++ +
Sbjct: 181 EGKNREIRRIFEYFGLKVNKLIRVQYGALKIGNLKPGDYKEISNKILKKII 231


>gi|33602225|ref|NP_889785.1| hypothetical protein BB3249 [Bordetella bronchiseptica RB50]
 gi|33576663|emb|CAE33741.1| conserved hypothetical protein [Bordetella bronchiseptica RB50]
          Length = 593

 Score =  175 bits (444), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 82/360 (22%), Positives = 132/360 (36%), Gaps = 11/360 (3%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             +       ++ KV+A AGI SRRE+E +I   RV VNG         V   D + V+G
Sbjct: 115 KYLNSEAVMPKLHKVLADAGIGSRREMEELIVAGRVSVNGEPA-HIGQRVAPNDQVRVNG 173

Query: 65  VPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            P+     K     +  +     +V+        S           + +SVGRLD+NTEG
Sbjct: 174 KPIARPNAKKPPRVILYHKPAGEIVSHDDPGGRASVFARLPKLRTGKWLSVGRLDLNTEG 233

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LL+ T  G +A  +  P     R Y VR  G++D  +   L +GI ++            
Sbjct: 234 LLIFTTSGDMANRIMHPRYGTEREYAVRVLGEMDDAQRKSLTEGIELEDGKAAFGSFEYL 293

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
              GSN W  V L+EG+NRE++++FE     V+RLIR  +G   L   L  G   E+   
Sbjct: 294 GGDGSNRWYRVTLQEGRNREVRRMFEAVGVTVSRLIRTRFGDIVLPRNLRRGRWEELDGS 353

Query: 240 -----ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
                +++  L     E           S ++ +      +     +  R+ +    + G
Sbjct: 354 LVTALMVQLGLLRDGDESEGRRKSRQPQSHDSALPPGFGTLERNGMNGARIGRRGKLQGG 413

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                                     H      +  R    + +         +R   +K
Sbjct: 414 RPGSAAACPSDPFGTGLMITGGYANGHPLGNDSAAGRGGKGKPAKGKAGGDKPQRGQGRK 473


>gi|33596480|ref|NP_884123.1| hypothetical protein BPP1859 [Bordetella parapertussis 12822]
 gi|33566249|emb|CAE37160.1| conserved hypothetical protein [Bordetella parapertussis]
          Length = 592

 Score =  175 bits (444), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 82/360 (22%), Positives = 132/360 (36%), Gaps = 11/360 (3%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             +       ++ KV+A AGI SRRE+E +I   RV VNG         V   D + V+G
Sbjct: 115 KYLNSEAVMPKLHKVLADAGIGSRREMEELIVAGRVSVNGEPA-HIGQRVAPNDQVRVNG 173

Query: 65  VPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            P+     K     +  +     +V+        S           + +SVGRLD+NTEG
Sbjct: 174 KPIARPNAKKPPRVILYHKPAGEIVSHDDPGGRASVFARLPKLRTGKWLSVGRLDLNTEG 233

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LL+ T  G +A  +  P     R Y VR  G++D  +   L +GI ++            
Sbjct: 234 LLIFTTSGDMANRIMHPRYGTEREYAVRVLGEMDDAQRKSLTEGIELEDGKAAFGSFEYL 293

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
              GSN W  V L+EG+NRE++++FE     V+RLIR  +G   L   L  G   E+   
Sbjct: 294 GGDGSNRWYRVTLQEGRNREVRRMFEAVGVTVSRLIRTRFGDIVLPRNLRRGRWEELDGS 353

Query: 240 -----ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
                +++  L     E           S ++ +      +     +  R+ +    + G
Sbjct: 354 LVTALMVQLGLLRDGDESEGRRKSRQPQSHDSALPPGFGTLERNGMNGARIGRRGKLQGG 413

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                                     H      +  R    + +         +R   +K
Sbjct: 414 RPGSAAACPSDPFGTGLMITGGYANGHPLGNDSAAGRGGKGKPAKGKAGGDKPQRGQGRK 473


>gi|298488132|ref|ZP_07006169.1| Pseudouridine synthase family protein [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|298157411|gb|EFH98494.1| Pseudouridine synthase family protein [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
          Length = 408

 Score =  175 bits (444), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 91/354 (25%), Positives = 140/354 (39%), Gaps = 15/354 (4%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG         V   D I
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDAT-LGQRVDLHDAI 62

Query: 61  EVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            VDG  +++ E     R  +        + T        +           R I++GRLD
Sbjct: 63  SVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           INT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++       
Sbjct: 123 INTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILKDGPARFT 182

Query: 176 QVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE+S+  + + L   +  +          + + + R +      +           +   
Sbjct: 243 REMSQYEV-DILAAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVRTLRPAAGA 301

Query: 294 GLSKQKKLATP-----VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
             +  +    P        R    +                +       S   P
Sbjct: 302 PATGDRAPRQPQITGSERDRPRGGDSTQRPSPRKDSGKPGSRAPRPADNSRGTP 355


>gi|332346017|gb|AEE59351.1| 23S rRNA pseudouridylate synthase F YjbC [Escherichia coli UMNK88]
          Length = 277

 Score =  175 bits (444), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 58/276 (21%), Positives = 107/276 (38%), Gaps = 5/276 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
             ++    A        ++     + +         
Sbjct: 239 SSSEAKPKAKAKPKTAGIKRPVVKMEKNGGKRRSPG 274


>gi|238794236|ref|ZP_04637850.1| Ribosomal small subunit pseudouridine synthase A [Yersinia
           intermedia ATCC 29909]
 gi|238726418|gb|EEQ17958.1| Ribosomal small subunit pseudouridine synthase A [Yersinia
           intermedia ATCC 29909]
          Length = 235

 Score =  175 bits (444), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 56/238 (23%), Positives = 109/238 (45%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    
Sbjct: 1   MRLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQTVGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +  D      +G+ +          Q+ +   +     V +
Sbjct: 121 ITSPRHHCEKTYLVTLEHPLADDTAQQFTEGVQLHNEKSLTKPAQLEVIEPQ----LVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
            L EG+  ++K++F     +V  L R   G  +L   L  G  R ++ + +     PH
Sbjct: 177 TLSEGRYHQVKRMFAAVGNRVVELHRERIGDIKLDDDLAPGEYRPLTAEEIASVGAPH 234


>gi|238761999|ref|ZP_04622972.1| Ribosomal small subunit pseudouridine synthase A [Yersinia
           kristensenii ATCC 33638]
 gi|238699727|gb|EEP92471.1| Ribosomal small subunit pseudouridine synthase A [Yersinia
           kristensenii ATCC 33638]
          Length = 246

 Score =  175 bits (444), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 56/242 (23%), Positives = 108/242 (44%), Gaps = 7/242 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
                R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++
Sbjct: 8   KVDLMRLDKFLSQQLGVSRALVARELRAKRVTIDGEIVKSGAIKLTPEQDVRFDGNPLQQ 67

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG 
Sbjct: 68  TVGPRYFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQ 127

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNA 187
            +  +  P     + Y V     V  D       G+ +          Q+ +   +    
Sbjct: 128 WSHRITSPRHHCEKTYLVTLEHPVADDTAQQFTDGVQLHNEKSLTKPAQLEVIEPQ---- 183

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
            V + + EG+  ++K++F     +V  L R   G  +L   L  G  R ++ + +     
Sbjct: 184 LVRLTISEGRYHQVKRMFGAVGNRVLELHRERIGDIKLDDDLAPGEYRPLTAEEIASVGA 243

Query: 247 PH 248
           PH
Sbjct: 244 PH 245


>gi|238650309|ref|YP_002916161.1| ribosomal large subunit pseudouridine synthase B [Rickettsia
           peacockii str. Rustic]
 gi|238624407|gb|ACR47113.1| ribosomal large subunit pseudouridine synthase B [Rickettsia
           peacockii str. Rustic]
          Length = 230

 Score =  175 bits (444), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 107/230 (46%), Positives = 148/230 (64%), Gaps = 2/230 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K+I+ AG+ SRR+ E++I + +VKV+GI +     NV  ++ IEV G  +    + R
Sbjct: 3   RLAKIISNAGVCSRRDAEKLIVEGQVKVDGITILSPTTNVDISNQIEVSGTLINNIHKPR 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LW+Y+KP+GL+TTH DP  R TVF+ L     RVIS+GRLD+N+EGLLLLTN G LAR  
Sbjct: 63  LWIYYKPVGLITTHKDPLSRKTVFEQLTG-LPRVISIGRLDLNSEGLLLLTNSGDLARQF 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPS++  RVY VR +G+ D    +   K + I GI Y    + L  Q  +N W  V L 
Sbjct: 122 ELPSSRLKRVYHVRAYGKYDILLKSN-YKNLEIDGIFYNPHSIKLLKQNKTNCWFEVVLF 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           EGKNREI+++FE+   KVN+LIRI YG F +  L  G  +E++ KIL   
Sbjct: 181 EGKNREIRRIFEYCGLKVNKLIRIQYGNFTIDNLKPGDYKEINNKILENN 230


>gi|312876843|ref|ZP_07736820.1| pseudouridine synthase [Caldicellulosiruptor lactoaceticus 6A]
 gi|311796358|gb|EFR12710.1| pseudouridine synthase [Caldicellulosiruptor lactoaceticus 6A]
          Length = 230

 Score =  175 bits (444), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 72/222 (32%), Positives = 115/222 (51%), Gaps = 2/222 (0%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRLWLY 78
           +A+ GIASRR+ E +I Q RVKVNG  + +    V    D +EVDG  +    +    + 
Sbjct: 1   MAQCGIASRRKCEEIILQGRVKVNGKTVNQLGFKVDPEKDVVEVDGKRISLQMQKVYIML 60

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLARVLELP 137
           +KP G++++  D  GR TV D +    +     VGRLD +T GL+LLTNDG  A  +  P
Sbjct: 61  NKPFGVISSAKDEKGRKTVVDLVKDKVNVRVFPVGRLDFDTTGLILLTNDGEFAYKVTHP 120

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGK 197
                + Y     G   +++++  +KG++I G      +  +      NA V + + EG+
Sbjct: 121 KHDIEKTYIALIRGIPSKEEIDRFEKGLLIDGKMTAPAKFKILKLINGNALVEIKIHEGR 180

Query: 198 NREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           NR+I+K+      +V +L R++ G  QLG L  G    + K+
Sbjct: 181 NRQIRKMCAQIGHEVLKLKRVAIGKLQLGKLKEGEFVFLDKE 222


>gi|206578740|ref|YP_002241036.1| ribosomal large subunit pseudouridine synthase F [Klebsiella
           pneumoniae 342]
 gi|290512420|ref|ZP_06551787.1| ribosomal large subunit pseudouridine synthase F [Klebsiella sp.
           1_1_55]
 gi|206567798|gb|ACI09574.1| ribosomal large subunit pseudouridine synthase F [Klebsiella
           pneumoniae 342]
 gi|289775415|gb|EFD83416.1| ribosomal large subunit pseudouridine synthase F [Klebsiella sp.
           1_1_55]
          Length = 291

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 60/301 (19%), Positives = 115/301 (38%), Gaps = 13/301 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSTRLNKYISESGICSRREADRFIEQGNVFINGKRAT-IGDQVKPGDLVKVNGRLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   R+  +GRLD +++GL+ LTN G L
Sbjct: 63  EADDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPVTDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLTGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
             ++                       +     +M+ ++ +    +  K+   P  ++  
Sbjct: 239 SSSEAK--------PKARPKAKAATPGIKRPVVKMENSNDKGRPAANGKRFTQPGRKKKG 290

Query: 311 A 311
            
Sbjct: 291 R 291


>gi|167751640|ref|ZP_02423767.1| hypothetical protein EUBSIR_02645 [Eubacterium siraeum DSM 15702]
 gi|167655448|gb|EDR99577.1| hypothetical protein EUBSIR_02645 [Eubacterium siraeum DSM 15702]
          Length = 251

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 119/233 (51%), Gaps = 3/233 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
              R+ K+IA +G  SRR+ E  I Q  VKVNG  +           D + V+G  +  +
Sbjct: 2   EKVRLQKIIADSGYCSRRKAEEYIEQGCVKVNGRPV-SLGDKADPKNDIVTVNGEKIASS 60

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             + R    +KP G VTT +D  GR  V D L  I  RV  VGRLD ++EGLL+LTNDG 
Sbjct: 61  GTQLRYIKLYKPRGYVTTMADTHGRKIVTDLLDDIDERVYPVGRLDKDSEGLLILTNDGA 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  +  PS    + YRV   G+V  DKL  L  G+ I         V +  ++ +   +
Sbjct: 121 LANAVMHPSRHIKKRYRVTVRGEVTDDKLTTLASGVKIDTGVTLPCTVAVLAEEENRTVI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
              + EGKNR+I+K+ E    ++ RL R + G  +LG L  G   +++ + L+
Sbjct: 181 EFTIAEGKNRQIRKMCEAVKLQIVRLKRNAVGNIKLGMLKPGEWADLTAEELK 233


>gi|303236518|ref|ZP_07323103.1| pseudouridylate synthase [Prevotella disiens FB035-09AN]
 gi|302483266|gb|EFL46276.1| pseudouridylate synthase [Prevotella disiens FB035-09AN]
          Length = 505

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 103/234 (44%), Gaps = 1/234 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +   P R++K +A AG+ SRRE +  I    V VNG ++      ++ +D I   G P+ 
Sbjct: 265 DPNEPLRLNKYLANAGVCSRREADEFIQAGVVTVNGEVVNELGTKILRSDVITFKGQPVT 324

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ++  + L      + T+      ++ +         R+  VGRLD NT G+LLLTNDG
Sbjct: 325 LEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKGICPERIYPVGRLDRNTTGVLLLTNDG 384

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     +VY V          L  +  GI ++                  + 
Sbjct: 385 DLASKLTHPKFLKKKVYHVYLDKPATPQTLQQISDGIELEDGEIK-ADAIEYADSLDQSQ 443

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           V + +  GKNR ++++FE   ++V +L R+ +       L  G  R ++++ + 
Sbjct: 444 VGIEIHSGKNRIVRRIFESLGYRVIKLDRVQFAGLTKKNLRRGDWRFLTEQEVD 497


>gi|229087098|ref|ZP_04219248.1| RNA pseudouridine synthase [Bacillus cereus Rock3-44]
 gi|228696166|gb|EEL49001.1| RNA pseudouridine synthase [Bacillus cereus Rock3-44]
          Length = 229

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 112/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-ER 72
            ++++ I++A   SRRE +R+I   RV +NG +       V + D + +DG  + K  + 
Sbjct: 1   MKINQFISKALSCSRRETDRLIKANRVAINGEICTH-GALVAADDIVSIDGKTIEKEAKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T ++    + +     +   R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KIYIAFHKPVGITCTAAEHIEGNIIEYI--NHPERIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ + +G+ I+       +VT       ++   + 
Sbjct: 118 QILHGDHEHEKEYIVTVDKPFTDWFIDSMSRGVKIKDGMTKPCKVT----GVDHSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+      L  L  G  R VS++ L E + 
Sbjct: 174 LTQGMNRQIRRMSRAFGYTVTKLKRVRIMNITLDGLEVGEWRNVSEQELIELMR 227


>gi|221632463|ref|YP_002521684.1| putative pseudouridine synthase [Thermomicrobium roseum DSM 5159]
 gi|221155848|gb|ACM04975.1| possible pseudouridine synthase [Thermomicrobium roseum DSM 5159]
          Length = 282

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 75/284 (26%), Positives = 123/284 (43%), Gaps = 3/284 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGV 65
           +    T QR+ +V+A  G+ASRR+ E +I   RV V+G+++      V      I VDG 
Sbjct: 1   MSVTMTEQRLQRVLAAHGVASRRKAEELILAGRVTVDGVVVRELGRKVDPERQEICVDGK 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL    R  + L+     + TT  +   ++ +  +L  +  RV+ VGRLD ++ GLLLLT
Sbjct: 61  PLHSEPRRYIVLHKPVGYITTTADEYGRKTVL--DLVQVPERVVPVGRLDRDSSGLLLLT 118

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG L   +  P  +  + Y V   G    +    L++G+ + G      ++     +  
Sbjct: 119 NDGDLIYRITHPRYELEKEYEVLVDGFPPPEVEEALRRGVPVDGRPVRIRRLEAIRVEPQ 178

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                V + EG+NR I++VFE   + V RL R+  GP +LG L  G  R+++   +    
Sbjct: 179 GTVYRVVIHEGRNRIIRRVFERVGYPVLRLQRVRVGPLRLGDLPPGRWRDLTASEVAALR 238

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
               L E           +              P    +  +  
Sbjct: 239 RAVGLPEFPEGAVGRERKARGGRGMPARRGDRRPSGVRKEHRRR 282


>gi|149182614|ref|ZP_01861084.1| 16S pseudouridylate synthase [Bacillus sp. SG-1]
 gi|148849692|gb|EDL63872.1| 16S pseudouridylate synthase [Bacillus sp. SG-1]
          Length = 239

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 102/232 (43%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV++ +      VNG +++     V    D + V G  +   E 
Sbjct: 1   MRIDKLLSNMGYGSRKEVKKHLKGGGTVVNGEVVKDPKFQVDPESDTVTVHGEEVVYREF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +   P  L  T             +         VGRLD +TEGLLL+TNDG L+ 
Sbjct: 61  IYLMMNKPPGVLSATEDAEGETVIDLLEMEDQIFNPFPVGRLDKDTEGLLLITNDGQLSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G+V ++ ++   +G+ +         ++ +    G  + + +
Sbjct: 121 QLLSPKKHVPKTYFAVIEGEVTEEDVSAFAEGVTLDDGYETKPGELEII-SSGIRSEINL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            + EGK  ++K++FE    +V  L RI+ G   L   L  G  RE++ + + 
Sbjct: 180 TITEGKFHQVKRMFESVGKRVIYLKRITMGLLPLDETLELGEYRELTDEEVE 231


>gi|260887142|ref|ZP_05898405.1| ribosomal large subunit pseudouridine synthase B [Selenomonas
           sputigena ATCC 35185]
 gi|330839088|ref|YP_004413668.1| pseudouridine synthase Rsu [Selenomonas sputigena ATCC 35185]
 gi|260863204|gb|EEX77704.1| ribosomal large subunit pseudouridine synthase B [Selenomonas
           sputigena ATCC 35185]
 gi|329746852|gb|AEC00209.1| pseudouridine synthase Rsu [Selenomonas sputigena ATCC 35185]
          Length = 242

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 85/239 (35%), Positives = 126/239 (52%), Gaps = 2/239 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K+I+RAG+ASRR+ E +IA  RV V+G ++        + T  IEVDG  +   ER
Sbjct: 3   ERLQKIISRAGVASRRKAEELIAAGRVTVDGAVVREPGTKADASTARIEVDGKRIPAEER 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP G V+T SD  GR TV D LP    RV  VGRLD NTEGL+LLTNDG L +
Sbjct: 63  LVYFLLNKPKGCVSTVSDERGRRTVLDLLPVKNVRVYPVGRLDQNTEGLILLTNDGTLTQ 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-KGSNAWVTV 191
            L  P     + YR +  G++  + L  L+ GI +        +V +    +   + V V
Sbjct: 123 ALLHPRFLVHKTYRAKVAGELTPEALKKLRSGIELADGMTAPAEVRVYGVTEKGLSDVEV 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
            L EG+NR+++++FE     V  L R  +    L  +  G++R ++K  +         
Sbjct: 183 TLHEGRNRQVRRMFEAVGCDVRALKRTRFAQLTLDGVKRGASRPLTKAEVEALYRLAEE 241


>gi|163942282|ref|YP_001647166.1| pseudouridine synthase [Bacillus weihenstephanensis KBAB4]
 gi|163864479|gb|ABY45538.1| pseudouridine synthase [Bacillus weihenstephanensis KBAB4]
          Length = 229

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 108/230 (46%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   R  +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRACINGEVCTH-GALVNEGDIVTIDGQVIVKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T ++    + +         R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAAEHIEDNIIDYI--DYPERIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT   Q    +   + 
Sbjct: 118 QILHGDHEHEKEYVVAVDKPFTDWFIDEMSSGVKIKDGMTKPCKVTRVNQ----STFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++   F + V +L R+     +L  L AG  R+++ K L 
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELNELEAGKWRDITPKELE 223


>gi|313892540|ref|ZP_07826127.1| pseudouridine synthase B, ribosomal large subunit [Dialister
           microaerophilus UPII 345-E]
 gi|313118937|gb|EFR42142.1| pseudouridine synthase B, ribosomal large subunit [Dialister
           microaerophilus UPII 345-E]
          Length = 240

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 71/238 (29%), Positives = 118/238 (49%), Gaps = 4/238 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K+I+ AG+ SRR+ E +I + RVKVNG  + +      S  D IEV+G  ++K   
Sbjct: 3   ERLQKIISHAGVCSRRKAEELIKEGRVKVNGHTVTKLGTEADSVRDCIEVNGKVIKKERL 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                      + +       R+        I  RV  VGRLD ++EGLLL+TNDG L  
Sbjct: 63  KYFLFNKPDKVITSMTDPAGRRTVSDYF-SQIKERVFPVGRLDYHSEGLLLMTNDGDLDY 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVT 190
           +L  PS +  ++Y V   G+  +     + +G+ I         + +    ++ +  ++ 
Sbjct: 122 ILTHPSHEVYKIYEVVVRGKFSERLAEKMSEGVKIDSGITAPCDIEIISYDKEKNKTFLK 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + L EGKNREI+K+ E F++ V +L R+ Y    L  +  G+ R +S + +R     H
Sbjct: 182 MVLHEGKNREIRKMMEAFHFPVFKLERVGYSFLTLKGVSRGTFRSLSPEEVRRLYELH 239


>gi|86141186|ref|ZP_01059732.1| pseudouridine synthase, Rsu [Leeuwenhoekiella blandensis MED217]
 gi|85831745|gb|EAQ50200.1| pseudouridine synthase, Rsu [Leeuwenhoekiella blandensis MED217]
          Length = 265

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 58/266 (21%), Positives = 108/266 (40%), Gaps = 7/266 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + EN    R++K ++  G  SRRE +++I   R+ VNG +       V S D I VDG  
Sbjct: 1   MSEN-KLTRINKFLSEVGYCSRREADKLIDAGRITVNGNIP-EMGTKVSSEDEIRVDGKI 58

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           + + +   ++L       +   +D         +  +  +R+  +GRLD  +EGL+ LTN
Sbjct: 59  VGEQKDPPVYLIFHKPVGIVCTTDTRVEKDNIIDYINYPTRIFPIGRLDKASEGLIFLTN 118

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG +   +        + Y V     +D   +  +  GI I        +     ++   
Sbjct: 119 DGDIVNKILRARNNHDKEYIVDVDKPIDASFVKRMSDGIPILDTITRKCE----VEQLGK 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               + L +G NR+I+++ E+ ++ V RL R+      L  +  G  R  +   L+E   
Sbjct: 175 KRFKIILTQGLNRQIRRMCEYLDYNVTRLKRVRIMNINL-DIPVGKYRAFTTAELKELNS 233

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRP 272
                      ++   +   +    P
Sbjct: 234 LLEGSSKTFEPESQTGNKPEIRPSGP 259


>gi|288918462|ref|ZP_06412813.1| pseudouridine synthase [Frankia sp. EUN1f]
 gi|288350102|gb|EFC84328.1| pseudouridine synthase [Frankia sp. EUN1f]
          Length = 308

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 81/234 (34%), Positives = 120/234 (51%), Gaps = 1/234 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
                 R+ KV+A AGI SRR  E +I   RV+V+G ++      V      IEVDG  +
Sbjct: 66  PEAEGIRLQKVLAAAGIGSRRASEELIDAGRVRVDGEVVREQGRRVDPERAVIEVDGERV 125

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                      HKP G+++T +D  GR T+ D L    +R+  VGRLD ++EGLLL+TND
Sbjct: 126 VTRTGLVHLALHKPRGVLSTMADDRGRPTIADLLTEFGTRLFHVGRLDADSEGLLLVTND 185

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS    + Y V   G V +D    L+ G+ ++          +     S  
Sbjct: 186 GDLAHRLMHPSYGVQKTYLVEITGPVRKDLPRRLRSGVELEDGPVKVDSARIIDMAASRV 245

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + + L EG+N  +++V E     V+RL+R+S+GP  LGTL AG  R +++  +
Sbjct: 246 MMEIVLHEGRNHVVRRVMESVGHPVHRLVRVSFGPVALGTLRAGRARHLTRHEV 299


>gi|117928443|ref|YP_872994.1| ribosomal large subunit pseudouridine synthase B [Acidothermus
           cellulolyticus 11B]
 gi|117648906|gb|ABK53008.1| ribosomal large subunit pseudouridine synthase B [Acidothermus
           cellulolyticus 11B]
          Length = 269

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 84/235 (35%), Positives = 125/235 (53%), Gaps = 1/235 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ KV+A AG+ SRR  E +IA  RV+V+G+ + R  V V   T  I VDG  +  A  
Sbjct: 32  VRLQKVLAAAGVGSRRACEELIAAGRVEVDGVPVTRLGVRVDPQTAVIRVDGKRIPPATP 91

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +  +KP G+VTT SDP GR  V D +  +  RV  VGRLD ++EGLLLLTNDG L  
Sbjct: 92  FAYFALNKPRGVVTTMSDPRGRPCVGDLVADLPVRVFHVGRLDTDSEGLLLLTNDGRLTH 151

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS    + Y     G++ +  ++LL+ G+ +         V +  + G+   V V 
Sbjct: 152 RLTHPSHAVPKTYVADVEGRLGRTGVHLLRSGVDLADGPAQADAVRILERYGARTLVEVV 211

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           + EG+   ++++       V RL+R + GP  LG L  G+ R+++ + L E L  
Sbjct: 212 VHEGRTHLVRRMLAAVGHPVRRLVRTAIGPVALGQLRPGARRQLTPRELGELLDL 266


>gi|329121295|ref|ZP_08249922.1| ribosomal large subunit pseudouridine synthase B [Dialister
           micraerophilus DSM 19965]
 gi|327470229|gb|EGF15692.1| ribosomal large subunit pseudouridine synthase B [Dialister
           micraerophilus DSM 19965]
          Length = 240

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 71/238 (29%), Positives = 117/238 (49%), Gaps = 4/238 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K+I+ AG+ SRR+ E +I   RVKVNG  + +      S  D IEV+G  ++K   
Sbjct: 3   ERLQKIISHAGVCSRRKAEELIKDGRVKVNGHTVTKLGTEADSVRDCIEVNGKVIKKERL 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                      + +       R+        I  RV  VGRLD ++EGLLL+TNDG L  
Sbjct: 63  KYFLFNKPDKVITSMTDPAGRRTVADYF-SQIKERVFPVGRLDYHSEGLLLMTNDGDLDY 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVT 190
           +L  PS +  ++Y V   G+  +     + +G+ I         + +    ++ +  ++ 
Sbjct: 122 ILTHPSHEVYKIYEVVVRGKFSERLAEKMSEGVKIDSGITAPCDIEIISYDKEKNKTFLK 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + L EGKNREI+K+ E F++ V +L R+ Y    L  +  G+ R +S + +R     H
Sbjct: 182 MVLHEGKNREIRKMMEAFHFPVFKLERVGYSFLTLKGVSRGTFRSLSPEEVRRLYELH 239


>gi|224585957|ref|YP_002639756.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|224470485|gb|ACN48315.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
          Length = 289

 Score =  175 bits (443), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 62/292 (21%), Positives = 116/292 (39%), Gaps = 5/292 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R++K I+ +GI SRRE +R I Q  V +NG         V++ D ++V+G  +  
Sbjct: 3   TDTSIRLNKYISESGICSRREADRFIEQGNVFINGKRAA-IGDQVVAGDVVKVNGRLIES 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   L L      +    +  DG      +  +   R+  +GRLD +++GL+ LTN G 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRIFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     +  + +  +  G+ I G            +K +    
Sbjct: 122 LVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +      
Sbjct: 178 RITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
              ++    A      T ++     I +  +            +   K+K  
Sbjct: 238 RSSSEAKPKAKAKPKTTGIKRPVVAIEKSNEKARPTSSGKRFTSPGRKKKGR 289


>gi|56416014|ref|YP_153089.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|197364941|ref|YP_002144578.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|56130271|gb|AAV79777.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|197096418|emb|CAR62024.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
          Length = 289

 Score =  175 bits (443), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 62/292 (21%), Positives = 116/292 (39%), Gaps = 5/292 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R++K I+ +GI SRRE +R I Q  V +NG         V++ D ++V+G  +  
Sbjct: 3   TDTSTRLNKYISESGICSRREADRFIEQGNVFINGKRAA-IGDQVVAGDIVKVNGRLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   L L      +    +  DG      +  +   R+  +GRLD +++GL+ LTN G 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRIFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     +  + +  +  G+ I G            +K +    
Sbjct: 122 LVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +      
Sbjct: 178 RITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
              ++    A      T ++     I +  +            +   K+K  
Sbjct: 238 RSSSEAKPKAKAKPKTTGIKRPVVAIEKSNEKARPASSGKRFTSPGRKKKGR 289


>gi|149175162|ref|ZP_01853785.1| ribosomal large subunit pseudouridine synthase B [Planctomyces
           maris DSM 8797]
 gi|148846140|gb|EDL60480.1| ribosomal large subunit pseudouridine synthase B [Planctomyces
           maris DSM 8797]
          Length = 352

 Score =  175 bits (443), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 89/349 (25%), Positives = 153/349 (43%), Gaps = 20/349 (5%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGV 65
           V +     R+ K +A  G+ SRR  E  I   RV V+G ++      +      IEVDG 
Sbjct: 16  VDDESHLIRLQKFLAATGLGSRRHCEEYIETGRVSVDGDVITELGAKIDPETQFIEVDGE 75

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +R   R    L      L T +     R  V D  P+   R+ +VGRLD N+EGL+L+T
Sbjct: 76  RVRLQPRRYYLLNKPSGFLCTNNDPAGRRRVV-DLFPNDGQRLFTVGRLDENSEGLILVT 134

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA+ L  P  +  R Y V+  G   ++KL+ L+KG+  +   +    +    ++G 
Sbjct: 135 NDGELAQRLAHPRYRVARTYHVQVVGNPPREKLDELRKGVRFKEGVFRVSGLKYLKKQGK 194

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           +A++ + L EG+NREI+++      KV +L+RI +GP  LG L  G +R +S   L++  
Sbjct: 195 SAFLELTLHEGQNREIRRMMARIGHKVIQLVRIRFGPLNLGKLKTGESRRLSDTELKKLR 254

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                + +              +R R    +  P      +K+  +++G        +  
Sbjct: 255 QLLNEKHS------------PDIRHRKGKKNAAPAKTRAPRKSVGKRSGERGAAAGKSVS 302

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            R +        + +       +G++       P    +R +   + K+
Sbjct: 303 ERISGGKKTGGKRSV------STGRKPAADSSKPKTTGRRIIGDVAEKR 345


>gi|253581558|ref|ZP_04858783.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           varium ATCC 27725]
 gi|251836628|gb|EES65163.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           varium ATCC 27725]
          Length = 236

 Score =  175 bits (443), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 66/230 (28%), Positives = 113/230 (49%), Gaps = 1/230 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K +A  GIASRREV++MI +  +K+NG       + V   D I + G  + K  
Sbjct: 2   EEMRINKYLASLGIASRREVDKMIEEGSIKINGEKAT-PGIKVSDKDEIYIRGKKIEKHT 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +++        V + S  D       +L +   R+  +GRLD NT GL++LTNDG L 
Sbjct: 61  EKKVYYILNKPLEVLSSSKDDRGRKTVVDLINCKERIFPIGRLDYNTSGLIILTNDGELF 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P  +  + Y V+  G++ ++ + LLK G+ +         V +  ++     + V
Sbjct: 121 NRIIHPKAEIFKEYYVKVLGEIKENNVELLKNGVELDDGITLPANVRILRREKGKTELLV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +REG+NR+++++ +  N  V  L R   G   LG L  G  RE++   +
Sbjct: 181 AIREGRNRQVRRMMDKINHPVITLRREKIGNLSLGNLKLGEYRELTNDEI 230


>gi|206977746|ref|ZP_03238637.1| RNA pseudouridine synthase family protein [Bacillus cereus
           H3081.97]
 gi|217962032|ref|YP_002340602.1| RNA pseudouridine synthase family protein [Bacillus cereus AH187]
 gi|222098014|ref|YP_002532071.1| tRNA pseudouridine synthase a [Bacillus cereus Q1]
 gi|229141278|ref|ZP_04269816.1| RNA pseudouridine synthase [Bacillus cereus BDRD-ST26]
 gi|206744047|gb|EDZ55463.1| RNA pseudouridine synthase family protein [Bacillus cereus
           H3081.97]
 gi|217063968|gb|ACJ78218.1| RNA pseudouridine synthase family protein [Bacillus cereus AH187]
 gi|221242072|gb|ACM14782.1| tRNA pseudouridine synthase A [Bacillus cereus Q1]
 gi|228642059|gb|EEK98352.1| RNA pseudouridine synthase [Bacillus cereus BDRD-ST26]
          Length = 229

 Score =  175 bits (443), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 108/230 (46%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTH-GALVSDGDRVTIDGQVIVKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D    + +     +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAADHIEDNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVTRV----DQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L 
Sbjct: 174 LTQGMNRQIRRMSRVFGFTVTKLKRVRIMNIELNELEVGKWRSVTAEELE 223


>gi|54297357|ref|YP_123726.1| hypothetical protein lpp1402 [Legionella pneumophila str. Paris]
 gi|53751142|emb|CAH12553.1| hypothetical protein lpp1402 [Legionella pneumophila str. Paris]
          Length = 248

 Score =  175 bits (443), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 79/240 (32%), Positives = 124/240 (51%), Gaps = 7/240 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--- 68
           + +R+ K++++AG+ SRRE+ER I    V+VNG   +    +   +D I V G  +    
Sbjct: 2   SSERLQKILSQAGLGSRREMERWIDNGWVQVNGKPAK-LGDSAGPSDKISVKGKLIPNPL 60

Query: 69  --KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
             K     L  +     + + H     ++   +       R + VGRLD+NT GLL+ TN
Sbjct: 61  KGKQNIRVLLYHKPVGEVSSRHDPKFEKTVFDNLPHLRQGRWVQVGRLDLNTSGLLIFTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G LA  L  P     R Y VR HGQV Q+ LN L KG+++        ++     +G+N
Sbjct: 121 NGELANQLMHPKYGLEREYAVRVHGQVSQESLNNLLKGVMLDDGLGKFTKIQFRGGEGTN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
           +W  V L EG+NRE+++++E    +V+RLIRI YG   +   L  G   E++ K + E L
Sbjct: 181 SWYHVTLNEGRNREVRRLWESQGVEVSRLIRIRYGMLTMPRFLSRGQFYELTPKEVTEFL 240


>gi|114705781|ref|ZP_01438684.1| High mobility group proteins HMG-I and HMG-Y:Pseudouridine
           synthase, Rsu:RNA-binding S4:Pseudouridine synthase
           [Fulvimarina pelagi HTCC2506]
 gi|114538627|gb|EAU41748.1| High mobility group proteins HMG-I and HMG-Y:Pseudouridine
           synthase, Rsu:RNA-binding S4:Pseudouridine synthase
           [Fulvimarina pelagi HTCC2506]
          Length = 639

 Score =  175 bits (443), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 165/349 (47%), Positives = 215/349 (61%), Gaps = 8/349 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +ARAGIASRR+ E MI   RVKVNG +++  A++V  TD IEVDG  L +AERT
Sbjct: 184 MRIARRLARAGIASRRDAEAMIVDGRVKVNGKIIDSPALDVKPTDRIEVDGALLPQAERT 243

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWL+HKP G VTT+ DP+GR TVFD LP    RV+S+GRLDINTEGLLLLTNDGGL+RV
Sbjct: 244 RLWLFHKPAGTVTTNKDPEGRRTVFDMLPEDMPRVLSIGRLDINTEGLLLLTNDGGLSRV 303

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELPST WLR YRVR HG + Q KL+ L+ GI + G+ YG ++ TLD ++GSN W+T+GL
Sbjct: 304 LELPSTGWLRRYRVRAHGSITQAKLDELRNGISVDGVFYGAIEATLDREQGSNVWITLGL 363

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNRE+K V      +VNRLIR+SYGPFQLG L  GS REV  + LR+QLG  L+EEA
Sbjct: 364 REGKNREVKNVLGALGLEVNRLIRLSYGPFQLGDLAEGSVREVKGRTLRDQLGDRLVEEA 423

Query: 254 QVNLDAP---IYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL-----ATPV 305
            V+ D P    +S+  +   +    S+  D  +   K   +  G  K+++        P 
Sbjct: 424 GVDFDGPINKPFSNAPVEGRQDARPSKKSDWVSAGGKVDRKTFGEKKREEALGRLDTKPR 483

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +          +G   S        E+   +      K   R     +
Sbjct: 484 GKFGDKPGDDRRRGDRRSDGPKRSFGEDRGGKGGGRFDKHDKREGFGDR 532



 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 18/100 (18%), Positives = 27/100 (27%), Gaps = 2/100 (2%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
                      +   R   +   E   D     ++   + G  +      P  +    SN
Sbjct: 504 PKRSFGEDRGGKGGGRFDKHDKREGFGDRVSGARSGGDRPGGDRDGPSRKPEGQGRRMSN 563

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           VWMA G       D G R            KR+L     +
Sbjct: 564 VWMAPGSKP--ERDPGARPAKTDGDGPKTGKRALADPKRR 601


>gi|114561788|ref|YP_749301.1| 23S rRNA pseudouridine synthase F [Shewanella frigidimarina NCIMB
           400]
 gi|114333081|gb|ABI70463.1| ribosomal large subunit pseudouridine synthase F [Shewanella
           frigidimarina NCIMB 400]
          Length = 293

 Score =  175 bits (443), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 66/302 (21%), Positives = 132/302 (43%), Gaps = 9/302 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + E+ T  R++K I+ +GI SRRE +R I Q  V +NG   +    +V   D ++V+G  
Sbjct: 1   MSESAT--RLNKYISESGICSRREADRYIEQGNVFINGKRAK-IGDSVEFGDKVKVNGHD 57

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +   +   L        +    +  +       +  +   RV  +GRLD +++GL+ LT+
Sbjct: 58  IAPRDEADLVFIALNKPVGIVSTTENTERDNIVDFVNHSERVFPIGRLDKDSQGLIFLTS 117

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G L   +        + Y V  +  + +  L  ++ G+ + G+     +V    ++ S 
Sbjct: 118 NGDLVNKILRAGNNHDKEYVVTVNKPITEAFLQGMRAGVPMLGVITKKCKV----EQVST 173

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               + L +G NR+I+++ E FN++V +L R S     L  L  G  R++ ++ L   + 
Sbjct: 174 FVFKIILVQGLNRQIRRMCEHFNFEVTKLERQSIMNVSLKGLPVGEWRDLDEQELSTLMK 233

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              +E +   +      ++           E P+ F + +    +K   +K K   +   
Sbjct: 234 L--IEHSSSEVKNAPKKAKKKPTQSLRDKIEGPEHFMQGRGAKPKKPAANKGKPSHSRKP 291

Query: 307 RR 308
           +R
Sbjct: 292 KR 293


>gi|329576942|gb|EGG58425.1| pseudouridylate synthase [Enterococcus faecalis TX1467]
          Length = 257

 Score =  175 bits (443), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 63/248 (25%), Positives = 109/248 (43%), Gaps = 5/248 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           I + G  L   +     L+     +  T    D             + +  VGRLD +TE
Sbjct: 61  IALMGEILTYQKFFYYMLHKPQGVISATEDQRDETVIDLLTDQDYRADLFPVGRLDKDTE 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVT 178
           GLLLLTNDG LA  L  P     + Y     G V  +   L  +G  +  G      ++ 
Sbjct: 121 GLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEMVKPSRLV 180

Query: 179 L--DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTRE 235
           +    ++   + V + ++EG+  ++K++       V  L R+  G   L   L  G  R 
Sbjct: 181 IETINEEEGTSVVRLVIQEGEFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEYRP 240

Query: 236 VSKKILRE 243
           +++  L++
Sbjct: 241 LTEAELQQ 248


>gi|320323233|gb|EFW79321.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. glycinea str. B076]
 gi|320329736|gb|EFW85725.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. glycinea str. race 4]
 gi|330881434|gb|EGH15583.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. glycinea str. race 4]
          Length = 408

 Score =  175 bits (443), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 91/354 (25%), Positives = 140/354 (39%), Gaps = 15/354 (4%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG         V   D I
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDATV-GQRVDLHDAI 62

Query: 61  EVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            VDG  +++ E     R  +        + T        +           R I++GRLD
Sbjct: 63  SVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           INT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++       
Sbjct: 123 INTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPARFT 182

Query: 176 QVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE+S+  + + L   +  +          + + + R +      +           +   
Sbjct: 243 REMSQYEV-DILAAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVRTLRPAAGA 301

Query: 294 GLSKQKKLATP-----VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
             +  +    P        R    +                +       S   P
Sbjct: 302 PATGDRAPRQPQITGSERDRPRGGDSTQRPSPRKDSGKPGSRAPRPADNSRGTP 355


>gi|188587870|ref|YP_001919826.1| RNA pseudouridine synthase family protein [Clostridium botulinum E3
           str. Alaska E43]
 gi|188498151|gb|ACD51287.1| RNA pseudouridine synthase family protein [Clostridium botulinum E3
           str. Alaska E43]
          Length = 238

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 110/231 (47%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K+I+  G  SR+E + +  +  ++V+G +++ ++VN+      ++++G  +   + 
Sbjct: 2   ERLDKIISNLGYGSRKEAKLLAKKGLIEVDGKIIKDSSVNIDPEKSIVKINGEEIFYRKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  TH   D        L         VGRLD +T GLLLLTNDG    
Sbjct: 62  IYLMMNKPTGVISATHDSKDETVIDLLELDHQIFDPFPVGRLDKDTVGLLLLTNDGDFNH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            +  P     +VY  +   +V++      KKG+V+       + ++ + +     + V +
Sbjct: 122 RMISPKWHVDKVYYAKIDKEVNEKDQEAFKKGVVLDDGYKCLEAKLDIISASPEGSEVRI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            ++EGK  ++K++FE  + KV  L R  +G   L   L  G  RE+S + L
Sbjct: 182 TIQEGKYHQVKRMFEARDKKVVYLKREEFGGLILDETLEEGEYRELSDEEL 232


>gi|260905260|ref|ZP_05913582.1| pseudouridine synthase, Rsu [Brevibacterium linens BL2]
          Length = 238

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 72/234 (30%), Positives = 116/234 (49%), Gaps = 1/234 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A AG+ SRR  E++I   RV+V+G ++      +   T  + VD V +    +
Sbjct: 1   MRLQKILAEAGLGSRRACEQLILDGRVEVDGSIVTELGTRIDTETQAVYVDAVRISTQTQ 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G+V+T SDPDGR  + D + +   R+  VGRLD  TEGL+LLTNDG L+ 
Sbjct: 61  KVYLVLNKPAGVVSTMSDPDGRPCLADYVKNRVDRLFHVGRLDTETEGLILLTNDGELSN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + Y  +  GQ+ +D  + LK G+ +           L       + V + 
Sbjct: 121 RLAHPRYEIPKTYLAQVRGQLAKDVGSRLKAGMDLDDGFVKVDSFKLVDSTPGKSVVELT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L  G+NR ++++ +     V RL+R  +GP  L     G  R +    + E   
Sbjct: 181 LHSGRNRIVRRLLKEVGHPVERLVRTKFGPITLDEQRQGKIRPLRSDEIGELFE 234


>gi|70728994|ref|YP_258728.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           fluorescens Pf-5]
 gi|68343293|gb|AAY90899.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           fluorescens Pf-5]
          Length = 396

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 87/360 (24%), Positives = 146/360 (40%), Gaps = 9/360 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           D+N  +     +++ KV+AR G+ SRR+VE  I+Q R+KVNG       + V   D I +
Sbjct: 5   DQNDQEIRPAGEKLQKVLARIGVGSRRDVESWISQGRIKVNGKEAT-LGLRVDLHDAISI 63

Query: 63  DGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           DG  +++ E     R  +        + T        +           R I++GRLDIN
Sbjct: 64  DGKVIKREEAAESVRRVIMYNKPDGEICTRDDPEGRPTVFDKLPRPREGRWINIGRLDIN 123

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLL+ T DG LA  L  PS +  R Y VR  G+VD + +  LK G++++        +
Sbjct: 124 TTGLLMFTTDGELANRLMHPSYEMDREYAVRVRGEVDDEMIERLKAGVMLEDGPAKFTDI 183

Query: 178 TLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTRE 235
                 +G N W    + EG+NRE+++++E     V+RL R+ +GP  L   L  G  RE
Sbjct: 184 QQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLNSDLPMGRWRE 243

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +S+  +        L    +         +     R +       +  R  + ++     
Sbjct: 244 MSQYEVDVLSAEVGLTPVAMPQLNAKSKDKLERMQRKSSRPVGKSERVRTLRPANGSAAT 303

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSG-QREENHRRSPSFPSKRSLRRTSAKK 354
            +  +       R          G   S        R       P+   + +   + +K+
Sbjct: 304 PRVSREPQIEGERPGRKPAARPDGERGSRAPRPATGRGTPVADRPADTKRPAKPASKSKR 363


>gi|197294800|ref|YP_001799341.1| 16S rRNA pseudouridylate synthase [Candidatus Phytoplasma
           australiense]
 gi|171854127|emb|CAM12116.1| 16S rRNA pseudouridylate synthase [Candidatus Phytoplasma
           australiense]
          Length = 243

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 71/233 (30%), Positives = 119/233 (51%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA A + SRR+VE +I Q+RVKVN  ++ +    V ++D + +D V ++K    
Sbjct: 2   ERLQKFIASANLVSRRKVEILILQKRVKVNNQVVSQLGTKVKASDVVTLDDVLIKKTTLF 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      L TT  D    + +     S   R+ SVGRLD NT GL+L+TNDG + + 
Sbjct: 62  YYLLNKPQGYLSTTKDDKKRPTVLDLIKESQNQRLYSVGRLDFNTTGLILITNDGEMTQK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----GSNAWV 189
           L  P     + Y V+ +  + +  L+LL KG++I        +     ++      + W+
Sbjct: 122 LTHPCFGIPKEYHVKINVFLTKKDLSLLLKGVIIDHNYLSIPKEINILKQRYLPKPSTWL 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + + EGKNR+I+K+ E   ++V +L R SY    +  L  G+ R +    ++
Sbjct: 182 KIVITEGKNRQIRKMMEALGYQVLKLRRYSYAFLTIEGLKTGAYRLLKIHEIK 234


>gi|146296790|ref|YP_001180561.1| pseudouridine synthase [Caldicellulosiruptor saccharolyticus DSM
           8903]
 gi|145410366|gb|ABP67370.1| ribosomal small subunit pseudouridine synthase A
           [Caldicellulosiruptor saccharolyticus DSM 8903]
          Length = 232

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 51/228 (22%), Positives = 104/228 (45%), Gaps = 7/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ + +A +G  +R EV+R+I +  VKVNG   +   + +    D ++V    +   +R
Sbjct: 1   MRLDRFLAHSGFGTRSEVKRLIKKGLVKVNGKQAKSPDLKIDEDKDVVQVGEEIVELQKR 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      + +                  +  + +VGRLD + EGLL++TN+G    
Sbjct: 61  VYIMMNKPQGYVCSNDDPLSPTIFSLIPENLKYRNLHTVGRLDKDAEGLLIITNNGEYTH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V+   +++++K+ + + G+V+         + T+      +  V++
Sbjct: 121 KVISPKKHIEKEYIVKLEKELNREKIKVFEDGVVLDDGYKTLPAKYTIL----DDFTVSL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            + EGK  +IK++FE    KV  L R+  G  +L   L  G  + + +
Sbjct: 177 TIYEGKYHQIKRMFESIGNKVVYLKRVRIGRLKLDENLNPGEYKVLDE 224


>gi|322615369|gb|EFY12289.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322618430|gb|EFY15319.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322622159|gb|EFY19009.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322627229|gb|EFY24021.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322631190|gb|EFY27954.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322637592|gb|EFY34293.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322642558|gb|EFY39155.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
 gi|322643574|gb|EFY40129.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322648310|gb|EFY44769.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322654619|gb|EFY50939.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322659579|gb|EFY55822.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
 gi|322662213|gb|EFY58429.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322666043|gb|EFY62221.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322672462|gb|EFY68573.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322675891|gb|EFY71962.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322680375|gb|EFY76413.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322684730|gb|EFY80734.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|323195994|gb|EFZ81160.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323197076|gb|EFZ82217.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323202220|gb|EFZ87270.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323206320|gb|EFZ91282.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323213332|gb|EFZ98134.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
 gi|323215701|gb|EGA00445.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323222124|gb|EGA06510.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323226535|gb|EGA10741.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323229161|gb|EGA13290.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323236230|gb|EGA20306.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323237651|gb|EGA21712.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323241684|gb|EGA25713.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323248169|gb|EGA32106.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2009159199]
 gi|323258439|gb|EGA42116.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008283]
 gi|323259719|gb|EGA43353.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
 gi|323265992|gb|EGA49488.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008285]
 gi|323270434|gb|EGA53882.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008287]
          Length = 289

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 63/292 (21%), Positives = 116/292 (39%), Gaps = 5/292 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R++K I+ +GI SRRE +R I Q  V +NG         V+S D ++V+G  +  
Sbjct: 3   TDTSTRLNKYISESGICSRREADRFIEQGNVFINGKRAA-IGDQVVSGDVVKVNGRLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   L L      +    +  DG      +  +   R+  +GRLD +++GL+ LTN G 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGERDNIVDFVNYSKRIFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     +  + +  +  G+ I G            +K +    
Sbjct: 122 LVNKILRVGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +      
Sbjct: 178 RITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
              ++    A      T ++     I +  +            +   K+K  
Sbjct: 238 RSSSEAKPKAKAKPKTTGIKRPVVAIEKSNEKARPTSSGKRFTSPGRKKKGR 289


>gi|307243938|ref|ZP_07526063.1| pseudouridylate synthase [Peptostreptococcus stomatis DSM 17678]
 gi|306492760|gb|EFM64788.1| pseudouridylate synthase [Peptostreptococcus stomatis DSM 17678]
          Length = 243

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 71/232 (30%), Positives = 116/232 (50%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA-E 71
            R++K IA AGIASRR+ E ++++ R+KVNG ++      V    D +E DG  +    E
Sbjct: 1   MRINKYIASAGIASRRKAENLVSEGRIKVNGQIIYDLGYQVNEDKDIVEYDGKKIDINSE 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +    L +KP G +T+  D  GR  V D +  I  R+  VGRLD  T GLLL+TNDG L 
Sbjct: 61  KLVYILLNKPEGYITSSKDQFGRKDVMDLVTDIKERIYPVGRLDYETSGLLLMTNDGDLT 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWV 189
             +  P  +  + Y     G    ++L   + G+ I+       ++ +     K + +  
Sbjct: 121 YKITHPKHEITKTYIASVKGIPTSEELERFENGLEIEDYVTSKAKIRVLKTDVKKNYSVC 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V + EG+NR+++K+F   N  V  L R++ G   +  +  G  R ++   +
Sbjct: 181 RVSIHEGRNRQVRKMFNAINHPVMNLKRVALGKISVNNVEVGKYRHLTDDEV 232


>gi|227325901|ref|ZP_03829925.1| 16S rRNA pseudouridylate synthase A [Pectobacterium carotovorum
           subsp. carotovorum WPP14]
          Length = 231

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 109/231 (47%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  QRV V+G +++  A  +    ++E DG PL++    
Sbjct: 1   MRLDKFLSQQLEISRSLVARELHAQRVTVDGEVVKSGAFKLSPEHNVEFDGEPLKQQNGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+LLT+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTILYFMDVPVAYKLHAAGRLDIDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  Q  + Y V     + +D       G+ +                +K ++  V +
Sbjct: 121 ITSPKHQCEKTYLVTLEQPLAEDTAAQFTAGVQLHNEKNLTKPAT----LEKITDYVVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F     +V  L R   G   L   L  G  RE+S + +
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVVELHRERIGGIYLDSELEPGEYRELSAEEI 227


>gi|146321792|ref|YP_001201503.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Streptococcus suis 98HAH33]
 gi|253752593|ref|YP_003025734.1| ribosomal small subunit pseudouridine synthase B [Streptococcus
           suis SC84]
 gi|253754419|ref|YP_003027560.1| ribosomal small subunit pseudouridine synthase B [Streptococcus
           suis P1/7]
 gi|253756353|ref|YP_003029493.1| ribosomal small subunit pseudouridine synthase B [Streptococcus
           suis BM407]
 gi|145692598|gb|ABP93103.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           Pseudouridylate synthase [Streptococcus suis 98HAH33]
 gi|251816882|emb|CAZ52530.1| putative ribosomal small subunit pseudouridine synthase B
           [Streptococcus suis SC84]
 gi|251818817|emb|CAZ56658.1| putative ribosomal small subunit pseudouridine synthase B
           [Streptococcus suis BM407]
 gi|251820665|emb|CAR47426.1| putative ribosomal small subunit pseudouridine synthase B
           [Streptococcus suis P1/7]
 gi|319759007|gb|ADV70949.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Streptococcus suis JS14]
          Length = 242

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 105/234 (44%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ SR EV++++  ++V VNG +       +    D I V G  L     
Sbjct: 1   MRLDKFLVDCGVGSRTEVKKLLKNKQVTVNGQVETSPKQQINEKKDQIAVAGQVLSHETF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  D         +  +    V  VGRLDI+T GLLLLTN G LA 
Sbjct: 61  VYYLLNKPKGVISATEDDHHRTVLDLLDNTARQKEVFPVGRLDIDTHGLLLLTNKGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            +  P     ++YR +  G + Q+ +     GI ++       Q+T+ +   +   + V 
Sbjct: 121 AMLSPKKHVDKLYRAQVDGIMTQEDVERFAAGIELKDFTCQPAQLTILSTDEAKQTSLVD 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           + +REGK  +IK++ +     V  L R++ GP +L   L  G  R ++   L++
Sbjct: 181 ITIREGKFHQIKRMVQACGKTVTDLQRLTMGPLRLDPKLALGEYRRLTAAELKQ 234


>gi|167552572|ref|ZP_02346325.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|168263493|ref|ZP_02685466.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|200389083|ref|ZP_03215695.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Virchow str. SL491]
 gi|199606181|gb|EDZ04726.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Virchow str. SL491]
 gi|205322854|gb|EDZ10693.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|205348000|gb|EDZ34631.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
          Length = 289

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 62/292 (21%), Positives = 116/292 (39%), Gaps = 5/292 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R++K I+ +GI SRRE +R I Q  V +NG         V++ D ++V+G  +  
Sbjct: 3   TDTSTRLNKYISESGICSRREADRFIEQGNVFINGKRAA-IGDQVVAGDVVKVNGRLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   L L      +    +  DG      +  +   R+  +GRLD +++GL+ LTN G 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRIFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     +  + +  +  G+ I G            +K +    
Sbjct: 122 LVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +      
Sbjct: 178 RITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
              ++    A      T ++     I +  +            +   K+K  
Sbjct: 238 RSSSEAKPKAKAKPKTTGIKRPVVAIEKSNEKARPTSSGKRFTSPGRKKKGR 289


>gi|315304474|ref|ZP_07874754.1| ribosomal small subunit pseudouridine synthase A [Listeria ivanovii
           FSL F6-596]
 gi|313627161|gb|EFR96014.1| ribosomal small subunit pseudouridine synthase A [Listeria ivanovii
           FSL F6-596]
          Length = 233

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 100/231 (43%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SRREV+ ++    V VNG + + + + V    D I V G P+   E 
Sbjct: 1   MRLDKLLSHTGYGSRREVKPLLKSGSVTVNGTIQKDSKLQVNPEKDQITVHGNPVVYQEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T  +               +    VGRLD +TEGLL++TNDG LA 
Sbjct: 61  VYFMLHKPQNVVSATEDNLSETVIDLLAQEDTLTNPFPVGRLDKDTEGLLIITNDGTLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y  +  G V    +   + GI +          + +     + + + V
Sbjct: 121 NLLSPKKHIDKTYYAKIEGNVTVADIEAFQTGITLDDGYTCKPAHLEII----TPSEINV 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            ++EGK  ++K++F      V  L RIS G  +L   L  G  R ++ + L
Sbjct: 177 TIQEGKFHQVKRMFAATGKTVTYLKRISMGKLKLDEALRLGEYRSLTDEEL 227


>gi|251779159|ref|ZP_04822079.1| RNA pseudouridine synthase family protein [Clostridium botulinum E1
           str. 'BoNT E Beluga']
 gi|243083474|gb|EES49364.1| RNA pseudouridine synthase family protein [Clostridium botulinum E1
           str. 'BoNT E Beluga']
          Length = 238

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 110/231 (47%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K+I+  G  SR+E + +  +  ++V+G +++ ++VN+      ++++G  +   + 
Sbjct: 2   ERLDKIISNLGYGSRKEAKLLAKKGLIEVDGKIIKDSSVNIDPEKSIVKINGEEIFYRKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  TH   D        L         VGRLD +T GLLLLTNDG    
Sbjct: 62  IYLMMNKPTGVISATHDSKDETVIDLLELDHQIFDPFPVGRLDKDTVGLLLLTNDGDFNH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            +  P     +VY  +   +V++      KKG+V+       + ++ + +     + V +
Sbjct: 122 RMISPKWHVDKVYYAKIDKEVNEKDQEAFKKGVVLDDGYKCLEAKLDIISASTEGSEVRI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            ++EGK  ++K++FE  + KV  L R  +G   L   L  G  RE+S + L
Sbjct: 182 TIQEGKYHQVKRMFEARDKKVVYLKREEFGGLILDETLEEGEYRELSDEEL 232


>gi|116629857|ref|YP_815029.1| 16S rRNA uridine-516 pseudouridylate synthase related
           pseudouridylate synthase [Lactobacillus gasseri ATCC
           33323]
 gi|116095439|gb|ABJ60591.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           gasseri ATCC 33323]
          Length = 245

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 66/238 (27%), Positives = 105/238 (44%), Gaps = 4/238 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E     R+ K +A   + SR+EV  +I ++ V VNG L+      V  TD + VDG  + 
Sbjct: 8   EKDIEMRIDKYLANMNVGSRKEVHSLIKKKVVTVNGELVTIPKQQVKETDLVAVDGNKIA 67

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             +     L      +  T                 +  +  VGRLD +T GLLLLTNDG
Sbjct: 68  YQQYHYFLLNKPKGVISATEDRSQQTVISLLKTKDRYQGIAPVGRLDKDTTGLLLLTNDG 127

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN- 186
            LA  L  P+    +VYR +  G  D +      +G+++  G      ++ +  Q   N 
Sbjct: 128 ALAHELLAPNKHVAKVYRAKIAGVPDPETAKKFAQGLILGDGTKLKPAKLKILKQDQDNN 187

Query: 187 -AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
            + + + ++EGK  +IK++F     KV  L R+S G   L   L  G  +E+    ++
Sbjct: 188 LSQIEIQIQEGKYHQIKRMFGAVGMKVLELDRVSMGKLHLPADLKRGEYKEIDLAEIK 245


>gi|66046810|ref|YP_236651.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. syringae
           B728a]
 gi|63257517|gb|AAY38613.1| Pseudouridine synthase, Rsu [Pseudomonas syringae pv. syringae
           B728a]
 gi|330897271|gb|EGH28690.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. japonica str.
           M301072PT]
 gi|330972281|gb|EGH72347.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. aceris str.
           M302273PT]
          Length = 409

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 90/355 (25%), Positives = 140/355 (39%), Gaps = 16/355 (4%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG         V   D I
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDAT-LGQRVDLHDAI 62

Query: 61  EVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            VDG  +++ E     R  +        + T        +           R I++GRLD
Sbjct: 63  SVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           INT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++       
Sbjct: 123 INTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPARFT 182

Query: 176 QVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE+S+  + + L   +  +          + + + R +      +           +   
Sbjct: 243 REMSQYEV-DILAAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVRTLRPAAGA 301

Query: 294 GLSKQKKLATPV------HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
             +  ++             R    +                +       S   P
Sbjct: 302 PATGGERAPRQPQITGSERDRPRGGDSTQRPSPRKDSGKPGSRAPRPADNSRGTP 356


>gi|326773388|ref|ZP_08232671.1| ribosomal large subunit pseudouridine synthase B [Actinomyces
           viscosus C505]
 gi|326636618|gb|EGE37521.1| ribosomal large subunit pseudouridine synthase B [Actinomyces
           viscosus C505]
          Length = 324

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 86/246 (34%), Positives = 123/246 (50%), Gaps = 10/246 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
           + QR+ KV+A AG+ASRR  E++IA  RV V+G+ +  A V V   T  I VDG  +   
Sbjct: 76  SGQRLQKVLAHAGVASRRACEQLIADGRVSVDGVTVTEAGVRVDPLTQEIRVDGSRILTN 135

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---------ISVGRLDINTEGL 121
                 + HKP G+VTT  DP+GR TV        +           + VGRLD  TEGL
Sbjct: 136 PELITLMLHKPAGVVTTMEDPEGRPTVAQYGRDYLTEHPELPDSLRLVHVGRLDTETEGL 195

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLL+NDG L+  L  PS +  + Y     GQV+      L++GI ++       +VT+  
Sbjct: 196 LLLSNDGELSHRLMHPSFEIAKTYVAIVEGQVEPWVPRKLRRGIELEDGEAKADRVTVKD 255

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                + V + L  GKNR ++++ +     V RL R   GP +LG L  G TR +S + +
Sbjct: 256 SGPRGSIVEITLHSGKNRIVRRMLDAVGHPVTRLARTRLGPLRLGNLRPGQTRPLSGEEI 315

Query: 242 REQLGP 247
                 
Sbjct: 316 AALQQE 321


>gi|330991270|ref|ZP_08315221.1| Putative RNA pseudouridine synthase [Gluconacetobacter sp. SXCC-1]
 gi|329761289|gb|EGG77782.1| Putative RNA pseudouridine synthase [Gluconacetobacter sp. SXCC-1]
          Length = 259

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 133/244 (54%), Positives = 173/244 (70%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +D +         R++K +AR+G+ASRR+ ERMIA+ RV++NG ++   A  V + D ++
Sbjct: 3   QDHSSSASAERGDRIAKWLARSGVASRRDAERMIAEGRVQLNGAVVNHPATFVGAGDIVQ 62

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           V+G  +   +RTRLW YHKP GLVTTH DP+GR TVF++LP    RVISVGRLD+N+EGL
Sbjct: 63  VNGSVVGAPDRTRLWRYHKPDGLVTTHRDPEGRPTVFESLPPGLPRVISVGRLDLNSEGL 122

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDG LAR LELPS  W+R YRVR  G VD+  L  L +G    G+ YG ++  LD+
Sbjct: 123 LLLTNDGELARRLELPSNGWIRRYRVRVFGVVDERMLASLARGSEFDGVRYGPIEAHLDS 182

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            KG NAW+TV LREGKNRE++KV +  N  V+RLIR SYGPFQLGTL  G   EV+ K++
Sbjct: 183 AKGDNAWLTVSLREGKNREVRKVMQGLNLHVSRLIRTSYGPFQLGTLTRGELEEVTGKVI 242

Query: 242 REQL 245
           REQ+
Sbjct: 243 REQV 246


>gi|323254500|gb|EGA38311.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
          Length = 289

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 63/292 (21%), Positives = 116/292 (39%), Gaps = 5/292 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R++K I+ +GI SRRE +R I Q  V +NG         V+S D ++V+G  +  
Sbjct: 3   TDTSTRLNKYISESGICSRREADRFIEQGNVFINGKRAA-IGDQVVSGDVVKVNGRLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   L L      +    +  DG      +  +   R+  +GRLD +++GL+ LTN G 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGERDNIVDFVNYSKRIFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     +  + +  +  G+ I G            +K +    
Sbjct: 122 LVNKILRVGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +      
Sbjct: 178 RITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
              ++    A      T ++     I +  +            +   K+K  
Sbjct: 238 RSSSEAKPKAKAKPKTTGIKRPVVAIEKSNEKARPTSSGKRLTSPGRKKKGR 289


>gi|325662260|ref|ZP_08150875.1| hypothetical protein HMPREF0490_01613 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|331086071|ref|ZP_08335154.1| hypothetical protein HMPREF0987_01457 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|325471512|gb|EGC74733.1| hypothetical protein HMPREF0490_01613 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|330406994|gb|EGG86499.1| hypothetical protein HMPREF0987_01457 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 255

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 64/243 (26%), Positives = 115/243 (47%), Gaps = 7/243 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K ++ AG+ SRRE +R+I   RV V+G       + V     + V    ++K +
Sbjct: 14  ESVRLNKFLSEAGVCSRREADRLIESGRVTVDGRRA-EMGMRVTKDQEVCVGKKVIQKKD 72

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R  L   +KP G+V T    + ++ +           I  GRLD ++EGLLL+TN+G + 
Sbjct: 73  RMVLLAVNKPTGIVCTEEKREKKNIIRFLNYPTRITYI--GRLDKDSEGLLLMTNNGDII 130

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y+V  + +V ++ +  + +G+ I        +V    +K       +
Sbjct: 131 NKMMRAGNCHEKEYKVTVNKEVTKEFVRKMSEGVPILDTVTRPCKV----EKTGKYKFRI 186

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ E+F ++V RL R+     +LG L +G  REV+ + L E        
Sbjct: 187 ILTQGLNRQIRRMCEYFGYQVTRLERVRVMNIELGNLKSGEYREVTGRELDELYEQLKGS 246

Query: 252 EAQ 254
              
Sbjct: 247 SNN 249


>gi|262067505|ref|ZP_06027117.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           periodonticum ATCC 33693]
 gi|291378768|gb|EFE86286.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           periodonticum ATCC 33693]
          Length = 234

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 73/231 (31%), Positives = 130/231 (56%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--RKAE 71
            R++K ++  GIASRR +++ I + R+KVNG++     ++V   D I +D   +  +K E
Sbjct: 1   MRINKFLSSLGIASRRAIDKYIEEGRIKVNGVIAST-GIDVTEDDEICIDDKKIETKKIE 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               ++ +KP+ +++  SD  GR TV D + +       +GRLD  T GL+LLTNDG L 
Sbjct: 60  EKVYFMLNKPLEVLSASSDDRGRKTVVDLIKTDKRI-FPIGRLDYMTSGLILLTNDGELF 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P ++  + Y ++  G+V +++++ LKKG++++       +V       +   + +
Sbjct: 119 NRLVHPKSEIYKKYYIKVFGEVKKEEIDELKKGVLLEDGKTLPAKVAGIKYDKNKTSMYI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +REG+NR+I+++ E F +KV  L R   G   LG L  G  RE++K+ + 
Sbjct: 179 SIREGRNRQIRRMIEKFGYKVLMLRREKIGELSLGDLKEGKYRELTKEEIE 229


>gi|15674222|ref|NP_268397.1| ribosomal small subunit pseudouridine synthase A [Lactococcus
           lactis subsp. lactis Il1403]
 gi|12725309|gb|AAK06338.1|AE006453_2 ribosomal small subunit pseudouridine synthase A [Lactococcus
           lactis subsp. lactis Il1403]
          Length = 273

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 102/241 (42%), Gaps = 9/241 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKA 70
              R+ K +A +G+ SR EV+ ++ + RV V G +       V      +  DG  L   
Sbjct: 30  KDMRLDKFLAESGLGSRSEVKILLKKGRVTVAGEVQRDGRFQVDKNSRQVAFDGEILDYQ 89

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E     L      +  T  +         +       +  VGRLD NTEGLL+LTNDG L
Sbjct: 90  EYYYYLLNKPQGLVSATKDNLFKTVVQLLSEKDFREDIFPVGRLDKNTEGLLILTNDGAL 149

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT------QK 183
              L  P     + Y  R  G+V  + +N   +G+ ++ G      ++ ++       Q 
Sbjct: 150 GHDLTQPKKHVEKEYFARIDGKVTDEIVNKFAEGLTLKNGEKARPGELFIENIYEGESQS 209

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           G  + + V + EGK  ++K++FE     V  L RI  G   L   L  G+ R ++ + + 
Sbjct: 210 GWISEIRVIIHEGKFHQVKRMFEAVEMYVLYLKRIRMGNLALDSDLALGAYRPLTTEEIE 269

Query: 243 E 243
            
Sbjct: 270 N 270


>gi|270160115|ref|ZP_06188771.1| ribosomal large subunit pseudouridine synthase B [Legionella
           longbeachae D-4968]
 gi|289165108|ref|YP_003455246.1| ribosomal large subunit pseudouridine synthase B (Pseudouridylate
           synthase) [Legionella longbeachae NSW150]
 gi|269988454|gb|EEZ94709.1| ribosomal large subunit pseudouridine synthase B [Legionella
           longbeachae D-4968]
 gi|288858281|emb|CBJ12149.1| putative ribosomal large subunit pseudouridine synthase B
           (Pseudouridylate synthase) [Legionella longbeachae
           NSW150]
          Length = 246

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 77/239 (32%), Positives = 120/239 (50%), Gaps = 7/239 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----- 68
           +R+ K++++AG+ SRRE+ER I    V+VNG  ++    +    D I V G  +      
Sbjct: 4   ERLQKILSQAGLGSRREMERWIENGWVQVNGKPVK-LGDSASEEDKITVKGKLIPNPLKV 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           K     L  +     + + H     ++           R + VGRLD+NT GLL+ TN G
Sbjct: 63  KKNVRILLYHKPVGEISSRHDPKFEKTVFDHLPHLRQGRWVQVGRLDLNTSGLLIFTNSG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P   + R Y VR  GQV Q+ LN L KG+ +        ++     +G+N+W
Sbjct: 123 ELANQLMHPKYGFEREYAVRVRGQVSQEVLNNLTKGVELDDGMAKFTRLEFRGGEGANSW 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
             V L EG+NRE+++++E    +V+RLIRI YG   +   L  G   E++ K + + L 
Sbjct: 183 YHVTLNEGRNREVRRLWESQGLEVSRLIRIRYGTITMPRYLSRGQHYELTPKEVSDLLA 241


>gi|189501858|ref|YP_001957575.1| hypothetical protein Aasi_0430 [Candidatus Amoebophilus asiaticus
           5a2]
 gi|189497299|gb|ACE05846.1| hypothetical protein Aasi_0430 [Candidatus Amoebophilus asiaticus
           5a2]
          Length = 252

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 64/237 (27%), Positives = 111/237 (46%), Gaps = 2/237 (0%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            +  +     R++K I+ AGI SRRE + +I   R+ VNG  +      V +TD ++   
Sbjct: 10  KVASDQINYVRLNKWISNAGICSRREADELIQAGRITVNGEKITTLGYQVKNTDIVKFRD 69

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L+  +   + L      + T       R+ +     +   RV  VGRLD NT GLL+L
Sbjct: 70  KVLKPNKHVYILLNKPRNCITTAFDPERRRTVLDFVKGACQERVYPVGRLDRNTTGLLVL 129

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG LA+ L  PS Q  ++Y+V     +    L  +K GI ++        +++   +G
Sbjct: 130 TNDGDLAQKLAHPSYQIKKIYQVELASPIQPKDLAAIKAGICLKDGIVQVDSISIV--QG 187

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             + + + +  GKNR I+++FE   +++  L R+ Y       L     R ++ + +
Sbjct: 188 DESKLGIEIHSGKNRIIRRLFEHLGYQIINLDRVMYANLTKKELPRSKWRFLTNQEV 244


>gi|90408174|ref|ZP_01216342.1| ribosomal large subunit pseudouridine synthase F [Psychromonas sp.
           CNPT3]
 gi|90310704|gb|EAS38821.1| ribosomal large subunit pseudouridine synthase F [Psychromonas sp.
           CNPT3]
          Length = 292

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 63/290 (21%), Positives = 118/290 (40%), Gaps = 11/290 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK- 69
            T +R++K I+ +G  SRRE +++I + RVK+NG +       V+  D + VDG  +   
Sbjct: 4   STGKRLNKYISDSGFCSRREADKLIEKSRVKINGTIP-ELGTKVLPGDIVLVDGRAINAV 62

Query: 70  ---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                      Y+KPIG+  T       + +         R+  +GRLD  +EGL+ LT+
Sbjct: 63  AENKSDRIYIAYNKPIGITCTTERDVRGNIIDAI--RHKKRIFPIGRLDKPSEGLIFLTS 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG +   +        + Y V     + +  +  +++G+ I         V +     S 
Sbjct: 121 DGDIVNKILRAENAHDKEYLVTVDKPLSERFVERMQRGVPILDTITKPCIVKVQ----SR 176

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
              ++ L +G NR+I+++ E+  ++V  L R       L  L  G  R +S + ++E   
Sbjct: 177 FVFSIILTQGLNRQIRRMCEYLGYEVQALQRTRIMQVTLKNLKPGQWRNLSVQEMQEINQ 236

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
                     +  P     T      +  ++      +  K+    N  +
Sbjct: 237 AVSHSSKTAQITTPANPPNTRKIYNQSGSTKKIFVNVKKTKSKPSANSRT 286


>gi|330960474|gb|EGH60734.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. maculicola
           str. ES4326]
          Length = 408

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 92/354 (25%), Positives = 142/354 (40%), Gaps = 15/354 (4%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG         V   D I
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDAT-LGQRVDLHDAI 62

Query: 61  EVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            VDG  +++ E     R  +        + T        +           R I++GRLD
Sbjct: 63  SVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           INT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++       
Sbjct: 123 INTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPARFT 182

Query: 176 QVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIKQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT-----RMKKN 288
           RE+S+  + + L   +  +          + + + R +      +          R    
Sbjct: 243 REMSQYEV-DILSAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVVRTLRPAAG 301

Query: 289 SSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
           +       +Q ++      R    +                +       S   P
Sbjct: 302 APTGERAPRQPQITGSERDRPRGGDSTQRPSPRKDSGKPGSRAPRPADNSRGTP 355



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 17/91 (18%), Positives = 24/91 (26%), Gaps = 2/91 (2%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
            E             +  +D     S  P      +     +      K+ A P  +R  
Sbjct: 317 SERDRPRGGDSTQRPSPRKDSGKPGSRAPRPADNSRGTPVAERPSDMNKRPAKPGPKRVG 376

Query: 311 AS--NVWMAKGIHSSFLSDSGQREENHRRSP 339
               N     G      + SGQR    RR P
Sbjct: 377 IKLVNDDAPSGKRRGPPAGSGQRPGFGRRKP 407


>gi|89895026|ref|YP_518513.1| hypothetical protein DSY2280 [Desulfitobacterium hafniense Y51]
 gi|89334474|dbj|BAE84069.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 257

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 89/233 (38%), Positives = 137/233 (58%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAER 72
           +R+ KV+A+AGIASRR  E +I Q RVKVNG ++      V+STD I VDG  L      
Sbjct: 16  ERLQKVLAQAGIASRRHAEEIILQGRVKVNGEVIRTLGTKVVSTDRIVVDGRLLSIPQND 75

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L HKP G +T+ +DP GR TV + +P I  RV  VGRLD +T GLLLLTNDG LA 
Sbjct: 76  YAYYLLHKPTGYITSVTDPQGRKTVMELMPKIPRRVYPVGRLDYDTSGLLLLTNDGDLAH 135

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA--WVT 190
            L  PS    + YRV    ++ +  L  L+KG++++       ++   + KG  +     
Sbjct: 136 RLMHPSYGVEKTYRVEVGEKIPEQALKRLEKGVLLEDGKTAPARIREVSPKGRGSLPTYE 195

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + + EG+NR+++++F+   + ++ L R+ +GP +L  +L  G+ R +SK  ++
Sbjct: 196 ITIHEGRNRQVRRMFKAVGFPLSTLKRLRFGPLELDPSLAPGAFRTLSKTEIQ 248


>gi|297626538|ref|YP_003688301.1| Pseudouridine synthase [Propionibacterium freudenreichii subsp.
           shermanii CIRM-BIA1]
 gi|296922303|emb|CBL56875.1| Pseudouridine synthase [Propionibacterium freudenreichii subsp.
           shermanii CIRM-BIA1]
          Length = 275

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 83/233 (35%), Positives = 127/233 (54%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
                R+ KV+A+AGIASRR  E +I + RV+VNG ++      V    D I VDG  + 
Sbjct: 35  KPEGIRLQKVLAQAGIASRRASEGLITEGRVEVNGHIVVELGTRVDPEHDSIRVDGARIP 94

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              R    L +KP G+V+T  DP+GR T+ + +P    R+  VGRLD  TEGL++LTNDG
Sbjct: 95  PPRRHMYLLLNKPRGVVSTMDDPEGRPTLAEYVPRH-QRLFHVGRLDTETEGLIILTNDG 153

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
                L  PS +  + Y V   G +D   +  L+KG+ ++       +V L ++   +  
Sbjct: 154 EFGHRLSHPSYEVRKTYLVDAEGLMDNRTIRRLEKGLTLEDGPIKPDRVKLVSRGPVHTM 213

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + L  G+NR ++++ +     V +L RI  GP +LG L  G TRE+S++ L
Sbjct: 214 LQITLHSGRNRIVRRMMDSVGHPVRQLARIGIGPVRLGNLAVGETRELSREEL 266


>gi|190890544|ref|YP_001977086.1| RNA-pseudouridine synthase, ribosomal large subunit B [Rhizobium
           etli CIAT 652]
 gi|190695823|gb|ACE89908.1| probable RNA-pseudouridine synthase protein, ribosomal large
           subunit B [Rhizobium etli CIAT 652]
          Length = 645

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 173/378 (45%), Positives = 230/378 (60%), Gaps = 31/378 (8%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           +     +R+SKV+ARAG+ASRR++ERMI + RV +NG +LE   VNV   D IEVDG+P+
Sbjct: 46  ESEAKAERISKVMARAGVASRRDIERMIMEGRVTLNGKVLETPVVNVTLADRIEVDGMPV 105

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R  ERTRLWLYHKP GLVTT++DP+GR TVFDNLP    RV+S+GRLDINTEGLLLLTND
Sbjct: 106 RGIERTRLWLYHKPAGLVTTNADPEGRPTVFDNLPEELPRVMSIGRLDINTEGLLLLTND 165

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GGLAR LELP+T WLR YRVR HG++DQ+ L+ LK GI + G+ YG ++ TLD  +GSN 
Sbjct: 166 GGLARALELPATGWLRRYRVRAHGEIDQEALDKLKDGIAVDGVLYGSIEATLDRTQGSNV 225

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+T+GLREGKNREIK V       VNRLIRISYGPFQLG L  G   EV  + LR+QLGP
Sbjct: 226 WITMGLREGKNREIKNVLGALGLDVNRLIRISYGPFQLGDLPEGHVIEVRGRTLRDQLGP 285

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK---------- 297
            L+EEA+ N DAPIY++  +  +    ++         +    ++  LS+          
Sbjct: 286 RLIEEAKANFDAPIYNAPAVAAEEEAEVAAPEKRERPRRDEDKRERALSRLDTKRDDRRG 345

Query: 298 ---------------------QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR 336
                                +K   +    +  ++NVWMA G        + +  +N +
Sbjct: 346 DDRRGGARRDDDRRDGGRRDDEKPKRSEPLGQRRSANVWMAPGARPLGEKAAAKAAKNAQ 405

Query: 337 RSPSFPSKRSLRRTSAKK 354
            +     +   +  +  +
Sbjct: 406 TARRRGEQAPAKSAAFDR 423



 Score = 41.3 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 16/125 (12%), Positives = 29/125 (23%), Gaps = 5/125 (4%)

Query: 233 TREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLV-----RDRPNIISEVPDDFTRMKK 287
            RE   + +R    P   +E +       +            +RP+       D  R  +
Sbjct: 435 VREEDGEWIRSSEQPRRKDEGEGFGRKRSFGDRPAREDRGFGERPSRGDRPFGDKPRGDR 494

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
                     +   A+    R+         G   S        +    R P        
Sbjct: 495 RPRADGDERPRATRASAGEGRSERPRGDRPFGDRPSRGDRPFGDKPRGDRRPREDGDERP 554

Query: 348 RRTSA 352
           R   +
Sbjct: 555 RAARS 559



 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 13/108 (12%), Positives = 26/108 (24%), Gaps = 1/108 (0%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH- 306
            + EE    + +          +         D   R  +   ++     +     P   
Sbjct: 434 RVREEDGEWIRSSEQPRRKDEGEGFGRKRSFGDRPAREDRGFGERPSRGDRPFGDKPRGD 493

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           RR  A      +   +S      +R    R     PS+         +
Sbjct: 494 RRPRADGDERPRATRASAGEGRSERPRGDRPFGDRPSRGDRPFGDKPR 541



 Score = 38.2 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 9/105 (8%), Positives = 19/105 (18%), Gaps = 1/105 (0%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
             G     +     D P        R       E P            +    ++     
Sbjct: 519 PRGDRPFGDRPSRGDRPFGDKPRGDRRPREDGDERPRAARSFAGEGRSERPRGERSFGDK 578

Query: 304 -PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            P  + +         G       +   + +  +     P     
Sbjct: 579 APGGKPSGDKPRGKGFGARPGGSKNFSGKPKGGKPGSDRPGGDRP 623



 Score = 37.1 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 8/109 (7%), Positives = 25/109 (22%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           ++        A  +       +            + P      + +    +     ++  
Sbjct: 488 DKPRGDRRPRADGDERPRATRASAGEGRSERPRGDRPFGDRPSRGDRPFGDKPRGDRRPR 547

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                R  A+  +  +G       +    ++     PS    R     +
Sbjct: 548 EDGDERPRAARSFAGEGRSERPRGERSFGDKAPGGKPSGDKPRGKGFGA 596



 Score = 36.3 bits (82), Expect = 7.2,   Method: Composition-based stats.
 Identities = 9/109 (8%), Positives = 23/109 (21%), Gaps = 4/109 (3%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              ++ + +        E     R +      +     +    + +   +         R
Sbjct: 485 PFGDKPRGDRRPRADGDERPRATRASAGEGRSERPRGDRPFGDRPSRGDRPFGDKPRGDR 544

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHR----RSPSFPSKRSLRRTSA 352
           R         +   S       +R    R    ++P         R   
Sbjct: 545 RPREDGDERPRAARSFAGEGRSERPRGERSFGDKAPGGKPSGDKPRGKG 593


>gi|237744367|ref|ZP_04574848.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           7_1]
 gi|229431596|gb|EEO41808.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           7_1]
          Length = 234

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 69/231 (29%), Positives = 129/231 (55%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAE 71
            R++K ++  GIASRR V++ I + R+ VNG +     +++   D+I +DG  ++    E
Sbjct: 1   MRINKFLSTLGIASRRAVDKYIEEGRITVNGNIATT-GMDISENDNIFIDGKKIKTDVNE 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               ++ +KP+ ++++ SD  GR TV D + +       +GRLD  T GL+LLTNDG L 
Sbjct: 60  EKVYFMLNKPLEVLSSSSDDRGRKTVVDLIKTDKRI-FPIGRLDYMTSGLILLTNDGELF 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P ++  + Y V+  G++ ++++  LKKG+++        +++      +   + +
Sbjct: 119 NRIVHPKSEIYKKYYVKIFGEIKKEEIAELKKGVLLNDGKTLPAKISGIKYDKNKTSMYI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            ++EG+NR+I+++ E F +KV  L R   G   LG L  G  RE++K+ + 
Sbjct: 179 SIKEGRNRQIRRMIERFGYKVLMLRREKIGELSLGDLEEGKYRELTKQEIE 229


>gi|156340515|ref|XP_001620471.1| hypothetical protein NEMVEDRAFT_v1g223077 [Nematostella vectensis]
 gi|156205434|gb|EDO28371.1| predicted protein [Nematostella vectensis]
          Length = 275

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 65/240 (27%), Positives = 109/240 (45%), Gaps = 1/240 (0%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +            R++K IA +G+ SRRE +  IA   V VNG ++      V  TD I 
Sbjct: 31  QSSTKKSSPEDGIRLNKYIANSGVCSRREADTYIASGNVVVNGKVITEMGFKVKPTDDIR 90

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
            DG  +   E+  + L      + T   D   ++ +     +   R+  VGRLD NT GL
Sbjct: 91  FDGTAISPEEKKYVLLNKPKNYITTMDDDRGRKTVMDLVQNAARERIYPVGRLDRNTTGL 150

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL TNDG LA+ L  P     ++Y      +++   L+ ++  ++I+G     +      
Sbjct: 151 LLFTNDGDLAKKLTHPKHNVQKLYHASLDRKLEVKDLHKMRDEVIIEGKRV-FIDEVDYV 209

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                  V + +  G+NR ++K+FE F +KV +L R+ +       L  G  RE++ + +
Sbjct: 210 AGEKKTEVGIKIHSGRNRIVRKIFEHFGYKVVKLDRVIFAGLTKKNLPRGRYRELTTQEV 269


>gi|153949734|ref|YP_001401683.1| 16S rRNA pseudouridylate synthase A [Yersinia pseudotuberculosis IP
           31758]
 gi|170025018|ref|YP_001721523.1| 16S rRNA pseudouridylate synthase A [Yersinia pseudotuberculosis
           YPIII]
 gi|152961229|gb|ABS48690.1| ribosomal small subunit pseudouridine synthase A [Yersinia
           pseudotuberculosis IP 31758]
 gi|169751552|gb|ACA69070.1| pseudouridine synthase [Yersinia pseudotuberculosis YPIII]
          Length = 235

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 55/238 (23%), Positives = 107/238 (44%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    
Sbjct: 1   MRLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQMVGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +  D       G+ +          Q+ +   +     V +
Sbjct: 121 VTSPRHHCEKTYLVTLEHPLSDDTAQQFADGVQLHNEKSLTKPAQLDVIEPQR----VRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
            + EG+  ++K++F     +V  L R   G   L   L  G  R ++ + +     PH
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVIELHRERIGDITLDDDLAPGEYRPLTAEEIASVGAPH 234


>gi|297565186|ref|YP_003684158.1| pseudouridine synthase [Meiothermus silvanus DSM 9946]
 gi|296849635|gb|ADH62650.1| pseudouridine synthase [Meiothermus silvanus DSM 9946]
          Length = 245

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 62/237 (26%), Positives = 112/237 (47%), Gaps = 8/237 (3%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDG 64
           + + + T +R+ KV+A  G+ SR+E+ ++    R+ V+G ++  A   +   +  I VDG
Sbjct: 1   MKKAHLTKERLDKVLAHLGLGSRKEIHKLARAGRITVDGEVITDAGFKLDPRSARIAVDG 60

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +   E   + L      + +T        +V   L  +    + VGRLD +TEGLLL+
Sbjct: 61  EEVFYREFFHVLLNKPAGYVTSTQDR--DGPSVTHLLEMVRDDWMPVGRLDKDTEGLLLI 118

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T DG LA  L  P  +  + Y         Q  +     G  ++G      ++TL    G
Sbjct: 119 TTDGELAHRLTHPRWKVPKRYYAELAEPATQADVEAFAAGFELEGEPLQPAELTL----G 174

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
            +  V + +REG+  ++K++F     +V  L R+++GP +L   L  G +R ++ + 
Sbjct: 175 KDRRVELVIREGRYHQVKRMFAARGNRVVYLKRVAFGPLELPEDLELGESRYLTAEE 231


>gi|257469264|ref|ZP_05633358.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           ulcerans ATCC 49185]
 gi|317063511|ref|ZP_07927996.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           ulcerans ATCC 49185]
 gi|313689187|gb|EFS26022.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           ulcerans ATCC 49185]
          Length = 236

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 66/230 (28%), Positives = 112/230 (48%), Gaps = 1/230 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K +A  GIASRREV++MI +  +KVNG       + V   D I + G  + K  
Sbjct: 2   EEMRINKYLASLGIASRREVDKMIEEGAIKVNGEKAA-PGIKVSDEDEIYIKGKKIEKNT 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +++        V + S  D       +L     R+  +GRLD NT GL++LTNDG L 
Sbjct: 61  EKKVYYILNKPLEVLSSSKDDRGRKTVVDLIKCKERIFPIGRLDYNTSGLIILTNDGELF 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P  +  + Y  +  G++ ++   LL+KG+ +         V +  ++     + V
Sbjct: 121 NRIIHPKAEIFKEYYAKVFGEIKEENAELLRKGVELDDGMTLPANVKILRRERGKTELLV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +REG+NR+++++ +  N  V  L R   G   LG L  G  RE++ + +
Sbjct: 181 AIREGRNRQVRRMLDKINHPVITLRREKIGDLSLGNLKLGEYRELTNEEV 230


>gi|330004789|ref|ZP_08305026.1| ribosomal large subunit pseudouridine synthase F [Klebsiella sp. MS
           92-3]
 gi|328536522|gb|EGF62861.1| ribosomal large subunit pseudouridine synthase F [Klebsiella sp. MS
           92-3]
          Length = 284

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 58/282 (20%), Positives = 111/282 (39%), Gaps = 5/282 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSTRLNKYISESGICSRREADRFIEQGNVFINGKRAT-IGDQVKPGDLVKVNGRLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   R+  +GRLD +++GL+ LTN G L
Sbjct: 63  EADDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPVTDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLTGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
             ++    A   +       +  ++     +       + ++
Sbjct: 239 SSSEAKPKARPKAKAATPGIKRPVVKMENSNDKGRPAGNGKR 280


>gi|251794145|ref|YP_003008876.1| pseudouridine synthase [Paenibacillus sp. JDR-2]
 gi|247541771|gb|ACS98789.1| pseudouridine synthase [Paenibacillus sp. JDR-2]
          Length = 233

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 105/233 (45%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+  G  SRRE ++++   RV +NG             D + +DG  + + +  
Sbjct: 1   MRINKFISETGYCSRREADKLVDSGRVTINGAKA-ELGSQAELGDDVRIDGKRIGEQKHH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+ +T            +      R+  +GRLD ++EGL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITSTTELHI--RGNIVDFVGHKERIFPIGRLDKDSEGLILLTNDGDVVNP 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     V  + +  +  G+ I G      QVT      +     + L
Sbjct: 118 ILRSEGKHEKEYIVTVDRPVTAEFVKGMSSGVRILGSMTLPCQVTRV----AERVFRIVL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            EGKNR+I+++ E F + V +L RI      LG L  G  R++++    E  G
Sbjct: 174 TEGKNRQIRRMCEAFGYHVRKLQRIRIMNIHLGQLPTGKWRDLTETEKAELFG 226


>gi|323705231|ref|ZP_08116807.1| pseudouridine synthase [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323535657|gb|EGB25432.1| pseudouridine synthase [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 240

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 60/232 (25%), Positives = 108/232 (46%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+E++  I +  V +N ++++     V    D I      +   E 
Sbjct: 4   MRIDKLLSNMGYGSRKEIKNFIKECLVAINDVIIDDPGFTVQPDKDVITFRNEKVSYKEY 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      +  T+   +              +V   GRLD +TEGLLL+TNDG L+ 
Sbjct: 64  IYIMMNKPKGVICATYDPSERTVVDLLPHHIKSRKVFPAGRLDKDTEGLLLITNDGELSH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G +D+D  +L  +GI++          + +    G+ + V +
Sbjct: 124 KLLSPKKHVFKKYYAEVLGFIDEDDASLFSEGILLDDGYKTMPATLEII-SSGNISKVYI 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            +REGK  +IK++FE  + KV  L R+S G  +L   L  G  RE++++ ++
Sbjct: 183 SIREGKYHQIKRMFEAIDSKVIYLKRLSIGKLKLDENLKEGEWRELNEEEIK 234


>gi|224543302|ref|ZP_03683841.1| hypothetical protein CATMIT_02502 [Catenibacterium mitsuokai DSM
           15897]
 gi|224523835|gb|EEF92940.1| hypothetical protein CATMIT_02502 [Catenibacterium mitsuokai DSM
           15897]
          Length = 231

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 106/234 (45%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A  G  SR++V++++    V  NG  +  +  +V    D I V    +  ++ 
Sbjct: 1   MRIDKLLAHCGYGSRKDVKQLLKDGLVTSNGKKIRSSGAHVDPEKDEIYVGDEKINYSKY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  +     TV D +      +  VGRLD++TEGLLL+TNDG LA 
Sbjct: 61  VYYMLNKPDGYVSATEDN--VYPTVIDLIKEYHPGLFPVGRLDVDTEGLLLITNDGQLAH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P T   + Y V+  G++    +N   KGI ++             +    +   V 
Sbjct: 119 RLLSPRTHVPKTYYVKVKGRLGIGDINAFTKGIPLEDFTCMP-SYLKIIKSDEISECEVT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           + EGK  ++K++F+    +V  L RIS G  +L   L  G  R ++ + +   L
Sbjct: 178 IYEGKFHQVKRMFQACGKEVVYLKRISMGELKLDENLKLGHYRPLTDEEINSIL 231


>gi|325954781|ref|YP_004238441.1| pseudouridine synthase Rsu [Weeksella virosa DSM 16922]
 gi|323437399|gb|ADX67863.1| pseudouridine synthase Rsu [Weeksella virosa DSM 16922]
          Length = 297

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 62/301 (20%), Positives = 129/301 (42%), Gaps = 6/301 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E     R++K I+ +G  SRRE ++ I  ++V VNG + +    +V   D + V+ + ++
Sbjct: 2   ERKETIRLNKFISDSGYCSRREADQYIENRQVYVNGRIAKV-GQHVQLHDQVVVNNIEIK 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ++           +  T +      T   +  S   R+  +GRLD +++GL+LLT+DG
Sbjct: 61  PRDKEMAIYIALNKPVGITCTTDPNDPTNIIDFLSFGERIFPIGRLDKDSQGLILLTSDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +     +  + Y V     +  D    ++ G+ I G+           +K +   
Sbjct: 121 DIVNKILRAGNKHEKEYIVTVDKPITDDFCTKMENGVPILGVNTKKCT----VEKLNTNT 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E+F+++V +L R       L  +  G  R+++K+ L E     
Sbjct: 177 FKIILIQGLNRQIRRMCEYFDYRVTKLERTRIMNIDL-NVPIGQYRDLTKEELMELKRLT 235

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
              E      A   +++     +  ++ +      R+ +    +  + K K    P  +R
Sbjct: 236 AQSEQHEKAKANKKTAKKKSTTKKTVLEKDTTPKKRITRKPKSQPRIGKSKPPEKPKRKR 295

Query: 309 N 309
            
Sbjct: 296 R 296


>gi|114798538|ref|YP_759667.1| pseudouridine synthase rsuA family protein [Hyphomonas neptunium
           ATCC 15444]
 gi|114738712|gb|ABI76837.1| pseudouridine synthase rsuA family protein [Hyphomonas neptunium
           ATCC 15444]
          Length = 305

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 119/271 (43%), Positives = 156/271 (57%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R++K +ARAG+ASRREVER+I    V VNG  L   A  V   + I+V    ++  
Sbjct: 35  SEGERIAKYLARAGVASRREVERLIEAGEVTVNGQKLTSPAFKVTGREAIKVGRKVIQAP 94

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + +RLW YHKP GL+TT +DP GR T+FD LP    R ++VGRLD+ TEGLLLLTNDG L
Sbjct: 95  DASRLWRYHKPSGLITTTNDPAGRRTIFDELPKSLPRTVTVGRLDLTTEGLLLLTNDGEL 154

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           AR LELP +   R YRVR  G V Q K++ L  GI ++G+ Y  ++   D + G+N+W+T
Sbjct: 155 ARFLELPKSALERTYRVRAKGTVTQLKIDELASGITVEGVKYQPIKAVFDREMGANSWLT 214

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           V L EGKNRE++K  E     VNRLIR+SYGPF L  L  G   EV   +L   L     
Sbjct: 215 VTLTEGKNREVRKALESVGLTVNRLIRVSYGPFLLADLKPGQVDEVPPDLLETALALLGH 274

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDD 281
           E           +   L R  P+   +    
Sbjct: 275 EVDTAPEKPAPAAKSRLGRRGPSARVKGKRS 305


>gi|16803988|ref|NP_465473.1| hypothetical protein lmo1949 [Listeria monocytogenes EGD-e]
 gi|46908183|ref|YP_014572.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes serotype 4b str. F2365]
 gi|47093378|ref|ZP_00231145.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes str. 4b H7858]
 gi|47097092|ref|ZP_00234662.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes str. 1/2a F6854]
 gi|224498601|ref|ZP_03666950.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes Finland 1988]
 gi|224501251|ref|ZP_03669558.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes FSL R2-561]
 gi|226224554|ref|YP_002758661.1| hypothetical protein Lm4b_01968 [Listeria monocytogenes Clip81459]
 gi|254825555|ref|ZP_05230556.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes FSL J1-194]
 gi|254827166|ref|ZP_05231853.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes FSL N3-165]
 gi|254831450|ref|ZP_05236105.1| hypothetical protein Lmon1_08853 [Listeria monocytogenes 10403S]
 gi|254852851|ref|ZP_05242199.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes FSL R2-503]
 gi|254899354|ref|ZP_05259278.1| hypothetical protein LmonJ_06059 [Listeria monocytogenes J0161]
 gi|254912507|ref|ZP_05262519.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes J2818]
 gi|254931879|ref|ZP_05265238.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes HPB2262]
 gi|254936834|ref|ZP_05268531.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes F6900]
 gi|254992999|ref|ZP_05275189.1| hypothetical protein LmonocytoFSL_08071 [Listeria monocytogenes FSL
           J2-064]
 gi|255026085|ref|ZP_05298071.1| hypothetical protein LmonocytFSL_06510 [Listeria monocytogenes FSL
           J2-003]
 gi|255520090|ref|ZP_05387327.1| hypothetical protein LmonocFSL_02452 [Listeria monocytogenes FSL
           J1-175]
 gi|284802394|ref|YP_003414259.1| hypothetical protein LM5578_2150 [Listeria monocytogenes 08-5578]
 gi|284995536|ref|YP_003417304.1| hypothetical protein LM5923_2101 [Listeria monocytogenes 08-5923]
 gi|300763739|ref|ZP_07073736.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes FSL N1-017]
 gi|16411402|emb|CAD00027.1| lmo1949 [Listeria monocytogenes EGD-e]
 gi|46881453|gb|AAT04749.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes serotype 4b str. F2365]
 gi|47014537|gb|EAL05500.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes str. 1/2a F6854]
 gi|47018249|gb|EAL09015.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes str. 4b H7858]
 gi|225877016|emb|CAS05725.1| Hypothetical protein of unknown function [Listeria monocytogenes
           serotype 4b str. CLIP 80459]
 gi|258599548|gb|EEW12873.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes FSL N3-165]
 gi|258606184|gb|EEW18792.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes FSL R2-503]
 gi|258609430|gb|EEW22038.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes F6900]
 gi|284057956|gb|ADB68897.1| hypothetical protein LM5578_2150 [Listeria monocytogenes 08-5578]
 gi|284061003|gb|ADB71942.1| hypothetical protein LM5923_2101 [Listeria monocytogenes 08-5923]
 gi|293583430|gb|EFF95462.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes HPB2262]
 gi|293590492|gb|EFF98826.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes J2818]
 gi|293594796|gb|EFG02557.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes FSL J1-194]
 gi|300515475|gb|EFK42525.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes FSL N1-017]
 gi|328466297|gb|EGF37454.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes 1816]
 gi|328472791|gb|EGF43640.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes 220]
 gi|332312390|gb|EGJ25485.1| Pseudouridine synthase [Listeria monocytogenes str. Scott A]
          Length = 244

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 77/238 (32%), Positives = 121/238 (50%), Gaps = 3/238 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E++I + +V VNG ++    V V  T+ IEV+G+ L K E  
Sbjct: 2   ERLQKVIANAGITSRRKAEKLIQEGKVTVNGKVVTELGVKVSGTERIEVEGIQLTKEEHR 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     +     D    +        I  R+  VGRLD +T GLLL+TNDG  A +
Sbjct: 62  YFLFYKPRGTVSAVTDDKGRTTVADYF-ADIPERLYPVGRLDYDTSGLLLMTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVTV 191
           L  P  +  + Y  R  G  +++ +  L++G+VI G      +V +    +    A V +
Sbjct: 121 LMHPKNEVSKTYIARIKGIPEREVIRQLERGVVIDGRKTAPAKVKVRSSDKTKDKAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + EG+NR+++K+FE   ++V +L R  Y    L  L AG  RE+S   +++      
Sbjct: 181 TIHEGRNRQVRKMFEAVGFEVQKLSREEYSFLNLRGLNAGERRELSHHEVKQLKTEAR 238


>gi|22126794|ref|NP_670217.1| 16S rRNA pseudouridylate synthase A [Yersinia pestis KIM 10]
 gi|45441149|ref|NP_992688.1| 16S rRNA pseudouridylate synthase A [Yersinia pestis biovar
           Microtus str. 91001]
 gi|108806980|ref|YP_650896.1| 16S rRNA pseudouridylate synthase A [Yersinia pestis Antiqua]
 gi|108812871|ref|YP_648638.1| 16S rRNA pseudouridylate synthase A [Yersinia pestis Nepal516]
 gi|145599700|ref|YP_001163776.1| 16S rRNA pseudouridylate synthase A [Yersinia pestis Pestoides F]
 gi|149366750|ref|ZP_01888784.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           CA88-4125]
 gi|162418753|ref|YP_001606002.1| 16S rRNA pseudouridylate synthase A [Yersinia pestis Angola]
 gi|165924511|ref|ZP_02220343.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165936140|ref|ZP_02224709.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|166009884|ref|ZP_02230782.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166211428|ref|ZP_02237463.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|167400432|ref|ZP_02305945.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167419607|ref|ZP_02311360.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167424159|ref|ZP_02315912.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|218928420|ref|YP_002346295.1| 16S rRNA pseudouridylate synthase A [Yersinia pestis CO92]
 gi|229841215|ref|ZP_04461374.1| 16S rRNA pseudouridylate 516 synthase [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229843320|ref|ZP_04463466.1| 16S rRNA pseudouridylate 516 synthase [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229903299|ref|ZP_04518412.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           Nepal516]
 gi|270487103|ref|ZP_06204177.1| pseudouridylate synthase [Yersinia pestis KIM D27]
 gi|294503270|ref|YP_003567332.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           Z176003]
 gi|34098649|sp|Q8ZGM2|RSUA_YERPE RecName: Full=Ribosomal small subunit pseudouridine synthase A;
           AltName: Full=16S pseudouridine 516 synthase; AltName:
           Full=16S pseudouridylate 516 synthase; AltName:
           Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|21959821|gb|AAM86468.1|AE013894_3 16S pseudouridylate 516 synthase [Yersinia pestis KIM 10]
 gi|45436008|gb|AAS61565.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Microtus str. 91001]
 gi|108776519|gb|ABG19038.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           Nepal516]
 gi|108778893|gb|ABG12951.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           Antiqua]
 gi|115347031|emb|CAL19923.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           CO92]
 gi|145211396|gb|ABP40803.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           Pestoides F]
 gi|149291124|gb|EDM41199.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           CA88-4125]
 gi|162351568|gb|ABX85516.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           Angola]
 gi|165915754|gb|EDR34362.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|165923571|gb|EDR40703.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165991280|gb|EDR43581.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166207199|gb|EDR51679.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|166962348|gb|EDR58369.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167050381|gb|EDR61789.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167057008|gb|EDR66771.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|229679069|gb|EEO75172.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           Nepal516]
 gi|229689667|gb|EEO81728.1| 16S rRNA pseudouridylate 516 synthase [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229697581|gb|EEO87628.1| 16S rRNA pseudouridylate 516 synthase [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|262361308|gb|ACY58029.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           D106004]
 gi|262365154|gb|ACY61711.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           D182038]
 gi|270335607|gb|EFA46384.1| pseudouridylate synthase [Yersinia pestis KIM D27]
 gi|294353729|gb|ADE64070.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           Z176003]
 gi|320015889|gb|ADV99460.1| Ribosomal small subunit pseudouridine synthaseA [Yersinia pestis
           biovar Medievalis str. Harbin 35]
          Length = 235

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 55/238 (23%), Positives = 107/238 (44%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    
Sbjct: 1   MRLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQMVGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +  D       G+ +          Q+ +   +     V +
Sbjct: 121 VTSPRHHCEKTYLVTLEHPLSDDTAQQFADGVQLYNEKSLTKPAQLDVIEPQR----VRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
            + EG+  ++K++F     +V  L R   G   L   L  G  R ++ + +     PH
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVIELHRERIGDITLDDDLAPGEYRPLTTEEIASVGAPH 234


>gi|312622542|ref|YP_004024155.1| pseudouridine synthase [Caldicellulosiruptor kronotskyensis 2002]
 gi|312203009|gb|ADQ46336.1| pseudouridine synthase [Caldicellulosiruptor kronotskyensis 2002]
          Length = 233

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 55/230 (23%), Positives = 105/230 (45%), Gaps = 7/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G  SR +V+++I +  V VNG  +      +    D +EVDG  ++ +++
Sbjct: 1   MRLDKFLTHCGFGSRSQVKKLIREGIVTVNGKQIVEVDFKINPEEDIVEVDGRVVKFSKQ 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      + +             +    +  + +VGRLD + EGLL++T+DG    
Sbjct: 61  IYIMMNKPKGYVCSNEELASLTVFSLISDDLKYRDLHTVGRLDKDAEGLLIITDDGEYTH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            +  P  +  + Y VR   +VD++KL   + GI++         + T+      +  V +
Sbjct: 121 RVISPKKRIEKEYLVRLEKEVDEEKLKEFENGIILDDGYKTLPAKYTII----DSTTVKL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + EGK  ++K++FE    KV  L R+  G   L  +L  G  R + ++ 
Sbjct: 177 CIYEGKYHQVKRMFEAIGNKVVDLKRLRIGGLNLDQSLKPGEYRVMKEEE 226


>gi|149180996|ref|ZP_01859497.1| tRNA pseudouridine synthase A [Bacillus sp. SG-1]
 gi|148851280|gb|EDL65429.1| tRNA pseudouridine synthase A [Bacillus sp. SG-1]
          Length = 238

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 67/226 (29%), Positives = 111/226 (49%), Gaps = 7/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +R+I + RV +NG   +     V   D I V G  +R A    
Sbjct: 5   RINKFISEAGKASRRGADRLIEEGRVTINGKKAK-IGDQVEPGDDIRVSGQQIRVARNNV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+ +T            +L +   RV ++GRLD +++GL+LLTNDG +   +
Sbjct: 64  YLALNKPVGITSTTEKNV--KGNIVDLVNHPLRVFNIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                Q  + Y V     +  + L  + +G+ I G      +V    ++ S     + L 
Sbjct: 122 LRAENQHEKEYIVSVDKPITPEFLTQMSEGVKILGTKTLPCKV----EQLSKFDFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +G NR+I+++ E   ++V RL R+      LG L  G  R+++KK 
Sbjct: 178 QGLNRQIRRMCEALGYEVFRLQRVRIMNIHLGNLPVGQWRDLTKKE 223


>gi|323167301|gb|EFZ53010.1| ribosomal large subunit pseudouridine synthase F [Shigella sonnei
           53G]
          Length = 291

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 60/292 (20%), Positives = 113/292 (38%), Gaps = 5/292 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDIVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++    A        ++     + +        +   S       +++ A
Sbjct: 239 SSSEAKPKAKAKPKTAGIKRPVVKMEKRRKKAVARRPTVSVLPRRGVKRRGA 290


>gi|238752726|ref|ZP_04614196.1| Ribosomal large subunit pseudouridine synthase F [Yersinia rohdei
           ATCC 43380]
 gi|238709057|gb|EEQ01305.1| Ribosomal large subunit pseudouridine synthase F [Yersinia rohdei
           ATCC 43380]
          Length = 290

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 63/296 (21%), Positives = 119/296 (40%), Gaps = 8/296 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRR+ +R + Q  V +NG         V + D ++V+G  +  
Sbjct: 3   TNSSTRLNKYISESGICSRRDADRYVEQGNVFINGKRAAV-GDQVYAGDVVKVNGQLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G 
Sbjct: 62  RDEDDLVLIALNKPVGIISTTEDGEHDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  V  + +  L  G+ + G            +K S    
Sbjct: 122 LVNKILRAGNDHEKEYVVTVNKPVTDEFILGLGAGVPMLGTV----TKKCKVKKESTFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ + F ++V +L R       L  L  G  R+++   L E      
Sbjct: 178 RITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNVTLKGLPQGEWRDLTDDELIELFKLI- 236

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
             E   + +AP+  S          +   P    +   N++ +   ++  +     
Sbjct: 237 --ENSSSDEAPVKKSPPKSVTNKKPVINGPKKTEKPDGNAAARKRFAQPGRKKKGR 290


>gi|121593577|ref|YP_985473.1| ribosomal large subunit pseudouridine synthase B [Acidovorax sp.
           JS42]
 gi|120605657|gb|ABM41397.1| ribosomal large subunit pseudouridine synthase B [Acidovorax sp.
           JS42]
          Length = 447

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 81/338 (23%), Positives = 136/338 (40%), Gaps = 8/338 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          V   D I+V+
Sbjct: 113 KRVLLPQPETPKLHKVLAQAGMGSRLEMEQLILEGRISVNNEPA-HIGQRVQFGDQIKVN 171

Query: 64  GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+R          +  +     +VT     +  +           +  SVGRLD+NTE
Sbjct: 172 GKPIRFRIAPPPVRVIAYHKPVGEVVTHDDPQNRPTVFRKLPRLQQGKWQSVGRLDLNTE 231

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL T+ G LA  L  P     R Y VR  G +  ++   L +G+ ++        V  
Sbjct: 232 GLLLFTSSGELANKLMHPRFGLEREYAVRVLGALSTEEKQRLLEGVPLEDGMASFGSVED 291

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E+ +
Sbjct: 292 GGGEGANCWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMMLPRGLKRGAWLELDE 351

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           + +R  +             A   S +     + +  S  P   +   ++ +        
Sbjct: 352 RDIRALMQAAGATLDG--GGARPTSGQGRGGRKGDRRSAGPGKASGSGRDKTGGRAGRPP 409

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR 336
              A P   +     +             +       R
Sbjct: 410 SPNAQPDPMKTSLGYIGADSFSRHRQQQRNNGPRRGGR 447


>gi|87307978|ref|ZP_01090120.1| ribosomal large subunit pseudouridine synthase B [Blastopirellula
           marina DSM 3645]
 gi|87289060|gb|EAQ80952.1| ribosomal large subunit pseudouridine synthase B [Blastopirellula
           marina DSM 3645]
          Length = 517

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 88/354 (24%), Positives = 146/354 (41%), Gaps = 7/354 (1%)

Query: 1   MKDKNIVQENFTP---QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M +     +N  P   +R+ KV+A AGI SRR+ E +I + RV+V+G  +    + V   
Sbjct: 1   MPENPAESDNPAPLRLERLHKVLAFAGIDSRRKCEALIQEGRVEVDGKFVTELGMKVDPE 60

Query: 58  -DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
              I VDG  L+  +R    L   P  L T          +      +     ++GRLD 
Sbjct: 61  HQEILVDGQRLKFGKRVYYMLNKPPGVLSTNFDPAGRTRVIDMVPQDVRL--FTIGRLDR 118

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
            +EGL+++TNDG LA  L  P  +  + YRV   G  + D +  +++G+ +       + 
Sbjct: 119 ASEGLIVVTNDGELANRLAHPRYEIEKTYRVEVAGHPEPDAITFVRRGVHLAEGFVQPVS 178

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V +  +   +  + V L EGKNREI+++      KV RL RI+ GP +LG +  G+ RE+
Sbjct: 179 VVMKRKNKQSTTLEVILDEGKNREIRRLMAKIGHKVLRLKRIAMGPLRLGEMPEGAFREL 238

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETL-VRDRPNIISEVPDDFTRMKKNSSQKNGL 295
                +          A          S T   R+ P           R     ++    
Sbjct: 239 KSAETKALRDAAFGVGAGKPKKPKPRKSSTPGEREGPIFPETKTIAKGRAGAKPTETGAK 298

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           S+     T    ++ ++    A    SS  +       +  R+ +  S  S  +
Sbjct: 299 SRATGKPTGAASKDRSTYKKSAGTGSSSRAAGKPAGSSSKDRASASKSSDSAPK 352


>gi|330989187|gb|EGH87290.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. lachrymans str. M301315]
          Length = 408

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 90/354 (25%), Positives = 139/354 (39%), Gaps = 15/354 (4%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG         V   D I
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDAT-LGQRVDLHDAI 62

Query: 61  EVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            VD   +++ E     R  +        + T        +           R I++GRLD
Sbjct: 63  SVDDRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           INT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++       
Sbjct: 123 INTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPARFT 182

Query: 176 QVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE+S+  + + L   +  +          + + + R +      +           +   
Sbjct: 243 REMSQYEV-DILAAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVRTLRPAAGA 301

Query: 294 GLSKQKKLATP-----VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
             +  +    P        R    +                +       S   P
Sbjct: 302 PATGDRAPRQPQITGSERDRPRGGDSTQRPSPRKDSGKPGSRAPRPADNSRGTP 355


>gi|16767443|ref|NP_463058.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|161617332|ref|YP_001591297.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|167991374|ref|ZP_02572473.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|168243582|ref|ZP_02668514.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|194448614|ref|YP_002048178.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|197263699|ref|ZP_03163773.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|34098651|sp|Q8ZKL1|RLUF_SALTY RecName: Full=Ribosomal large subunit pseudouridine synthase F;
           AltName: Full=rRNA pseudouridylate synthase F; AltName:
           Full=rRNA-uridine isomerase F
 gi|16422749|gb|AAL23017.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|161366696|gb|ABX70464.1| hypothetical protein SPAB_05187 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|194406918|gb|ACF67137.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL476]
 gi|197241954|gb|EDY24574.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|205330127|gb|EDZ16891.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|205337314|gb|EDZ24078.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|261249293|emb|CBG27155.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. D23580]
 gi|267996496|gb|ACY91381.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 14028S]
 gi|301160685|emb|CBW20216.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. SL1344]
 gi|312915294|dbj|BAJ39268.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhimurium str. T000240]
 gi|321223059|gb|EFX48129.1| Ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           TN061786]
 gi|323132528|gb|ADX19958.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|332991008|gb|AEF09991.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 289

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 62/292 (21%), Positives = 116/292 (39%), Gaps = 5/292 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R++K I+ +GI SRRE +R I Q  V +NG         V++ D ++V+G  +  
Sbjct: 3   TDTSTRLNKYISESGICSRREADRFIEQGNVFINGKRAA-IGDQVVAGDIVKVNGRLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   L L      +    +  DG      +  +   R+  +GRLD +++GL+ LTN G 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRIFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     +  + +  +  G+ I G            +K +    
Sbjct: 122 LVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +      
Sbjct: 178 RITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
              ++    A      T ++     I +  +            +   K+K  
Sbjct: 238 RSSSEAKPKAKAKPKTTGIKRPVVAIEKSNEKARPTSSGKRFTSPGRKKKGR 289


>gi|229825370|ref|ZP_04451439.1| hypothetical protein GCWU000182_00724 [Abiotrophia defectiva ATCC
           49176]
 gi|229790374|gb|EEP26488.1| hypothetical protein GCWU000182_00724 [Abiotrophia defectiva ATCC
           49176]
          Length = 234

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 67/236 (28%), Positives = 115/236 (48%), Gaps = 5/236 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K ++ AG+ SRR  +R+I + RV VNG         V ++D + VDG  +    
Sbjct: 2   EAVRINKYLSEAGVCSRRGADRLIEEGRVSVNGNHAF-LGSVVKNSDEVRVDGNLVTPVI 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  L  ++KP G+V T +DP  +        +   R+  VGRLD  +EGL+LL+NDG L+
Sbjct: 61  KKILIAFNKPRGIVCTTADPKSKDVNIIEYINYPERIFPVGRLDKESEGLILLSNDGDLS 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V      D + L  + +G+ I         +    ++       +
Sbjct: 121 NKIMKARNFHEKEYEVEVDKPFDDEFLKKMSEGVPILDTITRKCTL----KRTGKTSFNI 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            L +G NR+I+++ E+F +KV +L RI     +LG L +G+ R ++ K   E +  
Sbjct: 177 ILTQGLNRQIRRMCEYFGYKVLKLKRIRIMNIKLGNLKSGTYRNITDKEYEELIKE 232


>gi|297583540|ref|YP_003699320.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
 gi|297141997|gb|ADH98754.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
          Length = 236

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 59/236 (25%), Positives = 105/236 (44%), Gaps = 5/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            RV K++A  G  SR++V++++ +    VNG +++ A  +V   TD +   G P+   E 
Sbjct: 1   MRVDKLLAHVGYGSRKDVKQLLKKGLFTVNGEVVKSAKAHVDPETDDLAFGGEPILYREH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + ++     L  T    +              +   VGRLD +T GLLLLTNDG  A 
Sbjct: 61  LYVMMHKPAGVLSATEDVSERTVVDLLEEEDRLFQPFPVGRLDKDTTGLLLLTNDGKWAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            +  P+ +  + Y V     V  +  + L++G+ +            +     S + + +
Sbjct: 121 GITSPARKIPKTYEVLTAEPVTDEMADQLQQGVTLDDGYETRPA--GVAFPDESRSRLYL 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
            + EGK  ++K++       V+ L RI  G   L   L AG+ RE+++K +     
Sbjct: 179 TIDEGKYHQVKRMLAAVGNHVDGLKRIRIGGLPLDESLEAGTYRELTEKEIEAFQN 234


>gi|187478887|ref|YP_786911.1| ribosomal large subunit pseudouridine synthase B [Bordetella avium
           197N]
 gi|115423473|emb|CAJ50007.1| ribosomal large subunit pseudouridine synthase B [Bordetella avium
           197N]
          Length = 457

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 80/348 (22%), Positives = 132/348 (37%), Gaps = 11/348 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----KA 70
           ++ KV+A AGI SRRE+E +I   RV VNG         V + D + V+G  +     K 
Sbjct: 3   KLHKVLADAGIGSRREMEELIVAGRVSVNGEPA-HIGQRVAANDQVRVNGKLISRPNAKK 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               +  +     +V+        +           + +SVGRLD+NTEGLL+ T  G +
Sbjct: 62  PPRVILYHKPAGEIVSHDDPNGRANVFTRLPKLRTGKWLSVGRLDLNTEGLLIFTTSGDM 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +  P     R Y VR  G++D+ +   L +GI +                GSN W  
Sbjct: 122 ANRIMHPRYGTEREYAVRVLGEMDEAQRTSLVEGIDLDDGKAAFGSFDYLGGDGSNRWYR 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK-----ILREQ 244
           V L+EG+NRE++++FE     V+RLIR  +G   L  +L  G   E+        +++  
Sbjct: 182 VTLQEGRNREVRRMFEAVGVTVSRLIRTRFGDLVLPRSLRRGRWEELDASLVSALMVQLG 241

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           L     E           S ++ +      +     +  R+ +    + G S     +  
Sbjct: 242 LLRDEEESGGRRKSRQPQSHDSALPPGFGTMERNGMNGARIGRRGKLQGGRSASSATSPS 301

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                           H        + +      P+   K      + 
Sbjct: 302 DPFGTGLMFAGGYANGHPLGNDAPSKAKPAGASKPARGRKPGSGGGTQ 349


>gi|313622662|gb|EFR93029.1| RNA pseudouridine synthase family protein [Listeria innocua FSL
           J1-023]
          Length = 233

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 99/231 (42%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D + V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPEKDQVTVHGTPVVYQEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T  +               +    VGRLD +TEGLL++TNDG LA 
Sbjct: 61  VYFMLHKPQNVVSATEDNVSETVIDLLAQEDTLTNPFPVGRLDKDTEGLLIITNDGTLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y  +  G V  + +     G+ +          + + T       + V
Sbjct: 121 NLLSPKKHIDKTYYAKIDGDVTAEDVEAFSAGVTLDDGYTCKPAHLEIITPN----EIKV 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            ++EGK  +IK++F      V+ L RIS G  QL   L  G  R +++  L
Sbjct: 177 TIQEGKFHQIKRMFAARGKTVSYLKRISMGNLQLDESLELGEYRPLTENEL 227


>gi|281492918|ref|YP_003354898.1| ribosomal small subunit pseudouridine synthase A [Lactococcus
           lactis subsp. lactis KF147]
 gi|281376570|gb|ADA66056.1| Ribosomal small subunit pseudouridine synthase A [Lactococcus
           lactis subsp. lactis KF147]
          Length = 273

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 102/241 (42%), Gaps = 9/241 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKA 70
              R+ K +A +G+ SR EV+ ++ + RV V G +       V      +  DG  L   
Sbjct: 30  KDMRLDKFLAESGLGSRSEVKILLKKGRVTVAGEVQRDGRFQVDKNSRQVAFDGEILDYQ 89

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E     L      +  T  +         +       +  VGRLD NTEGLL+LTNDG L
Sbjct: 90  EYYYYLLNKPQGLVSATKDNLFKTVVQLLSEKDFREDIFPVGRLDKNTEGLLILTNDGAL 149

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT------QK 183
              L  P     + Y  R  G+V  + +N   +G+ ++ G      ++ ++       Q 
Sbjct: 150 GHDLTQPKKHVEKEYFARIDGKVTDEIVNKFAEGLTLKNGEKARPGELFIENIYKGESQS 209

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           G  + + V + EGK  ++K++FE     V  L RI  G   L   L  G+ R ++ + + 
Sbjct: 210 GWISEIRVIIHEGKFHQVKRMFEAVEMYVLYLKRIRMGNLALDSDLALGAYRPLTTEEIE 269

Query: 243 E 243
            
Sbjct: 270 N 270


>gi|312863597|ref|ZP_07723835.1| pseudouridylate synthase [Streptococcus vestibularis F0396]
 gi|311101133|gb|EFQ59338.1| pseudouridylate synthase [Streptococcus vestibularis F0396]
          Length = 243

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 106/234 (45%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+  + +++V VNG L       +    D I      L     
Sbjct: 1   MRLDKFLVDCGVGSRSQVKNFLKKKQVTVNGQLETSPKTQIDENKDRIAYLDQELTHETF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T +          +  +   +V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPQGVISATENPRHKTVLDLLDDTARHKQVFPVGRLDIDTHGLLLLTNNGDLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVT 190
            +  P     ++Y+ +  G +D++ +   +KGI ++       ++ +    +  S +WV 
Sbjct: 121 AMLSPKKHVDKIYQAKVAGVMDEEDILAFEKGIKLKDHTCQPAKLEIVSVDRNESTSWVQ 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           + + EGK  ++K++      +V  L R+S GP  L   L  G+ R ++++ L  
Sbjct: 181 ITIAEGKFHQVKRMVAACGKEVTELQRLSMGPLSLPNDLELGTWRRLTEEELEA 234


>gi|150392376|ref|YP_001322425.1| RNA-binding S4 domain-containing protein [Alkaliphilus
           metalliredigens QYMF]
 gi|149952238|gb|ABR50766.1| RNA-binding S4 domain protein [Alkaliphilus metalliredigens QYMF]
          Length = 235

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 108/236 (45%), Gaps = 13/236 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++  I+  G  SRRE + +I Q++V VNG +       V   D + + G PL+     
Sbjct: 1   MRLNNFISSTGKCSRREADELIKQKKVTVNGKIAT-LGCKVDPGDQVMLKGKPLQAKNND 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T       + +     +   R+  +GRLD ++EGL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCTTERHIRGNIIDFI--NHPERIFPIGRLDKDSEGLILLTNDGSIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI------QGICYGDMQVTLDTQKGSNA 187
           +     +  + Y V  + ++    +  + KG+ I      +       ++       ++ 
Sbjct: 118 ILAEENKHEKDYIVTVNKKITPSFIEGMSKGVKIYNPVKNKDTMTKRCKLVRI----NDR 173

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
              + L +G NR+I+++   F ++V +L R+      L  L  G  R ++++ +++
Sbjct: 174 TFKITLCQGLNRQIRRMCTHFGYRVVKLKRVRIMNLTLKDLTIGKWRNLTEEEVKD 229


>gi|223933741|ref|ZP_03625714.1| pseudouridine synthase [Streptococcus suis 89/1591]
 gi|302024514|ref|ZP_07249725.1| ribosomal small subunit pseudouridine synthase B [Streptococcus
           suis 05HAS68]
 gi|330833556|ref|YP_004402381.1| pseudouridine synthase [Streptococcus suis ST3]
 gi|223897583|gb|EEF63971.1| pseudouridine synthase [Streptococcus suis 89/1591]
 gi|329307779|gb|AEB82195.1| pseudouridine synthase [Streptococcus suis ST3]
          Length = 242

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 108/234 (46%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR EV++++  ++V VNG +       +    D I V G  L     
Sbjct: 1   MRLDKFLVDCGVGSRTEVKKLLKNKQVTVNGQVETSPKQQIDEKSDQIAVAGQVLSHETF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  D         +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYVLNKPKGVISATEDDRHRTVLDLLDNTARQKEVFPVGRLDIDTHGLLLLTNNGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
           V+  P     ++YR +  G + Q+ +     GI ++ +     Q+T+ +   +   + V 
Sbjct: 121 VMLSPKKHVDKLYRAQVDGIMTQEDVERFAAGIELKDLTCQPAQLTILSTDEAKQTSLVD 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           + +REGK  ++K++ +     V  L R++ GP +L   L  G  R ++   L++
Sbjct: 181 ITIREGKFHQVKRMVQACGKTVTDLQRLTMGPLRLDPKLALGEYRRLTAAELKQ 234


>gi|313617518|gb|EFR89863.1| RNA pseudouridine synthase family protein [Listeria innocua FSL
           S4-378]
          Length = 233

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 100/231 (43%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D + V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQVTVHGTPVIYQEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T  +               +    VGRLD +TEGLL++TNDG LA 
Sbjct: 61  VYFMLHKPQNVVSATEDNLSETVIDLLEQEDTLTNPFPVGRLDKDTEGLLIITNDGTLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y  +  G+V  + +     G+ +          + + T       + V
Sbjct: 121 NLLSPKKHIDKTYYAKIDGEVTAEDVEAFSAGVTLDDGYTCKPAHLEIITPN----EIKV 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            ++EGK  ++K++F      V+ L RIS G  QL   L  G  R +++  L
Sbjct: 177 TIQEGKFHQVKRMFAARGKTVSYLKRISMGNLQLDESLELGEYRPLTENEL 227


>gi|298717565|ref|YP_003730207.1| pseudouridylate synthase [Pantoea vagans C9-1]
 gi|298361754|gb|ADI78535.1| pseudouridylate synthase [Pantoea vagans C9-1]
          Length = 292

 Score =  174 bits (441), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 59/293 (20%), Positives = 114/293 (38%), Gaps = 5/293 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           +  R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +   +
Sbjct: 5   SSTRLNKYISESGICSRRDADRYIEQGNVFINGKRASV-GAQVFAGDVVKVNGQLIEPRD 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L L      +    +  +G      +  +   RV  +GRLD +++GL+ LTN G L 
Sbjct: 64  EDDLVLIALNKPVGIITTMEEGERDNISDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLV 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     +  + +  +  G+ + G            +K +     +
Sbjct: 124 NKILRAGNNHEKEYVVTVDKPITDEFIAGMSAGVPMLGTV----TKKCKVKKEAPFVFRI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ + F ++V +L R       L  L  G  R+++   L E        
Sbjct: 180 TLVQGLNRQIRRMCKHFGFEVTKLERTRIMNVNLKGLPLGEWRDLTDDELVELFKLLENS 239

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
            ++        +    V  +    S            +S+K  +   +K    
Sbjct: 240 SSEDKPAKKAKAPAKAVAAKKPQKSAAKPAEKADAAGASRKRFVQPGRKKKGR 292


>gi|315283394|ref|ZP_07871600.1| ribosomal small subunit pseudouridine synthase A [Listeria marthii
           FSL S4-120]
 gi|313612966|gb|EFR86902.1| ribosomal small subunit pseudouridine synthase A [Listeria marthii
           FSL S4-120]
          Length = 233

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 99/231 (42%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SRREV+ ++    V VNG + + +   V    D + V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRREVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQVTVHGTPVVYQEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T  +               +    VGRLD +TEGLL++TNDG LA 
Sbjct: 61  VYFMLHKPQNVVSATEDNVSETVIDLLAQEDTLTDPFPVGRLDKDTEGLLIITNDGTLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y  +  G V    +     GI +         ++ + T       + V
Sbjct: 121 NLLSPKKHIDKTYYAKIDGDVTATDVEAFAAGIELDDGYTCKPARLEIITPN----EIKV 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            ++EGK  ++K++F      V+ L RIS G  QL   L  G  R +++  L
Sbjct: 177 TIQEGKFHQVKRMFAARGKTVSYLKRISMGNLQLDESLELGEYRPLTETEL 227


>gi|256617552|ref|ZP_05474398.1| pseudouridine synthase [Enterococcus faecalis ATCC 4200]
 gi|256597079|gb|EEU16255.1| pseudouridine synthase [Enterococcus faecalis ATCC 4200]
          Length = 244

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 62/235 (26%), Positives = 104/235 (44%), Gaps = 5/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD I   G  L   + 
Sbjct: 1   MRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQIAFMGEILTYQKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T    D             + +  VGRLD +TEGLLLLTNDG LA 
Sbjct: 61  FYYMLHKPQGVISATEDQRDETVIDLLTDQDYRADLFPVGRLDKDTEGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTL--DTQKGSNAWV 189
            L  P     + Y     G V  +   L  +G  +  G      ++ +    ++   + V
Sbjct: 121 QLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEMVKPSRLVIETINEEEGTSVV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
            + ++EGK  ++K++       V  L R+  G   L   L  G  R +++  L++
Sbjct: 181 RLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGGYRPLTEAELQQ 235


>gi|302188863|ref|ZP_07265536.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. syringae 642]
          Length = 409

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 90/355 (25%), Positives = 141/355 (39%), Gaps = 16/355 (4%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG         V   D I
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDAT-LGQRVDLHDAI 62

Query: 61  EVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            VDG  +++ E     R  +        + T        +           R I++GRLD
Sbjct: 63  SVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           INT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++       
Sbjct: 123 INTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPARFT 182

Query: 176 QVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE+S+  + + L   +  +          + + + R +      +           +   
Sbjct: 243 REMSQYEV-DILAAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVRTLRPAAGA 301

Query: 294 GLSKQKKLATPV------HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
             +  ++             R    +                +     + S   P
Sbjct: 302 PATGGERAPRQPQITGSERDRPRGGDSTQRPSPRKDSGKPGSRAPRPPKTSRGTP 356


>gi|166030628|ref|ZP_02233457.1| hypothetical protein DORFOR_00294 [Dorea formicigenerans ATCC
           27755]
 gi|166029630|gb|EDR48387.1| hypothetical protein DORFOR_00294 [Dorea formicigenerans ATCC
           27755]
          Length = 246

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 115/241 (47%), Gaps = 13/241 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K ++ AG+ SRRE +R+I   RV V+G+      + V     I V    ++ AE+ 
Sbjct: 2   IRLNKYLSEAGVCSRREADRLIEAGRVTVDGVRA-VPGMKVSEEQKICVGKKVIQGAEQK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +   +KP G+V T                   RV   GRLD ++EGLL++TNDG L   
Sbjct: 61  VVLAVNKPAGIVCT--GDMKVKNNIIRFLHYPVRVTYAGRLDKDSEGLLIMTNDGELINS 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC------YGDMQVTLDTQKGSNA 187
           +        + Y VR   ++  + +  + +G+ IQ +           +V    ++    
Sbjct: 119 MMRARYHHEKEYHVRVDKEITSEFVRQMSEGVHIQDVEKNLDAVTRPCEV----KQIGKY 174

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
             ++ L +G NR+I+++ E   +KV +L+RI     +LG+L +G+ R++  + L++    
Sbjct: 175 TFSIILTQGLNRQIRRMCEALGYKVTKLVRIRIMNVELGSLKSGAVRKIEGQELKKLYEQ 234

Query: 248 H 248
            
Sbjct: 235 A 235


>gi|259906718|ref|YP_002647074.1| 23S rRNA pseudouridine synthase F [Erwinia pyrifoliae Ep1/96]
 gi|224962340|emb|CAX53795.1| Ribosomal large subunit pseudouridine synthase F [Erwinia
           pyrifoliae Ep1/96]
 gi|283476501|emb|CAY72316.1| putative pseudouridylate synthase [Erwinia pyrifoliae DSM 12163]
          Length = 292

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/292 (20%), Positives = 113/292 (38%), Gaps = 5/292 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++K I  +GI SRR+ +R I Q  V +NG         V + D ++V+G  +     
Sbjct: 6   SIRLNKYIGESGICSRRDADRYIEQGNVFINGKRASV-GDRVFAGDVVKVNGQLIEPRNE 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +    +  +G      +  +   RV  +GRLD +++GL+ LTN G L  
Sbjct: 65  EDLVVIALNKPVGIISTTEEGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  V ++ +  L  G+ + G            +K S     + 
Sbjct: 125 KILRAGNDHEKEYLVTVNKPVTEEFIRGLGAGVPMLGTV----TKKCKVKKESTFVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E F ++V++L R       L  L  G  R+++   L E         
Sbjct: 181 LVQGLNRQIRRMSEHFGYEVSKLERTRIMNVSLKGLPPGEWRDLTDDELIELFKLIENSS 240

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           ++           T  +      ++     T     + +K      +K    
Sbjct: 241 SEDGTAKKTKPKATTAKKPAASGAKGGAKATGNANPAPRKRFAQPGRKKKGR 292


>gi|323490333|ref|ZP_08095548.1| ribosomal large subunit pseudouridine synthase F [Planococcus
           donghaensis MPA1U2]
 gi|323396003|gb|EGA88834.1| ribosomal large subunit pseudouridine synthase F [Planococcus
           donghaensis MPA1U2]
          Length = 235

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 58/228 (25%), Positives = 111/228 (48%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K ++  GI SRR  ++ I   RV +NG L       + S+D ++VDG  + +  + 
Sbjct: 1   MRINKFLSETGITSRRGADKFIEAGRVTINGNLA-ELGSKIESSDEVKVDGKVIEQPNQQ 59

Query: 74  R-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP+G+ +T       + V  +  +   R+  +GRLD ++EGL+LLTNDG +  
Sbjct: 60  YVYLALNKPVGITSTTERHIEGNIV--DFVNHAERIFHIGRLDKDSEGLILLTNDGDIVN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V+    + +  L+ +++G+ I        +     +K S+    + 
Sbjct: 118 EILRVENEHEKEYVVKVDMPITESFLSKMEEGVEILDTKTLPAKA----EKLSSYTFKLT 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           LR+G NR+I+++     ++V  L R+      LG L  G  R+++   
Sbjct: 174 LRQGLNRQIRRMCTALGYEVRSLKRVRIINIFLGDLPVGEWRDLTDVE 221


>gi|238757900|ref|ZP_04619082.1| Ribosomal small subunit pseudouridine synthase A [Yersinia aldovae
           ATCC 35236]
 gi|238703885|gb|EEP96420.1| Ribosomal small subunit pseudouridine synthase A [Yersinia aldovae
           ATCC 35236]
          Length = 236

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 55/238 (23%), Positives = 109/238 (45%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    
Sbjct: 1   MRLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQTVGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +  D       G+ +          ++ +   +     V +
Sbjct: 121 ITSPRHHCEKTYLVTLEHPLADDTAQQFTDGVQLHNEESLTKPARLEVIEPQ----LVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
            L EG+  ++K++F     +V  L R   G  +L   L  G  R ++++ +     PH
Sbjct: 177 TLSEGRYHQVKRMFAAVGNRVLELHRERIGEIKLDDDLAPGEYRPLTEEEIASVGAPH 234


>gi|238789715|ref|ZP_04633498.1| Ribosomal small subunit pseudouridine synthase A [Yersinia
           frederiksenii ATCC 33641]
 gi|238722268|gb|EEQ13925.1| Ribosomal small subunit pseudouridine synthase A [Yersinia
           frederiksenii ATCC 33641]
          Length = 235

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 55/238 (23%), Positives = 109/238 (45%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    
Sbjct: 1   MRLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQTVGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     + +D       G+ +          Q+ +   +     V +
Sbjct: 121 ITSPRHHCEKTYLVTLEHPLAEDTAQQFADGVQLHNEQSLTKPAQLEVIEPQ----VVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
            + EG+  ++K++F     +V  L R   G  +L   L  G  R ++ + +     PH
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVLELHRERIGEIKLDDDLAPGEYRPLTAEEIASVGAPH 234


>gi|229586865|ref|YP_002845366.1| Ribosomal large subunit pseudouridine synthase [Rickettsia africae
           ESF-5]
 gi|228021915|gb|ACP53623.1| Ribosomal large subunit pseudouridine synthase [Rickettsia africae
           ESF-5]
          Length = 230

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 106/230 (46%), Positives = 148/230 (64%), Gaps = 2/230 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K+I+ AG+ SRR+ E++I + +VKV+G+ +     NV  ++ IEV G  +    + R
Sbjct: 3   RLAKIISNAGVCSRRDAEKLIVEGQVKVDGVTILSPTTNVDISNQIEVSGTLINNIHKPR 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LW+Y+KP+GL+TTH DP  R TVF+ L     RVIS+GRLD+N+EGLLLLTN G LAR  
Sbjct: 63  LWIYYKPVGLITTHKDPLSRKTVFEQLTG-LPRVISIGRLDLNSEGLLLLTNSGDLARQF 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPS++  RVY VR +G+ D    +   K + I GI Y    + L  Q  +N W  V L 
Sbjct: 122 ELPSSRLKRVYHVRAYGKSDILLKSN-YKNLEIDGIFYNPHSIKLLKQNKTNCWFEVVLF 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           EGKNREI+++FE+   KVN+LIRI YG F +  L  G  +E++ KIL   
Sbjct: 181 EGKNREIRRIFEYCGLKVNKLIRIQYGSFTIDNLKPGDYKEINNKILENH 230


>gi|256424973|ref|YP_003125626.1| pseudouridine synthase [Chitinophaga pinensis DSM 2588]
 gi|256039881|gb|ACU63425.1| pseudouridine synthase [Chitinophaga pinensis DSM 2588]
          Length = 389

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 69/345 (20%), Positives = 128/345 (37%), Gaps = 15/345 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
                ++K I+  G  SRRE + +I   RV +N              D +EVDG  +  A
Sbjct: 2   DQSISLNKFISDTGYCSRREADNLITSGRVLLNDRPAA-LGNRYKPGDTVEVDGSLITAA 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ++ +            T +          +  +   R+  +GRLD ++EGL+ LTNDG +
Sbjct: 61  KKEKRVYLALNKPPGITTTTELHIKDNIISFVNYPQRIFPIGRLDKDSEGLIFLTNDGDI 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +   +    + Y VR +  +D + L+ + +G+ I        +V +           
Sbjct: 121 INKILRAANNHEKEYVVRVNKPIDTNFLHQMSQGVPILDTRTLPCKVQM----TGRQTFR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E+  + V  L R+     +L  L  G  R +S+  +        +
Sbjct: 177 ITLTQGLNRQIRRMCEYLGYTVVGLQRVRIMNVRLDKLPLGKWRYLSEAEI------AFI 230

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           +E+  +              R      V +       ++ +    +  K++A P   R  
Sbjct: 231 KESVADSTKVSG-ESKPSGARRKTAKPVEEKEHLRTGSTPKNKPATGHKRVAAPAKHREE 289

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRS--PSFPSKRSLRRTSAK 353
               +M K    S   +       HR    P+F  K        K
Sbjct: 290 QEPAFMPKN-KPSAGHNRAAAPAKHREQQEPAFTPKNKSSTHKHK 333


>gi|163753337|ref|ZP_02160461.1| pseudouridine synthase, Rsu [Kordia algicida OT-1]
 gi|161327069|gb|EDP98394.1| pseudouridine synthase, Rsu [Kordia algicida OT-1]
          Length = 244

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 54/234 (23%), Positives = 108/234 (46%), Gaps = 8/234 (3%)

Query: 11  FTPQ--RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
             PQ  R++K ++ AG  SRR  +++I Q+RV +NG++       +   D + VDG  + 
Sbjct: 2   SEPQLTRINKFLSEAGYCSRRAADKLIEQRRVTINGVVPA-MGTKIAPGDEVRVDGELIS 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             +   ++L       +   +D         +  +  SR+  +GRLD  +EGL+ LT+DG
Sbjct: 61  DPKEKPVYLAFNKPIGIVCTTDTKVEKDNIIDYINYPSRIFPIGRLDKPSEGLIFLTSDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y V  +  +  D +  +  GI I G      +     ++ +   
Sbjct: 121 DIVNKILRARNNHEKEYEVTVNRPITSDFIQKMGNGIPILGTLTRKCK----VEQLTKYT 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
             + L +G NR+I+++ E+ +++V +L R       L  +  G  R ++++ L+
Sbjct: 177 FKIILTQGLNRQIRRMCEYLDYRVVKLKRTRIMNVSL-DIPVGKWRHLTEEELQ 229


>gi|170722948|ref|YP_001750636.1| RNA-binding S4 domain-containing protein [Pseudomonas putida W619]
 gi|169760951|gb|ACA74267.1| RNA-binding S4 domain protein [Pseudomonas putida W619]
          Length = 354

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 87/357 (24%), Positives = 152/357 (42%), Gaps = 13/357 (3%)

Query: 1   MKDKNIVQENFTP---QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M ++++     TP   +++ KV+AR G+ SRR+VE  I+Q R+KVNG+        V   
Sbjct: 1   MSEQDLQNTEITPPAGEKLQKVLARIGVGSRRDVEAWISQGRIKVNGVEAT-LGQRVDLH 59

Query: 58  DHIEVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
           D I VDG  +++ E     R  +        + T        +           R I++G
Sbjct: 60  DAIAVDGKLIKREEAAEATRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIG 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RLDINT GLLL T DG LA  L  PS +  R Y VR  G+VD + +  LK G++++    
Sbjct: 120 RLDINTTGLLLFTTDGELANRLMHPSYEMDREYAVRVRGEVDDEMIERLKAGVMLEDGPA 179

Query: 173 GDMQVTLDTQ-KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
               +      +G N W    + EG+NRE+++++E     V+RL R+ +GP  L   L  
Sbjct: 180 KFTDIQKAPGGEGFNHWYHCVVMEGRNREVRRLWESQGMVVSRLKRVRFGPVFLNSDLPM 239

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G  RE+++  + + L   +  +        + + + + R +      +           +
Sbjct: 240 GRWREMTQGEI-DILAAEVGLQPVALPAMNLKAKDKMERLQRKSTRPMGRSERVRSLRPA 298

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
           Q+   + ++    P        +   A     S +     + +  + +     K   
Sbjct: 299 QEA-AAAERPARQPREEAPRKGSRGSAVAERPSEMRKRPAKTDGDKPAGRGRGKPRG 354


>gi|294672844|ref|YP_003573460.1| ribosomal large subunit pseudouridine synthase B [Prevotella
           ruminicola 23]
 gi|294472710|gb|ADE82099.1| ribosomal large subunit pseudouridine synthase B [Prevotella
           ruminicola 23]
          Length = 449

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 110/250 (44%), Gaps = 1/250 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K I  +   P R++K +A AG+ SRRE +  I    V VNG ++      ++ TD +
Sbjct: 201 IEYKEINYDPNEPLRLNKFLANAGVCSRREADEFIQAGVVSVNGEIVTELGTKILRTDVV 260

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P+   ++  + L      + T+      ++ +     +   R+  VGRLD NT G
Sbjct: 261 KFHDQPVNIEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKNACPERIYPVGRLDRNTTG 320

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     V    L  + +GI ++        V   
Sbjct: 321 VLLLTNDGDLASKLTHPKYLKKKIYHVYLDKNVTAHDLAQIAEGIQLEDGEIKADDVQYA 380

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                   V + +  GKNR ++++FE   ++V +L R+ +       L  G  R ++++ 
Sbjct: 381 HPTDKKQ-VGIEIHSGKNRIVRRIFESLGYRVQKLDRVQFAGLTKKNLKRGDWRYLTEEE 439

Query: 241 LREQLGPHLL 250
           +         
Sbjct: 440 VDRLRMGAYE 449


>gi|168231182|ref|ZP_02656240.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
 gi|194472572|ref|ZP_03078556.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|194458936|gb|EDX47775.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|205334218|gb|EDZ20982.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
          Length = 289

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 62/292 (21%), Positives = 116/292 (39%), Gaps = 5/292 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R++K I+ +GI SRRE +R I Q  V +NG         V++ D ++V+G  +  
Sbjct: 3   TDTSTRLNKYISESGICSRREADRFIEQGNVFINGKRAA-IGDQVVAGDVVKVNGRLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   L L      +    +  DG      +  +   R+  +GRLD +++GL+ LTN G 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRIFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     +  + +  +  G+ I G            +K +    
Sbjct: 122 LVNKILRAGNDHEKEYLVAVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +      
Sbjct: 178 RITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
              ++    A      T ++     I +  +            +   K+K  
Sbjct: 238 RSSSEAKPKAKAKPKTTGIKRPVVAIEKSNEKARPTSSGKRFTSPGRKKKGR 289


>gi|104773906|ref|YP_618886.1| pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|116513914|ref|YP_812820.1| 16S rRNA uridine-516 pseudouridylate synthase related enzyme
           [Lactobacillus delbrueckii subsp. bulgaricus ATCC
           BAA-365]
 gi|103422987|emb|CAI97669.1| Pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|116093229|gb|ABJ58382.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC BAA-365]
 gi|325125580|gb|ADY84910.1| Ribosomal large subunit pseudouridine synthase B [Lactobacillus
           delbrueckii subsp. bulgaricus 2038]
          Length = 239

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 78/231 (33%), Positives = 120/231 (51%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRRE E+MI   RV+V+G ++ +    V S + + VD  P+ +    
Sbjct: 4   ERLQKVIAQAGIASRREAEKMILAGRVRVDGQVVTKLGTKVSSIEQVVVDNQPIERESHH 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     +++   D  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA +
Sbjct: 64  TYLFYKPRG-VISAVKDNKGRKTVADYFTDLPYRLYPVGRLDYDTSGLLLMTNDGELANL 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVTV 191
           L  P  +  +VY  +  G +  D++  LKKG+ I        QV +           V +
Sbjct: 123 LMHPRNEVDKVYVAKIKGILQPDEIKALKKGVQIGRYKTKPAQVKVLKTNPRAQTQIVQL 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EG   ++K++F+  N  V++L R  Y    L  L +G  RE++ K + 
Sbjct: 183 TIHEGHYHQVKEMFKAVNHLVDKLSRERYSFLDLQGLTSGQYRELNHKEVD 233


>gi|52424446|ref|YP_087583.1| RsuA protein [Mannheimia succiniciproducens MBEL55E]
 gi|52306498|gb|AAU36998.1| RsuA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 246

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 52/232 (22%), Positives = 106/232 (45%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R +  +++ Q  V+VNG +++  ++ +   D +  +G  L   E  
Sbjct: 17  MRLDKFLAENTGLTRSQAAKILRQGNVQVNGQVVKSGSLKITPQDEVLFEGESLEWLEDG 76

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP G V +H D +  +        +  ++ + GRLD +T GL+LLT+DG  +  
Sbjct: 77  VYIMLNKPQGYVCSHDDGEYPTVYQFFDYPLAGKLHTAGRLDADTSGLVLLTDDGKWSHR 136

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+ +     ++GI+++G         + +      +  V +
Sbjct: 137 VTSPKYHCQKTYLVTLADPVESNYRQACEQGILLRGEKEPTKPAILEII----DDYNVNL 192

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EG+  ++K++F     KV  L R   G  +L   L  G  R ++ + ++
Sbjct: 193 TISEGRYHQVKRMFAALGNKVVGLHRWKIGNIELDEDLPEGEFRVLTAEEIQ 244


>gi|226330601|ref|ZP_03806119.1| hypothetical protein PROPEN_04519 [Proteus penneri ATCC 35198]
 gi|225201396|gb|EEG83750.1| hypothetical protein PROPEN_04519 [Proteus penneri ATCC 35198]
          Length = 244

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 51/238 (21%), Positives = 105/238 (44%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  + R +    V ++G +++  +  +     +  DG  L +    
Sbjct: 11  MRLDKFLSQQLGISRSLILRELRAGLVTIDGEMVKSGSTKIAPEQEVAYDGKVLTQILGP 70

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KPIG V +  DP   + ++     +  ++ + GRLDI+T GL+LLT++G  +  
Sbjct: 71  RYFMLNKPIGYVCSTDDPVNPTILYFIDEPLAHKLHAAGRLDIDTTGLVLLTDNGQWSHR 130

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     + +      +KG+ + G        ++ +     +   V +
Sbjct: 131 ITAPKHHCEKTYLVTLEEPIGEGVAEQFQKGVQLNGEKDLTKPAKLEIL----TPTEVKL 186

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
            + EGK  ++K++F      V+ L R   G   L   L  G  R ++++ +     P 
Sbjct: 187 TISEGKYHQVKRMFAAVGNHVSALHRERIGDITLDETLAEGEYRPLTEEEINSIHLPQ 244


>gi|325688986|gb|EGD30994.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK115]
          Length = 242

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 64/232 (27%), Positives = 105/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++++ +  V VNG   +     +  T D I V G  L   + 
Sbjct: 1   MRLDKFLAENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDETADEIIVSGQRLTYEKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  D         +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPQGVISATEDDRHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
           V+  P     ++YR +  G ++Q        GI ++       Q+ +     +   + V 
Sbjct: 121 VMLSPKKHVEKIYRAQVAGLMNQADEERFAAGIELKDFTCQPAQLKILELDEAKETSLVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + L EGK  ++K++      +V  L R++ GP QL   L  G  R +++K +
Sbjct: 181 ITLAEGKFHQVKRMVASCGKEVTDLQRLTMGPLQLDPALALGEWRRLTEKEI 232


>gi|254818897|ref|ZP_05223898.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           intracellulare ATCC 13950]
          Length = 247

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 73/236 (30%), Positives = 111/236 (47%), Gaps = 4/236 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
                R+ KV+++AGIASRR  E++I + RV+V+G ++      V      I VDG  + 
Sbjct: 3   EAEGIRLQKVLSQAGIASRRAAEKLIIEGRVEVDGQVVTELGTRVDPDVSVIRVDGARIV 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLT 125
             +       +KP G+ +T SD  GR  + D +         +  VGRLD +TEGL+LLT
Sbjct: 63  LDDSQVYLALNKPRGVHSTMSDDRGRPCIGDLIERRVRGNKNLFHVGRLDADTEGLILLT 122

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  PS +  + Y     G V +     L+ GI +        +  +      
Sbjct: 123 NDGELAHRLMHPSHEVPKTYLATVTGSVPRGVGKALRAGIELDDGPARVDEFAVVDAIPG 182

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              V V L EG+NR ++++     + V  L+R   GP  LG    GS R + +  +
Sbjct: 183 KTLVRVTLHEGRNRIVRRLLAAAGFPVEALVRTDIGPVSLGKQRPGSFRALGRDEI 238


>gi|222529534|ref|YP_002573416.1| pseudouridine synthase [Caldicellulosiruptor bescii DSM 6725]
 gi|222456381|gb|ACM60643.1| pseudouridine synthase [Caldicellulosiruptor bescii DSM 6725]
          Length = 230

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 71/222 (31%), Positives = 116/222 (52%), Gaps = 2/222 (0%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRLWLY 78
           +A+ G+ASRR+ E +I Q RVKVNG  + +    V    D +EVDG  +    +    + 
Sbjct: 1   MAQCGVASRRKCEEIILQGRVKVNGKTVNQLGFKVDPEKDVVEVDGKRISLQMQKVYIML 60

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLARVLELP 137
           +KP G++++  D  GR TV D +    +     VGRLD +T GL++LTNDG  A  +  P
Sbjct: 61  NKPFGVISSAKDEKGRKTVVDLVKDKVNVRVFPVGRLDFDTTGLIILTNDGEFAYKVTHP 120

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGK 197
                + Y V   G   ++++   +KG++I G      +  +      NA V + + EG+
Sbjct: 121 KHDIEKTYIVLIKGIPSKEEIERFEKGLLIDGKMTAPAKFKILKLINGNALVEIKIHEGR 180

Query: 198 NREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           NR+I+K+ +    KV +L R++ G  QLG L  G    + ++
Sbjct: 181 NRQIRKMCDQIGHKVLKLKRVAIGKLQLGKLKEGEFVFLDRE 222


>gi|37523966|ref|NP_927343.1| hypothetical protein glr4397 [Gloeobacter violaceus PCC 7421]
 gi|35214972|dbj|BAC92338.1| glr4397 [Gloeobacter violaceus PCC 7421]
          Length = 248

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 83/237 (35%), Positives = 118/237 (49%), Gaps = 4/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A  GIASRR+ E +I   +V VNG +++R    V    D IEV G PL     
Sbjct: 5   IRLQKLLAEHGIASRRKAEALIVSGQVCVNGTVVDRLGTRVDPQIDLIEVFGQPLHCMPP 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTNDGG 129
               L HKP+G ++T  DP GR TV D L         +  VGRLD ++ G L+++NDG 
Sbjct: 65  LLYVLLHKPVGWLSTCFDPRGRRTVLDLLPAEWRTGQGLHPVGRLDCDSSGALIVSNDGE 124

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
               L  P  Q  + YRV   G+     L   + G+V++G       VT+ ++      +
Sbjct: 125 FTFRLTHPRHQLPKTYRVWVRGRPTAAVLGRWRAGVVLEGQKTLPAAVTVVSRAAEATEL 184

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            V L EG+NR+I+KV E     V RL R + GP  L  L  G+ R +S   +   L 
Sbjct: 185 EVVLVEGRNRQIRKVAELLGHPVERLHRTAIGPVALAGLPPGAHRLLSASQIERLLQ 241


>gi|328944867|gb|EGG39027.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1087]
          Length = 242

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 106/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++++ +  V VNG   +     +  T D I V G  L   + 
Sbjct: 1   MRLDKFLAENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDETADEIAVSGQRLTYEKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  D         +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPRGVISATEDDRHQTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVT 190
            +  P     ++YR +  G ++Q  +     GI ++        + +    ++  ++ V 
Sbjct: 121 AMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKDFTCQPAHLKILELDEEKEDSLVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + L EGK  ++K++      +V  L R++ GP QL   L  G  R ++++ +
Sbjct: 181 ITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDFALALGEWRRLTEEEM 232


>gi|117618383|ref|YP_857355.1| ribosomal small subunit pseudouridine synthase A [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
 gi|117559790|gb|ABK36738.1| ribosomal small subunit pseudouridine synthase A [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
          Length = 230

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 108/231 (46%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +      +R    ++I Q  V V+GI++++ A ++     +E DGV L   +R 
Sbjct: 1   MRLDKFLCDCSDLTRSLAGKLIRQGEVMVDGIVVKQPAFHINEQSQVEFDGVTLTLDQRN 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V ++ DPD  +  F        ++  VGRLD++T GL+L+T+DG  +  
Sbjct: 61  RYFMLHKPEGYVCSNEDPDHPTVFFLMDEPAMGKLHVVGRLDLDTTGLVLVTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y V     V  D + L  +G+++  +       Q+ +           +
Sbjct: 121 ITSPRHECAKTYHVWLADPVSPDAIALFAEGVLLRSETEKTRPAQLEIL----GECEARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R   G   L   L  G  RE++   +
Sbjct: 177 TIHEGKYHQVKRMFAAIGNKVVGLHRERVGGLTLDEELAPGEYRELTADEI 227


>gi|300856844|ref|YP_003781828.1| ribosomal small subunit pseudouridine synthase A [Clostridium
           ljungdahlii DSM 13528]
 gi|300436959|gb|ADK16726.1| ribosomal small subunit pseudouridine synthase A [Clostridium
           ljungdahlii DSM 13528]
          Length = 244

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 107/231 (46%), Gaps = 3/231 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A  G  +R+E++ ++    VK+NG +++ +++ +      IEV G  +   +  
Sbjct: 9   RIDKILANLGFGTRKEIKAVVKNGEVKINGTVIKDSSMKIDPDKSTIEVGGNVVEYKKNI 68

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L +      +  T  + D              +   VGRLD +TEGLLL+TNDG L   
Sbjct: 69  YLLMNKPQGVVSATFDNYDETVIDILEPEYQAFKPFPVGRLDKDTEGLLLITNDGELNHR 128

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVG 192
           +  P     +VY       +D+  +N  KKGI ++        ++ +       A V V 
Sbjct: 129 MISPKNHVDKVYYAEIDKYLDERDVNRFKKGIQLKDGYKCLPGKLHIIESDEDGAKVEVT 188

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           ++EGK  ++K++F      V  L RI +GP  L   L  G  RE+SK  + 
Sbjct: 189 IQEGKFHQVKRMFNALGKNVVYLKRIKFGPIDLDKDLNLGQYRELSKNEIE 239


>gi|332365802|gb|EGJ43559.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK355]
          Length = 242

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 104/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++++ +  V VNG   +     +  T D I V G  L   + 
Sbjct: 1   MRLDKFLAENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDETADEIIVSGQRLIYEKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  D         +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPQGVISVTEDDRHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            +  P     ++YR +  G ++Q  +     GI ++       Q+ +     +   + V 
Sbjct: 121 AMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKDFICQPAQLKIVELDEAKETSLVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + L EGK  ++K++      +V  L R+  GP QL + L  G  R +++  +
Sbjct: 181 ITLAEGKFHQVKRMVASCGKEVTDLQRLRMGPLQLDSALSLGEWRRLTEAEI 232


>gi|332293444|ref|YP_004432053.1| pseudouridine synthase [Krokinobacter diaphorus 4H-3-7-5]
 gi|332171530|gb|AEE20785.1| pseudouridine synthase [Krokinobacter diaphorus 4H-3-7-5]
          Length = 260

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 53/265 (20%), Positives = 103/265 (38%), Gaps = 6/265 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E     R++K ++  G  SRR  +++I Q RV +NG +       +   D + V+G  + 
Sbjct: 2   EERKQTRINKYLSEVGYCSRRAADKLIEQGRVTINGRIP-EMGTKISQGDEVHVNGELIS 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 +++       +   +D         +  +  SR+  +GRLD  +EGL+ LTNDG
Sbjct: 61  APTEKPVYIAFNKPVGIVCTTDTRVEKDNIIDYINYPSRIFPIGRLDKPSEGLIFLTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y V     +    +  +  G+ I              ++ S   
Sbjct: 121 DIVNKILRARNNHEKEYEVWVDRPITPSFIQQMGNGVPILDTVTRTCH----VEQLSRFS 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E  +++V RL R       L  +  G  R ++++ ++E     
Sbjct: 177 FKIILTQGLNRQIRRMCEALDYEVTRLKRNRIMNVSL-DVEEGKWRYITEEEMKEIYVLV 235

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPN 273
              E            + L   R  
Sbjct: 236 ADSEKTQAEKDAEPKFKDLRSSRNR 260


>gi|304395011|ref|ZP_07376895.1| pseudouridine synthase [Pantoea sp. aB]
 gi|304357264|gb|EFM21627.1| pseudouridine synthase [Pantoea sp. aB]
          Length = 292

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 57/295 (19%), Positives = 111/295 (37%), Gaps = 5/295 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +  
Sbjct: 3   TDSSTRLNKYISESGICSRRDADRYIEQGNVFINGKRASV-GAQVFAGDVVKVNGQLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   L L      +    +  +G      +  +   RV  +GRLD +++GL+ LTN G 
Sbjct: 62  RDEDDLVLIALNKPVGIITTMEEGERDNISDFVNHSKRVFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     +  + +  +  G+ + G            +K +    
Sbjct: 122 LVNKILRAGNNHEKEYVVTVDKPITDEFIAGMSAGVPMLGTV----TKKCKVKKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ + F ++V +L R       L  L  G  R+++   L E      
Sbjct: 178 RITLVQGLNRQIRRMCKHFGFEVTKLERTRIMNVNLKGLPLGEWRDLTDDELVELFKLLE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
              ++        +                         +S+K  +   +K    
Sbjct: 238 NSSSEDKPAKKAKAPAKAAAASKPQKRAAKPAEKADANGASRKRFVQPGRKKKGR 292


>gi|326407871|gb|ADZ64942.1| ribosomal small subunit pseudouridine synthase A [Lactococcus
           lactis subsp. lactis CV56]
          Length = 273

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 102/241 (42%), Gaps = 9/241 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKA 70
              R+ K +A +G+ SR EV+ ++ + RV V G +       V      +  DG  L   
Sbjct: 30  KDMRLDKFLAESGLGSRSEVKILLKKGRVTVAGEVQRDGRFQVDKNSRQVAFDGEILDYQ 89

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E     L      +  T  +         +       +  VGRLD NTEGLL+LTNDG L
Sbjct: 90  EYYYYLLNKPQGLVSATKDNLFKTVVQLLSEKDFREDIFPVGRLDKNTEGLLILTNDGAL 149

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT------QK 183
              L  P     + Y  R  G+V  + +N   +G+ ++ G      ++ ++       Q 
Sbjct: 150 GHDLTQPKRHVEKEYFARIDGKVTDEIVNKFAEGLTLKNGEKARPGELFIENIYKGESQS 209

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           G  + + V + EGK  ++K++FE     V  L RI  G   L   L  G+ R ++ + + 
Sbjct: 210 GWISEIRVIIHEGKFHQVKRMFEAVEMYVLYLKRIRMGNLALDSDLALGAYRPLTTEEIE 269

Query: 243 E 243
            
Sbjct: 270 N 270


>gi|225572683|ref|ZP_03781438.1| hypothetical protein RUMHYD_00872 [Blautia hydrogenotrophica DSM
           10507]
 gi|225039919|gb|EEG50165.1| hypothetical protein RUMHYD_00872 [Blautia hydrogenotrophica DSM
           10507]
          Length = 262

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 70/265 (26%), Positives = 120/265 (45%), Gaps = 8/265 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K ++ AG+ SRRE + +I Q RV V+G         V     I VD   +R+ +
Sbjct: 4   EKIRLNKYLSDAGVCSRREADSLILQGRVTVDGRKAVT-GEKVSVDQQIRVDNREIRQGQ 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L L +KP G++ T  +         +  +   RV  VGRLD++++GL+LLTN G L 
Sbjct: 63  PKVLLLLNKPRGIICTAKNQ---KDNIVDFVNYPIRVYPVGRLDVDSQGLILLTNQGELV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y+V     V ++ L+ + KG+ I G      Q+    +K       +
Sbjct: 120 NKIMRAGNYHEKEYQVTVDHPVTKEFLSKMAKGVPILGTVTRPCQIKRTGEKS----FQI 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ E+F ++V RL R      +LG L  G+ REV+ +  RE     +  
Sbjct: 176 ILTQGLNRQIRRMCEYFGYRVVRLNRTRIMNLKLGKLPVGAYREVTSEEWRELQRLLVDS 235

Query: 252 EAQVNLDAPIYSSETLVRDRPNIIS 276
            +            +   ++     
Sbjct: 236 SSVPCRKTGGIYGHSSGENQRAGTK 260


>gi|213163156|ref|ZP_03348866.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
          Length = 289

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 60/292 (20%), Positives = 114/292 (39%), Gaps = 5/292 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R++K I+ +GI SRRE +R I Q  V +NG         V++ D ++V+G  +  
Sbjct: 3   TDTSTRLNKYISESGICSRREADRFIEQGNVFINGKRAA-IGDQVVAGDVVKVNGRLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   L L      +    +  DG      +  +   R+  +GRLD +++GL+ LTN G 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRIFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     +  + +  +  G+ I G            +K +    
Sbjct: 122 LVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F ++V +L R       L  +  G   +++   L +      
Sbjct: 178 RITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWHDLTDDELIDLFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
              ++    A        ++     I +  +            +   K+K  
Sbjct: 238 GSSSEAKPKAKAKPKTAGIKRPVVAIEKSNEKARPASSGKRFTSPGRKKKGR 289


>gi|55823410|ref|YP_141851.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           thermophilus CNRZ1066]
 gi|55739395|gb|AAV63036.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           thermophilus CNRZ1066]
          Length = 243

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 57/234 (24%), Positives = 103/234 (44%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+  + +++V VNG +       +    D I   G  L     
Sbjct: 1   MRLDKFLVDCGVGSRSQVKTFLKKKQVTVNGQVETSPKTQIDEDKDQIAYLGQELTHETF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T            +  +   +V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPQGVISATEDSRHKTVLDLLDETARHKQVFPVGRLDIDTHGLLLLTNNGDLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVT 190
            +  P     ++Y+ +  G +D++ +   +KGI ++       ++ + +     S + V 
Sbjct: 121 AMLSPKRHVDKIYQAKVAGIMDEEDILAFEKGIKLKDHTCQPAKLEIVSVDRNASTSLVQ 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           + + EGK  ++K++      +V  L R+  GP  L   L  G  R ++++ L  
Sbjct: 181 ITIAEGKFHQVKRMVAACGKEVADLQRLKMGPLSLPNDLELGDWRRLTQEELDA 234


>gi|55821481|ref|YP_139923.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           thermophilus LMG 18311]
 gi|55737466|gb|AAV61108.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           thermophilus LMG 18311]
 gi|312278820|gb|ADQ63477.1| Pseudouridine synthase [Streptococcus thermophilus ND03]
          Length = 243

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 57/234 (24%), Positives = 103/234 (44%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+  + +++V VNG +       +    D I   G  L     
Sbjct: 1   MRLDKFLVDCGVGSRSQVKTFLKKKQVTVNGQVETSPKTQIDEDKDQIAYLGQELTHETF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T            +  +   +V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPQGVISATEDSRHKTVLDLLDETARHKQVFPVGRLDIDTHGLLLLTNNGDLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVT 190
            +  P     ++Y+ +  G +D++ +   +KGI ++       ++ + +     S + V 
Sbjct: 121 AMLSPKKHVDKIYQAKVAGIMDEEDILAFEKGIKLKDHTCQPAKLEIVSVDRNASTSLVQ 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           + + EGK  ++K++      +V  L R+  GP  L   L  G  R ++++ L  
Sbjct: 181 ITIAEGKFHQVKRMVAACGKEVADLQRLKMGPLSLPNDLELGDWRRLTQEELDA 234


>gi|270291299|ref|ZP_06197521.1| ribosomal large subunit pseudouridine synthase B [Pediococcus
           acidilactici 7_4]
 gi|304385048|ref|ZP_07367394.1| ribosomal large subunit pseudouridine synthase B [Pediococcus
           acidilactici DSM 20284]
 gi|270280145|gb|EFA25981.1| ribosomal large subunit pseudouridine synthase B [Pediococcus
           acidilactici 7_4]
 gi|304329242|gb|EFL96462.1| ribosomal large subunit pseudouridine synthase B [Pediococcus
           acidilactici DSM 20284]
          Length = 237

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 79/231 (34%), Positives = 127/231 (54%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR+ E++IA+  VKVNG +++     V   D IEVD VP++  E+ 
Sbjct: 4   ERLQKVMAEAGVASRRKSEKLIAEGHVKVNGRVVKELGTKVEQHDRIEVDEVPIQ-REQN 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++T+ SD   R TV D  P +  R+  VGRLD +T G +L+TNDG LA  
Sbjct: 63  VYFLLNKPRGVITSVSDDKNRKTVMDFFPDVTERIYPVGRLDYDTSGAVLMTNDGELANR 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           L  P  ++ + Y  +  G V+   L  L++G+VI        +  L +       + V +
Sbjct: 123 LMHPKFKFEKTYTAKVKGLVNGSALKRLEEGVVIDHRKTAKAKAKLISTDLEKKTSIVQL 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EG+N ++KK+F      V +L R SY    +  + +G  R +    ++
Sbjct: 183 TIHEGRNHQVKKMFMAVGHPVQKLHRNSYSFLSIDDVQSGKWRALKLSEVK 233


>gi|91776224|ref|YP_545980.1| ribosomal large subunit pseudouridine synthase B [Methylobacillus
           flagellatus KT]
 gi|91710211|gb|ABE50139.1| ribosomal large subunit pseudouridine synthase B [Methylobacillus
           flagellatus KT]
          Length = 383

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 87/347 (25%), Positives = 144/347 (41%), Gaps = 13/347 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
             +  PQR+ K++A AG  SRRE+E +IA  R+ +NG   E  A  V  +D + +D  PL
Sbjct: 23  DPDAVPQRLHKLLALAGFGSRREMETLIASGRITINGKTAEVGASVV-PSDVVRLDSRPL 81

Query: 68  ----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                      L  +     +V+     +  S           + I++GRLD+NT GLL+
Sbjct: 82  RLPFEPELPQVLLYHKPEGEIVSHDDPENRASVFDKLPRIRNGKWIAIGRLDMNTSGLLI 141

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T  G LA     P  +  R Y VR  G++ + ++  L  GI +         +     +
Sbjct: 142 FTTSGELANRFMHPRYEVEREYAVRIFGELTEGEMAQLTYGIELDDGPANFDSIRPQGGE 201

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           G+N W  V LREG+NRE++++FE F   V+RLIR+ +GP  L   L  G    +  K + 
Sbjct: 202 GANHWYEVILREGRNREVRRLFEAFQKPVSRLIRVRFGPVNLPPRLKRGQMIHLGAKEVT 261

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             L           L  P      L       + +V     R  +   + +  S+  +  
Sbjct: 262 ALLE-------WAELAVPKAVPRQLSPREKEKLGKVFTPKARKSRFDPEAHLESRGPRRV 314

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           T      +   +   +    S      +  +   R  + P+++ + R
Sbjct: 315 TKAREEGMRQELGKQQAGRRSRHGAETEEAQRPSRQGAKPARKPVNR 361


>gi|15604401|ref|NP_220917.1| hypothetical protein RP544 [Rickettsia prowazekii str. Madrid E]
 gi|6647946|sp|Q9ZD06|Y544_RICPR RecName: Full=Uncharacterized RNA pseudouridine synthase RP544;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|3861093|emb|CAA14993.1| unknown [Rickettsia prowazekii]
 gi|292572159|gb|ADE30074.1| Ribosomal large subunit pseudouridine synthase [Rickettsia
           prowazekii Rp22]
          Length = 235

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 108/235 (45%), Positives = 153/235 (65%), Gaps = 2/235 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K+I+ AG+ SRR  E++I   +VK++GI +   A NV  ++ IEV G  +   ++ R
Sbjct: 3   RLAKIISNAGVCSRRNAEKLIVGGKVKIDGITILSPATNVDMSNQIEVSGRLINNTQKPR 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LW+Y+KP+GL+TTH DP  R TVF+ L     RVIS+GRLD+N+EGLLLLTN G LA   
Sbjct: 63  LWIYYKPVGLITTHKDPLSRKTVFEQLIG-LPRVISIGRLDLNSEGLLLLTNSGDLAHQF 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           E+P+++  RVY VR +G  +    N   K + I GI Y    + L  Q  SN+W  V L 
Sbjct: 122 EMPASKLKRVYNVRAYGNPNILLKNN-YKNLKIDGIFYNPHSIKLLRQNKSNSWFEVVLF 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           EGKNREI+++FE+F  +VN+LIRI YG  ++G L  G+ +E+S KIL +QL    
Sbjct: 181 EGKNREIRRIFEYFGLQVNKLIRIQYGALKIGNLKPGNYQEISNKILEKQLVMCF 235


>gi|257086025|ref|ZP_05580386.1| pseudouridine synthase [Enterococcus faecalis D6]
 gi|256994055|gb|EEU81357.1| pseudouridine synthase [Enterococcus faecalis D6]
          Length = 244

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 62/235 (26%), Positives = 105/235 (44%), Gaps = 5/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD I + G  L   + 
Sbjct: 1   MRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQIALMGEILTYQKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T    D             + +  VGRLD +TEGLLLLTNDG LA 
Sbjct: 61  FYYMLHKPQGVISATEDQRDETVIDLLTDQDYRADLFPVGRLDKDTEGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTL--DTQKGSNAWV 189
            L  P     + Y     G V  +   L  +G  +  G      ++ +    ++   + V
Sbjct: 121 QLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEMVKPSRLVIETINEEEGTSVV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
            + ++EGK  ++K++       V  L R+  G   L   L  G  R +++  L++
Sbjct: 181 RLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGGYRPLTEAELQQ 235


>gi|270263002|ref|ZP_06191272.1| ribosomal large subunit pseudouridine synthase F [Serratia
           odorifera 4Rx13]
 gi|270042690|gb|EFA15784.1| ribosomal large subunit pseudouridine synthase F [Serratia
           odorifera 4Rx13]
          Length = 287

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/287 (21%), Positives = 113/287 (39%), Gaps = 5/287 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++K I+ +GI SRR+ +R I Q  V +NG  +      V   D ++V+G  +     
Sbjct: 6   STRLNKYISESGICSRRDADRYIEQGNVFINGKRVA-LGDRVFPGDVVKVNGQLIEPRNE 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L        +    +  +G      +  +  +R+  +GRLD +++GL+ LTN G L  
Sbjct: 65  DNLIFIALNKPVGIVSTTEEGEKDNIVDFVNHSTRIFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + YRV  +  V  D +  L  G+ + G            +K +     + 
Sbjct: 125 KILRAGNDHEKEYRVTVNKPVTDDFIRGLGAGVPMLGTV----TKKCKVKKEAPFVFRIV 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E F ++V +L R       +  L  G  R+++   L E         
Sbjct: 181 LVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSMAGLPPGEWRDLTDDELVELFKSIEGSS 240

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
           ++         +           +E P      +K  +Q     K +
Sbjct: 241 SEAKPAKKAKPAVKKPAGSAPKSTEKPAGNAAARKRFAQPGRKKKGR 287


>gi|237708147|ref|ZP_04538628.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           9_1_42FAA]
 gi|229457700|gb|EEO63421.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           9_1_42FAA]
          Length = 485

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 116/241 (48%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K+I+ +   P R++K +A AGI SRRE +  I    V VNG ++      +  TD +
Sbjct: 237 IEYKDILTDPNEPIRLNKFLANAGICSRREADEFITAGVVSVNGEVVTELGTKIKRTDEV 296

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P+    +T + L      + T+    + ++ +     +   R+  VGRLD NT G
Sbjct: 297 KFHDEPVSIERKTYILLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTTG 356

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     V +  L+ +  G+ +         ++  
Sbjct: 357 VLLLTNDGDLASKLTHPKYLKKKIYHVYCDKNVTKADLDQIAAGVTLDDGEIHADAISYA 416

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++    + V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++ 
Sbjct: 417 SET-DKSQVGIEIHSGKNRIVRRIFESLGYKVIKLDRVYFAGLTKKGLRRGDWRYLTEQE 475

Query: 241 L 241
           +
Sbjct: 476 V 476


>gi|227112086|ref|ZP_03825742.1| 16S rRNA pseudouridylate synthase A [Pectobacterium carotovorum
           subsp. brasiliensis PBR1692]
          Length = 231

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 109/231 (47%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  QRV V+G +++  A  +    ++E DG PL++    
Sbjct: 1   MRLDKFLSQQLEISRSLVARELHAQRVTVDGEVVKSGAFKLSPEHNVEFDGNPLKQQNGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+LLT+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTILYFMDVPVAYKLHAAGRLDIDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  Q  + Y V     + +D       G+ +                +K ++  V +
Sbjct: 121 ITSPKHQCEKTYLVTLEQPLAEDTAAQFTAGVQLHNEKNLTKPAT----LEKITDYVVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F     +V  L R   G   L   L  G  RE+S + +
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVVELHRERIGGIYLDSELEPGEYRELSAEEI 227


>gi|78044539|ref|YP_360363.1| ribosomal small subunit pseudouridine synthase A [Carboxydothermus
           hydrogenoformans Z-2901]
 gi|77996654|gb|ABB15553.1| ribosomal small subunit pseudouridine synthase A [Carboxydothermus
           hydrogenoformans Z-2901]
          Length = 231

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 108/231 (46%), Gaps = 9/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +A  G  +R+EV +++  ++V+VNG++++    N+   TD + V G  ++    
Sbjct: 1   MRIDKFLAHMGFGTRKEVRKLLKARKVEVNGVVVKDPGYNLNVDTDKVIVKGEEVKYKPF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T            +L  +  ++  VGRLDI+TEGLL+LT+DG LA 
Sbjct: 61  VYFMLNKPKGYVSATVDRRYPTVV---DLVPVHRKIFPVGRLDIDTEGLLILTDDGQLAH 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTV 191
            L  P  +  + Y       ++++  + +K GI ++        +  L  + G     T+
Sbjct: 118 HLTSPKKEVEKEYYFELDKPLEEEDFSKIKTGIRLEDNYLTKPAR--LLGKVGDKHG-TI 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++F      V  L RI  G   L   L  G  RE++ + +
Sbjct: 175 VITEGKYHQVKRMFLALGKTVVYLKRIRIGGLILDNKLSPGEYRELTPEEI 225


>gi|86130476|ref|ZP_01049076.1| pseudouridylate synthase [Dokdonia donghaensis MED134]
 gi|85819151|gb|EAQ40310.1| pseudouridylate synthase [Dokdonia donghaensis MED134]
          Length = 260

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 55/265 (20%), Positives = 103/265 (38%), Gaps = 6/265 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E     R++K ++ AG  SRR  +++I Q RV +NG +       +   D + V+G  + 
Sbjct: 2   EEKKQTRINKYLSEAGYCSRRAADKLIDQGRVTINGKVP-EMGTKITEGDEVRVNGELIT 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            +    +++       +   +D         +  +  SR+  +GRLD  +EGL+ LTNDG
Sbjct: 61  SSTEKPVYIALNKPVGIVCTTDTRVEKDNIIDFINYPSRIFPIGRLDKPSEGLIFLTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y V     +    +  +  G+ I              ++ S   
Sbjct: 121 DIVNKILRARNNHEKEYEVWVDKPITPSFIQQMSNGVPILDTVTRKCH----VEQLSRFS 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E  +++V RL R      +L  +  G  R +S   + E     
Sbjct: 177 FKIILTQGLNRQIRRMCEALDYEVTRLKRNRIMNIEL-DVPVGKWRYISDTEMEEINRLV 235

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPN 273
                             L R+R  
Sbjct: 236 EDSAKTHTDAPKEPRHPNLRRNRNR 260


>gi|315103786|gb|EFT75762.1| conserved hypothetical protein [Propionibacterium acnes HL050PA2]
          Length = 245

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 77/241 (31%), Positives = 110/241 (45%), Gaps = 2/241 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
            N    R+ KV+A+AG+ASRR  E MIA  RV+VNG L+      V    D I VDG  +
Sbjct: 2   SNEQGIRLQKVLAQAGLASRRAAEDMIAAGRVEVNGELIVEQGRRVDPERDEIRVDGSRI 61

Query: 68  R-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                     L      + T                    R+  VGRLD  T GL+LLTN
Sbjct: 62  PTARRHVYYVLNKPQGVVSTMDDPEGRPCLSDLEGVPRGIRLFHVGRLDTETSGLILLTN 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  A  +  PS + L+ Y     G+VD   ++ L KG+ ++        V L      +
Sbjct: 122 DGEFANRMTHPSYKVLKTYLADVEGRVDDKVIHRLSKGLTLEDGPVKPDAVRLVQASEEH 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + V V L EG+NR ++++ +     V RL R + GP +L  L  G  RE++ + L + L 
Sbjct: 182 SLVEVSLHEGRNRIVRRIMDSVAHPVRRLSRTAIGPVRLKRLGRGDMRELTHEELGQLLD 241

Query: 247 P 247
            
Sbjct: 242 L 242


>gi|257420928|ref|ZP_05597918.1| pseudouridine synthase [Enterococcus faecalis X98]
 gi|300861842|ref|ZP_07107922.1| pseudouridylate synthase [Enterococcus faecalis TUSoD Ef11]
 gi|257162752|gb|EEU92712.1| pseudouridine synthase [Enterococcus faecalis X98]
 gi|300848367|gb|EFK76124.1| pseudouridylate synthase [Enterococcus faecalis TUSoD Ef11]
          Length = 244

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/235 (25%), Positives = 105/235 (44%), Gaps = 5/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD I + G  L   + 
Sbjct: 1   MRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQIALMGEILTYQKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T    D             + +  VGRLD +TEGLLLLTNDG LA 
Sbjct: 61  FYYMLHKPQGVISATEDQRDETVIDLLTDQDYRADLFPVGRLDKDTEGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTL--DTQKGSNAWV 189
            L  P     + Y     G V  +   L  +G  ++        ++ +    ++   + V
Sbjct: 121 QLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEIVKPSRLVIETINEEEGTSVV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
            + ++EGK  ++K++       V  L R+  G   L   L  G  R +++  L++
Sbjct: 181 RLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGGYRPLTEAELQQ 235


>gi|322375796|ref|ZP_08050307.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           C300]
 gi|321279064|gb|EFX56106.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           C300]
          Length = 240

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 100/233 (42%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQINEERDEIRFDGQVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    V  VGRLDI+T GLLLLTNDG LA 
Sbjct: 61  VYYMMNKPQGVISATEDSKHRTVLDLLDDIARTKEVFPVGRLDIDTHGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVT 190
            L  P     + Y     G + Q+ +    KGI ++       ++ + +     + + V 
Sbjct: 121 ALLSPKRHVDKTYLAHVEGIMTQEDVETFVKGIPLKDFTCQPAKLEIVSVDSVKNQSLVR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 181 VTIAEGKFHQVKRMVAYCGKEVVDLQRLTMGTLVLDENLEQGEWRRLTKEELE 233


>gi|317492524|ref|ZP_07950952.1| RNA pseudouridylate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316919516|gb|EFV40847.1| RNA pseudouridylate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 240

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 53/231 (22%), Positives = 103/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  + R +  +RV V+G +++  A  +     +  DG  L +    
Sbjct: 1   MRLDKFLSQQLGISRALIARELRAKRVTVDGEIVKSGAHKLTPEQEVAFDGQVLEQIHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V +  DPD  + ++     +  ++ + GRLD++T GL+LLT+DG  +  
Sbjct: 61  RYFMLHKPEGYVCSTDDPDHSTILYFIDEPLAEKLHAAGRLDLDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y V     +  D       G+ + G         +           V +
Sbjct: 121 ITSPKHECDKTYLVTLEHPLADDTAEQFAHGVQLHGEKDLTKPATLEQLDAN----VVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F     +V  L R   G  +L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVVELHRERIGAIELDEDLAPGEYRPLTEEEI 227


>gi|217963899|ref|YP_002349577.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes HCC23]
 gi|290892109|ref|ZP_06555105.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes FSL J2-071]
 gi|217333169|gb|ACK38963.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes HCC23]
 gi|290558232|gb|EFD91750.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes FSL J2-071]
 gi|307571531|emb|CAR84710.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes L99]
 gi|313607907|gb|EFR84057.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes FSL F2-208]
          Length = 244

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 77/238 (32%), Positives = 121/238 (50%), Gaps = 3/238 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E++I + +V VNG ++    V V  T+ IEV+G+ L K E  
Sbjct: 2   ERLQKVIANAGITSRRKAEKLIQEGKVTVNGKVVTELGVKVSGTERIEVEGIQLTKEEHR 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     +     D    +        I  R+  VGRLD +T GLLL+TNDG  A +
Sbjct: 62  YFLFYKPRGTVSAVTDDKGRTTVADYF-ADIPERLYPVGRLDYDTSGLLLMTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           L  P  +  + Y  R  G  +++ +  L++G+VI G      +V + +       A V +
Sbjct: 121 LMHPKNEVSKTYIARIKGIPEREVIRQLERGVVIDGRKTAPAKVKVRSSDKAKDKAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + EG+NR+++K+FE   ++V +L R  Y    L  L AG  RE+S   +++      
Sbjct: 181 TIHEGRNRQVRKMFEAVGFEVQKLSREEYSFLNLRGLNAGERRELSHHEVKQLKTEAR 238


>gi|167766754|ref|ZP_02438807.1| hypothetical protein CLOSS21_01260 [Clostridium sp. SS2/1]
 gi|167711508|gb|EDS22087.1| hypothetical protein CLOSS21_01260 [Clostridium sp. SS2/1]
          Length = 249

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/243 (25%), Positives = 120/243 (49%), Gaps = 5/243 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +     R++K +++AGI SRR+ +  + + RV+V+G +       V+    +  DG P++
Sbjct: 12  KTEDAVRINKYLSQAGICSRRQADTYVEEGRVEVDGEVAVS-GTKVLPGQSVTFDGKPVK 70

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             E      +HKP G+V T S  +  + +     +  +R+  VGRLD +++GL+LLTNDG
Sbjct: 71  IQEDLIFLAFHKPRGIVCTASKEEKDNIIDYI--NYPTRIYPVGRLDKDSQGLILLTNDG 128

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             A  +        + Y V  + ++  + ++ ++  + +  I     +  +  +  +   
Sbjct: 129 EAANQIMKARNYHEKEYEVTVNKRITNEFIHDMRNPVPLDEINAVTRRCKVIKEGPN--E 186

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E F ++V +L R+     +LG L  G  R+++   LRE     
Sbjct: 187 FRIILTQGLNRQIRRMCEHFGYRVTKLKRVRVMNIKLGDLKEGRYRKLTPDELRELKKEL 246

Query: 249 LLE 251
             E
Sbjct: 247 KSE 249


>gi|317475710|ref|ZP_07934970.1| S4 domain-containing protein [Bacteroides eggerthii 1_2_48FAA]
 gi|316908166|gb|EFV29860.1| S4 domain-containing protein [Bacteroides eggerthii 1_2_48FAA]
          Length = 331

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 59/241 (24%), Positives = 104/241 (43%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +   D +
Sbjct: 83  IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRGDEV 142

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +     +    +  + L      + T+      R+ +     +   R+  VGRLD NT G
Sbjct: 143 KFHDQAVSIERKIYVLLNKPKDTVTTSDDPQARRTVMDLVKGACSERIYPVGRLDRNTTG 202

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     + +  +  +  GI +             
Sbjct: 203 VLLLTNDGDLASKLTHPKYLKKKIYHVHLDKNLTKADMEQIAAGIQLDDGEIQ-ADAISY 261

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           T       V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++ 
Sbjct: 262 TDDFKKDEVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLTEQE 321

Query: 241 L 241
           +
Sbjct: 322 V 322


>gi|255994193|ref|ZP_05427328.1| ribosomal large subunit pseudouridine synthase B [Eubacterium
           saphenum ATCC 49989]
 gi|255993861|gb|EEU03950.1| ribosomal large subunit pseudouridine synthase B [Eubacterium
           saphenum ATCC 49989]
          Length = 250

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 82/250 (32%), Positives = 126/250 (50%), Gaps = 16/250 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA+ GI SRR+ + +I + RV V GI L    VNV     I +DG P+   ++T
Sbjct: 1   MRINKYIAKCGICSRRKADELIKEGRVTVGGIPLLECGVNVDEDAVIAIDGRPIEIQKKT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G V T SD  GR TV+D L  I  R+ ++GRLD ++EGL+LLTNDG LA+ 
Sbjct: 61  VYIAMNKPCGYVCTVSDELGRRTVYDLLTDIDERLFTIGRLDKDSEGLILLTNDGDLAQK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC----------------YGDMQV 177
           L  P  +  + Y V   G    + +  L  GI I                        ++
Sbjct: 121 LLSPKRKIEKNYEVVVRGVPGANDIKKLSGGITIDVEISQTKQNKPVKSIVKYHTKPAKI 180

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               QK  +  +++ ++EGK R+I+K+F+    +V +L R+ +   +LG L  G  R +S
Sbjct: 181 FEIGQKQGDMKLSMIIKEGKKRQIRKMFDVIGHEVIKLKRVKFAGIELGDLRPGEFRHLS 240

Query: 238 KKILREQLGP 247
           +  +R     
Sbjct: 241 EDEVRSLCSL 250


>gi|289810128|ref|ZP_06540757.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 256

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 57/257 (22%), Positives = 107/257 (41%), Gaps = 5/257 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R++K I+ +GI SRRE +R I Q  V +NG         V++ D ++V+G  +  
Sbjct: 3   TDTSTRLNKYISESGICSRREADRFIEQGNVFINGKRAA-IGDQVVAGDVVKVNGRLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   L L      +    +  DG      +  +   R+  +GRLD +++GL+ LTN G 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRIFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     +  + +  +  G+ I G            +K +    
Sbjct: 122 LVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +      
Sbjct: 178 RITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIE 237

Query: 250 LEEAQVNLDAPIYSSET 266
              ++        + + 
Sbjct: 238 GSSSEAKPKGQSEAEDR 254


>gi|51595642|ref|YP_069833.1| 16S rRNA pseudouridylate synthase A [Yersinia pseudotuberculosis IP
           32953]
 gi|186894712|ref|YP_001871824.1| 16S rRNA pseudouridylate synthase A [Yersinia pseudotuberculosis
           PB1/+]
 gi|51588924|emb|CAH20541.1| ribosomal small subunit pseudouridine synthase A [Yersinia
           pseudotuberculosis IP 32953]
 gi|186697738|gb|ACC88367.1| pseudouridine synthase [Yersinia pseudotuberculosis PB1/+]
          Length = 235

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 56/238 (23%), Positives = 108/238 (45%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    
Sbjct: 1   MRLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQMVGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +  D       G+ +          Q+ +   +     V +
Sbjct: 121 VTSPRHHCEKTYLVTLEHPLSDDTAQQFADGVQLHNEKSLTKPAQLDVIEPQR----VRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
            +REG+  ++K++F     +V  L R   G   L   L  G  R ++ + +     PH
Sbjct: 177 TIREGRYHQVKRMFAAVGNRVIELHRERIGDITLDDDLAPGEYRPLTAEEIASVGAPH 234


>gi|292486534|ref|YP_003529400.1| putative pseudouridylate synthase [Erwinia amylovora CFBP1430]
 gi|292897771|ref|YP_003537140.1| ribosomal large subunit pseudouridine synthase F [Erwinia amylovora
           ATCC 49946]
 gi|291197619|emb|CBJ44713.1| ribosomal large subunit pseudouridine synthase F [Erwinia amylovora
           ATCC 49946]
 gi|291551947|emb|CBA18984.1| putative pseudouridylate synthase [Erwinia amylovora CFBP1430]
 gi|312170602|emb|CBX78865.1| putative pseudouridylate synthase [Erwinia amylovora ATCC BAA-2158]
          Length = 288

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/288 (21%), Positives = 110/288 (38%), Gaps = 5/288 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++K I  +GI SRR+ +R I Q  V +NG         V + D ++V+G  +     
Sbjct: 6   SIRLNKYIGESGICSRRDADRYIEQGNVFINGKRAAV-GDRVFAGDVVKVNGQLIEPRNE 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +    +   G      +  +   RV  +GRLD +++GL+ LTN G L  
Sbjct: 65  DDLVIIALNKPVGIVSTTEGGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  V  + +  L  G+ + G            +K S     + 
Sbjct: 125 KILRAGNDHEKEYLVTVNKPVTAEFIRGLGAGVPMLGTV----TKKCKVKKESTFVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E F + V +L R       L  L  G  R+++   L E         
Sbjct: 181 LVQGLNRQIRRMSEHFGYDVTKLERTRIMNVSLKGLPPGEWRDLTDDELIELFKLIENSS 240

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           ++           T  +      ++V        +    + G  K+ +
Sbjct: 241 SEDAAVKKAKPKATAAKKPAASGAKVTSSANAAPRKRFAQPGRKKKGR 288


>gi|288801457|ref|ZP_06406910.1| ribosomal large subunit pseudouridine synthase B [Prevotella sp.
           oral taxon 299 str. F0039]
 gi|288331668|gb|EFC70153.1| ribosomal large subunit pseudouridine synthase B [Prevotella sp.
           oral taxon 299 str. F0039]
          Length = 479

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 109/230 (47%), Gaps = 1/230 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      VM TD ++     +   ++
Sbjct: 243 PVRLNKFLANAGVCSRREADEYIQAGSVTVNGQVVTELGTKVMRTDEVKFGDNLVSLEKK 302

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      + T+      ++ +     +   R+  VGRLD NT G+LLLTNDG LA 
Sbjct: 303 VYILINKPKDCVTTSDDPQQRKTVLDLVKNACPERIYPVGRLDRNTTGVLLLTNDGDLAS 362

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VY V     V Q+ L  + +GI ++       ++    ++     V + 
Sbjct: 363 KLTHPKFLKKKVYHVFLDKPVAQEDLQKIAEGIELEDGEIHADEIAYANEEDKKQ-VGIE 421

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +  GKNR ++++FE   ++V +L R+ +       L  G  R +++K + 
Sbjct: 422 IHSGKNRIVRRIFEHLGYRVIKLDRVQFAGLTKKNLRRGDWRFLTEKEVD 471


>gi|205374821|ref|ZP_03227614.1| tRNA pseudouridine synthase A [Bacillus coahuilensis m4-4]
          Length = 235

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 64/227 (28%), Positives = 111/227 (48%), Gaps = 7/227 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ AG ASRR  +++I + RV +NG   +     V   D + V+G  +R A   
Sbjct: 1   MRINKYISDAGKASRRGADKLIEEGRVYINGRRAK-IGDQVNPGDDVLVNGNHVRLARNN 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+ +T            +L +   R+ ++GRLD  ++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITSTTEKGV--KGNIIDLVNHPLRIFNIGRLDKESDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     + Q+ L+ +  G+ I G      ++    ++ S     + L
Sbjct: 118 ILRAENKHEKEYFVSVDKPITQEFLDNMASGVKILGTKTLPCKI----EQISKYDFQITL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +G NR+I+++ E   ++V RL R       LG L  G  R++SKK 
Sbjct: 174 TQGLNRQIRRMCEALGYEVYRLQRTRIMNIHLGNLPVGQWRDLSKKE 220


>gi|37526757|ref|NP_930101.1| 16S rRNA pseudouridylate synthase A [Photorhabdus luminescens
           subsp. laumondii TTO1]
 gi|36786189|emb|CAE15241.1| ribosomal small subunit pseudouridine synthase A (16S
           pseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (uracil hydrolyase) [Photorhabdus luminescens
           subsp. laumondii TTO1]
          Length = 233

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 50/231 (21%), Positives = 103/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR +V R +   R+ V+  +++  A  +     +  DG  L + +  
Sbjct: 1   MRLDKFLSQQLGISRNDVGRELRAGRITVDDEIVKTGAYKLTPEQQVMFDGSLLEQQQGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DP   + ++        ++ + GRLD++T GL+LLT+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPINPTVLYFIDEPAAHKLHTAGRLDMDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  +  +    G+ + G        Q+ +   + +     +
Sbjct: 121 ITSPKHHCKKTYLVTLECPVAAETADKFLAGVQLNGEKTVTKPAQLEILEPQIA----RL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVTALHRERIGEIILAPELEPGEYRSLTEQEI 227


>gi|254775517|ref|ZP_05217033.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           avium subsp. avium ATCC 25291]
          Length = 247

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 73/236 (30%), Positives = 108/236 (45%), Gaps = 4/236 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLR 68
                R+ KV+++AGIASRR  E++I   RV+V+G ++      V      I VDG  + 
Sbjct: 3   EAQGIRLQKVLSQAGIASRRAAEKLIVDGRVEVDGQVVTELGTRVDPDAAVIRVDGARVV 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLLT 125
             E       +KP G+ +T SD  GR  + D +            VGRLD  TEGL+LLT
Sbjct: 63  LDESQVYLALNKPRGVHSTMSDDRGRPCIGDLIERRVRGNKNLFHVGRLDAETEGLILLT 122

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  PS +  + Y     G + +     L+ GI +        +  +      
Sbjct: 123 NDGELAHRLMHPSHEVPKTYLATVTGSIPRGLGKTLRAGIELDDGMARVDEFAVVDATPG 182

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              V V L EG+NR ++++     + V  L+R   GP  LG    GS R + +  +
Sbjct: 183 KTLVRVTLHEGRNRIVRRLLAAAGFPVESLVRTDIGPISLGKQRPGSIRALGRDEV 238


>gi|330830231|ref|YP_004393183.1| 23S rRNA pseudouridine synthase F [Aeromonas veronii B565]
 gi|328805367|gb|AEB50566.1| 23S rRNA pseudouridine synthase F [Aeromonas veronii B565]
          Length = 338

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 65/298 (21%), Positives = 115/298 (38%), Gaps = 8/298 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   NESMRLNKYISESGICSRREADRFIEQGHVFINGKRA-GIGDQVQVGDLVKVNGQVIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +   G      +  +  +RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EADSLVLIALNKPVGIVSTTEAGEKDNIVDFVNHSTRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V  + +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPVTDEFVRGMAAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L RI      L  L  G  R+++   L +       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGFEVTKLERIRIMNVSLKGLPVGEWRDLTDDELIDLFKLI-- 236

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
            E   +   P    +      P   S  P    + +++   + G            ++
Sbjct: 237 -EDSSSEVKPAKGDKPKAAKAPAAQSAKPGQGKKPRRDDDHEIGGRPNVPGPEAFEKK 293


>gi|150015235|ref|YP_001307489.1| pseudouridine synthase [Clostridium beijerinckii NCIMB 8052]
 gi|149901700|gb|ABR32533.1| pseudouridine synthase [Clostridium beijerinckii NCIMB 8052]
          Length = 238

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 108/231 (46%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K+I+  G  SR++V+    +  ++V+G++++ +A+ V      I+++G  +   + 
Sbjct: 2   ERLDKIISNLGYGSRKDVKSFAKKGIIEVDGLIVKDSAMLVDPEKSVIKINGEEVLYRKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      +  TH + D       NL         +GRLD +T GLLLLTNDG L  
Sbjct: 62  IYIMMNKPDGVISATHDNRDETVIDLLNLEHQVFDPFPIGRLDKDTVGLLLLTNDGELNH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY       VD+  +   K GI +       +  + + +     + + +
Sbjct: 122 RLISPKWHVDKVYYAEIDKSVDEKDIKAFKDGITLDDGYKCLEANLEILSSSNDGSEIRL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            ++EGK  ++K++FE    KV  L R  +G   L   L  G  RE++ + L
Sbjct: 182 TIQEGKFHQVKRMFEAVGKKVTYLKREEFGGLLLDPDLEEGEYRELTDEEL 232


>gi|118465035|ref|YP_882249.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           avium 104]
 gi|118166322|gb|ABK67219.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           avium 104]
          Length = 248

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 73/239 (30%), Positives = 110/239 (46%), Gaps = 4/239 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGV 65
           +       R+ KV+++AGIASRR  E++I   RV+V+G ++      V      I VDG 
Sbjct: 1   MMVEAQGIRLQKVLSQAGIASRRAAEKLIVDGRVEVDGQVVTELGTRVDPDAAVIRVDGA 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLL 122
            +   E       +KP G+ +T SD  GR  + D +         +  VGRLD  TEGL+
Sbjct: 61  RVVLDESQVYLALNKPRGVHSTMSDDRGRPCIGDLIERRVRGNKNLFHVGRLDAETEGLI 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTNDG LA  L  PS +  + Y     G + +     L+ GI +        +  +   
Sbjct: 121 LLTNDGELAHRLMHPSHEVPKTYLATVTGSIPRGLGKTLRAGIELDDGMARVDEFAVVDA 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                 V V L EG+NR ++++     + V  L+R   GP  LG    GS R + +  +
Sbjct: 181 IPGKTLVRVTLHEGRNRIVRRLLAAAGFPVESLVRTDIGPISLGKQRPGSIRALGRDEV 239


>gi|306830208|ref|ZP_07463392.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           mitis ATCC 6249]
 gi|304427734|gb|EFM30830.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           mitis ATCC 6249]
          Length = 240

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 63/233 (27%), Positives = 103/233 (44%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEERDQIRFDGQVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T  +         +  +    V  VGRLDI+T GLLLLTNDG LA 
Sbjct: 61  VYYMMNKPQGVISATEDNKHRTVLDLLDDYARAKEVFPVGRLDIDTHGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVT 190
            L  P     + Y  +  G + Q+ ++   KGI ++       ++ L +     + + V 
Sbjct: 121 ALLSPKRHVDKTYLAQVEGIMSQEDVDTFAKGIPLKDFTCQPAKLELVSVDPEKNQSLVR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 181 VTIAEGKFHQVKRMVAYCGKEVVDLQRLTMGTLALDENLERGEWRRLTKEELE 233


>gi|317499032|ref|ZP_07957313.1| RNA pseudouridylate synthase [Lachnospiraceae bacterium 5_1_63FAA]
 gi|291560717|emb|CBL39517.1| ribosomal large subunit pseudouridine synthase F
           [butyrate-producing bacterium SSC/2]
 gi|316893682|gb|EFV15883.1| RNA pseudouridylate synthase [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 244

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/243 (25%), Positives = 120/243 (49%), Gaps = 5/243 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +     R++K +++AGI SRR+ +  + + RV+V+G +       V+    +  DG P++
Sbjct: 7   KTEDAVRINKYLSQAGICSRRQADTYVEEGRVEVDGEVAVS-GTKVLPGQSVTFDGKPVK 65

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             E      +HKP G+V T S  +  + +     +  +R+  VGRLD +++GL+LLTNDG
Sbjct: 66  IQEDLIFLAFHKPRGIVCTASKEEKDNIIDYI--NYPTRIYPVGRLDKDSQGLILLTNDG 123

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             A  +        + Y V  + ++  + ++ ++  + +  I     +  +  +  +   
Sbjct: 124 EAANQIMKARNYHEKEYEVTVNKRITNEFIHDMRNPVPLDEINAVTRRCKVIKEGPN--E 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E F ++V +L R+     +LG L  G  R+++   LRE     
Sbjct: 182 FRIILTQGLNRQIRRMCEHFGYRVTKLKRVRVMNIKLGDLKEGRYRKLTPDELRELKKEL 241

Query: 249 LLE 251
             E
Sbjct: 242 KSE 244


>gi|218128464|ref|ZP_03457268.1| hypothetical protein BACEGG_00034 [Bacteroides eggerthii DSM 20697]
 gi|217989355|gb|EEC55668.1| hypothetical protein BACEGG_00034 [Bacteroides eggerthii DSM 20697]
          Length = 234

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 56/225 (24%), Positives = 97/225 (43%), Gaps = 1/225 (0%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW 76
           +K +A AG+ SRRE +  I    V VNG ++      +   D ++     +    +  + 
Sbjct: 2   NKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRGDEVKFHDQAVSIERKIYVL 61

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L      + T+      R+ +     +   R+  VGRLD NT G+LLLTNDG LA  L  
Sbjct: 62  LNKPKDTVTTSDDPQARRTVMDLVKGACSERIYPVGRLDRNTTGVLLLTNDGDLASKLTH 121

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
           P     ++Y V     + +  +  +  GI +             T       V + +  G
Sbjct: 122 PKYLKKKIYHVHLDKNLTKADMEQIAAGIQLDDGEIQ-ADAISYTDDFKKDEVGIEIHSG 180

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           KNR ++++FE   +KV +L R+ +       L  G  R ++++ +
Sbjct: 181 KNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLTEQEV 225


>gi|315645600|ref|ZP_07898724.1| RNA pseudouridine synthase family protein [Paenibacillus vortex
           V453]
 gi|315279078|gb|EFU42388.1| RNA pseudouridine synthase family protein [Paenibacillus vortex
           V453]
          Length = 230

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 106/234 (45%), Gaps = 10/234 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--E 71
            R++K I++ G  SRRE  R+IA  R+ +NG + E+    V   D + +DG  +     E
Sbjct: 1   MRINKYISQTGFCSRRETNRLIASGRITINGKVCEK-GAEVEPEDIVLIDGQEIPHNDSE 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L L      + T   + +G         +  SR+ ++GRLD  +EGL+LLTNDG + 
Sbjct: 60  PVYLALNKPMGIVCTAAEEVEG---NIIRYVNYPSRIFAIGRLDKASEGLILLTNDGDIV 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     V  + +  + +G+ I  +     +V       S A   +
Sbjct: 117 NKMMRSEHDHEKEYVVTVDRPVTDEFMRRMSQGVEILDVVTKPCEVFRQ----SEAVFRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            L +G N +I+++ +   ++V +L RI      L  L  G  R + ++ L + L
Sbjct: 173 ILTQGLNLQIRRMCKALGYRVLKLERIRIMNITLDQLERGKWRHLEERELHKLL 226


>gi|33592372|ref|NP_880016.1| hypothetical protein BP1244 [Bordetella pertussis Tohama I]
 gi|33572017|emb|CAE41540.1| conserved hypothetical protein [Bordetella pertussis Tohama I]
 gi|332381788|gb|AEE66635.1| hypothetical protein BPTD_1234 [Bordetella pertussis CS]
          Length = 588

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 82/355 (23%), Positives = 132/355 (37%), Gaps = 6/355 (1%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             +       ++ KV+A AGI SRRE+E +I   RV VNG         V   D + V+G
Sbjct: 108 KYLNSEAVMPKLHKVLADAGIGSRREMEELIVAGRVSVNGEPA-HIGQRVAPNDQVRVNG 166

Query: 65  VPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            P+     K     +  +     +V+        S           + +SVGRLD+NTEG
Sbjct: 167 KPIARPNAKKPPRVILYHKPAGEIVSHDDPGGRASVFARLPKLRTGKWLSVGRLDLNTEG 226

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LL+ T  G +A  +  P     R Y VR  G++D  +   L +GI ++            
Sbjct: 227 LLIFTTSGDMANRIMHPRYGTEREYAVRVLGEMDDAQRKSLTEGIELEDGKAAFGSFEYL 286

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
              GSN W  V L+EG+NRE++++FE     V+RLIR  +G   L   L  G   E+   
Sbjct: 287 GGDGSNRWYRVTLQEGRNREVRRMFEAVGVTVSRLIRTRFGDIVLPRNLRRGRWEELDGS 346

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
           ++   +    L       +    S +    D          +   M      + G  +  
Sbjct: 347 LVTALMVQLGLLRDGDESEGRRKSRQPQSHDSALPPGFGTLERNGMNGARIGRRGKLQGG 406

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +  +     +      +      +     G      R     P+K        ++
Sbjct: 407 RPGSAAACPSDPFGTGLMITGGYANGHPLGNDSAAGRGGKGKPAKGKAGGDKPQR 461


>gi|327330001|gb|EGE71755.1| ribosomal large subunit pseudouridine synthase B [Propionibacterium
           acnes HL097PA1]
          Length = 245

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 77/241 (31%), Positives = 110/241 (45%), Gaps = 2/241 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
            N    R+ KV+A+AG+ASRR  E MIA  RV+VNG L+      V    D I VDG  +
Sbjct: 2   SNEQGIRLQKVLAQAGLASRRAAEDMIAAGRVEVNGELIVDQGRRVDPERDEIRVDGSRI 61

Query: 68  R-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                     L      + T                    R+  VGRLD  T GL+LLTN
Sbjct: 62  PTARRHVYYVLNKPQGVVSTMDDPEGRPCLSDLEGVPRGIRLFHVGRLDTETSGLILLTN 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  A  +  PS + L+ Y     G+VD   ++ L KG+ ++        V L      +
Sbjct: 122 DGEFANRMTHPSYKVLKTYLADVEGRVDDKVIHRLSKGLTLEDGPVKPDAVRLVQAGEEH 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + V V L EG+NR ++++ +     V RL R + GP +L  L  G  RE++ + L + L 
Sbjct: 182 SLVEVSLHEGRNRIVRRIMDSVAHPVRRLSRTAIGPVRLKRLGRGDMRELTHEELGQLLD 241

Query: 247 P 247
            
Sbjct: 242 L 242


>gi|210617504|ref|ZP_03291607.1| hypothetical protein CLONEX_03829 [Clostridium nexile DSM 1787]
 gi|210149291|gb|EEA80300.1| hypothetical protein CLONEX_03829 [Clostridium nexile DSM 1787]
          Length = 253

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 64/260 (24%), Positives = 121/260 (46%), Gaps = 10/260 (3%)

Query: 7   VQENFTPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           ++EN T +   R++K ++ AG+ SRRE +R+I   +V V+G       + V  +  + V 
Sbjct: 1   MRENQTTETTVRLNKFLSEAGVCSRREADRLIENGKVTVDGKRA-EMGMRVSPSQRVCVG 59

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
              +R+     L   +KP+G+V T    +          +  +RV  +GRLD ++EGLLL
Sbjct: 60  KKEVRQKNEMVLLAVNKPVGIVCTEEKKE--KNNIIRFLNYPTRVTYIGRLDKDSEGLLL 117

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           +TN+G +   +     Q  + Y+V  +  V ++ +  + +G+ I        +V +    
Sbjct: 118 MTNNGDIINKMMRAGNQHEKEYKVTVNKPVTKEFIEKMAEGVPILDTVTRKCKVEML--- 174

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
                  + L +G NR+I+++ E+  +KV RL RI      LG L  G  R+V++  +++
Sbjct: 175 -GKYKFRIILTQGLNRQIRRMCEYLGYKVTRLERIRVMNITLGELKPGEYRKVTEAEIQK 233

Query: 244 QLGPHLLEEAQVNLDAPIYS 263
                     +  +      
Sbjct: 234 LYELIKDSSNETVIPKKQEQ 253


>gi|238786961|ref|ZP_04630761.1| Ribosomal large subunit pseudouridine synthase F [Yersinia
           frederiksenii ATCC 33641]
 gi|238724749|gb|EEQ16389.1| Ribosomal large subunit pseudouridine synthase F [Yersinia
           frederiksenii ATCC 33641]
          Length = 289

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 63/296 (21%), Positives = 120/296 (40%), Gaps = 8/296 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           + +  R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +  
Sbjct: 2   SNSSIRLNKYISESGICSRRDADRYIEQGNVFINGKRA-VIGDQVYAGDVVKVNGQLIDA 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   L L      +    +  D       +  +   R+  +GRLD +++GL+ LTN G 
Sbjct: 61  RDEDDLVLIVLNKPVGIISTTEDSEHNNIVDFVNHSKRIFPIGRLDKDSQGLIFLTNQGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  V ++ +  L  G+ + G            +K S    
Sbjct: 121 LVNKVLRAGNDHEKEYVVTVNKPVTEEFILGLGAGVPMLGTV----TKKCKVKKVSTFVF 176

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ ++F ++V +L R       L  L  G  R+++   L   +G   
Sbjct: 177 NITLVQGLNRQIRRMCQYFGYEVTKLERTRIMNINLKGLPLGEWRDLNDDEL---IGLFK 233

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           L E   +        +T         S  P    +   NS+ +   ++  +     
Sbjct: 234 LIENSSSEGKTAKKVQTKSVTHKKTNSNGPKKAEKPDGNSASRKRFAQPGRKKKGR 289


>gi|15892730|ref|NP_360444.1| ribosomal large subunit pseudouridine synthase B [Rickettsia
           conorii str. Malish 7]
 gi|26006907|sp|Q92HG4|Y807_RICCN RecName: Full=Uncharacterized RNA pseudouridine synthase RC0807;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|15619906|gb|AAL03345.1| ribosomal large subunit pseudouridine synthase B [Rickettsia
           conorii str. Malish 7]
          Length = 230

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 107/230 (46%), Positives = 147/230 (63%), Gaps = 2/230 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K+I+ AG+ SRR+ E++I   +VKV+GI +     NV  ++ IEV G  +    + R
Sbjct: 3   RLAKIISNAGVCSRRDAEKLIVAGQVKVDGITILSPTTNVDISNQIEVSGTLINNIHKPR 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LW+Y+KP+GL+TTH DP  R TVF+ L     RVIS+GRLD+N+EGLLLLTN G LAR  
Sbjct: 63  LWIYYKPVGLITTHKDPLSRKTVFEQLTG-LPRVISIGRLDLNSEGLLLLTNSGDLARQF 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPS++  RVY VR +G+ D    +   K + I GI Y    + L  Q  +N W  V L 
Sbjct: 122 ELPSSRLKRVYHVRAYGKSDILLKSN-YKNLEIDGIFYNPHSIKLLKQNKTNCWFEVVLF 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           EGKNREI+++FE+   KVN+LIRI YG F +  L  G  +E++ KIL   
Sbjct: 181 EGKNREIRRIFEYCGLKVNKLIRIQYGSFTIDNLKPGDYKEINNKILENN 230


>gi|289422766|ref|ZP_06424605.1| RNA pseudouridine synthase family protein [Peptostreptococcus
           anaerobius 653-L]
 gi|289156821|gb|EFD05447.1| RNA pseudouridine synthase family protein [Peptostreptococcus
           anaerobius 653-L]
          Length = 244

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 62/237 (26%), Positives = 105/237 (44%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K++   G  +R E+++   Q  V+VNG   +++ V+V    D I  +G  +   E 
Sbjct: 1   MRLDKLLGNLGYGTRSEIKKYCKQGFVRVNGAEAKKSDVHVDPENDEIVFNGELVNYREF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L      +  T    D           +      VGRLD +TEGLL++TNDG L+ 
Sbjct: 61  VYLLLNKPAGYVSATFDKYDPTVIDLIGEEYLPFEPFPVGRLDKDTEGLLVITNDGKLSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQ----VTLDTQKGS-N 186
            +  P     + Y      +VD   + + +KG+ I +       +       + + GS  
Sbjct: 121 RVLSPKNHVPKKYYAIIDKEVDDMDVRIFEKGVYIGEDYTTKPSKLEVLNPFEFEDGSLG 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + V V + EGK  ++K++FE    +V  L RI  G  +L   L  G  RE++ + + 
Sbjct: 181 SEVHVTISEGKFHQVKRMFEAVGKEVVYLQRIQMGGLELDEELDLGEYRELTPEEVE 237


>gi|218960682|ref|YP_001740457.1| ribosomal large subunit pseudouridine synthase B [Candidatus
           Cloacamonas acidaminovorans]
 gi|167729339|emb|CAO80250.1| ribosomal large subunit pseudouridine synthase B [Candidatus
           Cloacamonas acidaminovorans]
          Length = 279

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 71/241 (29%), Positives = 127/241 (52%), Gaps = 1/241 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
              R+++ +A  G+ SRR+VE  I   R+ VNG L++  +  ++   D + +DG P++ A
Sbjct: 38  KTLRLNRYLADCGLGSRRKVEEFITTGRIAVNGNLVQDLSRQIIPGKDKVTLDGKPIQPA 97

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +     + +KP G V + +D  GR TV+  LP    ++   GRLD  +EGLL  TND  L
Sbjct: 98  KEKFYLILNKPRGYVVSQNDELGRKTVYSLLPPKGKQLAYAGRLDKESEGLLFFTNDTAL 157

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             +L  P  +  +VYRV  +  ++  +LN+L+KG+ I+G       + + ++  +   + 
Sbjct: 158 INLLTHPKNKVEKVYRVDINRPLNNMELNMLRKGVEIEGGKTLPAGIFVKSKNANGMTLK 217

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + + EG+ R+I+++ E    KV  L R+ +GP +L  L  G  R +    ++  L     
Sbjct: 218 IVITEGRKRQIRQMIEAVGAKVTYLKRLQFGPLKLKDLPVGRWRLLEPGEVKALLSLKKE 277

Query: 251 E 251
           +
Sbjct: 278 K 278


>gi|269836469|ref|YP_003318697.1| pseudouridine synthase [Sphaerobacter thermophilus DSM 20745]
 gi|269785732|gb|ACZ37875.1| pseudouridine synthase [Sphaerobacter thermophilus DSM 20745]
          Length = 337

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 74/337 (21%), Positives = 133/337 (39%), Gaps = 3/337 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ +V+A  G+ASRR+ E +I   RV V+G ++    V V      I VDG  LR   R
Sbjct: 2   ERLQRVLAAHGVASRRKAEELITAGRVTVDGQVVRELGVRVDPERQEIRVDGKRLRPERR 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L   P  + T   +   R+ +  +L  +  RV+  GRLD  T GLLLLTNDG L  
Sbjct: 62  RYIMLNKPPGYITTVSDERGRRTVM--DLVQVPERVVPAGRLDRPTAGLLLLTNDGDLLF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + Y V   G    + L+ L++G+ + G      QV     + +   + + 
Sbjct: 120 RITHPRYELEKEYEVLVDGHPPPEVLDQLRRGVTVDGERVVPDQVRPLRIEEAGTVLRIV 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           + EG+NR ++++ +   + V +L R   GP  +  +  G+ R+++   + + L    L+ 
Sbjct: 180 IHEGRNRIVRRMMDRVGYPVLKLTRTRIGPIHVRGVPLGAWRDLTPGEVMQLLEAVGLDP 239

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
           A      P     +   +R              +   S     +++ +            
Sbjct: 240 ASAGRPLPEPGRRSDPGERRGEPRRSGPTRRGERPAPSGARPPARRGERRGGPGTGPRER 299

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                 G   +      +             +R    
Sbjct: 300 FGRGRGGERGARRPPGRRDRRPGGGRQDHRGERGGPP 336


>gi|238764926|ref|ZP_04625865.1| Ribosomal large subunit pseudouridine synthase F [Yersinia
           kristensenii ATCC 33638]
 gi|238696867|gb|EEP89645.1| Ribosomal large subunit pseudouridine synthase F [Yersinia
           kristensenii ATCC 33638]
          Length = 256

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 59/256 (23%), Positives = 105/256 (41%), Gaps = 5/256 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRR+ +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   TNSSIRLNKYISESGICSRRDADRYIEQGNVFINGKRAAV-GDQVYVGDVVKVNGQLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   L L      +    +  DG S    +  +   RV  +GRLD +++GL+ LTN G 
Sbjct: 62  RDENDLVLIALNKPVGIISTTEDGESDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  V  + +  L  G+ + G            +K +    
Sbjct: 122 LVNKILRAGNDHEKEYVVTVNKPVTDEFILGLGAGVPMLGTV----TKKCKVKKEAAFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           ++ L +G NR+I+++ + F ++V +L R       L  L  G  R+++   L E      
Sbjct: 178 SITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNVNLKGLPQGEWRDLTDDELTELFKLIE 237

Query: 250 LEEAQVNLDAPIYSSE 265
              +         S  
Sbjct: 238 NSSSDEKPYKKAESQS 253


>gi|84496363|ref|ZP_00995217.1| pseudouridine synthase, Rsu [Janibacter sp. HTCC2649]
 gi|84383131|gb|EAP99012.1| pseudouridine synthase, Rsu [Janibacter sp. HTCC2649]
          Length = 306

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 75/239 (31%), Positives = 118/239 (49%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +    R+ K++A AG+ SRR  E MI + RV+V+G ++    V + S   + VDGV +  
Sbjct: 66  DPDGIRLQKLLASAGVGSRRVCENMITEGRVEVDGQIVTELGVRINSEQVVHVDGVRVTL 125

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E      ++KP+ +VT+ +D  GR  + D       R+  VGRLD +TEGLLLLTNDG 
Sbjct: 126 DETRVYLAFNKPLNVVTSMNDDLGRIDIGDYFGDRKERLFHVGRLDSDTEGLLLLTNDGD 185

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L+ P    L+ Y  +  G V +D    L++GI ++          +   +   A V
Sbjct: 186 LAHRLQHPKYGVLKTYLAQIRGPVPRDLGKKLREGIELEDGPVKVDSFRVVDSQPGKAIV 245

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            V L EG+   ++++       V  L+R   GP +LG    G  R ++K  + +     
Sbjct: 246 EVILHEGRKHIVRRMLAEAGHPVLSLVRTQIGPIRLGDTKPGKFRRLTKGEVGDLHTAA 304


>gi|296114351|ref|ZP_06833005.1| RNA-binding S4 domain protein [Gluconacetobacter hansenii ATCC
           23769]
 gi|295979112|gb|EFG85836.1| RNA-binding S4 domain protein [Gluconacetobacter hansenii ATCC
           23769]
          Length = 258

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 134/244 (54%), Positives = 170/244 (69%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           KD +         R++K + R+G+ASRR+ ERMI + RV++NG ++   A  V   D ++
Sbjct: 3   KDASPAPTTPHGDRIAKWLGRSGVASRRDAERMIEEGRVRLNGDIVRHPATFVSDGDIVQ 62

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           VD   +   +RTRLW YHKP GLVTTH DPDGR TVF +LP    RVISVGRLD+N+EGL
Sbjct: 63  VDDKVIAAPDRTRLWRYHKPDGLVTTHRDPDGRPTVFASLPEGMPRVISVGRLDLNSEGL 122

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDG LAR LELPS  W+R YRVR  G V++D+L  L +G V +G+ YG ++  LD+
Sbjct: 123 LLLTNDGELARKLELPSNGWIRRYRVRVFGVVNEDQLADLAQGSVFEGVHYGPIEAALDS 182

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +G NAW+TV LREGKNREI+KV    N  V+RLIR SYGPFQLGTL      EV+ K+L
Sbjct: 183 SRGDNAWLTVSLREGKNREIRKVMRGLNLHVSRLIRTSYGPFQLGTLEREELEEVTGKVL 242

Query: 242 REQL 245
           REQ+
Sbjct: 243 REQV 246


>gi|332093194|gb|EGI98254.1| ribosomal small subunit pseudouridine synthase A [Shigella boydii
           5216-82]
          Length = 231

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 102/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+TNDG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTNDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEVI----TPTQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 227


>gi|331265615|ref|YP_004325245.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           oralis Uo5]
 gi|326682287|emb|CBY99904.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           oralis Uo5]
          Length = 240

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 63/233 (27%), Positives = 100/233 (42%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEERDEIRFDGQVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    V  VGRLDI+T GLLLLTNDG LA 
Sbjct: 61  VYYMMNKPQGVISATEDPKHRTVLDLLDDYARAKEVFPVGRLDIDTHGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVT 190
            L  P     + Y  +  G + Q+ +    KGI ++       ++   +     + + V 
Sbjct: 121 ALLSPKRHVDKTYLAQVEGIMSQEDVETFAKGIPLKDFTCQPAKLEFVSVDPEKNQSLVR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  ++K++  F   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 181 VTIAEGKFHQVKRMVAFCGKEVVDLQRLTMGTLVLDENLEQGEWRRLTKEELE 233


>gi|217963560|ref|YP_002349238.1| RNA pseudouridine synthase family protein [Listeria monocytogenes
           HCC23]
 gi|290893629|ref|ZP_06556611.1| rsuA protein [Listeria monocytogenes FSL J2-071]
 gi|217332830|gb|ACK38624.1| RNA pseudouridine synthase family protein [Listeria monocytogenes
           HCC23]
 gi|290556831|gb|EFD90363.1| rsuA protein [Listeria monocytogenes FSL J2-071]
 gi|307571864|emb|CAR85043.1| ribosomal small subunit pseudouridine synthase A [Listeria
           monocytogenes L99]
          Length = 233

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 99/231 (42%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D + V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQVTVHGTPVVYQEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T  +               +    VGRLD +TEGLL++TNDG LA 
Sbjct: 61  VYFMLHKPQNVVSATEDNVSETVIDLLAQEDTLTNPFPVGRLDKDTEGLLIITNDGTLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y  +  G V  + +     GI +         ++ +         + V
Sbjct: 121 NLLSPKKHIDKTYYAKIDGDVVAEDVTAFADGITLDDGYTCKPARLEIINPN----EIKV 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            ++EGK  ++K++F      V+ L RIS G  QL   L  G  R +++  L
Sbjct: 177 TIQEGKFHQVKRMFAARGKTVSYLKRISMGNLQLDESLELGEYRPLTETEL 227


>gi|289435297|ref|YP_003465169.1| ribosomal large subunit pseudouridine synthase B [Listeria
           seeligeri serovar 1/2b str. SLCC3954]
 gi|289171541|emb|CBH28087.1| ribosomal large subunit pseudouridine synthase B [Listeria
           seeligeri serovar 1/2b str. SLCC3954]
 gi|313632602|gb|EFR99592.1| ribosomal large subunit pseudouridine synthase B [Listeria
           seeligeri FSL N1-067]
 gi|313637139|gb|EFS02679.1| ribosomal large subunit pseudouridine synthase B [Listeria
           seeligeri FSL S4-171]
          Length = 243

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 76/238 (31%), Positives = 120/238 (50%), Gaps = 3/238 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E +I + +V VNG ++    V V  ++ IEV+G+ L K E  
Sbjct: 2   ERLQKVIANAGITSRRKAETLIKEGKVTVNGKVVTELGVKVSGSERIEVEGIQLTKEEHR 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     +     D    +        I  R+  VGRLD +T GLLL+TNDG  A +
Sbjct: 62  YFLFYKPRGTVSAVTDDKGRTTVADYF-TDIPERLYPVGRLDYDTSGLLLMTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           L  P  +  + Y  R  G  +++ +  L++G+VI G      +V + +       A V +
Sbjct: 121 LMHPKNEVSKTYIARIKGIPEREVIRELERGVVIDGRKTAPAKVKIRSSDKAKDKAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + EG+NR+++K+FE   ++V +L R  Y    L  L AG  RE+S   +++      
Sbjct: 181 TIHEGRNRQVRKMFEAVGFEVQKLSREEYSFLNLRGLNAGERRELSHHEVKQLKTEAR 238


>gi|251790037|ref|YP_003004758.1| 16S rRNA pseudouridylate synthase A [Dickeya zeae Ech1591]
 gi|247538658|gb|ACT07279.1| pseudouridine synthase [Dickeya zeae Ech1591]
          Length = 232

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 56/231 (24%), Positives = 104/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  QRV V+G +++  A  ++    +  D   L +    
Sbjct: 1   MRLDKFLSQQLGISRSLVARELRAQRVTVDGEVIKNGAFKLLPEHEVAFDDNVLVQQNGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP+G V +  DPD  + ++     +  ++ + GRLDI+T GL+LLT+DG  +  
Sbjct: 61  RYFMLNKPLGYVCSTDDPDHPTILYFIDEPVAHKLHAAGRLDIDTSGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +  D     + G+ + G         + +     S   V +
Sbjct: 121 ITSPKHHCEKTYLVTLDQPLAPDTAEKFQAGVQLHGEQSLTRPATLEII----SEHQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L AG  R ++ + +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVALHRERIGAITLDDALEAGEYRPLTPEEI 227


>gi|254293362|ref|YP_003059385.1| RNA-binding S4 domain protein [Hirschia baltica ATCC 49814]
 gi|254041893|gb|ACT58688.1| RNA-binding S4 domain protein [Hirschia baltica ATCC 49814]
          Length = 508

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 130/347 (37%), Positives = 184/347 (53%), Gaps = 4/347 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R++K +A AG+ SRRE ER+I +  V VNG +L+ AA  V   + I V+G  +   
Sbjct: 31  SKGERIAKWLAAAGVCSRREAERLIEEGLVAVNGQVLDSAAFKVTGNEKITVEGKRVGGP 90

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ++TRLW +HKP GLVTT+SDP+GR TVF++LP    RV+++GRLD+NTEGLLLLTNDG L
Sbjct: 91  DKTRLWRFHKPKGLVTTNSDPEGRPTVFEHLPKKLPRVMTIGRLDLNTEGLLLLTNDGEL 150

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           AR LELP+T   R YR R  G++ Q +L+ L++G++ +G+ Y  +  TLD  KG N W+ 
Sbjct: 151 ARTLELPTTGLKRCYRARAFGKITQAELDKLQEGVLFEGVVYRSIIATLDKTKGDNNWID 210

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI-LREQLGPHL 249
           + L EGK RE ++  E     VNRLIR+SYGPF+LG L+ G   E+     L E      
Sbjct: 211 MTLTEGKKREARRALESVGLIVNRLIRVSYGPFELGDLVEGGVAEIPAGELLSEFGDSIS 270

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
            +        P    E   + R     +     T   K  +      + +K   P   R 
Sbjct: 271 RKRRPDPASVPQSYLEPDTKRRRTKGRDEDTSQTAPAKKPAATIKPLRGEKFEKPSSGRE 330

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRR---SPSFPSKRSLRRTSAK 353
            A      +  H       G       R    P+ P +  +  + AK
Sbjct: 331 PAQRSHKRQTPHRYAALREGAETNPEPRDFSKPAKPGEAVVPASLAK 377


>gi|270262758|ref|ZP_06191029.1| ribosomal small subunit pseudouridine synthase A [Serratia
           odorifera 4Rx13]
 gi|270043442|gb|EFA16535.1| ribosomal small subunit pseudouridine synthase A [Serratia
           odorifera 4Rx13]
          Length = 237

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 57/238 (23%), Positives = 110/238 (46%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  +RV V+G +++  AV +     +  DG PL++    
Sbjct: 1   MRLDKFLSQQLGVSRALVARELRAKRVTVDGEVVKSGAVKLTPEQEVAFDGNPLQQLSGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     + +D      +G+ +          Q     +K  +  V +
Sbjct: 121 VTSPKHHCEKTYLVTLEHPLAEDTAQQFAEGVQLHNEKDLTRPAQ----LEKIEDTLVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
            + EG+  ++K++F     +V  L R   G   +   L  G  R ++++ +     PH
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVVELHRERIGAIVMDEDLAPGEYRPLTEEEIASVGAPH 234


>gi|238755438|ref|ZP_04616779.1| Ribosomal small subunit pseudouridine synthase A [Yersinia ruckeri
           ATCC 29473]
 gi|238706375|gb|EEP98751.1| Ribosomal small subunit pseudouridine synthase A [Yersinia ruckeri
           ATCC 29473]
          Length = 235

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 55/238 (23%), Positives = 107/238 (44%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  +RV V+G +++  A+ +     +  DG  L++    
Sbjct: 1   MRLDKFLSQQLGVSRALVARELRAKRVTVDGEIVKTGALKLTPEQEVMFDGNLLQQQVGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D       G+ +          Q+ +   +     V +
Sbjct: 121 ITSPKHHCEKTYLVTLEHPVADDTAEQFAVGVQLHNEPTLTKPAQLEVIEPQQ----VRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
            + EG+  ++K++F     +V  L R   G   +   L  G  R ++++ +     PH
Sbjct: 177 TISEGRYHQVKRMFGAVGNRVVALHRERIGAIVMDDDLAPGEYRPLTEEEIASVGAPH 234


>gi|323350518|ref|ZP_08086180.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis VMC66]
 gi|322123200|gb|EFX94885.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis VMC66]
          Length = 242

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 106/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++++ +  V VNG + +     +  T D I V G  L   + 
Sbjct: 1   MRLDKFLAENGLGSRAQVKQLLKKGLVLVNGRVEKSPKTQIDETADEIIVSGQRLTYEKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  D         +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPQGVISATEDDRHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            +  P     ++YR +  G + Q  ++    GI ++       Q+ +     +   + V 
Sbjct: 121 AMLSPKKHVEKIYRAQVAGLMKQADVDRFAAGIELKDFTCQPAQLKVLELDEAKETSLVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + L EGK  ++K++      +V  L R++ GP QL   +  G  R ++++ +
Sbjct: 181 ITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDPAVALGEWRRLTEEEM 232


>gi|229815391|ref|ZP_04445726.1| hypothetical protein COLINT_02438 [Collinsella intestinalis DSM
           13280]
 gi|229809171|gb|EEP44938.1| hypothetical protein COLINT_02438 [Collinsella intestinalis DSM
           13280]
          Length = 272

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 76/242 (31%), Positives = 116/242 (47%), Gaps = 13/242 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE 71
           P R+ + +ARAG+ASRR  E ++   RV+VNG +       V    D + VDG P+    
Sbjct: 20  PMRLQRFLARAGVASRRGSEGLMTAGRVRVNGEVKTELGTKVDPRCDEVTVDGAPVVLGS 79

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGL 130
                + +KP G +TT SDP GR TV + +PS        VGRLD++T GLLL T DG L
Sbjct: 80  GPAYIMLNKPAGFLTTMSDPHGRPTVAELVPSKKFPGLFPVGRLDMDTTGLLLFTTDGDL 139

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN---- 186
            + L  PS    + YR    G+     L  L++G+ +        +  +     ++    
Sbjct: 140 GQRLLHPSHHVWKTYRAIVDGRCLDGDLEPLRRGLTLDDGPCQPARCRVLEPADAHIPGF 199

Query: 187 -------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                    V V +REG+  ++K++       V  L R  +G  +LG L  GS RE++ +
Sbjct: 200 PRLVTGATAVEVIIREGRKNQVKRMLSKIGHPVIALHRCRFGELRLGDLAEGSWRELTDE 259

Query: 240 IL 241
            +
Sbjct: 260 EV 261


>gi|297570484|ref|YP_003691828.1| pseudouridine synthase [Desulfurivibrio alkaliphilus AHT2]
 gi|296926399|gb|ADH87209.1| pseudouridine synthase [Desulfurivibrio alkaliphilus AHT2]
          Length = 240

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 84/235 (35%), Positives = 132/235 (56%), Gaps = 1/235 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +ARAGIASRR+ E  IAQ RV+V+G  + +  + +      +  DG P+    R
Sbjct: 3   ERLQKFLARAGIASRRKAEEYIAQGRVQVDGRPVAQMGLTIDPERQQVTFDGQPVLPPSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G VTT +DP GR  V   +     R+  VGRLD++TEG LLLTNDG LA+
Sbjct: 63  KLTVLLNKPAGYVTTMADPQGRPIVTSLINEPGLRLFPVGRLDLDTEGALLLTNDGELAQ 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  PS Q  R Y     G+ +++ L  L++GI+++G      ++    +   +  + V 
Sbjct: 123 NILHPSRQINRTYHATVKGRPNREALQQLRRGIMLEGRRTWPARIRELRRNQESTTLEVI 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           + EG+ R+++K+F   N  V +L R++YG  +LG+L  G  R +S + L+    P
Sbjct: 183 IHEGRKRQVRKMFAAINHPVLQLKRVAYGGLRLGSLPTGRYRRLSPEDLQLLFRP 237


>gi|150025290|ref|YP_001296116.1| pseudouridylate synthase [Flavobacterium psychrophilum JIP02/86]
 gi|149771831|emb|CAL43305.1| Pseudouridylate synthase [Flavobacterium psychrophilum JIP02/86]
          Length = 266

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 59/263 (22%), Positives = 115/263 (43%), Gaps = 11/263 (4%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           ++EN T  R++K ++  G  SRRE ++++ + R+ +NG ++      V   D + VDG  
Sbjct: 1   MEENLT--RINKFLSETGHCSRREADKLLDEGRITING-IVPEMGTKVSHHDEVRVDGKL 57

Query: 67  LRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +R+  E+     ++KP+G+  T +     + V     +   R+  +GRLD  +EGL+ +T
Sbjct: 58  VREKTEKPVYLAFNKPVGIECTTNLDVRYNIVDFI--NYPKRIFPIGRLDKASEGLIFMT 115

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +   +        + Y V  +  +    +  +  GI I        +V    ++ S
Sbjct: 116 NDGDIVNKILRARNNHEKEYTVTVNKLITDRFIQKMSNGIPILDTVTKKCKV----EQIS 171

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++ E+  ++V  L RI      L  +  G  R+++   + E  
Sbjct: 172 KTTFKIVLTQGLNRQIRRMCEYLGYEVTSLKRIRIINISL-DIPVGRYRDLTDAEITELN 230

Query: 246 GPHLLEEAQVNLDAPIYSSETLV 268
                         P   +    
Sbjct: 231 NLIEPSSKTEEASFPKVEAPKRR 253


>gi|332884211|gb|EGK04479.1| hypothetical protein HMPREF9456_00806 [Dysgonomonas mossii DSM
           22836]
          Length = 289

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 64/297 (21%), Positives = 125/297 (42%), Gaps = 10/297 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ +G  SRRE +++I Q  V +NG         V++   ++V G  +    + 
Sbjct: 1   MRINKYISDSGYCSRREADKLIEQGSVTINGKRA-SIGSQVLAGQEVKVYGETVTCNTQP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y+KP+G+V+T    +       +      R+  +GRLD +++GL++LTN+G +   
Sbjct: 60  VFIAYNKPVGIVSTTDLDE--PNNIIDAVGHDERIFPIGRLDKDSQGLIILTNEGDMVNK 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V     +++D +  ++ G+ I G+     +V     K       + L
Sbjct: 118 MLRADNNHEKEYHVTVDKLINEDFVKKMQGGVPILGVVTRKCEVV----KTGTHSFNIVL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           R+G NR+I+++ E+  + V RL RI     +LG +  G  R ++K+ L E L        
Sbjct: 174 RQGLNRQIRRMCEYLGYNVVRLERIRIMHIKLGNIKVGQWRNITKEEL-EILRKKTASSV 232

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL--SKQKKLATPVHRR 308
           +        +     +              +      +++G      K       R+
Sbjct: 233 KTESAPKKKTKPQEAKTPQPKGKSANSYKEKKTPTGYKESGSGMRNGKSSVKKKTRK 289


>gi|255535081|ref|YP_003095452.1| pseudouridine synthase, Rsu [Flavobacteriaceae bacterium 3519-10]
 gi|255341277|gb|ACU07390.1| pseudouridine synthase, Rsu [Flavobacteriaceae bacterium 3519-10]
          Length = 239

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 65/241 (26%), Positives = 110/241 (45%), Gaps = 6/241 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++  G  SRRE +RM+ Q R+ VNG +       V   D I VDGV +RK E   
Sbjct: 4   RINKYLSEVGFCSRREADRMLEQGRITVNGNIP-EMGTKVSGEDEILVDGVSIRKVEEEH 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +++       +   +D            +   R+  +GRLD  +EGL+LLT+DG +   +
Sbjct: 63  VYIALNKPVGIVCTTDTKRERDNIVEFVNHPKRIFPIGRLDKPSEGLILLTSDGDIVNKI 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +    L+ ++ G+ I GI     +     ++       + L 
Sbjct: 123 LRARNNHEKEYIVRVDKPISPQFLHKMRNGVPILGIITNKCE----VEQIDTLSFRIILT 178

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E+  ++V +L RI     +L  L  G  R++S + L E        E  
Sbjct: 179 QGLNRQIRRMCEYLGYEVKKLKRIRIMNIKL-DLPIGKWRDLSAQELAELNALLGDSEKT 237

Query: 255 V 255
           V
Sbjct: 238 V 238


>gi|315282990|ref|ZP_07871273.1| ribosomal large subunit pseudouridine synthase B [Listeria marthii
           FSL S4-120]
 gi|313613361|gb|EFR87222.1| ribosomal large subunit pseudouridine synthase B [Listeria marthii
           FSL S4-120]
          Length = 244

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 77/232 (33%), Positives = 122/232 (52%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E++I + +V VNG +++   V V  T+ IEV+G+ L K E  
Sbjct: 2   ERLQKVIANAGITSRRKAEKLIQEGKVTVNGKVVKELGVKVSGTERIEVEGIQLTKEEHR 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     +     D    +        I  R+  VGRLD +T GLLL+TNDG  A +
Sbjct: 62  YFLFYKPRGTVSAVTDDKGRTTVADYF-ADIPERLYPVGRLDYDTSGLLLMTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVTV 191
           L  P  +  + Y  R  G  +++ +  L++G+VI G      +V +    +    A V +
Sbjct: 121 LMHPKNEVSKTYIARIKGIPEREVIRQLERGVVIDGRKTAPAKVKVRSSDKTKDKAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + EG+NR+++K+FE   ++V +L R  Y    L  L AG  RE+S   +++
Sbjct: 181 TIHEGRNRQVRKMFEAVGFEVQKLSREEYSFLNLRGLNAGERRELSHHEVKQ 232


>gi|16804380|ref|NP_465865.1| hypothetical protein lmo2342 [Listeria monocytogenes EGD-e]
 gi|224503528|ref|ZP_03671835.1| hypothetical protein LmonFR_13647 [Listeria monocytogenes FSL
           R2-561]
 gi|16411830|emb|CAD00420.1| lmo2342 [Listeria monocytogenes EGD-e]
          Length = 233

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 100/231 (43%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D I V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQITVHGTPVVYQEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T  +               +    VGRLD +TEGLL++TNDG LA 
Sbjct: 61  VYFMLHKPQNVVSATEDNVSETVIDLLAQEDTLTDPFPVGRLDKDTEGLLIITNDGTLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y  +  G V  + +     GI +         ++ + T       + V
Sbjct: 121 NLLSPKKHIDKTYYAKIDGDVTAEDVEAFAAGIELDDGYTCKPARLEIITPN----EIKV 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            ++EGK  ++K++F      V+ L RIS G  QL   L  G  R +++  L
Sbjct: 177 TIQEGKFHQVKRMFAARGKSVSYLKRISMGNLQLDESLALGEYRPLTEAEL 227


>gi|313623106|gb|EFR93379.1| ribosomal large subunit pseudouridine synthase B [Listeria innocua
           FSL J1-023]
          Length = 244

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 76/238 (31%), Positives = 121/238 (50%), Gaps = 3/238 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ SRR+ E++I + +V VNG ++    V V  T+ IEV+G+ L K E  
Sbjct: 2   ERLQKVIANAGVTSRRKAEKLIQEGKVTVNGKVVTELGVKVTGTERIEVEGIQLTKEEHR 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     +     D    +        I  R+  VGRLD +T GLLL+TNDG  A +
Sbjct: 62  YFLFYKPRGTVSAVTDDKGRTTVADYF-TDIPERLYPVGRLDYDTSGLLLMTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           L  P  +  + Y  R  G  +++ +  L++G+VI G      +V + +       A V +
Sbjct: 121 LMHPKNEVSKTYIARIKGIPEREVIRELERGVVIDGRKTAPAKVKVRSSDKAKDKAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + EG+NR+++K+FE   ++V +L R  Y    L  L AG  RE+S   +++      
Sbjct: 181 TIHEGRNRQVRKMFEAVGFEVQKLAREEYSFLNLRGLNAGERRELSHHEVKQLKTEAR 238


>gi|295702668|ref|YP_003595743.1| pseudouridine synthase F [Bacillus megaterium DSM 319]
 gi|294800327|gb|ADF37393.1| pseudouridine synthase F (ribosomal large subunit) [Bacillus
           megaterium DSM 319]
          Length = 238

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 65/226 (28%), Positives = 109/226 (48%), Gaps = 7/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +G ASRR  +++I++ RV VNG + +     V   D I V G  LR A    
Sbjct: 5   RLNKFISESGKASRRGADKLISEGRVTVNGKVAKV-GDQVKPGDDIRVSGQQLRIARNNV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+ +T            +L +   R+  VGRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITSTSEKKV--KGNIIDLVNHPLRIHHVGRLDKDSDGLILLTNDGDIINEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  + +  + +G+ I G      +VT      S     + L 
Sbjct: 122 LRAENKHEKEYIVAVDKPITPEFIKNMSEGVKILGTKTLPCKVTQL----SKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +G NR+I+++ E   ++V RL R       L  L  G  R+++KK 
Sbjct: 178 QGLNRQIRRMCEVLGYEVYRLQRTRIMNIHLNNLPVGQWRDLTKKE 223


>gi|300812160|ref|ZP_07092604.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           delbrueckii subsp. bulgaricus PB2003/044-T3-4]
 gi|300496845|gb|EFK31923.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           delbrueckii subsp. bulgaricus PB2003/044-T3-4]
          Length = 239

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 78/231 (33%), Positives = 121/231 (52%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRRE E+MI   RV+V+G ++ +    V S + + VD  P+ +    
Sbjct: 4   ERLQKVIAQAGIASRREAEKMILAGRVRVDGQVVTKLGTKVSSIEQVVVDNQPIERESHH 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     +++   D  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA +
Sbjct: 64  TYLFYKPRG-VISAVKDNKGRKTVADYFTDLPYRLYPVGRLDYDTSGLLLMTNDGELANL 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVTV 191
           L  P  +  +VY  +  G +  D++  LKKG+ I        QV +           V +
Sbjct: 123 LMHPRNEVDKVYVAKIKGILQPDEIKALKKGVQIGRYKTKPAQVKVLKTNPRAQTQIVQL 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EG   ++K++F+  N  V++L R  Y    L  L +G  RE+++K + 
Sbjct: 183 TIHEGHYHQVKEMFKAVNHLVDKLSRERYSFLDLQGLTSGQYRELNRKEVD 233


>gi|299141527|ref|ZP_07034663.1| ribosomal large subunit pseudouridine synthase B [Prevotella oris
           C735]
 gi|298576863|gb|EFI48733.1| ribosomal large subunit pseudouridine synthase B [Prevotella oris
           C735]
          Length = 490

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 61/242 (25%), Positives = 108/242 (44%), Gaps = 1/242 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I+   V VNG ++      V+ +D +
Sbjct: 242 IEYKETHIDPNEPIRLNKYLANAGVCSRREADEFISAGVVSVNGTVVTELGTKVLRSDEV 301

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +     +   ++  + L      + T+      ++ +         R+  VGRLD NT G
Sbjct: 302 KFHDQLVSLEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKDVCPERIYPVGRLDRNTTG 361

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     +VY V     V ++ L  +  GI ++            
Sbjct: 362 VLLLTNDGDLASKLTHPKFLKKKVYHVHLDKNVAEEDLQKIASGIELEDGEIH-ADAIEY 420

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                   V + +  GKNR ++++FE   ++V RL R+ +       L  G  R ++++ 
Sbjct: 421 ADDRDKKQVGIEIHSGKNRIVRRIFESLGYRVVRLDRVQFAGLTKKNLRRGDWRFLTEQE 480

Query: 241 LR 242
           + 
Sbjct: 481 VE 482


>gi|218133030|ref|ZP_03461834.1| hypothetical protein BACPEC_00891 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991903|gb|EEC57907.1| hypothetical protein BACPEC_00891 [Bacteroides pectinophilus ATCC
           43243]
          Length = 238

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 65/235 (27%), Positives = 115/235 (48%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K ++ AG  SRRE +R++   RV ++G +       V     + VDG  +    R 
Sbjct: 4   ERINKYLSEAGYCSRREADRLVEAGRVTIDG-VAAVCGSKVADGQKVCVDGKEVSGRSRH 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L  ++KP G+V T +D  G + + D +     R+  VGRLD ++EGL+L+TNDG +   
Sbjct: 63  ILLAFNKPAGIVCTTTDKQGSNNIVDFIGY-PERIYPVGRLDKDSEGLILMTNDGAMMDR 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKGSNAWVTV 191
           +   +    + Y VR +  V  + +  +  G+ ++               +K +     +
Sbjct: 122 ILRSTNGHEKEYIVRVNKPVTDEFVKGMSDGVYLKELDRTTKVC----VVEKVTKFCFRI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            L +G NR+I+++ E F +KV +L RI      LG L  G  R+V+ +   E + 
Sbjct: 178 VLTQGLNRQIRRMCENFGYKVMKLKRIRIMNIMLGDLKQGCYRDVTDEEYAELVR 232


>gi|167765418|ref|ZP_02437531.1| hypothetical protein BACSTE_03806 [Bacteroides stercoris ATCC
           43183]
 gi|167697046|gb|EDS13625.1| hypothetical protein BACSTE_03806 [Bacteroides stercoris ATCC
           43183]
          Length = 234

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 56/225 (24%), Positives = 97/225 (43%), Gaps = 1/225 (0%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW 76
           +K +A AG+ SRRE +  I    V VNG ++      +   D ++     +    +  + 
Sbjct: 2   NKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRGDEVKFHDQTVSIERKIYVL 61

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L      + T+      R+ +     +   R+  VGRLD NT G+LLLTNDG LA  L  
Sbjct: 62  LNKPKDTVTTSDDPQARRTVMDLVKGACDERIYPVGRLDRNTTGVLLLTNDGDLASKLTH 121

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
           P     ++Y V     + +  +  +  GI +             T       V + +  G
Sbjct: 122 PKYLKKKIYHVHLDKNLTKADMEQIAAGIQLDDGEIQ-ADAISYTDDFKKDEVGIEIHSG 180

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           KNR ++++FE   +KV +L R+ +       L  G  R ++++ +
Sbjct: 181 KNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLTEQEV 225


>gi|294497295|ref|YP_003560995.1| pseudouridine synthase F (ribosomal large subunit) [Bacillus
           megaterium QM B1551]
 gi|294347232|gb|ADE67561.1| pseudouridine synthase F (ribosomal large subunit) [Bacillus
           megaterium QM B1551]
          Length = 238

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 65/226 (28%), Positives = 109/226 (48%), Gaps = 7/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +G ASRR  +++I++ RV VNG + +     V   D I V G  LR A    
Sbjct: 5   RLNKFISESGKASRRGADKLISEGRVTVNGKVAKV-GDQVKPGDDIRVSGQQLRIARNNV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+ +T            +L +   R+  VGRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITSTSEKKV--KGNIIDLVNHPLRIHHVGRLDKDSDGLILLTNDGDIINEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  + +  + +G+ I G      +VT      S     + L 
Sbjct: 122 LRAENKHEKEYIVAVDKPITPEFIKNMSEGVKILGTKTLPCEVTQL----SKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +G NR+I+++ E   ++V RL R       L  L  G  R+++KK 
Sbjct: 178 QGLNRQIRRMCEVLGYEVYRLQRTRIMNIHLNNLPVGQWRDLTKKE 223


>gi|116873391|ref|YP_850172.1| ribosomal large subunit pseudouridine synthase B [Listeria
           welshimeri serovar 6b str. SLCC5334]
 gi|116742269|emb|CAK21393.1| ribosomal large subunit pseudouridine synthase B [Listeria
           welshimeri serovar 6b str. SLCC5334]
          Length = 244

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 76/238 (31%), Positives = 121/238 (50%), Gaps = 3/238 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E++I + +V VNG ++    V V  T+ IEV+G+ L K E  
Sbjct: 2   ERLQKVIANAGITSRRKAEKLIQEGKVTVNGKVVTELGVKVSGTERIEVEGIQLTKEEHR 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     +     D    +        I  R+  VGRLD +T GLLL+TNDG  A +
Sbjct: 62  YFLFYKPRGTVSAVTDDKGRTTVADYF-TDIPERLYPVGRLDYDTSGLLLMTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW--VTV 191
           L  P  +  + Y  R  G  +++ +  L++G+VI G      +V + +   +     V +
Sbjct: 121 LMHPKNEVSKTYIARIKGIPEREVIRELERGVVIDGRKTAPAKVKVRSSDKAKNKAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + EG+NR+++K+FE   ++V +L R  Y    L  L AG  RE+S   +++      
Sbjct: 181 TIHEGRNRQVRKMFEAVGFEVQKLSREEYSFLNLRGLNAGERRELSHHEVKQLKTEAR 238


>gi|225874153|ref|YP_002755612.1| pseudouridine synthase rsuA family protein [Acidobacterium
           capsulatum ATCC 51196]
 gi|225791360|gb|ACO31450.1| pseudouridine synthase rsuA family protein [Acidobacterium
           capsulatum ATCC 51196]
          Length = 406

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 97/352 (27%), Positives = 149/352 (42%), Gaps = 13/352 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAE 71
            +R+ K++A AG+ASRR+ E +I   RV+VNG ++         ++DHI VDG  L+  E
Sbjct: 23  GERLQKILASAGVASRRKAEELILAGRVQVNGQVVTEMGFKADAASDHIRVDGKLLQGPE 82

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDG 128
           + R ++ +KP G VTT SDP+GR TV +          R+  VGRLD  +EGLLL+TNDG
Sbjct: 83  KLRYFMLNKPKGYVTTVSDPEGRHTVMEFFHGRGKGGERLYPVGRLDYASEGLLLMTNDG 142

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-------CYGDMQVTLDT 181
            LA  L   S+   +VY V+  G+  +++L  ++ GI+I                     
Sbjct: 143 ALANTLTKASSHVEKVYLVKVSGRPTEEQLEQIRAGIMIDRGRPGEGRVMTAPA-GVRMV 201

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +   N W  + L EG+NREI+K+FE     V ++ RI YGP  L  +  G  RE++ + +
Sbjct: 202 RDAENPWFELTLIEGRNREIRKMFEETGHFVEKIRRIGYGPLVL-DVEPGEVRELNPEEV 260

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
                    + A     A      T++                         G   +   
Sbjct: 261 DSLRRAAQRKRAPKPKAATKTKRLTMLPKAKPARKSATGGRPGRAGAGRPAAGRPGRAGQ 320

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                R               +    S   E    RS +    +   R   +
Sbjct: 321 GGQNARSGQGGASSERPARKLAPEGASRATERAGSRSGAKAGNKPAARPGTR 372


>gi|255767687|ref|NP_390882.2| 16S pseudouridylate synthase [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|269849526|sp|O32068|YTZG_BACSU RecName: Full=Uncharacterized RNA pseudouridine synthase ytzG;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|225185315|emb|CAB14982.2| putative 16S pseudouridylate synthase [Bacillus subtilis subsp.
           subtilis str. 168]
          Length = 239

 Score =  173 bits (438), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 58/224 (25%), Positives = 96/224 (42%), Gaps = 3/224 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A +G  SR+EV+ ++    V ++G   +    +V      + V G P+   E 
Sbjct: 1   MRLDKLLANSGYGSRKEVKAVVKAGAVMIDGKPAKDVKEHVDPDTQEVTVYGEPVDYREF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      L  T                +       GRLD +TEG LLLTNDG LA 
Sbjct: 61  IYLMMNKPQGVLSATEDSRQQTVVDLLTPEEMRFEPFPAGRLDKDTEGFLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V    Q+ ++ ++ L+ G+ I+G       +  + T    N  + +
Sbjct: 121 RLLSPKKHVPKTYEVHLKSQISREDISDLETGVYIEGGYKTKPAKAEIKTNDSGNTVIYL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
            + EGK  ++K++ +    +V  L R+S G   L   L  G  R
Sbjct: 181 TITEGKYHQVKQMAKAVGNEVVYLKRLSMGRVSLDPALAPGEYR 224


>gi|332637861|ref|ZP_08416724.1| ribosomal large subunit pseudouridine synthase B [Weissella cibaria
           KACC 11862]
          Length = 255

 Score =  173 bits (438), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 79/240 (32%), Positives = 123/240 (51%), Gaps = 11/240 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A+AG+ASRR  E++I   +V VNG  +      V  +D IEV G P+   E+ 
Sbjct: 3   ERLQKVMAQAGVASRRASEQLILDGKVTVNGKTVRELGTKVEPSDKIEVSGEPIDSREKL 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G+VTT +D  GR TV D +     RV  VGRLD +T G+LLLTNDG LA  
Sbjct: 63  VYFLLNKPRGVVTTTNDDKGRQTVMDIV-DEPERVYPVGRLDYDTTGVLLLTNDGELANR 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--------CYGDMQVTLDTQKGS 185
           L  PS +  +VY  +  G    ++L  L+ G+ ++               +  + +    
Sbjct: 122 LMHPSYRIDKVYVAKVKGIPTNEQLEQLRHGVTVRTKQNGRYTTFKAAPARAEITSTNTK 181

Query: 186 NAW--VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           N    V + + EGK  ++K++ +    +V +L R  YG   L  L  G  R +  + ++ 
Sbjct: 182 NHTAIVKLTIHEGKYHQVKEMMKAVGHEVLKLTRERYGMLDLAGLTPGEYRPLRYEEVQA 241


>gi|223940522|ref|ZP_03632370.1| pseudouridine synthase [bacterium Ellin514]
 gi|223890803|gb|EEF57316.1| pseudouridine synthase [bacterium Ellin514]
          Length = 235

 Score =  173 bits (438), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 80/233 (34%), Positives = 122/233 (52%), Gaps = 2/233 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A AG+ASRR  ER+I   RV VNG  +      V    D I +DG PLR   +
Sbjct: 2   VRLQKFLAEAGVASRRASERIILGGRVSVNGDTVRELGTKVDPIHDSIALDGAPLRLKRK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + +   D      + D LP+ +  + SVGRLD ++EGL+ LTNDG  + 
Sbjct: 62  LYVALNKPRGYVCSRKDDRKR-KVIGDLLPAEWDNLYSVGRLDSDSEGLIFLTNDGEFSL 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  + L+ Y     G+V+Q+ L   K GIV +G      +    + + S + V + 
Sbjct: 121 HLTHPRYRVLKKYLATVEGRVEQEMLQRFKHGIVHEGEKLKVDRARTLSVQNSTSLVELE 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           L EGKNREI+++FE     V+RL+R+  G  +LG L +G  R +++  ++  L
Sbjct: 181 LTEGKNREIRRLFESQGLTVSRLVRMQIGKIKLGELRSGKWRMLTEAEIKSLL 233


>gi|157828676|ref|YP_001494918.1| ribosomal large subunit pseudouridine synthase B [Rickettsia
           rickettsii str. 'Sheila Smith']
 gi|157801157|gb|ABV76410.1| ribosomal large subunit pseudouridine synthase B [Rickettsia
           rickettsii str. 'Sheila Smith']
          Length = 230

 Score =  173 bits (438), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 107/230 (46%), Positives = 148/230 (64%), Gaps = 2/230 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K+I+ AG+ SRR+ E++I + +VKV+GI +     NV  ++ IEV G  +    + R
Sbjct: 3   RLAKIISNAGVCSRRDAEKLIVEGQVKVDGITILSPTTNVDISNQIEVSGTLINNIHKPR 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LW+Y+KP+GL+TTH DP  R TVF+ L     RVIS+GRLD+N+EGLLLLTN G LAR  
Sbjct: 63  LWIYYKPVGLITTHKDPLSRKTVFEQLTG-LPRVISIGRLDLNSEGLLLLTNSGDLARQF 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPS++  RVY VR +G+ D    +   K + I GI Y    + L  Q  +N W  V L 
Sbjct: 122 ELPSSRLKRVYHVRAYGKSDVLLKSN-YKNLEIDGIFYNPHSIKLLKQNKTNCWFEVVLF 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           EGKNREI+++FE+   KVN+LIRI YG F +  L  G  +E++ KIL   
Sbjct: 181 EGKNREIRRIFEYCGLKVNKLIRIQYGSFTIDNLKPGDYKEINNKILENN 230


>gi|34581547|ref|ZP_00143027.1| ribosomal large subunit pseudouridine synthase B [Rickettsia
           sibirica 246]
 gi|28262932|gb|EAA26436.1| ribosomal large subunit pseudouridine synthase B [Rickettsia
           sibirica 246]
          Length = 230

 Score =  173 bits (438), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 107/230 (46%), Positives = 148/230 (64%), Gaps = 2/230 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K+I+ AG+ SRR+ E++I + +VKV+GI +     NV  ++ IEV G  +    + R
Sbjct: 3   RLAKIISNAGVCSRRDAEKLIVEGQVKVDGITILSPTTNVDISNQIEVSGTLINNIHKPR 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LW+Y+KP+GL+TTH DP  R TVF+ L     RVIS+GRLD+N+EGLLLLTN G LAR  
Sbjct: 63  LWIYYKPVGLITTHKDPLSRKTVFEQLTG-LPRVISIGRLDLNSEGLLLLTNSGDLARQF 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPS++  RVY VR +G+ D    +   K + I GI Y    + L  Q  +N W  V L 
Sbjct: 122 ELPSSRLKRVYHVRAYGKSDILLKSN-YKNLEIDGIFYNPHSIKLLKQNKTNCWFEVVLF 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           EGKNREI+++FE+   KVN+LIRI YG F +  L  G  +E++ KIL   
Sbjct: 181 EGKNREIRRIFEYCGLKVNKLIRIQYGSFTIDNLKPGDYKEINNKILENN 230


>gi|50842867|ref|YP_056094.1| ribosomal large subunit pseudouridine synthase B [Propionibacterium
           acnes KPA171202]
 gi|282853641|ref|ZP_06262978.1| pseudouridylate synthase [Propionibacterium acnes J139]
 gi|50840469|gb|AAT83136.1| ribosomal large subunit pseudouridine synthase B [Propionibacterium
           acnes KPA171202]
 gi|282583094|gb|EFB88474.1| pseudouridylate synthase [Propionibacterium acnes J139]
 gi|313813285|gb|EFS50999.1| conserved hypothetical protein [Propionibacterium acnes HL025PA1]
 gi|314923703|gb|EFS87534.1| conserved hypothetical protein [Propionibacterium acnes HL001PA1]
 gi|314967055|gb|EFT11154.1| conserved hypothetical protein [Propionibacterium acnes HL082PA2]
 gi|314983150|gb|EFT27242.1| conserved hypothetical protein [Propionibacterium acnes HL110PA3]
 gi|315092372|gb|EFT64348.1| conserved hypothetical protein [Propionibacterium acnes HL110PA4]
 gi|315092741|gb|EFT64717.1| conserved hypothetical protein [Propionibacterium acnes HL060PA1]
 gi|315105956|gb|EFT77932.1| conserved hypothetical protein [Propionibacterium acnes HL030PA1]
 gi|327327189|gb|EGE68965.1| ribosomal large subunit pseudouridine synthase B [Propionibacterium
           acnes HL103PA1]
          Length = 245

 Score =  173 bits (438), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 77/241 (31%), Positives = 110/241 (45%), Gaps = 2/241 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
            N    R+ KV+A+AG+ASRR  E MIA  RV+VNG L+      V    D I VDG  +
Sbjct: 2   SNEQGIRLQKVLAQAGLASRRAAEDMIAAGRVEVNGELIVEQGRRVDPERDEIRVDGSRI 61

Query: 68  R-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                     L      + T                    R+  VGRLD  T GL+LLTN
Sbjct: 62  PTARRHVYYVLNKPQGVVSTMDDPEGRPCLSDLEGVPRGIRLFHVGRLDTETSGLILLTN 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  A  +  PS + L+ Y     G+VD   ++ L KG+ ++        V L      +
Sbjct: 122 DGEFANRMTHPSYKVLKTYLADVEGRVDDKVIHRLSKGLTLEDGPVKPDAVRLVQAGEEH 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + V V L EG+NR ++++ +     V RL R + GP +L  L  G  RE++ + L + L 
Sbjct: 182 SLVEVSLHEGRNRIVRRIMDSVAHPVRRLSRTAIGPVRLKRLGRGDMRELTHEELGQLLD 241

Query: 247 P 247
            
Sbjct: 242 L 242


>gi|163791560|ref|ZP_02185963.1| hypothetical protein CAT7_05483 [Carnobacterium sp. AT7]
 gi|159873165|gb|EDP67266.1| hypothetical protein CAT7_05483 [Carnobacterium sp. AT7]
          Length = 239

 Score =  173 bits (438), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 64/233 (27%), Positives = 106/233 (45%), Gaps = 5/233 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K++A  G  +R+ V+ ++  + V VNG++ +    +V   TD IEV G  ++  E 
Sbjct: 1   MRLDKLLANMGFGTRKTVKNVLKAKEVTVNGLVEKDGKTHVNPETDKIEVSGEVIQYQEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T                       VGRLD +TEGLL+LTNDG LA 
Sbjct: 61  MYFMLHKPQGVVSATTDHVHKTVIDLLQPQDQVMDPFPVGRLDKDTEGLLILTNDGTLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQK--GSNAWV 189
            L  P     + Y     G VD+  +   + GI +         ++ + +      ++ +
Sbjct: 121 NLLSPKKHVDKCYEAIIEGVVDEQDVQAFENGITLDDGFNCQSAKLEILSVDFEKESSVI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            V + EGK  ++K++FE  +  V  L R+S G  QL   L  G  R+++K+ L
Sbjct: 181 QVTIHEGKFHQVKRMFEAVDKSVIYLKRLSMGSLQLDETLELGEYRQLTKEEL 233


>gi|153004984|ref|YP_001379309.1| pseudouridine synthase [Anaeromyxobacter sp. Fw109-5]
 gi|152028557|gb|ABS26325.1| pseudouridine synthase [Anaeromyxobacter sp. Fw109-5]
          Length = 354

 Score =  173 bits (438), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 81/319 (25%), Positives = 123/319 (38%), Gaps = 1/319 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R+ K +A AG+ASRR+ E +I   RVKVN   +      V    D + VDG  + +
Sbjct: 9   PDGVRLQKYLAEAGVASRRKAEELILAGRVKVNARAVTVLGSKVDPARDLVTVDGRLVSR 68

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +E    +L +KP G VTT SDP+GR T  + L  +  RV SVGRLD + EG +L T+DG 
Sbjct: 69  SETRSYYLLYKPPGCVTTASDPEGRPTALEYLRGVKERVFSVGRLDFDAEGAVLFTDDGE 128

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  P     R Y V+  G+     L  L  G+ ++      ++     +   N W+
Sbjct: 129 LANRLAHPRYGHRRTYLVKVRGEPPPAALERLVAGVRLEDGPARALEAVPHERAERNVWI 188

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            V + EG+   +K++ E    +V RL R  +G   +  L  G  R ++   +R       
Sbjct: 189 RVVVGEGRFHLVKRLCEAVGLQVQRLYRPEFGGITVEGLRPGQFRPLAPVEVRALKTAVG 248

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
           L      +                          R  +         K+         R 
Sbjct: 249 LAGGAPAVAPRELPRAARRHGHGPPAPPELAPARREGERGEPGRREGKELPPRGEPRVRG 308

Query: 310 LASNVWMAKGIHSSFLSDS 328
              +               
Sbjct: 309 RGEDAGRGPRGEQRQRGRG 327


>gi|320667979|gb|EFX34882.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O157:H7 str.
           LSU-61]
          Length = 231

 Score =  173 bits (438), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 103/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D  +   KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTADQFAKGVQLHNEKDLTKPAVLEVI----TPTQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 227


>gi|311110505|ref|ZP_07711902.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           gasseri MV-22]
 gi|311065659|gb|EFQ45999.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           gasseri MV-22]
          Length = 240

 Score =  173 bits (438), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 66/240 (27%), Positives = 106/240 (44%), Gaps = 4/240 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + E     R+ K +A   + SR+EV  +I ++ V VNG L+      V  TD + VDG  
Sbjct: 1   MFEKDIEMRIDKYLANMNVGSRKEVHSLIKKKVVTVNGELVTIPKQQVKETDLVAVDGNK 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +   +     L      +  T                 +  +  VGRLD +T GLLLLTN
Sbjct: 61  IAYQQYHYFLLNKPKGVISATEDRSQQTVISLLKTKDRYQGIAPVGRLDKDTTGLLLLTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGS 185
           DG LA  L  P+    +VYR +  G  D +      +G+++  G      ++ +  Q   
Sbjct: 121 DGALAHELLAPNKHVAKVYRAKIAGVPDPETAKKFAQGLILGDGTKLKPAKLKILKQDQD 180

Query: 186 N--AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           N  + + + ++EGK  +IK++F     KV  L R+S G   L   L  G  +E+    ++
Sbjct: 181 NNLSQIEIQIQEGKYHQIKRMFGAVGMKVLELDRVSMGKLHLPADLKRGEYKEIDLAEIK 240


>gi|187733584|ref|YP_001879484.1| 16S rRNA pseudouridylate synthase A [Shigella boydii CDC 3083-94]
 gi|187430576|gb|ACD09850.1| ribosomal small subunit pseudouridine synthase A [Shigella boydii
           CDC 3083-94]
          Length = 231

 Score =  173 bits (438), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 102/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRYHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEVI----TPTQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 227


>gi|253989148|ref|YP_003040504.1| 16S rRNA pseudouridylate synthase A [Photorhabdus asymbiotica
           subsp. asymbiotica ATCC 43949]
 gi|253780598|emb|CAQ83760.1| ribosomal small subunit pseudouridine synthase A [Photorhabdus
           asymbiotica]
          Length = 233

 Score =  173 bits (438), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 52/229 (22%), Positives = 101/229 (44%), Gaps = 3/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR EV R +   R+ V+  +++  A  +     I  DG  L + +  
Sbjct: 1   MRLDKFLSQQLGISRNEVGRELRAGRITVDDEIIKTGAYKITPEQQIMFDGSLLEQQQGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DP   + ++        ++ + GRLD++T GL+LLT+DG  +  
Sbjct: 61  RYFMLNKPSGYVCSTDDPVNPTVLYFIDEPAAHKLHTAGRLDMDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  +  +    G+ + G         L+  +       + +
Sbjct: 121 ITSPKHHCKKTYLVTLECPVAAETADKFLAGVQLHGEKTLTKPAQLEMLEPQVT--RLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVIELHRERIGEIILDPALEPGEYRPLTEQEV 227


>gi|16801129|ref|NP_471397.1| hypothetical protein lin2063 [Listeria innocua Clip11262]
 gi|16414564|emb|CAC97293.1| lin2063 [Listeria innocua Clip11262]
 gi|313618115|gb|EFR90216.1| ribosomal large subunit pseudouridine synthase B [Listeria innocua
           FSL S4-378]
          Length = 244

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 76/238 (31%), Positives = 121/238 (50%), Gaps = 3/238 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ SRR+ E++I + +V VNG ++    V V  T+ IEV+G+ L K E  
Sbjct: 2   ERLQKVIANAGVTSRRKAEKLIQEGKVTVNGKVVTELGVKVSGTERIEVEGIQLTKEEHR 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     +     D    +        I  R+  VGRLD +T GLLL+TNDG  A +
Sbjct: 62  YFLFYKPRGTVSAVTDDKGRTTVADYF-TDIPERLYPVGRLDYDTSGLLLMTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           L  P  +  + Y  R  G  +++ +  L++G+VI G      +V + +       A V +
Sbjct: 121 LMHPKNEVSKTYIARIKGIPEREVIRELERGVVIDGRKTAPAKVKVRSSDKAKDKAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + EG+NR+++K+FE   ++V +L R  Y    L  L AG  RE+S   +++      
Sbjct: 181 TIHEGRNRQVRKMFEAVGFEVQKLAREEYSFLNLRGLNAGERRELSHHEVKQLKTEAR 238


>gi|150004186|ref|YP_001298930.1| ribosomal large subunit pseudouridine synthase B [Bacteroides
           vulgatus ATCC 8482]
 gi|149932610|gb|ABR39308.1| ribosomal large subunit pseudouridine synthase B [Bacteroides
           vulgatus ATCC 8482]
          Length = 488

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 116/241 (48%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K+I+ +   P R++K +A AGI SRRE +  I    V VNG ++      +  TD +
Sbjct: 240 IEYKDILTDPNEPIRLNKFLANAGICSRREADEFITAGVVSVNGEVVTELGTKIKRTDEV 299

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P+    +T + L      + T+    + ++ +     +   R+  VGRLD NT G
Sbjct: 300 KFHDEPVSIERKTYILLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTTG 359

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     V +  L+ +  G+ +         ++  
Sbjct: 360 VLLLTNDGDLASKLTHPKYLKKKIYHVYCDKNVTKADLDQIAAGVTLDDGEIHADAISYA 419

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++    + V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++ 
Sbjct: 420 SET-DKSQVGIEIHSGKNRIVRRIFESLGYKVIKLDRVYFAGLTKKGLRRGDWRYLTEQE 478

Query: 241 L 241
           +
Sbjct: 479 V 479


>gi|306831693|ref|ZP_07464850.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|304426118|gb|EFM29233.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
          Length = 253

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 63/242 (26%), Positives = 104/242 (42%), Gaps = 4/242 (1%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEV 62
           KN+        R+ K +  AGI SR EV++++ +++V VNG +       +    D I  
Sbjct: 2   KNVRIGKGKKMRLDKFLVEAGIGSRTEVKQLLKKKQVLVNGKVEISPKTQIDEKADRISC 61

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
            G  L   +     L      +  T  +         +  +    V  VGRLDI+T GLL
Sbjct: 62  QGQTLSYEKYVYYMLNKPKGVISATEDNHHKTVLDLLDKTAWDKEVFPVGRLDIDTHGLL 121

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTN+G LA  +  P     + YR +  G +    +     GI ++       Q+ +   
Sbjct: 122 LLTNNGKLAHAMLSPKKHVDKTYRAKVAGLMTTADVAAFANGIDLKDFTCQPAQLVILET 181

Query: 183 KGS--NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK 239
             +   + V + ++EGK  ++K++ +    KV  L R+S  P QL   L  G  R ++  
Sbjct: 182 NEAERTSVVEITIKEGKFHQVKRMVQACGKKVTDLQRLSMVPLQLDKQLALGEWRRLTDD 241

Query: 240 IL 241
            L
Sbjct: 242 EL 243


>gi|165933395|ref|YP_001650184.1| ribosomal large subunit pseudouridine synthase B [Rickettsia
           rickettsii str. Iowa]
 gi|165908482|gb|ABY72778.1| ribosomal large subunit pseudouridine synthase B [Rickettsia
           rickettsii str. Iowa]
          Length = 230

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 107/230 (46%), Positives = 148/230 (64%), Gaps = 2/230 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K+I+ AG+ SRR+ E++I + +VKV+GI +     NV  ++ IEV G  +    + R
Sbjct: 3   RLAKIISNAGVCSRRDAEKLIVEGQVKVDGITILSPTTNVDISNQIEVSGTLINNIHKPR 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LW+Y+KP+GL+TTH DP  R TVF+ L     RVIS+GRLD+N+EGLLLLTN G LAR  
Sbjct: 63  LWIYYKPVGLITTHKDPLSRKTVFEQLTG-LPRVISIGRLDLNSEGLLLLTNSGDLARQF 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPS++  RVY VR +G+ D    +   K + I GI Y    + L  Q  +N W  V L 
Sbjct: 122 ELPSSRLKRVYHVRAYGKSDVLLKSN-YKNLEIDGIFYNPHSIKLLKQNKTNCWFEVVLF 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           EGKNREI+++FE+   KVN+LIRI YG F +  L  G  +E++ KIL   
Sbjct: 181 EGKNREIRRIFEYCGLKVNKLIRIQYGSFTIDNLKPGDYKEINNKILENN 230


>gi|218549599|ref|YP_002383390.1| 16S rRNA pseudouridylate synthase A [Escherichia fergusonii ATCC
           35469]
 gi|218357140|emb|CAQ89774.1| 16S rRNA pseudouridylate 516 synthase [Escherichia fergusonii ATCC
           35469]
 gi|324114400|gb|EGC08369.1| RNA pseudouridylate synthase [Escherichia fergusonii B253]
          Length = 231

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 102/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHEVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEVI----TPTQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEV 227


>gi|300902164|ref|ZP_07120164.1| hypothetical protein HMPREF9536_00353 [Escherichia coli MS 84-1]
 gi|301306200|ref|ZP_07212275.1| hypothetical protein HMPREF9347_04814 [Escherichia coli MS 124-1]
 gi|300405683|gb|EFJ89221.1| hypothetical protein HMPREF9536_00353 [Escherichia coli MS 84-1]
 gi|300838566|gb|EFK66326.1| hypothetical protein HMPREF9347_04814 [Escherichia coli MS 124-1]
 gi|315255301|gb|EFU35269.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           MS 85-1]
          Length = 268

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 102/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    
Sbjct: 38  MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGP 97

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 98  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHR 157

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 158 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEVI----TPTQVRL 213

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 214 TISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 264


>gi|254884798|ref|ZP_05257508.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           4_3_47FAA]
 gi|319644140|ref|ZP_07998665.1| pseudouridine synthase [Bacteroides sp. 3_1_40A]
 gi|254837591|gb|EET17900.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           4_3_47FAA]
 gi|317384262|gb|EFV65233.1| pseudouridine synthase [Bacteroides sp. 3_1_40A]
          Length = 487

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 116/241 (48%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K+I+ +   P R++K +A AGI SRRE +  I    V VNG ++      +  TD +
Sbjct: 239 IEYKDILTDPNEPIRLNKFLANAGICSRREADEFITAGVVSVNGEVVTELGTKIKRTDEV 298

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P+    +T + L      + T+    + ++ +     +   R+  VGRLD NT G
Sbjct: 299 KFHDEPVSIERKTYILLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTTG 358

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     V +  L+ +  G+ +         ++  
Sbjct: 359 VLLLTNDGDLASKLTHPKYLKKKIYHVYCDKNVTKADLDQIAAGVTLDDGEIHADAISYA 418

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++    + V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++ 
Sbjct: 419 SET-DKSQVGIEIHSGKNRIVRRIFESLGYKVIKLDRVYFAGLTKKGLRRGDWRYLTEQE 477

Query: 241 L 241
           +
Sbjct: 478 V 478


>gi|281425341|ref|ZP_06256254.1| ribosomal large subunit pseudouridine synthase B [Prevotella oris
           F0302]
 gi|281400504|gb|EFB31335.1| ribosomal large subunit pseudouridine synthase B [Prevotella oris
           F0302]
          Length = 234

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 58/226 (25%), Positives = 101/226 (44%), Gaps = 1/226 (0%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW 76
           +K +A AG+ SRRE +  I+   V VNG ++      V+ +D ++     +   ++  + 
Sbjct: 2   NKYLANAGVCSRREADEFISAGVVSVNGTVVTELGTKVLRSDEVKFHDQLVSLEKKVYVL 61

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L      + T+      ++ +         R+  VGRLD NT G+LLLTNDG LA  L  
Sbjct: 62  LNKPKDYVTTSDDPQQRKTVMDLVKDVCPERIYPVGRLDRNTTGVLLLTNDGDLASKLTH 121

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
           P     +VY V     V ++ L  +  GI ++                    V + +  G
Sbjct: 122 PKFLKKKVYHVHLDKNVAEEDLQKIASGIELEDGEIH-ADAIEYADDRDKKQVGIEIHSG 180

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           KNR ++++FE   ++V RL R+ +       L  G  R ++++ + 
Sbjct: 181 KNRIVRRIFESLGYRVVRLDRVQFAGLTKKNLRRGDWRFLTEQEVE 226


>gi|237723682|ref|ZP_04554163.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           D4]
 gi|265756803|ref|ZP_06090791.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           3_1_33FAA]
 gi|229437893|gb|EEO47970.1| ribosomal large subunit pseudouridine synthase B [Bacteroides dorei
           5_1_36/D4]
 gi|263233589|gb|EEZ19209.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           3_1_33FAA]
          Length = 485

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 116/241 (48%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K+I+ +   P R++K +A AGI SRRE +  I    V VNG ++      +  TD +
Sbjct: 237 IEYKDILTDPNEPIRLNKFLANAGICSRREADEFITAGVVSVNGEVVTELGTKIKRTDEV 296

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P+    +T + L      + T+    + ++ +     +   R+  VGRLD NT G
Sbjct: 297 KFHDEPVSIERKTYILLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTTG 356

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     V +  L+ +  G+ +         ++  
Sbjct: 357 VLLLTNDGDLASKLTHPKYLKKKIYHVYCDKNVTKADLDQIAAGVTLDDGEIHADAISYA 416

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++    + V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++ 
Sbjct: 417 SET-DKSQVGIEIHSGKNRIVRRIFESLGYKVIKLDRVYFAGLTKKGLRRGDWRYLTEQE 475

Query: 241 L 241
           +
Sbjct: 476 V 476


>gi|238751859|ref|ZP_04613346.1| Ribosomal small subunit pseudouridine synthase A [Yersinia rohdei
           ATCC 43380]
 gi|238709988|gb|EEQ02219.1| Ribosomal small subunit pseudouridine synthase A [Yersinia rohdei
           ATCC 43380]
          Length = 235

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 56/238 (23%), Positives = 109/238 (45%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++   +
Sbjct: 1   MRLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQMVGS 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +  D       G+ +          Q+ +   +     V +
Sbjct: 121 ITSPRHHCEKTYLVTLEHPLADDTAQQFADGVQLHNEKSLTKPAQLEVIEPQ----LVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
            L EG+  ++K++F     +V  L R   G  +L   L  G  R ++ + +     PH
Sbjct: 177 TLSEGRYHQVKRMFAAVGNRVLELHRERIGAIKLDDDLAPGEYRRLTAEEIASVGAPH 234


>gi|294775216|ref|ZP_06740740.1| pseudouridylate synthase [Bacteroides vulgatus PC510]
 gi|294450921|gb|EFG19397.1| pseudouridylate synthase [Bacteroides vulgatus PC510]
          Length = 488

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 116/241 (48%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K+I+ +   P R++K +A AGI SRRE +  I    V VNG ++      +  TD +
Sbjct: 240 IEYKDILTDPNEPIRLNKFLANAGICSRREADEFITAGVVSVNGEVVTELGTKIKRTDEV 299

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P+    +T + L      + T+    + ++ +     +   R+  VGRLD NT G
Sbjct: 300 KFHDEPVSIERKTYILLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTTG 359

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     V +  L+ +  G+ +         ++  
Sbjct: 360 VLLLTNDGDLASKLTHPKYLKKKIYHVYCDKNVTKADLDQIAAGVTLDDGEIHADAISYA 419

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++    + V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++ 
Sbjct: 420 SET-DKSQVGIEIHSGKNRIVRRIFESLGYKVIKLDRVYFAGLTKKGLRRGDWRYLTEQE 478

Query: 241 L 241
           +
Sbjct: 479 V 479


>gi|213424484|ref|ZP_03357281.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. E02-1180]
          Length = 267

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 59/269 (21%), Positives = 110/269 (40%), Gaps = 5/269 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R++K I+ +GI SRRE +R I Q  V +NG         V++ D ++V+G  +  
Sbjct: 3   TDTSTRLNKYISESGICSRREADRFIEQGNVFINGKRAA-IGDQVVAGDVVKVNGRLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   L L      +    +  DG      +  +   R+  +GRLD +++GL+ LTN G 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRIFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     +  + +  +  G+ I G            +K +    
Sbjct: 122 LVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +      
Sbjct: 178 RITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEV 278
              ++    A        ++     I + 
Sbjct: 238 GSSSEAKPKAKAKPKTAGIKRPVVAIEKR 266


>gi|313123532|ref|YP_004033791.1| pseudouridine synthase [Lactobacillus delbrueckii subsp. bulgaricus
           ND02]
 gi|312280095|gb|ADQ60814.1| Pseudouridine synthase [Lactobacillus delbrueckii subsp. bulgaricus
           ND02]
 gi|325684293|gb|EGD26466.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 239

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 77/231 (33%), Positives = 120/231 (51%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRRE E+MI   RV+V+G ++ +    V S + + VD  P+ +    
Sbjct: 4   ERLQKVIAQAGIASRREAEKMILAGRVRVDGQVVTKLGTKVSSIEQVVVDNQPIERESHH 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     +++   D  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA +
Sbjct: 64  TYLFYKPRG-VISAVKDNKGRKTVADYFTDLPYRLYPVGRLDYDTSGLLLMTNDGELANL 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVTV 191
           L  P  +  +VY  +  G +  D++  LKKG+ I        +V +           V +
Sbjct: 123 LMHPRNEVDKVYVAKIKGILQPDEIKALKKGVQIGRYKTKPARVKVLKTNPRAQTQIVQL 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EG   ++K++F+  N  V++L R  Y    L  L +G  RE++ K + 
Sbjct: 183 TIHEGHYHQVKEMFKAVNHLVDKLSRERYSFLDLQGLTSGQYRELNHKEVD 233


>gi|222099396|ref|YP_002533964.1| Pseudouridine synthase [Thermotoga neapolitana DSM 4359]
 gi|221571786|gb|ACM22598.1| Pseudouridine synthase [Thermotoga neapolitana DSM 4359]
          Length = 240

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 62/242 (25%), Positives = 113/242 (46%), Gaps = 7/242 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++  GI +R+EV  +I   RV VN   +   A  +   D ++VDG  +   E+ 
Sbjct: 1   MRLDRYLSNRGIGTRKEVRALIKHGRVTVNDRTVLDPAYKLSDKDVVKVDGKVIDLPEKV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +  Y     + +T       S            +  VGRLD + EGLLL+TNDG  A  
Sbjct: 61  YILFYKPAGYVTSTRDP---HSETIMEFLPDIKGIFPVGRLDKDAEGLLLVTNDGEFAHR 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y V+  G++ +DKL  L++G+ ++   +   +     +K SN  V + +
Sbjct: 118 VISPRWKVEKEYVVKVEGEITEDKLEKLRRGVSLRDGFFAKAKHV---EKISNDTVKIVI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHLLEE 252
            EGK  ++K++      K   L R+  G  +L   +  G  R +S++ +R+    +  +E
Sbjct: 175 TEGKYHQVKRMMAAVGLKTIHLKRVRIGGLRLPQEMKPGEYRFLSEEEVRQVFEGNDQKE 234

Query: 253 AQ 254
            +
Sbjct: 235 DR 236


>gi|237799081|ref|ZP_04587542.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. oryzae str. 1_6]
 gi|331021935|gb|EGI01992.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. oryzae str. 1_6]
          Length = 409

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 91/354 (25%), Positives = 136/354 (38%), Gaps = 14/354 (3%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG         V   D I
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDAT-LGQRVDLHDAI 62

Query: 61  EVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            VDG  +++ E     R  +        + T        +           R I++GRLD
Sbjct: 63  SVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           INT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++       
Sbjct: 123 INTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPARFT 182

Query: 176 QVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE+S+  +        L+             +     R +       +        +   
Sbjct: 243 REMSQYEVDILAAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVVRTLRPAAGA 302

Query: 294 GLSKQKKLATP-----VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
             +  +    P        R    +                +       S   P
Sbjct: 303 PANSDRAPRQPQITGSERDRPRGGDSTQRPSPRKDSGKPGSRAPRPADNSRGTP 356



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 17/91 (18%), Positives = 24/91 (26%), Gaps = 2/91 (2%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
            E             +  +D     S  P      +     +      K+ A P  +R  
Sbjct: 318 SERDRPRGGDSTQRPSPRKDSGKPGSRAPRPADNSRGTPVAERPSEMNKRPAKPGPKRVG 377

Query: 311 AS--NVWMAKGIHSSFLSDSGQREENHRRSP 339
               N     G      + SGQR    RR P
Sbjct: 378 IKLVNDDAPSGKRRGPPAGSGQRPGFGRRKP 408


>gi|315648476|ref|ZP_07901575.1| pseudouridine synthase [Paenibacillus vortex V453]
 gi|315276170|gb|EFU39516.1| pseudouridine synthase [Paenibacillus vortex V453]
          Length = 253

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 68/244 (27%), Positives = 118/244 (48%), Gaps = 8/244 (3%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDG 64
           +  +  T QR+ KV++  G  SR E+++M  Q  + VNG +++    +V   TD IE +G
Sbjct: 1   MSAKGRTTQRLDKVLSNLGFGSRAELKKMAKQGSIVVNGTVMKDPGKHVDPYTDIIEFEG 60

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             ++  E   + L+  P  +  T    D       +   +      VGRLD +TEGLLLL
Sbjct: 61  ETIQYREYVYIMLHKPPGVVSATEDLRDRTVLDLLDKDYLVFEPFPVGRLDKDTEGLLLL 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQK 183
           TNDG LA  L  P     + Y     G+V ++   L   G+ +         ++ + + +
Sbjct: 121 TNDGKLAHELLSPRKHIPKTYEAIVEGRVGEEDARLFAAGVTLDDGYATMPAELVIHSHE 180

Query: 184 GSN-----AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVS 237
             +     + +++ + EGK  ++K++FE    KV  L R+S G  +L   L  G+ RE++
Sbjct: 181 ERDDGVILSRISLTIHEGKFHQVKRMFEAVGKKVVYLKRVSMGELRLDKSLEIGTYRELT 240

Query: 238 KKIL 241
           ++ L
Sbjct: 241 EEEL 244


>gi|322516330|ref|ZP_08069256.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           vestibularis ATCC 49124]
 gi|322125168|gb|EFX96557.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           vestibularis ATCC 49124]
          Length = 243

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 105/234 (44%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+  + +++V VNG +       +    D I      L     
Sbjct: 1   MRLDKFLVDCGVGSRSQVKNFLKKKQVIVNGQVETSPKTQIDENKDRITYLDQELTHETF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T            +  +   RV  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPQGVISATEDPRHKTVLDLLDDTARHKRVFPVGRLDIDTHGLLLLTNNGDLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVT 190
            +  P     ++Y+ +  G +D++ +   +KGI ++       ++ +    +  S +WV 
Sbjct: 121 AMLSPKKHVDKIYQAKVAGVMDEEDILAFEKGIKLKDHTCQPAKLEIVSVDRNESTSWVQ 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           + + EGK  ++K++      +V  L R+S GP  L   L  G+ R ++++ L  
Sbjct: 181 ITIAEGKFHQVKRMVAACGKEVTELQRLSMGPLSLPNDLELGTWRRLTEEELEA 234


>gi|309810348|ref|ZP_07704183.1| pseudouridylate synthase [Dermacoccus sp. Ellin185]
 gi|308435661|gb|EFP59458.1| pseudouridylate synthase [Dermacoccus sp. Ellin185]
          Length = 303

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 77/232 (33%), Positives = 121/232 (52%), Gaps = 1/232 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRK 69
               R+ KV+A+AG+ SRR  E +IA+ RV+V+G ++      +      I VDG  ++ 
Sbjct: 63  EEGTRLQKVLAQAGVGSRRHCENLIAEGRVEVDGQVVTELGTRIDPESAVIHVDGDRIQL 122

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +      ++KP G+V+T  D +GR  V + L     R+  VGRLD +TEGLLLLTNDG 
Sbjct: 123 DDTLVYLAFNKPTGVVSTMQDEEGRPCVGEYLEGRTERLFHVGRLDYDTEGLLLLTNDGN 182

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L+ P     +VY     G V +D    +++GI ++          +   +   A V
Sbjct: 183 LANRLQHPRYGVEKVYLATIPGPVPRDLGKRMREGIELEDGPAAVDSFKVVDSQPGMALV 242

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + L EG+NR ++++FE     V  L R   GP ++G L  G  R ++K+ +
Sbjct: 243 EIVLHEGRNRIVRRMFEEVGHPVIALARPQVGPVKVGDLRPGKMRPLNKREV 294


>gi|157372205|ref|YP_001480194.1| 23S rRNA pseudouridine synthase F [Serratia proteamaculans 568]
 gi|157323969|gb|ABV43066.1| pseudouridine synthase [Serratia proteamaculans 568]
          Length = 286

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 59/288 (20%), Positives = 112/288 (38%), Gaps = 7/288 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++K I+ +GI SRR+ +R I Q  V +NG  +      V   D ++V+G  +     
Sbjct: 6   STRLNKYISESGICSRRDADRYIEQGNVFINGKRVT-LGDQVFPGDVVKVNGQLIEPRNE 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L        +    +  +G      +  +  +R+  +GRLD +++GL+ LTN G L  
Sbjct: 65  DNLIFIALNKPVGIVSTTEEGEKDNIVDFVNHSTRIFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  V  D +  L  G+ + G            +K +     + 
Sbjct: 125 KILRAGNDHEKEYLVTVNKPVTDDFIRGLGAGVPMLGTV----TKKCKVKKEAPFVFRIV 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E F ++V +L R       +  L  G  R+++   L E      +E 
Sbjct: 181 LVQGLNRQIRRMCEHFGYEVTKLERTRIMNVGMAGLPPGEWRDLTDDELVELF--KSIEG 238

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           +         +     +      S          +    + G  K+ +
Sbjct: 239 SSSEAKPAKKAKPAAKKPASAPKSVEKPAGGAPARKRFAQPGRKKKGR 286


>gi|75763968|ref|ZP_00743593.1| Ribosomal large subunit pseudouridine synthase F [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
 gi|74488543|gb|EAO52134.1| Ribosomal large subunit pseudouridine synthase F [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
          Length = 254

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 65/239 (27%), Positives = 114/239 (47%), Gaps = 7/239 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K  ++++    R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+
Sbjct: 10  KFFLEKDVPNLRINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVN 68

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G  LR A        +KP+G+  T            +L +   R+  +GRLD +++GL+L
Sbjct: 69  GEQLRIARDHVYIALNKPVGITCTSEKAV--KGNIIDLVNHPLRISHIGRLDKDSDGLIL 126

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG +   +     +  + Y V     +  D L  +  G+ I G      ++T     
Sbjct: 127 LTNDGDIVNEILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEITQL--- 183

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            S     + L +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R
Sbjct: 184 -SKYEFQIILTQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKR 241


>gi|269302650|gb|ACZ32750.1| RNA pseudouridine synthase [Chlamydophila pneumoniae LPCoLN]
          Length = 235

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 69/236 (29%), Positives = 106/236 (44%), Gaps = 4/236 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T  R++K +A AG+ASRR+ + +I    V VNG + E   V V   D ++V G  +   +
Sbjct: 2   TKVRLNKFLASAGVASRRKCDEIIFSGSVTVNGRVAEGPFVLVDPEDKVQVGGTSVHLTK 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +    ++     L ++     G   V D    +  RV +VGRLD  T GL+L+TNDG  A
Sbjct: 62  KVYFMVHKAIGYLCSSEKKFPGTKLVIDLFAHLPYRVFTVGRLDKETSGLILVTNDGEFA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  PS+   + Y ++    V    L  L +G  I G     + VT   +      V +
Sbjct: 122 NKIIHPSSGITKEYLLKVSRDVSAKDLEKLMEGTFIDGKHVRPVSVTKIRRG----TVKI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + EGK  EI+   +     +  L RI  G   LG L  G  RE++   L   +  
Sbjct: 178 VVSEGKKHEIRLFADAAGLPILELKRIRIGSLVLGGLRYGEYRELTDAELGTYMKL 233


>gi|82776214|ref|YP_402563.1| 16S rRNA pseudouridylate synthase A [Shigella dysenteriae Sd197]
 gi|309786649|ref|ZP_07681269.1| RNA pseudouridylate synthase family protein [Shigella dysenteriae
           1617]
 gi|81240362|gb|ABB61072.1| 16S pseudouridylate 516 synthase [Shigella dysenteriae Sd197]
 gi|308925342|gb|EFP70829.1| RNA pseudouridylate synthase family protein [Shigella dysenteriae
           1617]
          Length = 231

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 103/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEVI----TPTQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L+ G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLVPGEYRPLTEEEI 227


>gi|15618773|ref|NP_225059.1| pseudouridine synthase [Chlamydophila pneumoniae CWL029]
 gi|4377181|gb|AAD19002.1| predicted pseudouridine synthase [Chlamydophila pneumoniae CWL029]
          Length = 235

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 69/236 (29%), Positives = 107/236 (45%), Gaps = 4/236 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T  R++K +A AG+ASRR+ + +I    V VNG + E   V V   D ++V G  +   +
Sbjct: 2   TKVRLNKFLASAGVASRRKCDEIIFSGSVTVNGRVAEGPFVLVDPEDKVQVGGTSVHLTK 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +    ++     L ++     G   V D    +  RV +VGRLD  T GL+L+TNDG  A
Sbjct: 62  KVYFMVHKAIGYLCSSEKKFPGTKLVIDLFAHLPYRVFTVGRLDKETSGLILVTNDGEFA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  PS+   + Y ++    V    L  L +G  I G     + VT   +      V +
Sbjct: 122 NKIIHPSSGITKEYLLKVSRDVSAKDLGKLMEGTFIDGKHVRPVSVTKIRRG----TVKI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + EGK  EI+   +   + +  L RI  G   LG L  G  RE++   L   +  
Sbjct: 178 VVSEGKKHEIRLFADAAGFPILELKRIRIGSLVLGGLRYGEYRELTDAELGTYMKL 233


>gi|288904878|ref|YP_003430100.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           gallolyticus UCN34]
 gi|288731604|emb|CBI13159.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           gallolyticus UCN34]
          Length = 238

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 104/229 (45%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++ +AG  SR +V+++I  ++V V+G L E   +NV  +   I V G  ++++  
Sbjct: 1   MRLDKLLGQAGFGSRNQVKKLIRSRQVYVDGRLAEADNLNVEPSLQKITVSGKQVKQSSE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                      ++  VGRLD +TEGLLL+TN+G L  
Sbjct: 61  KYFLLNKPAGVVSAVSDKEHQTVIDLIKEADCVPKLYPVGRLDRSTEGLLLITNNGPLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V  +  +  D     + G+           ++ + T     +   V
Sbjct: 121 RMLHPKYHVAKTYYVEVNAFLADDVPAFFENGVSFDDGTICKPAKLEIITASPEKSSAYV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + EGK  +IKK+F  +  KV  L R+++G FQLG L +G  RE++   
Sbjct: 181 TISEGKFHQIKKMFLAYGVKVTYLKRLTFGEFQLGDLPSGQYRELTSTE 229


>gi|58039267|ref|YP_191231.1| tRNA pseudouridine synthase A [Gluconobacter oxydans 621H]
 gi|58001681|gb|AAW60575.1| tRNA pseudouridine synthase A [Gluconobacter oxydans 621H]
          Length = 264

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 134/241 (55%), Positives = 167/241 (69%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           ++       +R++K +ARAG+ASRR++ERMI   R+K+ G ++   A  V   D + VDG
Sbjct: 12  DMETSGPKGERIAKALARAGVASRRDIERMIEDGRIKLGGQIVTHPATFVQPGDIVLVDG 71

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P+   ERTRLW YHKP GL+TTH DP GR TVFD LP    RVISVGRLDIN+EGLLLL
Sbjct: 72  KPVDSPERTRLWRYHKPDGLMTTHKDPQGRQTVFDTLPEGMPRVISVGRLDINSEGLLLL 131

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG LAR LELP   W+R YRVR  G VD+ +L  L  G   +G+ YG ++  LD+ KG
Sbjct: 132 TNDGELARRLELPGNSWVRRYRVRVFGVVDEKRLASLIDGFEYEGVRYGSIEAALDSTKG 191

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            N+W+TV LREGKNREI++V E  N  V+RLIR+SYGPFQLG+L A    EV  K LREQ
Sbjct: 192 DNSWLTVSLREGKNREIRRVMEGLNLHVSRLIRLSYGPFQLGSLKARELEEVPGKTLREQ 251

Query: 245 L 245
           +
Sbjct: 252 V 252


>gi|330836580|ref|YP_004411221.1| pseudouridine synthase Rsu [Spirochaeta coccoides DSM 17374]
 gi|329748483|gb|AEC01839.1| pseudouridine synthase Rsu [Spirochaeta coccoides DSM 17374]
          Length = 248

 Score =  173 bits (437), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 113/247 (45%), Gaps = 4/247 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +   P R+   +A++G  SRR  E++I   RVKVN  ++      V   D + VDGV   
Sbjct: 2   KTEYPIRLQSFLAKSGWGSRRSCEQLIIDGRVKVNSQVVRELGTKVDKDDAVYVDGVLAE 61

Query: 69  KAERTRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             ERT  +  +     + +     +             + + ++GRLD  + GL+L TND
Sbjct: 62  PNERTYYYALHKPAGYVCSNADPNESYFARDLIDVPERNLLFNIGRLDKESTGLVLFTND 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +++++  PS +  + Y V     +  + L   + GI I        +++   +  +  
Sbjct: 122 GEISQLITHPSYEIEKEYLVNTDRTIMIEDLQEARHGIRIDDG--RPYRISR-YKLETKR 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           WV + L EG+NREI+K+F +  + V +LIRI  G  +LG L     R V+K  +   +  
Sbjct: 179 WVRIILTEGRNREIRKIFTYLGYDVKKLIRIRIGTLELGDLAPAQFRRVTKDEIMSIVSN 238

Query: 248 HLLEEAQ 254
              +   
Sbjct: 239 ARNKGQG 245


>gi|306814702|ref|ZP_07448864.1| 16S rRNA pseudouridylate synthase A [Escherichia coli NC101]
 gi|305852096|gb|EFM52548.1| 16S rRNA pseudouridylate synthase A [Escherichia coli NC101]
 gi|320196056|gb|EFW70680.1| 16S rRNA pseudouridylate synthase A [Escherichia coli WV_060327]
          Length = 231

 Score =  173 bits (437), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 102/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEVI----TPTQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 227


>gi|291485437|dbj|BAI86512.1| hypothetical protein BSNT_04375 [Bacillus subtilis subsp. natto
           BEST195]
          Length = 239

 Score =  173 bits (437), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 58/224 (25%), Positives = 96/224 (42%), Gaps = 3/224 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A +G  SR+EV+ ++    V ++G   +    +V      + V G P+   E 
Sbjct: 1   MRLDKLLANSGYGSRKEVKAVVKAGAVMIDGKPAKDVKAHVDPDTQEVTVYGEPVDYREF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      L  T                +       GRLD +TEG LLLTNDG LA 
Sbjct: 61  IYLMMNKPQGVLSATEDSRQQTVVDLLTPEEMRFEPFPAGRLDKDTEGFLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V    Q+ ++ ++ L+ G+ I+G       +  + T    N  + +
Sbjct: 121 RLLSPKKHVPKTYEVHLKSQISREDISDLETGVYIEGGYKTKPARAEIKTNDSGNTVIYL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
            + EGK  ++K++ +    +V  L R+S G   L   L  G  R
Sbjct: 181 TITEGKYHQVKQMAKAVGNEVVYLKRLSMGRVSLDPALAPGEYR 224


>gi|15802739|ref|NP_288766.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O157:H7
           EDL933]
 gi|15832329|ref|NP_311102.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O157:H7 str.
           Sakai]
 gi|16130121|ref|NP_416688.1| 16S rRNA U516 pseudouridine synthase [Escherichia coli str. K-12
           substr. MG1655]
 gi|24113572|ref|NP_708082.1| 16S rRNA pseudouridylate synthase A [Shigella flexneri 2a str. 301]
 gi|30063626|ref|NP_837797.1| 16S rRNA pseudouridylate synthase A [Shigella flexneri 2a str.
           2457T]
 gi|82544599|ref|YP_408546.1| 16S rRNA pseudouridylate synthase A [Shigella boydii Sb227]
 gi|89109001|ref|AP_002781.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli str. K-12
           substr. W3110]
 gi|110642394|ref|YP_670124.1| 16S rRNA pseudouridylate synthase A [Escherichia coli 536]
 gi|117624381|ref|YP_853294.1| 16S rRNA pseudouridylate synthase A [Escherichia coli APEC O1]
 gi|157155587|ref|YP_001463536.1| 16S rRNA pseudouridylate synthase A [Escherichia coli E24377A]
 gi|157161665|ref|YP_001458983.1| 16S rRNA pseudouridylate synthase A [Escherichia coli HS]
 gi|161486177|ref|NP_754606.2| 16S rRNA pseudouridylate synthase A [Escherichia coli CFT073]
 gi|162138407|ref|YP_541459.2| 16S rRNA pseudouridylate synthase A [Escherichia coli UTI89]
 gi|168749590|ref|ZP_02774612.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4113]
 gi|168759074|ref|ZP_02784081.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4401]
 gi|168767807|ref|ZP_02792814.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4486]
 gi|168773096|ref|ZP_02798103.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4196]
 gi|168780036|ref|ZP_02805043.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4076]
 gi|168789002|ref|ZP_02814009.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC869]
 gi|170019500|ref|YP_001724454.1| 16S rRNA pseudouridylate synthase A [Escherichia coli ATCC 8739]
 gi|170081805|ref|YP_001731125.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli str. K-12
           substr. DH10B]
 gi|170681582|ref|YP_001744379.1| 16S rRNA pseudouridylate synthase A [Escherichia coli SMS-3-5]
 gi|188495180|ref|ZP_03002450.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           53638]
 gi|191165380|ref|ZP_03027222.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           B7A]
 gi|191170122|ref|ZP_03031676.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           F11]
 gi|193062338|ref|ZP_03043433.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           E22]
 gi|194427231|ref|ZP_03059782.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           B171]
 gi|194434188|ref|ZP_03066455.1| ribosomal small subunit pseudouridine synthase A [Shigella
           dysenteriae 1012]
 gi|194436203|ref|ZP_03068305.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           101-1]
 gi|195935565|ref|ZP_03080947.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O157:H7 str.
           EC4024]
 gi|208805677|ref|ZP_03248014.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4206]
 gi|208814565|ref|ZP_03255894.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4045]
 gi|208818354|ref|ZP_03258674.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4042]
 gi|209400555|ref|YP_002271597.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4115]
 gi|209919643|ref|YP_002293727.1| 16S rRNA pseudouridylate synthase A [Escherichia coli SE11]
 gi|215487405|ref|YP_002329836.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O127:H6 str.
           E2348/69]
 gi|217327530|ref|ZP_03443613.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. TW14588]
 gi|218559104|ref|YP_002392017.1| 16S rRNA pseudouridylate synthase A [Escherichia coli S88]
 gi|218695798|ref|YP_002403465.1| 16S rRNA pseudouridylate synthase A [Escherichia coli 55989]
 gi|218700655|ref|YP_002408284.1| 16S rRNA pseudouridylate synthase A [Escherichia coli IAI39]
 gi|218705715|ref|YP_002413234.1| 16S rRNA pseudouridylate synthase A [Escherichia coli UMN026]
 gi|227887240|ref|ZP_04005045.1| 16S rRNA pseudouridylate synthase A [Escherichia coli 83972]
 gi|237704656|ref|ZP_04535137.1| ribosomal small subunit pseudouridine synthase A [Escherichia sp.
           3_2_53FAA]
 gi|238901360|ref|YP_002927156.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli BW2952]
 gi|253772890|ref|YP_003035721.1| 16S rRNA pseudouridylate synthase A [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254162198|ref|YP_003045306.1| 16S rRNA pseudouridylate synthase A [Escherichia coli B str.
           REL606]
 gi|254794084|ref|YP_003078921.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O157:H7 str.
           TW14359]
 gi|256017648|ref|ZP_05431513.1| 16S rRNA pseudouridylate synthase A [Shigella sp. D9]
 gi|256022132|ref|ZP_05435997.1| 16S rRNA pseudouridylate synthase A [Escherichia sp. 4_1_40B]
 gi|260844789|ref|YP_003222567.1| 16S rRNA pseudouridylate 516 synthase RsuA [Escherichia coli
           O103:H2 str. 12009]
 gi|260856157|ref|YP_003230048.1| 16S rRNA pseudouridylate 516 synthase RsuA [Escherichia coli
           O26:H11 str. 11368]
 gi|260868884|ref|YP_003235286.1| 16S rRNA pseudouridylate 516 synthase RsuA [Escherichia coli
           O111:H- str. 11128]
 gi|261223356|ref|ZP_05937637.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli O157:H7
           str. FRIK2000]
 gi|261259093|ref|ZP_05951626.1| 16S rRNA pseudouridylate 516 synthase RsuA [Escherichia coli
           O157:H7 str. FRIK966]
 gi|291283437|ref|YP_003500255.1| Pseudouridine synthase [Escherichia coli O55:H7 str. CB9615]
 gi|293405651|ref|ZP_06649643.1| 16S rRNA pseudouridylate synthase A [Escherichia coli FVEC1412]
 gi|293410547|ref|ZP_06654123.1| 16S rRNA pseudouridylate synthase A [Escherichia coli B354]
 gi|293415469|ref|ZP_06658112.1| 16S rRNA pseudouridylate synthase A [Escherichia coli B185]
 gi|293446535|ref|ZP_06662957.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           B088]
 gi|298381333|ref|ZP_06990932.1| 16S rRNA pseudouridylate synthase A [Escherichia coli FVEC1302]
 gi|300819120|ref|ZP_07099322.1| conserved hypothetical protein [Escherichia coli MS 107-1]
 gi|300822636|ref|ZP_07102774.1| conserved hypothetical protein [Escherichia coli MS 119-7]
 gi|300897756|ref|ZP_07116149.1| conserved hypothetical protein [Escherichia coli MS 198-1]
 gi|300918831|ref|ZP_07135400.1| conserved hypothetical protein [Escherichia coli MS 115-1]
 gi|300926291|ref|ZP_07142094.1| hypothetical protein HMPREF9548_04311 [Escherichia coli MS 182-1]
 gi|300930419|ref|ZP_07145828.1| conserved hypothetical protein [Escherichia coli MS 187-1]
 gi|300935111|ref|ZP_07150142.1| conserved hypothetical protein [Escherichia coli MS 21-1]
 gi|300950052|ref|ZP_07163999.1| conserved hypothetical protein [Escherichia coli MS 116-1]
 gi|300956858|ref|ZP_07169118.1| hypothetical protein HMPREF9547_02661 [Escherichia coli MS 175-1]
 gi|300981435|ref|ZP_07175516.1| hypothetical protein HMPREF9553_01804 [Escherichia coli MS 200-1]
 gi|300982903|ref|ZP_07176367.1| conserved hypothetical protein [Escherichia coli MS 45-1]
 gi|301021043|ref|ZP_07185086.1| conserved hypothetical protein [Escherichia coli MS 69-1]
 gi|301024319|ref|ZP_07188008.1| conserved hypothetical protein [Escherichia coli MS 196-1]
 gi|301048923|ref|ZP_07195916.1| conserved hypothetical protein [Escherichia coli MS 185-1]
 gi|301328667|ref|ZP_07221728.1| conserved hypothetical protein [Escherichia coli MS 78-1]
 gi|301644209|ref|ZP_07244217.1| conserved hypothetical protein [Escherichia coli MS 146-1]
 gi|307138843|ref|ZP_07498199.1| 16S rRNA pseudouridylate synthase A [Escherichia coli H736]
 gi|307311237|ref|ZP_07590881.1| pseudouridine synthase [Escherichia coli W]
 gi|309793067|ref|ZP_07687495.1| conserved hypothetical protein [Escherichia coli MS 145-7]
 gi|312967483|ref|ZP_07781698.1| conserved hypothetical protein [Escherichia coli 2362-75]
 gi|331642812|ref|ZP_08343947.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli H736]
 gi|331647839|ref|ZP_08348931.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli M605]
 gi|331653617|ref|ZP_08354618.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli M718]
 gi|331658264|ref|ZP_08359226.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli TA206]
 gi|331663688|ref|ZP_08364598.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli TA143]
 gi|331668887|ref|ZP_08369735.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli TA271]
 gi|331673705|ref|ZP_08374468.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli TA280]
 gi|331678137|ref|ZP_08378812.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli H591]
 gi|332278659|ref|ZP_08391072.1| 16S rRNA pseudouridylate 516 synthase [Shigella sp. D9]
 gi|76364197|sp|P0AA43|RSUA_ECOLI RecName: Full=Ribosomal small subunit pseudouridine synthase A;
           AltName: Full=16S pseudouridine 516 synthase; AltName:
           Full=16S pseudouridylate 516 synthase; AltName:
           Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|88941974|sp|P0AA45|RSUA_ECO57 RecName: Full=Ribosomal small subunit pseudouridine synthase A;
           AltName: Full=16S pseudouridine 516 synthase; AltName:
           Full=16S pseudouridylate 516 synthase; AltName:
           Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|88941975|sp|P0AA44|RSUA_ECOL6 RecName: Full=Ribosomal small subunit pseudouridine synthase A;
           AltName: Full=16S pseudouridine 516 synthase; AltName:
           Full=16S pseudouridylate 516 synthase; AltName:
           Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|88941976|sp|P0AA46|RSUA_SHIFL RecName: Full=Ribosomal small subunit pseudouridine synthase A;
           AltName: Full=16S pseudouridine 516 synthase; AltName:
           Full=16S pseudouridylate 516 synthase; AltName:
           Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|12516515|gb|AAG57321.1|AE005451_2 16S pseudouridylate 516 synthase [Escherichia coli O157:H7 str.
           EDL933]
 gi|405907|gb|AAA16377.1| yejD [Escherichia coli]
 gi|1042177|gb|AAB34905.1| 16S RNA pseudouridine 516 synthase, 16S RNA psi 516 synthase=rsuA
           gene product [Escherichia coli, Peptide, 231 aa]
 gi|1788510|gb|AAC75244.1| 16S rRNA U516 pseudouridine synthase [Escherichia coli str. K-12
           substr. MG1655]
 gi|13362544|dbj|BAB36498.1| 16S pseudouridylate 516 synthase [Escherichia coli O157:H7 str.
           Sakai]
 gi|24052623|gb|AAN43789.1| 16S pseudouridylate 516 synthase [Shigella flexneri 2a str. 301]
 gi|30041879|gb|AAP17606.1| 16S pseudouridylate 516 synthase [Shigella flexneri 2a str. 2457T]
 gi|81246010|gb|ABB66718.1| 16S pseudouridylate 516 synthase [Shigella boydii Sb227]
 gi|85675292|dbj|BAE76648.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli str. K12
           substr. W3110]
 gi|110343986|gb|ABG70223.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           536]
 gi|115513505|gb|ABJ01580.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli APEC O1]
 gi|157067345|gb|ABV06600.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           HS]
 gi|157077617|gb|ABV17325.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           E24377A]
 gi|169754428|gb|ACA77127.1| pseudouridine synthase [Escherichia coli ATCC 8739]
 gi|169889640|gb|ACB03347.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli str. K-12
           substr. DH10B]
 gi|170519300|gb|ACB17478.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           SMS-3-5]
 gi|187771075|gb|EDU34919.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4196]
 gi|188016070|gb|EDU54192.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4113]
 gi|188490379|gb|EDU65482.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           53638]
 gi|189002071|gb|EDU71057.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4076]
 gi|189354270|gb|EDU72689.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4401]
 gi|189363003|gb|EDU81422.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4486]
 gi|189371377|gb|EDU89793.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC869]
 gi|190904543|gb|EDV64250.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           B7A]
 gi|190909638|gb|EDV69223.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           F11]
 gi|192932004|gb|EDV84603.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           E22]
 gi|194414852|gb|EDX31123.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           B171]
 gi|194417517|gb|EDX33619.1| ribosomal small subunit pseudouridine synthase A [Shigella
           dysenteriae 1012]
 gi|194424931|gb|EDX40916.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           101-1]
 gi|208725478|gb|EDZ75079.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4206]
 gi|208735842|gb|EDZ84529.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4045]
 gi|208738477|gb|EDZ86159.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4042]
 gi|209161955|gb|ACI39388.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4115]
 gi|209765918|gb|ACI81271.1| 16S pseudouridylate 516 synthase [Escherichia coli]
 gi|209765920|gb|ACI81272.1| 16S pseudouridylate 516 synthase [Escherichia coli]
 gi|209765922|gb|ACI81273.1| 16S pseudouridylate 516 synthase [Escherichia coli]
 gi|209765924|gb|ACI81274.1| 16S pseudouridylate 516 synthase [Escherichia coli]
 gi|209765926|gb|ACI81275.1| 16S pseudouridylate 516 synthase [Escherichia coli]
 gi|209912902|dbj|BAG77976.1| ribosomal small subunit pseudouridine synthase [Escherichia coli
           SE11]
 gi|215265477|emb|CAS09878.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli O127:H6
           str. E2348/69]
 gi|217319897|gb|EEC28322.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. TW14588]
 gi|218352530|emb|CAU98307.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli 55989]
 gi|218365873|emb|CAR03614.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli S88]
 gi|218370641|emb|CAR18450.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli IAI39]
 gi|218432812|emb|CAR13706.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli UMN026]
 gi|222033944|emb|CAP76685.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           LF82]
 gi|226901022|gb|EEH87281.1| ribosomal small subunit pseudouridine synthase A [Escherichia sp.
           3_2_53FAA]
 gi|227835590|gb|EEJ46056.1| 16S rRNA pseudouridylate synthase A [Escherichia coli 83972]
 gi|238859736|gb|ACR61734.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli BW2952]
 gi|242377823|emb|CAQ32589.1| 16S rRNA pseudouridine 516 synthase [Escherichia coli BL21(DE3)]
 gi|253323934|gb|ACT28536.1| pseudouridine synthase [Escherichia coli 'BL21-Gold(DE3)pLysS AG']
 gi|253974099|gb|ACT39770.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli B str.
           REL606]
 gi|253978266|gb|ACT43936.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli BL21(DE3)]
 gi|254593484|gb|ACT72845.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli O157:H7
           str. TW14359]
 gi|257754806|dbj|BAI26308.1| 16S rRNA pseudouridylate 516 synthase RsuA [Escherichia coli
           O26:H11 str. 11368]
 gi|257759936|dbj|BAI31433.1| 16S rRNA pseudouridylate 516 synthase RsuA [Escherichia coli
           O103:H2 str. 12009]
 gi|257765240|dbj|BAI36735.1| 16S rRNA pseudouridylate 516 synthase RsuA [Escherichia coli
           O111:H- str. 11128]
 gi|260448722|gb|ACX39144.1| pseudouridine synthase [Escherichia coli DH1]
 gi|281179275|dbj|BAI55605.1| ribosomal small subunit pseudouridine synthase [Escherichia coli
           SE15]
 gi|284922167|emb|CBG35249.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           042]
 gi|290763310|gb|ADD57271.1| Pseudouridine synthase [Escherichia coli O55:H7 str. CB9615]
 gi|291323365|gb|EFE62793.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           B088]
 gi|291427859|gb|EFF00886.1| 16S rRNA pseudouridylate synthase A [Escherichia coli FVEC1412]
 gi|291433117|gb|EFF06096.1| 16S rRNA pseudouridylate synthase A [Escherichia coli B185]
 gi|291471015|gb|EFF13499.1| 16S rRNA pseudouridylate synthase A [Escherichia coli B354]
 gi|294489663|gb|ADE88419.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           IHE3034]
 gi|298278775|gb|EFI20289.1| 16S rRNA pseudouridylate synthase A [Escherichia coli FVEC1302]
 gi|299880416|gb|EFI88627.1| conserved hypothetical protein [Escherichia coli MS 196-1]
 gi|300299299|gb|EFJ55684.1| conserved hypothetical protein [Escherichia coli MS 185-1]
 gi|300307508|gb|EFJ62028.1| hypothetical protein HMPREF9553_01804 [Escherichia coli MS 200-1]
 gi|300316339|gb|EFJ66123.1| hypothetical protein HMPREF9547_02661 [Escherichia coli MS 175-1]
 gi|300358471|gb|EFJ74341.1| conserved hypothetical protein [Escherichia coli MS 198-1]
 gi|300398295|gb|EFJ81833.1| conserved hypothetical protein [Escherichia coli MS 69-1]
 gi|300408703|gb|EFJ92241.1| conserved hypothetical protein [Escherichia coli MS 45-1]
 gi|300414074|gb|EFJ97384.1| conserved hypothetical protein [Escherichia coli MS 115-1]
 gi|300417720|gb|EFK01031.1| hypothetical protein HMPREF9548_04311 [Escherichia coli MS 182-1]
 gi|300450542|gb|EFK14162.1| conserved hypothetical protein [Escherichia coli MS 116-1]
 gi|300459692|gb|EFK23185.1| conserved hypothetical protein [Escherichia coli MS 21-1]
 gi|300461741|gb|EFK25234.1| conserved hypothetical protein [Escherichia coli MS 187-1]
 gi|300524836|gb|EFK45905.1| conserved hypothetical protein [Escherichia coli MS 119-7]
 gi|300528273|gb|EFK49335.1| conserved hypothetical protein [Escherichia coli MS 107-1]
 gi|300845059|gb|EFK72819.1| conserved hypothetical protein [Escherichia coli MS 78-1]
 gi|301077507|gb|EFK92313.1| conserved hypothetical protein [Escherichia coli MS 146-1]
 gi|306908743|gb|EFN39240.1| pseudouridine synthase [Escherichia coli W]
 gi|307554252|gb|ADN47027.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           ABU 83972]
 gi|307626276|gb|ADN70580.1| 16S rRNA pseudouridylate synthase A [Escherichia coli UM146]
 gi|308123353|gb|EFO60615.1| conserved hypothetical protein [Escherichia coli MS 145-7]
 gi|309702498|emb|CBJ01824.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           ETEC H10407]
 gi|312287680|gb|EFR15585.1| conserved hypothetical protein [Escherichia coli 2362-75]
 gi|312946803|gb|ADR27630.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O83:H1 str.
           NRG 857C]
 gi|313651297|gb|EFS15695.1| hypothetical protein SF2457T_0264 [Shigella flexneri 2a str. 2457T]
 gi|315061493|gb|ADT75820.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli W]
 gi|315136817|dbj|BAJ43976.1| pseudouridine synthase [Escherichia coli DH1]
 gi|315285741|gb|EFU45181.1| conserved hypothetical protein [Escherichia coli MS 110-3]
 gi|315294447|gb|EFU53795.1| conserved hypothetical protein [Escherichia coli MS 153-1]
 gi|315297949|gb|EFU57219.1| conserved hypothetical protein [Escherichia coli MS 16-3]
 gi|315615429|gb|EFU96061.1| RNA pseudouridylate synthase family protein [Escherichia coli 3431]
 gi|320174783|gb|EFW49909.1| 16S rRNA pseudouridylate synthase A [Shigella dysenteriae CDC
           74-1112]
 gi|320178861|gb|EFW53824.1| 16S rRNA pseudouridylate synthase A [Shigella boydii ATCC 9905]
 gi|320184699|gb|EFW59492.1| 16S rRNA pseudouridylate synthase A [Shigella flexneri CDC 796-83]
 gi|320192188|gb|EFW66833.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O157:H7 str.
           EC1212]
 gi|320199781|gb|EFW74370.1| 16S rRNA pseudouridylate synthase A [Escherichia coli EC4100B]
 gi|320641254|gb|EFX10732.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O157:H7 str.
           G5101]
 gi|320646643|gb|EFX15554.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O157:H- str.
           493-89]
 gi|320651898|gb|EFX20273.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O157:H- str.
           H 2687]
 gi|320657623|gb|EFX25421.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320663228|gb|EFX30537.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O55:H7 str.
           USDA 5905]
 gi|323152225|gb|EFZ38515.1| RNA pseudouridylate synthase [Escherichia coli EPECa14]
 gi|323161735|gb|EFZ47617.1| RNA pseudouridylate synthase [Escherichia coli E128010]
 gi|323171836|gb|EFZ57480.1| RNA pseudouridylate synthase [Escherichia coli LT-68]
 gi|323176916|gb|EFZ62506.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           1180]
 gi|323184191|gb|EFZ69568.1| RNA pseudouridylate synthase [Escherichia coli 1357]
 gi|323188090|gb|EFZ73385.1| RNA pseudouridylate synthase [Escherichia coli RN587/1]
 gi|323377926|gb|ADX50194.1| pseudouridine synthase [Escherichia coli KO11]
 gi|323936800|gb|EGB33085.1| RNA pseudouridylate synthase [Escherichia coli E1520]
 gi|323940746|gb|EGB36934.1| RNA pseudouridylate synthase [Escherichia coli E482]
 gi|323951979|gb|EGB47853.1| RNA pseudouridylate synthase [Escherichia coli H252]
 gi|323955953|gb|EGB51706.1| RNA pseudouridylate synthase [Escherichia coli H263]
 gi|323961577|gb|EGB57184.1| RNA pseudouridylate synthase [Escherichia coli H489]
 gi|323972934|gb|EGB68131.1| RNA pseudouridylate synthase [Escherichia coli TA007]
 gi|324006506|gb|EGB75725.1| hypothetical protein HMPREF9532_03776 [Escherichia coli MS 57-2]
 gi|324013929|gb|EGB83148.1| hypothetical protein HMPREF9533_01960 [Escherichia coli MS 60-1]
 gi|324020657|gb|EGB89876.1| hypothetical protein HMPREF9542_00685 [Escherichia coli MS 117-3]
 gi|324117976|gb|EGC11875.1| RNA pseudouridylate synthase [Escherichia coli E1167]
 gi|326339539|gb|EGD63350.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O157:H7 str.
           1125]
 gi|326344000|gb|EGD67761.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O157:H7 str.
           1044]
 gi|330912016|gb|EGH40526.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           AA86]
 gi|331039610|gb|EGI11830.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli H736]
 gi|331043563|gb|EGI15701.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli M605]
 gi|331048466|gb|EGI20542.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli M718]
 gi|331056512|gb|EGI28521.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli TA206]
 gi|331059487|gb|EGI31464.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli TA143]
 gi|331064081|gb|EGI35992.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli TA271]
 gi|331068978|gb|EGI40370.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli TA280]
 gi|331074597|gb|EGI45917.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli H591]
 gi|332093691|gb|EGI98749.1| ribosomal small subunit pseudouridine synthase A [Shigella boydii
           3594-74]
 gi|332096238|gb|EGJ01241.1| ribosomal small subunit pseudouridine synthase A [Shigella
           dysenteriae 155-74]
 gi|332101011|gb|EGJ04357.1| 16S rRNA pseudouridylate 516 synthase [Shigella sp. D9]
 gi|332343965|gb|AEE57299.1| conserved hypothetical protein [Escherichia coli UMNK88]
 gi|332754826|gb|EGJ85191.1| ribosomal small subunit pseudouridine synthase A [Shigella flexneri
           4343-70]
 gi|332755230|gb|EGJ85594.1| ribosomal small subunit pseudouridine synthase A [Shigella flexneri
           K-671]
 gi|332756177|gb|EGJ86528.1| ribosomal small subunit pseudouridine synthase A [Shigella flexneri
           2747-71]
 gi|332765997|gb|EGJ96207.1| 16S rRNA pseudouridine synthase [Shigella flexneri 2930-71]
 gi|333001324|gb|EGK20892.1| ribosomal small subunit pseudouridine synthase A [Shigella flexneri
           VA-6]
 gi|333001796|gb|EGK21362.1| ribosomal small subunit pseudouridine synthase A [Shigella flexneri
           K-218]
 gi|333002908|gb|EGK22464.1| ribosomal small subunit pseudouridine synthase A [Shigella flexneri
           K-272]
 gi|333016616|gb|EGK35945.1| ribosomal small subunit pseudouridine synthase A [Shigella flexneri
           K-304]
 gi|333016912|gb|EGK36236.1| ribosomal small subunit pseudouridine synthase A [Shigella flexneri
           K-227]
          Length = 231

 Score =  173 bits (437), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 102/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEVI----TPTQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 227


>gi|320534116|ref|ZP_08034657.1| hypothetical protein HMPREF9057_02553 [Actinomyces sp. oral taxon
           171 str. F0337]
 gi|320133695|gb|EFW26102.1| hypothetical protein HMPREF9057_02553 [Actinomyces sp. oral taxon
           171 str. F0337]
          Length = 324

 Score =  173 bits (437), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 86/246 (34%), Positives = 123/246 (50%), Gaps = 10/246 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
           + QR+ KV+A AG+ASRR  E++IA  RV V+GI +  A V V   T  I +DG  +   
Sbjct: 76  SGQRLQKVLAHAGVASRRACEQLIADGRVSVDGITVTEAGVRVDPLTQEIRLDGSRILTN 135

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---------ISVGRLDINTEGL 121
                 + HKP G+VTT  DP+GR TV        +           + VGRLD  TEGL
Sbjct: 136 PELITLMLHKPAGVVTTMDDPEGRPTVAQYGRDYLAEHPELPDSLRLVHVGRLDTETEGL 195

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLL+NDG L+  L  PS +  + Y     GQV+      L++GI ++       +VT+  
Sbjct: 196 LLLSNDGELSHRLMHPSFEIAKTYVAIVEGQVEPWVPRKLRRGIELEDGEAKADRVTVKD 255

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                + V + L  GKNR ++++ +     V RL R   GP +LG L  G TR +S + +
Sbjct: 256 SGPRGSIVEITLHSGKNRIVRRMLDAVGHPVTRLARTRLGPLRLGNLRPGETRPLSGEEI 315

Query: 242 REQLGP 247
                 
Sbjct: 316 AALQQE 321


>gi|288929146|ref|ZP_06422991.1| ribosomal large subunit pseudouridine synthase B [Prevotella sp.
           oral taxon 317 str. F0108]
 gi|288329248|gb|EFC67834.1| ribosomal large subunit pseudouridine synthase B [Prevotella sp.
           oral taxon 317 str. F0108]
          Length = 509

 Score =  173 bits (437), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 65/241 (26%), Positives = 110/241 (45%), Gaps = 3/241 (1%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K++NI  +   P R++K +A AG+ SRRE ++ I    VKVNG ++      V+ +D I 
Sbjct: 264 KEENI--DPNEPLRLNKFLANAGVCSRREADQFIQSGMVKVNGNVVTELGTKVLRSDEII 321

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
               P+   ++  + +      + T+      ++ +         R+  VGRLD NT G+
Sbjct: 322 FHDQPVTLEKKVYVLINKPKDYVTTSDDPQQRKTVMDLVKGVCPERIYPVGRLDRNTTGV 381

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDG LA  L  P     +VY V    +V +  L  +  G+ +              
Sbjct: 382 LLLTNDGDLASKLAHPKFLKKKVYHVFLDKEVTEHDLQQIATGVTLDDGEVH-ADAIEYA 440

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                  V + +  GKNR ++++FE   ++V RL R+ +       L  G  R +++K +
Sbjct: 441 NDKDKTQVGIEIHSGKNRIVRRIFESLGYRVVRLDRVQFAGLTKKNLKRGDWRFLTEKEV 500

Query: 242 R 242
            
Sbjct: 501 D 501


>gi|15836397|ref|NP_300921.1| pseudouridine synthase [Chlamydophila pneumoniae J138]
 gi|16752175|ref|NP_445542.1| ribosomal large subunit pseudouridine synthase B [Chlamydophila
           pneumoniae AR39]
 gi|33242224|ref|NP_877165.1| putative pseudouridine synthase [Chlamydophila pneumoniae TW-183]
 gi|7189918|gb|AAF38783.1| ribosomal large subunit pseudouridine synthase B [Chlamydophila
           pneumoniae AR39]
 gi|8979238|dbj|BAA99072.1| pseudouridine synthase [Chlamydophila pneumoniae J138]
 gi|33236735|gb|AAP98822.1| putative pseudouridine synthase [Chlamydophila pneumoniae TW-183]
          Length = 235

 Score =  173 bits (437), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 69/236 (29%), Positives = 106/236 (44%), Gaps = 4/236 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T  R++K +A AG+ASRR+ + +I    V VNG + E   V V   D ++V G  +   +
Sbjct: 2   TKVRLNKFLASAGVASRRKCDEIIFSGSVTVNGRVAEGPFVLVDPEDKVQVGGTSVHLTK 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +    ++     L ++     G   V D    +  RV +VGRLD  T GL+L+TNDG  A
Sbjct: 62  KVYFMVHKAIGYLCSSEKKFPGTKLVIDLFAHLPYRVFTVGRLDKETSGLILVTNDGEFA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  PS+   + Y ++    V    L  L +G  I G     + VT   +      V +
Sbjct: 122 NKIIHPSSGITKEYLLKVSRDVSAKDLGKLMEGTFIDGKHVRPVSVTKIRRG----TVKI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + EGK  EI+   +     +  L RI  G   LG L  G  RE++   L   +  
Sbjct: 178 VVSEGKKHEIRLFADAAGLPILELKRIRIGSLVLGGLRYGEYRELTDAELGTYMKL 233


>gi|260494080|ref|ZP_05814211.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           3_1_33]
 gi|260198226|gb|EEW95742.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           3_1_33]
          Length = 234

 Score =  173 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 69/231 (29%), Positives = 129/231 (55%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAE 71
            R++K ++  GIASRR V++ I + R+ VNG +     +++   D+I +DG  ++    E
Sbjct: 1   MRINKFLSTLGIASRRAVDKYIEEGRITVNGNIATT-GMDISENDNIFIDGKKIKTDVNE 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               ++ +KP+ ++++ SD  GR TV D + +       +GRLD  T GL+LLTNDG L 
Sbjct: 60  EKVYFMLNKPLEVLSSSSDDRGRKTVVDLIKTDKRI-FPIGRLDYMTSGLILLTNDGELF 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P ++  + Y V+  G++ ++++  LKKG+++        +++      +   + +
Sbjct: 119 NRIVHPKSEIYKKYYVKIFGEIKKEEIAELKKGVLLNDGKTLPAKISGIKYDKNKTSMYI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +REG+NR+I+++ E F +KV  L R   G   LG L  G  R+++K+ + 
Sbjct: 179 SIREGRNRQIRRMIEKFGYKVLMLRREKIGELSLGDLEEGKYRKLTKQEIE 229


>gi|46908512|ref|YP_014901.1| ribosomal small subunit pseudouridine synthase A [Listeria
           monocytogenes serotype 4b str. F2365]
 gi|47092440|ref|ZP_00230230.1| ribosomal small subunit pseudouridine synthase A [Listeria
           monocytogenes str. 4b H7858]
 gi|226224887|ref|YP_002758994.1| 16S pseudouridylate synthase [Listeria monocytogenes Clip81459]
 gi|254825083|ref|ZP_05230084.1| ribosomal small subunit pseudouridine synthase A [Listeria
           monocytogenes FSL J1-194]
 gi|254854294|ref|ZP_05243642.1| ribosomal small subunit pseudouridine synthase A [Listeria
           monocytogenes FSL R2-503]
 gi|254933330|ref|ZP_05266689.1| ribosomal small subunit pseudouridine synthase A [Listeria
           monocytogenes HPB2262]
 gi|254992010|ref|ZP_05274200.1| 16S pseudouridylate synthase [Listeria monocytogenes FSL J2-064]
 gi|255521704|ref|ZP_05388941.1| 16S pseudouridylate synthase [Listeria monocytogenes FSL J1-175]
 gi|300763910|ref|ZP_07073906.1| ribosomal small subunit pseudouridine synthase A [Listeria
           monocytogenes FSL N1-017]
 gi|46881784|gb|AAT05078.1| ribosomal small subunit pseudouridine synthase A [Listeria
           monocytogenes serotype 4b str. F2365]
 gi|47019217|gb|EAL09960.1| ribosomal small subunit pseudouridine synthase A [Listeria
           monocytogenes str. 4b H7858]
 gi|225877349|emb|CAS06063.1| Putative 16S pseudouridylate synthase [Listeria monocytogenes
           serotype 4b str. CLIP 80459]
 gi|258607686|gb|EEW20294.1| ribosomal small subunit pseudouridine synthase A [Listeria
           monocytogenes FSL R2-503]
 gi|293584891|gb|EFF96923.1| ribosomal small subunit pseudouridine synthase A [Listeria
           monocytogenes HPB2262]
 gi|293594326|gb|EFG02087.1| ribosomal small subunit pseudouridine synthase A [Listeria
           monocytogenes FSL J1-194]
 gi|300515251|gb|EFK42302.1| ribosomal small subunit pseudouridine synthase A [Listeria
           monocytogenes FSL N1-017]
 gi|328465377|gb|EGF36624.1| 16S pseudouridylate synthase [Listeria monocytogenes 1816]
 gi|328471562|gb|EGF42442.1| 16S pseudouridylate synthase [Listeria monocytogenes 220]
 gi|332312766|gb|EGJ25861.1| Ribosomal small subunit pseudouridine synthase A [Listeria
           monocytogenes str. Scott A]
          Length = 233

 Score =  173 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 100/231 (43%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D + V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQVTVHGTPVVYQEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T  +               +    VGRLD +TEGLL++TNDG LA 
Sbjct: 61  VYFMLHKPQNVVSATEDNVSETVIDLLAQEDTLTDPFPVGRLDKDTEGLLIITNDGTLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y  +  G V    +     GI +         ++ + T    N    V
Sbjct: 121 NLLSPKKHIDKTYYAKIDGDVTLADVEAFAAGIELDDGYTCKPARLEIITPNEIN----V 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            ++EGK  ++K++F     KV+ L RIS G  QL   L  G  R +++  L
Sbjct: 177 TIQEGKFHQVKRMFAARGKKVSYLKRISMGNLQLDESLGLGEYRPLTESEL 227


>gi|325978633|ref|YP_004288349.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
 gi|325178561|emb|CBZ48605.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
          Length = 242

 Score =  173 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 101/232 (43%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +  AGI SR EV++++ +++V VNG +       +    D I   G  L   + 
Sbjct: 1   MRLDKFLVEAGIGSRTEVKQLLKKKQVLVNGKVEISPKTQIDEKADRISCQGQTLSYEKY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  +         +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYMLNKPKGVISATEDNHHKTVLDLLDKTAWDKEVFPVGRLDIDTHGLLLLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVT 190
            +  P     + YR +  G +    +     GI ++       Q+ +     +   + V 
Sbjct: 121 AMLSPKKHVDKTYRAKVAGLMTTADVAAFANGIDLKDFTCQPAQLVILETNEAERTSVVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + ++EGK  ++K++ +    KV  L R+S  P QL   L  G  R ++   L
Sbjct: 181 ITIKEGKFHQVKRMVQACGKKVTDLQRLSMVPLQLDKQLALGEWRRLTDDEL 232


>gi|227496094|ref|ZP_03926400.1| possible pseudouridine synthase Rsu [Actinomyces urogenitalis DSM
           15434]
 gi|226834328|gb|EEH66711.1| possible pseudouridine synthase Rsu [Actinomyces urogenitalis DSM
           15434]
          Length = 325

 Score =  173 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 85/243 (34%), Positives = 119/243 (48%), Gaps = 13/243 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
           T +R+ KV+A AG+ASRR  E +IA  RV V+G+++    V V  +   I VDG  +   
Sbjct: 74  TGERLQKVLAHAGVASRRACEEIIAAGRVSVDGVVVTEPGVRVDPSRQEIRVDGSRVLTD 133

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------------ISVGRLDINT 118
                 L HKP G+VTT  DP GR TV D      S              + VGRLD  T
Sbjct: 134 PDVITVLLHKPAGVVTTMEDPQGRPTVADLAEQFISEHRTELEHPESVRLVHVGRLDTET 193

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLLLL+NDG LA  L  PS +  + Y     GQV+      L++GI +        +V 
Sbjct: 194 EGLLLLSNDGDLAHRLMHPSFEISKTYVAIVEGQVEGWVPRKLRRGIELDDGLAQADRVV 253

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +     S + V + L  GKNR ++++ +     V RL R   GP  +G L  G  R ++ 
Sbjct: 254 VKDAGPSGSIVEITLHSGKNRIVRRMLDAVGHPVTRLARTKLGPLGIGGLRPGQMRRLTG 313

Query: 239 KIL 241
           + +
Sbjct: 314 EEI 316


>gi|323968113|gb|EGB63523.1| RNA pseudouridylate synthase [Escherichia coli M863]
 gi|323977618|gb|EGB72704.1| RNA pseudouridylate synthase [Escherichia coli TW10509]
 gi|327252432|gb|EGE64091.1| RNA pseudouridylate synthase [Escherichia coli STEC_7v]
          Length = 231

 Score =  173 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 102/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAMLEVI----TPTQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 227


>gi|218660352|ref|ZP_03516282.1| putative ribosomal large subunit pseudouridine synthase B
           [Rhizobium etli IE4771]
          Length = 296

 Score =  173 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 150/264 (56%), Positives = 183/264 (69%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           +     +R+SKV+ARAG+ASRR++ERMI + RV +NG +LE   VNV   D IEVDGVP+
Sbjct: 33  ESEAKAERISKVMARAGVASRRDIERMIMEGRVTLNGRVLETPVVNVTLADRIEVDGVPI 92

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R  ERTRLWLYHKP GLVTT++DP+GR+TVFDNLP    RV+S+GRLDINTEGLLLLTND
Sbjct: 93  RGIERTRLWLYHKPAGLVTTNADPEGRATVFDNLPEELPRVMSIGRLDINTEGLLLLTND 152

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GGLAR LELP+T WLR YRVR HG++DQ+ L+ LK GI + G+ YG ++ TLD  +GSN 
Sbjct: 153 GGLARALELPATGWLRRYRVRAHGEIDQEALDKLKDGIAVDGVLYGSIEATLDRTQGSNV 212

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+T+GLREGKNREIK V       VNRLIRISYGPFQLG L  G   EV          P
Sbjct: 213 WITMGLREGKNREIKNVMGALGLDVNRLIRISYGPFQLGDLPEGHVIEVRGPHAARSARP 272

Query: 248 HLLEEAQVNLDAPIYSSETLVRDR 271
                +   +     +    +  R
Sbjct: 273 APDRGSPRRISMHRSTMRRPLPPR 296


>gi|260598642|ref|YP_003211213.1| 16S rRNA pseudouridylate synthase A [Cronobacter turicensis z3032]
 gi|260217819|emb|CBA32307.1| Ribosomal small subunit pseudouridine synthase A [Cronobacter
           turicensis z3032]
          Length = 235

 Score =  173 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 105/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV VNG +++  A  ++    IE DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRASRVTVNGDIVKDTAFKLLPDHEIEYDGNPLTQQNGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAHKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D   L  KG+ +          Q+ +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAALFAKGVQLNNEKDLTKPAQLEVI----TPTEVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G  +L   L  G  R +++  +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVGLHRERIGAIELDPELAPGEYRPLTEDEI 227


>gi|254418155|ref|ZP_05031879.1| conserved hypothetical protein, putative [Brevundimonas sp. BAL3]
 gi|196184332|gb|EDX79308.1| conserved hypothetical protein, putative [Brevundimonas sp. BAL3]
          Length = 519

 Score =  173 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 137/356 (38%), Positives = 194/356 (54%), Gaps = 16/356 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K +ARAGIASRREVER+I   +V VNG +L+  A  V   D I VDG P+   + T
Sbjct: 86  ERIAKTMARAGIASRREVERLIGLGKVAVNGRILDTPATLVTRDDVITVDGKPIGSTQAT 145

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+W YHKP GL+T+HSDP GR TVFD LP+   RVISVGRLD+ TEGLLLLTNDG L+R 
Sbjct: 146 RVWRYHKPAGLLTSHSDPTGRPTVFDALPAGLPRVISVGRLDLATEGLLLLTNDGELSRA 205

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA------ 187
           LELP+T  +R YR R  G++ Q++L+ LK G+V+ G+ YG ++ TLD  K S +      
Sbjct: 206 LELPATSLVRQYRARARGKITQEQLDKLKDGVVVDGVSYGPIEATLDKAKESKSEDGRAP 265

Query: 188 ---WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
              W++V + EGKNRE++KV E     VNRLIR++YGPF+L  L  GS  EV  +++RE 
Sbjct: 266 ANLWISVSITEGKNREVRKVLESVGLTVNRLIRLAYGPFRLDVLPIGSVEEVGPRVIREL 325

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ------ 298
           L  ++  E     +     +    R     I +          +       + +      
Sbjct: 326 LADYIRPENLPTGNTVETPAPIPGRRVSTPIVKGRSGSAMSDPSRKPSRVRAAETAQADA 385

Query: 299 -KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            ++   P  +   A           SF    G   +  R + ++  +    R +  
Sbjct: 386 VERRERPPKKEGWAKAAPKTGHPKKSFKPREGAPTDGERPARTYKPREEGDRPARA 441


>gi|261821191|ref|YP_003259297.1| 16S rRNA pseudouridylate synthase A [Pectobacterium wasabiae
           WPP163]
 gi|261605204|gb|ACX87690.1| pseudouridine synthase [Pectobacterium wasabiae WPP163]
          Length = 231

 Score =  173 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 109/231 (47%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  QRV V+G +++  A  +    ++E DG PL++    
Sbjct: 1   MRLDKFLSQQLEISRSLVARELHAQRVTVDGEVVKSGAFKLSPEHNVEFDGNPLKQQSGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+LLT+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTILYFMDVPVAYKLHAAGRLDIDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y V     + +D       G+ +                +K ++  V +
Sbjct: 121 ITSPKHECEKTYLVTLEQPLAEDTAAQFTAGVQLHSEKNLTKPAS----LEKVTDYVVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F     +V  L R   G   L   L  G  RE+S + +
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVVELHRERIGGISLDSELEPGEYRELSAEEV 227


>gi|50121666|ref|YP_050833.1| 16S rRNA pseudouridylate synthase A [Pectobacterium atrosepticum
           SCRI1043]
 gi|49612192|emb|CAG75642.1| ribosomal small subunit pseudouridine synthase [Pectobacterium
           atrosepticum SCRI1043]
          Length = 231

 Score =  173 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 109/231 (47%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  QRV V+G +++  A  +    ++E DG PL++    
Sbjct: 1   MRLDKFLSQQLEISRSLVARELHAQRVTVDGEVVKSGAFKLSPEHNVEFDGNPLKQQNGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+LLT+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTILYFMDVPVAYKLHAAGRLDIDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y V     + +D       G+ +                +K ++  V +
Sbjct: 121 ITSPKHECEKTYLVTLELPLAEDTAEQFTVGVQLHNEKNLTKPAT----LEKITDHVVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F     +V  L R   G   L   L  G  RE+S + +
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVVELHRERIGGICLDSELEPGEFRELSAEEV 227


>gi|264679428|ref|YP_003279335.1| Pseudouridine synthase, Rsu [Comamonas testosteroni CNB-2]
 gi|262209941|gb|ACY34039.1| Pseudouridine synthase, Rsu [Comamonas testosteroni CNB-2]
          Length = 529

 Score =  173 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 84/363 (23%), Positives = 140/363 (38%), Gaps = 12/363 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          +   D +
Sbjct: 150 MPAKRVLAPQVDSPKLHKVLAQAGMGSRLEMEQLILEGRISVNNEPAHV-GQRIQFGDIV 208

Query: 61  EVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           +V+G P+R          +  +     +VT     +  +           +  SVGRLD+
Sbjct: 209 KVNGQPIRFRIDPPPARVIAYHKPVGEVVTHDDPQNRPTVFRKLPKLQHGKWQSVGRLDL 268

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NTEGLLL T+ G LA  L  P     R Y  R  G + +++   L  G+ ++        
Sbjct: 269 NTEGLLLFTSSGELANSLMHPRFGLEREYAARVLGALSKEEKQRLLDGVQLEDGEASFGA 328

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTRE 235
           V     +G+N W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E
Sbjct: 329 VEDGGGEGANCWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMMLPRGLKRGAWVE 388

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           + +  ++  +    ++E          +     R   N  S    +     +    +   
Sbjct: 389 LDQADIQALMSAAGVKERAPVERNNGGARGANNRGGRNSRSGGRGNGMNADRAPQGRREG 448

Query: 296 SK------QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                         P                  S  S  G + +  R S  +    SL R
Sbjct: 449 GGQRRGEWDGNRPAPSGMLGDNPRNKSGGRSGGSGRSQGGGQPDPMRTSVGYIGGDSLSR 508

Query: 350 TSA 352
              
Sbjct: 509 ARQ 511


>gi|237745585|ref|ZP_04576065.1| ribosomal large subunit pseudouridine synthase B [Oxalobacter
           formigenes HOxBLS]
 gi|229376936|gb|EEO27027.1| ribosomal large subunit pseudouridine synthase B [Oxalobacter
           formigenes HOxBLS]
          Length = 510

 Score =  173 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 83/348 (23%), Positives = 138/348 (39%), Gaps = 12/348 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K +  +       ++ KV+A AG+ SRR++E +I   RV VNG         ++ TD + 
Sbjct: 162 KARRELTAEDDAPKLHKVLADAGLGSRRDMEELIVAGRVSVNGEPA-HIGQRILPTDQVR 220

Query: 62  VDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           ++G  +++         L  +     +V+        S          S+ ++VGRLD N
Sbjct: 221 LNGKLIQRKIAKSLPRVLTYHKPAGEIVSRDDPEKRPSVFDRLPLLKNSKWLAVGRLDFN 280

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLLL TN G LA  L  P     R Y VR  G++++     L  G+ +        ++
Sbjct: 281 TEGLLLFTNSGDLANRLMHPRYNIEREYAVRTLGELEEGMRQKLLAGVDLGDGIGQFSKI 340

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G N W  V + EG+NRE++++FE     V+RLIR  YG   L  +L  G   E+
Sbjct: 341 VDGGGEGVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAVVLSQSLKRGRWDEL 400

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVP------DDFTRMKKNSS 290
            +  +R  L    L+            S       P+                + +K S 
Sbjct: 401 EENAVRNLLRLSGLDNKDDKKTQGKTRSRNASGQYPDFPKSQSLSIRELQLQGQHQKKSP 460

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS 338
                S + +   P+      + +        +     G+ +   RR 
Sbjct: 461 GGQKGSPRNRQPDPLQTAFGYAGMGQNPPKGGTGQRARGRGQPGQRRR 508


>gi|66818983|ref|XP_643151.1| hypothetical protein DDB_G0276449 [Dictyostelium discoideum AX4]
 gi|60471215|gb|EAL69178.1| hypothetical protein DDB_G0276449 [Dictyostelium discoideum AX4]
          Length = 401

 Score =  173 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 94/265 (35%), Positives = 136/265 (51%), Gaps = 3/265 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +R+ K++ARAGIASRR+ E +I   RVKVNG +++   + V   D I VD  P++  + 
Sbjct: 137 TERIQKILARAGIASRRKAEELIIDGRVKVNGKIIKMEEILVKPHDIITVDDKPIKVDKP 196

Query: 73  TRLWLYH-KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                +    +       D                 +ISVGRLD  TEGL+L TNDG LA
Sbjct: 197 KIWMHFKNPQVLTSEYDPDGRDCLLPIIRKVIGIDHLISVGRLDYYTEGLILFTNDGELA 256

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           R L LP   + RVY+VR  G+   +    L KG+VI  + Y  + V ++++  SN W+ +
Sbjct: 257 RYLTLPQNLFFRVYKVRIFGKFTDEMKFSLAKGMVINEVFYRPVSVQVESETDSNTWLRI 316

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVS-KKILREQLGPHL 249
            L+EGK REI+ + E+FN KV RLIR++YGP+ L   L  G T EV  K  L+  +  + 
Sbjct: 317 TLQEGKKREIRTLLEYFNVKVLRLIRVAYGPYVLPNSLKHGETIEVPIKDELKPFINKYN 376

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNI 274
             E            E   ++  N 
Sbjct: 377 STERLKKTLQEQKKIENFNKNNVNK 401


>gi|157371489|ref|YP_001479478.1| 16S rRNA pseudouridylate synthase A [Serratia proteamaculans 568]
 gi|157323253|gb|ABV42350.1| pseudouridine synthase [Serratia proteamaculans 568]
          Length = 237

 Score =  173 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 55/238 (23%), Positives = 109/238 (45%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  +RV V+G +++  A+ +     +  DG PL++    
Sbjct: 1   MRLDKFLSQQLGVSRALVARELRAKRVTVDGEVVKSGALKLTPEQEVTFDGNPLQRQNGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +  D      +G+ +          Q     ++  +  V +
Sbjct: 121 ITSPKHHCEKTYLVTLEHPLAADTAQQFAEGVQLHNEKDLTRPAQ----LEQIEDKLVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
            + EG+  ++K++F     +V  L R   G   +   L  G  R ++++ +     PH
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVLELHRERIGAIVMDEDLAEGEYRPLTEEEIASVGAPH 234


>gi|297585561|ref|YP_003701341.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
 gi|297144018|gb|ADI00776.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
          Length = 237

 Score =  173 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 58/227 (25%), Positives = 106/227 (46%), Gaps = 7/227 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K ++  G  SRR  +++I + +V +NG   +     V   D + V+G P+   +  
Sbjct: 3   VRINKYVSETGKTSRRGADKLIQEGKVTINGKPAQ-LGDQVEPGDDVIVNGEPVHIVKEN 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+ +T            +L +   R+  +GRLD ++EGL+LLTNDG +   
Sbjct: 62  VYIALNKPVGITSTTERKV--KGNIIDLVNHPLRIFHIGRLDKDSEGLILLTNDGDIVNE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V  +  +  + L  + +G+ I        +V       S     + L
Sbjct: 120 ILRAENKHEKEYIVTVNKPITPEFLKQMSEGVDILDTTTLPCKVKKL----SKYEFNITL 175

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +G NR+I+++ +   + V RL+R       LG L  G  R++SKK 
Sbjct: 176 TQGLNRQIRRMCDALGYDVQRLLRTRIMNIHLGKLPPGQWRDLSKKE 222


>gi|193068120|ref|ZP_03049084.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           E110019]
 gi|331683863|ref|ZP_08384459.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli H299]
 gi|192958399|gb|EDV88838.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           E110019]
 gi|323945000|gb|EGB41065.1| RNA pseudouridylate synthase [Escherichia coli H120]
 gi|331078815|gb|EGI50017.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli H299]
          Length = 231

 Score =  173 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 102/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLVQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEVI----TPTQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 227


>gi|169334035|ref|ZP_02861228.1| hypothetical protein ANASTE_00428 [Anaerofustis stercorihominis DSM
           17244]
 gi|169258752|gb|EDS72718.1| hypothetical protein ANASTE_00428 [Anaerofustis stercorihominis DSM
           17244]
          Length = 238

 Score =  172 bits (436), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 76/237 (32%), Positives = 121/237 (51%), Gaps = 1/237 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRK 69
               R++K +A  G+ASRR+ E +I++ +V VNG ++      +    D ++V G  +  
Sbjct: 2   EEKMRINKYLASCGVASRRKCEEIISRGKVTVNGEVVRELGTIINVEKDLVKVYGKEVSL 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             +   ++ +KP G+++      G  TV D L     R+  VGRLD +T GL++LTNDG 
Sbjct: 62  DTKKVYYMLNKPQGVISASKSKYGEETVVDLLGKKEHRLFPVGRLDKDTTGLIILTNDGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  L  P  +  + Y     G+VD   L+ LK+G+VI G      +V L    G N+ V
Sbjct: 122 FAYKLTHPKYEKEKTYEALVKGKVDSKSLDKLKQGVVIDGKKTSRAKVRLVKMIGVNSLV 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            + L EG+ R++KK+ E    KV +L R       LG L  G  R+++K  + + L 
Sbjct: 182 EITLIEGRKRQVKKMCEKVGHKVIKLNRTMENGLSLGDLEIGEYRKLTKNEVSKLLK 238


>gi|295105192|emb|CBL02736.1| ribosomal small subunit pseudouridine synthase A [Faecalibacterium
           prausnitzii SL3/3]
          Length = 233

 Score =  172 bits (436), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 97/230 (42%), Gaps = 4/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R E + M+A+ RV+VNG + ++    +   D + VDG PLR  +  
Sbjct: 1   MRLDKYLAETAQCTRSEAKTMLAKGRVQVNGAVCKKGDTQLKDNDTVTVDGAPLRYQKFV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L      +  +    D               +   GRLD  + G +LLT+DGG A  
Sbjct: 61  YLMLNKPEGVVSASTDKRDTTVVDLVGDAYPRRELFPAGRLDKTSTGFVLLTDDGGFAHD 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG-DMQVTLDTQKGSNAWVTVG 192
           +  P     + Y V     + Q+       G+ +         +VT  +  G    V V 
Sbjct: 121 ILSPRHHVSKTYTVTIDTPLTQEMRTGFAAGVTLADGTALSPAEVTALSPDG--CTVRVV 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           LR+G   +IK++F  +   VN L R + G   L   L  G  RE+S + +
Sbjct: 179 LRQGVYHQIKRMFGVYGAGVNALHREAIGGLALDAQLAPGQWRELSDEEV 228


>gi|296103839|ref|YP_003613985.1| 16S rRNA pseudouridylate synthase A [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
 gi|295058298|gb|ADF63036.1| 16S rRNA pseudouridylate synthase A [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
          Length = 235

 Score =  172 bits (436), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 103/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G ++  +A  +     +E DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRASRVTVDGDIVRDSAFKLQPDHQVEYDGNPLTQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPEGYVCSTDDPDHPTVLYFLDEPVAHKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEVI----TPTEVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G  +L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVGLHRERIGAIELDPDLAPGEYRPLTEEEI 227


>gi|302533645|ref|ZP_07285987.1| pseudouridine synthase [Streptomyces sp. C]
 gi|302442540|gb|EFL14356.1| pseudouridine synthase [Streptomyces sp. C]
          Length = 239

 Score =  172 bits (436), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 70/230 (30%), Positives = 112/230 (48%), Gaps = 1/230 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +R+ KV+ARAG+ SRR  E +I Q RV+VNG ++      V   D I+VDG+ +    
Sbjct: 2   EGERLQKVLARAGMGSRRACEELIEQARVEVNGEIVTEQGKRVQPKDEIKVDGLTVATQS 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                L      + T       +  + D + +  +R+  VGRLD  TEG++LLTN G LA
Sbjct: 62  FLFFALNKPAGVVSTMEDPDGRQ-CLGDYVTNRETRLFHVGRLDTETEGIILLTNHGELA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y     G + +D    LK+GI ++          +  Q G N  V V
Sbjct: 121 HRLTHPKYGVQKTYVAAITGSLPRDIGKRLKEGIELEDGYARADNFRVVDQVGKNYLVEV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            L EG+   ++++     + V++L+R S+GP +LG   +G  R ++   +
Sbjct: 181 TLHEGRKHIVRRMLAEAGFPVDKLVRTSFGPIELGDQKSGWLRRLTNTEV 230


>gi|74312704|ref|YP_311123.1| 16S rRNA pseudouridylate synthase A [Shigella sonnei Ss046]
 gi|73856181|gb|AAZ88888.1| 16S pseudouridylate 516 synthase [Shigella sonnei Ss046]
 gi|323168668|gb|EFZ54348.1| RNA pseudouridylate synthase [Shigella sonnei 53G]
          Length = 231

 Score =  172 bits (436), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 102/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLVSPVADDTAEQFAKGVQLHNEKDLTKPAVLEVI----TPTQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 227


>gi|330980378|gb|EGH78489.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. aptata str.
           DSM 50252]
          Length = 408

 Score =  172 bits (436), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 96/371 (25%), Positives = 151/371 (40%), Gaps = 28/371 (7%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG         V   D I
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDAT-LGQRVDLHDAI 62

Query: 61  EVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            VDG  +++ E     R  +        + T        +           R I++GRLD
Sbjct: 63  SVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           INT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++       
Sbjct: 123 INTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPARFT 182

Query: 176 QVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           RE+S+     L  ++G   + + Q+N            +    +         R    + 
Sbjct: 243 REMSQYEVDILAAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVRTLRPAAGAP 302

Query: 291 QKNGLSKQKKL----------------ATPVHRRNLASNVWMAKGIHSSFLSDSGQREEN 334
              G    ++                   P  + +        +   +S  +   +R  +
Sbjct: 303 ATGGERAPRQPQITGSERDRPRGGDSTQRPSRKDSGKPGSRTPRPADNSRGTPVAERPSD 362

Query: 335 HRRSPSFPSKR 345
             + P+ P  +
Sbjct: 363 MNKRPAKPGPK 373


>gi|170767473|ref|ZP_02901926.1| ribosomal small subunit pseudouridine synthase A [Escherichia
           albertii TW07627]
 gi|170123807|gb|EDS92738.1| ribosomal small subunit pseudouridine synthase A [Escherichia
           albertii TW07627]
          Length = 231

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 103/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G ++  AA  ++   ++  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRANRVTVDGEIVRNAAFKLLPEHNVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEVI----TPTQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVELHRERIGGIMLDADLAPGEYRPLTEEEI 227


>gi|153956083|ref|YP_001396848.1| hypothetical protein CKL_3486 [Clostridium kluyveri DSM 555]
 gi|219856417|ref|YP_002473539.1| hypothetical protein CKR_3074 [Clostridium kluyveri NBRC 12016]
 gi|146348941|gb|EDK35477.1| RsuA [Clostridium kluyveri DSM 555]
 gi|219570141|dbj|BAH08125.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 238

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 107/231 (46%), Gaps = 3/231 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERT 73
           R+ KV+A  G  +R+EV+ ++    VK++G++++  ++ +   +  IEV+   +   +  
Sbjct: 3   RLDKVLANLGYGTRKEVKAIVKSGAVKIDGLVVKDNSMKIDPDECKIEVEETVVEYKKNI 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +      +  T  +                +   VGRLD +T+GLLL+TNDG L   
Sbjct: 63  YILMNKPEGVVCATFDNYQETVIDILEPKYQAFKPFPVGRLDKDTKGLLLITNDGELNHR 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTVG 192
           L  P     +VY      +VD D +   K GIV++        ++ +     + A V V 
Sbjct: 123 LISPKNHVDKVYYAEIDKKVDMDDIRKFKMGIVLKDEYTCMPAELKIIESDENGARVEVT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           ++EGK  +IK++F      V  L RI +GP  L   L  G  RE+  + + 
Sbjct: 183 VQEGKFHQIKRMFNSLGKNVIYLERIKFGPLSLDDNLQEGEYRELYGEEIE 233


>gi|327468371|gb|EGF13856.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK330]
          Length = 242

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 100/233 (42%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++++ +  V VNG   +     +    D I V G  L   + 
Sbjct: 1   MRLDKFLAENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDEAADDIVVSGQRLIYEKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  D         +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPQGVISATEDDHHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            +  P     ++YR +  G ++Q  +     GI ++        + +         + V 
Sbjct: 121 AMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKDFTCQPAHLKILELDEEKEASLVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + L EGK  ++K++      +V  L R++ GP QL   L  G  R ++   L 
Sbjct: 181 ITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDPALALGEWRRLTADELE 233


>gi|238755840|ref|ZP_04617170.1| Ribosomal large subunit pseudouridine synthase F [Yersinia ruckeri
           ATCC 29473]
 gi|238705925|gb|EEP98312.1| Ribosomal large subunit pseudouridine synthase F [Yersinia ruckeri
           ATCC 29473]
          Length = 290

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 61/291 (20%), Positives = 113/291 (38%), Gaps = 5/291 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           +  R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +   +
Sbjct: 5   SSTRLNKYISESGICSRRDADRYIEQGNVFINGKRAA-IGDQVYAADVVKVNGQLIEPRD 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L 
Sbjct: 64  EDDLVLIALNKPVGIISTTEDGEQDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLV 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V  +  V  + +  L  G+ + G            +K +     +
Sbjct: 124 NKILRAGNDHEKDYVVTVNKPVTDEFILGLSAGVPMLGTV----TKKCKVKKEATFVFRI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++   F ++V +L R       L  L  G  R+ +   L E        
Sbjct: 180 TLVQGLNRQIRRMCSHFGYEVTKLERTRIMNINLKGLPQGEWRDFTDDELIELFKLIEHS 239

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            ++        S     +       +V +       +  +     ++KK  
Sbjct: 240 SSEDKPTKKAQSKPAAEKKPSIKRPKVAEKSDGNAASRKRFAQPGRKKKGR 290


>gi|312793399|ref|YP_004026322.1| pseudouridine synthase [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|312877026|ref|ZP_07736999.1| pseudouridine synthase [Caldicellulosiruptor lactoaceticus 6A]
 gi|311796167|gb|EFR12523.1| pseudouridine synthase [Caldicellulosiruptor lactoaceticus 6A]
 gi|312180539|gb|ADQ40709.1| pseudouridine synthase [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 232

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 54/230 (23%), Positives = 102/230 (44%), Gaps = 7/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G  SR +V+++I +  V VNG  +      +    D +EVDG   + + +
Sbjct: 1   MRLDKFLTHCGFGSRSQVKKLIREGIVTVNGKRIVEVDFKINPEEDVVEVDGRVAKFSRQ 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      + +             +    +  + +VGRLD + EGLL++T+DG    
Sbjct: 61  IYIMMNKPKGYVCSNDDPASLTVFSLISDDLKYRDLHTVGRLDKDAEGLLIITDDGEYTH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            +  P  +  + Y VR   +VD++KL   + GI++         + T+      +  V +
Sbjct: 121 RVISPKKRIEKEYLVRLEKEVDEEKLKEFENGIILDDGYKTLPAKYTII----DSTTVKL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + EGK  ++K++FE    KV  L R+  G   L   L  G  + + ++ 
Sbjct: 177 CIYEGKYHQVKRMFEAIGNKVVDLKRLRIGGLNLDQNLKPGEYKVIDREE 226


>gi|257056522|ref|YP_003134354.1| ribosomal large subunit pseudouridine synthase B [Saccharomonospora
           viridis DSM 43017]
 gi|256586394|gb|ACU97527.1| ribosomal large subunit pseudouridine synthase B [Saccharomonospora
           viridis DSM 43017]
          Length = 247

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 72/234 (30%), Positives = 118/234 (50%), Gaps = 1/234 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
           ++    R+ KV+A+AG+ASRR  E +IA  RV V+G+++      V      I VDG+ +
Sbjct: 5   DSSEGVRLQKVLAKAGVASRRASEELIAAGRVSVDGVVVRELGRRVDPDTAVIHVDGIRV 64

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +  +       +KP G+ +T SD  GR  V D +     R+  VGRLD +TEGLLLLTND
Sbjct: 65  QVRDDLVYLALNKPRGVHSTMSDAQGRPCVGDYVADRPERLFHVGRLDADTEGLLLLTND 124

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS    + Y     G V +     L+ G+ +           +   + + +
Sbjct: 125 GDLAHKLMHPSFHVTKTYLAEVEGAVARGLGKRLRAGVQLSDGPVTADAFRIKDVRPNRS 184

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V + L EG+   ++++       V +L+R + G  +LGT   G+ R ++++ +
Sbjct: 185 LVEIVLHEGRKHIVRRLLAEVGHPVRKLVRTAIGEVRLGTTKPGTLRTLTQQEI 238


>gi|304382274|ref|ZP_07364781.1| ribosomal large subunit pseudouridine synthase B [Prevotella
           marshii DSM 16973]
 gi|304336631|gb|EFM02860.1| ribosomal large subunit pseudouridine synthase B [Prevotella
           marshii DSM 16973]
          Length = 481

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 60/242 (24%), Positives = 107/242 (44%), Gaps = 1/242 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      ++ TD +
Sbjct: 233 IEYKEEHTDPNEPIRLNKYLANAGVCSRREADEFIQAGVVTVNGQVITELGTKIVRTDEV 292

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P+   ++  + L      + T+      ++ +     +   R+  VGRLD NT G
Sbjct: 293 KFHDQPVTLEKKVYVLLNKPRDYVTTSDDPQQRKTVMELVKGACPERIYPVGRLDRNTTG 352

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LL TNDG LA  L  P     +VY V    +V    +  +  GI +             
Sbjct: 353 VLLFTNDGDLASKLTHPKFLKKKVYHVFLDKEVTMHDMQQIATGITLDDGEIH-ADAIEY 411

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +      V + +  G+NR ++++FE   ++V RL R+ +       L  G  R +++K 
Sbjct: 412 AKDNDKKQVGIEIHSGRNRIVRRIFESLGYRVVRLDRVQFAGLTKKYLRRGDWRFLTEKE 471

Query: 241 LR 242
           + 
Sbjct: 472 VD 473


>gi|222150708|ref|YP_002559861.1| tRNA pseudouridine synthase A homolog [Macrococcus caseolyticus
           JCSC5402]
 gi|222119830|dbj|BAH17165.1| tRNA pseudouridine synthase A homolog [Macrococcus caseolyticus
           JCSC5402]
          Length = 236

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 53/234 (22%), Positives = 98/234 (41%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K ++ AGI SRR  ++ I   R+K+NG+        V   D +EVD   +      
Sbjct: 1   MRINKFLSEAGICSRRGADKWIEAGRIKINGVKA-ELGSKVTEGDSVEVDNKVVTLNTDK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                        T +          +      R+  +GRLD ++EGL+LLTNDG +   
Sbjct: 60  GYVYIKLNKPRGITSTTERHIKGNIVDFVGHSERIFHIGRLDKDSEGLILLTNDGDIVNE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  D +  + +G+ I        +V    +K +     + L
Sbjct: 120 ILRKEGRHEKEYIVTVDKPITDDFVKQMSEGVAILDTVTLPAEV----EKLNTKTFKIIL 175

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            +G NR+I+++ E   ++V +L RI      +  L  G  +++++    E    
Sbjct: 176 TQGLNRQIRRMTEALGYEVKQLRRIRVMNILVDDLKLGEWKDLTEAEKDELFSM 229


>gi|291522303|emb|CBK80596.1| ribosomal large subunit pseudouridine synthase F [Coprococcus catus
           GD/7]
          Length = 261

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 65/263 (24%), Positives = 121/263 (46%), Gaps = 8/263 (3%)

Query: 3   DKNIVQENFTP--QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
            K+I+ EN      R+++ ++ AG  SRRE +R+I   RV V+G         V     +
Sbjct: 5   KKDILHENEDKSDVRLNRFLSDAGFCSRREADRLIEAGRVTVDGTKA-ELGTRVRPGQVV 63

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +V    +R+ +R  L  ++KP G+V T  D         +      R+  +GRLD ++EG
Sbjct: 64  KVGSKVVRQNDRMVLIAFNKPRGIVCTT-DRVREKNNIIDYIHYPERIYPIGRLDKDSEG 122

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+LLTNDG +   +   S    + Y VR + ++  + +  + KG+ I         +   
Sbjct: 123 LILLTNDGTIVNHILKASQYHEKEYIVRVNKKITDEFIQGMSKGVPILDTVTRPCTLRRI 182

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   ++ L +G NR+I+ +   F++ V +L R+     +LG+L  G  R+V+ + 
Sbjct: 183 ----DDYTFSIILTQGLNRQIRYMCRHFDYHVTKLKRVRIMNIRLGSLPVGKWRDVTAEE 238

Query: 241 LREQLGPHLLEEAQVNLDAPIYS 263
           L +     +  + +   +     
Sbjct: 239 LEQLKRQFIANDRRNQSNRRKSR 261


>gi|302345864|ref|YP_003814217.1| pseudouridylate synthase [Prevotella melaninogenica ATCC 25845]
 gi|302150213|gb|ADK96475.1| pseudouridylate synthase [Prevotella melaninogenica ATCC 25845]
          Length = 514

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 61/242 (25%), Positives = 109/242 (45%), Gaps = 1/242 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG +++     VM TD +
Sbjct: 266 IEYKEENYDPNEPIRLNKYLANAGVCSRREADEFILSGAVTVNGEVVKELGSKVMRTDEV 325

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 +   ++  + L      + T+      ++ +     +   R+  VGRLD NT G
Sbjct: 326 YFQDKLVSLEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKGACPERIYPVGRLDRNTTG 385

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     +VY V     +  + L  +  GI ++        +   
Sbjct: 386 VLLLTNDGDLASKLTHPKFLKKKVYHVFLDKAITANDLQKISDGIELEDGEIKADAIEYA 445

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             +     V + +  GKNR ++++FE   ++V +L R+ +       +  G  R +++K 
Sbjct: 446 DPQ-DQTQVGIEIHSGKNRIVRRIFESLGYRVVKLDRVQFAGLTKKNVRRGDWRFLTEKE 504

Query: 241 LR 242
           + 
Sbjct: 505 VD 506


>gi|213968651|ref|ZP_03396793.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. tomato T1]
 gi|301384619|ref|ZP_07233037.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. tomato Max13]
 gi|302059631|ref|ZP_07251172.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. tomato K40]
 gi|302130734|ref|ZP_07256724.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. tomato NCPPB 1108]
 gi|213926584|gb|EEB60137.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. tomato T1]
 gi|330879716|gb|EGH13865.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. morsprunorum str. M302280PT]
          Length = 408

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 92/371 (24%), Positives = 143/371 (38%), Gaps = 28/371 (7%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG         V   D I
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDAT-LGQRVDLHDAI 62

Query: 61  EVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            VDG  +++ E     R  +        + T        +           R I++GRLD
Sbjct: 63  SVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           INT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++       
Sbjct: 123 INTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPARFT 182

Query: 176 QVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIKQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKILR------------EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD 281
           RE+S+  +             +       ++    L                 +      
Sbjct: 243 REMSQYEVDILSAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVVRTLRPAAGA 302

Query: 282 FTRMKKNSSQKN-------GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREEN 334
                +   Q                   P  + +        +   +S  +   +R  +
Sbjct: 303 PATGDRTPRQPQITGSERDRPRGGDSTQRPARKDSGKPGSRAPRPADNSRGTPVAERPSD 362

Query: 335 HRRSPSFPSKR 345
             + P+ P  +
Sbjct: 363 MNKRPAKPGPK 373



 Score = 39.4 bits (90), Expect = 0.92,   Method: Composition-based stats.
 Identities = 18/100 (18%), Positives = 27/100 (27%), Gaps = 2/100 (2%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R    P +    +        +     +D     S  P      +     +      K+ 
Sbjct: 308 RTPRQPQITGSERDRPRGGDSTQRPARKDSGKPGSRAPRPADNSRGTPVAERPSDMNKRP 367

Query: 302 ATPVHRRNLAS--NVWMAKGIHSSFLSDSGQREENHRRSP 339
           A P  +R      N     G      + SGQR    RR P
Sbjct: 368 AKPGPKRVGIKLVNDDAPSGKRRGPPAGSGQRPGFGRRKP 407


>gi|312973563|ref|ZP_07787735.1| conserved hypothetical protein [Escherichia coli 1827-70]
 gi|310332158|gb|EFP99393.1| conserved hypothetical protein [Escherichia coli 1827-70]
          Length = 231

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 102/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKSYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEVI----TPTQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 227


>gi|299530511|ref|ZP_07043931.1| Pseudouridine synthase, Rsu [Comamonas testosteroni S44]
 gi|298721487|gb|EFI62424.1| Pseudouridine synthase, Rsu [Comamonas testosteroni S44]
          Length = 529

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 84/363 (23%), Positives = 141/363 (38%), Gaps = 12/363 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          +   D +
Sbjct: 150 MPAKRVLAPQVDSPKLHKVLAQAGMGSRLEMEQLILEGRISVNNEPAHV-GQRIQFGDIV 208

Query: 61  EVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           +V+G P+R          +  +     +VT     +  +           +  SVGRLD+
Sbjct: 209 KVNGQPIRFRIDPPPARVIAYHKPVGEVVTHDDPQNRPTVFRKLPKLQHGKWQSVGRLDL 268

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NTEGLLL T+ G LA  L  P     R Y  R  G + +++   L  G+ ++        
Sbjct: 269 NTEGLLLFTSSGELANSLMHPRFGLEREYAARVLGALSKEEKQRLLDGVQLEDGEASFGA 328

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTRE 235
           V     +G+N W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E
Sbjct: 329 VEDGGGEGANCWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMMLPRGLKRGAWVE 388

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           + +  ++  +    ++E      +   +     R   N  S    +     +    +   
Sbjct: 389 LDQADIQALMSAAGVKERAPVERSSGGARGANNRGGRNNRSGGRGNGMNADRAPQGRREG 448

Query: 296 SK------QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                         P                  S  S  G + +  R S  +    SL R
Sbjct: 449 GGQRRGEWDGNRPAPSGMLGDNPRNKSGGRSGGSGRSQGGGQPDPMRTSVGYIGSDSLSR 508

Query: 350 TSA 352
              
Sbjct: 509 ARQ 511


>gi|253996068|ref|YP_003048132.1| pseudouridine synthase [Methylotenera mobilis JLW8]
 gi|253982747|gb|ACT47605.1| pseudouridine synthase [Methylotenera mobilis JLW8]
          Length = 374

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 87/346 (25%), Positives = 143/346 (41%), Gaps = 13/346 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL----R 68
            QR+ K++A AG+ SRR++E +IA  RV VNG + E     V   D + +D  PL     
Sbjct: 36  TQRLHKLLALAGLGSRRDMEELIASGRVTVNGKVAEV-GAGVTEHDVVRLDSRPLRLPFE 94

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 L  +     +V+        S           + I++GRLD+NT GLL+ T  G
Sbjct: 95  PELPQVLIYHKPEGEIVSQDDPEGRASVFDKLPKVKHGKWIAIGRLDMNTSGLLIFTTSG 154

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA     P  +  R Y VR  G++ + ++  LK+GI ++        +     +G+N W
Sbjct: 155 ELANRFMHPRYEVEREYAVRIFGELTEGQIAQLKEGIELEDGPANFDSIIPQGGEGANHW 214

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             V LREG+NRE++++FE F   V+RL+R+ +GP     L     R    K+L+ +    
Sbjct: 215 YQVILREGRNREVRRLFEAFQLPVSRLMRVRFGPV---NLPP---RVKRGKMLKLEQKEV 268

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
           +      +L  P      L +      + V     R ++ S+         +     +R 
Sbjct: 269 VGLLEWADLPVPKAPLRQLTQREKLKSTAVFTPKVRKQRVSALDRPPRDAAEGEAGGYRG 328

Query: 309 NLASNVWMAKGIH--SSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
              S    A          ++   R+ +   +P    K    R   
Sbjct: 329 KPGSARGPATKKPIARKPAANRRVRQSSDLNAPQMQKKSDRNRGRG 374


>gi|239997156|ref|ZP_04717680.1| RNA pseudouridine synthase family protein [Alteromonas macleodii
           ATCC 27126]
          Length = 252

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 62/237 (26%), Positives = 108/237 (45%), Gaps = 11/237 (4%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
               P+R++K I+  G+ SRRE +++I Q RV VN          V   D ++VDG  + 
Sbjct: 2   SEQAPKRLNKYISDTGLCSRREADKLIEQNRVTVNNQPP-ELGTKVGPGDTVKVDGKVVG 60

Query: 69  K----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                       +Y+KPIG+  T       + +         R+  VGRLD  +EGL++L
Sbjct: 61  AVASDKSDRVYIVYNKPIGITCTTERHVKGNIIDAI--GHKERIFPVGRLDKPSEGLIIL 118

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T+DG +   +        + Y V  +  + +  +N + +G+ I G            +  
Sbjct: 119 TSDGDIVNKILRAENAHDKEYEVTVNQPISERFVNRMSRGVPILGTVTKPC----VVKPT 174

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                T+ L +G NR+I+++ EF  ++V +L R      +LG+L  G  R ++ + L
Sbjct: 175 GKNTFTIILTQGLNRQIRRMCEFLGYEVTKLKRTRIMHLELGSLKPGQWRNLTSREL 231


>gi|317153278|ref|YP_004121326.1| pseudouridine synthase [Desulfovibrio aespoeensis Aspo-2]
 gi|316943529|gb|ADU62580.1| pseudouridine synthase [Desulfovibrio aespoeensis Aspo-2]
          Length = 251

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 79/241 (32%), Positives = 120/241 (49%), Gaps = 6/241 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGV 65
           + ++ +  R++K IA+ G+ SRR  + ++   RV VNG   +   + V    DH+ VDG 
Sbjct: 1   MSDDSSLMRLNKFIAQCGVTSRRGADDLVFGGRVAVNGEKADSPGIKVDPARDHVTVDGR 60

Query: 66  PLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGL 121
           P+           + HKP+ +VTT  DP GR+TV D LP      R   VGRLD  +EGL
Sbjct: 61  PVVLPGSGGDITIMLHKPVEIVTTARDPQGRTTVLDLLPPEIVELRPFPVGRLDYYSEGL 120

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLD 180
           LLLT DG L   L  P     +VY V   G V +  +  ++ G+ ++ G         L 
Sbjct: 121 LLLTTDGELCHRLTHPKWHLPKVYEVTIRGSVPEKAIRTMQSGMTLKAGDRLAPADAILH 180

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +  + + L +G NR+I+++ E     + RL R+  GP +LG L  G  RE++   
Sbjct: 181 PPVAGSQVLEITLIQGLNRQIRRMCEELGLTILRLHRVKQGPMELGNLKRGQWRELTAAE 240

Query: 241 L 241
           L
Sbjct: 241 L 241


>gi|41407511|ref|NP_960347.1| hypothetical protein MAP1413 [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|41395864|gb|AAS03730.1| hypothetical protein MAP_1413 [Mycobacterium avium subsp.
           paratuberculosis K-10]
          Length = 247

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 73/236 (30%), Positives = 108/236 (45%), Gaps = 4/236 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLR 68
                R+ KV+++AGIASRR  E++I   RV+V+G ++      V      I VDG  + 
Sbjct: 3   EAQGIRLQKVLSQAGIASRRAAEKLIVDGRVEVDGQVVTELGTRVDPDAAVIRVDGARVV 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLLT 125
             E       +KP G+ +T SD  GR  + D +            VGRLD  TEGL+LLT
Sbjct: 63  LDESQVYLALNKPRGVHSTMSDDRGRPCIGDLIERRVRGNKNLFHVGRLDAETEGLILLT 122

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  PS +  + Y     G + +     L+ GI +        +  +      
Sbjct: 123 NDGELAHRLMHPSHEVPKTYLATVTGSIPRGLGKTLRAGIELDDGMARVDEFAVVDPIPG 182

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              V V L EG+NR ++++     + V  L+R   GP  LG    GS R + +  +
Sbjct: 183 KTLVRVTLHEGRNRIVRRLLAAAGFPVESLVRTDIGPISLGKQRPGSIRALGRDEV 238


>gi|237740448|ref|ZP_04570929.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           2_1_31]
 gi|229422465|gb|EEO37512.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           2_1_31]
          Length = 234

 Score =  172 bits (435), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 71/231 (30%), Positives = 130/231 (56%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--RKAE 71
            R++K ++  GIASRR +++ I + R+KVNG ++    ++V   D I +D   +  ++ E
Sbjct: 1   MRINKFLSSLGIASRRAIDKYIEEGRIKVNG-VITSTGIDVTEDDEIYIDNKKIETKRIE 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               ++ +KP+ +++  SD  GR TV D + +       +GRLD  T GL+LLTNDG L 
Sbjct: 60  EKVYFMLNKPLEVLSASSDDRGRKTVVDLIKTDKRI-FPIGRLDYMTSGLILLTNDGELF 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P ++  + Y ++  G+V ++++  LKKG++++       +++      +   + +
Sbjct: 119 NRLVHPKSEIYKKYYIKVFGEVKKEEIEELKKGVLLEDGKTLPAKISGIKYDKNKTSMYI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +REG+NR+I+++ E F +KV  L R   G   LG L  G  RE++K+ + 
Sbjct: 179 SIREGRNRQIRRMIEKFGYKVLMLRREKIGELSLGDLKEGKYRELTKEEIE 229


>gi|322383949|ref|ZP_08057679.1| pseudouridylate synthase B-like large subunit [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321151426|gb|EFX44613.1| pseudouridylate synthase B-like large subunit [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 250

 Score =  172 bits (435), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 66/234 (28%), Positives = 114/234 (48%), Gaps = 9/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+  G+ SRRE ++ IA  RV +NG+        V   D I VDG PL + ++ 
Sbjct: 1   MRINKFISETGVCSRREADKWIAANRVTINGVPA-ELGSTVEEGDEIRVDGKPLGEKKKG 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T            +  +   R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCTTEK--HVKGNIIDFVNHPERIFPIGRLDKDSQGLILLTNDGDIVNQ 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y VR +  V  + +  +  G+ I G      +VT      ++    + L
Sbjct: 118 ILRAENNHEKEYVVRVNKPVTDEFVKGMAGGVRILGTKTKPCKVTRI----NDHVFRIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKILREQL 245
            +G NR+I+++ E F ++V +L R+      L    L  G  R+++++ LRE L
Sbjct: 174 TQGLNRQIRRMCEVFGYQVVQLERVRIMNIHLDKPKLRLGEWRDLAREELRELL 227


>gi|300121522|emb|CBK22041.2| Pseudouridine synthase [Blastocystis hominis]
          Length = 271

 Score =  172 bits (435), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 91/232 (39%), Positives = 126/232 (54%), Gaps = 6/232 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++K IAR+G+ SRRE ER I   RV +NG ++   A+NV   D I VD  PL   +R
Sbjct: 10  SMRIAKRIARSGVCSRREAERWIEMGRVTLNGKVITSPAINVTQQDIIHVDNKPLSPIQR 69

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
           TR+ + +K  G + T SD   R T+FD L        ++ VG+LD +TEGLLLLTNDG  
Sbjct: 70  TRVIIANKLDGELVTTSDSQHRLTIFDRLRKTGLECHIMPVGQLDFHTEGLLLLTNDGDY 129

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS----N 186
           AR LE PS    R YR + +G+ D  ++  L    +I G  Y    V  D  + S     
Sbjct: 130 ARYLEHPSNAIPRRYRAKVYGRWDDSRVLALSHSNIIDGKRYKGCLVKRDLDRSSANAME 189

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            W T+ + EGK  E+K +  F    V +L+R ++G + LG L+ G  REV  
Sbjct: 190 HWCTIQVTEGKYHEVKNLLGFVGLNVEKLVRTNFGAYSLGNLVPGEFREVKP 241


>gi|47096040|ref|ZP_00233642.1| ribosomal small subunit pseudouridine synthase A [Listeria
           monocytogenes str. 1/2a F6854]
 gi|254826833|ref|ZP_05231520.1| ribosomal small subunit pseudouridine synthase A [Listeria
           monocytogenes FSL N3-165]
 gi|254901132|ref|ZP_05261056.1| hypothetical protein LmonJ_14998 [Listeria monocytogenes J0161]
 gi|254914018|ref|ZP_05264030.1| ribosomal small subunit pseudouridine synthase A [Listeria
           monocytogenes J2818]
 gi|254938333|ref|ZP_05270030.1| ribosomal small subunit pseudouridine synthase A [Listeria
           monocytogenes F6900]
 gi|47015637|gb|EAL06568.1| ribosomal small subunit pseudouridine synthase A [Listeria
           monocytogenes str. 1/2a F6854]
 gi|258599211|gb|EEW12536.1| ribosomal small subunit pseudouridine synthase A [Listeria
           monocytogenes FSL N3-165]
 gi|258610945|gb|EEW23553.1| ribosomal small subunit pseudouridine synthase A [Listeria
           monocytogenes F6900]
 gi|293592036|gb|EFG00371.1| ribosomal small subunit pseudouridine synthase A [Listeria
           monocytogenes J2818]
          Length = 233

 Score =  172 bits (435), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 99/231 (42%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D I V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQITVHGTPVVYQEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T  +               +    VGRLD +TEGLL++TNDG LA 
Sbjct: 61  VYFMLHKPQNVVSATEDNVSETVIDLLAQEDTLTDPFPVGRLDKDTEGLLIITNDGTLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y  +  G V    +     GI +         ++ + T       + V
Sbjct: 121 NLLSPKKHIDKTYYAKIDGDVTAADVEAFAAGIELDDGYTCKPARLEIITPN----EIKV 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            ++EGK  ++K++F      V+ L RIS G  QL   L  G  R +++  L
Sbjct: 177 TIQEGKFHQVKRMFAARGKSVSYLKRISMGNLQLDESLALGEYRPLTEAEL 227


>gi|311742416|ref|ZP_07716225.1| ribosomal large subunit pseudouridine synthase B [Aeromicrobium
           marinum DSM 15272]
 gi|311314044|gb|EFQ83952.1| ribosomal large subunit pseudouridine synthase B [Aeromicrobium
           marinum DSM 15272]
          Length = 247

 Score =  172 bits (435), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 74/233 (31%), Positives = 118/233 (50%), Gaps = 1/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
           +    R+ KV+A+AG+ SRR  E+++A+  V+VNG +  +  + V   TD I VDG  L 
Sbjct: 6   STDGIRLQKVLAQAGLGSRRRCEQLMAEGHVEVNGEITTQMGIRVDPATDVIHVDGRRLP 65

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   L +KP G+VT+ +D  GR  +   L     R+  VGRLD +T GLL++TNDG
Sbjct: 66  PPSDHVYVLLNKPRGVVTSMADERGRPDLRSLLADRTERLFHVGRLDTDTSGLLMMTNDG 125

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS ++ + Y     G VD      LK G+ +        +  +       + 
Sbjct: 126 DLAHRLAHPSFEFTKTYVALVEGVVDPAVGTRLKSGVELDDGPATVDRFRIKDTSQGRSL 185

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + L  G+NR ++++       V  L R ++GP +L  L +G  R++++  L
Sbjct: 186 VELDLHMGRNRIVRRLLAEVGHPVVELTRTAFGPLRLAGLGSGRARDLTRDEL 238


>gi|88801341|ref|ZP_01116869.1| putative ribosomal large subunit pseudouridine synthase
           [Polaribacter irgensii 23-P]
 gi|88781999|gb|EAR13176.1| putative ribosomal large subunit pseudouridine synthase
           [Polaribacter irgensii 23-P]
          Length = 305

 Score =  172 bits (435), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 64/241 (26%), Positives = 109/241 (45%), Gaps = 1/241 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            +  T  R++K IA +G+ SRRE +  I    V+VNG L+      V   D +  DG  +
Sbjct: 66  SDESTGIRLNKYIANSGVCSRREADTYIEHGSVEVNGNLVTEMGYKVQPDDVVRFDGTGI 125

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              ++  + L      + T   D   ++ +     +   R+  VGRLD NT GLLL TND
Sbjct: 126 TPEQKKYILLNKPKNYITTMDDDRGRKTVMDLISNATKERIYPVGRLDRNTTGLLLFTND 185

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA+ L  P     ++Y      +++   L  L+  ++I+G     +           +
Sbjct: 186 GELAKKLTHPKHDVRKLYHASLDKKLELKDLEKLRGEVLIEGKKV-FIDAVSYVDGQPKS 244

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V + +  G+NR ++K+FE   +KV++L R+ +       L  G  RE++ + L      
Sbjct: 245 EVGIEIHSGRNRIVRKIFEHLGYKVSKLDRVIFAELTKRNLPRGRWRELTNQELSNLQML 304

Query: 248 H 248
            
Sbjct: 305 K 305


>gi|228960820|ref|ZP_04122455.1| RNA pseudouridine synthase [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228798842|gb|EEM45821.1| RNA pseudouridine synthase [Bacillus thuringiensis serovar
           pakistani str. T13001]
          Length = 229

 Score =  172 bits (435), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 108/230 (46%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +N  +       V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINSEICTH-GALVSDGDRVTIDGQVIVKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D    + +     +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAADHIEDNIINYI--NYPERIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ + +G+ I+       +VT        +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSRGVKIKDGMTKPCKVTRV----DQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L 
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTAEELE 223


>gi|315611910|ref|ZP_07886829.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis ATCC 49296]
 gi|315316088|gb|EFU64121.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis ATCC 49296]
          Length = 240

 Score =  172 bits (435), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 63/233 (27%), Positives = 102/233 (43%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQINEERDEIRFDGQVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    V  VGRLDI+T GLLLLTNDG LA 
Sbjct: 61  VYYMMNKPQGVISATEDTKHRTVLDLLDDYARAKEVFPVGRLDIDTHGLLLLTNDGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVT 190
            L  P     + Y  +  G + Q+ ++   KGI ++       ++ L +     + + V 
Sbjct: 121 ALLSPKRHVDKTYLAQVKGIMTQEDVDAFAKGIPLKDFTCQPARLELVSVDPEKNQSLVR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 181 VTIAEGKFHQVKRMVAYCGKEVVDLQRLTMGTLVLDENLEQGEWRRLTKEELE 233


>gi|325497996|gb|EGC95855.1| 16S rRNA pseudouridylate synthase A [Escherichia fergusonii ECD227]
          Length = 231

 Score =  172 bits (435), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 101/231 (43%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G  +  AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGETVRNAAFKLLPEHEVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEVI----TPTQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEV 227


>gi|317492193|ref|ZP_07950623.1| RNA pseudouridylate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316919898|gb|EFV41227.1| RNA pseudouridylate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 317

 Score =  172 bits (435), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 93/319 (29%), Positives = 132/319 (41%), Gaps = 10/319 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+A AG  SRRE+E MI + RV V+G L      V V     I VDG  +   E
Sbjct: 2   SEKLQKVLANAGHGSRREIEAMIKEGRVSVDGKLATLGDRVEVTPAMKIRVDGRVVSIRE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T        +          SR I+VGRLDINT GLLL T 
Sbjct: 62  STESVCRVLAYYKPEGELCTRRDPEGRPTVFDRLPKLRGSRWIAVGRLDINTSGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD +K+  L +G+ ++        ++    +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDEKIRQLSRGVQLEDGPASFKTISFQGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+    L +  
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDLPLPKGLPRGGWAELP---LNDIN 238

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
               L E      + +       R + N I        +    ++               
Sbjct: 239 YLRELVELDAETVSKLPVERERRRMKANQIRRAVKRHGQGGSAAAAAPNRRSGSANKGTS 298

Query: 306 HRRNLASNVWMAKGIHSSF 324
             R  A+N   +       
Sbjct: 299 STRGSAANKGTSNRGAKRG 317


>gi|160915077|ref|ZP_02077290.1| hypothetical protein EUBDOL_01085 [Eubacterium dolichum DSM 3991]
 gi|158432876|gb|EDP11165.1| hypothetical protein EUBDOL_01085 [Eubacterium dolichum DSM 3991]
          Length = 230

 Score =  172 bits (435), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 107/231 (46%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A A + +R+EV+++I  +RV+VN  +  +    +   D + VD   L   E  
Sbjct: 1   MRLDKYLAHAQLGTRKEVKKLIRSKRVRVNDEICTKEDRQLQKEDCVYVDDELLVYDELV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L LY     +++   D    + +      +      VGRLDI++EGLLL+TNDG LA  
Sbjct: 61  YLMLYKPQG-VISATEDRVHTTVMDIFDAPLPKNCFPVGRLDIDSEGLLLITNDGQLAHQ 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           L  P     + Y V     +  + L LL+   I +        Q    +       + + 
Sbjct: 120 LLSPKKHVDKTYYVECEKTLSSEDLQLLESGTIQLDKEHVLPAQAKRISANS----LYLT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           ++EGK  ++K++ +    KV  L RIS G  QL   L  G  R +S++ +R
Sbjct: 176 IQEGKFHQVKRMLQACGNKVCYLKRISMGSLQLDKSLAPGEWRYLSEEEIR 226


>gi|313837519|gb|EFS75233.1| conserved hypothetical protein [Propionibacterium acnes HL037PA2]
 gi|314927273|gb|EFS91104.1| conserved hypothetical protein [Propionibacterium acnes HL044PA1]
 gi|314972725|gb|EFT16822.1| conserved hypothetical protein [Propionibacterium acnes HL037PA3]
 gi|328907871|gb|EGG27634.1| pseudouridylate synthase [Propionibacterium sp. P08]
          Length = 245

 Score =  172 bits (435), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 84/241 (34%), Positives = 123/241 (51%), Gaps = 2/241 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
            +    R+ KV+A+AG+ASRR  E MIA  RV+VNG L+      V    D I VDG  +
Sbjct: 2   SDEQGIRLQKVLAQAGLASRRAAEEMIAAGRVEVNGELIVEQGRRVDPEHDEIRVDGSRI 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTN 126
             A R   ++ +KP G+V+T  DP+ R  + D            VGRLD  T GL+LLTN
Sbjct: 62  PTARRHVYYVLNKPRGVVSTMDDPESRPCLSDLEGVPRGIRLFHVGRLDTETSGLILLTN 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  A  +  PS + L+ Y     G+VD   +  L KG+ ++        V L      +
Sbjct: 122 DGEFANRMTHPSYKVLKTYLADVEGRVDDKVIRRLSKGLTLEDGPVKPDAVRLVQAGDEH 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + V V L EG+NR ++++ +     V RL R + GP +L  L  G  RE++++ L + L 
Sbjct: 182 SLVEVSLHEGRNRIVRRMMDSVAHPVRRLSRTAIGPVRLKRLSRGDMRELTREELGQLLD 241

Query: 247 P 247
            
Sbjct: 242 L 242


>gi|291522211|emb|CBK80504.1| ribosomal small subunit pseudouridine synthase A [Coprococcus catus
           GD/7]
          Length = 250

 Score =  172 bits (435), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 73/247 (29%), Positives = 115/247 (46%), Gaps = 11/247 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A   + +R EV+ +I +  V VNG ++ +    V    D +   G P+      
Sbjct: 6   RLDKYLADMSVGTRSEVKNLIKKGLVTVNGEVIRKPEYKVDIEKDDLVCRGEPVAYQTLV 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      +++  +DP  ++ +          +  VGRLD +TEGLLL+TNDG LA  
Sbjct: 66  YYMLNKPAG-VISATNDPKQKTVLDLITDKSRKDLFPVGRLDKDTEGLLLITNDGDLAHQ 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI----CYGDMQVTLDTQKGSNAWV 189
           L  P     +VYR R  GQV  +   L  KG+ I            ++ +    G  + +
Sbjct: 125 LLSPKKHVDKVYRARIEGQVTAEDAALFAKGLGIDDEDGAWRAMPAKLNIL-SSGPESEI 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI---LREQL 245
            + +REGK  +IK++FE  + KV  L R+S G  +L   L  G  RE+++     L+E  
Sbjct: 184 EITIREGKFHQIKRMFEAVDKKVVYLKRLSMGSLRLDETLALGEYRELTEDEVQALKESK 243

Query: 246 GPHLLEE 252
           G    EE
Sbjct: 244 GHTNDEE 250


>gi|261367368|ref|ZP_05980251.1| ribosomal large subunit pseudouridine synthase B [Subdoligranulum
           variabile DSM 15176]
 gi|282570129|gb|EFB75664.1| ribosomal large subunit pseudouridine synthase B [Subdoligranulum
           variabile DSM 15176]
          Length = 267

 Score =  172 bits (435), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 78/264 (29%), Positives = 127/264 (48%), Gaps = 5/264 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGV--PLRKA 70
           QR+ KV+A  GI SRRE ER+IA  +VKVNG  +      +    D + +DG    + + 
Sbjct: 4   QRIQKVLADQGICSRREAERLIAAGKVKVNGRPV-GLGDKMDPDYDKVSIDGKNVRIVRK 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            +    + HKP G +TT SD  GR TV D +  + + +  VGRLD ++EGLLL+T+DG  
Sbjct: 63  RQYTYIMLHKPRGYLTTRSDDRGRKTVMDLVADVPAMLRPVGRLDKDSEGLLLMTDDGAF 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWV 189
             +L  PS    ++YRV  + +  ++++  +  G+V+          + + T +     +
Sbjct: 123 INLLTHPSGGVGKLYRVTVNPRATEEQVVQMASGVVLDDGVRTQPCVIHVVTDEPGRTVL 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L EG+NR+I+++      +V RL R + GP +LG L  G  RE+ K  +        
Sbjct: 183 EITLHEGRNRQIRRMCSAVGLQVVRLKRSAEGPVKLGMLQPGEYRELKKSEVSALRNAAQ 242

Query: 250 LEEAQVNLDAPIYSSETLVRDRPN 273
                  +             R  
Sbjct: 243 KNTRSAPVREENAPRRPGPLPRKK 266


>gi|238853950|ref|ZP_04644307.1| RNA pseudouridine synthase family protein [Lactobacillus gasseri
           202-4]
 gi|282851629|ref|ZP_06260994.1| pseudouridylate synthase [Lactobacillus gasseri 224-1]
 gi|238833395|gb|EEQ25675.1| RNA pseudouridine synthase family protein [Lactobacillus gasseri
           202-4]
 gi|282557597|gb|EFB63194.1| pseudouridylate synthase [Lactobacillus gasseri 224-1]
          Length = 233

 Score =  172 bits (435), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 65/233 (27%), Positives = 104/233 (44%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I ++ V VNG L+      V  TD + VDG  +   +  
Sbjct: 1   MRIDKYLANMNVGSRKEVHSLIKKKVVTVNGELVTIPKQQVKETDLVAVDGNKIAYQQYH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      +  T                 +  +  VGRLD +T GLLLLTNDG LA  
Sbjct: 61  YFLLNKPKGVISATEDRSQQTVISLLKTKDRYQGIAPVGRLDKDTTGLLLLTNDGALAHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN--AWVT 190
           L  P+    +VYR +  G  D +      +G+++  G      ++ +  Q   N  + + 
Sbjct: 121 LLAPNKHVAKVYRAKIAGVPDPETAKKFAQGLILGDGTKLKPAKLKILKQDQDNNLSQIE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           + ++EGK  +IK++F     KV  L R+S G   L   L  G  +E+    ++
Sbjct: 181 IQIQEGKYHQIKRMFGAVGMKVLELDRVSMGKLHLPADLKRGEYKEIDLAEIK 233


>gi|222529211|ref|YP_002573093.1| pseudouridine synthase [Caldicellulosiruptor bescii DSM 6725]
 gi|222456058|gb|ACM60320.1| pseudouridine synthase [Caldicellulosiruptor bescii DSM 6725]
          Length = 233

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 57/230 (24%), Positives = 104/230 (45%), Gaps = 7/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G  SR +V+++I +  V VNG  +      +    D IEVDG   + +++
Sbjct: 1   MRLDKFLTHCGFGSRSQVKKLIREGIVTVNGKQIVEVDFKINPEEDIIEVDGRVAKFSKQ 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      + +             +    +  + +VGRLD + EGLL++T+DG    
Sbjct: 61  IYIMMNKPKGYVCSNEELASLTVFSLISDDLKYRDLHTVGRLDKDAEGLLIITDDGEYTH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            +  P  +  + Y VR   +VD++KLN  + GI++         + T+      +  V +
Sbjct: 121 RVISPKKRIEKEYLVRLEKEVDEEKLNEFENGIILDDGYKTLPAKYTII----DSTTVKL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + EGK  ++K++FE    KV  L R+  G   L  +L  G  R +  + 
Sbjct: 177 CIYEGKYHQVKRMFEAIGNKVVDLKRLRIGGLNLDQSLKPGEYRVMKVEE 226


>gi|308068498|ref|YP_003870103.1| RNA pseudouridine synthase (RNA-uridine isomerase) [Paenibacillus
           polymyxa E681]
 gi|305857777|gb|ADM69565.1| Hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Paenibacillus polymyxa E681]
          Length = 260

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 67/240 (27%), Positives = 111/240 (46%), Gaps = 10/240 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
             QR+ KV+   G  SR +++R + Q  + VNG + + + + V    D IEV+G  +   
Sbjct: 7   QTQRLDKVLTHMGYGSRSDIKRQMKQGMITVNGKITKDSGLQVHPYQDQIEVNGERVVFR 66

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   + L+  P  +  T    +       +          VGRLD +TEGLLLLTNDG L
Sbjct: 67  EYIYIMLHKPPGVISATEDSRERTVLDLLSAEERHFEPFPVGRLDKDTEGLLLLTNDGKL 126

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSN--- 186
           A  L  P     + Y     G V ++ ++    G+ +         Q+T+   +      
Sbjct: 127 AHELLSPRRHVPKTYEATVSGHVTEEDIHQFTAGVELDDGYVTLPAQLTILRHEHPYQAD 186

Query: 187 ----AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
               +++++ + EGK  ++K++FE    KV  L R + GP +L   L  GS RE++ + L
Sbjct: 187 GGVISYISLVIHEGKFHQVKRMFEAVGKKVTYLKRTAMGPLKLDEQLPMGSYRELTNEEL 246


>gi|77457719|ref|YP_347224.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           fluorescens Pf0-1]
 gi|77381722|gb|ABA73235.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           fluorescens Pf0-1]
          Length = 405

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 89/364 (24%), Positives = 145/364 (39%), Gaps = 11/364 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +  K+  +     +++ KV+AR G+ SRR+VE  IA  R+KVNG       + V   D I
Sbjct: 4   INQKDDQEIGPAGEKLQKVLARIGVGSRRDVESWIAAGRIKVNGKDAT-LGLRVDMHDAI 62

Query: 61  EVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            +DG  +++ E     R  +        + T        +           R I++GRLD
Sbjct: 63  TIDGKVIKREEAAESVRRVIMYNKPDGEICTRDDPEGRPTVFDKLPRPKEGRWINIGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           INT GLL+ T DG LA  L  PS +  R Y VR  G+VD + +  LK G+V++       
Sbjct: 123 INTTGLLMFTTDGELANRLMHPSYEMDREYAVRVRGEVDDEMIERLKAGVVLEDGPARFT 182

Query: 176 QVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ +GP  L   L  G  
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLNSDLPMGRW 242

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           RE+S+     L  ++G   +   Q+N  +         +    +         R    + 
Sbjct: 243 REMSQYEVDVLSAEVGLTPVAMPQLNAKSKDKLDRMQRKSSRPMARTERVRTLRPANGAP 302

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
              G    ++      R                    +  R E      +  + R +   
Sbjct: 303 IGAGPRPVREPQIEGERPGRKPAARPDGERGPRSPRPANGRTERGEGRGTPVADRPVDTK 362

Query: 351 SAKK 354
              K
Sbjct: 363 RPAK 366


>gi|116625544|ref|YP_827700.1| ribosomal large subunit pseudouridine synthase B [Candidatus
           Solibacter usitatus Ellin6076]
 gi|116228706|gb|ABJ87415.1| ribosomal large subunit pseudouridine synthase B [Candidatus
           Solibacter usitatus Ellin6076]
          Length = 249

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 81/243 (33%), Positives = 131/243 (53%), Gaps = 2/243 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++++AG++SRR+ E+++ + RV VNG ++           DHI+VDG  L+  + 
Sbjct: 4   ERLQKILSQAGVSSRRQAEKLMQEGRVTVNGSVITELGSKADLDRDHIKVDGRLLKAPKH 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP G VTT  DP+GR TV D L  +  RV  VGRLD ++EGLLLLTNDG LA 
Sbjct: 64  QIYIALNKPKGTVTTVHDPEGRETVMDLLHRVKERVYPVGRLDYHSEGLLLLTNDGELAN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +   +T   + Y V+  G +  ++    + G+ + G       + L ++   N W  V 
Sbjct: 124 SIMSAATHLEKTYVVKVTGTLTAEQEEKFRTGVPLSGRRTLPAGLKLLSR-AENPWYEVK 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L EG+N +I+ +F  F   V +L R+  GP +LGTL  G+ R + ++ + +         
Sbjct: 183 LTEGRNNQIRMMFRHFGKLVEKLKRVRIGPIELGTLKTGAFRYLDEEDVAKLKRAIQRSS 242

Query: 253 AQV 255
            + 
Sbjct: 243 QKP 245


>gi|258654177|ref|YP_003203333.1| pseudouridine synthase [Nakamurella multipartita DSM 44233]
 gi|258557402|gb|ACV80344.1| pseudouridine synthase [Nakamurella multipartita DSM 44233]
          Length = 249

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 73/234 (31%), Positives = 115/234 (49%), Gaps = 1/234 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK 69
               R+ KV+A AG+ASRR+ E +I   RVKV+GI++      +      + VDG  +  
Sbjct: 9   DDGVRLQKVLASAGVASRRKAEELIRDGRVKVDGIVVREMGTRIDPENAVVHVDGNRITT 68

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                    +K  G+++T SD  GR  +   L     R+  VGRLD+ +EGLLLLTNDG 
Sbjct: 69  RTDLVYLALNKERGVLSTMSDELGRPHIGQMLEDRSERLFHVGRLDMESEGLLLLTNDGD 128

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  PS    + Y     G + +D    LK G+ ++          +     + A V
Sbjct: 129 LAHRLTHPSYGVAKTYVAEVPGPIPKDLGRRLKAGVELEDGPAKVDSFDVMDLHHNRAVV 188

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            V + EG+   ++++ E  +  V+RL+R   GP QLG    G+ R+++   + +
Sbjct: 189 EVVIHEGRKHIVRRLLEAVDRPVSRLVRTQIGPVQLGHQRPGTLRKLNPVEVSQ 242


>gi|126668319|ref|ZP_01739278.1| Pseudouridine synthase, Rsu [Marinobacter sp. ELB17]
 gi|126627236|gb|EAZ97874.1| Pseudouridine synthase, Rsu [Marinobacter sp. ELB17]
          Length = 367

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 84/313 (26%), Positives = 131/313 (41%), Gaps = 7/313 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
           P+R+ K++ARAG+ SRRE+E  +   R+ VNG  +         +D  E+DG  L  A  
Sbjct: 56  PERIQKLLARAGVGSRREIEGWMDAGRLLVNGKPVT-PGQKATVSDVFELDGKRLEVAAA 114

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R  L        + T        +           R IS+GRLD+NT GL++ T D
Sbjct: 115 AEVLRRVLIYNKPEGEVTTRKDPEGRPTVFDRLPRLREHRWISIGRLDLNTTGLVMFTTD 174

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS++  R Y VR  G+VD   +  L+ G+ ++        ++     G N 
Sbjct: 175 GELANRLMHPSSEIDREYAVRIFGEVDDAMIERLRTGVTLEDGEAKFSDISAAGGTGMNR 234

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V L EG+NRE+++++E    +V+RL R+ YG   L   L  G   E+ +K +     
Sbjct: 235 WFHVTLLEGRNREVRRLWESQGVRVSRLKRVRYGSIFLPSRLTVGKWEELDQKAVDLLSR 294

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              L +  V    P  ++    + R         +       S    G  K     +   
Sbjct: 295 TVGLAKMAVPQQTPDEAAAQARQQRKAAPVTNRSNRAASSPGSKSGQGARKWAVADSKPQ 354

Query: 307 RRNLASNVWMAKG 319
           R    +     +G
Sbjct: 355 RSGGKARNDKPRG 367


>gi|238796852|ref|ZP_04640357.1| Ribosomal small subunit pseudouridine synthase A [Yersinia
           mollaretii ATCC 43969]
 gi|238719340|gb|EEQ11151.1| Ribosomal small subunit pseudouridine synthase A [Yersinia
           mollaretii ATCC 43969]
          Length = 235

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 57/238 (23%), Positives = 107/238 (44%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  +RV ++G +++  A  +     +  DG PL++    
Sbjct: 1   MRLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGATKLTPESDVRFDGNPLQQTLGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V +D       G+ +          Q+ +   +     V +
Sbjct: 121 ITSPRHHCEKTYLVTLEHPVAEDTAQRFADGVQLHNETSLTKPAQLEIIEPQ----LVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
            L EG+  ++K++F     +V  L R   G   L   L  G  R ++ + +     PH
Sbjct: 177 TLSEGRYHQVKRMFGAVGNRVLALHRERIGAMILDDDLAPGEYRPLTAEEIASVGAPH 234


>gi|303233760|ref|ZP_07320414.1| putative pseudouridine synthase B, ribosomal large subunit
           [Finegoldia magna BVS033A4]
 gi|302495194|gb|EFL54946.1| putative pseudouridine synthase B, ribosomal large subunit
           [Finegoldia magna BVS033A4]
          Length = 242

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 71/243 (29%), Positives = 120/243 (49%), Gaps = 2/243 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA++G  SRR  + +I   +V VNG +L   +  V  TD +EV+G  +   E  
Sbjct: 1   MRINKFIAQSGYCSRRNADELIKNSKVYVNGTILLDLSYQVNDTDIVEVEGKKINLKEDK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KPIG  +T  D         +L    +RV  VGRLD ++ GLL+LTNDG     
Sbjct: 61  IYIAINKPIGYASTVKDKFADK-KVVDLIKSDTRVYPVGRLDKDSHGLLILTNDGEFTYE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  ++Y V   G+ ++ ++  LK GI++ G      ++       ++    V +
Sbjct: 120 LTHPKFEHKKIYEVLVKGKPNKTEIKQLKDGILLDGYKLKKSKIEFIENVKNDTKYRVTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLLEE 252
            EG+NR+I+++F+F N  V  L R+  G +++   L +G  + +  K L    G +   +
Sbjct: 180 FEGRNRQIRRMFDFINHPVLDLKRVQIGNYKMDNSLKSGEYKLLKSKDLDLIRGNNDRSK 239

Query: 253 AQV 255
              
Sbjct: 240 TSK 242


>gi|225028067|ref|ZP_03717259.1| hypothetical protein EUBHAL_02337 [Eubacterium hallii DSM 3353]
 gi|224954615|gb|EEG35824.1| hypothetical protein EUBHAL_02337 [Eubacterium hallii DSM 3353]
          Length = 273

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 63/247 (25%), Positives = 110/247 (44%), Gaps = 7/247 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
            N  P R++K ++ AG+ SRR+ +R + Q R+ V+G   +     V +   I VDG  + 
Sbjct: 31  SNGEPMRLNKFLSDAGVCSRRQADRYVEQGRILVDGEPAQ-MGQKVHAGQDIRVDGKRVS 89

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            + +  +   +KP G+V T    +       +      R+  VGRLD ++EGL+L+TNDG
Sbjct: 90  VSRKQIVLAVNKPKGIVCTTEKRE--KDNIVDFIGYPERIYPVGRLDKDSEGLILMTNDG 147

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   +        + Y V  +  V    L  + +G+ I        +V           
Sbjct: 148 ELMNEILKARNYHEKEYEVTINRPVTNVFLKQMSEGVEILDTVTRPCKVKRTGV----YT 203

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E   ++V  L R+      LG+L  G  RE++ + L +     
Sbjct: 204 FRIILTQGLNRQIRRMCEACGYRVRELKRLRIMNIHLGSLPTGKYREITGEELSKLEKLA 263

Query: 249 LLEEAQV 255
             +   V
Sbjct: 264 GRKPGGV 270


>gi|183599526|ref|ZP_02961019.1| hypothetical protein PROSTU_03005 [Providencia stuartii ATCC 25827]
 gi|188021773|gb|EDU59813.1| hypothetical protein PROSTU_03005 [Providencia stuartii ATCC 25827]
          Length = 234

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 59/238 (24%), Positives = 105/238 (44%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +   +V V+  +++  AV V     +  +G  L      
Sbjct: 1   MRLDKFLSQQLGISRSLVARELRAGKVTVDDEIVKSGAVQVSPEQVVAYEGSVLVHVTGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V +  DP   + ++     +  ++ S GRLDI+T GL+LLT+DG  +  
Sbjct: 61  RYFMLHKPQGYVCSTDDPAHPTILYFIDEPLADKLHSAGRLDIDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + YRV     +  D      +G+++ G        Q+ +     S   V +
Sbjct: 121 ITSPKHHCEKTYRVELENDIADDVAKRFAEGVMLNGEKYPTKPAQLEVI----SPKEVLL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
            + EG+  ++K++F      V  L R   G   L   L  G  RE+++  +   + P 
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVCGLHRERIGDIWLDDDLAPGEYRELTEDEINSVIVPR 234


>gi|312127717|ref|YP_003992591.1| pseudouridine synthase [Caldicellulosiruptor hydrothermalis 108]
 gi|311777736|gb|ADQ07222.1| pseudouridine synthase [Caldicellulosiruptor hydrothermalis 108]
          Length = 233

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 55/230 (23%), Positives = 102/230 (44%), Gaps = 7/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G  SR +V+++I    V VNG  +      +    D +EVDG  ++ + R
Sbjct: 1   MRLDKFLTHCGFGSRSQVKKLIRGGIVTVNGKRIVEVDFKINPEEDVVEVDGRIVKFSRR 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      + +             +    +  + +VGRLD + EGLL++T+DG    
Sbjct: 61  IYIMMNKPKGYVCSNDDPASLTVFSLISDNLKYRDLHTVGRLDKDAEGLLIITDDGEYTH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            +  P  +  + Y VR   +VD+++L   + GI++         + T+      +  V +
Sbjct: 121 RVISPRKRIEKEYLVRLEKEVDEERLKEFENGIILDDGYKTLPAKYTII----DSTTVKL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
            + EGK  ++K++FE    KV  L R+  G   L   L  G  R + ++ 
Sbjct: 177 CIYEGKYHQVKRMFEAIGNKVVDLKRLRIGGLNLDESLKPGEYRVMKEEE 226


>gi|166154065|ref|YP_001654183.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis 434/Bu]
 gi|301335269|ref|ZP_07223513.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis L2tet1]
 gi|165930053|emb|CAP03536.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis 434/Bu]
          Length = 241

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 68/230 (29%), Positives = 102/230 (44%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R++K +A AG+ASRR+ + +I    V VNG +     V V    D +EV G  +   ++
Sbjct: 4   VRLNKFLASAGVASRRKCDEIIFAGSVTVNGRVATGPFVTVDEEFDSVEVGGQRIGAEKK 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               ++     L ++     G   V D L     R+ +VGRLD  T GL+L+TNDG  A 
Sbjct: 64  VYFMVHKPLGYLCSSERKFPGSKLVIDLLSHCPYRLFTVGRLDKETSGLILVTNDGEFAN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  PS    + Y ++    V    L  L  G VI G     + V    +      + + 
Sbjct: 124 RVIHPSFGITKEYLLKVSRDVTARDLETLMAGTVIDGKVVRPVSVKKVRRG----TIKII 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGK  EI+   E    ++  L RI  G   LG L  G  RE++   L 
Sbjct: 180 VNEGKKHEIRLFAEAAGLQLLELKRIRIGSLVLGGLPYGKYRELTDSELD 229


>gi|146309893|ref|YP_001174967.1| 23S rRNA pseudouridine synthase F [Enterobacter sp. 638]
 gi|145316769|gb|ABP58916.1| ribosomal large subunit pseudouridine synthase F [Enterobacter sp.
           638]
          Length = 289

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 59/291 (20%), Positives = 106/291 (36%), Gaps = 5/291 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   NQSTRLNKYISESGICSRREADRYIEQGNVFINGKRAA-IGDQVAPGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               L        +    +  DG      +  +  SR+  +GRLD +++GL+ LTN G L
Sbjct: 63  NEEDLVFIALNKPVGIVSTTEDGERDNIVDFVNHSSRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  +  D +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYVVTVNKPITDDFIRGMGAGVPILGTV----TKKCKVKKEAPFAFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L E       
Sbjct: 179 ITLVQGLNRQIRRMCEHFGFEVTKLERTRIMNVSLSGIPLGEWRDLNGDELIELFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
             +              ++          +                K+K  
Sbjct: 239 SSSDAKPKTKAKPKTQGIKRPVVNAPASAEKERNKPAGKRFVQPGRKKKGR 289


>gi|322388650|ref|ZP_08062250.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           infantis ATCC 700779]
 gi|321140570|gb|EFX36075.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           infantis ATCC 700779]
          Length = 240

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 64/233 (27%), Positives = 98/233 (42%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +    + SR EV+  +   RV VNG   + A + +   TD I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNFLKSGRVTVNGKKEKSAKLQIDEETDEICFDGQKLDYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    V  VGRLDI+T GLLLLTNDG LA 
Sbjct: 61  VYYMMNKPQGVISATEDPKHKTVLDLLDDYARAKEVFPVGRLDIDTHGLLLLTNDGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVT 190
            L  P     + Y  +  G +    +    KGI ++       ++ L     +   + V 
Sbjct: 121 ALLSPKRHVDKTYLAQVKGIMTDTDVETFAKGIPLKDFTCQPAKLELVSIDTEKDQSLVR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  ++K++  +   +V  L R++ G   L   L  G  R +SK+ L 
Sbjct: 181 VTIAEGKFHQVKRMVAYCGKEVVDLQRLTMGTLTLDEDLKRGEWRRLSKEELE 233


>gi|148994694|ref|ZP_01823798.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP9-BS68]
 gi|168489757|ref|ZP_02713956.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           SP195]
 gi|147927094|gb|EDK78134.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP9-BS68]
 gi|183571795|gb|EDT92323.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           SP195]
 gi|332075138|gb|EGI85608.1| hypothetical protein SPAR50_0282 [Streptococcus pneumoniae GA17570]
          Length = 240

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 102/233 (43%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    +  VGRLDI+T GLLLLTNDG LA 
Sbjct: 61  VYYMMNKPKGVISATEDPKHRTVLDLLDDLARSKEIFPVGRLDIDTHGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVT 190
           VL  P     + Y  +  G + Q+ + +  +GI ++         ++     + + + + 
Sbjct: 121 VLLSPKRHVDKTYLAQVKGIMTQEDVEIFAEGIPLKDFTCQPAILELVSIDTEKNQSQIR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 181 VTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELE 233


>gi|169832770|ref|YP_001693807.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           Hungary19A-6]
 gi|168995272|gb|ACA35884.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           Hungary19A-6]
          Length = 240

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 101/233 (43%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    V  VGRLDI+T GLLLLTNDG LA 
Sbjct: 61  VYYMMNKPKGVISATEDPKHRTVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVT 190
           VL  P     + Y  +  G + Q+ +    +GI ++         ++     + + + + 
Sbjct: 121 VLLSPKRHVDKTYLAQVKGIMTQEDVETFAEGIPLKDFTCQPAILELVSIDTEKNQSQIR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 181 VTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELE 233


>gi|310659128|ref|YP_003936849.1| pseudouridylate synthase [Clostridium sticklandii DSM 519]
 gi|308825906|emb|CBH21944.1| pseudouridylate synthase [Clostridium sticklandii]
          Length = 236

 Score =  172 bits (435), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 58/234 (24%), Positives = 107/234 (45%), Gaps = 13/234 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++  I+ +G+ SRR+ + +I   +VKVN  +       V   D +EVDG  ++  E  
Sbjct: 1   MRLNNYISSSGLCSRRKADELIKNNKVKVNSKIA-DLGYQVSEGDIVEVDGTIIKPKEDK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T  +    + V     +   R+  +GRLD ++EGL+LLTNDG +   
Sbjct: 60  VYIALYKPVGITCTTEEHIEGNIVDYV--NYKERIFPIGRLDKDSEGLILLTNDGDIVNR 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG------ICYGDMQVTLDTQKGSNA 187
           +        + Y V     +D   L  + +G+ I              ++   ++K    
Sbjct: 118 ILREENHHEKEYIVTVDKPLDSKTLKQMSQGVRIYNPVKNTYTTTKPCKIHKISEKS--- 174

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              + L +G NR+I+++ + F +KV +L R+      L  L  G  R +++  +
Sbjct: 175 -FKIVLSQGLNRQIRRMCQHFGYKVRKLKRVRILNITLDGLSYGKWRFLNQAEV 227


>gi|253688026|ref|YP_003017216.1| pseudouridine synthase [Pectobacterium carotovorum subsp.
           carotovorum PC1]
 gi|251754604|gb|ACT12680.1| pseudouridine synthase [Pectobacterium carotovorum subsp.
           carotovorum PC1]
          Length = 231

 Score =  172 bits (435), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 109/231 (47%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  QRV V+G +++  A  +    ++E DG PL++    
Sbjct: 1   MRLDKFLSQQLEISRSLVARELHAQRVTVDGEVVKSGAFKLSPEHNVEFDGNPLKQQNGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+LLT+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTILYFMDVPVAYKLHAAGRLDIDTTGLVLLTDDGKWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  Q  + Y V     + +D       G+ +                +K ++  V +
Sbjct: 121 ITSPKHQCEKTYLVTLEQPLAEDTAAQFTAGVQLHNEKNLTKPAT----LEKITDHVVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F     +V  L R   G   L   L  G  RE+S + +
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVVELHRERIGDIWLDSELEPGEFRELSDEEI 227


>gi|269127043|ref|YP_003300413.1| pseudouridine synthase [Thermomonospora curvata DSM 43183]
 gi|268312001|gb|ACY98375.1| pseudouridine synthase [Thermomonospora curvata DSM 43183]
          Length = 250

 Score =  172 bits (435), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 79/244 (32%), Positives = 121/244 (49%), Gaps = 2/244 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDH 59
           M       E+    R+ KV+A AG+ SRR+ ER+I + RVKV+G ++      V      
Sbjct: 1   MNTDTGTAEHKEGVRLQKVLAEAGLGSRRQCERLIVEGRVKVDGEVVSWLGARVDPAKAV 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           I VDG+ +      R +  +KP G+V+     +       +   +  R+  VGRLD +TE
Sbjct: 61  IHVDGLRVETRPEMRYYALNKPRGVVS-TMADERGRKSLADYVDVPERLFHVGRLDTDTE 119

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GL+LLTNDG LA  L  PS    +VY     G + +D    L+ GI ++       +  L
Sbjct: 120 GLILLTNDGDLAHRLTHPSFGVEKVYLAEIVGPIRRDLGRRLRAGIELEDGLAKADRFRL 179

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             Q G  A V + L EG+   ++++ +     V +L RI +GP +LG L  GS R ++ K
Sbjct: 180 VEQVGKRALVEITLHEGRKHIVRRMLKEAGHPVQKLARIRFGPIKLGRLKPGSLRALTIK 239

Query: 240 ILRE 243
            + E
Sbjct: 240 EVGE 243


>gi|169350449|ref|ZP_02867387.1| hypothetical protein CLOSPI_01217 [Clostridium spiroforme DSM 1552]
 gi|169292769|gb|EDS74902.1| hypothetical protein CLOSPI_01217 [Clostridium spiroforme DSM 1552]
          Length = 239

 Score =  172 bits (435), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 64/230 (27%), Positives = 108/230 (46%), Gaps = 4/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  GI +R+EV+  I +  V+VNG ++++    V    D I  DG  +     
Sbjct: 3   MRLDKLLANYGIGTRKEVKSYIRKGFVEVNGEIIKKDDYKVDYQKDEIIFDGELIEYRPY 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L      + +   D    + +   +      +  VGRLDI+TEGLLL++NDG  A 
Sbjct: 63  VYLMLNKPKGYV-SATKDNVHPTVIDLIVGYENYDLFPVGRLDIDTEGLLLISNDGDFAH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P+    +VY  R  G +++  +   K G+++          + +      +  V +
Sbjct: 122 RLMSPNRNHAKVYVARIAGIMNEFDILAFKDGVILDNGYKCKPANLKILEVFDDSCEVEI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + EGK  ++KK+ E  N KV  L RIS     +  +L  G  RE++K+ 
Sbjct: 182 EIFEGKFHQVKKMVEACNKKVTYLKRISIKGLTIDRSLQLGDFRELTKEE 231


>gi|321312541|ref|YP_004204828.1| putative 16S pseudouridylate synthase [Bacillus subtilis BSn5]
 gi|320018815|gb|ADV93801.1| putative 16S pseudouridylate synthase [Bacillus subtilis BSn5]
          Length = 239

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 58/224 (25%), Positives = 96/224 (42%), Gaps = 3/224 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A +G  SR+EV+ ++    V ++G   +    +V      + V G P+   E 
Sbjct: 1   MRLDKLLANSGYGSRKEVKAVVKAGAVMIDGKPAKDVKAHVNPDTQEVTVYGEPVDYREF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      L  T                +       GRLD +TEG LLLTNDG LA 
Sbjct: 61  IYLMMNKPQGVLSATEDSRQQTVVDLLTPEEMRFEPFPAGRLDKDTEGFLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V    Q+ ++ ++ L+ G+ I+G       +  + T    N  + +
Sbjct: 121 RLLSPKKHVPKTYEVHLKSQISREDISDLETGVYIEGGYKTKPARAEIKTNDSGNTVIYL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
            + EGK  ++K++ +    +V  L R+S G   L   L  G  R
Sbjct: 181 TITEGKYHQVKQMAKAVGNEVVYLKRLSMGRVSLDPALAPGEYR 224


>gi|288803207|ref|ZP_06408641.1| ribosomal large subunit pseudouridine synthase B [Prevotella
           melaninogenica D18]
 gi|288334248|gb|EFC72689.1| ribosomal large subunit pseudouridine synthase B [Prevotella
           melaninogenica D18]
          Length = 514

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 106/234 (45%), Gaps = 1/234 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +   P R++K +A AG+ SRRE +  I    V VNG +++     V+ TD +      + 
Sbjct: 274 DPNEPIRLNKYLANAGVCSRREADEFILSGAVTVNGEVVKELGSKVLRTDEVYFQDKLVS 333

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ++  + L      + T+      ++ +     +   R+  VGRLD NT G+LLLTNDG
Sbjct: 334 LEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKGACPERIYPVGRLDRNTTGVLLLTNDG 393

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     +VY V     V  + L  +  GI ++        +     +     
Sbjct: 394 DLASKLTHPKFLKKKVYHVFLDKAVTANDLQKISDGIELEDGEIKADAIEYADPQ-DQTQ 452

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           V + +  GKNR ++++FE   ++V +L R+ +       +  G  R +++K + 
Sbjct: 453 VGIEIHSGKNRIVRRIFESLGYRVVKLDRVQFAGLTKKNVRRGDWRFLTEKEVD 506


>gi|170660220|ref|YP_001740050.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. tomato str. DC3000]
 gi|170652970|gb|ACB22026.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. tomato str. DC3000]
 gi|331017433|gb|EGH97489.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. lachrymans str. M302278PT]
          Length = 408

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 93/371 (25%), Positives = 144/371 (38%), Gaps = 28/371 (7%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG         V   D I
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDAT-LGQRVDLHDAI 62

Query: 61  EVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            VDG  +++ E     R  +        + T        +           R I++GRLD
Sbjct: 63  SVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           INT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++       
Sbjct: 123 INTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPARFT 182

Query: 176 QVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIKQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKILR------------EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD 281
           RE+S+  +             +       ++    L                 +      
Sbjct: 243 REMSQYEVDILSAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVVRTLRPAAGA 302

Query: 282 FTRMKKNSSQKN-------GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREEN 334
                +   Q                   PV + +        +   +S  +   +R  +
Sbjct: 303 PATGDRTPRQPQITGSERDRPRGGDSTQRPVRKDSGKPGSRAPRPADNSRGTPVAERPSD 362

Query: 335 HRRSPSFPSKR 345
             + P+ P  +
Sbjct: 363 MNKRPAKPGPK 373



 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 18/100 (18%), Positives = 28/100 (28%), Gaps = 2/100 (2%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R    P +    +        +   + +D     S  P      +     +      K+ 
Sbjct: 308 RTPRQPQITGSERDRPRGGDSTQRPVRKDSGKPGSRAPRPADNSRGTPVAERPSDMNKRP 367

Query: 302 ATPVHRRNLAS--NVWMAKGIHSSFLSDSGQREENHRRSP 339
           A P  +R      N     G      + SGQR    RR P
Sbjct: 368 AKPGPKRVGIKLVNDDAPSGKRRGPPAGSGQRPGFGRRKP 407


>gi|160900456|ref|YP_001566038.1| pseudouridine synthase [Delftia acidovorans SPH-1]
 gi|160366040|gb|ABX37653.1| pseudouridine synthase [Delftia acidovorans SPH-1]
          Length = 467

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 81/356 (22%), Positives = 136/356 (38%), Gaps = 8/356 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          +   D I+V+
Sbjct: 103 KRVLLPQVDSPKLHKVLAQAGLGSRLEMEQLILEGRISVNNEPAHV-GQRIQFGDQIKVN 161

Query: 64  GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+R          +  +     +VT     +  +           +  SVGRLD+NTE
Sbjct: 162 GQPIRFRIDPPPARVIAYHKPVGEVVTHDDPQNRPTVFRKLPRLQHGKWQSVGRLDLNTE 221

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL T+ G LA  L  P     R Y  R  G + +++   L  G+ ++        +  
Sbjct: 222 GLLLFTSSGELANSLMHPRFGLEREYAARVLGALSKEEKQRLTDGVQLEDGVAAFGSIED 281

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E+ +
Sbjct: 282 GGGEGANCWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMVLPRGLKRGAWVELDQ 341

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDF--TRMKKNSSQKNGLS 296
             ++       ++        P            N +            +   +      
Sbjct: 342 ADIQSLASAAGMQARAPAAPKPPAGGRRGGPADRNTVRREGGGRYFDGNRPAPNAMLDGP 401

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           + K  A                G          Q+ +  R S  +    SL R   
Sbjct: 402 RAKPAAKGGKADGGQGQGKGQGGAGGRGKGGGSQQPDPMRTSVGYIGSDSLSRARQ 457


>gi|320529017|ref|ZP_08030109.1| hypothetical protein HMPREF9555_00165 [Selenomonas artemidis F0399]
 gi|320138647|gb|EFW30537.1| hypothetical protein HMPREF9555_00165 [Selenomonas artemidis F0399]
          Length = 244

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 79/231 (34%), Positives = 130/231 (56%), Gaps = 1/231 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++A AGIASRR  E MI   RV V+G+ +        +    I VDG+P++K   
Sbjct: 4   ERLQKILANAGIASRRSAEEMIRAGRVTVDGVCVTELGRKYDAALHEIAVDGIPVQKETE 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP+G ++T  D  GR TV D LP   +R+  VGRLD +TEGLLL+TNDG + +
Sbjct: 64  RVYLLLNKPVGYLSTARDDRGRKTVLDLLPHTSARLYPVGRLDADTEGLLLITNDGAMTQ 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  +VYR    G +  +KL  L+ GI+++       ++ + +   +   + + 
Sbjct: 124 GLLHPRYEIDKVYRAEIEGALTPEKLRHLRGGILLEDGITAPARMRILSADDTVTTIEIV 183

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + EG+NR+++++F     +V RL R+ +    L  L  G++R +S + +RE
Sbjct: 184 IHEGRNRQVRRMFAAVGCRVLRLRRVRFAMLTLKDLPCGASRPLSAEEIRE 234


>gi|296164607|ref|ZP_06847174.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           parascrofulaceum ATCC BAA-614]
 gi|295900026|gb|EFG79465.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           parascrofulaceum ATCC BAA-614]
          Length = 247

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 75/236 (31%), Positives = 110/236 (46%), Gaps = 4/236 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           +    R+ KV+++AGIASRR  E++I   RV+V+G ++      V      I VDG  + 
Sbjct: 3   DTEGIRLQKVLSQAGIASRRAAEKLIIDGRVEVDGRVVTELGTRVDPDASVIRVDGARVV 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLLT 125
             E       +KP G+ +T SD  GR  + D +            VGRLD +TEGL+LLT
Sbjct: 63  LDESLVYLALNKPRGMHSTMSDDRGRPCIGDLVERKVRGNKNLFHVGRLDADTEGLILLT 122

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  PS +  + Y     G V +     LK GI +           +      
Sbjct: 123 NDGELAHRLMHPSHEVPKTYLATVTGSVPRGIGKKLKAGIELDDGPARVDDFAVVDAIPG 182

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              V V L EG+NR ++++     + V  L+R   GP  LG    GS R +++  +
Sbjct: 183 KTLVRVVLHEGRNRIVRRLLGAAGFPVEALVRTDIGPVSLGKQRPGSIRALNQGEV 238


>gi|283785995|ref|YP_003365860.1| ribosomal small subunit pseudouridine synthase A [Citrobacter
           rodentium ICC168]
 gi|282949449|emb|CBG89062.1| ribosomal small subunit pseudouridine synthase A [Citrobacter
           rodentium ICC168]
          Length = 231

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 103/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G ++  AA  ++    +E DG  L +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRASRVTVDGEIVRNAAFKLLPEHAVEYDGNTLVQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +          ++ +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTRPAELEVI----TPTQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVALHRERIGAIALDADLAPGEYRPLTEEEI 227


>gi|253577342|ref|ZP_04854659.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
 gi|251843242|gb|EES71273.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
          Length = 234

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 55/230 (23%), Positives = 103/230 (44%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+  G  SRRE ++++   +V +NG+            D + V+G P+      
Sbjct: 1   MRINKFISETGFCSRREADKLVESGQVTINGVKA-VLGSQAEPGDDVRVNGRPIAAKRSK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++       +  T +          +      R+  +GRLD ++EGL+LLT+DG +   
Sbjct: 60  HVY-IALNKPVGITCTTETHVKGNIVDFVGHPERIFPIGRLDKDSEGLILLTSDGDIVNK 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +    +  + +G+ I G      +VT      S+    + L
Sbjct: 119 ILRAEGKHEKEYIVTVDRPITPSFVKAMSEGVKILGEMTLPCKVTRV----SDRVFRIIL 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            EGKNR+I+++     ++V RL RI      LG    G+ R+++++  RE
Sbjct: 175 TEGKNRQIRRMCSALGYEVRRLQRIRIMNIHLGQQKVGTWRDLTEQEKRE 224


>gi|298293868|ref|YP_003695807.1| RNA-binding S4 domain protein [Starkeya novella DSM 506]
 gi|296930379|gb|ADH91188.1| RNA-binding S4 domain protein [Starkeya novella DSM 506]
          Length = 764

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 140/329 (42%), Positives = 196/329 (59%), Gaps = 3/329 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +RV+KVIARAG+ SRRE+E  I   RV VNG +LE  A  V   D I VDG PL   E
Sbjct: 28  EAERVAKVIARAGLGSRREIEEWILAGRVAVNGEVLESPARTVTPEDAITVDGNPLPAKE 87

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RTRL++YHKP G+VTT+ DP+GR T+F+ LP+   R++SVGRLD+NTEGL+LLTNDGGL+
Sbjct: 88  RTRLFMYHKPKGVVTTNYDPEGRPTLFEILPAGLPRLVSVGRLDLNTEGLILLTNDGGLS 147

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           RVLELP T WLR YRVR  G + QDKL+ L +G+ + G+ YG ++  LD  +G+N+W+T+
Sbjct: 148 RVLELPETGWLRRYRVRAKGDITQDKLDALMEGVTVDGVHYGPIEAKLDRVQGANSWLTL 207

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            LREGKNRE++ V      +VNRLIR+SYGPFQLG +  G   EV  ++L +QLG  L  
Sbjct: 208 ALREGKNREVRNVLGSLGLEVNRLIRVSYGPFQLGEIPQGEVEEVRTRVLADQLGEALSA 267

Query: 252 EAQVNLDAP---IYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
            A  + + P       +   +      ++         ++  ++  +  +      V   
Sbjct: 268 AAGADFEGPLFNHNDEDEAPKAGKPRGAKARYAAAEGAEDRHRRRPIDVEPGEGRSVTAG 327

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRR 337
            +A        +     +++    E  RR
Sbjct: 328 VVADRKGRQVLVQRVRSTEAEPEPEGRRR 356



 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 15/124 (12%), Positives = 37/124 (29%)

Query: 227 TLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
            +  G  R V+  ++ ++ G  +L +   + +A           R     E   +  R  
Sbjct: 315 DVEPGEGRSVTAGVVADRKGRQVLVQRVRSTEAEPEPEGRRRPQREVERREAEREAARAP 374

Query: 287 KNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +    ++   ++     P      A      + + +       +  +     PS P +  
Sbjct: 375 RAPRGRSEGGERTFRKRPSRPFEEAPGGEEERPMRARPARTPSRDRQIGGPRPSRPREDR 434

Query: 347 LRRT 350
             R 
Sbjct: 435 APRD 438



 Score = 35.9 bits (81), Expect = 9.6,   Method: Composition-based stats.
 Identities = 9/94 (9%), Positives = 19/94 (20%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
                       R       E P    R +    + +   + ++       R      + 
Sbjct: 532 RVKSEQHRGRPDRFEERGEGERPARPFRERAPRPEGDRAPRGERPFRERTPRAEGDRPFR 591

Query: 317 AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
            +G          +R        SF  +      
Sbjct: 592 ERGPRPEGDRPFRERGPRPEGERSFRPRAPRPEG 625


>gi|163786127|ref|ZP_02180575.1| pseudouridine synthase, Rsu [Flavobacteriales bacterium ALC-1]
 gi|159877987|gb|EDP72043.1| pseudouridine synthase, Rsu [Flavobacteriales bacterium ALC-1]
          Length = 255

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 60/263 (22%), Positives = 115/263 (43%), Gaps = 10/263 (3%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + +N T  R++K ++ AG  SRRE +R+I   RV +N  ++      V S D ++VDG  
Sbjct: 1   MSDNLT--RLNKYLSEAGYCSRREADRLIDAGRVTIND-VVPEMGTKVASGDIVKVDGEI 57

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           + + ++  ++L       +   +D         +  +   R+  +GRLD  +EGL+LLT+
Sbjct: 58  IGERKQGFVYLAFNKPVGIVCTTDTRVEKDNIIDYINYPKRIFPIGRLDKPSEGLILLTD 117

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKG 184
           DG +   +   S    + Y V     + Q  +  +  GI I+  G      +     +K 
Sbjct: 118 DGDIVNKILRASNNHEKEYIVTVDKPISQTFVARMAGGIYIEELGKRTKKCE----VKKI 173

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
                ++ L +G NR+I+++ E+ N++V  L R+     +L  +  G  RE++K+  +  
Sbjct: 174 DKFTFSIILTQGLNRQIRRMCEYLNYEVQTLKRVRIMNIKL-DMPLGKYRELTKEEFKTL 232

Query: 245 LGPHLLEEAQVNLDAPIYSSETL 267
                  +               
Sbjct: 233 SNLISESKKTFEAKQHTPRRNRR 255


>gi|110806162|ref|YP_689682.1| 16S rRNA pseudouridylate synthase A [Shigella flexneri 5 str. 8401]
 gi|26108971|gb|AAN81174.1|AE016763_133 Ribosomal small subunit pseudouridine synthase A [Escherichia coli
           CFT073]
 gi|91073047|gb|ABE07928.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           UTI89]
 gi|110615710|gb|ABF04377.1| 16S pseudouridylate 516 synthase [Shigella flexneri 5 str. 8401]
 gi|281601638|gb|ADA74622.1| Ribosomal small subunit pseudouridine synthase A [Shigella flexneri
           2002017]
          Length = 263

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 102/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    
Sbjct: 33  MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGP 92

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 93  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHR 152

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 153 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEVI----TPTQVRL 208

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 209 TISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 259


>gi|238754970|ref|ZP_04616319.1| Ribosomal large subunit pseudouridine synthase B [Yersinia ruckeri
           ATCC 29473]
 gi|238706829|gb|EEP99197.1| Ribosomal large subunit pseudouridine synthase B [Yersinia ruckeri
           ATCC 29473]
          Length = 321

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 89/320 (27%), Positives = 135/320 (42%), Gaps = 10/320 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN-VMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I Q RV V+G +        V  +  I +DG  L   E
Sbjct: 2   SEKLQKVLARAGHGSRREIEAIIQQGRVSVDGKVATLGDRVDVTPSTKIRLDGRILPITE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T        +          SR ++VGRLD+NT GLLL T 
Sbjct: 62  SEEAVCRVLAYYKPEGELCTRSDPDGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQ+D +K+ LL +G+ ++        ++    +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQIDDEKIKLLSRGVQLEDGPAAFRTISFQGGEGLN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK---ILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  K    LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELDLKATNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E +   +   +++ ++      +     R            +           S ++   
Sbjct: 242 ELVELDVETVSKLPVEKDRRRVKANQIRRAVKRHTEVAGRQQTAGRQGSARKSSTRQNTG 301

Query: 303 TPVHRRNLASNVWMAKGIHS 322
                    S    A     
Sbjct: 302 NTASSGAPVSGRRRAPAKRG 321


>gi|304397506|ref|ZP_07379384.1| pseudouridine synthase [Pantoea sp. aB]
 gi|304355124|gb|EFM19493.1| pseudouridine synthase [Pantoea sp. aB]
          Length = 239

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 102/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I++    SR    R I  QRV VNG ++   A  ++    +  DG  L+     
Sbjct: 1   MRLDKFISQQLEISRAIAHREIRGQRVTVNGEVVRDTAFKLLPDHEVVYDGNVLQMQTGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+LLT+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTIIYFIEEPMSFKLHAAGRLDIDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + YRV     +  D       G+ +          Q+ + T       V +
Sbjct: 121 ITSPRHHCEKTYRVTLESPISDDTAAQFTAGVQLHNEKSLTKPAQLEVITPTD----VRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            L EG+  ++K++F     +V  L R   G   L   L  G  R +++  +
Sbjct: 177 TLSEGRYHQVKRMFAAVGNRVIELHRERIGDIVLDEDLEPGEYRALTEDEI 227


>gi|229060031|ref|ZP_04197402.1| Pseudouridine synthase [Bacillus cereus AH603]
 gi|228719250|gb|EEL70858.1| Pseudouridine synthase [Bacillus cereus AH603]
          Length = 227

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 61/227 (26%), Positives = 107/227 (47%), Gaps = 7/227 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ AG ASRR  +++I +++V +NG + +     V   D + V+G  LR A   
Sbjct: 1   MRINKFISEAGKASRRGADKLINERKVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCTSEKAV--KGNIIDLVNHPLRINHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  + L  +  G+ I        ++T      S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPEFLEKMAAGVKILDTKTLPCEITQL----SKYEFEIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK 
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKKE 220


>gi|255281792|ref|ZP_05346347.1| ribosomal small subunit pseudouridine synthase A [Bryantella
           formatexigens DSM 14469]
 gi|255267859|gb|EET61064.1| ribosomal small subunit pseudouridine synthase A [Bryantella
           formatexigens DSM 14469]
          Length = 250

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 110/250 (44%), Gaps = 5/250 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
              R+ K++A  G  +R EV+  I + RV VNG + + A   V +  D I +DG P+   
Sbjct: 2   ETIRLDKLLAATGAGTRSEVKNAIRKGRVTVNGAVCKSADSKVDADKDVICLDGAPVVYT 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                 LY     + T   D    + +     +    +  VGRLD++TEGLLL+TNDG L
Sbjct: 62  RYEYHMLYKPAGCV-TAVRDARYPTVMDYISSARKKDLFPVGRLDLDTEGLLLITNDGEL 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y  R  G+V  + +   ++GI I +       ++ +    G  + V
Sbjct: 121 AHRLLAPGWHVDKTYYARVQGEVTAEDIRRFQEGIDIGEKRPTMPAELEILAA-GQESEV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
            V + EGK  ++K++F      V  L R+  G   L   L AG +R ++++         
Sbjct: 180 RVTIHEGKYHQVKRMFAAIGKPVLYLKRLRMGSLTLDENLQAGGSRLLTQEETEALHSLA 239

Query: 249 LLEEAQVNLD 258
             +  +    
Sbjct: 240 ASDIRKGEAH 249


>gi|229030086|ref|ZP_04186150.1| Pseudouridine synthase [Bacillus cereus AH1271]
 gi|228731256|gb|EEL82174.1| Pseudouridine synthase [Bacillus cereus AH1271]
          Length = 248

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 67/242 (27%), Positives = 115/242 (47%), Gaps = 7/242 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K  ++++    R++K I+ AG ASRR  +++I ++RV +NG + +     V   D +
Sbjct: 1   MSLKFCLEKDVPNLRINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDV 59

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            V+G  LR A        +KP+G+  T            +L +   R+  +GRLD +++G
Sbjct: 60  RVNGEQLRIARDHVYIALNKPVGITCTSEKAV--KGNIIDLVNHPLRISHIGRLDKDSDG 117

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+LLTNDG +   +     +  + Y V     +  D L  +  G+ I G      ++T  
Sbjct: 118 LILLTNDGDIVNEILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEITQL 177

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
               S     + L +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK 
Sbjct: 178 ----SKYEFNIILTQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKKE 233

Query: 241 LR 242
            R
Sbjct: 234 KR 235


>gi|160947164|ref|ZP_02094331.1| hypothetical protein PEPMIC_01096 [Parvimonas micra ATCC 33270]
 gi|158446298|gb|EDP23293.1| hypothetical protein PEPMIC_01096 [Parvimonas micra ATCC 33270]
          Length = 230

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 76/229 (33%), Positives = 124/229 (54%), Gaps = 4/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA +G  SRR  + ++ Q +V VNG L  +  +++   D + V+G  ++  E  
Sbjct: 1   MRINKFIANSGYCSRRNADLLLEQGKVFVNGKLATK-GIDISENDEVLVEGKKIKLEEAK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + +L +KPIG  +T         V  +L     R+  VGRLD ++ GLLLLTNDG LA  
Sbjct: 60  KYYLLNKPIGYSSTAKAQFQEKIV-LDLIDSKERIYPVGRLDKDSFGLLLLTNDGDLAFR 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  PS    + Y V+    + +  L  L  GI+++G      +  +      +  V V L
Sbjct: 119 LTHPSHNVEKEYIVKVDKTLKESDLKKLSSGIMLEGKITRKARFEML--DFKSNIVKVFL 176

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +EG+NR+I+K+F+  ++ V  L RI++G  +LG L  G+ RE+SK+ + 
Sbjct: 177 KEGRNRQIRKMFKTLDYNVISLERIAFGKIKLGKLKVGNYRELSKEEIE 225


>gi|331697591|ref|YP_004333830.1| pseudouridine synthase Rsu [Pseudonocardia dioxanivorans CB1190]
 gi|326952280|gb|AEA25977.1| pseudouridine synthase Rsu [Pseudonocardia dioxanivorans CB1190]
          Length = 252

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 70/243 (28%), Positives = 113/243 (46%), Gaps = 7/243 (2%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDG 64
           +  +N    R+ KV+A+AG+ASRR  E +IA  RV V+G ++      V      + VDG
Sbjct: 1   MTTQNSDGVRLQKVLAQAGVASRRAAEELIAAGRVSVDGEIVREMGRRVDPDTAVVHVDG 60

Query: 65  VPLRKAERTRLWLYHKPIGLVTT------HSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
             +   +       +KP G+++T                   L +   R+  VGRLD +T
Sbjct: 61  SRIVLRDDLVYLALNKPRGMLSTMSDDRGRECVGDLVADRAELLNQAGRLFHVGRLDADT 120

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLLLLTNDG L   L  PS +  + Y     GQV +D    L+ G+ ++          
Sbjct: 121 EGLLLLTNDGELGHRLMHPSFEVQKTYVAEVAGQVARDVGKRLRTGVELEDGPVVVHSFR 180

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           L    G  + V + L EG+   ++++ +   + V RL+R + G  +LG    G  R +++
Sbjct: 181 LVDSSGGRSMVEIVLHEGRKHVVRRLMDEVGYPVLRLVRTAIGDVRLGDQRPGKLRPLNQ 240

Query: 239 KIL 241
             +
Sbjct: 241 AEV 243


>gi|289550491|ref|YP_003471395.1| Ribosomal small subunit pseudouridine synthase A [Staphylococcus
           lugdunensis HKU09-01]
 gi|289180023|gb|ADC87268.1| Ribosomal small subunit pseudouridine synthase A [Staphylococcus
           lugdunensis HKU09-01]
          Length = 230

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 104/232 (44%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G  +R EV++ + +  V VNG + + A   +    D +++ G  +   E 
Sbjct: 2   MRLDKFLAHMGQGTRTEVKQSLKKGNVTVNGKVEKSAKTQIDPHHDVVQIHGHQIDYVET 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L      + +   DP   + +       +  +  VGRLD +TEGLLL+TNDG  + 
Sbjct: 62  VYLMLNKPKGYI-SATEDPKQATVIDLIKDYKYLDLFPVGRLDKDTEGLLLITNDGQFSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+    + Y V     V +D   + K+G+++        ++T+     S     V 
Sbjct: 121 NLMNPNKHVAKTYLVTSKYPVTKDNQYMFKQGVMLSDGLTKPAELTIIDDYHS----KVT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           + EG+  +IK++F     +V  L RI     +L   L  G  R +++  + +
Sbjct: 177 IYEGRYHQIKRMFHSIENEVLELKRIQIANLRLDEELDEGQYRVLTQTDIEQ 228


>gi|289428195|ref|ZP_06429891.1| pseudouridylate synthase [Propionibacterium acnes J165]
 gi|295130922|ref|YP_003581585.1| pseudouridylate synthase [Propionibacterium acnes SK137]
 gi|289158576|gb|EFD06783.1| pseudouridylate synthase [Propionibacterium acnes J165]
 gi|291375273|gb|ADD99127.1| pseudouridylate synthase [Propionibacterium acnes SK137]
 gi|313764054|gb|EFS35418.1| conserved hypothetical protein [Propionibacterium acnes HL013PA1]
 gi|313771915|gb|EFS37881.1| conserved hypothetical protein [Propionibacterium acnes HL074PA1]
 gi|313807148|gb|EFS45643.1| conserved hypothetical protein [Propionibacterium acnes HL087PA2]
 gi|313809640|gb|EFS47376.1| conserved hypothetical protein [Propionibacterium acnes HL083PA1]
 gi|313816404|gb|EFS54118.1| conserved hypothetical protein [Propionibacterium acnes HL059PA1]
 gi|313819344|gb|EFS57058.1| conserved hypothetical protein [Propionibacterium acnes HL046PA2]
 gi|313819993|gb|EFS57707.1| conserved hypothetical protein [Propionibacterium acnes HL036PA1]
 gi|313823215|gb|EFS60929.1| conserved hypothetical protein [Propionibacterium acnes HL036PA2]
 gi|313824997|gb|EFS62711.1| conserved hypothetical protein [Propionibacterium acnes HL063PA1]
 gi|313827299|gb|EFS65013.1| conserved hypothetical protein [Propionibacterium acnes HL063PA2]
 gi|313829960|gb|EFS67674.1| conserved hypothetical protein [Propionibacterium acnes HL007PA1]
 gi|313833036|gb|EFS70750.1| conserved hypothetical protein [Propionibacterium acnes HL056PA1]
 gi|314914915|gb|EFS78746.1| conserved hypothetical protein [Propionibacterium acnes HL005PA4]
 gi|314917860|gb|EFS81691.1| conserved hypothetical protein [Propionibacterium acnes HL050PA1]
 gi|314919749|gb|EFS83580.1| conserved hypothetical protein [Propionibacterium acnes HL050PA3]
 gi|314924832|gb|EFS88663.1| conserved hypothetical protein [Propionibacterium acnes HL036PA3]
 gi|314930009|gb|EFS93840.1| conserved hypothetical protein [Propionibacterium acnes HL067PA1]
 gi|314956415|gb|EFT00727.1| conserved hypothetical protein [Propionibacterium acnes HL027PA1]
 gi|314957284|gb|EFT01387.1| conserved hypothetical protein [Propionibacterium acnes HL002PA1]
 gi|314960611|gb|EFT04713.1| conserved hypothetical protein [Propionibacterium acnes HL002PA2]
 gi|314967733|gb|EFT11832.1| conserved hypothetical protein [Propionibacterium acnes HL037PA1]
 gi|314972874|gb|EFT16971.1| conserved hypothetical protein [Propionibacterium acnes HL053PA1]
 gi|314975703|gb|EFT19798.1| conserved hypothetical protein [Propionibacterium acnes HL045PA1]
 gi|314978089|gb|EFT22183.1| conserved hypothetical protein [Propionibacterium acnes HL072PA2]
 gi|314984113|gb|EFT28205.1| conserved hypothetical protein [Propionibacterium acnes HL005PA1]
 gi|314986250|gb|EFT30342.1| conserved hypothetical protein [Propionibacterium acnes HL005PA2]
 gi|314989536|gb|EFT33627.1| conserved hypothetical protein [Propionibacterium acnes HL005PA3]
 gi|315080909|gb|EFT52885.1| conserved hypothetical protein [Propionibacterium acnes HL078PA1]
 gi|315084832|gb|EFT56808.1| conserved hypothetical protein [Propionibacterium acnes HL027PA2]
 gi|315086005|gb|EFT57981.1| conserved hypothetical protein [Propionibacterium acnes HL002PA3]
 gi|315088276|gb|EFT60252.1| conserved hypothetical protein [Propionibacterium acnes HL072PA1]
 gi|315095697|gb|EFT67673.1| conserved hypothetical protein [Propionibacterium acnes HL038PA1]
 gi|315098205|gb|EFT70181.1| conserved hypothetical protein [Propionibacterium acnes HL059PA2]
 gi|315101641|gb|EFT73617.1| conserved hypothetical protein [Propionibacterium acnes HL046PA1]
 gi|315109460|gb|EFT81436.1| conserved hypothetical protein [Propionibacterium acnes HL030PA2]
 gi|327327900|gb|EGE69674.1| ribosomal large subunit pseudouridine synthase B [Propionibacterium
           acnes HL096PA3]
 gi|327330039|gb|EGE71792.1| ribosomal large subunit pseudouridine synthase B [Propionibacterium
           acnes HL096PA2]
 gi|327442730|gb|EGE89384.1| hypothetical protein HMPREF9570_02678 [Propionibacterium acnes
           HL043PA1]
 gi|327443872|gb|EGE90526.1| hypothetical protein HMPREF9571_02471 [Propionibacterium acnes
           HL043PA2]
 gi|327443940|gb|EGE90594.1| hypothetical protein HMPREF9568_01854 [Propionibacterium acnes
           HL013PA2]
 gi|327452345|gb|EGE98999.1| hypothetical protein HMPREF9581_01384 [Propionibacterium acnes
           HL087PA3]
 gi|327452780|gb|EGE99434.1| hypothetical protein HMPREF9586_02253 [Propionibacterium acnes
           HL083PA2]
 gi|328752647|gb|EGF66263.1| hypothetical protein HMPREF9588_02444 [Propionibacterium acnes
           HL025PA2]
 gi|328753801|gb|EGF67417.1| hypothetical protein HMPREF9579_01456 [Propionibacterium acnes
           HL087PA1]
 gi|328755029|gb|EGF68645.1| hypothetical protein HMPREF9563_01406 [Propionibacterium acnes
           HL020PA1]
 gi|328761441|gb|EGF74967.1| ribosomal large subunit pseudouridine synthase B [Propionibacterium
           acnes HL099PA1]
 gi|332675803|gb|AEE72619.1| ribosomal large subunit pseudouridine synthase B [Propionibacterium
           acnes 266]
          Length = 245

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 77/241 (31%), Positives = 109/241 (45%), Gaps = 2/241 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
            N    R+ KV+A+AG+ASRR  E MIA  RV+VNG L+      V    D I VDG  +
Sbjct: 2   SNEQGIRLQKVLAQAGLASRRAAEDMIAAGRVEVNGELIVEQGRRVDPERDEIRVDGSRI 61

Query: 68  R-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                     L      + T                    R+  VGRLD  T GL+LLTN
Sbjct: 62  PTARRHVYYVLNKPQGVVSTMDDPEGRPCLSDLEGVPRGIRLFHVGRLDTETSGLILLTN 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  A  +  PS + L+ Y     G+VD   +  L KG+ ++        V L      +
Sbjct: 122 DGEFANRMTHPSYKVLKTYLADVEGRVDDKVIRRLSKGLTLEDGPVKPDAVRLVQAGEEH 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + V V L EG+NR ++++ +     V RL R + GP +L  L  G  RE++ + L + L 
Sbjct: 182 SLVEVSLHEGRNRIVRRIMDSVAHPVRRLSRTAIGPVRLKRLGRGDMRELTHEELGQLLD 241

Query: 247 P 247
            
Sbjct: 242 L 242


>gi|218554753|ref|YP_002387666.1| 16S rRNA pseudouridylate synthase A [Escherichia coli IAI1]
 gi|218361521|emb|CAQ99110.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli IAI1]
          Length = 231

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 102/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEVI----TPTQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 177 IISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 227


>gi|168485953|ref|ZP_02710461.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           CDC1087-00]
 gi|183570820|gb|EDT91348.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           CDC1087-00]
          Length = 240

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 101/233 (43%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYMMNKPKGVISATEDPKHRTVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNNGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVT 190
           VL  P     + Y  +  G + Q+ +    +GI ++         ++     + + + + 
Sbjct: 121 VLLSPKRHVDKTYLAQVKGIMTQEDVETFAEGIPLKDFTCQPAILELVSIDTEKNQSQIR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 181 VTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELE 233


>gi|296124373|ref|YP_003632151.1| pseudouridine synthase [Planctomyces limnophilus DSM 3776]
 gi|296016713|gb|ADG69952.1| pseudouridine synthase [Planctomyces limnophilus DSM 3776]
          Length = 554

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 83/338 (24%), Positives = 138/338 (40%), Gaps = 9/338 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
           E    +R+ KV+A AG  SRR  E  I   RV ++G++ +   V V  +   + VDG  L
Sbjct: 32  EASAGERLQKVLASAGYGSRRACEEYIEMGRVTIDGVVAKELGVRVDLSRQKVAVDGEKL 91

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R  E+     +     L T          +    P++     +VGRLD  TEGLL++TND
Sbjct: 92  RVEEKRYFLFHKPAGVLCTNSDPAGRTRVIDCFPPNVGRL-FTVGRLDDGTEGLLIVTND 150

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P     R+YR    G    + +N L +G+      +    V     +GS  
Sbjct: 151 GDLAERLTHPKFGIPRIYRAVVAGNPSTEAINQLLEGLYFAEGRFRMSSVNRVKSQGSAT 210

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + + +REG+NREI+++      KV +L R  +GP +LG L  G+ R++S++ L      
Sbjct: 211 VLEITMREGQNREIRRLLARVGHKVMKLKRTHFGPIKLGDLERGAHRKLSEEEL------ 264

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               +  +       +     R R    +      TR   + +   G + + +L      
Sbjct: 265 -SKLQDVITGKWKEPAPRKPQRTRDAGKATSAGGVTRASSSRAGSAGATPRARLERTALP 323

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
                 + +         S    + +      + P +R
Sbjct: 324 ATGLEPLTIPGSKLKRLGSSKALKSQVLNSPEANPKRR 361


>gi|238784264|ref|ZP_04628276.1| Ribosomal small subunit pseudouridine synthase A [Yersinia
           bercovieri ATCC 43970]
 gi|238714831|gb|EEQ06831.1| Ribosomal small subunit pseudouridine synthase A [Yersinia
           bercovieri ATCC 43970]
          Length = 235

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 57/238 (23%), Positives = 109/238 (45%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    
Sbjct: 1   MRLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPESDVRFDGNPLQQTLGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V +D       G+ +          Q+ +   +     V +
Sbjct: 121 ITSPRHHCEKTYLVTLEHPVAEDTAQRFADGVQLHNETSLTKPAQLEIIEPQ----LVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
            L EG+  ++K++F     +V  L R   G  +L   L  G  R ++ + +     PH
Sbjct: 177 TLSEGRYHQVKRMFGAVGNRVLALHRERIGAMKLDDDLAPGEYRPLTAEEIASVGAPH 234


>gi|224499021|ref|ZP_03667370.1| hypothetical protein LmonF1_04688 [Listeria monocytogenes Finland
           1988]
 gi|254831233|ref|ZP_05235888.1| hypothetical protein Lmon1_07742 [Listeria monocytogenes 10403S]
          Length = 233

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 98/231 (42%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D I V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQITVHGTPVVYQEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T  +               +    VGRLD +TEGLL++TNDG LA 
Sbjct: 61  VYFMLHKPQNVVSATEDNVSETVIDLLAQEDTLTDPFPVGRLDKDTEGLLIITNDGTLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y  +  G V    +     GI +          + + T    N    V
Sbjct: 121 NLLSPKKHIDKTYYAKIDGDVTAADVEAFAAGIELDDGYTCKPASLEIITPNEIN----V 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            ++EGK  ++K++F      V+ L RIS G  QL   L  G  R +++  L
Sbjct: 177 TIQEGKFHQVKRMFAARGKTVSYLKRISMGNLQLDESLELGEYRPLTEAEL 227


>gi|302342638|ref|YP_003807167.1| pseudouridine synthase [Desulfarculus baarsii DSM 2075]
 gi|301639251|gb|ADK84573.1| pseudouridine synthase [Desulfarculus baarsii DSM 2075]
          Length = 271

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 82/268 (30%), Positives = 132/268 (49%), Gaps = 2/268 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++ARAG+ASRR  E +IA  RV V+G ++ +           I +DG P+ +AE 
Sbjct: 4   ERLQKILARAGVASRRAAEELIAAGRVAVDGQIVRQPGHKADPDTQSIAIDGKPIARAEA 63

Query: 73  TRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              W  +     + T H        +    P I +R+  VGRLD+++EGL+LLTNDG LA
Sbjct: 64  KEYWLAHKPAGYVSTVHDPQGRPRVLDLLPPEIRARLYPVGRLDLDSEGLMLLTNDGDLA 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + YRV   G+ ++  L  L+ G+ I+G       +T+      ++ V++
Sbjct: 124 LRLTHPRYGVPKTYRVWLSGRPNRADLEALRAGVEIEGRQTAPAMITVKAAADGHSKVSM 183

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            LREG+ REIK +++     V RL+R+  GP +LG L  G+ R +S   ++         
Sbjct: 184 VLREGRKREIKLMWKARGLNVIRLVRVGLGPLRLGDLPPGAVRRLSPAEIQALRRQCHAL 243

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVP 279
               +    +  S    R+ P+  S   
Sbjct: 244 SGCKDSADGVQKSARGARNAPSKKSTGR 271


>gi|241896291|ref|ZP_04783587.1| pseudouridylate synthase [Weissella paramesenteroides ATCC 33313]
 gi|241870452|gb|EER74203.1| pseudouridylate synthase [Weissella paramesenteroides ATCC 33313]
          Length = 255

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 81/240 (33%), Positives = 124/240 (51%), Gaps = 11/240 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A+AG+ASRR  E+MI + +V VNG ++      V  TDHIEV+G P+   E+ 
Sbjct: 3   ERLQKVMAQAGVASRRASEKMITEGQVTVNGQVIRELGTKVEPTDHIEVNGTPIDSKEKL 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L  KP G+VTT+SD  GR TV D +     RV  VGRLD +T G LLLTNDG LA  
Sbjct: 63  VYFLLDKPRGVVTTNSDDKGRQTVMDIV-DEPERVYPVGRLDYDTTGALLLTNDGDLANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--------YGDMQVTLDTQKGS 185
           L  P  +  +VY  +  G    ++L  L+ G+ ++ +                + +    
Sbjct: 122 LMHPKYRIDKVYVAKVKGIPTNEELEKLRHGVTVKTVQNGRHYTFNAAPAHAEILSTDKK 181

Query: 186 NAW--VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
                V + + EGK  ++K++ +    +V +L R  YG   L  L  G  R +  + ++ 
Sbjct: 182 KHTAIVKLTIHEGKYHQVKEMLKSVGHEVIKLTRERYGMLDLTGLTPGEYRPLRHEEVQA 241


>gi|299822093|ref|ZP_07053979.1| ribosomal small subunit pseudouridine synthase A [Listeria grayi
           DSM 20601]
 gi|299815622|gb|EFI82860.1| ribosomal small subunit pseudouridine synthase A [Listeria grayi
           DSM 20601]
          Length = 242

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 72/243 (29%), Positives = 110/243 (45%), Gaps = 4/243 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G  SR+EV++ + +  V VNG  ++     ++ T D + V    +   E 
Sbjct: 1   MRLDKFLAHHGYGSRKEVKQFLKKTEVTVNGKRVQDGKQAIVPTSDIVRVQDEVILYQEY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              W+ HKP G ++   D                 V  VGRLD +TEGLLLLT+DG LA 
Sbjct: 61  -VYWMLHKPSGYISATEDQAKTVLDLLKPKDAGRAVFPVGRLDKDTEGLLLLTDDGQLAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY     G V  D ++  KKGIV+         ++ +    G    + +
Sbjct: 120 ELLSPKKHVNKVYEATIEGVVTGDDVHAFKKGIVLEDDYQCKPAKLEILQVNGVKTDIRI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLL 250
            ++EGK  +IK++F   + KV  L RI  G  QL   L  G  R ++ + L +     L 
Sbjct: 180 TIQEGKYHQIKRMFLAVDKKVIYLKRIQMGSLQLDENLARGEYRPLTVEELEQLSKKRLE 239

Query: 251 EEA 253
            + 
Sbjct: 240 IQE 242


>gi|116628203|ref|YP_820822.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           thermophilus LMD-9]
 gi|116101480|gb|ABJ66626.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           thermophilus LMD-9]
          Length = 243

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 58/234 (24%), Positives = 104/234 (44%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+  + +++V VNG +       +    D I   G  L     
Sbjct: 1   MRLDKFLVDCGVGSRSQVKTFLKKKQVTVNGQVETSPKTQIDEDKDQIAYLGQELTHETF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T            +  +   +V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPQGVISATEDSRHKTVLDLLDETARHKQVFPVGRLDIDTHGLLLLTNNGDLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVT 190
            +  P     ++Y+ +  G +D++ +   +KGI ++       ++ + +     S + V 
Sbjct: 121 AMLSPKKHVDKIYQAKVAGIMDEEDILAFEKGIKLKDHTCQPAKLEIVSVDRNASTSLVQ 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           + + EGK  ++K++      KV  L R+  GP  L   L  G+ R ++++ L  
Sbjct: 181 ITVAEGKFHQVKRMVAACGKKVADLQRLKMGPLSLPNDLELGAWRRLTQEELDA 234


>gi|31789454|gb|AAP58568.1| pseudouridylate synthase [uncultured Acidobacteria bacterium]
          Length = 317

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 80/261 (30%), Positives = 125/261 (47%), Gaps = 5/261 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK--- 69
           +R+ K+IA AGIASRR  E++I    V VNG ++        +  DHI+V G  +     
Sbjct: 57  ERLQKIIATAGIASRRHAEQLITAGEVTVNGKVVTELGTKADAQNDHIKVRGKLINPTLK 116

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                  L +KP G +++ SDP+GR TV + LP+   RV  VGRLD NTEGLLLLTNDG 
Sbjct: 117 RVEKNYILLNKPRGYLSSVSDPEGRPTVLELLPASLGRVYPVGRLDFNTEGLLLLTNDGD 176

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAW 188
               +     +  +VY  +  G   +  +  L++G+ +         ++ L  +  SNAW
Sbjct: 177 FTNFITSARNKVDKVYEAKVKGVPTEASVERLRRGVTLDDGVRTAPAKIRLLGETESNAW 236

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             V L EGKN++I+++F+     V +L R   G  +   L  G  R +S+  ++      
Sbjct: 237 FEVLLHEGKNQQIRRMFDLIGHSVVKLRRSRIGGLRDDELKPGKWRRLSEYEVKLLTTTR 296

Query: 249 LLEEAQVNLDAPIYSSETLVR 269
                +           +  +
Sbjct: 297 SRTRKKPPQKTHAAGHGSSRQ 317


>gi|323135793|ref|ZP_08070876.1| RNA-binding S4 domain protein [Methylocystis sp. ATCC 49242]
 gi|322398884|gb|EFY01403.1| RNA-binding S4 domain protein [Methylocystis sp. ATCC 49242]
          Length = 640

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 153/361 (42%), Positives = 205/361 (56%), Gaps = 14/361 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
             +F  +R++K +ARAG+ SRRE E+ IA+ RV VNG++L  AA NV   D I +DG P+
Sbjct: 81  TSSFEGERIAKAMARAGVCSRREAEQWIAEGRVAVNGVVLPNAAFNVKEGDRITIDGAPM 140

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLL 124
           ++ ERTRL+L+HKP G VTT  DP+GR TVF  L        RV+SVGRLDINTEGLLLL
Sbjct: 141 QERERTRLFLFHKPAGYVTTAHDPEGRPTVFAFLEERHGELPRVVSVGRLDINTEGLLLL 200

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDGGLAR LELP+T W R YRVR HG  DQ +L+ L+KG+ I G+ Y  ++  L+  +G
Sbjct: 201 TNDGGLARTLELPATGWTRRYRVRVHGDTDQAQLDELRKGVTIDGVVYAPIEARLERVQG 260

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +NAW+ + L EGKNREIK+V       V RLIR+SYGPFQLG L  G+  EV  KILREQ
Sbjct: 261 ANAWIAMSLTEGKNREIKRVMAHLGLDVTRLIRVSYGPFQLGELAEGAVEEVKLKILREQ 320

Query: 245 LGPHLLEEAQVNLDAPIYSSETLV----RDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           LG  L E A V+  +P+           R+R            R +++     G   + +
Sbjct: 321 LGKSLAELAGVDFSSPVRERTATEEQEMRERAEKRPRKHVSVLRKQRDEKSGKGPRARIE 380

Query: 301 LATPVHRRNLA-------SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                 R+  A            A+   ++  +   +      R P     R+ R    +
Sbjct: 381 RGATADRKGRAVVVERVTPTARKAESETTTRNARRFEAMRGEGRRPGPEGGRAERPAREE 440

Query: 354 K 354
           +
Sbjct: 441 R 441


>gi|54309646|ref|YP_130666.1| pseudouridine synthase family 1 protein [Photobacterium profundum
           SS9]
 gi|46914084|emb|CAG20864.1| putative pseudouridine synthase family 1 protein [Photobacterium
           profundum SS9]
          Length = 377

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 80/362 (22%), Positives = 137/362 (37%), Gaps = 20/362 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
            +++ KV+ARAG  SRRE+E MI   RV ++G++ +        +  + +DG  +     
Sbjct: 5   SEKLQKVLARAGQGSRREIELMIQSGRVSIDGVVAKLGDRLDDFSVLVRIDGHKIDLVSP 64

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L        L T H     R+           R +SVGRLD NT GLLL T D
Sbjct: 65  SEEVCRVLAYNKPEGELCTRHDPEGRRTVFDRLPRLSSGRWVSVGRLDANTSGLLLFTTD 124

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS    R Y VR  G+++++ +  L +G+ ++        V     +G N 
Sbjct: 125 GELANRLMHPSRSVEREYMVRVFGEINENMVKNLVQGVELEDGMARFEDVVYSGGEGMNH 184

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI---LRE 243
              V + EG+NRE++++++     V+RL R+ YG   L   +  G   E+  K    LRE
Sbjct: 185 TFYVVITEGRNREVRRLWDSQGVTVSRLKRVRYGDIYLTKDMPRGGWMELELKEVNYLRE 244

Query: 244 QLGPHLLEEAQVN-----LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
            +     E   +          +      VR     ++E P           ++   ++ 
Sbjct: 245 VVELEAEENTMLTVEGLKRKRGVRQIRRAVRRHEERVTETPRGRRGRTNTPDERRSSTRN 304

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS------FPSKRSLRRTSA 352
            +                      +    S  +     R  +         ++     + 
Sbjct: 305 SEAEGQNVPVGKRKPSGKPSTAKPTRGKPSAGKPAQGNRRKTDDCNEPAGKRKPSGNGAQ 364

Query: 353 KK 354
           ++
Sbjct: 365 RR 366


>gi|306830930|ref|ZP_07464092.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325977819|ref|YP_004287535.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
 gi|304426953|gb|EFM30063.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325177747|emb|CBZ47791.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
          Length = 238

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 104/229 (45%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++ +AG  SR +V+++I  ++V V+G L E   +NV  +   I V G  ++++  
Sbjct: 1   MRLDKLLGQAGFGSRNQVKKLIRSRQVYVDGRLAEADNLNVEPSLQKITVSGKQVKQSSE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                      ++  VGRLD +TEGLLL+TN+G L  
Sbjct: 61  KYFLLNKPAGVVSAVSDKEHQTVIDLIKEADRVPKLYPVGRLDRSTEGLLLVTNNGPLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V  +  +  D     + G+           ++ + T     +   V
Sbjct: 121 RMLHPKYHVAKTYYVEVNAFLADDAPAFFENGVSFDDGTICKPAKLEIITASPETSSAYV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + EGK  +IKK+F  +  KV  L R+++G FQLG L +G  RE++   
Sbjct: 181 TISEGKFHQIKKMFLAYGVKVTYLKRLTFGEFQLGDLPSGQYRELTSTE 229


>gi|298707966|emb|CBJ30337.1| pseudouridine synthase [Ectocarpus siliculosus]
          Length = 468

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 72/349 (20%), Positives = 128/349 (36%), Gaps = 14/349 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA-- 70
           +R+ K ++ AG+ SRR+ E+MI   RV+VNG +++   V V    D + VDG  +     
Sbjct: 35  ERLQKFLSHAGLDSRRQCEQMILDGRVRVNGKMVKELGVKVNPRRDQVHVDGNRVSMRPD 94

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   + L      + T   +    + V      +  R++ VGRLD ++ GLLLLTN+  
Sbjct: 95  SEIKWVALNKPKGVICTVSDELGRPTAVASIPRGLEMRLVPVGRLDRDSCGLLLLTNENS 154

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI---CYGDMQVTLDTQKGSN 186
               L  PS    + YRV         +   +    ++            V +       
Sbjct: 155 WINPLTHPSYGHEKTYRVALTSGYPTTEEWDVLTQGMLLDGDPNPTRPCIVEVVNYDRRT 214

Query: 187 --AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
               V + +REGKNR+I+++FE    +V  + R+S+GP +L  L  G  RE+ +  + + 
Sbjct: 215 RVTTVDIIIREGKNRQIRRMFEGIGHEVKSITRVSHGPIRLKNLRPGEWRELEQWEIEKL 274

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
                       L +P                +         + +SQ+     + +    
Sbjct: 275 KNL-----TTKTLKSPAKQLAPTPTRAEGRHRQAAAAGRMSSRMTSQQQYHGSEYRRDAL 329

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               +  + V                R      + S     +  +    
Sbjct: 330 DEEEDEWNQVGAWDRSGVRKAVAPSARAGAPATTASARGGGTPPQGEPA 378


>gi|120404251|ref|YP_954080.1| pseudouridine synthase [Mycobacterium vanbaalenii PYR-1]
 gi|119957069|gb|ABM14074.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           vanbaalenii PYR-1]
          Length = 247

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 74/239 (30%), Positives = 111/239 (46%), Gaps = 4/239 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
            +    R+ KV+++AGIASRR  E+MI   RV+V+G ++      V      I VDG  +
Sbjct: 2   TDNDGIRLQKVLSQAGIASRRVAEKMIRDGRVEVDGRIVTELGTRVDPAASVIRVDGARI 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLL 124
              +       +KP G+ +T SD  GR  V D +            VGRLD +TEGLLLL
Sbjct: 62  TVDDTLVYLAINKPRGMHSTMSDDRGRPCVGDLVEHRVRGNKKLFHVGRLDADTEGLLLL 121

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG LA  L  PS +  + Y     G V +     L++G+ ++          +     
Sbjct: 122 TNDGELAHRLMHPSFEVPKSYVATVLGSVPKGLGRKLREGVELEDGPVQVDDFAVVDTTP 181

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
               V V L EG+   ++++     + V  L+R   G   LG    GS R +++K + E
Sbjct: 182 GRTLVRVTLHEGRKHIVRRLLAEVGFPVQELVRTDIGTVSLGDQRPGSIRVLTQKEIGE 240


>gi|329962610|ref|ZP_08300558.1| pseudouridylate synthase [Bacteroides fluxus YIT 12057]
 gi|328529641|gb|EGF56539.1| pseudouridylate synthase [Bacteroides fluxus YIT 12057]
          Length = 234

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 56/225 (24%), Positives = 97/225 (43%), Gaps = 1/225 (0%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW 76
           +K +A AG+ SRRE +  I    V VNG ++      +   D ++     +    +  + 
Sbjct: 2   NKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRGDEVKFHDQAVSIERKIYVL 61

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L      + T+      R+ +     +   R+  VGRLD NT G+LLLTNDG LA  L  
Sbjct: 62  LNKPKDTVTTSDDPQARRTVMDLVKGACSERIYPVGRLDRNTTGVLLLTNDGDLASKLTH 121

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
           P     ++Y V     + +  +  +  GI +             T       V + +  G
Sbjct: 122 PKYLKKKIYHVHLDKNLTKADMEQIAAGIQLDDGEIH-ADAISYTDDFKKDDVGIEIHSG 180

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           KNR ++++FE   +KV +L R+ +       L  G  R ++++ +
Sbjct: 181 KNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLTEQEV 225


>gi|293395241|ref|ZP_06639526.1| ribosomal small subunit pseudouridine synthase A [Serratia
           odorifera DSM 4582]
 gi|291422198|gb|EFE95442.1| ribosomal small subunit pseudouridine synthase A [Serratia
           odorifera DSM 4582]
          Length = 237

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 55/238 (23%), Positives = 106/238 (44%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  +RV V+G ++   A+ +     +  DG  L +    
Sbjct: 1   MRLDKFLSQQLGISRALVARELRAKRVTVDGEVVRSGALKLTPETEVAFDGNVLEQLNGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLEEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +  D  +    G+ +          Q     ++     V +
Sbjct: 121 ITSPKHHCEKTYLVTLEQPLAADTASHFAAGVQLHNEKDLTRPAQ----LEQLDEHRVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
            + EG+  ++K++F     +V  L R   G  +L   L  G  R ++++ +     PH
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVVDLHRERIGAIRLDDDLAPGEYRPLTEEEIASVGAPH 234


>gi|256820536|ref|YP_003141815.1| RNA-binding S4 domain-containing protein [Capnocytophaga ochracea
           DSM 7271]
 gi|256582119|gb|ACU93254.1| RNA-binding S4 domain protein [Capnocytophaga ochracea DSM 7271]
          Length = 387

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 60/228 (26%), Positives = 111/228 (48%), Gaps = 1/228 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGI SRR  +  I+   V VNG ++      V  TD +  DG  L   ++ 
Sbjct: 154 VRLNKYIADAGICSRRNADMYISAGNVTVNGEVMTTLGYRVKPTDEVRFDGKLLSSEKKE 213

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L      + TT+ +   ++ +     +   R++ VGRLD  T GLLLLTNDG L + 
Sbjct: 214 YILLNKPKGFITTTNDEKGRKTVMDLVANATNVRILPVGRLDRATTGLLLLTNDGELTKK 273

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P+    ++Y V    ++D      ++ G+ ++       +++    K  N  + + +
Sbjct: 274 LTHPTHGVRKIYHVILDRKLDYKDFMKVQDGLELEDGLIEVDEISYVNDKPKN-EIGIKI 332

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             G+NR ++++FE   ++V +L R+ +       L  G  R ++++ +
Sbjct: 333 HSGRNRIVRRIFEHLGYQVEKLDRVVFAGLTKKDLPRGHWRRLTQQEV 380


>gi|197286701|ref|YP_002152573.1| ribosomal large subunit pseudouridine synthase F [Proteus mirabilis
           HI4320]
 gi|227355108|ref|ZP_03839519.1| RluF protein [Proteus mirabilis ATCC 29906]
 gi|194684188|emb|CAR45657.1| ribosomal large subunit pseudouridine synthase F [Proteus mirabilis
           HI4320]
 gi|227164895|gb|EEI49742.1| RluF protein [Proteus mirabilis ATCC 29906]
          Length = 292

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 64/292 (21%), Positives = 118/292 (40%), Gaps = 8/292 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++K I+ +GI SRRE +R I Q  V +NG         V + D ++V+G  +   + 
Sbjct: 6   STRLNKYISESGICSRREADRYIEQGLVLINGKRA-GIGDRVTAGDEVKVNGRLIEAQDN 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + L L      +    +  +G      +  +  +RV  +GRLD +++GL+ LTN G L  
Sbjct: 65  SELVLIALNKPVGIVSTTDEGEKDNIVDYVNHSTRVFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V     +  + +  +  G+ I G            +K +     + 
Sbjct: 125 KILRAGNSHEKEYLVTVDKPITDEFIRGMGAGVPILGQK----TKKCKVKKEAAMVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI---LREQLGPHL 249
           L +G NR+I+++ E+F ++V +L RI      L  L  G  R+++      L + +    
Sbjct: 181 LVQGLNRQIRRMCEYFGYEVTKLERIRIMNVSLAGLPVGEWRDLTDDELIKLFDAIEASS 240

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            E  +   + P     +  +     I +     T             K+KK 
Sbjct: 241 SEAPKQKQNKPKKQISSNAKALGIHIPKTKAKETENNTRKRFAQPGRKKKKR 292


>gi|149374978|ref|ZP_01892751.1| putative pseudouridine synthase [Marinobacter algicola DG893]
 gi|149360867|gb|EDM49318.1| putative pseudouridine synthase [Marinobacter algicola DG893]
          Length = 324

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 90/305 (29%), Positives = 133/305 (43%), Gaps = 8/305 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
           P+R+ K++ARAG+ SRREVE  I   R+ +NG  +      V   D I++DG  L  A  
Sbjct: 22  PERIQKLLARAGVGSRREVESWIEAGRLSINGKPV-EPGQKVTVNDRIDLDGKRLDIAAG 80

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R  L        + T        +           R I++GRLDINT GL+L T D
Sbjct: 81  AEVVRRVLIYNKPEGEVTTRRDPEGRPTVFDSLPRLRDHRWIAIGRLDINTTGLVLFTTD 140

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G+VD+  +  L +G+++         ++    KG N 
Sbjct: 141 GELANRLMHPSRQIDREYAVRVFGEVDEAMIKRLSEGVLLDDGMAKFSDISEAGGKGINQ 200

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V L EG+NRE+++++E    +V+RL R+ YGP  L   L  G   E+ +K + + L 
Sbjct: 201 WFHVTLLEGRNREVRRLWESQGVRVSRLKRVRYGPIFLPSRLSVGKWEELDQKAV-DSLS 259

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
             +  +            +TL R R       P      +         + +K    P  
Sbjct: 260 KAVDLKPVEIPAKTPSEQKTLDRKRRKQAGTGPRKSGGARWQVDSAGPSTGRKSSGKPPA 319

Query: 307 RRNLA 311
           R    
Sbjct: 320 RSGKR 324


>gi|323494539|ref|ZP_08099644.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           brasiliensis LMG 20546]
 gi|323311266|gb|EGA64425.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           brasiliensis LMG 20546]
          Length = 233

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 51/230 (22%), Positives = 96/230 (41%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  A+R+E  ++I    V VN ++ +  +V V     +E  G  + K    
Sbjct: 1   MRLDKYLCDALGATRKEATKIIKSGDVTVNDVVQKSGSVKVTDDCTVEWQGREIHKPGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+     + +     +  +            +   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLFKPDGFVCSHEDGFNQ-TAFMLLDEVKMEDLHFAGRLDVDTTGLVLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     V  D       GI ++      +   ++        V + +
Sbjct: 120 ITSPKHKCEKTYRVWLADPVQDDYAEKFANGIQLRNEKDLTLPAQMELVDAQENEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
            EGK  ++K++F     KV  L R   G  +L  TL  G  R ++++ + 
Sbjct: 180 TEGKYHQVKRMFAALGNKVEHLHRERIGDIELCDTLEPGEYRYLTQQEID 229


>gi|222640395|gb|EEE68527.1| hypothetical protein OsJ_26969 [Oryza sativa Japonica Group]
          Length = 1502

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 67/252 (26%), Positives = 114/252 (45%), Gaps = 19/252 (7%)

Query: 1    MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
            M D   +       R++K IA  G  SRRE +R+IA +RV VNG      AV V   D +
Sbjct: 1257 MPDNRAMTT-----RLNKHIADTGFCSRREADRLIAARRVTVNGHPAGTGAV-VGEEDQV 1310

Query: 61   EVDGVPLRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
             VDG PLR          R      +KP+G+  T            +      R+  +GR
Sbjct: 1311 LVDGQPLRARVARKPGARRHVYIALNKPVGVTCTTETSV--KGNIVDFVGHEQRIFPIGR 1368

Query: 114  LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
            LD ++EGL+L+T++G +   +        + Y V  +  V  + L  + +G+ I      
Sbjct: 1369 LDKDSEGLILMTSNGDIVNQILRAENGHQKEYLVAVNKPVTDEFLRGMARGVRIHDQMTL 1428

Query: 174  DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
              + +   + G      + L++G NR+I+ +   F ++V +L R+     ++G L  G  
Sbjct: 1429 PCKTSRIAKFG----FRITLQQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKIGALKPGQW 1484

Query: 234  REVSKKILREQL 245
            R ++++ L+  L
Sbjct: 1485 RNLTEQELQGLL 1496


>gi|149920284|ref|ZP_01908755.1| ribosomal large subunit pseudouridine synthase B [Plesiocystis
           pacifica SIR-1]
 gi|149818871|gb|EDM78311.1| ribosomal large subunit pseudouridine synthase B [Plesiocystis
           pacifica SIR-1]
          Length = 300

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 73/277 (26%), Positives = 126/277 (45%), Gaps = 5/277 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGV 65
           ++E     R+ K +A AG+ASRR+ E +I    V+VNG ++      V    D + V G 
Sbjct: 24  LREQRDGVRLQKFMASAGVASRRKAEELITAGVVRVNGQVVRELGTRVFPERDRVTVRGE 83

Query: 66  PLRKAERTRLWLYHKPIGLVTT--HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           P++   +    L      + +     D  GR TV   L  +  R+  VGRLD ++ G+LL
Sbjct: 84  PIQAESKVYYVLNKPDGVVSSAAGSVDERGRPTVISLLHGVSERLYPVGRLDFHSRGVLL 143

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGD-MQVTLDT 181
           LTNDGGLA  L  P    ++ Y V+F G++ +++  LL+ G+ +          ++    
Sbjct: 144 LTNDGGLAEALTHPRHGVVKTYHVKFQGKLTEEQEQLLRDGVELDDGAITRPVAELFAFR 203

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +  +N W  +G+REG NR+I+++ E     V +LIR++ G      +  G  R ++   +
Sbjct: 204 ETATNVWYQIGIREGLNRQIRRMGEAIGHPVLKLIRVAIGDITADGVPEGEFRALNATEV 263

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEV 278
            + L    L        +         +       + 
Sbjct: 264 GQLLANVKLAPEGRRGRSGGAGRPRGGQRDRPKAKKS 300


>gi|152967064|ref|YP_001362848.1| pseudouridine synthase [Kineococcus radiotolerans SRS30216]
 gi|151361581|gb|ABS04584.1| pseudouridine synthase [Kineococcus radiotolerans SRS30216]
          Length = 322

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 77/240 (32%), Positives = 119/240 (49%), Gaps = 1/240 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           +    R+ KV+A+AG  SRR  E MIA  RV V+G ++    V +  T   + VDG+   
Sbjct: 81  DPEGVRLQKVLAQAGAGSRRACEEMIAAGRVTVDGEVVTELGVRIDPTRQVVHVDGMRFS 140

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             +     + +KP G+V+T  D +GR  + D +     R+  VGRLD+ TEGL+LLTNDG
Sbjct: 141 IDDELVYIMVNKPKGVVSTMYDEEGRLNLADMVGPREERLFHVGRLDLETEGLILLTNDG 200

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L+ PS    + Y     G V +D    L+ GI +           L   K   A 
Sbjct: 201 ALTHRLQHPSFGVQKTYLAEVRGPVKRDLGRNLRAGIELDDGPVSVDSFKLVDSKPGYAL 260

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           V V L EG+   ++++ E   + V +L+R+  GP  LG L  G  R +++  +++ +   
Sbjct: 261 VEVVLHEGRKHIVRRMLEAEGYPVLKLVRVQMGPIVLGDLKPGKNRRLTRGEVQQLMAVA 320


>gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum
           seropedicae SmR1]
 gi|300075686|gb|ADJ65085.1| 16S rRNA uridine-516 pseudouridylate synthase protein
           [Herbaspirillum seropedicae SmR1]
          Length = 560

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 82/358 (22%), Positives = 139/358 (38%), Gaps = 10/358 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
             +  +       ++ KV+A AG+ SRR++E +I   RV VNG         ++ TD + 
Sbjct: 185 NGRRDLTAEDDAPKLHKVLADAGLGSRRDMEELIVAGRVSVNGEPA-HIGQRILPTDAVR 243

Query: 62  VDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           ++G  ++    K     L  +     +V+        S           + ++VGRLD N
Sbjct: 244 INGKLIQRKVSKRPPRVLVYHKPAGEIVSHADPEGRNSVFDRLPTMKAGKWLAVGRLDYN 303

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLLL T  G LA  L  P     R Y VR  G++++     L  G+ +        ++
Sbjct: 304 TEGLLLFTTSGDLANRLMHPRYNIEREYAVRTLGELEEGMRQKLLSGVELDDGPAQFSRI 363

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                +G N W  V + EG+NRE++++FE     V+RLIR  YG   L  TL  G   E+
Sbjct: 364 ADGGGEGVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTLPQTLRRGRWEEL 423

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            +  +R  +    LE+          S       +       P       K   +  G +
Sbjct: 424 EENAVRNLMAACGLEKQAGE----GKSGNGGHAGKGQGNGNGPRGNAMQNKGPQKGRGGN 479

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              +     ++     N     G  +       ++ +  + +  FP     R    ++
Sbjct: 480 YGNQGGNYGNQGGNYGNQGGGYGGGNKGGQPKSRQPDPLQTALGFPDAGQRRNNRPQR 537


>gi|324326400|gb|ADY21660.1| RNA pseudouridine synthase family protein [Bacillus thuringiensis
           serovar finitimus YBT-020]
          Length = 235

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 109/229 (47%), Gaps = 7/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+G  LR A   
Sbjct: 1   MRINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCTSEKSV--KGNIIDLVNHPLRISHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  D L  +  G+ I G      ++T      S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEITQL----SKYEFKIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKR 222


>gi|170078952|ref|YP_001735590.1| RNA pseudouridylate synthase [Synechococcus sp. PCC 7002]
 gi|169886621|gb|ACB00335.1| RNA pseudouridylate synthase [Synechococcus sp. PCC 7002]
          Length = 259

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 68/235 (28%), Positives = 111/235 (47%), Gaps = 5/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
           +RV K++AR GIASRR  E++I   RV +NG  ++         D + VDG PL+  E  
Sbjct: 3   ERVQKILARWGIASRRGAEKLILAGRVTLNGKPVQLGDQADPEGDRLCVDGKPLKATERP 62

Query: 72  -RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDG 128
                 ++     + T        + +    P       +  +GRLD  + G LLLTNDG
Sbjct: 63  RHYYYLIHKPKGVVSTCADPKGRSTVLDLLPPPLRQGKGIHPIGRLDAQSTGALLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
                L  P     + YRV   G+V +  L+  ++G+++        Q+ L T       
Sbjct: 123 NFTLALTHPRYHIPKTYRVWLKGKVPEHVLDQWRQGVMLGDRRTLPTQIHLKTITQDKTC 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + + L EG+NR+I++V E   + V +L R++ G   LG L  G  R ++K  +++
Sbjct: 183 IDIMLTEGRNRQIRRVAEQLGFPVVKLHRLAIGNLHLGDLQRGQARPLTKAEIKQ 237


>gi|165870573|ref|ZP_02215227.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0488]
 gi|167639629|ref|ZP_02397899.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0193]
 gi|170687035|ref|ZP_02878254.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0465]
 gi|170706712|ref|ZP_02897171.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0389]
 gi|177649814|ref|ZP_02932816.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0174]
 gi|190565285|ref|ZP_03018205.1| RNA pseudouridine synthase family protein [Bacillus anthracis
           Tsiankovskii-I]
 gi|196033723|ref|ZP_03101134.1| RNA pseudouridine synthase family protein [Bacillus cereus W]
 gi|196039867|ref|ZP_03107170.1| RNA pseudouridine synthase family protein [Bacillus cereus
           NVH0597-99]
 gi|196043149|ref|ZP_03110387.1| RNA pseudouridine synthase family protein [Bacillus cereus 03BB108]
 gi|218903519|ref|YP_002451353.1| RNA pseudouridine synthase family protein [Bacillus cereus AH820]
 gi|225864348|ref|YP_002749726.1| RNA pseudouridine synthase family protein [Bacillus cereus 03BB102]
 gi|227814804|ref|YP_002814813.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           CDC 684]
 gi|229604604|ref|YP_002866722.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0248]
 gi|254684963|ref|ZP_05148823.1| ribosomal large subunit pseudouridine synthase F [Bacillus
           anthracis str. CNEVA-9066]
 gi|254722369|ref|ZP_05184157.1| ribosomal large subunit pseudouridine synthase F [Bacillus
           anthracis str. A1055]
 gi|254737410|ref|ZP_05195114.1| ribosomal large subunit pseudouridine synthase F [Bacillus
           anthracis str. Western North America USA6153]
 gi|254751725|ref|ZP_05203762.1| ribosomal large subunit pseudouridine synthase F [Bacillus
           anthracis str. Vollum]
 gi|254760244|ref|ZP_05212268.1| ribosomal large subunit pseudouridine synthase F [Bacillus
           anthracis str. Australia 94]
 gi|301053904|ref|YP_003792115.1| pseudouridylate synthase [Bacillus anthracis CI]
 gi|164713728|gb|EDR19251.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0488]
 gi|167512338|gb|EDR87714.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0193]
 gi|170128443|gb|EDS97311.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0389]
 gi|170669086|gb|EDT19830.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0465]
 gi|172084888|gb|EDT69946.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0174]
 gi|190563312|gb|EDV17277.1| RNA pseudouridine synthase family protein [Bacillus anthracis
           Tsiankovskii-I]
 gi|195993403|gb|EDX57360.1| RNA pseudouridine synthase family protein [Bacillus cereus W]
 gi|196025458|gb|EDX64127.1| RNA pseudouridine synthase family protein [Bacillus cereus 03BB108]
 gi|196029126|gb|EDX67730.1| RNA pseudouridine synthase family protein [Bacillus cereus
           NVH0597-99]
 gi|218536034|gb|ACK88432.1| RNA pseudouridine synthase family protein [Bacillus cereus AH820]
 gi|225790118|gb|ACO30335.1| RNA pseudouridine synthase family protein [Bacillus cereus 03BB102]
 gi|227006328|gb|ACP16071.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           CDC 684]
 gi|229269012|gb|ACQ50649.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0248]
 gi|300376073|gb|ADK04977.1| pseudouridylate synthase [Bacillus cereus biovar anthracis str. CI]
          Length = 235

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 109/229 (47%), Gaps = 7/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+G  LR A   
Sbjct: 1   MRINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCTSEKSV--KGNIIDLVNHPLRISHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  D L  +  G+ I G      ++T      S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEITQL----SKYEFKIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKR 222


>gi|217979006|ref|YP_002363153.1| RNA-binding S4 domain protein [Methylocella silvestris BL2]
 gi|217504382|gb|ACK51791.1| RNA-binding S4 domain protein [Methylocella silvestris BL2]
          Length = 676

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 146/344 (42%), Positives = 199/344 (57%), Gaps = 3/344 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++KVIARAG  SRR+ E +I++ RV +NG +L   A+NV   D I +DG PL +  RT
Sbjct: 25  ERIAKVIARAGACSRRDAETLISEGRVALNGAILISPAINVGPDDVILIDGAPLAERART 84

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGL 130
           RL+L+HKP GLVTT  DP+GR TVFD +        R++S+GRLDINTEGLLLLTNDGGL
Sbjct: 85  RLFLFHKPRGLVTTEHDPEGRPTVFDYVREHSPEAPRLVSIGRLDINTEGLLLLTNDGGL 144

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           ARVLELP+T W R YRVR  G +DQ  L+ L++G+ ++G+ Y  ++ TLD  +G+N W+T
Sbjct: 145 ARVLELPATGWARRYRVRAKGSIDQPTLDRLRQGVTVEGVDYAQIEATLDRIQGANCWLT 204

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + LREGKNREIK+V E    +VNRLIR+SYGPFQL  L  G   EV  ++LR+QLG  L 
Sbjct: 205 MSLREGKNREIKRVLEHLGLEVNRLIRLSYGPFQLADLEEGKVEEVRTRVLRDQLGAALA 264

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           E A V+   P   + T   + P             K    ++                  
Sbjct: 265 EAAAVDFVGPAGDALTPPPEEPAPRPPRQKSLRNQKAFRDEERPRRDSGPFRKAEGGGRP 324

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           A    +A+       +    +   ++ +P      S  R  A +
Sbjct: 325 AGAGLLARRRGPDPAAFDPAQPRKNKPAPGPRKHISSLRAEASE 368


>gi|227499448|ref|ZP_03929559.1| pseudouridylate synthase [Anaerococcus tetradius ATCC 35098]
 gi|227218510|gb|EEI83753.1| pseudouridylate synthase [Anaerococcus tetradius ATCC 35098]
          Length = 234

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 70/229 (30%), Positives = 117/229 (51%), Gaps = 3/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IAR+G  SRR+ + +I    VKVN  +++   ++V   D +EVDG  L   ++ 
Sbjct: 2   MRINKFIARSGYTSRRKADELIKNGLVKVNYKIIKEPGIDVKENDLVEVDGQILEIEDKF 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L LY     + +     + +      L  +  R  + GRLD ++EGLL++TNDG     
Sbjct: 62  YLKLYKPVGFITSNFDPYNDKDLNN--LLDLDKRFFAAGRLDKDSEGLLIITNDGDFTNE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  PS +  + Y V+    ++  +++L +KGI I           +   K +N    V +
Sbjct: 120 IIHPSKKLDKTYIVKVSKLLNNKEISLFEKGIDIGNGEVTSDSKIVLIDKKTN-KYKVTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++FE+F+ KV  L RIS GP QL  +    TR+ +   L 
Sbjct: 179 HQGYNRQIRRMFEYFSSKVINLKRISIGPIQLSNMKPYETRQFTADELE 227


>gi|118618582|ref|YP_906914.1| pseudouridylate synthase [Mycobacterium ulcerans Agy99]
 gi|183982541|ref|YP_001850832.1| pseudouridylate synthase [Mycobacterium marinum M]
 gi|118570692|gb|ABL05443.1| pseudouridylate synthase [Mycobacterium ulcerans Agy99]
 gi|183175867|gb|ACC40977.1| pseudouridylate synthase [Mycobacterium marinum M]
          Length = 253

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 75/237 (31%), Positives = 111/237 (46%), Gaps = 4/237 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
           E     R+ KV+++AGIASRR  E++I   RV+V+G ++      V      I VDGV +
Sbjct: 8   EQERGIRLQKVLSQAGIASRRAAEKLIIDGRVEVDGQVVTELGTRVDPDTSLIRVDGVRV 67

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLL 124
              +       +KP G+ +T SD  GR  + D +            VGRLD +TEGL+LL
Sbjct: 68  ILDDSLVYLALNKPRGMHSTMSDDRGRPCIGDLIERKVRGNKNLFHVGRLDADTEGLILL 127

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG LA  L  PS +  + Y     G V +     L+ GI ++          +     
Sbjct: 128 TNDGELAHRLMHPSHEVPKTYLATVAGTVPRGLGKKLRAGIELEDGPVRVDGFAVVDAIP 187

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
               V V L EG+NR ++++     + V  L+RI  G   LG    GS R + +  +
Sbjct: 188 GKTLVRVTLHEGRNRIVRRMLAAVGFPVQALVRIDIGGVSLGEQRPGSVRALRRDEI 244


>gi|310778392|ref|YP_003966725.1| ribosomal large subunit pseudouridine synthase B [Ilyobacter
           polytropus DSM 2926]
 gi|309747715|gb|ADO82377.1| ribosomal large subunit pseudouridine synthase B [Ilyobacter
           polytropus DSM 2926]
          Length = 236

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 74/231 (32%), Positives = 127/231 (54%), Gaps = 2/231 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K ++  G+ASRRE++R++ +  +KVNG +     + V  +D IE++G   RK  
Sbjct: 3   EKMRINKYLSSIGVASRREIDRLVEKGSIKVNGAIAT-PGMQVSESDTIEINGKKFRKNR 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               ++ +KP G+++   D  GR TV  +L     R+  VGRLD +TEGL+LLTNDG   
Sbjct: 62  GKVYFMLYKPTGVISAAKDDRGRKTV-VDLVKYQERIYPVGRLDFDTEGLILLTNDGDFF 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P ++  + Y V   G+V++ +++ LK+G+ ++       +V L       + + +
Sbjct: 121 NKIMHPKSEVYKEYHVDVMGKVNKLEIDKLKRGVRLEDGITLPAKVELLDSSHETSKLRI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +REG+NR+I+++ +     V  L R   G   LG L  G  RE+SKK + 
Sbjct: 181 SIREGRNRQIRRMCKAVGHPVTHLKREKIGELSLGRLKKGGFRELSKKEIE 231


>gi|229823225|ref|ZP_04449294.1| hypothetical protein GCWU000282_00523 [Catonella morbi ATCC 51271]
 gi|229787391|gb|EEP23505.1| hypothetical protein GCWU000282_00523 [Catonella morbi ATCC 51271]
          Length = 243

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 105/231 (45%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G  SR+++++++AQ+ V +N  +  +    V    D + V G  +     
Sbjct: 1   MRIEKYLADTGWGSRKDIKQLLAQKIVTINDQVCSKGGTQVTPGSDCVAVGGQLVPYQRY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      L  T          +         +  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  HYYLLNKPEGILSATEDRHHQTVIDWLGEGYQHLDLFPVGRLDIDTTGLLLLTNNGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVT 190
            L  P  +  + Y     G VDQ  +   + G+ +        ++T+ +Q      + + 
Sbjct: 121 QLLSPKKKVDKTYTATIRGLVDQADIAAFEAGLDLGDFTSLPAELTVLSQDVDQGTSQIQ 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
           V ++EGK  ++K++F+    +V  L R++ GP +L   L  G  R ++++ 
Sbjct: 181 VIIQEGKFHQVKRMFQAVGKEVLSLHRLAMGPLRLESDLAHGQWRSLTEQE 231


>gi|329915247|ref|ZP_08276235.1| Ribosomal large subunit pseudouridine synthase B [Oxalobacteraceae
           bacterium IMCC9480]
 gi|327544952|gb|EGF30293.1| Ribosomal large subunit pseudouridine synthase B [Oxalobacteraceae
           bacterium IMCC9480]
          Length = 621

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 82/374 (21%), Positives = 146/374 (39%), Gaps = 27/374 (7%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           +  +  +    ++ KV+A AG+ SRR++E +I   RV VNG         +++ D + ++
Sbjct: 197 RRDLTADDDAPKLHKVLAEAGLGSRRDMEELIISGRVSVNGEPA-HIGQRILAQDQVRIN 255

Query: 64  GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G  ++    K     L  +     +V+        S           + ++VGRLD NTE
Sbjct: 256 GKLIQRRVSKKPPRVLVYHKPAGEIVSHDDPDGRPSVFERLPNMKAGKWLAVGRLDFNTE 315

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL T  G LA  L  P     R Y VR  G++++     L  G+ +        +V  
Sbjct: 316 GLLLFTTSGDLANRLMHPRYNIDREYAVRTLGELEEGMRQKLLAGVELDDGVAQFSRVAD 375

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G N W  V + EG+NRE++++FE     V+RLIR  YG   L   L  G   E+ +
Sbjct: 376 GGGEGVNKWYRVTIGEGRNREVRRMFEAIGLTVSRLIRTRYGAMVLPPNLKRGRWEEMDE 435

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSET-------LVRDRPNIISEVPDDFTRMKKNSSQ 291
             +R+ L    LE+     +     S+                 +          + ++ 
Sbjct: 436 HSVRDLLKISGLEKTVGKSEPSRGRSDEHDSEGGVNGNRIERAPATARHGAPNGNRANAP 495

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHS--------------SFLSDSGQREENHRR 337
           + G  + K  + P       +     +G  +              +      ++ +  + 
Sbjct: 496 EPGQWQGKGRSGPARGPGGFAGQGQPRGPGAYPAQGQGGQGQGRGAPAKARSRQPDPMQT 555

Query: 338 SPSFPSKRSLRRTS 351
           +  FP     RR++
Sbjct: 556 ALGFPGMGQPRRSN 569


>gi|206973507|ref|ZP_03234425.1| RNA pseudouridine synthase family protein [Bacillus cereus
           H3081.97]
 gi|217959884|ref|YP_002338440.1| RNA pseudouridine synthase family protein [Bacillus cereus AH187]
 gi|206747663|gb|EDZ59052.1| RNA pseudouridine synthase family protein [Bacillus cereus
           H3081.97]
 gi|217067986|gb|ACJ82236.1| RNA pseudouridine synthase family protein [Bacillus cereus AH187]
          Length = 235

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 109/229 (47%), Gaps = 7/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+G  LR A   
Sbjct: 1   MRINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCTSEKSV--KGNIIDLVNHPLRISHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  D L  +  G+ I G      ++T      S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEITQL----SKYEFKIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKR 222


>gi|308069018|ref|YP_003870623.1| 16S rRNA uridine-516 pseudouridylate synthase [Paenibacillus
           polymyxa E681]
 gi|305858297|gb|ADM70085.1| 16S rRNA uridine-516 pseudouridylate synthase [Paenibacillus
           polymyxa E681]
          Length = 230

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 57/224 (25%), Positives = 94/224 (41%), Gaps = 10/224 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--E 71
            R++K I+  G  SRRE  R+IA  R+ +NG +   A   V   D + +DG  +     E
Sbjct: 1   MRINKYISETGFCSRRETNRLIAAGRITINGNVC-EAGAEVEPQDIVLIDGEAIPLNSSE 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L L      + T      G    +    +  SR+ ++GRLD  +EGL+LLTNDG + 
Sbjct: 60  PVYLALNKPIGIVCTAAEQVAGNIISYV---NYPSRIFAIGRLDKASEGLILLTNDGSIV 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     V  +    +  G+ I  +     +V       S     +
Sbjct: 117 NQMMRSEHGHEKEYVVTVDKPVTNEFTQAMSCGVEILNVITKPCKVDR----TSEYEFRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
            L +G N +I+++ +   ++V +L R+      L  L  G  R 
Sbjct: 173 ILTQGLNLQIRRMCKALGYRVLKLERVRIMNITLDHLERGQWRH 216


>gi|19704091|ref|NP_603653.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           nucleatum subsp. nucleatum ATCC 25586]
 gi|296328700|ref|ZP_06871217.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           nucleatum subsp. nucleatum ATCC 23726]
 gi|19714293|gb|AAL94952.1| Ribosomal large subunit pseudouridine synthase B [Fusobacterium
           nucleatum subsp. nucleatum ATCC 25586]
 gi|296154299|gb|EFG95100.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           nucleatum subsp. nucleatum ATCC 23726]
          Length = 234

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 68/231 (29%), Positives = 129/231 (55%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--E 71
            R++K ++  GIASRR +++ I + R+ VNG       +++   D+I +DG  ++    E
Sbjct: 1   MRINKFLSTLGIASRRAIDKYIEEGRITVNGNTATT-GMDINENDNIFIDGKKIKTKIDE 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               ++ +KP+ ++++ SD  GR TV D + +       +GRLD  T GL+LLTNDG L 
Sbjct: 60  EKVYFMLNKPLEVLSSSSDDRGRKTVVDLIKTDKRI-FPIGRLDYMTSGLILLTNDGELF 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P ++  + Y ++  G++ +++++ LKKG+++        +++      +   + +
Sbjct: 119 NRVVHPKSEIYKKYYIKVFGEIKKEEIDELKKGVLLDDGKTLPAKISGIKYDKNKTSMYI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +REG+NR+I+++ E F +KV  L R   G   LG L  G  RE++K+ + 
Sbjct: 179 SIREGRNRQIRRMIEKFEYKVLMLRREKIGELSLGDLPEGKYRELTKQEVE 229


>gi|255505461|ref|ZP_05346261.3| ribosomal large subunit pseudouridine synthase F [Bryantella
           formatexigens DSM 14469]
 gi|255267773|gb|EET60978.1| ribosomal large subunit pseudouridine synthase F [Bryantella
           formatexigens DSM 14469]
          Length = 267

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 75/254 (29%), Positives = 126/254 (49%), Gaps = 8/254 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +D   + +   P R++K +A+AGI SRRE +R+IA+ +V V+G     A   V+ +  I 
Sbjct: 17  EDFRKITDTAEPVRINKYLAQAGICSRREADRLIAEGKVLVDGA-AAVAGQKVLPSQDIR 75

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           V+G    +++   L + +KP G+V T     G +T+ + L    SRV   GRLD ++EGL
Sbjct: 76  VEGEQAVRSQERILLVVNKPRGVVCTTDKTWGDTTLEE-LVDYPSRVFYAGRLDKDSEGL 134

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTL 179
           +L+TNDG L   +   + +  + Y V+    VD   L  + KG+ +          +V  
Sbjct: 135 ILMTNDGELQDKIMRAANRHEKEYLVKVDRTVDDTFLKKMAKGVYLRELDTVTRPCRV-- 192

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +K       + L +G NR+I+++     ++V  L R+     +LG L AG  RE + +
Sbjct: 193 --EKTGRRAFRIVLTQGLNRQIRRMCAALGYQVQELRRVRIMNIRLGGLPAGQYREATDE 250

Query: 240 ILREQLGPHLLEEA 253
            LRE        + 
Sbjct: 251 ELREICALAEAGKP 264


>gi|322373412|ref|ZP_08047948.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           C150]
 gi|321278454|gb|EFX55523.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           C150]
          Length = 243

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 56/233 (24%), Positives = 102/233 (43%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+  + +++V VNG +       +    D I      L     
Sbjct: 1   MRLDKFLVDCGLGSRSQVKIYLKKKQVTVNGQVETSPKTQIDEKKDQIAYQSQELTHETF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T            +  +   +V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPKGVISATEDARHKTVLDLLDETARHKQVFPVGRLDIDTHGLLLLTNNGDLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVT 190
            +  P     ++Y+ +  G +D+  +   +KGI ++       ++ + +   +   + V 
Sbjct: 121 AMLSPRKHVDKIYQAKVAGVMDEADMQAFEKGIELKDHTCQPAKLEILSVDQAVKTSTVQ 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           V + EGK  ++K++      +V  L R+S G   L   L  G+ R ++++ L 
Sbjct: 181 VTIAEGKFHQVKRMVAACGKEVTDLQRLSMGSLVLPDDLEIGTWRRLTQEELD 233


>gi|259503200|ref|ZP_05746102.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           antri DSM 16041]
 gi|259168857|gb|EEW53352.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           antri DSM 16041]
          Length = 238

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 71/237 (29%), Positives = 107/237 (45%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K +A AG+ASRR  E++IA   V+VNG  +      V + D IEVDGVPL + +  
Sbjct: 2   ERLQKAMAEAGVASRRASEKLIATGHVQVNGQTVTTLGTKVAARDRIEVDGVPLHREKHV 61

Query: 74  RLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              L      + +                  I  R+  VGRLD +T GLLLLTNDG LA 
Sbjct: 62  YYLLNKPRGVISSAHDEKGRRTVVDILREDEIEERIYPVGRLDYDTTGLLLLTNDGALAN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVT 190
            L  P     + Y  +  G V  D L  L+ G+ + G      +  L    ++   + V 
Sbjct: 122 KLMHPKFAVDKTYVAKVKGLVSNDDLKRLRTGVKVDGRRTQPAKARLKATDREKRTSIVQ 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           + + EG   ++K++       V +L R SYG   L  +  G  RE+  + ++     
Sbjct: 182 LTIHEGHYHQVKRMLAAVGHPVIKLHRESYGFLTLQGVQPGDYRELRPEEVKRLTRL 238


>gi|306824439|ref|ZP_07457785.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
 gi|304433226|gb|EFM36196.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
          Length = 240

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 100/233 (42%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQINEERDEIRFDGQVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    V  VGRLDI+T GLLLLTNDG LA 
Sbjct: 61  VYYIMNKPKGVISATEDSKHRTVLDLLDDLARTKEVFPVGRLDIDTHGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVT 190
            L  P     + Y  +  G + Q+ +    KGI ++       ++ + +       + V 
Sbjct: 121 ALLSPKRHVDKTYLAQVKGIMSQEDVETFAKGISLKDFTCQPAKLEILSVDSGKDESQVR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 181 VTIAEGKFHQVKRMVSYCGKEVVDLQRLTMGTLALDENLERGEWRRLTKEELE 233


>gi|218231829|ref|YP_002367069.1| RNA pseudouridine synthase family protein [Bacillus cereus B4264]
 gi|218159786|gb|ACK59778.1| RNA pseudouridine synthase family protein [Bacillus cereus B4264]
          Length = 235

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 109/229 (47%), Gaps = 7/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+G  LR A   
Sbjct: 1   MRINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCTSEKSV--KGNIIDLVNHPLRISHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  D L  +  G+ I G      ++T      S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPDFLEKMATGVKILGTKTLPCEITQL----SKYEFQIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKR 222


>gi|298209211|ref|YP_003717390.1| pseudouridine synthase, Rsu [Croceibacter atlanticus HTCC2559]
 gi|83849138|gb|EAP87007.1| pseudouridine synthase, Rsu [Croceibacter atlanticus HTCC2559]
          Length = 244

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 56/249 (22%), Positives = 103/249 (41%), Gaps = 7/249 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
            P R++K     G  SRR+ +++I    V VNG         +    D + V+G  + + 
Sbjct: 2   EPIRINKYFTTIGFCSRRKADKLIEAGYVTVNGKRP-EMGQKIDPAKDKVRVNGKLVGQE 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   ++L       +   +D         +  +  SR+  +GRLD  +EGL+ LTNDG +
Sbjct: 61  EEKPVYLVFNKPVGIVCTTDTHVEKDNIIDYINYPSRIFPIGRLDKPSEGLIFLTNDGDI 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  D +N +K GI I      + +     +K ++    
Sbjct: 121 VNKILRARNHHEKEYIVTVDRVISDDFVNRMKSGIPILDTVTRECE----VEKITDYMFK 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E+  ++V  L RI      L  +  G  R+ + +  +E       
Sbjct: 177 IVLTQGLNRQIRRMCEYLGYEVLTLKRIRIMNVTL-DIPVGEYRDFTDQEFKELQDLLED 235

Query: 251 EEAQVNLDA 259
            E     + 
Sbjct: 236 SEKTAPENN 244


>gi|312962716|ref|ZP_07777205.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           fluorescens WH6]
 gi|311283091|gb|EFQ61683.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           fluorescens WH6]
          Length = 402

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 93/370 (25%), Positives = 155/370 (41%), Gaps = 17/370 (4%)

Query: 1   MKDKNIVQEN--FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M D++   +      +++ KV+AR G+ SRR+VE  I Q+R+KVNG+        V   D
Sbjct: 1   MNDQDHKDQEIGPAGEKLQKVLARIGVGSRRDVEAWITQKRIKVNGVEAT-LGQRVDLHD 59

Query: 59  HIEVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
            I +DG  +++ E     R  +        + T        +           R I++GR
Sbjct: 60  AITIDGKVIKREEAAESVRRVIMYNKPDGEICTRDDPEGRPTVFDKMPKPKEGRWINIGR 119

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LDINT GLL+ T DG LA  L  PS +  R Y VR  G+VD + +  LK G+V++     
Sbjct: 120 LDINTTGLLMFTTDGELANRLMHPSYEMDREYAVRVRGEVDDEMIERLKAGVVLEDGPAK 179

Query: 174 DMQVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAG 231
              +      +G N W    + EG+NRE+++++E     V+RL R+ +GP  L   L  G
Sbjct: 180 FTDIKQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLNSDLPMG 239

Query: 232 STREVSKKI---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
             RE+S+     L  ++G   +   Q+N  +         +    +        T     
Sbjct: 240 RWREMSQYEVDILSAEVGLTPVAMPQMNAKSKDKLERMQRKSSRPVARTERVARTLRPAL 299

Query: 289 SSQKNGLSKQKKLATPVHRR----NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
            +   G    ++      RR    +        +    +       R E  R + +  +K
Sbjct: 300 DAPATGGRISRQPQIEGERRPTAPSRQEGERAPRTPRPAPAGGRSNRGEADRPADNASTK 359

Query: 345 RSLRRTSAKK 354
           R  +  + K+
Sbjct: 360 RPAKPAANKR 369


>gi|300714626|ref|YP_003739429.1| Pseudouridine synthase [Erwinia billingiae Eb661]
 gi|299060462|emb|CAX57569.1| Pseudouridine synthase [Erwinia billingiae Eb661]
          Length = 292

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 60/297 (20%), Positives = 106/297 (35%), Gaps = 7/297 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I  +GI SRR+ +R I Q  V +NG         V + D ++V+G  +  
Sbjct: 3   TNSSIRLNKYIGESGICSRRDADRYIEQGNVFINGKRAAV-GDQVYAGDVVKVNGQLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L L      +    +  +G      N  +   RV  +GRLD  ++GL+ LTN G 
Sbjct: 62  RNEDDLVLIALNKPVGIISTTEEGERDNIVNFVNHSKRVFPIGRLDKESQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  V  + +  L  G+ + G            +K +    
Sbjct: 122 LVNKILRAGNDHEKEYVVTVNKLVTDEFIAGLGAGVPMLGTV----TKKCKVKKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ + F ++V +L R       L  L  G  RE +   L E      
Sbjct: 178 RITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNVSLKGLPIGEWREFTDDELIELFKL-- 235

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           +E +    +    +            +            +        Q        
Sbjct: 236 IEHSSSEENPEKKAKPKAKPAAVKKPTIAGPKTAEKPTANGAARKRFVQPGRKKKGR 292


>gi|282878147|ref|ZP_06286944.1| pseudouridylate synthase [Prevotella buccalis ATCC 35310]
 gi|281299725|gb|EFA92097.1| pseudouridylate synthase [Prevotella buccalis ATCC 35310]
          Length = 488

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 63/233 (27%), Positives = 107/233 (45%), Gaps = 1/233 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +   P R++K +A AG+ SRRE +  I    VKVNG ++      VM TD +     P+ 
Sbjct: 248 DPTVPVRLNKFLANAGVCSRREADEFIQAGVVKVNGEVVTELGTKVMRTDEVVFHDQPVS 307

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ++  + L      + T+      ++ +         R+  VGRLD NT G+LLLTNDG
Sbjct: 308 LEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKNVCPERIYPVGRLDRNTTGVLLLTNDG 367

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     +VY V     V    +  + +GI ++        +    +   N  
Sbjct: 368 DLASKLTHPKYLKKKVYHVFLDKNVTAHDMQKIAEGIELEDGEVHADAIEYAHETDKNQ- 426

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + +  GKNR ++++FE   ++V +L R+ +       L  G  R ++++ +
Sbjct: 427 VGIEIHSGKNRIVRRIFESLGYRVIKLDRVQFAGLTKKNLRRGDWRFLTEEEV 479


>gi|284802783|ref|YP_003414648.1| hypothetical protein LM5578_2540 [Listeria monocytogenes 08-5578]
 gi|284995925|ref|YP_003417693.1| hypothetical protein LM5923_2490 [Listeria monocytogenes 08-5923]
 gi|284058345|gb|ADB69286.1| hypothetical protein LM5578_2540 [Listeria monocytogenes 08-5578]
 gi|284061392|gb|ADB72331.1| hypothetical protein LM5923_2490 [Listeria monocytogenes 08-5923]
          Length = 233

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 99/231 (42%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D I V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQITVHGTPVVYQEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T  +               + +  VGRLD +TEGLL++TNDG LA 
Sbjct: 61  VYFMLHKPQNVVSATEDNVSETVIDLLAQEDTLTDLFPVGRLDKDTEGLLIITNDGTLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y  +  G V    +     GI +          + + T    N    V
Sbjct: 121 NLLSPKKHIDKTYYAKIDGDVTAADVEAFAAGIELDDGYTCKPASLEIITPNEIN----V 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            ++EGK  ++K++F      V+ L RIS G  QL   L  G  R +++  L
Sbjct: 177 TIQEGKFHQVKRMFAARGKTVSYLKRISMGNLQLDESLELGEYRPLTEAEL 227


>gi|291301885|ref|YP_003513163.1| pseudouridine synthase [Stackebrandtia nassauensis DSM 44728]
 gi|290571105|gb|ADD44070.1| pseudouridine synthase [Stackebrandtia nassauensis DSM 44728]
          Length = 244

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 72/236 (30%), Positives = 107/236 (45%), Gaps = 2/236 (0%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGV 65
           +       R+ KV+A AGI SRR  E +IA  RV VNG   +     V      I VDG 
Sbjct: 1   MTAEPEGVRLQKVMAAAGIGSRRACENLIAAGRVTVNGKKAQ-LGNRVDPQHAVIHVDGE 59

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +    +   +  +KP G V+T  D   R  + +    I  RV  VGRLD  +EGLLLLT
Sbjct: 60  RVITDTKLVHFALNKPRGYVSTMDDELKRPDLNEFTAGISERVFHVGRLDTESEGLLLLT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG L   L  PS +  + YR +  G         L  G+V++          +  +   
Sbjct: 120 NDGELGNRLTHPSYEIAKTYRCQVTGYAGPAIARRLAAGVVLEDGPVTVDDFKVIDEHAD 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            A V + + EG+   ++++       VNRL+R + G  +L  L  G+ R++    +
Sbjct: 180 QALVEIVVHEGRKHVVRRLLAEVGLPVNRLVRTAIGDIRLANLKPGTLRKLRPDEI 235


>gi|313901058|ref|ZP_07834546.1| 16S pseudouridylate 516 synthase [Clostridium sp. HGF2]
 gi|312954016|gb|EFR35696.1| 16S pseudouridylate 516 synthase [Clostridium sp. HGF2]
          Length = 233

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 110/231 (47%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A AG+ +R+EV+  I + RV VNG +  +    +    D + +D   +   E 
Sbjct: 1   MRLDKYLAHAGLGTRKEVKLAIRKGRVSVNGEVCRKDDRKIQEGVDVVCLDKEEI-YYEA 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP  +V+  SDP   + +      +      VGRLD++TEGLLL+TNDG LA 
Sbjct: 60  VVYIMLNKPQDVVSATSDPTYETVLDCIDAFLPKDCFPVGRLDMDTEGLLLITNDGKLAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V     + +     L+   IV+        +V +      +  + +
Sbjct: 120 RLLSPKHHVEKTYLVDLAQPLQEGDQKKLENGSIVLDEEPVLPARVEIL----EDTQILL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            ++EG+  ++K++      +V  L RI+ GP +L   L +G  R +S++ +
Sbjct: 176 HIQEGRFHQVKRMLHAIGNEVVHLKRIAMGPLRLDEALASGEWRYLSEEEI 226


>gi|157371821|ref|YP_001479810.1| pseudouridine synthase [Serratia proteamaculans 568]
 gi|157323585|gb|ABV42682.1| pseudouridine synthase [Serratia proteamaculans 568]
          Length = 266

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 55/258 (21%), Positives = 102/258 (39%), Gaps = 5/258 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
              +  R++K I+ +GI SRR+ +R I   +V +N    E     V   D + V+G  + 
Sbjct: 2   PTQSSIRLNKYISDSGICSRRQADRYIKLGKVFINDNQAEV-GAPVFIGDVVSVNGQRIE 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 L L      +    S          +  +   R   VGRLD +++GL+ LTN G
Sbjct: 61  PRNDADLVLIALNKPVGIITSMGKHVPNNIGDFVNHSQRTFPVGRLDKDSQGLIFLTNRG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   +        + Y V     +  + +  +  G+ I G      QV    ++ +   
Sbjct: 121 ELVNKILRAGNNHQKEYLVTVDKPLTDEFIQGMGAGVPILGKVTHKCQV----EQEAPQV 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + + L +G NR+I+++ ++F ++V +L R+      L  L  G  R++S+    E     
Sbjct: 177 LRITLVQGLNRQIRRMCKYFGYQVTKLERVRIMNISLQGLALGEWRDLSEDERTELFKLL 236

Query: 249 LLEEAQVNLDAPIYSSET 266
               ++            
Sbjct: 237 EHSSSEEPDLPQRDEIPP 254


>gi|206971481|ref|ZP_03232431.1| RNA pseudouridine synthase family protein [Bacillus cereus AH1134]
 gi|229178726|ref|ZP_04306090.1| Pseudouridine synthase [Bacillus cereus 172560W]
 gi|206733466|gb|EDZ50638.1| RNA pseudouridine synthase family protein [Bacillus cereus AH1134]
 gi|228604884|gb|EEK62341.1| Pseudouridine synthase [Bacillus cereus 172560W]
          Length = 235

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 109/229 (47%), Gaps = 7/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+G  LR A   
Sbjct: 1   MRINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCTSEKSV--KGNIIDLVNHPLRISHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  D L  +  G+ I G      ++T      S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEITQL----SKYEFQIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKR 222


>gi|332359960|gb|EGJ37774.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1056]
          Length = 242

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 104/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++ + +  V VNG   +     +  T D I V G  L   + 
Sbjct: 1   MRLDKFLAENGLGSRAQVKQFLKKGLVLVNGRAEKSPKTQIDETADEIVVSGQRLTYEKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  D         +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPQGVISATEDDRHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            +  P     ++YR +  G ++Q  +     GI ++       Q+ +     +   + V 
Sbjct: 121 AMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKDFTCQPAQLKIVELDEAKETSLVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + L EGK  ++K++      +V  L R++ G  QL + L  G  R ++++ +
Sbjct: 181 ITLAEGKFHQVKRMVASCGKEVTDLQRLTMGSLQLDSALALGEWRRLTEEEM 232


>gi|156933241|ref|YP_001437158.1| 16S rRNA pseudouridylate synthase A [Cronobacter sakazakii ATCC
           BAA-894]
 gi|156531495|gb|ABU76321.1| hypothetical protein ESA_01053 [Cronobacter sakazakii ATCC BAA-894]
          Length = 235

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 108/231 (46%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G +++ +A  +++ + +E DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRASRVTVDGEIVKDSAFKLLADNDVEYDGNPLIQQNGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAHKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D   L  KG+ +          Q+ +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAALFAKGVQLNNEKDLTKPAQLEVI----TPTEVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G  +L   L  G  R +++  +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVGLHRERIGAIELDPELAPGEYRPLTEDEI 227


>gi|121604769|ref|YP_982098.1| pseudouridine synthase [Polaromonas naphthalenivorans CJ2]
 gi|120593738|gb|ABM37177.1| ribosomal large subunit pseudouridine synthase B [Polaromonas
           naphthalenivorans CJ2]
          Length = 527

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 81/373 (21%), Positives = 142/373 (38%), Gaps = 23/373 (6%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          +   D ++V+
Sbjct: 86  KRVLSPQPETPKLHKVLAQAGLGSRLEMEQLILEGRISVNAEPA-HIGQRIQFGDTVKVN 144

Query: 64  GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+R          +  +     +VT     +  +           +  SVGRLD+NTE
Sbjct: 145 GKPIRVQIDPPPPRVIAYHKPAGEVVTHDDPQNRPTVFRRLPKLFQGKWQSVGRLDLNTE 204

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLLT+ G LA  L  P     R Y VR  G ++ ++   L  G+ +         +  
Sbjct: 205 GLLLLTSSGELANKLMHPRFGLEREYAVRVLGALNNEEKKRLLDGVTLDDGVAQFGSIEA 264

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E+ +
Sbjct: 265 GGGEGANCWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMVLPRGLKRGAFVELDE 324

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             +          E++ +             +        P    R +  + +   L   
Sbjct: 325 NDIHALTSAVSRSESRPDPRGEAAGPGQSEGEGGVQQRRGPRRNERPRSGAGRPRNLDAG 384

Query: 299 KKL-------ATPVHRRNLASNVWMAKG----------IHSSFLSDSGQREENHRRSPSF 341
           +         + P   R  ++     +                     +  +     P  
Sbjct: 385 QSGVQQPLDDSQPPMNRTDSAPRGNRRNAGGGAGPRGRSQGGNSGPGARFGQAGAGGPQG 444

Query: 342 PSKRSLRRTSAKK 354
             +R  R   + K
Sbjct: 445 QKRRDDRNPRSDK 457


>gi|301156469|emb|CBW15940.1| 16S rRNA pseudouridylate 516 synthase [Haemophilus parainfluenzae
           T3T1]
          Length = 232

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 61/236 (25%), Positives = 110/236 (46%), Gaps = 7/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  A  V   D I  +   L   E  
Sbjct: 1   MRLDKFIAENTGLTRSQATKAIRQSAVKINGEIVKNGATKVSLEDEIYFEDELLPWVEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ HKP G V +H D D  +      P +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYFMLHKPQGYVCSHDDGDYPTIYQFFEPPLSGKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  Q  + Y V     V+    +  ++GI+++G        ++ +      +  V +
Sbjct: 121 ITSPKHQCEKTYLVTLADPVENHYASACEEGILLRGEKEPTKPAKLEVL----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
            + EG+  ++K++F     KV  L R   G  +L   L  G  R ++++ +   + 
Sbjct: 177 TISEGRYHQVKRMFAALGNKVVALHRWRIGNVELDESLEEGEFRPLTQEEIDNLVK 232


>gi|218897335|ref|YP_002445746.1| RNA pseudouridine synthase family protein [Bacillus cereus G9842]
 gi|218544394|gb|ACK96788.1| RNA pseudouridine synthase family protein [Bacillus cereus G9842]
          Length = 235

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 109/229 (47%), Gaps = 7/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+G  LR A   
Sbjct: 1   MRINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCTSEKAV--KGNIIDLVNHPLRISHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  D L  +  G+ I G      ++T      S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEITQL----SKYEFQIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKR 222


>gi|110597201|ref|ZP_01385490.1| Pseudouridine synthase, Rsu [Chlorobium ferrooxidans DSM 13031]
 gi|110341392|gb|EAT59857.1| Pseudouridine synthase, Rsu [Chlorobium ferrooxidans DSM 13031]
          Length = 247

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 69/254 (27%), Positives = 117/254 (46%), Gaps = 10/254 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DH 59
           MK+      N    R+++ +A  GIASRR  ++++ + RV VNG ++ +    V    D 
Sbjct: 1   MKN----STNSEEVRINRFLALCGIASRRAADQLVLEGRVMVNGTVITQPGTKVNPDKDE 56

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           + VDG    + E  ++++       V + S  +    +  +   +  RV  VGRLD  T 
Sbjct: 57  VIVDGQKYAQPESRKVYILFNKPRNVISTSSDEKNREMVLDYIDVKERVFPVGRLDRKTT 116

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQV 177
           GL+LLTNDG LA  L  PS+   + Y      +     L  L  G+ ++         + 
Sbjct: 117 GLILLTNDGTLANKLMHPSSNVKKEYIAVLGEKFPASMLPQLTGGMRLKDTGEKVRPCRA 176

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L  +      V + + EGKN +++++FE   ++V RL R++Y    +G L  G  R +S
Sbjct: 177 KLLDEG---MQVLLSIHEGKNHQVRRMFETLGYEVKRLERVAYAGLTIGELRRGEWRYLS 233

Query: 238 KKILREQLGPHLLE 251
           +  +RE        
Sbjct: 234 RNEVRELYKLAESP 247


>gi|288553832|ref|YP_003425767.1| pseudouridine synthase [Bacillus pseudofirmus OF4]
 gi|288544992|gb|ADC48875.1| pseudouridine synthase [Bacillus pseudofirmus OF4]
          Length = 233

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 59/223 (26%), Positives = 104/223 (46%), Gaps = 4/223 (1%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTRLWLY 78
           ++  G  SR+EV++++    V++N  +++  +  V      + V G  +       L L 
Sbjct: 2   LSNMGYGSRKEVKKVLKSGSVRINEKVIKDGSYKVDPDQSDVTVHGELVEYKPYVYLMLN 61

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
                +  T  +         +   +      VGRLD +TEG+LLLTNDG  +  L  P 
Sbjct: 62  KPQGVISATEDNHHKTVIDLLDESYLLYDPFPVGRLDKDTEGMLLLTNDGKFSHSLMSPK 121

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVGLREGK 197
               + Y  +  G V ++ + L KKG+ +          +T+ T  G  + V + + EGK
Sbjct: 122 KHVKKTYYAKVKGTVTEEDIGLFKKGVTLDDGYVTKPADLTIITA-GEQSEVELTITEGK 180

Query: 198 NREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
             ++K++FE  + KV  L RIS G  +L  +L  G  RE++++
Sbjct: 181 FHQVKRMFEAVDKKVTFLKRISIGGLKLDPSLEKGMVRELTEE 223


>gi|157363887|ref|YP_001470654.1| RNA-binding S4 domain-containing protein [Thermotoga lettingae TMO]
 gi|157314491|gb|ABV33590.1| RNA-binding S4 domain protein [Thermotoga lettingae TMO]
          Length = 234

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 56/234 (23%), Positives = 105/234 (44%), Gaps = 6/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A A I +R EV ++I +  + VNG +++  + ++  TD +E  G  +    + 
Sbjct: 1   MRLDRFLANAKIGTRSEVRKIIKKGEISVNGEIVKNISFHINETDIVEYMGKTVVPYRKI 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L        +  +       S           ++   GRLD + EGLL+LTNDG     
Sbjct: 61  YLIFNKPAGFV--SDKTNAQPSVFDLIDHPFIDQMHVAGRLDRDVEGLLILTNDGLFTHR 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     + Y + F G +  +K+ +++ GIV+    +   ++ L +        T+ +
Sbjct: 119 LISPKFHVEKEYMIWFEGNLTAEKIQIVENGIVLAQNRFKPAKIKLLSSNIM----TLTI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            EGK  ++KK+ +       ++ RI  G   LG +  G+ RE+ +  L E +  
Sbjct: 175 TEGKYHQVKKMIKIMGLTYRKIKRIRIGNINLGNMSTGNYRELDENELNELMNL 228


>gi|311031252|ref|ZP_07709342.1| ribosomal small subunit pseudouridine synthase A [Bacillus sp.
           m3-13]
          Length = 236

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 61/224 (27%), Positives = 103/224 (45%), Gaps = 4/224 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A +G  +R+EV++++    VKV+G +++ A V+V      + V    +   E 
Sbjct: 1   MRLDKMLANSGFGTRKEVKKLLKTGVVKVDGNVVKDAKVHVDPEVQEVTVHDDIVEYREF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L ++  P  L  T                       VGRLD +TEGLLLLTNDG LA 
Sbjct: 61  IYLMMHKPPGLLSATEDHRQETVVDILQEEDKMFEPFPVGRLDKDTEGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y  +  G+V  + +   KKG+ +         ++ +  + G  + + +
Sbjct: 121 QLLSPKKHVPKTYYAKIDGEVTTEDMEAFKKGVTLDDGYETLPAELVIL-EAGPESQIEI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
            + EGK  ++K++F+     V  L R+S G  +L   L  G  R
Sbjct: 180 TIVEGKFHQVKRMFQAVGKTVTYLKRLSMGELKLDEDLELGEYR 223


>gi|30020453|ref|NP_832084.1| tRNA pseudouridine synthase A [Bacillus cereus ATCC 14579]
 gi|229109805|ref|ZP_04239390.1| Pseudouridine synthase [Bacillus cereus Rock1-15]
 gi|29896004|gb|AAP09285.1| tRNA pseudouridine synthase A [Bacillus cereus ATCC 14579]
 gi|228673650|gb|EEL28909.1| Pseudouridine synthase [Bacillus cereus Rock1-15]
          Length = 235

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 65/229 (28%), Positives = 109/229 (47%), Gaps = 7/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+G  LR A   
Sbjct: 1   MRINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCTSEKSV--KGNIIDLVNHPLRISHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  D L  +  G+ I G      +VT      S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEVTQL----SKYEFQIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKR 222


>gi|256845054|ref|ZP_05550512.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           3_1_36A2]
 gi|256718613|gb|EEU32168.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           3_1_36A2]
          Length = 234

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 69/231 (29%), Positives = 126/231 (54%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAE 71
            R++K ++  GIASRR ++R I + R+ VNG       +++   D+I +DG  +     E
Sbjct: 1   MRINKFLSTLGIASRRTIDRYIEEGRITVNGNTATT-GMDISGNDNIFIDGKKIETNIDE 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               ++ +KP+ ++++ SD  GR TV D + +       +GRLD  T GL+LLTNDG L 
Sbjct: 60  EKIYFMLNKPLEVLSSSSDDRGRKTVVDLIKTDKRI-FPIGRLDYMTSGLILLTNDGDLF 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P ++  + Y V+  G++ ++++  LKKG+++        +++      +   + +
Sbjct: 119 NRIVHPKSEIYKKYYVKIFGEIKKEEIEELKKGVLLDDGKTLPAKISGIKYDKNKTSMYI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +REG+NR+I+++ E F +KV  L R   G   LG L  G  RE++ + + 
Sbjct: 179 SIREGRNRQIRRMIEKFGYKVLMLKREKIGELSLGDLPEGKYRELTVQEVE 229


>gi|183599733|ref|ZP_02961226.1| hypothetical protein PROSTU_03236 [Providencia stuartii ATCC 25827]
 gi|188021992|gb|EDU60032.1| hypothetical protein PROSTU_03236 [Providencia stuartii ATCC 25827]
          Length = 291

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 60/292 (20%), Positives = 115/292 (39%), Gaps = 5/292 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           +  R++K I+ +GI SRR+ +R I Q  V +NG         V S D ++V+G  +    
Sbjct: 5   SSTRLNKYISESGICSRRDADRYIEQGNVFINGKRAA-IGDQVFSGDVVKVNGQLIEPRN 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L L      +    +   G      +  +   RV  +GRLD +++GL+ LTN G L 
Sbjct: 64  EEDLVLIALNKPVGIVSTTESGERDNIVDYVNHSKRVFPIGRLDKDSQGLIFLTNHGDLV 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +     +  + Y V  +  +  D +  +  G+ I G            +K +     +
Sbjct: 124 NKILRAGNEHEKEYLVTVNKPITDDFIRGMGAGVPILGTV----TKKCKVKKEAPFVFRI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ E+F ++V +L R+      L  +  G  R+++   L +        
Sbjct: 180 TLVQGLNRQIRRMCEYFGFEVTKLERVRIMNVNLSGIPLGEWRDLTDDELIKLFEMIEKS 239

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           E++           +      +  +            S ++     +KK   
Sbjct: 240 ESEAKPKKSAKPKTSTAGKTGSKPNAGSKPKGMADTASRKRFTQPGRKKKRR 291


>gi|152978349|ref|YP_001343978.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
 gi|150840072|gb|ABR74043.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
          Length = 231

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 61/235 (25%), Positives = 110/235 (46%), Gaps = 7/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    +R +  + I Q  V+VNG + +  A+ V   D I  DG PL   E  
Sbjct: 1   MRLDKFIAQQTGLTRSQATKSIRQGVVEVNGNMEKSGALKVSPQDEIVFDGEPLPWLEGL 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ +KP G V +H D D  +        +  ++ + GRLD +T GL+LLT+DG  +  
Sbjct: 61  QYFMLNKPQGYVCSHEDGDYPTVYQFFDYPLAGKLHTAGRLDADTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+ +  +  ++GI+++G        ++ +      +  V +
Sbjct: 121 VTSPKHYCEKTYLVTLADPVESNYQSACEQGILLRGEKEATKPAKLEII----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
            + EG+  ++K++F     KV  L R   G   L   L  G  R ++++ +   L
Sbjct: 177 TITEGRYHQVKRMFAALGNKVVALHRWRVGTVVLDDDLEEGGFRALTQQEIEALL 231


>gi|294806727|ref|ZP_06765554.1| pseudouridylate synthase [Bacteroides xylanisolvens SD CC 1b]
 gi|294446009|gb|EFG14649.1| pseudouridylate synthase [Bacteroides xylanisolvens SD CC 1b]
          Length = 319

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 107/241 (44%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +  +D +
Sbjct: 71  IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVV 130

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P+    +  + L      + T+    + R+ +     +   R+  VGRLD NT G
Sbjct: 131 KFHDEPVSIERKVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTTG 190

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     + +  +  +  GI ++            
Sbjct: 191 VLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADMEQIAAGIQLEDGEIH-ADAISY 249

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           T       V + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+  
Sbjct: 250 TDDFKKDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSEAE 309

Query: 241 L 241
           +
Sbjct: 310 V 310


>gi|294645459|ref|ZP_06723160.1| pseudouridylate synthase [Bacteroides ovatus SD CC 2a]
 gi|292639160|gb|EFF57477.1| pseudouridylate synthase [Bacteroides ovatus SD CC 2a]
          Length = 320

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 107/241 (44%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +  +D +
Sbjct: 72  IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVV 131

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P+    +  + L      + T+    + R+ +     +   R+  VGRLD NT G
Sbjct: 132 KFHDEPVSIERKVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTTG 191

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     + +  +  +  GI ++            
Sbjct: 192 VLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADMEQIAAGIQLEDGEIH-ADAISY 250

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           T       V + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+  
Sbjct: 251 TDDFKKDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSEAE 310

Query: 241 L 241
           +
Sbjct: 311 V 311


>gi|332141187|ref|YP_004426925.1| RNA pseudouridine synthase family protein [Alteromonas macleodii
           str. 'Deep ecotype']
 gi|327551209|gb|AEA97927.1| RNA pseudouridine synthase family protein [Alteromonas macleodii
           str. 'Deep ecotype']
          Length = 248

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 59/254 (23%), Positives = 110/254 (43%), Gaps = 11/254 (4%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL- 67
            +  P+R++K I+  G+ SRRE +++I Q+RV VN          +   D ++VDG  + 
Sbjct: 2   SDQAPKRLNKYISDTGLCSRREADKLIEQKRVSVNNHPP-ELGTKIGPNDIVKVDGKIVG 60

Query: 68  ---RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
              +        +Y+KPIG+  T       + +        +R+  VGRLD  +EGL++L
Sbjct: 61  AVAKDKSDRVYIVYNKPIGITCTTERHVKGNIIDAI--GHKARIFPVGRLDKPSEGLIIL 118

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T+DG +   +        + Y V  +  + +  +  + +G+ I G            +  
Sbjct: 119 TSDGDIVNKILRAENAHDKEYEVTVNQPISERFVKRMARGVPILGTVTKPC----VVKPT 174

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
                T+ L +G NR+I+++ EF  ++V +L R      +L  L  G  R +++  L   
Sbjct: 175 GKNTFTIILTQGLNRQIRRMCEFLGYEVTKLKRTRIMHLELKALKPGQWRNLTQHELTTL 234

Query: 245 LGPHLLEEAQVNLD 258
                        +
Sbjct: 235 QNAVKASSKTAPSN 248


>gi|296502925|ref|YP_003664625.1| tRNA pseudouridine synthase A [Bacillus thuringiensis BMB171]
 gi|296323977|gb|ADH06905.1| tRNA pseudouridine synthase A [Bacillus thuringiensis BMB171]
 gi|326940067|gb|AEA15963.1| tRNA pseudouridine synthase A [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 235

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 65/229 (28%), Positives = 109/229 (47%), Gaps = 7/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+G  LR A   
Sbjct: 1   MRINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCTSEKAV--KGNIIDLVNHPLRISHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  D L  +  G+ I G      +VT      S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEVTQL----SKYEFQIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKR 222


>gi|331703388|ref|YP_004400075.1| 23S rRNA pseudouridine synthase [Mycoplasma mycoides subsp. capri
           LC str. 95010]
 gi|328801943|emb|CBW54097.1| 23S rRNA pseudouridine synthase [Mycoplasma mycoides subsp. capri
           LC str. 95010]
          Length = 252

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 72/249 (28%), Positives = 123/249 (49%), Gaps = 5/249 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--RKAE 71
           +R+ KVI+  G  SRR  E++I + RVKVN  ++    V +     I++D   +      
Sbjct: 4   ERLQKVISSRGYCSRRAAEKLILENRVKVNDQIINTLGVKIDPKAEIKIDNKLVLSDSNN 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +   +L++KP  ++TT  DP  R TV D    +  RV  VGRLD +  GLLL+TNDG L+
Sbjct: 64  QKYYYLFYKPRLVLTTMYDPKKRKTVNDYFKDLNHRVYPVGRLDYDVSGLLLMTNDGVLS 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD--MQVTLDTQKGSNAW 188
             +  P  ++L+ Y+    GQV++ ++N L KG+ I           ++    +  + + 
Sbjct: 124 NFIMHPKYEFLKTYQGLCQGQVNKQQINQLIKGVYIDNDYLTKAYSAKLVKYDKLKNTSI 183

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           V + + EGK   +KK+FE    ++ +L R      ++  L  G  RE+    ++   G +
Sbjct: 184 VELTINEGKKHHVKKMFESIQAQLLKLKRTKIEFLEIADLKPGQYRELKTHEVKRLYGIY 243

Query: 249 LLEEAQVNL 257
              +   N 
Sbjct: 244 HSLKQNNNK 252


>gi|322835106|ref|YP_004215133.1| pseudouridine synthase [Rahnella sp. Y9602]
 gi|321170307|gb|ADW76006.1| pseudouridine synthase [Rahnella sp. Y9602]
          Length = 290

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 58/293 (19%), Positives = 116/293 (39%), Gaps = 5/293 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +  
Sbjct: 3   TNSSIRLNKYISESGICSRRDADRYIEQGNVFINGRRAAV-GAQVFAGDVVKVNGQIIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   L L      +    +  +G      +  +   RV  +GRLD +++GL+LLTN G 
Sbjct: 62  RDEEDLVLIALNKPVGIITTMEEGERDNIRDFVNHSKRVFPIGRLDKDSQGLILLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  +  + +  +  G+ + G            +K +    
Sbjct: 122 LVNKILRAGNDHEKEYIVTVNKPITDEFIAGMGAGVPMLGTV----TKKCKVKKEAPMVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ + F + V +L R+      L  L  G  R+++   L E      
Sbjct: 178 RITLVQGLNRQIRRMTKHFGFDVTKLERVRIMNINLKGLPLGEWRDLTDDELIELFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
              ++        S     +      ++  +       +  +     ++KK  
Sbjct: 238 NSSSEDKPAKKGPSKPAQAKKPAVTKTKNSEKPEANSASRKRFAQPGRKKKGR 290


>gi|290890516|ref|ZP_06553591.1| hypothetical protein AWRIB429_0981 [Oenococcus oeni AWRIB429]
 gi|290479912|gb|EFD88561.1| hypothetical protein AWRIB429_0981 [Oenococcus oeni AWRIB429]
          Length = 237

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 77/231 (33%), Positives = 117/231 (50%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA+AG+ASRR+ E MI   +VKVNG ++ +    V S D + VD   + +    
Sbjct: 5   ERLQKRIAQAGVASRRKAEEMIVNGQVKVNGKIITKLGKKVSSDDIVYVDNKKINEESFE 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      + +  S P+  S +   L    +R+ SVGRLD +T G+LLLTNDG L + 
Sbjct: 65  YYLLNKPAGYVSSNRSYPNQPSVIE--LIKTKTRIFSVGRLDQDTTGVLLLTNDGELTQK 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD--MQVTLDTQKGSNAWVTV 191
           L  P  +  R Y     G V++D+L  L K I   G  Y     ++    QK   + + +
Sbjct: 123 LTHPKHRIKRTYAAWVKGIVNEDELEQLTKPIRFDGEIYFPQAARILKVDQKRQESLIEI 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EGKN EIKK+ +F    V +L R  +    +G L  G  R +S++ + 
Sbjct: 183 TIAEGKNHEIKKILDFIGHPVIKLNRDMFDGITIGNLKKGQYRALSEQEVE 233


>gi|307705665|ref|ZP_07642514.1| conserved hypothetical protein [Streptococcus mitis SK597]
 gi|307620791|gb|EFN99878.1| conserved hypothetical protein [Streptococcus mitis SK597]
          Length = 240

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 101/233 (43%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    V  VGRLDI+T GLLLLTNDG LA 
Sbjct: 61  VYYMMNKPKGVISATEDPKHRTVLDLLDDIARSKEVFPVGRLDIDTHGLLLLTNDGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVT 190
            L  P     + Y  +  G + Q+ +    KGI ++       ++ L     + + + + 
Sbjct: 121 DLLSPKRHVDKTYLAQVKGIMTQEDVETFAKGIPLKDFTCKPARLELVSIDAEKNQSQIR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 181 VTIAEGKFHQVKRMVGYCGKEVVDLQRLTMGTLVLDENLQRGEWRRLTKEELE 233


>gi|325697447|gb|EGD39333.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK160]
          Length = 242

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 63/233 (27%), Positives = 102/233 (43%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++ + +  V VNG   +     +  T D I V G  L   + 
Sbjct: 1   MRLDKFLAENGLGSRAQVKQFLKKGLVLVNGRAEKSPKTQIDETADEIVVSGQRLTYEKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  D         +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPQGVISATEDDRHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            +  P     ++YR +  G ++Q  +     GI ++       Q+ +     +   + V 
Sbjct: 121 AMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKDFTCQPAQLKIVELDEAKETSLVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + L EGK  ++K++      +V  L R++ GP QL   L  G  R ++   L 
Sbjct: 181 ITLAEGKFHQVKRMVASCGKEVTDLQRLTMGPLQLDPALALGEWRRLTADELE 233


>gi|300361439|ref|ZP_07057616.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           gasseri JV-V03]
 gi|300354058|gb|EFJ69929.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           gasseri JV-V03]
          Length = 248

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 66/238 (27%), Positives = 105/238 (44%), Gaps = 4/238 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E     R+ K +A   + SR+EV  +I ++ V VNG L+      V   D + VDG  + 
Sbjct: 11  EKDIEMRIDKYLANMNVGSRKEVHSLIKKKVVTVNGELVTAPKQQVKEDDLVVVDGNEIA 70

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             +     L      +  T                 +  +  VGRLD NT GLLLLTNDG
Sbjct: 71  YQQYHYFLLNKPKGVISATEDRSQQTVISLLKTKDRYQGIAPVGRLDKNTTGLLLLTNDG 130

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN- 186
            LA  L  P+    +VYR +  G   ++ +     GI +  G      ++ +  Q   + 
Sbjct: 131 ALAHELLAPNKHVTKVYRAKISGVASEETIKTFASGITLGDGTKLKPAKLEILAQDKVHD 190

Query: 187 -AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
            + + + ++EGK  +IK++F     KV  L RIS G   L   L  G  +E+++  ++
Sbjct: 191 LSQIEIQIQEGKYHQIKRMFGAVGMKVLELDRISMGKLSLPTDLKRGQYQEITRDKIK 248


>gi|229592262|ref|YP_002874381.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           fluorescens SBW25]
 gi|229364128|emb|CAY51757.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           fluorescens SBW25]
          Length = 403

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 96/368 (26%), Positives = 157/368 (42%), Gaps = 16/368 (4%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           KD+N  QE     +++ KV+AR G+ SRR+VE  I Q+R+KVNG+        V   D I
Sbjct: 4   KDQNDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQKRIKVNGVEAT-LGQRVDLHDAI 62

Query: 61  EVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            +DG  +++ E     R  +        + T        +           R I++GRLD
Sbjct: 63  TIDGKVIKREEAAESVRRVIMYNKPDGEICTRDDPEGRPTVFDKMPKPKEGRWINIGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           INT GLL+ T DG LA  L  PS +  R Y VR  G+VD + +  LK G+V++       
Sbjct: 123 INTTGLLMFTTDGELANRLMHPSYEMDREYAVRVRGEVDDEMIERLKAGVVLEDGPAKFT 182

Query: 176 QVTLDTQ-KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ +GP  L   L  G  
Sbjct: 183 DIKQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLNSDLPMGRW 242

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           RE+S+     L  ++G   +   Q+N  +         +    +        T     ++
Sbjct: 243 REMSQYEVDILSAEVGLTPVAMPQMNAKSKDKLERMQRKSSRPVARTERVARTLRPALNA 302

Query: 291 QKNGLSKQKKLATPVHRR----NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
              G    ++      RR    +        +    +       R E  R + +  +KR 
Sbjct: 303 PATGGRISREPQIEGERRPTAPSRQEGERAPRTPRPAPAGGRSNRGEADRPADNASTKRP 362

Query: 347 LRRTSAKK 354
            +  + K+
Sbjct: 363 AKPAANKR 370


>gi|172039420|ref|YP_001805921.1| pseudouridine synthase [Cyanothece sp. ATCC 51142]
 gi|171700874|gb|ACB53855.1| pseudouridine synthase [Cyanothece sp. ATCC 51142]
          Length = 259

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 67/240 (27%), Positives = 115/240 (47%), Gaps = 12/240 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           QRV K++++ G+ASRR  E MI   RV++NG ++           D +EVDG  ++  +R
Sbjct: 3   QRVQKILSQWGVASRRHAEDMIVAGRVRLNGEIVT-LGDKADPNCDRLEVDGKLIQPNQR 61

Query: 73  T---RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTND 127
                + +      + T +   +    +       S  + +  VGRLD N+ G LLLTND
Sbjct: 62  PQLLYILMNKPIGVVCTCNDPQNRSIVLDFLPKAFSQGTGIHPVGRLDFNSSGALLLTND 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  P     + Y V   G   +++L   ++G+++ G      QV +  +   + 
Sbjct: 122 GELTLRLTHPRYHLPKTYEVWVQGYPTEERLQQWREGVMLMGKKTLPAQVEVIRRSRQHT 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-----GTLLAGSTREVSKKILR 242
            + V L EG+NR+I+++ +   + V RL R + GP  L      +L +G  R ++   +R
Sbjct: 182 CLKVVLTEGRNRQIRRIVQHLGFHVLRLHRTAIGPLVLSSPNESSLPSGQHRLLTPSEIR 241


>gi|146306872|ref|YP_001187337.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           mendocina ymp]
 gi|145575073|gb|ABP84605.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           mendocina ymp]
          Length = 385

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 93/374 (24%), Positives = 143/374 (38%), Gaps = 29/374 (7%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           Q     +++ KV+AR G+ASRRE+E  I + RVKVNG         V + D I +DG  L
Sbjct: 6   QPRPAGEKLQKVLARMGLASRREIETWIGEGRVKVNGAAAT-LGQRVDANDAIALDGRLL 64

Query: 68  RKAERT-----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           ++ E T      L        + T        +           R I++GRLDINT GLL
Sbjct: 65  KREEITGSVRRVLIYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLDINTTGLL 124

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT- 181
           L T DG LA  L  PS Q  R Y VR  G+V ++ L  LKKG++++        +     
Sbjct: 125 LFTTDGELANRLMHPSYQMDREYAVRVRGEVTEEMLENLKKGVMLEDGPAKFTDIKEAPG 184

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
            +G N W    + EG+NRE+++++E     V+RL R+ +GP  L   L  G  RE+ ++ 
Sbjct: 185 GEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLTSDLTMGRWREMDQRE 244

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDR--------------PNIISEVPDDFTRMK 286
           +        L    +         +     R                   E   +  R  
Sbjct: 245 VDILSAEVGLAPQALPAMKEKTREKLDRLQRKSAKPVEVRGKRVLRPAKDEAGAEGARPS 304

Query: 287 KNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREE-------NHRRSP 339
           +   + +G  +  +           S            +     R           +  P
Sbjct: 305 RAPRRDDGEQRAPRGPRKEGGERRESGRGTPVAERPGDVKKRQPRPAVELADRPARKPRP 364

Query: 340 SFPSKRSLRRTSAK 353
           + P KR       +
Sbjct: 365 AAPGKRPPAGDGQR 378


>gi|15902300|ref|NP_357850.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae R6]
 gi|116516048|ref|YP_815778.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae D39]
 gi|15457806|gb|AAK99060.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae R6]
 gi|116076624|gb|ABJ54344.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae D39]
          Length = 240

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 63/233 (27%), Positives = 101/233 (43%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A   +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKFQIDEKIDEIRFDGQVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    V  VGRLDINT GLLLLTNDG LA 
Sbjct: 61  VYYMMNKPKGVISATEDPKHRTVLDLLDDLARSKEVFPVGRLDINTHGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVT 190
           VL  P     + Y  +  G + Q+ +    +GI ++       ++ +     + + + + 
Sbjct: 121 VLLSPKRHVDKTYLAQVKGIMTQEDVETFAEGIPLKDFTCQPARLEILSTDAEKNQSQIR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 181 VTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELE 233


>gi|229155962|ref|ZP_04284063.1| Pseudouridine synthase [Bacillus cereus ATCC 4342]
 gi|228627569|gb|EEK84295.1| Pseudouridine synthase [Bacillus cereus ATCC 4342]
          Length = 238

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 64/228 (28%), Positives = 109/228 (47%), Gaps = 7/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCTSEKSV--KGNIIDLVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T      S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMATGVKILGTKTLPCEITQL----SKYEFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKR 225


>gi|256383874|gb|ACU78444.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           mycoides subsp. capri str. GM12]
 gi|256384705|gb|ACU79274.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           mycoides subsp. capri str. GM12]
 gi|296455832|gb|ADH22067.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [synthetic Mycoplasma mycoides JCVI-syn1.0]
          Length = 252

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 72/249 (28%), Positives = 123/249 (49%), Gaps = 5/249 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--RKAE 71
           +R+ KVI+  G  SRR  E++I + RVKVN  ++    V +     I++D   +      
Sbjct: 4   ERLQKVISSRGYCSRRAAEKLILENRVKVNDQIINTLGVKIDPKAEIKIDNKLVLSDSNN 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +   +L++KP  ++TT  DP  R TV D    +  RV  VGRLD +  GLLL+TNDG L+
Sbjct: 64  QKYYYLFYKPRLVLTTMYDPKKRKTVNDYFKDLNHRVYPVGRLDYDVSGLLLMTNDGVLS 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD--MQVTLDTQKGSNAW 188
             +  P  ++L+ Y+    GQV++ ++N L KG+ I           ++    +  + + 
Sbjct: 124 NFIMHPKYEFLKTYQGLCQGQVNKQQINQLIKGVYIDNDYLTKAYSAKLVKYDKLKNTSI 183

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           V + + EGK   +KK+FE    ++ +L R      ++  L  G  RE+    ++   G +
Sbjct: 184 VELTINEGKKHHVKKMFESIQAQLLKLKRTKIEFLEIADLKPGQYRELKTHEVKRLYGIY 243

Query: 249 LLEEAQVNL 257
              +   N 
Sbjct: 244 HSLKQDNNK 252


>gi|90412191|ref|ZP_01220197.1| putative pseudouridine synthase family 1 protein [Photobacterium
           profundum 3TCK]
 gi|90326915|gb|EAS43300.1| putative pseudouridine synthase family 1 protein [Photobacterium
           profundum 3TCK]
          Length = 374

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 81/348 (23%), Positives = 141/348 (40%), Gaps = 13/348 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
            +++ KV+ARAG  SRRE+E MI   RV ++G++ +        +  + +DG  +     
Sbjct: 2   SEKLQKVLARAGQGSRREIELMIQSGRVSIDGVVAKLGDRLDDLSVLVRLDGHKIDLVSP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L        L T H     R+           R +SVGRLD NT GLLL T D
Sbjct: 62  SDEVCRVLAYNKPEGELCTRHDPEGRRTVFDRLPRLSSGRWVSVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS    R Y VR  G+++++ +  L +G+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRSVEREYMVRVFGEINENMVKNLVQGVELEDGMARFEDVVYSGGEGMNH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
              V + EG+NRE++++++     V+RL R+ YG   L   +  G   E+    L+E   
Sbjct: 182 TFYVVITEGRNREVRRLWDSQGVTVSRLKRVRYGDIYLTKDMPRGGWMEL---ELKEVNY 238

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              + E +        +  T+   +            R  +    +    ++ + + P  
Sbjct: 239 LREVVELEAE----ENTMLTVEGQKRKRGVRQIRRAVRRHEERVTETPRGRRGRTSNPDE 294

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           RR+   N  +      +       +    + +   PS     + + +K
Sbjct: 295 RRSSTRNSEVEGQNAPAGKRKPSGKPSTAKPTRGKPSAGKPAQGNRRK 342


>gi|86158107|ref|YP_464892.1| ribosomal large subunit pseudouridine synthase B [Anaeromyxobacter
           dehalogenans 2CP-C]
 gi|85774618|gb|ABC81455.1| ribosomal large subunit pseudouridine synthase B [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 328

 Score =  171 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 83/281 (29%), Positives = 126/281 (44%), Gaps = 1/281 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +A AGIASRR+ E +I+  RV+VN   +      V    D + VDG  + + ++
Sbjct: 4   ERLQKYLAGAGIASRRKAEALISAGRVRVNQRTVTELGTKVDPGRDLVTVDGALVSQPDQ 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP G VTT SDP GR T  + L  +  R   VGRLD + EG LLLT+DG LA 
Sbjct: 64  RSYYLLYKPSGCVTTASDPQGRPTAMEYLRGVPGRPFPVGRLDYDAEGALLLTDDGELAN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     RVY V+  G    + L  +K G+ ++      ++  +      N W+ V 
Sbjct: 124 RLAHPRYGHQRVYLVKVKGDPPAEALERMKAGVRLEDGPARAIEAAVHDHADRNVWIRVV 183

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           + EG+   +K++ E    +V RL R  +G   +G L  G  R +  + +R       LE 
Sbjct: 184 VGEGRFHLVKRLCEAVGLQVQRLFRPEFGGIGVGGLRPGKFRRLQPEEVRALRQRVGLES 243

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
                   +       R   +     P       +  S   
Sbjct: 244 GTPARGPSVRELPKAARRHGHGPPAAPGAAPAPAEPGSPDE 284


>gi|301320594|gb|ADK69237.1| pseudouridylate synthase [Mycoplasma mycoides subsp. mycoides SC
           str. Gladysdale]
          Length = 252

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 71/249 (28%), Positives = 122/249 (48%), Gaps = 5/249 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--RKAE 71
           +R+ KVI+  G  SRR  E++I + RVKVN  ++    V +     I++D   +      
Sbjct: 4   ERLQKVISSRGYCSRRAAEKLILENRVKVNDQIINTLGVKIDPKAEIKIDNRLVLSDSNN 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +   +L++KP  ++TT  DP  R TV D    +  RV  VGRLD +  GLLL+TNDG L 
Sbjct: 64  QKYYYLFYKPRLVLTTMYDPKKRKTVNDYFKDLNHRVYPVGRLDYDVSGLLLMTNDGVLF 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD--MQVTLDTQKGSNAW 188
             +  P  ++L+ Y+    GQV++ ++N L KG+ I           ++    +  + + 
Sbjct: 124 NFIMHPKYEFLKTYQGLCQGQVNKQQINQLIKGVYIDNDYLTKAYSAKLVKYDKLKNTSI 183

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           V + + EGK   +KK+F+    ++ +L R      ++  L  G  RE+    ++   G +
Sbjct: 184 VELTINEGKKHHVKKMFDSIQAQLLKLKRTKIEFLEIADLKPGQYRELKTHEVKRLYGIY 243

Query: 249 LLEEAQVNL 257
              +   N 
Sbjct: 244 HSLKQNNNK 252


>gi|325268750|ref|ZP_08135378.1| ribosomal large subunit pseudouridine synthase B [Prevotella
           multiformis DSM 16608]
 gi|324988918|gb|EGC20873.1| ribosomal large subunit pseudouridine synthase B [Prevotella
           multiformis DSM 16608]
          Length = 509

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 107/234 (45%), Gaps = 1/234 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +   P R++K +A AG+ SRRE +  I    V VNG +++     V+ +D +     P+ 
Sbjct: 269 DPNEPIRLNKYLANAGVCSRREADEFILSGAVTVNGEVVKELGSKVLRSDVVLFQEKPVS 328

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ++  + L      + T+      ++ +     +   R+  VGRLD NT G+LLLTNDG
Sbjct: 329 LEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKGACPERIYPVGRLDRNTTGVLLLTNDG 388

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     +VY V     V  + L  +  GI ++        +     +     
Sbjct: 389 DLASKLTHPKFLKKKVYHVFLDKPVTANDLQKISDGIELEDGEIKADAIEYADPQ-DQTQ 447

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           V + +  GKNR ++++FE   ++V +L R+ +       +  G  R +++K + 
Sbjct: 448 VGIEIHSGKNRIVRRIFESLGYRVVKLDRVQFAGLTKKNVRRGDWRFLTEKEVD 501


>gi|291297121|ref|YP_003508519.1| RNA-binding S4 domain-containing protein [Meiothermus ruber DSM
           1279]
 gi|290472080|gb|ADD29499.1| RNA-binding S4 domain protein [Meiothermus ruber DSM 1279]
          Length = 295

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 78/303 (25%), Positives = 133/303 (43%), Gaps = 12/303 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R+ + +ARAGIASRR+ E +I   RV +N  +       V   D + +DG  +R  ++
Sbjct: 3   GMRLQQFLARAGIASRRKAEDLIRAGRVTINEQVA-SIGAVVQPGDIVRLDGERVRMPQK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +   HKP G  TTH D      V++ +P       +VGRLD +TEGLLLLTNDG L +
Sbjct: 62  KVVIALHKPKGYTTTHEDEHAEKIVYELVPKHPGL-HAVGRLDKDTEGLLLLTNDGHLTQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDK-LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P  Q  ++YR         +K    L +G+V+       ++        +   V +
Sbjct: 121 HLTHPRNQVPKLYRAWCKNGRVSEKACQQLVQGVVLGDGLAQALE-----AHPTRNGVKL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L EG+ RE++++     + V RL+R++ GP +LG L AG  R ++   ++         
Sbjct: 176 VLTEGRKREVRRMLNKVGYPVERLVRLAVGPIELGELEAGEWRYLTPDEIK----LLYTS 231

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
                            + +     +     +  ++ S+++   + +       H R   
Sbjct: 232 AQLPRPKTQAQKPTPTPKAKTGTRPQKSTVESSSERLSTRQRQGTNRGSTDRQAHTRAGR 291

Query: 312 SNV 314
           +N 
Sbjct: 292 TNK 294


>gi|47565741|ref|ZP_00236781.1| pseudouridine synthase family 1 protein VC2223 [Bacillus cereus
           G9241]
 gi|228985473|ref|ZP_04145630.1| Pseudouridine synthase [Bacillus thuringiensis serovar tochigiensis
           BGSC 4Y1]
 gi|47557377|gb|EAL15705.1| pseudouridine synthase family 1 protein VC2223 [Bacillus cereus
           G9241]
 gi|228774238|gb|EEM22647.1| Pseudouridine synthase [Bacillus thuringiensis serovar tochigiensis
           BGSC 4Y1]
          Length = 238

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 64/228 (28%), Positives = 109/228 (47%), Gaps = 7/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCTSEKSV--KGNIIDLVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T      S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEITQL----SKYEFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKR 225


>gi|167756918|ref|ZP_02429045.1| hypothetical protein CLORAM_02467 [Clostridium ramosum DSM 1402]
 gi|167703093|gb|EDS17672.1| hypothetical protein CLORAM_02467 [Clostridium ramosum DSM 1402]
          Length = 239

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 63/236 (26%), Positives = 111/236 (47%), Gaps = 4/236 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A  GI +R+EV+ +I +  VKVNG+++++    V    D I  D   +     
Sbjct: 3   MRLDKLLANYGIGTRKEVKSLIRKGFVKVNGMIIKKDDFKVDHEIDEIVFDDELIEYRPY 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + +   D    + +          +  VGRLD++TEGLLL+TNDG  + 
Sbjct: 63  VYIMLNKPAGYI-SATKDNLHPTVLELIEGYENYDLFPVGRLDLDTEGLLLITNDGDFSH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  PS    ++Y     G +D+  +   K GI++  G       + +  +   +  V +
Sbjct: 122 KLLAPSRNHSKIYFANIAGVMDEQDIQAFKDGIILNTGYHCKPANLEIINKNNDSCDVRI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
            + EGK  ++KK+ E    +V  L R+S    +L  +L  G  RE+S + L + + 
Sbjct: 182 EIFEGKFHQVKKMVEVCGKEVIYLKRLSIRNLELDRSLSLGDFRELSNEELVDLME 237


>gi|320536822|ref|ZP_08036818.1| hypothetical protein HMPREF9554_01551 [Treponema phagedenis F0421]
 gi|320146331|gb|EFW37951.1| hypothetical protein HMPREF9554_01551 [Treponema phagedenis F0421]
          Length = 239

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 72/246 (29%), Positives = 120/246 (48%), Gaps = 13/246 (5%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M DK I        R+   +A++GIASRR  E++I   RV VNGI +      V+ +D +
Sbjct: 1   MPDKEI--------RLQVYLAKSGIASRRASEKLILDGRVSVNGIKVTELGTKVLPSDIV 52

Query: 61  EVDGVPLRKAERTRL-WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
             D   ++  +  R   L      + +   +    +       +   R+ ++GRLD+ + 
Sbjct: 53  CFDNQQIKFEKEKRYVLLNKPVGYVCSLSDEMGRATAADLLKEAYTERLYNIGRLDMYSG 112

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G +L TNDG  +  +E PS +  + Y +     +    +    +GI I+GI Y      +
Sbjct: 113 GAILFTNDGDFSARIEHPSAEIEKEYLIETTQDIPDTLIERFTRGIRIEGIFYR----CV 168

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             ++ ++   ++ L EGKNREI+KVF+FF   + RLIR+  G  QL  L  G  R ++K+
Sbjct: 169 SAKRQASRKASIVLIEGKNREIRKVFDFFKIPIKRLIRVRIGGIQLNGLKPGEFRNLTKE 228

Query: 240 ILREQL 245
            + E L
Sbjct: 229 EIAELL 234


>gi|254385863|ref|ZP_05001182.1| pseudouridine synthase [Streptomyces sp. Mg1]
 gi|194344727|gb|EDX25693.1| pseudouridine synthase [Streptomyces sp. Mg1]
          Length = 260

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 69/232 (29%), Positives = 110/232 (47%), Gaps = 1/232 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R+ KV+ARAG+ SRR  E +I Q RV+VNG ++      V   D I+VDG+ +  
Sbjct: 21  EEEGERLQKVLARAGMGSRRACEELIEQARVEVNGEIVLEQGKRVQPKDEIKVDGLTVAT 80

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                  L      + T       +  + D + +  +R+  VGRLD  TEG++LLTN G 
Sbjct: 81  QSYLFFALNKPAGVVSTMEDPDGRQ-CLGDYVTNRETRLFHVGRLDTETEGIILLTNHGE 139

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  P     + Y     G + ++    LK GI ++          +  Q G N  V
Sbjct: 140 LAHRLTHPKYGVKKTYVAAITGPLPREIGKRLKDGIELEDGYARADHFRVVDQVGKNYLV 199

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V L EG+   ++++     + V +L+R S+GP +LG   +G  R ++   +
Sbjct: 200 EVTLHEGRKHIVRRMMAEAGFPVEKLVRTSFGPIELGDQKSGWLRRLTNTEV 251


>gi|49185230|ref|YP_028482.1| RNA pseudouridylate synthase [Bacillus anthracis str. Sterne]
 gi|49477651|ref|YP_036487.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus
           thuringiensis serovar konkukian str. 97-27]
 gi|52143096|ref|YP_083735.1| tRNA pseudouridine synthase A [Bacillus cereus E33L]
 gi|118477786|ref|YP_894937.1| ribosomal large subunit pseudouridine synthase F [Bacillus
           thuringiensis str. Al Hakam]
 gi|228914973|ref|ZP_04078578.1| Pseudouridine synthase [Bacillus thuringiensis serovar pulsiensis
           BGSC 4CC1]
 gi|228927441|ref|ZP_04090497.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228933676|ref|ZP_04096524.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228945990|ref|ZP_04108331.1| Pseudouridine synthase [Bacillus thuringiensis serovar monterrey
           BGSC 4AJ1]
 gi|229091360|ref|ZP_04222575.1| Pseudouridine synthase [Bacillus cereus Rock3-42]
 gi|229121932|ref|ZP_04251151.1| Pseudouridine synthase [Bacillus cereus 95/8201]
 gi|229184594|ref|ZP_04311796.1| Pseudouridine synthase [Bacillus cereus BGSC 6E1]
 gi|270000600|ref|YP_003329039.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           Ames]
 gi|291612215|ref|YP_003541029.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           'Ames Ancestor']
 gi|49179157|gb|AAT54533.1| RNA pseudouridylate synthase [Bacillus anthracis str. Sterne]
 gi|49329207|gb|AAT59853.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus
           thuringiensis serovar konkukian str. 97-27]
 gi|51976565|gb|AAU18115.1| tRNA pseudouridine synthase A [Bacillus cereus E33L]
 gi|118417011|gb|ABK85430.1| ribosomal large subunit pseudouridine synthase F [Bacillus
           thuringiensis str. Al Hakam]
 gi|224552841|gb|ACN55054.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           'Ames Ancestor']
 gi|228598911|gb|EEK56529.1| Pseudouridine synthase [Bacillus cereus BGSC 6E1]
 gi|228661581|gb|EEL17202.1| Pseudouridine synthase [Bacillus cereus 95/8201]
 gi|228691989|gb|EEL45731.1| Pseudouridine synthase [Bacillus cereus Rock3-42]
 gi|228813683|gb|EEM59963.1| Pseudouridine synthase [Bacillus thuringiensis serovar monterrey
           BGSC 4AJ1]
 gi|228826003|gb|EEM71788.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228832234|gb|EEM77815.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228844769|gb|EEM89815.1| Pseudouridine synthase [Bacillus thuringiensis serovar pulsiensis
           BGSC 4CC1]
 gi|269850305|gb|ACZ49999.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           Ames]
          Length = 238

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 64/228 (28%), Positives = 109/228 (47%), Gaps = 7/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCTSEKSV--KGNIIDLVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T      S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEITQL----SKYEFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKR 225


>gi|270284888|ref|ZP_06194282.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           muridarum Nigg]
 gi|270288916|ref|ZP_06195218.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           muridarum Weiss]
 gi|11279963|pir||E81741 ribosomal large chain pseudouridine synthase B TC0096 [imported] -
           Chlamydia muridarum (strain Nigg)
          Length = 241

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 66/230 (28%), Positives = 102/230 (44%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R++K +A AG+ASRR+ + +I    V +NG +     V V    D+IEV G  +   ++
Sbjct: 4   VRLNKFLASAGVASRRKCDEIIFAGSVTINGKVAAGPFVTVDEEFDYIEVGGQRIGAEKK 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               ++     L ++         V D L     R+ +VGRLD  T GL+L+TNDG  A 
Sbjct: 64  VYFMVHKPLGYLCSSERKFPQSKLVIDLLSHCPYRLFTVGRLDKETSGLILVTNDGEFAN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  PS    + Y ++    V    L  L  G +I G     + V    +      + + 
Sbjct: 124 RVIHPSFGITKEYLLKVSRDVTAKDLESLMSGTMIDGRIVRPVSVKKVRRG----TIKII 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGK  EI+   E    ++  L RI  G   LG L  G  RE++   L 
Sbjct: 180 VNEGKKHEIRLFAEAAGLQLLELKRIRIGSLVLGGLPYGKYRELTDAELD 229


>gi|254496468|ref|ZP_05109345.1| pseudouridine synthase [Legionella drancourtii LLAP12]
 gi|254354324|gb|EET12982.1| pseudouridine synthase [Legionella drancourtii LLAP12]
          Length = 252

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 77/241 (31%), Positives = 121/241 (50%), Gaps = 7/241 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--- 68
           + +R+ K++++AG+ SRRE+ER I    V+VNG  ++    +    D I V G  +    
Sbjct: 2   SSERLQKILSQAGLGSRREMERWIENGWVQVNGKPVK-LGDSASGDDKITVKGKLIPNPL 60

Query: 69  --KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
             K     L  +     + + H     ++           R + VGRLD+NT GLL+ TN
Sbjct: 61  KIKQNTRILLYHKPVGEISSRHDPKFEKTVFDRLPHLRQGRWVQVGRLDLNTSGLLIFTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G LA  L  P     R Y VR HGQV Q+ L +L+KG+ +        ++      G+N
Sbjct: 121 NGELANQLMHPRYGLEREYAVRVHGQVTQEMLTVLQKGVELDDGPAKFSRLESRGGDGAN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
            W  V L EG+NRE+++++E    +V+RLIRI YG   +   L    T E++ K + + L
Sbjct: 181 TWYHVTLNEGRNREVRRLWESQGVEVSRLIRIRYGMLTMPRFLGRAQTYELTPKEVTDFL 240

Query: 246 G 246
            
Sbjct: 241 A 241


>gi|213963701|ref|ZP_03391952.1| ribosomal large subunit pseudouridine synthase B [Capnocytophaga
           sputigena Capno]
 gi|213953696|gb|EEB65027.1| ribosomal large subunit pseudouridine synthase B [Capnocytophaga
           sputigena Capno]
          Length = 410

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 60/228 (26%), Positives = 112/228 (49%), Gaps = 1/228 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGI SRR  +  I+   V VNG ++      V  TD +  DG  L   ++ 
Sbjct: 177 VRLNKYIADAGICSRRNADMYISSGNVTVNGEVMTTLGYRVKPTDEVRFDGKLLSSEKKE 236

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L      + TT+ +   ++ +     +  +R++ VGRLD  T GLLLLTNDG L + 
Sbjct: 237 YILLNKPKGFITTTNDEKGRKTVMDLVANATSARILPVGRLDRATTGLLLLTNDGELTKK 296

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P+    ++Y V    ++D      ++ G+ ++       +++    K  N  + + +
Sbjct: 297 LTHPTHGVRKIYHVILDRKLDYKDFMKIQDGLELEDGFIEVDEISYVNDKPKN-EIGIKI 355

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             G+NR ++++FE   ++V +L R+ +       L  G  R ++++ +
Sbjct: 356 HSGRNRIVRRIFEHLGYQVEKLDRVVFAGLTKKDLPRGHWRRLTQQEV 403


>gi|261416560|ref|YP_003250243.1| RNA-binding S4 domain protein [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|261373016|gb|ACX75761.1| RNA-binding S4 domain protein [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|302327436|gb|ADL26637.1| pseudouridine synthase B, ribosomal large subunit [Fibrobacter
           succinogenes subsp. succinogenes S85]
          Length = 243

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 83/242 (34%), Positives = 123/242 (50%), Gaps = 6/242 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA-- 70
            R++K I+ +G ASRR  + ++A  RV+VNG  +      V  T D + VDG  L+    
Sbjct: 1   MRINKYISLSGFASRRAADELVADGRVQVNGETISDLGHQVDETKDQVTVDGKLLKLPTN 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ++T++ ++HKP G V T  DP GR TV+D LP  +     VGRLD+ + GLLL T+DG L
Sbjct: 61  KKTKVIMFHKPAGCVCTKDDPQGRRTVYDYLPPGYHNFKYVGRLDLQSRGLLLFTDDGEL 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---SNA 187
              L  PS +  R Y V     + +     L  G+ I+     D Q  +         N 
Sbjct: 121 LYRLTHPSFEVPRSYYVWTTRPLSESAAQRLVDGVDIRDPEDPDAQEEIAFATDVYLENG 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           +  + L EGKNREI+++     +++  L R+SY   QLG L AG  RE++   L +    
Sbjct: 181 FAELVLIEGKNREIRRMMRAIGYEIRDLKRVSYCQIQLGDLPAGEFRELTPNELNKLRQA 240

Query: 248 HL 249
             
Sbjct: 241 VH 242


>gi|161507296|ref|YP_001577250.1| 16S pseudouridylate synthase [Lactobacillus helveticus DPC 4571]
 gi|160348285|gb|ABX26959.1| 16S Pseudouridylate synthase [Lactobacillus helveticus DPC 4571]
 gi|328468687|gb|EGF39674.1| 16S pseudouridylate synthase [Lactobacillus helveticus MTCC 5463]
          Length = 236

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 103/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I +  V VNG +++     V  +D + VDG  +   +  
Sbjct: 1   MRIDKYLANMNVGSRKEVHVLIKKGIVTVNGDVVKTPKQQVKESDEVLVDGQEVNYQKYH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +      L  T                 +  +  VGRLD +T GLLLLTNDG L   
Sbjct: 61  YFLMNKPKGVLSATEDRSQRTVISLLKPQDQYQGITPVGRLDKDTTGLLLLTNDGQLNHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG--SNAWVT 190
           L  P+    ++YR +  G  D + +     G+ +  G      ++ +  Q     ++ + 
Sbjct: 121 LLAPNKHVDKIYRAKIAGVADDETVKTFASGMTLGDGTKLKPAELKILVQDEEHDSSEIE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           + +REGK  +IK++F     KV  L RIS G  +L   L  G+  E+S   +
Sbjct: 181 IKIREGKYHQIKRMFGAVGMKVVELERISMGKLKLPKDLKRGNYIELSLDDV 232


>gi|315657981|ref|ZP_07910855.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           lugdunensis M23590]
 gi|315497017|gb|EFU85338.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           lugdunensis M23590]
          Length = 230

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 104/232 (44%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G  +R EV++ + +  V VNG + + A   +    D +++ G  +   E 
Sbjct: 2   MRLDKFLAHMGQGTRTEVKQSLKKGNVTVNGKVEKSAKTQINPHHDVVQIHGHQIDYVET 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L      + +   DP   + +       +  +  VGRLD +TEGLLL+TNDG  + 
Sbjct: 62  VYLMLNKPKGYI-SATEDPKQATVIDLIKDYKYLDLFPVGRLDKDTEGLLLITNDGQFSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+    + Y V     V +D   + K+G+++        ++T+     S     V 
Sbjct: 121 NLMNPNKHVAKTYLVTSKYPVTKDNQYMFKQGVMLSDGLTKPAELTIIDDYHS----KVT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           + EG+  +IK++F     +V  L RI     +L   L  G  R +++  + +
Sbjct: 177 IYEGRYHQIKRMFHSIENEVLELKRIQIANLRLDEELDEGQYRVLTQTDIEQ 228


>gi|124515286|gb|EAY56796.1| Pseudouridine synthase, Rsu [Leptospirillum rubarum]
          Length = 616

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 93/343 (27%), Positives = 159/343 (46%), Gaps = 3/343 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K++A  G+ASRR  E MI    VKVNGI++      V   TD + VDG  +     
Sbjct: 18  IRLQKLLAHRGLASRRNAEEMIRGGLVKVNGIVVTVPGTKVHPETDRVTVDGKTVPVEPE 77

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L+L++KP G+V+T  DPD ++T+ D  P I + +I VGRLDI +EG+LLLTN+G LA+
Sbjct: 78  PFLFLFYKPKGIVSTLHDPDEKTTLKDFFPQI-NPLIHVGRLDIQSEGVLLLTNNGDLAQ 136

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
            +  P  +  R Y V+  G V  + L+ L+   + + G     +++  +    +N+W  +
Sbjct: 137 RILHPRYEIPRTYLVKVQGVVKPEHLDRLRSGKVRLDGRPVQPLELEQERLTETNSWYRI 196

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L EG+NRE++++F+  ++ V +L RI++G   L  L  G  R V+ + +   L     +
Sbjct: 197 TLTEGRNREVRRLFDALHYFVLKLTRIAFGNLDLAGLEPGEYRLVTPEEIALLLSGARWK 256

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
             +          +       +         +R        +G +   +   P  R+   
Sbjct: 257 RKESIPPPERSPRKPNPATPSSPDFRRHSFRSRTTSPDRTFSGPADGDQEEDPFPRQTGQ 316

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +                +R  N R      +K+    +S K+
Sbjct: 317 GHRSRPDTRSRGLSQSDSERFFNGRPRHRSDNKQQSGPSSQKR 359


>gi|228921081|ref|ZP_04084416.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228838627|gb|EEM83933.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 238

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 64/228 (28%), Positives = 109/228 (47%), Gaps = 7/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCTSEKAV--KGNIIDLVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T      S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEITQL----SKYEFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKR 225


>gi|309799641|ref|ZP_07693863.1| RNA pseudouridine synthase family protein [Streptococcus infantis
           SK1302]
 gi|308116732|gb|EFO54186.1| RNA pseudouridine synthase family protein [Streptococcus infantis
           SK1302]
          Length = 240

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 63/237 (26%), Positives = 102/237 (43%), Gaps = 4/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +    + SR EV+  +   RV VNG   + A + +   TD I  DG  L   E 
Sbjct: 1   MRLDKYLVACAVGSRTEVKNFLKAGRVMVNGKKEKSAKLQINEETDEICFDGQKLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    V  VGRLDI+T GLLLLTNDG LA 
Sbjct: 61  VYYMMNKPQGVISATEDSKHKTVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVT 190
            L  P     + Y  +  G + Q+ +    +GI ++         ++    ++ + + V 
Sbjct: 121 ALLSPKRHVDKTYLAQVGGIMTQEDVETFAQGIPLKDFTCQPAILELVSIDREKNQSLVR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K+ L   L 
Sbjct: 181 VTIAEGKFHQVKRMVAYCGKEVVDLQRLTMGTLTLDEGLKRGEWRRLTKEELEALLE 237


>gi|237732236|ref|ZP_04562717.1| 16S rRNA pseudouridylate synthase A [Citrobacter sp. 30_2]
 gi|226907775|gb|EEH93693.1| 16S rRNA pseudouridylate synthase A [Citrobacter sp. 30_2]
          Length = 235

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 56/231 (24%), Positives = 103/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G +++ +A  ++    +E DG  L +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRANRVTVDGEIVKNSAFKLLPEHDVEYDGNSLVQQNGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D       G+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAHGVQLHNEKDLTKPAVLEVI----TPTQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G  +L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVELHRERIGDIRLDDDLEPGEYRPLTEEEI 227


>gi|237755405|ref|ZP_04584032.1| ribosomal large subunit pseudouridine synthase B
           [Sulfurihydrogenibium yellowstonense SS-5]
 gi|237692446|gb|EEP61427.1| ribosomal large subunit pseudouridine synthase B
           [Sulfurihydrogenibium yellowstonense SS-5]
          Length = 244

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 64/237 (27%), Positives = 120/237 (50%), Gaps = 4/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R++K IA++GI SRR+ + +I +  VKVNG +++     +    D +EV+G  ++  E+
Sbjct: 3   VRLNKYIAQSGICSRRKADELIKEGIVKVNGEIIKDLGAKINPEKDVVEVEGNIIKPVEK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGG 129
                 +KP+G ++             +L    +I   +  VGRLD N+EGLL+LTNDG 
Sbjct: 63  KIYIKIYKPVGYLSAVGKDKFGRKTLTDLLKELNIKENLFPVGRLDYNSEGLLILTNDGE 122

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P  +  ++Y V    +V++++LN +KKG +++   +   +V +      + W+
Sbjct: 123 FANKIAHPRHEIRKIYHVEVVPKVNEERLNQMKKGAILEDGFFKPDKVEILKHTKDSTWL 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
              +  GK R +++    FN KV RL+R+      +  L     + ++ K ++    
Sbjct: 183 LFEIHSGKKRILRRYVSKFNHKVRRLVRVKIDSISIENLKPHQFKHLTDKEVKSIYE 239


>gi|91215957|ref|ZP_01252926.1| pseudouridine synthase, Rsu [Psychroflexus torquis ATCC 700755]
 gi|91185934|gb|EAS72308.1| pseudouridine synthase, Rsu [Psychroflexus torquis ATCC 700755]
          Length = 235

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 55/234 (23%), Positives = 110/234 (47%), Gaps = 6/234 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N    R++K +++AG  SRRE ++++ Q RV +NG  +      V S D + VDG  + K
Sbjct: 2   NKESIRINKYLSQAGFCSRREADKLMEQGRVTINGEYI-EMGTKVNSGDKVYVDGKLVEK 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               +++L       V   ++         +     +R+  +GRLD  +EGL+L+TNDG 
Sbjct: 61  ETEEKVYLAVYKPKGVVCTTNSKVEKNNIVDFVDYPTRIFPIGRLDKMSEGLILMTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +        + Y V  +  +  D +  ++KG+ I        +     +K  +   
Sbjct: 121 IVNHILRARHFHDKEYLVTVNKTITDDFIEKMRKGVPILDTMSRRCE----VEKLGDRSF 176

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + L +G NR+I+++ E  +++V  L R       L  +  G+ R ++++ +++
Sbjct: 177 KIVLTQGLNRQIRRMCEALDYRVRTLKRTRIKNITL-DVEKGNYRNLTEEEIKD 229


>gi|260102596|ref|ZP_05752833.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           helveticus DSM 20075]
 gi|260083623|gb|EEW67743.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           helveticus DSM 20075]
          Length = 236

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 103/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I +  V VNG +++     V  +D + VDG  +   +  
Sbjct: 1   MRIDKYLANMNVGSRKEVHVLIKKGIVTVNGDVVKTPKQQVKESDEVLVDGQEVNYQKYH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +      L  T                 +  +  VGRLD +T GLLLLTNDG L   
Sbjct: 61  YFLMNKPKGVLSATEDRSQRTVISLLKPQDQYQGITPVGRLDKDTTGLLLLTNDGQLNHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG--SNAWVT 190
           L  P+    ++YR +  G  D + +     G+ +  G      ++ +  Q     ++ + 
Sbjct: 121 LLAPNKHVDKIYRAKIAGVADDETVKTFASGMTLGDGTKLKPAELKILAQDEEHDSSEIE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           + +REGK  +IK++F     KV  L RIS G  +L   L  G+  E+S   +
Sbjct: 181 IKIREGKYHQIKRMFGAVGMKVVELERISMGKLKLPKDLKRGNYIELSLDDV 232


>gi|169824529|ref|YP_001692140.1| ribosomal large subunit pseudouridine synthase B [Finegoldia magna
           ATCC 29328]
 gi|167831334|dbj|BAG08250.1| ribosomal large subunit pseudouridine synthase B [Finegoldia magna
           ATCC 29328]
          Length = 242

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 71/243 (29%), Positives = 120/243 (49%), Gaps = 2/243 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA++G  SRR  + +I   +V VNG +L   +  V  TD +EV+G  +   E  
Sbjct: 1   MRINKFIAQSGYCSRRNADELIKNSKVYVNGTILLDLSYQVNDTDIVEVEGKKINLKEDK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KPIG  +T  D         +L    +RV  VGRLD ++ GLL+LTNDG     
Sbjct: 61  IYIAINKPIGYASTVKDKFADK-KVVDLIKSDTRVYPVGRLDKDSHGLLILTNDGEFTYE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  ++Y V   G+ ++ ++  LK GI++ G      ++       ++    V +
Sbjct: 120 LTHPKFEHKKIYEVLVKGKPNKTEIKQLKDGILLDGYKLKKSKIEFIENVKNDTKYRVTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLLEE 252
            EG+NR+I+++F+F N  V  L R+  G +++   L +G  + +  K L    G +   +
Sbjct: 180 FEGRNRQIRRMFDFINHPVLDLKRVQIGNYKMENSLKSGEYKLLKSKDLDLIRGNNDRSK 239

Query: 253 AQV 255
              
Sbjct: 240 TSK 242


>gi|302380740|ref|ZP_07269205.1| putative pseudouridine synthase B, ribosomal large subunit
           [Finegoldia magna ACS-171-V-Col3]
 gi|302311683|gb|EFK93699.1| putative pseudouridine synthase B, ribosomal large subunit
           [Finegoldia magna ACS-171-V-Col3]
          Length = 242

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 71/243 (29%), Positives = 120/243 (49%), Gaps = 2/243 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA++G  SRR  + +I   +V VNG +L   +  V  TD +EV+G  +   E  
Sbjct: 1   MRINKFIAQSGYCSRRNADELIKNSKVYVNGTILLDLSYQVNDTDIVEVEGKKINLKEDK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KPIG  +T  D         +L    +RV  VGRLD ++ GLL+LTNDG     
Sbjct: 61  IYIAINKPIGYASTVKDKFADK-KVVDLIKSDTRVYPVGRLDKDSHGLLILTNDGEFTYE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  ++Y V   G+ ++ ++  LK GI++ G      ++       ++    V +
Sbjct: 120 LTHPKFEHKKIYEVLVKGKPNKTEIKQLKDGILLDGYKLKKSKIEFIENIKNDTKYRVTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLLEE 252
            EG+NR+I+++F+F N  V  L R+  G +++   L +G  + +  K L    G +   +
Sbjct: 180 FEGRNRQIRRMFDFINHPVLDLKRVQIGNYKMENSLKSGEYKLLKSKDLDLIRGNNDRSK 239

Query: 253 AQV 255
              
Sbjct: 240 TSK 242


>gi|300717592|ref|YP_003742395.1| ribosomal small subunit pseudouridine synthase A [Erwinia
           billingiae Eb661]
 gi|299063428|emb|CAX60548.1| Ribosomal small subunit pseudouridine synthase A [Erwinia
           billingiae Eb661]
          Length = 234

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 53/238 (22%), Positives = 101/238 (42%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR    R +   +V V+G ++ + A  +   + +E DG PL      
Sbjct: 1   MRLDKFLSQQLEISRAIALRELRAHKVTVDGEVVRQGAFKLKPENQVEYDGNPLHLQFGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++        ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLEEPTAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +  D       G+ +           + +     S   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPLADDTAAQFTAGVQLHNEKYLTKPATLEVV----SECQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
            + EG+  ++K++F      V  L R   G   +   L  G  R ++ + +   + P 
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVALHRERIGAIVMDEDLGEGEYRPLTAEEIASVVVPR 234


>gi|160876688|ref|YP_001556004.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|160862210|gb|ABX50744.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|315268888|gb|ADT95741.1| pseudouridine synthase [Shewanella baltica OS678]
          Length = 236

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 64/233 (27%), Positives = 109/233 (46%), Gaps = 11/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMST----DHIEVDGVPLR 68
            R++K +A+ GI SRRE  R+I   R+ +NG +      + +       D IE+DG P+ 
Sbjct: 1   MRLAKYLAQCGIGSRREACRLIEAGRITLNGHIARHTDPIRLDELLNCLDRIELDGAPIT 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + E    W+++K +G      + D   T   +L     R+  VGRLD ++ GLLLLTNDG
Sbjct: 61  QTETLAYWVFNKAVGTDCRLLEQDE--TSLVHLLPKAPRLYPVGRLDKDSRGLLLLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P     + Y VR       + +  +  G+  + +     QV   +       
Sbjct: 119 ELTHKLMHPCFAHSKTYHVRLDRPFTDEFVEQMASGVRYKDVQTLPCQVRRLSSDS---- 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             + L +G NR+I+++     +KV  L R++     L +L  G+ R ++ + +
Sbjct: 175 FEIVLTQGLNRQIRRMAIALGYKVIDLQRVALMTLTLESLAEGAMRPLTPQEV 227


>gi|222095973|ref|YP_002530030.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus
           Q1]
 gi|229139077|ref|ZP_04267654.1| Pseudouridine synthase [Bacillus cereus BDRD-ST26]
 gi|229196600|ref|ZP_04323344.1| Pseudouridine synthase [Bacillus cereus m1293]
 gi|221240031|gb|ACM12741.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus
           Q1]
 gi|228586956|gb|EEK45030.1| Pseudouridine synthase [Bacillus cereus m1293]
 gi|228644432|gb|EEL00687.1| Pseudouridine synthase [Bacillus cereus BDRD-ST26]
          Length = 238

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 64/228 (28%), Positives = 109/228 (47%), Gaps = 7/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCTSEKSV--KGNIIDLVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T      S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEITQL----SKYEFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKR 225


>gi|163940156|ref|YP_001645040.1| RNA-binding S4 domain-containing protein [Bacillus
           weihenstephanensis KBAB4]
 gi|163862353|gb|ABY43412.1| RNA-binding S4 domain protein [Bacillus weihenstephanensis KBAB4]
          Length = 235

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 62/227 (27%), Positives = 107/227 (47%), Gaps = 7/227 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ AG ASRR  +++I +++V +NG + +     V   D + V+G  LR A   
Sbjct: 1   MRINKFISEAGKASRRGADKLINERKVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCTSEKAV--KGNIIDLVNHPLRINHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  + L  +  G+ I        +VT      S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPEFLEKMAAGVKILDTKTLPCEVTQL----SKYEFEIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK 
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKKE 220


>gi|262182363|ref|ZP_06041784.1| putative pseudouridylate synthase [Corynebacterium aurimucosum ATCC
           700975]
          Length = 286

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 81/245 (33%), Positives = 127/245 (51%), Gaps = 4/245 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DH 59
           ++ KN        +R+ KV+A+AG+ASRR  E +I + RV+VNG ++ +    V    D 
Sbjct: 33  VEGKNKKNSQNQGERLQKVLAKAGVASRRHAEILIDEGRVEVNGQVIIKQGTRVDPNKDV 92

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDI 116
           I VDG  +   E T+ ++ +KP G+ +T SD  GR  V D +        R+  VGRLD 
Sbjct: 93  IRVDGTRINVNEETQYFVLNKPRGMQSTMSDDMGRPCVGDVVADRVVAGQRLFHVGRLDA 152

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +TEGLLLLTNDG LA  L  P  +  + Y     G+ D+  +  L++GI ++        
Sbjct: 153 DTEGLLLLTNDGELANRLMHPKYEVTKTYLATVLGEADKKLIRQLREGIELEDGLAQADY 212

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V +  +    + V V L EG+   ++++ +   + V RL+R      QLG +  GS R +
Sbjct: 213 VQIVDKNQGYSLVRVELHEGRKHIVRRMLKEAGYPVQRLVRTKLHTVQLGDMKPGSLRAL 272

Query: 237 SKKIL 241
           +   L
Sbjct: 273 NSNEL 277


>gi|21324194|dbj|BAB98819.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Corynebacterium glutamicum
           ATCC 13032]
          Length = 252

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 75/236 (31%), Positives = 117/236 (49%), Gaps = 4/236 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           +    R+ KV+A+AG+ASRR  E +I Q RV+VN  ++    V V    D I VDGV + 
Sbjct: 8   DSDGVRLQKVLAQAGVASRRHAEILIDQGRVEVNDRIVTTQGVRVDPNNDVIRVDGVRIH 67

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLT 125
             E    ++ +KP G+ +T SD  GR  V D +        R+  VGRLD +TEGLLLLT
Sbjct: 68  INEDLEYFVLNKPRGMHSTMSDELGRPCVGDLVSEKTASGQRLFHVGRLDADTEGLLLLT 127

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  P  +  + Y     G+     ++ L+ G+ ++          +      
Sbjct: 128 NDGELANRLMHPKYEVSKTYLATVRGEATNKLVSALRDGVELEDGPAKADFAQIIDVFQG 187

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + + + + EG+   ++++F+   + V RL+R      QLG    GS R ++   L
Sbjct: 188 KSLLRIEIHEGRKHIVRRLFDELGFPVERLVRTKLHTVQLGDQKPGSLRALNSSEL 243


>gi|37679411|ref|NP_934020.1| pseudouridine synthase family 1 protein [Vibrio vulnificus YJ016]
 gi|320156837|ref|YP_004189216.1| ribosomal large subunit pseudouridine synthase B [Vibrio vulnificus
           MO6-24/O]
 gi|37198154|dbj|BAC93991.1| pseudouridine synthase family 1 protein [Vibrio vulnificus YJ016]
 gi|319932149|gb|ADV87013.1| ribosomal large subunit pseudouridine synthase B [Vibrio vulnificus
           MO6-24/O]
          Length = 320

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 90/321 (28%), Positives = 131/321 (40%), Gaps = 9/321 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
           +++ KV+ARAG  SRRE+E +I   RV VNGI+ +           + +DG  +      
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKSGRVSVNGIVAKLGERLEDEQAVVRIDGHVVSVKAQE 62

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 L  Y     L T H     R+          SR ISVGRLD NT GLLL T DG
Sbjct: 63  EVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS Q  R Y VR  G+V++ K+  L  G+ +         V     +G N  
Sbjct: 123 ELANRLMHPSRQVEREYLVRVFGEVNEHKVRNLVNGVELDDGLARFEDVVYTGGEGMNHT 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGP 247
             V + EG+NRE+++++E  +  V+RL R+ YG   L   L  G   E+    L++    
Sbjct: 183 FYVVINEGRNREVRRLWESQDCTVSRLKRVRYGDIYLDKKLPRGGWMEL---ELKDVNYL 239

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
             L E +   +  I  + +  +       ++     R ++  S   G S       P   
Sbjct: 240 RELVELRPEKETMIELNNSSRKRDRARSQKIRRAVKRHEERVSTPKGRSNNAARRKPSKA 299

Query: 308 RNLASNVWMAKGIHSSFLSDS 328
               S         S      
Sbjct: 300 AGQTSKTNSRNQAGSRSKPQR 320


>gi|228965356|ref|ZP_04126448.1| Pseudouridine synthase [Bacillus thuringiensis serovar sotto str.
           T04001]
 gi|228794346|gb|EEM41860.1| Pseudouridine synthase [Bacillus thuringiensis serovar sotto str.
           T04001]
          Length = 238

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 64/228 (28%), Positives = 109/228 (47%), Gaps = 7/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCTSEKAV--KGNIIDLVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T      S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKSITPDFLEKMAAGVKILGTKTLPCEITQL----SKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKR 225


>gi|168576293|ref|ZP_02722176.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           MLV-016]
 gi|183577841|gb|EDT98369.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           MLV-016]
          Length = 240

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 103/233 (44%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYMMNKPKGVISATEDPKHRTVLDLLDDLAQSKEVFPVGRLDIDTHGLLLLTNNGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVT 190
           VL  P     + Y+ +  G + Q+ +    KGI ++       ++ +     + + + + 
Sbjct: 121 VLLSPKRHVDKTYQAQVKGIMTQEDVETFIKGIPLKDFTCQPARLEILSTDAEKNQSQIR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 181 VTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELE 233


>gi|312796184|ref|YP_004029106.1| ribosomal large subunit pseudouridine synthase B [Burkholderia
           rhizoxinica HKI 454]
 gi|312167959|emb|CBW74962.1| Ribosomal large subunit pseudouridine synthase B (EC 4.2.1.70)
           [Burkholderia rhizoxinica HKI 454]
          Length = 563

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 85/359 (23%), Positives = 140/359 (38%), Gaps = 11/359 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K  +  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 185 KRALSADDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 243

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 244 GKPVKRKLPNKPPRVLIYHKPAGEIVSHADPEGRPSVFDKLPPMKTAKWLAVGRLDFNTE 303

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLLT  G LA     P  Q  R Y VR  G++ +     L  G+ +       +++  
Sbjct: 304 GLLLLTTSGDLANRFMHPRYQVEREYAVRVIGELAESARQKLLNGVELDDGPASFLRIQD 363

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+  
Sbjct: 364 GGGEGTNRWYHVALAEGRNREVRRMFEAVGLTVSRLIRTRHGPIVLPRGLKRGRWEELED 423

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNII-----SEVPDDFTRMKKNSSQKN 293
             +R  +    L+    +      ++     D           + P    R  + +    
Sbjct: 424 NQVRALMSAVGLKGPGEDKAERSKATPRRQPDPMQTALGYISYDAPGPQRRFGRGARGGA 483

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             +              A       G        +G +      + +   K    R + 
Sbjct: 484 NWTSSTPPVPGYTGFAAAHGHGNMTGGKHDNRDVNGNQASGKGGNRAQKGKPRGGRGAQ 542


>gi|238916961|ref|YP_002930478.1| ribosomal small subunit pseudouridine synthase A [Eubacterium
           eligens ATCC 27750]
 gi|238872321|gb|ACR72031.1| ribosomal small subunit pseudouridine synthase A [Eubacterium
           eligens ATCC 27750]
          Length = 244

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 55/233 (23%), Positives = 102/233 (43%), Gaps = 6/233 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +A   + +R EV+ +I ++RV VN  ++ +    +    D + VDG  +   E 
Sbjct: 3   IRLDKYLADMQVGTRSEVKELIRKKRVTVNDNIVTKPESKINTDGDSVNVDGNAVGYHEY 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +V+   D    + +          +  VGRLD +TEGLL++TNDG +A 
Sbjct: 63  EYFMLNKPAG-VVSATDDNTCTTVIDLIKNKNRKDLFPVGRLDKDTEGLLIITNDGAMAH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLD--TQKGSNAWV 189
            L  P     + Y  +  G++   ++     G+ +          + +         + +
Sbjct: 122 DLLSPKKHVDKTYYAKVKGKISDMEVKQFADGLFVDEELTALPAILKVLSYNSDKDYSEI 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            V + EGK  ++K++F     +V  L RI++G   L   L  G  R ++K+ +
Sbjct: 182 HVTIHEGKFHQVKRMFTAIGSEVLFLKRITFGALPLDESLKTGEYRALTKEEI 234


>gi|77408873|ref|ZP_00785599.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae COH1]
 gi|77172512|gb|EAO75655.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae COH1]
          Length = 239

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 59/230 (25%), Positives = 106/230 (46%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++ +AG  SR +V+++I  ++V V+G ++ +  V V S    I V    +   E 
Sbjct: 1   MRLDKLLGQAGFGSRNQVKKLIRSRQVSVDGQIVTKDNVIVDSGLQSIFVGKERVCLKES 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +   LY     +               +       +  +GRLD +TEGLL++TN+G L  
Sbjct: 61  SYYLLYKPSGVVSAVRDSEHKTVIDLISEKDKVEGLYPIGRLDRDTEGLLIITNNGPLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V  +G +++D +   ++G+V          ++T+DT     +   +
Sbjct: 121 RMLHPKHHVAKTYYVEVNGFLERDAITFFEEGVVFDDGTKCKPAELTIDTANNDKSTARI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + EGK  ++KK+F  +  KV  L RIS+G  +L   L  G  R +    
Sbjct: 181 TITEGKFHQVKKMFLAYGVKVIYLRRISFGDLRLDMNLKPGQYRRLRDSE 230


>gi|300855314|ref|YP_003780298.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           ljungdahlii DSM 13528]
 gi|300435429|gb|ADK15196.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           ljungdahlii DSM 13528]
          Length = 229

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 68/226 (30%), Positives = 111/226 (49%), Gaps = 4/226 (1%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRLWLY 78
           +A  GIASRR+ E +I Q RVKVNG  ++     +    D I VD V + K  +    L 
Sbjct: 1   MAYCGIASRRKCESIILQGRVKVNGETIKSLGTKIDDKVDKITVDDVKIEKENKKVYILL 60

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           +KP G V+     D       ++  +  R+  +GRLD NT G+++LTNDG +   +  P 
Sbjct: 61  NKPTGYVS-TVKDDRGRNTILDIVKVKERIYPIGRLDYNTSGIIILTNDGEVYNKVAHPK 119

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVTVGLREG 196
            +  +VY     G   ++ ++  K G+ I G         +    +  +N+ V + + EG
Sbjct: 120 MEKNKVYVAVIKGIPSKEDIDKFKNGVNIDGYITAKADFNILNINKSKNNSKVRIKIHEG 179

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           KNR+I+K+ +     V  L RIS G   +G L  G  R +++  ++
Sbjct: 180 KNRQIRKMCDAIGHPVISLTRISIGNINVGNLEEGKWRYLNEDEIK 225


>gi|330999160|ref|ZP_08322879.1| pseudouridine synthase B, ribosomal large subunit [Parasutterella
           excrementihominis YIT 11859]
 gi|329575360|gb|EGG56904.1| pseudouridine synthase B, ribosomal large subunit [Parasutterella
           excrementihominis YIT 11859]
          Length = 313

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 84/308 (27%), Positives = 126/308 (40%), Gaps = 13/308 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
           +++ KV+A AGI SRR++E  IA+ R+ VNG         V  +D I  DG  +R++   
Sbjct: 12  EKLHKVLADAGIGSRRDMEERIAEGRISVNGEPAHV-GQRVTPSDVIRFDGRIVRRSALE 70

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  +     +V+        +          +R I+VGRLD NTEGLLL T+ 
Sbjct: 71  NNDVPKVLIYHKPAGEIVSKDDPEGRPTVFDHLPRIGGARWIAVGRLDFNTEGLLLFTDS 130

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P  +  R Y VR  G +  +  + L KGI +         +     KG N 
Sbjct: 131 GNLANFLMHPRHEIEREYAVRVQGTMSPEAKDKLLKGIKLDDGIAKFTTLEEGGGKGFNR 190

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V L EG+NRE++++FE     V+RLIR+ YG  +L   L  G TR +S +       
Sbjct: 191 WYNVTLSEGRNREVRRMFEAVGLPVSRLIRVKYGNLELPSDLPRGKTRRMSTEE-----T 245

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              L+            +       P   +               +   S   + + P+ 
Sbjct: 246 EKWLDSISYKKGMSTAPAPRAPERTPRPAASRAPASAPKAGRKFGQRDTSSAIRSSRPMR 305

Query: 307 RRNLASNV 314
            R      
Sbjct: 306 SRGTRGPK 313


>gi|330791888|ref|XP_003284023.1| hypothetical protein DICPUDRAFT_147740 [Dictyostelium purpureum]
 gi|325086069|gb|EGC39465.1| hypothetical protein DICPUDRAFT_147740 [Dictyostelium purpureum]
          Length = 377

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 101/245 (41%), Positives = 145/245 (59%), Gaps = 7/245 (2%)

Query: 2   KDKNIVQENFT----PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-RAAVNVMS 56
           KDK I  E        +R++KV++R+G+ASRR+ + MI + RVKVNG++        V  
Sbjct: 94  KDKIIENEQDEIKGHKERLNKVLSRSGVASRRKADEMIREGRVKVNGVVTTLENDHFVSI 153

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLD 115
            D +EVDG  ++K        + KP  LVT        S V      +     I+VGRLD
Sbjct: 154 IDEVEVDGKIIKKPMPRMWMHFKKPKVLVTHSEVEGRESLVPILKKVLKKDHLITVGRLD 213

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
             +EGL+LLTNDG L+R LE P  ++ R YRVR  G++ Q+  ++  KGIVI  I Y  +
Sbjct: 214 YYSEGLILLTNDGNLSRYLEHPDNEFERTYRVRIFGKITQEMQDIFTKGIVIDNIKYKPI 273

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           +V +D +  +N+WV + ++EGKNREI+K+ E+FN KV RLIR+ YGP++L   L  G T 
Sbjct: 274 EVIVDKESKNNSWVVIKIKEGKNREIRKILEYFNIKVLRLIRVGYGPYELPESLKHGETI 333

Query: 235 EVSKK 239
           E+  K
Sbjct: 334 EIPLK 338


>gi|313676846|ref|YP_004054842.1| RNA-binding s4 domain protein [Marivirga tractuosa DSM 4126]
 gi|312943544|gb|ADR22734.1| RNA-binding S4 domain protein [Marivirga tractuosa DSM 4126]
          Length = 286

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 113/234 (48%), Gaps = 2/234 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           +E     R++K I+ AGI SRRE ++ IA  +VKVN  ++      V   D +  +G P+
Sbjct: 48  KELKEGIRLNKFISNAGICSRREADKHIADGKVKVNNKVVTELGFKVKPMDDVAFEGKPI 107

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +   + L      + T       ++ +     +   R+  VGRLD NT GLLL TND
Sbjct: 108 KREKLVYVLLNKPKGFITTMDDPKGRKTVMDLIATAGDERIYPVGRLDRNTTGLLLFTND 167

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA+ L  P  +  ++Y+V     + ++    +++GI ++        + + T    + 
Sbjct: 168 GELAKKLTHPKHKIKKIYQVELDKPITEEDFLKIQEGITLEDGEVKVDNLAILTPDAKS- 226

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + + +R G+NR +++ FE   + V +L R ++       L  G  R + +K +
Sbjct: 227 -IGMEIRMGRNRIVRRTFEHLGYDVVKLDRTTFAGLTKKDLARGKWRFLKEKEV 279


>gi|289641301|ref|ZP_06473467.1| pseudouridine synthase [Frankia symbiont of Datisca glomerata]
 gi|289508899|gb|EFD29832.1| pseudouridine synthase [Frankia symbiont of Datisca glomerata]
          Length = 248

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 83/235 (35%), Positives = 125/235 (53%), Gaps = 1/235 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVP 66
             N    R+ KV+A AG+ SRR  E +IA  RV+V+G ++E   + V   T  IEVDG  
Sbjct: 5   DANAEGVRLQKVLAAAGVGSRRHSEELIAAGRVRVDGRVVETQGMRVDPQTAIIEVDGER 64

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +           +KP+G+++  SD  GR TV D +      +  VGRLD+++EGLLL+TN
Sbjct: 65  VVTRAGLVHLALNKPVGVLSAMSDDRGRPTVADLVTDAGPGLFHVGRLDVDSEGLLLVTN 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  + Y V   G V +D    L++G+ +         V +    GS 
Sbjct: 125 DGELAHRLSHPSFEVAKTYLVEVAGPVGRDVPRRLREGVELADGPVRADAVRIVGSAGSR 184

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             + + L EG+NR ++++ E  +  V RL+R   GP  LG+L  G TR +S+  +
Sbjct: 185 VMLEITLHEGRNRVVRRLMEAVDHPVRRLVRTRIGPVHLGSLRVGRTRHLSRGEV 239


>gi|307707699|ref|ZP_07644178.1| RNA pseudouridine synthase family protein [Streptococcus mitis NCTC
           12261]
 gi|307616197|gb|EFN95391.1| RNA pseudouridine synthase family protein [Streptococcus mitis NCTC
           12261]
          Length = 240

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 63/237 (26%), Positives = 104/237 (43%), Gaps = 4/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEERDEIRFDGKVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    V  VGRLDI+T GLLLLTNDG LA 
Sbjct: 61  VYYMMNKPQGVISATEDPKHRTVLDLLDDIARSKEVFPVGRLDIDTHGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVT 190
            L  P     + Y V+  G + Q  +++  +GI ++       ++ L     + + + + 
Sbjct: 121 ALLSPKRHVNKTYLVQVKGIMTQGDVDIFAEGIPLKDFTCQPARLELVSIDTEKNQSQIR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K+ L   L 
Sbjct: 181 VTIAEGKFHQVKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELENLLA 237


>gi|153853074|ref|ZP_01994483.1| hypothetical protein DORLON_00468 [Dorea longicatena DSM 13814]
 gi|149753860|gb|EDM63791.1| hypothetical protein DORLON_00468 [Dorea longicatena DSM 13814]
          Length = 237

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 60/235 (25%), Positives = 107/235 (45%), Gaps = 7/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ +R+EV++ I Q +V VNG +++ A   +  T D + + G  +     
Sbjct: 2   MRLDKYLAEMGVGTRQEVKKQIRQGKVTVNGTVVKAADTKIDETCDEVTIGGRNISYVSY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +V+   D    + +          +  VGRLD +TEGLLL+TNDG LA 
Sbjct: 62  EYYMLNKPGG-VVSATEDRRDTTVIDLIKDKKRKDLFPVGRLDKDTEGLLLITNDGDLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWV 189
            L  P     +VY  +  G V ++ +    +GI I   +       ++ +  +    + +
Sbjct: 121 RLLAPKKHVDKVYYAKIDGMVTEEDVKRFAEGIDIGAEEEEMTRPAKLDI-MKSAEESEI 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
            + + EGK  ++K++F     +V  L R   GP  L   L  G  R ++++ +  
Sbjct: 180 RLTIHEGKFHQVKRMFLAVGKEVTYLKRERMGPLCLDENLKPGEYRLLTEEEIEN 234


>gi|297571446|ref|YP_003697220.1| pseudouridine synthase [Arcanobacterium haemolyticum DSM 20595]
 gi|296931793|gb|ADH92601.1| pseudouridine synthase [Arcanobacterium haemolyticum DSM 20595]
          Length = 251

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 79/242 (32%), Positives = 126/242 (52%), Gaps = 1/242 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDH 59
           M  K+    N   +R+ KV+A AG+ASRR  E MI Q RV V G ++ +  + V   +  
Sbjct: 1   MSRKSQDLHNPQGERLQKVLAHAGVASRRAAEDMIQQGRVSVEGTIVRQLGIRVDPQSAV 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           I VDG  ++  +       +KP G+V+T SD  GR T+ D +     R++ VGRLD++TE
Sbjct: 61  IHVDGNRVQLDQELITVALYKPPGVVSTMSDDQGRKTLADFVEDYPQRLVHVGRLDVDTE 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GL+LL+NDG L   L  PS +  + Y  R  G V +    +++KGI ++       +  +
Sbjct: 121 GLILLSNDGELVHRLTHPSYEVPKTYIARVEGTVTRGLQRVMEKGITLEDGPVHADRFII 180

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                 N+ V + L  G+NR ++++ E     V  L+R+ +G    G L  G  R+++  
Sbjct: 181 REVAKKNSIVEITLHSGRNRIVRRMMEEVGHPVMELVRMQFGNIVAGHLKPGQVRQIAGS 240

Query: 240 IL 241
            L
Sbjct: 241 EL 242


>gi|228952702|ref|ZP_04114776.1| Pseudouridine synthase [Bacillus thuringiensis serovar kurstaki
           str. T03a001]
 gi|228958637|ref|ZP_04120355.1| Pseudouridine synthase [Bacillus thuringiensis serovar pakistani
           str. T13001]
 gi|229069893|ref|ZP_04203175.1| Pseudouridine synthase [Bacillus cereus F65185]
 gi|229079559|ref|ZP_04212096.1| Pseudouridine synthase [Bacillus cereus Rock4-2]
 gi|228703728|gb|EEL56177.1| Pseudouridine synthase [Bacillus cereus Rock4-2]
 gi|228713296|gb|EEL65189.1| Pseudouridine synthase [Bacillus cereus F65185]
 gi|228801058|gb|EEM47957.1| Pseudouridine synthase [Bacillus thuringiensis serovar pakistani
           str. T13001]
 gi|228806978|gb|EEM53523.1| Pseudouridine synthase [Bacillus thuringiensis serovar kurstaki
           str. T03a001]
          Length = 238

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 64/228 (28%), Positives = 109/228 (47%), Gaps = 7/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCTSEKSV--KGNIIDLVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T      S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEITQL----SKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKR 225


>gi|329117728|ref|ZP_08246445.1| pseudouridylate synthase [Streptococcus parauberis NCFD 2020]
 gi|326908133|gb|EGE55047.1| pseudouridylate synthase [Streptococcus parauberis NCFD 2020]
          Length = 238

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 62/229 (27%), Positives = 106/229 (46%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++   GI SR +V+ +I  Q+VKVN  ++     NV  +   I   G P++    
Sbjct: 1   MRIDKLLEEEGIGSRNQVKTLIKSQQVKVNEKVITDGKTNVDPSLQVITASGTPIQAEGH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +               ++   ++++  +GRLD +TEGL+LLT++G L  
Sbjct: 61  HYFILNKPNGVVSARSDGLHQTVIDCLSVEDRYAKLYPIGRLDRDTEGLVLLTDNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            +  PS    + Y VR +GQ+  D L   ++GIV           + +  +    +   V
Sbjct: 121 RMLHPSHHVSKTYLVRVNGQLKDDALVFFEEGIVFHDGTKCKPAHLQILKKDEKCSEAVV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + EGK  ++KK+F  +  KV  L RIS+    LG L  G  R++++  
Sbjct: 181 TISEGKFHQVKKMFLAYGLKVIYLKRISFAGLTLGELPVGQYRKLTELE 229


>gi|30248452|ref|NP_840522.1| pseudouridylate synthase family protein 1 [Nitrosomonas europaea
           ATCC 19718]
 gi|30138338|emb|CAD84346.1| possible pseudouridylate synthase family 1 [Nitrosomonas europaea
           ATCC 19718]
          Length = 292

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 77/262 (29%), Positives = 120/262 (45%), Gaps = 6/262 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R+ K++AR G+ SRRE+E MIA  RV +NG+  +         D I +DG  +R   
Sbjct: 32  ETSRLQKLLARNGLGSRREIEDMIAAGRVSINGVTAK-PGDRAGPGDMIRIDGKIIRFRL 90

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  +  +     +V+        S          S+ I++GRLD NT GLL+ T D
Sbjct: 91  AALLPRVIIYHKPEGEIVSVRDPQGRPSVFDKLPHIRSSKWIAIGRLDFNTSGLLIFTTD 150

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P  Q  R Y VR  G++  +++  L  GI ++       Q+  +   G+N 
Sbjct: 151 GTLANHLMHPRYQMEREYAVRIVGELTPEQITRLTTGIELEDGLAKFDQLLDEGGTGTNH 210

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  + L+EG+NRE++++FE     V+RLIR+ +GP  L   L  G   E+    + + L 
Sbjct: 211 WYRIMLKEGRNREVRRMFEALGLTVSRLIRVRFGPVNLPPRLKRGMWIELMDIEVEQLLK 270

Query: 247 PHLLEEAQVNLDAPIYSSETLV 268
                 A +    P   +    
Sbjct: 271 LVSQPGAGIPDKPPSMQAGRRS 292


>gi|302871978|ref|YP_003840614.1| RNA-binding S4 domain protein [Caldicellulosiruptor obsidiansis
           OB47]
 gi|302574837|gb|ADL42628.1| RNA-binding S4 domain protein [Caldicellulosiruptor obsidiansis
           OB47]
          Length = 233

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 53/230 (23%), Positives = 100/230 (43%), Gaps = 7/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G  SR +V+++I +  V VNG  +      +    D +EVDG  ++ +  
Sbjct: 1   MRLDKFLTHCGFGSRTQVKKLIREGIVTVNGKQIVEVDFKINPEEDVVEVDGRVVKFSRW 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      + +             +       + +VGRLD + EGLL++T++G    
Sbjct: 61  IYIMMNKPKGYVCSNEDPMSLTVFSLISDDLKHRDLHTVGRLDKDAEGLLIITDNGEYTH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            +  P  +  + Y VR   +VD+++L   + GI++         + T+      +  V +
Sbjct: 121 RVISPKKRIEKEYLVRLEKEVDEERLKEFENGIILDDGYKTLPAKYTII----DSTTVKL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
            + EGK  ++K++FE    KV  L R   G   L   L  G  R + ++ 
Sbjct: 177 CIYEGKYHQVKRMFEAIGNKVVDLKRRRIGGLNLDESLKPGEYRVMKEEE 226


>gi|228900980|ref|ZP_04065193.1| Pseudouridine synthase [Bacillus thuringiensis IBL 4222]
 gi|228908132|ref|ZP_04071980.1| Pseudouridine synthase [Bacillus thuringiensis IBL 200]
 gi|229190444|ref|ZP_04317444.1| Pseudouridine synthase [Bacillus cereus ATCC 10876]
 gi|228593057|gb|EEK50876.1| Pseudouridine synthase [Bacillus cereus ATCC 10876]
 gi|228851550|gb|EEM96356.1| Pseudouridine synthase [Bacillus thuringiensis IBL 200]
 gi|228858678|gb|EEN03125.1| Pseudouridine synthase [Bacillus thuringiensis IBL 4222]
          Length = 238

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 64/228 (28%), Positives = 109/228 (47%), Gaps = 7/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCTSEKAV--KGNIIDLVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T      S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEITQL----SKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKR 225


>gi|325851841|ref|ZP_08171006.1| pseudouridylate synthase [Prevotella denticola CRIS 18C-A]
 gi|325484683|gb|EGC87596.1| pseudouridylate synthase [Prevotella denticola CRIS 18C-A]
          Length = 507

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 107/234 (45%), Gaps = 1/234 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +   P R++K +A AG+ SRRE +  I    V VNG +++     V+ +D +     P+ 
Sbjct: 267 DPNEPIRLNKYLANAGVCSRREADEFILSGAVTVNGEVVKELGSKVLRSDVVLFQEKPVS 326

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ++  + L      + T+      ++ +     +   R+  VGRLD NT G+LLLTNDG
Sbjct: 327 LEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKGACPERIYPVGRLDRNTTGVLLLTNDG 386

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     +VY V     V  + L  +  GI ++        +     +     
Sbjct: 387 DLASKLTHPKFLKKKVYHVFLDKPVTANDLQKISDGIELEDGEIKADAIEYADPQ-DQTQ 445

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           V + +  GKNR ++++FE   ++V +L R+ +       +  G  R +++K + 
Sbjct: 446 VGIEIHSGKNRIVRRIFESLGYRVVKLDRVQFAGLTKKNVRRGDWRFLTEKEVD 499


>gi|256027784|ref|ZP_05441618.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           D11]
 gi|289765737|ref|ZP_06525115.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           D11]
 gi|289717292|gb|EFD81304.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           D11]
          Length = 234

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 70/231 (30%), Positives = 129/231 (55%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAE 71
            R++K ++  GIASRR V++ I + R+ VNG +     +N+   D+I +DG  ++    E
Sbjct: 1   MRINKFLSTLGIASRRAVDKYIEEGRINVNGNIATT-GMNISENDNIFIDGKKIKTDVNE 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               ++ +KP+ ++++ SD  GR TV D + +       +GRLD  T GL+LLTNDG L 
Sbjct: 60  EKVYFMLNKPLEVLSSSSDDRGRKTVVDLIKTDKRI-FPIGRLDYMTSGLILLTNDGELF 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P ++  + Y V+  G++ ++++  LKKG+++        +++      +   + +
Sbjct: 119 NRIVHPKSEIYKKYYVKIFGEIKKEEIAELKKGVLLNDGKTLPAKISGIKYNKNKTSMYI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +REG+NR+I+++ E F +KV  L R   G   LG L  G  R+++K+ + 
Sbjct: 179 SIREGRNRQIRRMIEKFGYKVLMLRREKIGELSLGDLEEGKYRKLTKQEIE 229


>gi|289425044|ref|ZP_06426821.1| pseudouridylate synthase [Propionibacterium acnes SK187]
 gi|289154022|gb|EFD02710.1| pseudouridylate synthase [Propionibacterium acnes SK187]
 gi|313792449|gb|EFS40542.1| conserved hypothetical protein [Propionibacterium acnes HL110PA1]
 gi|313801506|gb|EFS42755.1| conserved hypothetical protein [Propionibacterium acnes HL110PA2]
 gi|313838267|gb|EFS75981.1| conserved hypothetical protein [Propionibacterium acnes HL086PA1]
 gi|314963143|gb|EFT07243.1| conserved hypothetical protein [Propionibacterium acnes HL082PA1]
 gi|315078206|gb|EFT50249.1| conserved hypothetical protein [Propionibacterium acnes HL053PA2]
 gi|327453532|gb|EGF00187.1| hypothetical protein HMPREF9584_01968 [Propionibacterium acnes
           HL092PA1]
          Length = 245

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 77/241 (31%), Positives = 108/241 (44%), Gaps = 2/241 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
            N    R+ KV+A+AG+ASRR  E MIA  RV+VNG L+      V    D I VDG  +
Sbjct: 2   SNEQGIRLQKVLAQAGLASRRAAEDMIAAGRVEVNGELIVEQGRRVDPERDEIRVDGSRI 61

Query: 68  R-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                     L      + T                    R+  VGRLD  T GL+LLTN
Sbjct: 62  PTARRHVYYVLNKPQGVVSTMDDPEGRPCLSDLEGVPRGIRLFHVGRLDTETSGLILLTN 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  A  +  PS + L+ Y     G+VD   +  L KG+ ++        V L      +
Sbjct: 122 DGEFANRMTHPSYKVLKTYLADVEGRVDDKVIRRLSKGLTLEDGPVKPDAVRLVQAGEEH 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + V V L EG+NR ++++ +     V RL R   GP +L  L  G  RE++ + L + L 
Sbjct: 182 SLVEVSLHEGRNRIVRRIMDSVAHPVRRLSRTVIGPVRLKRLGRGDMRELTHEELGQLLD 241

Query: 247 P 247
            
Sbjct: 242 L 242


>gi|324992460|gb|EGC24381.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK405]
 gi|327460692|gb|EGF07027.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1]
 gi|327472413|gb|EGF17844.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK408]
 gi|327488766|gb|EGF20565.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1058]
          Length = 242

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 103/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++++ +  V VNG + +     +  T D I V G  L   + 
Sbjct: 1   MRLDKFLAENGLGSRAQVKQLLKKGLVLVNGRVEKSPKTQIDETADEIVVSGQRLTYEKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  D         +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPQGVISATEDDRHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            +  P     ++YR +  G ++Q        GI ++       Q+ +     +   + V 
Sbjct: 121 AMLSPKKHVEKIYRAQVAGLMNQTDEERFAAGIELKDFTCQPAQLKILELDEAKETSLVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + L EGK  ++K++      +V  L R++ GP Q    L  G  R +++  +
Sbjct: 181 ITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQSDPALALGEWRRLTEVEM 232


>gi|218690332|ref|YP_002398544.1| 16S rRNA pseudouridylate synthase A [Escherichia coli ED1a]
 gi|218427896|emb|CAR08815.2| 16S rRNA pseudouridylate 516 synthase [Escherichia coli ED1a]
          Length = 231

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 101/231 (43%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEVI----TPTQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L     R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPSEYRPLTEEEI 227


>gi|229127761|ref|ZP_04256750.1| Pseudouridine synthase [Bacillus cereus BDRD-Cer4]
 gi|229144960|ref|ZP_04273356.1| Pseudouridine synthase [Bacillus cereus BDRD-ST24]
 gi|229150585|ref|ZP_04278800.1| Pseudouridine synthase [Bacillus cereus m1550]
 gi|228632894|gb|EEK89508.1| Pseudouridine synthase [Bacillus cereus m1550]
 gi|228638482|gb|EEK94916.1| Pseudouridine synthase [Bacillus cereus BDRD-ST24]
 gi|228655838|gb|EEL11687.1| Pseudouridine synthase [Bacillus cereus BDRD-Cer4]
          Length = 238

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 65/228 (28%), Positives = 109/228 (47%), Gaps = 7/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCTSEKSV--KGNIIDLVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      +VT      S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEVTQL----SKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKR 225


>gi|194246524|ref|YP_002004163.1| 16S rRNA pseudouridylate synthase [Candidatus Phytoplasma mali]
 gi|193806881|emb|CAP18310.1| 16S rRNA pseudouridylate synthase [Candidatus Phytoplasma mali]
          Length = 242

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 63/240 (26%), Positives = 118/240 (49%), Gaps = 4/240 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+++ + +ASRR+ E++I ++RVKVNG L+ +  V V   D I VD   ++ +E  
Sbjct: 2   ERLQKILSYSNVASRRKSEKLILEKRVKVNGKLVTKLGVKVSKKDIILVDDQIIKNSENC 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +      + T   + +  + +     +   R+  VGRLD NT GLLL+TNDG L + 
Sbjct: 62  YYLINKPSGCISTVKDEKNRPTVIDLIKDTEKKRIYPVGRLDFNTTGLLLITNDGQLTKK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----ICYGDMQVTLDTQKGSNAWV 189
           L  PS+   + Y V+ +  +   +L  L++G++I      +      +        + W+
Sbjct: 122 LTHPSSLIEKEYHVKINYCLSSLELKKLQQGVIIDENYLSVPKKIKILKKRLLPKPSTWL 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + + EGKN +I+K+ E   + + +LIR  Y    +  +  G  R +    +++      
Sbjct: 182 QIIITEGKNHQIRKMMEKLGFHILKLIRYRYAFLTIKGIKKGQYRILKIHEIKKLKILKY 241


>gi|312196764|ref|YP_004016825.1| pseudouridine synthase [Frankia sp. EuI1c]
 gi|311228100|gb|ADP80955.1| pseudouridine synthase [Frankia sp. EuI1c]
          Length = 285

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 77/235 (32%), Positives = 122/235 (51%), Gaps = 3/235 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
           +    R+ KV+A AG+ SRR  E +I   RV+V+G ++      V   T  IEVDG  + 
Sbjct: 42  SQEGIRLQKVLASAGVGSRRHNEELIDAGRVRVDGKVVREQGRRVDPETAVIEVDGERVV 101

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTN 126
                     +KP G+V+T SDP+ R T+ D L    +      VGRLD+++EGLLL+TN
Sbjct: 102 TRTGLVHLALNKPRGVVSTMSDPEDRPTISDLLTEFGASAGLFHVGRLDVDSEGLLLVTN 161

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G LA  L  PS Q  + Y+V+ +G + ++ +  L   + +           +  Q GS 
Sbjct: 162 NGDLAHRLTHPSYQVPKTYQVQINGPLRKETMRRLHTRVELSDGPVRVDSARIIDQVGSQ 221

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             + + L EG+NR ++++ E     V RL+R  +G   LGTL +G  R ++   +
Sbjct: 222 ILLEIVLHEGRNRIVRRMMEEVGHPVVRLLRTEFGAVHLGTLRSGRARHLTLHEV 276


>gi|333029320|ref|ZP_08457381.1| pseudouridine synthase Rsu [Bacteroides coprosuis DSM 18011]
 gi|332739917|gb|EGJ70399.1| pseudouridine synthase Rsu [Bacteroides coprosuis DSM 18011]
          Length = 437

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 113/241 (46%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG +++     V  +D +
Sbjct: 189 IEYKQQFVDPNEPIRLNKYLANAGVCSRREADEFIETGAVTVNGEIVKELGTKVKRSDEV 248

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           + +G  +   ++  + L      + T     + ++ +     +   R+  VGRLD  T G
Sbjct: 249 KFNGELVSIEKKVYVLLNKPKDCVTTMDDPQERQTVMDFVKNACDERIYPVGRLDRKTTG 308

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     + +  L  + +GI ++       +V   
Sbjct: 309 VLLLTNDGDLASKLTHPKYDKKKIYHVTLDRNIVKADLEKIAEGIELEDGLIKADEVGYT 368

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +   N  V + +  GKNR ++++FE   ++V +L R+ +       L  G  R +S++ 
Sbjct: 369 DEFKRNQ-VGIEIHSGKNRIVRRIFESLGYRVTKLDRVYFAGLTKKGLRRGQWRYLSEQE 427

Query: 241 L 241
           +
Sbjct: 428 V 428


>gi|327312548|ref|YP_004327985.1| pseudouridylate synthase [Prevotella denticola F0289]
 gi|326945115|gb|AEA21000.1| pseudouridylate synthase [Prevotella denticola F0289]
          Length = 507

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 107/234 (45%), Gaps = 1/234 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +   P R++K +A AG+ SRRE +  I    V VNG +++     V+ +D +     P+ 
Sbjct: 267 DPNEPIRLNKYLANAGVCSRREADEFILSGAVTVNGEVVKELGSKVLRSDVVLFQEKPVS 326

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ++  + L      + T+      ++ +     +   R+  VGRLD NT G+LLLTNDG
Sbjct: 327 LEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKGACPERIYPVGRLDRNTTGVLLLTNDG 386

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     +VY V     V  + L  +  GI ++        +     +     
Sbjct: 387 DLASKLTHPKFLKKKVYHVFLDKPVTANDLQKISDGIELEDGEIKADAIEYADPQ-DQTQ 445

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           V + +  GKNR ++++FE   ++V +L R+ +       +  G  R +++K + 
Sbjct: 446 VGIEIHSGKNRIVRRIFESLGYRVIKLDRVQFAGLTKKNVRRGDWRFLTEKEVD 499


>gi|228939520|ref|ZP_04102108.1| Pseudouridine synthase [Bacillus thuringiensis serovar berliner
           ATCC 10792]
 gi|228972373|ref|ZP_04132984.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228978987|ref|ZP_04139351.1| Pseudouridine synthase [Bacillus thuringiensis Bt407]
 gi|229044113|ref|ZP_04191799.1| Pseudouridine synthase [Bacillus cereus AH676]
 gi|228725226|gb|EEL76497.1| Pseudouridine synthase [Bacillus cereus AH676]
 gi|228780698|gb|EEM28912.1| Pseudouridine synthase [Bacillus thuringiensis Bt407]
 gi|228787390|gb|EEM35358.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228820220|gb|EEM66257.1| Pseudouridine synthase [Bacillus thuringiensis serovar berliner
           ATCC 10792]
          Length = 238

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 65/228 (28%), Positives = 109/228 (47%), Gaps = 7/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCTSEKAV--KGNIIDLVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      +VT      S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEVTQL----SKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKR 225


>gi|301793545|emb|CBW35921.1| putative ribosomal small subunit pseudouridine synthase B
           [Streptococcus pneumoniae INV104]
          Length = 240

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 101/233 (43%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    V  VGRLDI+T GLLLLTNDG LA 
Sbjct: 61  VYYMMNKPKGVISATEDPKHRTVMDLLDDLARSKEVFPVGRLDIDTHGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVT 190
           VL  P     + Y  +  G + Q+ +    +GI ++         ++     + + + + 
Sbjct: 121 VLLSPKRHVDKTYLAQVKGIMTQEDVETFAEGIPLKDFTCQPAILELVSIDTEKNQSQIR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 181 VTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELE 233


>gi|116873710|ref|YP_850491.1| ribosomal small subunit pseudouridine synthase A [Listeria
           welshimeri serovar 6b str. SLCC5334]
 gi|116742588|emb|CAK21712.1| ribosomal small subunit pseudouridine synthase A [Listeria
           welshimeri serovar 6b str. SLCC5334]
          Length = 233

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 103/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    V VNG + + + + V    D I V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKMQVNPDKDEITVHGTPVVYQEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T  +               +    VGRLD +TEGLL++TNDG LA 
Sbjct: 61  VYFMLHKPQNVVSATEDNVSETVIDLLAQEDTLTNPFPVGRLDKDTEGLLIITNDGTLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y  +  G+V  + +    +GIV+         ++ +         + V
Sbjct: 121 NLLSPKKHIDKTYYAKIDGEVLLEDVKAFAEGIVLDDGYICKPARLEIINPN----EIKV 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            ++EGK  ++K++F      V+ L RIS G  QL   L  G  R +++  L
Sbjct: 177 TIQEGKFHQVKRMFAARGKTVSYLKRISMGQLQLDESLELGEYRPLTETEL 227


>gi|58337102|ref|YP_193687.1| 16s pseudouridylate synthase [Lactobacillus acidophilus NCFM]
 gi|227903674|ref|ZP_04021479.1| 16S pseudouridylate synthase [Lactobacillus acidophilus ATCC 4796]
 gi|58254419|gb|AAV42656.1| 16s pseudouridylate synthase [Lactobacillus acidophilus NCFM]
 gi|227868561|gb|EEJ75982.1| 16S pseudouridylate synthase [Lactobacillus acidophilus ATCC 4796]
          Length = 236

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 99/234 (42%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV ++I +  V VNG  ++     +   D + V+G  +   +  
Sbjct: 1   MRIDKYLANMNVGSRKEVHQLIKKGLVDVNGKTVKTPKEKINEDDVVTVNGEKVAYQKYH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      L  T                 +  +  VGRLD +T GLLLLTNDG L   
Sbjct: 61  YFLLNKPTGVLSATEDRSQKTVISLLKPEDRYQGIAPVGRLDKDTTGLLLLTNDGQLNHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN--AWVT 190
           L  P+    +VYR +  G  D + +     G+ +  G      ++ +  Q   N  + + 
Sbjct: 121 LLAPNKHVAKVYRAQIAGVADDETVKTFASGMTLGDGTKLKPAKLRILKQDRENATSEIE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           + + EGK  +IK++F     KV  L R++ G   L   L  G   E+S   +  
Sbjct: 181 IEISEGKYHQIKRMFGAVGMKVMALDRLAMGKLCLPADLKRGKYVELSLDEIEN 234


>gi|323466841|gb|ADX70528.1| Pseudouridine synthase [Lactobacillus helveticus H10]
          Length = 246

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 103/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I +  V VNG +++     V  +D + VDG  +   +  
Sbjct: 11  MRIDKYLANMNVGSRKEVHVLIKKGIVTVNGDVVKTPKQQVKESDEVLVDGQEVNYQKYH 70

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +      L  T                 +  +  VGRLD +T GLLLLTNDG L   
Sbjct: 71  YFLMNKPKGVLSATEDRSQRTVISLLKPQDQYQGITPVGRLDKDTTGLLLLTNDGQLNHE 130

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG--SNAWVT 190
           L  P+    ++YR +  G  D + +     G+ +  G      ++ +  Q     ++ + 
Sbjct: 131 LLAPNKHVDKIYRAKIAGVADDETVKTFASGMTLGDGTKLKPAELKILAQDEEHDSSEIE 190

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           + +REGK  +IK++F     KV  L RIS G  +L   L  G+  E+S   +
Sbjct: 191 IKIREGKYHQIKRMFGAVGMKVVELERISMGKLKLPKDLKRGNYIELSLDDV 242


>gi|221066029|ref|ZP_03542134.1| pseudouridine synthase [Comamonas testosteroni KF-1]
 gi|220711052|gb|EED66420.1| pseudouridine synthase [Comamonas testosteroni KF-1]
          Length = 529

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 83/363 (22%), Positives = 140/363 (38%), Gaps = 12/363 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          +   D +
Sbjct: 150 MPAKRVLAPQVDSPKLHKVLAQAGMGSRLEMEQLILEGRISVNNEPAHV-GQRIQFGDIV 208

Query: 61  EVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           +V+G P+R          +  +     +VT     +  +           +  SVGRLD+
Sbjct: 209 KVNGQPIRFRIDPPPARVIAYHKPVGEVVTHDDPQNRPTVFRKLPKLQHGKWQSVGRLDL 268

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NTEGLLL T+ G LA  L  P     R Y  R  G + +++   L  G+ ++        
Sbjct: 269 NTEGLLLFTSSGELANSLMHPRFGLEREYAARVLGALSKEEKQRLLDGVQLEDGEASFGA 328

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTRE 235
           V     +G+N W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E
Sbjct: 329 VEDGGGEGANCWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMMLPRGLKRGAWVE 388

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           + +  ++  +    ++E          +     R   N  S    +     +    +   
Sbjct: 389 LDQADIQALMSAAGVKERAPVERNNSGARGANNRGGRNSRSGGRGNGMNADRAPQGRREG 448

Query: 296 SK------QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                         P                  +  S  G + +  R S  +    SL R
Sbjct: 449 GGQRRGEWDGNRPAPSGMLGDNPRNKPGGRSGGAGRSQGGGQPDPMRTSVGYIGSDSLSR 508

Query: 350 TSA 352
              
Sbjct: 509 ARQ 511


>gi|319892809|ref|YP_004149684.1| Ribosomal small subunit pseudouridine synthase A [Staphylococcus
           pseudintermedius HKU10-03]
 gi|317162505|gb|ADV06048.1| Ribosomal small subunit pseudouridine synthase A [Staphylococcus
           pseudintermedius HKU10-03]
 gi|323464159|gb|ADX76312.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           pseudintermedius ED99]
          Length = 232

 Score =  170 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 53/231 (22%), Positives = 105/231 (45%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A+ G+ +R EV+ ++ +  V  NG  ++ +   +    D +EV G  +     
Sbjct: 1   MRIDKFLAQMGVGTRTEVKALLKKGHVLHNGAKIKSSKTQIDPEHDVVEVKGRVIAYEPF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +++   D   ++ +          +  VGRLD +TEGLLL+TNDG    
Sbjct: 61  VYLMMNKPQ-NVISATVDDQHQTVIDIIEGYRHLDLFPVGRLDKDTEGLLLITNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+    + Y V+    +  +     ++GI ++        + +      +    V 
Sbjct: 120 ALMNPNKHVSKTYWVKAKYALKTNDPKRFEEGITLKEGRLQPAHLEIL---DDSMTAFVT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           ++EGK  ++K++F   + +V  L R+S G   L  +L  G+ R +++  L+
Sbjct: 177 IQEGKYHQVKRMFHAIDNEVVGLKRVSIGDLTLDSSLSPGAYRSLTEDELK 227


>gi|149006033|ref|ZP_01829762.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP18-BS74]
 gi|307126496|ref|YP_003878527.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           670-6B]
 gi|147762389|gb|EDK69350.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP18-BS74]
 gi|306483558|gb|ADM90427.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           670-6B]
 gi|332076726|gb|EGI87188.1| hypothetical protein SPAR148_0259 [Streptococcus pneumoniae
           GA17545]
          Length = 240

 Score =  170 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 102/233 (43%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    +  VGRLDI+T GLLLLTNDG LA 
Sbjct: 61  VYYMMNKPKGVISATEDPKHRTVLDLLDDLARSKEIFPVGRLDIDTHGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVT 190
           VL  P     + Y  +  G + Q+ + +  +GI ++         ++     + + + + 
Sbjct: 121 VLLSPKRHVDKTYLAQVKGIMTQEDVEIFAEGIPLKDFTCQPAILELVSIDTEKNQSQIR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 181 VTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELE 233


>gi|39934240|ref|NP_946516.1| pseudouridine synthase Rsu [Rhodopseudomonas palustris CGA009]
 gi|39648088|emb|CAE26608.1| Pseudouridine synthase, Rsu:RNA-binding S4:Pseudouridine synthase
           [Rhodopseudomonas palustris CGA009]
          Length = 731

 Score =  170 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 140/331 (42%), Positives = 195/331 (58%), Gaps = 2/331 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           + +   +R++KV+ARAG+ SRR+ E  I + RV VNG +++  A++V ++D I +DG PL
Sbjct: 399 KSDKAGERIAKVVARAGLCSRRDAEAWITEGRVTVNGKVIDSPALDVKASDIITIDGKPL 458

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            + ERTRL+LYHKP GL+TTHSDP+GR TVFD+LP    R+IS+GRLD NTEGLLLLTND
Sbjct: 459 PERERTRLFLYHKPRGLMTTHSDPEGRPTVFDHLPEGLPRLISIGRLDFNTEGLLLLTND 518

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GGLAR LELP T WLR YRVR HG++ Q +L+ L+ GI + G+ YG ++  L+  +G+N 
Sbjct: 519 GGLARALELPETGWLRRYRVRAHGEITQAQLDELQNGIEVDGVQYGPIEAKLERDQGANV 578

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+   +REGKNRE++ V      +VNRLIR+SYGPFQL  L  G   EV  ++LR+QLG 
Sbjct: 579 WLVFAIREGKNREVRNVLAHLGLEVNRLIRVSYGPFQLLELGEGEVDEVKTRVLRDQLGE 638

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ--KNGLSKQKKLATPV 305
            ++  A  +   P  S           +S              +      + + +    V
Sbjct: 639 KVIALAGCDFAGPSPSETKPKPRAGKAVSAEEWAVADAAPAPKKTITKRGAVEDRKGRKV 698

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHR 336
                AS                G+R+   R
Sbjct: 699 KVERTASEGGDRPLSRGPARRYHGKRDLAPR 729



 Score = 36.3 bits (82), Expect = 7.4,   Method: Composition-based stats.
 Identities = 15/109 (13%), Positives = 32/109 (29%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G    +  +   D P +S     + R +        F + + +  + +   +  +     
Sbjct: 220 GDRDRKFDKGGFDKPRFSKSRDDKPRFDRDRGDKPRFDKPRGDKPRFDRGERSDRPERSG 279

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            R   +      +G    F   S  R    R     P +   +R  A +
Sbjct: 280 DRPKFSRPRDGDRGEQRPFRERSFDRPREDRPRSDRPREDRPQRDRAAR 328



 Score = 35.9 bits (81), Expect = 9.5,   Method: Composition-based stats.
 Identities = 10/102 (9%), Positives = 25/102 (24%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           ++ G      ++   D P +  +   + R +        F R +++   +    + K   
Sbjct: 227 DKGGFDKPRFSKSRDDKPRFDRDRGDKPRFDKPRGDKPRFDRGERSDRPERSGDRPKFSR 286

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
                R                      R    R      ++
Sbjct: 287 PRDGDRGEQRPFRERSFDRPREDRPRSDRPREDRPQRDRAAR 328


>gi|15900214|ref|NP_344818.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae TIGR4]
 gi|111656756|ref|ZP_01407636.1| hypothetical protein SpneT_02001953 [Streptococcus pneumoniae
           TIGR4]
 gi|148988021|ref|ZP_01819484.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP6-BS73]
 gi|149011151|ref|ZP_01832456.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP19-BS75]
 gi|168493975|ref|ZP_02718118.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae CDC3059-06]
 gi|225856037|ref|YP_002737548.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae P1031]
 gi|225858129|ref|YP_002739639.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae 70585]
 gi|225860315|ref|YP_002741824.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|298229569|ref|ZP_06963250.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae str. Canada MDR_19F]
 gi|298254034|ref|ZP_06977620.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae str. Canada MDR_19A]
 gi|298502097|ref|YP_003724037.1| pseudouridylate synthase [Streptococcus pneumoniae TCH8431/19A]
 gi|14971752|gb|AAK74458.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae TIGR4]
 gi|147764787|gb|EDK71717.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP19-BS75]
 gi|147926485|gb|EDK77558.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP6-BS73]
 gi|183576148|gb|EDT96676.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae CDC3059-06]
 gi|225721053|gb|ACO16907.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae 70585]
 gi|225725053|gb|ACO20905.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae P1031]
 gi|225728111|gb|ACO23962.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|298237692|gb|ADI68823.1| pseudouridylate synthase [Streptococcus pneumoniae TCH8431/19A]
          Length = 240

 Score =  170 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 101/233 (43%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    V  VGRLDI+T GLLLLTNDG LA 
Sbjct: 61  VYYMMNKPKGVISATEDPKHRTVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVT 190
           VL  P     + Y  +  G + Q+ +    +GI ++         ++     + + + + 
Sbjct: 121 VLLSPKRHVDKTYLAQVKGIMTQEDVETFAEGIPLKDFTCQPAILELVSIDTEKNQSQIR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 181 VTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELE 233


>gi|15605456|ref|NP_220242.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis D/UW-3/CX]
 gi|76789463|ref|YP_328549.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis A/HAR-13]
 gi|237803153|ref|YP_002888347.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis B/Jali20/OT]
 gi|237805074|ref|YP_002889228.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis B/TZ1A828/OT]
 gi|255311554|ref|ZP_05354124.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis 6276]
 gi|255317855|ref|ZP_05359101.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis 6276s]
 gi|255349118|ref|ZP_05381125.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis 70]
 gi|255503655|ref|ZP_05382045.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis 70s]
 gi|255507334|ref|ZP_05382973.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis D(s)2923]
 gi|3329180|gb|AAC68318.1| predicted pseudouridine synthase [Chlamydia trachomatis D/UW-3/CX]
 gi|76167993|gb|AAX51001.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis A/HAR-13]
 gi|231273374|emb|CAX10289.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis B/TZ1A828/OT]
 gi|231274387|emb|CAX11182.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis B/Jali20/OT]
 gi|289525767|emb|CBJ15248.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis Sweden2]
 gi|296435342|gb|ADH17520.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis E/150]
 gi|296436269|gb|ADH18443.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis G/9768]
 gi|296437198|gb|ADH19368.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis G/11222]
 gi|296438129|gb|ADH20290.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis G/11074]
 gi|296439059|gb|ADH21212.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis E/11023]
 gi|297140630|gb|ADH97388.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis G/9301]
 gi|297748854|gb|ADI51400.1| Ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis D-EC]
 gi|297749734|gb|ADI52412.1| Ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis D-LC]
          Length = 241

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 68/230 (29%), Positives = 102/230 (44%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R++K +A AG+ASRR+ + +I    V VNG +     V V    D +EV G  +   ++
Sbjct: 4   VRLNKFLASAGVASRRKCDEIIFAGSVTVNGRVAAGPFVTVDEEFDSVEVGGQRIGAEKK 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               ++     L ++     G   V D L     R+ +VGRLD  T GL+L+TNDG  A 
Sbjct: 64  VYFMVHKPLGYLCSSERKFPGSKLVIDLLSHCPYRLFTVGRLDKETSGLILVTNDGEFAN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  PS    + Y ++    V    L  L  G VI G     + V    +      + + 
Sbjct: 124 RVIHPSFGITKEYLLKVSRDVTARDLETLMAGTVIDGKVVRPVSVKKVRRG----TIKII 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGK  EI+   E    ++  L RI  G   LG L  G  RE++   L 
Sbjct: 180 VNEGKKHEIRLFAEAAGLQLLELKRIRIGSLVLGGLPYGKYRELTDSELD 229


>gi|88798249|ref|ZP_01113835.1| pseudouridine synthase (makes pseudouridine2605 in 23 S RNA)
           [Reinekea sp. MED297]
 gi|88779025|gb|EAR10214.1| pseudouridine synthase (makes pseudouridine2605 in 23 S RNA)
           [Reinekea sp. MED297]
          Length = 282

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 84/277 (30%), Positives = 126/277 (45%), Gaps = 5/277 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A+AG  SRRE+ER I   RV+VNG + +     V   D + +DG  +      
Sbjct: 6   ERIQKVLAKAGQGSRREMERAIESGRVQVNGEVAK-LGDKVSEKDELRLDGKKISVEAEK 64

Query: 74  R---LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               L        + T        +           R I+VGRLDINT GLLL TNDG L
Sbjct: 65  VRRVLIYNKPEGEICTRKDPEGRHTVFDRLPRIPGERWIAVGRLDINTSGLLLFTNDGEL 124

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS Q  R Y VR  G V Q+ ++ + +G+ ++        V     KGSN W  
Sbjct: 125 ANRLMHPSHQIEREYAVRVLGDVQQENIDAMCEGVELEDGPAKFTDVQFFDGKGSNLWFH 184

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHL 249
           V + EG+NRE+++++E   ++V+RL R+ YG   L   + AG+ +E++KK + +      
Sbjct: 185 VVIMEGRNREVRRLWESQGFQVSRLKRVRYGSVFLDSDVRAGTWQEMAKKDIDQLAKTVD 244

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
           L  A               +             +R  
Sbjct: 245 LAPAPWKSIVKHKRDPMKRKMEKQRTRRSVGKTSRKP 281


>gi|25010876|ref|NP_735271.1| hypothetical protein gbs0821 [Streptococcus agalactiae NEM316]
 gi|77414995|ref|ZP_00791079.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae 515]
 gi|23095255|emb|CAD46465.1| Unknown [Streptococcus agalactiae NEM316]
 gi|77158953|gb|EAO70180.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae 515]
          Length = 239

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 59/230 (25%), Positives = 106/230 (46%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++ +AG  SR +V+++I  ++V V+G ++ +  V V S    I V    +   E 
Sbjct: 1   MRLDKLLGQAGFGSRNQVKKLIRSRQVSVDGQIVTKDNVIVDSGLQSIFVGKERVCLKES 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +   LY     +               +       +  +GRLD +TEGLL++TN+G L  
Sbjct: 61  SYYLLYKPSGVVSAVRDSEHKTVIDLISEKDRVEGLYPIGRLDRDTEGLLIITNNGPLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V  +G +++D +   ++G+V          ++T+DT     +   +
Sbjct: 121 RMLHPKHHVAKTYYVEVNGFLERDAITFFEEGVVFDDGTKCKPAELTIDTANNDKSTARI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + EGK  ++KK+F  +  KV  L RIS+G  +L   L  G  R +    
Sbjct: 181 TITEGKFHQVKKMFLAYGVKVIYLRRISFGDLRLDMNLKPGQYRRLRDSE 230


>gi|196233446|ref|ZP_03132289.1| pseudouridine synthase [Chthoniobacter flavus Ellin428]
 gi|196222442|gb|EDY16969.1| pseudouridine synthase [Chthoniobacter flavus Ellin428]
          Length = 237

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 78/242 (32%), Positives = 124/242 (51%), Gaps = 5/242 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +A AG+ SRR VE +I   +V++NG ++   +  V  TD ++V G  L + E+ 
Sbjct: 1   MRLNRFLASAGLGSRRGVEELITSGQVRINGQVVTDLSTQVGPTDAVKV-GSRLLRTEQK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L +KP G V T SD   R T+FD LP+ + RV  VGRLD ++EGLLL+TNDG L+  
Sbjct: 60  ITVLLNKPAGYVCTASDERDRKTIFDLLPANWPRVYHVGRLDKDSEGLLLVTNDGDLSLA 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  + Y V      +      L KG  I G      +V +     +   +++ L
Sbjct: 120 LTHPRYKIEKEYEVLLDKPFNPQDREKLLKGFHIIGGRAKAERVEIL----NPTHLSLTL 175

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
            +G  R+I+ +     ++V RL RI  GP ++G +  G  R ++ K +    GP      
Sbjct: 176 TQGIKRQIRLMLYDLGYEVERLARIRLGPLKIGEMRPGEWRLLTSKEIAALKGPAQPSAP 235

Query: 254 QV 255
           + 
Sbjct: 236 KA 237


>gi|322832033|ref|YP_004212060.1| pseudouridine synthase [Rahnella sp. Y9602]
 gi|321167234|gb|ADW72933.1| pseudouridine synthase [Rahnella sp. Y9602]
          Length = 235

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 54/231 (23%), Positives = 107/231 (46%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  +RV V+G +++  ++ +     +E DG  L +    
Sbjct: 1   MRLDKFLSQQLGVSRALVLRELRNKRVTVDGEIVKTGSMKISPEQRVEFDGNVLDQITGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLEEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +  D     + G+ +  +       Q     +K  +  V +
Sbjct: 121 ITSPRHHCEKTYLVTLEHPLADDTAAQFEAGVQLHNEDSLTKPAQ----LEKIEDCLVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            L EG+  ++K++F     +V  L R   G   +   L  G  R ++++ +
Sbjct: 177 TLSEGRYHQVKRMFAAVGNRVVALHRERIGEIVMDEDLEPGQYRPLTEQEV 227


>gi|192289766|ref|YP_001990371.1| RNA-binding S4 domain protein [Rhodopseudomonas palustris TIE-1]
 gi|192283515|gb|ACE99895.1| RNA-binding S4 domain protein [Rhodopseudomonas palustris TIE-1]
          Length = 736

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 140/331 (42%), Positives = 195/331 (58%), Gaps = 2/331 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           + +   +R++KV+ARAG+ SRR+ E  I + RV VNG +++  A++V ++D I +DG PL
Sbjct: 404 KSDKAGERIAKVVARAGLCSRRDAEAWITEGRVTVNGKVIDSPALDVKASDVITIDGKPL 463

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            + ERTRL+LYHKP GL+TTHSDP+GR TVFD+LP    R+IS+GRLD NTEGLLLLTND
Sbjct: 464 PERERTRLFLYHKPRGLMTTHSDPEGRPTVFDHLPEGLPRLISIGRLDFNTEGLLLLTND 523

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GGLAR LELP T WLR YRVR HG++ Q +L+ L+ GI + G+ YG ++  L+  +G+N 
Sbjct: 524 GGLARALELPETGWLRRYRVRAHGEITQAQLDELQNGIEVDGVQYGPIEAKLERDQGANV 583

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+   +REGKNRE++ V      +VNRLIR+SYGPFQL  L  G   EV  ++LR+QLG 
Sbjct: 584 WLVFAIREGKNREVRNVLAHLGLEVNRLIRVSYGPFQLLELGEGEVDEVKTRVLRDQLGE 643

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ--KNGLSKQKKLATPV 305
            ++  A  +   P  S           +S              +      + + +    V
Sbjct: 644 KVIALAGCDFAGPSPSETKPKPRAGKAVSAEEWAVADAAPAPKKTITKRGAVEDRKGRKV 703

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHR 336
                AS                G+R+   R
Sbjct: 704 KVERTASEGGDRPLSRGPARRYHGKRDLAPR 734



 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 12/108 (11%), Positives = 27/108 (25%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           ++ G      ++   D P +  +   + R +        F R +++   +    + K   
Sbjct: 227 DKGGFDKPRFSKSRDDKPRFDRDRGDKPRFDKPRGDKPRFDRGERSERPERSGDRPKFSR 286

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                R                      R  + R     P +    R 
Sbjct: 287 PRDGDRGEQRPFRERSFDRPREDRPRSDRPRSDRPREDRPQRDRAARH 334



 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 9/102 (8%), Positives = 21/102 (20%), Gaps = 1/102 (0%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
                +     +                     +    +     ++    P   R    +
Sbjct: 232 DKPRFSKSRDDKPRFDRDRGDKPRFDKPRGDKPRFDRGERSERPERSGDRPKFSRPRDGD 291

Query: 314 VWMAKGIH-SSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               +     SF      R  + R     P +   +R  A +
Sbjct: 292 RGEQRPFRERSFDRPREDRPRSDRPRSDRPREDRPQRDRAAR 333


>gi|22298198|ref|NP_681445.1| pseudouridylate synthase [Thermosynechococcus elongatus BP-1]
 gi|22294377|dbj|BAC08207.1| pseudouridylate synthase [Thermosynechococcus elongatus BP-1]
          Length = 250

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 85/236 (36%), Positives = 120/236 (50%), Gaps = 7/236 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
           T +R+ KV+A  G+ASRR  E +I   +V VNG   +     V    D IE  G  L   
Sbjct: 2   TTERLQKVLAHWGVASRRHAETLIRSGQVFVNGQRAK-LGDKVDPARDRIEYKGERLNPP 60

Query: 71  ERTR--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLLT 125
              +    L HKP G++ T  DP GR+TV D LP ++ RV     VGRLD ++ G LLLT
Sbjct: 61  RPPQRLYLLLHKPKGVLCTCHDPQGRTTVLDLLPPMYQRVGGLHPVGRLDADSSGALLLT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG     L  P     + YRV   GQ  ++ L   ++GI + G+      V     +G 
Sbjct: 121 NDGAFTYYLSHPRHHIPKTYRVWVQGQPPENVLQRWRQGIPLDGVMTLPATVKRLRSEGD 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            A + + L EG+NR+I++V +   + V  L RI+ GP  LG L   + R +S+  L
Sbjct: 181 RALLEIILHEGRNRQIRRVADQLGYPVLALQRIAIGPVHLGHLRPRAVRPLSRHEL 236


>gi|257465344|ref|ZP_05629715.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           minor 202]
 gi|257451004|gb|EEV25047.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           minor 202]
          Length = 230

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 53/231 (22%), Positives = 104/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + +    V VN  + +  +V + + D I  DG  L   +  
Sbjct: 1   MRLDKFIAENTGLTRSQAAKALKSGLVTVNQKVEKSGSVKISAQDEIRYDGELLEWMDEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ +KP G V +H D +  +        + +++ + GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYFMLYKPQGYVCSHDDGEYPTVFQFFDYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+       ++GI+++G        ++ +      +  V +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEDFYAQRFEEGILLRGEREPCLPAKMEVL----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F     KV  L R   G   L   L  G  R +++  +
Sbjct: 177 TISEGRYHQVKRMFAALGNKVEALHRWRIGDVVLDEDLQEGEFRPLTEDEM 227


>gi|229017689|ref|ZP_04174580.1| Pseudouridine synthase [Bacillus cereus AH1273]
 gi|229023908|ref|ZP_04180391.1| Pseudouridine synthase [Bacillus cereus AH1272]
 gi|228737421|gb|EEL87933.1| Pseudouridine synthase [Bacillus cereus AH1272]
 gi|228743615|gb|EEL93724.1| Pseudouridine synthase [Bacillus cereus AH1273]
          Length = 238

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 63/228 (27%), Positives = 108/228 (47%), Gaps = 7/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCTSEKAV--KGNIIDLVNHPLRINHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  + L  +  G+ I        ++T      S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPEFLEKMAAGVKILDTKTLPCEITQL----SKYEFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK  R
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKKEKR 225


>gi|237714337|ref|ZP_04544818.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           D1]
 gi|229445501|gb|EEO51292.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           D1]
          Length = 234

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 58/225 (25%), Positives = 100/225 (44%), Gaps = 1/225 (0%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW 76
           +K +A AG+ SRRE +  I    V VNG ++      +  +D ++    P+    +  + 
Sbjct: 2   NKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVVKFHDEPVSIERKVYVL 61

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L      + T+    + R+ +     +   R+  VGRLD NT G+LLLTNDG LA  L  
Sbjct: 62  LNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTTGVLLLTNDGDLASKLTH 121

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
           P     ++Y V     + +  +  +  GI ++            T       V + +  G
Sbjct: 122 PKFLKKKIYHVHLDKNLTKADMEQIAAGIQLEDGEIH-ADAISYTDDFKKDQVGIEIHSG 180

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           KNR ++++FE   +KV +L R+ +       L  G  R +S+  +
Sbjct: 181 KNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSEAEV 225


>gi|229096863|ref|ZP_04227832.1| Pseudouridine synthase [Bacillus cereus Rock3-29]
 gi|228686473|gb|EEL40382.1| Pseudouridine synthase [Bacillus cereus Rock3-29]
          Length = 235

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 66/229 (28%), Positives = 109/229 (47%), Gaps = 7/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+G  LR A   
Sbjct: 1   MRINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCTSEKAV--KGNIIDLVNHPLRISHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  D L  +  G+ I G      +VT      S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEVTQL----SKYEFQIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK  R
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKKEKR 222


>gi|149017975|ref|ZP_01834434.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP23-BS72]
 gi|147931539|gb|EDK82517.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP23-BS72]
          Length = 240

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 63/233 (27%), Positives = 101/233 (43%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    V  VGRLDINT GLLLLTNDG LA 
Sbjct: 61  VYYMMNKPKGVISATEDPKHRTVLDLLDDLARSKEVFPVGRLDINTHGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVT 190
           VL  P     + Y  +  G + Q+ +    +GI ++         ++     + + + + 
Sbjct: 121 VLLSPKRHVGKTYLAQVKGIMTQEDVETFAEGIPLKDFTCKPAILELVSIDTEKNQSQIR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 181 VTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELE 233


>gi|229496471|ref|ZP_04390186.1| ribosomal large subunit pseudouridine synthase B [Porphyromonas
           endodontalis ATCC 35406]
 gi|229316611|gb|EEN82529.1| ribosomal large subunit pseudouridine synthase B [Porphyromonas
           endodontalis ATCC 35406]
          Length = 459

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 62/235 (26%), Positives = 114/235 (48%), Gaps = 1/235 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +  TP R++K +A +G+ SRR  +++I    V VNG ++ +   +V   D I VDG P+ 
Sbjct: 219 DPKTPLRLNKFLASSGVCSRRVADQLIVDGHVSVNGEIVTQLGKHVTREDFISVDGKPVS 278

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ++  + L      + T+       + +     +   R+  VGRLD NT GLLLLTNDG
Sbjct: 279 IEKKIYVLLNKPRNCVTTSSDPEKRLTAIDLVRNACNERIYPVGRLDRNTTGLLLLTNDG 338

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P  +  ++Y+V     V  + +  +  GI ++        ++   +    A 
Sbjct: 339 DLAAKLMHPKYEKKKIYQVTLDKPVSVEHMQQIASGIELEDGEIHADAISYVDENNL-AI 397

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           V + +  G+NR ++++F+   ++V +L R+ +       L  G  R +++  +R 
Sbjct: 398 VGIEIHSGRNRIVRRIFKHLGYRVYKLDRVYFAGLTKKDLPRGRWRYLTEDEVRN 452


>gi|312135036|ref|YP_004002374.1| RNA-binding S4 domain-containing protein [Caldicellulosiruptor
           owensensis OL]
 gi|311775087|gb|ADQ04574.1| RNA-binding S4 domain protein [Caldicellulosiruptor owensensis OL]
          Length = 233

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 54/230 (23%), Positives = 100/230 (43%), Gaps = 7/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G  SR +V+++I +  V VNG  +      +    D +EVDG  ++ +  
Sbjct: 1   MRLDKFLTHCGFGSRTQVKKLIREGIVTVNGKQIVEVDFKINPEEDVVEVDGRIVKFSRW 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      + +             +       + +VGRLD + EGLL++T+DG    
Sbjct: 61  IYIMMNKPKGYVCSNEDPMSLTVFSLISDDLKHRDLHTVGRLDKDAEGLLIITDDGEYTH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            +  P  +  + Y VR   +VD+++L   + GI++         + T+      +  V +
Sbjct: 121 RVISPKKRIEKEYLVRLEKEVDEERLKEFENGIILDDGYKTLPAKYTII----DSTTVKL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
            + EGK  ++K++FE    KV  L R   G   L   L  G  R + ++ 
Sbjct: 177 CIYEGKYHQVKRMFEAIGNKVVDLKRRRIGGLNLDESLKPGEYRLMKEEE 226


>gi|162147095|ref|YP_001601556.1| ribosomal large subunit pseudouridine synthase B [Gluconacetobacter
           diazotrophicus PAl 5]
 gi|209544155|ref|YP_002276384.1| RNA-binding S4 domain-containing protein [Gluconacetobacter
           diazotrophicus PAl 5]
 gi|161785672|emb|CAP55243.1| putative ribosomal large subunit pseudouridine synthase B
           [Gluconacetobacter diazotrophicus PAl 5]
 gi|209531832|gb|ACI51769.1| RNA-binding S4 domain protein [Gluconacetobacter diazotrophicus PAl
           5]
          Length = 264

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 131/247 (53%), Positives = 167/247 (67%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R++K +AR+G+ASRR+ ER++ + RV++NG  +   A  V + D ++V+G  +   
Sbjct: 18  ERGERIAKWLARSGVASRRDAERLVEEGRVRLNGEPVTHPATFVAAGDIVQVNGAVVEAP 77

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ERTRLW YHKP GLVTTH DP+ R TVF +LP    RVISVGRLD+N+EGLLLLTNDG L
Sbjct: 78  ERTRLWRYHKPDGLVTTHRDPEKRPTVFASLPPGMPRVISVGRLDLNSEGLLLLTNDGEL 137

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           AR LELPS  WLR YRVR  G VD+ +L  L  G V +G+ YG ++  LD++KG NAW+T
Sbjct: 138 ARRLELPSNGWLRRYRVRVFGVVDEARLAALAGGSVFEGVRYGPIEAGLDSRKGDNAWLT 197

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           V LREGKNRE++KV    N  V+RLIR SYGPFQLGTL      EV  K+LREQ+     
Sbjct: 198 VALREGKNREVRKVMRGLNLHVSRLIRTSYGPFQLGTLQRSELEEVPGKVLREQVPGLGP 257

Query: 251 EEAQVNL 257
                  
Sbjct: 258 APRPARR 264


>gi|308187558|ref|YP_003931689.1| 16S pseudouridylate 516 synthase [Pantoea vagans C9-1]
 gi|308058068|gb|ADO10240.1| 16S pseudouridylate 516 synthase [Pantoea vagans C9-1]
          Length = 239

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 102/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I++    SR    R I  QRV VNG ++   A  ++    +  DG  L+     
Sbjct: 1   MRLDKFISQQLEISRAIAHREIRGQRVTVNGEVVRDTAFKLLPDHEVAYDGNVLQMLTGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+LLT+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTILYFIEEPMSFKLHAAGRLDIDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + YRV     +  D       G+ +          Q+ + T       V +
Sbjct: 121 ITSPRHHCEKTYRVTLESPIGDDTAAQFTAGVQLHNEKDLTKPAQLEVITPTD----VRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            L EG+  ++K++F     +V  L R   G   L   L  G  R +++  +
Sbjct: 177 TLSEGRYHQVKRMFAAVGNRVIELHRERIGDIALDDDLEPGDYRALTEDEI 227


>gi|296877269|ref|ZP_06901309.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           parasanguinis ATCC 15912]
 gi|296431789|gb|EFH17596.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           parasanguinis ATCC 15912]
          Length = 242

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 60/232 (25%), Positives = 103/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR EV++++ Q+++ VNG       + +    D +   G  L     
Sbjct: 1   MRLDKFLVDCGVGSRTEVKQLLKQKKIAVNGKKETAGKLQIDPGKDRVTFMGEDLVHETF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  D         +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPAGVISATEDDHHQTVLDLLDETARHKEVFPVGRLDIDTHGLLLLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            +  P     ++YR +  G +D+  +   + GI ++       ++ +     +N  ++V 
Sbjct: 121 AMLSPKKHVSKIYRAQVAGIMDEADVARFEAGIALKDFTTLPARLQILEVNEANASSYVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EGK  ++K++      +V  L RIS GP  L  +L  G  R +    L
Sbjct: 181 IEIAEGKFHQVKRMVAACGKEVADLERISMGPLTLDPSLKLGEWRRLQPSEL 232


>gi|253734463|ref|ZP_04868628.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|253727517|gb|EES96246.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|329733199|gb|EGG69536.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           21193]
          Length = 231

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 55/228 (24%), Positives = 100/228 (43%), Gaps = 7/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E 
Sbjct: 1   MRIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDKITVRGELIEYIEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + +   D   ++ +          +  VGRLD +TEGLLL+TNDG    
Sbjct: 61  VYIMLNKPKGYI-SATEDHHSKTVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+    + Y V     + +D +   K+G+ +         +T    + S     V 
Sbjct: 120 ELMSPNKHVSKKYEVISANPITEDDIQAFKEGVTLSDGKVKPAILTYIDNQTS----HVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           + EGK  ++K++F     +V  L RI     +L   L +G  R +++ 
Sbjct: 176 IYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYRLLTEN 223


>gi|189463704|ref|ZP_03012489.1| hypothetical protein BACINT_00037 [Bacteroides intestinalis DSM
           17393]
 gi|189438654|gb|EDV07639.1| hypothetical protein BACINT_00037 [Bacteroides intestinalis DSM
           17393]
          Length = 234

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 59/225 (26%), Positives = 99/225 (44%), Gaps = 1/225 (0%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW 76
           +K +A AG+ SRRE +  I    V VNG ++      +   D ++    P+    +  + 
Sbjct: 2   NKFLANAGVCSRREADEFITAGVVSVNGAVVTELGTKIKRGDEVKFHDQPVSIERKIYIL 61

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L      + T+      R+ +     +   R+  VGRLD NT G+LLLTNDG LA  L  
Sbjct: 62  LNKPKDTVTTSDDPQARRTVMDLVKGACDERIYPVGRLDRNTTGVLLLTNDGDLASKLTH 121

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
           P     ++Y V     V +  ++ +  GI +             T       V + +  G
Sbjct: 122 PKFLKKKIYHVHTDKNVTKADMDQIAAGIQLDDGEIH-ADAISYTDDVRRDEVGIEIHSG 180

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           KNR ++++FE   +KV +L R+ +       L  G  R +S++ +
Sbjct: 181 KNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLSEQEV 225


>gi|332883058|gb|EGK03342.1| hypothetical protein HMPREF9456_01979 [Dysgonomonas mossii DSM
           22836]
          Length = 482

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 59/233 (25%), Positives = 109/233 (46%), Gaps = 1/233 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +  TP R++K +A AG+ SRRE +  I    VKVNG ++++    V   D +     P+R
Sbjct: 242 DPSTPLRLNKYLANAGVCSRREADAFITSGVVKVNGEVVDQLGAKVTRGDLVTFHDQPVR 301

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              +  + L      + T+    +  + +     +   R+  VGRLD NT G+LLLTNDG
Sbjct: 302 LESKVYVLLNKPKNCVTTSDDPQNRLTVMDLVKNACPERIYPVGRLDRNTTGVLLLTNDG 361

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P  +  ++Y+V     V  + +  +  G+ +         +    +   N  
Sbjct: 362 DLASKLMHPKFKKKKIYQVTLDRDVAIEDMQAIADGVELDDGEIHADSIAYQAEDVLN-V 420

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + +  G+NR ++++FE   ++V +L R+ +       +     R +++K +
Sbjct: 421 VGIEIHSGRNRIVRRIFEKLGYQVVKLDRVYFAGLTKKNIPRSKWRYLTEKEV 473


>gi|301336267|ref|ZP_07224469.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           muridarum MopnTet14]
          Length = 241

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 66/229 (28%), Positives = 104/229 (45%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R++K +A AG+ASRR+ + ++    V VNG +     V V    D +EV+G  +   ++
Sbjct: 4   VRLNKFLASAGVASRRKCDEIVFAGAVTVNGKVAAGPFVIVDEELDSVEVEGQRIGTEKK 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               ++     L ++     G   V D L     R+ +VGRLD  T GL+L+TNDG  + 
Sbjct: 64  VYFMVHKPLGYLCSSERKFPGSKLVIDLLSHCPYRLFTVGRLDKETSGLILVTNDGEFSN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  PS    + Y ++    V    L  L  G+VI G     + V    +      + + 
Sbjct: 124 RVIHPSFGITKEYLLKVSRDVSARDLETLMAGVVIDGRIVRPVSVKKVRRG----TIKII 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGK  EI+   E    ++  L RI  G   LG L  G  RE++   L
Sbjct: 180 VNEGKKHEIRLFAEAAGLQLLELKRIRIGSLVLGGLPYGQYRELTDAEL 228


>gi|189220438|ref|YP_001941078.1| 16S rRNA uridine-516 pseudouridylate synthase or related enzyme
           [Methylacidiphilum infernorum V4]
 gi|189187296|gb|ACD84481.1| 16S rRNA uridine-516 pseudouridylate synthase or related enzyme
           [Methylacidiphilum infernorum V4]
          Length = 256

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 74/234 (31%), Positives = 130/234 (55%), Gaps = 4/234 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+++ +A  G+ SRR  E ++ + R+KVNG ++      + + D +E+DG  L + ++
Sbjct: 10  PIRINRYLASCGLGSRRSCEDLVREGRIKVNGQIVRTLGQKISAEDKVEIDGFLLLRPQQ 69

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + +L++KP G+V +  DP G  T++D LPS    + SVGRLD ++EGLLLLTNDG LA 
Sbjct: 70  KQYFLFYKPRGIVCSRKDPFGGKTIYDLLPSSLHHLFSVGRLDKDSEGLLLLTNDGLLAN 129

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P   + + Y V      ++     L KG+ I+G      +V ++ +      + + 
Sbjct: 130 AVLHPRYHFAKTYIVTLCPSFEEKHQKDLLKGMYIEGKRAKADKVIIENKN----TLKIV 185

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G  R+I+ +     +KVNRL R++ GP  L  +  G  R ++++ ++   G
Sbjct: 186 LSQGMKRQIRTMLSLLGYKVNRLRRVALGPLTLKRMKPGELRSLTEREIKSLYG 239


>gi|327439180|dbj|BAK15545.1| 16S rRNA uridine-516 pseudouridylate synthase [Solibacillus
           silvestris StLB046]
          Length = 240

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 61/224 (27%), Positives = 106/224 (47%), Gaps = 4/224 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV+ ++ Q+ V V+G+ ++ +A++V     ++ V G  +   E 
Sbjct: 5   MRLDKLLANMGYGSRKEVKLLLKQKAVTVDGVTVKDSAMHVNPEKQNVSVFGERVEYVEF 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +   P  +  T    D       +          VGRLD +TEGLLL+TNDG LA 
Sbjct: 65  IYLMMNKPPGVISATEDRYDQTVIDLLDPEYQHFEPFPVGRLDKDTEGLLLITNDGNLAH 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y  +  G V +  +    +G+ ++        ++ +    G  + + +
Sbjct: 125 NLLSPKKHVPKWYYAKIDGVVTEADIEAFAQGVTLEDGYHTKPGELKIL-VSGEQSEIEL 183

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
            ++EGK  ++K++FE    KV  L R+S G  +L   L  G  R
Sbjct: 184 MIQEGKFHQVKRMFEAVGKKVTYLKRLSMGTLKLDEELALGEYR 227


>gi|322390862|ref|ZP_08064371.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           parasanguinis ATCC 903]
 gi|321142447|gb|EFX37916.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           parasanguinis ATCC 903]
          Length = 242

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 104/233 (44%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR EV++++ Q+++ VNG       + +    D +   G  L     
Sbjct: 1   MRLDKFLVDCGMGSRTEVKQLLKQKKIAVNGKKETAGKLQIDPGKDRVTFMGEDLVHETF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  D         +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPAGVISATEDDHHQTVLDLLDETARHKEVFPVGRLDIDTHGLLLLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            +  P     ++YR +  G +D+  +   + GI ++       ++ +     +N  ++V 
Sbjct: 121 AMLSPKKHVSKIYRAQVAGIMDEADVARFEAGIALKDFTTLPARLQILEVNEANASSYVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + + EGK  ++K++      +V  L RIS GP  L  TL  G  R +    L+
Sbjct: 181 IEIAEGKFHQVKRMVAACGKEVVDLERISMGPLMLDPTLQLGEWRRLQPSELK 233


>gi|161502618|ref|YP_001569730.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160863965|gb|ABX20588.1| hypothetical protein SARI_00665 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 231

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 103/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G +++ AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVTDDTAAQFAKGVQLHNEKELTKPATLEVV----TPVQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVELHRERIGAITLDEDLAPGEYRPLTEEEI 227


>gi|257068695|ref|YP_003154950.1| pseudouridine synthase family protein [Brachybacterium faecium DSM
           4810]
 gi|256559513|gb|ACU85360.1| pseudouridine synthase family protein [Brachybacterium faecium DSM
           4810]
          Length = 306

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 83/233 (35%), Positives = 126/233 (54%), Gaps = 3/233 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
             +R+ KV+ARAG  SRR  E +I+  RV+V+G +++   V +      + VDG  L+  
Sbjct: 65  DGERLQKVLARAGFGSRRACETLISTGRVRVDGAVVQEQGVRIDPAAQVVHVDGRRLQLD 124

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E     + +KP G+V+  SDP+GR  + +   +   R+  VGRLD  TEGLLLLTNDG L
Sbjct: 125 ETKLTLVLNKPRGVVSAMSDPEGRRDLSEFTAAHSQRLYHVGRLDYETEGLLLLTNDGEL 184

Query: 131 ARVLELPSTQWLRVYRVRFHGQ--VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           A  L  PS +  + Y  RF       +  +  L+ G+ ++       +  +  Q G  A 
Sbjct: 185 AHRLTHPSFEVAKTYVCRFDAPGGPPRGLVRTLRDGVELEDGPARADRARVLAQDGREAV 244

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L EG+NR ++++F    +++  LIR   GP  LG L  G+TRE+S + L
Sbjct: 245 VEVTLHEGRNRIVRRMFASRGFELTALIRTRIGPVLLGDLAPGTTRELSGREL 297


>gi|256850915|ref|ZP_05556304.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           jensenii 27-2-CHN]
 gi|260661129|ref|ZP_05862043.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           jensenii 115-3-CHN]
 gi|256615977|gb|EEU21165.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           jensenii 27-2-CHN]
 gi|260548066|gb|EEX24042.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           jensenii 115-3-CHN]
          Length = 234

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 65/229 (28%), Positives = 100/229 (43%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I  ++V VNG L+++A   V  TD ++V    +   +  
Sbjct: 1   MRIDKYLANMKVGSRKEVHDLIKAKKVTVNGQLVKQAKQQVADTDIVKVADETIAYEQFY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      +  T                 +  +  VGRLD +T GLLLLTNDG L   
Sbjct: 61  YFMLNKPAGVITATEDPQQKTVLDLIEHKDRYQGLSPVGRLDKDTTGLLLLTNDGQLNHN 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     + Y V    +V  + +    KG+ +           L   K +     + +
Sbjct: 121 LLSPKKHVAKTYFVELDYEVSDELIVNFAKGVTLADG-TKVSPSQLKIDKSNKKQGFITI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EGK  +IK++F  F+  V RL RIS G   L   LL G  R+++K  +
Sbjct: 180 HEGKFHQIKRMFGLFDLGVVRLKRISMGNLSLDENLLLGKYRKLTKAEI 228


>gi|15924743|ref|NP_372277.1| 16S psudouridylate synthase [Staphylococcus aureus subsp. aureus
           Mu50]
 gi|15927330|ref|NP_374863.1| hypothetical protein SA1574 [Staphylococcus aureus subsp. aureus
           N315]
 gi|57652051|ref|YP_186636.1| pseudouridine synthase family 1 protein [Staphylococcus aureus
           subsp. aureus COL]
 gi|87160516|ref|YP_494393.1| pseudouridine synthase family 1 protein [Staphylococcus aureus
           subsp. aureus USA300_FPR3757]
 gi|88195567|ref|YP_500373.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus NCTC 8325]
 gi|148268231|ref|YP_001247174.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus JH9]
 gi|150394299|ref|YP_001316974.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus JH1]
 gi|151221858|ref|YP_001332680.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus str. Newman]
 gi|156980070|ref|YP_001442329.1| hypothetical protein SAHV_1739 [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|161509971|ref|YP_001575630.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|221141491|ref|ZP_03565984.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus str.
           JKD6009]
 gi|253315873|ref|ZP_04839086.1| pseudouridine synthase family 1 protein [Staphylococcus aureus
           subsp. aureus str. CF-Marseille]
 gi|255006539|ref|ZP_05145140.2| pseudouridine synthase family 1 protein [Staphylococcus aureus
           subsp. aureus Mu50-omega]
 gi|257794136|ref|ZP_05643115.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A9781]
 gi|258415840|ref|ZP_05682111.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A9763]
 gi|258420669|ref|ZP_05683608.1| pseudouridine synthase, family 1 [Staphylococcus aureus A9719]
 gi|258438319|ref|ZP_05689603.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A9299]
 gi|258443777|ref|ZP_05692116.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A8115]
 gi|258445988|ref|ZP_05694164.1| pseudouridylate synthase [Staphylococcus aureus A6300]
 gi|258448285|ref|ZP_05696412.1| pseudouridylate synthase [Staphylococcus aureus A6224]
 gi|258452304|ref|ZP_05700317.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A5948]
 gi|258454188|ref|ZP_05702159.1| pseudouridine synthase family 1 protein [Staphylococcus aureus
           A5937]
 gi|262049062|ref|ZP_06021940.1| hypothetical protein SAD30_2267 [Staphylococcus aureus D30]
 gi|262053064|ref|ZP_06025237.1| hypothetical protein SA930_1121 [Staphylococcus aureus 930918-3]
 gi|269203391|ref|YP_003282660.1| pseudouridine synthase family 1 protein [Staphylococcus aureus
           subsp. aureus ED98]
 gi|282893247|ref|ZP_06301481.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A8117]
 gi|282925640|ref|ZP_06333289.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A9765]
 gi|282927882|ref|ZP_06335493.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A10102]
 gi|284024800|ref|ZP_06379198.1| pseudouridine synthase family 1 protein [Staphylococcus aureus
           subsp. aureus 132]
 gi|294849914|ref|ZP_06790653.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A9754]
 gi|295406064|ref|ZP_06815872.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A8819]
 gi|296276053|ref|ZP_06858560.1| pseudouridine synthase family 1 protein [Staphylococcus aureus
           subsp. aureus MR1]
 gi|297245011|ref|ZP_06928888.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A8796]
 gi|304380652|ref|ZP_07363323.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|7328274|emb|CAB82472.1| hypothetical protein [Staphylococcus aureus subsp. aureus COL]
 gi|13701549|dbj|BAB42842.1| SA1574 [Staphylococcus aureus subsp. aureus N315]
 gi|14247525|dbj|BAB57915.1| similar to 16S psudouridylate synthase [Staphylococcus aureus
           subsp. aureus Mu50]
 gi|57286237|gb|AAW38331.1| pseudouridine synthase, family 1 [Staphylococcus aureus subsp.
           aureus COL]
 gi|87126490|gb|ABD21004.1| pseudouridine synthase, family 1 [Staphylococcus aureus subsp.
           aureus USA300_FPR3757]
 gi|87203125|gb|ABD30935.1| ribosomal small subunit pseudouridine synthase A, putative
           [Staphylococcus aureus subsp. aureus NCTC 8325]
 gi|147741300|gb|ABQ49598.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus JH9]
 gi|149946751|gb|ABR52687.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus JH1]
 gi|150374658|dbj|BAF67918.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus str. Newman]
 gi|156722205|dbj|BAF78622.1| hypothetical protein [Staphylococcus aureus subsp. aureus Mu3]
 gi|160368780|gb|ABX29751.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|257788108|gb|EEV26448.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A9781]
 gi|257839433|gb|EEV63906.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A9763]
 gi|257843273|gb|EEV67683.1| pseudouridine synthase, family 1 [Staphylococcus aureus A9719]
 gi|257848363|gb|EEV72354.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A9299]
 gi|257851183|gb|EEV75126.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A8115]
 gi|257855230|gb|EEV78169.1| pseudouridylate synthase [Staphylococcus aureus A6300]
 gi|257858524|gb|EEV81400.1| pseudouridylate synthase [Staphylococcus aureus A6224]
 gi|257860029|gb|EEV82864.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A5948]
 gi|257863640|gb|EEV86397.1| pseudouridine synthase family 1 protein [Staphylococcus aureus
           A5937]
 gi|259159041|gb|EEW44112.1| hypothetical protein SA930_1121 [Staphylococcus aureus 930918-3]
 gi|259162879|gb|EEW47443.1| hypothetical protein SAD30_2267 [Staphylococcus aureus D30]
 gi|262075681|gb|ACY11654.1| pseudouridine synthase family 1 protein [Staphylococcus aureus
           subsp. aureus ED98]
 gi|269941231|emb|CBI49619.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           TW20]
 gi|282590392|gb|EFB95471.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A10102]
 gi|282592420|gb|EFB97434.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A9765]
 gi|282764565|gb|EFC04691.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A8117]
 gi|285817435|gb|ADC37922.1| 16S pseudouridine synthase A [Staphylococcus aureus 04-02981]
 gi|294823253|gb|EFG39683.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A9754]
 gi|294969061|gb|EFG45082.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A8819]
 gi|297178091|gb|EFH37339.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A8796]
 gi|302751580|gb|ADL65757.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus str. JKD6008]
 gi|304340759|gb|EFM06688.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|312830131|emb|CBX34973.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           ECT-R 2]
 gi|315130607|gb|EFT86593.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           CGS03]
 gi|315197223|gb|EFU27562.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           CGS01]
 gi|320140780|gb|EFW32631.1| hypothetical protein HMPREF9528_00946 [Staphylococcus aureus subsp.
           aureus MRSA131]
 gi|320143781|gb|EFW35555.1| hypothetical protein HMPREF9529_00791 [Staphylococcus aureus subsp.
           aureus MRSA177]
 gi|329314428|gb|AEB88841.1| Pseudouridine synthase [Staphylococcus aureus subsp. aureus T0131]
 gi|329726944|gb|EGG63401.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           21189]
 gi|329727428|gb|EGG63884.1| putative 16S pseudouridylate 516 synthase [Staphylococcus aureus
           subsp. aureus 21172]
          Length = 231

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 55/228 (24%), Positives = 100/228 (43%), Gaps = 7/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E 
Sbjct: 1   MRIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDKITVRGELIEYIEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + +   D   ++ +          +  VGRLD +TEGLLL+TNDG    
Sbjct: 61  VYIMLNKPKGYI-SATEDHHSKTVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+    + Y V     + +D +   K+G+ +         +T    + S     V 
Sbjct: 120 ELMSPNKHVSKKYEVISANPITEDDIQAFKEGVTLTDGKVKPAILTYIDNQTS----HVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           + EGK  ++K++F     +V  L RI     +L   L +G  R +++ 
Sbjct: 176 IYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYRLLTEN 223


>gi|78485288|ref|YP_391213.1| pseudouridine synthase, Rsu [Thiomicrospira crunogena XCL-2]
 gi|78363574|gb|ABB41539.1| pseudouridine synthase homolog [Thiomicrospira crunogena XCL-2]
          Length = 261

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 114/238 (47%), Gaps = 7/238 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            + I+  +F+  R++K+I++AG+ S+++ +  I Q RV VNG +       V   D + +
Sbjct: 21  KQKIIATDFSSMRLNKLISQAGLGSKKQADAWIMQNRVTVNGQVASV-GQKVNQHDQVLL 79

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG P+  +    L  YHKP+G+V TH      + V      +     ++GRLD  +EGL+
Sbjct: 80  DGRPVAWSSEVLLMAYHKPVGVVCTHDLSVANNLVVS--TGLMQHFSAMGRLDKASEGLM 137

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           +LTN G L   +  P     + Y V     + +  L  +++G+ I G      ++    +
Sbjct: 138 ILTNQGDLTNHILQPGFAHEKEYWVEVDQPLTEYFLTNMQQGVEIMGQVTRPCEI----E 193

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                   + L +G N++I+++ +   ++V RL R+      L  L   + RE++   
Sbjct: 194 ATGEHCFRIVLTQGLNKQIRRMCKSLGYRVLRLQRVRIAQVWLDDLPVNTLRELNDVE 251


>gi|260664647|ref|ZP_05865499.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii SJ-7A-US]
 gi|260561712|gb|EEX27684.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii SJ-7A-US]
          Length = 234

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 98/229 (42%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I  ++V +N  L+++A   V   D ++VD   +   +  
Sbjct: 1   MRIDKYLANMNVGSRKEVHNLIKAKKVTINEKLVKQAKQQVTENDMVKVDNQTITYQQFH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      +  T                 +S +  VGRLD +T GLLL+TNDG L   
Sbjct: 61  YFMLNKPTGVITATEDPQQKTVLDLIASKDRYSDLAPVGRLDKDTTGLLLITNDGQLNHN 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     + Y V    ++  +  +   KG+ +           L   K +     + +
Sbjct: 121 LLSPKKHVAKTYFVELDQEIANEVDSAFAKGVALADG-TQVGSAQLIIDKSNKKQGLITI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EGK  +IK++F  F+  V +L RI  G   L   L  G  RE+++  +
Sbjct: 180 HEGKFHQIKRMFGLFDLGVVKLKRIKMGNLSLDENLPQGKYRELTEAEI 228


>gi|253732405|ref|ZP_04866570.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
 gi|297207533|ref|ZP_06923969.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus ATCC 51811]
 gi|253723857|gb|EES92586.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
 gi|296887869|gb|EFH26766.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus ATCC 51811]
          Length = 231

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 56/228 (24%), Positives = 102/228 (44%), Gaps = 7/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E 
Sbjct: 1   MRIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDKITVRGELIEYIEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP   ++   D   ++ +          +  VGRLD +TEGLLL+TNDG    
Sbjct: 61  -VYIMLNKPKDYISATEDHHSKTVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+    + Y V     + +D +   K+G+ +         +T    + S     V 
Sbjct: 120 ELMSPNKHVSKKYEVISANPITEDDIQAFKEGVTLSDGKVKPAILTYIDNQTS----HVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           + EGK  ++K++F     +V  L RI     +L   L +G  R +++ 
Sbjct: 176 IYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYRLLTEN 223


>gi|76787803|ref|YP_329548.1| RNA pseudouridine synthase family protein [Streptococcus agalactiae
           A909]
 gi|77406572|ref|ZP_00783621.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae H36B]
 gi|77411336|ref|ZP_00787684.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae CJB111]
 gi|76562860|gb|ABA45444.1| RNA pseudouridine synthase family protein [Streptococcus agalactiae
           A909]
 gi|77162596|gb|EAO73559.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae CJB111]
 gi|77174825|gb|EAO77645.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae H36B]
          Length = 239

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 59/230 (25%), Positives = 106/230 (46%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++ +AG  SR +V+++I  ++V V+G ++ +  V V S    I V    +   E 
Sbjct: 1   MRLDKLLGQAGFGSRNQVKKLICSRQVSVDGQIVTKDNVIVDSGLQSIFVGKERVCLKES 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +   LY     +               +       +  +GRLD +TEGLL++TN+G L  
Sbjct: 61  SYYLLYKPSGVVSAVRDSEHKTVIDLISEKDKVEGLYPIGRLDRDTEGLLIITNNGPLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V  +G +++D +   ++G+V          ++T+DT     +   +
Sbjct: 121 RMLHPKHHVAKTYYVEVNGFLERDAITFFEEGVVFDDGTKCKPAELTIDTANNDKSTARI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + EGK  ++KK+F  +  KV  L RIS+G  +L   L  G  R +    
Sbjct: 181 TITEGKFHQVKKMFLAYGVKVIYLRRISFGDLRLDMNLKPGQYRRLRDSE 230


>gi|330811302|ref|YP_004355764.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
 gi|327379410|gb|AEA70760.1| Ribosomal large subunit pseudouridine synthase B [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
          Length = 411

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 89/378 (23%), Positives = 147/378 (38%), Gaps = 26/378 (6%)

Query: 1   MKDKNIVQEN---FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           MKD++           +++ KV+AR G+ SRR+VE  I Q R+KVNG       + V   
Sbjct: 1   MKDQDQNDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDAT-LGLRVDMH 59

Query: 58  DHIEVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
           D I +DG  +++ E     R  +        + T        +           R I++G
Sbjct: 60  DAITIDGKVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDKMPRPKEGRWINIG 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RLDINT GLL+ T DG LA  L  PS +  R Y VR  G+VD + +  LK G+V++    
Sbjct: 120 RLDINTTGLLMFTTDGELANRLMHPSYEMDREYAVRVRGEVDDEMIERLKAGVVLEDGPA 179

Query: 173 GDMQVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
               +      +G N W    + EG+NRE+++++E     V+RL R+ +GP  L   L  
Sbjct: 180 RFTDIKQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLNSDLPM 239

Query: 231 GSTREVSKKI---------LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD 281
           G  RE+S+           L+    P +  +++  L+     S   +     + +  P  
Sbjct: 240 GRWREMSQYEVDILAAEVGLKPVAMPQMTAKSKDKLERMQRKSSRPMGKTERVRTLRPAA 299

Query: 282 FTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGI------HSSFLSDSGQREENH 335
                     +    + ++ A     R                            R    
Sbjct: 300 EGAPTGPRPSREPQIEGERPARKPAPRQDGERGPRTPRPANGRTERGEGRGAPAGRGTPV 359

Query: 336 RRSPSFPSKRSLRRTSAK 353
              P+   + +      +
Sbjct: 360 ADRPADTKRPAKPAPKKR 377


>gi|300072082|gb|ADJ61482.1| ribosomal small subunit pseudouridine synthase A [Lactococcus
           lactis subsp. cremoris NZ9000]
          Length = 242

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 63/239 (26%), Positives = 102/239 (42%), Gaps = 9/239 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
            R+ K +A +G+ SR EV+ ++ + RV V G +       V      +  DG  L   E 
Sbjct: 1   MRLDKFLAESGLGSRSEVKVLLKKGRVTVAGEIQRDGRFQVDKNSRQVAFDGQILDYQEY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  +         +       +  VGRLD NTEGLL+LTNDG L  
Sbjct: 61  YYYLLNKPQGVVSATKDNVFKTVVQLLSEKDFRKDIFPVGRLDKNTEGLLILTNDGALGH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT------QKGS 185
            L  P     + Y  R  G+V  + +N   +G+ ++ G      ++ ++       Q G 
Sbjct: 121 DLTQPKKHVEKEYFARIDGKVTDEIINKFAEGLTLKNGEKARPGELFVEKTYKGDSQSGW 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
            + + V + EGK  ++K++FE     V  L RI  G   L   L  G+ R ++ + +  
Sbjct: 181 VSEIRVIIHEGKFHQVKRMFEAVEMYVLYLKRIRMGNLALDSDLALGAYRPLTIEEIEN 239


>gi|293364698|ref|ZP_06611415.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           oralis ATCC 35037]
 gi|307702946|ref|ZP_07639893.1| putative ribosomal large subunit pseudouridine synthase B
           [Streptococcus oralis ATCC 35037]
 gi|291316148|gb|EFE56584.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           oralis ATCC 35037]
 gi|307623339|gb|EFO02329.1| putative ribosomal large subunit pseudouridine synthase B
           [Streptococcus oralis ATCC 35037]
          Length = 240

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 102/233 (43%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQINEERDEIRFDGQVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    V  VGRLDI+T GLLLLTNDG LA 
Sbjct: 61  VYYMMNKPQGVISATEDSKHRTVLDLLDDVARSKGVFPVGRLDIDTHGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVT 190
            L  P     + Y  +  G + Q+ +    KGI ++       ++ + +     + + + 
Sbjct: 121 ALLSPKRHVDKTYLAQVKGIMSQEDVETFAKGIPLKDFTCQPARLEIISIDTEKNQSKIR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  ++K++  +   +V  L R++ G   LG  L  G  R ++K+ L 
Sbjct: 181 VTIAEGKFHQVKRMVAYCGKEVVDLQRLTMGTLALGENLERGEWRRLTKEELE 233


>gi|124022690|ref|YP_001016997.1| pseudouridylate synthase specific to ribosomal small subunit
           [Prochlorococcus marinus str. MIT 9303]
 gi|123962976|gb|ABM77732.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Prochlorococcus marinus str. MIT 9303]
          Length = 244

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 77/231 (33%), Positives = 117/231 (50%), Gaps = 3/231 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
             QR+ K+IA +G+ SRR  E+++ Q+RV +NG L +          D I VDG  L   
Sbjct: 2   KQQRLQKLIAASGLCSRRHAEQLLLQERVTLNGHLAK-LGDKADPELDKISVDGRVLNSN 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGG 129
             TR+ L++KP G++T+  DP GR TVF  LP    +    VGRLD ++ G LL+TN G 
Sbjct: 61  TETRVLLFNKPAGVITSCHDPHGRVTVFSLLPDKLCKGLHPVGRLDADSRGALLITNRGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     + Y+V   G+     L+  + G+++ G      ++ L     S + +
Sbjct: 121 LTLRLTHPRYAHDKTYQVLVEGKPSPLVLSSWRHGVMLDGKTTLPAELELLQSHPSQSLL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            V LREG+NR+I++V E     V  L R +     L  L  G  R + ++ 
Sbjct: 181 KVVLREGRNRQIRRVAEQLGHPVLDLQRTAIANVALDALPEGCWRALDERE 231


>gi|297567379|ref|YP_003686351.1| RNA-binding S4 domain-containing protein [Meiothermus silvanus DSM
           9946]
 gi|296851828|gb|ADH64843.1| RNA-binding S4 domain protein [Meiothermus silvanus DSM 9946]
          Length = 369

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 79/349 (22%), Positives = 139/349 (39%), Gaps = 21/349 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +ARAG+ASRR+ E +I + RV +N  +      +V  +D + +DG  +R  E+ 
Sbjct: 1   MRLQQFLARAGVASRRKAEDLIREGRVTINDQIA-GIGSSVSESDVVCLDGERVRLPEKK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +   HKP+G+ TT SDP    TV+  L      +  VGRLD ++EGLLLLTNDG L   
Sbjct: 60  VVIALHKPVGVTTTKSDPHAERTVYQ-LVPDVPGLHPVGRLDKDSEGLLLLTNDGDLTLK 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQD-KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           L  P     +VYR         +     L +G+ +       ++     +        + 
Sbjct: 119 LTHPRYGVRKVYRAWCKHGRVSEADCRRLVEGVALDDGLAQALEAEPTQEGA-----RIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           + EGK RE++++     + V RL+R+  GP +LG L  G  R ++ + +    G   L+ 
Sbjct: 174 MAEGKKREVRRMLGRLGYPVTRLVRLQVGPIKLGKLNPGEWRYLTPEEIGLLQGQKPLKP 233

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN-------------SSQKNGLSKQK 299
            +    A    ++   +   +   + P    + +               +         +
Sbjct: 234 RKKEGWAKAKPAKFAQQREESRAIKPPSRTEQGRAGFTVRTKSPGDTPQAGTDRWARWAR 293

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           +      R               +   +          S   P +R+  
Sbjct: 294 ESDRSAQRSGRWGTSRRPYQGKRTAELEPKGLGSKSTSSTKTPGERTRP 342


>gi|238855289|ref|ZP_04645608.1| putative ribosomal small subunit pseudouridine synthase A
           [Lactobacillus jensenii 269-3]
 gi|282932418|ref|ZP_06337843.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           jensenii 208-1]
 gi|313471899|ref|ZP_07812391.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           jensenii 1153]
 gi|238832181|gb|EEQ24499.1| putative ribosomal small subunit pseudouridine synthase A
           [Lactobacillus jensenii 269-3]
 gi|239529181|gb|EEQ68182.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           jensenii 1153]
 gi|281303367|gb|EFA95544.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           jensenii 208-1]
          Length = 234

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 97/229 (42%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I  ++V +N  L+++A   V   D ++VD   +   +  
Sbjct: 1   MRIDKYLANMNVGSRKEVHNLIKAKKVTINEKLVKQAKQQVTENDMVKVDNQTITYQQFH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      +  T                 +  +  VGRLD +T GLLL+TNDG L   
Sbjct: 61  YFMLNKPTGVITATEDPQQKTVLDLIASKDRYPDLAPVGRLDKDTTGLLLITNDGQLNHN 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     + Y V    ++  +  +   KG+ +           L   K +     + +
Sbjct: 121 LLSPKKHVAKTYFVELDQEIANEVDSAFAKGVALADG-TQVGSAQLIIDKSNKKQGLITI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EGK  +IK++F  F+  V +L RI  G   L   L  G  RE+++  +
Sbjct: 180 HEGKFHQIKRMFGLFDLGVVKLKRIKMGNLSLDENLPQGKYRELTEAEI 228


>gi|221134960|ref|ZP_03561263.1| pseudouridine synthase (makes pseudouridine2605 in 23 S RNA)
           [Glaciecola sp. HTCC2999]
          Length = 331

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 91/331 (27%), Positives = 142/331 (42%), Gaps = 17/331 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
             ++ KV+A  G+ SRRE+E  I Q R+ VNG +       V  +D I VDG  L++ + 
Sbjct: 2   SDKLQKVLANQGVGSRREMETWIEQGRISVNGTIAT-LGDRVEPSDQIRVDGHLLKRDQK 60

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 L        L +       ++           R I+VGRLD+NT GLLL TNDG
Sbjct: 61  APVCRVLMYNKPEGELCSRTDPLGRQTVFDRLPNIQSGRWIAVGRLDLNTAGLLLFTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--N 186
            LA  L  P  +  R Y VR  G+V+   L LL+ G+ ++       ++     +    N
Sbjct: 121 ELANRLMHPRHEVEREYAVRVFGEVEPKTLKLLESGVELEDGLAKFTKIIARPNEEESIN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI---LR 242
           AW  V L EG+NRE+++++E    +V+RLIR+ YGP  L   L  G+  E+       LR
Sbjct: 181 AWYNVSLSEGRNREVRRLWESQGVQVSRLIRLRYGPLSLQKRLPQGAWIELELNDVNALR 240

Query: 243 EQLGPHLLEEAQVNLDAPI------YSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           +Q+      E  V ++               V+   +  ++ P        +   K    
Sbjct: 241 KQVQLPPETETLVGVNDNKLNHTKLSRMRKSVKKHKDRNAKAPIKGEGESASDDTKRTSR 300

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSD 327
           ++     P   RN A    + +    +  S 
Sbjct: 301 RKPNNGKPQANRNNAKKGNLGRTRAGTGGSR 331


>gi|22536965|ref|NP_687816.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae 2603V/R]
 gi|22533819|gb|AAM99688.1|AE014228_9 ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus agalactiae 2603V/R]
          Length = 239

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 59/230 (25%), Positives = 106/230 (46%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++ +AG  SR +V+++I  ++V V+G ++ +  V V S    I V    +   E 
Sbjct: 1   MRLDKLLGQAGFGSRNQVKKLICSRQVSVDGQIVTKDNVIVDSGLQSIFVGKERVCLKES 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +   LY     +               +       +  +GRLD +TEGLL++TN+G L  
Sbjct: 61  SYYLLYKPSGVVSAVRDSEHKTVIDLISEKDKVEGLYPIGRLDRDTEGLLIVTNNGPLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V  +G +++D +   ++G+V          ++T+DT     +   +
Sbjct: 121 RMLHPKHHVAKTYYVEVNGFLERDAITFFEEGVVFDDGTKCKPAELTIDTANNDKSTARI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + EGK  ++KK+F  +  KV  L RIS+G  +L   L  G  R +    
Sbjct: 181 TITEGKFHQVKKMFLAYGVKVIYLRRISFGDLRLDMNLKPGQYRRLRDSE 230


>gi|326331280|ref|ZP_08197572.1| ribosomal large subunit pseudouridine synthase B [Nocardioidaceae
           bacterium Broad-1]
 gi|325950913|gb|EGD42961.1| ribosomal large subunit pseudouridine synthase B [Nocardioidaceae
           bacterium Broad-1]
          Length = 255

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 73/233 (31%), Positives = 120/233 (51%), Gaps = 1/233 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A AGIASRR  E ++    V+VNG ++ R    V    D + V G  L     
Sbjct: 18  IRLQKLLALAGIASRRGSEILMLNGEVEVNGEVVTRLGTKVDPGKDVVRVGGKRLPPISG 77

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G+V+T SDP+GR  + D +     R+  VGRLD +TEGL++LTNDG  A 
Sbjct: 78  KVYLVLNKPRGVVSTMSDPEGRRNLSDLVADRPERLFHVGRLDTDTEGLIILTNDGDFAH 137

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS +  + Y     G++  +    L  G+ ++       +  +   +   + + + 
Sbjct: 138 RLAHPSYEVDKTYVAEVKGEIFPNVRKRLLAGVTLEDGPVTVTKARIMETRKDKSIIELV 197

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + EG+NR ++++ +     V RL R   GP +LG +  G  R++S++ L E L
Sbjct: 198 IHEGRNRIVRRLLDHLGHPVTRLTRTRIGPVRLGAMKPGDMRDLSREELGELL 250


>gi|315038031|ref|YP_004031599.1| 16S pseudouridylate synthase [Lactobacillus amylovorus GRL 1112]
 gi|325956483|ref|YP_004291895.1| 16S pseudouridylate synthase [Lactobacillus acidophilus 30SC]
 gi|312276164|gb|ADQ58804.1| 16S pseudouridylate synthase [Lactobacillus amylovorus GRL 1112]
 gi|325333048|gb|ADZ06956.1| 16S pseudouridylate synthase [Lactobacillus acidophilus 30SC]
 gi|327183311|gb|AEA31758.1| 16S pseudouridylate synthase [Lactobacillus amylovorus GRL 1118]
          Length = 236

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 103/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I +  V VNG +++     V  +D + VDG  +   +  
Sbjct: 1   MRIDKYLANMNVGSRKEVHVLIKKGIVTVNGDVVKTPKQQVKESDEVLVDGQEINYQKYH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +      L  T                 +  +  VGRLD +T GLLLLTNDG L   
Sbjct: 61  YFLMNKPKGVLSATEDRSQRTVISLLKPQDQYQGITPVGRLDKDTTGLLLLTNDGQLNHK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKG--SNAWVT 190
           L  P+    ++YR +  G  D + + +   G+ +         ++ + +Q     ++ + 
Sbjct: 121 LLAPNKHVDKIYRAKIAGVADDETVKIFASGMTLGDSTKLKPAELKILSQDEEHDSSEIE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           + +REGK  +IK++F     KV  L RIS G  +L   L  G   E++   +
Sbjct: 181 IRIREGKYHQIKRMFGAVGMKVVELERISMGKLKLPKDLKRGEYIELNLDDV 232


>gi|238926990|ref|ZP_04658750.1| pseudouridylate synthase [Selenomonas flueggei ATCC 43531]
 gi|238885224|gb|EEQ48862.1| pseudouridylate synthase [Selenomonas flueggei ATCC 43531]
          Length = 290

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 83/287 (28%), Positives = 135/287 (47%), Gaps = 1/287 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K+I+ AG ASRR  E +I   RV V+G+ +        +    I VDG P+R+ ER
Sbjct: 3   ERLQKIISNAGAASRRAAEALIRAGRVTVDGLPVTALGGKYDAARHEIAVDGTPIRRNER 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L HKP G ++T  D  GR TV D LP   +R+  VGRLD +TEGLL++TNDG + +
Sbjct: 63  RFYILLHKPRGCLSTAYDDRGRRTVLDLLPHFPARLYPVGRLDADTEGLLIITNDGAMTQ 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  +VYR    G V +D L  L+ GI++        ++ +  ++G    V   
Sbjct: 123 GLLHPRFEIDKVYRAEVTGNVTEDGLTALRNGILLDDGRTAPARLRVLHREGERTVVETI 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           + EG+ R+++++F     +V RL R+ +    L  +  GS R ++   + E      +  
Sbjct: 183 IHEGRKRQVRRMFAAIGCRVQRLCRVRFAMLTLDGVSCGSFRHLTSDEIHELKKIAGVMH 242

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
           +  +      S         +      D   +     +Q +   K  
Sbjct: 243 SGEDSRRRRGSCGNDGGRCGSGTRGQCDPARKDAARRAQDDDHGKGA 289


>gi|307245181|ref|ZP_07527272.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|307254128|ref|ZP_07535973.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 9 str. CVJ13261]
 gi|307258592|ref|ZP_07540327.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 11 str. 56153]
 gi|306853825|gb|EFM86039.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|306862828|gb|EFM94777.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 9 str. CVJ13261]
 gi|306867249|gb|EFM99102.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 11 str. 56153]
          Length = 230

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 106/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  R +    V VNG L +  +V +  TD I  +G  L   +  
Sbjct: 1   MRLDKFIAENTGLTRSQAARALKSGLVTVNGKLEKSGSVKIGDTDEICYEGERLEWVDEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ +KP G V +H D +  +        + +++ + GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYFMLYKPQGYVCSHDDGEYPTVFQFFDYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+      L +GI+++G        Q+ +      +  V +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEDFYAKKLAEGILLRGEREPCLPAQMEII----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EG+  ++K++F     KV  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAALGNKVEALHRWRIGDVVLDESLEEGEYRPLTEQEI 227


>gi|317048876|ref|YP_004116524.1| pseudouridine synthase [Pantoea sp. At-9b]
 gi|316950493|gb|ADU69968.1| pseudouridine synthase [Pantoea sp. At-9b]
          Length = 240

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 61/244 (25%), Positives = 111/244 (45%), Gaps = 7/244 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I++    SR    R I  +++ +NG ++   A  V+  D +  DG PL +    
Sbjct: 1   MRLDKFISQQLEISRAISAREIRAKKITINGEVVRDTAYKVLPDDDVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + +F     +  ++ + GRLDI+T GL+LLT+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTILFFIEEPMVGKLHAAGRLDIDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     +VYRV     +D   +     GI +           + +   + +     +
Sbjct: 121 ITSPRHHCEKVYRVGVESPIDPSLVEKFAAGIQLHNEKDLTKPATLEIVGPQEA----LL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLL 250
            + EG+  ++K++F      V  L R   G   L   L  G  RE++++ +     P  L
Sbjct: 177 TISEGRYHQVKRMFAASGNHVVTLHRERIGDIVLDADLAEGEYRELTEEEVASIGLPDEL 236

Query: 251 EEAQ 254
           ++ +
Sbjct: 237 KQPK 240


>gi|315223635|ref|ZP_07865489.1| ribosomal large subunit pseudouridine synthase B [Capnocytophaga
           ochracea F0287]
 gi|314946416|gb|EFS98411.1| ribosomal large subunit pseudouridine synthase B [Capnocytophaga
           ochracea F0287]
          Length = 387

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 60/228 (26%), Positives = 111/228 (48%), Gaps = 1/228 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGI SRR  +  I+   V VNG ++      V  TD +  DG  L   ++ 
Sbjct: 154 VRLNKFIADAGICSRRNADMYISAGNVMVNGEVMTTLGYRVKPTDEVRFDGKLLSSEKKE 213

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L      + TT+ +   ++ +     +   R++ VGRLD  T GLLLLTNDG L + 
Sbjct: 214 YILLNKPKGFITTTNDEKGRKTVMDLVANATNVRILPVGRLDRATTGLLLLTNDGELTKK 273

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P+    ++Y V    ++D      ++ G+ ++       +++    K  N  + + +
Sbjct: 274 LTHPTHGVRKIYHVILDRKLDYKDFMKVQDGLELEDGLIEVDEISYVNNKPKN-EIGIKI 332

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             G+NR ++++FE   ++V +L R+ +       L  G  R ++++ +
Sbjct: 333 HSGRNRIVRRIFEHLGYQVEKLDRVVFAGLTKKDLPRGHWRRLTQQEV 380


>gi|251811134|ref|ZP_04825607.1| pseudouridylate synthase [Staphylococcus epidermidis BCM-HMP0060]
 gi|282875829|ref|ZP_06284696.1| pseudouridylate synthase [Staphylococcus epidermidis SK135]
 gi|293366306|ref|ZP_06612986.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|251805354|gb|EES58011.1| pseudouridylate synthase [Staphylococcus epidermidis BCM-HMP0060]
 gi|281294854|gb|EFA87381.1| pseudouridylate synthase [Staphylococcus epidermidis SK135]
 gi|291319544|gb|EFE59910.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|329737233|gb|EGG73487.1| putative 16S pseudouridylate 516 synthase [Staphylococcus
           epidermidis VCU028]
 gi|329737517|gb|EGG73770.1| putative 16S pseudouridylate 516 synthase [Staphylococcus
           epidermidis VCU045]
          Length = 230

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 58/227 (25%), Positives = 101/227 (44%), Gaps = 7/227 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  VKVN  +++   ++V    D I V+   +     
Sbjct: 1   MRLDKFLANMGVGTRSEVKQLLKKGSVKVNQNIVKLPKLHVNPNSDEIMVNDEVVSYI-D 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G ++   D    + +          +  VGRLD +TEGLLL+TNDG    
Sbjct: 60  KVYIMLNKPKGYISATEDEVHPTIIDLIPEYAHLNIFPVGRLDKDTEGLLLVTNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P+    + Y V     + Q  ++  K GI +              +K  N    V 
Sbjct: 120 EVMNPNKHVSKTYEVYSKHPITQFDIDKFKSGIELSDGKLKPA----ILKKVDNYVSHVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
           + EGK  ++K++F     +V  L RI     +L   L  GS R +++
Sbjct: 176 IYEGKYHQVKRMFHSIENEVLELKRIKIAQLELDHNLDLGSYRLLTQ 222


>gi|56478942|ref|YP_160531.1| pseudouridylate synthase [Aromatoleum aromaticum EbN1]
 gi|56314985|emb|CAI09630.1| pseudouridylate synthase [Aromatoleum aromaticum EbN1]
          Length = 317

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 76/266 (28%), Positives = 121/266 (45%), Gaps = 6/266 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA- 70
            P+R+ KV+A+ G+ SRRE+E  +   R+ VNG+        +   D ++ +G  +    
Sbjct: 53  EPERLQKVLAQIGLGSRREIEEWVVAGRISVNGLPA-ELGQKIGPGDRVKYNGKLIPLRF 111

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  +     +V+        +           R I+VGRLD NT GLLL TND
Sbjct: 112 TVRTPRVLIYHKPEGEIVSREDPEGRPTVFERLPILRKGRWIAVGRLDFNTSGLLLFTND 171

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P  +  R Y VR  GQ+D ++L  LK GI ++        ++ +  +G+N 
Sbjct: 172 GTLANRLMHPRYELEREYAVRLLGQLDDEQLESLKTGIQLEDGLARFTSISDEGGEGANH 231

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
           W  V L EG+NRE++++FE     V+RL+R+ YGP  L + L  G   E+ +  +    G
Sbjct: 232 WYRVTLSEGRNREVRRMFEAVGLTVSRLMRVRYGPVTLSSRLKRGMWMEMPEAEVCSLAG 291

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRP 272
               +         +  +        
Sbjct: 292 LPKPQGQAARPGEQVRKTRLHRTTPR 317


>gi|307565246|ref|ZP_07627740.1| pseudouridylate synthase [Prevotella amnii CRIS 21A-A]
 gi|307346059|gb|EFN91402.1| pseudouridylate synthase [Prevotella amnii CRIS 21A-A]
          Length = 528

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 61/235 (25%), Positives = 110/235 (46%), Gaps = 1/235 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            +   P R++K +A AG+ SRRE +  I+  ++ VNG ++      ++ TD I+  G  +
Sbjct: 287 TDPTEPLRLNKYLANAGVCSRREADNYISSGQITVNGEVVTELGTKILRTDEIKFKGQTV 346

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              ++  L L      + T+      +  V     +   R+  VGRLD NT G+LL TND
Sbjct: 347 SLEKKVYLLLNKPKDYVTTSDDPQQRKKVVDLVKDACPERIYPVGRLDRNTTGVLLFTND 406

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P     +VY V     V  + L  + +GI+++        +   +     +
Sbjct: 407 GDLASKLTHPKFLKKKVYHVFLDKPVAANDLQKIAEGIMLEDGEIKADAIEYASPDDL-S 465

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V + +  GKNR ++++FE   ++V +L R+ +       +  G  R +++K + 
Sbjct: 466 QVGIEIHSGKNRIVRRIFESLGYRVVKLDRVMFAGLTKKNVRRGDWRFLTQKEVE 520


>gi|332830420|gb|EGK03048.1| hypothetical protein HMPREF9455_01298 [Dysgonomonas gadei ATCC
           BAA-286]
          Length = 444

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 65/241 (26%), Positives = 115/241 (47%), Gaps = 2/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K K  +  N TP R++K +A AG+ SRRE +  I    VKVNG ++++    V   D +
Sbjct: 197 VKYKENIDPN-TPLRLNKYLANAGVCSRREADAYITSGVVKVNGEVVDQLGAKVTRGDLV 255

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                P+R   +  + L      + T+    +  + +     +   R+  VGRLD NT G
Sbjct: 256 TFQDKPVRLESKVYVLLNKPKNCVTTSDDPQNRLTVMDLVKNACPERIYPVGRLDRNTTG 315

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P  +  ++Y+V     V  + +  +  G+ +         +   
Sbjct: 316 VLLLTNDGDLASKLMHPKFKKKKIYQVTLDRDVAIEDMQAIADGVELDDGEIHADSIAYQ 375

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +   N  V + +  G+NR ++++FE   ++V +L R+ +       +L G  R +S+K 
Sbjct: 376 AEDVLN-VVGIEIHSGRNRIVRRIFEKLGYQVMKLDRVYFAGLTKKNVLRGKWRYLSEKE 434

Query: 241 L 241
           +
Sbjct: 435 V 435


>gi|227495415|ref|ZP_03925731.1| pseudouridylate synthase [Actinomyces coleocanis DSM 15436]
 gi|226830962|gb|EEH63345.1| pseudouridylate synthase [Actinomyces coleocanis DSM 15436]
          Length = 248

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 77/240 (32%), Positives = 124/240 (51%), Gaps = 1/240 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R+ KVI++AG+ASRR  E++I   RVKV+G ++    + V  +   I VDG  +  
Sbjct: 8   EDGVRLQKVISQAGVASRRHAEKLIISGRVKVDGNIVRTLGIRVDPSVQTIHVDGNQIML 67

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             ++     +KP G+V+T  DPDGR  + + +     R+  VGRLD +T GL+LLTNDG 
Sbjct: 68  DTKSLTIALNKPAGVVSTMDDPDGRPCLAEFVEQYNQRLYHVGRLDTDTAGLILLTNDGE 127

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L+  L  PS +  + Y    HG+V +     L +GI ++          +    G    V
Sbjct: 128 LSHRLMHPSWEVPKTYVATVHGEVPRGLGRKLARGITLEDGPVKVEDFQITDHYGEMTLV 187

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L EG+NR ++++ +   + V  L+R  +GP  +G L +G TR +   +L+E      
Sbjct: 188 QLTLHEGRNRIVRRIMDHVGFPVIELVRTQFGPVHIGRLHSGVTRRIEGPVLQELYRAVN 247


>gi|163816624|ref|ZP_02207987.1| hypothetical protein COPEUT_02814 [Coprococcus eutactus ATCC 27759]
 gi|158447881|gb|EDP24876.1| hypothetical protein COPEUT_02814 [Coprococcus eutactus ATCC 27759]
          Length = 239

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 106/233 (45%), Gaps = 6/233 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    I SR +V++ I +  V VNG     + + +    D I+ +G  L  ++ 
Sbjct: 1   MRLDKFLVEMNIGSRSQVKQYIKKGMVSVNGTNAASSDMKINEDTDTIKYNGKQLCYSKY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      + +   D   ++ +          +  VGRLD++TEGLL++TNDG LA 
Sbjct: 61  RYFLLNKPAGCV-SATKDNVHQTVIDLLNGENTKDLFPVGRLDLDTEGLLIITNDGRLAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN--AWV 189
            L  P+    + Y     G VD   ++L K+GI I          + +     S   + +
Sbjct: 120 HLLSPAHHIAKTYYADIDGYVDDQTISLFKQGIDIGDDTPTLPASLKIIEADRSTGSSRI 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            + + EG+  ++K++F+  N  V  L RIS G   +   L  GS RE++ + +
Sbjct: 180 ELTITEGRFHQVKRMFQAVNMSVTFLKRISMGNLHIADDLPTGSYRELTPEEV 232


>gi|320451314|ref|YP_004203410.1| ribosomal large subunit pseudouridine synthase B [Thermus
           scotoductus SA-01]
 gi|320151483|gb|ADW22861.1| ribosomal large subunit pseudouridine synthase B [Thermus
           scotoductus SA-01]
          Length = 236

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 82/242 (33%), Positives = 116/242 (47%), Gaps = 8/242 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+   +ARAG+ SRR+ E +I Q RV+VNG +       V   D +EVDG P+   
Sbjct: 2   EKPLRLQAFLARAGVGSRRKAEELIRQGRVRVNGKVA-VLGQKVNPGDVVEVDGKPVEPP 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               +   HKP G  TT  DP  + TVFD LP I      +GRLD ++EGLLLLTNDG L
Sbjct: 61  RERIVLALHKPRGYTTTRHDPHAQKTVFDLLPDIPGL-HPIGRLDRDSEGLLLLTNDGHL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
              L  P     +VYRV              L +G+ ++      +              
Sbjct: 120 TLRLTHPRYGVRKVYRVYTERGTLPLAICQRLLEGVDLEDGPARALACRPAPGGA----- 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L EG+ RE++++ +   + V RLIR+  GP  LG L  G  R++S + +   L    
Sbjct: 175 LLTLAEGRKREVRRMLKAVGYPVKRLIRLQVGPIHLGHLPPGKWRQLSPREVEALLRETP 234

Query: 250 LE 251
           +E
Sbjct: 235 VE 236


>gi|296117982|ref|ZP_06836565.1| RNA pseudouridylate synthase [Corynebacterium ammoniagenes DSM
           20306]
 gi|295969213|gb|EFG82455.1| RNA pseudouridylate synthase [Corynebacterium ammoniagenes DSM
           20306]
          Length = 308

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 79/243 (32%), Positives = 123/243 (50%), Gaps = 4/243 (1%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIE 61
           +K+    N   +R+ KV+A+AG+ASRR  E +I   RV+VNG +++R  V V    D I 
Sbjct: 57  EKSTQNPNTEGERLQKVLAKAGVASRRHAEVLIDAGRVEVNGKIIKRQGVRVNPNADVIR 116

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINT 118
           VDGV +   E    ++ +KP G+ +T  D  GR  V D +        R+  VGRLD +T
Sbjct: 117 VDGVRVNVNEDHEYFILNKPRGVQSTMQDDMGRPCVGDMVAEKTASGQRLFHVGRLDADT 176

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLL+LTNDG LA  L  P  +  + Y     G+ D+  +  LK GI +         V 
Sbjct: 177 EGLLILTNDGELANRLMHPKYEVSKTYLATVLGEADKSLVRTLKDGIELDDGMANADFVQ 236

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +  +    + + + L EG+   ++++ +   + V RL+R      QLG +  G  R ++ 
Sbjct: 237 IVDKNQGMSLIRLELHEGRKHIVRRMLKAAGYPVQRLVRTKIHTVQLGDMKPGGIRALNS 296

Query: 239 KIL 241
             L
Sbjct: 297 AEL 299


>gi|168484154|ref|ZP_02709106.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CDC1873-00]
 gi|172042547|gb|EDT50593.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CDC1873-00]
 gi|332203445|gb|EGJ17512.1| hypothetical protein SPAR93_0315 [Streptococcus pneumoniae GA47368]
          Length = 240

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 63/233 (27%), Positives = 102/233 (43%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    V  VGRLDI+T GLLLLTNDG LA 
Sbjct: 61  VYYMMNKPKGVISATEDPKHRTVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVT 190
           VL  P     + Y  +  G + Q+ +    KGI ++       ++ +     + + + + 
Sbjct: 121 VLLSPKRHVDKTYLAQVKGIMTQEDVETFIKGIPLKDFTCQPARLEILSTDAEKNQSQIR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 181 VTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELE 233


>gi|33863340|ref|NP_894900.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Prochlorococcus marinus str. MIT 9313]
 gi|33640789|emb|CAE21244.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Prochlorococcus marinus str. MIT 9313]
          Length = 244

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 77/231 (33%), Positives = 117/231 (50%), Gaps = 3/231 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
             QR+ K+IA +G+ SRR  E+++ Q+RV +NG L +          D I VDG  L   
Sbjct: 2   KQQRLQKLIAASGLCSRRHAEQLLLQERVTLNGHLAK-LGDKADPELDKISVDGRVLNSN 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGG 129
             TR+ L++KP G++T+  DP GR TVF  LP    +    VGRLD ++ G LL+TN G 
Sbjct: 61  TETRVLLFNKPAGVITSCHDPHGRVTVFSMLPDKLCKGLHPVGRLDADSRGALLITNQGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     + Y+V   G+     L+  + G+++ G      ++ L     S + +
Sbjct: 121 LTLRLTHPRYAHDKTYQVLVEGKPSALVLSSWRHGVMLDGKTTLPAELELLQSHPSQSLL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            V LREG+NR+I++V E     V  L R +     L  L  G  R + ++ 
Sbjct: 181 KVVLREGRNRQIRRVAEQLGHPVLDLQRTAIANVALNALPEGCWRALDERE 231


>gi|225018711|ref|ZP_03707903.1| hypothetical protein CLOSTMETH_02661 [Clostridium methylpentosum
           DSM 5476]
 gi|224948439|gb|EEG29648.1| hypothetical protein CLOSTMETH_02661 [Clostridium methylpentosum
           DSM 5476]
          Length = 255

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 87/234 (37%), Positives = 129/234 (55%), Gaps = 2/234 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--K 69
              R+ K+IA +G  SRR+ E++I ++RVKVNG   +         D + VD   +   +
Sbjct: 11  EKIRLQKIIAESGFCSRRKAEQLIEERRVKVNGHPAKIGDKADPRKDVVTVDDERITVAR 70

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               R  + HKP G VTT SD  GR  V D +  I  R+  VGRLD+N+EGLLL TNDG 
Sbjct: 71  RPTYRYVMLHKPRGYVTTMSDEKGRRCVADLVADIDERLYPVGRLDVNSEGLLLFTNDGR 130

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  +  PS    + YRV     +  ++   L +G+VI G      QV + T++ +   +
Sbjct: 131 LANDIMHPSRHVTKTYRVTVRPDITDEQAARLAEGVVIDGRKTAPAQVHVLTKEPNRVVM 190

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            V +REG+NR+I+K+ E    +V RL R S GP +LG L  G+ R+++ + L+ 
Sbjct: 191 EVVIREGRNRQIRKMMEAVGLEVARLKRTSLGPIKLGMLKPGAHRDLTAEELKA 244


>gi|320539063|ref|ZP_08038735.1| putative 23S rRNA U2604 pseudouridine synthase [Serratia symbiotica
           str. Tucson]
 gi|320030873|gb|EFW12880.1| putative 23S rRNA U2604 pseudouridine synthase [Serratia symbiotica
           str. Tucson]
          Length = 288

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 58/291 (19%), Positives = 116/291 (39%), Gaps = 5/291 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           + +  R++K I+ +GI SRR+ +R I Q  V +NG  +      V   D ++V+G  +  
Sbjct: 3   SKSSLRLNKYISESGICSRRDADRYIEQGNVFINGKRVT-LGDRVFPGDVVKVNGQVIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        +    +  DG      +  +  +R+  +GRLD +++GL+ LTN G 
Sbjct: 62  RNEDNLIFIALNKPVGIVSTTEDGEKDNIVDFVNHSTRIFPIGRLDKDSQGLIFLTNQGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + YRV  +  +  D +  L  G+ + G            +K +    
Sbjct: 122 LVNKILRAGNGHEKEYRVTVNKPLTDDVIRGLGDGVPMLGTV----TKKCKVKKETPLVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F ++V +L R       L  L  G  R+++     +      
Sbjct: 178 RIVLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLIGLPLGEWRDLTDDERGQLFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
              ++V        +   +       +      +   +    + G  K+ +
Sbjct: 238 DSSSEVKSVKKAKPAVKNLAGNNGPRNGNRSGSSLAARKRFTQPGRKKKGR 288


>gi|240948999|ref|ZP_04753353.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           minor NM305]
 gi|240296586|gb|EER47204.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           minor NM305]
          Length = 230

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 53/231 (22%), Positives = 104/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + +    V VN  + +  +V + + D I  DG  L   +  
Sbjct: 1   MRLDKFIAENTGLTRSQAAKALKSGLVTVNQKVEKSGSVKISAQDEIRYDGELLEWMDEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ +KP G V +H D +  +        + +++ + GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYFMLYKPQGYVCSHDDGEYPTVFQFFDYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+       ++GI+++G        ++ +      +  V +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEDFYAQRFEEGILLRGEREPCLPAKMEVL----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F     KV  L R   G   L   L  G  R +++  +
Sbjct: 177 TISEGRYHQVKRMFAALGNKVEALHRWRIGDVVLDENLQEGEFRPLTEDEM 227


>gi|331002924|ref|ZP_08326437.1| hypothetical protein HMPREF0491_01299 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330413217|gb|EGG92591.1| hypothetical protein HMPREF0491_01299 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 242

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 60/247 (24%), Positives = 110/247 (44%), Gaps = 11/247 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG------VPL 67
            R++K +A  G+ SRRE ++ I   RV +NG +       V   D + +DG        +
Sbjct: 1   MRLNKFLASIGVCSRREADKAIEAGRVMINGEVA-ELGAMVGEEDLVSLDGRYIATGKDV 59

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            K +   +        + TT  +    + V      +  R+  VGRLD ++ GLLLLTN 
Sbjct: 60  EKVKPIIIAFNKPEGIVCTTSDNDGATNVVDYI--GMKERIYPVGRLDKDSSGLLLLTNQ 117

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L   +    + Y V+ +  +D D +N +  GI +  +     +  +  +K +  
Sbjct: 118 GSLTNSLLRAANYHEKEYIVKVNKDIDDDFINKMSNGIYLYELKTKTRKCKV--KKLNKN 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
             ++ L +G NR+I+++      KV +L R+     +L  L  G+ R +S + +++    
Sbjct: 176 TFSIVLTQGLNRQIRRMCLACGMKVQKLNRVRIVNIKLDGLALGAYRNLSDEEIKKLYKE 235

Query: 248 HLLEEAQ 254
             + E  
Sbjct: 236 LGIRENG 242


>gi|188533404|ref|YP_001907201.1| 16S rRNA pseudouridylate synthase A [Erwinia tasmaniensis Et1/99]
 gi|188028446|emb|CAO96308.1| Ribosomal small subunit pseudouridine synthase A [Erwinia
           tasmaniensis Et1/99]
          Length = 234

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 52/229 (22%), Positives = 103/229 (44%), Gaps = 3/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR    R +  ++V V+G ++   +  + +   IE DG  L++    
Sbjct: 1   MRLDKFLSQQLEVSRAIAARELRAKKVTVDGEVVRDGSYKLSADSAIEYDGNALQQQLGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP+G V +  DPD  + ++        ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPVGYVCSTDDPDHPTILYFLEEPSAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D       G+ +           L+  + +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPIGHDTAQQFADGVQLHNEKTLTKPAALEVIEPN--LVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G   L   +  G  R +S + +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVALHRERIGAILLDTGMQPGEYRPLSDEEI 227


>gi|71280912|ref|YP_268861.1| ribosomal small subunit pseudouridine synthase A [Colwellia
           psychrerythraea 34H]
 gi|71146652|gb|AAZ27125.1| ribosomal small subunit pseudouridine synthase A [Colwellia
           psychrerythraea 34H]
          Length = 243

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 58/243 (23%), Positives = 105/243 (43%), Gaps = 13/243 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I ++   +R E ++++    V+VN  + + AA+ V   + I +DG  L      
Sbjct: 1   MRLDKFICKSTELTRTEAKKVLKSGEVRVNNEVAKNAAMQVHENNLITIDGQQLSARGS- 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HK +  + ++ D    S +          +   GRLD +T GL+L+T+DG  +  
Sbjct: 60  RYYILHKIVDTICSNVDEIYPSVLHSLEVDKAFDLHIAGRLDADTTGLVLITDDGRWSHN 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI------VIQGICYGDMQVTLDTQKG--- 184
           +  P  Q  + YRV    ++D DKL+ L            +        +T         
Sbjct: 120 VISPKKQCQKTYRVWLRSEIDDDKLSALVARFDSGLQLQGEDSLTRPAILTRVEIDNLVD 179

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                + V + + EGK  ++K++F     +V  L R   G   LG L  G  RE+++  +
Sbjct: 180 EASYRSEVLLTITEGKYHQVKRMFAAVGNRVVGLHREQIGKITLGDLAPGEWRELTEDEI 239

Query: 242 REQ 244
            + 
Sbjct: 240 TQF 242


>gi|282934173|ref|ZP_06339451.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           jensenii 208-1]
 gi|297205793|ref|ZP_06923188.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           jensenii JV-V16]
 gi|281301787|gb|EFA94053.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           jensenii 208-1]
 gi|297148919|gb|EFH29217.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           jensenii JV-V16]
          Length = 234

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 65/229 (28%), Positives = 100/229 (43%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I  ++V VNG L+++A   V  TD ++V    +   +  
Sbjct: 1   MRIDKYLANMKVGSRKEVHDLIKAKKVTVNGQLVKQAKQQVADTDIVKVADETIAYEQFH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      +  T                 +  +  VGRLD +T GLLLLTNDG L   
Sbjct: 61  YFMLNKPAGVITATEDPQQKTVLDLIEHKDRYQGLSPVGRLDKDTTGLLLLTNDGQLNHN 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     + Y V    +V  + +    KG+ +           L   K +     + +
Sbjct: 121 LLSPKKHVAKTYFVELDYEVSDELIVNFAKGVTLADG-TKVSPSQLKIDKSNKKQGFITI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EGK  +IK++F  F+  V RL RIS G   L   LL G  R+++K  +
Sbjct: 180 HEGKFHQIKRMFGLFDLGVVRLKRISMGNLSLDENLLLGKYRKLTKAEI 228


>gi|325695507|gb|EGD37407.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK150]
          Length = 242

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 63/233 (27%), Positives = 102/233 (43%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++++ ++ V VNG   +     +  T D I V G  L   + 
Sbjct: 1   MRLDKFLAENGLGSRAQVKQLLKKELVLVNGRAEKSPKTQIDETADEIIVSGQRLTYEKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  D         +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPQGVISATEDDRHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVT 190
            +  P     ++YR +  G ++Q        GI ++       Q+ +         + V 
Sbjct: 121 AMLSPKKHVEKIYRAQVAGLMNQADEERFAAGIELKDFTCQPAQLKILELDAAKETSLVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + L EGK  ++K++      +V  L R++ GP QL   L  G  R ++   L 
Sbjct: 181 ITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDFALALGEWRRLTTDELE 233


>gi|295098123|emb|CBK87213.1| ribosomal small subunit pseudouridine synthase A [Enterobacter
           cloacae subsp. cloacae NCTC 9394]
          Length = 235

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 105/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G +++ +A  +     +E DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRASRVTVDGDIVKDSAFKLQPEHQVEYDGNPLTQQNGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPEGYVCSTDDPDHPTVLYFLDEPVAHKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + YRV     V  D      KG+ +           + + T       V +
Sbjct: 121 ITSPRHHCDKTYRVMLESPVSDDTAEQFAKGVQLHNEKDLTKPAVLEILTPTD----VRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G  +L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVGLHRERIGAIELDPDLAPGEYRPLTEEEI 227


>gi|150391402|ref|YP_001321451.1| pseudouridine synthase [Alkaliphilus metalliredigens QYMF]
 gi|149951264|gb|ABR49792.1| pseudouridine synthase [Alkaliphilus metalliredigens QYMF]
          Length = 243

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 66/234 (28%), Positives = 107/234 (45%), Gaps = 4/234 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
             QR+ K++A  G  SR ++ R+  Q  V VNG +++ ++ +V    D I V    +   
Sbjct: 3   KTQRLDKILANLGHGSRSDIRRLCRQGVVTVNGAVVKSSSQHVEPENDKITVGEEEIYYR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   + +      +  T    +               V  VGRLD +TEGLL+LTNDG L
Sbjct: 63  EFVYIMMNKPQDVISATEDFKEKTVVDLLESKYQAFDVFPVGRLDKDTEGLLMLTNDGKL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y  +  G V    +   +KGI I+        Q+ +       + V
Sbjct: 123 AHQLLSPKKHVPKTYYAKIEGVVTDADVEAFEKGIFIEENLQTMPSQLKILKADEI-SEV 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            V + EGK  ++K++F+  + +V  L R+S G   L   L  G+ RE+S++ L+
Sbjct: 182 EVTIYEGKYHQVKRMFQATDKEVVYLKRLSMGSLMLDNSLDLGTYRELSEEELQ 235


>gi|291619766|ref|YP_003522508.1| RluF [Pantoea ananatis LMG 20103]
 gi|291154796|gb|ADD79380.1| RluF [Pantoea ananatis LMG 20103]
          Length = 297

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 57/299 (19%), Positives = 114/299 (38%), Gaps = 11/299 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +  
Sbjct: 10  TQSSTRLNKYISESGICSRRDADRFIEQGNVFINGKRAAV-GAQVFAGDVVKVNGQLIEP 68

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   L L           +  +G      +  +   RV  +GRLD +++GL+ LTN G 
Sbjct: 69  RDEDDLVLIALNKPTGIITTMEEGERDNISDFVNHSKRVFPIGRLDKDSQGLIFLTNHGD 128

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     V  + +  +  G+ + G            +K +    
Sbjct: 129 LVNKILRAGNNHEKEYVVTVDKPVTDEFIAGMASGVPMLGTV----TKKCKVKKEAPYVF 184

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ + F ++V +L R       L  +  G  R+++     E      
Sbjct: 185 RITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNVNLKGIPLGEWRDLTDDERVELFKL-- 242

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
                 N  +    ++   +  P       +   + +K+  +     +  +       R
Sbjct: 243 ----LENSSSEDKPAKKTPQKSPAAKKPAKNAVKQGEKSEDKPASRKRFTQPGRKKKGR 297


>gi|283458425|ref|YP_003363049.1| 16S rRNA uridine-516 pseudouridylate synthase [Rothia mucilaginosa
           DY-18]
 gi|283134464|dbj|BAI65229.1| 16S rRNA uridine-516 pseudouridylate synthase [Rothia mucilaginosa
           DY-18]
          Length = 378

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 83/234 (35%), Positives = 133/234 (56%), Gaps = 2/234 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLR 68
           +    R+ K++A+AG+ASRR  E MI + RV VNG ++    V V  +   ++VDG+ ++
Sbjct: 136 DHDGVRLQKLLAQAGVASRRVCEEMITEGRVTVNGEVVTELGVRVDPSKVTVQVDGMTVQ 195

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
             ++     ++KP G+V+T  DP+GR  + D L S +  RV  VGRLD+ TEGLLLLTND
Sbjct: 196 TNDKLVYMAFNKPAGVVSTMEDPEGRPCISDFLRSSMSERVFHVGRLDVETEGLLLLTND 255

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  + Y V+  G ++      +KKGI ++       +  L      + 
Sbjct: 256 GELANRLTHPSYEVPKTYLVQVPGPMEPGVGAAMKKGIRLEDGVTRVDEFKLVDSTPGHV 315

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V V +  GKNR ++++F+   + V RL+R+  GP ++G+   G+ R +SK  +
Sbjct: 316 LVEVTIHSGKNRIVRRLFDAVGYPVERLVRVEMGPIRIGSQKQGTVRNLSKVEI 369


>gi|268319723|ref|YP_003293379.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           johnsonii FI9785]
 gi|262398098|emb|CAX67112.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           johnsonii FI9785]
          Length = 233

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 105/233 (45%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I ++ V VNG +++     V   D + V+G  +   +  
Sbjct: 1   MRIDKYLANMNVGSRKEVHNLIKKKIVTVNGEVVKTPKEQVKEEDQVAVNGEKVAYQQYH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      +  T                 +  +  VGRLD +T GLLLLTNDG LA  
Sbjct: 61  YFLLNKPKGVISATEDRSQKTVLSLLKPKDRYKDIAPVGRLDKDTTGLLLLTNDGALAHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG--SNAWVT 190
           L  P+    + YR +  G  D++ + +   G+ +  G      ++ +  Q      + + 
Sbjct: 121 LLAPNKHVTKKYRAKIAGVADEETVKIFAIGMTLGDGTKLKPAELKILMQDKESDQSEIE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           + ++EGK  +IK++F     KV  L RIS G   L   L  G  +E++ K ++
Sbjct: 181 IEIQEGKYHQIKRMFGAVGMKVIELDRISMGKLVLPANLKRGQYQEITLKEIK 233


>gi|317402968|gb|EFV83508.1| pseudouridine synthase [Achromobacter xylosoxidans C54]
          Length = 469

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 83/353 (23%), Positives = 130/353 (36%), Gaps = 11/353 (3%)

Query: 1   MKDK--NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M+ +    +       ++ KV+A AGI SRRE+E +I   RV VNG         V   D
Sbjct: 98  MEQRLGKYLNSEAVMPKLHKVLADAGIGSRREMEELIVAGRVSVNGEPA-HIGQRVAPND 156

Query: 59  HIEVDGVPL----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
            + V+G P+     K     +  +     +V+        S           + +SVGRL
Sbjct: 157 QVRVNGKPIMRANTKKPPRVILYHKPAGEIVSHDDPGGRASVFARLPKLRTGKWLSVGRL 216

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D+NTEGLL+ T  G +A  +  P     R Y VR  G++D+ +   L  GI ++      
Sbjct: 217 DLNTEGLLIFTTSGDMANRIMHPRYGTEREYAVRVLGEMDEAQRQSLVDGIELEDGVAAF 276

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
             +      GSN W  V L+EG+NRE++++FE     V+RLIR  +G   L  +L  G  
Sbjct: 277 GALDYLGGDGSNRWYRVTLQEGRNREVRRMFEAVGVTVSRLIRTRFGDVVLPRSLRRGRW 336

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
            E+   ++   +    L             S+        +              +    
Sbjct: 337 EELDASLVTALMVQLGLLREDDESGGNRRRSKQPQSHDSALPPGFGTMDRNGMNGARIGR 396

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKG---IHSSFLSDSGQREENHRRSPSFPS 343
               Q   A    +     +     G               E N  R    P+
Sbjct: 397 RGKIQGGRAGSAGQAAACPSDPFGTGLMIAGGYANGHPLAGEANGNRKGGKPA 449


>gi|295090937|emb|CBK77044.1| ribosomal large subunit pseudouridine synthase F [Clostridium cf.
           saccharolyticum K10]
          Length = 271

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 66/272 (24%), Positives = 119/272 (43%), Gaps = 6/272 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +++     R++K ++ +G  SRRE +R+I   +V V+G +     + +     IE DG  
Sbjct: 6   MEKERQEIRLNKFLSESGFCSRREADRLIEAGKVLVDGAVA-SMGMKIREGQQIEADGTL 64

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +   +R  + L +KP G+V T SD D    + D +         VGRLD ++EGL+L+TN
Sbjct: 65  ISGKDRPVVLLVNKPRGIVCTTSDRDRAENIVDFIGYPLRV-YPVGRLDKDSEGLILMTN 123

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
            G L   +        + Y V    ++ +  LN ++KG+ I         V    +K   
Sbjct: 124 QGELVNRILKGRYGHEKEYLVSVDREITEQFLNRMRKGVKILDTVTRPCTV----EKTGE 179

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               + L +G NR+I+++ E   ++V  L R+     +L  L  G  RE+++   +E   
Sbjct: 180 KSFRIILTQGLNRQIRRMCEALGYRVRTLKRVRIMNLRLDGLKTGEYREITRGEWKELTE 239

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEV 278
               +  +   D       + +  R       
Sbjct: 240 LLEGKGERRKADQKNAEKHSELGQREPEKGGR 271


>gi|229011635|ref|ZP_04168818.1| Pseudouridine synthase [Bacillus mycoides DSM 2048]
 gi|228749593|gb|EEL99435.1| Pseudouridine synthase [Bacillus mycoides DSM 2048]
          Length = 235

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 62/227 (27%), Positives = 107/227 (47%), Gaps = 7/227 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ AG ASRR  +++I +++V +NG + +     V   D + V+G  LR A   
Sbjct: 1   MRINKFISEAGKASRRGADKLINERKVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCTSEKAV--KGNIIDLVNHPLRINHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  + L  +  G+ I        +VT      S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPEFLEKMAAGVKILDTKTLPCEVTQL----SKYEFQIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK 
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKKE 220


>gi|254303780|ref|ZP_04971138.1| pseudouridylate synthase [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
 gi|148323972|gb|EDK89222.1| pseudouridylate synthase [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
          Length = 234

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 68/231 (29%), Positives = 129/231 (55%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAE 71
            R++K ++  GIASRR +++ I + R+ VNG       +++   D+I +DG  ++    E
Sbjct: 1   MRINKFLSTLGIASRRAIDKYIEEGRITVNGNTATT-GMDINENDNIFIDGKKIKTSINE 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               ++ +KP+ ++++ SD  GR TV D + +       +GRLD  T GL+LLTNDG L 
Sbjct: 60  EKVYFMLNKPLEVLSSSSDDRGRKTVVDLIKTDKRI-FPIGRLDYMTSGLILLTNDGELF 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P ++  + Y ++  G++ +++++ LKKG+++        +++      +   + +
Sbjct: 119 NRVVHPKSEIYKKYYIKILGELKKEEIDELKKGVLLDDGKTLPAKISGIKYDKNKTSMFI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +REG+NR+I+++ E F +KV  L R   G   LG L  G  RE++K+ + 
Sbjct: 179 SIREGRNRQIRRMIEKFEYKVLMLRREKIGELALGDLPEGKYRELTKQEVE 229


>gi|159897316|ref|YP_001543563.1| pseudouridine synthase [Herpetosiphon aurantiacus ATCC 23779]
 gi|159890355|gb|ABX03435.1| pseudouridine synthase [Herpetosiphon aurantiacus ATCC 23779]
          Length = 728

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 87/341 (25%), Positives = 135/341 (39%), Gaps = 10/341 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +ARAG+ SRR  E ++   RV VNG +       +    D I VDG  +     
Sbjct: 2   ERLHKFLARAGVDSRRACEELMLAGRVSVNGRVQRELGTQIDPDKDDIRVDGEQITPPTE 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L HKP  ++TT  DP+G      +L    +R+  VGRLD ++EGLLLLT+DG L  
Sbjct: 62  LHYVLLHKPSSVMTTLHDPEG-RQTVADLVKSHNRLFPVGRLDYDSEGLLLLTDDGDLTF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS +  + Y+   +     ++L   + G+ +         + L  +     WV V 
Sbjct: 121 RLTHPSFEVEKEYQALLNQTPSVEQLREWRNGVELDDGKTAPAWIELLNETADGTWVRVV 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           + EG+NR+I++V E    +V RLIR+  GP  LG L AG  R ++   +          +
Sbjct: 181 IHEGRNRQIRRVAEALGLEVRRLIRLREGPLTLGELQAGQWRALTPTEIDRLRMHGKQSK 240

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP-------- 304
           A   +     +     R +   I        R      +                     
Sbjct: 241 AWTPVRPQENAEGGKPRRQVRRIDRSGQLVERRADVEPRLQRAPHFTSQENTMSFEDFSI 300

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
              R+        +       SD G R +    S     +R
Sbjct: 301 EEERSTDRPRRRPEPRREGGFSDRGPRRDGGSPSDDRGPRR 341


>gi|148983686|ref|ZP_01817005.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP3-BS71]
 gi|148996705|ref|ZP_01824423.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP11-BS70]
 gi|168490791|ref|ZP_02714934.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           CDC0288-04]
 gi|182683261|ref|YP_001835008.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae CGSP14]
 gi|194398298|ref|YP_002036978.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae G54]
 gi|225853878|ref|YP_002735390.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           JJA]
 gi|303255185|ref|ZP_07341259.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae BS455]
 gi|303259389|ref|ZP_07345366.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP-BS293]
 gi|303261144|ref|ZP_07347093.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP14-BS292]
 gi|303263472|ref|ZP_07349395.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae BS397]
 gi|303265764|ref|ZP_07351662.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae BS457]
 gi|303267805|ref|ZP_07353607.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae BS458]
 gi|307066956|ref|YP_003875922.1| 16S rRNA uridine-516 pseudouridylate synthase-like pseudouridylate
           synthase [Streptococcus pneumoniae AP200]
 gi|147757280|gb|EDK64319.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP11-BS70]
 gi|147923833|gb|EDK74945.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP3-BS71]
 gi|182628595|gb|ACB89543.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae CGSP14]
 gi|183574853|gb|EDT95381.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           CDC0288-04]
 gi|194357965|gb|ACF56413.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae G54]
 gi|225722369|gb|ACO18222.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           JJA]
 gi|301799421|emb|CBW31958.1| putative ribosomal small subunit pseudouridine synthase B
           [Streptococcus pneumoniae OXC141]
 gi|301801222|emb|CBW33896.1| putative ribosomal small subunit pseudouridine synthase B
           [Streptococcus pneumoniae INV200]
 gi|302597818|gb|EFL64890.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae BS455]
 gi|302637981|gb|EFL68467.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP14-BS292]
 gi|302639323|gb|EFL69781.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP-BS293]
 gi|302642501|gb|EFL72846.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae BS458]
 gi|302644672|gb|EFL74921.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae BS457]
 gi|302647245|gb|EFL77469.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae BS397]
 gi|306408493|gb|ADM83920.1| 16S rRNA uridine-516 pseudouridylate synthase-like pseudouridylate
           synthase [Streptococcus pneumoniae AP200]
 gi|332077581|gb|EGI88042.1| hypothetical protein SPAR68_0323 [Streptococcus pneumoniae GA41301]
 gi|332202193|gb|EGJ16262.1| hypothetical protein SPAR69_0304 [Streptococcus pneumoniae GA41317]
 gi|332204287|gb|EGJ18352.1| hypothetical protein SPAR120_0252 [Streptococcus pneumoniae
           GA47901]
          Length = 240

 Score =  169 bits (427), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 103/233 (44%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYMMNKPKGVISATEDPKHRTVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNNGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVT 190
           VL  P     + Y+ +  G + Q+ +    KGI ++       ++ +     + + + + 
Sbjct: 121 VLLSPKRHVDKTYQAQVKGIMTQEDVETFIKGIPLKDFTCQPARLEILSTDAEKNQSQIR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 181 VTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELE 233


>gi|322514615|ref|ZP_08067646.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           ureae ATCC 25976]
 gi|322119449|gb|EFX91548.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           ureae ATCC 25976]
          Length = 230

 Score =  169 bits (427), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 55/231 (23%), Positives = 106/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + +    V VNG + +  +  +  TD I  +G  L   +  
Sbjct: 1   MRLDKFIAENTGLTRSQAGKALKSGLVTVNGKIEKSGSAKISETDEICYEGECLEWVDEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ +KP G V +H D +  +        + +++ + GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYFMLYKPQGYVCSHDDGEYPTVFQFFDYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+   +  L +GI+++G        Q+ +      +  V +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEDFYVEKLAEGILLRGEREPCLPAQMEII----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EG+  ++K++F     KV  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAALGNKVEALHRWRIGDVVLDESLEEGEYRLLTEQEI 227


>gi|323342596|ref|ZP_08082828.1| ribosomal small subunit pseudouridine synthase A [Erysipelothrix
           rhusiopathiae ATCC 19414]
 gi|322463708|gb|EFY08902.1| ribosomal small subunit pseudouridine synthase A [Erysipelothrix
           rhusiopathiae ATCC 19414]
          Length = 229

 Score =  169 bits (427), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 53/230 (23%), Positives = 108/230 (46%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +A  G  +R++V+ ++ +  V VN  ++  A + +    D + V G  +   + 
Sbjct: 1   MRLDKFLAHNGFGTRKDVKILVKKGMVTVNHDVVRDAGMVLNLEKDEVFVKGESVSYQKD 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +     +P+   +V + + S    ++ VGRLD +TEGLLL+TNDG  + 
Sbjct: 61  IYFMMNKPAGYI--CEHNPEMYPSVLELIESYHRDLVFVGRLDADTEGLLLITNDGQFSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +    +   + Y V      D      L+KG+++        QV +  ++     + + 
Sbjct: 119 RVAHSKSNVHKQYYVELDKPFDLRFCEELEKGMMLGDELLKPAQVEVVGERA----IHLT 174

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++    + +V  L RI  G  +L  +L  G+ R++S++ +
Sbjct: 175 IGEGKYHQVKRMMHACDNEVTYLKRIKIGALELDSSLQPGAYRDLSEEEI 224


>gi|319949182|ref|ZP_08023271.1| pseudouridylate synthase [Dietzia cinnamea P4]
 gi|319437168|gb|EFV92199.1| pseudouridylate synthase [Dietzia cinnamea P4]
          Length = 252

 Score =  169 bits (427), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 77/238 (32%), Positives = 120/238 (50%), Gaps = 4/238 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAE 71
           P R+ K++A+AG+ASRR  E +IA+ RV+V+G ++    V V   T  I VDG  +   +
Sbjct: 11  PVRLQKILAQAGVASRRASEDLIARGRVEVDGKIVREMGVKVDPATAVIRVDGTRIVLDD 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTNDG 128
                  +KP G  TT SD  GR  V D +        R+  VGRLD +TEGLLL+TNDG
Sbjct: 71  TLVHLALNKPRGYHTTMSDEMGRPCVGDLVADRIDAGQRLFHVGRLDADTEGLLLVTNDG 130

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  + Y     G V +     L++G+ ++       Q +L       + 
Sbjct: 131 ELAHRLMHPSYEVSKTYMATVTGVVGKGIGKQLREGVELEDGPAKVDQFSLLDVHDGRSL 190

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           V V L EG+   ++++       V  L+R  +G   LG   AG+ R+++++ + +   
Sbjct: 191 VKVVLHEGRKHIVRRLLAEVGHPVESLVRTRFGSVALGDQRAGTFRKLNRREVSDLYE 248


>gi|117620907|ref|YP_857421.1| ribosomal large subunit pseudouridine synthase B [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
 gi|117562314|gb|ABK39262.1| ribosomal large subunit pseudouridine synthase B [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
          Length = 307

 Score =  169 bits (427), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 83/307 (27%), Positives = 133/307 (43%), Gaps = 10/307 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +       V     I VDG  ++    
Sbjct: 2   SEKLQKVLARAGHGSRREMEALITAGRVSVDGKVAT-LGDRVEVNAVIRVDGHQIKTRAA 60

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  +     + T H      +          +R I+VGRLD+NT GLLL T D
Sbjct: 61  EEVICRVLAYHKPEGEMCTRHDPEGRPTVFDRLPKMEGARWIAVGRLDVNTSGLLLFTTD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G++ +  L  L+KG+ ++       ++     +G N 
Sbjct: 121 GELANRLMHPSHEVEREYAVRVFGEITEAMLQRLRKGVQLEDGMAKFNKIKPAGGEGLNQ 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LRE 243
           W  V L EG+NRE+++++E    +V+RL+RI YG  QL   +  G  +E+       LR 
Sbjct: 181 WFNVTLTEGRNREVRRLWESQEVQVSRLMRIRYGDVQLDRGIPRGGWQELKLPEVNYLRG 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +      E++V+L     +S      +     +   +    +  +       K      
Sbjct: 241 LVNLPNETESKVDLQQDGKTSRHKQAAQIRRAVKRHKEMQGKEPRARATTARRKPTSSTR 300

Query: 304 PVHRRNL 310
                + 
Sbjct: 301 NSGTGSK 307


>gi|238760641|ref|ZP_04621767.1| Ribosomal large subunit pseudouridine synthase F [Yersinia aldovae
           ATCC 35236]
 gi|238701130|gb|EEP93721.1| Ribosomal large subunit pseudouridine synthase F [Yersinia aldovae
           ATCC 35236]
          Length = 290

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 60/293 (20%), Positives = 115/293 (39%), Gaps = 5/293 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRR+ +R I Q  V +NG         V   + ++V+G  +  
Sbjct: 3   TNSSIRLNKYISESGICSRRDADRYIEQGNVFINGKRAAV-GDQVYVGNVVKVNGQLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   L L      +    +  +G S    +  +   RV  +GRLD +++GL+LLTN G 
Sbjct: 62  RDENDLVLIALNKPVGIISTTEEGESDNIVDFVNHSKRVFPIGRLDKDSQGLILLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  V  + +  L  G+ + G            +K +    
Sbjct: 122 LVNKILRAGNDHEKEYVVTVNKPVTDEFIVGLAAGVPMMGTV----TKKCKVKKIAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ + F ++V +L R       L  L  G  R++    L E      
Sbjct: 178 NITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNVTLKGLPQGEWRDLLDDELIELFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
              +         +    V+       +  +    +  +  +     ++KK  
Sbjct: 238 NSSSDEKPVKKTQAKPVAVKKPSTSGPKKAEKSDGISASRKRFAQPGRKKKGR 290


>gi|166154940|ref|YP_001653195.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis L2b/UCH-1/proctitis]
 gi|165930928|emb|CAP06490.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           trachomatis L2b/UCH-1/proctitis]
          Length = 241

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 68/230 (29%), Positives = 101/230 (43%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R++K +A AG+ASRR+ + +I    V VNG       V V    D +EV G  +   ++
Sbjct: 4   VRLNKFLASAGVASRRKCDEIIFAGSVTVNGRAATGPFVTVDEEFDSVEVGGQRIGAEKK 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               ++     L ++     G   V D L     R+ +VGRLD  T GL+L+TNDG  A 
Sbjct: 64  VYFMVHKPLGYLCSSERKFPGSKLVIDLLSHCPYRLFTVGRLDKETSGLILVTNDGEFAN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  PS    + Y ++    V    L  L  G VI G     + V    +      + + 
Sbjct: 124 RVIHPSFGITKEYLLKVSRDVTARDLETLMAGTVIDGKVVRPVSVKKVRRG----TIKII 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGK  EI+   E    ++  L RI  G   LG L  G  RE++   L 
Sbjct: 180 VNEGKKHEIRLFAEAAGLQLLELKRIRIGSLVLGGLPYGKYRELTDSELD 229


>gi|261253105|ref|ZP_05945678.1| ribosomal small subunit pseudouridine synthase A [Vibrio orientalis
           CIP 102891]
 gi|260936496|gb|EEX92485.1| ribosomal small subunit pseudouridine synthase A [Vibrio orientalis
           CIP 102891]
          Length = 233

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 53/229 (23%), Positives = 99/229 (43%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  A+RRE  R+I    V VN ++ +  +V V     +E  G  L+K    
Sbjct: 1   MRLDKYLCDALGATRREATRIIKSGDVTVNDVVQKSGSVKVTDGCTVEWQGRELQKPGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+     + +     +  +            +   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLFKPDGFVCSHEDGFNQ-TAFMLLDEVKIEELHFAGRLDVDTTGLVLITDDGKWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     +  D +    +GI ++      +   L+        V + +
Sbjct: 120 ITSPKHKCEKTYRVWLADPIQADYVEKFAEGIQLRNEKGLTLPAQLEIVDEEENEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            EGK  ++K++F     KV  L R   G  +L  +L  G  R ++++ +
Sbjct: 180 TEGKYHQVKRMFAALGNKVEHLHRERIGDIELCESLEPGEYRYLTEEEV 228


>gi|332365597|gb|EGJ43357.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1059]
          Length = 242

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 63/233 (27%), Positives = 102/233 (43%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++ + +  V VNG   +     +  T D I V G  L   + 
Sbjct: 1   MRLDKFLAENGLGSRAQVKQFLKKGLVLVNGRAEKSPKTQIDETADEIAVSGQRLTYEKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  D         +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPQGVISATEDDRHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            +  P     ++YR +  G ++Q  +     GI ++       Q+ +     +   + V 
Sbjct: 121 AMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKAFTCQPAQLKILELDEAKETSLVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + L EGK  ++K++      +V  L R++ GP QL   L  G  R ++   L 
Sbjct: 181 ITLAEGKFHQVKRMVAACGKEVTNLQRLTMGPLQLDPALALGEWRRLTTDELE 233


>gi|320451356|ref|YP_004203452.1| ribosomal small subunit pseudouridine synthase A [Thermus
           scotoductus SA-01]
 gi|320151525|gb|ADW22903.1| ribosomal small subunit pseudouridine synthase A [Thermus
           scotoductus SA-01]
          Length = 238

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 65/229 (28%), Positives = 110/229 (48%), Gaps = 6/229 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +R+ K++AR G+ SR+EV R++   +V+V G ++   A +V     +EVDG PL    
Sbjct: 2   RGERLDKLLARLGLGSRKEVARLVRSGQVQVEGQVVRDPAFHVPPGARLEVDGEPLVLRC 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              + L+     + +    P   + +        S    VGRLD +TEGLLL T DG L 
Sbjct: 62  HHHILLHKPAGYVTSRREGPSVYALLEGFPTRDLS---PVGRLDKDTEGLLLFTTDGELL 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P  +  + Y V       ++     ++G+V++G      +++          V +
Sbjct: 119 HRLTHPRHKVEKRYLVHLERPATREDQEAFREGLVLEGTRLLPAELSW---DQDPTRVEL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            LREG+  ++K++F+    +V  L R+S GP  LG L  G  R +S++ 
Sbjct: 176 VLREGRFHQVKRMFQARGNRVLYLKRLSLGPLTLGDLPVGQARYLSQEE 224


>gi|295093016|emb|CBK82107.1| ribosomal small subunit pseudouridine synthase A [Coprococcus sp.
           ART55/1]
          Length = 241

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 107/233 (45%), Gaps = 6/233 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   GI SR +V++ + +  V VNG  ++ + V +    D I+ +G  L  +  
Sbjct: 1   MRLDKFLVEMGIGSRSQVKQYVKKGTVTVNGAPVKSSDVKIDENNDTIKYNGRILNYSRY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      + +   D   ++ +          +  VGRLDI+TEGLLLLTNDG L  
Sbjct: 61  RYFLLNKPAGCV-SATKDNVHQTVIDLLKGENTKDLSPVGRLDIDTEGLLLLTNDGALTH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKG--SNAWV 189
            L  P+    + Y     G V  D +NL   G+ I          + + +     + + +
Sbjct: 120 HLLSPAHHIPKTYYAEIDGYVTDDTINLFATGVDIGDEKPTLPADLRILSSDSTAARSEI 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + + EG+  ++K++FE    KV  L RI+ G  ++   L  G+ R +S++ +
Sbjct: 180 ELIITEGRFHQVKRMFEAVGMKVTFLRRIAMGELKIDESLPTGAYRSLSEEEV 232


>gi|228994293|ref|ZP_04154184.1| Pseudouridine synthase [Bacillus pseudomycoides DSM 12442]
 gi|228997453|ref|ZP_04157072.1| Pseudouridine synthase [Bacillus mycoides Rock3-17]
 gi|229005098|ref|ZP_04162822.1| Pseudouridine synthase [Bacillus mycoides Rock1-4]
 gi|228756200|gb|EEM05521.1| Pseudouridine synthase [Bacillus mycoides Rock1-4]
 gi|228762329|gb|EEM11256.1| Pseudouridine synthase [Bacillus mycoides Rock3-17]
 gi|228765443|gb|EEM14106.1| Pseudouridine synthase [Bacillus pseudomycoides DSM 12442]
          Length = 235

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 63/227 (27%), Positives = 108/227 (47%), Gaps = 7/227 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ +G ASRR  +++I ++RV +NG + +     V   D + V+G  LR A   
Sbjct: 1   MRINKFISESGKASRRGADKLINERRVIINGKVAK-IGDQVQPGDDVRVNGEQLRIARDH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T            +L +   R+  VGRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCTSEKAV--KGNIIDLVNHPLRINHVGRLDKDSDGLILLTNDGDIINE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  + L  +  G+ I G      ++T      S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPEFLKEMAAGVKILGTKTLPCEITQL----SKYEFQIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +G NR+I+++ E   ++V  L R      QL  L  G  R+++KK 
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIQLNNLPVGQWRDLTKKE 220


>gi|224476843|ref|YP_002634449.1| RNA pseudouridine synthase [Staphylococcus carnosus subsp. carnosus
           TM300]
 gi|222421450|emb|CAL28264.1| RNA pseudouridine synthase [Staphylococcus carnosus subsp. carnosus
           TM300]
          Length = 231

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 55/231 (23%), Positives = 110/231 (47%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ + +V+VNG   +++  ++    D I VDG  +   ++
Sbjct: 1   MRLDKYLANMGVGTRSEVKQLLKKNKVQVNGKNEKQSKAHINPDTDEITVDGNLIEYVDK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + +   D +  + V         ++  VGR+  +TEGL+LLTNDG    
Sbjct: 61  VYIMLNKPAGYI-SATEDEEQSTIVSLIKDFQHMKIFPVGRVGKDTEGLILLTNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P+    ++YRV     +  D +    +G+ +        Q     +  +     V 
Sbjct: 120 DIMSPNKHVSKIYRVEAKNPITDDDIKQFAEGVELSDGKTKPAQ---LERTENEKVAFVS 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           +REG+  ++K++F   + +V  L R+  G  +L   L  GS RE++++ + 
Sbjct: 177 IREGRYHQVKRMFHAIDNEVLNLKRVQIGKLKLDSNLPKGSYRELTQEEIE 227


>gi|229102971|ref|ZP_04233660.1| Pseudouridine synthase [Bacillus cereus Rock3-28]
 gi|229115851|ref|ZP_04245249.1| Pseudouridine synthase [Bacillus cereus Rock1-3]
 gi|229173064|ref|ZP_04300615.1| Pseudouridine synthase [Bacillus cereus MM3]
 gi|228610397|gb|EEK67668.1| Pseudouridine synthase [Bacillus cereus MM3]
 gi|228667594|gb|EEL23038.1| Pseudouridine synthase [Bacillus cereus Rock1-3]
 gi|228680386|gb|EEL34574.1| Pseudouridine synthase [Bacillus cereus Rock3-28]
          Length = 238

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 66/228 (28%), Positives = 109/228 (47%), Gaps = 7/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCTSEKAV--KGNIIDLVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      +VT      S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEVTQL----SKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK  R
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKKEKR 225


>gi|327396520|dbj|BAK13941.1| ribosomal large subunit pseudouridine synthase F [Pantoea ananatis
           AJ13355]
          Length = 290

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 57/299 (19%), Positives = 114/299 (38%), Gaps = 11/299 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +  
Sbjct: 3   TQSSTRLNKYISESGICSRRDADRFIEQGNVFINGKRAAV-GAQVFAGDVVKVNGQLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   L L           +  +G      +  +   RV  +GRLD +++GL+ LTN G 
Sbjct: 62  RDEDDLVLIALNKPTGIITTMEEGERDNISDFVNHSKRVFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     V  + +  +  G+ + G            +K +    
Sbjct: 122 LVNKILRAGNNHEKEYVVTVDKPVTDEFIAGMASGVPMLGTV----TKKCKVKKEAPYVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ + F ++V +L R       L  +  G  R+++     E      
Sbjct: 178 RITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNVNLKGIPLGEWRDLTDDERVELFKL-- 235

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
                 N  +    ++   +  P       +   + +K+  +     +  +       R
Sbjct: 236 ----LENSSSEDKPAKKTPQKSPAAKKPAKNAVKQGEKSEDKPASRKRFTQPGRKKKGR 290


>gi|325578607|ref|ZP_08148707.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           parainfluenzae ATCC 33392]
 gi|325159843|gb|EGC71973.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           parainfluenzae ATCC 33392]
          Length = 232

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 60/236 (25%), Positives = 109/236 (46%), Gaps = 7/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+N  +++  A  V   D I  +   L   E  
Sbjct: 1   MRLDKFIAENTGLTRSQATKAIRQSAVKINDEIVKNGATKVSQEDEIYFEDELLSWVEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ HKP G V +H D D  +      P +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYFMLHKPQGYVCSHDDDDYPTIYQFFEPPLSGKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  Q  + Y V     V+    +  ++GI+++G        ++ +      +  V +
Sbjct: 121 ITSPKHQCEKTYLVTLADPVENHYASACEEGILLRGEKEPTKPAKLEVL----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
            + EG+  ++K++F     KV  L R   G  +L   L  G  R ++++ +   + 
Sbjct: 177 TISEGRYHQVKRMFAALGNKVVALHRWRIGNVELDESLEEGEFRPLTQEEIDNLVK 232


>gi|62180809|ref|YP_217226.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|62128442|gb|AAX66145.1| 16S rRNA pseudouridylate 516 synthase [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
          Length = 231

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 104/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G +++ AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     ++Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKIYLVTLESPVADDTAAQFAKGVQLHNEKDLTKPATLEVI----TPVQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNCVVELHRERIGAITLDENLAPGEYRPLTEEEI 227


>gi|21283425|ref|NP_646513.1| hypothetical protein MW1696 [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49486578|ref|YP_043799.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|300911616|ref|ZP_07129060.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus TCH70]
 gi|21204866|dbj|BAB95561.1| MW1696 [Staphylococcus aureus subsp. aureus MW2]
 gi|49245021|emb|CAG43482.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|300887037|gb|EFK82238.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus TCH70]
          Length = 231

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 56/228 (24%), Positives = 103/228 (45%), Gaps = 7/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E 
Sbjct: 1   MRIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDKITVRGELIEYIEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP   ++   D   ++ +          + +VGRLD +TEGLLL+TNDG    
Sbjct: 61  -VYIMLNKPKDYISATEDHHSKTVIDLIPEYQHLNIFTVGRLDKDTEGLLLITNDGDFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+    + Y V     + +D +   K+G+ +         +T    + S     V 
Sbjct: 120 ELMSPNKHVSKKYEVISANPITEDDIQAFKEGVTLSDGKVKPAILTYIDNQTS----HVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           + EGK  ++K++F     +V  L RI     +L   L +G  R +++ 
Sbjct: 176 IYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYRLLTEN 223


>gi|229085292|ref|ZP_04217534.1| Pseudouridine synthase [Bacillus cereus Rock3-44]
 gi|228698011|gb|EEL50754.1| Pseudouridine synthase [Bacillus cereus Rock3-44]
          Length = 238

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 64/226 (28%), Positives = 108/226 (47%), Gaps = 7/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +G ASRR  +++I ++RV +NG + +     V   D + V+G  LR A    
Sbjct: 5   RINKFISESGKASRRGADKLINERRVIINGKVAK-IGDQVQPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T            +L +   RV  VGRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCTSEKAV--KGNIIDLVNHPLRVNHVGRLDKDSDGLILLTNDGDIINEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  + L  +  G+ I G      ++T      S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPEFLKQMAAGVKILGTKTLPCEITQL----SKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +G NR+I+++ E   ++V  L R      QL  L  G  R+++KK 
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIQLNNLPVGQWRDLTKKE 223


>gi|88705955|ref|ZP_01103663.1| ribosomal large subunit pseudouridine synthase B (Pseudouridylate
           synthase) [Congregibacter litoralis KT71]
 gi|88699669|gb|EAQ96780.1| ribosomal large subunit pseudouridine synthase B (Pseudouridylate
           synthase) [Congregibacter litoralis KT71]
          Length = 332

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 81/316 (25%), Positives = 134/316 (42%), Gaps = 5/316 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
             +++ KV+AR+G+ SRRE+ER I Q+RV ++G         V++   IEVDG PL    
Sbjct: 18  DGEKLQKVLARSGLGSRREMERWIEQERVTIDGKAAR-LGDRVVAAQRIEVDGRPLVASD 76

Query: 70  -AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             +   L  +     + +       R+           R IS+GRLD NT GLLL T DG
Sbjct: 77  GEKTRCLLYHKPTGEVCSRKDPEGRRTVFERLPKVKSGRWISIGRLDYNTSGLLLFTTDG 136

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS    R Y VR  G V +D L  + +G++++        +      G N+W
Sbjct: 137 ELANALMHPSANIEREYMVRVMGDVTEDHLKAMLEGVMLEDGVARFTDIQSGGGDGINSW 196

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
             V L EG+NRE+++++E     V+RL R+ YG   +   +  G  +E++   +      
Sbjct: 197 YYVVLMEGRNREVRRLWESQGLTVSRLKRVRYGDLFVPSKVKKGQWQELAPNEINGLYRM 256

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
             ++   V   +    S+    +               +  +   +  S++   +     
Sbjct: 257 AGMQAKDVEPPSREDRSKHKRMEGKRGRVRGNRHAKSARDKTGAPDKGSRKPSRSRKPGS 316

Query: 308 RNLASNVWMAKGIHSS 323
               S     KG   +
Sbjct: 317 GKRESAPVKNKGRSRA 332


>gi|324989740|gb|EGC21683.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK353]
          Length = 242

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 99/233 (42%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V++++ +  V VNG   +     +    D I V G  L   + 
Sbjct: 1   MRLDKFLTENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDEAADDIVVSGQRLIYEKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  D         +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPQGVISATEDDHHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            +  P     ++YR +  G ++Q  +     GI ++        + +         + V 
Sbjct: 121 AMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKDFTCQPAHLKILELDEEKEASLVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + L EGK  ++K++      +V  L R++ GP QL   L  G  R ++   L 
Sbjct: 181 ITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDPALALGEWRRLTADELE 233


>gi|225569254|ref|ZP_03778279.1| hypothetical protein CLOHYLEM_05336 [Clostridium hylemonae DSM
           15053]
 gi|225162053|gb|EEG74672.1| hypothetical protein CLOHYLEM_05336 [Clostridium hylemonae DSM
           15053]
          Length = 247

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 62/251 (24%), Positives = 113/251 (45%), Gaps = 13/251 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K ++ AG+ SRRE +R+I + RV V+G       + V  +  + V    +R  ++ 
Sbjct: 1   MRLNKFLSEAGVCSRREADRLIEEGRVTVDGKKA-VPGMQVDPSSEVRVGKKRIRSKDKK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +   HKP G+V T                   R+   GRLD  +EGLL++T+DG L   
Sbjct: 60  TVLAVHKPAGIVCTEDKRV--KNNIIRFLKYPERITYAGRLDKESEGLLIMTDDGELING 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI------QGICYGDMQVTLDTQKGSNA 187
           +        + Y+V  +  V ++ +N +  G+ +              +V    ++    
Sbjct: 118 MMRSRYGHEKEYKVWVNKPVTEEFVNRMSSGVRLVDKEKGLDEVTRPCEV----RQCGTY 173

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
             T+ L +G NR+I+++ E   +KV RL+RI     +LG L  G+ R+++++ L E    
Sbjct: 174 IFTIILTQGLNRQIRRMCEALGYKVKRLVRIRIMNIELGNLKPGAYRKLTEQELNELYEQ 233

Query: 248 HLLEEAQVNLD 258
               +      
Sbjct: 234 TEKGKNAGTGR 244


>gi|20664188|pdb|1KSK|A Chain A, Structure Of Rsua
 gi|20664191|pdb|1KSL|A Chain A, Structure Of Rsua
 gi|20664194|pdb|1KSV|A Chain A, Structure Of Rsua
          Length = 234

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 58/230 (25%), Positives = 99/230 (43%), Gaps = 7/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    R
Sbjct: 5   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGPR 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +  +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L T+DG  +  +
Sbjct: 65  YFXLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLXTDDGQWSHRI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTVG 192
             P     + Y V     V  D      KG+ +           + +     +   V + 
Sbjct: 125 TSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEVI----TPTQVRLT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EG+  ++K+ F      V  L R   G   L   L  G  R ++++ +
Sbjct: 181 ISEGRYHQVKRXFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 230


>gi|239917903|ref|YP_002957461.1| pseudouridine synthase family protein [Micrococcus luteus NCTC
           2665]
 gi|281413596|ref|ZP_06245338.1| pseudouridine synthase family protein [Micrococcus luteus NCTC
           2665]
 gi|289706509|ref|ZP_06502862.1| pseudouridylate synthase [Micrococcus luteus SK58]
 gi|239839110|gb|ACS30907.1| pseudouridine synthase family protein [Micrococcus luteus NCTC
           2665]
 gi|289556767|gb|EFD50105.1| pseudouridylate synthase [Micrococcus luteus SK58]
          Length = 318

 Score =  169 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 79/233 (33%), Positives = 130/233 (55%), Gaps = 1/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
           + + +R+ KV+A AG+ASRR  E +IA+ RV+V+G+++    V V   T  I VDG+ ++
Sbjct: 77  DESGERLQKVLAAAGVASRRVSEDLIAEGRVEVDGVVVTEPGVRVDPATAVIRVDGISVQ 136

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                + ++++KP G+++T  DP+GR ++   L      +  VGRLD  TEGLL+LTNDG
Sbjct: 137 TDVTKQYFVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVGRLDNETEGLLILTNDG 196

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  + Y V+  G + +   N L++G+ ++          L      +  
Sbjct: 197 ELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVAQVDSFKLVDSTPGHVL 256

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L  GKNR ++++F+     V RL+R+  GP  LG    G+ R ++ + L
Sbjct: 257 VEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGTVRALNAQEL 309


>gi|149001603|ref|ZP_01826576.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP14-BS69]
 gi|237649412|ref|ZP_04523664.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae CCRI 1974]
 gi|237821288|ref|ZP_04597133.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae CCRI 1974M2]
 gi|147760061|gb|EDK67050.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP14-BS69]
          Length = 240

 Score =  169 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 100/233 (42%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    V  VGRLDI+T GLLLL NDG LA 
Sbjct: 61  VYYMMNKPKGVISATEDPKHRTVLDLLDDLARSKEVFPVGRLDIDTHGLLLLANDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVT 190
           VL  P     + Y  +  G + Q+ +    +GI ++         ++     + + + + 
Sbjct: 121 VLLSPKRHVDKTYLAQVKGIMTQEDVETFAEGIPLKDFTCQPAILELVSIDTEKNQSQIR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 181 VTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELE 233


>gi|332359298|gb|EGJ37119.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK49]
          Length = 242

 Score =  169 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 63/233 (27%), Positives = 105/233 (45%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++++ +  V VNG   +     +    D I V G  L   + 
Sbjct: 1   MRLDKFLAENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDERADEIVVSGQRLTYEKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  D         +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPQGVISATEDDRHQTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVT 190
            +  P     ++YR +  G ++Q  +     GI ++       Q+ +    ++  ++ V 
Sbjct: 121 AMLSPKKHVEKIYRAQVAGLMEQADVERFAAGIELKDFTCQPAQLKILELDEEKESSLVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + L EGK  ++K++      +V  L R++ GP QL  TL  G  R ++   L 
Sbjct: 181 ITLAEGKFHQVKRMVAACRKEVTDLQRLTMGPLQLDPTLALGEWRRLTTDELE 233


>gi|27366329|ref|NP_761857.1| ribosomal large subunit pseudouridine synthase B [Vibrio vulnificus
           CMCP6]
 gi|34098527|sp|Q8D8C0|RLUB_VIBVU RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|27362530|gb|AAO11384.1| Ribosomal large subunit pseudouridine synthase B [Vibrio vulnificus
           CMCP6]
          Length = 320

 Score =  169 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 89/321 (27%), Positives = 131/321 (40%), Gaps = 9/321 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
           +++ KV+ARAG  SRRE+E +I   RV VNGI+ +           + +DG  +      
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKSGRVSVNGIVAKLGERLEDEQAVVRIDGHVVSVKAQE 62

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 L  Y     L T H     R+          SR ISVGRLD NT GLLL T DG
Sbjct: 63  EVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS Q  R Y VR  G+V++ K+  L  G+ +         V     +G N  
Sbjct: 123 ELANRLMHPSRQVEREYLVRVFGEVNEHKVRNLVNGVELDDGLARFEDVVYTGGEGMNHT 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGP 247
             V + EG+NRE+++++E  +  V+RL R+ YG   L   L  G   E+    L++    
Sbjct: 183 FYVVINEGRNREVRRLWESQDCTVSRLKRVRYGDIYLDKKLPRGGWMEL---ELKDVNYL 239

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
             L E +   +  I  + +  +       ++     R ++  S   G S       P   
Sbjct: 240 RELVELRPEKETMIELNNSSRKRDRARSQKIRRAVKRHEERVSTPKGRSNNAARRKPSKA 299

Query: 308 RNLASNVWMAKGIHSSFLSDS 328
               +         S      
Sbjct: 300 DGQTNKTNSRNQAGSRSKPQR 320


>gi|229161332|ref|ZP_04289317.1| Pseudouridine synthase [Bacillus cereus R309803]
 gi|228622146|gb|EEK78987.1| Pseudouridine synthase [Bacillus cereus R309803]
          Length = 238

 Score =  169 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 65/228 (28%), Positives = 109/228 (47%), Gaps = 7/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCTSEKAV--KGNIIDLVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T      S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEITQL----SKYEFNIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK  R
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKKEKR 225


>gi|296327880|ref|ZP_06870416.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium
           nucleatum subsp. nucleatum ATCC 23726]
 gi|296155014|gb|EFG95795.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium
           nucleatum subsp. nucleatum ATCC 23726]
          Length = 226

 Score =  169 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 69/229 (30%), Positives = 106/229 (46%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   GI SR+EV+++I+   + VNG+    A  N+    D IE +G  L   E 
Sbjct: 1   MRLDKFLVECGIGSRKEVKKLISNGEITVNGMSYILAKDNIDENSDTIEYNGERLEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +  K   +  T    +           I   +  VGRLD +TEGLLL TNDG L  
Sbjct: 61  RYYIMNKKAGYITATEDFKEDTVMDLLPEWVIKKDLAPVGRLDKDTEGLLLFTNDGKLNH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VY V     +  + +  L++G+ I        +V    +K S+  + + 
Sbjct: 121 KLLSPKNHIDKVYYVEIEKNILDEDILKLEQGVDIGNYITQPAKV----EKISDNKIYLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++EGK  ++KK+ E  N KV  L R S+G   L  L  G  +EVS + +
Sbjct: 177 IKEGKFHQVKKMLEAVNNKVCYLRRESFGKLTLNDLTLGEVKEVSLEDI 225


>gi|322377564|ref|ZP_08052054.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           M334]
 gi|321281329|gb|EFX58339.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           M334]
          Length = 240

 Score =  168 bits (426), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 100/233 (42%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEERDEIRFDGQVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    V  VGRLDI+T GLLLLTNDG LA 
Sbjct: 61  VYYMMNKPQGVISATEDPKHRTVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNDGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVT 190
            L  P     + Y  +  G + Q+ +    KGI ++         ++     + + + + 
Sbjct: 121 ALLSPKRHVDKTYLAQVKGIMTQEDVETFAKGISLKDFTCQPAILELVSIDPEKNQSQIR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 181 VTIAEGKFHQVKRMVTYCGKEVVDLQRLTMGTLVLDESLQRGEWRRLTKEELE 233


>gi|294340472|emb|CAZ88853.1| putative Pseudouridine synthase [Thiomonas sp. 3As]
          Length = 562

 Score =  168 bits (426), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 85/347 (24%), Positives = 143/347 (41%), Gaps = 12/347 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           + ++       ++ KV+A++G+ SRRE+E +I   RV VNG         ++ TD I V+
Sbjct: 165 RRVLAPAEDAPKLHKVLAQSGVGSRREMEDLILAGRVSVNGEPA-HLGQRILPTDQIRVN 223

Query: 64  GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G  ++     A+   L  +     +V+        +          ++  +VGRLDINTE
Sbjct: 224 GKIIKRRLRPAQARVLAYHKPTGEVVSFKDPEGRPTVFQHLPKLQGAKWTAVGRLDINTE 283

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL T  G LA  L  PS    R Y VR  G++D    + L +G+ +       + +  
Sbjct: 284 GLLLFTTSGDLANRLMHPSYGAEREYAVRVLGELDAAARDELLEGVQLGDGPARFLSLEE 343

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V + EG+NRE++++FE     V+RLIR+ Y    L   L  G   E+ K
Sbjct: 344 AGGEGANRWWRVVISEGRNREVRRMFEAVGLTVSRLIRVRYASVVLPAGLRRGDFVELDK 403

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
            +++   G      +                +  N      D     +    +  G  +Q
Sbjct: 404 SLVQALQGRSGEAPSGA------GDRPARRPNGQNQGGRRNDSRGSGRGGRGKGQGGDQQ 457

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
           +       R  + +    +  + S   S  G    +    P   S+R
Sbjct: 458 QPGPDSYARTTVEALFGKSPVVRSGGGSWGGAGNFSTGNKPGGQSRR 504


>gi|56412865|ref|YP_149940.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|168261760|ref|ZP_02683733.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|197361796|ref|YP_002141432.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|56127122|gb|AAV76628.1| ribosomal small subunit pseudouridine synthase [Salmonella enterica
           subsp. enterica serovar Paratyphi A str. ATCC 9150]
 gi|197093272|emb|CAR58718.1| ribosomal small subunit pseudouridine synthase [Salmonella enterica
           subsp. enterica serovar Paratyphi A str. AKU_12601]
 gi|205349524|gb|EDZ36155.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
          Length = 231

 Score =  168 bits (426), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 103/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G +++ AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKDLTKPATLEVI----TPVQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVELHRERIGAITLDENLAPGEYRPLTEEEI 227


>gi|306833047|ref|ZP_07466179.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           bovis ATCC 700338]
 gi|304424946|gb|EFM28080.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           bovis ATCC 700338]
          Length = 238

 Score =  168 bits (426), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 105/229 (45%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++ +AG  SR +V+++I  ++V V+G L E   +NV ++   I V G  ++++  
Sbjct: 1   MRLDKLLGQAGFGSRNQVKKLIRSRQVYVDGRLAEADNLNVETSLQKITVSGKQVKQSSE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                      ++  VGRLD +TEGLLL+TN+G L  
Sbjct: 61  KYFLLNKPAGVVSAVSDKEHQTVIDLIKESDRVPQLYPVGRLDRSTEGLLLITNNGPLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V  +  +  D     + G+           ++ + T     +   V
Sbjct: 121 RMLHPKYHVAKTYYVEVNAFLADDAPAFFENGVSFDDGTICKPAKLEIITASTEESSAYV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + EGK  +IKK+F  +  KV  L R+++G FQLG L +G  RE++   
Sbjct: 181 TISEGKFHQIKKMFLAYGVKVTYLKRLTFGEFQLGDLPSGQYRELTSTE 229


>gi|330830517|ref|YP_004393469.1| ribosomal large subunit pseudouridine synthase B [Aeromonas veronii
           B565]
 gi|328805653|gb|AEB50852.1| Ribosomal large subunit pseudouridine synthase B [Aeromonas veronii
           B565]
          Length = 307

 Score =  168 bits (426), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 82/306 (26%), Positives = 131/306 (42%), Gaps = 7/306 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +       V     I VDG  ++    
Sbjct: 2   SEKLQKVLARAGHGSRREMEALITAGRVSVDGKVAT-LGDRVEVNAVIRVDGHQVKTRAA 60

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  +     + T H      +          +R I+VGRLD+NT GLLL T D
Sbjct: 61  EEVICRVLAYHKPEGEMCTRHDPEGRPTVFDRLPKMEGARWIAVGRLDVNTSGLLLFTTD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G++ +  L  L+KG+ ++       ++     +G N 
Sbjct: 121 GELANRLMHPSHEVEREYAVRVFGEITEAMLQRLRKGVQLEDGTAKFNKIKPAGGEGLNQ 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           W  V L EG+NRE+++++E    +V+RL+RI YG  +L   +  G  +E+    +    G
Sbjct: 181 WFNVTLTEGRNREVRRLWESQEVQVSRLMRIRYGDVKLDRGIPRGGWQELKLPEVNYLRG 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              L     +        +T    +   I         M+    +    + ++K      
Sbjct: 241 LVNLPPETESKVDLQQDGKTSRHKQAAQIRRAVQRHKEMQGKEPRARATTARRKPQASTR 300

Query: 307 RRNLAS 312
                S
Sbjct: 301 NSGTGS 306


>gi|28897989|ref|NP_797594.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus RIMD 2210633]
 gi|153838627|ref|ZP_01991294.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AQ3810]
 gi|260364226|ref|ZP_05776929.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus K5030]
 gi|260877145|ref|ZP_05889500.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AN-5034]
 gi|260898993|ref|ZP_05907434.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus Peru-466]
 gi|260902058|ref|ZP_05910453.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AQ4037]
 gi|34098481|sp|Q87QD4|RSUA_VIBPA RecName: Full=Ribosomal small subunit pseudouridine synthase A;
           AltName: Full=16S pseudouridine 516 synthase; AltName:
           Full=16S pseudouridylate 516 synthase; AltName:
           Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|28806203|dbj|BAC59478.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus RIMD 2210633]
 gi|149747999|gb|EDM58859.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AQ3810]
 gi|308088663|gb|EFO38358.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus Peru-466]
 gi|308093845|gb|EFO43540.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AN-5034]
 gi|308109089|gb|EFO46629.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AQ4037]
 gi|308111860|gb|EFO49400.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus K5030]
 gi|328473055|gb|EGF43903.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus 10329]
          Length = 233

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 49/230 (21%), Positives = 96/230 (41%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  A+R++  ++I    V V+G + +  +  V     +E DG  +      
Sbjct: 1   MRLDKYLCDALGATRKQATKIIKSGEVLVDGEVQKSGSFKVPEGGVVEWDGREVGAPGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + LY     + +     +  +            +   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLYKPADFVCSHEDGYNP-TAFVLLDEPKVENLHFAGRLDVDTTGLVLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     +  D +    +GI ++      +   L+    +   V + +
Sbjct: 120 ITSPKHKCKKTYRVWLADAIQPDYVEKFAQGIELRNEREATLPAHLEIVNEAENEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            EGK  ++K++F     KV  L R   G   L   L  G  R ++++ + 
Sbjct: 180 VEGKYHQVKRMFAALGNKVELLHRERIGDIVLDDTLEPGDYRYLTQEEVD 229


>gi|239906975|ref|YP_002953716.1| pseudouridine synthase [Desulfovibrio magneticus RS-1]
 gi|239796841|dbj|BAH75830.1| pseudouridine synthase [Desulfovibrio magneticus RS-1]
          Length = 322

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 93/300 (31%), Positives = 137/300 (45%), Gaps = 6/300 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
            +    R++K +A AG+ SRR  + +IA  RV VNG ++  A + +    D + VDG P+
Sbjct: 4   TDSRLTRINKALASAGVCSRRHADDLIAAGRVTVNGAVVTEAGLRIDPARDALAVDGAPV 63

Query: 68  R-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLL 124
               E       HK  G+VTT SDP+GR TVFD LP      R+  VGRLD  +EGLLLL
Sbjct: 64  NLAPEIPITLALHKKPGVVTTASDPEGRPTVFDGLPEVWRGKRLFPVGRLDFFSEGLLLL 123

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGD-MQVTLDTQ 182
           T DG LA  L  P     + YRV   GQV  D L  + +G+ + +G          ++  
Sbjct: 124 TTDGELALRLTHPRWHVPKRYRVTVRGQVTPDMLGTMARGMRLAEGERLAPVAARVVEGP 183

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
               + + + L +G NR+I+++       V RL R+S GP  LG L  G+ RE++   L 
Sbjct: 184 AQDRSILEMELHQGVNRQIRRMCRDLGLTVLRLARVSQGPVALGDLPLGACRELTPAELA 243

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
                  L++A V    P          +       P      +  +    G ++     
Sbjct: 244 TLRQSVGLDDADVAPAPPRPRPTAEGDTKRPPRPARPPQAGGKRPATKASGGETETGPRR 303


>gi|282891010|ref|ZP_06299515.1| hypothetical protein pah_c045o010 [Parachlamydia acanthamoebae str.
           Hall's coccus]
 gi|281499003|gb|EFB41317.1| hypothetical protein pah_c045o010 [Parachlamydia acanthamoebae str.
           Hall's coccus]
          Length = 261

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 71/231 (30%), Positives = 116/231 (50%), Gaps = 4/231 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           + T QR+SKV+A AG+ASRR  E +I    V VNG +       V   D I   G  + K
Sbjct: 29  DKTKQRLSKVMAAAGVASRRACEMLIFDGCVTVNGEVTLVPQTLVDENDVITCKGQSVGK 88

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +    ++ +KPIG + ++        V D   ++  R+ +VGRLD +T GL+++TNDG 
Sbjct: 89  KQNKVYYILNKPIGYICSNKRNKDSKIVLDLFDTVEERLFTVGRLDKDTSGLIIVTNDGH 148

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  PS    + Y V+ + +V+ + L+ L  G +++      ++V+   +      +
Sbjct: 149 FANRVIHPSANIHKEYLVKTNEEVEAEHLSALSSGTLVEKTFVRPIRVSKVRRG----TL 204

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + + EGK REI+ + E     V  L RI  G   LG L  G  RE++ + 
Sbjct: 205 KITIAEGKKREIRLLMESAKLPVLELTRIRIGGLHLGPLQPGEWREMTARE 255


>gi|229824809|ref|ZP_04450878.1| hypothetical protein GCWU000182_00158 [Abiotrophia defectiva ATCC
           49176]
 gi|229790812|gb|EEP26926.1| hypothetical protein GCWU000182_00158 [Abiotrophia defectiva ATCC
           49176]
          Length = 242

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 94/237 (39%), Gaps = 7/237 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRK 69
               R+ K ++     +R +V+  I + RV  NG++++     V    D I +DG P+  
Sbjct: 2   SKTIRLDKYLSDMTSETRSKVKEYIRKGRVTANGVVIKSPETKVDTDNDEICIDGKPVGY 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI----SVGRLDINTEGLLLLT 125
            E     +      + +T                           VGRLD +TEGLLL+T
Sbjct: 62  VEYYYYMMNKPQGVITSTEKGRTKTVMDVFKETGTGCPRFNELSPVGRLDKDTEGLLLIT 121

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG L   L  P     +VY       V    + +   G+ +        ++ +      
Sbjct: 122 NDGELNHKLLSPKNHVDKVYYAELKSPVKVSDIEIFAGGLDLGDFICKPARLEI-CDDVK 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
                + + EGK  ++K++FE    +V  L R+S G  +L   L  G  R ++++ +
Sbjct: 181 KFAAKITISEGKFHQVKRMFEAVENEVIYLKRLSMGSLKLDDNLELGEVRALTEEEI 237


>gi|291618129|ref|YP_003520871.1| RsuA [Pantoea ananatis LMG 20103]
 gi|291153159|gb|ADD77743.1| RsuA [Pantoea ananatis LMG 20103]
          Length = 239

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 103/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I++    SR    R I  QRV VNG ++   A  +     +E DG  L+     
Sbjct: 1   MRLDKFISQQLEISRAIAAREIRGQRVTVNGDVVRDTAFKLQPDHEVEYDGNVLQMQTGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + V+     +  ++ + GRLDI+T GL+LLT+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTIVYFIEEPMAFKLHAAGRLDIDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + YRV     V  D       G+ +          Q+ +     +   V +
Sbjct: 121 ITSPRHHCEKTYRVTLEAPVSDDTAAQFSAGVQLHNEKSLTKPAQLEVI----TPTEVLL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            L EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TLSEGRYHQVKRMFAAVGNRVVGLHRERIGEIVLDEALEPGEYRPLTEEEI 227


>gi|296136237|ref|YP_003643479.1| RNA-binding S4 domain protein [Thiomonas intermedia K12]
 gi|295796359|gb|ADG31149.1| RNA-binding S4 domain protein [Thiomonas intermedia K12]
          Length = 562

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 85/347 (24%), Positives = 143/347 (41%), Gaps = 12/347 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           + ++       ++ KV+A++G+ SRRE+E +I   RV VNG         ++ TD I V+
Sbjct: 162 RRVLAPAEDAPKLHKVLAQSGVGSRREMEDLILAGRVSVNGEPA-HLGQRILPTDQIRVN 220

Query: 64  GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G  ++     A+   L  +     +V+        +          ++  +VGRLDINTE
Sbjct: 221 GKIIKRRLRPAQARVLAYHKPTGEVVSFKDPEGRPTVFQHLPKLQGAKWTAVGRLDINTE 280

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL T  G LA  L  PS    R Y VR  G++D    + L +G+ +       + +  
Sbjct: 281 GLLLFTTSGDLANRLMHPSYGAEREYAVRVLGELDAAARDELLEGVQLGDGPARFLSLEE 340

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V + EG+NRE++++FE     V+RLIR+ Y    L   L  G   E+ K
Sbjct: 341 AGGEGANRWWRVVISEGRNREVRRMFEAVGLTVSRLIRVRYASVVLPAGLRRGDFVELDK 400

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
            +++   G      +                +  N      D     +    +  G  +Q
Sbjct: 401 SLVQALQGRSGEAPSGA------GDRPARRPNGQNQGGRRNDSRGSGRGGRGKGQGGDQQ 454

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
           +       R  + +    +  + S   S  G    +    P   S+R
Sbjct: 455 QPGPDSYARTTVEALFGKSPVVRSGGGSWGGAGNFSTGNKPGGQSRR 501


>gi|220905836|ref|YP_002481147.1| pseudouridine synthase [Cyanothece sp. PCC 7425]
 gi|219862447|gb|ACL42786.1| pseudouridine synthase [Cyanothece sp. PCC 7425]
          Length = 261

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 74/260 (28%), Positives = 112/260 (43%), Gaps = 13/260 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR- 68
            + +R+ K++A+ GIASRR+ E+MI   RV +NG              D I+VDG  L+ 
Sbjct: 2   DSGERLQKILAQWGIASRRQAEQMILDGRVWLNGEPAT-LGQKADPHCDRIQVDGRTLQS 60

Query: 69  -KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTN 126
            + +   L LY     + T        + +    P   +  +  VGRLD  T G LL+TN
Sbjct: 61  DRPDLLYLLLYKPTGVISTCSDPQGRPTILDLLPPHYRNLGLHPVGRLDSETTGALLITN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L   L  P  Q  +VY+V   G   +  L   + G+++ G      QV L  +    
Sbjct: 121 DGWLTHALTHPCHQVSKVYQVWVSGHPPESVLQQWRDGVMLAGRLTLPAQVRLLERTEIP 180

Query: 187 A---WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-----TLLAGSTREVSK 238
           +    + V L EG+NR+I++V +   + V  L R   GP QL      TL  G  R ++ 
Sbjct: 181 SALTCLEVILWEGRNRQIRRVAKKLGYPVVHLHRTGIGPVQLQATDQPTLAKGHYRHLTP 240

Query: 239 KILREQLGPHLLEEAQVNLD 258
             L        +        
Sbjct: 241 GELEALREQVGILSIAAPAR 260


>gi|283832379|ref|ZP_06352120.1| ribosomal small subunit pseudouridine synthase A [Citrobacter
           youngae ATCC 29220]
 gi|291072028|gb|EFE10137.1| ribosomal small subunit pseudouridine synthase A [Citrobacter
           youngae ATCC 29220]
          Length = 235

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 56/231 (24%), Positives = 105/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G +++ +A  ++    +E DG  L +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRANRVTVDGEIVKNSAFKLLPEHDVEYDGNSLIQQNGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V +D      +G+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVAEDTAEQFARGVQLHNEKDLTKPAVLEVI----TPTQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G  +L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVELHRERIGAIKLDDDLEPGEYRPLTEEEI 227


>gi|257126979|ref|YP_003165093.1| RNA-binding S4 domain protein [Leptotrichia buccalis C-1013-b]
 gi|257050918|gb|ACV40102.1| RNA-binding S4 domain protein [Leptotrichia buccalis C-1013-b]
          Length = 228

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 117/229 (51%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA  G  SRR+ + +I + RV VN        ++V   D + +DG  ++   R 
Sbjct: 1   MRLNKFIAETGFCSRRKADELINEGRVTVN-KHEAIIGMDVKPEDVVRIDGERVKLNTRY 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP  ++ ++ D  GR    D + S  +R+ + GRLD  TEGL++++NDG +   
Sbjct: 60  EYYILNKPKRVLCSNEDKFGRRLAVDFIKS-RARLFTYGRLDFMTEGLIIISNDGEVYNH 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y  +   +++   +  L+ G+VI G      +V    +K     + + +
Sbjct: 119 VMHPRKKLYKSYIAKVSREIEDKDIEALQHGVVIDGKRTAPAKV----KKIDKKELRIAI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EG+NR+I+K+ E   + VN L RI  G   LG L  G  R +++  ++
Sbjct: 175 FEGRNRQIRKMLETLGYNVNSLKRIKVGELTLGNLQVGEYRALNEDEIK 223


>gi|332288671|ref|YP_004419523.1| 16S rRNA pseudouridylate synthase A [Gallibacterium anatis UMN179]
 gi|330431567|gb|AEC16626.1| 16S rRNA pseudouridylate synthase A [Gallibacterium anatis UMN179]
          Length = 234

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 63/236 (26%), Positives = 109/236 (46%), Gaps = 7/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ K ++     SR +  + + Q  VKVN  L++  A+ V   D +E DG  L      
Sbjct: 3   QRLDKFLSEYTGLSRSQATKALRQNLVKVNQQLVKDGALKVSPEDVVEFDGETLEWVSGN 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + +L +KP G V +H D +  +        + SR+ + GRLD++T GL+LLT+DG  +  
Sbjct: 63  QYFLLYKPEGYVCSHDDGEYPTVYQFFDYPLSSRLHTAGRLDVDTTGLVLLTDDGQWSHR 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P   + + Y V     V+   L    +GI+++G        Q+ +      +  + +
Sbjct: 123 ITSPKYHYKKTYLVTLAAPVEDFYLEQCAQGILLRGEKQPTKPAQIEII----DDYNLNL 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
            + EGK  ++K++F     KV  L R   G   L   L  G  R ++   ++  L 
Sbjct: 179 TIVEGKYHQVKRMFAALGNKVIALHRWRIGQIILDPQLEEGQYRALTDAEVQSFLK 234


>gi|319790166|ref|YP_004151799.1| pseudouridine synthase [Thermovibrio ammonificans HB-1]
 gi|317114668|gb|ADU97158.1| pseudouridine synthase [Thermovibrio ammonificans HB-1]
          Length = 251

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 83/251 (33%), Positives = 134/251 (53%), Gaps = 10/251 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R++K +A AG  +RR+VE +I Q RV+VNG +++  AV V    D ++VDG  +R   +
Sbjct: 1   MRLNKFLAYAGFGARRKVEELIKQGRVEVNGQVVDSPAVEVDPKKDVVKVDGERVRLPNK 60

Query: 73  TRLWLYHKPIGLVT--THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                ++KP G++T    +  D R  V D   +   R+  VGRLD NTEGLL++TNDG L
Sbjct: 61  FVYIAFNKPQGVLTAMERAPGDKRPIVADYFRNYPVRLFPVGRLDYNTEGLLIMTNDGEL 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-----YGDMQVTLDT--QK 183
           A  L  P     + Y  +  G+V   ++  +KKG ++            + V L    + 
Sbjct: 121 ADRLAHPRYHVPKTYIAKVKGRVKPAEIERMKKGALLVDDKGKKFFIKPLDVKLLHPSKT 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           G N +V + + +GKNR +++ F+ F+  V +L R++ GP +LG L  G  RE++ + ++ 
Sbjct: 181 GRNTYVQITIDQGKNRVVRRFFDRFDHGVLKLKRVAIGPVKLGDLPKGYYRELTPEEVKR 240

Query: 244 QLGPHLLEEAQ 254
                 LEE  
Sbjct: 241 LKKAAGLEEEG 251


>gi|310768104|gb|ADP13054.1| 16S rRNA pseudouridylate synthase A [Erwinia sp. Ejp617]
          Length = 234

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 54/229 (23%), Positives = 103/229 (44%), Gaps = 3/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I++    SR    R +  ++V V+G ++   +  + +   +E DG  L +    
Sbjct: 1   MRLDKFISQQLEVSRAIAARELRARKVTVDGEVVREGSYKLNADSTVEYDGNVLEQQLGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP+G V +  DPD  + ++        R+ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPVGYVCSTDDPDHPTILYFLEEPGAYRLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D       G+ +           L+  + +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESAISDDNAQQFADGVQLHNEKTLTKPAALEVIEPN--VVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G  +L   L  G  R +S + +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVGLHRERIGAIRLDSDLHPGEYRPLSAEEI 227


>gi|304403869|ref|ZP_07385531.1| pseudouridine synthase [Paenibacillus curdlanolyticus YK9]
 gi|304346847|gb|EFM12679.1| pseudouridine synthase [Paenibacillus curdlanolyticus YK9]
          Length = 260

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 59/242 (24%), Positives = 108/242 (44%), Gaps = 9/242 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
                R+ K++A  G  +R E+++ + Q +V V+G +++ + + +      +   G  + 
Sbjct: 11  TDKRMRLDKLLANMGYGTRSEIKKAVKQGKVTVDGRVVKDSGLQIKPNEQQVAFSGELVV 70

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             +   L L+  P  +  T    D       +      +   VGRLD +TEGLLLLTNDG
Sbjct: 71  YRDVVYLMLHKPPGVVSATEDSRDETVIDLLDADDRILQPFPVGRLDKDTEGLLLLTNDG 130

Query: 129 GLARVLELPSTQWLRVYRVRF--HGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGS 185
            LA  L  P     + Y  R      V Q        G+ +         ++ ++  + S
Sbjct: 131 QLAHDLLSPRKHVPKTYFARVLGEEPVGQADRERFAAGVELDDGYVTMPAELEVEQAEQS 190

Query: 186 N----AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
           +    + + + ++EGK  +IK++F+    +V  L R+S GP  L   L  G+ RE+++  
Sbjct: 191 DDGWVSLIRITIQEGKFHQIKRMFQAVGKQVIYLKRLSMGPLHLDETLPIGAYRELTEDE 250

Query: 241 LR 242
           + 
Sbjct: 251 IE 252


>gi|90422426|ref|YP_530796.1| pseudouridine synthase Rsu [Rhodopseudomonas palustris BisB18]
 gi|90104440|gb|ABD86477.1| Pseudouridine synthase, Rsu [Rhodopseudomonas palustris BisB18]
          Length = 743

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 142/324 (43%), Positives = 194/324 (59%), Gaps = 3/324 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +R++KV++RAG+ SRR+ E  + Q RV VNG ++   A++V + D I VDG PL   ER
Sbjct: 422 GERIAKVVSRAGLCSRRDAEEWVTQGRVAVNGRIINSPALDVTTRDVITVDGKPLPLPER 481

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TRL++YHKP GL+TTH+DP+GR TVFD+LP    R+IS+GRLD NTEGLLLLTNDGGLAR
Sbjct: 482 TRLFMYHKPRGLMTTHADPEGRPTVFDHLPDGLPRLISIGRLDFNTEGLLLLTNDGGLAR 541

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            LELP T WLR YRVR HG+V Q +L+ LKKG+ + G+ YG +  TL+  +G+N W+   
Sbjct: 542 TLELPDTGWLRRYRVRAHGEVTQGQLDELKKGVEVDGVKYGSIDATLERDQGANVWLVFA 601

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           +REGKNRE++ V      +VNRLIR+SYGPFQLG L  G   EV  ++LREQLG  +   
Sbjct: 602 IREGKNREVRNVLAHLGLEVNRLIRVSYGPFQLGELEEGQVEEVKTRVLREQLGEKIAAA 661

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
           +  +    I S   +  D   +   V   + R      +   +  Q+  +     RN A 
Sbjct: 662 SGADFARQIPSKGDVDLDPVVVKKPV---YKRGTVEDRKGRRVLVQRTGSEEARARNEAE 718

Query: 313 NVWMAKGIHSSFLSDSGQREENHR 336
                     +      +  +   
Sbjct: 719 ANGYGPPRRPTRGYKGKRDLKPRD 742


>gi|330966753|gb|EGH67013.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. actinidiae str. M302091]
          Length = 408

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 92/371 (24%), Positives = 143/371 (38%), Gaps = 28/371 (7%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG         V   D I
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQSRIKVNGKDAT-LGQRVDLHDAI 62

Query: 61  EVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            VDG  +++ E     R  +        + T        +           R I++GRLD
Sbjct: 63  SVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           INT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++       
Sbjct: 123 INTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPARFT 182

Query: 176 QVTLDTQ-KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIKQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKILR------------EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD 281
           RE+S+  +             +       ++    L                 +      
Sbjct: 243 REMSQYEVDILSAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVVRTLRPAAGA 302

Query: 282 FTRMKKNSSQKN-------GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREEN 334
                +   Q                   P  + +        +   +S  +   +R  +
Sbjct: 303 PATGDRTPRQPQITGSERDRPRGGDSTQRPARKDSGKPGSRAPRPADNSRGTPVAERPSD 362

Query: 335 HRRSPSFPSKR 345
             + P+ P  +
Sbjct: 363 MNKRPAKPGPK 373



 Score = 39.4 bits (90), Expect = 0.91,   Method: Composition-based stats.
 Identities = 18/100 (18%), Positives = 27/100 (27%), Gaps = 2/100 (2%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R    P +    +        +     +D     S  P      +     +      K+ 
Sbjct: 308 RTPRQPQITGSERDRPRGGDSTQRPARKDSGKPGSRAPRPADNSRGTPVAERPSDMNKRP 367

Query: 302 ATPVHRRNLAS--NVWMAKGIHSSFLSDSGQREENHRRSP 339
           A P  +R      N     G      + SGQR    RR P
Sbjct: 368 AKPGPKRVGIKLVNDDAPSGKRRGPPAGSGQRPGFGRRKP 407


>gi|226325127|ref|ZP_03800645.1| hypothetical protein COPCOM_02919 [Coprococcus comes ATCC 27758]
 gi|225206475|gb|EEG88829.1| hypothetical protein COPCOM_02919 [Coprococcus comes ATCC 27758]
          Length = 234

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 110/231 (47%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G  +R E++++I   RV V+G  +++  + +  T   + ++G  +  A++
Sbjct: 2   MRIDKYLAEMGQGTRSEIKKLIRSGRVMVDGETVKKPELKIDETTQKVSLEGKQIGYAKK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               LY     +++   D   ++ +        + +  VGRLD +TEGLLL+TNDG LA 
Sbjct: 62  EYYMLYKPAG-VISATKDDRDKTVLDLITDKKRNDLFPVGRLDKDTEGLLLITNDGELAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VY  +  G+VD+  +     G+ I              + G  + + + 
Sbjct: 121 RLLSPKKHVDKVYYAKVQGKVDESDVKAFADGVDIGDDTPAKSADLRILKSGEESEIELT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           + EG+  ++K++F     +V  L R+S G   L   L  G  R ++++ ++
Sbjct: 181 ITEGRFHQVKRMFHAVGKEVIYLKRLSMGSLALDKTLTKGEYRSLTEEEIK 231


>gi|261403960|ref|YP_003240201.1| pseudouridine synthase [Paenibacillus sp. Y412MC10]
 gi|261280423|gb|ACX62394.1| pseudouridine synthase [Paenibacillus sp. Y412MC10]
          Length = 233

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 62/234 (26%), Positives = 109/234 (46%), Gaps = 7/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+  G  SRRE ++++   +V +NG++           D + + G PL+  ++ 
Sbjct: 1   MRINKFISETGYCSRREADKLVESGKVTINGVVA-VLGSQAEEGDDVRIQGKPLQDKKKH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+ +T            +      R+  +GRLD ++EGL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITSTTESHI--KGNIVDFVGHNERIFPIGRLDKDSEGLILLTNDGDIVNK 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     V +  L  +  G+ I G      +VT      S     + L
Sbjct: 118 ILRSEGKHEKEYIVTVDRPVTESFLRGMAGGVKILGEMTLPCEVTRM----SERVFRIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            EGKNR+I+++   F ++V +L RI     +LG+   GS R+++ K   E    
Sbjct: 174 TEGKNRQIRRMCSAFGYEVRKLQRIRIMNIRLGSQRIGSWRDLNDKEKEELGRL 227


>gi|306820425|ref|ZP_07454061.1| ribosomal large subunit pseudouridine synthase B [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
 gi|304551500|gb|EFM39455.1| ribosomal large subunit pseudouridine synthase B [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
          Length = 232

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 59/227 (25%), Positives = 110/227 (48%), Gaps = 2/227 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA     SRR+ + +I  ++VK+NG +LE  A  V   D +E+DG  +   +  
Sbjct: 1   MRINKFIATKTAYSRRKADELIKDKKVKINGEVLENLAYTVNDDDEVELDGRIISDIKVK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + +        V +    +       +       V  VGRLD ++ GL+++TNDG LA  
Sbjct: 61  KYYYLFNKPKNVVSTVSDEFGRYCITDFFPPDISVFPVGRLDYDSTGLIIVTNDGDLANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  PS    + Y     G++ + ++ +  +G+VI        +  ++    S     + +
Sbjct: 121 IAHPSHHVKKTYIATLDGRLSEAQMKIFSEGVVIDSKKTLPAE--IELYDFSETQYKISI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            EG+NR+I+K+ +     V  L RIS G  +LG ++ G  R+++++ 
Sbjct: 179 YEGRNRQIRKMIDVLGRNVRELKRISIGKIKLGRIVEGKYRKLTEEE 225


>gi|158424014|ref|YP_001525306.1| pseudouridine synthase [Azorhizobium caulinodans ORS 571]
 gi|158330903|dbj|BAF88388.1| pseudouridine synthase [Azorhizobium caulinodans ORS 571]
          Length = 717

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 151/340 (44%), Positives = 203/340 (59%), Gaps = 4/340 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +R++KVIARAG+ SRRE+E  I   RV VNG +L   A  V + D I VDG PL + E
Sbjct: 28  EAERIAKVIARAGLGSRREIEEWITAGRVSVNGEVLASPAFTVTAEDEIRVDGEPLPERE 87

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RTRL+LYHKPIG+VTT+ DP+GR+T+F+ LP    R++SVGRLDIN+EGLLLLTNDGGLA
Sbjct: 88  RTRLFLYHKPIGVVTTNRDPEGRTTLFELLPGHLPRLVSVGRLDINSEGLLLLTNDGGLA 147

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           RVLELP T WLR YRVR  G VDQ +L+ L KGIV++G+ YG ++  LD  +G+N W+TV
Sbjct: 148 RVLELPETGWLRRYRVRAKGTVDQAQLDALIKGIVVEGVEYGPIEAVLDRVQGANVWITV 207

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            LREGKNRE++ V      +VNRLIRISYGPFQLG +  G   EV  +ILR+Q+G  +  
Sbjct: 208 ALREGKNREVRNVLGALGLQVNRLIRISYGPFQLGEIAEGGVEEVRTRILRDQIGNDIAA 267

Query: 252 EAQVNLDAPIYSSETLVRDRPNI----ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            A  + + P+   E               ++P         ++      ++++ A P   
Sbjct: 268 AAGADFNGPLVEREPEEEAPRRPLGLDKRKLPRAAEVADAKAAVSKPARRERRSAEPEID 327

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
                 V + K +               R+  +   +R L
Sbjct: 328 PERPPRVPLRKRMQDEERKVVKVGTVADRKGRAVKVERKL 367



 Score = 35.9 bits (81), Expect = 9.2,   Method: Composition-based stats.
 Identities = 10/99 (10%), Positives = 20/99 (20%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
                           +      E P      +  + +  G   ++  +    R      
Sbjct: 594 DKPRGERRTDKPFGRPEGGRTRREQPAGEGGFEGRAPRGRGGFAKEGASERPARSGFDKP 653

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                   S        R    + +   P   +  RT A
Sbjct: 654 RGERSFGKSEGRPPREDRSPGGKPAGKRPGFGAGPRTGA 692


>gi|304321112|ref|YP_003854755.1| hypothetical protein PB2503_07789 [Parvularcula bermudensis
           HTCC2503]
 gi|303300014|gb|ADM09613.1| hypothetical protein PB2503_07789 [Parvularcula bermudensis
           HTCC2503]
          Length = 253

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 131/246 (53%), Positives = 167/246 (67%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + E    +R++KV+ARAG+ASRR  E +IA+ RV ++G  +E  A  V   + I VDG  
Sbjct: 1   MDEEMKGERLAKVMARAGVASRRGAETLIAEGRVTIDGRPVETPATLVTGDEDIRVDGSR 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           LRK E  RLW YHKP GLVTTH DP GR TVFDNLP+   RV+SVGRLD+ TEGLLLLTN
Sbjct: 61  LRKPEAPRLWRYHKPSGLVTTHKDPQGRQTVFDNLPTDLPRVLSVGRLDLTTEGLLLLTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGGL+R+LELPST W R YRVR +G++    L  L +G+ ++G+ YG +Q  LD ++G N
Sbjct: 121 DGGLSRLLELPSTGWKRRYRVRAYGRLAGGSLGRLSEGLTVEGVRYGPIQAKLDRRQGDN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            W+TV + EGKNRE++ +       VNRLIR+SYGPFQLG L  G   EV +K L EQ+G
Sbjct: 181 LWLTVAIAEGKNREVRAICRHLGLTVNRLIRVSYGPFQLGHLAEGEVEEVPRKQLIEQVG 240

Query: 247 PHLLEE 252
                 
Sbjct: 241 RRHAAS 246


>gi|229133216|ref|ZP_04262048.1| Pseudouridine synthase [Bacillus cereus BDRD-ST196]
 gi|229167200|ref|ZP_04294941.1| Pseudouridine synthase [Bacillus cereus AH621]
 gi|228616238|gb|EEK73322.1| Pseudouridine synthase [Bacillus cereus AH621]
 gi|228650235|gb|EEL06238.1| Pseudouridine synthase [Bacillus cereus BDRD-ST196]
          Length = 238

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 62/226 (27%), Positives = 107/226 (47%), Gaps = 7/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I +++V +NG + +     V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERKVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCTSEKAV--KGNIIDLVNHPLRINHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  + L  +  G+ I        +VT      S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPEFLEKMAAGVKILDTKTLPCEVTQL----SKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK 
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKKE 223


>gi|330443912|ref|YP_004376898.1| RNA pseudouridylate synthase [Chlamydophila pecorum E58]
 gi|328807022|gb|AEB41195.1| RNA pseudouridylate synthase [Chlamydophila pecorum E58]
          Length = 234

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 67/231 (29%), Positives = 107/231 (46%), Gaps = 5/231 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
           T  R++K ++ AGIASRR+ + +I    V +NG + +   V V    D + V G P+   
Sbjct: 2   TKVRLNKFLSAAGIASRRKCDEIIFAGEVTINGRVAQGPFVQVDDQHDRVLVRGKPIAST 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ++    ++     + T+     G   V D    +  RV +VGRLD  T GL+L+TNDG  
Sbjct: 62  KKVYFMVHKPLGFVCTSERKFPGTKLVIDLFSHLPYRVFTVGRLDKETSGLILVTNDGDF 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +  PS    + Y ++ +  V +  LN L +G +I G         +   K     + 
Sbjct: 122 ANKIIHPSYGITKEYLLKVNRDVIEKDLNSLMQGTMIDGKRVRP----VAVSKVRRGTIK 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + EGK  EI+   E    ++  L RI  G   LG L  G  RE++   +
Sbjct: 178 IVVNEGKKHEIRLFAEAAGLQILELKRIRIGSLVLGGLRYGEYRELTDAEI 228


>gi|256832502|ref|YP_003161229.1| pseudouridine synthase [Jonesia denitrificans DSM 20603]
 gi|256686033|gb|ACV08926.1| pseudouridine synthase [Jonesia denitrificans DSM 20603]
          Length = 265

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 81/231 (35%), Positives = 120/231 (51%), Gaps = 1/231 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKA 70
              R+ KV+A AG+ SRRE E +I Q RV+V+G ++    V V  T   + VDG+ +   
Sbjct: 26  DGIRLQKVMADAGVGSRRECENLIRQGRVEVDGQIVMELGVRVDPTAHVVTVDGLRIMAD 85

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                   +KP  +V T  DP+GR+TV D +     R+  VGRLD  +EGLLLLTNDG L
Sbjct: 86  ASKITIAVNKPQKMVATMHDPEGRATVADLVSKRTERLFHVGRLDYESEGLLLLTNDGEL 145

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     + Y V   G+V     + L +GI ++          +  Q  +   + 
Sbjct: 146 ANRLSHPRYNVRKTYVVTVKGRVANGVGSQLLRGITLEDGEVALDSYRVIDQTDTETMIE 205

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V L  G+NR ++++F+     V RL+R S GP +LG L  G TR +++  +
Sbjct: 206 VQLHSGRNRIVRRIFDSLGHPVTRLVRTSIGPIKLGDLKQGRTRVLNRTEV 256


>gi|329930177|ref|ZP_08283790.1| ribosomal large subunit pseudouridine synthase F [Paenibacillus sp.
           HGF5]
 gi|328935199|gb|EGG31680.1| ribosomal large subunit pseudouridine synthase F [Paenibacillus sp.
           HGF5]
          Length = 233

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 62/234 (26%), Positives = 109/234 (46%), Gaps = 7/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+  G  SRRE ++++   +V +NG++           D + + G PL+  ++ 
Sbjct: 1   MRINKFISETGYCSRREADKLVESGKVTINGVVA-VLGSQAEEGDDVRIQGKPLQDKKKH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+ +T            +      R+  +GRLD ++EGL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITSTTESHI--KGNIVDFVGHNERIFPIGRLDKDSEGLILLTNDGDIVNK 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     V +  L  +  G+ I G      +VT      S     + L
Sbjct: 118 ILRSEGKHEKEYIVTVDRPVTESFLRGMAGGVKILGEITLPCEVTRM----SERVFRIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            EGKNR+I+++   F ++V +L RI     +LG+   GS R+++ K   E    
Sbjct: 174 TEGKNRQIRRMCSAFGYEVRKLQRIRIMNIRLGSQRIGSWRDLNDKEKEELGRL 227


>gi|313636574|gb|EFS02285.1| ribosomal small subunit pseudouridine synthase A [Listeria
           seeligeri FSL S4-171]
          Length = 233

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 98/231 (42%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SRREV+ ++    V VNG++ + + + V    D I V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRREVKPLLKSGSVVVNGVIQKDSKLQVNPEKDQITVHGNPVIYQEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T  +               +    VGRLD +TEGLL++TNDG LA 
Sbjct: 61  VYFMLHKPQNVVSATEDNLSETVIDLLAQEDTLTNPFPVGRLDKDTEGLLIITNDGTLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y  +  G V    +   + GI +          + +         + V
Sbjct: 121 NLLSPKKHIDKTYYAKIEGDVTATDVEAFRTGITLDDGYTCKPAHLEIMAPN----EIRV 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            ++EGK  ++K++F      V  L R+S G   L   L  G  R +++  L
Sbjct: 177 TIQEGKFHQVKRMFAATGKTVTYLKRLSMGKLMLDESLGLGEYRSLTEDEL 227


>gi|289435619|ref|YP_003465491.1| ribosomal small subunit pseudouridine synthase A [Listeria
           seeligeri serovar 1/2b str. SLCC3954]
 gi|289171863|emb|CBH28409.1| ribosomal small subunit pseudouridine synthase A [Listeria
           seeligeri serovar 1/2b str. SLCC3954]
          Length = 233

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 97/231 (41%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SRREV+ ++    V VNG++ + +   V    D I V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRREVKPLLKSGSVVVNGVIQKDSKSQVNPEKDQITVHGNPVIYQEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T  +               +    VGRLD +TEGLL++TNDG LA 
Sbjct: 61  VYFMLHKPQNVVSATEDNLSETVIDLLAQEDTLTNPFPVGRLDKDTEGLLIITNDGTLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y  +  G V    +   + GI +          + +         + V
Sbjct: 121 NLLSPKKHIDKTYYAKIEGDVTATDVEAFRTGITLDDGYTCKPAHLEIMAPN----EIRV 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            ++EGK  ++K++F      V  L R+S G   L   L  G  R +++  L
Sbjct: 177 TIQEGKFHQVKRMFAATGKTVIYLKRLSMGKLMLDESLGLGEYRSLTEDEL 227


>gi|241203270|ref|YP_002974366.1| RNA-binding S4 domain protein [Rhizobium leguminosarum bv. trifolii
           WSM1325]
 gi|240857160|gb|ACS54827.1| RNA-binding S4 domain protein [Rhizobium leguminosarum bv. trifolii
           WSM1325]
          Length = 698

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 174/370 (47%), Positives = 226/370 (61%), Gaps = 26/370 (7%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
             +   +R+SKV+ARAG+ASRR++ERMI + RV +NG +L+   VNV   D IEVDGVP+
Sbjct: 46  DSDAKAERISKVMARAGVASRRDIERMIMEGRVTLNGRVLDTPVVNVTLADRIEVDGVPI 105

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R  ERTRLWLYHKP GLVTT++DP+GRSTVFDNLP    RV+S+GRLDINTEGLLLLTND
Sbjct: 106 RGIERTRLWLYHKPTGLVTTNADPEGRSTVFDNLPEELPRVMSIGRLDINTEGLLLLTND 165

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GGLAR LELP+T WLR YRVR HG++DQD L+ LK GI + G+ YG ++ TLD  +GSN 
Sbjct: 166 GGLARALELPATGWLRRYRVRAHGEIDQDALDKLKDGIAVDGVLYGSIEATLDRTQGSNV 225

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+T+GLREGKNREIK V       VNRLIRISYGPFQLG L      EV  + LR+QLGP
Sbjct: 226 WITMGLREGKNREIKNVLGALGLDVNRLIRISYGPFQLGDLPESHVVEVRGRTLRDQLGP 285

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK---------- 297
            L+EEA+ N DAPIY++  +  +     +         +    ++  LS+          
Sbjct: 286 RLIEEAKANFDAPIYNTTAVAAEEEAEPAAPEKRERPRRDEDKRERALSRLDTKRDDRHG 345

Query: 298 ----------------QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF 341
                           +K        +  ++NVWMA G        + +  +N + +   
Sbjct: 346 GARKEDDRRDGGRRDDEKPKRPQPLGQRRSANVWMAPGARPLGEKAAAKAAKNAQTARRR 405

Query: 342 PSKRSLRRTS 351
             +   +   
Sbjct: 406 GEQAPAKNDR 415



 Score = 42.5 bits (98), Expect = 0.094,   Method: Composition-based stats.
 Identities = 13/107 (12%), Positives = 22/107 (20%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P           +     +    DRP+       D  R  +          +    +P 
Sbjct: 506 RPRAARSPAGEGRSERPRGDRPFGDRPSRGDRPFGDKPRGDRKPRADGDERPRAARTSPG 565

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             R+         G   S        +    R P        R   +
Sbjct: 566 EGRSERPRSDRPSGDRPSRGDRPFGDKPRGDRRPREDGDERPRAARS 612



 Score = 40.2 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 22/112 (19%), Gaps = 1/112 (0%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E        +                + R +       D       S    G S++ +  
Sbjct: 566 EGRSERPRSDRPSGDRPSRGDRPFGDKPRGDRRPREDGDERPRAARSFAGEGRSERPRGD 625

Query: 303 TPVHRR-NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            P   R +             S     G +  + +   + P           
Sbjct: 626 KPSGDRPSGDRPRGKGFAAKPSGAKPGGAKSFSGKPKGTKPGGDRPGGDRPA 677



 Score = 40.2 bits (92), Expect = 0.56,   Method: Composition-based stats.
 Identities = 13/126 (10%), Positives = 26/126 (20%), Gaps = 6/126 (4%)

Query: 233 TREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
            RE   + +R    P   +E +       +       DR +       D     +     
Sbjct: 427 VREEDGEWIRSSEQPRGKDEGEGFGRKRGFGDRPAREDRGSGDRPARGDRPFGDRPPRGD 486

Query: 293 NGLSKQKKLATPVHR------RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
                + +             R   S     +          G R     R      +  
Sbjct: 487 RPFGDKPRGDRKPRADGDERPRAARSPAGEGRSERPRGDRPFGDRPSRGDRPFGDKPRGD 546

Query: 347 LRRTSA 352
            +  + 
Sbjct: 547 RKPRAD 552



 Score = 39.8 bits (91), Expect = 0.61,   Method: Composition-based stats.
 Identities = 18/133 (13%), Positives = 28/133 (21%), Gaps = 12/133 (9%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE      R   G     +     D P        R       E P            + 
Sbjct: 462 REDRGSGDRPARGDRPFGDRPPRGDRPFGDKPRGDRKPRADGDERPRAARSPAGEGRSER 521

Query: 294 GLSKQKKLATPVH------------RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF 341
               +     P              R+  A      +   +S      +R  + R S   
Sbjct: 522 PRGDRPFGDRPSRGDRPFGDKPRGDRKPRADGDERPRAARTSPGEGRSERPRSDRPSGDR 581

Query: 342 PSKRSLRRTSAKK 354
           PS+         +
Sbjct: 582 PSRGDRPFGDKPR 594



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 12/102 (11%), Positives = 24/102 (23%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               +      A    +     +RP       D  +R  +    K    ++ +       
Sbjct: 498 KPRADGDERPRAARSPAGEGRSERPRGDRPFGDRPSRGDRPFGDKPRGDRKPRADGDERP 557

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           R   ++    +         SG R     R      +   R 
Sbjct: 558 RAARTSPGEGRSERPRSDRPSGDRPSRGDRPFGDKPRGDRRP 599



 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 11/103 (10%), Positives = 17/103 (16%)

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
                           +    DRP        D  R  +          +   +     R
Sbjct: 459 RPAREDRGSGDRPARGDRPFGDRPPRGDRPFGDKPRGDRKPRADGDERPRAARSPAGEGR 518

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
           +         G   S        +    R P        R   
Sbjct: 519 SERPRGDRPFGDRPSRGDRPFGDKPRGDRKPRADGDERPRAAR 561



 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 9/107 (8%), Positives = 17/107 (15%), Gaps = 1/107 (0%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               +     D P        R       E P            +     +     P   
Sbjct: 576 RPSGDRPSRGDRPFGDKPRGDRRPREDGDERPRAARSFAGEGRSERPRGDKPSGDRPSGD 635

Query: 308 RNLASN-VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           R           G           + +  +     P         ++
Sbjct: 636 RPRGKGFAAKPSGAKPGGAKSFSGKPKGTKPGGDRPGGDRPAGGPSR 682



 Score = 38.2 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 10/105 (9%), Positives = 24/105 (22%), Gaps = 1/105 (0%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              ++ + +        E     R +      +     + +  + +   +         R
Sbjct: 538 PFGDKPRGDRKPRADGDERPRAARTSPGEGRSERPRSDRPSGDRPSRGDRPFGDKPRGDR 597

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           R         +   S       +R    + S   PS     R   
Sbjct: 598 RPREDGDERPRAARSFAGEGRSERPRGDKPSGDRPS-GDRPRGKG 641



 Score = 38.2 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 17/108 (15%), Positives = 27/108 (25%), Gaps = 1/108 (0%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               +      A   S      +RP       D  +R  +    K    ++ +       
Sbjct: 548 KPRADGDERPRAARTSPGEGRSERPRSDRPSGDRPSRGDRPFGDKPRGDRRPREDGDERP 607

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSP-SFPSKRSLRRTSAKK 354
           R   S     +         SG R    R     F +K S  +    K
Sbjct: 608 RAARSFAGEGRSERPRGDKPSGDRPSGDRPRGKGFAAKPSGAKPGGAK 655


>gi|312868136|ref|ZP_07728340.1| pseudouridylate synthase [Streptococcus parasanguinis F0405]
 gi|311096540|gb|EFQ54780.1| pseudouridylate synthase [Streptococcus parasanguinis F0405]
          Length = 242

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 104/233 (44%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR EV++++ Q+++ VNG       + +    D +   G  L     
Sbjct: 1   MRLDKFLVDCGVGSRTEVKQLLKQKKIAVNGKKETAGKLQIDPDKDQVTFMGEDLVHETF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  D         +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPAGVISATEDDHHQTVLDLLDETARHKEVFPVGRLDIDTHGLLLLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVT 190
            +  P     + YR +  G +D+  +   ++GI ++       ++ +       ++++V 
Sbjct: 121 AMLSPKKHVSKNYRAQVAGIMDEADVARFEEGIALKDFTTLPARLQILEVNEASASSYVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + + EGK  ++K++      +V  L RIS GP  L  TL  G  R +    L+
Sbjct: 181 IEIAEGKFHQVKRMVAACGKEVVDLERISMGPLTLDPTLQLGEWRRLHTSELK 233


>gi|126455204|ref|YP_001066028.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1106a]
 gi|242317672|ref|ZP_04816688.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1106b]
 gi|254198293|ref|ZP_04904715.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei S13]
 gi|126228846|gb|ABN92386.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1106a]
 gi|169655034|gb|EDS87727.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei S13]
 gi|242140911|gb|EES27313.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1106b]
          Length = 554

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 84/355 (23%), Positives = 146/355 (41%), Gaps = 8/355 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 173 KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 231

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 232 GKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNTE 291

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 292 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQRLLHGVELDDGPANFLRIRD 351

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 352 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 411

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             +R  +    L+    +            R    + + +          +  +    ++
Sbjct: 412 AQVRRLMSTVGLKAPTEDKGG-KRGGPAERRQPDPMQTSMGFINREPVLTTHGQLDQPRR 470

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            +                A        S  G R+ +  R+ S+    + +R + K
Sbjct: 471 GRRGPAGGGFGAGLGGGYAGLPGYGGASRQGGRDVDGNRA-SYGGAGANKRGAGK 524


>gi|42518880|ref|NP_964810.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           johnsonii NCC 533]
 gi|41583166|gb|AAS08776.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           johnsonii NCC 533]
          Length = 233

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 104/233 (44%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I ++ V VNG +++     V   D + VDG  +   +  
Sbjct: 1   MRIDKYLANMNVGSRKEVHNLIKKKIVTVNGEVVKTPKEQVKEEDQVAVDGEKVAYQQYH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      +  T                 +  +  VGRLD +T GLLLLTNDG LA  
Sbjct: 61  YFLLNKPKGVISATEDKSQKTVLSLLKPKDRYKDIAPVGRLDKDTTGLLLLTNDGALAHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG--SNAWVT 190
           L  P+    + YR +  G  D++ + +   G+ +  G      ++ +  Q      + + 
Sbjct: 121 LLAPNKHVTKKYRAKIAGVADEETVKVFASGMTLGDGTKLKPAELKILMQDKESDQSEIE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           + ++EGK  +IK++F     KV  L RIS G   L   L  G  +E++   ++
Sbjct: 181 IEIQEGKYHQIKRMFGAVGMKVIELDRISMGKLVLPANLKRGQYQEITLTDIK 233


>gi|53719535|ref|YP_108521.1| hypothetical protein BPSL1921 [Burkholderia pseudomallei K96243]
 gi|126440981|ref|YP_001058776.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 668]
 gi|217423361|ref|ZP_03454862.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 576]
 gi|237812039|ref|YP_002896490.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei MSHR346]
 gi|254179983|ref|ZP_04886582.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1655]
 gi|254259934|ref|ZP_04950988.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1710a]
 gi|52209949|emb|CAH35921.1| conserved hypothetical protein [Burkholderia pseudomallei K96243]
 gi|126220474|gb|ABN83980.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 668]
 gi|184210523|gb|EDU07566.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1655]
 gi|217393219|gb|EEC33240.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 576]
 gi|237504108|gb|ACQ96426.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei MSHR346]
 gi|254218623|gb|EET08007.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1710a]
          Length = 554

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 84/355 (23%), Positives = 146/355 (41%), Gaps = 8/355 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 173 KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 231

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 232 GKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNTE 291

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 292 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRIRD 351

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 352 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 411

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             +R  +    L+    +            R    + + +          +  +    ++
Sbjct: 412 AQVRRLMSTVGLKAPTEDKGG-KRGGPAERRQPDPMQTSMGFINREPVLTTHGQLDQPRR 470

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            +                A        S  G R+ +  R+ S+    + +R + K
Sbjct: 471 GRRGPAGGGFGAGLGGGYAGLPGYGGASRQGGRDVDGNRA-SYGGAGANKRGAGK 524


>gi|260890551|ref|ZP_05901814.1| RNA pseudouridine synthase [Leptotrichia hofstadii F0254]
 gi|260859793|gb|EEX74293.1| RNA pseudouridine synthase [Leptotrichia hofstadii F0254]
          Length = 228

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 117/229 (51%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA  G  SRR+ + +I + RV VN        ++V   D + +DG  ++   R 
Sbjct: 1   MRLNKFIAETGFCSRRKADELINEGRVTVN-KHEAIIGMDVKPEDVVRIDGERVKLNTRY 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP  ++ ++ D  GR    D + S  +R+ + GRLD  TEGL++++NDG +   
Sbjct: 60  EYYILNKPKRVICSNEDKFGRRLAVDFIKS-RARLFTYGRLDFMTEGLIIISNDGEVYNH 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y  +   +++   +  L+ G+VI G      +V    +K     + + +
Sbjct: 119 VMHPRKKLYKSYIAKVSREIEDKDIEALQHGVVIDGKRTAPAKV----KKIDKKELRIAI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EG+NR+I+K+ E   + VN L RI  G   LG L  G  R +++  ++
Sbjct: 175 FEGRNRQIRKMLETLGYNVNSLKRIKVGELTLGNLQVGEYRALNEDEIK 223


>gi|240173130|ref|ZP_04751788.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           kansasii ATCC 12478]
          Length = 250

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 75/233 (32%), Positives = 109/233 (46%), Gaps = 4/233 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE 71
             R+ KV+++AGIASRR  E+MI   RV+V+G L+      V      I VDG  +   E
Sbjct: 9   GIRLQKVLSQAGIASRRAAEKMIIDGRVEVDGKLVTELGTRVDPDVSVIRVDGARVVLDE 68

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTNDG 128
                  +KP G+ +T +D  GR  + D +         +  VGRLD +TEGL+LLTNDG
Sbjct: 69  SLVYLALNKPRGMHSTMADDRGRPCIGDLIERKVRGNKNLFHVGRLDADTEGLILLTNDG 128

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  + Y     G V +     L+ GI +           +         
Sbjct: 129 ELAHRLMHPSHEVPKTYLATVAGTVPRGLGKKLRTGIELDDGLARVDGFAVVDAIPGKTL 188

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L EG+NR ++++     + V  L+R   GP  LG    GS R + +  +
Sbjct: 189 VRVTLHEGRNRIVRRLLAAAGFPVEALVRTDIGPVTLGKQRPGSVRALGRDEI 241


>gi|330445592|ref|ZP_08309244.1| 23S rRNA pseudouridine 2605 synthase [Photobacterium leiognathi
           subsp. mandapamensis svers.1.1.]
 gi|328489783|dbj|GAA03741.1| 23S rRNA pseudouridine 2605 synthase [Photobacterium leiognathi
           subsp. mandapamensis svers.1.1.]
          Length = 364

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 84/351 (23%), Positives = 133/351 (37%), Gaps = 12/351 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E MI   RV V+G++ +        T ++ VDG  +     
Sbjct: 2   SEKLQKVLARAGQGSRREIELMIQNGRVSVDGVVAKLGDRLEDMTANVRVDGHRIELISS 61

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L        L T H     R+           R +SVGRLD NT GLLL T D
Sbjct: 62  DEEICRILAYNKPEGELCTRHDPEGRRTVFDRLPRLNTGRWVSVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS    R Y VR  G V +  +  L KG+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRTVEREYMVRVFGDVTEQMVKNLVKGVELEDGLARFEDVVYAGGEGMNH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
              V + EG+NRE++++++     V+RL R+ YG   L   +  G   E+    L+E   
Sbjct: 182 TFYVVITEGRNREVRRLWDSQGVTVSRLKRVRYGDVYLTKDMPRGGWSEL---ELKEVNE 238

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                E     +  +       +     I           +  +      + +       
Sbjct: 239 LRATVELPPETETALTVEGQKRKKGIRQIRRAVRRHEERIETGNGNARGRRGRNNDRRNP 298

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRR---SPSFPSKRSLRRTSAKK 354
             +  ++V   +            +  ++R     P    KR     +A +
Sbjct: 299 GASRNADVESQQNERRGSGRSQPVKGRDNRNDSGKPQSSGKRKPSGNAANR 349


>gi|225870791|ref|YP_002746738.1| ribosomal small subunit pseudouridine synthase B [Streptococcus
           equi subsp. equi 4047]
 gi|225700195|emb|CAW94370.1| putative ribosomal small subunit pseudouridine synthase B
           [Streptococcus equi subsp. equi 4047]
          Length = 237

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 99/234 (42%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +  AG+ SR +V+ ++ +++V VNG+        V   TD +   G  L     
Sbjct: 1   MRLDKFLVDAGLGSRSQVKLLLKKKQVSVNGVSQTSPKYQVNEMTDEVSYQGQRLNYEAF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T            +  +    V  VGRLD +T GLLL+TNDG LA 
Sbjct: 61  VYYMLNKPKGVISATEDSSHKTVLDLLDDTARQKAVFPVGRLDKDTHGLLLVTNDGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVT 190
            L  P     + Y     G + Q+ +    +GI ++        + +     S   + V 
Sbjct: 121 ALLSPKKHVAKQYLAVVDGMMTQEDVKHFAQGITLKDHQCMPAHLDILEINESLKTSLVK 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
           + + EGK  ++K++       V+ L RIS GP QL + L  G+ R ++   L  
Sbjct: 181 ITIEEGKFHQVKRMVAACGKTVSDLQRISMGPLQLDSALAPGAYRRLTAAELEA 234


>gi|121600285|ref|YP_992840.1| RNA pseudouridine synthase family protein [Burkholderia mallei
           SAVP1]
 gi|124385307|ref|YP_001026183.1| RNA pseudouridine synthase family protein [Burkholderia mallei NCTC
           10229]
 gi|126448664|ref|YP_001080547.1| RNA pseudouridine synthase family protein [Burkholderia mallei NCTC
           10247]
 gi|167004349|ref|ZP_02270107.1| RNA pseudouridine synthase family protein [Burkholderia mallei
           PRL-20]
 gi|238562585|ref|ZP_00440124.2| RNA pseudouridine synthase family protein [Burkholderia mallei GB8
           horse 4]
 gi|254177730|ref|ZP_04884385.1| RNA pseudouridine synthase family protein [Burkholderia mallei ATCC
           10399]
 gi|254199711|ref|ZP_04906077.1| RNA pseudouridine synthase family protein [Burkholderia mallei FMH]
 gi|254358407|ref|ZP_04974680.1| RNA pseudouridine synthase family protein [Burkholderia mallei
           2002721280]
 gi|121229095|gb|ABM51613.1| RNA pseudouridine synthase family protein [Burkholderia mallei
           SAVP1]
 gi|124293327|gb|ABN02596.1| RNA pseudouridine synthase family protein [Burkholderia mallei NCTC
           10229]
 gi|126241534|gb|ABO04627.1| RNA pseudouridine synthase family protein [Burkholderia mallei NCTC
           10247]
 gi|147749307|gb|EDK56381.1| RNA pseudouridine synthase family protein [Burkholderia mallei FMH]
 gi|148027534|gb|EDK85555.1| RNA pseudouridine synthase family protein [Burkholderia mallei
           2002721280]
 gi|160698769|gb|EDP88739.1| RNA pseudouridine synthase family protein [Burkholderia mallei ATCC
           10399]
 gi|238522261|gb|EEP85706.1| RNA pseudouridine synthase family protein [Burkholderia mallei GB8
           horse 4]
 gi|243060317|gb|EES42503.1| RNA pseudouridine synthase family protein [Burkholderia mallei
           PRL-20]
          Length = 554

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 82/377 (21%), Positives = 138/377 (36%), Gaps = 27/377 (7%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 173 KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 231

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 232 GKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNTE 291

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 292 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRIRD 351

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 352 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 411

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRP---------------------NIISE 277
             +R  +    L+    +            +  P                          
Sbjct: 412 AQVRRLMSTVGLKAPTEDKGGKRGGPVERRQPDPMQTSMGFINREPVLTTHGQLDQPRRG 471

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
                                                  + G   +    +G+   N   
Sbjct: 472 RRGPAGGGFGAGLGGGYAGLPGYGGASRQGGRDVDGNRASYGGAGANKRGAGKGGRNPNG 531

Query: 338 SPSFPSKRSLRRTSAKK 354
           + +    R   RT  ++
Sbjct: 532 NRAEGGARGGPRTPQQR 548


>gi|165975813|ref|YP_001651406.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 3 str. JL03]
 gi|190149629|ref|YP_001968154.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|303252597|ref|ZP_07338760.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 2 str. 4226]
 gi|307247349|ref|ZP_07529397.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 2 str. S1536]
 gi|307249573|ref|ZP_07531560.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 4 str. M62]
 gi|307256398|ref|ZP_07538180.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 10 str. D13039]
 gi|307260827|ref|ZP_07542513.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 12 str. 1096]
 gi|307262953|ref|ZP_07544575.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 13 str. N273]
 gi|165875914|gb|ABY68962.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 3 str. JL03]
 gi|189914760|gb|ACE61012.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|302648565|gb|EFL78758.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 2 str. 4226]
 gi|306856193|gb|EFM88348.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 2 str. S1536]
 gi|306858428|gb|EFM90497.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 4 str. M62]
 gi|306865028|gb|EFM96929.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 10 str. D13039]
 gi|306869394|gb|EFN01185.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 12 str. 1096]
 gi|306871579|gb|EFN03301.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 13 str. N273]
          Length = 230

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 106/232 (45%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  R +    V VNG L +  +V +  TD I  +G  L   +  
Sbjct: 1   MRLDKFIAENTGLTRSQAARALKSGLVTVNGKLEKSGSVKIGDTDEICYEGERLEWVDEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ +KP G V +H D +  +        + +++ + GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYFMLYKPQGYVCSHDDGEYPTVFQFFDYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+      L +GI+++G        ++ +      +  V +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEDFYAKKLAEGILLRGEREPCLPAKMEVI----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EG+  ++K++F     KV  L R   G   L   L  G  R +S++ + 
Sbjct: 177 TISEGRYHQVKRMFAALGNKVEALHRWRIGDVVLDENLEEGEYRPLSEQEVE 228


>gi|170728200|ref|YP_001762226.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169813547|gb|ACA88131.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 245

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 63/243 (25%), Positives = 108/243 (44%), Gaps = 14/243 (5%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--------VMSTD 58
           ++ N T  R++K +A+ G+ SRR   R I    + + G +               + S++
Sbjct: 1   MEHNPTQMRLAKYLAQTGLCSRRAATRYIRDGLITIEGRIANHIDTVTLIETPQGIESSE 60

Query: 59  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
            +  DG P+   E    W +HK   + T        S+   +L     R+  VGRLD ++
Sbjct: 61  QLTFDGAPISAVEEKEYWAFHKA--VGTDSRLLIDDSSSLLHLLPATPRLYPVGRLDKDS 118

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLLLTNDG L + L  P     ++Y VR     D + L  + +G+  + +      +T
Sbjct: 119 RGLLLLTNDGELTQTLMHPDFGHSKIYHVRVDRDFDDNFLQAMAQGVSYRDVTTLPCTLT 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              +        + L +G NR+I+++ +   +KV  L R+      LG L  G  R+++ 
Sbjct: 179 RLAKDQ----FEITLTQGLNRQIRRMSQALGFKVIDLKRVKIQSLALGDLKEGEMRQLTS 234

Query: 239 KIL 241
             L
Sbjct: 235 SEL 237


>gi|126659748|ref|ZP_01730876.1| hypothetical protein CY0110_23321 [Cyanothece sp. CCY0110]
 gi|126618996|gb|EAZ89737.1| hypothetical protein CY0110_23321 [Cyanothece sp. CCY0110]
          Length = 259

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 67/240 (27%), Positives = 112/240 (46%), Gaps = 12/240 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           QRV K++++ G+ASRR  E MI   RVK+NG ++         + D +EVDG  ++ ++R
Sbjct: 3   QRVQKILSQWGVASRRHAEDMIIAGRVKLNGEIVT-LGDKADPSCDRLEVDGRMIQPSQR 61

Query: 73  T---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTND 127
                + +      + T     +    +          + +  VGRLD N+ G LLLTND
Sbjct: 62  PQLLYILINKPVGVVCTCDDPQNRSIVLDLLPKQLSKGTGIHPVGRLDFNSSGALLLTND 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  P     + Y V   G   +++L   ++G+++ G      QV +  +   N 
Sbjct: 122 GELTLRLTHPRYHLPKTYEVLIQGHPTEERLQQWREGVMLMGKKTLPAQVEVICRYRQNT 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-----GTLLAGSTREVSKKILR 242
            + V L EG+NR+I+ + +   + V RL R + G   L      +L  G  R ++   +R
Sbjct: 182 RLKVILTEGRNRQIRHIVQHLGFHVLRLHRTAIGSLVLSSPNESSLPNGHYRLLTPSEIR 241


>gi|49484000|ref|YP_041224.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|257425866|ref|ZP_05602290.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257428533|ref|ZP_05604931.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257431166|ref|ZP_05607543.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257433848|ref|ZP_05610206.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257436765|ref|ZP_05612809.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           M876]
 gi|282904328|ref|ZP_06312216.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus C160]
 gi|282906153|ref|ZP_06314008.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus Btn1260]
 gi|282909070|ref|ZP_06316888.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282911378|ref|ZP_06319180.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282914547|ref|ZP_06322333.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus M899]
 gi|282919515|ref|ZP_06327250.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus C427]
 gi|282924893|ref|ZP_06332559.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus C101]
 gi|283958507|ref|ZP_06375958.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus A017934/97]
 gi|293503625|ref|ZP_06667472.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus 58-424]
 gi|293510641|ref|ZP_06669346.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus M809]
 gi|293537182|ref|ZP_06671862.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus M1015]
 gi|295428329|ref|ZP_06820958.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus EMRSA16]
 gi|297590707|ref|ZP_06949345.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus MN8]
 gi|49242129|emb|CAG40829.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|257271560|gb|EEV03706.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257275374|gb|EEV06861.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257278114|gb|EEV08762.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257281941|gb|EEV12078.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257284116|gb|EEV14239.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           M876]
 gi|282313259|gb|EFB43655.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus C101]
 gi|282317325|gb|EFB47699.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus C427]
 gi|282321728|gb|EFB52053.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus M899]
 gi|282325073|gb|EFB55383.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282327334|gb|EFB57629.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282331445|gb|EFB60959.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus Btn1260]
 gi|282595946|gb|EFC00910.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus C160]
 gi|283790656|gb|EFC29473.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus A017934/97]
 gi|290920027|gb|EFD97095.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus M1015]
 gi|291095291|gb|EFE25556.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus 58-424]
 gi|291466532|gb|EFF09053.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus M809]
 gi|295127729|gb|EFG57366.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus EMRSA16]
 gi|297575593|gb|EFH94309.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus MN8]
 gi|312437790|gb|ADQ76861.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus TCH60]
 gi|315195667|gb|EFU26054.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           CGS00]
          Length = 231

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 55/228 (24%), Positives = 100/228 (43%), Gaps = 7/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E 
Sbjct: 1   MRIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDKISVRGELIEYVEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + +   D   ++ +          +  VGRLD +TEGLLL+TNDG    
Sbjct: 61  VYIMLNKPKGYI-SATEDHHSKTVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+    + Y V     + ++ +   K+GI +         +T    + S     V 
Sbjct: 120 ELMSPNKHVSKKYEVISANPITEEDIQAFKEGITLSDGKVKPAILTYIDNQTS----HVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           + EGK  ++K++F     +V  L RI     +L   L +G  R +++ 
Sbjct: 176 IYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYRLLTEN 223


>gi|117924345|ref|YP_864962.1| ribosomal large subunit pseudouridine synthase B [Magnetococcus sp.
           MC-1]
 gi|117608101|gb|ABK43556.1| ribosomal large subunit pseudouridine synthase B [Magnetococcus sp.
           MC-1]
          Length = 332

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 83/257 (32%), Positives = 131/257 (50%), Gaps = 5/257 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA- 70
              R+ K +A  G+ SRRE E  I + RV +NG ++    V V   D + VDG  +    
Sbjct: 68  EAPRLQKWLAEQGLCSRREGEVWIQEGRVSINGEVVTELGVKVAKRDRVAVDGQLVTPQR 127

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
              T + L+     + T       R+          SR+I+VGRLDIN+EGL++LT+DG 
Sbjct: 128 SRDTAIILHKPKSIICTRSDPQGRRTIFDLIENHGSSRLITVGRLDINSEGLIILTSDGQ 187

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLD--TQKGSN 186
           LA  L  PS +  RVYRV+ HG +   +L  ++   + ++    G +++ LD   ++G+N
Sbjct: 188 LAHGLMHPSREVPRVYRVKTHGILLASQLEQIRTVGVRLEDGPTGPLEIVLDRGREQGNN 247

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +W T+ LREG+NRE++++F+ F  +V RL+R+ YG   LG L  G+ R V+         
Sbjct: 248 SWYTITLREGRNREVRRIFDHFGLQVARLLRVGYGGISLGNLEPGAWRPVTVDEWNMLQK 307

Query: 247 PHLLEEAQVNLDAPIYS 263
                    +  A    
Sbjct: 308 ISKRPIPGESAQAIPER 324


>gi|320527331|ref|ZP_08028516.1| hypothetical protein HMPREF9430_00622 [Solobacterium moorei F0204]
 gi|320132355|gb|EFW24900.1| hypothetical protein HMPREF9430_00622 [Solobacterium moorei F0204]
          Length = 233

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 110/231 (47%), Gaps = 8/231 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ +++A A + SR EV++++ ++RV+VNG + + + + V      I VD +P+   +  
Sbjct: 3   RLDRILANARVGSRSEVKKLVKEKRVRVNGEIAKSSDMRVDENTAEIFVDDIPVTYEKYV 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      +  T        TV D +   +  +   GRLD +TEGLL++TNDG LA  
Sbjct: 63  YYMLNKPAGYISATEGK--NCPTVLDLITEDYKGMFPCGRLDKDTEGLLMITNDGPLAHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     + Y V     + ++ +  ++ G+   G+ Y         +K S+   T+ +
Sbjct: 121 LLSPKKHVEKEYYVEHTLPLTEEDIAKIESGVTYNGVSYKPA----VYKKISDTSCTLTI 176

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
           +EGK  EIK +F     KV  L R+      L   L  G  R ++K+ L +
Sbjct: 177 QEGKYHEIKFIFNSVGDKVVYLKRLRMKNLVLDETLKPGEYRPLTKEELED 227


>gi|300691724|ref|YP_003752719.1| ribosomal large subunit pseudouridine synthase B [Ralstonia
           solanacearum PSI07]
 gi|299078784|emb|CBJ51444.1| Ribosomal large subunit pseudouridine synthase B [Ralstonia
           solanacearum PSI07]
          Length = 594

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 86/370 (23%), Positives = 148/370 (40%), Gaps = 19/370 (5%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K + +  E+  P ++ K++A AG+ SRR++E +I Q RV VNG+        ++ TD + 
Sbjct: 204 KVRELTSEDDAP-KLHKILADAGLGSRRDMEDLILQGRVSVNGLPA-HIGQRILPTDQVR 261

Query: 62  VDGVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           V+G  +++         L  +     +V+        +           + ++VGRLD N
Sbjct: 262 VNGKLIQRKLPNKAPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRMKTGKWVAVGRLDFN 321

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+ T  G +A     P     R Y VR  G++ +     L +G+ +       +  
Sbjct: 322 TEGLLIFTTSGDIANRFMHPRYGVEREYAVRTLGELSESDRQKLLQGVRLDDGEANFLSC 381

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EV
Sbjct: 382 ADGGGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEV 441

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDF------------TR 284
           S + +R  +G   L+    +             +R                       +R
Sbjct: 442 SAEEVRVLMGLLGLKVPTASAGGGQGGQGGRQGNRRREAQPALTGPMSSGFTGEATFQSR 501

Query: 285 MKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
                +    L   ++  +P     + +++        + L+   +     R  P   S 
Sbjct: 502 GMGVENGNRALPAPRRQPSPRQPDPMQTSMGYINVGGPTTLTARTRMGGGGRALPGAGSG 561

Query: 345 RSLRRTSAKK 354
              R    K+
Sbjct: 562 NGNRAPGNKR 571


>gi|118470853|ref|YP_888039.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           smegmatis str. MC2 155]
 gi|118172140|gb|ABK73036.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           smegmatis str. MC2 155]
          Length = 247

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 78/241 (32%), Positives = 111/241 (46%), Gaps = 4/241 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
                R+ KV+++AGIASRR  ERMI   RV+V+G ++      V      I VDG  + 
Sbjct: 3   EEQGVRLQKVLSQAGIASRRVAERMIIDGRVEVDGQIVTELGTRVDPAVADIRVDGSRII 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLLT 125
             +       +KP G+ +T SD  GR  V D +            VGRLD +TEGLLLLT
Sbjct: 63  LDDTMVYLAINKPRGMHSTMSDDRGRPCVGDLVEHRVRGNKKLFHVGRLDADTEGLLLLT 122

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  PS +  + Y     G V +     LK G+ +           +      
Sbjct: 123 NDGELAHRLMHPSFEVPKTYVATVMGTVPRGLGKKLKAGVELDDGPAHVDDFAVVDTVPG 182

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
              V V L EG+NR ++++    ++ V  L+R   G   LG    GS R +++K + E  
Sbjct: 183 KTMVKVTLHEGRNRIVRRLLAAVDFPVQELVRTEIGSVSLGDQRPGSIRALTRKEVGELY 242

Query: 246 G 246
            
Sbjct: 243 Q 243


>gi|289624030|ref|ZP_06456984.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. aesculi str. NCPPB3681]
          Length = 308

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 87/307 (28%), Positives = 134/307 (43%), Gaps = 10/307 (3%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG         V   D I
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDAT-LGQRVDLHDAI 62

Query: 61  EVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            VDG  +++ E     R  +        + T        +           R I++GRLD
Sbjct: 63  SVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           INT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++       
Sbjct: 123 INTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPARFT 182

Query: 176 QVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE+S+  + + L   +  +          + + + R +      +           +   
Sbjct: 243 REMSQYEV-DILAAEVGLQPVAQPQMNAKTKDKMERLQRQPSRPLGKGERVRTLRPAAGA 301

Query: 294 GLSKQKK 300
             +  + 
Sbjct: 302 PATGDRA 308


>gi|319744819|gb|EFV97158.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae ATCC 13813]
          Length = 239

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 59/230 (25%), Positives = 106/230 (46%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++ +AG  SR  V+++I  ++V V+G ++ +  V V S+   I V    +   E 
Sbjct: 1   MRLDKLLGQAGFGSRNHVKKLIRSRQVSVDGQIVTKDNVIVDSSLQSIFVGKERVCLKES 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +   LY     +               +       +  +GRLD +TEGLL++TN+G L  
Sbjct: 61  SYYLLYKPSGVVSAVRDSEHKTVIDLISEKDKVEGLYPIGRLDRDTEGLLIITNNGPLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V  +G +++D +   ++G+V          ++T+DT     +   +
Sbjct: 121 RMLHPKHHVAKTYYVEVNGFLERDAITFFEEGVVFDDGTKCKPAELTIDTANNDKSTARI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + EGK  ++KK+F  +  KV  L RIS+G  +L   L  G  R +    
Sbjct: 181 TITEGKFHQVKKMFLAYGVKVIYLRRISFGDLRLDMNLKPGQYRRLRDSE 230


>gi|323343010|ref|ZP_08083241.1| ribosomal large subunit pseudouridine synthase B [Erysipelothrix
           rhusiopathiae ATCC 19414]
 gi|322463074|gb|EFY08269.1| ribosomal large subunit pseudouridine synthase B [Erysipelothrix
           rhusiopathiae ATCC 19414]
          Length = 262

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 62/241 (25%), Positives = 109/241 (45%), Gaps = 5/241 (2%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           I  E     R++K I+ +G  SRR+ +R IA+  V ++G+        V+    + V+G 
Sbjct: 18  IQHEARESLRLNKYISDSGYCSRRQADRFIAEGVVAIDGVTATV-GQQVLPGQRVTVEGN 76

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +   +       +KP G+  T       +    +  +    +  +GRLD ++ GL+LLT
Sbjct: 77  HVTIDDEKVYIALNKPRGITCTTDGAIEGNIS--DFMNYPKMIFPIGRLDKDSSGLILLT 134

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQK 183
           NDG +   +        + Y V  +  +D+D +  + KG+ I       MQVT   D ++
Sbjct: 135 NDGDIVNKILREEYGHDKEYIVSVNKTIDEDFITKMSKGVEIYNQQTHRMQVTNPSDVEQ 194

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            +     + L +G NR+I+++ +   +KV  L R+      LG L  G  R +S   L E
Sbjct: 195 VAPKTFRIVLNQGLNRQIRRMTKALGFKVTTLNRVRIMNINLGDLKVGEWRYLSVHELEE 254

Query: 244 Q 244
            
Sbjct: 255 M 255


>gi|269124110|ref|YP_003306687.1| pseudouridine synthase [Streptobacillus moniliformis DSM 12112]
 gi|268315436|gb|ACZ01810.1| pseudouridine synthase [Streptobacillus moniliformis DSM 12112]
          Length = 228

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 60/229 (26%), Positives = 111/229 (48%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA +G  SRR+ + +I   RV +N  +       V   D + +DG  +   +  
Sbjct: 1   MRINKYIAESGFCSRRKADELIIDGRVTINKNIA-VIGSEVEDGDIVRIDGEKVTVKKEY 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP  ++   ++     T+  +L     R+ + GRLD  TEGL++++NDG +   
Sbjct: 60  EYYILNKPKRVLC-SNEDRQGRTLAVSLIKSKKRLFTYGRLDYMTEGLIIISNDGDIYNN 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y  +    +  D +  LK G+VI G+     +V    +  +   V V +
Sbjct: 119 VMHPKKKLYKSYIAKIDSDITDDHIEALKYGVVIDGVRTLPAKV----KTITKREVRVAI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EG+NR+I+K+FE   + V  L R+  G   L  L  G  R+++   ++
Sbjct: 175 HEGRNRQIRKMFEVLGYTVKTLRRVKVGELSLKGLEVGKYRKMTDDEIK 223


>gi|126173147|ref|YP_001049296.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|125996352|gb|ABN60427.1| pseudouridine synthase [Shewanella baltica OS155]
          Length = 236

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 67/233 (28%), Positives = 110/233 (47%), Gaps = 11/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMST----DHIEVDGVPLR 68
            R++K +A+ GI SRRE  R+I   R+ +NG +      + +  +    D IE+DG P+ 
Sbjct: 1   MRLAKYLAQCGIGSRREACRLIEAGRITLNGHIARHTDPIRLDESLNCLDSIELDGAPIT 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           K E    W+ +K +G      + D   T    L     R+  VGRLD ++ GLLLLTNDG
Sbjct: 61  KTETLAYWILNKAVGTDCRLLEQDE--TSLIRLLPKAPRLYPVGRLDKDSRGLLLLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS    + Y VR +     + +  +  G+  + +     QV   +       
Sbjct: 119 ELTHKLMHPSFAHSKTYHVRLNRPFTDEFVEQMASGVRYKDLQTLPCQVRRLSSDS---- 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             + L +G NR+I+++     +KV  L R++     L +L  G+ R ++ K +
Sbjct: 175 FEIVLTQGLNRQIRRMSSALGYKVIDLQRVALMTLTLKSLAEGAMRPLTPKEV 227


>gi|283471019|emb|CAQ50230.1| RNA pseudouridine synthase family protein [Staphylococcus aureus
           subsp. aureus ST398]
          Length = 231

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 54/228 (23%), Positives = 100/228 (43%), Gaps = 7/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E 
Sbjct: 1   MRIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDKISVRGELIEYVEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + +   D   ++ +          +  VGRLD +TEGLLL+TNDG    
Sbjct: 61  VYIMLNKPKGYI-SATEDHHSKTVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+    + Y V     + ++ +   K+G+ +         +T    + S     V 
Sbjct: 120 ELMSPNKHVSKKYEVISANPITEEDIQAFKEGVTLSDGKVKPAILTYIDNQTS----HVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           + EGK  ++K++F     +V  L RI     +L   L +G  R +++ 
Sbjct: 176 IYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYRLLTEN 223


>gi|197262149|ref|ZP_03162223.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|197240404|gb|EDY23024.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
          Length = 231

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 105/229 (45%), Gaps = 3/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G +++ AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +    Y     TL+        V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKYLTKPATLEVITP--VQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEEEI 227


>gi|260890235|ref|ZP_05901498.1| ribosomal small subunit pseudouridine synthase A [Leptotrichia
           hofstadii F0254]
 gi|260859855|gb|EEX74355.1| ribosomal small subunit pseudouridine synthase A [Leptotrichia
           hofstadii F0254]
          Length = 238

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 55/233 (23%), Positives = 107/233 (45%), Gaps = 5/233 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A +GI +R+EV+ ++  +++ VN   ++   + +    D ++ +   +     
Sbjct: 1   MRLDKFLANSGIGTRKEVKEILKNKKISVNDAFVKDGKIQIDEEKDIVKYEDNIIYYKPF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      +  T  +         N       +  VGRLDI+TEGLLLLTNDG L+ 
Sbjct: 61  VYIMMNKPAGVISATEDNHHRTVIDLLNDEYRTYDIFPVGRLDIDTEGLLLLTNDGILSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQ--KGSNAWV 189
            L  P     + Y V+    + ++ +  L+ GI + +       +V +     + +    
Sbjct: 121 NLLSPKKHVDKKYYVKISNPLTEEDIKTLENGIKLEENFVTKKAKVKIICNNSEKNENLA 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + + EGK  ++K++F+  N +V  L R+  G   L   L  G  RE++++ L
Sbjct: 181 YITISEGKFHQVKRMFKAVNNEVLYLKRVKMGSLSLDEKLKLGEYRELTEEEL 233


>gi|91975753|ref|YP_568412.1| pseudouridine synthase Rsu [Rhodopseudomonas palustris BisB5]
 gi|91682209|gb|ABE38511.1| Pseudouridine synthase, Rsu [Rhodopseudomonas palustris BisB5]
          Length = 795

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 137/321 (42%), Positives = 192/321 (59%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++KV+ARAG+ SRR+ E  I + RV VNG +++  A++V  +D I VDG PL + ER
Sbjct: 475 GDRIAKVVARAGLCSRRDAEAWIVEGRVAVNGRVIDSPALDVTYSDVITVDGKPLPERER 534

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TRL+LYHKP GL+TTH+DP+GR TVFDNLP    R+IS+GRLD NTEGLLLLTNDGGLAR
Sbjct: 535 TRLFLYHKPRGLMTTHADPEGRPTVFDNLPEDLPRLISIGRLDFNTEGLLLLTNDGGLAR 594

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            LELP T WLR YRVR HG+V Q +L+ L  G+ + G+ YG ++  L+  +G+N W+   
Sbjct: 595 ALELPETGWLRRYRVRAHGEVTQAQLDQLASGVEVDGVKYGPIEAKLERDQGANVWLVFA 654

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           +REGKNRE++ V      +VNRLIR+SYGPFQL  +  G   EV  ++LREQLG  +++ 
Sbjct: 655 IREGKNREVRNVLAHLGLEVNRLIRVSYGPFQLLEIEEGQVEEVKTRVLREQLGEKIIKL 714

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
           A+ +   P  S           ++       + K    +     ++ +        +   
Sbjct: 715 AEADFGGPSPSETRPKPRPGKPVAAEDGPAPKKKAVVKRGAVEDRKGRKVKVERTGSGDR 774

Query: 313 NVWMAKGIHSSFLSDSGQREE 333
           +             +   RE+
Sbjct: 775 DPSRGPARRYHGKREPAPRED 795



 Score = 40.9 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 17/141 (12%), Positives = 33/141 (23%), Gaps = 6/141 (4%)

Query: 219 SYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEV 278
            +G  + G    G  R  + +   ++      E  +     P    E           + 
Sbjct: 199 RFGDKKFGDKKFGEKRPYTPREGGDKRPYTPREGGEKRPYTPREGGEKRPYAAREGGEKR 258

Query: 279 PDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAK------GIHSSFLSDSGQRE 332
           P       +  S        K+  TP                    G   S     G  +
Sbjct: 259 PYTPRDGGEKRSYAPREGGDKRPYTPRGEGFRKDGERSRPTGDRPFGARPSRDGKFGGDK 318

Query: 333 ENHRRSPSFPSKRSLRRTSAK 353
           +  R +P    ++       +
Sbjct: 319 KFGRGAPDRGPRKDFGSRPDR 339


>gi|168242327|ref|ZP_02667259.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|194449422|ref|YP_002046277.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194407726|gb|ACF67945.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL476]
 gi|205338506|gb|EDZ25270.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
          Length = 231

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 104/229 (45%), Gaps = 3/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G +++ AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V    DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCATDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +    Y     TL+        V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKYLTKPATLEVITP--VQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEEEI 227


>gi|116250666|ref|YP_766504.1| ribosomal large subunit pseudouridine synthase B [Rhizobium
           leguminosarum bv. viciae 3841]
 gi|115255314|emb|CAK06389.1| putative ribosomal large subunit pseudouridine synthase B
           [Rhizobium leguminosarum bv. viciae 3841]
          Length = 701

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 173/331 (52%), Positives = 219/331 (66%), Gaps = 3/331 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R+SKV+ARAG+ASRR++ERMI + RV +NG +LE   VNV   D IEVDGVP+R 
Sbjct: 48  EAKAERISKVMARAGVASRRDIERMIMEGRVTLNGRVLETPVVNVTLADRIEVDGVPIRG 107

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ERTRLWLYHKP GLVTT++DP+GRSTVFDNLP    RV+S+GRLDINTEGLLLLTNDGG
Sbjct: 108 IERTRLWLYHKPAGLVTTNADPEGRSTVFDNLPEELPRVMSIGRLDINTEGLLLLTNDGG 167

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LAR LELP+T WLR YRVR HG++DQD L+ LK GI + G+ YG ++ TLD  +GSN W+
Sbjct: 168 LARALELPATGWLRRYRVRAHGEIDQDALDKLKDGIAVDGVLYGSIEATLDRTQGSNVWI 227

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           T+GLREGKNREIK V       VNRLIRISYGPFQLG L  G   EV  + LR+QLGP L
Sbjct: 228 TMGLREGKNREIKNVLGALGLDVNRLIRISYGPFQLGDLPEGHVVEVRGRTLRDQLGPRL 287

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
           +EEA+ N DAPIY++  +  +     +         +    ++  LS   +L T    R+
Sbjct: 288 IEEAKANFDAPIYNAAAVAAEEEAEPAAAERRERPRRDEDKRERALS---RLDTKRDDRH 344

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
             +     +        +  +R +   +  S
Sbjct: 345 GGARKEDDRRDGGRRDDERPKRPQPLGQRRS 375



 Score = 40.9 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 14/118 (11%), Positives = 28/118 (23%), Gaps = 4/118 (3%)

Query: 233 TREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
            RE   + +R    P   +E +       +       DR +       +     + S   
Sbjct: 430 VREEDGEWIRSSEEPRRKDEGEGFGRKRGFGDRPAREDRGSGDRPARGERPFGDRPSRGD 489

Query: 293 NGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                + +      R+         +   SS      +R    R     P +      
Sbjct: 490 RPFGDKPRGD----RKPRTDGDERPRAARSSAGDARSERPRGDRPFGDRPPRGDRPFG 543



 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 16/129 (12%), Positives = 26/129 (20%), Gaps = 12/129 (9%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE      R   G     +     D P        R       E P        ++  + 
Sbjct: 465 REDRGSGDRPARGERPFGDRPSRGDRPFGDKPRGDRKPRTDGDERPRAARSSAGDARSER 524

Query: 294 GLSKQKKLATPVH------------RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF 341
               +     P              R+         +   SS      +R  + R     
Sbjct: 525 PRGDRPFGDRPPRGDRPFGDKPRGDRKPRTDGDERPRAARSSAGEGRSERPRSDRPFGDR 584

Query: 342 PSKRSLRRT 350
           P +      
Sbjct: 585 PPRGDRPFG 593



 Score = 38.2 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 13/102 (12%), Positives = 23/102 (22%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               +      A   S+     +RP       D   R  +    K    ++ +       
Sbjct: 501 KPRTDGDERPRAARSSAGDARSERPRGDRPFGDRPPRGDRPFGDKPRGDRKPRTDGDERP 560

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           R   S+    +          G R     R      +   R 
Sbjct: 561 RAARSSAGEGRSERPRSDRPFGDRPPRGDRPFGDKPRADRRP 602



 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 9/112 (8%), Positives = 21/112 (18%), Gaps = 1/112 (0%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E        +       P        + R +       D       S    G S++ +  
Sbjct: 569 EGRSERPRSDRPFGDRPPRGDRPFGDKPRADRRPREDGDERPRAARSFAGEGRSERPRGE 628

Query: 303 TP-VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                + +                   G +  + +   + P           
Sbjct: 629 RSFGDKPSGDKPRGKGFAAKPGGTKPGGAKSFSGKPKGAKPGGDRPGGDRPA 680


>gi|313632172|gb|EFR99245.1| ribosomal small subunit pseudouridine synthase A [Listeria
           seeligeri FSL N1-067]
          Length = 233

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 97/231 (41%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SRREV+ ++    V VNG++ + +   V    D I V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRREVKPLLKSGSVVVNGVIQKDSKSQVNPEKDQITVHGNPVIYQEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T  +               +    VGRLD +TEGLL++TNDG LA 
Sbjct: 61  VYFMLHKPQNVVSATEDNLSETVIDLLAQEDTLTNPFPVGRLDKDTEGLLIITNDGTLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y  +  G V    +   + GI +          + +         + V
Sbjct: 121 NLLSPKKHIDKTYYAKIEGDVTATDVEAFRTGITLDDGYTCKPAHLEIMAPN----EIRV 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            ++EGK  ++K++F      V  L R+S G   L   L  G  R +++  L
Sbjct: 177 TIQEGKFHQVKRMFAATGKTVTYLKRLSMGKLMLDESLGLGEYRSLTEDEL 227


>gi|269795291|ref|YP_003314746.1| pseudouridine synthase family protein [Sanguibacter keddieii DSM
           10542]
 gi|269097476|gb|ACZ21912.1| pseudouridine synthase family protein [Sanguibacter keddieii DSM
           10542]
          Length = 263

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 77/232 (33%), Positives = 120/232 (51%), Gaps = 1/232 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R+ KV+A AG+ SRR  E +I   RV V+ + +    V +    + + VDG+ ++ 
Sbjct: 23  PDGVRLQKVLATAGLGSRRACENLITAGRVTVDDVPVHELGVRIDPDKNVVHVDGLRIQL 82

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                    +KP+G+V+T  DP+GR T+   +     R+  VGRLD ++EGLLLLTNDG 
Sbjct: 83  DMSLLTLALNKPLGVVSTMHDPEGRPTLAQFVADRPERLFHVGRLDADSEGLLLLTNDGE 142

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  P  +  + Y V+  G+V  +    L KGI ++       +  L       + +
Sbjct: 143 LANRLTHPKYKITKTYTVQVEGRVPANLGTTLLKGIELEDGVATVDKYRLVDATPQASLI 202

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V L EG+NR I+++FE   + V +L+R   GP +LG L  G  R + +  L
Sbjct: 203 EVELHEGRNRIIRRMFETAGYPVTQLVRTKIGPIRLGDLRQGRVRVIGQTEL 254


>gi|323496683|ref|ZP_08101734.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           sinaloensis DSM 21326]
 gi|323318265|gb|EGA71225.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           sinaloensis DSM 21326]
          Length = 233

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 51/230 (22%), Positives = 97/230 (42%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  A+R+E  ++I    V VN  + +  A  V     +E  G  ++K    
Sbjct: 1   MRLDKYLCDALGATRKEATKIIKSGDVTVNDAVQKSGAFKVTDECVVEWQGREIQKPGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+     + +     +  +            +   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLFKPDGFVCSHEDGFNQ-TAFALLDEVKMEDLHFAGRLDVDTTGLVLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     + +D      +GI ++      +   LD        V + +
Sbjct: 120 ITSPKHKCEKTYRVWLVDPIGEDYAEKFAQGIELRSEKEPTLPAQLDIVNQDENEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            EGK  ++K++F     KV  L R   G  +L  +L  G  R ++++ + 
Sbjct: 180 TEGKYHQVKRMFAALGNKVEHLHRERIGAIELDYSLEPGEYRFLTEEEID 229


>gi|282917013|ref|ZP_06324771.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus D139]
 gi|283770831|ref|ZP_06343723.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus H19]
 gi|282319500|gb|EFB49852.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus D139]
 gi|283460978|gb|EFC08068.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus H19]
 gi|302333417|gb|ADL23610.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus JKD6159]
          Length = 231

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 55/228 (24%), Positives = 100/228 (43%), Gaps = 7/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E 
Sbjct: 1   MRIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDKISVRGELIEYVEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + +   D   ++ +          +  VGRLD +TEGLLL+TNDG    
Sbjct: 61  VYIMLNKPKGYI-SATEDHHSKTVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+    + Y V     + +D +   K+G+ +         +T    + S     V 
Sbjct: 120 ELMSPNKHVSKKYEVISANPITEDDIQAFKEGVTLSDGKVKPAILTYIDNQTS----HVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           + EGK  ++K++F     +V  L RI     +L   L +G  R +++ 
Sbjct: 176 IYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYRLLTEN 223


>gi|59711487|ref|YP_204263.1| 16S rRNA pseudouridylate 516 synthase [Vibrio fischeri ES114]
 gi|197335138|ref|YP_002155642.1| ribosomal small subunit pseudouridine synthase A [Vibrio fischeri
           MJ11]
 gi|59479588|gb|AAW85375.1| 16S rRNA pseudouridylate 516 synthase [Vibrio fischeri ES114]
 gi|197316628|gb|ACH66075.1| ribosomal small subunit pseudouridine synthase A [Vibrio fischeri
           MJ11]
          Length = 234

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 53/235 (22%), Positives = 99/235 (42%), Gaps = 2/235 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +     A+R+E  R+I    V V+G+  +  +V V     +E DG  L+     
Sbjct: 1   MRLDKFLCETLGATRKEATRIIKSGTVTVDGVKTKVTSVKVTDDSTVEWDGRELKFHGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+     + +        S +         ++   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLFKPDGYVCSHEDSTHP-SALSLLDEVNLEKLHFAGRLDVDTTGLVLITDDGQWSHK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     +  D    L+ GI ++      M   ++        + + +
Sbjct: 120 ITSPKRKCAKTYRVWLADPIGADYAEKLEAGIQLKSEKDLTMPAVMEIVDEEEHELLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGP 247
            EGK  ++K++F     KV  L R   G   L  +L  G  R ++++ +    G 
Sbjct: 180 HEGKYHQVKRMFAALGNKVEGLHRAQIGGLGLDYSLEPGEYRYLTEEEVEAVFGE 234


>gi|160943235|ref|ZP_02090471.1| hypothetical protein FAEPRAM212_00721 [Faecalibacterium prausnitzii
           M21/2]
 gi|158445474|gb|EDP22477.1| hypothetical protein FAEPRAM212_00721 [Faecalibacterium prausnitzii
           M21/2]
          Length = 233

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 96/230 (41%), Gaps = 4/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R E + M+A+ RV+VNG + ++    +  TD + VDG  L   +  
Sbjct: 1   MRLDKYLAETAQCTRSEAKTMLAKGRVQVNGAVCKKGDTQLKDTDTVAVDGALLTYQKFV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L      +  +    D               +   GRLD  + G +LLT+DGG A  
Sbjct: 61  YLMLNKPEGVVSASTDKRDTTVVDLVGDAYPRRELFPAGRLDKTSTGFVLLTDDGGFAHD 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG-DMQVTLDTQKGSNAWVTVG 192
           +  P     + Y V     + Q+       G+ +         +VT  +  G    V V 
Sbjct: 121 ILSPRHHVSKTYTVTIDTPLTQEMCTGFAAGVTLADGTALSPAEVTALSPDGL--TVRVV 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           LR+G   +IK++F  +   VN L R + G   L   L  G  RE+S + +
Sbjct: 179 LRQGVYHQIKRMFGVYGAGVNALHREAIGGLALDAQLAPGQWRELSDEEV 228


>gi|134282285|ref|ZP_01768990.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 305]
 gi|134246323|gb|EBA46412.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 305]
          Length = 554

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 83/355 (23%), Positives = 145/355 (40%), Gaps = 8/355 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 173 KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 231

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 232 GKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNTE 291

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 292 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRIRD 351

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++ E     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 352 GGGEGTNHWYHVALAEGRNREVRRMLEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 411

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             +R  +    L+    +            R    + + +          +  +    ++
Sbjct: 412 AQVRRLMSTVGLKAPTEDKGG-KRGGPAERRQPDPMQTSMGFINREPVLTTHGQLDQPRR 470

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            +                A        S  G R+ +  R+ S+    + +R + K
Sbjct: 471 GRRGPAGGGFGAGLGGGYAGLPGYGGASRQGGRDVDGNRA-SYGGAGANKRGAGK 524


>gi|21673314|ref|NP_661379.1| ribosomal small subunit pseudouridine synthase A [Chlorobium
           tepidum TLS]
 gi|21646406|gb|AAM71721.1| ribosomal small subunit pseudouridine synthase A [Chlorobium
           tepidum TLS]
          Length = 247

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 64/241 (26%), Positives = 109/241 (45%), Gaps = 2/241 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVP 66
           Q      R++K +A  G+ASRR  ++++ + +V VNG + +     V    D + VDG  
Sbjct: 4   QVQEEKVRINKYLAMCGVASRRAADQLVLEGKVSVNGHIADEPGFKVDPRNDEVIVDGRL 63

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +   E  ++++       V T +  +       +   +  RV  VGRLD  + GLLLLTN
Sbjct: 64  MATPEARKVYILFNKPRNVITTNHDERDRQQILDFIDVPERVFPVGRLDRKSTGLLLLTN 123

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS+Q  + Y      +     L  L  G+ ++                  
Sbjct: 124 DGTLAHRLMHPSSQVQKEYLAALDAKFPPAMLQKLTGGMRLKDTGEKVSPCRAKILDDGM 183

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + + V + EGKN +++++F    ++V RL R++Y    LG L  G  R +S+  + +   
Sbjct: 184 SVL-VSIHEGKNHQVRRMFSTLGFEVKRLDRVAYAGLTLGELRRGEWRFLSRNEVEKLYR 242

Query: 247 P 247
            
Sbjct: 243 L 243


>gi|300716948|ref|YP_003741751.1| ribosomal large subunit pseudouridine synthase B [Erwinia
           billingiae Eb661]
 gi|299062784|emb|CAX59904.1| Ribosomal large subunit pseudouridine synthase B [Erwinia
           billingiae Eb661]
          Length = 315

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 94/318 (29%), Positives = 140/318 (44%), Gaps = 12/318 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM--STDHIEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E MI+  RV V+G L       V    +  I VDG  +  A
Sbjct: 2   SEKLQKVLARAGHGSRREIETMISAGRVSVDGKLAT-LGDRVDSSPSIKIRVDGHLVSVA 60

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E        L  Y     L T +      +          +R I+VGRLD+NT GLLL T
Sbjct: 61  ESTAEVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  G +D DK+  L +G+ ++        +     +G 
Sbjct: 121 TDGELANRLMHPSREVEREYAVRVFGAIDDDKIRQLSRGVQLEDGPASFKTLKFTGGEGI 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           N W TV L EG+NRE+++++E    +V+RLIR  YG  QL   L  G   E+    L   
Sbjct: 181 NQWYTVTLTEGRNREVRRLWESVGVQVSRLIRTRYGDIQLPKGLPRGGWTEL---ELAPT 237

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
                L +    + + +   +   R + N I       +++   S + +G +  K  A  
Sbjct: 238 NYLRELVDLPPEITSKVAVEKDRRRTKANQIRRAVKRHSQVAPGSRRPSGKASGKAAAAK 297

Query: 305 VHRRNLASNVWMAKGIHS 322
              ++ A           
Sbjct: 298 PAGKSSARTSGKPSAKRG 315


>gi|34762584|ref|ZP_00143579.1| Ribosomal small subunit pseudouridine synthase A [Fusobacterium
           nucleatum subsp. vincentii ATCC 49256]
 gi|237741688|ref|ZP_04572169.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           4_1_13]
 gi|256845012|ref|ZP_05550470.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           3_1_36A2]
 gi|294785701|ref|ZP_06750989.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           3_1_27]
 gi|27887750|gb|EAA24824.1| Ribosomal small subunit pseudouridine synthase A [Fusobacterium
           nucleatum subsp. vincentii ATCC 49256]
 gi|229429336|gb|EEO39548.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           4_1_13]
 gi|256718571|gb|EEU32126.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           3_1_36A2]
 gi|294487415|gb|EFG34777.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           3_1_27]
          Length = 226

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 67/229 (29%), Positives = 106/229 (46%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   GI SR+EV+++I+   + VNG+       N+    D IE +G  L   E 
Sbjct: 1   MRLDKFLVECGIGSRKEVKKLISNDEITVNGMSDILPKDNIDENSDIIEYNGERLEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +  K   +  T    +           I   +  VGRLD +TEGLLL TNDG L  
Sbjct: 61  RYYIMNKKAGYITATEDFKENTVMDLLPEWVIRKDLAPVGRLDKDTEGLLLFTNDGKLNH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VY V     +  + +  L++G+ I        +V    +K S+  + + 
Sbjct: 121 RLLSPKNHIDKVYYVEIENNILDEDILKLEQGVNIGNYITQPAKV----EKISDNKIYLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++EGK  ++KK+ E  N KV  L R+S+G   L  L  G  +EV+ + +
Sbjct: 177 IKEGKFHQVKKMLEAVNNKVCYLKRVSFGKLTLNDLTLGEVKEVNLEDI 225


>gi|322715286|gb|EFZ06857.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
          Length = 231

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 103/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G +++ AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKDLTKPATLEVI----TPVQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNCVVELHRERIGAITLDENLAPGEYRPLTEEEI 227


>gi|259907987|ref|YP_002648343.1| 16S rRNA pseudouridylate synthase A [Erwinia pyrifoliae Ep1/96]
 gi|224963609|emb|CAX55102.1| Ribosomal small subunit pseudouridine synthase A [Erwinia
           pyrifoliae Ep1/96]
 gi|283477874|emb|CAY73790.1| putative 16S pseudouridylate 516 synthase [Erwinia pyrifoliae DSM
           12163]
          Length = 234

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 54/229 (23%), Positives = 102/229 (44%), Gaps = 3/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I++    SR    R +  ++V V+G ++   A  + +   +E DG  L +    
Sbjct: 1   MRLDKFISQQLEVSRAIAARELRARKVTVDGEVVREGAYKLSADSTVEYDGNVLEQQLGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP+G V +  DPD  + ++        R+ + GRLD +T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPVGYVCSTDDPDHPTILYFLEEPGAYRLHAAGRLDNDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D       G+ +           L+  + +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESAISDDNAQQFADGVQLHNEKTLTKPAMLEVIEPN--VVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G  +L   L  G  R +S + +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVGLHRERIGAIRLDSDLQPGEYRPLSAEEI 227


>gi|268591199|ref|ZP_06125420.1| ribosomal small subunit pseudouridine synthase A [Providencia
           rettgeri DSM 1131]
 gi|291313360|gb|EFE53813.1| ribosomal small subunit pseudouridine synthase A [Providencia
           rettgeri DSM 1131]
          Length = 235

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 56/238 (23%), Positives = 105/238 (44%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +    V V+  +++  A  V     +  DG  L +    
Sbjct: 1   MRLDKFLSQQLGISRSLVARELRAGLVTVDDEIVKSGAFQVTIDHEVAYDGNVLVQVTGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G + +  DP   + +F     +  ++ S GRLDI+T GL+LLT+DG  +  
Sbjct: 61  RYFMLHKPQGYICSTDDPTHPTILFFIDEPLAQKLHSAGRLDIDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + YRV+    +  D      +G+++ G        ++ + + +     V +
Sbjct: 121 ITSPKHHCEKTYRVQLSDDIANDVAEQFAQGVMLNGEKYLTKPAKLEIISPRD----VRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
            + EG+  ++K++F      V  L R   G   L   L  G  R ++++ +     P 
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVCGLHRERVGEIWLDETLEPGEYRPLTEEEINSINVPR 234


>gi|116513179|ref|YP_812086.1| ribosomal small subunit pseudouridine synthase A [Lactococcus
           lactis subsp. cremoris SK11]
 gi|116108833|gb|ABJ73973.1| ribosomal small subunit pseudouridine synthase A [Lactococcus
           lactis subsp. cremoris SK11]
          Length = 242

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 62/239 (25%), Positives = 102/239 (42%), Gaps = 9/239 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
            R+ K +A +G+ SR EV+ ++ + RV V G +       V      +  DG  L   E 
Sbjct: 1   MRLDKFLAESGLGSRSEVKVLLKKGRVTVAGEIQRDGRFQVDKNSRQVAFDGQILDYQEY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  +         +       +  VGRLD NTEGLL+L+NDG L  
Sbjct: 61  YYYLLNKPQGVVSATKDNVFKTVVQLLSEKDFRKDIFPVGRLDKNTEGLLILSNDGALGH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT------QKGS 185
            L  P     + Y  R  G+V  + +N   +G+ ++ G      ++ ++       Q G 
Sbjct: 121 DLTQPKKHVEKEYFARIDGKVTDEIINKFAEGLTLKNGEKARPGELFVEKTYKGDSQSGW 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
            + + V + EGK  ++K++FE     V  L RI  G   L   L  G+ R ++ + +  
Sbjct: 181 VSEIRVIIHEGKFHQVKRMFEAVEMYVLYLKRIRMGNLALDSDLALGAYRPLTIEEIEN 239


>gi|116491036|ref|YP_810580.1| ribosomal large subunit pseudouridine synthase B [Oenococcus oeni
           PSU-1]
 gi|116091761|gb|ABJ56915.1| ribosomal large subunit pseudouridine synthase B [Oenococcus oeni
           PSU-1]
          Length = 237

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 76/231 (32%), Positives = 117/231 (50%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA+AG+ASRR+ E MI   +VKVNG ++ +    V S D + VD   + +    
Sbjct: 5   ERLQKRIAQAGVASRRKAEEMIVNGQVKVNGKIITKLGKKVSSDDIVYVDNKKINEESFE 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      + +  S P+  S +   L    +R+ SVGRLD +T G+LLLTNDG L + 
Sbjct: 65  YYLLNKPAGYVSSNRSYPNQPSVIE--LIKTKTRIFSVGRLDQDTTGVLLLTNDGELTQK 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD--MQVTLDTQKGSNAWVTV 191
           L  P  +  R Y     G V++D++  L K I   G  Y     ++    QK   + + +
Sbjct: 123 LTHPKHRIKRTYAAWVKGIVNEDEIEQLTKPIRFDGEIYFPQAARILKVDQKRQESLIEI 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EGKN EIKK+ +F    V +L R  +    +G L  G  R +S++ + 
Sbjct: 183 TIAEGKNHEIKKILDFIGHPVIKLNRDMFDGITIGNLKKGQHRALSEQEVE 233


>gi|326791990|ref|YP_004309811.1| pseudouridine synthase Rsu [Clostridium lentocellum DSM 5427]
 gi|326542754|gb|ADZ84613.1| pseudouridine synthase Rsu [Clostridium lentocellum DSM 5427]
          Length = 240

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 63/230 (27%), Positives = 109/230 (47%), Gaps = 9/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+++  GI SR +  ++I   RVKVNG L       V  TD I +D  P+++ ER 
Sbjct: 1   MRINKLLSNKGICSRSQAHQLIVAGRVKVNGQLC-IPGQWVEETDEILLDDRPVKEKERL 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L      + T                +  + +  VGRLD +++GL+LLTNDG LA  
Sbjct: 60  YIILNKPVGIVCTAAEGV---KDNIIRYMNYPAYLFPVGRLDKDSQGLILLTNDGDLASD 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           +        + Y V+     ++D L+ + +G+ +  G+     QV+   +        + 
Sbjct: 117 ILEAEKGHEKEYMVQVDRPYEEDFLHKMSQGVNLGDGVITRICQVSAINED----TFRII 172

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++ + F + V RL RI      LG L  G  R+++   + 
Sbjct: 173 LTQGMNRQIRRMTKAFGYNVVRLERIRLLNIALGPLAYGEWRKLTNLEVE 222


>gi|33861215|ref|NP_892776.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Prochlorococcus marinus subsp. pastoris str.
           CCMP1986]
 gi|33639947|emb|CAE19117.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Prochlorococcus marinus subsp. pastoris str.
           CCMP1986]
          Length = 240

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 55/236 (23%), Positives = 104/236 (44%), Gaps = 11/236 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---KAE 71
           R++K ++  G  SRR  + +I + +V +NG +       V   D +EV+G  +    K E
Sbjct: 4   RINKYLSEVGYCSRRVADSLIEEGKVTINGEIP-EMGTKVEEGDQVEVEGQRIEKSMKHE 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  L        + TT    +  + +        +R+  +GRLD  +EGL+ LTNDG + 
Sbjct: 63  KIYLVFNKPVGIVCTTDRRVESDNIIDFI--KYPTRIFPIGRLDKPSEGLIFLTNDGDIV 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V  +  +++D +  +  G+ I G    +       ++       +
Sbjct: 121 NKILRARNNHEKEYIVSVNRPINRDFIQSMSNGVEILGTITKNC----FVKQLGPKKFRI 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            L +G NR+I+++ E   ++V  L R+     +L  +  G  RE +K+ L E    
Sbjct: 177 ILTQGLNRQIRRMCESLGFRVKSLKRVRIMNIKL-DVSIGEYREFTKEELFELNKL 231


>gi|327394528|dbj|BAK11950.1| ribosomal small subunit pseudouridine synthase A RsuA [Pantoea
           ananatis AJ13355]
          Length = 239

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 103/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I++    SR    R I  QRV VNG ++   A  +     +E DG  L+     
Sbjct: 1   MRLDKFISQQLEISRAIAAREIRGQRVTVNGDVVRDTAFKLQPDHEVEYDGNVLQMQTGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + V+     +  ++ + GRLDI+T GL+LLT+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTIVYFIEEPMAFKLHAAGRLDIDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + YRV     V  D       G+ +          Q+ +     +   V +
Sbjct: 121 ITSPRHHCEKTYRVTLEAPVSDDTAAQFSAGVQLHNEKSLTKPAQLEVI----TPTEVLL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            L EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TLSEGRYHQVKRMFAAVGNRVVGLHRERIGEIVLDEALEPGEYRLLTEEEI 227


>gi|295676258|ref|YP_003604782.1| pseudouridine synthase [Burkholderia sp. CCGE1002]
 gi|295436101|gb|ADG15271.1| pseudouridine synthase [Burkholderia sp. CCGE1002]
          Length = 589

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 85/356 (23%), Positives = 145/356 (40%), Gaps = 10/356 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRR++E +I   RV VNG         +M TD + ++
Sbjct: 188 KRVLSPDDDAPKLHKVLAEAGMGSRRDMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 246

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 247 GKPVKRKLASKPPRVLLYHKPTGEIVSHADPEGRPSVFDKLPPMKTAKWVAVGRLDFNTE 306

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ ++      +++  
Sbjct: 307 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELAEGMRQKLLHGVELEDGPANFLRIRD 366

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+  
Sbjct: 367 GGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPISLPRGLKRGRWEELED 426

Query: 239 KILR---EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
             +R     +G     E + + +A     +                     +   Q  G 
Sbjct: 427 NQVRALMASVGLKAPTEERGSRNAAPERRQPDPMQTSMGFINREPVLMSHSRFEQQPRGQ 486

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
            ++                + A   + +     G R+ +  R+PS    R+     
Sbjct: 487 GRRGAAGGGFGAGMGGGAGFGAGAGNRAPGGQRG-RDVDGNRAPSPNGNRARTGGK 541


>gi|91793104|ref|YP_562755.1| 23S rRNA pseudouridine synthase F [Shewanella denitrificans OS217]
 gi|91715106|gb|ABE55032.1| ribosomal large subunit pseudouridine synthase F [Shewanella
           denitrificans OS217]
          Length = 309

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 58/294 (19%), Positives = 116/294 (39%), Gaps = 5/294 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRR+ +R + Q  V +NG   +     V   D ++V+G  +  
Sbjct: 2   TDSAIRLNKYISESGICSRRDADRYVEQGNVFINGRRAQV-GDLVSIGDKVKVNGQDIEP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   L        +    +          +  +  SR+  +GRLD +++GL+ LTN+G 
Sbjct: 61  RDAENLVFIALNKPVGIVSTTEGSERDNIVDFVNHSSRIFPIGRLDKDSQGLIFLTNNGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  +  D +  +  G+ I G+           ++ S    
Sbjct: 121 LVNKILRAGNNHDKEYVVTVNKPITDDFIKGMGAGVPILGVVTKKC----VVEQVSPFAF 176

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F ++V +L R       L  L  G  R++ K+ L        
Sbjct: 177 KIVLVQGLNRQIRRMCEYFGFEVTKLERQQIMNVSLKGLPIGEWRDLDKQELDVLFDMIK 236

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
              ++    A     +   +           +       S++  G +K +    
Sbjct: 237 DSSSEDKNAAAKKKPKPKPKVASLRDKIEGPEHFMQHNRSTKHKGQAKGQPKGQ 290


>gi|226199665|ref|ZP_03795218.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei Pakistan 9]
 gi|225928251|gb|EEH24285.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei Pakistan 9]
          Length = 554

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 84/355 (23%), Positives = 146/355 (41%), Gaps = 8/355 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 173 KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 231

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 232 GKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNTE 291

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 292 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQRLLHGVELDDGPANFLRIRD 351

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 352 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 411

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             +R  +    L+    +            R    + + +          +  +    ++
Sbjct: 412 AQVRRLMSTVGLKAPTEDKGG-KRGGPAERRQPDPMQTSMGFINREPVLTTHGQLDQPRR 470

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            +                A        S  G R+ +  R+ S+    + +R + K
Sbjct: 471 GRRGPAGGGFGAGLGGGYAGLPGYGGASRQGGRDVDGNRA-SYGGAGANKRGAGK 524


>gi|221214882|ref|ZP_03587850.1| RNA pseudouridine synthase family protein [Burkholderia multivorans
           CGD1]
 gi|221165109|gb|EED97587.1| RNA pseudouridine synthase family protein [Burkholderia multivorans
           CGD1]
          Length = 554

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 83/341 (24%), Positives = 141/341 (41%), Gaps = 8/341 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 170 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRI 228

Query: 63  DGVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           +G P+++         L  +     +V+        S      P   ++ ++VGRLD NT
Sbjct: 229 NGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNT 288

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLL+LT  G LA     P     R Y VR  G++ +     L  GI +       +++ 
Sbjct: 289 EGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSESARQKLLHGIELDDGPANFLRIR 348

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
               +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ 
Sbjct: 349 DGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELD 408

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +  +R+ +    L+                 R +P+ +       +R    ++       
Sbjct: 409 EAQVRKLMATVGLKAPSEEKGKRGGGQ--AERRQPDPMQTSMGFISREPVLTTHGQLDQP 466

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS 338
           ++            S                G+  + +R S
Sbjct: 467 RRGGRRGGPGLPGLSGYGSLPVASGYGNRAGGRDVDGNRAS 507


>gi|294782467|ref|ZP_06747793.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           1_1_41FAA]
 gi|294481108|gb|EFG28883.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           1_1_41FAA]
          Length = 234

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 72/231 (31%), Positives = 129/231 (55%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--RKAE 71
            R++K ++  GIASRR +++ I + R+KVNG +     ++V   D I +D   +  ++ E
Sbjct: 1   MRINKFLSSLGIASRRAIDKYIEEGRIKVNGAIP-SIGIDVNEDDEIYIDNKKIETKRIE 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               ++ +KP+ +++  SD  GR TV D + +       +GRLD  T GL+LLTNDG L 
Sbjct: 60  EKVYFILNKPLEVLSASSDDRGRRTVVDLIKTDKRI-FPIGRLDYMTSGLILLTNDGELF 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P ++  + Y ++  G+V ++++  LKKG++++       +V+      +   + +
Sbjct: 119 NRLVHPKSEIYKKYYIKVFGEVKKEEIEELKKGVLLEDGKTLPAKVSGIKYDKNKTSMYI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +REG+NR+I+++ E F +KV  L R   G   LG L  G  RE++K+ + 
Sbjct: 179 SIREGRNRQIRRMIEKFGYKVLMLRREKIGELSLGDLKEGKYRELTKEEIE 229


>gi|237741726|ref|ZP_04572207.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           4_1_13]
 gi|294785660|ref|ZP_06750948.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           3_1_27]
 gi|229429374|gb|EEO39586.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           4_1_13]
 gi|294487374|gb|EFG34736.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           3_1_27]
          Length = 234

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 70/231 (30%), Positives = 129/231 (55%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAE 71
            R++K ++  GIASRR +++ I + R+ VNG       +++   D+I +DG  ++    E
Sbjct: 1   MRINKFLSTLGIASRRTIDKYIEEGRITVNGNTAIT-GMDISENDNIFIDGEKIKTNIDE 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +   ++ +KP+ ++++ SD  GR TV D + +       VGRLD  T GL+LLTNDG L 
Sbjct: 60  KKVYFMLNKPLEVLSSSSDNRGRKTVVDLIKTDKRI-FPVGRLDYMTSGLILLTNDGELF 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P ++  + Y V+  G++ ++++  LKKG+++        +++      +   + +
Sbjct: 119 NRIVHPKSEIYKKYYVKILGEIKKEEIEELKKGVLLDDSKTLPAKISGIKYDKNKTSMYI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +REG+NR+I+++ E F +KV  L R   G   LG L  G  RE++K+ + 
Sbjct: 179 SIREGRNRQIRRMIEKFGYKVLMLRREKIGELSLGDLPEGKYRELTKQEVE 229


>gi|254495132|ref|ZP_05108056.1| pseudouridylate synthase [Polaribacter sp. MED152]
 gi|85819482|gb|EAQ40639.1| pseudouridylate synthase [Polaribacter sp. MED152]
          Length = 282

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 63/236 (26%), Positives = 106/236 (44%), Gaps = 1/236 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++K IA +G+ SRRE +  I    VKVNG L+      V   D ++ DG  +   ++
Sbjct: 48  GIRLNKYIANSGVCSRREADTYIEHGSVKVNGKLVTEMGYKVQPDDVVQFDGTSITPEQK 107

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + T   D   ++ +     +   R+  VGRLD NT GLLL TNDG LA+
Sbjct: 108 RYILLNKPKNYITTMDDDRGRKTVMDLVSNASKERIYPVGRLDRNTTGLLLFTNDGDLAK 167

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     ++Y      ++D   L  L+  ++I+G     +             + + 
Sbjct: 168 KLTHPKHNVRKLYHASLDRKLDLKDLEKLRGEVIIEGRKV-FIDAVSYVDGQPKTEIGIE 226

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +  G+NR ++K+FE   +KVN+L R+ +       L  G  R ++ + +       
Sbjct: 227 IHSGRNRIVRKIFEHVGYKVNKLDRVIFAELTKKNLPRGRWRALTNQEVSNLQMMK 282


>gi|315644423|ref|ZP_07897556.1| pseudouridine synthase [Paenibacillus vortex V453]
 gi|315280173|gb|EFU43466.1| pseudouridine synthase [Paenibacillus vortex V453]
          Length = 233

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 64/233 (27%), Positives = 113/233 (48%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+  G  SRRE ++++   +V +NG++           D + + G PL+  ++ 
Sbjct: 1   MRINKFISETGYCSRREADKLVESGKVTINGVVA-VLGSQAEEGDDVRIQGRPLQDKKKH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+ +T            +      R+  +GRLD ++EGL+LLTNDG +   
Sbjct: 60  VYIALYKPVGITSTTELHI--KGNIVDFVGHKERIFPIGRLDKDSEGLILLTNDGDIVNK 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +    L  +  G+ I G      +VT      S     + L
Sbjct: 118 ILRSEGKHEKEYIVTVDRPLTDTFLRGMSSGVKILGEMTLPCEVTRM----SERVFRIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            EGKNR+I+++   F ++V +L RI     +LG+   GS R++++K  RE+LG
Sbjct: 174 TEGKNRQIRRMCSAFGYEVRKLQRIRIMNIRLGSQRVGSWRDLNEKE-REELG 225


>gi|330502861|ref|YP_004379730.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           mendocina NK-01]
 gi|328917147|gb|AEB57978.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           mendocina NK-01]
          Length = 385

 Score =  168 bits (424), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 91/374 (24%), Positives = 141/374 (37%), Gaps = 29/374 (7%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           Q     +++ KV+AR G+ASRRE+E  IA+ RVKVNG         V + D I +DG  L
Sbjct: 6   QPRPAGEKLQKVLARLGLASRREIETWIAEGRVKVNGAAAT-LGQRVDANDAIALDGRLL 64

Query: 68  RKAERT-----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           ++ E T      L        + T        +           R I++GRLDINT GLL
Sbjct: 65  KREEITGSVRRVLIYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLDINTTGLL 124

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT- 181
           L T DG LA  L  PS Q  R Y VR  G+V ++ L  LK G++++        +     
Sbjct: 125 LFTTDGELANRLMHPSYQMDREYAVRVRGEVTEEMLENLKTGVMLEDGPAKFTDIKEAPG 184

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTRE----- 235
            +G N W    + EG+NRE+++++E     V+RL R+ +GP  L   L     RE     
Sbjct: 185 GEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLTSELTMARWREMDQRE 244

Query: 236 ---------VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
                    ++ + L         +  ++   +         R       E   D  R  
Sbjct: 245 VDILSAEVGLTPQALPAMKEKTREKLDRLQRKSAKPVEVRGKRVLRPAKDEAGADSARPS 304

Query: 287 KNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREE-------NHRRSP 339
           +   +     +  +           +            +     R           +  P
Sbjct: 305 RAPRRDEAEQRTPRGPRKEGGERRENGRGTPVAERPGDVKKRQPRPAVELSERPARKPRP 364

Query: 340 SFPSKRSLRRTSAK 353
           + P KR       +
Sbjct: 365 ASPGKRPPSGDGQR 378


>gi|325520892|gb|EGC99873.1| ribosomal large subunit pseudouridine synthase B [Burkholderia sp.
           TJI49]
          Length = 328

 Score =  168 bits (424), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 77/274 (28%), Positives = 126/274 (45%), Gaps = 6/274 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 38  NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRI 96

Query: 63  DGVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           +G P+++         L  +     +V+        S      P   ++ ++VGRLD NT
Sbjct: 97  NGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNT 156

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++ 
Sbjct: 157 EGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELTEASRQKLLHGVELDDGPANFLRIR 216

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
               +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ 
Sbjct: 217 DGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELE 276

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDR 271
           +  +R+ +    L+            +E    D 
Sbjct: 277 EAQVRKLMATVGLKAPSEEKGRRGGETERRQPDP 310


>gi|167761342|ref|ZP_02433469.1| hypothetical protein CLOSCI_03750 [Clostridium scindens ATCC 35704]
 gi|167661008|gb|EDS05138.1| hypothetical protein CLOSCI_03750 [Clostridium scindens ATCC 35704]
          Length = 247

 Score =  168 bits (424), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 64/243 (26%), Positives = 117/243 (48%), Gaps = 5/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K ++ AG+ SRRE +R+I   +V V+G       + V     ++V    +R     
Sbjct: 2   VRLNKYLSDAGVCSRREADRLIESGQVSVDGQRA-VPGMKVADGQEVKVGKKVIRSNTEK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +   +KP G+V T    + ++ +         RV   GRLD ++EGLL++TNDG L   
Sbjct: 61  IVLAVNKPAGIVCTEDVREKKNIIRYL--KYPIRVTYAGRLDKDSEGLLIMTNDGDLING 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--DMQVTLDTQKGSNAWVTV 191
           +        + Y+V  +  V QD ++ +K+GI I                +K      ++
Sbjct: 119 MMRARHGHEKEYKVTVNKPVTQDFISKMKEGIRIVDKEKRLDVATRPCKAEKLGKYTFSI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ E   +KV RL+R+     +LG+L  G+ R+++++ L+E        
Sbjct: 179 TLTQGLNRQIRRMCEALGYKVERLVRVRIMNIELGSLKPGAYRKLTEQELKELYEQVKES 238

Query: 252 EAQ 254
           +  
Sbjct: 239 QNA 241


>gi|324117539|gb|EGC11445.1| RNA pseudouridylate synthase [Escherichia coli E1167]
          Length = 299

 Score =  168 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 88/298 (29%), Positives = 132/298 (44%), Gaps = 10/298 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEV 62
           K  ++ +   +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +
Sbjct: 2   KATLKGSSMSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRI 61

Query: 63  DGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           DG  +   E        L  Y     L T +      +          +R I+VGRLD+N
Sbjct: 62  DGHLISVRESAEQICRVLVYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVN 121

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLL T DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +
Sbjct: 122 TCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTI 181

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+
Sbjct: 182 KFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTEL 241

Query: 237 S---KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
                  LRE +       ++V ++      +     R            R    ++ 
Sbjct: 242 DLAQTNYLRELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGGRRSGGRNNG 299


>gi|311279823|ref|YP_003942054.1| pseudouridine synthase [Enterobacter cloacae SCF1]
 gi|308749018|gb|ADO48770.1| pseudouridine synthase [Enterobacter cloacae SCF1]
          Length = 299

 Score =  168 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 87/301 (28%), Positives = 135/301 (44%), Gaps = 10/301 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E MI   RV V+G +      V +     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESMIEAGRVSVDGKIATLGDRVEITPGLKIRIDGHLISVKE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SVEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD +K+  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDNKVRELARGVQLEDGPAAFKTIKFTGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+    L +  
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELD---LAQTN 238

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
               L E +   ++ +   +   R + N I       +++    ++  G     + +   
Sbjct: 239 YLRELVELKPETESKVAVEKDRRRMKANQIRRAVKRHSQVNSKPARSTGRRASSRNSGSG 298

Query: 306 H 306
            
Sbjct: 299 S 299


>gi|167745885|ref|ZP_02418012.1| hypothetical protein ANACAC_00579 [Anaerostipes caccae DSM 14662]
 gi|317470613|ref|ZP_07929999.1| RNA pseudouridylate synthase [Anaerostipes sp. 3_2_56FAA]
 gi|167654749|gb|EDR98878.1| hypothetical protein ANACAC_00579 [Anaerostipes caccae DSM 14662]
 gi|316901904|gb|EFV23832.1| RNA pseudouridylate synthase [Anaerostipes sp. 3_2_56FAA]
          Length = 242

 Score =  168 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 60/232 (25%), Positives = 119/232 (51%), Gaps = 5/232 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K +++AG+ SRR+ +  + Q +V V+G         V     +  +G P+R  
Sbjct: 6   NSAVRINKFLSQAGLCSRRQADFYVEQGKVTVDGKTA-EPGTKVCEGQEVCFNGKPVRMD 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            +T    Y+KP G+V T S  +  + +        SR+  VGRLD +++GL+LLTNDG  
Sbjct: 65  TQTVYLAYNKPKGIVCTSSKEEANNIIDAV--GYPSRIYPVGRLDKDSQGLILLTNDGEA 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +        + Y V  + ++  D +  ++ G+ +  +     + T+  +   +    
Sbjct: 123 ANEIMKARNYHEKEYEVTVNKRITNDFIQGMRNGVPLSELDTVTRKCTVKKEGPDS--FR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + L +G NR+I+++ E+F ++V +L R+     +LG L  GS R+++ + ++
Sbjct: 181 IILTQGLNRQIRRMCEYFGYRVTKLRRVRVMNIRLGNLKEGSYRKLTPEEIK 232


>gi|163789367|ref|ZP_02183806.1| ribosomal small subunit pseudouridine synthase A [Carnobacterium
           sp. AT7]
 gi|159875221|gb|EDP69286.1| ribosomal small subunit pseudouridine synthase A [Carnobacterium
           sp. AT7]
          Length = 239

 Score =  168 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 69/231 (29%), Positives = 107/231 (46%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++   G  SRR V+R++  ++V+VNG  +   ++NV      + V GVP+     
Sbjct: 1   MRLDKLLFETGFGSRRTVKRLLKSKQVQVNGQTIMVDSLNVDPQLQEVTVAGVPIDYQPH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +       +               +  VGRLD +TEGLLLLTN+G L  
Sbjct: 61  VYYMLHKPAGVVSAVSDAVNQTVIDLIEPSQRVPGLFPVGRLDKDTEGLLLLTNNGQLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L +P  +  + Y V  + +V  D       GIV  G       Q+T+ +Q  + + V +
Sbjct: 121 QLLIPKKEVTKCYEVVVNERVTDDDQLAFTAGIVFDGGVICKPAQLTILSQSDTESRVLL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++KK+F     KV  L R+S GP QL   L  GS R +  + L
Sbjct: 181 EISEGKFHQVKKMFLSVGKKVIYLKRLSMGPLQLDKTLSLGSYRPLHAEEL 231


>gi|293391815|ref|ZP_06636149.1| ribosomal small subunit pseudouridine synthase A [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290952349|gb|EFE02468.1| ribosomal small subunit pseudouridine synthase A [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 233

 Score =  168 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 103/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R +  + + Q  V +NG + +  A  V   D I  DG  L   +  
Sbjct: 1   MRLDKFLAEHTGLTRSQATKALRQSAVTINGKIEKSGATKVSPQDAIYFDGELLTWLDVG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +  +++KP G V +H + +  S        + +R+ S GRLDI+T GL+LLT+DG  +  
Sbjct: 61  QYLMFNKPQGYVCSHDEDEHPSIYQFFDYPLSARLHSAGRLDIDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+ +      +GI+++G         + +      N  V +
Sbjct: 121 VTSPKHHQPKTYLVTLADPVEANYAQACAEGILLRGEKDPTKPAVLEIL----DNYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EG+  ++K++F     KV  L R   G   L   L  G  R ++ + +
Sbjct: 177 TISEGRYHQVKRMFAALGNKVLGLHRWKIGNLTLDDNLAEGDFRVLNAEEI 227


>gi|242374043|ref|ZP_04819617.1| pseudouridylate synthase [Staphylococcus epidermidis M23864:W1]
 gi|242348249|gb|EES39851.1| pseudouridylate synthase [Staphylococcus epidermidis M23864:W1]
          Length = 230

 Score =  168 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 55/228 (24%), Positives = 104/228 (45%), Gaps = 7/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V+VN   ++    ++    DH+ V+G  +   E 
Sbjct: 1   MRIDKFLANMGVGTRNEVKQLLKKGAVEVNDKKIKTPKTHINPNEDHVTVNGSTISYIEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      +++   D   ++ +          +  VGRLD +TEGLLLLTNDG    
Sbjct: 61  VYIMLNKPKG-VISATEDDSHKTVIDLIPEYSHLGIFPVGRLDKDTEGLLLLTNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+    + Y V     + Q  +   + G+ +        ++     KG++    V 
Sbjct: 120 ELMNPNKHVSKTYEVVSKYPIKQADIEAFESGVELSDGKVKPAKLI----KGNDHLSYVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           + EGK  ++K++F     +V  L RI     +L  +L  G  R ++++
Sbjct: 176 IYEGKYHQVKRMFHSIENEVLELKRIKIANLELDQSLNDGEFRFLNEQ 223


>gi|331091189|ref|ZP_08340030.1| hypothetical protein HMPREF9477_00673 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330404636|gb|EGG84175.1| hypothetical protein HMPREF9477_00673 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 234

 Score =  168 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 108/234 (46%), Gaps = 3/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +    + SR EV++ I Q R+ V+G    +    +   +  + VD   +     
Sbjct: 2   MRLDKYLCEMNVGSRSEVKKYIRQGRITVDGKTAVKPEEKIDEHSQKVCVDSRVIGYEAF 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               LY     +V+  +D   ++ +          +  VGRLD +TEGLLL+TNDG +A 
Sbjct: 62  EYYMLYKPSG-VVSATTDRKEKTVLDLIEEKKRKDLFPVGRLDKDTEGLLLITNDGEMAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VY  +  G+V + ++ +  +G+ I    Y         ++G+ + + + 
Sbjct: 121 RLLSPKKHVDKVYYAKIDGKVTEREVQIFSEGLSIGNDEYAKPSALKILKEGNISEIELT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
           ++EGK  ++K++F     +V  L RIS G   L   L  G  R +++K + +  
Sbjct: 181 IQEGKFHQVKRMFHAVGMEVIYLKRISMGNLVLDESLKKGEYRRLTEKEVEQLC 234


>gi|325261871|ref|ZP_08128609.1| ribosomal large subunit pseudouridine synthase F [Clostridium sp.
           D5]
 gi|324033325|gb|EGB94602.1| ribosomal large subunit pseudouridine synthase F [Clostridium sp.
           D5]
          Length = 256

 Score =  168 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 109/233 (46%), Gaps = 7/233 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
              P R++K ++ AG+ SRRE +R+I   +VKV+G       + V     + +    + +
Sbjct: 12  KKEPVRLNKYLSEAGVCSRREADRLIESGKVKVDGK-AAGMGMKVSPGQEVRIGRKIVSR 70

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +E   +   +KP G+V T    +          +   RV  VGRLD ++ GLLL+TN+G 
Sbjct: 71  SEEMIVLAVNKPAGIVCTEETRE--RKSIVRFLNYPVRVTYVGRLDKDSRGLLLMTNNGD 128

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +     +  + Y+V     +  + L  +  G+ I G      +V    QK      
Sbjct: 129 IINKMMRAGNRHEKEYKVTVDKALTPEFLEKMSSGVAILGTVTRPCRV----QKIGKYTF 184

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           T+ L +G NR+I+++ E   ++V  L+R      +LG L  G  R+++ K L 
Sbjct: 185 TIILTQGLNRQIRRMCEVLGYEVKDLVRTRIMNIELGKLKEGEYRKLTDKELD 237


>gi|262038781|ref|ZP_06012135.1| ribosomal large subunit pseudouridine synthase B [Leptotrichia
           goodfellowii F0264]
 gi|261747192|gb|EEY34677.1| ribosomal large subunit pseudouridine synthase B [Leptotrichia
           goodfellowii F0264]
          Length = 228

 Score =  168 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 63/228 (27%), Positives = 114/228 (50%), Gaps = 6/228 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K +A AG+ SRR+ + MI + RV VN        + + S D + VDG  ++     
Sbjct: 1   MRLNKYMADAGVCSRRKADEMIKEGRVTVN-KKEAVLGMEISSGDIVRVDGEKIKLNTVY 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP  ++ ++ D  GR    D + S      + GRLD  TEGL++++NDG +   
Sbjct: 60  EYYMLNKPKRVICSNEDRFGRRLAIDYIKSKKRL-FTYGRLDYMTEGLIIISNDGEVYNH 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y  +   +V++  +   K G+VI G      +V    +K     + + +
Sbjct: 119 VMHPRKKLYKSYIAKLSREVEEKDMEAWKHGVVIDGKRTAPAKV----KKIDKKEIRIAI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            EG+NR+I+K+ E   + V  L R+  G   LG L  G  R ++++ +
Sbjct: 175 FEGRNRQIRKMVEILGYTVESLKRVKVGELTLGYLQPGDYRALTEEEV 222


>gi|238917131|ref|YP_002930648.1| ribosomal large subunit pseudouridine synthase F [Eubacterium
           eligens ATCC 27750]
 gi|238872491|gb|ACR72201.1| ribosomal large subunit pseudouridine synthase F [Eubacterium
           eligens ATCC 27750]
          Length = 244

 Score =  168 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 102/231 (44%), Gaps = 7/231 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +R++K ++  GI SRRE +RMI + R+ ++G +       V     I VDG  +  +  
Sbjct: 10  SERINKYLSAHGICSRREADRMIQEGRITIDGRIAA-MGEMVDDNTIICVDGRKVDNSTP 68

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            ++ +       +   +          +      R+  VGRLD  ++GL+LLTNDG +  
Sbjct: 69  PQVVIAFNKPVGIVCTTTDKQGKNNIVDFIGYKERIYPVGRLDKESDGLILLTNDGDMMD 128

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKGSNAWVT 190
            L        + Y V  +  +++D +  +  GI ++               +K S+    
Sbjct: 129 RLLRSVNGHEKEYIVSVNKPINKDFIKRMSGGIYLKELDRTTRKC----VVEKISDRTFR 184

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + L +G NR+I+++     + V +L RI     +LG L  G  RE+  K L
Sbjct: 185 IILTQGLNRQIRRMCAECGYSVTKLTRIRIMNVELGDLKTGEYRELDGKEL 235


>gi|91200876|emb|CAJ73931.1| conserved hypothetical protein [Candidatus Kuenenia
           stuttgartiensis]
          Length = 260

 Score =  168 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 65/259 (25%), Positives = 119/259 (45%), Gaps = 2/259 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV+A AGI SRRE E +I   RV V+G  +      V +    I  DG+P+R   +
Sbjct: 3   ERLQKVLASAGIGSRRECENVILAGRVTVDGERVTALGATVDAGKSVIYCDGMPIRPEAK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      L T + + +      D + ++  R+ ++GRLD  +EGL+++TNDG L+ 
Sbjct: 63  IYYLLNKPKDCLCTNYDELNRLR-AIDIIKNVKQRLYTIGRLDKQSEGLIIITNDGELSN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + Y +   G +  + +  L+ G+ +       +++    +    +   + 
Sbjct: 122 KLSHPKYEVNKTYFIEIDGYLSNETITALQSGVWLAFGKTQPVRIKKMHRSFKKSRFEMI 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L EGKNREI+++      KV  L RI  G      L  G  R+++++ ++        + 
Sbjct: 182 LCEGKNREIRRMLADHGHKVRTLRRIKIGSLCDPDLKVGKYRKLTEQEIKSLYSMTEKKP 241

Query: 253 AQVNLDAPIYSSETLVRDR 271
            +       Y + T  + +
Sbjct: 242 IEKKSGKQRYDTVTASKKK 260


>gi|118586875|ref|ZP_01544309.1| ribosomal pseudouridine synthase B, large subunit [Oenococcus oeni
           ATCC BAA-1163]
 gi|118432707|gb|EAV39439.1| ribosomal pseudouridine synthase B, large subunit [Oenococcus oeni
           ATCC BAA-1163]
          Length = 237

 Score =  168 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 76/231 (32%), Positives = 116/231 (50%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA+AG+ASRR+ E MI   +VKVNG ++ +    V S D + VD   + +    
Sbjct: 5   ERLQKRIAQAGVASRRKAEEMIVNGQVKVNGKIITKLGKKVSSDDIVYVDNKKINEESFE 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      + +  S P+  S +   L    +R+ SVGRLD +T G+LLLTNDG L + 
Sbjct: 65  YYLLNKPAGYVSSNRSYPNQPSVIE--LIKTKTRIFSVGRLDQDTTGVLLLTNDGELTQK 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD--MQVTLDTQKGSNAWVTV 191
           L  P  +  R Y     G V++D+L  L K I   G  Y     ++    QK   + + +
Sbjct: 123 LTHPKHRIKRTYAAWVKGIVNEDELEQLTKPIRFDGEIYFPQAARILKVDQKRQESLIEI 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EGK  EIKK+ +F    V +L R  +    +G L  G  R +S++ + 
Sbjct: 183 TIAEGKTHEIKKILDFIGHPVIKLNRDMFDGITIGNLKKGQYRALSEQEVE 233


>gi|127513903|ref|YP_001095100.1| pseudouridine synthase [Shewanella loihica PV-4]
 gi|126639198|gb|ABO24841.1| ribosomal small subunit pseudouridine synthase A [Shewanella
           loihica PV-4]
          Length = 230

 Score =  168 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 47/231 (20%), Positives = 97/231 (41%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I+ +   +R   ++ + +  V V+G +++  +  +  +  + +DG P+      
Sbjct: 1   MRLDKFISESTQLTRSLAKKALHRGEVTVDGQVIKDGSFKLNESQQVCLDGEPISLI-GP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + HKP   + +  D    S +          +   GRLD +T GL+L+T+DG  +  
Sbjct: 60  RFIMLHKPADTLCSTVDEVYPSVLNLLDLPHKEDLHIAGRLDADTTGLVLITSDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y V+    +  + +     G+ +  +        + L      +    +
Sbjct: 120 VTSPKRECGKTYLVQLADPLKAEWVEQFATGLALRSEEGLTKPATLELL----GSHEARL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R S G   L   L  G  R +++  +
Sbjct: 176 TITEGKYHQVKRMFAAVGNKVVGLHRESVGEIVLDESLAPGEWRYLTEAEI 226


>gi|46445794|ref|YP_007159.1| putative ribosomal large chain pseudouridine synthase B [Candidatus
           Protochlamydia amoebophila UWE25]
 gi|46399435|emb|CAF22884.1| putative ribosomal large chain pseudouridine synthase B [Candidatus
           Protochlamydia amoebophila UWE25]
          Length = 234

 Score =  168 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 68/230 (29%), Positives = 111/230 (48%), Gaps = 5/230 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
              R+SKV+A AGIASRR  E +I Q  VKVNG +++     V    D I V    + + 
Sbjct: 2   ETNRLSKVLAAAGIASRRACEELIFQGLVKVNGEVIKVPQTKVNPEIDTITVRDEVINRK 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E    +L +KP G + +         + D       R+ +VGRLD +T+GLL++TNDG  
Sbjct: 62  EDKVYYLLNKPPGYICSARKSGQTKIILDLFQDEDHRLFTVGRLDKDTQGLLIVTNDGHF 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +  PS    + Y  +   ++  + L  +  G +++G+    ++V    +      + 
Sbjct: 122 ANQIIHPSANIQKEYLAKTDQEISHEHLIAIANGTLVEGVFVKPIRVQKVRKG----TIK 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           + + EGK RE++ +      KV  L RI  G   LG L  G+ R +++  
Sbjct: 178 IIIGEGKKREVRMLLSAAGLKVQELTRIRLGGLHLGRLPIGNWRPLTETE 227


>gi|289167140|ref|YP_003445407.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           mitis B6]
 gi|288906705|emb|CBJ21539.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           mitis B6]
          Length = 240

 Score =  168 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 62/234 (26%), Positives = 101/234 (43%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKSGRVTVNGKKEKSAKLQIDEERDEIRFDGQVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    V  VGRLDI+T GLLLLTNDG LA 
Sbjct: 61  VYYMMNKPKGVISATEDPKHRTVLDLLDDIARSKEVFPVGRLDIDTHGLLLLTNDGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVT 190
            L  P     + Y  +  G + Q+      KGI ++       ++ L +     + + + 
Sbjct: 121 ALLSPKRHVDKTYLAQVKGIMTQEDAETFAKGIPLKDFTCQPARLELVSVDTKKNQSQIR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K+ L +
Sbjct: 181 VTIAEGKFHQVKRMVGYCGKEVVDLQRLTMGTLVLDENLQRGEWRRLTKEELED 234


>gi|303249716|ref|ZP_07335920.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|307251902|ref|ZP_07533803.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|302651283|gb|EFL81435.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|306860594|gb|EFM92606.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
          Length = 230

 Score =  168 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 106/232 (45%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  R +    V VNG L +  +V +  TD I  +G  L   +  
Sbjct: 1   MRLDKFIAENTGLTRSQAARALKSGLVTVNGKLEKSGSVKIGDTDEICYEGERLEWVDEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ +KP G V +H D +  +        + +++ + GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYFMLYKPQGYVCSHDDGEYPTVFQFFGYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+      L +GI+++G        ++ +      +  V +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEDFYAKKLAEGILLRGEREPCLPAKMEVI----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EG+  ++K++F     KV  L R   G   L   L  G  R +S++ + 
Sbjct: 177 TISEGRYHQVKRMFAALGNKVEALHRWRIGDVVLDENLEEGEYRPLSEQEVE 228


>gi|218779269|ref|YP_002430587.1| pseudouridine synthase [Desulfatibacillum alkenivorans AK-01]
 gi|218760653|gb|ACL03119.1| pseudouridine synthase [Desulfatibacillum alkenivorans AK-01]
          Length = 234

 Score =  168 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 70/231 (30%), Positives = 121/231 (52%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +A AG+ SRR  E +I+Q +V VNG ++ +  V +    D I V+G  +   + 
Sbjct: 4   ERLQKYLAHAGVCSRRHAEELISQGKVAVNGEIVTQMGVKIDPDKDEIAVNGKKVEPKQS 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G +TT         +  +L  +  R+  +GRLD N+ GLLLLT+DG +  
Sbjct: 64  RTYIMLNKPAGYLTT--CKQPGRKIVLDLIDLPQRLFPIGRLDNNSTGLLLLTDDGRIHH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS    + Y V          L+ +++G++++G      +V    + G  +  T+ 
Sbjct: 122 RLSHPSFDHEKEYEVETVKDAPDQALDAMRRGMILEGKKTRPAKVK---RTGPRS-FTIV 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           L+EG+NR+I+K+ E    KV RL R+     +LG L +G  R +++K ++ 
Sbjct: 178 LKEGRNRQIRKMVELTKNKVKRLHRVRMSTIRLGGLPSGKWRRLNEKEIQA 228


>gi|83720156|ref|YP_443084.1| RNA pseudouridylate synthase family protein [Burkholderia
           thailandensis E264]
 gi|83653981|gb|ABC38044.1| RNA pseudouridylate synthase family protein [Burkholderia
           thailandensis E264]
          Length = 502

 Score =  168 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 82/357 (22%), Positives = 142/357 (39%), Gaps = 9/357 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 122 KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 180

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 181 GKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNTE 240

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 241 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRIRD 300

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 301 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 360

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             +R  +    L+           ++E   R    + + +          +  +    ++
Sbjct: 361 AQVRRLMSTVGLKAPVEEKGKRGGAAE--RRQPDPMQTSMGFINREPVLTTHGQLDQPRR 418

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP-SFPSKRSLRRTSAKK 354
            +                A           G R+ +  R+P               +
Sbjct: 419 GRRGPAGGGFGAGLGGGYAGLPGYGGAPRQGGRDVDGNRAPHGGAGANKRGAGKGAR 475


>gi|27366125|ref|NP_761653.1| ribosomal small subunit pseudouridine synthase A [Vibrio vulnificus
           CMCP6]
 gi|37679610|ref|NP_934219.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio vulnificus
           YJ016]
 gi|34098531|sp|Q8D8X2|RSUA_VIBVU RecName: Full=Ribosomal small subunit pseudouridine synthase A;
           AltName: Full=16S pseudouridine 516 synthase; AltName:
           Full=16S pseudouridylate 516 synthase; AltName:
           Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|27362325|gb|AAO11180.1| Ribosomal small subunit pseudouridine synthase A [Vibrio vulnificus
           CMCP6]
 gi|37198354|dbj|BAC94190.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio vulnificus
           YJ016]
          Length = 233

 Score =  168 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 52/232 (22%), Positives = 98/232 (42%), Gaps = 6/232 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  A+R+E  +++    V VN  + +  AV V     +E  G  L      
Sbjct: 1   MRLDKFLCDALGATRKEATKILKSGEVTVNEQVQKSGAVKVTEECVVEWQGRELAMQGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + LY     + +     +  +            +   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLYKPEGFVCSHEDGFNH-TAFVLLDEVKMDELHFAGRLDVDTTGLVLITDDGKWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + YRV     +  D    L +G+ ++         Q+T+     +   V +
Sbjct: 120 ITSPKHKCDKTYRVWLADPIGSDYAEKLAEGVQLRNEKELTLPAQMTIVNADEN--EVLL 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            + EGK  ++K++F     KV +L R   G  +L   L  G  R ++++ + 
Sbjct: 178 TIHEGKYHQVKRMFAALGNKVEQLHRERIGAIELDESLEPGEYRYLTQEEID 229


>gi|320104277|ref|YP_004179868.1| pseudouridine synthase [Isosphaera pallida ATCC 43644]
 gi|319751559|gb|ADV63319.1| pseudouridine synthase [Isosphaera pallida ATCC 43644]
          Length = 655

 Score =  168 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 98/341 (28%), Positives = 146/341 (42%), Gaps = 3/341 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVP 66
           + +  PQR+ K++A AGIASRR  E +I Q RV VNG  +             I +DG P
Sbjct: 120 EPSDQPQRLQKILAHAGIASRRACEELILQGRVTVNGETVRELGARYNPYESKIAIDGEP 179

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           ++  E+   +  +KP G + ++ DPD R  V D LP I  RV ++GRLD  + GL+LLTN
Sbjct: 180 IKL-EKLVYFAVNKPKGYICSNEDPDNRPRVVDLLPEIPQRVYTIGRLDEASTGLILLTN 238

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  P     + Y V   G  D+D L  L  G+ +        +V    ++G +
Sbjct: 239 DGELANKLTHPKFGVEKRYEVVVAGHPDRDVLRKLIDGVWLSDGKVRAKKVRELGRRGDS 298

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + + + L EGKNREI+++      KV  L R++ GP  L  L  G  R +    +     
Sbjct: 299 SILELVLAEGKNREIRRMLARLGHKVMSLTRVAVGPITLKGLRTGEVRVLGTAEVDRLKQ 358

Query: 247 PHLLEEAQVN-LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                      LD+   SS    RDR    S    D +R      +  G ++    +   
Sbjct: 359 IARNPFPPTESLDSDAGSSAPAQRDRDYDRSAKRSDLSRRSAPGFRLGGGNRFGGGSNRP 418

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
             R + +         S    +            + P  R 
Sbjct: 419 LGRPVYTPGNEPPEDRSDRRPNRLGGGNRFGEGGNRPLGRP 459


>gi|291536368|emb|CBL09480.1| ribosomal large subunit pseudouridine synthase F [Roseburia
           intestinalis M50/1]
 gi|291538762|emb|CBL11873.1| ribosomal large subunit pseudouridine synthase F [Roseburia
           intestinalis XB6B4]
          Length = 251

 Score =  168 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 64/257 (24%), Positives = 115/257 (44%), Gaps = 9/257 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R++K ++ AG+ SRRE +R +    V ++G++       V+    +   G P++K 
Sbjct: 2   QEPVRINKYLSEAGVCSRREADRQVEAGNVTIDGVVA-SMGAKVLPDQTVLFCGKPVKKE 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L  +HKP G+V T    +  + V     +   R+  +GRLD ++EGLLL+TN+G +
Sbjct: 61  EEMILLAFHKPTGIVCTAEKREKNNVVDYI--NYPKRIYPIGRLDKDSEGLLLMTNNGDI 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAW 188
              +        + Y V  +  V    L  L  G+ +          +V           
Sbjct: 119 VNRIMRAGNMHEKEYIVTVNKPVTDSFLRGLAGGVPLVELNATTRKCKVW----GIGKRQ 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E+F ++V +L+R      +LG L AG+ REV+ +  +E +   
Sbjct: 175 FGIILTQGLNRQIRRMCEYFGYRVEKLVRTRIMNIELGDLKAGTYREVTPQEYKELMRLV 234

Query: 249 LLEEAQVNLDAPIYSSE 265
                   +        
Sbjct: 235 KDSSNTTVIHGRDGGDR 251


>gi|145224079|ref|YP_001134757.1| pseudouridine synthase [Mycobacterium gilvum PYR-GCK]
 gi|315444416|ref|YP_004077295.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium sp.
           Spyr1]
 gi|145216565|gb|ABP45969.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           gilvum PYR-GCK]
 gi|315262719|gb|ADT99460.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium sp.
           Spyr1]
          Length = 247

 Score =  168 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 74/239 (30%), Positives = 109/239 (45%), Gaps = 4/239 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPL 67
            +    R+ KV+++AGIASRR  E+MI   RV+V+  ++      V      I VDG  +
Sbjct: 2   TDNDGVRLQKVLSQAGIASRRVAEKMIRDGRVEVDDRIVTELGTRVDPAESVIRVDGARI 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLL 124
              +       +KP G+ +T SD  GR  V D +            VGRLD +TEGLLLL
Sbjct: 62  TVDDTLVHLAINKPRGMHSTMSDDRGRPCVGDLVEHRVRGNKKLFHVGRLDADTEGLLLL 121

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG LA  L  PS +  + Y     G V +     L++G+ +           L     
Sbjct: 122 TNDGELAHRLMHPSYEVPKSYVATVLGSVPRGLGRKLREGVELDDGPVQVDDFALVDTTP 181

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
               V V L EG+   ++++     + V  L+R   G   LG    GS R +++K + E
Sbjct: 182 GRTLVRVTLHEGRKHIVRRLLAEVGFPVQNLVRTDIGGVSLGDQRPGSIRALTQKEIGE 240


>gi|328957900|ref|YP_004375286.1| uncharacterized RNA pseudouridine synthase YtzG [Carnobacterium sp.
           17-4]
 gi|328674224|gb|AEB30270.1| uncharacterized RNA pseudouridine synthase YtzG [Carnobacterium sp.
           17-4]
          Length = 239

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 106/231 (45%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++   G  SRR V+R+I  ++V+VNG++     +NV      + V G  +R    
Sbjct: 1   MRLDKLLFETGFGSRRTVKRLIKSKQVQVNGLIALVDNLNVDPQLQEVIVSGELIRFQPH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +       +               +  VGRLD +TEGLLLLTN+G L  
Sbjct: 61  VYYMLHKPAGVVSAVSDVLNQTVIDLIEPSQRVPGLFPVGRLDKDTEGLLLLTNNGQLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L +P  + ++ Y    + +V  +       GIV  G       ++T+ ++  + + V +
Sbjct: 121 QLLIPKKEVIKCYEAVVNERVTSEDQFAFASGIVFNGGVKCKPAKLTILSESDAESKVLL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++KK+F     KV  L R+S GP QL   L  GS R +  + L
Sbjct: 181 EISEGKFHQVKKMFLSVGKKVIYLKRLSMGPLQLDKTLPLGSYRALHSEEL 231


>gi|197301581|ref|ZP_03166654.1| hypothetical protein RUMLAC_00307 [Ruminococcus lactaris ATCC
           29176]
 gi|197299311|gb|EDY33838.1| hypothetical protein RUMLAC_00307 [Ruminococcus lactaris ATCC
           29176]
          Length = 266

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 56/263 (21%), Positives = 113/263 (42%), Gaps = 7/263 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +   P R++K ++ AG+ SRRE +R+I   +V V+G       + +     ++V    + 
Sbjct: 11  QKKEPVRLNKYLSEAGVCSRREADRLIETGKVSVDGKRA-GMGMKIYPGQTVKVGNKTVS 69

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + +   +   +KP G+V T    +          +   RV  +GRLD ++ GLLL+TN+G
Sbjct: 70  RQDEMIVLAVNKPKGIVCTEERRE--RDSIVRFLNYPVRVTYIGRLDKDSRGLLLMTNNG 127

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +   +    + Y+V    ++ +D L  + +G+ I        +V    +K     
Sbjct: 128 DIINKIMRAANYHEKEYKVTVDHEITEDFLKKMSRGVAILDTVTRPCKV----EKLGKYT 183

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E   ++V  L+R+      L  L  G  R+++ + L E     
Sbjct: 184 FKIILTQGLNRQIRRMCEALGYEVKDLLRVRVMNITLDGLKEGKYRKLTDRELNELDQLL 243

Query: 249 LLEEAQVNLDAPIYSSETLVRDR 271
               +           +     +
Sbjct: 244 EQSSSLPGGRESRQERKDGAGKK 266


>gi|167551196|ref|ZP_02344951.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|168466080|ref|ZP_02699950.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|205353355|ref|YP_002227156.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|207857656|ref|YP_002244307.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|195631355|gb|EDX49915.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|205273136|emb|CAR38093.1| ribosomal small subunit pseudouridine synthase [Salmonella enterica
           subsp. enterica serovar Gallinarum str. 287/91]
 gi|205324100|gb|EDZ11939.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|206709459|emb|CAR33800.1| ribosomal small subunit pseudouridine synthase [Salmonella enterica
           subsp. enterica serovar Enteritidis str. P125109]
 gi|326628444|gb|EGE34787.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Gallinarum str. 9]
          Length = 231

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 105/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G +++ AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D +    KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTVAQFAKGVQLHNEKDLTKPATLEVI----TPVQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEEEI 227


>gi|161524931|ref|YP_001579943.1| pseudouridine synthase [Burkholderia multivorans ATCC 17616]
 gi|189350319|ref|YP_001945947.1| ribosomal large subunit pseudouridine synthase B [Burkholderia
           multivorans ATCC 17616]
 gi|160342360|gb|ABX15446.1| pseudouridine synthase [Burkholderia multivorans ATCC 17616]
 gi|189334341|dbj|BAG43411.1| ribosomal large subunit pseudouridine synthase B [Burkholderia
           multivorans ATCC 17616]
          Length = 554

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 83/341 (24%), Positives = 141/341 (41%), Gaps = 8/341 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 170 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRI 228

Query: 63  DGVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           +G P+++         L  +     +V+        S      P   ++ ++VGRLD NT
Sbjct: 229 NGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNT 288

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLL+LT  G LA     P     R Y VR  G++ +     L  GI +       +++ 
Sbjct: 289 EGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSESARQKLLHGIELDDGPANFLRIR 348

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
               +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ 
Sbjct: 349 DGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELD 408

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +  +R+ +    L+                 R +P+ +       +R    ++       
Sbjct: 409 EAQVRKLMATVGLKAPSEEKGKRGGGQ--AERRQPDPMQTSMGFISREPVLTTHGQLDQP 466

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS 338
           ++            S                G+  + +R S
Sbjct: 467 RRGGRRGGPGLPGLSGYGSLPVASGYGNRAGGRDVDGNRAS 507


>gi|293604235|ref|ZP_06686643.1| pseudouridine synthase [Achromobacter piechaudii ATCC 43553]
 gi|292817460|gb|EFF76533.1| pseudouridine synthase [Achromobacter piechaudii ATCC 43553]
          Length = 614

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 81/356 (22%), Positives = 131/356 (36%), Gaps = 12/356 (3%)

Query: 1   MKDK--NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M+ +    +  +    ++ KV+A AGI SRRE+E +I   RV VNG         V   D
Sbjct: 100 MEQRLGKYLNSDSVMPKLHKVLADAGIGSRREMEELIVAGRVSVNGEPA-HIGQRVAPND 158

Query: 59  HIEVDGVPL----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
            + V+G P+     K     +  +     +V+        S           + +SVGRL
Sbjct: 159 QVRVNGKPIMRTNTKKPPRVILYHKPAGEIVSHDDPGGRASVFARLPKLRTGKWLSVGRL 218

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D+NTEGLL+ T  G +A  +  P     R Y VR  G++D+ +   L  GI ++      
Sbjct: 219 DLNTEGLLIFTTSGDMANRIMHPRYGTEREYAVRVLGEMDEAQRQSLVDGIELEDGVAAF 278

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
             +      GSN W  V L+EG+NRE++++FE     V+RLIR  +G   L  TL  G  
Sbjct: 279 GALDYLGGDGSNRWYRVTLQEGRNREVRRMFEAVGVTVSRLIRTRFGDVVLPRTLRRGRW 338

Query: 234 REVSKKILREQLG----PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
            E+   ++   +         +E+  N               P   +   +     +   
Sbjct: 339 EELDGSLVTALMVQLGLLRDDDESGGNRRRSKQPVSHDSALPPGFGTMDRNGMNGARIGR 398

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
             K    +           +      +      +             R    P   
Sbjct: 399 RGKLQGGRVGSAGQAAACPSDPFGTGLMIAGGYANGHPLASEGAGGNRKGGKPGGD 454


>gi|237737269|ref|ZP_04567750.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium
           mortiferum ATCC 9817]
 gi|229421131|gb|EEO36178.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium
           mortiferum ATCC 9817]
          Length = 230

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 111/232 (47%), Gaps = 5/232 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R+ K +   G+ SRREV++++   +++VN I+++    N+  + D IE DG  L  
Sbjct: 2   EDKMRLDKFLTECGLGSRREVKKLLDNGKIRVNDIIVKNPQANIKESIDKIEYDGNKLEY 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E     +  K   +  T    +           I   +  VGRLD +TEGLLL TNDG 
Sbjct: 62  KEFRYYIMNKKGGYITATEDPKEKTVMELLPEWVIKKDLAPVGRLDKDTEGLLLFTNDGK 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     + Y  +   ++ + ++  L++G+ I G      +  +  +K     +
Sbjct: 122 LGHSLLSPKKHVDKTYYAKLEKEIGEVEIKKLEEGVDIGGYITQPAKAKIVGEK----EI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + +REGK  ++KK+ E  N KV  L R+++G  +L  +  G  RE++ + +
Sbjct: 178 ELTIREGKFHQVKKMLEAVNNKVVYLKRVTFGKLELKDMELGEVREINLEDI 229


>gi|218553820|ref|YP_002386733.1| 23S rRNA pseudouridylate synthase B [Escherichia coli IAI1]
 gi|218694839|ref|YP_002402506.1| 23S rRNA pseudouridylate synthase B [Escherichia coli 55989]
 gi|218351571|emb|CAU97283.1| 23S rRNA pseudouridylate synthase [Escherichia coli 55989]
 gi|218360588|emb|CAQ98146.1| 23S rRNA pseudouridylate synthase [Escherichia coli IAI1]
 gi|323947451|gb|EGB43455.1| RNA pseudouridylate synthase [Escherichia coli H120]
          Length = 299

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 88/298 (29%), Positives = 132/298 (44%), Gaps = 10/298 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEV 62
           K  ++ +   +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +
Sbjct: 2   KATLKGSSMSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRI 61

Query: 63  DGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           DG  +   E        L  Y     L T +      +          +R I+VGRLD+N
Sbjct: 62  DGHLISVRESAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVN 121

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLL T DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +
Sbjct: 122 TCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTI 181

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+
Sbjct: 182 KFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTEL 241

Query: 237 S---KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
                  LRE +       ++V ++      +     R            R    ++ 
Sbjct: 242 DLAQTNYLRELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGGRRSGGRNNG 299


>gi|62185473|ref|YP_220258.1| putative 16S pseudouridine synthase [Chlamydophila abortus S26/3]
 gi|62148540|emb|CAH64311.1| putative 16S pseudouridine synthase [Chlamydophila abortus S26/3]
          Length = 232

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 67/229 (29%), Positives = 105/229 (45%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R++K +A +G+ASRR+ + +I    V VNG +     V V   TD ++VDG  +   ++
Sbjct: 4   IRLNKFLASSGVASRRKCDEIIFSGHVTVNGRVAPGPFVLVDEETDTVKVDGRRVGMTKK 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               ++     L ++     G   V D    +  RV +VGRLD  T GL+L+TNDG  + 
Sbjct: 64  VYFMVHKPLGYLCSSERTFPGDKLVIDLFSHLPYRVFTVGRLDKETSGLILVTNDGEFSN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  PS    + Y ++    V    L  L +G VI G         +  +K     + + 
Sbjct: 124 KIIHPSFGITKEYLLKVSRDVTAKNLEDLMEGTVIDGKRVRP----VSVEKIRRGTLKII 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGK  EI+   E     +  L RI  G F LG L  G  RE++   +
Sbjct: 180 VNEGKKHEIRLFAEAAGLPILELSRIRIGSFVLGGLRYGEYRELTDAEI 228


>gi|259046491|ref|ZP_05736892.1| ribosomal small subunit pseudouridine synthase A [Granulicatella
           adiacens ATCC 49175]
 gi|259036656|gb|EEW37911.1| ribosomal small subunit pseudouridine synthase A [Granulicatella
           adiacens ATCC 49175]
          Length = 238

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 109/230 (47%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV+ ++  +++ VNG ++    V V   TD I  DG  ++  E 
Sbjct: 1   MRIDKCLADCGLGTRSEVKSLLKSKKITVNGKVVTNGKVQVNPETDEILFDGEKIQYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      +  T  +         N       V  VGRLDI+T GLLLLTNDG LA 
Sbjct: 61  VYIMMNKPKGVVSATEDNLHKTVLDLINPLYFKKGVFPVGRLDIDTHGLLLLTNDGELAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     ++Y+ R  G +  +     ++GIV+  G      ++ + +     + V +
Sbjct: 121 RLLSPKKHVTKIYQARVEGVMTPEDAAAFERGIVLSDGTECMPARLDILSTTQDESIVQI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
            L+EGK  ++K++ +     V  L R++ G  +L   L  G +R ++++ 
Sbjct: 181 HLKEGKFHQVKRMVKACGKNVVDLQRLTMGTLKLDERLALGESRPLTEEE 230


>gi|292493543|ref|YP_003528982.1| RNA-binding S4 domain protein [Nitrosococcus halophilus Nc4]
 gi|291582138|gb|ADE16595.1| RNA-binding S4 domain protein [Nitrosococcus halophilus Nc4]
          Length = 266

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 84/252 (33%), Positives = 125/252 (49%), Gaps = 7/252 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-----R 68
           +R+ K++AR G+ SRRE+E  I   RV+VNG+  +     V   D + +DG P+     +
Sbjct: 3   ERLQKILARGGLGSRREIEAWIKAGRVRVNGVPAQ-LGDKVSVKDRVTIDGRPISPKRLQ 61

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 +  +     + +        +           R ISVGRLDINT GLLLLT DG
Sbjct: 62  PPSSQVIIYHKPAGEVCSRKDPEGRPNVFQSLPRPQQGRWISVGRLDINTSGLLLLTTDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PSTQ  R Y VR  G V +D +  L+ G+ ++       Q+     +G+N W
Sbjct: 122 ELANRLMHPSTQVEREYAVRVLGTVAEDVIERLQGGVTLEDGLARFEQILDAGGEGANHW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
             V LREG+NRE+++++E    +V+RLIRI +GP +L   L  G  R + +  L+  L  
Sbjct: 182 YHVILREGRNREVRRLWESQGVRVSRLIRIRFGPIRLPPGLRLGRWRFLERPELKALLEA 241

Query: 248 HLLEEAQVNLDA 259
             +E        
Sbjct: 242 AGMEPRPTQSRP 253


>gi|259908330|ref|YP_002648686.1| 23S rRNA pseudouridylate synthase B [Erwinia pyrifoliae Ep1/96]
 gi|224963952|emb|CAX55457.1| Ribosomal large subunit pseudouridine synthase B [Erwinia
           pyrifoliae Ep1/96]
 gi|283478269|emb|CAY74185.1| ribosomal large subunit pseudouridine synthase B [Erwinia
           pyrifoliae DSM 12163]
          Length = 295

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 89/295 (30%), Positives = 128/295 (43%), Gaps = 12/295 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E MI+  RV V+G L       V       I +DG  +  +
Sbjct: 2   SEKLQKVLARAGHGSRREIETMISAGRVSVDGKLAT-LGDRVEPGASLKIRIDGHVVPVS 60

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E        L  Y     L T        +          +R I+VGRLD+NT GLLL T
Sbjct: 61  ESISEVCRVLAYYKPEGELCTRSDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  G VD +K+ LL +G+ ++        +     +G 
Sbjct: 121 TDGELANRLMHPSREVEREYAVRVFGAVDDEKIKLLSRGVQLEDGPAAFKTLKFTGGEGI 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKIL 241
           N W  V L EG+NRE+++++E    +V+RLIRI YG   L   L  G   E+       L
Sbjct: 181 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRIRYGDIDLPKGLPRGGWTELDLSPTNYL 240

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           RE +G      ++V ++     ++     R                    K    
Sbjct: 241 RELVGLAPETVSKVPVEKDRRRTKANQIRRAVKRHTTTKVSKPGSGRRPSKRQQG 295


>gi|16761163|ref|NP_456780.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. CT18]
 gi|16765551|ref|NP_461166.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|29141142|ref|NP_804484.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|161613070|ref|YP_001587035.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|168229594|ref|ZP_02654652.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
 gi|168236410|ref|ZP_02661468.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           SL480]
 gi|168818048|ref|ZP_02830048.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|194446350|ref|YP_002041497.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194469360|ref|ZP_03075344.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|194737206|ref|YP_002115312.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|197249585|ref|YP_002147195.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|198241888|ref|YP_002216306.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|204929076|ref|ZP_03220219.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|213023702|ref|ZP_03338149.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
 gi|213052312|ref|ZP_03345190.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
 gi|213424223|ref|ZP_03357082.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E02-1180]
 gi|213581650|ref|ZP_03363476.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-0664]
 gi|213646821|ref|ZP_03376874.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. J185]
 gi|224583280|ref|YP_002637078.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|238913797|ref|ZP_04657634.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Tennessee str. CDC07-0191]
 gi|54039570|sp|P65841|RSUA_SALTI RecName: Full=Ribosomal small subunit pseudouridine synthase A;
           AltName: Full=16S pseudouridine 516 synthase; AltName:
           Full=16S pseudouridylate 516 synthase; AltName:
           Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|54042084|sp|P65840|RSUA_SALTY RecName: Full=Ribosomal small subunit pseudouridine synthase A;
           AltName: Full=16S pseudouridine 516 synthase; AltName:
           Full=16S pseudouridylate 516 synthase; AltName:
           Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|25324010|pir||AG0785 pseudouridylate synthase (EC 4.2.1.70) - Salmonella enterica subsp.
           enterica serovar Typhi (strain CT18)
 gi|16420760|gb|AAL21125.1| 16S rRNA pseudouridylate 516 synthase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|16503461|emb|CAD02605.1| ribosomal small subunit pseudouridine synthase [Salmonella enterica
           subsp. enterica serovar Typhi]
 gi|29136768|gb|AAO68333.1| ribosomal small subunit pseudouridine synthase [Salmonella enterica
           subsp. enterica serovar Typhi str. Ty2]
 gi|161362434|gb|ABX66202.1| hypothetical protein SPAB_00778 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|194405013|gb|ACF65235.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Newport str. SL254]
 gi|194455724|gb|EDX44563.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|194712708|gb|ACF91929.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           CVM19633]
 gi|197213288|gb|ACH50685.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Agona str. SL483]
 gi|197290459|gb|EDY29814.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           SL480]
 gi|197936404|gb|ACH73737.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Dublin str.
           CT_02021853]
 gi|204321620|gb|EDZ06819.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|205335593|gb|EDZ22357.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
 gi|205345073|gb|EDZ31837.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|224467807|gb|ACN45637.1| ribosomal small subunit pseudouridine synthase [Salmonella enterica
           subsp. enterica serovar Paratyphi C strain RKS4594]
 gi|261247434|emb|CBG25259.1| ribosomal small subunit pseudouridine synthase [Salmonella enterica
           subsp. enterica serovar Typhimurium str. D23580]
 gi|267994304|gb|ACY89189.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 14028S]
 gi|301158783|emb|CBW18295.1| ribosomal small subunit pseudouridine synthase [Salmonella enterica
           subsp. enterica serovar Typhimurium str. SL1344]
 gi|312913212|dbj|BAJ37186.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhimurium str. T000240]
 gi|320086666|emb|CBY96437.1| 16S pseudouridylate 516 synthase [Salmonella enterica subsp.
           enterica serovar Weltevreden str. 2007-60-3289-1]
 gi|321224878|gb|EFX49941.1| Ribosomal small subunit pseudouridine synthase A ; SSU Psi
           [Salmonella enterica subsp. enterica serovar Typhimurium
           str. TN061786]
 gi|322615249|gb|EFY12171.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322617839|gb|EFY14735.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322624567|gb|EFY21398.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322626983|gb|EFY23779.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322634168|gb|EFY30904.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322635640|gb|EFY32350.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322640225|gb|EFY36889.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
 gi|322646353|gb|EFY42865.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322649320|gb|EFY45756.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322656440|gb|EFY52729.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322660683|gb|EFY56918.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
 gi|322665695|gb|EFY61879.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322667221|gb|EFY63388.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322671226|gb|EFY67354.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322675134|gb|EFY71211.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322680742|gb|EFY76777.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322686917|gb|EFY82894.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|323130552|gb|ADX17982.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|323192682|gb|EFZ77909.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323198887|gb|EFZ83986.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323205103|gb|EFZ90081.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323208146|gb|EFZ93090.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323211199|gb|EFZ96045.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
 gi|323215829|gb|EGA00572.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323221865|gb|EGA06265.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323223805|gb|EGA08108.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323231275|gb|EGA15390.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323233708|gb|EGA17800.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323237780|gb|EGA21840.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323245761|gb|EGA29755.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323246500|gb|EGA30479.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2009159199]
 gi|323255132|gb|EGA38915.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008283]
 gi|323259561|gb|EGA43196.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
 gi|323266058|gb|EGA49551.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008285]
 gi|323271866|gb|EGA55282.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008287]
 gi|326624057|gb|EGE30402.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
 gi|332989156|gb|AEF08139.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 231

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 104/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G +++ AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKDLTKPATLEVI----TPVQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEEEI 227


>gi|300724003|ref|YP_003713317.1| 16S rRNA pseudouridylate 516 synthase [Xenorhabdus nematophila ATCC
           19061]
 gi|297630534|emb|CBJ91199.1| 16S rRNA pseudouridylate 516 synthase [Xenorhabdus nematophila ATCC
           19061]
          Length = 235

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 53/239 (22%), Positives = 101/239 (42%), Gaps = 7/239 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR +V R +    V V+  +++  A  +     +  DG   ++    
Sbjct: 1   MRLDKFLSQQLGISRNDVGRELRAGLVTVDNEVIKTGAYKLKLDQQVAYDGTIFQQLNGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DP   + ++     +  ++ S GRLDI+T GL+LLT+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPSNPTVLYFIDEPVAHKLHSAGRLDIDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     + ++       GI + G        ++ +   +     V +
Sbjct: 121 ITSPKHHCEKTYLVTLEQPISEETEEKFLAGIQLNGEKTLTKPAKLEIIEPQI----VRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHL 249
            + EG+  ++K++F      V  L R   G   L   L AG  R ++   +     P  
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVELHRERIGEIYLDPALEAGEYRALTDSEINSIQMPRF 235


>gi|289577308|ref|YP_003475935.1| RNA-binding S4 domain protein [Thermoanaerobacter italicus Ab9]
 gi|289527021|gb|ADD01373.1| RNA-binding S4 domain protein [Thermoanaerobacter italicus Ab9]
          Length = 240

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 63/224 (28%), Positives = 100/224 (44%), Gaps = 4/224 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K+++  GI +R+EV++ I +  V VNG  ++ A + V    D I  DG  +   E 
Sbjct: 4   MRIDKLLSNIGIGTRKEVKKFIKEGLVLVNGNTVKDAGLIVDTEFDEILFDGEKINYKEF 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      +  T+   +                   GRLD +TEGLL +TNDG LA 
Sbjct: 64  IYIMMNKPKGVISATYDPIEKTVIDLLPQELKARNPFPAGRLDKDTEGLLFITNDGNLAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P    ++ Y     G V++  +   K+GIV++         + +       + V V
Sbjct: 124 KLLSPKKNVIKKYYAEILGFVNERDIKAFKEGIVLEDGYKTLPADLEILLSSEV-SKVYV 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
            +REGK  +IK++FE    KV  L R++ G   L   L  G  R
Sbjct: 183 YIREGKYHQIKRMFESVGKKVVYLKRLAMGSLTLDENLKPGQWR 226


>gi|157150331|ref|YP_001449642.1| pseudouridine synthase rRNA-specific [Streptococcus gordonii str.
           Challis substr. CH1]
 gi|157075125|gb|ABV09808.1| pseudouridine synthase rRNA-specific [Streptococcus gordonii str.
           Challis substr. CH1]
          Length = 242

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 107/233 (45%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+ ++ +  V VNG   +    ++  T D I V G  L   + 
Sbjct: 1   MRLDKFLVENGLGSRSQVKEVLKKGLVLVNGRAEKSPKTHINETADEIVVSGQKLTYEKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  +         +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPKGYISATEDERHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVT 190
            +  P     ++YR +  G ++Q  +    +GI ++       Q+ +    ++   + V 
Sbjct: 121 AMLSPKKHVEKIYRAQVAGLMNQSDVEQFARGIELKDFTCQPAQLKIVELDEEKETSLVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + L EGK  ++K++      +V  L R++ GP QL   L  G  R ++K+ ++
Sbjct: 181 ITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDSGLALGEWRRLTKEEMK 233


>gi|313895603|ref|ZP_07829159.1| pseudouridine synthase B, ribosomal large subunit [Selenomonas sp.
           oral taxon 137 str. F0430]
 gi|312975729|gb|EFR41188.1| pseudouridine synthase B, ribosomal large subunit [Selenomonas sp.
           oral taxon 137 str. F0430]
          Length = 243

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 81/231 (35%), Positives = 129/231 (55%), Gaps = 1/231 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++A AGIASRR  E MI   RV V+G+ +        +    I VDG+P++K   
Sbjct: 3   ERLQKILANAGIASRRSAEEMIRAGRVTVDGVCVTGLGRKYDAALHEIAVDGIPVQKETE 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP+G ++T  D  GR TV D LP   +R+  VGRLD +TEGLLL+TNDG + +
Sbjct: 63  RVYLLLNKPVGYLSTARDDRGRKTVLDLLPHTSTRLYPVGRLDADTEGLLLITNDGAMTQ 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  +VYR    G +  +KL  L+ GI+++       +V +     +   V + 
Sbjct: 123 GLLHPRYEIDKVYRAEIEGALTPEKLRHLRGGILLEDGITAPARVRIFAADSTVTTVEIV 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + EG+NR+++++F     +V RL R+ +    L  L  G++R +S + +RE
Sbjct: 183 IHEGRNRQVRRMFAAVGCRVLRLRRVRFAMLTLKDLPCGASRPLSAEEIRE 233


>gi|27468344|ref|NP_764981.1| 16S pseudouridylate synthase [Staphylococcus epidermidis ATCC
           12228]
 gi|57867194|ref|YP_188884.1| pseudouridine synthase family 1 protein [Staphylococcus epidermidis
           RP62A]
 gi|27315890|gb|AAO05025.1|AE016748_259 16S pseudouridylate synthase [Staphylococcus epidermidis ATCC
           12228]
 gi|57637852|gb|AAW54640.1| pseudouridine synthase, family 1 [Staphylococcus epidermidis RP62A]
          Length = 230

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 57/227 (25%), Positives = 101/227 (44%), Gaps = 7/227 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  VKVN  +++   ++V    D I V+   +     
Sbjct: 1   MRLDKFLANMGVGTRSEVKQLLKKGSVKVNQNIVKLPKLHVNPNSDEIMVNDEVVSYI-D 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G ++   D    + +          +  VGRLD +TEGLLL+TNDG    
Sbjct: 60  KVYIMLNKPKGYISATEDELHPTIIDLIPEYAHLNIFPVGRLDKDTEGLLLVTNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P+    + Y V     + Q  ++  K GI +              +K  +    V 
Sbjct: 120 EVMNPNKHVSKTYEVYSKHPITQFDIDKFKSGIELSDGKLKPA----ILKKVDDYVSHVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
           + EGK  ++K++F     +V  L RI     +L   L  GS R +++
Sbjct: 176 IYEGKYHQVKRMFHSIENEVLELKRIKIAQLELDHNLDLGSYRLLTQ 222


>gi|329851127|ref|ZP_08265884.1| S4 domain protein [Asticcacaulis biprosthecum C19]
 gi|328839973|gb|EGF89545.1| S4 domain protein [Asticcacaulis biprosthecum C19]
          Length = 760

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 144/356 (40%), Positives = 196/356 (55%), Gaps = 14/356 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K+        +R++KV+ARAG+ASRREVER+I   ++ VNG +LE  AV V S D I V+
Sbjct: 43  KDGKPPPKATERIAKVLARAGLASRREVERLIGLGKIAVNGRILETPAVLVSSADIITVE 102

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G  + KAE TR+W YHKP+GL+TTHSDP GR T+FD LP+   RVISVGRLD+N+EGLLL
Sbjct: 103 GQVIGKAEPTRVWRYHKPVGLITTHSDPQGRPTLFDQLPTHLPRVISVGRLDLNSEGLLL 162

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ- 182
           LTNDG LAR LE PS+ W+R YRVR  G   Q +L+ LK G  ++G+ YG M+ T+D   
Sbjct: 163 LTNDGELARSLEKPSSGWVRRYRVRALGHASQSRLDALKDGTTVEGVIYGPMEATIDKVA 222

Query: 183 ----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
                 +N W+TV + EGKNRE++KV E    KVNRLIR++YGPFQLG L  G   EV  
Sbjct: 223 EKADGRANVWLTVAITEGKNREVRKVLESIGLKVNRLIRLAYGPFQLGNLETGEVEEVGP 282

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           +++RE L          ++ +             +   E P       +    + G   +
Sbjct: 283 RVIRELL---------ADVVSLKNLPPEGASQTGDAPRERPARGDARGEGFGGRRGGGDR 333

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                   R +  S+          F      +E +  + P F      R    ++
Sbjct: 334 FDKGDRPDRGDRTSSRPQNARGKPEFAEKREFKERDFDQRPRFEGDGEARDRKPER 389


>gi|317502014|ref|ZP_07960198.1| pseudouridine synthase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|316896694|gb|EFV18781.1| pseudouridine synthase [Lachnospiraceae bacterium 8_1_57FAA]
          Length = 249

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 55/227 (24%), Positives = 111/227 (48%), Gaps = 7/227 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K ++ AG+ SRRE +R+I   +V V+G+  +   + V +   ++V    + K +
Sbjct: 19  ESVRLNKYLSEAGVCSRREADRLIESGKVTVDGVTAQ-MGMRVTAGQIVKVGKKTVSKQD 77

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              +   +KP G+V T    +          +   RV   GRLD ++ GLLL+TN+G + 
Sbjct: 78  EMIVLAVNKPKGIVCTEDQRE--RDSIVRFLNYPVRVTYAGRLDKDSRGLLLMTNNGDII 135

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +   + +  + Y+V    ++ +  +  + +G+ I         V    +K      ++
Sbjct: 136 NQMMRAANRHEKEYKVTVDKEITEQFIKKMSEGVPILDTVTRPCTV----KKIGKYTFSI 191

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            L +G NR+I+++   F ++V  L+RI     +LG+L  G+ R+++ 
Sbjct: 192 ILTQGLNRQIRRMCAAFGYEVKDLVRIRIMNIRLGSLKEGAYRKLTD 238


>gi|319778229|ref|YP_004129142.1| Ribosomal large subunit pseudouridine synthase B [Taylorella
           equigenitalis MCE9]
 gi|317108253|gb|ADU90999.1| Ribosomal large subunit pseudouridine synthase B [Taylorella
           equigenitalis MCE9]
          Length = 418

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 83/325 (25%), Positives = 134/325 (41%), Gaps = 9/325 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           V EN +  ++ K++A AG+ SRR++E +I Q RV VNG+        +   D ++V+G  
Sbjct: 98  VAENSSKPKLHKILADAGVGSRRDMEDLIIQGRVSVNGVPA-HIGQRISDEDVVKVNGRI 156

Query: 67  LRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           + + +  R+      +     +VT     +  +          ++ +SVGRLDINTEGLL
Sbjct: 157 INRPKSNRVPRVILYHKPAGEIVTQDDPKNRATVFARLPKMKTAKWVSVGRLDINTEGLL 216

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + T  G LA  L  P     R Y VR  G++D  +L  L +GI ++        +     
Sbjct: 217 IFTTSGDLANRLMHPRYGNEREYAVRILGELDSTQLKTLTEGIHLEDGLAKFGSIDYIGG 276

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            GSN W  V + EG+NRE++++FE     V+RLIR  +G   L   L  G   E+    +
Sbjct: 277 DGSNKWYRVTIEEGRNREVRRMFEALGLTVSRLIRSRFGDVHLPRNLKRGRWEELDPSQV 336

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
              LG           D              N +    +      K+ S           
Sbjct: 337 ---LGLMECLGLNKKNDEDGRKGRRGPVSHGNALPPGFEKSIDPSKDFSIHKVRKSAGGP 393

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLS 326
              +  R + S        +++   
Sbjct: 394 QRGLTGRGVPSQRRGRSTRNNTTNR 418


>gi|251791839|ref|YP_003006559.1| ribosomal small subunit pseudouridine synthase A [Aggregatibacter
           aphrophilus NJ8700]
 gi|247533226|gb|ACS96472.1| ribosomal small subunit pseudouridine synthase A [Aggregatibacter
           aphrophilus NJ8700]
          Length = 233

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 102/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R +  +++ Q  V +NG + +  A  V   D I  DG  L      
Sbjct: 1   MRLDKFLAEMTDLTRSQATKVLRQSAVTINGKIEKSGAAKVGPNDEICYDGERLAWVAEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +  + +KP G + +H D D  +        + +R+ S GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYIMLNKPQGYICSHEDGDHPTIYQFFGYPLSARLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+ + +    +GI+++G         + +      +  V +
Sbjct: 121 ITSPKHHQPKTYLVTLADPVEANYVQACTEGILLRGEKDPTKPATLEIL----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EG+  +IK++F     KV  L R   G   L   L  G  R ++   +
Sbjct: 177 TISEGRYHQIKRMFAALGNKVVGLHRWKIGALVLDDSLEEGEYRALTAAEV 227


>gi|134101741|ref|YP_001107402.1| pseudouridylate synthase ribosomal large subunit [Saccharopolyspora
           erythraea NRRL 2338]
 gi|291003087|ref|ZP_06561060.1| pseudouridylate synthase ribosomal large subunit [Saccharopolyspora
           erythraea NRRL 2338]
 gi|133914364|emb|CAM04477.1| pseudouridylate synthase ribosomal large subunit [Saccharopolyspora
           erythraea NRRL 2338]
          Length = 253

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 76/235 (32%), Positives = 118/235 (50%), Gaps = 1/235 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
             +    R+ KV+++AG+ASRR  E+MI + RV+VNG ++      V      I VDG  
Sbjct: 10  SPSAEGVRLQKVLSQAGVASRRAAEQMIVEGRVEVNGEIVLELGTRVDPDTAVIHVDGNR 69

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +         L +KP G++ T SD  GR  + D L     R+  VGRLD+++EGLLL+TN
Sbjct: 70  IMVNADLTHLLLNKPKGILCTMSDDQGRPCIGDYLRERQGRLYHVGRLDVDSEGLLLITN 129

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS + L+ Y     G + ++    L+ GI ++          L       
Sbjct: 130 DGELAHRLMHPSYRILKTYLAEVPGPIPKNLGRELRNGIELEDGPVKVDSFKLVDVNEGR 189

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           A V V L EG+   ++++ +     V RL+R + G  +L T   G+ R + +K +
Sbjct: 190 ALVEVVLHEGRKHVVRRLLKQVGHPVLRLVRTAVGDVRLTTERQGAIRPLDRKEI 244


>gi|85059383|ref|YP_455085.1| 23S rRNA pseudouridylate synthase B [Sodalis glossinidius str.
           'morsitans']
 gi|84779903|dbj|BAE74680.1| putative pseudouridine synthase [Sodalis glossinidius str.
           'morsitans']
          Length = 297

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 88/296 (29%), Positives = 135/296 (45%), Gaps = 10/296 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN-VMSTDHIEVDGVPLRK 69
              +++ KV+AR+G  SRRE+E +I Q RV V+G +        V ST  I +DG  +  
Sbjct: 2   SESEKLQKVLARSGQGSRREIEAVIEQGRVSVDGKVATLGDRVDVTSTTKIRIDGRIIAI 61

Query: 70  AE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                     L  Y     L T        +          +R ++VGRLDINT GLLL 
Sbjct: 62  KPVEDAVCRVLTYYKPEGELCTRRDPEGRPTVFDRLPRLNNARWVAVGRLDINTSGLLLF 121

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T DG LA  L  PS +  R Y +R  G+VD+DK   L +G+ +         +T    +G
Sbjct: 122 TTDGELANRLMHPSCKIEREYALRVFGEVDEDKQRQLTRGVQLDDGPAAFRSLTFQGGEG 181

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI--- 240
            N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  +    
Sbjct: 182 LNQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDVTLPKGLPRGGWTELPLEQTNY 241

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           LRE++   L    ++ ++      +     R    +       R  ++  + NG+ 
Sbjct: 242 LREKVQLPLESVTKLPVERDRRRLKATQIRRVVKRNSQRAPSRRGGQSIKRNNGVG 297


>gi|162419712|ref|YP_001606744.1| 23S rRNA pseudouridylate synthase B [Yersinia pestis Angola]
 gi|162352527|gb|ABX86475.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           Angola]
          Length = 344

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 95/325 (29%), Positives = 142/325 (43%), Gaps = 16/325 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
            +++ K++ARAG  SRRE+E +I Q RV V+G +  +    V  T    I +DG  L   
Sbjct: 28  GEKLQKILARAGHGSRREIEAIIQQGRVSVDGKV-SKLGDRVEVTQSTKIRLDGHLLSIK 86

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E        L  Y     L T +      +          SR ++VGRLD+NT GLLL T
Sbjct: 87  ESEENVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFT 146

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  GQ+D DK+  L +G+ ++        ++    +G 
Sbjct: 147 TDGELANCLMHPSREVEREYAVRVFGQIDDDKIKQLSRGVQLEDGPAAFRTISYQGGEGI 206

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+    L+  
Sbjct: 207 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELD---LKAT 263

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
                L E  V       S   + +DR  + +       +     S +    +Q      
Sbjct: 264 NYLRELVELDVETV----SKLPVEKDRRRVKANQIRRAVKRHTEVSGRQVAGRQGSARKG 319

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSG 329
             R+N+ +    A     S     G
Sbjct: 320 STRQNVGNAAPAATASRRSGPKKRG 344


>gi|293414601|ref|ZP_06657250.1| 23S rRNA pseudouridylate synthase B [Escherichia coli B185]
 gi|291434659|gb|EFF07632.1| 23S rRNA pseudouridylate synthase B [Escherichia coli B185]
          Length = 311

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 87/292 (29%), Positives = 129/292 (44%), Gaps = 10/292 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLR 68
           +   +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  + 
Sbjct: 20  SSMSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLIS 79

Query: 69  KAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
             E        L  Y     L T +      +          +R I+VGRLD+NT GLLL
Sbjct: 80  VRESAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLL 139

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +
Sbjct: 140 FTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGE 199

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KK 239
           G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+      
Sbjct: 200 GINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTN 259

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
            LRE +       ++V ++      +     R            R    ++ 
Sbjct: 260 YLRELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGGRRSGGRNNG 311


>gi|260773017|ref|ZP_05881933.1| ribosomal large subunit pseudouridine synthase B [Vibrio
           metschnikovii CIP 69.14]
 gi|260612156|gb|EEX37359.1| ribosomal large subunit pseudouridine synthase B [Vibrio
           metschnikovii CIP 69.14]
          Length = 346

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 88/345 (25%), Positives = 134/345 (38%), Gaps = 14/345 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E +I   RV VNG +          T  + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAILGERLEDETAVVRIDGHAVSAKAP 61

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  Y     L T H     R+          SR ISVGRLD NT GLLL T D
Sbjct: 62  EEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G+++++K+  L +G+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRQVEREYLVRVFGEINEEKIRNLVRGVQLEDGMARFEDVMYAGGEGMNH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI---LRE 243
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+  K    LR+
Sbjct: 182 TFYVVINEGRNREVRRLWESQGTTVSRLKRVRYGDIFLDKKLPRGGWVELDLKQVNYLRD 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL-----SKQ 298
            +     +E  ++      S +        I   V     R+   +++         +  
Sbjct: 242 LVELRPEKETMLDESKDNTSRKRERSRSQKIRRAVKRHEERITTTTAKPKSRVTNGTTTG 301

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
                   R                      +      ++P    
Sbjct: 302 GSTGNAPTRARRKPGSSTRNSAQEQSSRQGTRAPSGKAKAPRRQG 346


>gi|310767747|gb|ADP12697.1| 23S rRNA pseudouridylate synthase B [Erwinia sp. Ejp617]
          Length = 295

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 87/295 (29%), Positives = 128/295 (43%), Gaps = 12/295 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E +I+  RV V+G L       V       I +DG  +  +
Sbjct: 2   SEKLQKVLARAGHGSRREIETLISAGRVSVDGKLAT-LGDRVEPGASLKIRIDGHVVPVS 60

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E        L  Y     L T        +          +R ++VGRLD+NT GLLL T
Sbjct: 61  ESISEVCRILAYYKPEGELCTRSDPEGRPTVFDRLPKLRGARWVAVGRLDVNTCGLLLFT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  G VD +K+ LL +G+ ++        +     +G 
Sbjct: 121 TDGELANRLMHPSREVEREYAVRVFGAVDDEKIKLLSRGVQLEDGPAAFKTLKFTGGEGI 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKIL 241
           N W  V L EG+NRE+++++E    +V+RLIRI YG   L   L  G   E+       L
Sbjct: 181 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRIRYGDIDLPKGLPRGGWTELDLAPTNYL 240

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           RE +G      ++V ++     ++     R                    K    
Sbjct: 241 RELVGLAPETVSKVPVEKDRRRTKANQIRRAVKRHTTTKVSKPGSGRRPSKRQQG 295


>gi|148981773|ref|ZP_01816521.1| pseudouridine synthase family 1 protein [Vibrionales bacterium
           SWAT-3]
 gi|145960740|gb|EDK26079.1| pseudouridine synthase family 1 protein [Vibrionales bacterium
           SWAT-3]
          Length = 305

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 94/307 (30%), Positives = 137/307 (44%), Gaps = 13/307 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E +I   RV VNG + +           I +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRRELEGLIKSGRVSVNGQVAKLGERLEDENSVIRIDGHTVSGKAS 61

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  Y     L T H     R+          SR ISVGRLD NT GLLL T D
Sbjct: 62  EEVVCRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G+V + K+  L +G+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRQVEREYLVRVFGEVTEQKVKNLVRGVELEDGMARFEDVVYAGGEGMNH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LRE 243
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G  +E+  +    LRE
Sbjct: 182 TFYVAINEGRNREVRRLWESQETTVSRLKRVRYGDIYLDKKLPRGGWKELDLQEVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +     +E  ++LD     S T  +   +   ++     R ++ ++   G S Q K   
Sbjct: 242 LVELKPEKETLLDLD----PSNTSRKRERSRSQKIRRAVRRHEERANAPKGRSNQAKRKK 297

Query: 304 PVHRRNL 310
           P  R   
Sbjct: 298 PATRGTT 304


>gi|153829628|ref|ZP_01982295.1| pseudouridine synthase family 1 protein [Vibrio cholerae 623-39]
 gi|148874904|gb|EDL73039.1| pseudouridine synthase family 1 protein [Vibrio cholerae 623-39]
          Length = 321

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 91/320 (28%), Positives = 132/320 (41%), Gaps = 9/320 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E +I   RV VNG +             + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGERLEDDNAVVRIDGHVVSVKAQ 61

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  Y     L T H     R+          SR ISVGRLD NT GLLL T D
Sbjct: 62  EEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G V ++K+  L +G+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRQVEREYLVRVFGDVTEEKVRNLVRGVQLEDGMARFEDVMYAGGEGINH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI---LRE 243
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+  K    LRE
Sbjct: 182 TFYVVINEGRNREVRRLWESQGTTVSRLKRVRYGDIFLDKKLPRGGWMELDLKQVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +     +E  +N+     + +        I   V     R+     +      ++K   
Sbjct: 242 LVELRPEKETVLNMAPDAATRKRERTRSQKIRRAVRRHEERISATPGRSGKAPARRKPGG 301

Query: 304 PVHRRNLASNVWMAKGIHSS 323
               RN  +N   +      
Sbjct: 302 EPSTRNKVANQQQSSRKPRG 321


>gi|329667573|gb|AEB93521.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           johnsonii DPC 6026]
          Length = 233

 Score =  167 bits (422), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 64/233 (27%), Positives = 106/233 (45%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I ++ V VNG +++     V   D + VDG  +   +  
Sbjct: 1   MRIDKYLANMNVGSRKEVHNLIKKKIVTVNGEVVKTPKEQVKEEDQVAVDGEKVAYQQYH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      +  T                 +  +  VGRLD +T GLLLLTNDG LA  
Sbjct: 61  YFLLNKPKGVISATEDRSQKTVLSLLKPKDRYKGIAPVGRLDKDTTGLLLLTNDGALAHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG--SNAWVT 190
           L  P+    + YR +  G  D++ + +   G+ +  G      ++ +  Q      + + 
Sbjct: 121 LLAPNKHVTKKYRAKIAGVADEETVEIFASGMTLGDGTKLKPAELKILIQDKEADRSEIE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           + ++EGK  +IK++F     KV  L RIS G   L  +L  G  +E+S K ++
Sbjct: 181 IEIQEGKYHQIKRMFGAVGMKVIELDRISMGKLVLPTSLKRGEYKEISLKEIK 233


>gi|46143798|ref|ZP_00204573.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|126207838|ref|YP_001053063.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae L20]
 gi|126096630|gb|ABN73458.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 5b str. L20]
          Length = 230

 Score =  167 bits (422), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 106/232 (45%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  R +    V +NG L +  +V +  TD I  +G  L   +  
Sbjct: 1   MRLDKFIAENTGLTRSQAARALKSGLVTINGKLEKSGSVKIGDTDEICYEGERLEWVDEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ +KP G V +H D +  +        + +++ + GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYFMLYKPQGYVCSHDDGEYPTVFQFFDYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+      L +GI+++G        ++ +      +  V +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEDFYAKKLAEGILLRGEREPCLPAKMEVI----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EG+  ++K++F     KV  L R   G   L   L  G  R +S++ + 
Sbjct: 177 TISEGRYHQVKRMFAALGNKVEALHRWRIGDVVLDENLEEGEYRPLSEQEVE 228


>gi|154248798|ref|YP_001409623.1| RNA-binding S4 domain-containing protein [Fervidobacterium nodosum
           Rt17-B1]
 gi|154152734|gb|ABS59966.1| RNA-binding S4 domain protein [Fervidobacterium nodosum Rt17-B1]
          Length = 245

 Score =  167 bits (422), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 54/241 (22%), Positives = 103/241 (42%), Gaps = 5/241 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K  +  +      R+ K ++ A I +R EV+++I + RV VN  ++     +V   D IE
Sbjct: 3   KKISKKESEIKSIRLDKFLSNAHIGTRNEVKKIIKEGRVSVNFEIIRNPDFHVKLDDIIE 62

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +DG  +   +   +  +     + TT       S +        + +   GRLD + EGL
Sbjct: 63  LDGNRIEPHKNVYIIFHKPSGFVSTTSDR--EPSVLNLIDHPYLNELHIAGRLDKDVEGL 120

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD-QDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+LTNDG     L  P     + Y +     V+    +  +    +        +   + 
Sbjct: 121 LILTNDGEFTHNLISPKKHIEKEYWIYTKENVEVTQNMVKMVSEGIELEKGTKTLPGKI- 179

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +K S   +++ + EGK  ++KK+      +  +++R+  G   L  L  G  +E+SK+ 
Sbjct: 180 -RKVSEKIISLTIVEGKYHQVKKMCISLGIEWEKIVRVRIGNLTLEGLEKGKWKELSKEE 238

Query: 241 L 241
           +
Sbjct: 239 I 239


>gi|312898944|ref|ZP_07758332.1| conserved hypothetical protein [Megasphaera micronuciformis F0359]
 gi|310620106|gb|EFQ03678.1| conserved hypothetical protein [Megasphaera micronuciformis F0359]
          Length = 231

 Score =  167 bits (422), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 75/225 (33%), Positives = 120/225 (53%), Gaps = 4/225 (1%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTRLWLY 78
           ++  G+ASRR  E MIA  RV+VNG++++   V V    D I VDG  L K  +      
Sbjct: 1   MSNCGVASRRASEEMIAAGRVRVNGVIVKTPGVKVDLQKDIIVVDGKRLEKPAKQYYLFN 60

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
                ++TT  D   R+TV D   ++  R+  VGRLD NTEGLL++TNDG LA +L  PS
Sbjct: 61  KPKG-VLTTVKDDRERNTVMDYFKNVKDRIYPVGRLDQNTEGLLIMTNDGALANILMHPS 119

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVGLREG 196
               + Y VR  G++    L  L +G+ ++        V      G+     V + + EG
Sbjct: 120 KLVDKTYNVRIKGRITDAVLEKLAQGVPLKDGMTAPAVVVYVGYDGATNITEVEITIHEG 179

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +NR+++++FE+F ++V+ L R  Y    L  +  G+ R ++++ +
Sbjct: 180 RNRQVRRMFEYFGFQVHNLRRTQYAFLTLSGVKRGAYRRLTREEV 224


>gi|154687141|ref|YP_001422302.1| YtzF [Bacillus amyloliquefaciens FZB42]
 gi|154352992|gb|ABS75071.1| YtzF [Bacillus amyloliquefaciens FZB42]
          Length = 239

 Score =  167 bits (422), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 58/224 (25%), Positives = 94/224 (41%), Gaps = 3/224 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A +G  SR++V++++    V ++G   +    +V      I V G P    E 
Sbjct: 1   MRLDKLLANSGFGSRKDVKKIVKAGAVMIDGEPAKDVKTHVDPEKQDITVYGEPADYREF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      L  T                        GRLD +TEG LLLTNDG LA 
Sbjct: 61  IYVMMNKPQGVLSATEDSRQQTVVDLLTPEEQRFEPFPAGRLDKDTEGFLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y VR    +  + +  L++G+VI+G        V + T+      + +
Sbjct: 121 RLLSPKKHVPKTYEVRLTSPLSPEDIVHLERGVVIEGGYKTKPAAVEIITESPDETVIHL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
            + EGK  ++K + +    +V  L R+S G   L   L  G  R
Sbjct: 181 TITEGKYHQVKLMAKAVGNEVAYLKRLSMGAVSLDPDLKPGEFR 224


>gi|139439675|ref|ZP_01773088.1| Hypothetical protein COLAER_02116 [Collinsella aerofaciens ATCC
           25986]
 gi|133775016|gb|EBA38836.1| Hypothetical protein COLAER_02116 [Collinsella aerofaciens ATCC
           25986]
          Length = 321

 Score =  167 bits (422), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 75/291 (25%), Positives = 119/291 (40%), Gaps = 14/291 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE 71
             R+ + +ARAG+ASRR  E ++   RV VNG++       V    DHIEVDGVP++  +
Sbjct: 29  TMRLQRFLARAGVASRRGSEDLMTAGRVTVNGLVATELGTKVDVDRDHIEVDGVPVKLNQ 88

Query: 72  -RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               L LY     L T     +          + F  +  VGRLD +T GLLL T DG L
Sbjct: 89  GAVYLMLYKPTGYLTTMSDPQERPCVADLVPRNRFPGLFPVGRLDRDTTGLLLFTTDGDL 148

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--------- 181
           ++ L  PS    + Y+    GQ+    L+ L++GI +           +           
Sbjct: 149 SQDLLHPSKHVHKTYQALVDGQLTDRDLDQLRRGIELDDGLCQPAICRVINAREAVAVAP 208

Query: 182 --QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
              K     V V +REG+  ++K++    +  V RL R ++   +L  +  GS RE++ +
Sbjct: 209 QGVKPGTTAVEVIIREGRKNQVKRMLGKIHHPVIRLHRCNFAGLELEGVAKGSWRELTDR 268

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
            + + L    +   Q +        +     R            R      
Sbjct: 269 EV-QILKSGGIPPKQASAKRNGDKPQDTPASRTRHHGSHGSAPKRNTYRER 318


>gi|119476913|ref|ZP_01617194.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [marine gamma proteobacterium
           HTCC2143]
 gi|119449720|gb|EAW30957.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [marine gamma proteobacterium
           HTCC2143]
          Length = 282

 Score =  167 bits (422), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 81/279 (29%), Positives = 130/279 (46%), Gaps = 6/279 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E+    ++ K++A+AG+ SRRE+E++IA +RV VNG + +       S D I VDG  + 
Sbjct: 5   ESPAGDKLQKLLAQAGVGSRREMEKVIADRRVTVNGKVAK-LGDRASSRDKIAVDGKLVG 63

Query: 69  KAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            AE+      L        + +       ++          SR I+VGRLD NT GL++ 
Sbjct: 64  VAEQDSAGRVLIYNKPEGEICSRSDPEGRKTVFERLPKLTGSRWIAVGRLDFNTSGLMIF 123

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T DG LA  L  PS++  R Y  R  G V    L  L  G++++        +     +G
Sbjct: 124 TTDGQLANALMHPSSEIDREYLCRVLGNVSDVVLQRLSDGVLLEDGTAKFTDIVDGGGEG 183

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           +N W  V L EG+NRE+++++E    +V+RL R+ +G   L   L  G  +E+  K ++E
Sbjct: 184 ANHWYYVALMEGRNREVRRLWESQEIQVSRLKRVRFGGVFLPSKLRQGQWQEMPYKEVQE 243

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDF 282
                 +E  +     P        + R N   + P   
Sbjct: 244 LYKMAGMEALKPQKMMPKELQSMERQQRKNRGIKHPRRS 282


>gi|221197754|ref|ZP_03570800.1| RNA pseudouridine synthase family protein [Burkholderia multivorans
           CGD2M]
 gi|221204688|ref|ZP_03577705.1| RNA pseudouridine synthase family protein [Burkholderia multivorans
           CGD2]
 gi|221175545|gb|EEE07975.1| RNA pseudouridine synthase family protein [Burkholderia multivorans
           CGD2]
 gi|221181686|gb|EEE14087.1| RNA pseudouridine synthase family protein [Burkholderia multivorans
           CGD2M]
          Length = 541

 Score =  167 bits (422), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 83/341 (24%), Positives = 141/341 (41%), Gaps = 8/341 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 157 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRI 215

Query: 63  DGVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           +G P+++         L  +     +V+        S      P   ++ ++VGRLD NT
Sbjct: 216 NGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNT 275

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLL+LT  G LA     P     R Y VR  G++ +     L  GI +       +++ 
Sbjct: 276 EGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSESARQKLLHGIELDDGPANFLRIR 335

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
               +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ 
Sbjct: 336 DGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELD 395

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +  +R+ +    L+                 R +P+ +       +R    ++       
Sbjct: 396 EAQVRKLMATVGLKAPSEEKGKRGAGQ--AERRQPDPMQTSMGFISREPVLTTHGQLDQP 453

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS 338
           ++            S                G+  + +R S
Sbjct: 454 RRGGRRGGPGLPGLSGYGSLPVASGYGNRAGGRDVDGNRAS 494


>gi|298695021|gb|ADI98243.1| pseudouridine synthase, family 1 [Staphylococcus aureus subsp.
           aureus ED133]
 gi|323439591|gb|EGA97311.1| 16S RNA pseudouridylate synthase [Staphylococcus aureus O11]
 gi|323441503|gb|EGA99155.1| 16S RNA pseudouridylate synthase [Staphylococcus aureus O46]
          Length = 231

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 55/228 (24%), Positives = 100/228 (43%), Gaps = 7/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E 
Sbjct: 1   MRIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDKISVRGELIEYVEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + +   D   ++ +          +  VGRLD +TEGLLL+TNDG    
Sbjct: 61  VYIMLNKPKGYI-SATEDHHSKTVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+    + Y V     + +D +   K+G+ +         +T    + S     V 
Sbjct: 120 ELMSPNKHVSKKYEVISANPITEDDIQAFKEGVKLSDGKVKPAILTYIDNQTS----HVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           + EGK  ++K++F     +V  L RI     +L   L +G  R +++ 
Sbjct: 176 IYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYRLLTEN 223


>gi|329725501|gb|EGG61981.1| pseudouridylate synthase [Staphylococcus epidermidis VCU144]
          Length = 230

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 57/227 (25%), Positives = 101/227 (44%), Gaps = 7/227 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  VKVN  +++   ++V    D I V+   +     
Sbjct: 1   MRLDKFLANMGVGTRSEVKQLLKKGSVKVNQNIVKLPKLHVNPNSDEIMVNDEVVSYI-D 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G ++   D    + +          +  VGRLD +TEGLLL+TNDG    
Sbjct: 60  KVYIMLNKPKGYISATEDELHPTIIDLLPEYAHLNIFPVGRLDKDTEGLLLVTNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P+    + Y V     + Q  ++  K GI +              +K  +    V 
Sbjct: 120 EVMNPNKHVSKTYEVYSKHPITQFDIDKFKSGIELSDGKLKPA----ILKKVDDYVSHVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
           + EGK  ++K++F     +V  L RI     +L   L  GS R +++
Sbjct: 176 IYEGKYHQVKRMFHSIENEVLELKRIKIAQLELDHNLDLGSYRLLTQ 222


>gi|120610106|ref|YP_969784.1| ribosomal large subunit pseudouridine synthase B [Acidovorax
           citrulli AAC00-1]
 gi|120588570|gb|ABM32010.1| ribosomal large subunit pseudouridine synthase B [Acidovorax
           citrulli AAC00-1]
          Length = 483

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 79/356 (22%), Positives = 133/356 (37%), Gaps = 29/356 (8%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          V   D ++V+
Sbjct: 139 KRVLPPQVEMPKLHKVLAQAGLGSRLEMEQLILEGRISVNNEPA-HIGQRVQYGDQVKVN 197

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+R          +  +     +VT     +  +           +  SVGRLD+NTE
Sbjct: 198 GRPIRYRIDPPAPRVIAYHKPVGEVVTHDDPQNRPTVFRKLPRLAHGKWQSVGRLDLNTE 257

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL T+ G LA  L  P     R Y VR  G +  ++   L  G+ ++        +  
Sbjct: 258 GLLLFTSAGELANKLMHPRFGLEREYAVRVLGALSNEEKQRLLDGVQLEDGMAAFGSIED 317

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +GSN W  V + EG+NRE++++ E     V+RLIRI YG   L   L  G+  E+ +
Sbjct: 318 GGGEGSNCWYRVTISEGRNREVRRMLESVGHAVSRLIRIRYGSMMLPRGLKRGAWLELDE 377

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           + +R  +     +  +                R               +           
Sbjct: 378 RDIRALMQAAGADMPRPAGPGAAAGDRKGGGPRKGGGRGQGGPGGPAPRGD--------- 428

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                               G      + S  + +  + S  +    SL R    +
Sbjct: 429 --------------YFNPPAGGRGKRAAPSSSQPDPMKTSVGYIGSDSLARHRQDQ 470


>gi|166031891|ref|ZP_02234720.1| hypothetical protein DORFOR_01592 [Dorea formicigenerans ATCC
           27755]
 gi|166028344|gb|EDR47101.1| hypothetical protein DORFOR_01592 [Dorea formicigenerans ATCC
           27755]
          Length = 243

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 58/238 (24%), Positives = 111/238 (46%), Gaps = 8/238 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K ++  G+ +R+EV++ I + +V+V+G + +R  + V  T  ++ +DG  +  A  
Sbjct: 7   IRLDKFLSEMGVGTRQEVKQYIRKGKVEVDGEIAKRPELKVDETKANVTLDGERIGYASY 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +V+   D   ++ +          +  VGRLD +T GLLL+TNDG LA 
Sbjct: 67  VYYMLNKPSG-VVSATEDKREKTVIDLIKGQKRKDLFPVGRLDKDTVGLLLITNDGNLAH 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGSNAW 188
            L  P     + Y  +  G V +D      +G+ I    +       ++ +  +    + 
Sbjct: 126 RLLSPKHHVDKCYFAKVQGNVTKDDAEKFAEGVNIGTEDEPEITMPGKLDII-KSDDLSE 184

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
           + + ++EGK  ++K++F+    +V  L R   G   L   L  G  R ++++ L+  L
Sbjct: 185 IRLTIQEGKFHQVKRMFQAVGKEVVYLKRERMGSLILDDNLAEGEYRMLTEEELKNLL 242


>gi|303256973|ref|ZP_07342987.1| ribosomal large subunit pseudouridine synthase B [Burkholderiales
           bacterium 1_1_47]
 gi|302860464|gb|EFL83541.1| ribosomal large subunit pseudouridine synthase B [Burkholderiales
           bacterium 1_1_47]
          Length = 355

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 84/308 (27%), Positives = 126/308 (40%), Gaps = 13/308 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
           +++ KV+A AGI SRR++E  IA+ R+ VNG         V  +D I  DG  +R++   
Sbjct: 54  EKLHKVLADAGIGSRRDMEERIAEGRISVNGEPAHV-GQRVTPSDVIRFDGRIVRRSALE 112

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  +     +V+        +          +R I+VGRLD NTEGLLL T+ 
Sbjct: 113 NNDVPKVLIYHKPAGEIVSKDDPEGRPTVFDHLPRIGGARWIAVGRLDFNTEGLLLFTDS 172

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P  +  R Y VR  G +  +  + L KGI +         +     KG N 
Sbjct: 173 GNLANFLMHPRHEIEREYAVRVQGTMSPEAKDKLLKGIKLDDGIAKFTTLEEGGGKGFNR 232

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V L EG+NRE++++FE     V+RLIR+ YG  +L   L  G TR +S +       
Sbjct: 233 WYNVTLSEGRNREVRRMFEAVGLPVSRLIRVKYGNLELPSDLPRGKTRRMSTEE-----T 287

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              L+            +       P   +               +   S   + + P+ 
Sbjct: 288 EKWLDSISYKKGMSTAPAPRAPERTPRPAASRAPASAPKAGRKFGQRDTSSAIRSSRPMR 347

Query: 307 RRNLASNV 314
            R      
Sbjct: 348 SRGTRGPK 355


>gi|153216913|ref|ZP_01950677.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           1587]
 gi|124114062|gb|EAY32882.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           1587]
          Length = 229

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 48/231 (20%), Positives = 95/231 (41%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSCVEWQGREITLHGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     + +       ++            +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDG-FNQTAFTLLDEVNVEDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + YRV     +  D      +GI ++G        Q+ +     S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELRGERELTLPAQLEVI----SETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R   G   L   L  G  R ++++ +
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEEEV 226


>gi|254507010|ref|ZP_05119148.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus 16]
 gi|219550005|gb|EED26992.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus 16]
          Length = 233

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 49/230 (21%), Positives = 100/230 (43%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  A+R+E  ++I    V VN ++ +  A  V     +E  G  ++K    
Sbjct: 1   MRLDKYLCDALGATRKEATKIIKSGDVTVNDVMQKSGAFKVTDACVVEWQGREIQKPGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+     + +     +  +            +   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLFKPDGFVCSHEDGFNQ-TAFALLDEVKMEDLHFAGRLDVDTTGLVLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     +  D  + L +G+ ++      +  T++        + + +
Sbjct: 120 ITSPKHKCEKTYRVWLVDPIGDDYADKLAQGVELRNEKEPTLPATMEVVNHDENELLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            EGK  ++K++F     KV  L R   G  +L  +L  G  R ++++ + 
Sbjct: 180 TEGKYHQVKRMFAALGNKVEHLHRERIGAIELDYSLEPGEYRYLTEEEVD 229


>gi|87124763|ref|ZP_01080611.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Synechococcus sp. RS9917]
 gi|86167642|gb|EAQ68901.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Synechococcus sp. RS9917]
          Length = 246

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 83/232 (35%), Positives = 121/232 (52%), Gaps = 1/232 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R+ K+IA AG+ SRR+ E ++ QQRV+VNG ++          D I VDG PLR  E
Sbjct: 2   TGERLQKLIAAAGLCSRRKAEELLRQQRVRVNGQIVALGDRADPEQDRICVDGRPLRAPE 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGL 130
            TRL L +KP+G++++  DP GR TV D +P+   R    +GRLD ++ G LLLTN G L
Sbjct: 62  ATRLLLLNKPVGVISSCYDPRGRRTVLDLIPNHLRRGLHPIGRLDADSRGALLLTNRGQL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + YRV   G      L   + G+ + G       V    ++G    + 
Sbjct: 122 TLRLSHPRYAHSKTYRVWLEGDPSPQHLQSWRDGVWLDGQRTQPATVQRLRREGGRTLLE 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           V L+EG+NR+I++  +     V  L RI+     LG+L  G  R + +   R
Sbjct: 182 VTLQEGRNRQIRRTADQLGHPVLDLQRIAIAGIPLGSLAEGEWRALHRGEWR 233


>gi|260776099|ref|ZP_05884994.1| ribosomal large subunit pseudouridine synthase B [Vibrio
           coralliilyticus ATCC BAA-450]
 gi|260607322|gb|EEX33587.1| ribosomal large subunit pseudouridine synthase B [Vibrio
           coralliilyticus ATCC BAA-450]
          Length = 314

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 91/312 (29%), Positives = 131/312 (41%), Gaps = 9/312 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
           +++ KV+ARAG  SRRE+E +I   RV VNG++ +           + +DG  +      
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKAGRVSVNGVVAKLGERLEDENAVVRIDGHTVSAKAQE 62

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 L  Y     L T H     R+          SR ISVGRLD NT GLLL T DG
Sbjct: 63  EVVCRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS Q  R Y VR  G VD+ K+  L  G+ ++        V      G N  
Sbjct: 123 ELANRLMHPSRQVEREYLVRVFGDVDEKKIRNLVGGVELEDGLARFEDVVYAGGDGMNHT 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI---LREQ 244
             V + EG+NRE+++++E  +  V+RL R+ YG   L   L  G   E+  K    LRE 
Sbjct: 183 FYVVINEGRNREVRRLWESQDCTVSRLKRVRYGDIFLDKKLPRGGWMELDLKEVNYLREL 242

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           +     +E  ++ +    S +        I   V     RM     + N  +++K     
Sbjct: 243 VELRPEKETMLDENKANTSRKRERSRSQKIRRAVKRHEERMNNGGGRSNNPARRKPRKGA 302

Query: 305 VHRRNLASNVWM 316
             +         
Sbjct: 303 GEQGARNKQRQR 314


>gi|78213141|ref|YP_381920.1| ribosomal large subunit pseudouridine synthase B [Synechococcus sp.
           CC9605]
 gi|78197600|gb|ABB35365.1| Pseudouridine synthase, Rsu [Synechococcus sp. CC9605]
          Length = 250

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 64/244 (26%), Positives = 102/244 (41%), Gaps = 1/244 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KA 70
           T QR+ K+IA AG+ SRR  E  +   RV V+G +             I VDG PL    
Sbjct: 2   TRQRLQKLIAAAGLCSRRRAEEWLQAGRVTVDGQVARVGDQADPQQQTIHVDGQPLPSPG 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               L +      + +       R+ +    P   + +  VGRLD ++ G LLLT+ G L
Sbjct: 62  MARVLLMNKPVGVICSCDDPQGRRTVLDLLPPEHRAGLHPVGRLDADSHGALLLTDLGEL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + YRV   G   +  L+  ++G+ + G      +V      G  + + 
Sbjct: 122 TLKLTHPRYSHAKTYRVWVQGVPSEPVLDRWRRGVPLDGRLTRPARVRQLRTWGDRSLLE 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + LREG+NR+I+++ E   + V  L R +     LG L  G    + +   +  L     
Sbjct: 182 IELREGRNRQIRRMAEALGYPVVDLQRTAIAGLPLGDLAEGCWIWLCEGEWKPLLERAGS 241

Query: 251 EEAQ 254
            +  
Sbjct: 242 MDLP 245


>gi|70726170|ref|YP_253084.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Staphylococcus haemolyticus JCSC1435]
 gi|68446894|dbj|BAE04478.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           Pseudouridylate synthase [Staphylococcus haemolyticus
           JCSC1435]
          Length = 230

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 104/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV+ ++ + +V VN  + +    ++  T D + V+G  +     
Sbjct: 1   MRLDKFLANMGVGTRTEVKHLLKKGKVTVNTSVEKSPKSHINPTEDIVHVNGKQVEFVNN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + +   D   R+ +          +  VGRLD +TEGLLL+TNDG  + 
Sbjct: 61  VYIMLNKPKGYI-SATHDESNRTVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGQFSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS    + Y V     V +  ++  KKGI++        Q+T   +  S     V 
Sbjct: 120 DLMSPSKHVSKTYEVTSKKPVTKVDIDAFKKGIILSDGPVKPAQLTRINETIS----HVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + EGK  ++K++F     +V  L R+      L   L +G  + +S K L+
Sbjct: 176 IYEGKYHQVKRMFHAIENEVLELKRLKIANLALDENLKSGEYKLLSDKELK 226


>gi|240145658|ref|ZP_04744259.1| ribosomal large subunit pseudouridine synthase B [Roseburia
           intestinalis L1-82]
 gi|257202246|gb|EEV00531.1| ribosomal large subunit pseudouridine synthase B [Roseburia
           intestinalis L1-82]
          Length = 251

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 64/257 (24%), Positives = 115/257 (44%), Gaps = 9/257 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R++K ++ AG+ SRRE +R +    V ++G++       V+    +   G P++K 
Sbjct: 2   QEPVRINKYLSEAGVCSRREADRQVEAGNVTIDGVVA-SMGAKVLPDQTVLFCGKPVKKE 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L  +HKP G+V T    +  + V     +   R+  +GRLD ++EGLLL+TN+G +
Sbjct: 61  EEMILLAFHKPTGIVCTAEKREKNNVVDYI--NYPKRIYPIGRLDKDSEGLLLMTNNGDI 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAW 188
              +        + Y V  +  V    L  L  G+ +          +V           
Sbjct: 119 VNRIMRAGNMHEKEYIVTVNKPVTDSFLRGLAGGVPLVELNATTRKCKVWRI----GKRQ 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E+F ++V +L+R      +LG L AG+ REV+ +  +E +   
Sbjct: 175 FGIILTQGLNRQIRRMCEYFGYRVEKLVRTRIMNIELGDLKAGTYREVTPQEYKELMRLV 234

Query: 249 LLEEAQVNLDAPIYSSE 265
                   +        
Sbjct: 235 KDSSNTTVIHGRDGGDR 251


>gi|163749124|ref|ZP_02156374.1| putative ribosomal RNA pseudouridylate synthase [Shewanella
           benthica KT99]
 gi|161331194|gb|EDQ02083.1| putative ribosomal RNA pseudouridylate synthase [Shewanella
           benthica KT99]
          Length = 250

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 62/254 (24%), Positives = 107/254 (42%), Gaps = 16/254 (6%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-------- 58
           + ++    R++K +A  G+ SRR   R I   ++ ++G L       +  TD        
Sbjct: 1   MTQDNPSIRLAKYLAMTGLCSRRAATRYIRDGQITLDGRLANHIDT-ISLTDSDSGFISQ 59

Query: 59  -HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
             ++ DGV ++  E  + W+ +K   + T         +   +L     R+  VGRLD +
Sbjct: 60  EILKFDGVLIQGIESKQYWMLNKS--VGTDCRLLPHDPSSLLHLLPASPRLYPVGRLDKD 117

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           + G LLLTNDG L + L  P     + Y V      D   L  + +G+  + +     Q+
Sbjct: 118 SRGQLLLTNDGELTQKLMHPDFGHSKTYHVLVDRNFDDSFLISMAQGVSYRDVTTLPCQM 177

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           T            + L +G NR+I+++ +   +KV  L R+     +LG L  G  RE++
Sbjct: 178 TRLDDDK----FEIILTQGLNRQIRRMSQALGYKVIDLKRVQIQTLKLGELEEGEMRELT 233

Query: 238 KKILREQLGPHLLE 251
              L   L      
Sbjct: 234 TNELALLLESCRPS 247


>gi|154504970|ref|ZP_02041708.1| hypothetical protein RUMGNA_02480 [Ruminococcus gnavus ATCC 29149]
 gi|153794853|gb|EDN77273.1| hypothetical protein RUMGNA_02480 [Ruminococcus gnavus ATCC 29149]
          Length = 241

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 111/229 (48%), Gaps = 3/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV+R I++ RV V+G  +++    +      +  DG  +   ++
Sbjct: 3   IRLDKYLADMGVGTRTEVKRAISKGRVSVDGACVKKPETKIDTEETTVVFDGQIVEYTKK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +++   D   ++ +   +      +  VGRLD +TEGLLL+TNDG LA 
Sbjct: 63  EYYMLHKPAG-VISATEDAREKTVIDLIVSRKRKDLFPVGRLDKDTEGLLLITNDGELAH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y  +  G V Q+ +    +G+ I         V    + G  + + + 
Sbjct: 122 RLLSPKKHVDKTYYAKVQGIVTQEDVRKFAEGVDIHEKKLTAPAVLEVVKSGEVSEILLT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
           + EGK  ++K++FE    KV  L R+S GP QL   L+ G  RE+++K 
Sbjct: 182 ICEGKFHQVKRMFEAVGKKVIYLKRLSMGPLQLDETLMPGEYRELTEKE 230


>gi|310641936|ref|YP_003946694.1| tRNA pseudouridine synthase a [Paenibacillus polymyxa SC2]
 gi|309246886|gb|ADO56453.1| tRNA pseudouridine synthase A [Paenibacillus polymyxa SC2]
          Length = 230

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 58/224 (25%), Positives = 96/224 (42%), Gaps = 10/224 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--E 71
            R++K I+  G  SRRE  R+IA  R+ +NG +   A   V   D + +DG P+     E
Sbjct: 1   MRINKYISETGFCSRRETNRLIAAGRITINGSVC-EAGAEVEPLDIVLIDGKPIPINHSE 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L L      + T     +G         +  SR+ ++GRLD  +EGL+LLTNDG + 
Sbjct: 60  PVYLALNKPIGIVCTAAEQVEG---NIIRYVNYPSRIFAIGRLDKASEGLILLTNDGSIV 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     V  +    + +G+ I  +     +V       S     +
Sbjct: 117 NQMMRSEHGHEKEYVVTVDKPVTDEFTQTMSRGVEILNVITKPCKVDRI----SEYEFRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
            L +G N +I+++ +   ++V +L R+      L  L  G  R 
Sbjct: 173 ILTQGLNLQIRRMCKALGYRVLKLERVRIMNITLDHLERGQWRH 216


>gi|200386647|ref|ZP_03213259.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Virchow str. SL491]
 gi|199603745|gb|EDZ02290.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Virchow str. SL491]
          Length = 231

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 102/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G +++ AA  ++    +  DG PL      
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLALQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTEDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKDLTKPATLEVI----TPVQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEEEI 227


>gi|297543604|ref|YP_003675906.1| RNA-binding S4 domain-containing protein [Thermoanaerobacter
           mathranii subsp. mathranii str. A3]
 gi|296841379|gb|ADH59895.1| RNA-binding S4 domain protein [Thermoanaerobacter mathranii subsp.
           mathranii str. A3]
          Length = 240

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 65/224 (29%), Positives = 102/224 (45%), Gaps = 4/224 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K+++  GI +R+EV++ I +  V VNG  ++ A + V    D I  DG  +   E 
Sbjct: 4   MRIDKLLSNIGIGTRKEVKKFIKEGLVLVNGNTVKDAGLIVDTEFDEILFDGEKINYKEF 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      +  T+   +                  VGRLD +TEGLLL+TNDG LA 
Sbjct: 64  IYIMMNKPKGVISATYDPIEKTVIDLLPQELKARNPFPVGRLDKDTEGLLLITNDGNLAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P    ++ Y     G V++  +   K+GIV++         + +       + V V
Sbjct: 124 KLLSPKKNVIKKYYAEILGFVNERDIKAFKEGIVLEDGYKTLPADLEILLSSEV-SKVYV 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
            +REGK  +IK++FE    KV  L R++ G   L   L  G  R
Sbjct: 183 YIREGKYHQIKRMFESVGKKVVYLKRLAMGSLTLDENLKPGQWR 226


>gi|226943690|ref|YP_002798763.1| Pseudouridine synthase [Azotobacter vinelandii DJ]
 gi|226718617|gb|ACO77788.1| Pseudouridine synthase [Azotobacter vinelandii DJ]
          Length = 382

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 92/350 (26%), Positives = 149/350 (42%), Gaps = 12/350 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +++ KV+AR G+ SRR++E  IA+ RV VNG +       V   D I +DG  LR+ E
Sbjct: 13  QGEKLQKVLARMGLGSRRDIEARIAEGRVMVNGTVAT-LGQRVGRHDAIALDGRLLRREE 71

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                R  L        + T +      +           R +++GRLDINT GLLL T 
Sbjct: 72  GAELVRRVLIYNKPDGEICTRNDPEGRPTVFDRLPRLKEGRWVNIGRLDINTTGLLLFTT 131

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-KGS 185
           DG LA  L  PS +  R Y VR  G+V ++ L  LK+G++++        +      +G 
Sbjct: 132 DGELANRLMHPSYEMDREYAVRVRGEVTEEMLETLKRGVMLEDGPARFTDIQEAPGGEGL 191

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           N W    + EG+NRE+++++E     V+RL R+ +GP  +   L  G  RE+++  + + 
Sbjct: 192 NHWFHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFMTSDLAMGRWREMTQDEV-DI 250

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK--LA 302
           L   +  E     +  +   E + R +      V     R +       G   Q++    
Sbjct: 251 LSREVGLEPLALPEMKLRFREKMERLQRKSAKPVGRGGARERVLRPAHEGAEAQERRAPR 310

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            P   R             +  +     R     RSP+   +R  R+   
Sbjct: 311 RPKEERAPRGRGTPVAERPAESVRKRPGRPAGE-RSPAESGERPARKPGP 359


>gi|332527848|ref|ZP_08403885.1| ribosomal large subunit pseudouridine synthase B [Rubrivivax
           benzoatilyticus JA2]
 gi|332112425|gb|EGJ12218.1| ribosomal large subunit pseudouridine synthase B [Rubrivivax
           benzoatilyticus JA2]
          Length = 487

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 82/339 (24%), Positives = 133/339 (39%), Gaps = 6/339 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +  K ++       ++ KV+A+AGI SRR++E+MI + R+ VNG         + + D I
Sbjct: 41  LPAKRVLAPEPDAPKLHKVLAQAGIGSRRDMEQMILEGRITVNGEPA-HIGQRIAAGDRI 99

Query: 61  EVDGVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G P+R          +  +     +VT        +           +  SVGRLDI
Sbjct: 100 AVGGKPVRYRIAPPPTRVIAYHKPAGEVVTHDDPQQRPTVFRRLPRLHQGKWQSVGRLDI 159

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NTEGLLL TN G LA  L  P     R Y VR  G +D      L +G+ I G       
Sbjct: 160 NTEGLLLFTNSGELANQLMHPRFGIEREYAVRSLGGLDDASRQKLLEGVEIDGQRCAFKS 219

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTRE 235
           +     +G+N W    + EG+NRE++K+F+     V+RLIRI YG   L   L  G   +
Sbjct: 220 IENGGGEGANQWYRCVITEGRNREVRKLFDAVGHAVSRLIRIRYGSVVLPKGLKRGVWVD 279

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +S++ +R       + E           +    R +        +      + +  +   
Sbjct: 280 LSEQDVRTLRRMTGVGERPEGEAREAREAGGDRRGKRGKRGRGGNAPEGAPRAARPQRRE 339

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREEN 334
             +        ++         +      + + G     
Sbjct: 340 GGEGPAIPNPLQQTFDKRAIQQERQRKREIPEDGPIPNP 378


>gi|320156638|ref|YP_004189017.1| ribosomal small subunit pseudouridine synthase A [Vibrio vulnificus
           MO6-24/O]
 gi|319931950|gb|ADV86814.1| ribosomal small subunit pseudouridine synthase A [Vibrio vulnificus
           MO6-24/O]
          Length = 233

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 52/232 (22%), Positives = 98/232 (42%), Gaps = 6/232 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  A+R+E  +++    V VN  + +  AV V     IE  G  L      
Sbjct: 1   MRLDKFLCDALGATRKEATKILKSGEVTVNEQVQKSGAVKVTEECVIEWQGRELAMQGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + LY     + +     +  +            +   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLYKPEGFVCSHEDGFNH-TAFVLLDEVKMDELHFAGRLDVDTTGLVLITDDGKWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + YRV     +  D    L +G+ ++         Q+++     +   V +
Sbjct: 120 ITSPKHKCDKTYRVWLADPIGSDYAEKLAEGVQLRNEKELTLPAQMSIVNADEN--EVLL 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            + EGK  ++K++F     KV +L R   G  +L   L  G  R ++++ + 
Sbjct: 178 TIHEGKYHQVKRMFAALGNKVEQLHRERIGAIELDESLEPGEYRYLTQEEID 229


>gi|262165811|ref|ZP_06033548.1| ribosomal small subunit pseudouridine synthase A [Vibrio mimicus
           VM223]
 gi|262025527|gb|EEY44195.1| ribosomal small subunit pseudouridine synthase A [Vibrio mimicus
           VM223]
          Length = 231

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 49/231 (21%), Positives = 94/231 (40%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  IE  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDLVQKSGAFKLKETSRIEWQGREITAHGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     + +       ++            +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDG-FNQTAFILLDEVNIQDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + YRV     +  D       GI ++G        Q+ +     S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQVDYAEQFTNGIELRGERELTLPAQLEVV----SETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R   G   L   L  G  R ++++ +
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDESLEPGEYRYLTEEEI 226


>gi|167562943|ref|ZP_02355859.1| RNA pseudouridylate synthase family protein [Burkholderia
           oklahomensis EO147]
          Length = 354

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 76/273 (27%), Positives = 123/273 (45%), Gaps = 6/273 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 48  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 106

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S          ++ ++VGRLD NTE
Sbjct: 107 GKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPTMKTAKWLAVGRLDFNTE 166

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 167 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELPEASRQKLLHGVELDDGPANFLRIRD 226

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 227 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELEE 286

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDR 271
             +R  +    L+            +E    D 
Sbjct: 287 AQVRRLMAAVGLKAPTEEKGKRGGVTERRQPDP 319


>gi|313901543|ref|ZP_07834987.1| ribosomal large subunit pseudouridine synthase B [Thermaerobacter
           subterraneus DSM 13965]
 gi|313468182|gb|EFR63652.1| ribosomal large subunit pseudouridine synthase B [Thermaerobacter
           subterraneus DSM 13965]
          Length = 327

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 77/321 (23%), Positives = 131/321 (40%), Gaps = 8/321 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL----- 67
           +R+ K+++RAG+ASRR+VE  IA  R+ VNG              D I +DG PL     
Sbjct: 4   ERLQKILSRAGVASRRQVEAWIAAGRLTVNGRPA-VLGTRADPARDVIALDGRPLAGLAE 62

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R + +  +  +     + T        +            +  VGRLD ++EGLLLLT+D
Sbjct: 63  RLSRKRYVLFHKPRGMVTTLRDPQGRPNVGDFCRRHGLQGLHPVGRLDFDSEGLLLLTDD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  P  +  +VY V   G +D  +L  L+ G+++           +   +    
Sbjct: 123 GELTFALTHPRHEVDKVYHVLVRGDLDPARLRRLRDGVLLDDGPARARIARVLRPRPGGG 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           WV V LREG+ R+++++ +   W+V RL+R++ GP +LG L AG+ R +S++ +      
Sbjct: 183 WVEVVLREGRKRQVRRMCQAVGWQVVRLVRVAVGPLRLGRLAAGAWRPLSRQEVESLRVA 242

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV-H 306
             L             +      R              +     + G + ++    P   
Sbjct: 243 AGLPPRPDEPAPRHRQAGEGRPARGPAWGRRVPAGLAGRPPGPARPGAAARRVSEGPALQ 302

Query: 307 RRNLASNVWMAKGIHSSFLSD 327
            +     V       +     
Sbjct: 303 GQGPRGRVSRPPSGRNRRRKA 323


>gi|225868275|ref|YP_002744223.1| ribosomal small subunit pseudouridine synthase B [Streptococcus
           equi subsp. zooepidemicus]
 gi|225701551|emb|CAW98765.1| putative ribosomal small subunit pseudouridine synthase B
           [Streptococcus equi subsp. zooepidemicus]
          Length = 237

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 101/233 (43%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +  AG+ SR +V+ ++ +++V VNG+        V   TD++   G  L     
Sbjct: 1   MRLDKFLVDAGLGSRSQVKLLLKKKQVSVNGVSQTSPKYQVNELTDNVTYQGQRLNYETF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T            +  +    V  VGRLD +T GLLLLTNDG LA 
Sbjct: 61  VYYMLNKPKGVISATEDPSHKTVLDLLDDTARQKAVFPVGRLDKDTHGLLLLTNDGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVT 190
            L  P     + Y  +  G + Q+ +    +GI ++        + +     S   + V 
Sbjct: 121 ALLSPKKHVAKQYLAKVDGTMTQEDVKHFAQGITLKDHQCMPAYLDILEINESLKTSLVK 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           + + EGK  ++K++       V+ L RIS GP QL + L  G+ R ++   L 
Sbjct: 181 ITIEEGKFHQVKRMVAACGKTVSDLQRISMGPLQLDSALAPGAYRRLTAAELE 233


>gi|167738823|ref|ZP_02411597.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 14]
          Length = 359

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 76/274 (27%), Positives = 124/274 (45%), Gaps = 6/274 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 49  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 107

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 108 GKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNTE 167

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 168 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQRLLHGVELDDGPANFLRIRD 227

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 228 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 287

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRP 272
             +R  +    L+    +            +  P
Sbjct: 288 AQVRRLMSTVGLKAPTEDKGGKRGGPAERRQPDP 321


>gi|254230520|ref|ZP_04923892.1| ribosomal large subunit pseudouridine synthase B [Vibrio sp. Ex25]
 gi|262393864|ref|YP_003285718.1| ribosomal large subunit pseudouridine synthase B [Vibrio sp. Ex25]
 gi|151936968|gb|EDN55854.1| ribosomal large subunit pseudouridine synthase B [Vibrio sp. Ex25]
 gi|262337458|gb|ACY51253.1| ribosomal large subunit pseudouridine synthase B [Vibrio sp. Ex25]
          Length = 312

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 90/313 (28%), Positives = 132/313 (42%), Gaps = 13/313 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E +I   RV VNG++ +        +  + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREIESLIKSGRVSVNGVVAKLGERLEDESSVVRIDGHIVSAKIQ 61

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  Y     L T H     R+          SR ISVGRLD NT GLLL T D
Sbjct: 62  EEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G+V + K+  L KG+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRQVEREYLVRVFGEVTEQKVRNLVKGVELEDGLARFEDVVYAGGEGMNH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LRE 243
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+  K    LRE
Sbjct: 182 TFYVVINEGRNREVRRLWESQECTVSRLKRVRYGDIFLDKKLPRGGWMELDLKEVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +     +E  ++L+       T  +       ++     R ++  +   G S       
Sbjct: 242 LVELRPEKETMLDLNK----DNTSRKRERARSQKIRRAVKRHEERVNTPKGRSNNPSRRK 297

Query: 304 PVHRRNLASNVWM 316
           P            
Sbjct: 298 PKKTAGDQGARSK 310


>gi|261210662|ref|ZP_05924954.1| ribosomal large subunit pseudouridine synthase B [Vibrio sp. RC341]
 gi|260840147|gb|EEX66727.1| ribosomal large subunit pseudouridine synthase B [Vibrio sp. RC341]
          Length = 319

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 85/319 (26%), Positives = 124/319 (38%), Gaps = 7/319 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E +I   RV VNG +             + VDG  +     
Sbjct: 2   SEKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGERLEDDNALVRVDGHVVSVKAQ 61

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  Y     L T H     R+          SR ISVGRLD NT GLLL T D
Sbjct: 62  EEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G V+++K+  L +G+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRQVEREYLVRVFGDVNEEKVRNLVRGVQLEDGMARFEDVMYAGGEGINH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+  K +   L 
Sbjct: 182 TFYVVINEGRNREVRRLWESQGTTVSRLKRVRYGDIFLDKKLPRGGWMELDLKQV-NYLR 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
             +    +              +       ++     R ++  S   G S   +      
Sbjct: 241 ELVELRPEKETVLNTAPDAATRKRERTRSQKIRRAVRRHEERVSTAPGRSSSARRKPGGE 300

Query: 307 RRNLASNVWMAKGIHSSFL 325
                      +       
Sbjct: 301 SSTRNKVANKQQSARKPRG 319


>gi|255326184|ref|ZP_05367270.1| ribosomal large subunit pseudouridine synthase B [Rothia
           mucilaginosa ATCC 25296]
 gi|255296638|gb|EET75969.1| ribosomal large subunit pseudouridine synthase B [Rothia
           mucilaginosa ATCC 25296]
          Length = 386

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 83/234 (35%), Positives = 133/234 (56%), Gaps = 2/234 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLR 68
           +    R+ K++A+AG+ASRR  E MI + RV VNG ++    V V  +   ++VDG+ ++
Sbjct: 144 DHDGVRLQKLLAQAGVASRRVCEEMITEGRVTVNGEVVTELGVRVDPSKVTVQVDGMTVQ 203

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
             ++     ++KP G+V+T  DP+GR  + D L S +  RV  VGRLD+ TEGLLLLTND
Sbjct: 204 TNDKLVYMAFNKPAGVVSTMEDPEGRPCISDFLRSSMSERVFHVGRLDVETEGLLLLTND 263

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  + Y V+  G ++      +KKGI ++       +  L      + 
Sbjct: 264 GELANRLTHPSYEVPKTYLVQVPGPMEPGVGAAMKKGIRLEDGVTRVDEFKLVDSTPGHV 323

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V V +  GKNR ++++F+   + V RL+R+  GP ++G+   G+ R +SK  +
Sbjct: 324 LVEVTIHSGKNRIVRRLFDAVGYPVERLVRVEMGPIRIGSQKQGTVRNLSKVEI 377


>gi|224825900|ref|ZP_03699004.1| RNA-binding S4 domain protein [Lutiella nitroferrum 2002]
 gi|224602124|gb|EEG08303.1| RNA-binding S4 domain protein [Lutiella nitroferrum 2002]
          Length = 242

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 68/244 (27%), Positives = 105/244 (43%), Gaps = 20/244 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
            P R+SK +A  GI SRRE +  I Q  VKV+G +       V+   HIE+D        
Sbjct: 2   EPVRLSKRLAELGICSRREADSYIEQGWVKVDGQVA-VLGFKVLPHQHIELDPRAKKAQL 60

Query: 64  -------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
                    P+          Y     L    +  +G  +     P+    +   GRLDI
Sbjct: 61  ERVTILLNKPVGYVSGQAEKGYKPAAMLAVPANHWEGDKSGIRFSPNHLKGLAPAGRLDI 120

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           ++ GLL+LT DG +A+ L   ++   + Y VR  G++  + L LL  G+ + G      +
Sbjct: 121 DSVGLLVLTQDGVVAKRLIGENSTVEKEYLVRVTGELSPEGLKLLNHGLSLDGQPLRPAK 180

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V+   +      +   LREGK R+I+++ E     V  L R+  G   LG L  G  R +
Sbjct: 181 VSWQNEDQ----LRFILREGKKRQIRRMCEQVGLYVVGLKRVRIGNVMLGDLPTGQWRYL 236

Query: 237 SKKI 240
            +  
Sbjct: 237 REDE 240


>gi|328955498|ref|YP_004372831.1| ribosomal large subunit pseudouridine synthase B [Coriobacterium
           glomerans PW2]
 gi|328455822|gb|AEB07016.1| ribosomal large subunit pseudouridine synthase B [Coriobacterium
           glomerans PW2]
          Length = 257

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 81/258 (31%), Positives = 125/258 (48%), Gaps = 5/258 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ + +ARAG+ASRR  E +++  RV+VNG++       V    D +EVDG+ +     
Sbjct: 1   MRLQRFLARAGVASRRGSEHLMSAGRVRVNGLVASELGTKVDVGADRVEVDGIEVVFGAP 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G +TT SDP GR  V + +P         VGRLD +T G+LL T DG LA
Sbjct: 61  PVYIVLNKPAGYLTTMSDPAGRPCVAELVPIRRFPGLFPVGRLDKDTTGVLLFTTDGDLA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWV 189
           + L  PS    + Y  R  G  D   L++L+ GI +        +  L  +   G ++ V
Sbjct: 121 QNLLHPSKHVAKTYLARVEGTPDSADLDVLRAGIELDDGPCLPARCRLVERRASGGSSLV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + +REG+  ++K++       V RL+R S+G      L  G  RE++   L   L P  
Sbjct: 181 ELIIREGRKNQVKRMLAAVGHPVQRLVRTSFGGVAASDLAEGEWRELTSCEL-ALLRPES 239

Query: 250 LEEAQVNLDAPIYSSETL 267
             +   +L  P  S +  
Sbjct: 240 PADPPAHLGRPGASRKES 257


>gi|262165448|ref|ZP_06033185.1| ribosomal large subunit pseudouridine synthase B [Vibrio mimicus
           VM223]
 gi|262402464|ref|ZP_06079025.1| ribosomal large subunit pseudouridine synthase B [Vibrio sp. RC586]
 gi|262025164|gb|EEY43832.1| ribosomal large subunit pseudouridine synthase B [Vibrio mimicus
           VM223]
 gi|262351246|gb|EEZ00379.1| ribosomal large subunit pseudouridine synthase B [Vibrio sp. RC586]
          Length = 319

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 85/319 (26%), Positives = 124/319 (38%), Gaps = 7/319 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E +I   RV VNG +             + VDG  +     
Sbjct: 2   SEKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGERLEDDNALVRVDGHVVSVKAQ 61

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  Y     L T H     R+          SR ISVGRLD NT GLLL T D
Sbjct: 62  EEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G V+++K+  L +G+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRQVEREYLVRVFGDVNEEKVRNLVRGVQLEDGMARFEDVMYAGGEGINH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+  K +   L 
Sbjct: 182 TFYVVINEGRNREVRRLWESQGTTVSRLKRVRYGDIFLDKKLPRGGWMELDLKQV-NYLR 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
             +    +              +       ++     R ++  S   G S   +      
Sbjct: 241 ELVELRPEKETVLNTAPDAATRKRERTRSQKIRRAVRRHEERVSTAPGRSGSARRKPGGE 300

Query: 307 RRNLASNVWMAKGIHSSFL 325
                      +       
Sbjct: 301 SSTRNKVASKQQSARKPRG 319


>gi|258621657|ref|ZP_05716688.1| pseudouridine synthase family 1 protein [Vibrio mimicus VM573]
 gi|258626398|ref|ZP_05721245.1| pseudouridine synthase family 1 protein [Vibrio mimicus VM603]
 gi|258581450|gb|EEW06352.1| pseudouridine synthase family 1 protein [Vibrio mimicus VM603]
 gi|258585888|gb|EEW10606.1| pseudouridine synthase family 1 protein [Vibrio mimicus VM573]
          Length = 319

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 85/319 (26%), Positives = 124/319 (38%), Gaps = 7/319 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E +I   RV VNG +             + VDG  +     
Sbjct: 2   SEKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGERLEDDNALVRVDGHVVSVKAQ 61

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  Y     L T H     R+          SR ISVGRLD NT GLLL T D
Sbjct: 62  EEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G V+++K+  L +G+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRQVEREYLVRVFGDVNEEKVRNLVRGVQLEDGMARFEDVMYAGGEGINH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+  K +   L 
Sbjct: 182 TFYVVINEGRNREVRRLWESQGTTVSRLKRVRYGDIFLDKKLPRGGWMELDLKQV-NYLR 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
             +    +              +       ++     R ++  S   G S   +      
Sbjct: 241 ELVELRPEKETVLNTAPDAATRKRERTRSQKIRRAVRRHEERVSTAPGRSASARRKPGGE 300

Query: 307 RRNLASNVWMAKGIHSSFL 325
                      +       
Sbjct: 301 SSTRNKVANKQQSARKPRG 319


>gi|82751342|ref|YP_417083.1| 16S RNA pseudouridylate synthase [Staphylococcus aureus RF122]
 gi|82656873|emb|CAI81302.1| 16S RNA pseudouridylate synthase [Staphylococcus aureus RF122]
          Length = 231

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 55/228 (24%), Positives = 100/228 (43%), Gaps = 7/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E 
Sbjct: 1   MRIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDMISVRGELIEYVEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + +   D   ++ +          +  VGRLD +TEGLLL+TNDG    
Sbjct: 61  VYIMLNKPKGYI-SGTEDHHSKTVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+    + Y V     + +D +   K+G+ +         +T    + S     V 
Sbjct: 120 ELMSPNKHVSKKYEVISANPITEDDIQAFKEGVTLSDGKVKPAILTYIDNQTS----HVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           + EGK  ++K++F     +V  L RI     +L   L +G  R +++ 
Sbjct: 176 IYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYRLLTEN 223


>gi|227833146|ref|YP_002834853.1| putative pseudouridylate synthase [Corynebacterium aurimucosum ATCC
           700975]
 gi|227454162|gb|ACP32915.1| putative pseudouridylate synthase [Corynebacterium aurimucosum ATCC
           700975]
          Length = 305

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 81/245 (33%), Positives = 127/245 (51%), Gaps = 4/245 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DH 59
           ++ KN        +R+ KV+A+AG+ASRR  E +I + RV+VNG ++ +    V    D 
Sbjct: 52  VEGKNKKNSQNQGERLQKVLAKAGVASRRHAEILIDEGRVEVNGQVIIKQGTRVDPNKDV 111

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDI 116
           I VDG  +   E T+ ++ +KP G+ +T SD  GR  V D +        R+  VGRLD 
Sbjct: 112 IRVDGTRINVNEETQYFVLNKPRGMQSTMSDDMGRPCVGDVVADRVVAGQRLFHVGRLDA 171

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +TEGLLLLTNDG LA  L  P  +  + Y     G+ D+  +  L++GI ++        
Sbjct: 172 DTEGLLLLTNDGELANRLMHPKYEVTKTYLATVLGEADKKLIRQLREGIELEDGLAQADY 231

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V +  +    + V V L EG+   ++++ +   + V RL+R      QLG +  GS R +
Sbjct: 232 VQIVDKNQGYSLVRVELHEGRKHIVRRMLKEAGYPVQRLVRTKLHTVQLGDMKPGSLRAL 291

Query: 237 SKKIL 241
           +   L
Sbjct: 292 NSNEL 296


>gi|227485055|ref|ZP_03915371.1| pseudouridylate synthase [Anaerococcus lactolyticus ATCC 51172]
 gi|227236888|gb|EEI86903.1| pseudouridylate synthase [Anaerococcus lactolyticus ATCC 51172]
          Length = 231

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 108/230 (46%), Gaps = 7/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG  SRR+ + +I + +VK+N  ++    ++V   D +EV+G  L   ++ 
Sbjct: 1   MRINKFIAHAGYTSRRKADELILKGKVKINDEVILEPGIDVCDDDRVEVEGKVLSIEKKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + LY     + +     + +      L  I  R  + GRLD ++EGLL++TNDG     
Sbjct: 61  YIKLYKPVGFITSNFDPYNEKDLNE--LVDIDKRFFAAGRLDKDSEGLLIITNDGEFTNN 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           L  P  +  + Y V+   ++   +     +G+ I  G    D ++        N    V 
Sbjct: 119 LIHPKYKLDKEYIVKVDKKLKDYQEKQFAQGLDIGNGEKTSDAKIEYL----ENNTYRVI 174

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + +G NR+I+++F+ F  KV  L RI  G   L  L     R  ++  L+
Sbjct: 175 IHQGYNRQIRRMFKVFGIKVVSLKRIRIGKISLSNLKEKEYRYFNEDELK 224


>gi|269119789|ref|YP_003307966.1| RNA-binding S4 domain protein [Sebaldella termitidis ATCC 33386]
 gi|268613667|gb|ACZ08035.1| RNA-binding S4 domain protein [Sebaldella termitidis ATCC 33386]
          Length = 228

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 67/229 (29%), Positives = 120/229 (52%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA +G  SRR+ + +I+Q RV +N    +   + V   D + +DG  ++     
Sbjct: 1   MRLNKYIAESGFCSRRKADELISQNRVTINKDTAK-LGMEVRDGDIVRIDGEKIKVDTDY 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP  ++ T+SD   R    D + S      + GRLD  TEG++L++NDG     
Sbjct: 60  EYYLLYKPKKVICTNSDNFARRLAVDFIRSKKRL-FTYGRLDYMTEGIILVSNDGDTYNK 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y  +    ++   L  L+KGI+I G      ++    +K  +A V V +
Sbjct: 119 VMHPRKKLFKTYIAKLDKPIEDKDLARLEKGILIDGQKTAPAKI----KKTDDAEVKVSI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EG+NR+I+K+FE  ++ V  L R++ G F++G L  G  R++++  + 
Sbjct: 175 FEGRNRQIRKMFENLHYNVKELKRVTIGEFKIGNLKPGEYRKLTEDEIE 223


>gi|237747775|ref|ZP_04578255.1| ribosomal large subunit pseudouridine synthase B [Oxalobacter
           formigenes OXCC13]
 gi|229379137|gb|EEO29228.1| ribosomal large subunit pseudouridine synthase B [Oxalobacter
           formigenes OXCC13]
          Length = 510

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 80/321 (24%), Positives = 130/321 (40%), Gaps = 6/321 (1%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
             K  ++      ++ KV+A AG+ SRR++E +I   RV VNG         ++ TD + 
Sbjct: 157 NAKRELRAEDDAPKLHKVLADAGLGSRRDMEELIIAGRVSVNGEPA-HIGQRILPTDQVR 215

Query: 62  VDGVPLRKAE----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           ++G  L++         +  +     +V+        S   +      S+ ++VGRLD N
Sbjct: 216 INGKLLQRKVTKSLPKVMLYHKPAGEIVSRDDPEKRASVFDNLPSLKNSKWLAVGRLDFN 275

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLLL TN+G LA  L  P     R Y VR  G++++     L  G+ +         +
Sbjct: 276 TEGLLLFTNNGDLANRLMHPRYNIEREYAVRTLGELEEGMRQKLLAGVDLGDGIGQFSSI 335

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                +G N W  V + EG+NRE++++FE     V+RLIR  YG   L   L  G   E+
Sbjct: 336 ADGGGEGINKWYRVTIGEGRNREVRRMFESVGLTVSRLIRTRYGVITLPQNLKRGRWDEL 395

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
               +R  +    +E              +    R     +     +        +N  S
Sbjct: 396 DDNAVRNLMRLSGMEPKGDKSATETAKGRSAGAKRQGQDRKGSFGRSETLSIHEFRNNDS 455

Query: 297 KQKKLATPVHRRNLASNVWMA 317
           + KK  T   +    S     
Sbjct: 456 RSKKGPTSAQKGAPRSRQPDP 476


>gi|42781479|ref|NP_978726.1| RNA pseudouridylate synthase family protein [Bacillus cereus ATCC
           10987]
 gi|42737401|gb|AAS41334.1| RNA pseudouridylate synthase family protein [Bacillus cereus ATCC
           10987]
          Length = 238

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 64/228 (28%), Positives = 108/228 (47%), Gaps = 7/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  ++ I ++RV +NG + +     V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKXINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCTSEKSV--KGNIIDLVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T      S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEITQL----SKYEFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKR 225


>gi|327538428|gb|EGF25099.1| ribosomal large subunit pseudouridine synthase B [Rhodopirellula
           baltica WH47]
          Length = 395

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 83/339 (24%), Positives = 139/339 (41%), Gaps = 3/339 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+++++A AG  SRR+ E +I + RV V+G  +      V      + VDG  LR  +  
Sbjct: 26  RINQLLASAGFGSRRQCEELIREGRVDVDGETITELGTTVDPDLQKVRVDGNYLRPQKLV 85

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +      + T          +  +L     RV  VGRLDI++EGL+LLTNDG LA+ 
Sbjct: 86  YYVVNKPVGIVTTNRDPRGRPRVI--DLVPPTERVFPVGRLDISSEGLILLTNDGDLAQK 143

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     +VYRV   G+V  + +  +++GI I           +   +     + + L
Sbjct: 144 LAHPKFGIQKVYRVVVAGEVRGETMKKMREGIYIAEGLVQVDGAKIIKARTKATEMEIRL 203

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           +EGKNREI+++   F  KV +L R++ GP +LG +  G+ R++++  + +        E 
Sbjct: 204 KEGKNREIRRILARFGHKVQQLRRVAIGPLKLGDVPRGAYRKLTRDEVDKLRRSIDAAEK 263

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
                 P   +      R    +             + K G    K   T   R +    
Sbjct: 264 AAKTAPPARPASKQSIKRRPGGASRNVAAKGTGGRPAFKGGRKAVKNSRTTETRSSATGP 323

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                    +  S           +P    K++ R T+ 
Sbjct: 324 KTSKPVKKRTLSSGGSTGTVIGADAPKESRKKTERGTNP 362


>gi|89094110|ref|ZP_01167053.1| ribosomal large subunit pseudouridine synthase B [Oceanospirillum
           sp. MED92]
 gi|89081585|gb|EAR60814.1| ribosomal large subunit pseudouridine synthase B [Oceanospirillum
           sp. MED92]
          Length = 276

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 84/273 (30%), Positives = 128/273 (46%), Gaps = 7/273 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
           +++ KV+AR+G+ SRRE+ER I + RV+VNG +       +   D +EVDG         
Sbjct: 4   EKLHKVLARSGVGSRREMERWIKEGRVQVNGQVAT-LGDRISEGDQVEVDGRKTPLIFDN 62

Query: 71  --ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ER  L        + T H      +      P    R I++GRLDINT GLLL T DG
Sbjct: 63  QAERRVLIYNKPVGEICTRHDPEGRPTVFRHLPPLKEGRWIAIGRLDINTSGLLLFTTDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS Q  R Y VR  G VD+  L  LK G++++        V     +G+N W
Sbjct: 123 ELANALMHPSAQIDREYAVRVLGDVDEAMLQRLKDGVLLEDGMARFTDVQFFDGEGANKW 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
               + EG+NRE+++++E    +VNRL R+ +GP  L   + +G+ +E++ K +      
Sbjct: 183 YHCVVMEGRNREVRRLWESQEIQVNRLKRVRFGPLFLPSDVRSGTWKELTVKEVNSLSKM 242

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
             L+  +          +   R +         
Sbjct: 243 LELKPKRAPKMTADEKQKYQRRFKKQKARRQEG 275


>gi|302039244|ref|YP_003799566.1| putative pseudouridine synthase [Candidatus Nitrospira defluvii]
 gi|300607308|emb|CBK43641.1| putative Pseudouridine synthase [Candidatus Nitrospira defluvii]
          Length = 236

 Score =  166 bits (421), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 63/227 (27%), Positives = 109/227 (48%), Gaps = 7/227 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K     G+ SRRE +R+IA+ RV +NG + +     V   D +  DGV L++  R 
Sbjct: 1   MRINKFFTEQGLCSRREADRLIAEGRVTINGRVAK-LGDQVSPQDAVARDGVVLQRGNRA 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               YHKP+G+ TT      R+ + +      +R+  +GRLD ++ GL+LLTNDG +   
Sbjct: 60  VYLKYHKPVGVTTTTEPHVRRNIIAEI--GHTARIFPIGRLDKDSSGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        R YRV    + D+  L  + +G+ I G+      +             + L
Sbjct: 118 ILRVEHGHEREYRVEVDREFDETFLARMARGVTILGVPTRPCTLARL----GPRRFRIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            EG+NR+I+++ +   ++V  L R+      +  L AG   +++   
Sbjct: 174 TEGRNRQIRRMCQALGYRVVSLHRVRIMHITIDGLHAGQWMDLTHDE 220


>gi|312899113|ref|ZP_07758491.1| conserved hypothetical protein [Megasphaera micronuciformis F0359]
 gi|310619780|gb|EFQ03362.1| conserved hypothetical protein [Megasphaera micronuciformis F0359]
          Length = 237

 Score =  166 bits (421), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 58/230 (25%), Positives = 99/230 (43%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K++  +G  +R+E++ +     V VNG ++  ++V V     + V G  +     +
Sbjct: 2   IRLDKLLGHSGYGTRKEIKSLCKSGDVTVNGEIVRDSSVKVDEGATVIVAGEKVEYEAVS 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L+     +  T                  SRV  VGRLDI+T GLLLL+NDG  A  
Sbjct: 62  YLMLHKPAGVVSATQDSRVRTVLDILPSRYAASRVAPVGRLDIDTTGLLLLSNDGTWAHK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVG 192
           +  P     +VY  +  G +  D       GIV++        +     +K +   + + 
Sbjct: 122 VISPKKHVPKVYEAQVEGVIPADVGERFAAGIVLEDGVECLPAR----AEKTAEGRLQIT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++       V  L R   G   L   L AG  R+++K+ +
Sbjct: 178 VCEGKFHQVKRMCSVVGLTVTSLHRSRIGGLALDKNLQAGEYRKLTKEEI 227


>gi|307151744|ref|YP_003887128.1| RNA-binding S4 domain-containing protein [Cyanothece sp. PCC 7822]
 gi|306981972|gb|ADN13853.1| RNA-binding S4 domain protein [Cyanothece sp. PCC 7822]
          Length = 259

 Score =  166 bits (421), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 79/256 (30%), Positives = 128/256 (50%), Gaps = 15/256 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK-- 69
            +RV K++++ GIASRR+ E++I   RV++NG +            D +EVDG  ++   
Sbjct: 2   TERVQKILSQWGIASRRQAEKLILAGRVRLNGNIA-SLGDKADPHQDLLEVDGTIIQPVN 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTN 126
             R    L +KP+G+V+T  DP  R TV + LP   +  + +  VGRLDIN+ G L+LTN
Sbjct: 61  RPRPIYILLNKPLGVVSTCHDPQNRPTVLELLPATLNQGTGIHPVGRLDINSTGALVLTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L   L  P     + Y+V   G   +  L   ++G+++ G      QV +  +    
Sbjct: 121 DGELTLSLTHPRYHLPKTYQVWIDGNPGEQILQQWREGVMLMGKKTQPAQVKVVKRHHQQ 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-----TLLAGSTREVSKKI- 240
             + V + EGKNR+I+++ +   + V +L R + G  QL      +L +G  R +     
Sbjct: 181 TQLQVVITEGKNRQIRRIVQLLGFNVLKLHRTAIGLIQLNPANEPSLASGDYRFLKTFEI 240

Query: 241 --LREQLGPHLLEEAQ 254
             LR  +   +  EA 
Sbjct: 241 DYLRNHVNLAIGTEAA 256


>gi|258624941|ref|ZP_05719868.1| ribosomal small subunit pseudouridine synthase A [Vibrio mimicus
           VM603]
 gi|258582797|gb|EEW07619.1| ribosomal small subunit pseudouridine synthase A [Vibrio mimicus
           VM603]
          Length = 257

 Score =  166 bits (421), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 49/238 (20%), Positives = 96/238 (40%), Gaps = 8/238 (3%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +Q +    R+ K +  A   +R+E   ++    V V+ ++ +  A  +  T  +E  G  
Sbjct: 20  LQADEVSMRLDKFLCDALGTTRKEATMLLKSGEVTVDDLVQKSGAFKLKETSRVEWQGRE 79

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +       + ++     + +       ++            +   GRLD++T GLLL+T+
Sbjct: 80  ITAHGPRYIMMHKPDGVVCSHEDG-FNQTAFILLDEVNIQDLHFAGRLDVDTTGLLLITD 138

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKG 184
           DG  +  +  P  +  + YRV     +  D       GI ++G        Q+ +     
Sbjct: 139 DGQWSHRVTSPKHKCEKTYRVWLADPIQADYAEQFTNGIELRGERELTLPAQLEVV---- 194

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           S   V + + EGK  ++K++F     KV  L R   G   L   L  G  R ++++ +
Sbjct: 195 SETEVLLTIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDESLEPGEYRYLTEEEI 252


>gi|254285421|ref|ZP_04960386.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           AM-19226]
 gi|150424693|gb|EDN16629.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           AM-19226]
          Length = 231

 Score =  166 bits (421), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 48/231 (20%), Positives = 95/231 (41%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSCVEWQGREITLHGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     + +       ++            +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDG-FNQTAFTLLDEVNIQDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + YRV     +  D      +GI ++G        Q+ +     S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELRGERELTLPAQLEVI----SETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R   G   L   L  G  R ++++ +
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEEEV 226


>gi|145298420|ref|YP_001141261.1| ribosomal large subunit pseudouridine synthase B [Aeromonas
           salmonicida subsp. salmonicida A449]
 gi|142851192|gb|ABO89513.1| ribosomal large subunit pseudouridine synthase B [Aeromonas
           salmonicida subsp. salmonicida A449]
          Length = 307

 Score =  166 bits (421), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 79/306 (25%), Positives = 131/306 (42%), Gaps = 7/306 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +       V     I VDG  ++    
Sbjct: 2   SEKLQKVLARAGHGSRREMEALITAGRVSVDGKVAT-LGDRVEVNAVIRVDGHTVKTRAE 60

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  +     + T H      +          +R I+VGRLD+NT GLLL T D
Sbjct: 61  EEMICRVLAYHKSEGEMCTRHDPEGRPTVFDRLPKLDSARWIAVGRLDVNTSGLLLFTTD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G++ +  L  L+KG+ ++       ++     +G N 
Sbjct: 121 GELANRLMHPSHEVEREYAVRVFGEITEAMLQRLRKGVQMEDGMAKFNKIKPAGGEGLNQ 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           W  V L EG+NRE+++++E    +V+RL+R+ YG   L   +  G  +E+    +    G
Sbjct: 181 WFNVTLTEGRNREVRRLWESQEVQVSRLMRVRYGDVTLDRGIPRGGWQELKLPEVNYLRG 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              +     +        ++    +   I         M+    +    + ++K  +   
Sbjct: 241 LVNMPPETESKVDLQQDGKSTRHKQAAQIRRAVKRHKDMQGMEPRARSTTARRKPTSSTR 300

Query: 307 RRNLAS 312
                S
Sbjct: 301 NSGTGS 306


>gi|110803687|ref|YP_698469.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           perfringens SM101]
 gi|110684188|gb|ABG87558.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           perfringens SM101]
          Length = 236

 Score =  166 bits (421), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 67/228 (29%), Positives = 114/228 (50%), Gaps = 2/228 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKAER 72
           +R+ K +AR G+ASRR+ E +I   +VKVN  +++     V  +  +   +   +   E 
Sbjct: 3   ERLQKYMARCGVASRRKCEEIICSGKVKVNDTVVDSLGTKVDPSVDVVSVNNKVISPEEN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G VTT+ D   R T+ D +     R+  +GRLD ++ GLLLLTNDG +  
Sbjct: 63  KVYIMLNKPEGYVTTNKDEKNRKTILDIVKVN-ERIYPIGRLDYDSSGLLLLTNDGDVYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y     G   ++++N  +KG+ I      + ++ L  +  ++  V + 
Sbjct: 122 KIIHPRVNLNKEYIALVKGIFTEEEMNKFRKGVDIGDYKTAECEIELLEKYTNSCKVKII 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           + EGKNR+I+++   FN +V  L R + G   L  L  G  R +S   
Sbjct: 182 IHEGKNRQIRRMCAAFNHEVVSLKREAIGSLTLKNLKKGEWRYLSSSE 229


>gi|188532201|ref|YP_001905998.1| 23S rRNA pseudouridine synthase F [Erwinia tasmaniensis Et1/99]
 gi|188027243|emb|CAO95082.1| Ribosomal large subunit pseudouridine synthase F [Erwinia
           tasmaniensis Et1/99]
          Length = 293

 Score =  166 bits (421), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 58/293 (19%), Positives = 112/293 (38%), Gaps = 5/293 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++K I  +GI SRR+ +R I Q  V +NG         V++ D ++V+G  +     
Sbjct: 6   SIRLNKYIGESGICSRRDADRYIEQGNVFINGKRASV-GDRVLAGDVVKVNGQLIEPRNE 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +    +  +G      +  +   RV  +GRLD +++GL+ LTN G L  
Sbjct: 65  EDLVVIALNKPVGIVSTTEEGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  V ++ +  L  G+ + G            +K S     + 
Sbjct: 125 KILRAGNDHEKEYLVTVNKPVTEEFIRGLGAGVPMLGTV----TKKCKVKKESTFVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E F ++V +L R       L  L  G  R+++   L E         
Sbjct: 181 LVQGLNRQIRRMSEHFGYEVTKLERTRIMNVSLKGLPPGEWRDLTDDELIELFKLIENSS 240

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           ++           +  +    +             N++ +    +  +     
Sbjct: 241 SEDGAAKKAKPKASSAKKPAAVSGAKAGAKAGGNANAAARKRFVQPGRKKKGR 293


>gi|15641192|ref|NP_230824.1| pseudouridine synthase family 1 protein [Vibrio cholerae O1 biovar
           El Tor str. N16961]
 gi|121587810|ref|ZP_01677569.1| pseudouridine synthase family 1 protein [Vibrio cholerae 2740-80]
 gi|121728227|ref|ZP_01681260.1| pseudouridine synthase family 1 protein [Vibrio cholerae V52]
 gi|153215349|ref|ZP_01949962.1| pseudouridine synthase family 1 protein [Vibrio cholerae 1587]
 gi|153819079|ref|ZP_01971746.1| pseudouridine synthase family 1 protein [Vibrio cholerae NCTC 8457]
 gi|153823509|ref|ZP_01976176.1| pseudouridine synthase family 1 protein [Vibrio cholerae B33]
 gi|153826657|ref|ZP_01979324.1| pseudouridine synthase family 1 protein [Vibrio cholerae MZO-2]
 gi|183179584|ref|ZP_02957795.1| pseudouridine synthase family 1 protein [Vibrio cholerae MZO-3]
 gi|227081351|ref|YP_002809902.1| pseudouridine synthase family 1 protein [Vibrio cholerae M66-2]
 gi|229505227|ref|ZP_04394737.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           BX 330286]
 gi|229511103|ref|ZP_04400582.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           B33]
 gi|229515560|ref|ZP_04405019.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           TMA 21]
 gi|229518222|ref|ZP_04407666.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           RC9]
 gi|229520392|ref|ZP_04409817.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           TM 11079-80]
 gi|229529733|ref|ZP_04419123.1| LSU pseudouridine synthase B [Vibrio cholerae 12129(1)]
 gi|229608246|ref|YP_002878894.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           MJ-1236]
 gi|254226705|ref|ZP_04920282.1| pseudouridine synthase family 1 protein [Vibrio cholerae V51]
 gi|254291998|ref|ZP_04962777.1| pseudouridine synthase family 1 protein [Vibrio cholerae AM-19226]
 gi|254848305|ref|ZP_05237655.1| pseudouridine synthase family 1 protein [Vibrio cholerae MO10]
 gi|255745589|ref|ZP_05419537.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholera
           CIRS 101]
 gi|262158338|ref|ZP_06029454.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           INDRE 91/1]
 gi|297578779|ref|ZP_06940707.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           RC385]
 gi|298498719|ref|ZP_07008526.1| pseudouridine synthase family 1 protein [Vibrio cholerae MAK 757]
 gi|34098735|sp|Q9KSS7|RLUB_VIBCH RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|9655656|gb|AAF94338.1| pseudouridine synthase family 1 protein [Vibrio cholerae O1 biovar
           El Tor str. N16961]
 gi|121547974|gb|EAX58055.1| pseudouridine synthase family 1 protein [Vibrio cholerae 2740-80]
 gi|121629478|gb|EAX61904.1| pseudouridine synthase family 1 protein [Vibrio cholerae V52]
 gi|124114792|gb|EAY33612.1| pseudouridine synthase family 1 protein [Vibrio cholerae 1587]
 gi|125620766|gb|EAZ49123.1| pseudouridine synthase family 1 protein [Vibrio cholerae V51]
 gi|126510362|gb|EAZ72956.1| pseudouridine synthase family 1 protein [Vibrio cholerae NCTC 8457]
 gi|126518977|gb|EAZ76200.1| pseudouridine synthase family 1 protein [Vibrio cholerae B33]
 gi|149739519|gb|EDM53747.1| pseudouridine synthase family 1 protein [Vibrio cholerae MZO-2]
 gi|150422075|gb|EDN14043.1| pseudouridine synthase family 1 protein [Vibrio cholerae AM-19226]
 gi|183012995|gb|EDT88295.1| pseudouridine synthase family 1 protein [Vibrio cholerae MZO-3]
 gi|227009239|gb|ACP05451.1| pseudouridine synthase family 1 protein [Vibrio cholerae M66-2]
 gi|229333507|gb|EEN98993.1| LSU pseudouridine synthase B [Vibrio cholerae 12129(1)]
 gi|229342490|gb|EEO07483.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           TM 11079-80]
 gi|229344937|gb|EEO09911.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           RC9]
 gi|229347329|gb|EEO12289.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           TMA 21]
 gi|229351068|gb|EEO16009.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           B33]
 gi|229357450|gb|EEO22367.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           BX 330286]
 gi|229370901|gb|ACQ61324.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           MJ-1236]
 gi|254844010|gb|EET22424.1| pseudouridine synthase family 1 protein [Vibrio cholerae MO10]
 gi|255736664|gb|EET92061.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholera
           CIRS 101]
 gi|262029779|gb|EEY48427.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           INDRE 91/1]
 gi|297536373|gb|EFH75206.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           RC385]
 gi|297543052|gb|EFH79102.1| pseudouridine synthase family 1 protein [Vibrio cholerae MAK 757]
 gi|327483880|gb|AEA78287.1| Ribosomal large subunit pseudouridine synthase B LSU Psi2605
           [Vibrio cholerae LMA3894-4]
          Length = 321

 Score =  166 bits (421), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 91/320 (28%), Positives = 132/320 (41%), Gaps = 9/320 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E +I   RV VNG +             + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGERLEDDNAVVRIDGHVVSVKAQ 61

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  Y     L T H     R+          SR ISVGRLD NT GLLL T D
Sbjct: 62  EEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G V ++K+  L +G+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRQVEREYLVRVFGDVTEEKVRNLVRGVQLEDGMARFEDVMYAGGEGINH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI---LRE 243
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+  K    LRE
Sbjct: 182 TFYVVINEGRNREVRRLWESQGTTVSRLKRVRYGDIFLDKKLPRGGWMELDLKQVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +     +E  +N+     + +        I   V     R+     +      ++K   
Sbjct: 242 LVELRPEKETVLNMAPDAATRKRERTRSQKIRRAVRRHEERISATPGRSGKAPARRKPGG 301

Query: 304 PVHRRNLASNVWMAKGIHSS 323
               RN  +N   +      
Sbjct: 302 ESSTRNKVANQQQSSRKPRG 321


>gi|288555072|ref|YP_003427007.1| RNA pseudouridine synthase family protein [Bacillus pseudofirmus
           OF4]
 gi|288546232|gb|ADC50115.1| RNA pseudouridine synthase family protein [Bacillus pseudofirmus
           OF4]
          Length = 229

 Score =  166 bits (421), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 66/228 (28%), Positives = 102/228 (44%), Gaps = 7/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+   ++  G  SRRE ER++A  R+ VNG    +    V + D I +DG P+   ER 
Sbjct: 1   MRIQLYMSNTGYCSRRETERLLAAGRITVNGKTATK-DTFVDTDDCILLDGSPVPMKERN 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L HKP G+V T            +  +   R+ +VGRLD ++EGLLLLTNDG +   
Sbjct: 60  IYLLLHKPTGIVCTAQRQV--KNNLIDYMNYRERIFAVGRLDKDSEGLLLLTNDGDIVNK 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V          L  +  G+ I         VT            + L
Sbjct: 118 IMRVENGHEKEYIVTVDRPYPDTFLKSMASGVEILDQVTEPCTVTRI----DEMTFRIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++G NR+I+++ + F + V RL R+      +  L  G  RE++ + L
Sbjct: 174 KQGLNRQIRRMTKEFGYYVTRLRRVRIMNLSIDRLPYGQWRELTDEEL 221


>gi|162447507|ref|YP_001620639.1| pseudouridylate synthase, 16S RNA-specific [Acholeplasma laidlawii
           PG-8A]
 gi|161985614|gb|ABX81263.1| pseudouridylate synthase, 16S RNA-specific [Acholeplasma laidlawii
           PG-8A]
          Length = 236

 Score =  166 bits (421), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 56/232 (24%), Positives = 106/232 (45%), Gaps = 5/232 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++  I++ G+ASRR  + +I   R+KVNG+      + +   D + +D   +   E  
Sbjct: 1   MRLNLYISKTGVASRRGADSLIEHGRIKVNGVTA-VLGMQITKNDVVTLDNNIIEPLEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L +KP+G+V+T +     +       +   ++  VGRLD ++ GL+LLTNDG +   
Sbjct: 60  FYILLNKPVGIVSTTNTAISGN--MITFMNFKEKIFPVGRLDKDSHGLILLTNDGSIVNK 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY--GDMQVTLDTQKGSNAWVTV 191
           +        + Y V  +   D   +  +  G+ I         M +    +       ++
Sbjct: 118 ILRVENGHDKEYHVTLNKPYDDYFIETMTSGVEIYNPVAHEKQMTMPSILKPLDERTFSL 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            +R+G NR+I+++ +   ++V  L R+      LG L  G  R ++   L+E
Sbjct: 178 TIRQGLNRQIRRMADSLGYRVESLERVRIMHLTLGDLPVGYWRYLTSDELKE 229


>gi|32472361|ref|NP_865355.1| ribosomal large subunit pseudouridine synthase B [Rhodopirellula
           baltica SH 1]
 gi|32443597|emb|CAD73039.1| ribosomal large subunit pseudouridine synthase B [Rhodopirellula
           baltica SH 1]
          Length = 395

 Score =  166 bits (421), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 84/339 (24%), Positives = 140/339 (41%), Gaps = 3/339 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+++++A AG  SRR+ E +I + RV V+G  +      V      + VDG  LR  +  
Sbjct: 26  RINQLLASAGFGSRRQCEELIREGRVDVDGETITELGTTVDPDLQKVRVDGNYLRPQKLV 85

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +      + T          +  +L     RV  VGRLDI++EGL+LLTNDG LA+ 
Sbjct: 86  YYVVNKPVGIVTTNRDPRGRPRVI--DLVPPTERVFPVGRLDISSEGLILLTNDGDLAQK 143

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     +VYRV   G+V  + +  +++GI I           +   +     + + L
Sbjct: 144 LAHPKFGIQKVYRVVVAGEVRGETMKKMREGIYIAEGLVQVDGAKIIKARTKATEMEIRL 203

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           +EGKNREI+++   F  KV +L R++ GP +LG +  G+ R++++  + +        E 
Sbjct: 204 KEGKNREIRRILARFGHKVQQLRRVAIGPLKLGDVPRGAYRKLTRDEVDKLRRSIDAAEK 263

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
                 P   +      R    +             + K G    KK  T   R +    
Sbjct: 264 AAKTAPPARPASKQSIKRRPGGASRNVAAKGTGGRPAFKGGRKAVKKSRTTETRSSATGP 323

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                    +  S           +P    K++ R T+ 
Sbjct: 324 KTSKPVKKRTLSSGGSTGTVIGADAPKESRKKTERGTNP 362


>gi|161503173|ref|YP_001570285.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160864520|gb|ABX21143.1| hypothetical protein SARI_01241 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 291

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 86/288 (29%), Positives = 128/288 (44%), Gaps = 10/288 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD+ KL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDESKLRDLSRGVQLEDGPAAFKTIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDILLPKGLPRGGWAELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           + +       ++V ++      +     R            R    ++
Sbjct: 242 DLVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQMAGGRRSGGRNN 289


>gi|13472018|ref|NP_103585.1| hypothetical protein mlr2177 [Mesorhizobium loti MAFF303099]
 gi|14022763|dbj|BAB49371.1| mlr2177 [Mesorhizobium loti MAFF303099]
          Length = 250

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 68/227 (29%), Positives = 110/227 (48%), Gaps = 1/227 (0%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTR 74
           +++ +++ G+ SR + E +IA+ RV+V G ++  AA+ V    D I VDG P+    +  
Sbjct: 19  LNRALSKLGLCSRTQAELLIAEGRVRVGGKVVRDAALRVDLNRDRIVVDGEPVIAERKVY 78

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L      + T        +            V  VGRLD  +EGLLL+TND   A  L
Sbjct: 79  VMLNKPRGLVTTRDDPQQRDTVYACLEGLDLPFVSPVGRLDKASEGLLLMTNDTHFANRL 138

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P++   + Y V+     D+  L  L+ G+ + G       + L    G  AW+ + L 
Sbjct: 139 MDPASHLPKTYHVQVGTVPDEAMLETLRAGVSVDGETLTANSIVLLRSGGRTAWLEIVLD 198

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           EG+NR I+++      +V RLIRI+ G   LG L  G+ R ++ + L
Sbjct: 199 EGRNRHIRRLLAAHGIEVKRLIRIAIGRLPLGDLAKGTARHLTPEEL 245


>gi|301165765|emb|CBW25337.1| putative RNA pseudouridylate synthase [Bacteriovorax marinus SJ]
          Length = 343

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 88/272 (32%), Positives = 130/272 (47%), Gaps = 4/272 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK-AER 72
           R+ K IA  GI SRR+ E +I Q RVKVNG  +      V    D + VDG      +  
Sbjct: 5   RLQKFIADCGITSRRKAEELIVQGRVKVNGETIRVLGTKVNPDIDAVIVDGQIADLGSVD 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G VTT  DP+GR TV D    +  R+  VGRLD  +EGLLLLTNDG +A 
Sbjct: 65  KVYLVMNKPRGYVTTVEDPEGRKTVMDLCKEVAERIYPVGRLDYLSEGLLLLTNDGEVAN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           ++  PS    +VY V+  G V +  L  L+ G+ ++      + V +  Q  +  WV   
Sbjct: 125 MVMHPSFNITKVYEVKVFGSVTETILKKLRAGVQLEEGFVKPLSVRVIKQLPNKTWVEFR 184

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL--L 250
           L EG+NREI+K+ E     V++L R++     +  +  G  R ++KK L   +G      
Sbjct: 185 LGEGRNREIRKICEACGLTVDKLKRVAIEGLTVEGIAPGKFRYINKKQLLSLIGLSEDGR 244

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDF 282
           +   V        +  L +      +   D+ 
Sbjct: 245 KLESVKAWVSSKKTVNLKKKGVQPGTAADDEA 276


>gi|290475293|ref|YP_003468181.1| Ribosomal large subunit pseudouridine synthase B [Xenorhabdus
           bovienii SS-2004]
 gi|289174614|emb|CBJ81408.1| Ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Xenorhabdus bovienii SS-2004]
          Length = 317

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 89/317 (28%), Positives = 135/317 (42%), Gaps = 8/317 (2%)

Query: 1   MKDK-NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTD 58
           M DK    Q+    +++ K++ARAG  SRRE+E  I + R+ ++G        + V  + 
Sbjct: 1   MSDKTQKTQKTERTEKLQKILARAGHGSRREIEGYIQEGRISIDGKTATLGDRIEVKPSI 60

Query: 59  HIEVDGVPLRKAERT-----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
            I +DG  L   E        L  Y     L T H      +          +R I+VGR
Sbjct: 61  KIRLDGRILSIKEPQKTICRVLAYYKPEGELCTRHDPEGRPTVFDRLPKMQDARWIAVGR 120

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LDINT GLLL T DG LA  L  PS +  R Y VR  G+VD  KL  L +G+ ++     
Sbjct: 121 LDINTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGEVDNAKLRQLTQGVQLEDGPAS 180

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGS 232
              V+    +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G 
Sbjct: 181 FKTVSFKGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIDLPKGLPRGG 240

Query: 233 TREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
             E+  +          L E  ++  A       +  ++     +        +    + 
Sbjct: 241 WTELGLEQTNYLRQLVDLNEETMSKVAVERDQRRIKANQIRRAVKRHSQVGSSRPAGKRP 300

Query: 293 NGLSKQKKLATPVHRRN 309
              S+Q        +  
Sbjct: 301 ASSSRQNAGRKAAPKGR 317


>gi|229551699|ref|ZP_04440424.1| pseudouridylate synthase [Lactobacillus rhamnosus LMS2-1]
 gi|258539094|ref|YP_003173593.1| pseudouridine synthase A [Lactobacillus rhamnosus Lc 705]
 gi|229314931|gb|EEN80904.1| pseudouridylate synthase [Lactobacillus rhamnosus LMS2-1]
 gi|257150770|emb|CAR89742.1| Pseudouridine synthase A [Lactobacillus rhamnosus Lc 705]
          Length = 236

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 94/228 (41%), Gaps = 2/228 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++     SR+EV+ +I  +RV++ G L+     N++    +EV+          
Sbjct: 1   MRLDKYLSHLQFGSRKEVKALIRDKRVRIAGELVTDPGYNILPGVAVEVNDAQADGPLEV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +      +  T                    +  VGRLD +T GLLLLT DG L   
Sbjct: 61  DYLMNKPAGVITATEDPTQSTVLDLIRPHDYRPGLYPVGRLDKDTTGLLLLTTDGNLGHT 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P+    + Y  +    +  +  + L+ G+ ++        V +      N  + + +
Sbjct: 121 LLAPNHHVPKTYAAKLAKALTTEMKHQLEHGVALKDFTTAPADVQVVPAT-DNKEIYITI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
            EGK  +IK++    + +V  L RI+ GP +L   L AG  R ++   
Sbjct: 180 TEGKYHQIKRMLLAVDNEVVALTRIAMGPLRLPEDLDAGEYRALTDDE 227


>gi|256391653|ref|YP_003113217.1| pseudouridine synthase [Catenulispora acidiphila DSM 44928]
 gi|256357879|gb|ACU71376.1| pseudouridine synthase [Catenulispora acidiphila DSM 44928]
          Length = 332

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 79/235 (33%), Positives = 127/235 (54%), Gaps = 2/235 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVP 66
             N    R+ KV+A+AG+ SRR  E +IA  RV+VNG ++    + V   T  I VDG+ 
Sbjct: 90  DANEEGIRLQKVLAQAGVGSRRVSEDLIAAGRVEVNGEIVRHQGMRVDPETAVIRVDGMR 149

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +  AE    + ++KP+G+V+   D   R  + D +     R+  +GRLD++TEGL+LLTN
Sbjct: 150 ISTAEGIVHFAFNKPMGVVS-AMDDPDRPNLGDYVRGRNERLFHIGRLDVDTEGLILLTN 208

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  +VYR + +G V +D    L++G+ ++          L    G N
Sbjct: 209 DGELAHRLAHPSYEIRKVYRAQVYGTVPKDLGRRLREGVDLEDGLARVDHFRLLDSVGRN 268

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           A V + + EG+NR ++++ +     V  L+R  +GP  LG       R ++K+ +
Sbjct: 269 ALVEITIHEGRNRIVRRIMDAVGLPVRGLVRTKFGPISLGDQKPERMRPLNKEEV 323


>gi|91228669|ref|ZP_01262584.1| pseudouridine synthase family 1 protein [Vibrio alginolyticus
           12G01]
 gi|269967050|ref|ZP_06181118.1| pseudouridine synthase family 1 protein [Vibrio alginolyticus 40B]
 gi|91187790|gb|EAS74107.1| pseudouridine synthase family 1 protein [Vibrio alginolyticus
           12G01]
 gi|269828309|gb|EEZ82575.1| pseudouridine synthase family 1 protein [Vibrio alginolyticus 40B]
          Length = 312

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 90/313 (28%), Positives = 132/313 (42%), Gaps = 13/313 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E +I   RV VNG++ +        +  + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREIESLIKSGRVSVNGVVAKLGERLEDESSVVRIDGHIVSAKIQ 61

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  Y     L T H     R+          SR ISVGRLD NT GLLL T D
Sbjct: 62  EEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G+V + K+  L KG+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRQVEREYLVRVFGEVTEQKVRNLVKGVELEDGLARFEDVVYAGGEGMNH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LRE 243
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+  K    LRE
Sbjct: 182 TFYVVINEGRNREVRRLWESQECTVSRLKRVRYGDIFLDKKLPRGGWMELDLKEVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +     +E  ++L+       T  +       ++     R ++  +   G S       
Sbjct: 242 LVELRPEKETMLDLNK----DNTSRKRERARSQKIRRAVKRHEERVNTPKGRSNNPSRRK 297

Query: 304 PVHRRNLASNVWM 316
           P            
Sbjct: 298 PKKTAGDQGARNK 310


>gi|297579215|ref|ZP_06941143.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           RC385]
 gi|297536809|gb|EFH75642.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           RC385]
          Length = 231

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 48/231 (20%), Positives = 95/231 (41%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSCVEWQGREITLHGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     + +       ++            +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDG-FNQTAFTLLDEVNIQDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + YRV     +  D      +GI ++G        Q+ +     S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELRGERELTLPAQLDVI----SETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R   G   L   L  G  R ++++ +
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEEEV 226


>gi|209886355|ref|YP_002290212.1| pseudouridine synthase, Rsu [Oligotropha carboxidovorans OM5]
 gi|209874551|gb|ACI94347.1| pseudouridine synthase, Rsu [Oligotropha carboxidovorans OM5]
          Length = 693

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 143/344 (41%), Positives = 199/344 (57%), Gaps = 4/344 (1%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K     + + + +R++KV+ARAG+ SRR+ E  I Q RV VNG ++   A++V + D I 
Sbjct: 354 KRAAPKKADKSGERIAKVVARAGLCSRRDAEDWIMQGRVAVNGRVIGSPALDVTARDVIT 413

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           VDG PL + ERTRL+LYHKP GL+TTH DP+GR TVFD+LP    R+IS+GRLD NTEGL
Sbjct: 414 VDGQPLPERERTRLFLYHKPRGLMTTHDDPEGRPTVFDHLPDGLPRLISIGRLDFNTEGL 473

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDGGL+R LE P T WLR YRVR HG V Q +L+ LK G+ + G+ YG +  TL+ 
Sbjct: 474 LLLTNDGGLSRALEHPDTGWLRRYRVRAHGDVTQARLDELKNGVEVDGVKYGSIDATLER 533

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +G+N W+T  +REGKNRE++ V      +VNRLIR+SYGPFQLG +  G   E+  ++L
Sbjct: 534 DQGANVWLTFAIREGKNREVRNVMAHLGLEVNRLIRVSYGPFQLGEIPEGQVEEIKSRVL 593

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           REQLG  ++  A    D P+   +          + +         N   K    + +K 
Sbjct: 594 REQLGDKIIALAGAQFDKPVQEGDDAEAKLGRDGTPLRSKAA----NKKIKRSAIEDRKG 649

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
              V +R+ +          +       + +  +     F  K 
Sbjct: 650 RRVVVQRSGSDEARARNEAEAGGYGPPRRPQRRYHGKRDFTPKD 693


>gi|262369297|ref|ZP_06062625.1| ribosomal large subunit pseudouridine synthase B [Acinetobacter
           johnsonii SH046]
 gi|262315365|gb|EEY96404.1| ribosomal large subunit pseudouridine synthase B [Acinetobacter
           johnsonii SH046]
          Length = 368

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 88/359 (24%), Positives = 150/359 (41%), Gaps = 19/359 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
            +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG  +     
Sbjct: 2   SEKLQKVLARVGLGSRRYMEEVIAAGRVSVNGQVAQV-GERIEPGDELRIDGRKVSFQIE 60

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R  L  Y     + + +      +           R + VGRLDIN+ GLLL TND
Sbjct: 61  DEIRRRVLIYYKPEGEICSRNDPESRPTVFDQLPAIANDRWVMVGRLDINSTGLLLFTND 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V     N + KG+V+          +    +G N 
Sbjct: 121 GELANRLMHPSNEVEREYAVRVMGEVTPQIKNNMLKGVVLDDGPAKFESFSEIGGEGINR 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V ++EG+NRE++++FE    KV+RL+R  YG   L   L  G   E+ K  + + L 
Sbjct: 181 WYQVVVKEGRNREVRRIFESQGLKVSRLLRTRYGTVILPRELRTGRWMELDKNDI-DNLT 239

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG---------LSK 297
             +  + +        +     R +   ++     F R ++  ++  G           +
Sbjct: 240 KAVELKPRQGTGLYGMAKRRTERMQEKPMAARRGGFLRQQRRDNEDEGQQQAKPAFNRER 299

Query: 298 QKKLATPVHRRNLASNV--WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           ++       RR   +       +   +S  +    R EN     ++  + +    + +K
Sbjct: 300 RENPNGHSQRRQDNAQTGYGQREPRQNSGYAQRDSRPENFGNKGTYGQRDARDENAPRK 358


>gi|262198800|ref|YP_003270009.1| pseudouridine synthase [Haliangium ochraceum DSM 14365]
 gi|262082147|gb|ACY18116.1| pseudouridine synthase [Haliangium ochraceum DSM 14365]
          Length = 553

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 69/285 (24%), Positives = 122/285 (42%), Gaps = 4/285 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R+ + +++ G+A+RR+ E +I    V VNG  +      V+   D + V G  +  
Sbjct: 2   DEAIRLQRYLSQCGVAARRKAEELITSGVVSVNGQRVTELGTKVVPGRDRVSVRGEAVYP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   + L      L       +   TV + L  + +RV+ VGRLD  +EG+LLLTNDG 
Sbjct: 62  EEPFYVLLNKPKGCLTAVTDPENR-PTVMEYLHGLPARVVPVGRLDFYSEGVLLLTNDGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNA- 187
           L+  L+ P     + Y V+   QV +  L +L++G+ ++        Q+ +     S   
Sbjct: 121 LSARLQSPRHHVEKTYHVKVRDQVTERHLEVLRQGVRLEDGTVTRPAQIDMLGGTKSRHD 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+ + L EGK+R+I ++     + V +L R+++G      L  G  RE+++  + +    
Sbjct: 181 WLVITLTEGKSRQIHRMLGVLGYTVMKLQRVAFGGLTFHGLRVGDARELTQAEVNDLREL 240

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
             L +  V         E   R R +                  +
Sbjct: 241 VGLPKDTVARGKWTSRREETERARRSRARARVGMSGGRDGGRDFR 285


>gi|116623183|ref|YP_825339.1| ribosomal large subunit pseudouridine synthase B [Candidatus
           Solibacter usitatus Ellin6076]
 gi|116226345|gb|ABJ85054.1| ribosomal large subunit pseudouridine synthase B [Candidatus
           Solibacter usitatus Ellin6076]
          Length = 264

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 69/264 (26%), Positives = 134/264 (50%), Gaps = 2/264 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DH 59
           M+ K   QE  T + + +V ++AG  SR +  + I+  +V+VNG ++      V    D 
Sbjct: 1   MEKKRNRQEKITLKTLERVFSKAGAGSRTDARKWISGGKVRVNGKVVLNPDHWVDPDHDK 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           + ++G PL+ A ++ + LY      +TT+ DP+GR TV+  L  +   +  VGRLD++T 
Sbjct: 61  VTLEGKPLKAATKSYILLYKPKG-YLTTYRDPEGRPTVYALLGDVGKWLSPVGRLDLDTS 119

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LTND   A  +  P  +  + Y+++    +  +++  L+ G+ +        +V  
Sbjct: 120 GLLVLTNDNDFAERITNPEHKVPKTYQIKAATVLSDEQIERLRAGVELSDGPTRPAEVKR 179

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                 + ++ + + EG+NR+++++ E    KV++L+R + GP ++G L  G  R ++  
Sbjct: 180 LRDGPKHTFLEMTITEGRNRQVRRMLEAVESKVSKLVRTAIGPVRIGELPIGKWRNLTAD 239

Query: 240 ILREQLGPHLLEEAQVNLDAPIYS 263
            + E  G    + +    D     
Sbjct: 240 EVHELRGQAAKKASGPARDKNRNK 263


>gi|313115054|ref|ZP_07800544.1| conserved hypothetical protein [Faecalibacterium cf. prausnitzii
           KLE1255]
 gi|310622616|gb|EFQ06081.1| conserved hypothetical protein [Faecalibacterium cf. prausnitzii
           KLE1255]
          Length = 233

 Score =  166 bits (420), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 53/230 (23%), Positives = 96/230 (41%), Gaps = 4/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R E + ++++ RV+VNG + ++    +  +D + VDG  L   +  
Sbjct: 1   MRLDKYLAETAQCTRSEAKALLSKGRVQVNGAVCKKGDTQLKESDTVAVDGRALSYQQFV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L      +  +    D              ++   GRLD  + G +LLT+DG  A  
Sbjct: 61  YIMLNKPEGVVSASTDKRDTTVVDLVGDAYPRRQLFPAGRLDKTSTGFVLLTDDGTFAHD 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG-DMQVTLDTQKGSNAWVTVG 192
           +  P     + Y V     + ++       G+ +         +VT  +  G    V V 
Sbjct: 121 ILAPKRHVSKTYTVVLDTPLTEEMRTGFAAGVTLADGTALSPAEVTALSADG--CTVRVV 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           L++G   +IK++F  +   VN L R + G   L   L  G  RE+S + +
Sbjct: 179 LKQGVYHQIKRMFGVYGAGVNGLHRDAIGGLALDPALAPGQWRELSAEEV 228


>gi|261408369|ref|YP_003244610.1| pseudouridine synthase [Paenibacillus sp. Y412MC10]
 gi|261284832|gb|ACX66803.1| pseudouridine synthase [Paenibacillus sp. Y412MC10]
          Length = 253

 Score =  166 bits (420), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 68/238 (28%), Positives = 112/238 (47%), Gaps = 8/238 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
           T QR+ KV++  G  SR E+++   Q  + VNG + +    +V    D IE +G  ++  
Sbjct: 7   TTQRLDKVLSNLGFGSRAELKKKAKQGSIVVNGTVTKDPGKHVDPYADIIEFEGETIQYR 66

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L+  P  +  T    D       +          VGRLD +TEGLLLLTNDG L
Sbjct: 67  EYVYLMLHKPPGVVSATEDLRDRTVLDLLDAEYRVFEPFPVGRLDKDTEGLLLLTNDGKL 126

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSN--- 186
           A  L  P     + Y     G+VD++ +     G+ +         ++ + + +      
Sbjct: 127 AHELLSPRKHIPKTYEATVEGRVDEEDVRRFAAGVTLDDGYVTLPGELAIHSHEEREDGV 186

Query: 187 --AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
             + +++ + EGK  ++K++FE    KV  L RIS G  +L   L  G+ RE++++ L
Sbjct: 187 QLSRISLTIHEGKFHQVKRMFEAVGKKVVYLKRISMGELRLDENLEIGTYRELTEQEL 244


>gi|320663977|gb|EFX31164.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 str.
           LSU-61]
          Length = 290

 Score =  166 bits (420), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 88/289 (30%), Positives = 129/289 (44%), Gaps = 10/289 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +GSN
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGSN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           E +       ++V ++      +     R            R    ++ 
Sbjct: 242 ELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGGRRSGGRNNG 290


>gi|171779572|ref|ZP_02920528.1| hypothetical protein STRINF_01409 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171281674|gb|EDT47108.1| hypothetical protein STRINF_01409 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 238

 Score =  166 bits (420), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 103/229 (44%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++ +AG  SR +V+++I  ++V V+G L E   +NV  +   I V G  L ++  
Sbjct: 1   MRLDKLLGQAGFGSRNQVKKLIRSRQVYVDGRLAEADNLNVEPSLQEIMVSGKRLEQSTE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                      R+  VGRLD +TEGLLL+TN+G L  
Sbjct: 61  KYFILNKPAGVVSAVSDKEHQTVIDLIAEADRVPRLYPVGRLDRDTEGLLLITNNGLLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V  +G + +D     + G+            + +       +   +
Sbjct: 121 RMLHPKYHVTKTYYVEVNGLLAEDAPAFFENGVTFDDGTVCKPANLEIIEASSEKSSAYI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + EGK  ++KK+F  +  KV  L R+++G F+LG L  G  RE++ K 
Sbjct: 181 SIAEGKFHQVKKMFLAYGVKVIYLKRMTFGDFELGDLPRGQYRELNTKE 229


>gi|189347479|ref|YP_001944008.1| pseudouridine synthase [Chlorobium limicola DSM 245]
 gi|189341626|gb|ACD91029.1| pseudouridine synthase [Chlorobium limicola DSM 245]
          Length = 252

 Score =  166 bits (420), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 65/251 (25%), Positives = 118/251 (47%), Gaps = 6/251 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DH 59
           MK +          R+++ +A  G+ASRR  ++++   RV +NG ++    + V  + D 
Sbjct: 1   MKKRTAENREERLVRINRYLAMCGVASRRASDQLVEAGRVMINGSIILEPGLKVDPSVDE 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           + VDG  L   E  ++++       V T +  +       N  S+  R+  VGRLD  T 
Sbjct: 61  VIVDGSMLALPEGKKVYILFNKPKNVITTNSDEKNRETVLNYISVKERIYPVGRLDRKTT 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQV 177
           G+LLLTNDG LA  L  PS+   + Y      +     L  L  G+ ++         Q 
Sbjct: 121 GVLLLTNDGNLAHKLMHPSSNVKKEYIAVLDKKFPHTLLLQLTGGMRLKDTGEKVSPCQA 180

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +  +      V + + EGKN +++++FE   ++V++L R++Y   ++G L  G  R + 
Sbjct: 181 KILDEG---FQVWLSIHEGKNHQVRRMFETLGFEVDKLERVAYAGLKVGDLRRGEWRALD 237

Query: 238 KKILREQLGPH 248
           +K +++     
Sbjct: 238 RKEIQQLFQQA 248


>gi|291612934|ref|YP_003523091.1| RNA-binding S4 domain protein [Sideroxydans lithotrophicus ES-1]
 gi|291583046|gb|ADE10704.1| RNA-binding S4 domain protein [Sideroxydans lithotrophicus ES-1]
          Length = 243

 Score =  166 bits (420), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 63/244 (25%), Positives = 106/244 (43%), Gaps = 19/244 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
              R+SK+++  G+ SRRE +  IA+  VKV+G ++      V+ T  I ++        
Sbjct: 2   EKIRLSKLMSEQGLCSRREADDFIAKGWVKVDGEIVSELGTKVLPTQKITLEKAAQAKQQ 61

Query: 64  -------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
                    P+          +   I L+   +  +  +       S    +   GRLDI
Sbjct: 62  GRVTILLNKPVGYVSGQAEEGHKPAILLLDAATRWEQDTAPHRFHRSQLLGLAPAGRLDI 121

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           ++ GLL+LT DG +A+ L    +   + Y VR  G++  + LNLL  G+ + G      +
Sbjct: 122 DSTGLLVLTQDGRIAKQLIGEDSPIEKEYLVRVQGKLVGNGLNLLNHGLSLDGKKLKPAK 181

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V+   +      +   L EGK R+I+++ E    KV  L R+  G  +LG L  G  R +
Sbjct: 182 VSWQNEDQ----LRFILNEGKKRQIRRMCEMVGLKVTALKRVRIGKVRLGDLPQGQWRYL 237

Query: 237 SKKI 240
               
Sbjct: 238 RADE 241


>gi|325954742|ref|YP_004238402.1| pseudouridine synthase Rsu [Weeksella virosa DSM 16922]
 gi|323437360|gb|ADX67824.1| pseudouridine synthase Rsu [Weeksella virosa DSM 16922]
          Length = 297

 Score =  166 bits (420), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 62/240 (25%), Positives = 109/240 (45%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K      ++    R++K IA AGI+SRRE + +I    V VNG ++      V  TD + 
Sbjct: 52  KKLKPAPKDDGTIRLNKYIANAGISSRREADELILTGVVTVNGKVITEMGYKVQPTDEVR 111

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
            DG  +   +     L      + TT  + + ++ +     +  +R+  VGRLD  T G+
Sbjct: 112 FDGKKISAEKNVYFILNKPKGYITTTKDEKNRQTVLDLMEGATTARIFPVGRLDRQTTGV 171

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL TNDG L + L  PS    +VY V    ++    +  ++KGI +       +      
Sbjct: 172 LLFTNDGFLTKKLTHPSHDVKKVYHVTLDRKLSSHDMAEIRKGIRLIPEGVATVDEVSFI 231

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
               +  + + L  G NR ++++FE   ++V +L R+S+       L  G  R ++ + +
Sbjct: 232 DGRPHNEIGLELHIGWNRVVRRIFESLGYQVEKLDRVSFAGLTKSKLRQGQYRALTPQEV 291


>gi|146318298|ref|YP_001198010.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Streptococcus suis 05ZYH33]
 gi|146320492|ref|YP_001200203.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Streptococcus suis 98HAH33]
 gi|253751463|ref|YP_003024604.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           suis SC84]
 gi|253753364|ref|YP_003026505.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           suis P1/7]
 gi|253755807|ref|YP_003028947.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           suis BM407]
 gi|145689104|gb|ABP89610.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           Pseudouridylate synthase [Streptococcus suis 05ZYH33]
 gi|145691298|gb|ABP91803.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           Pseudouridylate synthase [Streptococcus suis 98HAH33]
 gi|251815752|emb|CAZ51353.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus suis SC84]
 gi|251818271|emb|CAZ56080.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus suis BM407]
 gi|251819610|emb|CAR45331.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus suis P1/7]
 gi|292558093|gb|ADE31094.1| Pseudouridine synthase, Rsu [Streptococcus suis GZ1]
 gi|319757880|gb|ADV69822.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Streptococcus suis JS14]
          Length = 238

 Score =  166 bits (420), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 107/231 (46%), Gaps = 2/231 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K + +A + SR++V+++   Q++K+NG   +  +  V      I+V G  +     
Sbjct: 1   MRLDKCLEKAKVGSRKQVKKLFKAQQIKINGQAAQSLSQIVDPELQTIQVSGKKVALEGS 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +               +       +  VGRLD +TEGL+L+TN+G L  
Sbjct: 61  AYYLLHKPAGVVSAVTDQEHQTVIDLISPQDSREGLYPVGRLDRDTEGLVLITNNGPLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVTV 191
            +  PS    +VY V  +G + +D       G+  + G       +T+      ++  T+
Sbjct: 121 RMLHPSHHVDKVYYVEVNGCLAEDASKFFASGVTFLDGTRCQPADLTVLEASLDHSRATI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            L EGK  ++KK+F  +  KV  L RIS+G F+LG L  G+ R+++   + 
Sbjct: 181 KLAEGKFHQVKKMFLAYGVKVTYLKRISFGGFELGDLERGTYRQLTPNEME 231


>gi|94497978|ref|ZP_01304542.1| hypothetical protein SKA58_10410 [Sphingomonas sp. SKA58]
 gi|94422561|gb|EAT07598.1| hypothetical protein SKA58_10410 [Sphingomonas sp. SKA58]
          Length = 315

 Score =  166 bits (420), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 113/232 (48%), Positives = 152/232 (65%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
              PQR++K++ARAG+ASRRE+ERMIA  R+ ++G  ++  A  + S   + VDGV +  
Sbjct: 72  KNEPQRIAKLLARAGVASRREIERMIADGRIALDGAPVDTPATLLTSLHGVTVDGVAIAA 131

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
              TRL+L+HKP G +TT  DP GR T++D LP    RV+ +GRLD+NTEGLLLLT DGG
Sbjct: 132 PAPTRLFLFHKPTGCLTTERDPAGRPTIYDRLPDGLPRVMPIGRLDMNTEGLLLLTTDGG 191

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
             R +ELP+T   R YR R  G+V Q +L  L  G+ I GI YG ++  L+ + G N W+
Sbjct: 192 FKRQMELPATGVPRTYRARAFGEVSQQQLEDLFDGLEIDGIRYGQIEANLERRTGRNQWI 251

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + L EGKNRE+++V E    KVNRLIR +YGPF LG L  G+  EV +  L
Sbjct: 252 EMTLTEGKNREVRRVLEHLGLKVNRLIRTAYGPFSLGELAVGTVEEVRQHDL 303


>gi|317121959|ref|YP_004101962.1| ribosomal large subunit pseudouridine synthase B [Thermaerobacter
           marianensis DSM 12885]
 gi|315591939|gb|ADU51235.1| ribosomal large subunit pseudouridine synthase B [Thermaerobacter
           marianensis DSM 12885]
          Length = 320

 Score =  166 bits (420), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 83/318 (26%), Positives = 131/318 (41%), Gaps = 9/318 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL----- 67
           QR+ K+++RAGIASRR+VE  IA  R+ VNG              D I VDG PL     
Sbjct: 4   QRLQKLLSRAGIASRRQVENWIAAGRITVNGRPA-VLGTRADPERDVIAVDGRPLADLRQ 62

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R A +  + L+     + T        S       +    +  VGRLD ++EGLLLLT+D
Sbjct: 63  RLARKRYVMLHKPRGMVTTLRDPQGRPSVGDFCRRAGLRGLHPVGRLDFDSEGLLLLTDD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  P  +  +VY V   G ++  +L  L+ G+++           +   +    
Sbjct: 123 GELTFALTHPRHEVDKVYHVLVRGPLEPQRLRRLRDGVLLDDGPARARSARILRPRPGGG 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           WV V LREG+ R+++++     W V RL+R++ GP +LG L AG  R +S++ +      
Sbjct: 183 WVEVVLREGRKRQVRRMCRAVGWDVVRLVRVAVGPLRLGRLTAGQWRPLSRQEVEALRAA 242

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISE--VPDDFTRMKKNSSQKNGLSKQKKLATPV 305
             L             +   +  R    S            +  S + G           
Sbjct: 243 AGLPIHGDEPAPREGGAAPAITSRWRAASPRAGGGIAAGRAETGSARTGGGVPATPGDAG 302

Query: 306 HRRNLASNVWMAKGIHSS 323
            + +        +G +  
Sbjct: 303 GKASGGRAAGRQQGRNRG 320


>gi|262171789|ref|ZP_06039467.1| ribosomal large subunit pseudouridine synthase B [Vibrio mimicus
           MB-451]
 gi|261892865|gb|EEY38851.1| ribosomal large subunit pseudouridine synthase B [Vibrio mimicus
           MB-451]
          Length = 319

 Score =  166 bits (420), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 85/319 (26%), Positives = 124/319 (38%), Gaps = 7/319 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E +I   RV VNG +             + VDG  +     
Sbjct: 2   SEKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGERLEDDNALVRVDGHVVSVKAQ 61

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  Y     L T H     R+          SR ISVGRLD NT GLLL T D
Sbjct: 62  EEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G V+++K+  L +G+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRQVEREYLVRVFGDVNEEKVRNLVRGVQLEDGMARFEDVMYAGGEGINH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+  K +   L 
Sbjct: 182 TFYVVINEGRNREVRRLWESQGTTVSRLKRVRYGDIFLDKKLPRGGWMELDLKQV-NYLR 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
             +    +              +       ++     R ++  S   G S   +      
Sbjct: 241 ELVELRPEKETVLNTAPDAATRKRERTRSQKIRRAVRRHEERVSTAPGRSGSARRKPGGE 300

Query: 307 RRNLASNVWMAKGIHSSFL 325
                      +       
Sbjct: 301 SSTRNKVANKQQSARKHRG 319


>gi|260913145|ref|ZP_05919627.1| ribosomal small subunit pseudouridine synthase A [Pasteurella
           dagmatis ATCC 43325]
 gi|260632732|gb|EEX50901.1| ribosomal small subunit pseudouridine synthase A [Pasteurella
           dagmatis ATCC 43325]
          Length = 233

 Score =  166 bits (420), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 109/231 (47%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A +   +R +  +++ Q  V +NG + +  +V V S D I  DG  L   E  
Sbjct: 1   MRLDKFLAESTGLTRSQANKVLKQSAVTMNGKVEKNGSVKVNSEDEICFDGELLTWIEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +  + +KP G V +H D D  +        + +++ S GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYIMLYKPQGYVCSHDDGDYPTIYQFFDYPLSTKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     ++ +     + GI+++G        ++ +      +  V +
Sbjct: 121 ITSPKHHCEKTYLVTLADPIESNYQQACEAGILLRGEKELTKPAKLEIL----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EG+  ++K++F     KV  L R   G  +L   L  G  R +S++ +
Sbjct: 177 TISEGRYHQVKRMFAALGNKVVGLHRWKIGCIELDETLEEGGYRSLSEQEI 227


>gi|153801570|ref|ZP_01956156.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           MZO-3]
 gi|124122897|gb|EAY41640.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           MZO-3]
          Length = 231

 Score =  166 bits (420), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 48/231 (20%), Positives = 95/231 (41%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSCVEWQGREITLHGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     + +       ++            +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDG-FNQTAFTLLDEVNVEDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + YRV     +  D      +GI ++G        Q+ +     S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELRGERELTLPAQLEVI----SETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R   G   L   L  G  R ++++ +
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEEEV 226


>gi|218768378|ref|YP_002342890.1| putative pseudouridine synthase [Neisseria meningitidis Z2491]
 gi|121052386|emb|CAM08718.1| putative pseudouridine synthase [Neisseria meningitidis Z2491]
          Length = 256

 Score =  166 bits (420), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 72/245 (29%), Positives = 121/245 (49%), Gaps = 7/245 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  ++   
Sbjct: 2   EPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLKW 60

Query: 72  RTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             RL      Y +   +V+        S       +  SR +++GRLDINT GLL+LT  
Sbjct: 61  ADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTTS 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN 186
           G L +    PS +  R Y VR  G +  +++ +L +  ++++       ++     +G+N
Sbjct: 121 GELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGAN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
            W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   E++   +   L
Sbjct: 181 KWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFYELNPAEVANIL 240

Query: 246 GPHLL 250
               +
Sbjct: 241 KWAEM 245


>gi|298206743|ref|YP_003714922.1| putative ribosomal large subunit pseudouridine synthase
           [Croceibacter atlanticus HTCC2559]
 gi|83849374|gb|EAP87242.1| putative ribosomal large subunit pseudouridine synthase
           [Croceibacter atlanticus HTCC2559]
          Length = 259

 Score =  166 bits (420), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 56/240 (23%), Positives = 117/240 (48%), Gaps = 1/240 (0%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K+K  V+      R++K IA AGI SRR+ +  I    V VNG  +      V  +D ++
Sbjct: 15  KNKPKVETVDGGIRLNKYIANAGICSRRDADIYITAGNVTVNGKTITEMGYKVKLSDEVK 74

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
            DG  +   ++    L       V+   +  G + +     +  +R+  +G+L+ +  GL
Sbjct: 75  FDGRSITPDKKEYYLLNKPKDVFVSGSLNESGMTVLDIVGRATKARLSPIGKLERSAMGL 134

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           ++LTNDG L++ L  P     ++Y V+ + ++ Q  L  +++GI ++      + ++   
Sbjct: 135 VVLTNDGTLSKSLANPRHGIRQIYHVQLNKELSQVDLEKIRQGITLEDGEIKVVDISYV- 193

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +  S   V + ++  K+  ++++F+  N+++  L R+ +G      L  G  R ++K+ +
Sbjct: 194 ENKSKREVGIEIKSTKSHIVQRLFKSLNYEIKYLDRVVFGTLTKKDLPRGMFRHLTKQEI 253


>gi|15641640|ref|NP_231272.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           O1 biovar El Tor str. N16961]
 gi|121591192|ref|ZP_01678495.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           2740-80]
 gi|153819727|ref|ZP_01972394.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           NCTC 8457]
 gi|153823785|ref|ZP_01976452.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           B33]
 gi|227081787|ref|YP_002810338.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           M66-2]
 gi|229508252|ref|ZP_04397757.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           BX 330286]
 gi|229511509|ref|ZP_04400988.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           B33]
 gi|229518648|ref|ZP_04408091.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           RC9]
 gi|229607826|ref|YP_002878474.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           MJ-1236]
 gi|254848756|ref|ZP_05238106.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           MO10]
 gi|255744936|ref|ZP_05418886.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholera
           CIRS 101]
 gi|262161779|ref|ZP_06030797.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           INDRE 91/1]
 gi|298498281|ref|ZP_07008088.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           MAK 757]
 gi|34098734|sp|Q9KRK5|RSUA_VIBCH RecName: Full=Ribosomal small subunit pseudouridine synthase A;
           AltName: Full=16S pseudouridine 516 synthase; AltName:
           Full=16S pseudouridylate 516 synthase; AltName:
           Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|9656147|gb|AAF94786.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           O1 biovar El Tor str. N16961]
 gi|121546947|gb|EAX57095.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           2740-80]
 gi|126509718|gb|EAZ72312.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           NCTC 8457]
 gi|126518696|gb|EAZ75919.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           B33]
 gi|227009675|gb|ACP05887.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           M66-2]
 gi|229343337|gb|EEO08312.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           RC9]
 gi|229351474|gb|EEO16415.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           B33]
 gi|229355757|gb|EEO20678.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           BX 330286]
 gi|229370481|gb|ACQ60904.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           MJ-1236]
 gi|254844461|gb|EET22875.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           MO10]
 gi|255737407|gb|EET92802.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholera
           CIRS 101]
 gi|262028511|gb|EEY47166.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           INDRE 91/1]
 gi|297542614|gb|EFH78664.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           MAK 757]
          Length = 231

 Score =  166 bits (420), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 48/231 (20%), Positives = 96/231 (41%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSCVEWQGREITLHGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     + +       ++ +          +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDG-FNQTALTLLDEVNIQDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + YRV     +  D      +GI ++G        Q+ +     S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELRGERELTLPAQLEVI----SETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R   G   L   L  G  R ++++ +
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEEEV 226


>gi|320093560|ref|ZP_08025451.1| ribosomal large subunit pseudouridine synthase B [Actinomyces sp.
           oral taxon 178 str. F0338]
 gi|319979487|gb|EFW10958.1| ribosomal large subunit pseudouridine synthase B [Actinomyces sp.
           oral taxon 178 str. F0338]
          Length = 249

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 87/236 (36%), Positives = 125/236 (52%), Gaps = 2/236 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE 71
             R+ KV+A+AG+ASRR  E+MIA  RV V+G ++    + V  T   I VDG  L   E
Sbjct: 10  GVRLQKVLAQAGVASRRAAEQMIADGRVSVDGQVVRGQGMRVDPTAQVIHVDGERLILDE 69

Query: 72  RT-RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               +   +KP+G+V+T SDP+GR TV D +     R+  VGRLDI+T GLLLLTNDG L
Sbjct: 70  TKHVVLAINKPVGVVSTMSDPEGRPTVADIVAGYPERLYHVGRLDIDTSGLLLLTNDGEL 129

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS +  + Y  R HG+V       L  GI ++          +    G    V 
Sbjct: 130 ANRLTHPSYEISKTYVARLHGEVRPGVKRRLMAGIELEDGPIAVDGFRVVDTYGDITTVE 189

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + + EG+NR ++++ +   + V  L+R  +GP +L  L  G++R V    L    G
Sbjct: 190 IVVHEGRNRLVRRMMDAVGFPVRELVRTGFGPIRLDHLQPGTSRRVKGNALTALYG 245


>gi|292488387|ref|YP_003531269.1| ribosomal large subunit pseudouridine synthase B [Erwinia amylovora
           CFBP1430]
 gi|292899583|ref|YP_003538952.1| ribosomal large subunit pseudouridine synthase B [Erwinia amylovora
           ATCC 49946]
 gi|291199431|emb|CBJ46548.1| ribosomal large subunit pseudouridine synthase B [Erwinia amylovora
           ATCC 49946]
 gi|291553816|emb|CBA20861.1| ribosomal large subunit pseudouridine synthase B [Erwinia amylovora
           CFBP1430]
 gi|312172530|emb|CBX80786.1| ribosomal large subunit pseudouridine synthase B [Erwinia amylovora
           ATCC BAA-2158]
          Length = 295

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 90/295 (30%), Positives = 129/295 (43%), Gaps = 12/295 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E MI+  RV V+G L       V       I +DG  +  +
Sbjct: 2   SEKLQKVLARAGHGSRREIETMISAGRVSVDGKLAT-LGDRVEPAASLKIRIDGHVVPVS 60

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E        L  Y     L T +      +          +R I+VGRLD+NT GLLL T
Sbjct: 61  ESISEVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  G VD DK+ LL +G+ ++        +     +G 
Sbjct: 121 TDGELANRLMHPSREVEREYAVRVFGAVDDDKIKLLSRGVQLEDGPAAFKTLKFTGGEGI 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKIL 241
           N W  V L EG+NRE+++++E    +V+RLIRI YG   L   L  G   E+       L
Sbjct: 181 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRIRYGDIDLPKGLPRGGWTELDLAPTNYL 240

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           RE +G      ++V ++     ++     R                    K    
Sbjct: 241 RELVGLAPETVSKVPVEKDRRRTKANQIRRAVKRHTTTKVSKPGSGRRPSKRQQG 295


>gi|83319317|ref|YP_424568.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           capricolum subsp. capricolum ATCC 27343]
 gi|83283203|gb|ABC01135.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           capricolum subsp. capricolum ATCC 27343]
          Length = 252

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 70/249 (28%), Positives = 123/249 (49%), Gaps = 5/249 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--RKAE 71
           +R+ KVI+  G  SRR  E++I + RVKVN  ++ +  V +     I +D   +      
Sbjct: 4   ERLQKVISSRGYCSRRTAEKLILENRVKVNNQIINKLGVKIDPKAEIIIDNKLVTSDSNN 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +   +L++KP  ++TT  DP  R TV D    +  RV  VGRLD +  GLL++TNDG L+
Sbjct: 64  QKYYYLFYKPRLVLTTMYDPKKRKTVADYFKDLNHRVYPVGRLDYDVSGLLIMTNDGELS 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---QVTLDTQKGSNAW 188
             +  P  ++L+ Y+    GQV++ ++N L KG+ I           ++    +  + + 
Sbjct: 124 NFIMHPKYEFLKTYQGLCQGQVNKQQVNQLIKGVYIDNNYLTKAYSSKLIKYDKLKNVSI 183

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           V + + EGK   +KK+FE    ++ +L R      ++  L  G  RE+    +++  G +
Sbjct: 184 VELTINEGKKHHVKKMFESIQAQLLKLKRTRIEFLEIDNLKPGQYRELKVHEIKKLYGIY 243

Query: 249 LLEEAQVNL 257
              +     
Sbjct: 244 HSLKQNNKK 252


>gi|199599098|ref|ZP_03212503.1| 16S rRNA uridine-516 pseudouridylate synthase related
           pseudouridylate synthase [Lactobacillus rhamnosus HN001]
 gi|199589991|gb|EDY98092.1| 16S rRNA uridine-516 pseudouridylate synthase related
           pseudouridylate synthase [Lactobacillus rhamnosus HN001]
 gi|328467827|gb|EGF38871.1| pseudouridine synthase A [Lactobacillus rhamnosus MTCC 5462]
          Length = 236

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 94/228 (41%), Gaps = 2/228 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++     SR+EV+ +I  +RV++ G L+     N++    +EV+          
Sbjct: 1   MRLDKYLSHLQFGSRKEVKALIRDKRVRIAGELVTDPGYNILPGVAVEVNDAQADGPLEV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +      +  T                    +  VGRLD +T GLLLLT DG L   
Sbjct: 61  DYLMNKPAGVITATEDPTQSTVLDLIRPHDYRPGLYPVGRLDKDTTGLLLLTTDGNLGHT 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P+    + Y  +    +  +  + L+ G+ ++        V +      N  + + +
Sbjct: 121 LLAPNHHVPKTYAAKLAKALTTEMKHQLEHGVALKDFTTAPADVQVVPAT-DNKEIHITI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
            EGK  +IK++    + +V  L RI+ GP +L   L AG  R ++   
Sbjct: 180 TEGKYHQIKRMLLAVDNEVVALTRIAMGPLRLPEDLDAGEYRALTDDE 227


>gi|89897918|ref|YP_515028.1| ribosomal large subunit pseudouridine synthase B [Chlamydophila
           felis Fe/C-56]
 gi|89331290|dbj|BAE80883.1| ribosomal large subunit pseudouridine synthase B [Chlamydophila
           felis Fe/C-56]
          Length = 239

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 67/236 (28%), Positives = 107/236 (45%), Gaps = 5/236 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGV 65
           ++   T  R++K +A +G+ASRR+ + +I    V VNG +     V V   TD ++VDG 
Sbjct: 4   MENIMTKVRLNKFLASSGVASRRKCDEIIFSGHVTVNGRVAPGPFVLVDEETDTVKVDGR 63

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +   ++    ++     L ++     G   V D    +  RV +VGRLD  T GL+L+T
Sbjct: 64  RVGMTKKVYFMVHKPLGYLCSSERKFPGDKLVIDLFSHLPYRVFTVGRLDKETSGLILVT 123

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG  +  +  PS    + Y ++    V    L  L  G +I G         +  +K  
Sbjct: 124 NDGEFSNKIIHPSFGITKEYLLKVSRDVTAKNLEDLMGGTIIDGKRVRP----VSVEKIR 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              + + + EGK  EI+   E     +  L RI  G F LG L  G  RE++   +
Sbjct: 180 RGTIKIIVNEGKKHEIRLFAEAAGLPILELSRIRIGSFVLGGLRYGEYRELTDAEI 235


>gi|261868654|ref|YP_003256576.1| ribosomal small subunit pseudouridine synthase A [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261413986|gb|ACX83357.1| ribosomal small subunit pseudouridine synthase A [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 233

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 104/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R +  + + Q  V +NG + +  A  V   D I  DG  L   +  
Sbjct: 1   MRLDKFLAEHTGLTRSQATKALRQSAVTINGKIEKSGATKVSPQDAIYFDGELLTWLDVG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +  +++KP G V +H + +  S        + +R+ S GRLDI+T GL+LLT+DG  +  
Sbjct: 61  QYLMFNKPQGYVCSHDEDEHPSIYQFFDYPLSARLHSAGRLDIDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+ + +    +GI+++G         + +      +  V +
Sbjct: 121 VTSPKHHQPKTYLVTLADPVEANYVQACAEGILLRGEKDPTKPAVLEIL----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EG+  ++K++F     KV  L R   G   L   L  G  R ++ + +
Sbjct: 177 TISEGRYHQVKRMFAALGNKVLGLHRWKIGNLTLDDNLAEGDFRVLNAEEI 227


>gi|229520766|ref|ZP_04410189.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           TM 11079-80]
 gi|229342321|gb|EEO07316.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           TM 11079-80]
          Length = 231

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 48/231 (20%), Positives = 94/231 (40%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSCVEWQGREITLHGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     + +       ++            +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDG-FNQTAFTLLDEVNVEDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + YRV     +  D      +GI ++G        Q+ +     S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELRGERELTLPAQLEVI----SETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R   G   L   L  G  R ++ + +
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTAEEV 226


>gi|319946247|ref|ZP_08020487.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           australis ATCC 700641]
 gi|319747629|gb|EFV99882.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           australis ATCC 700641]
          Length = 247

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 61/236 (25%), Positives = 106/236 (44%), Gaps = 4/236 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
                R+ K +   G+ SR EV++++ +++++VNG +     +++    D +   G  L 
Sbjct: 2   KEASMRLDKYLVDCGVGSRTEVKQVLKKKKIQVNGKVETSPKIHIDPDKDQVTYLGESLF 61

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             E     L      +  T  D         +  +    V  VGRLDI+T GLLLLTN+G
Sbjct: 62  HEEFVYYLLNKPKGVISATEDDHHQTVLDLLDDTARHKEVFPVGRLDIDTHGLLLLTNNG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SN 186
            LA  +  P     +VYR +  G + Q+ ++  K+GI ++       ++ +       ++
Sbjct: 122 KLAHAMLSPKKHVDKVYRAQVAGIMTQEDIDRFKEGIELKDFTTLPAELEMLEVDQEANS 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
             V + + EGK  ++K++      +V  L RIS GP  L   L  G  R +    L
Sbjct: 182 CLVQIRIAEGKFHQVKRMVAACGKEVTDLERISMGPLSLDPALKLGQWRRLQSSEL 237


>gi|258507847|ref|YP_003170598.1| pseudouridine synthase A [Lactobacillus rhamnosus GG]
 gi|257147774|emb|CAR86747.1| Pseudouridine synthase A [Lactobacillus rhamnosus GG]
 gi|259649175|dbj|BAI41337.1| pseudouridine synthase [Lactobacillus rhamnosus GG]
          Length = 236

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 95/228 (41%), Gaps = 2/228 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++     SR+EV+ +I  +RV++ G L+     N++    +EV+          
Sbjct: 1   MRLDKYLSHLQFGSRKEVKALIRDKRVRIAGELVTDPGYNILPGVAVEVNDAQADGPLEV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +      +  T                    +  VGRLD +T GLLLLT DG L   
Sbjct: 61  DYLMNKPAGVITATEDPTQSTVLDLIRPHDYRPGLYPVGRLDKDTTGLLLLTTDGNLGHT 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P+    + Y  +    +  +  + L++G+ ++        V +      N  + + +
Sbjct: 121 LLAPNHHVPKTYAAKLAKALTTEMKHQLEQGVALKDFTTAPADVQVVPAT-DNKEIHITI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
            EGK  +IK++    + +V  L RI+ GP +L   L AG  R ++   
Sbjct: 180 TEGKYHQIKRMLLAVDNEVVALTRIAMGPLRLPEDLDAGEYRALTDDE 227


>gi|237744301|ref|ZP_04574782.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           7_1]
 gi|256027971|ref|ZP_05441805.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           D11]
 gi|289765917|ref|ZP_06525295.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           D11]
 gi|229431530|gb|EEO41742.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           7_1]
 gi|289717472|gb|EFD81484.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           D11]
          Length = 226

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 69/229 (30%), Positives = 107/229 (46%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   GI SR+EV+++I+   + VNGI    A  N+    D IE +   L   + 
Sbjct: 1   MRLDKFLVECGIGSRKEVKKLISNNEITVNGISNISAKDNIDENSDIIEYNEEKLEYKKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +  K   +  T    +           I   +  VGRLD +TEGLLL TNDG L  
Sbjct: 61  RYYIMNKKSGYITATEDFKENTVMDLLPEWVIKKDLAPVGRLDKDTEGLLLFTNDGKLNH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VY V     +  + +  L++G+ I        +V    +K S+  + + 
Sbjct: 121 KLLSPKNHVDKVYYVEIKNNISDEDIFKLEQGVDIGNYITQPAKV----EKISDNEIYLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++EGK  +IKK+ E  N KV  L R+S+G  +L  L  G  REV+ + +
Sbjct: 177 IKEGKFHQIKKMLEAINNKVCYLKRVSFGRLKLNDLALGEVREVNLEDI 225


>gi|163841326|ref|YP_001625731.1| ribosomal large subunit pseudouridine synthase B [Renibacterium
           salmoninarum ATCC 33209]
 gi|162954802|gb|ABY24317.1| ribosomal large subunit pseudouridine synthase B [Renibacterium
           salmoninarum ATCC 33209]
          Length = 345

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 84/235 (35%), Positives = 128/235 (54%), Gaps = 3/235 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLR 68
           +    R+ KV+A AG+ASRR  E MI   RV+V+G ++    + V   T  I VDG+ L+
Sbjct: 102 DPEGVRLQKVMAAAGVASRRVCEEMIEDGRVEVDGSIVTELGLRVNVETAVISVDGIRLQ 161

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTN 126
             E     +++KP G+V+T  DP+GR  + D L + ++      VGRLD  TEGLLLLTN
Sbjct: 162 LKENMIYLVFNKPRGVVSTMDDPEGRRNISDFLKNKYAHERLFHVGRLDQATEGLLLLTN 221

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  + Y V+  G ++    N ++KGI ++          L      +
Sbjct: 222 DGELANRLTHPSYEVPKTYLVQTKGPMETGVSNQMRKGIELEDGVTKIDAFKLVDSTPGH 281

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             V V L  GKNR ++++F+   + V RL+R+  GP +LG    GS R + ++ +
Sbjct: 282 VLVEVVLHSGKNRIVRRLFDAVGYPVERLVRLQVGPIRLGDQKQGSIRALGQQEV 336


>gi|317496566|ref|ZP_07954915.1| RNA pseudouridylate synthase [Gemella moribillum M424]
 gi|316913369|gb|EFV34866.1| RNA pseudouridylate synthase [Gemella moribillum M424]
          Length = 235

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 56/232 (24%), Positives = 101/232 (43%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K I    + SR E +++I +  V VNG +++     +    D + V+   L   + 
Sbjct: 1   MRLDKYIGHTTLLSRAESKKIIKKG-VLVNGNIVKAPDFKIDELNDEVIVNEKKLIYQKY 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      +  T                       VGRLD +TEGL+LLTNDG L  
Sbjct: 60  IYIMMNKPKGVISATEDSISRTVIDLLEEKDCIFEPFPVGRLDKDTEGLMLLTNDGNLGH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V  +G +  + +  LK+GI+++        ++ + T   S +   +
Sbjct: 120 QLTSPKKDVEKQYYVEVNGVLKVEHIPYLKEGIILEDGYKCKSAKLDILTSDVSKSTAYI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            + EGK  ++K++ +    +V  L R+S G   L   L  G  R ++++ L+
Sbjct: 180 YVTEGKFHQVKRMMKALGCEVTYLKRLSIGELVLDETLELGKYRYLTEQELK 231


>gi|261340615|ref|ZP_05968473.1| ribosomal small subunit pseudouridine synthase A [Enterobacter
           cancerogenus ATCC 35316]
 gi|288317026|gb|EFC55964.1| ribosomal small subunit pseudouridine synthase A [Enterobacter
           cancerogenus ATCC 35316]
          Length = 235

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 104/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G +++ +A  +     +E DG  L +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRASRVTVDGDIVKDSAFKLQPEHQVEYDGNTLTQQNGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLHKPEGYVCSTDDPDHPTVLYFLDEPVAHKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEHFAKGVQLHNEKDLTRPAVLEVI----TPTEVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F     +V  L R   G  +L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVVGLHRERIGAIELDPELAPGEYRPLTEEEI 227


>gi|209695469|ref|YP_002263398.1| ribosomal small subunit pseudouridine synthase A (16S pseudouridine
           516 synthase) [Aliivibrio salmonicida LFI1238]
 gi|208009421|emb|CAQ79703.1| ribosomal small subunit pseudouridine synthase A (16S pseudouridine
           516 synthase) [Aliivibrio salmonicida LFI1238]
          Length = 234

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 99/233 (42%), Gaps = 2/233 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +     A+R E  R++    V VNG+  +  +V V     +E DG  L+     
Sbjct: 1   MRLDKFLCETTGATRSEATRIVKSGTVTVNGVKTKVTSVKVTDDSTVEWDGRELKFHGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+     + +        S +         ++   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLFKPDGYVCSHEDSTHP-SALTLLDEVNLEKLHFAGRLDVDTTGLVLITDDGQWSHK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     +       L +GI ++      M  T++        + + +
Sbjct: 120 ITSPKRKCPKTYRVWLDEPIGAYYAEQLTEGIQLKSETGLIMPATMEVVNEEEHELLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           +EGK  ++K++F     KV  L R   G   L  +L  G  R ++ + ++  L
Sbjct: 180 QEGKYHQVKRMFAALGNKVEGLHRSQIGGLGLDYSLEPGEYRYLTAEEVKAVL 232


>gi|327390694|gb|EGE89034.1| hypothetical protein SPAR5_0271 [Streptococcus pneumoniae GA04375]
          Length = 240

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 102/234 (43%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQINEERDQIHFDGQKLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    V  VGRLDI+T GLLLLTNDG LA 
Sbjct: 61  VYYMMNKPKGVISATEDPKHRTVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNDGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVT 190
            L  P     + Y+ +  G + ++ +    +GI ++       ++ L     + + + + 
Sbjct: 121 TLLSPKRHVDKTYQAQVKGMMTREDVETFAEGIPLKDFTCQPAKLELVSIDTEKNQSQIR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L  
Sbjct: 181 VTIAEGKFHQIKRMVAYCGKEVMDLQRLTMGTLVLDENLGRGEWRRLTKEELEN 234


>gi|242243012|ref|ZP_04797457.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
 gi|242233613|gb|EES35925.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
          Length = 230

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 57/227 (25%), Positives = 100/227 (44%), Gaps = 7/227 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  VKVN   ++   ++V    D I V+   +     
Sbjct: 1   MRLDKFLANMGVGTRSEVKQLLKKGAVKVNQNKVKSPKLHVNPNSDEIMVNDEVVSYI-D 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G ++   D    + +          +  VGRLD +TEGLLL+TNDG    
Sbjct: 60  KVYIMLNKPKGYISATEDELHPTIIDLIPEYAHLNIFPVGRLDKDTEGLLLVTNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P+    + Y V     + Q  ++  K GI +              +K  +    V 
Sbjct: 120 EVMNPNKHVSKTYEVYSKHPITQFDIDEFKSGIELSDGKLKPA----ILKKVDDYVSHVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
           + EGK  ++K++F     +V  L RI     +L   L  GS R +++
Sbjct: 176 IYEGKYHQVKRMFHSIENEVLELKRIKIAELELDHNLDLGSYRLLTQ 222


>gi|78779587|ref|YP_397699.1| ribosomal large subunit pseudouridine synthase F [Prochlorococcus
           marinus str. MIT 9312]
 gi|78713086|gb|ABB50263.1| ribosomal large subunit pseudouridine synthase F [Prochlorococcus
           marinus str. MIT 9312]
          Length = 240

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 53/236 (22%), Positives = 103/236 (43%), Gaps = 11/236 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---KAE 71
           R++K ++  G  SRR+ +R+I + +V +NG +       V   D +EV+G  ++   K +
Sbjct: 4   RINKYLSEVGYCSRRKADRLIEEGKVTINGKIP-EIGAKVEDGDQVEVEGQRIKKSTKQK 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L        + TT            +      R+  +GRLD ++EGL+ LTNDG + 
Sbjct: 63  NIYLAFNKPIGVVCTTDRG--VEPDNIIDFIKYPKRIFPIGRLDKSSEGLIFLTNDGDIV 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V  +  ++++ +  +  G+ I      +       +K       +
Sbjct: 121 NKILRARNNHEKEYIVSVNRPINREFIQTMSNGVEILETKTKNC----FVKKLGPKKFKI 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            L +G NR+I+++ E   ++V  L R+     +L  L  G  RE +K+ + +    
Sbjct: 177 ILTQGLNRQIRRMCESLGYRVQSLKRVRIMNIKL-DLPIGKYREFTKEEISDLNAL 231


>gi|237731717|ref|ZP_04562198.1| 23S rRNA pseudouridylate synthase B [Citrobacter sp. 30_2]
 gi|226907256|gb|EEH93174.1| 23S rRNA pseudouridylate synthase B [Citrobacter sp. 30_2]
          Length = 291

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 89/288 (30%), Positives = 128/288 (44%), Gaps = 10/288 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +IA  RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIAAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRDARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           E +       ++V ++      +     R            R    S+
Sbjct: 242 ELVELKPETTSKVAVEKDRRRMKANQIRRAVKRHSQVGSSRRPGGRSN 289


>gi|212712415|ref|ZP_03320543.1| hypothetical protein PROVALCAL_03504 [Providencia alcalifaciens DSM
           30120]
 gi|212685161|gb|EEB44689.1| hypothetical protein PROVALCAL_03504 [Providencia alcalifaciens DSM
           30120]
          Length = 235

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 56/238 (23%), Positives = 106/238 (44%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +    V V+  +++  ++ V   + +  DG  L +    
Sbjct: 1   MRLDKFLSQQLGISRSLVARELRAGNVTVDDEVVKSGSMQVGLDNEVAYDGNVLVQVTGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DP   + ++     I   + + GRLDI+T GL+LLT+DG  +  
Sbjct: 61  RYFMLNKPEGYVCSTDDPTHPTILYFIDEPIAQNLHAAGRLDIDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + YRV+    +  D     ++G+++ G        Q+ +     S   V +
Sbjct: 121 ITSPKHHCEKTYRVQLSEDIADDVTIQFEQGVMLNGEKSPTKPAQLEII----SPREVLL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
            + EG+  ++K++F      V  L R   G   L   L  G  R +++  ++    P 
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVCGLHRERVGEIHLDEQLEPGEYRPLTEAEIKSITVPR 234


>gi|28898725|ref|NP_798330.1| pseudouridine synthase family 1 protein [Vibrio parahaemolyticus
           RIMD 2210633]
 gi|153839754|ref|ZP_01992421.1| RNA pseudouridine synthase family protein [Vibrio parahaemolyticus
           AQ3810]
 gi|260363727|ref|ZP_05776503.1| pseudouridine synthase B, ribosomal large subunit [Vibrio
           parahaemolyticus K5030]
 gi|260877279|ref|ZP_05889634.1| pseudouridine synthase B, ribosomal large subunit [Vibrio
           parahaemolyticus AN-5034]
 gi|260897774|ref|ZP_05906270.1| pseudouridine synthase B, ribosomal large subunit [Vibrio
           parahaemolyticus Peru-466]
 gi|260903494|ref|ZP_05911889.1| pseudouridine synthase B, ribosomal large subunit [Vibrio
           parahaemolyticus AQ4037]
 gi|34098479|sp|Q87NB7|RLUB_VIBPA RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|28806943|dbj|BAC60214.1| pseudouridine synthase family 1 protein [Vibrio parahaemolyticus
           RIMD 2210633]
 gi|149746721|gb|EDM57709.1| RNA pseudouridine synthase family protein [Vibrio parahaemolyticus
           AQ3810]
 gi|308087596|gb|EFO37291.1| pseudouridine synthase B, ribosomal large subunit [Vibrio
           parahaemolyticus Peru-466]
 gi|308090332|gb|EFO40027.1| pseudouridine synthase B, ribosomal large subunit [Vibrio
           parahaemolyticus AN-5034]
 gi|308106753|gb|EFO44293.1| pseudouridine synthase B, ribosomal large subunit [Vibrio
           parahaemolyticus AQ4037]
 gi|308114915|gb|EFO52455.1| pseudouridine synthase B, ribosomal large subunit [Vibrio
           parahaemolyticus K5030]
 gi|328474711|gb|EGF45516.1| pseudouridine synthase family 1 protein [Vibrio parahaemolyticus
           10329]
          Length = 312

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 91/313 (29%), Positives = 131/313 (41%), Gaps = 13/313 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
            +++ KV+ARAG  SRRE+E +I   RV VNG++ +        +  + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREIESLIKSGRVSVNGVVAKLGERLEDESSVVRIDGHIVSAKVQ 61

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  Y     L T H     R+          SR ISVGRLD NT GLLL T D
Sbjct: 62  EEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G+V + K+  L KG+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRQVEREYLVRVFGEVTEQKVRNLVKGVELEDGLARFEDVVYAGGEGMNH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LRE 243
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+  K    LRE
Sbjct: 182 TFYVVINEGRNREVRRLWESQECTVSRLKRVRYGDIFLDKKLPRGGWMELDLKEVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +     +E  ++L        T  +       ++     R ++  S   G S       
Sbjct: 242 LVELRPEKETMLDLSK----DNTSRKRERARSQKIRRAVKRHEERVSTSKGRSNNPARRK 297

Query: 304 PVHRRNLASNVWM 316
           P            
Sbjct: 298 PKKNAGEQGARNK 310


>gi|220904481|ref|YP_002479793.1| pseudouridine synthase [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
 gi|219868780|gb|ACL49115.1| pseudouridine synthase [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
          Length = 243

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 82/232 (35%), Positives = 125/232 (53%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA +G+ SRR+ + +I   RV VNGI     A  V   D + VDG PL  A+  
Sbjct: 1   MRLNKAIAASGLCSRRKADELILSGRVTVNGIAEPNPARQVSPEDALGVDGRPLTGAQDF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
              + +KP+ +V T +DP+GR TV + LP      R+  VGRLD  +EGLLLLTNDG LA
Sbjct: 61  YYLMLNKPVQVVCTVNDPEGRPTVMEYLPKNMRALRLYPVGRLDYFSEGLLLLTNDGQLA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
           + L  PS    + Y V   G V    L  ++ G+ + +G     ++V     KG    + 
Sbjct: 121 QRLTHPSHHQPKTYEVLVRGAVSDASLAAMRHGMRLAEGEDLMPVEVEASFTKG-RTLLR 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + L +G NR+I+++       +  L R+S GP +LG L +G  R+++   ++
Sbjct: 180 MVLHQGLNRQIRRMCRDLGLTILYLKRVSQGPIELGGLASGRARQLTAAEIK 231


>gi|283832909|ref|ZP_06352650.1| ribosomal large subunit pseudouridine synthase B [Citrobacter
           youngae ATCC 29220]
 gi|291071514|gb|EFE09623.1| ribosomal large subunit pseudouridine synthase B [Citrobacter
           youngae ATCC 29220]
          Length = 291

 Score =  166 bits (419), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 89/288 (30%), Positives = 128/288 (44%), Gaps = 10/288 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +IA  RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIAAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRDARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           E +       ++V ++      +     R            R    S+
Sbjct: 242 ELVELKPETTSKVAVEKDRRRMKANQIRRAVKRHSQVGGSRRPGGRSN 289


>gi|270262113|ref|ZP_06190385.1| ribosomal large subunit pseudouridine synthase B [Serratia
           odorifera 4Rx13]
 gi|270043989|gb|EFA17081.1| ribosomal large subunit pseudouridine synthase B [Serratia
           odorifera 4Rx13]
          Length = 298

 Score =  166 bits (419), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 92/300 (30%), Positives = 136/300 (45%), Gaps = 10/300 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V ++  I +DG  L   E
Sbjct: 2   SEKLQKVLARAGHGSRREIETIIEAGRVSVDGKVAKLGDRVEVTASMKIRLDGHVLSIKE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T        +          SR ++VGRLD+NT GLLL T 
Sbjct: 62  SEETVCRVLAYYKPEGELCTRSDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQ+D +K+  L KG+ ++        +T    +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQIDDEKVKQLSKGVQLEDGPAAFRTITFQGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+    L    
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIDLPKGLPRGGWTEL---ELPAIN 238

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
               L E +    + +       R + N I       T++  +  +    SK  K +   
Sbjct: 239 YLRELVELKPETVSKMPVERERRRVKANQIRRAVKRHTQVAGSGRRSAPGSKSGKPSKRS 298


>gi|195978395|ref|YP_002123639.1| ribosomal small subunit pseudouridine synthase A RsuA
           [Streptococcus equi subsp. zooepidemicus MGCS10565]
 gi|195975100|gb|ACG62626.1| ribosomal small subunit pseudouridine synthase A RsuA
           [Streptococcus equi subsp. zooepidemicus MGCS10565]
          Length = 237

 Score =  166 bits (419), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 98/233 (42%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +  AG+ SR +V+ ++ +++V VNG+        V    D +   G  L     
Sbjct: 1   MRLDKFLVDAGLGSRSQVKLLLKKKQVSVNGVSQTSPKYQVNEMADEVSYQGQRLNYEAF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T            +  +    V  VGRLD +T GLLL+TNDG LA 
Sbjct: 61  VYYMLNKPKGVISATEDSSHKTVLDLLDDTARQKAVFPVGRLDKDTHGLLLVTNDGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVT 190
            L  P     + Y     G + Q+ +    +GI ++        + +     S   + V 
Sbjct: 121 ALLSPKKHVAKQYLAVVDGMMTQEDVKHFAQGITLKDHQCMPAYLDILEINESLKTSLVK 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           + + EGK  ++K++       V+ L RIS GP QL + L  G+ R ++   L 
Sbjct: 181 ITIEEGKFHQVKRMVAACGKTVSDLQRISMGPLQLDSALAPGAYRRLTAAELE 233


>gi|183221647|ref|YP_001839643.1| ribosomal small subunit pseudouridine synthase A [Leptospira
           biflexa serovar Patoc strain 'Patoc 1 (Paris)']
 gi|189911725|ref|YP_001963280.1| pseudouridylate synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|167776401|gb|ABZ94702.1| Pseudouridylate synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|167780069|gb|ABZ98367.1| Ribosomal small subunit pseudouridine synthase A (rRNA
           pseudouridylate synthase A) [Leptospira biflexa serovar
           Patoc strain 'Patoc 1 (Paris)']
          Length = 243

 Score =  166 bits (419), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 99/229 (43%), Gaps = 3/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+   G  +R +V++ I Q  VKVNG++++     +  TD +      L + E  
Sbjct: 4   ERLDKVLGNYGFGTRSDVKKEIYQGNVKVNGLVVKDPGYKITLTDIVVYYDETLNRKEFY 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +   P  +  T    +     + +       +  +GRLD  TEGLLL T DG LA  
Sbjct: 64  YFMMNKAPDCITATEDPREKTVMDYLSERHRNMNLFPIGRLDKETEGLLLFTTDGTLAHY 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVG 192
              P     + Y       V    ++  + GI +         ++ +          TV 
Sbjct: 124 YTSPKHFVEKEYYAEISAPVTAFDISQFESGITLDDGYKTLPARLAIPDPSNP-HIATVW 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
           LREGK R+I+++F+    +V  L R+  G  +L   L  GS RE+++  
Sbjct: 183 LREGKYRQIRRMFQSLGKEVQYLKRVKMGNLELDRDLEVGSYRELTEAE 231


>gi|242239776|ref|YP_002987957.1| 16S rRNA pseudouridylate synthase A [Dickeya dadantii Ech703]
 gi|242131833|gb|ACS86135.1| pseudouridine synthase [Dickeya dadantii Ech703]
          Length = 232

 Score =  166 bits (419), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 55/232 (23%), Positives = 104/232 (44%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  + R +  QRV V+G +++  A  +     +  DG PL +    
Sbjct: 1   MRLDKFLSQQLGISRSLIARELRAQRVTVDGDVIKNGAFKLAPEHQVAFDGNPLVQQTGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V +  DPD  + ++     +  ++ + GRLDI+T GL+LLT+DG  +  
Sbjct: 61  RYFMLHKPQGYVCSTDDPDHPTILYFIDEPVAHKLHAAGRLDIDTSGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     ++         GI + G         + +  ++       +
Sbjct: 121 ITSPKHHCEKTYLVALDRPIEPGTAEHFAAGIQLNGEKELTKPAVLEVLDEQ----LARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EG+  ++K++F      V  L R   G   L  +L  G  R ++++ + 
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVTALHRERIGAIVLDSSLEPGEYRALTQEEVD 228


>gi|254481782|ref|ZP_05095025.1| conserved hypothetical protein, putative [marine gamma
           proteobacterium HTCC2148]
 gi|214037911|gb|EEB78575.1| conserved hypothetical protein, putative [marine gamma
           proteobacterium HTCC2148]
          Length = 298

 Score =  166 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 75/280 (26%), Positives = 118/280 (42%), Gaps = 5/280 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---K 69
            +++ KV+AR G+ SRRE+ER I Q RV ++G         V   + I VDG P+     
Sbjct: 20  GEKLQKVLARTGLGSRREMERWIEQGRVSIDGKPAT-LGDRVTHRERISVDGRPVNTTPA 78

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   +  +     + +       R+           R IS+GRLD NT GLLL T DG 
Sbjct: 79  QETRCILYHKPTGEVCSRKDPQGRRTVFERLPKLKSGRWISIGRLDYNTSGLLLFTTDGD 138

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  PS+   R Y VR  G+  +D L  L  G++++        +      G N W 
Sbjct: 139 LANKLMHPSSNIEREYMVRVMGEWKEDMLQRLLDGVMLEDGVARFSDIQDGGGDGINHWF 198

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
            V + EG+NRE+++++E     V+RL R+ YG   +   +  G   E++ K ++      
Sbjct: 199 YVVIMEGRNREVRRLWESQGLTVSRLKRVRYGEVFIPSKVKQGQWVELAGKEIKSLYRMA 258

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
            L    +         +   +             +  K  
Sbjct: 259 DLPLKDMKRGTIKEREKMERQFSKRKGPGGSSARSGRKPR 298


>gi|229112170|ref|ZP_04241712.1| Pseudouridine synthase [Bacillus cereus Rock1-15]
 gi|228671286|gb|EEL26588.1| Pseudouridine synthase [Bacillus cereus Rock1-15]
          Length = 233

 Score =  166 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 58/223 (26%), Positives = 99/223 (44%), Gaps = 4/223 (1%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTRLWLYHKP 81
            G  SR+EV++++    VK++G  ++ A V+V      + + G  +   E   L ++   
Sbjct: 1   MGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKEFVYLMMHKPQ 60

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
             +  T  D          L         VGRLDI+TEG LL+TNDG L+  L  P    
Sbjct: 61  GVISATEDDNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKLSHQLLSPKKHV 120

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
            + Y     G V ++ +    KG+++          +T+  +    + + + + EGK  +
Sbjct: 121 PKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEIELVITEGKFHQ 179

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           +K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 180 VKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 222


>gi|53726360|ref|YP_102763.1| RNA pseudouridylate synthase family protein [Burkholderia mallei
           ATCC 23344]
 gi|52429783|gb|AAU50376.1| RNA pseudouridylate synthase family protein [Burkholderia mallei
           ATCC 23344]
          Length = 380

 Score =  166 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 81/375 (21%), Positives = 137/375 (36%), Gaps = 27/375 (7%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++G 
Sbjct: 1   MLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRINGK 59

Query: 66  PLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           P+++         L  +     +V+        S      P   ++ ++VGRLD NTEGL
Sbjct: 60  PVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNTEGL 119

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           L+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++    
Sbjct: 120 LMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRIRDGG 179

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
            +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +  
Sbjct: 180 GEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDEAQ 239

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRP---------------------NIISEVP 279
           +R  +    L+    +            +  P                            
Sbjct: 240 VRRLMSTVGLKAPTEDKGGKRGGPVERRQPDPMQTSMGFINREPVLTTHGQLDQPRRGRR 299

Query: 280 DDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
                                                + G   +    +G+   N   + 
Sbjct: 300 GPAGGGFGAGLGGGYAGLPGYGGASRQGGRDVDGNRASYGGAGANKRGAGKGGRNPNGNR 359

Query: 340 SFPSKRSLRRTSAKK 354
           +    R   RT  ++
Sbjct: 360 AEGGARGGPRTPQQR 374


>gi|229917541|ref|YP_002886187.1| RNA-binding S4 domain protein [Exiguobacterium sp. AT1b]
 gi|229468970|gb|ACQ70742.1| RNA-binding S4 domain protein [Exiguobacterium sp. AT1b]
          Length = 236

 Score =  166 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 63/227 (27%), Positives = 110/227 (48%), Gaps = 7/227 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ +G ASRR+ +R++ + RV +NG   +     V   D + V+G   R A   
Sbjct: 1   MRINKFISESGKASRRQADRLVEEGRVTINGKKAK-IGDQVKPGDEVLVNGSVARVARNN 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                HKP+G+ +T       + V     +   R+ ++GRLD ++EGL+L+TNDG +   
Sbjct: 60  VYIAVHKPVGITSTTEKKVKGNLVDMV--NHPLRIFNIGRLDKDSEGLILMTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  + +  ++ G+ I G      +V       S     + L
Sbjct: 118 ILRAEGEHEKEYIVSVDKPITPEFVEQMEAGVKILGQKTLPCKVRPL----SKFDFNITL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +G NR+I+++ E   ++V RL R+      LG L  G  R++SKK 
Sbjct: 174 TQGLNRQIRRMCEALGYEVFRLQRVRVMNITLGKLPPGQWRDLSKKE 220


>gi|145639224|ref|ZP_01794831.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae PittII]
 gi|145271786|gb|EDK11696.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae PittII]
 gi|309750799|gb|ADO80783.1| 16S RNA U516 pseudouridine synthase [Haemophilus influenzae R2866]
          Length = 232

 Score =  166 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 57/236 (24%), Positives = 108/236 (45%), Gaps = 7/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  +V +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENTGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWIEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ HKP G V ++ D D  +        +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYFMLHKPQGCVCSNDDGDYPTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+++      +GI+++G        ++ +      +  V +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEENYAAACSEGILLRGEKEPTKPAKLEIL----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
            + EG+  ++K++F     KV  L R   G   L   L  G  R +++  + + + 
Sbjct: 177 TISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLVK 232


>gi|290961534|ref|YP_003492716.1| pseudouridine synthase [Streptomyces scabiei 87.22]
 gi|260651060|emb|CBG74179.1| putative pseudouridine synthase [Streptomyces scabiei 87.22]
          Length = 313

 Score =  166 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 112/233 (48%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
               +R+ K++ARAG  SRR  E +I Q RV+VNG ++      V    D ++VDG+ + 
Sbjct: 73  EQEGERLQKILARAGYGSRRSCEELIEQARVEVNGEIVLEQGKRVDPEKDEVKVDGLTVA 132

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   L      + T   +   +  + D + +  +R+  VGRLD  TEG++LLTN G
Sbjct: 133 TQSYQFFSLNKPAGVVSTMEDNEGRQ-CLGDYVTNRETRLFHVGRLDTETEGVILLTNHG 191

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     +VY     G + +D    LK GI ++          +  Q G N  
Sbjct: 192 ELAHRLTHPKYGVKKVYLAHIVGPIPRDLGKQLKDGIQLEDGYARADHFRVVQQTGKNYL 251

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L EG+   ++++     + V++L+R+++GP  LG   +G  R +S   +
Sbjct: 252 VEVTLHEGRKHIVRRMLAEAGFPVDKLVRVAFGPITLGDQKSGWLRRLSNTEV 304


>gi|220929584|ref|YP_002506493.1| pseudouridine synthase [Clostridium cellulolyticum H10]
 gi|219999912|gb|ACL76513.1| pseudouridine synthase [Clostridium cellulolyticum H10]
          Length = 245

 Score =  166 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 58/245 (23%), Positives = 107/245 (43%), Gaps = 13/245 (5%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DH 59
           MK K         QR+ KV++  G  SR  ++  + +  V V+G +++ + ++V      
Sbjct: 1   MKQK---------QRLDKVLSNFGFGSRNYIKGAVKKGLVTVDGRIIKDSGIHVDPEVSI 51

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           IE+DG  L   +   + L      +  T                    +   GRLDI+TE
Sbjct: 52  IEIDGERLNYRKYIYIMLNKPQGVISATSDRKQKTVFDILPEEYKCFDLFPAGRLDIDTE 111

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVT 178
           GL+L+TNDG L+  +  P     + Y  +  G+V+Q+      +G+ +          + 
Sbjct: 112 GLVLMTNDGQLSHEILSPKKHVPKQYYAKVMGRVNQEDAEAFSRGVTLDDGYQTLPAVLE 171

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVS 237
           +  +    + + + + EGK  ++K++FE    KV  L R+S G  +L   L  G  +E+ 
Sbjct: 172 IL-KSDDLSEIKLTIVEGKFHQVKRMFEAVGKKVIYLKRLSMGNLRLDESLQLGECKELG 230

Query: 238 KKILR 242
           +  + 
Sbjct: 231 ESDIE 235


>gi|242279370|ref|YP_002991499.1| RNA-binding S4 domain protein [Desulfovibrio salexigens DSM 2638]
 gi|242122264|gb|ACS79960.1| RNA-binding S4 domain protein [Desulfovibrio salexigens DSM 2638]
          Length = 251

 Score =  166 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 82/240 (34%), Positives = 130/240 (54%), Gaps = 7/240 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPL 67
              T  R++K IA AGIASRR  + ++ + +VKVNG L +   + V    D +EV+G  +
Sbjct: 2   TEKTTIRLNKYIASAGIASRRGADELVQKGKVKVNGELADSPGIQVDPDNDRVEVNGKLV 61

Query: 68  RKAERTR--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLL 123
           +  E+++    L HK I  VTT  DP GR TV D LP          VGRLD  +EG+LL
Sbjct: 62  QHDEKSKDLYILLHKTIETVTTAKDPQGRKTVLDLLPPDVINRRVFPVGRLDFYSEGMLL 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDT 181
           LT DG L   +  P     ++Y V   G++ + +L++++ G+ ++        +++   +
Sbjct: 122 LTTDGELCNRMTHPKWHLPKIYHVTIRGKLSEKELSVMQNGMYLEDKGELLAPVKIKAIS 181

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + G      + LR+G NR+I+++F  F+  + RL R+  G  +LG L  G  RE+S K L
Sbjct: 182 EVGETTKYEMELRQGINRQIRRMFGEFDKTILRLKRVRQGRIELGALKPGKWRELSAKEL 241


>gi|291087005|ref|ZP_06345121.2| ribosomal large subunit pseudouridine synthase B [Clostridium sp.
           M62/1]
 gi|291076613|gb|EFE13977.1| ribosomal large subunit pseudouridine synthase B [Clostridium sp.
           M62/1]
          Length = 283

 Score =  166 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 66/272 (24%), Positives = 118/272 (43%), Gaps = 6/272 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +++     R++K ++ +G  SRRE +R+I    V V+G +     + +     IE DG  
Sbjct: 18  MEKGTQEIRLNKFLSESGFCSRREADRLIEAGEVLVDGAVA-SMGMKIREGQQIEADGTL 76

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +   +R  + L +KP G+V T SD D    + D +         VGRLD ++EGL+L+TN
Sbjct: 77  ISGKDRPVVLLVNKPRGIVCTTSDRDRAENIVDFIGYPLRV-YPVGRLDKDSEGLILMTN 135

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
            G L   +        + Y V    ++ +  LN ++KG+ I         V    +K   
Sbjct: 136 QGELVNRILKGRYGHEKEYLVSVDREITEQFLNRMRKGVKILDTVTRPCTV----EKTGE 191

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               + L +G NR+I+++ E   ++V  L R+     +L  L  G  RE+++   +E   
Sbjct: 192 KSFRIILTQGLNRQIRRMCEALGYRVRTLKRVRIMNLRLDGLKTGEYREITRGEWKELTE 251

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEV 278
               +  +   D       + +  R       
Sbjct: 252 LLEGKGERRKADQKNAGKHSELGQREPEKGGR 283


>gi|209548084|ref|YP_002280001.1| RNA-binding S4 domain protein [Rhizobium leguminosarum bv. trifolii
           WSM2304]
 gi|209533840|gb|ACI53775.1| RNA-binding S4 domain protein [Rhizobium leguminosarum bv. trifolii
           WSM2304]
          Length = 689

 Score =  166 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 170/329 (51%), Positives = 213/329 (64%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R+SKV+ARAG+ASRR++ERMI + RV +NG +L+   VNV   D IEVDGVP+R 
Sbjct: 44  EAKAERISKVMARAGVASRRDIERMIMEGRVTLNGAVLDTPVVNVTLADRIEVDGVPIRG 103

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ERTRLWLYHKP GLVTT++DP+GR+TVFDNLP    RV+S+GRLDINTEGLLLLTNDGG
Sbjct: 104 IERTRLWLYHKPAGLVTTNADPEGRATVFDNLPEELPRVMSIGRLDINTEGLLLLTNDGG 163

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LAR LELP+T WLR YRVR HG +DQD L+ LK GI + G+ YG ++ TLD  +GSN W+
Sbjct: 164 LARALELPATGWLRRYRVRAHGDIDQDALDKLKDGIAVDGVLYGSIEATLDRTQGSNVWI 223

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           T+GLREGKNREIK V       VNRLIRISYGPFQLG L  G   EV  + LR+QLGP L
Sbjct: 224 TMGLREGKNREIKNVMGALGLDVNRLIRISYGPFQLGDLPEGHVIEVRGRTLRDQLGPRL 283

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
           +EEA+ N DAPIY++  +  +             R +++  ++     +        R  
Sbjct: 284 IEEAKANFDAPIYNAPAVAAEEEAEAPVPERREQRPRRDEDKRERALSRLDTKRDDRRGG 343

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRS 338
              +     G           +    RRS
Sbjct: 344 GRRDDDRRDGGRFDDDKPKRPQPLGQRRS 372



 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 10/115 (8%), Positives = 27/115 (23%), Gaps = 2/115 (1%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           + ++    +    + + +    S +   +D          D    +            ++
Sbjct: 415 IEDRPRTQINRVREEDGEWIRSSEQPNRKDEGEGRKRSFGDRPAREDRGFGDRPARGDRR 474

Query: 301 LATPVHRRNL-ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                  R    S+    +          G R     R PS   +    +    +
Sbjct: 475 PREGGDERPRSRSSAGEGRPERPRGDRPFGDRPSRGDR-PSRGDRPFGDKPRGDR 528



 Score = 42.1 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 14/121 (11%), Positives = 29/121 (23%), Gaps = 2/121 (1%)

Query: 233 TREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
            RE   + +R    P+  +E +    +         R   +  +              + 
Sbjct: 426 VREEDGEWIRSSEQPNRKDEGEGRKRSFGDRPAREDRGFGDRPARGDRRPREGGDERPRS 485

Query: 293 NGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
              + + +   P   R        ++G   S        +    R P        R   A
Sbjct: 486 RSSAGEGRPERPRGDRPFGDRP--SRGDRPSRGDRPFGDKPRGDRKPRGDGDERPRAARA 543

Query: 353 K 353
            
Sbjct: 544 S 544



 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 18/118 (15%), Positives = 28/118 (23%), Gaps = 7/118 (5%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R   G     E          S+     +RP       D  +R  + S        + + 
Sbjct: 467 RPARGDRRPREGGDERPRSRSSAGEGRPERPRGDRPFGDRPSRGDRPSRGDRPFGDKPRG 526

Query: 302 ATPVHR------RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                       R   ++   A+          G R     R P     R  RR   +
Sbjct: 527 DRKPRGDGDERPRAARASTGEARSERPRGDRPFGDRPSRGDR-PFGDKPRGERRPREE 583



 Score = 39.4 bits (90), Expect = 0.78,   Method: Composition-based stats.
 Identities = 12/115 (10%), Positives = 21/115 (18%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
                           +       +       DRP+       D  R  +          
Sbjct: 479 GDERPRSRSSAGEGRPERPRGDRPFGDRPSRGDRPSRGDRPFGDKPRGDRKPRGDGDERP 538

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           +   A+    R+         G   S        +    R P        R   +
Sbjct: 539 RAARASTGEARSERPRGDRPFGDRPSRGDRPFGDKPRGERRPREEGDERPRAARS 593



 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 11/108 (10%), Positives = 23/108 (21%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G H +E+        +   +          +   +   R +    +     +        
Sbjct: 411 GSHHIEDRPRTQINRVREEDGEWIRSSEQPNRKDEGEGRKRSFGDRPAREDRGFGDRPAR 470

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R             SS      +R    R     PS+        +
Sbjct: 471 GDRRPREGGDERPRSRSSAGEGRPERPRGDRPFGDRPSRGDRPSRGDR 518


>gi|331677046|ref|ZP_08377742.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli H591]
 gi|331075735|gb|EGI47033.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli H591]
          Length = 299

 Score =  166 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 87/292 (29%), Positives = 129/292 (44%), Gaps = 10/292 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLR 68
           +   +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  + 
Sbjct: 8   SSMSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLIS 67

Query: 69  KAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
             E        L  Y     L T +      +          +R I+VGRLD+NT GLLL
Sbjct: 68  VRESAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLL 127

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +
Sbjct: 128 FTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGE 187

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KK 239
           G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+      
Sbjct: 188 GINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTN 247

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
            LRE +       ++V ++      +     R            R    ++ 
Sbjct: 248 YLRELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGGRRSGGRNNG 299


>gi|213859463|ref|ZP_03385167.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
          Length = 231

 Score =  166 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 104/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G +++ AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNRKSLTKPATLEVI----TPVQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEEEI 227


>gi|258621922|ref|ZP_05716952.1| ribosomal small subunit pseudouridine synthase A [Vibrio mimicus
           VM573]
 gi|258585860|gb|EEW10579.1| ribosomal small subunit pseudouridine synthase A [Vibrio mimicus
           VM573]
          Length = 257

 Score =  166 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 49/238 (20%), Positives = 96/238 (40%), Gaps = 8/238 (3%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +Q +    R+ K +  A   +R+E   ++    V V+ ++ +  A  +  T  +E  G  
Sbjct: 20  LQADEVSMRLDKFLCDALGTTRKEATMLLKSGEVTVDDLVQKSGAFKLKETSCVEWQGRE 79

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +       + ++     + +       ++            +   GRLD++T GLLL+T+
Sbjct: 80  ITAHGPRYIMMHKPDGVVCSHEDG-FNQTAFILLDEVNIQDLHFAGRLDVDTTGLLLITD 138

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKG 184
           DG  +  +  P  +  + YRV     +  D       GI ++G        Q+ +     
Sbjct: 139 DGQWSHRVTSPKHKCEKTYRVWLADPIQADYAEQFTNGIELRGERELTLPAQLEIV---- 194

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           S   V + + EGK  ++K++F     KV  L R   G   L   L  G  R ++++ +
Sbjct: 195 SETEVLLTIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDESLEPGDYRYLTEEEI 252


>gi|258424167|ref|ZP_05687049.1| RNA pseudouridine synthase [Staphylococcus aureus A9635]
 gi|257845788|gb|EEV69820.1| RNA pseudouridine synthase [Staphylococcus aureus A9635]
          Length = 231

 Score =  166 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 54/228 (23%), Positives = 101/228 (44%), Gaps = 7/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E 
Sbjct: 1   MRIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKAHIEPKNDKISVRGELIEYVEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + +   D   ++ +          +  VGRLD +TEGLLL+TNDG    
Sbjct: 61  VYIMLNKPKGYI-SATEDHHSKTVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+    + Y V     + ++ +   K+G+ +         +T    + S     V 
Sbjct: 120 ELMSPNKHVSKKYEVISANPITEEDIQAFKEGVTLSDGKVKPAILTYIDNQTS----HVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           + EGK  ++K++F     +V  L RI     +L   L +G+ R +++ 
Sbjct: 176 IYEGKYHQVKRMFHSIQNEVIHLKRIKIADLELDSNLESGNYRLLTEN 223


>gi|300863940|ref|ZP_07108855.1| ribosomal large subunit pseudouridine synthase B [Oscillatoria sp.
           PCC 6506]
 gi|300338060|emb|CBN54001.1| ribosomal large subunit pseudouridine synthase B [Oscillatoria sp.
           PCC 6506]
          Length = 263

 Score =  166 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 82/239 (34%), Positives = 122/239 (51%), Gaps = 12/239 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR--KA 70
           +R+ K++A+ GIASRR+ E MI   RV+VNG  ++         +D IEVDGV ++  + 
Sbjct: 3   ERLQKILAQWGIASRRQAEEMILAGRVRVNGNTVQ-LGQKANPASDRIEVDGVRVKSERR 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTND 127
            +    L +KP G+V+T SDP  R+TV D LP        +  VGRLD+ + G LLLTND
Sbjct: 62  PQPVYLLLNKPAGVVSTCSDPAQRTTVLDLLPPKLRAGCGIHPVGRLDVESTGALLLTND 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  P     + Y+V   G   +  L    +G+++        QV +  + GS  
Sbjct: 122 GNLTFALTHPRHCVPKTYQVWVEGDPPKSVLQTWSQGVLLSRRMTLPAQVRVQERNGSQT 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-----TLLAGSTREVSKKIL 241
            + V L EG+NR++++V E   + V  L R + GP  L       L AG  R +    +
Sbjct: 182 LLEVILYEGRNRQVRRVAEQLGYPVIHLHRTAIGPILLQPPGEPELPAGHYRPLLDSEI 240


>gi|315180431|gb|ADT87345.1| pseudouridine synthase family 1 protein [Vibrio furnissii NCTC
           11218]
          Length = 315

 Score =  166 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 86/315 (27%), Positives = 130/315 (41%), Gaps = 7/315 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E +I   RV VNG +             + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGERLEDENAVVRIDGHAVSAKAQ 61

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  Y     L T H     R+          SR ISVGRLD NT GLLL T D
Sbjct: 62  EEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G V +DK+  L +G+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRQVEREYLVRVFGDVTEDKIRNLVRGVQLEDGLARFEDVVYAGGEGMNH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+  K +   L 
Sbjct: 182 TFYVVINEGRNREVRRLWESQETTVSRLKRVRYGDIFLDKKLPRGGWMELDLKDV-NYLR 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
             +  + +      +    T  +   +   ++     R ++  +   G S   +      
Sbjct: 241 ELVELKPEKTTMLDVSKDNTSRKRERSRSQKIRRAVRRHEERVTAPAGRSGSSRRKDAAS 300

Query: 307 RRNLASNVWMAKGIH 321
           R+   +     +   
Sbjct: 301 RQKAGNTSAAPRKGR 315


>gi|282860273|ref|ZP_06269343.1| pseudouridylate synthase [Prevotella bivia JCVIHMP010]
 gi|282586947|gb|EFB92182.1| pseudouridylate synthase [Prevotella bivia JCVIHMP010]
          Length = 555

 Score =  166 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 59/242 (24%), Positives = 111/242 (45%), Gaps = 1/242 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I   +V VNG ++      ++ TD +
Sbjct: 307 IEYKEEHIDPTEPLRLNKFLANAGVCSRREADDFILAGQVTVNGEVINELGTKILRTDEV 366

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +     +   ++  + L      + T+      ++ +     +   R+  VGRLD NT G
Sbjct: 367 KFQDKLVSLEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKDACPERIYPVGRLDRNTTG 426

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LL TNDG LA  L  P     +VY V     +  ++L  +  GI ++        +   
Sbjct: 427 VLLFTNDGDLASKLTHPKFLKKKVYHVFLDKPITANELQKISDGIELEDGEIKADAIEYA 486

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             +   A V + +  GKNR ++++FE   ++V +L R+ +       +  G  R +++K 
Sbjct: 487 NPE-DQAQVGIEIHSGKNRIVRRIFESLGYRVVKLDRVMFAGLTKKNVRRGDWRFLTEKE 545

Query: 241 LR 242
           + 
Sbjct: 546 VE 547


>gi|222098177|ref|YP_002532234.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus
           Q1]
 gi|221242235|gb|ACM14945.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus
           Q1]
          Length = 233

 Score =  166 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 59/223 (26%), Positives = 100/223 (44%), Gaps = 4/223 (1%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTRLWLYHKP 81
            G  SR+EV++++    VK++GI ++ A V+V      + + G  +   E   L ++   
Sbjct: 1   MGYGSRKEVKKLLKDGVVKIDGIPVKDAKVHVNVEEQEVMIHGEVVEYKEFVYLMMHKPQ 60

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
             +  T  D          L         VGRLDI+TEG LL+TNDG L+  L  P    
Sbjct: 61  GVISATEDDNHETVIDLLELEDAIFNPFPVGRLDIDTEGFLLITNDGKLSHQLLSPKKHV 120

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
            + Y     G V ++ +    KG+++          +T+  +    + + + + EGK  +
Sbjct: 121 PKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEIELVITEGKFHQ 179

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           +K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 180 VKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 222


>gi|147673214|ref|YP_001216750.1| pseudouridine synthase family 1 protein [Vibrio cholerae O395]
 gi|262169496|ref|ZP_06037188.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           RC27]
 gi|262191635|ref|ZP_06049813.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           CT 5369-93]
 gi|146315097|gb|ABQ19636.1| pseudouridine synthase family 1 protein [Vibrio cholerae O395]
 gi|227013096|gb|ACP09306.1| pseudouridine synthase family 1 protein [Vibrio cholerae O395]
 gi|262022309|gb|EEY41018.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           RC27]
 gi|262032477|gb|EEY51037.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           CT 5369-93]
          Length = 321

 Score =  166 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 91/320 (28%), Positives = 131/320 (40%), Gaps = 9/320 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E +I   RV VNG +             + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGERLEDDNAVVRIDGHVVSVKAQ 61

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  Y     L T H     R+          SR ISVGRLD NT GLLL T D
Sbjct: 62  EEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G V ++K+  L +G+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRQVEREYLVRVFGDVTEEKVRNLVRGVQLEDGMARFEDVMYAGGEGINH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI---LRE 243
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+  K    LRE
Sbjct: 182 TFYVVINEGRNREVRRLWESQGTTVSRLKRVRYGDIFLDKKLPRGGWMELDLKQVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +     +E  +N+     + +        I   V     R+     +       +K   
Sbjct: 242 LVELRPEKETVLNMAPDAATRKRERTRSQKIRRAVRRHEERISATPGRSGKAPACRKPGG 301

Query: 304 PVHRRNLASNVWMAKGIHSS 323
               RN  +N   +      
Sbjct: 302 ESSTRNKVANQQQSSRKPRG 321


>gi|121635067|ref|YP_975312.1| putative pseudouridine synthase [Neisseria meningitidis FAM18]
 gi|120866773|emb|CAM10526.1| putative pseudouridine synthase [Neisseria meningitidis FAM18]
 gi|325138220|gb|EGC60789.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis ES14902]
          Length = 256

 Score =  166 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 71/245 (28%), Positives = 121/245 (49%), Gaps = 7/245 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P+R+ KV+A +G+ SRRE+E  I    + VNG   +     V   DH+ V G  ++   
Sbjct: 2   EPERLQKVLAASGVGSRREMEEWITNGWITVNGKTAQ-LGDKVTPDDHVTVKGSIIKLKW 60

Query: 72  RTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             RL      Y +   +V+        S       +  SR +++GRLDINT GLL+LT  
Sbjct: 61  ADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTTS 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN 186
           G L +    PS +  R Y VR  G +  +++ +L +  ++++       ++     +G+N
Sbjct: 121 GELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGAN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
            W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   E++   +   L
Sbjct: 181 KWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFYELNPAEVANIL 240

Query: 246 GPHLL 250
               +
Sbjct: 241 KWAEM 245


>gi|319776127|ref|YP_004138615.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           influenzae F3047]
 gi|329123291|ref|ZP_08251859.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           aegyptius ATCC 11116]
 gi|317450718|emb|CBY86938.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           influenzae F3047]
 gi|327471500|gb|EGF16948.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           aegyptius ATCC 11116]
          Length = 232

 Score =  166 bits (419), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 58/236 (24%), Positives = 108/236 (45%), Gaps = 7/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  AV +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENTGLTRSQATKAIRQSAVKINGEIVKSGAVQISQEDKIYFEDELLTWVEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ HKP G V ++ D D  +        +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYFMLHKPQGCVCSNDDGDYPTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+++      +GI+++G        ++ +      +  V +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEENYAAACSEGILLRGEKEPTKPAKLEIL----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
            + EG+  ++K++F     KV  L R   G   L   L  G  R +++  + + + 
Sbjct: 177 TISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLVK 232


>gi|120554089|ref|YP_958440.1| RNA-binding S4 domain-containing protein [Marinobacter aquaeolei
           VT8]
 gi|120323938|gb|ABM18253.1| ribosomal large subunit pseudouridine synthase B [Marinobacter
           aquaeolei VT8]
          Length = 328

 Score =  166 bits (419), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 87/309 (28%), Positives = 134/309 (43%), Gaps = 8/309 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
           P+RV K++ARAG+ SRREVE  I   R+ VNG+ ++       ++D  E+DG  L  +  
Sbjct: 21  PERVQKLLARAGVGSRREVEGWIEAGRLLVNGVPVQ-PGQKASTSDRFELDGKLLDVSSA 79

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R  L        + +        +           R IS+GRLDINT GL+L T D
Sbjct: 80  AEVVRRVLIYNKPEGEVTSRKDPEGRPTVFDRLPRLKDQRWISIGRLDINTTGLVLFTTD 139

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS+Q  R Y VR  G+VD   +  LK+G++++        ++    KG N 
Sbjct: 140 GELANRLMHPSSQIDREYAVRVFGEVDDAMIERLKEGVLLEDGMAKFTDISPAGGKGMNQ 199

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V L EG+NRE+++++E    +V+RL R+ YGP  L   L  G   E+ +K +     
Sbjct: 200 WFHVTLLEGRNREVRRLWESQGVRVSRLKRVRYGPIFLPSRLTMGRWEELDQKGVDALSR 259

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISE-VPDDFTRMKKNSSQKNGLSKQKKLATPV 305
              L    V    P   +    + R +              + +      ++      P 
Sbjct: 260 AVGLGSVAVPQKTPGEQAAHDRKRRKSPGKSLQRTRKGGSWQVADGAPPKARSDSRGKPS 319

Query: 306 HRRNLASNV 314
             +      
Sbjct: 320 AGKGRKPAR 328


>gi|223985762|ref|ZP_03635806.1| hypothetical protein HOLDEFILI_03112 [Holdemania filiformis DSM
           12042]
 gi|223962272|gb|EEF66740.1| hypothetical protein HOLDEFILI_03112 [Holdemania filiformis DSM
           12042]
          Length = 237

 Score =  166 bits (419), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 61/242 (25%), Positives = 105/242 (43%), Gaps = 9/242 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A AG  +R+ V+ ++ + RV+VNG  +++    +    D I+VDG  +     
Sbjct: 2   MRLDKFLAHAGFGTRKAVKELVRKGRVEVNGQRVKKDDQKIDERQDQIQVDGRIVTYETE 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      +  T             L +  S +  VGRLDI+TEGLLL+TNDG LA 
Sbjct: 62  VYIMLNKPQGVVSATEDSRYETVLDC--LETNRSDLFPVGRLDIDTEGLLLITNDGALAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V      D      ++ GI I               ++ +   + +
Sbjct: 120 DLLSPKKHVDKTYEVHLERPWDPQYEAAIQMGIRISDEEVCLPAT----LRQTAEHIILL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLL 250
            ++EGK  ++K++    + +V  L R++ GP +L   L  G  R  + + +         
Sbjct: 176 TIQEGKFHQVKRMMHACDNEVVYLKRLTMGPLKLDAALQPGQWRNCTPQEIEALKNHKKA 235

Query: 251 EE 252
           E+
Sbjct: 236 EK 237


>gi|18310062|ref|NP_561996.1| pseudouridylate synthase [Clostridium perfringens str. 13]
 gi|18144741|dbj|BAB80786.1| pseudouridylate synthase [Clostridium perfringens str. 13]
          Length = 236

 Score =  166 bits (419), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 68/228 (29%), Positives = 115/228 (50%), Gaps = 2/228 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKAER 72
           +R+ K +AR G+ASRR+ E +I   +VKVN  +++     V  +  +   +   +R  E 
Sbjct: 3   ERLQKYMARCGVASRRKCEEIICSGKVKVNDTVVDSLGTKVDPSVDVVSVNNKVIRPEEN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G VTT+ D   R T+ D +     R+  +GRLD ++ GLLLLTNDG +  
Sbjct: 63  KVYIMLNKPEGYVTTNKDEKNRKTILDIVKVN-ERIYPIGRLDYDSSGLLLLTNDGDVYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y     G   ++++N  +KG+ I      + ++ L  +  ++  V + 
Sbjct: 122 KIIHPRVNLNKEYIALVKGIFTEEEMNKFRKGVDIGDYKTAECEIELLEKYTNSCKVKII 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           + EGKNR+I+++   FN +V  L R + G   L  L  G  R +S   
Sbjct: 182 IHEGKNRQIRRMCAAFNHEVVSLKREAIGSLTLKNLKKGEWRYLSSSE 229


>gi|295692663|ref|YP_003601273.1| pseudouridine synthase [Lactobacillus crispatus ST1]
 gi|295030769|emb|CBL50248.1| Pseudouridine synthase [Lactobacillus crispatus ST1]
          Length = 234

 Score =  165 bits (418), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 102/232 (43%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I +  V VNG+ ++     V  +D + V+G  +   +  
Sbjct: 1   MRIDKYLANMNVGSRKEVHLLIKKGIVAVNGVTVKTPKQQVKESDQVTVNGDAVAYQKYH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      L  T                 +  ++ VGRLD +T GLLLLTNDG L   
Sbjct: 61  YFLLNKPKGVLSATEDRSQPTVISLLAPQDRYQGIVPVGRLDKDTTGLLLLTNDGQLNHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG--SNAWVT 190
           L  P+    ++YR +  G  D + +     G+ +  G      ++ + +Q    + +   
Sbjct: 121 LLAPNKHVDKIYRAKIAGVADDETVKTFAAGMTLGDGTKLQPAELKILSQDEEHNRSTTE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           + +REGK  +IK++F     KV  L RIS G   L   L  G   E+  + +
Sbjct: 181 IKIREGKYHQIKRMFGAVGMKVVELERISMGDLTLPANLKRGEYLELKLEDI 232


>gi|149365868|ref|ZP_01887903.1| putative RNA pseudouridylate synthase-family protein [Yersinia
           pestis CA88-4125]
 gi|153947333|ref|YP_001400903.1| 23S rRNA pseudouridylate synthase B [Yersinia pseudotuberculosis IP
           31758]
 gi|229894897|ref|ZP_04510075.1| 23S rRNA pseudouridylate synthase [Yersinia pestis Pestoides A]
 gi|229897640|ref|ZP_04512796.1| 23S rRNA pseudouridylate synthase [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229898285|ref|ZP_04513432.1| 23S rRNA pseudouridylate synthase [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229902144|ref|ZP_04517265.1| 23S rRNA pseudouridylate synthase [Yersinia pestis Nepal516]
 gi|34098644|sp|Q8ZEG0|RLUB_YERPE RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|115347920|emb|CAL20842.1| putative RNA pseudouridylate synthase-family protein [Yersinia
           pestis CO92]
 gi|149292281|gb|EDM42355.1| putative RNA pseudouridylate synthase-family protein [Yersinia
           pestis CA88-4125]
 gi|152958828|gb|ABS46289.1| ribosomal large subunit pseudouridine synthase B [Yersinia
           pseudotuberculosis IP 31758]
 gi|229681040|gb|EEO77135.1| 23S rRNA pseudouridylate synthase [Yersinia pestis Nepal516]
 gi|229688575|gb|EEO80644.1| 23S rRNA pseudouridylate synthase [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229693977|gb|EEO84026.1| 23S rRNA pseudouridylate synthase [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229701992|gb|EEO90013.1| 23S rRNA pseudouridylate synthase [Yersinia pestis Pestoides A]
 gi|320014878|gb|ADV98449.1| 23S rRNA pseudouridylate synthase [Yersinia pestis biovar
           Medievalis str. Harbin 35]
          Length = 318

 Score =  165 bits (418), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 95/325 (29%), Positives = 142/325 (43%), Gaps = 16/325 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
            +++ K++ARAG  SRRE+E +I Q RV V+G +  +    V  T    I +DG  L   
Sbjct: 2   GEKLQKILARAGHGSRREIEAIIQQGRVSVDGKV-SKLGDRVEVTQSTKIRLDGHLLSIK 60

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E        L  Y     L T +      +          SR ++VGRLD+NT GLLL T
Sbjct: 61  ESEENVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  GQ+D DK+  L +G+ ++        ++    +G 
Sbjct: 121 TDGELANRLMHPSREVEREYAVRVFGQIDDDKIKQLSRGVQLEDGPAAFRTISYQGGEGI 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+    L+  
Sbjct: 181 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELD---LKAT 237

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
                L E  V       S   + +DR  + +       +     S +    +Q      
Sbjct: 238 NYLRELVELDVETV----SKLPVEKDRRRVKANQIRRAVKRHTEVSGRQVAGRQGSARKG 293

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSG 329
             R+N+ +    A     S     G
Sbjct: 294 STRQNVGNAAPAATASRRSGPKKRG 318


>gi|254743404|ref|ZP_05201089.1| ribosomal large subunit pseudouridine synthase F [Bacillus
           anthracis str. Kruger B]
          Length = 235

 Score =  165 bits (418), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 109/229 (47%), Gaps = 7/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+G  LR A   
Sbjct: 1   MRINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCTSEKSV--KGNIIDLVNHPLRISHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  D L  +  G+ I G      ++T      S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEITQL----SKYEFKIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQRRDLTKKEKR 222


>gi|220935178|ref|YP_002514077.1| ribosomal large subunit pseudouridine synthase B [Thioalkalivibrio
           sp. HL-EbGR7]
 gi|219996488|gb|ACL73090.1| ribosomal large subunit pseudouridine synthase B [Thioalkalivibrio
           sp. HL-EbGR7]
          Length = 268

 Score =  165 bits (418), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 78/268 (29%), Positives = 112/268 (41%), Gaps = 5/268 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---K 69
            +R+ K++AR G  SRRE+ER I +  V VNG +           D + + G  +     
Sbjct: 2   TERLQKLLARLGHGSRREIERWIEEGLVTVNGKVA-SLGDQAGPDDKVAIRGRVVPLDVA 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   +  +     L T        +           R I+VGRLD NT GLLL T DG 
Sbjct: 61  PKPRVIAYHKPDGELTTRKDPEGRPTVFEHLPRLRNGRWIAVGRLDYNTSGLLLFTTDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  PS +  R Y VR  G+V  D L  L  G+ ++        +      G+N W 
Sbjct: 121 LAAKLMHPSGEVEREYAVRILGEVSPDALKQLTTGVELEDGPARFETLREAGGTGANRWY 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
            V LREG+NRE+++++E     V+RL R+ YGP  LG  L AG  R++    +       
Sbjct: 181 HVTLREGRNREVRRLWEAVGLTVSRLTRVRYGPISLGRDLRAGRWRDLEPGEMGALYAVA 240

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIIS 276
            L      +           R       
Sbjct: 241 GLPWTPPKIRREDRRPPKPPRTARRPKR 268


>gi|326316275|ref|YP_004233947.1| pseudouridine synthase Rsu [Acidovorax avenae subsp. avenae ATCC
           19860]
 gi|323373111|gb|ADX45380.1| pseudouridine synthase Rsu [Acidovorax avenae subsp. avenae ATCC
           19860]
          Length = 485

 Score =  165 bits (418), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 78/356 (21%), Positives = 132/356 (37%), Gaps = 29/356 (8%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          V   D ++V+
Sbjct: 141 KRVLPPQVEMPKLHKVLAQAGLGSRLEMEQLILEGRISVNNEPA-HIGQRVQYGDQVKVN 199

Query: 64  GVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+R          +  +     +VT     +  +           +  SVGRLD+NTE
Sbjct: 200 GRPIRYRIDPPAPRVIAYHKPVGEVVTHDDPQNRPTVFRKLPRLAHGKWQSVGRLDLNTE 259

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL T+ G LA  L  P     R Y VR  G +  ++   L  G+ ++        +  
Sbjct: 260 GLLLFTSAGELANKLMHPRFGLEREYAVRVLGALSNEEKQRLLDGVQLEDGMAAFGSIED 319

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +GSN W  V + EG+NRE++++ E     V+RLIRI YG   L   L  G+  E+ +
Sbjct: 320 GGGEGSNCWYRVTISEGRNREVRRMLESVGHAVSRLIRIRYGSMMLPRGLKRGAWLELDE 379

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           + +R  +     +  +                R               +           
Sbjct: 380 RDIRALMQAAGADMPRPAGPGAAAGDRKGGGPRKGGGRGQGGPGGPAPRGD--------- 430

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                               G      +    + +  + S  +    SL R    +
Sbjct: 431 --------------YFNPPAGGRGQRAAPPSSQPDPMKTSVGYIGSDSLARHRQDQ 472


>gi|121728919|ref|ZP_01681926.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           V52]
 gi|147673094|ref|YP_001217185.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           O395]
 gi|262169651|ref|ZP_06037342.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           RC27]
 gi|121628805|gb|EAX61267.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           V52]
 gi|146314977|gb|ABQ19516.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           O395]
 gi|227013543|gb|ACP09753.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           O395]
 gi|262021885|gb|EEY40595.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           RC27]
          Length = 231

 Score =  165 bits (418), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 48/231 (20%), Positives = 95/231 (41%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSCVEWQGREIMLHGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     + +       ++            +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDG-FNQTAFTLLDEVNVEDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + YRV     +  D      +GI ++G        Q+ +     S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELRGERELTLPAQLEVI----SETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R   G   L   L  G  R ++++ +
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEEEV 226


>gi|269959632|ref|ZP_06174012.1| pseudouridine synthase family 1 protein [Vibrio harveyi 1DA3]
 gi|269835555|gb|EEZ89634.1| pseudouridine synthase family 1 protein [Vibrio harveyi 1DA3]
          Length = 312

 Score =  165 bits (418), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 90/313 (28%), Positives = 131/313 (41%), Gaps = 13/313 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E +I   RV VNGI+ +           + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREIESLIKSGRVSVNGIVAKLGERLEDENSVVRIDGHIVSAKAQ 61

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  Y     L T H     R+          SR ISVGRLD NT GLLL T D
Sbjct: 62  EEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G+V++ K+  L  G+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRQVEREYLVRVFGEVNEKKVRNLVSGVELEDGMARFEDVVHAGGEGMNH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LRE 243
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+  K    LRE
Sbjct: 182 TFYVVINEGRNREVRRLWESQECTVSRLKRVRYGDIFLDKKLPRGGWMELDLKEVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +     +E  ++L+       T  +       ++     R ++  +   G S       
Sbjct: 242 LVELRPEKETMLDLNK----DNTSRKRERARSQKIRRAVKRHEERVNTPKGRSNNPSRRK 297

Query: 304 PVHRRNLASNVWM 316
           P            
Sbjct: 298 PKKAAGDQGARNK 310


>gi|113953004|ref|YP_730229.1| 16S rRNA pseudouridylate synthase [Synechococcus sp. CC9311]
 gi|113880355|gb|ABI45313.1| 16S rRNA pseudouridylate synthase [Synechococcus sp. CC9311]
          Length = 244

 Score =  165 bits (418), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 73/231 (31%), Positives = 110/231 (47%), Gaps = 3/231 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
           T QR+ K+IA AGI SRR  E ++ + RV VN  +          + D IEVDG PL  A
Sbjct: 2   TRQRLQKLIAAAGICSRRHAEELMREGRVTVN-QVTAGLGDQADPSIDRIEVDGRPLSHA 60

Query: 71  ERTRL-WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            R RL  L      + +        + +     S+   +  VGRLD ++ G LLLTN G 
Sbjct: 61  SRPRLILLNKPRGVISSCSDPQGRETVLDLIPKSLRRGLHPVGRLDGDSRGALLLTNQGA 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   L  P     + Y+V+  G      LN    G+ + G+     +V+L  Q  + + +
Sbjct: 121 ITLQLTHPRYSHSKTYKVQVRGTPTNTTLNRWCNGVELDGVPTQPAEVSLLKQGANQSLL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            V LREG+NR+I++V +     V  L R +     LG+L  G  RE+++  
Sbjct: 181 KVILREGRNRQIRRVADALGHPVLDLQRTAISSIDLGSLPEGHWRELTRSE 231


>gi|237808158|ref|YP_002892598.1| pseudouridine synthase [Tolumonas auensis DSM 9187]
 gi|237500419|gb|ACQ93012.1| pseudouridine synthase [Tolumonas auensis DSM 9187]
          Length = 231

 Score =  165 bits (418), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 59/232 (25%), Positives = 104/232 (44%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAER 72
            R+ K + +    SR +  +++   R+ VN ++++  A +V   D + +D  PL    E+
Sbjct: 1   MRLDKHLHQCLGISRSQASQLLKAGRISVNSLIIKSGAQHVTEQDSVLLDDKPLDTPGEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ HKP G V  + D               S + + GRLD +T GL+L+TNDG  + 
Sbjct: 61  LYYFMLHKPQGYVCANGDASHPGITRLFDLPCASELHAAGRLDADTTGLVLVTNDGQWSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--CYGDMQVTLDTQKGSNAWVT 190
            +  P  Q  + YRV     +  +   +  KGI+++         Q     +  +   V 
Sbjct: 121 RVTSPRKQCDKTYRVWLAEPISPETEEIFAKGILLRSETQVTRPAQ----LETITPQEVL 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EGK  ++K++F      V RL R   G   L   L  GS RE++ + +
Sbjct: 177 LTIHEGKYHQVKRMFAAVGNHVERLHRERIGELVLDADLPEGSYRELTPEEI 228


>gi|312865980|ref|ZP_07726201.1| putative 16S pseudouridylate 516 synthase [Streptococcus downei
           F0415]
 gi|311098384|gb|EFQ56607.1| putative 16S pseudouridylate 516 synthase [Streptococcus downei
           F0415]
          Length = 242

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 61/239 (25%), Positives = 104/239 (43%), Gaps = 4/239 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +    + SR +V+ ++ ++ V+VNG +       +    D + + G  L+    
Sbjct: 1   MRLDKFLVDCTVGSRSQVKAILKKKEVQVNGQIESSPKRQIDEKKDRVTLAGQLLKHETF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T            + P+   +V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPQGVVSATEDSQHQTVLDLLDEPAHQKQVFPVGRLDIDTTGLLLLTNNGPLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            +  P     +VY+ +  G +  + +    +GI ++       Q+ +     +     V 
Sbjct: 121 AMLSPKKHVAKVYQAKVEGLMTDEDVVAFGQGIRLKDFVCRPAQLQILESDQAQGSCLVQ 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
           + + EGK  ++K++      KV  L RIS GP  L   L  G  R +S + L +  G H
Sbjct: 181 IEIAEGKFHQVKRMVASRGKKVLELKRISMGPLHLPHDLSEGHYRRLSAQELADLSGFH 239


>gi|110801071|ref|YP_695782.1| ribosomal small subunit pseudouridine synthase B [Clostridium
           perfringens ATCC 13124]
 gi|168212063|ref|ZP_02637688.1| ribosomal small subunit pseudouridine synthase B [Clostridium
           perfringens B str. ATCC 3626]
 gi|169342630|ref|ZP_02863674.1| ribosomal small subunit pseudouridine synthase B [Clostridium
           perfringens C str. JGS1495]
 gi|110675718|gb|ABG84705.1| ribosomal small subunit pseudouridine synthase B [Clostridium
           perfringens ATCC 13124]
 gi|169299272|gb|EDS81341.1| ribosomal small subunit pseudouridine synthase B [Clostridium
           perfringens C str. JGS1495]
 gi|170710018|gb|EDT22200.1| ribosomal small subunit pseudouridine synthase B [Clostridium
           perfringens B str. ATCC 3626]
          Length = 236

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 69/228 (30%), Positives = 116/228 (50%), Gaps = 2/228 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKAER 72
           +R+ K +AR G+ASRR+ E +I   +VKVN I+++     V  +  +   +   +R  E 
Sbjct: 3   ERLQKYMARCGVASRRKCEEIICSGKVKVNDIVVDSLGTKVDPSVDVVSVNNKVIRPEEN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G VTT+ D   R T+ D +     R+  +GRLD ++ GLLLLTNDG +  
Sbjct: 63  KVYIMLNKPEGYVTTNKDEKNRKTILDIVKVN-ERIYPIGRLDYDSSGLLLLTNDGDVYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y     G   ++++N  +KG+ I      + ++ L  +  ++  V + 
Sbjct: 122 KIIHPRVNLNKEYIALVKGIFTEEEMNKFRKGVDIGDYKTAECEIELLEKYTNSCKVKII 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           + EGKNR+I+++   FN +V  L R + G   L  L  G  R +S   
Sbjct: 182 IHEGKNRQIRRMCAAFNHEVVSLKREAIGSLTLKNLKKGEWRYLSSSE 229


>gi|94987310|ref|YP_595243.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Lawsonia intracellularis
           PHE/MN1-00]
 gi|94731559|emb|CAJ54922.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Lawsonia intracellularis
           PHE/MN1-00]
          Length = 270

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 59/249 (23%), Positives = 109/249 (43%), Gaps = 9/249 (3%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIE 61
             +      T  R++K +A AG+ SRR V++ I    V +NG  + +  + +    D I 
Sbjct: 13  RNHTQSSTTTSIRINKALANAGVCSRRNVDKYILNGEVTINGKSVTQPGIYIHPDKDIIA 72

Query: 62  VDGVPL----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDI 116
           + G  +    +  +   L +Y     + +     +  + +        +     VGRLD 
Sbjct: 73  LHGRRVDIQLKNKKYYYLSMYKPIKVISSVKDPQNRLTVLDFIPFPWKNYRLYPVGRLDF 132

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDM 175
            +EGLLL+TNDG L + L  P     +VY V    ++    L  + KGI +  G      
Sbjct: 133 FSEGLLLITNDGELTQRLTHPRYHISKVYHVLIRERILNTTLKNISKGITLSDGTKLPPA 192

Query: 176 QVTLD--TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
           +V +     + +  W+ + L++G NR+I+++ +     + +LIR+  G   L  L  G  
Sbjct: 193 KVRVLSSITETNTTWLEITLQQGINRQIRRMCKELGLTILKLIRVKQGNINLSNLQPGEV 252

Query: 234 REVSKKILR 242
           R +    ++
Sbjct: 253 RPLKNDEIK 261


>gi|30062791|ref|NP_836962.1| 23S rRNA pseudouridylate synthase B [Shigella flexneri 2a str.
           2457T]
 gi|110805271|ref|YP_688791.1| 23S rRNA pseudouridylate synthase B [Shigella flexneri 5 str. 8401]
 gi|34098404|sp|P59815|RLUB_SHIFL RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|30041039|gb|AAP16769.1| hypothetical protein S1356 [Shigella flexneri 2a str. 2457T]
 gi|110614819|gb|ABF03486.1| conserved hypothetical protein [Shigella flexneri 5 str. 8401]
 gi|281600690|gb|ADA73674.1| Ribosomal large subunit pseudouridine synthase B [Shigella flexneri
           2002017]
 gi|313649457|gb|EFS13888.1| ribosomal large subunit pseudouridine synthase B [Shigella flexneri
           2a str. 2457T]
 gi|332757920|gb|EGJ88247.1| ribosomal large subunit pseudouridine synthase B [Shigella flexneri
           4343-70]
 gi|332759264|gb|EGJ89572.1| ribosomal large subunit pseudouridine synthase B [Shigella flexneri
           2747-71]
 gi|332760363|gb|EGJ90653.1| ribosomal large subunit pseudouridine synthase B [Shigella flexneri
           K-671]
 gi|332767503|gb|EGJ97697.1| 23S rRNA pseudouridine synthase [Shigella flexneri 2930-71]
 gi|333005742|gb|EGK25260.1| ribosomal large subunit pseudouridine synthase B [Shigella flexneri
           K-218]
 gi|333019134|gb|EGK38424.1| ribosomal large subunit pseudouridine synthase B [Shigella flexneri
           K-304]
          Length = 290

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 87/289 (30%), Positives = 128/289 (44%), Gaps = 10/289 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           E +       ++V ++      +     R            R    ++ 
Sbjct: 242 ELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGSRRSGGRNNG 290


>gi|331088168|ref|ZP_08337088.1| hypothetical protein HMPREF1025_00671 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|330408824|gb|EGG88287.1| hypothetical protein HMPREF1025_00671 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 244

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 55/227 (24%), Positives = 111/227 (48%), Gaps = 7/227 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K ++ AG+ SRRE +R+I   +V V+G+  +   + V +   ++V    + K +
Sbjct: 14  ESVRLNKYLSEAGVCSRREADRLIESGKVTVDGVTAQ-MGMRVTAGQIVKVGKKTVSKQD 72

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              +   +KP G+V T    +          +   RV   GRLD ++ GLLL+TN+G + 
Sbjct: 73  EMIVLAVNKPKGIVCTEDQRE--RDSIVRFLNYPVRVTYAGRLDKDSRGLLLMTNNGDII 130

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +   + +  + Y+V    ++ +  +  + +G+ I         V    +K      ++
Sbjct: 131 NQMMRAANRHEKEYKVTVDKEITEQFIKKMSEGVPILDTVTRPCTV----KKIGKYTFSI 186

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            L +G NR+I+++   F ++V  L+RI     +LG+L  G+ R+++ 
Sbjct: 187 ILTQGLNRQIRRMCAAFGYEVKDLVRIRIMNIRLGSLKEGAYRKLTD 233


>gi|15601868|ref|NP_244940.1| hypothetical protein PM0003 [Pasteurella multocida subsp. multocida
           str. Pm70]
 gi|34098699|sp|Q9CPN4|RSUA_PASMU RecName: Full=Ribosomal small subunit pseudouridine synthase A;
           AltName: Full=16S pseudouridine 516 synthase; AltName:
           Full=16S pseudouridylate 516 synthase; AltName:
           Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|12720202|gb|AAK02087.1| RsuA [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 232

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 60/229 (26%), Positives = 104/229 (45%), Gaps = 3/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R +  +++ Q  V VNG + +  A  V  TD I ++G  L      
Sbjct: 1   MRLDKFLAENTGLTRSQANKVLKQSAVTVNGHVEKNGAQKVSQTDEICLEGEHLPWVSAG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +  + +KP G V +H D D  +        +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYLMLYKPQGYVCSHEDGDYPTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGKWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+        +G++++G        TL+     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVESHYQQACAEGMLLRGEKTPTKPATLEILDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EG+  ++K++F     KV  L R   G  +L   L  G  R +S + +
Sbjct: 179 SEGRYHQVKRMFAALGNKVVGLHRWKIGQIELDDRLAEGEYRSLSAEEI 227


>gi|15801910|ref|NP_287930.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7
           EDL933]
 gi|15831095|ref|NP_309868.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 str.
           Sakai]
 gi|74312362|ref|YP_310781.1| 23S rRNA pseudouridylate synthase B [Shigella sonnei Ss046]
 gi|82544277|ref|YP_408224.1| 23S rRNA pseudouridylate synthase B [Shigella boydii Sb227]
 gi|157154729|ref|YP_001462565.1| 23S rRNA pseudouridylate synthase B [Escherichia coli E24377A]
 gi|168751157|ref|ZP_02776179.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4113]
 gi|168758353|ref|ZP_02783360.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4401]
 gi|168763584|ref|ZP_02788591.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4501]
 gi|168771267|ref|ZP_02796274.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4486]
 gi|168775077|ref|ZP_02800084.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4196]
 gi|168783771|ref|ZP_02808778.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4076]
 gi|168790068|ref|ZP_02815075.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC869]
 gi|168801615|ref|ZP_02826622.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC508]
 gi|191166646|ref|ZP_03028474.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           B7A]
 gi|193062722|ref|ZP_03043816.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           E22]
 gi|193069992|ref|ZP_03050940.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           E110019]
 gi|194426137|ref|ZP_03058693.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           B171]
 gi|195939202|ref|ZP_03084584.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 str.
           EC4024]
 gi|208810912|ref|ZP_03252745.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4206]
 gi|208815453|ref|ZP_03256632.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4045]
 gi|208820806|ref|ZP_03261126.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4042]
 gi|209396722|ref|YP_002270323.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4115]
 gi|209918508|ref|YP_002292592.1| 23S rRNA pseudouridylate synthase B [Escherichia coli SE11]
 gi|217329090|ref|ZP_03445170.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. TW14588]
 gi|254792857|ref|YP_003077694.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 str.
           TW14359]
 gi|256018485|ref|ZP_05432350.1| 23S rRNA pseudouridylate synthase B [Shigella sp. D9]
 gi|260843616|ref|YP_003221394.1| 23S rRNA pseudouridylate synthase RluB [Escherichia coli O103:H2
           str. 12009]
 gi|260854966|ref|YP_003228857.1| 23S rRNA pseudouridylate synthase RluB [Escherichia coli O26:H11
           str. 11368]
 gi|260867717|ref|YP_003234119.1| 23S rRNA pseudouridylate synthase RluB [Escherichia coli O111:H-
           str. 11128]
 gi|261224251|ref|ZP_05938532.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 str.
           FRIK2000]
 gi|261257493|ref|ZP_05950026.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 str.
           FRIK966]
 gi|291282356|ref|YP_003499174.1| Ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O55:H7 str. CB9615]
 gi|300820147|ref|ZP_07100316.1| conserved hypothetical protein [Escherichia coli MS 107-1]
 gi|300822569|ref|ZP_07102708.1| conserved hypothetical protein [Escherichia coli MS 119-7]
 gi|300904135|ref|ZP_07122008.1| hypothetical protein HMPREF9536_02226 [Escherichia coli MS 84-1]
 gi|300919449|ref|ZP_07135950.1| conserved hypothetical protein [Escherichia coli MS 115-1]
 gi|301304781|ref|ZP_07210887.1| hypothetical protein HMPREF9347_03390 [Escherichia coli MS 124-1]
 gi|307309978|ref|ZP_07589628.1| pseudouridine synthase [Escherichia coli W]
 gi|309793259|ref|ZP_07687686.1| conserved hypothetical protein [Escherichia coli MS 145-7]
 gi|331667653|ref|ZP_08368517.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli TA271]
 gi|332279541|ref|ZP_08391954.1| ribosomal large subunit pseudouridine synthase B [Shigella sp. D9]
 gi|34098616|sp|Q8X4Q8|RLUB_ECO57 RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|12515528|gb|AAG56546.1|AE005380_5 orf, hypothetical protein [Escherichia coli O157:H7 str. EDL933]
 gi|13361306|dbj|BAB35264.1| hypothetical protein [Escherichia coli O157:H7 str. Sakai]
 gi|73855839|gb|AAZ88546.1| conserved hypothetical protein [Shigella sonnei Ss046]
 gi|81245688|gb|ABB66396.1| conserved hypothetical protein [Shigella boydii Sb227]
 gi|157076759|gb|ABV16467.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           E24377A]
 gi|187769333|gb|EDU33177.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4196]
 gi|188014796|gb|EDU52918.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4113]
 gi|188998981|gb|EDU67967.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4076]
 gi|189354811|gb|EDU73230.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4401]
 gi|189359963|gb|EDU78382.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4486]
 gi|189366282|gb|EDU84698.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4501]
 gi|189370413|gb|EDU88829.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC869]
 gi|189376287|gb|EDU94703.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC508]
 gi|190903295|gb|EDV63016.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           B7A]
 gi|192931844|gb|EDV84444.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           E22]
 gi|192956745|gb|EDV87200.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           E110019]
 gi|194416192|gb|EDX32458.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           B171]
 gi|208724418|gb|EDZ74126.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4206]
 gi|208732101|gb|EDZ80789.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4045]
 gi|208740929|gb|EDZ88611.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4042]
 gi|209158122|gb|ACI35555.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4115]
 gi|209772018|gb|ACI84321.1| hypothetical protein ECs1841 [Escherichia coli]
 gi|209772020|gb|ACI84322.1| hypothetical protein ECs1841 [Escherichia coli]
 gi|209772022|gb|ACI84323.1| hypothetical protein ECs1841 [Escherichia coli]
 gi|209772024|gb|ACI84324.1| hypothetical protein ECs1841 [Escherichia coli]
 gi|209772026|gb|ACI84325.1| hypothetical protein ECs1841 [Escherichia coli]
 gi|209911767|dbj|BAG76841.1| putative pseudouridine synthase [Escherichia coli SE11]
 gi|217317529|gb|EEC25957.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. TW14588]
 gi|254592257|gb|ACT71618.1| 23S rRNA pseudouridylate synthase [Escherichia coli O157:H7 str.
           TW14359]
 gi|257753615|dbj|BAI25117.1| 23S rRNA pseudouridylate synthase RluB [Escherichia coli O26:H11
           str. 11368]
 gi|257758763|dbj|BAI30260.1| 23S rRNA pseudouridylate synthase RluB [Escherichia coli O103:H2
           str. 12009]
 gi|257764073|dbj|BAI35568.1| 23S rRNA pseudouridylate synthase RluB [Escherichia coli O111:H-
           str. 11128]
 gi|290762229|gb|ADD56190.1| Ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O55:H7 str. CB9615]
 gi|300403900|gb|EFJ87438.1| hypothetical protein HMPREF9536_02226 [Escherichia coli MS 84-1]
 gi|300413471|gb|EFJ96781.1| conserved hypothetical protein [Escherichia coli MS 115-1]
 gi|300524985|gb|EFK46054.1| conserved hypothetical protein [Escherichia coli MS 119-7]
 gi|300527302|gb|EFK48364.1| conserved hypothetical protein [Escherichia coli MS 107-1]
 gi|300839902|gb|EFK67662.1| hypothetical protein HMPREF9347_03390 [Escherichia coli MS 124-1]
 gi|306909696|gb|EFN40190.1| pseudouridine synthase [Escherichia coli W]
 gi|308122846|gb|EFO60108.1| conserved hypothetical protein [Escherichia coli MS 145-7]
 gi|315060519|gb|ADT74846.1| 23S rRNA pseudouridylate synthase [Escherichia coli W]
 gi|315254773|gb|EFU34741.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           MS 85-1]
 gi|320176684|gb|EFW51722.1| 23S rRNA pseudouridylate synthase B [Shigella dysenteriae CDC
           74-1112]
 gi|320187507|gb|EFW62193.1| 23S rRNA pseudouridylate synthase B [Shigella flexneri CDC 796-83]
 gi|320189980|gb|EFW64632.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 str.
           EC1212]
 gi|320199303|gb|EFW73894.1| 23S rRNA pseudouridylate synthase B [Escherichia coli EC4100B]
 gi|320637163|gb|EFX06989.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 str.
           G5101]
 gi|320642529|gb|EFX11777.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H- str.
           493-89]
 gi|320647882|gb|EFX16590.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H- str.
           H 2687]
 gi|320653484|gb|EFX21589.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320659184|gb|EFX26773.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O55:H7 str.
           USDA 5905]
 gi|323153300|gb|EFZ39558.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           EPECa14]
 gi|323162371|gb|EFZ48226.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           E128010]
 gi|323168243|gb|EFZ53928.1| ribosomal large subunit pseudouridine synthase B [Shigella sonnei
           53G]
 gi|323172376|gb|EFZ58013.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           LT-68]
 gi|323179780|gb|EFZ65341.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           1180]
 gi|323185573|gb|EFZ70934.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           1357]
 gi|323378918|gb|ADX51186.1| pseudouridine synthase [Escherichia coli KO11]
 gi|326341071|gb|EGD64864.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 str.
           1125]
 gi|326343312|gb|EGD67079.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 str.
           1044]
 gi|331065238|gb|EGI37133.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli TA271]
 gi|332094735|gb|EGI99779.1| ribosomal large subunit pseudouridine synthase B [Shigella boydii
           3594-74]
 gi|332101893|gb|EGJ05239.1| ribosomal large subunit pseudouridine synthase B [Shigella sp. D9]
 gi|333004583|gb|EGK24107.1| ribosomal large subunit pseudouridine synthase B [Shigella flexneri
           VA-6]
 gi|333007605|gb|EGK27083.1| ribosomal large subunit pseudouridine synthase B [Shigella flexneri
           K-272]
 gi|333019539|gb|EGK38819.1| ribosomal large subunit pseudouridine synthase B [Shigella flexneri
           K-227]
          Length = 290

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 87/289 (30%), Positives = 128/289 (44%), Gaps = 10/289 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           E +       ++V ++      +     R            R    ++ 
Sbjct: 242 ELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGGRRSGGRNNG 290


>gi|153826173|ref|ZP_01978840.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           MZO-2]
 gi|153830671|ref|ZP_01983338.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           623-39]
 gi|229523730|ref|ZP_04413135.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           bv. albensis VL426]
 gi|148873851|gb|EDL71986.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           623-39]
 gi|149740114|gb|EDM54279.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           MZO-2]
 gi|229337311|gb|EEO02328.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           bv. albensis VL426]
          Length = 231

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 47/231 (20%), Positives = 94/231 (40%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +     +E  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKEASRVEWQGREIMLHGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     + +       ++            +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDG-FNQTAFTLLDEVNIQDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + YRV     +  D      +GI ++G        Q+ +     S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELRGERELTLPAQLEVI----SETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R   G   L   L  G  R ++++ +
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEEEV 226


>gi|320546398|ref|ZP_08040713.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           equinus ATCC 9812]
 gi|320448783|gb|EFW89511.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           equinus ATCC 9812]
          Length = 238

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 101/229 (44%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++ +AG  SR +V+++I  ++V V+G L E   +NV  +   I V G  +  +  
Sbjct: 1   MRLDKLLGQAGFGSRNQVKKLIRSRQVYVDGRLAEADNLNVEPSLQEITVSGKQVTLSTE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                      ++  VGRLD +TEG LL+TN+G L  
Sbjct: 61  KYFILNKPAGVVSAVSDKEHQTVIDLIVESDRVPKLYPVGRLDRDTEGFLLITNNGPLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V  +G++  D     + G+           ++ +       +   +
Sbjct: 121 RMLHPKYHVTKTYYVEVNGRLADDTPAFFENGVTFDDGTVCKPAKLEIIESSSEKSSAYI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + EGK  ++KK+F  +  KV  L R+++G F+LG L  G  RE++   
Sbjct: 181 TIAEGKFHQVKKMFLAYGVKVTYLKRMTFGEFELGDLPTGHYRELTINE 229


>gi|316932709|ref|YP_004107691.1| RNA-binding S4 domain-containing protein [Rhodopseudomonas
           palustris DX-1]
 gi|315600423|gb|ADU42958.1| RNA-binding S4 domain protein [Rhodopseudomonas palustris DX-1]
          Length = 717

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 138/330 (41%), Positives = 194/330 (58%), Gaps = 2/330 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
            +   +R++KV+ARAG+ SRR+ E  I + RV VNG +++  A++V ++D I +DG PL 
Sbjct: 386 SDKAGERIAKVVARAGLCSRRDAEAWITEGRVAVNGKVIDSPALDVKASDVITIDGKPLP 445

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRL+LYHKP GL+TTHSDP+GR TVFD+LP    R+IS+GRLD NTEGLLLLTNDG
Sbjct: 446 ERERTRLFLYHKPRGLMTTHSDPEGRPTVFDHLPEGLPRLISIGRLDFNTEGLLLLTNDG 505

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GLAR LELP T WLR YRVR HG++ Q +L+ L+ GI + G+ YG +   L+  + +N W
Sbjct: 506 GLARALELPETGWLRRYRVRAHGEITQAQLDELQNGIEVDGVQYGPIDAKLERDQSANVW 565

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +   +REGKNRE++ V      +VNRLIR+SYGPFQL  L  G   EV  ++LR+QLG  
Sbjct: 566 LVFAIREGKNREVRNVLAHLGLEVNRLIRVSYGPFQLLELGEGEVDEVKTRVLRDQLGEK 625

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ--KNGLSKQKKLATPVH 306
           ++  A  +   P  S          ++S              +      + + +    + 
Sbjct: 626 VIALAGCDFAGPSPSETKPKPRAGKVVSAEEWSVVEGAAKPKKTITKRGAVEDRKGRRIK 685

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHR 336
               AS+               G+R+   R
Sbjct: 686 VERTASDGGERPLSRGPARRYHGKRDLAPR 715



 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 11/102 (10%), Positives = 19/102 (18%), Gaps = 1/102 (0%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
                A     +                     +          ++    P   R     
Sbjct: 213 DKPRFAKSRDDKPRFDRDRGDKPRFDKPRGDKPRFDRGARSERPERSGDRPKFSRPRDGE 272

Query: 314 VWMAKGIH-SSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               +     SF      R  + R     P +   +R  A K
Sbjct: 273 RGEQRPFRERSFDRPREDRPRSDRPRSDRPREDRPQRDRAAK 314



 Score = 37.1 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 12/108 (11%), Positives = 26/108 (24%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           ++ G      A+   D P +  +   + R +        F R  ++   +    + K   
Sbjct: 208 DKGGFDKPRFAKSRDDKPRFDRDRGDKPRFDKPRGDKPRFDRGARSERPERSGDRPKFSR 267

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                R                      R  + R     P +    + 
Sbjct: 268 PRDGERGEQRPFRERSFDRPREDRPRSDRPRSDRPREDRPQRDRAAKH 315


>gi|238920493|ref|YP_002934008.1| 16S rRNA pseudouridylate synthase A [Edwardsiella ictaluri 93-146]
 gi|238870062|gb|ACR69773.1| conserved hypothetical protein [Edwardsiella ictaluri 93-146]
          Length = 235

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 58/238 (24%), Positives = 101/238 (42%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I++    SR  V R +   RV V+G++    ++ V     +  +G  L      
Sbjct: 1   MRLDKFISQQLGISRSLVIRELRAARVTVDGVVARSGSLQVTPDQEVAYEGNVLTFITGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V +  DPD  + ++     +  ++ + GRLD++T GL+LLT+DG  +  
Sbjct: 61  RYFMLHKPEGYVCSTDDPDHATILYFIDEPMAEKLHAAGRLDLDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +      L  +GI++ G        Q+           V +
Sbjct: 121 ITSPRHHCEKSYLVTLEQPLAPQTAALFAQGIMLNGETDLTKPAQLEAF----DEHHVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
            + EG+  ++K++F     +V  L R   G   L   L  G  R +S   +   L   
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVVGLHRERIGAIALDAALAPGEYRALSDDEVASALAGR 234


>gi|188533752|ref|YP_001907549.1| 23S rRNA pseudouridylate synthase B [Erwinia tasmaniensis Et1/99]
 gi|188028794|emb|CAO96656.1| Ribosomal large subunit pseudouridine synthase B [Erwinia
           tasmaniensis Et1/99]
          Length = 295

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 88/295 (29%), Positives = 131/295 (44%), Gaps = 12/295 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E MI+  RV V+G L       V  +    I +DG  +  +
Sbjct: 2   SEKLQKVLARAGHGSRREIETMISAGRVSVDGKLAT-LGDRVEPSVSLKIRIDGHVVPVS 60

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E        L  Y     L T +      +          +R ++VGRLD+NT GLLL T
Sbjct: 61  ESISEVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWVAVGRLDVNTCGLLLFT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  G VD +K+  L +G+ ++        +     +G 
Sbjct: 121 TDGELANRLMHPSREVEREYAVRVFGAVDDEKIKQLSRGVQLEDGPAAFKTLKFTGGEGI 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKIL 241
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       L
Sbjct: 181 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIDLPKGLPRGGWTELDLAPTNYL 240

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           RE +G      ++V ++     ++T    R                  S K    
Sbjct: 241 RELVGLAPETVSKVPVEKDRRRTKTNQIRRAVKRHTTTKVSKPGSGRRSSKRQQG 295


>gi|296282690|ref|ZP_06860688.1| hypothetical protein CbatJ_03660 [Citromicrobium bathyomarinum
           JL354]
          Length = 252

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 106/240 (44%), Positives = 153/240 (63%), Gaps = 4/240 (1%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + ++     R++K++ARAG+ASRREVERMIA +R+ ++G  +E  A  + +   + VDG 
Sbjct: 1   MAEDERKGDRIAKLLARAGVASRREVERMIADKRIAIDGKTVETPATLLETLRGVTVDGK 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGL 121
           P+ K E TRL+ +HKP GL+T   DP GR T++D L +   +     + +GRLD NTEGL
Sbjct: 61  PVAKPEPTRLFAFHKPTGLITAEHDPRGRPTIYDALRNSLPKDAPRVMPIGRLDFNTEGL 120

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDG   R+LELP+    R YR R HG V Q +L  L +GI I G+ YG +   L+ 
Sbjct: 121 LLLTNDGEFKRMLELPANAVERTYRARAHGGVTQAQLEELSEGITIDGVHYGPINANLER 180

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + G+N W+ V + EGKNRE+++V E    +VNRL+R+++GP  LG L  G   E+ K  +
Sbjct: 181 RTGANQWIEVTITEGKNREVRRVLEHLGLEVNRLVRVAFGPVALGDLPRGQAMEIRKHEI 240


>gi|167570132|ref|ZP_02363006.1| RNA pseudouridylate synthase family protein [Burkholderia
           oklahomensis C6786]
          Length = 371

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 76/273 (27%), Positives = 123/273 (45%), Gaps = 6/273 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 60  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 118

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S          ++ ++VGRLD NTE
Sbjct: 119 GKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPTMKTAKWLAVGRLDFNTE 178

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 179 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELPEASRQKLLHGVELDDGPANFLRIRD 238

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 239 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 298

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDR 271
             +R  +    L+            +E    D 
Sbjct: 299 AQVRRLMAAVGLKAPTEEKGKRGGVTERRQPDP 331


>gi|148827048|ref|YP_001291801.1| malic enzyme [Haemophilus influenzae PittGG]
 gi|148718290|gb|ABQ99417.1| malic enzyme [Haemophilus influenzae PittGG]
          Length = 232

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 58/236 (24%), Positives = 108/236 (45%), Gaps = 7/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  AV +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENTGLTRSQATKAIRQSAVKINGEIVKSGAVQISQKDEIYFEDELLTWVEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ HKP G V ++ D D  +        +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYFMLHKPQGCVCSNDDGDYPTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+++      +GI+++G        ++ +      +  V +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEKNYAEACAEGILLRGEKEPTKPAKLEIL----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
            + EG+  ++K++F     KV  L R   G   L   L  G  R +++  + + + 
Sbjct: 177 TISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLVK 232


>gi|46200149|ref|YP_005816.1| ribosomal small subunit pseudouridine synthase A [Thermus
           thermophilus HB27]
 gi|55980117|ref|YP_143414.1| ribosomal large subunit pseudouridine synthase B [Thermus
           thermophilus HB8]
 gi|46197777|gb|AAS82189.1| ribosomal small subunit pseudouridine synthase A [Thermus
           thermophilus HB27]
 gi|55771530|dbj|BAD69971.1| ribosomal large subunit pseudouridine synthase B [Thermus
           thermophilus HB8]
          Length = 243

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 67/245 (27%), Positives = 109/245 (44%), Gaps = 6/245 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +R+ KV+AR G+ SR+EV R++ Q +V+V G +++     V     +EV+G PL    
Sbjct: 2   KGERLDKVLARLGLGSRKEVARLVRQGKVRVLGQVVKDPGFRVPEGAALEVEGRPLEVRR 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              + L+  P  + +    P   + +             VGRLD + EGLLL T DG L 
Sbjct: 62  HLHVLLHKPPGFVTSRTEGPSVYALLQGFPTRDL---SPVGRLDKDAEGLLLFTTDGLLL 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P  +  + Y V     V        ++GI++ G      ++T         W  V
Sbjct: 119 HRLTHPRHKVAKRYLVHLERPVGPKDQEAFREGILLDGKKTLPAELTPL---EDPTWAEV 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L+EG+  +IK++F     +V RL R++ GP +LG L  G  R +++   +       L 
Sbjct: 176 VLKEGRFHQIKRMFRARGNRVLRLKRLALGPLELGDLPPGKARPLTEAEEKALYAAVGLG 235

Query: 252 EAQVN 256
                
Sbjct: 236 GEDPE 240


>gi|332283699|ref|YP_004415610.1| pseudouridylate synthase [Pusillimonas sp. T7-7]
 gi|330427652|gb|AEC18986.1| pseudouridylate synthase [Pusillimonas sp. T7-7]
          Length = 598

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 90/368 (24%), Positives = 149/368 (40%), Gaps = 20/368 (5%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             +  +    ++ KV+A AG+ SRRE+E +I   RV VNG         V + D + V+G
Sbjct: 144 KYLNSDALTPKLHKVLADAGVGSRREMEELIVAGRVSVNGEPA-HIGQRVGANDQVRVNG 202

Query: 65  VPL----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            P+     K     +  +     +V+        +           + +SVGRLD+NTEG
Sbjct: 203 RPIVRPNAKKPPRIILYHKPAGEIVSHDDPEGRATVFARLPKMRVGKWLSVGRLDLNTEG 262

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LL+LT  G LA  L  P     R Y VR  G++ +++ + L KGI ++        +   
Sbjct: 263 LLILTTSGDLANRLMHPRYGAEREYAVRVLGELGEEQQDKLLKGIQLEDGLAQFGSLEYL 322

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
             +GSN W  V L+EG+NRE++++FE     V+RLIR  +G   L   L  G   E+   
Sbjct: 323 GGEGSNRWYRVTLKEGRNREVRRMFEAAGVTVSRLIRTRFGEVVLPRNLRRGRWEELDSS 382

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
            L   L   L    + + D     S    R   +  S +P  F  +++N +    +S++ 
Sbjct: 383 -LVTALMLQLGLLREDDSDERGAGSGRGERQPVSHDSALPPGFGTLERNGTNGAKVSRRG 441

Query: 300 KLATPVHRRNLASNV-------------WMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           KL+    +R   +                     H +         +             
Sbjct: 442 KLSGGRPQRAATAQAYPSDPYGTGLMFSGGLPNGHPTAGRGKPGTSKAGGNKAHGNKAGG 501

Query: 347 LRRTSAKK 354
             +T+  +
Sbjct: 502 RGKTADGR 509



 Score = 37.1 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 6/100 (6%), Positives = 16/100 (16%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
                         +         ++           S +  G ++ +           A
Sbjct: 473 PNGHPTAGRGKPGTSKAGGNKAHGNKAGGRGKTADGRSQKPAGQARDEGEVRTTAGAGDA 532

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                      +    S  R             R+    +
Sbjct: 533 RRRGAGARPAKAAGPKSAARPSRGENKAKSAGPRARSGAA 572


>gi|253989545|ref|YP_003040901.1| 23S rRNA pseudouridylate synthase B [Photorhabdus asymbiotica
           subsp. asymbiotica ATCC 43949]
 gi|253780995|emb|CAQ84157.1| ribosomal large subunit pseudouridine synthase B [Photorhabdus
           asymbiotica]
          Length = 310

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 92/309 (29%), Positives = 131/309 (42%), Gaps = 12/309 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPL 67
           +    +++ K++AR+G  SRRE+E  I Q RV V+G +      + V     I +DG  L
Sbjct: 4   KTQKSEKLQKILARSGHGSRREIEGYIQQGRVSVDGKIATLGDRIEVQPATKIRLDGRIL 63

Query: 68  RKAERT-----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
              E        L  Y     L T H      +        + SR I+VGRLD+NT GLL
Sbjct: 64  SIKESQKAICRVLAYYKPEGELCTRHDPEGRPTVFDRLPKLLGSRWIAVGRLDVNTCGLL 123

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L T DG LA  L  PS +  R Y VR  G+VD  KL  L KGI ++        V     
Sbjct: 124 LFTTDGELANRLMHPSREVEREYAVRVFGEVDDAKLKQLAKGIQLEDGPAAFRTVAFKGG 183

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI- 240
           +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  +  
Sbjct: 184 EGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIGLPKGLPRGGWAELGLEQT 243

Query: 241 --LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             LR+ +G H  EE    +                 +       +R        +     
Sbjct: 244 NYLRQLVGLH--EETVSKVAVERDQRRMKANQIRRAVKRHAQVASRPSAGKRPGSSRQNA 301

Query: 299 KKLATPVHR 307
            +      R
Sbjct: 302 GRTTAQKGR 310


>gi|221231179|ref|YP_002510331.1| ribosomal small subunit pseudouridine synthase B [Streptococcus
           pneumoniae ATCC 700669]
 gi|220673639|emb|CAR68127.1| putative ribosomal small subunit pseudouridine synthase B
           [Streptococcus pneumoniae ATCC 700669]
          Length = 240

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 63/233 (27%), Positives = 100/233 (42%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ M+   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNMLKSGRVTVNGKKEKSAKLQIDEERDEIRFDGQVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    V  VGRLDI+T GLLLLTNDG LA 
Sbjct: 61  VYYMMNKPKGVISATEDPKHRTVLDLLDDIARSKEVFPVGRLDIDTHGLLLLTNDGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVT 190
            L  P     + Y  +  G + Q+      KGI ++       ++ L +     + + + 
Sbjct: 121 ALLSPKRHVDKTYLAQVKGIMTQEDAETFAKGIPLKDFTCQPARLELVSVDTKKNQSQIR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 181 VTIAEGKFHQVKRMVGYCGKEVVDLQRLTMGTLVLDENLQRGEWRRLTKEELE 233


>gi|157376397|ref|YP_001474997.1| putative ribosomal small subunit pseudouridine synthase A
           [Shewanella sediminis HAW-EB3]
 gi|157318771|gb|ABV37869.1| conserved hypothetical ribosomal small subunit pseudouridine
           synthase A [Shewanella sediminis HAW-EB3]
          Length = 232

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 51/230 (22%), Positives = 97/230 (42%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   +R E   +I    V VNG  +  A+  V   + I +DG  L      
Sbjct: 1   MRLDKFLCKSTELTRIEATALIVAGEVLVNGQTVTSASTQVHENNRITLDGQVLTPRASR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     L +             ++  +    I+ GRLD +T GL+L+T+DG  +  
Sbjct: 61  YIMMHKPLDTLSSNVDGDYPSVMNCLDVDKVCDLHIA-GRLDADTTGLVLVTDDGRWSFN 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--CYGDMQVTLDTQKGSNAWVTV 191
           +  P     +VYRV     ++ D       G+ +QG        ++ +     S   V +
Sbjct: 120 IINPKYHCEKVYRVSLRDPINDDVAGKFACGVQLQGEASLTLPAKLEVV----SPTEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + EG+  ++K++F     +VN L R   G  +L  +  G  R ++ + +
Sbjct: 176 TITEGRYHQVKRMFAAVGNRVNGLHRQQVGDIKL-DIGLGQWRYLTTEEI 224


>gi|148253231|ref|YP_001237816.1| putative pseudouridine synthase, Rsu [Bradyrhizobium sp. BTAi1]
 gi|146405404|gb|ABQ33910.1| Putative Pseudouridine synthase, Rsu [Bradyrhizobium sp. BTAi1]
          Length = 690

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 141/306 (46%), Positives = 193/306 (63%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++KV+ARAG+ASRR+ E M+ Q RV VNG ++   A++V   D I+VDG PL + ER
Sbjct: 373 GDRIAKVLARAGLASRRDAEEMVTQGRVTVNGRVINSPALDVTENDVIQVDGAPLPQRER 432

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TRL+LYHKP GL+TTHSDP+GR TVFDNLP    R+IS+GRLD NTEGLLLLTNDGGLAR
Sbjct: 433 TRLFLYHKPRGLMTTHSDPEGRPTVFDNLPEGLPRLISIGRLDFNTEGLLLLTNDGGLAR 492

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           VLELP T W R YRVR HG++ Q +L+ L  G+ + G+ YG ++ TL+  +G+N W+ V 
Sbjct: 493 VLELPDTGWTRRYRVRAHGEITQAQLDQLAAGVEVDGVKYGPIEATLERDQGANVWLIVA 552

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           +REGKNRE++ V  +   +VNRLIR+SYGPFQL  L  G  +EV  ++LREQLG  ++ +
Sbjct: 553 IREGKNREVRNVLAYLGLEVNRLIRVSYGPFQLLELPEGEVQEVKTRVLREQLGEKVIAQ 612

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
           +  +L      +   + D             + ++   Q+ G  + +       R     
Sbjct: 613 SGADLGPAGKGNREPLPDPKPKPKREVVADRKGRRVLVQRTGSEEARARHEAEARFPGPP 672

Query: 313 NVWMAK 318
                 
Sbjct: 673 RRPKRG 678



 Score = 36.3 bits (82), Expect = 7.0,   Method: Composition-based stats.
 Identities = 13/123 (10%), Positives = 32/123 (26%)

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G  +  + +       P+               ++    DRP    + P+     ++  S
Sbjct: 152 GERKPYAARERDGDKRPYTPRGEGARDRGDRPRADRSFGDRPPRTGDRPERKFGGERKFS 211

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
           +     + ++      R          +   +      G   +   RSP  P +      
Sbjct: 212 RGAEGDRGERKFGAGPRGPRKEFGDRPQRGETKPWQKRGADGDRPERSPRAPREGGRSFD 271

Query: 351 SAK 353
             +
Sbjct: 272 RPR 274


>gi|229525790|ref|ZP_04415195.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           bv. albensis VL426]
 gi|229339371|gb|EEO04388.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           bv. albensis VL426]
          Length = 322

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 88/322 (27%), Positives = 129/322 (40%), Gaps = 7/322 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E +I   RV VNG +             + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAILGERLEEDNAVVRIDGHVVSVKAQ 61

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  Y     L T H     R+          SR ISVGRLD NT GLLL T D
Sbjct: 62  EEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G V +DK+  L +G+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRQVEREYLVRVFGDVTEDKVRNLVRGVQLEDGMARFEDVMYAGGEGINH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+  K +   L 
Sbjct: 182 TFYVVINEGRNREVRRLWESQGTTVSRLKRVRYGDIFLDKKLPRGGWMELDLKQV-NYLR 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
             +    +      +       +       ++     R ++  S   G S +        
Sbjct: 241 ELVELRPEKETVLNMAPDAATRKRERTRSQKIRRAVRRHEERISTPAGRSGKAPARRKPG 300

Query: 307 RRNLASNVWMAKGIHSSFLSDS 328
               ++   +A    SS     
Sbjct: 301 SGESSTRNKVANQQQSSRKPRG 322


>gi|318061409|ref|ZP_07980130.1| pseudouridine synthase [Streptomyces sp. SA3_actG]
 gi|318078007|ref|ZP_07985339.1| pseudouridine synthase [Streptomyces sp. SA3_actF]
          Length = 416

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 70/232 (30%), Positives = 111/232 (47%), Gaps = 1/232 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R+ KV+ARAG  SRR  E +I Q RV+VNG ++    + V  +D I+VDG+ +  
Sbjct: 177 EQEGERLQKVLARAGYGSRRACEELIEQARVEVNGEIVLEQGLRVKPSDEIKVDGLTVAT 236

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                  L      + T       ++   D + +  +R+  VGRLD  TEG++LLTN G 
Sbjct: 237 QSYQFFSLNKPAGVVATMEDPEGRQNLG-DYVNNRETRLFHVGRLDTETEGVILLTNHGE 295

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  P     + Y     G + +D    LK GI ++          +  Q G N  V
Sbjct: 296 LAHRLTHPRYGVRKTYLAHIVGPIPRDLGKRLKDGIELEDGWARADHFRVVEQTGKNYLV 355

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V L EG+   ++++     + V++L+R ++GP  LG   +G  R +S   +
Sbjct: 356 EVTLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPITLGDQKSGWLRRLSNTEV 407


>gi|16129230|ref|NP_415785.1| 23S rRNA pseudouridylate synthase [Escherichia coli str. K-12
           substr. MG1655]
 gi|89108115|ref|AP_001895.1| 23S rRNA pseudouridylate synthase [Escherichia coli str. K-12
           substr. W3110]
 gi|157160774|ref|YP_001458092.1| 23S rRNA pseudouridylate synthase B [Escherichia coli HS]
 gi|170020367|ref|YP_001725321.1| 23S rRNA pseudouridylate synthase B [Escherichia coli ATCC 8739]
 gi|170080946|ref|YP_001730266.1| 23S rRNA pseudouridylate synthase [Escherichia coli str. K-12
           substr. DH10B]
 gi|170682451|ref|YP_001743918.1| 23S rRNA pseudouridylate synthase B [Escherichia coli SMS-3-5]
 gi|188492201|ref|ZP_02999471.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           53638]
 gi|194435058|ref|ZP_03067297.1| ribosomal large subunit pseudouridine synthase B [Shigella
           dysenteriae 1012]
 gi|218699976|ref|YP_002407605.1| 23S rRNA pseudouridylate synthase B [Escherichia coli IAI39]
 gi|238900502|ref|YP_002926298.1| 23S rRNA pseudouridylate synthase [Escherichia coli BW2952]
 gi|253773734|ref|YP_003036565.1| 23S rRNA pseudouridylate synthase B [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254161349|ref|YP_003044457.1| 23S rRNA pseudouridylate synthase B [Escherichia coli B str.
           REL606]
 gi|256023023|ref|ZP_05436888.1| 23S rRNA pseudouridylate synthase B [Escherichia sp. 4_1_40B]
 gi|300927775|ref|ZP_07143339.1| conserved hypothetical protein [Escherichia coli MS 187-1]
 gi|300940072|ref|ZP_07154682.1| conserved hypothetical protein [Escherichia coli MS 21-1]
 gi|300951921|ref|ZP_07165725.1| conserved hypothetical protein [Escherichia coli MS 116-1]
 gi|300955866|ref|ZP_07168205.1| hypothetical protein HMPREF9547_01723 [Escherichia coli MS 175-1]
 gi|301019493|ref|ZP_07183662.1| conserved hypothetical protein [Escherichia coli MS 69-1]
 gi|301022795|ref|ZP_07186637.1| conserved hypothetical protein [Escherichia coli MS 196-1]
 gi|301647237|ref|ZP_07247056.1| conserved hypothetical protein [Escherichia coli MS 146-1]
 gi|307137906|ref|ZP_07497262.1| 23S rRNA pseudouridylate synthase B [Escherichia coli H736]
 gi|312971458|ref|ZP_07785633.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           1827-70]
 gi|331641827|ref|ZP_08342962.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli H736]
 gi|331652309|ref|ZP_08353328.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli M718]
 gi|1175678|sp|P37765|RLUB_ECOLI RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|1742064|dbj|BAA14806.1| 23S rRNA pseudouridylate synthase [Escherichia coli str. K12
           substr. W3110]
 gi|1787524|gb|AAC74351.1| 23S rRNA pseudouridylate synthase [Escherichia coli str. K-12
           substr. MG1655]
 gi|157066454|gb|ABV05709.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           HS]
 gi|169755295|gb|ACA77994.1| pseudouridine synthase [Escherichia coli ATCC 8739]
 gi|169888781|gb|ACB02488.1| 23S rRNA pseudouridylate synthase [Escherichia coli str. K-12
           substr. DH10B]
 gi|170520169|gb|ACB18347.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           SMS-3-5]
 gi|188487400|gb|EDU62503.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           53638]
 gi|194416715|gb|EDX32845.1| ribosomal large subunit pseudouridine synthase B [Shigella
           dysenteriae 1012]
 gi|218369962|emb|CAR17736.1| 23S rRNA pseudouridylate synthase [Escherichia coli IAI39]
 gi|238859761|gb|ACR61759.1| 23S rRNA pseudouridylate synthase [Escherichia coli BW2952]
 gi|242377048|emb|CAQ31772.1| 23S rRNA pseudouridine 2605 synthase [Escherichia coli BL21(DE3)]
 gi|253324778|gb|ACT29380.1| pseudouridine synthase [Escherichia coli 'BL21-Gold(DE3)pLysS AG']
 gi|253973250|gb|ACT38921.1| 23S rRNA pseudouridylate synthase [Escherichia coli B str. REL606]
 gi|253977464|gb|ACT43134.1| 23S rRNA pseudouridylate synthase [Escherichia coli BL21(DE3)]
 gi|260449601|gb|ACX40023.1| pseudouridine synthase [Escherichia coli DH1]
 gi|299881096|gb|EFI89307.1| conserved hypothetical protein [Escherichia coli MS 196-1]
 gi|300317268|gb|EFJ67052.1| hypothetical protein HMPREF9547_01723 [Escherichia coli MS 175-1]
 gi|300399234|gb|EFJ82772.1| conserved hypothetical protein [Escherichia coli MS 69-1]
 gi|300448865|gb|EFK12485.1| conserved hypothetical protein [Escherichia coli MS 116-1]
 gi|300455107|gb|EFK18600.1| conserved hypothetical protein [Escherichia coli MS 21-1]
 gi|300464168|gb|EFK27661.1| conserved hypothetical protein [Escherichia coli MS 187-1]
 gi|301074599|gb|EFK89405.1| conserved hypothetical protein [Escherichia coli MS 146-1]
 gi|309701567|emb|CBJ00874.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           ETEC H10407]
 gi|310336055|gb|EFQ01255.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           1827-70]
 gi|315135905|dbj|BAJ43064.1| 23S rRNA pseudouridylate synthase B [Escherichia coli DH1]
 gi|315297258|gb|EFU56538.1| conserved hypothetical protein [Escherichia coli MS 16-3]
 gi|315619347|gb|EFU99891.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           3431]
 gi|320181709|gb|EFW56620.1| 23S rRNA pseudouridylate synthase B [Shigella boydii ATCC 9905]
 gi|320195718|gb|EFW70343.1| 23S rRNA pseudouridylate synthase B [Escherichia coli WV_060327]
 gi|323937590|gb|EGB33858.1| RNA pseudouridylate synthase [Escherichia coli E1520]
 gi|323942383|gb|EGB38553.1| RNA pseudouridylate synthase [Escherichia coli E482]
 gi|323962569|gb|EGB58149.1| RNA pseudouridylate synthase [Escherichia coli H489]
 gi|323973491|gb|EGB68677.1| RNA pseudouridylate synthase [Escherichia coli TA007]
 gi|331038625|gb|EGI10845.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli H736]
 gi|331050587|gb|EGI22645.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli M718]
 gi|332091659|gb|EGI96739.1| ribosomal large subunit pseudouridine synthase B [Shigella boydii
           5216-82]
 gi|332097910|gb|EGJ02883.1| ribosomal large subunit pseudouridine synthase B [Shigella
           dysenteriae 155-74]
 gi|332342861|gb|AEE56195.1| 23S rRNA pseudouridylate synthase RluB [Escherichia coli UMNK88]
          Length = 291

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 87/288 (30%), Positives = 128/288 (44%), Gaps = 10/288 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           E +       ++V ++      +     R            R    ++
Sbjct: 242 ELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGGRRSGGRNN 289


>gi|145641141|ref|ZP_01796722.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           influenzae R3021]
 gi|145274302|gb|EDK14167.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           influenzae 22.4-21]
          Length = 232

 Score =  165 bits (417), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 58/236 (24%), Positives = 108/236 (45%), Gaps = 7/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  AV +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENTGLTRSQATKAIRQSAVKINGEIVKSGAVQISQEDKIYFEDELLTWLEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ HKP G V ++ D D  +        +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYFMLHKPQGCVCSNDDGDYPTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+++      +GI+++G        ++ +      +  V +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEENYAAACSEGILLRGEKEPTKPAKLEIL----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
            + EG+  ++K++F     KV  L R   G   L   L  G  R +++  + + + 
Sbjct: 177 TISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLVK 232


>gi|229515031|ref|ZP_04404491.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           TMA 21]
 gi|229347736|gb|EEO12695.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           TMA 21]
          Length = 231

 Score =  165 bits (417), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 48/231 (20%), Positives = 96/231 (41%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSRVEWQGREITLHGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     + +       ++            +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDG-FNQTAFTLLDEVNIQDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + YRV     +  D      +GI ++G        Q+ +     S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELRGERELTLPAQLEVI----SETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R   G   L   L +G  R ++++ +
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLESGEYRYLTEEEV 226


>gi|294635983|ref|ZP_06714424.1| ribosomal large subunit pseudouridine synthase B [Edwardsiella
           tarda ATCC 23685]
 gi|291090692|gb|EFE23253.1| ribosomal large subunit pseudouridine synthase B [Edwardsiella
           tarda ATCC 23685]
          Length = 291

 Score =  165 bits (417), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 91/290 (31%), Positives = 134/290 (46%), Gaps = 10/290 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I + RV V+G L      V V +   I VDG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIEALIKEGRVSVDGKLATLGDRVEVTANMKIRVDGRVVSIRE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T        +          SR I+VGRLDINT GLLL T 
Sbjct: 62  SEQEICRVLAYYKPEGELCTRRDPEGRPTVFDRLPRLRGSRWIAVGRLDINTSGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD+DKL  L +G+ ++        ++    +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDEDKLRQLSRGVQLEDGPASFKSISFQGGEGLN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK---ILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G  +E+  +    LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDLTLPKGLPRGGWQELPLENINYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
           E +       +++ ++      +     R           +R    + + 
Sbjct: 242 ELVELKAESTSKLPVERERRRMKANQIRRAVKRHSQHGSSSRRAPAAKRG 291


>gi|51596461|ref|YP_070652.1| 23S rRNA pseudouridylate synthase B [Yersinia pseudotuberculosis IP
           32953]
 gi|170024274|ref|YP_001720779.1| 23S rRNA pseudouridylate synthase B [Yersinia pseudotuberculosis
           YPIII]
 gi|186895510|ref|YP_001872622.1| 23S rRNA pseudouridylate synthase B [Yersinia pseudotuberculosis
           PB1/+]
 gi|51589743|emb|CAH21373.1| putative RNA pseudouridylate synthase-family protein [Yersinia
           pseudotuberculosis IP 32953]
 gi|169750808|gb|ACA68326.1| pseudouridine synthase [Yersinia pseudotuberculosis YPIII]
 gi|186698536|gb|ACC89165.1| pseudouridine synthase [Yersinia pseudotuberculosis PB1/+]
          Length = 344

 Score =  165 bits (417), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 96/325 (29%), Positives = 143/325 (44%), Gaps = 16/325 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
            +++ K++ARAG  SRRE+E +I Q RV V+G +  +    V  T    I +DG  L   
Sbjct: 28  GEKLQKILARAGHGSRREIEAIIQQGRVSVDGKV-SKLGDRVEVTQSTKIRLDGHLLSIK 86

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E        L  Y     L T +      +          SR ++VGRLD+NT GLLL T
Sbjct: 87  ESEENVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFT 146

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  GQ+D DK+  L +G+ ++        ++    +G 
Sbjct: 147 TDGELANRLMHPSREVEREYAVRVFGQIDDDKIKQLSRGVQLEDGPAAFRTISYQGGEGI 206

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+    L+  
Sbjct: 207 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELD---LKAT 263

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
                L E  V       S   + +DR  + +       +     S +    +Q      
Sbjct: 264 NYLRELVELDVETV----SKLPVEKDRRRVKANQIRRAVKRHTEVSGRQVAGRQGSARKG 319

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSG 329
             R+N+ + V  A     S     G
Sbjct: 320 STRQNVGNAVPAATASRRSGPKKRG 344


>gi|158316819|ref|YP_001509327.1| pseudouridine synthase [Frankia sp. EAN1pec]
 gi|158112224|gb|ABW14421.1| pseudouridine synthase [Frankia sp. EAN1pec]
          Length = 259

 Score =  165 bits (417), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 80/242 (33%), Positives = 118/242 (48%), Gaps = 2/242 (0%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHI 60
            D           R+ KV+A AGI SRR  E +I   RV+V+G ++      V   T  I
Sbjct: 9   PDTRRRDPASEGIRLQKVLASAGIGSRRHNEELIDSGRVRVDGEVVREQGRRVDPETAVI 68

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTE 119
           EVDG  +           +KP G+++  SD  GR T+ D L    S     VGRLD ++E
Sbjct: 69  EVDGERVVTRTGLVHLALNKPRGVLSAMSDDRGRPTIADFLTEFGSVGLFHVGRLDGDSE 128

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL+TNDG LA  L  PS    + Y V   G V +D    L+ G+ ++          +
Sbjct: 129 GLLLVTNDGDLAHRLTHPSFGVPKTYLVEISGPVRRDVPRRLRSGVTLEDGPVSVDAARI 188

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                S   + + L EG+   ++++ E     V+RL+R+S+GP  LGTL AG  R +++ 
Sbjct: 189 VDVAASRVMMELTLHEGRKHVVRRMMEAVGHPVHRLVRVSFGPVTLGTLRAGRARHLTRH 248

Query: 240 IL 241
            +
Sbjct: 249 EV 250


>gi|145630872|ref|ZP_01786649.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae R3021]
 gi|260582948|ref|ZP_05850732.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae NT127]
 gi|144983532|gb|EDJ91000.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae R3021]
 gi|260094048|gb|EEW77952.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae NT127]
          Length = 232

 Score =  165 bits (417), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 57/236 (24%), Positives = 108/236 (45%), Gaps = 7/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  AV +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENTGLTRSQATKAIRQSAVKINGEIVKSGAVQISQEDEIYFEDQLLTWVEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ +KP G V ++ D D  +        +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYFMLNKPQGCVCSNDDGDYPTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+++      +GI+++G        ++ +      +  V +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEENYATACAEGILLRGEKEPTKPAKLEIL----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
            + EG+  ++K++F     KV  L R   G   L  +L  G  R +++  +   + 
Sbjct: 177 TISEGRYHQVKRMFAALGNKVVGLHRWKIGNVVLDQSLDEGEYRPLTQSEIESLVK 232


>gi|123966487|ref|YP_001011568.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Prochlorococcus marinus str. MIT 9515]
 gi|123200853|gb|ABM72461.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Prochlorococcus marinus str. MIT 9515]
          Length = 240

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 54/226 (23%), Positives = 103/226 (45%), Gaps = 7/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++  G  SRR  +R+I + +V +NG +       V   D +EV+G+ + K  + +
Sbjct: 4   RINKYLSEVGYCSRRVADRLIEEGKVTINGKI-SEIGTKVKEDDQVEVEGIIIDKPTKQK 62

Query: 75  LWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                    + +   +D         +  +  +R+  +GRLD N+EGL+ LTNDG +   
Sbjct: 63  YIYLAFNKPVGIVCTTDRRVEPDNIIDFINYSTRIFPIGRLDKNSEGLIFLTNDGDIVNK 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V  +  +++D ++ +  G+ I      +  V     K       + L
Sbjct: 123 ILRARNNHEKEYIVSVNRPINRDFIHNMSNGVKILDTITKNCFVKQLGVKK----FKIIL 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            +G NR+I+++ E   ++V  L RI     +L  +  G  RE +K 
Sbjct: 179 TQGLNRQIRRMCESLGYRVQSLKRIRIMNIKL-DIPTGKYREFTKD 223


>gi|19704052|ref|NP_603614.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium
           nucleatum subsp. nucleatum ATCC 25586]
 gi|19714248|gb|AAL94913.1| Ribosomal small subunit pseudouridine synthase A [Fusobacterium
           nucleatum subsp. nucleatum ATCC 25586]
          Length = 226

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 69/229 (30%), Positives = 106/229 (46%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   GI SR+EV+++I+   + VNG+    A  N+    D IE +G  L   E 
Sbjct: 1   MRLDKFLVECGIGSRKEVKKLISNGEIAVNGMSDILAKDNIDENSDTIEYNGERLEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +  K   +  T    +           I   +  VGRLD +TEGLLL TNDG L  
Sbjct: 61  RYYIMNKKAGYITATEDFKEDTVMDLLPEWVIKKDLAPVGRLDKDTEGLLLFTNDGKLNH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VY V     +  + +  L++G+ I        +V    +K S+  + + 
Sbjct: 121 KLLSPKNHIDKVYYVEIEKNILDEDILKLEQGVDIGNYITQPAKV----EKISDNKIYLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++EGK  ++KK+ E  N KV  L R S+G   L  L  G  +EVS + +
Sbjct: 177 IKEGKFHQVKKMLEAVNNKVCYLRRESFGKLTLNDLTLGEVKEVSLEDI 225


>gi|223043526|ref|ZP_03613571.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Staphylococcus capitis
           SK14]
 gi|222443014|gb|EEE49114.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Staphylococcus capitis
           SK14]
          Length = 230

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 56/228 (24%), Positives = 103/228 (45%), Gaps = 7/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V+VN   ++     +   TD + VDG  +   + 
Sbjct: 1   MRIDKFLANMGLGTRTEVKQLLKKGLVEVNEKKIKTPKSQIDPETDKVVVDGEEISYVDN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP   ++   D   ++ +          +  VGRLD +TEGLLLLTNDG    
Sbjct: 61  -VYMMLNKPKDYISATEDNAHQTVLDLIPEFSHLGIFPVGRLDKDTEGLLLLTNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V     + Q  +   K G+ +        ++     KG++    V 
Sbjct: 120 ELMSPKKHVSKTYEVISKYPIKQSDIEAFKLGVELSDGKVKPAELI----KGNDRLSYVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK 239
           + EGK  ++K++F     +V  L R+     +L   L +G  R ++++
Sbjct: 176 IYEGKYHQVKRMFHSIENEVLELKRVKIANLELDETLNSGEYRFLNEQ 223


>gi|223933287|ref|ZP_03625276.1| pseudouridine synthase [Streptococcus suis 89/1591]
 gi|223898017|gb|EEF64389.1| pseudouridine synthase [Streptococcus suis 89/1591]
          Length = 238

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 107/231 (46%), Gaps = 2/231 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K + +A + SR++V+++   Q++K+NG   +  +  V      I+V G  +     
Sbjct: 1   MRLDKCLEKAKVGSRKQVKKLFKAQQIKINGHAAQSLSQIVDPELQTIQVSGKKVALEGS 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +               +       +  VGRLD +TEGL+L+TN+G L  
Sbjct: 61  AYYLLHKPAGVVSAVTDQEHQTVIDLISPQDSREGLYPVGRLDRDTEGLVLITNNGPLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVTV 191
            +  PS    +VY V  +G + +D       G+  + G       +T+      ++  T+
Sbjct: 121 RMLHPSHHVDKVYYVEVNGCLAEDASKFFASGVTFLDGTRCQPADLTVLEASLDHSRATI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            L EGK  ++KK+F  +  KV  L RIS+G F+LG L  G+ R+++   + 
Sbjct: 181 KLAEGKFHQVKKMFLAYGVKVTYLKRISFGGFELGDLERGAYRQLTPNEME 231


>gi|206576604|ref|YP_002237397.1| ribosomal small subunit pseudouridine synthase A [Klebsiella
           pneumoniae 342]
 gi|288934323|ref|YP_003438382.1| pseudouridine synthase [Klebsiella variicola At-22]
 gi|290508526|ref|ZP_06547897.1| ribosomal small subunit pseudouridine synthase A [Klebsiella sp.
           1_1_55]
 gi|206565662|gb|ACI07438.1| ribosomal small subunit pseudouridine synthase A [Klebsiella
           pneumoniae 342]
 gi|288889052|gb|ADC57370.1| pseudouridine synthase [Klebsiella variicola At-22]
 gi|289777920|gb|EFD85917.1| ribosomal small subunit pseudouridine synthase A [Klebsiella sp.
           1_1_55]
          Length = 239

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 57/243 (23%), Positives = 104/243 (42%), Gaps = 7/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G +++ A+  +     +E DG  L +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGSRVTVDGDIVKDASFKLQPEHEVEYDGNTLTQQNGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTILYFLDEPVAHKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     + +    L  KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVELESPLAEGTAELFAKGVQLHNEKDLTKPAVLEVI----TPTEVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLL 250
            + EG+  ++K++F      V  L R   G   L   L  G  R +++  +     P   
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVGLHRERIGDILLDDALAPGEYRPLTETEIASVGAPQAR 236

Query: 251 EEA 253
            + 
Sbjct: 237 SKT 239


>gi|300787858|ref|YP_003768149.1| ribosomal large subunit pseudouridine synthase B [Amycolatopsis
           mediterranei U32]
 gi|299797372|gb|ADJ47747.1| ribosomal large subunit pseudouridine synthase B [Amycolatopsis
           mediterranei U32]
          Length = 250

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 75/238 (31%), Positives = 113/238 (47%), Gaps = 4/238 (1%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
            E+    R+ KV+++AG+ASRR  E +I   RV+V+G ++      V      I VDG  
Sbjct: 4   SEHPDGVRLQKVLSQAGVASRRAAEDLIVAGRVEVDGEVVTELGRRVDPDAAIIHVDGTR 63

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLL 123
           +   +       +KP G+ +T SD  GR  V D L   +      + VGRLD NTEGLLL
Sbjct: 64  VNLRDDLIYLALNKPKGVHSTMSDDRGRPCVGDYLRGRYEETPGVVHVGRLDENTEGLLL 123

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG L   L  PS + L+ Y     G V +     L+ G  +        Q  +    
Sbjct: 124 LTNDGDLGHRLMHPSYRVLKTYLAEVDGLVPRGLGKELRNGWELPDGIVKVDQFRVKDMH 183

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              + V + + EGK   ++++ +     V +L+R + G  QLG    GS R ++K  +
Sbjct: 184 SGKSLVELVIHEGKKHIVRRLLKDTGHPVLKLVRTAVGDVQLGNQRVGSIRRLTKTEV 241


>gi|182439522|ref|YP_001827241.1| putative pseudouridine synthase [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|178468038|dbj|BAG22558.1| putative pseudouridine synthase [Streptomyces griseus subsp.
           griseus NBRC 13350]
          Length = 434

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 109/233 (46%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLR 68
               +R+ KV+ARAG+ SRR  E +I Q RV+VNG ++    + V    D I+VDG+ + 
Sbjct: 194 EQEGERLQKVLARAGMGSRRACEELIEQARVEVNGEIVVEQGMRVDVHKDEIKVDGLTVA 253

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   L      + +       +  + D + +  +R+  VGRLD  TEG+++LTN G
Sbjct: 254 AQSYLFFALNKPAGVVSSMEDPDGRQ-CLGDYVTNRETRLFHVGRLDTETEGIIMLTNHG 312

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     + Y     G + +D    LK GI ++          +    G N  
Sbjct: 313 ELAHRLTHPKYGVKKTYLAAIQGPLPRDLGKRLKDGIQLEDGYARADHFRVVENTGKNYL 372

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L EG+   ++++     + V RL+R S+GP  LG   +G  R ++   +
Sbjct: 373 VEVTLHEGRKHIVRRMLAEAGFPVERLVRTSFGPIPLGDQKSGWLRRLTNTEV 425


>gi|325846603|ref|ZP_08169518.1| pseudouridylate synthase [Anaerococcus hydrogenalis ACS-025-V-Sch4]
 gi|325481361|gb|EGC84402.1| pseudouridylate synthase [Anaerococcus hydrogenalis ACS-025-V-Sch4]
          Length = 240

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 67/229 (29%), Positives = 111/229 (48%), Gaps = 3/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA+AG+ASRR+ E  I +  V VNG  L+  +  V   D ++V G  L   E+ 
Sbjct: 10  MRINKYIAKAGLASRRKSEEYIKKGLVFVNGKKLDDLSYQVKENDEVKVMGKLLEIKEKF 69

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      + +            ++L  I  R    GRLD ++ GL+L+TNDG +   
Sbjct: 70  YYKLNKPIGFISSN--YDPHNKKDLNSLVKIDQRFFCAGRLDKDSHGLMLITNDGKITNK 127

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  PS +  + Y V+    +++D   L +KGI +           ++    +     V +
Sbjct: 128 LIHPSKKIEKTYIVKVDKLLNKDDEALFRKGIKLSDNE-KTSDAKINLIDENRKIYEVII 186

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+++++F +F  KV  L RI  G  +LG L  G  ++++KK L 
Sbjct: 187 HQGFNRQVRRMFLYFGSKVIDLKRIKIGQIELGKLEDGKYKKLNKKELE 235


>gi|91070007|gb|ABE10933.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [uncultured Prochlorococcus marinus clone
           ASNC3046]
          Length = 240

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 55/236 (23%), Positives = 104/236 (44%), Gaps = 11/236 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---AE 71
           R++K ++  G  SRRE +++I + +V +NG +       V   D +EV G  + K    E
Sbjct: 4   RINKYLSEVGYCSRREADKLILEGKVTINGKIP-EIGAKVEEIDQVEVKGQRIEKSDRQE 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  L        + TT            +      R+  +GRLD  +EGL+ LTNDG + 
Sbjct: 63  KIYLAFNKPLGIVCTTDRK--VEPNNVIDFIKYPKRIFPIGRLDKLSEGLIFLTNDGDIV 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V+ +  ++ + +  +  G+ I      +       ++       +
Sbjct: 121 NKILRARNNHEKEYIVKVNRPINSEFIQKMSNGVEILDTITKNCS----VKQLGPRKFKI 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            L +G NR+I+++ E   ++V  L R+     +L  + +G  RE S++ L+E  G 
Sbjct: 177 ILTQGLNRQIRRMCETLGYRVRSLKRVRIMNIKL-DMPSGKYREFSREELQELNGL 231


>gi|311113298|ref|YP_003984520.1| pseudouridine synthase [Rothia dentocariosa ATCC 17931]
 gi|310944792|gb|ADP41086.1| pseudouridine synthase [Rothia dentocariosa ATCC 17931]
          Length = 357

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 87/234 (37%), Positives = 130/234 (55%), Gaps = 2/234 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-VDGVPLR 68
           +    R+ K++A+AG+ASRR  E MI + RV VNG ++    V V   D I  VDG+ ++
Sbjct: 115 DHEGVRLQKLMAQAGVASRRVCEEMITEGRVTVNGEVVTELGVRVNPADVIVQVDGMTVQ 174

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
             E+     ++KP G+V+T  DPDGR  + D L   +  RV  VGRLD+ TEGLLLLTND
Sbjct: 175 TNEKLIYMAFNKPAGVVSTMEDPDGRPCIKDFLRDSMNERVFHVGRLDVETEGLLLLTND 234

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  + Y V+  G V+      LKKGI ++          L      + 
Sbjct: 235 GELANRLTHPSYEVPKTYLVQVRGPVESGIGAELKKGIRLEDGVSRVDSFKLVDSAPGHV 294

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + V +  GKNR ++++FE   + V +L+R+  GP ++G+   G+ R +SK  +
Sbjct: 295 LIEVTIHSGKNRIVRRLFEAVGYPVEKLVRVQMGPIRIGSQKQGTVRNLSKVEI 348


>gi|28209926|ref|NP_780870.1| tRNA pseudouridine synthase A [Clostridium tetani E88]
 gi|28202361|gb|AAO34807.1| tRNA pseudouridine synthase A [Clostridium tetani E88]
          Length = 235

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 110/231 (47%), Gaps = 5/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++  I+  GI SRRE + +I Q++VKVNG +       V S D IEV+G  L+K +  
Sbjct: 1   MRLNNFISSTGICSRREADELIKQKKVKVNGEIAP-LGYIVNSKDKIEVNGKLLQKKKND 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T            +  +   R+  +GRLD ++EGL+LLTNDG +   
Sbjct: 60  IYIALNKPVGITCTTERHI--KGNIIDFINHTERIFPIGRLDKDSEGLILLTNDGSIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--DMQVTLDTQKGSNAWVTV 191
           +        + Y V  +  +    +N + KG+ I         +       K ++    +
Sbjct: 118 ILREENNHEKDYIVTVNKPITPAFINGMSKGVKIYNPVKNQYTITNKCKVVKINSNTFKI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            L +G NR+I+++   F++KV +L RI      L  L  G  R ++ + +R
Sbjct: 178 TLSQGLNRQIRRMCSSFSYKVVKLKRIRIINITLKGLNVGKWRNLTDEEVR 228


>gi|307544267|ref|YP_003896746.1| RNA-binding S4 domain protein [Halomonas elongata DSM 2581]
 gi|307216291|emb|CBV41561.1| RNA-binding S4 domain protein [Halomonas elongata DSM 2581]
          Length = 287

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 84/287 (29%), Positives = 123/287 (42%), Gaps = 7/287 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           + T +++ KV+ARAG+ SRRE+E  IA  RVKVNG +       V   D +  D  P+  
Sbjct: 2   SNTSEKLQKVLARAGLGSRREMETAIADGRVKVNGQVAT-LGDRVELRDKVAFDDRPVAL 60

Query: 70  A-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                  R  +        L T       R+           R I++GRLDINT GLLL 
Sbjct: 61  RGADEVPRRVIMYNKPEGELCTRKDPEGRRTVFDRLPRLKGERWIAIGRLDINTSGLLLF 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T DG LA  L  PSTQ  R Y VR  G+V  D +  + +G+++         V     +G
Sbjct: 121 TTDGELANRLMHPSTQIEREYAVRVMGEVTMDHIKAMVEGVMLDDGPARFTDVQEFGGEG 180

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
            N W  V + EG+NRE+++++E  N  V+RL R+ YG   L     AG   E+ +  + +
Sbjct: 181 INTWFHVVIMEGRNREVRRLWESQNLTVSRLKRVRYGNIFLDKRAKAGEWVELGQDEIDD 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
                 L   +V    P   +            +        +    
Sbjct: 241 LAEQAGLPSRKVPELTPDEKNRWSRDKNKRRPVQGVRKPKSSRSRGR 287


>gi|229529332|ref|ZP_04418722.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           12129(1)]
 gi|229333106|gb|EEN98592.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           12129(1)]
          Length = 231

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 47/231 (20%), Positives = 94/231 (40%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +     +E  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKEASRVEWQGREIMLHGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     + +       ++            +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDG-FNQTAFTLLDEVNVEDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + YRV     +  D      +GI ++G        Q+ +     S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELRGERELTLPAQLEVI----SETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R   G   L   L  G  R ++++ +
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEEEV 226


>gi|327484245|gb|AEA78652.1| Ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           LMA3894-4]
          Length = 231

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 47/231 (20%), Positives = 94/231 (40%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +     +E  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKEASRVEWQGREIMLHGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     + +       ++            +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGIVCSHEDG-FNQTAFTLLDEVNVEDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + YRV     +  D      +GI ++G        Q+ +     S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELRGERELTLPAQLEVI----SETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R   G   L   L  G  R ++++ +
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEEEV 226


>gi|281354990|ref|ZP_06241484.1| pseudouridine synthase [Victivallis vadensis ATCC BAA-548]
 gi|281317870|gb|EFB01890.1| pseudouridine synthase [Victivallis vadensis ATCC BAA-548]
          Length = 241

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 109/234 (46%), Gaps = 5/234 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           EN   +R+ K+++ AGIASRR    +I   RV VNG  +      V   D +E DGVP+ 
Sbjct: 2   ENDNRERLVKILSAAGIASRRGAGDLIKAGRVTVNGETVFEPGFRVAPGDRVEYDGVPVL 61

Query: 69  KAERTRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             ER    +       + T          V     +   R+ S GRLD ++EGL+L +ND
Sbjct: 62  AEERKVYIMLNKPRGYVCTNADPHADLKAVDLIRLTPPLRLFSAGRLDKDSEGLILFSND 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G     L  P  + L+VY+VR   +    +L  +++G++ +G             +  + 
Sbjct: 122 GDYVARLTHPRHEILKVYQVRVRREFKPAELEQMRRGVLERGELLK----VHAVSRCGDC 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              + L EGKNREI+++         RL R+  G  +LG L  G+ RE++   +
Sbjct: 178 TYLITLNEGKNREIRRLTAALGSPTRRLKRLQIGALRLGGLPVGNWRELTPAEI 231


>gi|326780186|ref|ZP_08239451.1| pseudouridine synthase Rsu [Streptomyces cf. griseus XylebKG-1]
 gi|326660519|gb|EGE45365.1| pseudouridine synthase Rsu [Streptomyces cf. griseus XylebKG-1]
          Length = 433

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 109/233 (46%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLR 68
               +R+ KV+ARAG+ SRR  E +I Q RV+VNG ++    + V    D I+VDG+ + 
Sbjct: 193 EQEGERLQKVLARAGMGSRRACEELIEQARVEVNGEIVVEQGMRVDVHKDEIKVDGLTVA 252

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   L      + +       +  + D + +  +R+  VGRLD  TEG+++LTN G
Sbjct: 253 AQSYLFFALNKPAGVVSSMEDPDGRQ-CLGDYVTNRETRLFHVGRLDTETEGIIMLTNHG 311

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     + Y     G + +D    LK GI ++          +    G N  
Sbjct: 312 ELAHRLTHPKYGVKKTYLAAIQGPLPRDLGKRLKDGIQLEDGYARADHFRVVENTGKNYL 371

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L EG+   ++++     + V RL+R S+GP  LG   +G  R ++   +
Sbjct: 372 VEVTLHEGRKHIVRRMLAEAGFPVERLVRTSFGPIPLGDQKSGWLRRLTNTEV 424


>gi|308187008|ref|YP_003931139.1| ribosomal large subunit pseudouridine synthase B [Pantoea vagans
           C9-1]
 gi|308057518|gb|ADO09690.1| ribosomal large subunit pseudouridine synthase B [Pantoea vagans
           C9-1]
          Length = 296

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 90/299 (30%), Positives = 130/299 (43%), Gaps = 12/299 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV--MSTDHIEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E MIA  RV V+G +       V    +  I +DG  +  A
Sbjct: 2   SEKLQKVLARAGHGSRREIESMIAAGRVSVDGKIAT-LGDRVESSKSLKIRIDGHLVSIA 60

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E        L  Y     L T        +          SR I+VGRLD+NT GL+L T
Sbjct: 61  ESATEVCRVLAYYKPEGELCTRSDPEGRPTVFDRLPRLRGSRWIAVGRLDVNTCGLMLFT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  GQVD DK+  L KG+ ++        +     +G 
Sbjct: 121 TDGELANRLMHPSREVEREYAVRVFGQVDDDKIRQLSKGVQLEDGPAAFKTLKFGGGEGI 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           N W  V L EG+NRE+++++E    +V+RL+R+ YG   L   L  G   E+    L   
Sbjct: 181 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLMRVRYGDITLPKGLPRGGWTELD---LPAV 237

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                L E        +   +   R + N I       +++             K+ + 
Sbjct: 238 NYLRNLVELDDETVTKLVVEKDRRRTKANQIRRAVKRHSKVSSTPRAPRRNPGSKRNSG 296


>gi|254229618|ref|ZP_04923030.1| ribosomal small subunit pseudouridine synthase A [Vibrio sp. Ex25]
 gi|262394552|ref|YP_003286406.1| ribosomal small subunit pseudouridine synthase A [Vibrio sp. Ex25]
 gi|151937901|gb|EDN56747.1| ribosomal small subunit pseudouridine synthase A [Vibrio sp. Ex25]
 gi|262338146|gb|ACY51941.1| ribosomal small subunit pseudouridine synthase A [Vibrio sp. Ex25]
          Length = 233

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 47/230 (20%), Positives = 97/230 (42%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  A+R++  ++I    + V+G + +  A  V     +  +   +      
Sbjct: 1   MRLDKYLCDALGATRKQATKIIKSGDITVDGEVQKSGAFKVPEGVEVMWEDRVIGAPGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + LY     + +     +  +            +   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLYKPADFVCSHEDGYNQ-TAFALLDEPKIENLHFAGRLDVDTTGLVLITDDGKWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     +  D    L++GI+++      +   L+    +   V + +
Sbjct: 120 ITSPKHKCEKTYRVWLVDAIQPDYAEKLEQGIILRNESEATLPARLEIVNEAENEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            EGK  ++K++F     KV  L R   G  +L   L  G  R ++++ + 
Sbjct: 180 VEGKYHQVKRMFAALGNKVEYLHRERIGSIELDEALEPGDYRYLTQEEID 229


>gi|22125944|ref|NP_669367.1| 23S rRNA pseudouridylate synthase B [Yersinia pestis KIM 10]
 gi|45441810|ref|NP_993349.1| 23S rRNA pseudouridylate synthase B [Yersinia pestis biovar
           Microtus str. 91001]
 gi|108807566|ref|YP_651482.1| 23S rRNA pseudouridylate synthase B [Yersinia pestis Antiqua]
 gi|108811842|ref|YP_647609.1| 23S rRNA pseudouridylate synthase B [Yersinia pestis Nepal516]
 gi|145598219|ref|YP_001162295.1| 23S rRNA pseudouridylate synthase B [Yersinia pestis Pestoides F]
 gi|165927423|ref|ZP_02223255.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165938234|ref|ZP_02226793.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|166010649|ref|ZP_02231547.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166210657|ref|ZP_02236692.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|167400806|ref|ZP_02306312.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167420205|ref|ZP_02311958.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167424996|ref|ZP_02316749.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|167470517|ref|ZP_02335221.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           FV-1]
 gi|218929309|ref|YP_002347184.1| 23S rRNA pseudouridylate synthase B [Yersinia pestis CO92]
 gi|270490618|ref|ZP_06207692.1| pseudouridylate synthase [Yersinia pestis KIM D27]
 gi|294503749|ref|YP_003567811.1| hypothetical protein YPZ3_1639 [Yersinia pestis Z176003]
 gi|21958885|gb|AAM85618.1|AE013808_1 hypothetical protein y2054 [Yersinia pestis KIM 10]
 gi|45436672|gb|AAS62226.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Yersinia pestis biovar
           Microtus str. 91001]
 gi|108775490|gb|ABG18009.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           Nepal516]
 gi|108779479|gb|ABG13537.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           Antiqua]
 gi|145209915|gb|ABP39322.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           Pestoides F]
 gi|165913895|gb|EDR32513.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|165920689|gb|EDR37937.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165990351|gb|EDR42652.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166207837|gb|EDR52317.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|166961900|gb|EDR57921.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167049659|gb|EDR61067.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167056183|gb|EDR65961.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|262362131|gb|ACY58852.1| hypothetical protein YPD4_1945 [Yersinia pestis D106004]
 gi|270339122|gb|EFA49899.1| pseudouridylate synthase [Yersinia pestis KIM D27]
 gi|294354208|gb|ADE64549.1| hypothetical protein YPZ3_1639 [Yersinia pestis Z176003]
          Length = 344

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 95/325 (29%), Positives = 142/325 (43%), Gaps = 16/325 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
            +++ K++ARAG  SRRE+E +I Q RV V+G +  +    V  T    I +DG  L   
Sbjct: 28  GEKLQKILARAGHGSRREIEAIIQQGRVSVDGKV-SKLGDRVEVTQSTKIRLDGHLLSIK 86

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E        L  Y     L T +      +          SR ++VGRLD+NT GLLL T
Sbjct: 87  ESEENVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFT 146

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  GQ+D DK+  L +G+ ++        ++    +G 
Sbjct: 147 TDGELANRLMHPSREVEREYAVRVFGQIDDDKIKQLSRGVQLEDGPAAFRTISYQGGEGI 206

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+    L+  
Sbjct: 207 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELD---LKAT 263

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
                L E  V       S   + +DR  + +       +     S +    +Q      
Sbjct: 264 NYLRELVELDVETV----SKLPVEKDRRRVKANQIRRAVKRHTEVSGRQVAGRQGSARKG 319

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSG 329
             R+N+ +    A     S     G
Sbjct: 320 STRQNVGNAAPAATASRRSGPKKRG 344


>gi|148555617|ref|YP_001263199.1| pseudouridine synthase [Sphingomonas wittichii RW1]
 gi|148500807|gb|ABQ69061.1| pseudouridine synthase [Sphingomonas wittichii RW1]
          Length = 286

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 116/230 (50%), Positives = 160/230 (69%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            PQR++K++ARAGIASRRE+ERMIA+ RV ++G  ++  A  + S   + VDG P+   E
Sbjct: 45  EPQRIAKLLARAGIASRREIERMIAEGRVAIDGAAIDTPATLLTSLKGVTVDGKPVAAPE 104

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            TRL+L+HKP GL+TT  DP GR T++D LP+   RV+ VGRLD+NTEGLLLLT DG   
Sbjct: 105 ATRLFLFHKPKGLLTTERDPKGRPTIYDRLPAGLPRVMPVGRLDLNTEGLLLLTTDGEFK 164

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           R LELPST   R+YR R +G V Q++L  L +GI I G+ YG +   ++ + G+N W+ +
Sbjct: 165 RQLELPSTGVERIYRARCYGTVHQEQLEALIEGIEIDGVRYGSIDANMERRTGANVWIEM 224

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            LREGKNRE+++V E    +V+RLIRI+YG F+LG L  G   E+++  L
Sbjct: 225 KLREGKNREVRRVLEHLGLEVSRLIRIAYGAFELGDLQPGEVGEIAQHQL 274


>gi|254226106|ref|ZP_04919703.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           V51]
 gi|125621341|gb|EAZ49678.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           V51]
          Length = 231

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 49/231 (21%), Positives = 95/231 (41%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSCVEWQGREITLHGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     + +       ++            +   GRLDI+T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDG-FNQTAFTLLDEVNVEDLHFAGRLDIDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + YRV     +  D      +GI ++G        Q+ +     S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELRGERELTLPAQLEVI----SETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R   G   L   L  G  R ++++ +
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRKRIGQITLDETLEPGEYRYLTEEEV 226


>gi|187731466|ref|YP_001880099.1| 23S rRNA pseudouridylate synthase B [Shigella boydii CDC 3083-94]
 gi|187428458|gb|ACD07732.1| ribosomal large subunit pseudouridine synthase B [Shigella boydii
           CDC 3083-94]
          Length = 290

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 87/289 (30%), Positives = 128/289 (44%), Gaps = 10/289 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKIIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           E +       ++V ++      +     R            R    ++ 
Sbjct: 242 ELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGGRRSGGRNNG 290


>gi|94984870|ref|YP_604234.1| pseudouridine synthase, Rsu [Deinococcus geothermalis DSM 11300]
 gi|94555151|gb|ABF45065.1| Pseudouridine synthase, Rsu [Deinococcus geothermalis DSM 11300]
          Length = 253

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 73/251 (29%), Positives = 108/251 (43%), Gaps = 10/251 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--A 70
            +R+ K +ARAG+ASRR  E +I   RV VNG +       VM  D + VDG  +     
Sbjct: 5   GERLQKRLARAGVASRRAAEDLITAGRVTVNGQIAT-LGRTVMPDDEVRVDGRLIEAPAQ 63

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E     LY     + T   +   R+ +          +  VGRLD ++EGLLLLT DG L
Sbjct: 64  ESVTFLLYKPAGYVTTARDEYGRRNVLSA--MPPIPGLHPVGRLDKDSEGLLLLTTDGQL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + YR    GQ    +L +L+ GI +       +               
Sbjct: 122 TLTLTHPRYGHEKAYRAWTAGQPVAAELRVLETGIELADGPARALSARPARGGA-----L 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           V L EG+NR+++++ +   + V+RL+R   G   LG L  G  R +S + L + L P  +
Sbjct: 177 VTLTEGRNRQVRRMLDAIGYPVHRLLRYRVGGLWLGDLEPGEYRLLSPRDLHDLLHPAQV 236

Query: 251 EEAQVNLDAPI 261
                      
Sbjct: 237 PRHVWERAERE 247


>gi|167632749|ref|ZP_02391075.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0442]
 gi|167531561|gb|EDR94226.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0442]
          Length = 238

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 64/228 (28%), Positives = 109/228 (47%), Gaps = 7/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG + +     V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIINGKVAK-IGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T            +L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCTSEKSV--KGNIIDLVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T      S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEITQL----SKYEFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQRRDLTKKEKR 225


>gi|319745443|gb|EFV97749.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae ATCC 13813]
          Length = 240

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 57/233 (24%), Positives = 104/233 (44%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+ ++ ++++ VNG       V V    D I+ +G  +   + 
Sbjct: 1   MRLDKFLVECGLGSRTQVKLILKKKQISVNGNSETSPKVQVDEYRDEIKYNGTLVSYEKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T            +  +    V  VGRLDI+T G LLLTN+G LA 
Sbjct: 61  VYYMLHKPKGVISATDDPSHKTVLDLLDKTARDKAVFPVGRLDIDTTGFLLLTNNGELAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVT 190
            +  P     + Y  +  G + +D +    KGI+++         ++    Q  + + V 
Sbjct: 121 KILSPKKHVDKCYEAKISGIMTEDDILAFDKGIILKDFTCLPALLEIVEVNQVKNQSLVK 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           + ++EGK  ++K++      +V  L R+S G  QL   L +G  R ++ K + 
Sbjct: 181 ITIKEGKFHQVKRMVAACGKEVLELKRLSMGNLQLDKQLESGQWRRLTIKEIE 233


>gi|153835311|ref|ZP_01987978.1| RNA pseudouridine synthase family protein [Vibrio harveyi HY01]
 gi|156975027|ref|YP_001445934.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio harveyi ATCC
           BAA-1116]
 gi|148868176|gb|EDL67329.1| RNA pseudouridine synthase family protein [Vibrio harveyi HY01]
 gi|156526621|gb|ABU71707.1| hypothetical protein VIBHAR_02753 [Vibrio harveyi ATCC BAA-1116]
          Length = 312

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 90/313 (28%), Positives = 132/313 (42%), Gaps = 13/313 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E +I   RV VNGI+ +           + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREIESLIKSGRVSVNGIVAKLGERLEDENSVVRIDGHVVSAKAQ 61

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  Y     L T H     R+          SR ISVGRLD NT GLLL T D
Sbjct: 62  EEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G+V + K+  L +G+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRQVEREYLVRVFGEVTEQKVKNLVRGVELEDGMARFEDVVYAGGEGMNH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LRE 243
              V + EG+NRE+++++E  +  V+RL R+ YG   L   L  G   E+  K    LRE
Sbjct: 182 TFYVAINEGRNREVRRLWESQDTTVSRLKRVRYGDIYLDKKLPRGGWMELDLKEVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +     +E  ++L+       T  +       ++     R ++  +   G S       
Sbjct: 242 LVELRPEKETMLDLNK----DNTSRKRERARSQKIRRAVKRHEERVNTPKGRSNNPSRRK 297

Query: 304 PVHRRNLASNVWM 316
           P            
Sbjct: 298 PKKTAGDQGARNK 310


>gi|325971205|ref|YP_004247396.1| pseudouridine synthase Rsu [Spirochaeta sp. Buddy]
 gi|324026443|gb|ADY13202.1| pseudouridine synthase Rsu [Spirochaeta sp. Buddy]
          Length = 250

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 66/249 (26%), Positives = 111/249 (44%), Gaps = 6/249 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+   +A++G  SRR  E +I   RV +N   +      V   D + VD   +  A+R
Sbjct: 6   PIRLQAYMAKSGCGSRRFCETLITAGRVTINTKRVTELGTKVNEEDVVMVDDQLIEPADR 65

Query: 73  TRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           T  +  Y     + T +   +          +  + +  +GRLD  + GL+L TNDG +A
Sbjct: 66  TYYYALYKPRGYVCTNYDPNEKLYARDLIDIADKNLLFHIGRLDKESSGLILYTNDGDVA 125

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
           + +  PS +  + Y V    +V ++ L    KGI I     Y   +  +     S  WV 
Sbjct: 126 QKIMHPSREIEKEYLVSCSTEVRREDLEEALKGIYIDIPQPYRIKRFEIL----SKKWVR 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L EGKNREI+K+F ++ + V +L+R+  G  +LG +  G  R +    +   L     
Sbjct: 182 IILTEGKNREIRKIFSYYGYDVKQLVRMRIGCIELGEMQPGQYRALFSSEIEAMLKGETE 241

Query: 251 EEAQVNLDA 259
              +  +  
Sbjct: 242 PVKKRKVTW 250


>gi|170768335|ref|ZP_02902788.1| ribosomal large subunit pseudouridine synthase B [Escherichia
           albertii TW07627]
 gi|170123101|gb|EDS92032.1| ribosomal large subunit pseudouridine synthase B [Escherichia
           albertii TW07627]
          Length = 291

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 87/288 (30%), Positives = 128/288 (44%), Gaps = 10/288 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLVSVRE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SVEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDTKLRDLSRGVQLEDGPAAFKTIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           E +       ++V ++      +     R            R    ++
Sbjct: 242 ELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQMSGGRRSGGRNN 289


>gi|325130402|gb|EGC53166.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis OX99.30304]
 gi|325204354|gb|ADY99807.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M01-240355]
          Length = 256

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 72/245 (29%), Positives = 121/245 (49%), Gaps = 7/245 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  ++   
Sbjct: 2   EPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLKW 60

Query: 72  RTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             RL      Y +   +V+        S       +  SR +++GRLDINT GLL+LT  
Sbjct: 61  ADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTTS 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN 186
           G L +    PS +  R Y VR  G +  +++ +L +  ++++       ++     +G+N
Sbjct: 121 GELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGAN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
            W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   E++   +   L
Sbjct: 181 KWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFYELNPAEVANIL 240

Query: 246 GPHLL 250
               +
Sbjct: 241 KWAEM 245


>gi|254515164|ref|ZP_05127225.1| ribosomal large subunit pseudouridine synthase B [gamma
           proteobacterium NOR5-3]
 gi|219677407|gb|EED33772.1| ribosomal large subunit pseudouridine synthase B [gamma
           proteobacterium NOR5-3]
          Length = 327

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 82/318 (25%), Positives = 135/318 (42%), Gaps = 12/318 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
             +++ KV+AR+G+ SRRE+ER I Q RV ++G         V++   IEVDG PL    
Sbjct: 18  DGEKLQKVLARSGLGSRREMERWIEQDRVTIDGKPA-SLGDRVVAGQRIEVDGRPLAAGD 76

Query: 70  -AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             +   L  +     + +       R+           R IS+GRLD NT GLLL T DG
Sbjct: 77  GEKTRCLLYHKPTGEVCSRKDPEGRRTVFERLPKVKSGRWISIGRLDYNTSGLLLFTTDG 136

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS    R Y VR  G V ++ ++ + +G++++        +      G NAW
Sbjct: 137 ELANALMHPSANIEREYMVRVMGDVTEENISAMLEGVMLEDGVARFTDIQSGGGDGINAW 196

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
             V L EG+NRE+++++E     V+RL R+ YG   +   +  G  +E++   +      
Sbjct: 197 YYVVLMEGRNREVRRLWESQGLTVSRLKRVRYGDLFVPSKVKKGQYQELASNEINGLYRM 256

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
             +    V          +      +   E      R  K++    G    +K  +   R
Sbjct: 257 AGMPAKDVE-------PPSREDRNKHKRMEGKRGRVRGNKHAKDDFGSRDARKEKSGKGR 309

Query: 308 RNLASNVWMAKGIHSSFL 325
           +  + +    K    +  
Sbjct: 310 KPGSKSTSAPKNKRRTRD 327


>gi|300741224|ref|ZP_07071245.1| ribosomal large subunit pseudouridine synthase B [Rothia
           dentocariosa M567]
 gi|300380409|gb|EFJ76971.1| ribosomal large subunit pseudouridine synthase B [Rothia
           dentocariosa M567]
          Length = 357

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 87/234 (37%), Positives = 130/234 (55%), Gaps = 2/234 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-VDGVPLR 68
           +    R+ K++A+AG+ASRR  E MI + RV VNG ++    V V   D I  VDG+ ++
Sbjct: 115 DHDGVRLQKLMAQAGVASRRVCEEMITEGRVTVNGEVVTELGVRVNPADVIVQVDGMTVQ 174

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
             E+     ++KP G+V+T  DPDGR  + D L   +  RV  VGRLD+ TEGLLLLTND
Sbjct: 175 TNEKLIYMAFNKPAGVVSTMEDPDGRPCIKDFLRDSMNERVFHVGRLDVETEGLLLLTND 234

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  + Y V+  G V+      LKKGI ++          L      + 
Sbjct: 235 GELANRLTHPSYEVPKTYLVQVRGPVESGIGAELKKGIRLEDGVSRVDSFKLVDSAPGHV 294

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + V +  GKNR ++++FE   + V +L+R+  GP ++G+   G+ R +SK  +
Sbjct: 295 LIEVTIHSGKNRIVRRLFEAVGYPVEKLVRVQMGPIRIGSQKQGTVRNLSKVEI 348


>gi|329116700|ref|ZP_08245417.1| putative 16S pseudouridylate 516 synthase [Streptococcus parauberis
           NCFD 2020]
 gi|326907105|gb|EGE54019.1| putative 16S pseudouridylate 516 synthase [Streptococcus parauberis
           NCFD 2020]
          Length = 238

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 59/232 (25%), Positives = 99/232 (42%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +  AGI SR +V+ ++ ++ V VNG +   A   + S  D I   G  L   E 
Sbjct: 1   MRLDKFLVDAGIGSRSQVKSLLKKKEVLVNGQVESSAKRQIDSDKDQIVFQGQKLVYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  +         +  +    V  VGRLD +T GLLLLTN+G LA 
Sbjct: 61  LYYMLNKPAGVVSATEDNLHQTVVDLLDDRARQKEVFPVGRLDKDTHGLLLLTNNGELAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVT 190
            L  P     ++Y     G + +      + GI +         + +    +      V 
Sbjct: 121 QLLTPKKHVDKIYLAHIEGMMTKKDQEAFENGIQLSDHHCLPATLEVLETDEHKQTCKVK 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + L+EGK  ++K++ +    +V  L R++ GP +L   L  G  R ++ + +
Sbjct: 181 ITLKEGKFHQVKRMVKACGKEVTDLQRLTMGPLKLDNQLQLGQFRRLTDEEI 232


>gi|260768728|ref|ZP_05877662.1| ribosomal large subunit pseudouridine synthase B [Vibrio furnissii
           CIP 102972]
 gi|260616758|gb|EEX41943.1| ribosomal large subunit pseudouridine synthase B [Vibrio furnissii
           CIP 102972]
          Length = 314

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 89/314 (28%), Positives = 132/314 (42%), Gaps = 7/314 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E +I   RV VNG +             + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGERLEDENAVVRIDGHAVSAKAQ 61

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  Y     L T H     R+          SR ISVGRLD NT GLLL T D
Sbjct: 62  EEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G V +DK+  L +G+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRQVEREYLVRVFGDVTEDKIRNLVRGVQLEDGLARFEDVVYAGGEGMNH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+  K +   L 
Sbjct: 182 TFYVVINEGRNREVRRLWESQETTVSRLKRVRYGDIFLDKKLPRGGWMELDLKDV-NYLR 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
             +  + +      +    T  +   +   ++     R ++  +   G S   +      
Sbjct: 241 ELVELKPEKTTMLDVSKDNTSRKRERSRSQKIRRAVRRHEERVTAPAGRSGSSRRKDAAS 300

Query: 307 RRNLASNVWMAKGI 320
           R+   +N    KG 
Sbjct: 301 RQKAGNNSSPRKGR 314


>gi|254519947|ref|ZP_05132003.1| RNA pseudouridine synthase [Clostridium sp. 7_2_43FAA]
 gi|226913696|gb|EEH98897.1| RNA pseudouridine synthase [Clostridium sp. 7_2_43FAA]
          Length = 227

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 57/228 (25%), Positives = 108/228 (47%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+++  G  SR+EV R I  +R+ VNG L       V  +D I +DG  ++  E+ 
Sbjct: 1   MRINKLLSNYGYCSRKEVSRWIEDKRIIVNGKLC-EQGQWVEESDEILLDGEKIKPKEKV 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L   P  + T+  + D       +  +    V  VGRLD +++GL+L+TNDG LA  
Sbjct: 60  YIALNKPPGIVCTSAREID---NNIIDFLNYKDYVFPVGRLDKDSQGLILMTNDGELANK 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +    +   + Y V      D+  +  +  G+ I G      ++    +       ++ L
Sbjct: 117 ILSSDSYHEKEYIVTIDRDFDESFIEGMSNGVEILGTITRPCKLRRIDKNI----FSIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +G NR+I+++ + F + V +L RI         +  G  + ++K+++
Sbjct: 173 TQGLNRQIRRMTKAFGYNVIKLERIRIMNIMSNDIELGQWKFINKEVI 220


>gi|210615570|ref|ZP_03290668.1| hypothetical protein CLONEX_02886 [Clostridium nexile DSM 1787]
 gi|210150237|gb|EEA81246.1| hypothetical protein CLONEX_02886 [Clostridium nexile DSM 1787]
          Length = 240

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 104/231 (45%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV+++I Q +V V+G + +     +  S   +   G  +     
Sbjct: 8   IRLDKYLADMGVGTRTEVKKLIRQGKVTVDGSIEKSPERKIDISHQKVCCMGEAVSYETH 67

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +V+  +D   ++ V          +  VGRLD +TEGLLL+TNDG LA 
Sbjct: 68  EYYMLNKPAG-VVSATTDRQDKTVVELISSKKRRDLFPVGRLDKDTEGLLLITNDGELAH 126

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VY  +  G VD+    +   G+ I                G  + + V 
Sbjct: 127 RLLSPKKHVDKVYYAKVQGIVDEVDQEIFAVGMSIGNGETALPSKLEILYSGEISEIRVT 186

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           ++EGK  ++K++F     +V  L R+S G   L   L +G  R ++K+ L+
Sbjct: 187 IQEGKFHQVKRMFHAVGKEVIYLKRLSMGTLLLDETLKSGEYRALTKEELK 237


>gi|269218469|ref|ZP_06162323.1| ribosomal large subunit pseudouridine synthase B [Actinomyces sp.
           oral taxon 848 str. F0332]
 gi|269211580|gb|EEZ77920.1| ribosomal large subunit pseudouridine synthase B [Actinomyces sp.
           oral taxon 848 str. F0332]
          Length = 247

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 74/238 (31%), Positives = 116/238 (48%), Gaps = 1/238 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK 69
            T +R+ KV+AR G+ SRR  E +IAQ RV V+G ++      V      I VDG+ ++ 
Sbjct: 7   PTGERLQKVLARNGVGSRRACEGLIAQGRVSVDGHVVRELGTRVDPVASVIHVDGIRVQT 66

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                    +KP G+V+T  D  GR  +   +     R+  VGRLD +TEGL+LL+NDG 
Sbjct: 67  DSSLLTLALYKPPGVVSTMYDDMGRPGLAQYVEDRPERLYHVGRLDQDTEGLILLSNDGE 126

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P  +  + Y  R  G V +    +L++GI ++       +  L      N+ V
Sbjct: 127 LTHRLTHPKYEVPKTYIARVEGSVTRGLGRVLERGITLEDGPARVDRFILRESAPRNSIV 186

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + L  G+NR ++++       V  L+R+ +G   +G L  G TR V+   L   +  
Sbjct: 187 EITLHSGRNRIVRRMMAEVGHPVMELVRMKFGTVVVGHLKPGKTRVVAGSELGALMKL 244


>gi|114046458|ref|YP_737008.1| pseudouridine synthase, Rsu [Shewanella sp. MR-7]
 gi|113887900|gb|ABI41951.1| Pseudouridine synthase, Rsu [Shewanella sp. MR-7]
          Length = 236

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 114/233 (48%), Gaps = 11/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-RAAVNVMST----DHIEVDGVPLR 68
            R++K +A+ GI+SRRE  R+I   R+ +NG + +   AV+V +     D + +D  P+ 
Sbjct: 1   MRLAKYLAQCGISSRREACRLIEAGRISLNGKIAKHTDAVHVDADGHCLDSLCLDEKPIS 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            AE    W+++K   + T     D   +   +L     R+  VGRLD ++ GLLLLTNDG
Sbjct: 61  GAEALSYWIFNKA--VGTDCRLLDADKSSLLHLLPTTPRLYPVGRLDKDSRGLLLLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS    + Y V+     +   +  +  G+  + +     QVT      S+  
Sbjct: 119 ELTHKLMHPSFAHSKTYHVQLDRPFNDAFIEQMASGVQYKEVRTLPCQVTRL----SDVS 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             + L +G NR+I+++     +KV  L R++     LG+L  G  R +S + +
Sbjct: 175 FEIVLTQGLNRQIRRMSNALGYKVVDLQRVALMTLTLGSLAEGEMRPLSPEEV 227


>gi|88808924|ref|ZP_01124433.1| Pseudouridine synthase, Rsu [Synechococcus sp. WH 7805]
 gi|88786866|gb|EAR18024.1| Pseudouridine synthase, Rsu [Synechococcus sp. WH 7805]
          Length = 247

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 77/241 (31%), Positives = 118/241 (48%), Gaps = 1/241 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T QR+ K+IA AGI SRR  E ++ Q RVKVNG L        +  D +EVDG PL++A 
Sbjct: 2   TRQRLQKLIAAAGICSRRRAEDLLRQHRVKVNGQLAAIGDQADLDQDDVEVDGRPLQRAL 61

Query: 72  RTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             R L L   P  + +       ++ +      +   +  VGRLD  + G LLL+N G L
Sbjct: 62  VPRVLLLNKPPGVICSCRDPQQRKTVLDLVPAHLRDGLHPVGRLDAESRGALLLSNQGEL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + YRV   G   + +L   ++G+V+ G      +VTL      ++ + 
Sbjct: 122 TLQLTHPRYNHCKTYRVTVAGLPPEKQLRQWRRGVVLDGTVTRPAEVTLLEGTTRSSVLE 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           V LREG+NR+I+++      +V  L RI+ G   LG++  G  RE+S++     +     
Sbjct: 182 VVLREGRNRQIRRIALSLGHRVLDLQRIAIGDLMLGSVAEGCWRELSRQEWSGLIQHRGR 241

Query: 251 E 251
            
Sbjct: 242 P 242


>gi|154497957|ref|ZP_02036335.1| hypothetical protein BACCAP_01937 [Bacteroides capillosus ATCC
           29799]
 gi|150272947|gb|EDN00104.1| hypothetical protein BACCAP_01937 [Bacteroides capillosus ATCC
           29799]
          Length = 246

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 81/245 (33%), Positives = 125/245 (51%), Gaps = 4/245 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K+++ AG+ASRR  E  +   RV VNG              D I +DG P+R A  
Sbjct: 3   ERIQKILSAAGLASRRRAEEYLTAGRVTVNGRTAA-LGEKADPQRDDIRLDGKPVRPAGA 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G VTT SD  GR TV   +    +RV  VGRLD+++EGLLL+T+DG   +
Sbjct: 62  HTYLMLYKPRGYVTTLSDERGRRTVAQLVSGCGARVWPVGRLDLDSEGLLLMTDDGNFTQ 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-SNAWVTV 191
            L  PS Q  + Y V   G VD+     L   + + GI     ++ + +++G   A ++V
Sbjct: 122 RLIHPSHQVEKEYLVTVEGDVDRAIPV-LSGPMELDGIPLAPARIGVLSREGADRARLSV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++      +V RL R+  G   LG L  G  R ++ + LR  LG     
Sbjct: 181 VIHEGRNRQVRRMCALAGLEVKRLKRVREGGLALGRLRPGEWRRLTPQELRLALGERGST 240

Query: 252 EAQVN 256
               +
Sbjct: 241 VPGKD 245


>gi|108799895|ref|YP_640092.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium sp.
           MCS]
 gi|119869005|ref|YP_938957.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium sp.
           KMS]
 gi|126435523|ref|YP_001071214.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium sp.
           JLS]
 gi|108770314|gb|ABG09036.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium sp.
           MCS]
 gi|119695094|gb|ABL92167.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium sp.
           KMS]
 gi|126235323|gb|ABN98723.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium sp.
           JLS]
          Length = 247

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 74/239 (30%), Positives = 111/239 (46%), Gaps = 4/239 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPL 67
                 R+ KV+++AGIASRR  E+MI   RV+V+G ++      V  T   I VDG  +
Sbjct: 2   TEPDGVRLQKVLSQAGIASRRVAEKMILDGRVEVDGHIVTELGTRVDPTAADIRVDGTRV 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLL 124
              +       +KP G+ +T SD  GR  + D +            VGRLD +TEGL+LL
Sbjct: 62  LLDDTLVHLAINKPRGMHSTMSDDRGRPCIGDLVEHRVRGNKGLFHVGRLDADTEGLMLL 121

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG LA  L  PS +  + Y     G V +     L+ G+ +           +     
Sbjct: 122 TNDGELAHRLMHPSYEVPKTYVATVLGTVPRGLGKKLRAGVELDDGPARVDDFAVVDAMP 181

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
             + V V L EG+ R ++++     + V  L+R   G   LG    GS R +++K + E
Sbjct: 182 GRSMVRVTLHEGRKRIVRRLLAAVGFPVQELVRTDIGAVSLGEQRPGSIRVLTRKEIGE 240


>gi|332295067|ref|YP_004436990.1| pseudouridine synthase Rsu [Thermodesulfobium narugense DSM 14796]
 gi|332178170|gb|AEE13859.1| pseudouridine synthase Rsu [Thermodesulfobium narugense DSM 14796]
          Length = 248

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 64/249 (25%), Positives = 116/249 (46%), Gaps = 3/249 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK-AE 71
            R++K ++ +G+ SRR+ E +I   +V+VN  ++   +  V    D ++V+G  ++   +
Sbjct: 1   MRINKFLSFSGLTSRRKAEDLILSGKVEVNDKVISDLSYKVDPNKDVVKVNGRLVKIRKK 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R  L  Y     L     DP G  T+ + +  +  R+   GRLD ++EGLLLLT+DG  A
Sbjct: 61  RHYLLFYKPRWVLTALGKDPGGLKTLDEYIKDLKIRLFPAGRLDFDSEGLLLLTDDGDFA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  PS + ++ Y+V  +   D      +  G V+ G         +       +W+ +
Sbjct: 121 HKIHHPSFEVVKKYQVLVNPIFDIVDKEKVLSGCVLMGKYVKPDSFKILKDLSDASWLEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
              EG    +K+  +   + V RLIR++ G F+L  +  GS R +S++ +      +  E
Sbjct: 181 AFHEGMKHLVKEYLKKMGYSVKRLIRVAIGDFRLTGV-PGSYRWLSEEEVSNFKKRYFGE 239

Query: 252 EAQVNLDAP 260
               N    
Sbjct: 240 MTGDNDGKY 248


>gi|317488196|ref|ZP_07946767.1| RNA pseudouridylate synthase [Eggerthella sp. 1_3_56FAA]
 gi|316912701|gb|EFV34239.1| RNA pseudouridylate synthase [Eggerthella sp. 1_3_56FAA]
          Length = 285

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 68/273 (24%), Positives = 107/273 (39%), Gaps = 33/273 (12%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE 71
           P R+ K +ARAG ASRR  E ++   RV VNG ++      V    D + VDG  +R A+
Sbjct: 13  PMRLQKFLARAGAASRRGSENLMTAGRVTVNGKVVTELGSKVDPLVDEVAVDGAVVRLAD 72

Query: 72  RTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + L+     + T       R+         +  +  +GRLD +T GLLL + DG L
Sbjct: 73  GPVTIMLHKPAGFVTTMSDPQGRRTVAELVPTERYPGLFPIGRLDFDTTGLLLFSTDGEL 132

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA--- 187
              L  P     + Y     G+  +  L LL++GI +         V +     +     
Sbjct: 133 GNGLLHPKHHVTKRYLACVEGRPTERDLALLRRGIELDDGPTQPADVRVVEGGAARHAER 192

Query: 188 ----------------------------WVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
                                        V +G+REG+ R++K++       V  L R S
Sbjct: 193 LLEIPAAVPPRSSKEYAAVCEGRATRRSIVRLGIREGRKRQVKRMLAAVGHPVLALHRDS 252

Query: 220 YGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           +GP +LG L  G+ R +  + +          E
Sbjct: 253 FGPLELGDLPRGAWRALDAEEVAALHQAIGRAE 285


>gi|284007498|emb|CBA72981.1| ribosomal large subunit pseudouridine synthase B [Arsenophonus
           nasoniae]
          Length = 322

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 83/304 (27%), Positives = 129/304 (42%), Gaps = 10/304 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPL 67
           +    +++ KV+AR G  SRRE+E  I   R+ V+G L      + V +   I +DG  L
Sbjct: 18  KKQKSEKLQKVLARCGYGSRREIESFIQSGRISVDGQLATLGDRIEVKANTKIRLDGHLL 77

Query: 68  RKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           R  E        L  Y     L T H      +          SR I++GRLD+NT GLL
Sbjct: 78  RIKEAEKSICRILAYYKPEGELCTHHDPEGRPTVFDRLPKLTGSRWIAIGRLDVNTCGLL 137

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L T DG LA  L  P  +  R Y VR  G+++  K+  L KG+ ++        +     
Sbjct: 138 LFTTDGELANRLMHPRHEVEREYAVRVFGEINDAKIRQLTKGVQLEDGEASFKTLKFRGG 197

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK--- 238
           +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+     
Sbjct: 198 EGMNQWFNVTLTEGRNREVRRLWEAVGIQVSRLIRVRYGDIYLPKGLPRGGWTELGLVQI 257

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             LR+ +G      +++ ++      +     R               K ++       +
Sbjct: 258 NYLRQLVGLSDETASKIAVEQDRRRIKANQIRRAVKRHTQVSSMRVANKRATGAAKGHNK 317

Query: 299 KKLA 302
               
Sbjct: 318 PARK 321


>gi|168214957|ref|ZP_02640582.1| ribosomal small subunit pseudouridine synthase B [Clostridium
           perfringens CPE str. F4969]
 gi|182626336|ref|ZP_02954091.1| ribosomal small subunit pseudouridine synthase B [Clostridium
           perfringens D str. JGS1721]
 gi|170713593|gb|EDT25775.1| ribosomal small subunit pseudouridine synthase B [Clostridium
           perfringens CPE str. F4969]
 gi|177908355|gb|EDT70900.1| ribosomal small subunit pseudouridine synthase B [Clostridium
           perfringens D str. JGS1721]
          Length = 236

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 69/228 (30%), Positives = 116/228 (50%), Gaps = 2/228 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKAER 72
           +R+ K +AR G+ASRR+ E +I   +VKVN I+++     V  +  +   +   +R  E 
Sbjct: 3   ERLQKYMARCGVASRRKCEEIICSGKVKVNDIVVDSLGTKVDPSVDVVSVNNKVIRPEEN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G VTT+ D   R T+ D +     R+  +GRLD ++ GLLLLTNDG +  
Sbjct: 63  KVYIMLNKPEGYVTTNKDEKNRKTILDIVKVN-ERIYPIGRLDYDSSGLLLLTNDGDVYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y     G   ++++N  +KG+ I      + ++ L  +  ++  V + 
Sbjct: 122 KIIHPRVNLNKEYIALVKGIFTEEEMNKFRKGVDIGDYKTAECEIELLEKYTNSCKVKII 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           + EGKNR+I+++   FN +V  L R + G   L  L  G  R +S   
Sbjct: 182 IHEGKNRQIRRMCAAFNHEVVSLKREAIGSLNLKNLKKGEWRYLSSSE 229


>gi|329943240|ref|ZP_08292014.1| hypothetical protein G5Q_0929 [Chlamydophila psittaci Cal10]
 gi|332287819|ref|YP_004422720.1| putative 16S pseudouridine synthase [Chlamydophila psittaci 6BC]
 gi|313848391|emb|CBY17395.1| putative 16S pseudouridine synthase [Chlamydophila psittaci RD1]
 gi|325507299|gb|ADZ18937.1| putative 16S pseudouridine synthase [Chlamydophila psittaci 6BC]
 gi|328814787|gb|EGF84777.1| hypothetical protein G5Q_0929 [Chlamydophila psittaci Cal10]
 gi|328915079|gb|AEB55912.1| ribosomal large subunit pseudouridine synthase B [Chlamydophila
           psittaci 6BC]
          Length = 232

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 67/229 (29%), Positives = 105/229 (45%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R++K +A +G+ASRR+ + +I    V VNG +     V V   TD ++VDG  +   ++
Sbjct: 4   VRLNKFLASSGVASRRKCDEIIFSGHVTVNGRVAPGPFVLVDEETDTVKVDGRRVGMTKK 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               ++     L ++     G   V D    +  RV +VGRLD  T GL+L+TNDG  + 
Sbjct: 64  VYFMVHKPLGYLCSSERKFPGDKLVIDLFSHLPYRVFTVGRLDKETSGLILVTNDGEFSN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  PS    + Y ++    V    L  L +G VI G         +  +K     + + 
Sbjct: 124 KIIHPSFGITKEYLLKVSRDVTAKNLEDLMEGTVIDGKRVRP----VSVEKIRRGTLKII 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGK  EI+   E     +  L RI  G F LG L  G  RE++   +
Sbjct: 180 VNEGKKHEIRLFAEAAGLSILELSRIRIGSFVLGGLRYGEYRELTDAEI 228


>gi|301062561|ref|ZP_07203199.1| pseudouridylate synthase [delta proteobacterium NaphS2]
 gi|300443326|gb|EFK07453.1| pseudouridylate synthase [delta proteobacterium NaphS2]
          Length = 295

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 74/239 (30%), Positives = 118/239 (49%), Gaps = 1/239 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
             P R++++++ AG+ SRR+ ++ I   R+ VNG  +           D I VDG  +  
Sbjct: 54  EKPWRLNRILSSAGLTSRRKADQWILSGRITVNGKPVNAPGTTAFWGRDDIRVDGQKIPL 113

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             +    + +KP G + +  DP+GR  V D    I  RV  VGRLD +T GLLLLTNDG 
Sbjct: 114 PPKKVYLMLNKPFGTICSLDDPEGRPLVTDLTKDIPIRVYPVGRLDFDTLGLLLLTNDGE 173

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  L  P     + Y+V   G +  + L  L+ GI +     G  +  L  +    + +
Sbjct: 174 FAHRLTHPRFHVPKTYKVTVQGAISDEALKRLQTGITLNDGPAGRARTELINRNNEKSIL 233

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + + +GK+R+++++ E   + V  LIRIS+G  QLG L  G  R +  + L +     
Sbjct: 234 RMTITQGKSRQVRRMLEKVGFTVIHLIRISFGTLQLGDLKIGHHRHLDSEELSKLKKMA 292


>gi|329894510|ref|ZP_08270324.1| Ribosomal large subunit pseudouridine synthase B [gamma
           proteobacterium IMCC3088]
 gi|328923035|gb|EGG30360.1| Ribosomal large subunit pseudouridine synthase B [gamma
           proteobacterium IMCC3088]
          Length = 303

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 81/271 (29%), Positives = 118/271 (43%), Gaps = 5/271 (1%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            K    ++   +++ KV+ARAG+ SRRE+E+ I+  RVK++G +       V     IEV
Sbjct: 21  KKTESSKSQKDEKLQKVLARAGLGSRREMEKWISDGRVKLDGRIA-ELGDRVCDNAAIEV 79

Query: 63  DGVPLRKAERTR---LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           DG  L +A       L  +     + T       R+           R IS+GRLD NT 
Sbjct: 80  DGQALSRAPAEAVRCLLYHKPTGEVCTRKDPEGRRTVFERLPKVKGGRWISIGRLDYNTS 139

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL T DG LA  L  PS    R Y VR  G+ D D L  L  G+ +         +  
Sbjct: 140 GLLLFTTDGELANALMHPSAVIEREYMVRVMGEWDTDTLQRLIHGVELDDGFARFTDIQD 199

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
               G N W  V L EG+NRE+++++E     V+RL R+ YG   +   +  G   E+ +
Sbjct: 200 GGGDGINHWFYVVLMEGRNREVRRLWESQGLTVSRLKRVRYGEVFIPSKVKQGKWMELDQ 259

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVR 269
           K +        L    V   +         +
Sbjct: 260 KDVDVLYAMASLPPKSVPNLSVDERKNMDRQ 290


>gi|297198681|ref|ZP_06916078.1| pseudouridine synthase [Streptomyces sviceus ATCC 29083]
 gi|297147171|gb|EDY58604.2| pseudouridine synthase [Streptomyces sviceus ATCC 29083]
          Length = 314

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 112/233 (48%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
               +R+ K++ARAG  SRR  E +I Q RV+VNG ++      V    D ++VDG+ + 
Sbjct: 74  EQEGERLQKILARAGYGSRRSCEELIEQARVEVNGEIVLEQGKRVDPERDEVKVDGLTVA 133

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   L      + T   +   +  + D + +  +R+  VGRLD  TEG++LLTN G
Sbjct: 134 TQSYQFFSLNKPAGVVSTMEDNEGRQ-CLGDYVTNRETRLFHVGRLDTETEGVILLTNHG 192

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     +VY     G + +D    LK GI ++          +  Q G N  
Sbjct: 193 ELAHRLTHPRYGVKKVYLAHIVGPIPRDLGKQLKDGIQLEDGYAKADHFRVVEQTGKNYL 252

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L EG+   ++++     + V++L+R+++GP  LG   +G  R +S   +
Sbjct: 253 VEVTLHEGRKHIVRRMLAEAGFPVDKLVRVAFGPITLGDQKSGWLRRLSNTEV 305


>gi|290968302|ref|ZP_06559844.1| pseudouridylate synthase [Megasphaera genomosp. type_1 str. 28L]
 gi|290781661|gb|EFD94247.1| pseudouridylate synthase [Megasphaera genomosp. type_1 str. 28L]
          Length = 238

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 95/229 (41%), Gaps = 7/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K ++ +G  SR+EV  +  Q RV VNG +    A  V +  D ++VD  P+   E  
Sbjct: 6   RLDKWLSHSGQGSRKEVRDLCRQGRVLVNGEICRDGAQLVETGVDRVQVDRQPVCYEEFY 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+     +  T          F   P     V  VGRLD +T GLLLLTNDG  A  
Sbjct: 66  YIMLHKPRGVISATTDAACRTVLDFLPPPCRTGGVFPVGRLDKDTTGLLLLTNDGVWAHR 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           +  P     +VY     G + +D        IV+  G      +      +     V + 
Sbjct: 126 ILSPKKHCYKVYEATVSGSIPEDLTVRFASRIVLADGTVCLPARALRIDGQ----TVEIT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
           + EG+  ++K++      +V  L R   G   L   L  G  R++++  
Sbjct: 182 VYEGRYHQVKRMCAAVGLQVLSLHRHKIGALGLDPALSPGQWRKLTEVE 230


>gi|37526345|ref|NP_929689.1| 23S rRNA pseudouridylate synthase B [Photorhabdus luminescens
           subsp. laumondii TTO1]
 gi|36785776|emb|CAE14826.1| unnamed protein product [Photorhabdus luminescens subsp. laumondii
           TTO1]
          Length = 310

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 90/305 (29%), Positives = 128/305 (41%), Gaps = 7/305 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV-NVMSTDHIEVDGVPLRK 69
              +++ K++AR+G  SRRE+E  I Q RV V+G +        V     I +DG  L  
Sbjct: 6   QKSEKLQKILARSGHGSRREIEGYIQQGRVSVDGKIATLGDRLEVQPATKIRLDGRILNI 65

Query: 70  AERT-----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            E        L  Y     L T H      +        + SR I+VGRLD+NT GLLL 
Sbjct: 66  KESQKTVCRVLAYYKPEGELCTRHDPEGRPTVFDRLPKLLGSRWIAVGRLDVNTCGLLLF 125

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T DG LA  L  PS +  R Y VR  G+VD  KL  L KGI ++        +     +G
Sbjct: 126 TTDGELANRLMHPSREVEREYAVRVFGEVDDAKLKQLAKGIQLEEGPASFRTIAFKGGEG 185

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  +    
Sbjct: 186 MNQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIGLPKGLPRGGWTELGLEQTNY 245

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                 L E  V+  A       L  ++     +             +     ++    T
Sbjct: 246 LRQLVDLNEETVSKVAVGRDQRRLKANQIRRAVKRHAQVASRPSAGKRPGSSRQKAGRTT 305

Query: 304 PVHRR 308
               R
Sbjct: 306 APKGR 310


>gi|114046295|ref|YP_736845.1| ribosomal small subunit pseudouridine synthase A [Shewanella sp.
           MR-7]
 gi|113887737|gb|ABI41788.1| ribosomal small subunit pseudouridine synthase A [Shewanella sp.
           MR-7]
          Length = 235

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 47/234 (20%), Positives = 99/234 (42%), Gaps = 8/234 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+ K I  +   +R   ++ + +  +  +G++++ +   V+    + +DG P+   
Sbjct: 4   SRPVRLDKFICESTSLTRSLAKKALHRGEITCDGVVVKDSGFKVLEGMQVCLDGEPISLV 63

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              R  + +KP+  + +  D    S +          +   GRLD +T GL+L+T+DG  
Sbjct: 64  -GERYLMLNKPVDTICSTIDEAYPSVLSLLDIEKPETLHIAGRLDADTTGLVLITSDGQW 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAW 188
           +  +  P     + Y V     VD+  + +   G+ +  +        + +   +     
Sbjct: 123 SHRITSPKKDCGKRYLVALADPVDESLVGIFAAGVELRNEDGLTKPAVLEIIEPQ----L 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           V + + EGK  ++K++F      V  L R S G  +L   L  G  R ++ + +
Sbjct: 179 VRLTITEGKYHQVKRMFAAVGNHVVGLHRESIGRIELDSDLAPGEWRYLTSEEI 232


>gi|304396082|ref|ZP_07377964.1| pseudouridine synthase [Pantoea sp. aB]
 gi|304356451|gb|EFM20816.1| pseudouridine synthase [Pantoea sp. aB]
          Length = 296

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 91/299 (30%), Positives = 130/299 (43%), Gaps = 12/299 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV--MSTDHIEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E MIA  RV V+G +       V    +  I +DG  +  A
Sbjct: 2   SEKLQKVLARAGHGSRREIESMIAAGRVSVDGKIAT-LGDRVESSKSLKIRIDGHLVSIA 60

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E        L  Y     L T        +          SR I+VGRLD+NT GL+L T
Sbjct: 61  ESATEVCRVLAYYKPEGELCTRSDPEGRPTVFDRLPRLRGSRWIAVGRLDVNTCGLMLFT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  GQVD DK+  L KG+ ++        +     +G 
Sbjct: 121 TDGELANRLMHPSREVEREYAVRVFGQVDDDKIRQLSKGVQLEDGPAAFKTLKFGGGEGI 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           N W  V L EG+NRE+++++E    +V+RL+R+ YG   L   L  G   E+    L   
Sbjct: 181 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLMRVRYGDITLPKGLPRGGWTELD---LPAV 237

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                L E        +   +   R + N I       T++             K+ + 
Sbjct: 238 NYLRNLVELDDETVTKLVVEKDRRRTKANQIRRAVKRHTKVSSTPRAPRRNPGSKRNSG 296


>gi|317124964|ref|YP_004099076.1| pseudouridine synthase [Intrasporangium calvum DSM 43043]
 gi|315589052|gb|ADU48349.1| pseudouridine synthase [Intrasporangium calvum DSM 43043]
          Length = 334

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 76/233 (32%), Positives = 122/233 (52%), Gaps = 1/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
           +    R+ K++A AG+ SRR  E +I Q RV+V+G ++    V +   +  + VDGV + 
Sbjct: 93  DPDGVRLQKLMAAAGVGSRRVCENLIEQGRVEVDGQVITELGVRINPQSQVVHVDGVRVN 152

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             E      ++KP G+VTT  D  GR ++ D + +   R+  VGRLD +TEGLLLLTNDG
Sbjct: 153 LDEERVYLAFNKPKGVVTTMHDELGRISLADYVGNREQRLFHVGRLDADTEGLLLLTNDG 212

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L+ P+   L+ Y     G V +D    L++G+ ++          +   +   A 
Sbjct: 213 DLAHRLQHPAYGVLKTYLATVRGPVGRDVGKQLREGVELEDGPVTVDSFKVVDSQPGKAL 272

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + V L EG+   ++++ E     V  L+R   GP +LG L +G  R ++K  +
Sbjct: 273 IEVVLHEGRKHVVRRMLELVGHPVLELVRTEVGPIRLGDLRSGRMRRLNKAEI 325


>gi|297161649|gb|ADI11361.1| putative pseudouridine synthase [Streptomyces bingchenggensis
           BCW-1]
          Length = 333

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 67/233 (28%), Positives = 110/233 (47%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
               +R+ KV+ARAG+ SRR  E +I Q RV+VNG ++    + V    D I+VDG+ + 
Sbjct: 93  EQEGERLQKVLARAGMGSRRACEELIDQARVEVNGKIVTEQGLRVDPEKDEIKVDGLTVA 152

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   L      + T       +  + D + +  +R+  VGRLD  TEG++LLTN G
Sbjct: 153 TQSYLFFALNKPAGVVSTMEDPDGRQ-CLGDYVTNRETRLFHVGRLDTETEGIILLTNHG 211

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L+  L  P     + Y     G + +D    LK GI ++          +    G N  
Sbjct: 212 ELSHRLTHPRYGVTKTYLAAIQGPLPRDLGKRLKDGIQLEDGYARADHFRVVQNTGKNYL 271

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L EG+   ++++     + V++L+R ++GP  LG   +G  R ++   +
Sbjct: 272 VEVSLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPIALGDQKSGWLRRLTNTEV 324


>gi|293192784|ref|ZP_06609679.1| ribosomal large subunit pseudouridine synthase B [Actinomyces
           odontolyticus F0309]
 gi|292820031|gb|EFF79029.1| ribosomal large subunit pseudouridine synthase B [Actinomyces
           odontolyticus F0309]
          Length = 249

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 89/236 (37%), Positives = 122/236 (51%), Gaps = 2/236 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE 71
             R+ KV+A+AG+ASRR  E+MIA  RV V+G ++    V V  T   I VDG  L   E
Sbjct: 10  GVRLQKVLAQAGVASRRASEQMIADGRVSVDGTVVRNQGVRVDPTKQVIHVDGERLILDE 69

Query: 72  RTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               +   +KPIG V+T SDP+GR T+ D +     R+  VGRLDI+T GLLLLTNDG L
Sbjct: 70  TKHIVLAVNKPIGTVSTMSDPEGRPTIADLIADYPERLYHVGRLDIDTSGLLLLTNDGEL 129

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P  +  + Y  R HG+V       L  GI ++          +    G    V 
Sbjct: 130 ANRLTHPKYEIRKTYVARLHGEVKPGVKRTLMNGIELEDGPIKVDSFRIVDTYGDITTVE 189

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + + EG+NR ++++ E   + V  L+R  +GP  L  L  G+TR V    L    G
Sbjct: 190 IVVHEGRNRLVRRMMEAVGYPVRELVRTGFGPISLDHLKQGTTRRVKGNALSALYG 245


>gi|323525722|ref|YP_004227875.1| pseudouridine synthase [Burkholderia sp. CCGE1001]
 gi|323382724|gb|ADX54815.1| pseudouridine synthase [Burkholderia sp. CCGE1001]
          Length = 618

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 84/352 (23%), Positives = 142/352 (40%), Gaps = 16/352 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRR++E +I   RV VNG         +M TD + ++
Sbjct: 208 KRVLSADDDAPKLHKVLAEAGMGSRRDMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRIN 266

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 267 GKPVKRKLANKPPRVLLYHKPTGEIVSHADPEGRPSVFDKLPPMKTAKWLAVGRLDFNTE 326

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 327 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELAEGMRQKLLNGVELDDGPANFLRIRD 386

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+  
Sbjct: 387 GGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPISLPKGLKRGRWEELED 446

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRD----------RPNIISEVPDDFTRMKKN 288
             +R  +    L+           + E    D          R  ++        + +  
Sbjct: 447 NQVRALMASVGLKAPSEERGGRNAAPERKQPDPMQTSMGFISREPVLMSHHRFEQQPRGQ 506

Query: 289 SSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
             +             +        V  + G      +  G R+ +  R+PS
Sbjct: 507 GRRGAAGGGFGGAGAGLGGGYGNRGVGRSAGGFGGTGAPRGGRDVDGNRAPS 558


>gi|239940238|ref|ZP_04692175.1| putative pseudouridine synthase [Streptomyces roseosporus NRRL
           15998]
 gi|239986727|ref|ZP_04707391.1| putative pseudouridine synthase [Streptomyces roseosporus NRRL
           11379]
 gi|291443668|ref|ZP_06583058.1| pseudouridine synthase [Streptomyces roseosporus NRRL 15998]
 gi|291346615|gb|EFE73519.1| pseudouridine synthase [Streptomyces roseosporus NRRL 15998]
          Length = 427

 Score =  164 bits (416), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 109/233 (46%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLR 68
               +R+ KV+ARAG+ SRR  E +I Q RV+VNG ++    + V    D I+VDG+ + 
Sbjct: 187 EQEGERLQKVLARAGMGSRRACEELIEQARVEVNGEIVVEQGMRVDVHKDEIKVDGLTVA 246

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   L      + +       +  + D + +  +R+  VGRLD  TEG+++LTN G
Sbjct: 247 AQSYLFFALNKPAGVVSSMEDPDGRQ-CLGDYVNNRETRLFHVGRLDTETEGIIMLTNHG 305

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     + Y     G + +D    LK GI ++          +    G N  
Sbjct: 306 ELAHRLTHPKYGVKKTYLAAIQGPLPRDLGKRLKDGIQLEDGYARADHFRVVENTGKNYL 365

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L EG+   ++++     + V RL+R S+GP  LG   +G  R ++   +
Sbjct: 366 VEVTLHEGRKHIVRRMLAEAGFPVERLVRTSFGPIPLGDQKSGWLRRLTNTEV 418


>gi|300723349|ref|YP_003712652.1| Ribosomal large subunit pseudouridine synthase B [Xenorhabdus
           nematophila ATCC 19061]
 gi|297629869|emb|CBJ90487.1| Ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Xenorhabdus nematophila ATCC 19061]
          Length = 307

 Score =  164 bits (416), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 85/306 (27%), Positives = 128/306 (41%), Gaps = 7/306 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLR 68
           +   +++ K++AR+G  SRRE+E  I Q R+ ++G        + V  +  I +DG  L 
Sbjct: 2   SDKTEKLQKILARSGHGSRREIEGYIQQGRISIDGKTATLGDRIEVKPSIKIRLDGRILN 61

Query: 69  KAERT-----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
             E        L  Y     L T H      +          +R I+VGRLDINT GLLL
Sbjct: 62  IKEPQKTVCRVLAYYKPEGELCTRHDPEGRPTVFDRLPRMQGARWIAVGRLDINTCGLLL 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T DG LA  L  PS +  R Y VR  G+VD  KL  L +G+ ++        +T    +
Sbjct: 122 FTTDGELANRLMHPSQEVEREYAVRVFGEVDTAKLRQLTQGVQLEDGPASFKTITFKGGE 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  +   
Sbjct: 182 GINQWYNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDINLPKGLPRGGWTELGLEQTN 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
                  L +  V   A       +  ++     +               +   +     
Sbjct: 242 YLRQLVGLGDEMVTKVAVERDQRRIKANQIRRAVKRHAKVASRPAGKRPASSSRQNAGRK 301

Query: 303 TPVHRR 308
           T    R
Sbjct: 302 TTPKGR 307


>gi|294501579|ref|YP_003565279.1| RNA pseudouridylate synthase [Bacillus megaterium QM B1551]
 gi|294351516|gb|ADE71845.1| RNA pseudouridylate synthase [Bacillus megaterium QM B1551]
          Length = 238

 Score =  164 bits (416), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 62/224 (27%), Positives = 99/224 (44%), Gaps = 4/224 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    VKV+G  ++ A V+V      I V G  +   E 
Sbjct: 1   MRLDKLLSTIGYGSRKEVKGLLKTGAVKVDGTAVKDAKVHVNPDEQEITVHGEAVSYREF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T             L         VGRLD +TEGLLLLTNDG LA 
Sbjct: 61  VYFMLHKPQGVISATEDSLHETVLDLLELDDAVYDPFPVGRLDKDTEGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y  + +  V ++     ++G+ +         ++ + T  G  + + +
Sbjct: 121 QLLSPKKHVPKTYFAKINAPVTEEDAEAFRQGVTLDDGYVTKSAELKILT-SGVESEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
            + EGK  ++K++FE    KV  L R+S G   L   L  G  R
Sbjct: 180 TIVEGKFHQVKRMFEARGKKVTYLKRLSMGALLLDESLDLGEYR 223


>gi|292488789|ref|YP_003531676.1| putative 16S pseudouridylate 516 synthase [Erwinia amylovora
           CFBP1430]
 gi|292899940|ref|YP_003539309.1| ribosomal small subunit pseudouridine synthase A [Erwinia amylovora
           ATCC 49946]
 gi|291199788|emb|CBJ46909.1| ribosomal small subunit pseudouridine synthase A [Erwinia amylovora
           ATCC 49946]
 gi|291554223|emb|CBA21490.1| putative 16S pseudouridylate 516 synthase [Erwinia amylovora
           CFBP1430]
 gi|312172942|emb|CBX81197.1| putative 16S pseudouridylate 516 synthase [Erwinia amylovora ATCC
           BAA-2158]
          Length = 234

 Score =  164 bits (416), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 54/229 (23%), Positives = 100/229 (43%), Gaps = 3/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I+R    SR    R +  ++V V+G ++   +  + +   +  DG  L +    
Sbjct: 1   MRLDKFISRQLEVSRAIAARELRARKVTVDGEVVREGSYQLSADSTVAYDGKVLEQQLGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP+G V +  DPD  + ++        R+ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPVGYVCSTDDPDHPTILYFLEEPGAFRLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D       G+ +           L     +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESAISDDTAQQFADGVQLHNEKTLTKPAMLAVIAPN--LVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G  +L   L  G  R +S + +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVALHRERIGAIRLDSDLQPGEYRPLSAEEI 227


>gi|330939561|gb|EGH42880.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. pisi str. 1704B]
          Length = 299

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 87/298 (29%), Positives = 132/298 (44%), Gaps = 10/298 (3%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG         V   D I
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDAT-LGQRVDLHDAI 62

Query: 61  EVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            VDG  +++ E     R  +        + T        +           R I++GRLD
Sbjct: 63  SVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           INT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++       
Sbjct: 123 INTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPARFT 182

Query: 176 QVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           RE+S+  + + L   +  +          + + + R +      +           + 
Sbjct: 243 REMSQYEV-DILAAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVRTLRPAA 299


>gi|269102962|ref|ZP_06155659.1| ribosomal large subunit pseudouridine synthase B [Photobacterium
           damselae subsp. damselae CIP 102761]
 gi|268162860|gb|EEZ41356.1| ribosomal large subunit pseudouridine synthase B [Photobacterium
           damselae subsp. damselae CIP 102761]
          Length = 385

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 93/360 (25%), Positives = 144/360 (40%), Gaps = 18/360 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E MI   RV V+G + +        T  + +DG  +     
Sbjct: 2   SEKLQKVLARAGQGSRREIELMIQNGRVSVDGDVAKLGDRLEDMTASVRIDGRRIELVAS 61

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L        L T H     R+           R +SVGRLD NT G+LL T D
Sbjct: 62  TDEVCRVLAYNKPEGELCTRHDPEGRRTVFDRLPRLNNGRWVSVGRLDANTSGMLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS    R Y VR  G++ +D +  L +G+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSHSVQREYMVRVFGEISEDMVRNLVRGVELEDGMARFEDVVYAGGEGMNH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV---SKKILRE 243
              V + EG+NRE+++++      V+RL R+ YG   L   L  G   E+       LRE
Sbjct: 182 TFYVVITEGRNREVRRLWASQGVTVSRLKRVRYGDIYLSKELPRGGWMELELNDVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG-------LS 296
            +G     E ++ ++            R     E   D T  ++ + +++         +
Sbjct: 242 LVGLQPETETELTVEGQKRKRNVRQIRRAVRRFEERADNTNSRRRNDRRSTTRNSDVEKA 301

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENH--RRSPSFPSKRSLRRTSAKK 354
              K   P  R +        K    S  +    + EN+  RR P      +     A+K
Sbjct: 302 GNDKPRRPSTRSSDVDKAGNQKPRRPSTRNSGADKAENNKPRRQPRQNDADNKGGNKARK 361


>gi|154508819|ref|ZP_02044461.1| hypothetical protein ACTODO_01329 [Actinomyces odontolyticus ATCC
           17982]
 gi|153798453|gb|EDN80873.1| hypothetical protein ACTODO_01329 [Actinomyces odontolyticus ATCC
           17982]
          Length = 249

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 88/236 (37%), Positives = 121/236 (51%), Gaps = 2/236 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAE 71
             R+ KV+A+AG+ASRR  E+MIA  RV V+G ++    V V      I VDG  L   E
Sbjct: 10  GVRLQKVLAQAGVASRRASEQMIADGRVSVDGTVVRNQGVRVDPAKQVIHVDGERLILDE 69

Query: 72  RTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               +   +KPIG V+T SDP+GR T+ D +     R+  VGRLDI+T GLLLLTNDG L
Sbjct: 70  TKHIVLAVNKPIGTVSTMSDPEGRPTIADLIADYPERLYHVGRLDIDTSGLLLLTNDGEL 129

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P  +  + Y  R HG+V       L  GI ++          +    G    V 
Sbjct: 130 ANRLTHPKYEIRKTYVARLHGEVKPGVKRTLMNGIELEDGPIKVDSFRIVDTYGDITTVE 189

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + + EG+NR ++++ E   + V  L+R  +GP  L  L  G+TR V    L    G
Sbjct: 190 IVVHEGRNRLVRRMMEAVGYPVRELVRTGFGPISLDHLKQGTTRRVKGNALSALYG 245


>gi|269968137|ref|ZP_06182172.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           alginolyticus 40B]
 gi|269827268|gb|EEZ81567.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           alginolyticus 40B]
          Length = 233

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 47/230 (20%), Positives = 97/230 (42%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  A+R++  ++I    + V+G + +  A  V     +  +   +      
Sbjct: 1   MRLDKYLCDALGATRKQATKIIKSGDITVDGEVQKSGAFKVPKGAEVMWEDRVIGAPGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + LY     + +     +  +            +   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLYKPADFVCSHEDGYNQ-TAFALLDEPKIENLHFAGRLDVDTTGLVLITDDGKWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     +  D    L++GI+++      +   L+    +   V + +
Sbjct: 120 ITSPKHKCEKTYRVWLVDAIQPDYAEKLEQGIILRNESEATLPARLEIVNEAENEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            EGK  ++K++F     KV  L R   G  +L   L  G  R ++++ + 
Sbjct: 180 VEGKYHQVKRMFAALGNKVEYLHRERIGSIELDEALEPGDYRYLTQEEID 229


>gi|300771415|ref|ZP_07081291.1| pseudouridylate synthase (ribosomal large subunit pseudouridine
           synthase B) [Sphingobacterium spiritivorum ATCC 33861]
 gi|300762085|gb|EFK58905.1| pseudouridylate synthase (ribosomal large subunit pseudouridine
           synthase B) [Sphingobacterium spiritivorum ATCC 33861]
          Length = 441

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 66/229 (28%), Positives = 109/229 (47%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+++ I+ AGI SRR+ + +I    + VNG ++      V    D I+ +G  L++ + 
Sbjct: 207 IRLNRYISNAGICSRRKADELITAGVISVNGEVVTELGSKVDPAKDEIKYNGERLKREKM 266

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + TT    + R+ +     +   R+  VGRLD NT GLLLLTNDG LA 
Sbjct: 267 VYVLLNKPKDYITTTDDPQERRTVMQLVANATKERIYPVGRLDRNTTGLLLLTNDGNLAE 326

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     ++Y V     ++Q   N +  G+ ++        ++   Q GS   V + 
Sbjct: 327 KLSHPRNNISKIYNVELDKSLNQGDFNKIVFGLELEDGFVKPDDLSYV-QGGSKREVGIQ 385

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +  GKNR ++++FE   + V +L R+ Y       L  G  R + +K L
Sbjct: 386 IHSGKNRIVRRIFESLGYDVVKLDRVVYANLTKKDLPRGRWRYLEEKEL 434


>gi|239637925|ref|ZP_04678886.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           warneri L37603]
 gi|239596488|gb|EEQ79024.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           warneri L37603]
          Length = 230

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 56/231 (24%), Positives = 103/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++ + +  VKVN  +++     +    D I V+   +   ++
Sbjct: 1   MRLDKFLANMGVGTRNEVKQSLKKGYVKVNNEVIKSPKTQIDPNEDIITVNDEKIIYIDK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      +V+   D   ++ +          +  VGRLD +TEGLLL+TNDG    
Sbjct: 61  VYIMLNKPSG-VVSATEDDKHQTVIDLIPEYQHLEIFPVGRLDKDTEGLLLITNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+    + Y V     V Q  +   K+G+ +        Q+ +   + S     V 
Sbjct: 120 DLMSPNKHVPKTYEVVSKNDVTQSDVERFKEGLELSDGLVKPAQLEIIENRRS----RVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + EGK  ++K++F     +V +L RI     +L  +L  G  R +++   +
Sbjct: 176 IYEGKYHQVKRMFHEIENEVLQLKRIKIANLELDTSLKLGEFRLLTENDFK 226


>gi|62261679|gb|AAX78007.1| unknown protein [synthetic construct]
          Length = 306

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 86/259 (33%), Positives = 124/259 (47%), Gaps = 9/259 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+  N   +   P+R+ K++A+ GI SRR++E  I Q RVKVNG +           D I
Sbjct: 27  MRRANQNNDKN-PERLQKLLAKYGIGSRRKIEEYIEQGRVKVNGKVAT-LGDKASEADKI 84

Query: 61  EVDGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
             DG  L            +  + +   + T+  + D ++          SR I VGRLD
Sbjct: 85  SFDGKALHSYGQPMTRPRVVIYHKREGEVCTSKDEKDRQTVFDSLPKLAKSRWIMVGRLD 144

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGD 174
           INT GLLL T DG LA  L  PS Q  R Y VR  GQ    + +N LK+GI ++      
Sbjct: 145 INTTGLLLFTTDGDLANRLMHPSYQIEREYAVRVFGQQLSDETINKLKEGIQLEDGMAKF 204

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGST 233
             +     +G+N W  V L EG+NRE++++FE     V+RL RI +G   L   +  G T
Sbjct: 205 NSIKFSGGEGANLWYYVTLSEGRNREVRRMFEAVGVTVSRLTRIRFGDIILPKFVSRGKT 264

Query: 234 REVSKKILREQLGPHLLEE 252
            E++   +        L+E
Sbjct: 265 LELNPSEVNRLRKSVKLKE 283


>gi|332653044|ref|ZP_08418789.1| ribosomal large subunit pseudouridine synthase B [Ruminococcaceae
           bacterium D16]
 gi|332518190|gb|EGJ47793.1| ribosomal large subunit pseudouridine synthase B [Ruminococcaceae
           bacterium D16]
          Length = 237

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 79/235 (33%), Positives = 116/235 (49%), Gaps = 2/235 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+I++ G+ASRR  E  I   RV VNG L +      +  D +EVDG PLR     
Sbjct: 3   ERLQKLISQCGLASRRTAEEWITAGRVTVNGFLAQLGDRADLDRDRVEVDGRPLRGGSPR 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP G VTT SD  GR TV   +     RV  VGRLD+++EGLLL+T+DG L   
Sbjct: 63  TYLMLNKPRGYVTTLSDEKGRKTVAALVSGCGKRVWPVGRLDLDSEGLLLMTDDGELTNS 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  PS Q  + Y V   G V+      L   + + G      +V    + G    +++ +
Sbjct: 123 LLHPSHQVEKEYLVWVTGDVETALPI-LSGPMELDGEPLAPAKVARGRESGGVTQLSITI 181

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGP 247
            +GKNR+++++      +V RL RI  G   L   L  G  R ++ + L      
Sbjct: 182 CQGKNRQVRRMCAQAGLEVTRLKRIREGQVSLDRKLKPGQWRPLTAQELAALRKH 236


>gi|78187542|ref|YP_375585.1| pseudouridine synthase, Rsu [Chlorobium luteolum DSM 273]
 gi|78167444|gb|ABB24542.1| ribosomal large subunit pseudouridine synthase B [Chlorobium
           luteolum DSM 273]
          Length = 250

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 70/247 (28%), Positives = 118/247 (47%), Gaps = 6/247 (2%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVD 63
           N+ ++     R+++ +A  GIASRR  ++M+ + RV +NG+L     V V+   D + VD
Sbjct: 4   NVEKKQNEAVRINRYLAMCGIASRRAADQMVLEGRVTINGVLASEPGVKVVPGKDEVIVD 63

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G    + E  ++++       V T S  +    +  +   +  RV  VGRLD  T G+LL
Sbjct: 64  GSKFAQPEGRKIYILFNKPRNVITTSSDERNREMVLDFIDVNERVYPVGRLDRKTTGVLL 123

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDT 181
           LTNDG LA  L  PS+   + Y         Q  L LL  G+ +          Q  +  
Sbjct: 124 LTNDGMLANKLMHPSSNVKKEYIAVLDAPFPQASLPLLTGGMRLSDTGEKVSPCQAKI-M 182

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             GS  W  + + EGKN +++++F+   ++V RL R +Y    +G L  G  R +++  +
Sbjct: 183 GDGSQVW--ISIHEGKNHQVRRMFKTLGFEVTRLDRPTYAGLTVGDLRRGQWRHLTRTEV 240

Query: 242 REQLGPH 248
           ++     
Sbjct: 241 QQLRHLA 247


>gi|92112979|ref|YP_572907.1| ribosomal large subunit pseudouridine synthase B [Chromohalobacter
           salexigens DSM 3043]
 gi|91796069|gb|ABE58208.1| ribosomal large subunit pseudouridine synthase B [Chromohalobacter
           salexigens DSM 3043]
          Length = 286

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 84/286 (29%), Positives = 125/286 (43%), Gaps = 7/286 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N   +++ KV+ARAG  SRRE+E  IA  RVKVNG +       + + D +  D  P+  
Sbjct: 2   NTPTEKLQKVLARAGFGSRREMETAIADGRVKVNGQVAT-LGDRIETRDRVTFDERPVNL 60

Query: 70  A-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                  R  +        L T       R+           R I+VGRLDINT GLLL 
Sbjct: 61  RDAEEVPRRVIMYNKPEGELCTRRDPEGRRTVFERLPRLKGERWIAVGRLDINTSGLLLF 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T DG LA  L  P+TQ  R Y VR  G V Q+ +N + +G++++        V     +G
Sbjct: 121 TTDGELANRLMHPATQVEREYAVRVMGNVRQEHVNAMVEGVMLEDGPARFTDVQEFGGEG 180

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
            N W  V + EG+NRE+++++E     V+RL R+ YG   L     AG   E+S+  + +
Sbjct: 181 INTWFHVVILEGRNREVRRLWESQGLTVSRLKRVRYGNIFLDKRAKAGEWVELSQDEIDD 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
                 L   +V    P   +                     +++ 
Sbjct: 241 LAQLADLPARKVPELTPDEQNRWSRDKNKRRPVNAMRKPKSSRRSR 286


>gi|330832619|ref|YP_004401444.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Streptococcus suis ST3]
 gi|329306842|gb|AEB81258.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Streptococcus suis ST3]
          Length = 238

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 106/231 (45%), Gaps = 2/231 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K + +A + SR++V+++   Q++K+NG   +  +  V      I+V G  +     
Sbjct: 1   MRLDKCLEKAKVGSRKQVKKLFKAQQIKINGQAAQSLSQIVDPELQTIQVSGKKVALEGS 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +               +       +  VGRLD +TEGL+L+TN+G L  
Sbjct: 61  AYYLLHKPAGVVSAVTDQEHQTVIDLISPQDSREGLYPVGRLDRDTEGLVLITNNGPLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVTV 191
            +  PS    + Y V  +G + +D       G+  + G       +T+      ++  T+
Sbjct: 121 RMLHPSHHVDKFYYVEVNGCLAEDASKFFASGVTFLDGTRCQPAVLTVLEASLDHSRATI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            L EGK  ++KK+F  +  KV  L RIS+G F+LG L  G+ R+++   + 
Sbjct: 181 KLAEGKFHQVKKMFLAYGVKVTYLKRISFGGFELGDLERGAYRQLTPNEME 231


>gi|315022583|gb|EFT35609.1| Ribosomal large subunit pseudouridine synthase B [Riemerella
           anatipestifer RA-YM]
          Length = 311

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 60/237 (25%), Positives = 113/237 (47%), Gaps = 1/237 (0%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            +VQ+     R++K IA +GI SRRE + +I Q  V++NG ++      V  TD +  DG
Sbjct: 70  KLVQQPKDTIRLNKYIANSGICSRREADELIQQGLVEINGKVVTELGYQVQKTDKVVFDG 129

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +   +   + L      + TT  +   ++ +     +   R+  VGRLD  T G++LL
Sbjct: 130 QSITPEKPVYVLLNKPKGYISTTKDEKARKTVMDLTANASPYRIFPVGRLDRQTTGVILL 189

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG L + L  PS    ++Y V    ++  + + ++ KGI ++        ++    K 
Sbjct: 190 TNDGHLTKKLTHPSFNIKKIYHVTLDRKLTGEDMAIIAKGIRLEEGVAEVDSISYIDGKP 249

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            N  + + +  G NR I+++F+   ++V  L R+ +       +  G  R +++  +
Sbjct: 250 KN-EIGIEIHIGWNRVIRRIFQRLGYEVEALDRVMFAGLTKKNIKRGHWRILTELEV 305


>gi|145636895|ref|ZP_01792560.1| malic enzyme [Haemophilus influenzae PittHH]
 gi|145269976|gb|EDK09914.1| malic enzyme [Haemophilus influenzae PittHH]
          Length = 232

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 57/236 (24%), Positives = 108/236 (45%), Gaps = 7/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  +V +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWVEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ HKP G V ++ D D  +        +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYFMLHKPQGCVCSNDDGDYPTIYQFFDYPLAGKLHSAGRLDMDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+++      +GI+++G        ++ +      +  V +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEENYAAACSEGILLRGEKEPTKPAKLEIL----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
            + EG+  ++K++F     KV  L R   G   L   L  G  R +++  + + + 
Sbjct: 177 TISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLVK 232


>gi|326334734|ref|ZP_08200941.1| ribosomal large subunit pseudouridine synthase B [Capnocytophaga
           sp. oral taxon 338 str. F0234]
 gi|325693184|gb|EGD35116.1| ribosomal large subunit pseudouridine synthase B [Capnocytophaga
           sp. oral taxon 338 str. F0234]
          Length = 294

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 57/234 (24%), Positives = 111/234 (47%), Gaps = 1/234 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            ++    R++K IA AGI +RRE +R I    V+VNG  +      V   D ++ DG  +
Sbjct: 54  TDDSKGIRLNKYIANAGICARREADRYITAGNVEVNGKPMTELGYRVQPNDIVKFDGKNI 113

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              ++  + L      + TT  +   ++ +   + +    +  VGRLD  T GLLLLTND
Sbjct: 114 SAEKKEYILLNKPKGFITTTQDEKGRKTVMELVVGAAQGNIKPVGRLDRLTTGLLLLTND 173

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L + L  PS    ++Y V    ++     + +++G+ ++        ++   +   + 
Sbjct: 174 GDLIKKLTHPSHGVRKIYHVILDKKLALPDFHKIQEGLTLEDGFIQVDDISFV-EGAPHN 232

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + V +  G+NR ++++FE   + V +L R+ +       L  G  R ++++ +
Sbjct: 233 EIGVKIHSGRNRIVRRIFESLGYTVEKLDRVVFAGLTKKDLPRGHWRPLTQQEV 286


>gi|225621236|ref|YP_002722494.1| pseudouridylate synthase [Brachyspira hyodysenteriae WA1]
 gi|225216056|gb|ACN84790.1| pseudouridylate synthase [Brachyspira hyodysenteriae WA1]
          Length = 229

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 67/233 (28%), Positives = 110/233 (47%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA   +ASRRE +R+I    VKVNGI+    A  V   D IE      +  E  
Sbjct: 1   MRLNKYIASLNLASRREADRLIQNGNVKVNGIINTNPATQVDENDKIEC--SIEQYKENK 58

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G V + +  +G+   ++ +   F  +  VGRLD ++ GL+L TNDG  A+ 
Sbjct: 59  IYIKLNKPRGYVVSSNKNEGKPI-YNLIKKDFDNIYPVGRLDKDSSGLILFTNDGVFAKQ 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +   +T   + Y VR    +    L  L+ GI + G      +V    +        + L
Sbjct: 118 IIGENTNCEKEYYVRVDDNIPDGALQKLEYGISLDGQKLKPAKVKRVNKNS----FHIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            EGKNR+I+++ +   ++V  L R+      L  L  G+ + ++K+ +   L 
Sbjct: 174 TEGKNRQIRRMCQKVGFEVIILKRLRISGILLEDLKEGTFKSLTKEEIESILK 226


>gi|315604212|ref|ZP_07879278.1| ribosomal large subunit pseudouridine synthase B [Actinomyces sp.
           oral taxon 180 str. F0310]
 gi|315313918|gb|EFU61969.1| ribosomal large subunit pseudouridine synthase B [Actinomyces sp.
           oral taxon 180 str. F0310]
          Length = 249

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 91/236 (38%), Positives = 123/236 (52%), Gaps = 2/236 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAE 71
             R+ KV+A+AGIASRR  E+MIA  RV V+G ++    V V   T  I VDG  L   E
Sbjct: 10  GVRLQKVLAQAGIASRRASEQMIADGRVSVDGTVVRTQGVRVDPATQVIHVDGERLILDE 69

Query: 72  RTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               +   +KPIG V+T SDP+GR T+ D +     R+  VGRLDI+T GLLLLTNDG L
Sbjct: 70  AKHIVLAVNKPIGTVSTMSDPEGRPTIADLIADYPERLYHVGRLDIDTSGLLLLTNDGEL 129

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS +  + Y  R HG+V       L  GI ++          L    G    V 
Sbjct: 130 ANRLTHPSYEIRKTYVARLHGEVKPGVRRRLLAGIELEDGPIAVDSFRLVDTYGDITTVE 189

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + + EG+NR ++++ E   + V  L+R  +GP  L  L  G+TR +    L    G
Sbjct: 190 IVVHEGRNRLVRRMMEAVGYPVRELVRTGFGPISLDHLKQGTTRRIKGNALTALYG 245


>gi|159037542|ref|YP_001536795.1| pseudouridine synthase [Salinispora arenicola CNS-205]
 gi|157916377|gb|ABV97804.1| pseudouridine synthase [Salinispora arenicola CNS-205]
          Length = 256

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 81/230 (35%), Positives = 119/230 (51%), Gaps = 1/230 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P+R+ KV+A AG+ SRR  E +I ++RV VNG + +       ++D I VDG  L+   R
Sbjct: 18  PERLQKVLAAAGVGSRRACEDLIFRRRVTVNGRIAQLGDRADPTSDTIHVDGERLQADTR 77

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLA 131
                 +KP G+V+T +D  GR+ + D L +        VGRLD ++EGLLLLTNDG LA
Sbjct: 78  LVYLAMNKPRGVVSTMADEKGRTAIADFLGNRVQERVYHVGRLDADSEGLLLLTNDGTLA 137

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  PS    + Y     G + +     L  GI +           +    G  A V V
Sbjct: 138 HRLTHPSYGVPKTYLCEVSGPIPRTLGRRLAAGIELTDGPATVDAFRVVDTLGRTAQVEV 197

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            L EG+   ++++F+     V+RL+R S GP +LG L AG TR ++   +
Sbjct: 198 TLHEGRKHIVRRLFDAVGHPVSRLVRTSIGPIRLGDLRAGRTRRLTNAEV 247


>gi|254506983|ref|ZP_05119121.1| ribosomal large subunit pseudouridine synthase B [Vibrio
           parahaemolyticus 16]
 gi|219549978|gb|EED26965.1| ribosomal large subunit pseudouridine synthase B [Vibrio
           parahaemolyticus 16]
          Length = 322

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 92/320 (28%), Positives = 134/320 (41%), Gaps = 9/320 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
           +++ KV+ARAG  SRRE+E +I   RV VNG++ +           + +DG  +      
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKAGRVSVNGVVAKLGERLEDENAIVRIDGHTVSAKAQE 62

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 L  Y     L T H     R+          SR ISVGRLD NT GLLL T DG
Sbjct: 63  EVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS Q  R Y VR  G+V + K+  L +G+ ++        V      G N  
Sbjct: 123 ELANRLMHPSRQVEREYLVRVFGEVTEQKVKNLVRGVELEDGMARFEDVVYAGGDGMNHT 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LREQ 244
             V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+  K    LRE 
Sbjct: 183 FYVAINEGRNREVRRLWESQETTVSRLKRVRYGDIYLDKKLPRGGWMELDLKQVNYLREL 242

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           +     +E  ++ +    S +        I   V     R+     + N  S++K     
Sbjct: 243 VELRPEKETLLDENKANSSRKRERSRSQKIRRAVKRHEERVNSGGGRSNNPSRRKPRKGA 302

Query: 305 VHRRNLASNVWMAKGIHSSF 324
             + + A          S  
Sbjct: 303 GEQGSRAKQGNSKPQRQSRK 322


>gi|324113141|gb|EGC07116.1| RNA pseudouridylate synthase [Escherichia fergusonii B253]
 gi|325497457|gb|EGC95316.1| 23S rRNA pseudouridylate synthase B [Escherichia fergusonii ECD227]
          Length = 290

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 86/289 (29%), Positives = 128/289 (44%), Gaps = 10/289 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V +     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEITPGLKIRIDGHLISVRE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           E +       ++V ++      +     R            R    ++ 
Sbjct: 242 ELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGGRRSGGRNNG 290


>gi|328948658|ref|YP_004365995.1| RNA-binding S4 domain protein [Treponema succinifaciens DSM 2489]
 gi|328448982|gb|AEB14698.1| RNA-binding S4 domain protein [Treponema succinifaciens DSM 2489]
          Length = 247

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 76/248 (30%), Positives = 121/248 (48%), Gaps = 5/248 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M   N  ++     R+ + +A+ G+ASRR  E +I   RV VNG ++      V   D +
Sbjct: 1   MPVNNSKEKKEDVMRLQQYMAKCGVASRRASEAIICAGRVTVNGTVVTELGTKVDVQDKV 60

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
            VD   +   E+    L +KP G V + SD  GR    D L      R+ +VGRLD+ + 
Sbjct: 61  CVDEKEIHLEEKKCYVLLNKPSGYVCSASDEKGRPVAADLLKEAYSERLYNVGRLDMFSS 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GL++ TNDG  A  L  PS +  + Y V     + +   +    GI I G+ Y       
Sbjct: 121 GLIIFTNDGDFAAKLSHPSAELEKEYIVDTSLPMPRFLADDFMDGIRIDGVFYR----CK 176

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           D ++ ++  + + L EGKNREI++VFE +   +  L+RI  G   +G L  G  R++++ 
Sbjct: 177 DARELNSHRMRIVLVEGKNREIRRVFEKYEVGIKSLMRIRIGCVGVGELQFGQFRDLTQD 236

Query: 240 ILREQLGP 247
            ++  L  
Sbjct: 237 EVKALLRL 244


>gi|194436993|ref|ZP_03069092.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           101-1]
 gi|194423976|gb|EDX39964.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           101-1]
          Length = 291

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 87/288 (30%), Positives = 127/288 (44%), Gaps = 10/288 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ +         +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLGDGPAAFKTIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           E +       ++V ++      +     R            R    ++
Sbjct: 242 ELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGGRRSGGRNN 289


>gi|323497601|ref|ZP_08102618.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio sinaloensis
           DSM 21326]
 gi|323317350|gb|EGA70344.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio sinaloensis
           DSM 21326]
          Length = 321

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 92/319 (28%), Positives = 133/319 (41%), Gaps = 9/319 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
           +++ KV+ARAG  SRRE+E +I   RV VNGI+ +           + +DG  +      
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKAGRVSVNGIVAKLGERLEDENAVVRIDGHTVSAKAQE 62

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 L  Y     L T H     R+          SR ISVGRLD NT GLLL T DG
Sbjct: 63  EVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS Q  R Y VR  G V + K+  L +G+ ++        V      G N  
Sbjct: 123 ELANRLMHPSRQVEREYLVRVFGDVTEQKVKNLVRGVELEDGMARFEDVVYAGGDGMNHT 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI---LREQ 244
             V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+  K    LRE 
Sbjct: 183 FYVAINEGRNREVRRLWESQETTVSRLKRVRYGDIYLDKKLPRGGWMELDLKQVNYLREM 242

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           +     +E  ++ +    S +        I   V     R+     + N  S++K     
Sbjct: 243 VELRPEKETLLDENKSNTSRKRERSRSQKIRRAVKRHEERVNSGGGRSNNPSRRKPRKGA 302

Query: 305 VHRRNLASNVWMAKGIHSS 323
             + + A      +     
Sbjct: 303 GEQGSRAKQGGKPQRQQRK 321


>gi|256822107|ref|YP_003146070.1| RNA-binding S4 domain-containing protein [Kangiella koreensis DSM
           16069]
 gi|256795646|gb|ACV26302.1| RNA-binding S4 domain protein [Kangiella koreensis DSM 16069]
          Length = 267

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 86/261 (32%), Positives = 128/261 (49%), Gaps = 7/261 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
            +++ K++A AG+ SRRE+E+ I   RV VNG + +         D I VDG  +     
Sbjct: 2   SEKLQKILANAGLGSRREIEKWIEGGRVSVNGSIAK-LGERATDKDTIRVDGRIISIISA 60

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L        + T        +   +   + F R IS+GRLDINT GLLL TN+
Sbjct: 61  EETYTRVLAYNKPLGEVSTKKDPEGRATVFDNLPNTSFGRWISIGRLDINTTGLLLFTNN 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR HG+V  + ++ L KG++I+G       V     +G+N 
Sbjct: 121 GELAHRLMHPSYQVERKYAVRVHGEVTPEMISNLTKGVLIEGDTCQFTYVQDKGGEGANH 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
           W  VGL EGKNRE++K++E    +V+RL+R+ YGP  L T L  G   ++ ++ + +   
Sbjct: 181 WYEVGLAEGKNREVRKLWESQGVEVSRLMRVQYGPISLPTRLSRGRWVDLEEQEINDLAK 240

Query: 247 PHLLEEAQVNLDAPIYSSETL 267
              LE         +   +  
Sbjct: 241 LVELEVTPRRARPEVQKRQKK 261


>gi|260587785|ref|ZP_05853698.1| ribosomal small subunit pseudouridine synthase A [Blautia hansenii
           DSM 20583]
 gi|331083787|ref|ZP_08332896.1| hypothetical protein HMPREF0992_01820 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|260542050|gb|EEX22619.1| ribosomal small subunit pseudouridine synthase A [Blautia hansenii
           DSM 20583]
 gi|330403212|gb|EGG82772.1| hypothetical protein HMPREF0992_01820 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 238

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 66/232 (28%), Positives = 108/232 (46%), Gaps = 6/232 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV+R I + R+ VNG +++     +   TD +  DG  +   E 
Sbjct: 4   IRLDKYLADMGLGTRTEVKRDIKKGRISVNGEIVKSPEYKIDIQTDVVLADGKEIAYEEL 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +V+   D   ++ +          +  VGRLD +TEGLLL+TNDG LA 
Sbjct: 64  VYYMLNKPQG-VVSATEDRRDKTVLDLISEKKRKDLFPVGRLDKDTEGLLLITNDGELAH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y VR    + ++    L++G+ I +        V +  +K   A   +
Sbjct: 123 NLLSPKKHVDKKYFVRLRDALSEEDKKHLEEGVDIGEDKLTLPSHVFVLNEKRDEA--EI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            +REGK  +IK++F     +V  L R+S G   L   LL G  R ++ + + 
Sbjct: 181 VIREGKFHQIKRMFHAVGNEVVFLKRLSMGSLTLDEALLTGEYRLLTPQEIE 232


>gi|325473332|gb|EGC76527.1| pseudouridine synthase [Treponema denticola F0402]
          Length = 234

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 69/236 (29%), Positives = 115/236 (48%), Gaps = 5/236 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R+   +AR G+ASRR  E +I   RV V+G ++      V   + I +DG  +    
Sbjct: 3   DEIRLQVYLARCGVASRRASENLILNGRVSVDGKIITELGTKVSGKEKICLDGKQIFPEA 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGL 130
             R  L +KP G V + +D   R      L   ++    ++GRLD+ + G +L TNDG  
Sbjct: 63  EKRYILLNKPEGYVCSLADEKDRPIAASLLKDTYTERLYNIGRLDMLSGGAILFTNDGDF 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  +E PS++  + Y V    +   + L    +G+ I+G+ Y  +      +        
Sbjct: 123 SAKVEHPSSEIEKEYEVITVFEYPDEVLQKFLRGVRIEGVFYKALSAERIAKNKM----R 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + L EGKNREI++V +FFN K+ +L R+  G   L  L +G  R ++ + ++  LG
Sbjct: 179 IVLIEGKNREIRRVLKFFNIKIKKLTRVRIGCVYLADLPSGKHRPLTSEEIKGLLG 234


>gi|313205697|ref|YP_004044874.1| ribosomal large subunit pseudouridine synthase b [Riemerella
           anatipestifer DSM 15868]
 gi|312445013|gb|ADQ81368.1| ribosomal large subunit pseudouridine synthase B [Riemerella
           anatipestifer DSM 15868]
 gi|325336858|gb|ADZ13132.1| 16S rRNA uridine-516 pseudouridylate synthase related
           pseudouridylate synthase [Riemerella anatipestifer
           RA-GD]
          Length = 311

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 60/237 (25%), Positives = 113/237 (47%), Gaps = 1/237 (0%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            +VQ+     R++K IA +GI SRRE + +I Q  V++NG ++      V  TD +  DG
Sbjct: 70  KLVQQPKDTIRLNKYIANSGICSRREADELIQQGLVEINGKVVTELGYQVQKTDKVVFDG 129

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +   +   + L      + TT  +   ++ +     +   R+  VGRLD  T G++LL
Sbjct: 130 QSITPEKPVYVLLNKPKGYISTTKDEKARKTVMDLTANASPYRIFPVGRLDRQTTGVILL 189

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG L + L  PS    ++Y V    ++  + + ++ KGI ++        ++    K 
Sbjct: 190 TNDGHLTKKLTHPSFNIKKIYHVTLDRKLTGEDMAIIAKGIRLEEGVAEVDSISYIDGKP 249

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            N  + + +  G NR I+++F+   ++V  L R+ +       +  G  R +++  +
Sbjct: 250 KN-EIGIEIHIGWNRVIRRIFQRLGYEVEALDRVMFAGLTKKNIKRGHWRILTELEV 305


>gi|160880922|ref|YP_001559890.1| pseudouridine synthase [Clostridium phytofermentans ISDg]
 gi|160429588|gb|ABX43151.1| pseudouridine synthase [Clostridium phytofermentans ISDg]
          Length = 240

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 66/245 (26%), Positives = 108/245 (44%), Gaps = 8/245 (3%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGV 65
           + ++ +  R+ K +A   + +R EV++MI + RV VNG         V S  D I VD  
Sbjct: 1   MSKSNSMLRLDKYLADLSVGTRTEVKQMIRKGRVMVNGNTETSPETKVDSNHDKIFVDSR 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            L         L      +V+  +D    + V     +    +  VGRLD +TEGLL++T
Sbjct: 61  ELSYVTLEYFMLNKPAG-VVSASNDKKQTTVVDLIDEAKRKDLFPVGRLDKDTEGLLIIT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKG 184
           NDG LA  L  P     +VY  +    + ++       G+ I         ++   +++ 
Sbjct: 120 NDGDLAHQLLSPKKHVDKVYFAKLRDPLKKEDEEAFAAGLKIDEEFTALPAKLERISEQE 179

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
           +     V +REGK  +IK++FE    +V  L RIS G   L   L  G  RE++++ +  
Sbjct: 180 A----YVTIREGKFHQIKRMFEATRNEVIYLKRISMGSLVLDESLSLGEYRELTEEEIEA 235

Query: 244 QLGPH 248
                
Sbjct: 236 LRENR 240


>gi|16760161|ref|NP_455778.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. CT18]
 gi|34098636|sp|Q8Z7D5|RLUB_SALTI RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|25324005|pir||AI0653 probable pseudouridine synthase STY1331 [imported] - Salmonella
           enterica subsp. enterica serovar Typhi (strain CT18)
 gi|16502455|emb|CAD08412.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Typhi]
          Length = 291

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 86/288 (29%), Positives = 127/288 (44%), Gaps = 10/288 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD+ KL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDESKLRDLSRGVQLEDGPAAFKTIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDFAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
             +       ++V ++      +     R            R    ++
Sbjct: 242 GLVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQIAGGRRSGGRNN 289


>gi|47565132|ref|ZP_00236175.1| ribosomal small subunit pseudouridine synthase A [Bacillus cereus
           G9241]
 gi|47557918|gb|EAL16243.1| ribosomal small subunit pseudouridine synthase A [Bacillus cereus
           G9241]
          Length = 233

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 59/223 (26%), Positives = 100/223 (44%), Gaps = 4/223 (1%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTRLWLYHKP 81
            G  SR+EV++++    VK++GI ++ A V+V      + + G  +   E   L ++   
Sbjct: 1   MGYGSRKEVKKLLKDGVVKIDGISVKDAKVHVNVEEQEVMIHGEVVEYKEFVYLMMHKPQ 60

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
             +  T  D          L         VGRLDI+TEG LL+TNDG L+  L  P    
Sbjct: 61  GVISATEDDNHETVIDLLELEDAIFNPFPVGRLDIDTEGFLLITNDGKLSHQLLSPKKHV 120

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
            + Y     G V ++ +    KG+++          +T+  +    + + + + EGK  +
Sbjct: 121 PKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEIELVITEGKFHQ 179

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           +K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 180 VKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 222


>gi|254525629|ref|ZP_05137681.1| ribosomal large subunit pseudouridine synthase F [Prochlorococcus
           marinus str. MIT 9202]
 gi|221537053|gb|EEE39506.1| ribosomal large subunit pseudouridine synthase F [Prochlorococcus
           marinus str. MIT 9202]
          Length = 240

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 104/236 (44%), Gaps = 11/236 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---AE 71
           R++K ++  G  SRRE +R+I + +V +NG + +     V  +D +EV G  ++K    +
Sbjct: 4   RINKYLSEVGYCSRREADRLIHEGKVTINGKIPK-IGSKVEESDQVEVKGQRIKKITGQK 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L        + TT            +      R+  +GRLD  +EGL+ LTNDG + 
Sbjct: 63  NIYLAFNKPVGIVCTTDRK--VEPNNVIDFIKYPKRIFPIGRLDKLSEGLIFLTNDGDIV 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V+ + Q++ D +  +  G+ I      +       ++       +
Sbjct: 121 NKILRARNNHEKEYIVKVNRQINSDFIQSMSSGVEILDTITKNC----FVKQLGPKKFKI 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            L +G NR+I+++ E   ++V  L R+     +L  +  G  RE +K+ L E    
Sbjct: 177 ILTQGLNRQIRRMCESLGYRVRSLKRVRIMNIEL-DVSTGKYREFTKEELFELNRL 231


>gi|212696088|ref|ZP_03304216.1| hypothetical protein ANHYDRO_00624 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212676717|gb|EEB36324.1| hypothetical protein ANHYDRO_00624 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 231

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 69/230 (30%), Positives = 114/230 (49%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA+AG+ASRR+ E  I +  V VNG  L+  +  V   D ++V G  L   E+ 
Sbjct: 1   MRINKYIAKAGLASRRKSEEYIKKGLVFVNGKKLDDLSYQVKENDQVKVMGKLLEIKEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      + +            ++L  I  R    GRLD ++ GL+L+TNDG +   
Sbjct: 61  YYKLNKPIGFISSN--YDPHNKKDLNSLVKIDHRFFCAGRLDKDSHGLMLITNDGKITNK 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVG 192
           L  PS +  + Y V+    +++D   L +KGI +       D ++ L     ++    V 
Sbjct: 119 LIHPSKKIEKTYIVKVDKLLNKDDEALFRKGIKLSVNEKTSDAKINLI--DENSKIYEVI 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + +G NR+++++F +F  KV  L RI  G  +LG L  G  ++++KK L 
Sbjct: 177 IHQGFNRQVRRMFLYFGSKVIDLKRIKIGQIELGKLEDGKYKKLNKKELE 226


>gi|78188520|ref|YP_378858.1| pseudouridine synthase, Rsu [Chlorobium chlorochromatii CaD3]
 gi|78170719|gb|ABB27815.1| ribosomal large subunit pseudouridine synthase B [Chlorobium
           chlorochromatii CaD3]
          Length = 251

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 66/253 (26%), Positives = 117/253 (46%), Gaps = 5/253 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DH 59
           MK +     N    R+++ +A  GIASRR  ++++ + RV +NG ++    V V  + D 
Sbjct: 3   MKQEK---SNNDGMRINRFLAMCGIASRRAADQLVQEGRVCINGKIVTTPGVKVNPSRDE 59

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           + +DG    + E  ++++       V T S  + +  +  +   +  R+  VGRLD  T 
Sbjct: 60  VIIDGKRFAQPENRKVYILLNKPRNVITTSSDERQREMVLDFIDVPERIFPVGRLDRKTT 119

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G++LLTNDG LA  L  PS+   + Y      +     L  L  G+ ++           
Sbjct: 120 GVILLTNDGELAHKLMHPSSGVKKEYIAELSERFPAAMLGKLTNGMRLKDTGEKVSPCRA 179

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                    + + + EGKN +++++F+   ++V RL R++Y   Q G L  G  R +S+ 
Sbjct: 180 KLLDDGMRVL-LSIHEGKNHQVRRMFDTLGFEVKRLDRVAYAGLQAGELRRGEWRYLSRN 238

Query: 240 ILREQLGPHLLEE 252
            +RE       E 
Sbjct: 239 EVRELYRISQEEA 251


>gi|294012129|ref|YP_003545589.1| ribosomal large subunit pseudouridine synthase B [Sphingobium
           japonicum UT26S]
 gi|292675459|dbj|BAI96977.1| ribosomal large subunit pseudouridine synthase B [Sphingobium
           japonicum UT26S]
          Length = 304

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 112/231 (48%), Positives = 150/231 (64%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             PQR++K++ARAG+ASRREVERMI + R+ +NG  +   A  + S   + VDG P+   
Sbjct: 63  NEPQRIAKLLARAGVASRREVERMIEEGRITLNGEAVSTPATLLSSLHGVAVDGNPVAAP 122

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              RL+L+HKP G +TT  DP GR T++D LP    RV+ +GRLD+ TEGLLLLT DG  
Sbjct: 123 APARLFLFHKPSGFLTTERDPRGRPTIYDKLPPDLPRVMPIGRLDMMTEGLLLLTTDGEF 182

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            R +ELPST   R YR R  G+V Q++L  L  G+ I GI YG ++  L+ + G N W+ 
Sbjct: 183 KRQMELPSTGVPRTYRARAFGEVSQNQLEDLFDGLEIDGIRYGRIEANLERRTGRNQWIE 242

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + L EGKNRE+++V E    +VNRLIR SYGPF LG L +G+  EV +  L
Sbjct: 243 MTLTEGKNREVRRVLEHLGLQVNRLIRTSYGPFHLGELASGAVEEVRQHDL 293


>gi|227540649|ref|ZP_03970698.1| pseudouridylate synthase (ribosomal large subunit pseudouridine
           synthase B) [Sphingobacterium spiritivorum ATCC 33300]
 gi|227239511|gb|EEI89526.1| pseudouridylate synthase (ribosomal large subunit pseudouridine
           synthase B) [Sphingobacterium spiritivorum ATCC 33300]
          Length = 441

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 66/229 (28%), Positives = 109/229 (47%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+++ I+ AGI SRR+ + +I    + VNG ++      V    D I+ +G  L++ + 
Sbjct: 207 IRLNRYISNAGICSRRKADELITAGVISVNGEVVTELGSKVDPAKDEIKYNGERLKREKM 266

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + TT    + R+ +     +   R+  VGRLD NT GLLLLTNDG LA 
Sbjct: 267 VYVLLNKPKDYITTTDDPQERRTVMQLVANATKERIYPVGRLDRNTTGLLLLTNDGNLAE 326

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     ++Y V     ++Q   N +  G+ ++        ++   Q GS   V + 
Sbjct: 327 KLSHPRNNISKIYNVELDKSLNQGDFNKIVFGLELEDGFVKPDDLSYV-QGGSKREVGIQ 385

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +  GKNR ++++FE   + V +L R+ Y       L  G  R + +K L
Sbjct: 386 IHSGKNRIVRRIFESLGYDVVKLDRVVYANLTKKDLPRGRWRYLEEKEL 434


>gi|16765063|ref|NP_460678.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|29142068|ref|NP_805410.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|56413355|ref|YP_150430.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|161613791|ref|YP_001587756.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|167993774|ref|ZP_02574867.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|168230158|ref|ZP_02655216.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
 gi|168237772|ref|ZP_02662830.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           SL480]
 gi|168241298|ref|ZP_02666230.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|168260059|ref|ZP_02682032.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|168462806|ref|ZP_02696737.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|168819542|ref|ZP_02831542.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|194444498|ref|YP_002040973.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194451051|ref|YP_002045766.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194471762|ref|ZP_03077746.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|194733904|ref|YP_002114751.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|197249960|ref|YP_002146307.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197265930|ref|ZP_03166004.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|197362279|ref|YP_002141916.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|198242127|ref|YP_002215422.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|200389338|ref|ZP_03215949.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Virchow str. SL491]
 gi|205352607|ref|YP_002226408.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|207856768|ref|YP_002243419.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|213163149|ref|ZP_03348859.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
 gi|213421199|ref|ZP_03354265.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
 gi|213424436|ref|ZP_03357249.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. E02-1180]
 gi|213582563|ref|ZP_03364389.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-0664]
 gi|213649101|ref|ZP_03379154.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. J185]
 gi|213855225|ref|ZP_03383465.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
 gi|224583789|ref|YP_002637587.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|238911889|ref|ZP_04655726.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Tennessee str. CDC07-0191]
 gi|289829089|ref|ZP_06546769.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
 gi|34098653|sp|Q8ZP51|RLUB_SALTY RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|16420249|gb|AAL20637.1| putative ribosomal large subunit pseudouridine synthase [Salmonella
           enterica subsp. enterica serovar Typhimurium str. LT2]
 gi|29137697|gb|AAO69259.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|56127612|gb|AAV77118.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|161363155|gb|ABX66923.1| hypothetical protein SPAB_01525 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|194403161|gb|ACF63383.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Newport str. SL254]
 gi|194409355|gb|ACF69574.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL476]
 gi|194458126|gb|EDX46965.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|194709406|gb|ACF88627.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           CVM19633]
 gi|195634468|gb|EDX52820.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|197093756|emb|CAR59230.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|197213663|gb|ACH51060.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Agona str. SL483]
 gi|197244185|gb|EDY26805.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|197289238|gb|EDY28605.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           SL480]
 gi|197936643|gb|ACH73976.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Dublin str.
           CT_02021853]
 gi|199601783|gb|EDZ00329.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Virchow str. SL491]
 gi|205272388|emb|CAR37268.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205328271|gb|EDZ15035.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|205335319|gb|EDZ22083.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
 gi|205339577|gb|EDZ26341.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|205343695|gb|EDZ30459.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|205350643|gb|EDZ37274.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|206708571|emb|CAR32892.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|224468316|gb|ACN46146.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|261246909|emb|CBG24726.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. D23580]
 gi|267993665|gb|ACY88550.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 14028S]
 gi|301158247|emb|CBW17746.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. SL1344]
 gi|312912712|dbj|BAJ36686.1| 23S rRNA pseudouridine synthase B [Salmonella enterica subsp.
           enterica serovar Typhimurium str. T000240]
 gi|320085782|emb|CBY95558.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           2007-60-3289-1]
 gi|321224350|gb|EFX49413.1| Ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           TN061786]
 gi|322614978|gb|EFY11903.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322621428|gb|EFY18282.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322623230|gb|EFY20072.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322628520|gb|EFY25308.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322633684|gb|EFY30424.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322638508|gb|EFY35203.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322640822|gb|EFY37471.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
 gi|322645314|gb|EFY41842.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322651803|gb|EFY48175.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322654300|gb|EFY50622.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322659265|gb|EFY55513.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
 gi|322662733|gb|EFY58940.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322667656|gb|EFY63816.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322671930|gb|EFY68051.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322677024|gb|EFY73088.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322680314|gb|EFY76353.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322685257|gb|EFY81253.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|323129991|gb|ADX17421.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|323195433|gb|EFZ80612.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323199316|gb|EFZ84410.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323204774|gb|EFZ89770.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323205930|gb|EFZ90893.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323217255|gb|EGA01976.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323220712|gb|EGA05157.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323227964|gb|EGA12116.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323232119|gb|EGA16226.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323234646|gb|EGA18733.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323238098|gb|EGA22157.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323243298|gb|EGA27317.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323248445|gb|EGA32380.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2009159199]
 gi|323252551|gb|EGA36394.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
 gi|323255424|gb|EGA39190.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008283]
 gi|323260826|gb|EGA44428.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
 gi|323267587|gb|EGA51070.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008285]
 gi|323270947|gb|EGA54383.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008287]
 gi|326623169|gb|EGE29514.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
 gi|326627671|gb|EGE34014.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
 gi|332988608|gb|AEF07591.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 291

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 86/288 (29%), Positives = 127/288 (44%), Gaps = 10/288 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD+ KL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDESKLRDLSRGVQLEDGPAAFKTIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
             +       ++V ++      +     R            R    ++
Sbjct: 242 GLVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQIAGGRRSGGRNN 289


>gi|319896936|ref|YP_004135131.1| ribosomal small subunit pseudouridine synthase a [Haemophilus
           influenzae F3031]
 gi|317432440|emb|CBY80795.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           influenzae F3031]
          Length = 232

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 58/236 (24%), Positives = 108/236 (45%), Gaps = 7/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  AV +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENTGLTRSQATKAIHQSAVKINGEIVKSGAVQISQEDKIYFEDELLTWVEED 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ HKP G V ++ D D  +        +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYFMLHKPQGCVCSNDDGDYPTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+++      +GI+++G        ++ +      +  V +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEENYAAACSEGILLRGEKEPTKPAKLEIL----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
            + EG+  ++K++F     KV  L R   G   L   L  G  R +++  + + + 
Sbjct: 177 TISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLVK 232


>gi|167549772|ref|ZP_02343530.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|204927933|ref|ZP_03219134.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|204323275|gb|EDZ08471.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|205324943|gb|EDZ12782.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
          Length = 291

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 86/288 (29%), Positives = 127/288 (44%), Gaps = 10/288 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD+ KL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDESKLRDLSRGVQLEDGPAAFKTIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLSQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
             +       ++V ++      +     R            R    ++
Sbjct: 242 GLVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQIAGGRRSGGRNN 289


>gi|26247598|ref|NP_753638.1| 23S rRNA pseudouridylate synthase B [Escherichia coli CFT073]
 gi|91210560|ref|YP_540546.1| 23S rRNA pseudouridylate synthase B [Escherichia coli UTI89]
 gi|110641498|ref|YP_669228.1| 23S rRNA pseudouridylate synthase B [Escherichia coli 536]
 gi|191171000|ref|ZP_03032551.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           F11]
 gi|215486564|ref|YP_002328995.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218549040|ref|YP_002382831.1| 23S rRNA pseudouridylate synthase B [Escherichia fergusonii ATCC
           35469]
 gi|218558254|ref|YP_002391167.1| 23S rRNA pseudouridylate synthase B [Escherichia coli S88]
 gi|218704792|ref|YP_002412311.1| 23S rRNA pseudouridylate synthase B [Escherichia coli UMN026]
 gi|227886303|ref|ZP_04004108.1| 23S rRNA pseudouridylate synthase [Escherichia coli 83972]
 gi|237705292|ref|ZP_04535773.1| ribosomal large subunit pseudouridine synthase B [Escherichia sp.
           3_2_53FAA]
 gi|293404810|ref|ZP_06648802.1| 23S rRNA pseudouridylate synthase B [Escherichia coli FVEC1412]
 gi|298380451|ref|ZP_06990050.1| 23S rRNA pseudouridylate synthase B [Escherichia coli FVEC1302]
 gi|300897321|ref|ZP_07115752.1| conserved hypothetical protein [Escherichia coli MS 198-1]
 gi|300971792|ref|ZP_07171626.1| hypothetical protein HMPREF9553_00034 [Escherichia coli MS 200-1]
 gi|300982412|ref|ZP_07176109.1| conserved hypothetical protein [Escherichia coli MS 45-1]
 gi|301046931|ref|ZP_07194045.1| conserved hypothetical protein [Escherichia coli MS 185-1]
 gi|306813708|ref|ZP_07447889.1| 23S rRNA pseudouridylate synthase B [Escherichia coli NC101]
 gi|312966803|ref|ZP_07781021.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           2362-75]
 gi|331646590|ref|ZP_08347693.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli M605]
 gi|331662681|ref|ZP_08363604.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli TA143]
 gi|331672793|ref|ZP_08373579.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli TA280]
 gi|331682754|ref|ZP_08383373.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli H299]
 gi|34098555|sp|Q8FHV4|RLUB_ECOL6 RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|26108000|gb|AAN80200.1|AE016760_59 Hypothetical protein yciL [Escherichia coli CFT073]
 gi|91072134|gb|ABE07015.1| hypothetical protein YciL [Escherichia coli UTI89]
 gi|110343090|gb|ABG69327.1| putative ribosomal large subunit pseudouridine synthase
           [Escherichia coli 536]
 gi|190908732|gb|EDV68320.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           F11]
 gi|215264636|emb|CAS09007.1| 23S rRNA pseudouridy late synthase [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218356581|emb|CAQ89204.1| 23S rRNA pseudouridylate synthase [Escherichia fergusonii ATCC
           35469]
 gi|218365023|emb|CAR02726.1| 23S rRNA pseudouridylate synthase [Escherichia coli S88]
 gi|218431889|emb|CAR12774.1| 23S rRNA pseudouridylate synthase [Escherichia coli UMN026]
 gi|222033073|emb|CAP75813.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           LF82]
 gi|226900049|gb|EEH86308.1| ribosomal large subunit pseudouridine synthase B [Escherichia sp.
           3_2_53FAA]
 gi|227836507|gb|EEJ46973.1| 23S rRNA pseudouridylate synthase [Escherichia coli 83972]
 gi|281178457|dbj|BAI54787.1| putative pseudouridine synthase [Escherichia coli SE15]
 gi|284921150|emb|CBG34216.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           042]
 gi|291427018|gb|EFF00045.1| 23S rRNA pseudouridylate synthase B [Escherichia coli FVEC1412]
 gi|294492436|gb|ADE91192.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           IHE3034]
 gi|298277893|gb|EFI19407.1| 23S rRNA pseudouridylate synthase B [Escherichia coli FVEC1302]
 gi|300301157|gb|EFJ57542.1| conserved hypothetical protein [Escherichia coli MS 185-1]
 gi|300309298|gb|EFJ63818.1| hypothetical protein HMPREF9553_00034 [Escherichia coli MS 200-1]
 gi|300358900|gb|EFJ74770.1| conserved hypothetical protein [Escherichia coli MS 198-1]
 gi|300408750|gb|EFJ92288.1| conserved hypothetical protein [Escherichia coli MS 45-1]
 gi|305852982|gb|EFM53427.1| 23S rRNA pseudouridylate synthase B [Escherichia coli NC101]
 gi|307553327|gb|ADN46102.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           ABU 83972]
 gi|307627157|gb|ADN71461.1| 23S rRNA pseudouridylate synthase B [Escherichia coli UM146]
 gi|312288267|gb|EFR16169.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           2362-75]
 gi|312945903|gb|ADR26730.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O83:H1 str.
           NRG 857C]
 gi|315289107|gb|EFU48505.1| conserved hypothetical protein [Escherichia coli MS 110-3]
 gi|315294756|gb|EFU54099.1| conserved hypothetical protein [Escherichia coli MS 153-1]
 gi|323187500|gb|EFZ72809.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           RN587/1]
 gi|323949128|gb|EGB45020.1| RNA pseudouridylate synthase [Escherichia coli H252]
 gi|323953860|gb|EGB49661.1| RNA pseudouridylate synthase [Escherichia coli H263]
 gi|323964605|gb|EGB60078.1| RNA pseudouridylate synthase [Escherichia coli M863]
 gi|323977101|gb|EGB72188.1| RNA pseudouridylate synthase [Escherichia coli TW10509]
 gi|324006121|gb|EGB75340.1| hypothetical protein HMPREF9532_04240 [Escherichia coli MS 57-2]
 gi|324011320|gb|EGB80539.1| hypothetical protein HMPREF9533_04708 [Escherichia coli MS 60-1]
 gi|327253958|gb|EGE65587.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           STEC_7v]
 gi|331045342|gb|EGI17469.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli M605]
 gi|331061103|gb|EGI33067.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli TA143]
 gi|331070014|gb|EGI41383.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli TA280]
 gi|331080385|gb|EGI51564.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli H299]
          Length = 291

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 86/288 (29%), Positives = 128/288 (44%), Gaps = 10/288 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V +     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEITPGLKIRIDGHLISVRE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           E +       ++V ++      +     R            R    ++
Sbjct: 242 ELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGGRRSGGRNN 289


>gi|257791082|ref|YP_003181688.1| pseudouridine synthase [Eggerthella lenta DSM 2243]
 gi|257474979|gb|ACV55299.1| pseudouridine synthase [Eggerthella lenta DSM 2243]
          Length = 282

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 68/273 (24%), Positives = 107/273 (39%), Gaps = 33/273 (12%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE 71
           P R+ K +ARAG ASRR  E ++   RV VNG ++      V    D + VDG  +R A+
Sbjct: 10  PMRLQKFLARAGAASRRGSENLMTAGRVTVNGKVVTELGSKVDPLVDEVAVDGAVVRLAD 69

Query: 72  RTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + L+     + T       R+         +  +  +GRLD +T GLLL + DG L
Sbjct: 70  GPVTIMLHKPAGFVTTMSDPQGRRTVAELVPTERYPGLFPIGRLDFDTTGLLLFSTDGEL 129

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA--- 187
              L  P     + Y     G+  +  L LL++GI +         V +     +     
Sbjct: 130 GNGLLHPKHHVTKRYLACVEGRPTERDLALLRRGIELDDGPTQPADVRVVEGGAARHAER 189

Query: 188 ----------------------------WVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
                                        V +G+REG+ R++K++       V  L R S
Sbjct: 190 LLEIPAAVPPRSSKEYAAVCEGRATRRSIVRLGIREGRKRQVKRMLAAVGHPVLALHRDS 249

Query: 220 YGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           +GP +LG L  G+ R +  + +          E
Sbjct: 250 FGPLELGDLPRGAWRALDAEEVAALHQAIGRAE 282


>gi|89095132|ref|ZP_01168058.1| 16S rRNA uridine-516 pseudouridylate synthase [Oceanospirillum sp.
           MED92]
 gi|89080627|gb|EAR59873.1| 16S rRNA uridine-516 pseudouridylate synthase [Oceanospirillum sp.
           MED92]
          Length = 230

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 55/231 (23%), Positives = 103/231 (44%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A++   SR+EV R +    V VN + ++  A+++   D + + G P+      
Sbjct: 1   MRLDKYLAQSTGFSRKEVRRFMKAGEVVVNDLEIKDPALHISDEDDVYLSGYPVEAPGEK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L+     + +             +LP      I  GRLD++T GL+L+T++G  A  
Sbjct: 61  YLMLHKPLGCVCSNDDSTHPTVLSLLDLPRAEELTI-CGRLDVDTTGLVLITSNGKWAHK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y+V     + QD +    KG+++  +       ++T+           V
Sbjct: 120 VTSPKHKTGKRYQVTTADPIPQDAITKFAKGLMLINEKERTKPAELTII----GEYEAEV 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            L EG+  ++K++F     KV  L R+S G   L   L  G  R ++ + +
Sbjct: 176 VLTEGRYHQVKRMFAAIGNKVEELHRVSIGAISLDEDLEPGEFRFLTDEEI 226


>gi|324996011|gb|EGC27922.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK678]
          Length = 242

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 60/232 (25%), Positives = 102/232 (43%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++++ +  V VNG   +     +    D I V G  L   + 
Sbjct: 1   MRLDKFLAENGLGSRAQVKQILKKGLVLVNGRAEKSPKTQIDERADEIVVSGQRLTYEKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T  D         +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPQGVISATEDDRHQTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            +  P     ++YR +  G ++Q  +     GI ++       Q+ +     +   + V 
Sbjct: 121 AMLSPKKHVEKIYRAQVAGLMEQADVERFAAGIELKDFTCQPAQLKILELDEAKETSLVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + L EGK  ++K++      +V  L R++ GP Q    L  G  R +++  +
Sbjct: 181 ITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQSDPALALGEWRRLTEVEM 232


>gi|83647424|ref|YP_435859.1| 16S rRNA uridine-516 pseudouridylate synthase-like protein [Hahella
           chejuensis KCTC 2396]
 gi|83635467|gb|ABC31434.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Hahella chejuensis KCTC 2396]
          Length = 323

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 82/318 (25%), Positives = 136/318 (42%), Gaps = 6/318 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL- 67
           E    +++ KVIAR G+ASRRE E  I+  RV+VNG +       V + D I VDG  + 
Sbjct: 7   EKAQGEKLQKVIARQGLASRREAEEWISGGRVRVNGKVA-HLGDRVTAEDKISVDGHKIA 65

Query: 68  --RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
                E   L        + +        +           R ++VGRLDINT GLL+ T
Sbjct: 66  MVDAEETMVLVYNKPEGEVTSRKDPEGRPTVFARLPKLKSGRWVAVGRLDINTTGLLIFT 125

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS+Q  R Y VR HG+V ++ +  L+ G++++        +      GS
Sbjct: 126 TDGELANRLMHPSSQIDREYAVRVHGEVTEEMVTRLQDGVLLEDGLAKFSDIKEAGGSGS 185

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           N W  V L+EG+NRE+++++E     V+RL R+ YG   L   +  G+     +K +   
Sbjct: 186 NRWFHVVLQEGRNREVRRLWESQGVTVSRLKRVRYGYMFLPSRVRLGNWEMAGQKDVNVL 245

Query: 245 LGPH-LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                +  +   +L           + +       P +     +  ++K   +  ++ + 
Sbjct: 246 YEMAGMQPKTVASLTPHTREKIQRQQGKSGASKPKPSNGRTGARAPARKPAAASDERRSA 305

Query: 304 PVHRRNLASNVWMAKGIH 321
           P+            +   
Sbjct: 306 PLRHSTGRKPGPGRRKPQ 323


>gi|330911132|gb|EGH39642.1| ribosomal large subunit pseudouridine synthase B LSU [Escherichia
           coli AA86]
          Length = 291

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 87/288 (30%), Positives = 129/288 (44%), Gaps = 10/288 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V +     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEITPGLKIRIDGHLISVRE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           E +       ++V ++      +T    R            R    ++
Sbjct: 242 ELVELPPETSSKVAVEKDRRRMKTNQIRRAVKRHSQVSGGRRSGGRNN 289


>gi|145594471|ref|YP_001158768.1| pseudouridine synthase [Salinispora tropica CNB-440]
 gi|145303808|gb|ABP54390.1| ribosomal large subunit pseudouridine synthase B [Salinispora
           tropica CNB-440]
          Length = 262

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 79/230 (34%), Positives = 120/230 (52%), Gaps = 1/230 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P+R+ KV+A AG+ SRR  E +I ++RV VNG + +       ++D I V+G  L+   R
Sbjct: 24  PERLQKVLAAAGVGSRRACEDLIFRRRVTVNGRVAQLGDRADPTSDTIYVNGERLQADTR 83

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLA 131
                 +KP G+V+T +D  GR+ + D L +   +    VGRLD ++EGLLLLTNDG LA
Sbjct: 84  LVYLAMNKPRGVVSTMADEKGRTAIGDFLGNRVEQRVYHVGRLDADSEGLLLLTNDGTLA 143

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  PS    + Y     G + +     L  G+ +           +    G  A V V
Sbjct: 144 HRLMHPSYGVPKTYLCEVSGPIPRSLGRRLAAGVELTDGPATVDAFRVVDTLGKTAQVEV 203

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            L EG+   ++++F+     V+RL+R S GP +LG L AG TR ++   +
Sbjct: 204 TLHEGRKHIVRRLFDAVGHPVSRLVRTSIGPIRLGDLRAGRTRRLTNAEV 253


>gi|295706927|ref|YP_003600002.1| RNA pseudouridylate synthase [Bacillus megaterium DSM 319]
 gi|294804586|gb|ADF41652.1| RNA pseudouridylate synthase [Bacillus megaterium DSM 319]
          Length = 238

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 62/224 (27%), Positives = 99/224 (44%), Gaps = 4/224 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    VKV+G  ++ A V+V      I V G  +   E 
Sbjct: 1   MRLDKLLSTIGYGSRKEVKGLLKTGAVKVDGSAVKDAKVHVNPDEQEITVHGEAVSYREF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T             L         VGRLD +TEGLLLLTNDG LA 
Sbjct: 61  VYFMLHKPQGVISATEDSLHETVLDLLELDDAVYDPFPVGRLDKDTEGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y  + +  V ++     ++G+ +         ++ + T  G  + + +
Sbjct: 121 QLLSPKKHVPKTYFAKINAPVTEEDAEAFRQGVTLDDGYVTKSAELKILT-SGVESEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
            + EGK  ++K++FE    KV  L R+S G   L   L  G  R
Sbjct: 180 TIVEGKFHQVKRMFEARGKKVTYLKRLSMGALLLDESLDLGEYR 223


>gi|49187595|ref|YP_030848.1| RNA pseudouridylate synthase [Bacillus anthracis str. Sterne]
 gi|229093808|ref|ZP_04224907.1| Pseudouridine synthase [Bacillus cereus Rock3-42]
 gi|229124274|ref|ZP_04253465.1| Pseudouridine synthase [Bacillus cereus 95/8201]
 gi|49181522|gb|AAT56898.1| RNA pseudouridylate synthase [Bacillus anthracis str. Sterne]
 gi|228659175|gb|EEL14824.1| Pseudouridine synthase [Bacillus cereus 95/8201]
 gi|228689693|gb|EEL43501.1| Pseudouridine synthase [Bacillus cereus Rock3-42]
          Length = 233

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 59/223 (26%), Positives = 100/223 (44%), Gaps = 4/223 (1%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTRLWLYHKP 81
            G  SR+EV++++    VK++GI ++ A V+V      + + G  +   E   L ++   
Sbjct: 1   MGYGSRKEVKKLLKDGVVKIDGISVKDAKVHVNVEEQEVMIHGEVVEYKEFVYLMMHKPQ 60

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
             +  T  D          L         VGRLDI+TEG LL+TNDG L+  L  P    
Sbjct: 61  GVISATEDDNHETVIDLLELEDAIFNPFPVGRLDIDTEGFLLITNDGKLSHQLLSPKKHV 120

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
            + Y     G V ++ +    KG+++          +T+  +    + + + + EGK  +
Sbjct: 121 PKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEIELVITEGKFHQ 179

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           +K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 180 VKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 222


>gi|261346079|ref|ZP_05973723.1| ribosomal small subunit pseudouridine synthase A [Providencia
           rustigianii DSM 4541]
 gi|282565731|gb|EFB71266.1| ribosomal small subunit pseudouridine synthase A [Providencia
           rustigianii DSM 4541]
          Length = 234

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 54/238 (22%), Positives = 108/238 (45%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +    + V+  +++  ++ + + + +  DG  L +    
Sbjct: 1   MRLDKFLSQQLGISRNLVARELRAGNITVDDKVVKSGSMQISADNEVSYDGNVLIQITGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V +  DP   + ++     +  ++ + GRLDI+T GL+LLT+DG  +  
Sbjct: 61  RYFMLHKPEGYVCSTDDPTHPTILYFIDEPVTQKLHAAGRLDIDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + YRV+    +  D +   + G+++ G        Q+ +     S   V +
Sbjct: 121 ITSPKHHCEKTYRVQLSEDITDDVIQKFEIGVMLNGEKSPTKPAQLEII----SPREVLL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
            + EG+  ++K++F      V  L R   G  +L   L  G  R +++  +     P 
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVCGLHRERVGEIRLDEQLEPGEYRPLTEDEINSITVPR 234


>gi|325201930|gb|ADY97384.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M01-240149]
          Length = 256

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 71/245 (28%), Positives = 121/245 (49%), Gaps = 7/245 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  ++   
Sbjct: 2   EPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLKW 60

Query: 72  RTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             RL      Y +   +V+        S       +  SR +++GRLDINT GLL+LT  
Sbjct: 61  ADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTTS 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN 186
           G L +    PS +  R Y VR  G +  +++ +L +  ++++       ++     +G+N
Sbjct: 121 GELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGAN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
            W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   E++   +   +
Sbjct: 181 KWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFYELNPAEVANII 240

Query: 246 GPHLL 250
               +
Sbjct: 241 KWADM 245


>gi|109899133|ref|YP_662388.1| pseudouridine synthase, Rsu [Pseudoalteromonas atlantica T6c]
 gi|109701414|gb|ABG41334.1| ribosomal large subunit pseudouridine synthase B [Pseudoalteromonas
           atlantica T6c]
          Length = 289

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 89/289 (30%), Positives = 126/289 (43%), Gaps = 8/289 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+A AG+ SRRE+E+ IA  R+ VNG +       V   D + VDG  +  A  
Sbjct: 2   SEKLQKVLANAGVGSRREMEKWIASGRISVNGKVAT-LGDRVEPLDQLRVDGNLITAAAK 60

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 L        L +        +           R I+VGRLDINT GLLL TNDG
Sbjct: 61  STICRVLMYNKPEGELCSRKDPQGRPTVFDRLPKIQNGRWIAVGRLDINTSGLLLFTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--N 186
            LA  L  P  +  R Y VR  G+VD D +  LKKG+ ++       +V          N
Sbjct: 121 ELANRLMHPKHEIEREYAVRVFGEVDDDMIKRLKKGVELEDGVSKFTEVRKRPGDDESLN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
           +W  V L EGKNRE+++++E    +V+RLIR+ YG   L   L  G   E+    L    
Sbjct: 181 SWYNVSLSEGKNREVRRLWESQGLQVSRLIRVRYGTLNLQNRLPQGGWIELPLTDLNTLR 240

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
               L+  Q +L     +    VR      S       + +  +  K  
Sbjct: 241 KSVQLDLEQESLIEDKQTKLDHVRLSRMRRSVQKHKVNQGRAKARPKKK 289


>gi|313665476|ref|YP_004047347.1| pseudouridylate synthase [Mycoplasma leachii PG50]
 gi|312949302|gb|ADR23898.1| pseudouridylate synthase [Mycoplasma leachii PG50]
          Length = 252

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 69/249 (27%), Positives = 122/249 (48%), Gaps = 5/249 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--RKAE 71
           +R+ KVI+  G  SRR  E++I + R+KVN  ++ +  V +     I +D   +      
Sbjct: 4   ERLQKVISSRGYCSRRTAEKLILENRIKVNNQIINKLGVKIDPKAEIIIDNKLVTSDSNN 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +   +L++KP  ++TT  DP  R TV D    +  RV  VGRLD +  GLL++TNDG L+
Sbjct: 64  QKYYYLFYKPRLVLTTMYDPKKRKTVADYFKDLNHRVYPVGRLDYDVSGLLIMTNDGELS 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD--MQVTLDTQKGSNAW 188
             +  P  ++L+ Y+    GQV + ++N L KG+ I           ++    +  + + 
Sbjct: 124 NFIMHPKYEFLKTYQGLCQGQVSKQQVNQLIKGVYIDNNYLTKAYSAKLVKYDKLKNVSI 183

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           V + + EGK   +KK+FE    ++ +L R      ++  L  G  RE+    +++  G +
Sbjct: 184 VELTINEGKKHHVKKMFESIQAQLLKLKRTKIEFLEIDNLKPGQYRELKIHEIKKLYGIY 243

Query: 249 LLEEAQVNL 257
              +     
Sbjct: 244 HSLKQNNKK 252


>gi|54112711|gb|AAV28989.1| NT02FT0029 [synthetic construct]
          Length = 271

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 86/259 (33%), Positives = 125/259 (48%), Gaps = 9/259 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+  N + +   P+R+ K++A+ GI SRR++E  I Q RVKVNG +           D I
Sbjct: 1   MRRANQINDKN-PERLQKLLAKYGIGSRRKIEEYIEQGRVKVNGKVAT-LGDKASEADKI 58

Query: 61  EVDGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
             DG  L            +  + +   + T+  + D ++          SR I VGRLD
Sbjct: 59  SFDGKALHSYGQPMTRPRVVIYHKREGEVCTSKDEKDRQTVFDSLPKLAKSRWIMVGRLD 118

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGD 174
           INT GLLL T DG LA  L  PS Q  R Y VR  GQ    + +N LK+GI ++      
Sbjct: 119 INTTGLLLFTTDGDLANRLMHPSYQIEREYAVRVFGQQLSDETINKLKEGIQLEDGMAKF 178

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGST 233
             +     +G+N W  V L EG+NRE++++FE     V+RL RI +G   L   +  G T
Sbjct: 179 NSIKFSGGEGANLWYYVTLSEGRNREVRRMFEAVGVTVSRLTRIRFGDIILPKFVSRGKT 238

Query: 234 REVSKKILREQLGPHLLEE 252
            E++   +        L+E
Sbjct: 239 LELNPSEVNRLRKSVKLKE 257


>gi|269214394|ref|ZP_05986473.2| ribosomal large subunit pseudouridine synthase B [Neisseria
           lactamica ATCC 23970]
 gi|269209982|gb|EEZ76437.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           lactamica ATCC 23970]
          Length = 350

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 74/256 (28%), Positives = 126/256 (49%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++     +F P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+
Sbjct: 85  LKERRSDLSHFEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHV 143

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 144 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 203

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++  L +  ++++       
Sbjct: 204 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTTEQMRSLTEEGVMLEDGLAKVE 263

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   
Sbjct: 264 RIYEQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFY 323

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   L    +
Sbjct: 324 ELNPAEVANILKWADM 339


>gi|117623529|ref|YP_852442.1| 23S rRNA pseudouridylate synthase B [Escherichia coli APEC O1]
 gi|115512653|gb|ABJ00728.1| 23S rRNA pseudouridylate synthase [Escherichia coli APEC O1]
          Length = 291

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 85/288 (29%), Positives = 128/288 (44%), Gaps = 10/288 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ K++ARAG  SRRE+E +I   RV V+G + +    V +     I +DG  +   E
Sbjct: 2   SEKLQKLLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEITPGLKIRIDGHLISVRE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           E +       ++V ++      +     R            R    ++
Sbjct: 242 ELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGGRRSGGRNN 289


>gi|224369318|ref|YP_002603482.1| RluB [Desulfobacterium autotrophicum HRM2]
 gi|223692035|gb|ACN15318.1| RluB [Desulfobacterium autotrophicum HRM2]
          Length = 230

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 100/231 (43%), Gaps = 5/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A AG+ SRR  E  I + RV VN  ++      +    D +EVD  P+  A  
Sbjct: 1   MRLQKFLAHAGVCSRRRGEVYILEGRVSVNHKVVISLGTKIDPEIDLVEVDKKPIVLASE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                           S       V  +L  I  RV  +GRLD ++ GLLLLT+DG L  
Sbjct: 61  KAKIYIALNKPAGVVSSCSHPGEKVVVDLIDIKDRVYPIGRLDKDSVGLLLLTDDGNLHN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS    + Y V     ++ + L  +  GIV+ G      +V   +         + 
Sbjct: 121 RLSHPSFDHEKEYVVETTAPINDEALAQMAAGIVLDGKITRKARVRRLSDNR----FNIV 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           L++G NR+I+++      +V  L R+  G  +LG L  G  R ++   +R 
Sbjct: 177 LKQGINRQIRRMVTAVGNRVKLLKRVRMGSVRLGNLGTGKWRYLTDTEVRA 227


>gi|311278834|ref|YP_003941065.1| pseudouridine synthase [Enterobacter cloacae SCF1]
 gi|308748029|gb|ADO47781.1| pseudouridine synthase [Enterobacter cloacae SCF1]
          Length = 235

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 101/231 (43%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G +++  A  +     +  DG  L +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRASRVTVDGDIVKDTAFKLQPEHDVAYDGNSLVQQTGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAHKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + YRV     + +D       GI +          Q+ + T       V +
Sbjct: 121 ITSPRHHCEKTYRVTLESPLAEDTAEQFAHGIQLHNEKALTKPAQLEVITA----TEVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F      V  L R   G   L   L  G  R +++  +
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVGLHRERIGAIALDPELEPGGYRPLTEDEI 227


>gi|295095683|emb|CBK84773.1| ribosomal large subunit pseudouridine synthase B [Enterobacter
           cloacae subsp. cloacae NCTC 9394]
          Length = 291

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 86/289 (29%), Positives = 129/289 (44%), Gaps = 12/289 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM--STDHIEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E +I   RV V+G +       V       I +DG  +   
Sbjct: 2   SEKLQKVLARAGHGSRREIEAIIEAGRVSVDGKIAT-LGDRVEIVPGLKIRIDGHLISVK 60

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E        L  Y     L T +      +          +R I+VGRLD+NT GLLL T
Sbjct: 61  ESAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  GQVD++KL  L +G+ ++        +     +G 
Sbjct: 121 TDGELANRLMHPSREVEREYAVRVFGQVDENKLRDLSRGVQLEDGPAAFKTIKFTGGEGI 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKIL 241
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       L
Sbjct: 181 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDILLPKGLPRGGYTELDLTQTNYL 240

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           R+ +G      ++V ++      +     R            R    ++
Sbjct: 241 RDLVGLTPETTSKVAVEKDRRRMKANQIRRAVKRHSQVSSNRRSGSRNN 289


>gi|94500050|ref|ZP_01306585.1| ribosomal small subunit pseudouridine synthase [Oceanobacter sp.
           RED65]
 gi|94427908|gb|EAT12883.1| ribosomal small subunit pseudouridine synthase [Oceanobacter sp.
           RED65]
          Length = 236

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 108/232 (46%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     SR E  + + Q+RV VNG L++  +  V + D + +DG  +      
Sbjct: 1   MRLDKFLANYSSLSRTEATKALKQKRVLVNGDLVKTGSHKVANDDQVWLDGRRIEMNTA- 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP   +  ++DP           +    + +VGRLD++T GLLL+T+DG  +  
Sbjct: 60  VYFMMNKPANYLCANADPQHALVFDLIDEASTYVLHTVGRLDLDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           L  P     + YRV     +  D     ++G+++  +       ++       ++  V +
Sbjct: 120 LTSPKHHIPKTYRVWLDEPLVADAEIQCEQGLLLRSESKPTLPAELNRI----TDTEVLI 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EG+  ++K++F     +V RL R   GP +L   L  G  R ++++ L 
Sbjct: 176 TISEGRYHQVKRMFAAMGNRVVRLHRERIGPLELDPNLAPGEYRSLTQQELD 227


>gi|293409653|ref|ZP_06653229.1| conserved hypothetical protein [Escherichia coli B354]
 gi|291470121|gb|EFF12605.1| conserved hypothetical protein [Escherichia coli B354]
          Length = 291

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 86/288 (29%), Positives = 128/288 (44%), Gaps = 10/288 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V +     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEITPGLKIRIDGHLISVRE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDTKLRDLSRGVQLEDGPAAFKTIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           E +       ++V ++      +     R            R    ++
Sbjct: 242 ELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGGRRSGGRNN 289


>gi|167824420|ref|ZP_02455891.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 9]
          Length = 374

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 76/274 (27%), Positives = 124/274 (45%), Gaps = 6/274 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 66  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 124

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 125 GKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNTE 184

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 185 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQRLLHGVELDDGPANFLRIRD 244

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 245 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 304

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRP 272
             +R  +    L+    +            +  P
Sbjct: 305 AQVRRLMSTVGLKAPTEDKGGKRGGPAERRQPDP 338


>gi|303326819|ref|ZP_07357261.1| ribosomal large subunit pseudouridine synthase B [Desulfovibrio sp.
           3_1_syn3]
 gi|302862807|gb|EFL85739.1| ribosomal large subunit pseudouridine synthase B [Desulfovibrio sp.
           3_1_syn3]
          Length = 244

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 78/236 (33%), Positives = 120/236 (50%), Gaps = 3/236 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA  G+ SRR+ + +I   +V++NG L E  A  V+  D I V+   L  A+  
Sbjct: 1   MRLNKAIAATGLCSRRKADELILAGQVRINGTLEENPARRVLPGDCIAVNDRELAAAQEY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
              L HKP+  V T +DP+GR TV   LP       +  VGRLD  +EGLLLLTNDG LA
Sbjct: 61  YYLLLHKPVQTVCTVNDPEGRPTVMAYLPPEVRHLRLYPVGRLDYFSEGLLLLTNDGELA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVT 190
           + L  P     + Y V   G V +  L  +++G+ +        + V   T +  N  + 
Sbjct: 121 QRLTHPRHHQPKTYEVLIRGSVPETALAAMRRGMRLDEGQALLPVDVEAKTAENGNTLLR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + L +G NR+I+++       + RL R++ GP  LG L  G+ R ++   + +   
Sbjct: 181 MVLHQGVNRQIRRMCRDLGLTILRLRRVAQGPLALGNLKPGAARALTTGEVADLRQ 236


>gi|294507508|ref|YP_003571566.1| ribosomal large subunit pseudouridine synthase B [Salinibacter
           ruber M8]
 gi|294343836|emb|CBH24614.1| ribosomal large subunit pseudouridine synthase B [Salinibacter
           ruber M8]
          Length = 261

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 68/241 (28%), Positives = 111/241 (46%), Gaps = 3/241 (1%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
             +    R++K IA AG+ SRR+ + ++ Q RV ++G  +++    V     + VDG  +
Sbjct: 17  SSDREGMRINKYIAHAGVCSRRDADDLVEQGRVHIDGERVDQHGTRVREGQTVTVDGEEV 76

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLT 125
              E   L L      + TT    D R+ +          S +  VGRLD NT G+LL++
Sbjct: 77  YPLEFEYLLLNKPKDTISTTDDPKDRRTVLDAIGVPEDNPSGLFPVGRLDRNTTGVLLVS 136

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  P  +  ++Y VR    V   +L+ LK+G+ +        QV     +  
Sbjct: 137 NDGDLAHRLMHPRYEIPKIYYVRLQDDVKPHQLDQLKRGVELSDGAAAADQVAYLDPQR- 195

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
              + + L EG+NR+I+++ E     + +L R  Y     G L  G  R +  + +RE  
Sbjct: 196 KTDIALELHEGRNRQIRRMMEALGHTIVQLERAKYATLTTGRLQRGEWRRLEPEEVRELY 255

Query: 246 G 246
            
Sbjct: 256 Q 256


>gi|91226537|ref|ZP_01261286.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           alginolyticus 12G01]
 gi|91189169|gb|EAS75450.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           alginolyticus 12G01]
          Length = 233

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 47/230 (20%), Positives = 97/230 (42%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  A+R++  ++I    + V+G + +  A  V     +  +   +      
Sbjct: 1   MRLDKYLCDALGATRKQATKIIKSGDITVDGEVQKSGAFKVPKGAEVMWEDRVIGAPGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + LY     + +     +  +            +   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLYKPADFVCSHEDGYNQ-TAFALLDEPKIENLHFAGRLDVDTTGLVLITDDGKWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     +  D    L++GI+++      +   L+    +   V + +
Sbjct: 120 ITSPKHKCEKTYRVWLVDAIQPDYAEKLEQGIILRNESEATLPARLEIVNEAENEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            EGK  ++K++F     KV  L R   G  +L   L  G  R ++++ + 
Sbjct: 180 VEGKYHQVKRMFAALGNKVEYLHRERIGSIELDEALEPGDYRHLTQEEID 229


>gi|302387646|ref|YP_003823468.1| pseudouridine synthase [Clostridium saccharolyticum WM1]
 gi|302198274|gb|ADL05845.1| pseudouridine synthase [Clostridium saccharolyticum WM1]
          Length = 262

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 66/246 (26%), Positives = 111/246 (45%), Gaps = 15/246 (6%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
                R++K ++ AGI SRRE +R I   +V +NG         V+    + ++G  ++ 
Sbjct: 2   ETEGIRLNKFLSEAGICSRREADRFIEAGKVSINGKAAAT-GQKVLPGQSVTINGRTVQA 60

Query: 70  -------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
                   E       HKP G+V T S  D    + D +     R+  VGRLD ++EGL+
Sbjct: 61  GKGDQSHKEEPVFLAVHKPRGIVCTTSHKDRAPNIVDMVDY-PVRIYPVGRLDKDSEGLI 119

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLD 180
           L+TN G L   +        + Y V+ +  V  D +  +KKG+ +    +      VT  
Sbjct: 120 LMTNQGSLVNKMMRSGNAHEKEYLVKVNRPVTDDFIRTMKKGVFLPELNVTTKPCFVTKA 179

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +K       + L +G NR+I+++     ++V  L R+     +LG L  G+ RE+SK+ 
Sbjct: 180 GEKA----FRIVLTQGLNRQIRRMCSQLGFEVRMLKRMRIMNIELGDLKPGAYRELSKRE 235

Query: 241 LREQLG 246
             +   
Sbjct: 236 YHQMKE 241


>gi|197301684|ref|ZP_03166754.1| hypothetical protein RUMLAC_00410 [Ruminococcus lactaris ATCC
           29176]
 gi|197299124|gb|EDY33654.1| hypothetical protein RUMLAC_00410 [Ruminococcus lactaris ATCC
           29176]
          Length = 246

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 65/245 (26%), Positives = 113/245 (46%), Gaps = 5/245 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R ++++ I++ +V VNG + + A   +    D +   G  +  AE  
Sbjct: 4   RLDKYLADMGLGTRSQIKKDISKGQVLVNGTVSKDAGTRIDTEKDQVSYLGQTVTYAEYE 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      +V+   D   R+ +          +  VGRLD +TEGLLL+TNDG LA  
Sbjct: 64  YYMLNKPAG-VVSATEDRHDRTVLDLIDTKQRKDLFPVGRLDKDTEGLLLITNDGALAHR 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           L  P +   +VY  R  G+V  + + L +KG+ I +       ++ +     + + + + 
Sbjct: 123 LLSPKSHVDKVYFARIEGKVTAEDVFLFQKGVDIGEQALTLPARLEIL-SSDTVSEIRLT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLLE 251
           + EGK  ++K++FE    KV  L R+S G   L   L  G+ R ++   +R        E
Sbjct: 182 ICEGKFHQVKRMFESVGKKVLYLKRLSMGTLILDDLLPPGAYRTLTAGEIRSLQTISKKE 241

Query: 252 EAQVN 256
                
Sbjct: 242 TGDKE 246


>gi|313668495|ref|YP_004048779.1| pseudouridine synthase [Neisseria lactamica ST-640]
 gi|313005957|emb|CBN87414.1| putative pseudouridine synthase [Neisseria lactamica 020-06]
          Length = 350

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 74/256 (28%), Positives = 127/256 (49%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++     +F P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+
Sbjct: 85  LKERRSDLSHFEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHV 143

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 144 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 203

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L +  ++++       
Sbjct: 204 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRMLTEEGVMLEDGLAKVE 263

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   
Sbjct: 264 RIYEQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFY 323

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   L    +
Sbjct: 324 ELNPAEVANILKWADM 339


>gi|167836825|ref|ZP_02463708.1| RNA pseudouridylate synthase family protein [Burkholderia
           thailandensis MSMB43]
          Length = 358

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 77/300 (25%), Positives = 126/300 (42%), Gaps = 9/300 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++       ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 60  KRVLSPEDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRIN 118

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 119 GKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNTE 178

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 179 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRIRD 238

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++F+     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 239 GGGEGTNHWYHVALAEGRNREVRRMFDAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 298

Query: 239 KILRE---QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
             +R     +G     E +          +                 T   +    + G 
Sbjct: 299 AQVRRLMSTVGLKAPTEEKGKRGGATERRQPDPMQTSMGFINREPVLTTHGQLDQPRRGR 358


>gi|254303709|ref|ZP_04971067.1| pseudouridylate synthase [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
 gi|148323901|gb|EDK89151.1| pseudouridylate synthase [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
          Length = 226

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 67/229 (29%), Positives = 106/229 (46%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   GI SR+EV+++I+   + VNG     A  N+    D IE +G  L   E 
Sbjct: 1   MRLDKFLVECGIGSRKEVKKLISNDEITVNGFNDISAKDNIDENSDIIEYNGEKLEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +  K   +  T    +           I   +  VGRLD +TEGLLL TNDG L  
Sbjct: 61  RYYIMNKKAGYITATEDFKENTVMDLLPEWVIRKDLAPVGRLDKDTEGLLLFTNDGKLNH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VY +     +    +  L++G+ I        +V    +K S+  + + 
Sbjct: 121 RLLSPKNHIDKVYYIEIENNILDKDILKLEQGVDIGNYITQPAKV----EKISDNKIYLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++EGK  ++KK+ E  N KV  L R+S+G  +L  L  G  +EV+ + +
Sbjct: 177 IKEGKFHQVKKMLEAVNNKVCYLKRVSFGKLKLDDLALGEVKEVNLEDI 225


>gi|77405184|ref|ZP_00782282.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae H36B]
 gi|77411049|ref|ZP_00787403.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae CJB111]
 gi|77162872|gb|EAO73829.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae CJB111]
 gi|77176186|gb|EAO78957.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae H36B]
          Length = 240

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 57/233 (24%), Positives = 104/233 (44%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+ ++ ++++ VNG       V V    D I+ +G  +   + 
Sbjct: 1   MRLDKFLVECGLGSRTQVKLILKKKQISVNGNSETSPKVQVDEYRDEIKYNGTLVSYEKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T            +  +    V  VGRLDI+T GLLL+TN+G LA 
Sbjct: 61  VYYMLHKPKGVISATDDPSHKTVLDLLDKTARDKAVFPVGRLDIDTTGLLLITNNGELAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVT 190
            +  P     + Y  +  G + +D +    KGI+++         ++    Q    + V 
Sbjct: 121 KMLSPKKHVDKCYEAKISGIMTEDDILAFDKGIILKDFTCLPALLEIVEVNQVKKQSLVK 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           + ++EGK  ++K++      +V  L R+S G  QL   L +G  R ++ K + 
Sbjct: 181 ITIKEGKFHQVKRMVAACGKEVLELKRLSMGNLQLDKQLESGQWRRLTIKEIE 233


>gi|328956893|ref|YP_004374279.1| 16S pseudouridylate synthase [Carnobacterium sp. 17-4]
 gi|328673217|gb|AEB29263.1| 16S pseudouridylate synthase [Carnobacterium sp. 17-4]
          Length = 239

 Score =  164 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 100/234 (42%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A  G  +R+ V+ ++  + V VNG + +     V    D I V G  +   E 
Sbjct: 1   MRLDKLLANMGFGTRKTVKNVLKAKEVTVNGTMEKDGKTQVDPDKDVIVVSGEAVHYQEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               ++     +  T  +                    VGRLD +TEGLLLLTNDG LA 
Sbjct: 61  VYFMMHKPQGVVSATIDNLHETVIDLLQPQDQVFDPFPVGRLDKDTEGLLLLTNDGTLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQK--GSNAWV 189
            L  P     + Y     G V++  +   K GI +         ++ + +         +
Sbjct: 121 NLLSPKKHVDKCYEAIIEGLVNEQDIQAFKDGITLNDGFICQSAKLEILSTDLEKEQTLI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            V + EGK  ++K++FE  +  VN L R+S G  QL   +  G+ R ++ + L 
Sbjct: 181 HVTIHEGKFHQVKRMFEAVDKSVNYLKRLSMGKLQLDETVEIGNYRPLTNEELE 234


>gi|332161874|ref|YP_004298451.1| 23S rRNA pseudouridylate synthase B [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|318605612|emb|CBY27110.1| ribosomal large subunit pseudouridine synthase B; LSU Psi2605
           [Yersinia enterocolitica subsp. palearctica Y11]
 gi|325666104|gb|ADZ42748.1| 23S rRNA pseudouridylate synthase B [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330860992|emb|CBX71265.1| ribosomal large subunit pseudouridine synthase B [Yersinia
           enterocolitica W22703]
          Length = 349

 Score =  164 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 92/333 (27%), Positives = 141/333 (42%), Gaps = 20/333 (6%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGV 65
           +     +++ K++ARAG  SRRE+E +I Q RV V+G +  +    V  T    I +DG 
Sbjct: 29  KTKVVGEKLQKILARAGHGSRREIETIIQQGRVSVDGKI-SKLGDRVEVTQATKIRLDGH 87

Query: 66  PLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            L   E        L  Y     L T +      +          SR ++VGRLD+NT G
Sbjct: 88  LLSIKESEEAVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSG 147

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLL T DG LA  L  PS +  R Y VR  GQ+D +K+  L +G+ ++        +T  
Sbjct: 148 LLLFTTDGELANRLMHPSREVEREYAVRVFGQIDDEKIKQLSRGVQLEDGPAAFRTITFQ 207

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
             +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+   
Sbjct: 208 GGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELD-- 265

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
            L+       L E      + +   +   R + N I                +    +  
Sbjct: 266 -LKATNYLRELVELDSETVSKLSVEKDRRRVKANQIRRAVKR--------HTEVAGRQVA 316

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQRE 332
                  + +   NV  A    ++    S +R 
Sbjct: 317 GRQGSARKGSTRQNVGNAAPAAATGRRGSNKRG 349


>gi|319763718|ref|YP_004127655.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
 gi|330824019|ref|YP_004387322.1| pseudouridine synthase Rsu [Alicycliphilus denitrificans K601]
 gi|317118279|gb|ADV00768.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
 gi|329309391|gb|AEB83806.1| pseudouridine synthase Rsu [Alicycliphilus denitrificans K601]
          Length = 451

 Score =  164 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 74/301 (24%), Positives = 122/301 (40%), Gaps = 6/301 (1%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          V   D I+V+
Sbjct: 121 KRVLLPQPESPKLHKVLAQAGMGSRLEMEQLILEGRISVNNEPA-HIGQRVQFGDQIKVN 179

Query: 64  GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+R          +  +     +VT     +  +           +  SVGRLD+NTE
Sbjct: 180 GKPIRFRVAPPPTRVIAYHKPVGEVVTHDDPQNRPTVFRKLPRLQQGKWQSVGRLDLNTE 239

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL T+ G LA  L  P     R Y VR  G +  ++   L  G+ ++        +  
Sbjct: 240 GLLLFTSSGELANKLMHPRFGLEREYAVRVLGALSDEERQRLLDGVSLEDGMAAFGSIED 299

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E+ +
Sbjct: 300 GGGEGANCWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMMLPRGLKRGAWLELDE 359

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             +R  +    +            +     R       +         +           
Sbjct: 360 HDIRALMQAAGVPADAGGGARAGRNGRRGERKPMGAKMQGEGRGKAAGRAGRSSGSSQPD 419

Query: 299 K 299
            
Sbjct: 420 P 420


>gi|262171355|ref|ZP_06039033.1| ribosomal small subunit pseudouridine synthase A [Vibrio mimicus
           MB-451]
 gi|261892431|gb|EEY38417.1| ribosomal small subunit pseudouridine synthase A [Vibrio mimicus
           MB-451]
          Length = 231

 Score =  164 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 47/231 (20%), Positives = 93/231 (40%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++ +  V V+ ++ +  A  +  T  +E     +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKRGEVTVDDVVQKSGAFKLKETSCVEWQDREITLHGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     + +       ++            +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDG-FNQTAFTLLDEVNIEDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + YRV     +  D       GI ++G        Q+ +     S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLAEPIQADYAEQFTNGIELRGERELTLPAQLEIV----SETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R   G   L   L  G  R +++  +
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDESLEPGEYRYLTEDEV 226


>gi|256825344|ref|YP_003149304.1| pseudouridine synthase family protein [Kytococcus sedentarius DSM
           20547]
 gi|256688737|gb|ACV06539.1| pseudouridine synthase family protein [Kytococcus sedentarius DSM
           20547]
          Length = 284

 Score =  164 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 74/239 (30%), Positives = 128/239 (53%), Gaps = 1/239 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
               +R+ KV+A AG+ SRR  E+MIA  RV+V+G+ +    V +  +   + VDG+P++
Sbjct: 43  TSQGERLQKVLAAAGLGSRRACEQMIADGRVEVDGVPVTELGVRIDPSRQKVAVDGLPVQ 102

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             +     +++KP+G+++T  D +GR +V D   +   R+  VGRLD +T GLLLLTNDG
Sbjct: 103 LDDSKVYLVFNKPVGVISTMEDEEGRLSVGDYTYTRKERLFHVGRLDQDTSGLLLLTNDG 162

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L+ PS    + Y  +  G V +   NLL++G+ ++         ++   +   A 
Sbjct: 163 ELAHRLQHPSYSVPKTYVAKVPGPVKKGLGNLLREGVELEDGVVKVDDFSVVASQPGWAM 222

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           V + + EG+   ++++ E   + V  L+R   G  ++G L  G+ R V+   L   +  
Sbjct: 223 VQLVIHEGRKHVVRRLLEEVGYPVEELVRTQVGEIRMGDLRPGNLRAVTPDELARTMKL 281


>gi|330015788|ref|ZP_08308280.1| 16S pseudouridylate 516 synthase [Klebsiella sp. MS 92-3]
 gi|328530489|gb|EGF57362.1| 16S pseudouridylate 516 synthase [Klebsiella sp. MS 92-3]
          Length = 239

 Score =  164 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 57/243 (23%), Positives = 103/243 (42%), Gaps = 7/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G +++ A+  +     +E DG  L +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGSRVTVDGDIVKDASFKLQPEHEVEYDGNTLTQQNGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTILYFLDEPVAHKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     + +    L  KG+ +                +  +   V +
Sbjct: 121 ITSPRHHCEKTYLVALENPLAEGTAELFAKGVQLHNEKDLTKPA----LLEVITPTEVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLL 250
            + EG+  ++K++F      V  L R   G   L   L  G  R +++  +     P   
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVGLHRERIGDILLDESLAPGEYRPLTEAEIASVGAPQPR 236

Query: 251 EEA 253
            + 
Sbjct: 237 SKT 239


>gi|320540531|ref|ZP_08040181.1| putative 23S rRNA pseudouridylate synthase [Serratia symbiotica
           str. Tucson]
 gi|320029462|gb|EFW11491.1| putative 23S rRNA pseudouridylate synthase [Serratia symbiotica
           str. Tucson]
          Length = 299

 Score =  164 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 87/298 (29%), Positives = 132/298 (44%), Gaps = 10/298 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E MI   RV V+G + +    V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIEAMIDAGRVSVDGKIAKLGDRVEVNPAMKIRMDGHVVSVKE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T        +          SR ++VGRLD+NT GLLL T 
Sbjct: 62  SEEAVCRVLAYYKPEGELCTHSDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  P+ +  R Y VR  GQ D D +  LKKG+ ++        +     +G N
Sbjct: 122 DGELANRLMHPNREVEREYAVRVFGQTDDDSVKQLKKGVQLEDGPAAFRTIDFQGGEGLN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK---KILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIALPKGLPRGGWAELDLNAINYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
             +G      +++ ++      +     R           +  +     K+G   +++
Sbjct: 242 ALVGLKPETVSKMPVERERRRMKANQIRRAVKRHIQVTGSSGRRNAPGSKSGRPSKRR 299


>gi|238757070|ref|ZP_04618258.1| Ribosomal large subunit pseudouridine synthase B [Yersinia aldovae
           ATCC 35236]
 gi|238704900|gb|EEP97429.1| Ribosomal large subunit pseudouridine synthase B [Yersinia aldovae
           ATCC 35236]
          Length = 349

 Score =  164 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 90/329 (27%), Positives = 137/329 (41%), Gaps = 16/329 (4%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGV 65
           +     +++ KV+ARAG  SRRE+E +I Q RV V+G +       V  T    I +DG 
Sbjct: 29  KTKVVGEKLQKVLARAGHGSRREIETIIQQGRVSVDGKI-STLGDRVEVTQATKIRLDGH 87

Query: 66  PLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            L   E        L  Y     L T +      +          SR ++VGRLD+NT G
Sbjct: 88  LLSIKESEETVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSG 147

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLL T DG LA  L  PS +  R Y VR  G +D +K+  L +G+ ++        ++  
Sbjct: 148 LLLFTTDGELANRLMHPSREVEREYAVRVFGLIDDEKIKQLSRGVQLEDGPAAFRTISFQ 207

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
             +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+   
Sbjct: 208 GGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELD-- 265

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
            L+       L E          S   + +DR  + +       +     + +    +Q 
Sbjct: 266 -LKATNYLRQLVEMDSETV----SKLPVEKDRRRVKANQIRRAVKRHTEVAGRQVAGRQG 320

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDS 328
                  R+N  +    A           
Sbjct: 321 SARKGSTRQNTGNAAPAATAGRRGTNKRG 349


>gi|260463018|ref|ZP_05811221.1| pseudouridine synthase [Mesorhizobium opportunistum WSM2075]
 gi|259031139|gb|EEW32412.1| pseudouridine synthase [Mesorhizobium opportunistum WSM2075]
          Length = 259

 Score =  164 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 65/227 (28%), Positives = 107/227 (47%), Gaps = 1/227 (0%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTR 74
           +++ +++ G+ SR + E +I + RV+V G ++   A+ V    D I VDG  +    +  
Sbjct: 28  LNRALSKLGLCSRTQAELLITEGRVRVGGKVVRDPALRVDLNRDSIVVDGEKVIAERKVY 87

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L      + T        +            +  VGRLD  +EGLLL+TND   A  L
Sbjct: 88  VMLNKPRGLVTTRDDPQQRDTVYACLEALDLPFISPVGRLDKASEGLLLMTNDTRFANRL 147

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P++   + Y V+     D   L  L+ G  + G       + L    G  AW+ V L 
Sbjct: 148 MDPASHLPKTYHVQVATVPDAAMLETLRAGATVDGEILTANSIDLLRSGGRTAWLEVVLD 207

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           EG+NR I+++    + +V RLIRI+ G  +LG L  G+ R ++ + L
Sbjct: 208 EGRNRHIRRLLAAHDIEVLRLIRIAIGGLRLGDLAKGTARHLTAEEL 254


>gi|116670095|ref|YP_831028.1| pseudouridine synthase, Rsu [Arthrobacter sp. FB24]
 gi|116610204|gb|ABK02928.1| Pseudouridine synthase, Rsu [Arthrobacter sp. FB24]
          Length = 406

 Score =  164 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 85/234 (36%), Positives = 127/234 (54%), Gaps = 2/234 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
           +    R+ KV+A AG+ASRR  E MI++ RV+V+G ++    V V   T  I VDG+ ++
Sbjct: 164 DADGIRLQKVMASAGVASRRVCEEMISEGRVEVDGKVVTELGVRVDPKTAVIHVDGLRIQ 223

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
             E     +++KP G+V+T  DPDGR  + D + +    R+  VGRLD+ TEGLLLLTND
Sbjct: 224 LDENMVYMVFNKPKGVVSTMEDPDGRPCISDFVRNTHGERLFHVGRLDVATEGLLLLTND 283

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  + Y V+  G   Q     LK G+ ++          L      + 
Sbjct: 284 GELANRLTHPSYEVPKTYLVQVRGPFPQGIGAQLKAGVELEDGMASVDSFKLVDSTPGHV 343

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + V L  GKNR ++++F+   + V RL+R+  GP  LG    GS R + K+ +
Sbjct: 344 LIEVVLHSGKNRIVRRLFDAVGFPVLRLVRVKVGPIGLGDQRQGSIRNLGKQEV 397


>gi|90581222|ref|ZP_01237020.1| putative pseudouridine synthase family 1 protein [Vibrio angustum
           S14]
 gi|90437593|gb|EAS62786.1| putative pseudouridine synthase family 1 protein [Vibrio angustum
           S14]
          Length = 376

 Score =  164 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 83/351 (23%), Positives = 133/351 (37%), Gaps = 9/351 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E MI   RV V+G++ +        +  + +DG  +     
Sbjct: 2   SEKLQKVLARAGQGSRREIELMIQNGRVSVDGVVAKLGDRLEDLSVSVRIDGHNIELISS 61

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L        L T H     R+           R +SVGRLD NT GLLL T D
Sbjct: 62  DEEICRILAYNKPEGELCTRHDPEGRRTVFDRLPRLNTGRWVSVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS    R Y VR  G+V +  +  + KG+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRTVEREYMVRVFGEVTEQMVKNVVKGVELEDGLARFEDVVYAGGEGMNH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK---ILRE 243
              V + EG+NRE++++++     V+RL R+ YG   L   +  G   E+  K    LR 
Sbjct: 182 TFYVVITEGRNREVRRLWDSQGVTVSRLKRVRYGDVYLTKDMPRGGWSELELKEVNELRA 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +      E  + ++            R     E   +    +    + N          
Sbjct: 242 TVELPPETETALTVEGQKRKKGIRQIRRAVRRHEERVETGGGRGRRGRGNDRRNPGSSRN 301

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                         +   +    +   R+    +S   P      ++S K+
Sbjct: 302 AEVEAQSNERRGNGRSQPAKGRDNRDSRDNGKPQSSGRPQTSGKPQSSGKR 352


>gi|257438983|ref|ZP_05614738.1| ribosomal large subunit pseudouridine synthase B [Faecalibacterium
           prausnitzii A2-165]
 gi|257198568|gb|EEU96852.1| ribosomal large subunit pseudouridine synthase B [Faecalibacterium
           prausnitzii A2-165]
          Length = 294

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 83/274 (30%), Positives = 134/274 (48%), Gaps = 3/274 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K++A  G+ SRR  E++IA+ RVKVNG  ++       + D + VD   +   +  
Sbjct: 21  ERIQKIMAEQGLCSRRAAEQIIAEGRVKVNGHPVKVGDKMDPNRDVLHVDDERIYIQKNQ 80

Query: 74  --RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                  +KP G VTT SD  GR TV + +  I +R+  VGRLD ++EGLLL+TNDG  A
Sbjct: 81  QLYYLALYKPRGYVTTASDELGRKTVMELVSDIPARLYPVGRLDKDSEGLLLMTNDGAFA 140

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVT 190
           + +  PS    ++YRV    + D+ ++  +  G+V+          + + T +     + 
Sbjct: 141 QAVTHPSGGISKLYRVTVQPRADESQILKMSSGVVLDDGTKTMPCAINVVTDEPGRTVME 200

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L+EGKNREI+++ E    +V RL R + G  +LG L  G+ RE++K  +         
Sbjct: 201 MTLKEGKNREIRRMCEAVGLEVVRLKRNAEGVVKLGMLKPGTYRELTKAEVSGLRAAAAK 260

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
             AQ    A    +       P      P    +
Sbjct: 261 GRAQTRSAALQSKAAARRPKGPVGSGNAPAKRRK 294


>gi|152971155|ref|YP_001336264.1| 16S rRNA pseudouridylate synthase A [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|238895743|ref|YP_002920479.1| 16S rRNA pseudouridylate synthase A [Klebsiella pneumoniae
           NTUH-K2044]
 gi|262040199|ref|ZP_06013451.1| ribosomal small subunit pseudouridine synthase A [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
 gi|150956004|gb|ABR78034.1| 16S pseudouridylate 516 synthase [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|238548061|dbj|BAH64412.1| 16S pseudouridylate 516 synthase [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
 gi|259042436|gb|EEW43455.1| ribosomal small subunit pseudouridine synthase A [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
          Length = 239

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 57/243 (23%), Positives = 103/243 (42%), Gaps = 7/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G +++ A+  +     +E DG  L +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGSRVTVDGDIVKDASFKLQPEHEVEYDGNTLTQQNGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTILYFLDEPVAHKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     + +    L  KG+ +                +  +   V +
Sbjct: 121 ITSPRHHCEKTYLVALESPLAEGTAELFAKGVQLHNEKDLTKPA----LLEVITPTEVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLL 250
            + EG+  ++K++F      V  L R   G   L   L  G  R +++  +     P   
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVGLHRERIGDILLDESLAPGEYRPLTEAEIASVGAPQPR 236

Query: 251 EEA 253
            + 
Sbjct: 237 SKT 239


>gi|145629302|ref|ZP_01785101.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae 22.1-21]
 gi|144978805|gb|EDJ88528.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae 22.1-21]
          Length = 232

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 57/236 (24%), Positives = 108/236 (45%), Gaps = 7/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  +V +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWIEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ HKP G V ++ D D  +        +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYFMLHKPQGCVCSNDDGDYPTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+++      +GI+++G        ++ +      +  V +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEENYAAACSEGILLRGEKEPTKPAKLEIL----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
            + EG+  ++K++F     KV  L R   G   L   L  G  R +++  + + + 
Sbjct: 177 TISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLVK 232


>gi|163803033|ref|ZP_02196919.1| anthranilate synthase component II [Vibrio sp. AND4]
 gi|159173207|gb|EDP58036.1| anthranilate synthase component II [Vibrio sp. AND4]
          Length = 312

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 90/313 (28%), Positives = 131/313 (41%), Gaps = 13/313 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E  I   RV VNGI+ +           + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREIESFIKSGRVSVNGIVAKLGERLEDENSVVRIDGHVVSAKIQ 61

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  Y     L T H     R+          SR ISVGRLD NT GLLL T D
Sbjct: 62  EEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G+V + K+  L +G+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRQVEREYLVRVFGEVTEQKVKNLVRGVELEDGMARFEDVVYAGGEGMNH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LRE 243
              V + EG+NRE+++++E  +  V+RL R+ YG   L   L  G   E+  K    LRE
Sbjct: 182 TFYVAINEGRNREVRRLWESQDTTVSRLKRVRYGDIYLDKKLPRGGWMELDLKEVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +     +E  ++L+       T  +       ++     R ++  +   G S       
Sbjct: 242 LVELRPEKETMLDLNK----DNTSRKRERARSQKIRRAVKRHEERVNTPKGRSNNPSRRK 297

Query: 304 PVHRRNLASNVWM 316
           P            
Sbjct: 298 PKKSAGDQGARNK 310


>gi|76809714|ref|YP_333311.1| RNA pseudouridylate synthase family protein [Burkholderia
           pseudomallei 1710b]
 gi|76579167|gb|ABA48642.1| RNA pseudouridylate synthase family protein [Burkholderia
           pseudomallei 1710b]
          Length = 513

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 84/355 (23%), Positives = 146/355 (41%), Gaps = 8/355 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 132 KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 190

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 191 GKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNTE 250

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 251 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRIRD 310

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 311 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 370

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             +R  +    L+    +            R    + + +          +  +    ++
Sbjct: 371 AQVRRLMSTVGLKAPTEDKGG-KRGGPAERRQPDPMQTSMGFINREPVLTTHGQLDQPRR 429

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            +                A        S  G R+ +  R+ S+    + +R + K
Sbjct: 430 GRRGPAGGGFGAGLGGGYAGLPGYGGASRQGGRDVDGNRA-SYGGAGANKRGAGK 483


>gi|309378850|emb|CBX22555.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 349

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 74/256 (28%), Positives = 126/256 (49%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++     +F P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+
Sbjct: 84  LKERRSDLSHFEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHV 142

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++  L +  ++++       
Sbjct: 203 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTTEQMRSLTEEGVMLEDGLAKVE 262

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   
Sbjct: 263 RIYEQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFY 322

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   L    +
Sbjct: 323 ELNPAEVANILKWAEM 338


>gi|118444660|ref|YP_877521.1| RNA pseudouridylate synthase family protein [Clostridium novyi NT]
 gi|118135116|gb|ABK62160.1| RNA pseudouridylate synthase family protein [Clostridium novyi NT]
          Length = 229

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 57/237 (24%), Positives = 105/237 (44%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+++  GI SR+E  R+I Q R+ VNG L       V  +D I +D   ++  ++ 
Sbjct: 1   MRINKLLSNYGICSRKEANRIIEQNRIIVNGKLC-IPGQWVEESDEILLDNKRIKPKKKV 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L        T+  D         +  +    +  VGRLD  +EGL++LTNDG L+  
Sbjct: 60  YILLNKPVGITCTSSKDI---KANIIDFVNYRDYIFPVGRLDKKSEGLIILTNDGELSNK 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V+     D + +  + KG+ ++G+           ++       + L
Sbjct: 117 ILESENMHEKEYVVKVDKPFDDEFIENMSKGVQLKGVKTRTC----IVRRIDECTFKIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
            +G NR+I+K+   F + V +L RI     ++  +  GS R  ++  L       + 
Sbjct: 173 TQGLNRQIRKMTRAFGYTVVKLKRIRIMNLKIDGIDIGSFRHFTEDELNNIRVMVMK 229


>gi|296102094|ref|YP_003612240.1| 23S rRNA pseudouridylate synthase B [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
 gi|295056553|gb|ADF61291.1| 23S rRNA pseudouridylate synthase B [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
          Length = 291

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 87/289 (30%), Positives = 131/289 (45%), Gaps = 12/289 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM--STDHIEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E +I   RV V+G +       V       I +DG  +   
Sbjct: 2   SEKLQKVLARAGHGSRREIEAIIEAGRVSVDGKIAT-LGDRVEIVPGLKIRIDGHLISVK 60

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E        L  Y     L T +      +          +R I+VGRLD+NT GLLL T
Sbjct: 61  ESAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  GQVD++KL  L +G+ ++        +     +G 
Sbjct: 121 TDGELANRLMHPSREVEREYAVRVFGQVDENKLRDLSRGVQLEDGPAAFKTIKFTGGEGI 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKIL 241
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       L
Sbjct: 181 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDILLPKGLPRGGYTELDLTQTNYL 240

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           RE +G      ++V ++      +     R        ++  R    ++
Sbjct: 241 RELVGLAPETTSKVAVEKDRRRMKANQIRRAVKRHSQVNNNRRAGSRNN 289


>gi|297588511|ref|ZP_06947154.1| ribosomal large subunit pseudouridine synthase B [Finegoldia magna
           ATCC 53516]
 gi|297573884|gb|EFH92605.1| ribosomal large subunit pseudouridine synthase B [Finegoldia magna
           ATCC 53516]
          Length = 242

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 76/241 (31%), Positives = 120/241 (49%), Gaps = 2/241 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA++G  SRR+ + +I   +V VNG +L   +  V  +D +EV+G  + K E  
Sbjct: 1   MRINKFIAQSGYCSRRKADELIKNSKVCVNGTILLDLSYQVNDSDIVEVEGKKISKKEEK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KPIG  +T  D         +L    +RV  VGRLD ++ GLL+LTNDG L   
Sbjct: 61  IYIAINKPIGYTSTVKDKFADK-KVVDLIKFKTRVYPVGRLDKDSHGLLILTNDGELTYE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  +VY V   G+  +DK+  LK GIV+ G       +        N    V +
Sbjct: 120 LTHPKFEHKKVYEVLVKGRPTKDKIQELKNGIVLDGYKLKKSSIEFIANVKDNTKYMVTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHLLEE 252
            EG+NR+I+K+F++ N  V  L R+  G +++   L +G    +  + L    G +   +
Sbjct: 180 YEGRNRQIRKMFDYINHPVLDLKRVQIGYYKMEDNLKSGEYVLLKNEDLDLIRGKYDRSK 239

Query: 253 A 253
            
Sbjct: 240 T 240


>gi|260885631|ref|ZP_05897074.1| ribosomal large subunit pseudouridine synthase B [Prevotella
           tannerae ATCC 51259]
 gi|260851764|gb|EEX71633.1| ribosomal large subunit pseudouridine synthase B [Prevotella
           tannerae ATCC 51259]
          Length = 230

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 56/222 (25%), Positives = 100/222 (45%), Gaps = 1/222 (0%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           +A AGI SRR+ ++ I    + VNG ++      V+ +D I     P+R  ++  + L  
Sbjct: 1   MANAGICSRRDADKYIQAGVITVNGKVVTELGTKVLRSDDILFHESPVRLEKKVYVLLNK 60

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
               + T+    + ++ +     +   R+  VGRLD NT G+LLLTNDG LA  L  P  
Sbjct: 61  PKGCITTSEDPQERKTVMNLVKGACQERIYPVGRLDRNTTGVLLLTNDGELAAKLTHPQF 120

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
              ++Y V     V    L  +  GI +         +   ++      + + +  GKNR
Sbjct: 121 MKKKIYHVYLDKNVSGVDLQKIADGITLDDGEIKADDIQYASETDKKQ-IGIEIHSGKNR 179

Query: 200 EIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            ++++FE   + V +L R+ +       L  G  R +++  +
Sbjct: 180 IVRRIFESLGYHVVKLDRVYFAGLTKKHLRRGDWRYLTQDEV 221


>gi|34763151|ref|ZP_00144119.1| Ribosomal large subunit pseudouridine synthase B [Fusobacterium
           nucleatum subsp. vincentii ATCC 49256]
 gi|27887180|gb|EAA24283.1| Ribosomal large subunit pseudouridine synthase B [Fusobacterium
           nucleatum subsp. vincentii ATCC 49256]
          Length = 234

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 69/231 (29%), Positives = 129/231 (55%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAE 71
            R++K ++  GIASRR +++ I + R+ VNG       +++   D+I +DG  ++    E
Sbjct: 1   MRINKFLSTLGIASRRTIDKYIEEGRITVNGNTAIT-GMDISENDNIFIDGEKIKTNIDE 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +   ++ +KP+ ++++ SD  GR TV D + +       VGRLD  T GL+LLTNDG L 
Sbjct: 60  KKVYFMLNKPLEVLSSSSDNRGRKTVVDLIKTDKRI-FPVGRLDYMTSGLILLTNDGELF 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P ++  + Y V+  G++ ++++  LKKG+++        +++      +   + +
Sbjct: 119 NRIVHPKSEIYKKYYVKILGEIKKEEIEELKKGVLLDDSKTLPAKISGIKYDKNKTSMYI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +REG+NR+I+++ E F ++V  L R   G   LG L  G  RE++K+ + 
Sbjct: 179 SIREGRNRQIRRMIEKFEYRVLMLRREKIGELSLGDLPEGKYRELTKQEVE 229


>gi|331268777|ref|YP_004395269.1| pseudouridine synthase [Clostridium botulinum BKT015925]
 gi|329125327|gb|AEB75272.1| pseudouridine synthase [Clostridium botulinum BKT015925]
          Length = 226

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 57/230 (24%), Positives = 105/230 (45%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+++  GI SR+E  R+I + R+ VNG +       V   D I +D  P++K E+ 
Sbjct: 1   MRINKLLSNYGICSRKEANRIIEENRIIVNGEVC-IPGQWVEEYDEILMDNEPIKKKEKI 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L        T   +         +  +    +  VGRLD ++EGL+L+TNDG L+  
Sbjct: 60  YIALNKPVGITCTAAREV---KDNIIDFLNYPEYIFPVGRLDKDSEGLILMTNDGELSNK 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     Q  + Y V      D   +  + +G+ + G       VT      +N    + L
Sbjct: 117 ILESENQHEKEYIVTVDKPFDDLFIKAMSEGVQLNGPKTRPCIVTRI----NNDTFRIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            +G NR+I+++   F + V +L RI     ++  +  G  + ++ + + E
Sbjct: 173 TQGLNRQIRRMTRAFGYTVIKLERIRILNIKINGIDNGKWKYLTDEEITE 222


>gi|325134403|gb|EGC57048.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M13399]
 gi|325142531|gb|EGC64931.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis 961-5945]
 gi|325198505|gb|ADY93961.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis G2136]
 gi|325200018|gb|ADY95473.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis H44/76]
          Length = 256

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 71/245 (28%), Positives = 121/245 (49%), Gaps = 7/245 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P+R+ KV+A +G+ SRRE+E  I    + VNG   +     V   DH+ V G  ++   
Sbjct: 2   EPERLQKVLAASGVGSRREMEEWITNGWITVNGKTAQ-LGDKVTPDDHVTVKGSIIKLKW 60

Query: 72  RTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             RL      Y +   +V+        S       +  SR +++GRLDINT GLL+LT  
Sbjct: 61  ADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTTS 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN 186
           G L +    PS +  R Y VR  G +  +++ +L +  ++++       ++     +G+N
Sbjct: 121 GELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGAN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
            W  V ++EG+NRE++++FE     V+RL+RI +GP  L   L  G   E++   +   +
Sbjct: 181 KWYNVVIKEGRNREVRRIFESQGLTVSRLVRIGFGPIGLPNRLKRGQFYELNPAEVANII 240

Query: 246 GPHLL 250
               +
Sbjct: 241 KWADM 245


>gi|319944113|ref|ZP_08018391.1| hypothetical protein HMPREF0551_1238 [Lautropia mirabilis ATCC
           51599]
 gi|319742607|gb|EFV95016.1| hypothetical protein HMPREF0551_1238 [Lautropia mirabilis ATCC
           51599]
          Length = 918

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 84/340 (24%), Positives = 135/340 (39%), Gaps = 10/340 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +++ K++A AGI SRR++E +I   RV VNG+        V + D I V+G PL +
Sbjct: 286 SPDAEKLHKILADAGIGSRRDMEELIIAGRVSVNGLPAHV-GQRVGTEDVIRVNGKPLSR 344

Query: 70  ------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                      L  +     LVT                   +R I+VGRLD+N+EGLL+
Sbjct: 345 KRSAASQTPQVLLYHKPTGELVTRDDPGSRPKVFDRLPRLRGARWIAVGRLDLNSEGLLI 404

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T  G LA  L  P   W R Y VR  G+VD      L  G+ ++        +     +
Sbjct: 405 FTTSGDLANKLMHPRYGWEREYAVRVLGRVDDGIRQQLLTGVTLEDGPATLQSIEDIGGE 464

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           G+N W  V + EG+NRE++++F+     V+RL+RI +GP  L   L  G    +++  +R
Sbjct: 465 GANHWYRVVILEGRNREVRRLFDAVGLTVSRLVRIRFGPIALPPRLQRGRLHALTEAEVR 524

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +         A++   A   + ET   +               ++         +     
Sbjct: 525 QLQQQMRRHVAEMTDGAADAARETRSGNAQGRGKGAGRGNDAPRRQGRGAGKAVQAGAGQ 584

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSD--SGQREENHRRSPS 340
               ++  AS      G           G R    +    
Sbjct: 585 QGSGQQGAASGSPQPSGSRHPARRRMLRGARGRAQQTGEG 624


>gi|332307254|ref|YP_004435105.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
 gi|332174583|gb|AEE23837.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
          Length = 289

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 86/289 (29%), Positives = 125/289 (43%), Gaps = 8/289 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL----R 68
            +++ KV+A AG+ SRRE+E+ IA  R+ VNG +       V   D + VDG  +    +
Sbjct: 2   SEKLQKVLANAGVGSRREMEKWIASGRISVNGKVAT-LGDRVEPVDQLRVDGNLITSAAK 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 L        L +        +           R I+VGRLDINT GLLL TNDG
Sbjct: 61  STMCRVLMYNKPEGELCSRKDPQGRPTVFDRLPKIQNGRWIAVGRLDINTSGLLLFTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--N 186
            LA  L  P  +  R Y VR  G+V+ D +  LKKG+ ++       ++          N
Sbjct: 121 ELANRLMHPKHEIEREYAVRVFGEVEDDMIKRLKKGVELEDGVSKFTEIRKRPGDDESLN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
           +W  V L EGKNRE+++++E    +V+RLIR+ YG   L   L  G   E+    L    
Sbjct: 181 SWYNVSLSEGKNREVRRLWESQGLQVSRLIRVRYGTLNLQNRLPQGGWIELPLTDLNTLR 240

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
               L+  Q +L     +    VR      S       + +     K  
Sbjct: 241 KSVQLDLEQESLVEDKQTKLDHVRLSRMRRSVQKHKVNQGRAKPRPKKK 289


>gi|22537618|ref|NP_688469.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae 2603V/R]
 gi|76787384|ref|YP_330112.1| RNA pseudouridine synthase family protein [Streptococcus agalactiae
           A909]
 gi|76797639|ref|ZP_00779909.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae 18RS21]
 gi|22534503|gb|AAN00342.1|AE014259_13 ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae 2603V/R]
 gi|76562441|gb|ABA45025.1| RNA pseudouridine synthase family protein [Streptococcus agalactiae
           A909]
 gi|76587000|gb|EAO63488.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae 18RS21]
          Length = 240

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 58/233 (24%), Positives = 104/233 (44%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+ ++ ++++ VNG       V V    D I+ +G  +   + 
Sbjct: 1   MRLDKFLVECGLGSRTQVKLILKKKQISVNGNSETSPKVQVDEYRDEIKYNGTLVSYEKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T            +  +    V  VGRLDI+T GLLLLTN+G LA 
Sbjct: 61  VYYMLHKPKGVISATDDPSHKTVLDLLDKTARDKAVFPVGRLDIDTTGLLLLTNNGELAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVT 190
            +  P     + Y V+  G + +D +    KGI+++         ++    Q    + V 
Sbjct: 121 KMLSPKKHVDKCYEVKISGIMTEDDILAFDKGIILKDFTCLPALLEIVEVNQVKKQSLVK 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           + ++EGK  ++K++      +V  L R+  G  QL   L +G  R ++ K + 
Sbjct: 181 ITIKEGKFHQVKRMVAACGKEVLELKRLRMGNLQLDKQLESGQWRRLTIKEIE 233


>gi|300870412|ref|YP_003785283.1| RNA pseudouridine synthase family protein [Brachyspira pilosicoli
           95/1000]
 gi|300688111|gb|ADK30782.1| RNA pseudouridine synthase family protein [Brachyspira pilosicoli
           95/1000]
          Length = 225

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 66/228 (28%), Positives = 111/228 (48%), Gaps = 9/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA   IASRRE + +I   +VKVNG ++   A  V  TD +E D    +  +  
Sbjct: 1   MRLNKYIASLNIASRREADNLIKDGKVKVNGEIILNPATQVSETDKVECD----KDEKNK 56

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G V + +  D   T+++ L +    V  VGRLD ++ GL+LLTNDG  A+ 
Sbjct: 57  IYIKLNKPRGYVVSTNK-DEGKTIYELLNNKLKGVYPVGRLDKDSNGLILLTNDGVFAKK 115

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +   ++   + Y V+ +  +    L  L+ GI + G      +    T+        + L
Sbjct: 116 IIGENSNCEKEYYVKVNDNIPDGALKKLEYGISLDGKKLKPAKTKRITKNS----FNIIL 171

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            EG+NR+I+++ E   ++V  L R+      L  L  G    ++K+ +
Sbjct: 172 TEGRNRQIRRMCEKVGFEVIILKRLRINNIFLNELKEGKFEYLTKEEI 219


>gi|222153299|ref|YP_002562476.1| ribosomal small subunit pseudouridine synthase B [Streptococcus
           uberis 0140J]
 gi|222114112|emb|CAR42564.1| putative ribosomal small subunit pseudouridine synthase B
           [Streptococcus uberis 0140J]
          Length = 239

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 67/239 (28%), Positives = 103/239 (43%), Gaps = 4/239 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +  AGI SR +V+ ++ ++ V VNG    +A + +    D +   G  L   E 
Sbjct: 1   MRLDKFLVEAGIGSRTQVKSILKKKEVFVNGKPESQAKLQIKPNQDQVSFGGQVLVYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T            +  +    V  VGRLD +T GLLLLTNDG LA 
Sbjct: 61  LYYLLNKPQGVVSATEDKVHQTVLDLLDDTARRKSVFPVGRLDKDTHGLLLLTNDGELAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA--WVT 190
            L  P     +VY  R  G + +  +    KGI +        Q+ ++          V 
Sbjct: 121 RLLSPKKHVDKVYMARVDGIMTEQDVEAFAKGITLSDHQCLPAQLQIEEVDVERTCCKVR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
           + +REGK  +IK++      +V  L RIS GP QL   L  G+ R +++  ++  L   
Sbjct: 181 ITIREGKFHQIKRMVLACGKEVTDLQRISMGPIQLDDSLALGAFRRLNETEMKALLALK 239


>gi|300704339|ref|YP_003745942.1| ribosomal large subunit pseudouridine synthase b [Ralstonia
           solanacearum CFBP2957]
 gi|299072003|emb|CBJ43333.1| Ribosomal large subunit pseudouridine synthase B [Ralstonia
           solanacearum CFBP2957]
          Length = 597

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 78/321 (24%), Positives = 131/321 (40%), Gaps = 9/321 (2%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             +       ++ K++A AG+ SRR++E +I Q RV VNG+        ++ TD + V+G
Sbjct: 205 RELTAEDDAPKLHKILADAGLGSRRDMEDLIMQGRVSVNGLPA-HIGQRILPTDQVRVNG 263

Query: 65  VPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
             +++         L  +     +V+        +           + ++VGRLD NTEG
Sbjct: 264 KLIQRKLPNKAPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRMKTGKWVAVGRLDFNTEG 323

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LL+ T  G +A     P     R Y VR  G++ +     L +G+ +       ++    
Sbjct: 324 LLIFTTSGDIANRFMHPRYGVEREYAVRTLGELAESDRQKLLQGVRLDDGEANFLRCADG 383

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
             +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EVS +
Sbjct: 384 GGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEVSAE 443

Query: 240 ILR---EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            +R     LG  +   +               R+   ++          +     +    
Sbjct: 444 EVRVLMGSLGLKVPSASVGGGQGGGRQQGGRRREAQPMLMGPMSSGFTGEATFQSRGQGV 503

Query: 297 KQKKLATPVHRRNLASNVWMA 317
           +    A P  RR  +      
Sbjct: 504 ENGNRALPAARRPSSPRQPDP 524


>gi|15608849|ref|NP_216227.1| hypothetical protein Rv1711 [Mycobacterium tuberculosis H37Rv]
 gi|15841171|ref|NP_336208.1| RNA pseudouridylate synthase [Mycobacterium tuberculosis CDC1551]
 gi|31792898|ref|NP_855391.1| hypothetical protein Mb1738 [Mycobacterium bovis AF2122/97]
 gi|121637619|ref|YP_977842.1| hypothetical protein BCG_1750 [Mycobacterium bovis BCG str. Pasteur
           1173P2]
 gi|148661509|ref|YP_001283032.1| RNA pseudouridylate synthase [Mycobacterium tuberculosis H37Ra]
 gi|148822917|ref|YP_001287671.1| hypothetical protein TBFG_11726 [Mycobacterium tuberculosis F11]
 gi|167967185|ref|ZP_02549462.1| hypothetical protein MtubH3_03737 [Mycobacterium tuberculosis
           H37Ra]
 gi|215403985|ref|ZP_03416166.1| hypothetical protein Mtub0_09916 [Mycobacterium tuberculosis
           02_1987]
 gi|215411359|ref|ZP_03420167.1| hypothetical protein Mtub9_08567 [Mycobacterium tuberculosis
           94_M4241A]
 gi|215427035|ref|ZP_03424954.1| hypothetical protein MtubT9_11867 [Mycobacterium tuberculosis T92]
 gi|215430604|ref|ZP_03428523.1| hypothetical protein MtubE_08018 [Mycobacterium tuberculosis
           EAS054]
 gi|215445897|ref|ZP_03432649.1| hypothetical protein MtubT_08146 [Mycobacterium tuberculosis T85]
 gi|218753419|ref|ZP_03532215.1| hypothetical protein MtubG1_08264 [Mycobacterium tuberculosis GM
           1503]
 gi|219557635|ref|ZP_03536711.1| hypothetical protein MtubT1_10192 [Mycobacterium tuberculosis T17]
 gi|224990094|ref|YP_002644781.1| hypothetical protein JTY_1725 [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|253799250|ref|YP_003032251.1| hypothetical protein TBMG_02284 [Mycobacterium tuberculosis KZN
           1435]
 gi|254550722|ref|ZP_05141169.1| hypothetical protein Mtube_09734 [Mycobacterium tuberculosis
           '98-R604 INH-RIF-EM']
 gi|260200774|ref|ZP_05768265.1| hypothetical protein MtubT4_11812 [Mycobacterium tuberculosis T46]
 gi|260204981|ref|ZP_05772472.1| hypothetical protein MtubK8_11835 [Mycobacterium tuberculosis K85]
 gi|289443169|ref|ZP_06432913.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           tuberculosis T46]
 gi|289569762|ref|ZP_06449989.1| conserved hypothetical protein [Mycobacterium tuberculosis T17]
 gi|289574379|ref|ZP_06454606.1| RNA pseudouridine synthase [Mycobacterium tuberculosis K85]
 gi|289745851|ref|ZP_06505229.1| RNA pseudouridylate synthase [Mycobacterium tuberculosis 02_1987]
 gi|289750268|ref|ZP_06509646.1| conserved hypothetical protein [Mycobacterium tuberculosis T92]
 gi|289753802|ref|ZP_06513180.1| RNA pseudouridylate synthase [Mycobacterium tuberculosis EAS054]
 gi|289757820|ref|ZP_06517198.1| RNA pseudouridylate synthase [Mycobacterium tuberculosis T85]
 gi|289761867|ref|ZP_06521245.1| RNA pseudouridylate synthase [Mycobacterium tuberculosis GM 1503]
 gi|294993179|ref|ZP_06798870.1| hypothetical protein Mtub2_01388 [Mycobacterium tuberculosis 210]
 gi|297634264|ref|ZP_06952044.1| hypothetical protein MtubK4_09092 [Mycobacterium tuberculosis KZN
           4207]
 gi|297731251|ref|ZP_06960369.1| hypothetical protein MtubKR_09182 [Mycobacterium tuberculosis KZN
           R506]
 gi|306972006|ref|ZP_07484667.1| hypothetical protein TMJG_03142 [Mycobacterium tuberculosis
           SUMu010]
 gi|313658583|ref|ZP_07815463.1| hypothetical protein MtubKV_09197 [Mycobacterium tuberculosis KZN
           V2475]
 gi|54040263|sp|P65843|Y1738_MYCBO RecName: Full=Uncharacterized RNA pseudouridine synthase Mb1738;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|54042595|sp|P65842|Y1711_MYCTU RecName: Full=Uncharacterized RNA pseudouridine synthase
           Rv1711/MT1751.1; AltName: Full=RNA pseudouridylate
           synthase; AltName: Full=RNA-uridine isomerase
 gi|2326754|emb|CAB10968.1| CONSERVED HYPOTHETICAL PROTEIN [Mycobacterium tuberculosis H37Rv]
 gi|13881392|gb|AAK46022.1| RNA pseudouridylate synthase [Mycobacterium tuberculosis CDC1551]
 gi|31618489|emb|CAD94441.1| CONSERVED HYPOTHETICAL PROTEIN [Mycobacterium bovis AF2122/97]
 gi|121493266|emb|CAL71737.1| Conserved hypothetical protein [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|148505661|gb|ABQ73470.1| RNA pseudouridylate synthase [Mycobacterium tuberculosis H37Ra]
 gi|148721444|gb|ABR06069.1| conserved hypothetical protein [Mycobacterium tuberculosis F11]
 gi|224773207|dbj|BAH26013.1| hypothetical protein JTY_1725 [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|253320753|gb|ACT25356.1| conserved hypothetical protein [Mycobacterium tuberculosis KZN
           1435]
 gi|289416088|gb|EFD13328.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           tuberculosis T46]
 gi|289538810|gb|EFD43388.1| RNA pseudouridine synthase [Mycobacterium tuberculosis K85]
 gi|289543516|gb|EFD47164.1| conserved hypothetical protein [Mycobacterium tuberculosis T17]
 gi|289686379|gb|EFD53867.1| RNA pseudouridylate synthase [Mycobacterium tuberculosis 02_1987]
 gi|289690855|gb|EFD58284.1| conserved hypothetical protein [Mycobacterium tuberculosis T92]
 gi|289694389|gb|EFD61818.1| RNA pseudouridylate synthase [Mycobacterium tuberculosis EAS054]
 gi|289709373|gb|EFD73389.1| RNA pseudouridylate synthase [Mycobacterium tuberculosis GM 1503]
 gi|289713384|gb|EFD77396.1| RNA pseudouridylate synthase [Mycobacterium tuberculosis T85]
 gi|308358526|gb|EFP47377.1| hypothetical protein TMJG_03142 [Mycobacterium tuberculosis
           SUMu010]
 gi|323719802|gb|EGB28916.1| hypothetical protein TMMG_00962 [Mycobacterium tuberculosis
           CDC1551A]
 gi|326903326|gb|EGE50259.1| hypothetical protein TBPG_01194 [Mycobacterium tuberculosis W-148]
          Length = 254

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 72/238 (30%), Positives = 106/238 (44%), Gaps = 4/238 (1%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
                  R+ KV+++AGIASRR  E+MI   RV+V+G ++      V      + VDG  
Sbjct: 8   SREPRGIRLQKVLSQAGIASRRAAEKMIVDGRVEVDGHVVTELGTRVDPQVAVVRVDGAR 67

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLL 123
           +   +       +KP G+ +T SD  GR  + D +            VGRLD +TEGL+L
Sbjct: 68  VVLDDSLVYLALNKPRGMHSTMSDDRGRPCIGDLIERKVRGTKKLFHVGRLDADTEGLML 127

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG LA  L  PS +  + Y     G V +     L+ GI +           +    
Sbjct: 128 LTNDGELAHRLMHPSHEVPKTYLATVTGSVPRGLGRTLRAGIELDDGPAFVDDFAVVDAI 187

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                V V L EG+NR ++++     + V  L+R   G   LG    GS R +    +
Sbjct: 188 PGKTLVRVTLHEGRNRIVRRLLAAAGFPVEALVRTDIGAVSLGKQRPGSVRALRSNEI 245


>gi|108759403|ref|YP_632021.1| ribosomal large subunit pseudouridine synthase B [Myxococcus
           xanthus DK 1622]
 gi|108463283|gb|ABF88468.1| ribosomal large subunit pseudouridine synthase B [Myxococcus
           xanthus DK 1622]
          Length = 745

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 89/362 (24%), Positives = 138/362 (38%), Gaps = 23/362 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +ARAG+ASRR  E +I   RV VN   +      V    D + VDG  +   + 
Sbjct: 4   ERLQKYLARAGVASRRHAEELITAGRVAVNNKTVTELGSRVEPGTDLVTVDGTLVTPPDE 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +  +L +KP+G+VTT SDP GR TV + +     R+  VGRLD + EG LL T+DG LA 
Sbjct: 64  SSYFLLYKPVGVVTTLSDPQGRPTVANYVEETGKRLFPVGRLDYDAEGALLFTDDGALAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS Q  R Y  +  G  D   L+ L+ G+ ++      + V++      N W+ + 
Sbjct: 124 KLTHPSFQVPRTYLAKVKGAPDTATLDKLRGGVRLEDGMATPVSVSVFEAAERNTWLKIV 183

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL----------- 241
           + EG+   IK++       V RL R SY    +  L  G  R +    +           
Sbjct: 184 VAEGRPHLIKRLCAAVGHPVVRLFRPSYAGVGVEGLRPGELRPLKTSEVELLNAVSDGKA 243

Query: 242 -----------REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
                      R         ++    +  +     +                 +  +S 
Sbjct: 244 APPTGELRLPPRRHGRAAPGFDSDDEAELSMDDDAPVAAKPARKAPARAAKTATVGGSSL 303

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
            + G  K         RR+   +    +G           R  +       P  RS    
Sbjct: 304 ARFGRPKGASAEGKPARRSFGGDEGAPRGRSFGGDKAGAPRGRSFGGDEGAPRGRSFGGD 363

Query: 351 SA 352
            A
Sbjct: 364 KA 365



 Score = 39.8 bits (91), Expect = 0.58,   Method: Composition-based stats.
 Identities = 12/111 (10%), Positives = 24/111 (21%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
              G     +         +  +     R +  S+      R   +   +          
Sbjct: 354 APRGRSFGGDKAGAPRGRSFGGDEGRPARRSFGSDEGKPARRSFGSDEGRPARRSFGGDE 413

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               RR+  S+                 R  +       P++RS      K
Sbjct: 414 GKPARRSFGSDEGRPARRSFGGDKAGSPRGRSFGSDEGRPARRSFGGDEGK 464



 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 14/123 (11%), Positives = 24/123 (19%), Gaps = 4/123 (3%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R       +        +E +    +         R         P   +     +    
Sbjct: 383 RSFGSDEGKPARRSFGSDEGRPARRSFGGDEGKPARRSFGSDEGRPARRSFGGDKAGSPR 442

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR----EENHRRSPSFPSKRSLRR 349
           G S       P  R         A+           +R    +E      SF       R
Sbjct: 443 GRSFGSDEGRPARRSFGGDEGKPARRSFGGDEGRPARRSFGGDEGRPARRSFGGDDGAPR 502

Query: 350 TSA 352
             +
Sbjct: 503 GRS 505



 Score = 37.9 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 16/99 (16%), Positives = 24/99 (24%), Gaps = 5/99 (5%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           +A           E   R R     +      R       +              RR+  
Sbjct: 339 KAGAPRGRSFGGDEGAPRGRSFGGDKAGAPRGRSFGGDEGRPARRSFGSDEGKPARRSFG 398

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
           S+         +  S  G   +  RRS      R  RR+
Sbjct: 399 SDEG-----RPARRSFGGDEGKPARRSFGSDEGRPARRS 432


>gi|82776628|ref|YP_402977.1| 23S rRNA pseudouridylate synthase B [Shigella dysenteriae Sd197]
 gi|309789069|ref|ZP_07683664.1| ribosomal large subunit pseudouridine synthase B [Shigella
           dysenteriae 1617]
 gi|81240776|gb|ABB61486.1| conserved hypothetical protein [Shigella dysenteriae Sd197]
 gi|308923340|gb|EFP68852.1| ribosomal large subunit pseudouridine synthase B [Shigella
           dysenteriae 1617]
          Length = 290

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 87/289 (30%), Positives = 128/289 (44%), Gaps = 10/289 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV ++G + +    V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSIDGRIAKLGDRVEVTPGLKIRIDGHLISVRE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           E +       ++V ++      +     R            R    +S 
Sbjct: 242 ELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGGRRSGGRNSG 290


>gi|332974446|gb|EGK11370.1| ribosomal large subunit pseudouridine synthase B [Kingella kingae
           ATCC 23330]
          Length = 390

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 74/255 (29%), Positives = 126/255 (49%), Gaps = 6/255 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +++K        P+R+ KV+A +G+ SRRE+E  I    V+VNG +       V   D +
Sbjct: 127 LREKRTDLSRIEPERLQKVLAASGVGSRREMEEWINNGWVQVNGRVAT-LGEKVSPDDQV 185

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 186 TVKGSAIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 245

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NT GLL+LT  G L +    PS +  R Y VR  G++  +++N L +G++++       +
Sbjct: 246 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGELSPEQMNDLCEGVMLEDGLAKVER 305

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTRE 235
           +     +G N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   E
Sbjct: 306 IYEQGGEGVNKWYNVIIKEGRNREVRRLFESQGVTVSRLVRVGFGPIGLPNRLKRGQFYE 365

Query: 236 VSKKILREQLGPHLL 250
           ++   +   L    +
Sbjct: 366 LNPAEVANILKWADM 380


>gi|297538013|ref|YP_003673782.1| pseudouridine synthase [Methylotenera sp. 301]
 gi|297257360|gb|ADI29205.1| pseudouridine synthase [Methylotenera sp. 301]
          Length = 374

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 81/346 (23%), Positives = 140/346 (40%), Gaps = 13/346 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            QR+ K++A AG+ SRR++E +I+  RV VNG    +    V   D + +D  P++    
Sbjct: 36  TQRLHKLLALAGLGSRRDMETLISSGRVTVNGAPATQ-GQGVTQFDTVRLDSRPVKLPFI 94

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 L  +     +V+        S           + I++GRLD+NT GLL+ T  G
Sbjct: 95  AELPQVLIYHKPEGEIVSQDDPEGRASVFDKLPKVKNGKWIAIGRLDMNTSGLLIFTTSG 154

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA     P  +  R Y VR  G++ + ++  LK+GI ++        ++    +G+N W
Sbjct: 155 ELANRFMHPRYEVEREYAVRIFGELTEGQMTQLKEGIELEDGPANFDSISAQGGEGANHW 214

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             V LREG+NRE++++FE F   V+RL+R+ +GP     L     R     +L+ +    
Sbjct: 215 YQVILREGRNREVRRLFEAFQLPVSRLMRVRFGPV---NLPP---RVKRGTMLKLEQKEV 268

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL--ATPVH 306
           +      +L  P      L +      + V     R ++ S+         +     P  
Sbjct: 269 VGLLEWADLPVPSAPLRQLTQREKLKATTVFMPKVRKQRISALDRVPRTDGEPYSKKPSV 328

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            R  A      +   +  +  +        +      K    R   
Sbjct: 329 ARKEAPKKPAPRKSENRRVRQTSDLPAPDAQKAGMQKKSDRNRGRG 374


>gi|295136030|ref|YP_003586706.1| ribosomal large subunit pseudouridine synthase [Zunongwangia
           profunda SM-A87]
 gi|294984045|gb|ADF54510.1| putative ribosomal large subunit pseudouridine synthase
           [Zunongwangia profunda SM-A87]
          Length = 284

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 64/242 (26%), Positives = 113/242 (46%), Gaps = 2/242 (0%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K KN  +++     R++K IA AGI SRR+ +  IA   V VNG ++      V  TD 
Sbjct: 38  IKRKNTALEKREDGMRLNKYIANAGICSRRDADIYIASGNVSVNGEVVTEMGYKVQLTDE 97

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           ++ DG  +   +     L       VT      G + +     +  S++  +G+LD  T 
Sbjct: 98  VKFDGRSITPDKPEYFVLNKSKGVFVTGSVHKGGLTVMDIMAKASKSKLDPIGKLDTQTT 157

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+ TNDG LA+ L  P     ++Y ++    + QD L  +++G+ I+        V+ 
Sbjct: 158 GLLVFTNDGALAKKLANPKNGIRQIYHIKLDHALSQDDLEKIREGVYIESKKINVTDVSY 217

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +      V + L   K   ++K+F+  ++++  L R+ YG      L  G  R ++K+
Sbjct: 218 V-KDRPKTEVGMELTSTKPHIVQKIFKSLSYEILNLDRVVYGGLTKKDLPRGRFRTLTKQ 276

Query: 240 IL 241
            +
Sbjct: 277 EV 278


>gi|325128449|gb|EGC51330.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis N1568]
          Length = 256

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 71/245 (28%), Positives = 121/245 (49%), Gaps = 7/245 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  ++   
Sbjct: 2   EPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLKW 60

Query: 72  RTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             RL      Y +   +V+        S       +  SR +++GRLDINT GLL+LT  
Sbjct: 61  ADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTTS 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN 186
           G L +    PS +  R Y VR  G +  +++ +L +  ++++       ++     +G+N
Sbjct: 121 GELVQRFAHPSFEVEREYAVRVLGGLTGEQIRVLTEEGVMLEDGLAKVERIREQGGEGAN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
            W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   E++   +   +
Sbjct: 181 KWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFYELNPAEVANII 240

Query: 246 GPHLL 250
               +
Sbjct: 241 KWADM 245


>gi|313890704|ref|ZP_07824329.1| putative 16S pseudouridylate 516 synthase [Streptococcus
           pseudoporcinus SPIN 20026]
 gi|313120805|gb|EFR43919.1| putative 16S pseudouridylate 516 synthase [Streptococcus
           pseudoporcinus SPIN 20026]
          Length = 238

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 97/229 (42%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++    I SR +V+++I  +R+ ++  +      NV      I VDG  L+    
Sbjct: 1   MRLDKLLETCQIGSRGQVKKLINAKRITIDDKVAIDGRQNVDPGLQRIGVDGNILQAKGH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                    F  +  VGRLD +TEGL+LLT++G L  
Sbjct: 61  HYFILNKPRGVVSALKDKEHPTVIDCLIEADRFPNLYPVGRLDRDTEGLVLLTDNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
            +  P+    + Y V  +G +D D  +  +   +   G       V + +     +   V
Sbjct: 121 RMLHPNHHVDKSYYVVVNGFLDDDLPSFFRAGVVFFDGTVCKAAAVEILSAGEKQSVAKV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            L EGK  +IKK+F  +  KV  L R+++  F LG L  G  R ++ + 
Sbjct: 181 TLSEGKFHQIKKMFLAYGVKVIYLKRMTFAEFTLGNLAEGEYRTLTDQE 229


>gi|260061659|ref|YP_003194739.1| ribosomal large subunit pseudouridine synthase B [Robiginitalea
           biformata HTCC2501]
 gi|88785791|gb|EAR16960.1| ribosomal large subunit pseudouridine synthase B [Robiginitalea
           biformata HTCC2501]
          Length = 303

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 67/228 (29%), Positives = 108/228 (47%), Gaps = 1/228 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGI SRRE +  IA   V VNG  +      V  TD +  DG  L++  + 
Sbjct: 70  IRLNKYIANAGICSRREADTYIAAGNVTVNGKTITEMGYKVQPTDEVRFDGRLLQRERKE 129

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L      + TT  +   R+ +     +  +R++ VGRLD NT GLLL TNDG LA+ 
Sbjct: 130 YVLLNKPRNFITTTRDEKGRRTVMELISRASNARLVPVGRLDRNTTGLLLFTNDGELAKK 189

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     ++Y V          L  L++G+ ++       + +      S   V V L
Sbjct: 190 LTHPKHGVRKIYHVELDKTFKSADLGKLREGLELEDGRIEVDEASYIDG-ASKKEVGVEL 248

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             G+NR ++++FE   ++V +L R+         L  G  R ++++ +
Sbjct: 249 HSGRNRIVRRIFEHLGYQVVKLDRVVLAGLTKKDLPRGHWRHLTEQEV 296


>gi|119944821|ref|YP_942501.1| pseudouridine synthase [Psychromonas ingrahamii 37]
 gi|119863425|gb|ABM02902.1| ribosomal large subunit pseudouridine synthase B [Psychromonas
           ingrahamii 37]
          Length = 293

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 79/283 (27%), Positives = 127/283 (44%), Gaps = 10/283 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
            +++ KV+ARAG+ SRR++E +I + RV V+G ++      V     I VDG  ++    
Sbjct: 2   SEKLQKVLARAGLGSRRKMEVVIQEGRVSVDGKVV-GLGERVTDVQVIRVDGHIVKNLTP 60

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L        + T   +    +          +R IS+GRLDINT GLLL T D
Sbjct: 61  ENTMCRILAYNKPEGEICTRSDEEGRTTVFERLPSLKGARWISIGRLDINTSGLLLFTTD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G  A  +  PS Q  R Y VR  G V +  LN L+ G+ ++      + +     +G N 
Sbjct: 121 GEFANKMMHPSQQIEREYAVRIFGDVTEAILNRLRMGVQLEDGEAKFLDIKESGGEGINR 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI---LRE 243
           W  V L EG+ RE+++++E    +V+RL+R+ YG   L   L  G   E++ K    LR+
Sbjct: 181 WFHVVLTEGRTREVRRLWESQGLQVSRLMRVRYGNITLSKQLPQGGWHELNLKEVNYLRK 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
            +      E++V +D                + +        +
Sbjct: 241 LVDMPKETESKVKVDVTESKFTNPQARIRRAVKKHAQHRKAGE 283


>gi|157370902|ref|YP_001478891.1| 23S rRNA pseudouridylate synthase B [Serratia proteamaculans 568]
 gi|157322666|gb|ABV41763.1| pseudouridine synthase [Serratia proteamaculans 568]
          Length = 299

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 86/298 (28%), Positives = 133/298 (44%), Gaps = 10/298 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V ++  I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIETIIEAGRVSVDGKIAKLGDRVEVTASMKIRLDGHVVSIKE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T        +          SR ++VGRLD+NT GLLL T 
Sbjct: 62  SEEEVCRVLAYYKPEGELCTRSDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQ+D +K+  L KG+ ++        ++    +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQIDDEKIKQLSKGVQLEDGPAAFRTISFQGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK---KILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIDLPKGLPRGGWTELDLPAINYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           E +       +++ ++      +     R            R     S+      ++ 
Sbjct: 242 ELVELKPETVSKMPIERERRRVKANQIRRAVKRHTQVAGSGRRSTAGSKPGNKPSKRS 299


>gi|254231907|ref|ZP_04925234.1| conserved hypothetical protein [Mycobacterium tuberculosis C]
 gi|254364550|ref|ZP_04980596.1| conserved hypothetical protein [Mycobacterium tuberculosis str.
           Haarlem]
 gi|289554516|ref|ZP_06443726.1| conserved hypothetical protein [Mycobacterium tuberculosis KZN 605]
 gi|298525209|ref|ZP_07012618.1| conserved hypothetical protein [Mycobacterium tuberculosis
           94_M4241A]
 gi|308231906|ref|ZP_07414234.2| hypothetical protein TMAG_01544 [Mycobacterium tuberculosis
           SUMu001]
 gi|308369503|ref|ZP_07418052.2| hypothetical protein TMBG_00254 [Mycobacterium tuberculosis
           SUMu002]
 gi|308370796|ref|ZP_07422771.2| hypothetical protein TMCG_03412 [Mycobacterium tuberculosis
           SUMu003]
 gi|308372033|ref|ZP_07427137.2| hypothetical protein TMDG_03429 [Mycobacterium tuberculosis
           SUMu004]
 gi|308373217|ref|ZP_07431453.2| hypothetical protein TMEG_01610 [Mycobacterium tuberculosis
           SUMu005]
 gi|308374378|ref|ZP_07435832.2| hypothetical protein TMFG_00797 [Mycobacterium tuberculosis
           SUMu006]
 gi|308375655|ref|ZP_07444660.2| hypothetical protein TMGG_00259 [Mycobacterium tuberculosis
           SUMu007]
 gi|308376799|ref|ZP_07440079.2| hypothetical protein TMHG_00891 [Mycobacterium tuberculosis
           SUMu008]
 gi|308377802|ref|ZP_07480471.2| hypothetical protein TMIG_01963 [Mycobacterium tuberculosis
           SUMu009]
 gi|308380151|ref|ZP_07488888.2| hypothetical protein TMKG_02217 [Mycobacterium tuberculosis
           SUMu011]
 gi|308401397|ref|ZP_07493409.2| hypothetical protein TMLG_00694 [Mycobacterium tuberculosis
           SUMu012]
 gi|124600966|gb|EAY59976.1| conserved hypothetical protein [Mycobacterium tuberculosis C]
 gi|134150064|gb|EBA42109.1| conserved hypothetical protein [Mycobacterium tuberculosis str.
           Haarlem]
 gi|289439148|gb|EFD21641.1| conserved hypothetical protein [Mycobacterium tuberculosis KZN 605]
 gi|298495003|gb|EFI30297.1| conserved hypothetical protein [Mycobacterium tuberculosis
           94_M4241A]
 gi|308215647|gb|EFO75046.1| hypothetical protein TMAG_01544 [Mycobacterium tuberculosis
           SUMu001]
 gi|308327365|gb|EFP16216.1| hypothetical protein TMBG_00254 [Mycobacterium tuberculosis
           SUMu002]
 gi|308330808|gb|EFP19659.1| hypothetical protein TMCG_03412 [Mycobacterium tuberculosis
           SUMu003]
 gi|308334631|gb|EFP23482.1| hypothetical protein TMDG_03429 [Mycobacterium tuberculosis
           SUMu004]
 gi|308338418|gb|EFP27269.1| hypothetical protein TMEG_01610 [Mycobacterium tuberculosis
           SUMu005]
 gi|308342141|gb|EFP30992.1| hypothetical protein TMFG_00797 [Mycobacterium tuberculosis
           SUMu006]
 gi|308345612|gb|EFP34463.1| hypothetical protein TMGG_00259 [Mycobacterium tuberculosis
           SUMu007]
 gi|308349928|gb|EFP38779.1| hypothetical protein TMHG_00891 [Mycobacterium tuberculosis
           SUMu008]
 gi|308354549|gb|EFP43400.1| hypothetical protein TMIG_01963 [Mycobacterium tuberculosis
           SUMu009]
 gi|308362465|gb|EFP51316.1| hypothetical protein TMKG_02217 [Mycobacterium tuberculosis
           SUMu011]
 gi|308366085|gb|EFP54936.1| hypothetical protein TMLG_00694 [Mycobacterium tuberculosis
           SUMu012]
 gi|328459002|gb|AEB04425.1| conserved hypothetical protein [Mycobacterium tuberculosis KZN
           4207]
          Length = 253

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 72/238 (30%), Positives = 106/238 (44%), Gaps = 4/238 (1%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
                  R+ KV+++AGIASRR  E+MI   RV+V+G ++      V      + VDG  
Sbjct: 7   SREPRGIRLQKVLSQAGIASRRAAEKMIVDGRVEVDGHVVTELGTRVDPQVAVVRVDGAR 66

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLL 123
           +   +       +KP G+ +T SD  GR  + D +            VGRLD +TEGL+L
Sbjct: 67  VVLDDSLVYLALNKPRGMHSTMSDDRGRPCIGDLIERKVRGTKKLFHVGRLDADTEGLML 126

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG LA  L  PS +  + Y     G V +     L+ GI +           +    
Sbjct: 127 LTNDGELAHRLMHPSHEVPKTYLATVTGSVPRGLGRTLRAGIELDDGPAFVDDFAVVDAI 186

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                V V L EG+NR ++++     + V  L+R   G   LG    GS R +    +
Sbjct: 187 PGKTLVRVTLHEGRNRIVRRLLAAAGFPVEALVRTDIGAVSLGKQRPGSVRALRSNEI 244


>gi|167816044|ref|ZP_02447724.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 91]
          Length = 358

 Score =  163 bits (412), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 76/274 (27%), Positives = 124/274 (45%), Gaps = 6/274 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 60  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 118

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 119 GKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNTE 178

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 179 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRIRD 238

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 239 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 298

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRP 272
             +R  +    L+    +            +  P
Sbjct: 299 AQVRRLMSTVGLKAPTEDKGGKRGGPAERRQPDP 332


>gi|25011583|ref|NP_735978.1| hypothetical protein gbs1541 [Streptococcus agalactiae NEM316]
 gi|77414111|ref|ZP_00790278.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae 515]
 gi|24413122|emb|CAD47200.1| unknown [Streptococcus agalactiae NEM316]
 gi|77159822|gb|EAO70966.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae 515]
          Length = 240

 Score =  163 bits (412), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 56/233 (24%), Positives = 103/233 (44%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+ ++ ++++ VNG       V V    D I+ +G  +   + 
Sbjct: 1   MRLDKFLVECGLGSRTQVKLILKKKQISVNGNSETSPKVQVDEYRDEIKYNGTLVSYEKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T            +  +    V  VGRLDI+T GLLL+TN+G LA 
Sbjct: 61  VYYMLHKPKGVISATDDPSHKTVLDLLDKTARDKAVFPVGRLDIDTTGLLLITNNGELAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVT 190
            +  P     + Y  +  G + +D +    KGI+++         ++    Q    + V 
Sbjct: 121 KMLSPKKHVDKCYEAKISGIMTEDDILAFDKGIILKDFTCLPALLEIVEVNQVKKQSLVK 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           + ++EGK  ++K++      +V  L R+  G  QL   L +G  R ++ K + 
Sbjct: 181 ITIKEGKFHQVKRMVAACGKEVLELKRLRMGNLQLDKQLESGQWRRLTIKEIE 233


>gi|257455144|ref|ZP_05620382.1| ribosomal small subunit pseudouridine synthase A [Enhydrobacter
           aerosaccus SK60]
 gi|257447477|gb|EEV22482.1| ribosomal small subunit pseudouridine synthase A [Enhydrobacter
           aerosaccus SK60]
          Length = 234

 Score =  163 bits (412), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 58/238 (24%), Positives = 107/238 (44%), Gaps = 11/238 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +++A   SR++ ++++    V VNG +++ A++++    D IE  G PL  A  
Sbjct: 1   MRLDKFLSKATELSRKDCKKILHAGEVTVNGEVVKDASLHIDEVGDDIEWAGEPLSVAMG 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R  L +KP G   T    +               +   GRLD++T G LLL++DGG   
Sbjct: 61  NRYLLLYKPEGFECTLKPKEWPIVTDLIDVPQLGSLRIAGRLDVDTTGALLLSDDGGFLH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKL----NLLKKGIVIQGI--CYGDMQVTLDTQKGSN 186
            +  P     +VY +     + + +       L KGI+++         +++      + 
Sbjct: 121 RVTSPKHHVAKVYELTLADPMTEAQQAFAIKELAKGIMLEDEYDKTKPAELSFSDATHA- 179

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
               + L EGK  ++K++  +F  KV  L R S G   L  L  G +R ++ + + + 
Sbjct: 180 ---KLVLTEGKYHQVKRMMGYFGNKVIELHRASIGNITLAGLEKGESRFLTAEEIDQF 234


>gi|86740160|ref|YP_480560.1| ribosomal large subunit pseudouridine synthase B [Frankia sp. CcI3]
 gi|86567022|gb|ABD10831.1| ribosomal large subunit pseudouridine synthase B [Frankia sp. CcI3]
          Length = 252

 Score =  163 bits (412), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 74/234 (31%), Positives = 113/234 (48%), Gaps = 1/234 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPL 67
                 R+ KV+A AG+ SRR  E +IA  RV+V+G ++      V   T  IEVDG  +
Sbjct: 10  PQDQGIRLQKVLAAAGVGSRRHGEELIAAGRVRVDGTVVREQGRRVDPETALIEVDGERI 69

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                      +KP G+++  SD  GR T+ D L      +  VGRLD ++EGLLL+TND
Sbjct: 70  VTRTGLVHLALNKPRGVLSAMSDDRGRPTIADLLTEFGGGLFHVGRLDADSEGLLLVTND 129

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS    + Y V   G + +D L  L+  + +           +        
Sbjct: 130 GELAHRLTHPSFAVPKTYLVEVSGPLRRDVLRQLRAEVELDDGPVRADSARIVDNANGRV 189

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V V + EG+   ++++ +     V+RL+R  +G   LGTL AG  R +++  +
Sbjct: 190 MVEVVVHEGRKHVVRRMMDAVGHPVHRLVRTRFGAVSLGTLRAGRARHLTRHEI 243


>gi|261340036|ref|ZP_05967894.1| ribosomal large subunit pseudouridine synthase B [Enterobacter
           cancerogenus ATCC 35316]
 gi|288317956|gb|EFC56894.1| ribosomal large subunit pseudouridine synthase B [Enterobacter
           cancerogenus ATCC 35316]
          Length = 291

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 86/289 (29%), Positives = 128/289 (44%), Gaps = 12/289 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM--STDHIEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E +I   RV V+G +       V       I +DG  +   
Sbjct: 2   SEKLQKVLARAGHGSRREIEAIIEAGRVSVDGKIAT-LGDRVEIVPGLKIRIDGHLISVK 60

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E        L  Y     L T +      +          +R I+VGRLD+NT GLLL T
Sbjct: 61  ESAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  GQVD++KL  L +G+ ++        +     +G 
Sbjct: 121 TDGELANRLMHPSREVEREYAVRVFGQVDENKLRDLSRGVQLEDGPAAFKTIKFTGGEGI 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKIL 241
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       L
Sbjct: 181 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDILLPKGLPRGGYTELDLAQTNYL 240

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           RE +       ++V ++      +     R            R    ++
Sbjct: 241 RELVELTPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSSNRRSGSRNN 289


>gi|238786125|ref|ZP_04630080.1| Ribosomal large subunit pseudouridine synthase B [Yersinia
           bercovieri ATCC 43970]
 gi|238712977|gb|EEQ05034.1| Ribosomal large subunit pseudouridine synthase B [Yersinia
           bercovieri ATCC 43970]
          Length = 342

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 89/317 (28%), Positives = 135/317 (42%), Gaps = 12/317 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E +I Q RV V+G +       V  T    I +DG  L   
Sbjct: 27  GEKLQKVLARAGHGSRREIEAIIQQGRVSVDGKI-STLGDRVEVTQATKIRLDGHLLSIT 85

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E        L  Y     L T +      +          SR ++VGRLD+NT GLLL T
Sbjct: 86  ESEEAVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFT 145

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  GQ+D +K+  L +G+ ++        ++    +G 
Sbjct: 146 TDGELANRLMHPSREVEREYAVRVFGQIDDEKIKQLSRGVQLEDGPAAFRTISFQGGEGL 205

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK---IL 241
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  K    L
Sbjct: 206 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELDLKATNYL 265

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           RE +       +++ ++      +     R               +  S + G ++Q   
Sbjct: 266 RELVELDSETVSKLPVEKDRRRVKANQIRRAVKRHTEVAGRQVAGRQGSARKGSTRQNVG 325

Query: 302 ATPVHRRNLASNVWMAK 318
                            
Sbjct: 326 NAAPAATAGRRGSNKRG 342


>gi|322372477|ref|ZP_08047013.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           C150]
 gi|321277519|gb|EFX54588.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           C150]
          Length = 239

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 59/230 (25%), Positives = 104/230 (45%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++ +AG  SR +V+++I  ++V V+G+L +R  +NV ++   I V G  L  A  
Sbjct: 1   MRLDKLLGQAGYGSRNQVKKLIRSRQVYVDGVLADRDNLNVDASLQTITVSGKELEHAPE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +                       +  VGRLD +TEGL+L+TN+G L  
Sbjct: 61  VYYLMNKPSGVVSARRDKEHQTVIDLIKPEDQREGLYPVGRLDRDTEGLVLITNNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V  +  +  +     + G+V +         + + +     +   +
Sbjct: 121 ALLHPRYHVAKRYYVEVNDVLGPEAPAFFESGVVFEDGTVCKPAHLKILSSASDKSCAHI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
            + EGK  ++KK+F  +  KV  L RIS+G F L   L  GS R ++++ 
Sbjct: 181 TISEGKFHQVKKMFLAYGVKVTYLKRISFGDFVLDEKLPRGSYRPLTEEE 230


>gi|89074056|ref|ZP_01160557.1| putative pseudouridine synthase family 1 protein [Photobacterium
           sp. SKA34]
 gi|89050194|gb|EAR55705.1| putative pseudouridine synthase family 1 protein [Photobacterium
           sp. SKA34]
          Length = 376

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 84/347 (24%), Positives = 132/347 (38%), Gaps = 9/347 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E MI   RV V+G++ +        +  + +DG  +     
Sbjct: 2   SEKLQKVLARAGQGSRREIELMIQNGRVSVDGVVAKLGDRLEDLSVSVRIDGHNIELISS 61

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L        L T H     R+           R +SVGRLD NT GLLL T D
Sbjct: 62  DEEICRILAYNKPEGELCTRHDPEGRRTVFDRLPRLNTGRWVSVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS    R Y VR  G+V +  +  + KG+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRTVEREYMVRVFGEVTEQMVKNVVKGVELEDGLARFEDVVYAGGEGMNH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
              V + EG+NRE++++++     V+RL R+ YG   L   +  G   E+    L+E   
Sbjct: 182 TFYVVITEGRNREVRRLWDSQGVTVSRLKRVRYGDVYLTKDMPRGGWSEL---ELKEVNE 238

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                E     +  +       +     I           +  + +    +      P  
Sbjct: 239 LRATVELPPETETALTVEGQKRKKGIRQIRRAVRRHEERVETGAARGRRGRGNDRRNPGS 298

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            RN        +   +     +  R+    R    P      +TS K
Sbjct: 299 SRNAEVEAQSNERRGNGRSQPAKGRDNRDSRDNGKPQSAGRPQTSGK 345


>gi|312885162|ref|ZP_07744842.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           caribbenthicus ATCC BAA-2122]
 gi|309367175|gb|EFP94747.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           caribbenthicus ATCC BAA-2122]
          Length = 233

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 50/230 (21%), Positives = 96/230 (41%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  A+R+E  ++I    V VN  + +  A  V     +E  G  ++K    
Sbjct: 1   MRLDKYLCDALGATRKEATKIIKSGDVTVNEQVQKSGAFKVDDHSIVEWQGREVQKPGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+     + +     +  +            +   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLFKPDGFVCSHEDGFNQ-TAFMLLDEVRIEDLHFAGRLDVDTTGLVLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     +     +   KGI ++      +   L+        V + +
Sbjct: 120 ITSPKHKCDKTYRVWLADPIQPHYADEFTKGIQLRNEKGLTLPAKLELVDAQENEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
            EGK  ++K++F     KV  L R   G  +L  +L  G  R ++++ + 
Sbjct: 180 NEGKYHQVKRMFAALGNKVEHLHRERIGQIELCESLEPGDYRYLTQEEVD 229


>gi|283785437|ref|YP_003365302.1| ribosomal large subunit pseudouridine synthase B [Citrobacter
           rodentium ICC168]
 gi|282948891|emb|CBG88493.1| ribosomal large subunit pseudouridine synthase B [Citrobacter
           rodentium ICC168]
          Length = 291

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 86/288 (29%), Positives = 127/288 (44%), Gaps = 10/288 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIARLGDRVEVTPGLKIRIDGHLISVKE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD  K+  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDAKIRDLSRGVQLEDGPAAFRTIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAKTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           E +       ++V ++      +     R            R    ++
Sbjct: 242 ELVELPPETTSKVAVEKDRRRMKANQIRRAVKRHSQMSGGRRSGGRNN 289


>gi|145633297|ref|ZP_01789028.1| malic enzyme [Haemophilus influenzae 3655]
 gi|145634426|ref|ZP_01790136.1| malic enzyme [Haemophilus influenzae PittAA]
 gi|148825838|ref|YP_001290591.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae PittEE]
 gi|229845029|ref|ZP_04465165.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae 6P18H1]
 gi|229846853|ref|ZP_04466960.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae 7P49H1]
 gi|144986143|gb|EDJ92733.1| malic enzyme [Haemophilus influenzae 3655]
 gi|145268406|gb|EDK08400.1| malic enzyme [Haemophilus influenzae PittAA]
 gi|148715998|gb|ABQ98208.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae PittEE]
 gi|229810342|gb|EEP46061.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae 7P49H1]
 gi|229812001|gb|EEP47694.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae 6P18H1]
 gi|309972980|gb|ADO96181.1| 16S rRNA U516 pseudouridine synthase [Haemophilus influenzae R2846]
          Length = 232

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 57/236 (24%), Positives = 108/236 (45%), Gaps = 7/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  +V +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWVEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ HKP G V ++ D D  +        +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYFMLHKPQGCVCSNDDGDYPTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+++      +GI+++G        ++ +      +  V +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEENYAAACAEGILLRGEKEPTKPAKLEIL----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
            + EG+  ++K++F     KV  L R   G   L   L  G  R +++  + + + 
Sbjct: 177 TISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLVK 232


>gi|19552642|ref|NP_600644.1| 16S rRNA uridine-516 pseudouridylate synthase [Corynebacterium
           glutamicum ATCC 13032]
 gi|62390310|ref|YP_225712.1| 16S rRNA uridine-516 pseudouridylate synthase or related
           pseudouridylate synthase [Corynebacterium glutamicum
           ATCC 13032]
 gi|41325647|emb|CAF21436.1| 16S rRNA uridine-516 pseudouridylate synthase or related
           pseudouridylate synthase [Corynebacterium glutamicum
           ATCC 13032]
          Length = 320

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 75/236 (31%), Positives = 117/236 (49%), Gaps = 4/236 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           +    R+ KV+A+AG+ASRR  E +I Q RV+VN  ++    V V    D I VDGV + 
Sbjct: 76  DSDGVRLQKVLAQAGVASRRHAEILIDQGRVEVNDRIVTTQGVRVDPNNDVIRVDGVRIH 135

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLT 125
             E    ++ +KP G+ +T SD  GR  V D +        R+  VGRLD +TEGLLLLT
Sbjct: 136 INEDLEYFVLNKPRGMHSTMSDELGRPCVGDLVSEKTASGQRLFHVGRLDADTEGLLLLT 195

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  P  +  + Y     G+     ++ L+ G+ ++          +      
Sbjct: 196 NDGELANRLMHPKYEVSKTYLATVRGEATNKLVSALRDGVELEDGPAKADFAQIIDVFQG 255

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + + + + EG+   ++++F+   + V RL+R      QLG    GS R ++   L
Sbjct: 256 KSLLRIEIHEGRKHIVRRLFDELGFPVERLVRTKLHTVQLGDQKPGSLRALNSSEL 311


>gi|260435028|ref|ZP_05788998.1| pseudouridine synthase [Synechococcus sp. WH 8109]
 gi|260412902|gb|EEX06198.1| pseudouridine synthase [Synechococcus sp. WH 8109]
          Length = 250

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 66/242 (27%), Positives = 103/242 (42%), Gaps = 1/242 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T QR+ K+IA AG+ SRR  E  +   RV V+G++             I VDG PL    
Sbjct: 2   TRQRLQKLIAAAGLCSRRRAEEWLQAGRVTVDGLVASVGDQADPQQQTIHVDGQPLPSRG 61

Query: 72  RTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             R L +      + +       R+ +    P   + +  VGRLD ++ G LLLT+ G L
Sbjct: 62  VARVLLMNKPVGVICSCDDPQGRRTVLDLLPPEHRAGLHPVGRLDADSHGALLLTDLGEL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + YRV   G   +  L+  ++G+ + G      +V      G  + + 
Sbjct: 122 TLKLTHPRYSHAKTYRVWVKGVPPEPVLDRWRRGLPLDGCLTRPARVRRLRTWGDRSLLE 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + LREG+NR+I+++ E     V  L R +     LG L  G    +S+      L     
Sbjct: 182 IELREGRNRQIRRMAEALGHPVLDLQRTAIAGLPLGDLAEGCWIWLSEGEWEPLLERADP 241

Query: 251 EE 252
            +
Sbjct: 242 MD 243


>gi|42526387|ref|NP_971485.1| ribosomal large subunit pseudouridine synthase B [Treponema
           denticola ATCC 35405]
 gi|41816499|gb|AAS11366.1| ribosomal large subunit pseudouridine synthase B [Treponema
           denticola ATCC 35405]
          Length = 234

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 69/236 (29%), Positives = 117/236 (49%), Gaps = 5/236 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R+   +AR G+ASRR  E +I   RV V+G ++    + V   + I +DG  +    
Sbjct: 3   DEIRLQVYLARCGVASRRASENLILNGRVSVDGKIITELGIKVSGKEKICLDGKQIFPEA 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGL 130
             R  L +KP G V + +D   R      L   ++    ++GRLD+ + G +L TNDG  
Sbjct: 63  EKRYILLNKPEGYVCSLADEKDRPIAASLLKDTYTERLYNIGRLDMLSGGAILFTNDGDF 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  +E PS++  + Y V    +   + L    +G+ I+G+ Y  +     ++        
Sbjct: 123 SAKVEHPSSEIEKEYEVITVFEYPDEILQKFLRGVRIEGVFYKALSAERISKNKM----R 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + L EGKNREI++V +FFN K+ +L R+  G   L  L +G  R ++ + ++  LG
Sbjct: 179 IVLIEGKNREIRRVLKFFNIKIKKLTRVRIGCVYLADLPSGKHRPLTSEEIKGLLG 234


>gi|320334680|ref|YP_004171391.1| pseudouridine synthase Rsu [Deinococcus maricopensis DSM 21211]
 gi|319755969|gb|ADV67726.1| pseudouridine synthase Rsu [Deinococcus maricopensis DSM 21211]
          Length = 250

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 71/234 (30%), Positives = 109/234 (46%), Gaps = 6/234 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +R+ K +ARAG+ASRR  E +I   RV VNG+  +     V   D + VDG P+ +   
Sbjct: 2   TERLQKRLARAGVASRRAAEALITSGRVTVNGVTAQ-LGQTVTEADEVLVDGQPIAQRPT 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +           T +  +       +       +  VGRLD ++EGLLLLT DG L  
Sbjct: 61  QHVTFALYKPRGFVTTARDELGRRTVLDAMPNVPGLHPVGRLDRDSEGLLLLTTDGDLTL 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VYR    GQ D+  L  L +G+ ++    G  +V             V 
Sbjct: 121 TLTHPRYGHEKVYRAWTDGQPDEAALGRLARGMNLEDGPTGPAEVRAAPDGAW-----VT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +REG+NR+++++ +   + V RL+R   G   L  L  G  RE+ ++ L+E L 
Sbjct: 176 IREGRNRQVRRMLDAVGYPVTRLVRTRVGGLWLEDLGPGEYRELDERALQELLN 229


>gi|256545246|ref|ZP_05472611.1| ribosomal large subunit pseudouridine synthase B [Anaerococcus
           vaginalis ATCC 51170]
 gi|256399073|gb|EEU12685.1| ribosomal large subunit pseudouridine synthase B [Anaerococcus
           vaginalis ATCC 51170]
          Length = 231

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 64/230 (27%), Positives = 111/230 (48%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA+ G ASRR+ E  I   +V VNG  LE  +  V   D +++DG  L+  +  
Sbjct: 1   MRINKYIAKTGFASRRKSEEYIKNGKVFVNGNKLEDLSYQVKEEDEVKIDGKILKIQKNF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      + + +   + +      L +I  R    GRLD ++ GL+++TNDG +   
Sbjct: 61  YYKLNKPIGYISSNYDPHNEKDLNK--LLNIDERFFCAGRLDKDSHGLMIITNDGKITNK 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           +  PS +  ++Y V+   ++   +      G+ + Q     D +++L           V 
Sbjct: 119 IIHPSKKIDKIYIVKVDKKLTAYQEKNFMDGLKLSQKEITSDAKISLI--DKEKITYKVT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + +G NR+I+++FE+F  KV  L RI  G   L  L  G  +++SKK + 
Sbjct: 177 IHQGYNRQIRRMFEYFKIKVIDLKRIKIGQICLDDLKDGDYKKLSKKEVE 226


>gi|157145597|ref|YP_001452916.1| 23S rRNA pseudouridylate synthase B [Citrobacter koseri ATCC
           BAA-895]
 gi|157082802|gb|ABV12480.1| hypothetical protein CKO_01343 [Citrobacter koseri ATCC BAA-895]
          Length = 291

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 85/276 (30%), Positives = 124/276 (44%), Gaps = 10/276 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V +     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEITPGLKIRIDGHLISVKE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEV 278
           E +       ++V ++      +     R       
Sbjct: 242 ELVQLAPETTSKVAVEKDRRRMKANQIRRAVKRHSQ 277


>gi|332140787|ref|YP_004426525.1| pseudouridine synthase (makes pseudouridine2605 in 23 S RNA)
           [Alteromonas macleodii str. 'Deep ecotype']
 gi|327550809|gb|AEA97527.1| pseudouridine synthase (makes pseudouridine2605 in 23 S RNA)
           [Alteromonas macleodii str. 'Deep ecotype']
          Length = 298

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 85/298 (28%), Positives = 129/298 (43%), Gaps = 12/298 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+A  G+ SRRE+ER I + RV VNG +       V  T  I VDG  L +   
Sbjct: 2   TEKLQKVLANQGLGSRREMERWIEEGRVSVNGSVAT-LGDRVDHTAQIRVDGHLLSRQTE 60

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 L        L + H      +           R I+VGRLD+NT GLLL TNDG
Sbjct: 61  QPICRVLMYNKPEGELCSRHDPEGRDTVFDRLPAIRLGRWITVGRLDMNTSGLLLFTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------QVTLDTQ 182
            LA  L  P  +  R Y VR  G+V    LN L+KG+ +       +            +
Sbjct: 121 ELANRLMHPKCEVEREYAVRVFGEVSTKTLNTLQKGVELDDGEAKFLTISGTPTPQHAEE 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           +  N W  V L+EG+NRE+++++E    +V+RLIR+ YGP +L   L  G+  E+  + +
Sbjct: 181 ESMNRWFNVTLKEGRNREVRRLWESQGVQVSRLIRVKYGPIELQKRLPQGAWVELGLEDV 240

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
                   L +    +           R      S       + +  + +    +K+K
Sbjct: 241 NALRNHVQLPDETQTMVNVRQGKLDHARLSRMRRSVKKHKVRKQQGLNKRAGRPAKRK 298


>gi|323492456|ref|ZP_08097604.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio brasiliensis
           LMG 20546]
 gi|323313243|gb|EGA66359.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio brasiliensis
           LMG 20546]
          Length = 312

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 89/310 (28%), Positives = 130/310 (41%), Gaps = 9/310 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
           +++ KV+ARAG  SRRE+E +I   RV VNGI+ +           + +DG  +      
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKAGRVSVNGIVAKLGERLEDENAVVRIDGHTVSAKAQE 62

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 L  Y     L T H     R+          SR ISVGRLD NT GLLL T DG
Sbjct: 63  EVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS Q  R Y VR  G+V + K+  L +G+ ++        V      G N  
Sbjct: 123 ELANRLMHPSRQVEREYLVRVFGEVTEQKVKNLVRGVELEDGMARFEDVVYAGGDGMNHT 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LREQ 244
             V + EG+NRE+++++E  +  V+RL R+ YG   L   L  G   E+  K    LRE 
Sbjct: 183 FYVAINEGRNREVRRLWESQDTTVSRLKRVRYGDIYLDKKLPRGGWMELDLKEVNYLREL 242

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           +      +  ++      S +        I   V     R+     + N  +++K     
Sbjct: 243 VELRPERQTLLDESKANSSRKRERSRSQKIRRAVKRHEERVNSGGGRSNNPARRKPKKGS 302

Query: 305 VHRRNLASNV 314
             +       
Sbjct: 303 GQQGARNKQR 312


>gi|299134222|ref|ZP_07027415.1| RNA-binding S4 domain protein [Afipia sp. 1NLS2]
 gi|298590969|gb|EFI51171.1| RNA-binding S4 domain protein [Afipia sp. 1NLS2]
          Length = 695

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 140/327 (42%), Positives = 193/327 (59%), Gaps = 1/327 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           +++ T +R++K +ARAG+ SRR+ E  I Q RV VNG ++   A++V   D I +DG PL
Sbjct: 364 KKDKTGERIAKAVARAGLCSRRDAEEWITQGRVAVNGRVINSPALDVTVRDVITIDGKPL 423

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            + ERTRL+LYHKP GL+TTH DP+GR TVFD+LP    R+IS+GRLD NTEGLLLLTND
Sbjct: 424 PERERTRLFLYHKPRGLMTTHDDPEGRPTVFDHLPEGLPRLISIGRLDFNTEGLLLLTND 483

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GGL+R LE P T WLR YRVR HG+V Q +L+ LK G+ + GI YG +  TL+  +G+N 
Sbjct: 484 GGLSRALEHPDTGWLRRYRVRAHGEVTQAQLDELKNGVEVDGIKYGSIDATLERDQGANV 543

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           WVT  +REGKNRE++ V      +VNRLIR+SYGPFQLG +  G   E+  ++LREQLG 
Sbjct: 544 WVTFAIREGKNREVRNVMAHLGLEVNRLIRVSYGPFQLGEIPEGQVEEIKSRVLREQLGE 603

Query: 248 HLLEEAQVNLDAPIY-SSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
            +   +    D P+       V      +    D+    +     + G +   + +    
Sbjct: 604 KIATMSGAQFDKPVREDEGPKVGRDGTPLRSKADNKKIKRSKIEDRKGRTVVVQRSGSDE 663

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREE 333
           +R          G           + +
Sbjct: 664 KRARNEAEANGYGPPRKPKRGYHGKRD 690


>gi|297520148|ref|ZP_06938534.1| 23S rRNA pseudouridylate synthase B [Escherichia coli OP50]
          Length = 281

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 86/276 (31%), Positives = 125/276 (45%), Gaps = 10/276 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEV 278
           E +       ++V ++      +     R       
Sbjct: 242 ELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQ 277


>gi|169629456|ref|YP_001703105.1| l RNA pseudouridine synthase [Mycobacterium abscessus ATCC 19977]
 gi|169241423|emb|CAM62451.1| Probablel RNA pseudouridine synthase [Mycobacterium abscessus]
          Length = 263

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 67/236 (28%), Positives = 108/236 (45%), Gaps = 4/236 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           +    R+ KV+++AGIASRR  ERMI   RV+V+G ++      +    + + VDG  + 
Sbjct: 19  SEEGIRLQKVLSQAGIASRRVAERMIYDGRVEVDGEIVTEQGRRIDPAVNVVRVDGARVI 78

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLT 125
                     +KP G+++T SD  GR  V   +           +VGRLD +T GL+LLT
Sbjct: 79  MNTDLVYLALNKPFGMLSTMSDDRGRPCVGKLIEERVRGNQGVRNVGRLDADTVGLILLT 138

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG L   L  PS +  + Y     G + +     L+ G+ +        +         
Sbjct: 139 NDGELTHRLMHPSYEVPKTYIATVAGTIPRGLGRQLRDGVELADGPAKVDEFKFLGTTDG 198

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + V + L EG+NR ++++ +     V  L+R   G   LG    GS R + +  +
Sbjct: 199 QSMVQLTLHEGRNRIVRRMMDAAGHPVVELVRTKIGDVTLGNQRPGSLRALGRDEI 254


>gi|16273162|ref|NP_439399.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae Rd KW20]
 gi|260581161|ref|ZP_05848981.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           influenzae RdAW]
 gi|1175857|sp|P45124|RSUA_HAEIN RecName: Full=Ribosomal small subunit pseudouridine synthase A;
           AltName: Full=16S pseudouridine 516 synthase; AltName:
           Full=16S pseudouridylate 516 synthase; AltName:
           Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|1574175|gb|AAC22895.1| 16s pseudouridylate 516 synthase (rsuA) [Haemophilus influenzae Rd
           KW20]
 gi|260092189|gb|EEW76132.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           influenzae RdAW]
          Length = 232

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 108/236 (45%), Gaps = 7/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  +V +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWIEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ +KP G V ++ D D  +        +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYFMLNKPQGCVCSNDDGDYPTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+++      +GI+++G        ++ +      +  V +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEENYSAACAEGILLRGEKEPTKPAKLEIL----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
            + EG+  ++K++F     KV  L R   G   L   L  G  R +++  + + + 
Sbjct: 177 TISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLVK 232


>gi|114330041|ref|YP_746263.1| pseudouridine synthase, Rsu [Nitrosomonas eutropha C91]
 gi|114307055|gb|ABI58298.1| ribosomal large subunit pseudouridine synthase F [Nitrosomonas
           eutropha C91]
          Length = 243

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 61/245 (24%), Positives = 99/245 (40%), Gaps = 19/245 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
              R+SK+++  G+ SRRE +  I Q  V V+G         +     I +D        
Sbjct: 2   EKVRLSKLMSAQGMCSRREADVYIEQGWVYVDGQPARELGTKIYPWQEITLDRTAQIKQN 61

Query: 64  -------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
                    P+          Y     L+   S      +           +   GRLDI
Sbjct: 62  QQVTILLNKPVGYVSGQPELGYKPAASLICHDSRFHRDRSSLKFTSQHLKNLAPAGRLDI 121

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +++GLL+ T DG +A+ L    ++  + Y VR  G + +  L LL  G+ + G      +
Sbjct: 122 DSQGLLVFTQDGRVAKQLIGEYSRIEKEYLVRVIGNLTRKGLALLNHGLQLDGQVLKPAK 181

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V+L  Q      +   L+EGK R+I+++ E     V+ L R+  G  +L  L  G  R +
Sbjct: 182 VSLLNQDQ----LRFILQEGKKRQIRRMCELVGLNVSGLKRVRIGQIRLADLPEGKWRYL 237

Query: 237 SKKIL 241
            K  L
Sbjct: 238 GKNEL 242


>gi|331657316|ref|ZP_08358278.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli TA206]
 gi|331055564|gb|EGI27573.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli TA206]
          Length = 291

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 86/288 (29%), Positives = 128/288 (44%), Gaps = 10/288 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E ++   RV V+G + +    V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESILEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           E +       ++V ++      +     R            R    ++
Sbjct: 242 ELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGGRRSGGRNN 289


>gi|251782725|ref|YP_002997028.1| ribosomal small subunit pseudouridine synthaseA [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
 gi|242391355|dbj|BAH81814.1| ribosomal small subunit pseudouridine synthaseA [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
          Length = 245

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 56/234 (23%), Positives = 97/234 (41%), Gaps = 4/234 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAE 71
             R+ K +   G+ SR +V+ ++ ++ + VN  +     V +    D +   G PL    
Sbjct: 2   TMRLDKFLVETGVGSRSQVKSLLKKKAILVNQEVETSPKVQINEHKDVVTYLGKPLTYEA 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                L      L  T            +  +    V  VGRLD +T GLLLLTN+G LA
Sbjct: 62  FVYYILNKPAGFLSATKDRAQATVIDLLDETARQKDVFPVGRLDKDTRGLLLLTNNGQLA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWV 189
             L  P     + Y  +  G +     +   KGI ++       ++ +  +        V
Sbjct: 122 HDLLSPKKHVTKEYLAKVAGIMTDADKDDFAKGISLKDHQCLPAKLEVLDKDLSQETCVV 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           ++ ++EGK  ++K++      +V  L R+S GP +L   L  G  R ++   L+
Sbjct: 182 SITIQEGKFHQVKRMVAACGKEVLELQRLSMGPLRLDPGLAEGDFRRLTSDELQ 235


>gi|311748732|ref|ZP_07722517.1| ribosomal large subunit pseudouridine synthase B [Algoriphagus sp.
           PR1]
 gi|311302834|gb|EFQ79272.1| ribosomal large subunit pseudouridine synthase B [Algoriphagus sp.
           PR1]
          Length = 434

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 60/227 (26%), Positives = 108/227 (47%), Gaps = 2/227 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA +GI SRRE + +IA+  V VNG ++    + V   D +   G  +   +   
Sbjct: 203 RLNKYIANSGICSRREADDLIAKGLVSVNGKVVTELGLKVSKFDRVVYQGKKINPEKPVY 262

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L      + TT    + ++ +     +   R+  VGRLD NT GLLL TNDG LA  L
Sbjct: 263 VLLNKPKDFITTTDDPLERKTVMALVGNACEERIFPVGRLDRNTTGLLLFTNDGELAAKL 322

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             PS Q  ++Y+V     +  +    + +G+ ++        + + +       + + + 
Sbjct: 323 SHPSNQIKKIYQVTLDKPLTHNDEKDILEGLTLEDGEVEVDDMQVLSVD--RKILGLEIH 380

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            GKNR ++++F    ++V  L R+ Y       L  G+ R +S++ +
Sbjct: 381 VGKNRIVRRIFAHLGYEVTALDRVMYAGLDKKDLKRGNYRFLSEQEV 427


>gi|319776559|ref|YP_004139047.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae F3047]
 gi|317451150|emb|CBY87383.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae F3047]
          Length = 357

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 90/288 (31%), Positives = 132/288 (45%), Gaps = 10/288 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QPKVEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 67  LRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +  +         L  Y     L T        +          SR I+VGRLDINT GL
Sbjct: 130 INLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPHLTGSRWIAVGRLDINTSGL 189

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++    
Sbjct: 190 LLFTTDGELANRLMHPSHEVEREYSVRVFGQVDDAMLARLRKGVQLEDGLANFKEIKFTG 249

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 250 GVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEMDLEN 309

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
              LRE +G     E ++++       ++    +        +   + 
Sbjct: 310 VNYLRELVGLPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>gi|312883597|ref|ZP_07743322.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio
           caribbenthicus ATCC BAA-2122]
 gi|309368820|gb|EFP96347.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio
           caribbenthicus ATCC BAA-2122]
          Length = 311

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 88/309 (28%), Positives = 127/309 (41%), Gaps = 9/309 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
           +++ KV+ARAG  SRRE+E +I   RV VNG++             + +DG  +      
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKAGRVSVNGVVARLGERLEDENAVVRIDGHIVSAKAQE 62

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 L  Y     L T H     R+          SR ISVGRLD NT GLLL T DG
Sbjct: 63  EVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS Q  R Y VR  G+V + K+  L +G+ ++        V      G N  
Sbjct: 123 ELANRLMHPSRQVEREYLVRVFGEVTEQKVKNLVRGVELEDGLARFEDVVYAGGDGMNHT 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LREQ 244
             V + EG+NRE+++++E  +  V+RL R+ YG   L   L  G   E+  K    LRE 
Sbjct: 183 FYVAINEGRNREVRRLWESQDTTVSRLKRVRYGDIYLDKKLPRGGWMELDLKEVNYLREL 242

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           +     ++  ++ +    S +        I   V     R+       N   +  K    
Sbjct: 243 VELRPEKQTLLDENKANSSRKRERSRSQKIRRAVKRHEERVNSGGRSNNPARRNPKKGAG 302

Query: 305 VHRRNLASN 313
                    
Sbjct: 303 KANTRSKQR 311


>gi|262404053|ref|ZP_06080608.1| ribosomal small subunit pseudouridine synthase A [Vibrio sp. RC586]
 gi|262349085|gb|EEY98223.1| ribosomal small subunit pseudouridine synthase A [Vibrio sp. RC586]
          Length = 231

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 48/231 (20%), Positives = 94/231 (40%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++ +  V V+ ++ +  A  +  T  +E     +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKRGEVTVDDVVQKSGAFKLKETSRVEWQDREITLHGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     + +       ++            +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDG-FNQTAFTLLDEVNIEDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + YRV     +  D      KGI ++G        Q+ +     S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQGDYAEQFTKGIELRGERELTLPAQLEVV----SETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R   G   L   L  G  R +++  +
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDESLEPGEYRYLTEDEV 226


>gi|227877298|ref|ZP_03995371.1| pseudouridylate synthase [Lactobacillus crispatus JV-V01]
 gi|256842860|ref|ZP_05548348.1| 16S pseudouridylate synthase [Lactobacillus crispatus 125-2-CHN]
 gi|256848766|ref|ZP_05554200.1| 16S pseudouridylate synthase [Lactobacillus crispatus MV-1A-US]
 gi|262045826|ref|ZP_06018790.1| 16S pseudouridylate synthase [Lactobacillus crispatus MV-3A-US]
 gi|293381695|ref|ZP_06627676.1| pseudouridine synthase [Lactobacillus crispatus 214-1]
 gi|312977621|ref|ZP_07789368.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           crispatus CTV-05]
 gi|227863154|gb|EEJ70600.1| pseudouridylate synthase [Lactobacillus crispatus JV-V01]
 gi|256614280|gb|EEU19481.1| 16S pseudouridylate synthase [Lactobacillus crispatus 125-2-CHN]
 gi|256714305|gb|EEU29292.1| 16S pseudouridylate synthase [Lactobacillus crispatus MV-1A-US]
 gi|260573785|gb|EEX30341.1| 16S pseudouridylate synthase [Lactobacillus crispatus MV-3A-US]
 gi|290921742|gb|EFD98763.1| pseudouridine synthase [Lactobacillus crispatus 214-1]
 gi|310895360|gb|EFQ44427.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           crispatus CTV-05]
          Length = 234

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 60/232 (25%), Positives = 98/232 (42%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV ++I +  V VN ++++     V  +D + V+G  +   +  
Sbjct: 1   MRIDKYLANMNVGSRKEVHQLIKKGIVAVNDVIVKTPKQQVKESDQVTVNGDAVAYQKYH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      L  T                 +  ++ VGRLD +T GLLLLTNDG L   
Sbjct: 61  YFLLNKPKGVLSATEDRNQPTVISLLAPQDRYQGIVPVGRLDKDTTGLLLLTNDGQLNHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG--SNAWVT 190
           L  P     +VYR    G  +   +     G+ +  G      ++ + +Q      +   
Sbjct: 121 LLAPGKHVDKVYRAEIAGVANDATVKTFASGMTLGDGTKLQPAELKILSQDEEHDRSTTE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           + + EGK  +IK++F     KV  L RIS G   L   L  G   E+  + +
Sbjct: 181 IKICEGKYHQIKRMFGAVGMKVVELERISMGKLSLPANLKRGEYLELKLEDI 232


>gi|152969819|ref|YP_001334928.1| 23S rRNA pseudouridylate synthase B [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|238894324|ref|YP_002919058.1| 23S rRNA pseudouridylate synthase B [Klebsiella pneumoniae
           NTUH-K2044]
 gi|262043008|ref|ZP_06016151.1| ribosomal large subunit pseudouridine synthase B [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
 gi|150954668|gb|ABR76698.1| pseudouridine synthase [Klebsiella pneumoniae subsp. pneumoniae MGH
           78578]
 gi|238546640|dbj|BAH62991.1| pseudouridine synthase [Klebsiella pneumoniae subsp. pneumoniae
           NTUH-K2044]
 gi|259039610|gb|EEW40738.1| ribosomal large subunit pseudouridine synthase B [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
          Length = 300

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 89/300 (29%), Positives = 131/300 (43%), Gaps = 12/300 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM--STDHIEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E  I   RV V+G +       V       I +DG  +   
Sbjct: 2   SEKLQKVLARAGHGSRREIEAKIEAGRVSVDGKIAT-LGDRVEIVPGLKIRIDGHLISVK 60

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E        L  Y     L T +      +          +R I+VGRLD+NT GLLL T
Sbjct: 61  ESAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  GQVD DKL  L +G+ ++        +     +G 
Sbjct: 121 TDGELANRLMHPSREVEREYAVRVFGQVDDDKLRQLSRGVQLEDGPAAFKTIKFTGGEGI 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKIL 241
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       L
Sbjct: 181 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDILLPKGLPRGGYTELDLAQTNYL 240

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           RE +       ++V ++      +     R            R   NS++++    +   
Sbjct: 241 RELVELTPETSSKVAVEKDRRRLKANQIRRAVKRHSQTSANPRQGNNSNRRSSTRNKTNG 300


>gi|206576006|ref|YP_002238999.1| ribosomal large subunit pseudouridine synthase B [Klebsiella
           pneumoniae 342]
 gi|288935908|ref|YP_003439967.1| pseudouridine synthase [Klebsiella variicola At-22]
 gi|290512947|ref|ZP_06552311.1| 23S rRNA pseudouridylate synthase B [Klebsiella sp. 1_1_55]
 gi|206565064|gb|ACI06840.1| ribosomal large subunit pseudouridine synthase B [Klebsiella
           pneumoniae 342]
 gi|288890617|gb|ADC58935.1| pseudouridine synthase [Klebsiella variicola At-22]
 gi|289774560|gb|EFD82564.1| 23S rRNA pseudouridylate synthase B [Klebsiella sp. 1_1_55]
          Length = 300

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 89/300 (29%), Positives = 131/300 (43%), Gaps = 12/300 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM--STDHIEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E  I   RV V+G +       V       I +DG  +   
Sbjct: 2   SEKLQKVLARAGHGSRREIEAKIEAGRVSVDGKIAT-LGDRVEIVPGLKIRIDGHLISVK 60

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E        L  Y     L T +      +          +R I+VGRLD+NT GLLL T
Sbjct: 61  ESAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  GQVD DKL  L +G+ ++        +     +G 
Sbjct: 121 TDGELANRLMHPSREVEREYAVRVFGQVDDDKLRQLSRGVQLEDGPAAFKTIKFTGGEGI 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKIL 241
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       L
Sbjct: 181 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDILLPKGLPRGGYTELDLAQTNYL 240

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           RE +       ++V ++      +     R            R   NS++++    +   
Sbjct: 241 RELVELTPETSSKVAVEKDRRRMKANQIRRAVKRHSQTSANPRQGNNSNRRSSTRNKTNG 300


>gi|296393714|ref|YP_003658598.1| pseudouridine synthase [Segniliparus rotundus DSM 44985]
 gi|296180861|gb|ADG97767.1| pseudouridine synthase [Segniliparus rotundus DSM 44985]
          Length = 272

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 79/240 (32%), Positives = 122/240 (50%), Gaps = 12/240 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           QR+ KV+ARAG+ASRR  E++IA+ RV+V+G L+    V V   T  +EVDG  +   +R
Sbjct: 19  QRLHKVLARAGVASRRGSEQLIAEGRVRVDGRLVTEQGVLVDPHTAVVEVDGKRIAVDDR 78

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-----------ISVGRLDINTEGL 121
              +  +KP G++T  SD   R        +                  VGRLD +T GL
Sbjct: 79  HATYALNKPKGVLTAMSDTRERCVGDLLREAGPDFAADGRAGLPAGLFHVGRLDADTTGL 138

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL++NDG LA  L  PS +  + Y     G V +  +  L+ G+V++       +V L  
Sbjct: 139 LLVSNDGELAHRLAHPSYEIPKTYIATVRGVVAKRAVEQLRAGVVLEDGPAKADEVCLRG 198

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +     V + L EG+NR ++++F+     V  L R+  GP +LG L +G+ R +S   +
Sbjct: 199 SQRDRTVVEITLHEGRNRIVRRMFDEVGHPVIELARLRIGPIRLGDLRSGALRALSSSEV 258


>gi|238064000|ref|ZP_04608709.1| pseudouridine synthase [Micromonospora sp. ATCC 39149]
 gi|237885811|gb|EEP74639.1| pseudouridine synthase [Micromonospora sp. ATCC 39149]
          Length = 256

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 72/230 (31%), Positives = 106/230 (46%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV+A AG+ SRR  E +I ++RV VNG + +        T D I VDG  L+   R
Sbjct: 19  ERLQKVLAAAGVGSRRACEDLIFRRRVTVNGKVAQ-LGDKADPTRDVILVDGERLQADTR 77

Query: 73  TRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                       + T   +    +        +  RV  VGRLD ++EGLLLLTNDG LA
Sbjct: 78  LVYLALNKPRGVVSTMADEKGRAALSDFIGNRVEQRVYHVGRLDADSEGLLLLTNDGDLA 137

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  PS    + Y     G + ++    L  GI ++          +    G  A V +
Sbjct: 138 HRLTHPSYGVPKTYLCEVAGPIPRNLGKRLAAGIELEDGPVTVDSFKVVDTLGKTAQVEL 197

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            L EG+   ++++       V RL+R S GP +LG L AG TR ++   +
Sbjct: 198 TLHEGRKHIVRRLLGEVGHPVFRLVRTSIGPIRLGDLRAGRTRRLTNAEV 247


>gi|194335646|ref|YP_002017440.1| pseudouridine synthase [Pelodictyon phaeoclathratiforme BU-1]
 gi|194308123|gb|ACF42823.1| pseudouridine synthase [Pelodictyon phaeoclathratiforme BU-1]
          Length = 247

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 114/250 (45%), Gaps = 10/250 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DH 59
           MK  N         R+++ +A  GIASRR  ++++   RV VNG ++    + V  T D 
Sbjct: 1   MKKSN----KDDEVRINRYLASCGIASRRAADQLVLDGRVMVNGTVITTPGIKVSPTRDE 56

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           + VDG    + E  ++++       V T +  +    +  +   +  RV  VGRLD  T 
Sbjct: 57  VIVDGEKFAQPEHRKVYILFNKPRNVITTNSDEKNREMVLDFIDVEERVFPVGRLDRKTT 116

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQV 177
           G++LLTNDG LA  L  PS+   + Y      +   + L  L  G+ ++         + 
Sbjct: 117 GVILLTNDGTLAHKLMHPSSNVKKEYIAELSEKFTPNLLPQLTGGMRLKDTGEKVSPCRA 176

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +         V V + EGKN +++++FE   ++V RL R++Y     G L  G  R +S
Sbjct: 177 KIL---EDGMQVLVSIHEGKNHQVRRMFETLGFEVKRLERVAYAGLLAGELRRGEWRYLS 233

Query: 238 KKILREQLGP 247
           +  ++     
Sbjct: 234 RNEVQALYKL 243


>gi|295100310|emb|CBK97855.1| ribosomal small subunit pseudouridine synthase A [Faecalibacterium
           prausnitzii L2-6]
          Length = 234

 Score =  163 bits (411), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 57/230 (24%), Positives = 93/230 (40%), Gaps = 4/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R E + ++A+ RV VNG +  +    +   D + VDG  L   +  
Sbjct: 1   MRLDKYLAETAQCTRSEAKALLAKGRVTVNGAVCRKGDTQLKEADAVAVDGKALAYRQFV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L      +  +    D               +   GRLD  + G +LLT+DGG A  
Sbjct: 61  YLMLNKPEGVVSASADKRDTTVVDLVGDAYPRRELFPAGRLDKTSTGFVLLTDDGGFAHD 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG-DMQVTLDTQKGSNAWVTVG 192
           +  P     + Y V     + ++       G+ +         +V+  T  G    V V 
Sbjct: 121 ILAPKRHVSKTYTVVIDTPLTEEMKAGFAAGVTLADGTALSPAEVSALTPDGL--TVRVL 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           LR+G   +IK++F  +   VN L R + G   L   L AG  RE++   +
Sbjct: 179 LRQGVYHQIKRMFGVYGAGVNALHRDAIGGLALDESLAAGQWRELTADEV 228


>gi|254361964|ref|ZP_04978095.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|261493683|ref|ZP_05990202.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
 gi|261494350|ref|ZP_05990844.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|153093511|gb|EDN74491.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|261309999|gb|EEY11208.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|261310683|gb|EEY11867.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
          Length = 233

 Score =  163 bits (411), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 55/236 (23%), Positives = 104/236 (44%), Gaps = 7/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  +++    V VNG + +  A  +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENTGLTRSQAAKVLKSGVVTVNGNIEKSGAAKISQEDEIYYEDQKLEWVEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ +KP G + +H D +  +        + +++ + GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYFMLYKPQGYICSHDDGEYPTVFQFFDYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+      L +GI+++G        Q+ +      +  V +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEDFYAQRLAEGILLRGEKEPTLPAQLEIL----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
            + EG+  ++K++F     KV  L R   G   L   L  G  R ++ + +    G
Sbjct: 177 TISEGRYHQVKRMFAALGNKVEALHRWRIGDVVLDERLEEGEFRSLTSEEIASFNG 232


>gi|146342900|ref|YP_001207948.1| putative pseudouridine synthase, Rsu:RNA-binding S4:pseudouridine
           synthase [Bradyrhizobium sp. ORS278]
 gi|146195706|emb|CAL79733.1| Putative Pseudouridine synthase, Rsu:RNA-binding S4:Pseudouridine
           synthase [Bradyrhizobium sp. ORS278]
          Length = 683

 Score =  163 bits (411), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 144/321 (44%), Positives = 199/321 (61%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           +   T +R++KV+ARAG+ASRR+ E M+ Q RV VNG ++   A++V   D I+VDG PL
Sbjct: 360 KPRKTGERIAKVLARAGLASRRDAEEMVTQGRVSVNGRIINSPALDVTENDEIKVDGAPL 419

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            + ERTRL+LYHKP GL+TTHSDP+GR TVFDNLP    R+IS+GRLD NTEGLLLLTND
Sbjct: 420 PERERTRLFLYHKPRGLMTTHSDPEGRPTVFDNLPEGLPRLISIGRLDFNTEGLLLLTND 479

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GGLARVLELP T W R YRVR HG++ Q +L+ L  G+ + G+ YG ++ TL+  +G+N 
Sbjct: 480 GGLARVLELPDTGWTRRYRVRAHGEITQGQLDQLAAGVEVDGVKYGPIEATLERDQGANV 539

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+ V +REGKNRE++ V      +VNRLIR+SYGPFQL  L  G  +EV  ++LREQLG 
Sbjct: 540 WLVVAIREGKNREVRNVLAHLGLEVNRLIRVSYGPFQLLELPEGEVQEVKTRVLREQLGE 599

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            ++ ++  +L     S+   + D             + ++   Q+ G  + ++      R
Sbjct: 600 KVIAQSGADLGPAGSSNREPLPDPKPKPKREIVADRKGRRVLVQRTGSEEARERHEAEAR 659

Query: 308 RNLASNVWMAKGIHSSFLSDS 328
                            +S  
Sbjct: 660 FPGPPRRPKRGYHGKRDISPR 680



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 9/113 (7%), Positives = 27/113 (23%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R++        A  + +    + +           +   +        ++ +     +  
Sbjct: 76  RDERPRGDRPYAARSGEGEKRAFKPRGDRPKFDRDDRGGEKRPYTPRGNRDDARPAGRSS 135

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                 R   +                G R+   R + SF  + S      ++
Sbjct: 136 ERKFGERKPYAPRERDGEKRPYTPRGEGARDRGDRPARSFGDRPSRGGDRPER 188


>gi|298373492|ref|ZP_06983481.1| ribosomal large subunit pseudouridine synthase B [Bacteroidetes
           oral taxon 274 str. F0058]
 gi|298274544|gb|EFI16096.1| ribosomal large subunit pseudouridine synthase B [Bacteroidetes
           oral taxon 274 str. F0058]
          Length = 396

 Score =  163 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 58/230 (25%), Positives = 107/230 (46%), Gaps = 2/230 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAE 71
           P R++K IA + I SRRE +  I    V VNG ++      ++  TD +      +   +
Sbjct: 160 PMRLNKFIANSNICSRREADEFIQAGVVSVNGQVVTELGTKIVPATDKVHFHDQLVSMEK 219

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +      + T     + R+ +     +   RV  VGRLD NT G+LL+TNDG L 
Sbjct: 220 KIYILMNKPKNIITTLDDPKERRTVLDLIKNACSERVYPVGRLDRNTTGVLLITNDGDLT 279

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P  +  ++Y VR   + +   +  ++ GIV++        ++   ++ +   V +
Sbjct: 280 SKLIHPKYEKKKIYHVRLDREFESQDMEAMRSGIVLEDGDIKADDISYV-KEDNKKEVGI 338

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +  GKNR ++++FE   +K+  L R+ +       L  G  R +S+  +
Sbjct: 339 EIHSGKNRIVRRMFEHLGYKIVALDRVYFAGLTKKNLPRGKWRYLSESEV 388


>gi|238919603|ref|YP_002933118.1| 23S rRNA pseudouridylate synthase B [Edwardsiella ictaluri 93-146]
 gi|269138896|ref|YP_003295597.1| 23S rRNA pseudouridylate synthase/pseudouridine synthase
           [Edwardsiella tarda EIB202]
 gi|238869172|gb|ACR68883.1| RNA pseudouridine synthase family protein [Edwardsiella ictaluri
           93-146]
 gi|267984557|gb|ACY84386.1| 23S rRNA pseudouridylate synthase/pseudouridine synthase
           [Edwardsiella tarda EIB202]
 gi|304558882|gb|ADM41546.1| Ribosomal large subunit pseudouridine synthase B [Edwardsiella
           tarda FL6-60]
          Length = 291

 Score =  163 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 92/292 (31%), Positives = 135/292 (46%), Gaps = 12/292 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I + RV V+G L      V VM    I VDG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIEALIKEGRVSVDGKLATLGDRVEVMPNMKIRVDGRVVSIRE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T        +          SR I+VGRLDINT GLLL T 
Sbjct: 62  SEQEICRVLAYYKPEGELCTRRDPEGRPTVFDRLPRLRGSRWIAVGRLDINTSGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD+DKL  L++G+ ++        ++    +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDEDKLRQLRRGVQLEDGPASFKSISFQGGEGLN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK---ILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G  +E+  +    LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDLPLPKGLPRGGWQELPLENINYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           E +       +++ ++                +          ++  + K G
Sbjct: 242 ELVELQAETASKLPVERERRRM--KANQIRRAVKRHGQHSGGSRRAPTTKRG 291


>gi|329124070|ref|ZP_08252617.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           aegyptius ATCC 11116]
 gi|327467495|gb|EGF12993.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           aegyptius ATCC 11116]
          Length = 357

 Score =  163 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 90/288 (31%), Positives = 132/288 (45%), Gaps = 10/288 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QSKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 67  LRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +  +         L  Y     L T        +          SR I+VGRLDINT GL
Sbjct: 130 INLSHAQKEICRVLMYYKPEGELCTRSDPKGRATVFDRLPHLTGSRWIAVGRLDINTSGL 189

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++    
Sbjct: 190 LLFTTDGELANRLMHPSHEVEREYSVRVFGQVDDAMLARLRKGVQLEDGLANFKEIKFTG 249

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 250 GVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEMDLEN 309

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
              LRE +G     E ++++       ++    +        +   + 
Sbjct: 310 VNYLRELVGLPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>gi|229916458|ref|YP_002885104.1| pseudouridine synthase [Exiguobacterium sp. AT1b]
 gi|229467887|gb|ACQ69659.1| pseudouridine synthase [Exiguobacterium sp. AT1b]
          Length = 237

 Score =  163 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 53/236 (22%), Positives = 104/236 (44%), Gaps = 3/236 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
            R+ K++A  G  SR++V+ ++ Q  V+V+  L++ A  +V  +   + V G  +     
Sbjct: 1   MRIDKLLANMGYGSRKDVKILLKQGAVRVDEALVKDAKRHVDPSSEKVTVFGEVVEYRPY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T    +       +       +  VGRLD +T GLLL+TNDG    
Sbjct: 61  IYFMMNKPEGVISATEDQVETTVIELIDSEYAHYDLFPVGRLDKDTTGLLLITNDGAFNH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY     G++  + +     G+ ++        ++ + ++ G  + + +
Sbjct: 121 ALMSPRKHVDKVYIAEVDGEMTVEDIKTFANGVELEDGYTTKPARLEILSRSGRRSVIRL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYG-PFQLGTLLAGSTREVSKKILREQLG 246
            L EGK  ++K++       V RL R+  G      TL  G+ RE++++ ++  L 
Sbjct: 181 TLSEGKYHQVKRMVAAVGKHVERLERVQIGELELDETLELGAYRELTEEEVQLFLQ 236


>gi|261253231|ref|ZP_05945804.1| ribosomal large subunit pseudouridine synthase B [Vibrio orientalis
           CIP 102891]
 gi|260936622|gb|EEX92611.1| ribosomal large subunit pseudouridine synthase B [Vibrio orientalis
           CIP 102891]
          Length = 312

 Score =  163 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 89/314 (28%), Positives = 134/314 (42%), Gaps = 13/314 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
           +++ KV+ARAG  SRRE+E +I   RV VNG++ +           + +DG  +      
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKAGRVSVNGVVAKLGERLEDENAIVRIDGHTVSAKAQE 62

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 L  Y     L T H     R+          SR ISVGRLD NT GLLL T DG
Sbjct: 63  EVVCRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS Q  R Y VR  G+V + K+  L +G+ ++        V      G N  
Sbjct: 123 ELANRLMHPSRQVEREYLVRVFGEVTEQKVKNLVRGVELEDGMARFEDVVYAGGDGMNHT 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LREQ 244
             V + EG+NRE+++++E  +  V+RL R+ YG   L   L  G   E+  K    LRE 
Sbjct: 183 FYVAINEGRNREVRRLWESQDTTVSRLKRVRYGDIYLDKKLPRGGWMELDLKEVNYLREL 242

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           +     +E  ++ +     + T  +   +   ++     R ++  S   G S       P
Sbjct: 243 VELRPEKETLLDENK----ANTSRKRERSRSQKIRRAVKRHEERVSSGGGRSNNPSRRKP 298

Query: 305 VHRRNLASNVWMAK 318
                  +     +
Sbjct: 299 KKGAGKPNARNKQR 312


>gi|329939210|ref|ZP_08288584.1| pseudouridine synthase [Streptomyces griseoaurantiacus M045]
 gi|329302095|gb|EGG45988.1| pseudouridine synthase [Streptomyces griseoaurantiacus M045]
          Length = 364

 Score =  163 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 108/233 (46%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
               +R+ KV+ARAG  SRR  E +I   RV+VNG ++      V    D I+VDG+ + 
Sbjct: 124 EQEGERLQKVLARAGYGSRRACEELIEDARVEVNGEIVLEQGKRVDPEHDEIKVDGLTVA 183

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   L      + T       +  + D + +  +R+  VGRLD  TEG++LLTN G
Sbjct: 184 TQSYQFFSLNKPAGVVSTMEDPEGRQ-CLGDYVTNRETRLFHVGRLDTETEGVILLTNHG 242

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     + Y     G + +D    LK GI ++          +  Q G N  
Sbjct: 243 ELAHRLTHPRYGVRKTYLAHIVGPIPRDLGKRLKDGIQLEDGYARADHFRVVEQTGKNYL 302

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L EG+   ++++     + V++L+R ++GP  LG   +G  R +S   +
Sbjct: 303 VEVTLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPITLGDQKSGWLRRLSNTEV 355


>gi|332290312|ref|YP_004421164.1| 23S rRNA pseudouridylate synthase B [Gallibacterium anatis UMN179]
 gi|330433208|gb|AEC18267.1| 23S rRNA pseudouridylate synthase B [Gallibacterium anatis UMN179]
          Length = 297

 Score =  163 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 95/282 (33%), Positives = 134/282 (47%), Gaps = 10/282 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPL---- 67
            +++ KV+ARAG+ SRREVE +IA  RV VNG +      V V +   I VDG  +    
Sbjct: 16  GEKLQKVLARAGVGSRREVETIIAAGRVSVNGKIASLGDRVEVKNDTKIRVDGGLVSLIA 75

Query: 68  -RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
            RK     L  Y     L T H      +          +R +SVGRLDINT GLLL T 
Sbjct: 76  ARKDICRVLMYYKPEGELCTRHDPEGRATVFERLPQISNARWVSVGRLDINTSGLLLFTT 135

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  G V +  L  L+KG+ ++       +++    +G N
Sbjct: 136 DGELANRLMHPSKEVEREYSVRVFGHVTEQMLAKLRKGVQLEDGPASFKKISAQGGQGMN 195

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK---ILR 242
            W +V L EG+NRE+++++E    +V+RLIR  YG   L   L  G   E+  +    LR
Sbjct: 196 QWFSVTLTEGRNREVRRLWESQGIQVSRLIRTRYGNIDLMKGLPRGGWIELPLEKVNYLR 255

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
           + +   L  E++V+           +R      S      TR
Sbjct: 256 QLVDLPLETESKVDTKNSRSFKSNQIRKAVKQHSLKKRYQTR 297


>gi|169343901|ref|ZP_02864897.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           C str. JGS1495]
 gi|169298021|gb|EDS80112.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           C str. JGS1495]
          Length = 228

 Score =  163 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 56/229 (24%), Positives = 104/229 (45%), Gaps = 8/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+ +  GI SR+E  ++I + R+ VNG         V  +D I +DG PL   E+ 
Sbjct: 1   MRINKLFSNFGICSRKETNKIIREGRIIVNGKPCIE-GQWVELSDEILLDGKPLVPKEKI 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L      + T   +         +   I   V  +GRLD +++GL++LTNDG LA  
Sbjct: 60  YIALNKPVGVVCTAAEEV---KDNIIDYLGIDDYVFPIGRLDKDSQGLIILTNDGDLANE 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V        D +  +++G+ I G      ++    +       ++ L
Sbjct: 117 VLAAENNHEKEYIVTLDQPFYDDFIEKMEQGVEILGQVTKPCKLKRINEN----TYSIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ + F + V +L RI      L  +  G  R ++++ + 
Sbjct: 173 TQGLNRQIRRMSKVFGFNVVKLERIRILNITLKDIEYGKWRYINREEIE 221


>gi|167582090|ref|ZP_02374964.1| RNA pseudouridylate synthase family protein [Burkholderia
           thailandensis TXDOH]
          Length = 379

 Score =  163 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 77/273 (28%), Positives = 125/273 (45%), Gaps = 6/273 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 73  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 131

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 132 GKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNTE 191

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 192 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRIRD 251

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 252 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 311

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDR 271
             +R  +    L+           ++E    D 
Sbjct: 312 AQVRRLMSTVGLKAPVEEKGKRGGAAERRQPDP 344


>gi|187928207|ref|YP_001898694.1| pseudouridine synthase [Ralstonia pickettii 12J]
 gi|187725097|gb|ACD26262.1| pseudouridine synthase [Ralstonia pickettii 12J]
          Length = 594

 Score =  163 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 83/321 (25%), Positives = 138/321 (42%), Gaps = 7/321 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K + +  E+  P ++ K++A AG+ SRR++E +I Q RV VNG+        +++TD + 
Sbjct: 202 KARELTSEDDAP-KLHKILADAGLGSRRDMEDLILQGRVSVNGLPA-HIGQRILATDQVR 259

Query: 62  VDGVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           V+G  +++         L  +     +V+        +           + ++VGRLD N
Sbjct: 260 VNGKLIQRKLPNKPPRVLLYHKPSGEIVSQSDPEGRPTVFDALPRMKTGKWVAVGRLDFN 319

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+ T  G +A     P     R Y VR  G++ +     L  GI +Q      ++ 
Sbjct: 320 TEGLLIFTTSGDIANRFMHPRYGVEREYAVRTLGELAETDRQKLLHGISLQDGEANFLRC 379

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EV
Sbjct: 380 VDGGGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEV 439

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           S + +R  +G   ++    +            R    ++          + N   +    
Sbjct: 440 SAEDVRTLMGTLGMKVPTASSGGGQDRQGNRRRGPAPVLMGPMSSGFAGEANFQSRGMGV 499

Query: 297 KQKKLATPVHRRNLASNVWMA 317
           +    A P  RR  +      
Sbjct: 500 ENGNRAQPAQRRPSSPRQPDP 520


>gi|168218095|ref|ZP_02643720.1| ribosomal small subunit pseudouridine synthase B [Clostridium
           perfringens NCTC 8239]
 gi|182379855|gb|EDT77334.1| ribosomal small subunit pseudouridine synthase B [Clostridium
           perfringens NCTC 8239]
          Length = 236

 Score =  163 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 69/228 (30%), Positives = 116/228 (50%), Gaps = 2/228 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKAER 72
           +R+ K +AR G+ASRR+ E +I   +VKVN I+++     V  +  +   +   +R  E 
Sbjct: 3   ERLQKYMARCGVASRRKCEEIICSGKVKVNDIVVDSLGTKVDPSVDVVSVNNKVIRPEEN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G VTT+ D   R T+ D +     R+  +GRLD ++ GLLLLTNDG +  
Sbjct: 63  KVYIMLNKPEGYVTTNKDEKNRKTILDIVKVN-ERIYPIGRLDYDSSGLLLLTNDGDVYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y     G   ++++N  +KG+ I      + ++ L  +  ++  V + 
Sbjct: 122 KIIHPRVNLNKEYIALVKGIFTEEEMNKFRKGVDIGDYKTAECEIELLEKYTNSCKVKII 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           + EGKNR+I+++   FN +V  L R + G   L  L  G  R +S   
Sbjct: 182 IHEGKNRQIRRMCAVFNHEVVSLKREAIGSLNLKNLKKGEWRYLSSSE 229


>gi|293395935|ref|ZP_06640216.1| ribosomal large subunit pseudouridine synthase B [Serratia
           odorifera DSM 4582]
 gi|291421433|gb|EFE94681.1| ribosomal large subunit pseudouridine synthase B [Serratia
           odorifera DSM 4582]
          Length = 297

 Score =  163 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 83/296 (28%), Positives = 133/296 (44%), Gaps = 7/296 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E MI   RV V+G + +    V V+    I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIETMIEAGRVSVDGKIAKLGDRVEVVQGMKIRLDGHVVSIKE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T        +          SR ++VGRLD+NT GLLL T 
Sbjct: 62  SEEAVCRVLAYYKPEGELCTRSDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQ+D DK+  L +G+ ++        ++    +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQIDDDKVKQLSRGVQLEDGPAAFRTISFQGGEGLN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   +  G   E+    +    
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGIPRGGWTELDLPAINYLR 241

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
               L+   V+          +  ++     +     +  +++++        K+ 
Sbjct: 242 ELVDLQPETVSKLPVERERRRVKANQIRRAVKRHSQVSTGRRSAAGGKPGKPSKRN 297


>gi|75908041|ref|YP_322337.1| ribosomal large subunit pseudouridine synthase B [Anabaena
           variabilis ATCC 29413]
 gi|75701766|gb|ABA21442.1| ribosomal large subunit pseudouridine synthase B [Anabaena
           variabilis ATCC 29413]
          Length = 288

 Score =  163 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 84/243 (34%), Positives = 123/243 (50%), Gaps = 12/243 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ KV+A+ GIASRRE E MI + RV++NG L       V    D I VDG  +      
Sbjct: 30  RLQKVLAQWGIASRREAEEMIRRSRVQINGTLA-ELGQKVNPERDIITVDGKSVSAQRHH 88

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLLTNDG 128
           R    L +KP G+V+T  DP GR TV D LP    +      VGRLD  + G L+LTNDG
Sbjct: 89  RLTYLLLNKPTGVVSTCYDPQGRKTVLDLLPEELRKGSGLHPVGRLDAYSTGALILTNDG 148

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS    + Y++   G   +  L + ++G+++ G      +V+L       + 
Sbjct: 149 DLTFKLTHPSHNIPKTYQILVKGHPPEAVLKMWREGVLLDGRKTRKAKVSLLESLAEKSR 208

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-----LLAGSTREVSKKILRE 243
           + + L+EG+NR+I++V E   + V +L R + G  QL T     L AG+ R +    +R 
Sbjct: 209 LEIVLQEGRNRQIRRVAEQLGYPVIKLHRTAIGSIQLQTSKQPLLRAGNYRILRDDEIRS 268

Query: 244 QLG 246
              
Sbjct: 269 LQE 271


>gi|296126048|ref|YP_003633300.1| RNA-binding S4 domain protein [Brachyspira murdochii DSM 12563]
 gi|296017864|gb|ADG71101.1| RNA-binding S4 domain protein [Brachyspira murdochii DSM 12563]
          Length = 227

 Score =  163 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 64/232 (27%), Positives = 113/232 (48%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA   IASRRE +++I    VK+NGI+    A  V + D +E D       +  
Sbjct: 1   MRLNKYIASLNIASRREADKLIQNGNVKINGIVNTNPAYQVSNDDKVECD--INEYKKDK 58

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G V + +  +G+   +  + + F+ +  VGRLD ++ GL++LTNDG  +R 
Sbjct: 59  IYIKLNKPRGYVVSSNKKEGKPI-YSLIKNDFNNIYPVGRLDKDSSGLIILTNDGVFSRK 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +   +T   + Y V+ +  +    L  L+ GI + G      +V    +        + L
Sbjct: 118 IIGENTNCKKEYFVKVNDNIPDGALKKLEYGISLDGQKLKPAEVKRINKNS----FHIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            EGKNR+I+++ +   ++V  L R+      L  L  G+ + ++K  +   L
Sbjct: 174 TEGKNRQIRRMCQKIGFEVIILKRLRIADILLDDLKEGTFKHLTKNEINSVL 225


>gi|302330665|gb|ADL20859.1| Putative pseudourin ine synthase B [Corynebacterium
           pseudotuberculosis 1002]
 gi|308276349|gb|ADO26248.1| 16S rRNA uridine-516 pseudouridylate synthase-like pseudouridylate
           synthase [Corynebacterium pseudotuberculosis I19]
          Length = 286

 Score =  163 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 77/245 (31%), Positives = 120/245 (48%), Gaps = 4/245 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DH 59
           ++ ++         R+ KV+A+AG+ASRR  E +I   R++VNG ++    V V    D 
Sbjct: 33  VEQRDFGSPTGEGIRLQKVLAQAGVASRRHAEILIDAGRIEVNGKIVLTQGVRVNPHADI 92

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDI 116
           I VDGV +   E  + ++ +KP GL +T SD  GR  V D +        R+  VGRLD 
Sbjct: 93  IRVDGVRINVNEDMQYFVLNKPRGLQSTMSDDMGRPCVGDIVGERIAAGQRLFHVGRLDA 152

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
            TEGLLLLTNDG LA  L  P  +  + Y     G+ D+  +  L+ GI +         
Sbjct: 153 ATEGLLLLTNDGELANRLMHPKYEVTKTYLATVLGEADKRLIKQLRDGIELDDGPAKADF 212

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V +       + + + L EG+   ++++ +   + V RL+R      QLG    G+ R +
Sbjct: 213 VQIVDAHQGKSLIRIELHEGRKHIVRRMLKTAGFPVERLVRTKIHTIQLGEQTPGAVRAL 272

Query: 237 SKKIL 241
           +   L
Sbjct: 273 NSSEL 277


>gi|239817945|ref|YP_002946855.1| RNA-binding S4 domain protein [Variovorax paradoxus S110]
 gi|239804522|gb|ACS21589.1| RNA-binding S4 domain protein [Variovorax paradoxus S110]
          Length = 273

 Score =  163 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 67/276 (24%), Positives = 100/276 (36%), Gaps = 47/276 (17%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           + +   P R++K +A  G+ SRRE +  IA   VKVNG       V V  +D IEVD   
Sbjct: 1   MTDAPAPIRLNKRMAELGLCSRREADEWIANGWVKVNGKPA-EMGVKVTPSDRIEVDKAA 59

Query: 64  ------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                         P+          +   + L T  +     +  F   P     +   
Sbjct: 60  KGQQANQVTILINKPIGYVSGQAEDGHEPAVTLFTPQNRWAEDNARFFFSPQQLRGLAPC 119

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ------------------- 152
           GRLDI++ GLL++T DG +AR L    +   + Y VR                       
Sbjct: 120 GRLDIDSIGLLVMTQDGRIARQLIGEDSVMEKEYLVRVAYHGLGQPAPTGQLVRMDDDDP 179

Query: 153 --------VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                        L  L+ G+ + G      +V     +     +   L EGK R+I+++
Sbjct: 180 VTTNVQAVFPPAMLARLRHGLSLDGQPLKPARVEWQNPEQ----LRFVLTEGKKRQIRRM 235

Query: 205 FEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            E    KV  L R+  G   LG L  G  R +    
Sbjct: 236 CELVGLKVVGLKRVRIGKVMLGNLPVGQWRYLGPHE 271


>gi|270264704|ref|ZP_06192969.1| ribosomal large subunit pseudouridine synthase F [Serratia
           odorifera 4Rx13]
 gi|270041387|gb|EFA14486.1| ribosomal large subunit pseudouridine synthase F [Serratia
           odorifera 4Rx13]
          Length = 253

 Score =  163 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 52/247 (21%), Positives = 96/247 (38%), Gaps = 5/247 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRR  +R I    V +N  L       V S D + V+   +  
Sbjct: 3   TQSSIRLNKYISDSGICSRRHADRHIKLGNVFINDRLAAV-GAQVFSGDRVRVNDRQIAP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   L L      +    S          +  +   R   +GRLD  ++GL+ LTN G 
Sbjct: 62  RDADDLVLIALNKPVGVLTSMGKHERDNIGDFVNHSQRTFPIGRLDKASQGLIFLTNQGE 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  +    +  +  G+ I G            +K ++   
Sbjct: 122 LVNKILRAGNNHEKEYLVTVNKPLTDAFIQGMGAGVPILGKVTHPC----LVEKEASQVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ ++F ++V +L R+      L  L  G  R+ +     E      
Sbjct: 178 RITLVQGLNRQIRRMCKYFGYEVTKLERVRIMNVDLTGLALGEWRDFTADERLELFKLIE 237

Query: 250 LEEAQVN 256
              ++  
Sbjct: 238 HSSSEEP 244


>gi|229823649|ref|ZP_04449718.1| hypothetical protein GCWU000282_00950 [Catonella morbi ATCC 51271]
 gi|229786886|gb|EEP23000.1| hypothetical protein GCWU000282_00950 [Catonella morbi ATCC 51271]
          Length = 238

 Score =  163 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 103/233 (44%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +V+ +AG+ SR +V+R++   +V+V+G +  R   NV      I+V G  L +   
Sbjct: 1   MRLDQVMNQAGLGSRNQVKRLLKSCQVQVDGQVERRPNRNVDPGLQEIKVQGRILTQPAE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T   L+     L     D                 +  VGRLD +T GL+ LT +G L  
Sbjct: 61  TYWLLHKPQGVLTAVTDDRFTTVIDCLAPQDQAPGLYPVGRLDRSTTGLVFLTTNGPLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y+V  +G + QD +    +GI+I          + ++      +   +
Sbjct: 121 RMLHPQYHVEKEYQVVVNGPLTQDHVASFAQGILIDQNRPCAPAHLVIEASGPQESRARL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
            +REGK  ++KK+F     KV +L R+  G   L   L  G+ R +  + L +
Sbjct: 181 TIREGKFHQVKKMFLSVGVKVTQLHRLRMGHLVLDQDLAPGAYRPLKPEELDQ 233


>gi|228471718|ref|ZP_04056491.1| ribosomal large subunit pseudouridine synthase B [Capnocytophaga
           gingivalis ATCC 33624]
 gi|228276871|gb|EEK15566.1| ribosomal large subunit pseudouridine synthase B [Capnocytophaga
           gingivalis ATCC 33624]
          Length = 329

 Score =  163 bits (411), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 108/234 (46%), Gaps = 1/234 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            +     R++K IA AGI +RRE +R IA   V+VNG  +      V  TD ++ DG  +
Sbjct: 89  TDQSKGIRLNKYIANAGICARREADRYIAAGNVEVNGKPMTELGYRVQPTDVVKFDGKNI 148

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              ++  + L      + TT  +   ++ +     +    +  VGRLD  T GLLLLTND
Sbjct: 149 SAEKKEYILLNKPKGFITTTQDEKGRKTVMDLVAGAAEGNIKPVGRLDRLTTGLLLLTND 208

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L + L  PS    ++Y V    ++     + +++G+ ++        +        N 
Sbjct: 209 GDLMKKLTHPSHGVRKIYHVILDKKLALADFHKIQEGLTLEDGFIQVDDINFVDGAPHN- 267

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + V +  G+NR ++++FE   + V +L R+ +       L  G  R ++ + +
Sbjct: 268 EIGVKIHSGRNRIVRRIFESLGYVVEKLDRVVFAGLTKKDLPRGHWRTLTAQEI 321


>gi|110801287|ref|YP_695597.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           ATCC 13124]
 gi|168209502|ref|ZP_02635127.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           B str. ATCC 3626]
 gi|110675934|gb|ABG84921.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           ATCC 13124]
 gi|170712304|gb|EDT24486.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           B str. ATCC 3626]
          Length = 228

 Score =  163 bits (411), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 104/229 (45%), Gaps = 8/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+ +  GI SR+E  ++I + RV VNG         V  +D I +DG PL   E+ 
Sbjct: 1   MRINKLFSNFGICSRKETNKIIREGRVIVNGKPCIE-GQWVELSDEILLDGKPLVPKEKI 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L      + T   +         +   I   V  +GRLD +++GL++LTNDG LA  
Sbjct: 60  YIALNKPVGVVCTAAEEV---KDNIIDYLGIDDYVFPIGRLDKDSQGLIILTNDGDLANE 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V        D +  +++G+ I G      ++    +       ++ L
Sbjct: 117 VLAAENNHEKEYIVTLDQPFYDDFIEKMERGVEILGQVTKPCKLKRINEN----TYSIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ + F + V +L RI      L  +  G  R ++++ + 
Sbjct: 173 TQGLNRQIRRMSKVFGFNVVKLERIRILNITLEDIEYGKWRYINREEIE 221


>gi|284991416|ref|YP_003409970.1| pseudouridine synthase [Geodermatophilus obscurus DSM 43160]
 gi|284064661|gb|ADB75599.1| pseudouridine synthase [Geodermatophilus obscurus DSM 43160]
          Length = 280

 Score =  163 bits (411), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 77/235 (32%), Positives = 121/235 (51%), Gaps = 1/235 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
             +   +R+ KV+ARAG+ SRR VE M+ Q R+ VNG  +    + V    D I VDGV 
Sbjct: 37  DASAEGERLQKVLARAGVGSRRVVENMVDQGRISVNGKTVAVQGMRVDPERDKIAVDGVR 96

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +   +    +  +KP G++T  SD   R TV D +  +   ++ VGRLD +TEGLLL+TN
Sbjct: 97  IELRDDRVTYALNKPPGVITAMSDDRNRPTVGDMVGDLAPGLVHVGRLDQDTEGLLLVTN 156

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  + Y  +  G V +D    L+ G+ ++          +       
Sbjct: 157 DGELAHRLAHPSYEVKKTYLAQVSGSVPRDMARRLRSGVELEDGPVKVDSFRVVDTHAGQ 216

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + V V L EG+   ++++       V+RL R + GP +L  + +GS R +S+  +
Sbjct: 217 SVVEVVLHEGRKHIVRRLLASVGLPVSRLTRTAVGPVKLERMRSGSIRRLSRAEV 271


>gi|149190891|ref|ZP_01869154.1| pseudouridine synthase family 1 protein [Vibrio shilonii AK1]
 gi|148835246|gb|EDL52220.1| pseudouridine synthase family 1 protein [Vibrio shilonii AK1]
          Length = 310

 Score =  163 bits (411), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 86/309 (27%), Positives = 125/309 (40%), Gaps = 9/309 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E +I   RV VNG +             I +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRRELEALIKSGRVSVNGQVARLGERLEDENAVIRIDGHTVSAKAQ 61

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  Y     L T H     R+          SR ISVGRLD NT GLLL T D
Sbjct: 62  EEVVCRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G++++ K+  +  G+ ++        V     +G N 
Sbjct: 122 GELANRLMHPSRQVEREYLVRVFGEINEKKVRNVVNGVELEDGMARFEDVVYAGGEGMNH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI---LRE 243
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E++ K    LRE
Sbjct: 182 TFYVVINEGRNREVRRLWESQETTVSRLKRVRYGDIYLDKKLPRGGWMELTLKEVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +     +E  ++L           R +    +    +                +K    
Sbjct: 242 LVELRPEKETMLDLSQNTSRQRERSRSQKIRRAVRRHEERANAPKGRSNQQRRNKKSAGE 301

Query: 304 PVHRRNLAS 312
              R     
Sbjct: 302 QSARSKTRR 310


>gi|62180286|ref|YP_216703.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|62127919|gb|AAX65622.1| putative ribosomal large subunit pseudouridine synthase [Salmonella
           enterica subsp. enterica serovar Choleraesuis str.
           SC-B67]
 gi|322714760|gb|EFZ06331.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
          Length = 291

 Score =  162 bits (410), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 87/284 (30%), Positives = 128/284 (45%), Gaps = 10/284 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD+ KL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDESKLRDLSRGVQLEDGPAAFKTIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+    L +  
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELD---LAQTN 238

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
               L E      + +   +   R + N I       +++    
Sbjct: 239 YLRGLVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQIAGGR 282


>gi|187924437|ref|YP_001896079.1| RNA-binding S4 domain protein [Burkholderia phytofirmans PsJN]
 gi|187715631|gb|ACD16855.1| RNA-binding S4 domain protein [Burkholderia phytofirmans PsJN]
          Length = 250

 Score =  162 bits (410), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 64/250 (25%), Positives = 102/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---------- 64
           R+SK+++  G+ SRRE +  I +  V V+G  ++     V     IE+D           
Sbjct: 3   RLSKLMSELGMCSRREADEWIEKGWVMVDGERIDTLGTKVRPDQRIEIDPAAEAAQMSQV 62

Query: 65  -----VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
                 P+          Y   I LVT  +  +G         +   ++   GRLDI++ 
Sbjct: 63  TVLIHKPVGLVSGQAEDGYQPAITLVTPENRWEGDHADIRFSVAHLRQLAPAGRLDIDST 122

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT DG +A+ L    ++  + Y VR                + L LL  G+ +  +
Sbjct: 123 GLLVLTQDGRIAKQLIGGHSEIDKEYLVRVAFGEHTTDVESHFPPESLELLCHGLSLDDV 182

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                QV     +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 183 PLKPAQVNWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPP 238

Query: 231 GSTREVSKKI 240
           G  R +S   
Sbjct: 239 GQWRYLSPDE 248


>gi|167855222|ref|ZP_02477992.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           parasuis 29755]
 gi|167853675|gb|EDS24919.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           parasuis 29755]
          Length = 339

 Score =  162 bits (410), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 90/291 (30%), Positives = 135/291 (46%), Gaps = 10/291 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDH 59
           ++ +N   +    +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S+  
Sbjct: 48  IETENKANDKIVGEKLQKILARAGQGSRREIEEVIAAGRVSVDGKIATLGDRVQVSSSTK 107

Query: 60  IEVDGVPLRKAERT-----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
           I +DG  +            L  Y     L T        +          SR I+VGRL
Sbjct: 108 IRIDGNLVNLIPTQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWIAVGRL 167

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DINT GLLL T DG LA  L  PS +  R Y VR  G+V+   +  L+KG+ ++      
Sbjct: 168 DINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGEVNDAMIQRLRKGVQLEDGPANF 227

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
            Q+      G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L  +L  G  
Sbjct: 228 KQIKAVGGTGINQWFDVTLTEGRNREVRRLWESQGIQVSRLIRIRYGNIKLEKSLPRGGW 287

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD 281
            E+  +    LRE +G     E +V++      + T    +          
Sbjct: 288 EEMGLEQVNYLRELVGLKPETETKVDVTKARRRTSTRQIRKAVKQHTKYRK 338


>gi|92118637|ref|YP_578366.1| pseudouridine synthase, Rsu [Nitrobacter hamburgensis X14]
 gi|91801531|gb|ABE63906.1| Pseudouridine synthase, Rsu [Nitrobacter hamburgensis X14]
          Length = 687

 Score =  162 bits (410), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 147/339 (43%), Positives = 200/339 (58%), Gaps = 10/339 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
              T +R++KV+ARAG+ASRR+ E  + Q RV VNG ++   A++V S D I +DG PL 
Sbjct: 355 SKKTGERIAKVMARAGVASRRDAEEWVTQGRVAVNGRVINSPALDVTSRDVITIDGQPLP 414

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRL+LYHKP GL+TTH+DP+GR TVFDNLP    R+IS+GRLD NTEGLLLLTNDG
Sbjct: 415 ERERTRLFLYHKPRGLMTTHADPEGRPTVFDNLPEGLPRLISIGRLDFNTEGLLLLTNDG 474

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GLAR LELP T WLR YRVR HG+V Q +L+ LK G+ + G+ YG +  TL+  +G+N W
Sbjct: 475 GLARALELPDTGWLRRYRVRAHGEVTQAQLDALKNGVEVDGVKYGSIDATLERDQGANVW 534

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +   +REGKNRE++ V      +VNRLIR+SYGPFQL  +  G   EV  ++LREQLG  
Sbjct: 535 LVFAIREGKNREVRNVMAHLGLEVNRLIRVSYGPFQLAEIAEGQVEEVKTRVLREQLGDK 594

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
           +   A  N               P +  +     ++    +  K  L + +K    V +R
Sbjct: 595 IAALANANFAGTAAE----AETEPKLGRDGTPLRSKKDNKARAKRSLIEDRKGRNVVVQR 650

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
             +          +   +++       R    +  KR L
Sbjct: 651 TGSDE------ARARNEAEANGYGPPRRPKRGYHGKRDL 683



 Score = 40.2 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 12/120 (10%), Positives = 22/120 (18%), Gaps = 1/120 (0%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT-RMKKNSSQKN 293
           E      RE                     +    DRP               +    + 
Sbjct: 191 ESKPWEKREARPRDDARRESRPSRDGAGRFDKPRFDRPRDDRGGSGRPRFSKPREDRPER 250

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                +        +          G    F      R +  R   S  + +   R + +
Sbjct: 251 TAGGDRGPRKFDRPQGDRPRYERPTGDRPRFDRPRQDRPDGDRPGGSRNAWQERPRRNDR 310



 Score = 36.7 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 11/103 (10%), Positives = 20/103 (19%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
                   P            +   E  +   R       +       +   P   R   
Sbjct: 171 SRGAPDRGPRKEFGDRADRGESKPWEKREARPRDDARRESRPSRDGAGRFDKPRFDRPRD 230

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                 +   S    D  +R     R P    +    R   ++
Sbjct: 231 DRGGSGRPRFSKPREDRPERTAGGDRGPRKFDRPQGDRPRYER 273


>gi|160945258|ref|ZP_02092484.1| hypothetical protein FAEPRAM212_02777 [Faecalibacterium prausnitzii
           M21/2]
 gi|158442989|gb|EDP19994.1| hypothetical protein FAEPRAM212_02777 [Faecalibacterium prausnitzii
           M21/2]
          Length = 275

 Score =  162 bits (410), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 86/273 (31%), Positives = 135/273 (49%), Gaps = 4/273 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K++A  G+ SRR  E++IA+ RVKVNG  ++       + D + VD   +   +  
Sbjct: 4   ERIQKIMAEQGLCSRRAAEQIIAEGRVKVNGHPVKVGDKMDPNRDVLHVDDERIYIQKNQ 63

Query: 74  --RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                  +KP G VTT SD  GR TV D +  I +R+  VGRLD ++EGLLL+TNDG  A
Sbjct: 64  QLYYLALYKPRGYVTTASDELGRKTVMDLVSDIPARLYPVGRLDKDSEGLLLMTNDGAFA 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVT 190
           + +  PS    ++YRV    + D+  +  L  G+V+          + + T +     + 
Sbjct: 124 QAVTHPSGGISKLYRVTVQPRADEATILKLSSGVVLDDGTKTMPCAINVVTDEPGRTVME 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L+EGKNREI+++ E    +V RL R + G  +LG L  G+ RE++K  +   L    +
Sbjct: 184 MTLKEGKNREIRRMCESVGLEVVRLKRNAEGVVKLGMLKPGTYRELTKAEV-NGLRAAAV 242

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
           +       A   S     R R  +    P    
Sbjct: 243 KGRAQTRSAAQQSKAAERRPRGPVGKNAPRKQK 275


>gi|59801084|ref|YP_207796.1| hypothetical protein NGO0657 [Neisseria gonorrhoeae FA 1090]
 gi|59717979|gb|AAW89384.1| conserved hypothetical protein [Neisseria gonorrhoeae FA 1090]
          Length = 350

 Score =  162 bits (410), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 72/256 (28%), Positives = 125/256 (48%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+
Sbjct: 85  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHV 143

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 144 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 203

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++  L +  ++++       
Sbjct: 204 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTTEQMRSLTEEGVMLEDGLAKVE 263

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  + ++EG+NRE++++FE     V+RL+R+++GP  L   L  G   
Sbjct: 264 RIYEQGGEGANKWYNIVIKEGRNREVRRIFESQGLTVSRLVRVAFGPIGLPNRLKRGQFY 323

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   L    +
Sbjct: 324 ELNPAEVANILKWADM 339


>gi|307252799|ref|ZP_07534689.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|307255057|ref|ZP_07536875.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 9 str. CVJ13261]
 gi|307261643|ref|ZP_07543310.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 12 str. 1096]
 gi|307263831|ref|ZP_07545436.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 13 str. N273]
 gi|306859698|gb|EFM91721.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|306861930|gb|EFM93906.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 9 str. CVJ13261]
 gi|306868635|gb|EFN00445.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 12 str. 1096]
 gi|306870820|gb|EFN02559.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 13 str. N273]
          Length = 373

 Score =  162 bits (410), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 91/286 (31%), Positives = 132/286 (46%), Gaps = 10/286 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGV- 65
           +E    +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S   I +DG  
Sbjct: 88  KEKVVGEKLQKILARAGQGSRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNL 147

Query: 66  ----PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
               P++K     L  Y     L T        +          +R I+VGRLDINT GL
Sbjct: 148 ISLIPVQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGARWIAVGRLDINTSGL 207

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  G +D+  L  L+KG+ ++       Q+    
Sbjct: 208 LLFTTDGELANRLMHPSREVEREYSVRVFGNIDEAMLQRLRKGVQLEDGPANFKQIKTVG 267

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 268 GTGLNQWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKLEKGLPRGGWEEMGLEQ 327

Query: 241 ---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
              LRE +G     E +V++      +      +            
Sbjct: 328 VNYLRELVGLPAETETKVDVTKNRRRTNIRQIRKAVKQHSKYRTKA 373


>gi|167719822|ref|ZP_02403058.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei DM98]
          Length = 399

 Score =  162 bits (410), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 76/304 (25%), Positives = 131/304 (43%), Gaps = 7/304 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 97  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 155

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 156 GKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNTE 215

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 216 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRIRD 275

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 276 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 335

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             +R  +    L+    +            R    + + +          +  +    ++
Sbjct: 336 AQVRRLMSTVGLKAPTEDKGG-KRGGPAERRQPDPMQTSMGFINREPVLTTHGQLDQPRR 394

Query: 299 KKLA 302
            +  
Sbjct: 395 GRRG 398


>gi|332704996|ref|ZP_08425081.1| ribosomal large subunit pseudouridine synthase B [Lyngbya majuscula
           3L]
 gi|332356173|gb|EGJ35628.1| ribosomal large subunit pseudouridine synthase B [Lyngbya majuscula
           3L]
          Length = 251

 Score =  162 bits (410), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 82/239 (34%), Positives = 123/239 (51%), Gaps = 12/239 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +RV K++++ GIASRR  E+MIA  +V++NG  +          TD IEVDG P+   +R
Sbjct: 3   ERVQKILSQWGIASRRRAEKMIAAGQVRLNGTTV-HLGQKADPETDVIEVDGKPINPYQR 61

Query: 73  T--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTND 127
                 L +KP G+V+T  D   R TV D LP        +  VGRLD ++ G LLLTND
Sbjct: 62  PQSIYLLLNKPAGVVSTCRDSRNRPTVIDLLPDKLTKGQGIHPVGRLDADSTGALLLTND 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  PS    + Y+V   G   +  L   ++G+ + G      QV +  +KG + 
Sbjct: 122 GELTFRLTHPSHHIPKTYQVWVRGNPPESVLQTWREGVNLLGKKTLPAQVRVLKRKGQST 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-----TLLAGSTREVSKKIL 241
            + V L EG+NR+I++V +  ++ V  L R + GP +L       L  G  R ++   +
Sbjct: 182 LLEVVLTEGRNRQIRRVAQLLSYPVIHLHRTAIGPIKLNLPGEPILPCGDYRALNDVEV 240


>gi|114330607|ref|YP_746829.1| pseudouridine synthase, Rsu [Nitrosomonas eutropha C91]
 gi|114307621|gb|ABI58864.1| ribosomal large subunit pseudouridine synthase B [Nitrosomonas
           eutropha C91]
          Length = 272

 Score =  162 bits (410), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 73/241 (30%), Positives = 114/241 (47%), Gaps = 6/241 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R+ K++AR G+ SRRE+E MIA  RV +N    +         D I +DG  +R + 
Sbjct: 31  ETDRLQKLLARNGLGSRREIEAMIAAGRVSINNTTAK-LGDRAGLGDKIRIDGRIIRLSM 89

Query: 72  R----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  +  +     +V+        S          S+ I++GRLD NT GLL+ T D
Sbjct: 90  PALLPRIIIYHKPEGEIVSARDPQGRLSVFDKLPHIQSSKWIAIGRLDFNTSGLLIFTTD 149

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P  Q  R Y VR  G++  +++  L  GI ++       Q+  +   G+N 
Sbjct: 150 GALANRLMHPRYQMEREYAVRIVGELSPEQITHLTTGIELEDGSAKFDQLLDEGGLGTNH 209

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  + L+EG+NRE++++FE     V+RL+R+ +GP  L   L  G   E+    +   L 
Sbjct: 210 WYRIVLKEGRNREVRRMFEALGITVSRLMRVRFGPVNLPPRLKRGMWLELVDTEVERLLA 269

Query: 247 P 247
            
Sbjct: 270 L 270


>gi|168206272|ref|ZP_02632277.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           E str. JGS1987]
 gi|170662280|gb|EDT14963.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           E str. JGS1987]
          Length = 228

 Score =  162 bits (410), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 56/229 (24%), Positives = 104/229 (45%), Gaps = 8/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+ +  GI SR+E  ++I + R+ VNG         V  +D I +DG PL   E+ 
Sbjct: 1   MRINKLFSNFGICSRKETNKIIREGRIIVNGKPCIE-GQWVELSDEILLDGKPLVPKEKI 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L      + T   +         +   I   V  +GRLD +++GL++LTNDG LA  
Sbjct: 60  YIALNKPVGVVCTAAEEV---KDNIIDYLGIDDYVFPIGRLDKDSQGLIILTNDGDLANE 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V        D +  +++G+ I G      ++    +       ++ L
Sbjct: 117 VLAAENNHEKEYIVTLDQPFYDDFIEKMEQGVEILGQVTKPCKLKRINEN----TYSIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ + F + V +L RI      L  +  G  R ++++ + 
Sbjct: 173 TQGLNRQIRRMSKVFGFNVVKLERIRILNITLEDIEYGKWRYINREEIE 221


>gi|317970403|ref|ZP_07971793.1| 16S rRNA pseudouridylate synthase [Synechococcus sp. CB0205]
          Length = 235

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 77/231 (33%), Positives = 116/231 (50%), Gaps = 5/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K+IA+AG+ SRR  E ++   RV VNG   +          D I +DG PL  +  
Sbjct: 4   ERLQKLIAQAGVCSRRRAEELLRDGRVTVNGQRAQ-LGDKADPNSDAISLDGQPLGASAE 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDGG 129
             + L +KP G++++  DP+GR  V D LP        +  VGRLD  + G LLL+NDG 
Sbjct: 63  PMVLLLNKPAGVLSSCFDPEGRPIVLDLLPPELARGQGLHPVGRLDFESRGALLLSNDGA 122

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     + YRV   GQ  Q  L+   +G+ + G+    +QV   + +     +
Sbjct: 123 LTLQLTHPRYAHSKTYRVWVQGQPSQRVLDQWARGVSLDGLPSQPVQVRSLSSEQGRTLL 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + + EGKNR+I++  E     V  L RI+ GP  LG L  G  R ++ + 
Sbjct: 183 ELVMGEGKNRQIRRTAELLGHHVLDLQRIAIGPIHLGALPEGRWRRINDQE 233


>gi|284007248|emb|CBA72545.1| ribosomal small subunit pseudouridine synthase A [Arsenophonus
           nasoniae]
          Length = 231

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 51/232 (21%), Positives = 103/232 (44%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +   +V V+  +++  +  +     +  DGV L+     
Sbjct: 2   MRLDKFLSQQLTISRGLVIRELRAGKVMVDNEIIKTGSYQITPEMIVSYDGVVLQHIIGP 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  D    + +        +++   GRLDI+T GL+++T+DG     
Sbjct: 62  RYFMLNKPQGYVCSTVDSVNLTILSFIDEPAITKLHIAGRLDIDTTGLVIITDDGKWTHK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  +  +    GI ++G        ++++ + K     V +
Sbjct: 122 MISPKHHCEKTYLVTLAQPVSTELADKFLAGIWLKGEKLPTKPAKLSIVSSKQ----VRL 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EG+  ++K++F      V  L R   G   L   L AG  R ++++ ++
Sbjct: 178 TISEGRYHQVKRMFAAVGNHVCALHRERIGGIYLDPALRAGEYRSLTQEEIK 229


>gi|239999104|ref|ZP_04719028.1| Pseudouridine synthase [Neisseria gonorrhoeae 35/02]
 gi|240013989|ref|ZP_04720902.1| Pseudouridine synthase [Neisseria gonorrhoeae DGI18]
 gi|240016430|ref|ZP_04722970.1| Pseudouridine synthase [Neisseria gonorrhoeae FA6140]
 gi|240113081|ref|ZP_04727571.1| Pseudouridine synthase [Neisseria gonorrhoeae MS11]
 gi|240115837|ref|ZP_04729899.1| Pseudouridine synthase [Neisseria gonorrhoeae PID18]
 gi|240121555|ref|ZP_04734517.1| Pseudouridine synthase [Neisseria gonorrhoeae PID24-1]
 gi|240125874|ref|ZP_04738760.1| Pseudouridine synthase [Neisseria gonorrhoeae SK-92-679]
 gi|240128384|ref|ZP_04741045.1| Pseudouridine synthase [Neisseria gonorrhoeae SK-93-1035]
 gi|268599167|ref|ZP_06133334.1| pseudouridine synthase [Neisseria gonorrhoeae MS11]
 gi|268601513|ref|ZP_06135680.1| pseudouridine synthase [Neisseria gonorrhoeae PID18]
 gi|268684473|ref|ZP_06151335.1| pseudouridine synthase [Neisseria gonorrhoeae SK-92-679]
 gi|268686783|ref|ZP_06153645.1| pseudouridine synthase [Neisseria gonorrhoeae SK-93-1035]
 gi|268583298|gb|EEZ47974.1| pseudouridine synthase [Neisseria gonorrhoeae MS11]
 gi|268585644|gb|EEZ50320.1| pseudouridine synthase [Neisseria gonorrhoeae PID18]
 gi|268624757|gb|EEZ57157.1| pseudouridine synthase [Neisseria gonorrhoeae SK-92-679]
 gi|268627067|gb|EEZ59467.1| pseudouridine synthase [Neisseria gonorrhoeae SK-93-1035]
          Length = 349

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 72/256 (28%), Positives = 125/256 (48%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+
Sbjct: 84  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHV 142

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++  L +  ++++       
Sbjct: 203 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTTEQMRSLTEEGVMLEDGLAKVE 262

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  + ++EG+NRE++++FE     V+RL+R+++GP  L   L  G   
Sbjct: 263 RIYEQGGEGANKWYNIVIKEGRNREVRRIFESQGLTVSRLVRVAFGPIGLPNRLKRGQFY 322

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   L    +
Sbjct: 323 ELNPAEVANILKWADM 338


>gi|103486547|ref|YP_616108.1| pseudouridine synthase, Rsu [Sphingopyxis alaskensis RB2256]
 gi|98976624|gb|ABF52775.1| Pseudouridine synthase, Rsu [Sphingopyxis alaskensis RB2256]
          Length = 285

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 106/229 (46%), Positives = 145/229 (63%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           PQR++K++ARAG+ SRR+VERMI + R+ +NG ++ + A  + S + + VDG P+ K   
Sbjct: 48  PQRIAKLLARAGVGSRRDVERMIEEGRIALNGEVVTQPAPLLASLEGLTVDGNPVAKPVS 107

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TRL+ +HKP G +T   DP GR T++D LP    R++ VGRLD NTEGLLLLTNDG   R
Sbjct: 108 TRLYRFHKPAGCLTAARDPKGRKTIYDVLPKGLPRLMPVGRLDYNTEGLLLLTNDGAFKR 167

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            LELP++   R YR R  G + Q +L  L  GI I GI YG +   L+ + G N W+ + 
Sbjct: 168 QLELPASGVERTYRARAFGDISQAQLEELVMGIEIDGIRYGKIDANLERRTGRNQWIEMT 227

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           L EGKNRE+++V E    +V+RLIR  YG F L  L  G+   V +  L
Sbjct: 228 LTEGKNREVRRVLEHLGLQVSRLIRTRYGEFTLAGLDMGAVEVVPRDEL 276


>gi|145589412|ref|YP_001156009.1| pseudouridine synthase [Polynucleobacter necessarius subsp.
           asymbioticus QLW-P1DMWA-1]
 gi|145047818|gb|ABP34445.1| pseudouridine synthase [Polynucleobacter necessarius subsp.
           asymbioticus QLW-P1DMWA-1]
          Length = 587

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 89/348 (25%), Positives = 134/348 (38%), Gaps = 7/348 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP----LR 68
             ++ KV+A  G+ SRR++E +I Q RV VNG+        +  TD + ++G P    ++
Sbjct: 196 TVKLHKVLADVGMGSRRDMEDLIIQGRVSVNGLPA-HIGQRIGPTDQVRINGKPVHRKIQ 254

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 +  +     +V+        +           R I+VGRLD NTEGLLL T  G
Sbjct: 255 TKPPRVIMYHKPAGEIVSQSDPEGRPTVFDRLPKPRQGRWIAVGRLDFNTEGLLLFTTSG 314

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     R Y VR  G + Q+   LLK GI +       +++ +   +G+N W
Sbjct: 315 ELANRLMHPRYGVEREYAVRILGDLSQENTALLKSGITLDDGQAKFLRLAMGGGEGANRW 374

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
             V L EG+NRE++++FE     V+RLIR  YG F L   L  G   E+    +   +  
Sbjct: 375 YHVALSEGRNREVRRMFEAVGHTVSRLIRTRYGIFLLPPRLRRGKWEEIEAGGIYNLMKS 434

Query: 248 HLLEEAQV-NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
             L+  Q  +       +    R         P   +     S     L+      T   
Sbjct: 435 AGLKMPQPSDKGRSPNPNNRDRRPAGEDFQPDPMQTSVSYWGSRDALTLASGHNGLTHQS 494

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           R         A      F   +                +   R  AKK
Sbjct: 495 RGGKPGGGGAASEGRGPFRGRTQGGRPGQGAGQGGQGGQGQNRNKAKK 542


>gi|314933904|ref|ZP_07841269.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           caprae C87]
 gi|313654054|gb|EFS17811.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           caprae C87]
          Length = 230

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 56/228 (24%), Positives = 103/228 (45%), Gaps = 7/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V+VN   ++     +   TD + VDG  +   + 
Sbjct: 1   MRIDKFLANMGLGTRTEVKQLLKKGLVEVNEKKIKTPKSQIDPETDKVVVDGEEISYVDN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G ++   D   ++ +          +  VGRLD +TEGLLLLTNDG    
Sbjct: 61  -VYMMLNKPKGYISATEDNAHQTVLDLIPEFSHLGIFPVGRLDKDTEGLLLLTNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V     + Q  +   K G+ +        ++     KG++    V 
Sbjct: 120 ELMSPKKHVSKTYEVISKYPIKQSDIEAFKLGVELSDGKVKPAELI----KGNDRLSYVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK 239
           + EGK  ++K++F     +V  L R+     +L   L +G    ++++
Sbjct: 176 IYEGKYHQVKRMFHSIENEVLELKRVKIANLELDKTLNSGEYCFLNEQ 223


>gi|302875820|ref|YP_003844453.1| pseudouridine synthase [Clostridium cellulovorans 743B]
 gi|307689254|ref|ZP_07631700.1| pseudouridine synthase [Clostridium cellulovorans 743B]
 gi|302578677|gb|ADL52689.1| pseudouridine synthase [Clostridium cellulovorans 743B]
          Length = 226

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 57/228 (25%), Positives = 103/228 (45%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+++  G  SRRE  RMI + R+ VNG    +    V   D I +D  P+   E+ 
Sbjct: 1   MRINKLLSNYGYCSRRETNRMIEENRITVNGQNCIK-GQWVEEDDIILIDNEPISLKEKI 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +          T             +  +    +  VGRLD  ++GL++LTNDG LA  
Sbjct: 60  YIAFNKPVGITCTLEKTV---KNNIGDYINFSDYIFPVGRLDKESQGLIILTNDGDLANK 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V  +   +   +N + +G+ I G+     QV     K S+    + L
Sbjct: 117 ILESENKHEKEYIVTLNRPFNDSFINGMSEGVEICGVKTRKCQV----SKISDNVFRIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +G N++I+++ + F + V +L RI     ++  +  G  R ++ + L
Sbjct: 173 TQGLNKQIRRMSKTFGYTVIKLERIRILNIKIDGIDIGKWRVLTDEEL 220


>gi|225389037|ref|ZP_03758761.1| hypothetical protein CLOSTASPAR_02782 [Clostridium asparagiforme
           DSM 15981]
 gi|225044895|gb|EEG55141.1| hypothetical protein CLOSTASPAR_02782 [Clostridium asparagiforme
           DSM 15981]
          Length = 247

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 67/244 (27%), Positives = 116/244 (47%), Gaps = 8/244 (3%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDG 64
           + +      R+ K +   G  +R +V+ M+ + R+ VNG  + +A + +    D I +DG
Sbjct: 1   MAERKKAMIRLDKFLTEMGRGTRSQVKEMVRKGRITVNGQAVRQADLKINPEADQICLDG 60

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +  A      L      +V+   D   ++       ++   +  VGRLDI+TEGLLLL
Sbjct: 61  AAVAYARTEYYMLNKPQG-VVSATEDGRYQTVTELITGALRGDIFPVGRLDIDTEGLLLL 119

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQK 183
           TNDG LA  L  P     +VY  R  GQ+ +D +     G+V++        ++ +    
Sbjct: 120 TNDGSLAHNLLSPRKHVDKVYFARIEGQLPEDAVGRAAAGLVLEDGTKTLPARLEILEPG 179

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
                V + +REGK  ++K++FE    +V  L R+S GP  L   L  G  R ++++ ++
Sbjct: 180 Q----VRLTIREGKFHQVKRMFEAMGCRVTYLKRLSMGPLVLDPALAPGEYRPLTEQEIQ 235

Query: 243 EQLG 246
           +  G
Sbjct: 236 DLQG 239


>gi|602963|gb|AAB59990.1| ORF4 [Escherichia coli str. K-12 substr. W3110]
          Length = 243

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 81/232 (34%), Positives = 114/232 (49%), Gaps = 7/232 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+ 
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELD 233


>gi|83815539|ref|YP_445618.1| ribosomal large subunit pseudouridine synthase B [Salinibacter
           ruber DSM 13855]
 gi|83756933|gb|ABC45046.1| ribosomal large subunit pseudouridine synthase B [Salinibacter
           ruber DSM 13855]
          Length = 249

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 68/241 (28%), Positives = 111/241 (46%), Gaps = 3/241 (1%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
             +    R++K IA AG+ SRR+ + ++ Q RV ++G  +++    V     + VDG  +
Sbjct: 5   SSDREGMRINKYIAHAGVCSRRDADDLVEQGRVHIDGERVDQHGTCVREGQTVTVDGEEV 64

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLT 125
              E   L L      + TT    D R+ +          S +  VGRLD NT G+LL++
Sbjct: 65  YPLEFEYLLLNKPKDTISTTDDPKDRRTVLDAIGVPEDNPSGLFPVGRLDRNTTGVLLVS 124

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  P  +  ++Y VR    V   +L+ LK+G+ +        QV     +  
Sbjct: 125 NDGDLAHRLMHPRYEIPKIYYVRVQDDVKPHQLDQLKRGVELSDGAAAADQVAYLDPQR- 183

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
              + + L EG+NR+I+++ E     + +L R  Y     G L  G  R +  + +RE  
Sbjct: 184 KTDIALELHEGRNRQIRRMMEALGHTIVQLERAKYATLTTGRLQRGEWRRLEPEEVRELY 243

Query: 246 G 246
            
Sbjct: 244 Q 244


>gi|168216005|ref|ZP_02641630.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           NCTC 8239]
 gi|182381895|gb|EDT79374.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           NCTC 8239]
          Length = 228

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 104/229 (45%), Gaps = 8/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+ +  GI SR+E  ++I + RV VNG         V  +D I +DG PL   E+ 
Sbjct: 1   MRINKLFSNFGICSRKETNKIIREGRVIVNGNPCIE-GQWVELSDEILLDGKPLVPKEKI 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L      + T   +         +   I   V  +GRLD +++GL++LTNDG LA  
Sbjct: 60  YIALNKPVGVVCTAAEEV---KNNIIDYLGIDDYVFPIGRLDKDSQGLIILTNDGDLANE 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V        D +  +++G+ I G      ++    +       ++ L
Sbjct: 117 VLAAENNHEKEYIVTLDQPFYDDFIEKMERGVEILGQVTKPCKLKRINEN----TYSIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ + F + V +L RI      L  +  G  R ++++ + 
Sbjct: 173 TQGLNRQIRRMSKVFGFNVIKLERIRILNITLEDIEYGKWRYINREEIE 221


>gi|192360200|ref|YP_001982275.1| RNA pseudouridylate synthase family protein [Cellvibrio japonicus
           Ueda107]
 gi|190686365|gb|ACE84043.1| RNA pseudouridylate synthase family protein [Cellvibrio japonicus
           Ueda107]
          Length = 376

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 84/289 (29%), Positives = 124/289 (42%), Gaps = 6/289 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL----RK 69
           +++ KV+ARAGI SRRE+ER I + RVKVN  +       V  TD I V G  +      
Sbjct: 89  EKLQKVLARAGIGSRREMERAIEEGRVKVNDRIAT-LGDRVTLTDKIFVGGQRVVLRTEA 147

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           A R  +        + + H      +           R ISVGRLD NT GLLL TNDG 
Sbjct: 148 ARRRVILYNKPEGEICSRHDPEGRPTVYDSLPSLKGERWISVGRLDFNTSGLLLFTNDGE 207

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  PS+   R Y VR  G VD D    L +G+++         +     +G N W 
Sbjct: 208 LANKLMHPSSVIDREYLVRIQGDVDDDMKERLLEGVLLDDGVARFTDIVDGAGEGKNRWF 267

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
              + EG+NRE+++++E    KV+RL R+ Y    +   +  G   E++++ +R+     
Sbjct: 268 YCVVMEGRNREVRRLWESQGVKVSRLKRVRYANIFIPSHVRVGQWTELTEQEIRDLCMTA 327

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
             +             E    +R            +  K   +K    K
Sbjct: 328 GFDSNNYTRIMRPSREEVAQIERHEKKLRSASSAPKRVKVDLRKRSPRK 376


>gi|163801131|ref|ZP_02195031.1| ribosomal small subunit pseudouridine synthase A [Vibrio sp. AND4]
 gi|159175480|gb|EDP60277.1| ribosomal small subunit pseudouridine synthase A [Vibrio sp. AND4]
          Length = 233

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 47/234 (20%), Positives = 97/234 (41%), Gaps = 2/234 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +     A+R++  ++I    V V+G + +  +  V     +E +G  +      
Sbjct: 1   MRLDKYLCDGLGATRKQATKIIKSGDVTVDGEVQKSGSFKVPEAGVVEWEGRLVGAPGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + LY     + +     +  +           ++   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLYKPADFVCSHEDGHNP-TAFVLLDEPKVEKLHFAGRLDVDTTGLVLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     +  D +    +GI ++      +   L+    +   V + +
Sbjct: 120 ITSPKHKCEKTYRVWLADAIQPDYIEKFAEGIELRNESGPTLPAHLEIVNEAENEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
            EGK  ++K++F     KV  L R   G   L   L  G  R ++++ +   + 
Sbjct: 180 VEGKYHQVKRMFAALGNKVEYLHRERIGSIVLDEALEPGDYRFLTEEEVESVVK 233


>gi|295100683|emb|CBK98228.1| ribosomal large subunit pseudouridine synthase B [Faecalibacterium
           prausnitzii L2-6]
          Length = 278

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 136/276 (49%), Gaps = 4/276 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+++  G+ SRR  E++IA+ RVKVNG  ++       + D + VD   +   +  
Sbjct: 4   ERIQKIMSEQGLCSRRAAEQIIAEGRVKVNGHPVKVGDKMDPNRDVLHVDDERIYIQKNQ 63

Query: 74  --RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                  +KP G VTT SD  GR TV + +  I +R+  VGRLD ++EGLLL+TNDG  A
Sbjct: 64  QMYYLALYKPRGYVTTASDELGRKTVMELVADIPARLYPVGRLDKDSEGLLLMTNDGAFA 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVT 190
           + +  PS    ++YRV    + D+ ++  L  G+V+          + + T +     + 
Sbjct: 124 QAVTHPSGGISKLYRVTVQPRADEAQILKLSSGVVLDDGTKTMPCAINVVTDEPGRTVME 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L+EGKNREI+++ E    +V RL R + G  +LG L  G  RE++K  +   L     
Sbjct: 184 MTLKEGKNREIRRMCEAVGLEVIRLKRNAEGVVKLGMLQPGRYRELTKAEV-NGLRAAAA 242

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
           +       A + S     R R  +         + K
Sbjct: 243 KGRAQTRSAALQSRAAARRPRGPVGGNKAAAGKKHK 278


>gi|207743366|ref|YP_002259758.1| rrna uridine-516 pseudouridylate synthase-related pseudouridylate
           synthase protein [Ralstonia solanacearum IPO1609]
 gi|206594763|emb|CAQ61690.1| rrna uridine-516 pseudouridylate synthase-related pseudouridylate
           synthase protein [Ralstonia solanacearum IPO1609]
          Length = 610

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 78/318 (24%), Positives = 133/318 (41%), Gaps = 6/318 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +       ++ K++A AG+ SRR++E +I Q RV VNG+        ++ TD + V+G  
Sbjct: 207 LTAEDDAPKLHKILADAGLGSRRDMEDLIMQGRVSVNGLPA-HIGQRILPTDQVRVNGKL 265

Query: 67  LRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           +++         L  +     +V+        +           + ++VGRLD NTEGLL
Sbjct: 266 IQRKLPNKAPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRMKTGKWVAVGRLDFNTEGLL 325

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + T  G +A     P     R Y VR  G++ +     L +G+ +       ++      
Sbjct: 326 IFTTSGDIANRFMHPRYGVEREYAVRTLGELAEFDRQKLLQGVRLDDGEANFLRCADGGG 385

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EVS + +
Sbjct: 386 EGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEVSAEEV 445

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R  +G   L+    +      S     R R      +    +     ++ ++     +  
Sbjct: 446 RVLMGSLGLKVPSASAGGGQGSRPQGGRRREAQPMLMGPMSSGFTGEATFQSRGQGVENG 505

Query: 302 ATPVHRRNLASNVWMAKG 319
              +      SN      
Sbjct: 506 NRALPAARRPSNPRQPDP 523


>gi|262275813|ref|ZP_06053622.1| ribosomal small subunit pseudouridine synthase A [Grimontia
           hollisae CIP 101886]
 gi|262219621|gb|EEY70937.1| ribosomal small subunit pseudouridine synthase A [Grimontia
           hollisae CIP 101886]
          Length = 234

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 55/231 (23%), Positives = 101/231 (43%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +      +R++  +++ ++RV V+G +++  A+ +     +E DG+ LR A   
Sbjct: 2   IRLDKFLCETVGVTRKQAAKILKEERVTVDGNIIKNGAIKIAEEADVEFDGMSLRLAGPR 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +      + +        +           ++   GRLD +T GLLLLT+DG  +  
Sbjct: 62  YYMMNKPAGYVCSHDDP-YNPTVFVLLDEIGAEKLHIAGRLDCDTTGLLLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  +  +VYRV     V  +      +GI ++G        Q+    +K     V +
Sbjct: 121 VTSPKHKCDKVYRVWLDDPVSPETEQCFAEGIKLRGERTETLPAQMQRVGEK----EVLL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R S G   L   L  G  RE++ + +
Sbjct: 177 TIHEGKYHQVKRMFAAVGNKVVGLHRESVGGLVLDEALEPGEYRELTDEEI 227


>gi|145295560|ref|YP_001138381.1| hypothetical protein cgR_1487 [Corynebacterium glutamicum R]
 gi|140845480|dbj|BAF54479.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 320

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 75/236 (31%), Positives = 117/236 (49%), Gaps = 4/236 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           +    R+ KV+A+AG+ASRR  E +I Q RV+VN  ++    V V    D I VDGV + 
Sbjct: 76  DSDGVRLQKVLAQAGVASRRHAEILIDQGRVEVNDRIVTTQGVRVNPNNDVIRVDGVRIH 135

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLT 125
             E    ++ +KP G+ +T SD  GR  V D +        R+  VGRLD +TEGLLLLT
Sbjct: 136 INEDLEYFVLNKPRGMHSTMSDELGRPCVGDLVSEKTASGQRLFHVGRLDADTEGLLLLT 195

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  P  +  + Y     G+     ++ L+ G+ ++          +      
Sbjct: 196 NDGELANRLMHPKYEVSKTYLATVRGEATNKLVSALRDGVELEDGPAKADFAQIIDVFQG 255

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + + + + EG+   ++++F+   + V RL+R      QLG    GS R ++   L
Sbjct: 256 KSLLRIEIHEGRKHIVRRLFDELGFPVERLVRTKLHTVQLGDQKPGSLRALNSSEL 311


>gi|187931629|ref|YP_001891613.1| 16S rRNA pseudouridine synthase [Francisella tularensis subsp.
           mediasiatica FSC147]
 gi|187712538|gb|ACD30835.1| 16S rRNA pseudouridine synthase [Francisella tularensis subsp.
           mediasiatica FSC147]
          Length = 271

 Score =  162 bits (410), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 86/259 (33%), Positives = 124/259 (47%), Gaps = 9/259 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+  N   +   P+R+ K++A+ GI SRR++E  I Q RVKVNG +           D I
Sbjct: 1   MRRANQNNDKN-PERLQKLLAKYGIGSRRKIEEYIEQGRVKVNGKVAT-LGDKASEADKI 58

Query: 61  EVDGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
             DG  L            +  + +   + T+  + D ++          SR I VGRLD
Sbjct: 59  SFDGKALHSYGQPMTRPRVVIYHKRAGEVCTSKDEKDRQTVFDSLPKLAKSRWIMVGRLD 118

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGD 174
           INT GLLL T DG LA  L  PS Q  R Y VR  GQ    + +N LK+GI ++      
Sbjct: 119 INTTGLLLFTTDGDLANRLMHPSYQIEREYAVRVFGQQLSDETINKLKEGIQLEDGMAKF 178

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGST 233
             +     +G+N W  V L EG+NRE++++FE     V+RL RI +G   L   +  G T
Sbjct: 179 NSIKFSGGEGANLWYYVTLSEGRNREVRRMFEAVGVTVSRLTRIRFGDIILPKFVSRGKT 238

Query: 234 REVSKKILREQLGPHLLEE 252
            E++   +        L+E
Sbjct: 239 LELNPSEVNRLRKSVKLKE 257


>gi|154502351|ref|ZP_02039411.1| hypothetical protein RUMGNA_00164 [Ruminococcus gnavus ATCC 29149]
 gi|153796976|gb|EDN79396.1| hypothetical protein RUMGNA_00164 [Ruminococcus gnavus ATCC 29149]
          Length = 252

 Score =  162 bits (410), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 61/245 (24%), Positives = 115/245 (46%), Gaps = 9/245 (3%)

Query: 1   MKDK--NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M ++     Q+     R++K ++ AG+ SRRE +R+I   RV V+G   +   + ++   
Sbjct: 1   MNNRILQEYQKTKEEVRLNKYLSEAGVCSRREADRLIESGRVSVDGKRAQT-GMKIVPGQ 59

Query: 59  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
            ++V    + K +   +   +KP G+V T    +              R+  VGRLD ++
Sbjct: 60  VVKVGKKVVSKQDEMVVLAVNKPAGIVCTEERRE--RNSIVRFLDYPIRITYVGRLDKDS 117

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           +GLLL+TN+G +   +     +  + Y+V    ++ Q+ L  +  G+ I        +V 
Sbjct: 118 KGLLLMTNNGDIINKMMRAGNRHEKEYKVTVDKEITQEFLEKMASGVPILDTVTRPCKV- 176

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              +K      ++ L +G NR+I+++ E   ++V  LIR+      LG L  G  R+++ 
Sbjct: 177 ---EKIGKYTFSIILTQGLNRQIRRMCEALGYQVRELIRVRIMNIHLGRLKEGEYRKLTD 233

Query: 239 KILRE 243
             L E
Sbjct: 234 AELNE 238


>gi|110802829|ref|YP_698310.1| ribosomal large subunit pseudouridine synthase f [Clostridium
           perfringens SM101]
 gi|110683330|gb|ABG86700.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           SM101]
          Length = 228

 Score =  162 bits (410), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 104/229 (45%), Gaps = 8/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+ +  GI SR+E  ++I + RV VNG         V  +D I +DG PL   E+ 
Sbjct: 1   MRINKLFSNFGICSRKETNKIIREGRVIVNGKPCIE-GQWVELSDEILLDGKPLVPKEKI 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L      + T   +         +   I   V  +GRLD +++GL++LTNDG LA  
Sbjct: 60  YIALNKPVGVVCTAAEEV---KDNIIDYLGIDDYVFPIGRLDKDSQGLIILTNDGDLANE 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V        D +  +++G+ I G      ++    +       ++ L
Sbjct: 117 VLAAENNHEKEYIVTLDQPFYDDFIEKMEQGVEILGQVTKPCKLKRINEN----TYSIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ + F + V +L RI      +  +  G  R +++K + 
Sbjct: 173 TQGLNRQIRRMSKVFGFNVVKLERIRILNITIDNIEYGKWRYINRKEIE 221


>gi|322517216|ref|ZP_08070098.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           vestibularis ATCC 49124]
 gi|322124203|gb|EFX95727.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           vestibularis ATCC 49124]
          Length = 239

 Score =  162 bits (409), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 63/239 (26%), Positives = 109/239 (45%), Gaps = 6/239 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++ +AG  SR +V+++I  ++V V+G+L +R  +NV ++   I V G  L  A  
Sbjct: 1   MRLDKLLGQAGYGSRNQVKKLIRSRQVYVDGVLADRDNLNVDASLQSITVSGKELEHAPE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +                       +  VGRLD +TEGL+L+TN+G L  
Sbjct: 61  VYYLMNKPAGVVSARSDKKHQTVIDLIKPEDQREGLYPVGRLDRDTEGLVLITNNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V  +  +  D     + G+V +        Q+ + +     +   +
Sbjct: 121 AMLHPRYHVAKTYYVEVNDILGPDTPAFFESGVVFEDGTICKSAQLEILSSASDKSCARI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LREQLG 246
            + EGK  ++KK+F  +  KV  L RIS+G F+L   +  GS R +++     LR  LG
Sbjct: 181 TISEGKFHQVKKMFLAYGVKVTYLKRISFGAFKLDEGIAVGSYRALTEAEKVILRTYLG 239


>gi|318040247|ref|ZP_07972203.1| 16S rRNA pseudouridylate synthase [Synechococcus sp. CB0101]
          Length = 241

 Score =  162 bits (409), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 75/235 (31%), Positives = 116/235 (49%), Gaps = 3/235 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+IA AG+ SRR  E ++   RV VNG   E         D I +DG PLR A+  
Sbjct: 4   ERLQKLIAAAGLGSRRYAETLLRAGRVSVNGRTAELGERADPERDAICIDGEPLRPAQPP 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTNDGGL 130
              L +KP G++ +  DP+GR  V D LP        +  VGRLD ++ G LLL+N+G L
Sbjct: 64  LALLLNKPAGVMCSCHDPEGRPIVLDLLPPELASGQGLHPVGRLDFHSRGALLLSNNGAL 123

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P  Q  + YR+   GQ  Q  L+   +G+ + G+    + +    Q+     + 
Sbjct: 124 TLQLTHPRFQHSKTYRIWVRGQPSQTVLDRWARGVPLDGLPSQPVTLHRLDQEHDATQLQ 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + + EG+NR+I++  E     V  L R++ G  +LG L  G  R +  +   +  
Sbjct: 184 LVMHEGRNRQIRRTAELLGHPVLDLQRVAIGSIELGELPEGRWRRLDPQEWPDTH 238


>gi|167919194|ref|ZP_02506285.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei BCC215]
          Length = 408

 Score =  162 bits (409), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 76/274 (27%), Positives = 124/274 (45%), Gaps = 6/274 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 99  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 157

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 158 GKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNTE 217

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 218 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRIRD 277

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 278 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 337

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRP 272
             +R  +    L+    +            +  P
Sbjct: 338 AQVRRLMSTVGLKAPTEDKGGKRGGPAERRQPDP 371


>gi|68250225|ref|YP_249337.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           influenzae 86-028NP]
 gi|68058424|gb|AAX88677.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           influenzae 86-028NP]
          Length = 232

 Score =  162 bits (409), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 106/236 (44%), Gaps = 7/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  AV +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGAVQISQEDKIYFEDELLTWVEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ HKP G V ++ D D  +        +  ++ S GRLD++T G +LLT+DG  +  
Sbjct: 61  QYFMLHKPQGCVCSNDDGDYPTIYQFFDYPLAGKLHSAGRLDVDTTGFVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+++      +GI++  +       ++ +      +  V +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEENYAAACSEGILLRREKEPTKPAKLEIL----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
            + EG+  ++K++F     KV  L R   G   L   L  G  R +++  + + + 
Sbjct: 177 TISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLVK 232


>gi|315500441|ref|YP_004089244.1| RNA-binding s4 domain protein [Asticcacaulis excentricus CB 48]
 gi|315418453|gb|ADU15093.1| RNA-binding S4 domain protein [Asticcacaulis excentricus CB 48]
          Length = 658

 Score =  162 bits (409), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 137/320 (42%), Positives = 190/320 (59%), Gaps = 5/320 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++KV+ARAG+ASRREVER+I   ++ VNG LL+  A  V   D I V+G P+RKAE T
Sbjct: 46  ERIAKVLARAGLASRREVERLIGLGKIAVNGRLLDTPATTVSPDDLITVEGKPIRKAEPT 105

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+W YHKP+GL+TTH DP GR TVF++LP    RVISVGRLDIN+EGLLLLTNDG LAR 
Sbjct: 106 RVWRYHKPVGLMTTHQDPQGRPTVFNSLPQELPRVISVGRLDINSEGLLLLTNDGELARA 165

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-----GSNAW 188
           LELP+T W RVYRVR  G+  Q+ L+ LK G+ ++G+ YG ++  LD  +      +N W
Sbjct: 166 LELPTTGWTRVYRVRALGRTTQEALDTLKTGVTVEGVQYGPIEAKLDKAQEKADGRANLW 225

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +TV L EGKNRE++KV +    KVNRLIR++YGPFQLG +  G   E+  +++RE LG  
Sbjct: 226 ITVSLNEGKNREVRKVLDSLGLKVNRLIRLAYGPFQLGDIEPGEVEEIGPRVVRELLGDK 285

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
           +      + +     +   +R      +          + +S+  G  ++++        
Sbjct: 286 IDPRNLPSENETQTRTPMRLRRTDGEGAPRTGRRGGGDRFASKSEGREERRERPLSRDEA 345

Query: 309 NLASNVWMAKGIHSSFLSDS 328
                     G         
Sbjct: 346 FRRKYEAKEFGERDFDERPR 365


>gi|238751905|ref|ZP_04613391.1| Ribosomal large subunit pseudouridine synthase B [Yersinia rohdei
           ATCC 43380]
 gi|238709885|gb|EEQ02117.1| Ribosomal large subunit pseudouridine synthase B [Yersinia rohdei
           ATCC 43380]
          Length = 346

 Score =  162 bits (409), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 87/321 (27%), Positives = 135/321 (42%), Gaps = 12/321 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVP 66
           +    +++ K++ARAG  SRRE+E +I Q RV V+G +  +    V  T    I +DG  
Sbjct: 27  DKIVGEKLQKILARAGHGSRREIETIIQQGRVSVDGKI-SKLGDRVEVTQATKIRLDGHL 85

Query: 67  LRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           L   E        L  Y     L T +      +          SR ++VGRLD+NT GL
Sbjct: 86  LSIKESEETVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGL 145

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQ+D +K+  L +G+ ++        +    
Sbjct: 146 LLFTTDGELANRLMHPSREVEREYAVRVFGQIDDEKIKQLSRGVQLEDGPAAFRTIKFQG 205

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
            +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  K 
Sbjct: 206 GEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELDLKA 265

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
              LRE +       +++ ++      +     R               +  S +   ++
Sbjct: 266 TNYLRELVELDSETVSKMPVEKDRRRVKANQIRRAVKRHSEVAGRQVAGRQGSARKSSTR 325

Query: 298 QKKLATPVHRRNLASNVWMAK 318
           Q                    
Sbjct: 326 QNVSNATPTATAGRRGSNKRG 346


>gi|327398425|ref|YP_004339294.1| pseudouridine synthase Rsu [Hippea maritima DSM 10411]
 gi|327181054|gb|AEA33235.1| pseudouridine synthase Rsu [Hippea maritima DSM 10411]
          Length = 240

 Score =  162 bits (409), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 74/229 (32%), Positives = 130/229 (56%), Gaps = 4/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA A   SRRE +  + + RVKVNG  +    V V  +D +EVDG  L   ++ 
Sbjct: 1   MRINKYIATALKISRREADNYVKEGRVKVNGKSITS-FVEVDGSDKVEVDGELLSLNKKK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + ++KP  ++++  D +GR+TV D   +I  ++I VGRLD  +EGLL++T+DG  A +
Sbjct: 60  SYFAFYKPPFVISSTKDNEGRTTVCDFFKNIEEKLICVGRLDYLSEGLLIITSDGEFANL 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  + Y V+  G +  + L  + KG+ ++   +  ++     +  S  WV + +
Sbjct: 120 LMHPRFKIRKTYLVKTKGPIKTETLKAMSKGVNLEDGFFRPIR---IKKTNSPNWVLISI 176

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
             G+NR I++  + F+ K+++L RI+ G  +LG L  G  RE++K+ + 
Sbjct: 177 DTGRNRIIRRFLKKFDIKIDKLKRIAIGNIELGNLRNGEFRELTKQEIE 225


>gi|309782266|ref|ZP_07676994.1| RNA pseudouridine synthase family protein [Ralstonia sp. 5_7_47FAA]
 gi|308918959|gb|EFP64628.1| RNA pseudouridine synthase family protein [Ralstonia sp. 5_7_47FAA]
          Length = 605

 Score =  162 bits (409), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 82/321 (25%), Positives = 138/321 (42%), Gaps = 7/321 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K + +  ++  P ++ K++A AG+ SRR++E +I Q RV VNG+        +++TD + 
Sbjct: 213 KTRELTSDDDAP-KLHKILADAGLGSRRDMEDLILQGRVSVNGLPA-HIGQRILATDQVR 270

Query: 62  VDGVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           V+G  +++         L  +     +V+        +           + ++VGRLD N
Sbjct: 271 VNGKLIQRKLPNKPPRVLLYHKPAGEIVSQSDPEGRPTVFDALPRMKTGKWVAVGRLDFN 330

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+ T  G +A     P     R Y VR  G++ +     L  GI +Q      ++ 
Sbjct: 331 TEGLLIFTTSGDIANRFMHPRYGVEREYAVRTLGELAETDRQKLLHGIPLQDGEANFLRC 390

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EV
Sbjct: 391 VDGGGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEV 450

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           S + +R  +G   ++    +            R    ++          + N   +    
Sbjct: 451 SAEDVRTLMGTLGMKVPTASSGGGQDRQGNRRRGPAPVLMGPMSSGFAGEANFQSRGMGI 510

Query: 297 KQKKLATPVHRRNLASNVWMA 317
           +    A P  RR  +      
Sbjct: 511 ENGNRAQPAQRRPSSPRQPDP 531


>gi|40890007|pdb|1VIO|A Chain A, Crystal Structure Of Pseudouridylate Synthase
 gi|40890008|pdb|1VIO|B Chain B, Crystal Structure Of Pseudouridylate Synthase
          Length = 243

 Score =  162 bits (409), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 56/235 (23%), Positives = 108/235 (45%), Gaps = 7/235 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  + I Q  VK+NG +++  +V +   D I  +   L   E  +
Sbjct: 4   RLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWIEEGQ 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V ++ D D  +        +  ++ S GRLD++T GL+LLT+DG  +  +
Sbjct: 64  YFMLNKPQGCVCSNDDGDYPTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSHRI 123

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTVG 192
             P     + Y V     V+++      +GI+++G        ++ +      +  V + 
Sbjct: 124 TSPKHHCEKTYLVTLADPVEENYSAACAEGILLRGEKEPTKPAKLEIL----DDYNVNLT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
           + EG+  ++K++F     KV  L R   G   L   L  G  R +++  + + + 
Sbjct: 180 ISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLVE 234


>gi|83748669|ref|ZP_00945686.1| Ribosomal large subunit pseudouridine synthase B [Ralstonia
           solanacearum UW551]
 gi|83724631|gb|EAP71792.1| Ribosomal large subunit pseudouridine synthase B [Ralstonia
           solanacearum UW551]
          Length = 614

 Score =  162 bits (409), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 78/320 (24%), Positives = 133/320 (41%), Gaps = 6/320 (1%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             +       ++ K++A AG+ SRR++E +I Q RV VNG+        ++ TD + V+G
Sbjct: 209 RELTAEDDAPKLHKILADAGLGSRRDMEDLIMQGRVSVNGLPA-HIGQRILPTDQVRVNG 267

Query: 65  VPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
             +++         L  +     +V+        +           + ++VGRLD NTEG
Sbjct: 268 KLIQRKLPNKAPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRMKTGKWVAVGRLDFNTEG 327

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LL+ T  G +A     P     R Y VR  G++ +     L +G+ +       ++    
Sbjct: 328 LLIFTTSGDIANRFMHPRYGVEREYAVRTLGELAEFDRQKLLQGVRLDDGEANFLRCADG 387

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
             +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EVS +
Sbjct: 388 GGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEVSAE 447

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
            +R  +G   L+    +      S     R R      +    +     ++ ++     +
Sbjct: 448 EVRVLMGSLGLKVPSASAGGGQGSRPQGGRRREAQPMLMGPMSSGFTGEATFQSRGQGVE 507

Query: 300 KLATPVHRRNLASNVWMAKG 319
                +      SN      
Sbjct: 508 NGNRALPAARRPSNPRQPDP 527


>gi|50365365|ref|YP_053790.1| 23S rRNA pseudouridine synthase [Mesoplasma florum L1]
 gi|50363921|gb|AAT75906.1| 23S rRNA pseudouridine synthase [Mesoplasma florum L1]
          Length = 251

 Score =  162 bits (409), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 69/248 (27%), Positives = 125/248 (50%), Gaps = 3/248 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+I+  G+ SRR  E++I + +VKVNG+++        +   IEV+G    K    
Sbjct: 2   ERLQKIISARGVTSRRNAEKLIVEGKVKVNGVVITELGFKTSTDADIEVNGKQTTKNNEK 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP  ++TT  DP  R TV D    + +RV  VGRLD +  GL+++TNDG  A  
Sbjct: 62  FYYLFNKPRLVLTTMYDPKQRKTVADYFKDVPTRVYPVGRLDYDVSGLIIMTNDGEFANF 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--QKGSNAWVT 190
           +  P  ++ + Y+    G+V + ++N L KG+ I        +Q  L    Q+   + + 
Sbjct: 122 VMHPRYEFFKTYQGLCKGKVSKQQVNQLLKGVKIEDDYFTKAIQAELLNYDQEKDQSIIE 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + + EGK   +K++F      + +L R      ++  L  G  RE+    +++  G +  
Sbjct: 182 MTIAEGKKHHVKQMFSAIEANLMKLKRTKIEFLEVDDLEVGRYRELKPHEVKKFYGIYQS 241

Query: 251 EEAQVNLD 258
            + + +L 
Sbjct: 242 TKRKEDLK 249


>gi|253681751|ref|ZP_04862548.1| ribosomal large subunit pseudouridine synthase F [Clostridium
           botulinum D str. 1873]
 gi|253561463|gb|EES90915.1| ribosomal large subunit pseudouridine synthase F [Clostridium
           botulinum D str. 1873]
          Length = 226

 Score =  162 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 58/230 (25%), Positives = 105/230 (45%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+++  GI SR+E  R+I + R+ VNG +       V   D I +D  P++K E+ 
Sbjct: 1   MRINKLLSNYGICSRKEANRIIEENRIIVNGEVC-IPGQWVEEYDEILMDNEPIKKKEKI 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L        T   +         +  +    +  VGRLD ++EGL+L+TNDG L+  
Sbjct: 60  YIALNKPVGITCTAAREV---KDNIIDFLNYPEYIFPVGRLDKDSEGLILMTNDGELSNK 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V      D   +  + +G+ + G+      VT      +N    + L
Sbjct: 117 ILESENHHEKEYIVTVDKPFDDSFIKGMSEGVQLNGVKTRPCIVTRI----NNDTFRIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            +G NR+I+++   F + V +L RI     ++  +  G  R ++ K + E
Sbjct: 173 TQGLNRQIRRMTRAFRYTVIKLERIRILNIKINEIDVGKWRYLTHKEIDE 222


>gi|163750152|ref|ZP_02157395.1| ribosomal small subunit pseudouridine synthase A [Shewanella
           benthica KT99]
 gi|161330209|gb|EDQ01191.1| ribosomal small subunit pseudouridine synthase A [Shewanella
           benthica KT99]
          Length = 241

 Score =  162 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 46/231 (19%), Positives = 92/231 (39%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  +   +R   ++ + +  V  +G +++ +   V     I +DG  +      
Sbjct: 13  VRLDKFICESTELTRSFAKKALHRGDVTCDGEVVKNSGFKVKVGQTICLDGKVISVV-GP 71

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP   +    D    + +          +   GRLDI+T GL+L+T DG  +  
Sbjct: 72  RFLMLNKPADTICATFDIVHPTVIDLLDIEKADTLHIAGRLDIDTTGLVLITTDGQWSHK 131

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V+   ++D   +    +G+ +  +        + +           +
Sbjct: 132 ITSPKKDCSKCYLVKLTDELDASLVETFAQGVELRNEDGLTKPAVLEII----DTHTARL 187

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R S G   L   L  G  R ++ + +
Sbjct: 188 TITEGKYHQVKRMFAAVGNKVVGLHRESVGKIVLDDDLAPGEWRYLTDEEV 238


>gi|113971512|ref|YP_735305.1| ribosomal small subunit pseudouridine synthase A [Shewanella sp.
           MR-4]
 gi|113886196|gb|ABI40248.1| ribosomal small subunit pseudouridine synthase A [Shewanella sp.
           MR-4]
          Length = 235

 Score =  162 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 47/234 (20%), Positives = 98/234 (41%), Gaps = 8/234 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+ K I  +   +R   ++ + +  +  +GI+++ +   V+    + ++G P+   
Sbjct: 4   SRPVRLDKFICESTSLTRSLAKKALHRGEITCDGIVVKDSGFKVLEGMQVCLEGEPISLV 63

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              R  + +KP+  + +  D    S +          +   GRLD +T GL+L+T+DG  
Sbjct: 64  -GERYLMLNKPVDTICSTIDEAYPSVLSLLDIEKPETLHIAGRLDADTTGLVLITSDGQW 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAW 188
           +  +  P     + Y V     VD   + +   G+ +  +        + +   +     
Sbjct: 123 SHRITSPKKDCGKRYLVTLADPVDGSLVGIFAAGVELRNEDGLTKPAVLEIIEPQ----L 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           V + + EGK  ++K++F      V  L R S G  +L   L  G  R ++ + +
Sbjct: 179 VRLTITEGKYHQVKRMFAAVGNHVVGLHRESIGRIELDSDLAPGEWRYLTSEEI 232


>gi|225377123|ref|ZP_03754344.1| hypothetical protein ROSEINA2194_02768 [Roseburia inulinivorans DSM
           16841]
 gi|225211028|gb|EEG93382.1| hypothetical protein ROSEINA2194_02768 [Roseburia inulinivorans DSM
           16841]
          Length = 260

 Score =  162 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 63/267 (23%), Positives = 125/267 (46%), Gaps = 7/267 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           ++EN    R++K ++ AG+ SRRE +R +    + ++G + E     V+    +   G  
Sbjct: 1   MEEN--GIRINKFLSEAGVCSRREADRQVELGNITIDGKVAET-GARVLPGQTVLFQGKK 57

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           + K E   L  +HKP+G+V T    +  + +     +   R+  +GRLD ++EGLLLLTN
Sbjct: 58  VSKEEEMILIAFHKPVGIVCTAEKREKNNVIDYI--NYPKRIYPIGRLDKDSEGLLLLTN 115

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G +   +        + Y V  +  V +  ++ L  G+ +  +     +  +  ++   
Sbjct: 116 NGDIVNKMMRSGNMHEKEYIVTVNRPVTESFIHGLANGVPLAELNTMTRKCHV--KQIGK 173

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               + L +G NR+I+++ E+F ++V +L+R      +LG L  G+ R+V+ +  R+ L 
Sbjct: 174 KQFKIILTQGLNRQIRRMCEYFGYRVEKLVRTRIMNIELGDLPVGTYRDVTTEEYRQLLS 233

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPN 273
                  +  +      SE +      
Sbjct: 234 LIKDSSNETVIPKKYPKSERMKEKSKK 260


>gi|256829185|ref|YP_003157913.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
 gi|256578361|gb|ACU89497.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
          Length = 250

 Score =  162 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 117/242 (48%), Gaps = 7/242 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGV 65
           + EN  P R++K +A AGIASRR  + +I   RV VNG++       V+   D +  +G 
Sbjct: 1   MPENS-PVRLNKYLADAGIASRRGADALIQGGRVCVNGLIQREPGTRVIPGQDTVLCNGA 59

Query: 66  PLRKAERT---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGL 121
           P+   +      + L+     + T +     ++ V      + +     VGRLD  +EGL
Sbjct: 60  PVSAKQNAPSSYIMLHKPVHTVTTVNDPQGRKTVVDLLPEELRTLRLFPVGRLDYMSEGL 119

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLD 180
           LLLTNDG +   L  PS +  + Y V     V +  L ++++G+ + +G     ++V   
Sbjct: 120 LLLTNDGEVTLRLTHPSYEHPKKYEVLVREAVTEKSLGIMRQGMRLQEGERLAPVEVESA 179

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +  G    + + LR+G NR+I+++       + RL RI  GP  LG L  G  R ++   
Sbjct: 180 SDAGGATLLRMTLRQGVNRQIRRMCRDLGLTILRLRRIELGPLFLGNLEPGKWRALTDAE 239

Query: 241 LR 242
           ++
Sbjct: 240 IK 241


>gi|227504286|ref|ZP_03934335.1| pseudouridine synthase B [Corynebacterium striatum ATCC 6940]
 gi|227199125|gb|EEI79173.1| pseudouridine synthase B [Corynebacterium striatum ATCC 6940]
          Length = 287

 Score =  162 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 80/237 (33%), Positives = 123/237 (51%), Gaps = 4/237 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
           +N   +R+ KV+A+AG+ASRR  E MI   RV+VNG ++ +  V V    D I VDGV +
Sbjct: 42  DNPKGERLQKVLAKAGVASRRHAEIMIDAGRVEVNGKIVMQQGVRVDPNVDVIRVDGVRI 101

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLL 124
              E TR ++ +KP GL +T SD  GR  + D +        R+  VGRLD +TEGL+L+
Sbjct: 102 NVNEETRYFILNKPRGLQSTMSDELGRPCIGDLIGDRVAAGQRLFHVGRLDADTEGLILI 161

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG LA  L  P  +  + Y     G+     +  LK+G+ ++        V +  +  
Sbjct: 162 TNDGELANRLMHPKYEVRKTYLATVLGEAGNGLVRTLKEGVELEDGLAKADYVQIVDKNQ 221

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             + V V L EG+   ++++ +   + V RL+R      QLG +  G  R ++   L
Sbjct: 222 GYSLVRVELHEGRKHIVRRMLKEAGFPVQRLVRTKLHTLQLGEMKPGILRALNSNEL 278


>gi|167620251|ref|ZP_02388882.1| RNA pseudouridylate synthase family protein [Burkholderia
           thailandensis Bt4]
          Length = 431

 Score =  162 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 78/304 (25%), Positives = 127/304 (41%), Gaps = 9/304 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 129 KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 187

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 188 GKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNTE 247

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 248 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRIRD 307

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 308 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 367

Query: 239 KILRE---QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
             +R     +G     E +          +                 T   +    + G 
Sbjct: 368 AQVRRLMSTVGLKAPVEEKGKRGGAAERRQPDPMQTSMGFINREPVLTTHGQLDQPRRGR 427

Query: 296 SKQK 299
               
Sbjct: 428 RGPA 431


>gi|207723237|ref|YP_002253636.1| rrna uridine-516 pseudouridylate synthase-related pseudouridylate
           synthase protein [Ralstonia solanacearum MolK2]
 gi|206588433|emb|CAQ35396.1| rrna uridine-516 pseudouridylate synthase-related pseudouridylate
           synthase protein [Ralstonia solanacearum MolK2]
          Length = 501

 Score =  162 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 78/320 (24%), Positives = 131/320 (40%), Gaps = 8/320 (2%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             +       ++ K++A AG+ SRR++E +I Q RV VNG+        ++ TD + V+G
Sbjct: 111 RELTAEDDAPKLHKILADAGLGSRRDMEDLIMQGRVSVNGLPA-HIGQRILPTDQVRVNG 169

Query: 65  VPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
             +++         L  +     +V+        +           + ++VGRLD NTEG
Sbjct: 170 KLIQRKLPNKAPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRMKTGKWVAVGRLDFNTEG 229

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LL+ T  G +A     P     R Y VR  G++ +     L +G+ +       ++    
Sbjct: 230 LLIFTTSGDIANRFMHPRYGVEREYAVRTLGELAESDRQKLLQGVRLDDGEANFLRCADG 289

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
             +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EVS +
Sbjct: 290 GGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEVSAE 349

Query: 240 ILREQLGPHLLE--EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            +R  +G   L+                   R+   ++          +     +    +
Sbjct: 350 EVRVLMGSLGLKVPSVSAGGGQGGRPQGGRRREAQPMLMGPMSSGFTGEATFQSRGQGVE 409

Query: 298 QKKLATPVHRRNLASNVWMA 317
               A P  RR  +      
Sbjct: 410 NGNRALPAARRPSSPRQPDP 429


>gi|325002515|ref|ZP_08123627.1| ribosomal large subunit pseudouridine synthase B [Pseudonocardia
           sp. P1]
          Length = 253

 Score =  162 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 76/239 (31%), Positives = 115/239 (48%), Gaps = 7/239 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
           +    R+ KV+ARAG+ASRR  E +IAQ RV+V+G  +      +   T  + VDG  + 
Sbjct: 6   DPDGVRLQKVLARAGVASRRAAEELIAQGRVQVDGETVREMGRRIDPETAVLHVDGARVT 65

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLL 122
             +       +KP+GL +T SD  GR  V D L       +   R+  VGRLD +TEGLL
Sbjct: 66  LRDDQVYLALNKPVGLHSTMSDDLGRPCVGDLLADRVELMNSAQRLFHVGRLDADTEGLL 125

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTNDG L   L  PS +  + Y     G++ +D    L+ GI ++          L   
Sbjct: 126 LLTNDGELGHRLMHPSYEVPKTYLAEVEGKIARDLGRRLRDGIELEDGIARVDAFKLVDA 185

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
               + V + L EG+   ++++       V RL+R + G  +LG    G  R + +  +
Sbjct: 186 VPGRSTVQLILHEGRKHIVRRMLSEVGHPVQRLVRTAVGEVRLGNQKPGKLRPLDRVEV 244


>gi|269123516|ref|YP_003306093.1| pseudouridine synthase [Streptobacillus moniliformis DSM 12112]
 gi|268314842|gb|ACZ01216.1| pseudouridine synthase [Streptobacillus moniliformis DSM 12112]
          Length = 230

 Score =  162 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 65/234 (27%), Positives = 115/234 (49%), Gaps = 6/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A +GI +R+EV+ +I  +++ VN  ++  + + +  T D I+ +   +   + 
Sbjct: 1   MRLDKFLANSGIGTRKEVKEIIKNRKIFVNDKIVMSSDLKIDETKDIIKYENNVINYTKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + +  +D   ++ +         ++  VGRLDI+TEGLLLLTNDG LA 
Sbjct: 61  RYIMLNKPKGYI-SATNDNKQKTVLDLITDFKTYKLFPVGRLDIDTEGLLLLTNDGDLAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V     +  D ++ ++KGI I       +   +   K  +  + + 
Sbjct: 120 NLLSPKKHVEKKYYVELSQDISSDDISNIEKGIDIGEGIITRLSKII---KVDDNKLYII 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
           + EGK  ++K++F+  N +V  L RIS G   L   L  G  RE++ + LR  L
Sbjct: 177 ITEGKFHQVKRMFKAVNNEVKYLKRISMGSLILDEKLNLGEYRELTYEELRSLL 230


>gi|119356331|ref|YP_910975.1| ribosomal large subunit pseudouridine synthase B [Chlorobium
           phaeobacteroides DSM 266]
 gi|119353680|gb|ABL64551.1| ribosomal large subunit pseudouridine synthase B [Chlorobium
           phaeobacteroides DSM 266]
          Length = 243

 Score =  162 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 71/243 (29%), Positives = 117/243 (48%), Gaps = 6/243 (2%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVP 66
            E+    R+++ +A  GIASRR  ++++A  RV VNG + +   + ++   D + VDG  
Sbjct: 4   TEDEGGIRINRYLAMCGIASRRAADKLVADGRVTVNGKIADEPGLRILPFKDEVIVDGRK 63

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
               E  ++++       V T S  +       +L S+  RV  VGRLD  T G++LLTN
Sbjct: 64  FVVPEAKKVYILLNKPRNVITTSHDEKDRETILDLVSVEERVYPVGRLDRKTTGVILLTN 123

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKG 184
           DG LA  L  PS+   + Y      +  Q  L+ L  G+ ++         Q  L    G
Sbjct: 124 DGILAHRLMHPSSNVKKEYVAELDKRFPQGLLSQLVGGMKLKDTGEKVSPCQAKLLD-DG 182

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
              W  + + EGKN +++++ E   + V +L R++Y   + G L  G+ R +SK  +RE 
Sbjct: 183 MRIW--ISIHEGKNHQVRRMLETLGFDVTKLERVAYAGLKAGDLRRGAWRHLSKNEVREL 240

Query: 245 LGP 247
              
Sbjct: 241 YRL 243


>gi|226942108|ref|YP_002797182.1| Pseudouridine synthase family protein [Laribacter hongkongensis
           HLHK9]
 gi|226717035|gb|ACO76173.1| Pseudouridine synthase family protein [Laribacter hongkongensis
           HLHK9]
          Length = 247

 Score =  162 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 62/249 (24%), Positives = 102/249 (40%), Gaps = 19/249 (7%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           +       R+SK +A  G+ SRRE +  IA+  V V+G ++      V     I +D   
Sbjct: 1   MDSQSDKIRLSKRMAELGLCSRREADDYIARGWVSVDGQIISELGSKVSPDQRITLDARA 60

Query: 64  ------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                         P+          Y     L+          +     P+    +   
Sbjct: 61  REAQNTRVTILLHKPIGYVSGQAEKGYQPAATLIVPERHWQQDPSRTVWKPAQLQGLAPA 120

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++ ++ L LL  G+ + G+ 
Sbjct: 121 GRLDIDSTGLLVLTQDGRIAKQLIGENSPVDKEYLVRVEGRLSEEGLRLLNHGLALDGVP 180

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
               +V    +      +   L EGK R+I+++ E    +V  L RI  G   LG L  G
Sbjct: 181 LKPARVWWQNRDQ----LRFVLVEGKKRQIRRMCELVGLRVVGLKRIRIGRIMLGDLPQG 236

Query: 232 STREVSKKI 240
             R ++   
Sbjct: 237 QWRYLAPGE 245


>gi|148239883|ref|YP_001225270.1| 16S rRNA pseudouridylate synthase [Synechococcus sp. WH 7803]
 gi|147848422|emb|CAK23973.1| 16S rRNA pseudouridylate synthase [Synechococcus sp. WH 7803]
          Length = 243

 Score =  162 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 75/230 (32%), Positives = 116/230 (50%), Gaps = 1/230 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KA 70
           T QR+ K+IA AG+ SRR+ E ++  +RV+VNG L        +  D IEVD  PL+   
Sbjct: 2   TRQRLQKLIASAGVCSRRKAEDLLRDRRVRVNGQLATLGDQADLDVDTIEVDDRPLQTAP 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L L   P  + +       R+ +    P +   +  VGRLD  + G LLL+N G L
Sbjct: 62  QARVLLLNKPPGVICSCRDPQRRRTVLELVPPDLREGLHPVGRLDAESRGALLLSNQGEL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + YRV   G   + +LN  ++G+V+ G      +V L  +    + + 
Sbjct: 122 TLQLTHPRYNHRKTYRVTVAGLPSEKQLNQWRRGVVLDGTVTRPAEVNLVKKSPQASVLE 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           V LREG+NR+I++V      +V  L RI+ G   LG++  G  RE+S++ 
Sbjct: 182 VILREGRNRQIRRVALSLGHRVLDLQRIAIGRLTLGSMREGCWRELSRQE 231


>gi|115522955|ref|YP_779866.1| pseudouridine synthase Rsu [Rhodopseudomonas palustris BisA53]
 gi|115516902|gb|ABJ04886.1| Pseudouridine synthase, Rsu [Rhodopseudomonas palustris BisA53]
          Length = 787

 Score =  162 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 143/323 (44%), Positives = 187/323 (57%), Gaps = 3/323 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +R++KV++RAG+ SRR+ E  I + RV VNG ++   A++V   D I VDG PL   ER
Sbjct: 466 GERIAKVVSRAGLCSRRDAEDWITEGRVAVNGRIINSPALDVTERDVITVDGKPLPPPER 525

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TRL+LYHKP GL+TTH+DP+GR TVFD+LP    R+IS+GRLD NTEGLLLLTNDGGLAR
Sbjct: 526 TRLFLYHKPRGLMTTHADPEGRPTVFDHLPEGLPRLISIGRLDFNTEGLLLLTNDGGLAR 585

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            LELP T WLR YRVR HG+V Q +LN LK G+ + G+ YG +  TL+  +G+N W+   
Sbjct: 586 TLELPDTGWLRRYRVRAHGEVTQAQLNELKDGVEVDGVKYGPIDATLERDQGANVWLVFA 645

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           +REGKNRE++ V      +VNRLIR+SYGPFQLG +  G   EV  ++LREQLG  +   
Sbjct: 646 IREGKNREVRNVLAHLGLEVNRLIRVSYGPFQLGEIEEGQVEEVKTRVLREQLGEKIALA 705

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
           A  N    I S      D   +   V     R      +   +  Q+  +     RN   
Sbjct: 706 AGANFARQIPSKGDTDLDPVVVKKPV---LKRSTVEDRKGRRVLVQRSGSEEARERNELE 762

Query: 313 NVWMAKGIHSSFLSDSGQREENH 335
                            +     
Sbjct: 763 AAGFGPPKRPKRGYKGKRDLAPR 785



 Score = 40.2 bits (92), Expect = 0.46,   Method: Composition-based stats.
 Identities = 13/117 (11%), Positives = 22/117 (18%), Gaps = 4/117 (3%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +    P      +    +            P   +E      R  +      G  K+   
Sbjct: 211 KRPFTPRPDRGDRPAARSDDRKFGERKPYAPREGAEKRPYSPRPDRGDRPDRGPRKEFGE 270

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP----SFPSKRSLRRTSAKK 354
             P   R        A             R       P     F   +   R +  +
Sbjct: 271 RKPYAPREGGEKRPYAPRDRKDGDRPFSPRPSRDGDRPQGERKFGGDKKFGRGAPDR 327



 Score = 36.7 bits (83), Expect = 4.9,   Method: Composition-based stats.
 Identities = 15/113 (13%), Positives = 28/113 (24%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +    P      + +        E           + P      + +        ++   
Sbjct: 176 KRPYSPRPDRGDRPDRGPRKEFGERKPYAPREGGEKRPFTPRPDRGDRPAARSDDRKFGE 235

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             P   R  A     +         D G R+E   R P  P +   +R  A +
Sbjct: 236 RKPYAPREGAEKRPYSPRPDRGDRPDRGPRKEFGERKPYAPREGGEKRPYAPR 288



 Score = 36.7 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 17/102 (16%), Positives = 25/102 (24%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                +      P           P   +E      R  +      G  K+     P   
Sbjct: 111 RPARSSDRPDRGPRKEFGEKRPYAPREGAEKRPYSPRPDRGDRPDRGPRKEFGERKPYAP 170

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           R  A     +         D G R+E   R P  P +   +R
Sbjct: 171 REGAEKRPYSPRPDRGDRPDRGPRKEFGERKPYAPREGGEKR 212


>gi|148658668|ref|YP_001278873.1| pseudouridine synthase [Roseiflexus sp. RS-1]
 gi|148570778|gb|ABQ92923.1| pseudouridine synthase [Roseiflexus sp. RS-1]
          Length = 624

 Score =  162 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 100/351 (28%), Positives = 149/351 (42%), Gaps = 11/351 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV+A AGIASRR+ E  IA  RV VNG ++      V    D I VDG P+ K   
Sbjct: 4   ERLQKVLASAGIASRRDCEEYIAAGRVMVNGKVVRIPGTRVDPEHDEILVDGRPIGKIHH 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + HKP G+V+T  DP GR TV  +L ++  R+  VGRLD ++EGLLLLT+DG L +
Sbjct: 64  RTYVMLHKPAGVVSTTDDPQGRPTVI-DLVNLEQRLFPVGRLDYDSEGLLLLTDDGELTQ 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS Q  + YRV  +       L   + G+ + G+      V L  +    AWV V 
Sbjct: 123 KLTHPSYQVEKEYRVLLNEAPSPAALRAWRTGVELDGVKTAPAWVELIERTPDGAWVRVI 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L EG+ R+I++V     ++V RLIR+  GP  LG L +G+ R ++ + +           
Sbjct: 183 LHEGRKRQIREVARVLGYEVRRLIRVREGPLTLGDLPSGTWRFLTDEEVDMLREHAERNA 242

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ---------KNGLSKQKKLAT 303
           A    + P    +   +              R+ +   Q            +   +    
Sbjct: 243 AVAEAEQPRRREQGETQVSGGRRLRRITPSARLLQKGDQVTDTTLPDLDEAVESVQPPPV 302

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              RR+   N  +              R+   R           R     +
Sbjct: 303 VDERRSSRDNERIRHDERPPRDVRHSGRDGYGREQRDRRGSGDGRGDRRDE 353



 Score = 36.3 bits (82), Expect = 6.4,   Method: Composition-based stats.
 Identities = 18/120 (15%), Positives = 29/120 (24%), Gaps = 3/120 (2%)

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G  RE  ++  R   GP      + +        E       +   +      R ++   
Sbjct: 439 GGYRE--RREERGGNGPRDFRRDERSGGYRERREERGANGPRDFRRDERGGGYRERREER 496

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
             NG    ++       R        A G       + G      R        R  RR 
Sbjct: 497 GANGPRDFRRDERSGGYRERREERG-ANGPRDFRRDERGGGYRERREERGANGPRDFRRN 555


>gi|269956363|ref|YP_003326152.1| pseudouridine synthase [Xylanimonas cellulosilytica DSM 15894]
 gi|269305044|gb|ACZ30594.1| pseudouridine synthase [Xylanimonas cellulosilytica DSM 15894]
          Length = 243

 Score =  162 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 73/233 (31%), Positives = 118/233 (50%), Gaps = 2/233 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK 69
               R+ KV+A AG  SRR+ E++I   RV V+G ++    V V    + I VDG+ L+ 
Sbjct: 2   PDGVRLQKVLADAGYGSRRKAEQLIEDGRVSVDGQIIIELGVRVDPAKNVIHVDGLRLQL 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                    +KP G+++  SD  GR T+ D + +   R+  VGRLD+++EGL+LLTNDG 
Sbjct: 62  DTNKVTLAVNKPAGVISAMSDEKGRPTLADLVRNREERLFHVGRLDLDSEGLILLTNDGE 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNL-LKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           L   L  P  +  + Y V   G     ++   L  G+ ++       +V +         
Sbjct: 122 LGNRLAHPKYEVPKTYLVTVSGGDVFPRIVRALLDGVDLEDGPARMDRVKIVQALEGMTM 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L +G+NR ++++F+  +  V RL+R   GP  LG    G+ R +S+  +
Sbjct: 182 VEVVLHDGRNRVVRRMFDAVDRPVERLVRTKIGPIALGDQRPGTHRVLSRTEV 234


>gi|296314446|ref|ZP_06864387.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           polysaccharea ATCC 43768]
 gi|296838734|gb|EFH22672.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           polysaccharea ATCC 43768]
          Length = 349

 Score =  162 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 73/256 (28%), Positives = 124/256 (48%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+
Sbjct: 84  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHV 142

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++  L +  ++++       
Sbjct: 203 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTTEQMRSLTEEGVMLEDGLAKVE 262

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   
Sbjct: 263 RIYEQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFY 322

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   L    +
Sbjct: 323 ELNPAEVANILKWAEM 338


>gi|295105527|emb|CBL03071.1| ribosomal large subunit pseudouridine synthase B [Faecalibacterium
           prausnitzii SL3/3]
          Length = 275

 Score =  162 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 86/273 (31%), Positives = 135/273 (49%), Gaps = 4/273 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K++A  G+ SRR  E++IA+ RVKVNG  ++       + D + VD   +   +  
Sbjct: 4   ERIQKIMAEQGLCSRRAAEQIIAEGRVKVNGHPVKVGDKMDPNRDVLHVDDERIYIQKNQ 63

Query: 74  --RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                  +KP G VTT SD  GR TV D +  I +R+  VGRLD ++EGLLL+TNDG  A
Sbjct: 64  QLYYLALYKPRGYVTTASDELGRKTVMDLVSDIPARLYPVGRLDKDSEGLLLMTNDGAFA 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVT 190
           + +  PS    ++YRV    + D+  +  L  G+V+          + + T +     + 
Sbjct: 124 QAVTHPSGGISKLYRVTVQPRADEATILKLSSGVVLDDGTKTMPCAINVVTDEPGRTVME 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L+EGKNREI+++ E    +V RL R + G  +LG L  G+ RE++K  +   L    +
Sbjct: 184 MTLKEGKNREIRRMCESVGLEVVRLKRNAEGVVKLGMLKPGTYRELTKAEV-NGLRAAAV 242

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
           +       A   S     R R  +    P    
Sbjct: 243 KGRAQTRSAAQQSKAAERRPRGPVGKNTPRKQK 275


>gi|227503690|ref|ZP_03933739.1| pseudouridine synthase B [Corynebacterium accolens ATCC 49725]
 gi|227075726|gb|EEI13689.1| pseudouridine synthase B [Corynebacterium accolens ATCC 49725]
          Length = 303

 Score =  162 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 79/240 (32%), Positives = 122/240 (50%), Gaps = 4/240 (1%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDG 64
           +  +    +R+ KV+A+AG+ASRR  E +I   RV+VNG ++ +  V V    D I VDG
Sbjct: 55  VDDDKPKGERLQKVLAKAGVASRRHAEILIDAGRVEVNGNVILKQGVKVNPAVDVIRVDG 114

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGL 121
           V +   E    ++ +KP G+ +T SD  GR  V D +        R+  VGRLD +TEGL
Sbjct: 115 VRVNVNEDQEYFILNKPRGMQSTMSDDLGRPCVGDVVSEKVASGQRLFHVGRLDADTEGL 174

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           L+LTNDG LA  L  P  +  + Y     G+ D   +  LK+GI ++        V +  
Sbjct: 175 LILTNDGELANRLMHPKYEVKKTYLATVLGEADNKLVRQLKEGIELEDGLAKADFVQVVD 234

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +    + V V L EG+   ++++ +   + V RL+R      QLG +  G  R ++   L
Sbjct: 235 KNQGFSLVRVELHEGRKHIVRRLLKEAGYPVQRLVRTKLHTVQLGDMKPGGLRALNSNEL 294


>gi|153001970|ref|YP_001367651.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|151366588|gb|ABS09588.1| pseudouridine synthase [Shewanella baltica OS185]
          Length = 242

 Score =  162 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 66/240 (27%), Positives = 111/240 (46%), Gaps = 16/240 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLER-----AAVNVMSTDHIEVDGVPLR 68
            R++K +A+ GI SRRE  R+I   R+ +NG +           ++   D+IE+DG P+ 
Sbjct: 1   MRLAKYLAQCGIGSRREACRLIEAGRITLNGHIARHTDPVRLGESLNCLDNIELDGAPIT 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           K E    W+ +K +G      + D   T   +L     R+  VGRLD ++ GLLLLTNDG
Sbjct: 61  KTETLAYWVLNKAVGTDCRLLEQDE--TSLIHLLPKAPRLYPVGRLDKDSRGLLLLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS    + Y V  +     + +  +  G+  + +     QV   +       
Sbjct: 119 ELTHKLMHPSFAHSKTYHVHLNRPFTDEFVEQMASGVRYKDVQTLPCQVRRLSSDS---- 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ-----LGTLLAGSTREVSKKILRE 243
             + L +G NR+I+++ +   ++V  L R++          LG L  G  R +++  + E
Sbjct: 175 FEIVLTQGLNRQIRRMSKALGYRVIDLERVAIMTLNLRELALGELQEGQMRRLTESEVAE 234


>gi|238790412|ref|ZP_04634183.1| Ribosomal large subunit pseudouridine synthase B [Yersinia
           frederiksenii ATCC 33641]
 gi|238721519|gb|EEQ13188.1| Ribosomal large subunit pseudouridine synthase B [Yersinia
           frederiksenii ATCC 33641]
          Length = 342

 Score =  162 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 139/328 (42%), Gaps = 16/328 (4%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVP 66
           +    +++ K++ARAG  SRRE+E +I Q RV V+G +  +    V  T    I +DG  
Sbjct: 23  DKIVGEKLQKILARAGHGSRREIETIIQQGRVSVDGKI-SKLGDRVEVTQATKIRLDGHL 81

Query: 67  LRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           L   E        L  Y     L T +      +          SR ++VGRLD+NT GL
Sbjct: 82  LSIKESEEAVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGL 141

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQ+D +K+  L +G+ ++        +    
Sbjct: 142 LLFTTDGELANRLMHPSREVEREYAVRVFGQIDDEKIKQLSRGVQLEDGPAAFRTIKFQG 201

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
            +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+    
Sbjct: 202 GEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELD--- 258

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
               L         V LD+   S   + +DR  + +       +     + +    +Q  
Sbjct: 259 ----LNATNYLRELVELDSETVSKLPVEKDRRRVKANQIRRAVKRHTEVAGRQVAGRQGS 314

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDS 328
                 R+N+ S                
Sbjct: 315 ARKSSSRQNVGSAAPATTAGRRGSNKRG 342


>gi|56708141|ref|YP_170037.1| ribosomal large subunit pseudouridine synthase B [Francisella
           tularensis subsp. tularensis SCHU S4]
 gi|110670612|ref|YP_667169.1| ribosomal large subunit pseudouridine synthase B [Francisella
           tularensis subsp. tularensis FSC198]
 gi|118497537|ref|YP_898587.1| 16S rRNA pseudouridine synthase [Francisella tularensis subsp.
           novicida U112]
 gi|195536233|ref|ZP_03079240.1| ribosomal large subunit pseudouridine synthase B [Francisella
           tularensis subsp. novicida FTE]
 gi|208779336|ref|ZP_03246682.1| ribosomal large subunit pseudouridine synthase B [Francisella
           novicida FTG]
 gi|224457237|ref|ZP_03665710.1| 16S rRNA pseudouridine synthase [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|254370626|ref|ZP_04986631.1| hypothetical protein [Francisella tularensis subsp. tularensis
           FSC033]
 gi|254874944|ref|ZP_05247654.1| rluB, ribosomal large subunit pseudouridine synthase B [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|56604633|emb|CAG45689.1| ribosomal large subunit pseudouridine synthase B [Francisella
           tularensis subsp. tularensis SCHU S4]
 gi|110320945|emb|CAL09072.1| ribosomal large subunit pseudouridine synthase B [Francisella
           tularensis subsp. tularensis FSC198]
 gi|118423443|gb|ABK89833.1| 16S rRNA pseudouridine synthase [Francisella novicida U112]
 gi|151568869|gb|EDN34523.1| hypothetical protein FTBG_00414 [Francisella tularensis subsp.
           tularensis FSC033]
 gi|194372710|gb|EDX27421.1| ribosomal large subunit pseudouridine synthase B [Francisella
           tularensis subsp. novicida FTE]
 gi|208745136|gb|EDZ91434.1| ribosomal large subunit pseudouridine synthase B [Francisella
           novicida FTG]
 gi|254840943|gb|EET19379.1| rluB, ribosomal large subunit pseudouridine synthase B [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|282159347|gb|ADA78738.1| 16S rRNA pseudouridine synthase [Francisella tularensis subsp.
           tularensis NE061598]
 gi|332184099|gb|AEE26353.1| Ribosomal large subunit pseudouridine synthase B [Francisella cf.
           novicida 3523]
          Length = 271

 Score =  162 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 86/259 (33%), Positives = 124/259 (47%), Gaps = 9/259 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+  N   +   P+R+ K++A+ GI SRR++E  I Q RVKVNG +           D I
Sbjct: 1   MRRANQNNDKN-PERLQKLLAKYGIGSRRKIEEYIEQGRVKVNGKVAT-LGDKASEADKI 58

Query: 61  EVDGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
             DG  L            +  + +   + T+  + D ++          SR I VGRLD
Sbjct: 59  SFDGKALHSYGQPMTRPRVVIYHKREGEVCTSKDEKDRQTVFDSLPKLAKSRWIMVGRLD 118

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGD 174
           INT GLLL T DG LA  L  PS Q  R Y VR  GQ    + +N LK+GI ++      
Sbjct: 119 INTTGLLLFTTDGDLANRLMHPSYQIEREYAVRVFGQQLSDETINKLKEGIQLEDGMAKF 178

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGST 233
             +     +G+N W  V L EG+NRE++++FE     V+RL RI +G   L   +  G T
Sbjct: 179 NSIKFSGGEGANLWYYVTLSEGRNREVRRMFEAVGVTVSRLTRIRFGDIILPKFVSRGKT 238

Query: 234 REVSKKILREQLGPHLLEE 252
            E++   +        L+E
Sbjct: 239 LELNPSEVNRLRKSVKLKE 257


>gi|85717175|ref|ZP_01048133.1| pseudouridine synthase, Rsu [Nitrobacter sp. Nb-311A]
 gi|85696008|gb|EAQ33908.1| pseudouridine synthase, Rsu [Nitrobacter sp. Nb-311A]
          Length = 635

 Score =  162 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 148/328 (45%), Positives = 194/328 (59%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           +     +RV+KVI+RAG+ASRR+ E  + Q RV VNG ++   A++V S D I VDG PL
Sbjct: 303 KPKKAGERVAKVISRAGLASRRDAEEWVTQGRVAVNGRVINSPALDVTSRDVITVDGEPL 362

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            + ERTRL+LYHKP GL+TTH+DP+GR TVFD+LP    R+ISVGRLD NTEGLLLLTND
Sbjct: 363 PERERTRLFLYHKPRGLMTTHADPEGRPTVFDHLPDGLPRLISVGRLDFNTEGLLLLTND 422

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GGLAR LELP T WLR YRVR HG+V Q +L+ LK G+ ++G+ YG +  TL+  +G+N 
Sbjct: 423 GGLARALELPDTGWLRRYRVRAHGEVTQPQLDALKNGVEVEGVKYGSIDATLERDQGANV 482

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+T  +REGKNRE++ V      +VNRLIRISYGPFQL  +  G   EV  ++LREQ G 
Sbjct: 483 WLTFAIREGKNREVRNVMAHLGLEVNRLIRISYGPFQLAEIAEGEVEEVKTRVLREQFGD 542

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            +   A +N       S  +   R         D     K +  ++   +   +      
Sbjct: 543 RIAALANMNPAGATAESGAVKLGRDGTPLRSKKDNKARTKRALIEDRKGRSVVVQRTGSD 602

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENH 335
              A N   A G         G   +  
Sbjct: 603 EARARNEAEANGYGPPRRPKRGYHGKRD 630


>gi|330816691|ref|YP_004360396.1| hypothetical protein bgla_1g17950 [Burkholderia gladioli BSR3]
 gi|327369084|gb|AEA60440.1| hypothetical protein bgla_1g17950 [Burkholderia gladioli BSR3]
          Length = 575

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 82/388 (21%), Positives = 143/388 (36%), Gaps = 39/388 (10%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++       ++ KV+A AG+ SRRE+E +I   RV VNG         ++ TD + ++
Sbjct: 178 KRVLAPEDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRILPTDQVRIN 236

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 237 GKPVKRKLANKPPRVLLYHKPTGEIVSHADPEGRASVFDRLPPMKTAKWLAVGRLDFNTE 296

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++++     L  G+ ++      +++  
Sbjct: 297 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELNEASRQKLLHGVELEDGPANFLRIRD 356

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +G   L   L  G   E+ +
Sbjct: 357 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGSIPLPRGLKRGRWEELDE 416

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             +R+ +    L+ A         + +   R    + + +          +  +    ++
Sbjct: 417 AQVRKLMATVGLKVAADEKGKRGGAGQAERRQPDPMQTSMGFLNREPVLTTHGQLDQPRR 476

Query: 299 KKLATPVHRRNLASNV---------------------------------WMAKGIHSSFL 325
                       A                                        G      
Sbjct: 477 GGRRGAQGGGFGAGAGFGGGAAGGGFGGNANGNGNRRGGGDVDGNRLSYGANNGNKRGGG 536

Query: 326 SDSGQREENHRRSPSFPSKRSLRRTSAK 353
              G R  N  R+    +     R   +
Sbjct: 537 KSQGPRGANGNRADGGGNAGGSARGGQR 564


>gi|302335698|ref|YP_003800905.1| ribosomal large subunit pseudouridine synthase B [Olsenella uli DSM
           7084]
 gi|301319538|gb|ADK68025.1| ribosomal large subunit pseudouridine synthase B [Olsenella uli DSM
           7084]
          Length = 267

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 64/244 (26%), Positives = 101/244 (41%), Gaps = 16/244 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA- 70
             R+ + +ARAG+ASRR  E +++  RV+VNG ++      V    D + VDGV  R + 
Sbjct: 11  TMRLQRFLARAGVASRRGSENLMSAGRVRVNGRVVSELGSKVTPGIDVVTVDGVECRLSD 70

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      L T                + +  +  VGRLD +T GLLL + DG +
Sbjct: 71  EHAYLMLNKPAGYLTTMSDPQGRPCVAELVPTARYPGLFPVGRLDADTTGLLLFSTDGEV 130

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA--- 187
           A  L  PS    + Y     G     +L +L+ G+ +           L       +   
Sbjct: 131 ANALLHPSRHVWKRYVALVRGTPTTRQLAMLRAGVPLDDGVARPADAHLLGADDPLSASV 190

Query: 188 ----------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                      V++ + EGK  ++K++ +    +V  L R  +GP  L   L AG  R +
Sbjct: 191 VTGGADPGCAVVSIRIHEGKKHQVKRMLKAVGHEVVHLHRSEFGPLVLTAELKAGRWRPL 250

Query: 237 SKKI 240
           +   
Sbjct: 251 TGDE 254


>gi|260582128|ref|ZP_05849922.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae NT127]
 gi|260094760|gb|EEW78654.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae NT127]
          Length = 357

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 90/288 (31%), Positives = 132/288 (45%), Gaps = 10/288 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QPKVEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 67  LRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +  +         L  Y     L T        +          SR I+VGRLDINT GL
Sbjct: 130 INLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPHLTGSRWIAVGRLDINTSGL 189

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++    
Sbjct: 190 LLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGPANFKEIKFTG 249

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 250 GVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEMDLEN 309

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
              LRE +G     E ++++       ++    +        +   + 
Sbjct: 310 VNYLRELVGLPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>gi|253688397|ref|YP_003017587.1| pseudouridine synthase [Pectobacterium carotovorum subsp.
           carotovorum PC1]
 gi|251754975|gb|ACT13051.1| pseudouridine synthase [Pectobacterium carotovorum subsp.
           carotovorum PC1]
          Length = 294

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 83/293 (28%), Positives = 125/293 (42%), Gaps = 7/293 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIEGIIQAGRVSVDGKVATLGDRVEVTKATKIRIDGHVVTVKE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          SR ++VGRLD+NT GLLL T 
Sbjct: 62  TEETVCRVLVYYKPEGELCTRNDPDGRPTVFDRLPKIQGSRWVAVGRLDVNTSGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  G+VD +K+  L KG+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGEVDDEKIKQLSKGVQLEDGPASFRTIRYQGGEGLN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  + L    
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDITLPKGLPRGGWAEMPLEQLNYLR 241

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
               L    V+          +  ++     +     +      +        
Sbjct: 242 ELVQLPAETVSKLPVERERRRVKANQIRRAVKRHSQISTAPARRTSPKPKRNG 294


>gi|238027587|ref|YP_002911818.1| hypothetical protein bglu_1g20050 [Burkholderia glumae BGR1]
 gi|237876781|gb|ACR29114.1| Hypothetical protein bglu_1g20050 [Burkholderia glumae BGR1]
          Length = 571

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 78/367 (21%), Positives = 140/367 (38%), Gaps = 15/367 (4%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
             K ++       ++ KV+A AG+ SRRE+E +I   RV VNG         ++ TD + 
Sbjct: 172 PQKRVLAPEDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRILPTDQVR 230

Query: 62  VDGVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           ++G P+++         L  +     +V+        S      P   ++ ++VGRLD N
Sbjct: 231 INGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRASVFDRLPPMKTAKWLAVGRLDFN 290

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++
Sbjct: 291 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRI 350

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                +G+N W  V L EG+NRE++++FE     V+RLIR  +G   L   L  G   E+
Sbjct: 351 RDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGSISLPRGLKRGRWEEL 410

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM---------KK 287
            +  +R+ +    L+ A         +     +    + + +                + 
Sbjct: 411 DEAQVRKLMATVGLKVAADEKGGKRGAGAAERKQPDPMQTSMGFLNREPVLTTHGQLDQP 470

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
               + G       A                G +++        + +  R     +    
Sbjct: 471 RRGGRRGAQGGGFGAGLGGGFAGGGASAGGYGGNANGNRRGAGGDVDGNRLSYGANGNKR 530

Query: 348 RRTSAKK 354
               + +
Sbjct: 531 GGGKSPR 537


>gi|260186664|ref|ZP_05764138.1| hypothetical protein MtubCP_11646 [Mycobacterium tuberculosis
           CPHL_A]
 gi|289447326|ref|ZP_06437070.1| conserved hypothetical protein [Mycobacterium tuberculosis CPHL_A]
 gi|289420284|gb|EFD17485.1| conserved hypothetical protein [Mycobacterium tuberculosis CPHL_A]
          Length = 254

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 72/238 (30%), Positives = 106/238 (44%), Gaps = 4/238 (1%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVP 66
                  R+ KV+++AGIASRR  E+MI   RV+V+G ++      V      + VDG  
Sbjct: 8   SREPRGIRLQKVLSQAGIASRRAAEKMIVDGRVEVDGHVVTELGTRVDPPVAVVRVDGAR 67

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLL 123
           +   +       +KP G+ +T SD  GR  + D +            VGRLD +TEGL+L
Sbjct: 68  VVLDDSLVYLALNKPRGMHSTMSDDRGRPCIGDLIERKVRGTKKLFHVGRLDADTEGLML 127

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG LA  L  PS +  + Y     G V +     L+ GI +           +    
Sbjct: 128 LTNDGELAHRLMHPSHEVPKTYLATVTGSVPRGLGRTLRAGIELDDGPAFVDDFAVVDAI 187

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                V V L EG+NR ++++     + V  L+R   G   LG    GS R +    +
Sbjct: 188 PGKTLVRVTLHEGRNRIVRRLLAAAGFPVEALVRTDIGAVSLGKQRPGSVRALRSNEI 245


>gi|227549324|ref|ZP_03979373.1| 16S rRNA uridine-516 pseudouridylate synthase [Corynebacterium
           lipophiloflavum DSM 44291]
 gi|227078643|gb|EEI16606.1| 16S rRNA uridine-516 pseudouridylate synthase [Corynebacterium
           lipophiloflavum DSM 44291]
          Length = 295

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 76/235 (32%), Positives = 115/235 (48%), Gaps = 4/235 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R+ KV+A+AG+ASRR  E MI Q RV+VNG  +    + V  + D I VDG  +  
Sbjct: 52  TEGVRLQKVLAQAGVASRRHAEIMITQGRVEVNGTRVTTQGMRVDPSRDVIRVDGTRINV 111

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTN 126
            E    ++++KP G+ +T  D   R++V   L        R+  VGRLD +TEGLLLLTN
Sbjct: 112 NEELEYFVFNKPRGVQSTMKDEMDRTSVGSYLSERTASGQRLFHVGRLDADTEGLLLLTN 171

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  P  +  + Y     G+     +  L++GI +         V +       
Sbjct: 172 DGELANRLMHPRYEIAKTYMATVLGEAKPALVKKLREGIELDDGPAKADYVQIVDTHNGQ 231

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + V L EG+   ++++ +     V RL+R      QLG +  GS R ++   L
Sbjct: 232 SIIRVELHEGRKHIVRRMLKAAGHPVQRLVRTKVHTVQLGDMKPGSLRALNAAEL 286


>gi|50121219|ref|YP_050386.1| 23S rRNA pseudouridylate synthase B [Pectobacterium atrosepticum
           SCRI1043]
 gi|49611745|emb|CAG75194.1| putative RNA pseudouridylate synthase [Pectobacterium atrosepticum
           SCRI1043]
          Length = 294

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 82/293 (27%), Positives = 125/293 (42%), Gaps = 7/293 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIQAGRVSVDGKIATLGDRVEVTKATKIRIDGHVVTVKE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          SR ++VGRLD+NT GLLL T 
Sbjct: 62  TEETVCRVLVYYKPEGELCTRNDPDGRPTVFDRLPKIQGSRWVAVGRLDVNTSGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  G+VD +K+  L KG+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSHEVEREYAVRVFGEVDDEKIKQLSKGVQLEDGPASFRTICYQGGEGLN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   +  G   E+  + L    
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDITLPKGIPRGGWTEMPLEQLNYLR 241

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
               L    V+          +  ++     +     +      +        
Sbjct: 242 ELVQLPAETVSKLPVERERRRVKANQIRRAVKRHSQISSAPARRTSPKSKRNG 294


>gi|320011602|gb|ADW06452.1| pseudouridine synthase [Streptomyces flavogriseus ATCC 33331]
          Length = 389

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 109/233 (46%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
               +R+ K++ARAG+ SRR  E +I Q RV+VNG ++    + V    D I+VDG+ + 
Sbjct: 149 EQEGERLQKILARAGMGSRRACEELIEQARVEVNGEIVLEQGMRVDPQKDEIKVDGLTVA 208

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   L      + T       ++   D + +  +R+  VGRLD  TEG++LLTN G
Sbjct: 209 TQSYLFFALNKPAGVVSTMGDPDGRQNLG-DYVNNRETRLFHVGRLDTETEGIILLTNHG 267

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     + Y     G + +D    LK GI ++          +    G N  
Sbjct: 268 ELAHRLTHPKYGVKKTYLAAIQGPLPRDLGKRLKDGIQLEDGYARADHFRVVENTGKNYL 327

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L EG+   ++++     + V RL+R S+GP  LG   +G  R ++   +
Sbjct: 328 VEVTLHEGRKHIVRRMLAEAGFPVERLVRTSFGPIPLGDQKSGWLRRLTNTEV 380


>gi|284045196|ref|YP_003395536.1| pseudouridine synthase [Conexibacter woesei DSM 14684]
 gi|283949417|gb|ADB52161.1| pseudouridine synthase [Conexibacter woesei DSM 14684]
          Length = 233

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 76/237 (32%), Positives = 126/237 (53%), Gaps = 6/237 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K +A AG+ASRR  E++IA+ R+ V G ++   A +V ++  +  DG P+R  E  
Sbjct: 1   MRLAKFLAHAGVASRRASEQLIAEGRIAVGGEIVLDPARDVDASSGVTYDGEPVRGEEPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++  HKP G+V+T +D  GR TV + L     R+  VGRLD ++ GL+LLTNDG LA  
Sbjct: 61  VVYALHKPAGVVSTAADTHGRRTVTE-LVPQGRRLYPVGRLDADSTGLILLTNDGELANR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           L  P  +  + YR    G    D+    L++G+ ++       +V       S   + + 
Sbjct: 120 LTHPRFEVPKTYRATVGGPQIGDRTLRQLREGVRLEDGMTAPARVRRL----SAHVLELT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           + EG+ R+++++ E     V  L+R  +GP  LG L  G +R ++ + +RE      
Sbjct: 176 IHEGRKRQVRRMCEEVGHPVKSLVRTQFGPLSLGDLGTGRSRRLTAREVRELAEAAN 232


>gi|271500649|ref|YP_003333674.1| pseudouridine synthase [Dickeya dadantii Ech586]
 gi|270344204|gb|ACZ76969.1| pseudouridine synthase [Dickeya dadantii Ech586]
          Length = 296

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 86/295 (29%), Positives = 127/295 (43%), Gaps = 10/295 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E MI   R+ V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESMIEAGRISVDGKIATLGDRVEVTRATKIRIDGHVVSVRE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T        +           R ++VGRLD+NT GLLL T 
Sbjct: 62  TEEAVCRVLMYYKPEGELCTRSDPEGRPTVFDRLPRIQGYRWVAVGRLDVNTSGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  G+V  DK+  L KG+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGEVGDDKIRQLSKGVQLEDGPAAFRAIRYQGGEGLN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV---SKKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG  QL   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIQLPKGLPRGGWTEMPLADVNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           E +       +++ ++      +     R           +R   N       + 
Sbjct: 242 ELVQLTPETVSKLPVERERRRVKANQIRRAVKRHGQTGAASRPSGNRRSAPKRNG 296


>gi|332993790|gb|AEF03845.1| pseudouridine synthase [Alteromonas sp. SN2]
          Length = 298

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 90/298 (30%), Positives = 131/298 (43%), Gaps = 15/298 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+A  G+ SRRE+ER I Q RV VNG L       V  T  I VDG  L +   
Sbjct: 2   TEKLQKVLANQGLGSRREMERWIEQGRVSVNGTLAT-LGDRVDETGQIRVDGHLLSRQTE 60

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 L        L + H      +           R I+VGRLD+NT GLLL TNDG
Sbjct: 61  QPVCRVLMYNKPEGELCSRHDPEGRDTVFDRLPAIRMGRWIAVGRLDMNTSGLLLFTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------TQ 182
            LA  L  P  +  R Y VR  G V    LN LKKG+ ++      + ++         +
Sbjct: 121 ELANRLMHPKCEVEREYAVRVFGDVTHQTLNTLKKGVQLEDGEAKFLSISGKVAPPGSEE 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI- 240
           +  N W  V L+EG+NRE+++++E    +V+RLIR+ YGP  L   L  G+  E+  +  
Sbjct: 181 ESMNRWFNVTLKEGRNREVRRLWESQGVQVSRLIRVKYGPMDLQKRLPQGAWVELGLEDV 240

Query: 241 --LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
             LR+ +      +  V++         L R R ++            K    +    
Sbjct: 241 NSLRDIVQLPEETQTMVDVRQGKLDHARLSRMRRSVKKHKVRKENGGVKKRVARTPKR 298


>gi|319900039|ref|YP_004159767.1| RNA-binding S4 domain protein [Bacteroides helcogenes P 36-108]
 gi|319415070|gb|ADV42181.1| RNA-binding S4 domain protein [Bacteroides helcogenes P 36-108]
          Length = 501

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 60/241 (24%), Positives = 103/241 (42%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +   D +
Sbjct: 253 IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRGDEV 312

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +     +    +  + L      + T+      R+ +     +   R+  VGRLD NT G
Sbjct: 313 KFHDQAVSIERKIYVLLNKPKDTVTTSDDPQARRTVMDLVKGACEERIYPVGRLDRNTTG 372

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     + +  +  +  GI +             
Sbjct: 373 VLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKSDMEQIAAGIQLDDGEIH-ADAISY 431

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           T       V + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+  
Sbjct: 432 TDDFKKDDVGIEIHSGKNRIVRRIFESLGYKVVKLDRVYFAGLTKKGLRRGEWRYLSEAE 491

Query: 241 L 241
           +
Sbjct: 492 V 492


>gi|294637088|ref|ZP_06715402.1| ribosomal small subunit pseudouridine synthase A [Edwardsiella
           tarda ATCC 23685]
 gi|291089716|gb|EFE22277.1| ribosomal small subunit pseudouridine synthase A [Edwardsiella
           tarda ATCC 23685]
          Length = 235

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 101/237 (42%), Gaps = 7/237 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I++    SR  V R +  + V V+G++    ++ + +   +   G  L      
Sbjct: 1   MRLDKFISQQLGISRALVARELRARYVTVDGVVARSGSLQITAEQEVAYQGNVLTFITGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLD++T GL+LLT+DG  +  
Sbjct: 61  RYFMLNKPEGYVCSTDDPDHATILYFIDEPMAEKLHAAGRLDLDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +D        +G+ + G        ++           V +
Sbjct: 121 ITSPRHHCEKTYLVTLEQPLDPQTAEQFAQGVQLHGEKDLTKPARLEAL----DEHQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGP 247
            + EG+  ++K++F     +V  L R   G   L   L  G  R +S   +   L P
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVVALHRERIGAIALDAALAPGEYRALSDDEVASVLAP 233


>gi|253584230|ref|ZP_04861428.1| pseudouridylate synthase [Fusobacterium varium ATCC 27725]
 gi|251834802|gb|EES63365.1| pseudouridylate synthase [Fusobacterium varium ATCC 27725]
          Length = 226

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 65/229 (28%), Positives = 101/229 (44%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SRREV+ ++    + VNGI+     +N+    D I      L   + 
Sbjct: 1   MRLDKFLTECGLGSRREVKEILNTGEITVNGIIANNPQMNIKENSDEIFYQERKLEYKKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L  K   +       D           I   +  VGRLD +TEGLLLLTNDG L  
Sbjct: 61  RYYILNKKAGYITAVEDSRDQTVMELLPDWVIKKDLAPVGRLDKDTEGLLLLTNDGALNH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y       + +D+L  L+ G+ I G      +         +A + + 
Sbjct: 121 KLLSPKNHVEKTYYAELEKDISEDELVKLRNGVDIGGYITMPAKADRI----DSAKIHLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++EGK  ++KK+ E    KV  L RIS+G  +L  L  G+ +EV+ + +
Sbjct: 177 IKEGKFHQVKKMLEAVGNKVIFLKRISFGKLKLDNLELGAVKEVNIEDI 225


>gi|238798380|ref|ZP_04641862.1| Ribosomal large subunit pseudouridine synthase B [Yersinia
           mollaretii ATCC 43969]
 gi|238717765|gb|EEQ09599.1| Ribosomal large subunit pseudouridine synthase B [Yersinia
           mollaretii ATCC 43969]
          Length = 342

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 92/324 (28%), Positives = 138/324 (42%), Gaps = 16/324 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E +I Q RV V+G +       V  T    I +DG  L   
Sbjct: 27  GEKLQKVLARAGHGSRREIETIIQQGRVSVDGKI-STLGDRVEVTQATKIRLDGHLLSIT 85

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E        L  Y     L T +      +          SR ++VGRLD+NT GLLL T
Sbjct: 86  ESEEAVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFT 145

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  GQ+D +K+  L +G+ ++        ++    +G 
Sbjct: 146 TDGELANRLMHPSREVEREYAVRVFGQIDDEKIKQLSRGVQLEDGPAAFRTISFQGGEGL 205

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+    L+  
Sbjct: 206 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELD---LKAT 262

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
                L E          S   + +DR  + +       +     + +    +Q      
Sbjct: 263 NYLRELVELDSETV----SKLPVEKDRRRVKANQIRRAVKRHTEVAGRQVAGRQGSARKG 318

Query: 305 VHRRNLASNVWMAKGIHSSFLSDS 328
             R+N+ S    A           
Sbjct: 319 STRQNVGSAAPAATTNRRGSNKRG 342


>gi|294628596|ref|ZP_06707156.1| LOW QUALITY PROTEIN: pseudouridine synthase, Rsu [Streptomyces sp.
           e14]
 gi|292831929|gb|EFF90278.1| LOW QUALITY PROTEIN: pseudouridine synthase, Rsu [Streptomyces sp.
           e14]
          Length = 358

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 109/233 (46%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
               +R+ KV+ARAG  SRR  E +I Q RV+VNG ++      V    D ++VDG+ + 
Sbjct: 118 EQEGERLQKVLARAGYGSRRACEELIEQARVEVNGEIVLEQGKRVDPEKDEVKVDGLTVA 177

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   L      + T       +  + D + +  +R+  VGRLD  TEG++LLTN G
Sbjct: 178 TQSYQFFSLNKPAGVVSTMEDPEGRQ-CLGDYVTNRETRLFHVGRLDTETEGVILLTNHG 236

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     + Y     G + +D    LK GI ++          +  Q G N  
Sbjct: 237 ELAHRLTHPKYGVRKTYLAHIVGPIPRDLGKRLKDGIQLEDGYARADHFRVVEQTGKNYL 296

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L EG+   ++++     + V++L+R ++GP  LG   +G  R +S   +
Sbjct: 297 VEVTLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPITLGDQKSGWLRRLSNTEV 349


>gi|313673524|ref|YP_004051635.1| RNA-binding s4 domain protein [Calditerrivibrio nitroreducens DSM
           19672]
 gi|312940280|gb|ADR19472.1| RNA-binding S4 domain protein [Calditerrivibrio nitroreducens DSM
           19672]
          Length = 233

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 57/228 (25%), Positives = 100/228 (43%), Gaps = 5/228 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ IA     SRRE + +I    V VNG  +      V   D + V G  + ++   
Sbjct: 1   MRLNRFIAFNSNYSRREADELIFNGHVTVNGKPVLVPGYEVKDDDKVSVLGKVISRSNFL 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +  Y     L +      GR  + D      +++   GRLD ++EGL+  +NDG +   
Sbjct: 61  YVKFYKPRGFLTSYGDP-YGRKNLDDFEFFKKTKLAYSGRLDNDSEGLIFFSNDGSIIHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           ++ P     + Y V     +  ++   ++ G+ I G  +         +K       V +
Sbjct: 120 MQTPKYDVEKEYIVYTKRPLGDEEKLAMENGLEIDGYKFKKCS----VEKIGRNKYRVII 175

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            EGK R+I+ +F+ FN +V RL+RI      LG L  G  + ++K  +
Sbjct: 176 TEGKKRQIRNMFKHFNIEVERLVRIRIANITLGELKPGDFKFLTKDEI 223


>gi|188026069|ref|ZP_02960759.2| hypothetical protein PROSTU_02727 [Providencia stuartii ATCC 25827]
 gi|188021498|gb|EDU59538.1| hypothetical protein PROSTU_02727 [Providencia stuartii ATCC 25827]
          Length = 313

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 84/304 (27%), Positives = 136/304 (44%), Gaps = 10/304 (3%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG 64
           +  +    +++ K++AR+G  SRRE+E  + + R+ V+G +      + V     I +DG
Sbjct: 9   MSAKPQKTEKLQKILARSGHGSRREIETFLKEGRISVDGKIATLGDRIEVKPATKIRLDG 68

Query: 65  VPLRKAERTRLWL-----YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
             L   E  +        Y     L T H      +        + +R I+VGRLD+NT 
Sbjct: 69  RILAIKEPEKEICRVMAYYKPEGELCTRHDPEGRPTVFTRLPKLVGARWIAVGRLDVNTS 128

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL T DG LA  L  PS +  R Y VR  G++   K+  L +G+ ++        V+ 
Sbjct: 129 GLLLFTTDGELANRLMHPSREVEREYAVRVFGEITDAKIRQLTQGVQLEDGPAAFKTVSF 188

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  
Sbjct: 189 RGGEGMNQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIDLPKGLPRGGWTELGL 248

Query: 239 KI---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +    LRE +G     E +V ++      +     R              K+ SS+    
Sbjct: 249 QQTNYLRELVGLEAETETKVAVERDQRRIKANQIRRAVKRHSQVAARPASKRQSSRPTAK 308

Query: 296 SKQK 299
            + +
Sbjct: 309 RRTR 312


>gi|218885473|ref|YP_002434794.1| pseudouridine synthase [Desulfovibrio vulgaris str. 'Miyazaki F']
 gi|218756427|gb|ACL07326.1| pseudouridine synthase [Desulfovibrio vulgaris str. 'Miyazaki F']
          Length = 251

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 79/245 (32%), Positives = 121/245 (49%), Gaps = 7/245 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R++K IA AG+ SRR+ + +I Q  V+VNG +++     V+   D IEV G  L     
Sbjct: 6   VRLNKAIAGAGVCSRRQADDLIQQGVVRVNGEVVDTPGARVVPGRDRIEVRGQLLELDAA 65

Query: 73  TR---LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTND 127
                  + HKP+ +V+T  DP GR TV   LP      R+  VGRLD  +EGLL+LT+D
Sbjct: 66  PAAFTYVMLHKPVQVVSTVRDPQGRPTVLGILPPDLRGGRLYPVGRLDYFSEGLLILTDD 125

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN 186
           G L   L  P     +VY V+  G V +  L  +++G+ + +G     + V L       
Sbjct: 126 GDLTNRLTHPRYHLPKVYMVKVRGHVTESTLAPMRQGMTLAEGEKLAPVDVRLLQSDRQA 185

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +   + L +G NR+I+++       V  L R+  GP +LG L  G+ R ++   +     
Sbjct: 186 SLFEMTLHQGVNRQIRRMCRDLGLTVLLLRRVRQGPLELGELPKGAARRLTPHEVAALRR 245

Query: 247 PHLLE 251
              LE
Sbjct: 246 AAGLE 250


>gi|218663826|ref|ZP_03519756.1| RNA-pseudouridine synthase protein, ribosomal large subunit B
           [Rhizobium etli IE4771]
          Length = 267

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 71/266 (26%), Positives = 119/266 (44%), Gaps = 12/266 (4%)

Query: 1   MKDKNIVQENFTPQRVS-----------KVIARAGIASRREVERMIAQQRVKVNGILLER 49
           M+D+   Q+     +++           + +++ G  SR + ER+IA+ RV V+G  +  
Sbjct: 1   MRDRRPPQKKRERPKLTADAAGKRVTLPRALSKLGYCSRTQAERLIAEGRVSVDGRTVND 60

Query: 50  AAVNVMS-TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
            +  V   T  I VDG+ +    +  L L      + T H      +            +
Sbjct: 61  PSAWVDLVTAEIRVDGLVIAAEAKIYLMLNKPRGLVTTRHDPEGRPTVYDCLKDFEIPHL 120

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
             VGRLD  +EGLLL TND   A++L  P T   + Y V+    +D + +  +  GI   
Sbjct: 121 SPVGRLDKASEGLLLFTNDTEFAQILLDPITHVTKTYHVQIDRIMDDEAIAAMTSGIRHD 180

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           G       V    Q   N+W+ V L EG+NR+I+++ E    +  RL+R++ G  +LG L
Sbjct: 181 GELLTATAVRRLRQGDRNSWIEVELDEGRNRQIRRMLEALGTECLRLVRVAIGGLELGEL 240

Query: 229 LAGSTREVSKKILREQLGPHLLEEAQ 254
             G+ R ++   L+        E A+
Sbjct: 241 PKGAVRALTAAELQALHRSAGTERAR 266


>gi|312863475|ref|ZP_07723713.1| pseudouridylate synthase [Streptococcus vestibularis F0396]
 gi|311101011|gb|EFQ59216.1| pseudouridylate synthase [Streptococcus vestibularis F0396]
          Length = 239

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 64/239 (26%), Positives = 108/239 (45%), Gaps = 6/239 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++ +AG  SR +V+++I  ++V V+GIL +R  +NV ++   I V G  L     
Sbjct: 1   MRLDKLLGQAGYGSRNQVKKLIRSRQVYVDGILADRDNLNVDASLQTITVSGKELEHTPE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +                       +  VGRLD NTEGL+L+TN+G L  
Sbjct: 61  VYYLMNKPAGVVSARSDKEHQTVIDLIKPEDQRDGLYPVGRLDRNTEGLVLITNNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V  +  +  D     + G+V +        Q+ + +     +   +
Sbjct: 121 AMLHPGYHVAKTYYVEVNDILGPDAPAFFESGVVFEDGTICKSAQLEILSSASDKSCARI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LREQLG 246
            + EGK  ++KK+F  +  KV  L RIS+G F+L   +  GS R +++     LR  LG
Sbjct: 181 TISEGKFHQVKKMFLAYGVKVTYLKRISFGAFKLDEGIAVGSYRVLTEAEKVILRTYLG 239


>gi|270292060|ref|ZP_06198275.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           M143]
 gi|270279588|gb|EFA25430.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           M143]
          Length = 240

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 99/229 (43%), Gaps = 4/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQINEERDEIRFDGQVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            +  +    V  VGRLDI+T GLLLLTNDG LA 
Sbjct: 61  VYYMMNKPQGVISATEDSKHRTVLDLLDDVARSKEVFPVGRLDIDTHGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVT 190
            L  P     + Y  +  G + Q+ +    +GI ++       ++ L +     + + V 
Sbjct: 121 ALLSPKRHVDKTYLAQVEGIMTQEDVETFAEGIPLKDFTCQPARLELVSVDPEKNQSLVR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSK 238
           V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K
Sbjct: 181 VTIAEGKFHQVKRMVAYCGKEVVDLQRLTMGALILDEKLKRGEWRRLTK 229


>gi|269102754|ref|ZP_06155451.1| ribosomal small subunit pseudouridine synthase A [Photobacterium
           damselae subsp. damselae CIP 102761]
 gi|268162652|gb|EEZ41148.1| ribosomal small subunit pseudouridine synthase A [Photobacterium
           damselae subsp. damselae CIP 102761]
          Length = 232

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 47/231 (20%), Positives = 97/231 (41%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +      +R+E  +++  + V+VNG +++  A+ V     +E  G  L      
Sbjct: 1   MRLDKFLCTTLGITRKEAGKILKDKLVEVNGEIVKNGALKVTDDCDVEFSGRTLSLQGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      + +   D    +           R+   GRLD +T GL+L+T+DG  +  
Sbjct: 61  YYMLNKPSGYVCSH-VDDFNPTVFILFDEVAPERMHVAGRLDGDTTGLVLVTDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +++  +   ++G+ ++G        ++ +  +K +     +
Sbjct: 120 ITSPRHVCEKTYYVETADPIEESYIQAFEEGVQLRGEKELTLPAKLEILEEKVA----LL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R   G  +L   L  G  R +++  +
Sbjct: 176 TITEGKYHQVKRMFAAMGNKVELLHRERVGAIELDDDLEPGEYRPLTEDEI 226


>gi|291279397|ref|YP_003496232.1| ribosomal small subunit pseudouridine synthase A [Deferribacter
           desulfuricans SSM1]
 gi|290754099|dbj|BAI80476.1| ribosomal small subunit pseudouridine synthase A [Deferribacter
           desulfuricans SSM1]
          Length = 239

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 68/234 (29%), Positives = 120/234 (51%), Gaps = 5/234 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
                R++K+IA +G  SRRE +R+I    V VNG+++   A      DH+ V+G  L  
Sbjct: 5   KKELIRLNKLIASSGKYSRREADRLIQNGFVLVNGVVITNPAEKFSINDHVVVNGEKLDF 64

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ++  +  Y     ++T++     + ++ D      +R+   GRLD  +EGL++ TNDG 
Sbjct: 65  NKKVYIKFYKPIK-VLTSYDKYRDKKSLLDIEFFKKNRLGYSGRLDYESEGLIIFTNDGD 123

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   ++ PS++  + Y V     +++ +L L++ G+  + I Y   ++        N   
Sbjct: 124 LIYKIQHPSSRIEKEYIVAVDKILEEKELELIRAGLKTKEIKYLPCKINYL----GNYTY 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + L EGK REI+ +F+FF   V +L R+  GP ++  L  G  + +SKK + E
Sbjct: 180 NIVLYEGKKREIRNIFKFFKINVKKLKRVRIGPIRIVDLKPGEYKHLSKKEIEE 233


>gi|218689259|ref|YP_002397471.1| 23S rRNA pseudouridylate synthase B [Escherichia coli ED1a]
 gi|218426823|emb|CAR07673.2| 23S rRNA pseudouridylate synthase [Escherichia coli ED1a]
          Length = 291

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 86/288 (29%), Positives = 128/288 (44%), Gaps = 10/288 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V +     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEITPRLKIRIDGHLISVRE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           E +       ++V ++      +     R            R    ++
Sbjct: 242 ELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGGRRSGGRNN 289


>gi|260494116|ref|ZP_05814247.1| pseudouridylate synthase [Fusobacterium sp. 3_1_33]
 gi|260198262|gb|EEW95778.1| pseudouridylate synthase [Fusobacterium sp. 3_1_33]
          Length = 226

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 68/229 (29%), Positives = 107/229 (46%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   GI SR+EV+++I+   + VNG+    A  N+    D IE +   L   + 
Sbjct: 1   MRLDKFLVECGIGSRKEVKKLISNNEITVNGMSNISAKDNIDENSDIIEYNEEKLEYKKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +  K   +  T    +           I   +  VGRLD +TEGLLL TNDG L  
Sbjct: 61  RYYIMNKKSGYITATEDFKENTVMDLLPEWVIKKDLAPVGRLDKDTEGLLLFTNDGKLNH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VY V     +  + +  L++G+ I        +V    +K S+  + + 
Sbjct: 121 KLLSPKNHVDKVYYVEIKNNISDEDIFKLEQGVDIGNYISQPAKV----EKISDNKIYLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++EGK  +IKK+ E  N KV  L R+S+G  +L  L  G  REV+ + +
Sbjct: 177 IKEGKFHQIKKMLEAINNKVCYLKRVSFGRLKLNDLALGEVREVNLEDI 225


>gi|291613735|ref|YP_003523892.1| RNA-binding S4 domain protein [Sideroxydans lithotrophicus ES-1]
 gi|291583847|gb|ADE11505.1| RNA-binding S4 domain protein [Sideroxydans lithotrophicus ES-1]
          Length = 280

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 76/275 (27%), Positives = 121/275 (44%), Gaps = 9/275 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           + +   +R+ KV+A+AGI SRRE+E  I+  RV VNG +     + V   D ++VDG  +
Sbjct: 6   ETSQPGERLQKVLAQAGIGSRREMEEWISAGRVTVNGTVAT-LGMRVAEGDKVQVDGRNV 64

Query: 68  RKA------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           R            L  + +   +V+     +  S           + I++GRLD NT GL
Sbjct: 65  RLQLQTEQTMPRILLYHKQEGEIVSRDDPGERASVFDALPKLRGQKWIAIGRLDFNTSGL 124

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLD 180
           L+ T  G LA  L  P  +  R Y VR  GQ+  + +  + K  I +        Q++ +
Sbjct: 125 LIFTTSGELANRLMHPRFEVEREYAVRVQGQMTPEHMRQVTKEGIELDDGVVRFEQLSDE 184

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
             +G N W  + L+EG+NR +++ FE     V+RL+R+ +G   L   +  G   E+   
Sbjct: 185 GGEGFNHWYRLVLKEGRNRVVRRTFEALGLPVSRLMRVRFGIIGLPPRIKRGMMAELGDN 244

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNI 274
            +R  L    L                L R R   
Sbjct: 245 EVRSILEWVGLPVGVARQVVDDGRRNKLQRARIRK 279


>gi|238898376|ref|YP_002924057.1| 16S rRNA pseudouridylate 516 synthase [Candidatus Hamiltonella
           defensa 5AT (Acyrthosiphon pisum)]
 gi|229466135|gb|ACQ67909.1| 16S rRNA pseudouridylate 516 synthase [Candidatus Hamiltonella
           defensa 5AT (Acyrthosiphon pisum)]
          Length = 240

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 49/244 (20%), Positives = 106/244 (43%), Gaps = 7/244 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     SR++V R + ++RV ++  ++   AV ++    +  D   L+     
Sbjct: 1   MRLDRFLSHQLGKSRKQVTRALKEKRVILDSKVITNGAVKLLPEQKVLFDQQLLKYPITG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G + +  DP           ++   + + GRLDI+  GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPKGYLCSTRDPHHPVVNDFFDETVSGELHAAGRLDIDATGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           L  P     + Y V     +  D       G+ ++         Q+ + T +       +
Sbjct: 121 LTSPKYHCKKTYWVTLASPISHDPTQNFLDGLRLKNEKTLTRPAQLKIVTPQSM----EL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLL 250
            + EG+  ++K++F      V  L R+  G  +L   L+ G  R ++K+ +   +    +
Sbjct: 177 TITEGRYHQVKRMFAAIGHHVTELHRMQIGSIKLDEALMPGQYRLLTKQEINSIISFEHM 236

Query: 251 EEAQ 254
           ++  
Sbjct: 237 DQRS 240


>gi|331085062|ref|ZP_08334149.1| hypothetical protein HMPREF0987_00452 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330408762|gb|EGG88227.1| hypothetical protein HMPREF0987_00452 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 241

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 65/237 (27%), Positives = 112/237 (47%), Gaps = 5/237 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A   + +R EV++MI +  V V+G+++++    V      +   G  +   +  
Sbjct: 7   RLDKYLADMQVGTRSEVKQMIRKGLVTVDGLIVKKPEEKVDCEKQVVVCSGAIVSYHQYE 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      +V+   DP  ++ +          +   GRLD +TEGLLL+TNDG LA  
Sbjct: 67  YYMLNKPAG-VVSATEDPRDKTVIDLIEDRRRKDLFPAGRLDKDTEGLLLITNDGALAHD 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           L  P     + Y  +  G V ++ + L  KGI I +        +T+    G  + +T+ 
Sbjct: 126 LLSPKKHVDKKYYAKIEGTVTEEDVELFGKGIDIGEKRVTLPAVLTIL-SSGEESEITLT 184

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
           +REGK  ++K++FE    KV  L R+S G   L   LL G  R+++++ L +     
Sbjct: 185 IREGKFHQVKRMFEAVGKKVTYLKRLSMGSLVLDEKLLPGEYRKLTEQELTQLKQMR 241


>gi|33152184|ref|NP_873537.1| pseudouridine synthase [Haemophilus ducreyi 35000HP]
 gi|33148406|gb|AAP95926.1| probable pseudouridine synthase [Haemophilus ducreyi 35000HP]
          Length = 354

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 91/284 (32%), Positives = 132/284 (46%), Gaps = 10/284 (3%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVD 63
              +     +++ K++ARAG  SRRE+E +IA  RV V+G +      V+V +T  I +D
Sbjct: 66  QDKKTKIVGEKLQKILARAGQGSRRELEEVIAAGRVSVDGKIASLGDRVHVNATTKIRID 125

Query: 64  GVPL-----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           G  +     +K     L  Y     L T        +          SR I+VGRLDINT
Sbjct: 126 GTLINLVTAQKEICRVLMYYKPEGELCTRADPEGRATVFDRLPRLSGSRWIAVGRLDINT 185

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       Q+ 
Sbjct: 186 SGLLLFTTDGDLANRLMHPSHEVEREYSVRVFGQVDDAMLQRLRKGVQLEDGPANFKQIK 245

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
                G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+ 
Sbjct: 246 AVGGTGLNQWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKLEKGLPRGGWEEMG 305

Query: 238 KKI---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEV 278
            +    LR+ +G     E +V++      +      +       
Sbjct: 306 LEQVNYLRDLVGLPAETETKVDVTKNRRRTNIRQIRKAVKQHSK 349


>gi|325962913|ref|YP_004240819.1| pseudouridine synthase family protein [Arthrobacter
           phenanthrenivorans Sphe3]
 gi|323469000|gb|ADX72685.1| pseudouridine synthase family protein [Arthrobacter
           phenanthrenivorans Sphe3]
          Length = 400

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 85/236 (36%), Positives = 128/236 (54%), Gaps = 4/236 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
           +    R+ KV+A AG+ASRR  E MIA+ RV+V+G ++    V V   T  I VDG+ ++
Sbjct: 156 DADGVRLQKVMASAGVASRRVCEEMIAEGRVEVDGQVVTELGVRVDPKTAVIHVDGIRIQ 215

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLLT 125
             E     +++KP G+V+T  DP+GR  + D L +  ++      VGRLD+ TEGLLLLT
Sbjct: 216 LDENMVYMVFNKPKGVVSTMEDPEGRPCISDFLKNAKNKGERLFHVGRLDVATEGLLLLT 275

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  PS +  + Y V+  G   Q     LK+G+ ++          L      
Sbjct: 276 NDGELANRLTHPSYEVPKTYLVQVRGPFPQGIGAQLKEGVELEDGFASVDSFRLVDSTPG 335

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +  + V L  GKNR ++++F+   + V RL+R+  GP  LG    GS R + K+ +
Sbjct: 336 HVLIEVVLHSGKNRIVRRLFDAVGFPVLRLVRVKVGPIGLGDQRQGSIRNLGKQEV 391


>gi|261211757|ref|ZP_05926044.1| ribosomal small subunit pseudouridine synthase A [Vibrio sp. RC341]
 gi|260839107|gb|EEX65739.1| ribosomal small subunit pseudouridine synthase A [Vibrio sp. RC341]
          Length = 231

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 47/231 (20%), Positives = 94/231 (40%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E     +      
Sbjct: 1   MRLDKFLCDALGTTRKESTQLLKSGEVTVDDVVQKSGAFKLKETSRVEWQEREITLHGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     + +       ++            +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDG-FNQTAFTLLDEVNIEDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + YRV     +  D  +   +GI ++G        Q+ +     S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYADQFTQGIELRGERELTLPAQLEVV----SETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R   G   L   L  G  R +++  +
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDEALEPGEYRYLTEDEV 226


>gi|241662811|ref|YP_002981171.1| pseudouridine synthase [Ralstonia pickettii 12D]
 gi|240864838|gb|ACS62499.1| pseudouridine synthase [Ralstonia pickettii 12D]
          Length = 594

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 83/321 (25%), Positives = 138/321 (42%), Gaps = 7/321 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K + +  E+  P ++ K++A AG+ SRR++E +I Q RV VNG+        +++TD + 
Sbjct: 202 KARELTSEDDAP-KLHKILADAGLGSRRDMEDLILQGRVSVNGLPA-HIGQRILATDQVR 259

Query: 62  VDGVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           V+G  +++         L  +     +V+        +           + ++VGRLD N
Sbjct: 260 VNGKLIQRKLPNKPPRVLLYHKPSGEIVSQSDPEGRPTVFDALPRMKTGKWVAVGRLDFN 319

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+ T  G +A     P     R Y VR  G++ +     L  GI +Q      ++ 
Sbjct: 320 TEGLLIFTTSGDIANRFMHPRYGVEREYAVRTLGELAETDRQKLLHGIPLQDGEANFLRC 379

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EV
Sbjct: 380 VDGGGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEV 439

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           S + +R  +G   ++    +            R    ++          + N   +    
Sbjct: 440 SAEDVRTLMGTLGMKVPTASSGGGQDRQGNRRRGPAPVLMGPMSSGFAGEANFQSRGMGI 499

Query: 297 KQKKLATPVHRRNLASNVWMA 317
           +    A P  RR  +      
Sbjct: 500 ENGNRAQPAQRRPSSPRQPDP 520


>gi|261378838|ref|ZP_05983411.1| ribosomal large subunit pseudouridine synthase F [Neisseria cinerea
           ATCC 14685]
 gi|269144818|gb|EEZ71236.1| ribosomal large subunit pseudouridine synthase F [Neisseria cinerea
           ATCC 14685]
          Length = 252

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 70/255 (27%), Positives = 110/255 (43%), Gaps = 20/255 (7%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K          R+SK IA+ G+ SRRE +  I Q  V VNG         V  TD I
Sbjct: 1   MNSKISSDHTEDTIRLSKRIAQLGLCSRREADGYIEQGWVTVNGKTA-VLGQKVSPTDRI 59

Query: 61  EVD---------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           E++                 P+          Y     L+T+ +  +G ++     P   
Sbjct: 60  ELNKKAHEQQAARITILLNKPVGYVSAQAEKGYKSAAELITSENRWEGDTSRIRFDPKHK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             +   GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+
Sbjct: 120 IGLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGL 179

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G      +V    +      +   L++GK R+I+++ E    +V  L RI  G  +L
Sbjct: 180 SLDGEKLRPAKVEWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>gi|254372898|ref|ZP_04988387.1| ribosomal large subunit pseudouridine synthase B [Francisella
           tularensis subsp. novicida GA99-3549]
 gi|254374352|ref|ZP_04989834.1| ribosomal large subunit pseudouridine synthase B [Francisella
           novicida GA99-3548]
 gi|151570625|gb|EDN36279.1| ribosomal large subunit pseudouridine synthase B [Francisella
           novicida GA99-3549]
 gi|151572072|gb|EDN37726.1| ribosomal large subunit pseudouridine synthase B [Francisella
           novicida GA99-3548]
 gi|332678236|gb|AEE87365.1| Ribosomal large subunit pseudouridine synthase B [Francisella cf.
           novicida Fx1]
          Length = 271

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 86/259 (33%), Positives = 124/259 (47%), Gaps = 9/259 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+  N   +   P+R+ K++A+ GI SRR++E  I Q RVKVNG +           D I
Sbjct: 1   MRRANQNNDKN-PERLQKLLAKYGIGSRRKIEEYIEQGRVKVNGKVAT-LGDKASEADKI 58

Query: 61  EVDGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
             DG  L            +  + +   + T+  + D ++          SR I VGRLD
Sbjct: 59  SFDGKALHSYGQPMTRPRVVIYHKREGEVCTSKDEKDRQTVFDSLPKLAKSRWIMVGRLD 118

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGD 174
           INT GLLL T DG LA  L  PS Q  R Y VR  GQ    + +N LK+GI ++      
Sbjct: 119 INTTGLLLFTTDGDLANRLMHPSYQIEREYAVRVFGQQLSDETINKLKEGIQLEDGMAKF 178

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGST 233
             +     +G+N W  V L EG+NRE++++FE     V+RL RI +G   L   +  G T
Sbjct: 179 NNIKFSGGEGANLWYYVTLSEGRNREVRRMFEAVGVTVSRLTRIRFGDIILPKFVSRGKT 238

Query: 234 REVSKKILREQLGPHLLEE 252
            E++   +        L+E
Sbjct: 239 LELNPSEVNRLRKSVKLKE 257


>gi|322412052|gb|EFY02960.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           dysgalactiae subsp. dysgalactiae ATCC 27957]
          Length = 243

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 56/233 (24%), Positives = 100/233 (42%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+ ++ ++ + VN  +     V +    D +   G PL     
Sbjct: 1   MRLDKFLVETGVGSRSQVKSLLKKKAILVNQEVETSPKVQINEHKDVVTYLGKPLTYEAF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      L  T            +  +    V  VGRLD +T GLLLLTN+G LA 
Sbjct: 61  VYYVLNKPAGFLSATKDRAQATVIDLLDETARQKDVFPVGRLDKDTRGLLLLTNNGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVT 190
            L  P     + Y  +  G + +   +   KGI ++       ++ +  +        V+
Sbjct: 121 DLLSPKKHVTKEYLAKVAGIMTEADKDDFAKGISLKDYQCLPAKLEVLDKDVSQETCVVS 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + ++EGK  ++K++      +V  L R+S GP +L  +L  G  R ++ + L+
Sbjct: 181 ITIQEGKFHQVKRMVAACGKEVLELQRLSMGPLRLDPSLAEGDFRRLTSEELQ 233


>gi|149907885|ref|ZP_01896553.1| ribosomal large subunit pseudouridine synthase B [Moritella sp.
           PE36]
 gi|149808891|gb|EDM68822.1| ribosomal large subunit pseudouridine synthase B [Moritella sp.
           PE36]
          Length = 335

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 88/337 (26%), Positives = 145/337 (43%), Gaps = 14/337 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG+ SRRE+E +IA+ RV VNG ++      V   D I +DG P+   + 
Sbjct: 2   SEKLQKVLARAGLGSRREMEAVIAEGRVSVNGEMVT-LGTRVEEVDRIRLDGNPVSVVKE 60

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  +     L T       ++      P    R I++GRLDINT GLLL T D
Sbjct: 61  EDAVCRILAYHKPEGELCTRKDPEGRKTVFDRLPPLKSGRWIAIGRLDINTSGLLLFTTD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----K 183
           G LA  L  PS +  R Y  R  G+V    +  L+ G+ ++       ++    +    +
Sbjct: 121 GELANRLMHPSHEVEREYSCRIFGEVTPKIIQNLRMGVELEDGPAKFQKIKGVAEGTGGE 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           G N W  V L EG+NRE+++++E    +V+RLIRI YG   L   L  G   E++ + + 
Sbjct: 181 GLNQWYNVLLSEGRNREVRRLWESQGIQVSRLIRIRYGSLVLDRRLPRGGWSELALEEIN 240

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
                  L        A     +     +  I   + ++  R K   S + G   ++   
Sbjct: 241 ---YLRTLVSLPPETTARSLERKETRIRQGRIRRSLKNNDARQKPTRSGRLGKEIEETTE 297

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
           +    R   +   +         +   +  +  +R+ 
Sbjct: 298 SRGKSRTKPTGSGIPLHRGKKGPAKQQRGPKAKKRTR 334


>gi|146312421|ref|YP_001177495.1| 16S rRNA pseudouridylate synthase A [Enterobacter sp. 638]
 gi|145319297|gb|ABP61444.1| ribosomal small subunit pseudouridine synthase A [Enterobacter sp.
           638]
          Length = 235

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 104/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G ++  +A  ++    +E DG  L +   +
Sbjct: 1   MRLDKFIAQQLSVSRAIAGREIRASRVTVDGDIVRDSAFKLLPEHDVEFDGNTLTQQIGS 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLEEPVAHKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVMLESPVADDTAEQFTKGVQLHNEKDLTKPAVLEVI----TPTEVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 177 TIIEGRYHQVKRMFAAVGNRVVGLHRERIGEIALDPELEPGEYRPLTEEEI 227


>gi|329768850|ref|ZP_08260278.1| hypothetical protein HMPREF0433_00042 [Gemella sanguinis M325]
 gi|328837213|gb|EGF86850.1| hypothetical protein HMPREF0433_00042 [Gemella sanguinis M325]
          Length = 235

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 104/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K I+   + SR E +++I +  V VN +L+++    V    D + +DG  L   + 
Sbjct: 1   MRLDKYISSITVYSRAETKKIIKKG-VLVNNVLVKQPDYQVDEENDQVVIDGKSLFYQKH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      +  T    D       N      +   VGRLD +TEGL+LLTNDG LA 
Sbjct: 60  VYIMMNKPGNIISATEDKKDTTVIDILNEKDRLFKPFPVGRLDKDTEGLMLLTNDGELAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P    ++ Y V   G++  + + +++ G+V++         + + T     +   +
Sbjct: 120 KLISPKKDVIKKYYVEVDGELKVEHVTIIRDGVVLEDGYKTKCAALEILTSNTEKSRAYI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            + EGK  ++K++ +     V  L R+S G   L   L  G  R ++   L+
Sbjct: 180 SITEGKFHQVKRMMKSLGVNVTYLKRLSIGSLVLDESLKLGEYRYLTDTELK 231


>gi|186685861|ref|YP_001869057.1| pseudouridine synthase [Nostoc punctiforme PCC 73102]
 gi|186468313|gb|ACC84114.1| pseudouridine synthase [Nostoc punctiforme PCC 73102]
          Length = 252

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 82/240 (34%), Positives = 126/240 (52%), Gaps = 12/240 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPL--RKA 70
           +R+ K++A+ GIASRRE E MI   RV++NG L       V    D I +DG  L  ++ 
Sbjct: 3   ERLQKILAQWGIASRREAEEMIRHSRVQINGKLA-HLGQKVDPQKDAIAIDGKTLSEKQR 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTND 127
                 L HKP G+V+T  DP  R TV D LP        +  VGRLD ++ G L+LTND
Sbjct: 62  PALIYLLLHKPAGVVSTCYDPHRRKTVLDLLPKELREGSGIHPVGRLDADSTGALILTND 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  P     + YRV   G   +  L + ++G+V++G      +V L   +   +
Sbjct: 122 GNLTFGLTHPRHSISKTYRVLVKGHPPEVVLQMWREGVVLEGRKTRAAEVHLIEHRAEQS 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-----LLAGSTREVSKKILR 242
           ++ + L+EG+NR+I+++ +   + V +L R + GP QL T     L  G  R ++ + +R
Sbjct: 182 FLEIVLQEGRNRQIRRIAQQLGYPVIKLHRTAIGPIQLQTPKEPLLSEGKYRSLTDREIR 241


>gi|257438815|ref|ZP_05614570.1| ribosomal small subunit pseudouridine synthase A [Faecalibacterium
           prausnitzii A2-165]
 gi|257198724|gb|EEU97008.1| ribosomal small subunit pseudouridine synthase A [Faecalibacterium
           prausnitzii A2-165]
          Length = 235

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 57/230 (24%), Positives = 94/230 (40%), Gaps = 4/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R E + ++ + RV VNG + ++    +   D + VDG PL   +  
Sbjct: 1   MRLDKYLAETAQCTRSEAKTLLNRGRVTVNGAVCKKGDTQLREGDSVAVDGAPLAYRQFV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L      +  +    D               +  VGRLD  + G +LLT+DGG A  
Sbjct: 61  YLMLNKPEGVVSASTDKRDTTVVDLIGDAYPRRELFPVGRLDKTSTGFVLLTDDGGFAHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG-DMQVTLDTQKGSNAWVTVG 192
           +  P     + Y V     + ++      +G+ +         +V   T  G    V   
Sbjct: 121 ILAPKRHVSKTYTVVIDTPLTEEMRRGFAEGVTLADGTALSPAEVEALTPDGLTVKVR-- 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           LR+G   +IK++F  +   VN L R + G   L   L  G  RE+S + +
Sbjct: 179 LRQGVYHQIKRMFGVYGAGVNALHRDAIGGLALDPALAPGQWRELSAEEV 228


>gi|240080549|ref|ZP_04725092.1| Pseudouridine synthase [Neisseria gonorrhoeae FA19]
 gi|240118135|ref|ZP_04732197.1| Pseudouridine synthase [Neisseria gonorrhoeae PID1]
 gi|240123684|ref|ZP_04736640.1| Pseudouridine synthase [Neisseria gonorrhoeae PID332]
 gi|260440347|ref|ZP_05794163.1| Pseudouridine synthase [Neisseria gonorrhoeae DGI2]
 gi|268603851|ref|ZP_06138018.1| pseudouridine synthase [Neisseria gonorrhoeae PID1]
 gi|268682316|ref|ZP_06149178.1| pseudouridine synthase [Neisseria gonorrhoeae PID332]
 gi|268587982|gb|EEZ52658.1| pseudouridine synthase [Neisseria gonorrhoeae PID1]
 gi|268622600|gb|EEZ55000.1| pseudouridine synthase [Neisseria gonorrhoeae PID332]
          Length = 349

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 72/256 (28%), Positives = 125/256 (48%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+
Sbjct: 84  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHV 142

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++  L +  ++++       
Sbjct: 203 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTTEQMRSLTEEGVMLEDGLAKVE 262

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  + ++EG+NRE++++FE     V+RL+R+++GP  L   L  G   
Sbjct: 263 RIREQGGEGANKWYNIVIKEGRNREVRRIFESQGLTVSRLVRVAFGPIGLPNRLKRGQFY 322

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   L    +
Sbjct: 323 ELNPAEVANILKWADM 338


>gi|283769551|ref|ZP_06342447.1| pseudouridylate synthase [Bulleidia extructa W1219]
 gi|283103819|gb|EFC05205.1| pseudouridylate synthase [Bulleidia extructa W1219]
          Length = 231

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 69/236 (29%), Positives = 109/236 (46%), Gaps = 9/236 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +V+A A + SR +V+ M+   RV VNG +   +++ V    D I +D   L+ A+ 
Sbjct: 1   MRLDRVLANASVGSRTQVKNMVKNGRVSVNGKIALASSMMVDPNQDVIRIDDEILQYAKY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L LY     +  T    D        L   +  +   GRLD +TEGLLL+TNDG LA 
Sbjct: 61  QYLMLYKPAGYISATEGRYDPTVLE---LVPNYKGLFPCGRLDKDTEGLLLMTNDGRLAH 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V     + Q+ +  +++GI  + I Y   ++ +      +   T+ 
Sbjct: 118 NLLSPKKHVEKEYYVEHQLPLSQEDVLCIERGIRYKNITYKGAKLKIL----DDLQCTII 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGP 247
           L+EGK  EIK +F   + KV  L RI      L   L  G  R +S++ + +    
Sbjct: 174 LQEGKYHEIKNIFLAIDNKVTYLKRIRMKNLILDETLKKGEYRPLSEEEIGDLKQL 229


>gi|291087689|ref|ZP_06572058.1| ribosomal small subunit pseudouridine synthase A [Clostridium sp.
           M62/1]
 gi|291074338|gb|EFE11702.1| ribosomal small subunit pseudouridine synthase A [Clostridium sp.
           M62/1]
          Length = 477

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 61/250 (24%), Positives = 112/250 (44%), Gaps = 14/250 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R+ + +      SR EV++MI   RV V+G +   A   +  +   + +DG  +  
Sbjct: 7   EKAMRLDRYLVEMKKGSRSEVKKMIKSGRVSVDGEICREAERKIQPSASEVSLDGTQVGY 66

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           A      L      +V+   D   ++ V     +    +  VGRLDI+TEGLLL+TNDG 
Sbjct: 67  AAYEYFMLNKPAG-VVSATEDGRHKTVVSLIEDAKRRDLFPVGRLDIDTEGLLLITNDGK 125

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKG---- 184
           LA  L  P     + Y  R  G++ ++ +   K+G+ ++        ++ +         
Sbjct: 126 LAHRLLSPKKHVDKTYFARVEGRLPENAIEQFKEGLTLEDGTRTLPARLVIQKASETAED 185

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVS 237
                 S + + + + EGK  ++K++FE    +V  L R+S G  +L   L  G+ R ++
Sbjct: 186 DGKADSSLSEIELTIHEGKFHQVKRMFEAVGCRVVYLKRLSMGSLRLDESLAPGAYRRLT 245

Query: 238 KKILREQLGP 247
           ++ + +  G 
Sbjct: 246 EEEISKLQGE 255


>gi|269139658|ref|YP_003296359.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthase [Edwardsiella tarda EIB202]
 gi|267985319|gb|ACY85148.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthase [Edwardsiella tarda EIB202]
 gi|304559528|gb|ADM42192.1| Ribosomal small subunit pseudouridine synthase A [Edwardsiella
           tarda FL6-60]
          Length = 235

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 56/231 (24%), Positives = 99/231 (42%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I++    SR  V R +   RV V+G++    ++ V     +  +G  L      
Sbjct: 1   MRLDKFISQQLGISRSLVIRELRASRVTVDGVVSRSGSLQVTPDQEVAYEGNVLAFITGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V +  DPD  + ++     +  ++ + GRLD++T GL+LLT+DG  +  
Sbjct: 61  RYFMLHKPEGYVCSTDDPDHATILYFIDEPMAEKLHAAGRLDLDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +         +GI++ G        Q+           V +
Sbjct: 121 ITSPRHHCEKSYLVTLEQPLAPQTAAQFAEGILLNGETDLTKPAQLEAF----DEHHVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F     +V  L R   G   L   L  G  R +S   +
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVVGLHRERIGAIALDAALAPGEYRALSDDEV 227


>gi|291294585|ref|YP_003505983.1| pseudouridine synthase [Meiothermus ruber DSM 1279]
 gi|290469544|gb|ADD26963.1| pseudouridine synthase [Meiothermus ruber DSM 1279]
          Length = 257

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 57/236 (24%), Positives = 101/236 (42%), Gaps = 6/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAER 72
           +R+ KV+   G+ SR+E+ R+     + +NG ++  A      +  HIEV G PL   + 
Sbjct: 19  ERLDKVLGHLGVGSRKEIHRLARAGLITINGKIVADAGFKFDPSQAHIEVAGEPLVYQKF 78

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L      + +T        T         +  + VGRLD +TEGLLLLT DG L  
Sbjct: 79  FYLLLNKPAGYITSTKDPSGTPITALLPEEFWRNDWMPVGRLDKDTEGLLLLTTDGELLH 138

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P  +  + Y V        + + +     + ++G      +            V +
Sbjct: 139 RLTHPRWKVTKRYYVELASPATPEDVAVFAAGTLELEGEPLQPAE---LYLGPDPRKVEL 195

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYG-PFQLGTLLAGSTREVSKKILREQLG 246
            LREG+  ++K++F     +V  L R+++G       L  G++R+++   ++    
Sbjct: 196 VLREGRFHQVKRMFAARGNQVTYLKRLAFGPLQLPPNLPPGASRQLTPDEIKALYE 251


>gi|330813627|ref|YP_004357866.1| ribosomal large subunit pseudouridine synthase B [Candidatus
           Pelagibacter sp. IMCC9063]
 gi|327486722|gb|AEA81127.1| ribosomal large subunit pseudouridine synthase B [Candidatus
           Pelagibacter sp. IMCC9063]
          Length = 246

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 89/239 (37%), Positives = 140/239 (58%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + +E     R+SK +A   + SRRE+ERMI   R+ +NG +L      V  TD I++DG 
Sbjct: 1   MKKELPEKVRISKFLASYNVGSRREIERMIENGRIYLNGEILTTPVHFVNKTDSIKLDGK 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            L   +  +++ ++KP   + + +  D R  V+D LP  F   I  GRLD+N+EGLL++T
Sbjct: 61  LLLFKKFKQIYKFYKPTDCICSKNKQDERKIVYDLLPKRFKNFIFAGRLDVNSEGLLIVT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +AR LELP  +++R YRVR +G  ++ K++ L KG  I GI Y      L  +   
Sbjct: 121 NDGEVARSLELPKNKFVRKYRVRVYGVCEEQKIDNLSKGRKIDGIQYRPFNYKLFNKDKK 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           N W+ + L+EGKNREI+++    + +VN+L R+ +GPF++  L  G  +    K +R+ 
Sbjct: 181 NFWIEMELKEGKNREIRELMRSIDLRVNKLTRLEFGPFKISNLKPGEIKTAEPKEIRQY 239


>gi|167894529|ref|ZP_02481931.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 7894]
          Length = 395

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 76/274 (27%), Positives = 124/274 (45%), Gaps = 6/274 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 90  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 148

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 149 GKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNTE 208

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 209 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRIRD 268

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 269 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 328

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRP 272
             +R  +    L+    +            +  P
Sbjct: 329 AQVRRLMSTVGLKAPTEDKGGKRGGPAERRQPDP 362


>gi|167845952|ref|ZP_02471460.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei B7210]
          Length = 384

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 76/303 (25%), Positives = 131/303 (43%), Gaps = 7/303 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 84  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 142

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 143 GKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNTE 202

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 203 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQRLLHGVELDDGPANFLRIRD 262

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 263 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 322

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             +R  +    L+    +            R    + + +          +  +    ++
Sbjct: 323 AQVRRLMSTVGLKAPTEDKGG-KRGGPAERRQPDPMQTSMGFINREPVLTTHGQLDQPRR 381

Query: 299 KKL 301
            + 
Sbjct: 382 GRR 384


>gi|153855785|ref|ZP_01996786.1| hypothetical protein DORLON_02807 [Dorea longicatena DSM 13814]
 gi|149751912|gb|EDM61843.1| hypothetical protein DORLON_02807 [Dorea longicatena DSM 13814]
          Length = 248

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 61/254 (24%), Positives = 112/254 (44%), Gaps = 13/254 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K ++ AG+ SRRE +R+I    V V+G       + V     + V    ++   + 
Sbjct: 2   IRLNKYLSEAGVCSRREADRLIESGVVTVDGKNA-VPGMKVEDGQEVCVGKKRIKSKTKK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +   +KP G+V T    +          +   RV   GRLD ++EGLL++TNDG L   
Sbjct: 61  TVLAVYKPAGIVCTEDKRE--KKNIIRFLNYPLRVTYAGRLDKDSEGLLIMTNDGDLING 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC------YGDMQVTLDTQKGSNA 187
           +        + Y+V  + ++  + +  + +G+ I+             +V    +K    
Sbjct: 119 MMRARFSHEKEYKVTVNKEITPEFIEKMSRGVHIRDREKNLDAVTRPCKV----RKNGKY 174

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
             ++ L +G NR+I+++ E   +KV  L RI     +LG L  G  R ++++ L+E  G 
Sbjct: 175 TFSIILTQGLNRQIRRMCEALGYKVTTLKRIRIMNVELGNLKPGEVRGLTEQELKELYGT 234

Query: 248 HLLEEAQVNLDAPI 261
               E +       
Sbjct: 235 VKERENERTGQPSE 248


>gi|300778150|ref|ZP_07088008.1| ribosomal large subunit pseudouridine synthase B [Chryseobacterium
           gleum ATCC 35910]
 gi|300503660|gb|EFK34800.1| ribosomal large subunit pseudouridine synthase B [Chryseobacterium
           gleum ATCC 35910]
          Length = 393

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 63/239 (26%), Positives = 113/239 (47%), Gaps = 1/239 (0%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K     +    R++K IA +GI SRRE + +I Q  V+VNG ++      V  TD +  
Sbjct: 150 NKIEKDVHKDSIRLNKYIANSGICSRREADELITQGLVEVNGKVVTEMGYQVQKTDRVVF 209

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG  +   +   + L      + TT  D   ++ +     +   R+  VGRLD +T G++
Sbjct: 210 DGQSITPEKPVYVLLNKPKGYISTTKDDKARKTVMDLVANASPYRLFPVGRLDRSTTGVI 269

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTNDG + + L  PS    ++Y V    ++  + L L+ +GI +        Q++    
Sbjct: 270 LLTNDGHMTKKLTHPSFDAKKIYHVTLDKKLTGEDLRLIAEGIRLDEGVAVVDQISYIEG 329

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           K  N  V + +  G NR I+++F+   ++V  L R+ +       +  G  R +++  +
Sbjct: 330 KPKN-EVGIEIHIGWNRVIRRIFQRLGYEVEALDRVMFAGLTKKNIKRGHWRILTELEV 387


>gi|300781239|ref|ZP_07091093.1| 16S rRNA uridine-516 pseudouridylate synthase [Corynebacterium
           genitalium ATCC 33030]
 gi|300532946|gb|EFK54007.1| 16S rRNA uridine-516 pseudouridylate synthase [Corynebacterium
           genitalium ATCC 33030]
          Length = 318

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 77/238 (32%), Positives = 118/238 (49%), Gaps = 4/238 (1%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
           ++     R+ KV+A+AG+ASRR  E MI + RV+VNG ++ +  V V    D I VDGV 
Sbjct: 72  KKRGDGIRLQKVLAQAGVASRRHSEVMIDEGRVEVNGKIVRQQGVRVDPNVDIIRVDGVR 131

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLL 123
           +   E  + +  +KP G+ TT  D  GR  V D +        R+  VGRLD +TEGLLL
Sbjct: 132 VNVNEDQQYFALNKPRGVHTTMEDELGRPCVGDFVADRVAAGQRLFHVGRLDADTEGLLL 191

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG L+  L  P     + Y     G+     +  LKKGI ++          +    
Sbjct: 192 LTNDGELSNRLMHPKYGVEKTYLATVLGEAKPALVRELKKGIELEDGVAKADYAQIVDTH 251

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              + + + + EG+   ++++ +   + V RL+R      QLG L  G+ R ++   L
Sbjct: 252 QGQSLIRLVIHEGRKHVVRRMLKEAGYPVQRLVRTKIHTVQLGELKPGAMRALNDSEL 309


>gi|295396784|ref|ZP_06806919.1| ribosomal large subunit pseudouridine synthase B [Brevibacterium
           mcbrellneri ATCC 49030]
 gi|294970368|gb|EFG46308.1| ribosomal large subunit pseudouridine synthase B [Brevibacterium
           mcbrellneri ATCC 49030]
          Length = 271

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 73/236 (30%), Positives = 118/236 (50%), Gaps = 1/236 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
           +  R+ KV+A AG+ SRR  E+MI   RV+V+G ++      +  T   + VD +P+  +
Sbjct: 32  SGVRLQKVMADAGLGSRRACEQMILDGRVEVDGHIVIELGTRIDPTKQRLVVDSMPIETS 91

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                +  +KP  +V++  DP+GR  + + +     R+  VGRLD  TEGLLLLTNDG +
Sbjct: 92  TEKVYFALNKPAKVVSSMGDPEGRRNLDEFVRDRTERLFHVGRLDYETEGLLLLTNDGDM 151

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P  +  + Y  +  G V +D    L++GI +           L   +   A V 
Sbjct: 152 ANRLTHPRYEIPKKYLAQVKGPVAKDVGARLREGIELDDGISRVDSFKLIDSQPGVALVE 211

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           V L  GKNR ++++       V RL+R  +GP +L     G  R++  + + E + 
Sbjct: 212 VILHSGKNRIVRRLLSAVGNPVLRLVRTEFGPIELAEQRQGKMRQLRPEEVSELMK 267


>gi|239623801|ref|ZP_04666832.1| pseudouridine synthase [Clostridiales bacterium 1_7_47_FAA]
 gi|239521832|gb|EEQ61698.1| pseudouridine synthase [Clostridiales bacterium 1_7_47FAA]
          Length = 243

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 63/235 (26%), Positives = 111/235 (47%), Gaps = 7/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G  +R +++ M+ + RV+VNG +++     +   TD + VD   +  A  
Sbjct: 1   MRLDKFLGEMGYGTRTQIKEMVRKGRVQVNGQVIKAPESKLAPETDQVMVDQSVVGYARM 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP  +V+  +D    + V     ++   +  VGRLD++TEGLL++TNDG +A 
Sbjct: 61  EYYM-LNKPKDVVSATTDSRYPTVVGLIGDALRKDLFPVGRLDVDTEGLLIITNDGEMAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSN---AW 188
            L  P     +VY  R  G++  +      +GIV+          +  +           
Sbjct: 120 NLLSPKKHVDKVYMARLSGRLPVNAKERFSEGIVLDDGVKTLPALLEYEGCGNGTEGLTE 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + +REGK  ++K++FE     V  L R+S GP  L   L  G  R ++++ +R
Sbjct: 180 VLLTIREGKFHQVKRMFEALGCHVEYLKRMSMGPLGLDPELEPGQYRPLTEEEIR 234


>gi|319782459|ref|YP_004141935.1| pseudouridine synthase [Mesorhizobium ciceri biovar biserrulae
           WSM1271]
 gi|317168347|gb|ADV11885.1| pseudouridine synthase [Mesorhizobium ciceri biovar biserrulae
           WSM1271]
          Length = 250

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 68/227 (29%), Positives = 109/227 (48%), Gaps = 1/227 (0%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTR 74
           +++ +++ G+ SR + E +IA+ RV+V G ++  AA+ V    D I VD  P+    +  
Sbjct: 19  LNRALSKLGLCSRTQAEVLIAEGRVRVGGKVVRDAALRVDLDRDRIVVDDRPVVAERKVY 78

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L      + T        +            V  VGRLD  +EGLLL+TND   A  L
Sbjct: 79  LMLNKPRGLVTTRDDPQQRDTVYACLEGLDLPFVSPVGRLDKASEGLLLMTNDTRFANRL 138

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P++   + Y V+     D   L  L+ G+++ G       + L    G  AW+ + L 
Sbjct: 139 MDPASHLPKTYHVQIGTVPDAPMLETLRAGVIVDGEVLTANAIELLRSGGRTAWLEIVLD 198

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           EG+NR I+++      +V RLIRI+ G   LG L  G+ R ++ + L
Sbjct: 199 EGRNRHIRRLLAAHGVEVLRLIRIAIGRLPLGDLAKGTARHLTAEEL 245


>gi|302879085|ref|YP_003847649.1| pseudouridine synthase [Gallionella capsiferriformans ES-2]
 gi|302581874|gb|ADL55885.1| pseudouridine synthase [Gallionella capsiferriformans ES-2]
          Length = 243

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 62/244 (25%), Positives = 102/244 (41%), Gaps = 19/244 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
              R+SK ++  G+ SRRE +  I +  V V+G  +      V     I +         
Sbjct: 2   EKIRLSKRMSELGLCSRREADSYIEKGWVDVDGETVSLLGTKVYPNQQITLRTAAQVVQH 61

Query: 64  -------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
                    P+          Y     L+   +      +      S F  +   GRLDI
Sbjct: 62  ERVTILINKPVGYVSGQAEHGYKPASALLDEATHWKDDPSPIKFHRSQFIGLAPAGRLDI 121

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +++GLL+LT DG +A+ L    ++  + Y VR  G+++   L LL +G+ + G      +
Sbjct: 122 DSQGLLILTQDGRVAKQLIGEDSKVDKEYLVRVQGKLESSGLALLCQGLKLDGEYLKPAK 181

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V+   +      +   LREGK R+I+++ E     V  L RI  G  +LG L AG  R +
Sbjct: 182 VSWQNEDQ----LRFVLREGKKRQIRRMCELVGLTVTGLKRIRIGKIKLGLLPAGQWRYL 237

Query: 237 SKKI 240
            +  
Sbjct: 238 GEHE 241


>gi|251789770|ref|YP_003004491.1| 23S rRNA pseudouridylate synthase B [Dickeya zeae Ech1591]
 gi|247538391|gb|ACT07012.1| pseudouridine synthase [Dickeya zeae Ech1591]
          Length = 301

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 83/300 (27%), Positives = 124/300 (41%), Gaps = 7/300 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E MI   R+ V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESMIEAGRISVDGKIATLGDRVEVTRATKIRIDGHVVSVRE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T        +           R ++VGRLD+NT GLLL T 
Sbjct: 62  TEEAVCRVLMYYKPEGELCTRSDPEGRPTVFDRLPRIQGYRWVAVGRLDVNTSGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  G+V  DK+  L KG+ +         +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGEVGDDKIRQLSKGVQLDDGPAAFRSIRYQGGEGLN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
            W  V L EG+NRE+++++E    +V+RLIR+ YG  QL   L  G   E+    +    
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIQLPKGLPRGGWMEMKLTDVNYLR 241

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
               L    V+          +  ++     +           +++  G  +        
Sbjct: 242 ELVQLTPETVSKLPVERERRRVKANQIRRAVKRHGGHGGQVGGNNRPAGSRRNAPKRNGG 301


>gi|226355753|ref|YP_002785493.1| RNA pseudouridylate synthase [Deinococcus deserti VCD115]
 gi|226317743|gb|ACO45739.1| putative RNA pseudouridylate synthase [Deinococcus deserti VCD115]
          Length = 253

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 69/256 (26%), Positives = 107/256 (41%), Gaps = 8/256 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           + +R+ K +ARAGIASRR  E MI   RV VNG++       V   D + VDG  +    
Sbjct: 2   SGERLQKRLARAGIASRRAAEEMITAGRVTVNGVVA-HLGQTVTDADDVRVDGSLVDSTA 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              +           T +  +       +       +  VGRLD ++EGLLLLT DG L 
Sbjct: 61  VPAVTYALYKPRGYVTTARDEYGRRNVLDAMPEIPGLHPVGRLDRDSEGLLLLTTDGQLT 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKL--NLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
             +  P     + YR    G  D  +   + L  G+ ++      +  +           
Sbjct: 121 LTMTHPRYGHEKAYRAWTEGPHDPTQGELDTLVSGVELEDGPARAVSASPAYGGAF---- 176

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            V L EG+NR+++++ E     V+RL+R   G   LG +  G  RE+++K L E + P  
Sbjct: 177 -VVLGEGRNRQVRRMLEAVGHPVSRLLRYRVGGLWLGDMEVGEYRELTRKDLDELVNPAS 235

Query: 250 LEEAQVNLDAPIYSSE 265
           +  A            
Sbjct: 236 IPRASWQRSWEHAQQR 251


>gi|254491124|ref|ZP_05104305.1| conserved hypothetical protein, putative [Methylophaga thiooxidans
           DMS010]
 gi|224463637|gb|EEF79905.1| conserved hypothetical protein, putative [Methylophaga thiooxydans
           DMS010]
          Length = 293

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 73/292 (25%), Positives = 126/292 (43%), Gaps = 7/292 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ KV+ARAG  SRR+VE  I + +V  NG         +   D +++D   L      
Sbjct: 3   ERIQKVLARAGYGSRRQVETWIKEGKVSCNGETAT-LGDQISEGDRLKLDNKLLSPKRLW 61

Query: 70  -AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              +  +        + T       R+           R +SVGRLD+NT GL++LT DG
Sbjct: 62  QQPQQVILYNKPVGEVCTRSDPEGRRTIFQALPTPEQGRWVSVGRLDLNTSGLIILTTDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  R Y VR  G+V  + +  L+ G++++        +     +G+N W
Sbjct: 122 ELANRLMHPSNEMDREYAVRVLGEVTPEIMQNLRDGVMLEDGEAHFADIQESGGEGANHW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
             V ++EG+NRE+++++E    +V+RL+R+ YGP  +   L  G   +V    L      
Sbjct: 182 YHVVIQEGRNREVRRLWESQGVQVSRLMRVRYGPIIIPNNLRMGHWTKVEGADLEHLYEQ 241

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
             ++  Q              +      S          K + +++   + +
Sbjct: 242 AGMKPQQTEKTGKRQQKPVRNQATAKKESPYRGKKQTQDKATGKRSPRIRGR 293


>gi|75676734|ref|YP_319155.1| pseudouridine synthase, Rsu [Nitrobacter winogradskyi Nb-255]
 gi|74421604|gb|ABA05803.1| pseudouridine synthase, Rsu [Nitrobacter winogradskyi Nb-255]
          Length = 680

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 147/328 (44%), Positives = 194/328 (59%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           +     +RV+K+I+RAG+ASRR+ E M+ Q RV VNG ++   A++V S D + VDG PL
Sbjct: 348 KPKKAGERVAKMISRAGLASRRDAEEMVTQGRVAVNGRVINSPALDVTSRDVVTVDGQPL 407

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            + ERTRL+LYHKP GL+TTH+DP+GR TVFD+LP    RVISVGRLD NTEGLLLLTND
Sbjct: 408 PERERTRLFLYHKPRGLMTTHADPEGRPTVFDHLPEGLPRVISVGRLDFNTEGLLLLTND 467

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GGLAR LELP T WLR YRVR HG+V Q +L+ LK G+ + G+ YG +  TL+  +G+N 
Sbjct: 468 GGLARALELPDTGWLRRYRVRAHGEVTQAQLDALKNGVEVDGVKYGSIDATLERDQGANV 527

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+T  +REGKNRE++ V      +VNRLIRISYGPFQL  +  G   EV  ++LREQLG 
Sbjct: 528 WLTFAIREGKNREVRNVMAHLGLEVNRLIRISYGPFQLAEIAEGEVEEVKTRVLREQLGD 587

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            +   A ++       +      R         D     K +  ++   +   +      
Sbjct: 588 RIATLANMDPSGAAAEAGAANLGRDGTPLRSKKDNKARTKRALIEDRQGRSVVVQRTGSD 647

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENH 335
              A N   A G         G   +  
Sbjct: 648 EARARNEAEANGYGPPRRPKRGYHGKRD 675


>gi|315506751|ref|YP_004085638.1| pseudouridine synthase [Micromonospora sp. L5]
 gi|315413370|gb|ADU11487.1| pseudouridine synthase [Micromonospora sp. L5]
          Length = 256

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 77/230 (33%), Positives = 117/230 (50%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV+A AG+ SRR  E +I ++RV VNG + +          D I VDG  L+   R
Sbjct: 19  ERLQKVLAAAGVGSRRACEDLIFRRRVTVNGRVAQ-LGDKADPARDVIVVDGERLQADVR 77

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLA 131
                 +KP G+VTT +D  GR+ + D + +   +    VGRLD ++EGLLLLTNDG LA
Sbjct: 78  LVYVAMNKPRGVVTTMADEKGRTELADFIGARLEQRVYHVGRLDADSEGLLLLTNDGTLA 137

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  PS + L+ Y     G + ++    L  G+ ++          +    G  A V +
Sbjct: 138 HKLMHPSYEVLKTYLAEVAGPIPRNLSKRLTAGVELEDGPVKVDGFKVVDTLGKTAQVEL 197

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            L EG+   ++++       V+RLIR S GP +LG L  G  R ++   +
Sbjct: 198 TLHEGRKHIVRRLMAEVGHPVSRLIRTSIGPIKLGDLRTGRMRRLTNAEV 247


>gi|255325636|ref|ZP_05366733.1| ribosomal large subunit pseudouridine synthase B [Corynebacterium
           tuberculostearicum SK141]
 gi|255297246|gb|EET76566.1| ribosomal large subunit pseudouridine synthase B [Corynebacterium
           tuberculostearicum SK141]
          Length = 303

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 77/240 (32%), Positives = 123/240 (51%), Gaps = 4/240 (1%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDG 64
           + ++    +R+ KV+A+AG+ASRR  E +I   RV+VNG ++ +  V V  + D I VDG
Sbjct: 55  VDEDKPKGERLQKVLAKAGVASRRHAEILIDAGRVEVNGKIISKQGVKVNPSVDVIRVDG 114

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGL 121
           V +   E    ++ +KP G+ +T SD  GR  V D +        R+  VGRLD +TEGL
Sbjct: 115 VRVNVNEEHEYFVLNKPRGMQSTMSDDLGRPCVGDVVSEKVAAGQRLFHVGRLDADTEGL 174

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           L+LTNDG LA  L  P  +  + Y     G+ D+  +  LK+GI ++          +  
Sbjct: 175 LILTNDGELANRLMHPKYEVTKTYLATVLGEADRKLVRQLKEGIELEDGLAKADFAQVVD 234

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                + V + L EG+   ++++ +   + V RL+R      QLG +  G  R ++   L
Sbjct: 235 TNQGYSLVRLELHEGRKHIVRRMLKEAGFPVQRLVRTKLHTVQLGDMKPGGLRALNSSEL 294


>gi|152981336|ref|YP_001353751.1| pseudouridylate synthase [Janthinobacterium sp. Marseille]
 gi|151281413|gb|ABR89823.1| pseudouridylate synthase [Janthinobacterium sp. Marseille]
          Length = 248

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 61/249 (24%), Positives = 102/249 (40%), Gaps = 23/249 (9%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------- 63
             P R+SK ++  G+ SRRE +  IA+  V+V+G ++      V+ T  + V+       
Sbjct: 2   NEPLRLSKRMSELGLCSRREADEWIARGWVRVDGKVVSELGSKVLPTQRVTVERQAAAEQ 61

Query: 64  --------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                     P+          Y   + LV   +            P+    ++  GRLD
Sbjct: 62  SKRVTVLINKPMGYVSGQAEDGYKPAVALVNASTRWSEDQAATQFHPTQLRSLVPAGRLD 121

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL----NLLKKGIVIQGIC 171
           I++ GLL+LT DG +A+ L    T   + Y VR                L  G+++ G  
Sbjct: 122 IDSVGLLVLTQDGRIAKHLIGEDTSVEKEYLVRVQYSKPGKLPEADLKRLNHGLMLDGKK 181

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
               +V    +      ++  LREGK R+I+++ +    KV  L R+  G  +LG L  G
Sbjct: 182 LLPAKVKWQNEDQ----LSFILREGKKRQIRRMCDMVGLKVIGLKRVRIGNVKLGDLPVG 237

Query: 232 STREVSKKI 240
             R + +  
Sbjct: 238 QWRYLREDE 246


>gi|145633070|ref|ZP_01788802.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae 3655]
 gi|144986296|gb|EDJ92875.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae 3655]
          Length = 357

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 90/288 (31%), Positives = 132/288 (45%), Gaps = 10/288 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QSKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 67  LRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +  +         L  Y     L T        +          SR I+VGRLDINT GL
Sbjct: 130 INLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPHLTGSRWIAVGRLDINTSGL 189

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++    
Sbjct: 190 LLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGSANFKEIKFTG 249

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 250 GVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEMDLQN 309

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
              LRE +G     E ++++       ++    +        +   + 
Sbjct: 310 VNYLRELVGLPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>gi|294142202|ref|YP_003558180.1| ribosomal small subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
 gi|293328671|dbj|BAJ03402.1| ribosomal small subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
          Length = 229

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 46/231 (19%), Positives = 94/231 (40%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  +   +R   ++ + +  V  +G +++ ++  V +   I +DG  +      
Sbjct: 1   MRLDKFICESTELTRSFAKKALHRGDVTCDGEVVKSSSFKVKAGQIICLDGKVISVV-GP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP   +    D    + +          +   GRLDI+T GL+L+T DG  +  
Sbjct: 60  RFLMLNKPADTICATFDIVHPTVIDLLDIEKADTLHIAGRLDIDTTGLVLITTDGQWSHK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V    ++D   +    +G+ +  +        + +      +    +
Sbjct: 120 ITSPKKDCGKCYLVTLTDELDASLVETFAQGVELRNEDGLTKPAVLEII----DSHHARL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R S G   L   L  G  R ++ + +
Sbjct: 176 TITEGKYHQVKRMFAAVGNKVVGLHRESVGKIVLDDDLAPGEWRFLTDEEI 226


>gi|257465549|ref|ZP_05629920.1| pseudouridine synthase [Actinobacillus minor 202]
 gi|257451209|gb|EEV25252.1| pseudouridine synthase [Actinobacillus minor 202]
          Length = 340

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 90/289 (31%), Positives = 131/289 (45%), Gaps = 10/289 (3%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVD 63
           N  +E    +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S   I +D
Sbjct: 52  NEKKEKVVGEKLQKILARAGQGSRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRID 111

Query: 64  GVPLRKAERT-----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           G  +            L  Y     L T        +          +R ++VGRLDINT
Sbjct: 112 GHLINLIPTQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGARWVAVGRLDINT 171

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLL T DG LA  L  PS +  R Y VR  G VD+  L  L+KG+ ++       Q+ 
Sbjct: 172 SGLLLFTTDGELANRLMHPSREVEREYSVRVFGNVDEAMLQRLRKGVQLEDGPANFKQIK 231

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
                G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L  +L  G   E+ 
Sbjct: 232 AVGGTGINQWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKLEKSLPRGGWEEMG 291

Query: 238 KKI---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
            +    LRE +G     E +V++      +      +            
Sbjct: 292 LEQVNYLRELVGLPAETETKVDVTRNRRRTNVRQIRKAVKQHAKYRSKA 340


>gi|268316878|ref|YP_003290597.1| RNA-binding S4 domain-containing protein [Rhodothermus marinus DSM
           4252]
 gi|262334412|gb|ACY48209.1| RNA-binding S4 domain protein [Rhodothermus marinus DSM 4252]
          Length = 268

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 74/270 (27%), Positives = 130/270 (48%), Gaps = 7/270 (2%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V +  +  R+++ +ARAG+  SRR+ + +IA  +V+VNG + +   + V   D +EV+G
Sbjct: 2   TVSDKSSLIRLNRYLARAGVCPSRRKADELIASGQVRVNGQVAQ-LGMRVGPDDIVEVNG 60

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGL 121
           V +    +    L +KP   +TT  D  GR TV D +       + +  VGRLD NT G+
Sbjct: 61  VRVVPQTQALYILMNKPHDTITTCDDERGRRTVLDLINLPPEQKNGLFPVGRLDRNTTGV 120

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDG LA  L  P  +  ++Y  R    V  ++   L++G+ ++      +QV ++ 
Sbjct: 121 LLLTNDGELANRLMHPRYRVEKIYVARTARPVKPEEAEQLRRGVQLEDGPARAVQVAVNP 180

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                  + + + EG+NR+++++ E    +V +L R  Y       +  G  R ++   +
Sbjct: 181 ADP--HEIALMIYEGRNRQVRRMLEAIGHEVVQLKRTHYAGLTTKGVRPGKWRRLTDAEV 238

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDR 271
           R       L+  +     PI   +     R
Sbjct: 239 RRLYRLAGLKPPKTFKTMPIGHGDANAVKR 268


>gi|148828349|ref|YP_001293102.1| methyltransferase [Haemophilus influenzae PittGG]
 gi|148719591|gb|ABR00719.1| predicted methyltransferase [Haemophilus influenzae PittGG]
          Length = 357

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 90/288 (31%), Positives = 132/288 (45%), Gaps = 10/288 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 67  LRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +  +         L  Y     L T        +          SR I+VGRLDINT GL
Sbjct: 130 INLSHAQKEICRVLMYYKPEGELCTRSDPKGRATVFDRLPHLTGSRWIAVGRLDINTSGL 189

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++    
Sbjct: 190 LLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGSANFKEIKFAG 249

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 250 GVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEMDLEN 309

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
              LRE +G     E ++++       ++    +        +   + 
Sbjct: 310 VNYLRELVGLPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>gi|119962911|ref|YP_947435.1| RNA pseudouridine synthase [Arthrobacter aurescens TC1]
 gi|119949770|gb|ABM08681.1| putative RNA pseudouridine synthase [Arthrobacter aurescens TC1]
          Length = 404

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 82/236 (34%), Positives = 127/236 (53%), Gaps = 4/236 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLR 68
           +    R+ KV+A+AG+ASRR  E MI + RV+V+G++     + V  T   I VDG+ ++
Sbjct: 160 DVDGVRLQKVMAQAGVASRRVCEEMILEGRVEVDGVVTTELGMRVDPTSAVIHVDGIRIQ 219

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLLT 125
             E     +++KP G+V+T  DP+GR  + D L +  ++      VGRLD+ TEGLLLLT
Sbjct: 220 LDETLVYMVFNKPKGVVSTMEDPEGRPCISDFLKNNKNKGERLFHVGRLDVATEGLLLLT 279

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  PS +  + Y V+  G   Q     LK G+ ++          L      
Sbjct: 280 NDGELANRLTHPSYEVPKTYLVQVRGPFPQGVGAKLKNGVELEDGVAAVDSFRLVDSTPG 339

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +  + V L  GKNR ++++F+   + V RL+R+  GP  LG    GS R + ++ +
Sbjct: 340 HVLIEVVLHSGKNRIVRRMFDAVGFPVERLVRVKVGPIGLGDQRQGSIRNLGRQEV 395


>gi|16331284|ref|NP_442012.1| hypothetical protein slr0361 [Synechocystis sp. PCC 6803]
 gi|3915377|sp|Q55578|Y361_SYNY3 RecName: Full=Uncharacterized RNA pseudouridine synthase slr0361;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|1001457|dbj|BAA10082.1| slr0361 [Synechocystis sp. PCC 6803]
          Length = 249

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 80/239 (33%), Positives = 116/239 (48%), Gaps = 11/239 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++++ GIASRR  E MI   RV VNG +            D + VDG  ++   R
Sbjct: 3   ERIQKLLSQWGIASRRHAEEMILAGRVSVNGKVA-NLGDKADPQQDFLSVDGKQIKADNR 61

Query: 73  TR--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLLTND 127
            R    L +KP  +++T  DP GR TV D LP    R      VGRLD N+ G LLLTND
Sbjct: 62  PRDIYLLVNKPRDVLSTCDDPRGRKTVLDLLPQDLQRGKGLHPVGRLDRNSTGALLLTND 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  P     + Y V   G    + L   + G+++ G       + + ++     
Sbjct: 122 GELTLRLTHPRYHLPKTYDVWLEGNPSDEDLEKWRSGMMLDGKKTLPATLEVISENKDQI 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT----LLAGSTREVSKKILR 242
            + V L EG+NR+I+++ E     V +L R + GP QL T    L +G  R +S   +R
Sbjct: 182 HLLVTLTEGRNRQIRRLAEELGLTVLKLHRRTIGPLQLHTRGKVLGSGQFRFLSPAEIR 240


>gi|288941903|ref|YP_003444143.1| pseudouridine synthase [Allochromatium vinosum DSM 180]
 gi|288897275|gb|ADC63111.1| pseudouridine synthase [Allochromatium vinosum DSM 180]
          Length = 299

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 89/286 (31%), Positives = 129/286 (45%), Gaps = 7/286 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-----V 65
             P R+ K++A AG+ SRR++E  I++ RV+VNG L +         D I VDG      
Sbjct: 15  DEPVRLQKLLAEAGLGSRRQIEGWISEGRVRVNGQLAK-LGDQATRADRIRVDGRDVTLK 73

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P R +E   +  +     LVT     +  +           R I+VGRLDINT GL+L T
Sbjct: 74  PKRDSETQIIVYHKPEGELVTRRDPEERPTVFRRLPRPKQGRWIAVGRLDINTSGLILFT 133

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  G+V  + L  L  GI +        ++T     G+
Sbjct: 134 TDGELANRLMHPSREIEREYSVRILGEVAPETLERLTAGIELDDGPAKFERITDQGGTGA 193

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           N W  V LREG+NRE+++++E     V+RLIRI YG  +LG  L  G+ R ++     E 
Sbjct: 194 NHWYNVVLREGRNREVRRLWEAAGCTVSRLIRIRYGNVELGRRLFPGNWRPLTDAERAEL 253

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           +    L   +              R           +  +  + S 
Sbjct: 254 MALAGLRVLERPRLRRPAPGAAKPRRPKPDDGSSSGEGLKWGRRSR 299


>gi|270295727|ref|ZP_06201927.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           D20]
 gi|317479868|ref|ZP_07938986.1| S4 domain-containing protein [Bacteroides sp. 4_1_36]
 gi|270273131|gb|EFA18993.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           D20]
 gi|316903977|gb|EFV25813.1| S4 domain-containing protein [Bacteroides sp. 4_1_36]
          Length = 494

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 59/241 (24%), Positives = 104/241 (43%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +   D +
Sbjct: 246 IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRGDEV 305

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +     +    +  + L      + T+      R+ +     +   R+  VGRLD NT G
Sbjct: 306 KFHDQTVSIERKIYVLLNKPKDTVTTSDDPQARRTVMDLVKGACDERIYPVGRLDRNTTG 365

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     + +  +  +  GI +             
Sbjct: 366 VLLLTNDGDLASKLTHPKYLKKKIYHVHLDKNLTKADMEQIAAGIQLDDGEIH-ADAISY 424

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           T       V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++ 
Sbjct: 425 TDDFKKDDVGIEIHSGKNRIVRRIFESLGYKVMKLDRVYFAGLTKKGLRRGEWRYLTEQE 484

Query: 241 L 241
           +
Sbjct: 485 V 485


>gi|325295025|ref|YP_004281539.1| pseudouridine synthase Rsu [Desulfurobacterium thermolithotrophum
           DSM 11699]
 gi|325065473|gb|ADY73480.1| pseudouridine synthase Rsu [Desulfurobacterium thermolithotrophum
           DSM 11699]
          Length = 252

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 82/239 (34%), Positives = 127/239 (53%), Gaps = 10/239 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R++K +A AG+ +RR+VE +I Q RV VNG ++E  AV V    D + VDG  +R  +R
Sbjct: 1   MRLNKFLAYAGLGARRKVEELIKQGRVTVNGEVVENPAVEVDPKKDEVRVDGERVRLPKR 60

Query: 73  TRLWLYHKPIGLVT--THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                ++KP G++T       D R  V D       R+  VGRLD NTEGLLL+TNDG L
Sbjct: 61  FIYLAFNKPQGVLTAMEREPGDKRPIVADYFRKYPVRLFPVGRLDYNTEGLLLMTNDGEL 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD-------MQVTLDTQK 183
           A  L  P     + Y  +  G+V   ++  +KKG  +              +++   ++ 
Sbjct: 121 AERLAHPRYHIPKTYIAKVKGRVTPAEIERMKKGAKLVDDKGKPFFAKPIDIKLLKPSRT 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           G N +V +    GKNR +++ F+ F+  V +L RI+ GP +LG L  G  RE++ + ++
Sbjct: 181 GRNTYVQISFDIGKNRVVRRFFDRFDHGVLKLKRIAIGPLKLGNLPKGMYRELTPEEVK 239


>gi|330685516|gb|EGG97168.1| putative 16S pseudouridylate 516 synthase [Staphylococcus
           epidermidis VCU121]
          Length = 230

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 104/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  GI +R EV++ + +  VKVN  + +     +    D I V+G  +     
Sbjct: 1   MRLDKFLANMGIGTRNEVKQSLKKGYVKVNDKVNKSPKTQINPDEDIITVNGEKIIYI-D 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP  +V+   D   ++ +          +  VGRLD +TEGLLL+TNDG    
Sbjct: 60  KVYIMLNKPSDVVSATEDDKHQTVIDLIPEYKHLGIFPVGRLDKDTEGLLLITNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+    + Y V     V Q  +   K+G+ +        Q+ +   + S     V 
Sbjct: 120 NLMSPNKHVPKTYEVVSKNDVTQSDVERFKEGLELSDGLLKPAQLEIIENRRS----RVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + EGK  ++K++F     +V +L RI     +L  +L  G  R ++++  +
Sbjct: 176 IYEGKYHQVKRMFHEIENEVLQLKRIKIANLELDTSLKLGEFRLLTEEDFK 226


>gi|311694421|gb|ADP97294.1| RNA-binding S4 domain protein [marine bacterium HP15]
          Length = 327

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 88/308 (28%), Positives = 128/308 (41%), Gaps = 8/308 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
           P+R+ K++ARAGI SRRE+E  +   R+ VNG  +          D  E+DG  L  +  
Sbjct: 22  PERIQKLLARAGIGSRREIEGWMEAGRLLVNGQPVA-PGQKATVEDRFELDGKRLEVSGA 80

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R  L        + T        +           R IS+GRLDINT GL+L T D
Sbjct: 81  AEVMRRVLIYNKPEGEVTTRKDPEGRPTVFDRLPRLKEHRWISIGRLDINTTGLVLFTTD 140

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G+VD  K+  L +G++++        ++     G N 
Sbjct: 141 GELANRLMHPSNQIDREYAVRIFGEVDDAKIERLLQGVLLEDGMAKFTDISPAGGSGINR 200

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V L EG+NRE+++++E    +V+RL R+ YGP  L   L  G   E+ ++ + + L 
Sbjct: 201 WFHVTLLEGRNREVRRLWESQGVRVSRLKRVRYGPIFLPSRLTVGKWEELDQRAV-DTLS 259

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
             +  EA               R R              K   S         +   P  
Sbjct: 260 RTVGLEAVEIPQKTPNEKAAHDRQRRKSPGRSGKKTPGNKWAVSDTKPAKPAGRAPRPER 319

Query: 307 RRNLASNV 314
            R+     
Sbjct: 320 ARSKTPRG 327


>gi|306836036|ref|ZP_07469026.1| ribosomal large subunit pseudouridine synthase B [Corynebacterium
           accolens ATCC 49726]
 gi|304568063|gb|EFM43638.1| ribosomal large subunit pseudouridine synthase B [Corynebacterium
           accolens ATCC 49726]
          Length = 303

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 79/240 (32%), Positives = 122/240 (50%), Gaps = 4/240 (1%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDG 64
           +  +    +R+ KV+A+AG+ASRR  E +I   RV+VNG ++ +  V V    D I VDG
Sbjct: 55  VDDDKPKGERLQKVLAKAGVASRRHAEILIDGGRVEVNGNVVLKQGVKVNPAVDVIRVDG 114

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGL 121
           V +   E    ++ +KP G+ +T SD  GR  V D +        R+  VGRLD +TEGL
Sbjct: 115 VRVNVNEDQEYFILNKPRGMQSTMSDDLGRPCVGDVVSEKVASGQRLFHVGRLDADTEGL 174

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           L+LTNDG LA  L  P  +  + Y     G+ D   +  LK+GI ++        V +  
Sbjct: 175 LILTNDGELANRLMHPKYEVKKTYLATVLGEADNKLVRQLKEGIELEDGLAKADFVQVVD 234

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +    + V V L EG+   ++++ +   + V RL+R      QLG +  G  R ++   L
Sbjct: 235 KNQGFSLVRVELHEGRKHIVRRLLKEAGYPVQRLVRTKLHTVQLGDMKPGGLRALNSNEL 294


>gi|186476490|ref|YP_001857960.1| pseudouridine synthase [Burkholderia phymatum STM815]
 gi|184192949|gb|ACC70914.1| pseudouridine synthase [Burkholderia phymatum STM815]
          Length = 597

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 75/274 (27%), Positives = 123/274 (44%), Gaps = 6/274 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRR++E +I   RV VNG         ++ TD + ++
Sbjct: 191 KRVLSPDDDAPKLHKVLADAGMGSRRDMEELIVAGRVSVNGEPA-HIGQRILPTDLVRIN 249

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 250 GKPIKRKLQSKPPRVLLYHKPTGEIVSHADPEGRPSVFDKLPPMKTAKWLAVGRLDFNTE 309

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 310 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELTEGNRQKLLHGVELDDGPANFLRIRD 369

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+  
Sbjct: 370 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIALPRGLKRGRWEELED 429

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRP 272
             +R  +    L+       A         +  P
Sbjct: 430 NQVRSLMASVGLKAPAEEKGAGRRGEPERRQPDP 463


>gi|309775612|ref|ZP_07670612.1| ribosomal small subunit pseudouridine synthase A
           [Erysipelotrichaceae bacterium 3_1_53]
 gi|308916706|gb|EFP62446.1| ribosomal small subunit pseudouridine synthase A
           [Erysipelotrichaceae bacterium 3_1_53]
          Length = 233

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 64/238 (26%), Positives = 110/238 (46%), Gaps = 8/238 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A AG  SR+EV++ I +  V++N +   +    +    D + V+G  +   E 
Sbjct: 1   MRLDKYLAHAGYGSRKEVKQAIRKGLVRINEVECRKDDTRIQEGIDVVCVNGEEVVY-EA 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP  +V+  SDP   + +      +      VGRLDI+TEGLLL+TNDG LA 
Sbjct: 60  VVYIMLNKPQDVVSATSDPTHETVLDCIDAILPRDCFPVGRLDIDTEGLLLITNDGKLAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P    ++ Y V+    + +     L+   IV+        +V L  +      + +
Sbjct: 120 RLLSPKNHVVKTYFVQLAKPLQEADKKRLEDGSIVLDEEPVQCARVELLEE----TQILL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
            ++EG+  ++K++      +V  L RI+ GP QL   L  G  R + ++ L       
Sbjct: 176 HIQEGRFHQVKRMLHAVGNEVVYLRRIAMGPLQLDEQLAPGDWRYLYEEELAALQEIA 233


>gi|257094536|ref|YP_003168177.1| RNA-binding S4 domain-containing protein [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
 gi|257047060|gb|ACV36248.1| RNA-binding S4 domain protein [Candidatus Accumulibacter phosphatis
           clade IIA str. UW-1]
          Length = 322

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 76/259 (29%), Positives = 122/259 (47%), Gaps = 6/259 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P+R+ K++A++GI SRRE+E +IA  R+ +NG           + D ++V+G  ++   
Sbjct: 65  KPERLHKLLAQSGIGSRREMEELIAAGRISINGETASV-GQTASAGDRVKVNGKLVQLRF 123

Query: 72  RTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             RL      +     +V+ +      +           R ++VGRLD NT GLLLLT  
Sbjct: 124 SDRLPRVILYHKPEGEIVSRNDPEHRPNVFTSMPRISAGRWVAVGRLDFNTSGLLLLTTS 183

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P  Q +R Y VR  G++ ++    L  GI +               +G+N 
Sbjct: 184 GDLANRLMHPRYQLVREYAVRILGELTEEVRRQLLDGIDLDDGPAQFASFQEAGGEGANR 243

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V L EG+NRE++++FE     V+RL+R+ YGPF L   L  G   E+S+  +++ L 
Sbjct: 244 WYRVSLHEGRNREVRRMFEAVGVVVSRLMRVRYGPFALPPGLKRGQVLELSEADVKKLLA 303

Query: 247 PHLLEEAQVNLDAPIYSSE 265
              +   +           
Sbjct: 304 DFGMANPEAGRAPRRPRER 322


>gi|163857448|ref|YP_001631746.1| pseudouridine synthase [Bordetella petrii DSM 12804]
 gi|163261176|emb|CAP43478.1| pseudouridine synthase [Bordetella petrii]
          Length = 588

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 80/320 (25%), Positives = 128/320 (40%), Gaps = 9/320 (2%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             +  +    ++ KV+A AGI SRRE+E +I   RV VNG         V  +D + V+G
Sbjct: 114 KYLNSDAAMPKLHKVLADAGIGSRREMEELITAGRVSVNGEPA-HIGQRVAPSDQVRVNG 172

Query: 65  VPL----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            P+     K     +  +     +V+        S           + +SVGRLD+NTEG
Sbjct: 173 KPVARPNTKKPPRVILYHKPAGEIVSHDDPGGRASVFARLPKLRTGKWLSVGRLDLNTEG 232

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LL+ T  G +A  +  P     R Y VR  G++D      L +GI ++        +   
Sbjct: 233 LLIFTTSGDMANRIMHPRYGTEREYAVRVLGEMDDATRKSLVEGIELEDGQAAFGALDYL 292

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
              GSN W  V L+EG+NRE++++FE     V+RLIR  +G   L  TL  G   E+   
Sbjct: 293 GGDGSNRWYRVTLQEGRNREVRRMFESVGVTVSRLIRTRFGDLVLPRTLRRGRWEELDSS 352

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
           ++       +      + D              +               +  + G   + 
Sbjct: 353 LV---TALMVQLGLLRDDDDADGGRNARQPRSHDSALPPGFGTMDRNGMNGARIGRRGKL 409

Query: 300 KLATPVHRRNLASNVWMAKG 319
           +   P    ++AS+     G
Sbjct: 410 QGGGPGSAGHVASSPSDPFG 429


>gi|148826192|ref|YP_001290945.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae PittEE]
 gi|148716352|gb|ABQ98562.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae PittEE]
          Length = 357

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 89/288 (30%), Positives = 132/288 (45%), Gaps = 10/288 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 67  LRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +  +         L  Y     L T        +          SR I+VGRLDINT GL
Sbjct: 130 INLSHAQKEICRVLMYYKPEGELCTRSDPKGRATVFDRLPRLTGSRWIAVGRLDINTSGL 189

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++    
Sbjct: 190 LLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGPANFKEIKFTG 249

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
             G N W  + L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 250 GVGINQWYDITLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEMDLEN 309

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
              LRE +G     E ++++       ++    +        +   + 
Sbjct: 310 VNYLRELVGLPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>gi|301169983|emb|CBW29587.1| 16S rRNA pseudouridylate 516 synthase [Haemophilus influenzae
           10810]
          Length = 232

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 57/236 (24%), Positives = 108/236 (45%), Gaps = 7/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  +V +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENVGLTRSQATKAIHQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWVEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ HKP G V ++ D D  +        +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYFMLHKPQGCVCSNDDGDYPTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V+++      +GI+++G        ++ +      +  V +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEENYAAACSEGILLRGEKEPTKPAKLEIL----DDYNVNL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
            + EG+  ++K++F     KV  L R   G   L   L  G  R +++  + + + 
Sbjct: 177 TISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRSLTQSEIEKLVK 232


>gi|297195213|ref|ZP_06912611.1| pseudouridine synthase [Streptomyces pristinaespiralis ATCC 25486]
 gi|297152696|gb|EFH31937.1| pseudouridine synthase [Streptomyces pristinaespiralis ATCC 25486]
          Length = 368

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 67/233 (28%), Positives = 111/233 (47%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           +   +R+ KV+ARAG+ SRR  E +I   RV+VNG ++    V V    D I+VDG+ + 
Sbjct: 128 DQEGERLQKVLARAGMGSRRACEELIDAGRVEVNGKIVIEQGVRVDPEQDEIKVDGLTVA 187

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   L      + T       +  + D + +  +R+  VGRLD  TEG++LLTN G
Sbjct: 188 TQSHLFFALNKPAGVVSTMEDPDGRQ-CLGDYVTNRETRLFHVGRLDTETEGIILLTNHG 246

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     + Y     G + ++    LK+GI ++          +    G N  
Sbjct: 247 ELAHRLTHPKYGVKKTYLAAIQGPLPRELGKRLKEGIQLEDGYARADHFRVVENTGKNYL 306

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L EG+   ++++     + V++L+R ++GP  LG   +G  R ++   +
Sbjct: 307 VEVTLHEGRKHIVRRMLSEAGFPVDKLVRTAFGPIALGDQKSGWLRRLTNTEV 359


>gi|326204454|ref|ZP_08194312.1| pseudouridine synthase [Clostridium papyrosolvens DSM 2782]
 gi|325985486|gb|EGD46324.1| pseudouridine synthase [Clostridium papyrosolvens DSM 2782]
          Length = 247

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 57/245 (23%), Positives = 110/245 (44%), Gaps = 13/245 (5%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DH 59
           MK K         QR+ KVI+  G  SR +++  + +  V V+G +++ + ++V      
Sbjct: 1   MKQK---------QRLDKVISNFGFGSRNDIKSAVKKGLVTVDGAIVKDSGIHVDPEASI 51

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           IE++G  L   +   + +      +  T                    +   GRLDI+TE
Sbjct: 52  IEINGERLNYRKFIYIMMNKPQGVISATSDRKQRTVFDILPEEYKCFELFPAGRLDIDTE 111

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVT 178
           GL+L+TNDG L+  +  P     + Y  +  G+V+Q+  +  ++G+ +          + 
Sbjct: 112 GLVLMTNDGQLSHEILSPKKHVPKQYYAKVLGRVNQEDADAFRQGVTLDDGYSTLPAVLE 171

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
           +  +    + + + + EGK  ++K++FE    KV  L R+S G  +L   L  G  +E+ 
Sbjct: 172 VL-KSDELSEIKLTIVEGKFHQVKRMFEAVGKKVIYLKRLSMGNLRLDENLKLGECKELG 230

Query: 238 KKILR 242
           +  + 
Sbjct: 231 ESDIE 235


>gi|319941976|ref|ZP_08016297.1| pseudouridine synthase [Sutterella wadsworthensis 3_1_45B]
 gi|319804629|gb|EFW01499.1| pseudouridine synthase [Sutterella wadsworthensis 3_1_45B]
          Length = 400

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 83/346 (23%), Positives = 139/346 (40%), Gaps = 8/346 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---- 68
            +++ K +A AG+ SRRE+ER+I    V VNG   +     V + D I V+G  +R    
Sbjct: 40  TEKLQKALADAGMGSRREMERLIESGIVTVNGNPAK-LGDRVSAEDVIRVEGRLVRRLSP 98

Query: 69  --KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  +     +V+        S           R I+VGRLD NTEGLLL T 
Sbjct: 99  EAADTPRVLLYHKPAGEIVSRDDPEGRPSVFNHLPRVPGGRWIAVGRLDFNTEGLLLFTT 158

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
            G LA  L  P  +  R Y VR  G++  +    L  G+ ++        +T +  KG N
Sbjct: 159 SGSLANRLMHPRYEMEREYAVRTVGELTPEDEAKLLAGVELEDGPAKFETLTDEGGKGLN 218

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
            W  V +REG+NRE++++FE  N  V+RLIR+ YG  +L   L+ G   E+    +R  +
Sbjct: 219 HWYVVTIREGRNREVRRLFESVNLTVSRLIRVRYGAVELPPGLVRGKREEMDPADVRRWI 278

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                 +   + +     +  +   +     +  +   R    + +        K     
Sbjct: 279 AELDRMDRASSPEEAAAKAAEVKALKAAARLKWRERLEREAAEAERAPRRGAPGKSDRTG 338

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
              + + ++   +   +   S++  R  N          +      
Sbjct: 339 VPFSESRDLSDRRTQRAYGKSNASSRTRNEEDGQRSEGVKRTPFGK 384


>gi|311739374|ref|ZP_07713209.1| ribosomal large subunit pseudouridine synthase B [Corynebacterium
           pseudogenitalium ATCC 33035]
 gi|311305190|gb|EFQ81258.1| ribosomal large subunit pseudouridine synthase B [Corynebacterium
           pseudogenitalium ATCC 33035]
          Length = 303

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 77/240 (32%), Positives = 123/240 (51%), Gaps = 4/240 (1%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDG 64
           + ++    +R+ KV+A+AG+ASRR  E +I   RV+VNG ++ +  V V  + D I VDG
Sbjct: 55  VDEDKPKGERLQKVLAKAGVASRRHAEILIDAGRVEVNGKIIAKQGVKVNPSVDVIRVDG 114

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGL 121
           V +   E    ++ +KP G+ +T SD  GR  V D +        R+  VGRLD +TEGL
Sbjct: 115 VRVNVNEEHEYFVLNKPRGMQSTMSDDLGRPCVGDVVSEKVAAGQRLFHVGRLDADTEGL 174

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           L+LTNDG LA  L  P  +  + Y     G+ D+  +  LK+GI ++          +  
Sbjct: 175 LILTNDGELANRLMHPKYEVTKTYLATVLGEADRKLVRQLKEGIELEDGLAKADFAQVVD 234

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                + V + L EG+   ++++ +   + V RL+R      QLG +  G  R ++   L
Sbjct: 235 TNQGYSLVRLELHEGRKHIVRRMLKEAGFPVQRLVRTKLHTVQLGDMKPGGLRALNSSEL 294


>gi|299067338|emb|CBJ38535.1| Ribosomal large subunit pseudouridine synthase B [Ralstonia
           solanacearum CMR15]
          Length = 601

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 78/321 (24%), Positives = 129/321 (40%), Gaps = 11/321 (3%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +       ++ K++A AG+ SRR++E +I Q RV VNG+        ++ TD + V+G  
Sbjct: 207 LTAEDDAPKLHKILADAGLGSRRDMEDLILQGRVSVNGLPA-HIGQRILPTDQVRVNGKL 265

Query: 67  LRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           +++         L  +     +V+        +           + ++VGRLD NTEGLL
Sbjct: 266 IQRKLPSKPPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRMKTGKWVAVGRLDFNTEGLL 325

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + T  G +A     P     R Y VR  G++ +     L  GI +       +       
Sbjct: 326 IFTTSGDIANRFMHPRYGVEREYAVRTLGELPESDRQKLLHGIRLDDGEANFLSCADGGG 385

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EVS   +
Sbjct: 386 EGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEVSADDV 445

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISE-----VPDDFTRMKKNSSQKNGLS 296
           R  +G   L+    +        +   +      ++             +     +    
Sbjct: 446 RGLMGLLGLKVPSASAGGGQQGGQGGRQGNRRREAQPVLMGPMSSGFTGEATFQSRGQGV 505

Query: 297 KQKKLATPVHRRNLASNVWMA 317
           +    A P  RR  +      
Sbjct: 506 ENGNRAMPAPRRQSSPRQPDP 526


>gi|156974936|ref|YP_001445843.1| ribosomal small subunit pseudouridine synthase A [Vibrio harveyi
           ATCC BAA-1116]
 gi|156526530|gb|ABU71616.1| hypothetical protein VIBHAR_02655 [Vibrio harveyi ATCC BAA-1116]
          Length = 233

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 47/234 (20%), Positives = 96/234 (41%), Gaps = 2/234 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +     A+R++  ++I    + V+G + +  A  V     +E +G  +      
Sbjct: 1   MRLDKYLCDGLGATRKQATKIIKSGEITVDGEVQKSGAFKVPEGGVVEWEGREVGAPGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + LY     + +     +  +            +   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLYKPADFVCSHEDGHNP-TAFVLLDEPKVENLHFAGRLDVDTTGLVLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     +  D +    +GI ++      +   L+    +   V + +
Sbjct: 120 ITSPKHKCEKTYRVWLVDAIQPDYVEKFAEGIELRNEREPTLPAHLEIVNEAENEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
            EGK  ++K++F     KV  L R   G   L   L  G  R ++++ +   + 
Sbjct: 180 VEGKYHQVKRMFAALGNKVEHLHRERIGSIVLDEALEPGDYRFLTEEEVESVVK 233


>gi|149926275|ref|ZP_01914537.1| hypothetical protein LMED105_02043 [Limnobacter sp. MED105]
 gi|149825093|gb|EDM84305.1| hypothetical protein LMED105_02043 [Limnobacter sp. MED105]
          Length = 458

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 90/383 (23%), Positives = 151/383 (39%), Gaps = 32/383 (8%)

Query: 2   KDKNIVQENFTPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           K+++ +     P+   ++ KV+A +G+ SRRE+E +I   RV VN          V+ TD
Sbjct: 54  KNRSKLNVRLDPELAPKLHKVLADSGMGSRREMEELIVAGRVSVNAEPA-HLGQRVLPTD 112

Query: 59  HIEVDGVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
            + V+G  +++         L  +     +V+        +           + I+VGRL
Sbjct: 113 QVRVNGKLIQRKNKSKPPRVLIYHKPAGEIVSMDDPQGRTTVFQKLPKISNGKWIAVGRL 172

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D NTEGLLL T+ G LA  L  P  +  R Y VR  G++ +++   L  GI ++      
Sbjct: 173 DFNTEGLLLFTSSGELANRLMHPRYEVQREYAVRILGELSEEQRQQLLTGIQLEDGPAKF 232

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
           + V     +G+N W  VGL+EG+NRE++++FE  N  V+RLIR  +G   +  TL  G  
Sbjct: 233 LYVDAAGGEGANRWYKVGLKEGRNREVRRMFEACNLTVSRLIRTRFGDIMMPSTLKRGRH 292

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISE------------- 277
            E+         + LG  + E AQ         +     ++                   
Sbjct: 293 MEMEALEAMSYMQSLGLKVDESAQEGAIRRDKKNIGSKNNKRRNGQPLIDPGLAFTTPTQ 352

Query: 278 -------VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ 330
                           +N+    G S ++         N A          +   + +G+
Sbjct: 353 TYLTVSGATAAAALSNQNNLSSAGGSARRNGGGGDRNGNRAGANGNGAAAPAGKFAGAGK 412

Query: 331 REENHRRSPSFPSKRSLRRTSAK 353
           R    R +       S  R   +
Sbjct: 413 RPSGPRNAGPRSGGPSAGRGPGR 435


>gi|302866907|ref|YP_003835544.1| pseudouridine synthase [Micromonospora aurantiaca ATCC 27029]
 gi|302569766|gb|ADL45968.1| pseudouridine synthase [Micromonospora aurantiaca ATCC 27029]
          Length = 256

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 77/230 (33%), Positives = 117/230 (50%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV+A AG+ SRR  E +I ++RV VNG + +          D I VDG  L+   R
Sbjct: 19  ERLQKVLAAAGVGSRRACEDLIFRRRVTVNGRVAQ-LGDKADPARDVIVVDGERLQADVR 77

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLA 131
                 +KP G+VTT +D  GR+ + D + +   +    VGRLD ++EGLLLLTNDG LA
Sbjct: 78  LVYVAMNKPRGVVTTMADEKGRTELADFIGARLEQRVYHVGRLDADSEGLLLLTNDGTLA 137

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  PS + L+ Y     G + ++    L  G+ ++          +    G  A V +
Sbjct: 138 HKLMHPSYEVLKTYLAEVAGPIPRNLGKRLTAGVELEDGPVKVDGFKVVDTLGKTAQVEL 197

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            L EG+   ++++       V+RLIR S GP +LG L  G  R ++   +
Sbjct: 198 TLHEGRKHIVRRLMAEVGHPVSRLIRTSIGPIKLGDLRTGRMRRLTNAEV 247


>gi|298490451|ref|YP_003720628.1| pseudouridine synthase ['Nostoc azollae' 0708]
 gi|298232369|gb|ADI63505.1| pseudouridine synthase ['Nostoc azollae' 0708]
          Length = 254

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 72/238 (30%), Positives = 115/238 (48%), Gaps = 12/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K+I++ GIASRRE E MI + RVK+NGIL       V    D I +DG P+ +++  
Sbjct: 4   RIQKIISQWGIASRREAEEMIKRSRVKINGILA-HLGQKVDPQIDTISIDGQPISQSQHP 62

Query: 74  ---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDG 128
               L L   P  + T        + +      +     +  VGRLD ++ G L+LTNDG
Sbjct: 63  SLIYLLLNKPPGVVSTCDDPQGRPTVLDLLPQKLRHGLGIHPVGRLDADSTGALILTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS    + Y +   G   +  L   ++G+ ++G      +V L       + 
Sbjct: 123 DLTFSLTHPSHNIAKTYHIVVKGHPPEVVLGRWREGVFLEGRKTRPAKVQLIESLAHQSK 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-----LLAGSTREVSKKIL 241
           + + L+EG+NR+I++V E   + V +L R + G  QL T     LL G  R ++ + +
Sbjct: 183 LEIILQEGRNRQIRRVAEQLGYPVIQLHRTAIGSIQLQTPKARFLLWGDYRHITPEEI 240


>gi|29833054|ref|NP_827688.1| pseudouridine synthase [Streptomyces avermitilis MA-4680]
 gi|29610175|dbj|BAC74223.1| putative pseudouridine synthase [Streptomyces avermitilis MA-4680]
          Length = 356

 Score =  161 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 71/233 (30%), Positives = 112/233 (48%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
               +R+ KV+ARAG  SRR  E +I Q RV+VNG ++    + V    D I+VDG+ + 
Sbjct: 116 EQEGERLQKVLARAGYGSRRSCEELIEQARVEVNGEIVLEQGLRVDPEKDEIKVDGLTVA 175

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   L      + T       +  + D + +  +R+  VGRLD  TEG++LLTN G
Sbjct: 176 TQSYQFFSLNKPAGVVSTMEDTEGRQ-CLGDYVTNRETRLFHVGRLDTETEGVILLTNHG 234

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     +VY     G + +D    LK GI ++          +  Q G N  
Sbjct: 235 ELAHRLTHPKYGVKKVYLAHIVGPIPRDLGKRLKDGIQLEDGYAKADHFRVVEQTGKNYL 294

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L EG+   ++++     + V++L+R+++GP  LG   +G  R +S   +
Sbjct: 295 VEVTLHEGRKHIVRRMLAEAGFPVDKLVRVAFGPITLGDQKSGWLRRLSNTEV 347



 Score = 36.7 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 7/84 (8%), Positives = 13/84 (15%)

Query: 268 VRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSD 327
                +   +      R  K   ++              +    +               
Sbjct: 16  RGAGNDRDQKQGQGQGRPSKPRPEERRYDVGPGATQDGPKAGRGNAARGGAKGGPKQSRQ 75

Query: 328 SGQREENHRRSPSFPSKRSLRRTS 351
            G R E  R            R  
Sbjct: 76  RGGRTEPARSREYETRAEERNRDR 99


>gi|330467060|ref|YP_004404803.1| pseudouridine synthase [Verrucosispora maris AB-18-032]
 gi|328810031|gb|AEB44203.1| pseudouridine synthase [Verrucosispora maris AB-18-032]
          Length = 256

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 76/231 (32%), Positives = 119/231 (51%), Gaps = 3/231 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAE 71
           P+R+ KV+A AG+ SRR  E +I +++V VNG + +     V   T  I V+G  L+   
Sbjct: 18  PERLQKVLAAAGVGSRRACEDLIFRRKVTVNGRVAQ-LGDKVDPATAVIHVNGERLQADT 76

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGL 130
           R      +KP G+V+T +D  GR+ + D L +   +    VGRLD ++EGLLLLTNDG L
Sbjct: 77  RLVYLAMNKPRGVVSTMADERGRTALADFLNNRVEQRVYHVGRLDADSEGLLLLTNDGTL 136

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS    + Y     G + ++    L  GI ++          +    G  A V 
Sbjct: 137 AHRLMHPSYGVQKTYLCEVAGPIPRNLGKRLAAGIELEDGPVSVDAFRVVDSLGRTAQVE 196

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + L EG+   ++++       V+RL+R + GP +LG L +G TR ++   +
Sbjct: 197 LSLHEGRKHIVRRLLAEVGHPVSRLVRTAIGPIRLGDLRSGRTRRLTNAEV 247


>gi|158337477|ref|YP_001518652.1| pseudouridine synthase family 1 protein [Acaryochloris marina
           MBIC11017]
 gi|158307718|gb|ABW29335.1| pseudouridine synthase family [Acaryochloris marina MBIC11017]
          Length = 269

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 61/248 (24%), Positives = 106/248 (42%), Gaps = 15/248 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK--- 69
            R+ K++++ G+ASRR+ E++I   +V++NG              D I ++G  L     
Sbjct: 3   IRLQKLLSQWGVASRRQAEQLILAGQVQLNGHTA-ELGQKADPDQDQITLNGQILNPTDR 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTND 127
            +   L +      + T       R+ +     +         VGRLD+ + G LLLTND
Sbjct: 62  PQPLYLLVNKPKGVVSTCQDPQHRRTVLELLPKTYQQGQGLHPVGRLDVASTGALLLTND 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  P     + Y+V   G    + L+  ++GI + G      QV +     S+ 
Sbjct: 122 GQLTFALTHPRFHIAKTYQVWIEGCPPPEILDRWRQGIHLDGRTTLPAQVEILKPYQSHT 181

Query: 188 ---WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-----LLAGSTREVSKK 239
               + V L+EG+NR+I+++ E   + V +L R   G   L +     L  G  R ++  
Sbjct: 182 NSICLEVILQEGRNRQIRRIAEQLGYPVRKLHRTQIGSISLHSPSGKLLPQGRYRSLTAS 241

Query: 240 ILREQLGP 247
            ++     
Sbjct: 242 EMKNLRRL 249


>gi|253578262|ref|ZP_04855534.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251850580|gb|EES78538.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 255

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 66/243 (27%), Positives = 115/243 (47%), Gaps = 15/243 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R+ K +A AG  +R EV++ I + +V+VNG+  +++ + V   D + +DG  + +A 
Sbjct: 3   KAVRLDKFLADAGAGTRSEVKKFIQKGKVQVNGVPAKKSEIKVSEEDEVVLDGNRISQAP 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               +L HKP G V+   +     TV + + S    +  VGRLD +TEGLLL+T+DG LA
Sbjct: 63  EFVYYLLHKPAGYVSAT-EDKRDKTVMELVASDRKDLFPVGRLDKDTEGLLLITDDGALA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLD---------- 180
             L  P     + Y     G + ++ +     G+ I         ++ +           
Sbjct: 122 HELLSPKKHVDKTYYAVTDGCMTKEDVQRFADGLEIGEKNPTMPAKLKILSTRKVEETEL 181

Query: 181 --TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
                G ++ + + ++EGK  ++K++ E    KV  L RIS G   L   L  G  R+++
Sbjct: 182 EQYPSGWSSEIQLTIKEGKFHQVKRMTEAVGKKVVYLKRISMGVLTLPDDLKKGECRQLT 241

Query: 238 KKI 240
            + 
Sbjct: 242 AEE 244


>gi|15805921|ref|NP_294620.1| ribosomal large subunit pseudouridine synthase B [Deinococcus
           radiodurans R1]
 gi|6458615|gb|AAF10472.1|AE001942_4 ribosomal large subunit pseudouridine synthase B [Deinococcus
           radiodurans R1]
          Length = 257

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 76/256 (29%), Positives = 106/256 (41%), Gaps = 12/256 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 71
           +R+ K +ARAGIASRR  E +I   RV VNG         V  TD + VDG  +     E
Sbjct: 4   ERLHKRLARAGIASRRAAEELIRAGRVTVNGQTA-GLGQGVNDTDDVRVDGRLVELTRPE 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                LY     + T H +   R+ +          +  VGRLD ++EGLLLLTNDG L 
Sbjct: 63  TVTYALYKPVGFVTTAHDEYGRRNVLDA--MPDVPGLHPVGRLDKDSEGLLLLTNDGDLT 120

Query: 132 RVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
             L  P                   Q +L++L +GI +       +              
Sbjct: 121 LTLTHPRYGHEKAYRAWTEGREPPTQAELDVLVRGIAMDDGPAQALSAAPAEDGA----- 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            V L EG+NR+++++ E     V RL+R   G   LG L  G  RE+  + L + L PH 
Sbjct: 176 YVVLGEGRNRQVRRMLEALGHPVGRLVRYRVGGLWLGDLNPGEYRELGPRDLEQLLHPHK 235

Query: 250 LEEAQVNLDAPIYSSE 265
              A  +         
Sbjct: 236 TPRAVWDGAWEQTQDR 251


>gi|327440834|dbj|BAK17199.1| 16S rRNA uridine-516 pseudouridylate synthase [Solibacillus
           silvestris StLB046]
          Length = 247

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 67/242 (27%), Positives = 112/242 (46%), Gaps = 24/242 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-----------RAAVNVMSTDHIEV 62
           +R+ KVIA AG+ASRR+ E++I           +E                V ++D IEV
Sbjct: 2   ERLQKVIAYAGVASRRKAEQLI-----------VEGKVKVNGVVVKELGTKVSNSDTIEV 50

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           +GV L K ++    LY     +     D   ++        +  R+  VGRLD +T GLL
Sbjct: 51  EGVKLEKEDKVYFLLYKPRAYISAVTDDKGRKTVTDIFKKHVHQRIFPVGRLDYDTTGLL 110

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLD 180
           LLTNDG  + ++  P  +  + Y  R  G   +  L  L+ GI ++       +  +T  
Sbjct: 111 LLTNDGEFSNLMTHPKFKIDKTYIARVKGIPTKQGLMKLQSGIKLEDGKTAPAKVSMTSF 170

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +K   A   + + EG+NR+++++FE     V +L R  +    L  L  G  R+++K  
Sbjct: 171 DEKAGKAICEITIHEGRNRQVRRMFEAIGTPVVKLKRERFAFLDLTGLSPGEYRQLTKHE 230

Query: 241 LR 242
           ++
Sbjct: 231 VK 232


>gi|319638171|ref|ZP_07992934.1| pseudouridine synthase [Neisseria mucosa C102]
 gi|317400444|gb|EFV81102.1| pseudouridine synthase [Neisseria mucosa C102]
          Length = 352

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 73/256 (28%), Positives = 129/256 (50%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++      F P+R+ KV+A +G+ SRRE+E  I+   V VNG + +     V   DH+
Sbjct: 87  LKERRSDLSRFEPERLQKVLAASGVGSRREMEEWISNGWVTVNGRVAQ-LGDKVTPDDHV 145

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 146 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRISIFDRLPQAASSRWVAIGRLDI 205

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G++  +++ +L +  ++++       
Sbjct: 206 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGELTTEQMRVLTEEGVMLEDGLAKVE 265

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   
Sbjct: 266 RIYEQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFY 325

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   +    +
Sbjct: 326 ELNPAEVANIIKWADM 341


>gi|325661183|ref|ZP_08149810.1| hypothetical protein HMPREF0490_00543 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325472690|gb|EGC75901.1| hypothetical protein HMPREF0490_00543 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 237

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 64/237 (27%), Positives = 112/237 (47%), Gaps = 5/237 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A   + +R EV++MI +  V V+G+++++    V      +   G  +   +  
Sbjct: 3   RLDKYLADMQVGTRSEVKQMIRKGLVTVDGLIVKKPEEKVDCEKQVVVCSGAIVSYHQYE 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      +V+   DP  ++ +          +   GRLD +TEGLLL+TNDG LA  
Sbjct: 63  YYMLNKPAG-VVSATEDPRDKTVIDLIEDRRRKDLFPAGRLDKDTEGLLLITNDGALAHD 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           L  P     + Y  +  G V ++ + L  KG+ I +        +T+    G  + +T+ 
Sbjct: 122 LLSPKKHVDKKYYAKIEGTVTEEDVELFGKGVDIGEKRVTLPAVLTIL-SSGEESEITLT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
           +REGK  ++K++FE    KV  L R+S G   L   LL G  R+++++ L +     
Sbjct: 181 IREGKFHQVKRMFEAVGKKVTYLKRLSMGSLVLDEKLLPGEYRKLTEQELTQLKQMR 237


>gi|217970106|ref|YP_002355340.1| pseudouridine synthase [Thauera sp. MZ1T]
 gi|217507433|gb|ACK54444.1| pseudouridine synthase [Thauera sp. MZ1T]
          Length = 379

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 73/267 (27%), Positives = 123/267 (46%), Gaps = 6/267 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P+R+ KV+A+AG+ASRRE+E  +   R+ VNG+        +   D ++V+G  +   
Sbjct: 114 SEPERLQKVLAQAGVASRREIEEWVVAGRISVNGLPA-SLGQKIGPGDRVKVNGKLVPLR 172

Query: 71  ERTR----LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
              R    L  +     +V+        +           R ++VGRLD NT GLLL TN
Sbjct: 173 FTQRSPRVLIYHKPEGEIVSRDDPEGRPTVFERLPILRKGRWLAVGRLDFNTSGLLLFTN 232

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  P  +  R Y VR  G++ ++++  L  GI ++        +  +  +G+N
Sbjct: 233 DGDLANKLMHPRYELEREYAVRILGELTEEQVKSLTDGIQLEDGPAKFNLLRDEGGEGAN 292

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
            W  V + EG+NRE++++FE     V+RL+R+ YG  +L   L  G   E+ +       
Sbjct: 293 HWYRVTISEGRNREVRRMFEAVGLTVSRLMRVRYGSVELPARLKRGMWMEMPEAEACALA 352

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRP 272
           G    ++++          +       
Sbjct: 353 GLPPPQQSRQQDLRDKRPVKLHRTQAR 379


>gi|254525127|ref|ZP_05137182.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
 gi|219722718|gb|EED41243.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
          Length = 240

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 70/228 (30%), Positives = 109/228 (47%), Gaps = 1/228 (0%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           +++V+++AG+ SR E  R IA+ RV+V+G ++      +      IEVDG PL   +R  
Sbjct: 5   LARVLSKAGVCSRSEAARWIAEGRVRVSGRIVRDPEFPIGQPAPPIEVDGQPLAAPQRLY 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L      + T   +    +       +    +  VGRLD  +EGLLL +ND   A  L
Sbjct: 65  LMLNKPRGVVTTVQDERGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAARL 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P T   + Y V+  G  D   L  L+ G+  +G       V +       AW+ V L 
Sbjct: 125 TDPQTGPDKTYHVQVDGMPDHATLAALQAGVEDEGEFLAAHAVRVLRSGDKTAWLEVVLD 184

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           EG+NR I+++   F+ +V RL+R++ G   LG L  G  R +    L+
Sbjct: 185 EGRNRHIRRLLAAFDLQVLRLVRVAIGGLVLGDLGKGQWRVLEVSDLQ 232


>gi|312139846|ref|YP_004007182.1| pseudouridylate synthase [Rhodococcus equi 103S]
 gi|325674277|ref|ZP_08153966.1| ribosomal large subunit pseudouridine synthase B [Rhodococcus equi
           ATCC 33707]
 gi|311889185|emb|CBH48499.1| pseudouridylate synthase [Rhodococcus equi 103S]
 gi|325554957|gb|EGD24630.1| ribosomal large subunit pseudouridine synthase B [Rhodococcus equi
           ATCC 33707]
          Length = 321

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 77/243 (31%), Positives = 116/243 (47%), Gaps = 4/243 (1%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIE 61
           D+          R+ KV+A+AG+ASRR  E +I Q RV+V+G ++    + V      + 
Sbjct: 70  DRERAPMKGDGVRLQKVLAQAGVASRRAAEELIDQGRVEVDGRIVLEQGLRVDPENAIVR 129

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINT 118
           VDG+ +   +       +KP G  +T SD  GR  + D +        R+  VGRLD +T
Sbjct: 130 VDGIRVVVKKDLVHIALNKPRGWQSTMSDDLGRPCIGDIVSERVSAGQRLFHVGRLDADT 189

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGL+LLTNDG LA  L  PS +  + Y     G VD++    LK G+ +          T
Sbjct: 190 EGLILLTNDGDLAHRLMHPSYEVPKTYLATVQGVVDRNVGKTLKAGVELDDGPAKVDAFT 249

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           L    G  + V V L EG+   ++++ E     V RL+R   G   LG    G+ R + +
Sbjct: 250 LLDVNGGKSLVRVVLHEGRKHIVRRLLEAVGHPVVRLVRTDIGNVALGDGRPGTLRVLGR 309

Query: 239 KIL 241
             +
Sbjct: 310 GEV 312


>gi|193214786|ref|YP_001995985.1| pseudouridine synthase [Chloroherpeton thalassium ATCC 35110]
 gi|193088263|gb|ACF13538.1| pseudouridine synthase [Chloroherpeton thalassium ATCC 35110]
          Length = 297

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 80/268 (29%), Positives = 124/268 (46%), Gaps = 7/268 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHI 60
           K K     N    R++K IA  G ASRR+ + MI Q  V VNG ++      V    D +
Sbjct: 31  KIKTEQNINDPIIRLNKFIALCGEASRRKADEMIEQGEVMVNGKVVMELGYKVDRRADEV 90

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            V+G  L +  +    L +KP  +VTT SD   R TV + L  +  RV  VGRLD +T G
Sbjct: 91  VVNGKKLHENTQKIYILLNKPKDVVTTSSDEKSRKTVVE-LVGLKDRVFPVGRLDRDTTG 149

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVT 178
           +LLLTNDG L   L  P+    + Y      ++    L  +KKG  ++            
Sbjct: 150 VLLLTNDGDLTYRLTHPTFGVQKQYVATLDKKITSVDLQNIKKGFRLKDTGEKVSPCNAR 209

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +         + V + EGKN +I ++F  F + V +L+R++YG  ++GT+  G  R +++
Sbjct: 210 IL---DDGYTIWVAIHEGKNHQIHRMFWSFGYNVKKLVRVAYGGLEVGTMRRGEWRFLTQ 266

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSET 266
             + +      LE  Q         ++ 
Sbjct: 267 LEVSKLYKQVQLEGKQRIQKNQSTHNKK 294


>gi|53729057|ref|ZP_00348305.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|126208628|ref|YP_001053853.1| ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae L20]
 gi|126097420|gb|ABN74248.1| ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 5b str. L20]
          Length = 349

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 91/286 (31%), Positives = 132/286 (46%), Gaps = 10/286 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGV- 65
           +E    +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S   I +DG  
Sbjct: 64  KEKVVGEKLQKILARAGQGSRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNL 123

Query: 66  ----PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
               P++K     L  Y     L T        +          +R I+VGRLDINT GL
Sbjct: 124 ISLIPVQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGARWIAVGRLDINTSGL 183

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  G +D+  L  L+KG+ ++       Q+    
Sbjct: 184 LLFTTDGELANRLMHPSREVEREYSVRVFGNIDEAMLQRLRKGVQLEDGPANFKQIKTVG 243

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 244 GTGLNQWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKLEKGLPRGGWEEMGLEQ 303

Query: 241 ---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
              LRE +G     E +V++      +      +            
Sbjct: 304 VNYLRELVGLPAETETKVDVTKNRRRTNIRQIRKAVKQHSKYRTKA 349


>gi|119513289|ref|ZP_01632329.1| hypothetical protein N9414_09736 [Nodularia spumigena CCY9414]
 gi|119462052|gb|EAW43049.1| hypothetical protein N9414_09736 [Nodularia spumigena CCY9414]
          Length = 264

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 87/239 (36%), Positives = 126/239 (52%), Gaps = 12/239 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL--RKAE 71
           R+ K++A+ GIASRRE E MI + RV++NG+L       V    D I VDG P+  ++  
Sbjct: 4   RLQKILAQWGIASRRESEEMIRRSRVRINGVLA-HLGQKVDPERDKISVDGKPVYAQQRP 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLLTNDG 128
                L HKP G+V+T  DP GR TV D LP    +      VGRLD  + G L+LTNDG
Sbjct: 63  PLIYLLLHKPAGVVSTCYDPQGRKTVLDLLPPELRKGSGLHPVGRLDAESTGALILTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS    + Y+V   G   +  L + +KG+V++G      +V L      N+ 
Sbjct: 123 DLTFGLTHPSHSIPKTYQVLVKGHPSEAVLEMWRKGVVLEGRKTRPAKVHLIESLAKNSH 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-----LLAGSTREVSKKILR 242
           + + L+EG+NR+I++V +   + V +L R S GP QL       L  G+ R +    +R
Sbjct: 183 LEIVLKEGRNRQIRRVAQQLGYPVIQLHRTSIGPIQLQMPKLPFLGEGNYRSLKSAEIR 241


>gi|255530412|ref|YP_003090784.1| RNA-binding S4 domain-containing protein [Pedobacter heparinus DSM
           2366]
 gi|255343396|gb|ACU02722.1| RNA-binding S4 domain protein [Pedobacter heparinus DSM 2366]
          Length = 472

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 67/236 (28%), Positives = 114/236 (48%), Gaps = 2/236 (0%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGV 65
           VQ++    R+++ I+ +GI SRR+ + +I    V VNG ++      +    D +  +G 
Sbjct: 230 VQKDDGLIRLNRYISNSGICSRRKADELIEAGVVSVNGEVVSELGHKIDPVKDQVRYNGE 289

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            L++ ++  + L      + TT    + R+ +     +   R+  VGRLD NT GLLL+T
Sbjct: 290 LLKREKKIYVLLNKPKDYITTTDDPQERRTVMQLVEKASRERIYPVGRLDRNTTGLLLMT 349

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  P     ++Y V     + Q  LN ++ G+ ++        V+  T  GS
Sbjct: 350 NDGDLADKLSHPKNGITKIYHVELSRSLSQGDLNKIQFGLELEDGIIKPDSVSYVTG-GS 408

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              V + +  GKNR ++++FE   + V +L R+ YG      L  G  R + +  L
Sbjct: 409 KREVGIQIHSGKNRIVRRIFEHLGYDVVKLDRVVYGNLTKKDLPRGRWRYLEEHEL 464


>gi|251771881|gb|EES52455.1| Pseudouridine synthase, Rsu [Leptospirillum ferrodiazotrophum]
          Length = 638

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 98/348 (28%), Positives = 160/348 (45%), Gaps = 3/348 (0%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIE 61
           D  I +E     R+ K++A  G+ASRR+ E++IA   V V+G ++      V      I 
Sbjct: 15  DSEIPEEADGRLRLHKILAHRGVASRRKSEQLIAAGSVTVDGEVVTEPGTRVDPKHQVIL 74

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           VDG PL +   T L+L++KP G+V+T  DP+GR T+ D  P I   ++ +GRLD  TEG 
Sbjct: 75  VDGRPLPREPETFLFLFYKPKGVVSTLFDPEGRPTLRDYFPGI-DPLLHIGRLDFQTEGA 133

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GIVIQGICYGDMQVTLD 180
           LLLTN+G L++ +  P  +  R Y V+  G +    L  + +  I + G     +++  +
Sbjct: 134 LLLTNNGDLSQRILHPRFEIPRTYLVKIQGGMSPAHLERMARGEIRLDGRPVVPLELVPE 193

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            Q  +NAW  + L EG+NRE++++FE  N+ V +L+R ++GP  L  L  G  R V+   
Sbjct: 194 RQTSTNAWYRITLTEGRNREVRRLFETLNYFVLKLVRTAFGPLTLAGLEPGEYRTVTPHE 253

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
               L     +    NLD+     +       +       +    + +   +    K   
Sbjct: 254 TELLLAGTRPQSLPKNLDSRFSRRDDDGGAPRSEGRRSGREEKVGQGSREPRRTTGKSAA 313

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                  R        ++G     +  +     +  RSP   S R  R
Sbjct: 314 PRGEGFDRPSRPRSAASRGSAFPKIRRTEGEWPSGVRSPREESGREAR 361



 Score = 36.3 bits (82), Expect = 6.7,   Method: Composition-based stats.
 Identities = 10/111 (9%), Positives = 24/111 (21%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                  +E +          +                    +  S ++    +  +   
Sbjct: 474 PRRESFRKEGRSASSPSRPVRQYANSPDRPARPHADRFERPERPASREERPEGRFDRTRK 533

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           P       S          +      +  +  RR  SF  +R  R    ++
Sbjct: 534 PYQPSGRPSVPRSGAPRGQAREDRQSRTRDEGRRENSFGDERKPRSPQGRQ 584


>gi|240948952|ref|ZP_04753308.1| pseudouridine synthase [Actinobacillus minor NM305]
 gi|240296767|gb|EER47378.1| pseudouridine synthase [Actinobacillus minor NM305]
          Length = 340

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 91/289 (31%), Positives = 131/289 (45%), Gaps = 10/289 (3%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVD 63
           N  +E    +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S   I +D
Sbjct: 52  NEKKEKVVGEKLQKILARAGQGSRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRID 111

Query: 64  GVPLRKAERT-----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           G  +            L  Y     L T        +          SR ++VGRLDINT
Sbjct: 112 GHLINLIPTQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWVAVGRLDINT 171

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLL T DG LA  L  PS +  R Y VR  G VD+  L  L+KG+ ++       Q+ 
Sbjct: 172 SGLLLFTTDGELANRLMHPSREVEREYSVRVFGNVDEAMLQRLRKGVQLEDGPANFKQIK 231

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
                G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L  +L  G   E+ 
Sbjct: 232 AVGGTGINQWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKLEKSLPRGGWEEMG 291

Query: 238 KKI---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
            +    LRE +G     E +V++      +      +            
Sbjct: 292 LEQVNYLRELVGLPAETETKVDVTKNRRRTNVRQIRKAVKQHAKYRAKA 340


>gi|193212142|ref|YP_001998095.1| pseudouridine synthase [Chlorobaculum parvum NCIB 8327]
 gi|193085619|gb|ACF10895.1| pseudouridine synthase [Chlorobaculum parvum NCIB 8327]
          Length = 247

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 110/241 (45%), Gaps = 2/241 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
                  R++K +A  GIASRR  ++++ + RV VNG + ++  + +    D + VDG  
Sbjct: 4   SAQDEKVRINKYLAMCGIASRRAADQLVLEGRVMVNGHVADQPGLQIDPKHDEVIVDGRH 63

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           + + E  ++++       V T S  +       +   +  RV  VGRLD  + GLL+LTN
Sbjct: 64  MAQPEHKKVYILFNKPRNVITTSHDERDRQQILDFVDVPERVFPVGRLDRKSTGLLILTN 123

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS+   + Y      +     L+ L  G+ ++                  
Sbjct: 124 DGTLAHRLMHPSSLVQKEYLAELDAKFPGSMLSKLTSGMRLKDTGEKVSPCRAKILDDGM 183

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + + V + EGKN +++++F    ++V RL R++Y     G L  G  R +S+K +     
Sbjct: 184 SVL-VSIHEGKNHQVRRMFSTLGFEVKRLDRVAYAGLTPGELRRGEWRYLSRKEVEHLYR 242

Query: 247 P 247
            
Sbjct: 243 L 243


>gi|261821582|ref|YP_003259688.1| 23S rRNA pseudouridylate synthase B [Pectobacterium wasabiae
           WPP163]
 gi|261605595|gb|ACX88081.1| pseudouridine synthase [Pectobacterium wasabiae WPP163]
          Length = 294

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 82/293 (27%), Positives = 125/293 (42%), Gaps = 7/293 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIEGIIQAGRVSVDGKVATLGDRVEVTKATKIRIDGHVVTVKE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          SR ++VGRLD+NT GLLL T 
Sbjct: 62  TEETVCRVLVYYKPEGELCTRNDPDGRPTVFDRLPKIQGSRWVAVGRLDVNTSGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  G+VD +K+  L KG+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGEVDDEKIKQLSKGVQLEDGPAAFRTIRYQGGEGLN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   +  G   E+  + L    
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDITLPKGIPRGGWAEMPLEQLNYLR 241

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
               L    V+          +  ++     +     +      +        
Sbjct: 242 ELVQLPAETVSKLPVERERRRVKANQIRRAVKRHSQISSAPARRTSPKPKRNG 294


>gi|191637730|ref|YP_001986896.1| Pseudouridine synthase [Lactobacillus casei BL23]
 gi|190712032|emb|CAQ66038.1| Pseudouridine synthase [Lactobacillus casei BL23]
 gi|327381795|gb|AEA53271.1| Ribosomal small subunit pseudouridine synthase A [Lactobacillus
           casei LC2W]
 gi|327384957|gb|AEA56431.1| Ribosomal small subunit pseudouridine synthase A [Lactobacillus
           casei BD-II]
          Length = 236

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 56/228 (24%), Positives = 91/228 (39%), Gaps = 2/228 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++     SR+EV+ +I  +RV+V G L+     NV+    +EV+          
Sbjct: 1   MRLDKYLSHLQFGSRKEVKALIRDKRVRVAGDLITDPGYNVLPGIAVEVNDAQADGPLEV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +      +  T                    +  VGRLD +T GLLLLT DG L   
Sbjct: 61  DYLMNKPAGVITATEDPTQSTVLDLIRPHDYRPGLYPVGRLDKDTTGLLLLTTDGNLGHA 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P+    + Y       +  D    L+ GI ++       QV +         + + +
Sbjct: 121 LLSPNRHIAKTYAATLAKTLTADMKQQLETGIDLKDFTTAPAQVVVLPDTDGKR-IQITI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
            EGK  ++K++    + +V  L RI+ GP  L   L AG  R ++   
Sbjct: 180 TEGKFHQVKRMLLAVDNEVTALTRIAMGPLSLPADLAAGEYRALTDDE 227


>gi|329767586|ref|ZP_08259107.1| hypothetical protein HMPREF0428_00804 [Gemella haemolysans M341]
 gi|328839213|gb|EGF88797.1| hypothetical protein HMPREF0428_00804 [Gemella haemolysans M341]
          Length = 235

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 106/233 (45%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K I+     SR E +++I +  V +N IL++     V   +D + V+G  L   + 
Sbjct: 1   MRLDKFISTTTTLSRAEAKKIIKKG-VLINNILVKSPDYKVDELSDQVIVNGERLVYQKY 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      +  T    +              +V  VGRLD +TEGL+LLTNDG LA 
Sbjct: 60  IYIMMNKPKNVVSATEDAVEKTVVDILEEKDRIHKVFPVGRLDKDTEGLMLLTNDGELAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V   G++  + + L++ GI+I G       ++ +       +  ++
Sbjct: 120 KLISPKKDVEKKYYVEVSGKLKDEYIELVENGIIIDGGYKCKSARLEILESNEEKSRASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
            + EGK  ++K++ +     V  L R+S G  +L   L  G  R +++K L+ 
Sbjct: 180 FITEGKFHQVKRMMKALGTTVTYLKRLSIGSLKLDENLKLGEYRYLTEKELKN 232


>gi|77164554|ref|YP_343079.1| pseudouridine synthase, Rsu [Nitrosococcus oceani ATCC 19707]
 gi|254433620|ref|ZP_05047128.1| conserved hypothetical protein, putative [Nitrosococcus oceani
           AFC27]
 gi|76882868|gb|ABA57549.1| ribosomal large subunit pseudouridine synthase B [Nitrosococcus
           oceani ATCC 19707]
 gi|207089953|gb|EDZ67224.1| conserved hypothetical protein, putative [Nitrosococcus oceani
           AFC27]
          Length = 268

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 81/267 (30%), Positives = 122/267 (45%), Gaps = 7/267 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
           +R+ K++AR G+ SRREVE  I   RV++NGI        V   D + V+G PL      
Sbjct: 3   ERLQKILARGGLGSRREVEEWIKAGRVRINGIPAR-LGDKVSDEDQVTVNGRPLSPRRLQ 61

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 +  +     + +        +           R +SVGRLDINT GLLL T DG
Sbjct: 62  APSSQVILYHKPAGEICSRKDPEGRPTVFRSLPRPRQGRWVSVGRLDINTSGLLLFTTDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PSTQ  R Y VR  G V +  L  L++G+ ++       ++     +G+N W
Sbjct: 122 ELANRLMHPSTQVEREYAVRVLGTVTEVILERLQRGVQLEDGLASFKRILDAGGEGANHW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
             V L EG+ RE+++++E    +V+RLIRI +GP  L   L  G  R +     +  L  
Sbjct: 182 YHVILWEGRKREVRRLWESQGIQVSRLIRIRFGPVSLPPGLRMGRWRFLEPSEFKALLEI 241

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNI 274
             +E+          ++    + R   
Sbjct: 242 GGVEQRTTRFQPRSKNNRRGRQGRKQG 268


>gi|117919365|ref|YP_868557.1| pseudouridine synthase, Rsu [Shewanella sp. ANA-3]
 gi|117611697|gb|ABK47151.1| Pseudouridine synthase, Rsu [Shewanella sp. ANA-3]
          Length = 236

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 65/233 (27%), Positives = 111/233 (47%), Gaps = 11/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-RAAVNVMST----DHIEVDGVPLR 68
            R++K +A+ GI+SRRE  R+I   R+ +NG + +   AV+  +     D + +D  P+ 
Sbjct: 1   MRLAKYLAQCGISSRREACRLIEAGRISLNGKIAKHTDAVHFDADGQCLDSLCLDEKPIS 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            AE    W+++K   + T     D   +   +L     R+  VGRLD ++ GLLLLTNDG
Sbjct: 61  GAEALSYWIFNKA--VGTDCRLLDADKSSLLHLLPTTPRLYPVGRLDKDSRGLLLLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS    + Y V+     +   +  +  G+  + +     QVT  +       
Sbjct: 119 ELTHKLMHPSFAHSKTYHVQLDRPFNDAFIAQMASGVQYKEVRTLPCQVTRLSADR---- 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             + L +G NR+I+++     +KV  L R++     L +L  G  R +S + +
Sbjct: 175 FEIVLTQGLNRQIRRMSNALGYKVIDLQRVALMTLTLASLAEGEMRPLSPEEI 227


>gi|145641201|ref|ZP_01796781.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae R3021]
 gi|145274038|gb|EDK13904.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae 22.4-21]
          Length = 357

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 89/288 (30%), Positives = 131/288 (45%), Gaps = 10/288 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 67  LRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +  +         L  Y     L T        +          SR I+VGRLDINT GL
Sbjct: 130 INLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWIAVGRLDINTSGL 189

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQVD   L  L+ G+ ++       ++    
Sbjct: 190 LLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRNGVQLEDGPANFKEIKFTG 249

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 250 GVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEMDLEN 309

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
              LRE +G     E ++++       ++    +        +   + 
Sbjct: 310 VNYLRELVGLPAETETKLDVKQASRRLKSGQIRKAVKRYSEMNKRYKK 357


>gi|229846229|ref|ZP_04466341.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae 7P49H1]
 gi|229811233|gb|EEP46950.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae 7P49H1]
          Length = 357

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 90/288 (31%), Positives = 132/288 (45%), Gaps = 10/288 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 67  LRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +  +         L  Y     L T        +          SR I+VGRLDINT GL
Sbjct: 130 INLSHAQKEICRVLMYYKPEGELCTRSDPKGRATVFDRLPRLTGSRWIAVGRLDINTSGL 189

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++    
Sbjct: 190 LLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGPANFKEIKFTG 249

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 250 GVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEMDLEN 309

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
              LRE +G     E ++++       ++    +        +   + 
Sbjct: 310 VNYLRELVGLPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>gi|254416564|ref|ZP_05030315.1| conserved hypothetical protein, putative [Microcoleus
           chthonoplastes PCC 7420]
 gi|196176530|gb|EDX71543.1| conserved hypothetical protein, putative [Microcoleus
           chthonoplastes PCC 7420]
          Length = 255

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 71/247 (28%), Positives = 115/247 (46%), Gaps = 19/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK--- 69
           +RV K+I++ GIASRR+ E+MI   RV++NG +++         TD IEV+G  L+    
Sbjct: 3   ERVQKIISQWGIASRRQAEKMIVAGRVRLNGTVVQ-LGQKANPETDLIEVNGQRLKPSNR 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------PSIFSRVISVGRLDINTEG 120
            +   L L      + T  +     + +                   +  VGRLD+ + G
Sbjct: 62  PQAIYLLLNKPVGVVSTCRNYRVCNTILEKRRTVLDLLPSTIRQGQGIHPVGRLDMESTG 121

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
            L+LTNDG L   L  P     + YRV   G   +  L+  ++G+ + G      QV + 
Sbjct: 122 ALILTNDGTLTYKLTHPRHHVPKTYRVWVKGHPPESILSAWRQGVDLSGRTTLPAQVRVL 181

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-----LLAGSTRE 235
            Q+     + + L EG+NR+I++V +   + V  L R + GP QL       LL+G  R 
Sbjct: 182 KQQPDKTLLEIVLTEGRNRQIRRVADLLGYPVIHLHRTAIGPIQLQRPGEPILLSGHYRY 241

Query: 236 VSKKILR 242
           + +  +R
Sbjct: 242 LEEFEIR 248


>gi|313113861|ref|ZP_07799427.1| conserved hypothetical protein [Faecalibacterium cf. prausnitzii
           KLE1255]
 gi|310623827|gb|EFQ07216.1| conserved hypothetical protein [Faecalibacterium cf. prausnitzii
           KLE1255]
          Length = 276

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 84/273 (30%), Positives = 133/273 (48%), Gaps = 3/273 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K++A  G+ SRR  E++IA+ RVKVNG  ++       + D + VD   +   +  
Sbjct: 4   ERIQKIMAEQGLCSRRAAEQIIAEGRVKVNGHPVKVGDKMDPNRDVLHVDDERIYIRKDQ 63

Query: 74  --RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                  +KP G VTT SD  GR TV + +  I +R+  VGRLD ++EGLLL+TNDG  A
Sbjct: 64  QMYYLALYKPRGYVTTASDELGRKTVMELVSDIPARLYPVGRLDKDSEGLLLMTNDGAFA 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVT 190
           + +  PS    ++YRV    + D+ ++  L  G+V+          + + T +     + 
Sbjct: 124 QAVTHPSGGISKLYRVTVQPRADESQILKLSSGVVLDDGTKTMPCAINVVTDEPGRTVME 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L+EGKNREI+++ E    +V RL R + G  +LG L  G+ RE++K  +         
Sbjct: 184 MTLKEGKNREIRRMCETVGLEVVRLKRNAEGVVKLGMLKPGTYRELTKAEINGLRAAAAK 243

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
             AQ    A    +       P      P    
Sbjct: 244 GRAQTRSAAVQSKAAERRPRGPVGKGTAPKKRK 276


>gi|268589491|ref|ZP_06123712.1| ribosomal large subunit pseudouridine synthase B [Providencia
           rettgeri DSM 1131]
 gi|291315159|gb|EFE55612.1| ribosomal large subunit pseudouridine synthase B [Providencia
           rettgeri DSM 1131]
          Length = 339

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 84/301 (27%), Positives = 135/301 (44%), Gaps = 10/301 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPL 67
           +    +++ K++AR+G  SRRE+E  +   R+ V+G +      V V     I +DG  L
Sbjct: 38  KPQKTEKLQKILARSGHGSRREIETFLQAGRISVDGKIATLGDRVEVTPATKIRLDGRLL 97

Query: 68  RKAERTRLWL-----YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
              E  +        Y     L T H      +          +R I+VGRLD+NT GLL
Sbjct: 98  AIKEPEKEICRVMAYYKPEGELCTRHDPEGRPTVFNRLPRLTGARWIAVGRLDVNTSGLL 157

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L T DG LA  L  PS +  R Y VR  G+++  K+  L +G+ ++        V+    
Sbjct: 158 LFTTDGELANRLMHPSREVEREYAVRVFGEINDAKIRQLTQGVQLEDGPASFKTVSYRGG 217

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI- 240
           +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  +  
Sbjct: 218 EGMNQWFNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDIDLPKGLPRGGWTELGLEQT 277

Query: 241 --LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             LRE +   +  E++V ++      +     R              K+ SS+     + 
Sbjct: 278 NYLRELVELPVETESKVAVERDQRRIKANQIRRAVKRHTQVASRPASKRQSSRPTAKRRT 337

Query: 299 K 299
           +
Sbjct: 338 R 338


>gi|304387883|ref|ZP_07370057.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           meningitidis ATCC 13091]
 gi|304338148|gb|EFM04284.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           meningitidis ATCC 13091]
          Length = 252

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 107/255 (41%), Gaps = 20/255 (7%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K          R+SK +A+ G+ SRRE +  I Q  V VNG         V   D I
Sbjct: 1   MNSKISSDHTEDTMRLSKRMAQLGLCSRREADGYIEQGWVTVNGKTA-VLGQKVSPADRI 59

Query: 61  EVD---------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           E++                 P+          Y     L+T  +  +G +      P   
Sbjct: 60  ELNKKAHEQQAARITILLNKPVGYVSAQAEKGYKSAAELITPENHWEGDTGRIRFDPKHK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             +   GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+
Sbjct: 120 IGLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGL 179

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G      QV    +      +   L++GK R+I+++ E    +V  L RI  G  +L
Sbjct: 180 SLDGEKLRPAQVEWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>gi|290475891|ref|YP_003468784.1| 16S rRNA pseudouridylate 516 synthase [Xenorhabdus bovienii
           SS-2004]
 gi|289175217|emb|CBJ82020.1| 16S rRNA pseudouridylate 516 synthase [Xenorhabdus bovienii
           SS-2004]
          Length = 235

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 103/237 (43%), Gaps = 7/237 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR +V R +   RV V+  +++  A  +     I  +G  L +   +
Sbjct: 1   MRLDKFLSQQLGISRNDVGRELRASRVTVDDEVIKSGAYKLKPDHQIAYEGSVLEQLGGS 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DP   + ++     +  ++ S GRLDI+T GL+LLT+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPTNPTILYFIDEPVAHKLHSAGRLDIDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +  D       G+ + G        ++ +         V +
Sbjct: 121 ITSPKHHCEKTYLVTLEYPISDDTEMKFLAGVQLNGEKTLTKPAKLEII----EPHRVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGP 247
            +REG+  ++K++F      V  L R   G   L + L  G  R ++K  +     P
Sbjct: 177 SIREGRYHQVKRMFAAVGNHVVELHRERVGQIYLDSTLEPGEYRALTKHEINSIQVP 233


>gi|145631249|ref|ZP_01787022.1| predicted methyltransferase [Haemophilus influenzae R3021]
 gi|144983176|gb|EDJ90671.1| predicted methyltransferase [Haemophilus influenzae R3021]
          Length = 357

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 90/288 (31%), Positives = 132/288 (45%), Gaps = 10/288 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QPKVEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 67  LRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +  +         L  Y     L T        +          SR I+VGRLDINT GL
Sbjct: 130 INLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWIAVGRLDINTSGL 189

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++    
Sbjct: 190 LLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGPANFKEIKFTG 249

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 250 GVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEMDLEN 309

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
              LRE +G     E ++++       ++    +        +   + 
Sbjct: 310 VNYLRELVGLPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>gi|309973338|gb|ADO96539.1| 23S rRNA pseudouridylate synthase RluB [Haemophilus influenzae
           R2846]
          Length = 357

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 89/288 (30%), Positives = 132/288 (45%), Gaps = 10/288 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 67  LRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +  +         L  Y     L T        +          SR I+VGRLDINT GL
Sbjct: 130 INLSHAQKEICRVLMYYKPEGELCTRSDPKGRATVFDRLPRLTGSRWIAVGRLDINTSGL 189

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++    
Sbjct: 190 LLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGPANFKEIKFTG 249

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
             G N W  + L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 250 GVGINQWYDITLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEMDLEN 309

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
              LRE +G     E ++++       ++    +        +   + 
Sbjct: 310 VNYLRELVGLPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>gi|219872044|ref|YP_002476419.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           parasuis SH0165]
 gi|219692248|gb|ACL33471.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           parasuis SH0165]
          Length = 339

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 90/291 (30%), Positives = 135/291 (46%), Gaps = 10/291 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDH 59
           ++ +N   +    +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S+  
Sbjct: 48  IETENKANDKIVGEKLQKILARAGQGSRREIEEVIAAGRVSVDGKIAMLGDRVQVSSSTK 107

Query: 60  IEVDGVPLRKAERT-----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
           I +DG  +            L  Y     L T        +          SR I+VGRL
Sbjct: 108 IRIDGNLVSLIPTQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWIAVGRL 167

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DINT GLLL T DG LA  L  PS +  R Y VR  G+V+   +  L+KG+ ++      
Sbjct: 168 DINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGEVNDAMIQRLRKGVQLEDGPANF 227

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
            Q+      G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L  +L  G  
Sbjct: 228 KQIKAVGGTGINQWFDVTLTEGRNREVRRLWESQGIQVSRLIRIRYGNIKLEKSLPRGGW 287

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD 281
            E+  +    LRE +G     E +V++      + T    +          
Sbjct: 288 EEMGLEQVNYLRELVGLKPETETKVDVTKARRRTSTRQIRKAVKQHTKYRK 338


>gi|291513764|emb|CBK62974.1| pseudouridine synthase family [Alistipes shahii WAL 8301]
          Length = 455

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 114/229 (49%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ IA++GI SRRE +  I    V VNG ++      V+ TD +  +  P++  ++ 
Sbjct: 221 MRLNRFIAQSGICSRREADDFITAGVVSVNGKIVTELGTKVLPTDEVRFNDEPVQGEKKV 280

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L      + +      G++ +     +   R+  VGRLD N+ GLLL TNDG L + 
Sbjct: 281 YLVLNKPKGYVTSLDDPHAGKTVMELVSGACTERIYPVGRLDKNSLGLLLFTNDGDLTKQ 340

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  PS +  ++Y+V     + +  ++ + +G+ ++       +  +   K +   V + +
Sbjct: 341 LTHPSYKKKKIYQVTLDKPLTRADMDRIAEGVTLEDGEIFADE--ISYVKENKQEVGIEI 398

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
             G+NR ++++FEF  + V +L R+ Y       L  G+ R ++++ + 
Sbjct: 399 HSGRNRIVRRIFEFLGYTVTKLDRVYYAGLTKKNLKRGAWRFLTREEVE 447


>gi|332969784|gb|EGK08795.1| ribosomal large subunit pseudouridine synthase B [Psychrobacter sp.
           1501(2011)]
          Length = 354

 Score =  160 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 77/310 (24%), Positives = 129/310 (41%), Gaps = 7/310 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
            +++ K +AR G+ SRR++E +I   RV +N          V  +D I VDG  ++    
Sbjct: 46  TEKLQKALARMGLGSRRQMEEVIKAGRVSINQKPAT-IGDRVEQSDEIRVDGRLIKYKSE 104

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R  L  Y     + + +      +           R I VGRLDIN+ GLLL TND
Sbjct: 105 REKRRRVLAYYKPEGEICSANDPEGRTTVFERLPKLTHDRWIMVGRLDINSTGLLLFTND 164

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS + +R Y VR  G++  + +  L  G++++        +     +G N 
Sbjct: 165 GELAHRLMHPSNEIVREYAVRILGELTPEMMRNLTDGVMLEDGLAKFEDIRQGGGEGVNK 224

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V L+EG+NRE++++ E    KV+RL+R SYG   L   L  G   E+ +K +   + 
Sbjct: 225 WYHVKLKEGRNREVRRLIESQGLKVSRLLRTSYGSVDLPKELRTGRFIELDRKEIHRLID 284

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              +   +          +     +  + +      +R  +  +   G +     +    
Sbjct: 285 LVGIRPREDMGVHGKAKEKKERFQKKPLKARTIRTSSRSGRAGTTATGRNSNPSSSNTRG 344

Query: 307 RRNLASNVWM 316
           R         
Sbjct: 345 RDTGNRGSKR 354


>gi|326796234|ref|YP_004314054.1| pseudouridine synthase Rsu [Marinomonas mediterranea MMB-1]
 gi|326546998|gb|ADZ92218.1| pseudouridine synthase Rsu [Marinomonas mediterranea MMB-1]
          Length = 298

 Score =  160 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 90/302 (29%), Positives = 132/302 (43%), Gaps = 11/302 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +++ KV+ARAG+ SRRE+E  I + RV VNG +       V   D IE+DG P+      
Sbjct: 3   EKLQKVLARAGLGSRREMENRIREGRVVVNGEVAT-LGDRVGLEDQIELDGYPVSVSGAG 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             R  +        + T        +           R I+VGRLDINT GLLL T DG 
Sbjct: 62  QNRRVIIYNKPEGEVCTRKDPEGRPTVFDRLPKLRGERWIAVGRLDINTSGLLLFTTDGE 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  PST+  R Y VR  GQV  + +  LKKG+++         V     +G N W 
Sbjct: 122 LANRLMHPSTEIDREYLVRVMGQVTDEHIATLKKGVLLDDGMASFSDVVDGGGEGINHWF 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
            V L EG+NRE+++++E    KVNRL R+ +GP  L      G   E+ +  +       
Sbjct: 182 YVCLMEGRNREVRRLWESQGLKVNRLKRVRFGPVFLPSKAKVGRWVEMEEAEVNGLCELV 241

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
            ++ A +         +   R      ++      R  K    ++   ++ K   P  R 
Sbjct: 242 DIKPAPIKQKTKQEQEDLKRRR-----AKQVPGKARRTKGFDWQSSDKQEFKPRKPGKRS 296

Query: 309 NL 310
             
Sbjct: 297 FR 298


>gi|308176960|ref|YP_003916366.1| pseudouridylate synthase [Arthrobacter arilaitensis Re117]
 gi|307744423|emb|CBT75395.1| pseudouridylate synthase [Arthrobacter arilaitensis Re117]
          Length = 373

 Score =  160 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 78/236 (33%), Positives = 127/236 (53%), Gaps = 3/236 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPL 67
           E     R+ K +A AG+ASRR  E MI + RV+VNG L+      V    D I VDG+ +
Sbjct: 129 EQQDGIRLQKAMANAGVASRRVCEEMILEGRVEVNGNLVVELGSRVDPAKDRIHVDGMRI 188

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLT 125
           +  +  R ++++KP  ++ T  DP+GR T+ D   +     R+  VGRLD  TEG+L+LT
Sbjct: 189 QMNQANRYFVFNKPKHVMCTMDDPEGRRTIADYFKNEHHSLRLFHVGRLDYKTEGVLILT 248

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L+ P  +  + Y V+  G + +   N L++G+ ++        + +      
Sbjct: 249 NDGELANRLQHPKYEVPKTYLVQIPGPLPRAVSNQLREGVKLEDGWIKVDDLKIIATTPK 308

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +  V V L  G+NR ++++F+     V RL+R++ GP QLG    G+ R +  + +
Sbjct: 309 HVMVEVTLHSGRNRIVRRMFDEVGHPVQRLVRVAVGPVQLGDQKQGTIRSLGNQEV 364


>gi|165976586|ref|YP_001652179.1| pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 3
           str. JL03]
 gi|303250091|ref|ZP_07336293.1| ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|303253264|ref|ZP_07339413.1| ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 2 str. 4226]
 gi|307246075|ref|ZP_07528157.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|307248183|ref|ZP_07530211.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 2 str. S1536]
 gi|307259493|ref|ZP_07541218.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 11 str. 56153]
 gi|165876687|gb|ABY69735.1| probable pseudouridine synthase [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|302647946|gb|EFL78153.1| ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 2 str. 4226]
 gi|302651154|gb|EFL81308.1| ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|306853010|gb|EFM85233.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|306855360|gb|EFM87535.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 2 str. S1536]
 gi|306866429|gb|EFM98292.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 11 str. 56153]
          Length = 349

 Score =  160 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 91/286 (31%), Positives = 132/286 (46%), Gaps = 10/286 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGV- 65
           +E    +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S   I +DG  
Sbjct: 64  KEKVVGEKLQKILARAGQGSRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNL 123

Query: 66  ----PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
               P++K     L  Y     L T        +          +R I+VGRLDINT GL
Sbjct: 124 ISLIPVQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGARWIAVGRLDINTSGL 183

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  G +D+  L  L+KG+ ++       Q+    
Sbjct: 184 LLFTTDGELANRLMHPSREVEREYSVRVFGNIDEAMLQRLRKGVQLEDGPANFKQIKTVG 243

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 244 GTGLNQWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKLEKGLPRGGWEEMGLEQ 303

Query: 241 ---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
              LRE +G     E +V++      +      +            
Sbjct: 304 VNYLRELVGLPAETETKVDVTKNRRRTNIRQIRKAVKQHSKYRTKA 349


>gi|307250415|ref|ZP_07532362.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 4 str. M62]
 gi|306857544|gb|EFM89653.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 4 str. M62]
          Length = 349

 Score =  160 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 91/286 (31%), Positives = 132/286 (46%), Gaps = 10/286 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGV- 65
           +E    +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S   I +DG  
Sbjct: 64  KEKVVGEKLQKILARAGQGSRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNL 123

Query: 66  ----PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
               P++K     L  Y     L T        +          +R I+VGRLDINT GL
Sbjct: 124 ISLIPVQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGARWIAVGRLDINTSGL 183

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  G +D+  L  L+KG+ ++       Q+    
Sbjct: 184 LLFTTDGELANRLMHPSREVEREYSVRVFGNIDEAMLQRLRKGVQLEDGPANFKQIKTVG 243

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 244 GTGLNQWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKLEKGLPRGGWEEMGLEQ 303

Query: 241 ---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
              LRE +G     E +V++      +      +            
Sbjct: 304 VNYLRELVGLPAETETKVDVTKNRRRTNIRQIRKAVKQHSKYRTKA 349


>gi|302550431|ref|ZP_07302773.1| pseudouridine synthase [Streptomyces viridochromogenes DSM 40736]
 gi|302468049|gb|EFL31142.1| pseudouridine synthase [Streptomyces viridochromogenes DSM 40736]
          Length = 372

 Score =  160 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 110/233 (47%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
               +R+ KV+ARAG  SRR  E +I + RV++NG ++      V    D I+VDG+ + 
Sbjct: 132 EQEGERLQKVLARAGFGSRRACEELIEEARVEINGEIVLEQGRRVDPEKDEIKVDGLTVA 191

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   L      + T       +  + D + +  +R+  VGRLD  TEG++LLTN G
Sbjct: 192 TQSYQFFSLNKPAGVVSTMEDPEGRQ-CLGDYVTNRETRLFHVGRLDTETEGVILLTNHG 250

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     + Y     G + +D    LK GI ++          +  Q G N  
Sbjct: 251 ELAHRLTHPKYGVKKTYLAHIVGPIPRDLGKQLKDGIQLEDGYARADHFRVVQQTGKNYL 310

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L EG+   ++++     + V++L+R+++GP  LG   +G  R +S   +
Sbjct: 311 VEVTLHEGRKHIVRRMLAEAGFPVDKLVRVAFGPITLGDQKSGWLRRLSNTEV 363


>gi|134301954|ref|YP_001121923.1| putative RNA pseudouridine synthase B [Francisella tularensis
           subsp. tularensis WY96-3418]
 gi|134049731|gb|ABO46802.1| putative RNA pseudouridine synthase B [Francisella tularensis
           subsp. tularensis WY96-3418]
          Length = 271

 Score =  160 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 86/259 (33%), Positives = 125/259 (48%), Gaps = 9/259 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+  N   +   P+R+ K++A+ GI SRR++E  I Q RVKVNG +        +  D I
Sbjct: 1   MRRANQNNDKN-PERLQKLLAKYGIGSRRKIEEYIEQGRVKVNGKVAT-LGDKAIEADKI 58

Query: 61  EVDGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
             DG  L            +  + +   + T+  + D ++          SR I VGRLD
Sbjct: 59  SFDGKALHSYGQPMTRPRVVIYHKREGEVCTSKDEKDRQTVFDSLPKLAKSRWIMVGRLD 118

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGD 174
           INT GLLL T DG LA  L  PS Q  R Y VR  GQ    + +N LK+GI ++      
Sbjct: 119 INTTGLLLFTTDGDLANRLMHPSYQIEREYAVRVFGQQLSDETINKLKEGIQLEDGMAKF 178

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGST 233
             +     +G+N W  V L EG+NRE++++FE     V+RL RI +G   L   +  G T
Sbjct: 179 NSIKFSGGEGANLWYYVTLSEGRNREVRRMFEAVGVTVSRLTRIRFGDIILPKFVSRGKT 238

Query: 234 REVSKKILREQLGPHLLEE 252
            E++   +        L+E
Sbjct: 239 LELNPSEVNRLRKSVKLKE 257


>gi|257462340|ref|ZP_05626755.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           D12]
 gi|317060006|ref|ZP_07924491.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           D12]
 gi|313685682|gb|EFS22517.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           D12]
          Length = 239

 Score =  160 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 66/236 (27%), Positives = 113/236 (47%), Gaps = 3/236 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           ++EN    R++K +A  G+ASRR+V+  I + R+ VNG L       V   D I V+G  
Sbjct: 1   MEENK--IRINKFLASKGLASRRQVDLWIEEGRISVNGSLATS-GQKVSEEDDIVVNGKS 57

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           + + ++ +++        V +    D       +      R+  VGRLD  T GL+LLTN
Sbjct: 58  ISQKKQKKVYYLLYKEEEVLSAVKDDRGRRTVVDCVLSPYRIFPVGRLDYRTSGLILLTN 117

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L   +  P  +  + Y V   G + +++L  L++G+ ++        +     +  N
Sbjct: 118 DGDLFNRMMHPRAEIFKSYEVLAKGHLTKEQLKTLEEGVELEEGKTLAALIAKVKYEKGN 177

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +  + +REGKNR+I+++ E    +V RL R   G   L  L  G  R + +K + 
Sbjct: 178 TFFEISIREGKNRQIRRMVEAVGSRVYRLRRTKIGKLSLDGLSLGEYRALEEKEIE 233


>gi|327394043|dbj|BAK11465.1| ribosomal large subunit pseudouridine synthase B RluB [Pantoea
           ananatis AJ13355]
          Length = 294

 Score =  160 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 90/296 (30%), Positives = 131/296 (44%), Gaps = 10/296 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E MIA  RV V+G L         S    I +DG  +  AE
Sbjct: 2   SEKLQKVLARAGHGSRREIEAMIAAGRVSVDGKLATLGDRIENSKALKIRIDGHLVSIAE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T        +          SR I+VGRLD+NT GL+L T 
Sbjct: 62  SATEVCRVLAYYKPEGELCTRSDPEGRPTVFDRLPRLRGSRWIAVGRLDVNTCGLMLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD DK+  L KG+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDDKIRQLSKGVQLEDGPAAFKTLRFAGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
            W  V L EG+NRE+++++E    +V+RL+R+ YG   L   +  G   E+    L    
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLMRVRYGDITLPKGVPRGGWMELD---LPAVN 238

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
               +          +   +   R + N I       ++     +++N  SK+   
Sbjct: 239 YLRNMVGMDDETVTKLAVEKDRRRTKANQIRRAVKRHSQTSGRPARRNPGSKRNAT 294


>gi|27382606|ref|NP_774135.1| hypothetical protein bll7495 [Bradyrhizobium japonicum USDA 110]
 gi|27355778|dbj|BAC52760.1| bll7495 [Bradyrhizobium japonicum USDA 110]
          Length = 696

 Score =  160 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 144/339 (42%), Positives = 198/339 (58%), Gaps = 13/339 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           +     +R++K +ARAG+ASRR+ E M+ Q RV VNG ++   A+++   D + VDG PL
Sbjct: 371 KPKKAGERIAKALARAGLASRRDAEEMVTQGRVAVNGRVINSPALDITPNDVVTVDGKPL 430

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              ERTRL+LYHKP GL+TTH DP+GR TVFDNLP    R+ISVGRLD NTEGLLLLTND
Sbjct: 431 PPRERTRLFLYHKPRGLMTTHDDPEGRPTVFDNLPEGLPRLISVGRLDFNTEGLLLLTND 490

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GGLAR LELP T WLR YRVR HG V Q +L+ LK GI ++G+ YG +  TL+  +G+N 
Sbjct: 491 GGLARTLELPDTGWLRRYRVRAHGDVTQAQLDELKAGIEVEGVKYGPIDATLERDQGANV 550

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+   +REGKNRE++ V      +VNRLIR+SYGPFQLG +  G   E+  ++LREQLG 
Sbjct: 551 WLVFAIREGKNREVRNVCAHLGLEVNRLIRVSYGPFQLGEVPEGQVEEIKSRVLREQLGD 610

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            ++E++    D P               +   DD    +K  + K  +   +K    + +
Sbjct: 611 KVIEKSGAQFDVPQK-------------AAATDDGAPHEKKPASKRAVINDRKGRRVLVQ 657

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           R  +          +S      + +  +        +  
Sbjct: 658 RTGSEEARERNEAEASGYGPPRRPKRGYHGKRDLTPRED 696



 Score = 37.5 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 8/107 (7%), Positives = 19/107 (17%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              EE       P        R   +                        + +  +    
Sbjct: 85  RGGEERGERSFKPRGDRPFSDRGARDGEKRPFKPRGDRPSYGRDDRPPRSRDRDDSRAAG 144

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           R         +           + +   + S   P +    R   ++
Sbjct: 145 RTGDRKFGDKRPSAPRGDRPERKFDGERKFSRGAPDRSDRPRDRGER 191


>gi|313890958|ref|ZP_07824580.1| pseudouridylate synthase [Streptococcus pseudoporcinus SPIN 20026]
 gi|313120682|gb|EFR43799.1| pseudouridylate synthase [Streptococcus pseudoporcinus SPIN 20026]
          Length = 239

 Score =  160 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 62/239 (25%), Positives = 102/239 (42%), Gaps = 4/239 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A AG  SR +V+ ++  ++V VNG    +A   +    D +EV+G  +   E 
Sbjct: 1   MRLDKFLAEAGFGSRSQVKNLLKTKKVCVNGKNESQAKKQINPNLDRVEVEGQEVLYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T            +  +    V  VGRLD +T GLLLLTN+G LA 
Sbjct: 61  VYYMLNKPKGVVSATQDKVHQTVLDLLDATAKQKAVFPVGRLDKDTHGLLLLTNNGDLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            L  P     +VY     G +    +   +KGI +         + +         + V 
Sbjct: 121 RLLSPKKHVNKVYVAEVDGLMTSQDIEAFEKGIQLSDHQCQPAVLEILASDRDKFQSRVK 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
           + ++EGK  ++K++      +V  L R+  GP QL + L  G+ R++ K  +   L   
Sbjct: 181 IVIKEGKFHQVKRMVLACGKEVRDLQRLEMGPLQLDSTLDLGAFRKLEKSEIEALLNLP 239


>gi|213618826|ref|ZP_03372652.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 276

 Score =  160 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 57/281 (20%), Positives = 109/281 (38%), Gaps = 5/281 (1%)

Query: 21  ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHK 80
           + +GI SRRE +R I Q  V +NG         V++ D ++V+G  +   E   L L   
Sbjct: 1   SESGICSRREADRFIEQGNVFINGKRAA-IGDQVVAGDVVKVNGRLIEPREADDLVLIAL 59

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
              +    +  DG      +  +   R+  +GRLD +++GL+ LTN G L   +      
Sbjct: 60  NKPVGIVSTTEDGERDNIVDFVNHSKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGND 119

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
             + Y V     +  + +  +  G+ I G            +K +     + L +G NR+
Sbjct: 120 HEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFRITLVQGLNRQ 175

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAP 260
           I+++ E+F ++V +L R       L  +  G  R+++   L +         ++    A 
Sbjct: 176 IRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEGSSSEAKPKAK 235

Query: 261 IYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
                  ++     I +  +            +   K+K  
Sbjct: 236 AKPKTAGIKRPVVAIEKSNEKARPASSGKRFTSPGRKKKGR 276


>gi|60683236|ref|YP_213380.1| putative ribosomal large subunit pseudouridine synthase
           [Bacteroides fragilis NCTC 9343]
 gi|60494670|emb|CAH09471.1| putative ribosomal large subunit pseudouridine synthase
           [Bacteroides fragilis NCTC 9343]
          Length = 466

 Score =  160 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 57/241 (23%), Positives = 106/241 (43%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +   D +
Sbjct: 218 IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRADVV 277

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +     +    +  + L      + T+       + +     +   R+  VGRLD NT G
Sbjct: 278 KFHDETVSIERKVYVLLNKPKDCVTTSDDPQARLTVMDLVKGACAERIYPVGRLDRNTTG 337

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     + +  ++ +  GI ++            
Sbjct: 338 VLLLTNDGDLASKLTHPKYLKKKIYHVYLDKNLTKADMDQIAAGIQLEDGEIH-ADAISY 396

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           + +     V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++ 
Sbjct: 397 SDEVKRDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLTEQE 456

Query: 241 L 241
           +
Sbjct: 457 V 457


>gi|315222342|ref|ZP_07864248.1| conserved hypothetical protein [Streptococcus anginosus F0211]
 gi|315188675|gb|EFU22384.1| conserved hypothetical protein [Streptococcus anginosus F0211]
          Length = 246

 Score =  160 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 63/235 (26%), Positives = 107/235 (45%), Gaps = 4/235 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
              R+ K +   G+ SR EV+R++ +++V VNG +   A + +    D I V+   L   
Sbjct: 3   KKMRLDKFLVEMGLGSRTEVKRLLKKKQVLVNGKIETSAKIQIDENQDEISVNNQVLIYE 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                 L      +  T  D         N  +    V  VGRLDI+T GLLLLTN+G L
Sbjct: 63  RFVYYLLNKPKGVISATEDDKHRTVLDLLNENARQKEVFPVGRLDIDTHGLLLLTNNGAL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAW 188
           A  +  P     +VYR +  G + +  +   + GI ++       ++T+    ++   + 
Sbjct: 123 AHAMLSPKKHVAKVYRAKVDGIITEKDVEHFEAGIELKDFTCQPAKLTILEVNEEQQTSL 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           V + + EGK  ++K++ +     V  L R+S GP  L   L   + R ++K+ L 
Sbjct: 183 VEIIISEGKFHQVKRMVQACGKTVTDLERLSMGPLMLDERLELVTFRRLTKEELE 237


>gi|34497861|ref|NP_902076.1| pseudouridylate synthase [Chromobacterium violaceum ATCC 12472]
 gi|34103717|gb|AAQ60078.1| probable pseudouridylate synthase [Chromobacterium violaceum ATCC
           12472]
          Length = 242

 Score =  160 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 68/244 (27%), Positives = 104/244 (42%), Gaps = 20/244 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
            P R+SK +A  G+ SRRE +  I Q  VKV+G +       V+  + IE+D        
Sbjct: 2   EPVRLSKRMAELGLCSRREADSYIEQGWVKVDGEVA-VLGQKVLPHNQIEIDKKAQDAQS 60

Query: 64  -------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
                    P+          Y     L+   +      +     PS    +   GRLDI
Sbjct: 61  ARVTILLNKPVGYVSGQAEDGYLPAAALIKPENRWAEDGSRKRFQPSHLRGLAPAGRLDI 120

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           ++ GLL+LT DG +A+ L    ++  + Y VR  G++    L LL  G+ + G      +
Sbjct: 121 DSVGLLVLTQDGRIAKQLIGEHSEVEKEYLVRVEGELTPSGLALLNHGLELDGKKLLPAK 180

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V    +      +   LREGK R+I+++ E    +V  L RIS G  +LG L  G  R +
Sbjct: 181 VGWQNEDQ----LRFVLREGKKRQIRRMCELVGLRVVGLKRISIGKVKLGNLPTGQWRYL 236

Query: 237 SKKI 240
               
Sbjct: 237 RDDE 240


>gi|78184950|ref|YP_377385.1| pseudouridine synthase, Rsu [Synechococcus sp. CC9902]
 gi|78169244|gb|ABB26341.1| ribosomal large subunit pseudouridine synthase B [Synechococcus sp.
           CC9902]
          Length = 247

 Score =  160 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 65/235 (27%), Positives = 104/235 (44%), Gaps = 1/235 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP-LRKA 70
           T QR+ K++A AG+ SRR  E  +   RV V+G +         ++  IEVDGVP +   
Sbjct: 2   TRQRLQKLMAAAGLCSRRRGEDWLQAGRVTVDGRVASLGDQADPNSQLIEVDGVPLISVQ 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E     L      + +        + +        S +  VGRLD ++ G LLLT+ G L
Sbjct: 62  EPRVFLLNKPVGVICSCRDPQGRATVLDCLPHQERSGLHPVGRLDADSRGALLLTDQGEL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + YRV   G      L   + G+++ G      +V     +G+++ + 
Sbjct: 122 TLRLTHPRYNHAKTYRVLVRGIPSSQALRRWRDGLLLDGRLTRPARVHCLRSRGASSLLE 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           V L+EG+NR+I++V E     V  L R++    +L  L  G  R +  +     L
Sbjct: 182 VELKEGRNRQIRRVAELLGHPVIDLQRVAIDGIRLDDLAEGCWRRLDAREWSTIL 236


>gi|53715301|ref|YP_101293.1| ribosomal large subunit pseudouridine synthase B [Bacteroides
           fragilis YCH46]
 gi|253567192|ref|ZP_04844642.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           3_2_5]
 gi|265767788|ref|ZP_06095320.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           2_1_16]
 gi|52218166|dbj|BAD50759.1| ribosomal large subunit pseudouridine synthase B [Bacteroides
           fragilis YCH46]
 gi|251944023|gb|EES84542.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           3_2_5]
 gi|263252460|gb|EEZ23988.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           2_1_16]
 gi|301164755|emb|CBW24314.1| putative ribosomal large subunit pseudouridine synthase
           [Bacteroides fragilis 638R]
          Length = 466

 Score =  160 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 57/241 (23%), Positives = 106/241 (43%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +   D +
Sbjct: 218 IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRADVV 277

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +     +    +  + L      + T+       + +     +   R+  VGRLD NT G
Sbjct: 278 KFHDETVSIERKVYVLLNKPKDCVTTSDDPQARLTVMDLVKGACAERIYPVGRLDRNTTG 337

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     + +  ++ +  GI ++            
Sbjct: 338 VLLLTNDGDLASKLTHPKYLKKKIYHVYLDKNLTKADMDQIAAGIQLEDGEIH-ADAISY 396

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           + +     V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++ 
Sbjct: 397 SDEVKRDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLTEQE 456

Query: 241 L 241
           +
Sbjct: 457 V 457


>gi|309379383|emb|CBX21950.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 252

 Score =  160 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 68/255 (26%), Positives = 109/255 (42%), Gaps = 20/255 (7%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K          R+SK +A+ G+ SRRE +  I Q RV VNG         V   D I
Sbjct: 1   MNSKISSDHTEDTMRLSKRMAQLGLCSRREADGYIEQGRVTVNGKTA-VLGQKVSPADRI 59

Query: 61  EVD---------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           E++                 P+          Y     L+T+ +  +  ++     P   
Sbjct: 60  ELNKKAHEQQAARITILLNKPVGYVSAQAEKGYKSAAELITSENRWESDTSRIRFDPKHK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             +   GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+
Sbjct: 120 IGLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGL 179

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G      +V    +      +   L++GK R+I+++ E    +V  L RI  G  +L
Sbjct: 180 SLDGEKLRPAKVEWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>gi|255011767|ref|ZP_05283893.1| ribosomal large subunit pseudouridine synthase B [Bacteroides
           fragilis 3_1_12]
 gi|313149605|ref|ZP_07811798.1| ribosomal large subunit pseudouridine synthase B [Bacteroides
           fragilis 3_1_12]
 gi|313138372|gb|EFR55732.1| ribosomal large subunit pseudouridine synthase B [Bacteroides
           fragilis 3_1_12]
          Length = 466

 Score =  160 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 57/241 (23%), Positives = 106/241 (43%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +   D +
Sbjct: 218 IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRADVV 277

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +     +    +  + L      + T+       + +     +   R+  VGRLD NT G
Sbjct: 278 KFHDETVSIERKVYVLLNKPKDCVTTSDDPQARLTVMDLVKGACAERIYPVGRLDRNTTG 337

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     + +  ++ +  GI ++            
Sbjct: 338 VLLLTNDGDLASKLTHPKYLKKKIYHVYLDKNLTKADMDQIAAGIQLEDGEIH-ADAISY 396

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           + +     V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++ 
Sbjct: 397 SDEVKRDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLTEQE 456

Query: 241 L 241
           +
Sbjct: 457 V 457


>gi|237785455|ref|YP_002906160.1| putative pseudouridylate synthase [Corynebacterium kroppenstedtii
           DSM 44385]
 gi|237758367|gb|ACR17617.1| putative pseudouridylate synthase [Corynebacterium kroppenstedtii
           DSM 44385]
          Length = 278

 Score =  160 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 77/234 (32%), Positives = 114/234 (48%), Gaps = 4/234 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
              R+ KV+A AG+ASRR  E++I + RV+VNG ++ R  V V    D I VDG  +   
Sbjct: 36  EGIRLQKVLAAAGVASRRMSEKLIDEGRVEVNGDIVTRQGVRVDPDYDVIRVDGSRVVVD 95

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTND 127
           E  + +  +KP G+ +T  D  GR  V D +        R+  VGRLD  T+GLLLLTND
Sbjct: 96  ESMQYFALNKPRGVQSTMHDDMGRPCVGDIVGEKVDAGQRLFHVGRLDAATQGLLLLTND 155

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P     + Y     G+VD+  L  L +GI +           +       +
Sbjct: 156 GELANRLIHPKYGIKKTYLATVLGEVDKKDLRRLTQGIELDDGTARADDADIIDVWQGRS 215

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V V L EG+   ++++ +   + V  L+R      QLG    G+ R +++  L
Sbjct: 216 LVKVVLHEGRKHIVRRMLKAAGFPVQELVRTKIHTVQLGEQTPGTLRALNRSEL 269


>gi|325106158|ref|YP_004275812.1| RNA-binding S4 domain protein [Pedobacter saltans DSM 12145]
 gi|324975006|gb|ADY53990.1| RNA-binding S4 domain protein [Pedobacter saltans DSM 12145]
          Length = 396

 Score =  160 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 65/245 (26%), Positives = 116/245 (47%), Gaps = 7/245 (2%)

Query: 3   DKNIVQENFTP-----QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS- 56
            KN  Q++ TP      R+++ IA +GI SRR+ + +I    + VN +++      V   
Sbjct: 145 RKNTSQQSSTPKEPDQIRLNRYIANSGICSRRKADELITSGAITVNDVVVSELGAKVNPT 204

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           TD ++ +G  L++ +   + L      + TT    + ++ +     +   R+  VGRLD 
Sbjct: 205 TDKVKYNGQLLKREKMVYVLLNKPKDFITTTEDPQERKTVMELVKNATSERIYPVGRLDR 264

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NT GLLLLTNDG LA  L  P     ++Y V     + Q   N +  G+ ++        
Sbjct: 265 NTTGLLLLTNDGDLAEKLSHPRNNITKIYNVELSKNLTQGDFNKIAFGVELEDGFIKPDA 324

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V+     G+   + + +  GKNR ++++FE   ++V +L R+ Y       L  G  R +
Sbjct: 325 VSYV-SGGTKKEIGIQIHSGKNRIVRRIFESLGYEVEKLDRVIYANLTKKDLTRGKWRFL 383

Query: 237 SKKIL 241
           ++  +
Sbjct: 384 TENEI 388


>gi|262375673|ref|ZP_06068905.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           lwoffii SH145]
 gi|262309276|gb|EEY90407.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           lwoffii SH145]
          Length = 350

 Score =  160 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 91/341 (26%), Positives = 148/341 (43%), Gaps = 13/341 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
            +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG  +     
Sbjct: 2   SEKLQKVLARVGLGSRRYMEEVIAAGRVSVNGQIAQV-GERIEPGDELRIDGRKVAFQIE 60

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R  +  Y     + +     +  +           R + VGRLDIN+ GLLL TND
Sbjct: 61  DEIRRRVIIYYKPEGEICSRSDPENRPTVFEQLPAIPGDRWVMVGRLDINSTGLLLFTND 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V     N + KG+V+          +     G N 
Sbjct: 121 GELANRLMHPSNEIEREYAVRVMGEVTPQIRNNMLKGVVLDDGPAKFESFSELGGDGINR 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V ++EG+NRE++++FE    KV+RL+R  YG   L   L  G   E+ K  + + L 
Sbjct: 181 WFQVVVKEGRNREVRRIFESQGLKVSRLLRTRYGTVILPRELRTGRWIELDKNDI-DNLT 239

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL---SKQKKLAT 303
             +  + +        +     R +   ++     F R ++  S +       ++++   
Sbjct: 240 KAVELKPRQGTGLFGMAKRRNERMQDKPMAARRGGFLRQQRRDSDEQPQNNTGRERRDEN 299

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDS--GQREENHRRSPSFP 342
              RR+ A N    + +      D   G+REE    +P  P
Sbjct: 300 AYGRRDRAENQNGTQFVRRENRPDQGFGRREERDENAPRRP 340


>gi|260171988|ref|ZP_05758400.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           D2]
 gi|315920300|ref|ZP_07916540.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           D2]
 gi|313694175|gb|EFS31010.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           D2]
          Length = 482

 Score =  160 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 108/241 (44%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +  +D +
Sbjct: 234 IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVV 293

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P+    +  + L      + T+    + R+ +     +   R+  VGRLD NT G
Sbjct: 294 KFHDEPVSIERKVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTTG 353

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     + +  ++ +  GI ++            
Sbjct: 354 VLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADMDQIAAGIQLEDGEIH-ADAISY 412

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           T       V + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+  
Sbjct: 413 TDDFKKDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSEAE 472

Query: 241 L 241
           +
Sbjct: 473 V 473


>gi|145637046|ref|ZP_01792709.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae PittHH]
 gi|145269700|gb|EDK09640.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae PittHH]
          Length = 357

 Score =  160 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 90/288 (31%), Positives = 132/288 (45%), Gaps = 10/288 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 67  LRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +  +         L  Y     L T        +          SR I+VGRLDINT GL
Sbjct: 130 INLSHAQKEICRVLMYYKPEGELCTRSDPKGRATVFDRLPRLTGSRWIAVGRLDINTSGL 189

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++    
Sbjct: 190 LLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGPANFKEIKFTG 249

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 250 GVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEMDLEN 309

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
              LRE +G     E ++++       ++    +        +   + 
Sbjct: 310 VNYLRELVGLPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>gi|332687173|ref|YP_004456947.1| ribosomal small subunit pseudouridine synthaseA [Melissococcus
           plutonius ATCC 35311]
 gi|332371182|dbj|BAK22138.1| ribosomal small subunit pseudouridine synthaseA [Melissococcus
           plutonius ATCC 35311]
          Length = 243

 Score =  160 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 61/243 (25%), Positives = 105/243 (43%), Gaps = 5/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K ++ +G+ SR+EV++++ Q+ +KVNG L +     +    D++   G  +   + 
Sbjct: 1   MRLDKFLSDSGLGSRKEVKQLLKQKCIKVNGTLAKDGKQQISQIDDYVTHAGEKIVYQKY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      + +T    +               +  VGRLD +TEGLLLLTNDG LA 
Sbjct: 61  FYYVLNKPKNVISSTKDPIERTVVDLLAKKHYRKDIFPVGRLDKDTEGLLLLTNDGDLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSN--AWV 189
            L  P     + Y     G V +  + L  KG  ++        ++ +D     +    V
Sbjct: 121 QLLSPKKHVDKEYLAEIDGIVTEQDIKLFAKGFTLKNGEAVKPARLIIDQMDEGHQMTIV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
            + ++EGK  ++K+VFE    +V  L R+  G   L   L  G  R ++   L +     
Sbjct: 181 HLTIQEGKFHQVKRVFETIGKRVTYLKRLKMGSLSLDSDLPLGKYRPLTTVELAQLKQFK 240

Query: 249 LLE 251
             +
Sbjct: 241 NEK 243


>gi|145639281|ref|ZP_01794887.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae PittII]
 gi|145271584|gb|EDK11495.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae PittII]
 gi|309751158|gb|ADO81142.1| 23S rRNA pseudouridylate synthase RluB [Haemophilus influenzae
           R2866]
          Length = 357

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 90/288 (31%), Positives = 132/288 (45%), Gaps = 10/288 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 67  LRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +  +         L  Y     L T        +          SR I+VGRLDINT GL
Sbjct: 130 INLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWIAVGRLDINTSGL 189

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++    
Sbjct: 190 LLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGPANFKEIKFTG 249

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 250 GVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEMDLEN 309

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
              LRE +G     E ++++       ++    +        +   + 
Sbjct: 310 VNYLRELVGLPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>gi|322434202|ref|YP_004216414.1| pseudouridine synthase [Acidobacterium sp. MP5ACTX9]
 gi|321161929|gb|ADW67634.1| pseudouridine synthase [Acidobacterium sp. MP5ACTX9]
          Length = 312

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 86/292 (29%), Positives = 134/292 (45%), Gaps = 22/292 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE 71
            +R+ K++A+AG+ASRR+ E +I   RV+VNG ++        +T DHI VDG  ++  E
Sbjct: 23  GERLQKILAQAGLASRRKAEEIILDGRVQVNGTVVTELGTRADATKDHIRVDGKLIKGPE 82

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLT 125
           + + ++ +KP G VTT  DP  R TV   +               VGRLD  +EGLLL+T
Sbjct: 83  QQKYYMVNKPRGYVTTLDDPQHRPTVMQLMTPKSGPHETQVRLYPVGRLDYLSEGLLLMT 142

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-------------Y 172
           NDG LA  L   ST   + Y V+  G      L+ +++GI+I                  
Sbjct: 143 NDGDLANALSKASTGVEKTYLVKTSGVPPDSALDQIRRGIMIDRGRLDEVRAGRRDRILT 202

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
              +V L  + G N W  V L EG+NR+++K+FE     V ++ RI YG  +L  +  G 
Sbjct: 203 APAKVELVRR-GDNPWYEVTLTEGRNRQLRKMFEEVGHHVEKIRRIGYGALRL-DVAPGE 260

Query: 233 TREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
            RE+    +         ++ +   + P +S            +        
Sbjct: 261 FRELKPGEVMALDRASKGKKVEPKRNLPEFSKLKAPVKPKRPGAGKSYAAKS 312


>gi|146292026|ref|YP_001182450.1| pseudouridine synthase [Shewanella putrefaciens CN-32]
 gi|145563716|gb|ABP74651.1| pseudouridine synthase [Shewanella putrefaciens CN-32]
          Length = 242

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 63/237 (26%), Positives = 103/237 (43%), Gaps = 16/237 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILL--ERAAVNVMST---DHIEVDGVPLR 68
            R++K +A+ GI SRRE  R+I   R+ +NG +                D I +D  P+ 
Sbjct: 1   MRLAKYLAQCGIGSRREACRLINAGRITLNGKIAKHTNLVQRDAQGLCLDSICLDAEPIV 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + E    W+++K   + T     +   T   +L     R+  VGRLD ++ GLLLLTNDG
Sbjct: 61  ETEALAYWIFNKA--VGTDCRLLEQDKTSLLHLLPKAPRLYPVGRLDKDSRGLLLLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS    + Y VR       D +  +  G+  + +     QV   +       
Sbjct: 119 ELTHKLMHPSFAHSKTYHVRLDKPFTDDFVEQMASGVRYKDLQTLPCQVRRLSLDS---- 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-----GTLLAGSTREVSKKI 240
             + L +G NR+I+ + +   ++V  L R++     L     G L  G  R ++ + 
Sbjct: 175 FEIVLTQGLNRQIRHMSKALGYRVIDLERVAIMALNLRELASGELPEGQMRPLTPQE 231


>gi|317048303|ref|YP_004115951.1| pseudouridine synthase [Pantoea sp. At-9b]
 gi|316949920|gb|ADU69395.1| pseudouridine synthase [Pantoea sp. At-9b]
          Length = 290

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 87/290 (30%), Positives = 130/290 (44%), Gaps = 9/290 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV--MSTDHIEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E MI+  RV V+G L       +    +  I +DG  +  A
Sbjct: 2   SEKLQKVLARAGHGSRREIETMISAGRVSVDGKLAT-LGDRIENDKSLKIRIDGHLVSIA 60

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E        L  Y     L T +      +          SR I+VGRLD+NT GLLL T
Sbjct: 61  ESTTEVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPRLRGSRWIAVGRLDVNTCGLLLFT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  G+V  DK+  L KG+ ++        +     +G 
Sbjct: 121 TDGELANRLMHPSREVEREYAVRVFGEVGDDKIRQLSKGVQLEDGPAAFKTLRFAGGEGI 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           N W  V L EG+NRE+++++E    +V+RL+R+ YG  QL   L  G   E+    +   
Sbjct: 181 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLMRVRYGDIQLPKGLPRGGWMELELPAVNYL 240

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
                + E  V   A          ++     +     +   + SS++  
Sbjct: 241 RTLVGMPEETVTKVAVEKDRRRTKANQIRRAVKRHSQVSNSPRRSSKRGA 290


>gi|227111426|ref|ZP_03825082.1| 23S rRNA pseudouridylate synthase B [Pectobacterium carotovorum
           subsp. brasiliensis PBR1692]
          Length = 294

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 82/293 (27%), Positives = 123/293 (41%), Gaps = 7/293 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIEGIIQAGRVSVDGKIATLGDRVEVTKATKIRIDGHVVTVKE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          SR ++VGRLD+NT GLLL T 
Sbjct: 62  TEESVCRVLMYYKPEGELCTRNDPDGRPTVFDRLPKIQGSRWVAVGRLDVNTSGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  G+VD +K+  L KG+ +         +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGEVDDEKIKQLSKGVQLDDGPASFRTIRYQGGEGLN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   +  G   E+  + L    
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDITLPKGIPRGGWTEMPLEQLNYLR 241

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
               L    V+          +  ++     +            +        
Sbjct: 242 ELVQLPAETVSKLPVERERRRVKANQIRRAVKRHSQINTAPARRTSPKPKRNG 294


>gi|329929427|ref|ZP_08283175.1| pseudouridylate synthase [Paenibacillus sp. HGF5]
 gi|328936514|gb|EGG32959.1| pseudouridylate synthase [Paenibacillus sp. HGF5]
          Length = 243

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 65/233 (27%), Positives = 108/233 (46%), Gaps = 8/233 (3%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERTRL 75
            KV++  G  SR E+++   Q  + VNG + +    +V    D IE +G  ++  E   L
Sbjct: 2   DKVLSNLGFGSRAELKKKAKQGSIVVNGTITKDPGKHVDPYADIIEFEGETIQYREYVYL 61

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L+  P  +  T    D       +          VGRLD +TEGLLLLTNDG LA  L 
Sbjct: 62  MLHKPPGVVSATEDLRDRTVLDLLDAEYRVFEPFPVGRLDKDTEGLLLLTNDGKLAHELL 121

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSN-----AWV 189
            P     + Y     G+VD++ +     G+ +         ++ + + +        + +
Sbjct: 122 SPRKHIPKTYEATVEGRVDEEDVRRFAAGVTLDDGYVTLPGELAIHSHEEREDGDQLSRI 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           ++ + EGK  ++K++FE    KV  L RIS G  +L   L  G+ RE++++ L
Sbjct: 182 SLTIHEGKFHQVKRMFEAVGKKVVYLKRISMGELRLDENLEIGTYRELTEQEL 234


>gi|292559208|gb|ADE32209.1| Pseudouridine synthase, Rsu [Streptococcus suis GZ1]
          Length = 235

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 61/226 (26%), Positives = 101/226 (44%), Gaps = 4/226 (1%)

Query: 22  RAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRLWLYHK 80
             G+ SR EV++++  ++V VNG +       +    D I V G  L         L   
Sbjct: 2   DCGVGSRTEVKKLLKNKQVTVNGQVETSPKQQINEKKDQIAVAGQVLSHETFVYYLLNKP 61

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
              +  T  D         +  +    V  VGRLDI+T GLLLLTN G LA  +  P   
Sbjct: 62  KGVISATEDDHHRTVLDLLDNTARQKEVFPVGRLDIDTHGLLLLTNKGQLAHAMLSPKKH 121

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVGLREGKN 198
             ++YR +  G + Q+ +     GI ++       Q+T+ +   +   + V + +REGK 
Sbjct: 122 VDKLYRAQVDGIMTQEDVERFAAGIELKDFTCQPAQLTILSTDEAKQTSLVDITIREGKF 181

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
            +IK++ +     V  L R++ GP +L   L  G  R ++   L++
Sbjct: 182 HQIKRMVQACGKTVTDLQRLTMGPLRLDPKLALGEYRRLTAAELKQ 227


>gi|85059548|ref|YP_455250.1| 16S rRNA pseudouridylate synthase A [Sodalis glossinidius str.
           'morsitans']
 gi|84780068|dbj|BAE74845.1| ribosomal small subunit pseudouridine synthase [Sodalis
           glossinidius str. 'morsitans']
          Length = 235

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 56/231 (24%), Positives = 104/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  +RV V+G ++++ A  +     +  DG  L +    
Sbjct: 1   MRLDKFLSQQLGVSRALVARELRAKRVTVDGEIIKQGAFQLRPEHQVRFDGNLLHQILTA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+LLT+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTILYFIDEPVPDKLHAAGRLDIDTTGLVLLTDDGQWSYR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           L  P     + Y V     +  +       GI+++G        ++       S   V +
Sbjct: 121 LTSPRHHCEKDYLVTLEQPLAAEITAQFAAGILLRGEKLPTRPARLATL----SPLKVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F     +V  L R   G   L   L  G  R ++   +
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVVALHRERIGAIVLDAHLQPGEYRALTAGEV 227


>gi|315652469|ref|ZP_07905454.1| pseudouridine synthase RluB [Eubacterium saburreum DSM 3986]
 gi|315485258|gb|EFU75655.1| pseudouridine synthase RluB [Eubacterium saburreum DSM 3986]
          Length = 242

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 59/247 (23%), Positives = 109/247 (44%), Gaps = 11/247 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG------VPL 67
            R++K +A  G+ SRRE +R I   RV +NG         V   D + +DG        +
Sbjct: 1   MRLNKFLASIGVCSRREADRAIEANRVMINGETA-ELGAIVGEEDLVSLDGRYIATGKDV 59

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            K +   +        + TT  +    + V      +  R+  VGRLD ++ GLLLLTN 
Sbjct: 60  EKVKPIIIAFNKPEGVVCTTSDNDGATNVVDYI--GMKERIYPVGRLDKDSSGLLLLTNQ 117

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L   +    + Y V+ +  +D + +N +  GI +  +     +  +  +K +  
Sbjct: 118 GSLTNSLLRAANYHEKEYIVKVNKDIDDEFINKISNGIYLYELKTKTRKCKV--RKLNKN 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
             ++ L +G NR+I+++      KV +L R+     +L  L  G  R +S + +++    
Sbjct: 176 TFSIVLTQGLNRQIRRMCAACGRKVQKLNRVRIVNIKLDGLAVGDYRNLSDEEIKKLYKE 235

Query: 248 HLLEEAQ 254
             +++  
Sbjct: 236 LGIKDNG 242


>gi|302528005|ref|ZP_07280347.1| pseudouridylate synthase ribosomal large subunit [Streptomyces sp.
           AA4]
 gi|302436900|gb|EFL08716.1| pseudouridylate synthase ribosomal large subunit [Streptomyces sp.
           AA4]
          Length = 250

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 72/238 (30%), Positives = 115/238 (48%), Gaps = 4/238 (1%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
           +++    R+ KV+++AG+ASRR  E +IA  RV+V+G ++      V      I VDG  
Sbjct: 4   EQHPDGIRLQKVLSQAGVASRRAAEDLIAAGRVEVDGEVVTELGRRVHPDEAVIHVDGTR 63

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLL 123
           +   +      ++KP G+ +T SD  GR  V D L         V+ VGRLD NTEGLLL
Sbjct: 64  VNLRDDLVYLAFNKPKGVHSTMSDDRGRPCVGDYLRGRWEETPGVVHVGRLDENTEGLLL 123

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG L   L  PS + L+ Y     G V +     L+ G  +        Q  +    
Sbjct: 124 LTNDGDLGHRLMHPSYRVLKTYFAEVEGLVPRGLGKELRAGWELPDGIVKVDQFRVKDMH 183

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              + + + + EG+   ++++       V +L+R + G  QLG    G+ R +++  +
Sbjct: 184 SGRSMIELVIHEGRKHIVRRLMAATGHPVRKLVRTAVGDVQLGNQRQGTIRRLNRGEV 241


>gi|120437946|ref|YP_863632.1| ribosomal large subunit pseudouridine synthase F [Gramella forsetii
           KT0803]
 gi|117580096|emb|CAL68565.1| ribosomal large subunit pseudouridine synthase F [Gramella forsetii
           KT0803]
          Length = 295

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 108/233 (46%), Gaps = 1/233 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
            N    R++K IA +G+ SRR+ +  IA   V VNG  +      V   D +  DG  L 
Sbjct: 58  TNSDGIRLNKYIANSGVCSRRDADMYIAAGNVTVNGKSITEMGYRVKLEDDVRFDGRRLN 117

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             +   + L       VT + +  G++ +     +  ++V  VG+LD   +GLLL TNDG
Sbjct: 118 PEKPEYILLNKPAGFFVTGNPEKGGKTVMELVARTTSAKVSPVGKLDNQAKGLLLFTNDG 177

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA+ L  P     ++Y+V  +  + ++ L  ++KG+ I+G     +      +   +  
Sbjct: 178 TLAKKLAKPKNGIRQIYQVTLNKNLTKEDLEGIEKGVYIEGSKVL-ITSISFIEDKPHNE 236

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + L   K   + ++F+   ++V  L R+ +G      L  G  R ++K+ +
Sbjct: 237 VGIELYSIKEHIVTRIFKSLGYEVESLDRVVFGGLTKKDLPRGRHRNLTKQEV 289


>gi|227890506|ref|ZP_04008311.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           salivarius ATCC 11741]
 gi|227867444|gb|EEJ74865.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           salivarius ATCC 11741]
          Length = 238

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 118/234 (50%), Gaps = 6/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +++ G  +R E +++I  +RV++NG +++   + +    D I +DG  L    +
Sbjct: 1   MRLDKFLSQTGKFTRAEAKKVIKAKRVRLNGEVVKDGKIKINEDSDKIFLDGELLALNNK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDN-LPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              ++ +KP G+V+   D   ++ +     P     +  VGRLD +T GLL++TNDG  A
Sbjct: 61  EVYYMLNKPAGVVSATRDDKDKTVIDLINFPGRKEDLFPVGRLDKDTTGLLIITNDGKFA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLD--TQKGSNAW 188
             +  P     + Y     G++ + ++ +  +G+ +  G      Q+ +   ++K   + 
Sbjct: 121 HNIISPKKHVSKTYEAVVTGKISEKEVKIFSQGMELANGDKLQPAQLDIISYSEKDDTSK 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           V V + EGK  +++++F   + +V  L R+  G  +L   L  G  RE+++K L
Sbjct: 181 VRVIIHEGKYHQVRRMFGAVSQRVLELDRVKIGLLELDDTLERGEYRELTEKEL 234


>gi|189461543|ref|ZP_03010328.1| hypothetical protein BACCOP_02202 [Bacteroides coprocola DSM 17136]
 gi|189431749|gb|EDV00734.1| hypothetical protein BACCOP_02202 [Bacteroides coprocola DSM 17136]
          Length = 253

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 113/241 (46%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K+++ +   P R++K +A AGI SRRE +  I    V VNG+++      V  TD I
Sbjct: 5   IEYKDVLTDPDEPIRLNKFLANAGICSRREADEFITAGVVSVNGVVVTELGTKVKRTDEI 64

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P+    +  + L      + T+    + ++ +     +   R+  VGRLD NT G
Sbjct: 65  KFHDQPVNIERKVYVLLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTTG 124

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     V +  L+ +  GI +             
Sbjct: 125 VLLLTNDGDLASKLTHPKYLKKKIYHVYCDKNVTKADLDQIVSGITLDDGEIH-ADAVSY 183

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             +   + V + +  GKNR ++++FE   ++V +L R+ +       L  G  R ++++ 
Sbjct: 184 ASETDKSQVGIEIHSGKNRIVRRIFEALGYRVIKLDRVYFAGLTKKGLRRGDWRYLTEQE 243

Query: 241 L 241
           +
Sbjct: 244 V 244


>gi|299538371|ref|ZP_07051654.1| ribosomal large subunit pseudouridine synthase B [Lysinibacillus
           fusiformis ZC1]
 gi|298725958|gb|EFI66550.1| ribosomal large subunit pseudouridine synthase B [Lysinibacillus
           fusiformis ZC1]
          Length = 243

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 80/237 (33%), Positives = 125/237 (52%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E++I + +VKVNG+++      V ++D IEV+GV L K ++ 
Sbjct: 2   ERLQKVIAYAGVASRRKAEQLILEGKVKVNGVVVRELGTKVSNSDTIEVEGVKLEKEDKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     +     D  GR TV D    I  R+  VGRLD +T GLLLLTNDG  + +
Sbjct: 62  YFLLYKPRGTISAVT-DDKGRKTVTDLFHHIPQRIFPVGRLDYDTSGLLLLTNDGEFSYM 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           L  P  +  + Y  R  G    + L  L++GI ++       +  +T   +K   A   +
Sbjct: 121 LTHPKFKIDKTYIARVKGVPTIEGLKKLQRGIKLEDGKTAPAKVSMTSFDEKAGKAICEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + EG+NR+++++FE     V +L R  +    L  L  G  RE+SK  +++     
Sbjct: 181 TIHEGRNRQVRRMFEAIGTPVVKLKRERFAFLDLFGLAPGEYRELSKHEVKQLRVLA 237


>gi|160946175|ref|ZP_02093386.1| hypothetical protein PEPMIC_00137 [Parvimonas micra ATCC 33270]
 gi|158447698|gb|EDP24693.1| hypothetical protein PEPMIC_00137 [Parvimonas micra ATCC 33270]
          Length = 235

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 58/235 (24%), Positives = 100/235 (42%), Gaps = 4/235 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ + +   GI SR E+++ +   RVK+NG   + +   V    D I  D   +   E 
Sbjct: 3   IRIDRFLCHMGIGSRSEIKKYLKTCRVKLNGKFEKNSNTQVDIEKDEILFDDEIVIYKEF 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L      +  T              P     +  VGRLDI+T G L+LTNDG  + 
Sbjct: 63  TYLMLNKPKDFISATFDTKLPTVLDLLEFPYSNMELFPVGRLDIDTTGFLILTNDGKFSY 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + Y V    ++  +++  L+ GI  +   +      +  +K S   + + 
Sbjct: 123 NVTNPKKKVNKKYFVTLRDEIISEQIEKLENGIYFEKEDFTTENAKV--EKISEKEINLT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
           + EGK  ++K++ E+   +V  L ++  G   L   L  G  RE++   L E   
Sbjct: 181 ISEGKFHQVKRMLEYVENEVVELKKVCIGNLNLDDSLKLGEYREITNSELEEIFR 235


>gi|194477231|ref|YP_002049410.1| Pseudouridine synthase, Rsu [Paulinella chromatophora]
 gi|171192238|gb|ACB43200.1| Pseudouridine synthase, Rsu [Paulinella chromatophora]
          Length = 242

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 69/235 (29%), Positives = 124/235 (52%), Gaps = 3/235 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ K+IA +G  SRR+ E+++ Q +V+VNG+L       +   D IE+DG P+R  +  
Sbjct: 4   QRLQKLIAISGFCSRRQAEKLLIQGQVRVNGLLAHLGDRAISHVDTIEIDGKPIRLPDNH 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDGGL 130
              L +KP G++++  DP GR T+ D +P       ++  +GRLD N+ G L+LT DG L
Sbjct: 64  VTLLINKPTGVISSCQDPQGRPTILDLIPQSILQNRKLHPIGRLDSNSRGALILTTDGSL 123

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + Y+V   G+     + + ++GI +       +++ +  ++ ++  + 
Sbjct: 124 TMNLSHPRYSHDKAYKVWVEGRPSSSVIKIWQQGIFLDKKMTSRVELKILCKRVTSTLLE 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + ++EG+ R+I++   F    V  L RI     +LG+L  G  R+++   L   L
Sbjct: 184 IVMKEGRKRQIRRTATFLGHPVIDLQRIGIASIRLGSLPEGRWRKLNSYELSASL 238


>gi|315634119|ref|ZP_07889408.1| ribosomal large subunit pseudouridine synthase B [Aggregatibacter
           segnis ATCC 33393]
 gi|315477369|gb|EFU68112.1| ribosomal large subunit pseudouridine synthase B [Aggregatibacter
           segnis ATCC 33393]
          Length = 328

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 91/293 (31%), Positives = 136/293 (46%), Gaps = 10/293 (3%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIE 61
              +   +   +++ KV+ARAG  SRRE+E +IA+ RV V+G +      +NV S   + 
Sbjct: 36  KNEMKTTSAEGEKLQKVLARAGQGSRREIESIIAENRVSVDGKIATLGDRINVNSGVKVR 95

Query: 62  VDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           +DG  +   +        L  Y     L T H      +          +R I+VGRLDI
Sbjct: 96  IDGNLINLTQAQKEVCRVLMYYKPEGELCTRHDPEGRATVFDRLPRLTGARWIAVGRLDI 155

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NT GLLL T DG LA  L  PS +  R Y VR  G VD   LN LKKG+ ++       +
Sbjct: 156 NTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGAVDDAMLNRLKKGVQLEDGPANFKE 215

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTRE 235
           +      G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G  +E
Sbjct: 216 IKFVGGVGMNQWFDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKNLPRGGWQE 275

Query: 236 V---SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
           +       LRE +G     E +++++      +T    +            + 
Sbjct: 276 MELADVNYLRELVGLPPETETKLDMNKQRRKPKTGKIRKAVKRYSELSKRYKK 328


>gi|59800833|ref|YP_207545.1| hypothetical protein NGO0389 [Neisseria gonorrhoeae FA 1090]
 gi|194098126|ref|YP_002001174.1| RNA-binding protein [Neisseria gonorrhoeae NCCP11945]
 gi|239998582|ref|ZP_04718506.1| RNA-binding protein [Neisseria gonorrhoeae 35/02]
 gi|240016146|ref|ZP_04722686.1| RNA-binding protein [Neisseria gonorrhoeae FA6140]
 gi|240112500|ref|ZP_04726990.1| RNA-binding protein [Neisseria gonorrhoeae MS11]
 gi|240115241|ref|ZP_04729303.1| RNA-binding protein [Neisseria gonorrhoeae PID18]
 gi|240117527|ref|ZP_04731589.1| RNA-binding protein [Neisseria gonorrhoeae PID1]
 gi|240125333|ref|ZP_04738219.1| RNA-binding protein [Neisseria gonorrhoeae SK-92-679]
 gi|240127785|ref|ZP_04740446.1| RNA-binding protein [Neisseria gonorrhoeae SK-93-1035]
 gi|254493303|ref|ZP_05106474.1| RNA-binding protein [Neisseria gonorrhoeae 1291]
 gi|260440942|ref|ZP_05794758.1| RNA-binding protein [Neisseria gonorrhoeae DGI2]
 gi|268594441|ref|ZP_06128608.1| RNA-binding protein [Neisseria gonorrhoeae 35/02]
 gi|268598568|ref|ZP_06132735.1| RNA-binding protein [Neisseria gonorrhoeae MS11]
 gi|268600921|ref|ZP_06135088.1| RNA-binding protein [Neisseria gonorrhoeae PID18]
 gi|268603228|ref|ZP_06137395.1| RNA-binding protein [Neisseria gonorrhoeae PID1]
 gi|268683935|ref|ZP_06150797.1| RNA-binding protein [Neisseria gonorrhoeae SK-92-679]
 gi|268686179|ref|ZP_06153041.1| RNA-binding protein [Neisseria gonorrhoeae SK-93-1035]
 gi|291044269|ref|ZP_06569978.1| RNA-binding protein [Neisseria gonorrhoeae DGI2]
 gi|293399462|ref|ZP_06643615.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           gonorrhoeae F62]
 gi|59717728|gb|AAW89133.1| conserved hypothetical protein [Neisseria gonorrhoeae FA 1090]
 gi|193933416|gb|ACF29240.1| RNA-binding protein [Neisseria gonorrhoeae NCCP11945]
 gi|226512343|gb|EEH61688.1| RNA-binding protein [Neisseria gonorrhoeae 1291]
 gi|268547830|gb|EEZ43248.1| RNA-binding protein [Neisseria gonorrhoeae 35/02]
 gi|268582699|gb|EEZ47375.1| RNA-binding protein [Neisseria gonorrhoeae MS11]
 gi|268585052|gb|EEZ49728.1| RNA-binding protein [Neisseria gonorrhoeae PID18]
 gi|268587359|gb|EEZ52035.1| RNA-binding protein [Neisseria gonorrhoeae PID1]
 gi|268624219|gb|EEZ56619.1| RNA-binding protein [Neisseria gonorrhoeae SK-92-679]
 gi|268626463|gb|EEZ58863.1| RNA-binding protein [Neisseria gonorrhoeae SK-93-1035]
 gi|291011163|gb|EFE03159.1| RNA-binding protein [Neisseria gonorrhoeae DGI2]
 gi|291610031|gb|EFF39153.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           gonorrhoeae F62]
 gi|317163855|gb|ADV07396.1| hypothetical protein NGTW08_0424 [Neisseria gonorrhoeae
           TCDC-NG08107]
          Length = 252

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 68/255 (26%), Positives = 108/255 (42%), Gaps = 20/255 (7%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K          R+SK +A+ G+ SRRE +  I Q  V VNG         V   D I
Sbjct: 1   MNSKISSDHTEDTIRLSKRMAQLGLCSRREADGHIEQGWVTVNGKTA-VLGQKVSPADRI 59

Query: 61  EVD---------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           E++                 P+          Y     L+T  +  +G ++     P   
Sbjct: 60  ELNKKAHEQQAARITILLNKPVGYVSAQAEKGYKSAAELITPENCWEGDTSRISFDPKHK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             +   GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+
Sbjct: 120 IGLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGL 179

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G      +V    +      +   L++GK R+I+++ E    +V  L RI  G  +L
Sbjct: 180 SLDGDKLRPAKVEWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>gi|313668715|ref|YP_004048999.1| RNA-binding protein [Neisseria lactamica ST-640]
 gi|313006177|emb|CBN87639.1| putative RNA-binding protein [Neisseria lactamica 020-06]
          Length = 252

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 71/255 (27%), Positives = 108/255 (42%), Gaps = 20/255 (7%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K          R+SK +A+ G+ SRRE +  I Q RV VNG         V   D I
Sbjct: 1   MNSKISSDHTEDTMRLSKRMAQLGLCSRREADGYIEQGRVTVNGKTA-VLGQKVSPADRI 59

Query: 61  EVD---------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           E+D                 P+          Y     L+T  +  +G +      P   
Sbjct: 60  ELDKKAHEQQAARITILLNKPVGYVSAQAEKGYKSAAELITPENRWEGDTGRIRFDPKHK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             +   GRLDI++ GLL+LT DG +AR L   ++   + Y VR  G++D+  L LL  G+
Sbjct: 120 IGLAPAGRLDIDSVGLLVLTQDGRIARQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGL 179

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G      +V    +      +   L++GK R+I+++ E    +V  L RI  G  +L
Sbjct: 180 SLDGEKLRPAKVEWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>gi|167627916|ref|YP_001678416.1| 16S rRNA pseudouridine synthase [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
 gi|167597917|gb|ABZ87915.1| 16S rRNA pseudouridine synthase [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
          Length = 271

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 85/259 (32%), Positives = 125/259 (48%), Gaps = 9/259 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+  N      TP+R+ K++A+ GI SRR++E  I Q RV+VNG +           D I
Sbjct: 1   MRRIN-QNTENTPERLQKLLAKYGIGSRRKIEEFIEQGRVRVNGKVAT-IGDKATDKDKI 58

Query: 61  EVDGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
             DG  L            +  + +   + T+  + D ++          SR I +GRLD
Sbjct: 59  SFDGKALHSYGQPMTRPRVIIYHKREGEVCTSKDEKDRKTVFDSLPRLAKSRWIMIGRLD 118

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGD 174
           INT GLLL T DG LA  L  PS +  R Y VR +GQ    + LN LK+GI ++      
Sbjct: 119 INTTGLLLFTTDGDLANRLMHPSYEIEREYAVRVYGQELSDETLNKLKEGIQLEDGMAKF 178

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGST 233
             +     +G+N W  V L EG+NRE++++FE     V+RL RI +G   L   +  G T
Sbjct: 179 NNIKFSGGEGANLWYYVTLSEGRNREVRRMFEAVGVTVSRLTRIRFGNIILPKFVSRGKT 238

Query: 234 REVSKKILREQLGPHLLEE 252
            E++   +        L+E
Sbjct: 239 LELNPSEVNRLRKSVKLKE 257


>gi|218441222|ref|YP_002379551.1| pseudouridine synthase [Cyanothece sp. PCC 7424]
 gi|218173950|gb|ACK72683.1| pseudouridine synthase [Cyanothece sp. PCC 7424]
          Length = 259

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 85/255 (33%), Positives = 132/255 (51%), Gaps = 13/255 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +RV K++++ GIASRR+ E++I   RV++NG +        +S D +EVDG  ++   R
Sbjct: 2   TERVQKILSQWGIASRRQAEKLILAGRVRLNGNIACLGDKADLSQDRLEVDGKIIQPVHR 61

Query: 73  TR--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTND 127
            R    L +KPIG+V+T  DP  R TV D LP   S    +  VGRLDIN+ G LLLTND
Sbjct: 62  PRSIYILLNKPIGVVSTCDDPQKRRTVLDLLPKKLSHETGIHPVGRLDINSTGALLLTND 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  P     + Y+V   G   ++ L   ++G+++ G      QV +  +     
Sbjct: 122 GELTLRLTHPRYHLPKTYQVWIDGDPGEEILQQWREGVMLMGKKTLPAQVNVIKRYQHQT 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-----TLLAGSTREVSKKI-- 240
            + V L EGKNR+I+++ +   + V +L R + G  QL      +L +G  R +      
Sbjct: 182 QLQVILTEGKNRQIRRIVQQMGFNVLKLHRTAIGLIQLTPSNDPSLASGHYRFLKSVEID 241

Query: 241 -LREQLGPHLLEEAQ 254
            L+  +   + +EA 
Sbjct: 242 FLKNHVNLAIGKEAA 256


>gi|152997397|ref|YP_001342232.1| RNA-binding S4 domain-containing protein [Marinomonas sp. MWYL1]
 gi|150838321|gb|ABR72297.1| RNA-binding S4 domain protein [Marinomonas sp. MWYL1]
          Length = 300

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 88/299 (29%), Positives = 125/299 (41%), Gaps = 6/299 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
           +++ KV+ARAG  SRRE+E  I + RV VNG +       V   D I +DG  +   E  
Sbjct: 3   EKLQKVLARAGQGSRREMETRIREGRVLVNGEVAT-LGDRVSVKDTITIDGYSIIATEAG 61

Query: 72  --RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             R  +        + T        +           R I+VGRLDINT GLLL T DG 
Sbjct: 62  ENRRVIIYNKPEGEVCTRKDPEGRPTVFDKLPKLRGERWIAVGRLDINTSGLLLFTTDGE 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  PST+  R Y VR  G+V  + L  LKKG+++         +     +G N W 
Sbjct: 122 LANRLMHPSTEIDREYLVRVMGEVTDENLAALKKGVILDDGIAKFTDIVDGGGEGINRWF 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
            V L EG+NRE+++++E    KVNRL R+ +GP  L      G   E+ +  +       
Sbjct: 182 YVCLMEGRNREVRRLWESQGVKVNRLKRVRFGPVFLPSKAKVGRWVEMEETDVNSLCAMV 241

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            L+ +++         E                  +     S      K KK      R
Sbjct: 242 DLKLSELTPKTQQEKLELKRHKNKATAGGARRAPPKGFDWQSNDKPEFKPKKPGKRSFR 300


>gi|300214283|gb|ADJ78699.1| Pseudouridine synthase [Lactobacillus salivarius CECT 5713]
          Length = 240

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 118/234 (50%), Gaps = 6/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +++ G  +R E +++I  +RV++NG +++   + +    D I +DG  L    +
Sbjct: 3   MRLDKFLSQTGKFTRAEAKKVIKAKRVRLNGEVVKDGKIKINEDSDKIFLDGELLALNNK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDN-LPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              ++ +KPIG+V+   D   ++ +     P     +  VGRLD  T GLL++TNDG  A
Sbjct: 63  EVYYMLNKPIGVVSATRDDKDKTVIDLINFPGRKEDLFPVGRLDKETTGLLIITNDGKFA 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLD--TQKGSNAW 188
             +  P     + Y     G++ + ++ +  +G+ +  G      Q+ +   ++K   + 
Sbjct: 123 HDIISPKKHVSKTYEAVVTGKISEKEVKIFSQGMELANGDKLQPAQLDIISYSEKDDTSK 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           V V + EGK  +++++F   + +V  L R+  G  +L   L  G  RE++++ L
Sbjct: 183 VRVIIHEGKYHQVRRMFGAVSQRVLELDRVKIGLLELDDTLERGEYRELTEEEL 236


>gi|261377503|ref|ZP_05982076.1| ribosomal large subunit pseudouridine synthase B [Neisseria cinerea
           ATCC 14685]
 gi|269146237|gb|EEZ72655.1| ribosomal large subunit pseudouridine synthase B [Neisseria cinerea
           ATCC 14685]
          Length = 349

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 72/256 (28%), Positives = 124/256 (48%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+
Sbjct: 84  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHV 142

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++  L +  ++++       
Sbjct: 203 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTTEQMRSLTEEGVMLEDGLAKVE 262

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   
Sbjct: 263 RIYEQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFY 322

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   +    +
Sbjct: 323 ELNPAEVANIIKWADM 338


>gi|134296032|ref|YP_001119767.1| RNA-binding S4 domain-containing protein [Burkholderia
           vietnamiensis G4]
 gi|134139189|gb|ABO54932.1| RNA-binding S4 domain protein [Burkholderia vietnamiensis G4]
          Length = 249

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 62/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I Q  V V+G  ++     V     IE+D          
Sbjct: 1   MRLSKRMSELGLCSRREADEWIEQGWVLVDGERIDTLGTKVRPDQKIEIDERASAAQAAQ 60

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     L+T  +   G  +     P     +   GRLDI++
Sbjct: 61  VTILLHKPVGYVSGQAEDGYEPAAVLITRANQWSGDRSQIRFSPQHLHALAPAGRLDIDS 120

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 121 TGLLVLTQNGRIAKQLIGEQSDIDKEYLVRVRYGEHLIDIDQHFPAESLAKLRHGLELDG 180

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 181 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCEMVGLEVIGLKRVRMGRVMLGALP 236

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 237 QGQWRYLSPDE 247


>gi|212550926|ref|YP_002309243.1| ribosomal large subunit pseudouridine synthase B [Candidatus
           Azobacteroides pseudotrichonymphae genomovar. CFP2]
 gi|212549164|dbj|BAG83832.1| putative ribosomal large subunit pseudouridine synthase B
           [Candidatus Azobacteroides pseudotrichonymphae
           genomovar. CFP2]
          Length = 290

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 58/241 (24%), Positives = 107/241 (44%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K   +   +  P R+++ +A +G+ SRR+ ++ I    VK NGI +      V  TD+I
Sbjct: 42  IKYYKVEPNSNGPIRLNRYLANSGLCSRRKADKYIQTGLVKKNGIPVTEFGTRVNRTDNI 101

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 +R   +  L L      + TT+      + +     +   ++  VGRLD NT G
Sbjct: 102 TFCNSLVRSEHKVYLLLNKPKNCVTTTNDPQGRLTVMDLIKTACKEQIFPVGRLDRNTTG 161

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG L+  L  P     ++Y V  +  +D   +  L KGI ++        ++  
Sbjct: 162 VLLLTNDGKLSAKLTHPRHMKKKIYHVWLNRGIDAADIKKLSKGIQLEDGGIWADDISYV 221

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                   + + +  G+N  I+++FE   + V +L R+ +       L  G    ++ + 
Sbjct: 222 N-DKDKTQINIEIHSGRNHIIRRMFESLGYHVVKLDRVYFAGLTKKKLKKGQWCFLNDRE 280

Query: 241 L 241
           +
Sbjct: 281 V 281


>gi|146311853|ref|YP_001176927.1| 23S rRNA pseudouridylate synthase B [Enterobacter sp. 638]
 gi|145318729|gb|ABP60876.1| ribosomal large subunit pseudouridine synthase B [Enterobacter sp.
           638]
          Length = 291

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 85/288 (29%), Positives = 131/288 (45%), Gaps = 10/288 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V++   I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIETIIEAGRVSVDGKIAKLGDRVEVVAGMKIRLDGHVISVKE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GL+L T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLMLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  G+VD+ KL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGEVDEHKLRDLSRGVQLEDGPAAFKTIKFTGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDILLPKGLPRGGYTELDLTQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           E +       ++V ++      +     R            R    ++
Sbjct: 242 ELVELKPETTSKVAVEKDRRRVKANQIRRAVKRHSQVSPTRRSGSRNN 289


>gi|227326052|ref|ZP_03830076.1| 23S rRNA pseudouridylate synthase B [Pectobacterium carotovorum
           subsp. carotovorum WPP14]
          Length = 294

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 82/293 (27%), Positives = 124/293 (42%), Gaps = 7/293 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIEVIIQAGRVSVDGKIATLGDRVEVTKATKIRIDGHVVTVKE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          SR ++VGRLD+NT GLLL T 
Sbjct: 62  TEESVCRVLMYYKPEGELCTRNDPDGRPTVFDRLPKIQGSRWVAVGRLDVNTSGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  G+VD +K+  L KG+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGEVDDEKIKQLSKGVQLEDGPASFRTIRYQGGEGLN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   +  G   E+  + L    
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDITLPKGIPRGGWTEMPLEQLNYLR 241

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
               L    V+          +  ++     +            +        
Sbjct: 242 ELVQLPAETVSKLPVERERRRVKANQIRRAVKRHSQINSAPARRTSPKPKRNG 294


>gi|194333285|ref|YP_002015145.1| pseudouridine synthase [Prosthecochloris aestuarii DSM 271]
 gi|194311103|gb|ACF45498.1| pseudouridine synthase [Prosthecochloris aestuarii DSM 271]
          Length = 248

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 65/239 (27%), Positives = 110/239 (46%), Gaps = 2/239 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
                 R++K +A  GIASRRE +R++    V +NG +     V V    D + V G  L
Sbjct: 6   TTEEGIRINKYLALCGIASRRESDRLVEAGEVMINGRIARTQGVKVHPGKDEVVVKGRIL 65

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              E  ++++       + T +  +       ++ S+  R+  VGRLD  + GLLLLTND
Sbjct: 66  ALPEEKKVYILLNKPRNIITTNRDEKDRETVLDIVSVPQRIFPVGRLDRKSTGLLLLTND 125

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS+   + Y  +      + +L  L  G+ ++                   
Sbjct: 126 GDLAHRLMHPSSLVEKEYLAQLEKPFLEKELKNLTGGMRLKDTGEKVSSCKAKLLSDGMQ 185

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            + V + EGKN +++++F    + V +L R+SY   ++G L  G  R ++KK ++E   
Sbjct: 186 VL-VTIHEGKNHQVRRMFWSLGYDVKKLDRVSYAGLKVGRLRRGEWRFLNKKEVKELYQ 243


>gi|149280291|ref|ZP_01886413.1| pseudouridylate synthase (ribosomal large subunit pseudouridine
           synthase B) [Pedobacter sp. BAL39]
 gi|149228980|gb|EDM34377.1| pseudouridylate synthase (ribosomal large subunit pseudouridine
           synthase B) [Pedobacter sp. BAL39]
          Length = 463

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 115/240 (47%), Gaps = 2/240 (0%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIE 61
            KN+  ++    R+++ IA +GI SRR+ + +IA   V VNG ++      +    D + 
Sbjct: 217 RKNVAVKDDGLIRLNRYIANSGICSRRKADELIAAGVVSVNGEVVSELGHKIDPAKDQVR 276

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
            +G  L++ ++  + L      + TT    + R+ +     +   R+  VGRLD NT GL
Sbjct: 277 YNGELLKREKKVYVLLNKPKDYITTTDDPQERRTVMQLVEKASRERIYPVGRLDRNTTGL 336

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL+TNDG LA  L  P     ++Y V     + Q  LN ++ G+ ++        V+   
Sbjct: 337 LLMTNDGELADKLSHPKNGITKIYHVELSRSLSQGDLNKIQFGLELEDGIIKPDSVSYVA 396

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             GS   V + +  GKNR ++++FE   + V +L R+ YG      L  G  R + +  L
Sbjct: 397 G-GSKREVGIQIHSGKNRIVRRIFEHLGYDVVKLDRVVYGNLTKKDLPRGRWRFLEEHEL 455


>gi|269467788|gb|EEZ79546.1| 16S rRNA uridine-516 pseudouridylate synthase [uncultured SUP05
           cluster bacterium]
          Length = 241

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 86/238 (36%), Positives = 134/238 (56%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ K+IA AG  SRR  ER+I Q RV+VN             TD +++DG  +      
Sbjct: 2   ERLQKLIATAGYGSRRWAERLIEQGRVEVNNKTA-SIGDKADITDKVKIDGRTIDLSRYN 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E T++ + +K  G++ ++ D +GR + +D LP      + VGRLD+NT GLLL TN+G 
Sbjct: 61  EEETKVIILNKQAGVICSNKDKEGRKSAYDLLPKESRW-VMVGRLDLNTSGLLLFTNNGD 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  PS++  R Y VR  G+V+ + L  L +GI ++       +VT+   +G+N W 
Sbjct: 120 LANKLMHPSSEIEREYAVRVLGKVENEDLKQLTEGIDLEDGFAKFSRVTIGGGQGANRWY 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
            V L+EGK RE+++++E   +KV+RLIRI +G  +L   L A     +  K ++  L 
Sbjct: 180 KVVLKEGKKREVRRLWEALGFKVSRLIRIRFGEIRLPDSLRANQYEYLKSKQVQSLLK 237


>gi|254805154|ref|YP_003083375.1| putative pseudouridine synthase [Neisseria meningitidis alpha14]
 gi|254668696|emb|CBA06445.1| putative pseudouridine synthase [Neisseria meningitidis alpha14]
          Length = 349

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 73/256 (28%), Positives = 125/256 (48%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+
Sbjct: 84  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHV 142

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L +  ++++       
Sbjct: 203 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVE 262

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   
Sbjct: 263 RIREQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFY 322

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   L    +
Sbjct: 323 ELNPAEVANILKWAEM 338


>gi|294788878|ref|ZP_06754119.1| ribosomal large subunit pseudouridine synthase B [Simonsiella
           muelleri ATCC 29453]
 gi|294483360|gb|EFG31046.1| ribosomal large subunit pseudouridine synthase B [Simonsiella
           muelleri ATCC 29453]
          Length = 353

 Score =  159 bits (402), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 73/255 (28%), Positives = 126/255 (49%), Gaps = 6/255 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K+K        P+R+ KV+A +G+ SRRE+E  I    V+VNG +       +   D +
Sbjct: 90  LKEKRTDLSRIQPERLQKVLAASGVGSRREMEEWINNGWVQVNGHVAR-LGEKITPNDQV 148

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            + G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 149 TIKGNAIKLKWADRLPRIILYYKQEGEIVSRDDPQGRISIFDRLPQAASSRWVAIGRLDI 208

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NT GLL+LT  G L +    PS +  R Y VR  G++  ++LN L +G++++       +
Sbjct: 209 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGELTPEQLNALSEGVMLEDGLAKVER 268

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTRE 235
           +     +G N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   E
Sbjct: 269 IYEQGGEGVNKWYNVIIKEGRNREVRRLFESQGLTVSRLVRVGFGPIGLPNRLKRGQFYE 328

Query: 236 VSKKILREQLGPHLL 250
           ++   +   +    +
Sbjct: 329 LNPMEVANIMKWADM 343


>gi|220912302|ref|YP_002487611.1| pseudouridine synthase [Arthrobacter chlorophenolicus A6]
 gi|219859180|gb|ACL39522.1| pseudouridine synthase [Arthrobacter chlorophenolicus A6]
          Length = 403

 Score =  159 bits (402), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 85/236 (36%), Positives = 126/236 (53%), Gaps = 4/236 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
           +    R+ KV+A AG+ASRR  E MIA+ RV+V+G ++    V +   T  I VDG+ ++
Sbjct: 159 DADGVRLQKVMASAGVASRRVCEEMIAEGRVEVDGQVVTELGVRIDPATAVIHVDGLRIQ 218

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLLT 125
             E     +++KP G+V+T  DPDGR  + D L +  +       VGRLD+ TEGLLLLT
Sbjct: 219 LDENLVYMVFNKPKGVVSTMEDPDGRPCISDFLKNNKNTGERLFHVGRLDVATEGLLLLT 278

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  PS +  + Y V+  G   Q     LK G+ ++          L      
Sbjct: 279 NDGELANRLTHPSYEVPKTYLVQVRGPFPQGIGAQLKAGVELEDGPAAVDSFRLVDSTPG 338

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +  + V L  GKNR ++++F+   + V RL+R+  GP  LG    GS R + K+ +
Sbjct: 339 HVLIEVVLHSGKNRIVRRMFDAVGFPVQRLVRVKVGPIGLGDQRQGSIRNLGKQEV 394


>gi|241760499|ref|ZP_04758592.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           flavescens SK114]
 gi|261380706|ref|ZP_05985279.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           subflava NJ9703]
 gi|241319003|gb|EER55505.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           flavescens SK114]
 gi|284796417|gb|EFC51764.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           subflava NJ9703]
          Length = 352

 Score =  159 bits (402), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 73/256 (28%), Positives = 129/256 (50%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++      F P+R+ KV+A +G+ SRRE+E  I+   V VNG + +     V   DH+
Sbjct: 87  LKERRSDLSRFEPERLQKVLAASGVGSRREMEEWISNGWVTVNGRVAQ-LGEKVTPDDHV 145

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 146 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 205

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G++  +++ +L +  ++++       
Sbjct: 206 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGELTTEQMRVLTEEGVMLEDGLAKVE 265

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   
Sbjct: 266 RIYEQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFY 325

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   +    +
Sbjct: 326 ELNPAEVANIIKWADM 341


>gi|17546005|ref|NP_519407.1| hypothetical protein RSc1286 [Ralstonia solanacearum GMI1000]
 gi|17428300|emb|CAD14988.1| putative rrna uridine-516 pseudouridylate synthase-related
           pseudouridylate synthase protein [Ralstonia solanacearum
           GMI1000]
          Length = 598

 Score =  159 bits (402), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 80/320 (25%), Positives = 130/320 (40%), Gaps = 10/320 (3%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +       ++ K++A AG+ SRR++E +I Q RV VNG+        ++ TD + V+G  
Sbjct: 207 LTAEDDAPKLHKILADAGLGSRRDMEDLILQGRVSVNGLPA-HIGQRILPTDQVRVNGKL 265

Query: 67  LRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           +++         L  +     +V+        +           + ++VGRLD NTEGLL
Sbjct: 266 IQRKLPSKPPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRMKTGKWVAVGRLDFNTEGLL 325

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + T  G +A     P     R Y VR  G++ +     L +GI +       ++      
Sbjct: 326 IFTTSGDIANRFMHPRYGVEREYAVRTLGELPESDRQKLLQGIRLDDGEANFLRCADGGG 385

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EVS + +
Sbjct: 386 EGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEVSAEDV 445

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISE----VPDDFTRMKKNSSQKNGLSK 297
           R  +G   L+    +      S      +R                  +     +    +
Sbjct: 446 RGLMGLLGLKVPSASASGGQGSQGGRQGNRRREAQPVLMGPMSSGFTGEATFQSRGQGIE 505

Query: 298 QKKLATPVHRRNLASNVWMA 317
               A P  RR         
Sbjct: 506 NGNRAMPAPRRQSNPRQPDP 525


>gi|225076444|ref|ZP_03719643.1| hypothetical protein NEIFLAOT_01490 [Neisseria flavescens
           NRL30031/H210]
 gi|224952123|gb|EEG33332.1| hypothetical protein NEIFLAOT_01490 [Neisseria flavescens
           NRL30031/H210]
          Length = 352

 Score =  159 bits (402), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 73/256 (28%), Positives = 129/256 (50%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++      F P+R+ KV+A +G+ SRRE+E  I+   V VNG + +     V   DH+
Sbjct: 87  LKERRSDLSRFEPERLQKVLAASGVGSRREMEEWISNGWVTVNGRVAQ-LGEKVTPDDHV 145

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 146 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 205

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G++  +++ +L +  ++++       
Sbjct: 206 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGELTTEQMRVLTEEGVMLEDGLAKVE 265

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   
Sbjct: 266 RIYEQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFY 325

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   +    +
Sbjct: 326 ELNPAEVANIIKWADM 341


>gi|119477504|ref|ZP_01617695.1| ribosomal small subunit pseudouridine synthase A [marine gamma
           proteobacterium HTCC2143]
 gi|119449430|gb|EAW30669.1| ribosomal small subunit pseudouridine synthase A [marine gamma
           proteobacterium HTCC2143]
          Length = 229

 Score =  159 bits (402), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 102/231 (44%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR E +R+I   RV+V G ++     NV +   I V+G  LR +   
Sbjct: 1   MRLDKYLSQVTDYSRSEGKRLIRSGRVRVAGHVVIDPRENVDNNAVIVVNGQQLR-SASP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G ++   D    + +         ++   GRLDI+T GLLL+++DG     
Sbjct: 60  RYFMLHKPDGYISATKDRQHLTALELFDEDNVDQLHIAGRLDIDTTGLLLVSDDGQWCHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P +   + YRV     +  + +  +++GI +  +        + L           +
Sbjct: 120 VTSPKSDCKKTYRVEAVDPITPEAIKNIEQGIHLSQEKKPTLPADLDLL----DEHTARL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R   G   L   L  G  R ++   +
Sbjct: 176 TITEGKYHQVKRMFAAVGNKVECLHRERIGNIVLDDDLAPGEYRSLTAAEI 226


>gi|269120981|ref|YP_003309158.1| pseudouridine synthase [Sebaldella termitidis ATCC 33386]
 gi|268614859|gb|ACZ09227.1| pseudouridine synthase [Sebaldella termitidis ATCC 33386]
          Length = 233

 Score =  159 bits (402), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 60/237 (25%), Positives = 107/237 (45%), Gaps = 6/237 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A +GI +R+EV+ ++ ++R+ VN  ++  A  ++    D +  DG  +   E 
Sbjct: 1   MRIDKFLANSGIGTRKEVKELLKKKRISVNDEVVTEAKTHIDEDNDFVAFDGKRIEFKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      +  T  +           P     +  VGRLD +TEGLL+LTNDG +A 
Sbjct: 61  LYIMLNKPQDVISATDDERHRTVLDLLEEPLTKVGLFPVGRLDKDTEGLLVLTNDGKMAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V     + +++  +L+ G+ ++       +V   T+      V + 
Sbjct: 121 ELLSPKKHVPKRYYVELKKTLSKEEAAILENGVELETFTTKPAKVEFITEDK----VYII 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           + EGK  ++K++F+    +V  L R   G   L   L  G  RE++   L +  G  
Sbjct: 177 ISEGKYHQVKRMFKCVGNRVLFLKRTGMGNLGLDENLAPGEYRELTSDELEQLQGLK 233


>gi|192361094|ref|YP_001982433.1| ribosomal small subunit pseudouridine synthase A [Cellvibrio
           japonicus Ueda107]
 gi|190687259|gb|ACE84937.1| ribosomal small subunit pseudouridine synthase A [Cellvibrio
           japonicus Ueda107]
          Length = 234

 Score =  159 bits (402), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 55/230 (23%), Positives = 96/230 (41%), Gaps = 4/230 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            QR+   I+     +R +++R+I   RV ++   + + A  +  T+ + VDG  +     
Sbjct: 2   SQRLDAFISNNSDFTRSQIQRLIKAGRVHIDDKPVSQGAQKLNGTESVRVDGELIEPLSL 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L+     +               +LP   +  I+ GRLD++T GL+LLT+DG    
Sbjct: 62  RYLMLHKPQGYVCANTDSEHPTVLDLIDLPRKQTLQIA-GRLDLDTTGLVLLTDDGQWNH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D  +    GI + G  +      L+     NAW+   
Sbjct: 121 RITSPRRECSKRYRVTTAEPIAADTAHYFTDGIQLHGEKHKTRPAHLELIDDYNAWLD-- 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G   L   L     R ++   +
Sbjct: 179 IHEGKYHQVKRMFAATGNKVIALHRTRIGSITLDNQLTPAHWRPLTPAEI 228


>gi|260772944|ref|ZP_05881860.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           metschnikovii CIP 69.14]
 gi|260612083|gb|EEX37286.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           metschnikovii CIP 69.14]
          Length = 231

 Score =  159 bits (402), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 50/231 (21%), Positives = 97/231 (41%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+GI+ +  +  V     +E  G  L  +   
Sbjct: 1   MRLDKFLCDALGTTRKESTQLLKSGDVTVDGIVRKSGSCQVTELSQVEWQGRALTLSGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+     + +       ++       +    +   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLHKPQGYVCSHEDS-FNQTAFVLLDEANQRDLHFAGRLDVDTTGLVLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + YRV     +  +      KGI ++G        Q+ +  Q+     V +
Sbjct: 120 VTSPKHHCEKTYRVWLADPIAAEYTEQFAKGIELRGERDLTRPAQLEIIDQQQ----VLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R   G   L   L  G +R +++  +
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVVGLHRERVGDIVLDPGLEPGESRYLTESEI 226


>gi|116494395|ref|YP_806129.1| 16S rRNA uridine-516 pseudouridylate synthase related
           pseudouridylate synthase [Lactobacillus casei ATCC 334]
 gi|239631097|ref|ZP_04674128.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           paracasei subsp. paracasei 8700:2]
 gi|301065904|ref|YP_003787927.1| 16S rRNA uridine-516 pseudouridylate synthase-like pseudouridylate
           synthase [Lactobacillus casei str. Zhang]
 gi|116104545|gb|ABJ69687.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           casei ATCC 334]
 gi|239525562|gb|EEQ64563.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           paracasei subsp. paracasei 8700:2]
 gi|300438311|gb|ADK18077.1| 16S rRNA uridine-516 pseudouridylate synthase related
           pseudouridylate synthase [Lactobacillus casei str.
           Zhang]
          Length = 236

 Score =  159 bits (402), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 56/228 (24%), Positives = 91/228 (39%), Gaps = 2/228 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++     SR+EV+ +I  +RV+V G L+     NV+    +EV+          
Sbjct: 1   MRLDKYLSHLQFGSRKEVKALIRDKRVRVAGDLITDPGYNVLPGIAVEVNDAQADGPLEV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +      +  T                    +  VGRLD +T GLLLLT DG L   
Sbjct: 61  DYLMNKPAGVITATEDPTQSTVLDLIRPHDYRPGLYPVGRLDKDTTGLLLLTTDGNLGHA 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P+    + Y       +  D    L+ GI ++       QV +         + + +
Sbjct: 121 LLSPNRHIAKTYAATLAKTLTADMKQRLETGIDLKDFTTAPAQVVVLPDTDGKR-IQITI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
            EGK  ++K++    + +V  L RI+ GP  L   L AG  R ++   
Sbjct: 180 TEGKFHQVKRMLLAVDNEVTALTRIAMGPLSLPADLAAGEYRALTDDE 227


>gi|307257215|ref|ZP_07538986.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 10 str. D13039]
 gi|306864257|gb|EFM96169.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 10 str. D13039]
          Length = 349

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 91/286 (31%), Positives = 133/286 (46%), Gaps = 10/286 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGV- 65
           +E    +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S   I +DG  
Sbjct: 64  KEKVVGEKLQKILARAGQGSRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNL 123

Query: 66  ----PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
               P++K     L  Y     L T        +          +R I+VGRLDINT GL
Sbjct: 124 ISLIPVQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGARWIAVGRLDINTSGL 183

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  G +D+  L  L+KG+ ++       Q+    
Sbjct: 184 LLFTTDGELANRLMHPSREVEREYSVRVFGNIDEAMLQRLRKGVQLEDGPANFKQIKTVG 243

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L  +L  G   E+  + 
Sbjct: 244 GTGLNQWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKLEKSLPRGGWEEMGLEQ 303

Query: 241 ---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
              LRE +G     E +V++      +      +            
Sbjct: 304 VNYLRELVGLPAETETKVDVTKNRRRTNIRQIRKAVKQHSKYRTKA 349


>gi|81429040|ref|YP_396040.1| pseudouridylate synthase, 16S-rRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
 gi|78610682|emb|CAI55733.1| Pseudouridylate synthase, 16S-rRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
          Length = 239

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 59/236 (25%), Positives = 103/236 (43%), Gaps = 4/236 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++   + +R+ ++ ++   RV+V   +++ A   V     + VD  P+R     
Sbjct: 1   MRIDRFLSHMNVGTRKTLKPLLKAGRVRVADKVIKEAKYQVTPETVVYVDDEPIRYQTNF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             WL +KP G+++  +DP                +  VGRLD +T GLLL+TNDG LA  
Sbjct: 61  -YWLLNKPAGVISATTDPQKTVMDLFAPADYREDLFPVGRLDKDTTGLLLITNDGDLAHD 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTV 191
           L  P     + YR +  G V          G+ ++       Q+T+     +   + + V
Sbjct: 120 LLSPKKHVAKTYRAKIAGVVTAADQAQFAAGLKLRDFDAQPAQLTILRTDTARQESLIEV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
            + EGK  ++K++F     +V  L RI  GP  L   L  G  R ++   +     
Sbjct: 180 EIHEGKFHQVKRMFHAVGKEVLTLERIKMGPLSLPADLKRGQYRALTTTEIDALQR 235


>gi|295091825|emb|CBK77932.1| pseudouridine synthase family/haloacid dehalogenase superfamily,
           subfamily IA, variant 3 with third motif having DD or ED
           [Clostridium cf. saccharolyticum K10]
          Length = 471

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 61/249 (24%), Positives = 114/249 (45%), Gaps = 13/249 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R+ + +      SR EV++MI   RV V+G +   A   +  +   + +DG  +  
Sbjct: 2   EKAMRLDRYLVEMKKGSRSEVKKMIKSGRVSVDGEICREAERKIQPSASEVSLDGTQVGY 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           A      L      +V+   D   ++ V     +    +  VGRLDI+TEGLLL+TNDG 
Sbjct: 62  AAYEYFMLNKPAG-VVSATEDGRHKTVVSLIEDAKRRDLFPVGRLDIDTEGLLLITNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQ------ 182
           LA  L  P     + Y  R  G++ ++ +   K+G+ ++        ++ +  +      
Sbjct: 121 LAHRLLSPKKHVDKTYFARVEGRLPENAIEQFKEGLTLEDGTRTLPARLLIQKEAGTAEE 180

Query: 183 ---KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
                S + + + + EGK  ++K++FE    +V  L R+S G  +L  +L  G+ R +++
Sbjct: 181 GKADSSLSEIELTIHEGKFHQVKRMFEAVGCRVVYLKRLSMGSLRLYESLAPGAYRRLTE 240

Query: 239 KILREQLGP 247
           + + +  G 
Sbjct: 241 EEISKLQGE 249


>gi|241668468|ref|ZP_04756046.1| 16S rRNA pseudouridine synthase [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254877002|ref|ZP_05249712.1| ribosomal large subunit pseudouridine synthase B [Francisella
           philomiragia subsp. philomiragia ATCC 25015]
 gi|254843023|gb|EET21437.1| ribosomal large subunit pseudouridine synthase B [Francisella
           philomiragia subsp. philomiragia ATCC 25015]
          Length = 271

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 85/259 (32%), Positives = 125/259 (48%), Gaps = 9/259 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+  N      TP+R+ K++A+ GI SRR++E  I Q RV+VNG +           D I
Sbjct: 1   MRRIN-QNIENTPERLQKLLAKYGIGSRRKIEEFIEQGRVRVNGKVAT-LGDKATDKDKI 58

Query: 61  EVDGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
             DG  L            +  + +   + T+  + D ++          SR I +GRLD
Sbjct: 59  SFDGKALHSYGQPMTRPRVIIYHKREGEVCTSKDEKDRKTVFDSLPKLAKSRWIMIGRLD 118

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGD 174
           INT GLLL T DG LA  L  PS +  R Y VR +GQ    + LN LK+GI ++      
Sbjct: 119 INTTGLLLFTTDGDLANRLMHPSYEIEREYAVRVYGQELSDETLNKLKEGIQLEDGMAKF 178

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGST 233
             +     +G+N W  V L EG+NRE++++FE     V+RL RI +G   L   +  G T
Sbjct: 179 NNIKFSGGEGANLWYYVTLSEGRNREVRRMFEAVGVTVSRLTRIRFGDIILPKFVSRGKT 238

Query: 234 REVSKKILREQLGPHLLEE 252
            E++   +        L+E
Sbjct: 239 LELNPSEVNRLRKSVKLKE 257


>gi|145635048|ref|ZP_01790754.1| predicted methyltransferase [Haemophilus influenzae PittAA]
 gi|145267656|gb|EDK07654.1| predicted methyltransferase [Haemophilus influenzae PittAA]
          Length = 357

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 90/288 (31%), Positives = 132/288 (45%), Gaps = 10/288 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QPKIEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 67  LRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +  +         L  Y     L T        +          SR I+VGRLDINT GL
Sbjct: 130 INLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWIAVGRLDINTSGL 189

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++    
Sbjct: 190 LLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGPANFKEIKFTG 249

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 250 GVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEMDLEN 309

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
              LRE +G     E ++++       ++    +        +   + 
Sbjct: 310 VNYLRELVGLPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>gi|308389478|gb|ADO31798.1| putative pseudouridine synthase [Neisseria meningitidis alpha710]
          Length = 349

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 73/256 (28%), Positives = 125/256 (48%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+
Sbjct: 84  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHV 142

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L +  ++++       
Sbjct: 203 NTSGLLILTTSGELVQRFTHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVE 262

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   
Sbjct: 263 RIREQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFY 322

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   L    +
Sbjct: 323 ELNPAEVANILKWAEM 338


>gi|257462423|ref|ZP_05626837.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           D12]
          Length = 231

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 60/229 (26%), Positives = 108/229 (47%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR+EV+ ++ +++++VN  ++      +    D +  +   L   + 
Sbjct: 1   MRMDKFLVECGLGSRKEVKELLKKRKIQVNASIVTSGQQIIDEEKDEVFYEKEKLVYKKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               LY K   +       +           I   ++ VGRLD +TEGLLL TNDG L  
Sbjct: 61  RYYILYKKAGYVTALEDSKERTVMELLPEWVIRKDLVPVGRLDKDTEGLLLFTNDGKLNH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P +   + Y V     + ++ +  L++G+ I        QV    ++     +++ 
Sbjct: 121 QLLSPKSHVDKTYHVCLEKIITEEAIEQLRQGVRIGDYTTLPAQVEQLEEQK----ISLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++EGK  ++KK+ E  + KV+ L R+S+G   LG L  G  REVS + +
Sbjct: 177 IQEGKFHQVKKMLEAVDNKVSYLKRVSFGRLVLGDLKPGEVREVSLEDI 225


>gi|42523444|ref|NP_968824.1| pseudouridylate synthase [Bdellovibrio bacteriovorus HD100]
 gi|39575650|emb|CAE79817.1| pseudouridylate synthase [Bdellovibrio bacteriovorus HD100]
          Length = 245

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 69/247 (27%), Positives = 115/247 (46%), Gaps = 18/247 (7%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + E+    R+SK++A  GI SRRE +  I++  V VNG ++ +    V     I ++   
Sbjct: 1   MSEDNK-VRLSKLMAEKGICSRREADDYISRGLVMVNGEVVSQLGTKVSPDVKITLEAQA 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-------------GR 113
           L++ +R    L +KP+G V+   +P  +  +    P                      GR
Sbjct: 60  LKQQKRLATILLNKPVGYVSAQPEPPYQPAIKLITPQNQFGNSKTRLKEEHFKGLAVAGR 119

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LDI+++GLLL T DG +A+ +    ++  + Y VR  G +  DKL LL  G+ + G    
Sbjct: 120 LDIDSQGLLLFTQDGRIAKKIIGEESKVEKEYIVRVQGTLPPDKLKLLNFGLSLDGKKLK 179

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
             +V    +      +   L+EGK R+I+++ E    KV  L R+  G  +LG L  G  
Sbjct: 180 PAKVEWLNEDQ----LRFILQEGKKRQIRRMCELVGLKVTGLKRVRIGKIRLGQLPEGQW 235

Query: 234 REVSKKI 240
           R + +  
Sbjct: 236 RFLEEDE 242


>gi|160939069|ref|ZP_02086420.1| hypothetical protein CLOBOL_03963 [Clostridium bolteae ATCC
           BAA-613]
 gi|158438032|gb|EDP15792.1| hypothetical protein CLOBOL_03963 [Clostridium bolteae ATCC
           BAA-613]
          Length = 262

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 70/234 (29%), Positives = 111/234 (47%), Gaps = 7/234 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE 71
           P R+ + +A  G  +R +V+ M+ + RV++NG  ++ A   V    D +EVD   +  A 
Sbjct: 16  PMRLDRFLAEMGYGTRTQVKDMVKKGRVRMNGEAVKDADRKVNPESDIVEVDRSRVAYAR 75

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                L      +V+   D    + V     ++   +  VGRLDI+TEGLLL+TNDG LA
Sbjct: 76  MEYYMLNKPQG-VVSATEDRKYPTVVGLIREALRKDLFPVGRLDIDTEGLLLITNDGELA 134

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSN---A 187
             L  P     +VY     G + +D +   ++GI ++        ++ +    G      
Sbjct: 135 HNLLSPKKHVDKVYLAHVSGGLPEDAVKRFEEGIKLEDGTMTLPAELKILKGAGPEEDAQ 194

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            V V +REGK  +IK++FE    +V  L RIS GP  L   L  G  R ++ + 
Sbjct: 195 EVLVTIREGKFHQIKRMFEALGCRVEYLKRISMGPLILDPNLEPGEYRPLTLQE 248


>gi|119898401|ref|YP_933614.1| pseudouridylate synthase [Azoarcus sp. BH72]
 gi|119670814|emb|CAL94727.1| pseudouridylate synthase [Azoarcus sp. BH72]
          Length = 356

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 80/272 (29%), Positives = 127/272 (46%), Gaps = 9/272 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P+R+ KV+A+AG+ASRRE+E ++   R+ VNG+        +   D ++++G  +    
Sbjct: 89  EPERLQKVLAQAGVASRREIEELVVAGRISVNGLPA-SLGQKIGPGDRVKLNGKLIPLRF 147

Query: 72  RTR----LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             R    L  +     +V+        +           R ++VGRLD NT GLLL TND
Sbjct: 148 SQRSPRVLVYHKPEGEIVSRDDPEGRPTVFERLPLLRKGRWLAVGRLDFNTSGLLLFTND 207

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P  +  R Y VR  GQ+ +++   L  GI ++      + +     +G N 
Sbjct: 208 GDLANRLMHPRYELTREYAVRLLGQLTEEQGQSLVDGIQLEDGPARFLSLVDAGGEGVNH 267

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V L EG+NRE++++FE     V+RL+R+ YGP +L   L  G   E+ +    +   
Sbjct: 268 WYRVTLAEGRNREVRRMFEAVGLTVSRLMRVRYGPVELPARLKRGMWMELPE---ADACA 324

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEV 278
              L   +V+  A     E   R    +  E 
Sbjct: 325 LAGLPPPRVDPSARGARREKAPRLHHTLPHER 356


>gi|239993811|ref|ZP_04714335.1| pseudouridine synthase (makes pseudouridine2605 in 23 S RNA)
           [Alteromonas macleodii ATCC 27126]
          Length = 298

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 85/307 (27%), Positives = 131/307 (42%), Gaps = 21/307 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+A  G+ SRRE+ER I + RV V+G         V  T  I VDG  L +   
Sbjct: 2   TEKLQKVLANQGLGSRREMERWIEEGRVSVDGTKAT-LGDRVDHTAQIRVDGHLLSRQTE 60

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 L        L + H      +           R I+VGRLD+NT GLLL TNDG
Sbjct: 61  QPICRVLMYNKPEGELCSRHDPEGRDTVFDRLPAIRLGRWITVGRLDMNTSGLLLFTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------QVTLDTQ 182
            LA  L  P  +  R Y VR  G+V    L+ L+KG+ ++      +             
Sbjct: 121 ELANRLMHPKCEVEREYAVRVFGEVTGKTLHTLQKGVELEDGEAKFLTISGAPTPQHAED 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           +  N W  V L+EG+NRE+++++E    +V+RLIR+ YGP +L   L  G+  E+     
Sbjct: 181 ESMNRWYNVTLKEGRNREVRRLWESQGVQVSRLIRVKYGPIELQKRLPQGAWVEL----- 235

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
               G   +   + ++  P  +   +   +  +         R  K    +      K+ 
Sbjct: 236 ----GLEDVNALRSHVQLPDETQTMVNVRQGKLDHARLSRMRRSVKKHKVRKQQGLNKRA 291

Query: 302 ATPVHRR 308
             P  R+
Sbjct: 292 GRPAKRK 298


>gi|296269471|ref|YP_003652103.1| pseudouridine synthase [Thermobispora bispora DSM 43833]
 gi|296092258|gb|ADG88210.1| pseudouridine synthase [Thermobispora bispora DSM 43833]
          Length = 426

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 81/242 (33%), Positives = 125/242 (51%), Gaps = 1/242 (0%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIE 61
           ++    E    +R+ KV+ARAG+ASRR  E +I Q RV V+G ++ R    V      I 
Sbjct: 178 EERDTTEVPGGERLQKVLARAGVASRRACEELIGQGRVTVDGQVVRRYGARVDPERQIIR 237

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           VDG  +  +     + ++KP G+V+T  DP+GR  + D +  +  R+  VGRLD  TEGL
Sbjct: 238 VDGKRIPTSTGLAYYAFNKPAGVVSTMDDPEGRPCLADYVQDLAPRLFHVGRLDTATEGL 297

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL TNDG LA  L  PS    + Y  +  G V +     L+ G+ ++         T+  
Sbjct: 298 LLFTNDGELAHRLTHPSYGVRKKYIAKVAGPVPRKLARTLRAGVELEDGKVTVDGFTVIQ 357

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           Q G  A V + L EG+   ++++ E     V  L RI +GP +LG L  G+ R ++ + +
Sbjct: 358 QHGRQALVEIVLHEGRKHIVRRLMEAVGHPVLELARIEFGPVKLGRLKPGTVRALTLREI 417

Query: 242 RE 243
            +
Sbjct: 418 GD 419


>gi|295115835|emb|CBL36682.1| ribosomal small subunit pseudouridine synthase A
           [butyrate-producing bacterium SM4/1]
          Length = 346

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 112/250 (44%), Gaps = 14/250 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R+ + +      SR EV++MI   RV V+G     A   +  +   + +DG  +  
Sbjct: 2   EKAMRLDRYLVEMKKGSRSEVKKMIKSGRVSVDGETCREAERKIQPSASEVSLDGTQVGY 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           A      L      +V+   D   ++ V     +    +  VGRLDI+TEGLLL+TNDG 
Sbjct: 62  AAYEYFMLNKPAG-VVSATEDGRHKTVVSLIEDAKRRDLFPVGRLDIDTEGLLLITNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKG---- 184
           LA  L  P     + Y  R  G++ ++ +   K+G+ ++        ++ +    G    
Sbjct: 121 LAHRLLSPKKHVDKTYFARVEGRLPENAIEQFKEGLTLEDGTRTLPARLVIQKASGTAED 180

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVS 237
                 S + + + + EGK  ++K++FE    +V  L R+S G  +L   L  G+ R ++
Sbjct: 181 DGKADSSLSEIELTIHEGKFHQVKRMFEAVGCRVVYLKRLSMGSLRLDESLAPGAYRRLT 240

Query: 238 KKILREQLGP 247
           ++ + +  G 
Sbjct: 241 EEEISKLQGE 250


>gi|293369516|ref|ZP_06616095.1| pseudouridylate synthase [Bacteroides ovatus SD CMC 3f]
 gi|292635401|gb|EFF53914.1| pseudouridylate synthase [Bacteroides ovatus SD CMC 3f]
          Length = 485

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 107/241 (44%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +  +D +
Sbjct: 237 IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVV 296

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P+    +  + L      + T+    + R+ +     +   R+  VGRLD NT G
Sbjct: 297 KFHDEPVSIERKVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTTG 356

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     + +  +  +  GI ++            
Sbjct: 357 VLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADMEQIAAGIQLEDGEIH-ADAISY 415

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           T       V + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+  
Sbjct: 416 TDDFKKDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSEAE 475

Query: 241 L 241
           +
Sbjct: 476 V 476


>gi|218246395|ref|YP_002371766.1| pseudouridine synthase [Cyanothece sp. PCC 8801]
 gi|257059438|ref|YP_003137326.1| pseudouridine synthase [Cyanothece sp. PCC 8802]
 gi|218166873|gb|ACK65610.1| pseudouridine synthase [Cyanothece sp. PCC 8801]
 gi|256589604|gb|ACV00491.1| pseudouridine synthase [Cyanothece sp. PCC 8802]
          Length = 252

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 69/240 (28%), Positives = 111/240 (46%), Gaps = 12/240 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK--- 69
           +RV K++++ GIASRR+ E +I   RVKVNG L++     V    D +EVDG  +     
Sbjct: 3   ERVQKILSQWGIASRRKAESLILAGRVKVNGNLVK-LGDKVDPYCDRLEVDGKRIEPTQR 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTND 127
            E   + +      + T     +  + +          + +  VGRLD N+ G LLLTND
Sbjct: 62  PEFLYILVNKPLGVVSTCDDPQNRPTVLELLPQELRKGTGIHPVGRLDFNSTGALLLTND 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  P     + Y V   G + +  L   ++G+++ G      QV +  +     
Sbjct: 122 GELTLRLTHPRYHLPKTYEVSISGDISETSLQQWREGVMLMGKKTLPAQVEVIHRCRQQT 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-----TLLAGSTREVSKKILR 242
            + V L EG+NR+I+++ E   + V RL R + G   L      +L +G  R +    +R
Sbjct: 182 CLKVILIEGRNRQIRRIVEHLGFSVLRLHRTAVGSIALHRPHEPSLPSGHYRLLKASEIR 241


>gi|319794363|ref|YP_004156003.1| pseudouridine synthase [Variovorax paradoxus EPS]
 gi|315596826|gb|ADU37892.1| pseudouridine synthase [Variovorax paradoxus EPS]
          Length = 601

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 76/341 (22%), Positives = 131/341 (38%), Gaps = 6/341 (1%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++       ++ KV+A+AG+ SR E+E +I Q R+ VN          +   D ++++
Sbjct: 175 KRVLLPEADSPKLHKVLAQAGLGSRLEMEALILQGRISVNNEPA-HIGQRIQYGDQVKIN 233

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+R          +  +     +VT     +  +           +  SVGRLD+NTE
Sbjct: 234 GKPIRYRIAPPPPRVIAYHKPVGEVVTHDDPQNRPTVFRKLPRLQQGKWQSVGRLDLNTE 293

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL ++ G LA  L  P     R Y VR  G +  ++   L  G+ ++        +  
Sbjct: 294 GLLLFSSSGDLANQLMHPRFGLEREYAVRVLGALSSEEKQKLLDGVRLEDGMAQFGTIEE 353

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +GSN W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E+ +
Sbjct: 354 GGGEGSNCWYRVTISEGRNREVRRLFESVGHAVSRLIRIRYGAMVLPRGLKRGAWMELDE 413

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           + +R          A+                R     +   +     +   Q     ++
Sbjct: 414 RDIRALFQASGGAAARPAAPQQRGPGGPEGGGRNGRNKKRRGNRNGGGQGQGQGQQQPRE 473

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
            +                         ++ G     +   P
Sbjct: 474 MRDDGREAPIPNPLGDGRPPRGDRGGRANRGGGGGGNGGPP 514


>gi|310778731|ref|YP_003967064.1| ribosomal small subunit pseudouridine synthase A [Ilyobacter
           polytropus DSM 2926]
 gi|309748054|gb|ADO82716.1| ribosomal small subunit pseudouridine synthase A [Ilyobacter
           polytropus DSM 2926]
          Length = 226

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 60/229 (26%), Positives = 107/229 (46%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +   G+ +RR+V+ +I++  + +N   +      +    D I++    L+  + 
Sbjct: 1   MRLDKFLTECGVGTRRDVKNIISKNEITINDKKVNSPKEKIDLENDVIKIGERVLKYKKD 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T    +           I   +  VGRLD +TEGLLL TN+G +A 
Sbjct: 61  RFYIMNKTSGFITATEDTREKTVMELLPEWVIKKDLFPVGRLDKDTEGLLLFTNNGKIAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V+   ++D+  +NLL++G+ I G      +V +     +N  + + 
Sbjct: 121 ELLSPKKHVDKTYLVKLLKEIDKKSVNLLEEGVDIGGYITKPSKVQII----NNTEILLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGK  ++KK+ E    KV  L R+S+G  +LG L  G  +EV  K +
Sbjct: 177 ICEGKFHQVKKMLEAVGNKVIYLKRLSFGNLELGDLPLGEVKEVDLKDI 225


>gi|291563383|emb|CBL42199.1| ribosomal small subunit pseudouridine synthase A
           [butyrate-producing bacterium SS3/4]
          Length = 265

 Score =  159 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 65/241 (26%), Positives = 110/241 (45%), Gaps = 12/241 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R+ K +A  G  +R E++ MI + R+ VNG+++++    +    D I +D  P+  
Sbjct: 19  EKAIRLDKYLADMGKGTRTELKEMIRRGRITVNGVIVKKPETKIKKGEDTICLDNAPVEY 78

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E     L      +++   D    + V          +  VGRLDI+TEGLLL+TNDG 
Sbjct: 79  VELEYYLLNKPQG-VISATEDRRRETVVDLIDEKSRKDLFPVGRLDIDTEGLLLITNDGA 137

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKG---- 184
           LA  L  P     +VY  R  G V  + +   ++G+ +         ++ +  +K     
Sbjct: 138 LAHRLLAPGHHVDKVYEARCKGFVPDEAVQRFREGMTLADGLSCMPSELEILERKPEDPE 197

Query: 185 ----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK 239
               + + V + L EGK  ++K++ E     V  L R+S GP +L   L  G  R+++ K
Sbjct: 198 TGTAAESLVRLTLHEGKFHQVKRMMEETGCPVLHLKRLSMGPLKLDDALKTGEYRKLTDK 257

Query: 240 I 240
            
Sbjct: 258 E 258


>gi|241889378|ref|ZP_04776679.1| ribosomal small subunit pseudouridine synthase A [Gemella
           haemolysans ATCC 10379]
 gi|241863921|gb|EER68302.1| ribosomal small subunit pseudouridine synthase A [Gemella
           haemolysans ATCC 10379]
          Length = 235

 Score =  159 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 54/231 (23%), Positives = 103/231 (44%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K I+     SR E +++I +  + +N  L++     V    D + +DG  L   + 
Sbjct: 1   MRLDKFISTTTTLSRAEAKKVIKKG-ILINDKLIKSPDYKVDEINDQVILDGKRLVYQKY 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      +  T    +              +V  VGRLD +TEGL+LLTNDG LA 
Sbjct: 60  VYIMMNKPQDTISATEDAIEKTVVDILKEEDRIHKVFPVGRLDKDTEGLMLLTNDGELAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P    ++ Y V   G++ ++ L +++ G+ ++        ++ +       +   +
Sbjct: 120 RLISPKKDVVKKYYVEVSGELKEEHLPIIEAGVTLEDGYKCKAAKLEILESNEDESKANI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++K++ +     V  L R+S G  +L   L  G  R ++++ L
Sbjct: 180 YITEGKFHQVKRMMKSLGTTVTYLKRLSIGSLKLDENLKLGDYRYLTEEEL 230


>gi|325266342|ref|ZP_08133021.1| ribosomal large subunit pseudouridine synthase B [Kingella
           denitrificans ATCC 33394]
 gi|324982304|gb|EGC17937.1| ribosomal large subunit pseudouridine synthase B [Kingella
           denitrificans ATCC 33394]
          Length = 362

 Score =  159 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 75/255 (29%), Positives = 128/255 (50%), Gaps = 6/255 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K+K        P+R+ KV+A +G+ SRRE+E  I    V+VNG +       +   D +
Sbjct: 99  LKEKRTDLSRIEPERLQKVLAASGVGSRREMEEWINNGWVQVNGRVA-VLGEKITPEDQV 157

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 158 TVKGSAIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 217

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NT GLL+LT  G L +    PS +  R Y VR  G++ Q+++N L +G++++       +
Sbjct: 218 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGELTQEQMNALSEGVMLEDGLARVER 277

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTRE 235
           +     +G+N W  V L+EG+NRE++++FE     V+RL+R+ +GP  L   L  G   E
Sbjct: 278 IYEQGGEGANKWYNVVLKEGRNREVRRLFESQGLTVSRLVRVGFGPIGLPNRLKRGQFYE 337

Query: 236 VSKKILREQLGPHLL 250
           ++   +   +    +
Sbjct: 338 LNPMEVANIMKWADM 352


>gi|237719081|ref|ZP_04549562.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           2_2_4]
 gi|229451460|gb|EEO57251.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           2_2_4]
          Length = 493

 Score =  159 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 108/241 (44%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +  +D +
Sbjct: 245 IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVV 304

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P+    +  + L      + T+    + R+ +     +   R+  VGRLD NT G
Sbjct: 305 KFHDEPVSIERKVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTTG 364

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     + +  ++ +  GI ++            
Sbjct: 365 VLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADMDQIAAGIQLEDGEIH-ADAISY 423

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           T       V + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+  
Sbjct: 424 TDDFKKDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSEAE 483

Query: 241 L 241
           +
Sbjct: 484 V 484


>gi|113475036|ref|YP_721097.1| ribosomal large subunit pseudouridine synthase B [Trichodesmium
           erythraeum IMS101]
 gi|110166084|gb|ABG50624.1| ribosomal large subunit pseudouridine synthase B [Trichodesmium
           erythraeum IMS101]
          Length = 254

 Score =  159 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 69/241 (28%), Positives = 113/241 (46%), Gaps = 13/241 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++++ GIASRR+ E+MI   RVKVNG +++          D+IEVDG+P+R   R
Sbjct: 3   ERLQKILSQWGIASRRQAEQMIIAGRVKVNGKIVQ-LGEKAQPDLDNIEVDGLPIRPEAR 61

Query: 73  T---RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTND 127
                L L      + T          +            +  VGRLD ++ G LLLTND
Sbjct: 62  PSPIYLLLNKPMGVISTCSEPRKRSKVLDILNAELRNGKGIHPVGRLDADSTGALLLTND 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-KGSN 186
           G +   L  P     + Y+V   G   +  L L ++GI++ G      +V +  +   S 
Sbjct: 122 GRVTYCLTHPKYCLSKTYQVLVEGHPQESILKLWRQGIILSGKKTLPAEVKVLKECNSSQ 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-----GTLLAGSTREVSKKIL 241
             + V + EG+NR+I++V +    +V +L R + G  +L       L  G  R++    +
Sbjct: 182 TLLEVVISEGRNRQIRRVADKLGHRVLKLHRTAIGQIKLQLPGESVLPIGHYRQLKDFEI 241

Query: 242 R 242
            
Sbjct: 242 E 242


>gi|228478281|ref|ZP_04062889.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus salivarius SK126]
 gi|228249960|gb|EEK09230.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus salivarius SK126]
          Length = 239

 Score =  159 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 104/230 (45%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++ +AG  SR +V+R+I  ++V V+GIL +R  +NV ++   I V G  L     
Sbjct: 1   MRLDKLLGQAGYGSRNQVKRLIRSRQVYVDGILADRDNLNVDASLQTITVSGKELEHTPE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +                       +  VGRLD +TEGL+L+TN+G L  
Sbjct: 61  VYYLMNKPAGVVSARKDKEHQTVIDLITPEDQRDGLYPVGRLDRDTEGLVLITNNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V  +  +  D     + G+V +        Q+ + +     +   +
Sbjct: 121 AMLHPRYHVAKTYYVEVNDVLGPDAPAFFESGVVFEDGTVCKSAQLEILSSARDKSSAHI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + EGK  ++KK+F  +  KV  L RIS+G F+L   +  GS R +++  
Sbjct: 181 TISEGKFHQVKKMFLAYGVKVTYLKRISFGAFKLDEGIAVGSYRTLTETE 230


>gi|77409420|ref|ZP_00786117.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae COH1]
 gi|77171978|gb|EAO75150.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae COH1]
          Length = 240

 Score =  159 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 56/233 (24%), Positives = 103/233 (44%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+ ++ ++++ VN        V V    D I+ +G  +   + 
Sbjct: 1   MRLDKFLVECGLGSRTQVKLILKKKQISVNSNSETSPKVQVDEYRDEIKYNGTLVSYEKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T            +  +    V  VGRLDI+T GLLL+TN+G LA 
Sbjct: 61  VYYMLHKPKGVISATDDPSHKTVLDLLDKTARDKAVFPVGRLDIDTTGLLLITNNGELAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVT 190
            +  P     + Y  +  G + +D +    KGI+++         ++    Q    + V 
Sbjct: 121 KMLSPKKHVDKCYEAKISGIMTEDDILAFDKGIILKDFTCLPALLEIVEVNQVKKQSLVK 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           + ++EGK  ++K++      +V  L R+S G  QL   L +G  R ++ K + 
Sbjct: 181 ITIKEGKFHQVKRMVAACGKEVLELKRLSMGNLQLDKQLESGQWRRLTIKEIE 233


>gi|260768255|ref|ZP_05877189.1| ribosomal small subunit pseudouridine synthase A [Vibrio furnissii
           CIP 102972]
 gi|260616285|gb|EEX41470.1| ribosomal small subunit pseudouridine synthase A [Vibrio furnissii
           CIP 102972]
          Length = 233

 Score =  159 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 48/229 (20%), Positives = 91/229 (39%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  ++R+E  +++    V V+G + +  +V V     +      L      
Sbjct: 1   MRLDKFLCDALGSTRKEATQILKSGDVTVDGKVQKSGSVQVTEASVVAWQERQLSLTGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + LY     + +     +  +            +   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLYKPEGFVCSHEDGFNQ-TAFVLLDEVNMRGLHFAGRLDVDTTGLVLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     V  D    L  GI ++      +   ++        V + +
Sbjct: 120 ITSPKHKCDKTYRVWLADAVQADYAEKLAHGIELRNERELTLPAHMELVNADENEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EGK  ++K++F     KV  L R   G   L   L  G  R +++  +
Sbjct: 180 HEGKYHQVKRMFAALGNKVEALHRERVGDIVLDESLEPGEYRYLTEAEV 228


>gi|209524582|ref|ZP_03273130.1| pseudouridine synthase [Arthrospira maxima CS-328]
 gi|209495040|gb|EDZ95347.1| pseudouridine synthase [Arthrospira maxima CS-328]
          Length = 257

 Score =  159 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 70/240 (29%), Positives = 105/240 (43%), Gaps = 13/240 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK--- 69
           +R+ K+I+  G+ASRR  E MI   RVKVNG              D IE+DG  L     
Sbjct: 3   ERLQKIISHWGVASRRHAEEMILSGRVKVNGDRAY-LGQKADPKCDRIEIDGRALHPSSQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTND 127
            +   L L      + T       ++ +      +        VGRLD ++ G LL+TND
Sbjct: 62  PQPLYLLLNKPLGVVCTCAEPQGRKAVLDLLPRQMRVGQGLHPVGRLDSDSTGALLITND 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-KGSN 186
           G L  +L  P     + Y+V   G   +  L   ++GI++ G      QV    +   S 
Sbjct: 122 GELTFLLTHPRYHVAKTYQVLVQGCPPESVLEQWRQGILLSGKNTLPAQVRPIGKPSRSQ 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-----TLLAGSTREVSKKIL 241
             + V LREG+NR+I++V E   + V +L R + GP  L       L +G  R +    +
Sbjct: 182 TLLEVVLREGRNRQIRRVAEALGYPVVQLHRTAIGPIYLNSTGKPELASGEYRSLKNSEV 241


>gi|119775259|ref|YP_927999.1| pseudouridine synthase, Rsu [Shewanella amazonensis SB2B]
 gi|119767759|gb|ABM00330.1| ribosomal large subunit pseudouridine synthase B [Shewanella
           amazonensis SB2B]
          Length = 295

 Score =  159 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 78/295 (26%), Positives = 131/295 (44%), Gaps = 7/295 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E  IA  RV +NG +       V +   + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRVSINGEIA-NLGDRVDADAKVRLDGRLVSIKSA 60

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  +     + +        +          +R ++VGRLDINT GLLL T+D
Sbjct: 61  DDIICRVLAYHKPEGEICSRKDPEGRPTVFDRLPKLRDARWVAVGRLDINTSGLLLFTSD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V+   +  L+ G++++        V     +G N 
Sbjct: 121 GELANRLMHPSNEVDREYAVRTFGEVNDFTIQKLRTGVMLEDGPAQFDYVKAAGGEGVNQ 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  VGLREG+NRE+++++E    +V+RLIR+ YG  +L  TL  G   E+  + +     
Sbjct: 181 WWHVGLREGRNREVRRLWESQEVQVSRLIRVRYGMIELPKTLPRGGWIELPLEQVNYLRQ 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
              ++    ++      S        +         +++   +  K     + + 
Sbjct: 241 LAGMDPETRSMIGTDKHSVARASQVRSAKIRRAVRKSKVGAATGSKRPKPTRTRS 295


>gi|307292742|ref|ZP_07572588.1| RNA-binding S4 domain protein [Sphingobium chlorophenolicum L-1]
 gi|306880808|gb|EFN12024.1| RNA-binding S4 domain protein [Sphingobium chlorophenolicum L-1]
          Length = 267

 Score =  159 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 112/231 (48%), Positives = 151/231 (65%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             PQR++K++ARAG+ASRREVERMI + R+ +NG  +   A  + S   + VDG P+   
Sbjct: 26  NEPQRIAKLLARAGVASRREVERMIEEGRITLNGEAITTPATLLASLHGVAVDGAPVAAP 85

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              RL+L+HKP G +TT  DP GR T++D LP+   RV+ +GRLD+ TEGLLLLT DG  
Sbjct: 86  APARLFLFHKPSGFLTTERDPRGRPTIYDKLPADLPRVMPIGRLDMTTEGLLLLTTDGEF 145

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            R +ELPST   R YR R  G V Q++L  L +GI I GI YG ++  L+ + G N W+ 
Sbjct: 146 KRQMELPSTGVPRTYRARAFGDVSQNQLEDLFEGIEIDGIRYGQIEANLERRTGRNQWIE 205

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + L EGKNRE+++V E    +V+RLIR SYGPF LG L +G+  EV +  L
Sbjct: 206 MTLTEGKNREVRRVLEHLGLQVSRLIRTSYGPFHLGELPSGAVEEVRQHDL 256


>gi|119486449|ref|ZP_01620507.1| hypothetical protein L8106_00605 [Lyngbya sp. PCC 8106]
 gi|119456351|gb|EAW37482.1| hypothetical protein L8106_00605 [Lyngbya sp. PCC 8106]
          Length = 250

 Score =  159 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 74/241 (30%), Positives = 111/241 (46%), Gaps = 13/241 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K++A  GIASRR+ E+MI  +RV+VNG +           +D IEVDG P++ + R
Sbjct: 3   ERLQKIMATWGIASRRQAEQMILAKRVRVNGNIA-HLGQKANPSSDDIEVDGKPIKPSHR 61

Query: 73  T---RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTND 127
                L L      + T       R+ +            V  VGRLD+++ G LLLTND
Sbjct: 62  PVPIYLLLNKPIGVVSTCADPGGRRNVLDLLPRRLQKGQGVHPVGRLDVDSTGALLLTND 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-GSN 186
           G L   L  P     + Y+V   G   +  L   ++G+++        +V    Q   S 
Sbjct: 122 GELTFRLTHPRHHVPKTYQVWVQGHPPESVLQAWRQGVILSSRKTLSAEVRRLQQSIDSQ 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-----TLLAGSTREVSKKIL 241
             + V L EG+NR+I+KV E   + V +L R + G  QL       L  G  R ++   L
Sbjct: 182 TLLEVILFEGRNRQIRKVAEQLGYPVVKLHRSAIGSIQLNPPGKPELAPGRYRPLTPSEL 241

Query: 242 R 242
            
Sbjct: 242 E 242


>gi|159903645|ref|YP_001550989.1| 16S rRNA uridine-516 pseudouridylate synthase [Prochlorococcus
           marinus str. MIT 9211]
 gi|159888821|gb|ABX09035.1| 16S rRNA uridine-516 pseudouridylate synthase [Prochlorococcus
           marinus str. MIT 9211]
          Length = 237

 Score =  159 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 63/229 (27%), Positives = 105/229 (45%), Gaps = 1/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-RKAER 72
           QR+ K+IA +GI SRR+ E +I Q +V VNG   +         D I V+G  + +    
Sbjct: 4   QRLQKIIAESGICSRRKAEELIIQHKVLVNGFAAKIGDKANPENDQIIVNGYRIPKVIFN 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + + +     ++ +      I   +  +GRLD  + G +LLTN+G L  
Sbjct: 64  RVILLNKPRGIISSCNDQFGRKTVLSLIPSDIRKGLYPIGRLDYESRGAILLTNNGDLTL 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V   G      L+  ++G V+ G      +V L       + + + 
Sbjct: 124 KLTHPKFNHTKSYFVWVKGLPSSSTLSEWRQGTVLDGKITMKAKVNLIKSLKHQSLIQIE 183

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++EG+NR+I+++ E F   V  L R++    +LG L  G  REV +  L
Sbjct: 184 MKEGRNRQIRRISEKFGHPVIDLKRVAISKIKLGNLQEGCWREVKEDEL 232


>gi|213965939|ref|ZP_03394129.1| ribosomal large subunit pseudouridine synthase B [Corynebacterium
           amycolatum SK46]
 gi|213951353|gb|EEB62745.1| ribosomal large subunit pseudouridine synthase B [Corynebacterium
           amycolatum SK46]
          Length = 324

 Score =  159 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 79/242 (32%), Positives = 120/242 (49%), Gaps = 4/242 (1%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEV 62
           K    E     R+ KV+A+AG+ASRR  E++I + RV+V+G ++ R  V V      I V
Sbjct: 74  KRAHSEAGEGVRLQKVLAQAGVASRRMAEKLIDEGRVEVDGKIVTRQGVRVDPNTSVIRV 133

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTE 119
           DG  +   E  + ++ +KP G+ +T  D  GR  V D +        R+  VGRLD  TE
Sbjct: 134 DGSRVIVNEDMQYFVLNKPRGVQSTMHDDMGRPCVGDIIGEKISAGQRLFHVGRLDAATE 193

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLLTNDG LA  L  PS +  + Y     G+VD   +  L+KGI +           +
Sbjct: 194 GLLLLTNDGELANRLMHPSYEVTKTYMATVVGEVDSKVMRELEKGIELDDGIAKADMAQI 253

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                  + V + L EG+   ++++ +   + V RL+R      QLG    G+ R +++ 
Sbjct: 254 IDVWQGRSIVRIELHEGRKHIVRRMLKTAGFPVERLVRTKIHTVQLGEQTPGALRALNRA 313

Query: 240 IL 241
            L
Sbjct: 314 EL 315


>gi|15602526|ref|NP_245598.1| hypothetical protein PM0661 [Pasteurella multocida subsp. multocida
           str. Pm70]
 gi|34098697|sp|Q9CMY9|RLUB_PASMU RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|12720938|gb|AAK02745.1| unknown [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 345

 Score =  159 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 93/290 (32%), Positives = 138/290 (47%), Gaps = 10/290 (3%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG 64
           +       +++ KV+ARAG  SRRE+E MIA+ RV V+G +      ++V +   I +DG
Sbjct: 56  VKNPLVEGEKLQKVLARAGQGSRREIEAMIAENRVSVDGKIATLGDRIDVHAGVKIRIDG 115

Query: 65  VPL-----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
             +     +K     L  Y     L T H      +          SR I+VGRLDINT 
Sbjct: 116 HLINLLHAQKEVCRVLMYYKPEGELCTRHDPEGRPTVFDRLPRLTGSRWIAVGRLDINTS 175

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL T DG LA  L  PS +  R Y VR  GQVD+  L+ LKKG+ ++       ++  
Sbjct: 176 GLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDEAMLHRLKKGVQLEDGPANFKEIKF 235

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
               G N W  V L EG+NRE+++++E    +V+RLIR  YG   L  +L  G   E+  
Sbjct: 236 AGGVGMNQWFDVTLMEGRNREVRRLWESQGVQVSRLIRTRYGNISLMKSLPRGGWEEMDL 295

Query: 239 ---KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
                LRE +G     E ++++  P   ++T    +        +   + 
Sbjct: 296 TNVNYLRELVGLPAEVETKLDVTKPRRRAKTGQIRKAVKRYAELNKRYKK 345


>gi|302518236|ref|ZP_07270578.1| pseudouridine synthase [Streptomyces sp. SPB78]
 gi|302427131|gb|EFK98946.1| pseudouridine synthase [Streptomyces sp. SPB78]
          Length = 447

 Score =  159 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 70/232 (30%), Positives = 111/232 (47%), Gaps = 1/232 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R+ KV+ARAG  SRR  E +I Q RV+VNG ++    + V  +D I+VDG+ +  
Sbjct: 208 EQEGERLQKVLARAGYGSRRACEELIEQARVEVNGEIVLEQGLRVKPSDEIKVDGLTVAT 267

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                  L      + T       ++   D + +  +R+  VGRLD  TEG++LLTN G 
Sbjct: 268 QSYQFFSLNKPAGVVATMEDPEGRQNLG-DYVNNRETRLFHVGRLDTETEGVILLTNHGE 326

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  P     + Y     G + +D    LK GI ++          +  Q G N  V
Sbjct: 327 LAHRLTHPRYGVRKTYLAHIVGPIPRDLGKRLKDGIELEDGWARADHFRVVEQTGKNYLV 386

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V L EG+   ++++     + V++L+R ++GP  LG   +G  R +S   +
Sbjct: 387 EVTLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPITLGDQKSGWLRRLSNTEV 438


>gi|333028084|ref|ZP_08456148.1| putative pseudouridine synthase [Streptomyces sp. Tu6071]
 gi|332747936|gb|EGJ78377.1| putative pseudouridine synthase [Streptomyces sp. Tu6071]
          Length = 455

 Score =  159 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 70/232 (30%), Positives = 111/232 (47%), Gaps = 1/232 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R+ KV+ARAG  SRR  E +I Q RV+VNG ++    + V  +D I+VDG+ +  
Sbjct: 216 EQEGERLQKVLARAGYGSRRACEELIEQARVEVNGEIVLEQGLRVKPSDEIKVDGLTVAT 275

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                  L      + T       ++   D + +  +R+  VGRLD  TEG++LLTN G 
Sbjct: 276 QSYQFFSLNKPAGVVATMEDPEGRQNLG-DYVNNRETRLFHVGRLDTETEGVILLTNHGE 334

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  P     + Y     G + +D    LK GI ++          +  Q G N  V
Sbjct: 335 LAHRLTHPRYGVRKTYLAHIVGPIPRDLGKRLKDGIELEDGWARADHFRVVEQTGKNYLV 394

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V L EG+   ++++     + V++L+R ++GP  LG   +G  R +S   +
Sbjct: 395 EVTLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPITLGDQKSGWLRRLSNTEV 446


>gi|325132446|gb|EGC55139.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M6190]
          Length = 349

 Score =  159 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 72/256 (28%), Positives = 125/256 (48%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    + VNG   +     V   DH+
Sbjct: 84  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWITNGWITVNGKTAQ-LGDKVTPDDHV 142

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L +  ++++       
Sbjct: 203 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVE 262

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   
Sbjct: 263 RIREQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFY 322

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   L    +
Sbjct: 323 ELNPAEVANILKWAEM 338


>gi|120600049|ref|YP_964623.1| pseudouridine synthase [Shewanella sp. W3-18-1]
 gi|120560142|gb|ABM26069.1| pseudouridine synthase [Shewanella sp. W3-18-1]
 gi|319425319|gb|ADV53393.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 242

 Score =  159 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 65/240 (27%), Positives = 105/240 (43%), Gaps = 16/240 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILL--ERAAVNVMST---DHIEVDGVPLR 68
            R++K +A+ GI SRRE  R+I   R+ +NG +                D I +D  P+ 
Sbjct: 1   MRLAKYLAQCGIGSRREACRLINAGRITLNGKIAKHTNLVQRDAQGLCLDSICLDAEPIV 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + E    W+++K   + T     +   T   +L     R+  VGRLD ++ GLLLLTNDG
Sbjct: 61  ETEALAYWIFNKA--VGTDCRLLEQDKTSLLHLLPKAPRLYPVGRLDKDSRGLLLLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS    + Y VR       D +  +  G+  + +     QV   +       
Sbjct: 119 ELTHKLMHPSFAHSKTYHVRLDKPFTDDFVEQMASGVRYKDLQTLPCQVRRLSLDS---- 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-----GTLLAGSTREVSKKILRE 243
             + L +G NR+I+ + +   ++V  L R++     L     G L  G  R ++K  + E
Sbjct: 175 FEIVLTQGLNRQIRHMSKALGYRVIDLERVTIMALNLRELASGELPEGQMRPLTKSEIAE 234


>gi|148653754|ref|YP_001280847.1| RNA-binding S4 domain-containing protein [Psychrobacter sp. PRwf-1]
 gi|148572838|gb|ABQ94897.1| ribosomal large subunit pseudouridine synthase B [Psychrobacter sp.
           PRwf-1]
          Length = 345

 Score =  159 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 77/305 (25%), Positives = 130/305 (42%), Gaps = 7/305 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
            +++ K +AR G+ SRR++E +I   RV +N          V   D I VDG  ++    
Sbjct: 42  TEKLQKALARMGLGSRRQMEEVIKAGRVSINQKPA-SIGDRVEQGDEIRVDGRLIKYKSE 100

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R  L  Y     + + +      +           R I VGRLDIN+ GLLL TND
Sbjct: 101 REKRRRVLAYYKPEGEICSANDPEGRTTVFERLPKLTHDRWIMVGRLDINSTGLLLFTND 160

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS + +R Y VR  G++  + +  L  G++++        +     +G N 
Sbjct: 161 GELAHRLMHPSNEIVREYAVRILGELTPEMMRNLTDGVMLEDGLAKFEDIKQGGGEGVNK 220

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V L+EG+NRE++++ E    KV+RL+R SYG   L   L  G   E+ +K +   + 
Sbjct: 221 WYHVKLKEGRNREVRRLIESQGLKVSRLLRTSYGSVDLPKELRTGRFIELDRKDIHRLID 280

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              +   +          +     +  + +      +R  + S+     +   +     +
Sbjct: 281 LVGIRPREDMGVHGKAKEKKERFQKKPMKARTIRTSSRSGRASTSTGKNTSATRGRDTGN 340

Query: 307 RRNLA 311
           R +  
Sbjct: 341 RGSKR 345


>gi|73541719|ref|YP_296239.1| ribosomal large subunit pseudouridine synthase B [Ralstonia
           eutropha JMP134]
 gi|72119132|gb|AAZ61395.1| ribosomal large subunit pseudouridine synthase B [Ralstonia
           eutropha JMP134]
          Length = 615

 Score =  159 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 72/303 (23%), Positives = 124/303 (40%), Gaps = 6/303 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +  +    ++ KV+A  G+ SRRE+E +I Q RV VNG+        ++ TD + V+G  
Sbjct: 211 LSADDDAPKLHKVLAEGGLGSRREMEELILQGRVSVNGLPA-HIGQRILPTDQVRVNGKL 269

Query: 67  LRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           + +         L  +     +V+        +           + ++VGRLD NTEGLL
Sbjct: 270 IHRKVSTKPPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRMKTGKWVAVGRLDFNTEGLL 329

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + T  G +A     P     R Y VR  G++ +     L  GI +       +++     
Sbjct: 330 IFTTSGDIANRFMHPRYGVEREYAVRTLGELAEADRQRLLHGIKLDDGEANFLRIADGGG 389

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           +G N W  V L EG+NRE++++FE     V+RLIR  YG F L   L  G  +E+    +
Sbjct: 390 EGVNQWYHVALTEGRNREVRRMFEAVGLTVSRLIRTRYGQFLLPRGLKRGRWQELEANEV 449

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +  +    L+    +       ++   R +    +              + +     +  
Sbjct: 450 KSMMTAIGLKVPGTSEQGGKGVTKVGGRKQRTEAAIAGMPMHTGMDGLPRVDKGGAGRGQ 509

Query: 302 ATP 304
             P
Sbjct: 510 PDP 512


>gi|289522957|ref|ZP_06439811.1| RNA pseudouridine synthase [Anaerobaculum hydrogeniformans ATCC
           BAA-1850]
 gi|289503500|gb|EFD24664.1| RNA pseudouridine synthase [Anaerobaculum hydrogeniformans ATCC
           BAA-1850]
          Length = 249

 Score =  159 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 67/231 (29%), Positives = 106/231 (45%), Gaps = 4/231 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K +A  G+ SRR+ E +I   RVKV+G +     + V ++ ++EVDG  +   
Sbjct: 13  DKLIRLNKYLAMCGLGSRRKTEALIVSGRVKVDGEIAAGPWIMVNTSYNVEVDGKIVAPL 72

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L +      +                   I  R+  VGRLD N+ GLL+LTNDG  
Sbjct: 73  KNLYLVMNKPRNCVCAVVDSRYTTVIDLLPKDLIGHRLFPVGRLDKNSSGLLILTNDGDF 132

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A+ +  P     + YRV  +  +    L   +KG+ +         V +     S+ W  
Sbjct: 133 AQDIIHPRNGITKTYRVMLNKPMTSGDLEKWRKGVYLDDRLIKPKDVKIL----SDKWCV 188

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + EGK REI+++ E   +KV  L+RI  G  +L TL  G   + SK  L
Sbjct: 189 IEIYEGKKREIRRMAECLGYKVVELVRIKIGRLELKTLDEGCFLKFSKDKL 239


>gi|153809092|ref|ZP_01961760.1| hypothetical protein BACCAC_03402 [Bacteroides caccae ATCC 43185]
 gi|149128425|gb|EDM19644.1| hypothetical protein BACCAC_03402 [Bacteroides caccae ATCC 43185]
          Length = 494

 Score =  159 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 108/241 (44%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +  +D +
Sbjct: 246 IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVV 305

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P+    +  + L      + T+    + R+ +     +   R+  VGRLD NT G
Sbjct: 306 KFHDEPVSIERKVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTTG 365

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     + +  ++ +  GI ++            
Sbjct: 366 VLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADMDQIAAGIQLEDGEIH-ADAISY 424

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           T       V + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+  
Sbjct: 425 TDDFKKDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSEAE 484

Query: 241 L 241
           +
Sbjct: 485 V 485


>gi|166366480|ref|YP_001658753.1| ribosomal large subunit pseudouridine synthase B [Microcystis
           aeruginosa NIES-843]
 gi|166088853|dbj|BAG03561.1| probable ribosomal large subunit pseudouridine synthase B
           [Microcystis aeruginosa NIES-843]
          Length = 248

 Score =  159 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 89/239 (37%), Positives = 125/239 (52%), Gaps = 10/239 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV K++A+ GIASRR  E MI   RV+ NG +++         DH+E+DG  +  A R 
Sbjct: 3   ERVQKILAQWGIASRRRAEEMIVAGRVRRNGKIVQLGEKADPEKDHLEIDGKKIEPANRP 62

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLLTNDG 128
           +    L +KPIG+V+T  DP  R TV D LP   +       VGRLDINT G LLLTNDG
Sbjct: 63  KRLYILVNKPIGVVSTCRDPQNRPTVIDLLPDSLASETGLHPVGRLDINTTGALLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P     + YRV   G +D+  L   ++GI+++G      QV +  Q      
Sbjct: 123 QLTLTLTHPRYHLPKTYRVWLDGAIDRLALQRWREGILLEGKKTLPAQVEILKQTDQKTL 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-----LLAGSTREVSKKILR 242
           + V L EG+NR+I+ V E   + V +L R + G  QL +     L  G  R ++   L+
Sbjct: 183 LEVILVEGRNRQIRSVAEELGYHVLKLHRSAIGRIQLNSGNNSPLPLGDYRFLTLDELK 241


>gi|261392364|emb|CAX49904.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B; rRNA pseudouridylate synthase B) [Neisseria
           meningitidis 8013]
          Length = 350

 Score =  159 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 72/256 (28%), Positives = 125/256 (48%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+
Sbjct: 85  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHV 143

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 144 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 203

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L +  ++++       
Sbjct: 204 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVE 263

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   
Sbjct: 264 RIREQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFY 323

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   +    +
Sbjct: 324 ELNPAEVANIIKWADM 339


>gi|257784526|ref|YP_003179743.1| pseudouridine synthase [Atopobium parvulum DSM 20469]
 gi|257473033|gb|ACV51152.1| pseudouridine synthase [Atopobium parvulum DSM 20469]
          Length = 279

 Score =  159 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 68/287 (23%), Positives = 114/287 (39%), Gaps = 36/287 (12%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS--------- 56
           + +E   P R+ + +ARAG+ASRR  ER++   RV VNG ++      V           
Sbjct: 1   MTEERIVPMRLQRFLARAGVASRRGSERLMTSGRVTVNGQVVTELGSKVDPLVDVVAVDG 60

Query: 57  -TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
               I          +   L L      L T        + V       +  +  VGRLD
Sbjct: 61  VVCSI--------AEKPVYLMLNKPAGYLTTMKDPQGRPTIVDMVPTDTYPGLFPVGRLD 112

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           ++T GLL  T DG +A+ L  PS    + Y     G   +++LN L++GI ++       
Sbjct: 113 MDTTGLLFFTTDGQMAQELLHPSKHVWKHYVAHVVGTPTEEQLNRLREGIELEDGPAAPA 172

Query: 176 QVTLDTQK------------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
           +V + +                      NA V+V +REG+  ++KK+    + +V  L R
Sbjct: 173 EVEIISDDVKMKNLLAPQGLGKTGGGEPNALVSVTIREGRKHQVKKMLLAIHHRVLALHR 232

Query: 218 ISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSS 264
            ++GP  L  +  G  R ++++ +         E     +     S 
Sbjct: 233 DTFGPLHLTRVKEGEWRLLTEEEVTALERTIGREPGTSPIMPLNTSK 279


>gi|319897335|ref|YP_004135531.1| ribosomal large subunit pseudouridine synthase b [Haemophilus
           influenzae F3031]
 gi|301169940|emb|CBW29544.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae 10810]
 gi|317432840|emb|CBY81205.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae F3031]
          Length = 357

 Score =  159 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 90/288 (31%), Positives = 132/288 (45%), Gaps = 10/288 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 67  LRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +  +         L  Y     L T        +          SR I+VGRLDINT GL
Sbjct: 130 INLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWIAVGRLDINTSGL 189

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++    
Sbjct: 190 LLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGPANFKEIKFTG 249

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 250 GVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEMDLEN 309

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
              LRE +G     E ++++       ++    +        +   + 
Sbjct: 310 VNYLRELVGLPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>gi|68249745|ref|YP_248857.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae 86-028NP]
 gi|68057944|gb|AAX88197.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae 86-028NP]
          Length = 357

 Score =  159 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 90/288 (31%), Positives = 132/288 (45%), Gaps = 10/288 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 67  LRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +  +         L  Y     L T        +          SR I+VGRLDINT GL
Sbjct: 130 INLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWIAVGRLDINTSGL 189

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++    
Sbjct: 190 LLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGPANFKEIKFTG 249

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 250 GVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEMDLEN 309

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
              LRE +G     E ++++       ++    +        +   + 
Sbjct: 310 VNYLRELVGLPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>gi|16273119|ref|NP_439355.1| hypothetical protein HI1199 [Haemophilus influenzae Rd KW20]
 gi|260581101|ref|ZP_05848922.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae RdAW]
 gi|1175679|sp|P45104|RLUB_HAEIN RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|1574128|gb|AAC22853.1| conserved hypothetical protein [Haemophilus influenzae Rd KW20]
 gi|260092230|gb|EEW76172.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae RdAW]
          Length = 357

 Score =  159 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 90/288 (31%), Positives = 132/288 (45%), Gaps = 10/288 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 67  LRKAERT-----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +  +         L  Y     L T        +          SR I+VGRLDINT GL
Sbjct: 130 INLSHTQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWIAVGRLDINTSGL 189

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++    
Sbjct: 190 LLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGLANFKEIKFTG 249

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 250 GVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEMDLEN 309

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
              LRE +G     E ++++       ++    +        +   + 
Sbjct: 310 VNYLRELVGLPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>gi|312277957|gb|ADQ62614.1| Pseudouridine synthase [Streptococcus thermophilus ND03]
          Length = 239

 Score =  159 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 63/239 (26%), Positives = 109/239 (45%), Gaps = 6/239 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++ ++G  SR +V+++I  ++V V+G+L +R  +NV ++   I V G  L  A  
Sbjct: 1   MRLDKLLGQSGYGSRNQVKKLIRSRQVYVDGVLADRDNLNVDASLQTIMVSGKELEHAPE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +                       +  VGRLD +TEGL+L+TN+G L  
Sbjct: 61  VYYLMNKPSGVVSARKDKEHQTVIDLIRPEDQREGLYPVGRLDRDTEGLVLITNNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V  +  +  D     + G+V +        Q+ + +     +   V
Sbjct: 121 AMLHPRYHVAKTYYVEVNDILGPDAPAFFESGVVFEDGTVCQSAQLEVLSSASDKSCARV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LREQLG 246
            + EGK  ++KK+F  +  KV  L RIS+G F+L   +  GS R +++     LR  LG
Sbjct: 181 TISEGKFHQVKKMFLAYGVKVTYLKRISFGEFKLDEGMAVGSYRTLTEAEKTILRTYLG 239


>gi|113969261|ref|YP_733054.1| pseudouridine synthase, Rsu [Shewanella sp. MR-4]
 gi|113883945|gb|ABI37997.1| Pseudouridine synthase, Rsu [Shewanella sp. MR-4]
          Length = 241

 Score =  159 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 68/238 (28%), Positives = 113/238 (47%), Gaps = 16/238 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-RAAVNVMST----DHIEVDGVPLR 68
            R++K +A+ GI+SRRE  R+I   R+ +NG + +   AV+V +     D + +D  P+ 
Sbjct: 1   MRLAKYLAQCGISSRREACRLIEAGRISLNGKIAKHTDAVHVDADGLCLDSLCLDEKPIS 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             E    WL++K   + T     D   +   +L     R+  VGRLD ++ GLLLLTNDG
Sbjct: 61  GVEALSYWLFNKA--VGTDCRLLDADKSSLLHLLPATPRLYPVGRLDKDSRGLLLLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-----KKGIVIQGICYGDMQVTLDTQK 183
            L   L  PS    + Y V+     +   +  +      K +  + +     QVT     
Sbjct: 119 ELTHKLMHPSFAHSKTYHVQLDSPFNDAFIEQMACGVQYKEVRNKEVRTLPCQVTRL--- 175

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            S+    + L +G NR+I+++     +KV  L R++     LG+L  G  R +S + +
Sbjct: 176 -SDVSFEIVLTQGLNRQIRRMSNALGYKVIDLQRVALMTLTLGSLAEGEMRPLSPEEV 232


>gi|167625168|ref|YP_001675462.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
 gi|167355190|gb|ABZ77803.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
          Length = 230

 Score =  159 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 47/232 (20%), Positives = 95/232 (40%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  +   SR   ++ + +  V  NG +++ +   V     I +DG  L      
Sbjct: 1   MRLDKFICESTSHSRVSAKKALHRGDVTCNGEVVKNSGFKVTDEHEIRLDGEVLTII-GP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP+  + +  D +  S +          +   GRLD +T GL+L+T DG  +  
Sbjct: 60  RFIMLNKPVDTICSTIDEEYPSVISLLDVIRPEDLHIAGRLDADTTGLVLITTDGQWSHK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y +     +  D +     G+ +  +       ++ +     +     +
Sbjct: 120 ITSPKKECGKRYLLETAESLSDDLVQQFVDGLQLNNEDGLTKPAELEILAPNQA----RL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++      KV +L R S G  +L   L  G  R ++   ++
Sbjct: 176 TITEGKYHQVKRMLAAVGNKVTKLHRESVGAIELDPNLELGQWRYLTAAEIK 227


>gi|116073056|ref|ZP_01470318.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Synechococcus sp. RS9916]
 gi|116068361|gb|EAU74113.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Synechococcus sp. RS9916]
          Length = 249

 Score =  159 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 79/243 (32%), Positives = 114/243 (46%), Gaps = 3/243 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
           E    +R+ K+IA AG+ SRR  E ++   RVKVN  + +          D I +DG PL
Sbjct: 8   ETVKAERLQKLIAAAGVCSRRHAEELLRAGRVKVNDRMAQ-LGDRAEPGLDRITIDGTPL 66

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTN 126
              +  RL L +KP G++++  DP GR  V D +P    R    VGRLD  + G LLLTN
Sbjct: 67  PANDPPRLLLLNKPRGVISSCQDPQGRPIVLDLVPKHLRRGLHPVGRLDAESRGALLLTN 126

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
            G L   L  P     + YRV   G+     L   ++G+ +        +V       + 
Sbjct: 127 QGELTLQLTHPRYSHAKTYRVWVQGRPSHGALEHWRRGLRLDQRLTQPAEVRELHHNANR 186

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
             + V LREG+NR+I++V E     V  L R +     LG+L  G  RE+++   R    
Sbjct: 187 TLLEVVLREGRNRQIRRVAELLGHPVLDLQRTAIATVVLGSLQEGRWRELTEGEWRALTR 246

Query: 247 PHL 249
           P  
Sbjct: 247 PSR 249


>gi|111221683|ref|YP_712477.1| pseudouridylate synthase [Frankia alni ACN14a]
 gi|111149215|emb|CAJ60900.1| Pseudouridylate synthase [Frankia alni ACN14a]
          Length = 254

 Score =  159 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 77/241 (31%), Positives = 122/241 (50%), Gaps = 3/241 (1%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEV 62
           ++         R+ KV+A AGI SRR  E +IA+ RV V+G+++      V   T  IEV
Sbjct: 5   RDPASAADEGIRLQKVLASAGIGSRRRGEELIAEGRVSVDGVVVREQGRRVNPETAIIEV 64

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEG 120
           DG  +           +KP G+++  SD  GR T+ D L        +  VGRLD ++EG
Sbjct: 65  DGDRIVTRTGLVHLALNKPRGVLSAMSDDRGRPTIADLLTEFDGGGGLFHVGRLDGDSEG 124

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLL+TNDG LA  L  PS +  + Y V   G + ++    L+ G+ ++        V L 
Sbjct: 125 LLLVTNDGELAHRLTHPSFEVPKTYLVEVSGPLRREVPRTLRTGVELEDGPARADSVQLV 184

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            Q      + + + EG+NR ++++ E   + V+RL+R   G   LGTL +G  R +++  
Sbjct: 185 DQANGRVMLEIVIHEGRNRIVRRMMETVGYPVHRLVRTRLGAVHLGTLRSGRARHLTRGE 244

Query: 241 L 241
           +
Sbjct: 245 V 245


>gi|238794709|ref|ZP_04638313.1| Ribosomal large subunit pseudouridine synthase B [Yersinia
           intermedia ATCC 29909]
 gi|238725940|gb|EEQ17490.1| Ribosomal large subunit pseudouridine synthase B [Yersinia
           intermedia ATCC 29909]
          Length = 342

 Score =  159 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 87/301 (28%), Positives = 135/301 (44%), Gaps = 12/301 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVP 66
           +    +++ K++ARAG  SRRE+E +I Q RV V+G +       V  T    I +DG  
Sbjct: 23  DKIVGEKLQKILARAGHGSRREIETIIQQGRVSVDGKI-STLGDRVEVTQATKIRLDGHL 81

Query: 67  LRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           L   E        L  Y     L T +      +          SR ++VGRLD+NT GL
Sbjct: 82  LSIKESEEAVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGL 141

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQ+D +K+  L +G+ +         ++   
Sbjct: 142 LLFTTDGELANRLMHPSREVEREYAVRVFGQIDDEKIKQLSRGVQLDDGPAAFRTISFQG 201

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
            +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  K 
Sbjct: 202 GEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELDLKA 261

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
              LRE +  +    +++ ++      +     R               +  S +   ++
Sbjct: 262 TNYLRELVELNSETVSKLPVEKDRRRVKANQIRRAVKRHTEVAGRQVAGRQGSARKSSTR 321

Query: 298 Q 298
           Q
Sbjct: 322 Q 322


>gi|46200069|ref|YP_005736.1| ribosomal large subunit pseudouridine synthase B [Thermus
           thermophilus HB27]
 gi|46197697|gb|AAS82109.1| ribosomal large subunit pseudouridine synthase B [Thermus
           thermophilus HB27]
          Length = 235

 Score =  158 bits (400), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 83/238 (34%), Positives = 121/238 (50%), Gaps = 8/238 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+   +ARAG+ASRR+ E +I + RV+VNG +       V   D +EVDG  +   ++  
Sbjct: 5   RLQAFLARAGVASRRKAEDLIREGRVRVNGKVA-VLGQKVGPEDLVEVDGKRVELPQKRL 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +   HKP G  TT  DP  R TVFD LP I      VGRLD ++EGLLLLTNDG L   L
Sbjct: 64  VLALHKPKGYTTTRHDPHARRTVFDLLPKIPGL-HPVGRLDRDSEGLLLLTNDGDLTHRL 122

Query: 135 ELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
             P     +VYRV   G    ++    L  G+ ++      +               + L
Sbjct: 123 THPRFGVRKVYRVWTEGGTLPKEVCRRLLLGVDLEDGPARALACCPAPGGAV-----LVL 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            EG+ RE++++ +   + V RL+R+  GP +LG L  G  R +S++ ++  L    LE
Sbjct: 178 AEGRKREVRRMLQRVGYPVRRLLRLQVGPIRLGDLPPGKWRRLSEREVKALLRLVGLE 235


>gi|89256369|ref|YP_513731.1| ribosomal large subunit pseudouridine synthase B [Francisella
           tularensis subsp. holarctica LVS]
 gi|115314814|ref|YP_763537.1| pseudouridylate synthase [Francisella tularensis subsp. holarctica
           OSU18]
 gi|156502454|ref|YP_001428519.1| RNA pseudouridine synthase B [Francisella tularensis subsp.
           holarctica FTNF002-00]
 gi|167010714|ref|ZP_02275645.1| ribosomal large subunit pseudouridine synthase B [Francisella
           tularensis subsp. holarctica FSC200]
 gi|254367705|ref|ZP_04983726.1| ribosomal large subunit pseudouridine synthase B [Francisella
           tularensis subsp. holarctica 257]
 gi|254369343|ref|ZP_04985355.1| pseudouridylate synthase [Francisella tularensis subsp. holarctica
           FSC022]
 gi|89144200|emb|CAJ79469.1| ribosomal large subunit pseudouridine synthase B [Francisella
           tularensis subsp. holarctica LVS]
 gi|115129713|gb|ABI82900.1| pseudouridylate synthase [Francisella tularensis subsp. holarctica
           OSU18]
 gi|134253516|gb|EBA52610.1| ribosomal large subunit pseudouridine synthase B [Francisella
           tularensis subsp. holarctica 257]
 gi|156253057|gb|ABU61563.1| RNA pseudouridine synthase B [Francisella tularensis subsp.
           holarctica FTNF002-00]
 gi|157122293|gb|EDO66433.1| pseudouridylate synthase [Francisella tularensis subsp. holarctica
           FSC022]
          Length = 271

 Score =  158 bits (400), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 85/259 (32%), Positives = 123/259 (47%), Gaps = 9/259 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+  N   +   P+R+ K++A+ GI SRR++E  I Q RVKVNG +           D I
Sbjct: 1   MRRANQNNDKN-PERLQKLLAKYGIGSRRKIEEYIEQGRVKVNGKVAT-LGDKASEADKI 58

Query: 61  EVDGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
             D   L            +  + +   + T+  + D ++          SR I VGRLD
Sbjct: 59  SFDSKALHSYGQPMTRPRVVIYHKREGEVCTSKDEKDRQTVFDSLPKLAKSRWIMVGRLD 118

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGD 174
           INT GLLL T DG LA  L  PS Q  R Y VR  GQ    + +N LK+GI ++      
Sbjct: 119 INTTGLLLFTTDGDLANRLMHPSYQIEREYAVRVFGQQLSDETINKLKEGIQLEDGIAKF 178

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGST 233
             +     +G+N W  V L EG+NRE++++FE     V+RL RI +G   L   +  G T
Sbjct: 179 NSIKFSGGEGANLWYYVTLSEGRNREVRRMFEAVGVTVSRLTRIRFGDIILPKFVSRGKT 238

Query: 234 REVSKKILREQLGPHLLEE 252
            E++   +        L+E
Sbjct: 239 LELNPSEVNRLRKSVKLKE 257


>gi|300870781|ref|YP_003785652.1| ribosomal large subunit pseudouridine synthase B [Brachyspira
           pilosicoli 95/1000]
 gi|300688480|gb|ADK31151.1| ribosomal large subunit pseudouridine synthase B [Brachyspira
           pilosicoli 95/1000]
          Length = 351

 Score =  158 bits (400), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 75/240 (31%), Positives = 126/240 (52%), Gaps = 6/240 (2%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           + N    R+ KVI  +G ASRR  E+ I   RV+VN  ++   A  V  +D + +D   +
Sbjct: 4   KTNKENVRLVKVILESGFASRRNCEKAIMSGRVRVNNQVILDPAYRVKESDSVSIDRNII 63

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            +  +  + LY     +V+T     GR  + +    I  R+   GRLD  + G++++TND
Sbjct: 64  ERQTKRYMALYKPLG-VVSTTKYLPGRRIITEFFKGIKERLFYAGRLDSESRGIMIITND 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G  A ++  PS + L+VY V  +G++D + L     GI I+ + Y   +  + ++    +
Sbjct: 123 GEFANIITHPSYEILKVYDVTVNGKIDSEALLKASAGITIKNVTYSPFKFKILSKGRVQS 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-----GTLLAGSTREVSKKILR 242
            + + + EGKNREI+K+F++  +KV  L RIS G         GTL AG  R+++KK + 
Sbjct: 183 KIRLTINEGKNREIRKIFDYLGYKVIDLERISVGCVSKYDDISGTLEAGHIRDLTKKEIE 242


>gi|91793788|ref|YP_563439.1| pseudouridine synthase, Rsu [Shewanella denitrificans OS217]
 gi|91715790|gb|ABE55716.1| ribosomal large subunit pseudouridine synthase B [Shewanella
           denitrificans OS217]
          Length = 290

 Score =  158 bits (400), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 125/289 (43%), Gaps = 7/289 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E  IA  RV V+G +       V     I +DG        
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRVSVDGEIAT-LGDRVEVDAKIRIDGRTTSIKTA 60

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  +     + +        +          SR ++VGRLDINT GLLL T+D
Sbjct: 61  DDMICRVLAYHKPEGEICSRKDPEGRPTVFERLPKIRDSRWVAVGRLDINTSGLLLFTSD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQV    +  L+ G++++        +     +G N+
Sbjct: 121 GDLANRLMHPSNEVEREYAVRTFGQVTDANVQSLRTGVMLEDGPAQFDTIKPAGGEGINS 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V L+EG+NRE+++++E    +V+RLIR+ YG  +L  TL  G   E+    +     
Sbjct: 181 WWHVTLKEGRNREVRRLWESQEIQVSRLIRVRYGMVELPKTLPRGGWIELPLDQVNYLRQ 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
              LE    ++      S    + + + I         +   +      
Sbjct: 241 LAGLEAETRSMLGSDKHSVARSKVKSSKIRRAVQKHKVISSRAKPSRQR 289


>gi|120600175|ref|YP_964749.1| pseudouridine synthase [Shewanella sp. W3-18-1]
 gi|146291897|ref|YP_001182321.1| pseudouridine synthase [Shewanella putrefaciens CN-32]
 gi|120560268|gb|ABM26195.1| ribosomal small subunit pseudouridine synthase A [Shewanella sp.
           W3-18-1]
 gi|145563587|gb|ABP74522.1| ribosomal small subunit pseudouridine synthase A [Shewanella
           putrefaciens CN-32]
 gi|319425188|gb|ADV53262.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 229

 Score =  158 bits (400), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 47/231 (20%), Positives = 98/231 (42%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  +   +R   ++ + +  +  +G++++ A   V     I ++G P+      
Sbjct: 1   MRLDKFICESTSLTRSLAKKALHRGDITCDGVVIKDAGFKVTEGMQICLEGEPIVLV-GE 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP+  + +  D    S +          +   GRLD +T GL+L+T+DG  +  
Sbjct: 60  RYVMLNKPVDTICSTIDEAYPSVLSLLDIPKPETLHIAGRLDADTTGLVLITSDGQWSHK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y V+    VD   + +  KG+ +  +        + +   +     V +
Sbjct: 120 ITSPKKECGKRYLVQLADPVDDGLIEVFAKGVALRNEDGLTKPAVLEIIDPQQ----VRL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++K++F      V  L R   G  +L   L  G  R ++ + +
Sbjct: 176 TITEGKYHQVKRMFAAVGNLVVGLHRERIGQIELDPDLALGEWRYLTAEEI 226


>gi|319410624|emb|CBY90993.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B; rRNA pseudouridylate synthase B) [Neisseria
           meningitidis WUE 2594]
          Length = 349

 Score =  158 bits (400), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 72/256 (28%), Positives = 125/256 (48%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+
Sbjct: 84  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHV 142

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L +  ++++       
Sbjct: 203 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVE 262

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   
Sbjct: 263 RIYEQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFY 322

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   +    +
Sbjct: 323 ELNPAEVANIIKWADM 338


>gi|291550320|emb|CBL26582.1| ribosomal small subunit pseudouridine synthase A [Ruminococcus
           torques L2-14]
          Length = 241

 Score =  158 bits (400), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 110/232 (47%), Gaps = 5/232 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  GI +R EV++ I + +V+VN   ++R  + +    DH+   G  +  AE  
Sbjct: 4   RLDKYLADMGIGTRTEVKKAITKGQVRVNEETVKRPEIKIDTEKDHVFYQGQMVAYAEYE 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      +V+   D +  + +          +  VGRLD +TEGLLL+TNDG LA  
Sbjct: 64  YYMLNKPAG-VVSATEDKNDSTVLDLIDEKQRKDLFPVGRLDKDTEGLLLITNDGELAHQ 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           L  P     +VY  R  G+V ++ +    +G+ I +        + +  ++   + + + 
Sbjct: 123 LLSPKKHVDKVYFARIDGKVTEEDVRRFAEGLEIGEEKPTLPAHLEILKREEI-SEIRLT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           +REGK  ++K++F     +V  L R+  G   L   L  G  RE++ + L  
Sbjct: 182 IREGKFHQVKRMFHAVGKEVIYLKRLQMGSLVLDPRLALGEYRELTGQELEA 233


>gi|184201169|ref|YP_001855376.1| pseudouridine synthase [Kocuria rhizophila DC2201]
 gi|183581399|dbj|BAG29870.1| pseudouridine synthase [Kocuria rhizophila DC2201]
          Length = 368

 Score =  158 bits (400), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 81/239 (33%), Positives = 126/239 (52%), Gaps = 2/239 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           +    R+ K++A+AG+ASRR  E MI   RV V+G ++    V V      + VDG+ ++
Sbjct: 126 DENGVRLQKLMAQAGVASRRVCEEMIQDGRVSVDGEIVTELGVRVDPALQAVHVDGMRIQ 185

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTND 127
             E+   + ++KP G+V+T  DPDGR  V D L     +    VGRLD+ TEGLLLLTND
Sbjct: 186 TDEKLVYYAFNKPAGVVSTMEDPDGRRCVSDFLDPRKHQRVFHVGRLDVETEGLLLLTND 245

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  PS +  + Y V+ HG V++   N +K+GI ++          L      + 
Sbjct: 246 GELTNRLTHPSYEVPKTYLVQVHGPVEKGIGNQMKQGIRLEDGIAKVDDFRLVDSTPGHV 305

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            + V L  G+NR ++++F+  +  V +L R   GP  +G    G+ R++S   +   L 
Sbjct: 306 LIEVVLHSGRNRIVRRMFDAVDHPVEKLARTHVGPIAIGDQKQGTVRKLSHTEVGNLLA 364


>gi|157413639|ref|YP_001484505.1| 16S rRNA uridine-516 pseudouridylate synthase-like protein
           [Prochlorococcus marinus str. MIT 9215]
 gi|157388214|gb|ABV50919.1| 16S rRNA uridine-516 pseudouridylate synthase-like protein
           [Prochlorococcus marinus str. MIT 9215]
          Length = 240

 Score =  158 bits (400), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 53/226 (23%), Positives = 100/226 (44%), Gaps = 11/226 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---AE 71
           R++K ++  G  SRRE +R+I + +V +NG + +     V  +D +EV G  ++K    +
Sbjct: 4   RINKYLSEVGYCSRREADRLIHEGKVTINGKIPK-IGSKVEESDQVEVKGQRIKKITGQK 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L        + TT            +      R+  +GRLD  +EGL+ LTNDG + 
Sbjct: 63  NIYLAFNKPVGIVCTTDRK--VEPNNVIDFIKYPKRIFPIGRLDKLSEGLIFLTNDGDIV 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V+ + Q++ D +  +  G+ I      +       ++       +
Sbjct: 121 NKILRARNNHEKEYIVKVNRQINSDFIQSMSSGVEILDTITKNC----FVKQLGPKKFKI 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L +G NR+I+++ E   ++V  L R+     +L  +  G  RE +
Sbjct: 177 ILTQGLNRQIRRMCESLGYRVRSLKRVRIMNIEL-DVSTGKYREFT 221


>gi|315179963|gb|ADT86877.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio furnissii
           NCTC 11218]
          Length = 233

 Score =  158 bits (400), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 48/229 (20%), Positives = 91/229 (39%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  ++R+E  +++    V V+G + +  +V V     +      L      
Sbjct: 1   MRLDKFLCDALGSTRKEATQILKSGDVTVDGKVQKSGSVQVTEASVVAWQERQLSLTGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + LY     + +     +  +            +   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLYKPEGFVCSHEDGFNQ-TAFVLLDEVNMRGLHFAGRLDVDTTGLVLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     V  D    L  GI ++      +   ++        V + +
Sbjct: 120 ITSPKHKCDKTYRVWLADAVQADYAEQLAHGIELRNERELTLPAHMELVNADENEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EGK  ++K++F     KV  L R   G   L   L  G  R +++  +
Sbjct: 180 HEGKYHQVKRMFAALGNKVEALHRERVGEIVLDESLEPGEYRYLTEAEV 228


>gi|167758122|ref|ZP_02430249.1| hypothetical protein CLOSCI_00460 [Clostridium scindens ATCC 35704]
 gi|167664019|gb|EDS08149.1| hypothetical protein CLOSCI_00460 [Clostridium scindens ATCC 35704]
          Length = 246

 Score =  158 bits (400), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 63/236 (26%), Positives = 107/236 (45%), Gaps = 8/236 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
            R+ K +A  GI +R+EV+R I Q RV ++GI  +     +      I  DG  +  A+ 
Sbjct: 7   IRLDKYLADMGIGTRQEVKRYIRQGRVSIDGIPAKSPETKIEEKARKITFDGREVDYADY 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +V+   D    + V          +  VGRLD +TEGLLL+TNDG L+ 
Sbjct: 67  EYYMLNKPSG-VVSATEDARCTTVVDLIRDKKRKDLFPVGRLDKDTEGLLLITNDGQLSH 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGSNAW 188
            L  P     + Y  +  G+V ++     ++G+ I    +        + +  +    + 
Sbjct: 126 RLLSPKKHVDKTYYAKVAGKVTKEDAKAFREGVNIGTEEKEEWTRPGVLDIL-KSEEVSE 184

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
           + + ++EGK  ++K++F+    +V  L R S G  +L   L  G  R ++KK L  
Sbjct: 185 IRLTIQEGKYHQVKRMFQAVGKEVLYLKRESMGCLKLDETLKPGEYRPLTKKELEN 240


>gi|323697859|ref|ZP_08109771.1| pseudouridine synthase [Desulfovibrio sp. ND132]
 gi|323457791|gb|EGB13656.1| pseudouridine synthase [Desulfovibrio desulfuricans ND132]
          Length = 251

 Score =  158 bits (400), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 69/236 (29%), Positives = 108/236 (45%), Gaps = 6/236 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R++K IA+ G+ASRR  + M+   RV VNG   +   + V    D + VDG  + +
Sbjct: 6   SDTLRLNKFIAQCGVASRRGADEMVFAGRVTVNGATADSPGLQVDPARDEVAVDGKVIGQ 65

Query: 70  AE---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLT 125
                   L L+     + T       ++ +    P     R   VGRLD  +EGLLLLT
Sbjct: 66  KASAGDLTLLLHKPVETVTTASDPQGRKTVLDLLPPEIRKKRPFPVGRLDFFSEGLLLLT 125

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG 184
            DG L   L  P     +VY V   G V Q  +  +++G+ + +G      +V L     
Sbjct: 126 TDGDLCYRLTHPKYHLPKVYVVTIRGSVPQKAVQTMRQGMTLREGDRLAPAKVRLLKPIA 185

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
               + + L +G NR+I+++ E     + RL R+  GP  LG L  G+ RE++ + 
Sbjct: 186 GTQQLEITLIQGVNRQIRRMCEELGLTILRLRRVRQGPVALGDLKPGAWRELTSEE 241


>gi|261400141|ref|ZP_05986266.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           lactamica ATCC 23970]
 gi|269210136|gb|EEZ76591.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           lactamica ATCC 23970]
          Length = 252

 Score =  158 bits (400), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 72/255 (28%), Positives = 110/255 (43%), Gaps = 20/255 (7%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K          R+SK +A+ G+ SRRE +  I Q RV VNG         V+  D I
Sbjct: 1   MNSKISSDHTEDTMRLSKRMAQLGLCSRREADGYIEQGRVTVNGKTA-VLGQKVLPADRI 59

Query: 61  EVD---------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           E+D                 P+          Y     L+T  +  +G +      P   
Sbjct: 60  ELDKKAHEQQAARITILLNKPVGYVSAQAEKGYKSAAELITPENRWEGDTGRIRFDPKHK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             + S GRLDI++ GLL+LT DG +AR L   ++   + Y VR  G++D+  L LL  G+
Sbjct: 120 IGLASAGRLDIDSVGLLVLTQDGRIARQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGL 179

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G      +V    +      +   L++GK R+I+++ E    +V  L RI  G  +L
Sbjct: 180 SLDGEKLRPAKVEWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>gi|225021516|ref|ZP_03710708.1| hypothetical protein CORMATOL_01537 [Corynebacterium matruchotii
           ATCC 33806]
 gi|224945898|gb|EEG27107.1| hypothetical protein CORMATOL_01537 [Corynebacterium matruchotii
           ATCC 33806]
          Length = 241

 Score =  158 bits (400), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 76/233 (32%), Positives = 116/233 (49%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ KV+A+AG+ASRR  E MI   RV+VNG ++ +  V V    D I VDGV +     
Sbjct: 1   MRLQKVLAQAGVASRRNAEIMIDSGRVEVNGAVVMQQGVRVNPEVDVIRVDGVRVNVNNN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTNDGG 129
            + ++ +KP G+ +T SD  GR  + D +         +  VGRLD +TEGL+LLTNDG 
Sbjct: 61  HQYFVLNKPRGIHSTMSDDLGRPCIGDLVSERISAGQGLFHVGRLDADTEGLILLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  P  +  + Y     G+ D+  +  LK G+ +         V +       + V
Sbjct: 121 LANRLSHPKYEVSKTYIAEVLGEADRSLVTTLKNGVELDDGPAAADYVQIVDVHQGRSLV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V L EG+   ++++ +   + V  L+R      QLG    G+ R ++   LR
Sbjct: 181 RVQLHEGRKHIVRRMLKAAGYPVQYLVRTKLHTVQLGEQKPGTIRALNDNELR 233


>gi|311104985|ref|YP_003977838.1| ribosomal large subunit pseudouridine synthase B [Achromobacter
           xylosoxidans A8]
 gi|310759674|gb|ADP15123.1| ribosomal large subunit pseudouridine synthase B [Achromobacter
           xylosoxidans A8]
          Length = 604

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 86/328 (26%), Positives = 135/328 (41%), Gaps = 14/328 (4%)

Query: 1   MKDK--NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M+ +    +  +    ++ KV+A AGI SRRE+E +I   RV VNG         V   D
Sbjct: 95  MEQRLGKYLNSDSVMPKLHKVLADAGIGSRREMEELIVAGRVSVNGEPA-HIGQRVAPND 153

Query: 59  HIEVDGVPL----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
            + V+G P+     K     +  +     +V+        S           + +SVGRL
Sbjct: 154 QVRVNGKPIMRVNTKKPPRVILYHKPAGEIVSHDDPGGRASVFARLPKLRTGKWLSVGRL 213

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D+NTEGLL+ T  G +A  +  P     R Y VR  G++D+ +   L  GI ++      
Sbjct: 214 DLNTEGLLIFTTSGDMANRIMHPRYGTEREYAVRVLGEMDEAQRQSLVDGIELEDGLAAF 273

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
             +      GSN W  V L+EG+NRE++++FE     V+RLIR  +G   L  TL  G  
Sbjct: 274 GALDYLGGDGSNRWYRVTLQEGRNREVRRMFEAVGVTVSRLIRTRFGDVVLPRTLRRGRW 333

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
            E+        +   +++   V  D     +    +   +  S +P  F  M +N    N
Sbjct: 334 EELDA----SLVTALMVQLGLVRDDDEAGGNRRRSKQPQSHDSALPPGFGTMDRNG--LN 387

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIH 321
           G    ++      R   A          
Sbjct: 388 GARIGRRGKLQGGRLGSAGQAAACPSDP 415


>gi|119469277|ref|ZP_01612216.1| pseudouridine synthase [Alteromonadales bacterium TW-7]
 gi|119447141|gb|EAW28410.1| pseudouridine synthase [Alteromonadales bacterium TW-7]
          Length = 289

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 82/288 (28%), Positives = 133/288 (46%), Gaps = 10/288 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N   +++ KV+ARAG+ SRRE+E+ I   RV VNG + +     V  TD I VDG  ++ 
Sbjct: 2   NIQGEKLQKVLARAGVGSRREMEKYIDANRVSVNGKVAK-LGDRVEETDLIRVDGHTVKI 60

Query: 70  AE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            E        +        L T       R+           R I+VGRLD+NT GL+L 
Sbjct: 61  EEKADRICRVIMYNKPEGELSTRKDPEGRRTVFDRLPRIDGDRWIAVGRLDVNTSGLMLF 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG LA  L  PS +  R Y  R  G+V  + L  L +G+ ++        +     +G
Sbjct: 121 TNDGELANRLMHPSYEVEREYSSRVFGEVTNETLKNLMRGVELEDGPAKFTNIKPLGGEG 180

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREV---SKKI 240
            N W  V L EG+NRE++++++  + +V+RLIRI YG  +L   +  G   E    +   
Sbjct: 181 INRWFNVTLNEGRNREVRRLWQSQDVEVSRLIRIRYGKLELDKRVPQGGWVEYDLETVNY 240

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
           LR+ +      + ++++       +    ++     +  +   +  K 
Sbjct: 241 LRKTVKLGRETQTKLSVMPEKRKDKRAKINQIRKAVKKHNQRVKSTKR 288


>gi|161829731|ref|YP_001596671.1| RNA pseudouridine synthase family protein [Coxiella burnetii RSA
           331]
 gi|161761598|gb|ABX77240.1| RNA pseudouridine synthase family protein [Coxiella burnetii RSA
           331]
          Length = 244

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 75/233 (32%), Positives = 115/233 (49%), Gaps = 5/233 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---KA 70
           +R+ KV+AR+G  SRRE+E+MIA+ R+KVN  L +     +   D + +DG         
Sbjct: 3   ERIQKVLARSGYGSRREIEKMIAEGRIKVNQRLAQ-LGDRITEQDLVYIDGQLSSLSAPE 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L  +     + T        +           R + +GRLDINT GLLL TN+G L
Sbjct: 62  QVRVLLYHKPEGEICTRKDPEWRTTVFETLPRLKDGRWVIIGRLDINTSGLLLFTNEGEL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS Q  R Y VR  G VD D    L  G+ ++        +      G N W  
Sbjct: 122 ANRLMHPSAQVEREYAVRVLGAVDADMTQKLAHGVGLEDGKARFEDIVDVGGDGKNRWFH 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           V + EG++R +++++E    KV+RLIR+ +GP  L  +L  G+ +E+    ++
Sbjct: 182 VVVVEGRHRLVRRLWESQGLKVSRLIRVRFGPIVLPKSLRRGAWKELESPEIK 234


>gi|298480189|ref|ZP_06998387.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           D22]
 gi|298273470|gb|EFI15033.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           D22]
          Length = 495

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 107/241 (44%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +  +D +
Sbjct: 247 IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVV 306

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P+    +  + L      + T+    + R+ +     +   R+  VGRLD NT G
Sbjct: 307 KFHDEPVSIERKVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTTG 366

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     + +  +  +  GI ++            
Sbjct: 367 VLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADMEQIAAGIQLEDGEIH-ADAISY 425

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           T       V + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+  
Sbjct: 426 TDDFKKDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSEAE 485

Query: 241 L 241
           +
Sbjct: 486 V 486


>gi|257469859|ref|ZP_05633951.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium
           ulcerans ATCC 49185]
 gi|317064088|ref|ZP_07928573.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium
           ulcerans ATCC 49185]
 gi|313689764|gb|EFS26599.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium
           ulcerans ATCC 49185]
          Length = 226

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 100/229 (43%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SRREV+ ++    + VNG + +   +N+    D +      L   + 
Sbjct: 1   MRLDKFLTECGLGSRREVKELLNTGEITVNGAVADNPQMNIKENDDEVFYQERKLEYKKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L  K   +       D           I   +  VGRLD +TEGLLLLT+DG L  
Sbjct: 61  RYYILNKKAGYITAVGDARDQTVMDLLPDWVIKKDLAPVGRLDKDTEGLLLLTSDGALNH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y      ++ +  L  L+ G+ I G      +      K  +  + + 
Sbjct: 121 KLLSPKNHVEKTYYAELEKEISEADLERLRNGVDIGGYITMPGKAV----KIDSCKIHLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++EGK  ++KK+ E    KV  L R+S+G  +L  L  G+ +EVS + +
Sbjct: 177 IKEGKFHQVKKMLEAVGNKVTFLRRVSFGKLKLEDLELGAVKEVSIEDI 225


>gi|116627439|ref|YP_820058.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           thermophilus LMD-9]
 gi|116100716|gb|ABJ65862.1| 16S rRNA uridine-516 pseudouridylate synthase or related
           pseudouridylate synthase [Streptococcus thermophilus
           LMD-9]
          Length = 239

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 62/239 (25%), Positives = 108/239 (45%), Gaps = 6/239 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++ ++G  SR +V+ +I  ++V V+G+L +R  +NV ++   I V G  L  A  
Sbjct: 1   MRLDKLLGQSGYGSRNQVKNLIRSRQVYVDGVLADRDNLNVDASLQTIMVSGKELEHAPE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +                       +  VGRLD +TEGL+L+TN+G L  
Sbjct: 61  VYYLMNKPSGVVSARKDKEHQTVIDLIRPEDQREGLYPVGRLDRDTEGLVLITNNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V  +  +  D     + G+V +        Q+ + +     +   +
Sbjct: 121 AMLHPRYHVAKTYYVEVNDILGPDAPAFFESGVVFEDGTVCQSAQLEILSSASDKSCARI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LREQLG 246
            + EGK  ++KK+F  +  KV  L RIS+G F+L   +  GS R +++     LR  LG
Sbjct: 181 TISEGKFHQVKKMFLAYGVKVTYLKRISFGEFKLDEGMAVGSYRTLTEAEKTILRTYLG 239


>gi|325982253|ref|YP_004294655.1| pseudouridine synthase Rsu [Nitrosomonas sp. AL212]
 gi|325531772|gb|ADZ26493.1| pseudouridine synthase Rsu [Nitrosomonas sp. AL212]
          Length = 276

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 70/238 (29%), Positives = 117/238 (49%), Gaps = 6/238 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--- 71
           ++ K++A+ G+ SRRE+E +IA  +VK+N  +           D + +    +R  E   
Sbjct: 38  KLQKLLAQKGLGSRREMEALIASGQVKLNDHIA-VIGDRAGPGDIVRIGRRVIRIHEEEE 96

Query: 72  -RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               L  +     +V+ +   D  S          S+ I++GRLD NT GLL+ TNDG L
Sbjct: 97  LPKVLLYHKPEGEIVSRNDPQDRPSVFDKLPYLRSSKWIAIGRLDFNTSGLLIFTNDGAL 156

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +  P  +  R Y VR  G++ ++++  L  GI ++        +     +G+N W  
Sbjct: 157 ANRMMHPRFEMEREYAVRILGELTEEQMQQLTTGITLEDGEAAFTYLADQGGEGANHWYR 216

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
           V L+EGKNRE++++F      V+RL+R+ +GP  L   +  G   E+ +K  R  L  
Sbjct: 217 VILKEGKNREVRRMFGAIGLTVSRLMRVRFGPINLPPRIKRGQWLELDEKETRRLLSL 274


>gi|307130978|ref|YP_003882994.1| 23S rRNA pseudouridylate synthase [Dickeya dadantii 3937]
 gi|306528507|gb|ADM98437.1| 23S rRNA pseudouridylate synthase [Dickeya dadantii 3937]
          Length = 296

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 87/298 (29%), Positives = 131/298 (43%), Gaps = 10/298 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E MI   R+ V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESMIEAGRISVDGKIATLGDRVEVTRATKIRIDGHVVSVRE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T        +           R ++VGRLD+NT GLLL T 
Sbjct: 62  TEESVCRVLMYYKPEGELCTRSDPEGRPTVFDRLPRIQGYRWVAVGRLDVNTSGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  G+V  DK+  L KG+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGEVGDDKIRQLSKGVQLEDGPAAFRSIRYQGGEGLN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
            W  V L EG+NRE+++++E  + +V+RLIR+ YG  QL   L  G   E+    L +  
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVDVQVSRLIRVRYGDIQLPKGLPRGGWMEMG---LTDVN 238

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
               L +      + +       R + N I       +++  ++   +G     K   
Sbjct: 239 YLRELVQLTPETVSKLPVERERRRVKANQIRRAVKRHSQVGVSNRPASGRRSAPKRNG 296


>gi|313159346|gb|EFR58710.1| pseudouridylate synthase [Alistipes sp. HGB5]
          Length = 423

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 57/239 (23%), Positives = 118/239 (49%), Gaps = 2/239 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K   ++     R+++ +A++G+ SRRE +  I    V VNG ++ +    V+ TD ++ +
Sbjct: 179 KFTPEKQIGEMRLNRFLAQSGLCSRREADDFITAGLVTVNGQIVTQLGTKVLPTDEVKFN 238

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
              ++  ++  L L      + +      G++ +     +   R+  VGRLD N+ GLLL
Sbjct: 239 DSRVQGEKKVYLVLNKPKGYVTSLDDPHAGKTVMELVQGACTERIYPVGRLDKNSLGLLL 298

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            TNDG L + L  P+ +  ++Y+V     + +  ++ + +GI ++       +  +   K
Sbjct: 299 FTNDGDLTKQLTHPAFRKKKIYQVSLDKPLTRADMDRIAEGITLEDGEIFADE--ISYVK 356

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +   V + +  G+NR ++++FEF  + V +L R+ Y       L  G+ R +S++ + 
Sbjct: 357 DNKQEVGIEIHSGRNRIVRRIFEFLGYTVTKLDRVYYAGLTKKNLKRGAWRFLSREEVE 415


>gi|298368371|ref|ZP_06979689.1| ribosomal large subunit pseudouridine synthase B [Neisseria sp.
           oral taxon 014 str. F0314]
 gi|298282374|gb|EFI23861.1| ribosomal large subunit pseudouridine synthase B [Neisseria sp.
           oral taxon 014 str. F0314]
          Length = 348

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 72/256 (28%), Positives = 124/256 (48%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+
Sbjct: 84  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHV 142

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++  L +  ++++       
Sbjct: 203 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTTEQMRSLTEEGVMLEDGLAKVE 262

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   
Sbjct: 263 RIYEQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFY 322

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   +    +
Sbjct: 323 ELNPAEVANIIKWADM 338


>gi|304384543|ref|ZP_07366889.1| ribosomal small subunit pseudouridine synthase A [Pediococcus
           acidilactici DSM 20284]
 gi|304328737|gb|EFL95957.1| ribosomal small subunit pseudouridine synthase A [Pediococcus
           acidilactici DSM 20284]
          Length = 239

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 101/234 (43%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            RV K +    + +R ++ ++I ++ V VN ++ +   V V    D + +    +   + 
Sbjct: 1   MRVDKFLHDMNVGTRSQIRKLIKEKAVFVNDVVAKSGRVKVDPVVDQVRLGEQVITYQQY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            N       +  VGRLD +TEGLLL+TN+G LA 
Sbjct: 61  FYFMMNKPLGVVTATEDRKQKTVMDLFNKVDFRKDLFPVGRLDKDTEGLLLITNNGPLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQK--GSNAWV 189
            L  P     + Y     GQ+    +     GIV++         +T+           V
Sbjct: 121 QLLAPERHVQKTYEAVVTGQITDPAVKQFADGIVLKDGTQLKPADLTILNYSALDEQTLV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
            V L+EGK  +++++F     +V  L RIS+GP QL   LL G+ RE+S + + 
Sbjct: 181 HVTLKEGKYHQVRRMFGSLGERVVSLKRISFGPLQLEEGLLPGTYRELSDEEIE 234


>gi|302037904|ref|YP_003798226.1| pseudouridine synthase, rsuA family [Candidatus Nitrospira
           defluvii]
 gi|300605968|emb|CBK42301.1| Pseudouridine synthase, rsuA family [Candidatus Nitrospira
           defluvii]
          Length = 255

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 79/254 (31%), Positives = 120/254 (47%), Gaps = 2/254 (0%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTR 74
           + +++++ GIASR + +  I   RV++N  L+      +    D + +D  P+ +     
Sbjct: 3   LDRLLSKLGIASRSQAQEWIRAGRVRINRRLVRMPDTWIDWPGDAVTLDDRPIEQRPPQF 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +  +     + T   +     T+FD LP     + +VGRLD  T GLLLLTND  L+  L
Sbjct: 63  ILFHKPKGVVTTHQDEKGR-PTIFDVLPPELKGLHAVGRLDQATSGLLLLTNDSTLSSFL 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  Q  R+Y V   G+V ++       G+  QG       VT+  + G  + + V L 
Sbjct: 122 TDPKQQVPRLYLVTVRGEVSEETGRAALDGVDDQGERLHCASVTIQKRSGRESHLVVTLT 181

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           EGKNREI+++F+    +V RL RI YGPF LG L  G+ RE+  +  R QL       A 
Sbjct: 182 EGKNREIRRLFKALGHEVTRLRRIQYGPFILGDLQPGAWRELPIEAARAQLRLPSAHAAG 241

Query: 255 VNLDAPIYSSETLV 268
           V    P        
Sbjct: 242 VPQAKPDPLDRRAT 255


>gi|261365463|ref|ZP_05978346.1| ribosomal large subunit pseudouridine synthase B [Neisseria mucosa
           ATCC 25996]
 gi|288566133|gb|EFC87693.1| ribosomal large subunit pseudouridine synthase B [Neisseria mucosa
           ATCC 25996]
          Length = 348

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 72/256 (28%), Positives = 124/256 (48%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+
Sbjct: 83  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHV 141

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 142 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 201

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++  L +  ++++       
Sbjct: 202 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTTEQMRSLTEEGVMLEDGLAKVE 261

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   
Sbjct: 262 RIYEQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFY 321

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   +    +
Sbjct: 322 ELNPAEVANIIKWADM 337


>gi|168212250|ref|ZP_02637875.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           CPE str. F4969]
 gi|170715946|gb|EDT28128.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           CPE str. F4969]
          Length = 228

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 56/229 (24%), Positives = 103/229 (44%), Gaps = 8/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+ +  GI SR+E  ++I + RV VNG         V  +D I +D  PL   E+ 
Sbjct: 1   MRINKLFSNFGICSRKETNKIIREGRVIVNGKPCIE-GQWVELSDEILLDEKPLVPKEKI 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L      + T   +         +   I   V  +GRLD +++GL++LTNDG LA  
Sbjct: 60  YIALNKPVGVVCTAAEEV---KDNIIDYLGIDDYVFPIGRLDKDSQGLIILTNDGDLANE 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V        D +  +++G+ I G      ++    +       ++ L
Sbjct: 117 VLAAENNHEKEYIVTLDQPFYDDFIKKMERGVEILGQVTKPCKLKRINEN----TYSIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ + F + V +L RI      L  +  G  R ++++ + 
Sbjct: 173 TQGLNRQIRRMSKVFGFNVVKLERIRILNITLEDIEYGKWRYINREEIE 221


>gi|325136137|gb|EGC58745.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M0579]
 gi|325136446|gb|EGC59053.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M0579]
 gi|325208319|gb|ADZ03771.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis NZ-05/33]
          Length = 349

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 72/256 (28%), Positives = 125/256 (48%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+
Sbjct: 84  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHV 142

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L +  ++++       
Sbjct: 203 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVE 262

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   
Sbjct: 263 RIREQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFY 322

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   +    +
Sbjct: 323 ELNPAEVANIIKWADM 338


>gi|262408169|ref|ZP_06084716.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           2_1_22]
 gi|262353721|gb|EEZ02814.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           2_1_22]
          Length = 495

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 107/241 (44%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +  +D +
Sbjct: 247 IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVV 306

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P+    +  + L      + T+    + R+ +     +   R+  VGRLD NT G
Sbjct: 307 KFHDEPVSIERKVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTTG 366

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     + +  +  +  GI ++            
Sbjct: 367 VLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADMEQIAAGIQLEDGEIH-ADAISY 425

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           T       V + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+  
Sbjct: 426 TDDFKKDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSEAE 485

Query: 241 L 241
           +
Sbjct: 486 V 486


>gi|282599636|ref|ZP_05971291.2| ribosomal large subunit pseudouridine synthase B [Providencia
           rustigianii DSM 4541]
 gi|282568029|gb|EFB73564.1| ribosomal large subunit pseudouridine synthase B [Providencia
           rustigianii DSM 4541]
          Length = 313

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 84/305 (27%), Positives = 138/305 (45%), Gaps = 10/305 (3%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG 64
           +  +    +++ K++AR+G  SRRE+E  + + R+ V+G +      V V ++  I +DG
Sbjct: 9   MSSKPQQTEKLQKILARSGHGSRREIEGFLKEGRISVDGKMATLGDRVEVTTSTKIRLDG 68

Query: 65  VPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
             L   E        +  Y     L T H      +          +R I+VGRLD+NT 
Sbjct: 69  RLLTIREPEKDICRVMAYYKPEGELCTRHDPEGRPTVFTRLPKLTGARWIAVGRLDVNTS 128

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL T DG LA  L  PS +  R Y VR  G++   K+  L  G+ ++        V+ 
Sbjct: 129 GLLLFTTDGELANRLMHPSREVEREYAVRVFGEITDAKIRQLTMGVQLEDGPASFKTVSF 188

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  
Sbjct: 189 RGGEGMNQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIDLPKGLPRGGWTELGL 248

Query: 239 KI---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +    LRE +G  +  E++V ++      +     R              K+ +S+    
Sbjct: 249 EQTNYLRELVGLSVETESKVAVERDQRRLKANQIRRAVKRHTQVASRPASKRQASRPTAK 308

Query: 296 SKQKK 300
            + + 
Sbjct: 309 KRTRA 313


>gi|294142422|ref|YP_003558400.1| ribosomal pseudouridine synthase family protein [Shewanella
           violacea DSS12]
 gi|293328891|dbj|BAJ03622.1| ribosomal pseudouridine synthase family protein [Shewanella
           violacea DSS12]
          Length = 250

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 55/242 (22%), Positives = 106/242 (43%), Gaps = 14/242 (5%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--------VMSTD 58
           + ++    R++K +A  G+ SR+   R I    + ++G L               + S +
Sbjct: 1   MTQDKPSMRLAKYLAMTGLCSRKAATRYIRDGHITLDGRLANHIDTISLIESPSGLTSLE 60

Query: 59  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
            ++ DGV ++  E  + W+ +K   + T         +   +L     R+  VGRLD ++
Sbjct: 61  ILKFDGVLIQGVESKQYWMLNKS--VGTDCRLLAHDPSSLLHLLPDNPRLYPVGRLDKDS 118

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            G L+LTNDG L + L  P     + Y V+  G  +   L  + +G+  + +     ++T
Sbjct: 119 RGQLILTNDGELTQQLMHPDFGHSKTYHVQVDGNFEDSFLIKMAQGVSYRDVTTLPCKMT 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
                       + L +G NR+I+++ +   +KV  L R++     LG L  G  R+++ 
Sbjct: 179 RLNDNK----FEIILTQGLNRQIRRMSQALGYKVVDLKRVNIQSLALGDLKEGEMRQLTA 234

Query: 239 KI 240
             
Sbjct: 235 LE 236


>gi|293390209|ref|ZP_06634543.1| ribosomal large subunit pseudouridine synthase B [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290950743|gb|EFE00862.1| ribosomal large subunit pseudouridine synthase B [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 322

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 91/284 (32%), Positives = 139/284 (48%), Gaps = 10/284 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKA 70
             +++ KV+ARAG  SRRE+E +IA+ RV V+G +      +NV +   + +DG  +   
Sbjct: 39  EGEKLQKVLARAGQGSRREIEAIIAENRVSVDGKIATLGDRINVYAGVKVRIDGHLINLT 98

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +        L  Y     L T H      +          +R I+VGRLDINT GLLL T
Sbjct: 99  QAQKEVCRVLMYYKPEGELCTRHDPEGRATVFDRLPRLTGARWIAVGRLDINTSGLLLFT 158

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  GQVD   LN LKKG+ ++       ++ +    G 
Sbjct: 159 TDGELANRLMHPSREVEREYSVRVFGQVDDAMLNRLKKGVQLEDGSANFKEIKVVGGVGM 218

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           N W  V L EG+NRE+++++E    +V+RLIRI YG  +L  TL  G  +E+    L + 
Sbjct: 219 NQWFDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKTLPRGGWQEM---ELADV 275

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
                L       +  + +++T  + +   I +    ++ + K 
Sbjct: 276 NYLRELVGLPPEAETKLGANKTRHKPKFGRIRKAVKRYSELNKR 319


>gi|67920373|ref|ZP_00513893.1| Pseudouridine synthase, Rsu [Crocosphaera watsonii WH 8501]
 gi|67857857|gb|EAM53096.1| Pseudouridine synthase, Rsu [Crocosphaera watsonii WH 8501]
          Length = 257

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 76/240 (31%), Positives = 125/240 (52%), Gaps = 12/240 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +RV K++++ G+ASRR  E MI  +RVK+NG ++         + D +EVDG  ++  +R
Sbjct: 3   ERVQKILSQWGVASRRRAEDMILARRVKLNGKIVT-LGDKADPSCDRLEVDGKLIQPNKR 61

Query: 73  TRLWLY--HKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTND 127
            +L     +KP+G+V+T  DP  RS V D LP   ++   +  VGRLD N+ G LLLTND
Sbjct: 62  PKLIYILLNKPVGVVSTCDDPQNRSIVLDLLPKKLTQGTGIHPVGRLDFNSSGALLLTND 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  P     + Y V   G   ++ L   ++G+++ G      +V +  +     
Sbjct: 122 GDLTLKLTHPRYHLPKTYEVLVKGHPPEETLQQWREGVILMGKKTLPAEVEVIRRSAQQT 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-----GTLLAGSTREVSKKILR 242
            + V L EG+NR+I+++ E   ++V RL R +     L      +L +G  R ++   + 
Sbjct: 182 QLKVVLTEGRNRQIRRIVEQLGFRVLRLHRTAIDSLCLSPNHKNSLSSGHYRLLTPSEID 241


>gi|239978707|ref|ZP_04701231.1| pseudouridine synthase [Streptomyces albus J1074]
 gi|291450599|ref|ZP_06589989.1| pseudouridine synthase [Streptomyces albus J1074]
 gi|291353548|gb|EFE80450.1| pseudouridine synthase [Streptomyces albus J1074]
          Length = 351

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 69/232 (29%), Positives = 110/232 (47%), Gaps = 2/232 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK 69
              +R+ KV+ARAG  SRR  E +I   RV+VNG ++    + V    D I+VDG+ +  
Sbjct: 112 NEGERLQKVLARAGYGSRRACEELIEDARVEVNGEIVLEQGLRVDPENDEIKVDGLTVAT 171

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                  L      + T       +  + D + +  +R+  VGRLD  TEG++LLTN G 
Sbjct: 172 QSYQFFSLNKPAGVVSTMEDPDGRQ-CLGDYVTNRETRLFHVGRLDTETEGVILLTNHGE 230

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  P     + Y     G + +D    LK GI ++          +  Q G N  V
Sbjct: 231 LAHRLTHPRYGVKKTYLAHIVGPIPRDLGKRLKDGIQLEDGYARADHFRVVEQTGKNYLV 290

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V L EG+   ++++     + V++L+R+++GP  LG   +G  R +S   +
Sbjct: 291 EVTLHEGRKHIVRRMLAEAGFPVDKLVRVAFGPITLGDQKSGWLRRLSNTEV 342


>gi|55820632|ref|YP_139074.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           thermophilus LMG 18311]
 gi|55736617|gb|AAV60259.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           thermophilus LMG 18311]
          Length = 239

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 62/239 (25%), Positives = 109/239 (45%), Gaps = 6/239 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++ ++G  SR +V+++I  ++V V+G+L +R  +NV ++   I V G  L  A  
Sbjct: 1   MRLDKLLGQSGYGSRNQVKKLIRSRQVYVDGVLADRDNLNVDASLQTIMVSGKELEHAPE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +                       +  VGRLD +TEGL+L+TN+G L  
Sbjct: 61  VYYLMNKPSGVVSARKDKEHQTVIDLIRPEDRREGLYPVGRLDRDTEGLVLITNNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V  +  +  D     + G+V +        Q+ + +     +   +
Sbjct: 121 AMLHPRYHVAKTYYVEVNDILGPDAPAFFESGVVFEDGTVCQSAQLEILSSASDKSCARI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LREQLG 246
            + EGK  ++KK+F  +  KV  L RIS+G F+L   +  GS R +++     LR  LG
Sbjct: 181 TISEGKFHQVKKMFLAYGVKVTYLKRISFGEFKLDEGMAVGSYRTLTEAEKTILRTYLG 239


>gi|68535954|ref|YP_250659.1| putative pseudouridylate synthase [Corynebacterium jeikeium K411]
 gi|260578661|ref|ZP_05846569.1| RNA pseudouridylate synthase [Corynebacterium jeikeium ATCC 43734]
 gi|68263553|emb|CAI37041.1| putative pseudouridylate synthase [Corynebacterium jeikeium K411]
 gi|258603158|gb|EEW16427.1| RNA pseudouridylate synthase [Corynebacterium jeikeium ATCC 43734]
          Length = 290

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 73/246 (29%), Positives = 119/246 (48%), Gaps = 4/246 (1%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVD 63
           N  +      R+ KV+A AG+ASRR  E++IA  RV+VNG ++ +    +  + D + VD
Sbjct: 41  NKPESEKAQVRLQKVLASAGVASRRMSEKLIAAGRVEVNGEVVVKMGTRIDPSVDIVRVD 100

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEG 120
           G  ++  E    ++ +KP G+ +T SD  GR  V D + +       +  VGRLD  TEG
Sbjct: 101 GERVQVNEEMVYFVLNKPRGVHSTMSDDLGRPCVGDLVGTRLKEGQGLFHVGRLDAQTEG 160

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLLLTNDG LA  L  P  +  + Y     G+  +  +  LK G+ +         V + 
Sbjct: 161 LLLLTNDGELANRLMHPKYEVKKTYMATVLGEASRKLIRELKDGVELDDGIARADSVQIV 220

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 + + V L EG+   ++++ +   + V  L+R      QLG    G+ R +++  
Sbjct: 221 DVWQGKSLIKVELHEGRKHIVRRMLKEAGFPVQALVRTKIHTVQLGEQKPGTIRALNQAE 280

Query: 241 LREQLG 246
           L+    
Sbjct: 281 LQSMYK 286


>gi|296314139|ref|ZP_06864080.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           polysaccharea ATCC 43768]
 gi|296839244|gb|EFH23182.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           polysaccharea ATCC 43768]
          Length = 252

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 70/255 (27%), Positives = 108/255 (42%), Gaps = 20/255 (7%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K          R+SK +A+ G+ SRRE +  I Q RV VNG         V   D I
Sbjct: 1   MNSKISSDHTEDTMRLSKRMAQLGLCSRREADGYIEQGRVTVNGKTA-VLGQKVSPADRI 59

Query: 61  EVD---------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           E++                 P+          Y     L+T  +  +G +      P   
Sbjct: 60  ELNKKAHEQQAARITILLNKPVGYVSAQAEKGYKSAAELITPENRWEGDTGRIRFDPKHK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             +   GRLDI++ GLL+LT DG +AR L   ++   + Y VR  G++D+  L LL  G+
Sbjct: 120 IGLAPAGRLDIDSVGLLVLTQDGRIARQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGL 179

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G      +V    +      +   L++GK R+I+++ E    +V  L RI  G  +L
Sbjct: 180 SLDGEKLRPAKVEWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRVIGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>gi|148241876|ref|YP_001227033.1| 16S rRNA pseudouridylate synthase [Synechococcus sp. RCC307]
 gi|147850186|emb|CAK27680.1| 16S rRNA pseudouridylate synthase [Synechococcus sp. RCC307]
          Length = 254

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 77/235 (32%), Positives = 114/235 (48%), Gaps = 5/235 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
           +   QR+ KV+++AG+ SRR  E ++ Q RV +NG              D I VDG  + 
Sbjct: 2   SSERQRLQKVLSQAGVCSRRRAEELMRQGRVLLNGRPA-SPGDQGDPLRDRILVDGELVS 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLT 125
                   L HKP G+ +T  DP GR TV D LP+       +  VGRLD ++ G LLL+
Sbjct: 61  PPAEELTVLLHKPRGVHSTCFDPRGRRTVLDLLPAELAEGQGLHPVGRLDCDSRGALLLS 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           N+G L   L  P     + YR+   G      L   + G+++ G       V    Q   
Sbjct: 121 NNGALTLALTHPRFSHRKSYRIWVSGHPSSAVLQQWRHGVLLDGRPTRSADVRELQQDAE 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++ + + +REG+NR+I++V E     V  L+R+S GP QLG L +G  R +    
Sbjct: 181 HSQLELVMREGRNRQIRRVAEQLGHPVRDLLRVSIGPVQLGDLPSGQWRRLHPDE 235


>gi|296158769|ref|ZP_06841598.1| pseudouridine synthase [Burkholderia sp. Ch1-1]
 gi|295890974|gb|EFG70763.1| pseudouridine synthase [Burkholderia sp. Ch1-1]
          Length = 626

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 82/354 (23%), Positives = 137/354 (38%), Gaps = 9/354 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRR++E +I   RV VNG         +M TD + ++
Sbjct: 202 KRVLAADDDAPKLHKVLAEAGMGSRRDMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRIN 260

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 261 GKPVKRKLANKPPRVLLYHKPTGEIVSHADPEGRPSVFDKLPPMKTAKWLAVGRLDFNTE 320

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 321 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELAEGMRQKLLHGVELDDGPANFLRIRD 380

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+  
Sbjct: 381 GGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPISLPKGLKRGRWEELED 440

Query: 239 KILR---EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
             +R     +G     E + + +A     +                     +   Q    
Sbjct: 441 NQVRALMASVGLKAPTEERGSRNAAPERKQPDPMQTSMGFINREPVLMSHGRFDQQPPRG 500

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
             ++  A        A   +     +      +G               R  R 
Sbjct: 501 QGRRGGAAGGGFAGGAGAGFGGGYGNRGAGRSAGGFSGPMGGGGGAGGPRGGRE 554


>gi|307730031|ref|YP_003907255.1| pseudouridine synthase [Burkholderia sp. CCGE1003]
 gi|307584566|gb|ADN57964.1| pseudouridine synthase [Burkholderia sp. CCGE1003]
          Length = 614

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 82/356 (23%), Positives = 139/356 (39%), Gaps = 16/356 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRR++E +I   RV VNG         +M TD + ++
Sbjct: 205 KRVLSADDDAPKLHKVLAEAGMGSRRDMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRIN 263

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 264 GKPVKRKLANKPPRVLLYHKPTGEIVSHADPEGRPSVFDKLPPMKTAKWLAVGRLDFNTE 323

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 324 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELAEGMRQKLLNGVELDDGPANFLRIRD 383

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+  
Sbjct: 384 GGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPISLPKGLKRGRWEELED 443

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRD----------RPNIISEVPDDFTRMKKN 288
             +R  +    L+           + E    D          R  ++        + +  
Sbjct: 444 NQVRALMASVGLKAPNEERGGRGAAPERKQPDPMQTSMGFISREPVLMSHHRFEQQPRGQ 503

Query: 289 SSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
             +          A         +                G R+ +  R+P+    
Sbjct: 504 GRRGAAGGGVGGGAGAGFGGGYGNRGTGRGAGGFGVGGPRGARDVDGNRAPTGSGN 559


>gi|254672143|emb|CBA04924.1| conserved hypothetical protein [Neisseria meningitidis alpha275]
          Length = 349

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 73/256 (28%), Positives = 125/256 (48%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+
Sbjct: 84  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHV 142

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L +  ++++       
Sbjct: 203 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVE 262

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  V ++EG+NRE++++FE     V+RL+RI +GP  L   L  G   
Sbjct: 263 RIREQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRIGFGPIGLPNRLKRGQFY 322

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   +    +
Sbjct: 323 ELNPAEVANIIKWADM 338


>gi|238763121|ref|ZP_04624087.1| Ribosomal large subunit pseudouridine synthase B [Yersinia
           kristensenii ATCC 33638]
 gi|238698620|gb|EEP91371.1| Ribosomal large subunit pseudouridine synthase B [Yersinia
           kristensenii ATCC 33638]
          Length = 324

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 87/322 (27%), Positives = 136/322 (42%), Gaps = 12/322 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGV 65
           +     +++ K++ARAG  SRRE+E +I Q RV V+G +  +    V  T    I +DG 
Sbjct: 4   KTKVVGEKLQKILARAGHGSRREIETIIQQGRVSVDGKI-SKLGDRVEVTQATKIRLDGH 62

Query: 66  PLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            L   E        L  Y     L T +      +          SR ++VGRLD+NT G
Sbjct: 63  LLSIKESEEAVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSG 122

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLL T DG LA  L  PS +  R Y VR  GQ+D +K+  L +G+ ++        ++  
Sbjct: 123 LLLFTTDGELANRLMHPSREVEREYAVRVFGQIDDEKIKQLSRGVQLEDGPAAFRTISFQ 182

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
             +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  K
Sbjct: 183 GGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELDLK 242

Query: 240 ---ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
               LRE +       +++ ++      +     R               +  S +   +
Sbjct: 243 ATNYLRELVELDSETVSKLPVEKDRRRVKANQIRRAVKRHTEVAGRQVAGRQGSARKSST 302

Query: 297 KQKKLATPVHRRNLASNVWMAK 318
           +Q                    
Sbjct: 303 RQHAGNAAPAAATGRRGSNKRG 324


>gi|87303407|ref|ZP_01086195.1| Pseudouridine synthase, Rsu [Synechococcus sp. WH 5701]
 gi|87282055|gb|EAQ74017.1| Pseudouridine synthase, Rsu [Synechococcus sp. WH 5701]
          Length = 241

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 79/240 (32%), Positives = 122/240 (50%), Gaps = 3/240 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T QR+ K++A AG+ SRR  E +I Q RV +NG +        +S+D +E+DG P+  A 
Sbjct: 2   TAQRLQKLLASAGLCSRRRAEELILQGRVTLNGAVARLGDQADLSSDRLELDGTPVAAAA 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLLTNDG 128
            T   L +KP G++ +  DP+GR+TV D LP   S       VGRLD  + G LLL+NDG
Sbjct: 62  PTITVLLNKPRGVICSCHDPEGRTTVLDLLPPELSEATGLHPVGRLDGASRGALLLSNDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P     + YRV   G+   + L   ++G+ + G     + V    +      
Sbjct: 122 ALTLRLTHPRFGHRKHYRVWVTGEPAAEALEQWRRGVPLDGQPSQPVGVRELARGQRGTL 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + + + EG+NR+I++  E     V  L R++ GP +LG L  G  R ++ +  R+     
Sbjct: 182 LELEMVEGRNRQIRRTAELLGHPVRDLQRVAIGPLRLGELPEGRWRHLAPQEWRDLDARR 241


>gi|291287278|ref|YP_003504094.1| pseudouridine synthase [Denitrovibrio acetiphilus DSM 12809]
 gi|290884438|gb|ADD68138.1| pseudouridine synthase [Denitrovibrio acetiphilus DSM 12809]
          Length = 229

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 73/231 (31%), Positives = 120/231 (51%), Gaps = 4/231 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A     SRR+ ++ I + RV+VNG L E   V +   D + +DG  +  AE   
Sbjct: 3   RINKYLAARSQLSRRDADKAIEEGRVRVNGKLPEGPWVQLSEKDKVTLDGNDISGAEDYF 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            W ++KP  ++T + D  G+ T+         +    GRLD ++EGL++ +NDG   R L
Sbjct: 63  YWAFYKPKSVLTAYGDGHGKDTLEIYPFLREKKPAYSGRLDYDSEGLIIFSNDGDFIRRL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           +    +  + Y V  +  + + +++ L+KGIV +GI Y +       ++ S+    V L 
Sbjct: 123 QRAEEKVEKEYIVTVNRVLKKGEMDDLRKGIVYEGIRYREC----IVEQHSHDRYQVVLH 178

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           EGK R+I+ +F  F  +V +L R+  G   L  L  G  RE S K +RE L
Sbjct: 179 EGKKRQIRHMFRNFGIRVKKLKRVRIGSVNLNELQPGEFREFSPKEMREML 229


>gi|254670545|emb|CBA06380.1| conserved hypothetical protein [Neisseria meningitidis alpha153]
          Length = 349

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 72/256 (28%), Positives = 125/256 (48%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+
Sbjct: 84  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHV 142

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L +  ++++       
Sbjct: 203 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVE 262

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   
Sbjct: 263 RIREQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFY 322

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   +    +
Sbjct: 323 ELNPAEVANIIKWADM 338


>gi|90410509|ref|ZP_01218525.1| hypothetical 16S rRNA uridine-516 pseudouridylate synthase
           [Photobacterium profundum 3TCK]
 gi|90328750|gb|EAS45034.1| hypothetical 16S rRNA uridine-516 pseudouridylate synthase
           [Photobacterium profundum 3TCK]
          Length = 232

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 49/236 (20%), Positives = 99/236 (41%), Gaps = 8/236 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R+E  R+++ + ++VNG +++ A++ +     +E +G  L      
Sbjct: 1   MRLDKFLATTLGITRKEAGRLLSNKMIEVNGNVVKSASLKITDDCDVEFNGKKLALQGPQ 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      + +   D    +           ++   GRLD +T GL LLT+DG  +  
Sbjct: 61  YFMLNKPEGFVCSH-VDDHNPTVFVLFDEVSPEKMHVAGRLDGDTTGLTLLTDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     +VY V     V ++ +    +G+ ++G        ++ +     S     +
Sbjct: 120 VTSPRHVCEKVYHVELADPVPEETIQTFLEGVQLRGEKDITRPAKLEIL----SEREAIL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
            + EGK  ++K++F     +V  L R   G   L   L  G  R ++++ +   L 
Sbjct: 176 TITEGKYHQVKRMFAAVGNRVVGLHREQVGAVVLDENLEPGEYRRLTEEEIASFLK 231


>gi|55822523|ref|YP_140964.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           thermophilus CNRZ1066]
 gi|55738508|gb|AAV62149.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           thermophilus CNRZ1066]
          Length = 239

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 63/239 (26%), Positives = 109/239 (45%), Gaps = 6/239 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++ ++G  SR +V+++I  ++V V+G+L +R  +NV ++   I V G  L  A  
Sbjct: 1   MRLDKLLGQSGYGSRNQVKKLIRSRQVYVDGVLADRDNLNVDASLQTIMVSGKELEHAPE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +                       +  VGRLD +TEGL+L+TN+G L  
Sbjct: 61  VYYLMNKPSGVVSARKDKEHQTVIDLIRPEDRREGLYPVGRLDRDTEGLVLITNNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V  +  +  D     + G+V +        Q+ + +     +   V
Sbjct: 121 AMLHPRYHVAKTYYVEVNDILGPDAPAFFESGVVFEDGTVCKSAQLEVLSSASDKSCARV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LREQLG 246
            + EGK  ++KK+F  +  KV  L RIS+G F+L   +  GS R +++     LR  LG
Sbjct: 181 TISEGKFHQVKKMFLAYGVKVTYLKRISFGEFKLDEGMAVGSYRTLTEAEKTILRTYLG 239


>gi|225028080|ref|ZP_03717272.1| hypothetical protein EUBHAL_02350 [Eubacterium hallii DSM 3353]
 gi|224954550|gb|EEG35759.1| hypothetical protein EUBHAL_02350 [Eubacterium hallii DSM 3353]
          Length = 242

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 67/237 (28%), Positives = 110/237 (46%), Gaps = 7/237 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + E     R+ K + +A   +R E ++ I +  V V+G ++++A + V S D I +DG  
Sbjct: 1   MPETLKKMRLDKFLTQAAELTRSEAKQKIKKGSVTVDGEVVKKAEMKVSSEDAICLDGEV 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +   +   + L+     +  T        TV D +      +  VGRLD +TEGLLLLTN
Sbjct: 61  VTYEKYRYIMLHKPAGVVSATEDAQCQ--TVLDLITEGRKGLFPVGRLDKDTEGLLLLTN 118

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGS 185
           DG LA  L  P     + Y     G+V + +  L  +G+ I         +  L+    +
Sbjct: 119 DGALAHNLLSPRKHVDKTYFAILDGEVGEKEQELFLQGLDIGDEKKTLPAK--LEITDKA 176

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           N    + ++EG+  ++K++ E    KV  L RIS GP  L   L  G  R + ++ L
Sbjct: 177 NEVF-ITVQEGRFHQVKRMAEAVGRKVEYLKRISMGPLVLDKELKKGEYRPLFEEEL 232


>gi|254393249|ref|ZP_05008402.1| pseudouridine synthase [Streptomyces clavuligerus ATCC 27064]
 gi|294811815|ref|ZP_06770458.1| Pseudouridine synthase [Streptomyces clavuligerus ATCC 27064]
 gi|326440444|ref|ZP_08215178.1| pseudouridine synthase [Streptomyces clavuligerus ATCC 27064]
 gi|197706889|gb|EDY52701.1| pseudouridine synthase [Streptomyces clavuligerus ATCC 27064]
 gi|294324414|gb|EFG06057.1| Pseudouridine synthase [Streptomyces clavuligerus ATCC 27064]
          Length = 376

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 109/233 (46%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
               +R+ KV+ARAG+ SRR  E +I   RV+VNG ++    V V    D I+VDG+ + 
Sbjct: 136 EQEGERLQKVLARAGVGSRRACEELIEAGRVEVNGSIVIEQGVRVDPENDEIKVDGLTVA 195

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   L      + T       +  + D + +  +R+  VGRLD  TEG++LLTN G
Sbjct: 196 TQSYLFFALNKPAGVVSTMEDPDGRQ-CLGDYVTNRETRLFHVGRLDTETEGIILLTNHG 254

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     + Y     G + ++    LK GI ++          +    G N  
Sbjct: 255 ELAHRLTHPRYGVKKTYLAAIQGPLPRELGKRLKDGIALEDGYARADHFRVVENTGKNYL 314

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L EG+   ++++     + V+RL+R ++GP  LG   +G  R +S   +
Sbjct: 315 VEVTLHEGRKHIVRRMLAEAGFPVDRLVRTAFGPIGLGDQKSGWLRRLSNTEV 367


>gi|325068740|ref|ZP_08127413.1| pseudouridine synthase family protein [Actinomyces oris K20]
          Length = 303

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 82/227 (36%), Positives = 116/227 (51%), Gaps = 10/227 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
           + QR+ KV+A AG+ASRR  E++IA  RV V+G+ +  A V V   T  I VDG  +   
Sbjct: 76  SGQRLQKVLAHAGVASRRACEQLIADGRVSVDGVTVTEAGVRVDPLTQEIRVDGSRILTN 135

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---------ISVGRLDINTEGL 121
                 + HKP G+VTT  DP+GR TV        +           + VGRLD  TEGL
Sbjct: 136 PELITLMLHKPAGVVTTMEDPEGRPTVAQYGRDYLAEHPELPDSLRLVHVGRLDTETEGL 195

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLL+NDG L+  L  PS +  + Y     GQV+      L++GI ++       +VT+  
Sbjct: 196 LLLSNDGELSHRLMHPSFEIAKTYVAIVEGQVEAWVPRKLRRGIELEDGEAKADRVTVKD 255

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                + V + L  GKNR ++++ +     V RL R   GP +LG L
Sbjct: 256 SGPRGSIVEITLHSGKNRIVRRMLDAVGHPVTRLARTRLGPLRLGNL 302


>gi|195977793|ref|YP_002123037.1| ribosomal small subunit pseudouridine synthase A RsuA
           [Streptococcus equi subsp. zooepidemicus MGCS10565]
 gi|225868904|ref|YP_002744852.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           equi subsp. zooepidemicus]
 gi|225870089|ref|YP_002746036.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           equi subsp. equi 4047]
 gi|195974498|gb|ACG62024.1| ribosomal small subunit pseudouridine synthase A RsuA
           [Streptococcus equi subsp. zooepidemicus MGCS10565]
 gi|225699493|emb|CAW93033.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus equi subsp. equi 4047]
 gi|225702180|emb|CAW99890.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus equi subsp. zooepidemicus]
          Length = 238

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 54/229 (23%), Positives = 97/229 (42%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++   G  SR +V+++I  + V ++G        +V S    I V+G  ++    
Sbjct: 1   MRLDKLLEVTGFGSRNQVKQLIKGRSVLIDGQPARAGCQSVDSGLQVIMVNGRQIKAFAH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +                     + +  +GRLD +T GL+LLT++G L  
Sbjct: 61  RYYLLHKPAGVVSACSDRKHQTVIDLIRKEDRVANLYPIGRLDRDTTGLVLLTDNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V  +G +  D +   + G+  + G       + +       +   V
Sbjct: 121 RMLHPKHHVNKTYLVTVNGSLAADAVPFFENGVTFLDGTRCKSAALRIIKADQMESQAEV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            L EGK  +IKK+F  +  KV +L RI +    LG L  G+ R+++ K 
Sbjct: 181 TLSEGKYHQIKKMFLSYGLKVTQLKRIGFAEIALGDLAEGAYRQLTVKE 229


>gi|229844846|ref|ZP_04464984.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae 6P18H1]
 gi|229812227|gb|EEP47918.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae 6P18H1]
          Length = 357

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 90/288 (31%), Positives = 132/288 (45%), Gaps = 10/288 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 67  LRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +  +         L  Y     L T        +          SR I+VGRLDINT GL
Sbjct: 130 INLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWIAVGRLDINTSGL 189

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++    
Sbjct: 190 LLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGSANFKEIKFTG 249

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 250 GVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEMDLEN 309

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
              LRE +G     E ++++       ++    +        +   + 
Sbjct: 310 VNYLRELVGLPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>gi|304387322|ref|ZP_07369514.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis ATCC 13091]
 gi|304338573|gb|EFM04691.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis ATCC 13091]
          Length = 350

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 72/256 (28%), Positives = 124/256 (48%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+
Sbjct: 85  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHV 143

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR  ++GRLDI
Sbjct: 144 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWGAIGRLDI 203

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L +  ++++       
Sbjct: 204 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVE 263

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   
Sbjct: 264 RIREQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFY 323

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   +    +
Sbjct: 324 ELNPAEVANIIKWADM 339


>gi|302338564|ref|YP_003803770.1| RNA-binding S4 domain protein [Spirochaeta smaragdinae DSM 11293]
 gi|301635749|gb|ADK81176.1| RNA-binding S4 domain protein [Spirochaeta smaragdinae DSM 11293]
          Length = 251

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 74/243 (30%), Positives = 120/243 (49%), Gaps = 6/243 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DH 59
           M   +  +      R+   +AR+G+ SRR  E++I++  V+VNG +     + V+   D 
Sbjct: 1   MDKDDKKKRPDEAVRLQLYLARSGVGSRRACEKLISEGCVRVNGQVANSQGIKVVPGRDS 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINT 118
           +   G P+    +      +KP+  + TH D +GR    D +   F     +VGRLD  +
Sbjct: 61  VTYRGKPVFPTGKHYYIALNKPVRYLCTHYDLEGRPLAEDLIKGKFPVRLFNVGRLDFLS 120

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GL+  TNDG  A+++  PS +  + Y V    ++  + L   +KG+V++G  Y      
Sbjct: 121 SGLIFFTNDGEFAKIITHPSHEIEKEYVVETAKRLSSELLEEFRKGVVVEGELYRIHAYN 180

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +     S   V + LREGKNREI+K+F   N KV RL R+  GP Q+  +  G  R +  
Sbjct: 181 II----SPVKVKIVLREGKNREIRKLFTSKNIKVKRLHRVRIGPVQIAGMHPGEFRNLKP 236

Query: 239 KIL 241
           K +
Sbjct: 237 KEI 239


>gi|284053272|ref|ZP_06383482.1| pseudouridine synthase [Arthrospira platensis str. Paraca]
 gi|291565993|dbj|BAI88265.1| putative pseudouridylate synthase [Arthrospira platensis NIES-39]
          Length = 257

 Score =  158 bits (398), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 70/240 (29%), Positives = 107/240 (44%), Gaps = 13/240 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK--- 69
           +R+ K+I+  G+ASRR  E MI   RVKVNG              D IE+DG  L     
Sbjct: 3   ERLQKIISHWGVASRRHAEEMILSGRVKVNGDQAY-LGQKADPKCDRIEIDGRALHPSSQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTND 127
            +   L L      + T       ++ +      +        VGRLD ++ G LL+TND
Sbjct: 62  PQPLYLLLNKPLGVVSTCAEPQGRKTVLDLLPRQLQVGQGLHPVGRLDTDSTGALLITND 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-KGSN 186
           G L  +L  P     + Y+V   G   +  L   ++GI++ G      +V    + +GS 
Sbjct: 122 GELTFLLTHPRYHVAKTYQVLVQGCPPESVLEQWRQGILLSGKNTLPAKVRRIGKPRGSQ 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-----TLLAGSTREVSKKIL 241
             + V LREG+NR+I++V E   + V +L R + GP  L       L +G  R +    +
Sbjct: 182 TLLEVVLREGRNRQIRRVAEALGYPVVQLHRTAIGPIYLNSTGKPELASGEYRSLKNSEV 241


>gi|212212525|ref|YP_002303461.1| ribosomal large subunit pseudouridine synthase B [Coxiella burnetii
           CbuG_Q212]
 gi|212010935|gb|ACJ18316.1| ribosomal large subunit pseudouridine synthase B [Coxiella burnetii
           CbuG_Q212]
          Length = 244

 Score =  158 bits (398), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 75/233 (32%), Positives = 115/233 (49%), Gaps = 5/233 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---KA 70
           +R+ KV+AR+G  SRRE+E+MIA+ R+KVN  L +     +   D + +DG         
Sbjct: 3   ERIQKVLARSGYGSRREIEKMIAEGRIKVNQRLAQ-LGDRITEQDLVYIDGQLSSLSVPE 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L  +     + T        +           R + +GRLDINT GLLL TN+G L
Sbjct: 62  QVRVLLYHKPEGEICTRKDPEWRTTVFETLPRLKDGRWVIIGRLDINTSGLLLFTNEGEL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS Q  R Y VR  G VD D    L  G+ ++        +      G N W  
Sbjct: 122 ANRLMHPSAQVEREYAVRVLGAVDADMTQKLAHGVGLEDGKARFEDIVDVGGDGKNRWFH 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           V + EG++R +++++E    KV+RLIR+ +GP  L  +L  G+ +E+    ++
Sbjct: 182 VVVVEGRHRLVRRLWESQGVKVSRLIRVRFGPIVLPKSLRRGAWKELEAPEIK 234


>gi|25028115|ref|NP_738169.1| hypothetical protein CE1559 [Corynebacterium efficiens YS-314]
 gi|259507172|ref|ZP_05750072.1| RNA pseudouridine synthase [Corynebacterium efficiens YS-314]
 gi|23493399|dbj|BAC18369.1| conserved hypothetical protein [Corynebacterium efficiens YS-314]
 gi|259165253|gb|EEW49807.1| RNA pseudouridine synthase [Corynebacterium efficiens YS-314]
          Length = 329

 Score =  158 bits (398), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 76/234 (32%), Positives = 116/234 (49%), Gaps = 4/234 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
              R+ KV+A+AG+ASRR  E +I   RV+VNG ++      V    D I VDGV +   
Sbjct: 87  EGIRLQKVLAQAGVASRRHAEILIDNGRVEVNGRIVTTQGTRVNPNSDVIRVDGVRININ 146

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTND 127
           E    ++ +KP G+ +T SD  GR  V D +        R+  VGRLD +TEGLLLLTND
Sbjct: 147 EDLEYFVLNKPRGMHSTMSDDLGRPCVGDLVSEKTASGQRLFHVGRLDADTEGLLLLTND 206

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P  +  + Y     G+   + +  L+KGI ++        V +       +
Sbjct: 207 GELANRLMHPKYEVRKTYLATVRGEAGPNLVTTLRKGIELEDGPAKADYVQIIDTFQGKS 266

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + + + EG+   ++++ +   + V RL+R      QLG    GS R ++   L
Sbjct: 267 LIRLEIHEGRKHIVRRMLDEAGFPVERLVRTKLHTVQLGEQKPGSLRALNASEL 320


>gi|326791171|ref|YP_004308992.1| pseudouridine synthase Rsu [Clostridium lentocellum DSM 5427]
 gi|326541935|gb|ADZ83794.1| pseudouridine synthase Rsu [Clostridium lentocellum DSM 5427]
          Length = 242

 Score =  158 bits (398), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 109/234 (46%), Gaps = 4/234 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
              R+ K +   G  +R  V+++I  ++VKV+G ++ +    V S T  +EV+G  +   
Sbjct: 4   KKIRLDKYLVHVGYGTRSTVQKIIRGKKVKVDGQVIIKPETAVNSLTSVVEVNGERMDYQ 63

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E     L      +  T    D               V  VGRLD +TEGLL+LTNDG +
Sbjct: 64  EFYHFILNKPRGYITATEDGRDQTVLDLLEERDQNKEVFPVGRLDKDTEGLLILTNDGKM 123

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     +VY  R  G++ ++ + +  +GI +  G  Y   ++ +  +    + +
Sbjct: 124 AHGLLSPKRHVDKVYYARVAGKMTEEDIKMFAEGIALTDGTKYAPGKLEII-RSDEESEI 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
            V + EGK  ++K++ +    +V  L RI  G  +L   L  G+ R ++K+ L 
Sbjct: 183 YVTIHEGKFHQVKRMVQAVGKEVVYLKRIKMGGLELPEDLSLGTYRTLTKEELD 236


>gi|71908073|ref|YP_285660.1| ribosomal large subunit pseudouridine synthase B [Dechloromonas
           aromatica RCB]
 gi|71847694|gb|AAZ47190.1| ribosomal large subunit pseudouridine synthase B [Dechloromonas
           aromatica RCB]
          Length = 340

 Score =  158 bits (398), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 77/240 (32%), Positives = 116/240 (48%), Gaps = 8/240 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
              P R+ KV+A AG+ SRRE+E  IA  +V VNG++       V  +D +++ G  +  
Sbjct: 82  EAKPVRLQKVLAEAGVGSRREMEEWIAAGKVSVNGVVATVGQSVVN-SDKVKIGGRLINI 140

Query: 70  A------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                      L  +     +V+        S           R I+VGRLD NT GLLL
Sbjct: 141 RFTGSSRPPRVLMYHKPEGEIVSRDDPDGRPSVFAALPRMRGGRWINVGRLDFNTSGLLL 200

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T  G LA  L  PS++ +R Y VR  G++  D    L  G+ ++        +     +
Sbjct: 201 FTTSGELANKLMHPSSELVREYAVRVLGELTLDAQQKLLHGVELEDGRANFGSLHDGGGE 260

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           G+N W  V + EG+NRE++++FE     V+RLIR+ YGPF L   L  G  RE+ +  ++
Sbjct: 261 GANHWYRVTISEGRNREVRRMFEAVGCTVSRLIRVRYGPFILPPQLKRGMARELKEAEIK 320


>gi|194098813|ref|YP_002001876.1| Pseudouridine synthase [Neisseria gonorrhoeae NCCP11945]
 gi|254493881|ref|ZP_05107052.1| pseudouridine synthase [Neisseria gonorrhoeae 1291]
 gi|268594941|ref|ZP_06129108.1| pseudouridine synthase [Neisseria gonorrhoeae 35/02]
 gi|193934103|gb|ACF29927.1| Pseudouridine synthase [Neisseria gonorrhoeae NCCP11945]
 gi|226512921|gb|EEH62266.1| pseudouridine synthase [Neisseria gonorrhoeae 1291]
 gi|268548330|gb|EEZ43748.1| pseudouridine synthase [Neisseria gonorrhoeae 35/02]
 gi|317164395|gb|ADV07936.1| Pseudouridine synthase [Neisseria gonorrhoeae TCDC-NG08107]
          Length = 416

 Score =  158 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 72/256 (28%), Positives = 125/256 (48%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+
Sbjct: 151 LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHV 209

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 210 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 269

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++  L +  ++++       
Sbjct: 270 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTTEQMRSLTEEGVMLEDGLAKVE 329

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  + ++EG+NRE++++FE     V+RL+R+++GP  L   L  G   
Sbjct: 330 RIYEQGGEGANKWYNIVIKEGRNREVRRIFESQGLTVSRLVRVAFGPIGLPNRLKRGQFY 389

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   L    +
Sbjct: 390 ELNPAEVANILKWADM 405


>gi|332704127|ref|ZP_08424215.1| pseudouridine synthase Rsu [Desulfovibrio africanus str. Walvis
           Bay]
 gi|332554276|gb|EGJ51320.1| pseudouridine synthase Rsu [Desulfovibrio africanus str. Walvis
           Bay]
          Length = 254

 Score =  158 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 66/240 (27%), Positives = 110/240 (45%), Gaps = 11/240 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPL----- 67
            R++K +A AG+ SRR+ + ++    V VNGI      + V    D + V G P+     
Sbjct: 1   MRLNKALAMAGVCSRRKADELVFAGNVAVNGITASSPGIQVDPQNDIVTVFGKPVAFLPQ 60

Query: 68  --RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLL 124
             +  E     L      + T       R+ +          RV  VGRLD  +EGLLLL
Sbjct: 61  EGQATEHAYYMLNKPVEVVTTASDPQGRRTVLEILPEEVRKRRVFPVGRLDFFSEGLLLL 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQK 183
           T+DG L   +  P     +VY V   G+V +DKL  +++G+ + +G     ++V +  ++
Sbjct: 121 TSDGDLTYRMTHPRYHLPKVYEVLVRGEVTRDKLEAMRRGMTLAEGEKLAPVEVKVLDKQ 180

Query: 184 -GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
                 + + L +G NR+I+++       V +L R   GP  LG L  G  R ++   ++
Sbjct: 181 MLGKTLLELTLIQGINRQIRRMCRDLGLTVLKLRRTCEGPLSLGALPTGKLRTLTPAEVK 240


>gi|325830888|ref|ZP_08164272.1| pseudouridine synthase B, ribosomal large subunit [Eggerthella sp.
           HGA1]
 gi|325487295|gb|EGC89738.1| pseudouridine synthase B, ribosomal large subunit [Eggerthella sp.
           HGA1]
          Length = 301

 Score =  158 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 69/273 (25%), Positives = 107/273 (39%), Gaps = 33/273 (12%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE 71
           P R+ K +ARAG ASRR  E ++   RV VNG ++      V    D + VDG  +R A+
Sbjct: 29  PMRLQKFLARAGAASRRGSENLMTAGRVTVNGKVVTELGSKVDPLVDEVAVDGAVVRLAD 88

Query: 72  RTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + L+     + T       R+         +  +  +GRLD +T GLLL + DG L
Sbjct: 89  GPVTIMLHKPAGFVTTMSDPQGRRTVAELVPTERYPGLFPIGRLDFDTTGLLLFSTDGEL 148

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA--- 187
              L  P     + Y     G+  +  L LL++GI +         V +     +     
Sbjct: 149 GNGLLHPKHHVTKRYLACVEGRPTERDLALLRRGIELDDGPTQPADVRMVEGGAARHAER 208

Query: 188 ----------------------------WVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
                                        V +G+REG+ R++K++       V  L R S
Sbjct: 209 LLEIPAAVPPRSSKEYAAVCEGRATRRSIVRLGIREGRKRQVKRMLAAVGHPVLALHRDS 268

Query: 220 YGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           +GP +LG L  GS R +  + +          E
Sbjct: 269 FGPLELGDLPRGSWRALDAEEVAALHQAIGRAE 301


>gi|315151609|gb|EFT95625.1| conserved hypothetical protein [Enterococcus faecalis TX0012]
          Length = 320

 Score =  158 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 69/267 (25%), Positives = 118/267 (44%), Gaps = 3/267 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGV 65
           +QE     R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G 
Sbjct: 54  IQEWSGTMRLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESQNVDAQLQMIKVKGQ 113

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +         L      +                       +  VGRLD +TEGLLLLT
Sbjct: 114 LISHKTHVYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLT 173

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKG 184
           ++G L   L  P+ +  + Y V+ +G V  +     K GIV+QG       ++T+     
Sbjct: 174 DNGQLGYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATE 233

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           + + V + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+ 
Sbjct: 234 TESHVFLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQL 293

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRD 270
            L    +E+ Q +            R 
Sbjct: 294 LLPYFFIEKQQTSKALLSNLKREEERK 320


>gi|239932155|ref|ZP_04689108.1| pseudouridine synthase [Streptomyces ghanaensis ATCC 14672]
 gi|291440523|ref|ZP_06579913.1| pseudouridine synthase [Streptomyces ghanaensis ATCC 14672]
 gi|291343418|gb|EFE70374.1| pseudouridine synthase [Streptomyces ghanaensis ATCC 14672]
          Length = 347

 Score =  158 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 109/233 (46%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
               +R+ KV+ARAG  SRR  E +I Q RV+VNG ++      V    D ++VDG+ + 
Sbjct: 107 EQEGERLQKVLARAGYGSRRACEELIEQARVEVNGEIVLEQGRRVDPEKDEVKVDGLTVA 166

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   L      + T       +  + D + +  +R+  VGRLD  TEG++LLTN G
Sbjct: 167 TQSYQFFSLNKPAGVVSTMEDPEGRQ-CLGDYVTNRETRLFHVGRLDTETEGVILLTNHG 225

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     + Y     G + +D    LK GI ++          +  Q G N  
Sbjct: 226 ELAHRLTHPRYGVKKTYLAHIVGPIPRDLGKRLKDGIQLEDGYARADHFRVVEQTGKNYL 285

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L EG+   ++++     + V++L+R ++GP  LG   +G  R +S   +
Sbjct: 286 VEVTLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPITLGDQKSGWLRRLSNTEV 338


>gi|240013706|ref|ZP_04720619.1| RNA-binding protein [Neisseria gonorrhoeae DGI18]
 gi|240080288|ref|ZP_04724831.1| RNA-binding protein [Neisseria gonorrhoeae FA19]
 gi|240120776|ref|ZP_04733738.1| RNA-binding protein [Neisseria gonorrhoeae PID24-1]
 gi|240123081|ref|ZP_04736037.1| RNA-binding protein [Neisseria gonorrhoeae PID332]
 gi|268596437|ref|ZP_06130604.1| RNA-binding protein [Neisseria gonorrhoeae FA19]
 gi|268681708|ref|ZP_06148570.1| RNA-binding protein [Neisseria gonorrhoeae PID332]
 gi|268550225|gb|EEZ45244.1| RNA-binding protein [Neisseria gonorrhoeae FA19]
 gi|268621992|gb|EEZ54392.1| RNA-binding protein [Neisseria gonorrhoeae PID332]
          Length = 252

 Score =  158 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 67/255 (26%), Positives = 108/255 (42%), Gaps = 20/255 (7%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K          R+SK +A+ G+ SRRE +  I Q  V VNG         V   D I
Sbjct: 1   MNSKISSDHTEDTIRLSKRMAQLGLCSRREADGHIEQGWVTVNGKTA-VLGQKVSPADRI 59

Query: 61  EVD---------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           E++                 P+          Y     L+T  +  +G ++     P   
Sbjct: 60  ELNKKAHEQQAARITILLNKPVGYVSAQAEKGYKSAAELITPENCWEGDTSRISFDPKHK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             +   GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+
Sbjct: 120 IGLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGL 179

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G      +V    +      +   L++GK R+I+++ E    ++  L RI  G  +L
Sbjct: 180 SLDGDKLRPAKVEWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRIVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>gi|170728059|ref|YP_001762085.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169813406|gb|ACA87990.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 230

 Score =  158 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 45/232 (19%), Positives = 99/232 (42%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  +   +R   ++ + +  V  +G +++ +   V     I ++G PL      
Sbjct: 1   MRLDKYICESTSLTRSLAKKALHRGDVTCDGKVIKDSGFKVTDKQVICLEGEPLSVI-GP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP+  + +  D +  S +          +   GRLD++T GL+L+TNDG  +  
Sbjct: 60  RFIMLNKPLDTICSTIDEEYPSVLGLLDVVKADELHIAGRLDVDTTGLVLITNDGQWSHK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y +     + Q+ +     G+ +  +        + +      +    +
Sbjct: 120 ITSPKKECGKRYLLETAEPLKQEWVEEFAAGLQLNNEDGLTKPATLEIL----GSHQARL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            + EGK  ++K++       V +L R S G  +L   L +G  R +++  ++
Sbjct: 176 TITEGKYHQVKRMLAAVGNCVTQLHRESVGEIELDESLASGEWRYLTEAEIK 227


>gi|29349280|ref|NP_812783.1| ribosomal large subunit pseudouridine synthase B [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|253570374|ref|ZP_04847783.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           1_1_6]
 gi|298384818|ref|ZP_06994377.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           1_1_14]
 gi|29341188|gb|AAO78977.1| ribosomal large subunit pseudouridine synthase B [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|251840755|gb|EES68837.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           1_1_6]
 gi|298261962|gb|EFI04827.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           1_1_14]
          Length = 496

 Score =  158 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 60/241 (24%), Positives = 108/241 (44%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +  +D +
Sbjct: 248 IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVV 307

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P+    +  + L      + T+    + R+ +     +   R+  VGRLD NT G
Sbjct: 308 KFHDEPVSIERKVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTTG 367

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     + +  ++ +  G+ ++            
Sbjct: 368 VLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADMDQIAAGVQLEDGEIH-ADAISY 426

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           T       V + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+  
Sbjct: 427 TDDFKKDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSEAE 486

Query: 241 L 241
           +
Sbjct: 487 V 487


>gi|255535111|ref|YP_003095482.1| Ribosomal large subunit pseudouridine synthase B [Flavobacteriaceae
           bacterium 3519-10]
 gi|255341307|gb|ACU07420.1| Ribosomal large subunit pseudouridine synthase B [Flavobacteriaceae
           bacterium 3519-10]
          Length = 371

 Score =  158 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 111/230 (48%), Gaps = 1/230 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K IA +GI SRRE + +I Q  V+VNG ++      V  TD +  DG  +   +
Sbjct: 137 ETIRLNKYIANSGICSRREADELITQGLVQVNGAVVTEMGYQVQKTDKVIFDGQGITPEK 196

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              + L      + TT  +   ++ +     +   RV  VGRLD +T G++LLTNDG + 
Sbjct: 197 PVYVLLNKPKGYISTTKDEKARKTVMDLVANASPYRVFPVGRLDRSTTGVILLTNDGHMT 256

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           + L  PS    ++Y V    ++D+  LN + +G+ ++        ++    K  N  V +
Sbjct: 257 KKLTHPSFNMKKIYHVTLDRKLDRADLNAIAEGVRLEEGVAEVDSISYIEGKPKN-EVGI 315

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +  G NR ++++F+   ++V  L R+ +       +  G  R +++  +
Sbjct: 316 EIHIGWNRVVRRIFQRLGYEVEALDRVMFAGLTKKNIKRGHWRILTELEV 365


>gi|15677226|ref|NP_274379.1| hypothetical protein NMB1361 [Neisseria meningitidis MC58]
 gi|7226606|gb|AAF41735.1| conserved hypothetical protein [Neisseria meningitidis MC58]
          Length = 350

 Score =  158 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 72/256 (28%), Positives = 125/256 (48%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    + VNG   +     V   DH+
Sbjct: 85  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWITNGWITVNGKTAQ-LGDKVTPDDHV 143

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 144 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 203

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L +  ++++       
Sbjct: 204 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVE 263

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  V ++EG+NRE++++FE     V+RL+RI +GP  L   L  G   
Sbjct: 264 RIREQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRIGFGPIGLPNRLKRGQFY 323

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   +    +
Sbjct: 324 ELNPAEVANIIKWADM 339


>gi|90578741|ref|ZP_01234551.1| hypothetical 16S rRNA uridine-516 pseudouridylate synthase [Vibrio
           angustum S14]
 gi|90439574|gb|EAS64755.1| hypothetical 16S rRNA uridine-516 pseudouridylate synthase [Vibrio
           angustum S14]
          Length = 231

 Score =  158 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 47/236 (19%), Positives = 101/236 (42%), Gaps = 8/236 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +      +RRE  +++  + ++V+G ++  A+ +V   + +E +G PL+     
Sbjct: 1   MRLDKFLGTTLGITRREAGKLLRDKMIEVDGEIVRSASFSVSDDNDVEFNGRPLKLQGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      + +   D    +           ++   GRLD +T GL+LLT+DG  +  
Sbjct: 61  YFMLNKPEGFVCSH-VDDFNPTVFVLFDEVSPEKMHVAGRLDGDTTGLVLLTDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     + +D +   + G+ +  +       ++ +  ++ +     +
Sbjct: 120 ITSPRHLCSKTYFVEAADPITEDYIKQFEAGVQLRSEKELTRPAKLEILGEREA----LL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
            + EGK  ++K++F     KV  L R   G  +L   L  G  R ++++ +   L 
Sbjct: 176 TISEGKYHQVKRMFAAMGNKVVGLHRERIGTVELDEDLAPGEYRPLTEEEIASFLK 231


>gi|218289710|ref|ZP_03493918.1| pseudouridine synthase [Alicyclobacillus acidocaldarius LAA1]
 gi|218240167|gb|EED07351.1| pseudouridine synthase [Alicyclobacillus acidocaldarius LAA1]
          Length = 242

 Score =  158 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 68/234 (29%), Positives = 109/234 (46%), Gaps = 4/234 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE 71
             RV K +  AG  +R E +++    RV++NG  ++ AA +     D +EVDG  +    
Sbjct: 3   TIRVDKWLTTAGYGTRSEAKKLCRAGRVRLNGETVKDAAKHADPAVDVLEVDGEIVPYEP 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                +Y  P  + +T    D       +   I+  V  VGRLD + EGLLLLTNDG LA
Sbjct: 63  LVYFMMYKPPGYVSSTEDPRDPVVIELLDEEDIWRDVFPVGRLDKDAEGLLLLTNDGPLA 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y VR  G + +D    L +G+V+         ++ +  + G+ +   
Sbjct: 123 HRLLAPKRHVPKRYFVRVRGALGEDDARALAEGVVLDDGYKAMPAELEIL-RSGAESEAI 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           + + EGK  ++K++F     +V  L RIS GP  L   L  G  R +++  +  
Sbjct: 182 IQVYEGKYHQVKRMFASLGKRVTFLKRISMGPLSLDPALKPGEYRRLTEGEIEA 235


>gi|77358718|ref|YP_338282.1| RNA pseudouridine synthase family protein [Coxiella burnetii RSA
           493]
 gi|71066708|gb|AAZ22630.1| ribosomal large subunit pseudouridine synthase B [Coxiella burnetii
           RSA 493]
          Length = 244

 Score =  158 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 75/233 (32%), Positives = 115/233 (49%), Gaps = 5/233 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---KA 70
           +R+ KV+AR+G  SRRE+E+MIA+ R+KVN  L +     +   D + +DG         
Sbjct: 3   ERIQKVLARSGYGSRREIEKMIAEGRIKVNQRLAQ-LGDRITEQDLVYIDGQLSSLSAPE 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L  +     + T        +           R + +GRLDINT GLLL TN+G L
Sbjct: 62  QVRVLLYHKPEGEICTRKDPEWRTTVFETLPRLKDGRWVIIGRLDINTSGLLLFTNEGEL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS Q  R Y VR  G VD D    L  G+ ++        +      G N W  
Sbjct: 122 ANRLMHPSAQVEREYAVRVLGAVDADMTQKLAHGVGLEDGKARFEDIVDVGGDGKNRWFH 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           V + EG++R +++++E    KV+RLIR+ +GP  L  +L  G+ +E+    ++
Sbjct: 182 VVVVEGRHRLVRRLWESQGVKVSRLIRVRFGPIVLPKSLRRGAWKELESPEIK 234


>gi|19746315|ref|NP_607451.1| 16S pseudouridylate synthase [Streptococcus pyogenes MGAS8232]
 gi|21910554|ref|NP_664822.1| putative 16S pseudouridylate synthase [Streptococcus pyogenes
           MGAS315]
 gi|19748507|gb|AAL97950.1| putative 16S pseudouridylate synthase [Streptococcus pyogenes
           MGAS8232]
 gi|21904754|gb|AAM79625.1| putative 16S pseudouridylate synthase [Streptococcus pyogenes
           MGAS315]
          Length = 243

 Score =  158 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 100/233 (42%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ +R +V+ ++ ++ + VN  +   A  ++    D +   G PL     
Sbjct: 1   MRLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEYKDLVTYQGTPLVYESF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T            +  +    V  VGRLD +T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPSGYVSATQDRQQATVMELLDDTARQKTVFPVGRLDKDTRGLLLLTNNGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVT 190
            L  P     + Y  +  G + +   +   +GI ++        + +     +   + V 
Sbjct: 121 DLLSPKKHVTKEYLAKVAGIMTEADKDYFARGISLKDHQCLPAHLEVLASDLQQQTSLVK 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + ++EGK  ++K++      +V  L R+S GP +L  +L  G  R ++ + L+
Sbjct: 181 ITIQEGKFHQVKRMVAACGKEVLDLQRLSMGPLKLDPSLAEGEFRRLTPEELQ 233


>gi|28895754|ref|NP_802104.1| 16S pseudouridylate synthase [Streptococcus pyogenes SSI-1]
 gi|50914410|ref|YP_060382.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS10394]
 gi|94994587|ref|YP_602685.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS10750]
 gi|28811003|dbj|BAC63937.1| putative 16S pseudouridylate synthase [Streptococcus pyogenes
           SSI-1]
 gi|50903484|gb|AAT87199.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS10394]
 gi|94548095|gb|ABF38141.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS10750]
          Length = 244

 Score =  158 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 100/233 (42%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ +R +V+ ++ ++ + VN  +   A  ++    D +   G PL     
Sbjct: 2   MRLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEYKDLVTYQGTPLVYESF 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T            +  +    V  VGRLD +T GLLLLTN+G LA 
Sbjct: 62  VYYLLNKPSGYVSATQDRQQATVMELLDDTARQKTVFPVGRLDKDTRGLLLLTNNGQLAH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVT 190
            L  P     + Y  +  G + +   +   +GI ++        + +     +   + V 
Sbjct: 122 DLLSPKKHVTKEYLAKVAGIMTEADKDYFARGISLKDHQCLPAHLEVLASDLQQQTSLVK 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + ++EGK  ++K++      +V  L R+S GP +L  +L  G  R ++ + L+
Sbjct: 182 ITIQEGKFHQVKRMVAACGKEVLDLQRLSMGPLKLDPSLAEGEFRRLTPEELQ 234


>gi|316984168|gb|EFV63146.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis H44/76]
 gi|325140419|gb|EGC62940.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis CU385]
 gi|325144504|gb|EGC66803.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M01-240013]
          Length = 349

 Score =  158 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 72/256 (28%), Positives = 125/256 (48%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    + VNG   +     V   DH+
Sbjct: 84  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWITNGWITVNGKTAQ-LGDKVTPDDHV 142

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L +  ++++       
Sbjct: 203 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVE 262

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  V ++EG+NRE++++FE     V+RL+RI +GP  L   L  G   
Sbjct: 263 RIREQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRIGFGPIGLPNRLKRGQFY 322

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   +    +
Sbjct: 323 ELNPAEVANIIKWADM 338


>gi|322515424|ref|ZP_08068415.1| ribosomal large subunit pseudouridine synthase B [Actinobacillus
           ureae ATCC 25976]
 gi|322118547|gb|EFX90780.1| ribosomal large subunit pseudouridine synthase B [Actinobacillus
           ureae ATCC 25976]
          Length = 347

 Score =  158 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 87/280 (31%), Positives = 127/280 (45%), Gaps = 10/280 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S   I +DG  +    
Sbjct: 67  GEKLQKILARAGQGSRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNLISLIP 126

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T        +          +R ++VGRLDINT GLLL T 
Sbjct: 127 AQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGARWVAVGRLDINTSGLLLFTT 186

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  G +D+  L  L+KG+ ++       Q+      G N
Sbjct: 187 DGELANRLMHPSREVEREYSVRVFGNIDEAMLQRLRKGVQLEDGPANFKQIKTVGGTGLN 246

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI---LR 242
            W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  +    LR
Sbjct: 247 QWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKLEKGLPRGGWEEMGLEQVNYLR 306

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDF 282
           E +G     E +V++      +      +           
Sbjct: 307 ELVGLPAETETKVDVIKNRRRTNIRQIRKAVKQHSKYRAK 346


>gi|114320248|ref|YP_741931.1| ribosomal large subunit pseudouridine synthase B [Alkalilimnicola
           ehrlichii MLHE-1]
 gi|114226642|gb|ABI56441.1| ribosomal large subunit pseudouridine synthase B [Alkalilimnicola
           ehrlichii MLHE-1]
          Length = 290

 Score =  158 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 99/277 (35%), Positives = 146/277 (52%), Gaps = 13/277 (4%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           D   + E    +++ KV+ARAG+ SRR++E  IA+ RVKVNG + +     V + D ++V
Sbjct: 4   DNTAMSEQANTEKLQKVLARAGVGSRRQMEAWIAEGRVKVNGHVAQ-LGDRVTAEDRLQV 62

Query: 63  DGVPL---RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           DG P+   +     R+ LY+KP G V T  DP+GR TVF+NLP    R + VGRLD+N++
Sbjct: 63  DGRPVARRKLQPERRVLLYYKPEGQVCTRDDPEGRPTVFENLPEADGRWVVVGRLDLNSQ 122

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL T DG LA  L  PS+   R Y VR +G+V  + L  L++G+ +        ++T 
Sbjct: 123 GLLLFTTDGELANRLMHPSSGIEREYAVRVYGEVTPEILRRLQQGVTLDDGEAAFTRITP 182

Query: 180 DTQK--------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLA 230
                         N W  V LREG+NRE+++++E    KV+RLIR+ YGP  L   L  
Sbjct: 183 VVDYRALGYEAPPGNEWYQVTLREGRNREVRRLWESQGLKVSRLIRVRYGPVSLPRGLRR 242

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETL 267
           G  R + +  +        LE      +    +    
Sbjct: 243 GEHRPLREGQVAALCQAVGLEHETQKDNDKRKAPRHK 279


>gi|308050759|ref|YP_003914325.1| ribosomal small subunit pseudouridine synthase A [Ferrimonas
           balearica DSM 9799]
 gi|307632949|gb|ADN77251.1| ribosomal small subunit pseudouridine synthase A [Ferrimonas
           balearica DSM 9799]
          Length = 232

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 50/230 (21%), Positives = 96/230 (41%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +      +R   ++++ +  V+ +G +++     V     + ++GVPL      
Sbjct: 1   MRLDKYLCSCTDLTRSMAKKLLHKGEVQCDGEVVKDPGFKVTDDTQVVLEGVPLGPVATR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+     L +   +          LP   +  I+ GRLD++T GL+LL+ DG     
Sbjct: 61  YIMLHKPAEFLCSNVDELYPSVLNLIELPKRETLRIA-GRLDVDTTGLVLLSEDGQWCHQ 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  Q  + YR      +  D    L +G+ +  +       ++       S+  V +
Sbjct: 120 ITSPRRQCSKRYRAWLAEPLVADAEQQLAQGVQLHNEEGLTRPAELVRI----SDTEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
            + EGK  ++K++F     KV  L R + G  +L   L  G  R +S+  
Sbjct: 176 TIEEGKYHQVKRMFAALGNKVVALHREAIGAIELDETLEPGEWRLLSEDE 225


>gi|302561440|ref|ZP_07313782.1| RNA pseudouridine synthase [Streptomyces griseoflavus Tu4000]
 gi|302479058|gb|EFL42151.1| RNA pseudouridine synthase [Streptomyces griseoflavus Tu4000]
          Length = 359

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 109/233 (46%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
               +R+ KV+ARAG  SRR  E +I Q RV+VNG ++      V    D ++VDG+ + 
Sbjct: 119 EQEGERLQKVLARAGYGSRRACEELIEQARVEVNGEIVLEQGKRVDPEKDEVKVDGLTVA 178

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   L      + T       +  + D + +  +R+  VGRLD  TEG++LLTN G
Sbjct: 179 TQSYQFFSLNKPAGVVSTMEDPEGRQ-CLGDYVTNRETRLFHVGRLDTETEGVILLTNHG 237

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     + Y     G + +D    LK GI ++          +  Q G N  
Sbjct: 238 ELAHRLTHPKYGVKKTYLAAIVGPIPRDLGKRLKDGIQLEDGYARADHFRVVEQTGKNYL 297

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L EG+   ++++     + V++L+R ++GP  LG   +G  R +S   +
Sbjct: 298 VEVTLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPITLGDQKSGWLRRLSNTEV 350


>gi|270291591|ref|ZP_06197811.1| ribosomal small subunit pseudouridine synthase A [Pediococcus
           acidilactici 7_4]
 gi|270279910|gb|EFA25748.1| ribosomal small subunit pseudouridine synthase A [Pediococcus
           acidilactici 7_4]
          Length = 239

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 101/234 (43%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            RV K +    + +R ++ ++I ++ V VN ++ +   V V    D + +    +   + 
Sbjct: 1   MRVDKFLHDMNVGTRSQIRKLIKEKVVFVNDVVAKSGRVKVDPVVDQVRLGEQVITYQQY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            N       +  VGRLD +TEGLLL+TN+G LA 
Sbjct: 61  FYFMMNKPLGVVTATEDRKQKTVMDLFNKVDFRKDLFPVGRLDKDTEGLLLITNNGPLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQK--GSNAWV 189
            L  P     + Y     GQ+    +     GIV++         +T+           V
Sbjct: 121 QLLAPERHVQKTYEAVVTGQITDPAVKQFADGIVLKDGTQLKPADLTILNYSALDEQTLV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
            V L+EGK  +++++F     +V  L RIS+GP QL   LL G+ RE+S + + 
Sbjct: 181 HVTLKEGKYHQVRRMFGSLGERVVSLKRISFGPLQLEEGLLPGTYRELSDEEIE 234


>gi|212710702|ref|ZP_03318830.1| hypothetical protein PROVALCAL_01769 [Providencia alcalifaciens DSM
           30120]
 gi|212686399|gb|EEB45927.1| hypothetical protein PROVALCAL_01769 [Providencia alcalifaciens DSM
           30120]
          Length = 313

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 85/304 (27%), Positives = 139/304 (45%), Gaps = 10/304 (3%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG 64
           +  +    +++ K++AR+G  SRRE+E ++ + R+ V+G +      V V +T  I +DG
Sbjct: 9   MSSKPQQTEKLQKILARSGHGSRREIEGLLKEGRISVDGKMATLGDRVEVKATTKIRLDG 68

Query: 65  VPLRKAERTRLWL-----YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
             L   E  +        Y     L T H      +          +R I+VGRLD+NT 
Sbjct: 69  RLLAIKEPEKEICRVMAYYKPEGELCTRHDPEGRPTVFNRLPRLTGARWIAVGRLDVNTS 128

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL T DG LA  L  PS +  R Y VR  G++   K+  L  G+ ++        V+ 
Sbjct: 129 GLLLFTTDGELANRLMHPSREVEREYAVRVFGEITDAKIRQLTTGVQLEDGPASFKTVSY 188

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  
Sbjct: 189 RGGEGMNQWYNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDIDLPKGLPRGGWTELGL 248

Query: 239 KI---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +    LRE +   +  E++V+++      +     R              K+ SS+    
Sbjct: 249 EQTNYLRELVELDVETESKVSVERDQRRIKANQIRRAVKRHTQVASRPAAKRQSSRPTAK 308

Query: 296 SKQK 299
            + +
Sbjct: 309 RRTR 312


>gi|300114572|ref|YP_003761147.1| RNA-binding S4 domain-containing protein [Nitrosococcus watsonii
           C-113]
 gi|299540509|gb|ADJ28826.1| RNA-binding S4 domain protein [Nitrosococcus watsonii C-113]
          Length = 268

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 81/267 (30%), Positives = 125/267 (46%), Gaps = 7/267 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
           +R+ K++AR G+ SRREVE  I   RV++NGI  +     V   D + ++G PL      
Sbjct: 3   ERLQKILARGGLGSRREVEAWIKAGRVRINGIPAQ-LGDKVSDEDQVTINGRPLSPRRLQ 61

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 +  +     + +        +           R +SVGRLDI+T GLLL T DG
Sbjct: 62  APSSQVILYHKSAGEICSRKDPEGRPTVFRSLPRPRQGRWVSVGRLDISTSGLLLFTTDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PSTQ  R Y VR  G V +  L  L++G+ ++       ++     +G+N W
Sbjct: 122 ELANRLMHPSTQVEREYAVRVLGAVTEATLERLQRGVQLEDGLASFKRILDAGGEGANHW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
             V LREG+ RE+++++E    +V+RLIRI +GP  L   L  G  R +     +  L  
Sbjct: 182 YHVILREGRKREVRRLWESQGIQVSRLIRIRFGPVSLPPGLRMGRWRFLEPSEFKALLEI 241

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNI 274
             +E     L +   ++    + R   
Sbjct: 242 GGVERRITGLQSRSKNNRRGRQGRKQG 268


>gi|157961474|ref|YP_001501508.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157846474|gb|ABV86973.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 290

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 83/290 (28%), Positives = 125/290 (43%), Gaps = 7/290 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E  IA  RV V+G +       V S   I +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRVSVDGEIA-SLGDRVESDAKIRIDGRTVSIRSE 60

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  +  +     + +        +       +  SR ++VGRLDINT GLLL T+D
Sbjct: 61  EDVVCRVIAYHKPEGEICSRKDPEGRPTVFDRLPKTRDSRWVAVGRLDINTSGLLLFTSD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V+   +  L+ G+ ++       +V     +G N 
Sbjct: 121 GELANRLMHPSNEVEREYAVRTFGEVNDACIQRLRMGVTLEDGPANFDKVKAAGGEGMNK 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + +     
Sbjct: 181 WWHVSLAEGRNREVRRLWESQEVQVSRLIRIRYGMIELPKALPRGGWIELPIEEVNYLRK 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
              +EE    L      S    + R   I                    S
Sbjct: 241 TAGMEEETRTLLGTDKHSVARNKVRSAKIKRAVHKHKVATGKPKPTRQRS 290


>gi|188590522|ref|YP_001921660.1| ribosomal large subunit pseudouridine synthase F [Clostridium
           botulinum E3 str. Alaska E43]
 gi|188500803|gb|ACD53939.1| ribosomal large subunit pseudouridine synthase F [Clostridium
           botulinum E3 str. Alaska E43]
          Length = 226

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 57/228 (25%), Positives = 104/228 (45%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+ +  GI SR++  ++I + R+ VNG+        V   D I +D  PL   E+ 
Sbjct: 1   MRINKLFSNLGICSRKDTSKLIEENRIIVNGLPC-IQGQWVELEDEILLDNKPLPIKEKI 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L        T   + +       N  +    +  VGRLD  ++GL+LLTNDG LA  
Sbjct: 60  YIALNKPVGVTCTAADEVEH---NIINFMNYNEYIFPVGRLDKASQGLILLTNDGDLANK 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V      + + +  +  G+ I  +     +V   ++        + L
Sbjct: 117 ILESENEHEKEYIVTLDRPFNDEFILGMTSGVEICNVKTRQCKVRRISED----TFNIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +G N++I+++ + F + V +L RI     +LG L  G  R +S++ L
Sbjct: 173 TQGLNKQIRRMSKAFGYNVKKLERIRIVNIELGNLEYGKWRYLSEEEL 220


>gi|91782986|ref|YP_558192.1| ribosomal large subunit pseudouridine synthase B [Burkholderia
           xenovorans LB400]
 gi|91686940|gb|ABE30140.1| ribosomal large subunit pseudouridine synthase B [Burkholderia
           xenovorans LB400]
          Length = 633

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 79/333 (23%), Positives = 134/333 (40%), Gaps = 9/333 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRR++E +I   RV VNG         +M TD + ++
Sbjct: 207 KRVLAADDDAPKLHKVLAEAGMGSRRDMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRIN 265

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 266 GKPVKRKLASKPPRVLLYHKPTGEIVSHADPEGRPSVFDKLPPMKTAKWLAVGRLDFNTE 325

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 326 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELAEGMRQKLLHGVELDDGPANFLRIRD 385

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+  
Sbjct: 386 GGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPISLPKGLKRGRWEELED 445

Query: 239 KILR---EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
             +R     +G     E + + +A     +                     +   Q    
Sbjct: 446 NQVRALMASVGLKAPTEERGSRNAAPERKQPDPMQTSMGFINREPVLMSHGRFDQQPPRG 505

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDS 328
             ++  A        A   +     +      +
Sbjct: 506 QGRRGGAAGGGFAGGAGAGFGGGYGNRGAGRSA 538


>gi|319787503|ref|YP_004146978.1| pseudouridine synthase [Pseudoxanthomonas suwonensis 11-1]
 gi|317466015|gb|ADV27747.1| pseudouridine synthase [Pseudoxanthomonas suwonensis 11-1]
          Length = 242

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 65/240 (27%), Positives = 110/240 (45%), Gaps = 9/240 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
                R++K IA  G  SRRE +R+IA++RV VNG      AV V   D + VDG PL+ 
Sbjct: 2   TEEAVRLNKHIAGTGFCSRREADRLIAERRVTVNGQPAGVGAV-VGEGDEVRVDGQPLKL 60

Query: 70  AE----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
                 + R         +  T +          +      R+  +GRLD ++EGL+LLT
Sbjct: 61  RAARPGKRRHVYIALNKPVGITCTTESSVKGNIVDFVGHEQRIFPIGRLDKDSEGLILLT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           ++G +   +        + Y V  +  V  + L  + +G+ I        + +   + G 
Sbjct: 121 SNGDIVNEILRAENGHQKEYLVAVNKPVTDEFLRGMSRGVRIHNQMTLPCRASRIAKFG- 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L++G NR+I+ +   F+++V +L R+     +LGTL  G  R ++ + LR  L
Sbjct: 180 ---FRIVLQQGLNRQIRLMAAAFDYRVTQLRRVRIDNIRLGTLKPGQWRNLTPEELRGLL 236


>gi|110636569|ref|YP_676776.1| ribosomal large subunit pseudouridine synthase B [Cytophaga
           hutchinsonii ATCC 33406]
 gi|110279250|gb|ABG57436.1| pseudouridylate synthase (ribosomal large subunit pseudouridine
           synthase B) [Cytophaga hutchinsonii ATCC 33406]
          Length = 562

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 60/229 (26%), Positives = 108/229 (47%), Gaps = 3/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ +GI SRRE +++I +  VKVNGI++      V   D ++ +   L   +  
Sbjct: 329 IRLNKYISNSGICSRREADQLIIEGTVKVNGIVVTELGYKVKPGDSVKYNNKVLNPEKSV 388

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L      + T   + D ++ +     +   R+  VGRLD NT GLLL TNDG LA+ 
Sbjct: 389 YVLLNKPKDFITTMEDENDRKTVMQLVANATKERIYPVGRLDRNTTGLLLFTNDGELAQK 448

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           L  PS +  ++Y V     +  +  + +    I +        +  +     S   + + 
Sbjct: 449 LTHPSNKVKKIYEVELDKPITAEDFDKIVDGKIHLFDGPVKVDEAAII--SPSKKIIGIE 506

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EG+NR ++++FE   + V +L R+ Y       +  GS R ++   +
Sbjct: 507 IHEGRNRIVRRIFESLGYDVLKLDRVMYAGLTKKNIPRGSWRYLTATEV 555



 Score = 36.7 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 13/108 (12%), Positives = 26/108 (24%), Gaps = 1/108 (0%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           + +       +  +     P   S++   D  +                  + G  +   
Sbjct: 144 IAQSGEDRRPQPDRGVERRPAKRSDSRGGDDRSPAKRSYTKRGEGSAEYKSRAGEGRSSA 203

Query: 301 LATP-VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
                  +R   S               SG REE+        ++RS 
Sbjct: 204 PKKTFGPKREDDSRSGRGPAAKFPNKRTSGSREESGDFKRKPTTRRSF 251


>gi|317131163|ref|YP_004090477.1| pseudouridine synthase [Ethanoligenens harbinense YUAN-3]
 gi|315469142|gb|ADU25746.1| pseudouridine synthase [Ethanoligenens harbinense YUAN-3]
          Length = 237

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 93/237 (39%), Gaps = 8/237 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV  ++   RV+V+G  +  A   V      + +DG  L      
Sbjct: 5   RLDKLLAGQGQGSRKEVHTLLRGGRVQVDGQTVTDAGQKVDPDRQRVTLDGHALLWRAHL 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L +      +  +                    +   GRLD +TEG LL+T+DG  A  
Sbjct: 65  YLMMNKPAGVISASRDPKARTVLDLLPADLCRPGLFPAGRLDKDTEGFLLITDDGAFAHD 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVG 192
           +  P     ++Y        D    +    G+ ++        ++ L     + A V   
Sbjct: 125 ILAPRRHVEKIYLATLDRPADTADTDAFATGLTLEDGLHCLPARLWLGEGTDAYAAVR-- 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
             EGK  +++++F     +V  L RI  G   L   L  G  RE++    R+++G  
Sbjct: 183 --EGKFHQVRRMFAARGKQVVHLRRIQIGGLALDESLAPGEARELTPAE-RDRIGLR 236


>gi|240047413|ref|YP_002960801.1| Pseudouridine synthase [Mycoplasma conjunctivae HRC/581]
 gi|239984985|emb|CAT04978.1| Pseudouridine synthase [Mycoplasma conjunctivae]
          Length = 233

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 71/229 (31%), Positives = 110/229 (48%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ K+IA+ G+ SRR+ E+MI   +V +NG             D IE+DG  + K  + 
Sbjct: 5   QRLQKLIAQVGLCSRRQAEQMIKDGKVYLNGEKA-NLGDRASWEDKIEIDGEQIAKKVKI 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G +TT  D   R TV D      + +  VGRLD NT GLLL+TNDG LA  
Sbjct: 64  VWYLLNKPAGYITTVRDQFNRPTVMDFF-DNKTHLFPVGRLDYNTTGLLLITNDGELANK 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  R+Y  +    +   +L+ L    +         +     +K S+    + +
Sbjct: 123 LLHPRNKIERIYLAKLDYSLADWELDFLNTTSLNLDGVISKQK----IEKVSSRKYKITI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G N  +KK+F     +V  L RI +   +L  L  G  R++S   ++
Sbjct: 179 WQGSNHHVKKIFAIAKKQVIELKRIGFANLELANLPEGQFRKLSDLEIK 227


>gi|209559583|ref|YP_002286055.1| Putative 16S pseudouridylate synthase [Streptococcus pyogenes
           NZ131]
 gi|209540784|gb|ACI61360.1| Putative 16S pseudouridylate synthase [Streptococcus pyogenes
           NZ131]
          Length = 243

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 100/233 (42%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ +R +V+ ++ ++ + VN  +   A  ++    D +   G PL     
Sbjct: 1   MRLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEYKDLVTYQGTPLVYESF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T            +  +    V  VGRLD +T GLLLLTN+G LA 
Sbjct: 61  VYYLLNKPSGYVSATQDRQQATVMELLDDTARQKAVFPVGRLDKDTRGLLLLTNNGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVT 190
            L  P     + Y  +  G + +   +   +GI ++        + +     +   + V 
Sbjct: 121 DLLSPKKHVTKEYLAKVAGIMTEADKDYFARGISLKDHQCLPAHLEVLASDLQQQTSLVK 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + ++EGK  ++K++      +V  L R+S GP +L  +L  G  R ++ + L+
Sbjct: 181 ITIQEGKFHQVKRMVAACGKEVLDLQRLSMGPLKLDPSLAEGEFRRLTPEELQ 233


>gi|15675276|ref|NP_269450.1| putative 16S pseudouridylate synthase [Streptococcus pyogenes M1
           GAS]
 gi|71910905|ref|YP_282455.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS5005]
 gi|94988765|ref|YP_596866.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS9429]
 gi|94992591|ref|YP_600690.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS2096]
 gi|139473614|ref|YP_001128330.1| ribosomal small subunit pseudouridine synthase B [Streptococcus
           pyogenes str. Manfredo]
 gi|13622451|gb|AAK34171.1| putative 16S pseudouridylate synthase [Streptococcus pyogenes M1
           GAS]
 gi|71853687|gb|AAZ51710.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS5005]
 gi|94542273|gb|ABF32322.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS9429]
 gi|94546099|gb|ABF36146.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS2096]
 gi|134271861|emb|CAM30097.1| putative ribosomal small subunit pseudouridine synthase B
           [Streptococcus pyogenes str. Manfredo]
          Length = 244

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 100/233 (42%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ +R +V+ ++ ++ + VN  +   A  ++    D +   G PL     
Sbjct: 2   MRLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEYKDLVTYQGTPLVYESF 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T            +  +    V  VGRLD +T GLLLLTN+G LA 
Sbjct: 62  VYYLLNKPSGYVSATQDRQQATVMELLDDTARQKAVFPVGRLDKDTRGLLLLTNNGQLAH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVT 190
            L  P     + Y  +  G + +   +   +GI ++        + +     +   + V 
Sbjct: 122 DLLSPKKHVTKEYLAKVAGIMTEADKDYFARGISLKDHQCLPAHLEVLASDLQQQTSLVK 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + ++EGK  ++K++      +V  L R+S GP +L  +L  G  R ++ + L+
Sbjct: 182 ITIQEGKFHQVKRMVAACGKEVLDLQRLSMGPLKLDPSLAEGEFRRLTPEELQ 234


>gi|311899116|dbj|BAJ31524.1| putative ribosomal large subunit pseudouridine synthase B
           [Kitasatospora setae KM-6054]
          Length = 428

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 68/232 (29%), Positives = 109/232 (46%), Gaps = 2/232 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK 69
              +R+ KV+ARAG+ SRR  E +IAQ RV VNG  +      V    D I+VDG+ +  
Sbjct: 189 EDGERLQKVLARAGMGSRRACEELIAQGRVDVNGETVLEQGRRVDPVKDEIKVDGLTVAT 248

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                  L      + T       +  + D + +  +R+  VGRLD  TEG++LLTN G 
Sbjct: 249 QSYLFFALNKPAGVVSTMEDPEGRQ-CLGDYVTNRETRLFHVGRLDTETEGIILLTNHGE 307

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  P     + Y     G + +D    L KG+ ++          + +  G N  V
Sbjct: 308 LAHRLTHPKYGVTKTYLAAIQGPLPRDLGKTLAKGVELEDGWARADSFKVISNLGKNYLV 367

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V L EG+   ++++     + V++L+R ++GP  LG   +G  R ++   +
Sbjct: 368 EVTLHEGRKHIVRRLLAEVGFPVDKLVRTAFGPITLGDQKSGWLRRLTNPEV 419


>gi|167622673|ref|YP_001672967.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
 gi|167352695|gb|ABZ75308.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
          Length = 244

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 64/251 (25%), Positives = 101/251 (40%), Gaps = 16/251 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD---------HIEVDG 64
            R++K +A  G  SRR   R+I   +V++N  L       V   D          I V+ 
Sbjct: 1   MRLAKYLALTGCCSRRAATRLIRDGQVRINDRLANHVDS-VSLIDTPEGQRSAEQIYVND 59

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +   E    WL++K   + T             +L     R+  +GRLD ++ GLL+L
Sbjct: 60  ELVCPIEAKAYWLFNKS--VGTDSRLLAHLPNSLIHLLPETPRLYPIGRLDKDSRGLLIL 117

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG L   L  P     + Y V+     D   L  +  G+  + +      +       
Sbjct: 118 TNDGELTHKLMHPDFGHAKTYHVQLDRDFDDAFLASMAAGVSYKDVTTLPCIMQRLAADK 177

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
                 + L +G NR+I+++ +   +KV  L R+S    QLG L  GS R +S   L + 
Sbjct: 178 ----YQITLTQGLNRQIRRMSQALGFKVIDLKRVSIQSLQLGDLAEGSMRPLSSAELADL 233

Query: 245 LGPHLLEEAQV 255
           L      E+  
Sbjct: 234 LASVACPESSA 244


>gi|145627819|ref|ZP_01783620.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae 22.1-21]
 gi|144979594|gb|EDJ89253.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae 22.1-21]
          Length = 357

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 89/288 (30%), Positives = 131/288 (45%), Gaps = 10/288 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QPKIEGEKLQKVLARAGQGSRREIETMIASGRVSVEGKIAILGDRIDVHSGVKVRIDGQI 129

Query: 67  LRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +  +         L  Y     L T        +          SR I+VGRLDINT GL
Sbjct: 130 INLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWIAVGRLDINTSGL 189

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++    
Sbjct: 190 LLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGPANFKEIKFTG 249

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 250 GVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEMDLEN 309

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
              LRE +G       ++++       ++    +        +   + 
Sbjct: 310 VNYLRELVGLPAETATKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>gi|51892665|ref|YP_075356.1| ribosomal small subunit pseudouridine synthase A [Symbiobacterium
           thermophilum IAM 14863]
 gi|51856354|dbj|BAD40512.1| ribosomal small subunit pseudouridine synthase A [Symbiobacterium
           thermophilum IAM 14863]
          Length = 251

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 59/253 (23%), Positives = 98/253 (38%), Gaps = 6/253 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++   G  SR+E+  ++   RV V+G  +      V      + VDG P+R    
Sbjct: 1   MRLDRLLGHMGFGSRKELRALLKAGRVTVDGRPVTDPGTLVDPGTSSVAVDGEPVRFQRH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L+     +  T                    ++ VGRLD +TEGLLLLT DG LA 
Sbjct: 61  FHVLLHKPAGVITATADPRQRTVMDVLPEDLRRRDLVPVGRLDKDTEGLLLLTTDGTLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y  R    +D         G+ +  G      ++ + + +       V
Sbjct: 121 RLMAPRWHQPKRYLARVDRPLDPADQEAFAAGVPLADGYVTLPARLEILSPQEGI----V 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            +REGK  +++++F     +V  L R+S GP  LG L  G+ R ++   +        L 
Sbjct: 177 TVREGKYHQVRRMFAARGKRVVYLKRLSMGPLSLGDLPPGAARPLTAAEVDALYRSASLP 236

Query: 252 EAQVNLDAPIYSS 264
                        
Sbjct: 237 NPDDPDVPLAGPP 249


>gi|227535644|ref|ZP_03965693.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           ATCC 25302]
 gi|227186774|gb|EEI66841.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           ATCC 25302]
          Length = 236

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 55/228 (24%), Positives = 91/228 (39%), Gaps = 2/228 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++     SR+EV+ +I  +RV+V G L+     NV+    +EV+          
Sbjct: 1   MRLDKYLSHLQFGSRKEVKALIRDKRVRVAGDLITDPGYNVLPGIAVEVNDAQADGPLEV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +      +  T                    +  VGRLD +T GLLLLT DG L   
Sbjct: 61  DYLMNKPAGVITATEDPTQSTVLDLIRPHDYRPGLYPVGRLDKDTTGLLLLTTDGNLGHA 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P+    + Y       +  D    L+ GI ++       QV +         + + +
Sbjct: 121 LLSPNRHIAKTYAATLAKTLTADMKQRLETGIDLKDFTTAPAQVVVLPDTDGKR-IQITI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
            EGK  ++K++    + +V  L RI+ GP  L   L AG  + ++   
Sbjct: 180 TEGKFHQVKRMLLAVDNEVTALTRIAMGPLSLPADLAAGEYQALTDDE 227


>gi|158319769|ref|YP_001512276.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
 gi|158139968|gb|ABW18280.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
          Length = 242

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 55/217 (25%), Positives = 101/217 (46%), Gaps = 3/217 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
             QR+ K+++  G  SR+++ ++     VKV+G +++ ++ +V      I +    +   
Sbjct: 3   KTQRIDKILSNLGYGSRKDIRQICKNGLVKVDGKVVKDSSAHVDPENSQIIIGNEVVNYR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L ++     +  T  + D       +   +   V  VGRLD +TEGLLLLTNDG L
Sbjct: 63  EFVYLMMHKPQGVISATEDNRDQTVVDLLDEEYLPFSVFPVGRLDKDTEGLLLLTNDGKL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y  +  G V +  +   K+G+ I +       ++ +  +    + +
Sbjct: 123 AHNLLSPKKNVPKTYYAKVLGTVTRSDIESFKEGVFIEEDYKTLPAELNIL-KSDEISEI 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
            + + EGK  ++K++FE  +  V  L R+S G   L 
Sbjct: 182 ELTIYEGKFHQVKRMFEAVDKTVVYLKRLSMGTLNLD 218


>gi|237740792|ref|ZP_04571273.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           2_1_31]
 gi|229422809|gb|EEO37856.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           2_1_31]
          Length = 226

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 68/229 (29%), Positives = 109/229 (47%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ + +   GI SR+EV+++I+ + +KVNG     A  N+   +D IE +G  L   E 
Sbjct: 1   MRLDRFLVECGIGSRKEVKKIISAKEIKVNGSYDISAKDNIDEYSDVIEYNGERLEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +  K   +  T    +           I   +  VGRLD +TEGLLLLTNDG L  
Sbjct: 61  RYYIMNKKAGYITATEDIREATVMDLLPEWVIRKDLAPVGRLDKDTEGLLLLTNDGKLNH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V     + Q+ +  L++G+ I        +V    +K S+  + + 
Sbjct: 121 KLLSPKNHVDKTYYVEIENNISQEDILKLEEGVDIGNYITLPAKV----EKISDTKIYLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++EGK  ++KK+ E  N KVN L R ++    L  L  G  +EV+ + +
Sbjct: 177 IKEGKFHQVKKMLEAVNNKVNYLQRTTFAKLSLDGLALGEVKEVNLEDI 225


>gi|145220277|ref|YP_001130986.1| ribosomal large subunit pseudouridine synthase B [Prosthecochloris
           vibrioformis DSM 265]
 gi|145206441|gb|ABP37484.1| ribosomal large subunit pseudouridine synthase B [Chlorobium
           phaeovibrioides DSM 265]
          Length = 247

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 114/247 (46%), Gaps = 8/247 (3%)

Query: 7   VQENFTPQ--RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVD 63
           + E    +  R+++ +A  GIASRR  ++M+ + RV VNG ++    + +    D + VD
Sbjct: 1   MTEKRRGEEVRINRYLAMCGIASRRAADQMVIEGRVMVNGQVVIEPGLQIKMGKDEVIVD 60

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G      E  ++++       V T S  +    +  +   +  RV  VGRLD  T G LL
Sbjct: 61  GQKYALPEERKVYILFNKPRNVITTSSDERDREMVLDYIKVKERVFPVGRLDRKTTGALL 120

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDT 181
            TNDG LA  L  PS+   + Y         Q  L LL  G+ ++         Q  +  
Sbjct: 121 FTNDGILANKLMHPSSNVKKEYLAVLDTAFPQSSLPLLTGGMRLKDTGEKVRPCQAKILD 180

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             G   W  + L EGKN +++++F    ++V RL R++Y   + G L  G  R ++++ +
Sbjct: 181 G-GMQVW--MSLHEGKNHQVRRMFWTLGFEVTRLERVTYAGLKTGDLRRGEWRYLNREEV 237

Query: 242 REQLGPH 248
           R+     
Sbjct: 238 RQLQELA 244


>gi|325202400|gb|ADY97854.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           meningitidis M01-240149]
 gi|325207848|gb|ADZ03300.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           meningitidis NZ-05/33]
          Length = 252

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 108/255 (42%), Gaps = 20/255 (7%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K          R+SK +A+ G+ SRRE +  I Q  V VNG         V   D I
Sbjct: 1   MNPKTPPDHTEDAVRLSKRMAQLGLCSRREADGYIEQGWVTVNGKTA-VLGQKVSPADRI 59

Query: 61  EVD---------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           E++                 P+          Y     L+T  +  +G ++     P   
Sbjct: 60  ELNKKAHEQQAARITILLNKPVGYVSAQAEKGYKSAAELITPENHWEGDTSRIRFDPKHK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             +   GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+
Sbjct: 120 IGLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGL 179

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G      QV    +      +   L++GK R+I+++ E    +V  L RI  G  +L
Sbjct: 180 SLDGEKLRPAQVEWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>gi|237745528|ref|ZP_04576008.1| pseudouridylate synthase [Oxalobacter formigenes HOxBLS]
 gi|229376879|gb|EEO26970.1| pseudouridylate synthase [Oxalobacter formigenes HOxBLS]
          Length = 249

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 65/249 (26%), Positives = 108/249 (43%), Gaps = 23/249 (9%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------- 63
             P R+SK ++  GI SRRE +  I +  VKV+G  + +    V+    I ++       
Sbjct: 3   SEPVRLSKRMSELGICSRREADEWIERGWVKVDGKTVSQLGSKVLPHQKISIEKQASQEQ 62

Query: 64  --------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                     P+          Y   + L++  +   G  +     PS    ++  GRLD
Sbjct: 63  ARRVTILINKPVGYVSGQAEDGYKPAVSLISEATRWKGDPSKEKFKPSQLRSLVPAGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG----QVDQDKLNLLKKGIVIQGIC 171
           I++ GLL+LT DG +A+ L   ++   + Y VR       ++ ++ L LL+ G+ + G  
Sbjct: 123 IDSVGLLVLTQDGRIAKRLIGENSATDKEYLVRVKYLKPGKLPENDLQLLRHGLKLDGKP 182

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
               +V           +   LREGK R+I+++ E    KV  L RI  G  +LG L  G
Sbjct: 183 LLPAKVNWQNDDQ----LRFVLREGKKRQIRRMCEAVGLKVIGLKRIRIGQIKLGDLPPG 238

Query: 232 STREVSKKI 240
             R +  + 
Sbjct: 239 QWRYLRPEE 247


>gi|227488999|ref|ZP_03919315.1| pseudouridine synthase B [Corynebacterium glucuronolyticum ATCC
           51867]
 gi|227091075|gb|EEI26387.1| pseudouridine synthase B [Corynebacterium glucuronolyticum ATCC
           51867]
          Length = 349

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 78/241 (32%), Positives = 120/241 (49%), Gaps = 4/241 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ KV+A+AG+ASRR  E +IAQ RV+VNG ++ R  V V      I VDGV ++  E 
Sbjct: 109 VRLQKVLAQAGVASRRMSEELIAQGRVEVNGEIVMRQGVRVDPDTAVIRVDGVRVKVNED 168

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGG 129
                 +KP+G+ +T  D  GR  V D +         +  VGRLD  TEGLLLLTNDG 
Sbjct: 169 LVYIALNKPLGVQSTMKDDMGRPCVGDIVGEKVDAGLHLFHVGRLDAKTEGLLLLTNDGE 228

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  P     + Y     G+ D++ +  L++G+ ++        V +       + +
Sbjct: 229 LANRLMHPKYHVSKTYLATVLGEADRELVKKLREGVDLEDGIAKADYVQIVDTYEGRSLI 288

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            V L EG+   ++++ +   + V +L+R      QLG L  G+ R ++   LR       
Sbjct: 289 RVELHEGRKHIVRRMLKELGFPVQQLVRTKIHTVQLGELTPGAIRHLNDSELRALYKAVE 348

Query: 250 L 250
           +
Sbjct: 349 M 349


>gi|262373293|ref|ZP_06066572.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter junii
           SH205]
 gi|262313318|gb|EEY94403.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter junii
           SH205]
          Length = 313

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 80/309 (25%), Positives = 130/309 (42%), Gaps = 7/309 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
            +++ KV+AR G+ SRR +E +IA  RV +NG + +     +  TD + +DG  ++    
Sbjct: 2   SEKLQKVLARVGLGSRRYMEEVIAAGRVSINGKIAQV-GERIEPTDELRIDGRKVQFQIE 60

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R  L  Y     + + +      +           R + VGRLDIN+ GLL+ TND
Sbjct: 61  DEIRRRVLIYYKPEGEICSRNDPEKRPTVFDHLPQIANDRWVMVGRLDINSTGLLIFTND 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V     N + KG+ ++         +     G N 
Sbjct: 121 GELANRLMHPSNEVEREYAVRVMGEVTPQIRNNMLKGVELEDGPAKFESFSEIGGDGINR 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V ++EG+NRE++++FE    KV+RL+R  YG   L   L  G   E+ K  +     
Sbjct: 181 WYQVVVKEGRNREVRRIFESQGLKVSRLLRTRYGTVILPRELRTGRWMELDKADIDNLAK 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              L+  Q      +    T       + +       + +++  Q               
Sbjct: 241 SVELKPRQGTGLFGMAKRRTERMSEKPMAARRGGYLRQQRRDDEQPEQQRPNTNNNGNSG 300

Query: 307 RRNLASNVW 315
           R+ +  N  
Sbjct: 301 RKTIGLNKG 309


>gi|317486146|ref|ZP_07944990.1| S4 domain-containing protein [Bilophila wadsworthia 3_1_6]
 gi|316922595|gb|EFV43837.1| S4 domain-containing protein [Bilophila wadsworthia 3_1_6]
          Length = 262

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 65/252 (25%), Positives = 114/252 (45%), Gaps = 21/252 (8%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R++K +A AG+ SRR  + +IA  RV VNG  +    + V    D +EVDG P++ 
Sbjct: 2   EKTVRINKALADAGVCSRRRADELIAAGRVSVNGEPVASPGLQVTPGTDKLEVDGKPVQP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTN 126
                  L L      + T +      + +        +R     GRLD  +EGL+LLT+
Sbjct: 62  IAQAPCYLLLNKPVRVVSTAYDPEGRTTVLDLVPAKWKARRLYPAGRLDFFSEGLVLLTD 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGS 185
           DG L   +  P     RVY V   G V    L +++KG+ + +G     +++ +   +  
Sbjct: 122 DGELTNRVVHPRHHMPRVYHVLIRGGVSDRALEVMRKGMTLAEGEKLAPVEIRVLPGQVH 181

Query: 186 N----------------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +                  + + L +G NR+I+++    +  + RL+R++ GP +LG + 
Sbjct: 182 DLSGVSRNAGPPAGQRGTLLEMTLHQGLNRQIRRMCRDLHLTILRLVRVAQGPLRLGVMK 241

Query: 230 AGSTREVSKKIL 241
            G  RE++   +
Sbjct: 242 PGEARELTPAEV 253


>gi|325142066|gb|EGC64494.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           meningitidis 961-5945]
 gi|325198023|gb|ADY93479.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           meningitidis G2136]
          Length = 252

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 67/255 (26%), Positives = 108/255 (42%), Gaps = 20/255 (7%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K          R+SK +A+ G+ SRRE +  I Q  V VNG         V+  D I
Sbjct: 1   MNPKTPPDHTEDAVRLSKRMAQLGLCSRREADGYIEQGWVTVNGKTA-VLGQKVLPADRI 59

Query: 61  EVD---------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           E++                 P+          Y     L+T  +  +  ++     P   
Sbjct: 60  ELNKKAHEQQAARITILLNKPVGYVSAQAEKGYKSAAELITPENHWEDDTSRIRFDPKHK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             +   GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+
Sbjct: 120 IGLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGL 179

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G      +V    +      +   L++GK R+I+++ E    +V  L RI  G  +L
Sbjct: 180 SLDGEKLRPAKVEWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>gi|163816856|ref|ZP_02208219.1| hypothetical protein COPEUT_03047 [Coprococcus eutactus ATCC 27759]
 gi|158448113|gb|EDP25108.1| hypothetical protein COPEUT_03047 [Coprococcus eutactus ATCC 27759]
          Length = 234

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 62/221 (28%), Positives = 109/221 (49%), Gaps = 7/221 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K ++ AG+ SRR  +  I   +V +NG         VM  D +   G  +++ 
Sbjct: 2   SDGIRLNKYLSEAGVCSRRAADTHIENGKVTINGETA-VMGQKVMPGDVVTFMGRKVQQK 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +RT +  Y+KPIGL  T S  D       +      R+  VGRLD +++GLLLLTNDG L
Sbjct: 61  DRTVILAYNKPIGLTCTASKAD--PDNIFDHIDYPIRLQYVGRLDKDSQGLLLLTNDGDL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  ++       + YRVR + ++ +D +  + +G+ I        +V    +K  +    
Sbjct: 119 SNAIQKSVNNHEKEYRVRVNREITEDFIRKMSEGVPILDTVTKKCKV----RKIDDRSFM 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           + L +G NR+I+++ +   ++V  L R+     +LG +  G
Sbjct: 175 IVLTQGLNRQIRRMCDALGYRVVNLKRVRVCNVKLGNMRPG 215


>gi|304410498|ref|ZP_07392116.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|307304591|ref|ZP_07584341.1| pseudouridine synthase [Shewanella baltica BA175]
 gi|304350982|gb|EFM15382.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|306911993|gb|EFN42417.1| pseudouridine synthase [Shewanella baltica BA175]
          Length = 242

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 67/240 (27%), Positives = 111/240 (46%), Gaps = 16/240 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMST----DHIEVDGVPLR 68
            R++K +A+ GI SRRE  R+I   R+ +NG +      + +  +    D IE+DG P+ 
Sbjct: 1   MRLAKYLAQCGIGSRREACRLIEAGRITLNGHIARHTDPIRLDESLNCLDRIELDGAPIT 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           K E    W+ +K +G      + D   T   +L     R+  VGRLD ++ GLLLLTNDG
Sbjct: 61  KTETLAYWILNKAVGTDCRLLEQDE--TSLIHLLPKAPRLYPVGRLDKDSRGLLLLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS    + Y VR +     D +  +  G+  + +     QV   +       
Sbjct: 119 ELTHKLMHPSFVHSKTYHVRLNRPFTDDFVEQMASGVRYKNLQTLPCQVRRLSSDS---- 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ-----LGTLLAGSTREVSKKILRE 243
             + L +G NR+I+++ +   ++V  L R++          LG L  G  + ++   + E
Sbjct: 175 FEIVLTQGLNRQIRRMSKALGYRVIDLERVAIMTLNLRELALGELQEGQMQPLTDSKIAE 234


>gi|73662319|ref|YP_301100.1| RNA pseudouridine synthase [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
 gi|72494834|dbj|BAE18155.1| RNA pseudouridine synthase [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
          Length = 232

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 51/231 (22%), Positives = 105/231 (45%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K ++  G+ +R EV++ + +++V ++  +       +    + ++V+   +     
Sbjct: 1   MRLDKFLSNMGVGTRTEVKQRLKKKQVTIDDKVETSPKKQINPELEIVKVNDQKIDFV-N 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP   ++  +D   ++ +       +  +  VGRLD +TEGLLL+TNDG    
Sbjct: 60  KVYLMLNKPKDYISATTDEQHKTVLDLIEDYRYLDLFPVGRLDKDTEGLLLITNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V     + ++ +N  K GI +        +  L      N    V 
Sbjct: 120 ELMSPGKHVAKTYEVISQKNITKNDINAFKVGIELNEGLAKPAK--LVQGDELNKSF-VT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           + EG+  ++K++F   + +V  L RI  G  QL + L +G  R ++++  +
Sbjct: 177 IYEGRYHQVKRMFHAIDNEVLALKRIRIGDLQLDSTLASGEYRHLTQQDFK 227


>gi|251779990|ref|ZP_04822910.1| ribosomal large subunit pseudouridine synthase F [Clostridium
           botulinum E1 str. 'BoNT E Beluga']
 gi|243084305|gb|EES50195.1| ribosomal large subunit pseudouridine synthase F [Clostridium
           botulinum E1 str. 'BoNT E Beluga']
          Length = 226

 Score =  157 bits (396), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 56/228 (24%), Positives = 104/228 (45%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+ +  GI SR++  ++I + R+ VNG+        V   D I +D   L   E+ 
Sbjct: 1   MRINKLFSNLGICSRKDTSKLIEENRIIVNGLPC-IQGQWVELEDEILLDNKLLPIKEKI 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L        T   + +       N  +    +  VGRLD  ++GL+LLTNDG LA  
Sbjct: 60  YIALNKPVGVTCTAADEVEH---NIINFMNYNEYIFPVGRLDKASQGLILLTNDGDLANK 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V      + + +  ++ G+ I  +     +V   ++        + L
Sbjct: 117 ILESENEHEKEYIVTLDRPFNDEFILGMENGVEICNVKTRQCKVRRISED----TFNIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +G N++I+++ + F + V +L RI     +LG L  G  R +S++ L
Sbjct: 173 TQGLNKQIRRMSKAFGYNVEKLERIRIVNIELGDLEYGKWRYLSEEEL 220


>gi|116492417|ref|YP_804152.1| ribosomal small subunit pseudouridine synthase A [Pediococcus
           pentosaceus ATCC 25745]
 gi|116102567|gb|ABJ67710.1| ribosomal small subunit pseudouridine synthase A [Pediococcus
           pentosaceus ATCC 25745]
          Length = 239

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 57/238 (23%), Positives = 104/238 (43%), Gaps = 5/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            RV K +    + +R ++ +MI  + + VN  +++   V V    D + +    +   + 
Sbjct: 1   MRVDKFLHDMNMGTRTQIRKMIKDKLIFVNDTVVKTGRVKVDPVVDEVRLKDQVIEYQQY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      L  T            N   + + +  VGRLD +T+GLLL+TN+G LA 
Sbjct: 61  FYFMMNKPLGVLTATEDRKQKTVMDLFNKVDLRNDLFPVGRLDKDTQGLLLITNNGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDT--QKGSNAWV 189
            L  P     + Y     G++    +   +KGI ++        Q+ ++   +      V
Sbjct: 121 DLLAPERHVDKTYEAVVTGKITDQAVEEFQKGITLRDGTTLKPAQLIIEHYSELDDQTVV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
            V L+EGK  +++++F     KV  L R S+GP +L   LL G+ RE++   +   + 
Sbjct: 181 KVVLKEGKYHQVRRMFGSLGEKVVTLRRTSFGPLELDVGLLPGTYRELTDDEINRLVE 238


>gi|83311576|ref|YP_421840.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthase [Magnetospirillum magneticum
           AMB-1]
 gi|82946417|dbj|BAE51281.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthase [Magnetospirillum magneticum
           AMB-1]
          Length = 247

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 94/234 (40%), Gaps = 3/234 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  T  R+ ++IA  G  S+R+V+ MI   RV +    +        + D I VDG PL 
Sbjct: 10  EGHTDMRLIRLIANLGYGSQRDVKAMIKAGRVTLADGTVLDDGTKA-AHDDIRVDGEPLD 68

Query: 69  KAERTRLWLYHKPIGLVTTHSD-PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                 L L+       +T          + +        V  VGRLD ++ GLLLLT+D
Sbjct: 69  PPPGLVLMLHKPEGYTCSTSDPGRIVYELLPERFMHRNPIVAPVGRLDRDSTGLLLLTDD 128

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  +  P     + Y V     +  ++  +   G ++       +        G   
Sbjct: 129 GPLAHRITSPKRHVPKTYEVTLARPLSGEEGAVFASGTLMLRSESTPLAPAELVVSGPQT 188

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              + + EG+  ++K++F      V RL R + G   LG L  G  R +S   +
Sbjct: 189 -ARITITEGRYHQVKRMFAAVGNHVERLHRAAIGGLDLGDLAEGQWRPLSPAEI 241


>gi|55980188|ref|YP_143485.1| ribosomal large subunit pseudouridine synthase B [Thermus
           thermophilus HB8]
 gi|55771601|dbj|BAD70042.1| ribosomal large subunit pseudouridine synthase B [Thermus
           thermophilus HB8]
          Length = 235

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 83/238 (34%), Positives = 121/238 (50%), Gaps = 8/238 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+   +ARAG+ASRR+ E +I + RV+VNG +       V   D +EVDG  +   ++  
Sbjct: 5   RLQAFLARAGVASRRKAEDLIREGRVRVNGKVA-VLGQKVGPEDLVEVDGKRVELPQKRL 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +   HKP G  TT  DP  R TVFD LP I      VGRLD ++EGLLLLTNDG L   L
Sbjct: 64  VLALHKPKGYTTTRHDPHARRTVFDLLPKIPGL-HPVGRLDRDSEGLLLLTNDGDLTHRL 122

Query: 135 ELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
             P     +VYRV   G    ++    L  G+ ++      +               + L
Sbjct: 123 THPRFGVRKVYRVWTEGGTLPKEVCRRLLLGVDLEDGPARALACRPAPGGAV-----LVL 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            EG+ RE++++ +   + V RL+R+  GP +LG L  G  R +S++ ++  L    LE
Sbjct: 178 AEGRKREVRRMLQRVGYPVRRLLRLQVGPIRLGDLPPGKWRRLSEREVKALLRLVGLE 235


>gi|330446105|ref|ZP_08309757.1| 16S rRNA pseudouridine 516 synthase [Photobacterium leiognathi
           subsp. mandapamensis svers.1.1.]
 gi|328490296|dbj|GAA04254.1| 16S rRNA pseudouridine 516 synthase [Photobacterium leiognathi
           subsp. mandapamensis svers.1.1.]
          Length = 231

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 95/236 (40%), Gaps = 8/236 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +      +R+E  +++  + V+VNG ++   +V V     +E +G  L      
Sbjct: 1   MRLDKFLGTTLGITRKEAGKILKDRMVEVNGEVVRNGSVQVSDDCDVEFNGRSLSLQGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      + +   D    +           ++   GRLD +T GL+L+T+DG  +  
Sbjct: 61  YYMLNKPQGFVCSH-VDDFNPTIFVLFDEISPEKMHVAGRLDGDTTGLVLVTDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     + +D +     G+ +  +       ++ +  +  +     +
Sbjct: 120 ITSPRHVCEKTYYVETADPITEDYIQQFADGVQLRSEKELTRPAKLEILGENEA----LL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
            + EGK  ++K++F     KV  L R   G  +L   L  G  R ++++ +   L 
Sbjct: 176 TITEGKYHQVKRMFAAMGNKVVGLHRERVGAVELDEELEPGEYRPLTEEEIASFLK 231


>gi|317506859|ref|ZP_07964631.1| RNA pseudouridylate synthase [Segniliparus rugosus ATCC BAA-974]
 gi|316254787|gb|EFV14085.1| RNA pseudouridylate synthase [Segniliparus rugosus ATCC BAA-974]
          Length = 278

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 74/249 (29%), Positives = 121/249 (48%), Gaps = 18/249 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK 69
              QR+ KV+ARAG+ASRR  E++IA+ RV V+G L+    + V   T  +EVDG  +  
Sbjct: 16  DKAQRLHKVLARAGVASRRGAEQLIAEGRVVVDGRLVVEQGMQVDPATAVVEVDGKRVAV 75

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                T L    K +    +         +    P + + +  VGRLD +T GLLL++ND
Sbjct: 76  DDRHATYLLNKPKGVVTAMSDQRERCVGDLLREQPDLPAGLFHVGRLDADTTGLLLVSND 135

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----- 182
           G LA  L  PS +  + Y     G V +  L+ L++G+ ++        V +  +     
Sbjct: 136 GELAHRLAHPSYEIPKTYLATVRGAVGKGALDALRRGVSLEDGPARADAVAVKGEARPAP 195

Query: 183 ----------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                      G+ + V + L EG+NR ++++F+     V  L R+  GP +LG L AG+
Sbjct: 196 LRKAQTGHASGGARSVVEITLHEGRNRIVRRMFDAVGHPVVELARLRIGPIRLGGLQAGA 255

Query: 233 TREVSKKIL 241
            R ++ + +
Sbjct: 256 LRALAPEEV 264


>gi|159026975|emb|CAO86693.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 248

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 90/239 (37%), Positives = 126/239 (52%), Gaps = 10/239 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV K++A+ GIASRR  E MI  +RV+ NG +++         DH+E+DG  +  A R 
Sbjct: 3   ERVQKILAQWGIASRRRAEEMIVARRVRRNGKIVQLGEKADPEKDHLEIDGKKIEPANRP 62

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLLTNDG 128
           +    L +KPIG+V+T  DP  R TV D LP   +       VGRLDINT G LLLTNDG
Sbjct: 63  KRLYILVNKPIGVVSTCKDPQNRPTVIDLLPDSLASETGLHPVGRLDINTTGALLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P     + YRV   G +D   L   ++GI+++G      QV +  Q      
Sbjct: 123 QLTLTLTHPRYHLPKTYRVWLDGAIDTLALQRWREGILLEGKKTLPAQVEILKQTDQKTL 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-----LLAGSTREVSKKILR 242
           + V L EG+NR+I+ V E   + V +L R + GP QL +     L  G  R ++   L+
Sbjct: 183 LEVILVEGRNRQIRCVAEELGYHVLKLHRSAIGPIQLNSGNNSPLPLGHYRFLTLDELK 241


>gi|194364580|ref|YP_002027190.1| pseudouridine synthase [Stenotrophomonas maltophilia R551-3]
 gi|194347384|gb|ACF50507.1| pseudouridine synthase [Stenotrophomonas maltophilia R551-3]
          Length = 268

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 112/233 (48%), Gaps = 4/233 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           +++V+++AG+ SR E  R IA+ RV+V+G ++      +      IEVDG P+   +R  
Sbjct: 33  LARVLSKAGVCSRSEAARWIAEGRVRVSGRIVRDPEFPIASPAPPIEVDGQPMAAPQRLY 92

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L      + T   +    +       +    +  VGRLD  +EGLLL +ND   A  L
Sbjct: 93  LMLNKPRGVVTTAQDERGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAAHL 152

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P T   + Y V+     D+D L  L+ G+  +G     + V +       AW+ V L 
Sbjct: 153 TDPETGPQKTYHVQVDRLPDEDTLAALRAGVEDEGEFLVALAVRVLRSGDKTAWLEVVLD 212

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           EG+NR I+++   F+ +V RL+R++ G   LG L  G  R +    + +Q   
Sbjct: 213 EGRNRHIRRLLAAFDLQVLRLVRVAIGELTLGDLGKGQWRVL---EVSDQQRL 262


>gi|328881450|emb|CCA54689.1| Ribosomal large subunit pseudouridine synthase B [Streptomyces
           venezuelae ATCC 10712]
          Length = 453

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 109/233 (46%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
               +R+ KV+ARAG+ SRR  E +I Q RV+VNG ++      V    D I+VDG+ + 
Sbjct: 213 EQEGERLQKVLARAGMGSRRACEELIEQARVEVNGEIVLEQGKRVDPEKDEIKVDGLTVA 272

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   L      + T       +  + D + +  +R+  VGRLD  TEG++LLTN G
Sbjct: 273 TQSYLFFALNKPSGVVSTMEDPDGRQ-CLGDYVTNRETRLFHVGRLDTETEGIILLTNHG 331

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     + Y     G + ++    LK GI ++          +  Q G N  
Sbjct: 332 ELAHRLTHPKYGVKKTYLAAITGPLPREVGKRLKDGIQLEDGYARADHFRVVEQTGKNYL 391

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L EG+   ++++     + V +L+R ++GP  LG   +G  R ++   +
Sbjct: 392 VEVTLHEGRKHIVRRMLAEAGFPVEKLVRTAFGPIALGDQKSGWLRRLTNTEV 444


>gi|167769669|ref|ZP_02441722.1| hypothetical protein ANACOL_01003 [Anaerotruncus colihominis DSM
           17241]
 gi|167668030|gb|EDS12160.1| hypothetical protein ANACOL_01003 [Anaerotruncus colihominis DSM
           17241]
          Length = 242

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 55/236 (23%), Positives = 96/236 (40%), Gaps = 5/236 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGV 65
           + +    +R+ KVIA     SRR+V+R++ + ++ VNG  +++A + +    D + V G 
Sbjct: 1   MPQKQKLERLDKVIAAQTKLSRRDVQRLVGRGQISVNGTPVKKADLKIDPDTDVVMVSGK 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            L       + L      +  T                +   +   GRLD +TEG +L+T
Sbjct: 61  TLALKRHVYIMLNKPRGVVCATSDAALPTVLDLVPDSLMRRGLFPAGRLDKDTEGFVLIT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG  A  +  P +   + Y  R    V Q  +     G+ + G      ++ +     +
Sbjct: 121 DDGAFAHRILAPKSHVPKTYTARLDAPVTQQMIEAFAAGVQLDGAVCMPAELCVL---DT 177

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
                V +R+G   +IK++F      V  L R   G   L   L  G  RE+S   
Sbjct: 178 PDTARVVIRQGMYHQIKRMFAACGAHVLALRRDRIGGLSLDIALGPGECRELSAAE 233


>gi|268596680|ref|ZP_06130847.1| pseudouridine synthase [Neisseria gonorrhoeae FA19]
 gi|268550468|gb|EEZ45487.1| pseudouridine synthase [Neisseria gonorrhoeae FA19]
          Length = 416

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 72/256 (28%), Positives = 125/256 (48%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+
Sbjct: 151 LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHV 209

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 210 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 269

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++  L +  ++++       
Sbjct: 270 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTTEQMRSLTEEGVMLEDGLAKVE 329

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  + ++EG+NRE++++FE     V+RL+R+++GP  L   L  G   
Sbjct: 330 RIREQGGEGANKWYNIVIKEGRNREVRRIFESQGLTVSRLVRVAFGPIGLPNRLKRGQFY 389

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   L    +
Sbjct: 390 ELNPAEVANILKWADM 405


>gi|15676704|ref|NP_273848.1| hypothetical protein NMB0806 [Neisseria meningitidis MC58]
 gi|7226040|gb|AAF41219.1| conserved hypothetical protein [Neisseria meningitidis MC58]
 gi|316984481|gb|EFV63449.1| conserved hypothetical protein [Neisseria meningitidis H44/76]
 gi|325140042|gb|EGC62571.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           meningitidis CU385]
 gi|325144157|gb|EGC66464.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           meningitidis M01-240013]
 gi|325200510|gb|ADY95965.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           meningitidis H44/76]
 gi|325203890|gb|ADY99343.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           meningitidis M01-240355]
 gi|325206353|gb|ADZ01806.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           meningitidis M04-240196]
          Length = 252

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 107/255 (41%), Gaps = 20/255 (7%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K          R+SK +A+ G+ SRRE +  I Q  V VNG         V   D I
Sbjct: 1   MNPKISSDHTEDAVRLSKRMAQLGLCSRREADGYIEQGWVTVNGKTA-VLGQKVSPADRI 59

Query: 61  EVD---------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           E++                 P+          Y     L+T  +  +G +      P   
Sbjct: 60  ELNKKAHEQQAARITILLNKPVGYVSAQAEKGYKSAAELITPENHWEGDTGRIRFDPKHK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             +   GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+
Sbjct: 120 IGLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGL 179

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G      QV    +      +   L++GK R+I+++ E    +V  L RI  G  +L
Sbjct: 180 SLDGEKLRPAQVEWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>gi|90961422|ref|YP_535338.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           salivarius UCC118]
 gi|90820616|gb|ABD99255.1| Ribosomal small subunit pseudouridine synthase A [Lactobacillus
           salivarius UCC118]
          Length = 240

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 56/234 (23%), Positives = 115/234 (49%), Gaps = 6/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +++ G  +R E +++I  +RV++N  +++   + +    D I +DG  L    +
Sbjct: 3   MRLDKFLSQTGKFTRAEAKKVIKAKRVRLNDEVVKDGKIKINEESDKIFLDGELLALNNK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDN-LPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              ++ +KP G+V+   D   ++ +     P     +  VGRLD  T GLL++TNDG  A
Sbjct: 63  EVYYMLNKPAGVVSATRDDKDKTVIDLINFPGRKEDLFPVGRLDKETTGLLIITNDGKFA 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDT--QKGSNAW 188
             +  P     + Y     G++ + ++ +  +G+ +         Q+ + +  +K   + 
Sbjct: 123 HDIISPKKHVSKTYEAVVTGKISEKEVKIFSQGMELSNGDKLQPAQLDIISYSEKDDTSK 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           V V + EGK  +++++F   + +V  L R+  G  +L   L  G  RE++++ L
Sbjct: 183 VRVIIHEGKYHQVRRMFGAVSQRVLELDRVKIGLLELDDTLERGEYRELTEEEL 236


>gi|260550972|ref|ZP_05825177.1| ribosomal large subunit pseudouridine synthase B [Acinetobacter sp.
           RUH2624]
 gi|260405920|gb|EEW99407.1| ribosomal large subunit pseudouridine synthase B [Acinetobacter sp.
           RUH2624]
          Length = 307

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 82/309 (26%), Positives = 132/309 (42%), Gaps = 13/309 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
            +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG  ++    
Sbjct: 2   SEKLQKVLARIGLGSRRYMEEVIAAGRVSVNGRVAQV-GERIEPGDELRIDGRKVQFQIE 60

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R  L  Y     + + +      +           R + VGRLDIN+ GLLL TND
Sbjct: 61  DEIRRRVLIYYKPEGEICSRNDPEKRPTVFDHLPQIANDRWVMVGRLDINSTGLLLFTND 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V       +  G+ ++         +    +G N 
Sbjct: 121 GELANRLMHPSNEIEREYAVRVMGEVTPQLRQNMVNGVELEDGPAKFESFSEIGGEGINR 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V ++EG+NRE++++FE    KV+RL+R  YG   L   L  G   E+ K  +     
Sbjct: 181 WYQVVVKEGRNREVRRIFESQGLKVSRLLRTRYGTVILPRELRTGRWMELDKTDIDNL-- 238

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                ++             + + R + ++E P    R      Q+    K+    T   
Sbjct: 239 ----AKSVELKPRQGTGLFGMAKRRTDRMTEKPMAARRGGYLRQQRRDDEKEAPTNTGNQ 294

Query: 307 RRNLASNVW 315
           R++   N  
Sbjct: 295 RKSTGFNRG 303


>gi|127513174|ref|YP_001094371.1| pseudouridine synthase [Shewanella loihica PV-4]
 gi|126638469|gb|ABO24112.1| ribosomal large subunit pseudouridine synthase B [Shewanella
           loihica PV-4]
          Length = 293

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 75/287 (26%), Positives = 127/287 (44%), Gaps = 7/287 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E  IA  RV ++G + +     + +   + +DG  +     
Sbjct: 7   SEKLQKVLARAGHGSRREMEAWIAAGRVSIDGEIAK-LGDRIEADAKVRIDGRTVSIKSE 65

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  +  +     + +        +       +  SR ++VGRLDINT GLLL T+D
Sbjct: 66  DDLVCRVIAYHKPEGEICSRKDPEGRPTVFDRLPKTRDSRWVAVGRLDINTSGLLLFTSD 125

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V    +  L+ G+ ++       ++     +G N 
Sbjct: 126 GELANRLMHPSHEVEREYAVRTFGEVTDACIQRLRSGVTLEDGPAHFDKIKPAGGEGMNK 185

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V L EG+NRE+++++E    +V+RLIRI YG   L  +L  G   E+  + +     
Sbjct: 186 WWHVSLAEGRNREVRRLWESQEVQVSRLIRIRYGMIDLPKSLPRGGWVELPIEQVNYLRK 245

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
              ++E    L      S    + +   I             + ++ 
Sbjct: 246 LAGMDEETRTLLGTDKHSVARAKVKSAKIRRAVRKHKTTAGKTPRQR 292


>gi|325205871|gb|ADZ01324.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M04-240196]
          Length = 349

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 71/256 (27%), Positives = 125/256 (48%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    + VNG   +     V   DH+
Sbjct: 84  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWITNGWITVNGKTAQ-LGDKVTPDDHV 142

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L +  ++++       
Sbjct: 203 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVE 262

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   
Sbjct: 263 RIREQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFY 322

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   +    +
Sbjct: 323 ELNPAEVANIIKWADM 338


>gi|257452584|ref|ZP_05617883.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           3_1_5R]
 gi|317059124|ref|ZP_07923609.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           3_1_5R]
 gi|313684800|gb|EFS21635.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           3_1_5R]
          Length = 235

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 62/229 (27%), Positives = 104/229 (45%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR+EV+ ++  ++++VNG+ +     N+    D +      L   E 
Sbjct: 1   MRIDKFLVECGVGSRKEVKELLKSRKIRVNGLFITSPKENIEEEKDEVYYGEKKLSYQEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+ K   +       +           I   +  VGRLD +TEGLLL TNDG L  
Sbjct: 61  RYYILHKKAGYVTALEDSREATVMDLLPEWVIKKDLAPVGRLDKDTEGLLLFTNDGKLNH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P +   + Y       + ++ L  L++G++I        +     +K  +  + + 
Sbjct: 121 RLLSPKSHVDKTYHASLECDITEEALEKLREGVMIGEYKTLPAKA----EKLEDRKIALT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +REGK  ++KK+ E    KV  L RIS+G   LG L  G  +EVS + +
Sbjct: 177 IREGKFHQVKKMLEAVGNKVIYLKRISFGKLVLGDLELGEVKEVSLEDI 225


>gi|77359062|ref|YP_338637.1| ribosomal RNA pseudouridylate synthase [Pseudoalteromonas
           haloplanktis TAC125]
 gi|76873973|emb|CAI85194.1| putative ribosomal RNA pseudouridylate synthase [Pseudoalteromonas
           haloplanktis TAC125]
          Length = 229

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 102/233 (43%), Gaps = 9/233 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T  R++K IA AG+ SR++  R+I +  V VN         +V   D I V+G  ++  
Sbjct: 2   STKIRLAKYIAHAGVCSRKQASRLIDEGAVIVNNRPANHID-HVDEQDQITVNGQIIKGT 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                + YHKP+G+               +     +RV  +GRLD ++ GLL+LTNDG L
Sbjct: 61  AELIYFAYHKPVGIDCK--LDQNDPASLYHHLPTITRVYPIGRLDKDSRGLLILTNDGEL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + Y V  +  +D +    +  G+ +              +K ++   +
Sbjct: 119 CNQLIHPDFHQPKRYLVSVNKSIDAEFCTKMAAGVPVDKQITLPCS----VEKIADKQFS 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKIL 241
           + L++G NR+I+K+  +  +KV  L R       L    L  G    ++K  +
Sbjct: 175 IILKQGLNRQIRKMAHYCGYKVIDLYREQISELTLQTLNLAQGQYIAINKSDI 227


>gi|89074204|ref|ZP_01160694.1| hypothetical 16S rRNA uridine-516 pseudouridylate synthase
           [Photobacterium sp. SKA34]
 gi|89049908|gb|EAR55442.1| hypothetical 16S rRNA uridine-516 pseudouridylate synthase
           [Photobacterium sp. SKA34]
          Length = 231

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 97/236 (41%), Gaps = 8/236 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +      +RRE  +++  + ++V+G ++  A+  V   + +E +G PL+     
Sbjct: 1   MRLDKFLGTTLGITRREASKLLRDKMIEVDGEIVRSASFAVSDDNDVEFNGRPLKLQGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      + +   D    +           ++   GRLD +T GL+L+T+DG  +  
Sbjct: 61  YFMLNKPEGFVCSH-VDDFNPTVFVLFDEVSPEKMHVAGRLDGDTTGLVLVTDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     + +D +   + G+ +  +       ++ +     S     +
Sbjct: 120 ITSPRHLCSKTYFVEAADPITEDYIKQFEAGVQLRSEKELTRPAKLEIL----SEREALL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
            + EGK  ++K++F     +V  L R   G  +L   L  G  R ++ + +   L 
Sbjct: 176 TISEGKYHQVKRMFAAMGNRVVGLHRERIGTVELDEDLAPGEYRLLTAEEIASFLK 231


>gi|194289952|ref|YP_002005859.1| ribosomal large subunit pseudouridine synthase b [Cupriavidus
           taiwanensis LMG 19424]
 gi|193223787|emb|CAQ69794.1| Ribosomal large subunit pseudouridine synthase B [Cupriavidus
           taiwanensis LMG 19424]
          Length = 613

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 73/320 (22%), Positives = 127/320 (39%), Gaps = 6/320 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +       ++ KV+A  G+ SRRE+E +I Q RV VNG+        ++  D + V+G  
Sbjct: 212 LSAEDDAPKLHKVLAEGGLGSRREMEELILQGRVSVNGLPA-HIGQRILPADQVRVNGKL 270

Query: 67  LRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           + +         L  +     +V+        +   +       + ++VGRLD NTEGLL
Sbjct: 271 IHRKVSTKPPRVLLYHKPAGEIVSQSDPEGRPTVFDNLPRIKTGKWVAVGRLDFNTEGLL 330

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + T  G +A     P     R Y VR  G++ +     L  GI +       +++     
Sbjct: 331 IFTTSGDIANRFMHPRYGVEREYAVRTLGELAEADRQRLLHGIKLDDGEANFLRIADGGG 390

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           +G N W  V L EG+NRE++++FE     V+RLIR  YG F L   L  G  +EV    +
Sbjct: 391 EGVNHWYHVALTEGRNREVRRMFEAVGLTVSRLIRTRYGQFLLPRGLKRGRWQEVEPNDV 450

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +  +    L+       AP  +++   R +    +              +      +   
Sbjct: 451 KALMTSVGLKVPGKGEQAPKGATKVGGRKQRTEAAIAGMPMHTGMDGLPRFEQGGARGGG 510

Query: 302 ATPVHRRNLASNVWMAKGIH 321
                   + +++       
Sbjct: 511 GRSSQPDPMKTSMGYISHGP 530


>gi|239815173|ref|YP_002944083.1| pseudouridine synthase [Variovorax paradoxus S110]
 gi|239801750|gb|ACS18817.1| pseudouridine synthase [Variovorax paradoxus S110]
          Length = 604

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 73/308 (23%), Positives = 126/308 (40%), Gaps = 6/308 (1%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++       ++ KV+A+AG+ SR E+E +I Q R+ VN          +   D ++++
Sbjct: 188 KRVLLPEADSPKLHKVLAQAGLGSRLEMEALILQGRISVNNEPA-HIGQRIQYGDQVKIN 246

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+R          +  +     +VT     +  +           +  SVGRLD+NTE
Sbjct: 247 GKPIRYRIAPPPPRVIAYHKPVGEVVTHDDPQNRPTVFRKLPRLQQGKWQSVGRLDLNTE 306

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL ++ G LA  L  P     R Y VR  G ++ ++   L +G+ +         +  
Sbjct: 307 GLLLFSSSGDLANQLMHPRFGLEREYAVRVLGALNAEEKKKLLEGVRLDDGMAQFGTIEE 366

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +GSN W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E+ +
Sbjct: 367 GGGEGSNHWYRVTISEGRNREVRRLFESVGHAVSRLIRIRYGAMVLPRGLKRGAWMELDE 426

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           + +            +          E     R     +   +          ++     
Sbjct: 427 RDISALFQASGGGAPRPPQQQRGPGQEGAGGGRNGRNKKRRGNRNAGGGQQQPRDMRDDG 486

Query: 299 KKLATPVH 306
           ++   P  
Sbjct: 487 REAPIPNP 494


>gi|134094557|ref|YP_001099632.1| putative pseudouridylate synthase [Herminiimonas arsenicoxydans]
 gi|133738460|emb|CAL61505.1| putative ribosomal large subunit pseudouridine synthase
           [Herminiimonas arsenicoxydans]
          Length = 248

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 61/249 (24%), Positives = 106/249 (42%), Gaps = 23/249 (9%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------- 63
             P R+SK ++  G+ SRRE +  IA+  V+V+G ++      ++ T  + V+       
Sbjct: 2   TEPLRLSKRMSELGLCSRREADEWIARGWVRVDGKVVSELGTKILPTQRVTVERQAAAEQ 61

Query: 64  --------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                     P+          Y   + LV   S     ++     P+    ++  GRLD
Sbjct: 62  SKRVTILINKPMGYVSGQAEDGYKPAVALVKAESRWKEDTSPTQFHPTQLRSLVPAGRLD 121

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL----NLLKKGIVIQGIC 171
           I++ GLL+LT DG +A+ L   ++   + Y VR                L  G+++ G  
Sbjct: 122 IDSVGLLVLTQDGRIAKHLIGENSSVEKEYLVRVQYIKPGKLPEADLQRLNHGLMLDGKK 181

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
               QV    +      ++  LREGK R+I+++ +    KV  L R+  G  +LG L  G
Sbjct: 182 LLPAQVKWQNEDQ----LSFILREGKKRQIRRMCDIVGLKVVGLKRVRIGRVKLGDLPVG 237

Query: 232 STREVSKKI 240
             R +++  
Sbjct: 238 EWRYLAEGE 246


>gi|315170843|gb|EFU14860.1| conserved hypothetical protein [Enterococcus faecalis TX1342]
          Length = 320

 Score =  156 bits (395), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 68/261 (26%), Positives = 116/261 (44%), Gaps = 3/261 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE 71
             R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +    
Sbjct: 60  TMRLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLISHKT 119

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                L      +                       +  VGRLD +TEGLLLLT++G L 
Sbjct: 120 HVYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQLG 179

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVT 190
             L  P+ +  + Y V+ +G V  +     K GIV+QG       ++T+     + + V 
Sbjct: 180 YQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHVF 239

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHL 249
           + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L    
Sbjct: 240 LTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYFF 299

Query: 250 LEEAQVNLDAPIYSSETLVRD 270
           +E+ Q +   P        R 
Sbjct: 300 IEKQQTSKALPSNLKREEERK 320


>gi|169634122|ref|YP_001707858.1| putative ribosomal large subunit pseudouridine synthase B
           (pseudouridylate synthase) (Uracil hydrolyase)
           [Acinetobacter baumannii SDF]
 gi|169796999|ref|YP_001714792.1| putative ribosomal large subunit pseudouridine synthase B
           (pseudouridylate synthase) (Uracil hydrolyase)
           [Acinetobacter baumannii AYE]
 gi|213156596|ref|YP_002318257.1| ribosomal large subunit pseudouridine synthase B [Acinetobacter
           baumannii AB0057]
 gi|215484461|ref|YP_002326694.1| Ribosomal large subunit pseudouridine synthase B [Acinetobacter
           baumannii AB307-0294]
 gi|239501231|ref|ZP_04660541.1| Ribosomal large subunit pseudouridine synthase B [Acinetobacter
           baumannii AB900]
 gi|301347312|ref|ZP_07228053.1| Ribosomal large subunit pseudouridine synthase B [Acinetobacter
           baumannii AB056]
 gi|301510844|ref|ZP_07236081.1| Ribosomal large subunit pseudouridine synthase B [Acinetobacter
           baumannii AB058]
 gi|301594338|ref|ZP_07239346.1| Ribosomal large subunit pseudouridine synthase B [Acinetobacter
           baumannii AB059]
 gi|332852087|ref|ZP_08433914.1| pseudouridine synthase B, ribosomal large subunit [Acinetobacter
           baumannii 6013150]
 gi|332867485|ref|ZP_08437638.1| pseudouridine synthase B, ribosomal large subunit [Acinetobacter
           baumannii 6013113]
 gi|169149926|emb|CAM87820.1| putative ribosomal large subunit pseudouridine synthase B
           (Pseudouridylate synthase) (Uracil hydrolyase)
           [Acinetobacter baumannii AYE]
 gi|169152914|emb|CAP01955.1| putative ribosomal large subunit pseudouridine synthase B
           (Pseudouridylate synthase) (Uracil hydrolyase)
           [Acinetobacter baumannii]
 gi|193076586|gb|ABO11248.2| putative ribosomal large subunit pseudouridine synthase B
           [Acinetobacter baumannii ATCC 17978]
 gi|213055756|gb|ACJ40658.1| ribosomal large subunit pseudouridine synthase B [Acinetobacter
           baumannii AB0057]
 gi|213987354|gb|ACJ57653.1| Ribosomal large subunit pseudouridine synthase B [Acinetobacter
           baumannii AB307-0294]
 gi|332729459|gb|EGJ60798.1| pseudouridine synthase B, ribosomal large subunit [Acinetobacter
           baumannii 6013150]
 gi|332733902|gb|EGJ65047.1| pseudouridine synthase B, ribosomal large subunit [Acinetobacter
           baumannii 6013113]
          Length = 307

 Score =  156 bits (395), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 82/309 (26%), Positives = 131/309 (42%), Gaps = 13/309 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
            +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG  ++    
Sbjct: 2   SEKLQKVLARIGLGSRRYMEEVIAAGRVSVNGRVAQV-GERIEPGDELRIDGRKVQFQIE 60

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R  L  Y     + + +      +           R + VGRLDIN+ GLLL TND
Sbjct: 61  DEIRRRVLIYYKPEGEICSRNDPEKRPTVFDHLPQIANDRWVMVGRLDINSTGLLLFTND 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V       +  G+ ++         +    +G N 
Sbjct: 121 GELANRLMHPSNEIEREYAVRVMGEVTPQLRQNMVNGVELEDGPAKFESFSEIGGEGINR 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V ++EG+NRE++++FE    KV+RL+R  YG   L   L  G   E+ K  +     
Sbjct: 181 WYQVVVKEGRNREVRRIFESQGLKVSRLLRTRYGTVILPRELRTGRWMELDKTDIDNL-- 238

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                ++             + + R   ++E P    R      Q+    K+    T   
Sbjct: 239 ----AKSVELKPRQGTGLFGMAKRRTERMTEKPMAARRGGYLRQQRRDDEKEAPANTGNQ 294

Query: 307 RRNLASNVW 315
           R++   N  
Sbjct: 295 RKSTGFNRG 303


>gi|317060087|ref|ZP_07924572.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           D12]
 gi|313685763|gb|EFS22598.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           D12]
          Length = 229

 Score =  156 bits (395), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 59/226 (26%), Positives = 106/226 (46%), Gaps = 5/226 (2%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRL 75
            K +   G+ SR+EV+ ++ +++++VN  ++      +    D +  +   L   +    
Sbjct: 2   DKFLVECGLGSRKEVKELLKKRKIQVNASIVTSGQQIIDEEKDEVFYEKEKLVYKKFRYY 61

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            LY K   +       +           I   ++ VGRLD +TEGLLL TNDG L   L 
Sbjct: 62  ILYKKAGYVTALEDSKERTVMELLPEWVIRKDLVPVGRLDKDTEGLLLFTNDGKLNHQLL 121

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
            P +   + Y V     + ++ +  L++G+ I        QV    ++     +++ ++E
Sbjct: 122 SPKSHVDKTYHVCLEKIITEEAIEQLRQGVRIGDYTTLPAQVEQLEEQK----ISLTIQE 177

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           GK  ++KK+ E  + KV+ L R+S+G   LG L  G  REVS + +
Sbjct: 178 GKFHQVKKMLEAVDNKVSYLKRVSFGRLVLGDLKPGEVREVSLEDI 223


>gi|225076290|ref|ZP_03719489.1| hypothetical protein NEIFLAOT_01331 [Neisseria flavescens
           NRL30031/H210]
 gi|224952414|gb|EEG33623.1| hypothetical protein NEIFLAOT_01331 [Neisseria flavescens
           NRL30031/H210]
          Length = 247

 Score =  156 bits (395), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 106/250 (42%), Gaps = 20/250 (8%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           +   +F   R+SK +A+ G+ SRRE +  I Q  VKVNG         V   D I+++  
Sbjct: 1   MQNNDFETMRLSKRMAQLGLCSRREADSYIEQGWVKVNGQTA-VLGQKVTELDRIDLNKQ 59

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                          P+          Y     L+T ++  +   +           +  
Sbjct: 60  AHEKQAARVTIILNKPVGYVSAQAEKGYKSAAELITANNHWEDDDSRIPFSEKHKFGLAP 119

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++D   L LL  G+ + G 
Sbjct: 120 AGRLDIDSVGLLVLTQDGRIAKQLIGENSNSEKEYLVRVRGKLDDKGLALLNHGLSLDGE 179

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                +V    +      +   LR+GK R+I+++ E    +V  L RI  G  +LG L  
Sbjct: 180 KLRPAKVEWQNEDQ----LRFILRQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPP 235

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 236 GKWRYLRADE 245


>gi|254786469|ref|YP_003073898.1| ribosomal large subunit pseudouridine synthase B [Teredinibacter
           turnerae T7901]
 gi|237684905|gb|ACR12169.1| ribosomal large subunit pseudouridine synthase B [Teredinibacter
           turnerae T7901]
          Length = 285

 Score =  156 bits (395), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 81/280 (28%), Positives = 126/280 (45%), Gaps = 7/280 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +++ KV+ARAG+ SRRE+ER+I+  +V VNG         V + D IE DG  ++ 
Sbjct: 7   EPQGEKLQKVLARAGLGSRREMERLISLGKVSVNGATAR-LGDRVGAEDKIEYDGKRIQA 65

Query: 70  -----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                     +        + + +      +   +      SR ISVGRLD NT GLLL 
Sbjct: 66  APVVKQRTRVILYNKPEGQICSRNDPEGRPTVYDNLPKIAQSRWISVGRLDFNTSGLLLF 125

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG LA  L  PST   R Y VR  G+VD D L  L+ G++++        +    ++ 
Sbjct: 126 TNDGELANKLMHPSTGIDREYLVRIQGEVDNDMLQRLRDGVLLEDGIARFTDIVEGQKES 185

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            N W    + EG+NRE+++++E    +V+RL R+ YG   +   + AG   E+++K + E
Sbjct: 186 KNRWFYCVVMEGRNREVRRLWESQEVRVSRLKRVRYGNIFIPSHVRAGQWVELTEKDVGE 245

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
                 L        +P          R    +       
Sbjct: 246 LCDTAGLAPPPKPKYSPELRRSRERHQRKLRKANTSRTRR 285


>gi|72080505|ref|YP_287563.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           hyopneumoniae 7448]
          Length = 237

 Score =  156 bits (395), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 63/229 (27%), Positives = 110/229 (48%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K ++  G+ SRR+ E++I Q R+K+N    +     V   D IE+D   + K    
Sbjct: 1   MRINKFLSEMGVCSRRQSEKLILQGRIKINNETAK-IGQIVSQNDVIELDQQKITKKPPI 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +  +KP   +T+  DP+ R T+ +        +  VGRLD  T GL+L+TNDG     
Sbjct: 60  FWYALNKPKNYITSRFDPENRPTIMEFFSKN-EYLFPVGRLDFQTTGLILITNDGKTTNK 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  PS++  R Y V+    +   ++  L    +         +     +K S+    V +
Sbjct: 119 LLHPSSKIERTYLVKTDFSLSDKEIRFLNDNKIQLDSV----KSIQKIKKCSSRTYLVTV 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G N  IKK+F   N KV +L R+S+   +L  +  G  R+++ + ++
Sbjct: 175 WQGSNHHIKKLFLSINKKVLKLKRVSFANIKLNNISEGKYRKLTNQEIK 223


>gi|301301292|ref|ZP_07207445.1| putative 16S pseudouridylate 516 synthase [Lactobacillus salivarius
           ACS-116-V-Col5a]
 gi|300851107|gb|EFK78838.1| putative 16S pseudouridylate 516 synthase [Lactobacillus salivarius
           ACS-116-V-Col5a]
          Length = 238

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 57/234 (24%), Positives = 117/234 (50%), Gaps = 6/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +++ G  +R E +++I  +RV++NG +++   + +    D I +DG  L    +
Sbjct: 1   MRLDKFLSQTGKFTRAEAKKVIKAKRVRLNGEVVKDGKIKINEDSDKIFLDGELLALNNK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDN-LPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              ++ +KPIG+++   D   ++ +     P     +  VGRLD  T GLL++TNDG  A
Sbjct: 61  EVYYMLNKPIGVLSATRDDKDKTVIDLINFPGRKEDLFPVGRLDKETTGLLIITNDGKFA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLD--TQKGSNAW 188
             +  P     + Y     G++ + ++    +G+ +  G      Q+ +   ++K   + 
Sbjct: 121 HDIISPKKHVSKTYEAVVTGKISEKEVKTFSQGMELANGDKLQPAQLDIISYSEKDDTSK 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           V V + EGK  +++++F   + +V  L R+  G  +L   L  G  R+++++ L
Sbjct: 181 VRVIIHEGKYHQVRRMFGAVSQRVLELDRVKIGLLELDDTLERGEYRKLTEEEL 234


>gi|163750232|ref|ZP_02157474.1| putative RNA pseudouridylate synthase [Shewanella benthica KT99]
 gi|161330088|gb|EDQ01072.1| putative RNA pseudouridylate synthase [Shewanella benthica KT99]
          Length = 288

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 78/287 (27%), Positives = 129/287 (44%), Gaps = 7/287 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E  IA  R+ ++G +       + +   I +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRISIDGEIA-NLGDRIEADVKIRIDGRAISIKSA 60

Query: 73  TRLWL-----YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             L       +     + +        +       +  SR ++VGRLDINT GLLL T+D
Sbjct: 61  EDLICRVIAYHKPEGEICSRKDPEGRPTVFDRLPKTRDSRWVAVGRLDINTSGLLLFTSD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V    +  L+ G+ ++       +V     +G N 
Sbjct: 121 GELANRLMHPSNEVEREYAVRTFGEVTDACIQRLRTGVTLEDGPASFDKVKAAGGEGMNK 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V L EG+NRE+++++E    +V+RLIRI YG  +L  +L  G   E++ + +     
Sbjct: 181 WWHVSLAEGRNREVRRLWESQEVQVSRLIRIRYGKIELPKSLPRGGWVELTMEEVNYLRK 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
              L+E    +      S    + + + I         +     +K 
Sbjct: 241 TAGLKEETRTVLGTDKHSVARSKVKGSKIRRAVRKHKAVASKPGRKR 287


>gi|262202716|ref|YP_003273924.1| pseudouridine synthase [Gordonia bronchialis DSM 43247]
 gi|262086063|gb|ACY22031.1| pseudouridine synthase [Gordonia bronchialis DSM 43247]
          Length = 329

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 73/234 (31%), Positives = 117/234 (50%), Gaps = 4/234 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
              R+ KV+A+AG+ASRR  E MIA  RV+++G ++    + +      I VDG  +   
Sbjct: 87  DGVRLQKVLAQAGVASRRGAEEMIAAGRVEIDGEIVTEQGLRIDPDTAIIRVDGARVIID 146

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTND 127
           E  +    +KP G  +T +D  GR  V D +        R+  VGRLD +TEGLLLLTND
Sbjct: 147 ETRQYLALNKPRGWQSTMADDQGRPCVGDIVAERVMAGQRLFHVGRLDADTEGLLLLTND 206

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  + Y     G+V +    +L+ G+ +        ++T+       +
Sbjct: 207 GELAHRLMHPSYEVPKTYLATVRGEVPRSLSRMLRDGVELDDGPVAVDKLTIVDVHEGQS 266

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + + L EG+NR ++++ +   + V  L+R   G   LG    GS R + +  +
Sbjct: 267 LLRITLHEGRNRIVRRMMDEVGFPVVELVRTHVGSVALGEQRPGSLRVLGRDEV 320


>gi|282600611|ref|ZP_05979218.2| ribosomal small subunit pseudouridine synthase A [Subdoligranulum
           variabile DSM 15176]
 gi|282571938|gb|EFB77473.1| ribosomal small subunit pseudouridine synthase A [Subdoligranulum
           variabile DSM 15176]
          Length = 237

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 55/231 (23%), Positives = 87/231 (37%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--RKAE 71
            R+ K ++     +R E  + I + RV VNG++  +A   V     I VDG PL     +
Sbjct: 2   MRLDKYLSERTGLTRSESRKAITKGRVAVNGMVCRKADTQVAEDAAIAVDGTPLAGSYQK 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              + L      +  +    D               +   GRLD  + G +LLT+DG LA
Sbjct: 62  YVYIMLNKPEGVVSASRDKRDTTVVDLVAADFPRRALFPAGRLDKTSTGFVLLTDDGALA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y V     +          G+ +            +        V V
Sbjct: 122 HDLLSPAHHVDKQYLVTLDTPLTDAMRAGFAAGVTLADGETM-APAEAEPAGEDPCVVKV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            L +G   +IK++F  +   VN L R + G   L   L  G  RE++ + L
Sbjct: 181 TLHQGVYHQIKRMFGVYGAGVNALHRYAIGGVALDAALAPGQWRELTAEEL 231


>gi|78485572|ref|YP_391497.1| pseudouridine synthase, Rsu [Thiomicrospira crunogena XCL-2]
 gi|78363858|gb|ABB41823.1| ribosomal large subunit pseudouridine synthase B [Thiomicrospira
           crunogena XCL-2]
          Length = 317

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 86/302 (28%), Positives = 140/302 (46%), Gaps = 11/302 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV-----PL 67
            +++ K++AR G  SRREVE++I+Q  VKVNG +          TD ++V+        L
Sbjct: 17  GEKLQKILARGGFGSRREVEKLISQGLVKVNGKVAT-LGDRAFPTDTLKVNDQLVKETRL 75

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            K     +        + +   +    +        I SR ISVGRLDINT GLL+LTN+
Sbjct: 76  EKQPTQVILYNKPEGQVCSRKDEKGRETIFTSLPRIINSRWISVGRLDINTSGLLILTNN 135

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---QVTLDTQKG 184
           G LA  L  PS +  R Y VR  G+V  + L+ LKKG+ ++          ++    +  
Sbjct: 136 GELANRLMHPSYEMEREYSVRVFGEVSDEILDRLKKGVKLEDGFAKFESIGKIPQQEEDS 195

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            N W  V ++EG+NRE+++++E    +V+RL+R  YG F L   L  G +  ++ K + +
Sbjct: 196 INQWYRVVIKEGRNREVRRIWESQGVQVSRLVRTRYGQFSLPRNLRRGKSEPLTWKQINQ 255

Query: 244 QLGPHL-LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            L      EE + +L      ++ +         +        +K  + +   SK K   
Sbjct: 256 LLKSVDLPEEPRPDLRNNPAKAKKMAARHAEPFKKETGRVKYKEKGENHREEKSKPKSAR 315

Query: 303 TP 304
             
Sbjct: 316 RR 317


>gi|242239360|ref|YP_002987541.1| 23S rRNA pseudouridylate synthase B [Dickeya dadantii Ech703]
 gi|242131417|gb|ACS85719.1| pseudouridine synthase [Dickeya dadantii Ech703]
          Length = 289

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 86/286 (30%), Positives = 127/286 (44%), Gaps = 10/286 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN-VMSTDHIEVDGVPLRKAE 71
            +++ KV+AR+G  SRRE+E +I Q RV V+G +        V     I +DG  +   E
Sbjct: 2   SEKLQKVLARSGHGSRREIESIIQQGRVSVDGKIATLGDRVDVTRATKIRIDGHVVTVRE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T        +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  TEETVCRVLMYYKPEGELCTRSDPEGRPTVFDRLPRIQGARWIAVGRLDVNTSGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  G+V  DK+  L KG+ +         +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGEVGDDKIRQLSKGVQLDDGPAAFRSIRHQGGEGLN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI---LR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG  QL   L  G   E+S +    LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIQLPKGLPRGGWSEMSLEDVNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
           E +       +++ ++      +     R      +        K 
Sbjct: 242 ELVQLSPETVSKLPVERERRRLKANQIRRAVKRHSLVGARRNAPKR 287


>gi|332533576|ref|ZP_08409438.1| ribosomal large subunit pseudouridine synthase B [Pseudoalteromonas
           haloplanktis ANT/505]
 gi|332036978|gb|EGI73437.1| ribosomal large subunit pseudouridine synthase B [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 289

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 82/286 (28%), Positives = 133/286 (46%), Gaps = 10/286 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +++ KV+ARAG+ SRRE+E+ I   RV VNG + +     V  TD I VDG  ++  E
Sbjct: 4   QGEKLQKVLARAGVGSRREMEKYIDANRVSVNGKVAK-LGDRVEETDLIRVDGHTVKIEE 62

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   +        L T       R+           R I+VGRLD+NT GL+L TN
Sbjct: 63  KADRICRVIMYNKPEGELSTRKDPEGRRTVFDRLPRIDGDRWIAVGRLDVNTSGLMLFTN 122

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y  R  G+V  + +  L +G+ ++        VT    +G N
Sbjct: 123 DGELANRLMHPSYEVEREYSARVFGEVTNETVKNLLRGVELEDGPAKFTTVTPMGGEGVN 182

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREV---SKKILR 242
            W  V L EG+NRE++++++  + +V+RLIRI YG  +L   +  G   E    +   LR
Sbjct: 183 RWFNVTLNEGRNREVRRLWQSQDAEVSRLIRIRYGKLELDKRVPQGGWMEYDLETVNYLR 242

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
           + +      + ++++       +    ++     +  +   +  K 
Sbjct: 243 KTVKLGRETQTKLSVMPEKRKDKRAKINQIRKAVKKHNQRVKPTKR 288


>gi|257453996|ref|ZP_05619272.1| RNA pseudouridine synthase family protein [Enhydrobacter aerosaccus
           SK60]
 gi|257448661|gb|EEV23628.1| RNA pseudouridine synthase family protein [Enhydrobacter aerosaccus
           SK60]
          Length = 287

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 86/286 (30%), Positives = 130/286 (45%), Gaps = 7/286 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
             +++ K +AR G+ SRR++E +I + RV VNG +       V   D I VDG  LR   
Sbjct: 2   KDEKLQKALARLGLGSRRQMEDVIREGRVSVNGTVAT-IGDRVGQGDEIRVDGRLLRYTA 60

Query: 70  ---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                R  L  Y     + + H      +      P    R + VGRLDIN+ GLLL TN
Sbjct: 61  ENEKRRRILMYYKPEGEICSAHDPEGRPTVFERLPPLNHDRWVMVGRLDINSTGLLLFTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  G+V  + +  LK+G++++        +     +G N
Sbjct: 121 DGELAHRLMHPSNEIEREYAVRVMGEVTPEIMLNLKRGVMLEDGMAQFDDIVEKGGEGIN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
            W  V L+EG+NRE++++FE    KV+RL+RI YG   L   L  G   E+ ++ +    
Sbjct: 181 KWYQVKLKEGRNREVRRLFESQGLKVSRLLRIRYGSVSLPRELRTGRYLELDRREIDTLA 240

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           G   +   Q      I        ++  + +     + R  K    
Sbjct: 241 GLVNIRPRQGTGLYGIAKRRQERFEKKPLKARRGGHYLRRDKEKRS 286


>gi|157374830|ref|YP_001473430.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
 gi|157317204|gb|ABV36302.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
          Length = 288

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 75/290 (25%), Positives = 126/290 (43%), Gaps = 10/290 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E  IA  R+ ++G +       + +   I +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRISIDGEIA-SLGDRIEADAKIRIDGRAISIKSE 60

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  +  +     + +        +       +  SR ++VGRLDINT GLLL T+D
Sbjct: 61  EDIVCRVIAYHKPEGEICSRKDPEGRPTVFDRLPKTRDSRWVAVGRLDINTSGLLLFTSD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G V    +  L+ G+ ++       +V     +G N 
Sbjct: 121 GELANRLMHPSNEVEREYAVRTFGDVSDACIQHLRTGVTLEDGPANFDKVKAAGGEGMNK 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V L EG+NRE+++++E    +V+RLIRI YG  +L  +L  G   E+    L +   
Sbjct: 181 WWHVTLSEGRNREVRRLWESQEVQVSRLIRIRYGSIELPKSLPRGGWIEL---ELEQVNY 237

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
                   +     + + +  V       +++     + K    +     
Sbjct: 238 LRKTAGLDIENRTMLGTDKHSVARSKVKSAKIKRAVHKHKATGGKNTRQR 287


>gi|149184427|ref|ZP_01862745.1| hypothetical protein ED21_26953 [Erythrobacter sp. SD-21]
 gi|148831747|gb|EDL50180.1| hypothetical protein ED21_26953 [Erythrobacter sp. SD-21]
          Length = 255

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 114/248 (45%), Positives = 159/248 (64%), Gaps = 7/248 (2%)

Query: 7   VQENFTPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           + +N  P+   R++K++ARAG+ASRRE+ERMIA  RV ++G +L+  AV + S   + VD
Sbjct: 1   MSDNRLPEAGDRIAKLLARAGVASRREIERMIADGRVSLDGKVLDTPAVKLESLRGVTVD 60

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTE 119
           G P+ +AE TRL+ +HKP GL+T   DP GR T++  L +   +     + VGRLD NTE
Sbjct: 61  GKPVGEAEETRLFAFHKPSGLLTAERDPKGRPTIYAALRNALPKDAGRVMPVGRLDFNTE 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLLTNDG + R +ELPST   R YR R  G + Q +L+ L +GI I GI YG ++  L
Sbjct: 121 GLLLLTNDGEMKRAMELPSTGVPRTYRARAFGDITQQRLDDLIEGIAIDGIRYGQIEANL 180

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +   G N W+ + LREGKNRE+++V E F  +VNRL+RI YGPF LG L  G   E+ + 
Sbjct: 181 ERGSGRNRWIEMTLREGKNREVRRVLEHFGLEVNRLLRIGYGPFHLGDLPRGQAVELKQG 240

Query: 240 ILREQLGP 247
            ++     
Sbjct: 241 DVQAFKRE 248


>gi|325578258|ref|ZP_08148393.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           parainfluenzae ATCC 33392]
 gi|325159994|gb|EGC72123.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           parainfluenzae ATCC 33392]
          Length = 336

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 89/278 (32%), Positives = 132/278 (47%), Gaps = 10/278 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V+G +      ++V S   + +DG  
Sbjct: 49  QSTVEGEKLQKVLARAGQGSRREIEAMIADNRVSVDGKMATLGDRIDVHSGVKVRIDGRI 108

Query: 67  LRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +   +        L  Y     L T        +          +R I+VGRLDINT GL
Sbjct: 109 INLQQAQKEVCRVLMYYKPEGELCTRSDPEGRPTVFDRLPRLNGARWIAVGRLDINTSGL 168

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQVD   L  L++G+ ++       ++    
Sbjct: 169 LLFTTDGELANCLMHPSREVEREYSVRVFGQVDDAMLARLRRGVQLEDGPANFKEIKFAG 228

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 229 GIGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEMDLEN 288

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNII 275
              LRE +G     E ++++  P    ++    +    
Sbjct: 289 VNYLRELVGLPPETETKLDVTKPRRRPKSGQIRKAVKR 326


>gi|150376249|ref|YP_001312845.1| pseudouridine synthase [Sinorhizobium medicae WSM419]
 gi|150030796|gb|ABR62912.1| pseudouridine synthase [Sinorhizobium medicae WSM419]
          Length = 260

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 63/228 (27%), Positives = 110/228 (48%), Gaps = 1/228 (0%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTR 74
           +++ +++ G  +R + E++IA+ RV V G  +   A  V    D I VDG  +    +  
Sbjct: 25  LARALSKLGYCTRTQAEKLIAEGRVSVGGRRVTDLAHWVDIEADRIAVDGTVIAAQPKVY 84

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L      + T        +            +  VGRLD  +EGLLL TND  LA+ L
Sbjct: 85  LMLNKPRGLVTTRDDPEGRPTVFTCLETVDAPSLSPVGRLDKASEGLLLFTNDTVLAQRL 144

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P T   + Y V+  G + +     + +G+   G      +V L      N+W+ V L 
Sbjct: 145 LDPQTHLGKRYHVQVRGFLGEAMAARMVEGVTEGGELLRAARVALLRGGDRNSWIEVELT 204

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           EG+NR+I+++ +   ++  RL+R++ G  +LG L  G++R +++  +R
Sbjct: 205 EGRNRQIRRMLDALGFECLRLLRVAIGEVRLGDLPKGASRPLAEAEIR 252


>gi|295093348|emb|CBK82439.1| ribosomal large subunit pseudouridine synthase F [Coprococcus sp.
           ART55/1]
          Length = 234

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 62/220 (28%), Positives = 108/220 (49%), Gaps = 7/220 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K ++ AG+ SRR  +  I   +V +NG         VM  D +   G  +++ +
Sbjct: 3   DGIRLNKYLSEAGVCSRRAADTHIENGKVTINGETA-VMGQKVMPGDVVTFMGRKVQQKD 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RT +  Y+KPIGL  T S  D       +      R+  VGRLD +++GLLLLTNDG L+
Sbjct: 62  RTVILAYNKPIGLTCTASKAD--PDNIFDHIDYPIRLQYVGRLDKDSQGLLLLTNDGDLS 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             ++       + YRVR + ++ +D +  +  G+ I        +V    +K  +    +
Sbjct: 120 NAIQKSVNNHEKEYRVRVNREITEDFIRKMSDGVPILDTVTKKCKV----RKIDDRSFMI 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
            L +G NR+I+++ +   ++V  L R+     +LG +  G
Sbjct: 176 VLTQGLNRQIRRMCDALGYRVVNLKRVRVCNVKLGNMRPG 215


>gi|40063061|gb|AAR37917.1| RNA pseudouridylate synthase family protein [uncultured marine
           bacterium 560]
          Length = 244

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 85/245 (34%), Positives = 135/245 (55%), Gaps = 7/245 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---- 68
            +R+ K+IA AG  SRR  ER+I Q RV +N   ++      +  D + +DG  +     
Sbjct: 2   SERLQKLIANAGYGSRRWAERLIEQGRVSLNNHDVK-LGDKAVLNDKVRIDGKLIDLKRY 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
               T++ + +K  G + +  DP+GR +VFD LP      I +GRLD+N+ GLLL TN+G
Sbjct: 61  AKTETKVLILNKQAGFICSTKDPEGRKSVFDLLPENSRW-IMIGRLDLNSSGLLLFTNNG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS Q  R Y VR  G+V ++ +  L  G+ ++       +VT    +G+N W
Sbjct: 120 ELASKLMHPSAQIDREYAVRVLGKVKEEHIKKLTNGVELEDGFAKFHKVTQGGGEGANRW 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
             V +REG+ RE+++++EF ++KV+RLIRI +G   L   L +  +  +  K L+  L  
Sbjct: 180 YRVVIREGRKREVRRLWEFLDFKVSRLIRIRFGDICLPDKLRSNQSEYLKPKQLKTLLNS 239

Query: 248 HLLEE 252
             L++
Sbjct: 240 VNLKD 244


>gi|260555709|ref|ZP_05827929.1| ribosomal large subunit pseudouridine synthase B [Acinetobacter
           baumannii ATCC 19606]
 gi|260410620|gb|EEX03918.1| ribosomal large subunit pseudouridine synthase B [Acinetobacter
           baumannii ATCC 19606]
          Length = 307

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 82/309 (26%), Positives = 131/309 (42%), Gaps = 13/309 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
            +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG  ++    
Sbjct: 2   SEKLQKVLARIGLGSRRYMEEVIAAGRVSVNGRVAQV-GERIEPGDELRIDGRKVQFQIE 60

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R  L  Y     + + +      +           R + VGRLDIN+ GLLL TND
Sbjct: 61  DEIRRRVLIYYKPEGEICSRNDPEKRPTVFDHLPQIANDRWVMVGRLDINSTGLLLFTND 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V       +  G+ ++         +    +G N 
Sbjct: 121 GELANRLMHPSNEIEREYAVRVMGEVTPQLRQNMVNGVELEDGPAKFESFSEIGGEGINR 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V ++EG+NRE++++FE    KV+RL+R  YG   L   L  G   E+ K  +     
Sbjct: 181 WYQVVVKEGRNREVRRIFESQGLKVSRLLRTRYGTVILPRELRTGRWMELDKTDIDNL-- 238

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                ++             + + R   ++E P    R      Q+    K+    T   
Sbjct: 239 ----AKSVELKPRQGTGLFGMAKRRTERMTEKPMAARRGGYLRQQRRDDEKEAPANTSNQ 294

Query: 307 RRNLASNVW 315
           R++   N  
Sbjct: 295 RKSTGFNRG 303


>gi|171463770|ref|YP_001797883.1| pseudouridine synthase [Polynucleobacter necessarius subsp.
           necessarius STIR1]
 gi|171193308|gb|ACB44269.1| pseudouridine synthase [Polynucleobacter necessarius subsp.
           necessarius STIR1]
          Length = 417

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 83/279 (29%), Positives = 128/279 (45%), Gaps = 6/279 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP-- 66
           ++    ++ KV+A  G+ SRR++E +I Q RV VNG+       ++  TD + ++G P  
Sbjct: 24  DDEDTMKLHKVLADVGMGSRRDMEDLIIQGRVSVNGLPA-HIGQSIGPTDQVRINGKPVH 82

Query: 67  --LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             ++      +  +     +V+        +           R I+VGRLD NTEGLLL 
Sbjct: 83  RKIQTKPPRVIMYHKPAGEIVSQSDPEGRPTVFDRLPKPRQGRWIAVGRLDFNTEGLLLF 142

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T  G LA  L  P     R Y VR  G + Q+   LLK GI +       +++ +   +G
Sbjct: 143 TTSGELANRLMHPRYGVEREYAVRILGDLSQENTVLLKSGITLDDGQAKFLRLAIGGGEG 202

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           +N W  V L EG+NRE++++FE     V+RLIR  YG F L   L  G   E+    +  
Sbjct: 203 ANRWYHVALSEGRNREVRRMFEAVGHTVSRLIRTRYGIFLLPPRLRRGKWEEIEAGDIYN 262

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDF 282
            +    L+  Q        +S +  RDR  I  +   D 
Sbjct: 263 LMKSAGLKMPQPQDKGRNPNSNSNGRDRRPIGEDFQPDP 301


>gi|94499317|ref|ZP_01305855.1| hypothetical protein RED65_11024 [Oceanobacter sp. RED65]
 gi|94428949|gb|EAT13921.1| hypothetical protein RED65_11024 [Oceanobacter sp. RED65]
          Length = 290

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 81/287 (28%), Positives = 131/287 (45%), Gaps = 9/287 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
            +++ K++A+AG+ SRRE+ER I Q RV++NG   +       + D I+VDG  +     
Sbjct: 2   SEKLQKILAQAGLGSRREMERWIEQGRVELNGSPAK-LGERAEAKDQIKVDGKVIEHGQR 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             R  L        + T H      +           R I+VGRLDINT GLLL T DG 
Sbjct: 61  KARRVLAYNKPEGEVCTRHDPEGRPTVFDRLPKLHGERWIAVGRLDINTSGLLLFTTDGE 120

Query: 130 LARVLELPSTQW-LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           LA  L  PST    R Y VR  G+V  + +  + +G++++        V      G N W
Sbjct: 121 LANKLMHPSTNTVDREYAVRVAGEVTDEAVKAMTEGVLLEDGMAKFTDVQYFDGDGFNQW 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK---KILREQ 244
             V + EG+NRE+++++E   +KV+RL R+ YG   L   + AG   E+++     L   
Sbjct: 181 YHVCIMEGRNREVRRLWESQGFKVSRLKRVRYGCVFLPKRVSAGKWTELNQADTDELSAL 240

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           +       A+++            R R    +    +  +    +++
Sbjct: 241 VDLPSKPVAKLDPQEMKRYEREFRRQRTRQKAGDQPNKPKGPSRNAR 287


>gi|295696969|ref|YP_003590207.1| pseudouridine synthase [Bacillus tusciae DSM 2912]
 gi|295412571|gb|ADG07063.1| pseudouridine synthase [Bacillus tusciae DSM 2912]
          Length = 250

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 57/245 (23%), Positives = 103/245 (42%), Gaps = 4/245 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAER 72
           QR+ +++A  G+ SRR++++M     ++V+G ++  A+++V     +  V G P+     
Sbjct: 4   QRLDRILAEMGVGSRRDIKKMARSGLIEVDGRVVRDASLHVDPGQQVLCVAGHPVHYQPF 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +   P  +               +      R+   GRLDI+TEG +L+T+DG LA 
Sbjct: 64  HYWMMNKPPGVVSAVIDPRHRTVIDLLDESDRTPRLFPAGRLDIDTEGFVLITDDGQLAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +  P     + YR    G+V    +    +G+V+  G       + +    G  + V +
Sbjct: 124 AILSPKRHVSKTYRATVQGRVSDADVAAFARGLVLGDGYRALPAHLQI-RDAGERSEVEI 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLL 250
            LREGK  +IK++F      V  L R++ G   L   L  G  R ++   +         
Sbjct: 183 VLREGKFHQIKRMFAALGKPVLYLKRVAIGGVPLDPALPPGGYRALADDEVARLRETDPR 242

Query: 251 EEAQV 255
                
Sbjct: 243 LPPHP 247


>gi|291617615|ref|YP_003520357.1| RluB [Pantoea ananatis LMG 20103]
 gi|291152645|gb|ADD77229.1| RluB [Pantoea ananatis LMG 20103]
          Length = 294

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 89/296 (30%), Positives = 132/296 (44%), Gaps = 10/296 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E MIA  RV V+G L         S    I +DG  +  AE
Sbjct: 2   SEKLQKVLARAGHGSRREIEAMIAAGRVSVDGKLATLGDRIENSKALKIRIDGHLVSIAE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T        +          SR I+VGRLD+NT GL+L T 
Sbjct: 62  SATEVCRVLAYYKPEGELCTRSDPEGRPTVFDRLPRLRGSRWIAVGRLDVNTCGLMLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD DK+  L KG+ ++        +     KG  
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDDKIRQLSKGVQLEDGPAAFKTLRFAGGKGLT 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
           + +T+ L EG+NRE+++++E    +V+RL+R+ YG   L   +  G   E+    L    
Sbjct: 182 SGITLTLTEGRNREVRRLWEAVGVQVSRLMRVRYGDITLPKGVPRGGWMELD---LPAVN 238

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
               +          +   +   R + N I       ++     +++N  SK+   
Sbjct: 239 YLRNMVGMDDETVTKLAVEKDRRRTKANQIRRAVKRHSQTSGRPARRNPGSKRNAT 294


>gi|256788622|ref|ZP_05527053.1| pseudouridine synthase [Streptomyces lividans TK24]
 gi|289772517|ref|ZP_06531895.1| pseudouridine synthase [Streptomyces lividans TK24]
 gi|289702716|gb|EFD70145.1| pseudouridine synthase [Streptomyces lividans TK24]
          Length = 371

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 108/233 (46%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
               +R+ KV+ARAG  SRR  E +I Q RV++NG ++      V    D ++VDG+ + 
Sbjct: 131 EQEGERLQKVLARAGYGSRRACEELIEQARVEINGEIVLEQGRRVDPEKDEVKVDGLTVA 190

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   L      + T       +  + D + +  +R+  VGRLD  TEG++LLTN G
Sbjct: 191 TQSYQFFSLNKPAGVVSTMEDPEGRQ-CLGDYVTNRETRLFHVGRLDTETEGVILLTNHG 249

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     + Y     G + +D    LK GI ++          +  Q G N  
Sbjct: 250 ELAHRLTHPRYGVKKTYLAHIVGPIPRDLGKRLKDGIQLEDGYARADHFRVVEQTGKNYL 309

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L EG+   ++++     + V+ L+R ++GP  LG   +G  R +S   +
Sbjct: 310 VEVTLHEGRKHIVRRMLAEAGFPVDNLVRTAFGPITLGDQKSGWLRRLSNTEV 362


>gi|323341451|ref|ZP_08081692.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           ruminis ATCC 25644]
 gi|323091062|gb|EFZ33693.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           ruminis ATCC 25644]
          Length = 240

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 57/235 (24%), Positives = 98/235 (41%), Gaps = 5/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A     +R EV+ ++  +RV VNG+        +   +D + +D   L     
Sbjct: 1   MRLDKFLAECNQGTRSEVKVLLKSKRVTVNGVTENSGKRQINEVSDVVCLDEKKLTYQSF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T            +       +  VGRLD +T GL+LLTNDG LA 
Sbjct: 61  AYYMLNKPKDVITATEDSVQKTVLDLIDKKDRIKGLFPVGRLDKDTTGLVLLTNDGALAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTL--DTQKGSNAWV 189
            L  P     +VY  +  G V + ++ L  K I ++ G      ++ +    +    + +
Sbjct: 121 NLLAPKKHVEKVYEAKIEGIVTEAEVELFSKPIELKNGEVTKPSRLVVKKADEDAGMSEI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
            + + EGK  +IK++F      V  L R+  G  +L   L  G  R +++  + E
Sbjct: 181 EITISEGKYHQIKRMFASTGMHVLELKRLKMGSLELDDRLDPGKYRALTQTEIEE 235


>gi|198283587|ref|YP_002219908.1| RNA-binding S4 domain-containing protein [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218666928|ref|YP_002426211.1| ribosomal large subunit pseudouridine synthase B [Acidithiobacillus
           ferrooxidans ATCC 23270]
 gi|198248108|gb|ACH83701.1| RNA-binding S4 domain protein [Acidithiobacillus ferrooxidans ATCC
           53993]
 gi|218519141|gb|ACK79727.1| ribosomal large subunit pseudouridine synthase B [Acidithiobacillus
           ferrooxidans ATCC 23270]
          Length = 292

 Score =  156 bits (394), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 87/287 (30%), Positives = 125/287 (43%), Gaps = 7/287 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
           +++ KV+AR G+ SRR +E  IA  RV VNG + +     V + D I VDG  LR     
Sbjct: 3   EKLQKVLARFGLGSRRLMEEWIAAGRVVVNGQIAK-LGDRVTAQDKIAVDGETLRIPSWV 61

Query: 71  --ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 L  +     L T +      +          SR I+VGRLD NTEGLLLLTNDG
Sbjct: 62  RPRLRVLRYHKPAGELTTRNDPAGRPTVFDRLPRLRGSRWIAVGRLDYNTEGLLLLTNDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     R Y VR  G+V  ++   L +G+V++      + +     +G+N W
Sbjct: 122 DLANALMHPRAGIEREYAVRVLGEVSPEQQVRLLQGVVLEDGEAHFVTLQEAGGEGANRW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGP 247
             V L EG+NRE++++FE     V+RLIR+ YG  ++   L  G   E+  +     L  
Sbjct: 182 YHVTLAEGRNREVRRLFEAVGLTVSRLIRVRYGVVEMPRLLKTGYFDELPDEERDALLAS 241

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
                        +      + D     S      T  +    Q   
Sbjct: 242 VQWVNPATPPSDSVERVTAPLPDARKNNSRREARQTPSRGRPGQGRR 288


>gi|291043642|ref|ZP_06569358.1| pseudouridine synthase [Neisseria gonorrhoeae DGI2]
 gi|291012105|gb|EFE04094.1| pseudouridine synthase [Neisseria gonorrhoeae DGI2]
          Length = 399

 Score =  156 bits (394), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 72/256 (28%), Positives = 125/256 (48%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+
Sbjct: 134 LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHV 192

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 193 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 252

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++  L +  ++++       
Sbjct: 253 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTTEQMRSLTEEGVMLEDGLAKVE 312

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  + ++EG+NRE++++FE     V+RL+R+++GP  L   L  G   
Sbjct: 313 RIREQGGEGANKWYNIVIKEGRNREVRRIFESQGLTVSRLVRVAFGPIGLPNRLKRGQFY 372

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   L    +
Sbjct: 373 ELNPAEVANILKWADM 388


>gi|254672187|emb|CBA05055.1| pseudouridylate synthase [Neisseria meningitidis alpha275]
 gi|325127918|gb|EGC50821.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           meningitidis N1568]
          Length = 252

 Score =  156 bits (394), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 68/255 (26%), Positives = 108/255 (42%), Gaps = 20/255 (7%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K          R+SK +A+ G+ SRRE +  I Q  V VNG         V   D I
Sbjct: 1   MNPKTPPDHTEDAVRLSKRMAQLGLCSRREADGYIEQGWVTVNGKTA-VLGQKVSPADRI 59

Query: 61  EVD---------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           E++                 P+          Y     L+T+ +  +  ++     P   
Sbjct: 60  ELNKKAHEQQAARITILLNKPVGYVSAQAEKGYKSAAELITSENRWESDTSRIRFDPKHK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             +   GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+
Sbjct: 120 IGLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGL 179

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G      QV    +      +   L++GK R+I+++ E    +V  L RI  G  +L
Sbjct: 180 SLDGEKLRPAQVEWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>gi|238899278|ref|YP_002924961.1| pseudouridine synthase (makes pseudouridine2605 in 23 S RNA)
           [Candidatus Hamiltonella defensa 5AT (Acyrthosiphon
           pisum)]
 gi|229467039|gb|ACQ68813.1| pseudouridine synthase (makes pseudouridine2605 in 23 S RNA)
           [Candidatus Hamiltonella defensa 5AT (Acyrthosiphon
           pisum)]
          Length = 288

 Score =  156 bits (394), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 87/287 (30%), Positives = 128/287 (44%), Gaps = 12/287 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM--STDHIEVDGVPLRKA 70
            +++ K++AR+G  SRRE+E  I +  V VNG +       V    +  I +DG  L   
Sbjct: 2   SEKLQKILARSGYGSRREIEEKIQRGLVSVNGKI-STLGDRVSVMPSTQIRLDGRILPIT 60

Query: 71  ERT-----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E        L  Y     + T        +          SR I +GRLDINT GLLL T
Sbjct: 61  EPQKIPCRVLAYYKIEGEICTRKDPKGRPTVFDRLPKLHHSRWIGIGRLDINTSGLLLFT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y  R  GQV++  +  L +GI ++       +VT    +G 
Sbjct: 121 TDGELAHRLMHPSQEIEREYASRIFGQVNEPSIKQLTQGIQLEDGMAAFRRVTFGGGEGL 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV---SKKIL 241
           N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G  +E+   +   L
Sbjct: 181 NHWYNVILTEGRNREVRRLWEAIGVQVSRLIRIRYGDIKLPKGLPRGGWKEMDISTIHYL 240

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
           RE +G        + ++          + R  +   V       KK 
Sbjct: 241 RELVGLKKDITNTLLIEKKEQRFFKPRQIRRAVKRHVMSSTRSFKKK 287


>gi|184157088|ref|YP_001845427.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           baumannii ACICU]
 gi|332872664|ref|ZP_08440632.1| pseudouridine synthase B, ribosomal large subunit [Acinetobacter
           baumannii 6014059]
 gi|183208682|gb|ACC56080.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           baumannii ACICU]
 gi|322506987|gb|ADX02441.1| Pseudouridine synthase [Acinetobacter baumannii 1656-2]
 gi|323516854|gb|ADX91235.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           baumannii TCDC-AB0715]
 gi|332739193|gb|EGJ70052.1| pseudouridine synthase B, ribosomal large subunit [Acinetobacter
           baumannii 6014059]
          Length = 307

 Score =  156 bits (394), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 82/309 (26%), Positives = 131/309 (42%), Gaps = 13/309 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
            +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG  ++    
Sbjct: 2   SEKLQKVLARIGLGSRRYMEEVIAAGRVSVNGRIAQV-GERIEPGDELRIDGRKVQFQIE 60

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R  L  Y     + + +      +           R + VGRLDIN+ GLLL TND
Sbjct: 61  DEIRRRVLIYYKPEGEICSRNDPEKRPTVFDHLPQIANDRWVMVGRLDINSTGLLLFTND 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V       +  G+ ++         +    +G N 
Sbjct: 121 GELANRLMHPSNEIEREYAVRVMGEVTPQLRQNMVNGVELEDGPAKFESFSEIGGEGINR 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V ++EG+NRE++++FE    KV+RL+R  YG   L   L  G   E+ K  +     
Sbjct: 181 WYQVVVKEGRNREVRRIFESQGLKVSRLLRTRYGTVILPRELRTGRWMELDKTDIDNL-- 238

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                ++             + + R   ++E P    R      Q+    K+    T   
Sbjct: 239 ----AKSVELKPRQGTGLFGMAKRRTERMTEKPMAARRGGYLRQQRRDDEKEAPANTGNQ 294

Query: 307 RRNLASNVW 315
           R++   N  
Sbjct: 295 RKSTGFNRG 303


>gi|225620831|ref|YP_002722089.1| pseudouridine synthase [Brachyspira hyodysenteriae WA1]
 gi|225215651|gb|ACN84385.1| pseudouridine synthase [Brachyspira hyodysenteriae WA1]
          Length = 359

 Score =  156 bits (394), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 82/332 (24%), Positives = 151/332 (45%), Gaps = 6/332 (1%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           Q+N    R+ KVI  +G ASRR  E+ I   RV+VN  ++   A  V   D + +D   +
Sbjct: 4   QQNEEAVRLVKVILESGFASRRNCEKAIMSGRVRVNNQVILDPAYRVKEDDSVSIDRELI 63

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++  +  + LY     +V+T     GR  + +    I  R+   GRLD  + G++++TND
Sbjct: 64  KRQTKRYMALYKPIG-VVSTTKYLPGRRIITEFFKGIKERLFYAGRLDSESRGIMIITND 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G  A ++  PS + L+VY V  +G++D + L    KGI I+ + Y   +  + ++    +
Sbjct: 123 GEFANIITHPSYEILKVYDVTVNGKIDSEALLNASKGITIKNVSYSPFKFKILSKGRIQS 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-----GTLLAGSTREVSKKILR 242
            + + + EGKNREI+K+F+   +KV  L RIS G         GTL AG  R+++KK + 
Sbjct: 183 KIRLTINEGKNREIRKIFDHLGYKVIDLERISVGCVSKYDEVSGTLEAGHIRDLTKKEID 242

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
                   +   +         +    +  + I    ++     K    ++  +K K   
Sbjct: 243 FFFKQKDKKLKDIESIFENIPDDIEDENYEDSILNSSNNDKEENKKVHDRSKWAKAKHKK 302

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREEN 334
             +  +  ++     +   S       ++++ 
Sbjct: 303 KRLITKKSSTFKGKMQKKSSKSEFSENRKDKK 334


>gi|88859932|ref|ZP_01134571.1| pseudouridine synthase [Pseudoalteromonas tunicata D2]
 gi|88817926|gb|EAR27742.1| pseudouridine synthase [Pseudoalteromonas tunicata D2]
          Length = 293

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 83/293 (28%), Positives = 131/293 (44%), Gaps = 10/293 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E+ I   RV V+G +       V     I +DG  ++  E 
Sbjct: 2   SEKLQKVLARAGKGSRREIEKFIEAHRVSVDGNVAR-LGDRVEPHQLIRLDGHIVKIEEP 60

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  +     L T        +     +     R I+VGRLD+NT GLLL TND
Sbjct: 61  EERVCRVLMYHKPEGELCTRKDPEGRPTVFDRLMRLDDDRWIAVGRLDVNTSGLLLFTND 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P  +  R Y VR  G+V  + L  L KG+ ++      +++     +G N 
Sbjct: 121 GELANRLMHPRYEVEREYAVRVFGEVTTETLKTLTKGVELEDGPAKFLKIMPHGGEGINK 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK---ILRE 243
           W  V L EG+NRE++++++    +V+RLIR+ YG  +L   L  G   E+       LR+
Sbjct: 181 WYNVLLTEGRNREVRRLWQSQGVEVSRLIRVRYGDLELNKRLPQGGWEELELDKVNYLRK 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            +G     E ++++       +     +           T  KK   +    +
Sbjct: 241 LVGLDRELETKLSVIPEKRKDKRAKIAQIRKAVNKHKQRTTGKKTDPKAKKRT 293


>gi|227818294|ref|YP_002822265.1| ribosomal pseudouridine synthase B [Sinorhizobium fredii NGR234]
 gi|227337293|gb|ACP21512.1| putative ribosomal pseudouridine synthase B [Sinorhizobium fredii
           NGR234]
          Length = 263

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 66/228 (28%), Positives = 111/228 (48%), Gaps = 1/228 (0%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTR 74
           +++ +++ G  SR + ER+IA+ RV V G      ++ +    D I VDG P+    R  
Sbjct: 28  LARALSKLGYCSRTQAERLIAEGRVSVGGRKTTDLSLWIDIDRDRITVDGTPVAAEARIY 87

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L      + T        +            +  VGRLD  +EGLLL TND  LA+ L
Sbjct: 88  LMLNKPRGLVTTRDDPEGRPTVFDCLGKVDARFMSPVGRLDKASEGLLLFTNDTVLAQRL 147

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P+T   + Y V+  G  D+     +  G+   G     + V        N+W+ V L+
Sbjct: 148 LDPATHLGKTYHVQVRGLFDEAAARAMMDGVSEGGEMLKAIDVRRLRSGDKNSWIEVELQ 207

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           EG+NR+I+++ +   ++  RL+R+S G  +LG L  G++R +S+  ++
Sbjct: 208 EGRNRQIRRMLDALGFECLRLVRVSIGEIRLGDLPKGASRPLSEAEVQ 255


>gi|187923621|ref|YP_001895263.1| pseudouridine synthase [Burkholderia phytofirmans PsJN]
 gi|187714815|gb|ACD16039.1| pseudouridine synthase [Burkholderia phytofirmans PsJN]
          Length = 626

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 75/301 (24%), Positives = 130/301 (43%), Gaps = 8/301 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRR++E +I   RV VNG         +M TD + ++
Sbjct: 202 KRVLAADDDAPKLHKVLAEAGMGSRRDMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRIN 260

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S   +  P   ++ ++VGRLD NTE
Sbjct: 261 GKPVKRKLANKPPRVLLYHKPTGEIVSHADPEGRASVFDNLPPMKTAKWLAVGRLDFNTE 320

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ ++      +++  
Sbjct: 321 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELAEGMRQKLLNGVELEDGPANFLRIRD 380

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+  
Sbjct: 381 GGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPISLPKGLKRGRWEELED 440

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             +R  +    L+                 +    + + +          S  +    + 
Sbjct: 441 NQVRALMASVGLKAPTEE--KGGRREAPERKQPDPMQTSMGFIGREPVLMSHSRFDQQQP 498

Query: 299 K 299
           +
Sbjct: 499 R 499


>gi|302670774|ref|YP_003830734.1| RNA pseudouridylate synthase [Butyrivibrio proteoclasticus B316]
 gi|302395247|gb|ADL34152.1| RNA pseudouridylate synthase [Butyrivibrio proteoclasticus B316]
          Length = 237

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 114/233 (48%), Gaps = 10/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ IA  GI SRRE ++++A  RVKVNGI  + A + V  +D + VD   +   +  
Sbjct: 1   MRLNQYIAACGICSRREADKLVAAGRVKVNGISAQ-AGIQVEDSDEVFVDNKKISLVKEN 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +  Y+KP+G+V T  D     TV   +        + GRLD ++EGLL+L+NDG L   
Sbjct: 60  VVLAYYKPVGVVCTEKDTHAERTVTSEVKYPTRVTYA-GRLDKDSEGLLILSNDGNLINA 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKGSNAWVTV 191
           +   S +  + Y V    ++  D LN +  G+ ++         +VT   +K       +
Sbjct: 119 MMKSSNKHEKEYEVSVDREISGDFLNRMSNGVYLEELDRTTRGCKVTRTGKKS----FRI 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKILR 242
            L +G NR+I+++     + V  L RI     +L    ++ G   E+ KK + 
Sbjct: 175 ILTQGLNRQIRRMCNALGYNVESLKRIRVMTVKLSDYDIMPGQYVELDKKSIE 227


>gi|255037667|ref|YP_003088288.1| pseudouridine synthase [Dyadobacter fermentans DSM 18053]
 gi|254950423|gb|ACT95123.1| pseudouridine synthase [Dyadobacter fermentans DSM 18053]
          Length = 555

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 111/238 (46%), Gaps = 2/238 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           ++  +E     R+++ IA AGI SRRE + +I+  ++ VNG ++      V  TD ++  
Sbjct: 313 RHKDKEETDEIRLNRYIANAGICSRREADDLISSGQISVNGKIVTEMGYKVRPTDVVKYG 372

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
              L   +   + +      + TT    + ++ +     +   RV  VGRLD NT GLLL
Sbjct: 373 KKALNPEKMVYILINKPKDYITTTDDPEERKTVLDIIAGACSERVYPVGRLDRNTTGLLL 432

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG LA  L  PS+   ++Y+      +  +    LK G+ ++       +  +    
Sbjct: 433 LTNDGELAEKLTHPSSGIKKIYQAELDKPITTEDFEQLKAGVELEDGFIRPDE--VGLVT 490

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                V + +  G+NR ++++FE   ++V +L R  +       L  G  R +++K +
Sbjct: 491 PDAQVVGLEIHSGRNRIVRRMFEHLGYEVQKLDRTVFAGLNKKDLPRGKWRFLTEKEV 548


>gi|71894432|ref|YP_278540.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Mycoplasma synoviae 53]
          Length = 232

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 65/233 (27%), Positives = 115/233 (49%), Gaps = 9/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K IA + + +R E++++I++  VKVN +++++ + ++    D I ++G+ L   E 
Sbjct: 1   MRIEKFIADSTLYTRNEIKKLISKGLVKVNDLIIKK-SQSIDPKLDKIYLEGILLEAREE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G +  + D + +      L          ++GRLDI+TEGLL++TNDG L
Sbjct: 60  FSYIMMNKPAGYICANFDWNKQVVFELLLDLEMNLKDFFTIGRLDIDTEGLLIITNDGKL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  L  P     + Y V     ++++   LL+K ++I  I Y            SN    
Sbjct: 120 SHNLLSPKKHIPKTYYVELDKPLEKNIKELLEKELLIDEIKYK----KSILNNISNNKWE 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + + EGK  +IK +F  F +KV  L RI      L   L  G  + ++K+ L 
Sbjct: 176 ITIFEGKFHQIKIIFAHFGYKVTYLKRIKMNNLSLDENLKPGEYKFLTKEELD 228


>gi|297620540|ref|YP_003708677.1| RNA pseudouridylate synthase family protein [Waddlia chondrophila
           WSU 86-1044]
 gi|297375841|gb|ADI37671.1| RNA pseudouridylate synthase family protein [Waddlia chondrophila
           WSU 86-1044]
          Length = 232

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 63/225 (28%), Positives = 113/225 (50%), Gaps = 4/225 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  GIASRR+ E +I   +V VNG ++ +  + V  ++ I V G  + + E+  
Sbjct: 5   RIAKHLASCGIASRRKCEDLIFAGKVSVNGEVVRQPQLLVDGSEKITVSGKKVNRQEKKV 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP+  + + +   G   V D    +  R+ +VGRLD  T GLL++TNDG     +
Sbjct: 65  YFMLNKPLNTLCSPNGKKGSKLVTDLFEGVKERLFTVGRLDKETTGLLIVTNDGEFTNQV 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             PS+   + Y  +   ++  D L  +  G  ++G+    +      +K   A + V + 
Sbjct: 125 IHPSSNIQKEYIAKTDCEISNDHLKAIAAGTSVEGVFVQPLS----VKKVRKATLKVVVG 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           EGK RE++ +      +V  L R   G   LG+L  G  R ++++
Sbjct: 181 EGKKREVRLLIAAAGLEVRALKRTRIGSLTLGSLPIGHWRSLTER 225


>gi|317498387|ref|ZP_07956682.1| RNA pseudouridylate synthase [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316894281|gb|EFV16468.1| RNA pseudouridylate synthase [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 242

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 111/241 (46%), Gaps = 4/241 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA 70
              R+ K +  +   +R+E +  + + +V VNG  +++    V    D +E D   ++  
Sbjct: 3   KKTRLDKFLCDSLNMTRKEAKESVKKGKVVVNGEAIKKPEYKVDAEQDQVEFDHKLIQFE 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L L+     +V+   D   ++ +         R+  VGRLD +TEGLLLLT+DG L
Sbjct: 63  QFHYLMLHKPQG-VVSATKDHHDQTVLDLIHEDYKDRLFPVGRLDKDTEGLLLLTDDGML 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     +VY  +  GQ  ++++   K+G+ I  G      ++ +       + V
Sbjct: 122 AHELLSPRKHVDKVYFAKVSGQFGENEIARFKEGLDIGNGEKSKQARLQILKADVQESEV 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
            + + EGK  ++K++ +    +V  L R+S G  +L   L  G  R ++K  L+E     
Sbjct: 182 LITIMEGKFHQVKRMVKAVGSEVLYLKRLSMGSLKLDEELKLGEYRRLTKAELQELKEHR 241

Query: 249 L 249
            
Sbjct: 242 R 242


>gi|154707706|ref|YP_001424364.1| ribosomal large subunit pseudouridine synthase B [Coxiella burnetii
           Dugway 5J108-111]
 gi|154356992|gb|ABS78454.1| ribosomal large subunit pseudouridine synthase B [Coxiella burnetii
           Dugway 5J108-111]
          Length = 244

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 75/233 (32%), Positives = 115/233 (49%), Gaps = 5/233 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---KA 70
           +R+ KV+AR+G  SRRE+E+MIA+ R+KVN  L +     +   D + +DG         
Sbjct: 3   ERIQKVLARSGYGSRREIEKMIAEGRIKVNQRLAQ-LGDRITEQDLVYIDGQLSSLSAPE 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L  +     + T        +           R + +GRLDINT GLLL TN+G L
Sbjct: 62  QVRVLLYHKPEGEICTRKDPEGRTTVFETLPRLKDGRWVIIGRLDINTSGLLLFTNEGEL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS Q  R Y VR  G VD D    L  G+ ++        +      G N W  
Sbjct: 122 ANRLMHPSAQVEREYAVRVLGAVDADMTQKLAHGVGLEDGKARFEDIVDVGGDGKNRWFH 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           V + EG++R +++++E    KV+RLIR+ +GP  L  +L  G+ +E+    ++
Sbjct: 182 VVVVEGRHRFVRRLWESQGVKVSRLIRVRFGPIVLSKSLRRGAWKELESPEIK 234


>gi|297623666|ref|YP_003705100.1| RNA-binding S4 domain-containing protein [Truepera radiovictrix DSM
           17093]
 gi|297164846|gb|ADI14557.1| RNA-binding S4 domain protein [Truepera radiovictrix DSM 17093]
          Length = 241

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 69/246 (28%), Positives = 110/246 (44%), Gaps = 8/246 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +R+ K +ARAG+ASRR+ E +I    V VNG+        V + D + V G  +     
Sbjct: 2   SERLQKFLARAGVASRRKAEALILSGAVTVNGVRA-ELGQRVAAGDEVRVRGERVAPPAA 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
              +  +KP G+++  +D  GR TV   +P          VGRLD ++EGLLLLT DG L
Sbjct: 61  HVTYALYKPKGVISAVTDDRGRVTVLQLVPPSARVPGLHPVGRLDADSEGLLLLTTDGEL 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + YRV        + L  L++G+ ++       +             T
Sbjct: 121 TLTLTHPRYGHEKTYRVWCEPVPGPEALRRLERGVALEDGPARARRARAAPGG-----CT 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L EG+NR+++++      +V RL+R   G   LG +  G  R +S   L +       
Sbjct: 176 LVLSEGRNRQVRRMLAALGCEVTRLLRTRIGGLSLGAMRPGELRRLSDAELAQLGYTRDR 235

Query: 251 EEAQVN 256
            + +  
Sbjct: 236 ADKRSP 241


>gi|21220260|ref|NP_626039.1| pseudouridine synthase [Streptomyces coelicolor A3(2)]
 gi|5738484|emb|CAB52832.1| putative pseudouridine synthase [Streptomyces coelicolor A3(2)]
          Length = 371

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 108/233 (46%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
               +R+ KV+ARAG  SRR  E +I Q RV++NG ++      V    D ++VDG+ + 
Sbjct: 131 EQEGERLQKVLARAGYGSRRACEELIEQARVEINGEIVLEQGRRVDPEKDEVKVDGLTVA 190

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   L      + T       +  + D + +  +R+  VGRLD  TEG++LLTN G
Sbjct: 191 TQSYQFFSLNKPAGVVSTMEDPEGRQ-CLGDYVTNRETRLFHVGRLDTETEGVILLTNHG 249

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     + Y     G + +D    LK GI ++          +  Q G N  
Sbjct: 250 ELAHRLTHPRYGVKKTYLAHIVGPIPRDLGKRLKDGIQLEDGYARADHFRVVEQTGKNYL 309

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L EG+   ++++     + V+ L+R ++GP  LG   +G  R +S   +
Sbjct: 310 VEVTLHEGRKHIVRRMLAEAGFPVDNLVRTAFGPITLGDQKSGWLRRLSNTEV 362


>gi|319787863|ref|YP_004147338.1| pseudouridine synthase [Pseudoxanthomonas suwonensis 11-1]
 gi|317466375|gb|ADV28107.1| pseudouridine synthase [Pseudoxanthomonas suwonensis 11-1]
          Length = 268

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 69/250 (27%), Positives = 112/250 (44%), Gaps = 4/250 (1%)

Query: 2   KDKNIVQENFTPQR--VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           KD+     +    R  +++V+++AG+ SR E  R I   RV+V+G ++      +     
Sbjct: 10  KDRAAPGSSTAGVRHGLARVLSKAGLCSRTEAARWIEAGRVQVDGRIVRDPEYPMRHGLR 69

Query: 60  -IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
            + VDG      ER  L L      + T   +    +       S    +  VGRLD  +
Sbjct: 70  GVLVDGRAPAGPERIYLALNKPRGLVTTARDEQGRDTVYRCLDGSGLPWLAPVGRLDRAS 129

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLLL +ND   A  +  P +   + Y V+     DQ  L  L+ G+   G     +  +
Sbjct: 130 EGLLLFSNDPAWAARVLDPDSGPDKTYHVQVDAIPDQTLLQALRTGVDADGEHLRAVSAS 189

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +      NAW+ + L EG+NR+I+++   F+  V RL+R++ G  QLG L  G  R +  
Sbjct: 190 VLRTGTRNAWLEIVLDEGRNRQIRRLLAAFDLSVLRLVRVAIGALQLGDLGKGQWRMLQP 249

Query: 239 KILREQLGPH 248
              R+ L   
Sbjct: 250 AE-RDALALP 258


>gi|320539364|ref|ZP_08039033.1| putative 16S rRNA pseudouridylate 516 synthase [Serratia symbiotica
           str. Tucson]
 gi|320030489|gb|EFW12499.1| putative 16S rRNA pseudouridylate 516 synthase [Serratia symbiotica
           str. Tucson]
          Length = 239

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 53/238 (22%), Positives = 108/238 (45%), Gaps = 7/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  +R+ V+G +++  AV +     ++ DG  L +    
Sbjct: 1   MRLDKFLSQQLGISRALVARELRARRITVDGEVVKNGAVKLAVEQEVKFDGNLLAQQNGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +   + + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYNLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +  +       G+ +             +  +K ++  V +
Sbjct: 121 VTSPKHHCEKTYLVTLEHSLAANTAQRFAAGVQLHNEKSLTRP----VQLEKINDRQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
            + EG+  ++K++F     +V  L R   G   +   L +G+ R ++ + +     PH
Sbjct: 177 AISEGRYHQVKRMFAAIGNRVIALHRERIGTIVMDKDLASGAYRPLTAEEIASVGAPH 234


>gi|241759798|ref|ZP_04757898.1| RNA pseudouridine synthase family protein [Neisseria flavescens
           SK114]
 gi|241319806|gb|EER56202.1| RNA pseudouridine synthase family protein [Neisseria flavescens
           SK114]
          Length = 247

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 104/250 (41%), Gaps = 20/250 (8%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           +   +    R+SK +A+ G+ SRRE +  I Q  VKVNG         V   D I+++  
Sbjct: 1   MQNNDSETMRLSKRMAQLGLCSRREADSYIEQGWVKVNGQTA-VLGQKVTERDRIDLNKQ 59

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                          P+          Y     L+T  +  +   +           +  
Sbjct: 60  AHEKQAARVTILLNKPVGYVSAQAEKGYKSAAELITADNHWEDDDSRIPFSEKHKFGLAP 119

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++D   L LL  G+ + G 
Sbjct: 120 AGRLDIDSVGLLVLTQDGRIAKQLIGENSSSEKEYLVRVRGKLDDKGLALLNHGLSLDGE 179

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                +V    +      +   LR+GK R+I+++ E    +V  L RI  G  +LG L  
Sbjct: 180 KLRPAKVEWQNEDQ----LRFILRQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPP 235

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 236 GKWRYLRTDE 245


>gi|325279694|ref|YP_004252236.1| pseudouridine synthase Rsu [Odoribacter splanchnicus DSM 20712]
 gi|324311503|gb|ADY32056.1| pseudouridine synthase Rsu [Odoribacter splanchnicus DSM 20712]
          Length = 407

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 58/238 (24%), Positives = 113/238 (47%), Gaps = 3/238 (1%)

Query: 5   NIVQENFTPQ-RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            +  E+   + R+++ I+  G+ SRR+ + +I   RVKVNG +++   + V   D +EVD
Sbjct: 166 RLKNEDENAELRLNRYISMGGVCSRRDADELIVAGRVKVNGEVVQTVGLKVRKKDKVEVD 225

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
            V +   ++  L L      + T     + ++ +     +   R+  VGRLD  T G+LL
Sbjct: 226 DVQIFPEKKVYLVLNKPKDYVTTVEDPLERKTVMALVEGACKERIYPVGRLDRQTTGVLL 285

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            TNDG LA+ L  P     ++Y V     + ++    +  G+ ++       +  +    
Sbjct: 286 FTNDGDLAKKLTHPKYDHKKIYHVFLDRVLTEEDFQAIANGVQLEDGFIKADE--ISYTS 343

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                V + +  GKNR ++++FE F +++ +L R+ +       L  G+ R ++ K +
Sbjct: 344 PDCTEVGIEIHSGKNRIVRRIFEHFGYQIIKLDRVYFAGITKKNLPRGTWRFLTPKEV 401


>gi|190150487|ref|YP_001969012.1| ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|189915618|gb|ACE61870.1| ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
          Length = 349

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 90/286 (31%), Positives = 132/286 (46%), Gaps = 10/286 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGV- 65
           +E    +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S   I +DG  
Sbjct: 64  KEKVVGEKLQKILARAGQGSRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNL 123

Query: 66  ----PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
               P++K     L  Y     L T        +          +R I+VGRLDINT GL
Sbjct: 124 ISLIPVQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGARWIAVGRLDINTSGL 183

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  G +D+  L  L+KG+ ++       Q+    
Sbjct: 184 LLFTTDGELANRLMHPSREVEREYSVRVFGNIDEAMLQRLRKGVQLEDGPANFKQIKTVG 243

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
             G N W  V L +G+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 244 GTGLNQWFDVTLTKGRNREVRRLWESQGVEVSRLIRIRYGNIKLEKGLPRGGWEEMGLEQ 303

Query: 241 ---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
              LRE +G     E +V++      +      +            
Sbjct: 304 VNYLRELVGLPAETETKVDVTKNRRRTNIRQIRKAVKQHSKYRTKA 349


>gi|72382440|ref|YP_291795.1| ribosomal large subunit pseudouridine synthase F [Prochlorococcus
           marinus str. NATL2A]
 gi|124026115|ref|YP_001015231.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Prochlorococcus marinus str. NATL1A]
 gi|72002290|gb|AAZ58092.1| ribosomal large subunit pseudouridine synthase F [Prochlorococcus
           marinus str. NATL2A]
 gi|123961183|gb|ABM75966.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Prochlorococcus marinus str. NATL1A]
          Length = 240

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 55/227 (24%), Positives = 102/227 (44%), Gaps = 11/227 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---KAE 71
           R++K ++  G  SRR  +R+I + +V +NG + E+    V   D ++VDG  +    K +
Sbjct: 4   RINKYLSEVGYCSRRVADRLIEEGKVVINGKIPEK-GTKVEEGDQVKVDGQRIEKSTKQK 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L        + TT    +  + +        +R+  +GRLD  +EGL+ LTNDG + 
Sbjct: 63  NIYLAFNKPVGIVCTTDRRVEHDNIIDFI--KYPTRIFPIGRLDKPSEGLIFLTNDGDIV 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V  +  +++D +  +  G+ I      +  V     K       +
Sbjct: 121 NKILRARNNHEKEYIVSVNRPINRDFIQSMSNGVEILETITKNCFVKQLGAKK----FKI 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            L +G NR+I+++ E   ++V  L R+     +L  +  G  RE +K
Sbjct: 177 ILTQGLNRQIRRMCESLGYRVESLKRVRIMNIKL-DVPIGKYREFTK 222


>gi|307328933|ref|ZP_07608102.1| pseudouridine synthase [Streptomyces violaceusniger Tu 4113]
 gi|306885443|gb|EFN16460.1| pseudouridine synthase [Streptomyces violaceusniger Tu 4113]
          Length = 366

 Score =  156 bits (393), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 110/233 (47%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
               +R+ KV+ARAG+ SRR  E +I Q RV+VNG ++    + V    D I+VDG+ + 
Sbjct: 126 EVEGERLQKVLARAGMGSRRACEELIDQARVEVNGKIVTEQGLRVDPEKDEIKVDGLTVA 185

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   L      + T       +  + D + +  +R+  VGRLD  TEG++LLTN G
Sbjct: 186 TQSYLFFALNKPAGVVSTMEDPDGRQ-CLGDYVTNRETRLFHVGRLDTETEGIILLTNHG 244

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     + Y     G + +D    LK GI ++          +    G N  
Sbjct: 245 ELAHRLTHPRYGVKKTYLAAIQGPLPRDLGKRLKSGIELEDGYARADHFRVVQNTGKNYL 304

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L EG+   ++++     + V++L+R ++GP  LG   +G  R ++   +
Sbjct: 305 VEVTLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPIALGDQKSGWLRRMTNTEV 357


>gi|319638629|ref|ZP_07993391.1| RNA-binding protein [Neisseria mucosa C102]
 gi|317400378|gb|EFV81037.1| RNA-binding protein [Neisseria mucosa C102]
          Length = 247

 Score =  156 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 105/250 (42%), Gaps = 20/250 (8%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           +   +    R+SK +A+ G+ SRRE +  I Q  VKVNG         V   D I+++  
Sbjct: 1   MQNNDSETMRLSKRMAQLGLCSRREADSYIEQGWVKVNGQTA-VLGQKVTERDRIDLNKQ 59

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                          P+          Y     L+T  +  +G  +           +  
Sbjct: 60  AHEKQAARVTILLNKPVGYVSAQAEKGYKSAAELITADNHWEGDDSRIPFSEKHKFGLAP 119

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++D   L LL  G+ + G 
Sbjct: 120 AGRLDIDSVGLLVLTQDGRIAKQLIGENSSSEKEYLVRVRGKLDNKGLALLNHGLSLDGE 179

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                +V    +      +   LR+GK R+I+++ E    +V  L RI  G  +LG L  
Sbjct: 180 KLRPAKVEWQNEDQ----LRFILRQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPP 235

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 236 GKWRYLRADE 245


>gi|85708946|ref|ZP_01040012.1| S4 domain protein [Erythrobacter sp. NAP1]
 gi|85690480|gb|EAQ30483.1| S4 domain protein [Erythrobacter sp. NAP1]
          Length = 260

 Score =  156 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 107/244 (43%), Positives = 152/244 (62%), Gaps = 6/244 (2%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           ++     R++K++ARAG+ASRRE+ERMIA  R+ +N  ++E  A  + S   + VDG P+
Sbjct: 9   EDRPEGDRIAKLLARAGVASRREIERMIADGRITLNDKVVETPATFLTSLQGVAVDGKPV 68

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLL 123
            K E  +L+ +HKP GL+T   DP GR+T++  L +   +     + +GRLD+NTEGLLL
Sbjct: 69  AKPEPAQLYAFHKPTGLITAERDPAGRATIYAALRNALPKDTPRLMPIGRLDLNTEGLLL 128

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ- 182
           LTNDGGL R +ELPS+   R YR R  G V Q++L  L +G+ I G+ YG +   L+   
Sbjct: 129 LTNDGGLKRQMELPSSGIPRTYRARAFGDVSQEQLEALIEGVEIDGVRYGSIDANLERGG 188

Query: 183 -KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             G N WV + + EGKNRE+++V E+   KVNRLIR +YGPF LG L  G    + K  L
Sbjct: 189 AGGKNQWVEMTITEGKNREVRRVLEYLGLKVNRLIRTAYGPFGLGDLPRGQAVRIRKGDL 248

Query: 242 REQL 245
              +
Sbjct: 249 DRFV 252


>gi|229546666|ref|ZP_04435391.1| pseudouridylate synthase [Enterococcus faecalis TX1322]
 gi|307296165|ref|ZP_07575995.1| hypothetical protein HMPREF9509_03087 [Enterococcus faecalis
           TX0411]
 gi|312905054|ref|ZP_07764179.1| conserved hypothetical protein [Enterococcus faecalis TX0635]
 gi|229308233|gb|EEN74220.1| pseudouridylate synthase [Enterococcus faecalis TX1322]
 gi|306496139|gb|EFM65719.1| hypothetical protein HMPREF9509_03087 [Enterococcus faecalis
           TX0411]
 gi|310631633|gb|EFQ14916.1| conserved hypothetical protein [Enterococcus faecalis TX0635]
 gi|315148327|gb|EFT92343.1| conserved hypothetical protein [Enterococcus faecalis TX4244]
 gi|315576566|gb|EFU88757.1| conserved hypothetical protein [Enterococcus faecalis TX0630]
          Length = 320

 Score =  156 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 68/261 (26%), Positives = 116/261 (44%), Gaps = 3/261 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE 71
             R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +    
Sbjct: 60  TMRLDKLLEELQFGSRKTVKRLIRGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLISHKT 119

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                L      +                       +  VGRLD +TEGLLLLT++G L 
Sbjct: 120 HVYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQLG 179

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVT 190
             L  P+ +  + Y V+ +G V  +     K GIV+QG       ++T+     + + V 
Sbjct: 180 YQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHVF 239

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHL 249
           + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L    
Sbjct: 240 LTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYFF 299

Query: 250 LEEAQVNLDAPIYSSETLVRD 270
           +E+ Q +   P        R 
Sbjct: 300 IEKQQTSKALPSNLKREEERK 320


>gi|54020392|ref|YP_115728.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           hyopneumoniae 232]
 gi|53987565|gb|AAV27766.1| conserved hypothetical protein [Mycoplasma hyopneumoniae 232]
 gi|144575306|gb|AAZ53540.2| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           hyopneumoniae 7448]
          Length = 240

 Score =  156 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 110/231 (47%), Gaps = 6/231 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K ++  G+ SRR+ E++I Q R+K+N    +     V   D IE+D   + K  
Sbjct: 2   KKIRINKFLSEMGVCSRRQSEKLILQGRIKINNETAK-IGQIVSQNDVIELDQQKITKKP 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               +  +KP   +T+  DP+ R T+ +        +  VGRLD  T GL+L+TNDG   
Sbjct: 61  PIFWYALNKPKNYITSRFDPENRPTIMEFFSKN-EYLFPVGRLDFQTTGLILITNDGKTT 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  PS++  R Y V+    +   ++  L    +         +     +K S+    V
Sbjct: 120 NKLLHPSSKIERTYLVKTDFSLSDKEIRFLNDNKIQLDSV----KSIQKIKKCSSRTYLV 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + +G N  IKK+F   N KV +L R+S+   +L  +  G  R+++ + ++
Sbjct: 176 TVWQGSNHHIKKLFLSINKKVLKLKRVSFANIKLNNISEGKYRKLTNQEIK 226


>gi|283782395|ref|YP_003373150.1| pseudouridine synthase [Pirellula staleyi DSM 6068]
 gi|283440848|gb|ADB19290.1| pseudouridine synthase [Pirellula staleyi DSM 6068]
          Length = 811

 Score =  156 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 77/291 (26%), Positives = 129/291 (44%), Gaps = 3/291 (1%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHI 60
            +K I  +    +R+ KV+A AGI SRR+ E +I + RV V+G ++      V      I
Sbjct: 22  PEKQIGPDGVVAERLQKVLAAAGIGSRRDCEELITEGRVDVDGKVVTELGTRVDPVKQTI 81

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            VDG  LRK +R    +      + T         T   +L     RV +VGRLD  +EG
Sbjct: 82  RVDGEALRKPQRLYFVVNKPEGVVTTN--YDQAGRTRVIDLVPTDERVFAVGRLDRASEG 139

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+++TNDG  A  +  P     + Y VR  G+    +L  L++GI +         + + 
Sbjct: 140 LIIVTNDGEFANRVTHPRYGVTKTYLVRVAGEASTAELAKLRRGIHLSDGFCKVDAIQVK 199

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +   +  + + L EGKNREI+++      KV +L R++ G  +LG L  G+ R + K+ 
Sbjct: 200 RRHKQSTDMVIQLSEGKNREIRRILARIGHKVLKLKRLAVGSLKLGELPLGAWRWLDKQE 259

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           +   L    L   +        ++    +  P   ++        +  S +
Sbjct: 260 IERLLSEARLRRKENKKGKSATATTADGKAAPKKPAKSAGAIRDEQGPSEE 310



 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/115 (11%), Positives = 30/115 (26%), Gaps = 3/115 (2%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           + + LG    +E      +    +     +R       P      + +   +     + +
Sbjct: 473 IEDSLGNEDGDEPPARRTSKRSPAGAPRAERVPRGDRAPRGDRPPRGDRPARTDRPARGE 532

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR-SPSFPSKRSLRRTSAKK 354
             +   R   A      +G   S     G+ E   R   P    + +       +
Sbjct: 533 RPSRGERPARAE--GAPQGDRPSRGDRPGRGERPARGERPQRGERPARGEGRPPR 585



 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 13/112 (11%), Positives = 26/112 (23%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R   G       +          +   R       E P    R ++      G  +  + 
Sbjct: 527 RPARGERPSRGERPARAEGAPQGDRPSRGDRPGRGERPARGERPQRGERPARGEGRPPRK 586

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               +  +   N         +     G++    R   +    RS  R   +
Sbjct: 587 PAGEYSESGYQNDAGGGPRRPTRGGRPGRKPTGPRPEGARSEFRSEGRPEGR 638



 Score = 44.8 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 9/122 (7%), Positives = 19/122 (15%), Gaps = 10/122 (8%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R +  P      + +            R          +   R +            +  
Sbjct: 500 RAERVPRGDRAPRGDRPPRGDRPARTDRPARGERPSRGERPARAEGAPQGDRPSRGDRPG 559

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQRE----------ENHRRSPSFPSKRSLRRTS 351
                 R                       E              R P+   +   + T 
Sbjct: 560 RGERPARGERPQRGERPARGEGRPPRKPAGEYSESGYQNDAGGGPRRPTRGGRPGRKPTG 619

Query: 352 AK 353
            +
Sbjct: 620 PR 621



 Score = 43.6 bits (101), Expect = 0.051,   Method: Composition-based stats.
 Identities = 12/128 (9%), Positives = 22/128 (17%), Gaps = 15/128 (11%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R           +         +    R          D   R ++ S  +     +   
Sbjct: 488 RRTSKRSPAGAPRAERVPRGDRAPRGDRPPRGDRPARTDRPARGERPSRGERPARAEGAP 547

Query: 302 ATPVHRRNLASNVWMAK--GIHSSFLSDSGQREENHRRSPSF-------------PSKRS 346
                 R            G          + E    R P+                +R 
Sbjct: 548 QGDRPSRGDRPGRGERPARGERPQRGERPARGEGRPPRKPAGEYSESGYQNDAGGGPRRP 607

Query: 347 LRRTSAKK 354
            R     +
Sbjct: 608 TRGGRPGR 615



 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 13/117 (11%), Positives = 25/117 (21%), Gaps = 4/117 (3%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R    P     A+ +  A         R      +   D  +R  +    +     ++  
Sbjct: 512 RGDRPPRGDRPARTDRPARGERPSRGERPARAEGAPQGDRPSRGDRPGRGERPARGERPQ 571

Query: 302 ATPVHRRNLASNVWMAKGIHSSFL----SDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                 R          G +S       +  G R       P           +  +
Sbjct: 572 RGERPARGEGRPPRKPAGEYSESGYQNDAGGGPRRPTRGGRPGRKPTGPRPEGARSE 628



 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 11/118 (9%), Positives = 22/118 (18%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
              ++  +            L   I  S                        + +     
Sbjct: 449 RANVISYEDDEAPAASETAALTGDIEDSLGNEDGDEPPARRTSKRSPAGAPRAERVPRGD 508

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +  +   P      A     A+G   S      + E   +        R  R     +
Sbjct: 509 RAPRGDRPPRGDRPARTDRPARGERPSRGERPARAEGAPQGDRPSRGDRPGRGERPAR 566


>gi|126696606|ref|YP_001091492.1| pseudouridine synthase, Rsu [Prochlorococcus marinus str. MIT 9301]
 gi|126543649|gb|ABO17891.1| Pseudouridine synthase, Rsu [Prochlorococcus marinus str. MIT 9301]
          Length = 240

 Score =  156 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 48/223 (21%), Positives = 95/223 (42%), Gaps = 11/223 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL---RKAE 71
           R++K ++  G  SRRE +++I + +V +NG +       V   D +EV G  +   ++ +
Sbjct: 4   RINKYLSEVGYCSRREADKLILEGKVTINGEIP-EIGTKVEDNDQVEVKGQRIEKSKRQK 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L        + TT            +      R+  +GRLD  +EGL+ LTNDG + 
Sbjct: 63  NIYLAFNKPVGIVCTTDKK--LEPNNVIDFIKYPKRIFPIGRLDKLSEGLIFLTNDGDIV 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V+ +  ++ + +  +  G+ I      +       ++       +
Sbjct: 121 NKILRARNNHEKEYIVKVNRPINSNFIKSMSNGVEILDTITKNC----FVEQLGPRNFKI 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            L +G NR+I+++ E   ++V  L R+     +L  +  G  R
Sbjct: 177 ILTQGLNRQIRRMCEALGYRVRSLKRVRIMNIKL-DVPTGEYR 218


>gi|171322053|ref|ZP_02910927.1| RNA-binding S4 domain protein [Burkholderia ambifaria MEX-5]
 gi|171092644|gb|EDT37945.1| RNA-binding S4 domain protein [Burkholderia ambifaria MEX-5]
          Length = 249

 Score =  156 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 60/251 (23%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V     IE+D          
Sbjct: 1   MRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPDQKIEIDERASAAQAAQ 60

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     L+T  +   G  +     P     +   GRLDI++
Sbjct: 61  VTILLHKPVGYVSGQAEDGYEPASVLITRANQWSGDRSPLRFSPQHLHALAPAGRLDIDS 120

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            G+L+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 121 TGMLVLTQNGRIAKQLIGEQSDIDKEYLVRVRFGERLLDIDQHFPAESLAKLRHGLELDG 180

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 181 VALKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 236

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 237 QGQWRYLSPDE 247


>gi|312601099|gb|ADQ90354.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           hyopneumoniae 168]
          Length = 236

 Score =  156 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 111/231 (48%), Gaps = 6/231 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K ++  G+ SRR+ E++I Q R+K+N    +     V   D IE+D   + K  
Sbjct: 2   KKIRINKFLSEMGVCSRRQSEKLILQGRIKINNETAK-IGQIVSQNDVIELDQQKITKKP 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               +  +KP   +T+  DP+ R T+ +        +  VGRLD  T GL+L+TNDG   
Sbjct: 61  PIFWYALNKPKNYITSRFDPENRPTIMEFFSKN-EYLFPVGRLDFQTSGLILITNDGKTT 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  PS++  R Y V+    +   ++  L    +         +     +K S+    V
Sbjct: 120 NKLLHPSSKIERTYLVKTDFSLSDKEIRFLNDNKIQLDSV----KSIQKIKKCSSRTYLV 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + +G N  IKK+F   N KV +L R+S+   +L  +  G  R+++K+ ++
Sbjct: 176 TVWQGSNHHIKKLFLSINKKVLKLKRVSFANIKLNNISEGKYRKLTKQEIK 226


>gi|193216644|ref|YP_001999886.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           arthritidis 158L3-1]
 gi|193001967|gb|ACF07182.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           arthritidis 158L3-1]
          Length = 251

 Score =  156 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 72/247 (29%), Positives = 117/247 (47%), Gaps = 6/247 (2%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
              E     ++ K I++ G  SRR+ E +I Q+R+K+N  +       V++ D I +DG 
Sbjct: 4   TKDEFEKTIKIQKAISQVGYCSRRQAEELIKQKRIKINHQVAT-LGQRVLADDQIFIDGK 62

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            L         +++KP   + T  DP+ R T+++    +     SVGRLD N+ G++L+T
Sbjct: 63  KLNIKPPKFYLVFNKPKNTICTLKDPEKRKTIYEY-MGLKEYAYSVGRLDFNSTGIILVT 121

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG  A ++  PS    RVY V    ++ +   N L    VI        + +    K +
Sbjct: 122 NDGDFANLIAHPSANIKRVYEVVLEKELSEGDFNYLNSNKVILNGK----KSSQSLSKLA 177

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
               +V L EG+N  +K +F   N  V  L R+SYGP     L  G TR +S+  ++   
Sbjct: 178 PFKYSVSLYEGRNHHVKNLFLLVNNYVKELHRVSYGPITDANLKIGKTRHLSESEVQNLK 237

Query: 246 GPHLLEE 252
              L ++
Sbjct: 238 TLALKQK 244


>gi|89890105|ref|ZP_01201616.1| ribosomal large subunit pseudouridine synthase F [Flavobacteria
           bacterium BBFL7]
 gi|89518378|gb|EAS21034.1| ribosomal large subunit pseudouridine synthase F [Flavobacteria
           bacterium BBFL7]
          Length = 326

 Score =  156 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 56/249 (22%), Positives = 110/249 (44%), Gaps = 10/249 (4%)

Query: 2   KDKNIVQENFTP---------QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV 52
           K + I+++              R++K I+ +GI SRR+ +  I    V VNG  +     
Sbjct: 73  KKEYIMRKKSEGAKSKPDDGTIRLNKYISNSGICSRRDADIYIKAGSVTVNGKPVSEMGY 132

Query: 53  NVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
            V  TD ++ DG  ++  ++  L L      +     +   ++ +     +  + +  VG
Sbjct: 133 RVKLTDEVKFDGQNIQPYQKQYLLLNKPKGFIAPRKGERASKTVLDLMQSAGVANLHYVG 192

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RL   + GL+L TND  +A  L  P+ +  ++Y+V        + L  L+ GI I G   
Sbjct: 193 RLGRQSVGLMLFTNDLEMANKLNNPNLEMRKIYQVALDRSFKHEDLMQLRNGIAINGEVI 252

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
            D++     + G N  + + +  GK+  ++ +FE   +++  L R+  G      L  G 
Sbjct: 253 -DVKEINYVEDGRNNEIGIEIHSGKDNIVQALFEAVKYEIKVLDRVVLGGLTKKDLPRGH 311

Query: 233 TREVSKKIL 241
            R ++++ +
Sbjct: 312 YRALTEQEI 320


>gi|289450385|ref|YP_003475159.1| pseudouridylate synthase [Clostridiales genomosp. BVAB3 str.
           UPII9-5]
 gi|289184932|gb|ADC91357.1| pseudouridylate synthase [Clostridiales genomosp. BVAB3 str.
           UPII9-5]
          Length = 317

 Score =  156 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 66/283 (23%), Positives = 115/283 (40%), Gaps = 39/283 (13%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR---- 68
            R++K IA  GIASRR  + ++A  R+ +NG         V   +D IE+DG PL+    
Sbjct: 31  IRINKYIAGLGIASRRAADELLADGRITINGETA-GLGEMVDPQSDRIELDGRPLKVECA 89

Query: 69  --------------------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
                                       +R  + L      + TT S             
Sbjct: 90  PLPYAPYGKASPPRLTSKDDNQATSNYPQRVYIALNKPKGIVCTTDSR---EPENITEYM 146

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
           +   R+  +GRLD  + GLLLLTNDG +   +        + YRV     + +  L  ++
Sbjct: 147 NFPIRIFPIGRLDKASSGLLLLTNDGSIVNRILRAHNHHEKEYRVEVDKPLTEAALQTMR 206

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP 222
            G+ I G+     ++ L     +   +T+ L +G NR+I+++ E+  +KV +L R     
Sbjct: 207 TGVPILGVVTLPCRIKLL----NPTTMTIILTQGLNRQIRRMCEYCGYKVVKLERRRIMN 262

Query: 223 FQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSE 265
             LG +  G+ R ++   L +     +      +L   + + +
Sbjct: 263 ITLGKMPVGAWRYLTYPELSQLDELLIGSSESASLQQKMSTVQ 305


>gi|307718784|ref|YP_003874316.1| pseudouridylate synthase [Spirochaeta thermophila DSM 6192]
 gi|306532509|gb|ADN02043.1| putative pseudouridylate synthase [Spirochaeta thermophila DSM
           6192]
          Length = 255

 Score =  156 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 76/230 (33%), Positives = 110/230 (47%), Gaps = 6/230 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA-ER 72
           R+   +AR G  SRR  E +I + RV+VNG ++   A  V    D + +DG  +    + 
Sbjct: 17  RLHVFLARCGEGSRRACEELIKKGRVRVNGRVITNPAHRVDPQEDRVTLDGRDVHLVGKF 76

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L  +  P  L T               P +  +V S+GRLD  + GLLLLTNDG  A 
Sbjct: 77  LYLAFHKPPGYLCTRSDPQGRPLVYDLIDPVLPYKVFSIGRLDFLSSGLLLLTNDGEFAD 136

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           ++  P  +  + Y V     + +  L    KGI I+G  Y    V    +  S   V + 
Sbjct: 137 IVMHPKHRVEKEYLVETKRPIPRALLESYLKGIRIEGERY----VLKAYKSKSPHKVHLI 192

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L EGKNREI+KVF   +  + R+ RI  GP +LG L  G  R ++K+ +R
Sbjct: 193 LEEGKNREIRKVFYSSHIPIVRIHRIRIGPVRLGRLRPGHFRNLTKEEIR 242


>gi|90412232|ref|ZP_01220237.1| hypothetical ribosomal small subunit pseudouridine synthase A
           [Photobacterium profundum 3TCK]
 gi|90326723|gb|EAS43116.1| hypothetical ribosomal small subunit pseudouridine synthase A
           [Photobacterium profundum 3TCK]
          Length = 232

 Score =  156 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 49/230 (21%), Positives = 97/230 (42%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I ++   +R E  ++I    + VN  ++   A  V   + + +DG+ L      
Sbjct: 5   MRLDKFICKSTDLTRTEATQLINAGNIIVNNEVVSNEATQVHENNDVLLDGIKLIARASR 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     + +   D    S            +   GRLD +T GL+L+T+DG  +  
Sbjct: 65  YILMHKPLNTICSN-IDEVYPSLFNYIDVEKADDLHIAGRLDADTTGLVLITDDGRWSFN 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P+ Q  + YRV     + +D      +G+ +QG        ++ + T       V +
Sbjct: 124 IITPNKQCEKTYRVGLRNPIAEDAAEKFAQGVKLQGEKQLTLPAKLDVVTSN----EVLL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + EGK  ++K++F     +V  L R   G  +L  +  G  R ++ + +
Sbjct: 180 TITEGKYHQVKRMFSAIGNRVVTLHREQIGNIKL-DVEVGKWRFLTPEEI 228


>gi|289208914|ref|YP_003460980.1| RNA-binding S4 domain protein [Thioalkalivibrio sp. K90mix]
 gi|288944545|gb|ADC72244.1| RNA-binding S4 domain protein [Thioalkalivibrio sp. K90mix]
          Length = 318

 Score =  156 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 83/318 (26%), Positives = 127/318 (39%), Gaps = 7/318 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +RV KV+A  G+ SRRE+E  I +  VKVN    +     V   D I V G  +  AE 
Sbjct: 2   SERVQKVLAARGLGSRREIEGWIERGEVKVNQRTAK-LGDQVGPNDVIRVRGRVIHMAEH 60

Query: 73  TRLW--LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              W   +     + +       +            R ++VGRLD+NT GLLL T DG L
Sbjct: 61  AHRWLVYHKPVGEICSRSDPEGRKPVFASLPRLKGQRWVAVGRLDLNTSGLLLFTTDGEL 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS    R Y VR  G+V  D   +L +G+ ++        +      G+N W  
Sbjct: 121 ANRLMHPSHSLEREYAVRVLGEVPDDTRRMLLEGVELEDGPARFDVLEERGGDGANHWFH 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LREQLG 246
           V + EG+NR ++++++     V+RLIR+ YGP  LG  L  G++R++  +    L E + 
Sbjct: 181 VVVSEGRNRLVRRLWDAVGVTVSRLIRVRYGPVVLGRGLKTGASRDLEVREVEALYEAVE 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
             + E  +           T         S           ++   +G  K  K      
Sbjct: 241 LPVPESIRERGRRRGPGRNTRPARGKRGKSGGRVREADRWTSTKPGSGPGKGGKTGRSGP 300

Query: 307 RRNLASNVWMAKGIHSSF 324
                       G  +  
Sbjct: 301 GGAGRKGGPRKPGGRARS 318


>gi|254361758|ref|ZP_04977893.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|153093293|gb|EDN74289.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
          Length = 355

 Score =  156 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 88/279 (31%), Positives = 128/279 (45%), Gaps = 10/279 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S+  I +DG  +    
Sbjct: 77  GEKLQKILARAGQGSRRELEEIIAAGRVSVDGKMATLGDRVQVSSSTKIRIDGHLVNLMP 136

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T        +          +R I+VGRLDINT GLLL T 
Sbjct: 137 AQKEICRVLMYYKPEGELCTRSDPEGRSTVFDRLPRLSGARWIAVGRLDINTSGLLLFTT 196

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  G +D   L  L+KG+ ++       Q+ +    G N
Sbjct: 197 DGELANRLMHPSREVEREYSVRVFGNIDDAMLQRLRKGVQLEDGPANFKQIKVVGGTGLN 256

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LR 242
            W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  +    LR
Sbjct: 257 QWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKLDKGLPRGGWEEMGLEQVNYLR 316

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD 281
           E +G     E +V +      +      +     +    
Sbjct: 317 ELVGLPPETETKVEVGVNRRRTNIRQIRKAVKQHQKYRG 355


>gi|167768019|ref|ZP_02440072.1| hypothetical protein CLOSS21_02562 [Clostridium sp. SS2/1]
 gi|167710348|gb|EDS20927.1| hypothetical protein CLOSS21_02562 [Clostridium sp. SS2/1]
          Length = 245

 Score =  156 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 111/241 (46%), Gaps = 4/241 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA 70
              R+ K +  +   +R+E +  + + +V VNG  +++    V    D +E D   ++  
Sbjct: 6   KKTRLDKFLCDSLNMTRKEAKESVKKGKVVVNGEAIKKPEYKVDAEQDQVEFDHKLIQFE 65

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L L+     +V+   D   ++ +         R+  VGRLD +TEGLLLLT+DG L
Sbjct: 66  QFHYLMLHKPQG-VVSATKDHHDQTVLDLIHEDYKDRLFPVGRLDKDTEGLLLLTDDGML 124

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     +VY  +  GQ  ++++   K+G+ I  G      ++ +       + V
Sbjct: 125 AHELLSPRKHVDKVYFAKVSGQFGENEIARFKEGLDIGNGERSKQARLQILKADVQESEV 184

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
            + + EGK  ++K++ +    +V  L R+S G  +L   L  G  R ++K  L+E     
Sbjct: 185 LITIMEGKFHQVKRMVKAVGSEVLYLKRLSMGSLKLDEELKLGEYRRLTKAELQELKEHR 244

Query: 249 L 249
            
Sbjct: 245 R 245


>gi|261494040|ref|ZP_05990543.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
 gi|261496199|ref|ZP_05992605.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|261308151|gb|EEY09448.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|261310206|gb|EEY11406.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
          Length = 355

 Score =  156 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 88/279 (31%), Positives = 128/279 (45%), Gaps = 10/279 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S+  I +DG  +    
Sbjct: 77  GEKLQKILARAGQGSRRELEEIIAAGRVSVDGKMATLGDRVQVSSSTKIRIDGHLVNLMP 136

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T        +          +R I+VGRLDINT GLLL T 
Sbjct: 137 AQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLSGARWIAVGRLDINTSGLLLFTT 196

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  G +D   L  L+KG+ ++       Q+ +    G N
Sbjct: 197 DGELANRLMHPSREVEREYSVRVFGNIDDAMLQRLRKGVQLEDGPANFKQIKVVGGTGLN 256

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LR 242
            W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  +    LR
Sbjct: 257 QWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKLDKGLPRGGWEEMGLEQVNYLR 316

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD 281
           E +G     E +V +      +      +     +    
Sbjct: 317 ELVGLPPETETKVEVGVNRRRTNIRQIRKAVKQHQKYRG 355


>gi|315126449|ref|YP_004068452.1| pseudouridine synthase [Pseudoalteromonas sp. SM9913]
 gi|315014963|gb|ADT68301.1| pseudouridine synthase [Pseudoalteromonas sp. SM9913]
          Length = 289

 Score =  156 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 80/286 (27%), Positives = 132/286 (46%), Gaps = 10/286 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +++ KV+ARAG+ SRRE+E+ I   RV VNG + +     V  TD I VDG  ++  E
Sbjct: 4   QGEKLQKVLARAGVGSRREMEKYIDANRVSVNGKVAK-LGDRVEETDLIRVDGHTVKIEE 62

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   +        L T       R+           R I+VGRLD+NT GL+L TN
Sbjct: 63  KADRICRVIMYNKPEGELSTRKDPEGRRTVFDRLPRIDGDRWIAVGRLDVNTSGLMLFTN 122

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y  R  G+V  + +  L +G+ ++        +     +G N
Sbjct: 123 DGELANRLMHPSYEVEREYSARVFGEVTDETMKNLLRGVELEDGPAKFTGIKPMGGEGIN 182

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREV---SKKILR 242
            W  V L EG+NRE++++++  + +V+RLIRI YG  +L   +  G   E    +   LR
Sbjct: 183 RWYNVTLNEGRNREVRRLWQSQDVEVSRLIRIRYGKLELDKRVPQGGWIEYDLDTVNYLR 242

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
           + +      + ++++       +    ++     +  +   +  K 
Sbjct: 243 KTVKLGKETQTKLSVIPEKRKDKRAKINQIRKAVKKHNQRVKPTKR 288


>gi|161869750|ref|YP_001598917.1| RNA-binding protein [Neisseria meningitidis 053442]
 gi|161595303|gb|ABX72963.1| RNA-binding protein [Neisseria meningitidis 053442]
          Length = 252

 Score =  156 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 68/255 (26%), Positives = 109/255 (42%), Gaps = 20/255 (7%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K          R+SK +A+ G+ SRRE +  I Q  V VNG         V   D I
Sbjct: 1   MNSKISSDHTEDAVRLSKRMAQLGLCSRREADGYIGQGWVTVNGKTA-VLGQKVSPADRI 59

Query: 61  EVD---------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           E++                 P+          Y     L+T+ +  +G ++     P   
Sbjct: 60  ELNKKAHEQQAARITILLNKPVGYVSAQAEKGYKSAAELITSENRWEGDTSRIRFDPKHK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             +   GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+
Sbjct: 120 IGLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGL 179

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G      +V    +      +   L++GK R+I+++ E    +V  L RI  G  +L
Sbjct: 180 SLDGEKLRPAKVEWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>gi|160935783|ref|ZP_02083158.1| hypothetical protein CLOBOL_00673 [Clostridium bolteae ATCC
           BAA-613]
 gi|158441527|gb|EDP19237.1| hypothetical protein CLOBOL_00673 [Clostridium bolteae ATCC
           BAA-613]
          Length = 251

 Score =  156 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 66/254 (25%), Positives = 114/254 (44%), Gaps = 12/254 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----K 69
           +R++K +++ G+ SRRE +R+I   +V V+          V     +  +G  +R    +
Sbjct: 3   ERLNKWLSQMGVCSRREADRLIEAGKVLVDNRPA-SMGQKVTPGQKVVCNGKMVRVDRSQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             R  L   +KP G+V T +D D    + D L     R+  VGRLD ++EGLLL+TN G 
Sbjct: 62  RPRPVLLAVNKPKGIVCTTTDKDRAENIVDFLGY-PERIYPVGRLDKDSEGLLLMTNQGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNA 187
           L   +        + Y V     V +  L  +  GI +          +V    +K    
Sbjct: 121 LVNKIMRSGNAHEKEYIVTIDKPVTERFLEQMAGGIRLPELDQVTRPCKV----KKVERN 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
             ++ L +G NR+I+++ E    +V RL+R+     +LG L  G+ R+++K+   E  G 
Sbjct: 177 TFSIILTQGLNRQIRRMCEACGCQVKRLVRVRIMNIRLGNLRTGAYRQITKEEYEELTGL 236

Query: 248 HLLEEAQVNLDAPI 261
                +    +   
Sbjct: 237 LKDSSSLSLKERKN 250


>gi|144575100|gb|AAZ43829.2| 16S rRNA uridine-516 pseudouridylate synthase and related
           Pseudouridylate synthase [Mycoplasma synoviae 53]
          Length = 234

 Score =  156 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 65/233 (27%), Positives = 115/233 (49%), Gaps = 9/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K IA + + +R E++++I++  VKVN +++++ + ++    D I ++G+ L   E 
Sbjct: 3   IRIEKFIADSTLYTRNEIKKLISKGLVKVNDLIIKK-SQSIDPKLDKIYLEGILLEAREE 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G +  + D + +      L          ++GRLDI+TEGLL++TNDG L
Sbjct: 62  FSYIMMNKPAGYICANFDWNKQVVFELLLDLEMNLKDFFTIGRLDIDTEGLLIITNDGKL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  L  P     + Y V     ++++   LL+K ++I  I Y            SN    
Sbjct: 122 SHNLLSPKKHIPKTYYVELDKPLEKNIKELLEKELLIDEIKYK----KSILNNISNNKWE 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + + EGK  +IK +F  F +KV  L RI      L   L  G  + ++K+ L 
Sbjct: 178 ITIFEGKFHQIKIIFAHFGYKVTYLKRIKMNNLSLDENLKPGEYKFLTKEELD 230


>gi|325132039|gb|EGC54737.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           meningitidis M6190]
 gi|325137793|gb|EGC60368.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           meningitidis ES14902]
          Length = 252

 Score =  156 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 107/255 (41%), Gaps = 20/255 (7%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K          R+SK +A+ G+ SRRE +  I Q  V VNG         V   D I
Sbjct: 1   MNPKISSDHTEDAVRLSKRMAQLGLCSRREADGYIEQGWVTVNGKTA-VLGQKVSPADRI 59

Query: 61  EVD---------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           E++                 P+          Y     L+T  +  +G +      P   
Sbjct: 60  ELNKKAHEQQAARITILLNKPVGYVSAQAEKGYKSAAELITPENRWEGDTGRIRFDPKHK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             +   GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+
Sbjct: 120 IGLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGL 179

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G      QV    +      +   L++GK R+I+++ E    +V  L RI  G  +L
Sbjct: 180 SLDGEKLRPAQVEWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>gi|153206799|ref|ZP_01945640.1| RNA pseudouridine synthase family protein [Coxiella burnetii 'MSU
           Goat Q177']
 gi|212218389|ref|YP_002305176.1| ribosomal large subunit pseudouridine synthase B [Coxiella burnetii
           CbuK_Q154]
 gi|120577162|gb|EAX33786.1| RNA pseudouridine synthase family protein [Coxiella burnetii 'MSU
           Goat Q177']
 gi|212012651|gb|ACJ20031.1| ribosomal large subunit pseudouridine synthase B [Coxiella burnetii
           CbuK_Q154]
          Length = 244

 Score =  156 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 78/233 (33%), Positives = 117/233 (50%), Gaps = 5/233 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--LRKAE 71
           +R+ KV+AR+G  SRRE+E+MIA+ R+KVN  L +     +   D + +DG    L   E
Sbjct: 3   ERIQKVLARSGYGSRREIEKMIAEGRIKVNQRLAQ-LGDRITEQDLVYIDGQLSSLSAPE 61

Query: 72  RTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + R L  +     + T        +           R + +GRLDINT GLLL TN+G L
Sbjct: 62  QVRILLYHKPEGEICTRKDPEGRTTVFETLPRLKDGRWVIIGRLDINTSGLLLFTNEGEL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS Q  R Y VR  G VD D    L  G+ ++        +      G N W  
Sbjct: 122 ANRLMHPSAQVEREYAVRVLGAVDADMTQKLAHGVGLEDGKARFEDIVDVGGDGKNRWFH 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           V + EG++R +++++E    KV+RLIR+ +GP  L  +L  G  +E+    ++
Sbjct: 182 VVVVEGRHRFVRRLWESQGVKVSRLIRVRFGPIVLPKSLRRGDWKELESPEIK 234


>gi|260584045|ref|ZP_05851793.1| ribosomal small subunit pseudouridine synthase A [Granulicatella
           elegans ATCC 700633]
 gi|260158671|gb|EEW93739.1| ribosomal small subunit pseudouridine synthase A [Granulicatella
           elegans ATCC 700633]
          Length = 243

 Score =  156 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 57/235 (24%), Positives = 100/235 (42%), Gaps = 5/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A +GIA+R +V+ ++ Q+RV+ N   +    V +    D I +D   +   + 
Sbjct: 1   MRLDKFLADSGIATRSQVKLILKQKRVRKNQETVTNGKVQIDEKLDEIYLDDERVYYEKY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T               +    V  VGRLDI+T G LLLTN+G L+ 
Sbjct: 61  LYYVMNKPKGVVSATEDTKHATVLDLIGELAQKRGVFPVGRLDIDTHGFLLLTNNGALSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSN--AWV 189
            +  P     + Y  +  G + Q+     +KGI +          + + +   ++  + V
Sbjct: 121 AMLSPKKHVEKTYVAKIEGIMTQEDQVSFEKGITLDDGYECMPAHLEILSVDKNHQASLV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
            + ++EGK  ++K++ +     V  L RIS GP  L   L  G  R +    L  
Sbjct: 181 QIKIKEGKFHQVKRMVKACGKTVIDLQRISMGPLHLDKSLKLGEFRSLKDSELEA 235


>gi|194365006|ref|YP_002027616.1| pseudouridine synthase [Stenotrophomonas maltophilia R551-3]
 gi|194347810|gb|ACF50933.1| pseudouridine synthase [Stenotrophomonas maltophilia R551-3]
          Length = 240

 Score =  156 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 65/238 (27%), Positives = 110/238 (46%), Gaps = 14/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---- 70
           R++K IA  G  SRRE +R+IA +RV VNG      AV V   D + VDG PLR      
Sbjct: 4   RLNKHIADTGFCSRREADRLIAARRVTVNGHPAGTGAV-VGEEDQVLVDGQPLRARVARK 62

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R      +KP+G+  T            +      R+  +GRLD  +EGL+L+T++
Sbjct: 63  PGTRRHVYIALNKPVGVTCTTETSV--KGNIVDFVGHEQRIFPIGRLDKESEGLILMTSN 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +        + Y V  +  V  + L  + +G+ I        + +   + G   
Sbjct: 121 GDIVNQILRAENGHQKEYLVAVNKPVTDEFLRGMARGVRIHDQMTLPCKTSRIAKFG--- 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
              + L++G NR+I+ +   F ++V +L R+     ++G L  G  R ++++ L+  L
Sbjct: 178 -FRITLQQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKIGALKPGQWRNLTEQELQGLL 234


>gi|94310972|ref|YP_584182.1| ribosomal large subunit pseudouridine synthase B [Cupriavidus
           metallidurans CH34]
 gi|93354824|gb|ABF08913.1| pseudouridine synthase, Rsu [Cupriavidus metallidurans CH34]
          Length = 631

 Score =  156 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 71/278 (25%), Positives = 118/278 (42%), Gaps = 6/278 (2%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             +  +    ++ KV+A  G+ SRRE+E +I Q RV VNG+        ++ TD + V+G
Sbjct: 226 RELSADDDAPKLHKVLAEGGLGSRREMEELILQGRVSVNGLPA-HIGQRILPTDQVRVNG 284

Query: 65  VPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
             + +         L  +     +V+        +           + ++VGRLD NTEG
Sbjct: 285 KLIHRKVTTKPPRVLLYHKPSGEIVSQSDPEGRPTVFDSLPRIKNGKWVAVGRLDFNTEG 344

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LL+ T  G +A     P     R Y VR  G++ +     L  GI +       +++   
Sbjct: 345 LLIFTTSGDIANRFMHPRYGVEREYAVRTLGELAEADRQRLLHGIQLDDGEANFLRIADG 404

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
             +G N W  V L EG+NRE++++FE     V+RLIR  YG F L   L  G  +E+   
Sbjct: 405 GGEGVNQWYHVALTEGRNREVRRMFEAVGLTVSRLIRTRYGQFLLPRGLKRGRWQELDPT 464

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISE 277
            +R  +    L+       +       +   +    + 
Sbjct: 465 DVRGLMANIGLKAPSKEAQSGGKGVTKVGGRKQREEAA 502


>gi|50084073|ref|YP_045583.1| putative ribosomal large subunit pseudouridine synthase B
           (pseudouridylate synthase) (Uracil hydrolyase)
           [Acinetobacter sp. ADP1]
 gi|49530049|emb|CAG67761.1| putative ribosomal large subunit pseudouridine synthase B
           (Pseudouridylate synthase) (Uracil hydrolyase)
           [Acinetobacter sp. ADP1]
          Length = 313

 Score =  155 bits (392), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 82/309 (26%), Positives = 131/309 (42%), Gaps = 7/309 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
            +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG  ++    
Sbjct: 2   SEKLQKVLARIGLGSRRYMEEVIAAGRVSVNGQIAQV-GERIEPGDELRIDGRKVQFQIE 60

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R  L  Y     + + +      +           R + VGRLDIN+ GLLL TND
Sbjct: 61  DEIRRRVLIYYKPEGEICSRNDPEQRPTVFDHLPQIANDRWVMVGRLDINSTGLLLFTND 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V       L  G+V+          +     G N 
Sbjct: 121 GELANRLMHPSNEIEREYAVRVMGEVTPQIRQTLLNGVVLDDGPAKFESFSELGGDGINR 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V ++EG+NRE++++FE    KV+RL+R  YG   L   L  G   E+ K  +     
Sbjct: 181 WYQVVVKEGRNREVRRLFESQGLKVSRLLRTRYGSVILPRELRTGRWIELDKGDIDNLTK 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              L+  Q      +    T       + +       + ++++      + + K      
Sbjct: 241 LVELKPRQGTGLYGMAKRRTERMVEKPMAARRGGYLRQQRRDNENGTENNNETKQPYAAA 300

Query: 307 RRNLASNVW 315
           R+ +A N  
Sbjct: 301 RKTVAVNKG 309


>gi|190573465|ref|YP_001971310.1| putative pseudouridine synthase [Stenotrophomonas maltophilia
           K279a]
 gi|254521293|ref|ZP_05133348.1| ribosomal large subunit pseudouridine synthase F [Stenotrophomonas
           sp. SKA14]
 gi|190011387|emb|CAQ45002.1| putative pseudouridine synthase [Stenotrophomonas maltophilia
           K279a]
 gi|219718884|gb|EED37409.1| ribosomal large subunit pseudouridine synthase F [Stenotrophomonas
           sp. SKA14]
          Length = 240

 Score =  155 bits (392), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 65/238 (27%), Positives = 110/238 (46%), Gaps = 14/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---- 70
           R++K IA  G  SRRE +R+IA +RV VNG      AV V   D + VDG PLR      
Sbjct: 4   RLNKHIADTGFCSRREADRLIAARRVTVNGHPAGTGAV-VGEEDQVLVDGQPLRARVARK 62

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R      +KP+G+  T            +      R+  +GRLD  +EGL+L+T++
Sbjct: 63  PGARRHVYIALNKPVGVTCTTETSV--KGNIVDFVGHEQRIFPIGRLDKESEGLILMTSN 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +        + Y V  +  V  + L  + +G+ I        + +   + G   
Sbjct: 121 GDIVNQILRAENGHQKEYLVAVNKPVTDEFLRGMARGVRIHDQMTLPCKTSRIAKFG--- 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
              + L++G NR+I+ +   F ++V +L R+     ++G L  G  R ++++ L+  L
Sbjct: 178 -FRITLQQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKIGALKPGQWRNLTEQELQGLL 234


>gi|165918548|ref|ZP_02218634.1| RNA pseudouridine synthase family protein [Coxiella burnetii RSA
           334]
 gi|165917794|gb|EDR36398.1| RNA pseudouridine synthase family protein [Coxiella burnetii RSA
           334]
          Length = 244

 Score =  155 bits (392), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 78/233 (33%), Positives = 118/233 (50%), Gaps = 5/233 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--LRKAE 71
           +R+ KV+AR+G  SRRE+E+MIA+ R+KVN  L +     +   D + +DG    L   E
Sbjct: 3   ERIQKVLARSGYGSRREIEKMIAEGRIKVNQRLAQ-LGDRITEQDLVYIDGQLSSLSAPE 61

Query: 72  RTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + R L  +     + T        +           R + +GRLDINT GLLL TN+G L
Sbjct: 62  QVRILLYHKPEGEICTRKDPEGRTTVFETLPRLKDGRWVIIGRLDINTSGLLLFTNEGEL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS Q  R Y VR  G VD D    L  G+ ++        +      G N W  
Sbjct: 122 ANRLMHPSAQVEREYAVRVLGAVDADMTQKLAHGVGLEDGKARFEDIVDVGGDGKNRWFH 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           V + EG++R +++++E    KV+RLIR+ +GP  L  +L  G+ +E+    ++
Sbjct: 182 VVVVEGRHRFVRRLWESQGVKVSRLIRVRFGPIVLPKSLRRGAWKELESPEIK 234


>gi|161870231|ref|YP_001599401.1| pseudouridine synthase [Neisseria meningitidis 053442]
 gi|161595784|gb|ABX73444.1| pseudouridine synthase [Neisseria meningitidis 053442]
          Length = 416

 Score =  155 bits (392), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 72/256 (28%), Positives = 125/256 (48%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+
Sbjct: 151 LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHV 209

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 210 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 269

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L +  ++++       
Sbjct: 270 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVE 329

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   
Sbjct: 330 RIREQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFY 389

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   +    +
Sbjct: 390 ELNPAEVANIIKWADM 405


>gi|258512547|ref|YP_003185981.1| pseudouridine synthase [Alicyclobacillus acidocaldarius subsp.
           acidocaldarius DSM 446]
 gi|257479273|gb|ACV59592.1| pseudouridine synthase [Alicyclobacillus acidocaldarius subsp.
           acidocaldarius DSM 446]
          Length = 245

 Score =  155 bits (392), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 67/234 (28%), Positives = 108/234 (46%), Gaps = 4/234 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE 71
             RV K +  AG  +R E +++    RV++NG  ++ AA +     D +EVDG  +    
Sbjct: 3   SIRVDKWLTTAGYGTRSEAKKLCRAGRVRLNGETVKDAAKHADPAVDVLEVDGELVPYEP 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                +Y  P  + +T    D       +   I+  V  VGRLD + EGLLLLTNDG LA
Sbjct: 63  LVYFMMYKPPGYVSSTEDPRDPVVIELLDEEDIWRDVFPVGRLDKDAEGLLLLTNDGPLA 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y VR  G + +     L +G+V+         ++ +  + G+ +   
Sbjct: 123 HRLLAPKRHVPKRYFVRVRGALGEGDARALAEGVVLDDGYKAMPAELEIL-RSGAESEAI 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           + + EGK  ++K++F     +V  L RIS GP  L   L  G  R +++  +  
Sbjct: 182 IQVYEGKYHQVKRMFASLGKRVTFLKRISMGPLSLDPALKPGEYRRLTEGEIEA 235


>gi|257066516|ref|YP_003152772.1| pseudouridine synthase [Anaerococcus prevotii DSM 20548]
 gi|256798396|gb|ACV29051.1| pseudouridine synthase [Anaerococcus prevotii DSM 20548]
          Length = 233

 Score =  155 bits (392), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 60/229 (26%), Positives = 114/229 (49%), Gaps = 3/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA +G  SRR+ + ++ + +VKVNG       +++  +D +E+DG  L   E+ 
Sbjct: 1   MRINKYIASSGYTSRRKADDLVKKGKVKVNGETTHELGLDIKDSDVVEIDGKVLEIEEKI 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + LY     + +     + R    ++L  +  R  + GRLD ++EGLL++TNDG     
Sbjct: 61  YIKLYKPRGYITSNFDPYNDRDL--NDLVKLDQRFFAAGRLDKDSEGLLIITNDGIFTNQ 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  PS +  + Y VR    +++++    + GI I           ++    ++    V +
Sbjct: 119 IIHPSKKLDKTYIVRVSRLLNKEECQQFESGIDIGDSE-MTSDSRIELIDKTSKTYKVTI 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++F +F+ +V  L RIS GP +L  +     R   +  + 
Sbjct: 178 HQGYNRQIRRMFAYFSSEVKMLKRISIGPIKLDGMKPYEKRNFDQAEMD 226


>gi|124004166|ref|ZP_01689012.1| ribosomal large subunit pseudouridine synthase B [Microscilla
           marina ATCC 23134]
 gi|123990236|gb|EAY29735.1| ribosomal large subunit pseudouridine synthase B [Microscilla
           marina ATCC 23134]
          Length = 391

 Score =  155 bits (392), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 60/240 (25%), Positives = 116/240 (48%), Gaps = 2/240 (0%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K++          R+++ I+ +G+ SRRE +++I    + VNG ++      V  TD ++
Sbjct: 147 KERTQRHNEPEKMRLNRFISNSGVCSRREADKLIEMGMISVNGKVITEMGFQVSPTDTVK 206

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
                L++ +   + L      + TT+   D ++ +     S   R+  VGRLD NT GL
Sbjct: 207 YGKRLLKREKFVYVLLNKPKDFITTTNDPQDRKTVMDLIKNSCDERIYPVGRLDRNTTGL 266

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL TNDG +A+ L  PS    +VY+V     +  + L+ + +G++++       ++ +  
Sbjct: 267 LLFTNDGEVAKKLSHPSHDVKKVYQVELDKPLKDEDLDSIAEGVILEDGYAAVDEIAIL- 325

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                  V V +  G+NR ++++F   +++V +L R  Y       +  G  R +S+K +
Sbjct: 326 -NPERTLVGVEIHIGRNRIVRRIFNHLDYEVVKLDRTMYAGLNKKNIDRGDWRYLSEKEV 384


>gi|33152188|ref|NP_873541.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           ducreyi 35000HP]
 gi|33148410|gb|AAP95930.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           ducreyi 35000HP]
          Length = 230

 Score =  155 bits (392), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 108/229 (47%), Gaps = 3/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R    + +    + VNG +++  A+ + S D +  +G  L   E  
Sbjct: 1   MRLDKFIAENIGLTRSLANKALKSSLITVNGQVVKSGAMKITSADGVCYEGNRLTWLESG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ +KP G + ++ D +  +        +  R+ + GRLD++T GL+LLT+DG  +  
Sbjct: 61  QYFMLYKPQGYICSNDDSEYPTVFQFFDYRLMVRLHTAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+QD    L KGI+++G     +   ++     N  V + +
Sbjct: 121 ITSPKYHCEKSYLVTLADPVEQDYALKLAKGILLRGERDPCLPAAMEIIDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EG+  ++K++F     KV  L R   G   L   L  G+ R ++K+ +
Sbjct: 179 CEGRYHQVKRMFAALGNKVQALHRWRIGEIILDETLQEGTFRHLTKQEI 227


>gi|313904334|ref|ZP_07837712.1| RNA-binding S4 domain protein [Eubacterium cellulosolvens 6]
 gi|313470884|gb|EFR66208.1| RNA-binding S4 domain protein [Eubacterium cellulosolvens 6]
          Length = 239

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 62/244 (25%), Positives = 120/244 (49%), Gaps = 5/244 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K ++ +G  SRRE +R++    V +NG +             + V G  +   E+ 
Sbjct: 1   MRINKYLSASGHCSRREADRLVEAGHVSINGKIA-EPGSQADENSIVTVKGKRVTLEEKK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+V T    +  + +     +   RV   GRLD N+EGLL+LTNDG L + 
Sbjct: 60  IYLKMYKPVGIVCTAEKRERDNLIEYL--NYPVRVTYAGRLDRNSEGLLILTNDGDLIQS 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V  +  + ++ L+ +++G+ ++ +       T+   +       + L
Sbjct: 118 MMAARNAHEKEYEVTVNKDLRKEDLDSMREGVYLRELEVRTRPCTIV--QTGERTFRIIL 175

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
            +G NR+I+++ + F++ V +L RI      L  L  G TRE+S++ +R+      +EE+
Sbjct: 176 TQGLNRQIRRMCKEFSYGVKKLKRIRVVNITLDGLKYGQTRELSEQEVRDLKKNLGIEES 235

Query: 254 QVNL 257
           + +L
Sbjct: 236 KNDL 239


>gi|261365431|ref|ZP_05978314.1| ribosomal large subunit pseudouridine synthase F [Neisseria mucosa
           ATCC 25996]
 gi|288566092|gb|EFC87652.1| ribosomal large subunit pseudouridine synthase F [Neisseria mucosa
           ATCC 25996]
          Length = 247

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 64/250 (25%), Positives = 105/250 (42%), Gaps = 20/250 (8%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           +   +    R+SK +A+ G+ SRRE +  I Q  VKVNG         V   D I+++  
Sbjct: 1   MDNTSEETMRLSKRMAQLGLCSRREADSYIEQGWVKVNGQTA-VLGQKVTERDRIDLNRQ 59

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                          P+          Y     L+T  +  +   +           +  
Sbjct: 60  AHERQAERVTILLNKPVGYVSAQAEKGYKSAAELITADNRWESDDSHIPFSEKHKFGLAP 119

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+ + G 
Sbjct: 120 AGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGE 179

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                +V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  
Sbjct: 180 KLRPAKVEWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGKLPP 235

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 236 GKWRYLRADE 245


>gi|149926779|ref|ZP_01915039.1| propable 16S pseudouridylate synthase [Limnobacter sp. MED105]
 gi|149824708|gb|EDM83924.1| propable 16S pseudouridylate synthase [Limnobacter sp. MED105]
          Length = 342

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 72/248 (29%), Positives = 120/248 (48%), Gaps = 18/248 (7%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + + F PQR+SK++A  G+ SRRE + +I    V+VNG +++     V+ T  I++D   
Sbjct: 97  MLDPFEPQRLSKIMAAKGLCSRREADYLIENGWVRVNGKVVDELGAKVLPTVTIDLDARA 156

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDG--------------RSTVFDNLPSIFSRVISVG 112
                +    LYHKPIG+V+   +                 R T     P++   +   G
Sbjct: 157 KNVLGKQVTILYHKPIGVVSGQPEGRYKAAMECLSLENQADRKTSTPFQPAMLKGLAPAG 216

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++    L +L+ G+ + G   
Sbjct: 217 RLDIDSTGLLVLTQDGRIAKQLIDANSTVEKEYLVRVEGELTDRGLEMLRYGLSLDGEAL 276

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
              +V+   +      +   L EGK R+I+++ E    KV  L R+  G   LG L  G 
Sbjct: 277 KPARVSWQNEDQ----LRFILNEGKKRQIRRMCEIVGLKVVGLKRVRIGRVMLGDLPVGQ 332

Query: 233 TREVSKKI 240
            R ++ + 
Sbjct: 333 WRLLTPEE 340


>gi|198283940|ref|YP_002220261.1| pseudouridine synthase [Acidithiobacillus ferrooxidans ATCC 53993]
 gi|198248461|gb|ACH84054.1| pseudouridine synthase [Acidithiobacillus ferrooxidans ATCC 53993]
          Length = 237

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 61/227 (26%), Positives = 97/227 (42%), Gaps = 2/227 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+  +++R G  SR EV  ++ + RV+V G LL +A+  V +   + VD  P+      
Sbjct: 6   ERMDHLLSRLGYCSRSEVRDLLREGRVRVAGELLRKASAKVNA-AEVWVDEEPIDHPHAF 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L  +     +                       + SVGRLD  T G+LLLT+DG     
Sbjct: 65  YLLYHKPLGKVCAHDDPRAIYQDFPLRWRYRRPALSSVGRLDRETSGVLLLTDDGDWLHH 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
              P     RVYRV     +  D  ++L  G ++        +        +   V + L
Sbjct: 125 WTSPRRAIPRVYRVTLQEPLRSDAADILAAGTLMLDGEDTPCRPAALHC-LTEREVRLTL 183

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            EG+  E++++F   +  V  L R +YGPF L  L AG  RE++   
Sbjct: 184 TEGRYHEVRRMFAALDNLVLTLHREAYGPFLLDDLPAGQWRELTVAE 230


>gi|227892643|ref|ZP_04010448.1| pseudouridylate synthase [Lactobacillus ultunensis DSM 16047]
 gi|227865514|gb|EEJ72935.1| pseudouridylate synthase [Lactobacillus ultunensis DSM 16047]
          Length = 233

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 63/233 (27%), Positives = 105/233 (45%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV ++I +  V VNG  ++     V  TD + V+G  +   +  
Sbjct: 1   MRIDKYLANMNVGSRKEVHQLIKKGIVSVNGQTVKTPKEKVAETDEVTVNGEKIVYQKYH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +      L  T            +L   +  ++ VGRLD +T GLLLLTNDG L   
Sbjct: 61  YFLMNKPKGVLSATEDRSQRTVISLLDLKDQYQGIVPVGRLDKDTTGLLLLTNDGQLNHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQK--GSNAWVT 190
           L  P+    +VYR +  G  D++ +     G+ +         ++T+  Q     ++ + 
Sbjct: 121 LLAPNKHVAKVYRAKIAGVADENTVKTFASGMTLGDETKLKPAKLTVLKQDLEHDSSEIE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           + + EGK  +IK++F     KV  L RIS G  +L   L  G   E+    ++
Sbjct: 181 IEISEGKYHQIKRMFGAVGMKVVELERISMGKLKLPNNLKRGQYIEIDVDEIK 233


>gi|296112282|ref|YP_003626220.1| ribosomal small subunit pseudouridine synthase A [Moraxella
           catarrhalis RH4]
 gi|295919976|gb|ADG60327.1| ribosomal small subunit pseudouridine synthase A [Moraxella
           catarrhalis RH4]
 gi|326561792|gb|EGE12127.1| ribosomal small subunit pseudouridine synthase A [Moraxella
           catarrhalis 7169]
 gi|326562268|gb|EGE12594.1| ribosomal small subunit pseudouridine synthase A [Moraxella
           catarrhalis 103P14B1]
 gi|326563228|gb|EGE13495.1| ribosomal small subunit pseudouridine synthase A [Moraxella
           catarrhalis 46P47B1]
 gi|326564754|gb|EGE14967.1| ribosomal small subunit pseudouridine synthase A [Moraxella
           catarrhalis 12P80B1]
 gi|326568983|gb|EGE19052.1| ribosomal small subunit pseudouridine synthase A [Moraxella
           catarrhalis BC1]
 gi|326569283|gb|EGE19344.1| ribosomal small subunit pseudouridine synthase A [Moraxella
           catarrhalis BC7]
 gi|326571959|gb|EGE21964.1| ribosomal small subunit pseudouridine synthase A [Moraxella
           catarrhalis BC8]
 gi|326575471|gb|EGE25396.1| ribosomal small subunit pseudouridine synthase A [Moraxella
           catarrhalis 101P30B1]
 gi|326576441|gb|EGE26349.1| ribosomal small subunit pseudouridine synthase A [Moraxella
           catarrhalis CO72]
 gi|326577913|gb|EGE27777.1| ribosomal small subunit pseudouridine synthase A [Moraxella
           catarrhalis O35E]
          Length = 234

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 106/236 (44%), Gaps = 7/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +++A   SR++ ++++    + VNG +++ ++ +V  + D I   G  L  A+ 
Sbjct: 1   MRLDKFLSKATELSRKDAKKVLHAGEITVNGTIIKDSSHHVDLANDEILWAGEALSVADG 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R  L +KP G   T    +             + +   GRLD++T G LLL++DG    
Sbjct: 61  NRYILLYKPDGFECTLKPKEYPMVTDLIAVPEVANLRIAGRLDVDTTGALLLSDDGAWLH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKL----NLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +  P     + Y++     +D+D        +  GI+++G         L     ++A 
Sbjct: 121 RVTSPKRHQPKQYQLTLADAMDKDAQAYAIKQIANGILLEGETEKTRPAVLSFIDETHAV 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +   L EGK  ++K++  +F  KV +L R S G   L  L  G  R ++   + + 
Sbjct: 181 L--TLTEGKYHQVKRMMAYFGNKVIKLHRASIGHISLEGLQMGECRFLTPDEINQF 234


>gi|293398946|ref|ZP_06643111.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           gonorrhoeae F62]
 gi|291610360|gb|EFF39470.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           gonorrhoeae F62]
          Length = 399

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 72/256 (28%), Positives = 126/256 (49%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+
Sbjct: 134 LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHV 192

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 193 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 252

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L +  ++++       
Sbjct: 253 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVE 312

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W  + ++EG+NRE++++FE     V+RL+R+++GP  L   L  G   
Sbjct: 313 RIREQGGEGANKWYNIVIKEGRNREVRRIFESQGLTVSRLVRVAFGPIGLPNRLKRGQFY 372

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   L    +
Sbjct: 373 ELNPAEVANILKWADM 388


>gi|118595060|ref|ZP_01552407.1| pseudouridine synthase, Rsu [Methylophilales bacterium HTCC2181]
 gi|118440838|gb|EAV47465.1| pseudouridine synthase, Rsu [Methylophilales bacterium HTCC2181]
          Length = 242

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 58/243 (23%), Positives = 106/243 (43%), Gaps = 18/243 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R+SK+++  G+ SRRE ++ I    V ++G  +         T  +E+         
Sbjct: 2   EKVRISKILSEQGLCSRREADKFIELGLVLLDGKTVSELGTKACRTQKVELKDRAQIAQS 61

Query: 72  RTRLWLYHKPIGLVTT--------------HSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
                + +KP+G ++                 D   ++            +   GRLDI+
Sbjct: 62  AKATIILNKPVGFISHLDDDKEFTPAASLVTPDKFYQTNDTRRPTFNTDGLAPAGRLDID 121

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           + GLL+LT DG +A+ +   +    + Y VR  G +  + L+LL  G+ + G      +V
Sbjct: 122 SSGLLVLTQDGRIAKQIIGENVIVEKEYLVRIEGTLTDEALSLLNHGLTLDGYELKPAKV 181

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                  ++A ++  L EG+NR+I+K+ +    KV  L R+  G  +LG + +GS R + 
Sbjct: 182 LWQ----NDAQLSFTLIEGRNRQIRKMCQLVGVKVTALKRVRIGNVRLGNIPSGSWRFLG 237

Query: 238 KKI 240
              
Sbjct: 238 ADE 240


>gi|332534428|ref|ZP_08410268.1| putative ribosomal RNA pseudouridylate synthase [Pseudoalteromonas
           haloplanktis ANT/505]
 gi|332036162|gb|EGI72637.1| putative ribosomal RNA pseudouridylate synthase [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 230

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 59/233 (25%), Positives = 102/233 (43%), Gaps = 9/233 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T  R++K IA AGI SR++  R+I +  V VN         +V   D I V+   ++ A
Sbjct: 2   STKIRLAKYIAHAGICSRKQASRLIDEGVVTVNNRPANHID-HVDEQDTIIVNEKEIKGA 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                + YHKP+G+               +     +RV  +GRLD ++ GLL+LTNDG  
Sbjct: 61  ADLVYFAYHKPVGIDCK--LNIDDPASLIHHLPTLTRVYPIGRLDKDSRGLLILTNDGDF 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + Y V  +  +D      +  G+ +        +      K ++   +
Sbjct: 119 CNQLIHPDFHQPKHYLVTVNKPLDDAFCKKMAAGVPVDKHITLPCE----VNKIASNQFS 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKIL 241
           + L++G NR+I+K+  +  +KV  L R+ +    L    L      +++K  +
Sbjct: 175 IVLKQGLNRQIRKMAHYCGYKVIDLFRVQFSDLTLSKLNLPENQYIQINKTDI 227


>gi|261380881|ref|ZP_05985454.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           subflava NJ9703]
 gi|284796358|gb|EFC51705.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           subflava NJ9703]
          Length = 247

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 105/250 (42%), Gaps = 20/250 (8%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           +   +    R+SK +A+ G+ SRRE +  I Q  VKVNG         V   D I+++  
Sbjct: 1   MQNNDSETMRLSKRMAQLGLCSRREADSYIEQGWVKVNGQTA-VLGQKVTERDRIDLNKQ 59

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                          P+          Y     L+T  +  +G  +           +  
Sbjct: 60  AHEKQAARVTILLNKPVGYVSAQAEKGYKSAAELITAENHWEGDDSRIPFSEKHKFGLAP 119

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++D   L LL  G+ + G 
Sbjct: 120 AGRLDIDSVGLLVLTQDGRIAKQLIGENSSSEKEYLVRVRGKLDDKGLALLNHGLSLDGE 179

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                +V    +      +   LR+GK R+I+++ E    +V  L RI  G  +LG L  
Sbjct: 180 KLRPAKVEWQNEDQ----LRFILRQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPP 235

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 236 GKWRYLRADE 245


>gi|254670635|emb|CBA06652.1| pseudouridylate synthase [Neisseria meningitidis alpha153]
          Length = 252

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 109/255 (42%), Gaps = 20/255 (7%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K          R+SK +A+ G+ SRRE +  I Q  V VNG         V   D I
Sbjct: 1   MNSKISSDHTEDAVRLSKRMAQLGLCSRREADGYIGQGWVTVNGKTA-VLGQKVSPADRI 59

Query: 61  EVD---------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           E++                 P+          Y     L+T+ +  +G ++     P   
Sbjct: 60  ELNKKAHEQQAARITILLNKPVGYVSAQAEKGYKSAAELITSENRWEGDTSRIRFDPKHK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             +   GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+
Sbjct: 120 IGLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGL 179

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G      QV    +      +   L++GK R+I+++ E    +V  L RI  G  +L
Sbjct: 180 SLDGEKLRPAQVEWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>gi|78048528|ref|YP_364703.1| pseudouridylate synthase [Xanthomonas campestris pv. vesicatoria
           str. 85-10]
 gi|78036958|emb|CAJ24658.1| Pseudouridylate synthase [Xanthomonas campestris pv. vesicatoria
           str. 85-10]
          Length = 253

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 64/241 (26%), Positives = 107/241 (44%), Gaps = 10/241 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++K IA +G  SRRE +R+I ++RV VNG+     AV V + D + VDG PLR  E 
Sbjct: 15  TIRLNKYIAESGFCSRREADRLIGERRVTVNGVPAGTGAV-VGAEDTVLVDGQPLRIREA 73

Query: 73  TRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            +L             +  T +                 R+  +GRLD ++EGL+L+T++
Sbjct: 74  KKLGGRKHVYIALNKPVGITCTTESSVKGNIVKFVGHEQRIFPIGRLDKDSEGLILMTSN 133

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +     +  + Y V  +  V  + L  + +G+ I        +     + G   
Sbjct: 134 GNIVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRIHNETTLPCRTARIAKFG--- 190

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR  L  
Sbjct: 191 -FRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELRGLLPQ 249

Query: 248 H 248
            
Sbjct: 250 R 250


>gi|109899770|ref|YP_663025.1| pseudouridine synthase, Rsu [Pseudoalteromonas atlantica T6c]
 gi|109702051|gb|ABG41971.1| ribosomal small subunit pseudouridine synthase A [Pseudoalteromonas
           atlantica T6c]
          Length = 241

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 52/223 (23%), Positives = 101/223 (45%), Gaps = 9/223 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ ++++  G  SR+E   ++  +RV V G   +  A+ V     + VDG  L   +   
Sbjct: 15  RLDQLLSNLGYCSRKEARYLLKGKRVTVKGEFAKSPALKVDP-ATVRVDGEALDAPDGIL 73

Query: 75  LWLYHKPIGLVTTHSD--PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + L      + +  ++        + +       +++SVGRLD +T GL+L+T+D  L  
Sbjct: 74  VMLNKPLGYVCSHDNNEGMRIYDLLPERWEFRNPKIVSVGRLDKDTSGLILVTDDTKLVH 133

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--CYGDMQVTLDTQKGSNAWVT 190
            L  P     +VY+V     +  D ++   KG+V+          ++ + ++  +N    
Sbjct: 134 QLTSPKHHVDKVYQVSVDCPLQSDIIDSFAKGVVLGEGAEQCLPAKIEIVSENVAN---- 189

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
           V L EGK  +++++F    + V  L R  +G ++L  L  G  
Sbjct: 190 VTLNEGKYHQVRRMFAACGYHVEALHRSQFGQYRLQDLAQGEW 232


>gi|255318614|ref|ZP_05359845.1| RNA pseudouridine synthase family protein [Acinetobacter
           radioresistens SK82]
 gi|262379160|ref|ZP_06072316.1| ribosomal large subunit pseudouridine synthase B [Acinetobacter
           radioresistens SH164]
 gi|255304296|gb|EET83482.1| RNA pseudouridine synthase family protein [Acinetobacter
           radioresistens SK82]
 gi|262298617|gb|EEY86530.1| ribosomal large subunit pseudouridine synthase B [Acinetobacter
           radioresistens SH164]
          Length = 301

 Score =  155 bits (392), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 77/301 (25%), Positives = 129/301 (42%), Gaps = 8/301 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
            +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG  ++    
Sbjct: 2   SEKLQKVLARIGLGSRRYMEEVIAAGRVSVNGRVAQV-GERIEPGDELRIDGRKVQFQIE 60

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R  L  Y     + + +      +           R + VGRLDIN+ GLLL TND
Sbjct: 61  DEIRRRVLIYYKPEGEICSRNDPESRPTVFDHLPTIANDRWVMVGRLDINSTGLLLFTND 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V       +  G+V+          +     G N 
Sbjct: 121 GELANRLMHPSNEIEREYAVRVMGEVTPQIRQNMLNGVVLDDGPAKFESFSEIGGDGINR 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V ++EG+NRE++++FE    KV+RL+R  YG   L   L  G   E+ K  + + L 
Sbjct: 181 WYQVVVKEGRNREVRRIFESQGLKVSRLLRTRYGTVILPRELRTGRWIELDKADI-DNLT 239

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
             +  + +        +     R     ++     + R ++  ++    +   +      
Sbjct: 240 KSVELKPRQGTGLYGMAKRRTERMAEKPMAARRGGYLRQQRRENEGTEQTAAPRKPYSPK 299

Query: 307 R 307
           +
Sbjct: 300 K 300


>gi|315125198|ref|YP_004067201.1| ribosomal RNA pseudouridylate synthase [Pseudoalteromonas sp.
           SM9913]
 gi|315013711|gb|ADT67049.1| putative ribosomal RNA pseudouridylate synthase [Pseudoalteromonas
           sp. SM9913]
          Length = 230

 Score =  155 bits (392), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 55/219 (25%), Positives = 94/219 (42%), Gaps = 7/219 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T  R++K IA AGI SR++  R+I +  V VN         +V   D + V+G  ++  
Sbjct: 2   DTKIRLAKYIAHAGICSRKQASRLIDEGVVIVNNRPANHID-HVDENDRVIVNGHAIKGP 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                + YHKP+G+           +   +     +RV  +GRLD ++ GL++LTNDG  
Sbjct: 61  ADLVYFAYHKPVGIDCK--LNHHDPSSLIHHLPQLTRVYPIGRLDKDSRGLIILTNDGDF 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + Y V  +  +D      +  G+ +        +V            +
Sbjct: 119 CNQLIHPDFHQPKRYLVTVNKPLDAHFCEKMAAGVPVDKQITRPCEVVKIASNQ----FS 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           + L++G NR+I+K+  +  + V  L R+      L  L 
Sbjct: 175 IVLKQGLNRQIRKMAHYCGYTVIDLYRVQISELLLDNLN 213


>gi|254427640|ref|ZP_05041347.1| conserved hypothetical protein, putative [Alcanivorax sp. DG881]
 gi|196193809|gb|EDX88768.1| conserved hypothetical protein, putative [Alcanivorax sp. DG881]
          Length = 280

 Score =  155 bits (392), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 73/280 (26%), Positives = 126/280 (45%), Gaps = 9/280 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG+ SRRE+E  I+  RV VNG +       V S D + VDG  ++    
Sbjct: 2   SEKLQKVLARAGLGSRRELETWISDGRVSVNGTVAT-LGDRVGSEDTLRVDGRMIKVKAE 60

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               +  +  +  P  + + +      +   +       R + VGRLDINT G++L T D
Sbjct: 61  EDTVQRVIMYHKPPGEVCSRNDPEGRPTVFDNLPRLQGMRWVQVGRLDINTTGMMLFTTD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD--MQVTLDTQKGS 185
           G LA  L  PS  ++R Y VR  G + Q+K   +  G++++        ++     ++G+
Sbjct: 121 GELAHRLMHPSNGFVREYAVRVRGGMTQEKRQAMLDGVLLEDGVSKFDSIEDAGGAEEGA 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           N W  V L  GK RE++++F+  + +V RL+RI +G   L   L  G   E+  + ++  
Sbjct: 181 NHWYKVTLTGGKYREVRRLFQSQDLEVARLMRIRFGDLNLPPQLRQGRWMELEPEQMKAL 240

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
           +    L+  +                           + R
Sbjct: 241 IDKVELKGKKYTGLYGRARLRHQRSGSKPPRKARRGPYRR 280


>gi|54308737|ref|YP_129757.1| hypothetical protein PBPRA1544 [Photobacterium profundum SS9]
 gi|46913167|emb|CAG19955.1| hypothetical 16S rRNA uridine-516 pseudouridylate synthase
           [Photobacterium profundum SS9]
          Length = 232

 Score =  155 bits (392), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 47/236 (19%), Positives = 98/236 (41%), Gaps = 8/236 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R+E  R++  + ++VNG +++  ++ +     +E +G  L      
Sbjct: 1   MRLDKFLATTLGITRKEAGRLLNNKMIEVNGDVVKSISLKITDDCDVEFNGKKLTLQGPQ 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      + +   D    +           ++   GRLD +T GL LLT+DG  +  
Sbjct: 61  YFMLNKPEGFVCSH-VDDHNPTVFVLFDEVSPEKMHVAGRLDGDTTGLTLLTDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     +VY V     V ++ +    +G+ ++G        ++ +  ++ +     +
Sbjct: 120 VTSPRHVCEKVYHVELADPVPEETIQTFLEGVQLRGEKDITRPAKLEILGEREAI----L 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
            + EGK  ++K++F     +V  L R   G   L   L  G  R ++ + +   L 
Sbjct: 176 TITEGKYHQVKRMFAAVGNRVVGLHREQVGAVVLDENLKPGEYRRLTDEEIASFLK 231


>gi|167747171|ref|ZP_02419298.1| hypothetical protein ANACAC_01885 [Anaerostipes caccae DSM 14662]
 gi|167654131|gb|EDR98260.1| hypothetical protein ANACAC_01885 [Anaerostipes caccae DSM 14662]
          Length = 243

 Score =  155 bits (392), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 105/234 (44%), Gaps = 5/234 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
              R+ K +      +R E  +MI Q RV     ++++    V    D I  DG  L   
Sbjct: 7   KTLRLDKFLCDVLGCTRSEARKMIRQGRVLAGDEIIKKPEYKVNPEEDEITADGQRLNFR 66

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L +      +VT   D   ++ +          +   GRLD +TEGLLL+TNDG L
Sbjct: 67  KYEYLMMNKPKG-VVTATKDGRDKTVMDLLTGRHRKGLFPAGRLDKDTEGLLLITNDGEL 125

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y V   G++ +++  + + G+ I         ++ + T  G  +  
Sbjct: 126 AHRLLSPKHHVTKCYSVTVTGEIGREQQEIFESGMDIGDDKPLKPAKLVILT-SGEVSQA 184

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            V + EG+  +IK++FE    KV  L R+S G   L   LL G  RE++++ ++
Sbjct: 185 EVFITEGRFHQIKRMFEAVGSKVLELKRLSMGSLVLDPELLPGQVRELTEEEIK 238


>gi|197285199|ref|YP_002151071.1| 23S rRNA pseudouridylate synthase B [Proteus mirabilis HI4320]
 gi|227355624|ref|ZP_03840018.1| ribosomal large subunit pseudouridine synthase B [Proteus mirabilis
           ATCC 29906]
 gi|194682686|emb|CAR42838.1| ribosomal large subunit pseudouridine synthase B [Proteus mirabilis
           HI4320]
 gi|227164231|gb|EEI49124.1| ribosomal large subunit pseudouridine synthase B [Proteus mirabilis
           ATCC 29906]
          Length = 308

 Score =  155 bits (392), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 79/309 (25%), Positives = 134/309 (43%), Gaps = 9/309 (2%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVD 63
           +  ++   +++ K++AR+G  SRRE+E  + + R+ ++G+  +     + +     I +D
Sbjct: 1   MSDKSQRTEKLQKILARSGHGSRREIEGYLQEGRISIDGVKAK-LGDRIDANSTAKIRLD 59

Query: 64  GVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           G  L   E        L  Y     L T        +          +R I+VGRLD+NT
Sbjct: 60  GRILSIREAQKDVCRVLAYYKPEGELCTRSDPQGRPTVFQRLPRLNSARWIAVGRLDVNT 119

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLL T DG LA  L  PS +  R Y VR  G++D  K+  L +G+ ++        V+
Sbjct: 120 SGLLLFTTDGELANRLMHPSREVEREYAVRVFGEIDDAKIRQLTRGVQLEDGPASFRSVS 179

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
               +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+ 
Sbjct: 180 YRGGEGINQWYNVSLTEGRNREVRRMWEAVGVQVSRLIRVRYGDIDLPKGLPRGGWVELG 239

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
              +        L +  V   A       +  ++     +     +     S  K   S+
Sbjct: 240 LNQINYLRQLVELNDETVTKVAVEKDQRRIKANQIRRAVKRHTKISARTSTSPAKRASSR 299

Query: 298 QKKLATPVH 306
           ++   +   
Sbjct: 300 RQSAGSKSK 308


>gi|261392828|emb|CAX50409.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F; rRNA pseudouridylate synthase F) [Neisseria
           meningitidis 8013]
 gi|325134050|gb|EGC56705.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           meningitidis M13399]
          Length = 252

 Score =  155 bits (391), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 108/255 (42%), Gaps = 20/255 (7%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K          R+SK +A+ G+ SRRE +  I Q  V VNG         V   D I
Sbjct: 1   MNPKTPPDHTEDAVRLSKRMAQLGLCSRREADGYIEQGWVTVNGKTA-VLGQKVSPADRI 59

Query: 61  EVD---------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           E++                 P+          Y     L+T+ +  +G +      P   
Sbjct: 60  ELNKKAHEQQAARITILLNKPVGYVSAQAEKGYKSAAELITSENRWEGDTGRIRFDPKHK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             +   GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+
Sbjct: 120 IGLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGL 179

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G      QV    +      +   L++GK R+I+++ E    +V  L RI  G  +L
Sbjct: 180 SLDGEKLRPAQVEWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>gi|209522381|ref|ZP_03270995.1| RNA-binding S4 domain protein [Burkholderia sp. H160]
 gi|209497187|gb|EDZ97428.1| RNA-binding S4 domain protein [Burkholderia sp. H160]
          Length = 325

 Score =  155 bits (391), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 107/250 (42%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---------- 64
           R+SK++++ G+ SRRE +  I +  V V+G  ++     V     I++D           
Sbjct: 78  RLSKLMSKLGLCSRREADEWIEKGWVMVDGERVDTLGTKVFPDQRIDIDPAAEAFQSSQV 137

Query: 65  -----VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
                 P+          Y   I LVT  +  +G  +      S   ++   GRLDI++ 
Sbjct: 138 TVIVHKPVGLVSGQAEDGYQPAITLVTPENRWEGDRSGVRFSVSHLRQLAPAGRLDIDST 197

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT DG +A+ L    +   + Y VR                +KL LL+ G+ +  +
Sbjct: 198 GLLVLTQDGRIAKQLIGGHSDVDKEYLVRVAYGEYTVDVESHFPAEKLALLRHGLSLDDV 257

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                QV+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 258 ALKPAQVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVVGLKRVRMGQVMLGALPP 313

Query: 231 GSTREVSKKI 240
           G  R +S+  
Sbjct: 314 GQWRYLSEDE 323


>gi|94990658|ref|YP_598758.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS10270]
 gi|306827141|ref|ZP_07460432.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes ATCC 10782]
 gi|94544166|gb|ABF34214.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS10270]
 gi|304430668|gb|EFM33686.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes ATCC 10782]
          Length = 244

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 99/233 (42%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ +R +V+ ++ ++ + VN  +   A  ++    D +   G PL     
Sbjct: 2   MRLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEYKDLVTYQGTPLVYESF 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T            +  +    V  VGRLD +T GLLLLTN+G LA 
Sbjct: 62  VYYLLNKPSGYVSATQDRQQATVMELLDDTARQKAVFPVGRLDKDTRGLLLLTNNGQLAH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVT 190
            L  P     + Y  +  G + +   +   +GI ++        + +     +   + V 
Sbjct: 122 DLLSPKKHVTKEYLAKVAGIMTEADKDYFARGISLKDHQCLPAHLEVLASDLQQQTSLVK 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + ++EGK  ++K++       V  L R+S GP +L  +L  G  R ++ + L+
Sbjct: 182 ITIQEGKFHQVKRMVAACGKGVLDLQRLSMGPLKLDPSLAEGEFRRLTPEELQ 234


>gi|121634598|ref|YP_974843.1| putative RNA-binding protein [Neisseria meningitidis FAM18]
 gi|218767923|ref|YP_002342435.1| putative RNA-binding protein [Neisseria meningitidis Z2491]
 gi|120866304|emb|CAM10045.1| putative RNA-binding protein [Neisseria meningitidis FAM18]
 gi|121051931|emb|CAM08237.1| putative RNA-binding protein [Neisseria meningitidis Z2491]
 gi|308388992|gb|ADO31312.1| putative RNA-binding protein [Neisseria meningitidis alpha710]
 gi|319410171|emb|CBY90507.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F; rRNA pseudouridylate synthase F) [Neisseria
           meningitidis WUE 2594]
 gi|325129963|gb|EGC52762.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           meningitidis OX99.30304]
 gi|325135973|gb|EGC58583.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           meningitidis M0579]
          Length = 252

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 107/255 (41%), Gaps = 20/255 (7%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K          R+SK +A+ G+ SRRE +  I Q  V VNG         V   D I
Sbjct: 1   MNPKTPPDHTEDAVRLSKRMAQLGLCSRREADGYIEQGWVTVNGKTA-VLGQKVSPADRI 59

Query: 61  EVD---------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           E++                 P+          Y     L+T  +  +G +      P   
Sbjct: 60  ELNKKAHEQQAARITILLNKPVGYVSAQAEKGYKSAAELITPENRWEGDTGRIRFDPKHK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             +   GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+
Sbjct: 120 IGLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGL 179

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G      QV    +      +   L++GK R+I+++ E    +V  L RI  G  +L
Sbjct: 180 SLDGEKLRPAQVEWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>gi|115380386|ref|ZP_01467383.1| ribosomal large subunit pseudouridine synthase B [Stigmatella
           aurantiaca DW4/3-1]
 gi|310821617|ref|YP_003953975.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|115362608|gb|EAU61846.1| ribosomal large subunit pseudouridine synthase B [Stigmatella
           aurantiaca DW4/3-1]
 gi|309394689|gb|ADO72148.1| Pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 648

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 90/342 (26%), Positives = 134/342 (39%), Gaps = 1/342 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +ARAG+ASRR  E +I   RV VN   +      V    D + VDG  +   E 
Sbjct: 3   ERLQKYLARAGVASRRHAEELITAGRVMVNNQKVTELGSRVEPGTDLVSVDGELVSLPET 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +  +L +KP G+VTT SDP GR TV   + +   R+  VGRLD + EG LL T+DG LA 
Sbjct: 63  SSYYLLYKPAGVVTTLSDPQGRPTVASYVEATGKRLFPVGRLDYDAEGALLFTDDGTLAH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS Q  R Y  +  G  D+  L  L+ G+ ++      + V L  Q   N W+ + 
Sbjct: 123 KLTHPSFQVPRTYLAKVKGSPDRATLEKLRGGVRLEDGMATPLSVDLFEQAERNTWLKIV 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           + EG+   IK++       V RL R +Y    +  +  G  R ++   +R          
Sbjct: 183 VAEGRPHLIKRLCAAVGHPVVRLFRPAYAGVGVSGVRPGELRPLTSTEVRLLQDVAEART 242

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
           A    +  +               E  + F      ++            T   R   A 
Sbjct: 243 APPEGELNLPPRRHGRAAPGFEEDEDGEGFEVEGAAAAPAKPSRSPAAAKTGRARPAAAG 302

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                    S             R S +  S+    R    +
Sbjct: 303 RPERKPAGKSPRTEGGTGLARFGRTSSAAVSEEGSERPRRSE 344


>gi|86358998|ref|YP_470890.1| pseudouridylate synthase, ribosomal large subunit protein
           [Rhizobium etli CFN 42]
 gi|86283100|gb|ABC92163.1| probable pseudouridylate synthase, ribosomal large subunit protein
           [Rhizobium etli CFN 42]
          Length = 312

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 71/266 (26%), Positives = 120/266 (45%), Gaps = 12/266 (4%)

Query: 1   MKDKNIVQENFT---------PQR--VSKVIARAGIASRREVERMIAQQRVKVNGILLER 49
           M+D+    +             +R  + + +++ G  SR + ER+IA+ RV V+G  +  
Sbjct: 46  MRDRRPSHKTRERLKPAADTAGKRVTLPRALSKLGYCSRTQAERLIAESRVAVDGRTVSD 105

Query: 50  AAVNVM-STDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           A+  V  ST  I VDG+ +    +  L L      + T        +            +
Sbjct: 106 ASAWVDLSTARISVDGLVIAAEAKIYLMLNKPRGLVTTRQDPEGRPTVYDCLKNFDIPHL 165

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
             VGRLD  +EGLLL TND   A+ L  P T   + Y V+    +D +++  +  GI   
Sbjct: 166 SPVGRLDKASEGLLLFTNDTEFAQTLLDPLTHVTKTYHVQIDRLMDDEEIAAMTSGIRHD 225

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           G            Q   N+W+ V L EG+NR+I+++ E    +  RL+R++ G  +LG L
Sbjct: 226 GELLTAAATRRLRQGDRNSWIEVELDEGRNRQIRRMLEALGAECLRLVRVAIGGLELGEL 285

Query: 229 LAGSTREVSKKILREQLGPHLLEEAQ 254
             G+ R +++  L+       +E A+
Sbjct: 286 PKGAVRALTEGELQGLRRRAGMERAR 311


>gi|291561019|emb|CBL39819.1| ribosomal small subunit pseudouridine synthase A
           [butyrate-producing bacterium SSC/2]
          Length = 242

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 111/241 (46%), Gaps = 4/241 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA 70
              R+ K +  +   +R+E +  + + +V VNG  +++    V    D +E D   ++  
Sbjct: 3   KKTRLDKFLCDSLNMTRKEAKESVKKGKVVVNGEAIKKPEYKVDAEQDQVEFDHKLIQFE 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L L+     +V+   D   ++ +         R+  VGRLD +TEGLLLLT+DG L
Sbjct: 63  QFHYLMLHKPQG-VVSATKDHHDQTVLDLIHEDYKDRLFPVGRLDKDTEGLLLLTDDGML 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     +VY  +  GQ  ++++   K+G+ I  G      ++ +       + V
Sbjct: 122 AHELLSPRKHVDKVYFAKVSGQFGENEIARFKEGLDIGNGERSKQARLQILKADVQESEV 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
            + + EGK  ++K++ +    +V  L R+S G  +L   L  G  R ++K  L+E     
Sbjct: 182 LITIMEGKFHQVKRMVKAVGSEVLYLKRLSMGSLKLDEELKLGEYRRLTKAELQELKEHR 241

Query: 249 L 249
            
Sbjct: 242 R 242


>gi|254418210|ref|ZP_05031934.1| conserved hypothetical protein, putative [Brevundimonas sp. BAL3]
 gi|196184387|gb|EDX79363.1| conserved hypothetical protein, putative [Brevundimonas sp. BAL3]
          Length = 259

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 63/242 (26%), Positives = 112/242 (46%), Gaps = 14/242 (5%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +   P RV+K + + G+ SRRE E +IA+  V ++G  +  A   +     + ++    +
Sbjct: 8   DGDEPVRVNKWLGQTGVCSRREAESLIAEGLVSIDGETISDAGRKIEPGQTLTLNDTAQQ 67

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI----------SVGRLDINT 118
                   + HKP+G V+   DP     V                       +GRLD ++
Sbjct: 68  ALASGMTLVLHKPVGYVSGQPDPGKIPAVRLLKIPNRIGEGETPARDASLPPIGRLDEDS 127

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLLL++DG +A+ +  P+++  + Y V   G + + KL+ L+ G+V+        +VT
Sbjct: 128 RGLLLLSSDGVVAKAVIGPASELDKEYLVVVDGVITEAKLSRLRHGLVLNDKPLKPARVT 187

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
               +     +   L EGK R+I+++ E    +V  L RI  GP ++G L  G  R ++ 
Sbjct: 188 QIEPQR----LRFVLTEGKYRQIRRMCELVGLEVVDLYRIRIGPLEIGDLPEGRWRHLTD 243

Query: 239 KI 240
           + 
Sbjct: 244 QE 245


>gi|110834248|ref|YP_693107.1| S4 domain-containing protein [Alcanivorax borkumensis SK2]
 gi|110647359|emb|CAL16835.1| S4 domain protein [Alcanivorax borkumensis SK2]
          Length = 280

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 71/280 (25%), Positives = 124/280 (44%), Gaps = 9/280 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG+ SRRE+E  I+  RV VNG +       V S D + VDG  ++    
Sbjct: 2   SEKLQKVLARAGLGSRRELETWISDGRVSVNGTVAT-LGDRVGSEDTLRVDGRIIKVKTE 60

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               +  +  +  P  + + +      +   +       R + VGRLDINT G++L T D
Sbjct: 61  EDTVQRVIMYHKPPGEVCSRNDPEGRPTVFDNLPRLQGMRWVQVGRLDINTTGMMLFTTD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD--MQVTLDTQKGS 185
           G LA  L  PS  ++R Y VR  G +  +K   +  G++++        ++     ++G+
Sbjct: 121 GELAHRLMHPSNGFVREYAVRVRGVMTPEKRQAMLDGVLLEDGVSKFDSIEDAGGAEEGA 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           N W    L  GK RE++++F+  + +V RL+RI +G   L   L  G   E+  + ++  
Sbjct: 181 NHWYKATLTGGKYREVRRLFQSQDLEVARLMRIRFGDLTLPPQLRQGRWMELEPEQMKAL 240

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
           +    L+  +                           + R
Sbjct: 241 IEKVDLKGKKYTGLYGRARLRHQRGGNKPPRKARRGPYRR 280


>gi|17231365|ref|NP_487913.1| hypothetical protein all3873 [Nostoc sp. PCC 7120]
 gi|17133007|dbj|BAB75572.1| all3873 [Nostoc sp. PCC 7120]
          Length = 262

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 85/243 (34%), Positives = 124/243 (51%), Gaps = 12/243 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ KV+A+ GIASRRE E MI + RV++NG L       V    D I VDG  +      
Sbjct: 4   RLQKVLAQWGIASRREAEEMIRRSRVQINGTLA-ELGQKVNPEKDIITVDGKSVSAQRHP 62

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLLTNDG 128
           R    L +KP G+V+T  DP GR TV D LP    +      VGRLD ++ G L+LTNDG
Sbjct: 63  RLTYLLLNKPTGVVSTCYDPQGRKTVLDLLPEELRKGPGLHPVGRLDADSTGALILTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS    + Y+V   G   +  L + ++G+++ G      +V+L       + 
Sbjct: 123 DLTFRLTHPSHSIPKTYQVLVKGHPPKAVLEMWREGVLLDGRKTRKAKVSLLESLAEKSR 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-----LLAGSTREVSKKILRE 243
           + + L+EG+NR+I++V E   + V +L R + G  QL T     L AG+ R +    +R 
Sbjct: 183 LEIVLQEGRNRQIRRVAEQLGYPVIKLHRTAIGSIQLQTSKQPLLRAGNYRILRDDEIRS 242

Query: 244 QLG 246
              
Sbjct: 243 LQE 245


>gi|218132204|ref|ZP_03461008.1| hypothetical protein BACPEC_00061 [Bacteroides pectinophilus ATCC
           43243]
 gi|217992897|gb|EEC58897.1| hypothetical protein BACPEC_00061 [Bacteroides pectinophilus ATCC
           43243]
          Length = 500

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 69/250 (27%), Positives = 114/250 (45%), Gaps = 22/250 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A   + +R +V+  I ++ V VNG+ + +  V V +  D I V G  +    +
Sbjct: 4   IRLDKYLADMQVGTRSQVKEQIRKKLVSVNGVTVTKPDVKVDTDRDKIMV-GSDIIGYTQ 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +KP G+++  +DP  ++ V     +I   +  VGRLD +TEGL+L+TNDG LA 
Sbjct: 63  FEYFMLNKPKGVLSAANDPKAQTVVDLITDNICRDLFPVGRLDKDTEGLMLITNDGELAH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---------------QGICYGDMQV 177
            L  P     + Y VRF G +  + +    KGI I               +       ++
Sbjct: 123 KLLSPRKHVDKSYYVRFEGIIADNTVESFAKGIDINIAKCADDEVDNNPKEIYHTKPAKL 182

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
            L +   +     + + EGK  +IK++F     +V  L RIS G  QL   L  G  R +
Sbjct: 183 RLMSADEAV----ITISEGKFHQIKRMFMAAGCRVTYLKRISMGTLQLDFDLKPGQYRRL 238

Query: 237 SKKILREQLG 246
           +        G
Sbjct: 239 TDSETDNLRG 248


>gi|157960503|ref|YP_001500537.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157845503|gb|ABV86002.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 238

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 65/241 (26%), Positives = 100/241 (41%), Gaps = 16/241 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD---------HIEVDG 64
            R++K +A  G  SRR   R+I    V+++  L       V   D          I V+ 
Sbjct: 1   MRLAKYLALTGCCSRRAATRLIRDGLVRIDERLANHVDS-VTLIDTPIGQRSIEQIYVND 59

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P+R  E    WL++K   + T             +L     R+  VGRLD ++ GLL+L
Sbjct: 60  EPIRVVEAKAYWLFNKA--VGTDSRLLAHLPNSLLHLLPESPRLYPVGRLDKDSRGLLIL 117

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG L   L  P     + Y V+     D   L  +  G+  + +      +       
Sbjct: 118 TNDGELTHKLMHPDFGHAKTYHVQVDRPFDDAFLVNMAAGVSYKDVVTLPCIMQRLAADK 177

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
                 + L +G NR+I+++ +   +KV  L R+S    QLG L  GS R +S   L + 
Sbjct: 178 ----YEITLTQGLNRQIRRMSQALGFKVIDLKRVSIQSLQLGDLPEGSMRPLSSAELADL 233

Query: 245 L 245
           L
Sbjct: 234 L 234


>gi|56964562|ref|YP_176293.1| 16S pseudouridylate synthase [Bacillus clausii KSM-K16]
 gi|56910805|dbj|BAD65332.1| 16S pseudouridylate synthase [Bacillus clausii KSM-K16]
          Length = 243

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 105/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A AG  +R EV++ + Q  V+V+G +++   ++V      +   G P+R    
Sbjct: 1   MRLDKMLANAGYGTRNEVKKALKQGVVEVDGAVVKDGKLHVQPERQSVCYAGTPVRYKAE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L      +  T                   +   VGRLD +T GLLLLT DG  + 
Sbjct: 61  LYLMLNKPAGVVTATEDARQKTVLDLMKNEWGHMKPFPVGRLDKDTTGLLLLTTDGAFSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            L  P     + YR    G+V Q  +   K G+V+         Q+ ++ + G  + +++
Sbjct: 121 ELMAPKKHIAKEYRALVEGKVTQADVEAFKNGVVLDDGYCTKPAQLEIE-ESGPLSAISL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            L EGK  ++K++F     KV +L RI  G   L  +L  G  RE++   ++
Sbjct: 180 ELTEGKFHQVKRMFAAVGKKVIKLERIRIGSLLLDSSLPKGGYRELTPAEIQ 231


>gi|319442276|ref|ZP_07991432.1| putative pseudouridylate synthase [Corynebacterium variabile DSM
           44702]
          Length = 282

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 74/244 (30%), Positives = 115/244 (47%), Gaps = 4/244 (1%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHI 60
             K   + +    R+ KV+A AG+ASRR  E++I   RV+VNG ++    + V    D I
Sbjct: 30  NQKKRTKSDNEKTRLQKVLAAAGVASRRMSEKLIEAGRVEVNGSIVTEQGMRVDPENDVI 89

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDIN 117
            VDGV +   E    +  +KP G+ +T  D  GR  + D +        R+  VGRLD  
Sbjct: 90  RVDGVRVIADEEIVTFALNKPRGIHSTMHDEFGRPCLSDLVGERVEAGQRLFHVGRLDAQ 149

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLLLLTNDG LA  L  P     + Y     G+ D+  +  L  GI +        +V
Sbjct: 150 TEGLLLLTNDGELANRLMHPRYGIKKTYLATVLGEADRRLVRQLLDGIELDDGIVIADEV 209

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EG+   ++++ +   + V  L+R      QLG    G+ R ++
Sbjct: 210 QIIDAWQGKSLIKVVIHEGRKHVVRRMLKEAGFPVQALVRTKVHTVQLGEQKPGTLRALN 269

Query: 238 KKIL 241
           +  L
Sbjct: 270 RSEL 273


>gi|315635454|ref|ZP_07890720.1| RNA pseudouridine synthase [Arcobacter butzleri JV22]
 gi|315480212|gb|EFU70879.1| RNA pseudouridine synthase [Arcobacter butzleri JV22]
          Length = 275

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 68/251 (27%), Positives = 123/251 (49%), Gaps = 18/251 (7%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
             F   R++K ++     SRRE +++I + +++VN  ++   A  V STD +E+    ++
Sbjct: 15  PKFELIRLNKFLSHNSNYSRREADKLIEEGKIRVNNKVVTDLATKVKSTDKVEIGKKLIK 74

Query: 69  KAERTRL--WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           + +       +Y+KP G + +  DP GR T++D L   +   +SVGRLD ++EGLLLL++
Sbjct: 75  EEKNKLYTVIVYNKPKGEIVSKKDPQGRKTIYDGLEHKYKHFLSVGRLDYSSEGLLLLSD 134

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICY 172
              +   L        RVY+++ +G +       ++ GI I+                  
Sbjct: 135 SVDIVNALMHSD--LERVYKIKLNGVITPAVEQAMQSGITIEDATSGAYKGTKIKSMSFA 192

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
             +   + T    ++ + V + EGKNRE+++ F  FN  V  L R+ YG   L  L  G 
Sbjct: 193 PFLAYDIQTNGTKHSKIKVVINEGKNRELRRFFAHFNLDVLDLKRLEYGGISLNNLPTGK 252

Query: 233 TREVSKKILRE 243
           +R ++K+  + 
Sbjct: 253 SRYLTKEEYKN 263


>gi|157736321|ref|YP_001489004.1| ribosomal large subunit pseudouridine synthase B [Arcobacter
           butzleri RM4018]
 gi|157698175|gb|ABV66335.1| ribosomal large subunit pseudouridine synthase B [Arcobacter
           butzleri RM4018]
          Length = 275

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 68/251 (27%), Positives = 123/251 (49%), Gaps = 18/251 (7%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
             F   R++K ++     SRRE +++I + +++VN  ++   A  V STD +E+    ++
Sbjct: 15  PKFELIRLNKFLSHNSNYSRREADKLIEEGKIRVNNKVVTDLATKVKSTDKVEIGKKLIK 74

Query: 69  KAERTRL--WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           + +       +Y+KP G + +  DP GR T++D L   +   +SVGRLD ++EGLLLL++
Sbjct: 75  EEKNKLYTVIVYNKPKGEIVSKKDPQGRKTIYDGLEHKYKHFLSVGRLDYSSEGLLLLSD 134

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICY 172
              +   L        RVY+++ +G +       ++ GI I+                  
Sbjct: 135 SVDIVNALMHSD--LERVYKIKLNGLITPAVEQAMQSGITIEDATSGAYKGTKIKSMSFA 192

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
             +   + T    ++ + V + EGKNRE+++ F  FN  V  L R+ YG   L  L  G 
Sbjct: 193 PFLAYDIQTNGTKHSKIKVVINEGKNRELRRFFAHFNLDVLDLKRLEYGGISLNNLPTGK 252

Query: 233 TREVSKKILRE 243
           +R ++K+  + 
Sbjct: 253 SRYLTKEEYKN 263


>gi|262068119|ref|ZP_06027731.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium
           periodonticum ATCC 33693]
 gi|291378207|gb|EFE85725.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium
           periodonticum ATCC 33693]
          Length = 226

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 68/229 (29%), Positives = 108/229 (47%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ + +   GI SR+EV+++I+ + VKVNG     A  N+   +D IE +G  L   E 
Sbjct: 1   MRLDRFLVECGIGSRKEVKKIISTKEVKVNGSYDISAKDNIDEYSDIIEYNGKKLEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +  K   +  T    +           I   +  VGRLD +TEGLLL TNDG L  
Sbjct: 61  RYYIMNKKAGYITATEDTREATVMDLLPEWVIKKDLAPVGRLDKDTEGLLLFTNDGKLNH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V     + Q+ +  L++G+ I        +V    +K S+  + + 
Sbjct: 121 RLLSPKNHVDKTYYVEIENNISQEDILKLEEGVDIGSYVTLPAKV----KKISDTKIFLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++EGK  ++KK+ E  N KV  L R S+   +L  L  G  +EV+ + +
Sbjct: 177 IKEGKFHQVKKMLEAVNNKVIYLQRTSFAKLKLADLALGEVKEVNLEDI 225


>gi|303228803|ref|ZP_07315617.1| putative 16S pseudouridylate 516 synthase [Veillonella atypica
           ACS-134-V-Col7a]
 gi|303232129|ref|ZP_07318832.1| putative 16S pseudouridylate 516 synthase [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302513235|gb|EFL55274.1| putative 16S pseudouridylate 516 synthase [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302516515|gb|EFL58443.1| putative 16S pseudouridylate 516 synthase [Veillonella atypica
           ACS-134-V-Col7a]
          Length = 232

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 60/235 (25%), Positives = 109/235 (46%), Gaps = 9/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILL--ERAAVNVMSTDHIEVDGVPLRKAE 71
            R+ K++A     SR+EV ++I   RV VNG ++  +  ++++   D I VDGV +   +
Sbjct: 1   MRLDKLLANKAFGSRKEVHQIIRDGRVTVNGAVILKKDQSIHID-DDIIAVDGVQISTKQ 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  +  +     +                       V  VGRLD +TEGLLLLTNDG  A
Sbjct: 60  QYYIKFHKPAGYITAVEDPTHPVVMDLLPPEFKKMGVFPVGRLDKDTEGLLLLTNDGIWA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             +        +VY V F+G++ +D L  ++ GIV+  G       + + +++     + 
Sbjct: 120 HSIINGHKHVPKVYYVEFNGKLTKDGLERIETGIVLGDGTQCKPANIDVLSEQS----LH 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQ 244
           + + EGK  ++K++      +V  L R+S G   L  + A  +  E+  + + + 
Sbjct: 176 ITIEEGKYHQVKRMIGAAGGEVTYLKRLSIGHITLNGIEAINTYSEIDDQDVVDF 230


>gi|261749610|ref|YP_003257296.1| hypothetical protein BPLAN_550 [Blattabacterium sp. (Periplaneta
           americana) str. BPLAN]
 gi|261497703|gb|ACX84153.1| conserved hypothetical protein [Blattabacterium sp. (Periplaneta
           americana) str. BPLAN]
          Length = 255

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 67/256 (26%), Positives = 124/256 (48%), Gaps = 5/256 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K I +E F   R++  ++ AGI SRRE +++I    ++VNG ++ +    V   D I
Sbjct: 5   MNQKKIEEEKF--IRLNHYLSNAGITSRREADKLIQSGLIEVNGKIVTKFGTVVHKNDVI 62

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +  G  ++  ++  + L      + +T    + ++ +         R+  VGRLD  T G
Sbjct: 63  KFHGSRIKNKKKIYILLNKPKGYITSTRDPFNRKTVMNLIPNFQNYRIYPVGRLDRLTTG 122

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG +   L  P  +  ++Y V  +  +    L+ +++G +      G +++   
Sbjct: 123 VLLLTNDGFITEKLTHPKYKIQKIYLVVLNKTIHYQDLDKIRQGKIYLNE--GRVKIDFL 180

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +   N  V +GL  G NR I+++F+   ++V +L RI +G F    L  GS   +SK+ 
Sbjct: 181 HKYAKN-IVKIGLHIGWNRVIRRIFKKLTYQVIKLERIHFGGFTNKNLKIGSWCFLSKQE 239

Query: 241 LREQLGPHLLEEAQVN 256
           +   +     E+ + N
Sbjct: 240 VDHTVKNLFHEKNKHN 255


>gi|163753329|ref|ZP_02160453.1| pseudouridylate synthase (ribosomal large subunit pseudouridine
           synthase B) [Kordia algicida OT-1]
 gi|161327061|gb|EDP98386.1| pseudouridylate synthase (ribosomal large subunit pseudouridine
           synthase B) [Kordia algicida OT-1]
          Length = 292

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 69/238 (28%), Positives = 112/238 (47%), Gaps = 1/238 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K     N    R++K I+ +GI SRRE +  I+   V VNG ++      V  TD +  D
Sbjct: 50  KQKTSSNPNEIRLNKYISNSGICSRREADMHISVGSVTVNGKVVTEMGYKVQLTDEVRFD 109

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G  +   + T + L      LVTT  +   ++ +     +  +R++ VGRL+  T GLLL
Sbjct: 110 GRIINPEKATYILLNKPKGFLVTTKDEKGRKTVMDLVATATTARIVPVGRLERQTTGLLL 169

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            TNDG LAR L  P     +++ V     + Q   N +K G+ I+G  YG  +++   Q 
Sbjct: 170 FTNDGELARKLTDPHQNVRKIFHVELDRNLSQTDFNKIKDGVNIRGDIYGVDEISWI-QG 228

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            S   V + +  G N  +K +FE  ++ V RL R+ +       L     R ++ + +
Sbjct: 229 ASKREVGIKVSTGSNGLVKAIFEHLSYTVARLDRVVFAGLTKKDLPRSHWRHLTAQEV 286


>gi|71903738|ref|YP_280541.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS6180]
 gi|71802833|gb|AAX72186.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS6180]
          Length = 244

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 99/233 (42%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ +R +V+ ++ ++ + VN  +   A  ++    D +   G PL     
Sbjct: 2   MRLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEYKDLVTYQGTPLVYESF 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T            +  +    V  VGRLD +T GLLLLTN+G LA 
Sbjct: 62  VYYLLNKPSGYVSATQDRQQATVMELLDDTARQKAVFPVGRLDKDTRGLLLLTNNGQLAH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVT 190
            L  P     + Y  +  G + +   +   +GI ++        + +     +   + V 
Sbjct: 122 DLLSPKKHVTKEYLAKVVGIMTEADKDYFARGISLKDHQCLPAHLEVLASDLQQRTSLVK 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + ++EGK  ++K++       V  L R+S GP +L  +L  G  R ++ + L+
Sbjct: 182 ITIQEGKFHQVKRMVAACGKGVLDLQRLSMGPLKLDPSLAEGEFRRLTPEELQ 234


>gi|329119926|ref|ZP_08248600.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           bacilliformis ATCC BAA-1200]
 gi|327464082|gb|EGF10393.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           bacilliformis ATCC BAA-1200]
          Length = 369

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 75/256 (29%), Positives = 128/256 (50%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G  SRRE+E  IA   V+VNG   +     V   D +
Sbjct: 105 LKERRSDLSRQEPERLQKVLAASGAGSRREMEEWIAAGLVQVNGKTAQ-LGDKVTPDDQV 163

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G P++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 164 TVKGSPIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 223

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G++  +++  L  +G+++        
Sbjct: 224 NTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGELTAEQMRELTTEGVMLDDGLAKVE 283

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G+N W +V ++EG+NRE++++FE F   V+RL+R+ +GP  L   L  G   
Sbjct: 284 RIFEQGGEGANKWYSVVIKEGRNREVRRIFEHFGLTVSRLVRVGFGPIGLPNRLKRGQFY 343

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   +    +
Sbjct: 344 ELNPAEVANIVKWADM 359


>gi|146329607|ref|YP_001209391.1| ribosomal large subunit pseudouridine synthase, RluB [Dichelobacter
           nodosus VCS1703A]
 gi|146233077|gb|ABQ14055.1| ribosomal large subunit pseudouridine synthase, RluB [Dichelobacter
           nodosus VCS1703A]
          Length = 266

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 78/265 (29%), Positives = 125/265 (47%), Gaps = 12/265 (4%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           ++N   QR+ K +A  G+ SRR++E  I + R+KV+G +       +   + + +DG PL
Sbjct: 3   KKNDDAQRIQKYLAARGVGSRRQIETWIKEGRLKVDGRVA-ELGQKISGNERLSLDGKPL 61

Query: 68  R-----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           R     K     L  +     + T        S           R +++GRLD+NT GLL
Sbjct: 62  RIAVEHKNPHMILMYHKPAGEICTRKDPEGRVSVFQHLPKISHGRWVAIGRLDLNTSGLL 121

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG-----DMQV 177
           L TNDG LA  L  PS +  R Y VR  G+V ++ L  L++GI +            ++ 
Sbjct: 122 LFTNDGALANQLMHPSAEIEREYWVRVAGEVTEEMLTALRQGIPLDDGLARFTEICPLKT 181

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
             +     N + +V L+EG+NRE+++++E    KV+RL RI YG   L  +L AG  R +
Sbjct: 182 LHEDDTQFNRYFSVTLKEGRNREVRRLWEAVGCKVSRLKRIRYGTISLPPSLSAGRHRLL 241

Query: 237 SKKILREQLGPHLLEEAQVNLDAPI 261
           +       +     +  + N   P 
Sbjct: 242 TAGEQASLISLVSEKNRRDNSPKPR 266


>gi|260913991|ref|ZP_05920465.1| ribosomal large subunit pseudouridine synthase B [Pasteurella
           dagmatis ATCC 43325]
 gi|260632078|gb|EEX50255.1| ribosomal large subunit pseudouridine synthase B [Pasteurella
           dagmatis ATCC 43325]
          Length = 358

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 93/283 (32%), Positives = 134/283 (47%), Gaps = 10/283 (3%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIE 61
              + +     +++ KV+ARAG  SRRE+E MIA+ RV V+G +      ++V S   + 
Sbjct: 66  KNTVKKPKVEGEKLQKVLARAGQGSRREIEAMIAENRVSVDGKMATLGDRIDVRSGVKVR 125

Query: 62  VDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           +DG  +            L  Y     L T H      +          SR I+VGRLDI
Sbjct: 126 IDGHIVNLMHAQKEVCRVLMYYKPEGELCTRHDPEGRATVFDRLPRLTGSRWIAVGRLDI 185

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NT GLLL T DG LA  L  PS +  R Y VR  GQVD   LN LKKG+ ++       +
Sbjct: 186 NTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLNRLKKGVQLEDGPANFKE 245

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTRE 235
           +      G N W  V L EG+NRE+++++E    +V+RLIR  YG   L  +L  G   E
Sbjct: 246 IKFAGGVGMNQWFDVTLMEGRNREVRRLWESQGVQVSRLIRTRYGNISLMKSLPRGGWEE 305

Query: 236 VSK---KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNII 275
           +       LRE +G     E ++++  P   ++T    +    
Sbjct: 306 MDLTNVNYLRELVGLPPEMETKLDVTKPRRRAKTSQIRKAVKR 348


>gi|257452524|ref|ZP_05617823.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           3_1_5R]
 gi|317059065|ref|ZP_07923550.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           3_1_5R]
 gi|313684741|gb|EFS21576.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           3_1_5R]
          Length = 238

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 64/236 (27%), Positives = 116/236 (49%), Gaps = 3/236 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           ++EN    R++K +A  G+ASRR+++  I + ++ VNGIL       V + D I V+G  
Sbjct: 1   MEENK--IRINKFLASKGVASRRQIDLWIEEGKILVNGILATS-GQKVSAEDKILVNGKM 57

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           + + E  +++        V +    +       +     +R+  VGRLD  T GL+LLTN
Sbjct: 58  ISEKEEKKVYYILYKEEEVLSAVKDERGRKTVVDCIPTKARIFPVGRLDYRTSGLILLTN 117

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L   +  P  +  + Y V   G + +++L  L++G+ ++     +  V     +  N
Sbjct: 118 DGELFNRVMHPRAEIFKTYEVLAKGHLTREQLKTLEEGVELEEGKTLEALVAKVKYEKGN 177

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +  + +REG+NR+I+++ E    +V RL R   G   L  L  G  R + ++ + 
Sbjct: 178 TFFEISIREGRNRQIRRMVEAVGSRVYRLRRTKIGRLSLEGLKLGQYRRLQEEEIE 233


>gi|325926524|ref|ZP_08187841.1| pseudouridine synthase family protein [Xanthomonas perforans
           91-118]
 gi|325543096|gb|EGD14542.1| pseudouridine synthase family protein [Xanthomonas perforans
           91-118]
          Length = 253

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 64/241 (26%), Positives = 106/241 (43%), Gaps = 10/241 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++K IA  G  SRRE +R+I ++RV VNG+     AV V + D + VDG PLR  E 
Sbjct: 15  TIRLNKYIAETGFCSRREADRLIGERRVTVNGVPAGTGAV-VGAEDTVLVDGQPLRIREA 73

Query: 73  TRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            +L             +  T +                 R+  +GRLD ++EGL+L+T++
Sbjct: 74  KKLGGRKHVYIALNKPVGITCTTESSVKGNIVEFVGHEQRIFPIGRLDKDSEGLILMTSN 133

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +     +  + Y V  +  V  + L  + +G+ I        +     + G   
Sbjct: 134 GNIVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRIHNETTLPCRTARIAKFG--- 190

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR  L  
Sbjct: 191 -FRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELRGLLPQ 249

Query: 248 H 248
            
Sbjct: 250 R 250


>gi|38233785|ref|NP_939552.1| putative pseudouridine synthase B [Corynebacterium diphtheriae NCTC
           13129]
 gi|38200046|emb|CAE49722.1| Putative pseudouridine synthase B [Corynebacterium diphtheriae]
          Length = 321

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 77/236 (32%), Positives = 117/236 (49%), Gaps = 4/236 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           +    R+ KV+A+AG+ASRR  E +I   RV+VNG ++    + V    D I VDGV + 
Sbjct: 77  STEGIRLQKVLAQAGVASRRHAEILIDAGRVEVNGKIVMTQGMRVNPNVDVIRVDGVRVN 136

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLT 125
             E  + ++ +KP GL +T SD  GR  V D +        R+  VGRLD  TEGLLLLT
Sbjct: 137 VNENLQYFVLNKPRGLQSTMSDDMGRPCVGDIVGERISAGQRLFHVGRLDAATEGLLLLT 196

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  P  +  + Y     G+ D+  +  L+ GI +         V +      
Sbjct: 197 NDGELANRLMHPRYEVSKTYLATVLGEADKRLVKQLRDGIELDDGPAKADLVQIIDTFQG 256

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + + + L EG+   ++++ +   + V RL+R      QLG    G+ R ++   L
Sbjct: 257 KSLIRIELHEGRKHIVRRMLKTAGFPVQRLVRTKIHTIQLGEQTPGAIRALNSSEL 312


>gi|225012606|ref|ZP_03703041.1| RNA-binding S4 domain protein [Flavobacteria bacterium MS024-2A]
 gi|225003139|gb|EEG41114.1| RNA-binding S4 domain protein [Flavobacteria bacterium MS024-2A]
          Length = 255

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 55/234 (23%), Positives = 95/234 (40%), Gaps = 2/234 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           ++     R++K ++ AG+ SRRE +  I    V VNG ++      V  TD ++ DG  +
Sbjct: 17  EKPSETVRLNKFLSNAGLCSRREADSHIEMGLVHVNGKIITEMGYQVKPTDEVKFDGARV 76

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++     L L      + T+      +S       ++ + V +VG +     GLL  TND
Sbjct: 77  QQTPPVYLLLNKPKGFVATSQGGKIVKSVQDLIRSAVKTPVPAVGDMGRPMTGLLFFTND 136

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
             L + L    +    +Y+V     V  D +  LK+G ++       +         S  
Sbjct: 137 EVLRKKLNNSKS-IPMIYQVLLDKNVTTDMMRQLKEGQMVFEKM-QKINEVSHMDGKSKK 194

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V + +       I K+F     KV  L RI+Y       L  G+ R ++ K +
Sbjct: 195 EVGIEVHSLSPAIIVKLFAAVGCKVVLLDRITYAGLTKKELPRGNWRRLNTKEV 248


>gi|71894334|ref|YP_278442.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           synoviae 53]
 gi|71851122|gb|AAZ43731.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           synoviae 53]
          Length = 231

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 63/226 (27%), Positives = 110/226 (48%), Gaps = 7/226 (3%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW 76
            K++++AG+ SRRE E++I +++VKVNG +           D I V+  P+ + E    +
Sbjct: 2   QKILSQAGVCSRREAEKLILEKKVKVNGQIAT-LGTKASFEDEILVNNKPITQREELVYF 60

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           + +KP   V      +       +L     ++  VGRLD +T G+LLLTNDG L+ +L  
Sbjct: 61  VLNKPKNTVC-TLKDNFNRVKVTDLIDTDKKIFPVGRLDYDTTGVLLLTNDGKLSNLLTH 119

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
           PS++  R+YR R    +   ++ +L K ++I        + T +          V L +G
Sbjct: 120 PSSEIKRIYRARISAPLTDKEMEILSKPVIINNQ-----RSTQEIYPADTKSYYVVLHQG 174

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
               +KK+FE  + KV  L R+ +    +  +  G  R ++   L+
Sbjct: 175 SYHHVKKLFELVDKKVLDLNRVEFANITVKNMQKGQYRRLTLHELK 220


>gi|119775746|ref|YP_928486.1| pseudouridine synthase, Rsu [Shewanella amazonensis SB2B]
 gi|119768246|gb|ABM00817.1| ribosomal small subunit pseudouridine synthase A [Shewanella
           amazonensis SB2B]
          Length = 230

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 49/231 (21%), Positives = 95/231 (41%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     SR   ++ I    V  +G++++  A  V     +   G  L      
Sbjct: 1   MRLDKYLAETTALSRGLAKKAINSGDVSCDGVVMKDPAFKVPQGARVCFQGEVLALVGVR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L+     + +T  +         ++       I+ GRLD +T GL+L+T+DG  +  
Sbjct: 61  YLMLHKPVDTICSTQDEYYPSVLSLLDIARPDKLHIA-GRLDADTTGLVLITDDGLWSHK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P     + YRV+    +  D +    +G+ +  +       ++ L     S+    +
Sbjct: 120 VTSPKRDCAKRYRVQLAESLTDDLIAQFAEGVQLNGEDGLTKPAKLELL----SDTEALL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R + G  +L   L  G  R +++  +
Sbjct: 176 SITEGKYHQVKRMFAAVGNKVIGLHREAVGAIELDPQLAPGEWRYLTEAEI 226


>gi|153810142|ref|ZP_01962810.1| hypothetical protein RUMOBE_00523 [Ruminococcus obeum ATCC 29174]
 gi|149833321|gb|EDM88402.1| hypothetical protein RUMOBE_00523 [Ruminococcus obeum ATCC 29174]
          Length = 257

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 71/252 (28%), Positives = 114/252 (45%), Gaps = 22/252 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
              R+ K +A AG  +R EV++ I + +V+VNG   ++  + V    D + + G  +  A
Sbjct: 3   KAVRLDKFLADAGKGTRSEVKKFIQKGQVQVNGAPAKKPELKVDPEKDTVILSGETVGVA 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                +L +KP G V+   +     TV + +PS    +  VGRLD +TEGLLL+T+DG L
Sbjct: 63  PEFVYYLLNKPAGCVSAT-EDRNDRTVMEYVPSDRKGIFPVGRLDKDTEGLLLITDDGML 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQK------ 183
           A  L  P     + Y VR  G++  +K+  L+ G+ I         +V +          
Sbjct: 122 AHELLAPGKHVDKTYFVRVEGKLTVEKIEKLENGVDIGEKKLTMPAKVEIVGGSWEGAGE 181

Query: 184 ------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLA 230
                            + + + EGK  ++K++ E     V  L RIS GP  L   L  
Sbjct: 182 PEPGRVRRENLPEVYTELHLTIHEGKFHQVKRMMEAVGTPVIYLKRISMGPLILPDDLKK 241

Query: 231 GSTREVSKKILR 242
           G  R ++ + LR
Sbjct: 242 GECRSLTDEELR 253


>gi|71893518|ref|YP_278964.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           hyopneumoniae J]
          Length = 237

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 110/229 (48%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K ++  G+ SRR+ E++I Q R+K+N    +     +   D IE+D   + K    
Sbjct: 1   MRINKFLSEMGVCSRRQSEKLILQGRIKINNETAK-IGQIISQNDVIELDQQKITKKPPI 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +  +KP   +T+  DP+ R T+ +        +  VGRLD  T GL+L+TNDG     
Sbjct: 60  FWYALNKPKNYITSRFDPENRPTIMEFFSKN-EYLFPVGRLDFQTTGLILITNDGKTTNK 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  PS++  R Y V+    +   ++  L    +         +     +K S+    V +
Sbjct: 119 LLHPSSKIERTYLVKTDFSLSDKEIRFLNDNKIQLDSV----KSIQKIKKCSSRTYLVTV 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G N  IKK+F   + KV +L R+S+   +L  +  G  R+++ + ++
Sbjct: 175 WQGSNHHIKKLFLSISKKVLKLKRVSFANIKLDNISEGKYRKLTNQEIK 223


>gi|77360285|ref|YP_339860.1| pseudouridine synthase (makes pseudouridine2605 in 23 S RNA)
           [Pseudoalteromonas haloplanktis TAC125]
 gi|76875196|emb|CAI86417.1| pseudouridine synthase (makes pseudouridine2605 in 23 S RNA)
           [Pseudoalteromonas haloplanktis TAC125]
          Length = 290

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 82/286 (28%), Positives = 133/286 (46%), Gaps = 10/286 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +++ KV+ARAG+ SRRE+E+ I   RV VNG + +     V  TD I VDG  ++  E
Sbjct: 5   QGEKLQKVLARAGVGSRREMEKYIDANRVSVNGKVAK-LGDRVEETDSIRVDGHTVKIEE 63

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   +        L T       R+           R I+VGRLDINT GL+L TN
Sbjct: 64  KADRICRVIMYNKPEGELSTRKDPEGRRTVFDRLPRIDGERWIAVGRLDINTAGLMLFTN 123

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y  R  G+V ++ +  L +G+ ++      + V     +G N
Sbjct: 124 DGELANRLMHPSYEVEREYSARVFGEVTKETIKNLTRGVELEDGPAKFLTVNPMGGEGIN 183

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREV---SKKILR 242
            W  V L EG+NRE++++++    +V+RLIRI YG  +L   +  G   E    +   LR
Sbjct: 184 RWYNVTLNEGRNREVRRLWQSQEVEVSRLIRIRYGKLELDKRVPQGGWIEYDLDTVNYLR 243

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
           + +      + ++++       +    ++     +  +   +  K 
Sbjct: 244 KTVKLGRETQTKLSVMPEKRKDKRAKINQIRKAVKKHNQRVKPTKR 289


>gi|304405744|ref|ZP_07387402.1| pseudouridine synthase [Paenibacillus curdlanolyticus YK9]
 gi|304344987|gb|EFM10823.1| pseudouridine synthase [Paenibacillus curdlanolyticus YK9]
          Length = 235

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 109/233 (46%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+  G  SRRE ++++ + RV +NGI+ +         D + ++G  +  + R 
Sbjct: 1   MRINKFISETGFCSRREADKLVDEGRVTINGIVAQ-LGSQAEQGDDVRINGKRIGASRRH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+ +T            +      R+  +GRLD ++EGL+L+TNDG +   
Sbjct: 60  VYIALNKPVGITSTTESQI--KGNIVDFVGHSERIFPIGRLDKDSEGLILMTNDGDIVNR 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     V    +  + +G+ I G      QVT      +     + L
Sbjct: 118 ILRAEGKHEKEYIVTVDRPVTPMFIKGMSEGVRILGTMTLPCQVTRI----AERIFKIVL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            EGKNR+I+++ E F ++V RL R+      LG L  G  R++ +  L E   
Sbjct: 174 TEGKNRQIRRMCEVFGYRVVRLRRVRIMNIHLGDLANGRWRDLHQDELDELFR 226


>gi|254804685|ref|YP_003082906.1| pseudouridylate synthase [Neisseria meningitidis alpha14]
 gi|254668227|emb|CBA05021.1| pseudouridylate synthase [Neisseria meningitidis alpha14]
          Length = 252

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 68/255 (26%), Positives = 108/255 (42%), Gaps = 20/255 (7%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K          R+SK +A+ G+ SRRE +  I Q  V VNG         V   D I
Sbjct: 1   MNPKTPPDHTEDAVRLSKRMAQLGLCSRREADGYIEQGWVTVNGKTA-VLGQKVSPADRI 59

Query: 61  EVD---------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           E++                 P+          Y     L+T+ +  +  ++     P   
Sbjct: 60  ELNKKAHEQQAARITILLNKPVGYVSAQAEKGYKSAAELITSENRWESDTSRIRFDPKHK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             +   GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+
Sbjct: 120 IGLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGL 179

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G      QV    +      +   L++GK R+I+++ E    +V  L RI  G  +L
Sbjct: 180 SLDGEKLRPAQVEWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPLGKWRYLAPGE 250


>gi|317473625|ref|ZP_07932914.1| RNA pseudouridylate synthase [Anaerostipes sp. 3_2_56FAA]
 gi|316898915|gb|EFV20940.1| RNA pseudouridylate synthase [Anaerostipes sp. 3_2_56FAA]
          Length = 238

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 105/234 (44%), Gaps = 5/234 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
              R+ K +      +R E  +MI Q RV     ++++    V    D I  DG  L   
Sbjct: 2   KTLRLDKFLCDVLGCTRSEARKMIRQGRVLAGDEIIKKPEYKVNPEEDEITADGQRLNFR 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L +      +VT   D   ++ +          +   GRLD +TEGLLL+TNDG L
Sbjct: 62  KYEYLMMNKPKG-VVTATKDGRDKTVMDLLTGRHRKGLFPAGRLDKDTEGLLLITNDGEL 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y V   G++ +++  + + G+ I         ++ + T  G  +  
Sbjct: 121 AHRLLSPKHHVTKCYSVTVTGEIGREQQEIFESGMDIGDDKPLKPAKLVILT-SGEVSQA 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            V + EG+  +IK++FE    KV  L R+S G   L   LL G  RE++++ ++
Sbjct: 180 EVFITEGRFHQIKRMFEAVGSKVLELKRLSMGSLVLDPELLPGQVRELTEEEIK 233


>gi|331644758|ref|ZP_08345875.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli H736]
 gi|331035733|gb|EGI07971.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli H736]
          Length = 227

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 55/221 (24%), Positives = 95/221 (42%), Gaps = 5/221 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     + ++ +  +  G+ I G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPILGTV----TKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           + L +G NR+I+++ E F ++V +L R       L  +  G
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLG 219


>gi|149198178|ref|ZP_01875225.1| RsuA protein [Lentisphaera araneosa HTCC2155]
 gi|149138780|gb|EDM27186.1| RsuA protein [Lentisphaera araneosa HTCC2155]
          Length = 239

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 51/240 (21%), Positives = 97/240 (40%), Gaps = 8/240 (3%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGV 65
           + +     R+ K+IA+    +R E  R +    VKVN I  +     +  + D +  DG 
Sbjct: 1   MAKIKAKIRLDKMIAKCTDLTRSEATRALKNGFVKVNDIPQKVGKSTIDLANDVVTFDGE 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            L   E     L      +     +                   S GRLDI+T GL++LT
Sbjct: 61  VLEYRETIYFMLNKPKGYVCAAKDERLKTVLDLLPPALASREPFSCGRLDIDTTGLVILT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQK 183
           +DG  A  +  P  +  + Y V    ++  + +  L++G+ +          ++    +K
Sbjct: 121 DDGTWAHGITSPKRKCEKSYLVGSVSELSDEDMRNLEQGVYLDGDDKITAPAKI----EK 176

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
                  + + EG+  ++K++FE  +  V  L R   G   L   L  G+ R+++ + ++
Sbjct: 177 IDEKTYRLKITEGRYHQVKRMFEAVDNMVKSLHREQIGGLSLDDDLDEGNWRDLTAEEVK 236


>gi|332305273|ref|YP_004433124.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
 gi|332172602|gb|AEE21856.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
          Length = 269

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 56/231 (24%), Positives = 101/231 (43%), Gaps = 13/231 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ ++++  G  SR+E   ++   RV V G   +  A  V +   + VDG PL   E   
Sbjct: 41  RLDQLLSNLGYCSRKEARYLLKDNRVTVAGEYAKSPAQKVDA-ATVRVDGEPLDFPEGIL 99

Query: 75  LWLYHKPIGLVTTH--SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + L      + +            + +       +++SVGRLD +T GL+L+T+D  L  
Sbjct: 100 VMLNKPLGYVCSHDSGEGMRIYDLLPERWEFRNPKIVSVGRLDKDTTGLILVTDDTKLVH 159

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--CYGDMQVTLDTQKGSNAWVT 190
            L  P     ++Y+V  +  +  D +    KG+V+          +V + ++  +N    
Sbjct: 160 QLTSPKHHVDKLYKVTVNSPLQPDIIEAFAKGVVLGDGAEQCLPAKVEIISENMAN---- 215

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG----TLLAGSTREVS 237
           V L EGK  +++++F    + V  L R  +GP+ L      L  G  + V 
Sbjct: 216 VTLNEGKYHQVRRMFAACGYHVEALHRSQFGPYSLHDLGQDLPQGDWQVVD 266


>gi|86148075|ref|ZP_01066376.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio sp. MED222]
 gi|85834135|gb|EAQ52292.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio sp. MED222]
          Length = 231

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 50/232 (21%), Positives = 99/232 (42%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +RRE   ++  + V VN ++ +  ++ V     +E  G  L      
Sbjct: 1   MRLDKFLCDALGVTRREATHLLKSKAVTVNDVIQKSGSLKVTEECVVEWQGNELNVHGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + LY     + +       R+           ++   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLYKPEGFVCSHEDG-SNRTAFELLDEIKMDKLHFAGRLDVDTTGLVLMTDDGKWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  ++YRV     V+ D +   K+GI +  +        + +     +   V +
Sbjct: 120 ITSPKHKCEKMYRVWLVEPVEDDYVEKFKEGIQLKSEDGLTLPAHLEV----RAEREVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            + EGK  ++K++F     KV  L R   G  ++   L  G  R ++++ + 
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVEALHRERIGEIEMDESLELGEYRYLTQEEVD 227


>gi|218709840|ref|YP_002417461.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio splendidus
           LGP32]
 gi|218322859|emb|CAV19036.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio splendidus
           LGP32]
          Length = 247

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 50/232 (21%), Positives = 99/232 (42%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +RRE   ++  + V VN ++ +  ++ V     +E  G  L      
Sbjct: 17  MRLDKFLCDALGVTRREATHLLKSKAVTVNDVIQKSGSLKVTEECVVEWQGNELNVHGPR 76

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + LY     + +       R+           ++   GRLD++T GL+L+T+DG  +  
Sbjct: 77  YIMLYKPEGFVCSHEDG-SNRTAFELLDEIKMDKLHFAGRLDVDTTGLVLMTDDGKWSHR 135

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  ++YRV     V+ D +   K+GI +  +        + +     +   V +
Sbjct: 136 ITSPKHKCEKMYRVWLVEPVEDDYVEKFKEGIQLKSEDGLTLPAHLEV----RAEREVLL 191

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            + EGK  ++K++F     KV  L R   G  ++   L  G  R ++++ + 
Sbjct: 192 TIHEGKYHQVKRMFAALGNKVEALHRERIGEIEMDESLELGEYRYLTQEEVD 243


>gi|297170719|gb|ADI21742.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [uncultured actinobacterium
           HF0130_15N16]
          Length = 239

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 78/236 (33%), Positives = 126/236 (53%), Gaps = 6/236 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + E    +R+ K ++RAG+ASRR  E MI   RV +N  +       V  TD IE+DG+P
Sbjct: 1   MTEEEPLERLQKALSRAGVASRRVSEGMIEAGRVTINRRVATV-GDRVSVTDRIELDGIP 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           + +      +L +KP+G+V+T  DP  R TV  +L S   R+  VGRLD ++EGL++LTN
Sbjct: 60  VIRDPDLVHYLLNKPVGVVSTSKDPQKRRTV-VDLVSSNERIFPVGRLDADSEGLIILTN 118

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L   L  PS    + Y V   G   +  L LL++G+ ++  C     V +       
Sbjct: 119 DGELTHRLTHPSFGVSKEYLVHVEGVPSRSSLRLLREGVELEDGCTAPANVAMPQDG--- 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
             + + + EG+NR+++++       V RL+R+  G  +  +L  G+ R +S + +R
Sbjct: 176 -VMRITIHEGRNRQVRRMCAAIGHPVQRLVRVRIGSIKDPSLRVGTARRLSVEEVR 230


>gi|167624536|ref|YP_001674830.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
 gi|167354558|gb|ABZ77171.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
          Length = 290

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 80/290 (27%), Positives = 127/290 (43%), Gaps = 7/290 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E  IA  RV V+G +       V +   I +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRVSVDGEIA-SLGDRVETDAKIRIDGRTVSIRSE 60

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  +  +     + +        +       +  SR ++VGRLDINT GLLL T+D
Sbjct: 61  EDVVCRVIAYHKPEGEICSRKDPEGRPTVFDRLPKTRDSRWVAVGRLDINTSGLLLFTSD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V+   +  L+ G+ ++       +V     +G N 
Sbjct: 121 GELANRLMHPSNEVEREYAVRTFGEVNDACIQRLRMGVTLEDGPANFDKVKAAGGEGMNK 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V L EG+NRE+++++E    +V+RLIRI YG  +L  +L  G   E+  + +     
Sbjct: 181 WWHVSLAEGRNREVRRLWESQEVQVSRLIRIRYGMIELPKSLPRGGWIELPIEQVNYLRK 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
              ++E   ++      S    + R   I                    S
Sbjct: 241 TAGMDEETRSILGTDKHSVARNKVRSAKIKRAVHKHKVASGRPKPSRQRS 290


>gi|312892173|ref|ZP_07751670.1| RNA-binding S4 domain protein [Mucilaginibacter paludis DSM 18603]
 gi|311295303|gb|EFQ72475.1| RNA-binding S4 domain protein [Mucilaginibacter paludis DSM 18603]
          Length = 517

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 66/241 (27%), Positives = 111/241 (46%), Gaps = 2/241 (0%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHI 60
           + K+    +    R+++ I+ AGI SRR+ + +I    V VNG ++      V    D I
Sbjct: 270 RKKSTTDADKGKIRLNRYISNAGICSRRKADELIVAGVVSVNGQVISELGFKVDPYKDEI 329

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
             +G  L++ +   + L      + TT    + R+ +     +   R+  +GRLD NT G
Sbjct: 330 RYNGETLKREKMVYVLLNKPKDYITTTEDPQERRTVMHLVDKASKERIYPIGRLDRNTTG 389

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLL+TNDG LA  L  P +   ++Y V     + Q  LN +  GI ++        V+  
Sbjct: 390 LLLMTNDGDLADKLSHPKSNISKLYHVELDKSLSQGDLNKIAYGIELEDGLIKPDSVSYV 449

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            Q  S   V + +  GKNR ++++FE   + V +L R  Y       L  G  R + ++ 
Sbjct: 450 -QGASKREVGIQIHSGKNRVVRRIFESLGYDVVKLDRAIYAGLTKKDLPRGRWRYLEEQE 508

Query: 241 L 241
           +
Sbjct: 509 V 509


>gi|166710887|ref|ZP_02242094.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzicola BLS256]
          Length = 245

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 111/243 (45%), Gaps = 7/243 (2%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERTRLWL 77
           +++ G+ SR E  R IA  RV V+  ++      + +     I VDG PL    R  L L
Sbjct: 2   LSKLGVCSRTEAARWIADGRVSVSTRVVRDPEFPIRADQQSSITVDGQPLTGPARCYLML 61

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
                 + T   +    +       +    +  VGRLD  +EGLLL +ND   A  +  P
Sbjct: 62  NKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAATVTDP 121

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNAWVTVG 192
           +T   + Y V+     +  +L  L+ G+V      +G+     QV++  +   NAW+ + 
Sbjct: 122 ATGPDKTYHVQIDCLPNVAQLAQLQAGVVDPDPEGEGVLLRAKQVSVLREGERNAWLEIV 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L EG+NR+I+++    +  V RL+R++ GP  +G L  G+ R +S + +R  +       
Sbjct: 182 LDEGRNRQIRRLLAAVDIGVLRLMRVAIGPLAMGELGKGAWRMLSAEEVRALVPAAHASA 241

Query: 253 AQV 255
              
Sbjct: 242 PDA 244


>gi|257466443|ref|ZP_05630754.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium
           gonidiaformans ATCC 25563]
 gi|315917599|ref|ZP_07913839.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium
           gonidiaformans ATCC 25563]
 gi|313691474|gb|EFS28309.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium
           gonidiaformans ATCC 25563]
          Length = 232

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 104/229 (45%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR+EV+ ++  ++++VNG+ +      +    D +      L   E 
Sbjct: 1   MRIDKFLVECGVGSRKEVKELLKSRKIRVNGLFITSPKETIEEEKDEVYYGEKKLSYQEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+ K   +       +           I   +  VGRLD +TEGLLL TNDG L  
Sbjct: 61  RYYILHKKAGYVTALEDSREATVMDLLPEWVIKKDLAPVGRLDKDTEGLLLFTNDGKLNH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P +   + Y       + ++ L  L++G++I        +     +K  +  + + 
Sbjct: 121 RLLSPKSHVDKTYHASLECDITEEALEKLREGVMIGEYKTLPAKA----EKLEDRKIALT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +REGK  ++KK+ E    KV  L RIS+G   LG L  G+ +EVS + +
Sbjct: 177 IREGKFHQVKKMLEAVGNKVIYLKRISFGKLVLGDLELGAVKEVSLEDI 225


>gi|170696462|ref|ZP_02887588.1| pseudouridine synthase [Burkholderia graminis C4D1M]
 gi|170138615|gb|EDT06817.1| pseudouridine synthase [Burkholderia graminis C4D1M]
          Length = 639

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 76/273 (27%), Positives = 123/273 (45%), Gaps = 6/273 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRR++E +I   RV VNG         +M TD + ++
Sbjct: 213 KRVLSADDDAPKLHKVLAEAGMGSRRDMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRIN 271

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G P+++         L  +     +V+        S      P   ++ ++VGRLD NTE
Sbjct: 272 GKPVKRKLANKPPRVLLYHKPTGEIVSHADPEGRPSVFDKLPPMKTAKWLAVGRLDFNTE 331

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 332 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELAEGMRQKLLNGVELDDGPANFLRIRD 391

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+  
Sbjct: 392 GGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPISLPKGLKRGRWEELED 451

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDR 271
             +R  +    L+           + E    D 
Sbjct: 452 NQVRALMASVGLKAPSEERGGRNAAPERKQPDP 484


>gi|119469659|ref|ZP_01612528.1| putative ribosomal RNA pseudouridylate synthase [Alteromonadales
           bacterium TW-7]
 gi|119446906|gb|EAW28177.1| putative ribosomal RNA pseudouridylate synthase [Alteromonadales
           bacterium TW-7]
          Length = 230

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 60/219 (27%), Positives = 100/219 (45%), Gaps = 7/219 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T  R++K IA AG+ SR++  R+I +  V VN         +V   D I V+G  ++ A
Sbjct: 2   STKIRLAKYIAHAGVCSRKQASRLIDEGVVTVNNRPANHID-HVDEQDDIIVNGQVVKGA 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                + YHKP+G+       +       +     +RV  +GRLD ++ GLL+LTNDG  
Sbjct: 61  ADLVYFAYHKPVGIDCK--LNENDPASLIHHLPTLTRVYPIGRLDKDSRGLLILTNDGDF 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + Y V     ++      +  GI +        +VT    K ++   +
Sbjct: 119 CNQLIHPDFHQPKRYLVTVDKPINNAFCEKMAAGIPVDKQITLPCEVT----KIADNQFS 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           + L++G NR+I+K+  +  +KV  L R+ +    L  L 
Sbjct: 175 IILKQGLNRQIRKMAHYCGFKVIDLFRVQFSELALSNLN 213


>gi|301156161|emb|CBW15632.1| 23S rRNA pseudouridylate synthase [Haemophilus parainfluenzae T3T1]
          Length = 336

 Score =  154 bits (390), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 90/278 (32%), Positives = 133/278 (47%), Gaps = 10/278 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA+ RV V+G +      ++V S   + +DG  
Sbjct: 49  QSTVEGEKLQKVLARAGQGSRREIEAMIAENRVSVDGKMATLGDRIDVHSGVKVRIDGRI 108

Query: 67  LRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +   +        L  Y     L T        +          +R I+VGRLDINT GL
Sbjct: 109 INLQQAQKEVCRVLMYYKPEGELCTRSDPEGRPTVFDRLPRLNGARWIAVGRLDINTSGL 168

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++    
Sbjct: 169 LLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGPANFKEIKFAG 228

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 229 GVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEMDLEN 288

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNII 275
              LRE +G     E ++++  P    ++    +    
Sbjct: 289 VNYLRELVGLPPETETKLDVTKPRRRPKSGQIRKAVKR 326


>gi|254432567|ref|ZP_05046270.1| RNA pseudouridine synthase family protein [Cyanobium sp. PCC 7001]
 gi|197627020|gb|EDY39579.1| RNA pseudouridine synthase family protein [Cyanobium sp. PCC 7001]
          Length = 242

 Score =  154 bits (390), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 77/239 (32%), Positives = 115/239 (48%), Gaps = 3/239 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            QR+ K+IA AG+ SRR  E ++ Q R++VNG             D I VDG PL +  R
Sbjct: 3   SQRLQKLIAAAGVCSRRHAEELLRQGRIQVNGAAARLGDSADPDRDSIAVDGRPLDRPAR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLLTNDGG 129
             L L +KP+G++ + SDP GR TV D LP    +      +GRLD ++ G LLLTN G 
Sbjct: 63  PVLLLLNKPLGVLCSCSDPQGRPTVLDLLPPELRQGQGLHPIGRLDADSRGALLLTNQGD 122

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     ++YRV   G      L     G+ + G+    + V +  +      +
Sbjct: 123 LTLRLTHPRYGHRKLYRVWVSGTPSATTLERWAAGVPLDGVASQPVDVRVLQRGKRGTRL 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + + EG+NR+I++        V  L R+  GP +LG+L  G  R +  +  +    P 
Sbjct: 183 ELAMGEGRNRQIRRTAALLGHPVLDLQRVGIGPLRLGSLAEGCWRALDHQEWQALADPP 241


>gi|222153366|ref|YP_002562543.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           uberis 0140J]
 gi|222114179|emb|CAR42705.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus uberis 0140J]
          Length = 236

 Score =  154 bits (390), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 55/226 (24%), Positives = 99/226 (43%), Gaps = 2/226 (0%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRL 75
            K++ +A I SR EV++MI  Q+V ++G + +  + NV +    + VDG  +        
Sbjct: 2   DKLLEKARIGSRTEVKKMIKNQKVVLDGKIAQSISQNVDTGFQELIVDGKKIEGYSHHYF 61

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            ++     +                       +  VGRLD +TEGL+L+T++G L   + 
Sbjct: 62  LIHKPAGYVTARLDQNHPTLFDLLKPEDRVEGLYPVGRLDRDTEGLVLVTDNGPLGFRML 121

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
            PS    + Y V  +G + +D     + GI  + G       + +   + + +   + + 
Sbjct: 122 HPSHHVEKTYYVEVNGFLGEDAPLFFRSGIVFLDGTVCKPAVLEVINCQQNLSKAYLTIS 181

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           EGK  ++KK+F  +  KV  L R+S+    LG L  G  R +    
Sbjct: 182 EGKFHQVKKMFLSYGLKVTYLRRVSFAGLSLGNLPLGKYRPLDWNE 227


>gi|40062484|gb|AAR37436.1| RNA pseudouridylate synthase, putative [uncultured marine bacterium
           105]
          Length = 255

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 85/248 (34%), Positives = 123/248 (49%), Gaps = 5/248 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ KV+A AGI+SRR  ER+I   RV VNG  + +         D I VDG  ++    
Sbjct: 6   VRLQKVLASAGISSRRAAERLIEVGRVTVNGRSVTKLGAKADPDLDDIRVDGRKVKTGRP 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L  KP G VTT  DP+GR T+ + + ++   V  VGRLD ++EGL++LTNDG LA 
Sbjct: 66  RIYLLVCKPRGYVTTRFDPEGRRTILNLISNVREYVYPVGRLDYDSEGLVILTNDGTLAA 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT----QKGSNAW 188
            L  P     RVY VR  G   Q  ++ L+ G++I G       V        +   NA 
Sbjct: 126 RLTHPRYGVERVYEVRVRGVPSQAAIDSLRHGVLINGRRTASSSVKFLRRLKAKSSENAL 185

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + V +REG+NR+++K+ E     V RL R   GP +  +L  G  R ++   +   +   
Sbjct: 186 LRVAIREGRNRQVRKMCEAIGHPVIRLRRTQIGPLRDSSLKVGKHRLLTTSEVAALMRAS 245

Query: 249 LLEEAQVN 256
            +   Q  
Sbjct: 246 EVSHPQDK 253


>gi|33865483|ref|NP_897042.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Synechococcus sp. WH 8102]
 gi|33632652|emb|CAE07464.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Synechococcus sp. WH 8102]
          Length = 250

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 68/230 (29%), Positives = 102/230 (44%), Gaps = 1/230 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA- 70
           T QR+ K+IA AG+ SRR  E  I   RVKV+G +          +  I VDG PL    
Sbjct: 2   TRQRLQKLIAAAGLCSRRTAEDWIDAGRVKVDGRISSLGDQADPESQLIHVDGRPLSFRG 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E T L +      + T        + +      +   +  VGRLD ++ G LLLT+ G L
Sbjct: 62  EPTVLLINKPAGVISTCRDPRGRSTVLDLLPQQLRQGLHPVGRLDADSRGALLLTDYGDL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + YRV   G      L   ++G+ + G      +V +  ++     + 
Sbjct: 122 TLRLTHPRYDHAKTYRVWVEGTPLDTSLQRWRQGVTLDGTRTRSAEVRVLQRRSDRTLLE 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           V L EG+NR+I++V E     V  L R++    +LG L  G  R +S+  
Sbjct: 182 VVLLEGRNRQIRRVAELLGHPVVDLQRVAIAGLRLGALPEGRWRRLSRGE 231


>gi|261867923|ref|YP_003255845.1| ribosomal large subunit pseudouridine synthase B [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261413255|gb|ACX82626.1| ribosomal large subunit pseudouridine synthase B [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 328

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 90/284 (31%), Positives = 139/284 (48%), Gaps = 10/284 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKA 70
             +++ KV+ARAG  SRRE+E +IA+ RV V+G +      +NV +   + +DG  +   
Sbjct: 39  EGEKLQKVLARAGQGSRREIEAIIAENRVSVDGKIATLGDRINVYAGVKLRIDGHLINLT 98

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +        +  Y     L T H      +          +R I+VGRLDINT GLLL T
Sbjct: 99  QAQKEVCRVVMYYKAEGELCTRHDPEGRATVFDRLPRLTGARWIAVGRLDINTSGLLLFT 158

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  GQVD   LN LKKG+ ++       ++ +    G 
Sbjct: 159 TDGELANRLMHPSREVEREYSVRVFGQVDDAMLNRLKKGVQLEDGPANFKEIKVVGGVGM 218

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           N W  V L EG+NRE+++++E    +V+RLIRI YG  +L  TL  G  +E+    L + 
Sbjct: 219 NQWFDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKTLPRGGWQEM---ELADV 275

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
                L       +  + +++T  + +   I +    ++ + K 
Sbjct: 276 NYLRELVGLPPETETKLGANKTRHKPKFGQIRKAVKRYSELNKR 319


>gi|302670814|ref|YP_003830774.1| RNA pseudouridylate synthase [Butyrivibrio proteoclasticus B316]
 gi|302395287|gb|ADL34192.1| RNA pseudouridylate synthase [Butyrivibrio proteoclasticus B316]
          Length = 242

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 64/240 (26%), Positives = 109/240 (45%), Gaps = 11/240 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    I +R++++  +   R  VNG ++ R  ++V    D I  DG  LR ++ 
Sbjct: 1   MRLDKFLGLFDIGTRKQIKEYLKNGRCSVNGEVVTRPDIHVDENNDEISFDGKTLRYSKY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               LY     +V+  +D    + +          +   GRLDI+TEGLLLLT+DGGL  
Sbjct: 61  HYYMLYKPQG-VVSATTDGRNTTVLDLLQEENVKGLSPAGRLDIDTEGLLLLTDDGGLIH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-------YGDMQVTLDTQKGS 185
            L  P     +VY V     +    +  L+KG+ I               +V    +   
Sbjct: 120 RLLSPKKHVDKVYEVHLRKDLSDKDIESLEKGVNIGDTKDNGEIDYTLPARVVRMDEDDE 179

Query: 186 NA-WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
           N   V + + EG+  ++K++ E    +V  L R+S GP  L   L  G  R+++++ L++
Sbjct: 180 NRPVVHLIIHEGRFHQVKRMMEAVGNEVLFLKRLSMGPLILDETLEPGEYRQLTQEELKQ 239


>gi|114562614|ref|YP_750127.1| pseudouridine synthase, Rsu [Shewanella frigidimarina NCIMB 400]
 gi|114333907|gb|ABI71289.1| ribosomal large subunit pseudouridine synthase B [Shewanella
           frigidimarina NCIMB 400]
          Length = 290

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 80/290 (27%), Positives = 126/290 (43%), Gaps = 7/290 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E  IA  RV V+G +       V +   I +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRVSVDGEI-SGLGDRVEADAKIRIDGRAVSLKSA 60

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  +     + +        +          +R ++VGRLDINT GLLL T D
Sbjct: 61  DDIICRVLAYHKPEGEICSRKDPEGRTTVFERLPKVRDARWVAVGRLDINTSGLLLFTCD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V +  +  L+ G+ ++        +     +G N 
Sbjct: 121 GELANRLMHPSNEVEREYAVRTFGEVPEAAVQRLRTGVTLEDGPAQFDTIKAAGGEGINQ 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V LREG+NRE+++++E  + +V+RLIR+ YG  +L  TL  G   E+    +     
Sbjct: 181 WWHVTLREGRNREVRRLWESQDVQVSRLIRVRYGKVELPKTLPRGGWIELPMDQVNYLRQ 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
              LE    ++      S    + +   I         +  +       S
Sbjct: 241 LAGLEAETRSVLGSDKHSVARSKVKSAKIRRAVHKHKVVGNHGKPTRQRS 290


>gi|294141568|ref|YP_003557546.1| ribosomal large subunit pseudouridine synthase B [Shewanella
           violacea DSS12]
 gi|293328037|dbj|BAJ02768.1| ribosomal large subunit pseudouridine synthase B [Shewanella
           violacea DSS12]
          Length = 288

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 78/287 (27%), Positives = 129/287 (44%), Gaps = 7/287 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E  IA  R+ ++G +       + +   I +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRISIDGEIA-NLGDRIEADVKIRIDGRTVSIKSE 60

Query: 73  TRLWL-----YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             L       +     + +        +       +  SR ++VGRLDINT GLLL T+D
Sbjct: 61  EDLICRVIAYHKPEGEICSRKDPEGRPTVFDRLPKTRDSRWVAVGRLDINTSGLLLFTSD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V+   +  L+ G+ ++       +V     +G N 
Sbjct: 121 GELANRLMHPSNEVEREYAVRTFGEVNDACIQRLRTGVTLEDGPASFDKVKAAGGEGMNK 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V L EG+NRE+++++E    +V+RLIRI YG  +L  +L  G   E++ + +     
Sbjct: 181 WWHVTLAEGRNREVRRLWESQEVQVSRLIRIRYGKIELPKSLPRGGWVELTMEQVNYLRK 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
              L E    +      S    + + + I         +     +K 
Sbjct: 241 TAGLNEETRTVLGTDKHSVARSKVKGSKIRRAVRKHKAVASKPGRKR 287


>gi|144227495|gb|AAZ44253.2| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           hyopneumoniae J]
          Length = 240

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 110/231 (47%), Gaps = 6/231 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K ++  G+ SRR+ E++I Q R+K+N    +     +   D IE+D   + K  
Sbjct: 2   KKIRINKFLSEMGVCSRRQSEKLILQGRIKINNETAK-IGQIISQNDVIELDQQKITKKP 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               +  +KP   +T+  DP+ R T+ +        +  VGRLD  T GL+L+TNDG   
Sbjct: 61  PIFWYALNKPKNYITSRFDPENRPTIMEFFSKN-EYLFPVGRLDFQTTGLILITNDGKTT 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  PS++  R Y V+    +   ++  L    +         +     +K S+    V
Sbjct: 120 NKLLHPSSKIERTYLVKTDFSLSDKEIRFLNDNKIQLDSV----KSIQKIKKCSSRTYLV 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + +G N  IKK+F   + KV +L R+S+   +L  +  G  R+++ + ++
Sbjct: 176 TVWQGSNHHIKKLFLSISKKVLKLKRVSFANIKLDNISEGKYRKLTNQEIK 226


>gi|329297659|ref|ZP_08254995.1| 23S rRNA pseudouridylate synthase B [Plautia stali symbiont]
          Length = 292

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 89/295 (30%), Positives = 131/295 (44%), Gaps = 12/295 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV--MSTDHIEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E MI+  R+ V+G L       +    T  I +DG  +  A
Sbjct: 2   SEKLQKVLARAGHGSRREIEAMISAGRISVDGKLAT-LGDRIENDKTLKIRIDGHLVSIA 60

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E        L  Y     L T +      +          SR I+VGRLD+NT GL+L T
Sbjct: 61  ESATEVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPRLRGSRWIAVGRLDVNTCGLMLFT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS    R Y VR  G+VD +K+  L KG+ ++        +     +G 
Sbjct: 121 TDGELANRLMHPSRAVEREYAVRVFGEVDDEKVRQLSKGVQLEDGPAAFKTIKFSGGEGI 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           N W  V L EG NRE+++++E    +V+RL+R+ YG  QL   L  G   E+    L   
Sbjct: 181 NQWYNVTLTEGCNREVRRLWEAVGVQVSRLMRVRYGDIQLPKGLPRGGWMEM---ELPAV 237

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
                L          +   +   R + N I       + +  NS ++N   +  
Sbjct: 238 NYLRKLVGLPEETVTKVAVEKDRRRTKANQIRRAVKRHSAVSNNSPRRNSNKRGA 292


>gi|127514108|ref|YP_001095305.1| pseudouridine synthase [Shewanella loihica PV-4]
 gi|126639403|gb|ABO25046.1| pseudouridine synthase [Shewanella loihica PV-4]
          Length = 238

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 66/240 (27%), Positives = 103/240 (42%), Gaps = 18/240 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERA----------AVNVMSTDHIEVD 63
            R+++ +A  G  SRR   R+I   RV +   L +                  +  + VD
Sbjct: 1   MRLAQYLALTGRCSRRAASRLIRNGRVSLGDRLAKHTDSIELIETPTGTQASLS--VCVD 58

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G PL        W+++K   + T        +T   +L     R+  VGRLD ++ GLLL
Sbjct: 59  GEPLPPIADKAYWIFNKA--VGTDCRLLAEDTTSLIHLLPRQPRLYPVGRLDKDSRGLLL 116

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG L + L  PS    + Y VR     D D +  +  G+  + +     QVT   Q 
Sbjct: 117 LTNDGELTQRLMHPSFAHHKRYHVRLDRPFDDDFVVKMAAGVSYKDVTTQPCQVTRLGQD 176

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
                  + L +G NR+I+++ +    KV  L R++     LG L  G  R +++  L E
Sbjct: 177 S----FEIVLTQGLNRQIRRMSKTLGHKVIDLKRVAIESLTLGDLPEGEMRPLTQAELDE 232


>gi|313884640|ref|ZP_07818398.1| 16S pseudouridylate 516 synthase [Eremococcus coleocola
           ACS-139-V-Col8]
 gi|312620150|gb|EFR31581.1| 16S pseudouridylate 516 synthase [Eremococcus coleocola
           ACS-139-V-Col8]
          Length = 242

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 98/231 (42%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR+EV+++I   +++VN + + +    V    D +   G  L     
Sbjct: 2   MRLDKFLATLGLGSRKEVKKLITSGQIQVNDVTVTKVNHGVDEDHDQVAYLGQELVYQAY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      +  T          +  L      +  VGRLDI+T GLLLLTN+G LA 
Sbjct: 62  YYVMLNKPDGLVSATEDKMHETVIDWVALDFDHVDLFPVGRLDIDTTGLLLLTNNGQLAH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVT 190
            L  P     + Y+    GQV +  +     GI ++       ++ +         +   
Sbjct: 122 QLLSPKKHVAKTYQALVTGQVSEVDIAAFAAGIRLKDFTAQAAELEILDYDPDKDQSLTK 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYG-PFQLGTLLAGSTREVSKKI 240
           V + EGK  ++K++F   + +V  L R+S G       L  G  RE++   
Sbjct: 182 VTIHEGKFHQVKRMFLARDHEVLHLHRVSMGPLDLDPDLDLGQYRELTAAE 232


>gi|330723277|gb|AEC45647.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           hyorhinis MCLD]
          Length = 242

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 107/229 (46%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +++ K+I++ G  SRR  E++I Q RV VN  L           D I++D   L+KAE  
Sbjct: 3   EKIQKLISQTGYCSRRNAEKLILQNRVFVNNQLAT-IGQKASFDDEIKIDNQILKKAEHI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     + T   + + +  +          +  VGRLD NT G++LLTNDG LA  
Sbjct: 62  YYAFYKPKRVVCTREDNFNRKKIIDFF--PKKEYLFPVGRLDFNTTGIILLTNDGELANK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  Q  R Y V  +G +  +++N   K ++        +      +K +     V L
Sbjct: 120 LIHPKFQIERTYLVHTNGDLSDEQINFANKNVIKLNNE---INSRQIIKKKATNKYIVKL 176

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           ++G N  +K++F+ F  +V  L R+ +    L  L  G  R+++ K ++
Sbjct: 177 KQGSNHHVKRLFDHFQIEVLDLKRVQFASINLANLSLGQYRKLTPKEIK 225


>gi|225568053|ref|ZP_03777078.1| hypothetical protein CLOHYLEM_04126 [Clostridium hylemonae DSM
           15053]
 gi|225163149|gb|EEG75768.1| hypothetical protein CLOHYLEM_04126 [Clostridium hylemonae DSM
           15053]
          Length = 256

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 63/247 (25%), Positives = 104/247 (42%), Gaps = 8/247 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  GI +R+EV++ I Q +VKV+  +++     V      +     P+R    
Sbjct: 7   IRLDKYLADMGIGTRQEVKKHIRQGKVKVDAAVVKSPEYKVNEKESTVLYGDSPVRYEAF 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +++   D   ++ V          +   GRLD +TEGLLL+TNDG LA 
Sbjct: 67  VYYMLNKPAG-VISATEDRREKTVVDLIKTKERKDLFPAGRLDKDTEGLLLITNDGKLAH 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGSNAW 188
            L  P     + Y  R  G V ++      +GI I             + +    G  + 
Sbjct: 126 SLLSPKKHVDKTYYARVKGIVTEEDARAFAEGIDIGTSALPEWTRPAVLEII-SSGQESA 184

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGP 247
           V + ++EGK  ++K++F     +V  L R   G   L  +L  G  R+++ + LR   G 
Sbjct: 185 VRLTIQEGKFHQVKRMFLARGKEVVYLKRERMGGLVLDSSLKPGEYRKLTDEELRNIYGT 244

Query: 248 HLLEEAQ 254
               E  
Sbjct: 245 DRHAEGH 251


>gi|304413779|ref|ZP_07395223.1| 23S rRNA pseudouridylate synthase [Candidatus Regiella insecticola
           LSR1]
 gi|304283870|gb|EFL92264.1| 23S rRNA pseudouridylate synthase [Candidatus Regiella insecticola
           LSR1]
          Length = 291

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 90/293 (30%), Positives = 134/293 (45%), Gaps = 12/293 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
            +++ KV+ARAG  SRR +E MI Q+R+ ++G +       V       I +DG  L   
Sbjct: 2   SEKLQKVLARAGHGSRRAIETMIMQRRISLDGKIAT-LGDRVDVRQSTKIRLDGRVLAIT 60

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E        L  Y     L T H      +          SR ++VGRLD+NT GLLL T
Sbjct: 61  ESNAAICRVLAYYKPEGELCTLHDPQGRPTVFDRLPKLRTSRWVAVGRLDVNTSGLLLFT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  P  +  R Y VR  GQ+D+DK+  L KGI ++       +++    +G 
Sbjct: 121 TDGELANRLMHPRHEVEREYAVRVFGQIDEDKIKQLNKGIQLEDGPASFHKISFQGGEGI 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           N W  V L EG+NRE+++++E  + KVNRLIRI YG   L   L  G   E+    L+  
Sbjct: 181 NQWYHVTLTEGRNREVRRLWEAVDVKVNRLIRIRYGDINLPKGLPRGGWTELD---LKAI 237

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
                L        + +   +   R + N I       +  K+  +++    +
Sbjct: 238 NYLRELVSLPAETVSKLPVEQERRRMKANQIRRAVKRHSEKKRADTRQIKKRR 290


>gi|320106004|ref|YP_004181594.1| pseudouridine synthase [Terriglobus saanensis SP1PR4]
 gi|319924525|gb|ADV81600.1| pseudouridine synthase [Terriglobus saanensis SP1PR4]
          Length = 301

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 92/302 (30%), Positives = 138/302 (45%), Gaps = 20/302 (6%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DH 59
           M  K  ++      R+ K++A AGIASRR+ E +I + RV+VNG ++           DH
Sbjct: 1   MAKKPELKAGPEGVRLQKILADAGIASRRKSEEVILEGRVQVNGKVVTELGTRANPEKDH 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLD 115
           I VDG  L+  E  R +L +KP G VTT  DP+ R T+ D L             VGRLD
Sbjct: 61  IRVDGKLLQGPEEHRYYLVNKPRGYVTTMHDPEKRPTIVDLLIKDGKMPDVRLYPVGRLD 120

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI----- 170
            N+EGLLL+TNDG LA  L   S    + Y V+  GQ  +  ++ L++G++I+       
Sbjct: 121 YNSEGLLLMTNDGELANALSKASNSVEKTYLVKVAGQPSEQAIDQLRRGVMIERGRLQET 180

Query: 171 --------CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP 222
                        +V L    G N W  V L EG+NR+++K+FE  +  V ++ RI YG 
Sbjct: 181 QGARRNRVMTAPAKVKLVRA-GLNPWFEVSLTEGRNRQLRKMFEEIDHHVEKIRRIGYGA 239

Query: 223 FQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDF 282
             L  +  G  RE+    +         ++ +     P  +  T+   +           
Sbjct: 240 LVL-DVAPGEFRELKPGEVTALGRAATGKKVERRRTMPEAAKLTVPGKKTGSRKAYKRPR 298

Query: 283 TR 284
             
Sbjct: 299 KE 300


>gi|218297269|ref|ZP_03497913.1| RNA-binding S4 domain protein [Thermus aquaticus Y51MC23]
 gi|218242409|gb|EED08950.1| RNA-binding S4 domain protein [Thermus aquaticus Y51MC23]
          Length = 235

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 79/241 (32%), Positives = 116/241 (48%), Gaps = 8/241 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R+  ++ARAG+ASRR+ E +I Q  V+VNG +       V   D +EV G  +    
Sbjct: 2   KAMRLQALLARAGVASRRQAEVLIRQGLVRVNGEVA-HLGQKVGPDDLVEVAGRRVEWPR 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              +   HKP G  TT SDP  R TVF+ LP +     +VGRLD  +EGLLL TNDG L 
Sbjct: 61  ERLVLALHKPRGYTTTRSDPHARRTVFELLPEVPGLQ-AVGRLDRESEGLLLFTNDGELL 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQD-KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     +VYRV        +     L +G+ ++      +               
Sbjct: 120 FRLTHPRYGVKKVYRVWTERGTLPEAVCRKLVEGVALEDGPARALSCRPAQGGAI----- 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L EG+ RE++++ +   + V RL+R+  GP +LG L  G  R +S + ++  L    L
Sbjct: 175 LTLGEGRKREVRRMLQAVGYPVKRLLRLQVGPIRLGNLPPGRWRRLSPEEVQALLKEVGL 234

Query: 251 E 251
           E
Sbjct: 235 E 235


>gi|222624207|gb|EEE58339.1| hypothetical protein OsJ_09447 [Oryza sativa Japonica Group]
          Length = 1194

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 66/238 (27%), Positives = 107/238 (44%), Gaps = 16/238 (6%)

Query: 4   KNIVQENF---TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDH 59
           +    EN     PQR++KV+A AG+ASRR  E +I Q +V VNG +       V  S D 
Sbjct: 65  RRFYNENIKEHEPQRLAKVLAAAGVASRRTCEELIFQGKVTVNGSVCTAPQTKVDISKDS 124

Query: 60  IEVDGVPLRKAERTRLWL--YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--------I 109
           I V+G  + K    +L+         + +        S   D L                
Sbjct: 125 IYVNGNRISKKLPPKLYFAVNKPKGYICSCGEPKSIISLFDDYLKGWNKIQPGVPKPRLF 184

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           +VGRLD+ T GL+++TNDG  A+ L  PS+  ++ Y V   G V ++ L  + +G  I G
Sbjct: 185 TVGRLDVATSGLIIITNDGEFAQKLSHPSSNIMKEYVVTIDGPVHRNHLIAISEGTKIDG 244

Query: 170 ICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +       +            + + + EG+N E++++ +    +V  L R+  G F+L
Sbjct: 245 VKCIPDLVEPLDVQSNTKRTRIRIAVHEGRNHEVRELVQNAGLEVYALKRVRIGRFRL 302


>gi|148651853|ref|YP_001278946.1| pseudouridine synthase [Psychrobacter sp. PRwf-1]
 gi|148570937|gb|ABQ92996.1| ribosomal small subunit pseudouridine synthase A [Psychrobacter sp.
           PRwf-1]
          Length = 234

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 56/232 (24%), Positives = 100/232 (43%), Gaps = 5/232 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K I++A   SR+E ++++    + VN  +++  +V+V    D +   G PL  A  
Sbjct: 1   MRLDKFISKATELSRKEAKKVLHASEITVNDEVVKDGSVHVDVLNDEVMWAGEPLSVATG 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +R  L HKP G   T    +             S +   GRLD++T G L+L++DG    
Sbjct: 61  SRYILLHKPEGFECTLKPKEYPIVTELIAVPELSNLRIAGRLDVDTTGALILSDDGSWLH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQD---KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            +  P     +VY +     +D++            ++    Y   +  L  +       
Sbjct: 121 RVTSPRHLHEKVYELTLADAMDEEAQAHAIKKVGQGILLDGDYEPTKPALL-EFIDETHA 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + L EGK  ++K++  +F  KV  L R S G   L  L  G +R +++  +
Sbjct: 180 RLILTEGKYHQVKRMMAYFGNKVVELHRASIGGITLEGLEKGDSRFLTEDEV 231


>gi|82702976|ref|YP_412542.1| pseudouridine synthase, Rsu [Nitrosospira multiformis ATCC 25196]
 gi|82411041|gb|ABB75150.1| ribosomal large subunit pseudouridine synthase B [Nitrosospira
           multiformis ATCC 25196]
          Length = 315

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 72/245 (29%), Positives = 120/245 (48%), Gaps = 6/245 (2%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
                 Q++ KV+A+AG+ SRRE+E +IA  +V +NG   +     + + D + V    +
Sbjct: 67  SPQPVTQKLHKVLAQAGLGSRREMEELIASGQVTINGKTAQV-GDRIAARDVVRVGKRVV 125

Query: 68  RKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                 RL      +     +V+        S          S+ I++GRLD NT GLL+
Sbjct: 126 HFRSARRLPRVMLYHKPEGEIVSQDDPQGRTSVFDKLPQLRSSKWIAIGRLDYNTSGLLV 185

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T DG LA  L  P  +  R Y VR  G++  ++  LL  G+ ++        ++ +  +
Sbjct: 186 FTTDGELANRLMHPRFEVEREYAVRIIGRLTPEQATLLTSGVELEDGAAKFDYLSDEGGE 245

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           GSN W  V L+EG+NRE++++FE     V+RL+R+ +GP  L   L  G + E+++  + 
Sbjct: 246 GSNHWYRVILKEGRNREVRRMFEAVGMTVSRLMRVRFGPINLPSRLKRGKSMELNEAEIG 305

Query: 243 EQLGP 247
             L  
Sbjct: 306 RLLEL 310


>gi|157376639|ref|YP_001475239.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
 gi|157319013|gb|ABV38111.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
          Length = 256

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 44/232 (18%), Positives = 93/232 (40%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  +   +R   ++ + +  V  +G +++ +   V     I +DG  L      
Sbjct: 27  VRLDKFICESTSLTRSLAKKAMHRGDVTCDGEIIKNSGFKVTDAHTICLDGEVLSII-GP 85

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP+  + +  D +  S +          +   GRLD +T GL+L+TNDG  +  
Sbjct: 86  RFIMINKPVDTICSTIDEEYPSVLGLIDVIKPEELHIAGRLDADTTGLVLITNDGQWSHK 145

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y +     +    +     G+ +  +        + +           +
Sbjct: 146 ITSPKKECGKRYLLETAEPLADSLVEQFATGLQLNNEDGLTKPAILDILGA----HEARL 201

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++      +V RL R   G  +L   L  G  R ++ + ++
Sbjct: 202 TITEGKYHQVKRMLAAVGNRVTRLHRECVGTIELDADLDLGEWRYLTDEEIK 253


>gi|251782848|ref|YP_002997151.1| putative 16S pseudouridylate synthetase [Streptococcus dysgalactiae
           subsp. equisimilis GGS_124]
 gi|242391478|dbj|BAH81937.1| putative 16S pseudouridylate synthetase [Streptococcus dysgalactiae
           subsp. equisimilis GGS_124]
          Length = 238

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 99/229 (43%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SRR+V+++I  Q V+++  +      NV      IE+ G  +   + 
Sbjct: 1   MRLDKLLEVVTDGSRRQVKQLIKGQDVRIDHEIAWSGRQNVDPGLQLIEISGKRISHPKH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +   L      +               +       +  VGRLD +TEGL+LLT++G L  
Sbjct: 61  SYFILNKPAGVVSARSDINHVTVLDQLSEKDRHPDLYPVGRLDRDTEGLVLLTDNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +  PS    + Y V  +G +D D  +    GI    G      Q+T+       +   +
Sbjct: 121 RMLHPSHHVAKTYMVTVNGFLDADAPDFFAAGIKFPTGEQCRPAQLTILQASQEKSQARL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + EGK  ++KK+F  +  KV  L R S+   +LG L +G+ R ++   
Sbjct: 181 VISEGKFHQVKKMFLTYGLKVISLKRASFAGLELGELASGAYRSLTDAE 229


>gi|217974541|ref|YP_002359292.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217499676|gb|ACK47869.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 242

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 67/240 (27%), Positives = 110/240 (45%), Gaps = 16/240 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLER-----AAVNVMSTDHIEVDGVPLR 68
            R++K +A+ GI SRRE  R+I   R+ +NG +           ++   D+IE+D  P+ 
Sbjct: 1   MRLAKYLAQCGIGSRREACRLIEAGRITLNGHIARHTDPIRLGESLNCLDNIELDSAPIT 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           K E    W+ +K +G      + D   T   +L     R+  VGRLD ++ GLLLLTNDG
Sbjct: 61  KTETLSYWILNKAVGTDCRLLEQDE--TSLIHLLPKAPRLYPVGRLDKDSRGLLLLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS    + Y VR +     D +  +  G+  + +     QV   +       
Sbjct: 119 ELTHKLMHPSFAHSKTYHVRLNRPFTDDFVEQMASGVRYKNLQTLPCQVRRLSSDS---- 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ-----LGTLLAGSTREVSKKILRE 243
             + L +G NR+I+++ +   + V  L R++          LG L  G  R +++  + E
Sbjct: 175 FEIVLIQGLNRQIRRMSKALGYHVIDLERVAIMTLNLRELALGELQEGQMRRLTESEVAE 234


>gi|149377680|ref|ZP_01895416.1| pseudouridylate synthase [Marinobacter algicola DG893]
 gi|149358033|gb|EDM46519.1| pseudouridylate synthase [Marinobacter algicola DG893]
          Length = 234

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 100/232 (43%), Gaps = 8/232 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R+   +A A   SRR+ ++ I+  RV+V+G    + A  V     + +D  PL   E 
Sbjct: 4   SMRLDYFVANATTLSRRDAKKAISAGRVRVDGETCRKPASPVAKDTRVSLDDQPLSLPEE 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L LY     +++  +D    + +      +   +   GRLD +T GLLLLT DG  + 
Sbjct: 64  RYLMLYKPAG-VISATTDSQQPTALDLLPADVRHGLHIAGRLDADTTGLLLLTTDGQWSH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--CYGDMQVTLDTQKGSNAWVT 190
            +  P  +  + YRV     +D   +  L++G+++ G         V L         + 
Sbjct: 123 RITSPRLKCHKTYRVTLAEPIDDFAITQLQQGVLLHGESRPTRPADVHLLNAG----EID 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + L EG+  ++K++       V  L R   GP  L   L  G  RE++ + +
Sbjct: 179 LTLSEGRYHQVKRMLAAVGNHVTGLHRWRVGPLILDDSLAPGDYRELTAEEV 230


>gi|237747726|ref|ZP_04578206.1| pseudouridylate synthase [Oxalobacter formigenes OXCC13]
 gi|229379088|gb|EEO29179.1| pseudouridylate synthase [Oxalobacter formigenes OXCC13]
          Length = 248

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 62/249 (24%), Positives = 105/249 (42%), Gaps = 23/249 (9%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------- 63
             P R+SK ++  GI+SRRE +  I +  VKV+G ++ +    V+    I ++       
Sbjct: 2   SEPVRLSKRMSELGISSRREADEWIEKGWVKVDGKVVSQLGSKVLPHQKITIEKQASQEQ 61

Query: 64  --------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                     P+          Y   + L++  +      +     PS    ++  GRLD
Sbjct: 62  SRRVTILINKPMGYVSGQAEDGYKPAVALISEDTHWKDDPSKEKFRPSQLRSLVPAGRLD 121

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL----NLLKKGIVIQGIC 171
           I++ GLL+LT DG +A+ L   ++   + Y VR              N+L+ G+ + G  
Sbjct: 122 IDSVGLLVLTQDGRIAKHLIGENSPTDKEYLVRVKYTRPGRLPDSELNMLRHGLKLDGKA 181

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
               +V           +   LREGK R+I+++ E    +V  L RI  G  +LG L  G
Sbjct: 182 LLPAKVEWQNDDQ----LRFVLREGKKRQIRRMCEAVGLRVIGLKRIRIGNVRLGDLPTG 237

Query: 232 STREVSKKI 240
             R +  + 
Sbjct: 238 QWRYLRPEE 246


>gi|299771357|ref|YP_003733383.1| Ribosomal large subunit pseudouridine synthase B [Acinetobacter sp.
           DR1]
 gi|298701445|gb|ADI92010.1| Ribosomal large subunit pseudouridine synthase B [Acinetobacter sp.
           DR1]
          Length = 307

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 83/312 (26%), Positives = 133/312 (42%), Gaps = 13/312 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
            +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG  ++    
Sbjct: 2   SEKLQKVLARIGLGSRRYMEEVIAAGRVSVNGRVAQV-GERIEPGDELRIDGRKVQFQIE 60

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R  L  Y     + + +      +           R + VGRLDIN+ GLLL TND
Sbjct: 61  DEIRRRVLIYYKPEGEICSRNDPEKRPTVFDHLPQIANDRWVMVGRLDINSTGLLLFTND 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V       +  G+ ++         +    +G N 
Sbjct: 121 GELANRLMHPSNEVEREYAVRVMGEVTPKIRQNMVNGVELEDGPAKFESFSEIGGEGINR 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V ++EG+NRE++++FE    KV+RL+R  YG   L   L  G   E+ K  +     
Sbjct: 181 WYQVVVKEGRNREVRRIFESQELKVSRLLRTRYGTVILPRELRTGRWMELDKTDIDNL-- 238

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                ++             + + R + ++E P    R      Q+    K+    T   
Sbjct: 239 ----AKSVELKPRQGTGLFGMAKRRTDRMTEKPMAARRGGYLRQQRRDEEKEAPANTGNQ 294

Query: 307 RRNLASNVWMAK 318
           R++   N    K
Sbjct: 295 RKSTGFNRGSKK 306


>gi|238019314|ref|ZP_04599740.1| hypothetical protein VEIDISOL_01178 [Veillonella dispar ATCC 17748]
 gi|237864013|gb|EEP65303.1| hypothetical protein VEIDISOL_01178 [Veillonella dispar ATCC 17748]
          Length = 234

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 62/237 (26%), Positives = 108/237 (45%), Gaps = 5/237 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A     SR+EV ++I  QRV +NG +  +  ++V   +D I VDG  +   + 
Sbjct: 1   MRLDKLLANKAYGSRKEVHQLIKDQRVTINGEVARKKDIHVDIESDVIAVDGQIVNTKQH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +  +     +                   I   V+ VGRLD +TEGLLLLTNDG  + 
Sbjct: 61  YYIKFHKPKGYVTAVEDASHPVVMDLLPPEYIKMGVVPVGRLDKDTEGLLLLTNDGVWSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +   +    +VY V F G++ +D +  +K+GIV+    +   +  L     S + V + 
Sbjct: 121 SIINGNKHVEKVYYVEFEGELTEDGIQRIKEGIVLGDGTH--CKPALIDILSSKS-VHIT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPH 248
           + EGK  ++K++       V  L R++ G   L  +   GS +++S   +       
Sbjct: 178 IEEGKYHQVKRMIGAAGGTVTYLKRLTIGHIDLTGIEEVGSAQDLSSDDIEAFKKIA 234


>gi|254429033|ref|ZP_05042740.1| conserved hypothetical protein, putative [Alcanivorax sp. DG881]
 gi|196195202|gb|EDX90161.1| conserved hypothetical protein, putative [Alcanivorax sp. DG881]
          Length = 243

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 55/237 (23%), Positives = 109/237 (45%), Gaps = 8/237 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E   P R+   +A +   +R+E +++I+   V V      +A + +     + + G  ++
Sbjct: 10  ETVLPMRLDYFLAHSAGLTRKEAKKLISGGAVTVADEAKPKANLQLRPDQVVMLHGEVVQ 69

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                R  + HKP+ +V +  DP+ R+ +      + ++V   GRLD +T GL+LLT+DG
Sbjct: 70  LP-GHRYLMLHKPVDVVCSTDDPEHRTVLDLLPAVLRTQVHPAGRLDRDTTGLVLLTSDG 128

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSN 186
             +  L  P+    + YRV     V  + L  L++GI++  +             ++ + 
Sbjct: 129 QWSHRLTSPNHACGKCYRVICADPVSDEDLQALREGILLRGEDSPTLPA----LAERVNT 184

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
             + + + EG+  ++K++      KV  L R   G   L   L  G  R ++++ +R
Sbjct: 185 HTLRLTITEGRYHQVKRMLAARGNKVVGLHREQIGDIVLDADLAPGEFRALTEEEIR 241


>gi|313202763|ref|YP_004041420.1| RNA-binding s4 domain protein [Paludibacter propionicigenes WB4]
 gi|312442079|gb|ADQ78435.1| RNA-binding S4 domain protein [Paludibacter propionicigenes WB4]
          Length = 514

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 110/241 (45%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K  V +   P R++K +A AGI SRRE +  I    + VNG ++    V V+ TD +
Sbjct: 266 LEFKKTVVDLTKPIRLNKFLANAGICSRREADEYIQAGVISVNGEIVTEMGVKVLLTDKV 325

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 +R   +  L L      + T+    D  + +     +   R+  VGRLD NT G
Sbjct: 326 MFHEQTVRSERKVYLLLNKPKDCVTTSEDTHDRLTVLDLVKNACSERIYPVGRLDRNTTG 385

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y       +++     +  G+ +  +          
Sbjct: 386 VLLLTNDGDLASKLTHPKYDKKKIYHATLDKPLEKADFETILAGVPLDDVNI-AADALEF 444

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            ++G    V + +  G+NR ++++FE   +K+ RL R+ +       L  G  R +S++ 
Sbjct: 445 VKEGDLKQVGIEIHSGQNRVVRRIFEKLGYKIIRLDRVYFAGLTKKQLPRGKYRFLSERE 504

Query: 241 L 241
           +
Sbjct: 505 V 505


>gi|295398834|ref|ZP_06808828.1| ribosomal small subunit pseudouridine synthase A [Aerococcus
           viridans ATCC 11563]
 gi|294972924|gb|EFG48757.1| ribosomal small subunit pseudouridine synthase A [Aerococcus
           viridans ATCC 11563]
          Length = 258

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 62/251 (24%), Positives = 105/251 (41%), Gaps = 9/251 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDH 59
           M +K         QR+ K ++     SR +V+ +I +  + VNG + ++    V  + D 
Sbjct: 1   MTNKKA---GKNTQRLDKFVSSMTPYSRSDVKTLIKKSAIYVNGSVAKKPNQPVNVTEDK 57

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINT 118
           +EVDG  L       + ++     +  T  +             I   +   VGRLD +T
Sbjct: 58  VEVDGQELVYEPYVYIMMHKPDGVISATEDNRWETVIDLLPEDLILTYQPFPVGRLDKDT 117

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQV 177
            GLLL+TNDG     L  P     + Y V   G +    ++  +KG+ I QG      Q+
Sbjct: 118 TGLLLITNDGQFNHALMAPKKHVEKEYAVLVDGLLSDKHIDQFEKGLDIGQGEKTKPAQL 177

Query: 178 TLDTQKG--SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
            +D        +   V + EGK  ++K++F   + +V +L R   G   L   L  G   
Sbjct: 178 FIDQVDEEAGQSLARVVIAEGKYHQVKRMFHAVDCEVVQLHRQRIGQLILPDALTEGEFV 237

Query: 235 EVSKKILREQL 245
           +V  + L + +
Sbjct: 238 QVDYQDLYDAI 248


>gi|271964497|ref|YP_003338693.1| pseudouridine synthase, Rsu [Streptosporangium roseum DSM 43021]
 gi|270507672|gb|ACZ85950.1| pseudouridine synthase, Rsu [Streptosporangium roseum DSM 43021]
          Length = 621

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 91/242 (37%), Positives = 127/242 (52%), Gaps = 1/242 (0%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIE 61
           D+    E     R+ KV+A+AG+ASRR  E MI   RV V+G ++ R    V      I 
Sbjct: 373 DERDTTEVPDGVRLQKVLAQAGVASRRACEDMIGDGRVTVDGQVVRRFGARVDPAKQVIH 432

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           VDG  L           +KPIG+V+T SDPDGR ++ D +     R+  VGRLD  TEGL
Sbjct: 433 VDGKRLPTMPDLVYLAINKPIGVVSTMSDPDGRPSLADFVADRTERLFHVGRLDTETEGL 492

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           +LLTNDG LA  L  PS    + Y  +  G++++D    LKKGI ++         TL  
Sbjct: 493 ILLTNDGELANRLTHPSYGVQKKYWAKVPGRIERDLGRRLKKGIELEDGIAKADSFTLVQ 552

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + G  A V V L EG+   ++++ E     V  L RI +GP +LG L  G+ R ++ K +
Sbjct: 553 EHGQQALVEVVLHEGRKHIVRRMLEEVGHPVIDLARIEFGPVKLGRLKPGTVRALTVKEV 612

Query: 242 RE 243
            E
Sbjct: 613 GE 614


>gi|303248052|ref|ZP_07334318.1| RNA-binding S4 domain protein [Desulfovibrio fructosovorans JJ]
 gi|302490609|gb|EFL50514.1| RNA-binding S4 domain protein [Desulfovibrio fructosovorans JJ]
          Length = 267

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 67/262 (25%), Positives = 111/262 (42%), Gaps = 7/262 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
            +    R++K +A AG+ SRR+ + +IA  RV V+G ++      +      + VDG  +
Sbjct: 2   TDDNGVRLNKALAEAGVCSRRQADALIAAGRVAVDGSVVTELGRKIDPARSRLSVDGKDV 61

Query: 68  RKAE---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLL 123
            K +      L L+ KP  + T        +           R   SVGRLD  +EGLLL
Sbjct: 62  VKPDTAGTLTLMLHKKPGCVTTARDPEGRPTVFDALPDPYRKRRLFSVGRLDFFSEGLLL 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGD-MQVTLDT 181
           LT DG LA  L  P     + Y V   G V  + +  + +G+ + +G          +  
Sbjct: 122 LTTDGELAYRLAHPRWHAPKRYLVTVRGHVGPEAIEAMGRGMRLAEGEPLAPVAARIVKR 181

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                  + + LR+G NR+++++       V +L+R++ GP +LG L  G  RE++ + L
Sbjct: 182 LAADRFVLEMELRQGINRQVRRMCRDLGLTVLKLVRVAQGPLELGGLAPGKCRELAGEEL 241

Query: 242 REQLGPHLLEEAQVNLDAPIYS 263
                   L             
Sbjct: 242 AALRRSVGLPAGDAAPSPRTGR 263


>gi|123968794|ref|YP_001009652.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Prochlorococcus marinus str. AS9601]
 gi|123198904|gb|ABM70545.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Prochlorococcus marinus str. AS9601]
          Length = 240

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 51/222 (22%), Positives = 95/222 (42%), Gaps = 11/222 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL---RKAE 71
           R++K ++  G  SRRE +R+I   +V +NG +       V  +D +EV G  +   ++ +
Sbjct: 4   RINKYLSEVGYCSRREADRLILDGKVTINGKIP-EIGTKVEDSDQVEVKGQRIEKSKRQK 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L        + TT            +      R+  +GRLD  +EGL+ LTNDG + 
Sbjct: 63  NIYLAFNKPVGIVCTTDRK--VEPDNVIDFIKYPKRIFPIGRLDKLSEGLIFLTNDGDIV 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V+ +  ++ D +  +  G+ I G    +       ++       +
Sbjct: 121 NKILRARNNHEKEYIVKVNRPINNDFIQSMSNGVEILGTITKNC----FVKQLGPRNFKI 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
            L +G NR+I+++ E   ++V  L RI     +L  +  G  
Sbjct: 177 ILTQGLNRQIRRMCEALGYRVQSLKRIRIMNIKL-DVPTGEY 217


>gi|150020759|ref|YP_001306113.1| RNA-binding S4 domain-containing protein [Thermosipho melanesiensis
           BI429]
 gi|149793280|gb|ABR30728.1| RNA-binding S4 domain protein [Thermosipho melanesiensis BI429]
          Length = 230

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 53/229 (23%), Positives = 96/229 (41%), Gaps = 9/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++ A + SR+EV+R+I    VK+NG ++      V   D + V+  P+      
Sbjct: 1   MRLDKFLSNAKVGSRKEVKRLIKFGIVKINGEIITNVDFKVKENDIVTVNNTPITPYHNV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +          +       R+            +   GRLD + EGLLL+TNDG     
Sbjct: 61  YIIFNKPTGYTSSKS--EFERNIFEFIDHPYVENLHIAGRLDKDVEGLLLITNDGIFTHK 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVG 192
           +  P ++  + Y V+   ++  + +   K GIV++    +    +          ++++ 
Sbjct: 119 ITSPKSKIEKEYIVKVDKEISDEMIQKAKDGIVLKNGTRFKPAIIKRLKDN----FISIT 174

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTREVSKK 239
           + EGK  EIK + +F      ++ RI  G  +L    L  G   E+  K
Sbjct: 175 ITEGKYHEIKLIVKFLGLSYKKIERIRIGKLKLEDFNLKRGEWSEIDYK 223


>gi|293609082|ref|ZP_06691385.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292829655|gb|EFF88017.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|325121143|gb|ADY80666.1| putative ribosomal large subunit pseudouridine synthase B
           [Acinetobacter calcoaceticus PHEA-2]
          Length = 307

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 83/312 (26%), Positives = 135/312 (43%), Gaps = 13/312 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
            +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG  ++    
Sbjct: 2   SEKLQKVLARIGLGSRRYMEEVIAAGRVSVNGRVAQV-GERIEPGDELRIDGRKVQFQIE 60

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R  L  Y     + + +      +           R + VGRLDIN+ GLLL TND
Sbjct: 61  DEIRRRVLIYYKPEGEICSRNDPEKRPTVFDHLPQIANDRWVMVGRLDINSTGLLLFTND 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V       +  G+ ++         +    +G N 
Sbjct: 121 GELANRLMHPSNEIEREYAVRVMGEVTPKLRQNMVNGVELEDGPAKFESFSEIGGEGINR 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V ++EG+NRE++++FE  + KV+RL+R  YG   L   L  G   E+ K  +     
Sbjct: 181 WYQVVVKEGRNREVRRIFESQDLKVSRLLRTRYGTVILPRELRTGRWMELDKTDIDNL-- 238

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                ++             + + R + ++E P    R      Q+    K+  + T   
Sbjct: 239 ----AKSVELKPRQGTGLFGMAKRRTDRMTEKPMAARRGGYLRQQRRDDEKEAPVNTGNQ 294

Query: 307 RRNLASNVWMAK 318
           R++   N    K
Sbjct: 295 RKSTGFNRGSKK 306


>gi|305680918|ref|ZP_07403725.1| putative pseudouridine synthase B, ribosomal large subunit
           [Corynebacterium matruchotii ATCC 14266]
 gi|305659123|gb|EFM48623.1| putative pseudouridine synthase B, ribosomal large subunit
           [Corynebacterium matruchotii ATCC 14266]
          Length = 285

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 76/236 (32%), Positives = 116/236 (49%), Gaps = 4/236 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R+ KV+A+AG+ASRR  E MI   RV+VNG ++ +  V V    D I VDGV +  
Sbjct: 42  TDGVRLQKVLAQAGVASRRNAEIMIDSGRVEVNGAVVMQQGVRVNPKVDVIRVDGVRVNV 101

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTN 126
               + ++ +KP G+ +T SD  GR  + D +         +  VGRLD +TEGL+LLTN
Sbjct: 102 NNNHQYFVLNKPRGIHSTMSDDLGRPCIGDLVSERISAGQGLFHVGRLDADTEGLILLTN 161

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  P  +  + Y     G+ D+  +  LK G+ +         V +       
Sbjct: 162 DGELANRLSHPKYEVSKTYIAEVLGEADRSLVTTLKNGVELDDGPAAADYVQIVDVHQGR 221

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + V V L EG+   ++++ +   + V  L+R      QLG    G+ R ++   LR
Sbjct: 222 SLVRVQLHEGRKHIVRRMLKAAGYPVQYLVRTKLHTVQLGEQKPGTIRALNDNELR 277


>gi|293384299|ref|ZP_06630185.1| putative ribosomal small subunit pseudouridine synthase A
           [Enterococcus faecalis R712]
 gi|307284346|ref|ZP_07564511.1| hypothetical protein HMPREF9515_02349 [Enterococcus faecalis
           TX0860]
 gi|307289480|ref|ZP_07569428.1| hypothetical protein HMPREF9505_02844 [Enterococcus faecalis
           TX0109]
 gi|312907104|ref|ZP_07766097.1| conserved hypothetical protein [Enterococcus faecalis DAPTO 512]
 gi|312951808|ref|ZP_07770699.1| conserved hypothetical protein [Enterococcus faecalis TX0102]
 gi|291078372|gb|EFE15736.1| putative ribosomal small subunit pseudouridine synthase A
           [Enterococcus faecalis R712]
 gi|306499576|gb|EFM68945.1| hypothetical protein HMPREF9505_02844 [Enterococcus faecalis
           TX0109]
 gi|306503286|gb|EFM72538.1| hypothetical protein HMPREF9515_02349 [Enterococcus faecalis
           TX0860]
 gi|310626881|gb|EFQ10164.1| conserved hypothetical protein [Enterococcus faecalis DAPTO 512]
 gi|310630211|gb|EFQ13494.1| conserved hypothetical protein [Enterococcus faecalis TX0102]
 gi|315154235|gb|EFT98251.1| conserved hypothetical protein [Enterococcus faecalis TX0031]
 gi|315156367|gb|EFU00384.1| conserved hypothetical protein [Enterococcus faecalis TX0043]
 gi|315164679|gb|EFU08696.1| conserved hypothetical protein [Enterococcus faecalis TX1302]
          Length = 320

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 68/261 (26%), Positives = 116/261 (44%), Gaps = 3/261 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE 71
             R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +    
Sbjct: 60  TMRLDKLLEELQFGSRKTVKRIIRGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLISHKT 119

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                L      +                       +  VGRLD +TEGLLLLT++G L 
Sbjct: 120 HVYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQLG 179

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVT 190
             L  P+ +  + Y V+ +G V  +     K GIV+QG       ++T+     + + V 
Sbjct: 180 YQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHVF 239

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHL 249
           + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L    
Sbjct: 240 LTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYFF 299

Query: 250 LEEAQVNLDAPIYSSETLVRD 270
           +E+ Q +   P        R 
Sbjct: 300 IEKQQTSKALPSNLKREEERK 320


>gi|294782058|ref|ZP_06747384.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           1_1_41FAA]
 gi|294480699|gb|EFG28474.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           1_1_41FAA]
          Length = 226

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 66/229 (28%), Positives = 107/229 (46%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ + +   GI SR+EV+++I+   +KVNG     A  N+   +D IE +G  L   + 
Sbjct: 1   MRLDRFLVECGIGSRKEVKKIISANEIKVNGSYDISAKDNINEYSDVIEYNGERLEYKKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +  K   +  T    +           I   +  VGRLD +TEGLLLLTNDG L  
Sbjct: 61  RYYIMNKKAGYITATEDIREATVMDLLPEWVIRKDLAPVGRLDKDTEGLLLLTNDGKLNH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V     + Q+ +  L++G+ I        +V    +K S+  + + 
Sbjct: 121 RLLSPKNHVDKTYYVEIENNISQEDVLKLEEGVDIGNYITLPAKV----EKISDTKIYLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++EGK  ++KK+ E  N KV  L R ++    L  L  G  +EV+ + +
Sbjct: 177 IKEGKFHQVKKMLEAVNNKVTYLQRTTFAKLSLADLALGEVKEVNLEDI 225


>gi|313200941|ref|YP_004039599.1| pseudouridine synthase [Methylovorus sp. MP688]
 gi|312440257|gb|ADQ84363.1| pseudouridine synthase [Methylovorus sp. MP688]
          Length = 237

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 95/237 (40%), Gaps = 6/237 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--EVDGVPLRKAERT 73
           + +++   G  SR+    +I    V VNG   +    +   TD +   V+  P    E+ 
Sbjct: 3   LERILHAQGFGSRKNCRILIRHHAVTVNGEPCDNPFADFD-TDKLAFTVNDEPWEYREKA 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L        +               P +   V  +GRLD +T GL+LL++DG     
Sbjct: 62  YLMLNKPANYECSHKPQHHPSVFALLPHPLLERGVQCIGRLDEDTTGLILLSDDGQFIHR 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  ++Y V     VD D++  L++G+ +           L  ++ S+  + + L
Sbjct: 122 MSSPKWKVPKIYEVGAKHAVDADQIRQLQEGVQLVDEPAPIA--ALACEQISDQVLHLTL 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHL 249
            EGK  ++K++      +V  L RI  G   L   L  G  R +++  L    G   
Sbjct: 180 AEGKYHQVKRMLAAVGNRVESLKRIRIGELVLPDDLAEGQWRWLTESELASLNGAAR 236


>gi|323127651|gb|ADX24948.1| Putative 16S pseudouridylate synthetase [Streptococcus dysgalactiae
           subsp. equisimilis ATCC 12394]
          Length = 238

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 100/229 (43%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SRR+V+++I  Q V+++  +      NV      IE+ G  +   + 
Sbjct: 1   MRLDKLLEVVTDGSRRQVKQLIKGQDVRIDHEIAWSGRQNVDPGLQLIEISGKRISHPKH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +   L      +               +       +  VGRLD +TEGL+LLT++G L  
Sbjct: 61  SYFILNKPAGVVSARSDINHVTVLDQLSEKDRHPDLYPVGRLDRDTEGLVLLTDNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +  PS    + Y V  +G +D+D  +    GI    G      Q+T+       +   +
Sbjct: 121 RMLHPSHHVAKTYMVTVNGFLDEDAPDFFAAGIKFPTGEQCRPAQLTILQASQEKSQARL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + EGK  ++KK+F  +  KV  L R S+   +LG L +G+ R V+   
Sbjct: 181 VISEGKFHQVKKMFLTYGLKVISLKRTSFAGLELGELASGAYRSVTDAE 229


>gi|113868284|ref|YP_726773.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Ralstonia eutropha H16]
 gi|113527060|emb|CAJ93405.1| Predicted 16S rRNA uridine-516 pseudouridylate synthase or related
           pseudouridylate synthase [Ralstonia eutropha H16]
          Length = 629

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 73/290 (25%), Positives = 122/290 (42%), Gaps = 6/290 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +  +    ++ KV+A  G+ SRRE+E +I Q RV VNG+        ++  D + V+G  
Sbjct: 217 LSADDDAPKLHKVLAEGGLGSRREMEELILQGRVSVNGLPA-HIGQRILPADQVRVNGKL 275

Query: 67  LRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           + +         L  +     +V+        +           + ++VGRLD NTEGLL
Sbjct: 276 IHRKVSTKPPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRIKTGKWVAVGRLDFNTEGLL 335

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + T  G +A     P     R Y VR  G++ +     L  GI +       +++     
Sbjct: 336 IFTTSGDIANRFMHPRYGVEREYAVRTLGELAEADRQRLLHGIKLDDGEANFLRIADGGG 395

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           +G N W  V L EG+NRE++++FE     V+RLIR  YG F L   L  G  +EV    +
Sbjct: 396 EGVNQWYHVALTEGRNREVRRMFEAVGLTVSRLIRTRYGQFLLPRGLKRGRWQEVEPNDV 455

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           +  +    L+       AP  +++   R +    +              +
Sbjct: 456 KALMAGVGLKVPGKGEQAPKGATKVGGRKQRTEAAIAGMPMPTGMDGLPR 505


>gi|257466391|ref|ZP_05630702.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           gonidiaformans ATCC 25563]
 gi|315917547|ref|ZP_07913787.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           gonidiaformans ATCC 25563]
 gi|313691422|gb|EFS28257.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           gonidiaformans ATCC 25563]
          Length = 238

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 63/236 (26%), Positives = 116/236 (49%), Gaps = 3/236 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           ++EN    R++K +A  G+ASRR+++  I + ++ VNGIL       V + D I V+G  
Sbjct: 1   MEENK--IRINKFLASKGVASRRQIDLWIEEGKILVNGILATS-GQKVSAEDKILVNGKM 57

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           + + E  +++        V +    +       +     +R+  VGRLD  T GL+LLTN
Sbjct: 58  ISEKEEKKVYYILYKEEEVLSAVKDERGRKTVVDCIPTKARIFPVGRLDYRTSGLILLTN 117

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L   +  P  +  + Y V   G + +++L  L++G+ ++     +  V     +  N
Sbjct: 118 DGELFNRVMHPRAEIFKTYEVLAKGHLTREQLKTLEEGVELEEGKTLEALVAKVKYEKGN 177

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +  + +REG+NR+I+++ E    +V +L R   G   L  L  G  R + ++ + 
Sbjct: 178 TFFEISIREGRNRQIRRMVEAVGSRVYQLRRTKIGRLSLEGLKLGQYRRLQEEEIE 233


>gi|126174904|ref|YP_001051053.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|217972846|ref|YP_002357597.1| RNA-binding S4 domain-containing protein [Shewanella baltica OS223]
 gi|125998109|gb|ABN62184.1| ribosomal large subunit pseudouridine synthase B [Shewanella
           baltica OS155]
 gi|217497981|gb|ACK46174.1| RNA-binding S4 domain protein [Shewanella baltica OS223]
          Length = 291

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 77/291 (26%), Positives = 127/291 (43%), Gaps = 7/291 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E  IA  RV ++G +       + +   + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRVSIDGEIA-SLGDRIEADAKVRIDGRAISLKSA 60

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  +     + +        +          SR ++VGRLDINT GLLL T+D
Sbjct: 61  EDVICRVLAYHKPEGEICSRKDPEGRPTVFDRLPKVRDSRWVAVGRLDINTSGLLLFTSD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G++ +  +  L+ G++++        +     +G N 
Sbjct: 121 GELANRLMHPSNEVDREYAVRTFGEIPEATVQRLRTGVMLEDGPAQFDSIKPAGGEGMNQ 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V LREG+NRE+++++E    +V+RLIRI YG  +L  +L  G   E+  + +     
Sbjct: 181 WWHVCLREGRNREVRRLWESQEVQVSRLIRIRYGMVELPKSLPRGGWVELPMEQVNYLRK 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
              LE     + A    S    + +   I               + +    
Sbjct: 241 LAGLEPETRTMLAADKHSVARAQVKSAKIRRAVRKHKVTGSGKPKPSRQRS 291


>gi|254468122|ref|ZP_05081528.1| ribosomal large subunit pseudouridine synthase B [beta
           proteobacterium KB13]
 gi|207086932|gb|EDZ64215.1| ribosomal large subunit pseudouridine synthase B [beta
           proteobacterium KB13]
          Length = 257

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 78/252 (30%), Positives = 123/252 (48%), Gaps = 7/252 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K+  +       +R+ K +A  G+ SRR +E +I Q+++ VN   +      V   + I 
Sbjct: 3   KNSPVEDSGNKKERIQKFLANMGMGSRRSIEELIKQKKITVNQKPI-DLGHMVYGNEIIH 61

Query: 62  VDGVPL-----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           ++G  +      K E   +  +     +V+       ++           + IS+GRLDI
Sbjct: 62  INGRRIYFKNAEKRESRLIIYHKPEGEIVSHSDPKHQKTVFQKLPKVKNGKWISIGRLDI 121

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NT GLLL+TNDG LA  +  PS Q  R Y VR  G+V ++ +N ++KG+ +         
Sbjct: 122 NTSGLLLITNDGKLANHMMHPSQQIDREYSVRILGEVTEEIINNIRKGVKLDDGVAHVDT 181

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTRE 235
                 +G+N W  + L+EG+NREI+++ E  N KV+RLIR  YGP  L   L  G   E
Sbjct: 182 FEHTGGEGANQWFRIILKEGRNREIRRLVESQNLKVSRLIRTRYGPLNLPSHLKRGQFME 241

Query: 236 VSKKILREQLGP 247
           + KK L +    
Sbjct: 242 LEKKNLEKIFKM 253


>gi|307276207|ref|ZP_07557337.1| hypothetical protein HMPREF9521_01835 [Enterococcus faecalis
           TX2134]
 gi|306507119|gb|EFM76259.1| hypothetical protein HMPREF9521_01835 [Enterococcus faecalis
           TX2134]
          Length = 320

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 68/261 (26%), Positives = 116/261 (44%), Gaps = 3/261 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE 71
             R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +    
Sbjct: 60  TMRLDKLLEELQFGSRKTVKRLIRGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLISHKT 119

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                L      +                       +  VGRLD +TEGLLLLT++G L 
Sbjct: 120 HVYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYRVGRLDGDTEGLLLLTDNGQLG 179

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVT 190
             L  P+ +  + Y V+ +G V  +     K GIV+QG       ++T+     + + V 
Sbjct: 180 YQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHVF 239

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHL 249
           + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L    
Sbjct: 240 LTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYFF 299

Query: 250 LEEAQVNLDAPIYSSETLVRD 270
           +E+ Q +   P        R 
Sbjct: 300 IEKQQTSKALPSNLKREEERK 320


>gi|260752916|ref|YP_003225809.1| pseudouridine synthase [Zymomonas mobilis subsp. mobilis NCIMB
           11163]
 gi|258552279|gb|ACV75225.1| pseudouridine synthase [Zymomonas mobilis subsp. mobilis NCIMB
           11163]
          Length = 509

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 114/231 (49%), Positives = 156/231 (67%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR++K+++RAGIASRR +E MI + R+ ++G+ +E+ A  + S D + VDG P+     T
Sbjct: 271 QRIAKLLSRAGIASRRMIEAMIEEGRIAIDGVTVEKPATLLTSLDGVTVDGKPVNAPTET 330

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL+LYHK  GL+TT  DP+GR T++D LP+   RV+ VGRLD+NTEGLLLLT DGG  R+
Sbjct: 331 RLFLYHKATGLLTTERDPEGRKTIYDRLPADLPRVMPVGRLDMNTEGLLLLTTDGGFKRM 390

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP+T   R YR R  G V QD+L  L +G+ I GI YG +   L+ + G N WV + L
Sbjct: 391 LELPATHIERCYRARVFGDVSQDQLEELIEGVTIDGIHYGSIDANLERRTGRNGWVEMKL 450

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            EG+NRE+++V  +   +V+RLIRISYGPF LG L  G+  EV    L+  
Sbjct: 451 HEGRNREVRRVLGYLGLQVSRLIRISYGPFLLGDLPVGAVEEVDPATLKAF 501


>gi|255067937|ref|ZP_05319792.1| ribosomal large subunit pseudouridine synthase F [Neisseria sicca
           ATCC 29256]
 gi|255047819|gb|EET43283.1| ribosomal large subunit pseudouridine synthase F [Neisseria sicca
           ATCC 29256]
          Length = 247

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 107/250 (42%), Gaps = 20/250 (8%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           +  ++    R+SK +A+ G+ SRRE +  I Q  VKVNG         V   D I+++  
Sbjct: 1   MEHDSNETMRLSKRMAQLGLCSRREADSYIEQGWVKVNGQTA-VLGQKVTERDRIDLNRQ 59

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                          P+          Y     L+T  +  +G  +           +  
Sbjct: 60  AHEKQAERVTILLNKPVGYVSAQAEKGYKSAAELITADNRWEGDDSRIPFNEKHKFGLAP 119

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+ + G 
Sbjct: 120 AGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGE 179

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                +V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  
Sbjct: 180 KLRPAKVEWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGKLPP 235

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 236 GKWRYLRADE 245


>gi|241761121|ref|ZP_04759210.1| pseudouridine synthase [Zymomonas mobilis subsp. mobilis ATCC
           10988]
 gi|241374740|gb|EER64201.1| pseudouridine synthase [Zymomonas mobilis subsp. mobilis ATCC
           10988]
          Length = 510

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 114/231 (49%), Positives = 156/231 (67%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR++K+++RAGIASRR +E MI + R+ ++G+ +E+ A  + S D + VDG P+     T
Sbjct: 272 QRIAKLLSRAGIASRRMIEAMIEEGRIAIDGVTVEKPATLLTSLDGVTVDGKPVNAPTET 331

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL+LYHK  GL+TT  DP+GR T++D LP+   RV+ VGRLD+NTEGLLLLT DGG  R+
Sbjct: 332 RLFLYHKATGLLTTERDPEGRKTIYDRLPADLPRVMPVGRLDMNTEGLLLLTTDGGFKRM 391

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP+T   R YR R  G V QD+L  L +G+ I GI YG +   L+ + G N WV + L
Sbjct: 392 LELPATHIERCYRARVFGDVSQDQLEELIEGVTIDGIHYGSIDANLERRTGRNGWVEMKL 451

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            EG+NRE+++V  +   +V+RLIRISYGPF LG L  G+  EV    L+  
Sbjct: 452 HEGRNREVRRVLGYLGLQVSRLIRISYGPFLLGDLPVGAVEEVDPATLKAF 502


>gi|120598427|ref|YP_963001.1| pseudouridine synthase [Shewanella sp. W3-18-1]
 gi|146293494|ref|YP_001183918.1| pseudouridine synthase [Shewanella putrefaciens CN-32]
 gi|120558520|gb|ABM24447.1| ribosomal large subunit pseudouridine synthase B [Shewanella sp.
           W3-18-1]
 gi|145565184|gb|ABP76119.1| ribosomal large subunit pseudouridine synthase B [Shewanella
           putrefaciens CN-32]
 gi|319426799|gb|ADV54873.1| RNA-binding S4 domain protein [Shewanella putrefaciens 200]
          Length = 291

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 77/291 (26%), Positives = 127/291 (43%), Gaps = 7/291 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E  IA  RV ++G +       + +   + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRVSIDGEIA-SLGDRIEADAKVRIDGRAISLKSA 60

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  +     + +        +          SR ++VGRLDINT GLLL T+D
Sbjct: 61  EDVICRVLAYHKPEGEICSRKDPEGRPTVFDRLPKVRDSRWVAVGRLDINTSGLLLFTSD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G++ +  +  L+ G++++        +     +G N 
Sbjct: 121 GELANRLMHPSNEVDREYAVRTFGEIPEATVQRLRTGVMLEDGPAQFDSIKPAGGEGMNQ 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V LREG+NRE+++++E    +V+RLIRI YG  +L  +L  G   E+  + +     
Sbjct: 181 WWHVCLREGRNREVRRLWESQEVQVSRLIRIRYGMVELPKSLPRGGWVELPVEQVNYLRQ 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
              LE     + A    S    + +   I              ++      
Sbjct: 241 LAGLEPETRTMLAADKHSVARAQVKSAKIRRAVRKHKVTGAGKAKPTRQRS 291


>gi|297823807|ref|XP_002879786.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
 gi|297325625|gb|EFH56045.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
          Length = 412

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 73/259 (28%), Positives = 125/259 (48%), Gaps = 18/259 (6%)

Query: 4   KNIVQENFT--PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHI 60
           +    ENF   PQR+SKV+A AG+ASRR  E +I   +V VNGIL       V  + D I
Sbjct: 150 RRFYNENFKEPPQRLSKVLAAAGVASRRTSEELIFDGKVTVNGILCNTPQTRVDPSRDII 209

Query: 61  EVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----------- 108
            V+G  + K       +  +KP G + +  + + +S +      + S             
Sbjct: 210 YVNGNRIPKKLPPKVYFALNKPKGYICSSGEKEIKSVISLFDEYLSSWDKRNPGTPKPRL 269

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            +VGRLD+ T GL+++TNDG  A+ L  PS+   + Y     G + +  L  + +G +++
Sbjct: 270 FTVGRLDVATTGLIVVTNDGDFAQKLSHPSSSLPKEYITTVVGDIHKRHLMAISEGTIVE 329

Query: 169 GICYGDMQVTLDTQK--GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL- 225
           G+      V L  ++     A + + + EG+N E++++ +    +V+ L R+  G F+L 
Sbjct: 330 GVHCVPDSVELMPKQHDIPRARLRIVVHEGRNHEVRELVKNAGLEVHSLKRVRIGGFRLP 389

Query: 226 GTLLAGSTREVSKKILREQ 244
             L  G   E+ +  L+  
Sbjct: 390 SDLGLGKHVELKQSELKAM 408


>gi|21232071|ref|NP_637988.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66767803|ref|YP_242565.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. 8004]
 gi|21113814|gb|AAM41912.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66573135|gb|AAY48545.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. 8004]
          Length = 240

 Score =  154 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 61/239 (25%), Positives = 106/239 (44%), Gaps = 10/239 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT- 73
           R++K IA  G  SRRE +R+I ++RV VNG++    AV V   D + VDG PLR  E   
Sbjct: 4   RLNKHIAETGFCSRREADRLIGERRVTVNGVIAGTGAV-VGEDDTVLVDGQPLRVREAKK 62

Query: 74  ----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               R         +  T +                 R+  +GRLD ++EGL+L+T++G 
Sbjct: 63  PGTRRHVYIALNKPVGITSTTESSVKGNIVEFVGHEQRIFPIGRLDKDSEGLILMTSNGN 122

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +     +  + Y V  +  V  + L  + +G+ +        +     + G     
Sbjct: 123 IVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRLHDETTLPCRTARIAKFG----F 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + L +G NR+I+ +   F ++V +L R+     +L  L  G  R ++ + L+  L   
Sbjct: 179 RIVLEQGLNRQIRLMAAAFGFRVTQLRRVRIDNIKLAALKPGQWRNLTDQELQGLLPQR 237


>gi|116328224|ref|YP_797944.1| pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116330948|ref|YP_800666.1| pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
 gi|116120968|gb|ABJ79011.1| Pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116124637|gb|ABJ75908.1| Pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
          Length = 244

 Score =  154 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 63/238 (26%), Positives = 107/238 (44%), Gaps = 4/238 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DH 59
           M+ KN         R+++ +A  G+ SRR+ E +I + ++ +NG  +      +    D 
Sbjct: 1   MQSKNDSNARDE-IRLNRFLADCGLGSRRKTEELILRGQITINGKRVTDLGTKIKPGSDV 59

Query: 60  IEVDGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           +   G  +    +  R+ + +KP+G + +H D     TVF  LP  +      GRLD+N+
Sbjct: 60  VSYLGNVVEPTRKPKRILILNKPVGYLCSHGDRFHEKTVFSLLPLTYKNFKIAGRLDLNS 119

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLL+LTNDG LA+ +  PS    + Y V  +    +  +    +  ++        ++ 
Sbjct: 120 RGLLILTNDGELAQKISHPSNGSEKEYLVTLNHDPGEKWIQAAFQKGILDAGEILRAKMV 179

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                G N    V L EGK R+I+++F      V  L RI  G  QL  L     + +
Sbjct: 180 KLVP-GKNCVYRVILAEGKKRQIRRMFHASGASVIDLQRIRIGSIQLEKLGIEEGKFL 236


>gi|307301432|ref|ZP_07581192.1| pseudouridine synthase [Sinorhizobium meliloti BL225C]
 gi|306903489|gb|EFN34077.1| pseudouridine synthase [Sinorhizobium meliloti BL225C]
          Length = 262

 Score =  154 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 64/226 (28%), Positives = 108/226 (47%), Gaps = 1/226 (0%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTR 74
           +++ +++ G  SR + E++IA+ RV V G  +   +  V    D I VDG  +    R  
Sbjct: 27  LARALSKLGYCSRTQAEKLIAEGRVSVAGRKITDLSHWVDIEADRIAVDGTVIAAQARVY 86

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L      + T        +            +  VGRLD  +EGLLL TND  LA+ L
Sbjct: 87  LMLNKPRGLVTTRDDPEGRPTVFSCLDNVDVPSLSPVGRLDKASEGLLLFTNDTVLAQRL 146

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P T   +VY V+  G   +     + +G+   G     ++V        N+W+ V L 
Sbjct: 147 LDPETHLGKVYHVQVRGIFGEAMAARMVEGVTEGGELLRALRVERLKSGDRNSWIEVELD 206

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           EG+NR+I+++ +   ++  RL+R+S G  +LG L  G++R +++  
Sbjct: 207 EGRNRQIRRMLDVLGFECLRLLRVSIGEIRLGDLPKGASRPLTEAE 252


>gi|72161610|ref|YP_289267.1| pseudouridine synthase, Rsu [Thermobifida fusca YX]
 gi|71915342|gb|AAZ55244.1| pseudouridine synthase, Rsu [Thermobifida fusca YX]
          Length = 375

 Score =  154 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 76/251 (30%), Positives = 127/251 (50%), Gaps = 4/251 (1%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHI 60
           ++++   +     R+ K +A+AG+ASRR  E +IA  RV V+G ++ R    V      I
Sbjct: 123 EERDTYVDVPGGIRLQKALAQAGVASRRACEELIAAGRVSVDGQIVRRFGARVDPEKSEI 182

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDIN 117
            VDG+ +  ++  R +  +KP G+V+T  DP+GR T+ D    +  I  R+  VGRLD +
Sbjct: 183 RVDGMRVVTSQNLRYYALNKPRGVVSTMFDPEGRPTIGDYAAQIGPIEERLFHVGRLDTD 242

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGL+LLTNDG LA  L  P  +  + Y  +  G V +D +  ++KG+ +          
Sbjct: 243 TEGLILLTNDGELANRLTHPRYKVTKTYLAKVPGPVPRDVIRQIRKGVELDDGFVKVDSF 302

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       A V + L EG+   ++++ +     V+ L R   GP  L  L +G+ R ++
Sbjct: 303 RVIDNIEPKALVEIRLHEGRKHIVRRLMKAVGHPVSDLARTQIGPVGLNNLKSGTIRALT 362

Query: 238 KKILREQLGPH 248
            + + E     
Sbjct: 363 SQEVSELYTAA 373


>gi|322388325|ref|ZP_08061929.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           infantis ATCC 700779]
 gi|321140997|gb|EFX36498.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           infantis ATCC 700779]
          Length = 241

 Score =  154 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 59/232 (25%), Positives = 108/232 (46%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + ++ + V+G +    A N+ +    +   G  ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLKKEILVDGQVAISLAQNIDTGLQELIFQGRKIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +  +                   +V ++GRLD +T GLLLLTN+G L  
Sbjct: 60  TYLMLHKPNGVVTASKDKKLPTVMDLLPQHLQSDQVYAIGRLDRDTTGLLLLTNNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   K GI  + G      Q+ + +   S +  T+
Sbjct: 120 QLLHPQYHVDKTYQVEVNGLLTPDHIQQFKNGIVFLDGTICKPAQLEILSSSPSISRATI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++KK+F     KV  L R+ +G F L   L  G  R ++++ L+
Sbjct: 180 TISEGKFHQVKKMFLSVGVKVTALKRVQFGDFLLDPDLAEGQYRLLNQEELK 231


>gi|212634749|ref|YP_002311274.1| pseudouridine synthase Rsu [Shewanella piezotolerans WP3]
 gi|212556233|gb|ACJ28687.1| Pseudouridine synthase, Rsu [Shewanella piezotolerans WP3]
          Length = 290

 Score =  154 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 76/292 (26%), Positives = 130/292 (44%), Gaps = 10/292 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E  IA  R+ V+G +       V S   + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRISVDGEIA-SLGDRVESDVKVRIDGRAISIKSE 60

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  +  +     + +        +       +  SR ++VGRLDINT GLLL T+D
Sbjct: 61  EDVVCRVIAYHKPEGEICSRKDPEGRPTVFDRLPKTRDSRWVAVGRLDINTSGLLLFTSD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V+   +  L+ G+ ++       +V     +G N 
Sbjct: 121 GELANRLMHPSNEVEREYAVRTFGEVNDACIQRLRMGVTLEDGPASFDKVKAAGGEGMNK 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V L EG+NRE+++++E    +V+RLIRI YG  +L  +L  G   E+    + +   
Sbjct: 181 WWHVSLAEGRNREVRRLWESQEVQVSRLIRIRYGMIELPKSLPRGGWIELP---IEQVNY 237

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
                       + + + +  V       +++     + K  ++       +
Sbjct: 238 LRQTAGMDEETRSILGTDKHSVARAKVRGAKIRRAVRKHKATATPNKPSRSR 289


>gi|94991824|ref|YP_599923.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS2096]
 gi|94545332|gb|ABF35379.1| Ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS2096]
          Length = 220

 Score =  154 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 65/221 (29%), Positives = 105/221 (47%), Gaps = 3/221 (1%)

Query: 34  MIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           MI Q  V +NG ++   A  V S D +E++G P+   E+    L      + +   D   
Sbjct: 1   MIKQGLVTLNGQVITDLATTVKSGDVVEIEGSPIYNEEKVYYLLNKPRGAISSVSDDKGR 60

Query: 94  RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
             TV D LP +  R+  VGRLD +T G+L+LTNDG     +  P  +  +VY  R  G  
Sbjct: 61  -KTVLDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDTMIHPRNEIDKVYLARVKGIA 119

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            ++ L  L +GIVI G      +  +       + + V + + EG+N ++KK+FE     
Sbjct: 120 TKENLRPLTRGIVIDGKKTKPARYNIVRVEADKNRSIVELTIHEGRNHQVKKMFESVGLL 179

Query: 212 VNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           V++L R  +G   L  L  G  R ++KK + +       ++
Sbjct: 180 VDKLSRTRFGTVDLKGLRPGEARRLNKKEISQLHNLANTKK 220


>gi|71065212|ref|YP_263939.1| ribosomal large subunit pseudouridine synthase B [Psychrobacter
           arcticus 273-4]
 gi|71038197|gb|AAZ18505.1| ribosomal large subunit pseudouridine synthase B [Psychrobacter
           arcticus 273-4]
          Length = 315

 Score =  154 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 88/315 (27%), Positives = 131/315 (41%), Gaps = 8/315 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
             +++ K +AR G+ SRR++E +I   RV VN          V   D I VDG  ++   
Sbjct: 2   KDEKLQKALARMGLGSRRQMEEVIKAGRVTVNNGPAT-IGDRVEQGDEIRVDGRQIKYTA 60

Query: 70  ---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                R  L  Y     + + +      +           R + VGRLDIN+ GLLL TN
Sbjct: 61  ENEKRRRVLAYYKPEGEVCSANDPEGRPTVFERLPKLTHDRWVMVGRLDINSTGLLLFTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG +A  L  PS++  R Y VR  G V  D    +  G++++        +     +G N
Sbjct: 121 DGEMAHRLMHPSSEVTREYAVRVLGDVTPDMARAMTTGVMLEDGMAKFEDIKEGGGEGVN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
            W  V L+EG+NRE++++FE    KV+RL+R SYG   L   L  G   E+ +K +    
Sbjct: 181 KWHHVKLKEGRNREVRRLFESQGLKVSRLLRTSYGNIALPKELRTGRFLELDRKDINILT 240

Query: 246 GPHLLEEA-QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
               L       L       +  +R++P                SS  N  +K K   +P
Sbjct: 241 DLVSLRPRYGTGLHGAAKEKQERIRNKPLKARRTDTRSDNRNSTSSSANSSTKPKTSGSP 300

Query: 305 VHRRNLASNVWMAKG 319
             R    S     K 
Sbjct: 301 ASRGTRNSRDRNDKR 315


>gi|283856285|ref|YP_162311.2| pseudouridine synthase [Zymomonas mobilis subsp. mobilis ZM4]
 gi|283775281|gb|AAV89200.2| pseudouridine synthase [Zymomonas mobilis subsp. mobilis ZM4]
          Length = 510

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 114/231 (49%), Positives = 156/231 (67%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR++K+++RAGIASRR +E MI + R+ ++G+ +E+ A  + S D + VDG P+     T
Sbjct: 272 QRIAKLLSRAGIASRRMIEAMIEEGRIAIDGVTVEKPATLLTSLDGVTVDGKPVNAPTET 331

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL+LYHK  GL+TT  DP+GR T++D LP+   RV+ VGRLD+NTEGLLLLT DGG  R+
Sbjct: 332 RLFLYHKATGLLTTERDPEGRKTIYDRLPADLPRVMPVGRLDMNTEGLLLLTTDGGFKRM 391

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP+T   R YR R  G V QD+L  L +G+ I GI YG +   L+ + G N WV + L
Sbjct: 392 LELPATHIERCYRARVFGDVSQDQLEELIEGVTIDGIHYGSIDANLERRTGRNGWVEMKL 451

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            EG+NRE+++V  +   +V+RLIRISYGPF LG L  G+  EV    L+  
Sbjct: 452 HEGRNREVRRVLGYLGLQVSRLIRISYGPFLLGDLPVGAVEEVDPATLKAF 502


>gi|258544383|ref|ZP_05704617.1| ribosomal large subunit pseudouridine synthase B [Cardiobacterium
           hominis ATCC 15826]
 gi|258520387|gb|EEV89246.1| ribosomal large subunit pseudouridine synthase B [Cardiobacterium
           hominis ATCC 15826]
          Length = 260

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 76/256 (29%), Positives = 126/256 (49%), Gaps = 12/256 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +R+ K +A  G+ SRRE+E  I + R++VNG L       +   + + +DG PLR 
Sbjct: 2   SNELERIQKWLAARGLGSRREIEGWIREGRLRVNGKLA-ELGQRISGYERLSLDGKPLRV 60

Query: 70  AE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
           +      R  L  +  P  + + +      +           R +S+GRLD+NT GLLL 
Sbjct: 61  SPEREAPRQILMYHKPPGEICSRNDPDGRPTVFRHLPKLRQGRWVSIGRLDLNTAGLLLF 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-----GDMQVTL 179
           TNDG LA  L  PS +  R Y VR  G+V++D L  L+ G+ ++           +Q   
Sbjct: 121 TNDGELANRLMHPSAEIEREYWVRVAGEVNEDTLQALRNGLELEDGFACFDDVQPLQALH 180

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
           +     N + +V L+EG+NRE+++++E    +V+RL RI +G   L   L AG  R ++ 
Sbjct: 181 EDDTQYNRYFSVVLKEGRNREVRRLWEAVGCQVSRLKRIRFGNLWLPKNLAAGRWRPLTA 240

Query: 239 KILREQLGPHLLEEAQ 254
             +   L     ++ +
Sbjct: 241 GEVNALLDLLQRKQRR 256


>gi|282864458|ref|ZP_06273514.1| pseudouridine synthase [Streptomyces sp. ACTE]
 gi|282560945|gb|EFB66491.1| pseudouridine synthase [Streptomyces sp. ACTE]
          Length = 382

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 108/233 (46%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
               +R+ K++ARAG+ SRR  E +I Q RV+VNG ++      V    D I+VDG+ + 
Sbjct: 142 EQEGERLQKILARAGMGSRRACEELIEQARVEVNGEIVLEQGKRVDPQKDEIKVDGLTVA 201

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   L      + T       ++   D + +  +R+  VGRLD  TEG++LLTN G
Sbjct: 202 TQSYLFFALNKPAGVVSTMGDPDGRQNLG-DYVTNRETRLFHVGRLDTETEGIILLTNHG 260

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     + Y     G + +D    LK GI ++          +    G N  
Sbjct: 261 ELAHRLTHPRYGVKKTYLAAIQGPLPRDLGKRLKDGIQLEDGYARADHFRVVENTGKNYL 320

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V L EG+   ++++     + V RL+R S+GP  LG   +G  R ++   +
Sbjct: 321 VEVTLHEGRKHIVRRMLAEAGFPVERLVRTSFGPIPLGDQKSGWLRRLTNTEV 373



 Score = 39.8 bits (91), Expect = 0.73,   Method: Composition-based stats.
 Identities = 11/104 (10%), Positives = 23/104 (22%), Gaps = 6/104 (5%)

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL------SKQKKLATPVHRRN 309
                  S            S       + ++   +             +  + P   R 
Sbjct: 22  PRSGSGGSFRPKAAGGTQGASGAGGRDDKREQRPRKPRPEERRYDVGADEPGSGPRKGRG 81

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            A+      G  S+     G R +     P     +  +R   +
Sbjct: 82  TAARGGAKGGPKSAQNVSKGGRRQGAPARPRELDAKIEQRNRDR 125


>gi|162448036|ref|YP_001621168.1| ribosomal small subunit pseudouridine synthase [Acholeplasma
           laidlawii PG-8A]
 gi|161986143|gb|ABX81792.1| ribosomal small subunit pseudouridine synthase [Acholeplasma
           laidlawii PG-8A]
          Length = 231

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 52/229 (22%), Positives = 93/229 (40%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K ++     SR+E++ M+    VKV  + ++ + V +    D I V+G  +   E 
Sbjct: 1   MRLDKFLSNLNYGSRKEIKLMVKNGLVKVGNLTVKSSDVKIDPNYDKIFVNGTEVIYKEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L  Y     L +  ++           P     +   GRLD ++EGL++LT  G L  
Sbjct: 61  VILSFYKPAGYLSSHKAEIYPSLFELIGAPYNQYDLKIAGRLDYDSEGLVILTTSGDLVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  +VY  +     ++     L +G+ I G                     + 
Sbjct: 121 QITHPKKKIRKVYEAKLDKHFNESSKLKLLQGVEIMGEDGMPYIGIALDLHYKEDVAYIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGK  ++KK+F    + V  L RI  G   L  L  G+ +E+ +  +
Sbjct: 181 IDEGKFHQVKKMFLEVGFLVTNLKRIQIGALTL-DLEPGTYKEIEENDI 228


>gi|304311685|ref|YP_003811283.1| Ribosomal small subunit pseudouridine synthase A [gamma
           proteobacterium HdN1]
 gi|301797418|emb|CBL45638.1| Ribosomal small subunit pseudouridine synthase A [gamma
           proteobacterium HdN1]
          Length = 248

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 52/238 (21%), Positives = 99/238 (41%), Gaps = 8/238 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
             N   QR+ + ++++G  SR    + I    V +NG L   A+  +   D +      +
Sbjct: 9   TPNQERQRLDRFLSQSGRLSRSMARKAILAGEVTINGTLCRDASTKIGPNDTVHHHHDIV 68

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L L+     +V    D   R+ +        S +   GRLDI+T GL+LLT+D
Sbjct: 69  VAPSHHYLMLHKPEG-VVCATEDGRHRTVIDLLGEPWRSDLHIAGRLDIDTTGLVLLTSD 127

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGS 185
           G  +  +  P     + Y V     +        ++G+++ G        Q+ +  +  +
Sbjct: 128 GDWSHRVTSPRHNKAKRYHVTTADPIASSWCASFEQGVMLDGETKLTRPAQLEILDEFHA 187

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           N    + L+EG+  ++K++F     +V +L R + G   L   L  G  R ++   ++
Sbjct: 188 N----LCLQEGRYHQVKRMFAAMGTRVVKLHRYAIGELILDNTLPLGHYRALTDCEIQ 241


>gi|326803925|ref|YP_004321743.1| pseudouridylate synthase [Aerococcus urinae ACS-120-V-Col10a]
 gi|326650643|gb|AEA00826.1| pseudouridylate synthase [Aerococcus urinae ACS-120-V-Col10a]
          Length = 243

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 67/233 (28%), Positives = 102/233 (43%), Gaps = 6/233 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K IA   + SR+EV+++I  +R+ VN  +  R  + +   TD I +DG  +     
Sbjct: 1   MRLDKFIANFTLYSRKEVKKLIKAKRITVNDSIASRPEMQIDEETDTISLDGQWIGYEPY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLA 131
               L      L TT   P    T F         +   VGRLD +TEGLLLLTNDG  A
Sbjct: 61  IYYLLNKPQNCLSTTRPGPTSIVTDFLPANEVEIYQPFPVGRLDKDTEGLLLLTNDGDFA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQK--GSNAW 188
             L  P     + Y     G V ++ +    KG+ I  G      Q+ +       + + 
Sbjct: 121 HDLLSPKKLVSKEYYAEIEGIVTEEDVKAFAKGLTIDQGDHCAPSQLDILATDPAKNRSE 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
           +TV L EGK  ++K++F+    +V  L R   G   L   L  G+  ++  + 
Sbjct: 181 ITVTLTEGKYHQVKRMFQAVGKEVIYLQRFRIGSLYLPEELELGTAFKLLPEE 233


>gi|218665791|ref|YP_002426574.1| ribosomal small subunit pseudouridine synthase A [Acidithiobacillus
           ferrooxidans ATCC 23270]
 gi|218518004|gb|ACK78590.1| ribosomal small subunit pseudouridine synthase A [Acidithiobacillus
           ferrooxidans ATCC 23270]
          Length = 251

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 62/236 (26%), Positives = 101/236 (42%), Gaps = 4/236 (1%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             +Q++   +R+  +++R G  SR EV  ++ + RV+V G LL +A+  V +   + VD 
Sbjct: 13  RPMQKSA--ERMDHLLSRLGYCSRSEVRDLLREGRVRVAGELLRKASAKVNA-AEVWVDE 69

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P+       L  +     +                       + SVGRLD  T G+LLL
Sbjct: 70  EPIDHPHAFYLLYHKPLGKVCAHDDPRAIYQDFPLRWRYRRPALSSVGRLDRETSGVLLL 129

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T+DG        P     RVYRV     +  D  ++L  G ++        +        
Sbjct: 130 TDDGDWLHHWTSPRRAIPRVYRVTLQEPLRSDAADILAAGTLMLDGEDTPCRPAALHC-L 188

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +   V + L EG+  E++++F   +  V  L R +YGPF L  L AG  RE++   
Sbjct: 189 TEREVRLTLTEGRYHEVRRMFAALDNLVLTLHREAYGPFLLDDLPAGQWRELTVAE 244


>gi|332522544|ref|ZP_08398796.1| putative 16S pseudouridylate 516 synthase [Streptococcus porcinus
           str. Jelinkova 176]
 gi|332313808|gb|EGJ26793.1| putative 16S pseudouridylate 516 synthase [Streptococcus porcinus
           str. Jelinkova 176]
          Length = 238

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 100/229 (43%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++    I SR +V+++I+ +++ V+  +      NV      I VDG  LR    
Sbjct: 1   MRLDKLLETCQIGSRGQVKKLISAKKIIVDDRVAIGGQQNVDPGLQTIIVDGKVLRAKGH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L      +                    F  +  VGRLD +TEGL+LLT++G L  
Sbjct: 61  HYFFLNKPRGVVSALKDREHPTVIDCLTEADRFPSLYPVGRLDRDTEGLVLLTDNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V  +G +  D L+  +   + + G       V + + +   +   V
Sbjct: 121 RMLHPKHHVDKSYYVVVNGFLGDDLLSFFRSGVVFLDGTVCKAAAVEILSAREKQSVAKV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            L EGK  +IKK+F  +  KV  L R+++  F +G L AG  R ++   
Sbjct: 181 TLSEGKFHQIKKMFLAYGVKVIYLKRLTFAEFSVGNLAAGEYRTLTAHE 229


>gi|188990917|ref|YP_001902927.1| Pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. B100]
 gi|167732677|emb|CAP50871.1| Pseudouridylate synthase [Xanthomonas campestris pv. campestris]
          Length = 260

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 62/248 (25%), Positives = 107/248 (43%), Gaps = 10/248 (4%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           I        R++K IA  G  SRRE +R+I ++RV VNG++    AV V   D + VDG 
Sbjct: 15  IADNPPMTTRLNKHIAETGFCSRREADRLIGERRVTVNGVIAGTGAV-VGEDDTVLVDGQ 73

Query: 66  PLRKAERT-----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           PLR  E       R         +  T +                 R+  +GRLD ++EG
Sbjct: 74  PLRVREAKKPGTRRHVYIALNKPVGITSTTESSVKGNIVEFVGHEQRIFPIGRLDKDSEG 133

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+L+T++G +   +     +  + Y V  +  V  + L  + +G+ +        +    
Sbjct: 134 LILMTSNGNIVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRLHDETTLPCRTARI 193

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + G      + L +G NR+I+ +   F ++V +L R+     +L  L  G  R ++ + 
Sbjct: 194 AKFG----FRIVLEQGLNRQIRLMAAAFGFRVTQLRRVRIDNIKLAALKPGQWRNLTDQE 249

Query: 241 LREQLGPH 248
           L+  L   
Sbjct: 250 LQGLLPQR 257


>gi|261855955|ref|YP_003263238.1| pseudouridine synthase [Halothiobacillus neapolitanus c2]
 gi|261836424|gb|ACX96191.1| pseudouridine synthase [Halothiobacillus neapolitanus c2]
          Length = 369

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 89/351 (25%), Positives = 150/351 (42%), Gaps = 13/351 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ K++A  G+ SRR +E  I+   VK+NG++ +       + D ++V G  +  ++ T
Sbjct: 4   QRLQKILATQGLGSRRMIEGWISAGEVKLNGVVAQ-LGDVAEAGDVLDVRGQKITVSDET 62

Query: 74  ----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                +  +     + +T       +           R I+VGRLD NT GLLL TNDG 
Sbjct: 63  PIRRVIIYHKPEGEITSTSDPEGRPTVFGSLPAIRQGRWITVGRLDFNTSGLLLATNDGE 122

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  PS Q  R Y VR  G + +D++  L   + +        Q++     G N W 
Sbjct: 123 LANRLMHPSHQIERTYAVRVLGGLTEDQVKQLTTEVQLDDGPAHFDQLSDAGGTGVNRWY 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI---LREQL 245
            V LREG+NREI+++ E     V+RLIRISY    L   L  G  +++  ++   L + +
Sbjct: 183 HVTLREGRNREIRRMIEAVGAVVSRLIRISYAGIPLPPRLKPGRAQDLPPEMEDALVKLV 242

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNII--SEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           G       +V  +     +    R R      ++ P +  R+   +  + G     +  +
Sbjct: 243 GLRPETRRKVQDEDTKRRALKPYRARVQTGTVAKRPAEPFRVPVRAESQEGADTAGRPTS 302

Query: 304 PVHRRN--LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
               R    +S     + + S       +   + R  P+    + +RR   
Sbjct: 303 RPIERATTRSSRPGEPRPVLSRARPQMTEEGSDKRGKPARAGGKPIRRERQ 353


>gi|120556507|ref|YP_960858.1| pseudouridine synthase [Marinobacter aquaeolei VT8]
 gi|120326356|gb|ABM20671.1| ribosomal small subunit pseudouridine synthase A [Marinobacter
           aquaeolei VT8]
          Length = 231

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 54/232 (23%), Positives = 108/232 (46%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     SR+E +++++  RVKV+G    +A   V +   + +DG P+      
Sbjct: 1   MRLDQYLSNGTELSRKEAKKVVSAGRVKVDGETCRQANRQVEAEQSVHLDGKPVNPPGDI 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L ++     +++  +D    + +      + SRV   GRLD +T GLLLLT+DG  +  
Sbjct: 61  YLMMHKPAG-VLSATTDSSQPTALDLLPRGLASRVHIAGRLDKDTTGLLLLTSDGQWSHA 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--CYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + YRV     + +     L+KG+++ G        +V +     +N  + +
Sbjct: 120 VTSPRRECRKSYRVWLAEAIPEQACRALEKGVMLNGETTETRPAEVRVH----NNQLIDL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            + EG+  ++K++      +V  L R   G  +L   L  G  R ++ + +R
Sbjct: 176 TIGEGRYHQVKRMLAAVGNRVEALHRFRIGSIELDDKLAPGEFRALTYQEIR 227


>gi|187935235|ref|YP_001886700.1| ribosomal large subunit pseudouridine synthase F [Clostridium
           botulinum B str. Eklund 17B]
 gi|187723388|gb|ACD24609.1| ribosomal large subunit pseudouridine synthase F [Clostridium
           botulinum B str. Eklund 17B]
          Length = 226

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 55/228 (24%), Positives = 102/228 (44%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+ +  GI SR++  ++I + R+ VNG         V   D I +D  PL   ++ 
Sbjct: 1   MRINKLFSNLGICSRKDTSKLIEENRIIVNGFPC-IQGQWVELEDEILLDNKPLPIKKKI 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L        T   + +       N  +    +  VGRLD  ++GL+LLTNDG LA  
Sbjct: 60  YIVLNKPIGITCTAADEVE---NNIINFMNYPEYIFPVGRLDKASQGLILLTNDGDLANK 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V      + + +  +  G+ I  +     +V   ++        + L
Sbjct: 117 ILESENKHEKEYIVTLDKPFNDEFILGMTSGVEICNVKTRQCKVRRISED----TFNIVL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +G N++I+++ + F + V +L RI     +LG L  G  R + ++ L
Sbjct: 173 TQGLNKQIRRMSKTFGYTVKKLERIRIVNIELGDLEYGKWRYLLEEEL 220


>gi|238924577|ref|YP_002938093.1| pseudouridylate synthase [Eubacterium rectale ATCC 33656]
 gi|238876252|gb|ACR75959.1| pseudouridylate synthase [Eubacterium rectale ATCC 33656]
 gi|291525250|emb|CBK90837.1| ribosomal large subunit pseudouridine synthase F [Eubacterium
           rectale DSM 17629]
 gi|291529291|emb|CBK94877.1| ribosomal large subunit pseudouridine synthase F [Eubacterium
           rectale M104/1]
          Length = 272

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 63/281 (22%), Positives = 118/281 (41%), Gaps = 11/281 (3%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           ++EN    R++K ++ AG+ SRRE +R I   +V ++G+  +     V+    +  +G  
Sbjct: 1   MEEN--GVRINKFLSEAGVCSRREADRQIEAGKVGIDGVTAKT-GDRVLKGQTVTYNGQV 57

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           + K E   L   +KP G+V T    +  + +     +   R+  +GRLD ++EGLLLLTN
Sbjct: 58  VSKEEEMILIALNKPAGIVCTAEKREKNNVIDYL--NYPKRIYPIGRLDKDSEGLLLLTN 115

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKG 184
           +G +   +     +  + Y V  +  +    +  L  G+ +   G+      V   + K 
Sbjct: 116 NGEIVNKMMRSGNRHEKEYIVTVNKTISDSFIRGLAGGVPLVELGVTTRKCHVKKLSSKQ 175

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
                 + L +G NR+I+++ E+F ++V +L R+     +LG L  G  R V+    +  
Sbjct: 176 ----FKIILTQGYNRQIRRMCEYFGYRVVKLERVRIMNIELGDLPRGKYRAVTPLEYKGL 231

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
                    Q  +                   +   D    
Sbjct: 232 KRLIADSSNQPVIPDTNKDHSDKKYTDKKHTDKKYQDRRAK 272


>gi|114799825|ref|YP_760545.1| ribosomal large subunit pseudouridine synthase F [Hyphomonas
           neptunium ATCC 15444]
 gi|114739999|gb|ABI78124.1| Ribosomal large subunit pseudouridine synthase F [Hyphomonas
           neptunium ATCC 15444]
          Length = 372

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 71/352 (20%), Positives = 137/352 (38%), Gaps = 37/352 (10%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R++K +A+ G+ SRRE + +I +  ++++G  +  A   V     + +     R+ 
Sbjct: 10  DEPLRINKWLAQEGVCSRREADALIEKGLIQLDGKPVTVAGERVTKGQTLSLTDAASRRL 69

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-----------LPSIFSRVISVGRLDINTE 119
           +     + +KP+G V+   +P     +              +P   +++  +GRLD ++ 
Sbjct: 70  DNQLSVILNKPVGYVSGTPEPGEIPAIRLISEENLSGSAHAIPQRSNKMAPLGRLDKDSH 129

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+L+ DG LA+ +  P +   + Y V+  G +   K+ LL+ G+ + G      +VT 
Sbjct: 130 GLLILSEDGVLAKAIIGPLSDMDKEYLVKVRGDITTAKVALLRHGLELDGRQLRPAEVTQ 189

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +  +     +   L+EG+NR+I+++ E    +V  L RI  GP  L  L  G  R +  K
Sbjct: 190 ERGQ----VLRFVLKEGRNRQIRRMCELVELRVLDLQRIRVGPILLAGLPQGKWRPLGAK 245

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
                                   +  L       +   P       + S        + 
Sbjct: 246 E----------------------RAALLAAGAGEEVRSSPARREDRLRTSDGPRRERSET 283

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
               P   R+ +       G        +G + +     P+ P  +  R  +
Sbjct: 284 GRDQPRTDRDRSGQFGTKPGQGRPDKPRTGPKPDRAGAKPARPGAKPARPGA 335


>gi|331004267|ref|ZP_08327745.1| hypothetical protein HMPREF0491_02607 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330411432|gb|EGG90844.1| hypothetical protein HMPREF0491_02607 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 239

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 57/233 (24%), Positives = 117/233 (50%), Gaps = 10/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            RV K+++  G  SR+E+++ +   ++K+N   +++    + S  D I  DG  +   E 
Sbjct: 3   VRVDKILSELGFGSRQEIKKYVKAGKIKINDRTVKKPEEKINSKNDIIYFDGKEIEVEEF 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               LY     +  T    +   TV + + S    ++ VGRLD++TEG+L+LTNDG L  
Sbjct: 63  ETYILYKPAGYVCAT--KDNVHRTVMELIDSKRKNIVPVGRLDLDTEGILILTNDGDLNH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P++   + Y   F G++D + + + + G+ I +G      ++ + ++      + +
Sbjct: 121 RLVSPASHVDKSYYAVFDGKLDSNAIEMTQAGLDIGEGEFSKPAELKILSEN----EILL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL--AGSTREVSKKILR 242
            + EGK  ++K++ +    +V  L R+++G  +L  L    G +R+++   + 
Sbjct: 177 TIHEGKFHQVKRMVKALGGEVTYLKRVAFGGLKLDDLKLEKGESRKITGDEME 229


>gi|307708437|ref|ZP_07644903.1| RNA pseudouridine synthase family protein [Streptococcus mitis NCTC
           12261]
 gi|307615536|gb|EFN94743.1| RNA pseudouridine synthase family protein [Streptococcus mitis NCTC
           12261]
          Length = 241

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 105/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+G      A N+ +    +   G  ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLKGEILVDGCPARSLAQNIDTGLQELLFQGRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                       + +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPTGVVTANKDRELPTVMDLLPPDIQSDMLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPARLEILSASPSLSQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++KK+F     KV  L RI +G F L   L  G  R ++++ L+
Sbjct: 180 TISEGKFHQVKKMFLSVGVKVTSLKRIQFGEFTLDPELAEGQYRPLNQEELK 231


>gi|300934025|ref|ZP_07149281.1| putative pseudouridylate synthase [Corynebacterium resistens DSM
           45100]
          Length = 335

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 70/239 (29%), Positives = 121/239 (50%), Gaps = 4/239 (1%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
           ++     R+ KV++ AG+ASRR  E++IA  RV+VNG ++++  + +  + D + VDG  
Sbjct: 89  KKEKQQVRLQKVLSSAGVASRRMSEKLIAAGRVEVNGEVVQQMGLRIDPSVDVVRVDGTR 148

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLL 123
           ++  E    +  +KP G+ +T  D  GR  V + +    +    +  VGRLD  TEGLLL
Sbjct: 149 VQVNEEMVYFALNKPRGVHSTMHDDLGRPHVGELIEAKFNQGQGLFHVGRLDAATEGLLL 208

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG LA  L  P  +  + Y     G+ D+  +  LK G+ ++        V +    
Sbjct: 209 LTNDGELANRLMHPKYEVSKTYMATVLGEADRGLIRTLKDGVDLEDGMARADYVQIVDVW 268

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
              + + V L EG+   ++++ +   + V  L+R      QLG    G+ R +++  L+
Sbjct: 269 QGKSLIKVELHEGRKHIVRRMLKAAGFPVQALVRTKIHTVQLGEQKPGTVRALNRSELQ 327


>gi|325283294|ref|YP_004255835.1| pseudouridine synthase Rsu [Deinococcus proteolyticus MRP]
 gi|324315103|gb|ADY26218.1| pseudouridine synthase Rsu [Deinococcus proteolyticus MRP]
          Length = 252

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 80/252 (31%), Positives = 125/252 (49%), Gaps = 8/252 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             + +R+ KV+ARAG+ASRR  E +I   RV VNGI      V V   D + VDG P+  
Sbjct: 2   TDSGERLQKVLARAGVASRRAAEELITAGRVAVNGIPA-GLGVRVQPGDRVTVDGEPVAA 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                 ++ HKP G VTT  D  GR TV  +       +  VGRLD ++EGLL+LT DG 
Sbjct: 61  PTPHVTYMLHKPAGFVTTAQDELGRRTV-LDAMPPVPGLHPVGRLDKDSEGLLILTTDGD 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P  +  +VYRV    +  + +L  L++G+ ++       +  ++   G    +
Sbjct: 120 LTLRLTHPRFEHEKVYRVWCFPEPGEQELAALRRGVELEEG---FARAEVEPAPGGALAL 176

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
              LREG+ R+++++F      V+RL+R   G   LG L  G   ++ ++ L   L P  
Sbjct: 177 ---LREGRKRQVRRMFAEVGCPVDRLLRYRVGGLWLGDLGPGEFVQLGEQELDWLLQPGT 233

Query: 250 LEEAQVNLDAPI 261
            +++    +   
Sbjct: 234 RQQSPAQREQEA 245


>gi|54302702|ref|YP_132695.1| ribosomal small subunit pseudouridine synthase A [Photobacterium
           profundum SS9]
 gi|46916126|emb|CAG22895.1| hypothetical ribosomal small subunit pseudouridine synthase A
           [Photobacterium profundum SS9]
          Length = 228

 Score =  153 bits (387), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 49/231 (21%), Positives = 92/231 (39%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I ++   +R E   +I    V VN  +    A  V   + + +D   L      
Sbjct: 1   MRLDKFICKSTDLTRNEATLLINAGNVTVNNEVASNEATQVHENNDVLLDEKKLIARASR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     + +   D    S            +   GRLD +T GL+L+T+DG  +  
Sbjct: 61  YILMHKPLGTICSN-IDEVYPSLFNYIDVEKADDLHIAGRLDADTTGLVLITDDGRWSFN 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P+ Q  + YRV     + +D       G+ +QG        ++ + T       V +
Sbjct: 120 IITPNKQCEKTYRVGLRNPIAEDAAEKFALGVQLQGEKQLTFPAKLDVVTSN----EVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EGK  ++K++F     +V  L R   G  +L  +  G  R ++ + + 
Sbjct: 176 TITEGKFHQVKRMFSAIGNRVVTLHREQIGNIKL-DVEVGKWRFLTPEEID 225


>gi|325479564|gb|EGC82660.1| pseudouridylate synthase [Anaerococcus prevotii ACS-065-V-Col13]
          Length = 233

 Score =  153 bits (387), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 68/230 (29%), Positives = 117/230 (50%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA++G  SRR+ + +I   +VKVNGIL+      V   D +E+DG  L   +  
Sbjct: 1   MRINKYIAKSGYTSRRKADDLIKASKVKVNGILINEPGYEVTDDDILEIDGKRLYIEKNF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     + + +   + +      L  +  R  + GRLD ++EGLL++TNDG     
Sbjct: 61  YKKLYKPVGYVTSNYDPHNEKDLNS--LIDMKERFFAAGRLDKDSEGLLIITNDGHFTNG 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           +  PS +  + Y V    ++ + +    +KGI I +G    + ++ L   K +     V 
Sbjct: 119 IIHPSNELEKTYIVTVSRKLSKSQEKKFEKGIDIGRGEITSNSKIKLLDSKTNK--YEVK 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + +G NR+I+++F +F+ KV  L RIS GP +L  +     R+ S+K + 
Sbjct: 177 IHQGYNRQIRRMFAYFSSKVINLKRISIGPIKLDDMKEYEIRDFSEKEME 226


>gi|308189716|ref|YP_003922647.1| Pseudouridylate synthase [Mycoplasma fermentans JER]
 gi|319776902|ref|YP_004136553.1| pseudouridine synthase [Mycoplasma fermentans M64]
 gi|307624458|gb|ADN68763.1| predicted Pseudouridylate synthase [Mycoplasma fermentans JER]
 gi|318037977|gb|ADV34176.1| Pseudouridine synthase [Mycoplasma fermentans M64]
          Length = 258

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 67/257 (26%), Positives = 115/257 (44%), Gaps = 9/257 (3%)

Query: 1   MKDKNIVQENF---TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M + N + E F      RV K+IA+ G  SRR+ E  I ++ VKVNG +++         
Sbjct: 1   MNEINFLVERFAMKELIRVQKLIAQTGYCSRRKAEEYIEKKLVKVNGKIVQ-LGDKASEN 59

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           D I+++   +   +   ++          +            +L +   R+  VGRLD +
Sbjct: 60  DEIKINNQLISLQKPNFVYFLLNKPKKTISTVKDPKGRKTVVDLINYSERIAPVGRLDYD 119

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T G LLLTND  +   L  P  + LR YRVR    +   +  L+  G+++ G     +  
Sbjct: 120 TTGALLLTNDWEMINKLTHPKYEILRTYRVRIDSPLSLKEFKLINAGLIVNGKFSKQIVD 179

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +DT+        V L  G    IK++F+  N +V  L R+S+    +  +  GS R ++
Sbjct: 180 QVDTKS-----YLVTLHVGSYHHIKELFKALNHEVINLKRVSFANLTVEKMPEGSYRTLT 234

Query: 238 KKILREQLGPHLLEEAQ 254
            K +++      L+E +
Sbjct: 235 LKEIKDLKVLISLQEKK 251


>gi|16263775|ref|NP_436567.1| ribosomal large subunit pseudouridine synthase B [Sinorhizobium
           meliloti 1021]
 gi|15139899|emb|CAC48427.1| ribosomal large subunit pseudouridine synthase B [Sinorhizobium
           meliloti 1021]
          Length = 320

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 63/226 (27%), Positives = 108/226 (47%), Gaps = 1/226 (0%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTR 74
           +++ +++ G  SR + E++IA+ RV V G  +   +  V    D I VDG  +    R  
Sbjct: 85  LARALSKLGYCSRTQAEKLIAEGRVSVAGRKITDLSHWVDIEADRIAVDGTVIAAQARVY 144

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L      + T        +            +  VGRLD  +EGLLL TND  LA+ L
Sbjct: 145 LMLNKPRGLVTTRDDPEGRPTVFSCLDNVDVPSLSPVGRLDKASEGLLLFTNDTVLAQRL 204

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P T   +VY V+  G   +     + +G+   G     ++V        N+W+ + L 
Sbjct: 205 LDPETHLGKVYHVQVRGIFGEAMAARMVEGVTEGGELLRALRVERLKGGDRNSWIEIELD 264

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           EG+NR+I+++ +   ++  RL+R+S G  +LG L  G++R +++  
Sbjct: 265 EGRNRQIRRMLDVLGFECLRLLRVSIGEIRLGDLPKGASRPLTEAE 310


>gi|325285743|ref|YP_004261533.1| RNA-binding S4 domain-containing protein [Cellulophaga lytica DSM
           7489]
 gi|324321197|gb|ADY28662.1| RNA-binding S4 domain protein [Cellulophaga lytica DSM 7489]
          Length = 276

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 55/233 (23%), Positives = 99/233 (42%), Gaps = 1/233 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
            +    R++K +A +G+ SRRE +  IA   V VNG ++      V   D ++ DG  L 
Sbjct: 38  SDPNSIRLNKYVANSGVCSRREADVFIAAGSVTVNGKVVSEMGYKVKLDDVVKFDGRHLN 97

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             +R  + L        T  ++   R+       +  + ++ V ++   + GLLL TND 
Sbjct: 98  PEKREYVLLNKPKDFSTTVRNEHGKRNVAGLISSASKATLLPVDKMAKASTGLLLFTNDK 157

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L R L  P     ++Y V     +    L  ++ G+ I         ++       N  
Sbjct: 158 ELTRRLLNPKNGLRKIYHVELSKALSPADLKKIQDGLAIDEKVVNVHDISYVDNAPKNQ- 216

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + L   ++  + K+FE   ++V +L R+ YG      L  G  R ++K+ +
Sbjct: 217 VGIELFSSRSNIVTKIFEHLGYEVAKLDRVVYGGLTKKDLPRGHWRYLTKQEV 269


>gi|193782973|gb|ACF20459.1| pseudouridine synthase [Serratia symbiotica]
          Length = 300

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 78/235 (33%), Positives = 112/235 (47%), Gaps = 10/235 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+AR G  SRRE+E MI   RV +NG + +    + +     I +DG  +   +
Sbjct: 2   SEKLHKVLARTGYGSRREIEAMINACRVSINGKIAKLGDRIEIHPMMKIRIDGNIISIKK 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGR---STVFDNLPSIFSRVISVGRLDINTEGLLL 123
                   L  Y     L T  +  +     +           R +SVGRLDINT GLLL
Sbjct: 62  AEETICRVLAYYKPEGELCTISNPSNPEGRLTVFDHLPKLRNLRWVSVGRLDINTSGLLL 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T +G LA  L  PS +  R Y VR  G+   + +  LK  I ++        +T    K
Sbjct: 122 FTTNGELANRLMHPSRKIEREYAVRVFGKPSAENIKKLKHNIELEDGPAFFRTITFQGGK 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
           G N W  V L EG+NRE+++++E    +V+RLIRI YG   L   L  GS  E+ 
Sbjct: 182 GLNQWYHVTLTEGRNREVRRLWEAVGIQVSRLIRIRYGNIVLPKGLPRGSWAELD 236


>gi|84393834|ref|ZP_00992579.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio splendidus
           12B01]
 gi|84375529|gb|EAP92431.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio splendidus
           12B01]
          Length = 231

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 50/232 (21%), Positives = 99/232 (42%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +RRE   ++  + V VN ++ +  ++ V     +E  G  L      
Sbjct: 1   MRLDKFLCDALGVTRREATHLLKSKAVTVNDVIQKSGSLKVTEECVVEWQGNELNVHGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + LY     + +     +  +    +   +     + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  YIMLYKPEGFVCSHEDGANRIAFELLDEIKMDKLHFA-GRLDIDTTGLVLITDDGKWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + YRV     V+ D +   K+GI +  +        + +     +   V +
Sbjct: 120 ITSPKHKCEKTYRVWLVEPVEDDYVEKFKEGIQLKSEDGLTLPAHLEV----RAEREVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            + EGK  ++K++F     KV  L R   G  ++   L  G  R ++++ + 
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVEGLHRERIGEIEMDESLELGEYRYLTQEEVD 227


>gi|303256756|ref|ZP_07342770.1| ribosomal large subunit pseudouridine synthase F [Burkholderiales
           bacterium 1_1_47]
 gi|302860247|gb|EFL83324.1| ribosomal large subunit pseudouridine synthase F [Burkholderiales
           bacterium 1_1_47]
          Length = 292

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 67/294 (22%), Positives = 112/294 (38%), Gaps = 26/294 (8%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           +        R+SK ++  G+ SRRE +  I++  VKV+G ++      V     I +D  
Sbjct: 1   MSDTPADLVRLSKRMSELGLCSRREADEWISKGWVKVDGQVVSELGSKVRPDQKITIDRK 60

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                          PL          +     L+T  +      +     PS    ++ 
Sbjct: 61  AKDQQNERVTIILNKPLGYVSGQAEDGHEPARILITPRNRWIDDPSPRRFNPSQLKSLVP 120

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF-------HGQVDQDKLNLLKK 163
            GRLDIN+ GLL+LT DG +A+ +   ++   + Y VR        + +    KL LL  
Sbjct: 121 AGRLDINSTGLLVLTQDGRIAKTIIGENSSVEKEYIVRVAMTDGRSNSEFPPAKLALLNH 180

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
           G+ + G      +V+   +      +   LREG+NR+I+++ +    KV  L R+  G  
Sbjct: 181 GLELDGKPLEKAEVSWLNEDQ----LKFVLREGRNRQIRRMCDLVGLKVLALKRVRVGNI 236

Query: 224 QLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISE 277
            LG L  G  R +          P     ++    AP        R      + 
Sbjct: 237 PLGNLPVGKWRYLEDGESFTGSAPKRAPSSRPAAGAPRRPKTFKPRKPNFRKTR 290


>gi|170727249|ref|YP_001761275.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169812596|gb|ACA87180.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 287

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 77/287 (26%), Positives = 127/287 (44%), Gaps = 7/287 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E  IA  R+ ++G +       V +   I +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRISIDGEIA-NLGDRVEADVKIRIDGRAVSIKSE 60

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  +  +     + +        +       +  SR ++VGRLDINT GLLL T+D
Sbjct: 61  EDLVCRVIAYHKPEGEICSRKDPEGRPTVFDRLPKTRDSRWVAVGRLDINTSGLLLFTSD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V    +  L+ G+ ++       +V     +G N 
Sbjct: 121 GELANRLMHPSNEVEREYAVRTFGEVTDACIQRLRTGVTLEDGPAHFDKVKAAGGEGMNK 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V L EG+NRE+++++E    +V+RLIRI YG  +L  +L  G   E+  + +     
Sbjct: 181 WWHVSLAEGRNREVRRLWESQEVQVSRLIRIRYGMIELPKSLPRGGWVELELEQVNYLRQ 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
              L      L      S    + +   I    +        ++++ 
Sbjct: 241 TAGLAIENRTLLGTDKHSVARAKVKSAKIKRAVNKHKVNAAKNTRQR 287


>gi|227872023|ref|ZP_03990406.1| pseudouridylate synthase [Oribacterium sinus F0268]
 gi|227842134|gb|EEJ52381.1| pseudouridylate synthase [Oribacterium sinus F0268]
          Length = 239

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 60/235 (25%), Positives = 114/235 (48%), Gaps = 6/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAER 72
            R+ K ++  G+ SR  ++R I +  VK+NG +++  ++ V   +  I     P+   E 
Sbjct: 1   MRLDKYLSDMGVESRSVLKREIRKGLVKINGEIVKDPSMEVQPGNSEIVYKDEPIHYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +   +      ++++  D   ++ +          +  VGRLD ++EGLLL+ NDG LA 
Sbjct: 61  SYYMMNKPVG-VLSSTEDRKQKTVLDLFSDKHRKDLFPVGRLDKDSEGLLLIMNDGALAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V   G++ +++L+ L++GI     +     +    +     + V V
Sbjct: 120 KLLSPKMHIEKKYLVEIPGKISEEELDRLRQGIQYDTDLIAMPAKARCLSSTEEGSRVEV 179

Query: 192 GLREGKNREIKKVFEFF--NWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
            + EGK  +IKK+F     ++ V +L R+S GP  L   L  G  R++S++ ++ 
Sbjct: 180 IIMEGKFHQIKKMFLALSTDYVVTKLQRLSMGPLHLDPALAPGEYRKLSEEEVQA 234


>gi|113460886|ref|YP_718953.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           somnus 129PT]
 gi|112822929|gb|ABI25018.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           somnus 129PT]
          Length = 325

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 87/290 (30%), Positives = 135/290 (46%), Gaps = 12/290 (4%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM--STDHIEVD 63
           + Q+    +R+ KV+ARAG  SRR +E MI+  R+ ++G +       V   S   I +D
Sbjct: 37  VNQQKVEGERLQKVLARAGQGSRRTIEAMISANRISIDGKMAT-LGDRVDIHSGVKIRID 95

Query: 64  GVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           G  +   +        L  Y     L T H      +          SR I+VGRLDINT
Sbjct: 96  GHIVNLTQAQKEVCRVLLYYKPEGELCTRHDPEGRATVFDRLPRLNGSRWIAVGRLDINT 155

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLL T DG LA  L  P  +  R Y VR  G+VD   +  L+KG+ ++        + 
Sbjct: 156 SGLLLFTTDGELANRLMHPRHEVEREYAVRVFGEVDDAMIARLRKGVQLEDGPANFTSIK 215

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
               +G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L  +L  G   E+ 
Sbjct: 216 ATGGQGMNQWFDVTLIEGRNREVRRLWESQGIQVSRLIRIRYGNIKLTKSLPRGGWEEMD 275

Query: 238 K---KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
                 LR+ +G     +++++   P       +R      +E+   + +
Sbjct: 276 LTNINYLRKLVGLPPETDSKIDTKKPRRIKTGQIRKAVKRYAELNKRYKK 325


>gi|298368564|ref|ZP_06979882.1| ribosomal large subunit pseudouridine synthase F [Neisseria sp.
           oral taxon 014 str. F0314]
 gi|298282567|gb|EFI24054.1| ribosomal large subunit pseudouridine synthase F [Neisseria sp.
           oral taxon 014 str. F0314]
          Length = 247

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 107/250 (42%), Gaps = 20/250 (8%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           +  ++    R+SK +A+ G+ SRRE +  I Q  VKVNG         V   D I+++  
Sbjct: 1   MEHDSNETMRLSKRMAQLGLCSRREADSYIEQGWVKVNGQTAA-LGQKVTERDRIDLNRQ 59

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                          P+          Y     L+T  +  +G  +           +  
Sbjct: 60  AHEKQAERVTILLNKPVGYVSAQAEKGYKSAAELITADNRWEGDDSRIPFSEKHKFGLAP 119

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+ + G 
Sbjct: 120 AGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGE 179

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                +V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  
Sbjct: 180 KLRPAKVKWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRVIGLKRIRMGKVKLGKLPP 235

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 236 GKWRYLRADE 245


>gi|222084363|ref|YP_002542892.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
 gi|221721811|gb|ACM24967.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
          Length = 278

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 62/261 (23%), Positives = 117/261 (44%), Gaps = 3/261 (1%)

Query: 9   ENFTPQR--VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGV 65
           +    +R  + + +++ G  SR + E +IA  RV V+G  +      +      I VDG 
Sbjct: 18  QESDGKRVTLPRALSKLGYCSRTQAEALIAAGRVTVDGREITDPTAWIDLDRARIAVDGE 77

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +   ++    L      + T        +            +  VGRLD  +EGLLL T
Sbjct: 78  AIAAEKKLYFMLNKPRGLVTTRDDPEGRPTVYDCLRDIDARHLAPVGRLDKASEGLLLFT 137

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           ND  LA+ L  P +   ++Y V+ +  ++Q+ L+ +++G++  G         L      
Sbjct: 138 NDTVLAQALLDPISHVGKIYHVQVNTIMEQELLDRMERGVIDDGELLTATAARLLRSGDR 197

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           N W+ V L+EG+NR+I+++ E    +  RL+R+++G   LG L  G+ R +++  +    
Sbjct: 198 NGWIEVELKEGRNRQIRRMLEVLGVECLRLVRVAFGDIALGDLAKGAVRALTEAEVLGLR 257

Query: 246 GPHLLEEAQVNLDAPIYSSET 266
               +E+   N      ++  
Sbjct: 258 RRAGMEKTGRNGMKAGRNAAP 278


>gi|238809688|dbj|BAH69478.1| hypothetical protein [Mycoplasma fermentans PG18]
          Length = 269

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 67/257 (26%), Positives = 115/257 (44%), Gaps = 9/257 (3%)

Query: 1   MKDKNIVQENF---TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M + N + E F      RV K+IA+ G  SRR+ E  I ++ VKVNG +++         
Sbjct: 12  MNEINFLVERFAMKELIRVQKLIAQTGYCSRRKAEEYIEKKLVKVNGKIVQ-LGDKASEN 70

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           D I+++   +   +   ++          +            +L +   R+  VGRLD +
Sbjct: 71  DEIKINNQLISLQKPNFVYFLLNKPKKTISTVKDPKGRKTVVDLINYSERIAPVGRLDYD 130

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T G LLLTND  +   L  P  + LR YRVR    +   +  L+  G+++ G     +  
Sbjct: 131 TTGALLLTNDWEMINKLTHPKYEILRTYRVRIDSPLSLKEFKLINAGLIVNGKFSKQIVD 190

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +DT+        V L  G    IK++F+  N +V  L R+S+    +  +  GS R ++
Sbjct: 191 QVDTKS-----YLVTLHVGSYHHIKELFKALNHEVINLKRVSFANLTVEKMPEGSYRTLT 245

Query: 238 KKILREQLGPHLLEEAQ 254
            K +++      L+E +
Sbjct: 246 LKEIKDLKVLISLQEKK 262


>gi|319796303|ref|YP_004157943.1| RNA-binding s4 domain protein [Variovorax paradoxus EPS]
 gi|315598766|gb|ADU39832.1| RNA-binding S4 domain protein [Variovorax paradoxus EPS]
          Length = 277

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 65/270 (24%), Positives = 97/270 (35%), Gaps = 47/270 (17%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------- 63
           P R++K +A   + SRRE +  IA   VKVNG       V V  +D IE+D         
Sbjct: 11  PVRLNKRMAELKMCSRREADEWIANGWVKVNGKPA-EMGVKVTPSDRIEIDKAAKGQQAN 69

Query: 64  ------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
                   P+          +   + L T  +     +  F   P     +   GRLDI+
Sbjct: 70  QVTILINKPIGYVSGQAEDGHEPAVTLFTPQNRWAEDNARFFFSPQQLRGLAPCGRLDID 129

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ------------------------- 152
           + GLL++T DG +AR L    +   + Y VR                             
Sbjct: 130 SIGLLVMTQDGRVARQLIGEDSVMEKEYLVRVAYYGPGQSAPTGQLIRMDDDDPVTQNVQ 189

Query: 153 --VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                  L  L+ G+ + G      +V     +     +   L EGK R+I+++ E    
Sbjct: 190 AVFPPAMLARLRHGLSLDGQQLKPARVEWQNPEQ----LRFVLTEGKKRQIRRMCELVGL 245

Query: 211 KVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           KV  L R+  G   LG L  G  R +    
Sbjct: 246 KVVGLKRVRIGKVMLGNLPVGQWRYLGPHE 275


>gi|118595131|ref|ZP_01552478.1| pseudouridylate synthase [Methylophilales bacterium HTCC2181]
 gi|118440909|gb|EAV47536.1| pseudouridylate synthase [Methylophilales bacterium HTCC2181]
          Length = 280

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 74/262 (28%), Positives = 125/262 (47%), Gaps = 6/262 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +R+ K++A++G  SRRE+E+ I + +V VN    +     +  +D I  +G  +     
Sbjct: 19  GERIHKLLAQSGYGSRREIEKAILEDKVLVNNQNAK-IGQLITPSDKIIFNGKAIFLNND 77

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 L  +     +VT +      +           + +S+GRLD NT GLL+ T+ G
Sbjct: 78  NNLPRVLIYHKPEGEIVTENDPGGRSTVFEKLPRIKKGKWMSIGRLDFNTSGLLIFTSYG 137

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P  +  R Y VR  G++ +D++   K GI I G       +  +  +G+N W
Sbjct: 138 ELANRLMHPKYEIEREYSVRILGELSEDQIKEFKSGIDIDGGKAKFESIYFEGGEGANKW 197

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
             V L+EG+NRE++++FE+F+  V+RLIR+ +G   L   L  G   E+++  +   L  
Sbjct: 198 YRVVLKEGRNREVRRMFEYFDLTVSRLIRVRFGIVILPSHLKRGMHTELTQAEVTRLLQK 257

Query: 248 HLLEEAQVNLDAPIYSSETLVR 269
           H +E    N        +   R
Sbjct: 258 HDIEPNDFNKPQLSNQRKRNKR 279


>gi|285017365|ref|YP_003375076.1| pseudouridylate synthase [Xanthomonas albilineans GPE PC73]
 gi|283472583|emb|CBA15088.1| probable pseudouridylate synthase protein [Xanthomonas albilineans]
          Length = 275

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 66/227 (29%), Positives = 108/227 (47%), Gaps = 1/227 (0%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTR 74
           +++ +++ G+ SR E  R IA  RV V+G ++      ++     + +DG PL  +ER  
Sbjct: 34  LARTLSKLGLCSRTEAVRWIAAGRVAVDGRIVTDPEFPILRGRHRLALDGAPLSASERLY 93

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L      + T   +    +       +    +  VGRLD  +EGLLL TND   A  +
Sbjct: 94  LMLNKPRGLVTTAQDERGRETVYRCFDGAGLPWLAPVGRLDKASEGLLLFTNDPQWAARV 153

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P T   + Y V+     D   L  ++ G++  G      QV L  Q   +AW+ + L 
Sbjct: 154 TDPGTGPDKTYHVQVDVLPDAALLQRMRAGVMADGEALCAKQVRLLRQGERHAWLEIVLD 213

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           EG+NR+I+++   F   V RL+R++ G   LG L  G+ R +S   +
Sbjct: 214 EGRNRQIRRLLAAFGVDVVRLVRVAIGTLVLGELGKGAWRTLSAAEV 260


>gi|329957324|ref|ZP_08297844.1| pseudouridylate synthase [Bacteroides clarus YIT 12056]
 gi|328523037|gb|EGF50140.1| pseudouridylate synthase [Bacteroides clarus YIT 12056]
          Length = 225

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 52/216 (24%), Positives = 90/216 (41%), Gaps = 1/216 (0%)

Query: 26  ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLV 85
            SRRE +  I    V VNG ++      +   D ++     +    +  + L      + 
Sbjct: 2   CSRREADEFITAGVVSVNGEVVTELGTKIKRGDEVKFHDQTVSIERKIYVLLNKPKDTVT 61

Query: 86  TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY 145
           T+      R+ +     +   R+  VGRLD NT G+LLLTNDG LA  L  P     ++Y
Sbjct: 62  TSDDPQARRTVMDLVKGACDERIYPVGRLDRNTTGVLLLTNDGDLASKLTHPKYLKKKIY 121

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
            V     + +  +  +  GI +             T +     V + +  GKNR ++++F
Sbjct: 122 HVHLDKNLTKADMEQIAAGIQLDDGEIQ-ADAISYTDEFKKDEVGIEIHSGKNRIVRRIF 180

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           E   +KV +L R+ +       L  G  R +++  +
Sbjct: 181 ESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLTEPEV 216


>gi|113868872|ref|YP_727361.1| 16S rRNA uridine-516 pseudouridylate synthase [Ralstonia eutropha
           H16]
 gi|113527648|emb|CAJ93993.1| 16S rRNA uridine-516 pseudouridylate synthase [Ralstonia eutropha
           H16]
          Length = 235

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 53/229 (23%), Positives = 89/229 (38%), Gaps = 6/229 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERA--AVNVMSTDHIEVDGVPLRKAERT 73
           + +++   G  +RR    +IA   V+VNG L E       V     + VDG       + 
Sbjct: 3   LDRILQSQGFGTRRYCGDLIAAGLVEVNGELCEDPRAQFEVD-GLRLTVDGEEWLACTKA 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L        +              +P     V +VGRLD +T GLLLLT+DG     
Sbjct: 62  YLMLNKPTGYECSQRPRHHPSVYNLLPVPLRQREVQAVGRLDHDTTGLLLLTDDGQFIHA 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
              P  +  ++Y V     V  ++   L  G+ +       +        G  + + + L
Sbjct: 122 QTSPKRKVPKIYEVTTAEPVTPEQAEALCSGVQLLDEPA-PIAAEACEITGERS-LRLTL 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            +GK  ++K++       V+ L R + G  +L   L  G  R ++ + L
Sbjct: 180 VQGKYHQVKRMVAAAGNHVSALHRSAIGGLRLDPALAEGEWRWLTAQEL 228


>gi|255323628|ref|ZP_05364758.1| S4 domain protein [Campylobacter showae RM3277]
 gi|255299342|gb|EET78629.1| S4 domain protein [Campylobacter showae RM3277]
          Length = 257

 Score =  153 bits (386), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 67/247 (27%), Positives = 114/247 (46%), Gaps = 15/247 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+     SRRE + +I Q +V VNG ++   A +V   D ++++G  +R  +   
Sbjct: 5   RLNKFISHNTSYSRREADELIKQGKVSVNGRVISELATSVSDEDKVKINGRIVRLKKEFT 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +YHK  G + +  D  GR T++D+L   F++ +S+GRLD  +EGLLLLT+   +A  L
Sbjct: 65  MIVYHKQKGELVSKKDDRGRKTIYDSLDRQFAKFVSIGRLDYASEGLLLLTDAPAIATAL 124

Query: 135 ELPSTQWLRVYRVRFHGQVD--QDKLNLLKKGIVIQGICYGDM----------QVTLDTQ 182
                +     +V+     +               +G                   +   
Sbjct: 125 MNSDVEREYYLKVKGEITPEVITAMNEGFFAADATKGAHAKTAIKSMEFKPFLDYKIFGS 184

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI-- 240
            G    + V + EG+NRE+++ F +F+ +V  L R+S+G   LG L  G  R        
Sbjct: 185 SGGFTKLKVVINEGQNRELRRFFGYFDLEVMDLKRVSFGRVDLGMLKPGKWRYFENGEYE 244

Query: 241 -LREQLG 246
            LR+ L 
Sbjct: 245 ALRDFLK 251


>gi|150017514|ref|YP_001309768.1| pseudouridine synthase [Clostridium beijerinckii NCIMB 8052]
 gi|149903979|gb|ABR34812.1| pseudouridine synthase [Clostridium beijerinckii NCIMB 8052]
          Length = 261

 Score =  153 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 56/260 (21%), Positives = 97/260 (37%), Gaps = 28/260 (10%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A A + SR+ V   I +  VKVN  L+   A+ +    D IE     +  A +
Sbjct: 1   MRLDKFLAEAAVGSRKNVRIYIKEGMVKVNKELVTEPAIEIDENCDVIEYLNEIVSYAGK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                      +     +   ++       +    +  VGRLD +TEGLLL TNDG    
Sbjct: 61  LYYMFNKPAGCITAKTDE-IHKTVFDFLGEAGTKGIFHVGRLDKDTEGLLLFTNDGEFEH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLD---------- 180
            +  P     + Y     G + ++    L++G  I    I     ++ +D          
Sbjct: 120 KIMYPEKHVEKTYFFWALGSLSEEDKKQLEQGTYIGQCKILTKPAKIEVDKFGIYEELKH 179

Query: 181 -------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
                                  + + EG+  ++K++ +     V  L RIS G   L  
Sbjct: 180 EMATDNVNNINSNHGTQPVVSGYLTISEGRKHQVKRMLKSVGCYVVYLKRISIGGLALDK 239

Query: 228 -LLAGSTREVSKKILREQLG 246
            L  G  R +++  +++ LG
Sbjct: 240 SLKKGQYRPLTELEIQKVLG 259


>gi|312132030|ref|YP_003999370.1| RNA-binding s4 domain protein [Leadbetterella byssophila DSM 17132]
 gi|311908576|gb|ADQ19017.1| RNA-binding S4 domain protein [Leadbetterella byssophila DSM 17132]
          Length = 500

 Score =  153 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 66/243 (27%), Positives = 113/243 (46%), Gaps = 5/243 (2%)

Query: 2   KDKNIVQENFTP---QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           K K  V E   P    R+++ IA +GI SRRE + +I   ++ VNG  +      V  TD
Sbjct: 253 KQKKKVAEKVVPSDLIRLNRYIANSGICSRREADDLIESGQITVNGKTITEMGYQVKKTD 312

Query: 59  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
            ++     L   +   + L      + TT      R+ +     +   R+  VGRLD  T
Sbjct: 313 VVKYGRKILNPEKLVYVLLNKPKDFITTTEDPEGRRTVMELVAKAGPERIYPVGRLDRAT 372

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLL TNDG LA  L  PS +  ++Y+V     + ++    L +G+ ++       QV+
Sbjct: 373 TGLLLFTNDGELAEKLSHPSNEIRKIYQVEIDKPLAKEDFEKLIEGVELEDGFIKPDQVS 432

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +         + + +  GKNR ++++FE   ++V +L R +Y       L  G+ R +++
Sbjct: 433 IV--TPDQQVIGIEIHSGKNRVVRRIFEHLGYEVTQLDRTTYAGLTKKDLPRGNWRFLTE 490

Query: 239 KIL 241
           K +
Sbjct: 491 KEV 493


>gi|58220684|gb|AAW67949.1| putative rRNA pseudouridine synthase B [Desulfovibrio gigas]
          Length = 253

 Score =  153 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 83/251 (33%), Positives = 121/251 (48%), Gaps = 16/251 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP----- 66
              R++KV+A+AG+ASRR  + ++   RV+VNG + E   + V   D IEVDG P     
Sbjct: 2   DAIRLNKVLAQAGVASRRGADELVFAGRVRVNGAVAESPGMRVTPDDRIEVDGAPMPRKD 61

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLL 123
           L         L HKP+ +V+T  DP GR TV D LP           VGRLD  +EGLLL
Sbjct: 62  LAAGHALNYILLHKPVEVVSTVRDPQGRRTVLDLLPQALRANTRLYPVGRLDYFSEGLLL 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--------QGICYGDM 175
           LT+DG LA  L  P     + Y V   G V    L  ++ G+ +         G     +
Sbjct: 122 LTDDGDLANRLMHPRHHVPKRYEVLVRGDVPTTALQTMRSGMTLPPQAGDPPAGTRLQTV 181

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              +   K     + + L +G NR+++++ E     + RL R+  G  +LGTL  GS R 
Sbjct: 182 PARILGIKDGKTLLELVLHQGVNRQVRRMCEALGLTILRLTRVGLGSLELGTLEKGSWRR 241

Query: 236 VSKKILREQLG 246
           ++K  ++    
Sbjct: 242 LTKDEVQALQQ 252


>gi|310779774|ref|YP_003968106.1| ribosomal small subunit pseudouridine synthase A [Ilyobacter
           polytropus DSM 2926]
 gi|309749097|gb|ADO83758.1| ribosomal small subunit pseudouridine synthase A [Ilyobacter
           polytropus DSM 2926]
          Length = 227

 Score =  153 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 56/229 (24%), Positives = 98/229 (42%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR+++++++ + RVK+NG++     + +    D I +D   L     
Sbjct: 1   MRLEKYLVNCGVGSRKDIKKIVEEGRVKINGLVTLNFGLWIEEDRDDITLDNRHLEFKTL 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               LY     +     D                 +  VGRLD +TEGLLL TNDG    
Sbjct: 61  RYYILYKTKGYITAVKDDRHPTIMELLPGWLETKDLFPVGRLDKDTEGLLLFTNDGDTNY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + Y V     + +  +  L+KG+ I        +V    Q      + + 
Sbjct: 121 KMTHPDKKISKKYYVELDKPISEGDIKDLEKGVDIGTHICLPAKVQYIEQNK----IFLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++EGK  ++KK+      KV+ L R+ +G   L  +  G  RE+  K +
Sbjct: 177 IQEGKYHQVKKMVGSIKNKVSYLKRVKFGNLTLEDMKPGELREIFLKDI 225


>gi|308050240|ref|YP_003913806.1| ribosomal large subunit pseudouridine synthase B [Ferrimonas
           balearica DSM 9799]
 gi|307632430|gb|ADN76732.1| ribosomal large subunit pseudouridine synthase B [Ferrimonas
           balearica DSM 9799]
          Length = 291

 Score =  153 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 79/291 (27%), Positives = 128/291 (43%), Gaps = 12/291 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM--STDHIEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E MIA  RV ++G + +     V   +   + +DG  +   
Sbjct: 2   SEKLQKVLARAGHGSRREIEAMIAAGRVSIDGQVAK-LGDRVDGRAELKVRIDGHAVSLK 60

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
                    L  Y     L +        +          SR ++VGRLDINT GLLL T
Sbjct: 61  AEEEVICRVLAYYKPEGELCSRSDPQGRPTVFERLPRVRDSRWVAVGRLDINTSGLLLFT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y +R  G+V ++ L  L+ G+ ++       ++     +G 
Sbjct: 121 TDGELANRLMHPSQEVEREYAIRVFGEVTEEMLKNLRTGVELEDGTAQFKRLVPAGGEGL 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI---L 241
           N W    L EG+NRE+++++E    +V+RL+RI YG   L   L  G   E+  +    L
Sbjct: 181 NTWYHGVLSEGRNREVRRLWESQEVQVSRLMRIRYGDITLPKGLPRGGWVELPLEQVNYL 240

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
           R+ +G        +  D      +  ++      +         K   ++ 
Sbjct: 241 RDLVGLERESRTLLAQDKLGARRQKTLKAGKIRRAVHKHRARPAKGRPNKG 291


>gi|237746975|ref|ZP_04577455.1| ribosomal small subunit pseudouridine synthase A protein
           [Oxalobacter formigenes HOxBLS]
 gi|229378326|gb|EEO28417.1| ribosomal small subunit pseudouridine synthase A protein
           [Oxalobacter formigenes HOxBLS]
          Length = 239

 Score =  153 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 91/237 (38%), Gaps = 4/237 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAE 71
              + K++   G  SR+    ++   RV++ G +       + + D    VDG      E
Sbjct: 2   SMTLEKILQSQGFGSRKFCRNLVLGHRVEIAGKICTDPDRKLETDDLAFRVDGETWEYRE 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  L L        +               P +   +  VGRLD +T GLLLLT+DG   
Sbjct: 62  KLYLVLNKPAGYECSRQPQHHPSVFALLPEPFVQRGLQCVGRLDQDTTGLLLLTDDGHFI 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
                P  +  ++Y V      +  +L  L  G+ ++          L  Q      + +
Sbjct: 122 HQYTSPRKKVPKIYTVTGVSPFEATQLEKLVTGVQLKDEKTL--TSALACQLIDEYRLRL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGP 247
            + EGK  ++K++      +V  L R + G F L   LL G  R +++  L+    P
Sbjct: 180 SITEGKYHQVKRMIAAAGNRVETLHRSAIGGFTLEETLLPGHWRFLNENDLKRLSEP 236


>gi|153001233|ref|YP_001366914.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|160875907|ref|YP_001555223.1| RNA-binding S4 domain-containing protein [Shewanella baltica OS195]
 gi|304411914|ref|ZP_07393525.1| RNA-binding S4 domain protein [Shewanella baltica OS183]
 gi|307303318|ref|ZP_07583073.1| RNA-binding S4 domain protein [Shewanella baltica BA175]
 gi|151365851|gb|ABS08851.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|160861429|gb|ABX49963.1| RNA-binding S4 domain protein [Shewanella baltica OS195]
 gi|304349774|gb|EFM14181.1| RNA-binding S4 domain protein [Shewanella baltica OS183]
 gi|306913678|gb|EFN44100.1| RNA-binding S4 domain protein [Shewanella baltica BA175]
 gi|315268098|gb|ADT94951.1| RNA-binding S4 domain protein [Shewanella baltica OS678]
          Length = 291

 Score =  153 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 77/291 (26%), Positives = 127/291 (43%), Gaps = 7/291 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E  IA  RV ++G +       + +   + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRVSIDGEIA-SLGDRIEADAKVRIDGRSISLKSA 60

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  +     + +        +          SR ++VGRLDINT GLLL T+D
Sbjct: 61  EDVICRVLAYHKPEGEICSRKDPEGRPTVFDRLPKVRDSRWVAVGRLDINTSGLLLFTSD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G++ +  +  L+ G++++        +     +G N 
Sbjct: 121 GELANRLMHPSNEVDREYAVRTFGEIPEATVQRLRTGVMLEDGPAQFDSIKPAGGEGMNQ 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V LREG+NRE+++++E    +V+RLIRI YG  +L  +L  G   E+  + +     
Sbjct: 181 WWHVCLREGRNREVRRLWESQEVQVSRLIRIRYGMVELPKSLPRGGWVELPMEQVNYLRK 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
              LE     + A    S    + +   I               + +    
Sbjct: 241 LAGLEPETRTMLAADKHSVARAQVKSAKIRRAVRKHKVTGSGKPKPSRQRS 291


>gi|302386350|ref|YP_003822172.1| pseudouridine synthase [Clostridium saccharolyticum WM1]
 gi|302196978|gb|ADL04549.1| pseudouridine synthase [Clostridium saccharolyticum WM1]
          Length = 241

 Score =  153 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 60/232 (25%), Positives = 106/232 (45%), Gaps = 6/232 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERT 73
           R+ K +   G  +R +++ M  + R+ V+G   ++    +      + VDG P+      
Sbjct: 5   RLDKYLTEMGEGTRSQIKEMARKGRIFVDGQPEKKTERKIHPEQNQVSVDGRPVSYVRYE 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      +V+   D    + +          +  VGRLDI+TEGLLL+TNDG LA  
Sbjct: 65  YYMLNKPQG-VVSATEDSRYDTVISLIKSRKRDDLFPVGRLDIDTEGLLLITNDGDLAHQ 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV- 191
           L  P     +VY  R  G++  D    +++G+V+  G       + +  Q    + + + 
Sbjct: 124 LLSPKKHVDKVYFARIQGELPPDAKEQMEEGLVLSDGTPTMPAHLEVLKQGREESSLEIL 183

Query: 192 -GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
             +REGK  ++K++FE    +V  L R++ G   L   L  G  R +S++ +
Sbjct: 184 LTIREGKFHQVKRMFETLGCRVIYLKRMTMGSLTLDEALAPGEYRPLSEEEI 235


>gi|257077689|ref|ZP_05572050.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis JH1]
 gi|256985719|gb|EEU73021.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis JH1]
          Length = 238

 Score =  153 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 108/232 (46%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +     
Sbjct: 1   MRLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLISHKTH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                       +  VGRLD +TEGLLLLT++G L  
Sbjct: 61  VYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            L  P+ +  + Y V+ +G V  +     K GIV+QG       ++T+     + + V +
Sbjct: 121 QLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHVFL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+
Sbjct: 181 TIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQ 232


>gi|145590213|ref|YP_001156810.1| pseudouridine synthase [Polynucleobacter necessarius subsp.
           asymbioticus QLW-P1DMWA-1]
 gi|145048619|gb|ABP35246.1| ribosomal large subunit pseudouridine synthase F [Polynucleobacter
           necessarius subsp. asymbioticus QLW-P1DMWA-1]
          Length = 245

 Score =  153 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 63/246 (25%), Positives = 107/246 (43%), Gaps = 20/246 (8%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRK 69
               RVSK+++  G+ SRRE +  I Q  V V+G ++    V       IE+  G   ++
Sbjct: 2   EEKVRVSKLLSELGLCSRREADSYIEQGLVTVDGEVVNELGVRAYRHQKIELQSGAKAQQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---------------ISVGRL 114
           A R  + L      +     + + +       P  +                     GRL
Sbjct: 62  ASRITVILNKPVGYISHFDDEQEYQPAASLITPDNYFASPLDKGRNPRFNTKGLAPAGRL 121

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DI++ GLL+LT DG +A++L   ++   + Y VR  G++  + L+ L+ G+ +  +    
Sbjct: 122 DIDSTGLLVLTQDGRIAKLLIGENSPIEKEYLVRVEGKLSFEDLDKLRHGLTLDDVVLKP 181

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            QV+   +      +   LREG+ R+I+++ E    KV  L R+  G   LG L  G  R
Sbjct: 182 AQVSWQNEDQ----LRFVLREGRKRQIRRMCEMVGLKVIGLKRVRIGRISLGPLPPGQWR 237

Query: 235 EVSKKI 240
            V  + 
Sbjct: 238 FVRPEE 243


>gi|188578415|ref|YP_001915344.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae PXO99A]
 gi|188522867|gb|ACD60812.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae PXO99A]
          Length = 286

 Score =  153 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 115/247 (46%), Gaps = 7/247 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      + +     I VDG PL    R 
Sbjct: 39  LARVLSKLGVCSRTEAARWIADGRVSVSARVVRDPEFPIRADQQFAITVDGQPLTGPARC 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L      + T   +    +       +    +  VGRLD  +EGLLL +ND   A  
Sbjct: 99  YLMLNKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAAT 158

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNAW 188
           +  P+T   + Y V+     +  +L  L+ G+V      +G+     QV++  +   NAW
Sbjct: 159 VTDPATGPDKTYHVQIDCLPNVAQLAQLQAGVVDPDPEGEGMLLRAKQVSVLREGERNAW 218

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + + L EG+NR+I+++    +  V RL+R++ GP  +G L  G+ R +S + +R  +   
Sbjct: 219 LEIVLDEGRNRQIRRLLAAVDIGVLRLMRVAIGPLAMGELGKGAWRMLSAEEVRALVPAA 278

Query: 249 LLEEAQV 255
                  
Sbjct: 279 HASAPDA 285


>gi|304373099|ref|YP_003856308.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           hyorhinis HUB-1]
 gi|304309290|gb|ADM21770.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           hyorhinis HUB-1]
          Length = 237

 Score =  153 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 107/229 (46%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +++ K+I++ G  SRR  E++I Q RV VN  L           D I++D   L+KAE  
Sbjct: 3   EKIQKLISQTGYCSRRNAEKLILQNRVFVNNQLAT-IGQKASFDDEIKIDNQILKKAEHI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               Y     + T   + + +  +          +  VGRLD NT G++LLTNDG LA  
Sbjct: 62  YYAFYKPKRVVCTREDNFNRKKIIDFF--PKKEYLFPVGRLDFNTTGIILLTNDGELANK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  Q  R Y V  +G +  +++N   K ++        +      +K +     V L
Sbjct: 120 LIHPKFQIERTYLVHTNGDLSDEQINFANKNVIKLNNE---INSRQIIKKKATNKYIVKL 176

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           ++G N  +K++F+ F  +V  L R+ +    L  L  G  R+++ K ++
Sbjct: 177 KQGSNHHVKRLFDHFQIEVLDLKRVQFASINLANLSLGQYRKLTPKEIK 225


>gi|157165467|ref|YP_001467825.1| putative peptide ABC transporter, permease protein [Campylobacter
           concisus 13826]
 gi|112801794|gb|EAT99138.1| hypothetical RNA pseudouridine synthase jhp_1352 (RNA-uridine
           isomerase) (RNA pseudouridylate synthase) [Campylobacter
           concisus 13826]
          Length = 257

 Score =  153 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 115/250 (46%), Gaps = 15/250 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K I+     SRRE + +I   +V + G ++   A +V   D + ++G  ++  +
Sbjct: 2   EKTRLNKFISHNTNYSRREADELIKAGKVSIAGRVVSDLATSVDEDDKVRINGRLIKLKK 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              + +YHK  G + +  D  GR T++D L   F++ +SVGRLD  +EGLLLLT+   +A
Sbjct: 62  EFTVIVYHKQKGELVSKKDDRGRKTIYDTLDKKFAKFVSVGRLDYASEGLLLLTDAPAIA 121

Query: 132 RVLELPSTQWLRVYRVR-----------FHGQVDQDKLNLLKKGIVIQGICYGD-MQVTL 179
             L     +     +V+            +G   +D          I+ + +   +   +
Sbjct: 122 TALMNSDLEREYYLKVKGEISKEVIEAMTNGFFAKDATKGAHAKTTIKSMEFKPFLAYKV 181

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               G    + V + EG+NRE+++ F +F+ +V  L R+S+G   L  L  G  R     
Sbjct: 182 FGSSGGYTKLKVIINEGQNRELRRFFGYFDLEVMDLKRVSFGRVSLDMLKPGKWRYFENS 241

Query: 240 I---LREQLG 246
               LR+ L 
Sbjct: 242 EYEDLRDFLK 251


>gi|294791854|ref|ZP_06757002.1| ribosomal small subunit pseudouridine synthase A [Veillonella sp.
           6_1_27]
 gi|294457084|gb|EFG25446.1| ribosomal small subunit pseudouridine synthase A [Veillonella sp.
           6_1_27]
          Length = 232

 Score =  153 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 103/232 (44%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A     SR+EV ++I  +RV +NG +  +   ++    D + VDG  +   + 
Sbjct: 1   MRLDKLLANKAYGSRKEVHQLIKDRRVTINGSITTKKDTHIDIDVDIVAVDGKVVSTTQL 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +  +     +                L  I   V+ VGRLD +TEGLLLLTNDG    
Sbjct: 61  YYVKFHKPKGYVTAVEDSNHPVVMDLLPLEFIKMGVVPVGRLDKDTEGLLLLTNDGVWGH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +   +    +VY V F G +  + +  +K+GI++  G      ++   +       V V
Sbjct: 121 SIINGNKHVPKVYYVEFEGTLSDEGIQRIKEGILLGDGTQCKPAEIEFVSL----HSVHV 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
            + EGK  ++K++       V  L R++ G   L  +   GS  E++ + + 
Sbjct: 177 TIEEGKYHQVKRMISAAGGTVTYLKRLTIGHIDLSGIEEVGSAMELTVEQIE 228


>gi|58583316|ref|YP_202332.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae KACC10331]
 gi|84625145|ref|YP_452517.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|58427910|gb|AAW76947.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae KACC10331]
 gi|84369085|dbj|BAE70243.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae MAFF
           311018]
          Length = 286

 Score =  153 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 115/247 (46%), Gaps = 7/247 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      + +     I VDG PL    R 
Sbjct: 39  LARVLSKLGVCSRTEAARWIADGRVSVSARVVRDPEFPIRADQQFSITVDGQPLTGPARC 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L      + T   +    +       +    +  VGRLD  +EGLLL +ND   A  
Sbjct: 99  YLMLNKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAAT 158

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNAW 188
           +  P+T   + Y V+     +  +L  L+ G+V      +G+     QV++  +   NAW
Sbjct: 159 VTDPATGPDKTYHVQIDCLPNVAQLAQLQAGVVDPDPEGEGMLLRAKQVSVLREGERNAW 218

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + + L EG+NR+I+++    +  V RL+R++ GP  +G L  G+ R +S + +R  +   
Sbjct: 219 LEIVLDEGRNRQIRRLLAAVDIGVLRLMRVAIGPLAMGELGKGAWRMLSAEEVRALVPAA 278

Query: 249 LLEEAQV 255
                  
Sbjct: 279 HASAPDA 285


>gi|325925343|ref|ZP_08186745.1| pseudouridine synthase family protein [Xanthomonas perforans
           91-118]
 gi|325544221|gb|EGD15602.1| pseudouridine synthase family protein [Xanthomonas perforans
           91-118]
          Length = 264

 Score =  153 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 64/247 (25%), Positives = 112/247 (45%), Gaps = 7/247 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      +       I VDG PL    R 
Sbjct: 17  LARVLSKLGVCSRTEAARWIADGRVSVSARVVRDPEFPIRGDQQSSITVDGQPLAGPARC 76

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L      + T   +    +       +    +  VGRLD  +EGLLL +ND   A  
Sbjct: 77  YLMLNKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAAT 136

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNAW 188
           +  P+    + Y V+   +    +L  L+ G+       +G+     QV++  +   NAW
Sbjct: 137 VTDPARGPDKTYHVQIDCRPSAAQLTQLQAGVADTDPEGEGVLLRAKQVSVLREGERNAW 196

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + + L EG+NR+I+++    +  V RL+R++ GP  +G L  G+ R +S + +R  +   
Sbjct: 197 LEIVLDEGRNRQIRRLLAAVDIGVLRLVRVAIGPLAMGELGKGAWRMLSAEEVRTLVPAA 256

Query: 249 LLEEAQV 255
                  
Sbjct: 257 RASAPDA 263


>gi|307316843|ref|ZP_07596285.1| pseudouridine synthase [Sinorhizobium meliloti AK83]
 gi|306897465|gb|EFN28209.1| pseudouridine synthase [Sinorhizobium meliloti AK83]
          Length = 262

 Score =  153 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 64/226 (28%), Positives = 108/226 (47%), Gaps = 1/226 (0%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTR 74
           +++ +++ G  SR + E++IA+ RV V G  +   +  V    D I VDG  +    R  
Sbjct: 27  LARALSKLGYCSRTQAEKLIAEGRVSVAGRKITDLSHWVDIEVDRIAVDGTVIAAQARVY 86

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L      + T        +            +  VGRLD  +EGLLL TND  LA+ L
Sbjct: 87  LMLNKPRGLVTTRDDPEGRPTVFSCLDNVDVPSLSPVGRLDKASEGLLLFTNDTVLAQRL 146

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P T   +VY V+  G   +     + +G+   G     ++V        N+W+ V L 
Sbjct: 147 LDPETHLGKVYHVQVRGIFGEAMAARMVEGVTEGGELLRALRVERLKSGDRNSWIEVELD 206

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           EG+NR+I+++ +   ++  RL+R+S G  +LG L  G++R +++  
Sbjct: 207 EGRNRQIRRMLDVLGFECLRLLRVSIGEIRLGDLPKGASRPLTEAE 252


>gi|114562021|ref|YP_749534.1| pseudouridine synthase, Rsu [Shewanella frigidimarina NCIMB 400]
 gi|114333314|gb|ABI70696.1| ribosomal small subunit pseudouridine synthase A [Shewanella
           frigidimarina NCIMB 400]
          Length = 229

 Score =  153 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 46/232 (19%), Positives = 100/232 (43%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  +   +R   +R + +  V  +G++++ +   V+    + +DG  +      
Sbjct: 1   MRLDKFICESTELTRSLAKRALHRGDVTCDGVVVKNSGFKVLPQMAVHLDGTLISVI-GE 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP+  + +  D +  S +          +   GRLD++T GL+L+T+DG  +  
Sbjct: 60  RYIMLNKPVDTICSTIDEEYPSVLSLIDIEKMDTLHIAGRLDVDTTGLVLITSDGQWSHK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     +D   + +   G+ +  +        + +      +  V +
Sbjct: 120 ITSPKKDCGKRYWVELAEPIDDSLIQVFADGVELRNEDGLTKPALLDII----DSTHVRL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++F     +V  L R + G  +L   L AG  R ++   ++
Sbjct: 176 TISEGKYHQVKRMFAAVGNRVVNLHREAVGAIELNADLAAGEWRFLTDAEVK 227


>gi|90408508|ref|ZP_01216666.1| probable pseudouridine synthase [Psychromonas sp. CNPT3]
 gi|90310387|gb|EAS38514.1| probable pseudouridine synthase [Psychromonas sp. CNPT3]
          Length = 295

 Score =  153 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 77/294 (26%), Positives = 133/294 (45%), Gaps = 14/294 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+AR+G+ SRR++E +I + RV V+G ++      V     + VDG  ++    
Sbjct: 2   SEKLQKVLARSGLGSRRKMETVIQEGRVSVDGQVV-GLGTRVTVEQILRVDGHTVKYITE 60

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L        + T   +   ++          +R IS+GRLDINT GLLL T D
Sbjct: 61  ENTICRILAYNKPEGEVCTRSDEAGRKTVFERLPRLNGARWISIGRLDINTSGLLLFTTD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---- 183
           G  A  +  PS +  R Y VR  G VD   LN L+ G+ ++      + +    ++    
Sbjct: 121 GEFANRMMHPSREVEREYAVRIFGNVDDAMLNRLRMGVKLEDGEAKFLSIKESGKEAGGE 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL- 241
           G N W  V L EG+ RE+++++E    +V+RL+R+ YG   L   L  G   E++ K + 
Sbjct: 181 GINRWYHVVLTEGRTREVRRLWESQGVQVSRLMRVRYGHLHLDKQLPQGGWIELNLKEVN 240

Query: 242 --REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
             R+ +      E +V +D     +      R              ++++++  
Sbjct: 241 YFRKLVDLSKETETKVRVDDNKTKNTQARIRRAVKKHTQHRKAGVRRRSTARTR 294


>gi|266622691|ref|ZP_06115626.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           hathewayi DSM 13479]
 gi|288865556|gb|EFC97854.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           hathewayi DSM 13479]
          Length = 266

 Score =  153 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 69/270 (25%), Positives = 114/270 (42%), Gaps = 15/270 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--- 67
               R++K ++ AGI SRRE +R+I + +V V G         +   + +  +G  +   
Sbjct: 3   EDGIRLNKFLSGAGICSRREADRLIEEGKVTVGGRTA-VPGQKIKKGETVVCNGRTIAAG 61

Query: 68  ----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                K     L   HKP G+V T SD D    + D +     R+   GRLD  +EGL+L
Sbjct: 62  SRGAEKKPERVLLAVHKPCGIVCTTSDKDRAPNIVDMVDC-PVRIYPAGRLDKESEGLIL 120

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDT 181
           +TN G L   +   S+   + Y V     V  + +  ++KG+ +    +           
Sbjct: 121 MTNQGDLVNRMMRGSSGHEKEYLVWIDRPVKPEFIQKMRKGVFLPELDVTTKPC----FA 176

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +K       + L +G NR+I+++ E    KV +L R+     +LG L AG +R VSKK  
Sbjct: 177 EKTGEKSFRIVLTQGLNRQIRRMCEQLGCKVRKLKRVRIMNIELGDLKAGESRPVSKKEY 236

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDR 271
            E +            D      +   + +
Sbjct: 237 AELMRRLEHTSGLSLKDREEKQKKDSGKRK 266


>gi|283850767|ref|ZP_06368054.1| pseudouridine synthase [Desulfovibrio sp. FW1012B]
 gi|283574010|gb|EFC21983.1| pseudouridine synthase [Desulfovibrio sp. FW1012B]
          Length = 285

 Score =  153 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 72/278 (25%), Positives = 119/278 (42%), Gaps = 8/278 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR----K 69
           R++K +A AG+ SRR+ + +I   RV V+G ++      +    + + VDG P+R     
Sbjct: 8   RLNKALADAGVCSRRQADALITAGRVTVDGAVVTELGNKIDPARNRLAVDGRPVRLSGAA 67

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDG 128
                L L  +P  + T +      +   +   +  +R    VGRLD  +EGLLLLT DG
Sbjct: 68  DAPLTLLLNKRPGCVTTANDPEGRPTVFDELPAAYRARRLFPVGRLDYFSEGLLLLTTDG 127

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTL-DTQKGSN 186
            LA  L  P     + Y V   G V+   L+ + KG+ + +G     ++  +        
Sbjct: 128 ELANRLAHPRWHVDKRYLVTVRGTVNGQTLDTMAKGMTLAEGEQLAPVRARITARLAADR 187

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
             + + L +G NR+I+++    +  V +L RI+ GP  LG L AG  RE++   L     
Sbjct: 188 FVLEMELSQGVNRQIRRMCRDLDLTVLKLCRIAQGPVSLGGLPAGKCRELAASELAALRR 247

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
              L  +       + +     R      S       R
Sbjct: 248 SVGLPSSAAPAKPSVKAPGKAPRKASESPSGKAPGRRR 285


>gi|118602371|ref|YP_903586.1| ribosomal large subunit pseudouridine synthase B [Candidatus Ruthia
           magnifica str. Cm (Calyptogena magnifica)]
 gi|118567310|gb|ABL02115.1| ribosomal large subunit pseudouridine synthase B [Candidatus Ruthia
           magnifica str. Cm (Calyptogena magnifica)]
          Length = 242

 Score =  153 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 78/233 (33%), Positives = 126/233 (54%), Gaps = 7/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK----A 70
           R+ K+IA AG  SRR  E +I Q R++V+         N   TD +++DG  +       
Sbjct: 4   RLQKLIANAGYGSRRWAEHLIEQGRIEVDNKTA-SIGDNAEITDCVKIDGQKIDLSRYLE 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +  ++ + +K  G++ ++ D  GR +V+  LP      + VGRLD+NT GLLL TN+G L
Sbjct: 63  QEIKVIILNKQAGVICSNLDDKGRKSVYSLLPKESRW-VMVGRLDLNTSGLLLFTNNGDL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS+Q  R Y VR  GQV+ + L  L +G+ +        Q+     +G+N W  
Sbjct: 122 ANKLMHPSSQIDREYAVRVLGQVEDEDLKKLTQGVKLDDGFAKFSQIIFGGGQGANRWYK 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           V L+EG+  E+++++E   +KV+RLIRI +G  +L   L A     +  + ++
Sbjct: 182 VVLKEGRKHEVRRLWEELGFKVSRLIRIRFGEIRLPNNLKANQYDYLKPRQVK 234


>gi|91776879|ref|YP_546635.1| pseudouridine synthase, Rsu [Methylobacillus flagellatus KT]
 gi|91710866|gb|ABE50794.1| Pseudouridine synthase, Rsu [Methylobacillus flagellatus KT]
          Length = 380

 Score =  153 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 68/251 (27%), Positives = 104/251 (41%), Gaps = 19/251 (7%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             V       R+SK +A  G+ SRRE +  IA   VKVNG +++     V     IEV  
Sbjct: 132 KPVPSQPELPRLSKRMAELGLCSRREADEFIANGWVKVNGEVVDVLGTRVAPDAKIEVSK 191

Query: 65  VPLRKAERTRLWLYHKPIGLVT---------------THSDPDGRSTVFDNLPSIFSRVI 109
              +    T   L HKP+G V+                 +      +           + 
Sbjct: 192 EAHQHQAETVTILLHKPVGYVSGQAEDGYEPAVVLVHPDNQWKEDPSQTVFKRGHLRGLA 251

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
             GRLDI++ GLL+LT DG +AR L    +   + Y VR  G + ++ L  L  G+ + G
Sbjct: 252 PAGRLDIDSTGLLVLTQDGRVARRLIGEDSTVEKEYLVRVTGTLSEEGLRKLNHGLSLDG 311

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +     +V+   +      +   LREG+ R+I+++ E     V  L R+  G   LG L 
Sbjct: 312 VKLKPAKVSWQNEDQ----LRFVLREGRKRQIRRMCELVGLTVVGLKRVRIGSVTLGKLP 367

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 368 VGMWRYLRPGE 378


>gi|262280085|ref|ZP_06057870.1| ribosomal large subunit pseudouridine synthase B [Acinetobacter
           calcoaceticus RUH2202]
 gi|262260436|gb|EEY79169.1| ribosomal large subunit pseudouridine synthase B [Acinetobacter
           calcoaceticus RUH2202]
          Length = 307

 Score =  153 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 77/306 (25%), Positives = 130/306 (42%), Gaps = 7/306 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
            +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG  ++    
Sbjct: 2   SEKLQKVLARIGLGSRRYMEEVIAAGRVSVNGRVAQV-GERIEPGDELRIDGRKVQFQIE 60

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R  L  Y     + + +      +           R + VGRLDIN+ GLLL TND
Sbjct: 61  DEIRRRVLIYYKPEGEICSRNDPEKRPTVFDHLPQIANDRWVMVGRLDINSTGLLLFTND 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V       +  G+ ++         +    +G N 
Sbjct: 121 GELANRLMHPSNEIEREYAVRVMGEVTPKIRQKMVTGVELEDGPAKFESFSEIGGEGINR 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V ++EG+NRE++++FE    KV+RL+R  YG   L   L  G   E+ K  +     
Sbjct: 181 WYQVVVKEGRNREVRRIFESQELKVSRLLRTRYGTVILPRELRTGRWMELDKTDIDNLAK 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              L+  Q      +    T       + +       + +++  ++  ++   +  +   
Sbjct: 241 SVELKPRQGTGLFGMAKRRTDRMTEKPMAARRGGFLRQQRRDDEKEAPVNTGNQRKSTGF 300

Query: 307 RRNLAS 312
            R    
Sbjct: 301 NRGSKK 306


>gi|325983703|ref|YP_004296105.1| pseudouridine synthase Rsu [Nitrosomonas sp. AL212]
 gi|325533222|gb|ADZ27943.1| pseudouridine synthase Rsu [Nitrosomonas sp. AL212]
          Length = 246

 Score =  153 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 109/247 (44%), Gaps = 22/247 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R+SK+++  G+ SRRE +R I    V V+G  +      +  T  I+++     +  
Sbjct: 2   EKIRLSKLMSEQGLCSRREADRYIELGWVFVDGEQISELGTKIYPTQKIKLNKAAQAQQI 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRST------------------VFDNLPSIFSRVISVGR 113
                L +KP+G V+   +P  R                         PS    +   GR
Sbjct: 62  SLVTILLNKPVGYVSGQPEPGYRPAIVLIKPENQFIPKQPAQPNKRFQPSHLKNLAPAGR 121

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LDI+++GLL+LT DG +A+ +    +   + Y VR  G + ++KL LL  G+ + G    
Sbjct: 122 LDIDSQGLLVLTQDGRIAKQMIGEDSNIEKEYLVRVEGVLPREKLALLNHGLSLDGQPLK 181

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
              VT   Q      +   L+EGK R+I+++ E  N KV  L R+  G  +LG L  G  
Sbjct: 182 PANVTWQNQDQ----LRFILQEGKKRQIRRMCELVNLKVTGLKRVRIGKVKLGNLPEGQW 237

Query: 234 REVSKKI 240
           R +    
Sbjct: 238 RYLEDGE 244


>gi|322374684|ref|ZP_08049198.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           C300]
 gi|321280184|gb|EFX57223.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           C300]
          Length = 241

 Score =  153 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 53/232 (22%), Positives = 104/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A+  + SR+ +++ + ++ + V+       A NV +    +   G  ++  E 
Sbjct: 1   MRLDRLLAQEKV-SRKAMKQALLKKEILVDDCPASSLAQNVDTGLQKLVFQGRQIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L+     +  +                   ++ ++GRLD +T GLLLLT++G L  
Sbjct: 60  NYLMLHKPNGVVTASKDKKLPTVMDLLPPDIQSDQLYAIGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   K GIV          Q+ + +   + +  ++
Sbjct: 120 QLLHPQYHVDKSYQVVVNGLLTSDHIQKFKDGIVFLDGITCKPAQLEILSSSPTESRASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++KK+F     KV  L R+ +G F L   L  G  R ++ + L+
Sbjct: 180 TISEGKFHQVKKMFLSVGVKVTALKRVQFGDFTLDPELAKGQYRPLNPEELK 231


>gi|298529600|ref|ZP_07017003.1| RNA-binding S4 domain protein [Desulfonatronospira thiodismutans
           ASO3-1]
 gi|298511036|gb|EFI34939.1| RNA-binding S4 domain protein [Desulfonatronospira thiodismutans
           ASO3-1]
          Length = 262

 Score =  153 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 73/255 (28%), Positives = 116/255 (45%), Gaps = 8/255 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R++K +ARAGI SRR  + ++   RVKVN  ++    + V    D I VDG P++ 
Sbjct: 2   SREMRLNKALARAGICSRRRADGLVFSGRVKVNDEVVREPGIRVDPEKDSIIVDGRPVKI 61

Query: 70  -----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLL 123
                 E   + L      + TT                +       VGRLD  + GLL+
Sbjct: 62  ETEQERELVHVMLNKPVQVVTTTSDPGGRAKVTDLLPDRLRRMRLFPVGRLDYFSRGLLI 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQ 182
           LTNDG LA  L  PS +  +VYRV+  G + + KL ++++G+V+ +G     ++V +  Q
Sbjct: 122 LTNDGDLAHSLTHPSRKIPKVYRVKMRGDLSKKKLQIMRRGMVLSEGEKLAPVEVKILQQ 181

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
              +    + L +G NR+I+++    +  V  L+RI  GP  LG L  G  R +    + 
Sbjct: 182 TRDSVLAEMTLVQGINRQIRRMCRDLDMVVLSLVRIRQGPLALGELKPGEWRYLEPGEVS 241

Query: 243 EQLGPHLLEEAQVNL 257
           +             L
Sbjct: 242 QLRKWSSRTNHPQPL 256


>gi|223038553|ref|ZP_03608847.1| RNA pseudouridine synthase family protein [Campylobacter rectus
           RM3267]
 gi|222880410|gb|EEF15497.1| RNA pseudouridine synthase family protein [Campylobacter rectus
           RM3267]
          Length = 257

 Score =  152 bits (384), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 114/247 (46%), Gaps = 15/247 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+     SRRE + +I Q +V +NG ++   A +V   D ++++G  +R  +   
Sbjct: 5   RLNKFISHNTSYSRREADELIKQGKVSINGRVVSELATSVSDEDKVKINGRIVRLKKEFT 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +YHK  G + +  D  GR T++D+L   F++ +S+GRLD  +EGLLLLT+   +A  L
Sbjct: 65  VIVYHKQKGELVSKKDDRGRKTIYDSLDRQFAKFVSIGRLDYASEGLLLLTDAPAIATAL 124

Query: 135 ELPSTQWLRVYRVRFHGQVD--QDKLNLLKKGIVIQGICYGDM----------QVTLDTQ 182
                +     +V+     +               +G                   +   
Sbjct: 125 MNSDVEREYYLKVKGEITPEVITAMNEGFFAADATKGAHAKTAIKSMEFRPFLDYKIFGS 184

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI-- 240
            G    + V + EG+NRE+++ F +F+ +V  L R+S+G   LG L  G  R        
Sbjct: 185 SGGFTKLKVVINEGQNRELRRFFGYFDLEVMDLKRVSFGRVDLGMLKPGKWRYFENGEYE 244

Query: 241 -LREQLG 246
            LR+ L 
Sbjct: 245 ALRDFLK 251


>gi|117919212|ref|YP_868404.1| ribosomal small subunit pseudouridine synthase A [Shewanella sp.
           ANA-3]
 gi|117611544|gb|ABK46998.1| ribosomal small subunit pseudouridine synthase A [Shewanella sp.
           ANA-3]
          Length = 235

 Score =  152 bits (384), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 46/234 (19%), Positives = 97/234 (41%), Gaps = 8/234 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+ K I  +   +R   ++ + +  +  +G +++ A   V+    + ++G  +   
Sbjct: 4   SRPVRLDKFICESTSLTRSLAKKALHRGDITCDGAVIKDAGFKVLEGMQVCLEGEFISLV 63

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              R  + +KP+  + +  D    S +          +   GRLD +T GL+L+T+DG  
Sbjct: 64  -GERYLMLNKPVDTICSTIDEVYPSVLSLLDIEKPETLHIAGRLDADTTGLVLITSDGQW 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAW 188
           +  +  P     + Y V     VD+  + +   G+ +  +        + +   +     
Sbjct: 123 SHRITSPKKDCGKRYLVTLAEPVDESLIGVFAAGVELRNEDCLTKPALLEIIEPQ----L 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           V + + EGK  ++K++F      V  L R S G  +L   L  G  R ++ + +
Sbjct: 179 VRLTITEGKYHQVKRMFAAVGNHVVGLHRESIGKIELDAELALGEWRYLTSEEI 232


>gi|294669327|ref|ZP_06734406.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           elongata subsp. glycolytica ATCC 29315]
 gi|291308737|gb|EFE49980.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           elongata subsp. glycolytica ATCC 29315]
          Length = 345

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 72/256 (28%), Positives = 125/256 (48%), Gaps = 7/256 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    V VNG   +     +   D +
Sbjct: 82  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKITPDDQV 140

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      Y +   +V+        S       +  SR +++GRLDI
Sbjct: 141 LVKGNIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 200

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDM 175
           NT GLL+LT  G L +    P  +  R Y VR  G +  +++ +L +  I+++       
Sbjct: 201 NTSGLLILTTSGELVQRFAHPRFEVEREYAVRTLGGLTTEQMRMLTEEGIMLEDGLAKVE 260

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G N W  V ++EG+NRE++++FE+F+  V+RL+RI +GP  L   L  G   
Sbjct: 261 RIREQGGEGVNKWYNVVIKEGRNREVRRIFEYFDLTVSRLVRIGFGPIGLPNRLKRGQFY 320

Query: 235 EVSKKILREQLGPHLL 250
           E++   +   +    +
Sbjct: 321 ELNPAEVANIVKWADM 336


>gi|315500451|ref|YP_004089254.1| pseudouridine synthase [Asticcacaulis excentricus CB 48]
 gi|315418463|gb|ADU15103.1| pseudouridine synthase [Asticcacaulis excentricus CB 48]
          Length = 255

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 62/245 (25%), Positives = 113/245 (46%), Gaps = 15/245 (6%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + +   P R++K +A++G+ SRRE +  IA   V V G ++  A   V +   +  +   
Sbjct: 8   IYDGAEPIRLNKWLAQSGVCSRREADAFIADGLVSVEGEVVRDAGRKVEAGQSVSFNPQA 67

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-----------SVGRLD 115
               +     +YHKP+G+V+   +      V           +            VGRLD
Sbjct: 68  QASLDAKLTVVYHKPVGIVSGQPEAGETPAVRMIRRPNHWGQLTQWPNQDSKLAPVGRLD 127

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
            ++ GLL+L+ DG LA+ +  P ++  + Y VR  G + + KL  L++G+ + G      
Sbjct: 128 KDSRGLLILSEDGVLAKAIIGPDSELEKDYTVRVRGPIFEAKLKWLRQGLELDGRKLKPA 187

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                 Q+     +   L+EG+NR+I+++ +    +V  L R   GP ++G L  G  R 
Sbjct: 188 ----VVQQVGEQTLRFVLKEGRNRQIRRMCDMCELRVLDLYRSRIGPVEIGDLPEGQWRL 243

Query: 236 VSKKI 240
           ++ + 
Sbjct: 244 LTLEE 248


>gi|157962993|ref|YP_001503027.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157847993|gb|ABV88492.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 230

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 46/232 (19%), Positives = 97/232 (41%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  +   SR   ++ + +  V  NG +++ +   V     I ++G  L      
Sbjct: 1   MRLDKFICESTSHSRVSAKKALHRGDVTCNGEVVKNSGFKVTDEHEIRLEGEVLTII-GP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP+  + +  D +  S +     S    +   GRLD +T GL+L+T DG  +  
Sbjct: 60  RFIMLNKPVDTICSTIDEEYPSVISLLDVSRPEDLHIAGRLDADTTGLVLITTDGQWSHK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y +     + +  +     G+ +  +       ++ +     +     +
Sbjct: 120 ITSPKKECGKRYLLETADPLSEALVQQFADGLQLNNEDGLTKPAELEMLGSNQA----RL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++      KV +L R S G  +L  +L  G  R ++   ++
Sbjct: 176 TITEGKYHQVKRMLAAVGNKVTKLHRESVGAIELDPSLELGEWRYLTDAEIK 227


>gi|325266582|ref|ZP_08133259.1| ribosomal large subunit pseudouridine synthase F [Kingella
           denitrificans ATCC 33394]
 gi|324982025|gb|EGC17660.1| ribosomal large subunit pseudouridine synthase F [Kingella
           denitrificans ATCC 33394]
          Length = 243

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 68/245 (27%), Positives = 109/245 (44%), Gaps = 20/245 (8%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------- 63
             P R+SK +A+ G+ SRRE +  I Q  VKVNG +       V+  D I++D       
Sbjct: 2   SEPIRLSKQMAQLGLCSRREADHYIEQGWVKVNGEVA-VLGQKVLPGDRIDLDKNAHQQQ 60

Query: 64  --------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                     P+          Y   + L+T  +  +G  +     P     +   GRLD
Sbjct: 61  AGRVTVLLNKPVGYVSGQPEKGYKAAVELITPENHWEGDQSRIAFQPQHLRGLAPAGRLD 120

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I++ GLL+LT DG +A+ L        + Y VR  G++ ++ LNLL  G+ + G      
Sbjct: 121 IDSVGLLVLTQDGRVAKQLVGEQDSREKEYLVRVRGKIIENGLNLLNHGLHLDGQSLRPA 180

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           +V+   +      +   L +GK R+I+++ E    +V  L R+  G  +LG L  G  R 
Sbjct: 181 KVSWQNEDQ----LRFILTQGKKRQIRRMCELVGLRVVGLKRVRIGRIKLGALPPGKWRY 236

Query: 236 VSKKI 240
           +S   
Sbjct: 237 LSPDE 241


>gi|302878407|ref|YP_003846971.1| pseudouridine synthase [Gallionella capsiferriformans ES-2]
 gi|302581196|gb|ADL55207.1| pseudouridine synthase [Gallionella capsiferriformans ES-2]
          Length = 302

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 74/270 (27%), Positives = 124/270 (45%), Gaps = 7/270 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+A+AG  SRR +E  IA  RV VNG       + V+  D ++ +   +R  ER
Sbjct: 15  GEKLQKVLAQAGFGSRRNMEEWIAAGRVSVNGEPAT-LGMRVVPGDLVKTERRTIRVGER 73

Query: 73  ----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 L  +     +V+        S           + I+VGRLD NT GLL+ T  G
Sbjct: 74  DHTARVLLYHKPEGEIVSRDDPEKRASVFDKLPKLRGQKWIAVGRLDFNTSGLLIFTTSG 133

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNL-LKKGIVIQGICYGDMQVTLDTQKGSNA 187
            LA  L  P  +  R Y VR  G + +D++   LK+G++++       ++  +  +G N 
Sbjct: 134 ELANRLMHPRFEVEREYAVRVQGSMTEDQITQVLKEGVMLEDGPVTFDKLEDNGGEGFNH 193

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V L+EG+NR +++ F+     V+RLIR+ +G   L   L  G + E+ +  + + L 
Sbjct: 194 WYKVMLKEGRNRIVRRTFDALALPVSRLIRVRFGIINLPPRLKRGMSAELGEGEIAQVLD 253

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIIS 276
              +   +V   AP + +            
Sbjct: 254 WVGISTDEVEPPAPKFVAPKPSVPGRTRNP 283


>gi|299139090|ref|ZP_07032266.1| pseudouridine synthase [Acidobacterium sp. MP5ACTX8]
 gi|298598770|gb|EFI54932.1| pseudouridine synthase [Acidobacterium sp. MP5ACTX8]
          Length = 307

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 86/300 (28%), Positives = 134/300 (44%), Gaps = 27/300 (9%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R+ K++A+AGIASRR  E +I + RV+VNG ++        +T DHI VDG  L  
Sbjct: 10  PRGDRLQKILAQAGIASRRAAETIILEGRVQVNGQVVTELGTRADATRDHIRVDGKLLHG 69

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-----------PSIFSRVISVGRLDINT 118
            E  R ++ +KP G VTT  DP+ R TV   L            +   R+  VGRLD  +
Sbjct: 70  PEPQRYFMVNKPRGYVTTLDDPEHRPTVMQLLGQDAQKKSVGEHNKLPRLYPVGRLDYLS 129

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC------- 171
           EGLLL+TNDG LA  L   +    + Y V+  G    + ++ L++GI+I           
Sbjct: 130 EGLLLMTNDGELANKLSKAAAGVEKTYLVKVSGSPTDEAIDQLRRGIMIDRGRLNEVRSG 189

Query: 172 ------YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                     ++    ++G N W  V L EG+NR+++K+FE     V ++ RI YG   L
Sbjct: 190 RRDRVLTSPAKIE-QVRRGENPWFEVTLTEGRNRQLRKMFEEIGHHVEKIRRIGYGALVL 248

Query: 226 GTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
             +  G  RE++   ++        ++ +     P  +             +        
Sbjct: 249 -DIPPGGFRELTTGEVQALGRAAAGKKVERKKTLPEAAQLKKPVPPKKRAFKKAVRKRAS 307


>gi|113969809|ref|YP_733602.1| ribosomal large subunit pseudouridine synthase B [Shewanella sp.
           MR-4]
 gi|114047038|ref|YP_737588.1| ribosomal large subunit pseudouridine synthase B [Shewanella sp.
           MR-7]
 gi|113884493|gb|ABI38545.1| ribosomal large subunit pseudouridine synthase B [Shewanella sp.
           MR-4]
 gi|113888480|gb|ABI42531.1| ribosomal large subunit pseudouridine synthase B [Shewanella sp.
           MR-7]
          Length = 291

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 77/290 (26%), Positives = 130/290 (44%), Gaps = 10/290 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E  IA  RV ++G++       + +   + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRVSIDGVIA-NLGDRIEADAKVRIDGRAISLKSA 60

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  +     + +        +          SR ++VGRLDINT GLLL T+D
Sbjct: 61  DDVICRVLAYHKPEGEICSRKDPEGRPTVFDRLPKVRDSRWVAVGRLDINTSGLLLFTSD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V +  +  L+ G++++        +     +G N 
Sbjct: 121 GELANRLMHPSNEVEREYAVRTFGEVPEAAVQRLRTGVMLEDGMAQFDAIKAAGGEGMNQ 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI---LRE 243
           W  V LREG+NRE+++++E    +V+RLIR+ YG  +L  +L  G   E+  +    LR+
Sbjct: 181 WWHVCLREGRNREVRRLWESQEVQVSRLIRVRYGMVELPKSLPRGGWVELPIEQVNYLRQ 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
             G        +  D    +   +   +              K   +++ 
Sbjct: 241 LAGLEPETRTMLAADKHSVARAQVKSAKIRRAVRKHKVTATPKAKPTRQR 290


>gi|296271690|ref|YP_003654321.1| RNA-binding S4 domain-containing protein [Arcobacter nitrofigilis
           DSM 7299]
 gi|296095865|gb|ADG91815.1| RNA-binding S4 domain protein [Arcobacter nitrofigilis DSM 7299]
          Length = 266

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 69/256 (26%), Positives = 126/256 (49%), Gaps = 18/256 (7%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           KN  +      R++K I+     SRRE + +IA+ RVKVN   +   +  V+ +D + +D
Sbjct: 2   KNQPEAKEENTRLNKFISHNSKYSRREADAIIAEGRVKVNKKTITDLSTKVLDSDIVAID 61

Query: 64  GVPLRKAERTRL--WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
             P++  +       +Y+KP G + T +DP GR  +FD L + +   + +GRLD  +EG+
Sbjct: 62  NKPIKFEKNKMYTVLVYNKPKGELVTKNDPQGRRIIFDTLGAKYKHFLPIGRLDYASEGV 121

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG------------ 169
           LLLT+   +A  L     Q   VY+++  G +++   + +  G+ ++             
Sbjct: 122 LLLTDSVDVANGLMHSDLQR--VYKIKVSGPINKQVEDAMLHGLELEDATKGAWKDSKVK 179

Query: 170 --ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
                  +   +D+ K + + + V + EGKNRE+++ F  F   V  L R+ YG   L  
Sbjct: 180 SMSFAPFLGYKIDSVKDTFSKLKVAITEGKNRELRRFFAHFGLDVMDLKRVEYGGISLNN 239

Query: 228 LLAGSTREVSKKILRE 243
           L  G +R ++++  + 
Sbjct: 240 LPTGKSRYLTREEYKN 255


>gi|332652688|ref|ZP_08418433.1| ribosomal small subunit pseudouridine synthase A [Ruminococcaceae
           bacterium D16]
 gi|332517834|gb|EGJ47437.1| ribosomal small subunit pseudouridine synthase A [Ruminococcaceae
           bacterium D16]
          Length = 239

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 67/231 (29%), Positives = 105/231 (45%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
           +R+ K++A  G  SR+EV+ +IA+ RV V+G    R           I+VDG  +  A  
Sbjct: 4   ERLDKLLASTGRWSRKEVKELIARGRVLVDGRPAGRPEDKCEPQSACIQVDGEIVDCAPC 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L+     L  T                    +  VGRLD +TEGLLLLT+DG L  
Sbjct: 64  VYIMLHKPAGLLSATQDKKQSTVLDLLPEHLRRRGLFPVGRLDKDTEGLLLLTDDGPLGH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VY  R  GQ+D++ + +L +G+ +                G  +   V 
Sbjct: 124 DLLSPRKHVDKVYYARVDGQIDKEDVQVLAQGMTLGDGLV--CLPAGLEPLGDGSECLVT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           LREGK  ++K++       V  L R+S GP +L   L  G  R ++++ ++
Sbjct: 182 LREGKYHQVKRMLAARGKPVLYLKRLSMGPLKLDEKLEKGQWRFLTEREVQ 232


>gi|323691878|ref|ZP_08106132.1| hypothetical protein HMPREF9475_00994 [Clostridium symbiosum
           WAL-14673]
 gi|323504085|gb|EGB19893.1| hypothetical protein HMPREF9475_00994 [Clostridium symbiosum
           WAL-14673]
          Length = 244

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 59/237 (24%), Positives = 104/237 (43%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
            R+ K +A     +R +V+  + + RV V+G +   +          + +DG P+  A  
Sbjct: 5   IRLDKFLAEMKKGTRSQVKEAVRKGRVTVDGAVCRSSDFKFDPEVSGVCMDGEPVSYARM 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +V+   D    + +     +    +  VGRLDI+TEGLLL+TNDG LA 
Sbjct: 65  EYFMLNKPQG-VVSATEDNLHPTVISLIGDAKRKDLFPVGRLDIDTEGLLLITNDGKLAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQ----KGSNA 187
            L  P     +VY  +  G + +D +     GI +         ++ +++          
Sbjct: 124 ELLSPKKHVDKVYFAKVKGTLREDIVQAFAGGITLADQTTVLPAELLIESSYEEAGEPVC 183

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
              + + EGK  ++K++FE    +V  L R+S GP  L   L  G +R ++ K ++ 
Sbjct: 184 EARLTIHEGKFHQVKRMFEAAGGQVVFLKRLSMGPLTLDPKLKPGESRLLTGKEIKA 240


>gi|160872807|ref|ZP_02062939.1| RNA pseudouridine synthase family protein [Rickettsiella grylli]
 gi|159121606|gb|EDP46944.1| RNA pseudouridine synthase family protein [Rickettsiella grylli]
          Length = 245

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 69/236 (29%), Positives = 116/236 (49%), Gaps = 7/236 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL----- 67
            +++ K++A  G+ SRRE+ER I   RV +NG   +   + +     + +D   +     
Sbjct: 2   SEKIQKILAHFGLGSRREIERWIHDGRVHINGQPAK-LGMRIHLKAKVTIDNQRIRLTTN 60

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +  ER  L  +     + +        +           R + +GRLD+NT GLL+ TN+
Sbjct: 61  KPFERRVLIYHKPLGEICSRSDPRHHVTVFEHLPRLRDQRWVMIGRLDMNTSGLLIFTNE 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G  A  L  PS Q  R Y VR  G+V++  L+ LKKG++++        +      G+N 
Sbjct: 121 GEFAYRLSHPSYQIEREYVVRVLGKVNKSMLDRLKKGVMLKEKRAAFTSIQASGGSGANR 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           W  V L+EG+NRE+++++E     V+RL+RI +G   L   L  G   E+  K ++
Sbjct: 181 WYHVVLKEGRNREVRRLWETQGVTVSRLMRIRFGNVSLPHDLKKGHFFELKTKAIK 236


>gi|322412114|gb|EFY03022.1| Putative 16S pseudouridylate synthetase [Streptococcus dysgalactiae
           subsp. dysgalactiae ATCC 27957]
          Length = 238

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 98/229 (42%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SRR+V+++I  Q V+++  +      NV      IEV    +   + 
Sbjct: 1   MRLDKLLELVANGSRRQVKQLIKGQDVRIDHEIAWSGRQNVDPGLQLIEVSRKRISHPKH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +   L      +                       +  VGRLD +TEGL+LLT++G L  
Sbjct: 61  SYFILNKPAGVVSARSDINHVTVLDQLAEKDRHPDLYPVGRLDRDTEGLVLLTDNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +  PS    + Y V  +G +D+D  +    GI    G      Q+T+       +   +
Sbjct: 121 RMLHPSHHVAKTYMVTVNGFLDEDAPDFFASGIKFPTGEQCRPAQLTILQASQEKSQARL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + EGK  ++KK+F  +  KV  L R S+   +LG L +G+ R ++   
Sbjct: 181 VISEGKFHQVKKMFLTYGLKVISLKRTSFAGLELGELASGAYRSLTDAE 229


>gi|302382584|ref|YP_003818407.1| RNA-binding S4 domain protein [Brevundimonas subvibrioides ATCC
           15264]
 gi|302193212|gb|ADL00784.1| RNA-binding S4 domain protein [Brevundimonas subvibrioides ATCC
           15264]
          Length = 251

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 63/244 (25%), Positives = 114/244 (46%), Gaps = 14/244 (5%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + +   P R++K + ++G+ SRRE + +IA   V ++G ++  A   +     + +    
Sbjct: 6   LYDGPEPSRINKWLGQSGVCSRREADALIADGLVSIDGEVVTDAGRKIEPGQTLTLSDRA 65

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI----------SVGRLDI 116
                     + HKP+G V+   +PD    V     +                 +GRLD 
Sbjct: 66  ETALAAGITIVMHKPLGYVSGQPEPDKVPAVRLLTEANRIGPGTAPAADASLPPIGRLDE 125

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           ++ GLLLL+ DG +A+ +  P +   + Y VR  G V + KL +L+ GI++ G       
Sbjct: 126 DSRGLLLLSADGVVAKAVIGPDSDLDKEYLVRVVGDVTEKKLKILRHGIMLDGRQLRPAY 185

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V+       +  +   LREG+NR+I+++    + +V  LIR+  GP +L  L  G  R +
Sbjct: 186 VSRM----ESFRLKFILREGRNRQIRRMCAMVDLEVVDLIRVRIGPLKLDNLPEGHWRML 241

Query: 237 SKKI 240
           + + 
Sbjct: 242 TAEE 245


>gi|225010107|ref|ZP_03700579.1| RNA-binding S4 domain protein [Flavobacteria bacterium MS024-3C]
 gi|225005586|gb|EEG43536.1| RNA-binding S4 domain protein [Flavobacteria bacterium MS024-3C]
          Length = 334

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 59/238 (24%), Positives = 108/238 (45%), Gaps = 1/238 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K   + +    R+++ I+ +G+ SRRE +  IA   +KVNG  +      V  +D +  D
Sbjct: 91  KPAKKGDDNSIRLNRYISNSGVCSRREADIFIAAGSIKVNGKAVVEMGYKVALSDVVSFD 150

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           GV L   +R  + L        +       +S +     +  S++  VGRLD +  GLLL
Sbjct: 151 GVVLNPEKRAYILLNKPKDFDSSATDASQPKSALGLVANATKSKIKPVGRLDKSASGLLL 210

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            TNDG L   L  P   + ++Y       +  D L  ++KGIV++       +++     
Sbjct: 211 FTNDGELQTKLTKPKNGFRKIYHATLSKSLKADDLEKVRKGIVLEDGPVRVHEISNIEGS 270

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +   V + +   KN  IK++F+   +++ +L R+ Y       L  G  R ++++ +
Sbjct: 271 PA-TEVGIEILSAKNNIIKRLFDHLGYELIKLDRVVYAGLTKKDLPRGQWRTLTEQEI 327


>gi|323484805|ref|ZP_08090162.1| pseudouridine synthase [Clostridium symbiosum WAL-14163]
 gi|323401911|gb|EGA94252.1| pseudouridine synthase [Clostridium symbiosum WAL-14163]
          Length = 244

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 59/236 (25%), Positives = 104/236 (44%), Gaps = 8/236 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
            R+ K +A     +R +V+  + + RV V+G +   +          + +DG P+  A  
Sbjct: 5   IRLDKFLAEMKKGTRSQVKEAVRKGRVTVDGAVCRSSDFKFDPEVSGVCMDGEPVSYARM 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +V+   D    + +     +    +  VGRLDI+TEGLLL+TNDG LA 
Sbjct: 65  EYFMLNKPQG-VVSATEDNLHPTVISLIGDAKRKDLFPVGRLDIDTEGLLLITNDGKLAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQ----KGSNA 187
            L  P     +VY  +  G + +D +     GI +         ++ +++          
Sbjct: 124 ELLSPKKHVDKVYFAKVKGTLREDIVQAFAGGITLADQTTVLPAELLIESSYEEAGEPVC 183

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
              + + EGK  ++K++FE    +V  L R+S GP  L   L  G +R ++ K ++
Sbjct: 184 EARLTIHEGKFHQVKRMFEAAGGQVVFLKRLSMGPLTLDPKLKPGESRLLTGKEIK 239


>gi|320528289|ref|ZP_08029451.1| hypothetical protein HMPREF9430_01576 [Solobacterium moorei F0204]
 gi|320131203|gb|EFW23771.1| hypothetical protein HMPREF9430_01576 [Solobacterium moorei F0204]
          Length = 243

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 75/251 (29%), Positives = 119/251 (47%), Gaps = 25/251 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILL-----------ERAAVNVMSTDHIEV 62
           +R+ K IA+AGIASRR+ E +I           +                 V   D I V
Sbjct: 2   ERLQKTIAKAGIASRRKAEELI-----------VSGKVKVNGVVVTELGTQVSPDDDISV 50

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           +GV L+K E+    L      + +   +    + +   L  +  R+  VGRLD +T G+L
Sbjct: 51  NGVVLKKEEKVYYLLNKPRRVISSVSDEKGRETVL-AYLSDVRERIYPVGRLDYDTSGIL 109

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTNDG  A  +  PS+   + Y V   G +  D LN L +GI++        +V L  +
Sbjct: 110 LLTNDGDFANAMMHPSSHLPKTYEVAVTGVLTDDMLNRLARGIMLSDGKTLPAEVVLLER 169

Query: 183 --KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             K +   + + ++EG+NRE++++ E+F+ +V RL RI YG   LG L  G  R++    
Sbjct: 170 STKKNKTVLHITIQEGRNREVRRMMEYFHCEVTRLNRIGYGFLDLGNLRQGQYRKLRSFE 229

Query: 241 LREQLGPHLLE 251
           +R+ L      
Sbjct: 230 VRKLLAMVKRS 240


>gi|332665442|ref|YP_004448230.1| pseudouridine synthase Rsu [Haliscomenobacter hydrossis DSM 1100]
 gi|332334256|gb|AEE51357.1| pseudouridine synthase Rsu [Haliscomenobacter hydrossis DSM 1100]
          Length = 274

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 66/234 (28%), Positives = 117/234 (50%), Gaps = 2/234 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E+    R++K +A  G+ASRRE   ++ Q  + VN ++       + + D ++  G  +R
Sbjct: 33  ESTEGMRLNKYVAHCGVASRREAAEIVKQGHITVNSVVETEPFYQIKTGDIVKYKGQVIR 92

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTND 127
              R   +L +KP  ++TT SD  GR TV D +          VGRLD +T GLLLLTND
Sbjct: 93  PEVRRVYYLMNKPKNVITTTSDEKGRKTVLDLVADRVEERVFPVGRLDRDTTGLLLLTND 152

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  +  PS +  ++Y    +  V ++ L  ++ G+ ++      +       +  ++
Sbjct: 153 GELALKMTHPSYKIKKIYHATLNKTVSKEDLEKIRAGLELEDGPA-PVDAADYIIERPHS 211

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V + +  G+NR ++++FE   ++V +L R+  G      L  G  R ++ + L
Sbjct: 212 EVGLTVHIGRNRIVRRIFEHLGYEVLKLDRVYLGGLTKKDLPRGFVRRLTSQEL 265


>gi|90415213|ref|ZP_01223147.1| ribosomal small subunit pseudouridine synthase A [marine gamma
           proteobacterium HTCC2207]
 gi|90332536|gb|EAS47706.1| ribosomal small subunit pseudouridine synthase A [marine gamma
           proteobacterium HTCC2207]
          Length = 235

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 104/234 (44%), Gaps = 4/234 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I+ A   SR EV+R I    V ++       A  V   + I ++G  +  AE  R
Sbjct: 3   RLDKYISNATDLSRVEVKRYIKYGDVTIDDEKAINGAQKVSGDETICIEGSAISFAEN-R 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G+V+   D +  + +          +   GRLDI+T GLLL+T+DG     L
Sbjct: 62  YFMLNKPAGVVSATKDSNNSTALDLIFEHRSDELQIAGRLDIDTTGLLLITDDGQWNHRL 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P +   ++YRV     +  D    L  G+ ++G  +  +  T   ++  +  V + + 
Sbjct: 122 TSPRSDCQKIYRVTLGIPITPDYAEKLANGVWLKGEKHPCLPAT--MEQIDDETVLLSIA 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGP 247
           EGK  ++K++F      V  L R   G   L   L  G  R ++   +   + P
Sbjct: 180 EGKYHQVKRMFAALGNHVEALHRTQVGGIILDESLEPGDYRALTDAEVASIMAP 233


>gi|253998847|ref|YP_003050910.1| pseudouridine synthase [Methylovorus sp. SIP3-4]
 gi|253985526|gb|ACT50383.1| pseudouridine synthase [Methylovorus sp. SIP3-4]
          Length = 237

 Score =  152 bits (383), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 95/237 (40%), Gaps = 6/237 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--EVDGVPLRKAERT 73
           + +++   G  SR+    +I    V VNG   +    +   TD +   V+  P    E+ 
Sbjct: 3   LERILHAQGFGSRKNCRILIRHHAVTVNGEPCDNPFADFD-TDKLAFTVNEEPWEYREKA 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L        +               P +   V  +GRLD +T GL+LL++DG     
Sbjct: 62  YLMLNKPANYECSHKPQHHPSVFALLPHPLLERGVQCIGRLDEDTTGLILLSDDGQFIHR 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  ++Y V     VD D++  L++G+ +           L  ++ S+  + + L
Sbjct: 122 MSSPKWKVPKIYEVGAKHAVDADQIRQLQEGVQLVDEPAPIA--ALACEQISDQVLHLTL 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHL 249
            EGK  ++K++      +V  L RI  G   L   L  G  R +++  L    G   
Sbjct: 180 AEGKYHQVKRMLAAVGNRVESLKRIRIGELVLPDDLAEGQWRWLTESELASLNGAAR 236


>gi|325918949|ref|ZP_08181018.1| pseudouridine synthase family protein [Xanthomonas vesicatoria ATCC
           35937]
 gi|325534836|gb|EGD06763.1| pseudouridine synthase family protein [Xanthomonas vesicatoria ATCC
           35937]
          Length = 244

 Score =  152 bits (383), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 107/229 (46%), Gaps = 7/229 (3%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERTRLWL 77
           +++ G+ SR E  R IA+ RV V+  ++      + +  H  I VDG PL    R  L L
Sbjct: 2   LSKLGVCSRTEAARWIAEGRVSVDARVIHDPEFPIRADQHEAITVDGQPLAGPARVYLML 61

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
                 + T   +    +       +    +  VGRLD  +EGLLL +ND   A  +  P
Sbjct: 62  NKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAAAVTDP 121

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNAWVTVG 192
           +    + Y V+   +   ++L  L+ G++       G      QV L  +   NAW+ + 
Sbjct: 122 AIGPDKTYHVQVDCRPGAEQLAQLQAGVIDPAPDGDGALLRAKQVRLLREGERNAWLEIV 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           L EG+NR+I+++    +  V RL+R++ GP  +G L  G+ R +S   +
Sbjct: 182 LDEGRNRQIRRLLAAVDIGVLRLVRVAIGPLAMGELGKGAWRMLSAAEV 230


>gi|58581175|ref|YP_200191.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae KACC10331]
 gi|188575692|ref|YP_001912621.1| ribosomal large subunit pseudouridine synthase F [Xanthomonas
           oryzae pv. oryzae PXO99A]
 gi|58425769|gb|AAW74806.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae KACC10331]
 gi|188520144|gb|ACD58089.1| ribosomal large subunit pseudouridine synthase F [Xanthomonas
           oryzae pv. oryzae PXO99A]
          Length = 240

 Score =  152 bits (383), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 63/239 (26%), Positives = 103/239 (43%), Gaps = 10/239 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA  G  SRR+ +R+I ++RV VNG+     AV V   D + VDG PLR  E  +
Sbjct: 4   RLNKYIAETGFCSRRQADRLIGERRVTVNGVPAGTGAV-VGEEDTVLVDGQPLRVREAKK 62

Query: 75  L-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           L             +  T +                 R+  +GRLD  +EGL+L+T++G 
Sbjct: 63  LGGRKHVYIALNKPVGITCTTESSVKGNIVEFVGHEQRIFPIGRLDKESEGLILMTSNGN 122

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +     +  + Y V  +  V  + L  + +G+ I              + G     
Sbjct: 123 IVNEILRAENRHKKEYLVAVNKPVTDEFLRGMARGVRIHNETTLPCHTARIAKFG----F 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR  L   
Sbjct: 179 RIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELRGLLPQR 237


>gi|299532986|ref|ZP_07046373.1| Pseudouridine synthase, Rsu [Comamonas testosteroni S44]
 gi|298719210|gb|EFI60180.1| Pseudouridine synthase, Rsu [Comamonas testosteroni S44]
          Length = 292

 Score =  152 bits (383), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 67/251 (26%), Positives = 104/251 (41%), Gaps = 29/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA  G+ SRRE +  +    V VNG +      NV+  D IE+D     + ++ 
Sbjct: 45  VRINKRIADMGMCSRREADEWVENGWVTVNGEVAT-MGQNVVPGDRIEIDQKAQERQDQQ 103

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---------------ISVGRLDINT 118
              L +KP+G V+  ++      V                             GRLDI++
Sbjct: 104 VTILLNKPMGYVSGQAEDGHEPAVVLITNENRWNEDRSKTRFNFSQLKGLAPCGRLDIDS 163

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQG 169
            GLL+LT DG +AR +    ++  + Y VR               ++KL LL+ G+ +  
Sbjct: 164 VGLLVLTQDGRVARQIIGEDSEVDKEYLVRVTFGDRDVDVQSVFPEEKLALLRHGLSLDE 223

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                 QV     +     +   L EGK R+I+++ E    KV  L RI  G   LG L 
Sbjct: 224 QPLKPAQVDWQNPEQ----LRFVLTEGKKRQIRRMCEQVGLKVVGLKRIRIGGVTLGNLP 279

Query: 230 AGSTREVSKKI 240
            G  R ++   
Sbjct: 280 TGQWRYLAAHE 290


>gi|21241779|ref|NP_641361.1| pseudouridylate synthase [Xanthomonas axonopodis pv. citri str.
           306]
 gi|21107153|gb|AAM35897.1| pseudouridylate synthase [Xanthomonas axonopodis pv. citri str.
           306]
          Length = 264

 Score =  152 bits (383), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 64/247 (25%), Positives = 109/247 (44%), Gaps = 7/247 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      +       I VDG PL    R 
Sbjct: 17  LARVLSKLGVCSRTEAARWIAAGRVSVSARVVRDPEFPIRGDQQSSIAVDGQPLAGLARC 76

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L      + T   +    +       +    +  VGRLD  +EGLLL +ND   A  
Sbjct: 77  YLMLNKPRGVVTTVRDEQGRDTVYRCFDDAGLPWIAPVGRLDKASEGLLLFSNDPQWAAT 136

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-----YGDMQVTLDTQKGSNAW 188
           +  P+T   + Y V+   +    +L  L  G+V              QV++  +   NAW
Sbjct: 137 VTDPATGPDKTYHVQIDCRPSAAQLVQLHAGVVDPDPQGQGLLLRAKQVSVLREGERNAW 196

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + + L EG+NR+I+++    +  V RL+R++ GP  +G L  G+ R +S + +   +   
Sbjct: 197 LEIVLDEGRNRQIRRLLAAVDIGVLRLVRVAIGPLAMGELGKGAWRMLSAEEVSALVPAA 256

Query: 249 LLEEAQV 255
                  
Sbjct: 257 HASAPDA 263


>gi|294102080|ref|YP_003553938.1| pseudouridine synthase [Aminobacterium colombiense DSM 12261]
 gi|293617060|gb|ADE57214.1| pseudouridine synthase [Aminobacterium colombiense DSM 12261]
          Length = 240

 Score =  152 bits (383), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 71/228 (31%), Positives = 109/228 (47%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K +A  G+ASRR+VE  +   RV +NG ++   +  V  TD + +DG  +    R 
Sbjct: 3   IRLNKYLASCGLASRRKVEEFVLSGRVALNGRVVRDLSTTVEETDTVTLDGKEVSPESRV 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +      +       D              R+  VGRLD  +EGLL+LTNDG  A  
Sbjct: 63  YIVMNKPQGVVCAVEDRFDMTVIDVLPPAYSKFRLFPVGRLDKESEGLLVLTNDGDFAHF 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  PS+   R Y V  + ++  +K+ L  KG  I+G     + V    +     WVTV +
Sbjct: 123 LMHPSSNIKRDYEVLLNEELTVEKMKLWLKGFEIEGGFVRPLSVQPLCRPPYGRWVTVSI 182

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            EG+ RE++ + E   +KV  LIR   G  +L  L  G T ++S+  L
Sbjct: 183 TEGQKREVRLMAEHLGYKVMVLIRRRIGRMELRNLNKGQTVKLSQDEL 230


>gi|293365020|ref|ZP_06611737.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           oralis ATCC 35037]
 gi|307702270|ref|ZP_07639230.1| conserved hypothetical protein [Streptococcus oralis ATCC 35037]
 gi|291316470|gb|EFE56906.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           oralis ATCC 35037]
 gi|307624283|gb|EFO03260.1| conserved hypothetical protein [Streptococcus oralis ATCC 35037]
          Length = 241

 Score =  152 bits (383), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 54/232 (23%), Positives = 105/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A+  + SR+ +++ + ++ + V+       A NV +    +   G  ++  E 
Sbjct: 1   MRLDRLLAQEMV-SRKAMKQALLKKEILVDDCPARSLAQNVDTGLQKLVFQGRQIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +  +                   ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPNGSVTASKDKGLPTVMDLLPPDIQSDQLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   K+GIV          ++ + +   + +  ++
Sbjct: 120 QLLHPQYHVDKSYQVVVNGLLTPDHIQYFKEGIVFLDGTTCKPAKLDILSASPTESRASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++KK+F     KV  L R+ +G F L   L  G  R ++ + L 
Sbjct: 180 TISEGKFHQVKKMFLSVGVKVTTLKRVQFGDFTLDSELAEGQYRPLNPEELE 231


>gi|217974709|ref|YP_002359460.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217499844|gb|ACK48037.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 250

 Score =  152 bits (383), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 46/231 (19%), Positives = 97/231 (41%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  +   +R   ++ + +  +  +GI+++ +   V     + ++G P+      
Sbjct: 22  VRLDKFICESTPLTRSLAKKALHRGDITCDGIVVKDSGFKVTEGMRVCLEGEPIALV-GV 80

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP+  + +  D    S +          +   GRLD +T GL+L+T DG  +  
Sbjct: 81  RYLMLNKPVDTICSTIDETYPSVLSLVDVPKPETLHIAGRLDADTTGLVLITTDGQWSHK 140

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y V+    VD   + +   G+ +  +        + +   +     V +
Sbjct: 141 ITSPKKECGKRYLVQLADPVDASLIAIFAAGVELRGEDGLTKPALLEIIEPQ----LVRL 196

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++K++F      V  L R S G  +L   L  G  R ++ + +
Sbjct: 197 TITEGKYHQVKRMFAAVGNHVQGLHRESVGQIELDPALALGEWRYLTAEEI 247


>gi|289668818|ref|ZP_06489893.1| pseudouridylate synthase [Xanthomonas campestris pv. musacearum
           NCPPB4381]
          Length = 285

 Score =  152 bits (383), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 68/246 (27%), Positives = 116/246 (47%), Gaps = 7/246 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      + +  H  I VDG PL    R 
Sbjct: 39  LARVLSKLGVCSRTEAARWIADGRVSVSARVVRDPEFPIRADQHSSITVDGSPLAGPARC 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L      + T   +    +       +    +  VGRLD  +EGLLL +ND   A  
Sbjct: 99  YLMLNKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAAT 158

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNAW 188
           +  P+T   + Y V+   +    +L  L+ G+V      +G+     +V++  +   NAW
Sbjct: 159 VTDPTTGPDKTYHVQIDCRPSAAQLAQLQAGVVDPDPEGEGMLLRAKRVSVLREGERNAW 218

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + + L EG+NR+I+++    +  V RLIR++ GP  +G L  G+ R +S + +R  L   
Sbjct: 219 LEIVLDEGRNRQIRRLLAAVDIGVLRLIRVAIGPLAMGELCKGAWRMLSAEEVRALLPAP 278

Query: 249 LLEEAQ 254
                 
Sbjct: 279 ASAPDA 284


>gi|21243538|ref|NP_643120.1| pseudouridylate synthase [Xanthomonas axonopodis pv. citri str.
           306]
 gi|21109103|gb|AAM37656.1| pseudouridylate synthase [Xanthomonas axonopodis pv. citri str.
           306]
          Length = 240

 Score =  152 bits (383), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 104/241 (43%), Gaps = 10/241 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++K IA  G  SRRE +R+I ++RV VNG+     AV V   D + VD  PLR  E 
Sbjct: 2   TIRLNKYIAETGFCSRREADRLIGERRVTVNGVPAGTGAV-VGEEDTVLVDDQPLRIREA 60

Query: 73  TRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            +L             +  T +                 R+  +GRLD ++EGL+L+T++
Sbjct: 61  KKLGGRKHVYIALNKPVGITCTTESSVKGNIVEFVGHEQRIFPIGRLDKDSEGLILMTSN 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +     +  + Y V  +  V  + L  + +G+ I        +     + G   
Sbjct: 121 GNIVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRIHNETTLPCRTARIAKFG--- 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR  L  
Sbjct: 178 -FRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELRGLLPQ 236

Query: 248 H 248
            
Sbjct: 237 R 237


>gi|119505054|ref|ZP_01627130.1| 16S rRNA uridine-516 pseudouridylate synthase [marine gamma
           proteobacterium HTCC2080]
 gi|119459036|gb|EAW40135.1| 16S rRNA uridine-516 pseudouridylate synthase [marine gamma
           proteobacterium HTCC2080]
          Length = 305

 Score =  152 bits (383), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 76/299 (25%), Positives = 124/299 (41%), Gaps = 8/299 (2%)

Query: 2   KDKNIVQENFTP---QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
            +K  V+    P    ++ K +A+ G+ SRRE+ER I Q R+ + G   +     VM  +
Sbjct: 8   PNKRAVEPPPEPGKGDKLQKALAKTGLGSRREIERWIEQGRLTIGGRKAK-LGDRVMLGE 66

Query: 59  HIEVDGVPLRKAERTR---LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            + +DG P+   E  R   L  +     + +       R+           R I VGRLD
Sbjct: 67  RVTLDGKPVELDETERVRCLLYHKPVGEVCSRKDPEGRRTVFDSLPELQGGRWIVVGRLD 126

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
            NT GLLL T DG LA  +  PS+   R Y VR  G    + L+ L+ G+++        
Sbjct: 127 FNTSGLLLFTTDGELAHKMMHPSSTIEREYLVRVMGNATDEILDTLRAGVILDDGPARFT 186

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTR 234
            +      G N W  V L EG+NRE+++++E     V+RL R+ YG   +   L  G   
Sbjct: 187 DIVDGGGDGINRWFYVVLMEGRNREVRRLWESQGLTVSRLKRVRYGEVFIPSKLKKGEWT 246

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           E+  + +    G   L    +        ++     + +    V    +       ++ 
Sbjct: 247 ELPDRDVEVLYGMAKLPAKPIMPLGDKSRAKLERLAKKSGRETVRRLASGKGGFQRRRK 305


>gi|303233542|ref|ZP_07320201.1| pseudouridylate synthase [Finegoldia magna BVS033A4]
 gi|302495346|gb|EFL55093.1| pseudouridylate synthase [Finegoldia magna BVS033A4]
          Length = 235

 Score =  152 bits (383), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 57/233 (24%), Positives = 121/233 (51%), Gaps = 9/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K+++   IA+R+E+++M+ +  + VN + +++++ ++    D +++    +   + 
Sbjct: 1   MRLDKMLSEMKIATRKEIKQMVKKGIITVNDVTVKKSSEHIDENNDVVKIYDEVIEYRKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +K  G+ +   DP  ++ + D        +  VGRLD++T GLL++TNDG  A 
Sbjct: 61  L-YFVMNKRKGVTSHSKDPMHKTVIDDMGELCVFDLNPVGRLDLDTTGLLIITNDGKFAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVT 190
            L  P  +  + Y+V    +VD+   +  +KGI +  + I     ++ +      +    
Sbjct: 120 NLISPKKEVSKKYKVTLRDKVDEKYNDTFEKGIKLMPEDIITKPAKMEII----DDYNCY 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           + ++EGK  ++K++FE    +V  L R+  G F+L   L  G  RE++ + LR
Sbjct: 176 LTIKEGKYHQVKRMFEKVGNEVVELQRVQIGDFKLPEDLEEGDFRELTDEELR 228


>gi|46370355|gb|AAS89963.1| hypothetical protein [Agrobacterium vitis]
          Length = 240

 Score =  152 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 137/237 (57%), Positives = 163/237 (68%)

Query: 34  MIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           MI + RV VNG +L+   +N    D IEVDG  +R  ERTRLWLYHKP GLVTT+SDP+G
Sbjct: 1   MIMEGRVAVNGKVLDSPVLNATLADRIEVDGEAIRGIERTRLWLYHKPSGLVTTNSDPEG 60

Query: 94  RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
           R TVFDNLP    RV+S+GRLDINTEGLLLLTNDGGLARVLELP+T WLR YRVR +G++
Sbjct: 61  RPTVFDNLPEELPRVMSIGRLDINTEGLLLLTNDGGLARVLELPTTGWLRRYRVRAYGEI 120

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           DQ KL+ LK GI + G+ YG +   LD  +G N W+T+GLREGKNREIK V      +VN
Sbjct: 121 DQAKLDTLKDGIAVDGVLYGAIDAVLDRAQGHNVWITMGLREGKNREIKNVLGALGLEVN 180

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRD 270
           RLIRISYGPFQLG L     +EV  ++LR+QLGP L+               T    
Sbjct: 181 RLIRISYGPFQLGDLPESQVQEVRGRMLRDQLGPRLISLKPREWSCARTIPPTDGPR 237


>gi|225017146|ref|ZP_03706338.1| hypothetical protein CLOSTMETH_01071 [Clostridium methylpentosum
           DSM 5476]
 gi|224950065|gb|EEG31274.1| hypothetical protein CLOSTMETH_01071 [Clostridium methylpentosum
           DSM 5476]
          Length = 248

 Score =  152 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 98/232 (42%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K ++   IA+R + + M+   RV VNG  ++ A + V    D I VDG      E 
Sbjct: 3   IRIDKFLSTQAIATRSQAKEMLRAGRVLVNGTPVKAADLKVDPEGDEIRVDGRVYGYQEH 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L      +  T                    +   GRLD +T G +L+T+DG  A 
Sbjct: 63  LYLMLNKPQGVVSATDDKVHRTVLDLVPPELRRRGLFPAGRLDRDTVGFVLITDDGEFAH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y     G + +++L++L +G+V+  G      ++T+  Q G    + +
Sbjct: 123 NILSPRHHVPKTYEAGLDGPIGENELSVLAQGVVLGDGTKCRPAELTVL-QSGERPLIQI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EG+  +IK++F     +V  L R   G   L  +L  G    +S   L 
Sbjct: 182 VIVEGRYHQIKRMFAAVGRRVLTLKRTKIGGLALDPSLKEGDCIAISPSNLE 233


>gi|296126235|ref|YP_003633487.1| RNA-binding S4 domain protein [Brachyspira murdochii DSM 12563]
 gi|296018051|gb|ADG71288.1| RNA-binding S4 domain protein [Brachyspira murdochii DSM 12563]
          Length = 381

 Score =  152 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 81/240 (33%), Positives = 132/240 (55%), Gaps = 6/240 (2%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           Q+N    R+ KVI  +G ASRR  E+ I   R++VN  ++   A  V  +D + +D   +
Sbjct: 4   QKNEEAVRLVKVILESGFASRRNCEKAIMSGRIRVNNEVILDPAYRVKESDSVSIDRKLI 63

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +R R    +KP+G+V+T     GR  + +    I  R+   GRLD  + G++++TND
Sbjct: 64  E-RQRKRYMALYKPLGVVSTTKYLPGRRIITEFFKGIKERLFYAGRLDSESRGIMIITND 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G  A ++  PS + L+VY V  +G++D +KL    KGI I+ I Y   +  + ++    +
Sbjct: 123 GEFANIITHPSYEILKVYDVTVNGKIDSEKLYEASKGITIKNITYSPFKFKILSKGRVQS 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-----GTLLAGSTREVSKKILR 242
            + + + EGKNREI+K+F++  +KV  L RIS G         GTL AG  R+++KK + 
Sbjct: 183 KIRLTINEGKNREIRKIFDYLGYKVIDLERISVGCVSKYDETSGTLEAGHIRDLTKKEIE 242


>gi|117919973|ref|YP_869165.1| ribosomal large subunit pseudouridine synthase B [Shewanella sp.
           ANA-3]
 gi|117612305|gb|ABK47759.1| ribosomal large subunit pseudouridine synthase B [Shewanella sp.
           ANA-3]
          Length = 291

 Score =  152 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 77/290 (26%), Positives = 130/290 (44%), Gaps = 10/290 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+ARAG  SRRE+E  IA  RV ++G++       + +   + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRVSIDGVIA-NLGDRIEADAKVRIDGRAVSLKSA 60

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  +     + +        +          SR ++VGRLDINT GLLL T+D
Sbjct: 61  DDVICRVLAYHKPEGEICSRKDPEGRPTVFDRLPKVRDSRWVAVGRLDINTSGLLLFTSD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V +  +  L+ G++++        +     +G N 
Sbjct: 121 GELANRLMHPSNEVEREYAVRTFGEVPEAAVQRLRTGVMLEDGMAQFDAIKAAGGEGMNQ 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI---LRE 243
           W  V LREG+NRE+++++E    +V+RLIR+ YG  +L  +L  G   E+  +    LR+
Sbjct: 181 WWHVCLREGRNREVRRLWESQEVQVSRLIRVRYGMVELPKSLPRGGWVELPIEQVNYLRQ 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
             G        +  D    +   +   +              K   +++ 
Sbjct: 241 LAGLEPETRTMLAADKHSVARAQVKSAKIRRAVRKHKVTATPKAKPTRQR 290


>gi|327188988|gb|EGE56177.1| RNA-pseudouridine synthase protein, ribosomal large subunit B
           [Rhizobium etli CNPAF512]
          Length = 267

 Score =  152 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 70/266 (26%), Positives = 121/266 (45%), Gaps = 12/266 (4%)

Query: 1   MKDKNIVQENFTPQRVS-----------KVIARAGIASRREVERMIAQQRVKVNGILLER 49
           M+D+   Q+     +++           + +++ G  SR + ER+IA+ RV ++G  +  
Sbjct: 1   MRDRRPPQKTRERPKLTADAAGKRVTLPRALSKLGYCSRTQAERLIAESRVSIDGRTVND 60

Query: 50  AAVNVMS-TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
            +  V   T  I VDG+ +    +  L L      + T H      +            +
Sbjct: 61  PSAWVDLVTAKIRVDGLVIAAEAKIYLILNKPRGLVTTRHDPEGRPTVYDCLRDFDIPHL 120

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
             VGRLD  +EGLLL TND   A++L  P T   + Y V+    +D +++  +  GI   
Sbjct: 121 SPVGRLDKASEGLLLFTNDTEFAQILLDPVTHVTKTYHVQIDRLLDDEEIAAMTSGIRHD 180

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           G       V    Q   N+W+ V L EG+NR+I+++ E    +  RL+R++ G  +LG L
Sbjct: 181 GELLTATAVRRLRQGDRNSWIEVELDEGRNRQIRRMLEALGTECLRLVRVAIGGLELGEL 240

Query: 229 LAGSTREVSKKILREQLGPHLLEEAQ 254
             G+ R ++   L+       +E A+
Sbjct: 241 PKGAARALTAAELQALRRSAGMERAK 266


>gi|313904278|ref|ZP_07837656.1| pseudouridine synthase [Eubacterium cellulosolvens 6]
 gi|313470828|gb|EFR66152.1| pseudouridine synthase [Eubacterium cellulosolvens 6]
          Length = 256

 Score =  152 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 59/254 (23%), Positives = 103/254 (40%), Gaps = 25/254 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++   + +R+E++  I +    VNGI +     ++   + +  DG P+R  E  
Sbjct: 1   MRLDKYLSDMNVGTRKELKTKIRKGAATVNGIRITDPGFSIKGDEDVTFDGKPIRYNEYE 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      ++T   D   ++ +          +  VGRLD NT GLLL+TNDG L   
Sbjct: 61  YYMLNKPAG-VITATEDRKQQTVLDLLGKDRRKDLFPVGRLDKNTVGLLLITNDGDLNHK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLD------------ 180
           L  P     + Y  +  G+V    +    KG+ I         ++ +             
Sbjct: 120 LLSPKKHTDKKYYAKIDGRVTDADVEAFAKGLRIDDELTALPAKLEILSFRETATDADRE 179

Query: 181 ----------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLL 229
                     +     + + V + EGK  +IK++F     +V  L R+S G   L  +L 
Sbjct: 180 DLLTAEHPESSLSSGVSEICVTIHEGKFHQIKRMFHAVEKEVLYLKRLSMGSLVLDPSLP 239

Query: 230 AGSTREVSKKILRE 243
            GS R +++  +R 
Sbjct: 240 EGSWRPLTEDEIRN 253


>gi|307304763|ref|ZP_07584513.1| pseudouridine synthase [Shewanella baltica BA175]
 gi|306912165|gb|EFN42589.1| pseudouridine synthase [Shewanella baltica BA175]
          Length = 250

 Score =  152 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 46/231 (19%), Positives = 97/231 (41%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  +   +R   ++ + +  +  +GI+++ +   V     + ++G P+      
Sbjct: 22  VRLDKFICESTPLTRSLAKKALHRGDITCDGIVVKDSGFKVTEGMRVCLEGEPIALV-GV 80

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP+  + +  D    S +          +   GRLD +T GL+L+T DG  +  
Sbjct: 81  RYLMLNKPVDTICSTIDETYPSVLSLVDVPKPDTLHIAGRLDADTTGLVLITTDGQWSHK 140

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y V+    VD   + +   G+ +  +        + +   +     V +
Sbjct: 141 ITSPKKECGKRYLVQLADPVDAGLIAIFAAGVELRGEDGLTKPALLEIIEPQ----LVRL 196

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++K++F      V  L R S G  +L   L  G  R ++ + +
Sbjct: 197 TITEGKYHQVKRMFAAVGNHVQGLHRESVGQIELDPALALGEWRYLTAEEI 247


>gi|257081068|ref|ZP_05575429.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis E1Sol]
 gi|256989098|gb|EEU76400.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis E1Sol]
          Length = 260

 Score =  152 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 68/260 (26%), Positives = 116/260 (44%), Gaps = 3/260 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +     
Sbjct: 1   MRLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLISHKTH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                       +  VGRLD +TEGLLLLT++G L  
Sbjct: 61  VYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            L  P+ +  + Y V+ +G V  +     K GIV+QG       ++T+     + + V +
Sbjct: 121 QLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITILAATETESHVFL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLL 250
            ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L    +
Sbjct: 181 TIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYFFI 240

Query: 251 EEAQVNLDAPIYSSETLVRD 270
           E+ Q +   P        R 
Sbjct: 241 EKQQTSKALPSNLKREEERK 260


>gi|30687794|ref|NP_181447.2| SVR1 (SUPPRESSOR OF VARIEGATION 1); RNA binding / pseudouridine
           synthase [Arabidopsis thaliana]
 gi|21617894|gb|AAM66944.1| unknown [Arabidopsis thaliana]
 gi|26450440|dbj|BAC42334.1| unknown protein [Arabidopsis thaliana]
 gi|330254545|gb|AEC09639.1| suppressor of variegation1 causing pseudouridine synthase-like
           protein [Arabidopsis thaliana]
          Length = 410

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 75/258 (29%), Positives = 124/258 (48%), Gaps = 18/258 (6%)

Query: 4   KNIVQENFT--PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHI 60
           +    ENF   PQR+SKV+A AG+ASRR  E +I   +V VNGIL       V  + D I
Sbjct: 148 RRFYNENFKEQPQRLSKVLAAAGVASRRTSEELIFDGKVTVNGILCNTPQTRVDPSRDII 207

Query: 61  EVDGVPLRKA-ERTRLWLYHKPIGLVTTH-----------SDPDGRSTVFDNLPSIFSRV 108
            V+G  + K       +  +KP G + +             D    S    N  +   R+
Sbjct: 208 YVNGNRIPKKLPPKVYFALNKPKGYICSSGEKEIKSAISLFDEYLSSWDKRNPGTPKPRL 267

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            +VGRLD+ T GL+++TNDG  A+ L  PS+   + Y     G + +  L  + +G +++
Sbjct: 268 FTVGRLDVATTGLIVVTNDGDFAQKLSHPSSSLPKEYITTVVGDIHKRHLMAISEGTMVE 327

Query: 169 GICYGDMQVTLDTQK--GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL- 225
           G+      V L  ++     A + + + EG+N E++++ +    +V+ L R+  G F+L 
Sbjct: 328 GVHCVPDSVELMPKQHDIPRARLRIVVHEGRNHEVRELVKNAGLEVHSLKRVRIGGFRLP 387

Query: 226 GTLLAGSTREVSKKILRE 243
             L  G   E+ +  L+ 
Sbjct: 388 SDLGLGKHVELKQSELKA 405


>gi|85712444|ref|ZP_01043493.1| RNA pseudouridylate synthase-family protein [Idiomarina baltica
           OS145]
 gi|85693722|gb|EAQ31671.1| RNA pseudouridylate synthase-family protein [Idiomarina baltica
           OS145]
          Length = 291

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 80/291 (27%), Positives = 133/291 (45%), Gaps = 11/291 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+AR+G  SRRE+E MI   R++VNG + +     + +   + +DG  +     
Sbjct: 2   TEKLQKVLARSGYGSRREIEAMIGAGRIRVNGKVAQV-GERIDADASVRIDGHEVVIKSE 60

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  +     L T        +          +R ++VGRLD+NT GLLL T D
Sbjct: 61  NSVVCRVLTYHKPEGELCTRKDPEGRPTVYERLPRMSGARWVAVGRLDVNTSGLLLFTTD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDTQKGSN 186
           G LA  L  PS +  R Y VR  G+V    +N LKKG+ ++        +  +   +G N
Sbjct: 121 GELANRLMHPSQEVEREYAVRIFGEVTDAMINRLKKGVQLEDGLAHFDTIKAVGGGEGMN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK---ILR 242
            W  V L+EG+NRE+++++E    +V+RLIR+ YG  +L   L  G   E+       LR
Sbjct: 181 RWYHVTLKEGRNREVRRLWESQEVQVSRLIRVRYGDIKLESGLPQGGWSELELDQVNELR 240

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
            ++G    +++ V+            + R              + N +++ 
Sbjct: 241 AKVGLQPEDKSFVDPRHQESKQRKFAKIRKATSKRKDRLREAQRVNKNKRK 291


>gi|242042191|ref|XP_002468490.1| hypothetical protein SORBIDRAFT_01g046770 [Sorghum bicolor]
 gi|241922344|gb|EER95488.1| hypothetical protein SORBIDRAFT_01g046770 [Sorghum bicolor]
          Length = 407

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 70/261 (26%), Positives = 115/261 (44%), Gaps = 18/261 (6%)

Query: 4   KNIVQENF---TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDH 59
           +    EN     PQR++KV+A AG+ASRR  E +I Q +V VNG +       V  S D 
Sbjct: 145 RRFYNENIKEREPQRLAKVLAAAGVASRRTSEELIFQGKVTVNGSVCTSPQTKVDISKDS 204

Query: 60  IEVDGVPLRKAERTRLWL--YHKPIGLVTTH---------SDPDGRSTVFDNLPSIFSRV 108
           I V+G  + K    +L+         + +            +   +            R+
Sbjct: 205 IYVNGNRISKKLPPKLYFAVNKPKGYICSCGEDSKSVVSLFNDYLKGWNKIQPGLPKPRL 264

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            +VGRLD+ T GL+++TNDG  A+ L  PS+   + Y V   G V +  L  + +G  I 
Sbjct: 265 FTVGRLDVATSGLIIVTNDGEFAQKLAHPSSNVTKEYVVTIDGAVHKKHLIAISEGTKID 324

Query: 169 GICYGDMQVTLDTQKGS--NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL- 225
           GI      V     +       + + + EG+N E++++ +    +V  L R+  G F+L 
Sbjct: 325 GIMCIPDLVESLDAQSDTRKTRLKIVVHEGRNHEVRELVQNAGLQVYALKRVRIGRFRLP 384

Query: 226 GTLLAGSTREVSKKILREQLG 246
             L  G   E+ +  ++   G
Sbjct: 385 ADLGIGKFVELKQADIKALEG 405


>gi|123442465|ref|YP_001006444.1| 23S rRNA pseudouridylate synthase B [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|122089426|emb|CAL12274.1| putative RNA pseudouridylate synthase-family protein [Yersinia
           enterocolitica subsp. enterocolitica 8081]
          Length = 309

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 90/321 (28%), Positives = 135/321 (42%), Gaps = 20/321 (6%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKAE-----R 72
           +ARAG  SRRE+E +I Q RV V+G +  +    V  T    I +DG  L   E      
Sbjct: 1   MARAGHGSRREIETIIQQGRVSVDGKI-SKLGDRVEVTQATKIRLDGHLLSIKESEEAVC 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L  Y     L T +      +          SR ++VGRLD+NT GLLL T DG LA 
Sbjct: 60  RVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFTTDGELAN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS +  R Y VR  GQ+D +K+  L +G+ ++        +T    +G N W  V 
Sbjct: 120 RLMHPSREVEREYAVRVFGQIDDEKIKQLSRGVQLEDGPAAFRTITFQGGEGINQWYNVT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHLLE 251
           L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+    L+       L 
Sbjct: 180 LTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELD---LKATNYLRELV 236

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           E      + +   +   R + N I                +    +         + +  
Sbjct: 237 ELDSETVSKLPVEKDRRRVKANQIRRAVKR--------HTEVAGRQVAGRQGSARKGSTR 288

Query: 312 SNVWMAKGIHSSFLSDSGQRE 332
            NV  A    ++    + +R 
Sbjct: 289 QNVGNAAPAAATGRRGANKRG 309


>gi|300858398|ref|YP_003783381.1| hypothetical protein cpfrc_00980 [Corynebacterium
           pseudotuberculosis FRC41]
 gi|300685852|gb|ADK28774.1| hypothetical protein cpfrc_00980 [Corynebacterium
           pseudotuberculosis FRC41]
 gi|302206111|gb|ADL10453.1| Putative ribosomal large subunit pseudourinine synthase B
           [Corynebacterium pseudotuberculosis C231]
          Length = 373

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 77/245 (31%), Positives = 120/245 (48%), Gaps = 4/245 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DH 59
           ++ ++         R+ KV+A+AG+ASRR  E +I   R++VNG ++    V V    D 
Sbjct: 120 VEQRDFGSPTGEGIRLQKVLAQAGVASRRHAEILIDAGRIEVNGKIVLTQGVRVNPHADI 179

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDI 116
           I VDGV +   E  + ++ +KP GL +T SD  GR  V D +        R+  VGRLD 
Sbjct: 180 IRVDGVRINVNEDMQYFVLNKPRGLQSTMSDDMGRPCVGDIVGERIAAGQRLFHVGRLDA 239

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
            TEGLLLLTNDG LA  L  P  +  + Y     G+ D+  +  L+ GI +         
Sbjct: 240 ATEGLLLLTNDGELANRLMHPKYEVTKTYLATVLGEADKRLIKQLRDGIELDDGPAKADF 299

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V +       + + + L EG+   ++++ +   + V RL+R      QLG    G+ R +
Sbjct: 300 VQIVDAHQGKSLIRIELHEGRKHIVRRMLKTAGFPVERLVRTKIHTIQLGEQTPGAVRAL 359

Query: 237 SKKIL 241
           +   L
Sbjct: 360 NSSEL 364


>gi|46202419|ref|ZP_00053237.2| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Magnetospirillum
           magnetotacticum MS-1]
          Length = 236

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 58/230 (25%), Positives = 93/230 (40%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKV-NGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+ ++IA  G  S+R+V+ MI    V   +G +L+  +  V   D I VDG PL     
Sbjct: 1   MRLIRLIANLGYGSQRDVKAMIKDGLVTRADGSVLDDTS-KVAHED-IRVDGEPLDPPPG 58

Query: 73  TRLWLYHKPIGLVTTHSD-PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             L L        +T          +          V  VGRLD ++ GLLLLT+DG LA
Sbjct: 59  LVLMLNKPEGYTCSTSDPGRVVYELLPPRFMHRNPIVAPVGRLDRDSSGLLLLTDDGPLA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P     + Y V     +  ++  +   G ++       +        G      +
Sbjct: 119 HRVTSPKRHVPKTYEVTLARPLTGEEGAVFASGTLMLRSENTPLAPAELMVTGPQT-ARI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + EG+  ++K++F      V RL R + G   LG L  G  R ++   +
Sbjct: 178 TITEGRYHQVKRMFAAVGNHVERLHRAAIGGLDLGDLPEGQWRMLTPDEI 227


>gi|283769102|ref|ZP_06342007.1| pseudouridylate synthase [Bulleidia extructa W1219]
 gi|283104288|gb|EFC05666.1| pseudouridylate synthase [Bulleidia extructa W1219]
          Length = 242

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 84/237 (35%), Positives = 132/237 (55%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ KVIA+AGIASRR+ E +IAQ +VKVNG +++   V V   D I V+G  ++  E  
Sbjct: 2   QRLQKVIAQAGIASRRKAEELIAQGKVKVNGKVVKEMGVQVSFDDEIMVNGQSIQ-KEEK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP  +++T  D   R+T+ D    +  R+  VGRLD  T GLLL+TNDG  A  
Sbjct: 61  VYFLLNKPKKMISTVHDDLKRATIMDCFRDVKQRIFPVGRLDYETTGLLLVTNDGEFANA 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  PS    ++Y V  +G ++   L  LKKGI ++        V +  +    +   + +
Sbjct: 121 MMHPSHHMDKIYEVYVNGYLEDHMLTKLKKGIPLEDGMTLPASVEVLERSRKTNKTRIRL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            ++EGKNRE++++  +F ++V+ L RI Y    LG L  G  R + K  +++ L   
Sbjct: 181 TIQEGKNREVRRMMAYFGFEVHTLQRIGYSFLNLGNLRQGEYRRLKKFEVKKLLTIA 237


>gi|284929158|ref|YP_003421680.1| ribosomal large subunit pseudouridine synthase B [cyanobacterium
           UCYN-A]
 gi|284809617|gb|ADB95322.1| ribosomal large subunit pseudouridine synthase B [cyanobacterium
           UCYN-A]
          Length = 254

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 73/238 (30%), Positives = 119/238 (50%), Gaps = 12/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           RV K++++ GIASRR  E +I ++R+K+NG ++           D +E+DG  ++  ++T
Sbjct: 4   RVQKILSQLGIASRRHAEILILEKRLKLNGQIV-LLGDKADPNHDLLELDGKIIKSHKKT 62

Query: 74  RLWLY--HKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDG 128
           +L+    +KP+G++ +  D   RS V D LP        +  VGRLD+N+ G LLLTNDG
Sbjct: 63  QLFYILVNKPVGIICSCKDSQNRSIVMDLLPSNLRKGMGIHPVGRLDMNSSGALLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P     ++Y V   G   Q  L   ++G+V+ G       + +         
Sbjct: 123 NLTLRLTHPRYHLPKIYEVLVRGNFTQAILKDWRQGVVLDGKKTLPAYLEVINNNRQYTN 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-----GTLLAGSTREVSKKIL 241
           + + L EGKNR I+++ + F   V +L R + GP  L       +  G  R +S   +
Sbjct: 183 LKIILTEGKNRHIRRIAQKFELDVIKLHRTAIGPISLSTSKVDNVKLGHYRLLSSSEI 240


>gi|304310662|ref|YP_003810260.1| Ribosomal large subunit pseudouridine synthase B [gamma
           proteobacterium HdN1]
 gi|301796395|emb|CBL44603.1| Ribosomal large subunit pseudouridine synthase B [gamma
           proteobacterium HdN1]
          Length = 282

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 78/241 (32%), Positives = 119/241 (49%), Gaps = 7/241 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
            +++ KV+ARAGI SRR +E  IA  RV VNG   +     V   D + VDG  +  +  
Sbjct: 2   SEKLQKVLARAGIGSRRSMEDWIASGRVSVNGKKAKV-GDRVERGDVLRVDGRSMDYSGE 60

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R  +  Y     + T        +           R ++VGRLD+NT+GLLL T D
Sbjct: 61  DSDSRRMIIYYKPEGEVCTRTDPEGRPTVFDRLPRLDNERWVAVGRLDVNTQGLLLFTTD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS++  R Y  R  G+V  + L+ L+ G+ +        ++     +G NA
Sbjct: 121 GDLANRLMHPSSEIEREYAARIFGEVTPEMLHNLRTGVQLFDGPAHFDEILHSGGEGMNA 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V ++EG+ RE+++++E    +V+RLIR+ YG   L   L AG   E+S+  + E   
Sbjct: 181 WYHVIIKEGRRREVRRMWETQGVQVSRLIRVRYGCVTLPRGLKAGRWEELSEDQISELAQ 240

Query: 247 P 247
            
Sbjct: 241 L 241


>gi|239624076|ref|ZP_04667107.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239522107|gb|EEQ61973.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 294

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 67/262 (25%), Positives = 115/262 (43%), Gaps = 15/262 (5%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR------- 68
           ++K +++ G+ SRRE +R+I   +V V+G         V     +  DGVP+        
Sbjct: 36  LNKWLSQMGVCSRREADRLIEAGKVWVDGSPAA-MGQKVKPGQKVVCDGVPVNGGSGADS 94

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           +  +  L + +KP G+V T SD D    + + L     R+  VGRLD ++EGLLL+TN G
Sbjct: 95  RKPKPVLLVVNKPRGIVCTTSDKDRAMNIVEYLDY-PERIYPVGRLDKDSEGLLLMTNQG 153

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSN 186
            L   +        + Y V     +  D ++ + KGI +          +V     K   
Sbjct: 154 DLVNKIMRSGNAHEKEYIVTVDRPLTDDAMDRMAKGIYLRELETVTRPCKVKRVDGK--- 210

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
              ++ L +G NR+I+++ E     V RL+R+     +L  L  G++REV ++  RE + 
Sbjct: 211 -TFSIILTQGLNRQIRRMCEACGCHVERLVRVRIMNIRLDGLETGASREVGQEEYRELMR 269

Query: 247 PHLLEEAQVNLDAPIYSSETLV 268
                 +           +   
Sbjct: 270 LLRDSSSLPGGRGRAVPHKART 291


>gi|296085982|emb|CBI31423.3| unnamed protein product [Vitis vinifera]
          Length = 296

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 77/258 (29%), Positives = 125/258 (48%), Gaps = 18/258 (6%)

Query: 4   KNIVQENFT--PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHI 60
           +    ENF   PQR+SKV+A AG+ASRR  E +I + RV VNG +       V    D I
Sbjct: 34  RRFYNENFRDPPQRLSKVLAAAGVASRRNSEELIFEGRVTVNGSVCNTPQTRVDPARDMI 93

Query: 61  EVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----------- 108
            V+G  L K          +KP G + +  + + +S +      + S             
Sbjct: 94  YVNGNRLPKKLPPKVYLALNKPKGYICSSGEKESKSVLCLFDDYLKSWNKQNPGVPKPRI 153

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            +VGRLD+ T GL++LTNDG  A+ L  PS++  + Y     G V++  L  + +G VI+
Sbjct: 154 FTVGRLDVATTGLIILTNDGDFAQKLSHPSSKLSKEYIATIDGVVNKRHLIAISEGTVIE 213

Query: 169 GICYGDMQVTLDTQKGSNAW--VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL- 225
           G+      V L   + + +   + V + EG+N E++++ +    +++ L RI  G F+L 
Sbjct: 214 GVHCTPDSVELLPPQPNISKPRLRVVVHEGRNHEVRELVKSAGLQIHSLKRIRIGGFRLP 273

Query: 226 GTLLAGSTREVSKKILRE 243
             L  G   E+ +  L+ 
Sbjct: 274 SDLGHGKHVELKQGDLKA 291


>gi|28378068|ref|NP_784960.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|254556281|ref|YP_003062698.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
 gi|300769229|ref|ZP_07079117.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|308180250|ref|YP_003924378.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
 gi|28270902|emb|CAD63807.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|254045208|gb|ACT62001.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
 gi|300493258|gb|EFK28438.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|308045741|gb|ADN98284.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
          Length = 246

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 55/233 (23%), Positives = 96/233 (41%), Gaps = 5/233 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            RV K +    I +R +V R+I    +  NG  +      +    D + +D V +R  + 
Sbjct: 1   MRVDKFLHAMRIGTRTQVRRLIKDGHITANGEPVISGKQQINPGSDTVFLDDVQVRYQQY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +  T            N       +  VGRLD +TEG+L++TNDG L+ 
Sbjct: 61  FYYVMNKPVGVITATTDSAAKTVMDLFNTTDFRDDLFPVGRLDKDTEGILVITNDGALSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLD--TQKGSNAWV 189
            L  P+    +VY     G++   +L     GI ++        Q  +    +  +   +
Sbjct: 121 DLLSPNHHVTKVYEAEVTGEITAAQLANFNDGITLKDGTELQPAQAEIVQFHEIENFTTI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + + EGK  ++K++      +V  L RI +G   L   LLAG+ R ++   L
Sbjct: 181 RIMIHEGKYHQVKRMVGTLGERVVGLRRIKFGSLTLPVGLLAGNYRALTDDEL 233


>gi|330999105|ref|ZP_08322826.1| pseudouridylate synthase [Parasutterella excrementihominis YIT
           11859]
 gi|329575494|gb|EGG57033.1| pseudouridylate synthase [Parasutterella excrementihominis YIT
           11859]
          Length = 292

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 67/294 (22%), Positives = 113/294 (38%), Gaps = 26/294 (8%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           +        R+SK ++  G+ SRRE +  I++  VKV+G ++      V     I +D  
Sbjct: 1   MSDTPADLVRLSKRMSELGLCSRREADEWISKGWVKVDGQVVSELGSKVRPDQKITIDRK 60

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                          PL          +     L+T  +      +     PS    ++ 
Sbjct: 61  AQDQQNERVTIILNKPLGYVSGQAEDGHEPARILITPRNRWIDDPSPRRFNPSQLKSLVP 120

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF-------HGQVDQDKLNLLKK 163
            GRLDIN+ GLL+LT DG +A+ +   ++   + Y VR        + +    KL LL  
Sbjct: 121 AGRLDINSTGLLVLTQDGRIAKTIIGENSSVEKEYIVRVAMTDGRSNSEFPPAKLALLNH 180

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
           G+ + G      +V+   +      +   LREG+NR+I+++ +    KV  L R+  G  
Sbjct: 181 GLELDGKPLEKAEVSWLNEDQ----LKFVLREGRNRQIRRMCDLVGLKVLALKRVRVGNV 236

Query: 224 QLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISE 277
           +LG L  G  R +          P     ++    AP        R      + 
Sbjct: 237 RLGKLPVGKWRYLEDGESFTGPAPKRASSSRPAAGAPRRPKTFKPRKPNFRKTR 290


>gi|225574967|ref|ZP_03783577.1| hypothetical protein RUMHYD_03046 [Blautia hydrogenotrophica DSM
           10507]
 gi|225037814|gb|EEG48060.1| hypothetical protein RUMHYD_03046 [Blautia hydrogenotrophica DSM
           10507]
          Length = 246

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 109/238 (45%), Gaps = 9/238 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKA 70
              R+ K +A AG  +R EV++ I++ +V+VNG  +   A  +   +  +   G  +   
Sbjct: 2   KKIRLDKYLADAGAGTRSEVKKYISKAQVQVNGKTVLNPAEKIEPEEVEVCCLGQVVHVD 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                 L+     +  T        TV + +PS    +  VGRLD +TEGLLL+TNDG L
Sbjct: 62  RYEYYLLHKPAGCVSATEDV--RERTVMEFVPSRRKDLFPVGRLDKDTEGLLLITNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSN--- 186
           A  L  P     + Y  +  G++ Q+     ++G+ I         ++ + + +      
Sbjct: 120 AHRLLAPRRHVPKQYFAQIKGKMTQEDAQKFRQGVEIGEKNPTLPAKLEILSVENGEEGW 179

Query: 187 -AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + + + EGK  +IK++ +    +V  L RIS GP  L   L  G  R +++K + 
Sbjct: 180 ISCINLTIEEGKFHQIKRMVQAVGKEVIYLKRISMGPLYLDENLERGQCRPLTEKEIE 237


>gi|84623097|ref|YP_450469.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|84367037|dbj|BAE68195.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae MAFF
           311018]
          Length = 240

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 63/239 (26%), Positives = 104/239 (43%), Gaps = 10/239 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA  G  SRR+ +R+I ++RV VNG+     AV V   D + VDG PLR  E  +
Sbjct: 4   RLNKYIAETGFCSRRQADRLIGERRVTVNGVPAGTGAV-VGEEDTVLVDGQPLRVREAKK 62

Query: 75  L-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           L             +  T +                 R+  +GRLD  +EGL+L+T++G 
Sbjct: 63  LGGRKHVYIALNKPVGITCTTESSVKGNIVEFVGHEQRIFPIGRLDKESEGLILMTSNGN 122

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +     +  + Y V  +  V  + L  + +G+ I        +     + G     
Sbjct: 123 IVNEILRAENRHKKEYLVAVNKPVTDEFLRGMARGVRIHNETTLPCRTARIAKFG----F 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR  L   
Sbjct: 179 RIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELRGLLPQR 237


>gi|315269053|gb|ADT95906.1| pseudouridine synthase [Shewanella baltica OS678]
          Length = 250

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 46/231 (19%), Positives = 97/231 (41%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  +   +R   ++ + +  +  +GI+++ +   V     + ++G P+      
Sbjct: 22  VRLDKFICESTPLTRSLAKKALHRGDITCDGIVVKDSGFKVTEGMRVCLEGEPIALV-GV 80

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP+  + +  D    S +          +   GRLD +T GL+L+T DG  +  
Sbjct: 81  RYLMLNKPVDTICSTIDETYPSVLSLVDVPKPETLHIAGRLDADTTGLVLITTDGQWSHK 140

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y V+    VD   + +   G+ +  +        + +   +     V +
Sbjct: 141 ITSPKKECGKRYLVQLADPVDAGLIAVFAAGVELRGEDGLTKPALLEIIEPQ----LVRL 196

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++K++F      V  L R S G  +L   L  G  R ++ + +
Sbjct: 197 TITEGKYHQVKRMFAAVGNHVQGLHRESVGQIELDPALALGEWRYLTAEEI 247


>gi|160876850|ref|YP_001556166.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|160862372|gb|ABX50906.1| pseudouridine synthase [Shewanella baltica OS195]
          Length = 256

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 46/231 (19%), Positives = 97/231 (41%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  +   +R   ++ + +  +  +GI+++ +   V     + ++G P+      
Sbjct: 28  VRLDKFICESTPLTRSLAKKALHRGDITCDGIVVKDSGFKVTEGMRVCLEGEPIALV-GV 86

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP+  + +  D    S +          +   GRLD +T GL+L+T DG  +  
Sbjct: 87  RYLMLNKPVDTICSTIDETYPSVLSLVDVPKPETLHIAGRLDADTTGLVLITTDGQWSHK 146

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y V+    VD   + +   G+ +  +        + +   +     V +
Sbjct: 147 ITSPKKECGKRYLVQLADPVDAGLIAVFAAGVELRGEDGLTKPALLEIIEPQ----LVRL 202

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++K++F      V  L R S G  +L   L  G  R ++ + +
Sbjct: 203 TITEGKYHQVKRMFAAVGNHVQGLHRESVGQIELDPALALGEWRYLTAEEI 253


>gi|153002130|ref|YP_001367811.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|151366748|gb|ABS09748.1| pseudouridine synthase [Shewanella baltica OS185]
          Length = 246

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 46/231 (19%), Positives = 97/231 (41%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  +   +R   ++ + +  +  +GI+++ +   V     + ++G P+      
Sbjct: 18  VRLDKFICESTPLTRSLAKKALHRGDITCDGIVVKDSGFKVTEGMRVCLEGEPIALV-GV 76

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP+  + +  D    S +          +   GRLD +T GL+L+T DG  +  
Sbjct: 77  RYLMLNKPVDTICSTIDETYPSVLSLVDVPKPETLHIAGRLDADTTGLVLITTDGQWSHK 136

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y V+    VD   + +   G+ +  +        + +   +     V +
Sbjct: 137 ITSPKKECGKRYLVQLADPVDAGLIAVFAAGVELRGEDGLTKPALLEIIEPQ----LVRL 192

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++K++F      V  L R S G  +L   L  G  R ++ + +
Sbjct: 193 TITEGKYHQVKRMFAAVGNHVQGLHRESVGQIELDPALALGEWRYLTAEEI 243


>gi|332976275|gb|EGK13136.1| ribosomal small subunit pseudouridine synthase A [Psychrobacter sp.
           1501(2011)]
          Length = 234

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 56/235 (23%), Positives = 104/235 (44%), Gaps = 11/235 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K I++A   SR+E ++++    + VN  +++  +++V    D +   G PL  A  
Sbjct: 1   MRLDKFISKATELSRKEAKKVLHASEITVNDEVVKDGSLHVDVLNDEVMWAGEPLSVATG 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +R  L +KP G   T    +               +   GRLD++T G LLL++DGG   
Sbjct: 61  SRYLLLYKPEGFECTLKPKEYPMVTDLIAVPELGNLRIAGRLDVDTTGALLLSDDGGWLH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKL----NLLKKGIVIQG--ICYGDMQVTLDTQKGSN 186
            +  P     +VY +     +D+ +       + +GI++ G         +    +  + 
Sbjct: 121 RVTSPRHLHEKVYELTLAEPMDEAEQAHAVKKVAQGILLDGDYEPTKPATLEFIDETHA- 179

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
               + L EGK  ++K++  +F  KV  L R S G   L  L  G +R +++  +
Sbjct: 180 ---RLILTEGKYHQVKRMMGYFGNKVIELHRASIGGVTLEGLEKGESRFLTEDEI 231


>gi|212637124|ref|YP_002313649.1| pseudouridine synthase Rsu [Shewanella piezotolerans WP3]
 gi|212558608|gb|ACJ31062.1| Pseudouridine synthase, Rsu [Shewanella piezotolerans WP3]
          Length = 240

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 67/241 (27%), Positives = 102/241 (42%), Gaps = 14/241 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA--VNVM--STDH----IEVDGV 65
            R++K +A  G  SRR   R+I   +V  N  L         +           + V+G 
Sbjct: 1   MRLAKYLAITGCCSRRAATRLIRDGQVIFNDRLANHVDSVTLIDTPEGQRCQEHVIVNGE 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            ++  E    WL++K   + T             +L  +  R+  VGRLD ++ GLLLLT
Sbjct: 61  LIQAVEAKAYWLFNKA--VGTDSRLLAELPNSLIHLLPVSPRLYPVGRLDKDSHGLLLLT 118

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG L   L  P     + Y V+     D+  L  +  G+  +G+      +T       
Sbjct: 119 NDGELTHQLMHPDFGHSKTYHVQVDRPFDEVFLANMAAGVSYKGVTTLPCTITRLDVDR- 177

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++     +KV  L RIS    QLG LL GS R +S   L + L
Sbjct: 178 ---YEIILTQGLNRQIRRMSHALGFKVIDLKRISIQSLQLGNLLEGSMRPLSSTELADLL 234

Query: 246 G 246
            
Sbjct: 235 A 235


>gi|74317276|ref|YP_315016.1| ribosomal large subunit pseudouridine synthase B [Thiobacillus
           denitrificans ATCC 25259]
 gi|74056771|gb|AAZ97211.1| pseudouridine synthase, Rsu [Thiobacillus denitrificans ATCC 25259]
          Length = 296

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 71/269 (26%), Positives = 117/269 (43%), Gaps = 6/269 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL- 67
                +R+ K +A AG+ SRRE+E  IA+ RV+VNG         V   D ++V G  + 
Sbjct: 29  PEAASERLHKALASAGLGSRREMEEWIAEGRVQVNGETATV-GSKVGPRDVVKVSGRRVY 87

Query: 68  ---RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               +     L  +     +V+        +          S+ I+VGRLD NT+GL++ 
Sbjct: 88  LRFDEKRTRILIYHKSEGEIVSRDDPGGRATVFDALPRLRGSKWIAVGRLDYNTDGLMIF 147

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T  G LA  L  P  +  R Y VR  G++ +D +  L  G+ +               +G
Sbjct: 148 TTSGDLANRLMHPRFEVEREYAVRVLGELTEDMIAELLAGVELDDGPAQLQSCFAAGGEG 207

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           +N W  V ++EG+ RE++++FE     V+RL RI +GP  L   L  G   E+   ++ +
Sbjct: 208 ANRWYRVVIKEGRKREVRRLFEHLGLTVSRLTRIRFGPIVLPPQLRRGQKTELDDDLVAQ 267

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRP 272
            +    +E +       +    T      
Sbjct: 268 VMRWAGMEASPRRKTRGVPDKHTRKPRIR 296


>gi|293115329|ref|ZP_05790945.2| ribosomal small subunit pseudouridine synthase A [Butyrivibrio
           crossotus DSM 2876]
 gi|292810441|gb|EFF69646.1| ribosomal small subunit pseudouridine synthase A [Butyrivibrio
           crossotus DSM 2876]
          Length = 241

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 103/231 (44%), Gaps = 5/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G  SR E++  I +  V +NG  ++ A     +  D +      ++  E 
Sbjct: 6   IRIDKYLADMGAGSRTEIKDDIRKGLVYINGNKVKSAGEKADTLNDEVAYKENIIKYIEF 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      +  T    +   TV D + S    +  VGRLD +TEGLLLLTNDG LA 
Sbjct: 66  EYILLNKPAGVVSATEDRKE--KTVLDIIDSKRKDLFPVGRLDKDTEGLLLLTNDGMLAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V   G +  +   L K GI +       + ++ + +     +   +
Sbjct: 124 ELLSPKKHVDKKYYVETDGLLTDEHRKLFKNGIKVDDEFTAKEAELQILSSGDKGSKAYL 183

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            +REGK  ++K++ E     V  L RIS GP  L   +  G++R ++   +
Sbjct: 184 TIREGKYHQVKRMMEAVGNTVTYLKRISMGPLTLPEDMETGTSRMLTDSEI 234


>gi|50914459|ref|YP_060431.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS10394]
 gi|50903533|gb|AAT87248.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS10394]
          Length = 238

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 56/229 (24%), Positives = 98/229 (42%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +   + 
Sbjct: 1   MRLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQRVTHPKH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + + L      +                       +  VGRLD +TEGL+LLT++G L  
Sbjct: 61  SYIILNKPSGVVSAKKDTNYLTVIDQLAEEDKSPDLYPVGRLDRDTEGLVLLTDNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +  PS    + Y V  +G + +D  +    GI    G      Q+T+       +  ++
Sbjct: 121 RMLHPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADIDQSQASL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R +++  
Sbjct: 181 TISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLTESE 229


>gi|30248036|ref|NP_840106.1| 16S pseudouridylate synthase [Nitrosomonas europaea ATCC 19718]
 gi|30179921|emb|CAD83916.1| possible 16S pseudouridylate synthase [Nitrosomonas europaea ATCC
           19718]
          Length = 243

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 64/244 (26%), Positives = 101/244 (41%), Gaps = 19/244 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
              R+SK+++  GI SRRE +  I Q  V V+G  +      +     I +D        
Sbjct: 2   EKVRLSKLMSARGICSRREADVYIEQGSVYVDGQPVRELGTKIYPWQEIVLDRAAQIRQN 61

Query: 64  -------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
                    P+          Y   I LV   S      +    +P     +   GRLDI
Sbjct: 62  QQVTILLNKPVGYVSGQPEPGYKSAISLVNNDSHFHQDRSSLRFVPQHLKNIAPAGRLDI 121

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +++GLL+ T DG +A+ L    +Q  + Y VR  G + ++ L LL  G+ + G      +
Sbjct: 122 DSQGLLVFTQDGRIAKQLIGEYSQIEKEYLVRVSGNLTREGLALLNHGLQLDGQALKPAR 181

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V+   Q      +   L+EGK R+I+++ E     V  L R+  G  +L  L  G  R +
Sbjct: 182 VSRLNQDQ----LRFILQEGKKRQIRRMCELVGLNVTGLKRVRIGQIRLADLPEGKWRYL 237

Query: 237 SKKI 240
            K  
Sbjct: 238 GKNE 241


>gi|329889172|ref|ZP_08267515.1| ribosomal large subunit pseudouridine synthase F [Brevundimonas
           diminuta ATCC 11568]
 gi|328844473|gb|EGF94037.1| ribosomal large subunit pseudouridine synthase F [Brevundimonas
           diminuta ATCC 11568]
          Length = 252

 Score =  151 bits (381), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 66/242 (27%), Positives = 112/242 (46%), Gaps = 14/242 (5%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +   P R++K + ++G+ SRRE E +IA   V ++G ++  A   +     + ++     
Sbjct: 8   DGPEPVRINKWLGQSGVCSRREAEGLIADGLVSIDGEVVRDAGRKIEPGQTLTLNDTGEA 67

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI----------SVGRLDINT 118
                   L HKP+G V+   +P     V     +                 VGRLD ++
Sbjct: 68  ALAAGVAILLHKPVGYVSGQPEPGKIPAVRLLTTANRVGDGETPARDASLPPVGRLDEDS 127

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLL+L++DG +A+ +  P +   + Y VR  G V + KL  L+ G+ + G      +VT
Sbjct: 128 RGLLMLSSDGVVAKAVIGPQSDLDKEYLVRVAGTVTEAKLTKLRHGLELDGRQLKPARVT 187

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
               +     +   LREG+NR+I+++ E    +V  L RI  GP +LG L  G  R ++ 
Sbjct: 188 QMEPQR----LRFILREGRNRQIRRMCELVGLEVVDLYRIRIGPVKLGDLPEGRWRMLTA 243

Query: 239 KI 240
             
Sbjct: 244 DE 245


>gi|227554937|ref|ZP_03984984.1| pseudouridylate synthase [Enterococcus faecalis HH22]
 gi|256761582|ref|ZP_05502162.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis T3]
 gi|256957315|ref|ZP_05561486.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis DS5]
 gi|257083740|ref|ZP_05578101.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis Fly1]
 gi|257086165|ref|ZP_05580526.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis D6]
 gi|294779203|ref|ZP_06744610.1| pseudouridylate synthase [Enterococcus faecalis PC1.1]
 gi|307270119|ref|ZP_07551437.1| hypothetical protein HMPREF9498_02235 [Enterococcus faecalis
           TX4248]
 gi|312901640|ref|ZP_07760910.1| conserved hypothetical protein [Enterococcus faecalis TX0470]
 gi|227175933|gb|EEI56905.1| pseudouridylate synthase [Enterococcus faecalis HH22]
 gi|256682833|gb|EEU22528.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis T3]
 gi|256947811|gb|EEU64443.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis DS5]
 gi|256991770|gb|EEU79072.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis Fly1]
 gi|256994195|gb|EEU81497.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis D6]
 gi|294453714|gb|EFG22109.1| pseudouridylate synthase [Enterococcus faecalis PC1.1]
 gi|306513554|gb|EFM82168.1| hypothetical protein HMPREF9498_02235 [Enterococcus faecalis
           TX4248]
 gi|311291251|gb|EFQ69807.1| conserved hypothetical protein [Enterococcus faecalis TX0470]
 gi|315027592|gb|EFT39524.1| conserved hypothetical protein [Enterococcus faecalis TX2137]
 gi|315031324|gb|EFT43256.1| conserved hypothetical protein [Enterococcus faecalis TX0017]
 gi|315035355|gb|EFT47287.1| conserved hypothetical protein [Enterococcus faecalis TX0027]
 gi|315166970|gb|EFU10987.1| conserved hypothetical protein [Enterococcus faecalis TX1341]
 gi|315172714|gb|EFU16731.1| conserved hypothetical protein [Enterococcus faecalis TX1346]
 gi|315575276|gb|EFU87467.1| conserved hypothetical protein [Enterococcus faecalis TX0309B]
 gi|315581359|gb|EFU93550.1| conserved hypothetical protein [Enterococcus faecalis TX0309A]
 gi|327534406|gb|AEA93240.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis OG1RF]
          Length = 260

 Score =  151 bits (381), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 68/260 (26%), Positives = 116/260 (44%), Gaps = 3/260 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +     
Sbjct: 1   MRLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLISHKTH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                       +  VGRLD +TEGLLLLT++G L  
Sbjct: 61  VYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            L  P+ +  + Y V+ +G V  +     K GIV+QG       ++T+     + + V +
Sbjct: 121 QLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHVFL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLL 250
            ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L    +
Sbjct: 181 TIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYFFI 240

Query: 251 EEAQVNLDAPIYSSETLVRD 270
           E+ Q +   P        R 
Sbjct: 241 EKQQTSKALPSNLKREEERK 260


>gi|120612927|ref|YP_972605.1| RNA-binding S4 domain-containing protein [Acidovorax citrulli
           AAC00-1]
 gi|120591391|gb|ABM34831.1| RNA-binding S4 domain protein [Acidovorax citrulli AAC00-1]
          Length = 264

 Score =  151 bits (381), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 72/250 (28%), Positives = 105/250 (42%), Gaps = 29/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ SRRE +  IA   V+VNG +     + V  TD IEVD     + ER  
Sbjct: 18  RLNKRMAELGLCSRREADDWIASGWVRVNGQVAA-MGLQVAPTDRIEVDPAARGQQERQA 76

Query: 75  LWLYHKPIGLVT---------------THSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+                 +      +     P     +   GRLDI++ 
Sbjct: 77  TILLHKPMGYVSGQAEDGHTPAVALINPRTHWREDPSRQRFSPPQLRGLAPCGRLDIDSV 136

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ---------VDQDKLNLLKKGIVIQGI 170
           GLL+LT DG +AR L    ++  + Y VR H               +L  L  G+ + G 
Sbjct: 137 GLLVLTQDGRVARHLIGEDSEVEKEYLVRVHYGDIATDVQSAFPAGQLARLCHGLSLDGQ 196

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                +V     +     +   L+EGK R+I+++ E    KV  L RI  G   LG L  
Sbjct: 197 ALKPAKVEWQNPEQ----LRFVLKEGKKRQIRRMCELVGLKVVGLKRIRIGRVVLGNLPV 252

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 253 GQWRYLGPNE 262


>gi|114776453|ref|ZP_01451498.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthase [Mariprofundus ferrooxydans
           PV-1]
 gi|114553283|gb|EAU55681.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthase [Mariprofundus ferrooxydans
           PV-1]
          Length = 289

 Score =  151 bits (381), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 79/249 (31%), Positives = 136/249 (54%), Gaps = 4/249 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P+R+++ +A  G+ SRRE +R I   RV +NG L+E   V V S D + VD   +   + 
Sbjct: 42  PERINRYLAHCGLCSRREADRWIQAGRVSINGQLIEAPGVIVKSGDTVMVDDKLVEPQQG 101

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               LY+KP G + +  D   R  ++D +    +   S+GRLD++TEGLL+LT+DG L R
Sbjct: 102 HTYILYNKPKGQLCSRLDKKKRPLIYDFIDVAPNVQ-SIGRLDMDTEGLLMLTDDGALTR 160

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GIVIQGICYGDM-QVTLDTQKGSNAWVT 190
            L  P+ +  R YR R  G V+ + L  L++ G+ I      D  +VT+D++   + W+ 
Sbjct: 161 ALTHPAAKVPREYRARVAGIVELETLAKLRRGGMDIGRGDTSDAWEVTVDSESAGHTWLN 220

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHL 249
           + +  G+ RE+++  E     V RL+R  +GP +L   +  G+ R +++  +R+     +
Sbjct: 221 IIILRGRWREVRRTLEECGHPVRRLMRTRFGPIKLDEDMPKGTWRALNRGEIRKLRDRVI 280

Query: 250 LEEAQVNLD 258
             +A+ + D
Sbjct: 281 NPDAKTDSD 289


>gi|328951538|ref|YP_004368873.1| pseudouridine synthase Rsu [Marinithermus hydrothermalis DSM 14884]
 gi|328451862|gb|AEB12763.1| pseudouridine synthase Rsu [Marinithermus hydrothermalis DSM 14884]
          Length = 243

 Score =  151 bits (381), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 55/225 (24%), Positives = 96/225 (42%), Gaps = 5/225 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++A  G  +R+EV+R++    V+V+G ++    + +      +EV G  +     
Sbjct: 6   ERIDKILAHLGFGTRKEVKRLLRAGGVRVDGRVVRDPGMKLDPARARLEVAGEVVVWQRH 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + LY     +  T                    ++ VGRLD +TEGLLLLT DG L  
Sbjct: 66  HHVMLYKPAGVVTATRDARHATVLDCLPASLARKDLLPVGRLDRDTEGLLLLTTDGALLH 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  +VY          +      +G+V+        ++ L         V + 
Sbjct: 126 RLTHPRWKVPKVYYAELEQPARPEDAQAFAEGLVLSEGRCLPAELELL---EDPRRVRLV 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
           L EG+  ++K++F     +V  L R++ GP +L   L  G  R +
Sbjct: 183 LWEGRYHQVKRMFAARGNRVTYLKRLAVGPLELDPKLKPGEARAL 227


>gi|190893225|ref|YP_001979767.1| RNA-pseudouridine synthase, ribosomal large subunit B [Rhizobium
           etli CIAT 652]
 gi|190698504|gb|ACE92589.1| RNA-pseudouridine synthase protein, ribosomal large subunit B
           [Rhizobium etli CIAT 652]
          Length = 267

 Score =  151 bits (381), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 70/266 (26%), Positives = 121/266 (45%), Gaps = 12/266 (4%)

Query: 1   MKDKNIVQENFTPQRVS-----------KVIARAGIASRREVERMIAQQRVKVNGILLER 49
           M+D+   Q+     +++           + +++ G  SR + ER+IA+ RV ++G  +  
Sbjct: 1   MRDRRPPQKTRERPKLTADAAGKRVTLPRALSKLGYCSRTQAERLIAESRVSIDGRTVND 60

Query: 50  AAVNVMS-TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
            +  V   T  I VDG+ +    +  L L      + T H      +            +
Sbjct: 61  PSAWVDLVTAKIRVDGLVIAAEAKIYLILNKPRGLVTTRHDPEGRPTVYDCLRDFDIPHL 120

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
             VGRLD  +EGLLL TND   A++L  P T   + Y V+    +D +++  +  GI   
Sbjct: 121 SPVGRLDKASEGLLLFTNDTEFAQILLDPVTHVTKTYHVQIDRVLDDEEIAAMTSGIRHD 180

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           G       V    Q   N+W+ V L EG+NR+I+++ E    +  RL+R++ G  +LG L
Sbjct: 181 GELLTATAVRRLRQGDRNSWIEVELDEGRNRQIRRMLEALGTECLRLVRVAIGGLELGEL 240

Query: 229 LAGSTREVSKKILREQLGPHLLEEAQ 254
             G+ R ++   L+       +E A+
Sbjct: 241 PKGAARALTAAELQALRRSAGMERAR 266


>gi|87119433|ref|ZP_01075330.1| ribosomal large subunit pseudouridine synthase B [Marinomonas sp.
           MED121]
 gi|86164909|gb|EAQ66177.1| ribosomal large subunit pseudouridine synthase B [Marinomonas sp.
           MED121]
          Length = 296

 Score =  151 bits (381), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 86/293 (29%), Positives = 133/293 (45%), Gaps = 6/293 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
           +++ KV+ARAG  SRRE+E  I + RV VNG +       V  TD I++DG  ++  E  
Sbjct: 3   EKLQKVLARAGQGSRREMENRIREGRVLVNGDVAT-LGDRVKVTDTIKLDGYEVKVTEAG 61

Query: 72  --RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             R  +        + T        +           R I+VGRLDINT GLLL T DG 
Sbjct: 62  ASRRVIIYNKPEGEVCTRKDPEGRPTVFDKLPKLRGERWIAVGRLDINTSGLLLFTTDGE 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  PST+  R Y VR  G+++ D +  LKKG+++         +     +G N W 
Sbjct: 122 LANKLMHPSTEIDREYLVRVMGEINDDHIETLKKGVLLDDGMANFTDIVDGGGEGINRWF 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
            V + EG+NRE+++++E    KVNRL R+ +GP  L      G + E+ +  +       
Sbjct: 182 YVCVMEGRNREVRRLWESQGVKVNRLKRVRFGPVFLPSKAKMGRSVEMDEAEVNGLCDLV 241

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            L  A+         S+   +   ++ +  P  F     +  +       K+ 
Sbjct: 242 GLTHAKSAPKTQQQKSDAKRQKGKSMGARKPKGFDWQSSDKPEFKPKKPGKRT 294


>gi|289664226|ref|ZP_06485807.1| pseudouridylate synthase [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 285

 Score =  151 bits (381), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 68/246 (27%), Positives = 116/246 (47%), Gaps = 7/246 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      + +  H  I VDG PL    R 
Sbjct: 39  LARVLSKLGVCSRTEAARWIADGRVSVSARVVRDPEFPIRADQHSSITVDGSPLAGPARC 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L      + T   +    +       +    +  VGRLD  +EGLLL +ND   A  
Sbjct: 99  YLMLNKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAAT 158

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNAW 188
           +  P+T   + Y V+   +    +L  L+ G+V      +G+     +V++  +   NAW
Sbjct: 159 VTDPTTGPDKTYHVQIDCRPSAAQLAQLQAGVVDPDPEGEGMLLRAKRVSVLREGERNAW 218

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + + L EG+NR+I+++    +  V RLIR++ GP  +G L  G+ R +S + +R  L   
Sbjct: 219 LEIVLDEGRNRQIRRLLAAVDIGVLRLIRVAIGPLAMGELCKGAWRMLSAEEVRALLPAP 278

Query: 249 LLEEAQ 254
                 
Sbjct: 279 ASAPDA 284


>gi|152995917|ref|YP_001340752.1| pseudouridine synthase [Marinomonas sp. MWYL1]
 gi|150836841|gb|ABR70817.1| pseudouridine synthase [Marinomonas sp. MWYL1]
          Length = 238

 Score =  151 bits (381), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 51/235 (21%), Positives = 99/235 (42%), Gaps = 12/235 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   +R+E  + I    V VNG ++   A  V   + + ++G  L+  +  
Sbjct: 5   MRLDKFVCKSTELTRKEAVQCIHSGEVCVNGEVVTSEATQVHENNTVLLNGDRLKTRDFR 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +      + +   +       + ++       I+ GRLD +T GL+L+T+DG  +  
Sbjct: 65  YILMNKPAGTVCSNIDEVYPSVFNYLDVDKASELHIA-GRLDADTTGLVLITDDGRWSFN 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI------QGICYGDMQVTLDTQKGSNA 187
           + LPS    +VYRV+    +  ++   L            +       ++ + T K    
Sbjct: 124 ITLPSNDCCKVYRVQLSQAIPAERSGELVTQFKQGLQLQGEQGLTRPAKLDIITPK---- 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V + + EGK  ++K++F     +V  L R   G   L  L  G  R +SK  + 
Sbjct: 180 EVLLTITEGKFHQVKRMFSAVGNRVVGLHREQIGEVYL-DLDVGQWRYLSKSEVE 233


>gi|309798849|ref|ZP_07693110.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           infantis SK1302]
 gi|308117498|gb|EFO54913.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           infantis SK1302]
          Length = 199

 Score =  151 bits (381), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 67/197 (34%), Positives = 108/197 (54%), Gaps = 3/197 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E  
Sbjct: 1   MRINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGVISSVTDDKGRKTVVDLLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGIANKENLRPLTRGVEIDGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFF 208
            + EG+N ++KK  +  
Sbjct: 180 TIHEGRNHQVKKCLKLL 196


>gi|197105098|ref|YP_002130475.1| RNA pseudouridylate synthase [Phenylobacterium zucineum HLK1]
 gi|196478518|gb|ACG78046.1| RNA pseudouridylate synthase [Phenylobacterium zucineum HLK1]
          Length = 272

 Score =  151 bits (381), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 60/241 (24%), Positives = 112/241 (46%), Gaps = 13/241 (5%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP-- 66
           +   PQRV+K +A++G+ SRRE E +IA   V ++G  +  A   ++    + +      
Sbjct: 13  DEAEPQRVNKWLAQSGVCSRREAEALIADGLVSIDGETIADAGRKILPGQTLTLADRAAA 72

Query: 67  -------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
                  +       +    +P  +           +     P   + +  +GRLD ++ 
Sbjct: 73  SLGGFTAVLNKPVGYVSGQPEPGHVPAVRLLTAANLSGEGAAPDARASLPPLGRLDEDSR 132

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+L++DG LA+ +  P +   + Y VR  GQVD+ KL  L+ G+ + G       V++
Sbjct: 133 GLLILSDDGVLAKAVIGPQSDLDKEYVVRVAGQVDERKLARLRHGLELDGRKLKPATVSV 192

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                    +   L+EG+ R+I+++ +    +V  L+R+  GP +LG L  G  R ++ +
Sbjct: 193 IQGN----TLRFVLKEGRKRQIRRMCDLVGLRVVDLLRVRIGPLKLGDLPEGRWRVLTPQ 248

Query: 240 I 240
            
Sbjct: 249 E 249


>gi|188590260|ref|YP_001922453.1| RNA pseudouridine synthase family protein [Clostridium botulinum E3
           str. Alaska E43]
 gi|188500541|gb|ACD53677.1| RNA pseudouridine synthase family protein [Clostridium botulinum E3
           str. Alaska E43]
          Length = 254

 Score =  151 bits (381), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 61/256 (23%), Positives = 101/256 (39%), Gaps = 25/256 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A + I  R+ V   I    VKVNG ++   ++++    D +E  G  +    +
Sbjct: 1   MRLDKFLAESAIGRRKIVRTYIKDGMVKVNGKIITEPSLDINEKLDDVEYLGKKVIHNGK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                      +  T  +     TVFD      + V  VGRLD +TEGLLLLTNDG    
Sbjct: 61  VYYMFNKPAGCVTATRDN--VHKTVFDYFHEDMNGVFHVGRLDKDTEGLLLLTNDGEFEH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDT--------- 181
            +  P     + Y     G  D +    L++GI I          ++ +           
Sbjct: 119 KVMYPEKHVEKTYFFWALGSFDDEDKKQLEEGIFIGNNESLTKPAKIDVHKSGLYKEFKE 178

Query: 182 -------QKGSNAWV---TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLA 230
                  +   +  V    + + EG+  ++K++ +     V  L RIS G  +L   L  
Sbjct: 179 EIPIKNLENKDHQLVVSGYLTISEGQKHQVKRMLKAVGCYVIYLKRISIGGLKLDESLKM 238

Query: 231 GSTREVSKKILREQLG 246
           G  R+++KK +     
Sbjct: 239 GDYRDLTKKEIERIFE 254


>gi|225024981|ref|ZP_03714173.1| hypothetical protein EIKCOROL_01870 [Eikenella corrodens ATCC
           23834]
 gi|224942211|gb|EEG23420.1| hypothetical protein EIKCOROL_01870 [Eikenella corrodens ATCC
           23834]
          Length = 325

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 76/254 (29%), Positives = 120/254 (47%), Gaps = 7/254 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+ K +A +G+ SRRE+E  I    V VNG + +     V   D + V G  ++   
Sbjct: 72  EPVRLQKALAASGVGSRREMEEWIQNGWVTVNGKVAQ-LGDKVQPEDQVLVKGSVIKLKW 130

Query: 72  RTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             RL      Y +   +V+        S       +  SR +++GRLDINT GLL+LT  
Sbjct: 131 PDRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTTS 190

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTLDTQKGSN 186
           G LA     PS +  R Y VR  G++  D++ LL  +G++++       ++     +G N
Sbjct: 191 GELANRFAHPSFEVEREYAVRVLGELGMDEMRLLTSEGVMLEDGLARVERIHSQGGEGVN 250

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
            W  V L+EG+NRE++++FE F   V+RL+R  +GP  L   L  G   E++   +   +
Sbjct: 251 KWYNVVLKEGRNREVRRIFEHFGLTVSRLVRTGFGPIGLPNRLKRGQFYELNAAEVASVM 310

Query: 246 GPHLLEEAQVNLDA 259
               L         
Sbjct: 311 KWADLPLPDSRRRP 324


>gi|149194803|ref|ZP_01871897.1| Pseudouridine synthase, Rsu [Caminibacter mediatlanticus TB-2]
 gi|149134962|gb|EDM23444.1| Pseudouridine synthase, Rsu [Caminibacter mediatlanticus TB-2]
          Length = 256

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 74/256 (28%), Positives = 122/256 (47%), Gaps = 13/256 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+     SRRE +++I   +VKVNG ++   A  V+  D + V+G P++K+ + 
Sbjct: 1   MRLNKFISHHTSFSRREADKLIFDGKVKVNGKVVTNPAYEVLDGDKVAVNGKPVKKSTKY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +Y+KP G + T  D  GR T++D+LP  +   I +GRLD  +EGLL+LT+   +A  
Sbjct: 61  TCIIYNKPRGELVTKKDDRGRKTIYDSLPKKYKHFIPIGRLDFASEGLLILTDSPKVADA 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQ--------VTLDTQK 183
           L       +   R++ +   + +K       I ++G        +          +    
Sbjct: 121 LMKSDLPRVYKLRIKGNITPEIEKAMQEGVEIGVEGAHEKTKQEKIKLKPFYSYQIIKND 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI--- 240
              + + V + EGKNRE+++ F  F   V  L R+SYG   L  L  G TR   K+    
Sbjct: 181 PKYSTLKVAITEGKNRELRRFFAHFGRDVLDLKRLSYGWVALNALPTGKTRYFDKREYKL 240

Query: 241 LREQLGPHLLEEAQVN 256
           L+E L     +    N
Sbjct: 241 LKEFLKERDAKAKNKN 256


>gi|331266782|ref|YP_004326412.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           oralis Uo5]
 gi|326683454|emb|CBZ01072.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           oralis Uo5]
          Length = 241

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 53/232 (22%), Positives = 104/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A+  + SR+ +++ + ++ + V+       + NV +    +   G  ++  E 
Sbjct: 1   MRLDRLLAQEKV-SRKAMKQALLKKEILVDNCPASSLSQNVDTGLQKLVFQGRQIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +  +                   ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLLLHKPNGVVTASKDKKLPTVMDLLPPDIKSYQLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y++  +G +  + +   K GIV          Q+ + +   + +  ++
Sbjct: 120 QLLHPQYHVDKSYQMVVNGPLTSEHIQKFKDGIVFLDGTTCKPAQLEILSSSPTESHASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L R+ +G F L   L  G  R ++ + L 
Sbjct: 180 TISEGKFHQIKKMFLSVGVKVTSLKRVQFGDFTLDPELSEGQFRSLNPEELE 231


>gi|34498841|ref|NP_903056.1| hypothetical protein CV_3386 [Chromobacterium violaceum ATCC 12472]
 gi|34104693|gb|AAQ61050.1| conserved hypothetical protein [Chromobacterium violaceum ATCC
           12472]
          Length = 479

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 70/280 (25%), Positives = 121/280 (43%), Gaps = 8/280 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K+  +      P R+ K ++ +G+ SRRE+E  I    V VNG         V   D +
Sbjct: 199 LKEVRVDHAEIEPVRLQKALSSSGVGSRREMEEWIEAGLVTVNGKKA-SLGDKVGPQDKV 257

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            V G  ++     RL      + +   +VT        +       +  SR +++GRLD+
Sbjct: 258 LVKGDQIKLKWPDRLPRVIMYHKEEGEIVTRDDPEGRVTVFDRLPQAKSSRWVAIGRLDV 317

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NT GLLL+T  G LA  +  PS +  R Y VR  G++  + +  + KG+ ++       +
Sbjct: 318 NTSGLLLITTSGELANRMMHPSFEVEREYSVRVLGELTPEIMKEMTKGVELEDGEARFDR 377

Query: 177 --VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
              T   ++ +N W  V ++EG+NRE++++FE F   V+RL+R+ +G   L   L  G  
Sbjct: 378 IFQTGGQEESANQWYNVVIKEGRNREVRRMFEHFGLTVSRLMRVRFGNIGLPPRLKRGQF 437

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPN 273
            E++   +   +    L                       
Sbjct: 438 YELNAAEVAAVMKWSNLTVTGGKKAGGQRRGSPRKPKAAR 477


>gi|126172935|ref|YP_001049084.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|125996140|gb|ABN60215.1| ribosomal small subunit pseudouridine synthase A [Shewanella
           baltica OS155]
          Length = 246

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 46/231 (19%), Positives = 97/231 (41%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  +   +R   ++ + +  +  +GI+++ +   V     + + G P+      
Sbjct: 18  VRLDKFICESTPLTRSLAKKALHRGDITCDGIVVKDSGFKVTEGMRVCLQGEPIALV-GV 76

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP+  + +  D    S +          +   GRLD +T GL+L+T+DG  +  
Sbjct: 77  RYLMLNKPVDTICSTIDETYPSVLSLVDVPKPETLHIAGRLDADTTGLVLVTSDGQWSHK 136

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y V+    VD   + +   G+ +  +        + +   +     V +
Sbjct: 137 ITSPKKECGKRYLVQLADPVDAGLIAIFAAGVELRGEDGLTKPALLEIIEPQ----LVRL 192

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++K++F      V  L R S G  +L   L  G  R ++ + +
Sbjct: 193 TITEGKYHQVKRMFAAVGNHVQELHRESVGQIELDPALALGEWRYLTAEEI 243


>gi|313105549|ref|ZP_07791817.1| putative pseudouridylate synthase [Pseudomonas aeruginosa 39016]
 gi|310878319|gb|EFQ36913.1| putative pseudouridylate synthase [Pseudomonas aeruginosa 39016]
          Length = 230

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 107/231 (46%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     SRR+ + +IA  R++V+G ++      V     +E+D   L+  +  
Sbjct: 1   MRLDRFLANLPELSRRDAQMLIAGGRLRVDGQVVRDGTHEVRVFSRVELDEQLLQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP+G V+   DP   + +          +   GRLD NT GL+LLTNDG  +R 
Sbjct: 61  RYYMLHKPMGCVSATRDPQHPTVLDLFPEDQRDDLHIGGRLDYNTTGLMLLTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L LP ++  +VY V     +DQ  ++          + +     Q+             +
Sbjct: 121 LTLPGSRRDKVYYVETEAPIDQRYVDAFAAGLHFRFEDLITLPAQLEPI----GPRCARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            L EG+  ++K++F  F+ KV RL R   G   L   L  G+ R ++ + +
Sbjct: 177 TLHEGRYHQVKRMFGHFDNKVLRLHRERMGDICLDPQLPPGAWRPLNAEEI 227


>gi|212636604|ref|YP_002313129.1| pseudouridine synthase Rsu [Shewanella piezotolerans WP3]
 gi|212558088|gb|ACJ30542.1| Pseudouridine synthase, Rsu [Shewanella piezotolerans WP3]
          Length = 230

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 45/232 (19%), Positives = 97/232 (41%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  +   SR   ++ + +  V  NG +++ +   V     I ++G  L+     
Sbjct: 1   MRLDKFICESTSHSRVSAKKALHRGDVTCNGEVVKTSGFKVTDEHEIRLEGEVLKVI-GP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP+  + +  D +  S +          +   GRLD +T GL+L+T DG  +  
Sbjct: 60  RFIMLNKPVDTICSTIDEEYPSVIGLLDVIRPEDLHIAGRLDADTTGLVLITTDGKWSHK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y +     + ++ +     G+ +  +       ++ L           +
Sbjct: 120 ITSPKKECGKRYLLETADPLTEELIGKFATGLQLNNEDGLTKPAKLELL----GTHQARL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++      KV +L R   G  +L  +L  G  R +++  ++
Sbjct: 176 TITEGKYHQVKRMLAAVGNKVTKLHREVVGEIELDSSLELGQWRFLTEAEIK 227


>gi|91214943|ref|ZP_01251915.1| putative ribosomal large subunit pseudouridine synthase
           [Psychroflexus torquis ATCC 700755]
 gi|91186548|gb|EAS72919.1| putative ribosomal large subunit pseudouridine synthase
           [Psychroflexus torquis ATCC 700755]
          Length = 272

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 53/239 (22%), Positives = 107/239 (44%), Gaps = 2/239 (0%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           DK I   +    R++K I+ +G+ SRR+ +  I    V VNG ++     +V   D ++ 
Sbjct: 30  DKQIKNPSA-GMRLNKYISNSGVCSRRDADIYIKSGNVTVNGEVIIEMGHHVKLEDEVKF 88

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG  +    +  + L       VT   +    + +     +  S++  VG+LD +  GL+
Sbjct: 89  DGRRINPEPKAYVLLNKPKSFYVTGSYEKGKLTALDLVQNASKSKLAPVGKLDTSAMGLI 148

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L TNDG LA+ L        ++Y+V     + +  L ++K G  I+G     ++      
Sbjct: 149 LFTNDGTLAKKLSGHKNGIRQIYQVELTKPLRESDLEVIKDGPFIEGSKVK-IEEAAFVD 207

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                 V + LR  +   ++++F+   +++ ++ R+ Y       L  G  R ++++ +
Sbjct: 208 NRPKNIVGLELRSQRAHIVQRIFKKLGYEIEKMDRVIYANLDKKNLPRGHYRHLTRQEV 266


>gi|119947129|ref|YP_944809.1| pseudouridine synthase [Psychromonas ingrahamii 37]
 gi|119865733|gb|ABM05210.1| ribosomal small subunit pseudouridine synthase A [Psychromonas
           ingrahamii 37]
          Length = 230

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 53/231 (22%), Positives = 98/231 (42%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  +   +R + +++I Q R+  +G ++      V+    I  DG  +     T
Sbjct: 1   MRLDKYICESTTMTRSQAKKVIIQGRITSDGTVMRNTGYKVLENTPICFDGNLINVR-GT 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP   + +  D    S +         ++   GRLD +T GL L+T+DG  +  
Sbjct: 60  RYIMLNKPKDFICSTVDEQFPSIINLIKVDKPDQLCIAGRLDADTTGLALITDDGQWSHK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P     + YR      V+Q+ + L K+GI +  + +      + + T       V +
Sbjct: 120 ITSPRRNCSKRYRATLAQPVEQNAVTLFKEGIQLKSENVPCLPATLEILTDN----EVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++K++F      V  L R   G  +L   L  G  R ++   +
Sbjct: 176 TIHEGKYHQVKRMFAAIGNLVVELHREQIGEIKLDTDLKLGEWRYLTTDEV 226


>gi|332971035|gb|EGK10006.1| ribosomal large subunit pseudouridine synthase F [Kingella kingae
           ATCC 23330]
          Length = 243

 Score =  151 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 69/245 (28%), Positives = 109/245 (44%), Gaps = 20/245 (8%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+SK +A   I SRRE +  I Q  VKVNG +       V+  D I++D    ++ 
Sbjct: 2   TEPIRLSKRMAELKICSRREADSYIEQGWVKVNGAVA-VLGQKVLPNDRIDLDKRAHQQQ 60

Query: 71  ERTRLWLYHKPIGLVT---------------THSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            +    L +KP+G V+                 +   G ++     PS    +   GRLD
Sbjct: 61  TQRVTILLNKPVGFVSGQPEKDYRAAIELITESNHWQGDTSRIAFHPSQLRGLAPAGRLD 120

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I++ GLL+LT DG +A+ L    +   + Y VR  G +    L LL  G+ + G      
Sbjct: 121 IDSVGLLVLTQDGRIAKQLIGEQSDSEKEYLVRVKGTLSPQGLALLNHGLSLDGEKLRPA 180

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           +V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R 
Sbjct: 181 KVEWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGALPTGQWRY 236

Query: 236 VSKKI 240
           + +  
Sbjct: 237 LGENE 241


>gi|289668229|ref|ZP_06489304.1| pseudouridylate synthase [Xanthomonas campestris pv. musacearum
           NCPPB4381]
          Length = 240

 Score =  151 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 64/239 (26%), Positives = 105/239 (43%), Gaps = 10/239 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA  G  SRRE +R+I ++RV VNG+     AV V   D + VDG PLR  E  +
Sbjct: 4   RLNKYIAETGFCSRREADRLIGERRVTVNGVSAGTGAV-VGEEDTVLVDGQPLRVREAKK 62

Query: 75  L-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           L             +  T +                 R+  +GRLD ++EGL+L+T++G 
Sbjct: 63  LGGRKHVYIALNKPVGITCTTESSVKGNIVEFVGHEQRIFPIGRLDKDSEGLILMTSNGN 122

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +     +  + Y V  +  V  + L  + +G+ I        +     + G     
Sbjct: 123 IVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRIHNETTLPCRTARIAKFG----F 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR  L   
Sbjct: 179 RIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELRGLLPQR 237


>gi|289663281|ref|ZP_06484862.1| pseudouridylate synthase [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 240

 Score =  151 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 64/236 (27%), Positives = 103/236 (43%), Gaps = 10/236 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA  G  SRRE +R+I ++RV VNG+     AV V   D + VDG PLR  E  +
Sbjct: 4   RLNKYIAETGFCSRREADRLIGERRVTVNGVSAGTGAV-VGEEDTVLVDGQPLRVREAKK 62

Query: 75  L-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           L             +  T +                 R+  +GRLD  +EGL+L+T++G 
Sbjct: 63  LGGRKHVYIALNKPVGITCTTESSVKGNIVEFVGHEQRIFPIGRLDKESEGLILMTSNGN 122

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +     +  + Y V  +  V    L  + +G+ I        +     + G     
Sbjct: 123 IVNEILRAENRHQKEYLVAVNKPVTDQFLRGMARGVRIHNETTLPCRTARIAKFG----F 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR  L
Sbjct: 179 RIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELRGLL 234


>gi|90021564|ref|YP_527391.1| ribosomal small subunit pseudouridine synthase A [Saccharophagus
           degradans 2-40]
 gi|89951164|gb|ABD81179.1| ribosomal small subunit pseudouridine synthase A [Saccharophagus
           degradans 2-40]
          Length = 242

 Score =  151 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 52/242 (21%), Positives = 102/242 (42%), Gaps = 14/242 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     SR EV+R+I  + V V+  +    +  V + + + +DG  +   +  
Sbjct: 1   MRLDKFIANNSSYSRTEVKRLIKNKTVCVDKKITTDPSFTVTNLNTVRIDGEIIEAIKPL 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-----------GRLDINTEGLL 122
            + L      +     +                   +            GRLD++T GL+
Sbjct: 61  YIMLNKPTGYVCANKDNIHSPVVDLITEQHARQSDQTPPKYRAQSLQIAGRLDVDTTGLV 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLT++G     +  P+    + YRV+    +D   + LL +G+++ G     +  T++  
Sbjct: 121 LLTDNGEWNHRVTSPNKACFKRYRVKLEKPLDDAAIKLLSEGVMLHGEKAATLPATVEL- 179

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
             SN  V + ++EG+  ++K++F      V +L R + G  +L   L  G  R ++ + +
Sbjct: 180 -ISNTEVLLSIQEGRFHQVKRMFVKVGTCVVKLHREAIGAIELDTNLKPGQWRHLTNEEI 238

Query: 242 RE 243
             
Sbjct: 239 EA 240


>gi|218893324|ref|YP_002442193.1| putative pseudouridylate synthase [Pseudomonas aeruginosa LESB58]
 gi|218773552|emb|CAW29366.1| probable pseudouridylate synthase [Pseudomonas aeruginosa LESB58]
          Length = 230

 Score =  151 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 108/231 (46%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     SRR+ + +IA  R++V+G ++      V     +E+D   L+  +  
Sbjct: 1   MRLDRFLANLPELSRRDAQMLIAGGRLRVDGQVVRDGTHEVRVFSRVELDEQLLQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP+G V+   DP   + +      +   +   GRLD NT GL+LLTNDG  +R 
Sbjct: 61  RYYMLHKPMGCVSATRDPQHPTVLDLFPEDLRDDLHIGGRLDYNTTGLMLLTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L LP ++  +VY V     +DQ  ++          + +     Q+             +
Sbjct: 121 LTLPGSRRDKVYYVETEAPIDQRYVDAFAAGLHFRFEDLVTLPAQLEPI----GPRCARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            L EG+  ++K++F  F+ KV RL R   G   L   L  G+ R ++ + +
Sbjct: 177 TLHEGRYHQVKRMFGHFDNKVLRLHRERMGDICLDPQLPPGAWRPLNAEEI 227


>gi|257126419|ref|YP_003164533.1| pseudouridine synthase [Leptotrichia buccalis C-1013-b]
 gi|257050358|gb|ACV39542.1| pseudouridine synthase [Leptotrichia buccalis C-1013-b]
          Length = 252

 Score =  151 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 57/247 (23%), Positives = 106/247 (42%), Gaps = 19/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A +GI +R+EV+ ++  ++V VN + ++   ++V    D ++ +   +     
Sbjct: 1   MRLDKFLANSGIGTRKEVKEILKNKKVSVNNVFVKDGKIHVDEEKDIVKYENKIINYKPF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +      +  T            N       +  VGRLDI+TEGL+LLTNDG L+ 
Sbjct: 61  VYIMMNKPAGVISATEDSHHKTVIDLLNDEYRTYDIFPVGRLDIDTEGLILLTNDGILSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN----- 186
            L  P     + Y V+    + +D +  L+ GI + +     + +V +            
Sbjct: 121 NLLSPKKHVDKKYYVKITKSLSEDDIKTLENGIKLEENFITKNAKVEIICNNSEKESEDF 180

Query: 187 -----------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG-PFQLGTLLAGSTR 234
                        V + + EGK  ++K++F+    +V  L R+  G       L  G  R
Sbjct: 181 DFGENENNKNENSVYITISEGKFHQVKRMFKAVGNEVLYLKRVKMGNLLLDENLELGGYR 240

Query: 235 EVSKKIL 241
           E+++K L
Sbjct: 241 ELTQKEL 247


>gi|152999616|ref|YP_001365297.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|151364234|gb|ABS07234.1| pseudouridine synthase [Shewanella baltica OS185]
          Length = 256

 Score =  151 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 54/230 (23%), Positives = 102/230 (44%), Gaps = 8/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +       R+ V  ++   RV+V+G++++     V    HI++D   L+      
Sbjct: 28  RLDRYLCTQLHTHRKAVRELLLSGRVRVDGLIVKDMDRQVDEFSHIQLDEHILQANAPVY 87

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L+     +V+   D   ++ +          +   GRLD+N+ GLLLLTND   +  L
Sbjct: 88  VMLHKPIG-VVSATKDIQHKTVIDLLDCEARDELHIAGRLDLNSSGLLLLTNDSRWSDAL 146

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTVG 192
             P+ +  +VYRV     + ++ +    +G+    + I     ++ +     +     V 
Sbjct: 147 MSPTHKVDKVYRVTLANPITEEYIAAFAEGMYFGFEDITTQPAKLVILADNVA----EVT 202

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           L EGK  +IK++F  F   V  L R+S G   L   L  G +R ++   +
Sbjct: 203 LHEGKYHQIKRMFGRFRNPVVGLHRLSIGDIVLDEKLAPGESRALTAAEV 252


>gi|86748296|ref|YP_484792.1| pseudouridine synthase Rsu [Rhodopseudomonas palustris HaA2]
 gi|86571324|gb|ABD05881.1| Pseudouridine synthase, Rsu [Rhodopseudomonas palustris HaA2]
          Length = 784

 Score =  151 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 143/325 (44%), Positives = 201/325 (61%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           ++ T  R++KV+ARAG+ SRR+ E  + + RV VNG++++  A++VM +D I VDG PL 
Sbjct: 458 DDKTGDRIAKVVARAGLCSRRDAETWVTEGRVAVNGLVIDSPALDVMPSDVITVDGKPLP 517

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ERTRL+LYHKP GL+TTH+DP+GR TVFDNLP    R+IS+GRLD NTEGLLLLTNDG
Sbjct: 518 ERERTRLFLYHKPRGLMTTHADPEGRPTVFDNLPEDLPRLISIGRLDFNTEGLLLLTNDG 577

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GLAR LELP T WLR YRVR HG+V Q +L+ LK GI + G+ YG+++  L+  +G+N W
Sbjct: 578 GLARALELPETGWLRRYRVRAHGEVTQAQLDELKNGIEVDGVKYGEIEAKLERDQGANVW 637

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +   +REGKNRE++ V      +VNRLIR+SYGPFQL  +  G   EV  ++LREQLG  
Sbjct: 638 LVFAIREGKNREVRNVLAHLGLEVNRLIRVSYGPFQLLEIEEGEVEEVKTRVLREQLGDK 697

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
           +++ A  +   P  S           ++         KK  +++  +  +K     V R 
Sbjct: 698 IIQLAGADFGGPSPSEARPKPRPGRPVAAAEAAPAPKKKAPTKRGAVEDRKGRKVKVERT 757

Query: 309 NLASNVWMAKGIHSSFLSDSGQREE 333
               +  + +G    +         
Sbjct: 758 GSGGDRGLTRGPARRYHGKREPAPR 782


>gi|94311676|ref|YP_584886.1| ribosomal small subunit pseudouridine synthase A [Cupriavidus
           metallidurans CH34]
 gi|93355528|gb|ABF09617.1| 16S rRNA pseudouridylate 516 synthase [Cupriavidus metallidurans
           CH34]
          Length = 238

 Score =  151 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 50/228 (21%), Positives = 87/228 (38%), Gaps = 4/228 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTR 74
           + +++   G  +RR    ++A   V+VNG L E            + VDG       +  
Sbjct: 5   LDRILQSQGFGTRRYCGDLVAAGLVEVNGELCEDPGARFEVDGLRLMVDGEEWLACTKAY 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        +              +P     V +VGRLD +T GLLLLT+DG      
Sbjct: 65  VMLNKPTGYECSQRPRHHPSVYNLLPVPLRQREVQAVGRLDHDTTGLLLLTDDGQFIHAQ 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  Q  ++Y V     V  +++  L+ G+ +            +     +  + + L 
Sbjct: 125 TSPKKQVPKIYEVTTFDPVTPEQVEALRTGVKLDDEPAPIAADACEATGERS--LRLTLL 182

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           +GK  ++K++       V  L R + G   L   L  G  R ++ + L
Sbjct: 183 QGKYHQVKRMVAAVGNHVTALHRSAIGGLVLDPALGPGEWRWLTPEDL 230


>gi|284039270|ref|YP_003389200.1| RNA-binding S4 domain protein [Spirosoma linguale DSM 74]
 gi|283818563|gb|ADB40401.1| RNA-binding S4 domain protein [Spirosoma linguale DSM 74]
          Length = 638

 Score =  151 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 105/232 (45%), Gaps = 2/232 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N    R+++ IA +G+ SRRE + +IA   + VNG ++      V   D ++     L  
Sbjct: 401 NDGTTRLNRFIANSGVCSRREADELIAHGDISVNGKIVTEMGYKVKEGDTVKYGTKVLNP 460

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L      + TT    + ++ +     +   R+  VGRLD NT GLLL+TNDG 
Sbjct: 461 ERFVYVLLNKPKDYITTTEDPEERKTVMELVADAGKFRMYPVGRLDRNTTGLLLITNDGE 520

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  PS    ++Y+V     +  +    +KKGI ++          +         V
Sbjct: 521 LADKLTHPSNNIRKIYQVELDKPITDEHFEAIKKGIELEDGPIKPD--AISIVTPDAYVV 578

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + +  G+NR ++++FE F ++V +L R +Y       L  G  R +  K +
Sbjct: 579 GIEIHSGRNRIVRRIFESFGYEVTKLDRTTYAGLTKKELPRGKWRFLDPKEV 630


>gi|307706267|ref|ZP_07643081.1| conserved hypothetical protein [Streptococcus mitis SK321]
 gi|307618358|gb|EFN97511.1| conserved hypothetical protein [Streptococcus mitis SK321]
          Length = 241

 Score =  151 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 55/232 (23%), Positives = 108/232 (46%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  + SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKV-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDQIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                      ++ ++GRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKELPTVMDLLPPDIQSDKLYALGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V+ +G +  D + + +KGI  + G      ++ +     S++  ++
Sbjct: 120 QLLHPQYHVDKTYQVQVNGLLTPDHIQVFQKGIVFLDGTVCKPARLKILAASPSHSQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++KK+F     KV  L RI +G F L   L  G+ R +++K L+
Sbjct: 180 TISEGKFHQVKKMFLSVGVKVTSLKRIQFGDFTLKPDLAEGNYRPLNQKELQ 231


>gi|94994641|ref|YP_602739.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS10750]
 gi|94548149|gb|ABF38195.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS10750]
          Length = 238

 Score =  151 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 55/229 (24%), Positives = 97/229 (42%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +   + 
Sbjct: 1   MRLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQRVTHPKH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + + L      +                       +  VGRLD +TEGL+LLT++G L  
Sbjct: 61  SYIILNKPSGVVSAKKDTNYLTVIDQLAEEDKSPDLYPVGRLDRDTEGLVLLTDNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V  +G + +D  +    GI    G      Q+T+       +  ++
Sbjct: 121 RMLHPIHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQSQASL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R +++  
Sbjct: 181 TISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLTESE 229


>gi|120599941|ref|YP_964515.1| pseudouridine synthase [Shewanella sp. W3-18-1]
 gi|146292123|ref|YP_001182547.1| pseudouridine synthase [Shewanella putrefaciens CN-32]
 gi|120560034|gb|ABM25961.1| pseudouridine synthase [Shewanella sp. W3-18-1]
 gi|145563813|gb|ABP74748.1| pseudouridine synthase [Shewanella putrefaciens CN-32]
          Length = 236

 Score =  151 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 57/230 (24%), Positives = 103/230 (44%), Gaps = 8/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++      R+ V  ++   RV+V+G +++     V    HI++D   L+      
Sbjct: 7   RLDRYLSAKMQMPRKLVRDLLLSGRVQVDGQIVKEMDRQVDEFSHIQLDDQVLQANT-PV 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             + HKP+G+V+   D   ++ +          +   GRLD+N+ GLLLLTND   +  L
Sbjct: 66  YMMLHKPVGVVSATKDNQHKTVIDLLDNEYRHELHIAGRLDLNSSGLLLLTNDSRWSEAL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
             P+ +  +VYRV     +  D +    +      + I     ++ +      +    V 
Sbjct: 126 MSPTEKVDKVYRVTLANPLTHDYVTAFAEGMYFGFEDITTQPAKLVIL----DSHLAEVT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           L+EGK  +IK++F  F   V  L R+S G   L   L  G +R ++   +
Sbjct: 182 LKEGKYHQIKRMFGRFRNPVIGLHRLSIGDIVLDEQLQPGESRTLTAAEI 231


>gi|126173257|ref|YP_001049406.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|125996462|gb|ABN60537.1| pseudouridine synthase [Shewanella baltica OS155]
          Length = 256

 Score =  151 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 53/230 (23%), Positives = 100/230 (43%), Gaps = 8/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +       R+ V  ++   RV V+G++++     V     I++D   L+      
Sbjct: 28  RLDRYLCSQLHTHRKAVRELLLSGRVCVDGLIVKDMDRQVDEFSRIQLDEQILQANAPVY 87

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L+     +V+   D   ++ +          +   GRLD+N+ GLLLLTND   +  L
Sbjct: 88  VMLHKPIG-VVSATKDTQHKTVIDLLDCEARDELHIAGRLDLNSSGLLLLTNDSRWSDAL 146

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTVG 192
             P+ +  +VYRV     + ++ +    +G+    + I     ++ +     +     V 
Sbjct: 147 MSPTHKVDKVYRVTLANPITEEYIAAFAEGMYFGFEDITTQPAKLVILADNVA----EVT 202

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           L EGK  +IK++F  F   V  L R+S G   L   L  G +R ++   +
Sbjct: 203 LHEGKYHQIKRMFGRFRNPVVGLHRLSIGDIVLDEKLAPGESRALTVAEV 252


>gi|256379430|ref|YP_003103090.1| pseudouridine synthase [Actinosynnema mirum DSM 43827]
 gi|255923733|gb|ACU39244.1| pseudouridine synthase [Actinosynnema mirum DSM 43827]
          Length = 246

 Score =  151 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 75/237 (31%), Positives = 117/237 (49%), Gaps = 1/237 (0%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDG 64
           +        R+ KV+A+AGIASRR  E +I   RV+V+G ++      +      + VDG
Sbjct: 1   MSDPGSEGVRLQKVLAKAGIASRRVAEELIELGRVQVDGEVVREQGRRIDPDKAVVHVDG 60

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
           V +   E     + +KP G+++T  D   R  V D L +   R+  VGRLD +TEGLLL+
Sbjct: 61  VRVVLQEDVVTLVLNKPRGMLSTMHDDAHRPCVGDLLVNRKERLFHVGRLDADTEGLLLV 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG LA  L  PS +  + Y     G + +D    L+ GI ++          L +   
Sbjct: 121 TNDGDLAHRLMHPSYEVPKTYLAEVPGPIPRDLGKRLRSGIELEDGPVKVDSFKLISSLP 180

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             A V V L EG+   ++++ E     V  L+R + G  +LG    GS R ++++ +
Sbjct: 181 GRALVEVVLHEGRKHIVRRLLEAVGHPVQTLVRTAVGEVRLGNQRPGSLRVLNRQEV 237


>gi|87199318|ref|YP_496575.1| pseudouridine synthase, Rsu [Novosphingobium aromaticivorans DSM
           12444]
 gi|87134999|gb|ABD25741.1| Pseudouridine synthase, Rsu [Novosphingobium aromaticivorans DSM
           12444]
          Length = 270

 Score =  151 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 104/229 (45%), Positives = 142/229 (62%), Gaps = 4/229 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K++ARAGIASRREVERMI + RVK+   ++   A  + S   + VDG P+    
Sbjct: 27  EGDRIAKLLARAGIASRREVERMIEEGRVKIGDEVVTTPATLLTSLKGVSVDGKPVAPMA 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTND 127
             RL+ +HKP GL+T   DP GR T++  L +   +    V+ VGRLD+NTEGLLL+TND
Sbjct: 87  PPRLFRFHKPSGLITAERDPTGRPTIYTALRNALPQGTPRVMPVGRLDVNTEGLLLMTND 146

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L R LELPST   R YR R  G + Q +L  L +GI I G+ YG +   L+   G N 
Sbjct: 147 GELKRALELPSTGIPRTYRARTFGDISQARLEELMEGIEIDGVRYGSINANLERSAGRNK 206

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           W+ + L EGKNRE+++V E    +V+RL+R  YGPF+L  L  G+  E+
Sbjct: 207 WIELTLTEGKNREVRRVLEHLGLQVSRLLRTKYGPFELADLPRGAAEEI 255


>gi|163750021|ref|ZP_02157265.1| hypothetical ribosomal small subunit pseudouridine synthase A
           [Shewanella benthica KT99]
 gi|161330295|gb|EDQ01276.1| hypothetical ribosomal small subunit pseudouridine synthase A
           [Shewanella benthica KT99]
          Length = 239

 Score =  151 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 51/234 (21%), Positives = 101/234 (43%), Gaps = 12/234 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   +R E   +I   +V+VNGI++      V   + I + G  L      
Sbjct: 1   MRLDKFLCKSTDFTRVESIDLIEAGKVRVNGIVIITPQTQVHENNSIMLSGQRLVARPSR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+      + ++ D D  S +          +   GRLD +T GLLLLT+DG  +  
Sbjct: 61  YIMLHKPI-NTLCSNVDGDYPSVMNYIHMDRAEDLHITGRLDADTTGLLLLTDDGRWSFN 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLN----LLKKGIVIQGIC--YGDMQVTLDTQKGSNA 187
           +  P     + YRV     ++++ ++      ++G+ +QG        ++ +     +  
Sbjct: 120 IINPKYHCEKTYRVTLRDPIEEEDIDELVSRFEQGLQLQGEKSLTLAAKLEVI----APH 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V + L EG+  ++K++F     +V  L R   G   L  +  G  R +++  +
Sbjct: 176 QVLLTLSEGRYHQVKRMFFTVGNRVVGLHRQQVGKLSL-DIELGEWRYLTEDEV 228


>gi|325920712|ref|ZP_08182618.1| pseudouridine synthase family protein [Xanthomonas gardneri ATCC
           19865]
 gi|325548764|gb|EGD19712.1| pseudouridine synthase family protein [Xanthomonas gardneri ATCC
           19865]
          Length = 240

 Score =  151 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 66/241 (27%), Positives = 106/241 (43%), Gaps = 14/241 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---- 70
           R++K IA  G  SRRE +R+I ++RV VNG+     AV V   D + VDG PLR      
Sbjct: 4   RLNKYIAETGFCSRREADRLIGERRVTVNGVPAGTGAV-VGEEDTVLVDGQPLRTRAASK 62

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               +      +KP+G+  T                   R+  VGRLD  +EGL+L+T++
Sbjct: 63  PGGRKHVYIALNKPVGITCTTESSV--KGNIVEFVGHEQRIFPVGRLDKESEGLILMTSN 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +     +  + Y V  +  V  + L  + +G+ I        +     + G   
Sbjct: 121 GNIVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRIHNETTLPCRTARIAKFG--- 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR  L  
Sbjct: 178 -FRIVLEQGLNRQIRLMASEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELRGLLPQ 236

Query: 248 H 248
            
Sbjct: 237 R 237


>gi|322833321|ref|YP_004213348.1| pseudouridine synthase [Rahnella sp. Y9602]
 gi|321168522|gb|ADW74221.1| pseudouridine synthase [Rahnella sp. Y9602]
          Length = 439

 Score =  151 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 89/302 (29%), Positives = 131/302 (43%), Gaps = 8/302 (2%)

Query: 2   KDKNIVQENF-TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDH 59
           K KN +       +++ KV+ARAG  SRREVE MI   RV V+G +      V V     
Sbjct: 138 KPKNALDSTEGQSEKLQKVLARAGHGSRREVEAMIQAGRVSVDGKISTLGDRVEVTGGTK 197

Query: 60  IEVDGVPLRKAERT-----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
           I +DG  L   E        L  Y     L T +      +          SR I+VGRL
Sbjct: 198 IRLDGHVLSVMESQDTVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKMRGSRWIAVGRL 257

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D+NT GLLL T DG LA  L  PS +  R Y VR  GQVD +K+  L +G+ ++      
Sbjct: 258 DVNTSGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDEKIKQLSRGVQLEDGPAAF 317

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
             +     +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G  
Sbjct: 318 RSIKFQGGEGLNQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDLNLPKGLPRGGY 377

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           +E+    +        + E  V+          +  ++     +        ++ +    
Sbjct: 378 KELDLPDINYLRTLVDMTEETVSKLPVERDRRRVKANQIRRAVKRHTQVAPTRRTTGPAK 437

Query: 294 GL 295
             
Sbjct: 438 RG 439


>gi|328951588|ref|YP_004368923.1| pseudouridine synthase Rsu [Marinithermus hydrothermalis DSM 14884]
 gi|328451912|gb|AEB12813.1| pseudouridine synthase Rsu [Marinithermus hydrothermalis DSM 14884]
          Length = 240

 Score =  151 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 76/225 (33%), Positives = 113/225 (50%), Gaps = 9/225 (4%)

Query: 12  TPQRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              R+ K +A+AG+AS RR+ E +I   RV +NG +       V   D + VDG P+   
Sbjct: 2   EAIRLQKYLAQAGVASSRRKAEALIRAGRVTINGQVAA-LGAKVTPGDEVCVDGRPVAPT 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            R  +   HKP G+ TT  D     TVF+ L      + +VGRLD ++EGLLLLTNDG L
Sbjct: 61  ARRVVLALHKPPGVTTTRRDRFAERTVFE-LVPAIPGLHTVGRLDRDSEGLLLLTNDGRL 119

Query: 131 ARVLELPSTQWLRVYR-VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            + L  P     +VYR     G+V    L  L+KG+ ++      ++             
Sbjct: 120 TQRLTHPRYGVPKVYRVWTAKGEVPPFILKRLEKGVRLEDGPARALKARPKVGGCV---- 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L EG+ RE++++     + V RL+R+  GP +LG L  G+ R
Sbjct: 176 -LTLAEGRKREVRRMLRAVGYPVVRLLRVKIGPIRLGGLKPGAWR 219


>gi|108804279|ref|YP_644216.1| ribosomal large subunit pseudouridine synthase B [Rubrobacter
           xylanophilus DSM 9941]
 gi|108765522|gb|ABG04404.1| ribosomal large subunit pseudouridine synthase B [Rubrobacter
           xylanophilus DSM 9941]
          Length = 236

 Score =  151 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 72/231 (31%), Positives = 110/231 (47%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE 71
            R+   +AR+G A SRR+ E MI   RV+VNG +       V  + D + +DG  +    
Sbjct: 4   VRLQAFLARSGAAPSRRKAEEMIRAGRVRVNGRVA-SLGERVDPSSDRVSLDGRRVEPPS 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               +  HKP G +TT  D  GR TV   L      ++ VGRLD +T GLLLLTNDG LA
Sbjct: 63  GYAYYALHKPRGYLTTMRDDFGRRTVAS-LMPRIPGLVPVGRLDRDTSGLLLLTNDGRLA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  PS++  + Y +   G   Q+ L  L  G  ++       +++   +        +
Sbjct: 122 HRIAHPSSRVEKEYELVVRGDPPQEALRRLAAGPTLEDGPMLPPRLSHLRRGPRATTFHL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EG+ R I++       ++  L R+  GP  LG L  G  R +S++ L 
Sbjct: 182 TIHEGRKRIIRRACAATGLELLSLRRVRVGPVLLGDLAPGRYRPLSEEELE 232


>gi|241206129|ref|YP_002977225.1| pseudouridine synthase [Rhizobium leguminosarum bv. trifolii
           WSM1325]
 gi|240860019|gb|ACS57686.1| pseudouridine synthase [Rhizobium leguminosarum bv. trifolii
           WSM1325]
          Length = 268

 Score =  150 bits (379), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 67/240 (27%), Positives = 113/240 (47%), Gaps = 1/240 (0%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTRLW 76
           + +++ G  SR + ER+IA+ RV V+G  +  A+  V  +T  I +DG+ +    +  L 
Sbjct: 29  RALSKLGYCSRTQAERLIAENRVAVDGRTVSDASAWVDLATASISIDGLVIAAEAKIYLM 88

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L      + T H      +            +  VGRLD  +EGLLL TND   A++L  
Sbjct: 89  LNKPRGLVTTRHDPEGRPTVYDCLRDFDIPHLSPVGRLDKASEGLLLFTNDTEFAQILLD 148

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
           P T   + Y V+    +D + +  +  GI   G            Q   N+W+ V L EG
Sbjct: 149 PVTHVTKTYHVQIDRIMDDEDIAAMTAGIRHDGELLTATAARRLRQGDRNSWIEVELDEG 208

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVN 256
           +NR+I+++ E    +  RL+R++ G  +LG L  G+ R +++  L+       +E  + N
Sbjct: 209 RNRQIRRMLEALGTECLRLVRVAIGGLELGELPKGAVRALTEPELQALRRKTGMERTRRN 268


>gi|315641811|ref|ZP_07896815.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           italicus DSM 15952]
 gi|315482486|gb|EFU73025.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           italicus DSM 15952]
          Length = 240

 Score =  150 bits (379), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 75/233 (32%), Positives = 116/233 (49%), Gaps = 5/233 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
            R+ KVI      SR+E++R+ A+  V+++G ++   + NV S  H + VDG  +   E 
Sbjct: 1   MRIDKVIETQLHTSRKEMKRLFAKGLVQIDGEIMRNQSFNVDSHLHCLTVDGQVVEWYE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLA 131
            R WL +KP G VT + D    +               +VGRLD +TEGL+L+T +G L 
Sbjct: 60  -RYWLMNKPAGYVTANHDKVVPTIFDLFATDDLVAGLYAVGRLDRDTEGLVLVTTNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVT 190
             L  P+ +  + Y VR + ++ +  +    +GIV  G       Q+ L +     +   
Sbjct: 119 YQLLHPTKKVDKKYSVRVNARLTEKDVQAFSEGIVFHGGTRCLPAQLLLKSCHDQESEAE 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           V L EGK  ++KK+F     KV  L RIS+GP +L TL  G  R ++K  L  
Sbjct: 179 VVLSEGKFHQVKKMFLACGKKVTFLKRISFGPLELKTLPVGEYRSLTKHELEA 231


>gi|19746361|ref|NP_607497.1| 16S pseudouridylate synthetase [Streptococcus pyogenes MGAS8232]
 gi|19748557|gb|AAL97996.1| putative 16S pseudouridylate synthetase [Streptococcus pyogenes
           MGAS8232]
          Length = 254

 Score =  150 bits (379), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 99/232 (42%), Gaps = 2/232 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
            T  R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +  
Sbjct: 14  TTNMRLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQRVTH 73

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + + + L      +                       +  VGRLD +TEGL+LLT++G 
Sbjct: 74  PKHSYIILNKPSGVVSAKKDTNYLTIIDQLAEEDKSPDLYPVGRLDRDTEGLVLLTDNGP 133

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAW 188
           L   +  PS    + Y V  +G + +D  +    GI    G      Q+T+       + 
Sbjct: 134 LGFRMLHPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQSQ 193

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            ++ + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R +++  
Sbjct: 194 ASLTISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLTESE 245


>gi|307704494|ref|ZP_07641403.1| conserved hypothetical protein [Streptococcus mitis SK597]
 gi|307621963|gb|EFO00991.1| conserved hypothetical protein [Streptococcus mitis SK597]
          Length = 241

 Score =  150 bits (379), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 55/232 (23%), Positives = 104/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  + SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKV-SRKAMKQALLKGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                L     ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKKLPTVMDLLPLDIQSDKLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPARLEILSASPSLSRASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++KK+F     KV  L R+ +G F L   L  G  R ++ + L 
Sbjct: 180 TISEGKFHQVKKMFLSIGVKVTSLKRVQFGDFTLDTELTEGHYRPLNPEELE 231


>gi|256617696|ref|ZP_05474542.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis ATCC 4200]
 gi|256854328|ref|ZP_05559692.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis T8]
 gi|257089238|ref|ZP_05583599.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis CH188]
 gi|256597223|gb|EEU16399.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis ATCC 4200]
 gi|256709888|gb|EEU24932.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis T8]
 gi|256998050|gb|EEU84570.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis CH188]
 gi|315030512|gb|EFT42444.1| conserved hypothetical protein [Enterococcus faecalis TX4000]
 gi|323480003|gb|ADX79442.1| conserved hypothetical protein [Enterococcus faecalis 62]
          Length = 260

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 68/260 (26%), Positives = 116/260 (44%), Gaps = 3/260 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +     
Sbjct: 1   MRLDKLLEELQFGSRKTVKRLIRGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLISHKTH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                       +  VGRLD +TEGLLLLT++G L  
Sbjct: 61  VYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            L  P+ +  + Y V+ +G V  +     K GIV+QG       ++T+     + + V +
Sbjct: 121 QLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHVFL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLL 250
            ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L    +
Sbjct: 181 TIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYFFI 240

Query: 251 EEAQVNLDAPIYSSETLVRD 270
           E+ Q +   P        R 
Sbjct: 241 EKQQTSKALPSNLKREEERK 260


>gi|268678707|ref|YP_003303138.1| RNA-binding S4 domain protein [Sulfurospirillum deleyianum DSM
           6946]
 gi|268616738|gb|ACZ11103.1| RNA-binding S4 domain protein [Sulfurospirillum deleyianum DSM
           6946]
          Length = 261

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 75/260 (28%), Positives = 123/260 (47%), Gaps = 19/260 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K+I+     SRRE + +I    VKV+G +++  +  V   + IE++G  L +  
Sbjct: 2   ELTRLNKMISHNTHYSRREADELIKAGHVKVDGNVVQDLSTQVSFKNKIELNGKALFEKH 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              + +YHK  G + +  D  GR T++D LPS F+  +SVGRLD  +EGLLLL +   + 
Sbjct: 62  GYSVIVYHKQKGELVSKKDDRGRKTIYDTLPSKFAHYLSVGRLDFASEGLLLLCDSPSVV 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQV 177
             L        RVY V+ +G V       +++G+ ++                    +  
Sbjct: 122 SALMHGD--LERVYYVKINGLVSPAMEKAMQEGLSLEDARRGGHAKSEIHAMDFAPFVNY 179

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +     + + + V + EGKNRE+++ F +F+  V  L R+SYG   LG L  G  R  S
Sbjct: 180 RIIKNSPTFSTIKVTINEGKNRELRRFFGYFDVDVVDLKRVSYGKIDLGMLKPGKHRFFS 239

Query: 238 KKI---LREQLGPHLLEEAQ 254
                 LR+ L     E+  
Sbjct: 240 ASEYTALRDYLEYVKKEQGN 259


>gi|326318971|ref|YP_004236643.1| pseudouridine synthase Rsu [Acidovorax avenae subsp. avenae ATCC
           19860]
 gi|323375807|gb|ADX48076.1| pseudouridine synthase Rsu [Acidovorax avenae subsp. avenae ATCC
           19860]
          Length = 347

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 72/250 (28%), Positives = 105/250 (42%), Gaps = 29/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ SRRE +  IA   V+VNG +     + V  TD IEVD     + ER  
Sbjct: 101 RLNKRMAELGLCSRREADDWIASGWVRVNGQVAA-MGLQVAPTDRIEVDPAARGQQERQV 159

Query: 75  LWLYHKPIGLVT---------------THSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+                 +      +     P     +   GRLDI++ 
Sbjct: 160 TILLHKPMGYVSGQAEDGHTPAVALINPRTHWREDPSRQRFSPPQLRGLAPCGRLDIDSV 219

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHG---------QVDQDKLNLLKKGIVIQGI 170
           GLL+LT DG +AR L    ++  + Y VR H               +L  L  G+ + G 
Sbjct: 220 GLLVLTQDGRVARHLIGEDSEVEKEYLVRVHYGDVATDVQSVFPAAQLARLCHGLSLDGQ 279

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                +V     +     +   L+EGK R+I+++ E    KV  L RI  G   LG L  
Sbjct: 280 ALKPAKVDWQNPEQ----LRFVLQEGKKRQIRRMCELVGLKVVGLKRIRIGRVVLGNLPV 335

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 336 GQWRYLGPNE 345


>gi|116048646|ref|YP_792554.1| putative pseudouridylate synthase [Pseudomonas aeruginosa
           UCBPP-PA14]
 gi|115583867|gb|ABJ09882.1| putative pseudouridylate synthase [Pseudomonas aeruginosa
           UCBPP-PA14]
          Length = 230

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 107/231 (46%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     SRR+ + +IA  R++V+G ++      V     +E+D   L+  +  
Sbjct: 1   MRLDRFLANLPELSRRDAQMLIAGGRLRVDGQVVRDGTHEVRVFSRVELDEQLLQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP+G V+   DP   + +          +   GRLD NT GL+LLTNDG  +R 
Sbjct: 61  RYYMLHKPMGCVSATRDPQHPTVLDLLPEDQRDDLHIGGRLDYNTTGLMLLTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L LP ++  +VY V     +DQ  ++          + +     Q+             +
Sbjct: 121 LTLPGSRRDKVYYVETEAPIDQRYVDAFAAGLHFRFEDLITLPAQLEPI----GPRCARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            L EG+  ++K++F  F+ KV RL R   G   L   L  G+ R ++ + +
Sbjct: 177 TLHEGRYHQVKRMFGHFDNKVLRLHRERMGDICLDPQLPPGAWRPLNAEEI 227


>gi|51922071|gb|AAU14148.1| rluB [Mycoplasma mobile 163K]
          Length = 235

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 73/240 (30%), Positives = 115/240 (47%), Gaps = 6/240 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R+ K+I++AGI+SRR  E +I ++RVK+NG++ +         D I VD   +   E
Sbjct: 2   EKIRIQKLISQAGISSRRAAEDLILKKRVKINGVIAK-IGDKASLEDVILVDEKVIS-KE 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               +L +KP  +VTT  D   RS + D +     ++  VGRLD +T G+++LTNDG  A
Sbjct: 60  EKVYYLLNKPKNVVTTLKDNFNRSIITDFIDEKKYKIFPVGRLDYDTTGIIILTNDGETA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P  +  R+Y V    ++  +++  L    V         +   +  K SN    +
Sbjct: 120 NKLLHPKYEIPRIYEVIIDKELSLEEIKYLNSQEVFLNSK----KSFQEVSKISNYKYKI 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G    IKK+FE    KV  L R  Y  F L  L  G+ R+++K  +   L     +
Sbjct: 176 KLHQGSYHHIKKLFEIVGKKVKDLNRTEYAFFNLENLSIGNYRKLNKHEIDRLLNFVKNK 235


>gi|225448976|ref|XP_002270186.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 393

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 77/258 (29%), Positives = 125/258 (48%), Gaps = 18/258 (6%)

Query: 4   KNIVQENFT--PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHI 60
           +    ENF   PQR+SKV+A AG+ASRR  E +I + RV VNG +       V    D I
Sbjct: 131 RRFYNENFRDPPQRLSKVLAAAGVASRRNSEELIFEGRVTVNGSVCNTPQTRVDPARDMI 190

Query: 61  EVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----------- 108
            V+G  L K          +KP G + +  + + +S +      + S             
Sbjct: 191 YVNGNRLPKKLPPKVYLALNKPKGYICSSGEKESKSVLCLFDDYLKSWNKQNPGVPKPRI 250

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            +VGRLD+ T GL++LTNDG  A+ L  PS++  + Y     G V++  L  + +G VI+
Sbjct: 251 FTVGRLDVATTGLIILTNDGDFAQKLSHPSSKLSKEYIATIDGVVNKRHLIAISEGTVIE 310

Query: 169 GICYGDMQVTLDTQKGSNAW--VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL- 225
           G+      V L   + + +   + V + EG+N E++++ +    +++ L RI  G F+L 
Sbjct: 311 GVHCTPDSVELLPPQPNISKPRLRVVVHEGRNHEVRELVKSAGLQIHSLKRIRIGGFRLP 370

Query: 226 GTLLAGSTREVSKKILRE 243
             L  G   E+ +  L+ 
Sbjct: 371 SDLGHGKHVELKQGDLKA 388


>gi|251779869|ref|ZP_04822789.1| RNA pseudouridine synthase family protein [Clostridium botulinum E1
           str. 'BoNT E Beluga']
 gi|243084184|gb|EES50074.1| RNA pseudouridine synthase family protein [Clostridium botulinum E1
           str. 'BoNT E Beluga']
          Length = 254

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 61/257 (23%), Positives = 97/257 (37%), Gaps = 27/257 (10%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A + +  R+ V   I    VKVNG ++   ++N+    D +E  G  +    +
Sbjct: 1   MRLDKFLAESAVGRRKIVRTYIKDGMVKVNGKIITEPSININEKLDDVEYLGKKVIHNGK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                      +  T  +     TVFD      + V  VGRLD +TEGLLLLTNDG    
Sbjct: 61  VYYIFNKPAGCITATRDN--IHKTVFDYFDEDMNGVFHVGRLDKDTEGLLLLTNDGEFEH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVT 190
            +  P     + Y     G +D +    L+ GI I          +     + G      
Sbjct: 119 KVMYPEKHVEKTYFFWALGSLDDEDKKQLEAGIFIGNNESLTKPAK-IDLYKSGLYKEFK 177

Query: 191 --------------------VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LL 229
                               + + EG+  ++K++ +     V  L RIS G  +L   L 
Sbjct: 178 EEIPIKNLENKDHQPVVSGYLTISEGQKHQVKRMLKAVGCYVIYLKRISIGGLKLDESLK 237

Query: 230 AGSTREVSKKILREQLG 246
            G  R ++KK +     
Sbjct: 238 MGDYRNLTKKEIESIFE 254


>gi|194290486|ref|YP_002006393.1| 16S rRNA pseudouridylate 516 synthase [Cupriavidus taiwanensis LMG
           19424]
 gi|193224321|emb|CAQ70332.1| 16S rRNA pseudouridylate 516 synthase [Cupriavidus taiwanensis LMG
           19424]
          Length = 235

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 54/234 (23%), Positives = 90/234 (38%), Gaps = 6/234 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERA--AVNVMSTDHIEVDGVPLRKAERT 73
           + +++   G  +RR    +IA   V+VNG L E       V     + VDG       + 
Sbjct: 3   LDRILQSQGFGTRRYCGDLIAAGLVEVNGELCEDPRAQFEVD-GLRLTVDGEEWLACTKA 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L        +              +P     V +VGRLD +T GLLLLT+DG     
Sbjct: 62  YLMLNKPAGYECSQRPRHHPSVYNLLPVPLRQREVQAVGRLDHDTTGLLLLTDDGQFIHA 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
              P  +  ++Y V     V  ++   L+ G+ +       +        G  + + + L
Sbjct: 122 QTSPKRKVPKIYEVTTAEPVTPEQAEALRSGVQLLDEPA-PIAAEACEITGERS-LRLTL 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
            +GK  ++K++       V+ L R + G   L   L  G  R ++ + L    G
Sbjct: 180 VQGKYHQVKRMVVAAGNHVDALHRSAIGSLPLDPALAEGEWRWLTAQELAALTG 233


>gi|114777044|ref|ZP_01452064.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthase [Mariprofundus ferrooxydans
           PV-1]
 gi|114552565|gb|EAU55025.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthase [Mariprofundus ferrooxydans
           PV-1]
          Length = 249

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 49/249 (19%), Positives = 91/249 (36%), Gaps = 5/249 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
            +   +R+ K+++  G  +R++V   I    + V G   E  A  V ++D + ++G PL 
Sbjct: 2   SDQKSERLDKLLSNLGYGARKDVRHWIKAGWITVQGEAAESPAQKVFASD-VLLEGEPLD 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             +   +  +     + +           +             VGRLD +T GLL++T+D
Sbjct: 61  HPDGLTIIYHKPLDTVCSRKEGGRLIYDDLPARWLDRKPPFSPVGRLDKDTSGLLIVTDD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  P     + Y V     +   +  ++  G ++                 S  
Sbjct: 121 GQLNHCLTSPKQHISKTYSVTLAEPLQGREAEIMAAGTLLLENDDRPCLPAELIVH-SPT 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTREVSKKILREQL 245
             ++ L EG+  + +++F      V  L R   G   L    L  G  +  +   L   +
Sbjct: 180 QASLTLHEGRYHQARRMFVALGNHVTALQRTHIGALALKDTGLKPGEYQVTTSAELMAMI 239

Query: 246 GPHLLEEAQ 254
            P     AQ
Sbjct: 240 QPVAPSSAQ 248


>gi|73540410|ref|YP_294930.1| ribosomal small subunit pseudouridine synthase A [Ralstonia
           eutropha JMP134]
 gi|72117823|gb|AAZ60086.1| ribosomal small subunit pseudouridine synthase A [Ralstonia
           eutropha JMP134]
          Length = 251

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 56/233 (24%), Positives = 92/233 (39%), Gaps = 7/233 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERA--AVNVMSTDHIEVDGVPLRKA 70
           P  + +++   G  +RR    +IA   V+VNG L E       V     + VDG      
Sbjct: 15  PMTLDRILQSQGFGTRRYCGDLIAAGLVEVNGELCEDPRAQFEVD-GLRLTVDGEEWLAC 73

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            +  L L        +              +P     V +VGRLD +T GLLLLT+DG  
Sbjct: 74  TKAYLMLNKPAGYECSQRPRHHPSVYNLLPVPLRQREVQAVGRLDHDTTGLLLLTDDGQF 133

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
                 P  +  +VY V     V Q++++ L+ G+ +            +        + 
Sbjct: 134 IHAQTSPKRKVPKVYEVTTAEPVTQEQVDALRTGVKLDDEPVPIAAEGCEIT--GECSLR 191

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKIL 241
           + L +GK  ++K++       VN L R + G  +L    L  G  R ++ + L
Sbjct: 192 LTLLQGKYHQVKRMVAAAGNHVNALHRSAVGGLRLDPAALPEGEWRWLTAEDL 244


>gi|323526492|ref|YP_004228645.1| pseudouridine synthase [Burkholderia sp. CCGE1001]
 gi|323383494|gb|ADX55585.1| pseudouridine synthase [Burkholderia sp. CCGE1001]
          Length = 243

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 59/245 (24%), Positives = 98/245 (40%), Gaps = 28/245 (11%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--------------- 64
           ++  G+ SRRE +  I +  V V+G  ++     V     IE+D                
Sbjct: 1   MSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPDQRIEIDPAAEAAQASQVTVLIH 60

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +          Y   I LVT  +  +G  +      +   ++   GRLDI++ GLL+L
Sbjct: 61  KTVGYVSGQAEDGYQPAITLVTPENRWEGDRSDIRFSVAHLRQLAPAGRLDIDSTGLLVL 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQGICYGDM 175
           T DG +A+ L    ++  + Y VR                + L LL+ G+ +  +     
Sbjct: 121 TQDGRIAKQLIGGHSEIDKEYLVRVAYGEHTVDVESHFPPESLALLRHGLSLDDVPLKPA 180

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           QV+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  G  R 
Sbjct: 181 QVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPPGQWRY 236

Query: 236 VSKKI 240
           +    
Sbjct: 237 LGPDE 241


>gi|71910951|ref|YP_282501.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS5005]
 gi|139473571|ref|YP_001128287.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes str. Manfredo]
 gi|71853733|gb|AAZ51756.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS5005]
 gi|134271818|emb|CAM30052.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pyogenes str. Manfredo]
          Length = 238

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 56/229 (24%), Positives = 97/229 (42%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +   + 
Sbjct: 1   MRLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQRVTHPKH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + + L      +                       +  VGRLD +TEGL+LLT++G L  
Sbjct: 61  SYIILNKPSGVVSAKKDTNYLTVIDQLAEEDKSPDLYPVGRLDRDTEGLVLLTDNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +  PS    + Y V  +G + +D  +    GI    G      Q+T+       +  ++
Sbjct: 121 RMLHPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQSQASL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R ++   
Sbjct: 181 TISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLTASE 229


>gi|93004862|ref|YP_579299.1| pseudouridine synthase, Rsu [Psychrobacter cryohalolentis K5]
 gi|92392540|gb|ABE73815.1| ribosomal small subunit pseudouridine synthase A [Psychrobacter
           cryohalolentis K5]
          Length = 234

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 54/235 (22%), Positives = 98/235 (41%), Gaps = 11/235 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +++A   SR+E ++++    V VN  +++   V+V    D ++  G PL  A  
Sbjct: 1   MRLDKFLSKATELSRKESKKILHAGEVTVNEQVIKDPGVHVDIVNDDVQWAGEPLSVATG 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R  L HKP G   T    +               +   GRLD++T G LL+++DGG   
Sbjct: 61  NRYILLHKPEGFECTLKAKEYPIVTDLIAVPELGSLRIAGRLDVDTTGALLISDDGGWLH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI------VIQGICYGDMQVTLDTQKGSN 186
            +  P  +  +VY +     +D D      K +                 +    +  + 
Sbjct: 121 RVTSPKHEHAKVYELTLADAMDSDAQANAIKEVAEGILLEGDHEETKPATLEFIDETHA- 179

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
               + L +GK  ++K++  +F  +V  L R S G   L  L  G +R ++ + +
Sbjct: 180 ---RLTLEQGKYHQVKRMMGYFGNRVVELHRASVGHITLDGLEKGDSRFLTPEEV 231


>gi|282897729|ref|ZP_06305728.1| Pseudouridine synthase, Rsu [Raphidiopsis brookii D9]
 gi|281197408|gb|EFA72305.1| Pseudouridine synthase, Rsu [Raphidiopsis brookii D9]
          Length = 252

 Score =  150 bits (378), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 68/238 (28%), Positives = 107/238 (44%), Gaps = 12/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL---RKA 70
           RV K+I++ GIASRR+ E MI Q RV+VNG L       V    D I +DG P+      
Sbjct: 4   RVQKIISQWGIASRRQAEEMIGQSRVRVNGNLAR-LGQKVDPKVDMISIDGKPVTQGSPP 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDG 128
               L L      + T +      + +          + +  VGRLD ++ G L+LTNDG
Sbjct: 63  ALVYLLLNKPAGVVSTCNDPQGRTTVLDLLPTKLRQGTGICPVGRLDADSTGALILTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   L  PS    + Y V   G    + L +  +G+++ G      QV L  Q  + + 
Sbjct: 123 DVTFALTHPSHDVPKTYHVVVEGHPPTNVLRMWSQGVMLDGRKTRTAQVKLIEQGFTQSK 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-----LLAGSTREVSKKIL 241
           + + L+EG+NR+I++V +   + V  L R + G  +L          G  R +    +
Sbjct: 183 LEIILQEGRNRQIRRVAQQLGYPVVHLDRRAIGTIELHNSDGKFTDVGKYRHLITSEI 240


>gi|187478145|ref|YP_786169.1| ribosomal large subunit pseudouridine synthase F [Bordetella avium
           197N]
 gi|115422731|emb|CAJ49259.1| ribosomal large subunit pseudouridine synthase F (pseudouridylate
           synthase) [Bordetella avium 197N]
          Length = 243

 Score =  150 bits (378), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 60/244 (24%), Positives = 104/244 (42%), Gaps = 19/244 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
              R+SK+++  G+ SRRE +  I +  V+V+G ++            I ++        
Sbjct: 2   EKVRISKLMSEQGLCSRREADSYIERGWVRVDGEVVSELGAKAYPHQKITLERAARAAQT 61

Query: 64  -------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
                    P+          Y   + LV   S  +G  +      +    +   GRLDI
Sbjct: 62  SLATILINKPVGYVSGQAEDGYKPAVALVDARSQYEGDRSGRRFDRANLRGLAVAGRLDI 121

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +++GLL+LT DG +A+ L    +   + Y VR  G++ +  L LL  G+++ G       
Sbjct: 122 DSQGLLVLTQDGRVAKQLIGEDSLVDKEYLVRVEGRLSERGLALLNHGLMLDGKPLKPAN 181

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V    +      +   LREGK R+I+++ E    +V  L R+  G  +LG L  G  R +
Sbjct: 182 VCWQNEDQ----LRFVLREGKKRQIRRMCELVGLRVVGLKRVRIGRVRLGDLPVGQWRYL 237

Query: 237 SKKI 240
            +  
Sbjct: 238 REDE 241


>gi|71903794|ref|YP_280597.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS6180]
 gi|94988815|ref|YP_596916.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS9429]
 gi|94992701|ref|YP_600800.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS2096]
 gi|71802889|gb|AAX72242.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS6180]
 gi|94542323|gb|ABF32372.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS9429]
 gi|94546209|gb|ABF36256.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS2096]
          Length = 238

 Score =  150 bits (378), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 55/229 (24%), Positives = 96/229 (41%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +   + 
Sbjct: 1   MRLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQRVTHPKH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + + L      +                       +  VGRLD +TEGL+LLT++G L  
Sbjct: 61  SYIILNKPSGVVSAKKDTNYLTVIDQLAEEDKSPDLYPVGRLDRDTEGLVLLTDNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V  +G + +D  +    GI    G      Q+T+       +  ++
Sbjct: 121 RMLHPIHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQSQASL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R ++   
Sbjct: 181 TISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLTASE 229


>gi|89099078|ref|ZP_01171957.1| ribosomal large subunit pseudouridine synthaseB (pseudouridylate
           synthase) (uracil hydrolyase) [Bacillus sp. NRRL
           B-14911]
 gi|89086208|gb|EAR65330.1| ribosomal large subunit pseudouridine synthaseB (pseudouridylate
           synthase) (uracil hydrolyase) [Bacillus sp. NRRL
           B-14911]
          Length = 224

 Score =  150 bits (378), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 67/219 (30%), Positives = 113/219 (51%), Gaps = 3/219 (1%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           VKVNG +++   + V S+D +EVDG+P+ + E   + LY     + +   +      V D
Sbjct: 6   VKVNGKVVKELGLKVSSSDRVEVDGIPVEREEPVYILLYKPRGVISSVTDEKGR-KVVTD 64

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
            LP I  RV  VGRLD +T GLLL+TNDG  A +L  P  +  +VY  +  G   ++KL 
Sbjct: 65  LLPQIKERVYPVGRLDFDTSGLLLMTNDGEFANLLMHPKNEVEKVYVAKIKGIPAREKLK 124

Query: 160 LLKKGIVIQGICYGDMQVTL--DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
            L++G+ ++       +V +    ++ + A V + + EG+NR+++++ E     V +L R
Sbjct: 125 SLERGVRLEDGKTAPARVKVLSIDKQKNTAIVELVIHEGRNRQVRRMLEAIGHPVMKLKR 184

Query: 218 ISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVN 256
             YG   L  L AG  RE++   +++          + N
Sbjct: 185 ERYGFLTLQGLSAGDARELTAHEVKQLRTLASSAGKKKN 223


>gi|319792471|ref|YP_004154111.1| pseudouridine synthase [Variovorax paradoxus EPS]
 gi|315594934|gb|ADU36000.1| pseudouridine synthase [Variovorax paradoxus EPS]
          Length = 249

 Score =  150 bits (378), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 50/248 (20%), Positives = 91/248 (36%), Gaps = 11/248 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  +RR    ++ Q  V ++G  +     +V     +  V G P    E+  
Sbjct: 3   LQDILYTQGFGTRRVCAGLVQQGHVTIDGKAVTDPFADVDPEGLLYTVQGTPWAYHEKAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGR-------STVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           L L+       +                            V ++GRLD +T GLLL+T+D
Sbjct: 63  LMLHKPAGTECSQKPSTYPSIYTLLPSPLRLRPNKGAVQGVQAIGRLDQDTTGLLLMTDD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G     +  P     +VY V     VD+ ++  L  G+V+       ++     +  S  
Sbjct: 123 GQFIHKMGSPKHHVPKVYEVTAKHPVDEAQIAKLLAGVVLDDDP-KPVR-AAACESDSPL 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
            + + L EGK  ++K++      +V  L R   G   L   L  G  R ++ + +     
Sbjct: 181 HLRLTLTEGKYHQVKRMLAAVGNRVEGLHRSRIGELSLPADLAPGQWRWLTAEEVAALRA 240

Query: 247 PHLLEEAQ 254
           P    +  
Sbjct: 241 PTKPAKPP 248


>gi|53719771|ref|YP_108757.1| pseudouridylate synthase-related protein [Burkholderia pseudomallei
           K96243]
 gi|53723742|ref|YP_103198.1| pseudouridine synthase family protein [Burkholderia mallei ATCC
           23344]
 gi|251768207|ref|ZP_02269850.2| RNA pseudouridine synthase family protein [Burkholderia mallei
           PRL-20]
 gi|52210185|emb|CAH36164.1| conserved pseudouridylate synthase-related protein [Burkholderia
           pseudomallei K96243]
 gi|52427165|gb|AAU47758.1| pseudouridine synthase family protein [Burkholderia mallei ATCC
           23344]
 gi|243060515|gb|EES42701.1| RNA pseudouridine synthase family protein [Burkholderia mallei
           PRL-20]
          Length = 249

 Score =  150 bits (378), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 1   MRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 60

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 61  VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 120

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 121 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDG 180

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 181 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 236

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 237 QGEWRYLGPDE 247


>gi|168482908|ref|ZP_02707860.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae CDC1873-00]
 gi|172043870|gb|EDT51916.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae CDC1873-00]
 gi|332203838|gb|EGJ17905.1| hypothetical protein SPAR93_0709 [Streptococcus pneumoniae GA47368]
          Length = 241

 Score =  150 bits (378), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 107/232 (46%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + + ++ V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLRGKILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                      ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKELPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSISQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K L+
Sbjct: 180 TISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKELQ 231


>gi|89095415|ref|ZP_01168328.1| putative ribosomal small subunit pseudouridine synthase A
           [Oceanospirillum sp. MED92]
 gi|89080322|gb|EAR59581.1| putative ribosomal small subunit pseudouridine synthase A
           [Oceanospirillum sp. MED92]
          Length = 237

 Score =  150 bits (378), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 59/230 (25%), Positives = 95/230 (41%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + IA+    S+ +V  +IA+ RV VN  +       +   D + +D   L+K     
Sbjct: 7   RLDRFIAKHTDHSKNDVRILIAKGRVYVNQTVAVSVDQIIKQFDEVILDDEVLQKNTPIY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L      +  T       +TV D L   +  +   GRLD  + GLLLLTNDG  +  L
Sbjct: 67  LMLNKPAGVVSATSDPQH--TTVIDLLDDHYKDLHIAGRLDRFSTGLLLLTNDGEWSNSL 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
             P  +  + Y V     +     +   K      + I     Q+    ++       V 
Sbjct: 125 SHPDNRVAKRYIVELKEPITDAYGDAFAKGMHFAYEDITTQPAQL----KQLEPRVAEVT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           L EG+  +IK++F  F  +V  L R+S G   L   L  G  R +++  +
Sbjct: 181 LHEGRYHQIKRMFGRFRNQVLSLHRVSIGNLPLDDALKPGEYRMLTRDEV 230


>gi|170717435|ref|YP_001784534.1| pseudouridine synthase [Haemophilus somnus 2336]
 gi|168825564|gb|ACA30935.1| pseudouridine synthase [Haemophilus somnus 2336]
          Length = 348

 Score =  150 bits (378), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 87/290 (30%), Positives = 134/290 (46%), Gaps = 12/290 (4%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM--STDHIEVD 63
           I Q+    +R+ KV+AR G  SRR +E MI+  R+ ++G +       V   S   I +D
Sbjct: 60  INQQKVEGERLQKVLARVGQGSRRTIEAMISANRISIDGKMAT-LGDRVDIHSGVKIRID 118

Query: 64  GVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           G  +   +        L  Y     L T H      +          SR I+VGRLDINT
Sbjct: 119 GHIVNLTQAQKEVCRVLLYYKPEGELCTRHDPEGRATVFDRLPRLNGSRWIAVGRLDINT 178

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLL T DG LA  L  P  +  R Y VR  G+VD   +  L+KG+ ++        + 
Sbjct: 179 SGLLLFTTDGELANRLMHPRHEVEREYAVRVFGEVDDTMIARLRKGVQLEDGPANFTSIK 238

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
               +G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L  +L  G   E+ 
Sbjct: 239 ATGGQGMNQWFDVTLIEGRNREVRRLWESQGIQVSRLIRIRYGNIKLTKSLPRGGWEEMD 298

Query: 238 K---KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
                 LR+ +G     +++++   P       +R      +E+   + +
Sbjct: 299 LTNINYLRKLVGLPPETDSKIDTKKPRRIKTGQIRKAVKRYTELNKRYKK 348


>gi|304410666|ref|ZP_07392284.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|304351150|gb|EFM15550.1| pseudouridine synthase [Shewanella baltica OS183]
          Length = 250

 Score =  150 bits (378), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 46/231 (19%), Positives = 97/231 (41%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  +   +R   ++ + +  +  +GI+++ +   V     + + G P+      
Sbjct: 22  VRLDKFICESTPLTRSLAKKALHRGDITCDGIVVKDSGFKVTEGMRVYLQGEPIALV-GV 80

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP+  + +  D    S +          +   GRLD +T GL+L+T+DG  +  
Sbjct: 81  RYLMLNKPVDTICSTIDETYPSVLSLVDVPKPETLHIAGRLDADTTGLVLVTSDGQWSHK 140

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y V+    VD   + +   G+ +  +        + +   +     V +
Sbjct: 141 ITSPKKECGKRYLVQLADPVDAGLIAIFAAGVELRGEDGLTKPALLEIIEPQ----LVRL 196

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++K++F      V  L R S G  +L   L  G  R ++ + +
Sbjct: 197 TITEGKYHQVKRMFAAVGNHVQGLHRESVGQIELDPALALGEWRYLTAEEI 247


>gi|295113966|emb|CBL32603.1| pseudouridine synthase family [Enterococcus sp. 7L76]
          Length = 260

 Score =  150 bits (378), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 67/260 (25%), Positives = 116/260 (44%), Gaps = 3/260 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I++ G  +     
Sbjct: 1   MRLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESQNVDAQLQMIKLKGQLISHKTH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                       +  VGRLD +TEGLLLLT++G L  
Sbjct: 61  VYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            L  P+ +  + Y V+ +G V  +     K GIV+QG       ++T+     + + V +
Sbjct: 121 QLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETKSHVFL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLL 250
            ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L    +
Sbjct: 181 TIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYFFI 240

Query: 251 EEAQVNLDAPIYSSETLVRD 270
           E+ Q +   P        R 
Sbjct: 241 EKQQTSKALPSNLKREEERK 260


>gi|260424785|ref|ZP_05733291.2| ribosomal small subunit pseudouridine synthase A [Dialister invisus
           DSM 15470]
 gi|260403192|gb|EEW96739.1| ribosomal small subunit pseudouridine synthase A [Dialister invisus
           DSM 15470]
          Length = 277

 Score =  150 bits (378), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 62/257 (24%), Positives = 103/257 (40%), Gaps = 25/257 (9%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +     R+ K ++   + +R E++R I +  V+VNG  +      V   D I   G P+ 
Sbjct: 13  DEEDVMRLDKFLSDMNMGTRTELKRDIRKGAVQVNGEKITDPGFMVNENDEIIFAGEPVP 72

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   L      ++T   D   ++ +          +  VGRLD +T GLLL+TNDG
Sbjct: 73  YFRYEYYMLNKPAG-VITATEDRYQKTVLDFFGERRRKDLSPVGRLDKDTVGLLLVTNDG 131

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLD------- 180
           G    L  P     + Y  R  G+VD+      +KGI +  I      ++ +D       
Sbjct: 132 GFHHRLLSPKKHIDKEYYARIDGRVDEADREKFEKGIYVDEIFTALPAKLMIDGYRENAL 191

Query: 181 ---------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                            +   + + V ++EGK  +IK++F     +V  L RI  G   L
Sbjct: 192 ESDFMDLANSRAPKSALENGVSEIRVVVQEGKFHQIKRMFHALGKEVIYLKRIRIGSVVL 251

Query: 226 G-TLLAGSTREVSKKIL 241
             TL  G+ R ++   +
Sbjct: 252 DPTLEEGTYRRLTAGEV 268


>gi|319425419|gb|ADV53493.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 236

 Score =  150 bits (378), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 57/230 (24%), Positives = 103/230 (44%), Gaps = 8/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++      R+ V  ++   RV+V+G +++     V    HI++D   L+      
Sbjct: 7   RLDRYLSAKMQMPRKLVRDLLLSGRVQVDGQIVKEMDRQVDEFSHIQLDDQVLQANT-PV 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             + HKP+G+V+   D   ++ +          +   GRLD+N+ GLLLLTND   +  L
Sbjct: 66  YMMLHKPVGVVSATKDNQHKTVIDLLDNEYRHELHIAGRLDLNSSGLLLLTNDSRWSEAL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
             P+ +  +VYRV     +  D +    +      + I     ++ +      +    V 
Sbjct: 126 MSPTEKVDKVYRVTLANPLTHDYVTAFAEGMYFGFEDITTQPAKLVIL----DSHLAEVT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           L+EGK  +IK++F  F   V  L R+S G   L   L  G +R ++   +
Sbjct: 182 LKEGKYHQIKRMFGRFRNPVIGLHRLSIGAIVLDEQLQPGESRTLTAAEI 231


>gi|322385908|ref|ZP_08059550.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           cristatus ATCC 51100]
 gi|321270087|gb|EFX53005.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           cristatus ATCC 51100]
          Length = 257

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 59/247 (23%), Positives = 105/247 (42%), Gaps = 6/247 (2%)

Query: 1   MKDKNIVQENFTP--QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST- 57
           +K K    +       R+ K +A A I SR+E+++ +  +++ ++G      + NV S  
Sbjct: 2   IKRKKNRSKPLKGKLMRLDKFLALAKI-SRKEMKQKLRLRQIVIDGQAARSLSQNVDSGL 60

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
             I + G  L         +      +                      ++ ++GRLD +
Sbjct: 61  QSISLAGKTLNHLAHRYFLMNKPAGAVTANSDADKLTVLELIAPEDFNDQLYAIGRLDRD 120

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GIVIQGICYGDMQ 176
           T GLLL+T++G L   L  P     + Y V  +G +DQ+     ++  + + G      Q
Sbjct: 121 TRGLLLITDNGPLGFQLLHPQYHIAKTYYVEVNGPLDQEATIAFQQGIVFLDGTRCKPAQ 180

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTRE 235
           + + T    ++  +V + EGK  ++KK+F     KV  L R  +G FQL   L  GS R 
Sbjct: 181 LQIHTTSPEHSTASVTISEGKFHQVKKMFLAVGVKVTYLKRTHFGDFQLDPNLTEGSYRP 240

Query: 236 VSKKILR 242
           ++   L 
Sbjct: 241 LNPSELE 247


>gi|209550726|ref|YP_002282643.1| pseudouridine synthase [Rhizobium leguminosarum bv. trifolii
           WSM2304]
 gi|209536482|gb|ACI56417.1| pseudouridine synthase [Rhizobium leguminosarum bv. trifolii
           WSM2304]
          Length = 268

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 67/240 (27%), Positives = 113/240 (47%), Gaps = 1/240 (0%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTRLW 76
           + +++ G  SR + ER+IA+ RV V+G  +   +  V  +T  I VDG+ +    +  L 
Sbjct: 29  RALSKLGYCSRTQAERLIAESRVAVDGRTISDISAWVDLATARISVDGLVIAAEAKIYLM 88

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L      + T        +            +  VGRLD  +EGLLL TND   A++L  
Sbjct: 89  LNKPRGLVTTRDDPEGRPTVYDCLREFDIPHLSPVGRLDKASEGLLLFTNDTEFAQILLD 148

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
           P T   + Y V+    +D + +  +  GI   G            Q   N+W+ V L EG
Sbjct: 149 PVTHVTKTYHVQIDRIMDDEGIAAMTSGIRHDGELLTATAARRLRQGDRNSWIEVELDEG 208

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVN 256
           +NR+I+++ E    +  RL+R++ G  +LG L  G+ R +++  L+       +E+A+ N
Sbjct: 209 RNRQIRRMLEALGTECLRLVRVAIGGLELGELPKGAVRALTEAELQSLRRKTGIEKARRN 268


>gi|56460844|ref|YP_156125.1| RNA pseudouridylate synthase-family protein [Idiomarina loihiensis
           L2TR]
 gi|56179854|gb|AAV82576.1| RNA pseudouridylate synthase-family protein [Idiomarina loihiensis
           L2TR]
          Length = 286

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 79/289 (27%), Positives = 128/289 (44%), Gaps = 10/289 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+AR+G  SRRE+E  I+  R++VNG + +     + +   + +DG  ++    
Sbjct: 2   TEKLQKVLARSGHGSRREIETKISAGRIRVNGKVAQ-LGERIDADAKVRIDGHEVQIKPE 60

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L  +     L T        +          +R ++VGRLD+NT GLLL T D
Sbjct: 61  EEVICRVLIYHKPEGELCTRKDPEGRPTVYDRLPRMSGARWVAVGRLDVNTSGLLLFTTD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G VD+  +  L+KG+ ++        +      G N 
Sbjct: 121 GELANRLMHPSQQVEREYAVRVFGDVDEAMMQRLRKGVQLEDGPAHFNSIKPAGGDGMNR 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           W  V + EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+S   L +   
Sbjct: 181 WFHVTISEGRNREVRRLWESQEVQVSRLIRVRYGDIPLEPGLPQGGWAEMS---LPQVNA 237

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
                      ++ +       + R            R+ K  S++ G 
Sbjct: 238 LRAQVNLPAEKESFLDPRHEESKQRRFAKIRKATARHRLDKKQSKRRGK 286


>gi|56808351|ref|ZP_00366108.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Streptococcus pyogenes M49
           591]
 gi|209559629|ref|YP_002286101.1| Putative 16S pseudouridylate synthetase [Streptococcus pyogenes
           NZ131]
 gi|209540830|gb|ACI61406.1| Putative 16S pseudouridylate synthetase [Streptococcus pyogenes
           NZ131]
          Length = 238

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 98/229 (42%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++    + SR +V+++I  Q V V+ +L      NV      IEV G  +   + 
Sbjct: 1   MRLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMLARNGRQNVDPGLQLIEVTGQRVTHPKH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + + L      +                       +  VGRLD +TEGL+LLT++G L  
Sbjct: 61  SYIILNKPSGVVSAKKDTNYLTVIDQLAEEDKSPDLYPVGRLDRDTEGLVLLTDNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +  PS    + Y V  +G + +D  +    GI    G      Q+T+       +  ++
Sbjct: 121 RMLHPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQSQASL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R ++   
Sbjct: 181 TISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLTASE 229


>gi|224100741|ref|XP_002311995.1| predicted protein [Populus trichocarpa]
 gi|222851815|gb|EEE89362.1| predicted protein [Populus trichocarpa]
          Length = 397

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 71/257 (27%), Positives = 119/257 (46%), Gaps = 18/257 (7%)

Query: 4   KNIVQEN--FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHI 60
           +    EN     QR+SKV+A AG+ASRR  E +I + +V VNG +       V    D I
Sbjct: 135 RRFYNENFRDQAQRLSKVLAAAGVASRRSSEALIFEGKVTVNGSVCNTPQTRVDPGRDSI 194

Query: 61  EVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----------- 108
            V+G  L K          +KP G + +  + + +S +        S             
Sbjct: 195 YVNGNRLPKKLPPKIYIALNKPKGYICSLGEKESKSVMCLLDDYFQSWDKRNPGLPKPRL 254

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            +VGRLD+ T GL+++TNDG  A+ +  PS+   + Y     G V +  L  + +G VI+
Sbjct: 255 FTVGRLDVATTGLIIVTNDGDFAQQIAHPSSNLSKEYIATVDGVVSKRHLFAVSEGTVIE 314

Query: 169 GICYGDMQVTLDTQKG--SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL- 225
           G+      V L  Q+       + + + EG+N E++++ +    +++ L R+  G F+L 
Sbjct: 315 GVRCVPDSVELLPQQPDRPRPRLRIVVHEGRNHEVRELVKNAGLEIHSLKRVRIGGFRLP 374

Query: 226 GTLLAGSTREVSKKILR 242
             L  G   E+ +  L+
Sbjct: 375 SDLGLGKHAELKQTDLK 391


>gi|262340872|ref|YP_003283727.1| pseudouridylate synthase (ribosomal large subunit pseudouridine
           synthase B) [Blattabacterium sp. (Blattella germanica)
           str. Bge]
 gi|262272209|gb|ACY40117.1| pseudouridylate synthase (ribosomal large subunit pseudouridine
           synthase B) [Blattabacterium sp. (Blattella germanica)
           str. Bge]
          Length = 238

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 60/236 (25%), Positives = 117/236 (49%), Gaps = 2/236 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +    R++  ++ AGI+SRR+ ++ I    ++VNG  + R    + + D +   G  ++ 
Sbjct: 2   HNNKIRLNHYLSNAGISSRRKADQFIQSGAIEVNGKPVRRLGTVIHTNDLVTFYGEKIKI 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             +  L L      + TT    + ++ +         R+  VGRLD +T G+LLLTNDG 
Sbjct: 62  QNKIYLLLNKPKGFITTTKDPFNRKTVMNLIPNLSKYRIFPVGRLDRSTTGVLLLTNDGS 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +A  L  P +   ++Y V    ++  + L+ ++KG +      G ++V    +  S   +
Sbjct: 122 IAEKLTHPKSHVQKIYHVLLDKEIKNEDLDQIRKGKIYLKE--GKVKVIFVNKGHSKYQI 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            +GL  G NR IK++F+  N++V +L R+++G      +  G+   +++K +   L
Sbjct: 180 KIGLYIGWNRIIKRIFKKLNYQVIQLDRVNFGGLSKKNIQIGNWCFLNQKEVENIL 235


>gi|207728125|ref|YP_002256519.1| ribosomal small subunit pseudouridine synthase a protein [Ralstonia
           solanacearum MolK2]
 gi|206591370|emb|CAQ56982.1| ribosomal small subunit pseudouridine synthase a protein [Ralstonia
           solanacearum MolK2]
          Length = 278

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 54/243 (22%), Positives = 89/243 (36%), Gaps = 4/243 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-VDGVPLRKAERTR 74
           + +++   G  +RR  + ++A   V VNGI  E     V +   +  VDG       R  
Sbjct: 36  LYRILQSQGFGTRRYCKDLVAAGLVHVNGIEAEDPDAQVDTAGLVLDVDGERWAYHARAY 95

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L+       +              +P     V  VGRLD +T GLLLLT+DG     L
Sbjct: 96  LMLHKPAGFECSQKPRHHPSVYTLLPVPLRERGVQCVGRLDQDTTGLLLLTDDGQFVHTL 155

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  Q  +VY +     V   ++  L +G+++            +        + + L 
Sbjct: 156 TSPRHQVPKVYEITTADPVTDAQVAQLCRGVLLDDEDATVAAAWAERVD--TCHLRMALT 213

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLLEEA 253
           +GK  ++K++       V  L R + G   L   L  G  R + +  L       +    
Sbjct: 214 QGKYHQVKRMVAAAGNHVTALHRSAIGALTLDAGLAPGQWRWLERDDLTALDTTPVHAAG 273

Query: 254 QVN 256
              
Sbjct: 274 AAT 276


>gi|52425093|ref|YP_088230.1| RsuA protein [Mannheimia succiniciproducens MBEL55E]
 gi|52307145|gb|AAU37645.1| RsuA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 402

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 93/287 (32%), Positives = 132/287 (45%), Gaps = 10/287 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLR 68
               +++ KV+ARAG  SRRE+E +I Q RV V+G +      V V     I +DG  + 
Sbjct: 116 TVEGEKLQKVLARAGQGSRREIESIIEQGRVSVDGKIATLGDRVTVHDGLKIRIDGHLVN 175

Query: 69  KAERTR-----LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                R     L  Y     L T H      +          SR I+VGRLDINT GLLL
Sbjct: 176 LTAAQREVCRVLMYYKPEGELCTRHDPEGRATVFDRLPRLTGSRWIAVGRLDINTSGLLL 235

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T DG LA  L  PS +  R Y VR  GQVD   ++ L+KG+ ++        +      
Sbjct: 236 FTTDGELANRLMHPSQEVEREYSVRVFGQVDDAMIHRLRKGVQLEDGPANFKAIKAVGGT 295

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK---K 239
           G N W  V L EG+NRE+++++E    +V+RLIRI YG  QL  TL  G   E+      
Sbjct: 296 GLNQWFDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIQLMKTLPRGGWEEMDLAKVN 355

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
            LRE +G     E ++++      ++T    +        +   +  
Sbjct: 356 YLRELVGLPPETETKLDVTNLRRRAKTGQIRKAVKRYSEMNKRYKKS 402


>gi|227431698|ref|ZP_03913728.1| ribosomal large subunit pseudouridine synthase B [Leuconostoc
           mesenteroides subsp. cremoris ATCC 19254]
 gi|227352522|gb|EEJ42718.1| ribosomal large subunit pseudouridine synthase B [Leuconostoc
           mesenteroides subsp. cremoris ATCC 19254]
          Length = 224

 Score =  149 bits (377), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 71/211 (33%), Positives = 115/211 (54%), Gaps = 2/211 (0%)

Query: 34  MIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           MI   RV+VNG  +      V + D ++VDG P+   E+   +L +KP G+VTT+ D  G
Sbjct: 1   MIINGRVQVNGQTVTELGTKVTANDKVQVDGAPIEGREKLVYYLLNKPRGVVTTNDDEKG 60

Query: 94  RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
           R TV D L  +  RV  VGRLD +T G+LLLTNDG +A  L  P T+  + Y  +  G  
Sbjct: 61  RRTVLDILEDVDQRVYPVGRLDYDTTGVLLLTNDGVVANQLMHPKTKVDKTYVAKVEGIA 120

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIKKVFEFFNWK 211
            ++KL  LK+G+V++G      +V+++  + +   + V + + EG+N ++K +       
Sbjct: 121 TEEKLAPLKRGVVLKGRKTAPARVSIERIEPTKRTSMVRLTIHEGRNHQVKNMLAKVGLP 180

Query: 212 VNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           V +L R  Y  F +  L  G  R+++   ++
Sbjct: 181 VQKLKREQYAFFDVTGLQPGEYRKLTSVEIK 211


>gi|296390923|ref|ZP_06880398.1| putative pseudouridylate synthase [Pseudomonas aeruginosa PAb1]
          Length = 230

 Score =  149 bits (377), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 107/231 (46%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     SRR+ + +IA  R++V+G ++      V     +E+D   L+  +  
Sbjct: 1   MRLDRFLANLPELSRRDAQMLIAGGRLRVDGQVVRDGTHEVRVFSRVELDERLLQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP+G V+   DP   + +          +   GRLD NT GL+LLTNDG  +R 
Sbjct: 61  RYYMLHKPMGCVSATRDPQHPTVLDLFPEDQRDDLHIGGRLDYNTTGLMLLTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L LP ++  +VY V     +DQ  ++          + +     Q+             +
Sbjct: 121 LTLPGSRRDKVYYVETEAPIDQRYVDAFAAGLHFRFEDLTTLPAQLEPI----GPRCARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            L EG+  ++K++F  F+ KV RL R   G   L   L  G+ R ++ + +
Sbjct: 177 TLHEGRYHQVKRMFGHFDNKVLRLHRERMGDICLDPQLPPGAWRPLNAEEI 227


>gi|161524427|ref|YP_001579439.1| RNA-binding S4 domain-containing protein [Burkholderia multivorans
           ATCC 17616]
 gi|160341856|gb|ABX14942.1| RNA-binding S4 domain protein [Burkholderia multivorans ATCC 17616]
          Length = 249

 Score =  149 bits (377), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 60/251 (23%), Positives = 101/251 (40%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 1   MRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDERAQAAQAAQ 60

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     L+T  +   G  +     P     +   GRLDI++
Sbjct: 61  VTILLHKPVGYVSGQAEDGYEPASVLITRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 120

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                ++L  L+ G+ + G
Sbjct: 121 TGLLVLTQNGRIAKQLIGEQSDVDKEYLVRVRFGDRLTDIDQHFPAERLAQLRHGLELDG 180

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREG+ R+I+++ E    +V  L R+  G   LG L 
Sbjct: 181 VALKPAMVSWQNGEQ----LRFVLREGRKRQIRRMCELVGLEVIGLKRVRMGRVTLGALP 236

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 237 QGQWRYLSADE 247


>gi|93005438|ref|YP_579875.1| pseudouridine synthase, Rsu [Psychrobacter cryohalolentis K5]
 gi|92393116|gb|ABE74391.1| ribosomal large subunit pseudouridine synthase B [Psychrobacter
           cryohalolentis K5]
          Length = 310

 Score =  149 bits (377), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 79/310 (25%), Positives = 126/310 (40%), Gaps = 7/310 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
             +++ K +AR G+ SRR++E +I   RV VN          V   D I VDG  ++   
Sbjct: 2   KDEKLQKALARMGLGSRRQMEEVIKAGRVTVNNGPAT-IGDRVEQGDEIRVDGRQIKYTS 60

Query: 70  ---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                R  L  Y     + + +      +           R + VGRLDIN+ GLLL TN
Sbjct: 61  ENEKRRRVLAYYKPEGEVCSANDPEGRPTVFERLPKLTHDRWVMVGRLDINSTGLLLFTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG +A  L  PS++  R Y VR  G V  D    +  G++++        +     +G N
Sbjct: 121 DGEMAHRLMHPSSEVTREYAVRVLGDVTPDMARAMTTGVMLEDGMAKFEDIKEGGGEGVN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
            W  V L+EG+NRE++++FE    KV+RL+R SYG   L   L  G   E+ +K +    
Sbjct: 181 KWHHVQLKEGRNREVRRLFESQGLKVSRLLRTSYGNITLPKELRTGRFLELDRKDINTLT 240

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
               L              +        + +   D     + ++S     S    ++   
Sbjct: 241 DLVSLRPRYGTGLHGAAKEKQERIRNKPLKARRTDTRGDNRNSTSSAKPKSSASPVSRGT 300

Query: 306 HRRNLASNVW 315
                 ++  
Sbjct: 301 RNTRDRNDKR 310


>gi|107100191|ref|ZP_01364109.1| hypothetical protein PaerPA_01001214 [Pseudomonas aeruginosa PACS2]
 gi|254239095|ref|ZP_04932418.1| hypothetical protein PACG_05277 [Pseudomonas aeruginosa C3719]
 gi|254244988|ref|ZP_04938310.1| hypothetical protein PA2G_05867 [Pseudomonas aeruginosa 2192]
 gi|126171026|gb|EAZ56537.1| hypothetical protein PACG_05277 [Pseudomonas aeruginosa C3719]
 gi|126198366|gb|EAZ62429.1| hypothetical protein PA2G_05867 [Pseudomonas aeruginosa 2192]
          Length = 230

 Score =  149 bits (377), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 108/231 (46%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     SRR+ + +IA  R++V+G ++      V     +E+D   L+  +  
Sbjct: 1   MRLDRFLANLPELSRRDAQMLIAGGRLRVDGQVVRDGTHEVRVFSRVELDERLLQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP+G V+   DP   + +      +   +   GRLD NT GL+LLTNDG  +R 
Sbjct: 61  RYYMLHKPMGCVSATRDPQHPTVLDLFPEDLRDDLHIGGRLDYNTTGLMLLTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L LP ++  +VY V     +DQ  ++          + +     Q+             +
Sbjct: 121 LTLPGSRRDKVYYVETEAPIDQRYVDAFAAGLHFRFEDLVTLPAQLEPI----GPRCARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            L EG+  ++K++F  F+ KV RL R   G   L   L  G+ R ++ + +
Sbjct: 177 TLHEGRYHQVKRMFGHFDNKVLRLHRERMGDICLDPQLPPGAWRPLNAEEI 227


>gi|329907292|ref|ZP_08274608.1| putative pseudouridylate synthase [Oxalobacteraceae bacterium
           IMCC9480]
 gi|327547030|gb|EGF31918.1| putative pseudouridylate synthase [Oxalobacteraceae bacterium
           IMCC9480]
          Length = 238

 Score =  149 bits (377), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 55/240 (22%), Positives = 102/240 (42%), Gaps = 23/240 (9%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------------G 64
           ++  G+ SRRE +  I +  V+V+G ++      V+ + H+ ++                
Sbjct: 1   MSELGLCSRREADVWIEKGWVRVDGKVVSELGSKVLPSQHVTIERQAAAEQSKLVTILIN 60

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P+          Y   + L+   +            P+    ++  GRLDI++ GLL+L
Sbjct: 61  KPMGYVSGQAEDGYQPAVTLIKPENRWAEDQATTQFHPTQLRSLVPAGRLDIDSIGLLVL 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVD----QDKLNLLKKGIVIQGICYGDMQVTLD 180
           T DG +A+ L   +T+  + Y VR          +++L  L+ G+ + G      +V   
Sbjct: 121 TQDGRVAKQLIGETTEVEKEYLVRVQYDRPGRLPENQLLKLQHGLTMDGKELLPAKVRWQ 180

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +      ++  LREGK R+I+++ +    KV  L R+  G  +LG L  G  R +    
Sbjct: 181 NEDQ----LSFILREGKKRQIRRMCDMVGLKVLGLKRVRIGNIKLGDLPVGEWRYLGADE 236


>gi|111017942|ref|YP_700914.1| pseudouridylate synthase ribosomal large subunit [Rhodococcus
           jostii RHA1]
 gi|110817472|gb|ABG92756.1| pseudouridylate synthase ribosomal large subunit [Rhodococcus
           jostii RHA1]
          Length = 241

 Score =  149 bits (377), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 75/232 (32%), Positives = 115/232 (49%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ KV+A+AG+ASRR  E +I+Q RV+V+G ++    + +      + VDGV +   + 
Sbjct: 1   MRLQKVLAQAGVASRRAAEELISQGRVEVDGRIVIEQGLRIDPENAVVRVDGVRVVVQKD 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTNDGG 129
                 +KP G  +T SD  GR  V D +        R+  VGRLD +TEGLLLLTNDG 
Sbjct: 61  LVHLALNKPRGWQSTMSDDLGRPCVGDIVSERVAAGQRLFHVGRLDADTEGLLLLTNDGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  PS +  + Y     G +++     LK+G+ +          TL       + V
Sbjct: 121 LAHRLMHPSFEVSKTYLATVSGALERGVGKKLKEGVELDDGPAKVDTFTLLDINEGKSLV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V L EG+   ++++F+     V RL+R   G   LG    G+ R + +  +
Sbjct: 181 RVTLHEGRKHIVRRLFDAVGHPVIRLVRTDIGAVALGDQRPGTLRVLGRGEV 232


>gi|163848780|ref|YP_001636824.1| pseudouridine synthase [Chloroflexus aurantiacus J-10-fl]
 gi|222526730|ref|YP_002571201.1| pseudouridine synthase [Chloroflexus sp. Y-400-fl]
 gi|163670069|gb|ABY36435.1| pseudouridine synthase [Chloroflexus aurantiacus J-10-fl]
 gi|222450609|gb|ACM54875.1| pseudouridine synthase [Chloroflexus sp. Y-400-fl]
          Length = 528

 Score =  149 bits (377), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 102/348 (29%), Positives = 159/348 (45%), Gaps = 6/348 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA 70
           +P+R+ KV+A AGIASRR+ E +IA  RV VNG ++      V    D + VDG PL+  
Sbjct: 2   SPERLQKVLASAGIASRRDCEALIAAGRVMVNGRVVVVPGTRVDLDHDEVLVDGQPLQMP 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            +    + HKP G+V+T  D  GR TV  +L ++ +RV  VGRLD+++EGL+LLT+DG L
Sbjct: 62  TKRTYIMLHKPAGVVSTAEDTHGRPTV-LDLVNVPARVFPVGRLDMDSEGLILLTDDGEL 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS +  + YRV     +  + L   + G+++ G       V L        WV 
Sbjct: 121 AYALTHPSFEVEKEYRVLLDRALTPEALRSWRNGVLLDGEMTAPAWVELIGTAPEGVWVR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + LREG+ R+I+ V +   ++V RLIR+  G   LG L   + R ++ + +         
Sbjct: 181 IVLREGRKRQIRAVAKLLGYEVRRLIRVREGDLVLGDLPPRAWRHLTDEEVAALRTHIAK 240

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR-- 308
               V     +  S    RD        PD  +R  ++   +    + +       R   
Sbjct: 241 RRPPVERSPGVAPSSVRNRDDERPSYRTPDIRSRGDRDDRGREFEREPRARRDSGERGWE 300

Query: 309 -NLASNVWMAKGIHSS-FLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                      G     F  +   R ++  R   F  +   RR S ++
Sbjct: 301 FEREPRARRDSGERGREFEREPRARRDSGERGREFEREPRARRDSGER 348


>gi|226953468|ref|ZP_03823932.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter sp.
           ATCC 27244]
 gi|226835753|gb|EEH68136.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter sp.
           ATCC 27244]
          Length = 314

 Score =  149 bits (377), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 80/304 (26%), Positives = 128/304 (42%), Gaps = 7/304 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
            +++ KV+AR G+ SRR +E +IA  RV +NG + +     +   D + +DG  ++    
Sbjct: 2   SEKLQKVLARVGLGSRRYMEEVIAAGRVSINGRIAQV-GERIEPGDELRIDGRKVQFQVE 60

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R  L  Y     + + +      +           R + VGRLDIN+ GLLL TND
Sbjct: 61  DEIRRRVLIYYKPEGEICSRNDPEKRPTVFDHLPQIANDRWVMVGRLDINSTGLLLFTND 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V     N + KG+ ++         +     G N 
Sbjct: 121 GELANRLMHPSNEVEREYAVRVMGEVTPQIRNNMLKGVELEDGPAKFESFSEIGGDGINR 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V ++EG+NRE++++FE  N KV+RL+R  YG   L   L  G   E+ K  +     
Sbjct: 181 WYQVVVKEGRNREVRRIFESQNLKVSRLLRTRYGTVILPRELRTGRWMELDKMDIDNLAK 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              L+  Q      +    T       + +       + +++  Q              +
Sbjct: 241 SVELKPRQGTGLFGMAKRRTERMTDKPMAARRGGYLRQQRRDDEQPEQRPNSNGGNHNNN 300

Query: 307 RRNL 310
            R  
Sbjct: 301 GRKT 304


>gi|328868084|gb|EGG16464.1| Putative synthase [Dictyostelium fasciculatum]
          Length = 444

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 88/247 (35%), Positives = 134/247 (54%), Gaps = 16/247 (6%)

Query: 2   KDKNIVQENFTP---QRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-RAAVNVMST 57
           +  + ++E   P   +R+ K ++R+G+ SRR+ ERMI + RV VNG +   +  + V  T
Sbjct: 149 RTSSPIEEKIDPNQVERLQKRLSRSGVTSRRQSERMIMEGRVCVNGKVASMKNDLFVKPT 208

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           D + VD   + ++      L       +                      ++SVGRLD  
Sbjct: 209 DIVTVDNKIIEESVPKICNLQDPEKDTLIPILQKMLNK----------DHLMSVGRLDYY 258

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           +EGL+L+TNDG L+R LELP + + + YRVR  G+V  D    L +G+ I GI Y  M++
Sbjct: 259 SEGLILITNDGELSRYLELPQSGFEKTYRVRIFGKVTPDMNMALTRGLTIDGIRYAPMKI 318

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREV 236
           +++ +  SN WV   L EGKNREI+++FE FN KV R+IR  +GP+ L   L  G T EV
Sbjct: 319 SVERETDSNTWVICTLTEGKNREIRRIFEHFNVKVLRIIRTQFGPYTLPETLKPGETVEV 378

Query: 237 S-KKILR 242
             K  ++
Sbjct: 379 HLKDEIK 385


>gi|255971278|ref|ZP_05421864.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis T1]
 gi|255962296|gb|EET94772.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis T1]
          Length = 260

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 68/260 (26%), Positives = 116/260 (44%), Gaps = 3/260 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +     
Sbjct: 1   MRLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESRNVDAQLQMIKVKGQLISHKTH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                       +  VGRLD +TEGLLLLT++G L  
Sbjct: 61  VYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            L  P+ +  + Y V+ +G V  +     K GIV+QG       ++T+     + + V +
Sbjct: 121 QLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHVFL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLL 250
            ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L    +
Sbjct: 181 TIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYFFI 240

Query: 251 EEAQVNLDAPIYSSETLVRD 270
           E+ Q +   P        R 
Sbjct: 241 EKQQTSKALPSNLKREEERK 260


>gi|326575652|gb|EGE25575.1| ribosomal large subunit pseudouridine synthase B [Moraxella
           catarrhalis CO72]
          Length = 328

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 80/318 (25%), Positives = 136/318 (42%), Gaps = 13/318 (4%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           ++         +++ K++AR G+ SRR +E +I   R+ +NG +       V+ TD I +
Sbjct: 13  NEQNATNKPAGEKLQKLLARLGLGSRRGLEEIIKSGRISINGKVAT-LGDRVILTDEIRI 71

Query: 63  DGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           DG  +R        R  +  Y     + +        +           R + VGRLDIN
Sbjct: 72  DGRQVRLKAEREKRRRVIAYYKPEGEICSASDPQGRPTVFDRLPKLTNDRWVMVGRLDIN 131

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           + GLLL TNDG LA  L  PS+  +R Y VR  G+V     + L  G+ ++        +
Sbjct: 132 SSGLLLFTNDGELAHRLMHPSSGIIREYAVRVLGEVTPQIASQLTTGVELEDGVAKFDDI 191

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                 G N W  V ++EG+ RE++++FE    KV+RLIR  YG   L   L  G   E+
Sbjct: 192 KEGGGIGVNKWYHVTIKEGRKREVRRMFESQTLKVSRLIRTRYGTVILPKELRTGRFIEL 251

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
               + + +      ++               +++   I + P     +++   + +   
Sbjct: 252 DASDIGKLV------DSVGLRQRQGTGLNHATKEKQARIHKKPLKSREIRRQKHEAHERR 305

Query: 297 KQKKLATPVHRRNLASNV 314
           +++K  TP HR    S  
Sbjct: 306 EERKKHTPKHRTPNLSRT 323


>gi|315159966|gb|EFU03983.1| conserved hypothetical protein [Enterococcus faecalis TX0312]
          Length = 260

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 68/260 (26%), Positives = 116/260 (44%), Gaps = 3/260 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +     
Sbjct: 1   MRLDKLLEELQFGSRKTVKRLIRGKQVTVDGIVTLNESHNVDAQLQMIKVKGQLISHKTH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                       +  VGRLD +TEGLLLLT++G L  
Sbjct: 61  VYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            L  P+ +  + Y V+ +G V  +     K GIV+QG       ++T+     + + V +
Sbjct: 121 QLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHVFL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLL 250
            ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L    +
Sbjct: 181 TIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYFFI 240

Query: 251 EEAQVNLDAPIYSSETLVRD 270
           E+ Q +   P        R 
Sbjct: 241 EKQQTSKALPSNLKREEERK 260


>gi|326565822|gb|EGE15984.1| ribosomal large subunit pseudouridine synthase B [Moraxella
           catarrhalis BC1]
          Length = 328

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 80/318 (25%), Positives = 136/318 (42%), Gaps = 13/318 (4%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           ++         +++ K++AR G+ SRR +E +I   R+ +NG +       V+ TD I +
Sbjct: 13  NEQNATNKPAGEKLQKLLARLGLGSRRGLEEIIKSGRISINGKVAT-LGDRVILTDEIRI 71

Query: 63  DGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           DG  +R        R  +  Y     + +        +           R + VGRLDIN
Sbjct: 72  DGRQVRLKAEREKRRRVIAYYKPEGEICSASDPQGRPTVFDRLPKLTNDRWVMVGRLDIN 131

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           + GLLL TNDG LA  L  PS+  +R Y VR  G+V     + L  G+ ++        +
Sbjct: 132 SSGLLLFTNDGELAHRLMHPSSGIIREYAVRVLGEVTSQIASQLTAGVELEDGVAKFDDI 191

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                 G N W  V ++EG+ RE++++FE    KV+RLIR  YG   L   L  G   E+
Sbjct: 192 KEGGGIGVNKWYHVTIKEGRKREVRRMFESQTLKVSRLIRTRYGTVILPKELRTGRFIEL 251

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
               + + +      ++               +++   I + P     +++   + +   
Sbjct: 252 DASDIGKLV------DSVGLRQRQGTGLNHATKEKQARIHKKPLKSREIRRQKHEAHERR 305

Query: 297 KQKKLATPVHRRNLASNV 314
           +++K  TP HR    S  
Sbjct: 306 EERKKHTPKHRTPNLSRT 323


>gi|190572990|ref|YP_001970835.1| putative RNA pseudouridine synthase [Stenotrophomonas maltophilia
           K279a]
 gi|190010912|emb|CAQ44521.2| putative RNA pseudouridine synthase [Stenotrophomonas maltophilia
           K279a]
          Length = 277

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 109/233 (46%), Gaps = 4/233 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           +++V+++AG+ SR E  R IA+ RV+V+G ++      +      IEVDG P+   +R  
Sbjct: 42  LARVLSKAGVCSRSEAARWIAEGRVRVSGRIVRDPEFPIGQPAPPIEVDGQPMGAPQRLY 101

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L      + T   +    +       +    +  VGRLD  +EGLLL +ND   A  L
Sbjct: 102 LMLNKPRGVVTTAQDERGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAARL 161

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P T   + Y V+     D   L  L+ G+  +G       V +       AW+ V L 
Sbjct: 162 TDPETGPQKTYHVQVDRLPDDATLAALQAGVDDEGEFLVAQAVRVLRSGDKTAWLEVVLD 221

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           EG+NR I+++   F+ +V RL+R++ G  QL  L  G  R +    + +Q   
Sbjct: 222 EGRNRHIRRLLAAFDLQVLRLVRVAIGGLQLADLGKGQWRML---EVNDQQRL 271


>gi|296113067|ref|YP_003627005.1| ribosomal large subunit pseudouridine synthase B [Moraxella
           catarrhalis RH4]
 gi|295920761|gb|ADG61112.1| ribosomal large subunit pseudouridine synthase B [Moraxella
           catarrhalis RH4]
 gi|326561647|gb|EGE11984.1| ribosomal large subunit pseudouridine synthase B [Moraxella
           catarrhalis 103P14B1]
 gi|326562610|gb|EGE12921.1| ribosomal large subunit pseudouridine synthase B [Moraxella
           catarrhalis 46P47B1]
 gi|326570476|gb|EGE20516.1| ribosomal large subunit pseudouridine synthase B [Moraxella
           catarrhalis BC8]
 gi|326573451|gb|EGE23419.1| ribosomal large subunit pseudouridine synthase B [Moraxella
           catarrhalis 101P30B1]
 gi|326577116|gb|EGE27010.1| ribosomal large subunit pseudouridine synthase B [Moraxella
           catarrhalis O35E]
          Length = 328

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 80/318 (25%), Positives = 136/318 (42%), Gaps = 13/318 (4%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           ++         +++ K++AR G+ SRR +E +I   R+ +NG +       V+ TD I +
Sbjct: 13  NEQNATNKPAGEKLQKLLARLGLGSRRGLEEIIKSGRISINGKVAT-LGDRVILTDEIRI 71

Query: 63  DGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           DG  +R        R  +  Y     + +        +           R + VGRLDIN
Sbjct: 72  DGRQVRLKAEREKRRRVIAYYKPEGEICSASDPQGRPTVFDRLPKLTNDRWVMVGRLDIN 131

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           + GLLL TNDG LA  L  PS+  +R Y VR  G+V     + L  G+ ++        +
Sbjct: 132 SSGLLLFTNDGELAHRLMHPSSGIIREYAVRVLGEVTPQIASQLTAGVELEDGVAKFDDI 191

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                 G N W  V ++EG+ RE++++FE    KV+RLIR  YG   L   L  G   E+
Sbjct: 192 KEGGGIGVNKWYHVTIKEGRKREVRRMFESQTLKVSRLIRTRYGTVILPKELRTGRFIEL 251

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
               + + +      ++               +++   I + P     +++   + +   
Sbjct: 252 DASDIGKLV------DSVGLRQRQGTGLNHATKEKQARIHKKPLKSREIRRQKHEAHERR 305

Query: 297 KQKKLATPVHRRNLASNV 314
           +++K  TP HR    S  
Sbjct: 306 EERKKHTPKHRTPNLSRT 323


>gi|149195571|ref|ZP_01872628.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           Pseudouridylate synthase [Lentisphaera araneosa
           HTCC2155]
 gi|149141033|gb|EDM29429.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           Pseudouridylate synthase [Lentisphaera araneosa
           HTCC2155]
          Length = 236

 Score =  149 bits (376), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 66/231 (28%), Positives = 113/231 (48%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R++K IA  G+ SRR+ E ++ +  + +N   +   +  V    D +     PL   ++
Sbjct: 1   MRIAKFIAACGVCSRRKAEELVNEGHITINNHRVTELSTQVDVDNDEVRYRRKPLVLEKK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      + T       +  +  +L     R+ +VGRLD  +EGL++LTNDG LA+
Sbjct: 61  LYYLLNKPVGYVCTNDDPFAEKKAI--DLLPDKGRLYTVGRLDKPSEGLIVLTNDGDLAK 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAWVTV 191
           ++  PS +  + YRV   G+V Q KL+ L +  +  +G+ Y  +   +  Q      +  
Sbjct: 119 IMTHPSFELEKKYRVTVKGRVSQKKLDYLVRDGLTFEGVNYRVLDARIKKQVPGGYMINF 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            L EGKNREI+K+ +  + +V RL R       LG L  G+ R +++  +R
Sbjct: 179 TLNEGKNREIRKICQSLDLQVKRLRRYEIAGIALGKLPPGAWRPMTQSEVR 229


>gi|326564224|gb|EGE14460.1| ribosomal large subunit pseudouridine synthase B [Moraxella
           catarrhalis 12P80B1]
          Length = 328

 Score =  149 bits (376), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 80/318 (25%), Positives = 136/318 (42%), Gaps = 13/318 (4%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           ++         +++ K++AR G+ SRR +E +I   R+ +NG +       V+ TD I +
Sbjct: 13  NEQNATNKPAGEKLQKLLARLGLGSRRGLEEIIKSGRISINGKVAT-LGDRVILTDEIRI 71

Query: 63  DGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           DG  +R        R  +  Y     + +        +           R + VGRLDIN
Sbjct: 72  DGRQVRLKAEREKRRRVIAYYKPEGEICSASDPQGRPTVFDRLPKLTNDRWVMVGRLDIN 131

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           + GLLL TNDG LA  L  PS+  +R Y VR  G+V     + L  G+ ++        +
Sbjct: 132 SSGLLLFTNDGELAHRLMHPSSGIIREYAVRVLGEVTPQIASQLTAGVELEDGVAKFDDI 191

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                 G N W  V ++EG+ RE++++FE    KV+RLIR  YG   L   L  G   E+
Sbjct: 192 KEGGGIGVNKWYHVTIKEGRKREVRRMFESQTLKVSRLIRTRYGTVILPKELRTGRFIEL 251

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
               + + +      ++               +++   I + P     +++   + +   
Sbjct: 252 DASDIGKLV------DSVGLRQRQGTGLNHATKEKQARIHKKPLKSREIRRQKHEAHERR 305

Query: 297 KQKKLATPVHRRNLASNV 314
           +++K  TP HR    S  
Sbjct: 306 EERKKHTPKHRTPNLSRT 323


>gi|255020930|ref|ZP_05292986.1| ribosomal small subunit pseudouridine synthase [Acidithiobacillus
           caldus ATCC 51756]
 gi|254969721|gb|EET27227.1| ribosomal small subunit pseudouridine synthase [Acidithiobacillus
           caldus ATCC 51756]
          Length = 234

 Score =  149 bits (376), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 52/227 (22%), Positives = 92/227 (40%), Gaps = 2/227 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ ++ +R G  SR E+   +   RV V    +   ++ V     +++DG PL   E  
Sbjct: 6   ERLDRLFSRLGYGSRSELREWLRAGRVSVGSRPVGSPSLRVDPK-LVQIDGQPLDHPEGL 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L  +     +                       + +VGRLD +T G+LL+T+DGG    
Sbjct: 65  YLLYHKPRGKVCAHGEPRSVYGDFPAAWSVRRPAINTVGRLDADTSGVLLVTDDGGWLHR 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
              P     R YRV     +    L  L+ G ++                     + + L
Sbjct: 125 WTHPRRAVPRTYRVGLAEPITDGALAQLRSGKLLLAGETSPCLPADVEVLAPRH-LRLTL 183

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           REG+  E++++      +V+ L R ++GPF++  L +GS R +    
Sbjct: 184 REGRYHEVRRMLAALGNRVDTLHREAFGPFRVDDLPSGSWRLLDPHE 230


>gi|306827091|ref|ZP_07460388.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes ATCC 10782]
 gi|304430725|gb|EFM33737.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes ATCC 10782]
          Length = 238

 Score =  149 bits (376), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 56/229 (24%), Positives = 97/229 (42%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +   + 
Sbjct: 1   MRLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQQVTHPKH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + + L      +                       +  VGRLD +TEGL+LLT++G L  
Sbjct: 61  SYIILNKPSGVVSAKKDTNYLTVIDQLAEEDKSPDLYPVGRLDRDTEGLVLLTDNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +  PS    + Y V  +G + +D  +    GI    G      Q+T+       +  ++
Sbjct: 121 RMLHPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQSQASL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R ++   
Sbjct: 181 TISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLTASE 229


>gi|257482791|ref|ZP_05636832.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. tabaci ATCC
           11528]
          Length = 241

 Score =  149 bits (376), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 82/238 (34%), Positives = 115/238 (48%), Gaps = 9/238 (3%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG         V   D I
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDAT-LGQRVDLHDAI 62

Query: 61  EVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            VDG  +++ E     R  +        + T        +           R I++GRLD
Sbjct: 63  SVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           INT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++       
Sbjct: 123 INTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPARFT 182

Query: 176 QVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAG 231
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMG 240


>gi|94990717|ref|YP_598817.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS10270]
 gi|94544225|gb|ABF34273.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS10270]
          Length = 238

 Score =  149 bits (376), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 56/229 (24%), Positives = 97/229 (42%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +   + 
Sbjct: 1   MRLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQQVTHPKH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + + L      +                       +  VGRLD +TEGL+LLT++G L  
Sbjct: 61  SYIILNKPSGVVSAKKDTNYLTVIDQLAEEDKSPDLYPVGRLDRDTEGLVLLTDNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +  PS    + Y V  +G + +D  +    GI    G      Q+T+       +  ++
Sbjct: 121 RMLHPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQSQASL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R ++   
Sbjct: 181 TISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLTASE 229


>gi|294649541|ref|ZP_06726962.1| ribosomal large subunit pseudouridine synthase B [Acinetobacter
           haemolyticus ATCC 19194]
 gi|292824602|gb|EFF83384.1| ribosomal large subunit pseudouridine synthase B [Acinetobacter
           haemolyticus ATCC 19194]
          Length = 310

 Score =  149 bits (376), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 80/304 (26%), Positives = 128/304 (42%), Gaps = 7/304 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
            +++ KV+AR G+ SRR +E +IA  RV +NG + +     +   D + +DG  ++    
Sbjct: 2   SEKLQKVLARVGLGSRRYMEEVIAAGRVSINGRIAQV-GERIEPGDELRIDGRKVQFQVE 60

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R  L  Y     + + +      +           R + VGRLDIN+ GLLL TND
Sbjct: 61  DEIRRRVLIYYKPEGEICSRNDPEKRPTVFDHLPQIANDRWVMVGRLDINSTGLLLFTND 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V     N + KG+ ++         +     G N 
Sbjct: 121 GELANRLMHPSNEVEREYAVRVMGEVTPQIRNNMLKGVELEDGPAKFESFSEIGGDGINR 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           W  V ++EG+NRE++++FE  N KV+RL+R  YG   L   L  G   E+ K  +     
Sbjct: 181 WYQVVVKEGRNREVRRIFESQNLKVSRLLRTRYGTVILPRELRTGRWMELDKMDIDNLAK 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              L+  Q      +    T       + +       + +++  Q              +
Sbjct: 241 SVELKPRQGTGLFGMAKRRTERMTDKPMAARRGGYLRQQRRDDEQPEQRPNSNGGNHNNN 300

Query: 307 RRNL 310
            R  
Sbjct: 301 GRKT 304


>gi|148979672|ref|ZP_01815644.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrionales
           bacterium SWAT-3]
 gi|145961649|gb|EDK26947.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrionales
           bacterium SWAT-3]
          Length = 231

 Score =  149 bits (376), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 50/232 (21%), Positives = 99/232 (42%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E   ++  + V VN ++ +  +V V     +E  G  L      
Sbjct: 1   MRLDKFLCDALGITRKEATHLLKTKTVTVNDVMQKSGSVKVTEQCVVEWQGNELNVHGPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + LY     + +       R+           ++   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLYKPEGFVCSHEDG-SNRTAFELLDEIKMDKLHFAGRLDVDTTGLVLITDDGKWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  ++YRV     V+ D +   K+GI +  +        + +     +   V +
Sbjct: 120 ITAPKHKCEKMYRVWLVDPVEPDYVEKFKEGIQLKSEDGLTLPAHLEV----RAEREVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            + EGK  ++K++F     KV  L R   G  ++   L  G  R ++++ + 
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVEALHRERIGEIEMDESLELGEYRYLTQEEVD 227


>gi|78046600|ref|YP_362775.1| pseudouridylate synthase [Xanthomonas campestris pv. vesicatoria
           str. 85-10]
 gi|78035030|emb|CAJ22675.1| Pseudouridylate synthase [Xanthomonas campestris pv. vesicatoria
           str. 85-10]
          Length = 286

 Score =  149 bits (376), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 64/247 (25%), Positives = 112/247 (45%), Gaps = 7/247 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      +       I VDG PL    R 
Sbjct: 39  LARVLSKLGVCSRTEAARWIADGRVSVSARVVRDPEFPIRGDQQSSITVDGQPLAGPARC 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L      + T   +    +       +    +  VGRLD  +EGLLL +ND   A  
Sbjct: 99  YLMLNKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAAT 158

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNAW 188
           +  P+    + Y V+   +    +L  L+ G+       +G+     QV++  +   NAW
Sbjct: 159 VTDPARGPDKTYHVQIDCRPSAAQLTQLQAGVADTDPEGEGVLLRAKQVSVLREGERNAW 218

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + + L EG+NR+I+++    +  V RL+R++ GP  +G L  G+ R +S + +R  +   
Sbjct: 219 LEIVLDEGRNRQIRRLLAAVDIGVLRLVRVAIGPLAMGELGKGAWRMLSAEEVRTLVPAA 278

Query: 249 LLEEAQV 255
                  
Sbjct: 279 RASAPDA 285


>gi|166711386|ref|ZP_02242593.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzicola BLS256]
          Length = 240

 Score =  149 bits (376), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 63/239 (26%), Positives = 104/239 (43%), Gaps = 10/239 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA  G  SRR+ +R+I ++RV VNG+     AV V   D + VDG PLR  E  +
Sbjct: 4   RLNKYIAETGFCSRRQADRLIGERRVTVNGVSAGTGAV-VGEEDTVLVDGQPLRVREAKK 62

Query: 75  L-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           L             +  T +                 R+  +GRLD  +EGL+L+T++G 
Sbjct: 63  LGGRRHVYIALNKPVGITCTTESSVKGNIVEFVGHEQRIFPIGRLDKESEGLILMTSNGN 122

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +     +  + Y V  +  V  + L  + +G+ I        +     + G     
Sbjct: 123 IVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRIHNETTLPCRTARIAKFG----F 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR  L   
Sbjct: 179 RIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELRGLLPQR 237


>gi|332202557|gb|EGJ16626.1| hypothetical protein SPAR69_0668 [Streptococcus pneumoniae GA41317]
          Length = 241

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 106/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLKGDILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                      ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKELPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSISQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K L+
Sbjct: 180 TISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKELQ 231


>gi|306829140|ref|ZP_07462330.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           mitis ATCC 6249]
 gi|304428226|gb|EFM31316.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           mitis ATCC 6249]
          Length = 241

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 53/232 (22%), Positives = 104/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A+  + SR+ +++ + ++ + V+       A NV +    +   G  ++  E 
Sbjct: 1   MRLDRLLAQEKV-SRKAMKQALLKKEILVDDCPTSSLAQNVDTGLQKLVFQGRQIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L+     +  +                   ++ ++GRLD +T GLLLLT++G L  
Sbjct: 60  IYLMLHKPNGVVTASKDKKLPTVMDLVPKNIQSGQLYAIGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   K+GIV          Q+ + +   + +  ++
Sbjct: 120 QLLHPQYHVDKSYQVVVNGPLTSDHIQKFKEGIVFLDGTTCKPAQLEILSSSPTESRASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++KK+F     KV  L R+ +G F L   L  G  R ++ + L 
Sbjct: 180 TISEGKFHQVKKMFLSVGVKVTSLKRVQFGDFTLDPELAEGQYRPLNPEELE 231


>gi|71064605|ref|YP_263332.1| ribosomal small subunit pseudouridine synthase A [Psychrobacter
           arcticus 273-4]
 gi|71037590|gb|AAZ17898.1| ribosomal small subunit pseudouridine synthase A [Psychrobacter
           arcticus 273-4]
          Length = 239

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 54/235 (22%), Positives = 98/235 (41%), Gaps = 11/235 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +++A   SR+E ++++    V VN  +++   V+V    D ++  G PL  A  
Sbjct: 6   MRLDKFLSKATELSRKESKKILHAGEVTVNEQVIKDPGVHVDIVNDDVQWAGEPLSVATG 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R  L HKP G   T    +               +   GRLD++T G LL+++DGG   
Sbjct: 66  NRYILLHKPEGFECTLKAKEYPIVTDLIAVPELGSLRIAGRLDVDTTGALLISDDGGWLH 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI------VIQGICYGDMQVTLDTQKGSN 186
            +  P  +  +VY +     +D D      K +                 +    +  + 
Sbjct: 126 RVTSPKHEHAKVYELTLADAMDSDAQANAIKEVAEGILLEGDHEETKPATLEFIDETHA- 184

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
               + L +GK  ++K++  +F  +V  L R S G   L  L  G +R ++ + +
Sbjct: 185 ---RLTLEQGKYHQVKRMMGYFGNRVVELHRASVGHITLDGLEKGDSRFLTPEEV 236


>gi|255021571|ref|ZP_05293614.1| hypothetical protein ACA_2484 [Acidithiobacillus caldus ATCC 51756]
 gi|254968959|gb|EET26478.1| hypothetical protein ACA_2484 [Acidithiobacillus caldus ATCC 51756]
          Length = 288

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 84/287 (29%), Positives = 124/287 (43%), Gaps = 7/287 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----- 68
           +++ KV+AR G+ SRR++E  I   RV++N          V S D + VDG PLR     
Sbjct: 3   EKLQKVLARHGLGSRRQMEAWIRAGRVQINDRPAT-IGDRVTSRDRLSVDGKPLRVPSWV 61

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           +     L  +     L T        +          SR ++VGRLD+NTEGLLL TNDG
Sbjct: 62  RPRLRVLRYHKPAGELATRQDPEGRPTVFDRLPRLRGSRWVAVGRLDLNTEGLLLFTNDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P  +  RVY VR  G +  ++   L  G+ ++      + +     +GSN W
Sbjct: 122 DLANALMHPRAELERVYAVRVLGSLSDEQKAALLAGVELEDGPARFLAIEEAGGEGSNRW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
             V L EG+NRE++++    +  V+RLIRI YGP  +   L  G   E+S       L  
Sbjct: 182 YHVSLAEGRNREVRRLLAAVHLSVSRLIRIRYGPIDMPRHLKLGYFEELSDAERSVLLDA 241

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
               + Q    A     +            +  +  R K      + 
Sbjct: 242 VQWSDPQATAAAEHGPEDRRPNRSRQHRHGLRTELQRGKGGPRSGHA 288


>gi|24214991|ref|NP_712472.1| pseudouridylate synthase [Leptospira interrogans serovar Lai str.
           56601]
 gi|24196034|gb|AAN49490.1| pseudouridylate synthase [Leptospira interrogans serovar Lai str.
           56601]
          Length = 246

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 62/224 (27%), Positives = 107/224 (47%), Gaps = 5/224 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA-E 71
            R+++ +A  G+ SRR+ E +I +  +++NG  +      +    D +   G  ++   E
Sbjct: 15  IRLNRFLADCGLGSRRKTEELIQKGHIEINGKRVTNLGTRIDPEIDVVSYLGDVVKPIVE 74

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +++KPIG + +H+D     T+F  LPS +      GRLD+N+ GLL+LTNDG LA
Sbjct: 75  SKKILIFNKPIGYLCSHADRFHEKTIFSLLPSDYKNFKIAGRLDLNSRGLLILTNDGALA 134

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           + +  PS    + Y V       +  +    +  ++        ++      G      V
Sbjct: 135 QKITHPSNGSEKEYLVTLKHDPGEKLIQAAFQKGILDAGEILHAKMVKLVP-GKKCVYRV 193

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGST 233
            L EGK R+I+++F +F   V  L RI  GP +L    L  G  
Sbjct: 194 ILEEGKKRQIRRMFRWFGVSVVDLQRIRIGPLKLEKFNLEEGQY 237


>gi|315651232|ref|ZP_07904262.1| ribosomal small subunit pseudouridine synthase A [Eubacterium
           saburreum DSM 3986]
 gi|315486528|gb|EFU76880.1| ribosomal small subunit pseudouridine synthase A [Eubacterium
           saburreum DSM 3986]
          Length = 235

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 114/233 (48%), Gaps = 10/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            RV K+++  G  SR E++R +   +V++N   +++    + +  D +  DG  +   E 
Sbjct: 6   VRVDKILSELGFGSRTEIKRYVKAGKVRINENPVKKPEEKINTEIDRLYFDGKDVVIEEF 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               LY     +  T  +     TV + + S    ++ VGRLD++TEGLL+LTNDG L  
Sbjct: 66  ETYVLYKPAGYVCATFDNVH--KTVMELIDSNRKNIVPVGRLDLDTEGLLILTNDGNLNH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  PS+   +VY  +F G +  D + +  KG+ I         ++ + ++      V +
Sbjct: 124 RLVSPSSHVDKVYYAKFDGVLADDAIEMTAKGLDIGDGEVSKPAKLEIVSKN----EVLL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL--AGSTREVSKKILR 242
            + EGK  ++K++ +    +V  L R ++G   L  L    G +R++S + +R
Sbjct: 180 TIHEGKFHQVKRMIKALGGEVTYLKRTAFGGLGLDDLNLKRGESRKISMEEMR 232


>gi|225023283|ref|ZP_03712475.1| hypothetical protein EIKCOROL_00135 [Eikenella corrodens ATCC
           23834]
 gi|224943928|gb|EEG25137.1| hypothetical protein EIKCOROL_00135 [Eikenella corrodens ATCC
           23834]
          Length = 246

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 63/249 (25%), Positives = 103/249 (41%), Gaps = 20/249 (8%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-- 64
           +       R+SK +A  G+ SRRE +  I +  V VNG         V   D IE+    
Sbjct: 1   MTTPDNTVRLSKRMAELGLCSRREADAYIERGWVSVNGEKA-VLGQKVGEGDRIELHRAA 59

Query: 65  -------------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                         P+          Y     L+T  +      +      +    +   
Sbjct: 60  HEEQAGRVTILLHKPVGFVSGQAEKGYRSAAELITEANHWPEDRSPQKFKAAHRHGLAPA 119

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++ ++ L LL  G+ + G  
Sbjct: 120 GRLDIDSVGLLVLTQDGRVAKSLIGENSGVEKEYLVRVKGKLSEEGLRLLNHGLKLDGEA 179

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
               +V+   Q      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G
Sbjct: 180 LRPAKVSWQNQDQ----LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRIGKVKLGALPPG 235

Query: 232 STREVSKKI 240
             R ++   
Sbjct: 236 QWRYLAPHE 244


>gi|189499452|ref|YP_001958922.1| pseudouridine synthase [Chlorobium phaeobacteroides BS1]
 gi|189494893|gb|ACE03441.1| pseudouridine synthase [Chlorobium phaeobacteroides BS1]
          Length = 254

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 68/251 (27%), Positives = 110/251 (43%), Gaps = 9/251 (3%)

Query: 1   MKDKNI---VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           MK K+    V+      R++K +A  GIASRR  +R++    V VNG ++ +    V   
Sbjct: 1   MKKKSSNAHVETPGAAVRINKYLALCGIASRRAADRLVESGEVMVNGRIMMKKGATVRPG 60

Query: 58  -DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            D + V    L   E  ++++         T S  +       +L  +  RV  VGRLD 
Sbjct: 61  VDEVVVSNRLLALPEEKKVYILLNKPRNYITTSSDEKERETVLDLVDVRERVFPVGRLDR 120

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGD 174
            T G+LLLTNDG LA  L  PS++  + Y         +  L  L  G+ ++        
Sbjct: 121 KTTGMLLLTNDGALAHRLMHPSSEVEKEYLAELETPFSEKDLPSLTGGMRLKDTGEKTSP 180

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +  +         V V + EGKN +++++F    + V RL R +Y   + G L  G  R
Sbjct: 181 CKGKIMQGGL---RVLVTIHEGKNHQVRRMFRSLGYDVKRLDRTAYAGLRAGKLRRGEWR 237

Query: 235 EVSKKILREQL 245
             + K + + +
Sbjct: 238 YATSKEVEQLM 248


>gi|194397181|ref|YP_002037336.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae G54]
 gi|194356848|gb|ACF55296.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae G54]
          Length = 241

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 106/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                      ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKELPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSISQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K L+
Sbjct: 180 TISEGKFHQIKKMFLSVGIKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKELQ 231


>gi|149010697|ref|ZP_01832068.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP19-BS75]
 gi|147765178|gb|EDK72107.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP19-BS75]
          Length = 241

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 106/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                      ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKELPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSISQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K L+
Sbjct: 180 TISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKELQ 231


>gi|160874235|ref|YP_001553551.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|160859757|gb|ABX48291.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|315266469|gb|ADT93322.1| pseudouridine synthase [Shewanella baltica OS678]
          Length = 256

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 53/230 (23%), Positives = 98/230 (42%), Gaps = 8/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +       R+ V  ++   RV V+G++++     V    HI++D   L+      
Sbjct: 28  RLDRYLCTQLHTHRKAVRELLLSGRVCVDGLIVKDMDRQVDEFSHIQLDEQILQANVPVY 87

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L+     +V+   D   ++ +          +   GRLD+N+ GLLLLTND   +  L
Sbjct: 88  VMLHKPIG-VVSATKDTQHKTVIDLLDCEARDELHIAGRLDLNSSGLLLLTNDSRWSDAL 146

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLK--KGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
             P+ +  +VYRV     + ++ +           + I     ++ +     +     V 
Sbjct: 147 MSPTHKVDKVYRVTLANPITEEYIAAFAAGMYFGFEDITTQPAKLVILADNVA----EVT 202

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           L EGK  +IK++F  F   V  L R+S G   L   L  G +R ++   +
Sbjct: 203 LHEGKYHQIKRMFGRFRNPVVGLHRLSIGDIVLDEKLAPGESRALTAAEV 252


>gi|45657519|ref|YP_001605.1| pseudouridylate synthase [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
 gi|45600758|gb|AAS70242.1| pseudouridylate synthase [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
          Length = 246

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 62/224 (27%), Positives = 107/224 (47%), Gaps = 5/224 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA-E 71
            R+++ +A  G+ SRR+ E +I +  +++NG  +      +    D +   G  ++   E
Sbjct: 15  IRLNRFLADCGLGSRRKTEELIQKGHIEINGKRVTNLGTRIDPEIDVVSYLGDVVKPIVE 74

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +++KPIG + +H+D     T+F  LPS +      GRLD+N+ GLL+LTNDG LA
Sbjct: 75  SKKILIFNKPIGYLCSHADRFHEKTIFSLLPSDYKNFKIAGRLDLNSRGLLILTNDGALA 134

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           + +  PS    + Y V       +  +    +  ++        ++      G      V
Sbjct: 135 QKITHPSNGSEKEYLVTLKHDPGEKLIQAAFQKGILDAGEILHAKMVKLVP-GKKCVYRV 193

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGST 233
            L EGK R+I+++F +F   V  L RI  GP +L    L  G  
Sbjct: 194 ILEEGKKRQIRRMFRWFGVSVVDLQRIRIGPLKLEKFNLEEGQY 237


>gi|254000317|ref|YP_003052380.1| RNA-binding S4 domain-containing protein [Methylovorus sp. SIP3-4]
 gi|253986996|gb|ACT51853.1| RNA-binding S4 domain protein [Methylovorus sp. SIP3-4]
          Length = 455

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 65/255 (25%), Positives = 101/255 (39%), Gaps = 19/255 (7%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M     V       R+SK +A  G+ SRRE +  I    V+VNG +++     V    +I
Sbjct: 203 MFTPKPVASQPDLPRLSKRMAELGLCSRREADEWIVNGWVRVNGQVVDELGSRVEPDANI 262

Query: 61  EVDG---------------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           EV                  P+          Y   + LV   +         +      
Sbjct: 263 EVSKEAEKHQSEIVTILLHKPVGYVSGQAEDGYEPAVVLVHPDNHWAEDPVQKEFRRGFL 322

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             +   GRLDI++ GLL+LT DG +AR L    +Q  + Y VR  G +  + L  L  G+
Sbjct: 323 KGLAPAGRLDIDSTGLLVLTQDGRVARQLIGEDSQTEKEYLVRVEGTLSDEGLRKLNHGL 382

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G+     +V+   +      +   LREG+ R+I+++ E     V  L R+  G   L
Sbjct: 383 SLDGVQLKPAKVSWQNEDQ----LRFVLREGRKRQIRRMCELVGLHVVGLKRVRIGSVAL 438

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R +    
Sbjct: 439 GKLPPGQWRYLRPGE 453



 Score = 37.1 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 15/93 (16%), Positives = 24/93 (25%), Gaps = 3/93 (3%)

Query: 265 ETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW---MAKGIH 321
           E  V D P               +  Q  G S   + A     R    N       +   
Sbjct: 94  EHQVADSPAENDRPRRVAADRDASERQPAGRSASDRPARSGESRPRTDNARPENRQRDER 153

Query: 322 SSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +  S+  +R    R       + + RR    +
Sbjct: 154 PAERSELPRRPAADRADRLASDRDTPRRGGKAR 186


>gi|294788618|ref|ZP_06753860.1| ribosomal large subunit pseudouridine synthase F [Simonsiella
           muelleri ATCC 29453]
 gi|294483495|gb|EFG31180.1| ribosomal large subunit pseudouridine synthase F [Simonsiella
           muelleri ATCC 29453]
          Length = 245

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 113/247 (45%), Gaps = 20/247 (8%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
               P R+SK +A   + SRRE +  I Q  VKVNG++       V+ TD I++D +  +
Sbjct: 2   TEIQPIRLSKRMAELKMCSRREADHYIEQGWVKVNGVVA-VLGQKVVPTDRIDLDKIAHQ 60

Query: 69  KAERTRLWLYHKPIGLVT---------------THSDPDGRSTVFDNLPSIFSRVISVGR 113
           +  +    L +KP+G V+                 +  +G ++     P     +   GR
Sbjct: 61  QQAQRVTILLNKPVGFVSGQPEKDYRAAIELIAADNHWNGDTSKIPFHPKQLKGLAPAGR 120

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LDI++ GLL+LT DG +A+ L    +   + Y VR  G + ++ L LL  G+ + G    
Sbjct: 121 LDIDSVGLLVLTQDGRIAKQLIGEHSDSEKEYLVRVKGNLIENGLALLNHGLSLDGEKLR 180

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
             +V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  
Sbjct: 181 PAKVEWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRIGKVKLGALPVGQW 236

Query: 234 REVSKKI 240
           R +    
Sbjct: 237 RYLGANE 243


>gi|127511849|ref|YP_001093046.1| pseudouridine synthase [Shewanella loihica PV-4]
 gi|126637144|gb|ABO22787.1| pseudouridine synthase [Shewanella loihica PV-4]
          Length = 236

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 57/235 (24%), Positives = 104/235 (44%), Gaps = 8/235 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I++     R++V  ++A+ RV V+G ++  A   +     + +DG  LR+ +   
Sbjct: 7   RLDRFISQHCQIPRKQVRLILAKGRVSVDGQVVRDADCQIDQFSQVMLDGQALRQEQPIY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L+     +V+   D + ++ +          +  VGRLD+NT GLLLLTND   ++ +
Sbjct: 67  LMLHKPVG-VVSATKDDEHKTVMDLLPDYQDKGLHIVGRLDLNTSGLLLLTNDSRWSKRI 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
             P  +  + Y V     + Q  +    +      + I     Q+ +           V 
Sbjct: 126 MSPEHKVAKQYLVTLKAPLTQAYVKAFAEGFYFAFENITTQPAQLEIL----EPHLARVT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
           L EG+  +IK++F  F  +V  L R+S G   L   L  G  R ++ + +    G
Sbjct: 182 LHEGRYHQIKRMFGRFRNQVMALHRLSVGNLILDETLAVGQYRPLTPQEVASIFG 236


>gi|46449495|gb|AAS96146.1| ribosomal large subunit pseudouridine synthase B [Desulfovibrio
           vulgaris str. Hildenborough]
          Length = 267

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 75/245 (30%), Positives = 121/245 (49%), Gaps = 9/245 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK-- 69
             R++K ++ AG+ SRR+ + +IA  +V+VNG ++      V   TD IEV+G  L    
Sbjct: 20  GTRLNKALSGAGVCSRRQADTLIAGGKVRVNGEVVTEMGRRVFPATDRIEVEGRLLACGE 79

Query: 70  ---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLL 124
                R    + +KP+ +V+T  DP GR+T+ D LP     V    VGRLD  +EGLLLL
Sbjct: 80  ALNRHRHTYVMLNKPVQVVSTVRDPQGRTTILDILPDDLKTVRLYPVGRLDFFSEGLLLL 139

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQK 183
           T+DG L   L  P     + YRV     +    L  ++ G+ + +G     ++  +  + 
Sbjct: 140 TDDGDLTHRLTHPKWHLPKYYRVLVREDIPPAALTAMRSGMTLAEGDRVAPVEAYIIDRS 199

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
                + + L +G NR+I+++       V RL+RI  GP +LG L  G+ R +    ++ 
Sbjct: 200 EYGVELEMVLHQGINRQIRRMCRDLGLTVLRLLRIQQGPVELGNLSRGACRRLEDHEVKA 259

Query: 244 QLGPH 248
                
Sbjct: 260 LRKAA 264


>gi|332522623|ref|ZP_08398875.1| pseudouridylate synthase [Streptococcus porcinus str. Jelinkova
           176]
 gi|332313887|gb|EGJ26872.1| pseudouridylate synthase [Streptococcus porcinus str. Jelinkova
           176]
          Length = 239

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 62/239 (25%), Positives = 101/239 (42%), Gaps = 4/239 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G  SR +V+ ++  ++V VNG    +A   +    D +EV+G  +   E 
Sbjct: 1   MRLDKFLAETGFGSRTQVKSLLKTKKVCVNGKKESQAKKQINPNLDRVEVEGQEVLYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +  T            +  +    V  VGRLD +T GLLLLTN+G LA 
Sbjct: 61  VYYMLNKPKGVVSATQDKVHQTVLDLLDATAKQKEVFPVGRLDKDTHGLLLLTNNGNLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVT 190
            L  P     +VY     G +    +   KKGI +          ++     + S + V 
Sbjct: 121 RLLSPKKHVNKVYVADVDGLMTNQDIEAFKKGIHLSDHQCQPALLEILALDYEKSQSRVK 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           + ++EGK  ++K++      +V  L R+  GP QL   L  G+ R++    +   L   
Sbjct: 181 IVIKEGKFHQVKRMVLACGKEVRDLQRLEMGPLQLDSKLALGAFRKLENTEIEALLSLP 239


>gi|171464311|ref|YP_001798424.1| RNA-binding S4 domain protein [Polynucleobacter necessarius subsp.
           necessarius STIR1]
 gi|171193849|gb|ACB44810.1| RNA-binding S4 domain protein [Polynucleobacter necessarius subsp.
           necessarius STIR1]
          Length = 245

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 61/246 (24%), Positives = 109/246 (44%), Gaps = 20/246 (8%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRK 69
               RVSK+++  G+ SRRE +  I Q  V ++G ++    V       IE+  G   ++
Sbjct: 2   EEKVRVSKLLSELGLCSRREADSYIEQGLVTIDGEVVNELGVRAYRHQKIELQSGAKAQQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---------------ISVGRL 114
           A R  + L      +     + + +       P+ +                     GRL
Sbjct: 62  ASRITVILNKPVGYISHYDDEQEYQPAASLITPANYFASPLDKGKSPRFNTKGLAPAGRL 121

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DI++ G+L+LT DG +A++L   ++   + Y VR  G++  + L+ L+ G+ +  +    
Sbjct: 122 DIDSTGMLVLTQDGRIAKLLIGENSPIEKEYLVRVAGRLSFEGLDRLRHGLSLDEVELKP 181

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            QV+   ++     +   LREG+ R+I+++ E    KV  L R+  G   LG+L  G  R
Sbjct: 182 AQVSWQNEEQ----LRFVLREGRKRQIRRMCEIVGLKVLGLKRVRMGRISLGSLPPGQWR 237

Query: 235 EVSKKI 240
            V    
Sbjct: 238 YVGPHE 243


>gi|28895711|ref|NP_802061.1| 16S pseudouridylate synthetase [Streptococcus pyogenes SSI-1]
 gi|28810960|dbj|BAC63894.1| putative 16S pseudouridylate synthetase [Streptococcus pyogenes
           SSI-1]
          Length = 238

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 56/229 (24%), Positives = 97/229 (42%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +   + 
Sbjct: 1   MRLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQRVTHPKH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + + L      +                       +  VGRLD +TEGL+LLT++G L  
Sbjct: 61  SYIILNKPSGVVSAKKDTNYLTVIDQLAEEDKSPDLYPVGRLDRDTEGLVLLTDNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +  PS    + Y V  +G + +D  +    GI    G      Q+T+       +  ++
Sbjct: 121 RMLDPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQSQASL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R ++   
Sbjct: 181 TISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLTASE 229


>gi|295688343|ref|YP_003592036.1| RNA-binding S4 domain-containing protein [Caulobacter segnis ATCC
           21756]
 gi|295430246|gb|ADG09418.1| RNA-binding S4 domain protein [Caulobacter segnis ATCC 21756]
          Length = 256

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 68/245 (27%), Positives = 122/245 (49%), Gaps = 17/245 (6%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +   PQRV+K +A++G+ SRRE E++I+   V ++G ++E     +     + +      
Sbjct: 8   DEAEPQRVNKWLAQSGVCSRREAEQLISDGLVSIDGEVVEDVGRKIQPGQTLVLADRATA 67

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-------------SVGRLD 115
           K + T  +L HKP G+V++  DP           +                    VGRLD
Sbjct: 68  KLDGTPTYLIHKPRGVVSSQPDPGQVPAARLLTRANLWGDARGVAIPQSGDLIPPVGRLD 127

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
            ++ GLLLL+ DG +A+ +  P +   + YRV   G++ ++KL LL+ G+ + G      
Sbjct: 128 KDSRGLLLLSQDGVVAKAVIGPQSDLEKEYRVAVMGELTEEKLELLRFGLELDGRELRPA 187

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           +V + + +     ++  LREG+NR+I+++ +  + KV  L R+  GP  LG +  G  R 
Sbjct: 188 EVEVISDQR----LSFVLREGRNRQIRRMCDLVDLKVVDLFRVRIGPLDLGDMPEGRWRP 243

Query: 236 VSKKI 240
           ++   
Sbjct: 244 LTSAE 248


>gi|217974432|ref|YP_002359183.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217499567|gb|ACK47760.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 235

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 54/230 (23%), Positives = 101/230 (43%), Gaps = 8/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +       R+ V  ++   RV V+G++++     V    HI++D   L+      
Sbjct: 7   RLDRYLCTQLHTHRKAVRELLLSGRVCVDGLIVKDMDRQVDEFSHIQLDEQILQANAPVY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L+     +V+   D   ++ +          +   GRLD+N+ GLLLLTND   +  L
Sbjct: 67  VMLHKPIG-VVSATKDIQHKTVIDLLDCEARDELHIAGRLDLNSSGLLLLTNDSRWSDAL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTVG 192
             P+ +  +VYRV     + ++ +    +G+    + I     ++ +     +     V 
Sbjct: 126 MSPTHKVDKVYRVTLANPITEEYIAAFAEGMYFGFEDITTQPAKLVILADNVA----EVT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           L EGK  +IK++F  F   V  L R+S G   L   L  G +R ++   +
Sbjct: 182 LHEGKYHQIKRMFGRFRNPVVGLHRLSIGDIVLDEKLAPGESRALTAAEV 231


>gi|291518121|emb|CBK73342.1| ribosomal small subunit pseudouridine synthase A [Butyrivibrio
           fibrisolvens 16/4]
          Length = 234

 Score =  149 bits (376), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 51/232 (21%), Positives = 94/232 (40%), Gaps = 10/232 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAER 72
            R+ K++    I +R EV+ ++ +  + V+G    +    V      I   G      + 
Sbjct: 2   MRLDKLLVELNIGTRSEVKALLKKGLIFVDGEKATKPEQKVDENSVVITYQGKEYTYQKF 61

Query: 73  TRLWLYHKPIGLVTTHSDPDG--RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   +      +  T    +       +   P     +  VGRLD +T GLLL+TNDG L
Sbjct: 62  SYYVINKPKGVITATEDAHEKTVMDVFYSLCPDAPKGLAPVGRLDKDTTGLLLITNDGQL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  +  P     + Y V   G++ ++ +  L+ G+ I +G       V  +  K      
Sbjct: 122 AHDMLSPKKHVDKTYFVTLDGELSEEDVAALEAGVHIGEGEPTAPATVKYEGGK----TC 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTREVSKK 239
            + + EGK  ++K++F      V  L R ++GP  L    +  G    ++ +
Sbjct: 178 YITIHEGKFHQVKRMFFAVGKTVLELKRTAFGPLVLDEEKVPEGHFITLNPE 229


>gi|224373604|ref|YP_002607976.1| ribosomal large subunit pseudouridine synthase B [Nautilia
           profundicola AmH]
 gi|223588928|gb|ACM92664.1| ribosomal large subunit pseudouridine synthase B [Nautilia
           profundicola AmH]
          Length = 253

 Score =  149 bits (375), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 71/253 (28%), Positives = 117/253 (46%), Gaps = 10/253 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+     SRRE +++I   RVKVNG +++     V   D + V+G P++K+ + 
Sbjct: 1   MRLNKFISHHTTYSRREADKLIFDGRVKVNGRVIKEPGFEVEEGDKVAVNGKPVKKSTKY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +Y+KP G + T  D  GR T++D+LP  +   I VGRLD N+EGLL+LT+   +A  
Sbjct: 61  TCIVYNKPRGELVTKKDDRGRKTIYDSLPKKYRHFIPVGRLDFNSEGLLILTDSPKVAHA 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLL---------KKGIVIQGICYGD-MQVTLDTQK 183
           L       +   +++        +              +   I+ +     +   +    
Sbjct: 121 LMNSDLPRVYKLKIKGEITDKMIEAMQNGVEVGDAGAHEENEIKKMVLKPFLSAQIIKNT 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
              + + V + EGKNRE+++ F  F  +V  L R+SYG   L  L  G TR   KK  + 
Sbjct: 181 PKYSTLKVAIGEGKNRELRRFFANFGSEVVDLKRLSYGWVSLNALPTGKTRYFDKKEYKL 240

Query: 244 QLGPHLLEEAQVN 256
                  E  +  
Sbjct: 241 LKEFLHKEAERKK 253


>gi|296158908|ref|ZP_06841736.1| RNA-binding S4 domain protein [Burkholderia sp. Ch1-1]
 gi|295890783|gb|EFG70573.1| RNA-binding S4 domain protein [Burkholderia sp. Ch1-1]
          Length = 243

 Score =  149 bits (375), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 59/245 (24%), Positives = 99/245 (40%), Gaps = 28/245 (11%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--------------- 64
           ++  G+ SRRE +  I +  V V+G  ++     V     IE+D                
Sbjct: 1   MSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPDQRIEIDPAAEAAQASQVTVLIH 60

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +          Y   I LVT  +  +G  +      +   ++   GRLDI++ GLL+L
Sbjct: 61  KTVGFVSGQAEDGYQPAITLVTPENRWEGDRSNIRFSVAHLRQLAPAGRLDIDSTGLLVL 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQGICYGDM 175
           T DG +A+ L    ++  + Y VR                + L LL+ G+ +  +     
Sbjct: 121 TQDGRIAKQLIGGHSEIDKEYLVRVAFGEHTTEVESHFPPESLALLRHGLSLDDVPLKPA 180

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           QV+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  G  R 
Sbjct: 181 QVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGHVMLGALPPGQWRY 236

Query: 236 VSKKI 240
           ++   
Sbjct: 237 LAADE 241


>gi|74316453|ref|YP_314193.1| ribosomal large subunit pseudouridine synthase F [Thiobacillus
           denitrificans ATCC 25259]
 gi|74055948|gb|AAZ96388.1| pseudouridine synthase, Rsu [Thiobacillus denitrificans ATCC 25259]
          Length = 245

 Score =  149 bits (375), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 68/245 (27%), Positives = 111/245 (45%), Gaps = 20/245 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK+++  G+ SRRE +  I +  V V+G  +      V     I +D    R+ +
Sbjct: 3   EPVRLSKLMSERGLCSRREADAFIERGLVFVDGKRVSELGTKVDPACAIRLDNAASRQQQ 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV----------------FDNLPSIFSRVISVGRLD 115
           +    L HKP+G V+   +P  +  V                   LP+    +   GRLD
Sbjct: 63  QRVTILLHKPVGYVSGQPEPGYQPAVALIRGETQWRDERRPGPAFLPAHLKGLAPAGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I++ GLL+LT DG +AR L    +   + Y VR  G++D   L LL  G+ + G+     
Sbjct: 123 IDSTGLLVLTQDGRVARQLIGDHSDVEKEYLVRVEGRLDARGLALLNHGLSLDGVRLRPA 182

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           +V           +   L+EG+ R+I+++ E    +V  L R+  G  +LG L  G  R 
Sbjct: 183 KVAWQNADQ----LRFSLKEGRKRQIRRMCELVGLRVVGLKRVRIGAVRLGDLPLGRWRY 238

Query: 236 VSKKI 240
           ++   
Sbjct: 239 LAPGE 243


>gi|294665479|ref|ZP_06730763.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 10535]
 gi|292604733|gb|EFF48100.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 10535]
          Length = 240

 Score =  149 bits (375), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 65/241 (26%), Positives = 106/241 (43%), Gaps = 10/241 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++K IA  G  SRRE +R+I ++RV VNG+     AV V   D + VDG PLR+ E 
Sbjct: 2   TIRLNKYIAETGSCSRREADRLIGERRVTVNGMPAGTGAV-VGEEDTVLVDGQPLRRREA 60

Query: 73  TRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            RL             +  T +                 R+  +GRLD ++EGL+L+T++
Sbjct: 61  KRLGGRKHVYIALNKPVGITCTTESSVKGNIVEFVGHEQRIFPIGRLDKDSEGLILMTSN 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +     +  + Y V  +  V  + L  + +G+ I        +     + G   
Sbjct: 121 GNIVNEILRAENRHQKEYLVAVNKPVTDEFLRRMARGVRIHNETTLPCRTARIAKFG--- 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR  L  
Sbjct: 178 -FRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELRGLLPQ 236

Query: 248 H 248
            
Sbjct: 237 R 237


>gi|116253609|ref|YP_769447.1| ribosomal large subunit pseudouridine synthase B [Rhizobium
           leguminosarum bv. viciae 3841]
 gi|115258257|emb|CAK09359.1| putative ribosomal large subunit pseudouridine synthase B
           [Rhizobium leguminosarum bv. viciae 3841]
          Length = 268

 Score =  149 bits (375), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 66/240 (27%), Positives = 112/240 (46%), Gaps = 1/240 (0%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTRLW 76
           + +++ G  SR + ER+IA+ RV V+G ++   +  V  +T  I +DG+ +    +  L 
Sbjct: 29  RALSKLGYCSRTQAERLIAENRVAVDGRIVNDTSAWVDLATARISIDGLVIAAEAKIYLM 88

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L      + T H      +            +  VGRLD  +EGLLL TND   A++L  
Sbjct: 89  LNKPRGLVTTRHDPEGRPTVYDCLRDFDIPHLSPVGRLDKASEGLLLFTNDTEFAQILLD 148

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
           P T   + Y V+    +D + +  +  GI   G                N+W+ V L EG
Sbjct: 149 PVTHVTKTYHVQIDRIMDDEDIAAMTSGIRHDGELLTATAARRLRHGDRNSWIEVELDEG 208

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVN 256
           +NR+I+++ E    +  RL+R++ G  +LG L  G+ R +S+  L+       +E  + N
Sbjct: 209 RNRQIRRMLEALGTECLRLVRVAIGGLELGELPKGAVRALSEPELQALRRKTGMERTRRN 268


>gi|83746231|ref|ZP_00943285.1| Ribosomal small subunit pseudouridine synthase A [Ralstonia
           solanacearum UW551]
 gi|207744140|ref|YP_002260532.1| ribosomal small subunit pseudouridine synthase a protein [Ralstonia
           solanacearum IPO1609]
 gi|83727197|gb|EAP74321.1| Ribosomal small subunit pseudouridine synthase A [Ralstonia
           solanacearum UW551]
 gi|206595544|emb|CAQ62471.1| ribosomal small subunit pseudouridine synthase a protein [Ralstonia
           solanacearum IPO1609]
          Length = 278

 Score =  149 bits (375), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 55/243 (22%), Positives = 89/243 (36%), Gaps = 4/243 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-VDGVPLRKAERTR 74
           + +++   G  +RR  + ++A   V VNGI  E     V +   +  VDG       R  
Sbjct: 36  LYRILQSQGFGTRRYCKDLVAAGLVHVNGIEAEDPDAQVDTAGLVLDVDGERWAYHARAY 95

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L LY       +              +P     V  VGRLD +T GLLLLT+DG     L
Sbjct: 96  LMLYKPAGFECSQKPRHHPSVYTLLPVPLRERGVQCVGRLDQDTTGLLLLTDDGQFVHTL 155

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  Q  +VY +     V   ++  L +G+++            +        + + L 
Sbjct: 156 TSPRHQVPKVYEITTADPVTDAQVAQLCRGVLLDDEDATVAAAWAERVD--TCDLRMALT 213

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLLEEA 253
           +GK  ++K++       V  L R + G   L   L  G  R + +  L       +    
Sbjct: 214 QGKYHQVKRMVAAAGNHVTALHRSAIGALTLDAGLAPGQWRWLERDDLTALDTTPVHAAG 273

Query: 254 QVN 256
              
Sbjct: 274 AAT 276


>gi|326796385|ref|YP_004314205.1| pseudouridine synthase Rsu [Marinomonas mediterranea MMB-1]
 gi|326547149|gb|ADZ92369.1| pseudouridine synthase Rsu [Marinomonas mediterranea MMB-1]
          Length = 228

 Score =  149 bits (375), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 50/230 (21%), Positives = 97/230 (42%), Gaps = 7/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+   +A     SR+E +R IA+ +++VNG ++ +   +V     +E  G  +   +  
Sbjct: 1   MRLDYFLAHTTSWSRKEAKRFIAKGKIRVNGDVVTKPNASVTEDCKVESHGEVILWRKEK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY     + +   D +    +    P     +  VGRLD +T GL+ LT DG     
Sbjct: 61  YFALYKPADYV-SALEDSESPVLIDLIEPEERKNLKIVGRLDKDTTGLIFLTTDGQWLHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--CYGDMQVTLDTQKGSNAWVTV 191
           +  P     + YRV     + +     L+ G+++ G        +V       S+  + +
Sbjct: 120 ITSPKHDCYKTYRVYCADPISEANCKSLETGVMLNGEDLPTSPAKVERV----SDTEILL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            ++EGK  ++K++      +V +L R +     L  L  G  R +++  +
Sbjct: 176 SIKEGKYHQVKRMLAAVGNRVEKLHREAISDVNLDGLQEGQYRILTEDEI 225


>gi|268608512|ref|ZP_06142239.1| 16s pseudouridylate synthase [Ruminococcus flavefaciens FD-1]
          Length = 255

 Score =  149 bits (375), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 51/235 (21%), Positives = 94/235 (40%), Gaps = 5/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K I+     +R +++ + A+  V VNG  ++R+   + +  D + V G  +     
Sbjct: 4   IRLDKFISERTEYTRSQIKSLCAKGSVTVNGSPVKRSDTKIDTGADDVTVCGNAISSERF 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + +T                    +   GRLD ++ G LL+T+DG LA 
Sbjct: 64  RYILLNKPKGYVSSTDDKDGETVIKLVPPEMRSKGLFPAGRLDKDSTGALLITDDGALAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +  P+    ++Y        +Q+ +    KGIV+  G      +  +   + ++    V
Sbjct: 124 RICSPNNHISKIYAAELSRPFEQEYVEKFAKGIVLANGEACSPCK--VQKAENADNLAFV 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
            L EG   ++K++F      V  L RIS G   L   L  G    +  K + +  
Sbjct: 182 ELHEGMYHQVKRMFAAVGNHVENLKRISIGGLILPKDLPLGKCMYLLPKDIEQMF 236


>gi|152988322|ref|YP_001350132.1| putative pseudouridylate synthase [Pseudomonas aeruginosa PA7]
 gi|150963480|gb|ABR85505.1| probable pseudouridylate synthase [Pseudomonas aeruginosa PA7]
          Length = 230

 Score =  149 bits (375), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 114/231 (49%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     SRR+ +R+IA  R++V+G ++      V     +E+D   L+  +  
Sbjct: 1   MRLDRFLANLPELSRRDAQRLIAGGRLRVDGQVVRDGTHEVRVFSRVELDERLLQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP+G V+   DP+  + +    P     +   GRLD NT GL+LLTNDG  +R 
Sbjct: 61  RYYMLHKPMGCVSATRDPEHPTVLELLPPDHRDDLHIGGRLDYNTTGLMLLTNDGRWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L LP ++  +VY V     +DQ  ++          + +     Q+     + +     +
Sbjct: 121 LTLPGSRRDKVYYVETEEPIDQRYVDAFAAGIHFRFEDLVTLPAQLEPLGPRSA----RL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            L EG+  ++K++F  F+ +V RL R   G  QL  TL  G+ R ++ + +
Sbjct: 177 TLHEGRYHQVKRMFGHFDNRVLRLHRERMGDIQLDPTLPPGAWRPLNAEEI 227


>gi|85374350|ref|YP_458412.1| hypothetical protein ELI_07615 [Erythrobacter litoralis HTCC2594]
 gi|84787433|gb|ABC63615.1| hypothetical protein ELI_07615 [Erythrobacter litoralis HTCC2594]
          Length = 266

 Score =  149 bits (375), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 111/252 (44%), Positives = 159/252 (63%), Gaps = 8/252 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           ++     +     R++K++ARAG+ASRREVERMI   RV ++G  +E  A  + S   + 
Sbjct: 7   QNHERSPDRPDGDRIAKLLARAGVASRREVERMITDGRVALHGKPVETPATFLESLRGVT 66

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDIN 117
           VDG P+ KAE TRL+ ++KP GL+T  +DP GR+T++D L +   +     + +GRLD N
Sbjct: 67  VDGKPVGKAEPTRLFAFNKPTGLLTAENDPKGRATIYDALKNALPKDAGRVMPIGRLDFN 126

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLLLLTNDGGL R +ELPS+   R YR R  G + Q++L  L +GI I G+ YG +  
Sbjct: 127 TEGLLLLTNDGGLKRRMELPSSGIPRTYRARAFGDITQEQLESLIEGIEIDGVRYGRIDA 186

Query: 178 TLDTQKGS----NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
            L+ +  S    N W+ + + EGKNRE+++V E F  +V+RL+R++YGPFQLG L  G  
Sbjct: 187 NLEQKTKSAGGRNQWIEMTITEGKNREVRRVLEHFGLEVSRLMRVAYGPFQLGDLPRGQA 246

Query: 234 REVSKKILREQL 245
            E+ K  L   L
Sbjct: 247 VEIRKGDLGRFL 258


>gi|294625115|ref|ZP_06703760.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 11122]
 gi|292600579|gb|EFF44671.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 11122]
          Length = 240

 Score =  149 bits (375), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 65/241 (26%), Positives = 106/241 (43%), Gaps = 10/241 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++K IA  G  SRRE +R+I ++RV VNG+     AV V   D + VDG PLR+ E 
Sbjct: 2   TIRLNKYIAETGSCSRREADRLIGERRVTVNGMPAGTGAV-VGEEDTVLVDGQPLRRREA 60

Query: 73  TRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            RL             +  T +                 R+  +GRLD ++EGL+L+T++
Sbjct: 61  KRLGGRKHVYIALNKPVGITCTTESSVKGNIVEFVGHEQRIFPIGRLDKDSEGLILMTSN 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +     +  + Y V  +  V  + L  + +G+ I        +     + G   
Sbjct: 121 GNIVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRIHNETTLPCRTARIAKFG--- 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR  L  
Sbjct: 178 -FRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELRGLLPQ 236

Query: 248 H 248
            
Sbjct: 237 R 237


>gi|332075974|gb|EGI86440.1| hypothetical protein SPAR68_0695 [Streptococcus pneumoniae GA41301]
          Length = 241

 Score =  149 bits (375), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 107/232 (46%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  + SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKV-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                      ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKELPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V+ +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVQVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSLSQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K L+
Sbjct: 180 TISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKELQ 231


>gi|169825022|ref|YP_001692633.1| 16S pseudouridylate synthase [Finegoldia magna ATCC 29328]
 gi|167831827|dbj|BAG08743.1| 16S pseudouridylate synthase [Finegoldia magna ATCC 29328]
          Length = 235

 Score =  149 bits (375), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 56/233 (24%), Positives = 120/233 (51%), Gaps = 9/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ ++++   IA+R+E+++M+ +  + VN + +++++ ++    D +++    +   + 
Sbjct: 1   MRLDRMLSEMKIATRKEIKQMVKKGIITVNDVTVKKSSEHIDENNDVVKIYDEVIEYRKF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +K  G+ +   DP  ++ + D        +  VGRLD++T GLL++TNDG  A 
Sbjct: 61  L-YFVMNKRKGVTSHSKDPMHKTVIDDMGELCVFDLNPVGRLDLDTTGLLIITNDGKFAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVT 190
            L  P     + Y+V    +VD+   +  +KGI +  + I     ++ +      +    
Sbjct: 120 NLISPKKDVSKKYKVTLRDKVDEKYNDTFEKGIKLMPEDIVTKPAKMEII----DDYNCY 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           + ++EGK  ++K++FE    +V  L R+  G F+L   L  G  RE++ + LR
Sbjct: 176 LTIKEGKYHQVKRMFEKVGNEVVELQRVQIGDFKLPEDLEEGDFRELTDEELR 228


>gi|311695566|gb|ADP98439.1| pseudouridine synthase, Rsu [marine bacterium HP15]
          Length = 232

 Score =  148 bits (374), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 105/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            ++S++++     SRR+   +IA  RV VN +    AA  V     + +DG  +++AE  
Sbjct: 1   MKLSRILSNRNDISRRQANFLIASGRVAVNDVTCRDAAAEVDRFSCVRMDGDIIQEAEAC 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + HKP G ++   D   R+ +    P +   +   GRLD  + GLL+LTNDG  +R 
Sbjct: 61  HHLMLHKPAGFLSATLDDTHRTVMELISPELREDLHIAGRLDRASTGLLILTNDGRWSRQ 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VYRV     +  +  +   +GI  +          + L     S     V
Sbjct: 121 LTEPRIKIPKVYRVSTAYPISPETPHRFAEGIWFEFEQLTTSPADLDLL----SPCEARV 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            + EG+  ++K++F     +V  L R   G  +L   L AG  R ++ + +
Sbjct: 177 TIYEGRYHQVKRMFHAVGNRVTALHREQMGNIRLDDDLAAGEYRSLTAEEI 227


>gi|16125108|ref|NP_419672.1| RNA pseudouridylate synthase [Caulobacter crescentus CB15]
 gi|221233835|ref|YP_002516271.1| ribosomal large subunit pseudouridine synthase F [Caulobacter
           crescentus NA1000]
 gi|13422112|gb|AAK22840.1| RNA pseudouridylate synthase, putative [Caulobacter crescentus
           CB15]
 gi|220963007|gb|ACL94363.1| ribosomal large subunit pseudouridine synthase F [Caulobacter
           crescentus NA1000]
          Length = 255

 Score =  148 bits (374), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 60/245 (24%), Positives = 116/245 (47%), Gaps = 17/245 (6%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPL 67
           +   PQRV+K +A++G+ SRRE E++I+   V ++G ++E     +     + + D    
Sbjct: 8   DEAEPQRVNKWLAQSGVCSRREAEQLISDGLVSIDGEVVEDVGRKIQPGQTLTLADRATA 67

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPD------------GRSTVFDNLPSIFSRVISVGRLD 115
           +        ++     + +                          +P     +  +GRLD
Sbjct: 68  KLDAVPTYLVHKPRGVVSSQPDPGQVPAARLLTRANLWGDARGVAIPQSGDLIPPIGRLD 127

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
            ++ GLLLL+ DG +A+ +  P ++  + YRV   G++ ++KL LL+ G+ + G      
Sbjct: 128 KDSRGLLLLSQDGVVAKAVIGPQSELEKEYRVAVMGELTEEKLELLRFGLELDGRELRPA 187

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           +V + + +     ++  LREG+NR+I+++ E  + KV  L R+  GP  LG +  G  R 
Sbjct: 188 EVEVISDQR----LSFVLREGRNRQIRRMCELVDLKVVDLFRVRVGPLDLGDMPEGHWRL 243

Query: 236 VSKKI 240
           ++   
Sbjct: 244 LTAAE 248


>gi|319779597|ref|YP_004130510.1| tRNA pseudouridine synthase A [Taylorella equigenitalis MCE9]
 gi|317109621|gb|ADU92367.1| tRNA pseudouridine synthase A [Taylorella equigenitalis MCE9]
          Length = 241

 Score =  148 bits (374), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 62/242 (25%), Positives = 105/242 (43%), Gaps = 18/242 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              RVSK+++  GI SRRE +  I +  VK +G ++      V+    + +D   L    
Sbjct: 2   EKVRVSKLLSEQGICSRREADVFIERGWVKADGNVV-SLGTKVLPNAKLTLDKKALESKS 60

Query: 72  RTRLWLYHKPIGLVTTHSD-------------PDGRSTVFDNLPSIFSRVISVGRLDINT 118
           +    + +KP+G V++  +                     +   S    + + GRLDI +
Sbjct: 61  KQVTIILNKPVGYVSSQPEKNYKSALSLITKANQYDRVHNEFSESHLKGLATAGRLDIES 120

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           +GLL++T DG +A+ L    ++  + Y VR  G++ +  L LL  G+ + G    D +V 
Sbjct: 121 QGLLVMTQDGSIAKQLIGEDSEVEKEYIVRVEGKLSERGLQLLNHGLSLDGQPLRDAEVE 180

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
                     +   L EGK R+I+++ E    KV  L R+  G   L  L  G  R +  
Sbjct: 181 WINDDQ----LRFILWEGKKRQIRRMCELVGLKVIGLKRVRMGNVTLADLPTGKWRYLKP 236

Query: 239 KI 240
             
Sbjct: 237 FE 238


>gi|91792450|ref|YP_562101.1| pseudouridine synthase, Rsu [Shewanella denitrificans OS217]
 gi|91714452|gb|ABE54378.1| ribosomal small subunit pseudouridine synthase A [Shewanella
           denitrificans OS217]
          Length = 229

 Score =  148 bits (374), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 47/232 (20%), Positives = 94/232 (40%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  A   SR   ++ + +  V  +G++++ +   V     + ++G  L      
Sbjct: 1   MRLDKFITEASELSRSLAKKALHRGDVTCDGVIVKDSGFKVEPGTKVCLEGRELSLF-GV 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP+  + +  D    S +        S +   GRLD +T GL+L+T+DG  +  
Sbjct: 60  RYLMLNKPVDTICSTIDEVYPSVLSLIDVEKASNLHIAGRLDADTTGLVLITSDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
              P     + Y V     +D+  +    +GI +  +        + +      +    +
Sbjct: 120 ATSPKKDCGKRYLVEVAEPLDESLIETFAEGIALRNEDGLTKPATLEII----DSHHARL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++F      V  L R   G  +L   L  G  R +++  + 
Sbjct: 176 TITEGKYHQVKRMFAATGNAVINLHRECVGSIELDPGLALGEWRYLTQAEID 227


>gi|77457562|ref|YP_347067.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           fluorescens Pf0-1]
 gi|77381565|gb|ABA73078.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           fluorescens Pf0-1]
          Length = 230

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 108/231 (46%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            RV + ++     +R++V  ++ ++RV+++G ++      V+    +EVD   L+  +  
Sbjct: 1   MRVDRFLSNLPRYNRKQVRLLLVEKRVRIDGKVVSDPHSEVLEFSRVEVDDEVLQPGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V+   DP+  + +          +   GRLD NT GL+L+TNDG  +R 
Sbjct: 61  RYFMLNKPQGCVSATRDPEHPTVLDLIHEPDKDDLHIAGRLDFNTTGLMLITNDGSWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V    ++  +      +      + +     Q+ +           +
Sbjct: 121 LTQPQTKLPKVYYVETEQEIGPEYAIKFAEGIYFAFEDLTTQPAQLQVL----GPRTARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EG+  ++K++F  FN KV RL R S GP  L   L  G  R +  + +
Sbjct: 177 SIVEGRYHQVKRMFGHFNNKVLRLHRESMGPLALDHALKPGEYRALRTEEI 227


>gi|312959535|ref|ZP_07774052.1| ribosomal small subunit pseudouridine synthase [Pseudomonas
           fluorescens WH6]
 gi|311286252|gb|EFQ64816.1| ribosomal small subunit pseudouridine synthase [Pseudomonas
           fluorescens WH6]
          Length = 230

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 60/232 (25%), Positives = 108/232 (46%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +RR+V  ++ ++RV V+G+ +     +V     + VD   ++  +  
Sbjct: 1   MRIDRFLSNLPRLNRRQVRLLLVERRVSVDGVAVSDPHHDVRDFSCVCVDDEVIQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V+  SDP   + +          +   GRLD NT GL+L+TNDG  +R 
Sbjct: 61  RYFMLHKPQGCVSATSDPQHPTVLDLLDEPDKDELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P+T+  +VYRV     +  +             + +     ++ L           +
Sbjct: 121 LTQPTTKLPKVYRVHTEDTIGPEYAPTFAAGLYFAFEDLTTQPAELALL----GPTTARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            + EG+  ++K++F  FN KV  L R   GP +L + L  G  R +S + +R
Sbjct: 177 SIIEGRYHQVKRMFGHFNNKVIGLHRERMGPLELDSALAPGEYRALSLEEIR 228


>gi|15900581|ref|NP_345185.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae TIGR4]
 gi|111658681|ref|ZP_01409324.1| hypothetical protein SpneT_02000187 [Streptococcus pneumoniae
           TIGR4]
 gi|14972155|gb|AAK74825.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae TIGR4]
          Length = 241

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 105/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                      ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPAGAVTANKDKELPTVMDLLPSNIQSDKLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   +KGI  +        ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVEVNGLLTPDHIQTFQKGIVFLDDTVCKPAKLEILSASPSLSQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K L+
Sbjct: 180 TISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKELQ 231


>gi|311105891|ref|YP_003978744.1| ribosomal large subunit pseudouridine synthase F [Achromobacter
           xylosoxidans A8]
 gi|310760580|gb|ADP16029.1| ribosomal large subunit pseudouridine synthase F [Achromobacter
           xylosoxidans A8]
          Length = 243

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 61/244 (25%), Positives = 101/244 (41%), Gaps = 19/244 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
              R+SK+++  G+ SRRE +  I +  V+V+G+++            I ++        
Sbjct: 2   EKVRISKLMSERGLCSRREADTYIERGWVRVDGVVVSELGARAYPDQVITLERAAQARQT 61

Query: 64  -------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
                    P+          Y   + L+ + S   G         +    +   GRLDI
Sbjct: 62  SRVTILINKPVGYVSGQAEKGYTPAVALIDSRSRYAGDRAPQRFERAHLDGLAVAGRLDI 121

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +++GLL+LT DG +A+ L    +   + Y VR  G +  + L LL  G+ + G      Q
Sbjct: 122 DSQGLLVLTQDGRIAKHLIGEDSSVDKEYLVRVQGNLSDNGLALLNHGLSLDGKALKPAQ 181

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V           +   LREGK R+I+++ E    KV  L R+  G   LG L  G  R +
Sbjct: 182 VRWQNSDQ----LRFVLREGKKRQIRRMCELVGLKVIGLKRVRIGRVSLGDLPLGQWRYL 237

Query: 237 SKKI 240
            +  
Sbjct: 238 REDE 241


>gi|302380106|ref|ZP_07268580.1| pseudouridylate synthase [Finegoldia magna ACS-171-V-Col3]
 gi|302312092|gb|EFK94099.1| pseudouridylate synthase [Finegoldia magna ACS-171-V-Col3]
          Length = 235

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 56/233 (24%), Positives = 119/233 (51%), Gaps = 9/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ ++++   IA+R+E+++M+ +  + VN + +++++ ++    D +++    +   + 
Sbjct: 1   MRLDRMLSEMKIATRKEIKQMVKKGIITVNDVTVKKSSEHIDENNDVVKIYDEVIEYRKY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +K  G+ +   DP  ++ + D        +  VGRLD++T GLL++TNDG  A 
Sbjct: 61  L-YFVMNKRKGVTSHSKDPMYKTVIDDMGELCVFDLNPVGRLDLDTTGLLIITNDGKFAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVT 190
            L  P     + Y+V    +VD+   +  +KGI +  + I      + +      +    
Sbjct: 120 NLISPKKDVSKKYKVTLRDKVDEKYNDTFEKGIKLMPEDIVTKPATMEII----DDYNCY 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           + ++EGK  ++K++FE    +V  L R+  G F+L   L  G  RE++ + LR
Sbjct: 176 LTIKEGKYHQVKRMFEKVGNEVVELQRVQIGDFKLPEDLEEGDFRELTDEELR 228


>gi|154174771|ref|YP_001407361.1| RNA-uridine isomerase [Campylobacter curvus 525.92]
 gi|112802450|gb|EAT99794.1| RNA-uridine isomerase [Campylobacter curvus 525.92]
          Length = 257

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 113/250 (45%), Gaps = 15/250 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K I+     SRRE + +I   ++ VN  L+   A +V   D +++ G  ++  +
Sbjct: 2   QKMRLNKFISHNTSYSRREADELIKSGKISVNNKLVSELATSVSDEDKVKIGGRLVKPKK 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              + +YHK  G + T  D  GR T++D LP  F++ +S+GRLD  +EGLLLLT+   +A
Sbjct: 62  DFTMIVYHKQKGELVTKKDDRGRKTIYDALPEGFAKFVSIGRLDYASEGLLLLTDAPAIA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLL-----------KKGIVIQGICYGD-MQVTL 179
             L     +     +V+     +                       I+ + +   +   +
Sbjct: 122 TALMSSDIEREYYLKVKGEITDEVKTAMREGFFAADASKGAHAKSKIKSMEFKPFVAFDI 181

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               G      V + EG+NRE+++ F +F+ +V  L R+S+G   LG L  G  R     
Sbjct: 182 FGSSGGYTKFRVIINEGQNRELRRFFGYFDLEVMDLKRVSFGRVDLGMLKPGKWRYFENG 241

Query: 240 I---LREQLG 246
               LR+ L 
Sbjct: 242 EYEDLRDFLK 251


>gi|167586851|ref|ZP_02379239.1| Pseudouridine synthase, Rsu [Burkholderia ubonensis Bu]
          Length = 298

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 100/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 50  MRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDERASAAQAAQ 109

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     L+T  +   G  +     P     +   GRLDI++
Sbjct: 110 VTILLHKPVGYVSGQAEDGYEPATVLITRENHWSGDRSALRFSPQHLHSLAPAGRLDIDS 169

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 170 TGLLVLTQNGRIAKQLIGEQSDIDKEYLVRVRFGERLIDIDQHFPAESLAKLRHGLELDG 229

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 230 VALKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 285

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 286 QGQWRYLSADE 296


>gi|322376975|ref|ZP_08051468.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           M334]
 gi|321282782|gb|EFX59789.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           M334]
          Length = 241

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 56/231 (24%), Positives = 105/231 (45%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  + SR+ +++ + +  + V+G      A N+ +    +      +R  E 
Sbjct: 1   MRLDNLLAQEKV-SRKAMKQALLKGEILVDGRPARSLAQNIDTGLQELLFQDQIIRGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +               +      ++ +VGRLD +T GLLL+T++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDRELPTVMDLLSPDIQSDKLYAVGRLDRDTTGLLLVTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + YRV  +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYRVEVNGLLTPDHIQAFQKGIVFLDGTVCKPARLEILSASPSLSQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++KK+F     KV  L R  +GP+ L   L AG  R ++ + L
Sbjct: 180 TISEGKFHQVKKMFLSVGVKVTSLKRTHFGPWSLDENLQAGDYRPLNSEEL 230


>gi|148994427|ref|ZP_01823650.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP9-BS68]
 gi|168488362|ref|ZP_02712561.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae SP195]
 gi|182683607|ref|YP_001835354.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae CGSP14]
 gi|303254738|ref|ZP_07340839.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae BS455]
 gi|303259951|ref|ZP_07345925.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP-BS293]
 gi|303261357|ref|ZP_07347305.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP14-BS292]
 gi|303264023|ref|ZP_07349944.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae BS397]
 gi|303266337|ref|ZP_07352227.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae BS457]
 gi|303268804|ref|ZP_07354592.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae BS458]
 gi|147927263|gb|EDK78297.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP9-BS68]
 gi|182628941|gb|ACB89889.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae CGSP14]
 gi|183573107|gb|EDT93635.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae SP195]
 gi|301801543|emb|CBW34235.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae INV200]
 gi|302598278|gb|EFL65323.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae BS455]
 gi|302637491|gb|EFL67978.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP14-BS292]
 gi|302638870|gb|EFL69331.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP-BS293]
 gi|302641669|gb|EFL72028.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae BS458]
 gi|302644148|gb|EFL74405.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae BS457]
 gi|302646428|gb|EFL76654.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae BS397]
 gi|332074486|gb|EGI84962.1| hypothetical protein SPAR50_0667 [Streptococcus pneumoniae GA17570]
          Length = 241

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 106/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  + SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKV-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                      ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKELPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSLSQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K L+
Sbjct: 180 TISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKELQ 231


>gi|257091858|ref|YP_003165499.1| pseudouridine synthase [Candidatus Accumulibacter phosphatis clade
           IIA str. UW-1]
 gi|257044382|gb|ACV33570.1| pseudouridine synthase [Candidatus Accumulibacter phosphatis clade
           IIA str. UW-1]
          Length = 305

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 104/250 (41%), Gaps = 18/250 (7%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +V       R+SK++A  G+ SRR+ +  IA+  V V+G  +            I +D  
Sbjct: 59  VVSAPPGGVRISKLMAERGLCSRRDADDYIARGWVFVDGRRVSELGTRADPGAAITLDTA 118

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRST--------------VFDNLPSIFSRVISV 111
              +  +    L HKP+G V+   +P                        PS    +   
Sbjct: 119 AQTQQRKQMTILLHKPVGYVSGQPEPGCTPAVTLIQPERQFRTPDTPVFHPSCLRGLAPA 178

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLDI++ GLL+LT DG +AR L    +   + Y VR  G++    L LL  G+ + G  
Sbjct: 179 GRLDIDSTGLLVLTQDGRVARQLIGEESTVEKEYLVRVDGRLADKDLALLNHGLSLDGRQ 238

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
               +V           +   LREG+ R+I+++ E    +V  L R+  G  +L  L  G
Sbjct: 239 LKPARVEWLNDDQ----LRFVLREGRKRQIRRMCELVGLRVTGLKRVRIGAVRLADLPLG 294

Query: 232 STREVSKKIL 241
             R +    +
Sbjct: 295 QWRFLRPDEV 304


>gi|269797973|ref|YP_003311873.1| pseudouridine synthase [Veillonella parvula DSM 2008]
 gi|269094602|gb|ACZ24593.1| pseudouridine synthase [Veillonella parvula DSM 2008]
          Length = 232

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 102/232 (43%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A     SR+EV ++I  +RV +NG +  +   ++    D + VDG  +   + 
Sbjct: 1   MRLDKLLANKAYGSRKEVHQIIKDRRVTINGSITTKKDTHIDIDVDIVAVDGKVVSTTQL 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +  +     +                   I   V+ VGRLD +TEGLLLLTNDG    
Sbjct: 61  YYVKFHKPKGYVTAVEDSNHPVVMDLLPPEFIKMGVVPVGRLDKDTEGLLLLTNDGVWGH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +   +    ++Y V F G +  + +  +KKGI++  G      ++   +       V V
Sbjct: 121 SIINGNKHVPKIYYVEFEGTLSDEGIQRIKKGILLGDGTQCKPAEIEFVSL----HSVHV 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
            + EGK  ++K++       V  L R++ G   L  +   GS  E++ + + 
Sbjct: 177 TIEEGKYHQVKRMIGAAGGTVTYLKRLTIGHIDLSGIEEVGSAMELTVEQIE 228


>gi|126664623|ref|ZP_01735607.1| 16S rRNA pseudouridylate 516 synthase [Marinobacter sp. ELB17]
 gi|126630949|gb|EBA01563.1| 16S rRNA pseudouridylate 516 synthase [Marinobacter sp. ELB17]
          Length = 230

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 55/231 (23%), Positives = 100/231 (43%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + IA +   SR+E +R IA   V+VNG + + +A  V +   + + G  +      
Sbjct: 1   MRLDQFIATSSELSRKEAKRAIAAGDVQVNGDVWKNSATAVPANAEVMLQGELVALPAER 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L      + +   D D  + +      +   +   GRLD +T GLLLLT+DG  +  
Sbjct: 61  YLMLNKPAGFI-SATRDSDQPTALDLLPAELTRNLHIAGRLDADTTGLLLLTSDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y+V     + Q  +  L+ G++++         QVT+   +     V +
Sbjct: 120 VTSPRVECPKTYQVALSVPISQAAIAALETGVMLRNDTKPTKPAQVTVLQSQ----LVEL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++       V  L R   G   L   L AG  R ++   +
Sbjct: 176 TISEGRYHQVKRMLAAVGNHVTALHRSRIGGVTLDPALAAGEHRFLTSAEI 226


>gi|293604951|ref|ZP_06687348.1| ribosomal large subunit pseudouridine synthase F [Achromobacter
           piechaudii ATCC 43553]
 gi|292816779|gb|EFF75863.1| ribosomal large subunit pseudouridine synthase F [Achromobacter
           piechaudii ATCC 43553]
          Length = 243

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 60/244 (24%), Positives = 98/244 (40%), Gaps = 19/244 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
              R+SK+++  G+ SRRE +  I +  V+V+G+++            I ++        
Sbjct: 2   EKVRISKLMSERGLCSRREADSYIERGWVRVDGVVVSELGAKAFPDQVITLERAAQARQT 61

Query: 64  -------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
                    P+          Y   + L+   S             +    +   GRLDI
Sbjct: 62  SRVTILINKPVGYVSGQAEKGYTPAVALIDARSRFANDRHPQRFERAHLEGLAVAGRLDI 121

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +++GLL+LT DG +A+ L    +   + Y VR  G++    L LL  G+ + G      Q
Sbjct: 122 DSQGLLVLTQDGRIAKHLIGEDSSVDKEYLVRVQGELSDRGLQLLNHGLSLDGKALKPAQ 181

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V           +   LREGK R+I+++ E    KV  L R+  G   LG L  G  R +
Sbjct: 182 VRWQNHDQ----LRFVLREGKKRQIRRMCELVGLKVVGLKRVRIGRVSLGDLPLGQWRYL 237

Query: 237 SKKI 240
               
Sbjct: 238 RDDE 241


>gi|114561758|ref|YP_749271.1| pseudouridine synthase, Rsu [Shewanella frigidimarina NCIMB 400]
 gi|114333051|gb|ABI70433.1| Pseudouridine synthase, Rsu [Shewanella frigidimarina NCIMB 400]
          Length = 238

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 60/232 (25%), Positives = 103/232 (44%), Gaps = 5/232 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM--STDHIEVDGVPLRK 69
           T  R+S  +A  G+ASRR+  R+I   RV +N  L +     V     + I VD  P+  
Sbjct: 2   TSMRLSHYLAVCGVASRRQAARLIDTGRVSINHQLAKHTD-RVNFCEIETILVDDKPILA 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +  + WLYHKP+G+               ++     R+   GRLD ++ GLLLLTNDG 
Sbjct: 61  VQDKQYWLYHKPVGIDCR--LLVDDPHSLLHVLPELPRLYPAGRLDKDSRGLLLLTNDGQ 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L + L  P     + Y V+    +    L+++  G+    +      +   +        
Sbjct: 119 LTQALMHPDYYHPKTYVVQVDKPISTSFLSMMANGVSYGDVQTRSCDIRPLSLTAEEDRF 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + L +G NR+I+++ +   +KV  L+R      ++  L   + R ++   L
Sbjct: 179 EIVLTQGLNRQIRRMCQTLGYKVIDLMRTQLLDIRIDELAEKTMRPLTAAEL 230


>gi|182412551|ref|YP_001817617.1| RNA-binding S4 domain-containing protein [Opitutus terrae PB90-1]
 gi|177839765|gb|ACB74017.1| RNA-binding S4 domain protein [Opitutus terrae PB90-1]
          Length = 237

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 57/237 (24%), Positives = 90/237 (37%), Gaps = 4/237 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ +++A  G  SRRE    I   RV + G     +     + D + +DG PL   +   
Sbjct: 3   RLDQLLANLGYCSRREARSWIEAGRVTIGGEAANDSGQKAAAAD-VRIDGEPLDHPDGLL 61

Query: 75  LWLYHKPIGLVTTHSD--PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L L+     + +      P+  S + +        V SVGRLD  T GLLLLT+   L  
Sbjct: 62  LLLHKPLGLVCSHDEREGPNIYSLLPERWRRRNPAVTSVGRLDKETSGLLLLTDQSLLVH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  +VYR      +  D + L   G +                 G      + 
Sbjct: 122 RLTSPKHKVPKVYRASVDRDLSPDLVPLFASGTLQLEGEAHPCAPAELRLLGPR-EAELT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           L EG+  +++++       V  L R  +G   L  L  G+ RE+       + G   
Sbjct: 181 LTEGRYHQVRRMLAACGLTVLTLHRARFGHLALDDLAPGAWRELPLDEFAARFGLAR 237


>gi|325917090|ref|ZP_08179323.1| pseudouridine synthase family protein [Xanthomonas vesicatoria ATCC
           35937]
 gi|325536666|gb|EGD08429.1| pseudouridine synthase family protein [Xanthomonas vesicatoria ATCC
           35937]
          Length = 240

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 108/243 (44%), Gaps = 14/243 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
             R++K IA  G  SRRE +R+I ++RV VNG++    AV V   D + VDG PLR  E 
Sbjct: 2   TIRLNKHIADTGFCSRREADRLIGERRVTVNGVVAGTGAV-VGEEDTVLVDGQPLRAREA 60

Query: 72  ------RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
                 +      +KP+G+  T                   R+  +GRLD  +EGL+L+T
Sbjct: 61  KKPGGRKHVYIALNKPVGITCTTESSV--KGNIVEFVGHEQRIFPIGRLDKESEGLILMT 118

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           ++G +   +     +  + Y V  +  V  + L  + +G+ I        +     + G 
Sbjct: 119 SNGNIVNEILRAENRHQKEYLVAVNKAVTDEFLRGMARGVRIHNETTLPCRTARIAKFG- 177

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+ +   F+++V +L R+     +L  L  G  R +S   L   L
Sbjct: 178 ---FRIVLEQGLNRQIRLMAAEFDYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELHGLL 234

Query: 246 GPH 248
              
Sbjct: 235 PQR 237


>gi|226306743|ref|YP_002766703.1| pseudouridine synthase [Rhodococcus erythropolis PR4]
 gi|226185860|dbj|BAH33964.1| putative pseudouridine synthase [Rhodococcus erythropolis PR4]
          Length = 267

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 74/243 (30%), Positives = 113/243 (46%), Gaps = 4/243 (1%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIE 61
            K+         R+ KV+A+AG+ASRR  E +I Q RV+V+G ++    + V      + 
Sbjct: 16  TKHDGPPKGDGVRLQKVLAQAGVASRRAAEELIDQGRVEVDGRIVVEQGLRVDPENAVVR 75

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINT 118
           VDGV +   +       +KP G   T SD  GR  V D +        R+  VGRLD +T
Sbjct: 76  VDGVRVVVQKDLVYLAMNKPRGWQCTMSDDLGRPCVGDIVSERVQSGQRLFHVGRLDADT 135

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLLL TNDG LA  L  PS +  + Y    HG V++     L+ G+ +          T
Sbjct: 136 EGLLLFTNDGDLAHRLMHPSFEVPKTYLATVHGVVERSTGKQLRDGVTLDDGPAKVDAFT 195

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +         V + L EG+   ++++ +     V RL+R + G   LG    G+ R + +
Sbjct: 196 VLEINEGKTLVKLVLHEGRKHIVRRLLDAVGHPVVRLVRTNVGVVALGDQRPGTQRVLGR 255

Query: 239 KIL 241
             +
Sbjct: 256 SEV 258


>gi|229548762|ref|ZP_04437487.1| pseudouridylate synthase [Enterococcus faecalis ATCC 29200]
 gi|255973897|ref|ZP_05424483.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis T2]
 gi|256964355|ref|ZP_05568526.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis HIP11704]
 gi|257418422|ref|ZP_05595416.1| ribosomal small subunit pseudouridine synthase [Enterococcus
           faecalis T11]
 gi|257421072|ref|ZP_05598062.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis X98]
 gi|293388465|ref|ZP_06632971.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis S613]
 gi|300859808|ref|ZP_07105896.1| pseudouridylate synthase [Enterococcus faecalis TUSoD Ef11]
 gi|307271422|ref|ZP_07552695.1| hypothetical protein HMPREF9514_00174 [Enterococcus faecalis
           TX0855]
 gi|312979317|ref|ZP_07791015.1| conserved hypothetical protein [Enterococcus faecalis DAPTO 516]
 gi|229306102|gb|EEN72098.1| pseudouridylate synthase [Enterococcus faecalis ATCC 29200]
 gi|255966769|gb|EET97391.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis T2]
 gi|256954851|gb|EEU71483.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis HIP11704]
 gi|257160250|gb|EEU90210.1| ribosomal small subunit pseudouridine synthase [Enterococcus
           faecalis T11]
 gi|257162896|gb|EEU92856.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis X98]
 gi|291082155|gb|EFE19118.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis S613]
 gi|300850626|gb|EFK78375.1| pseudouridylate synthase [Enterococcus faecalis TUSoD Ef11]
 gi|306511886|gb|EFM80883.1| hypothetical protein HMPREF9514_00174 [Enterococcus faecalis
           TX0855]
 gi|311287911|gb|EFQ66467.1| conserved hypothetical protein [Enterococcus faecalis DAPTO 516]
 gi|315145203|gb|EFT89219.1| conserved hypothetical protein [Enterococcus faecalis TX2141]
 gi|315161890|gb|EFU05907.1| conserved hypothetical protein [Enterococcus faecalis TX0645]
          Length = 260

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 68/260 (26%), Positives = 116/260 (44%), Gaps = 3/260 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +     
Sbjct: 1   MRLDKLLEELQFGSRKTVKRIIRGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLISHKTH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                       +  VGRLD +TEGLLLLT++G L  
Sbjct: 61  VYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            L  P+ +  + Y V+ +G V  +     K GIV+QG       ++T+     + + V +
Sbjct: 121 QLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHVFL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLL 250
            ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L    +
Sbjct: 181 TIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYFFI 240

Query: 251 EEAQVNLDAPIYSSETLVRD 270
           E+ Q +   P        R 
Sbjct: 241 EKQQTSKALPSNLKREEERK 260


>gi|332298341|ref|YP_004440263.1| pseudouridine synthase Rsu [Treponema brennaborense DSM 12168]
 gi|332181444|gb|AEE17132.1| pseudouridine synthase Rsu [Treponema brennaborense DSM 12168]
          Length = 249

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 59/245 (24%), Positives = 99/245 (40%), Gaps = 14/245 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
             +R+ K+++  G  SR++V +++    V VNG +     V+V    D + VDG  +   
Sbjct: 2   KTERLDKILSHHGFGSRKDVRKLLHAGSVAVNGTVCVSPDVHVDPDADELTVDGSSVPMR 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTN 126
               + +      + +             +           +  VGRLDI+TEGLLLLT 
Sbjct: 62  RHIYIMMNKCAGVVCSARDGLHRTVFDLLDDSYRQEFLGGSLHMVGRLDIDTEGLLLLTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD--MQVTLDTQKG 184
           DG L   L  P T   + Y +R    V  +   L+ +     GI           D +  
Sbjct: 122 DGTLTHRLTSPKTHVTKTYTIRLKNCVPDEAQPLITRRFS-DGIHIAPDGDDGEYDCKPA 180

Query: 185 SNAWV-----TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              W      ++ + EG+  ++K++      +V  L RI+ G   L   L  G+ RE+S 
Sbjct: 181 DLHWFSGTECSLVITEGRFHQVKRMIAAAGNEVVYLKRIAIGALLLDPALENGAYRELSL 240

Query: 239 KILRE 243
           + L  
Sbjct: 241 RELEN 245


>gi|152989816|ref|YP_001355538.1| RNA pseudouridine synthase [Nitratiruptor sp. SB155-2]
 gi|151421677|dbj|BAF69181.1| RNA pseudouridine synthase [Nitratiruptor sp. SB155-2]
          Length = 260

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 81/251 (32%), Positives = 123/251 (49%), Gaps = 19/251 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+     SRRE +R+I +  VKVN  +++    +V   D + V G  ++     
Sbjct: 1   MRLNKYISHNTTYSRREADRLIQEGFVKVNRQIVKEPFYDVQEGDKVFVKGKLIKPKVDY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +Y+KP G + T  D  GR T++D+LP  F+  I VGRLD  +EGLLLLT+   +A+ 
Sbjct: 61  TVIVYNKPKGELVTKKDDRGRKTIYDSLPKKFAHYIPVGRLDFASEGLLLLTDSPKIAQA 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQVTL 179
           L        RVY V+  G+V       +++G+ ++                        +
Sbjct: 121 LMESD--IPRVYNVKIKGEVTPKMEEAMREGLELEDATAGGHEKSRVTSMKFAPFFAYRI 178

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           D    + + + V L EGKNREI++ F  F   V  L R+ YG  +L  L  G TR +SKK
Sbjct: 179 DKNAPTFSKLKVALTEGKNREIRRFFAHFGKDVVDLKRVEYGWIKLNALPTGKTRYLSKK 238

Query: 240 I---LREQLGP 247
               LRE L  
Sbjct: 239 EYEKLREFLKE 249


>gi|209694915|ref|YP_002262843.1| ribosomal small subunit pseudouridine synthase A [Aliivibrio
           salmonicida LFI1238]
 gi|208008866|emb|CAQ79074.1| ribosomal small subunit pseudouridine synthase A [Aliivibrio
           salmonicida LFI1238]
          Length = 229

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 53/230 (23%), Positives = 101/230 (43%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   ++ E    IA+ RVKVN  ++   +  V   +H+ ++G  L      
Sbjct: 1   MRLDKFVCKSTTLTKNEALECIAEGRVKVNAKIVTVESTQVHENNHVTLNGDLLTARPFR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L +      + +   D    S          S +   GRLD +T GL+L+T+DG  +  
Sbjct: 61  YLLMNKPANTICSN-IDEAYPSLFNYIKEGNNSELHIAGRLDSDTTGLVLITDDGRWSYN 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  PS +  +VYRV     +  + +  ++ G+ +QG        ++ + T+      V +
Sbjct: 120 IITPSKKCEKVYRVGLRNIITSEAIIKIELGVQLQGEVELTRPAKLKIITE----REVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R  +G   L  +  G  R ++   +
Sbjct: 176 TIIEGKFHQVKRMFSAVGNKVILLHREQFGEISL-DVNEGEWRYLTDYEV 224


>gi|194366464|ref|YP_002029074.1| RNA-binding S4 domain-containing protein [Stenotrophomonas
           maltophilia R551-3]
 gi|194349268|gb|ACF52391.1| RNA-binding S4 domain protein [Stenotrophomonas maltophilia R551-3]
          Length = 549

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 81/352 (23%), Positives = 140/352 (39%), Gaps = 13/352 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV----PLRK 69
           +R+ KV+A+AG+ SRR +E+ IA+  VKVNG + +   ++V S D IE+DG         
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIAEGLVKVNGEVAQT-GMSVKSGDKIELDGRGFVATALA 86

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + T        +      P   +R I+VGRLDINT GLLL T DG 
Sbjct: 87  EPSRVLVYNKPEGEVTTREDPEGRPTVFESLPPLKGARWIAVGRLDINTTGLLLATTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR      ++      ++ L +G+ ++       ++       
Sbjct: 147 LANAMMHPSFEVEREYVVRVRAPEGEEKVSDAIIDRLGRGVALEDGPAKFDEIERIGGTD 206

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   L  G + E+    +  
Sbjct: 207 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGKVTLPRELARGHSVELGSAQVEA 266

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                 LEE   +              +  +               +  +   + ++   
Sbjct: 267 LRAQLKLEEGAPSALTLQPVIGQRRAAKTTVRVREGGRGNAYVNGHNTADEGRELRRFDN 326

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR--SPSFPSKRSLRRTSAK 353
               R                +S     +++ +     +  + RSL   +  
Sbjct: 327 VREDRGRGRGGKGGGFKGGLTVSGEAAAKQSQKPFKQRAQKNDRSLPEGNPA 378


>gi|294793715|ref|ZP_06758852.1| ribosomal small subunit pseudouridine synthase A [Veillonella sp.
           3_1_44]
 gi|294455285|gb|EFG23657.1| ribosomal small subunit pseudouridine synthase A [Veillonella sp.
           3_1_44]
          Length = 232

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 102/232 (43%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A     SR+EV ++I  +RV +NG +  +   ++    D + VDG  +   + 
Sbjct: 1   MRLDKLLANKAYGSRKEVHQIIKDRRVTINGSITTKKDTHIDIDVDIVAVDGKIVSTTQL 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +  +     +                   I   V+ VGRLD +TEGLLLLTNDG    
Sbjct: 61  YYVKFHKPKGYVTAVEDSSHPVVMDLLPPEFIKMGVVPVGRLDKDTEGLLLLTNDGVWGH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +   +    +VY V F G +  + +  +K+GI++  G      ++   +       V V
Sbjct: 121 SIINGNKHVPKVYYVEFEGTLSDEGIQRIKEGILLGDGTQCKPAEIEFVSL----HSVHV 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
            + EGK  ++K++       V  L R++ G   L  +   GS  E++ + + 
Sbjct: 177 TIEEGKYHQVKRMIGAAGGTVTYLKRLTIGHIDLSGIEEVGSAMELTVEQIE 228


>gi|260584747|ref|ZP_05852492.1| ribosomal small subunit pseudouridine synthase A [Granulicatella
           elegans ATCC 700633]
 gi|260157404|gb|EEW92475.1| ribosomal small subunit pseudouridine synthase A [Granulicatella
           elegans ATCC 700633]
          Length = 237

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 56/232 (24%), Positives = 100/232 (43%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++ +    SR++++++I+   V ++       + NV      I V G  +    +
Sbjct: 1   MRLEHLLMKHFDISRKQMKKLISSGEVLIDSTPATHVSNNVDPQIQVITVQGSRMEDNSQ 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      ++T  +D    + +          +  +GRLD +TEGLL++TN+G L  
Sbjct: 61  KYYLLNKPKG-VITATTDSQLPTVIDLFKNENIEGLYPIGRLDRDTEGLLIITNNGPLGY 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V  +G +D   +     GI+          ++++     S +  TV
Sbjct: 120 RLLNPIQHIEKEYYVEVNGPLDNSCIQRFYDGIMFHDGTICKPAKLSILESSPSFSKATV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L  G  R ++   L+
Sbjct: 180 TISEGKFHQIKKMFLCVGVKVTFLKRIRFGEFLLDESLSPGEYRPLNFSELQ 231


>gi|187933363|ref|YP_001887508.1| RNA pseudouridine synthase family protein [Clostridium botulinum B
           str. Eklund 17B]
 gi|187721516|gb|ACD22737.1| RNA pseudouridine synthase family protein [Clostridium botulinum B
           str. Eklund 17B]
          Length = 264

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 59/257 (22%), Positives = 102/257 (39%), Gaps = 27/257 (10%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A + +  R+ V   I    VKVNG ++   ++++    D +E     +    +
Sbjct: 1   MRLDKFLAESAVGRRKIVRTYIKDGMVKVNGEIITEPSIDINEKLDDVEYLEKKVVHTGK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                      +  T    +   TVFD      + V  VGRLD +TEGLLLLTNDG    
Sbjct: 61  VYYMFNKPSGCITAT--KDNIHRTVFDYFDEDMNGVFHVGRLDKDTEGLLLLTNDGEFEH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVT 190
            +  P     + Y     G +D +    L++G+ I          ++ +  + GS     
Sbjct: 119 KVMHPEKHVEKTYFFWALGSLDDEDKKQLQEGVFIGSNEALTKPAKIDI-HKSGSYIEFK 177

Query: 191 --------------------VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LL 229
                               + + EG+  ++K++ +     V  L RIS G  +L   L 
Sbjct: 178 EEIPINSLKNKDHQPVVSGYLTISEGQKHQVKRMLKAVGCYVIYLKRISIGGLKLDESLK 237

Query: 230 AGSTREVSKKILREQLG 246
            G  R+++KK ++    
Sbjct: 238 MGDYRDLTKKEIKRIFE 254


>gi|295108497|emb|CBL22450.1| ribosomal small subunit pseudouridine synthase A [Ruminococcus
           obeum A2-162]
          Length = 257

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 66/241 (27%), Positives = 110/241 (45%), Gaps = 22/241 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
              R+ K +A AG  +R EV+++I + +V+VNG+  ++  + V+   D + + G  +  A
Sbjct: 3   KAVRLDKFLADAGKGTRSEVKKIIQKGQVQVNGVPAKKPEMKVVPENDVVVLSGETVGAA 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                +L +KP G V+   +     TV + +PS    +  VGRLD +TEGLLL+T+DG L
Sbjct: 63  PEFVYYLLNKPAGCVSAT-EDRNDRTVMEYVPSDRKGLFPVGRLDKDTEGLLLITDDGML 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQK------ 183
           A  L  P     + Y VR  G++  + +  L+ G+ I +       +V +          
Sbjct: 122 AHELLAPGKHVDKTYFVRVEGKLTVENIRNLENGVDIGEEKMTMPAKVEIVGGSWEGAGD 181

Query: 184 ------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLA 230
                            + + + EGK  ++K++       V  L RIS GP  L   L  
Sbjct: 182 SQSGRVRIENLPEVYTELHLTIHEGKFHQVKRMMAAVGNPVIYLKRISMGPLTLPDNLKK 241

Query: 231 G 231
           G
Sbjct: 242 G 242


>gi|257870927|ref|ZP_05650580.1| pseudouridine synthase [Enterococcus gallinarum EG2]
 gi|257805091|gb|EEV33913.1| pseudouridine synthase [Enterococcus gallinarum EG2]
          Length = 237

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 109/231 (47%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+I      SR+E++R+  Q +V V+  +    + NV S    I+V GV L+    
Sbjct: 1   MRIDKLIEERLATSRKEMKRLFQQGKVLVDQQIERNPSRNVDSRLHEIKVAGVLLQTR-D 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                     + + +VGRLD +TEGL+LLT +G L  
Sbjct: 60  VYYLLNKPAGVVTANIDHQHATVIDLLQPEDRQATLYAVGRLDRDTEGLVLLTTNGQLGY 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            L  P+ +  + Y V  +G V  + +    +GIV  G       ++T++   G  ++V +
Sbjct: 120 ELLHPNKKVPKRYDVIVNGPVTAEDVAAFAQGIVFHGGVVCQPAKLTIEMTSGRRSFVHL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EGK  ++KK+F     KV  L R++ GP +LG LL+G  R +++  L 
Sbjct: 180 EIAEGKFHQVKKMFLARGKKVIALKRVAIGPLELGDLLSGEYRNLTQFELE 230


>gi|255021078|ref|ZP_05293131.1| pseudouridylate synthase [Acidithiobacillus caldus ATCC 51756]
 gi|254969492|gb|EET27001.1| pseudouridylate synthase [Acidithiobacillus caldus ATCC 51756]
          Length = 247

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 64/227 (28%), Positives = 112/227 (49%), Gaps = 3/227 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERTR 74
           +++V+++ G+ SR    + I   RV V+G ++          D  I +DG+P ++A R  
Sbjct: 6   LARVLSKWGLCSRTVAAQWIRAGRVAVDGRIVRDPEAPQRGLDLWISIDGIPQQRARRQV 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L+ K   +V+   +    +   D        +  +GRLD  + GLLL +ND   ++ L
Sbjct: 66  LMLHKKRGVVVSRSDERGRPTVFADI--PQEPWLAPIGRLDRASSGLLLFSNDPIWSQRL 123

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P+    + YRV+    +  + L+ +    V+ G     M+V      G   W+   L+
Sbjct: 124 LDPAGHLPKTYRVQIRPPLAAEALHHIATASVLDGRPCLPMEVRAVACGGKTQWLEFVLQ 183

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           EG+NR+I+++ E    +V RLIRI++G   LG L  GS R +S+  +
Sbjct: 184 EGRNRQIRRLLEAQGVEVLRLIRIAFGSVILGDLAPGSWRWLSEAEI 230


>gi|332284234|ref|YP_004416145.1| pseudouridylate synthase [Pusillimonas sp. T7-7]
 gi|330428187|gb|AEC19521.1| pseudouridylate synthase [Pusillimonas sp. T7-7]
          Length = 244

 Score =  148 bits (372), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 60/244 (24%), Positives = 102/244 (41%), Gaps = 19/244 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
              R+SK++A  G+ SRRE +  I +  V+V+G+++            I +D        
Sbjct: 2   EKIRISKLMAERGLCSRREADAYIERGWVRVDGVVVSELGSKAWPDQKITLDKQAQRRQT 61

Query: 64  -------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
                    P+          Y   + L++  +      +     P     +   GRLDI
Sbjct: 62  SRVTILLNKPVGYVSGQAEQGYRPAVSLISASTRYRVDKSPLKFEPGHLRGLAPAGRLDI 121

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +++GLL+LT DG +AR L    ++  + Y VR  G++  + L  L  G+ + G       
Sbjct: 122 DSQGLLVLTQDGRIARQLINEDSEIDKEYLVRVQGKIAGNGLAQLNFGLSLDGKPLRRAH 181

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V    +      +   L+EGK R+I+++ E    KV  L R+  G   LG L  G  R +
Sbjct: 182 VEWQNEDQ----LRFVLQEGKKRQIRRMCEQVGLKVIGLKRVRMGRIVLGDLPPGQWRYL 237

Query: 237 SKKI 240
            +  
Sbjct: 238 KEGE 241


>gi|295696420|ref|YP_003589658.1| pseudouridine synthase [Bacillus tusciae DSM 2912]
 gi|295412022|gb|ADG06514.1| pseudouridine synthase [Bacillus tusciae DSM 2912]
          Length = 245

 Score =  148 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 91/230 (39%), Positives = 130/230 (56%), Gaps = 1/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KVIA AG+ SRR+ E+ IAQ RV+VNG ++      V    D IEVDG  +   +R
Sbjct: 3   ERLQKVIAGAGLTSRRKAEQWIAQGRVRVNGRVVVEQGFKVDPEVDRIEVDGRSVAIPDR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T  +L++KPIG+VTT  DP GR  V D +  +  RV  VGRLDIN+ GLLLLTNDG LA 
Sbjct: 63  TVCFLFYKPIGVVTTLHDPQGRPAVADYVRDLPKRVFPVGRLDINSSGLLLLTNDGELAH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + YRV   G +D   +  L+ GIV+ G+     +V L  +    +   + 
Sbjct: 123 RLMHPRFGVEKTYRVAVRGYLDNPGIRRLETGIVLDGVRTAPARVRLWGRGRERSEFDIT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L EG+NR+++++ +     V  L RI YG   +  L  G  R ++++  R
Sbjct: 183 LHEGRNRQVRRMCKAVGHPVLELTRIQYGNLTIDGLAPGEIRPLTEEEER 232


>gi|49081896|gb|AAT50348.1| PA0733 [synthetic construct]
          Length = 231

 Score =  148 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 107/231 (46%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     SRR+ + +IA   ++V+G ++      V     +E+D   L+  +  
Sbjct: 1   MRLDRFLANLPELSRRDAQMLIAGGHLRVDGQVVRDGTHEVRVFSRVELDERLLQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP+G V+   DP   + +      +   +   GRLD NT GL+LLTNDG  +R 
Sbjct: 61  RYYMLHKPMGCVSATRDPQHPTVLDLFPEDLRDDLHIGGRLDYNTTGLMLLTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L LP ++  +VY V     +DQ  ++          + +     Q+             +
Sbjct: 121 LTLPGSRRDKVYYVETEAPIDQRYVDAFAAGLHFRFEDLVTLPAQLEPI----GPRCARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            L EG+  ++K++F  F+ KV RL R   G   L   L  G+ R ++ + +
Sbjct: 177 TLHEGRYHQVKRMFGHFDNKVLRLHRERMGDICLDPQLPPGAWRPLNAEEI 227


>gi|15595930|ref|NP_249424.1| pseudouridylate synthase [Pseudomonas aeruginosa PAO1]
 gi|34098724|sp|Q9I5J6|RSUA_PSEAE RecName: Full=Ribosomal small subunit pseudouridine synthase A;
           AltName: Full=16S pseudouridine 516 synthase; AltName:
           Full=16S pseudouridylate 516 synthase; AltName:
           Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|9946618|gb|AAG04122.1|AE004508_7 probable pseudouridylate synthase [Pseudomonas aeruginosa PAO1]
          Length = 230

 Score =  148 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 107/231 (46%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     SRR+ + +IA   ++V+G ++      V     +E+D   L+  +  
Sbjct: 1   MRLDRFLANLPELSRRDAQMLIAGGHLRVDGQVVRDGTHEVRVFSRVELDERLLQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP+G V+   DP   + +      +   +   GRLD NT GL+LLTNDG  +R 
Sbjct: 61  RYYMLHKPMGCVSATRDPQHPTVLDLFPEDLRDDLHIGGRLDYNTTGLMLLTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L LP ++  +VY V     +DQ  ++          + +     Q+             +
Sbjct: 121 LTLPGSRRDKVYYVETEAPIDQRYVDAFAAGLHFRFEDLVTLPAQLEPI----GPRCARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            L EG+  ++K++F  F+ KV RL R   G   L   L  G+ R ++ + +
Sbjct: 177 TLHEGRYHQVKRMFGHFDNKVLRLHRERMGDICLDPQLPPGAWRPLNAEEI 227


>gi|293363190|ref|ZP_06610074.1| pseudouridylate synthase [Mycoplasma alligatoris A21JP2]
 gi|292553049|gb|EFF41798.1| pseudouridylate synthase [Mycoplasma alligatoris A21JP2]
          Length = 237

 Score =  148 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 61/244 (25%), Positives = 107/244 (43%), Gaps = 8/244 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K++A+AGIASRR+ E +I +  VK+NG +           D I V+G  + + ++ 
Sbjct: 2   ERIQKLLAQAGIASRRKAEELITKGLVKINGDVAT-IGQKATFNDKISVNGKEIVQEKKV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      + T   + + R     +L     R+  VGRLD +T G+L+LTNDG L+  
Sbjct: 61  YFVLNKPSKTVCTLKDNFNRRKV--VDLIETNLRIFPVGRLDYDTTGVLILTNDGELSNK 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P    +R YR R    + +D +  L    +I G      +  +  ++       V L
Sbjct: 119 LIHPKYNIIRKYRARLDEPLSKDDIKELNNEQLING---KPSKQVV--EQIDTKSYLVTL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
            +G    +K++F      V  L R+ +    +  +  G  R ++ K ++        E+ 
Sbjct: 174 TQGTYHHVKELFSKVGRLVINLKRVEFAGIGVDKIPMGEYRSLNMKEIKTLHNLVKEEKN 233

Query: 254 QVNL 257
               
Sbjct: 234 VKEK 237


>gi|104783290|ref|YP_609788.1| 16S rRNA pseudouridylate 516 synthase [Pseudomonas entomophila L48]
 gi|95112277|emb|CAK17004.1| 16S rRNA pseudouridylate 516 synthase [Pseudomonas entomophila L48]
          Length = 249

 Score =  148 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 59/252 (23%), Positives = 111/252 (44%), Gaps = 7/252 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +      +R++V  ++A +RV+V+G++       V     +EVD   ++     
Sbjct: 1   MRLDRFLGNLPCYNRQQVRLLLASKRVRVDGVVASDPLHEVREFSRVEVDDQVVQAGYPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + HKP G V+  SDP   + +      +   +   GRLD NT GL++LTNDG  +R 
Sbjct: 61  RYLMLHKPTGCVSATSDPLHPTVLDLLPAELRDGLHIAGRLDYNTTGLMILTNDGQWSRH 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V    ++    ++  ++      + +     Q+ +           +
Sbjct: 121 LTQPRTKLPKVYLVHTEDEIGAHYVDKFREGFYFAFEDLTTQPAQLDIL----GPREARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLL 250
            + EG+  ++K++F +F  KV  L R   G   L   L  G  RE+S + +         
Sbjct: 177 TIVEGRYHQVKRMFGYFQNKVVGLHRERMGAIALDPGLAPGEYRELSAEEISTVCRSGFS 236

Query: 251 EEAQVNLDAPIY 262
            +   ++  P+ 
Sbjct: 237 RDEHTSVWHPLR 248


>gi|326508874|dbj|BAJ86830.1| predicted protein [Hordeum vulgare subsp. vulgare]
 gi|326510163|dbj|BAJ87298.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 404

 Score =  148 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 71/252 (28%), Positives = 117/252 (46%), Gaps = 14/252 (5%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPL 67
           +   PQR++KV+A AG+ASRR  E +I Q +V VNG +       V  S D I V+G  +
Sbjct: 151 KEHEPQRLAKVLAAAGVASRRTSEELIFQGKVTVNGSVCTAPQTKVDISKDSIYVNGNRI 210

Query: 68  RKAERTRLWL--YHKPIGLVTTHSDPDGRSTVFDNLPSI--------FSRVISVGRLDIN 117
            K    +L+         + ++  +    S + D L             R+ +VGRLD+ 
Sbjct: 211 SKKLPPKLYFAVNKPKGYICSSGEEKSVISLLDDYLKGWNKLQPGVPKPRLFTVGRLDVA 270

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GL+++TNDG  A+ +  PS+   + Y V   G V +  L  +  G VI G+      V
Sbjct: 271 TTGLIIVTNDGEFAQKVSHPSSNITKEYVVTIDGAVHKKHLVAISGGTVIDGVKVVPDLV 330

Query: 178 TLDTQKGSNA--WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTR 234
                +       + + + EG+N E++++ +    KV  L R+  G F+L   L  G   
Sbjct: 331 EPLDTQADTKRMRLKIVVHEGRNHEVRELVQNAGLKVYALKRVRIGRFRLPSDLGIGKMV 390

Query: 235 EVSKKILREQLG 246
           E+ +  ++   G
Sbjct: 391 ELKEADIKALDG 402


>gi|91775308|ref|YP_545064.1| pseudouridine synthase, Rsu [Methylobacillus flagellatus KT]
 gi|91775452|ref|YP_545208.1| ribosomal small subunit pseudouridine synthase A [Methylobacillus
           flagellatus KT]
 gi|91709295|gb|ABE49223.1| Pseudouridine synthase, Rsu [Methylobacillus flagellatus KT]
 gi|91709439|gb|ABE49367.1| ribosomal small subunit pseudouridine synthase A [Methylobacillus
           flagellatus KT]
 gi|167042455|gb|ABZ07181.1| putative RNA pseudouridylate synthase [uncultured marine
           microorganism HF4000_ANIW133B20]
 gi|167042899|gb|ABZ07615.1| putative RNA pseudouridylate synthase [uncultured marine
           microorganism HF4000_ANIW137K11]
          Length = 237

 Score =  148 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 52/238 (21%), Positives = 90/238 (37%), Gaps = 4/238 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAER 72
            ++ +++   G  SR+    MI    V VNG + +           +  V G      E+
Sbjct: 1   MQLERILHSQGFGSRKICRSMIRHGEVAVNGEVCDFPFTEFDPEHLVFTVRGETWTYREK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L        +               P +   V S+GRLD +T GLLLL++DG    
Sbjct: 61  AYLMLNKPAHYECSHKPQHHPSIFSLLPAPLLERGVQSIGRLDEDTTGLLLLSDDGQFIH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  +VY V     +D+ ++  L  G+ +           L  +   +  + + 
Sbjct: 121 RMSSPKWKVPKVYEVTTKHPLDETQVTSLLSGVQLLDEPAPVA--ALSAKIVGDHVLHLT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHL 249
           L EGK  ++K++    + +V  L RI  G   L   L  G+ R +   +L        
Sbjct: 179 LAEGKYHQVKRMLAAVSNRVEALKRIRIGSLDLPEDLAPGAWRWLDAAMLAAVAPMRQ 236


>gi|282902023|ref|ZP_06309921.1| Pseudouridine synthase, Rsu [Cylindrospermopsis raciborskii CS-505]
 gi|281193110|gb|EFA68109.1| Pseudouridine synthase, Rsu [Cylindrospermopsis raciborskii CS-505]
          Length = 252

 Score =  148 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 71/238 (29%), Positives = 110/238 (46%), Gaps = 12/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL---RKA 70
           RV K+I++ GIASRRE E MI Q RV++NGIL       V    D I +DG P+    + 
Sbjct: 4   RVQKIISQWGIASRREAEEMIGQSRVRINGILAR-LGQKVDPRVDIISIDGKPVIQGNRP 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDG 128
               L L      + T +      + +          + +  VGRLD ++ G L+LTNDG
Sbjct: 63  ALVYLLLNKPTGVVSTCNDPQGRTTVLDLLPAKLRQGTGIHPVGRLDADSTGALILTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS    + Y V   G    + L +  +G+++ G      QV L  Q  + + 
Sbjct: 123 DLTFALTHPSHDISKTYHVVVEGHPPTNVLRMWSQGVMLDGRKTRTAQVKLIEQGVTQSK 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-----LLAGSTREVSKKIL 241
           + + L+EG+NR+I++V +   + V  L R + G  QL       +  G  R +    +
Sbjct: 183 LEIILQEGRNRQIRRVAQQLGYPVVHLDRRAVGTIQLHNSYGKFIDIGKYRHLITSEI 240


>gi|226503651|ref|NP_001152020.1| LOC100285657 [Zea mays]
 gi|195651911|gb|ACG45423.1| ribosomal large subunit pseudouridine synthase B [Zea mays]
          Length = 406

 Score =  148 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 67/261 (25%), Positives = 113/261 (43%), Gaps = 18/261 (6%)

Query: 4   KNIVQENF---TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDH 59
           +    EN     PQR++KV+A AG+ASRR  E +I Q +  VNG +       V  S D 
Sbjct: 144 RRFYNENIKEREPQRLAKVLAAAGVASRRTSEELIFQGKXTVNGSVCTSPQTKVDISKDS 203

Query: 60  IEVDGVPLRKAERTRLWL--YHKPIGLVTTH---------SDPDGRSTVFDNLPSIFSRV 108
           I V+G  + K    +L+         + +            +   +            R+
Sbjct: 204 IYVNGNRISKKLPPKLYFAVNKPKGYICSCGEESKSVVSLFNDYLKGWNKIQPGLPKPRL 263

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            +VGRLD+ T GL+++TNDG  A+ L  PS+   + Y V   G V +  L  + +G  I 
Sbjct: 264 FTVGRLDVATAGLIIVTNDGEFAQKLAHPSSNVTKEYVVTIDGAVHKKHLIAISEGTKID 323

Query: 169 GICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL- 225
           G+       +            + + + EG+N E++++ +    +V  L R+  G F+L 
Sbjct: 324 GVMCIPDLVEPLAAQSDTRKTRLRIVVHEGRNHEVRELVQNAGLQVYALKRVRIGRFRLP 383

Query: 226 GTLLAGSTREVSKKILREQLG 246
             L  G   E+ +  ++   G
Sbjct: 384 ADLGIGKFVELKQADIKALDG 404


>gi|282850202|ref|ZP_06259581.1| pseudouridylate synthase [Veillonella parvula ATCC 17745]
 gi|282579695|gb|EFB85099.1| pseudouridylate synthase [Veillonella parvula ATCC 17745]
          Length = 232

 Score =  148 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 102/232 (43%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A     SR+EV ++I  +RV +NG +  +   ++    D + VDG  +   + 
Sbjct: 1   MRLDKLLANKAYGSRKEVHQIIKDRRVTINGSITTKKDTHIDIDVDIVAVDGKVVSTTQL 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +  +     +                   I   V+ VGRLD +TEGLLLLTNDG    
Sbjct: 61  YYVKFHKPKGYVTAVEDSNHPVVMDLLPPEFIKMGVVPVGRLDKDTEGLLLLTNDGVWGH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +   +    +VY V F G +  + +  +K+GI++  G      +     +  S   V V
Sbjct: 121 SIINGNKHVPKVYYVEFEGTLSDEGIQRIKEGILLGDGTQCKPAE----IESVSLHSVHV 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
            + EGK  ++K++       V  L R++ G   L  +   GS  E++ + + 
Sbjct: 177 TIEEGKYHQVKRMIGAAGGTVTYLKRLTIGHIDLSGIEEVGSAMELTVEQIE 228


>gi|332534329|ref|ZP_08410172.1| 16S rRNA pseudouridylate synthase [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332036239|gb|EGI72712.1| 16S rRNA pseudouridylate synthase [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 232

 Score =  148 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 99/233 (42%), Gaps = 8/233 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K I+      R +    I ++ V VNG ++      +   D +   G PL     
Sbjct: 4   PCRLDKFISHLAEIPRTQARASIKRKEVSVNGEVITSHNFQLAQQDEVLHQGTPLVFL-G 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R ++ +KP+G V  +SD   ++          S     GRLDI+T GL+++TNDG  + 
Sbjct: 63  KRYYMLNKPVGYVCANSDELHKTVFDLLDEPNMSDFHVAGRLDIDTTGLVIITNDGDWSH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVT 190
            +  P     + Y V     +  + L  L+ G+++                ++ +N  + 
Sbjct: 123 KITSPKNNKFKTYLVETQEPITDEALEQLRTGVMLHNEKDLTRPA----IAERLANYGLR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + + EGK  ++K++    + KV  L R       L   L +G  R ++ + ++
Sbjct: 179 LSISEGKYHQVKRMLYAVDNKVVELHREQIAGITLDENLASGEYRLLTPEEIK 231


>gi|71280018|ref|YP_270193.1| ribosomal large subunit pseudouridine synthase B [Colwellia
           psychrerythraea 34H]
 gi|71145758|gb|AAZ26231.1| ribosomal large subunit pseudouridine synthase B [Colwellia
           psychrerythraea 34H]
          Length = 355

 Score =  148 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 83/299 (27%), Positives = 142/299 (47%), Gaps = 10/299 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K +     +   ++V KV+ARAG  SRRE+E MI++ RV ++G +       +  T+ I
Sbjct: 58  VKVEFQKATHSDSEKVQKVLARAGKGSRREMETMISEGRVSIDGKVAF-LGDRITGTEQI 116

Query: 61  EVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            +DG  ++           L        + T        +      P    R ++VGRLD
Sbjct: 117 RLDGHHVKLTAQDEDICRVLVYNKPEGEMCTRKDPEGRPTVFDRLPPLDAGRWVAVGRLD 176

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           INT G+LL T DG LA  L  PS +  R Y VR  G++++  L  L+ G+ ++       
Sbjct: 177 INTSGMLLFTTDGELANRLMHPSQKVEREYAVRVFGEINEAMLQTLRAGVKLEDGMARFQ 236

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTR 234
           ++T    +G N W  V L EG+NRE+++++E  + +V+RLIR+ YG  ++   L  G  R
Sbjct: 237 KITYRGGEGRNHWFHVVLSEGRNREVRRLWESQDVQVSRLIRVRYGDMEMQRQLPMGGWR 296

Query: 235 EVSKKIL---REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           E++ K +   R+ +      E++V +D     +    R R ++           ++   
Sbjct: 297 ELALKEVNYYRQLVNLTPEAESKVKVDEKAMDNAKSRRIRRSVKKHQQRHQQSTRRRHK 355


>gi|157374135|ref|YP_001472735.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
 gi|157316509|gb|ABV35607.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
          Length = 247

 Score =  148 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 63/230 (27%), Positives = 105/230 (45%), Gaps = 8/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I+     +R+ V  M+A+ RV+V+G L       V    HI +D   L+  E + 
Sbjct: 21  RLDRFISVNTGINRKHVRLMLAKGRVRVDGELARDIDQVVDEFSHICLDDKVLQANEASY 80

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L+     +V+   D   R+ +          +  VGRLD+NT GLLLLTNDG  ++ L
Sbjct: 81  VMLHKPVG-VVSATIDDKHRTVIDLLEQDDKESLHIVGRLDLNTSGLLLLTNDGRWSKRL 139

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
             P  +  ++YRV     +  D ++   +      + I     ++ +      +    V 
Sbjct: 140 MDPEHKVGKLYRVHLQNPLTPDYISGFAQGMYFEFEDITTLPAELEII----DSYTALVT 195

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           L EG+  +IK++F  F   V  L RIS G   L   L  G +R ++ K +
Sbjct: 196 LYEGRYHQIKRMFGRFRNPVIGLHRISVGNIVLDNNLKPGESRVLTPKEI 245


>gi|297586934|ref|ZP_06945579.1| ribosomal small subunit pseudouridine synthase A [Finegoldia magna
           ATCC 53516]
 gi|297574915|gb|EFH93634.1| ribosomal small subunit pseudouridine synthase A [Finegoldia magna
           ATCC 53516]
          Length = 235

 Score =  148 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 56/233 (24%), Positives = 119/233 (51%), Gaps = 9/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ ++++   IA+R+E+++M+ +  + VN + +++++ ++    D +++    +   + 
Sbjct: 1   MRLDRMLSEMKIATRKEIKQMVKKGIITVNDVTVKKSSEHIDENKDVVKIYDEVIEYRKY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +K  G+ +   DP  R+ + D        +  VGRLD++T GLL++TNDG  A 
Sbjct: 61  L-YFVMNKRKGVTSHSKDPMHRTVIDDMGELCVFDLNPVGRLDLDTTGLLIITNDGKFAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVT 190
            L  P     + Y+V    +VD+   +  +KGI +  + I      + +      +    
Sbjct: 120 NLISPKKDVSKKYKVTLRYKVDEKYNDTFEKGIKLMPEDIITKPATMEII----DDYNCY 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           + ++EGK  ++K++FE    +V  L R+  G F+L   L  G  RE++ + L+
Sbjct: 176 LTIKEGKYHQVKRMFEKVGNEVVELQRVQIGSFKLPEDLEEGDFRELTDEELK 228


>gi|119469122|ref|ZP_01612106.1| 16S rRNA pseudouridylate 516 synthase [Alteromonadales bacterium
           TW-7]
 gi|119447374|gb|EAW28642.1| 16S rRNA pseudouridylate 516 synthase [Alteromonadales bacterium
           TW-7]
          Length = 232

 Score =  148 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 102/233 (43%), Gaps = 8/233 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K I+      R +    I ++ V VNG ++      +   D +  +G PL     
Sbjct: 4   PCRLDKFISHLAEVPRTQARASIKRKEVSVNGEVITAHNFQLAKDDVVLHNGEPLVFL-G 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R ++ +KP+G V  +SD   ++          S     GRLDI+T GL+++TNDG  + 
Sbjct: 63  KRYFMLNKPVGYVCANSDDLHKTVFDLLDEPNMSDFHVAGRLDIDTTGLVIITNDGDWSH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVT 190
            +  P +   + Y V     +  + L  L++G+++                ++ +N  + 
Sbjct: 123 KITSPRSNKFKTYLVETQEPITDEALEQLREGVMLHNEKDATRPA----IAERLANYGLR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + + EGK  ++K++    + KV  L R      +L   L  G  R +++  ++
Sbjct: 179 LSISEGKYHQVKRMLYAVDNKVVELHREQIAGIKLDEDLAPGEYRLLTENEIK 231


>gi|254448673|ref|ZP_05062131.1| ribosomal large subunit pseudouridine synthase B [gamma
           proteobacterium HTCC5015]
 gi|198261681|gb|EDY85968.1| ribosomal large subunit pseudouridine synthase B [gamma
           proteobacterium HTCC5015]
          Length = 298

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 74/297 (24%), Positives = 122/297 (41%), Gaps = 12/297 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ K +A+ G+ SRR++E  I   ++ VNG + +     +  +D + +DG  +      
Sbjct: 3   ERIQKRLAQLGMGSRRQIEHWIRDGKITVNGKVAQ-LGDTLEWSDRVTLDGKAIDLEQVD 61

Query: 70  -AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              +  L  +     + T        +           R ISVGRLD+NT GLLL T DG
Sbjct: 62  TIPKEVLLYHKPEGEVCTRSDPQGRTTVFERLPRLRAGRWISVGRLDVNTAGLLLFTTDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----TQKG 184
            LA  L  PS +  R Y VR  G V  + LN L +G+ ++       ++ +         
Sbjct: 122 ELANRLMHPSREIDREYAVRVLGDVSDEMLNQLVEGVQLEDGAAKFSEIVIGDHEYDSDR 181

Query: 185 SNAWVTVGLREGKNREIKKVFEFF-NWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           +N W  V L+EG+NRE+++++E F    V+RL R+ Y    L  TL  G  +       +
Sbjct: 182 ANRWYYVCLQEGRNREVRRLWESFSGVTVSRLKRVRYANIFLPKTLARGQWKRAEYDEFQ 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
           E      L        A           R            + ++ S+ +      +
Sbjct: 242 ELYRSVELTPPSQKTYAESGGKRKEKHTRRARDINQKRRQQQNRRRSASQMRRRNPR 298


>gi|167645656|ref|YP_001683319.1| pseudouridine synthase [Caulobacter sp. K31]
 gi|167348086|gb|ABZ70821.1| pseudouridine synthase [Caulobacter sp. K31]
          Length = 255

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 65/245 (26%), Positives = 118/245 (48%), Gaps = 15/245 (6%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + +   PQRV++ +A+ G+ SRRE E +I Q  V ++G+ ++     +     + +    
Sbjct: 6   LYDEAEPQRVNRWLAQNGVCSRREAEALILQGLVSIDGLRVDDVGRKIEPGQTLVLSDRA 65

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRST-----------VFDNLPSIFSRVISVGRLD 115
             + E     + HKPIG+V+   D                     +P   +++  VGRLD
Sbjct: 66  QAQLEGALTVMIHKPIGIVSAQPDTGQVPAVRLLTREALYGQSPVIPGFENKLAPVGRLD 125

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           +++ GLL+L+ DG +A+ +  P+++  + Y V   G +  +KL LL+ G+ +        
Sbjct: 126 MDSRGLLILSEDGVVAKAVIGPASEMEKEYLVWVDGWITDEKLVLLRHGLELDERALRPA 185

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           QV +  ++     +   L+EG+NR+I+++ E     V  L+RI  G   LG L  G  R 
Sbjct: 186 QVEVVGRQQ----LKFILQEGRNRQIRRMCELVELTVVDLLRIRIGNVMLGDLPEGRWRP 241

Query: 236 VSKKI 240
           +S   
Sbjct: 242 LSAAE 246


>gi|239617854|ref|YP_002941176.1| pseudouridine synthase [Kosmotoga olearia TBF 19.5.1]
 gi|239506685|gb|ACR80172.1| pseudouridine synthase [Kosmotoga olearia TBF 19.5.1]
          Length = 235

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 55/235 (23%), Positives = 101/235 (42%), Gaps = 6/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+   ++R G  SRR+  ++I   RV+VNG  +      +     I +DG  +    + 
Sbjct: 1   MRLDTFLSRFGGISRRQSRKLIKTGRVEVNGAKIRNPEFKIPENSSIFLDGNRIVPYGKL 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +      + +     +G S          S++   GRLD N+ GLLLL+NDG     
Sbjct: 61  YIAMNKPVGYVCSKSRT-EGLSVYDLINEVFSSKLSIAGRLDKNSRGLLLLSNDGNFVHE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y V+   ++  ++L +L + + I    Y   +             ++ L
Sbjct: 120 IISPRKKIEKEYIVKVEEKILPEQLQILLQHVDIGKGEYARAESVQF---IDIVTFSIVL 176

Query: 194 REGKNREIKKVFE-FFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
            EGK  EI+++ +      V  L RI  G + L G L  G  R ++++ ++   G
Sbjct: 177 TEGKYHEIRRMVKSALKNNVVDLKRIRIGGYHLPGDLHEGEWRILTEEEIKAATG 231


>gi|254525039|ref|ZP_05137094.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
 gi|219722630|gb|EED41155.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
          Length = 546

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 80/352 (22%), Positives = 140/352 (39%), Gaps = 13/352 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV----PLRK 69
           +R+ KV+A+AG+ SRR +E+ IA+  VKVNG + +   ++V S D IE+DG         
Sbjct: 24  ERLHKVLAQAGLGSRRALEQRIAEGLVKVNGEVAQT-GMSVKSGDKIELDGRGFVATALA 82

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + T        +      P   +R I++GRLDINT GLLL T DG 
Sbjct: 83  EPSRVLVYNKPEGEVTTREDPEGRPTVFESLPPLKGARWIAIGRLDINTTGLLLATTDGE 142

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR      ++      ++ L +G+ ++       ++       
Sbjct: 143 LANAMMHPSFEVEREYVVRVRAPEGEEKVSDAIVDRLSRGVALEDGPAKFDEIERIGGTD 202

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   L  G + E+    +  
Sbjct: 203 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGKVSLPRELARGHSVELGTAQVEA 262

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                 LEE   +              +  +               +  +   + ++   
Sbjct: 263 LRAQLKLEEGAPSALTLQPVIGQRRAAKTTVRVREGGRGNAYVNGHNTADEGRELRRFDN 322

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR--SPSFPSKRSLRRTSAK 353
               R                +S     +++ +     +  + RSL   +  
Sbjct: 323 VREDRGRGRGGKGGGFKGGLTVSGEAAAKQSQKPFKQRAQKNDRSLPEGNPA 374


>gi|326560444|gb|EGE10826.1| ribosomal large subunit pseudouridine synthase B [Moraxella
           catarrhalis 7169]
 gi|326571160|gb|EGE21184.1| ribosomal large subunit pseudouridine synthase B [Moraxella
           catarrhalis BC7]
          Length = 328

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 79/318 (24%), Positives = 135/318 (42%), Gaps = 13/318 (4%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           ++         +++ K++AR G+ SRR +E +I   R+ +N  +       V+ TD I +
Sbjct: 13  NEQNATNKPAGEKLQKLLARLGLGSRRGLEEIIKSGRISINDKVAT-LGDRVILTDEIRI 71

Query: 63  DGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           DG  +R        R  +  Y     + +        +           R + VGRLDIN
Sbjct: 72  DGRQVRLKAEREKRRRVIAYYKPEGEICSASDPQGRPTVFDRLPKLTNDRWVMVGRLDIN 131

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           + GLLL TNDG LA  L  PS+  +R Y VR  G+V     + L  G+ ++        +
Sbjct: 132 SSGLLLFTNDGELAHRLMHPSSGIIREYAVRVLGEVTPQIASQLTAGVELEDGVAKFDDI 191

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                 G N W  V ++EG+ RE++++FE    KV+RLIR  YG   L   L  G   E+
Sbjct: 192 KEGGGIGVNKWYHVTIKEGRKREVRRMFESQTLKVSRLIRTRYGTVILPKELRTGRFIEL 251

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
               + + +      ++               +++   I + P     +++   + +   
Sbjct: 252 DASDIGKLV------DSVGLRQRQGTGLNHATKEKQARIHKKPLKSREIRRQKHEAHERR 305

Query: 297 KQKKLATPVHRRNLASNV 314
           +++K  TP HR    S  
Sbjct: 306 EERKKHTPKHRTPNLSRT 323


>gi|152993935|ref|YP_001359656.1| RNA pseudouridine synthase [Sulfurovum sp. NBC37-1]
 gi|151425796|dbj|BAF73299.1| RNA pseudouridine synthase [Sulfurovum sp. NBC37-1]
          Length = 281

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 73/285 (25%), Positives = 127/285 (44%), Gaps = 18/285 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA     SRRE +R+I +  V +N  +L   A +V   DHI V   P++ +   
Sbjct: 1   MRLNKYIAHHTKYSRREADRLIEEGEVTLNKKVLRDFAYDVQEGDHIYVKSRPIKPSNEI 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +Y+KP G++ T  D  GR+T++  LP  F   + VGRLD  +EGLL+LT+   +   
Sbjct: 61  TVIVYNKPKGVLVTKKDDRGRATIYHKLPGKFRHFVPVGRLDYASEGLLILTDSVEVVTA 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQVTL 179
           L        R Y ++    V Q+ +  + +G+V+                         +
Sbjct: 121 LMGSD--LERTYNLKIDKPVTQEMVAAMNEGLVLDDARAGGHEKSKIYGMEFAPFAHFEI 178

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            ++  S   + V + EGKNRE+++ F  F+ KV  L R++YG  +L  L    TR  S+K
Sbjct: 179 RSEGKSYTKLRVTITEGKNRELRRFFGHFDAKVLDLKRVAYGGIELNNLPTNKTRFFSRK 238

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
              +      +++ +      + +    ++           D   
Sbjct: 239 EYDDL--HKFMKQLKAEKKVEVKNRANALKQEEANKKAKKSDRRD 281


>gi|300704912|ref|YP_003746515.1| 16S rRNA pseudouridylate 516 synthase [Ralstonia solanacearum
           CFBP2957]
 gi|299072576|emb|CBJ43926.1| 16S rRNA pseudouridylate 516 synthase [Ralstonia solanacearum
           CFBP2957]
          Length = 252

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 54/228 (23%), Positives = 86/228 (37%), Gaps = 4/228 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-VDGVPLRKAERTR 74
           + +++   G  +RR  + ++    V VNGI  E     V +   +  VDG       R  
Sbjct: 10  LYRILQSQGFGTRRYCKDLVLAGLVHVNGIEAENPDAQVDTAGLVLDVDGERWAYHARAY 69

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L+       +              +P     V  VGRLD +T GLLLLT+DG     L
Sbjct: 70  LMLHKPAGFECSQKPRHHPSVYTLLPVPLRERGVQCVGRLDQDTTGLLLLTDDGQFVHTL 129

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  Q  +VY +     V   +L  L +G+++            +        + + L 
Sbjct: 130 TSPRHQVPKVYEITTADPVTDAQLAQLCQGVLLDDEDATVAAAWAERVD--TCHLRMALT 187

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           +GK  ++K++       V  L R + G   L   L  G  R +    L
Sbjct: 188 QGKYHQVKRMVAAAGNHVTALHRSAIGALTLDAGLAPGQWRWLEHDDL 235


>gi|152979359|ref|YP_001344988.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
 gi|150841082|gb|ABR75053.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
          Length = 373

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 93/283 (32%), Positives = 133/283 (46%), Gaps = 10/283 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN-VMSTDHIEVDGVPL---- 67
            +++ KV+ARAG  SRRE+E +IA+ RV V+G +        V S   I +DG  +    
Sbjct: 91  GEKLQKVLARAGQGSRREIEAVIAEGRVSVDGKIAALGDRVIVHSGLKIRIDGHLVNLTG 150

Query: 68  -RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
            +K     L  Y     L T H      +          SR ++VGRLDINT GLLL T 
Sbjct: 151 VQKDVCRVLMYYKPEGELCTRHDPEGRATVFERLPRLTGSRWVAVGRLDINTSGLLLFTT 210

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  G VD   L  L+KG+ ++        +      G N
Sbjct: 211 DGELANRLMHPSREVEREYSVRVFGNVDDAMLARLQKGVQLEDGPANFTAIKPAGGTGMN 270

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK---ILR 242
            W  V L EG+NRE+++++E    +V+RLIRI YG  +L  TL  G  +E+  +    LR
Sbjct: 271 RWFDVTLIEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKTLPRGGWQEMDLENVNYLR 330

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
           E +G     E ++++      ++T    R            R 
Sbjct: 331 ELVGLPPETETRLDVTQSNRRAKTGQIRRAVKRYSDVTRRYRK 373


>gi|302546514|ref|ZP_07298856.1| pseudouridine synthase RluB [Streptomyces hygroscopicus ATCC 53653]
 gi|302464132|gb|EFL27225.1| pseudouridine synthase RluB [Streptomyces himastatinicus ATCC
           53653]
          Length = 226

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 62/217 (28%), Positives = 98/217 (45%), Gaps = 2/217 (0%)

Query: 26  ASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRLWLYHKPIGL 84
            SRR  E +I Q RV+VNG ++    + V    D I+VDG+ +         L      +
Sbjct: 2   GSRRACEDLIDQARVEVNGKIVTEQGLRVDPEKDEIKVDGLTVATQSYLFFALNKPAGVV 61

Query: 85  VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV 144
            T       +  + D + +  +R+  VGRLD  TEG++LLTN G LA  L  P     + 
Sbjct: 62  STMEDPDGRQ-CLGDYVTNRETRLFHVGRLDTETEGIILLTNHGELAHRLTHPRYGVKKT 120

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
           Y     G + +D    LK GI ++          +    G N  V V L EG+   ++++
Sbjct: 121 YLAAIQGPLPRDLGKQLKNGIELEDGYARADHFKVVQNTGKNYLVEVSLHEGRKHIVRRM 180

Query: 205 FEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                + V +L+R S+GP  LG   +G  R ++   +
Sbjct: 181 LSEAGFPVEKLVRTSFGPIPLGDQKSGWLRRLTNTEV 217


>gi|120555818|ref|YP_960169.1| pseudouridine synthase [Marinobacter aquaeolei VT8]
 gi|120325667|gb|ABM19982.1| ribosomal small subunit pseudouridine synthase A [Marinobacter
           aquaeolei VT8]
          Length = 230

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 104/228 (45%), Gaps = 2/228 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            ++ +++      SRR+ + ++A  RV V+G       +++     + VD   ++ A  +
Sbjct: 1   MKLLRILTNQNGISRRQAKALLAAGRVHVDGERCHDPDLDIPRFREVCVDQRIIQSAAPS 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP G ++   D    + +    P +   V   GRLD  + GLL+LT+DG  +R 
Sbjct: 61  YYLMLNKPSGYLSATRDDQHPTVMELIDPLLRPHVHIAGRLDRASTGLLILTSDGVWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P+ +  +VYRV     +  +  +  ++GI  +         +L+        V + +
Sbjct: 121 LTEPAVKIPKVYRVTTAYAISPETEDRFREGIWFEYEQLRTSPASLEPL--GEREVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R S G   +  L  GS R +S + +
Sbjct: 179 YEGRYHQVKRMFHAVGNRVTSLHRESMGGLTVDGLEPGSYRHLSAQEV 226


>gi|56477738|ref|YP_159327.1| propable 16S pseudouridylate synthase [Aromatoleum aromaticum EbN1]
 gi|56313781|emb|CAI08426.1| propable 16S pseudouridylate synthase [Aromatoleum aromaticum EbN1]
          Length = 314

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 109/247 (44%), Gaps = 18/247 (7%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            +     R+SK+++  G+ SRRE + +I +  V V+G  +    + +     I +     
Sbjct: 70  TDAPEGVRLSKIMSERGLCSRREADEIIERGWVFVDGQRVSELGIRIDPNAEITLAAQAK 129

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRST--------------VFDNLPSIFSRVISVGR 113
           R+       L HKP+G V+   +P                        PS    +   GR
Sbjct: 130 RRQMEQVTILLHKPVGYVSGQPEPGFEPAVSLIGPDNQFDRADAQRFHPSHLKGIAPAGR 189

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LDI++ GLL+LT DG +AR L    ++  + Y VR  G++D+  L LL  G+ + G    
Sbjct: 190 LDIDSTGLLVLTQDGRIARQLIGDDSKVEKEYLVRVEGRLDERGLALLNHGLELDGRTLR 249

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
             +V    +      +   LREG+ R+I+++ E    KV  L R+  G  +LG L  G  
Sbjct: 250 PAKVEWLNEDQ----LRFVLREGRKRQIRRMCELVGLKVVGLKRVRIGRVKLGDLPLGQW 305

Query: 234 REVSKKI 240
           R + +  
Sbjct: 306 RFLREDE 312


>gi|168487228|ref|ZP_02711736.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae CDC1087-00]
 gi|183569856|gb|EDT90384.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae CDC1087-00]
          Length = 241

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 106/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLKGDILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                      ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKELPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVEVNGLLTPDHIQTFQKGIVFLDGTICKPARLEILSASPSLSQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K L+
Sbjct: 180 TISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKELQ 231


>gi|270293127|ref|ZP_06199338.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           M143]
 gi|270279106|gb|EFA24952.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           M143]
          Length = 241

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 55/232 (23%), Positives = 106/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A+  + SR+ +++ + ++ + V+       A N+ +    +   G  +R  E 
Sbjct: 1   MRLDRLLAQEKV-SRKAMKQALLKKEILVDDCPASSLAQNIDTGLQELLFQGRIIRGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                       + +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKELPTVMDLLPPDIQSDSLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   K+GIV          ++ + +   + +  ++
Sbjct: 120 QLLHPQYHVDKSYQVVVNGPLTSDHIQQFKEGIVFLDEITCKPAKLDILSASPTESRASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++KK+F   + KV  L R+ +G F L   L  G  R +++K L+
Sbjct: 180 TISEGKFHQVKKMFLSVSVKVTALKRVQFGDFTLDSELAEGQYRPLNQKELQ 231


>gi|323466661|gb|ADX70348.1| Pseudouridine synthase [Lactobacillus helveticus H10]
          Length = 216

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 57/216 (26%), Positives = 100/216 (46%), Gaps = 3/216 (1%)

Query: 34  MIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           MI   RVKV+G ++ +    V +  +I VD  P+ +        Y     + T   D   
Sbjct: 1   MIVAGRVKVDGKVVTKLGTKVETFSNITVDDEPIERESLHTYLFYKPRGVVSTADDDKGR 60

Query: 94  RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
           ++ V      +  R+  VGRLD +T GLLL+TNDG LA +L  P  +  +VY  +  G +
Sbjct: 61  KTVVDYF-EDVPCRLYPVGRLDYDTSGLLLMTNDGKLANLLMHPRNEVSKVYVAKIKGIL 119

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             D++  L  G+ +        +V +    ++     + + + EG   ++K++F+     
Sbjct: 120 TPDEIKTLTTGVKLDRFKAAPAKVKILKTDKRKDTQIIQLTIHEGHYHQVKRMFKAVGHL 179

Query: 212 VNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           V +L R  Y    L +L +G  RE+SK  + + +  
Sbjct: 180 VEKLSREKYAFLTLDSLTSGQYRELSKHEVDKLMRL 215


>gi|71909080|ref|YP_286667.1| pseudouridine synthase, Rsu [Dechloromonas aromatica RCB]
 gi|71848701|gb|AAZ48197.1| Pseudouridine synthase, Rsu [Dechloromonas aromatica RCB]
          Length = 379

 Score =  147 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 111/247 (44%), Gaps = 19/247 (7%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
            +    R+SKV++  G+ SRRE +  I +  V VNG  +      +  +   I V     
Sbjct: 135 PSPEGVRLSKVMSERGMCSRREADLWIERGWVFVNGEQVSELGSRIDPSVSEITVSQEAK 194

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTV--------------FDNLPSIFSRVISVGR 113
           +   +    L HKP+G V+   +P     V               +  P +   +   GR
Sbjct: 195 KDQAKAVTILLHKPVGYVSGQPEPGCIPAVTLITAETQVEQSGGPEFKPWMLRGLAPAGR 254

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LDI++ GLL+LT+DG +A+ L    ++  + Y VR  G++ +  L+LL+ G+ + G    
Sbjct: 255 LDIDSTGLLVLTSDGRVAKRLIGEDSEAEKEYLVRVSGEMIKGGLDLLRHGLELDGKPLK 314

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
              V    +      + + L+EGK R+I+++ E    +V  L R+  G  +LG L  G  
Sbjct: 315 PAWVKQLNEDQ----LHIILKEGKKRQIRRMCELVGLQVIGLKRVRIGRIRLGDLPMGQW 370

Query: 234 REVSKKI 240
           R +    
Sbjct: 371 RFLRADE 377


>gi|34495844|ref|NP_900059.1| pseudouridine synthase A, small subunit [Chromobacterium violaceum
           ATCC 12472]
 gi|34101699|gb|AAQ58067.1| pseudouridine synthase A, small subunit [Chromobacterium violaceum
           ATCC 12472]
          Length = 234

 Score =  147 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 99/229 (43%), Gaps = 5/229 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           + +++ + G   R+E  ++I    V+VNG +++         D   + VDG P       
Sbjct: 3   LYRLLQQQGFGGRKECRQLIEYGLVEVNGEVVDDYRAQFELADIASLAVDGEPWPLVTGP 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
              L HKP    T+H      S             V +VGRLD++T GL+LL+NDG    
Sbjct: 63  LYLLLHKPANYETSHKPQCHPSVYRLLPDQFARLDVSAVGRLDVDTTGLILLSNDGQFIH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VYRV    +   + +  L+ G+ +          ++  ++     + + 
Sbjct: 123 ALSSPKKLVPKVYRVTLKHEATPELIAKLQSGVYLNDEAREFAADSV--EQIDPHTILLT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGK  ++K++    + +V  L R S G   LG L  G  R ++ + L
Sbjct: 181 ITEGKYHQVKRMVAAASNRVEALHRESLGAIVLGDLPVGEWRHLTAEEL 229


>gi|328947715|ref|YP_004365052.1| pseudouridine synthase Rsu [Treponema succinifaciens DSM 2489]
 gi|328448039|gb|AEB13755.1| pseudouridine synthase Rsu [Treponema succinifaciens DSM 2489]
          Length = 269

 Score =  147 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 63/260 (24%), Positives = 109/260 (41%), Gaps = 24/260 (9%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGV 65
           + +    +R+ K+++  GI +RR+V+R+I   ++ VN I++     +V  S+D I VDG 
Sbjct: 1   MSDLKNTERLDKILSNNGIGTRRDVKRLIRSGKISVNRIIVREPEFHVDGSSDEILVDGK 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGL 121
           PL   +     +      + +T SD       +               +VGRLD +TEGL
Sbjct: 61  PLTVEQNAYFMMNKASGAVCSTKSDRRKTVFEYIFSEDNRKYPGGNLSTVGRLDADTEGL 120

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ----DKLNLLKKGIVIQGI------C 171
           L++T+DG L   +  P  +  + Y V     VD          L  G+ I+         
Sbjct: 121 LIITSDGNLIHRVTFPKYEVPKTYLVYLRDSVDDSEKLSYEKKLAAGVHIEAEGKDGEAD 180

Query: 172 YGDMQVTLDTQKGSNAW--------VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
                +    +   +            + + EGK  E+K++F+    +V  L RI     
Sbjct: 181 CRPAVIEWKEKNQYHTKTSECPSEVCCLTVTEGKFHEVKRIFKALGNEVVYLKRIRINNL 240

Query: 224 QLGT-LLAGSTREVSKKILR 242
            L   L  GS R ++K+ +R
Sbjct: 241 FLDETLKEGSYRPLTKEEIR 260


>gi|171910347|ref|ZP_02925817.1| Pseudouridine synthase, Rsu [Verrucomicrobium spinosum DSM 4136]
          Length = 229

 Score =  147 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 54/224 (24%), Positives = 96/224 (42%), Gaps = 4/224 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ +++A  G  +RREV  M+ +  VKV G++ E     V  T  + V G PL       
Sbjct: 6   RLDQLLASLGYGTRREVRNMVDRGLVKVGGVVAEDFDARVDPT-TVTVKGEPLDAPFGLV 64

Query: 75  LWLYHKPIGLVTT--HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +     + +      P     +    P     V SVGRLD +T G+LLLT+ G L +
Sbjct: 65  AVFHKPVGYVCSHASDEGPTIYDLLPKRWPFRNPTVTSVGRLDKDTSGILLLTDQGKLVQ 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P ++  +VY V     +++  + +  +G ++                 +     + 
Sbjct: 125 KWTSPKSEMDKVYEVTVDRPLEERLIGVFAEGTLLLESENKPCLPAKLEIVDALH-ARLT 183

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           L+EG+  +++++F    W V  L R  +G ++L  L  G  R +
Sbjct: 184 LQEGRYHQVRRMFASQGWHVEALHRSRFGEYELEGLEVGQWRVL 227


>gi|238021066|ref|ZP_04601492.1| hypothetical protein GCWU000324_00963 [Kingella oralis ATCC 51147]
 gi|237868046|gb|EEP69052.1| hypothetical protein GCWU000324_00963 [Kingella oralis ATCC 51147]
          Length = 243

 Score =  147 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 70/245 (28%), Positives = 110/245 (44%), Gaps = 20/245 (8%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+SK +A  GI SRRE +  I +  V+VNGI        V   D I+++     + 
Sbjct: 2   TDPVRLSKRMAELGICSRREADSYIEKGWVRVNGIPA-VLGQKVSPADRIDLNKQAHEQQ 60

Query: 71  ERTRLWLYHKPIGLVTTH---------------SDPDGRSTVFDNLPSIFSRVISVGRLD 115
                 L +KP+G V+                 +  +G ++     PS    +   GRLD
Sbjct: 61  ANRVTILLNKPVGFVSGQPEKDYRAAVELITAENQWEGDTSRIAFHPSHTRNLAPAGRLD 120

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I++ GLL+LT DG +A+ L   +    + Y VR  G + ++ L LL  G+ + G      
Sbjct: 121 IDSVGLLVLTQDGRIAKQLIGDNGNSEKEYLVRVKGSLKENGLALLNHGLSLDGEKLRPA 180

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           QV+   Q      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R 
Sbjct: 181 QVSWQNQDQ----LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRVGRIKLGALPQGKWRY 236

Query: 236 VSKKI 240
           +    
Sbjct: 237 LQANE 241


>gi|113971332|ref|YP_735125.1| pseudouridine synthase, Rsu [Shewanella sp. MR-4]
 gi|113886016|gb|ABI40068.1| Pseudouridine synthase, Rsu [Shewanella sp. MR-4]
          Length = 241

 Score =  147 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 102/230 (44%), Gaps = 8/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A      R+ V  ++  +RV V+G   +   + V    HI  DG  L+  +   
Sbjct: 7   RLDRYLAVKLQIHRKAVRELLLAERVYVDGAPAKSLDLLVDEFSHIVFDGQVLQANQPVY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L LY     +V+   D + R+ +          +   GRLD+N+ GLLLLTND   +  L
Sbjct: 67  LMLYKPVG-VVSATKDKEHRTVIDLLDCDTRQELHIAGRLDLNSSGLLLLTNDSRWSEAL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTVG 192
             P  +  +VYRV     +  + +    +G+    + I     ++ +     +     V 
Sbjct: 126 MSPEQKVDKVYRVTLANPLSDEYIAAFAQGMYFGFEDITTQPAKLVIL----APHVAEVT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           LREGK  +IK++F  F   V  L R+S G   L   L  G +R ++ + +
Sbjct: 182 LREGKYHQIKRMFGRFRNPVLGLHRLSIGEITLDEALKPGESRMLTAQEV 231


>gi|315612784|ref|ZP_07887695.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis ATCC 49296]
 gi|315314894|gb|EFU62935.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis ATCC 49296]
          Length = 241

 Score =  147 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 55/232 (23%), Positives = 104/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A+  + SR+ +++ + ++ + V+       A NV +    +   G  ++  E 
Sbjct: 1   MRLDRLLAQEKV-SRKAMKQALLKKEILVDDCPASSLAQNVDTGLQKLVFQGRQIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L+     +  +                   ++ ++GRLD +T GLLLLT++G L  
Sbjct: 60  NYLMLHKPNGAVTASKDKKLPTVMDLLPPDIQSDQLYAIGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   K+GIV          Q+ + +   S +  ++
Sbjct: 120 QLLHPQYHVNKSYQVVVNGPLTSDHIQSFKEGIVFLDGTTCKPAQLEILSSSPSESHASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L R+ +G F L   L  G  R ++ + L 
Sbjct: 180 TISEGKFHQIKKMFLSVGVKVTALKRVQFGDFTLDPELAEGQYRPLNPEELE 231


>gi|187734754|ref|YP_001876866.1| pseudouridine synthase [Akkermansia muciniphila ATCC BAA-835]
 gi|187424806|gb|ACD04085.1| pseudouridine synthase [Akkermansia muciniphila ATCC BAA-835]
          Length = 467

 Score =  147 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 66/333 (19%), Positives = 127/333 (38%), Gaps = 5/333 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M ++    E     R++K +A  GI SRR  +R+I + RV+VNG +++   + V   D +
Sbjct: 1   MSEEQHGSEENGGIRINKFLASCGIDSRRVADRLIGEGRVEVNGKVIDTPGMRVTEKDFV 60

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +VDG  +   E   + L      + +  +     +  +D LP     +  VGRLD ++EG
Sbjct: 61  KVDGRHMTPMEEVVVLLNKPRGYVCSREAQGAIGTV-YDLLPPRLRHLNYVGRLDADSEG 119

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LL++TN G L +VL  P+    + Y V      D   L    +G+ I         V   
Sbjct: 120 LLIMTNKGELTQVLSHPTGGIEKEYWVTVDQNFDNSVLMQFLRGVRIPEGNAKAKYVCRA 179

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           + + +     + L +G  R+++++F+    +V +L+R+  G    G L  G  + +    
Sbjct: 180 SARRAC----IVLEQGLKRQVRQMFQCLGLRVRKLVRVRIGSLWGGDLEPGGWKFLDDAD 235

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           +   L     +   +     +             +    D     +   +  +     + 
Sbjct: 236 VALSLKNPPRQRKYLGASQLVAGGGAKGEQGGRGVDSDEDYVFNPEDFEAGDSYEPTPEM 295

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREE 333
               V   +             S      +R +
Sbjct: 296 KTRFVETEDEREVKEDGYFRGDSGFRSRDRRGD 328


>gi|15902641|ref|NP_358191.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae R6]
 gi|116516226|ref|YP_816091.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae D39]
 gi|15458178|gb|AAK99401.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae R6]
 gi|116076802|gb|ABJ54522.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae D39]
          Length = 241

 Score =  147 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 106/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + + ++ V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLRGKILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                      ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKELPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSISQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L   + R +++K L+
Sbjct: 180 TISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAESNYRPLNQKELQ 231


>gi|227517791|ref|ZP_03947840.1| pseudouridylate synthase [Enterococcus faecalis TX0104]
 gi|227074752|gb|EEI12715.1| pseudouridylate synthase [Enterococcus faecalis TX0104]
          Length = 260

 Score =  147 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 68/260 (26%), Positives = 116/260 (44%), Gaps = 3/260 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +     
Sbjct: 1   MRLDKLLEELQFGSRKTVKRIIRGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLISHKTH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                       +  VGRLD +TEGLLLLT++G L  
Sbjct: 61  VYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            L  P+ +  + Y V+ +G V  +     K GIV+QG       ++T+     + + V +
Sbjct: 121 QLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHVFL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLL 250
            ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L    +
Sbjct: 181 TIQEGKFHQVKKMFLSVGKKVTALKRQTMGPVRLDPQLPLGAYRSLTREELQLLLPYFFI 240

Query: 251 EEAQVNLDAPIYSSETLVRD 270
           E+ Q +   P        R 
Sbjct: 241 EKQQTSKALPSNLKREEERK 260


>gi|119776069|ref|YP_928809.1| pseudouridine synthase, Rsu [Shewanella amazonensis SB2B]
 gi|119768569|gb|ABM01140.1| pseudouridine synthase, Rsu [Shewanella amazonensis SB2B]
          Length = 254

 Score =  147 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 66/239 (27%), Positives = 106/239 (44%), Gaps = 9/239 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+ K +A AG+ASRR   R+I   RV ++G      +  V  ++ + VDG PL  A
Sbjct: 7   SKGTRLCKYLAEAGVASRRGASRLIETGRVCIDGQQASH-SDRVFDSNRVTVDGAPLCPA 65

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +    +LYHKP+G+       D  S +      +       GRLD ++ GLLLLTNDG L
Sbjct: 66  QAKAYFLYHKPVGIDCRLRAEDPHSLIHCLPGDLRL--FPAGRLDKDSRGLLLLTNDGEL 123

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------QVTLDTQKG 184
            + L  P     + Y +  +     D +  +  G                      T+ G
Sbjct: 124 TQRLMHPDFHHQKGYLITLNKAPQPDDIAAIAAGFDYGEGPTRPCVVEAAIDCGYATEDG 183

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           +   + + L EGK R+I++++    ++V  L+R S     +G L  G  R ++   LR+
Sbjct: 184 NPRKLRMRLTEGKKRQIRRLWRARGYRVLDLLRESIQQLNIGKLEQGEIRSLTASELRQ 242


>gi|190575146|ref|YP_001972991.1| ribosomal large subunit pseudouridine synthase B [Stenotrophomonas
           maltophilia K279a]
 gi|190013068|emb|CAQ46700.1| ribosomal large subunit pseudouridine synthase B [Stenotrophomonas
           maltophilia K279a]
          Length = 542

 Score =  147 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 86/353 (24%), Positives = 146/353 (41%), Gaps = 15/353 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV----PLRK 69
           +R+ KV+A+AG+ SRR +E+ IA+  VKVNG + +   ++V S D IE+DG         
Sbjct: 24  ERLHKVLAQAGLGSRRALEQRIAEGLVKVNGEVAQT-GMSVKSGDKIELDGRGFVATALA 82

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + T        +      P   +R I++GRLDINT GLLL T DG 
Sbjct: 83  EPSRVLVYNKPEGEVTTREDPEGRPTVFESLPPLKGARWIAIGRLDINTTGLLLATTDGE 142

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR      ++      ++ L +G+ ++       ++       
Sbjct: 143 LANAMMHPSFEVEREYVVRVRAPEGEEKVSDAIVDRLARGVALEDGPAKFDEIERIGGTD 202

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK---KI 240
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   L  G + E+     + 
Sbjct: 203 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGKVSLPRELARGHSVELGTAQVEA 262

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           LR QL       + + L   I                  + +      + +   L +   
Sbjct: 263 LRAQLKLEEGAPSALTLQPVIGQRRAAKTTVRVREGGRGNAYVNGHNTADEGRELRRFDN 322

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +     R           G+  S  + + Q ++  ++       RSL   +  
Sbjct: 323 VREDRGRGRGGKGGGFKGGLTVSGEAAAKQSQKPFKQRTQKND-RSLPEGNPA 374


>gi|305432596|ref|ZP_07401757.1| RNA pseudouridine synthase [Campylobacter coli JV20]
 gi|304444307|gb|EFM36959.1| RNA pseudouridine synthase [Campylobacter coli JV20]
          Length = 253

 Score =  146 bits (369), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 76/250 (30%), Positives = 119/250 (47%), Gaps = 20/250 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+     SRRE + +I Q  VK+N  +    +  V + D + V G  LRK  + 
Sbjct: 1   MRINKFISHNSPYSRREADELIKQGLVKINNKIA-LLSDEVKTNDKVFVKGKALRKKTQF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +YHK  G + +  D  GR T++D LP  FS  +SVGRLD  +EGLLLLT+   +A  
Sbjct: 60  SVIIYHKQKGEIVSKKDDRGRKTIYDTLPRQFSTWLSVGRLDFASEGLLLLTDSPVIADA 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--------------YGDMQVTL 179
           L        R Y ++  G V +  +  ++ G+ I+                    +   +
Sbjct: 120 LMHSD--LEREYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEI 177

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               G    + V + EGKNRE+++ F  F+ +V  L R+++G   LG L AG  R +   
Sbjct: 178 FGSSGGYTKLRVVINEGKNRELRRFFGHFDLEVMDLKRVAFGALDLGMLKAGKYRYLENG 237

Query: 240 I---LREQLG 246
               LR+ L 
Sbjct: 238 EYEKLRDFLK 247


>gi|125975639|ref|YP_001039549.1| ribosomal small subunit pseudouridine synthase A [Clostridium
           thermocellum ATCC 27405]
 gi|281416647|ref|ZP_06247667.1| pseudouridine synthase [Clostridium thermocellum JW20]
 gi|125715864|gb|ABN54356.1| ribosomal small subunit pseudouridine synthase A [Clostridium
           thermocellum ATCC 27405]
 gi|281408049|gb|EFB38307.1| pseudouridine synthase [Clostridium thermocellum JW20]
 gi|316939756|gb|ADU73790.1| pseudouridine synthase [Clostridium thermocellum DSM 1313]
          Length = 244

 Score =  146 bits (369), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 64/239 (26%), Positives = 109/239 (45%), Gaps = 16/239 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERA------AVNVMS-TDHIEVDG 64
             QR+ K+++ +G  +R+E++++I       NG +          A+ V      IEV G
Sbjct: 3   DTQRIDKILSNSGFGTRKEIKKLIK------NGEVKVDGVVVKDSAMQVNPKESVIEVAG 56

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L+  E   + +      +  T+ +              F  +  VGRLDI+TEGLLLL
Sbjct: 57  EILKYREYIYIMMNKPQGVISATYDNRHRTVIDILPDEYKFFNLFPVGRLDIDTEGLLLL 116

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQK 183
           TNDG LA  L  P     + Y     G V    +++ ++G+V+         ++ +  + 
Sbjct: 117 TNDGQLAHELLSPRKHVPKKYYALIDGIVTTKDVDVFREGVVLDDGYKTLPSELFIL-KS 175

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           G  + V + + EGK  ++K++FE    KV  L RI  G  +L   L  G  RE++ + +
Sbjct: 176 GPYSEVEIVIYEGKFHQVKRMFEAVGKKVKYLRRIGMGKLKLDETLEPGDVRELTDEEM 234


>gi|326387186|ref|ZP_08208796.1| pseudouridine synthase, Rsu [Novosphingobium nitrogenifigens DSM
           19370]
 gi|326208367|gb|EGD59174.1| pseudouridine synthase, Rsu [Novosphingobium nitrogenifigens DSM
           19370]
          Length = 316

 Score =  146 bits (369), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 103/231 (44%), Positives = 149/231 (64%), Gaps = 4/231 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +R++K++ARAGIASRR+VERMI + R+K+N  L+   A  +++   + VD  P+    
Sbjct: 74  EGERIAKLLARAGIASRRDVERMIGEGRIKLNDELVTTPATLLLNLKGVTVDDKPVAAPA 133

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----RVISVGRLDINTEGLLLLTND 127
             RL+ +HKP GL+T   DP GR T+++ L +       RV+ VGRLD+NTEGLLLLTND
Sbjct: 134 PARLFRFHKPEGLITAERDPAGRPTIYNALRNALPAGTPRVMPVGRLDLNTEGLLLLTND 193

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L R +ELP++   R YR R  G + QD+L  L +G+ I+GI YG +   ++ + G N 
Sbjct: 194 GELKRAMELPASGIPRTYRARTFGDISQDQLEALIEGVEIEGIRYGSIDANMERRTGRNQ 253

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           W+ + L EGKNRE+++V E    +V+RLIR +YGPF L  L  G+  EV +
Sbjct: 254 WIEMTLTEGKNREVRRVLEHLGLQVSRLIRTAYGPFMLLDLPRGAADEVRQ 304


>gi|327479891|gb|AEA83201.1| pseudouridylate synthase [Pseudomonas stutzeri DSM 4166]
          Length = 230

 Score =  146 bits (369), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 107/233 (45%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +      SR++V R+++  R +VNG +       V   D +E+DG  L+  +  
Sbjct: 1   MRLDRYLGSRAQLSRQDVRRLVSDGRARVNGEVTRTLDREVRIFDCVELDGQVLQPGKVA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + HKP G V+   D   R+ +          +   GRLD NT GL+LLTNDG  +R 
Sbjct: 61  RYLMLHKPPGCVSATRDAAHRTVIDLIDEPDKDDLHIAGRLDFNTTGLMLLTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P++   +VY V    ++D   +    +      + +     ++ L   + +     +
Sbjct: 121 LTQPTSLQGKVYLVETEDEIDPGCVEAFARGLYFRFEDLTTLPAELVLLGPRRA----RL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
            L EG+  ++K++F  F  KV  L R S GP  L  +L  G  R ++   + +
Sbjct: 177 TLHEGRYHQVKRMFGHFGNKVTALHRESMGPLLLDASLSPGCYRPLTDNEIAQ 229


>gi|88810635|ref|ZP_01125892.1| Pseudouridine synthase, Rsu [Nitrococcus mobilis Nb-231]
 gi|88792265|gb|EAR23375.1| Pseudouridine synthase, Rsu [Nitrococcus mobilis Nb-231]
          Length = 267

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 79/267 (29%), Positives = 128/267 (47%), Gaps = 7/267 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +++ KV+ARAG+ SRR++E  I   R++VNG +       V     I VDG PLR+ 
Sbjct: 2   SETEKLQKVLARAGMGSRRQMEHWIRDGRIRVNGRIAR-LGERVAPRMQITVDGRPLRRR 60

Query: 71  E----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  +     + T        +           R I+VGRLDINT GLLL T 
Sbjct: 61  SLSGLPRMLLYHKPVGVVTTRSDPAGRPTVFQHLPRIKKGRWIAVGRLDINTCGLLLFTT 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-KGS 185
           DG LA  L  PS + +R Y VR +G+V  + +  L++G+ ++       ++ +  + + +
Sbjct: 121 DGELANRLMHPSFRLVREYAVRVYGEVTAEMITRLQQGVELEDGRGAFDRIEVLCEAQAA 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           N W  V L EG+ RE+++++E    +V+RLIR+ YGP +L   L  G  R++    +   
Sbjct: 181 NGWYRVSLAEGRRREVRRLWESQGVRVSRLIRLRYGPVRLPPGLRQGQIRKLGPAEIVRL 240

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDR 271
                L+ A     A        +++ 
Sbjct: 241 CRAVDLDPAWPKQQACTRRLSEALKNE 267


>gi|163857342|ref|YP_001631640.1| pseudouridylate synthase [Bordetella petrii DSM 12804]
 gi|163261070|emb|CAP43372.1| pseudouridylate synthase [Bordetella petrii]
          Length = 243

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 65/244 (26%), Positives = 100/244 (40%), Gaps = 19/244 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
              R+SK++A  G+ SRRE +  I +  VKV+G+++            I ++        
Sbjct: 2   EKIRISKLMAERGLCSRREADSYIERGWVKVDGVVVAELGARAFPDQVITLERAAQARQT 61

Query: 64  -------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
                    P+          Y     LV   S      +      +    +   GRLDI
Sbjct: 62  ARVTILINKPVGYVSGQAEKGYTPASALVDARSRYARDRSPLRFTRAHLQGLAVAGRLDI 121

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +++GLL+LT DG +AR L    +   + Y VR  G++D   L LL  G+ + G      Q
Sbjct: 122 DSQGLLVLTQDGRIARQLIGEDSSVDKEYLVRVQGRLDAGGLALLNHGLSLDGKPLRPAQ 181

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V           +   LREGK R+I+++ E    KV  L R+  G  +LG L  G  R +
Sbjct: 182 VRWQNADQ----LCFVLREGKKRQIRRMCELVGLKVVGLKRVRIGRVKLGDLPPGQWRYL 237

Query: 237 SKKI 240
               
Sbjct: 238 RDDE 241


>gi|319955817|ref|YP_004167080.1| RNA-binding s4 domain protein [Nitratifractor salsuginis DSM 16511]
 gi|319418221|gb|ADV45331.1| RNA-binding S4 domain protein [Nitratifractor salsuginis DSM 16511]
          Length = 263

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 70/250 (28%), Positives = 123/250 (49%), Gaps = 18/250 (7%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +++N    R++K I+     SRR+ +++I +  V VN + ++     V   D + V G  
Sbjct: 1   MKQNEEGMRLNKYISHNTPYSRRDADKLIEEGLVTVNRLPVKDFGYKVRPEDKVAVRGKL 60

Query: 67  LRKAERTRLWL--YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
           +   +R  + +  Y+KP G++ T  D  GR+T++  LP  F   I VGRLD  +EGLLLL
Sbjct: 61  IHPRKRGEVTMVVYNKPRGVLVTKRDDRGRTTIYHKLPGKFRHFIPVGRLDYASEGLLLL 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------I 170
           T++  +A VL     +  R Y ++    +  +    +K+G++++                
Sbjct: 121 TDNPEVADVLMGS--KLPRTYNLKIDKPLTPEMEKAMKEGLILEDAREGGHKESEITRME 178

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
               ++V    Q G N  + V + EGKNRE+++ F  F  KV  L R+ +G  +L  L  
Sbjct: 179 FAPFLEVQYRGQSGKNTKLRVTIAEGKNRELRRFFGHFGAKVLDLKRVGFGWVELNNLPE 238

Query: 231 GSTREVSKKI 240
             TR  +++ 
Sbjct: 239 NKTRYFTRQE 248


>gi|300692311|ref|YP_003753306.1| 16S rRNA pseudouridylate 516 synthase [Ralstonia solanacearum
           PSI07]
 gi|299079371|emb|CBJ52043.1| 16S rRNA pseudouridylate 516 synthase [Ralstonia solanacearum
           PSI07]
          Length = 252

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 52/228 (22%), Positives = 87/228 (38%), Gaps = 4/228 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-VDGVPLRKAERTR 74
           + +++   G  +RR  + ++    V VNG+  E     V +   +  VDG       R  
Sbjct: 10  LYRILQSQGFGTRRYCKDLVFAGLVHVNGVEAEDPDTQVDTAGLVLDVDGERWAYHARAY 69

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L+       +               P     V  VGRLD +T GLLLLT+DG     L
Sbjct: 70  LMLHKPAGFECSQKPRHHPSVYTLLPAPLRERGVQCVGRLDQDTTGLLLLTDDGQFVHTL 129

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  Q  +VY +     V   ++  L +G+++            +     +  + + L 
Sbjct: 130 TSPRHQVPKVYEITTAEPVTDAQVAQLCQGVLLDDEDVSVAAAWAERVDALH--LRMALT 187

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           +GK  ++K++       V  L R + G   L   L  G  R + +  L
Sbjct: 188 QGKYHQVKRMVAAAGNHVAALHRSAIGALTLDAGLAPGQWRWLERDDL 235


>gi|294627879|ref|ZP_06706458.1| Pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 11122]
 gi|292597793|gb|EFF41951.1| Pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 11122]
          Length = 286

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 113/247 (45%), Gaps = 7/247 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      +       I VDG PL    R 
Sbjct: 39  LARVLSKLGVCSRTEAARWIADGRVSVSARVVRDPEFPIRGDQQSSIAVDGQPLAGLARC 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L      + T   +    +       +    +  VGRLD  +EGLLL +ND   A  
Sbjct: 99  YLMLNKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAAA 158

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNAW 188
           +  P+T   + Y V+   +    +L  L+ G+V      QG+     QV++  +   NAW
Sbjct: 159 VTDPATGPDKTYHVQIDCRPSAAQLAQLQAGVVDPDPQGQGVLLRAKQVSVLREGERNAW 218

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + + L EG+NR+I+++    +  V RL+R++ GP  +G L  G+ R +S + +   +   
Sbjct: 219 LEIVLDEGRNRQIRRLVAAVDIGVLRLVRVAIGPLAMGELGKGAWRMLSAEEVSALVPAA 278

Query: 249 LLEEAQV 255
                  
Sbjct: 279 HASAPDA 285


>gi|225850577|ref|YP_002730811.1| ribosomal large subunit pseudouridine synthase B [Persephonella
           marina EX-H1]
 gi|225645869|gb|ACO04055.1| ribosomal large subunit pseudouridine synthase B [Persephonella
           marina EX-H1]
          Length = 241

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 66/235 (28%), Positives = 120/235 (51%), Gaps = 4/235 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+++ IAR+G  SRR+ +++I   +VKVNG +++     V    D +E+DG  ++   +
Sbjct: 3   MRLNRFIARSGYCSRRKADQLIEMGKVKVNGKVVKDFGYRVDTEKDRVEIDGKLIKLELK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDGG 129
                 +KP G +T             +L     I   V   GRLD  +EGLLLLTNDG 
Sbjct: 63  KVYIKLYKPRGYLTQLGKDKFGRKTLTDLFKEVGIKDNVFPAGRLDYESEGLLLLTNDGD 122

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A ++  P ++  + Y V+  G+V+ +  N ++KG +++       ++ +  +  +  W+
Sbjct: 123 FANMIMHPKSKIKKTYVVKVKGRVNLESFNRMRKGALLEDGFIKPDEIKILKKGKNYTWL 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + +  GK R I++  ++F + V RLIR   G  +LG+L     + + +KI+   
Sbjct: 183 EITIHSGKKRIIRRFTKYFGYPVERLIRTRIGSIELGSLKEKEWKYIDEKIINRM 237


>gi|182417049|ref|ZP_02948427.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           butyricum 5521]
 gi|237669150|ref|ZP_04529134.1| ribosomal large subunit pseudouridine synthase F [Clostridium
           butyricum E4 str. BoNT E BL5262]
 gi|182379058|gb|EDT76562.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           butyricum 5521]
 gi|237657498|gb|EEP55054.1| ribosomal large subunit pseudouridine synthase F [Clostridium
           butyricum E4 str. BoNT E BL5262]
          Length = 270

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 61/272 (22%), Positives = 102/272 (37%), Gaps = 47/272 (17%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+ +  GI SR+E  ++I Q+R+K+NG         V   D I  DG  ++  E+ 
Sbjct: 1   MRINKLFSNLGICSRKETNKLIEQKRIKINGEYC-VLGQWVEDNDEILFDGERVKSMEKV 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L  Y       T   +  G         +    V  VGRLD ++EGL++LTNDG  +  
Sbjct: 60  YLAFYKPKGITCTLEKNAQG---NIGEYINYNQYVFPVGRLDKDSEGLIILTNDGVFSNH 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-------------------------- 167
           +     +  + Y V+     D + L  ++ G+ I                          
Sbjct: 117 ILECDNKHEKEYIVKVDKPFDDNFLLSMRTGVEISAKSGSGVKRISDSEGIVIKDGKDEI 176

Query: 168 -------------QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                          +     +V    +        + L +G NR+I+K+     +KV  
Sbjct: 177 IMLDEAKNGKMKKDIVKTRPCKVERINED----TFKIILTQGLNRQIRKMSSVLGYKVIS 232

Query: 215 LIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L RI      L  L  G  R + K+ + E + 
Sbjct: 233 LKRIRIMNIHLDYLECGEYRLIPKEHIDELMK 264


>gi|118475394|ref|YP_892916.1| pseudouridine synthase, Rsu:RNA-binding S4:pseudouridine synthase
           [Campylobacter fetus subsp. fetus 82-40]
 gi|118414620|gb|ABK83040.1| pseudouridine synthase, Rsu:RNA-binding S4:Pseudouridine synthase
           [Campylobacter fetus subsp. fetus 82-40]
          Length = 254

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 65/248 (26%), Positives = 115/248 (46%), Gaps = 15/248 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+     SRRE + ++   +V +N  +++  A +V   D I+++G  +R  +  
Sbjct: 1   MRINKFISHNTNYSRREADELVKNGKVSINNKVIDNLATDVKEDDKIKINGRFIRLKKEF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +Y+K  G + T  D  GR T++DNLP   S+ IS+GRLD  +EGLLLLT+   +A  
Sbjct: 61  SIIVYNKQKGELVTKKDDRGRKTIYDNLPRGISKFISIGRLDFASEGLLLLTDAPAIAEA 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLL------------KKGIVIQGICYGDMQVTLDT 181
           L     +     +++     +                    +   I       +   + +
Sbjct: 121 LMGSDIEREYYLKIKGEITPNVIAAMQEGFFAKDATKGAHARTKQISMEFKPFLAYKIIS 180

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI- 240
             G    + V + EG+NRE+++ F +F+ +V  L R+S+G   L  L  G  R  +    
Sbjct: 181 FSGGYTRLKVIINEGQNRELRRFFGYFDLEVMDLKRVSFGRVSLDQLGEGKWRYFTNSEY 240

Query: 241 --LREQLG 246
             LR+ L 
Sbjct: 241 DDLRDFLK 248


>gi|168492245|ref|ZP_02716388.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae CDC0288-04]
 gi|183573539|gb|EDT94067.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae CDC0288-04]
          Length = 241

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 106/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  + SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKV-SRKAMKQALLRGDILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                      ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKELPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVEVNGLLTPDHIQTFQKGIVFLDGTICKPARLEILSASPSLSQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K L+
Sbjct: 180 TISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKELQ 231


>gi|256959950|ref|ZP_05564121.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis Merz96]
 gi|256950446|gb|EEU67078.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis Merz96]
          Length = 260

 Score =  146 bits (368), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 67/260 (25%), Positives = 115/260 (44%), Gaps = 3/260 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +     
Sbjct: 1   MRLDKLLEELQFGSRKTVKRIIRGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLISHKTH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                       +  VGRLD +TE LLLLT++G L  
Sbjct: 61  VYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYPVGRLDGDTERLLLLTDNGQLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            L  P+ +  + Y V+ +G V  +     K GIV+QG       ++T+     + + V +
Sbjct: 121 QLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHVFL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLL 250
            ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L    +
Sbjct: 181 TIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYFFI 240

Query: 251 EEAQVNLDAPIYSSETLVRD 270
           E+ Q +   P        R 
Sbjct: 241 EKQQTSKALPSNLKREEERK 260


>gi|207723350|ref|YP_002253749.1| ribosomal small subunit pseudouridine synthase a protein [Ralstonia
           solanacearum MolK2]
 gi|206588549|emb|CAQ35512.1| ribosomal small subunit pseudouridine synthase a protein [Ralstonia
           solanacearum MolK2]
          Length = 253

 Score =  146 bits (368), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 95/251 (37%), Gaps = 32/251 (12%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------DGVP 66
            R+SK ++  G+ SRRE +  I +  V V+G  +      V     IE+        G  
Sbjct: 1   MRLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVRPDAEIEILPAARSEQGER 60

Query: 67  LR--------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           +                  Y     L T  +  +   T           +   GRLDI++
Sbjct: 61  VTVLLHKPMGYVSGQAEDGYEPAATLFTAENQWEEDPTHKRFAAWQHKGLAPAGRLDIDS 120

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-------------VDQDKLNLLKKGI 165
            GLL+LT DG +AR L    +   + Y VR                   ++ L  L+ G+
Sbjct: 121 TGLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWDAPQGPVEHDISKVFPEELLEKLRHGL 180

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G      +V+   ++     +   LREGK R+I+++ E     V  L RI  G   L
Sbjct: 181 SLDGEALKPAKVSWQNEEQ----LRFVLREGKKRQIRRMCEQVGLTVVGLKRIRMGSVVL 236

Query: 226 GTLLAGSTREV 236
           G L  G  R +
Sbjct: 237 GDLPVGKWRFL 247


>gi|304410386|ref|ZP_07392004.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|307304478|ref|ZP_07584228.1| pseudouridine synthase [Shewanella baltica BA175]
 gi|304350870|gb|EFM15270.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|306911880|gb|EFN42304.1| pseudouridine synthase [Shewanella baltica BA175]
          Length = 235

 Score =  146 bits (368), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 52/230 (22%), Positives = 98/230 (42%), Gaps = 8/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +       R+ V  ++   RV V+G++++     V     I++D   L+      
Sbjct: 7   RLDRYLCTQLHTHRKAVRELLLSGRVCVDGLIVKDMDRQVDEFSRIQLDEHILQANAPVY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L+     +V+   D   ++ +          +   GRLD+N+ GLLLLTND   +  L
Sbjct: 67  VMLHKPIG-VVSATKDTQHKTVIDLLDCEARDELHIAGRLDLNSSGLLLLTNDSRWSDAL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
             P+ +  +VYRV     + ++ +    +      + I     ++ +     +     V 
Sbjct: 126 MSPTHKVDKVYRVTLANSITKEYIAAFAEGMYFGFEDITTQPAKLVILADNVA----EVT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           L EGK  +IK++F  F   V  L R+S G   L   L  G +R ++   +
Sbjct: 182 LHEGKYHQIKRMFGRFRNPVVGLHRLSIGEIVLDEKLAPGESRALTAAEV 231


>gi|183220850|ref|YP_001838846.1| putative ribosomal subunit pseudouridine synthase [Leptospira
           biflexa serovar Patoc strain 'Patoc 1 (Paris)']
 gi|189910947|ref|YP_001962502.1| pseudouridylate synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|167775623|gb|ABZ93924.1| Pseudouridylate synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|167779272|gb|ABZ97570.1| Putative ribosomal subunit pseudouridine synthase [Leptospira
           biflexa serovar Patoc strain 'Patoc 1 (Paris)']
          Length = 247

 Score =  146 bits (368), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 119/247 (48%), Gaps = 13/247 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
            R++  +A+ G+ SRR+VE ++   RVK+NG  +   +  V   D I  DG P+ K E  
Sbjct: 1   MRINAFLAKLGLGSRRKVEELVLAGRVKINGSTITDLSFQVNEEDSILFDGKPVTKEEGS 60

Query: 72  --RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             R ++  ++KP G +T+H D    +T+F  LP  F +    GRLD+++ GL+LL+ DG 
Sbjct: 61  DSRPKIIAFNKPPGFLTSHEDKHHENTIFTLLPESFQKYNYAGRLDLDSRGLILLSIDGN 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY------GDMQVTLDTQK 183
             + +  P  +  + Y +     V   K+       V +G             V  +   
Sbjct: 121 FIQKVTHPKNKIDKEYIISLKQPVSWKKIAEEFMLGVREGGETLRALAVKPANVFPEKTP 180

Query: 184 GS-NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKI 240
               +++++ L+EGK R+I+++ +  +  V  L RI  G   L    LL G  + V+++ 
Sbjct: 181 PGFTSYLSIVLKEGKKRQIRRMCKTKDLVVLDLYRIRIGKLDLRNFDLLEGKYKVVTEEQ 240

Query: 241 LREQLGP 247
           +   L P
Sbjct: 241 VLGNLNP 247


>gi|254468136|ref|ZP_05081542.1| ribosomal large subunit pseudouridine synthase F [beta
           proteobacterium KB13]
 gi|207086946|gb|EDZ64229.1| ribosomal large subunit pseudouridine synthase F [beta
           proteobacterium KB13]
          Length = 239

 Score =  146 bits (368), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 64/238 (26%), Positives = 106/238 (44%), Gaps = 15/238 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+SK+++  G+ SRRE +  I    V V+GI +            IE+ G   R  +  
Sbjct: 4   VRISKLLSNQGVCSRREADHFIELGFVYVDGIKVTELGAKANPEQKIELRGEGHRLQKSK 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV-----------FDNLPSIFSRVISVGRLDINTEGLL 122
           +  L +KPIG V+   D     +             + L  +  ++   GRLDI++ GLL
Sbjct: 64  KTILLNKPIGFVSHADDEGKYKSSLSLILKENFFGDEKLDKLSFKLAPAGRLDIDSTGLL 123

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           +LT DG +A+ +    ++  + Y VR  G +  + L LLK G+ +         V+   +
Sbjct: 124 VLTEDGVIAKKIIQEDSEIEKEYLVRVSGNLIPNGLKLLKHGLFLDNKPLKKAIVSWINE 183

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 +   L+EGK R+I+++ E    KV  L R+  G  +L  L  G  R +    
Sbjct: 184 DQ----LKFILKEGKKRQIRRMCELVGLKVVGLKRVRIGKIRLSNLPIGKWRFLQGNE 237


>gi|169834407|ref|YP_001694153.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae Hungary19A-6]
 gi|168996909|gb|ACA37521.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae Hungary19A-6]
          Length = 241

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 106/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLKGEILVDGCPARSLAQNIDTGLQELLFQDQIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                      ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKSAGVVTANKDRELPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVEVNGLLTPDHIQTFQKGIVFLDGTICKPARLEILSASPSLSQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K L+
Sbjct: 180 TISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKELQ 231


>gi|229588965|ref|YP_002871084.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           fluorescens SBW25]
 gi|229360831|emb|CAY47689.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           fluorescens SBW25]
          Length = 230

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 57/233 (24%), Positives = 105/233 (45%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            RV + ++     +R++V  ++ ++RV ++G+ +      V +   + VD   L+  +  
Sbjct: 1   MRVDRFLSNLPRFNRKQVRLLLVERRVSIDGVAVSDPHHEVRTFSRVCVDDEVLQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V+  +DP   + +          +   GRLD NT GL+L+TNDG  +R 
Sbjct: 61  RYFMLHKPQGCVSATADPQHPTVLDLLDEPDKDELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +  +             + +     ++ L           +
Sbjct: 121 LTQPQTKLPKVYHVETEQDIGPEYATTFAGGLYFAFEDLTTQPAELELL----GPTTARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
            + EG+  ++K++F  F+ KV  L R   GP  L  TL  G  R ++   +R+
Sbjct: 177 SIIEGRYHQVKRMFGHFDNKVIGLHRERMGPLVLDATLAPGQYRALTDDEIRQ 229


>gi|307128557|ref|YP_003880587.1| putative ribosomal large subunit pseudouridine synthase [Candidatus
           Sulcia muelleri CARI]
 gi|306483019|gb|ADM89889.1| putative ribosomal large subunit pseudouridine synthase [Candidatus
           Sulcia muelleri CARI]
          Length = 237

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 53/230 (23%), Positives = 107/230 (46%), Gaps = 3/230 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              +++  ++++GI+SRR  + +I    +KVNG ++++    + + D ++     L   +
Sbjct: 5   EKLKLNSYLSKSGISSRRNADNLIKSGNIKVNGKIIKKLGYIISNNDIVKYKDKRLYPEK 64

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  L L      + +        + +  +L  I  ++ S+GRLDI T G+LL TNDG L+
Sbjct: 65  KIYLILNKPKGYVSS--MKKQDNNNIVLDLIKINYKIFSIGRLDIETSGVLLFTNDGYLS 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     ++Y V  + +++   L  +K     +        ++   +   N  + +
Sbjct: 123 NKLTHPKFNIKKIYHVVLNKKINNKDLLKIKNSFSFKEGKLKIYNISYIKKLPKNN-IKL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            L  G N+ +K++F    +KV  L RI++G   +  L  G  R + K  +
Sbjct: 182 ELHIGWNKIVKRIFNKIKYKVLYLKRINFGGITIKGLKIGEYRYLKKNEI 231


>gi|313202274|ref|YP_004040932.1| RNA-binding s4 domain-containing protein [Methylovorus sp. MP688]
 gi|312441590|gb|ADQ85696.1| RNA-binding S4 domain protein [Methylovorus sp. MP688]
          Length = 425

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 65/255 (25%), Positives = 101/255 (39%), Gaps = 19/255 (7%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M     V       R+SK +A  G+ SRRE +  I    V+VNG +++     V    +I
Sbjct: 173 MFTPKPVASQPDLPRLSKRMAELGLCSRREADEWIVNGWVRVNGQVVDELGSRVEPDANI 232

Query: 61  EVDG---------------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           EV                  P+          Y   + LV   +         +      
Sbjct: 233 EVSKEAEKHQSEIVTILLHKPVGYVSGQAEDGYEPAVVLVHPDNHWAEDPVQKEFRRGFL 292

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             +   GRLDI++ GLL+LT DG +AR L    +Q  + Y VR  G +  + L  L  G+
Sbjct: 293 KGLAPAGRLDIDSTGLLVLTQDGRVARQLIGEDSQTEKEYLVRVEGTLSDEGLRKLNHGL 352

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G+     +V+   +      +   LREG+ R+I+++ E     V  L R+  G   L
Sbjct: 353 SLDGVQLKPAKVSWQNEDQ----LRFVLREGRKRQIRRMCELVGLHVVGLKRVRIGSVAL 408

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R +    
Sbjct: 409 GKLPPGQWRYLRPGE 423



 Score = 37.5 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 9/94 (9%), Positives = 26/94 (27%)

Query: 261 IYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGI 320
                       +    V  D    ++  ++++   +  +      R + A      +  
Sbjct: 63  HEHQVAESPAENDCPRRVAADRDASERQPARRSASDRPARSGESRPRADNARPENRQRDE 122

Query: 321 HSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             +  S+  +R    R       + + RR    +
Sbjct: 123 RPAERSERPRRPAADRADRLASDRDTPRRGGKAR 156


>gi|225860671|ref|YP_002742180.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|298229808|ref|ZP_06963489.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae str. Canada MDR_19F]
 gi|298254812|ref|ZP_06978398.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae str. Canada MDR_19A]
 gi|298502474|ref|YP_003724414.1| pseudouridylate synthase [Streptococcus pneumoniae TCH8431/19A]
 gi|225728241|gb|ACO24092.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|298238069|gb|ADI69200.1| pseudouridylate synthase [Streptococcus pneumoniae TCH8431/19A]
 gi|327390410|gb|EGE88751.1| hypothetical protein SPAR5_0652 [Streptococcus pneumoniae GA04375]
          Length = 241

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 105/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLKGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                      ++ +VGRLD +T GLLLLT+ G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKELPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDSGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V+ +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVQVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSLSQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L   + R +++K L+
Sbjct: 180 TISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAESNYRPLNQKELQ 231


>gi|77359432|ref|YP_339007.1| 16S rRNA pseudouridylate 516 synthase [Pseudoalteromonas
           haloplanktis TAC125]
 gi|76874343|emb|CAI85564.1| 16S rRNA pseudouridylate 516 synthase [Pseudoalteromonas
           haloplanktis TAC125]
          Length = 232

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 55/233 (23%), Positives = 100/233 (42%), Gaps = 8/233 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K I+      R +    I +Q   VNG ++      +   D +   G  L     
Sbjct: 4   PCRLDKFISHLAELPRSKARASIKRQAALVNGEVVTAFDFQIKQQDEVVFQGEQLVFL-G 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R ++ +KP+G V+ +SD   ++          S     GRLDI+T GL++LTNDG  + 
Sbjct: 63  KRYFMLNKPVGYVSANSDELHKTVFDLIDEPNMSDFHVAGRLDIDTTGLVILTNDGDWSH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVT 190
            +  P     + Y V     +  + L+ L++G+ +          +        +N  + 
Sbjct: 123 KITSPKNNKFKTYLVETQEPITDESLDALREGVQLHNEKALTRPAKAERL----ANYGLR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + + EGK  ++K++    + KV  L R   G  +L   L AG  R ++ + ++
Sbjct: 179 LSICEGKYHQVKRMLAAVDNKVVELHREQIGNIKLDENLAAGEYRLLTAEEIK 231


>gi|57504573|ref|ZP_00370685.1| RNA pseudouridine synthase, RsuA family [Campylobacter coli RM2228]
 gi|57019468|gb|EAL56162.1| RNA pseudouridine synthase, RsuA family [Campylobacter coli RM2228]
          Length = 253

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 76/250 (30%), Positives = 119/250 (47%), Gaps = 20/250 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+     SRRE + +I Q  VK+N  +    +  V + D + V G  LRK  + 
Sbjct: 1   MRINKFISHNSPYSRREADELIKQGLVKINNKIA-LLSDEVKTNDKVFVKGKALRKKTQF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +YHK  G + +  D  GR T++D LP  FS  +SVGRLD  +EGLLLLT+   +A  
Sbjct: 60  SVIIYHKQKGEIVSKKDDRGRKTIYDTLPRQFSTWLSVGRLDFASEGLLLLTDSPVIADA 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--------------YGDMQVTL 179
           L        R Y ++  G V +  +  ++ G+ I+                    +   +
Sbjct: 120 LMHSD--LEREYYLKVKGTVGKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEI 177

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               G    + V + EGKNRE+++ F  F+ +V  L R+++G   LG L AG  R +   
Sbjct: 178 FGSSGGYTKLRVVINEGKNRELRRFFGHFDLEVMDLKRVAFGALDLGMLKAGKYRYLENG 237

Query: 240 I---LREQLG 246
               LR+ L 
Sbjct: 238 EYEKLRDFLK 247


>gi|260438469|ref|ZP_05792285.1| ribosomal large subunit pseudouridine synthase B [Butyrivibrio
           crossotus DSM 2876]
 gi|292809058|gb|EFF68263.1| ribosomal large subunit pseudouridine synthase B [Butyrivibrio
           crossotus DSM 2876]
          Length = 240

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 115/232 (49%), Gaps = 5/232 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K I+++G+ SRR  +++I +  V +NG++ E     V   D + +D   +   +
Sbjct: 2   EEIRINKYISKSGVCSRRAADKLINEGHVTINGVVAET-GSKVTEKDIVRIDDDIINLIK 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +++ ++KP+G +++    D + T   +       +  VGRLD ++EGL+L+TNDG L 
Sbjct: 61  DIKVYAFYKPVGYISS--LSDEQGTGIASFLPQGMGLFPVGRLDKDSEGLMLITNDGNLM 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWV 189
             +   S    + Y V    + + D L  + KG+ I     G   +T   +  +  +   
Sbjct: 119 NEILNASNGHEKEYIVTTRQKFNNDFLVKMAKGVPITNRATGKKIITAPCKTEALEDNSF 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + + +G NR+I+++  +F+  V  L R+      LG +  G  +E+S+  L
Sbjct: 179 KITIIQGLNRQIRRMCGYFDIDVVSLKRVRIMNIMLGNMRPGELKELSQSEL 230


>gi|217968594|ref|YP_002353828.1| pseudouridine synthase [Thauera sp. MZ1T]
 gi|217505921|gb|ACK52932.1| pseudouridine synthase [Thauera sp. MZ1T]
          Length = 245

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 47/236 (19%), Positives = 82/236 (34%), Gaps = 10/236 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-------IEVDGVP 66
            ++ +++   G  SR++   +I    V V G + +                    VD  P
Sbjct: 1   MQLERLLHAQGFGSRKDCRALIRAGYVSVAGEVCDDPTEEFDPGSRDGSPGLEFTVDDQP 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
            R   +  + L+       +                 +   V  VGRLD +T GLLLL++
Sbjct: 61  WRFRAQAYVVLHKPAGYECSQKPTFHPSVFTLLPPQLLARGVQCVGRLDQDTTGLLLLSD 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG           +  +VY V     V+QD  + L  G+ +            +      
Sbjct: 121 DGQFIHQWSSGKKRTPKVYEVTLKHAVEQDFADRLVAGVELNDEPVPIAAAACELLSP-- 178

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
             + + + EGK  ++K++      +V  L R   G   L   L  G  R +  + L
Sbjct: 179 TTLRLTICEGKYHQVKRMVGAAGNRVEVLHRSRVGGLDLPAGLAPGQWRWLEAEDL 234


>gi|116072478|ref|ZP_01469745.1| Pseudouridine synthase, Rsu [Synechococcus sp. BL107]
 gi|116065000|gb|EAU70759.1| Pseudouridine synthase, Rsu [Synechococcus sp. BL107]
          Length = 238

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 58/223 (26%), Positives = 92/223 (41%), Gaps = 3/223 (1%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP-LRKAERTRLWL 77
           +A AG+ SRR  E  +   RV V+G +              I VDG+P +   E     L
Sbjct: 1   MAAAGLCSRRRGEDWLQAGRVTVDGRVA-SLGDQADPDCQLIAVDGIPLISVREPRVFLL 59

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
                 + +        + +          +  VGRLD ++ G LLLT+ G L   L  P
Sbjct: 60  NKPVGVICSCRDPQGRSTVLDCLPHQERPGLHPVGRLDADSRGALLLTDQGELTLRLTHP 119

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGK 197
                + YRV   G  +   L   ++G+ + G       V     +G+++ + V LREG+
Sbjct: 120 RYSHAKTYRVLVKGIPNALVLRRWREGLQLDGRLTRPALVRCLRSRGTSSLLEVELREGR 179

Query: 198 NREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           NR+I++V E     V  L R++     L  L  G  R +  + 
Sbjct: 180 NRQIRRVAELLGHPVIDLQRVAIDGIHLDDLAEGCWRRLDARE 222


>gi|325529283|gb|EGD06232.1| putative RNA pseudouridylate synthase [Burkholderia sp. TJI49]
          Length = 306

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 101/251 (40%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +  HIE+D          
Sbjct: 58  MRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQHIEIDERAQAAQAAQ 117

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     L+T  +   G  +     P     +   GRLDI++
Sbjct: 118 VTILLHKPVGYVSGQAEDGYEPAAVLITRDNHWSGDRSPLRFSPQHLRTLAPAGRLDIDS 177

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 178 TGLLVLTQNGRIAKQLIGEQSDVDKEYLVRVKFGERLTDIDQHFPAESLAKLRHGLELDG 237

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREG+ R+I+++ E    +V  L R+  G   LG L 
Sbjct: 238 VALKPAMVSWQNGEQ----LRFVLREGRKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 293

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 294 QGQWRYLSADE 304


>gi|148549519|ref|YP_001269621.1| pseudouridine synthase [Pseudomonas putida F1]
 gi|148513577|gb|ABQ80437.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           putida F1]
          Length = 232

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 110/231 (47%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     +R++V  M+AQ+RV+V+G +      +V     +E+D   L+     
Sbjct: 1   MRLDRFLANLPSYNRQQVRLMLAQRRVRVDGKVASDPLTDVREFSRVELDEQLLQAGRPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP G V+   DP  R+ +     ++   +   GRLD NT GL++LTNDG  +R 
Sbjct: 61  RYLMLYKPTGCVSATHDPQHRTVLDLLPTALRDDLHIAGRLDFNTTGLMILTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P+T+  + Y V    ++ +  +   ++      + +     Q+ +           +
Sbjct: 121 LTQPATKLPKHYLVDTEDEIGEHYVAKFREGFYFAFEDLTTQPAQLDIL----GPHRARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F  FN KV  L R S G  +L   L  G  RE++   +
Sbjct: 177 AIVEGRYHQVKRMFGHFNNKVVGLHRESMGAIRLDPGLAPGEYRELTANEI 227


>gi|299067788|emb|CBJ38998.1| 16S rRNA pseudouridylate 516 synthase [Ralstonia solanacearum
           CMR15]
          Length = 239

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 53/224 (23%), Positives = 86/224 (38%), Gaps = 4/224 (1%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-VDGVPLRKAERTRLWLY 78
           +   G  +RR  + ++    V VNG+  E     V +   +  VDG       R  L L+
Sbjct: 1   MQSQGFGTRRYCKDLVFAGLVHVNGVEAEDPDAQVDTAGLVLDVDGERWAYHARAYLMLH 60

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
                  +              +P     V  VGRLD +T GLLLLT+DG     L  P 
Sbjct: 61  KPTGFECSQKPRHHPSVYTLLPVPLRERGVQCVGRLDQDTTGLLLLTDDGQFVHTLTSPR 120

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
            Q  +VY +     V   ++  L +G++++      +    +        + + L +GK 
Sbjct: 121 HQVPKVYEITTAEPVTDAQVTQLCQGVLLEDEDVPVVAAWAERVDA--CHLRMALTQGKY 178

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            ++K++       V  L R + G   LG  L  G  R +    L
Sbjct: 179 HQVKRMVAAAGNHVVALHRSAIGGLTLGADLAPGQWRWLEGDDL 222


>gi|146281644|ref|YP_001171797.1| pseudouridylate synthase [Pseudomonas stutzeri A1501]
 gi|145569849|gb|ABP78955.1| probable pseudouridylate synthase [Pseudomonas stutzeri A1501]
          Length = 230

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 107/233 (45%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +      SR++V R+++  R +VNG +       V   D +E+DG  L+  +  
Sbjct: 1   MRLDRYLGSRAQLSRQDVRRLVSDGRARVNGEVTRTLDREVRIFDCVELDGQVLQPGKVA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + HKP G V+   D   R+ +          +   GRLD NT GL+LLTNDG  +R 
Sbjct: 61  RYVMLHKPPGCVSATRDAAHRTVIDLIDEPDKDDLHIAGRLDFNTTGLMLLTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P++   +VY V    ++D   +    +      + +     ++ L   + +     +
Sbjct: 121 LTQPTSLQGKVYLVETEDEIDPGCVGAFARGLYFRFEDLTTLPAELVLLGPRRA----RL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
            L EG+  ++K++F  F  KV  L R S GP  L  +L  G  R ++   + +
Sbjct: 177 TLHEGRYHQVKRMFGHFGNKVTALHRESMGPLLLDASLTPGCYRPLTDNEIAQ 229


>gi|170692138|ref|ZP_02883301.1| RNA-binding S4 domain protein [Burkholderia graminis C4D1M]
 gi|170142568|gb|EDT10733.1| RNA-binding S4 domain protein [Burkholderia graminis C4D1M]
          Length = 346

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 62/261 (23%), Positives = 108/261 (41%), Gaps = 28/261 (10%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           +  +++     R+SK+++  G+ SRRE +  I +  V V+G  ++     V     IE+D
Sbjct: 88  RRDIEDAPGTLRLSKLMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPDQRIEID 147

Query: 64  G---------------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                             +          Y   I LVT  +  +G  +      +   ++
Sbjct: 148 PAAEAVQASQVTVLIHKTVGYVSGQAEDGYQPAITLVTPENRWEGDHSDIRFSVAHLRQL 207

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLN 159
              GRLDI++ GLL+LT DG +A+ L    ++  + Y VR                + L 
Sbjct: 208 APAGRLDIDSTGLLVLTQDGRIAKQLIGGHSEIDKEYLVRVAYGEHTVDVESHFPAESLE 267

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
           LL+ G+ +  +     QV+    +     +   LREGK R+I+++ E    +V  L R+ 
Sbjct: 268 LLRHGLSLDDVPLKPAQVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVR 323

Query: 220 YGPFQLGTLLAGSTREVSKKI 240
            G   LG L  G  R ++   
Sbjct: 324 MGRVVLGALPPGQWRYLAADE 344


>gi|152995450|ref|YP_001340285.1| pseudouridine synthase [Marinomonas sp. MWYL1]
 gi|150836374|gb|ABR70350.1| pseudouridine synthase [Marinomonas sp. MWYL1]
          Length = 229

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 53/231 (22%), Positives = 101/231 (43%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+   ++     +R+  +   ++ RV VNG ++++A   V   D I +D + L      
Sbjct: 1   MRLDFYLSHVTELARKAAKIAASKGRVTVNGEVVKKANYTVQEGDQICLDDILLAWPSEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L+     +     DPD  + +      +   +  VGRLD +T GLLLLT DG     
Sbjct: 61  YYLLHKPAGYV-CATQDPDHPTVLDLLPSHLGQELKIVGRLDKDTTGLLLLTTDGQWLHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--CYGDMQVTLDTQKGSNAWVTV 191
           +  P     + YR+     +  + L  L++G+++ G              ++ S+  + +
Sbjct: 120 ITSPRNACNKRYRMMLADPISDEDLKQLEEGVMLNGESQPTLPA----IAERISDCDIYL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            ++EGK  ++K++      KV  L R   G   L   + AG  RE++++ +
Sbjct: 176 TIQEGKYHQVKRMLAAVGNKVEELHRDQIGLLSLDADIQAGEFRELTEEEV 226


>gi|154499812|ref|ZP_02037850.1| hypothetical protein BACCAP_03469 [Bacteroides capillosus ATCC
           29799]
 gi|150271410|gb|EDM98667.1| hypothetical protein BACCAP_03469 [Bacteroides capillosus ATCC
           29799]
          Length = 238

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 98/231 (42%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN-VMSTDHIEVDGVPLRKAER 72
           +R+ K++A  G  SRREV+ ++   RV  NG ++             + VDG  +     
Sbjct: 2   ERLDKILASTGRWSRREVKELVRAGRVTANGAVVRSPEEKYQREGLDLRVDGQSVLCERY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +  T                    +   GRLD +TEGLLLLTNDG LA 
Sbjct: 62  TYLMLHKPAGLVSATEDPRQATVLELLPEHLRKIGLFPAGRLDRDTEGLLLLTNDGALAH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V+  GQ+DQ  +   + G+ +          + L     +     V
Sbjct: 122 DLLSPRKHVDKTYFVQVEGQLDQSDVEAFQGGMTLGDGLVCLPAGLKLL---EAPDEALV 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            LREGK  +IK++       V  L R++ GP  L   L  G  R ++++ L
Sbjct: 179 TLREGKYHQIKRMLAARGKPVRYLKRLTMGPLVLDEGLEKGQWRPLTEEEL 229


>gi|294670358|ref|ZP_06735240.1| hypothetical protein NEIELOOT_02076 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
 gi|291307822|gb|EFE49065.1| hypothetical protein NEIELOOT_02076 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
          Length = 245

 Score =  146 bits (367), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 68/245 (27%), Positives = 106/245 (43%), Gaps = 20/245 (8%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------- 63
             P R+SK +A   + SRRE +  I Q  VKVNG         V  +D IE+        
Sbjct: 4   QEPVRLSKRMAELKLCSRREADGYIEQGWVKVNGQTA-VLGQKVTPSDRIELAKQAHETQ 62

Query: 64  --------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                     P+          Y   + L+T  +  DG ++      S    +   GRLD
Sbjct: 63  AQRVTVLLNKPVGYVSGQPEKDYRAAVELITAENRWDGDTSRIPYRDSHKKGLAPAGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I++ GLL+LT DG +A+ L    +   + Y VR  G++ ++ L LL  G+ + G      
Sbjct: 123 IDSVGLLVLTQDGRIAKQLIGGDSGIEKEYLVRVKGRLSEEGLRLLNYGLSLDGEKLRPA 182

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           +V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R 
Sbjct: 183 KVEWQNEDQ----LRFILKQGKKRQIRRMCELVGLRVIGLKRIRMGQVKLGALPPGKWRY 238

Query: 236 VSKKI 240
           + K  
Sbjct: 239 LGKDE 243


>gi|21230406|ref|NP_636323.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66769600|ref|YP_244362.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. 8004]
 gi|188992811|ref|YP_001904821.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. B100]
 gi|21111965|gb|AAM40247.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66574932|gb|AAY50342.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. 8004]
 gi|167734571|emb|CAP52781.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris]
          Length = 285

 Score =  146 bits (367), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 66/234 (28%), Positives = 107/234 (45%), Gaps = 7/234 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV--NVMSTDHIEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R +A  RV V G ++            D I +DG PL    R 
Sbjct: 37  LARVLSKLGVCSRTEAARWVADGRVSVAGRVVRDPEFPLRADQHDGIAIDGQPLAGPARL 96

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L      + T   +    +       +    +  VGRLD  +EGLLL +ND   A  
Sbjct: 97  YLMLNKPRGVVTTVRDEQGRDTVYRCFDGAGLPWLAPVGRLDKASEGLLLFSNDPQWAAA 156

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-----VIQGICYGDMQVTLDTQKGSNAW 188
           +  P+T   + Y V+   + D  +L  +  G+        G      QV +  +   NAW
Sbjct: 157 VTDPATGPDKTYHVQVDCRPDALQLARMHDGVADTDPESDGSLLRAKQVRVLREGERNAW 216

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + + L EG+NR+I+++       V RL+R++ GP  +G L  GS R +S   +R
Sbjct: 217 LEIVLDEGRNRQIRRLLAALEIGVLRLVRVAIGPLAMGELGKGSWRLLSAAEVR 270


>gi|309798788|ref|ZP_07693052.1| RNA pseudouridine synthase family protein [Streptococcus infantis
           SK1302]
 gi|308117605|gb|EFO55017.1| RNA pseudouridine synthase family protein [Streptococcus infantis
           SK1302]
          Length = 241

 Score =  146 bits (367), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 59/232 (25%), Positives = 110/232 (47%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A+  I SR+ +++ + ++ + V+G+     A N  +    +   G+ ++  E 
Sbjct: 1   MRLDKLLAQEKI-SRKAMKQALLKKEILVDGLPASSLAQNTDTGLQELMFQGIRIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +  +                   ++ ++GRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPNGVVTASKDKKLPTVMDLLPQHLQSDQLYAIGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   K GI+ + G      Q+ + +   S +  T+
Sbjct: 120 QLLHPQYHVDKTYQVEVNGPLTPDHIQEFKDGIIFLDGTICKPAQLEILSSSPSLSKATI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++KK+F     KV  L R+ +G F L   L  G  R ++K+ L+
Sbjct: 180 TISEGKFHQVKKMFLSVGVKVTALKRVQFGNFILNPDLAEGDFRLLNKEELQ 231


>gi|325697062|gb|EGD38949.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK160]
          Length = 241

 Score =  146 bits (367), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 103/231 (44%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++ + Q+++ V+G    + + NV +    I   G  +     
Sbjct: 1   MRLDQLLA-ANHISRKKMKQSLLQKQILVDGKPAYKLSQNVDTGLQQITFQGKQVSDPAH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +               +       + S+GRLD +TEGLLL+T++G L  
Sbjct: 60  RYYMLNKPAGAVTANRDAEKLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V  +G +        ++GI  + G      Q+++ +   S +  TV
Sbjct: 120 QLLHPQYHVEKTYYVEVNGPLTSQDKLAFQEGIRFLDGTICQPAQLSILSTSSSLSRATV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  +IKK+F     KV  L RI +G F L   L  G  R ++++ L
Sbjct: 180 KISEGKFHQIKKMFLALGVKVTYLKRIQFGNFTLDPDLATGDCRPLNQEEL 230


>gi|157377068|ref|YP_001475668.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
 gi|157319442|gb|ABV38540.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
          Length = 261

 Score =  146 bits (367), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 58/239 (24%), Positives = 98/239 (41%), Gaps = 14/239 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN---VMSTDHIE-----VD 63
              R++K +A  G+ SRR   R I    + + G                  I       D
Sbjct: 21  KKIRLAKYLALTGLCSRRAATRYIRDGLIMIEGRQANHIDTVTLIESPDGLICKELLLFD 80

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G+ +   E  +  + +K +G        D  S +   L     R+  VGRLD ++ GLLL
Sbjct: 81  GMAVEGIEPKQYRMLNKCVGTDCRLLPDDSDSLLH--LLPASPRLYPVGRLDKDSRGLLL 138

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG L + L  P     + YRVR       + L  + +G+  + +      +T  ++ 
Sbjct: 139 LTNDGELTQHLMHPDFGHTKTYRVRVDRPYGDEFLQKMAQGVSYRDVTTLPCTMTRLSED 198

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
                  + L +G NR+I+++ +   +KV  L R+      L  L  G  RE++ + + 
Sbjct: 199 Q----FEIVLTQGLNRQIRRMSQALGFKVIDLKRVKIQTLMLEDLNEGEMRELTVEEID 253


>gi|325688213|gb|EGD30232.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK72]
          Length = 241

 Score =  146 bits (367), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 59/232 (25%), Positives = 105/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++ + Q+++ V+G    + + NV +    I   G  +     
Sbjct: 1   MRLDQLLA-ANHISRKKMKQSLLQKQILVDGKPAYKLSQNVDTGLQQITFQGKHVSGPAH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +               +       + S+GRLD +TEGLLL+T++G L  
Sbjct: 60  RYYMLNKPSGAVTANRDAEKLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V  +G +        ++GI  + G      Q+++ +   S +  TV
Sbjct: 120 QLLHPQYHVEKTYYVEVNGPLTSQDKIAFQEGIRFLDGTICQPAQLSILSSSSSLSRATV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F+LG  L  G  R ++++ L 
Sbjct: 180 KISEGKFHQIKKMFLAVGVKVIYLKRIRFGNFKLGPELTTGEYRPLNQEELE 231


>gi|301793860|emb|CBW36253.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae INV104]
 gi|332204697|gb|EGJ18762.1| hypothetical protein SPAR120_0662 [Streptococcus pneumoniae
           GA47901]
          Length = 241

 Score =  146 bits (367), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 55/232 (23%), Positives = 105/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  + SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKV-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                      ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKELPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V+ +  +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVQVNELLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSLSQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L   + R +++K L+
Sbjct: 180 TISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAESNYRPLNQKELQ 231


>gi|71905658|ref|YP_283245.1| ribosomal small subunit pseudouridine synthase A [Dechloromonas
           aromatica RCB]
 gi|71845279|gb|AAZ44775.1| ribosomal small subunit pseudouridine synthase A [Dechloromonas
           aromatica RCB]
          Length = 235

 Score =  146 bits (367), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 98/231 (42%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            ++ +++ + G  SRRE   +I + RV VNG + +   V +        VDGV    AE 
Sbjct: 1   MQLERILQKHGFGSRRECRGLIRRDRVAVNGQVCDDPFVELDTEGLVFTVDGVDWPYAEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L+       +              +P     V  +GRLD +T GLLL+TNDG L  
Sbjct: 61  ATLMLHKPAGYECSRKPKHHAGVLELLPIPLRERDVQPIGRLDEDTTGLLLITNDGQLNH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L     +  +VY       +DQ +++ L  G+++    Y  +        G    + + 
Sbjct: 121 QLSSAKRKVPKVYLATTKHPLDQAQIDQLVAGVLLADE-YEPISAAAAEIVGEK-LLRLT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           L EGK  ++K++    + +V  L R + G   L   L  G  R +S   L+
Sbjct: 179 LTEGKYHQVKRMVAAVSNRVEALHREAVGELTLPPDLKPGEWRWLSAADLQ 229


>gi|330502301|ref|YP_004379170.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           mendocina NK-01]
 gi|328916587|gb|AEB57418.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           mendocina NK-01]
          Length = 230

 Score =  146 bits (367), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 53/231 (22%), Positives = 105/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     SR++   +I+  R++V+G ++     ++     +E+D   L+     
Sbjct: 1   MRLDRFLSNFSRFSRQDSRLLISAGRLRVDGEIIIDPRFDIRDFQRVELDDELLQAGRSA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R W+ HKP+G+V+     + R+ +          +   GRLD+NT GLLL+TNDG  +R 
Sbjct: 61  RYWMLHKPVGVVSATEHDEHRTVLDLLDEPDKHELHLAGRLDLNTSGLLLITNDGLWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  +VY V     + ++   +  +      + +     Q+ +      +    +
Sbjct: 121 ITQPQQRKPKVYHVTTEQPITEEYAEVFARGLYFAFEDLTTLPAQLDVL----DSHHARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            L EG+  ++K++F  F  +V  L R S G   L   L  G  R ++   +
Sbjct: 177 TLFEGRYHQVKRMFGHFRNRVVALHRESMGEIVLDPQLAPGQYRALTAAEI 227


>gi|315125461|ref|YP_004067464.1| 16S rRNA pseudouridylate 516 synthase [Pseudoalteromonas sp.
           SM9913]
 gi|315013974|gb|ADT67312.1| 16S rRNA pseudouridylate 516 synthase [Pseudoalteromonas sp.
           SM9913]
          Length = 232

 Score =  146 bits (367), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 56/233 (24%), Positives = 94/233 (40%), Gaps = 8/233 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K I+      R +    I  Q   VNG ++      V   D +     PL     
Sbjct: 4   PCRLDKFISHLAELPRSKARAAIKSQAATVNGEVITAFDFQVSQQDDVLFYDEPLVFL-G 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R ++ +KP+G V  +SD   ++          S     GRLDI+T GL+L+TNDG  + 
Sbjct: 63  KRYFMLNKPVGYVCANSDELHKTVFDLLDEPNLSDFHVAGRLDIDTTGLVLITNDGDWSH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVT 190
            +  P     + Y V     +    L  L+ G+ +                ++  N  + 
Sbjct: 123 KITSPKKNKFKTYLVETQEPITDAALQQLRDGVQLHNEKDLTRPA----IAERLGNYGLR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + + EGK  ++K++    + KV  L R      +LG  L AG  R ++   ++
Sbjct: 179 LSISEGKYHQVKRMLAAVDNKVVELHREQIAGIKLGEDLAAGEYRPLTAAEIK 231


>gi|17545393|ref|NP_518795.1| ribosomal small subunit pseudouridine synthase A protein [Ralstonia
           solanacearum GMI1000]
 gi|17427685|emb|CAD14204.1| probable ribosomal small subunit pseudouridine synthase a protein
           [Ralstonia solanacearum GMI1000]
          Length = 252

 Score =  146 bits (367), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 89/228 (39%), Gaps = 4/228 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-VDGVPLRKAERTR 74
           + +++   G  +RR  + ++    V VNG+  E     V +   +  VDG       R  
Sbjct: 10  LYRILQSQGFGTRRYCKDLVFAGLVHVNGVEAEDPDAQVDTAGLVLDVDGERWAYHARAY 69

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L+       +              +P     V  VGRLD +T GLLLLT+DG     L
Sbjct: 70  LMLHKPTGFECSQKPRHHPSVYTLLPVPLRERGVQCVGRLDQDTTGLLLLTDDGQFVHTL 129

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  Q  +VY +     V   ++  L +G++++             ++     + + L 
Sbjct: 130 TSPRHQVPKVYEITTAEPVTDAQVTQLCQGVLLEDEDVPV--AAAWAERADACHLRMALT 187

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           +GK  ++K++       V  L R + G   LG  L  G  R +    L
Sbjct: 188 QGKYHQVKRMVAAAGNHVAALHRSAIGGLTLGADLAPGQWRWLESDDL 235


>gi|148989054|ref|ZP_01820454.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP6-BS73]
 gi|147925551|gb|EDK76628.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP6-BS73]
          Length = 241

 Score =  146 bits (367), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 57/230 (24%), Positives = 105/230 (45%), Gaps = 4/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                      ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKELPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V+ +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVQVNGLLTPDHIQTFQKGIVFLDGTICKPARLEILSASPSLSQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K 
Sbjct: 180 TISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKE 229


>gi|94970889|ref|YP_592937.1| pseudouridine synthase, Rsu [Candidatus Koribacter versatilis
           Ellin345]
 gi|94552939|gb|ABF42863.1| Pseudouridine synthase, Rsu [Candidatus Koribacter versatilis
           Ellin345]
          Length = 680

 Score =  145 bits (366), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 91/374 (24%), Positives = 152/374 (40%), Gaps = 38/374 (10%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
           + +R+ K+IA AG+ASRR+ E ++   RV VNG +           TD I VDG PL+  
Sbjct: 2   SSERLQKIIAAAGMASRRKAEELVTAGRVTVNGEVKNELGSKADPETDDIRVDGKPLKAE 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   + L+     + T        +   D +  I +R+  VGRLD  +EGLLLLTNDG +
Sbjct: 62  QLVYVLLHKPKGYVTTVSDPEGRETV-MDLVKGIPARLYPVGRLDYLSEGLLLLTNDGEM 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-------------------- 170
           A  L   ST   + Y V+  G+  ++++  L+ G+ +                       
Sbjct: 121 AAKLTHASTHVPKKYLVKVSGEPTEEQIQELRNGVQLPPEQGHIHADPREGGRFGGEKRR 180

Query: 171 ----CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
                    ++   T++G N W  V L EG+NR+I+++F+F    V ++ R+ YGP +L 
Sbjct: 181 STAVKTAPCKIE-LTREGDNPWYEVTLNEGRNRQIRRMFDFIGHHVEKIKRVEYGPLKL- 238

Query: 227 TLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
            +  G  R ++   +         +                  +RP       DD    +
Sbjct: 239 DVENGEFRLLNPAEVARLKKAAEGKHEAPRARDEKPRFAKARGERPAFGRGRSDDRAPFQ 298

Query: 287 KNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGI----------HSSFLSDSGQREENHR 336
           K S +     + +K       R  A    M +              +  +  G+R++   
Sbjct: 299 KGSYKDRSELESEKGERTRTARFDADGKRMEEAPRERRERPKFDRGARPAFRGKRDDARG 358

Query: 337 RSPSFPSKRSLRRT 350
             P+F  KR   R 
Sbjct: 359 ERPAFRGKRDDARG 372



 Score = 41.7 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 14/101 (13%), Positives = 30/101 (29%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
            ++A+    A     +    +RP   +   D      +   ++ G     +      R  
Sbjct: 367 RDDARGERPAFRGKRDDARSERPAFRARRDDQAGDRPRFPRREEGERPAFRGKRDDARGE 426

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
             +             +  G+R++     P+F  KR   R 
Sbjct: 427 RPAFRGKRDDARGERPAFRGKRDDARGERPAFRGKRDDARG 467



 Score = 40.9 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 12/104 (11%), Positives = 19/104 (18%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G    +       A    +                 F        +  G  +    A   
Sbjct: 519 GESRGKSFDRPARAGARPNFGDRPKFGPRKEGGDRPFRGKPGEKKEFRGKREGGSAARGD 578

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
            +           G       D   R +   + P  P K    R
Sbjct: 579 RKPGGFGRDRREGGERPFRGGDRPARGDRFGKKPGGPRKDFRPR 622



 Score = 40.5 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 14/101 (13%), Positives = 27/101 (26%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
            ++A+    A     +    DRP        +    +       G     +      R  
Sbjct: 381 RDDARSERPAFRARRDDQAGDRPRFPRREEGERPAFRGKRDDARGERPAFRGKRDDARGE 440

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
             +             +  G+R++     P+F  KR   R 
Sbjct: 441 RPAFRGKRDDARGERPAFRGKRDDARGERPAFRGKRDDARG 481



 Score = 40.2 bits (92), Expect = 0.44,   Method: Composition-based stats.
 Identities = 11/96 (11%), Positives = 18/96 (18%)

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW 315
             D            R +   + P    R +       G     +   P  R        
Sbjct: 380 KRDDARSERPAFRARRDDQAGDRPRFPRREEGERPAFRGKRDDARGERPAFRGKRDDARG 439

Query: 316 MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                        G+R     +      +R   R  
Sbjct: 440 ERPAFRGKRDDARGERPAFRGKRDDARGERPAFRGK 475



 Score = 39.8 bits (91), Expect = 0.62,   Method: Composition-based stats.
 Identities = 11/107 (10%), Positives = 24/107 (22%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              ++   +        E           +   +    +       G     +      R
Sbjct: 393 ARRDDQAGDRPRFPRREEGERPAFRGKRDDARGERPAFRGKRDDARGERPAFRGKRDDAR 452

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               +             +  G+R++     P+F  KR   R    K
Sbjct: 453 GERPAFRGKRDDARGERPAFRGKRDDARGERPAFRGKRDDARGERPK 499



 Score = 38.2 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 12/101 (11%), Positives = 31/101 (30%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
            ++A+    A     +    +RP    +  D  +      ++++  +  +          
Sbjct: 353 RDDARGERPAFRGKRDDARGERPAFRGKRDDARSERPAFRARRDDQAGDRPRFPRREEGE 412

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
             +             +  G+R++     P+F  KR   R 
Sbjct: 413 RPAFRGKRDDARGERPAFRGKRDDARGERPAFRGKRDDARG 453



 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 13/109 (11%), Positives = 23/109 (21%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P     A                       + P    R +       G   +KK     
Sbjct: 509 RPFRARPAGDGESRGKSFDRPARAGARPNFGDRPKFGPRKEGGDRPFRGKPGEKKEFRGK 568

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                A+      G       + G+R       P+   +   +    +K
Sbjct: 569 REGGSAARGDRKPGGFGRDRREGGERPFRGGDRPARGDRFGKKPGGPRK 617


>gi|297521296|ref|ZP_06939682.1| 16S rRNA pseudouridylate synthase A [Escherichia coli OP50]
          Length = 207

 Score =  145 bits (366), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 54/211 (25%), Positives = 93/211 (44%), Gaps = 6/211 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEVI----TPTQVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGP 222
            + EG+  ++K++F      V  L R   G 
Sbjct: 177 TISEGRYHQVKRMFAAVGNHVVELHRERIGG 207


>gi|253995406|ref|YP_003047470.1| RNA-binding S4 domain-containing protein [Methylotenera mobilis
           JLW8]
 gi|253982085|gb|ACT46943.1| RNA-binding S4 domain protein [Methylotenera mobilis JLW8]
          Length = 427

 Score =  145 bits (366), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 62/246 (25%), Positives = 101/246 (41%), Gaps = 24/246 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SKV+A  G+ SRRE +  I+   VKV+G ++E     +     I +            
Sbjct: 184 RLSKVMAERGLCSRREADEWISNGWVKVDGEIIETLGTRIKPDAEIIISSYAQEYQAENV 243

Query: 75  LWLYHKPIGLVTTHSDPDGRS--------------------TVFDNLPSIFSRVISVGRL 114
             + HKP+G V+  ++   +                             +   +   GRL
Sbjct: 244 TIILHKPVGYVSGQAEDGYQPAIVLVHPDNQWEDDPELHKHNPKQFHRGMLQGLAPAGRL 303

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DI++ G+L+LT DG +AR L    +   + Y VR  G++    +  L  G+ + G     
Sbjct: 304 DIDSTGMLVLTQDGRIARHLIGEDSTVEKEYLVRVTGELSDADMKRLNYGLSLDGEKLKP 363

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +V+   +      +   LREGK R+I+++ E     V  L RI  G   LG L  G  R
Sbjct: 364 AKVSWQNEDQ----LRFVLREGKKRQIRRMCEMVGLHVVGLKRIRMGSITLGKLPVGQWR 419

Query: 235 EVSKKI 240
            +    
Sbjct: 420 YLRSDE 425


>gi|260655287|ref|ZP_05860775.1| RNA pseudouridine synthase [Jonquetella anthropi E3_33 E1]
 gi|260629735|gb|EEX47929.1| RNA pseudouridine synthase [Jonquetella anthropi E3_33 E1]
          Length = 241

 Score =  145 bits (366), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 71/230 (30%), Positives = 104/230 (45%), Gaps = 1/230 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++K +A  G+ SRR+VE++I   RV VNG L+      V   D + VD V +    +
Sbjct: 2   TVRLNKYLASCGVGSRRKVEQLITAGRVTVNGYLVSDLGHQVEDGDAVAVDDVEVHVEAK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T + +      +    +                 R+  VGRLD+ +EG+L+LTNDG  A 
Sbjct: 62  TYIVIRKPRGYICAVTNPDYPVVLDLLPRSYDRLRLFPVGRLDLQSEGILILTNDGDFAN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTV 191
            L  PS    + Y VR +  +    L  L+ G V +G     + V L   +     W T 
Sbjct: 122 DLIHPSNGVTKTYEVRMNRVLTAADLENLRGGTVFEGRRLVPLSVDLLPDRRPEGQWATF 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            L EG  REI+ + E     V  L R + G  +L TL +G   EV+ K L
Sbjct: 182 VLGEGVKREIRLMAEGCGMTVEVLFRRAIGRMELRTLKSGEFVEVTLKDL 231


>gi|254448899|ref|ZP_05062354.1| ribosomal small subunit pseudouridine synthase A [gamma
           proteobacterium HTCC5015]
 gi|198261436|gb|EDY85726.1| ribosomal small subunit pseudouridine synthase A [gamma
           proteobacterium HTCC5015]
          Length = 231

 Score =  145 bits (366), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 49/231 (21%), Positives = 98/231 (42%), Gaps = 8/231 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I      +RREV+ ++    + VN  +  +  +++   D + V G  +   +   
Sbjct: 4   RLDRYIGNNTELTRREVKFLLKAGEITVNDEVPSKPGLHLKEGDVVAVQGRVVEPRQPRY 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             L+  P  + +  S  +    +          +  VGRLD++T GLLL+T+DG  ++ L
Sbjct: 64  FMLHKPPECI-SARSTEEHLGALDLIEEPFHDELHIVGRLDLDTTGLLLVTDDGQWSQRL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTVG 192
             P  +  +VY V     +        + GI +  +       Q+ +     +     + 
Sbjct: 123 RSPRHKVPKVYWVTTAKPIASTVAARFEAGIYLKTEDHTTAPAQLDVV----AECRARLT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + EGK  ++K++F   + +V  L R S G   L   L  G  R ++ + ++
Sbjct: 179 ITEGKFHQVKRMFAAVDNEVTALHRASVGEIVLDEDLEPGEYRALTAQEIQ 229


>gi|257415389|ref|ZP_05592383.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis AR01/DG]
 gi|257157217|gb|EEU87177.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis ARO1/DG]
          Length = 252

 Score =  145 bits (366), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 106/230 (46%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +     
Sbjct: 1   MRLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLISHKTH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                       +  VGRLD +TEGLLLLT++G L  
Sbjct: 61  VYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQLGY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            L  P+ +  + Y V+ +G V  +     K GIV+QG       ++T+     + + V +
Sbjct: 121 QLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHVFL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ 
Sbjct: 181 TIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREE 230


>gi|324990675|gb|EGC22611.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK353]
          Length = 241

 Score =  145 bits (366), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 103/231 (44%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++ + Q+++ V+G    + + NV +    I   G  +     
Sbjct: 1   MRLDQLLA-ANHISRKKMKQSLLQKQILVDGKPAYKLSQNVDTGLQQITFQGKYVSGPAH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +               +       + S+GRLD +TEGLLL+T++G L  
Sbjct: 60  RYYMLNKPAGAVTANRDAEKLTVLDLLDKEVEKENLYSIGRLDRDTEGLLLITDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V  +G +        ++GI  + G      Q+++ +   S +  TV
Sbjct: 120 QLLHPQYHVEKTYYVEVNGPLTSQDKIAFQEGIRFLDGTICQPAQLSILSSSSSLSRATV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  +IKK+F     KV  L RI +G F L   L  G  R ++++ L
Sbjct: 180 KISEGKFHQIKKMFLAVGVKVIYLKRIQFGDFTLDPDLAKGDYRALNQEEL 230


>gi|114048569|ref|YP_739119.1| pseudouridine synthase, Rsu [Shewanella sp. MR-7]
 gi|113890011|gb|ABI44062.1| Pseudouridine synthase, Rsu [Shewanella sp. MR-7]
          Length = 241

 Score =  145 bits (366), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 102/230 (44%), Gaps = 8/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A      R+ V  ++  +RV V+G   +   + V    HI  DG  L+  +   
Sbjct: 7   RLDRYLAVKLQIHRKAVRELLLAERVYVDGAPAKALDLLVDEFSHIVFDGQVLQANQPVY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L LY     +V+   D + R+ +          +   GRLD+N+ GLLLLTND   +  L
Sbjct: 67  LMLYKPVG-VVSATKDKEHRTVIDLLDCDTRQELHIAGRLDLNSSGLLLLTNDSRWSEAL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTVG 192
             P  +  +VYRV     +  + +    +G+    + I     ++ +     +     V 
Sbjct: 126 MSPEQKVDKVYRVTLANPLSDEYIAAFAQGMYFGFEDITTQPAKLVIL----APHVAEVT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           LREGK  +IK++F  F   V  L R+S G   L   L  G +R ++ + +
Sbjct: 182 LREGKYHQIKRMFGRFRNPVLGLHRLSIGEITLDEALKPGESRMLTAQEV 231


>gi|257486528|ref|ZP_05640569.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tabaci ATCC 11528]
 gi|331010014|gb|EGH90070.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tabaci ATCC 11528]
          Length = 230

 Score =  145 bits (366), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 98/231 (42%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R+ V   +A  RV+V+G         V     + +DG  L+  +  
Sbjct: 1   MRLDRFLSNLPSLNRKSVRLALASGRVQVDGQTTSDPHHEVREFSRVALDGEILQAGKAA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V+   D    + +          +   GRLD NT GL+L+TNDG  +R 
Sbjct: 61  RYFMLHKPEGCVSATVDTQHPTVLDLLDEPDRHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLK--KGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+              + I     Q+TL           +
Sbjct: 121 LTQPQTKMPKVYYVETEQPIDERYAATFAAGMYFSFENITTQPAQLTLL----GPHSARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F  FN KV RL R + G   L   L  G  R +    +
Sbjct: 177 TIVEGRYHQVKRMFGHFNNKVLRLHRENIGALALDPALAPGGYRALHAAEI 227


>gi|149908051|ref|ZP_01896719.1| hypothetical ribosomal small subunit pseudouridine synthase A
           [Moritella sp. PE36]
 gi|149809057|gb|EDM68988.1| hypothetical ribosomal small subunit pseudouridine synthase A
           [Moritella sp. PE36]
          Length = 229

 Score =  145 bits (366), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 53/230 (23%), Positives = 95/230 (41%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   +R +   MI    V VN  ++   A  V   +HI  +G  L      
Sbjct: 1   MRLDKFVCKSTELTRVDATAMITGGCVSVNHDVILDVATQVHENNHISFNGEVLTARPSR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+     + +   D    S          S +   GRLD +T GL+L+T+DG  +  
Sbjct: 61  YILLHKPADTICSN-IDEAYPSLFNYIDVENASELHVAGRLDADTTGLVLVTDDGRWSFN 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P+    +VYRV     +  D +     G+ +QG         + +     S+  V +
Sbjct: 120 IITPTKHCQKVYRVGLSRPIGDDVVAKFAHGVQLQGEQQLTRPAILEVV----SSKEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + EGK  ++K++F     +V  L R   G  QL  +  G  R ++ + +
Sbjct: 176 TITEGKFHQVKRMFSAVGNRVVSLHREKIGAIQL-DVEVGQWRYLTDREV 224


>gi|170725411|ref|YP_001759437.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169810758|gb|ACA85342.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 236

 Score =  145 bits (366), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 112/234 (47%), Gaps = 8/234 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I++    +R+ V  M+A+ +V+V+G L     + V    HI V+   ++  + + 
Sbjct: 7   RLDRFISQHLKINRKNVRLMLAKGQVRVDGELARDIDLIVDEFSHICVNDEVIQAKQASY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L+     +V+   D   ++ +        + +  VGRLD+NT GLLLLTNDG  ++ L
Sbjct: 67  IMLHKPVG-VVSATVDDKHKTVIELLKCDDRNSLHIVGRLDLNTSGLLLLTNDGRWSKQL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
             P  +  ++YRV     +  + ++   K      + I     ++ +      +    V 
Sbjct: 126 MDPEYKVGKLYRVELQNPLTVEYISAFAKGMYFEFEDITTLPAELEIV----DSHTALVT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
           L EG+  +IK++F  F   V  L RIS G   L   L +G +R ++ + ++ +L
Sbjct: 182 LYEGRYHQIKRMFGRFRNPVVGLHRISVGQIVLDKTLASGQSRPLTPEEIKHKL 235


>gi|299115182|emb|CBN74013.1| RNA pseudouridylate synthase domain-containing protein (C-terminal)
           RNA pseudouridylate synthase dom [Ectocarpus
           siliculosus]
          Length = 490

 Score =  145 bits (366), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 118/376 (31%), Positives = 168/376 (44%), Gaps = 35/376 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+S+ IAR+GIASRRE ERM+    V VNG  ++  A+NV   D ++V+          
Sbjct: 113 MRLSRRIARSGIASRREAERMVEAGVVMVNGATVQTPALNVGPRDIVKVNVGLFQQPGNG 172

Query: 64  --------GVPLRKAERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISV 111
                   G  L + E    +LW+ HK    + T  DP+GR TVFD L  +      + V
Sbjct: 173 TDCFTFVQGKVLERPESHTPKLWMVHKMRNELVTRHDPEGRPTVFDRLTKLKLPDTLMPV 232

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD NTEGLLLLTNDG LAR +ELPS+  +R Y VR +G + ++KL  ++ G  I G+ 
Sbjct: 233 GRLDYNTEGLLLLTNDGDLARKMELPSSNIVRTYSVRVYGNITEEKLRAMRSGCTIDGVR 292

Query: 172 YGDM-----QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
           Y  M           ++G NAW+T+   EGKNR+I+K+ ++    VNRL R  YGPF LG
Sbjct: 293 YKGMFVRVEGGGGKGREGRNAWLTIECTEGKNRQIRKICKYLCLTVNRLARTRYGPFSLG 352

Query: 227 TLLAGST--REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
            + AG     E+ K  +R                +   SS   V   P        +   
Sbjct: 353 KVRAGGVAAVEIPKAFMRRLEDGGGSPGGAGGGGSGSGSSRRRVGPGPGNGMRREMEAGG 412

Query: 285 ------MKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS 338
                     +   N +   +                  +G   S+    G R      +
Sbjct: 413 MKVSEVSSPGTGLSNTVGGGRDTGDRAGSSGGRHWGGGFRGAGRSWGEKGGPRIRKGVGA 472

Query: 339 PSFPSKRSLRRTSAKK 354
           P      S R T+ ++
Sbjct: 473 PMSRGDNSARPTAQQR 488


>gi|313678211|ref|YP_004055951.1| pseudouridine synthase B, ribosomal large subunit [Mycoplasma bovis
           PG45]
 gi|312950215|gb|ADR24810.1| pseudouridine synthase B, ribosomal large subunit [Mycoplasma bovis
           PG45]
          Length = 246

 Score =  145 bits (366), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 83/242 (34%), Positives = 116/242 (47%), Gaps = 9/242 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           RV K+IA++G+ SRRE E+MI+   V VNGI          + D I+V+G  L   +   
Sbjct: 6   RVQKLIAQSGLMSRREAEKMISSGLVFVNGIKA-SLGDKASADDEIKVNGKILNLTKSPV 64

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP   +TT +DP GR TV  +L +   R++ VGRLD NT G+LLLT D  L  
Sbjct: 65  FKYFLLNKPKNSITTSNDPKGRRTVI-DLINTNERIVPVGRLDRNTTGVLLLTTDYELVN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  RVYR R    +   +   L   I I G     +   +DT+        V 
Sbjct: 124 KLTHPKYEIERVYRARIDSPLTLKEFKELNARIEIDGKMSRQIVDQVDTKS-----YLVS 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L  G    +KK+FE    KV  L R+SY    +  L  G  RE++ K +R        +E
Sbjct: 179 LHVGSYHHVKKLFEKIGHKVLTLKRVSYANLTVDKLPEGMYRELTLKEVRNLKLLVEKQE 238

Query: 253 AQ 254
             
Sbjct: 239 KN 240


>gi|146299144|ref|YP_001193735.1| RNA-binding S4 domain-containing protein [Flavobacterium johnsoniae
           UW101]
 gi|146153562|gb|ABQ04416.1| ribosomal large subunit pseudouridine synthase B [Flavobacterium
           johnsoniae UW101]
          Length = 302

 Score =  145 bits (366), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 58/234 (24%), Positives = 112/234 (47%), Gaps = 1/234 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           Q+     R++K I+ +G+ SRR+ +  I    VKVNG+ +      V   D +  DGV L
Sbjct: 64  QKASDEIRLNKYISNSGVCSRRDADLYIQSGNVKVNGVPVTEMGYLVKLNDVVNFDGVTL 123

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              ++  + L              + R+ +     +  +++  +GR+D NT GLLL TND
Sbjct: 124 TPEKKEYILLNKPKNFTTALDEGQEYRNVLELVRAATNAKIAPIGRMDKNTTGLLLFTND 183

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
             + R   LP+ +  ++Y+V     +  + L  + KG+V+ G      +++   +K   +
Sbjct: 184 TDMIRKFSLPNQKSPKIYQVSLDKNLKFEDLEKISKGLVLDGHRVSVEEISYI-EKEPKS 242

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V + LR    + ++ +FE F++ V R+ R+S+       L  G+ R ++ + +
Sbjct: 243 EVGLKLRSSNVKVVRAIFENFDYNVLRIDRVSFAGLTKKNLPRGNWRFLTDQEV 296


>gi|89902309|ref|YP_524780.1| RNA-binding S4 [Rhodoferax ferrireducens T118]
 gi|89347046|gb|ABD71249.1| RNA-binding S4 [Rhodoferax ferrireducens T118]
          Length = 304

 Score =  145 bits (366), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 71/269 (26%), Positives = 107/269 (39%), Gaps = 48/269 (17%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---------- 64
           R++K +A  G+ASRRE +  IA+  VKVNG++     + V+    IE+D           
Sbjct: 39  RLNKRMAELGLASRREADDWIAKGWVKVNGVVAT-MGMQVLPDVRIEIDKQAQGQQAKQV 97

Query: 65  -----VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
                 P+          +   I LV   +     +  F   PS    ++  GRLDI++ 
Sbjct: 98  TVLVHKPIGLVSGQAEDGHLPAITLVQPQNRWAQDNARFFFHPSQLKSLVPAGRLDIDST 157

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------------------------ 155
           GLL+LT DG +AR L        + Y VR     DQ                        
Sbjct: 158 GLLVLTQDGRVARQLIGEDAVMEKEYLVRVVYNADQGAATSTGQLSRIDDDDPVSTDVQS 217

Query: 156 ----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +KL LL+ G+ + G      +V     +     +   L EGK R+I+++ E    K
Sbjct: 218 VFPREKLALLRHGLSLDGQALQPAKVDWQNPEQ----LRFILTEGKKRQIRRMCELVGLK 273

Query: 212 VNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           V  L R+  G   LG L  G  R ++   
Sbjct: 274 VVGLKRVRIGKVMLGNLPLGQWRYLAPHE 302


>gi|125717504|ref|YP_001034637.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK36]
 gi|125497421|gb|ABN44087.1| Ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus sanguinis SK36]
          Length = 241

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 103/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++ + Q+++ V+G    + + NV +    I   G  +     
Sbjct: 1   MRLDQLLA-ANHISRKKMKQSLLQKQILVDGKPAYKLSQNVDTGLQQITFQGKHVSGPAH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +               +       + S+GRLD +TEGLLL+T++G L  
Sbjct: 60  RYYMLNKPSGAVTANRDAEKLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V  +G +        ++GI  + G      Q+++ +   S +  TV
Sbjct: 120 QLLHPQYHVEKTYYVEVNGPLTSQDKIAFQEGIRFLDGTICQPAQLSILSSSSSLSRATV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L  G  R ++++ L 
Sbjct: 180 KISEGKFHQIKKMFLAVGVKVTYLKRIQFGDFTLDPDLAKGDYRALNQEELE 231


>gi|33240564|ref|NP_875506.1| 16S rRNA pseudouridylate synthase [Prochlorococcus marinus subsp.
           marinus str. CCMP1375]
 gi|33238092|gb|AAQ00159.1| 16S rRNA pseudouridylate synthase [Prochlorococcus marinus subsp.
           marinus str. CCMP1375]
          Length = 237

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 59/232 (25%), Positives = 108/232 (46%), Gaps = 2/232 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERA--AVNVMSTDHIEVDGVPLRKAE 71
           +R+ K+I+ +GI SR++ E +I Q+RV +N  +      A  ++    I+   +P     
Sbjct: 3   ERLQKIISNSGICSRKKAEALIDQKRVFINNEIASLGEKADILIDIIRIDDYIIPKNIKS 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              + L      + T       ++ +     ++   +  VGRLD ++ G L+++N+G L 
Sbjct: 63  SKVILLNKPTGVISTCRDTHGRKTVLDLLPDNLQKGMHPVGRLDKDSRGALIISNNGLLT 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y V   G   ++ L   + GI I         V +  ++G+N  + +
Sbjct: 123 LHLTHPRFNHKKRYSVLITGVPSKNTLKKWRNGIEIDKKTTRKALVNIVKRQGNNTLLEI 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            L EG+NR+I+KV +     V  LIRI  G  +L  L  G+ RE+++    +
Sbjct: 183 VLFEGRNRQIRKVADKLGHPVIDLIRIEIGNIKLNGLKEGAWREINELEWNQ 234


>gi|323352745|ref|ZP_08087715.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis VMC66]
 gi|322121781|gb|EFX93527.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis VMC66]
          Length = 241

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 59/232 (25%), Positives = 104/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++++ Q+++ V+G    + + NV +    I   G  +     
Sbjct: 1   MRLDQLLA-ANHISRKKMKQILLQKQILVDGNPACKLSQNVDTGLQQITFQGKHVSGPAH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +               +       + S+GRLD +TEGLLL+T++G L  
Sbjct: 60  RYYMLNKPAGAVTANRDAEKLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V  +G +        ++GI  + G      Q+++ +   S +  TV
Sbjct: 120 QLLHPQYHVEKTYYVEVNGPLTSQDKITFQEGIRFLDGTVCQPAQLSILSTSSSLSRATV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L  G  R +++K L 
Sbjct: 180 KISEGKFHQIKKMFLAVGVKVTYLKRIQFGDFTLDPDLAKGDYRALNQKELE 231


>gi|317403818|gb|EFV84295.1| pseudouridylate synthase [Achromobacter xylosoxidans C54]
          Length = 243

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 61/244 (25%), Positives = 100/244 (40%), Gaps = 19/244 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
              R+SK+++  G+ SRRE +  I +  V+V+G ++            I ++        
Sbjct: 2   EKVRISKLMSERGLCSRREADSYIERGWVRVDGEVVSELGARAFPNQVITLERAAQARQT 61

Query: 64  -------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
                    P+          Y   + L+   S   G  +           +   GRLDI
Sbjct: 62  SRVTILINKPVGYVSGQAEKGYTPAVALIDARSRFAGDRSPQRFERGHLDGLAVAGRLDI 121

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +++GLL+LT DG +A++L    +   + Y VR  G + ++ L LL  G+ + G      Q
Sbjct: 122 DSQGLLVLTQDGRVAKLLIGEDSSIDKEYLVRVQGDLSENGLALLNHGLSLDGKALKPAQ 181

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V           +   LREGK R+I+++ E    KV  L R+  G   LG L  G  R +
Sbjct: 182 VRWQNHDQ----LRFVLREGKKRQIRRMCELVGLKVVGLKRVRIGRVALGELPLGQWRYL 237

Query: 237 SKKI 240
               
Sbjct: 238 RDDE 241


>gi|269114930|ref|YP_003302693.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           hominis]
 gi|268322555|emb|CAX37290.1| Ribosomal large subunit pseudouridine synthaseB (rRNA-uridine
           isomerase B, rRNA pseudouridylatesynthase B) [Mycoplasma
           hominis ATCC 23114]
          Length = 240

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 68/244 (27%), Positives = 117/244 (47%), Gaps = 12/244 (4%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           ++E     R+ K+++  GI SRR+ E +I   ++ +N  + +     V   D I+++   
Sbjct: 1   MEEKAK--RIQKILSEQGICSRRKAEELILSGKILINNKIAK-LGECVTINDEIKINNRI 57

Query: 67  LRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           ++         +  + +KP+  + T SDP  R T+++ L     R+ S+GRLD NT G++
Sbjct: 58  IKLNNNIANNFKYIVLNKPMNTICTASDPQNRKTIYEYL-KAKERLFSIGRLDFNTTGII 116

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L+TNDG  A +L  PS++  R+Y      ++   +LNLL    V+        +VT    
Sbjct: 117 LITNDGEFANLLSHPSSEIPRIYIATLEREMLDGELNLLNSNHVLLNGKISKQKVTKL-- 174

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
             S     V L EG+N  +K +F   N  V +L R S+G      L  G  R ++   + 
Sbjct: 175 --SAFKYEVLLYEGRNHHVKNLFLLVNNYVKKLHRKSFGCIDDSNLKIGQYRNLTSSEIN 232

Query: 243 EQLG 246
           + L 
Sbjct: 233 KLLA 236


>gi|148997238|ref|ZP_01824892.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP11-BS70]
 gi|168575350|ref|ZP_02721286.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae MLV-016]
 gi|307067298|ref|YP_003876264.1| 16S rRNA uridine-516 pseudouridylate synthase-like pseudouridylate
           synthase [Streptococcus pneumoniae AP200]
 gi|147756938|gb|EDK63978.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP11-BS70]
 gi|183578472|gb|EDT99000.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae MLV-016]
 gi|306408835|gb|ADM84262.1| 16S rRNA uridine-516 pseudouridylate synthase-like pseudouridylate
           synthase [Streptococcus pneumoniae AP200]
          Length = 241

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 106/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLKGDILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                      ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKELPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVEVNGLLTPDHIQTFQKGIVFLDGTICKPARLEILSASPSLSQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K L+
Sbjct: 180 TISEGKFHQIKKMFLSVGVKVTILKRIQFGDFTLNPDLAEGNYRPLNQKELQ 231


>gi|118369895|ref|XP_001018150.1| conserved hypothetical protein [Tetrahymena thermophila]
 gi|89299917|gb|EAR97905.1| conserved hypothetical protein [Tetrahymena thermophila SB210]
          Length = 484

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 90/274 (32%), Positives = 146/274 (53%), Gaps = 14/274 (5%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            K ++ E    +R+SK ++R+G+ SRR+ E+MI    +KV+G +     + V   ++IE+
Sbjct: 169 RKQVMNE----ERLSKYLSRSGVCSRRQAEKMIKDGLIKVDGKVATS-NLPVTPKNNIEI 223

Query: 63  ---DGVPLRK--AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRL 114
               G               Y     + +        S       +       +I+VGRL
Sbjct: 224 FTQRGEKFAPVKQNAKIWIFYKPRGMICSHDDPLKRPSVFNYIYNNTKIKEPHIIAVGRL 283

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D N+EGL+LLTNDG +A+ LE P +   R YRVR  G++D+ KL  L++G VI G+ YG 
Sbjct: 284 DYNSEGLILLTNDGDIAQCLEQPESNIYRQYRVRVQGELDERKLLKLRQGTVINGVQYGP 343

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             V +D ++ SN W+TVGL  GKNREI+KV + F+ +V+RL R+SYGP+++G++L G   
Sbjct: 344 FNVEIDKRQSSNTWLTVGLYTGKNREIRKVMQKFDLRVSRLKRLSYGPYKIGSMLPGQIF 403

Query: 235 E-VSKKILREQLGPHLLEEAQVNLDAPIYSSETL 267
           E      L+ ++  ++ +  Q++           
Sbjct: 404 ETYVNDELKRKIYLYMRKRLQLSQADMKAYLVDK 437


>gi|304569705|ref|YP_010887.2| ribosomal large subunit pseudouridine synthase B [Desulfovibrio
           vulgaris str. Hildenborough]
 gi|311233922|gb|ADP86776.1| RNA-binding S4 domain protein [Desulfovibrio vulgaris RCH1]
          Length = 292

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 75/245 (30%), Positives = 121/245 (49%), Gaps = 9/245 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK-- 69
             R++K ++ AG+ SRR+ + +IA  +V+VNG ++      V   TD IEV+G  L    
Sbjct: 45  GTRLNKALSGAGVCSRRQADTLIAGGKVRVNGEVVTEMGRRVFPATDRIEVEGRLLACGE 104

Query: 70  ---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLL 124
                R    + +KP+ +V+T  DP GR+T+ D LP     V    VGRLD  +EGLLLL
Sbjct: 105 ALNRHRHTYVMLNKPVQVVSTVRDPQGRTTILDILPDDLKTVRLYPVGRLDFFSEGLLLL 164

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQK 183
           T+DG L   L  P     + YRV     +    L  ++ G+ + +G     ++  +  + 
Sbjct: 165 TDDGDLTHRLTHPKWHLPKYYRVLVREDIPPAALTAMRSGMTLAEGDRVAPVEAYIIDRS 224

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
                + + L +G NR+I+++       V RL+RI  GP +LG L  G+ R +    ++ 
Sbjct: 225 EYGVELEMVLHQGINRQIRRMCRDLGLTVLRLLRIQQGPVELGNLSRGACRRLEDHEVKA 284

Query: 244 QLGPH 248
                
Sbjct: 285 LRKAA 289


>gi|307709844|ref|ZP_07646293.1| conserved hypothetical protein [Streptococcus mitis SK564]
 gi|307619393|gb|EFN98520.1| conserved hypothetical protein [Streptococcus mitis SK564]
          Length = 220

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 57/217 (26%), Positives = 93/217 (42%), Gaps = 4/217 (1%)

Query: 34  MIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPD 92
           M+   RV VNG   + A + +    D I  DG  L   E     +      +  T     
Sbjct: 1   MLKAGRVTVNGKKEKSAKLQIDEERDEIIFDGQVLEYEEFVYYMMNKPKGVISATEDPKH 60

Query: 93  GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152
                  +  +    V  VGRLDI+T GLLLLTNDG LA  L  P     + Y+ +  G 
Sbjct: 61  RTVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNDGQLAHALLSPKRHVDKTYQAQVKGI 120

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           + Q+ + +  KGI ++       ++ +     +   + + V + EGK  ++K++  +   
Sbjct: 121 MTQEDVEIFAKGIPLKDFTCQPAKLEIVSIDTEKIQSQIRVTIAEGKFHQVKRMVAYCGK 180

Query: 211 KVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           +V  L R++ G   L   L  G  R ++K+ L   L 
Sbjct: 181 EVVDLQRLTMGTLVLDENLQRGEWRRLTKEELEALLA 217


>gi|126666853|ref|ZP_01737829.1| Pseudouridine synthase, Rsu [Marinobacter sp. ELB17]
 gi|126628569|gb|EAZ99190.1| Pseudouridine synthase, Rsu [Marinobacter sp. ELB17]
          Length = 250

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 56/228 (24%), Positives = 100/228 (43%), Gaps = 3/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            ++S++++     SR++   +IA  +V VN +    A  +V     + V+G  L++    
Sbjct: 16  MKLSRIVSNQPDISRKQANWLIATGQVYVNDLSCRTADADVDEFAAVSVNGKTLQQGHCA 75

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + HKP G ++   D    + +    P +   +   GRLD  T GL++LTN+G  +R 
Sbjct: 76  HYIMLHKPAGYLSATEDDTHPTVLQLLPPGLSQCLHIAGRLDRATTGLMILTNNGTWSRQ 135

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L LP     +VYRV     +  D      +GI  +         TL+  +       + +
Sbjct: 136 LTLPGMGIAKVYRVTTAYPIGPDTPQRFAEGIWFEYEQLTTAPATLELLEP--TLARLTI 193

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            EG+  ++K++F     +V  L R   G  QL   L  G+ R ++   
Sbjct: 194 YEGRYHQVKRMFHAVGNRVIALHREQIGHLQLNSDLAEGNFRMLTGSE 241


>gi|33592133|ref|NP_879777.1| putative RNA pseudouridylate synthase [Bordetella pertussis Tohama
           I]
 gi|33571777|emb|CAE41283.1| putative RNA pseudouridylate synthase [Bordetella pertussis Tohama
           I]
 gi|332381549|gb|AEE66396.1| putative RNA pseudouridylate synthase [Bordetella pertussis CS]
          Length = 243

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 61/244 (25%), Positives = 102/244 (41%), Gaps = 19/244 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG------- 64
              R+SK+++  G+ SRRE +  I +  V+V+G+++       +    I ++        
Sbjct: 2   EKVRISKLMSERGLCSRREADSYIERGWVRVDGVVVSELGARALPDQVITLERAAAARQT 61

Query: 65  --------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
                    P+          Y   + L+   S   G              +   GRLDI
Sbjct: 62  ARVTILLHKPVGYVSGQAEKGYTPAVALIDARSRYAGDRAPQRFERGQLQGLAVAGRLDI 121

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +++GLL+LT DG +A+ L    ++  + Y VR  G++ +  L LL  G+ + G      Q
Sbjct: 122 DSQGLLVLTQDGRIAKKLIGEDSEVDKEYLVRVQGRLSEAGLALLNHGLSLDGKPLRPAQ 181

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V           +   LREGK R+I+++ E    +V  L R+  G   LG L AG  R +
Sbjct: 182 VRWQNADQ----LRFVLREGKKRQIRRMCELVGLRVVGLKRVRIGRVSLGDLPAGQWRYL 237

Query: 237 SKKI 240
               
Sbjct: 238 RADE 241


>gi|117921613|ref|YP_870805.1| pseudouridine synthase, Rsu [Shewanella sp. ANA-3]
 gi|117613945|gb|ABK49399.1| Pseudouridine synthase, Rsu [Shewanella sp. ANA-3]
          Length = 241

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 103/230 (44%), Gaps = 8/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A      R+ V  ++  +RV V+GI  +   + V    HI  DG  L+  +   
Sbjct: 7   RLDRYLAVKLQIHRKAVRELLLTERVYVDGIPAKALDLLVDEFSHIVFDGQVLQANKPVY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L+     +V+   D + R+ +          +   GRLD+N+ GLLLLTND   +  L
Sbjct: 67  LMLHKPVG-VVSATKDTEHRTVIDLLDCDARHELHIAGRLDLNSSGLLLLTNDSRWSEAL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTVG 192
             P  +  +VYRV     + ++ +    +G+    + I     ++T+           V 
Sbjct: 126 MSPDQKVDKVYRVTLANPLSEEYIAAFAQGMYFGFEDITTQPAKLTIL----DTHIAEVT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           LREGK  +IK++F  F   V  L R S G   L   L  G +R ++ + +
Sbjct: 182 LREGKYHQIKRMFGRFRNPVVGLHRHSIGEITLDDGLKPGESRMLTAQEV 231


>gi|304410785|ref|ZP_07392402.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|307305043|ref|ZP_07584793.1| pseudouridine synthase [Shewanella baltica BA175]
 gi|304350682|gb|EFM15083.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|306912445|gb|EFN42869.1| pseudouridine synthase [Shewanella baltica BA175]
          Length = 233

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 59/232 (25%), Positives = 99/232 (42%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   +R      I    V VNG++    A+ V   + + ++G PL      
Sbjct: 1   MRLDKFLCKSTDLNRDAASVAILSGSVTVNGVIATDCAMQVHENNAVSLNGKPLAPRPS- 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP   + ++ D    S            +  VGRLD +T GL+LLT+DG  +  
Sbjct: 60  RYFVLHKPADTLCSNVDGAYPSLFHLLDIERAFDLHIVGRLDADTTGLVLLTDDGRWSFN 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKG----IVIQGICYGDMQVTLDTQKGSNAWV 189
           +  P  Q  +VYRV+    +D +    +       + +QG     +  TL         V
Sbjct: 120 IISPQYQCKKVYRVQLRDPLDSEATAAIAATFAAGLQLQGETALTLPATLQQVDDK--TV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + L EGK  ++K++F     KV  L R   G   L  +  G  RE++   +
Sbjct: 178 LLTLTEGKFHQVKRMFAAVGNKVVALHRAQIGAVTL-DVDVGEWRELTLTEI 228


>gi|221231495|ref|YP_002510647.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae ATCC 700669]
 gi|225854205|ref|YP_002735717.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae JJA]
 gi|220673955|emb|CAR68464.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae ATCC 700669]
 gi|225723188|gb|ACO19041.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae JJA]
          Length = 241

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 106/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + + ++ V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLRGKILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                      ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKELPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSISQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L   + R +++K L+
Sbjct: 180 TISEGKFHQIKKMFLSVGVKVTILKRIQFGDFTLNPDLAESNYRPLNQKELQ 231


>gi|297621361|ref|YP_003709498.1| RNA pseudouridylate synthase family protein [Waddlia chondrophila
           WSU 86-1044]
 gi|297376662|gb|ADI38492.1| RNA pseudouridylate synthase family protein [Waddlia chondrophila
           WSU 86-1044]
          Length = 239

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 65/237 (27%), Positives = 105/237 (44%), Gaps = 15/237 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK+++  GI SRRE +RMI +  V+ NG ++      V     IE+     +      
Sbjct: 5   RLSKLMSLRGICSRREADRMIEKGLVRANGKVISELGTKVPENAEIELLPHAKKWQAEKV 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-----------GRLDINTEGLLL 123
             + +KPIG V+T  +   +  +    P       S            GRLDI+++G+L+
Sbjct: 65  TIILNKPIGYVSTQPEKGYKQALDLITPERQWNSKSFDPKHLRKLSVAGRLDIDSKGILI 124

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LT DG +A+ +    ++  + Y VR  G V    +  L  G+V+              Q+
Sbjct: 125 LTQDGVIAKKIIGNESEIEKEYLVRVDGAVTPGIIKRLSFGLVLDNTPLKKAN----IQQ 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   L EGK R+I+++ E    KV  L R+  G  +LG L  G  R + K  
Sbjct: 181 LDEHLMKFTLIEGKKRQIRRMCELVGLKVVDLKRVRIGKIRLGDLPTGYWRYLKKSE 237


>gi|224826317|ref|ZP_03699419.1| RNA-binding S4 domain protein [Lutiella nitroferrum 2002]
 gi|224601418|gb|EEG07599.1| RNA-binding S4 domain protein [Lutiella nitroferrum 2002]
          Length = 497

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 75/252 (29%), Positives = 122/252 (48%), Gaps = 6/252 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++D  +  E   P R+ K +A +G+ SRRE+E  I    + VNG         V   D +
Sbjct: 235 LRDTRVDMEQIEPVRLQKALAASGVGSRREMEEWIEAGLILVNGKKAT-LGDRVGPQDRV 293

Query: 61  EVDGVPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
              G P+R     RL      + +   LVT        +       +  SR ++VGRLD+
Sbjct: 294 TAKGNPIRLKWPDRLPRVILYHKQEGELVTRDDPEGRVTIFDRLPQAKSSRWVAVGRLDV 353

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NT GLL++T  G LA  L  PS +  R Y VR  GQ++ +++  + +GI ++       +
Sbjct: 354 NTSGLLIVTTSGELANRLMHPSFEAEREYAVRVLGQLEPEQMKEMTRGIELEDGPAHFQR 413

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTRE 235
           +     +G N W  V ++EG+NRE++++FE F   V+RLIR+ +G   L   L  G   E
Sbjct: 414 IVEQGGEGVNHWYRVVIKEGRNREVRRIFEHFGLTVSRLIRVRFGNIGLPARLKRGQFYE 473

Query: 236 VSKKILREQLGP 247
           ++   +   +  
Sbjct: 474 LNSAEVAAVMKW 485


>gi|269792389|ref|YP_003317293.1| pseudouridine synthase [Thermanaerovibrio acidaminovorans DSM 6589]
 gi|269100024|gb|ACZ19011.1| pseudouridine synthase [Thermanaerovibrio acidaminovorans DSM 6589]
          Length = 234

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 63/218 (28%), Positives = 101/218 (46%), Gaps = 4/218 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +AR G+ SRR+VE +I   RVK+NG+++      V   DH+EVDG  +   ++ 
Sbjct: 1   MRLNQYLARCGLGSRRKVEALIVTGRVKLNGLVVSDLGCRVEEGDHVEVDGCSVHPLDKI 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +      +                      R   VGRLD  ++GLL+LTNDG     
Sbjct: 61  YIVMNKPRGVVCAVEDRRYRTVLDLLPPQIRALRPFPVGRLDKESQGLLILTNDGDFCDA 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P    ++ Y V     V  + L+ LK G+   G     + V+L         V V +
Sbjct: 121 ILHPRRGIIKTYEVTVDRDVPSESLDRLKGGVWSDGEILEPLMVSLM----GPRTVRVDI 176

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           +EGK RE++++     +KV  L+R   G  +L  L AG
Sbjct: 177 QEGKKREVRRMMAALGFKVLSLLRRRIGKMELRRLRAG 214


>gi|167957384|ref|ZP_02544458.1| pseudouridine synthase [candidate division TM7 single-cell isolate
           TM7c]
 gi|169835712|ref|ZP_02868900.1| ribosomal large subunit pseudouridine synthase B [candidate
           division TM7 single-cell isolate TM7a]
          Length = 237

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 59/232 (25%), Positives = 111/232 (47%), Gaps = 4/232 (1%)

Query: 8   QENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
                 +R++K +A + G+ SRR+ + +IA+Q+V +N    +     +  +D I ++   
Sbjct: 9   NRTEKIERLNKFLAFQLGV-SRRQADNLIAKQKVYINNQPAQ-LGARIGESDTITINNHI 66

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +         + +KPI  V +        T++  LP  F  +  VGRLD N+ GLLLLTN
Sbjct: 67  VGGRSSYTYLMLNKPINYVCSRKQQGKTPTIYSLLPDKFHNLKPVGRLDANSSGLLLLTN 126

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  A  +  P  +  + Y V    ++      ++    +        + ++  + +  +
Sbjct: 127 DGDFAFRMTHPKFKKNKQYNVTLDKELAPLHQQMIADFGIQLNDGLSKLGLSRQSNQDRH 186

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            W+ V + EG+NR+I++ F    + V +L R  +G ++LGTL AG    ++ 
Sbjct: 187 NWI-VTMSEGRNRQIRRTFAALGYTVIKLHRTHFGTYKLGTLGAGDYIVINP 237


>gi|305666250|ref|YP_003862537.1| ribosomal large subunit pseudouridine synthase B [Maribacter sp.
           HTCC2170]
 gi|88708241|gb|EAR00478.1| ribosomal large subunit pseudouridine synthase B [Maribacter sp.
           HTCC2170]
          Length = 278

 Score =  144 bits (364), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 56/233 (24%), Positives = 107/233 (45%), Gaps = 1/233 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
            N    R++K +A +G+ SRR+ +  I+   V VNG  +      V  TD ++ DG  L 
Sbjct: 40  SNPDLIRLNKYVANSGVCSRRDADIYISAGNVTVNGKPITEMGYKVRKTDEVKFDGRLLN 99

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ++  + L        T   +   R+       +  S+++ V ++D N  GLLL TNDG
Sbjct: 100 PEKKEYVLLNKPKDFSTTIRDERGKRNVNGLISSASNSKLLPVDKMDKNATGLLLFTNDG 159

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L R L+ P     ++Y V  +  +    L  +++G+V+        +V+          
Sbjct: 160 DLTRRLKSPKNGLRKIYHVVLNRDLRSADLKKIQEGVVLDEKPVRVQEVSFID-NAPKRE 218

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + +   KN+ ++++FE   ++V ++ R+SY       L  G  R ++++ +
Sbjct: 219 VGIEIYSSKNKVVERIFEELEYEVAKIDRVSYAGLTKKDLPRGHWRFLTEQEV 271


>gi|325473314|gb|EGC76509.1| pseudouridine synthase [Treponema denticola F0402]
          Length = 245

 Score =  144 bits (364), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 108/237 (45%), Gaps = 9/237 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ +++A +G+ SR +V++MI ++   V+G+ +   +  + +  + I +DG PL      
Sbjct: 4   RLDRILALSGLGSRSDVKKMIRKKNCCVDGVRIVSPSFILDTDLNKITIDGEPLVLRTNV 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L        + +T          +   P     +  +GRLDI+TEGLL++T+DG +   
Sbjct: 64  YLMFNKPQGCVTSTSDPVHKTVMDYIKAPFDRMTLFPIGRLDIDTEGLLIITDDGEITHK 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVIQ-GICYGDMQV-TLDTQKGS-N 186
           +  P +  ++ Y +    +   +         +KGI+++ G      +      + GS  
Sbjct: 124 ITSPKSGTVKTYYLELSREPSDEEFTNYCEEFEKGIMLKNGYKCLPAKFEKCGNKTGSFR 183

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           +   + + EGK  ++KK+      ++  L RI+ G   L   L  G  RE+S + + 
Sbjct: 184 SGFLMHITEGKFHQVKKMCLSAGNELCYLRRIAVGSIVLDETLKTGEYRELSAEEID 240


>gi|329571723|gb|EGG53404.1| pseudouridine synthase B, ribosomal large subunit [Enterococcus
           faecalis TX1467]
          Length = 205

 Score =  144 bits (364), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 63/204 (30%), Positives = 97/204 (47%), Gaps = 3/204 (1%)

Query: 47  LERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           ++     V   D +EVDGVP+ + E      Y     +++  SD  GR  V D    +  
Sbjct: 2   VKELGTQVSKQDTVEVDGVPIYQEEYGYYLFYKPRG-VISAVSDDKGRKVVTDYFTDVTE 60

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
           R+  VGRLD +T GLLLLTNDG  ++ L  P  +  +VY  +  G   +  L  L KGI 
Sbjct: 61  RIYPVGRLDYDTSGLLLLTNDGSFSQKLTHPKHEVDKVYVAKIKGVPTKRDLLPLAKGIR 120

Query: 167 IQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
           I G         + +       + V + + EG+N ++KK+F+   + V +L R  YG   
Sbjct: 121 IDGKRTAPANFQILSADIKTGSSVVELTIHEGRNHQVKKMFQAVGFPVQKLKRERYGELT 180

Query: 225 LGTLLAGSTREVSKKILREQLGPH 248
           L  L  G  R+++KK + + L   
Sbjct: 181 LQGLRPGQYRDLTKKEISQLLNQA 204


>gi|168492837|ref|ZP_02716980.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae CDC3059-06]
 gi|183576842|gb|EDT97370.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae CDC3059-06]
          Length = 241

 Score =  144 bits (364), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 56/232 (24%), Positives = 106/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  + SR+ +++ + + ++ V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKV-SRKAMKQALLRGKILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                      ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKELPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSISQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L   + R +++K L+
Sbjct: 180 TISEGKFHQIKKMFLSVGVKVTILKRIQFGDFTLNPDLAESNYRPLNQKELQ 231


>gi|167824765|ref|ZP_02456236.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 9]
          Length = 300

 Score =  144 bits (364), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 52  VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 111

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 112 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 171

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 172 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDG 231

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 232 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 287

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 288 QGEWRYLGPDE 298


>gi|319952524|ref|YP_004163791.1| ribosomal large subunit pseudouridine synthase b [Cellulophaga
           algicola DSM 14237]
 gi|319421184|gb|ADV48293.1| ribosomal large subunit pseudouridine synthase B [Cellulophaga
           algicola DSM 14237]
          Length = 280

 Score =  144 bits (364), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 53/227 (23%), Positives = 102/227 (44%), Gaps = 1/227 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ +A +G+ SRRE +  IA   V VNG  +      V  +D +  DG  L   ++  
Sbjct: 48  RLNRYVANSGVCSRREADIYIAAGSVTVNGKPVIEMGYKVQLSDEVRFDGRLLNPIKKEY 107

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        +T      R+ +     +  ++++ VG++D ++ GLLL TNDG L   L
Sbjct: 108 VVLNKPKDFATSTRDGAGNRTAMGLVSNASKAKLLPVGKMDKSSTGLLLFTNDGDLTARL 167

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     +++ V     +    L  +K+GI I+      +Q     +      V V + 
Sbjct: 168 NSPKNGLRKIFHVELTKPLKSTDLKRIKEGIEIEESVVR-IQDISYIENAPKTQVGVEIF 226

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             +N  ++++FE  ++ V +L  + Y       L  G  R ++++ +
Sbjct: 227 STRNNIVRRLFEKLDYDVVKLDLVVYAGLTKKDLPRGHWRPLTEQEI 273


>gi|149002375|ref|ZP_01827317.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP14-BS69]
 gi|149005797|ref|ZP_01829536.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP18-BS74]
 gi|237650299|ref|ZP_04524551.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae CCRI 1974]
 gi|237821983|ref|ZP_04597828.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae CCRI 1974M2]
 gi|307126876|ref|YP_003878907.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae 670-6B]
 gi|147759690|gb|EDK66681.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP14-BS69]
 gi|147762737|gb|EDK69697.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP18-BS74]
 gi|306483938|gb|ADM90807.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae 670-6B]
 gi|332077107|gb|EGI87569.1| hypothetical protein SPAR148_0640 [Streptococcus pneumoniae
           GA17545]
          Length = 241

 Score =  144 bits (364), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 106/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                      ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKELPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V+ +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVQVNGLLTPDHIQTFQKGIVFLDGTICKPARLEILSASPSFSQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L   + R +++K L+
Sbjct: 180 TISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAESNYRPLNQKELQ 231


>gi|229828352|ref|ZP_04454421.1| hypothetical protein GCWU000342_00410 [Shuttleworthia satelles DSM
           14600]
 gi|229792946|gb|EEP29060.1| hypothetical protein GCWU000342_00410 [Shuttleworthia satelles DSM
           14600]
          Length = 265

 Score =  144 bits (364), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 56/241 (23%), Positives = 111/241 (46%), Gaps = 9/241 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +  + QR++K +  AG+ SRRE +  I   +V ++G         V+    + V+G  + 
Sbjct: 19  DPASGQRLNKFLTNAGVCSRREADHRIRAGQVTIDGQTA-ELGQRVLPGQRVAVNGRIIE 77

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             E   + L+HKP G+V T    +       +     SRV  VGRLD  + GL+L+TN G
Sbjct: 78  GKEEEIILLFHKPRGIVCTAEKRE--KNNIVDFIGYPSRVYPVGRLDKESRGLILMTNQG 135

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKGSN 186
            +   +   + +  + Y+V  +  + +  +  ++ GI ++  G      Q+     +  +
Sbjct: 136 DIVNRMMRAANRHEKEYQVTVNRGISETFVRRMRAGIYLKELGETTRPCQIH----QTGD 191

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
              T+ L +G NR+I+++     ++V  L+R+     +L  +  G  R++ ++   E   
Sbjct: 192 RTFTIILTQGLNRQIRRMCHTLGYEVTDLLRVRIMNLRLDGIPEGEYRKIGRREREELNR 251

Query: 247 P 247
            
Sbjct: 252 L 252


>gi|108760801|ref|YP_630635.1| RsuA family pseudouridine synthase [Myxococcus xanthus DK 1622]
 gi|108464681|gb|ABF89866.1| pseudouridine synthase, RsuA family [Myxococcus xanthus DK 1622]
          Length = 268

 Score =  144 bits (364), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 59/244 (24%), Positives = 100/244 (40%), Gaps = 11/244 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPL 67
              P  +S+ +ARAG+  ++E E  I   RV +NG + + A   V     ++VDG  V L
Sbjct: 20  KEKPDWLSRALARAGVFPQKEAEDAIRAGRVSINGRVAKMALTPVPPGATVKVDGLVVSL 79

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGRLDINTEGLL 122
                  L  +     L +T       +     LP +          +VGRLD+++ GLL
Sbjct: 80  EAPPTRVLAFHKPAGLLSSTERQHRTGTVFEALLPQLPPELAGYTWHAVGRLDVDSTGLL 139

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L TND  L      P     + Y          +++  L++G+ +        +V +   
Sbjct: 140 LFTNDDKLVAHATSPDAHLPKRYVATVFSTASDERVEPLRRGMTLDDGPARPAKVNV--- 196

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
                 V V L EG++ ++K++       V  L R + G   L  +  G+ R ++   +R
Sbjct: 197 -RDEHTVEVTLTEGRHHQVKRMLGAVGLPVRALHREAVGSVDLEGIPEGTFRLLTDDEVR 255

Query: 243 EQLG 246
           E L 
Sbjct: 256 EGLR 259


>gi|309780778|ref|ZP_07675519.1| ribosomal small subunit pseudouridine synthase A [Ralstonia sp.
           5_7_47FAA]
 gi|308920460|gb|EFP66116.1| ribosomal small subunit pseudouridine synthase A [Ralstonia sp.
           5_7_47FAA]
          Length = 248

 Score =  144 bits (364), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 52/241 (21%), Positives = 87/241 (36%), Gaps = 3/241 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-VDGVPLRKAERTR 74
           + +++   G  +RR  + ++    V VNG+ +E     V +   +  VDG       R  
Sbjct: 9   LYRILQSQGFGTRRYCKDLVLAGLVFVNGVEMESPDALVDTAGLVLDVDGERWAYHARAY 68

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L        +              +P     V  VGRLD +T GLLLLT+DG     +
Sbjct: 69  LMLNKPAGVECSQKPKHHPSVYTLLPVPLRERAVQCVGRLDQDTTGLLLLTDDGQFVHTI 128

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  Q  +VY +     V + ++  L  G+++            +        + + L 
Sbjct: 129 TSPRHQVPKVYEITTAEPVTEAQIAQLCAGVLLADENENVAAAWAERV--GTHHLRMALT 186

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +GK  ++K++       V  L R + G   LG L  G  R +    L             
Sbjct: 187 QGKYHQVKRMVAAAGNHVAGLHRSAIGGLSLGDLAPGEWRWLEAADLEALNTTPPHATGP 246

Query: 255 V 255
            
Sbjct: 247 S 247


>gi|110835398|ref|YP_694257.1| pseudouridylate synthase [Alcanivorax borkumensis SK2]
 gi|110648509|emb|CAL17985.1| pseudouridylate synthase [Alcanivorax borkumensis SK2]
          Length = 229

 Score =  144 bits (364), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 110/232 (47%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+   +A +   +R+E +++I++  V V G    +A + +     + V G  ++     
Sbjct: 1   MRLDYFLAHSAGLTRKEAKQLISRGAVTVEGEAKPKANLQLRPDQAVTVHGERVQPP-GH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + HKP+ +V +  DP  R+ +    P + ++V   GRLD +T GL+LLT+DG  +  
Sbjct: 60  RYLMLHKPVDVVCSTEDPGHRTVLDLLPPELRAQVHPAGRLDRDTTGLVLLTSDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           L  P+    + YRV+    V  + +  L++G+++  +       QV         A + +
Sbjct: 120 LTSPNHACGKRYRVQCADPVSDEDMQALREGVLLRGEDKPTLPAQVERL----DEACLLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            +REG+  ++K++      KV  L R   G  QL   L  G  R +++  + 
Sbjct: 176 TIREGRYHQVKRMLAACGNKVLGLHREQIGEIQLDAALAPGEYRALTEDEVE 227


>gi|313500364|gb|ADR61730.1| Pseudouridine synthase [Pseudomonas putida BIRD-1]
          Length = 230

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 110/231 (47%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     +R+ V  M+AQ+RV+V+G ++     +V     +E+D   L+     
Sbjct: 1   MRLDRFLANLPSYNRQHVRLMLAQRRVRVDGQVVSDPLTDVREFSRVELDEQLLQAGRPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP G V+   DP  R+ +     ++   +   GRLD NT GL++LTNDG  +R 
Sbjct: 61  RYLMLYKPTGCVSATHDPQHRTVLDLLPAALRDDLHIAGRLDFNTTGLMILTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P+T+  + Y V    ++ +  +   ++      + +     Q+ +           +
Sbjct: 121 LTQPATKLPKHYLVDTEDEIGEHYVAKFREGFYFAFEDLTTQPAQLDIL----GPHRARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F  FN KV  L R S G  +L   L  G  RE++   +
Sbjct: 177 AIVEGRYHQVKRMFGHFNNKVIGLHRESMGAIRLDPGLAPGEYRELTANEI 227


>gi|42526372|ref|NP_971470.1| ribosomal small subunit pseudouridine synthase A [Treponema
           denticola ATCC 35405]
 gi|41816484|gb|AAS11351.1| ribosomal small subunit pseudouridine synthase A [Treponema
           denticola ATCC 35405]
          Length = 245

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 108/237 (45%), Gaps = 9/237 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ +++A +G+ SR +V++MI ++   V+G+ +   +  + +  + I +DG PL      
Sbjct: 4   RLDRILALSGLGSRSDVKKMIRKKNCCVDGVRIVSPSFILDTDLNKITIDGEPLVLRTNV 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L        + +T          +   P     +  +GRLDI+TEGLL++T+DG +   
Sbjct: 64  YLMFNKPQGCVTSTSDPVHKTVMDYIKAPFDRMTLFPIGRLDIDTEGLLIITDDGEITHK 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVIQGI-CYGDMQV-TLDTQKGS-N 186
           +  P +  ++ Y +    +   +         +KGIV++        +    + + GS  
Sbjct: 124 ITSPKSGTVKTYYLELSREPSDEEFKNYCEEFEKGIVLKNGYKCLPAKFEKCENKTGSFR 183

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           +   + + EGK  ++KK+      ++  L RI+ G   L   L  G  RE+S + + 
Sbjct: 184 SGFLMHITEGKFHQVKKMCLSAGNELCYLRRIAVGSIVLDETLKTGEYRELSAEEID 240


>gi|259047770|ref|ZP_05738171.1| ribosomal small subunit pseudouridine synthase A [Granulicatella
           adiacens ATCC 49175]
 gi|259035447|gb|EEW36702.1| ribosomal small subunit pseudouridine synthase A [Granulicatella
           adiacens ATCC 49175]
          Length = 230

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 61/224 (27%), Positives = 105/224 (46%), Gaps = 4/224 (1%)

Query: 22  RAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRLWLYHK 80
           +  + SRRE++++I  + V ++GI     + NV +T   I V+G  +    +    L   
Sbjct: 2   KHLVLSRREMKKLIKNEAVLIDGIPATHVSNNVDATLQVITVNGTRIHDDSQKYYMLNKP 61

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
              + +  +D +  + +          +  +GRLD +TEGLLL+TN+G L   +  P   
Sbjct: 62  QGLI-SATTDKEHTTVIDLFANENVEGLYPLGRLDGDTEGLLLVTNNGPLGYRMLNPDQH 120

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
             + Y V  +G +D D +   K+G+   G        +T+     +    TV + EGK  
Sbjct: 121 IEKEYYVEVNGPLDNDAVETFKRGVTFHGGYQCKPSMLTIIESSDNLGRATVTISEGKFH 180

Query: 200 EIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           ++KK+F     KV  L RI +G F L   L  G  RE+++  L+
Sbjct: 181 QVKKMFLCVGVKVTYLKRIRFGEFVLDESLAPGEYRELNEAELQ 224


>gi|90416540|ref|ZP_01224471.1| probable pseudouridine synthase [marine gamma proteobacterium
           HTCC2207]
 gi|90331739|gb|EAS46967.1| probable pseudouridine synthase [marine gamma proteobacterium
           HTCC2207]
          Length = 278

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 80/278 (28%), Positives = 120/278 (43%), Gaps = 11/278 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+A AG+ SRRE+E+ I+  RV VNG + +       + D I VDG  ++    
Sbjct: 2   SEKLQKVLATAGLGSRRELEKWISAGRVSVNGSIAK-LGDRAAADDRILVDGRLIKIVTD 60

Query: 72  --RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + TT       +           R I++GRLDINT GLLL TN G 
Sbjct: 61  DSPRVLMYSKPEGEVCTTSDPDGRPTVFDRLPRLSRGRWIAIGRLDINTSGLLLFTNHGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ------K 183
           LA  L  PS +  R Y  R HG+VD+  +  L  G+V++        V            
Sbjct: 121 LANRLMHPSYEVQREYMARIHGEVDEAMIKRLTDGVVLEDGLASFKSVKAQHARSSEDLG 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL-LAGSTREVSKKILR 242
           G N W  V L EG+ RE+++++E  + +VNRL RISYGP +L ++       E+  K + 
Sbjct: 181 GRNRWFKVILAEGRTREVRRLWESQDVEVNRLKRISYGPIELPSIVRRSDFLELDPKQVV 240

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
                  L   +      +         +         
Sbjct: 241 SLFKAVALHPPRFTERHVLKDMRERKERKLRARGNTWK 278


>gi|90409123|ref|ZP_01217244.1| hypothetical ribosomal small subunit pseudouridine synthase A
           [Psychromonas sp. CNPT3]
 gi|90309774|gb|EAS37938.1| hypothetical ribosomal small subunit pseudouridine synthase A
           [Psychromonas sp. CNPT3]
          Length = 230

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 52/231 (22%), Positives = 98/231 (42%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  +   +R + +++I+Q R+  +  ++   A        I  DG  +      
Sbjct: 1   MRLDKTICESTTLTRSQAKKVISQGRITCDDKIIRSCAFKPRKDAVIVFDGKTIAIR-GP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP   + ++ D    S            +   GRLD +T GL L+T+DG  +  
Sbjct: 60  RYMMLNKPENFICSNVDEQLPSLFNLVDVDKKELLFIAGRLDADTTGLTLITDDGKWSHK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  + ++ YRV     + +D + L K GI +  +       ++ +     S+  V +
Sbjct: 120 ITSPRNKCIKRYRVGLDAPICEDAVALFKAGIQLKSENQPCLPAELNIL----SSTEVIL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++K++F      V  L R   G  +L   L  G  R ++ K +
Sbjct: 176 SISEGKYHQVKRMFGAIGNVVIELHREKIGDIELDNTLALGEWRYLTDKEV 226


>gi|306825646|ref|ZP_07458985.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
 gi|304432007|gb|EFM34984.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
          Length = 241

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 54/232 (23%), Positives = 106/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A+  I SR+ +++ + ++ + V+       + NV +    +   G  ++  E 
Sbjct: 1   MRLDRLLAQEKI-SRKAMKQALLKKEILVDECPARFLSQNVDTGLQKLVFQGRQIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L+     +  +            +      ++ ++GRLD +T GLLLLT++G L  
Sbjct: 60  NYLMLHKPNGVVTASRDKNLPTVMDLLSPDIQSDQIYAIGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   K+GIV           + + +   S++  T+
Sbjct: 120 QLLHPQYHVDKSYQVVVNGPLTPDHIQRFKEGIVFLDGTTCKPATLEILSSSPSSSQATI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++KK+F     KV  L R+ +G F L   L  G  R ++++ L 
Sbjct: 180 TISEGKFHQVKKMFFSVGVKVVSLKRVQFGDFTLDSELAEGQYRFLNQEELE 231


>gi|148981446|ref|ZP_01816412.1| hypothetical ribosomal small subunit pseudouridine synthase A
           [Vibrionales bacterium SWAT-3]
 gi|145960868|gb|EDK26199.1| hypothetical ribosomal small subunit pseudouridine synthase A
           [Vibrionales bacterium SWAT-3]
          Length = 229

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 49/230 (21%), Positives = 98/230 (42%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   ++ E    I    V VN   +   +  V  ++ I ++G  L      
Sbjct: 1   MRLDKYLCKSTDLTKSEAIERIHNGEVSVNSEFVLDESTQVHESNTILLNGDALTLRAFR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     + +   +       +  L  +    I+ GRLD +T GL+L+T+DG  +  
Sbjct: 61  YILMHKPAGTICSNIDEVYPSLFNYLELDKVSELHIA-GRLDADTTGLVLITDDGRWSFN 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           + LP+    +VYRV     +  D  +  K G+ +QG        ++ +     S   V +
Sbjct: 120 ITLPTKSCKKVYRVTLSRDIKDDVADKFKAGVPLQGEKNLTRPAELEVI----SPKEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + EGK  ++K++F     +V  L R   G  +L  +  G  R +++  +
Sbjct: 176 TITEGKFHQVKRMFAAVGNRVVGLHREQIGDVRL-DVEEGHWRYLTEDEV 224


>gi|198284085|ref|YP_002220406.1| pseudouridine synthase [Acidithiobacillus ferrooxidans ATCC 53993]
 gi|198248606|gb|ACH84199.1| pseudouridine synthase [Acidithiobacillus ferrooxidans ATCC 53993]
          Length = 268

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 60/228 (26%), Positives = 101/228 (44%), Gaps = 7/228 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM---STDHIEVDGVPLRKAER 72
           +++++++AG+ SR      I   RV+V+G  +               I +DG+ +  + R
Sbjct: 26  LARILSKAGLCSRTVAVEWIRAGRVEVDGRRILDPEARFPLSGPG--IRIDGLDITASTR 83

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L+     L T   +    +    +L      +  VGRLD  + GLLL +ND   A+
Sbjct: 84  QVLLLHKPRGVLTTRQDERGRATVY--DLLPGSPWLAPVGRLDQASSGLLLFSNDPHWAQ 141

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V+    +  D +  L    V+ G     MQ+      G   W+   
Sbjct: 142 RLLDPDQHVAKTYHVQIRPPLSTDTVVQLAADSVLDGEPCLPMQIRELRCGGKTQWLEFI 201

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           L+EG+NR+I+++    + +V RLIR++ G   LG L AG  R +    
Sbjct: 202 LQEGRNRQIRRLLAACDREVLRLIRVAVGNLPLGELRAGEWRWLHSGE 249


>gi|90577330|ref|ZP_01233141.1| hypothetical ribosomal small subunit pseudouridine synthase A
           [Vibrio angustum S14]
 gi|90440416|gb|EAS65596.1| hypothetical ribosomal small subunit pseudouridine synthase A
           [Vibrio angustum S14]
          Length = 231

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 50/235 (21%), Positives = 104/235 (44%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I ++   ++ E    I    + VN  ++   A  V  ++ + +DG  L   E  
Sbjct: 1   MRLDKFICKSTQLTKAEAIERIHDGDISVNDAVIINEATQVHESNTVIMDGKRLIAREFR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     + +   +       + ++ +     I+ GRLD +T G++L+T++G  +  
Sbjct: 61  YILMHKPAGTICSNIDEVYPSLFNYLDIENTAELHIA-GRLDADTTGMVLITDNGRWSFN 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P+ +  +VYRV    ++  D     K GI +QG         +T+ + K     V +
Sbjct: 120 ITSPNQKCSKVYRVGLSREIAADVAEKFKAGIKLQGEQKLTAPALLTVISAK----EVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            + EGK  ++K++F     +V  L R + G  +L  L  G  R +++  +   + 
Sbjct: 176 TITEGKFHQVKRMFAAVGNRVVSLHREAIGEVRL-DLEVGQWRYLTQDEVASFVR 229


>gi|291460666|ref|ZP_06600056.1| ribosomal large subunit pseudouridine synthase F [Oribacterium sp.
           oral taxon 078 str. F0262]
 gi|291416625|gb|EFE90344.1| ribosomal large subunit pseudouridine synthase F [Oribacterium sp.
           oral taxon 078 str. F0262]
          Length = 247

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 61/242 (25%), Positives = 103/242 (42%), Gaps = 18/242 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----- 68
            R++K ++  G+ SRRE +R IA+ RV++NG         V   D +E+DG  ++     
Sbjct: 1   MRINKCLSELGLCSRREADRWIAEGRVRLNGETA-EMGQQVEEKDRLELDGKLVKKAGKA 59

Query: 69  ----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                  R  L  Y     + +       ++ V   L +   RV  +GRLD ++EGL+LL
Sbjct: 60  VRAQAPRRVLLACYKPRGVVCSCSDKDRAKNIVE--LVNYPERVYPIGRLDKDSEGLILL 117

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVT---L 179
           TN G L   +        + Y V     + ++ L+ L  G+ +          +V     
Sbjct: 118 TNQGELVNRINRGGRN-EKEYVVTVDRPLTREALDRLADGVELSELNQKTRPCEVWQDLR 176

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                      + L +G NR+I+++ E   ++V RL R+     +L  L  G  RE+   
Sbjct: 177 LPPGRRQRQFHIVLSQGLNRQIRRMCEALGYEVKRLKRVRILSLRLEGLRPGEFREIGLS 236

Query: 240 IL 241
            L
Sbjct: 237 EL 238


>gi|167911508|ref|ZP_02498599.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 112]
          Length = 298

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 50  VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 109

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 110 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 169

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 170 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDG 229

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 230 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 285

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 286 QGEWRYLGPDE 296


>gi|84623687|ref|YP_451059.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|188576662|ref|YP_001913591.1| ribosomal large subunit pseudouridine synthase B [Xanthomonas
           oryzae pv. oryzae PXO99A]
 gi|84367627|dbj|BAE68785.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|188521114|gb|ACD59059.1| ribosomal large subunit pseudouridine synthase B [Xanthomonas
           oryzae pv. oryzae PXO99A]
          Length = 546

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 86/360 (23%), Positives = 137/360 (38%), Gaps = 24/360 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG         
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGTVAQT-GMSVRSGDKIELDGRSFVASALT 86

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + T        +          SR I++GRLDINT GLLLLT DG 
Sbjct: 87  EPSRVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR      ++      +  L +G++++       ++       
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV---SKKI 240
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + EV       
Sbjct: 207 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGQSVEVAQDKVDA 266

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEV----------PDDFTRMKKNSS 290
           LR +L       + + L   I                             D  R  +   
Sbjct: 267 LRAELKLEEGAPSALTLQPVIGQRRAAKSTVHVSRDGRSNAYVNGHTSGADEGRELRRFD 326

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                  +     P   +   +    A    S       +      R        +  R+
Sbjct: 327 NLREDRGRGGRGKPGDFKGGLTVSGEAAARQSQQRPFKQRGPAKGDRGALPEGNPAAFRS 386


>gi|217076810|ref|YP_002334526.1| ribosomal large subunit pseudouridine synthase B [Thermosipho
           africanus TCF52B]
 gi|217036663|gb|ACJ75185.1| ribosomal large subunit pseudouridine synthase B [Thermosipho
           africanus TCF52B]
          Length = 247

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 70/248 (28%), Positives = 117/248 (47%), Gaps = 2/248 (0%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + +     ++ K +   G A RR+ ++ I   RV VNG ++++   +V   D + +D   
Sbjct: 1   MLKGDEIIKLQKYLQMCGFA-RRKADQYIIAGRVTVNGKVVDKPWFDVKDDDIVMLDNKK 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L+  ++   ++ HKP G  TT  DP  + T+ + +  I + V   GRLD +  G+L+LTN
Sbjct: 60  LKINQKFEYYVLHKPKGYATTLYDPKQKKTIKELIKHIKTPVKPAGRLDKDATGVLILTN 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L  +L        + Y V+  G V  + L  LKKGI  +          +  +    
Sbjct: 120 DGKLIDILTNAKYGVKKEYIVKVSGSVSFNDLLKLKKGIYDERDFLKLEYFDILEKGFDY 179

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL-LAGSTREVSKKILREQL 245
           + + V L +GK  EIK++F+    KV  L RI++GP  +  +   G   ++  K L   L
Sbjct: 180 SIIKVVLIKGKKHEIKRLFKSIGHKVLELKRIAHGPISISIVPNEGDLTKLKGKDLERLL 239

Query: 246 GPHLLEEA 253
                EE 
Sbjct: 240 KLKKGEEK 247


>gi|167563192|ref|ZP_02356108.1| pseudouridine synthase family protein [Burkholderia oklahomensis
           EO147]
          Length = 321

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 73  VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 132

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y   + LVT  +   G  +     P     +   GRLDI++
Sbjct: 133 VTILLHKPVGYVSGQAEDGYAPAVTLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 192

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 193 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERMADIDQHFPAESLAKLRHGLELDG 252

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                  V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 253 APLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 308

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 309 QGEWRYLGPDE 319


>gi|170727748|ref|YP_001761774.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169813095|gb|ACA87679.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 239

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 55/238 (23%), Positives = 100/238 (42%), Gaps = 13/238 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRKAER 72
            R+ K + ++   +R E   +I   +V VNG  +   +  V   +HI ++ G  L     
Sbjct: 1   MRLDKFLCKSTQLTRHEACELILAGKVLVNGESVVSPSAQVHENNHIRLEGGQRLTARAS 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L+     L +           F NL       I+ GRLD +T GLLL+T+DG  + 
Sbjct: 61  RYIMLHKPADTLSSNVDGDHPSVFNFINLEHTSELHIA-GRLDADTTGLLLITDDGRWSF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDK--------LNLLKKGIVIQGICYGDMQVTLDTQKG 184
            +  P     +VYRV     ++ +             K+G+ +QG     +   L+    
Sbjct: 120 NVFNPKYHCEKVYRVYLRDSIEGEIAGEIDAELKARFKQGLDLQGEQALTLPAKLEFVSP 179

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
               V + + EG+  ++K++F     +VN L R   G  +L  +  G  R ++++ + 
Sbjct: 180 K--EVLLTITEGRYHQMKRMFARVGNRVNALHREQVGKIKL-DMPVGQWRYLTREEID 234


>gi|254457105|ref|ZP_05070533.1| RNA pseudouridylate synthase family protein [Campylobacterales
           bacterium GD 1]
 gi|207085897|gb|EDZ63181.1| RNA pseudouridylate synthase family protein [Campylobacterales
           bacterium GD 1]
          Length = 263

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 71/263 (26%), Positives = 117/263 (44%), Gaps = 17/263 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R++K IA     SRRE ++ I    V++NG + +  A  V    D + V G  +   ++
Sbjct: 3   MRLNKYIAHHSSYSRREADKAILDGYVRINGEIQDNPATQVDEKDDIVYVSGKQITPKDK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +Y+KP G + T SDP GR T++D L   +   I VGRLD  TEG+LLLT+   +A 
Sbjct: 63  YTVIVYNKPKGELVTKSDPKGRRTIYDGLEKKYKHYIPVGRLDYATEGVLLLTDASKIAS 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQVT 178
            L        R+Y+V+  G+V  +    +  G+ +                     +   
Sbjct: 123 ALMNS--NLERIYKVKIKGEVTPEIEAAMMNGLELLDATAGGHSHSKVTSMTFAPFLGYK 180

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +   + + + + + + EG+NREI++ F  F  +V  L RIS+   +L  L  G  R +S+
Sbjct: 181 IQKNEHNYSVLKIAISEGQNREIRRFFAHFGTEVADLKRISFAEVELNNLPTGKVRFLSR 240

Query: 239 KILREQLGPHLLEEAQVNLDAPI 261
                       EE         
Sbjct: 241 SEYSALFTFMKAEEKLAREKGKK 263


>gi|327458771|gb|EGF05119.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1057]
          Length = 241

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 102/232 (43%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++ + Q+++ V+G    + + NV      I   G  +     
Sbjct: 1   MRLDQLLA-ANHISRKKMKQSLLQKQILVDGKPACKLSQNVDIGLQQITFQGKHVSGPAH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +               +       + S+GRLD +TEGLLL+T++G L  
Sbjct: 60  RYYMLNKPAGAVTANRDAEKLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V  +G +        ++GI  + G      Q+++ +   S +  TV
Sbjct: 120 QLLHPQYHVEKTYYVEVNGPLTSQDKIAFQEGIRFLDGTICQPAQLSILSSSSSLSRATV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L  G  R ++++ L 
Sbjct: 180 KISEGKFHQIKKMFLAVGVKVIYLKRIQFGDFTLDPDLAKGDYRALNQEELE 231


>gi|320535214|ref|ZP_08035340.1| hypothetical protein HMPREF9554_00054 [Treponema phagedenis F0421]
 gi|320147952|gb|EFW39442.1| hypothetical protein HMPREF9554_00054 [Treponema phagedenis F0421]
          Length = 259

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 55/237 (23%), Positives = 109/237 (45%), Gaps = 9/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            RV K++A  G  SR++V   + +    +NG+     A ++  T D + V+G+ ++    
Sbjct: 1   MRVDKILASNGYGSRKDVRVFLKKNNCCINGVRCINPAQHIDPTKDTVTVNGISVQLRTS 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L+     + +T          F   P     +  +GRLDI+TEGLL++TNDG L  
Sbjct: 61  VYIMLHKPAGCVSSTKDPIHKTVMDFLPAPFNAMDLFPIGRLDIDTEGLLIITNDGNLTH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-----VIQGICYGDM--QVTLDTQKGS 185
            +  P +  ++ Y +     + + +++   + +     +  G        ++T +    +
Sbjct: 121 SITAPKSNCVKTYYLELERPLTETEIHNFTEKLAQGILLHTGYTCLPAALELTENIHTKN 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
                + + EGK  +IKK+   F  K+  L R+S    +L  +L AG+ RE++ + +
Sbjct: 181 AQAFLIHITEGKYHQIKKMCTAFGVKLTYLKRVSMAGLELDPSLAAGNCRELTSEEI 237


>gi|319947493|ref|ZP_08021725.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           australis ATCC 700641]
 gi|319746433|gb|EFV98694.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           australis ATCC 700641]
          Length = 240

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 51/232 (21%), Positives = 98/232 (42%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A   I  R+E+++ +A++++ V+G+   + + NV +    +      L     
Sbjct: 1   MRLDQLLAHYQI-PRKEIKQSLAKRQILVDGLAATKLSQNVDTGLQEVRWKDQVLTDCSH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +  T                   +   +GRLD +T GLLLLT++G L  
Sbjct: 60  HYFLLHKPQGLVTATKDAQHSTVLDLLRTEDRTPKTYPIGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y    +G ++   +   ++GI           ++ + +   + +   V
Sbjct: 120 QLLHPQYHIEKEYAATVNGPLEPAHIEKFQEGITFLDGTTCKPAKLEILSSSLTESQALV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            L EGK  ++KK+      KV  L RI +G F L   L  G  R +++  L+
Sbjct: 180 TLSEGKFHQVKKMLLSVGVKVTSLKRIKFGDFSLDPNLAEGQYRPLNQDELQ 231


>gi|307710882|ref|ZP_07647309.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           mitis SK321]
 gi|307617327|gb|EFN96500.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           mitis SK321]
          Length = 220

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 58/217 (26%), Positives = 93/217 (42%), Gaps = 4/217 (1%)

Query: 34  MIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPD 92
           M+   RV VNG   + A + +    D I +DG  L   E     +      +  T     
Sbjct: 1   MLKAGRVTVNGKKEKSAKLQIDEERDEIRLDGQVLEYEEFVYYMMNKPQGVISATEDPKH 60

Query: 93  GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152
                  +  +    V  VGRLDI+T GLLLLTNDG LA  L  P     + Y  +  G 
Sbjct: 61  RTVLDLLDDLARTKEVFPVGRLDIDTHGLLLLTNDGQLAHALLSPKRHVDKTYLAQVKGI 120

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTVGLREGKNREIKKVFEFFNW 210
           + Q+ +    KGI ++       ++ L +     + + + V + EGK  ++K++  +   
Sbjct: 121 MTQEDVETFAKGIPLKDFTCQPARLELVSIDTAKNQSQIRVTIAEGKFHQVKRMVAYCGK 180

Query: 211 KVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           +V  L R++ G   L   L  G  R ++K+ L   L 
Sbjct: 181 EVVDLQRLTMGTLMLDENLQRGEWRRLTKEELENLLA 217


>gi|148244476|ref|YP_001219170.1| ribosomal large subunit pseudouridine synthase B [Candidatus
           Vesicomyosocius okutanii HA]
 gi|146326303|dbj|BAF61446.1| ribosomal large subunit pseudouridine synthase B [Candidatus
           Vesicomyosocius okutanii HA]
          Length = 241

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 86/233 (36%), Positives = 128/233 (54%), Gaps = 7/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK----A 70
           R+ K+IA AG  SRR VER+I Q R++VN  +          T  +++DG  +       
Sbjct: 4   RLQKLIANAGYGSRRWVERLIEQGRIEVNNKIA-IIGDKTEITSLVKIDGRKINLSRYVE 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + T++ + +K  G++ ++ D  GR +V+  LP      I VGRLD+NT GLLL+TN+G L
Sbjct: 63  QETKVIILNKQAGVICSNRDDKGRKSVYSLLPKESRW-IMVGRLDLNTSGLLLVTNNGDL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS++  R Y VR  GQV    L  L +G+V         Q+T    KG+N W  
Sbjct: 122 ANKLMHPSSEIDREYAVRVLGQVKNKDLKKLTQGVVFDDGFSKFNQITFSGGKGANRWYK 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           V LREGK RE+++++E   +KV+RLIRI +G  +L   L A     +    ++
Sbjct: 182 VVLREGKKREVRRLWEVLGFKVSRLIRIRFGEIRLPDNLKANQYDYLKTVQIK 234


>gi|124268226|ref|YP_001022230.1| ribosomal small subunit pseudouridine synthase A [Methylibium
           petroleiphilum PM1]
 gi|124261001|gb|ABM95995.1| ribosomal small subunit pseudouridine synthase A [Methylibium
           petroleiphilum PM1]
          Length = 233

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 50/228 (21%), Positives = 90/228 (39%), Gaps = 3/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAER 72
            R+S+V+   G  +RR+   +I    V+V G +++     + + D +  V G      ++
Sbjct: 1   MRISQVLFSQGFGTRRDCAGLIHAGAVEVAGRVVDDPDEELPTEDLVFSVQGRAWPFHDK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L+       +               P     +  VGRLD +T G LLLT+DG L  
Sbjct: 61  ALVLLHKPTHYECSQKPRHHPGVLSLLPTPLRVRGLQPVGRLDEDTTGALLLTDDGTLIH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VY +     +  +++  L +G+V+       ++     + G    + + 
Sbjct: 121 RLTSPKHHVPKVYEITAKHALADEQIARLTEGVVLDDDP-QPVRAAAAERTG-EFTLRLT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           L EGK  ++K++      +   L R   G   L  L  G  R V    
Sbjct: 179 LTEGKYHQVKRMLAAVGNRCEALHRSRIGALALDDLPVGQWRWVGPDE 226


>gi|307708856|ref|ZP_07645316.1| conserved hypothetical protein [Streptococcus mitis SK564]
 gi|307620192|gb|EFN99308.1| conserved hypothetical protein [Streptococcus mitis SK564]
          Length = 241

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 56/231 (24%), Positives = 104/231 (45%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  + SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKV-SRKAMKQALLKGDILVDGCPARSLAQNIDTGLQELLFQEQIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                      ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKELPTVMDLLPPDIQSDKLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + YRV  +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYRVEVNGLLTLDHIQAFQKGIVFLDGTICKPARLEILSASPSLSQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++KK+F     KV  L R  +GP+ L   L AG  R ++ + L
Sbjct: 180 TISEGKFHQVKKMFLSVGVKVTSLKRTHFGPWSLDENLQAGDYRPLNSEEL 230


>gi|241662183|ref|YP_002980543.1| pseudouridine synthase [Ralstonia pickettii 12D]
 gi|240864210|gb|ACS61871.1| pseudouridine synthase [Ralstonia pickettii 12D]
          Length = 248

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 51/237 (21%), Positives = 87/237 (36%), Gaps = 3/237 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-VDGVPLRKAERTR 74
           + +++   G  +RR  + ++    V +NG+ +E     V +   +  VDG       R  
Sbjct: 9   LYRILQSQGFGTRRYCKDLVLAGLVCINGVEMESPDALVDTAGLVLDVDGERWAYHARAY 68

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L        +              +P     V  VGRLD +T GLLLLT+DG     +
Sbjct: 69  LMLNKPAGVECSQKPKHHPSVYTLLPVPLRERAVQCVGRLDQDTTGLLLLTDDGQFVHTI 128

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  Q  +VY +     V + ++  L  G+++            +        + + L 
Sbjct: 129 TSPRHQVPKVYEITTAEPVTEAQIAQLCAGVLLADENENVAAAWAERV--GTHHLRMALT 186

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
           +GK  ++K++       V  L R + G   LG L  G  R +    L          
Sbjct: 187 QGKYHQVKRMVAAAGNHVVGLHRSAIGGLSLGDLAPGEWRWLEAADLEALNTTPPHA 243


>gi|312879945|ref|ZP_07739745.1| RNA-binding S4 domain protein [Aminomonas paucivorans DSM 12260]
 gi|310783236|gb|EFQ23634.1| RNA-binding S4 domain protein [Aminomonas paucivorans DSM 12260]
          Length = 242

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 72/232 (31%), Positives = 110/232 (47%), Gaps = 1/232 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   QR+++ +AR G+ASRR+ E +I   RV++NG ++   AV V   D +EVDG P+  
Sbjct: 2   SEDSQRLNQYLARCGVASRRKAEALILGGRVRLNGCVVLDLAVRVQGEDRVEVDGEPVLP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L L+     L       +              R   VGRLD ++EGLLLLTNDG 
Sbjct: 62  RVALYLVLHKPRGVLSAVEDRREQTVVDLLPSRFRPERPFPVGRLDKDSEGLLLLTNDGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A+ L  PS   ++ Y V+    +  +    + +G+  +G     + +          W 
Sbjct: 122 FAQRLLHPSAGIVKSYEVQLDRPLAPEHRERMLEGLWSEGEFLRPLSIRSLGV-PDRRWT 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              L EGK REI+++   F + V RLIR   G  +L  L  G  +E+S + L
Sbjct: 181 VFDLVEGKKREIRRLAALFEYGVLRLIRRRVGKLELRRLETGVAQELSGEAL 232


>gi|212633763|ref|YP_002310288.1| pseudouridine synthase Rsu [Shewanella piezotolerans WP3]
 gi|212555247|gb|ACJ27701.1| Pseudouridine synthase, Rsu [Shewanella piezotolerans WP3]
          Length = 233

 Score =  144 bits (362), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 65/244 (26%), Positives = 107/244 (43%), Gaps = 16/244 (6%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+ K          R+ + I+     SR+ V  ++A+  VKV+G +       V    HI
Sbjct: 1   MESKRA--------RLDRFISATKRVSRKHVRVLLAKGLVKVDGEIARDIDQIVDEFSHI 52

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            ++G  L+      L L+     +V+   D   ++ +         ++  VGRLD+NT G
Sbjct: 53  TLEGEVLQANTPIYLMLHKPVG-VVSATVDDKHKTVIDLLSHPDKQQLHIVGRLDLNTSG 111

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVT 178
           LLLLTNDG  ++ L  P  +  ++YRV     +D   +    +      + I     ++ 
Sbjct: 112 LLLLTNDGRWSKRLMSPEHKVAKLYRVSLENPIDASYIQAFHEGMYFEFEDITTLPAKLE 171

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVS 237
           +           V L EG+  +IK++F  F   V  L RIS G   L + LLAG +R +S
Sbjct: 172 IV----DPHTALVTLMEGRYHQIKRMFGRFRNPVIGLHRISVGEIVLDSQLLAGQSRVLS 227

Query: 238 KKIL 241
              +
Sbjct: 228 TAEI 231


>gi|307824285|ref|ZP_07654511.1| RNA-binding S4 domain protein [Methylobacter tundripaludum SV96]
 gi|307734665|gb|EFO05516.1| RNA-binding S4 domain protein [Methylobacter tundripaludum SV96]
          Length = 279

 Score =  144 bits (362), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 80/270 (29%), Positives = 124/270 (45%), Gaps = 7/270 (2%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            ++   +R+ KV+AR G+ SRRE+ER I + R+K+NG  +      + + DH+ ++   +
Sbjct: 11  NQSVDGERIQKVLARGGVGSRREIERWIDEGRLKINGKPV-GLGDRLKAGDHLLINDRVV 69

Query: 68  RK-----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
                       L  +     +VT                   SR I+VGRLDINT GLL
Sbjct: 70  HWEKFVEQPTRVLLYHKPVGEVVTRRDPEGRPVVFTQLPKLAISRWIAVGRLDINTSGLL 129

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L+TN+G LA  L  PSTQ  R Y VR  G+V    L  LK+G+ ++        +     
Sbjct: 130 LVTNNGELANRLMHPSTQVEREYAVRILGEVSDATLAKLKQGVELEDGKAKFDDIIFFGG 189

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           +G+N W  V + EG+NR +++++E     V+RL+R+ YGP  L   L   S  E++ K L
Sbjct: 190 EGANKWYNVIVAEGRNRLVRRLWESQELIVSRLMRVRYGPVVLPERLKTHSFYELTDKEL 249

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDR 271
                   +   +                R
Sbjct: 250 ELLFEFAGMAGEKPVHITKPEVKAHKSGKR 279


>gi|313682886|ref|YP_004060624.1| ribosomal small subunit pseudouridine synthase a [Sulfuricurvum
           kujiense DSM 16994]
 gi|313155746|gb|ADR34424.1| ribosomal small subunit pseudouridine synthase A [Sulfuricurvum
           kujiense DSM 16994]
          Length = 234

 Score =  144 bits (362), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 56/229 (24%), Positives = 97/229 (42%), Gaps = 4/229 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K+++  G  SRREV  +I +  +     L  ++   V   D I  +G PL   +   
Sbjct: 6   RLDKLLSSLGYCSRREVALLIREGIITHAHNLPLKSDTKVS-HDEILCEGEPLDPPQGIV 64

Query: 75  LWLYHKPIGLVTTHSDPDG--RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++     + +            + +       ++ +VGRLD +T GLLLLT+DG L  
Sbjct: 65  ILMHKPAGLVCSHDDGEGKLVYDLLPERWRLRDPKISTVGRLDKDTSGLLLLTDDGALLH 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  +VY  R    +  D+  +   G ++             T       VT+ 
Sbjct: 125 RLTSPKHKVPKVYEARLDRALKGDEAEIFASGTLMLNGEKTPCLPAKLTVIDDTH-VTLE 183

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EG+  +++++F      V  L R S+G   LG L AG  R +  + L
Sbjct: 184 IVEGRYHQVRRMFAAVGNHVTALHRCSFGTLTLGDLKAGEYRLIDAQSL 232


>gi|58581784|ref|YP_200800.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae KACC10331]
 gi|58426378|gb|AAW75415.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae KACC10331]
          Length = 566

 Score =  144 bits (362), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 86/360 (23%), Positives = 137/360 (38%), Gaps = 24/360 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG         
Sbjct: 48  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGTVAQT-GMSVRSGDKIELDGRSFVASALT 106

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + T        +          SR I++GRLDINT GLLLLT DG 
Sbjct: 107 EPSRVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 166

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR      ++      +  L +G++++       ++       
Sbjct: 167 LANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGGAKFDEIERIGGTD 226

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV---SKKI 240
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + EV       
Sbjct: 227 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGQSVEVAQDKVDA 286

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEV----------PDDFTRMKKNSS 290
           LR +L       + + L   I                             D  R  +   
Sbjct: 287 LRAELKLEEGAPSALTLQPVIGQRRAAKSTVHVSRDGRSNAYVNGHTSGADEGRELRRFD 346

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                  +     P   +   +    A    S       +      R        +  R+
Sbjct: 347 NLREDRGRGGRGKPGDFKGGLTVSGEAAARQSQQRPFKQRGPAKGDRGALPEGNPAAFRS 406


>gi|154248736|ref|YP_001409561.1| pseudouridine synthase [Fervidobacterium nodosum Rt17-B1]
 gi|154152672|gb|ABS59904.1| pseudouridine synthase [Fervidobacterium nodosum Rt17-B1]
          Length = 265

 Score =  144 bits (362), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 62/228 (27%), Positives = 101/228 (44%), Gaps = 3/228 (1%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            I  +     ++ K +   G A RR+ +  I  +RV VNG  ++     V   D++ VDG
Sbjct: 17  KISLKGDENIKLQKYLQLCGFA-RRKADEYITSKRVIVNGKTVDEPWFEVNEDDNVLVDG 75

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L+  +     L+     + T         T+ + +  I + +   GRLD +  G+L+L
Sbjct: 76  KILKPNQFEYYVLHKPKDYVTTLFDPKQK-KTIGELIKHIKTPLKPAGRLDKDATGVLIL 134

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG L  +L     +  + Y V+    V  ++L  LKKGI  +G         +  +  
Sbjct: 135 TNDGELIDILTNAKYRVKKEYIVKVKSVVSAEELVKLKKGIYDKGEFLKLEHFKIIEKSS 194

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
             + V V L +GK  EIK++F      V  L RIS+GP  +  L+   
Sbjct: 195 EYSIVRVELIKGKKHEIKRLFSSIGHNVLELKRISHGPISIS-LVPNE 241


>gi|294666869|ref|ZP_06732101.1| Pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 10535]
 gi|292603386|gb|EFF46805.1| Pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 10535]
          Length = 286

 Score =  144 bits (362), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 112/247 (45%), Gaps = 7/247 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      +       I VDG PL    R 
Sbjct: 39  LARVLSKLGVCSRTEAARWIADGRVSVSARVVRDPEFPIRGDQQSSIAVDGQPLAGLARC 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L      + T   +    +       +    +  VGRLD  +EGLLL +ND   A  
Sbjct: 99  YLMLNKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAAA 158

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNAW 188
           +  P+T   + Y V+   +    +L  L+ G+V      QG+     QV++  +   NAW
Sbjct: 159 VTDPATGPDKTYHVQIDCRPSAAQLAQLQAGVVDPDPQGQGVLLRAKQVSVLREGERNAW 218

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + + L EG+NR+I+++    +  V RL+R++ GP  +G L   + R +S + +   +   
Sbjct: 219 LEIVLDEGRNRQIRRLVAAVDIGVLRLVRVAIGPLAMGELGKSAWRMLSAEEVSALVPAA 278

Query: 249 LLEEAQV 255
                  
Sbjct: 279 HASAPDA 285


>gi|291320012|ref|YP_003515270.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           agalactiae]
 gi|290752341|emb|CBH40312.1| Ribosomal large subunit pseudouridine synthaseB [Mycoplasma
           agalactiae]
          Length = 246

 Score =  144 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 105/247 (42%), Gaps = 11/247 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               RV K+IA++G+ SRR+ E+MI++  V VNG +           D I+V+G  +   
Sbjct: 2   PELVRVQKLIAQSGLMSRRDAEKMISKGLVFVNG-IKSSIGDKASINDEIKVNGKIINLT 60

Query: 71  ERT---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           + T      L      + T+       + +  +L +   R++ VGRLD NT G+LLLT D
Sbjct: 61  KNTVFKYYLLNKPKNTITTSKDPKGRHTVI--DLINTSERIVPVGRLDRNTTGVLLLTTD 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
             L   L  P  +  RVYR R    +   +   L  GI I G             +    
Sbjct: 119 YELVNKLTHPKYEIERVYRARIDSPLTLKEFKELNAGIEIDGKM-----SYQIVDQVDTK 173

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L  G    +KK+FE     V  L R+SY    +  L  G  RE++ K ++     
Sbjct: 174 SYLISLHVGSYHHVKKLFEKIGHSVLTLKRVSYANLTVDKLPEGMYRELTIKEVKNLKLL 233

Query: 248 HLLEEAQ 254
              +E +
Sbjct: 234 VEQQEKK 240


>gi|169633279|ref|YP_001707015.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter baumannii SDF]
 gi|169152071|emb|CAP00958.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter baumannii]
          Length = 234

 Score =  144 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 48/226 (21%), Positives = 91/226 (40%), Gaps = 3/226 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V ++G ++          +    V G   +  E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVSIDGEVVSDLKKQFSPENFEFSVFGQNYQYREKIY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        + H               I   V +VGRLD +T GLLLLT+DG   +VL
Sbjct: 63  IALRKPQGFECSHHPQHHQSVFSLLPETMIHRGVQAVGRLDQDTTGLLLLTDDGKYLQVL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     +VY V  +  V  +++ +L +G+ +           +         +T+ + 
Sbjct: 123 THPRKHVPKVYHVTTYDPVTPEQIEMLIQGVNLHQEKEVFAATDVALL--GTHQLTMTIH 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +G   ++K++      KV +L R   G   L  +  G    +S++ 
Sbjct: 181 QGVYHQVKRMIAAVGNKVEKLHRHQIGQLVLPEIEDGDWVYLSEQE 226


>gi|254785989|ref|YP_003073418.1| ribosomal small subunit pseudouridine synthase A [Teredinibacter
           turnerae T7901]
 gi|237683937|gb|ACR11201.1| ribosomal small subunit pseudouridine synthase A [Teredinibacter
           turnerae T7901]
          Length = 238

 Score =  144 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 51/237 (21%), Positives = 97/237 (40%), Gaps = 12/237 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     SR +V  ++  +R++VNG      +  + S D + +D  PL+     
Sbjct: 1   MRLDKFVADNTSYSRSQVRGLLKAKRIRVNGQTALAPSAALKSDDEVTLDDAPLQARSDV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-----ISVGRLDINTEGLLLLTNDG 128
            L L+     +                  + +S          GRLD++T GL+L+T+DG
Sbjct: 61  YLMLHKPAGYVCANTDAEHPTVFDLPGFSARYSNADIARLQIAGRLDLDTTGLVLITSDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSN 186
                +  P  +  + Y V     +  +  +   +G+++ G        ++ L +   +N
Sbjct: 121 QWNHRITSPRQKCRKAYYVECAAPIAAETKSAFAEGVLLHGEKRPTLPAELELLSANTAN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
               + + +G   ++K++F     KV RL R   G   L   LL G  R ++   +R
Sbjct: 181 ----LYIEQGIYHQVKRMFASTGNKVLRLHRFQIGALALETDLLPGDMRALTSDEIR 233


>gi|218667427|ref|YP_002426740.1| RNA pseudouridine synthase family protein [Acidithiobacillus
           ferrooxidans ATCC 23270]
 gi|218519640|gb|ACK80226.1| RNA pseudouridine synthase family protein [Acidithiobacillus
           ferrooxidans ATCC 23270]
          Length = 264

 Score =  144 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 60/228 (26%), Positives = 101/228 (44%), Gaps = 7/228 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM---STDHIEVDGVPLRKAER 72
           +++++++AG+ SR      I   RV+V+G  +               I +DG+ +  + R
Sbjct: 22  LARILSKAGLCSRTVAVEWIRAGRVEVDGRRILDPEARFPLSGPG--IRIDGLDITASTR 79

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L+     L T   +    +    +L      +  VGRLD  + GLLL +ND   A+
Sbjct: 80  QVLLLHKPRGVLTTRQDERGRATVY--DLLPGSPWLAPVGRLDQASSGLLLFSNDPHWAQ 137

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V+    +  D +  L    V+ G     MQ+      G   W+   
Sbjct: 138 RLLDPDQHVAKTYHVQIRPPLSTDTVVQLAADSVLDGEPCLPMQIRELRCGGKTQWLEFI 197

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           L+EG+NR+I+++    + +V RLIR++ G   LG L AG  R +    
Sbjct: 198 LQEGRNRQIRRLLAACDREVLRLIRVAVGNLPLGELRAGEWRWLHSGE 245


>gi|187927714|ref|YP_001898201.1| pseudouridine synthase [Ralstonia pickettii 12J]
 gi|187724604|gb|ACD25769.1| pseudouridine synthase [Ralstonia pickettii 12J]
          Length = 248

 Score =  144 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 51/229 (22%), Positives = 88/229 (38%), Gaps = 3/229 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-VDGVPLRKAERTR 74
           + +++   G  +RR  + ++    V +NG+ +E     V +   +  VDG       R  
Sbjct: 9   LYRILQSQGFGTRRYCKDLVLAGLVFINGVEMESPDALVDTAGLVLDVDGERWAYHARAY 68

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L        +              +P     V  VGRLD +T GLLLLT+DG     +
Sbjct: 69  LMLNKPAGVECSQKPKHHPSVYTLLPVPLRERAVQCVGRLDQDTTGLLLLTDDGQFVHTI 128

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  Q  +VY +     V + ++  L  G+++            +        + + L 
Sbjct: 129 TSPRHQVPKVYEITTAEPVTEAQIAQLYAGVLLADENENVAAAWAERVD--THHLRMALT 186

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           +GK  ++K++       V+ L R + G   LG L  G  R +    L  
Sbjct: 187 QGKYHQVKRMVAAAGNHVDGLHRSAIGGLSLGDLAPGEWRWLEAADLEA 235


>gi|224826005|ref|ZP_03699108.1| pseudouridine synthase [Lutiella nitroferrum 2002]
 gi|224601642|gb|EEG07822.1| pseudouridine synthase [Lutiella nitroferrum 2002]
          Length = 236

 Score =  144 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 56/231 (24%), Positives = 100/231 (43%), Gaps = 5/231 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRKAERT 73
           + +++ + G  SR+E  +++    V+++G +++   + +     D + +DG P       
Sbjct: 3   LYRLMQQQGFGSRKECRKLVEHGLVELDGAVVDDYRLEIDPAAIDELVIDGEPWEILMLP 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLAR 132
              L HKP G  T+H      S             I+ VGRLD++T GLLLLT DG    
Sbjct: 63  LYILLHKPAGYETSHKPMHNPSVFTLLPWQFSQLGIAAVGRLDVDTTGLLLLTTDGQFVH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V     V +  +  LK G+ ++      +   ++        + + 
Sbjct: 123 ALTSPKKHVPKCYEVTLKHPVSEALVKHLKAGVFLKDDNEKVVADQVEVVD--EITIRMT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + +GK  ++K++      +V  L R++ G  QLG L  G  R +    L E
Sbjct: 181 ITQGKYHQVKRMIAAAGNRVQELHRVALGTLQLGELDEGEWRHLDAAELAE 231


>gi|162447734|ref|YP_001620866.1| rRNA pseudouridylate synthase [Acholeplasma laidlawii PG-8A]
 gi|161985841|gb|ABX81490.1| rRNA pseudouridylate synthase [Acholeplasma laidlawii PG-8A]
          Length = 238

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 111/232 (47%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+SKVIA+AG ASRR+ E +I + +VKVN  ++      V   D I V+G PL K    
Sbjct: 2   ERLSKVIAQAGCASRRKAENLITEGKVKVNDEVINVLGYKVSPKDIITVEGKPLVKEPLV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLAR 132
              L      L TT      R+ +   L    +     + +L+ +T GLLL+TNDG L +
Sbjct: 62  YYLLNKPTGYLSTTADIHKRRNILDLILKEDQNVRLFPIHKLEYDTSGLLLVTNDGELTK 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            L   S    + Y +R  G + ++++  +K+GI ++      + + +     ++    V 
Sbjct: 122 KLTSQSESIQKEYVIRTKGIMIKERIREIKRGIKVENKIIKPVDIAIVELDKAHQSTLVK 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + +     +E+K +F+    +V  + RI +    L  +  GS R++    ++
Sbjct: 182 MIITNESAKELKTMFKQLGHEVKNMTRIRFDSLTLEGVNRGSYRKLKSHEVK 233


>gi|193077698|gb|ABO12547.2| 16S rRNA pseudouridylate 516 synthase [Acinetobacter baumannii ATCC
           17978]
          Length = 234

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 48/226 (21%), Positives = 91/226 (40%), Gaps = 3/226 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V ++G ++          +    V G   +  E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVIIDGEVVSDLKKQFSPENFEFSVFGQNYQYREKIY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        + H               I   V +VGRLD +T GLLLLT+DG   + L
Sbjct: 63  IALRKPQGFECSHHPQHHQSVFSLLPETMIHRGVQAVGRLDQDTTGLLLLTDDGKYLQAL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     +VY V  +  V  +++ +L +G+ +     G     +         +T+ + 
Sbjct: 123 THPRKHVPKVYHVTTYDPVTPEQIEMLTQGVNLHQEKGGFAATDVALL--GTHQLTMTIH 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +G   ++K++      KV +L R   G   L  +  G    +S++ 
Sbjct: 181 QGVYHQVKRMIAAVGNKVEKLHRHQIGQLVLPEIEEGGWVYLSEQE 226


>gi|239814633|ref|YP_002943543.1| pseudouridine synthase [Variovorax paradoxus S110]
 gi|239801210|gb|ACS18277.1| pseudouridine synthase [Variovorax paradoxus S110]
          Length = 249

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 52/249 (20%), Positives = 91/249 (36%), Gaps = 11/249 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  +RR    ++ Q  V + G  +     ++   D +  V G      E+  
Sbjct: 3   LQDILYSQGFGTRRVCAGLVQQGHVSIAGAAVTDPFADLDPEDLLFTVQGTEWAYHEKAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGR-------STVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           L L+       +                            V ++GRLD +T GLLLLT+D
Sbjct: 63  LMLHKPAGTECSQKPSTYPSIYTLLPSPLRLRPNKGAVQGVQAIGRLDQDTTGLLLLTDD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G     +  P     +VY V     VD  ++  L  G+V+       ++     +  S  
Sbjct: 123 GQFIHKMGSPKHHVPKVYEVTAKHPVDAAQIEKLLAGVVLDDDP-KPVR-AAACESDSPL 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
            + + L EGK  ++K++      +V  L R   G   L G L AG  R ++ + +     
Sbjct: 181 HLRLTLTEGKYHQVKRMLAAVGNRVEGLHRSRIGDLALPGDLAAGQWRWLTAEQVAALRA 240

Query: 247 PHLLEEAQV 255
           P    +   
Sbjct: 241 PAKPPKTPK 249


>gi|153814849|ref|ZP_01967517.1| hypothetical protein RUMTOR_01064 [Ruminococcus torques ATCC 27756]
 gi|317500363|ref|ZP_07958587.1| hypothetical protein HMPREF1026_00530 [Lachnospiraceae bacterium
           8_1_57FAA]
 gi|331089629|ref|ZP_08338528.1| hypothetical protein HMPREF1025_02111 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|145847880|gb|EDK24798.1| hypothetical protein RUMTOR_01064 [Ruminococcus torques ATCC 27756]
 gi|316898118|gb|EFV20165.1| hypothetical protein HMPREF1026_00530 [Lachnospiraceae bacterium
           8_1_57FAA]
 gi|330404997|gb|EGG84535.1| hypothetical protein HMPREF1025_02111 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 261

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 60/259 (23%), Positives = 109/259 (42%), Gaps = 29/259 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +   G  +R +V++ I +  V VNG + ++A   V    D I   G  +  A   
Sbjct: 4   RLDKYLTEMGCGTRSQVKKEILKGSVSVNGEIAKKAERKVDTEKDEIIFKGEKIFYAGYE 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      +V+   D   R+ +     S    +   GRLD +TEGLLL+TNDG LA  
Sbjct: 64  YFMLNKPAG-VVSATEDKKERTVIDLIKESKRKDLFPAGRLDKDTEGLLLITNDGQLAHR 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDM----------------- 175
           L  P     ++Y  +  G V ++ + L +KG+ I                          
Sbjct: 123 LLSPKKHVDKIYYAKIKGIVTEEDVRLFEKGVHIGDEKPTMPAALEILSVQKERRKEKIK 182

Query: 176 --------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG- 226
                   +   D ++   + + + ++EG+  ++K++F     +V  L RI +G   L  
Sbjct: 183 EQKILPETKNETDEKEDGYSEIYLTIKEGRFHQVKRMFRAVGKEVVYLKRIQFGTLTLDP 242

Query: 227 TLLAGSTREVSKKILREQL 245
           +L  G  R+++++ + +  
Sbjct: 243 SLKPGQYRKLTEEEVEQLC 261


>gi|157149724|ref|YP_001449971.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           gordonii str. Challis substr. CH1]
 gi|157074518|gb|ABV09201.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           gordonii str. Challis substr. CH1]
          Length = 241

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 51/232 (21%), Positives = 99/232 (42%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A+A I SR+ ++R + +  + ++       + NV +    I  D   +     
Sbjct: 1   MRLDRLLAQASI-SRKSMKRALLRGAILIDQTPARSLSQNVDTGLQEILFDKQKVPAPAH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +                       + S+GRLD +T GLLL+T++G L  
Sbjct: 60  RYFMMNKPRGYITANSDASKETVIDLIQKEDYSGELYSIGRLDRDTTGLLLITDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V+ +G ++   +   ++G+           Q+T+ +     +  +V
Sbjct: 120 QLLHPQYHVDKTYYVQVNGLLNNQAIEAFQQGVRFLDGKVCKPAQLTIHSTTPVLSTASV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++KK+F     KV  L R  +G FQL  +L  G  R +++  L+
Sbjct: 180 TISEGKFHQVKKMFLAIGVKVTYLKRTHFGDFQLDPSLAEGDYRSLNQDELK 231


>gi|298488650|ref|ZP_07006680.1| Ribosomal small subunit pseudouridine synthase A [Pseudomonas
           savastanoi pv. savastanoi NCPPB 3335]
 gi|298156991|gb|EFH98081.1| Ribosomal small subunit pseudouridine synthase A [Pseudomonas
           savastanoi pv. savastanoi NCPPB 3335]
          Length = 230

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 100/231 (43%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R+ V   +A  RV+V+G         V     + +DG  L+  +  
Sbjct: 1   MRLDRFLSNLPSLNRKSVRLALASGRVQVDGQTTSDPHHEVREFSRVALDGEILQAGKAA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V+   D    + +          +   GRLD NT GL+L+TNDG  +R 
Sbjct: 61  RYFMLHKPEGCVSATVDTQHPTVLDLLDEPDRHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLK--KGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+              + I     Q+TL   + +     +
Sbjct: 121 LTQPQTKMPKVYYVETEQPIDERYAATFAAGMYFSFENITTQPAQLTLLGPRSA----RL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F  FN KV RL R + G   L   L  G  R +    +
Sbjct: 177 TIVEGRYHQVKRMFGHFNNKVLRLHRENIGALALDPALAPGGYRALHAAEI 227


>gi|71276521|ref|ZP_00652796.1| Pseudouridine synthase, Rsu [Xylella fastidiosa Dixon]
 gi|71900738|ref|ZP_00682860.1| Pseudouridine synthase, Rsu [Xylella fastidiosa Ann-1]
 gi|170729744|ref|YP_001775177.1| ribosomal small subunit pseudouridine synthase [Xylella fastidiosa
           M12]
 gi|71162698|gb|EAO12425.1| Pseudouridine synthase, Rsu [Xylella fastidiosa Dixon]
 gi|71729508|gb|EAO31617.1| Pseudouridine synthase, Rsu [Xylella fastidiosa Ann-1]
 gi|167964537|gb|ACA11547.1| ribosomal small subunit pseudouridine synthase [Xylella fastidiosa
           M12]
          Length = 236

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 97/230 (42%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGI-LLERAAVNVMSTDHIEVDGVPLRKAER 72
            ++ K IA  G  SR+EV R+  + R+  NG   +  A  +V  T  +  DG PL     
Sbjct: 1   MKLLKYIANLGYGSRKEVARIFREGRIT-NGEGEVLYADDHVQHTA-VRFDGEPLDPPPG 58

Query: 73  TRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             + L+     + +T          +          + +VGRLD +T GLLLLT+DG L 
Sbjct: 59  LMVMLHKPSGYICSTKDAGRLVYDLLPARFRLRSPLLSTVGRLDGDTSGLLLLTDDGALL 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P T   +VY       +  D+  L   G ++       +Q  +    G    V +
Sbjct: 119 HRMISPKTHLPKVYEATLVQALRGDEATLFASGTLLLDGDTKPLQPAVLEVLGP-CQVRL 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            L EG+  +++++F     +VN L R + G   L  L  G  R +  + L
Sbjct: 178 TLYEGRYHQVRRMFGATGNRVNTLHRSAIGGLVLDGLPEGQWRVLEAQDL 227


>gi|33601504|ref|NP_889064.1| putative RNA pseudouridylate synthase [Bordetella bronchiseptica
           RB50]
 gi|33575940|emb|CAE33019.1| putative RNA pseudouridylate synthase [Bordetella bronchiseptica
           RB50]
          Length = 243

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 60/244 (24%), Positives = 100/244 (40%), Gaps = 19/244 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG------- 64
              R+SK+++  G+ SRRE +  I +  V+V+G+++            I ++        
Sbjct: 2   EKVRISKLMSERGLCSRREADSYIERGWVRVDGVVVSELGARAFPDQAITLERAAAARQT 61

Query: 65  --------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
                    P+          Y   + L+   S   G              +   GRLDI
Sbjct: 62  ARVTILLHKPVGYVSGQAEKGYTPAVALIDARSRYAGDRAPLRFERGQLQGLAVAGRLDI 121

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +++GLL+LT DG +A+ L    ++  + Y VR  G++ +  L LL  G+ + G      Q
Sbjct: 122 DSQGLLVLTQDGRIAKKLIGEDSEVDKEYLVRVQGRLSEAGLALLNHGLSLDGKPLRPAQ 181

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V           +   LREGK R+I+++ E    +V  L R+  G   LG L  G  R +
Sbjct: 182 VRWQNADQ----LRFVLREGKKRQIRRMCELVGLRVVGLKRVRIGRVSLGDLPVGQWRYL 237

Query: 237 SKKI 240
               
Sbjct: 238 RADE 241


>gi|71901117|ref|ZP_00683224.1| Pseudouridine synthase, Rsu [Xylella fastidiosa Ann-1]
 gi|71729122|gb|EAO31246.1| Pseudouridine synthase, Rsu [Xylella fastidiosa Ann-1]
          Length = 236

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 96/230 (41%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGI-LLERAAVNVMSTDHIEVDGVPLRKAER 72
            ++ K IA  G  SR+EV R+    R+  NG   +  A  +V  T  +  DG PL     
Sbjct: 1   MKLLKYIANLGYGSRKEVARIFRDGRIT-NGEGEVLYADDHVQHTA-VRFDGEPLDPPPG 58

Query: 73  TRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             + L+     + +T          +          + +VGRLD +T GLLLLT+DG L 
Sbjct: 59  LMVMLHKPSGYICSTKDAGRLVYDLLPARFRLRSPLLSTVGRLDGDTSGLLLLTDDGALL 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P T   +VY       +  D+  L   G ++       +Q  +    G    V +
Sbjct: 119 HRMISPKTHLPKVYEATLVQALRGDEATLFASGTLLLDGDTKPLQPAVLEVLGP-CQVRL 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            L EG+  +++++F     +VN L R + G   L  L  G  R +  + L
Sbjct: 178 TLYEGRYHQVRRMFGATGNRVNTLHRSAIGGLVLDGLPEGQWRVLEAQDL 227


>gi|167739176|ref|ZP_02411950.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 14]
          Length = 313

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 65  VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 124

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 125 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 184

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 185 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDG 244

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 245 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 300

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 301 QGEWRYLGPDE 311


>gi|167720171|ref|ZP_02403407.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei DM98]
          Length = 305

 Score =  143 bits (361), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 57  VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 116

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 117 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 176

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 177 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDG 236

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 237 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 292

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 293 QGEWRYLGPDE 303


>gi|145514343|ref|XP_001443082.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124410443|emb|CAK75685.1| unnamed protein product [Paramecium tetraurelia]
          Length = 337

 Score =  143 bits (361), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 96/252 (38%), Positives = 155/252 (61%), Gaps = 8/252 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVP 66
              P R+SK +A+  + SRRE E+MI    + V+G  +E   + V S + I+V   +G  
Sbjct: 32  QPEPMRLSKYLAQTSVCSRREAEKMIESGMILVDGKKVES-NIPVTSENKIQVFTKNGEK 90

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLL 123
           +   + T++W+++KP+G++ +H+DP  R + +D           +ISVGRLD N+EGL++
Sbjct: 91  MPTKQSTKVWIFYKPVGMICSHNDPFKRPSFYDFAKLRLKTDQHIISVGRLDFNSEGLIV 150

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           +TNDG LAR +ELP T+  R+YRVR +G   ++KL  ++ GI I G+ YG   V ++ ++
Sbjct: 151 VTNDGELARCMELPETKLQRIYRVRVYGTFTEEKLKKIRNGITIAGVNYGPYWVNVENRQ 210

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK-ILR 242
             N W+ + L +GKNREI+KV + F+ +VNRLIR SYGP++L  L  G   E   +  ++
Sbjct: 211 SRNTWLIMRLEQGKNREIRKVMQKFDLRVNRLIRQSYGPYKLMGLKPGDFYEAQIEPEIK 270

Query: 243 EQLGPHLLEEAQ 254
            +L  H  ++ Q
Sbjct: 271 RKLYLHTRKKLQ 282


>gi|289623710|ref|ZP_06456664.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. aesculi str. NCPPB3681]
 gi|289648096|ref|ZP_06479439.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. aesculi str. 2250]
 gi|330871273|gb|EGH05982.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. aesculi str. 0893_23]
          Length = 230

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 99/231 (42%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R+ V   +A  RV+V+G         V     + +DG  L+  +  
Sbjct: 1   MRLDRFLSNLPSLNRKSVRLALASGRVQVDGQTTSDPHHEVREFSRVALDGEILQAGKAA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V+   D    + +          +   GRLD NT GL+L+TNDG  +R 
Sbjct: 61  RYFMLHKPEGCVSATVDTQHPTILDLLDEPDRHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLK--KGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VY V     +D+              + I     Q+TL   + +     +
Sbjct: 121 LTQPQNKMPKVYYVETEQPIDERYAATFAAGMYFSFENITTQPAQLTLLGPRSA----RL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F  FN KV RL R + G   L   L  G  R +    +
Sbjct: 177 TIVEGRYHQVKRMFGHFNNKVLRLHRENIGALALDPALAPGGYRALHAAEI 227


>gi|330808044|ref|YP_004352506.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
 gi|327376152|gb|AEA67502.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
          Length = 230

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 108/231 (46%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            RV + ++     +R++V  ++ ++RV+++G  +      V     +EVD   L+     
Sbjct: 1   MRVDRFLSNLPRFNRQQVRLLLVERRVRIDGQTVSDPHAQVREFSRVEVDDDVLQAGRPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V+   DP   + +        + +   GRLD NT GL+L+TNDG  +R 
Sbjct: 61  RYFMLHKPPGCVSATRDPQHPTVLDWLDEPDKNDLHIAGRLDFNTTGLMLITNDGSWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +  +  +   +      + +     ++TL   + +     +
Sbjct: 121 LTQPQTKLPKVYYVETEQIITAEYADTFARGLYFAFEDLTTQPAELTLLGPRSA----RL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F  FN KV RL R   GP  L   L  G  R +S + +
Sbjct: 177 SIVEGRYHQVKRMFGHFNNKVLRLHRERMGPLTLDAHLEPGQYRALSPEEV 227


>gi|317505008|ref|ZP_07962956.1| ribosomal large subunit pseudouridine synthase B [Prevotella
           salivae DSM 15606]
 gi|315663890|gb|EFV03609.1| ribosomal large subunit pseudouridine synthase B [Prevotella
           salivae DSM 15606]
          Length = 490

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 63/242 (26%), Positives = 108/242 (44%), Gaps = 1/242 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      V+  D +
Sbjct: 242 IEYKETHIDPNEPIRLNKYLANAGVCSRREADEFILAGVVTVNGNVVTELGTKVLRADEV 301

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P+   ++  + L      + T+      ++ +         R+  VGRLD NT G
Sbjct: 302 KFHDQPVSLEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKDVCPERIYPVGRLDRNTTG 361

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     +VY V     V +D L  +  GI ++            
Sbjct: 362 VLLLTNDGDLASKLTHPKFLKKKVYHVHLDKNVTEDDLQKIASGIELEDGEIH-ADAIEY 420

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             +     V + +  GKNR ++++FE   ++V RL R+ +       L  G  R ++++ 
Sbjct: 421 ADERDKKQVGIEIHSGKNRIVRRIFESLGYRVLRLDRVQFAGLTKKNLRRGDWRFLTEQE 480

Query: 241 LR 242
           + 
Sbjct: 481 VD 482


>gi|329851025|ref|ZP_08265782.1| ribosomal large subunit pseudouridine synthase F [Asticcacaulis
           biprosthecum C19]
 gi|328839871|gb|EGF89443.1| ribosomal large subunit pseudouridine synthase F [Asticcacaulis
           biprosthecum C19]
          Length = 253

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 58/243 (23%), Positives = 110/243 (45%), Gaps = 19/243 (7%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPL 67
           +   P R++K +A++G+ SRRE + +I +  V + G  +  A   ++    + +D G  L
Sbjct: 8   DGAEPVRLNKWLAQSGVCSRREADTLIEEGCVAIAGETVRDAGRKILPGQTVTLDRGETL 67

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN----------LPSIFSRVISVGRLDIN 117
                  +        +       +  +                P   S++  +GRLD +
Sbjct: 68  PM----TVIYNKPIGIVSGQPEPGETPAVRMIRRANVFGPADVYPDQTSKLAPIGRLDKD 123

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           + GLL+L+ DG LA+ +  P ++  + Y V+  GQ+ + KL  L+ G+ + G      ++
Sbjct: 124 SHGLLVLSEDGVLAKAVIGPDSELDKAYHVQVRGQIIEAKLAWLRHGLELDGRKLKPAEI 183

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           T    +     +T  L+EG+ R+I+++ +    +V  L R   GP QLG L  G  R ++
Sbjct: 184 T----QTGPQSLTFVLKEGRKRQIRRMCDMVELRVTDLYRDRIGPLQLGDLPEGQWRFMT 239

Query: 238 KKI 240
              
Sbjct: 240 PDE 242


>gi|33596106|ref|NP_883749.1| putative RNA pseudouridylate synthase [Bordetella parapertussis
           12822]
 gi|33573109|emb|CAE36753.1| putative RNA pseudouridylate synthase [Bordetella parapertussis]
          Length = 243

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 60/244 (24%), Positives = 100/244 (40%), Gaps = 19/244 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG------- 64
              R+SK+++  G+ SRRE +  I +  V+V+G+++            I ++        
Sbjct: 2   EKVRISKLMSERGLCSRREADSYIERGWVRVDGVVVSELGARAFPDQAITLERAAAARQT 61

Query: 65  --------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
                    P+          Y   + L+   S   G              +   GRLDI
Sbjct: 62  ARVTILLHKPVGYVSGQAEKGYTPAVALIDARSRHAGDRAPLRFERGQLQGLAVAGRLDI 121

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +++GLL+LT DG +A+ L    ++  + Y VR  G++ +  L LL  G+ + G      Q
Sbjct: 122 DSQGLLVLTQDGRIAKKLIGEDSEVDKEYLVRVQGRLSEAGLALLNHGLSLDGKPLRPAQ 181

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V           +   LREGK R+I+++ E    +V  L R+  G   LG L  G  R +
Sbjct: 182 VRWQNADQ----LRFVLREGKKRQIRRMCELVGLRVVGLKRVRIGRVSLGDLPVGQWRYL 237

Query: 237 SKKI 240
               
Sbjct: 238 RADE 241


>gi|297538780|ref|YP_003674549.1| pseudouridine synthase [Methylotenera sp. 301]
 gi|297258127|gb|ADI29972.1| pseudouridine synthase [Methylotenera sp. 301]
          Length = 245

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 48/228 (21%), Positives = 92/228 (40%), Gaps = 4/228 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTR 74
           + ++I   G  +R+    +I  Q V VNG + +              V G      E++ 
Sbjct: 11  LERIICNQGFGARKLCRILILNQEVTVNGEICDDPDAVFDTENLQYTVKGEAWDYREKSY 70

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L+       +  +            P +   V  +GRLD +T GL+L+++DG     +
Sbjct: 71  LMLHKPSNYECSHKTQHHPTIYSLLPHPLVVRDVQCIGRLDEDTTGLILISDDGQFIHRM 130

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  +VY V     +  +++  + KG+ +           L   + +   + + L 
Sbjct: 131 SSPKHKVPKVYEVTCKHPMSDEQIAHILKGVQLVDEDAPIA--ALACTRITQNIIHMTLA 188

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           EGK  ++K++    + +V  L RI  G  +L   L  G  R +++  L
Sbjct: 189 EGKYHQVKRMVAAISNRVEGLKRIQIGEVKLPDDLAVGEWRWLTESEL 236


>gi|283956165|ref|ZP_06373650.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 1336]
 gi|283792319|gb|EFC31103.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 1336]
          Length = 253

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 73/250 (29%), Positives = 118/250 (47%), Gaps = 20/250 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+     SRRE + +I Q  +K+N  +    +  V   D + V G  ++K  + 
Sbjct: 1   MRINKFISHNTCYSRREADELIKQGLIKINNKIA-LLSDEVKFDDKVFVKGKRVQKRTQF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +YHK  G + +  D  GR T++D LP  FS  +SVGRLD  +EGLLLLT+   +A  
Sbjct: 60  SVIIYHKQKGEIVSKKDDRGRKTIYDTLPRQFSTWLSVGRLDYASEGLLLLTDSPVIADA 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--------------YGDMQVTL 179
           L        R Y ++  G V +  +  ++ G+ I+                    +   +
Sbjct: 120 LMHSD--LEREYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEI 177

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               G    + V + EGKNRE+++ F  F+ +V  L R+++G   LG L AG  R +   
Sbjct: 178 FGSSGGYTKLRVVINEGKNRELRRFFGHFDLEVMDLKRVAFGALDLGMLKAGKHRYLENG 237

Query: 240 I---LREQLG 246
               LR+ L 
Sbjct: 238 EYEKLRDFLK 247


>gi|148985263|ref|ZP_01818486.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP3-BS71]
 gi|147922461|gb|EDK73580.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP3-BS71]
 gi|301799717|emb|CBW32282.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae OXC141]
          Length = 241

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 105/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+       A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLKGDILVDSCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                      ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKELPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTICKPARLEILSASPSLSQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K L+
Sbjct: 180 TISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKELQ 231


>gi|120602463|ref|YP_966863.1| pseudouridine synthase [Desulfovibrio vulgaris DP4]
 gi|120562692|gb|ABM28436.1| ribosomal large subunit pseudouridine synthase B [Desulfovibrio
           vulgaris DP4]
          Length = 292

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 76/245 (31%), Positives = 120/245 (48%), Gaps = 9/245 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK-- 69
             R++K ++ AG+ SRR+ +  IA  +V+VNG ++      V   TD IEV+G  L    
Sbjct: 45  GTRLNKALSGAGVCSRRQADTFIAGGKVRVNGEVVTEMGRRVFPATDRIEVEGRLLACGE 104

Query: 70  ---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLL 124
                R    + +KP+ +V+T  DP GR+T+ D LP     V    VGRLD  +EGLLLL
Sbjct: 105 ALNRHRHTYVMLNKPVQVVSTVRDPQGRTTILDILPDDLKTVRLYPVGRLDFFSEGLLLL 164

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQK 183
           T+DG L   L  P     + YRV     +    L  ++ G+ + +G     ++  +  + 
Sbjct: 165 TDDGDLTHRLTHPKWHLPKYYRVLVREDIPPAALTAMRSGMTLAEGDRVAPVEAYIIDRS 224

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
                + + L +G NR+I+++       V RL+RI  GP +LG L  GS R +    ++ 
Sbjct: 225 EYGVELEMVLHQGINRQIRRMCRDLGLTVLRLLRIQQGPVELGNLSRGSCRRLEDHEVKA 284

Query: 244 QLGPH 248
                
Sbjct: 285 LRKAA 289


>gi|121612851|ref|YP_001001353.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|167006242|ref|ZP_02272000.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|87248974|gb|EAQ71936.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 81-176]
          Length = 253

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 74/250 (29%), Positives = 118/250 (47%), Gaps = 20/250 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+     SRRE + +I Q  VK+N  +    +  V   D + V G  ++K  + 
Sbjct: 1   MRINKFISHNTRYSRREADELIKQGLVKINNKIA-LLSDEVKFDDKVFVKGKRVQKRTQF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +YHK  G + +  D  GR T++D LP  FS  +SVGRLD  +EGLLLLT+   +A  
Sbjct: 60  SVIIYHKQKGEIVSKKDDRGRKTIYDTLPRQFSTWLSVGRLDYASEGLLLLTDSPVIANA 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--------------YGDMQVTL 179
           L        R Y ++  G V +  +  ++ G+ I+                    +   +
Sbjct: 120 LMHSD--LEREYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEI 177

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               G    + V + EGKNRE+++ F  F+ +V  L R+++G   LG L AG  R +   
Sbjct: 178 FGSSGGYTKLRVVINEGKNRELRRFFGHFDLEVMDLKRVAFGALDLGMLKAGKHRYLENG 237

Query: 240 I---LREQLG 246
               LR+ L 
Sbjct: 238 EYEKLRDFLK 247


>gi|307578345|gb|ADN62314.1| RNA-binding S4 domain-containing protein [Xylella fastidiosa subsp.
           fastidiosa GB514]
          Length = 519

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 82/351 (23%), Positives = 142/351 (40%), Gaps = 12/351 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ KV+A+AG+ SRR +E+ I+   +KVNG + +   ++V S D IE+DG         
Sbjct: 27  ERLHKVLAQAGLGSRRALEQRISNGLIKVNGDIAQ-LGMSVKSGDKIELDGRSFVASALT 85

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + T        +          +R I++GRLDINT GLLLLT DG 
Sbjct: 86  EPARVLIYNKPEGEVTTREDPEGRPTVFETLPVLKGARWIAIGRLDINTTGLLLLTTDGE 145

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLN-----LLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS++  R Y VR      ++ +       L +G++++        +       
Sbjct: 146 LANAMMHPSSEIEREYVVRVRSPEGEEHVQDELLEQLTRGVMLEDGTAKFDTIERIGNTD 205

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + E+ K  +  
Sbjct: 206 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGSVLLPRELLRGQSTELPKTQVEA 265

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                 LE+                  +  +     D+      N+      S++ +   
Sbjct: 266 LRTQLKLEKDMPLALTLQPVIGQRRSAKATLHVNRNDNNKHAYHNNHSTADESRELRRFD 325

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK-RSLRRTSAK 353
            +                 +   ++  ++ +       P   RSL   S  
Sbjct: 326 TLRDDRGRGQGKHHFKDRLTVSGEAAAKQAHKPFKQYKPKNDRSLSEGSPA 376


>gi|227817496|ref|YP_002817505.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           CDC 684]
 gi|227006383|gb|ACP16126.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           CDC 684]
          Length = 214

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 53/205 (25%), Positives = 94/205 (45%), Gaps = 3/205 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++GI ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGISVKDAKVHVNVEEQEVMIHGEVVEYKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L ++     +  T  D          L         VGRLDI+TEG LL+TNDG L+ 
Sbjct: 61  VYLMMHKPQGVISATEDDNHETVIDLLELEDAIFNPFPVGRLDIDTEGFLLITNDGKLSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G V ++ +    KG+++          +T+  +    + + +
Sbjct: 121 QLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLI 216
            + EGK  ++K++FE    K + L 
Sbjct: 180 VITEGKFHQVKRMFEAVGEKSSLLK 204


>gi|82701397|ref|YP_410963.1| pseudouridine synthase, Rsu [Nitrosospira multiformis ATCC 25196]
 gi|82409462|gb|ABB73571.1| ribosomal large subunit pseudouridine synthase F [Nitrosospira
           multiformis ATCC 25196]
          Length = 243

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 63/244 (25%), Positives = 103/244 (42%), Gaps = 19/244 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG------- 64
              R+SK++++ G+ SRRE +  I +  V V+G  + +  + V  T  I++         
Sbjct: 2   EKIRLSKLMSQKGLCSRREADDYIERGWVFVDGERISQLGIKVFPTQEIKLARMAQAQQC 61

Query: 65  --------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
                    P+          Y   I L+   S+           P     +   GRLDI
Sbjct: 62  DQITVLLHKPVGYVSGQPERGYKPAISLINRESEFQDSKASSSFSPLNLKGMAPAGRLDI 121

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           ++ GLL+ T DG +AR L    ++  + Y VR  G+V Q  LNLL  G+ + G       
Sbjct: 122 DSSGLLVFTQDGRIARKLIGAESEIEKEYLVRAEGEVSQRTLNLLSHGLSLDGQALKRA- 180

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                 + +   +   L+EG+ R+I+++ E    KV  L R+  G  +LG L  G  R +
Sbjct: 181 ---VVVQQNKDQLRFILKEGRKRQIRRMCELVGLKVTGLKRVRIGKVRLGELPLGKWRYL 237

Query: 237 SKKI 240
               
Sbjct: 238 RPGE 241


>gi|332362872|gb|EGJ40665.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK49]
          Length = 241

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 104/231 (45%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++ + Q+++ V+G    + + NV +    I   G  +     
Sbjct: 1   MRLDQLLA-ANHISRKKMKQSLLQKQILVDGKPAYKLSQNVDTGLQQITFQGKHVSGPAH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +               +       + S+GRLD +TEGLLL+T++G L  
Sbjct: 60  RYYMLNKPAGAVTANRDAEKLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V  +G +        ++GI  + G      Q+T+ + + S +  +V
Sbjct: 120 QLLHPQYHVEKTYYVEVNGPLTPQDKIAFQEGIRFLDGTVCQPAQLTIFSSRSSLSRASV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  +IKK+F     KV  L RI +G F L   L  G  R ++++ L
Sbjct: 180 RISEGKFHQIKKMFLAVGVKVTYLKRIQFGDFTLDPDLAKGDYRALNQEEL 230


>gi|134094904|ref|YP_001099979.1| 16S rRNA pseudouridylate 516 synthase [Herminiimonas
           arsenicoxydans]
 gi|133738807|emb|CAL61854.1| putative 16S rRNA uridine-516 pseudouridylate synthase
           [Herminiimonas arsenicoxydans]
          Length = 244

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 41/229 (17%), Positives = 81/229 (35%), Gaps = 5/229 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + +++   G  +R+    +I    V +NG++++     V +TD    +     R  E   
Sbjct: 6   LDRILQSQGFGTRKYCRGLIEDGEVSINGVVVDNFKTAVDTTDLEFTIFDEVWRYREHVY 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        +                  +  +  VGRLD +T G+LL+++DG      
Sbjct: 66  IVLNKPANFECSRKPSHHPGVLTLLPEQFTWRDLQPVGRLDHDTTGMLLMSDDGPFIHAQ 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     ++Y    H  V  + +  L  G+ +          T      +   + + L 
Sbjct: 126 SSPKRHIPKIYVATTHDPVTPELIAQLLGGVQLHDEPAPLAAQTCRML--AEHQIEIVLE 183

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKIL 241
           +GK  ++K++        + L R   G   L    L  G    +  + L
Sbjct: 184 QGKYHQVKRMLAAAGNHCSALNRAEIGELTLESLGLEEGEWTYLDAEQL 232


>gi|57236895|ref|YP_179848.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           RM1221]
 gi|57165699|gb|AAW34478.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           RM1221]
          Length = 253

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 74/250 (29%), Positives = 118/250 (47%), Gaps = 20/250 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+     SRRE + +I Q  VK+N  +    +  V   D + V G  ++K  + 
Sbjct: 1   MRINKFISHNTRYSRREADELIKQGLVKINNKIA-LLSDEVKFDDKVFVKGKRVQKRTQF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +YHK  G + +  D  GR T++D LP  FS  +SVGRLD  +EGLLLLT+   +A  
Sbjct: 60  SVIIYHKQKGEIVSKKDDRGRKTIYDTLPRQFSTWLSVGRLDYASEGLLLLTDSPVIADA 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--------------YGDMQVTL 179
           L        R Y ++  G V +  +  ++ G+ I+                    +   +
Sbjct: 120 LMHSD--LEREYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEI 177

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               G    + V + EGKNRE+++ F  F+ +V  L R+++G   LG L AG  R +   
Sbjct: 178 FGSSGGYTKLRVVINEGKNRELRRFFGHFDLEVMDLKRVAFGALDLGMLKAGKHRYLENG 237

Query: 240 I---LREQLG 246
               LR+ L 
Sbjct: 238 EYEKLRDFLK 247


>gi|226952690|ref|ZP_03823154.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter sp. ATCC
           27244]
 gi|226836558|gb|EEH68941.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter sp. ATCC
           27244]
          Length = 238

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 49/225 (21%), Positives = 90/225 (40%), Gaps = 3/225 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V ++    +    N  + D   +V G   +  E   
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGAVSIDSQTCDHPKQNFSTEDLSFQVFGEQYQYREHIY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L+       +  +              I   V  VGRLD +T GLLLLT+DG   + L
Sbjct: 63  IVLHKPQGYECSHQATHHRSVFSLLPEILIHRGVQCVGRLDQDTTGLLLLTDDGQYLQAL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     +VY V     V  ++   L+ G+ ++      +    D +  S   + + + 
Sbjct: 123 THPKKHVPKVYCVSTADPVTTEQKQQLELGVELRNE--KGIYAATDIKLISERQLEMTIH 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G   ++K++      KV RL R   G  +L  L  G    ++ +
Sbjct: 181 QGVYHQVKRMIAAVGNKVERLHRQQIGLLELPNLEEGHWDYLTLE 225


>gi|86150527|ref|ZP_01068751.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni CF93-6]
 gi|86152349|ref|ZP_01070559.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 260.94]
 gi|86154122|ref|ZP_01072321.1| ribosomal large subunit pseudouridine synthase B [Campylobacter
           jejuni subsp. jejuni HB93-13]
 gi|88597657|ref|ZP_01100890.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 84-25]
 gi|157415931|ref|YP_001483187.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 81116]
 gi|205355723|ref|ZP_03222493.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8421]
 gi|218563295|ref|YP_002345075.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni NCTC 11168]
 gi|85838979|gb|EAQ56244.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni CF93-6]
 gi|85840646|gb|EAQ57898.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 260.94]
 gi|85842362|gb|EAQ59578.1| ribosomal large subunit pseudouridine synthase B [Campylobacter
           jejuni subsp. jejuni HB93-13]
 gi|88189961|gb|EAQ93937.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 84-25]
 gi|112361002|emb|CAL35803.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni NCTC 11168]
 gi|157386895|gb|ABV53210.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 81116]
 gi|205346500|gb|EDZ33133.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8421]
 gi|284926900|gb|ADC29252.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni IA3902]
 gi|307748569|gb|ADN91839.1| Pseudouridine synthase [Campylobacter jejuni subsp. jejuni M1]
 gi|315926636|gb|EFV06016.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni DFVF1099]
 gi|315931323|gb|EFV10292.1| conserved hypothetical protein [Campylobacter jejuni subsp. jejuni
           327]
          Length = 253

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 74/250 (29%), Positives = 118/250 (47%), Gaps = 20/250 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+     SRRE + +I Q  VK+N  +    +  V   D + V G  ++K  + 
Sbjct: 1   MRINKFISHNTRYSRREADELIKQGLVKINNKIA-LLSDEVKFDDKVFVKGKRVQKRTQF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +YHK  G + +  D  GR T++D LP  FS  +SVGRLD  +EGLLLLT+   +A  
Sbjct: 60  SVIIYHKQKGEIVSKKDDRGRKTIYDTLPRQFSTWLSVGRLDYASEGLLLLTDSPVIADA 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--------------YGDMQVTL 179
           L        R Y ++  G V +  +  ++ G+ I+                    +   +
Sbjct: 120 LMHSD--LEREYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEI 177

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               G    + V + EGKNRE+++ F  F+ +V  L R+++G   LG L AG  R +   
Sbjct: 178 FGSSGGYTKLRVVINEGKNRELRRFFGHFDLEVMDLKRVAFGALDLGMLKAGKHRYLENG 237

Query: 240 I---LREQLG 246
               LR+ L 
Sbjct: 238 EYEKLRDFLK 247


>gi|297559952|ref|YP_003678926.1| pseudouridine synthase [Nocardiopsis dassonvillei subsp.
           dassonvillei DSM 43111]
 gi|296844400|gb|ADH66420.1| pseudouridine synthase [Nocardiopsis dassonvillei subsp.
           dassonvillei DSM 43111]
          Length = 694

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 76/246 (30%), Positives = 118/246 (47%), Gaps = 1/246 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEV 62
           ++   +     R+ K +A AG+ASRR  E MIA  RV V+G ++ R    V      I V
Sbjct: 447 RDTYTDVENGIRLQKALAAAGVASRRASEEMIAAGRVSVDGQVVRRFGARVDPESSEIRV 506

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG+ +  A     +  +KP G+V+T  DP+GR T+ D       R+  VGRLD  TEGL+
Sbjct: 507 DGMRVVTAPDKLYFALNKPRGVVSTMWDPEGRPTLADYTGQTEERIFHVGRLDTETEGLI 566

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTNDG LA  L  P  + ++ Y  +  G V    +  ++KG+ ++          +   
Sbjct: 567 LLTNDGELANRLTHPRYKVVKTYIAKVPGPVPHRVVREVQKGVELEDGPVEVDSFRVVDN 626

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +   A V + L EG+   ++++ E     V  L R   GP  L  L  G+ R ++ + + 
Sbjct: 627 EPPKALVEIRLHEGRKHIVRRLMEAVGHPVADLARTQVGPIDLNALKLGTMRALTSREVS 686

Query: 243 EQLGPH 248
           E     
Sbjct: 687 ELYEAA 692


>gi|148926800|ref|ZP_01810479.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8486]
 gi|145844525|gb|EDK21632.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8486]
          Length = 253

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 74/250 (29%), Positives = 118/250 (47%), Gaps = 20/250 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+     SRRE + +I Q  VK+N  +    +  V   D + V G  ++K  + 
Sbjct: 1   MRINKFISHNTRYSRREADELIKQGLVKINNKIA-LLSDEVQFDDKVFVKGKRVQKRTQF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +YHK  G + +  D  GR T++D LP  FS  +SVGRLD  +EGLLLLT+   +A  
Sbjct: 60  SVIIYHKQKGEIVSKKDDRGRKTIYDTLPRQFSTWLSVGRLDYASEGLLLLTDSPVIADA 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--------------YGDMQVTL 179
           L        R Y ++  G V +  +  ++ G+ I+                    +   +
Sbjct: 120 LMHSD--LEREYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEI 177

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               G    + V + EGKNRE+++ F  F+ +V  L R+++G   LG L AG  R +   
Sbjct: 178 FGSSGGYTKLRVVINEGKNRELRRFFGHFDLEVMDLKRVAFGALDLGMLKAGKHRYLENG 237

Query: 240 I---LREQLG 246
               LR+ L 
Sbjct: 238 EYEKLRDFLK 247


>gi|184158637|ref|YP_001846976.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           baumannii ACICU]
 gi|332874333|ref|ZP_08442245.1| pseudouridylate synthase [Acinetobacter baumannii 6014059]
 gi|183210231|gb|ACC57629.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           baumannii ACICU]
 gi|322507599|gb|ADX03053.1| rsuA [Acinetobacter baumannii 1656-2]
 gi|323518555|gb|ADX92936.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           baumannii TCDC-AB0715]
 gi|332737461|gb|EGJ68376.1| pseudouridylate synthase [Acinetobacter baumannii 6014059]
          Length = 234

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 47/226 (20%), Positives = 91/226 (40%), Gaps = 3/226 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V ++G ++          +    V G   +  E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVSIDGEVVSDLKKQFAPENFEFSVFGQNYQYREKIY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        + H               I   V +VGRLD +T GLLLLT+DG   + L
Sbjct: 63  IALRKPQGFECSHHPQHHQSVFSLLPETMIHRGVQAVGRLDQDTTGLLLLTDDGKYLQAL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     +VY V  +  V  +++ +L +G+ +           +   +     +T+ + 
Sbjct: 123 THPRKHVPKVYHVTTYDPVTPEQIEMLIQGVNLHQEKGVFAATDVALLE--THQLTMTIH 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +G   ++K++      KV +L R   G   L  +  G    +S++ 
Sbjct: 181 QGVYHQVKRMIAAVGNKVEKLHRHQIGQLVLPEIEDGDWVYLSEQE 226


>gi|300926650|ref|ZP_07142426.1| hypothetical protein HMPREF9548_04653 [Escherichia coli MS 182-1]
 gi|300417316|gb|EFK00627.1| hypothetical protein HMPREF9548_04653 [Escherichia coli MS 182-1]
          Length = 276

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 117/276 (42%), Gaps = 10/276 (3%)

Query: 26  ASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE-----RTRLWLYH 79
             RRE+E +I   RV V+G + +    V V     I +DG  +   E        L  Y 
Sbjct: 1   GPRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRESAEQICRVLAYYK 60

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
               L T +      +          +R I+VGRLD+NT GLLL T DG LA  L  PS 
Sbjct: 61  PEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSR 120

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
           +  R Y VR  GQVD  KL  L +G+ ++        +     +G N W  V L EG+NR
Sbjct: 121 EVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNR 180

Query: 200 EIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILREQLGPHLLEEAQV 255
           E+++++E    +V+RLIR+ YG   L   L  G   E+       LRE +       ++V
Sbjct: 181 EVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLRELVELPPETSSKV 240

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
            ++      +     R            R    ++ 
Sbjct: 241 AVEKDRRRMKANQIRRAVKRHSQVSGGRRSGGRNNG 276


>gi|225856373|ref|YP_002737884.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae P1031]
 gi|225725742|gb|ACO21594.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae P1031]
          Length = 241

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 56/232 (24%), Positives = 105/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  + SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKV-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                      ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKELPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVEVNGLLTPDHIQTFQKGIVFLDGTICKPARLEILSASPSLSQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L  G+   +++K L+
Sbjct: 180 TISEGKFHQIKKMFLSVGVKVTNLKRIQFGDFTLNPDLAEGNYHPLNQKELQ 231


>gi|71737959|ref|YP_276115.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. phaseolicola 1448A]
 gi|71558512|gb|AAZ37723.1| Ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. phaseolicola 1448A]
 gi|320325537|gb|EFW81599.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. glycinea str. B076]
 gi|320327176|gb|EFW83190.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. glycinea str. race 4]
 gi|330879332|gb|EGH13481.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. glycinea str. race 4]
          Length = 230

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 100/231 (43%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R+ V   +A  RV+V+G         V     + +DG  L+  +  
Sbjct: 1   MRLDRFLSNLPSLNRKSVRLALASGRVQVDGQTTSDPHHEVREFSRVALDGEILQAGKAA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V+   D    + +          +   GRLD NT GL+L+TNDG  +R 
Sbjct: 61  RYFMLHKPEGCVSATVDTQHPTVLDLLDEPDRHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLK--KGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+              + I     Q+TL   + +     +
Sbjct: 121 LTQPKTKMPKVYYVETEQPIDERYAATFAAGMYFSFENITTQPAQLTLLGPRSA----RL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F  FN KV RL R + G   L   L  G  R +    +
Sbjct: 177 TIVEGRYHQVKRMFGHFNNKVLRLHRENIGALALDPALAPGGYRALHAAEI 227


>gi|293374527|ref|ZP_06620849.1| pseudouridylate synthase [Turicibacter sanguinis PC909]
 gi|325841216|ref|ZP_08167341.1| putative 16S pseudouridylate 516 synthase [Turicibacter sp. HGF1]
 gi|292646906|gb|EFF64894.1| pseudouridylate synthase [Turicibacter sanguinis PC909]
 gi|325490073|gb|EGC92419.1| putative 16S pseudouridylate 516 synthase [Turicibacter sp. HGF1]
          Length = 244

 Score =  143 bits (359), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 58/241 (24%), Positives = 97/241 (40%), Gaps = 19/241 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-------STDHIEVDGVP 66
            R+ K++A  G  +R EV++++  +       +     V          S   + V    
Sbjct: 1   MRLDKLLAHTGYGTRTEVKKLLKSK------EVKVDGVVVKDAKVKVDLSKQCVTVFDEV 54

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +   E   L +      L  T            +   +   V   GRLD +TEGL+LLTN
Sbjct: 55  VEYREFVYLMMNKPQDCLSATRDQRYRTVIDLLDDYYLMFDVAPAGRLDRDTEGLVLLTN 114

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-----YGDMQVTLDT 181
           DG LA  +  P     + Y     G++  +KLN L+ G+ I             +V +  
Sbjct: 115 DGKLAHEIISPKKDVYKRYVAHVTGELTDEKLNQLETGVEILDGTGEVFSTKPAKVKILQ 174

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
           +      V + + EGK  ++K++F     KV  L R++ G  +L   L  G  RE++ + 
Sbjct: 175 KNDEWTEVEICITEGKFHQVKRMFASVGGKVIYLKRLAIGGLELDESLELGEYRELTDEE 234

Query: 241 L 241
           L
Sbjct: 235 L 235


>gi|88858554|ref|ZP_01133196.1| 16S rRNA pseudouridylate 516 synthase [Pseudoalteromonas tunicata
           D2]
 gi|88820171|gb|EAR29984.1| 16S rRNA pseudouridylate 516 synthase [Pseudoalteromonas tunicata
           D2]
          Length = 233

 Score =  143 bits (359), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 54/232 (23%), Positives = 93/232 (40%), Gaps = 8/232 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K I+      R + +  I ++  KVNG ++      V  +D +      L     
Sbjct: 4   PCRLDKFISHLTELPRTKTKAGIKRKYAKVNGTVITSFDYQVTESDVVLWQDKQLEVLGD 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +    SD   ++ +      + S++   GRLD++T GL+L+TNDG  + 
Sbjct: 64  RYFMLNKPEGYV-CATSDELHQTVLELLDEPVMSKLHIAGRLDLDTTGLVLITNDGEWSH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVT 190
            +  P  Q  + Y V     +  D L  L+ G+ + G         V L     +   V 
Sbjct: 123 KVTSPKYQKYKTYLVETLEPMTDDALQELRDGVQLHGEKGLTQPAIVELL----AEYSVR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EGK  ++K++F     KV  L R       L   L  G  R ++ + +
Sbjct: 179 ISICEGKYHQVKRMFAAVGNKVEVLHREKIAGITLDQDLAPGQYRLLTAEEI 230


>gi|15837802|ref|NP_298490.1| ribosomal small subunit pseudouridine synthase [Xylella fastidiosa
           9a5c]
 gi|9106172|gb|AAF84010.1|AE003954_7 ribosomal small subunit pseudouridine synthase [Xylella fastidiosa
           9a5c]
          Length = 236

 Score =  143 bits (359), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 58/234 (24%), Positives = 95/234 (40%), Gaps = 13/234 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-----EVDGVPLR 68
            ++ K IA  G  SR+EV R+  + R+  NG         + + D +       DG PL 
Sbjct: 1   MKLLKYIANLGYGSRKEVARIFREGRIT-NGE-----GEVLYADDQVQHIAVRFDGEPLD 54

Query: 69  KAERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                 + L+     + +T          +          + +VGRLD +T GLLLLT+D
Sbjct: 55  PPPGLMVMLHKPSDYICSTKDAGRLVYDLLPPRFRLRSPLLSTVGRLDGDTSGLLLLTDD 114

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +  P T   +VY       +  D+  L   G ++       +Q  +    G   
Sbjct: 115 GALLHRMISPKTHLPKVYEATLVQALRGDEATLFASGTLLLDGDTKPLQPAVLEVLGP-C 173

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V + L EG+  +++++F     +VN L R + G   L  L  G  R +  + L
Sbjct: 174 QVRLTLYEGRYHQVRRMFGATGNRVNTLHRSAIGGLVLDGLPEGQWRVLEAQDL 227


>gi|15827715|ref|NP_301978.1| pseudouridine synthase [Mycobacterium leprae TN]
 gi|221230192|ref|YP_002503608.1| putative pseudouridine synthase [Mycobacterium leprae Br4923]
 gi|13093266|emb|CAC31751.1| possible pseudouridine synthase [Mycobacterium leprae]
 gi|219933299|emb|CAR71465.1| possible pseudouridine synthase [Mycobacterium leprae Br4923]
          Length = 257

 Score =  143 bits (359), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 71/245 (28%), Positives = 109/245 (44%), Gaps = 4/245 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGV 65
           +       R+ K+++RAGIASRR  E++I + RV+V+G L+      V      + VDGV
Sbjct: 10  MDRGAGAVRLQKILSRAGIASRRAAEKLIIEGRVEVDGQLVRELGTRVDPDVSVVRVDGV 69

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLL 122
            +   +       +KP G+ +T SD  GR  V D +            VGRLD +TEGL+
Sbjct: 70  KVVVDDSLVYLALNKPRGMYSTMSDDRGRPCVGDLIERRVRGNKKLFHVGRLDADTEGLI 129

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTNDG LA  L  PS +  + Y     G V +     L  G+ +           +   
Sbjct: 130 LLTNDGELAHRLMHPSHEVSKTYLATVKGAVPRGLGKKLSVGLELDDGPAHVDDFAVVDA 189

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
                 V + L EG+ R ++++     + V  L+R   G   LG    G  R + +  +R
Sbjct: 190 IPGKTLVRLTLHEGRKRIVRRLLTAAGFPVEMLVRTDIGAVSLGDQRPGCLRALLRDEIR 249

Query: 243 EQLGP 247
           +    
Sbjct: 250 QLYKE 254


>gi|160877136|ref|YP_001556452.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|160862658|gb|ABX51192.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|315269341|gb|ADT96194.1| pseudouridine synthase [Shewanella baltica OS678]
          Length = 233

 Score =  143 bits (359), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 99/233 (42%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++    R      I    V VNG +    A+ V   + + ++G PL      
Sbjct: 1   MRLDKFLCKSTDLDRDAASVAIINGSVTVNGTIATDCAMQVHENNAVCLNGKPLAPRPS- 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP   + ++ D    S            +  VGRLD +T GL+LLT+DG  +  
Sbjct: 60  RYFMLHKPADTLCSNVDGAYPSLFHLLDIEHAFDLHIVGRLDADTTGLVLLTDDGRWSFN 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKG----IVIQGICYGDMQVTLDTQKGSNAWV 189
           +  P  Q  +VYRV+    +D +    +       + +QG     +  TL  Q+     V
Sbjct: 120 IISPQYQCEKVYRVQLRDPLDSEATAAIATTFAAGLQLQGETALTLPATL--QQVDEKTV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + L EGK  ++K++F     KV  L R   G   L  +  G  RE++   + 
Sbjct: 178 LLTLTEGKFHQVKRMFAAVGNKVIALHRAQIGAVVL-DVDIGEWRELTLAEID 229


>gi|78776413|ref|YP_392728.1| pseudouridine synthase, Rsu [Sulfurimonas denitrificans DSM 1251]
 gi|78496953|gb|ABB43493.1| Pseudouridine synthase, Rsu [Sulfurimonas denitrificans DSM 1251]
          Length = 312

 Score =  143 bits (359), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 68/242 (28%), Positives = 117/242 (48%), Gaps = 17/242 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R++K IA     SRRE ++ I    V+VNG + +  A ++    D + V G P+   ++
Sbjct: 1   MRLNKYIAHHSSYSRREADKAIQDGYVRVNGEIQDNPATDIYEGVDVVYVSGKPVTPRDK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +Y+KP G + T SDP  R T++D LP  +   + VGRLD  +EGLLLLT+   +A 
Sbjct: 61  YTVIVYNKPKGELVTKSDPKERKTIYDTLPKEYKHYVPVGRLDYASEGLLLLTDASKVAS 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQVT 178
            L        R+Y+++  G+V  +    +  G+++                     +   
Sbjct: 121 ALMES--NLERIYKIKIKGEVTSEMEAAMLNGMMLDDATAGGHSHSKVTSMEFKPFIGYK 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +   + + + + V L EGKNRE+++ F  F   +  L R+S+   +L  L  G  R +S+
Sbjct: 179 IQKNEPNYSILKVALSEGKNRELRRFFAHFGTDIVDLKRVSFAEIELNNLPTGKVRFLSR 238

Query: 239 KI 240
             
Sbjct: 239 SE 240


>gi|222823063|ref|YP_002574636.1| ribosomal pseudouridine synthase [Campylobacter lari RM2100]
 gi|222538284|gb|ACM63385.1| putative ribosomal pseudouridine synthase [Campylobacter lari
           RM2100]
          Length = 253

 Score =  143 bits (359), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 74/255 (29%), Positives = 122/255 (47%), Gaps = 20/255 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+     SRRE + +I Q  VK+N         +V + D + ++G  L K  + 
Sbjct: 1   MRINKFISHNSKYSRREADELIKQGLVKINKKTA-LLNDSVNAEDKVFINGKKLHKKTQF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +YHK  G + +  D  GR T++  LP  FS  +SVGRLD  +EGLLLLT+   +A  
Sbjct: 60  SVIIYHKQKGEIVSKKDDRGRKTIYHTLPKQFSTWLSVGRLDFASEGLLLLTDSPVIADA 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--------------YGDMQVTL 179
           L        R Y ++  G +D++ +  ++ G+ IQ                    +   +
Sbjct: 120 LMHSD--LEREYYLKVKGNIDKNVIEAMQNGLEIQNEKKGAHAKTKITSMSFAPFLGFEI 177

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               G    + V + EGKNRE+++ F  F+ +V  L R+++G   LG L AG  R +   
Sbjct: 178 FGSSGGYTKLKVIINEGKNRELRRFFGHFDLEVMDLKRVAFGALDLGMLKAGKYRYLENG 237

Query: 240 I---LREQLGPHLLE 251
               LR+ L  + ++
Sbjct: 238 EYEKLRDFLKTNNIK 252


>gi|149020294|ref|ZP_01835186.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP23-BS72]
 gi|147930596|gb|EDK81578.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP23-BS72]
          Length = 241

 Score =  143 bits (359), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 56/232 (24%), Positives = 105/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  + SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKV-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                      ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKELPTVMNLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVEVNGLLTPDHIQTFQKGIVFLDGTICKPARLEILSASPSLSQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L  G+   +++K L+
Sbjct: 180 TISEGKFHQIKKMFLSIGVKVTNLKRIQFGDFTLNPDLAEGNYHPLNQKELQ 231


>gi|325299016|ref|YP_004258933.1| pseudouridine synthase Rsu [Bacteroides salanitronis DSM 18170]
 gi|324318569|gb|ADY36460.1| pseudouridine synthase Rsu [Bacteroides salanitronis DSM 18170]
          Length = 431

 Score =  143 bits (359), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 112/241 (46%), Gaps = 1/241 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+ K ++ +   P R++K +A AG+ SRRE +  I    V VNG+++      V  +D +
Sbjct: 183 MEYKEVLADPNEPIRLNKFLANAGLCSRREADEFITAGVVSVNGVVVTELGTKVKRSDEV 242

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P++   +  + L      + T+    + ++ +     +   R+  VGRLD NT G
Sbjct: 243 KFHDQPVKIERKVYVLLNKPKDCVTTSDDPQERKTVLDLVKDACTERIYPVGRLDRNTTG 302

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     ++Y V     V +  L+ +  GI +             
Sbjct: 303 VLLLTNDGDLASKLTHPKYLKKKIYHVFLDKNVTKADLDQIASGITLDDGEIH-ADAISY 361

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 + V + +  GKNR ++++FE   ++V +L R+ +       L  G  R ++++ 
Sbjct: 362 ASDTDKSQVGIEIHSGKNRIVRRIFESLGYRVIKLDRVYFAGLTKKGLRRGDWRYLTERE 421

Query: 241 L 241
           +
Sbjct: 422 V 422


>gi|3915542|sp|O05668|Y1370_MYCLE RecName: Full=Uncharacterized RNA pseudouridine synthase ML1370;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|2065214|emb|CAB08276.1| unnamed protein product [Mycobacterium leprae]
          Length = 256

 Score =  143 bits (359), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 71/245 (28%), Positives = 109/245 (44%), Gaps = 4/245 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGV 65
           +       R+ K+++RAGIASRR  E++I + RV+V+G L+      V      + VDGV
Sbjct: 9   MDRGAGAVRLQKILSRAGIASRRAAEKLIIEGRVEVDGQLVRELGTRVDPDVSVVRVDGV 68

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLL 122
            +   +       +KP G+ +T SD  GR  V D +            VGRLD +TEGL+
Sbjct: 69  KVVVDDSLVYLALNKPRGMYSTMSDDRGRPCVGDLIERRVRGNKKLFHVGRLDADTEGLI 128

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTNDG LA  L  PS +  + Y     G V +     L  G+ +           +   
Sbjct: 129 LLTNDGELAHRLMHPSHEVSKTYLATVKGAVPRGLGKKLSVGLELDDGPAHVDDFAVVDA 188

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
                 V + L EG+ R ++++     + V  L+R   G   LG    G  R + +  +R
Sbjct: 189 IPGKTLVRLTLHEGRKRIVRRLLTAAGFPVEMLVRTDIGAVSLGDQRPGCLRALLRDEIR 248

Query: 243 EQLGP 247
           +    
Sbjct: 249 QLYKE 253


>gi|148377344|ref|YP_001256220.1| ribosomal large subunit pseudouridine synthaseB [Mycoplasma
           agalactiae PG2]
 gi|148291390|emb|CAL58774.1| Ribosomal large subunit pseudouridine synthaseB [Mycoplasma
           agalactiae PG2]
          Length = 246

 Score =  142 bits (358), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 105/247 (42%), Gaps = 11/247 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               RV K+IA++G+ SRR+ E+MI++  V VNG +           D I+V+G  +   
Sbjct: 2   PELVRVQKLIAQSGLMSRRDAEKMISKGLVFVNG-IKSSIGDKASMNDEIKVNGKIINLT 60

Query: 71  ERT---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           + T      L      + T+       + +  +L +   R++ VGRLD NT G+LLLT D
Sbjct: 61  KNTVFKYYLLNKPKNTITTSKDPKGRHTVI--DLINTSERIVPVGRLDRNTTGVLLLTTD 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
             L   L  P  +  RVYR R    +   +   L  GI I G             +    
Sbjct: 119 YELVNKLTHPKYEIERVYRARIDSPLTLKEFRELNAGIEIDGKM-----SYQIVDQVDTK 173

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L  G    +KK+FE     V  L R+SY    +  L  G  RE++ K ++     
Sbjct: 174 SYLISLHVGSYHHVKKLFEKIGHSVLTLKRVSYANLTVDKLPEGMYRELTIKEVKNLKLL 233

Query: 248 HLLEEAQ 254
              +E +
Sbjct: 234 VEQQEKK 240


>gi|329118296|ref|ZP_08247005.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           bacilliformis ATCC BAA-1200]
 gi|327465520|gb|EGF11796.1| ribosomal large subunit pseudouridine synthase F [Neisseria
           bacilliformis ATCC BAA-1200]
          Length = 245

 Score =  142 bits (358), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 65/245 (26%), Positives = 100/245 (40%), Gaps = 20/245 (8%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---------- 60
             P R+SK +A  G+ SRRE +  I +  V+VNG         V   D I          
Sbjct: 4   QEPLRLSKRMAELGLCSRREADAYIERGWVRVNGQTA-VLGQKVSPADRIDLAREAHETQ 62

Query: 61  -----EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                 +   P+          Y   + L T  +  +G  +     P     +   GRLD
Sbjct: 63  ARRVTVLLNKPVGYVSGQPEKGYRAAVELFTPENRWEGDQSRIPFDPRHLRGLAPAGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I++ GLL+LT DG  A+ L        + Y VR  G++ ++ L LL  G+ + G      
Sbjct: 123 IDSVGLLVLTQDGRTAKQLVGADGGSEKEYLVRVRGRLKENGLALLNHGLSLDGEPLRPA 182

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           +V    +      +   LR+GK R+I+++ E     V  L RI  G  +LG L  G  R 
Sbjct: 183 KVEWQNRDQ----LRFVLRQGKKRQIRRMCELVGLTVVGLKRIRIGRVKLGALPPGKWRY 238

Query: 236 VSKKI 240
           ++   
Sbjct: 239 LASDE 243


>gi|322389007|ref|ZP_08062577.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           parasanguinis ATCC 903]
 gi|321144312|gb|EFX39720.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           parasanguinis ATCC 903]
          Length = 251

 Score =  142 bits (358), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 52/238 (21%), Positives = 107/238 (44%), Gaps = 4/238 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGV 65
           + E     R+ +++A     +R+++++++A++++ V+ +  ++ + N+      I++   
Sbjct: 4   ISEKEPSMRLDQLMANHQY-TRKDIKQLLARRQILVDHLPAQKLSQNIDPGLQQIQIGER 62

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +++       L+     +               +    +  +  +GRLD +T GLLLLT
Sbjct: 63  IIQEPRHHYYMLHKPIGAVTAKRDAHHPTVIDLVDPQQEYPDLYPLGRLDRDTSGLLLLT 122

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKG 184
           ++G L   L  P     +VY V  +G +    +   + GI            +T+     
Sbjct: 123 DNGPLGFQLLHPQYHVEKVYEVEVNGPLYAAHIEQFQNGISFTDGPICKPASLTILESTP 182

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           S +   V + EGK  ++KK+F     KV  L R+S+GPF L   L  G +R +++  L
Sbjct: 183 SYSKAQVRISEGKYHQVKKMFLAIGVKVMTLKRLSFGPFTLDPQLAPGESRPLNEVEL 240


>gi|294155697|ref|YP_003560081.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           crocodyli MP145]
 gi|291600028|gb|ADE19524.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           crocodyli MP145]
          Length = 237

 Score =  142 bits (358), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 64/243 (26%), Positives = 106/243 (43%), Gaps = 8/243 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K++++AGIASRR  E +I +  VK+N  +           D I V+G  + + ++ 
Sbjct: 2   ERIQKLLSQAGIASRRSSEELIKKGLVKINDKVALV-GQKASFNDKITVNGKEILQEKKV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      + T   + D +     +L     R+  VGRLD +T G+LLLTNDG L+  
Sbjct: 61  YYILNKPAKYVCTNKDNFDRKKV--IDLLPNDVRIFPVGRLDYDTTGVLLLTNDGELSNK 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  PS + LR YR R    + +  LN L K  +I G        +   ++  N    V L
Sbjct: 119 LIHPSFKILRKYRARLDEPLSRQDLNELNKDQIINGKL-----SSQSVEQLDNKTYLVSL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
            +G    +K++F      V  L R+ +    +  +  G  R ++ K ++           
Sbjct: 174 HQGTYHHVKELFSKVGRLVINLKRVEFAGLGVEKIPVGEFRSLTMKEIKSLHNLVKEVRK 233

Query: 254 QVN 256
              
Sbjct: 234 NEK 236


>gi|324018876|gb|EGB88095.1| hypothetical protein HMPREF9542_02380 [Escherichia coli MS 117-3]
          Length = 277

 Score =  142 bits (358), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 80/274 (29%), Positives = 117/274 (42%), Gaps = 10/274 (3%)

Query: 28  RREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE-----RTRLWLYHKP 81
           RRE+E +I   RV V+G + +    V V     I +DG  +   E        L  Y   
Sbjct: 4   RREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRESAEQICRVLAYYKPE 63

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
             L T +      +          +R I+VGRLD+NT GLLL T DG LA  L  PS + 
Sbjct: 64  GELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREV 123

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
            R Y VR  GQVD  KL  L +G+ ++        +     +G N W  V L EG+NRE+
Sbjct: 124 EREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREV 183

Query: 202 KKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILREQLGPHLLEEAQVNL 257
           ++++E    +V+RLIR+ YG   L   L  G   E+       LRE +       ++V +
Sbjct: 184 RRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLRELVELPPETSSKVAV 243

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           +      +     R            R    ++ 
Sbjct: 244 EKDRRRMKANQIRRAVKRHSQVSGGRRSGGRNNG 277


>gi|84385630|ref|ZP_00988661.1| hypothetical ribosomal small subunit pseudouridine synthase A
           [Vibrio splendidus 12B01]
 gi|84379610|gb|EAP96462.1| hypothetical ribosomal small subunit pseudouridine synthase A
           [Vibrio splendidus 12B01]
          Length = 232

 Score =  142 bits (358), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 54/235 (22%), Positives = 102/235 (43%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   ++ E    I    V VN   +   +  V  ++ I ++G PL+  E  
Sbjct: 1   MRLDKYLCKSTDLTKPEAIERIHNGEVNVNSETVTDESTQVHESNTILLNGTPLKLREFR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L ++     + +   +       +  +       I+ GRLD +T GL+L+T+DG  +  
Sbjct: 61  YLLMHKPAGTICSNVDEVYPSLFKYIEIDKASELHIA-GRLDADTTGLVLITDDGRWSFN 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           + LP+    +VYRV     +  D  +  K G+ +QG        ++ + T K     V +
Sbjct: 120 ITLPTKSCKKVYRVTLSRDIKDDVADKFKAGVKLQGEQNLTRPAELEVITSK----EVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            + EGK  ++K++F     +V  L R   G  +L  + AG  R ++K  +     
Sbjct: 176 TITEGKFHQVKRMFAAVGNRVVGLHREQIGDVRL-DVEAGQWRYLTKAEVDSFQQ 229


>gi|15639450|ref|NP_218900.1| hypothetical protein TP0459 [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|189025691|ref|YP_001933463.1| hypothetical protein TPASS_0459 [Treponema pallidum subsp. pallidum
           SS14]
 gi|3322747|gb|AAC65447.1| conserved hypothetical protein [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|189018266|gb|ACD70884.1| hypothetical protein TPASS_0459 [Treponema pallidum subsp. pallidum
           SS14]
          Length = 261

 Score =  142 bits (358), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 71/255 (27%), Positives = 115/255 (45%), Gaps = 21/255 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+   +AR+G ASRR  E +IA  RV V+G  +      V + + + VDG  ++     R
Sbjct: 11  RLQVYLARSGCASRRACEALIASGRVTVDGQTVTTQGRTVCAQNVVCVDGTVVQLERVQR 70

Query: 75  LWLYHKPIGLVTT-----------------HSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
             L +KP+G + +                  S  +    +    P+   R+  +GRLD+ 
Sbjct: 71  YVLLYKPVGYICSLAPQFPAGYAHTQVRAGPSKQEYARAIDLVQPAYQERLYHIGRLDVR 130

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           +EG LL TNDG  A+ L  P +   + Y V     V    L+   +G+ ++G  Y  ++ 
Sbjct: 131 SEGALLFTNDGSFAQALGHPRSGIEKEYIVETREPVPAALLSSFVRGVWVEGCRYRCVRA 190

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                +     V + L EGK REI+ VFE +   V RL+R+  G  +LG L  G+ R + 
Sbjct: 191 RHLAAQ----CVQLVLVEGKKREIRVVFEAWGQDVVRLVRVRIGRVRLGPLRPGAFRTMR 246

Query: 238 KKILREQLGPHLLEE 252
            + + + L       
Sbjct: 247 LQEVAQLLQCAGCAR 261


>gi|301327006|ref|ZP_07220295.1| conserved hypothetical protein [Escherichia coli MS 78-1]
 gi|300846389|gb|EFK74149.1| conserved hypothetical protein [Escherichia coli MS 78-1]
          Length = 274

 Score =  142 bits (358), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 80/274 (29%), Positives = 117/274 (42%), Gaps = 10/274 (3%)

Query: 28  RREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE-----RTRLWLYHKP 81
           RRE+E +I   RV V+G + +    V V     I +DG  +   E        L  Y   
Sbjct: 1   RREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRESAEQICRVLAYYKPE 60

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
             L T +      +          +R I+VGRLD+NT GLLL T DG LA  L  PS + 
Sbjct: 61  GELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREV 120

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
            R Y VR  GQVD  KL  L +G+ ++        +     +G N W  V L EG+NRE+
Sbjct: 121 EREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREV 180

Query: 202 KKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILREQLGPHLLEEAQVNL 257
           ++++E    +V+RLIR+ YG   L   L  G   E+       LRE +       ++V +
Sbjct: 181 RRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLRELVELPPETSSKVAV 240

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           +      +     R            R    ++ 
Sbjct: 241 EKDRRRMKANQIRRAVKRHSQVSGGRRSGGRNNG 274


>gi|254293522|ref|YP_003059545.1| RNA-binding S4 domain protein [Hirschia baltica ATCC 49814]
 gi|254042053|gb|ACT58848.1| RNA-binding S4 domain protein [Hirschia baltica ATCC 49814]
          Length = 315

 Score =  142 bits (358), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 65/313 (20%), Positives = 124/313 (39%), Gaps = 19/313 (6%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +   PQR++K + ++G+ SRRE E ++ Q  + ++G+ +      +   + + +      
Sbjct: 8   DGEEPQRINKWLGQSGVCSRREAEGLVEQGLISIDGVKVTEPGRKIEKGETLTLADAATD 67

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-----------LPSIFSRVISVGRLDIN 117
           K       + +KPI  V+ H +      V              +P   +R+  VGRLD +
Sbjct: 68  KLASAMSVILNKPIDYVSAHPNEGEVPAVRLLTKANLSGQSETIPDRDTRLAPVGRLDKD 127

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           + GLL+LT DG L + +  P     + Y V  +G +  +K+  L  G+ + G       V
Sbjct: 128 SRGLLILTEDGVLTKAVIGPDADSEKEYLVTVNGTITHEKIRRLCHGLRMDGRALKPAIV 187

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           T +  +     +   L EG+NR+I+++ E     V  L RI  G   +G L  G  R ++
Sbjct: 188 THEGGQ----VLRFILTEGRNRQIRRMAELVQLHVVDLFRIRIGHVHIGELPEGKWRTMT 243

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT---RMKKNSSQKNG 294
               R+ L      +  +  D    +     +    +  +             +   K  
Sbjct: 244 THE-RDGLIDKSKADKSLKPDPISSTFVPPEKPEKPVRRQGTSAKKLDPYRNADGYSKRN 302

Query: 295 LSKQKKLATPVHR 307
              + +   P  +
Sbjct: 303 YKAKSRPKYPGTK 315


>gi|146306387|ref|YP_001186852.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           mendocina ymp]
 gi|145574588|gb|ABP84120.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           mendocina ymp]
          Length = 230

 Score =  142 bits (358), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 54/231 (23%), Positives = 105/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     SR++   +I+  R++V+G  +     +V     +E+D   L+     
Sbjct: 1   MRLDRFLSNFPRFSRQDSRLLISAGRLRVDGETVRDPRFDVRDFQRVELDDELLQAGRSA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R W+ HKP+G+V+  +  + R+ +          +   GRLD+NT GLLL+TNDG  +R 
Sbjct: 61  RYWMLHKPVGVVSATAHDEHRTVLDLLDEPDRHDLHLAGRLDLNTSGLLLITNDGRWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  +VY V     +  +   + ++      + +     ++ L      +    +
Sbjct: 121 ITQPQQRKPKVYHVSTEQPITAEYAEVFERGLYFAFEDLTTLPARLELL----GSHSARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            L EG+  ++K++F  F  +V  L R S G   L   L  G  R ++   +
Sbjct: 177 TLFEGRYHQVKRMFGHFRNRVVALHRESMGEIVLDPQLAPGQYRALTAAEI 227


>gi|325193088|emb|CCA27453.1| RNA pseudouridine synthase putative [Albugo laibachii Nc14]
          Length = 285

 Score =  142 bits (358), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 96/250 (38%), Positives = 138/250 (55%), Gaps = 10/250 (4%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVD 63
           NI        R+SK IA AGI SRR+ E+ I   +V +NG +L     ++    D + VD
Sbjct: 28  NIESSTDQKMRISKWIAMAGICSRRQAEKKILSNQVVLNGNVLRDVGQSINPKVDRVTVD 87

Query: 64  GVPL-------RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRL 114
           G+ L       + +   +LWL HK  G + T  DP GR T+FD    +     ++ VGRL
Sbjct: 88  GIDLMRRKPEDKASYPRKLWLAHKLKGELVTTEDPQGRRTIFDRFRQMGLKQHLMPVGRL 147

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D NTEGLL+ TNDG  AR LE P     R YR    G V + K++ L +G ++ G+ Y  
Sbjct: 148 DYNTEGLLVFTNDGEYARQLEHPKFCVERTYRALVRGNVLRSKIDELARGAIVNGVKYRP 207

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +QV++ +    ++W+ V LREGKNRE++         V RLIR+ +GP++L  L +GS  
Sbjct: 208 IQVSIHSTDKKDSWLQVKLREGKNREVRNALAHVRLIVKRLIRVRFGPYRLADLPSGSVL 267

Query: 235 EVSKKILREQ 244
           EV  K+L +Q
Sbjct: 268 EVVPKVLEKQ 277


>gi|239501492|ref|ZP_04660802.1| hypothetical protein AbauAB_04211 [Acinetobacter baumannii AB900]
          Length = 234

 Score =  142 bits (358), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 47/226 (20%), Positives = 90/226 (39%), Gaps = 3/226 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V ++G ++          +    V G   +  E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVSIDGEVVGDLKKQFSPENFEFSVFGQNYQYREKIY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        + H               I   V +VGRLD +T GLLLLT+DG   + L
Sbjct: 63  IALRKPQGFECSHHPQHHQSVFSLLPETMIHRGVQAVGRLDQDTTGLLLLTDDGKYLQAL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     +VY V  +  V  +++ +L +G+ +           +         +T+ + 
Sbjct: 123 THPRKHVPKVYHVTTYDPVTPEQIEMLTQGVNLHQEKGVFAATDVALL--GTHQLTMTIH 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +G   ++K++      KV +L R   G   L  +  G    +S++ 
Sbjct: 181 QGVYHQVKRMIAAVGNKVEKLHRHQIGQLVLPEIEEGGWVYLSEQE 226


>gi|319786881|ref|YP_004146356.1| RNA-binding S4 domain protein [Pseudoxanthomonas suwonensis 11-1]
 gi|317465393|gb|ADV27125.1| RNA-binding S4 domain protein [Pseudoxanthomonas suwonensis 11-1]
          Length = 509

 Score =  142 bits (358), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 84/350 (24%), Positives = 145/350 (41%), Gaps = 12/350 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ KV+A+AG+ SRR +E+ IA   VKVNG + +    ++ S D +E+DG         
Sbjct: 29  ERLHKVLAQAGLGSRRALEQRIADGLVKVNGEVAQV-GQSIRSGDRVELDGKAFVASALT 87

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + T        +          +R I++GRLDINT GLLLLT DG 
Sbjct: 88  EPARVLVYNKPEGEVTTREDPEGRPTIFESLPRLKGARWIAIGRLDINTTGLLLLTTDGE 147

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           +A  +  PS +  R Y VR      Q+      ++ L +G+ ++       Q+       
Sbjct: 148 IANAMMHPSYEVEREYVVRVRAPEGQESVPDNIVDRLARGVALEDGPAKFDQIERIGGTD 207

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           S+ W  V ++EG+NRE+++++E    +V+RL R+ YG   L   LL G ++E+  +   E
Sbjct: 208 SHDWFKVVVKEGRNREVRRLWESQGCQVSRLKRVRYGKVSLPRELLRGQSQEL-PQEQVE 266

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            L   L  E        +       R     +         +  +++   G   ++    
Sbjct: 267 ALRKELKLEDSAASTLTLQPVIGQRRATKTAVRVGQGGQAYVNGHNTADEGRELRRFDHV 326

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              RR          G+  S    + Q ++  ++       + L   +  
Sbjct: 327 REDRRGGRGGKKPHGGLTVSGEMAAKQSQKPFKQRAQKGGLKPLPDGNPA 376


>gi|167894879|ref|ZP_02482281.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 7894]
          Length = 307

 Score =  142 bits (358), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 59  VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 118

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 119 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 178

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 179 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDG 238

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 239 VPLKPAMVSWQNGEQ----LCFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 294

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 295 QGEWRYLGPDE 305


>gi|332530024|ref|ZP_08405974.1| RNA-binding s4 domain protein [Hylemonella gracilis ATCC 19624]
 gi|332040497|gb|EGI76873.1| RNA-binding s4 domain protein [Hylemonella gracilis ATCC 19624]
          Length = 302

 Score =  142 bits (358), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 62/269 (23%), Positives = 96/269 (35%), Gaps = 48/269 (17%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---------- 64
           R++K +A  G+ SRRE +  +    VKVNG +       V   D IEVD           
Sbjct: 37  RLNKRMAELGLCSRREADAWVENGWVKVNGRVA-EMGQQVSPADRIEVDPQAQNQQATQV 95

Query: 65  -----VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
                 P+          +   + LV   +                  +   GRLDI++ 
Sbjct: 96  TILLHKPIGYVSGQAEDGHEPAVVLVQAQNRWREDRAPHRFNGGQLRGLAPAGRLDIDST 155

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVR----------------------------FHG 151
           GLL+LT DG +AR L    ++  + Y VR                               
Sbjct: 156 GLLVLTQDGRVARQLIGEDSEIEKEYLVRVVYLGTPAAASAPTELQPIHANDPVSANVQA 215

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 L  L+ G+ + G      +V  +  +     +   L+EGK R+I+++ E    K
Sbjct: 216 VFPPAMLAKLRHGLSLDGQALKPARVDWENTEQ----LRFVLKEGKKRQIRRMCELVGLK 271

Query: 212 VNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           V  L R+  G   LG L  G  R ++   
Sbjct: 272 VVGLKRVRIGRVMLGQLPQGQWRYLAPHE 300


>gi|315059155|gb|ADT73484.1| Putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni S3]
          Length = 253

 Score =  142 bits (358), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 69/248 (27%), Positives = 111/248 (44%), Gaps = 16/248 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+     SRRE + +I Q  VK+N  +    +  V   D + V G  ++K  + 
Sbjct: 1   MRINKFISHNTRYSRREADELIKQGLVKINNKIA-LLSDEVKFDDKVFVKGKRVQKRTQF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +YHK  G + +  D  GR T++D LP  FS  +SVGRLD  +EGLLLLT+   +A  
Sbjct: 60  SVIIYHKQKGEIVSKKDDRGRKTIYDTLPRQFSTWLSVGRLDYASEGLLLLTDSPVIADA 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI------------CYGDMQVTLDT 181
           L     +     +V+        +       +  +                  +   +  
Sbjct: 120 LMHSDLEREYYLKVKGTVSKQVIEAMQNGLEVKNEKKGAHAKTKITSMSFAPFIDFEIFG 179

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI- 240
             G    + V + EGKNRE+++ F  F+ +V  L R+++G   LG L AG  R +     
Sbjct: 180 SSGGYTKLRVVINEGKNRELRRFFGHFDLEVMDLKRVAFGALDLGMLKAGKHRYLENGEY 239

Query: 241 --LREQLG 246
             LR+ L 
Sbjct: 240 EKLRDFLK 247


>gi|312113041|ref|YP_004010637.1| pseudouridine synthase [Rhodomicrobium vannielii ATCC 17100]
 gi|311218170|gb|ADP69538.1| pseudouridine synthase [Rhodomicrobium vannielii ATCC 17100]
          Length = 800

 Score =  142 bits (358), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 133/327 (40%), Positives = 182/327 (55%), Gaps = 11/327 (3%)

Query: 34  MIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           MI ++RV VNG ++E AA++V  TD + VDG PL   E  RLW YHKP G VTTH DP+G
Sbjct: 1   MIGEKRVSVNGSIIESAALDVSPTDRVAVDGHPLPAREPPRLWRYHKPKGRVTTHKDPEG 60

Query: 94  RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
           R TVF+ LP    R+IS+GRLD NTEGLLLLTNDG LAR +ELPST W R YRVR  G++
Sbjct: 61  RPTVFEALPDNLPRLISIGRLDFNTEGLLLLTNDGELARHMELPSTGWARRYRVRAFGEI 120

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           DQ  L+ LK G+ I G+ YG ++ +L+ + G N W+T+ +REGKNRE++++ E     VN
Sbjct: 121 DQASLDKLKNGVRIAGVNYGPVEASLERETGDNVWITLLIREGKNREVRRIMEHLGLTVN 180

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQV--NLDAPIYSSETLVRDR 271
           RLIRIS+GPF LG L  G   EV   +L++QLGP L     V   +        T  R +
Sbjct: 181 RLIRISFGPFMLGDLEPGQVEEVKTSVLKDQLGPRLARSLGVRREVVREEKRLSTPSRGK 240

Query: 272 PNIISEVPDDFTRMKKNSSQKNGLSK----QKKLATP-----VHRRNLASNVWMAKGIHS 322
           P  +     +  R ++   +     +    +     P        +   ++         
Sbjct: 241 PTYLRRKEAEPERPRRAFEEPQMRRRRVLSEDASEAPIVELVPVPKPPRADRGERGEKRD 300

Query: 323 SFLSDSGQREENHRRSPSFPSKRSLRR 349
               D G+R  +  R  +   +RS  R
Sbjct: 301 FAPRDRGERSFDRPRDDAGGERRSFGR 327



 Score = 40.5 bits (93), Expect = 0.41,   Method: Composition-based stats.
 Identities = 13/118 (11%), Positives = 23/118 (19%), Gaps = 1/118 (0%)

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G  R    +                +                    E    F R +    
Sbjct: 567 GERRSFRPRE-GGGERKSFGPRDGADRPPFRKREGDRTDRPSRAAGEDRPRFRRSEDGGD 625

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
              G    +        R+ ++         S       +RE    R+P    +R   
Sbjct: 626 SARGPRPDRAPGDRPAYRSRSNEGGAGGERKSFDKPFRERREGAGDRAPQREGERQAS 683


>gi|332363998|gb|EGJ41777.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK355]
          Length = 241

 Score =  142 bits (358), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 56/231 (24%), Positives = 102/231 (44%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++ + Q+++ V+     + + NV ++   I   G  +     
Sbjct: 1   MRLDQLLA-ANHISRKKMKQSLLQKQILVDDKPACKLSQNVDTSLQQITFQGKHVSGPAH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +               +       + S+GRLD +TEGLLL+T++G L  
Sbjct: 60  RYYMLNKPAGAVTANRDAEKLTVLDLLDEEVEKENLYSIGRLDRDTEGLLLITDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V  +G +     +  ++GI           Q+++ +   S +  TV
Sbjct: 120 QLLHPQYHVEKTYYVEVNGPLTPKDKSSFQEGIRFLDGTTCQPAQLSILSTSSSLSCATV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  +IKK+F     KV  L RI +G F L   L  G  R ++++ L
Sbjct: 180 KISEGKFHQIKKMFLAVGVKVTYLKRIQFGDFTLDPELATGDYRPLNQEEL 230


>gi|227889739|ref|ZP_04007544.1| pseudouridylate synthase [Lactobacillus johnsonii ATCC 33200]
 gi|227849603|gb|EEJ59689.1| pseudouridylate synthase [Lactobacillus johnsonii ATCC 33200]
          Length = 233

 Score =  142 bits (358), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 104/233 (44%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I ++ V VNG +++     V   D + VDG  +   +  
Sbjct: 1   MRIDKYLANMNVGSRKEVHNLIKKKIVTVNGEVVKTPKEQVKEEDQVAVDGEKVAYQQYH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L      +  T                 +  +  VGRLD +T GLLLLTNDG LA  
Sbjct: 61  YFLLNKPKGVISATEDRSQKTVLSLLKPKDRYKDIAPVGRLDKDTTGLLLLTNDGALAHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG--SNAWVT 190
           L  P+    + YR +  G  D++ + +   G+ +  G      ++ +  Q      + + 
Sbjct: 121 LLAPNKHVTKKYRAKIAGVADEETVKIFASGMTLGDGTKLKPARLKILMQDKESDESEIE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           + ++EGK  +IK++F     KV  L RIS     L  +L  G  +E+  K ++
Sbjct: 181 IEIQEGKYHQIKRMFGAVGMKVIELDRISMEKLVLPTSLKRGEYKEIRLKEIK 233


>gi|330889469|gb|EGH22130.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. mori str. 301020]
          Length = 230

 Score =  142 bits (358), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 100/231 (43%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R+ V   +A  RV+V+G         V     + +DG  L+  +  
Sbjct: 1   MRLDRFLSNLPSLNRKSVRLALASGRVQVDGQTTSDPHHEVRDFSRVALDGEILQAGKAA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V+   D    + +          +   GRLD NT GL+L+TNDG  +R 
Sbjct: 61  RYFMLHKPEGCVSATVDTQHPTVLDLLDEPDRHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLK--KGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+              + I     Q+TL   + +     +
Sbjct: 121 LTQPQTKMPKVYYVETEQPIDERYAATFAAGMYFSFENITTQPAQLTLLRPRSA----RL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F  FN KV RL R + G   L   L  G  R +    +
Sbjct: 177 TIVEGRYHQVKRMFGHFNNKVLRLHRENIGALALDPALAPGGYRALHAAEI 227


>gi|121997382|ref|YP_001002169.1| pseudouridine synthase [Halorhodospira halophila SL1]
 gi|121588787|gb|ABM61367.1| ribosomal large subunit pseudouridine synthase B [Halorhodospira
           halophila SL1]
          Length = 278

 Score =  142 bits (357), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 98/251 (39%), Positives = 143/251 (56%), Gaps = 13/251 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRK 69
            +++ KV+ARAG+ SRRE+E  I   RV++ G   +         DH+E+DG     + +
Sbjct: 11  GEKLQKVLARAGLGSRREMEAAIQAGRVRIEGRTAK-LGDRARPRDHVELDGRTVQRVHR 69

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               R+ LY+KP G VTT SDP+GRSTVF+ LP    R I+VGRLDIN++GLLL TNDG 
Sbjct: 70  EPPRRVLLYNKPEGEVTTRSDPEGRSTVFERLPRTPGRWIAVGRLDINSQGLLLFTNDGE 129

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-----VTLDTQKG 184
           LA  L  PST   R Y  R HG+V ++ ++ L  G+ ++                + Q+G
Sbjct: 130 LANALMHPSTGVEREYACRIHGEVTEEMVHRLVDGVELEDGPAHFEVVESGMPVDEPQEG 189

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK---KI 240
           +NAW  V + EG+ RE+++++E     V+RLIR+ YGP  +   L  G  RE+ +   + 
Sbjct: 190 TNAWYHVIVTEGRRREVRRLWESQGVTVSRLIRVRYGPMVMPRDLRRGQLRELDEAGKRE 249

Query: 241 LREQLGPHLLE 251
           L E +G    E
Sbjct: 250 LYEHVGLTPPE 260


>gi|282856276|ref|ZP_06265557.1| RNA pseudouridine synthase family protein [Pyramidobacter piscolens
           W5455]
 gi|282585853|gb|EFB91140.1| RNA pseudouridine synthase family protein [Pyramidobacter piscolens
           W5455]
          Length = 239

 Score =  142 bits (357), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 62/242 (25%), Positives = 99/242 (40%), Gaps = 20/242 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--------- 64
            R+SK +A  G+ SRRE +  I++  V VNG+        V   D IE++          
Sbjct: 1   MRLSKRMAELGLCSRREADEYISRGLVSVNGVPA-VLGQKVTERDRIEMNRVAERDQSRR 59

Query: 65  ------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  PL          Y     L+   +   G  +           ++  GRLD+N+
Sbjct: 60  VTILLHKPLGYVSGQAEDGYRPARVLIRPENCWSGDKSPLRFDLRQLQNLVPAGRLDVNS 119

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLL+LT DG +AR L    +   + Y VR  G + +  L LL  G+ + G      +V 
Sbjct: 120 TGLLVLTQDGRVARRLVGEDSAVEKEYLVRVAGSLSERGLALLNHGLSLDGEELLPARVR 179

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
                     +   L++GK R+I+++      +V  L R+  G  +LG L  G  R +  
Sbjct: 180 WQNDDQ----LRFVLQQGKKRQIRRMCALVGLEVLALKRVRVGSVRLGALPPGQWRYLLP 235

Query: 239 KI 240
           + 
Sbjct: 236 EE 237


>gi|294650005|ref|ZP_06727393.1| ribosomal small subunit pseudouridine synthase A [Acinetobacter
           haemolyticus ATCC 19194]
 gi|292824098|gb|EFF82913.1| ribosomal small subunit pseudouridine synthase A [Acinetobacter
           haemolyticus ATCC 19194]
          Length = 238

 Score =  142 bits (357), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 48/225 (21%), Positives = 90/225 (40%), Gaps = 3/225 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V ++    +    N  + D   +V G   +  E   
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGAVSIDSQTCDNPKQNFSTEDLSFQVFGEQYQYREYVY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L+       +  +              +   V  VGRLD +T GLLLLT+DG   + L
Sbjct: 63  IVLHKPQGYECSHQATHHRSVFSLLPEILVHRGVQCVGRLDQDTTGLLLLTDDGQYLQAL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     +VY V     V  ++   L+ G+ ++      +    D +  S   + + + 
Sbjct: 123 THPKKHVPKVYCVSTADPVTTEQKQQLELGVELRNE--KGIYAATDIKLISERQLAMTIH 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G   ++K++      KV RL R   G  +L  L  G    ++ +
Sbjct: 181 QGVYHQVKRMIAAVGNKVERLHRQQIGLLELPNLEEGHWDYLTPQ 225


>gi|15828808|ref|NP_326168.1| ribosomal large subunit pseudouridine synthase B (pseudouridylate
           synthase) (uracil hydrolyase) [Mycoplasma pulmonis UAB
           CTIP]
 gi|14089751|emb|CAC13510.1| RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE B (PSEUDOURIDYLATE
           SYNTHASE) (URACIL HYDROLYASE) [Mycoplasma pulmonis]
          Length = 232

 Score =  142 bits (357), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 66/229 (28%), Positives = 105/229 (45%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            ++ K IA  G  SRR+ E +I Q +VKVN          V   D IE++G  L + E  
Sbjct: 1   MKIQKRIAHLGYCSRRQAEALILQNKVKVNSSFAT-IGQIVSDQDIIEINGKILVEKENE 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + +          + +  +    V  +L    SRV  VGRLD NT G+L+LTNDG L + 
Sbjct: 60  KEYYLLHKPPKTISSTKDEKNRQVVTDLVKSKSRVYPVGRLDYNTTGVLILTNDGDLTQK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  Q  R+Y  +    +++ +L  L +  +                +       V L
Sbjct: 120 LLHPKYQIKRLYHCKLDIPLEEKELIYLNEEKIYIDKKL----SIHKVLQVEKKSYLVEL 175

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G    +KK+FE  N KV +L R+++GP  +  L  G  R+++ K ++
Sbjct: 176 HQGSYHHVKKIFEKVNRKVVKLKRLAFGPITIDNLPEGYFRKLTFKEIK 224


>gi|153954187|ref|YP_001394952.1| RNA pseudouridine synthase-related protein [Clostridium kluyveri
           DSM 555]
 gi|146347068|gb|EDK33604.1| RNA pseudouridine synthase-related protein [Clostridium kluyveri
           DSM 555]
          Length = 239

 Score =  142 bits (357), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 69/230 (30%), Positives = 123/230 (53%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +A  G+ASRR+ E +I++ RVKVNG+++ +    +    D I VD   ++K  +
Sbjct: 3   ERLHKYMAACGVASRRKCEHIISEGRVKVNGVVVNKLGTTIDDERDEILVDNKIIKKENK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G +++  D  GR T+ D +     RV  +GRLD NT G ++LTNDG +  
Sbjct: 63  KVYILLNKPRGYISSVKDDRGRKTLLDIVKVN-ERVYPIGRLDYNTSGAIILTNDGEVYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P +   ++Y     G    +++   + GI I G      +    +    ++ V + 
Sbjct: 122 NIAHPGSNKSKIYIAAIKGIPSSEEIKRFENGIDIGGYITAKAKFDFISSNKESSKVKIE 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGKNR+++K+ +     V  L+RI+ G  +LG L  G+ R +++K ++
Sbjct: 182 IHEGKNRQVRKMCDAIGHPVITLMRIAIGDIKLGNLKEGAWRYLTEKEIQ 231


>gi|166712399|ref|ZP_02243606.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzicola BLS256]
          Length = 553

 Score =  142 bits (357), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 86/360 (23%), Positives = 136/360 (37%), Gaps = 24/360 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG         
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGTVAQT-GMSVRSGDKIELDGRSFVASALT 86

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + T        +          SR I++GRLDINT GLLLLT DG 
Sbjct: 87  EPSRVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR      ++      +  L +G++++       ++       
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV---SKKI 240
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + EV       
Sbjct: 207 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGQSVEVAQDKVDA 266

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEV----------PDDFTRMKKNSS 290
           LR +L       + + L   I                             D  R  +   
Sbjct: 267 LRAELKLEEGAPSALTLQPVIGQRRAAKSTVHVTRDGRSNAYVNGHTSGADEGRELRRFD 326

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                  +     P       +    A    S       +      R        +  R+
Sbjct: 327 NLREDRGRGGRGKPGDFMGGLTVSGEAAARQSQQRPFKQRGPAKGDRGALPEGNPAAFRS 386


>gi|289168287|ref|YP_003446556.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           mitis B6]
 gi|288907854|emb|CBJ22694.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           mitis B6]
          Length = 241

 Score =  142 bits (357), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 56/231 (24%), Positives = 105/231 (45%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+       A N+ +    +   G  ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLKGDILVDSCPARSLAQNIDTGLQELLFQGRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +             F        ++ +VGRLD +T GLLL+T++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKKLPTVMDFLPPDIQSDKLYAVGRLDRDTTGLLLVTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V  +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVEVNGLLTPDHIQTFQKGIVFLDGTVCKAARLEILSASPSLSQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++KK+F     KV  L R  +GP+ L   L AG  R ++ + L
Sbjct: 180 TISEGKFHQVKKMFLSVGVKVTSLKRTHFGPWSLDDNLQAGDYRPLNSEEL 230


>gi|295111666|emb|CBL28416.1| pseudouridine synthase family [Synergistetes bacterium SGP1]
          Length = 244

 Score =  142 bits (357), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 99/233 (42%), Gaps = 1/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
                R++  +A  G+ASRR  E +I   RV+V   ++      V    D +  DG  L+
Sbjct: 2   EVRGTRLNAFLAACGVASRRRAEEVIRAGRVRVGDRIVLAPFFQVDPEVDEVTCDGRTLK 61

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             E   + +      +       D              RV   GRLD  +EGLL+LTNDG
Sbjct: 62  ATEPVYVVMNKPGGVVCAVSDKYDPVVVDLLPEAVKSRRVYPAGRLDRESEGLLILTNDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L + +  PS    + Y    +  +++ +L   + G  I+G     + VTL  ++    W
Sbjct: 122 ALTQEVMHPSKGLHKEYEALLNVPINERQLARWRGGFEIEGRRAVPISVTLMDREPEGRW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V+V + EG  RE++ +     + V RL+R   G   L  L  G   ++S   L
Sbjct: 182 VSVVIGEGLKREVRVMANLAGFSVERLVRRRLGKMVLEKLRPGEFVDLSFSEL 234


>gi|260554617|ref|ZP_05826838.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter baumannii ATCC
           19606]
 gi|260411159|gb|EEX04456.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter baumannii ATCC
           19606]
          Length = 234

 Score =  142 bits (357), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 47/226 (20%), Positives = 90/226 (39%), Gaps = 3/226 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V ++G ++          +    V G   +  E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVIIDGEVVSDLKKQFSPENFEFSVFGQNYQYREKIY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        + H               I   V +VGRLD +T GLLLLT+DG   + L
Sbjct: 63  IALRKPQGFECSHHPQHHQSVFSLLPETMIHRGVQAVGRLDQDTTGLLLLTDDGKYLQAL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     +VY V  +  V  +++ +L +G+ +           +         +T+ + 
Sbjct: 123 THPRKHVPKVYHVTTYDPVTPEQIEMLTQGVNLHQEKGVFAATDVALL--GTHQLTMTIH 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +G   ++K++      KV +L R   G   L  +  G    +S++ 
Sbjct: 181 QGVYHQVKRMIAAVGNKVEKLHRHQIGQLVLPEIEEGGWVYLSEQE 226


>gi|229062234|ref|ZP_04199556.1| RNA pseudouridine synthase [Bacillus cereus AH603]
 gi|228717062|gb|EEL68741.1| RNA pseudouridine synthase [Bacillus cereus AH603]
          Length = 203

 Score =  142 bits (357), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 52/202 (25%), Positives = 92/202 (45%), Gaps = 8/202 (3%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
           +NG +       V   D + ++G  + K E+      +HKP+G+  T +D    + +   
Sbjct: 3   INGEICTH-GTRVRDGDIVTINGQVIEKEEKEKVYIAFHKPVGITCTAADHIEDNIIDYI 61

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
             +   R+  VGRLD  +EGL+LLTNDG +A  +     +  + Y V          ++ 
Sbjct: 62  --NYPERIFPVGRLDKASEGLILLTNDGTIANQILHGDHEHEKEYVVTVDKPFTDWFIDE 119

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           +  G+ I+       +VT        +   V L +G NR+I+++   F + V +L R+  
Sbjct: 120 MSGGVKIKDGMTKPCKVTRI----DQSTFRVVLTQGMNRQIRRMSRAFGFTVTKLKRVRI 175

Query: 221 GPFQLGTLLAGSTREVSKKILR 242
              +L  L AG  R+++ K L 
Sbjct: 176 MNIELNELEAGKWRDITPKELE 197


>gi|169795557|ref|YP_001713350.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter baumannii AYE]
 gi|213158501|ref|YP_002319800.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter baumannii
           AB0057]
 gi|215483044|ref|YP_002325249.1| hypothetical protein ABBFA_001346 [Acinetobacter baumannii
           AB307-0294]
 gi|301347860|ref|ZP_07228601.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter baumannii
           AB056]
 gi|301597806|ref|ZP_07242814.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter baumannii
           AB059]
 gi|332850625|ref|ZP_08432872.1| pseudouridylate synthase [Acinetobacter baumannii 6013150]
 gi|332867094|ref|ZP_08437391.1| pseudouridylate synthase [Acinetobacter baumannii 6013113]
 gi|169148484|emb|CAM86350.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter baumannii AYE]
 gi|213057661|gb|ACJ42563.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter baumannii
           AB0057]
 gi|213985713|gb|ACJ56012.1| conserved hypothetical protein [Acinetobacter baumannii AB307-0294]
 gi|332730462|gb|EGJ61778.1| pseudouridylate synthase [Acinetobacter baumannii 6013150]
 gi|332734287|gb|EGJ65416.1| pseudouridylate synthase [Acinetobacter baumannii 6013113]
          Length = 234

 Score =  142 bits (357), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 46/226 (20%), Positives = 89/226 (39%), Gaps = 3/226 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V ++G ++          +    V G   +  E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVIIDGEVVSDLKKQFSPENFEFSVFGQNYQYREKIY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        +                 I   V +VGRLD +T GLLLLT+DG   + L
Sbjct: 63  IALRKPQGFECSHQPQHHQSVFSLLPETMIHRGVQAVGRLDQDTTGLLLLTDDGKYLQAL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     +VY V  +  V  +++ +L +G+ +           +         +T+ + 
Sbjct: 123 THPRKHVPKVYHVTTYDPVTPEQIEMLTQGVNLHQEKGVFAATDVALL--GTHQLTMTIH 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +G   ++K++      KV +L R   G   L  +  G    +S++ 
Sbjct: 181 QGVYHQVKRMIAAVGNKVEKLHRHQIGQLVLPEIEEGGWVYLSEQE 226


>gi|219115295|ref|XP_002178443.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217410178|gb|EEC50108.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 252

 Score =  142 bits (357), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 64/242 (26%), Positives = 108/242 (44%), Gaps = 10/242 (4%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + +     R++K++A  G  SRRE  R I Q  VKVNG++   A   V  TD +E+    
Sbjct: 1   MNKLGVSIRLNKLLAHQGWCSRREANRFIEQGLVKVNGVVSRDA--RVAPTDTVELLPQA 58

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD-----NLPSIFSRVISVGRLDINTEGL 121
           +    + +  L HKP+G V++  + D              P       + GRLDIN+ GL
Sbjct: 59  VTVQAQQKTILVHKPVGYVSSQPETDSIPQEQASSRRLFHPRTQLGWATAGRLDINSTGL 118

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGIC--YGDMQVT 178
           L+LT  G +A+ L  P  +  + Y VR       D+       +  ++      G++   
Sbjct: 119 LVLTQSGRVAKTLIGPDVRVDKEYLVRVRPSPFFDRNQSTAAVLERLRDGIRDAGELLHA 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +  ++ +   +   L EGK+R I+++      +V+ L R+  G   LG L  G  R ++ 
Sbjct: 179 VSVERVNTDQLRFVLHEGKHRHIRRMCRAVGLEVDGLKRVRIGEIVLGNLPVGQWRYLAP 238

Query: 239 KI 240
             
Sbjct: 239 HE 240


>gi|145503394|ref|XP_001437673.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124404826|emb|CAK70276.1| unnamed protein product [Paramecium tetraurelia]
          Length = 336

 Score =  142 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 96/284 (33%), Positives = 160/284 (56%), Gaps = 8/284 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVP 66
              P R+SK +A+  + SRRE E+MI    + V+G  ++   + V S + I+V   +G  
Sbjct: 32  QSEPMRLSKYLAQTSVCSRREAEKMIESGMILVDGKKVDS-NIPVTSENKIQVFTKNGER 90

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLL 123
           +   + T++W+++KPIG++ +H+DP  R + +D           +ISVGRLD N+EGL++
Sbjct: 91  MPVKQSTKVWIFYKPIGMICSHNDPFKRPSFYDFAKLRLKTDQHIISVGRLDFNSEGLIV 150

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           +TNDG LAR +ELP T+  R+YRVR +G   ++KL  ++ G+ I G+ YG   V ++ ++
Sbjct: 151 VTNDGELARCMELPETKLQRIYRVRVYGTFTEEKLKKIRNGLTIAGVNYGPYWVNVENRQ 210

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK-ILR 242
             N W+ + L  GKNREI+KV + F+ +VNRLIR SYGP++L  L  G   E   +  ++
Sbjct: 211 SRNTWLIMRLESGKNREIRKVMQKFDLRVNRLIRQSYGPYKLMGLKPGDFYEAQIEPEIK 270

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
            +L     ++ Q   +        L     +  S+      + +
Sbjct: 271 RKLYLQARKKLQNVQEQIQLEQTKLNIKALDEQSKNEKQIEKQE 314


>gi|187735933|ref|YP_001878045.1| pseudouridine synthase [Akkermansia muciniphila ATCC BAA-835]
 gi|187425985|gb|ACD05264.1| pseudouridine synthase [Akkermansia muciniphila ATCC BAA-835]
          Length = 230

 Score =  142 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 51/232 (21%), Positives = 80/232 (34%), Gaps = 6/232 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+  +++R G  SRRE    I +  +   G         V +   I +DG P+   +  
Sbjct: 1   MRLDALLSRYGYCSRREAPGWIKRHSITFKGKPCSSPTDKVQAEG-ILLDGEPVEFPDGL 59

Query: 74  RLWLYHKPIGLVTTHSDPDG--RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              LY       +            +          V SVGRLD  T GLLLLT+DG   
Sbjct: 60  YAALYKPEGYTCSHDDGEGNLIYDLLPFQWRHRNPAVSSVGRLDKETSGLLLLTDDGKFI 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P     +VY       +  + + L   G +            L   +     + +
Sbjct: 120 HRMTSPRHHVAKVYEAVTEEDIPTEAVELFASGTLTLNGETRPCAPALLEIREPRRAL-L 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKIL 241
            L EGK  +++++       V  L R+S G   L    L  G    +    L
Sbjct: 179 TLTEGKYHQVRRMLAAVGAPVLSLCRVSIGSLHLDSLNLKPGEWAPIRPDAL 230


>gi|219681647|ref|YP_002468033.1| 23S rRNA pseudouridine synthase (YciL) [Buchnera aphidicola str. 5A
           (Acyrthosiphon pisum)]
 gi|219682204|ref|YP_002468588.1| 23S rRNA pseudouridine synthase (YciL) [Buchnera aphidicola str.
           Tuc7 (Acyrthosiphon pisum)]
 gi|257471336|ref|ZP_05635335.1| 23S rRNA pseudouridine synthase (YciL) [Buchnera aphidicola str.
           LSR1 (Acyrthosiphon pisum)]
 gi|219621937|gb|ACL30093.1| 23S rRNA pseudouridine synthase (YciL) [Buchnera aphidicola str.
           Tuc7 (Acyrthosiphon pisum)]
 gi|219624490|gb|ACL30645.1| 23S rRNA pseudouridine synthase (YciL) [Buchnera aphidicola str. 5A
           (Acyrthosiphon pisum)]
 gi|311086019|gb|ADP66101.1| 23S rRNA pseudouridine synthase (YciL) [Buchnera aphidicola str.
           LL01 (Acyrthosiphon pisum)]
 gi|311086593|gb|ADP66674.1| 23S rRNA pseudouridine synthase (YciL) [Buchnera aphidicola str.
           TLW03 (Acyrthosiphon pisum)]
 gi|311087176|gb|ADP67256.1| 23S rRNA pseudouridine synthase (YciL) [Buchnera aphidicola str.
           JF99 (Acyrthosiphon pisum)]
 gi|311087705|gb|ADP67784.1| 23S rRNA pseudouridine synthase (YciL) [Buchnera aphidicola str.
           JF98 (Acyrthosiphon pisum)]
          Length = 250

 Score =  142 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 69/250 (27%), Positives = 114/250 (45%), Gaps = 10/250 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
            +++ K+++  G  SRR +E MI    V +NG  +      + + +   I + G  +   
Sbjct: 2   SEKIQKILSHLGYGSRRNIENMIKFGDVSINGKKI-VIGQRLNNKNIEVITIKGETVSIK 60

Query: 71  ER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +       +        + T +                  R IS+GRLDINT GLLL TN
Sbjct: 61  KTDFKTKIIIYNKPEGEICTRNDYKKRPIVFDKLPLLNIHRWISIGRLDINTRGLLLFTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY--GDMQVTLDTQKG 184
           +G LA  L  PS +  R Y +R  G+++++ +N+LK G+ I+        +Q        
Sbjct: 121 NGNLANELMHPSNKIEREYYIRVFGKINKNTMNILKNGVKIKDGYAAFKSIQTIDHACSK 180

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            N W    L EG+NREI+ +++    +V+RLIRI YG   L   L  G   E+S + +  
Sbjct: 181 KNKWFKGVLCEGRNREIRSMWQAVQCQVSRLIRIRYGNIFLPKNLKLGDWSELSSESVNN 240

Query: 244 QLGPHLLEEA 253
                 L+++
Sbjct: 241 LSNLVSLKDS 250


>gi|262276796|ref|ZP_06054589.1| ribosomal large subunit pseudouridine synthase B [alpha
           proteobacterium HIMB114]
 gi|262223899|gb|EEY74358.1| ribosomal large subunit pseudouridine synthase B [alpha
           proteobacterium HIMB114]
          Length = 245

 Score =  142 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 78/235 (33%), Positives = 131/235 (55%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N    R++K++A     SRRE+E +I+ Q++K+N  ++   A  V   D I ++G  +  
Sbjct: 2   NHAKIRIAKLLASYNYGSRREIENLISNQKIKLNNKIILTPATFVNEEDKITINGKKVLF 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ++  +   +KP  ++ + +  D R  +++ L S +   I  GRLD  +EGL++LTND  
Sbjct: 62  KKKISILKLYKPKNVICSKNKQDKREIIYEILDSKYKNFIFAGRLDFKSEGLIILTNDSS 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L R LELP  ++ R Y VR  G  + +KL +  +G  I GI Y      + ++   N  +
Sbjct: 122 LTRNLELPKNKFERKYEVRIFGDFNVEKLKIKSRGTKINGIQYKPFDFKIKSKIKKNTLI 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + L+EGK  EI+ +F+  N +VN+L R+SYGPF+L  +L G  ++ SK  L + 
Sbjct: 182 EMNLKEGKKNEIRNIFKELNLQVNKLKRVSYGPFKLDNMLPGDLKKPSKIELEKY 236


>gi|225164913|ref|ZP_03727129.1| RNA-binding S4 domain protein [Opitutaceae bacterium TAV2]
 gi|224800471|gb|EEG18851.1| RNA-binding S4 domain protein [Opitutaceae bacterium TAV2]
          Length = 277

 Score =  142 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 68/278 (24%), Positives = 111/278 (39%), Gaps = 8/278 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGV 65
           + ++ T  R+ K +A AGI SRR  E +IA   V VNG         +    D I V G 
Sbjct: 1   MSDHATT-RLQKFLADAGICSRRAAETLIADGEVWVNGQPAT-LGQKITPDVDKITVRGK 58

Query: 66  PLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLL 122
            +R     +  L ++     + +     +  +        +   R    GRLD ++EGLL
Sbjct: 59  NVRTVAQPKLTLAMHKPRGLVCSNDDPHNPETVFDLLPREMARHRFFCAGRLDKDSEGLL 118

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           +LT DG LA  L  PST  ++ Y V         +L  L +G+ I+G         L   
Sbjct: 119 ILTTDGDLANRLMHPSTVVVKRYHVVLAEPFPAKRLGALLRGVTIEGERLKVEYAALVNP 178

Query: 183 KGSN--AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             +     + V L  GK REI+++F    ++V RL R   G F L  +   + + ++ + 
Sbjct: 179 NAAELSTSLDVHLHHGKKREIRQLFMALGFEVRRLRRYQIGAFPLRGIPVRAMKLLTPRE 238

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEV 278
           +        ++ A          +   V  +    S  
Sbjct: 239 IATLFAQPGIQPAATTRRYGRPQARNAVSQKKLQSSRQ 276


>gi|28198396|ref|NP_778710.1| ribosomal small subunit pseudouridine synthase [Xylella fastidiosa
           Temecula1]
 gi|182681039|ref|YP_001829199.1| pseudouridine synthase [Xylella fastidiosa M23]
 gi|28056466|gb|AAO28359.1| ribosomal small subunit pseudouridine synthase [Xylella fastidiosa
           Temecula1]
 gi|182631149|gb|ACB91925.1| pseudouridine synthase [Xylella fastidiosa M23]
 gi|307579507|gb|ADN63476.1| ribosomal small subunit pseudouridylate synthase [Xylella
           fastidiosa subsp. fastidiosa GB514]
          Length = 236

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 98/231 (42%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVN--GILLERAAVNVMSTDHIEVDGVPLRKAE 71
            ++ K IA  G  SR+EV R+  + R+  N  G +L  A  +V  T  +  DG PL    
Sbjct: 1   MKLLKYIANLGYGSRKEVARIFREGRIT-NDEGEVLY-ADDHVQHTA-VRFDGEPLDPPP 57

Query: 72  RTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              + L+     + +T          +          + +VGRLD +T GLLLLT+DG L
Sbjct: 58  GLMVMLHKPSGYICSTKDAGRLVYDLLPARFRLRSPLLSTVGRLDGDTSGLLLLTDDGAL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P T   +VY       +  D+  L   G ++       +Q  +    G    V 
Sbjct: 118 LHRMISPKTHLPKVYEATLVQALRGDEATLFASGTLLLDGDTKPLQPAVLEVLGP-CQVR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + L EG+  +++++F     +VN L R + G   L  L  G  R +  + L
Sbjct: 177 LTLYEGRYHQVRRMFGATGNRVNTLHRSAIGGLVLDGLPEGQWRVLEAQDL 227


>gi|291001465|ref|XP_002683299.1| predicted protein [Naegleria gruberi]
 gi|284096928|gb|EFC50555.1| predicted protein [Naegleria gruberi]
          Length = 362

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 98/279 (35%), Positives = 150/279 (53%), Gaps = 12/279 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA-- 70
           +RVSK +AR G+ S+++   +I   +VKVNGIL+  +   +    D + V GV + K   
Sbjct: 83  ERVSKFLARVGVCSKQQGVDLIKAGQVKVNGILITESGQKMNPFYDVVTVKGVNITKKDV 142

Query: 71  ----ERTRLWLYHKPIGLVTTHSDP--DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               E  +L+ YHKP G++ +  D   +  +         F  +ISVGRLD N+EGL+LL
Sbjct: 143 ESNLENVKLYAYHKPRGVLCSRVDNGGNRETIYQRLERMGFGHLISVGRLDYNSEGLILL 202

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG L+R LELP T   R Y VR HGQV Q  L+ L+KG  I+G+ Y  M+ TL  +  
Sbjct: 203 TNDGNLSRHLELPQTGLERQYLVRVHGQVSQPLLDSLQKGSTIEGVHYAGMKATLHREGE 262

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
             +W+ V L EGKNREI+K+F+  N  V+R++RI YGP++L  +  G  + +    L+E+
Sbjct: 263 KTSWIKVILHEGKNREIRKIFQQLNLPVSRIMRIQYGPYKLENIQKGQIKVL---ELKEE 319

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
                    +  + +     E   ++      +  +   
Sbjct: 320 FKQKCSNIYKTAVRSKEKELERDFKNNRAGNPKSNNSKR 358


>gi|293609407|ref|ZP_06691709.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292827859|gb|EFF86222.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 234

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 47/225 (20%), Positives = 88/225 (39%), Gaps = 3/225 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V V+G + +         +    + G   +  E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVSVDGEVADDLKKQFSPENLEFSLFGETYQYREKVY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L        +                 I   V ++GRLD +T GLLLLT+DG   + L
Sbjct: 63  LALKKPKGFECSHQPHHHQSVFSLLPEIMIQRGVQAIGRLDQDTTGLLLLTDDGKYLQAL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     +VY V     V  +++ +L +G+ +           +   +     +T+ + 
Sbjct: 123 THPRKHVPKVYHVTTIDPVTPEQIEMLSQGVSLHQEKGIFAATDVAILE--MHQLTMTIH 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G   ++K++      KV  L R   G   L  L  G    +S++
Sbjct: 181 QGVYHQVKRMIAAVGNKVEALHRHQVGQLVLPELEDGEWVYLSEE 225


>gi|325122669|gb|ADY82192.1| 16S rRNA synthase [Acinetobacter calcoaceticus PHEA-2]
          Length = 234

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 46/225 (20%), Positives = 87/225 (38%), Gaps = 3/225 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V ++G + +              + G   +  E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGYVSIDGEVADDLKKQFSSENLEFSLFGETYQYREKVY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L        +                 I   V ++GRLD +T GLLLLT+DG   + L
Sbjct: 63  LALKKPKGFECSHQPHHHQSVFSLLPEIMIQRGVQAIGRLDQDTTGLLLLTDDGKYLQAL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     +VY V     V  +++ +L +G+ +           +   +     +T+ + 
Sbjct: 123 THPRKHVPKVYHVTTIDPVTPEQIEMLSQGVSLHQEKGLFAATDVAILE--THQLTMTIH 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G   ++K++      KV  L R   G   L  L  G    +S++
Sbjct: 181 QGVYHQVKRMIAAVGNKVEALHRHQVGQLVLPELEDGEWVYLSEQ 225


>gi|327473408|gb|EGF18828.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK408]
          Length = 241

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 101/231 (43%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++ + Q+++ V+G    + + NV +    I      +     
Sbjct: 1   MRLGQLLA-ANHISRKKMKQSLLQKQIFVDGKPACKLSQNVDTGLQQITFQSKHVSGPAH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +               +       + S+GRLD +TEGLLL+T++G L  
Sbjct: 60  RYYMLNKPAGSVTANRDAEKLTVLDLLDKEVEKENLYSIGRLDRDTEGLLLITDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V  +G +     +  ++GI           Q+++ +   S +  TV
Sbjct: 120 QLLHPQYHVEKTYYVEVNGPLTPKDKSSFQEGIRFLDGTTCQPAQLSILSTNSSLSCATV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  +IKK+F     KV  L RI +G F L   L  G  R +++K L
Sbjct: 180 KISEGKFHQIKKMFLAVGVKVTYLKRIQFGDFTLDPDLATGDYRPLNQKEL 230


>gi|219854796|ref|YP_002471918.1| hypothetical protein CKR_1453 [Clostridium kluyveri NBRC 12016]
 gi|219568520|dbj|BAH06504.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 245

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 69/230 (30%), Positives = 123/230 (53%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +A  G+ASRR+ E +I++ RVKVNG+++ +    +    D I VD   ++K  +
Sbjct: 9   ERLHKYMAACGVASRRKCEHIISEGRVKVNGVVVNKLGTTIDDERDEILVDNKIIKKENK 68

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G +++  D  GR T+ D +     RV  +GRLD NT G ++LTNDG +  
Sbjct: 69  KVYILLNKPRGYISSVKDDRGRKTLLDIVKVN-ERVYPIGRLDYNTSGAIILTNDGEVYN 127

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P +   ++Y     G    +++   + GI I G      +    +    ++ V + 
Sbjct: 128 NIAHPGSNKSKIYIAAIKGIPSSEEIKRFENGIDIGGYITAKAKFDFISSNKESSKVKIE 187

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EGKNR+++K+ +     V  L+RI+ G  +LG L  G+ R +++K ++
Sbjct: 188 IHEGKNRQVRKMCDAIGHPVITLMRIAIGDIKLGNLKEGAWRYLTEKEIQ 237


>gi|330937693|gb|EGH41591.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. pisi str.
           1704B]
          Length = 230

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 104/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R++V   +A  RV+V+G         V     + +D   L+  +  
Sbjct: 1   MRLDRFLSNLPRFNRQQVRLALASGRVQVDGQATRDPHHEVGEFSCVALDEEILQAGKVP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V+  SD    + +          +   GRLD NT GL+L+TNDG  +R 
Sbjct: 61  RYFMLHKPEGCVSATSDAQHPTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+       +      + +     Q+TL   + +     +
Sbjct: 121 LTQPQTKMPKVYYVETEQPIDERYAAKFAEGLYFAFENLTTQPAQLTLLGPQSA----RL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F  F+ KV RL R + G   L   L  GS R ++   +
Sbjct: 177 SIVEGRYHQVKRMFGHFDNKVLRLHRETIGALALDPDLCPGSYRALNAGEI 227


>gi|324993413|gb|EGC25333.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK405]
 gi|324995275|gb|EGC27187.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK678]
 gi|327461687|gb|EGF08018.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1]
 gi|327469033|gb|EGF14505.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK330]
 gi|327489540|gb|EGF21333.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1058]
          Length = 241

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 103/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++ + Q+++ V+G    + + NV +    I   G  +     
Sbjct: 1   MRLDQLLA-ANHISRKKMKQSLLQKQILVDGKPACKLSQNVDTGLQQITFQGKQVSGPAH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +               +       + S+GRLD +TEGLLL+T++G L  
Sbjct: 60  HYYMLNKPAGAVTANRDAEKLTVLDLLDKEVEKENLYSIGRLDRDTEGLLLITDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V  +G +        ++GI  + G      Q+T+ +   S +  +V
Sbjct: 120 QLLHPQYHVEKTYYVEVNGPLTPQDKIAFQEGIRFLDGTVCQPAQLTIFSSCFSLSRASV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     K+  L RI +G F L   L  G  R ++++ L 
Sbjct: 180 RISEGKFHQIKKMFLVVGVKIIYLKRIQFGNFTLDPDLATGDCRPLNQEELE 231


>gi|260549355|ref|ZP_05823574.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter sp. RUH2624]
 gi|260407464|gb|EEX00938.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter sp. RUH2624]
          Length = 234

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 46/226 (20%), Positives = 89/226 (39%), Gaps = 3/226 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V + G ++          +    + G   R  E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVSIEGEIVTDLKKQFSPENLEFSLFGETYRYREKVY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L        + +               I   V ++GRLD +T GLLLLT+DG   + L
Sbjct: 63  LALKKPQGFECSHNPQHHQSVFSLLPEIMIQRGVQAIGRLDQDTTGLLLLTDDGKYLQAL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     +VY V     V  +++ +L +G+ +           +      +  +T+ + 
Sbjct: 123 THPRKHVPKVYHVTTIDSVTPEQIEMLTQGVNLHQEKDVFAATDVALL--GSHQLTMTIH 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +G   ++K++      KV +L R   G   L  +  G    +S++ 
Sbjct: 181 QGVYHQVKRMIAAVGNKVEKLHRHQIGQLVLPEIEEGDWVYLSEQE 226


>gi|153002415|ref|YP_001368096.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|151367033|gb|ABS10033.1| pseudouridine synthase [Shewanella baltica OS185]
          Length = 233

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 96/232 (41%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++    R      I    V VNG++    A+ V   + +  +G  L      
Sbjct: 1   MRLDKFLCKSTDLDRDAASVAILSGSVTVNGVIATDCAMQVHENNAVCFNGKSLVPRPS- 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP   + ++ D    S            +  VGRLD +T GL+LLT+DG  +  
Sbjct: 60  RYFMLHKPADTLCSNVDGAYPSLFHLLDIERAFDLHIVGRLDADTTGLVLLTDDGRWSFN 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKG----IVIQGICYGDMQVTLDTQKGSNAWV 189
           +  P  Q  +VYRV+    +D +    +       + +QG     +  TL         V
Sbjct: 120 IISPQYQCKKVYRVQLRDPLDSEATAAIAATFTAGLQLQGETALTLPATLQQVDDK--TV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + L EGK  ++K++F     KV  L R   G   L  +  G  RE++   +
Sbjct: 178 LLTLTEGKFHQVKRMFAAVGNKVVALHRAQIGAVTL-DVDVGEWRELTLAEI 228


>gi|313680897|ref|YP_004058636.1| ribosomal large subunit pseudouridine synthase b [Oceanithermus
           profundus DSM 14977]
 gi|313153612|gb|ADR37463.1| ribosomal large subunit pseudouridine synthase B [Oceanithermus
           profundus DSM 14977]
          Length = 252

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 75/253 (29%), Positives = 106/253 (41%), Gaps = 6/253 (2%)

Query: 12  TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              R+ K +  AG A SRR+ E +I   RV VNG ++      V   D + V G      
Sbjct: 5   DGIRLQKYLVLAGAAPSRRKAEDLIRAGRVSVNGAVV-GLGARVYPGDEVRVGGRRAELP 63

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ER  +   HKP G  TT     G  TV++ LP     +  VGRLD ++EGLLL TNDG L
Sbjct: 64  ERRVVLALHKPKGYETTRQSRSGAPTVYELLPD-LPGLHPVGRLDRDSEGLLLFTNDGAL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            + L  P     +VYRV          L    +  ++         +    + G      
Sbjct: 123 TQRLTHPRYGVKKVYRVWSRKGTPPPDLLRKLERGLVLKSGVRVQALKARPKDGGAV--- 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L EGK RE++ +     + V RL+R+  GP +LG    G+ RE+S   L+        
Sbjct: 180 ITLTEGKKREVRYMMAAIGYPVERLVRVKMGPIRLGGQKPGTWRELSASELKALDRAAFG 239

Query: 251 EEAQVNLDAPIYS 263
            E           
Sbjct: 240 PEEDEAKPRSAKR 252


>gi|170720236|ref|YP_001747924.1| pseudouridine synthase [Pseudomonas putida W619]
 gi|169758239|gb|ACA71555.1| pseudouridine synthase [Pseudomonas putida W619]
          Length = 233

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 106/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     +R++V  ++ Q+RV+V+G  +      V     IEVD   L+     
Sbjct: 1   MRLDRFLANLPSYNRQQVRLLLVQRRVRVDGETVADPRAEVREFSRIEVDDQLLQAGRPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + HKP+G V+   D   R+ +      + + +   GRLD NT GL++LTNDG  +R 
Sbjct: 61  RYLMLHKPVGCVSATHDSQHRTVLDLLPEPLRADLHIAGRLDYNTTGLMILTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P+T+  + Y V    ++    +   +       + +     Q+ +           +
Sbjct: 121 LTQPATKLPKHYLVETEDEIGAHYIEKFRAGFYFAFEDLTTLPAQLDIL----GPRTARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F +F+ KV  L R + G  QL   L  G  R ++   +
Sbjct: 177 AIIEGRYHQVKRMFGYFDNKVVGLHRETMGAIQLDPGLAPGEFRALTAAEI 227


>gi|119897119|ref|YP_932332.1| pseudouridylate synthase [Azoarcus sp. BH72]
 gi|119669532|emb|CAL93445.1| pseudouridylate synthase [Azoarcus sp. BH72]
          Length = 500

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 107/247 (43%), Gaps = 18/247 (7%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  +  R+SKV+A  GI SRRE + +I +  V V+G  +      +     + +     +
Sbjct: 257 EAPSGVRLSKVMADRGICSRREADELIERGWVFVDGRRVSELGTRIDPDARVVLAPEAKK 316

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRS--------------TVFDNLPSIFSRVISVGRL 114
              +    L HKP+G V+   +P                        PS    +   GRL
Sbjct: 317 AQAQRVTILLHKPVGYVSGQPEPGYEPAVTLIGGDNQFDRDVAQRFHPSQLKGLAPAGRL 376

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DI++ GLL+LT DG +AR L    ++  + Y VR  G++  D L LL  G+ +       
Sbjct: 377 DIDSTGLLVLTQDGRIARQLIGDDSKVEKEYLVRVEGELVDDGLALLNHGLSLDDKPLRP 436

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +V    +      +   L+EG+ R+I+++ E    +V  L R+  G  +LG L  G  R
Sbjct: 437 AKVEWINEDQ----LRFVLKEGRKRQIRRMCELVGLRVVGLKRVRIGRVKLGDLPLGEWR 492

Query: 235 EVSKKIL 241
            +    +
Sbjct: 493 YLRDDEV 499



 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 9/106 (8%), Positives = 19/106 (17%), Gaps = 2/106 (1%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           EE +           +                 R  +         +             
Sbjct: 58  EEGRAPRSGARGGQASRGERPRQDAEPRRQPRARPAQEGEAPRRSRRDPGDGGTERHPRR 117

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRR--SPSFPSKRSLRRTSAKK 354
            +     +        +   R    RR   P+    R  R    ++
Sbjct: 118 DAGASEERPRRREAADERQARPGYGRRDDGPARAGARPAREQGRER 163



 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 8/113 (7%), Positives = 23/113 (20%), Gaps = 2/113 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +          +    +         R           +  R      ++      ++  
Sbjct: 38  DPAQSVAAGSDKRARPSSAGEEGRAPRSGARGGQASRGERPRQDAEPRRQPRARPAQEGE 97

Query: 303 TPVHRRNLASNVWMAKGIHSSFLS--DSGQREENHRRSPSFPSKRSLRRTSAK 353
            P   R    +    +       +  +  +R E      + P         A+
Sbjct: 98  APRRSRRDPGDGGTERHPRRDAGASEERPRRREAADERQARPGYGRRDDGPAR 150



 Score = 36.3 bits (82), Expect = 6.5,   Method: Composition-based stats.
 Identities = 9/109 (8%), Positives = 17/109 (15%), Gaps = 3/109 (2%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                                    N  S    D  +     S K              R
Sbjct: 5   RKNPPQPAPSRIAGTLKLRKPAADDNGESAAGADPAQSVAAGSDKRARPSSAGEEGRAPR 64

Query: 308 ---RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              R   ++        +        R      +P    +      + +
Sbjct: 65  SGARGGQASRGERPRQDAEPRRQPRARPAQEGEAPRRSRRDPGDGGTER 113


>gi|332876893|ref|ZP_08444647.1| pseudouridylate synthase [Capnocytophaga sp. oral taxon 329 str.
           F0087]
 gi|332685176|gb|EGJ58019.1| pseudouridylate synthase [Capnocytophaga sp. oral taxon 329 str.
           F0087]
          Length = 215

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 50/208 (24%), Positives = 102/208 (49%), Gaps = 1/208 (0%)

Query: 34  MIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
            I+   V VNG ++      V  TD +  DG  L   ++  + L      + TT+ +   
Sbjct: 2   YISAGNVTVNGEVMTTLGYRVKPTDEVRFDGKLLSSEKKEYILLNKPKGFITTTNDEKGR 61

Query: 94  RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
           ++ +     +  +R++ VGRLD  T GLLLLTNDG L + L  P+    ++Y V    ++
Sbjct: 62  KTVMDLVANATNARILPVGRLDRATTGLLLLTNDGELTKKLTHPTHGVRKIYHVILDRKL 121

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +      +++G+ ++       +++   QK  N  + + +  G+NR ++++FE   ++V+
Sbjct: 122 EYKDFIAIEQGLELEDGFIQVDEISYVDQKPKN-EIGIKIHSGRNRIVRRIFEHLGYQVD 180

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +L R+ +       L  G  R ++++ +
Sbjct: 181 KLDRVVFAGLTKKDLPRGHWRRLTQQEV 208


>gi|167035395|ref|YP_001670626.1| pseudouridine synthase [Pseudomonas putida GB-1]
 gi|166861883|gb|ABZ00291.1| pseudouridine synthase [Pseudomonas putida GB-1]
          Length = 230

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 108/231 (46%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     +R++   M+AQ+RV+V+G ++      V     +E+D   L+     
Sbjct: 1   MRLDRFLANLPSHNRQQARLMLAQRRVRVDGQVVSDPLAEVREFSRVELDEQLLQAGRPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + HKP G V+   DP   + +     ++   +   GRLD NT GL++LTNDG  +R 
Sbjct: 61  RYLMLHKPTGCVSATQDPQHPTVLDLLPAALRDDLHIAGRLDFNTTGLMILTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P+T+  + Y V    ++ +  +   ++      + +      + +   + +     +
Sbjct: 121 LTQPATKLPKHYLVDTEDEIGEHYVARFREGFYFAFENLTTQPALLDILGPRQA----RL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F  FN KV  L R S G   L   L  G  RE++   +
Sbjct: 177 AIVEGRYHQVKRMFGHFNNKVVGLHRESMGAICLDPGLAPGEFRELTADEI 227


>gi|153864123|ref|ZP_01997120.1| ribosomal large subunit pseudouridine synthase B [Beggiatoa sp. SS]
 gi|152146384|gb|EDN72882.1| ribosomal large subunit pseudouridine synthase B [Beggiatoa sp. SS]
          Length = 230

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 76/219 (34%), Positives = 110/219 (50%), Gaps = 7/219 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---- 68
            +++ KV+AR G+ SRRE+E  I + RVKVN   +      V   D I V+   +R    
Sbjct: 2   TEKLQKVLARVGLGSRREIETWIEEGRVKVN-QYIATLGARVSPHDEIRVNERRIRQSDL 60

Query: 69  --KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
              + +  L  +     + T H +    +           R IS+GRLD+NT GLLLLT 
Sbjct: 61  QTPSRQQILCYHKPIGEVCTRHDEEGRTTIFERLPSPKHGRWISIGRLDLNTAGLLLLTT 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS    R Y VR  G+VD D L  L++GI ++       +V      G+N
Sbjct: 121 DGDLAHRLMHPSYDIEREYAVRILGEVDLDMLKRLREGIELEDGMAQFKRVFDAGGSGAN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            W  V L EG+  E+++++E     V+RL+RI +GP  L
Sbjct: 181 HWYHVTLMEGRKHEVRRLWESQGVTVSRLMRIRFGPVSL 219


>gi|285018816|ref|YP_003376527.1| rrna pseudouridine synthase [Xanthomonas albilineans GPE PC73]
 gi|283474034|emb|CBA16535.1| probable rrna pseudouridine synthase protein [Xanthomonas
           albilineans]
          Length = 252

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 63/244 (25%), Positives = 110/244 (45%), Gaps = 13/244 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
             R++K IA +G  SRRE +R+IA +RV VN  L       V   D ++VDG PLR    
Sbjct: 15  STRLNKHIAESGFCSRREADRLIAARRVTVND-LPGGVGSVVGEGDEVKVDGQPLRARAK 73

Query: 71  ----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                       +KP+G+  T            +      R+  +GRLD ++EGL+L+T+
Sbjct: 74  HKGGRHHVYIALNKPVGVTCTTEREV--KGNIVDFVGHEQRIFPIGRLDKDSEGLILMTS 131

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G +   +     +  + Y V  +  V  + L  + +G+ +        +     + G  
Sbjct: 132 NGDIVNEILRAENRHQKEYLVAVNKPVTDEFLRGIARGVRVHDQMTLPCRTARIAKFG-- 189

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               + L +G NR+I+ +   F+++V +L R+     +LG L  G  R ++++ LR  L 
Sbjct: 190 --FRIVLEQGLNRQIRLMAAAFDYRVTQLRRVRIDNIKLGALKPGQWRNLTEQELRGLLP 247

Query: 247 PHLL 250
               
Sbjct: 248 QRQQ 251


>gi|295397550|ref|ZP_06807631.1| ribosomal small subunit pseudouridine synthase A [Aerococcus
           viridans ATCC 11563]
 gi|294974221|gb|EFG49967.1| ribosomal small subunit pseudouridine synthase A [Aerococcus
           viridans ATCC 11563]
          Length = 247

 Score =  141 bits (355), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 51/230 (22%), Positives = 109/230 (47%), Gaps = 3/230 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTR 74
           + ++I  AG  +R+  +R++    V V+G ++ + A  V  +   I VD + + +     
Sbjct: 3   LGQLIMDAGQVTRKACKRLLKDGHVTVDGQVVTQFATVVDPSWQEIAVDQIVIDRHFGHT 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
            +L HKP G ++ + D    + +    P+     ++  GRLD +  GL+ +TN+G L  +
Sbjct: 63  YYLVHKPKGYLSANKDQTHPTVIDLIQPADNPGDLAITGRLDRDAHGLVFVTNNGQLHYI 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVG 192
            + P     + YR+  +G +D+  +   + G++ Q        ++ + +    ++   V 
Sbjct: 123 FQQPKFDIPKTYRITVNGLIDKKMVAQFQAGVIFQDGTICKAARLEIISASPQSSTGLVT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EG+  ++KK+F     KV  L R   G  ++  L  G  R +++  ++
Sbjct: 183 ISEGRRHQVKKMFLACGVKVTDLYRQKIGDLRIDDLAVGDYRRLNEAEIQ 232


>gi|94968658|ref|YP_590706.1| pseudouridine synthase, Rsu [Candidatus Koribacter versatilis
           Ellin345]
 gi|94550708|gb|ABF40632.1| Pseudouridine synthase, Rsu [Candidatus Koribacter versatilis
           Ellin345]
          Length = 254

 Score =  141 bits (355), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 66/241 (27%), Positives = 108/241 (44%), Gaps = 5/241 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTR 74
           +++V+++ G  SR     +I    V+VNG +            D +EV  + +R A    
Sbjct: 15  LARVLSKLGYCSRARAFELIRADEVRVNGKVERNPERPTDPARDRVEVAHIAIRAARFLY 74

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             +      + T   +    +  +  LP     V  VGRLD  +EGLLLLTND   A  +
Sbjct: 75  YVVNKPRGLITTASDEKGRETI-YSLLPPDSPWVAPVGRLDKASEGLLLLTNDSEWAAKI 133

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P++   + Y V+      +  +  L +GI   G      +V++    G N W+ + L 
Sbjct: 134 TDPNSHLDKTYHVQVSTLPSEQMVEALSRGIRSDGELLLAKRVSILRAGGKNGWLEIVLE 193

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK---ILREQLGPHLLE 251
           EGKNR+I+++      +V RLIR++ GP  LG L  G  R ++ +    L + L     E
Sbjct: 194 EGKNRQIRRMVAALQIEVLRLIRVAIGPLTLGELPKGGCRALTAEEKAELDDALRLVRGE 253

Query: 252 E 252
            
Sbjct: 254 H 254


>gi|212636851|ref|YP_002313376.1| ribosomal small subunit pseudouridine synthase A [Shewanella
           piezotolerans WP3]
 gi|212558335|gb|ACJ30789.1| Ribosomal small subunit pseudouridine synthase A, putative
           [Shewanella piezotolerans WP3]
          Length = 228

 Score =  141 bits (355), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 52/234 (22%), Positives = 96/234 (41%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   +R     ++A   V VNG ++  A   V   + +   G  L      
Sbjct: 1   MRLDKFLCKSTKLTRSAATEVLALGEVSVNGSIVTEARFQVHENNSVLWRGERLIARPSR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+      ++++ D D  S            +  VGRLD +T GL+LLT+DG  +  
Sbjct: 61  YIMLHKPL-NTLSSNVDGDYPSLFHCIDIERAEDLHIVGRLDADTSGLVLLTDDGRWSFE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--CYGDMQVTLDTQKGSNAWVTV 191
           +  P     + YRV     +  D       G+ +Q          + +  +      V +
Sbjct: 120 IIRPDKLCPKTYRVTLRDPIAADVAEKFNVGVQLQNESKLTAPAMLKVINE----REVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG+  ++K++F     +VN L R   G  QL  ++ G+ R +S + +   L
Sbjct: 176 TITEGRYHQVKRMFAAVGNRVNGLHREQIGDLQL-DVVLGNWRFLSPQEVAGFL 228


>gi|70728809|ref|YP_258558.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           fluorescens Pf-5]
 gi|68343108|gb|AAY90714.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           fluorescens Pf-5]
          Length = 230

 Score =  141 bits (355), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 110/232 (47%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R++V  ++ Q+R++++G  +      V     +E+D   L+  +  
Sbjct: 1   MRIDRFLSNLPRFNRQQVRVLLVQRRIRIDGQPVSDPKAEVREFSRVELDDEVLQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP+G V+   DP+ ++ +          +   GRLD NT GL+L+TNDG  +R 
Sbjct: 61  RYFMLHKPMGCVSATRDPEHKTVLELIHEPDPQDLHIAGRLDYNTTGLMLITNDGNWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  ++Y V    ++  + +           + +     Q+ +   + +     +
Sbjct: 121 LTQPQTKLPKLYYVETEQEIGPEYVETFAHGLYFAFEDLTTLPAQLQILGPRSA----RL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            + EG+  ++K++F  FN KV RL R   GP  L   L  G  R +S   +R
Sbjct: 177 SIVEGRYHQVKRMFGHFNNKVLRLHRERMGPLLLDERLAPGEYRALSDAEIR 228


>gi|89072330|ref|ZP_01158909.1| hypothetical ribosomal small subunit pseudouridine synthase A
           [Photobacterium sp. SKA34]
 gi|89051862|gb|EAR57314.1| hypothetical ribosomal small subunit pseudouridine synthase A
           [Photobacterium sp. SKA34]
          Length = 231

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 52/235 (22%), Positives = 103/235 (43%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I ++   ++ E    I    + VN  ++   A  V  ++ + +DG  L   E  
Sbjct: 1   MRLDKFICKSTQLTKAEAIERIHAGDINVNSAVIINEATQVHESNTVIMDGKRLIAREFR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     + +   +       + ++ +I    I+ GRLD +T G++L+T++G  +  
Sbjct: 61  YILIHKPAGTICSNIDEVYPSLFNYLDVDNIAELHIA-GRLDADTMGMVLITDNGRWSFN 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           +  P+ +  +VYRV     +  D     K GI +QG         +T+ + K     V +
Sbjct: 120 ITSPNQKCSKVYRVGLSRDITADVAEKFKAGIKLQGAQKLTAPALLTIISAK----EVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            + EGK  ++K++F     +V  L R + G   L  L  G  R ++K  +   + 
Sbjct: 176 TITEGKFHQVKRMFASVGNRVVSLHREAIGEVTL-DLEVGQWRYLTKDEVASFVK 229


>gi|167646666|ref|YP_001684329.1| pseudouridine synthase [Caulobacter sp. K31]
 gi|167349096|gb|ABZ71831.1| pseudouridine synthase [Caulobacter sp. K31]
          Length = 245

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 47/229 (20%), Positives = 93/229 (40%), Gaps = 7/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD----HIEVDGVPLRKA 70
           R+ +++A  G  SRR+V+ +++  +V ++G+ ++ A   +  T      + + GVP+   
Sbjct: 8   RLDRLLANLGYGSRRDVQALVSTGKVTLDGVAIKDAGQKIAVTADLPLRMRIRGVPVDPP 67

Query: 71  ERTRLWLYHKPIGLVTTHSD-PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               L ++     + +   D       +          + SVGRLD +T GLLL+T+DG 
Sbjct: 68  APLVLLMHKPLGVVCSHREDGERIYDLLPKRWQIRDPALSSVGRLDKDTSGLLLITDDGD 127

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
               +  P     +VYR      ++  +      G ++       +        G     
Sbjct: 128 FLHRVISPKRHVPKVYRATLDRPLNGTEGAAFASGALMLEGEEKPLLPATLDVLGD-HEA 186

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
            + + EG+  +++++F      V  L R   G   L   L  G  R ++
Sbjct: 187 RLTITEGRYHQVRRMFAAVGNHVVGLHRERIGGIDLPEDLAPGEHRILT 235


>gi|225858508|ref|YP_002740018.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae 70585]
 gi|225721992|gb|ACO17846.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae 70585]
          Length = 241

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 56/232 (24%), Positives = 105/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+       A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLKGDILVDSCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +                      ++ +VGRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPAGVVTANKDKELPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y+V+ +G +  D +   +KGI  + G      ++ + +   S +  ++
Sbjct: 120 QLLHPQYHVDKTYQVQVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSLSQASI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F L   L   + R +++K L+
Sbjct: 180 TISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAESNYRPLNQKELQ 231


>gi|270308102|ref|YP_003330160.1| pseudouridine synthase, RsuA family [Dehalococcoides sp. VS]
 gi|270153994|gb|ACZ61832.1| pseudouridine synthase, RsuA family [Dehalococcoides sp. VS]
          Length = 249

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 69/230 (30%), Positives = 110/230 (47%), Gaps = 5/230 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTR 74
           + KV+  A + SRR++   I Q  V +NG   E  +  V +  D +  +G P+  +   R
Sbjct: 11  LVKVLVEARLGSRRKMAEAIKQGLVTLNGQKAESYSQPVNTQQDKVTFEGKPVELSRIRR 70

Query: 75  -LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
              + +KP  +V+T SD  GR TV D L   +       VGRLD  T GLLLLTNDG L 
Sbjct: 71  IYLMLNKPPEIVSTTSDELGRKTVMDLLHRRYEGAGLFPVGRLDEATTGLLLLTNDGELT 130

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  PS Q  + Y +     + Q     L+KG+++        +++  T +       +
Sbjct: 131 NRLTHPSYQIEKEYLISIDAALTQADKESLEKGMLLDDGLTSPARLSRVTDEPPYN-YKL 189

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + EGK R ++++F    +++  L R      +LG L  G TRE++   +
Sbjct: 190 IIHEGKKRIVRRMFAHLGYQIKALKRSRIATLRLGKLEEGKTRELTPGEI 239


>gi|254284223|ref|ZP_04959191.1| ribosomal small subunit pseudouridine synthase A [gamma
           proteobacterium NOR51-B]
 gi|219680426|gb|EED36775.1| ribosomal small subunit pseudouridine synthase A [gamma
           proteobacterium NOR51-B]
          Length = 311

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 64/226 (28%), Positives = 106/226 (46%), Gaps = 7/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++     R+ V  M+AQ RV ++G+L   AA  +     I VDGV L       
Sbjct: 91  RLDKHLSKQTGVPRKAVRLMLAQARVTIDGVLARDAAEVINPFSRIAVDGVGLPTNTPHY 150

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L      +  T            +LP   +  I VGRLDI + GL+LLTNDG  +R L
Sbjct: 151 IMLNKPSGVVCATRDARHRTVIDILDLPFQHTLHI-VGRLDIQSTGLVLLTNDGQWSRRL 209

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            LP +++ + YRV     +  +++   +       +G+     ++ L     +N    V 
Sbjct: 210 SLPQSKFAKHYRVTTEQAITSEQIAGFEAGIFFAYEGLTTRPARLHLINSHEAN----VT 265

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           L EG+  +I+++F  +  +V  + R + GP+ L  L  G  RE+S 
Sbjct: 266 LTEGRYHQIRRMFGRYGNRVLSIHRYATGPYVLSNLRPGQYREISP 311


>gi|294141981|ref|YP_003557959.1| ribosomal small subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
 gi|293328450|dbj|BAJ03181.1| ribosomal small subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
          Length = 238

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 49/232 (21%), Positives = 95/232 (40%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   SR E   +I   +V+VN +++  A   V   + I + G  L      
Sbjct: 1   MRLDKFLCKSTDFSRAESIDLIEAGQVRVNELVIVTAQTQVHENNCIMLAGRRLVARPSR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+     L +           +  +       I  GRLD +T GL+L+T+DG  +  
Sbjct: 61  YIMLHKPIDTLCSNVDGDYPSVMNYIQVDRAEDLHI-TGRLDADTTGLVLITDDGRWSFN 119

Query: 134 LELPSTQWLRVYRVRFHGQVD----QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +  P     + YRV     ++     + ++  ++G+ +QG     +   L+        V
Sbjct: 120 IINPKYHCEKTYRVTLRDPIEDGDIDELVSRFEQGLQLQGEKKLTLAAKLEVITP--HQV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + L EG+  ++K++F     +V  L R   G   L  +  G  R ++   +
Sbjct: 178 LLTLSEGRYHQVKRMFFTVGNRVVGLHRQQVGKLSL-DIELGEWRHLTADEV 228


>gi|217969527|ref|YP_002354761.1| pseudouridine synthase [Thauera sp. MZ1T]
 gi|217506854|gb|ACK53865.1| pseudouridine synthase [Thauera sp. MZ1T]
          Length = 234

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 63/235 (26%), Positives = 100/235 (42%), Gaps = 18/235 (7%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           +A  G+ SRRE +  I +  V V+G  +    V V     + +     R  ++    L H
Sbjct: 1   MAERGLCSRREADEFIERGWVFVDGRRVSELGVRVGQDARVTLAPEATRTQQQRATILLH 60

Query: 80  KPIGLVTTHSDPDGRS--------------TVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           KP+G V+   +P                        PS    +   GRLDI++ GLL+LT
Sbjct: 61  KPVGYVSGQPEPGYSPAVSLIGPDNQADRDVAQRFHPSHLKNLAPAGRLDIDSTGLLVLT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG +AR L    ++  + Y VR  G + ++ L LL  G+ +        +V        
Sbjct: 121 QDGRIARQLIGEDSKVEKEYIVRVEGTLAENGLALLNHGLWLDDRPLRPAEVEWINDDQ- 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
              +   LREG+ R+I+++ E    KV  L R+  G  +LG L  G  R + +  
Sbjct: 180 ---LRFVLREGRKRQIRRMCELVGLKVVGLKRVRIGHVKLGDLPLGQWRFLREDE 231


>gi|254252056|ref|ZP_04945374.1| Pseudouridine synthase Rsu [Burkholderia dolosa AUO158]
 gi|124894665|gb|EAY68545.1| Pseudouridine synthase Rsu [Burkholderia dolosa AUO158]
          Length = 243

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 57/245 (23%), Positives = 95/245 (38%), Gaps = 28/245 (11%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------------G 64
           ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D                
Sbjct: 1   MSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDERAQAAQAAQVTILLH 60

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P+          Y     L+T  +   G  +     P     +   GRLDI++ GLL+L
Sbjct: 61  KPVGYVSGQAEDGYEPATVLITRENHWSGDRSPLRFSPQHLRTLAPAGRLDIDSTGLLVL 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQGICYGDM 175
           T +G +A+ L    +   + Y VR                + L  L+ G+ + G+     
Sbjct: 121 TQNGRIAKQLIGEQSDVDKEYLVRVRYGDMLTDIDRHFPAESLAKLRHGLELDGVALKPA 180

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
            V+    +     +   LREG+ R+I+++ E     V  L R+  G   LG L  G  R 
Sbjct: 181 MVSWQNGEQ----LRFVLREGRKRQIRRMCELVGLDVIGLKRVRMGRVMLGALPQGQWRY 236

Query: 236 VSKKI 240
           +S   
Sbjct: 237 LSADE 241


>gi|285019685|ref|YP_003377396.1| ribosomal small subunit pseudouridine synthase a protein
           [Xanthomonas albilineans GPE PC73]
 gi|283474903|emb|CBA17402.1| probable ribosomal small subunit pseudouridine synthase a protein
           [Xanthomonas albilineans]
          Length = 232

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 54/235 (22%), Positives = 89/235 (37%), Gaps = 5/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVK-VNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            ++ K +A  G  SR++V  M  + R+   +G +L  A   V     I VDG  L     
Sbjct: 1   MKLVKHLANLGYGSRKQVALMFREGRITDADGDVLY-ADDQV-PHAAIRVDGEVLDPPPG 58

Query: 73  TRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             L L+       +           +          + +VGRLD +T GLLL+T+DG L 
Sbjct: 59  LILALHKPVGYTCSTKDPGRIVYDLLPSRFRLRSPLMSTVGRLDRDTSGLLLMTDDGALL 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P ++  ++Y       +  D+      G ++       +        G    V V
Sbjct: 119 HRIVSPKSRLAKIYEATLAEDLRGDEAAQFASGTLLLDGETTPLLPVQLEVLGPRQ-VRV 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            L EG+  +++++F      V  L R   G   L  L AG  R +    L +   
Sbjct: 178 VLHEGRYHQVRRMFAAVGNHVLALHRSRIGGLALDALPAGQWRALEPMELAQVFE 232


>gi|325681054|ref|ZP_08160586.1| putative 16S pseudouridylate 516 synthase [Ruminococcus albus 8]
 gi|324107283|gb|EGC01567.1| putative 16S pseudouridylate 516 synthase [Ruminococcus albus 8]
          Length = 246

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 59/243 (24%), Positives = 106/243 (43%), Gaps = 10/243 (4%)

Query: 12  TPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              R+ K++A      SR +V+++  ++++ VNG L+ R+   V + D I V+G  L   
Sbjct: 3   EIMRLDKLVASQFSDVSRADVKKLCLKKKISVNGKLMARSDAKVDTDDEIFVNGERLVYK 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   + L      + +T                + + +   GRLD +TEG +LLT+DG L
Sbjct: 63  KHVYIMLNKPAGVVCSTKEGDSMTVLDLVPPELMRNGLFPAGRLDKDTEGFVLLTDDGEL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI------QGICYGDMQVTLDTQKG 184
           +  +  P T   + Y VR       +  +++  G+ I      +       Q +      
Sbjct: 123 SHRMLSPKTHVPKTYFVRLEKPYQPEYADIMAAGMTIKGLDGGEDEKCLPAQFS--GSDE 180

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           ++   T+ L EGK  ++K++F     KV  L R + G   L G L +G   E+  K + +
Sbjct: 181 NDCECTLILHEGKFHQVKRMFAELGNKVVYLKRTAIGEMPLNGELASGKCLEILHKDVEK 240

Query: 244 QLG 246
            L 
Sbjct: 241 LLA 243


>gi|254426889|ref|ZP_05040596.1| conserved hypothetical protein, putative [Alcanivorax sp. DG881]
 gi|196193058|gb|EDX88017.1| conserved hypothetical protein, putative [Alcanivorax sp. DG881]
          Length = 241

 Score =  141 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 65/239 (27%), Positives = 116/239 (48%), Gaps = 8/239 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +++    SR  +  ++A  RV+VNG+ +      +   D +E+DG PL+ +E  R
Sbjct: 7   RLDRFLSQVLQVSRSGLRPVLAAGRVRVNGVPVRDRQQRIGPFDRVELDGQPLQ-SEAPR 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             + +KP G+V+  SD    + +     S    +   GRLD N+ GL+LLTNDG  +R L
Sbjct: 66  YLMVNKPAGVVSATSDDQHTTVMDLLPASQRQGLHLAGRLDFNSTGLVLLTNDGAWSRQL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTVG 192
             P +Q  + YRV     + +  +    +G+    +GI     ++ + +   ++ W    
Sbjct: 126 SQPQSQVRKHYRVTVEQPLTEAYVAAFSEGMWFAFEGIKTRPAEIKIRSAYEADVW---- 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLL 250
           L EG+  +IK++F  F+ KV  L R++ G   L   L  G +R++    +    G    
Sbjct: 182 LCEGRYHQIKRMFGRFDNKVLTLHRLAIGHLVLDESLAPGESRDLMPGEVAGIAGLSSR 240


>gi|126662471|ref|ZP_01733470.1| pseudouridylate synthase (ribosomal large subunit pseudouridine
           synthase B) [Flavobacteria bacterium BAL38]
 gi|126625850|gb|EAZ96539.1| pseudouridylate synthase (ribosomal large subunit pseudouridine
           synthase B) [Flavobacteria bacterium BAL38]
          Length = 297

 Score =  141 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 50/233 (21%), Positives = 107/233 (45%), Gaps = 1/233 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
            N    R+++ I+ +G+ SRR+ +  I    VKVNG ++      V  TD ++ DGV + 
Sbjct: 59  SNPDEIRLNRYISNSGMCSRRDADIYIQSGNVKVNGEVITEMGYRVKLTDSVQFDGVNIT 118

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ++  + L                 + +     +  + ++ VGR+D  T GLLL TND 
Sbjct: 119 PEKKEYILLNKPKNFSTAGDDSAGSANVLDLVRNATKANLMPVGRMDKTTTGLLLFTNDT 178

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            + +   +P+ +  +VY+V     +  + L  ++KG+ I       ++     Q    + 
Sbjct: 179 EIVQKFTVPNQRSSKVYQVTLDKNLKFEDLEKIQKGLTIDDHKV-FVEEVTYIQDQPKSE 237

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + ++    + ++K+FE F + V ++ R+++       L  G  R ++++ +
Sbjct: 238 IGIKMKTSNVKVVRKIFEHFKYDVLKVDRVTFAGLTKKNLPRGDWRFLTEQEI 290


>gi|227874423|ref|ZP_03992604.1| RluF protein [Oribacterium sinus F0268]
 gi|227839739|gb|EEJ50188.1| RluF protein [Oribacterium sinus F0268]
          Length = 240

 Score =  141 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 63/240 (26%), Positives = 112/240 (46%), Gaps = 13/240 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL------ 67
            R++K ++  GI SRRE +R I++ ++ VNG       + ++  + I +DG  +      
Sbjct: 1   MRINKWLSAMGICSRREADRYISEGKLLVNGEKA-SLGMEILGKEEILLDGKLISGKGHK 59

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++  +  L  Y+KP G++ T  + D    V + +     R+  +GRLD ++EGLLLLTN 
Sbjct: 60  KEKPKPVLLKYYKPRGIICTTGEKDRGKNVIEAIGY-KERIYPIGRLDKDSEGLLLLTNQ 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDM---QVTLDTQ 182
           G L   +   S    + Y V     V ++ L  +  G+ +             Q     +
Sbjct: 119 GDLVNQINKASGYKEKEYIVSVDKPVTKEFLQEMSSGVYLPELERTTRRAVLWQDPKLPK 178

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +       + L EG NR+I+++ E   ++V RL RI     +LG +  G   E+ ++ L 
Sbjct: 179 EIQRRQFHIVLTEGLNRQIRRMCEALGYEVTRLKRIRVMNIELGKMKPGEYFEIKREELE 238


>gi|323143095|ref|ZP_08077798.1| putative 16S pseudouridylate 516 synthase [Succinatimonas hippei
           YIT 12066]
 gi|322417145|gb|EFY07776.1| putative 16S pseudouridylate 516 synthase [Succinatimonas hippei
           YIT 12066]
          Length = 248

 Score =  141 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 55/242 (22%), Positives = 101/242 (41%), Gaps = 7/242 (2%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +V +    +R+ K +++    SR+E   +I + RV V+G     AA+ +     I +D  
Sbjct: 1   MVSDKVQKERLDKCVSKLTGLSRKEASALIKEGRVLVDGQAALEAALKIPVNSIITIDDD 60

Query: 66  PLRKAE----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
            +   E    +    L      +           T           +   GRLDI+T GL
Sbjct: 61  EISLYEEGFKKRVYMLNKPSDMVCADRDRNHRIVTSLFVEELRPDTLHCAGRLDIDTTGL 120

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           L++T+DG L   +  P  +  ++YR      + +  ++   KGI      +   +    T
Sbjct: 121 LIVTDDGELIHEITHPKKEITKLYRAVTDKPIPEKAVSAFLKGIKHPEEKF-PYKSAKLT 179

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
            + +N  + V ++EG+  E+K++FE    +V  L R+  G  +L   L  G  R +S   
Sbjct: 180 IESANVGL-VEVKEGRFHEVKRLFECVGCEVIELTRLKIGSLELDDSLEEGEYRLLSDDE 238

Query: 241 LR 242
           + 
Sbjct: 239 VD 240


>gi|86147718|ref|ZP_01066026.1| hypothetical ribosomal small subunit pseudouridine synthase A
           [Vibrio sp. MED222]
 gi|85834499|gb|EAQ52649.1| hypothetical ribosomal small subunit pseudouridine synthase A
           [Vibrio sp. MED222]
          Length = 232

 Score =  141 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 57/235 (24%), Positives = 101/235 (42%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   ++ E    I    V VN   +   +  V  ++ I ++G PL+  E  
Sbjct: 1   MRLDKYLCKSTDLTKPEAIERIHNGEVNVNSETVTDESAQVHESNTILLNGTPLKLREFR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L ++     + +   D    S          S +   GRLD +T GL+L+T+DG  +  
Sbjct: 61  YLLMHKPAGTICSN-IDEVYPSLFNYIEIDKASELHIAGRLDADTTGLVLITDDGRWSFN 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--CYGDMQVTLDTQKGSNAWVTV 191
           + LP+    +VYRV     +  D  +  K GI +QG        ++ + T K     V +
Sbjct: 120 ITLPTKSCKKVYRVTLSRGIKDDVADKFKAGIQLQGEQKPTRPAELEVITSKQ----VLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            + EGK  ++K++F     +V  L R   G  +L  + AG  R ++K  +     
Sbjct: 176 TITEGKFHQVKRMFAAVGNRVVGLHREQIGDVRL-DVEAGQWRYLTKAEVDSFQQ 229


>gi|291059845|gb|ADD72580.1| RNA pseudouridine synthase superfamily [Treponema pallidum subsp.
           pallidum str. Chicago]
          Length = 284

 Score =  141 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 71/255 (27%), Positives = 115/255 (45%), Gaps = 21/255 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+   +AR+G ASRR  E +IA  RV V+G  +      V + + + VDG  ++     R
Sbjct: 34  RLQVYLARSGCASRRACEALIASGRVTVDGQTVTTQGRTVCAQNVVCVDGTVVQLERVQR 93

Query: 75  LWLYHKPIGLVTT-----------------HSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
             L +KP+G + +                  S  +    +    P+   R+  +GRLD+ 
Sbjct: 94  YVLLYKPVGYICSLAPQFPAGYAHTQVRAGPSKQEYARAIDLVQPAYQERLYHIGRLDVR 153

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           +EG LL TNDG  A+ L  P +   + Y V     V    L+   +G+ ++G  Y  ++ 
Sbjct: 154 SEGALLFTNDGSFAQALGHPRSGIEKEYIVETREPVPAALLSSFVRGVWVEGCRYRCVRA 213

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                +     V + L EGK REI+ VFE +   V RL+R+  G  +LG L  G+ R + 
Sbjct: 214 RHLAAQ----CVQLVLVEGKKREIRVVFEAWGQDVVRLVRVRIGRVRLGPLRPGAFRTMR 269

Query: 238 KKILREQLGPHLLEE 252
            + + + L       
Sbjct: 270 LQEVAQLLQCAGCAR 284


>gi|167581475|ref|ZP_02374349.1| pseudouridine synthase family protein [Burkholderia thailandensis
           TXDOH]
          Length = 324

 Score =  141 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 76  VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAEQAAQ 135

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 136 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWGGDRSPLRFSPQHLRALAPAGRLDIDS 195

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 196 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTTDIERHFPAESLAKLRHGLELDG 255

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 256 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 311

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 312 QGQWRYLGPDE 322


>gi|153951436|ref|YP_001398988.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. doylei 269.97]
 gi|152938882|gb|ABS43623.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. doylei 269.97]
          Length = 253

 Score =  141 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 74/250 (29%), Positives = 118/250 (47%), Gaps = 20/250 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+     SRRE + +I Q  VK+N  +    +  V   D + V G  ++K  + 
Sbjct: 1   MRINKFISHNTRYSRRESDELIKQGLVKINNKIA-LLSDEVKFDDKVFVKGKRVQKRTQF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +YHK  G + +  D  GR T++D LP  FS  +SVGRLD  +EGLLLLT+   +A V
Sbjct: 60  SVLIYHKQKGEIVSKKDDRGRKTIYDTLPRQFSTWLSVGRLDYASEGLLLLTDSPVIADV 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--------------YGDMQVTL 179
           L        R Y ++  G V +  +  ++ G+ I+                    +   +
Sbjct: 120 LMHSD--LEREYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEI 177

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               G    + V + EGKNRE+++ F  F+ +V  L R+++G   LG L  G  R +   
Sbjct: 178 FGSSGGYTKLRVVINEGKNRELRRFFGHFDLEVMDLKRVAFGALDLGMLKVGKHRYLENG 237

Query: 240 I---LREQLG 246
               LR+ L 
Sbjct: 238 EYEKLRDFLK 247


>gi|325273368|ref|ZP_08139630.1| pseudouridine synthase [Pseudomonas sp. TJI-51]
 gi|324101491|gb|EGB99075.1| pseudouridine synthase [Pseudomonas sp. TJI-51]
          Length = 230

 Score =  141 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 56/231 (24%), Positives = 114/231 (49%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     +R++   M+AQ+RV+++G ++      V     +++D   L+     
Sbjct: 1   MRLDRFLANLPHCNRQQARLMLAQRRVRLDGQVISDPLAEVREFSRVQLDEQLLQAGRPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + HKP G V+   DP   + +     ++ + +   GRLD NT GL++LTNDG  +R 
Sbjct: 61  RYLMLHKPAGCVSATHDPQHPTVLELLPAALRADLHIAGRLDFNTTGLMILTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P+T+  + Y V    ++ +  +   ++      + +     Q+ +   + +     +
Sbjct: 121 LTQPATKLPKQYLVETEDEIAEHYVAKFREGFYFAFENLTTQPAQLDILGPRQA----RL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F FF+ KV  L R S G  +L   L  G+ R+++ + +
Sbjct: 177 AIVEGRYHQVKRMFGFFDNKVVGLHRESMGAIRLDPGLAPGAFRQLTPEEI 227


>gi|299769553|ref|YP_003731579.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter sp. DR1]
 gi|298699641|gb|ADI90206.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter sp. DR1]
          Length = 234

 Score =  141 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 46/225 (20%), Positives = 88/225 (39%), Gaps = 3/225 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V ++G + +         +    + G   +  E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVSIDGEVADDLKKQFSPENLEFSLFGETYQYREKVY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L        +                 I   V ++GRLD +T GLLLLT+DG   + L
Sbjct: 63  LALKKPKGFECSHQPHHHQSVFSLLPEILIQRGVQAIGRLDQDTTGLLLLTDDGKYLQAL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     +VY V     V  +++ +L +G+ +           +   +     +T+ + 
Sbjct: 123 THPRKHVPKVYHVTTIDPVTPEQIEMLSQGVSLHQEKGVFAATDVKILE--THQLTMTIH 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G   ++K++      KV  L R   G   L  L  G    +S++
Sbjct: 181 QGVYHQVKRMIAAVGNKVEALHRHQVGQLVLPELEDGEWVYLSEQ 225


>gi|330720777|gb|EGG98994.1| Ribosomal small subunit pseudouridine synthase A [gamma
           proteobacterium IMCC2047]
          Length = 239

 Score =  141 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 61/235 (25%), Positives = 106/235 (45%), Gaps = 8/235 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R+ + I+     S++ V  ++AQ RV V+G +       + +   I +DG  L+   
Sbjct: 4   KSARLDRFISSKMAISQKAVRPILAQGRVAVDGCVCRDRQQIINTFSRITLDGQILQANT 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L +      +V+   D   ++ +        S++  VGRLD N+ GLLLLTND G +
Sbjct: 64  PLYLMMNKPKG-VVSATRDNQYQTVIDLLDHPERSKLHLVGRLDFNSTGLLLLTNDSGWS 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLK--KGIVIQGICYGDMQVTLDTQKGSNAWV 189
           + L  P  +  + YRV  +  +DQ  ++          +        + +     ++   
Sbjct: 123 QQLMKPDQKVSKRYRVTVNNPLDQQTVDAFAAGMYFAYEDATTRPAGLNII----NDYEA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
            V L EG+  +IK++F   N KV  L RI+ G   L  +L AG +RE+S   + +
Sbjct: 179 EVTLTEGRYHQIKRMFARCNNKVLALHRIAIGNLLLDPSLSAGQSRELSAAEVTD 233


>gi|285018093|ref|YP_003375804.1| ribosomal large subunit pseudouridine synthase b (rrna
           pseudouridylate synthase b) protein [Xanthomonas
           albilineans GPE PC73]
 gi|283473311|emb|CBA15816.1| probable ribosomal large subunit pseudouridine synthase b (rrna
           pseudouridylate synthase b) protein [Xanthomonas
           albilineans]
          Length = 511

 Score =  141 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 82/350 (23%), Positives = 144/350 (41%), Gaps = 13/350 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ KV+A+AG+ SRR +E+ IA   VKVNG + +   +++ S D IE+DG         
Sbjct: 29  ERLHKVLAQAGLGSRRALEQRIADGLVKVNGEVAQT-GMSIKSGDRIELDGRSFVASALT 87

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + T        +          +R I++GRLDINT GLLLLT DG 
Sbjct: 88  EPARVLIYNKPEGEVTTREDPEGRPTIFEALPALKGARWIAIGRLDINTTGLLLLTTDGE 147

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR      ++      +  L +G+V++       ++       
Sbjct: 148 LANAMMHPSYEIEREYVVRVRAPEGEESVPDSMIERLARGVVLEDGSAKFDEIERIGGTD 207

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   +L G + E+++  +  
Sbjct: 208 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGKVALPREVLRGQSMELAQDKVEA 267

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                 LEE      A         R     + +V           +  +   + ++  T
Sbjct: 268 LRAELKLEEGTP--SALTLQPVIGQRKAAKAVVQVGRGGNAYVNGHNAADEGRELRRFDT 325

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               R          G  +     + ++ +   +  +    + L   +  
Sbjct: 326 FREDRGRGRGGKKPHGGLTVSGEMAAKQAQKPFKQRTPKGPKPLPDGNPA 375


>gi|167837045|ref|ZP_02463928.1| pseudouridine synthase family protein [Burkholderia thailandensis
           MSMB43]
          Length = 325

 Score =  141 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 98/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 77  VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 136

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 137 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 196

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 197 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDG 256

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                  V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 257 APLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 312

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 313 QGQWRYLGLDE 323


>gi|289665762|ref|ZP_06487343.1| pseudouridylate synthase [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 527

 Score =  141 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 82/356 (23%), Positives = 142/356 (39%), Gaps = 17/356 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG         
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKIELDGRSFVASALT 86

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + T        +          SR I++GRLDINT GLLLLT DG 
Sbjct: 87  EPSRVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR      ++      +  L +G++++       ++       
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + EV+++ +  
Sbjct: 207 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGQSVEVAQEKVDA 266

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL-- 301
                 LEE   +              +  +               +      ++ +   
Sbjct: 267 LRAELKLEEGAPSALTLQPVIGQRRAAKSTVHVSRDGRSNAYVNGHTSGADEGRELRRFD 326

Query: 302 ----ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                     R           +     +   Q+    +R P+   + +L   +  
Sbjct: 327 NLREDRGRGGRGKPGGFKGGLTVSGEAAARQSQQRPFKQRGPAKGDRGALPEGNPA 382


>gi|319944612|ref|ZP_08018880.1| ribosomal large subunit pseudouridine synthase F [Lautropia
           mirabilis ATCC 51599]
 gi|319742149|gb|EFV94568.1| ribosomal large subunit pseudouridine synthase F [Lautropia
           mirabilis ATCC 51599]
          Length = 275

 Score =  140 bits (353), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 66/254 (25%), Positives = 104/254 (40%), Gaps = 29/254 (11%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------- 63
              +R++K +AR G+ SRRE +  I+Q  V++NG  +      VM  D +EV        
Sbjct: 25  PEGERLNKHLARTGVCSRREADDWISQGWVRINGRPV-EMGQKVMPGDVVEVRQAARARQ 83

Query: 64  --------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                     P+          Y   + L+   S   G +       +    +   GRLD
Sbjct: 84  QDKVTILLNKPVGYVSGQAEDGYRPAVTLIDAQSRWAGDTNPRRFERNQLRGLAVAGRLD 143

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG---------QVDQDKLNLLKKGIV 166
           I++ GLL+LT DG +AR L    +   + Y VR                D+L LL+ G+ 
Sbjct: 144 IDSVGLLVLTQDGRVARQLIGEDSSTTKEYLVRVRYGEVERNVQAAFPPDRLKLLRHGLS 203

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
           + G      QV  +  +     +   L+EG++R+I+++ E     V  L RI  G   LG
Sbjct: 204 LDGHKLKPAQVDWENPEQ----LRFVLQEGRHRQIRRMCELVGLAVTGLKRIRVGNVLLG 259

Query: 227 TLLAGSTREVSKKI 240
            L  G  R +    
Sbjct: 260 RLPPGQWRYLGLDE 273


>gi|222151679|ref|YP_002560835.1| 16S pseudouridylate synthase homolog [Macrococcus caseolyticus
           JCSC5402]
 gi|222120804|dbj|BAH18139.1| 16S pseudouridylate synthase homolog [Macrococcus caseolyticus
           JCSC5402]
          Length = 234

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 52/242 (21%), Positives = 98/242 (40%), Gaps = 27/242 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQ------------RVKVNGILLERAAVNVMSTDHIE 61
            R+ K +   G  +R+EV+ ++ +              +K+           V   D + 
Sbjct: 1   MRLDKFLGNHGFGTRKEVKLLVKRGAVKVNDVVVKKSDIKI-----------VPENDTVT 49

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           V    +       + L      + ++  D    + +          +  VGRLD +TEGL
Sbjct: 50  VYDEVVMYEPFVYIMLNKPAGYI-SSTKDYKDETVLELIEGFEHYDLHPVGRLDKDTEGL 108

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLD 180
           L+LTNDG  +  +  P     + Y  R  G V  D + L K GI +         ++ + 
Sbjct: 109 LILTNDGQFSHDVLSPRKHVNKTYFARVDGYVTDDTVELFKAGITLDDGYKAMPAELQII 168

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK 239
           +  G  + + + ++EGK  ++K++F   +  V  L RI  G   L   L  G+ R+++ +
Sbjct: 169 SA-GEISEIELVIQEGKFHQVKRMFIAVDMIVIYLKRIKMGGLPLDESLTPGAYRKLTLE 227

Query: 240 IL 241
            +
Sbjct: 228 EI 229


>gi|294139593|ref|YP_003555571.1| ribosomal small subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
 gi|293326062|dbj|BAJ00793.1| ribosomal small subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
          Length = 236

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 64/235 (27%), Positives = 108/235 (45%), Gaps = 8/235 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++      R+++  M+AQ RV+V+GI+ +     V    H+ VD   L+    + 
Sbjct: 7   RLDRFLSSELKIKRKDIRLMLAQNRVRVDGIVAKDIQQLVDEFSHVSVDDAVLKNNRPSY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L      +V+   D   ++ +        S +  VGRLD+NT GL+LLTNDG  +R L
Sbjct: 67  VMLNKPVG-VVSATKDDKHKTVIDLLDHPAKSELHIVGRLDLNTSGLMLLTNDGRWSRKL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
             P ++  + YRV     +  + ++   K      + I     ++ +     S     V 
Sbjct: 126 MSPESKVEKRYRVTLQNPLSTEYIDAFAKGFYFEFEDITTQAAKLEII----SEHIAEVT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           L EGK  +IK++F  F   V  L R S G   L   L  G +RE+S + + +  G
Sbjct: 182 LTEGKYHQIKRMFGRFRNPVIGLHRYSVGELLLDPDLDEGGSRELSVEEVNDIFG 236


>gi|237752429|ref|ZP_04582909.1| RNA pseudouridine synthase [Helicobacter winghamensis ATCC BAA-430]
 gi|229375918|gb|EEO26009.1| RNA pseudouridine synthase [Helicobacter winghamensis ATCC BAA-430]
          Length = 262

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 67/241 (27%), Positives = 117/241 (48%), Gaps = 16/241 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ IA     SRRE +R+I + +V +N  ++   +  V     + ++G  LR+ ++ 
Sbjct: 1   MRLNQYIAHHSKFSRREADRLIKEGKVTINKEVVSDFSYQVDKNTKVYLNGKCLREQDQY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +Y+KP G + +  D  GR  ++D+LP  FS    VGRLD  +EGLLLL++   + R 
Sbjct: 61  SVIVYNKPKGELVSKRDDRGRRVIYDSLPKRFSHFKPVGRLDFASEGLLLLSDSVKVVRS 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQVTL 179
           L     +  RVY ++  G +     + ++ GI ++                    +  T 
Sbjct: 121 LMES--ELERVYLLKLSGLIKDSVFDAMESGITLEDASAGGHSKSKIKAMEFAPFVGYTC 178

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                  + + V L+EGKNRE+++ F  F  +V  L RI+YG   L  L +G  R + + 
Sbjct: 179 IKNTPKYSKIKVILKEGKNRELRRFFAHFGLEVLDLKRIAYGFVHLNNLPSGKVRFLERG 238

Query: 240 I 240
            
Sbjct: 239 E 239


>gi|218709591|ref|YP_002417212.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio splendidus
           LGP32]
 gi|218322610|emb|CAV18769.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio splendidus
           LGP32]
          Length = 241

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 54/235 (22%), Positives = 103/235 (43%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   ++ E  + I    V VN +++   +  V  ++ I ++G  L   E  
Sbjct: 10  MRLDKYLCKSTELTKLEAVQRIQNGEVSVNSVVVLDESTQVHESNAILLNGDALTLREFR 69

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     + +   +       +  L       I+ GRLD +T GL+L+T+DG  +  
Sbjct: 70  YILMHKPAGTICSNIDEVYPSLFNYLELEKASELHIA-GRLDADTTGLVLITDDGRWSFN 128

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           + LP+    +VYRV     +  D  +  K GI +QG        ++ + T K     V +
Sbjct: 129 ITLPTKSCKKVYRVILSRDIKDDVADKFKAGIQLQGEQKLTRPAELEVITSK----EVLL 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            + EGK  ++K++F     +V  L R   G  +L  + AG  R ++K  +     
Sbjct: 185 TITEGKFHQVKRMFAAVGNRVVGLHREQIGDVRL-DVEAGQWRYLTKAEVDSFQQ 238


>gi|315221963|ref|ZP_07863874.1| conserved hypothetical protein [Streptococcus anginosus F0211]
 gi|315188929|gb|EFU22633.1| conserved hypothetical protein [Streptococcus anginosus F0211]
          Length = 250

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 56/232 (24%), Positives = 104/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+A   SR+++++ + ++++ V+     + + NV +    I ++  P+     
Sbjct: 10  MRLDILLAQA-HISRKKMKQALLKKKILVDDCPARKLSQNVDTGLQTITLEEQPVLGKPH 68

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +                       + SVGRLD +T GLLL+T++G L  
Sbjct: 69  QYFMMNKPLGVVTANSDAKFQTVLDLIRPEDFSEDLYSVGRLDRDTSGLLLITDNGPLGF 128

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
           +L  P     + Y V  +G +D   +   +KGI  + G       +T+ +   + +  TV
Sbjct: 129 LLLHPQYHVTKTYEVEVNGLLDDQAVQSFQKGIVFLDGTICKPATLTIRSSSSNKSRATV 188

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L RI +G F+L   L  G  R +++  L 
Sbjct: 189 TISEGKFHQIKKMFLTVGVKVTSLKRIHFGDFELEPNLATGEYRVLNQAELE 240


>gi|313678967|ref|YP_004056706.1| ribosomal small subunit pseudouridine synthase a [Oceanithermus
           profundus DSM 14977]
 gi|313151682|gb|ADR35533.1| ribosomal small subunit pseudouridine synthase A [Oceanithermus
           profundus DSM 14977]
          Length = 233

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 60/220 (27%), Positives = 102/220 (46%), Gaps = 9/220 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAER 72
           +R+ +V+A  G+ +R+EV ++I    V+V+G ++      +      IEV G P+R A  
Sbjct: 3   ERLDRVLAHLGLGTRKEVGKLIRAGAVRVDGAVVRDRGYKLDPEAARIEVRGEPVRYARH 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L+     L  T S+ +               +  VGRLD +TEGLLLLTN G L  
Sbjct: 63  FYVLLHKPAGVLTATRSERETTVLDLLPDALWRDDLRPVGRLDRDTEGLLLLTNHGELLH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  +VY      ++ +D      +G++     +   ++     + +     V 
Sbjct: 123 RLTHPRWKVAKVYFAELASELPEDAARRFAEGVLD----FAPAELEALGPRAA----RVT 174

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
           L EGK+R+++++F      V  L R  +GP +LG L  G 
Sbjct: 175 LYEGKHRQVRRMFAALGAPVAYLRRERFGPLELGGLEPGQ 214


>gi|254251646|ref|ZP_04944964.1| Pseudouridine synthase [Burkholderia dolosa AUO158]
 gi|124894255|gb|EAY68135.1| Pseudouridine synthase [Burkholderia dolosa AUO158]
          Length = 238

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 52/234 (22%), Positives = 88/234 (37%), Gaps = 4/234 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV V G           +   +  VDG       R  
Sbjct: 3   LESILYTQGFGSRRQCRGLIEAGRVAVGGATATDPDTAFDTDGLVFTVDGTAWPFHARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L        +               P +   V  VGRLD +T GLLLL++DG      
Sbjct: 63  LTLNKPAGYECSRDPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFVHAY 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y       +   +L+ L+ G+ + G     +       + ++  V + + 
Sbjct: 123 TSPKRKVPKTYVATVRHPLSDTQLHTLRTGVQLHGEP-KPIAAVAADARDAHTLV-LTVV 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
           EGK  ++K++    + +V+ L R S G   L   L  G+ R + +  L     P
Sbjct: 181 EGKYHQVKRMVAAVSNRVDALHRESIGGLTLPDNLAPGTWRWLDEAELAALRNP 234


>gi|172040768|ref|YP_001800482.1| putative pseudouridylate synthase [Corynebacterium urealyticum DSM
           7109]
 gi|171852072|emb|CAQ05048.1| putative pseudouridylate synthase [Corynebacterium urealyticum DSM
           7109]
          Length = 291

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 66/235 (28%), Positives = 101/235 (42%), Gaps = 4/235 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+ KV+A AG+ASRR  E++IA  RV+VNG +++R  V +     +        + 
Sbjct: 48  EDKVRLQKVLAAAGVASRRMSEKLIAAGRVEVNGKVVDRMGVRIDPNKDVVRVDGVRVQV 107

Query: 71  --ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTN 126
             E              T   D    S        +        VGRLD  TEGLLLLTN
Sbjct: 108 NDEMHYYIFNKPRGVQSTMSDDMGRPSVGNFIDERLKQGQGLFHVGRLDAQTEGLLLLTN 167

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  + Y     G+  +  ++ LKKGI +         V +       
Sbjct: 168 DGELANRLMHPSYEVSKTYMATVLGEAKKGLVHELKKGIELDDGIAKADDVQIVDVWQGK 227

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + + L EG+   ++++ +   + V  L+R      QLG    GS R +++  L
Sbjct: 228 SLIKLELHEGRKHIVRRLLKAAGFPVQALVRTKIHTVQLGDQKPGSVRALNRSEL 282


>gi|188991361|ref|YP_001903371.1| putative pseudouridine synthase [Xanthomonas campestris pv.
           campestris str. B100]
 gi|167733121|emb|CAP51319.1| putative pseudouridine synthase [Xanthomonas campestris pv.
           campestris]
          Length = 538

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 87/359 (24%), Positives = 146/359 (40%), Gaps = 25/359 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG     +  T
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKIELDGRSFVASALT 86

Query: 74  ----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + T        +          SR I++GRLDINT GLLLLT DG 
Sbjct: 87  ESSRVLVYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR      ++      +  L +G++++       ++       
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVPDSMIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV---SKKI 240
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + E+       
Sbjct: 207 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGKVSLPRELLRGQSVELAQEKVDA 266

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRP-----------NIISEVPDDFTRMKKNS 289
           LR +L       + + L   I                      N  +   D+   +++  
Sbjct: 267 LRAELKLEEGAPSALTLQPVIGQRRAAKSTVHVSRDGRSNAYVNGQTSGADEGRELRRFD 326

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           + +     +     P   +   +    A    S       +      RS    +  + R
Sbjct: 327 NLREDRGGRGGRGKPGGFKGGLTVSGEAAAKQSQQRPFKQRGPAKGDRSLPDGNPAAFR 385


>gi|91792047|ref|YP_561698.1| pseudouridine synthase, Rsu [Shewanella denitrificans OS217]
 gi|91714049|gb|ABE53975.1| Pseudouridine synthase, Rsu [Shewanella denitrificans OS217]
          Length = 238

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 62/237 (26%), Positives = 102/237 (43%), Gaps = 15/237 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRK 69
           T  R++  +A+ G+ASRR+  R+I   RV +NG         +   +   + VDG  +  
Sbjct: 2   TSIRLAHYLAQCGVASRRQASRLIEAGRVLLNGNQASHTDY-IDEHNASSLRVDGKAIAP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E    WLY+KPIG+       D  S +     +    +   GRLD ++ GLLLLTNDG 
Sbjct: 61  -EAKAYWLYNKPIGIDCRLLAQDPASLIHQLPSAPR--LYPAGRLDKDSRGLLLLTNDGD 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     + Y V+ +  +  + +  L  G+   G+     +V            
Sbjct: 118 LTHKLMHPDFYHPKTYHVQVNQPLKDEDIMALSTGVAYPGVLTRRCEVRRLADDK----F 173

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-----LLAGSTREVSKKIL 241
            + L +G NR+I+++ +   +KV  L R +    +L +     L     R +    L
Sbjct: 174 EMILTQGLNRQIRRMCKALGYKVIDLQRTAIMKLELNSKEFEQLADNKMRPLEAAEL 230


>gi|322392364|ref|ZP_08065825.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           peroris ATCC 700780]
 gi|321144899|gb|EFX40299.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           peroris ATCC 700780]
          Length = 241

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 106/232 (45%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++ +  + SR+ +++ + ++ + V+ +     A NV +    +   G  ++  E 
Sbjct: 1   MRLDKLLTQEKV-SRKAIKQALLKKEILVDELPATSLAQNVDTGLQELIFQGRKIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L+     +  +                    + ++GRLD +T GLLLLT++G L  
Sbjct: 60  TYLMLHKPNGVVTASKDKKLPTVMDLLPQSLQSEELYAIGRLDRDTTGLLLLTDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + YRV  +G +  DK+   K GI  + G      Q+ + +   S++   +
Sbjct: 120 QLLHPQYHVDKTYRVEVNGPLTPDKVQEFKDGIVFLDGTVCKPAQLDILSSSSSHSKAII 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++KK+F     KV  L RI +G F L   L  G  R ++++ L 
Sbjct: 180 TIAEGKFHQVKKMFLSIGVKVTSLKRIQFGDFTLDSELAEGQYRSLNQEELE 231


>gi|160932777|ref|ZP_02080166.1| hypothetical protein CLOLEP_01618 [Clostridium leptum DSM 753]
 gi|156867851|gb|EDO61223.1| hypothetical protein CLOLEP_01618 [Clostridium leptum DSM 753]
          Length = 256

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 104/231 (45%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K+++  G+ SR+E   +I +  V VNGIL  R         D I ++G PLR    
Sbjct: 6   ERLDKILSSQGVGSRKEAGILIRRGLVHVNGILATRPETKTDPERDQITIEGKPLRFQRH 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +      +  +    +               +   GRLD +T GLL+LT+DG LA 
Sbjct: 66  VYLMMNKPAGVVSASRDSREKTVVDLVPPVLSRRDLFPAGRLDRDTTGLLILTDDGELAH 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            +  P     ++Y     G V  +++     G+ ++         +T+  Q  +   + V
Sbjct: 126 RMLSPKKHVYKLYEASVDGPVGAEEIEKFAAGVALEDGTVCLPAGLTVVKQGTAWETL-V 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            +REGK  ++KK+F     +V RL R+  G  +L   L  G  RE++K+ L
Sbjct: 185 EIREGKFHQVKKMFLAVGRRVLRLKRVRIGGLELDKTLKEGECRELTKEEL 235


>gi|162533084|ref|YP_001621408.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tomato str. DC3000]
 gi|213971148|ref|ZP_03399267.1| Ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tomato T1]
 gi|301381835|ref|ZP_07230253.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tomato Max13]
 gi|302061563|ref|ZP_07253104.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tomato K40]
 gi|302132803|ref|ZP_07258793.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tomato NCPPB 1108]
 gi|118201622|gb|ABK79685.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tomato str. DC3000]
 gi|213924137|gb|EEB57713.1| Ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tomato T1]
 gi|331015567|gb|EGH95623.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. lachrymans str. M302278PT]
          Length = 230

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 102/231 (44%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R+ V   +A  RV+V+G +      +V     +  D   L+  +  
Sbjct: 1   MRLDRFLSNLPRFNRKSVRLALASGRVQVDGQITTDPHYDVREFSCVAFDMQILQPGKAA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V+  +D    + +          +   GRLD NT GL+L+TNDG  +R 
Sbjct: 61  RYFMLHKPQGCVSATTDAQHATVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+       +      + I     Q+T+   + +     +
Sbjct: 121 LTQPHTKMPKVYYVETEQLIDERYALTFAEGLFFSFENIITQPAQLTVLGPRSA----RL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F  F+ KV +L R S G   L   L  G  R +    +
Sbjct: 177 SIIEGRYHQVKRMFGHFDNKVLQLHRESIGALILDPALPPGGYRSLQAAEI 227


>gi|323356708|ref|YP_004223104.1| 16S rRNA uridine-516 pseudouridylate synthase [Microbacterium
           testaceum StLB037]
 gi|323273079|dbj|BAJ73224.1| 16S rRNA uridine-516 pseudouridylate synthase [Microbacterium
           testaceum StLB037]
          Length = 245

 Score =  140 bits (352), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 75/238 (31%), Positives = 111/238 (46%), Gaps = 21/238 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILL----------ERAAVNVMS-TDHIEV 62
            R+ KV+A AG+ASRR  E MI          +                 +   TD ++V
Sbjct: 1   MRLQKVLANAGVASRRVSEEMI----------VAGRVRVNGVVVTELGSRIHPETDLVDV 50

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG  ++     R  + +KP G+V++ SD  GR  +         R+ +VGRLD +T GLL
Sbjct: 51  DGTAIQLDTSKRYVILNKPTGVVSSMSDDRGRPDLRQYTKDWDERLFNVGRLDADTSGLL 110

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           +LTNDG LA VL  PS    +VY  +  GQV    +  L KG+ ++       +  L   
Sbjct: 111 VLTNDGDLAHVLAHPSFGVTKVYIAKVEGQVLPQTIQHLLKGVDLEDGRIAADKARLLDS 170

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
               + V + L  GKNR ++++       V  L+R  +GP  LGTL  G  RE++   
Sbjct: 171 SRGESLVELTLHSGKNRIVRRLMAEVGHPVIELVRRQFGPLHLGTLPVGKARELTTVE 228


>gi|114800237|ref|YP_759483.1| ribosomal small subunit pseudouridine synthase A [Hyphomonas
           neptunium ATCC 15444]
 gi|114740411|gb|ABI78536.1| ribosomal small subunit pseudouridine synthase A [Hyphomonas
           neptunium ATCC 15444]
          Length = 224

 Score =  140 bits (352), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 50/231 (21%), Positives = 88/231 (38%), Gaps = 15/231 (6%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              ++++K +A  G  SR+E+E  I + RV                 + +E DG PL   
Sbjct: 2   TETRKLAKYLASLGYGSRKEMEVAIRRGRVT-------------GWGEDVEFDGEPLDPG 48

Query: 71  ERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               + ++       +           +         ++ SVGRLD +T GLLL T+DG 
Sbjct: 49  PGMVILMHKPAGYTCSHQDQGKLVYDLLPPRFLKRDPKISSVGRLDADTTGLLLFTDDGA 108

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P +   + Y       ++  +      G +I                G     
Sbjct: 109 LLHRLISPKSDIPKTYEATLARPLEGFEKEFFASGSLILRGEDKPCLPAELEVTGERT-A 167

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + L EG+  +++++F      V  L R  +GP +LG L  G+ R +++  
Sbjct: 168 RLTLSEGRYHQVRRMFAAAGNHVEALHRSRFGPLELGDLSEGAWRLLTEAE 218


>gi|228999324|ref|ZP_04158904.1| RNA pseudouridine synthase [Bacillus mycoides Rock3-17]
 gi|229006879|ref|ZP_04164511.1| RNA pseudouridine synthase [Bacillus mycoides Rock1-4]
 gi|228754372|gb|EEM03785.1| RNA pseudouridine synthase [Bacillus mycoides Rock1-4]
 gi|228760521|gb|EEM09487.1| RNA pseudouridine synthase [Bacillus mycoides Rock3-17]
          Length = 203

 Score =  140 bits (352), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 53/206 (25%), Positives = 96/206 (46%), Gaps = 8/206 (3%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
           +NG +       V   D + +DG  + K  +      +HKP+G+  T +D    + +   
Sbjct: 3   INGEVCTH-GTIVTENDIVTIDGKTIEKEDKEKIYIAFHKPVGITCTAADHIDGNIIEYI 61

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
             +   R+  VGRLD  +EGL+LLTNDG +A  +     +  + Y V          ++ 
Sbjct: 62  --NHPERIFPVGRLDKASEGLILLTNDGRIANQILHGDHEHEKEYIVTVDKPFTDWFIDG 119

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           + +G+ I+       +VT      +++   + L +G NR+I+++   F + V +L R+  
Sbjct: 120 MSRGVKIKDGITKQCKVTRV----NSSTFRIILTQGMNRQIRRMSRAFGYTVTKLKRVRI 175

Query: 221 GPFQLGTLLAGSTREVSKKILREQLG 246
              +L  L AG  R V+ + L+E L 
Sbjct: 176 MNIKLDGLEAGEWRNVTVQELQELLK 201


>gi|229158156|ref|ZP_04286224.1| RNA pseudouridine synthase [Bacillus cereus ATCC 4342]
 gi|228625318|gb|EEK82077.1| RNA pseudouridine synthase [Bacillus cereus ATCC 4342]
          Length = 203

 Score =  140 bits (352), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 51/202 (25%), Positives = 90/202 (44%), Gaps = 8/202 (3%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
           +NG +       V   D + +DG  + K E+      +HKP+G+  T +D    + +   
Sbjct: 3   INGEICTH-GALVSDGDRVTIDGQVIVKEEKEKVYIAFHKPVGITCTAADHIEDNIIDYI 61

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
             +   R+  VGRLD  +EGL+LLTNDG +A  +     +  + Y V          ++ 
Sbjct: 62  --NYPERIFPVGRLDKASEGLILLTNDGAIANQILHGDHEHEKEYVVTVDKPFTDWFIDE 119

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           +  G+ I+       +VT        +   + L +G NR+I+++   F + V +L R+  
Sbjct: 120 MSSGVKIKDGMTKPCKVTRV----DQSTFRIVLTQGMNRQIRRMSRAFGFTVTKLKRVRI 175

Query: 221 GPFQLGTLLAGSTREVSKKILR 242
              +L  L  G  R V+ + L 
Sbjct: 176 MNIELNELEVGKWRSVTAEELE 197


>gi|325925508|ref|ZP_08186898.1| ribosomal large subunit pseudouridine synthase B [Xanthomonas
           perforans 91-118]
 gi|325544075|gb|EGD15468.1| ribosomal large subunit pseudouridine synthase B [Xanthomonas
           perforans 91-118]
          Length = 532

 Score =  140 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 85/356 (23%), Positives = 144/356 (40%), Gaps = 17/356 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG         
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKIELDGRSFVASALT 86

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + T        +          SR I++GRLDINT GLLLLT DG 
Sbjct: 87  EPSRVLIYNKPEGEVTTREDPEGRPTVFESLPVLKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR      ++      +  L +G++++       ++       
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + EV++  +  
Sbjct: 207 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGHSVEVAQDKVDA 266

Query: 244 QL-GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
                 L E A   L       +         +S        +   +S  +   + ++  
Sbjct: 267 LRAELKLEEGAPSALTLQPVIGQRRAAKSTVHVSRDGRSNAYVNGQTSGADEGRELRRFD 326

Query: 303 TPVHRRNLASNVWMAKGIH-----SSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                R                      +   Q+    +R P+   + +L   +  
Sbjct: 327 NLREDRGRGGRGKPGGFRGGLTVSGEAAAKQSQQRPFKQRGPAKGDRGALPDGNPA 382


>gi|302187757|ref|ZP_07264430.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. syringae 642]
          Length = 230

 Score =  140 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 106/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R++V   +A  RV+V+G         V     + +DG  L+  +  
Sbjct: 1   MRLDRFLSNLPRFNRQQVRLALASGRVQVDGQATRDPHHEVREFSCVALDGEILQAGKAP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V+  SD    + +          +   GRLD NT GL+L+TNDG  +R 
Sbjct: 61  RYFMLHKPQGCVSATSDAQHPTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+       +      +G+     Q+TL   + +     +
Sbjct: 121 LTQPQTKMPKVYYVETEQPIDERYAAKFAEGLYFAFEGLTTQPAQLTLLGPRSA----RL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F  F+ KV RL R + G   L   L  GS R ++   +
Sbjct: 177 SIVEGRYHQVKRMFGHFDNKVLRLHRENIGALALDPGLRPGSYRALNAGEI 227


>gi|328945586|gb|EGG39737.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1087]
          Length = 241

 Score =  140 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 103/231 (44%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++ + Q+++ V+G    + + NV +    I   G  +     
Sbjct: 1   MRIDQLLA-ANHISRKKMKQSLLQKQILVDGKPACKLSQNVDTGLQQINFQGKHVSGPAH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +               +       + S+GRLD +TEGLLL+T++G L  
Sbjct: 60  RYYMLNKPAGAVTANRDAEKLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V  +G +        ++GI  + G      Q+++ +   S +  TV
Sbjct: 120 QLLHPQYHVEKTYYVEVNGPLTPQDKIAFQEGIRFLDGTICQPAQLSILSTSSSLSRATV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  +IKK+F     KV  L RI +G F L   L  G  R ++++ L
Sbjct: 180 KISEGKFHQIKKMFLAIGVKVTYLKRIQFGDFTLDPDLAKGDYRALNQEEL 230


>gi|313681268|ref|YP_004059006.1| RNA-binding s4 domain protein [Sulfuricurvum kujiense DSM 16994]
 gi|313154128|gb|ADR32806.1| RNA-binding S4 domain protein [Sulfuricurvum kujiense DSM 16994]
          Length = 315

 Score =  140 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 75/308 (24%), Positives = 134/308 (43%), Gaps = 20/308 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R++K IA     SRRE ++ I    V+++G +    A  V     ++ + G  +   ++
Sbjct: 2   MRLNKFIAHYSTYSRREADQAILDGYVRIDGEIETNPATQVDERHANVMISGNKITPTDQ 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +Y+KP G + T  DP GR T++D+L   +   I +GRLD  +EGLLLLT+      
Sbjct: 62  FTVIVYNKPRGELVTKKDPQGRKTIYDSLAKQYRHYIPIGRLDFASEGLLLLTDA--SRV 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV--------------T 178
              L +++  RVY+++  G V +     + +G+ ++    G  +                
Sbjct: 120 ATALMTSKMERVYKIKIKGPVTEAMKVAMGEGLELEDASAGAHEHAEAGPMSFAPFYAYQ 179

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +   +G  + + V + EG+NRE+++ F  F  +V  L R+S+G   L  L  G  R + +
Sbjct: 180 VQKDQGDYSVLKVAIGEGQNRELRRFFAHFGAEVVDLKRLSFGGIDLNNLPTGKVRFLER 239

Query: 239 KI---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
                LRE L      E Q               +     +   +      K+S++  G 
Sbjct: 240 SEYASLREFLDALEKAEKQKQKSEKKAPRAEGKSEFKPAKTFTKEKSKAKPKSSNEPFGT 299

Query: 296 SKQKKLAT 303
           +K K    
Sbjct: 300 NKYKPEKK 307


>gi|308801140|ref|XP_003075351.1| propable 16S pseudouridylate synthase (ISS) [Ostreococcus tauri]
 gi|116061905|emb|CAL52623.1| propable 16S pseudouridylate synthase (ISS) [Ostreococcus tauri]
          Length = 337

 Score =  140 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 58/249 (23%), Positives = 98/249 (39%), Gaps = 24/249 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEV--DGVPLRKA 70
           +RVSK++AR G  SRRE E++IA  RV+VNG ++           D +E+  DG     +
Sbjct: 84  ERVSKILARRGACSRREAEQLIADGRVRVNGTVITEQGHKCDVNSDRVEITSDGSAWLSS 143

Query: 71  ERTRLWLYHKPIGL---VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           + T L +   P  +    +             N      + +++  L   T         
Sbjct: 144 KLT-LAVNKPPGLVSNLPSADEVAACSIVEPSNAWMRSMKWVAMDDLRRATSDPSRFNVC 202

Query: 128 GGLARVLEL---------------PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           G L +                        ++ Y V     V +  +  L   +++ G+  
Sbjct: 203 GRLDKDSRGLLILTEDGALARSVIGGNGVVKRYVVTTDADVRESHMQSLNGTVMLDGVEL 262

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
             M V        +  +   LREGKNR+I++V E F  +V  L R+  G   +G L  G+
Sbjct: 263 LPMNVKRL--GRGSRTLEFNLREGKNRQIRRVCEKFGLRVVDLHRVQIGEIDIGDLPEGA 320

Query: 233 TREVSKKIL 241
            R +S+  +
Sbjct: 321 WRILSEDEV 329


>gi|121607481|ref|YP_995288.1| RNA-binding S4 domain-containing protein [Verminephrobacter
           eiseniae EF01-2]
 gi|121552121|gb|ABM56270.1| RNA-binding S4 domain protein [Verminephrobacter eiseniae EF01-2]
          Length = 305

 Score =  140 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 68/250 (27%), Positives = 103/250 (41%), Gaps = 29/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ SRRE +  IAQ RV+VNG +     + V ++D I VD        +  
Sbjct: 59  RLNKRMAELGLCSRREADDWIAQGRVRVNGQVAP-IGLRVTASDRIAVDKQARGAQRQRV 117

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---------------ISVGRLDINTE 119
             L HKP+G V+  ++   R  V         R                   GRLDI++ 
Sbjct: 118 TILLHKPMGYVSGQAEDGHRPAVALIDQRTHWRDDTSRNRFAPAQLRGLAPAGRLDIDSV 177

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHG---------QVDQDKLNLLKKGIVIQGI 170
           GLL+LT DG +AR L    +   + Y VR                 +L  L  G+ + G 
Sbjct: 178 GLLVLTQDGRVARQLIGADSTVDKEYLVRVQYGAVALDVRSVFPAGQLASLCHGLSLDGQ 237

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V     +     +   L EG+ R+I+++       V  L R+  G  +LG L A
Sbjct: 238 PLKPAVVDWQNPEQ----LRFVLTEGRKRQIRRMCALVGLTVVGLKRVRIGRVRLGLLPA 293

Query: 231 GSTREVSKKI 240
           G  R ++   
Sbjct: 294 GQWRYLAADE 303


>gi|167846297|ref|ZP_02471805.1| pseudouridine synthase family protein [Burkholderia pseudomallei
           B7210]
          Length = 334

 Score =  140 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 86  VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 145

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 146 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 205

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 206 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDG 265

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 266 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 321

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 322 QGEWRYLGPDE 332


>gi|15616893|ref|NP_240106.1| hypothetical protein BU282 [Buchnera aphidicola str. APS
           (Acyrthosiphon pisum)]
 gi|11387285|sp|P57369|RLUB_BUCAI RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|25323981|pir||H84962 hypothetical protein [imported] - Buchnera sp. (strain APS)
 gi|10038957|dbj|BAB12992.1| hypothetical protein [Buchnera aphidicola str. APS (Acyrthosiphon
           pisum)]
          Length = 250

 Score =  140 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 68/250 (27%), Positives = 114/250 (45%), Gaps = 10/250 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
            +++ K+++  G  SRR +E MI    + +NG  +      + + +   I + G  +   
Sbjct: 2   SEKIQKILSHLGYGSRRNIENMIKFGDISINGKKI-VIGQRLNNKNIEVITIKGETVSIK 60

Query: 71  ER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +       +        + T +                  R IS+GRLDINT GLLL TN
Sbjct: 61  KTDFKTKIIIYNKPEGEICTRNDYKKRPIVFDKLPLLNIHRWISIGRLDINTRGLLLFTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY--GDMQVTLDTQKG 184
           +G LA  L  PS +  R Y +R  G+++++ +N+LK G+ I+        +Q        
Sbjct: 121 NGNLANELMHPSNKIEREYYIRVFGKINKNTMNILKNGVKIKDGNAAFKSIQTIDHACSK 180

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            N W    L EG+NREI+ +++    +V+RLIRI YG   L   L  G   E+S + +  
Sbjct: 181 KNKWFKGVLCEGRNREIRSMWQAVQCQVSRLIRIRYGNIFLPKNLKLGDWSELSSESVNN 240

Query: 244 QLGPHLLEEA 253
                 L+++
Sbjct: 241 LSNLVSLKDS 250


>gi|319761272|ref|YP_004125209.1| RNA-binding s4 domain protein [Alicycliphilus denitrificans BC]
 gi|330823139|ref|YP_004386442.1| pseudouridine synthase Rsu [Alicycliphilus denitrificans K601]
 gi|317115833|gb|ADU98321.1| RNA-binding S4 domain protein [Alicycliphilus denitrificans BC]
 gi|329308511|gb|AEB82926.1| pseudouridine synthase Rsu [Alicycliphilus denitrificans K601]
          Length = 306

 Score =  139 bits (351), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 73/251 (29%), Positives = 108/251 (43%), Gaps = 29/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K +A  G+ SRRE +  IAQ  V+VNG +     + V   D IEVD     +  + 
Sbjct: 59  MRLNKRMADLGLCSRREADDWIAQGWVRVNGQVA-VMGLQVGPQDRIEVDRAAQGRQSQQ 117

Query: 74  RLWLYHKPIGLVTTHSDPDGRS---------------TVFDNLPSIFSRVISVGRLDINT 118
              L HKP+G V+  ++                    +     P+    +   GRLDI++
Sbjct: 118 VTILLHKPMGYVSGQAEDGHTPAVALVNARSHWQGDASRMRFAPAQLKGLAPCGRLDIDS 177

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG---------QVDQDKLNLLKKGIVIQG 169
            GLL+LT DG +AR L    +   + Y VR                D+L LL  G+++ G
Sbjct: 178 VGLLVLTQDGRVARQLIGEDSAVDKEYLVRVQYGERTQDVRAVFPADRLALLCHGLLLDG 237

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                 QV     +     +   LREGK R+I+++ E    KV  L RI  G   LG L 
Sbjct: 238 QPLKPAQVDWQNPEQ----LRFVLREGKKRQIRRMCELVGLKVVGLKRIRIGRVLLGNLP 293

Query: 230 AGSTREVSKKI 240
            G  R ++   
Sbjct: 294 VGQWRYLAPGE 304


>gi|330002604|ref|ZP_08304373.1| pseudouridine synthase B, ribosomal large subunit [Klebsiella sp.
           MS 92-3]
 gi|328537255|gb|EGF63515.1| pseudouridine synthase B, ribosomal large subunit [Klebsiella sp.
           MS 92-3]
          Length = 292

 Score =  139 bits (351), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 82/285 (28%), Positives = 120/285 (42%), Gaps = 12/285 (4%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVM--STDHIEVDGVPLRKAE-----RTRLWLYHK 80
           RRE+E  I   RV V+G +       V       I +DG  +   E        L  Y  
Sbjct: 9   RREIEAKIEAGRVSVDGKIAT-LGDRVEIVPGLKIRIDGHLISVKESAEQICRVLAYYKP 67

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
              L T +      +          +R I+VGRLD+NT GLLL T DG LA  L  PS +
Sbjct: 68  EGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSRE 127

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
             R Y VR  GQVD DKL  L +G+ ++        +     +G N W  V L EG+NRE
Sbjct: 128 VEREYAVRVFGQVDDDKLRQLSRGVQLEDGPAAFKTIKFTGGEGINQWYNVTLTEGRNRE 187

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILREQLGPHLLEEAQVN 256
           +++++E    +V+RLIR+ YG   L   L  G   E+       LRE +       ++V 
Sbjct: 188 VRRLWEAVGVQVSRLIRVRYGDILLPKGLPRGGYTELDLAQTNYLRELVELTPETSSKVA 247

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           ++      +     R            R   NS++++    +   
Sbjct: 248 VEKDRRRLKANQIRRAVKRHSQTSANPRQGNNSNRRSSTRNKTNG 292


>gi|325929292|ref|ZP_08190423.1| ribosomal small subunit pseudouridine synthase A [Xanthomonas
           perforans 91-118]
 gi|325929321|ref|ZP_08190452.1| ribosomal small subunit pseudouridine synthase A [Xanthomonas
           perforans 91-118]
 gi|325540314|gb|EGD11925.1| ribosomal small subunit pseudouridine synthase A [Xanthomonas
           perforans 91-118]
 gi|325540343|gb|EGD11954.1| ribosomal small subunit pseudouridine synthase A [Xanthomonas
           perforans 91-118]
          Length = 237

 Score =  139 bits (351), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 52/232 (22%), Positives = 89/232 (38%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVN--GILLERAAVNVMSTDHIEVDGVPLRKAE 71
            ++ K IA  G  SR++V ++  Q  +  +  G +L  A   V   D I +DG PL    
Sbjct: 1   MKLVKHIANLGYGSRKQVTQLFRQGAIT-DAQGEVLY-ADDQV-EHDAIRIDGEPLDPPA 57

Query: 72  RTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              L L+       +   +       +          +  VGRLD  T G+LL+T+DG L
Sbjct: 58  GLSLLLHKPSGYTCSTKDTGRLIYELLPPRFRLRAPVLAPVGRLDRETSGMLLMTDDGAL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P +   +VY +     +  ++  L   G ++       +        G      
Sbjct: 118 LHRIISPKSALDKVYDITLAEDLHGEEAALFASGSLLLDGETKPLLPAELEVLGPRQ-AR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + L EG+  +++++F      V  L R   G   L  L +G  R +    L 
Sbjct: 177 LTLHEGRYHQVRRMFAAAGNHVVALHRSRIGGLSLDGLPSGQWRALEANDLE 228


>gi|294054852|ref|YP_003548510.1| pseudouridine synthase [Coraliomargarita akajimensis DSM 45221]
 gi|293614185|gb|ADE54340.1| pseudouridine synthase [Coraliomargarita akajimensis DSM 45221]
          Length = 243

 Score =  139 bits (351), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 73/239 (30%), Positives = 112/239 (46%), Gaps = 6/239 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
                QR+ K+IA AG+ SRRE ER+I   +V+VNG + +        +D I V+  PL 
Sbjct: 2   TEVEKQRIQKLIANAGLCSRREAERLIEDGKVRVNGKIAQ-LGDKARISDDIFVNNKPLN 60

Query: 69  K---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           K      T L    K +    +    D        L     R+   GRLD ++EGLL+LT
Sbjct: 61  KHVERSVTVLMNKPKGVLCTNSDPHADRTVFDLLPLDLQRQRMFCAGRLDKDSEGLLVLT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QK 183
           NDG LA  +  P++  ++ YRV  H   D+  +  L  G+  +G      +V       +
Sbjct: 121 NDGDLAHRITHPTSNVVKRYRVVLHRDFDKADIPKLLNGVDYEGDFLKAEKVIPAPAVGE 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           G    + V L  GK REI+++FE   + V +L+R+  G   L  +  G  + + KK + 
Sbjct: 181 GHLRRLEVHLHHGKKREIRRLFEANRYYVKKLVRVQIGGMVLKNMPKGGIKVLGKKDIE 239


>gi|78048073|ref|YP_364248.1| pseudouridylate synthase [Xanthomonas campestris pv. vesicatoria
           str. 85-10]
 gi|78036503|emb|CAJ24194.1| Pseudouridylate synthase [Xanthomonas campestris pv. vesicatoria
           str. 85-10]
          Length = 547

 Score =  139 bits (351), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 86/356 (24%), Positives = 145/356 (40%), Gaps = 17/356 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG         
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKIELDGRSFVASALT 86

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + T        +          SR I++GRLDINT GLLLLT DG 
Sbjct: 87  EPSRVLIYNKPEGEVTTREDPEGRPTVFESLPVLKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLN-----LLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR      ++K+       L +G++++       ++       
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVPDAIIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + EV++  +  
Sbjct: 207 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGHSVEVAQDKVDA 266

Query: 244 QL-GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
                 L E A   L       +         +S        +   +S  +   + ++  
Sbjct: 267 LRAELKLEEGAPSALTLQPVIGQRRAAKSTVHVSRDGRSNAYVNGQTSGADEGRELRRFD 326

Query: 303 TPVHRRNLASNVWMAKGIH-----SSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                R                      +   Q+    +R P+   + +L   +  
Sbjct: 327 NLREDRGRGGRGKPGGFRGGLTVSGEAAAKQSQQRPFKQRGPAKGDRGALPDGNPA 382


>gi|124267222|ref|YP_001021226.1| putative arginine/proline rich protein [Methylibium petroleiphilum
           PM1]
 gi|124259997|gb|ABM94991.1| putative arginine/proline rich protein [Methylibium petroleiphilum
           PM1]
          Length = 421

 Score =  139 bits (351), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 63/252 (25%), Positives = 103/252 (40%), Gaps = 30/252 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---------- 64
           R+SK ++  G+ASRRE +  I Q  V+V+G ++++    V     I +D           
Sbjct: 171 RLSKRMSELGLASRREADEWIEQGYVRVDGEVVDQLGARVRPEQQITIDPQARLEQAQRV 230

Query: 65  -----VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
                 PL          +     LVT  +      +      S    ++  GRLD+++ 
Sbjct: 231 TILLHKPLGYVSGQAEDGHAPAFTLVTAANRWATDGSKQRFNASQLKHLVPAGRLDLDST 290

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQ 168
           GLL+LT DG +A++L    +   + Y VR                  + L  L+ G+ + 
Sbjct: 291 GLLVLTQDGRVAKLLIGEDSPVEKEYVVRVQWTARPELTDLKQHFPPEALARLRHGLALD 350

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           G      +V+   ++     +   LREGK R+I+++ E    KV  L RI  G   LG L
Sbjct: 351 GEKLKPAKVSWQNEQH----LRFVLREGKKRQIRRMCELVGLKVESLKRIRIGRVGLGEL 406

Query: 229 LAGSTREVSKKI 240
             G  R +    
Sbjct: 407 PPGQWRYLGPFE 418


>gi|126172676|ref|YP_001048825.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|125995881|gb|ABN59956.1| pseudouridine synthase [Shewanella baltica OS155]
          Length = 233

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 59/232 (25%), Positives = 97/232 (41%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++    R      I    V VNG +    A+ V   + + ++  PL      
Sbjct: 1   MRLDKFLCKSTDLDRDAASVAIINGSVTVNGAIATDCAMQVHENNAVCLNEKPLMPRPS- 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP   + ++ D    S            +  VGRLD +T GL+LLT+DG  +  
Sbjct: 60  RYFMLHKPADTLCSNVDGAYPSLFHLLDIEHAFDLHIVGRLDADTTGLVLLTDDGRWSFN 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKG----IVIQGICYGDMQVTLDTQKGSNAWV 189
           +  P  Q  +VYRV     +D +    +       + +QG     +  TL  Q+     V
Sbjct: 120 IISPQYQCEKVYRVTLRDPLDSEATAAIAATFAAGLQLQGETALTLPATL--QQVDEKTV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + L EGK  ++K++F     KV  L R   G   L  +  G  RE++   +
Sbjct: 178 LLTLTEGKFHQVKRMFAAVGNKVVALHRAQIGAVTL-DVDVGEWRELTLAEI 228


>gi|294664707|ref|ZP_06730039.1| Pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 10535]
 gi|292605532|gb|EFF48851.1| Pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 10535]
          Length = 544

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 86/358 (24%), Positives = 138/358 (38%), Gaps = 24/358 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG         
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKIELDGRSFVASALT 86

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        ++T        +          SR I++GRLDINT GLLLLT DG 
Sbjct: 87  EPSRVLIYNKPEGEVITREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR      ++      +  L +G++++       ++       
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV---SKKI 240
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + EV       
Sbjct: 207 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGHSVEVAQDKVDA 266

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEV----------PDDFTRMKKNSS 290
           LR +L       + + L   I                             D  R  +   
Sbjct: 267 LRAELKLEEGAPSALTLQPVIGQRRAAKSTVHVSRDGRSNAYVNGQTSGADEGRELRRFD 326

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                   +        +   +    A    S       +      RS    +  + R
Sbjct: 327 NLREDRGGRGRGKSGGFKGGLTVSGEAAAKQSQQRPFKQRGPAKGDRSLPEGNPAAFR 384


>gi|254292636|ref|YP_003058659.1| pseudouridine synthase [Hirschia baltica ATCC 49814]
 gi|254041167|gb|ACT57962.1| pseudouridine synthase [Hirschia baltica ATCC 49814]
          Length = 247

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 51/241 (21%), Positives = 99/241 (41%), Gaps = 7/241 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST----DHIEV 62
           +  N  P R+ K+++  G  +R+E++ +   QR+ +     +  +  V       + + +
Sbjct: 1   MSGNAKPVRLDKLLSNMGYGTRKEIDALARYQRILLGDKGFKSGSDKVTPNEDLQNRLTI 60

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-SVGRLDINTEGL 121
           D  P+       + L        +        + +F +       ++  +GRLD  T GL
Sbjct: 61  DDKPVDPLPGFAVMLNKPAGVTCSRKDSGTLITELFPSRWDKRDPLLSPIGRLDKETSGL 120

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLT+DG L   +  P TQ  + Y V     ++ D+ ++   G ++       +     +
Sbjct: 121 LLLTDDGQLNHRVSSPKTQTPKRYHVILDRDLNGDEDSIFAAGELMLESETKPLLPAELS 180

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
             G      + L EG+  +++++F      VN L R S G   L   L  G  R +S+  
Sbjct: 181 ALG-KREAILTLHEGRYHQVRRMFAAVGNHVNALHRESIGGLTLPEDLQQGQWRIMSETD 239

Query: 241 L 241
           +
Sbjct: 240 I 240


>gi|91786512|ref|YP_547464.1| ribosomal large subunit pseudouridine synthase F [Polaromonas sp.
           JS666]
 gi|91695737|gb|ABE42566.1| ribosomal large subunit pseudouridine synthase F [Polaromonas sp.
           JS666]
          Length = 266

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 65/251 (25%), Positives = 101/251 (40%), Gaps = 29/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R++K +A  G+ SRRE +  IA+  V VNG         V     IEVD          
Sbjct: 19  VRLNKRMAELGLCSRREADDWIARGWVLVNGAPA-VMGQPVAPDARIEVDRQAEQQQRQQ 77

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          +   + LV   +     ++     P     +   GRLDI++
Sbjct: 78  VTILINKPVGYVSGQAEDGHEPAVVLVQPQNRWRECNSRMRWGPEQLRGLAPAGRLDIDS 137

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQG 169
            GLL+LT DG +AR L   +++  + Y VR               ++KL LL+ G+ + G
Sbjct: 138 IGLLVLTQDGRVARQLIGENSEIEKEYLVRVSYGAETSNVQAVFPREKLALLRHGLSLDG 197

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                 QV     +     +   L+EGK R+I+++ E     V  L R+  G   LG L 
Sbjct: 198 QALRPAQVDWQNPEQ----LRFVLKEGKKRQIRRMCEQVGLFVTGLKRVRIGRVNLGHLP 253

Query: 230 AGSTREVSKKI 240
            G  R ++   
Sbjct: 254 VGQWRYLAAHE 264


>gi|262279508|ref|ZP_06057293.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           calcoaceticus RUH2202]
 gi|262259859|gb|EEY78592.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           calcoaceticus RUH2202]
          Length = 234

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 45/225 (20%), Positives = 88/225 (39%), Gaps = 3/225 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V V+G + +         +    + G   +  E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVSVDGEIADDLKKQFSPENLEFSLFGQTYQYREQVY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        +                 I   V ++GRLD +T GLLLLT+DG   + L
Sbjct: 63  IALKKPKGFECSHQPQHHQSVFSLLPEIMIHRGVQAIGRLDQDTTGLLLLTDDGKYLQAL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     +VY V     V  +++ +L +G+ +           +   +     +T+ + 
Sbjct: 123 THPRKHVPKVYHVTTLDPVTPEQIAMLSEGVSLHQEKGIFAATDVAMLE--THQLTMTIH 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G   ++K++      KV  L R   G   L  +  G    +S++
Sbjct: 181 QGVYHQVKRMIAAVGNKVEALHRHQVGQLVLPEIADGEWVYLSEQ 225


>gi|227542008|ref|ZP_03972057.1| pseudouridine synthase B [Corynebacterium glucuronolyticum ATCC
           51866]
 gi|227182223|gb|EEI63195.1| pseudouridine synthase B [Corynebacterium glucuronolyticum ATCC
           51866]
          Length = 225

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 68/216 (31%), Positives = 105/216 (48%), Gaps = 4/216 (1%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSD 90
           E +IAQ RV+VNG ++ R  V V      I VDGV ++  E       +KP+G+ +T  D
Sbjct: 3   EELIAQGRVEVNGEIVMRQGVRVDPDTAVIRVDGVRVKVNEDLVYIALNKPLGVQSTMKD 62

Query: 91  PDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
             GR  V D +         +  VGRLD  TEGLLLLTNDG LA  L  P     + Y  
Sbjct: 63  DMGRPCVGDIVGEKVDAGLHLFHVGRLDAKTEGLLLLTNDGELANRLMHPKYHVSKTYLA 122

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
              G+ D++ +  L++G+ ++        V +       + + V L EG+   ++++ + 
Sbjct: 123 TVLGEADRELVKKLREGVDLEDGIAKADYVQIVDTYEGRSLIRVELHEGRKHIVRRMLKE 182

Query: 208 FNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
             + V +L+R      QLG L  G+ R ++   LR 
Sbjct: 183 LGFPVQQLVRTKIHTVQLGELTPGAIRHLNDSELRA 218


>gi|325922798|ref|ZP_08184528.1| ribosomal large subunit pseudouridine synthase B [Xanthomonas
           gardneri ATCC 19865]
 gi|325546740|gb|EGD17864.1| ribosomal large subunit pseudouridine synthase B [Xanthomonas
           gardneri ATCC 19865]
          Length = 442

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 85/347 (24%), Positives = 141/347 (40%), Gaps = 14/347 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG         
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKIELDGRSFVASALT 86

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + T        +          SR I++GRLDINT GLLLLT DG 
Sbjct: 87  EPSRVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR      +D      +  L +G++++       ++       
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEDKVSDAIIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV---SKKI 240
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + EV       
Sbjct: 207 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGQSVEVAQEKVDA 266

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           LR +L       + + L   I                  + +   + + + +    ++  
Sbjct: 267 LRAELKLEEGAPSALTLQPVIGQRRAAKSTVHVSRDGRSNAYVNGQTSGADEGRELRRFD 326

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
                            KG  +     + ++ +     P  P K   
Sbjct: 327 NPRDDRGGRGRGKPGGFKGGLTVSGEAAARQSQQRPFKPRAPGKGDR 373


>gi|325694128|gb|EGD36046.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK150]
          Length = 241

 Score =  139 bits (350), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 59/233 (25%), Positives = 103/233 (44%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVER--MIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
            R+ +++A A   SR+++++  +  Q+++ V+G    + + NV +    I   G  +   
Sbjct: 1   MRLDQLLA-ANHISRKKMKQSHL--QKQILVDGKPAYKLSQNVDTGLQQITFQGKHVSGP 57

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                 L      +   H           +       + S+GRLD +TEGLLL+T++G L
Sbjct: 58  AHRYYMLNKPAGAVTANHDAEKLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V  +G +         +GI  + G      Q+++ +   S +  
Sbjct: 118 GFQLLHPQYHVEKTYYVEVNGPLTPQDKIAFHEGIRFLDGTVCQPAQLSILSTSSSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           TV + EGK  +IKK+F     KV  L RI +G F L   L  G  R ++++ L
Sbjct: 178 TVKISEGKFHQIKKMFLAVGVKVTYLKRIQFGDFTLDPDLAKGDYRALNQEEL 230


>gi|226227546|ref|YP_002761652.1| ribosomal small subunit pseudouridine synthase A [Gemmatimonas
           aurantiaca T-27]
 gi|226090737|dbj|BAH39182.1| ribosomal small subunit pseudouridine synthase A [Gemmatimonas
           aurantiaca T-27]
          Length = 245

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 60/243 (24%), Positives = 99/243 (40%), Gaps = 5/243 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVK-VNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           +S+ +AR G  SR++V+ +I Q RV   +G+ L          D + VDG PL   E   
Sbjct: 3   LSRYLARLGYGSRKQVDILIRQHRVTTRDGVALRDGEC--PPHDTLAVDGEPLDPPEGAV 60

Query: 75  LWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + L+     + +     P     +     S    + +VGRLD +T GLLLLT+DG L   
Sbjct: 61  VLLHKPLGYVCSTNDRPPIVYELLPSRFLSRSPVMATVGRLDADTSGLLLLTDDGALNHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P T   + YRV     +  D+      G ++       ++        +   V + L
Sbjct: 121 ITSPRTHVPKTYRVTLAESLHGDEAAQFASGTLMLKGEDAPLRPATLFVHDART-VDLSL 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
            EG+  +++++F      V  L RI+ G   L  L  G  R +S   +            
Sbjct: 180 VEGRYHQVRRMFAATGNHVVTLQRIALGSLTLEGLAEGEWRVLSAAEVETLRLAARRSGG 239

Query: 254 QVN 256
           +  
Sbjct: 240 EAP 242


>gi|163851700|ref|YP_001639743.1| pseudouridine synthase [Methylobacterium extorquens PA1]
 gi|163663305|gb|ABY30672.1| pseudouridine synthase [Methylobacterium extorquens PA1]
          Length = 242

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 56/233 (24%), Positives = 97/233 (41%), Gaps = 7/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV----MSTDHIEVDGVPLRKA 70
           R+ +++A  G  SRREVE +     V+++G  L  A+  V      +  + V G  L   
Sbjct: 5   RLDRLLANLGYGSRREVEGLARAGLVRLDGQALRDASQRVPLEPDLSARMTVQGEALDPL 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               L L+       +         S + +        + +VGRLD  T GLLL+T+DG 
Sbjct: 65  PGVCLMLHKPLGVTCSHKEVGPLVYSLLPERWRRRDPALSTVGRLDKETSGLLLMTDDGA 124

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +  P  +  + YRV     +  D+  +L  G ++       + + ++ +       
Sbjct: 125 LLHRIISPKAKVSKRYRVTLARPLQGDETAILASGEMMLEGEDKPL-LPVEMETDDPTHC 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           TV L EG+  +++++F      V+ L R   G   L   L AG  R +    +
Sbjct: 184 TVTLHEGRYHQVRRMFAALGNHVDALHRDRVGGLALPADLPAGEFRILGPGEI 236


>gi|91792155|ref|YP_561806.1| pseudouridine synthase, Rsu [Shewanella denitrificans OS217]
 gi|91714157|gb|ABE54083.1| Pseudouridine synthase, Rsu [Shewanella denitrificans OS217]
          Length = 233

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 58/237 (24%), Positives = 99/237 (41%), Gaps = 11/237 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   SR E  ++I  +RV VNG+ +   A  V   +HI +DG  L      
Sbjct: 1   MRLDKFVCKSTPLSRTEAVQVIHHERVLVNGVAIVDEAAQVHENNHIILDGKHLVPRPFR 60

Query: 74  RLWLYHKPIG----LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            L L+         +          S          S +  VGRLD +T GLLL T+DG 
Sbjct: 61  YLLLHKPANCLSANISEPSKSTKYPSVFDVLNIDNSSELHLVGRLDADTTGLLLATDDGR 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNA 187
            +  +  P++   +VYRV     +  +  +    GI++QG        ++ + +      
Sbjct: 121 WSFTITSPNSDCSKVYRVGLAKPLGPEVADKFLAGILLQGEHELTLPAKLEVISPNQ--- 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            V + L +GK  ++K++F     KV  L R   G   L  +  G  R +++  +   
Sbjct: 178 -VLLTLTQGKFHQVKRMFAAVGNKVVSLHREKIGAISL-DVPQGQWRALTEAEVNAM 232


>gi|332361775|gb|EGJ39579.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1056]
          Length = 241

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 60/244 (24%), Positives = 106/244 (43%), Gaps = 11/244 (4%)

Query: 14  QRVSKVIARAGIASRREVER--MIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
            R+ +++A A   SR+++++  +  Q+++ V+G    + + NV +    I   G  +   
Sbjct: 1   MRLDQLLA-ANHISRKKMKQSHL--QKQILVDGKPAYKLSQNVDTGLQQITFQGKHVSGP 57

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                 L      +               +       + S+GRLD +TEGLLL+T++G L
Sbjct: 58  AHRYYMLNKPSGAVTANRDAEKLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V  +G +        ++GI  + G      Q+++ +   S +  
Sbjct: 118 GFQLLHPQYHVEKTYYVEVNGPLTSQDKIAFQEGIRFLDGTICQPAQLSILSSSSSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL---REQL 245
           TV + EGK  +IKK+F     KV  L RI +G F L   L  G  R ++++ L   +E L
Sbjct: 178 TVKISEGKFHQIKKMFLAVGVKVIYLKRIQFGNFTLDPDLAKGDCRPLNQEELEIIKESL 237

Query: 246 GPHL 249
               
Sbjct: 238 EKSW 241


>gi|256372131|ref|YP_003109955.1| pseudouridine synthase [Acidimicrobium ferrooxidans DSM 10331]
 gi|256008715|gb|ACU54282.1| pseudouridine synthase [Acidimicrobium ferrooxidans DSM 10331]
          Length = 254

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 77/233 (33%), Positives = 115/233 (49%), Gaps = 7/233 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           +    +V  ++ARAG  SRR +E  I   RV++NG +       V    D +E DG+ + 
Sbjct: 2   SAESVKVHVLLARAGCGSRRVLEDAIRDGRVRINGEVAT-IGARVRPGVDRVEFDGLEIA 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             E+   WL +KP G+V++  DP+GR TV   L +  SRV  VGRLD+++EGLL+LTNDG
Sbjct: 61  TEEQREYWLLNKPRGVVSSVVDPEGRPTVRS-LVATTSRVYPVGRLDVDSEGLLILTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P     + Y V     V +     L++G+ + G       V           
Sbjct: 120 PLTYQLTHPRFHVPKEYLVWVDRPVPRRLGRELREGVEVDGELLRASSV----GTVGPRL 175

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + L EG+NR+I+++       V RL+R+  GP     L  G  R +  + L
Sbjct: 176 VRIVLTEGRNRQIRRMVGAVGLSVERLVRVRIGPLVDPHLPPGVARRLEPREL 228


>gi|167619584|ref|ZP_02388215.1| pseudouridine synthase family protein [Burkholderia thailandensis
           Bt4]
          Length = 364

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 116 VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAEQAAQ 175

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 176 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWGGDRSPLRFSPQHLRALAPAGRLDIDS 235

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 236 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTTDIERHFPAESLAKLRHGLELDG 295

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 296 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 351

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 352 QGQWRYLGPDE 362


>gi|28199352|ref|NP_779666.1| pseudouridylate synthase [Xylella fastidiosa Temecula1]
 gi|182682078|ref|YP_001830238.1| RNA-binding S4 domain-containing protein [Xylella fastidiosa M23]
 gi|34098468|sp|Q87BI2|RLUB_XYLFT RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|28057458|gb|AAO29315.1| pseudouridylate synthase [Xylella fastidiosa Temecula1]
 gi|182632188|gb|ACB92964.1| RNA-binding S4 domain protein [Xylella fastidiosa M23]
          Length = 476

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 82/351 (23%), Positives = 142/351 (40%), Gaps = 12/351 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ KV+A+AG+ SRR +E+ I+   +KVNG + +   ++V S D IE+DG         
Sbjct: 27  ERLHKVLAQAGLGSRRALEQRISNGLIKVNGDIAQ-LGMSVKSGDKIELDGRSFVASALT 85

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + T        +          +R I++GRLDINT GLLLLT DG 
Sbjct: 86  EPARVLIYNKPEGEVTTREDPEGRPTVFETLPVLKGARWIAIGRLDINTTGLLLLTTDGE 145

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLN-----LLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS++  R Y VR      ++ +       L +G++++        +       
Sbjct: 146 LANAMMHPSSEIEREYVVRVRSPEGEEHVQDELLEQLTRGVMLEDGTAKFDTIERIGNTD 205

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + E+ K  +  
Sbjct: 206 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGSVLLPRELLRGQSTELPKTQVEA 265

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                 LE+                  +  +     D+      N+      S++ +   
Sbjct: 266 LRTQLKLEKDMPLALTLQPVIGQRRSAKATLHVNRNDNNKHAYHNNHSTADESRELRRFD 325

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK-RSLRRTSAK 353
            +                 +   ++  ++ +       P   RSL   S  
Sbjct: 326 TLRDDRGRGQGKHHFKDRLTVSGEAAAKQAHKPFKQYKPKNDRSLSEGSPA 376


>gi|254425390|ref|ZP_05039108.1| conserved hypothetical protein [Synechococcus sp. PCC 7335]
 gi|196192879|gb|EDX87843.1| conserved hypothetical protein [Synechococcus sp. PCC 7335]
          Length = 223

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 74/212 (34%), Positives = 108/212 (50%), Gaps = 4/212 (1%)

Query: 34  MIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           MI   RV VNG + E      +S D I VDGV +    +   +L HKP G+V+T  DP  
Sbjct: 1   MILSGRVTVNGEVAELGQRADVSHDQICVDGVEIGGPPQAAYFLLHKPRGVVSTCHDPRQ 60

Query: 94  RSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
           R TV D L         +  VGRLD ++ G L+LTNDG    +L  P  Q  +VY+V+  
Sbjct: 61  RKTVLDLLDSAFQRREGIHPVGRLDADSTGALILTNDGDFTYLLTHPRHQMSKVYQVKVR 120

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFN 209
           G   QD L   ++G++I G      +V+L     ++   + + L+EG+NR+I++V E   
Sbjct: 121 GIPSQDTLRQWREGVIIDGRKTLPARVSLLKSHSADGTLLQIDLKEGRNRQIRRVAEMLG 180

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             V  L R   G   LG L  G  R +++K +
Sbjct: 181 HPVTALHRTKIGSLSLGNLACGRYRSLTEKEI 212


>gi|297539905|ref|YP_003675674.1| RNA-binding S4 domain-containing protein [Methylotenera sp. 301]
 gi|297259252|gb|ADI31097.1| RNA-binding S4 domain protein [Methylotenera sp. 301]
          Length = 412

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 65/251 (25%), Positives = 100/251 (39%), Gaps = 24/251 (9%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------ 63
           +    R+SKV+A  GI SRRE +  I    V V+G++++     +     I +       
Sbjct: 164 STELPRLSKVMAERGICSRREADEWIMNSWVMVDGVIIDTLGTRINPDAEIVISSYAHEV 223

Query: 64  ---------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI----- 109
                      P+          Y   I LV   ++      +       F R       
Sbjct: 224 QAETVTIILHKPVGYVSGQAEDGYQPAIVLVHPDNEWLDDPELNQLHEREFQRRYLNGLA 283

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
             GRLDI++ G+L+LT DG +AR L    +   + Y VR  G +D D L  L  G+ + G
Sbjct: 284 PAGRLDIDSTGMLVLTQDGRVARHLIGEDSTVEKEYLVRVEGSLDDDGLKRLNHGLSLDG 343

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                 +V+   +      +   LREGK R+I+++ E     V  L R+  G   LG L 
Sbjct: 344 EKLKPAKVSWQNEDQ----LRFVLREGKKRQIRRMCEMVGLHVVGLKRVRIGSVNLGKLP 399

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 400 VGQWRYLRNGE 410


>gi|167816387|ref|ZP_02448067.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 91]
          Length = 351

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 103 VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 162

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 163 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 222

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 223 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDG 282

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 283 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 338

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 339 QGEWRYLGPDE 349


>gi|289665491|ref|ZP_06487072.1| ribosomal small subunit pseudouridylate synthase [Xanthomonas
           campestris pv. vasculorum NCPPB702]
 gi|289668330|ref|ZP_06489405.1| ribosomal small subunit pseudouridylate synthase [Xanthomonas
           campestris pv. musacearum NCPPB4381]
          Length = 237

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 54/232 (23%), Positives = 91/232 (39%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVN--GILLERAAVNVMSTDHIEVDGVPLRKAE 71
            ++ K IA  G  SR++V ++  Q  V  +  G ++  A   V   D I +DG PL    
Sbjct: 1   MKLVKHIANLGYGSRKQVTQLFRQGAVT-DAQGEVVY-ADDQV-EHDAIRIDGEPLDPPP 57

Query: 72  RTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              L L+       +   +       +     S    +  VGRLD +T G+LL+T+DG L
Sbjct: 58  GFSLLLHKPSGYTCSTKDTGRLIYELLPPRFRSRAPVLAPVGRLDRDTSGMLLMTDDGAL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P +   +VY +     +  D+  L   G ++       +        G      
Sbjct: 118 LHRIISPKSALDKVYDITLAEDLRGDEAALFASGTLLLEGETKPLLPAELEVLGLR-EAR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + L EG+  +++++F      V  L R   G   L  L +G  R +    L 
Sbjct: 177 LTLHEGRYHQVRRMFAAAGNHVVALHRSRIGGLLLDGLPSGQWRALEASDLE 228


>gi|283953680|ref|ZP_06371211.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 414]
 gi|283794721|gb|EFC33459.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 414]
          Length = 253

 Score =  139 bits (350), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 72/250 (28%), Positives = 117/250 (46%), Gaps = 20/250 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K ++     SRRE + +I Q  VK+N  +    +  V   D I + G  ++K  + 
Sbjct: 1   MRINKFVSHNTRYSRREADELIKQGLVKINNKIA-LLSDEVKFDDKIFIKGKRVQKKTQF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +YHK  G + +  D  GR T++D LP  FS  +SVGRLD  +EGLLLLT+   +A  
Sbjct: 60  SVIIYHKQKGEIVSKKDDRGRKTIYDTLPKQFSTWLSVGRLDYASEGLLLLTDSPVIADA 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--------------YGDMQVTL 179
           L        R Y ++  G V +  +  ++ G+ I+                    +   +
Sbjct: 120 LMHSD--LEREYYLKVKGIVTKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIGFEI 177

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               G    + V + EGKNRE+++ F  F+ +V  L R+++G   LG L  G  R +   
Sbjct: 178 FGSSGGYTKLRVIINEGKNRELRRFFGHFDVEVMDLKRVAFGVLDLGMLKPGKHRYLENG 237

Query: 240 I---LREQLG 246
               LR+ L 
Sbjct: 238 EYEKLRDFLK 247


>gi|255319548|ref|ZP_05360762.1| RNA pseudouridine synthase [Acinetobacter radioresistens SK82]
 gi|262378431|ref|ZP_06071588.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter radioresistens
           SH164]
 gi|255303488|gb|EET82691.1| RNA pseudouridine synthase [Acinetobacter radioresistens SK82]
 gi|262299716|gb|EEY87628.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter radioresistens
           SH164]
          Length = 235

 Score =  139 bits (350), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 43/229 (18%), Positives = 93/229 (40%), Gaps = 6/229 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    + +N  +           +   EV G      E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKSGAISINHEICADTKAKFDLKNFTFEVHGEEFEYREKVY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        +  +          +   +   +  VGRLD +T GLLLLT+DG   + L
Sbjct: 63  IALNKPQGYECSHQAQYHFSVFDLFDPALLNRGIQCVGRLDQDTTGLLLLTDDGQFLQAL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGL 193
             P     +VY +     +  +++ LL++G+ +     +    +    ++ S+  +++ +
Sbjct: 123 THPRKHVAKVYDLITVDPITPEQIRLLEQGVELRNDGIFKASNI----KQTSSHQLSLAI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G   ++K++      KV +L R   G  +L  L  G    + +  + 
Sbjct: 179 HQGVYHQVKRMLAAVGNKVEKLHRSKIGELELPMLAEGEWTYLDQTEIE 227


>gi|325478230|gb|EGC81349.1| putative 16S pseudouridylate 516 synthase [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 232

 Score =  139 bits (349), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 50/232 (21%), Positives = 102/232 (43%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+I  +G+ +R+ ++R   +  + VNG +++ ++  V    D +   G  +   E 
Sbjct: 1   MRLDKMIGNSGLDTRKNIKRNAKKGAILVNGEVIKDSSYQVDPEVDEVYYMGQFVDYFEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +       ++   D D       +       +   GRLD +T GLLLL+ DG    
Sbjct: 61  IYIMMNKPQG-YLSATEDKDPTVIDLLDDFYRVLDLSIAGRLDKDTTGLLLLSTDGKFIH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVT 190
            +  P++   + Y  +    +D+  ++L K+G+ I          ++ +  +  +     
Sbjct: 120 RVTSPNSNIEKTYIAKTRDPIDESLIDLFKEGVYIKEDDYTARSAKLEIIGKNEA----K 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           V + EGK   +K++F     +V  L R++ G  +L + L  G  RE+S   +
Sbjct: 176 VTVTEGKFHLVKRLFSNSGNEVVDLKRVAIGDLKLDSHLGLGEYRELSDDEV 227


>gi|307720120|ref|YP_003891260.1| RNA-binding S4 domain-containing protein [Sulfurimonas autotrophica
           DSM 16294]
 gi|306978213|gb|ADN08248.1| RNA-binding S4 domain protein [Sulfurimonas autotrophica DSM 16294]
          Length = 267

 Score =  139 bits (349), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 74/268 (27%), Positives = 123/268 (45%), Gaps = 17/268 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R++K IA     SRRE ++ +    V+VN  +    A  V    D + + G  +   E+
Sbjct: 2   MRLNKYIAHYSTYSRREADKAVQDGYVRVNSEIETNPATQVQEGVDIVYISGKQVSPQEK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +Y+KP G + T +DP GR T++D+L   F   I VGRLD  +EGLLLLT+   +A 
Sbjct: 62  YTVIVYNKPKGELVTKNDPKGRKTIYDSLSKEFRHFIPVGRLDFASEGLLLLTDASHVAT 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--------------DMQVT 178
            L        R+Y+++  G+V  D  + +  GI +     G               +   
Sbjct: 122 SLMESD--LERIYKLKIKGEVTPDMEDAMLNGIYLDDASAGAHSHSKITSMDIKPFIGYK 179

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +   + + + + V L+EGKNRE+++ F  F  +V  L R+S+   +L  L  G TR +S+
Sbjct: 180 IQKNQPNYSILKVALKEGKNRELRRFFAHFGAEVADLKRVSFAEIELNNLPTGKTRYLSR 239

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSET 266
                       E+ +   +      E 
Sbjct: 240 SEYSALYKFLKEEKKRARDNKRKEDKEQ 267


>gi|222109684|ref|YP_002551948.1| RNA-binding s4 domain-containing protein [Acidovorax ebreus TPSY]
 gi|221729128|gb|ACM31948.1| RNA-binding S4 domain protein [Acidovorax ebreus TPSY]
          Length = 248

 Score =  139 bits (349), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 72/251 (28%), Positives = 103/251 (41%), Gaps = 29/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K +A   + SRRE +  IAQ  V+VNG +     + V   D I+VD        + 
Sbjct: 1   MRLNKRMADLRLCSRREADDWIAQGWVRVNGQVAA-MGLQVGPHDRIDVDRAAQGHQRQQ 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---------------ISVGRLDINT 118
              L HKP+G V+  ++      V    P    +                   GRLDI++
Sbjct: 60  VTILLHKPMGYVSGQAEDGHTPAVALINPRTHWKDDESRTRFAPAQLKGLAPCGRLDIDS 119

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG---------QVDQDKLNLLKKGIVIQG 169
            GLL+LT DG +AR L    +   + Y VR                DKL LL  G+ + G
Sbjct: 120 VGLLVLTQDGRVARQLIGEDSTVDKEYLVRVQYGDRAQDVRAVFPADKLALLNHGLALDG 179

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                  V     +     +   LREGK R+I+++ E    KV  L RI  G   LG L 
Sbjct: 180 QQLKPALVEWQNPEQ----LRFVLREGKKRQIRRMCELVGLKVVGLKRIRIGQVLLGKLP 235

Query: 230 AGSTREVSKKI 240
            G  R ++   
Sbjct: 236 PGQWRYLAPGE 246


>gi|325915913|ref|ZP_08178209.1| ribosomal small subunit pseudouridine synthase A [Xanthomonas
           vesicatoria ATCC 35937]
 gi|325537880|gb|EGD09580.1| ribosomal small subunit pseudouridine synthase A [Xanthomonas
           vesicatoria ATCC 35937]
          Length = 237

 Score =  139 bits (349), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 91/231 (39%), Gaps = 5/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVK-VNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            ++ K IA  G  SR++V ++  Q  V  V G +L  A   V   D I +DG PL     
Sbjct: 1   MKLVKHIANLGYGSRKQVTQLFRQGAVTDVQGEVLY-ADDQV-EHDAIRIDGEPLDPPPG 58

Query: 73  TRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             L L+       +   +       +     S    +  VGRLD +T G+LL+T+DG L 
Sbjct: 59  FSLLLHKPSGYTCSTKDTGRLIYELLPPRFRSRAPVLAPVGRLDRDTSGMLLMTDDGALL 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P +   +VY V     +  D+  L   G ++       +        G      +
Sbjct: 119 HRIISPKSALDKVYEVSLAEDLRGDEAALFASGTLLLEGETKPLLPAELEVLGPRQ-ARL 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            L EG+  +++++F      V  L R   G   L  L AG  R +    L 
Sbjct: 178 TLHEGRYHQVRRMFAAAGNHVAALHRSRIGGLSLDALPAGQWRALDASDLE 228


>gi|163787355|ref|ZP_02181802.1| pseudouridylate synthase (ribosomal large subunit pseudouridine
           synthase B) [Flavobacteriales bacterium ALC-1]
 gi|159877243|gb|EDP71300.1| pseudouridylate synthase (ribosomal large subunit pseudouridine
           synthase B) [Flavobacteriales bacterium ALC-1]
          Length = 279

 Score =  139 bits (349), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 54/232 (23%), Positives = 108/232 (46%), Gaps = 2/232 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N    R++K +A +G+ SRRE +  IA   V VNG ++      V  TD +  DG  +  
Sbjct: 44  NPDEIRLNKYVANSGMCSRREADENIAIGLVSVNGKVVTEMGYKVKRTDEVRFDGQRITP 103

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E     L +KP G  TT ++  GR+ +     +  + V  +GRL  N+ GLLL TND  
Sbjct: 104 -EAKVYVLLNKPKGFATTTAEGKGRTVMDLVANATNANVKPIGRLGRNSLGLLLFTNDDK 162

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           + +          R+++V     +  + L  +K+G  ++G     ++     +  S   +
Sbjct: 163 IVQKFTNSKNGVARLFQVELDKNLKYEDLKKIKEGFKVEGKLI-TVEDISYIEGESKNKI 221

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + ++   N  ++ +F+ FN+ + ++  ++ G      +  G  + ++++ +
Sbjct: 222 GLKIKNTGNTILRTIFDNFNYDIVKIDCVAIGHLTKKDIPRGHWKHLTEQEV 273


>gi|325915975|ref|ZP_08178268.1| ribosomal large subunit pseudouridine synthase B [Xanthomonas
           vesicatoria ATCC 35937]
 gi|325537785|gb|EGD09488.1| ribosomal large subunit pseudouridine synthase B [Xanthomonas
           vesicatoria ATCC 35937]
          Length = 545

 Score =  139 bits (349), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 85/355 (23%), Positives = 143/355 (40%), Gaps = 16/355 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG         
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKIELDGRSFVASALT 86

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + T        +          SR I++GRLDINT GLLLLT DG 
Sbjct: 87  EPSRVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR      ++      +  L +G++++       ++       
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + EV++  +  
Sbjct: 207 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGQSIEVAQDKVDA 266

Query: 244 QL-GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
                 L E A   L       +         +S        +   +S  +   + ++  
Sbjct: 267 LRAELKLEEGAPSALTLQPVIGQRRAAKSTVHVSRDGRSNAYVNGQTSGADEGRELRRFD 326

Query: 303 TPVHRRNLASNVWMAKGIH----SSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                R                 S   +    ++   ++       RSL   +  
Sbjct: 327 NLREDRGRGGRGKPGGFKGGLTVSGEAAAKQSQQRPFKQRGPAKGDRSLPDGNPA 381


>gi|332366092|gb|EGJ43848.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1059]
          Length = 241

 Score =  139 bits (349), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 103/231 (44%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+ +++ + Q+++ V+G    + + NV +    I   G  +     
Sbjct: 1   MRLEQLLA-ANHISRKNMKQSLLQKQILVDGKPAYKLSQNVDTGLQQITFQGKHVSGPAH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +               +       + S+GRLD +TEGLLL+T++G L  
Sbjct: 60  RYYMLNKPAGAVTANRDAEKLTVLDLLDKEVEKENLYSIGRLDRDTEGLLLITDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V  +G +   K    ++GI  + G      Q+++ +   S +  TV
Sbjct: 120 QLLHPQYHVEKTYYVEVNGPLTSQKKISFQEGIRFLDGTVCQPAQLSILSTSSSLSRTTV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  +IKK+F     KV  L RI +G F L   L  G  R ++K+ L
Sbjct: 180 RISEGKFHQIKKMFLAVGVKVTYLKRIQFGDFTLDPDLAKGDYRALNKEEL 230


>gi|300087878|ref|YP_003758400.1| pseudouridine synthase [Dehalogenimonas lykanthroporepellens
           BL-DC-9]
 gi|299527611|gb|ADJ26079.1| pseudouridine synthase [Dehalogenimonas lykanthroporepellens
           BL-DC-9]
          Length = 266

 Score =  139 bits (349), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 73/261 (27%), Positives = 111/261 (42%), Gaps = 6/261 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR- 74
           + K +  AG  SRRE+   +   RV VNG   E  +  +   D I +D  P+  AE  R 
Sbjct: 8   LLKALRDAGCGSRRELAEAVKAGRVAVNGTTAESFSAAITPADVITLDSRPVVTAESARV 67

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L +KP+G++TT  DP GR TV D LP      R+  VGRLD NT GL++LTNDG L  
Sbjct: 68  YLLLNKPLGVITTTEDPQGRPTVIDLLPPDWQQKRLFPVGRLDENTTGLIILTNDGELTN 127

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V     ++ +    +K G + +        +  +     +     +
Sbjct: 128 RLTHPRYGVEKEYLVGIDRSLNSEDFEKIKSGGLELDDGPASPAR--ISPVNAAPFNYRI 185

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+ R ++++F     +V  L RI  G  +LG L  G+ R+++   LR         
Sbjct: 186 SIHEGRKRIVRRLFAALGHQVRVLRRIRVGSLELGNLKEGNWRQLTPLELRRLEAVPRRP 245

Query: 252 EAQVNLDAPIYSSETLVRDRP 272
                                
Sbjct: 246 GRAGGRYQSASGDRPRNPRSR 266


>gi|288575064|ref|ZP_06393421.1| pseudouridine synthase [Dethiosulfovibrio peptidovorans DSM 11002]
 gi|288570805|gb|EFC92362.1| pseudouridine synthase [Dethiosulfovibrio peptidovorans DSM 11002]
          Length = 238

 Score =  139 bits (349), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 61/220 (27%), Positives = 101/220 (45%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +A  G+ASRR  E +I   RVKV  +     A+++   D + VDG  +   +  
Sbjct: 1   MRLNRYLALCGVASRRRSEDIIRTGRVKVENVTATDPAMDISEEDQVSVDGKSVCFQKSV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +      +               +      R+  VGRLD  +EGLL+LTNDG     
Sbjct: 61  YIVMNKPKGYVCAVEDRFYPTVVGLLSPDLRAKRIYPVGRLDRQSEGLLVLTNDGDFCNS 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  PS  + + Y V     + ++ L   +KG+ I G     + + +  +K +  WV++ L
Sbjct: 121 LIHPSAGYQKTYEVLLGEALTEENLFSWRKGVPINGKVVSPVSIRVMDRKPARRWVSIVL 180

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
           +EG  REI+ +   F+  VN L R   G  +L  L +G  
Sbjct: 181 QEGLKREIRIMASHFSLSVNVLFRRKVGRMELRKLKSGEY 220


>gi|121592905|ref|YP_984801.1| RNA-binding S4 domain-containing protein [Acidovorax sp. JS42]
 gi|120604985|gb|ABM40725.1| RNA-binding S4 domain protein [Acidovorax sp. JS42]
          Length = 360

 Score =  139 bits (349), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 73/251 (29%), Positives = 104/251 (41%), Gaps = 29/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K +A  G+ SRRE +  IAQ  V+VNG +     + V   D I+VD        + 
Sbjct: 113 MRLNKRMADLGLCSRREADDWIAQGWVRVNGQVAA-MGLQVGPHDRIDVDRAAQGHQRQQ 171

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---------------ISVGRLDINT 118
              L HKP+G V+  ++      V    P    +                   GRLDI++
Sbjct: 172 VTILLHKPMGYVSGQAEDGHTPAVALINPRTHWKDDESRTRFSPAQLKGLAPCGRLDIDS 231

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG---------QVDQDKLNLLKKGIVIQG 169
            GLL+LT DG +AR L    +   + Y VR                DKL LL  G+ + G
Sbjct: 232 VGLLVLTQDGRVARQLIGEDSTVDKEYLVRVQYGDRAQDVRAVFPADKLALLNHGLALDG 291

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                  V     +     +   LREGK R+I+++ E    KV  L RI  G   LG L 
Sbjct: 292 QQLKPAVVEWQNPEQ----LRFVLREGKKRQIRRMCELVGLKVVGLKRIRIGQVLLGKLP 347

Query: 230 AGSTREVSKKI 240
            G  R ++   
Sbjct: 348 PGQWRYLAPGE 358


>gi|325921245|ref|ZP_08183105.1| ribosomal small subunit pseudouridine synthase A [Xanthomonas
           gardneri ATCC 19865]
 gi|325548212|gb|EGD19206.1| ribosomal small subunit pseudouridine synthase A [Xanthomonas
           gardneri ATCC 19865]
          Length = 237

 Score =  139 bits (349), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 90/231 (38%), Gaps = 5/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVK-VNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            ++ K IA  G  SR++V ++  Q  V  V G +L  A   V   D I +DG PL     
Sbjct: 1   MKLVKHIANLGYGSRKQVTQLFRQGAVTDVQGEVLY-ADDQV-EHDAIRIDGEPLDPPSG 58

Query: 73  TRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             L L+       +   +       +     S    +  VGRLD  T G+LL+T+DG L 
Sbjct: 59  FSLLLHKPSGYTCSTKDTGRLIYELLPLRFRSRAPVLAPVGRLDRETSGMLLMTDDGALL 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P +   +VY V     +  D+  L   G ++       +        G      +
Sbjct: 119 HRIISPKSALDKVYDVTLAEDLRGDEAALFSSGTLLLEGETKPLLPAELDVLGPR-EARL 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            L EG+  +++++F      V  L R   G   L  L +G  R +    L 
Sbjct: 178 TLHEGRYHQVRRMFAAAGNHVVALHRSRIGGLSLEGLPSGQWRTLEAPDLE 228


>gi|282855434|ref|ZP_06264755.1| ribosomal large subunit pseudouridine synthase B [Pyramidobacter
           piscolens W5455]
 gi|282586730|gb|EFB91977.1| ribosomal large subunit pseudouridine synthase B [Pyramidobacter
           piscolens W5455]
          Length = 238

 Score =  139 bits (349), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 101/234 (43%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K +A  G+ SRR+VE  I   RV   G  +     +V   + + VD V +R   + 
Sbjct: 1   MRLNKYLALCGVGSRRKVEEFIFAGRVVCGGYQVTEPGYDVPDGEIVTVDDVEVRPERKI 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+     +                    + R+  VGRLD+ +EGLL+LTNDG  ++ 
Sbjct: 61  YMVLHKPRGYICAVSDRNYPVILDLLPREYDYYRLFPVGRLDLQSEGLLMLTNDGDFSQE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V      ++ ++  L+ G V +G     + V    ++    W+   L
Sbjct: 121 MIHPRAGITKEYEVLLDRMPNEREMRQLRDGTVFEGKRLHPVGVDFLQREPEGRWLRFVL 180

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            EG  REI+ + E    KV  L R   G  +L  L +G  RE S   LR  +  
Sbjct: 181 NEGVKREIRLIAEGAGLKVQVLFRRRIGRMELRHLKSGCAREYSADQLRRMIRH 234


>gi|294625442|ref|ZP_06704073.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 11122]
 gi|292600265|gb|EFF44371.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 11122]
          Length = 552

 Score =  139 bits (349), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 85/356 (23%), Positives = 144/356 (40%), Gaps = 17/356 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG         
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKIELDGRSFVASALT 86

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + T        +          SR I++GRLDINT GLLLLT DG 
Sbjct: 87  EPSRVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR      ++      +  L +G++++       ++       
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + EV++  +  
Sbjct: 207 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGHSVEVAQDKVDA 266

Query: 244 QL-GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
                 L E A   L       +         +S        +   +S  +   + ++  
Sbjct: 267 LRAELKLEEGAPSALTLQPVIGQRRAAKSTVHVSRDGRSNAYVNGQTSGADEGRELRRFD 326

Query: 303 TPVHRRNLASNVWMAKGIH-----SSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                R                      +   Q+    +R P+   + +L   +  
Sbjct: 327 NLREDRGRGGRGKPGGFKGGLTVSGEAAARQSQQRPFKQRGPAKGDRGALPDGNPA 382


>gi|226939001|ref|YP_002794072.1| RsuA [Laribacter hongkongensis HLHK9]
 gi|226713925|gb|ACO73063.1| RsuA [Laribacter hongkongensis HLHK9]
          Length = 231

 Score =  139 bits (349), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 48/229 (20%), Positives = 83/229 (36%), Gaps = 3/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            ++ +++ R G +SR+    +I Q RV V G + +   + V        VD       E 
Sbjct: 1   MQLERLLHREGWSSRKGCRILINQGRVCVAGEVADDPGLEVEPEGLAYSVDDEAAIAREH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L        +                     V  VGRLD +T GLLLL++DG    
Sbjct: 61  LYLILNKPLDLECSRKPTVRTGVLTLFPPRYSERGVQPVGRLDADTSGLLLLSDDGQFIH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y       V+ + L  L  G+V+       +      +      + + 
Sbjct: 121 RITSPKHLVPKTYVATCARPVEPEHLRQLLAGVVLNDDPAPVV--ARSARTLDEHTLELV 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EG+  +++++        + L R   G   L  L  G  RE++   L
Sbjct: 179 VTEGRYHQVRRMIAAVGNHCDALHRSRIGELVLDGLAPGQWRELTAAEL 227


>gi|218296286|ref|ZP_03497042.1| pseudouridine synthase [Thermus aquaticus Y51MC23]
 gi|218243358|gb|EED09888.1| pseudouridine synthase [Thermus aquaticus Y51MC23]
          Length = 245

 Score =  138 bits (348), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 62/235 (26%), Positives = 104/235 (44%), Gaps = 6/235 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +R+ K++AR G+ SR+EV R+I   +V+V G ++     +V     +EV+G PL    
Sbjct: 11  RGERLDKLLARLGLGSRKEVGRLIRSGKVRVGGGVVLDPGFHVPEGAALEVEGRPLAVRR 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L L+     + +    P   + +             VGRLD +TEGLLL T DG L 
Sbjct: 71  HLHLLLHKPAGYVTSRKEGPSVYALLEGFPTRDL---SPVGRLDKDTEGLLLFTTDGELL 127

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P  +  + Y V          +   ++GI++ G      +           WV +
Sbjct: 128 HRLTHPRHKVEKRYLVHLLHPATAADVRAFQEGILLSGEKTLPAR---LHLGEDPTWVEL 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            L EG+  ++K++F+    +V  L R++ GP  L  L  G+ R ++ +  R    
Sbjct: 185 TLLEGRFHQVKRMFQARGNQVLYLKRLALGPLTLEDLPLGAARPLTPEEERALYQ 239


>gi|73748599|ref|YP_307838.1| RsuA family pseudouridine synthase [Dehalococcoides sp. CBDB1]
 gi|147669359|ref|YP_001214177.1| ribosomal large subunit pseudouridine synthase B [Dehalococcoides
           sp. BAV1]
 gi|289432625|ref|YP_003462498.1| pseudouridine synthase [Dehalococcoides sp. GT]
 gi|73660315|emb|CAI82922.1| pseudouridine synthase, RsuA family [Dehalococcoides sp. CBDB1]
 gi|146270307|gb|ABQ17299.1| ribosomal large subunit pseudouridine synthase B [Dehalococcoides
           sp. BAV1]
 gi|288946345|gb|ADC74042.1| pseudouridine synthase [Dehalococcoides sp. GT]
          Length = 249

 Score =  138 bits (348), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 66/230 (28%), Positives = 107/230 (46%), Gaps = 5/230 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERTR 74
           + KV+  A + SRR++   I Q  V +NG   E  +  V +  D +  +G  +  +   R
Sbjct: 11  LVKVLVEARLGSRRKMAEAIKQGLVTLNGQKAESYSQPVNTQKDKVTFEGKLVVLSRVRR 70

Query: 75  -LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
              + +KP  +V+T SD  GR TV D L   +       VGRLD  T GL+LLTNDG + 
Sbjct: 71  IYLMLNKPPEIVSTTSDELGRKTVMDLLHRRYEGAGLFPVGRLDEATTGLILLTNDGEMT 130

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  PS +  + Y +     + Q     L+KGI++        +++  T +       +
Sbjct: 131 NRLTHPSYEIEKEYLISIDAALTQADKESLEKGILLDDGLTSPARLSRVTDEPPYN-YKL 189

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + EGK R ++++F      +  L R      +LG L  G TRE++   +
Sbjct: 190 IIHEGKKRIVRRMFARLGHPIKALKRSRIATLRLGKLEEGKTRELTPGEI 239


>gi|167919518|ref|ZP_02506609.1| pseudouridine synthase family protein [Burkholderia pseudomallei
           BCC215]
          Length = 361

 Score =  138 bits (348), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 113 VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 172

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 173 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 232

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 233 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDG 292

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 293 VPLKPAMVSWQNGEQ----LCFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 348

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 349 QGEWRYLGPDE 359


>gi|229048259|ref|ZP_04193827.1| RNA pseudouridine synthase [Bacillus cereus AH676]
 gi|228722984|gb|EEL74361.1| RNA pseudouridine synthase [Bacillus cereus AH676]
          Length = 203

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 52/202 (25%), Positives = 92/202 (45%), Gaps = 8/202 (3%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
           +NG +       V   D + +DG  + K E+      +HKP+G+  T +D    + +   
Sbjct: 3   INGEICTH-GALVSDGDRVTIDGQVIVKEEKEKVYIAFHKPVGITCTAADHIEDNIIDYI 61

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
             +   R+  VGRLD  +EGL+LLTNDGG+A  +     +  + Y V          ++ 
Sbjct: 62  --NYPERIFPVGRLDKASEGLILLTNDGGIANQILHGDHEHEKEYVVTVDKPFTDWFIDE 119

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           + +G+ I+       +VT        +   + L +G NR+I+++   F + V +L R+  
Sbjct: 120 MSRGVKIKDGMTKPCKVTRV----DQSTFRIVLTQGMNRQIRRMSRAFGFTVIKLKRVRI 175

Query: 221 GPFQLGTLLAGSTREVSKKILR 242
              +L  L  G  R V+ + L 
Sbjct: 176 MNIELNELEVGKWRSVTAEELE 197


>gi|21231653|ref|NP_637570.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|34098581|sp|Q8P8M6|RLUB_XANCP RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|21113349|gb|AAM41494.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
          Length = 492

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 87/359 (24%), Positives = 146/359 (40%), Gaps = 25/359 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG     +  T
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKIELDGRSFVASALT 86

Query: 74  ----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + T        +          SR I++GRLDINT GLLLLT DG 
Sbjct: 87  ESSRVLVYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR      ++      +  L +G++++       ++       
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVPDSMIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV---SKKI 240
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + E+       
Sbjct: 207 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGKVSLPRELLRGQSVELAQEKVDA 266

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRP-----------NIISEVPDDFTRMKKNS 289
           LR +L       + + L   I                      N  +   D+   +++  
Sbjct: 267 LRAELKLEEGAPSALTLQPVIGQRRAAKSTVHVSRDGRSNAYVNGQTSGADEGRELRRFD 326

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           + +     +     P   +   +    A    S       +      RS    +  + R
Sbjct: 327 NLREDRGGRGGRGKPGGFKGGLTVSGEAAAKQSQQRPFKQRGPAKGDRSLPDGNPAAFR 385


>gi|228993274|ref|ZP_04153190.1| RNA pseudouridine synthase [Bacillus pseudomycoides DSM 12442]
 gi|228766342|gb|EEM14985.1| RNA pseudouridine synthase [Bacillus pseudomycoides DSM 12442]
          Length = 203

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 53/206 (25%), Positives = 97/206 (47%), Gaps = 8/206 (3%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
           +NG + +     V   D + +DG  + K  +      +HKP+G+  T +D    + +   
Sbjct: 3   INGEVCKH-GTIVTENDIVMIDGKTIEKEDKEKIYIAFHKPVGITCTAADHIDGNIIEYI 61

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
             +   R+  VGRLD  +EGL+LLTNDG +A  +     +  + Y V          ++ 
Sbjct: 62  --NHPERIFPVGRLDKASEGLILLTNDGRIANQILHGDYEHEKEYIVTVDKPFTDWFIDG 119

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           + +G+ I+       +VT      +++   + L +G NR+I+++   F + V +L R+  
Sbjct: 120 MSRGVKIKDGITKQCKVTRV----NSSTFRIILTQGMNRQIRRMSRAFGYTVTKLKRVRI 175

Query: 221 GPFQLGTLLAGSTREVSKKILREQLG 246
              +L  L AG  R V+ + L+E L 
Sbjct: 176 MNIKLDGLEAGEWRNVTVQELQELLK 201


>gi|91787681|ref|YP_548633.1| ribosomal small subunit pseudouridine synthase A [Polaromonas sp.
           JS666]
 gi|91696906|gb|ABE43735.1| ribosomal small subunit pseudouridine synthase A [Polaromonas sp.
           JS666]
          Length = 239

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 92/236 (38%), Gaps = 10/236 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN-VMSTDHIEVDGVPLRKAER 72
            ++  ++   G  +RR    +I Q  V V GI     A+  V       V GV     E+
Sbjct: 1   MQLQDILFSQGFGTRRVCAGLIQQGFVAVAGIPCTEPAMEFVAEDLRFTVQGVAWEYHEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDG------RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
             L L+       +              S +        + V +VGRLD +T GLLLL++
Sbjct: 61  AYLMLHKPAGYECSQKPSTYPSIYTLLPSPIRQRGGGAAAGVQAVGRLDQDTTGLLLLSD 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG     +  P     +VY V     VD  ++  L  G+V+       ++     +K   
Sbjct: 121 DGKFIHRMSSPRHHVPKVYEVTAKHAVDDRQVQKLLAGVVLDDDP-KPVR-AAACEKTGE 178

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
             +++ L EGK  ++K++      +V  L R   G   L   L  G  R ++ + L
Sbjct: 179 LQLSLTLTEGKYHQVKRMIAAVGNRVEDLHRSQLGGLMLPEDLKPGQWRWLTAQDL 234


>gi|167570375|ref|ZP_02363249.1| pseudouridine synthase family protein [Burkholderia oklahomensis
           C6786]
          Length = 414

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 166 VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 225

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y   + LVT  +   G  +     P     +   GRLDI++
Sbjct: 226 VTILLHKPVGYVSGQAEDGYAPAVTLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 285

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 286 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERMADIDQHFPAESLAKLRHGLELDG 345

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                  V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 346 APLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 401

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 402 QGEWRYLGPDE 412


>gi|157963031|ref|YP_001503065.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157848031|gb|ABV88530.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 239

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 53/240 (22%), Positives = 96/240 (40%), Gaps = 12/240 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I ++   +R+     I +  V VNG ++      V  ++ +   G  L      
Sbjct: 1   MRLDKFICKSTELNRKHASDCIERAEVSVNGEVITDVRFQVHESNEVRYKGQRLVARPSR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+      ++++ D D  S            +  VGRLD +T GL+LLT+DG  +  
Sbjct: 61  YIMLHKPI-HTLSSNVDGDYPSLFRCIDIDRVEDLHIVGRLDADTTGLVLLTDDGRWSFD 119

Query: 134 LELPSTQWLRVYRVRFHGQV----DQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNA 187
           +  P  Q  + YRV     +      D +   + G+ +Q         ++ +     +  
Sbjct: 120 IIRPDKQCAKTYRVMLRDPIAGDVAADVIARFEAGLQLQNEQALTLPAKLEIV----APR 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V + + EGK  ++K++F     +V  L R   G   L  L  G  R +S   ++    P
Sbjct: 176 EVLLTITEGKYHQVKRMFAAVGNRVIGLHREQIGDLSL-DLKVGEWRYLSDTEVKRLSTP 234


>gi|78049355|ref|YP_365530.1| ribosomal small subunit pseudouridylate synthase [Xanthomonas
           campestris pv. vesicatoria str. 85-10]
 gi|78037785|emb|CAJ25530.1| ribosomal small subunit pseudouridylate synthase [Xanthomonas
           campestris pv. vesicatoria str. 85-10]
          Length = 237

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 52/232 (22%), Positives = 89/232 (38%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVN--GILLERAAVNVMSTDHIEVDGVPLRKAE 71
            ++ K IA  G  SR++V ++  Q  +  +  G +L  A   V   D I +DG PL    
Sbjct: 1   MKLVKHIANLGYGSRKQVTQLFRQGAIT-DAQGEVLY-ADDQV-EHDAIRIDGEPLDPPA 57

Query: 72  RTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              L L+       +   +       +          +  VGRLD  T G+LL+T+DG L
Sbjct: 58  GLSLLLHKPSGYTCSTKDTGRLIYELLPPRFRLRAPVLAPVGRLDRETSGMLLMTDDGAL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P +   +VY +     +  ++  L   G ++       +        G      
Sbjct: 118 LHRIISPKSALDKVYDITLAEDLRGEEAALFASGSLLLDGETKPLLPAELEVLGPRQ-AR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + L EG+  +++++F      V  L R   G   L  L +G  R +    L 
Sbjct: 177 LTLHEGRYHQVRRMFAAAGNHVVALHRSRIGGLSLDGLSSGQWRALEANDLE 228


>gi|86142065|ref|ZP_01060589.1| putative ribosomal large subunit pseudouridine synthase
           [Leeuwenhoekiella blandensis MED217]
 gi|85831628|gb|EAQ50084.1| putative ribosomal large subunit pseudouridine synthase
           [Leeuwenhoekiella blandensis MED217]
          Length = 284

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 62/235 (26%), Positives = 103/235 (43%), Gaps = 2/235 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++K IA +GI SRRE +  I+  +V VNG ++      V   D +  DG  +   E 
Sbjct: 52  GIRLNKYIANSGICSRREADLYISTGQVTVNGEIINEMGFKVNLDDDVRFDGRRINP-EA 110

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G   T S+  G + +     S  SR+  VGRL  N  GLLL TND  + +
Sbjct: 111 KAYVLLNKPKGFSVTTSNAKGMTVMDLVASSTKSRIQPVGRLGRNATGLLLFTNDDKVMK 170

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L    T   R++ +     +  + L+ +KKG+ + G     ++            V + 
Sbjct: 171 KLTNSKTGLPRLFHIELDKNLKAEDLDKIKKGLTVDGKRLE-IEDLSYVDGAPKKEVGLK 229

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           +R   N  I+ +FE   ++V R+  +  G      L  G  R + ++ +   +  
Sbjct: 230 MRNVGNSIIRSIFEHLGYQVVRVDCVILGTLTKKDLPRGKYRHLKEQEIHNLMML 284


>gi|15839044|ref|NP_299732.1| hypothetical protein XF2453 [Xylella fastidiosa 9a5c]
 gi|34098741|sp|Q9PAP2|RLUB_XYLFA RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|9107649|gb|AAF85252.1|AE004054_4 conserved hypothetical protein [Xylella fastidiosa 9a5c]
          Length = 476

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 82/351 (23%), Positives = 142/351 (40%), Gaps = 12/351 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ KV+A+AG+ SRR +E+ I+   +KVNG + +   ++V S D IE+DG         
Sbjct: 27  ERLHKVLAQAGLGSRRALEQRISNGLIKVNGDIAQ-LGMSVKSGDKIELDGRSFVASALT 85

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + T        +          +R I++GRLDINT GLLLLT DG 
Sbjct: 86  EPARVLIYNKPEGEVTTREDPEGRPTVFETLPVLKGARWIAIGRLDINTTGLLLLTTDGE 145

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLN-----LLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS++  R Y VR      ++ +       L +G++++        +       
Sbjct: 146 LANAMMHPSSEIEREYVVRVRSPEGEEHVQDELLEQLTRGVMLEDGTAKFDTIERIGNTD 205

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + E+ K  +  
Sbjct: 206 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGSVLLPRELLRGQSTELPKTQVEA 265

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                 LE+                  +  +     D+      N+      S++ +   
Sbjct: 266 LRTQLKLEKDMPLALTLQPIIGQRRSAKATLHVNRNDNNKHAYHNNHSTADESRELRRFD 325

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK-RSLRRTSAK 353
            +                 +   ++  ++ +       P   RSL   S  
Sbjct: 326 TLRDDRGRGQGKHHFKDRLTVSGEAAAKQAHKPFKQYKPKNDRSLSEGSPA 376


>gi|21243053|ref|NP_642635.1| pseudouridylate synthase [Xanthomonas axonopodis pv. citri str.
           306]
 gi|34098587|sp|Q8PK58|RLUB_XANAC RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|21108565|gb|AAM37171.1| pseudouridylate synthase [Xanthomonas axonopodis pv. citri str.
           306]
          Length = 550

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 85/356 (23%), Positives = 144/356 (40%), Gaps = 17/356 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG         
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKIELDGRSFVASALT 86

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + T        +          SR I++GRLDINT GLLLLT DG 
Sbjct: 87  EPSRVLIYNKPEGEVTTREDPEGRPTVFESLPVLKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR      ++      +  L +G++++       ++       
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + EV++  +  
Sbjct: 207 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGHSVEVAQDKVDA 266

Query: 244 QL-GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
                 L E A   L       +         +S        +   +S  +   + ++  
Sbjct: 267 LRAELKLEEGAPSALTLQPVIGQRRAAKSTVHVSRDGRSNAYVNGQTSGADEGRELRRFD 326

Query: 303 TPVHRRNLASNVWMAKGIH-----SSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                R                      +   Q+    +R P+   + +L   +  
Sbjct: 327 NLREDRGRGGRGKPGGFKGGLTVSGEAAARQSQQRPFKQRGPAKGDRGALPDGNPA 382


>gi|296876964|ref|ZP_06901008.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           parasanguinis ATCC 15912]
 gi|296431999|gb|EFH17802.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           parasanguinis ATCC 15912]
          Length = 241

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 51/231 (22%), Positives = 105/231 (45%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A    A R+++++++A++++ V+ +  ++ + N+      I++    +++   
Sbjct: 1   MRLDQLMADHQYA-RKDIKQLLARRQILVDHLPAQKLSQNIDPGLQQIQIGERIIQEPRH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +               +    +  +  +GRLD +T GLLL+T++G L  
Sbjct: 60  HYYMLHKPIGAVTAKRDAHHPTVIDLVDPQQEYPDLYPLGRLDRDTSGLLLITDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY V  +G +    +   + GI            +T+     S +   V
Sbjct: 120 QLLHPQYHVEKVYEVEVNGPLYAAHIEQFQNGISFTDGPICKPASLTILESTPSYSKAQV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++KK+F     KV  L R+S+GPF L   L  G +R +++  L
Sbjct: 180 RISEGKYHQVKKMFLAIGVKVMTLKRLSFGPFTLDPQLAPGESRPLNEVEL 230


>gi|262375390|ref|ZP_06068623.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter lwoffii SH145]
 gi|262309644|gb|EEY90774.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter lwoffii SH145]
          Length = 235

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 92/229 (40%), Gaps = 3/229 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V +   +++     +       EV G      E+  
Sbjct: 3   LEKMLQSQGFGSRKHCQQLIKNGAVSIQDEVIDNPKHKLDLNHLNFEVYGKSQTYREKVY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        +  +          +   +   +  VGRLD +T GLLLLT+DG   + L
Sbjct: 63  IALNKPQGYECSHQATHHFSVFDLFDDILLNRGIQCVGRLDHDTTGLLLLTDDGQFLQAL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     +VY+++    V  +++  L++G+ ++          +     +   + + + 
Sbjct: 123 THPKKHVAKVYQMQTADPVTDEQIQQLEQGVELRNEKGIFAATEVARLAENR--LQMTIH 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           +G   ++K++      KV +L R   G   L  L  G    ++ + + +
Sbjct: 181 QGVYHQVKRMLAAVGNKVEQLHRAQIGALALPELAEGEWLYLNAEQVAQ 229


>gi|226943478|ref|YP_002798551.1| Pseudouridine synthase, Rsu A [Azotobacter vinelandii DJ]
 gi|226718405|gb|ACO77576.1| Pseudouridine synthase, Rsu A [Azotobacter vinelandii DJ]
          Length = 230

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 103/232 (44%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +      +RR    ++A  RV+V+G ++      +     IEVDG  L+     
Sbjct: 1   MRLDRFLGNLPDFNRRNSRLLLASGRVRVDGQVVRDGCSEIREFSRIEVDGRILQPGRAA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ HKP G+V+       R+ +          +   GRLD+ T GLLLLTNDG  +R 
Sbjct: 61  LYFMLHKPAGVVSATRHERHRTVLDLLDEPDRQGLHLAGRLDLGTTGLLLLTNDGHWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  +VY V     + ++ +    +      + +      + L      +    +
Sbjct: 121 ITHPRYKLAKVYYVETAEPIGEEYIETFARGLYFAFEDLVTQPAHLELL----GSHSARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            L EG+  ++K++F +F   V RL R S GP +L   L  G  R ++ + ++
Sbjct: 177 TLFEGRYHQVKRMFGYFRNPVLRLHRESMGPLRLESELPPGHYRPLTSEEIQ 228


>gi|154147941|ref|YP_001407262.1| RNA pseudouridine synthase [Campylobacter hominis ATCC BAA-381]
 gi|153803950|gb|ABS50957.1| hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           (RNA pseudouridylate synthase) [Campylobacter hominis
           ATCC BAA-381]
          Length = 253

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 64/247 (25%), Positives = 117/247 (47%), Gaps = 17/247 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+     SRRE + +I   +V VNG ++    + +  +D I ++   ++  +  
Sbjct: 1   MRLNKFISHNTGYSRREADELIKNGKVSVNGRIISD-FIEINESDKIRINKHLIKLKKDF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +Y+KP G + +  D  GR T++D+LP  FS+ +S+GRLD  +EGLLLLT+   +A  
Sbjct: 60  TMIIYNKPKGELVSKKDDRGRKTIYDSLPKGFSKFVSIGRLDYASEGLLLLTDAPAIATA 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQVTL 179
           L   + +     +V+    +  +    +K G   +                    +   +
Sbjct: 120 LMQSNIEREYYLKVKGE--ITDEIKTAMKDGFFAKDATKGAHPKTEIKSMNFAPFVAFDI 177

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               G    + V ++EG+NRE+++ F +F+ +V  L R+S+G   LG L     R  +  
Sbjct: 178 FGSSGGYTKLRVLIKEGQNRELRRFFGYFDLEVMDLKRVSFGIIDLGMLKESKWRYFTNS 237

Query: 240 ILREQLG 246
              E  G
Sbjct: 238 EYEELRG 244


>gi|330898470|gb|EGH29889.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. japonica str.
           M301072PT]
          Length = 230

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 104/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R++V   +A  RV+V+G         V     + +D   L+  +  
Sbjct: 1   MRLDRFLSNLPRFNRQQVRLALASGRVQVDGQATRDPHHEVREFSCVALDEEILQAGKVP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V+  SD    + +          +   GRLD NT GL+L+TNDG  +R 
Sbjct: 61  RYFMLHKPEGCVSATSDAQHPTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+       +      + +     Q+TL   + +     +
Sbjct: 121 LTQPQTKMPKVYYVETEQPIDERYAIKFAEGLYFAFENLTTQPAQLTLLGPQSA----RL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F  F+ KV RL R + G   L   L  GS R ++   +
Sbjct: 177 SIVEGRYHQVKRMFGHFDNKVLRLHRETIGALALDPGLRPGSYRALNAGEI 227


>gi|319785914|ref|YP_004145389.1| pseudouridine synthase [Pseudoxanthomonas suwonensis 11-1]
 gi|317464426|gb|ADV26158.1| pseudouridine synthase [Pseudoxanthomonas suwonensis 11-1]
          Length = 236

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 56/233 (24%), Positives = 91/233 (39%), Gaps = 9/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVK-VNGILLERAAVNVMS--TDHIEVDGVPLRKA 70
            ++ K +A  G  SR+EV  M  + RV   +G +L            D++ VDG PL   
Sbjct: 1   MKLVKHLANLGYGSRKEVAWMFREGRVTDADGEVL----YQDDPLDHDNVRVDGEPLDPP 56

Query: 71  ERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   L L+       +           +          + +VGRLD  T GLLL+T+DG 
Sbjct: 57  QGLLLMLHKPAGYTCSTKDKGRIVYDLLPPRFRLRDPVLSTVGRLDRETTGLLLMTDDGQ 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +  P ++  +VY       +  D+  L   G ++       +        G     
Sbjct: 117 LLHRIVSPKSKLAKVYEADLAEDLRGDEAQLFASGTLMLESETTPLLPAQMEVLGPRR-A 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V L EG+  +++++F      V  L R   G   LG L  G  R++ +  L 
Sbjct: 176 RVVLHEGRYHQVRRMFAAVGNNVVALHRPRIGGLALGDLAEGQWRQLGQDDLD 228


>gi|121606483|ref|YP_983812.1| pseudouridine synthase [Polaromonas naphthalenivorans CJ2]
 gi|120595452|gb|ABM38891.1| pseudouridine synthase [Polaromonas naphthalenivorans CJ2]
          Length = 278

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 63/252 (25%), Positives = 99/252 (39%), Gaps = 29/252 (11%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------- 63
             R++K +A  G+ SRRE +  IA+  V+VNG+        V +   IEV          
Sbjct: 30  TVRLNKRMADLGLCSRREADDWIARGWVRVNGLPA-VMGQPVAANARIEVAREAEQQQRQ 88

Query: 64  ------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
                   P+          +   + LV   +     ++           +   GRLDI+
Sbjct: 89  QVTILINKPVGYVSGQAEDGHEPAVALVQPENRWRECNSRMRWGFEQLRGLAPAGRLDID 148

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQ 168
           + GLL+LT DG +AR L    +   + Y VR     +          +KL LL  G+ + 
Sbjct: 149 SIGLLVLTQDGRVARQLIGEDSDMEKEYLVRVSYGAENVNVQAAFPREKLALLCHGLSLD 208

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           G      QV+    +     +   L+EGK R+I+++ E     V  L R+  G   LG L
Sbjct: 209 GQLLRPAQVSWQNPEQ----LRFVLKEGKKRQIRRMCEQVGLFVTGLKRVRIGRVNLGHL 264

Query: 229 LAGSTREVSKKI 240
             G  R +    
Sbjct: 265 PIGQWRYLMPHE 276


>gi|71276226|ref|ZP_00652505.1| Pseudouridine synthase, Rsu [Xylella fastidiosa Dixon]
 gi|170730719|ref|YP_001776152.1| pseudouridylate synthase [Xylella fastidiosa M12]
 gi|71162987|gb|EAO12710.1| Pseudouridine synthase, Rsu [Xylella fastidiosa Dixon]
 gi|167965512|gb|ACA12522.1| pseudouridylate synthase [Xylella fastidiosa M12]
          Length = 476

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 81/351 (23%), Positives = 142/351 (40%), Gaps = 12/351 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ KV+A+AG+ SRR +E+ I+   +KVNG + +   ++V S D IE+DG         
Sbjct: 27  ERLHKVLAQAGLGSRRALEQRISNGLIKVNGDIAQ-LGMSVKSGDKIELDGRSFVASALT 85

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + T        +          +R I++GRLDINT GLLLLT DG 
Sbjct: 86  EPARVLIYNKPEGEVTTREDPEGRPTVFETLPVLKGARWIAIGRLDINTTGLLLLTTDGE 145

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLN-----LLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS++  R Y VR      ++ +       L +G++++        +       
Sbjct: 146 LANAMMHPSSEIEREYVVRVRSPEGEEHVQDELLEQLTRGVMLEDGTAKFDTIERIGNTD 205

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           S+ W  + ++EG+NRE+++++E    +V+RL R  YG   L   LL G + E+ K  +  
Sbjct: 206 SHDWFRIVVKEGRNREVRRLWESQGCQVSRLKRTRYGSVLLPRELLRGQSTELPKTQVEA 265

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                 LE+                  +  +     D+      N+      S++ +   
Sbjct: 266 LRTQLKLEKDMPLALTLQPVIGQRRSAKATLHVNRNDNNKHAYHNNHSTADESRELRRFD 325

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK-RSLRRTSAK 353
            +                 +   ++  ++ +       P   RSL   S  
Sbjct: 326 TLRDDRGHGQGKHHFKDRLTVSGEAAAKQAHKPFKQYKPKNDRSLSEGSPA 376


>gi|71898735|ref|ZP_00680904.1| Pseudouridine synthase, Rsu [Xylella fastidiosa Ann-1]
 gi|71731500|gb|EAO33562.1| Pseudouridine synthase, Rsu [Xylella fastidiosa Ann-1]
          Length = 476

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 81/351 (23%), Positives = 142/351 (40%), Gaps = 12/351 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ KV+A+AG+ SRR +E+ I+   +KVNG + +   ++V S D IE+DG         
Sbjct: 27  ERLHKVLAQAGLGSRRALEQRISNGLIKVNGDIAQ-LGMSVKSGDKIELDGRSFVASALT 85

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + T        +          +R I++GRLDINT GLLLLT DG 
Sbjct: 86  EPARVLIYNKPEGEVTTREDPEGRPTVFETLPVLKGARWIAIGRLDINTTGLLLLTTDGE 145

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLN-----LLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS++  R Y VR      ++ +       L +G++++        +       
Sbjct: 146 LANAMMHPSSEIEREYVVRVRSPEGEEHVQDELLEQLTRGVMLEDGTAKFDTIERIGNTD 205

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           S+ W  + ++EG+NRE+++++E    +V+RL R  YG   L   LL G + E+ K  +  
Sbjct: 206 SHDWFRIVVKEGRNREVRRLWESQGCQVSRLKRTRYGSVLLPRELLRGQSTELPKTQVEA 265

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                 LE+                  +  +     D+      N+      S++ +   
Sbjct: 266 LRTQLKLEKDMPLALTLQPVIGQRRSAKATLHVNRNDNNKHAYHNNHSTADESRELRRFD 325

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK-RSLRRTSAK 353
            +                 +   ++  ++ +       P   RSL   S  
Sbjct: 326 TLRDDRGHGQGKHHFKDRLTVSGEAAAKQAHKPFKQYKPKNDRSLSEGSPA 376


>gi|257867046|ref|ZP_05646699.1| pseudouridine synthase [Enterococcus casseliflavus EC30]
 gi|257873381|ref|ZP_05653034.1| pseudouridine synthase [Enterococcus casseliflavus EC10]
 gi|257877124|ref|ZP_05656777.1| pseudouridine synthase [Enterococcus casseliflavus EC20]
 gi|257801102|gb|EEV30032.1| pseudouridine synthase [Enterococcus casseliflavus EC30]
 gi|257807545|gb|EEV36367.1| pseudouridine synthase [Enterococcus casseliflavus EC10]
 gi|257811290|gb|EEV40110.1| pseudouridine synthase [Enterococcus casseliflavus EC20]
          Length = 238

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 103/232 (44%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ KVI +    SR+E++R+  Q +V V+  +  R   NV S    I V G  L   ER
Sbjct: 1   MRLDKVIEQQLNTSRKEMKRLFQQGKVLVDQRIEGRPERNVDSAIHQIIVAGRQLETQER 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +                       + +VGRLD +TEGL+L+T +G L  
Sbjct: 61  -YYIVNKPNGVVTANVDQQHQTVIDLIAPKDQHPDLYAVGRLDRDTEGLVLVTTNGQLGY 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            L  P+ +  + Y V  +  V  + +     GI   G        +T+   + + ++V++
Sbjct: 120 DLLHPTKKVTKRYEVVVNDLVTPEDVAAFATGITFHGGVTCKPAALTIIDARAARSFVSL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
            + EGK  ++KK+F     KV +L R + G   L   L  GS R ++++ L+
Sbjct: 180 EIAEGKFHQVKKMFLARGKKVIQLKRTAMGSLVLPDDLAVGSYRSLTQEELK 231


>gi|301094302|ref|XP_002896257.1| RNA pseudouridine synthase, putative [Phytophthora infestans T30-4]
 gi|262109652|gb|EEY67704.1| RNA pseudouridine synthase, putative [Phytophthora infestans T30-4]
          Length = 238

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 94/235 (40%), Positives = 137/235 (58%), Gaps = 3/235 (1%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTRLWLYHKP 81
           +G+ SRRE E+ I    V VNG ++   A  V    D + VDG  L K ++T++W+ +K 
Sbjct: 2   SGLCSRREAEKRIQSFDVTVNGHVVADVATKVDAEKDVVAVDGRVLSKTQKTKVWMAYKM 61

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
            G + T+SDP  R+T+FD L  +     ++ VGRLD NTEGLLL TNDG  AR LE P T
Sbjct: 62  KGELVTNSDPQDRATIFDRLRVMGLTQHMMPVGRLDFNTEGLLLFTNDGDYARELEHPKT 121

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
              RVYR    G V + KL  LK+G ++ G+ Y  ++VT+ +    ++W+ V + EGKNR
Sbjct: 122 GVSRVYRALVRGNVAESKLEELKRGPLVDGVKYRPIKVTVQSTDKKDSWLQVKVAEGKNR 181

Query: 200 EIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           E++K        V +LIR+ YGP++L  L +G+  EV  K L ++      E+ Q
Sbjct: 182 EVRKALAHVRLVVKQLIRVQYGPYRLADLPSGAVLEVRPKSLEKKQYRKRDEDEQ 236


>gi|152981396|ref|YP_001353640.1| ribosomal small subunit pseudouridine synthase A protein
           [Janthinobacterium sp. Marseille]
 gi|151281473|gb|ABR89883.1| ribosomal small subunit pseudouridine synthase A protein
           [Janthinobacterium sp. Marseille]
          Length = 238

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 39/229 (17%), Positives = 79/229 (34%), Gaps = 5/229 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + +++   G  +R+    +I    V +NG  +        ++D    +     R  +   
Sbjct: 6   LDRILQSQGFGTRKYCRNLIEDGEVSINGESVTDYRAAFDTSDLEFTIFDEVWRYRQHVY 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        +                  +  +  VGRLD +T G+LL+++DG      
Sbjct: 66  IVLNKPANFECSRKPSHHPGVLTLLPEQFTWRELQPVGRLDHDTTGMLLMSDDGPFIHAQ 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     +VY    H  V  + +  L  G+ +          T      +   + + L 
Sbjct: 126 SSPKRHIPKVYVATTHDPVTPELIAQLLGGVQLHDEPAPLAAQTCRMLGAN--ELEIVLE 183

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKIL 241
           +GK  ++K++        + L R++ G   L    L  G    ++   L
Sbjct: 184 QGKYHQVKRMLAAAGNHCSALRRVAIGALTLESLELDEGEWAYLTDAQL 232


>gi|240138865|ref|YP_002963340.1| 16S rRNA pseudouridylate 516 synthase [Methylobacterium extorquens
           AM1]
 gi|240008837|gb|ACS40063.1| 16S rRNA pseudouridylate 516 synthase [Methylobacterium extorquens
           AM1]
          Length = 242

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 55/233 (23%), Positives = 97/233 (41%), Gaps = 7/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV----MSTDHIEVDGVPLRKA 70
           R+ +++A  G  SRREVE +     V+++G  L  A+  +      +  + V G  L   
Sbjct: 5   RLDRLLANLGYGSRREVEGLARAGLVRLDGQALRDASQRIPLEPDLSARMTVQGEALDPL 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               L L+       +         S + +        + +VGRLD  T GLLL+T+DG 
Sbjct: 65  PGVCLMLHKPLGVTCSHKEVGPLVYSLLPERWRRRDPALSTVGRLDKETSGLLLMTDDGA 124

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +  P  +  + YRV     +  D+  +L  G ++       + + ++ +       
Sbjct: 125 LLHRIISPKAKVSKRYRVTLARPLQGDETAILASGEMMLEGEDKPL-LPVEMETDDPTHC 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           TV L EG+  +++++F      V+ L R   G   L   L AG  R +    +
Sbjct: 184 TVTLHEGRYHQVRRMFAALGNHVDALHRDRVGGLALPADLPAGEFRILGPGEI 236


>gi|260222138|emb|CBA31404.1| hypothetical protein Csp_F37360 [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 282

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 67/285 (23%), Positives = 103/285 (36%), Gaps = 63/285 (22%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R++K +A  G+ASRRE +  IA+  VKVNG +     + V+    IE+D          
Sbjct: 1   MRLNKRMADLGMASRREADEWIAKGWVKVNGKVA-EMGMQVLPDVRIEIDKQAQGQQANQ 59

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  PL          +   I L+   +     +  F    S    ++  GRLDI++
Sbjct: 60  VTILLNKPLGIVSGQAEDGHEPAIKLIQPQNRWRDDNARFFFHGSQLKSLVPAGRLDIDS 119

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-------------------------- 152
            GLL+LT DG +AR L    +   + Y VR                              
Sbjct: 120 TGLLVLTQDGRVARQLIGEDSVMEKEYLVRVAYTGVENPGAANSPAATYPALAGRGKPQQ 179

Query: 153 -----------------VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
                               +KL LL+ G+++        +V     +     +   L E
Sbjct: 180 LIRLDDDDPVTSDVQSVFPPEKLQLLRHGLILDDQRLKPAKVEWQNPEQ----LRFVLTE 235

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           GK R+I+++ E    KV  L R+  G   LG L  G  R +    
Sbjct: 236 GKKRQIRRMCELVGLKVVGLKRVRVGKVMLGNLPVGQWRYLLPHE 280


>gi|289677892|ref|ZP_06498782.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. syringae FF5]
          Length = 230

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 104/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R++V   +A  RV+V+G         V     + +D   L+  +  
Sbjct: 1   MRLDRFLSNLPRFNRQQVRLALASGRVQVDGQATRDPHHEVREFSCVALDEEILQAGKVP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V+  SD    + +          +   GRLD NT GL+L+TNDG  +R 
Sbjct: 61  RYFMLHKPEGCVSATSDAQHPTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+       +      + +     Q+TL   + +     +
Sbjct: 121 LTQPQTKMPKVYYVETEQPIDERYAAKFAEGLYFAFENLTTQPAQLTLLGPQSA----RL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F  F+ KV RL R + G   L   L  GS R ++   +
Sbjct: 177 SIVEGRYHQVKRMFGHFDNKVLRLHRETIGALALDPGLRPGSYRALNAGEI 227


>gi|257066980|ref|YP_003153236.1| pseudouridine synthase [Anaerococcus prevotii DSM 20548]
 gi|256798860|gb|ACV29515.1| pseudouridine synthase [Anaerococcus prevotii DSM 20548]
          Length = 232

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 57/230 (24%), Positives = 102/230 (44%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+I  +G+ +R+ +++   +  + VNG +++  A  V    D +   G  +   E 
Sbjct: 1   MRLDKMIGNSGLDTRKNIKKNAKKGAILVNGEVVKDTATQVDPEVDEVYYMGHFVDYFEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +       ++   D D       +       +   GRLD +T GLLLL+ DG    
Sbjct: 61  IYVMMNKPAG-FLSATEDKDPTVIDLLDDFYKVIDLSIAGRLDKDTTGLLLLSTDGKFIH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P++   + Y V    ++D+  ++L K+G+ I+   Y      L+  +   A V V 
Sbjct: 120 KVTSPNSNIEKTYLVECRDKIDESLIDLFKEGVYIKEDDYTARSAKLEILEEKKAIVKVT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
             EGK   +K++F     KV +L RI+ G   L   L  G  RE+S   +
Sbjct: 180 --EGKFHLVKRLFSNCCNKVEKLKRIAIGDLSLDEHLAEGEYRELSDDEI 227


>gi|58580326|ref|YP_199342.1| ribosomal small subunit pseudouridylate synthase [Xanthomonas
           oryzae pv. oryzae KACC10331]
 gi|166713553|ref|ZP_02244760.1| ribosomal small subunit pseudouridylate synthase [Xanthomonas
           oryzae pv. oryzicola BLS256]
 gi|188578738|ref|YP_001915667.1| ribosomal small subunit pseudouridylate synthase [Xanthomonas
           oryzae pv. oryzae PXO99A]
 gi|58424920|gb|AAW73957.1| ribosomal small subunit pseudouridylate synthase [Xanthomonas
           oryzae pv. oryzae KACC10331]
 gi|188523190|gb|ACD61135.1| ribosomal small subunit pseudouridylate synthase [Xanthomonas
           oryzae pv. oryzae PXO99A]
          Length = 237

 Score =  138 bits (347), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 55/232 (23%), Positives = 90/232 (38%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVN--GILLERAAVNVMSTDHIEVDGVPLRKAE 71
            ++ K IA  G  SR++V ++  Q  V  +  G +L  A   V   D I +DG PL    
Sbjct: 1   MKLVKHIANLGYGSRKQVTQLFRQGAVT-DAQGEVLY-ADDQV-EHDAIRIDGEPLDPPP 57

Query: 72  RTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              L L+       +   +       +     S    +  VGRLD  T G+LL+T+DG L
Sbjct: 58  GFSLLLHKPGGYTCSTKDTGRLIYELLPPRFRSRAPVLAPVGRLDRETSGMLLMTDDGAL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P +   +VY +     +  D+  L   G ++       +        G      
Sbjct: 118 LHRIISPKSALDKVYDITLAEDLRGDEAALFASGSLLLEGETKPLLPAELEVLGPR-EAR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + L EG+  +++++F      V  L R   G   L  L +G  R +    L 
Sbjct: 177 LTLHEGRYHQVRRMFAAAGNHVVALHRSRIGGLSLDGLPSGQWRALEASDLE 228


>gi|168025695|ref|XP_001765369.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162683422|gb|EDQ69832.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 560

 Score =  138 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 67/253 (26%), Positives = 112/253 (44%), Gaps = 18/253 (7%)

Query: 4   KNIVQEN--FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHI 60
           +    E      +R+SKV+A AG+ASRR  E +I   RVKVNG +       V    D I
Sbjct: 230 RRFYNETYRAECERLSKVLAAAGVASRRGSEDIIFAGRVKVNGKVCTVPQTPVNPLKDTI 289

Query: 61  EVDGVPLRKAERTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----------- 108
            +DG  L K    +  +  +KP G + + +    +  +                      
Sbjct: 290 FLDGRSLPKKPPPKFYFALNKPKGYICSSAKDAPKPALSLLEDYWKIWDKKNPGVSRPRL 349

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            +VGRLD+ T GLLL+TNDG  A+ +  PS+   + Y      +V + +L L+  G  +Q
Sbjct: 350 FTVGRLDVATSGLLLITNDGDFAQRVSHPSSGLTKEYIATVTERVTKRQLQLIAGGTKVQ 409

Query: 169 GICYGDMQVTLDTQKG--SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
            +     +V L   +   +   + + + EG+NRE++++      +V  L R+  G   L 
Sbjct: 410 DVHCVPTEVELLPPEPGDARNRIRIVVCEGRNREVRELVANAGLEVLALKRVRIGGLSLS 469

Query: 227 -TLLAGSTREVSK 238
             L  G    +++
Sbjct: 470 RKLSPGKFEVLTE 482


>gi|218512381|ref|ZP_03509221.1| probable RNA-pseudouridine synthase protein, ribosomal large
           subunit B [Rhizobium etli 8C-3]
          Length = 244

 Score =  138 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 141/218 (64%), Positives = 166/218 (76%)

Query: 48  ERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
               VNV   D IEVDG+P+R  ERTRLWLYHKP GLVTT++DP+GR TVFDNLP    R
Sbjct: 16  RNPVVNVTLADRIEVDGMPIRGIERTRLWLYHKPAGLVTTNADPEGRPTVFDNLPEELPR 75

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           V+S+GRLDINTEGLLLLTNDGGLAR LELP+T WLR YRVR HG++DQ+ L+ LK GI +
Sbjct: 76  VMSIGRLDINTEGLLLLTNDGGLARALELPATGWLRRYRVRAHGEIDQEALDKLKDGIAV 135

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G+ YG ++ TLD  +GSN W+T+GLREGKNREIK V       VNRLIRISYGPFQLG 
Sbjct: 136 DGVLYGSIEATLDRTQGSNVWITMGLREGKNREIKNVLGALGLDVNRLIRISYGPFQLGD 195

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSE 265
           L  G   EV  + LR+QLGP L+EEA+ N DAPIY++ 
Sbjct: 196 LPEGHVIEVRGRTLRDQLGPRLIEEAKANFDAPIYNAP 233


>gi|150016675|ref|YP_001308929.1| pseudouridine synthase [Clostridium beijerinckii NCIMB 8052]
 gi|149903140|gb|ABR33973.1| pseudouridine synthase [Clostridium beijerinckii NCIMB 8052]
          Length = 281

 Score =  138 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 56/277 (20%), Positives = 104/277 (37%), Gaps = 52/277 (18%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+ +  GI SR+E  R+I ++R+ +NG         V  +D I  DG P+   E+ 
Sbjct: 1   MRINKLFSNYGICSRKETNRLIEEKRIIINGRYCVE-GQWVNDSDEIIFDGKPISTVEKV 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L        T  +        +         +  VGRLD +++GL+L+TNDG +A  
Sbjct: 60  YIVLNKPVGITCTAENKVSDNIISY---MKYPHYIFPVGRLDKDSQGLILMTNDGEVANR 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-------------ICYGDMQVT-- 178
           +        + Y V+ +   D + L  +  G+ I G               Y  ++    
Sbjct: 117 ILESDNMHEKEYLVQVNKNFDDEFLKRMSNGVEITGNKSSGVRRISDKLGLYKKIEDKEI 176

Query: 179 ---------------------------------LDTQKGSNAWVTVGLREGKNREIKKVF 205
                                               ++  +    + L +G N++I+K+ 
Sbjct: 177 LLGEEDPGDSSIVQLKELKNIEREQNKFVKTRPCQVERVDDNTFKIILTQGMNKQIRKMS 236

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
               +KV +L RI     +L  L  G  R + +  ++
Sbjct: 237 GALGYKVIKLERIRIMNIKLNDLETGKWRYLEENEMK 273


>gi|226226929|ref|YP_002761035.1| pseudouridine synthase [Gemmatimonas aurantiaca T-27]
 gi|226090120|dbj|BAH38565.1| pseudouridine synthase [Gemmatimonas aurantiaca T-27]
          Length = 237

 Score =  138 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 64/228 (28%), Positives = 100/228 (43%), Gaps = 3/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            RV + +AR G  SRRE ++ +A+ RV+VNG         V    D I +DG P+     
Sbjct: 1   MRVQRALARVGAVSRREADKAVAEGRVQVNGTTAIV-GQLVDPARDRITLDGTPVATQVT 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              W+       V T            +L      ++ VGRLD  TEG+LLLT DG  A 
Sbjct: 60  AHRWIVLHKPAAVMTTRKDPEGRATVFDLVDDAPGLVYVGRLDFMTEGVLLLTTDGTAAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           VL  PS +  R Y     G          ++G+ +        +VT            + 
Sbjct: 120 VLTHPSHEVERTYVATVRGDAVTAAREA-RRGVKLDDGLVVPSEVTAYPLGERRWAFELT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           + EG+  E++++ +    +V RL+R  +GP +LG L +G+ R ++   
Sbjct: 179 ITEGRTHEVRRICDALGLEVERLVRTRFGPVRLGELPSGAARALTSAE 226


>gi|254561472|ref|YP_003068567.1| 16S rRNA pseudouridylate 516 synthase [Methylobacterium extorquens
           DM4]
 gi|254268750|emb|CAX24711.1| 16S rRNA pseudouridylate 516 synthase [Methylobacterium extorquens
           DM4]
          Length = 242

 Score =  138 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 55/233 (23%), Positives = 97/233 (41%), Gaps = 7/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV----MSTDHIEVDGVPLRKA 70
           R+ +++A  G  SRREVE +     V+++G  L  A+  +      +  + V G  L   
Sbjct: 5   RLDRLLANLGYGSRREVEGLARAGLVRLDGQALRDASQRIPLEPDLSARMTVQGEALDPL 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               L L+       +         S + +        + +VGRLD  T GLLL+T+DG 
Sbjct: 65  PGVCLMLHKPLGVTCSHKEVGPLVYSLLPERWRRRDPALSTVGRLDKETSGLLLMTDDGA 124

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +  P  +  + YRV     +  D+  +L  G ++       + + ++ +       
Sbjct: 125 LLHRIISPKAKVSKRYRVTLARPLQGDETAILASGEMMLEGEDKPL-LPVEMETDDPTHC 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           TV L EG+  +++++F      V+ L R   G   L   L AG  R +    +
Sbjct: 184 TVTLHEGRYHQVRRMFAALGNHVDALHRDRVGGLVLPADLPAGEFRILGPGEI 236


>gi|84622298|ref|YP_449670.1| ribosomal small subunit pseudouridylate synthase [Xanthomonas
           oryzae pv. oryzae MAFF 311018]
 gi|84366238|dbj|BAE67396.1| ribosomal small subunit pseudouridylate synthase [Xanthomonas
           oryzae pv. oryzae MAFF 311018]
          Length = 237

 Score =  138 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 55/232 (23%), Positives = 91/232 (39%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVN--GILLERAAVNVMSTDHIEVDGVPLRKAE 71
            ++ K IA  G  SR++V ++  Q  V  +  G +L  A   V   D I +DG PL    
Sbjct: 1   MKLVKHIANLGYGSRKQVTQLFRQGAVT-DAQGEVLY-ADDQV-EHDAIRIDGEPLDPPP 57

Query: 72  RTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              L L+       +   +       +     S    +  VGRLD  T G+LL+T+DG L
Sbjct: 58  GFSLLLHKPGGYTCSTKDTGRLIYELLPPRFRSRAPVLAPVGRLDRETSGMLLMTDDGAL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P +   +VY +    ++  D+  L   G ++       +        G      
Sbjct: 118 LHRIISPKSALDKVYDITLAEELRGDEAALFASGSLLLEGETKPLLPAELEVLGPR-EAR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + L EG+  +++++F      V  L R   G   L  L +G  R +    L 
Sbjct: 177 LTLHEGRYHQVRRMFAAAGNHVVALHRSRIGGLSLDGLPSGQWRALEASDLE 228


>gi|121605680|ref|YP_983009.1| pseudouridine synthase [Polaromonas naphthalenivorans CJ2]
 gi|120594649|gb|ABM38088.1| ribosomal small subunit pseudouridine synthase A [Polaromonas
           naphthalenivorans CJ2]
          Length = 244

 Score =  138 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 52/236 (22%), Positives = 92/236 (38%), Gaps = 10/236 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN-VMSTDHIEVDGVPLRKAER 72
            ++ +++   G  +RR    ++ Q  V V G+     A+  +       V GV     E+
Sbjct: 1   MQLQEILFSQGFGTRRVCAGLVQQGFVTVAGVPCTEPAMEFIAVGLRFTVQGVAWEYHEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTV------FDNLPSIFSRVISVGRLDINTEGLLLLTN 126
             L L+       +                         + V +VGRLD +T GLLLL++
Sbjct: 61  AYLMLHKPAGHECSQKPSTYPSIYTLLPAPIRQRGGGAAAGVQAVGRLDQDTTGLLLLSD 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG     +  P     +VY V     VD  ++  L  G+V+       ++     ++ S 
Sbjct: 121 DGKFIHRMSSPRHHVPKVYEVTAKHPVDAQQVQKLLAGVVLDDDP-KPVR-AAACEQTSE 178

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
             +++ L EGK  ++K++      +V  L R   G   L   L  G  R ++ + L
Sbjct: 179 LQLSLTLTEGKYHQVKRMIAAVGNRVEGLHRSRIGSLALPADLKPGEWRWLTVQDL 234


>gi|317055194|ref|YP_004103661.1| pseudouridine synthase [Ruminococcus albus 7]
 gi|315447463|gb|ADU21027.1| pseudouridine synthase [Ruminococcus albus 7]
          Length = 246

 Score =  138 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 58/246 (23%), Positives = 102/246 (41%), Gaps = 11/246 (4%)

Query: 12  TPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              R+ K++A      SR +V+++  ++++ VNG L+ R+   V + D I +DG  L   
Sbjct: 3   EIMRLDKLVASQFADISRADVKKLCLKKKIMVNGKLMARSDAKVDTDDEIIIDGRKLTYK 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   + L      + +T                    +   GRLD +TEG +L+T+DG L
Sbjct: 63  KHIYIMLNKPAGVVCSTKEGASTTVLDLVPDELRRDGLFPAGRLDKDTEGFVLITDDGEL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-------ICYGDMQVTLDTQK 183
           +  +  P T   + Y VR     +    +++  G+ I G             Q       
Sbjct: 123 SHRVLSPKTHVPKTYFVRLEKPWEDSYKDIMAAGMTIDGLHEGDSEEKCQPAQ--FLASD 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            +    T+ + EGK  ++K++FE    KV  L R++ G   L   L  G   E+  K + 
Sbjct: 181 ENVCECTLIIHEGKFHQVKRMFEKLGNKVVYLKRVAIGEMPLDRGLELGECLEIMHKDVE 240

Query: 243 EQLGPH 248
           + L   
Sbjct: 241 KLLARK 246


>gi|218530506|ref|YP_002421322.1| pseudouridine synthase [Methylobacterium chloromethanicum CM4]
 gi|218522809|gb|ACK83394.1| pseudouridine synthase [Methylobacterium chloromethanicum CM4]
          Length = 242

 Score =  138 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 55/233 (23%), Positives = 97/233 (41%), Gaps = 7/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV----MSTDHIEVDGVPLRKA 70
           R+ +++A  G  SRREVE +     V+++G  L  A+  +      +  + V G  L   
Sbjct: 5   RLDRLLANLGYGSRREVEGLARAGLVRLDGQALRDASQRIPLEPDLSARMTVQGEALDPL 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               L L+       +         S + +        + +VGRLD  T GLLL+T+DG 
Sbjct: 65  PGVCLMLHKPLGVTCSHKEVGPLVYSLLPERWRRRDPALSTVGRLDKETSGLLLMTDDGA 124

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +  P  +  + YRV     +  D+  +L  G ++       + + ++ +       
Sbjct: 125 LLHRIISPKAKVSKRYRVTLARPLQGDETAILASGEMMLEGEDKPL-LPVEMETDDPTHC 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           TV L EG+  +++++F      V+ L R   G   L   L AG  R +    +
Sbjct: 184 TVTLHEGRYHQVRRMFAALGNHVDALHRDRVGGLVLPTDLPAGEFRILGPGEI 236


>gi|330877468|gb|EGH11617.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. morsprunorum str. M302280PT]
          Length = 230

 Score =  138 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 57/230 (24%), Positives = 102/230 (44%), Gaps = 7/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R+ V   +A  RV+V+G +      +V     + +D   L+  +  
Sbjct: 1   MRLDRFLSNLPRFNRKSVRLALASGRVQVDGQITTDPHYDVREFSCVALDAEILQPGKAA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V+  +D    + +          +   GRLD NT GL+L+TNDG  +R 
Sbjct: 61  RYFMLHKPQGCVSATTDAQHATVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+       +      + I     Q+T+   + +     +
Sbjct: 121 LTQPQTKMPKVYYVETEQLIDERYALTFAEGLFFSFENIITQPAQLTVLGPRSA----RL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + EG+  ++K++F  F+ KV +L R S G   L   L  G  R +    
Sbjct: 177 SIIEGRYHQVKRMFGHFDNKVLQLHRESIGALILDPALPPGGYRSLQAAE 226


>gi|322379744|ref|ZP_08054054.1| pseudouridine synthase [Helicobacter suis HS5]
 gi|321147815|gb|EFX42405.1| pseudouridine synthase [Helicobacter suis HS5]
          Length = 257

 Score =  138 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 63/245 (25%), Positives = 110/245 (44%), Gaps = 13/245 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ IA     SRR+ +++I + +VK+N  L    A      D I V+G  L   E+ 
Sbjct: 6   MRLNQFIAHNLPCSRRQADKLIKEGKVKINHQLA-SFATPFSPYDKIFVEGRMLNSYEKR 64

Query: 74  RL--WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                +YHKP G + +  D  GR T+F++L S F     +GRLD  + GLLLL++   + 
Sbjct: 65  SYTVLVYHKPKGELVSRIDHRGRKTIFESLESKFRHFTPIGRLDFASMGLLLLSDSKQVV 124

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI----------CYGDMQVTLDT 181
             L   S + + + +++ +      +       +                   M   +  
Sbjct: 125 NALMHSSLERVYLVKIQGNITQTMLEAMQTGLELQGLEGAHPKSKYTRMHIAPMACQILK 184

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              + + + + L+EG NREI++ F  F  +V  L R+S+G   L  L  G TR ++ K  
Sbjct: 185 NHRNYSKIKITLQEGHNREIRRFFAHFKKEVLDLRRVSFGFVSLNALPVGKTRYLNPKEY 244

Query: 242 REQLG 246
           ++   
Sbjct: 245 KQLHQ 249


>gi|330964551|gb|EGH64811.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. actinidiae str. M302091]
          Length = 230

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 57/230 (24%), Positives = 101/230 (43%), Gaps = 7/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R+ V   +A  RV+V+G +      +V     +  D   L+  +  
Sbjct: 1   MRLDRFLSNLPRFNRKSVRLALASGRVQVDGQITTDPHYDVREFSCVAFDTEILQPGKAA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V+  +D    + +          +   GRLD NT GL+L+TNDG  +R 
Sbjct: 61  RYFMLHKPQGCVSATTDAQHATVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+       +      + I     Q+T+   + +     +
Sbjct: 121 LTQPQTKMPKVYYVETEQLIDERYALTFAEGLFFSFENIITQPAQLTVLGPRSA----RL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + EG+  ++K++F  F+ KV +L R S G   L   L  G  R +    
Sbjct: 177 SIIEGRYHQVKRMFGHFDNKVLQLHRESIGALILDPALPPGGYRSLQAAE 226


>gi|257095422|ref|YP_003169063.1| RNA-binding S4 domain-containing protein [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
 gi|257047946|gb|ACV37134.1| RNA-binding S4 domain protein [Candidatus Accumulibacter phosphatis
           clade IIA str. UW-1]
          Length = 415

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 54/243 (22%), Positives = 100/243 (41%), Gaps = 18/243 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK++++  + SRRE +  I    V V+G+++ R    V     IE+     +   
Sbjct: 175 EPPRLSKLVSQLALCSRREADEWIENGWVTVDGVVVTRLGARVSPKAKIEITNAASQHQT 234

Query: 72  RTRLWLYHKP--------------IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
            +   +++KP                L+   +      T      S    +   G+LD  
Sbjct: 235 ASVTIVFNKPIGDAAAPDAGLAAIATLIRPDTHWAEDGTCRRFQASHLRGLAVAGKLDTE 294

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
             G+L+ T DG +AR L     +    Y +R  G++  D L LL+ G+ +  +     QV
Sbjct: 295 EHGMLVFTQDGSVARRLTGGGARLENEYHLRVQGELSPDGLQLLRHGLSLDNVRLERAQV 354

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +  +++     +   + E + R+I++  E    +V  + R+  G   LG L  G  R + 
Sbjct: 355 SWLSEQQ----LRFVVHENRKRQIQRQCELVGLQVTDIKRVRIGGVSLGKLPPGQWRYLR 410

Query: 238 KKI 240
              
Sbjct: 411 PDE 413


>gi|182415600|ref|YP_001820666.1| RNA-binding S4 domain-containing protein [Opitutus terrae PB90-1]
 gi|177842814|gb|ACB77066.1| RNA-binding S4 domain protein [Opitutus terrae PB90-1]
          Length = 266

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 71/264 (26%), Positives = 111/264 (42%), Gaps = 7/264 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           +F P R+ K +A AG+ SRR  E +IA   V VNG   +     V    D +   G P+R
Sbjct: 3   SFEPIRLQKYLADAGVCSRRAAEALIASGEVWVNGAPAQV-GQKVTPGVDRVTTGGKPVR 61

Query: 69  --KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
                R  L ++     + T     +  +            R    GRLD ++EGL++LT
Sbjct: 62  TTAQPRVTLAMHKPRGLVCTNEDPHNPETIFSVLPREFAKLRFFCAGRLDKDSEGLVILT 121

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS   ++ Y V         +L LL KG++ QG      +  L     S
Sbjct: 122 TDGDLAHRLMHPSNLVVKRYHVTLEKPFPAKRLPLLVKGVIAQGERLKVERAALINPSVS 181

Query: 186 N--AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           +    + V +  GK REI+ +F    + V RL R   G F+L  +   + +++S   +  
Sbjct: 182 HEATNLDVHMHHGKKREIRLLFTELGYPVKRLRRYQIGGFRLKGIPLRAMKKMSPAEIES 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETL 267
                    A + + A  ++S   
Sbjct: 242 LFRVPRTPHAAIEVTAESFASHHA 265


>gi|149375301|ref|ZP_01893072.1| 16S rRNA pseudouridylate 516 synthase [Marinobacter algicola DG893]
 gi|149360337|gb|EDM48790.1| 16S rRNA pseudouridylate 516 synthase [Marinobacter algicola DG893]
          Length = 245

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 54/233 (23%), Positives = 105/233 (45%), Gaps = 3/233 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N    ++S++++     SR+    +IA   V V+G +    A  +     +  +G  ++ 
Sbjct: 12  NIATMKLSRILSNQNGVSRKRANALIAAGTVTVDGCICRETAREIDRFSTVACNGRVIQH 71

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ++    + +KP G ++  +D   ++ +    P +   +   GRLD  + GLL+LTNDG 
Sbjct: 72  GDQAHYLMLNKPAGYLSATADKVHKTVMELIDPELRKDLHIAGRLDRASTGLLILTNDGA 131

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            +R L  P  +  +VYRV     V  + +    +GI  +          L+    + +  
Sbjct: 132 WSRRLTEPRIKLPKVYRVTTVEPVSTNAIERFAQGIWFEYERLTTSPARLEPLSANES-- 189

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V + EG+  +IK++F     +V+ L R   G   L  TL  G +R ++ + +
Sbjct: 190 RVTIYEGRYHQIKRMFHATGNRVSSLHREQMGAITLDPTLEPGESRPLTSREI 242


>gi|312867227|ref|ZP_07727437.1| putative 16S pseudouridylate 516 synthase [Streptococcus
           parasanguinis F0405]
 gi|311097356|gb|EFQ55590.1| putative 16S pseudouridylate 516 synthase [Streptococcus
           parasanguinis F0405]
          Length = 241

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 50/231 (21%), Positives = 105/231 (45%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A    A R+++++++A++++ V+ +  ++ + N+      I++    +++   
Sbjct: 1   MRLDQLMADHQYA-RKDIKQLLARRQILVDHLPAQKLSQNIDPGLQQIQIGDRIIQEPRH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L+     +               +    +  +  +GRLD +T GLLL+T++G L  
Sbjct: 60  HYYMLHKPIGAVTAKRDAHHPTVIELVDPQQEYPDLYPLGRLDRDTSGLLLITDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY V  +G +    +   + GI            +T+     S +   +
Sbjct: 120 QLLHPQYHVEKVYEVEVNGPLYAAHIEQFQNGISFTDGPICKPASLTILESTLSYSKAQI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++KK+F     KV  L R+S+GPF L   L  G +R +++  L
Sbjct: 180 RISEGKYHQVKKMFLAIGVKVMTLNRLSFGPFTLDPQLAPGESRPLNEVEL 230


>gi|167625202|ref|YP_001675496.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
 gi|167355224|gb|ABZ77837.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
          Length = 238

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 55/244 (22%), Positives = 97/244 (39%), Gaps = 11/244 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I ++   +R +    I    + VNG  +   +  V  ++ +   G  L      
Sbjct: 1   MRLDKFICKSTELNRAQASECIECAEISVNGETITEVSFQVHESNSVVFKGQRLVARPSR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+      ++++ D D  S            +  VGRLD +T GL+LLT+DG  +  
Sbjct: 61  YIMLHKPI-HTLSSNVDGDYPSLFRCINIERAEELHIVGRLDADTTGLVLLTDDGRWSFD 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQ---DKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAW 188
           +  P  Q  + YRV     +     D +     G+ +Q         ++ + T+K     
Sbjct: 120 IIRPDKQCEKTYRVTLRDAIRDDVADMVARFAHGLQLQNEPALTLPAKLEVVTEK----E 175

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           V + + EGK  ++K++F     +VN L R   G   L  L  G  R +S+  +     P 
Sbjct: 176 VLLTITEGKYHQVKRMFAAVGNRVNGLHRERIGGLSL-ELDVGCWRHLSEDEVNRLSTPT 234

Query: 249 LLEE 252
               
Sbjct: 235 PQSP 238


>gi|66047208|ref|YP_237049.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. syringae
           B728a]
 gi|63257915|gb|AAY39011.1| Pseudouridine synthase, Rsu [Pseudomonas syringae pv. syringae
           B728a]
          Length = 230

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 105/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R++V   +A  RV+V+G         V     + +D   L+  +  
Sbjct: 1   MRLDRFLSNLPRFNRQQVRLALASGRVQVDGQATRDPHHEVREFSCVALDEEILQAGKVP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V+  SD    + +          +   GRLD NT GL+L+TNDG  +R 
Sbjct: 61  RYFMLHKPEGCVSATSDAQHPTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P ++  +VY V     +D+       +      +GI     Q+TL   + +     +
Sbjct: 121 LTQPQSKMPKVYYVETEQPIDERYAAKFAEGLYFAFEGITTQPAQLTLLGPRSA----RL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F  F+ KV RL R + G   L   L  GS R ++   +
Sbjct: 177 SIVEGRYHQVKRMFGHFDNKVLRLHRETIGALLLDPDLRPGSYRALNAGEI 227


>gi|325690206|gb|EGD32210.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK115]
          Length = 241

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 58/234 (24%), Positives = 105/234 (44%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVER--MIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
            R+ +++A A   SR+++++  +  Q+++ V+G    + + NV +    I   G  +   
Sbjct: 1   MRLDQLLA-ANHISRKKMKQSHL--QKQILVDGKPAYKLSQNVDTGLQQITFQGKHVSGP 57

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                 L      +               +       + S+GRLD +TEGLLL+T++G L
Sbjct: 58  AHRYYMLNKPAGAVTANRDAEKLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V  +G +  +  +  ++GI  + G      Q+++ +   S +  
Sbjct: 118 GFQLLHPQYHVEKTYYVEVNGPLTPNDSSSFQEGIRFLDGTVCQPAQLSILSTSSSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           +V + EGK  +IKK+F     KV  L RI +G F L   L  G  R +++K L 
Sbjct: 178 SVRISEGKFHQIKKMFLAVGVKVTYLKRIQFGDFTLDPDLAKGDYRALNQKELE 231


>gi|144900938|emb|CAM77802.1| Ribosomal small subunit pseudouridylate synthase [Magnetospirillum
           gryphiswaldense MSR-1]
          Length = 230

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 95/231 (41%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVK-VNG-ILLERAAVNVMSTDHIEVDGVPLRKAE 71
            R+ ++IA  G  S+R++  ++   RV+  +G  L+E     V + D I VDG PL    
Sbjct: 1   MRLVRLIANLGYGSQRDIRFLLRDGRVRHADGRELVES--DKV-AHDDIRVDGEPLDPPA 57

Query: 72  RTRLWLYHKPIGLVTTHSD-PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              + L+       ++          +          +  VGRLD +T GLLLLT+DG L
Sbjct: 58  GLVIMLHKPAGYTCSSSDPGRIVYELLPPRFMHRNPVLAPVGRLDRDTTGLLLLTDDGKL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + Y V     ++  +  +   G ++       +        G N    
Sbjct: 118 LHRLTSPRHHVPKTYDVTLDRPLEGTEAEIFASGTLMLRSEKTPLAPAQLQVLGPNQ-AR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + L EG+  ++K++F      V  L R   GP  LG L  G  R ++ + L
Sbjct: 177 LTLHEGRYHQVKRMFAAVGNHVVSLHRAGLGPLTLGDLPEGQWRVMAAEEL 227


>gi|217974985|ref|YP_002359736.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217500120|gb|ACK48313.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 233

 Score =  137 bits (345), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 59/232 (25%), Positives = 97/232 (41%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++    R      I    V VNG +    A+ V   + + ++  PL      
Sbjct: 1   MRLDKFLCKSTDLDRDAASVAIINGSVTVNGAIATDCAMQVHENNAVCLNEKPLMPRPS- 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP   + ++ D    S            +  VGRLD++T GL+LLT+DG  +  
Sbjct: 60  RYFMLHKPADTLCSNVDGAYPSLFHLLDIERAFDLHIVGRLDVDTTGLVLLTDDGRWSFN 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKG----IVIQGICYGDMQVTLDTQKGSNAWV 189
           +  P  Q  +VYRV     +D +    +       + +QG     +  TL         V
Sbjct: 120 IISPQYQCKKVYRVTLRDPLDSEATAAIAATFAAGLQLQGETALTLPATLQQVDDK--TV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + L EGK  ++K++F     KV  L R   G F L  +  G  RE++   +
Sbjct: 178 LLTLTEGKFHQVKRMFAAVGNKVVALHRAQIGAFIL-DVDIGEWRELTLAEI 228


>gi|150024420|ref|YP_001295246.1| pseudouridylate synthase [Flavobacterium psychrophilum JIP02/86]
 gi|149770961|emb|CAL42428.1| Pseudouridylate synthase [Flavobacterium psychrophilum JIP02/86]
          Length = 302

 Score =  137 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 109/230 (47%), Gaps = 1/230 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K I+ +G  SRR+ +  I    VKVNGI +      V   D +  DG  L   +
Sbjct: 68  DEIRLNKYISNSGACSRRDADIYIQSGNVKVNGIPVIEMGYMVKPGDVVNFDGSVLTPEK 127

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + L              + R+ +     S  S++ +VGR+D NT GLLL TND  + 
Sbjct: 128 KEYILLNKPKNFTTAFDEGQENRNVLELVRGSTNSKIAAVGRMDKNTTGLLLFTNDTDMI 187

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           R   LPS +  ++Y+V     +  + L  + KG+VI G     ++     +K + + V +
Sbjct: 188 RRFSLPSQKSSKIYQVSLDKNLKFEDLEKISKGLVIDGHRV-FVEEISYIEKEAKSEVGL 246

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            L+    + ++ +FE F + V R+ R+S+       L  G+ R ++++ +
Sbjct: 247 KLKTANVKVVRAIFESFKYDVLRIDRVSFAGLTKKNLPRGNWRFLTEQEI 296


>gi|323343342|ref|ZP_08083569.1| ribosomal large subunit pseudouridine synthase B [Prevotella oralis
           ATCC 33269]
 gi|323095161|gb|EFZ37735.1| ribosomal large subunit pseudouridine synthase B [Prevotella oralis
           ATCC 33269]
          Length = 479

 Score =  137 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 61/242 (25%), Positives = 111/242 (45%), Gaps = 1/242 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AGI SRRE +  I    V VNG ++      V+ +D +
Sbjct: 231 IEYKEEHIDPNEPIRLNKYLANAGICSRREADEFIQAGVVTVNGNVVTELGTKVLRSDEV 290

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +    P+   ++  + L      + T+      ++ +     +   R+  VGRLD NT G
Sbjct: 291 KFHEQPVSLEKKVYVLLNKPKDYVTTSDDPQQRKTVMELVKGACEERIYPVGRLDRNTTG 350

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +LLLTNDG LA  L  P     +VY V     V ++ +  + +GI ++            
Sbjct: 351 VLLLTNDGDLASKLTHPKFLKKKVYHVFLDKAVTEEDMQKIAEGIELEDGEIH-ADAIEY 409

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             +     V + +  GKNR ++++FE   ++V +L R+ +       +  G  R +++K 
Sbjct: 410 ADERDKKQVGIEIHSGKNRIVRRIFESLGYRVIKLDRVQFAGLTKKNVRRGDWRYLTEKE 469

Query: 241 LR 242
           + 
Sbjct: 470 VD 471


>gi|241766432|ref|ZP_04764306.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
 gi|241363374|gb|EER58885.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
          Length = 237

 Score =  137 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 66/239 (27%), Positives = 95/239 (39%), Gaps = 29/239 (12%)

Query: 26  ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLV 85
            SRRE +  IAQ  VKVNG +     + V +TD IEVD       E+    L HKP+G V
Sbjct: 2   CSRREADDWIAQGWVKVNGQVAP-MGLQVHATDRIEVDKKAQGFQEQRVTILLHKPMGYV 60

Query: 86  T---------------THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +                 +      +     P     +   GRLDI++ GLL+LT DG +
Sbjct: 61  SGQAEDGHTPAVALINPRTHWREDPSRNRFSPPQLRGLAPAGRLDIDSVGLLVLTQDGRV 120

Query: 131 ARVLELPSTQWLRVYRVRFHG---------QVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           AR +    +   + Y VR                 +L  L  G+ + G      +V    
Sbjct: 121 ARQIIGEDSSMDKEYLVRVQYGDVATNVQAVFPAQQLARLCHGLSLDGQALKPARVEWQN 180

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +     +   L EGK R+I+++ E    +V  L RI  G   LG L  G  R +    
Sbjct: 181 PEQ----LRFVLTEGKKRQIRRMCELVGLRVVGLKRIRIGRVTLGNLPVGQWRYLGPHE 235


>gi|110004423|emb|CAK98761.1| probable ribosomal large subunit pseudouridine synthase b protein
           [Spiroplasma citri]
          Length = 267

 Score =  137 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 110/237 (46%), Gaps = 7/237 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-RKAER 72
           +R+ KVIA  G  SRR+ E +I Q RVKVN +++      V   D I  +   L  +   
Sbjct: 2   ERLQKVIAAKGYCSRRKAEELIIQGRVKVNNVVVTTLGTKVGKNDQI--NNQILMNENSN 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +K    V+T  DP  R TV   +  I  R+  VGRLD +T GLLLLTNDG    
Sbjct: 60  KIYLMLNKRRNCVSTMYDPQHRKTVLTYVKGISERIYPVGRLDYDTSGLLLLTNDGEFTN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG---DMQVTLDTQKGSNAWV 189
           ++  PS    + Y V   G + + +L  L  GI I+          ++    +  + + +
Sbjct: 120 IITHPSHIINKTYHVLLSGYLSKQQLQQLATGIEIEPGIIRSQAQAKLVKYEEVKNVSIL 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
            + + E    ++KK+ +    +V +L RI+ G  QL   L  G  R +  K ++   
Sbjct: 180 LLTIHEVTKHQVKKMIQSLGHEVIKLKRIAIGFLQLDETLKPGEWRYLKPKEIKRFF 236


>gi|307545292|ref|YP_003897771.1| pseudouridine synthase [Halomonas elongata DSM 2581]
 gi|307217316|emb|CBV42586.1| pseudouridine synthase [Halomonas elongata DSM 2581]
          Length = 233

 Score =  137 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 61/235 (25%), Positives = 104/235 (44%), Gaps = 12/235 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A +   +R   +R + +  V VNG L ++AA +V  TD I   G  L     T
Sbjct: 1   MRLDRFLAESTELTRGLAKRALIRGEVSVNGELEKKAARHVQETDRITWLGERLSLV-GT 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + HKP G+  T         V         R+  VGRLD+ T GLLL+T+DG  +  
Sbjct: 60  RYIMLHKPEGVECTARRGLYPRAVDLLDVPKVERLQPVGRLDVETTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDK----LNLLKKGIVIQGI--CYGDMQVTLDTQKGSNA 187
           +  P  +  + Y  R    ++ D+    +    +GIV++G        ++T       + 
Sbjct: 120 ITSPRRRCPKAYVARLARPLEGDEARRAMQAFAEGIVLEGEDAPTRPAELTCL----DDH 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            V + + EG+  +++++       V  L R S G   L   L  G  RE++ + +
Sbjct: 176 RVRLVIDEGRYHQVRRMLAAIGNHVETLHRESVGALVLDDTLEPGEWRELTPEEV 230


>gi|56477113|ref|YP_158702.1| ribosomal small subunit pseudouridine synthase A protein
           [Aromatoleum aromaticum EbN1]
 gi|56313156|emb|CAI07801.1| ribosomal small subunit pseudouridine synthase A protein
           [Aromatoleum aromaticum EbN1]
          Length = 239

 Score =  137 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 46/228 (20%), Positives = 87/228 (38%), Gaps = 4/228 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           + +++   G  SR+    +I   RV ++G + +    ++ + D +  VD    R  ++  
Sbjct: 3   IERILHSQGFGSRKVCRALIRAGRVTISGQIQDNPFADLPTADLVFTVDRETWRFRDKAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L+       +               P +   V  +GRLD +T GLLLL++DG    V 
Sbjct: 63  LMLHKPSGYECSRQPQFHAPVFALLPEPLVNRGVQPIGRLDQDTTGLLLLSDDGQFIHVW 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  ++Y V     V++     L  G+ +              ++     + + + 
Sbjct: 123 SSGRKRVPKIYEVAVRHPVNETMTEALLAGVQLHDDPEPVA--AAACERTGERSLKLTIT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           EGK  ++K++      +V  L R   G   L   L  G  R +    L
Sbjct: 181 EGKYHQVKRMVAAAGNRVESLHRSGIGGLMLPDDLAPGQWRWLDDGDL 228


>gi|296140073|ref|YP_003647316.1| pseudouridine synthase [Tsukamurella paurometabola DSM 20162]
 gi|296028207|gb|ADG78977.1| pseudouridine synthase [Tsukamurella paurometabola DSM 20162]
          Length = 319

 Score =  137 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 71/238 (29%), Positives = 111/238 (46%), Gaps = 4/238 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
            +    R+ KV+A+AG+ASRR  E MIA  RV+V+G ++    + V  +  +        
Sbjct: 74  PDGEKIRLQKVLAQAGVASRRVAEEMIADGRVEVDGEIVTEQGLRVDPSVAVVRVDGVRV 133

Query: 69  K-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLL 124
              E       +KP G  +T SD  GR  V D +        R+  VGRLD +TEGLLL+
Sbjct: 134 VVNENLVHLALNKPRGWHSTMSDDMGRPCVGDIVAERVAAGQRLFHVGRLDADTEGLLLV 193

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG LA  L  PS +  + Y     G+V ++    L+ G+ ++       + ++     
Sbjct: 194 TNDGELAHRLMHPSYEVPKTYLAWVAGEVPRNLGKKLRDGVELEDGPVTVDRFSVLEAAE 253

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
             + V V L EG+   ++++       V RL+R   G   LG    GS R + +  + 
Sbjct: 254 GKSTVRVVLHEGRKHIVRRLLAEVGHPVQRLVRTHVGTVALGDQRPGSLRVLGRDEVE 311


>gi|262281963|ref|ZP_06059732.1| pseudouridine synthase rRNA-specific [Streptococcus sp. 2_1_36FAA]
 gi|262262417|gb|EEY81114.1| pseudouridine synthase rRNA-specific [Streptococcus sp. 2_1_36FAA]
          Length = 237

 Score =  136 bits (343), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 54/212 (25%), Positives = 95/212 (44%), Gaps = 4/212 (1%)

Query: 35  IAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           + +  V VNG   +     +  T D + V G  L   +     L      +  T  +   
Sbjct: 17  LEKGLVLVNGRAEKSPKTQINETEDEVVVSGQKLTYEKFVYYLLNKPKGYISATEDERHK 76

Query: 94  RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
                 +  ++   V  VGRLDI+T GLLLLTN+G LA  +  P     ++YR +  G +
Sbjct: 77  TVLDLLDETALQKEVFPVGRLDIDTHGLLLLTNNGKLAHAMLSPKKHVEKIYRAQVAGLM 136

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +Q  +    +GI ++       Q+ +    ++   + V + L EGK  ++K++      +
Sbjct: 137 NQSDVEQFARGIELKDFTCQPAQLKILEVDEEKETSLVEISLAEGKFHQVKRMVAACGKE 196

Query: 212 VNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V  L R++ GP QL   L  G  R ++++ L+
Sbjct: 197 VTDLQRLTMGPLQLDPELALGEWRRLTEEELK 228


>gi|119896376|ref|YP_931589.1| pseudouridylate synthase [Azoarcus sp. BH72]
 gi|119668789|emb|CAL92702.1| pseudouridylate synthase [Azoarcus sp. BH72]
          Length = 248

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 40/233 (17%), Positives = 77/233 (33%), Gaps = 10/233 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-------HIEVDG 64
              ++ +++   G  SR++   ++    V V G+  +                    VD 
Sbjct: 2   QAMQIERLLHSQGFGSRKDCRALLRAGYVSVAGVPCDDPRAEFDPGSKDGSPGLEFTVDD 61

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                  +  L L+       +                 +   V  +GRLD +T GLLLL
Sbjct: 62  EIWHFRAQAYLMLHKPAGYECSHKPTFHPSVFTLLPPQLLNRGVQCIGRLDQDTTGLLLL 121

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           ++DG           +  +VY +      D   +  L  G+ +            +    
Sbjct: 122 SDDGQFIHQWSSGKKRTPKVYEIGLKHAADDALVAALLAGVELHDEPTPIAAAACEIT-- 179

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
           ++  + + + EGK  ++K++      +V  L R   G   L   L  G  R +
Sbjct: 180 ASHALRLTITEGKYHQVKRMVAAAGNRVETLHRSRVGGLTLDPALKPGEWRWL 232


>gi|27904757|ref|NP_777883.1| ribosomal large subunit pseudouridine synthase B [Buchnera
           aphidicola str. Bp (Baizongia pistaciae)]
 gi|34098502|sp|Q89AL1|RLUB_BUCBP RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|27904154|gb|AAO26988.1| ribosomal large subunit pseudouridine synthase B [Buchnera
           aphidicola str. Bp (Baizongia pistaciae)]
          Length = 247

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 63/237 (26%), Positives = 110/237 (46%), Gaps = 9/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRKA- 70
           +++ K++AR G  SRR +E +I    VK+N  +++     +       + ++    +   
Sbjct: 3   EKIQKILARHGYGSRRYIESLIKSHSVKINDEVVKV-GQRISINVIQKVIINNNNYKPKL 61

Query: 71  ----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L        + T     + R+          +R I++GRLD+N+ GLLL T 
Sbjct: 62  NINKSLKVLLYNKPEGEICTRKDQRNRRTIFEKLPKLSNARWINIGRLDLNSSGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS    R+Y+VR  GQ  ++ L  L   + +         +     +G N
Sbjct: 122 DGELAYRLTHPSFNIERIYKVRVFGQFTENILKQLNVRVKLLDGYANFKSIQFKYGEGKN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
            W  V L EG++R +++++E   ++VN+L+RISY    L  TL  G+   ++K  + 
Sbjct: 182 KWFNVSLCEGRHRIVRRIWEKLGFQVNKLVRISYAHLTLPKTLFPGTWITLNKHDID 238


>gi|92114073|ref|YP_574001.1| ribosomal small subunit pseudouridine synthase A [Chromohalobacter
           salexigens DSM 3043]
 gi|91797163|gb|ABE59302.1| ribosomal small subunit pseudouridine synthase A [Chromohalobacter
           salexigens DSM 3043]
          Length = 232

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 50/232 (21%), Positives = 99/232 (42%), Gaps = 5/232 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++ +   +R   ++ + +  V+VNG +++ AA  +     +   G PL +    
Sbjct: 1   MRLDRFLSESTELTRSLAKKALHRGEVEVNGDVVKNAAFKLGDEHVVRWLGEPLARIGVR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L        TT            ++       I+ GRLD++T GL+L+T DG  +  
Sbjct: 61  YLMLNKPAGYECTTRPGRYPSVIELLDVAKRGRLHIA-GRLDVDTTGLVLITEDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--CYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  + Y V     + +     L +G++++G        ++           V +
Sbjct: 120 LTSPRRRCDKHYLVTLARPLAEGAETALAEGLMLEGEDKPTLPARLERLD-DADGVRVRL 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            ++EG+  +IK++F   + +V  L R   G   L   L AG  RE+++  + 
Sbjct: 179 VIQEGRFHQIKRMFAALDNEVVALHRERIGEIALDPALAAGEWRELTQAEID 230


>gi|332292171|ref|YP_004430780.1| RNA-binding S4 domain protein [Krokinobacter diaphorus 4H-3-7-5]
 gi|332170257|gb|AEE19512.1| RNA-binding S4 domain protein [Krokinobacter diaphorus 4H-3-7-5]
          Length = 296

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 62/240 (25%), Positives = 106/240 (44%), Gaps = 2/240 (0%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K +   +++    R++K IA +GI SRRE +  I+  +V VNG ++      V   D + 
Sbjct: 53  KKQAPRKKDDGTMRLNKYIANSGICSRREADMYISIGQVTVNGKVVNEMGYQVKLEDDVR 112

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
            DG  +   E     L +KP G  TT S+  G + +     S  SR+  +GRL  N  GL
Sbjct: 113 FDGRRINP-EAKAYVLLNKPKGFATTTSNDKGNTVMDLVAGSTKSRIQPIGRLGRNAMGL 171

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL TND  L +          ++Y V     +    +  + +G+ I G      +++   
Sbjct: 172 LLFTNDDELVQKFTNSKKGVDKLYHVELSNNLKGADIERINEGLKIDGKTITVDEISYVD 231

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                  V + +R   N  I+ +FE  N++V R+  ++        L  G  R ++K+ +
Sbjct: 232 G-APKKEVGLRIRNTGNSVIRTIFEHLNYEVVRVDCVTIAGLTKKDLPRGHWRYLTKQEV 290


>gi|78066801|ref|YP_369570.1| pseudouridine synthase, Rsu [Burkholderia sp. 383]
 gi|77967546|gb|ABB08926.1| Pseudouridine synthase, Rsu [Burkholderia sp. 383]
          Length = 623

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 375 MRLSKRMSELGMCSRREADEWIEKGWVLVDGERIDTLGTKVRADQKIEIDERASAAQAAQ 434

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     L+T  +   G  +     P     +   GRLDI++
Sbjct: 435 VTILLHKPVGYVSGQAEDGYEPAAVLITRANRWSGDHSPVRFSPQHLHALAPAGRLDIDS 494

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 495 TGLLVLTQNGVVAKQLIGEQSDIDKEYLVRVRFGERLIDIDQHFPAESLAKLRHGLELDG 554

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E     V  L R+  G   LG L 
Sbjct: 555 VALKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLDVIGLKRVRMGRVMLGALP 610

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 611 QGQWRYLSADE 621


>gi|115375833|ref|ZP_01463084.1| ribosomal large subunit pseudouridine synthase B [Stigmatella
           aurantiaca DW4/3-1]
 gi|310820267|ref|YP_003952625.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|115367143|gb|EAU66127.1| ribosomal large subunit pseudouridine synthase B [Stigmatella
           aurantiaca DW4/3-1]
 gi|309393339|gb|ADO70798.1| Pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 270

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 68/243 (27%), Positives = 109/243 (44%), Gaps = 11/243 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
              P  +S+ +ARAG    +E E  I + RV VNG ++ +    V     + VDG  +R+
Sbjct: 26  KTKPDWLSRALARAGALPLQEAEDAIQEGRVTVNGRVVRQPLAPVPEGAVLRVDGTEVRR 85

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGRLDINTEGLLL 123
              TR+  +HKP  L+T+        TV++ L              +VGRLD  T GLLL
Sbjct: 86  EVETRVLAFHKPADLLTSTVSQHRTGTVYEVLLPQLPSELARYTWHAVGRLDRGTTGLLL 145

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            TND  L      P T   + Y     G  D+ ++  L++G+ ++       QV +    
Sbjct: 146 FTNDEKLVAHATSPETHLAKRYVATVQGTADEARVAPLRQGVQLEDGPTRPAQVRI---- 201

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
                V V + EG+N ++K++       V  L R + G   L  +  G+ R ++ + + E
Sbjct: 202 RDAHTVEVIVTEGRNHQVKRMLGAVGLPVRALHREAIGGVAL-DVPVGTFRLLTPEEVTE 260

Query: 244 QLG 246
            LG
Sbjct: 261 GLG 263


>gi|325524840|gb|EGD02796.1| ribosomal small subunit pseudouridine synthase A [Burkholderia sp.
           TJI49]
          Length = 238

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 52/234 (22%), Positives = 86/234 (36%), Gaps = 4/234 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV + G           +   +  VDG P     R  
Sbjct: 3   LESILYTQGFGSRRQCRGLIDAGRVAIAGAPATDPDARFDTDGLVFTVDGTPWPFHARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L        +               P +   V  VGRLD +T GLLLL++DG      
Sbjct: 63  LALNKPAGYECSRDPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFVHAY 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y       +D  +L+ L+ G+ + G     +   +         + + + 
Sbjct: 123 TSPKRKVPKTYVATVRHPLDDAQLDALRTGVQLHGEP-RPI-AAVAADARDTHALALTVL 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
           EGK  ++K++    + +V  L R   G F L   L  G+ R +    L     P
Sbjct: 181 EGKYHQVKRMVAAASNRVEALHRERIGGFTLPDDLAPGAWRWLDDADLSALRNP 234


>gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudouridine synthase A [Herbaspirillum
           seropedicae SmR1]
 gi|300073839|gb|ADJ63238.1| ribosomal small subunit pseudouridine synthase A protein
           [Herbaspirillum seropedicae SmR1]
          Length = 240

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 41/229 (17%), Positives = 81/229 (35%), Gaps = 5/229 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           + +++   G  SR+    +I    V +NG +++       + D +  +        E   
Sbjct: 6   LDRILQSQGFGSRKYCRELIEDGEVVINGEVVDDYRATPDTKDLVLTIFEEEWEYREHVY 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +   P    +                  +  V  VGRLD +T GLLL+++DG      
Sbjct: 66  IAINKPPNIECSRKPSHHPGVLTLLPEQFTWRDVQPVGRLDHDTTGLLLMSDDGAFIHAQ 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     +VY       V +  +  LK G+ +              ++     + + L 
Sbjct: 126 SSPKRHVPKVYAATTAEPVTEALIAQLKAGVQLHDEPAPLAATR--CRQLGENLLEIVLE 183

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKIL 241
           +GK  ++K++        + L R + G  QL    L  G    +  + +
Sbjct: 184 QGKYHQVKRMLAAAGNHCSALQRTAIGGLQLEALALEEGEWTYLDAEQM 232


>gi|226360073|ref|YP_002777851.1| pseudouridine synthase [Rhodococcus opacus B4]
 gi|226238558|dbj|BAH48906.1| pseudouridine synthase [Rhodococcus opacus B4]
          Length = 350

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 75/234 (32%), Positives = 115/234 (49%), Gaps = 4/234 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
              R+ KV+A+AG+ASRR  E +I+Q RV+V+G ++    + +      + VDGV +   
Sbjct: 108 DGMRLQKVLAQAGVASRRAAEELISQGRVEVDGRIVIEQGLRIDPENAVVRVDGVRVVVQ 167

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTND 127
           +       +KP G  +T SD  GR  V D +        R+  VGRLD +TEGLLLLTND
Sbjct: 168 KDLVHLALNKPRGWQSTMSDDLGRPCVGDIVSERVAAGQRLFHVGRLDADTEGLLLLTND 227

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  + Y     G +++     LK+G+ +          TL       +
Sbjct: 228 GDLAHRLMHPSFEVSKTYLATVSGALERGVGKKLKEGVELDDGPAKVDTFTLLDINEGKS 287

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V V L EG+   ++++F+     V RL+R   G   LG    G+ R + +  +
Sbjct: 288 LVRVTLHEGRKHIVRRLFDAVGHPVIRLVRTDIGAVALGDQRPGTLRVLGRGEV 341


>gi|262282747|ref|ZP_06060515.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           2_1_36FAA]
 gi|262262038|gb|EEY80736.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           2_1_36FAA]
          Length = 241

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 50/232 (21%), Positives = 96/232 (41%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A+A I SR+ +++ + ++ + V+       + NV +    I      +     
Sbjct: 1   MRLDRLLAQASI-SRKSMKQALLRRAILVDQTPARNLSQNVDTGLQDILFYKQKISAPAH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +                       + S+GRLD +T GLLL+T++G L  
Sbjct: 60  RYFMMNKPRGYITANSDASKATVIDLIQKEDFSEELYSIGRLDRDTTGLLLITDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V+ +G +D   +   ++G+           Q+ + +     +  +V
Sbjct: 120 QLLHPQYHVDKTYFVQVNGLLDNQAIEAFQQGVRFLDGKVCKPAQLIIHSATPVLSTASV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++KK+F     KV  L R   G FQL   L  G  R +++  L+
Sbjct: 180 TISEGKFHQVKKMFLAIGVKVTYLKRTHLGDFQLDPNLDEGDYRSLNQDELK 231


>gi|229494843|ref|ZP_04388596.1| pseudouridine synthase, Rsu [Rhodococcus erythropolis SK121]
 gi|229318201|gb|EEN84069.1| pseudouridine synthase, Rsu [Rhodococcus erythropolis SK121]
          Length = 354

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 74/243 (30%), Positives = 113/243 (46%), Gaps = 4/243 (1%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIE 61
            K+         R+ KV+A+AG+ASRR  E +I Q RV+V+G ++    + V      + 
Sbjct: 103 TKHDGPPKGDGVRLQKVLAQAGVASRRAAEELIDQGRVEVDGRIVVEQGLRVDPENAVVR 162

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINT 118
           VDGV +   +       +KP G   T SD  GR  V D +        R+  VGRLD +T
Sbjct: 163 VDGVRVVVQKDLVYLAMNKPRGWQCTMSDDLGRPCVGDIVSERVQSGQRLFHVGRLDADT 222

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLLL TNDG LA  L  PS +  + Y    HG V++     L+ G+ +          T
Sbjct: 223 EGLLLFTNDGDLAHRLMHPSFEVPKTYLATVHGVVERSTGKQLRDGVTLDDGPAKVDAFT 282

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +         V + L EG+   ++++ +     V RL+R + G   LG    G+ R + +
Sbjct: 283 VLEINEGKTLVKLVLHEGRKHIVRRLLDAVGHPVVRLVRTNVGVVALGDQRPGTQRVLGR 342

Query: 239 KIL 241
             +
Sbjct: 343 SEV 345


>gi|330981482|gb|EGH79585.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. aptata str.
           DSM 50252]
          Length = 230

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 104/231 (45%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R++V   +A  RV+V+G         V     + +D   L+  +  
Sbjct: 1   MRLDRFLSNLPRFNRQQVRLALASGRVQVDGQATRDPHHEVREFSCVALDEEILQAGKVP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V+  SD    + +          +   GRLD NT GL+L+TNDG  +R 
Sbjct: 61  RHFMLHKPEGCVSATSDAQHPTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+       +      + +     Q+TL   + +     +
Sbjct: 121 LTQPQTKMPKVYYVETEQPIDERYAAKFAEGLYFAFENLTTQPAQLTLLGPQSA----RL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F  F+ KV RL R + G   L   L  GS R ++   +
Sbjct: 177 SIVEGRYHQVKRMFGHFDNKVLRLHRETIGALALDPNLRPGSYRALNAGEI 227


>gi|237798683|ref|ZP_04587144.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. oryzae str. 1_6]
 gi|331021536|gb|EGI01593.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. oryzae str. 1_6]
          Length = 230

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 60/232 (25%), Positives = 103/232 (44%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R+ V   +A  RV+V+G+        V     +  D   L+  +  
Sbjct: 1   MRLDRFLSNLPRFNRKSVRLALASGRVQVDGLTTSDPHHEVREFSCVMFDTEILQPGKAA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V+  +D    + +          +   GRLD NT GL+L+TNDG  +R 
Sbjct: 61  RYFMLHKPPGCVSATTDAQHPTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D   +    +      + I     Q+ +   + +     +
Sbjct: 121 LTQPQTKMPKVYYVETEQLIDDRYVLKFAEGLYFSFENITTQPAQLNVLGPRSA----HL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EG+  ++K++F  F+ KV RL R S G   L  TL AGS R +    + 
Sbjct: 177 SIVEGRYHQVKRMFGHFDNKVLRLHRESIGALTLDPTLAAGSYRALHAAEID 228


>gi|253996871|ref|YP_003048935.1| pseudouridine synthase [Methylotenera mobilis JLW8]
 gi|253983550|gb|ACT48408.1| pseudouridine synthase [Methylotenera mobilis JLW8]
          Length = 245

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 50/237 (21%), Positives = 96/237 (40%), Gaps = 7/237 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGV 65
           + +  + +R+   +   G  SR+    ++  + V VNG L +           H  + G 
Sbjct: 4   MAKKLSIERI---LHNQGFGSRKLCRILVINEEVTVNGELCDDPDTTFELENLHYTIKGE 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
                E++ L ++       +  +            P +   V  +GRLD +T GL+L++
Sbjct: 61  AWVYHEKSYLMMHKPSNYECSHKTQHHPTIYSLLPHPLVERGVQCIGRLDEDTTGLILIS 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG     +  P  +  +VY V     V  +++  + KG+ +           L   K +
Sbjct: 121 DDGQFIHRMSSPKHKVPKVYEVTCKHAVSDEQIAHILKGVQLVDEDAPIA--ALACTKIN 178

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           +  + + L EGK  ++K++    + +V  L RI  G  +L   L  G  R +S   L
Sbjct: 179 DHVIHMTLAEGKYHQVKRMVAAISNRVEALKRIKIGRLELPQDLKVGEWRWLSASDL 235


>gi|307946012|ref|ZP_07661347.1| ribosomal small subunit pseudouridine synthase A [Roseibium sp.
           TrichSKD4]
 gi|307769676|gb|EFO28902.1| ribosomal small subunit pseudouridine synthase A [Roseibium sp.
           TrichSKD4]
          Length = 233

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 51/227 (22%), Positives = 85/227 (37%), Gaps = 5/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVK-VNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+ K+IA  G  SR+E++  I    V   +G  L+  +      + I  D  PL  A  
Sbjct: 1   MRLVKLIANLGYGSRKEIQTAIKNGWVTDRDGNTLKATSQ--TPHEDILFDDEPLDPAPG 58

Query: 73  TRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             L +        +           + D        + ++GRLD  T GLLL T+DG   
Sbjct: 59  MVLAMNKPLGYTCSTNDQGKLVYDLLPDRYRMRKPVLSTIGRLDKETSGLLLFTDDGTFL 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P     +VY V     +  ++  L   G ++       ++  +           V
Sbjct: 119 HKVISPKANVGKVYEVTLDRPMKGNETALFASGEMMLESEDKPLKPAMLEVLDDTH-ARV 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            L EG+  +++++F      V  L R   G   LG L  G  R + +
Sbjct: 178 ILHEGRYHQVRRMFAATGNHVTNLSRTQIGGLSLGCLEDGQWRMLDE 224


>gi|225419695|ref|ZP_03761998.1| hypothetical protein CLOSTASPAR_06033 [Clostridium asparagiforme
           DSM 15981]
 gi|225041659|gb|EEG51905.1| hypothetical protein CLOSTASPAR_06033 [Clostridium asparagiforme
           DSM 15981]
          Length = 300

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 112/303 (36%), Gaps = 47/303 (15%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----- 68
           +R++K+++  G+ SRRE +R+I   +V V+G+  +     V     +   G  +      
Sbjct: 4   ERLNKLLSAMGVCSRREADRLIESGKVLVDGVPAK-MGQKVRMDQTVVCRGKVVGRGEAA 62

Query: 69  ----------------------------------KAERTRLWLYHKPIGLVTTHSDPDGR 94
                                             K  R  L   +KP G+V T SD D  
Sbjct: 63  AGAGNGKTARRVGSGRADGTAAQDARPASLPRSMKKPRPVLLAVNKPKGVVCTASDKDKA 122

Query: 95  STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD 154
             + D +         VGRLD ++EGL+L+TN G L   +        + Y+V     V 
Sbjct: 123 PNIVDMIQYPVRVYY-VGRLDKDSEGLVLMTNQGDLVNKIMRSGNAHEKEYQVVVDRPVT 181

Query: 155 QDKLNLLKKGIVIQ--GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            + L  ++KG+ ++         +V    +K  +   ++ L +G NR+I+++ E     V
Sbjct: 182 AEFLARMEKGVRLKELDRTTLPCKV----RKTGDKRFSIVLTQGLNRQIRRMCEACGCHV 237

Query: 213 NRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRP 272
             L R+      LG L +G  R+V     RE +                        +  
Sbjct: 238 RSLKRVRVMNICLGDLKSGEYRQVEGAEYREFMKLLEHSTNLSFRQQNAARGPINRMENE 297

Query: 273 NII 275
           N  
Sbjct: 298 NGR 300


>gi|258645939|ref|ZP_05733408.1| ribosomal large subunit pseudouridine synthase B [Dialister invisus
           DSM 15470]
 gi|260403308|gb|EEW96855.1| ribosomal large subunit pseudouridine synthase B [Dialister invisus
           DSM 15470]
          Length = 239

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 69/239 (28%), Positives = 114/239 (47%), Gaps = 5/239 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ K+++ AG+ SRR+ E +I   RV+VNG ++          TD IE  G  ++    
Sbjct: 3   ERLQKILSHAGVCSRRKAEELILAGRVRVNGRVVRELGTEADVCTDKIEALGEIVKPEPL 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +     + +      GR TV D    +  RV  VGRLD ++EGLLL+TNDG L  
Sbjct: 63  RYYLFHKPDCVITSVSDP-AGRRTVMDYFRRVRERVFPVGRLDYHSEGLLLVTNDGQLDF 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVT 190
           +L  P  +  + Y V   G+  +     ++KG+ I        ++ +     + +   + 
Sbjct: 122 ILTHPCHEVQKEYEVVVRGKFSEKLAKKMEKGVKIDSGVTAPCEIEVLGYDAEKNKTRLR 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           + L EGKNREI+K+ E F++ V  L RI Y    L  +  G  R ++   +++    H 
Sbjct: 182 MVLHEGKNREIRKMMEIFHYPVFELKRIRYSFLTL-DVNRGQYRRLTAAEVKKLYELHR 239


>gi|315639358|ref|ZP_07894520.1| RNA pseudouridine synthase [Campylobacter upsaliensis JV21]
 gi|315480684|gb|EFU71326.1| RNA pseudouridine synthase [Campylobacter upsaliensis JV21]
          Length = 253

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 67/248 (27%), Positives = 116/248 (46%), Gaps = 16/248 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K ++     SRRE + +I Q  VK+N  + +  +  V   D I +    + K  + 
Sbjct: 1   MRINKFLSHNTSYSRREADELIKQGLVKINQKIAQ-LSDEVKEEDKIFLKNKRIHKKTQF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +YHK  G + +  D  GR T+++NLP  FS  +SVGRLD  +EGLLLLT+   +A  
Sbjct: 60  SVIIYHKQKGELVSRKDDRGRKTIYENLPKNFSTWLSVGRLDYASEGLLLLTDSPVIADA 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNL--LKKGIVIQGICYG----------DMQVTLDT 181
           L     +     +++        +     L+     +G               +   +  
Sbjct: 120 LMHSDLEREYYLKIKGQISKKVIEAMQNGLEIQNSTKGAHAKTKINSMKFAPFLDFEIFG 179

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI- 240
             G    + V + EG+NRE+++ F +F+ +V  L R+++G  +LG L AG  R + +   
Sbjct: 180 WSGGYTKLRVVINEGQNRELRRFFGYFDLEVMDLKRVAFGIVELGMLKAGKYRFLERGEY 239

Query: 241 --LREQLG 246
             LR+ L 
Sbjct: 240 EKLRDFLK 247


>gi|331005142|ref|ZP_08328543.1| Ribosomal small subunit pseudouridine synthase A [gamma
           proteobacterium IMCC1989]
 gi|330421061|gb|EGG95326.1| Ribosomal small subunit pseudouridine synthase A [gamma
           proteobacterium IMCC1989]
          Length = 232

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 50/229 (21%), Positives = 100/229 (43%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K ++     SR EV+R++    + VN +  + AA+ + +  D I +   PL     
Sbjct: 1   MRLDKYVSSVTDYSRAEVKRLLKNGSITVNDVSTKNAALQLDTQKDIICLFDEPLSAP-A 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R ++ +KPI  +    D    + +         ++   GRLD +T GL+L+T+DG  + 
Sbjct: 60  PRYFMLNKPIDTICATEDSMHPTVIDLLDEPNTQQLHIAGRLDKDTTGLVLITDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P+   ++ YRV       +     L++G+++        + +      +   + + 
Sbjct: 120 QITSPNKHCIKTYRVELEEAFTETAKKALEEGVLLHNEK-KPTRSSTVNI-INKYCIELA 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
           + EGK  ++K++       V +L R   G  QL  +L  G  R ++   
Sbjct: 178 ISEGKYHQVKRMLAAVGNHVKQLHRQQIGHIQLDSSLSLGQYRALTTDE 226


>gi|114563729|ref|YP_751242.1| pseudouridine synthase, Rsu [Shewanella frigidimarina NCIMB 400]
 gi|114335022|gb|ABI72404.1| Pseudouridine synthase, Rsu [Shewanella frigidimarina NCIMB 400]
          Length = 229

 Score =  136 bits (342), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 103/231 (44%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + I ++    + +  ++I    V VNG+++   AV V   + I ++G  L      
Sbjct: 1   MRLDRFICKSTELVKYDAIQLIHNGEVFVNGVVVRNEAVQVHENNDISLNGQKLAARAF- 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  L +KP   + ++ D    S          S +   GRLD NT GL+L+T+DG     
Sbjct: 60  RYMLINKPANTLCSNVDGVYPSLFSLIDVERPSELHIAGRLDANTTGLVLITDDGRWTFA 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  PS Q  +VYRV+    +  D      +GI +QG        Q+ + T +     V +
Sbjct: 120 ITSPSGQCHKVYRVKLAKPIAADAGESFLQGIALQGEQELTLPAQLQIITPQ----EVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            L EGK  ++K++F     KV  L R S G   +  +  G  R +S   ++
Sbjct: 176 TLTEGKFHQVKRMFAAVGNKVVSLHRESIGAVSV-DVAEGEWRYLSVDEVQ 225


>gi|313894552|ref|ZP_07828116.1| putative 16S pseudouridylate 516 synthase [Veillonella sp. oral
           taxon 158 str. F0412]
 gi|313440948|gb|EFR59376.1| putative 16S pseudouridylate 516 synthase [Veillonella sp. oral
           taxon 158 str. F0412]
          Length = 232

 Score =  136 bits (341), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 102/232 (43%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-RAAVNVMSTDHIEVDGVPLRKAER 72
            R+ K++A     SR+EV ++I  +RV +NG +   +     +  D + VDG  +   + 
Sbjct: 1   MRLDKLLANKAFGSRKEVHQIIKDRRVTINGEITTKKDIHIDIDIDTVAVDGQTVNTTQL 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +  +     +                   +   V+ VGRLD +TEGLLLLTNDG    
Sbjct: 61  YYVKFHKPKGYVTAVEDSTHPVVMDLLPPEYLKMGVVPVGRLDKDTEGLLLLTNDGVWGH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +        +VY V F G++ ++ +  +K+GIV+  G       + L     SN   T+
Sbjct: 121 SIINGHKHVPKVYYVEFEGELSEEGIQRIKEGIVLGDGTQCKPALIELL----SNQSATI 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
            + EGK  ++K++       V  L R++ G   L  +   GS  +++   + 
Sbjct: 177 TIEEGKYHQVKRMIGAAGGTVTYLKRLTIGHVDLSGIEEVGSVMDLTIDEVE 228


>gi|170693595|ref|ZP_02884753.1| pseudouridine synthase [Burkholderia graminis C4D1M]
 gi|170141377|gb|EDT09547.1| pseudouridine synthase [Burkholderia graminis C4D1M]
          Length = 239

 Score =  136 bits (341), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 54/231 (23%), Positives = 91/231 (39%), Gaps = 6/231 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD---HIEVDGVPLRKAER 72
           +  ++   G  SRR+   +IA  RV + GI+      +  + D      VDGVP    E 
Sbjct: 3   LESILFSQGFGSRRQCRALIADARVAIGGIVCTDPDADFATDDASFSFSVDGVPWPYREH 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L        +                     V  VGRLD +T GLLLL++DG    
Sbjct: 63  AYLLLNKPAGYECSRDPQHHLSVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGKFVH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +   P  +  +VY       +D  +L+ L+ G+++ G         +D        + + 
Sbjct: 123 MFTSPKRKVPKVYVATTRHPIDDRQLSALRDGVMLHGE--SKAVAAIDAHARGEHSLALT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           + EGK  ++K++      +   L R   G   L  TL  G+ + + +  L+
Sbjct: 181 VMEGKYHQVKRMIAAAGNRCEALHRERVGGLALPATLAPGAWQWLDETELK 231


>gi|329849476|ref|ZP_08264322.1| hypothetical protein ABI_23690 [Asticcacaulis biprosthecum C19]
 gi|328841387|gb|EGF90957.1| hypothetical protein ABI_23690 [Asticcacaulis biprosthecum C19]
          Length = 233

 Score =  136 bits (341), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 47/231 (20%), Positives = 94/231 (40%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVN--GILLERAAVNVMSTDHIEVDGVPLRKAE 71
            ++ K++A  G  SR+E++++I +  +  +  G  L+  +    + D I + G PL  A+
Sbjct: 1   MKLIKLLANLGYGSRKEMQQLIRRGTIT-DAAGQPLDDDSAI--AHDDIRLRGKPLDPAQ 57

Query: 72  RTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              L L+     + +           + +        + +VGRLD +T GLLL+T+DG  
Sbjct: 58  GMILLLHKPTGFVCSTKDRGRLVYELLPERFSLRKPVISTVGRLDSDTSGLLLMTDDGDF 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P     ++Y V     +    + +   G ++       ++       G      
Sbjct: 118 LHKVISPRNHVAKIYEVTTARPISPTYVPVFASGELMLESEKEPLKPAQMEITG-ETTAR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + L EG+  +++++F      V  L R   G   L  L  G  R ++   +
Sbjct: 177 LTLYEGRYHQVRRMFAAVGNHVEALHRAQMGELTLDDLAPGKWRLMTPDDI 227


>gi|242310659|ref|ZP_04809814.1| RNA pseudouridine synthase [Helicobacter pullorum MIT 98-5489]
 gi|239523057|gb|EEQ62923.1| RNA pseudouridine synthase [Helicobacter pullorum MIT 98-5489]
          Length = 250

 Score =  136 bits (341), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 68/241 (28%), Positives = 120/241 (49%), Gaps = 16/241 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ IA     SRRE +R+IAQ +V +N  +++  +  V     + V+G  LRK+E  
Sbjct: 1   MRLNQYIAHHSKYSRREADRLIAQGKVSINKEIIKDFSYQVDDKVKVYVNGKCLRKSEEY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +Y+KP G + +  D  GR T++++LP  F+  I VGRLD  +EGLLLL++D  +   
Sbjct: 61  TVIVYNKPKGELVSKKDDRGRRTIYESLPKRFAHFIPVGRLDFASEGLLLLSDDARVVTK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQVTL 179
           L     +  R+Y ++  G++ ++    ++ G+ +Q                    +   +
Sbjct: 121 LMES--KMERIYLLKLSGKIQEEVFEAMENGLSLQDARAGGHKESKIQSMEFAPFLGYWV 178

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                  + + V + EGKNRE+++ F  F  ++  L RISYG   L  L     R + + 
Sbjct: 179 LKNSTRYSKIKVAINEGKNRELRRFFAHFGLEILDLKRISYGFVSLNNLPTQKVRFLERG 238

Query: 240 I 240
            
Sbjct: 239 E 239


>gi|221194614|ref|ZP_03567671.1| ribosomal large subunit pseudouridine synthase B [Atopobium rimae
           ATCC 49626]
 gi|221185518|gb|EEE17908.1| ribosomal large subunit pseudouridine synthase B [Atopobium rimae
           ATCC 49626]
          Length = 269

 Score =  136 bits (341), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 80/265 (30%), Positives = 130/265 (49%), Gaps = 17/265 (6%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
           E   P R+ + +ARAG+ASRR  ER++ + RV+VNG+++      V  T D +EVDG  +
Sbjct: 4   ERIVPMRLQRFLARAGVASRRGSERLMTEGRVRVNGVVVSELGSKVDPTRDTVEVDGHIV 63

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTN 126
             A+     + +KP G +TT SDP GR T+   +P+        VGRLD++T GLLL T 
Sbjct: 64  GIADAPVYLMLNKPEGYLTTMSDPQGRPTIKTMVPTKRYPGLFPVGRLDMDTSGLLLFTT 123

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------- 179
           DG +A+ L  PS    + Y     G   + +L  L++GI++        +V L       
Sbjct: 124 DGTMAQELLHPSRHVWKHYLALVLGVPTEAELERLRRGIMLDDGMAQPAKVELRDDLLEL 183

Query: 180 --------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                   +  K  NA V + + EG+  ++KK+      +V  L R ++GP +L  +  G
Sbjct: 184 HGTSRYPQNPNKPQNAIVGIWIHEGRKHQVKKMMSAIGHRVLVLHRDAFGPLRLTNVEEG 243

Query: 232 STREVSKKILREQLGPHLLEEAQVN 256
             RE+  + +         ++   +
Sbjct: 244 CWRELRDEEIAALREQTSADKEDAD 268


>gi|157960717|ref|YP_001500751.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157845717|gb|ABV86216.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 234

 Score =  135 bits (340), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 60/245 (24%), Positives = 107/245 (43%), Gaps = 16/245 (6%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+ K          R+ + I+     +++ V  ++A+ +V V+G +       +    H+
Sbjct: 1   MESKRA--------RLDRFISAKTGINKKHVRLLLAKGQVLVDGEVARDIDQIIDEFSHV 52

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            +DG  L+    + + LY     +V+   D   R+ +          +  VGRLD+NT G
Sbjct: 53  CLDGKVLQANAPSYVMLYKPVG-VVSATVDDKHRTVIDLLERDDKHSLHIVGRLDLNTSG 111

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK--KGIVIQGICYGDMQVT 178
           LLLLTNDG  ++ L  P  +  +VYRV     +D+  +           + I     ++ 
Sbjct: 112 LLLLTNDGRWSKKLMSPDHKVGKVYRVTLKNPIDESYIAAFAGGMYFAFEDITTQPAKLE 171

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
           +           V L EG+  +IK++F  F   V  L R+S G  +L   L  G +R++S
Sbjct: 172 IV----DEHTALVTLVEGRYHQIKRMFGRFRNPVIGLHRLSVGAIELDPQLAVGQSRDLS 227

Query: 238 KKILR 242
              ++
Sbjct: 228 MTEIQ 232


>gi|257458444|ref|ZP_05623584.1| ribosomal small subunit pseudouridine synthase A [Treponema
           vincentii ATCC 35580]
 gi|257444145|gb|EEV19248.1| ribosomal small subunit pseudouridine synthase A [Treponema
           vincentii ATCC 35580]
          Length = 246

 Score =  135 bits (340), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 51/237 (21%), Positives = 96/237 (40%), Gaps = 9/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A  G+ S++++ R++ ++  ++NG  +  A   +    D +  +G  L     
Sbjct: 3   VRIDKILAANGLGSQKDIRRLLRKEDFRINGTRVTDAGTLLDPEHDALSRNGETLHLRTC 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L      + +T              P     +  +GRLD++TEGLL++TNDG L  
Sbjct: 63  CYLMLNKPAGVVTSTADPLHSTVMELLPPPFPAMELFPIGRLDLDTEGLLIITNDGALTH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNA 187
            L  P +  ++ Y +       +      +          +            T +    
Sbjct: 123 RLTAPKSACIKSYYLETAEPFTESTFTAARIACAEGLPLGKNFTCLPATFERTTSQRVKT 182

Query: 188 W--VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
                + + EGK  ++KK+ +    +V  L RI+ G   L   L AGS RE++   +
Sbjct: 183 EWAFLMHICEGKYHQVKKMVKALGNEVVYLKRIAMGGVTLDPKLPAGSCRELTPDEI 239


>gi|254446535|ref|ZP_05060011.1| conserved hypothetical protein, putative [Verrucomicrobiae
           bacterium DG1235]
 gi|198260843|gb|EDY85151.1| conserved hypothetical protein, putative [Verrucomicrobiae
           bacterium DG1235]
          Length = 249

 Score =  135 bits (340), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 68/239 (28%), Positives = 115/239 (48%), Gaps = 7/239 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
           ++    R  K++A AGI SRR  E  I    V +NG         V    D + ++G  +
Sbjct: 2   DSPQLIRTQKLLADAGICSRRVAEEYIKNGEVTINGKTA-ELGSKVDPAIDDVRLNGRRI 60

Query: 68  RKAERTRL-WLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLL 124
           +  +  +L    +KP G + ++ DP    TVFD LP      R+   GRLD ++EGLL+L
Sbjct: 61  KVVKHKQLVIALNKPKGFICSNDDPHNDRTVFDLLPTDYNRERLFCAGRLDKDSEGLLIL 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQ 182
           TNDG LA  L  PS    + Y V       + K+  L +G+ ++G      +     D  
Sbjct: 121 TNDGDLANRLMHPSNLVTKRYHVSLKQPFPKAKIFRLMRGVTVEGEKLKVEKAVFAGDKN 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           K  +  + + +  GK REI+++F+  ++ V +L R   G + +  +  G++  +S + +
Sbjct: 181 KAESTELDLAMHHGKKREIRRLFQALHYDVKKLKRYQIGRYSIKGMPKGASIGLSPRDI 239


>gi|311696250|gb|ADP99123.1| pseudouridine synthase, Rsu [marine bacterium HP15]
          Length = 230

 Score =  135 bits (340), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 52/230 (22%), Positives = 98/230 (42%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + IA +   SR+E +R I +  V +N  + + A   +   + + + G PL      
Sbjct: 1   MRLDQFIANSTELSRKEAKRAIGRGEVTINEQICKGANTRLAGDERVALSGTPLSLPGER 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L +      +V+  +D D  + +      I   +   GRLD +T GLLLLT DG  +  
Sbjct: 61  YLMMNKPAG-VVSATTDSDHPTALDLLPAEITRHLHIAGRLDADTTGLLLLTTDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           +  P T   + YRV  +  +       L++G+ +          +V        +  + +
Sbjct: 120 VTSPRTDCPKTYRVTLNEPLSDAAAQQLERGVDLHNDPRPTRPARVHFL----EDRIIEL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
            + EG+  ++K++       V  L R+  G  +L   L+ G  RE++ + 
Sbjct: 176 TISEGRYHQVKRMMAAVGNHVEALHRVRIGQVELDDALMPGEYRELTAEE 225


>gi|221234852|ref|YP_002517288.1| ribosomal small subunit pseudouridine synthase A [Caulobacter
           crescentus NA1000]
 gi|220964024|gb|ACL95380.1| ribosomal small subunit pseudouridine synthase A [Caulobacter
           crescentus NA1000]
          Length = 246

 Score =  135 bits (340), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 45/229 (19%), Positives = 95/229 (41%), Gaps = 7/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMST--DHIEVDGVPLRKA 70
           R+ +++A  G  SR+EV+ ++A  +V ++G +L+ A     V +T  + + + G P+   
Sbjct: 8   RLDRLLANLGYGSRKEVQALVAGGKVVLDGAILKDAGARIAVDATLPERMTIRGAPVDPP 67

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               L ++     + +           +          + +VGRLD +T GL+L+T+DG 
Sbjct: 68  APLVLIMHKPLGVVCSHKEDGEKIYDLLPRRWRLRDPGLSTVGRLDKDTSGLILITDDGD 127

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
               +  P     + Y       ++  +  +   G ++       +         ++A  
Sbjct: 128 FLHRVISPKRHVPKTYLATLDRPLNGSEGEVFAAGTLMLDSEEKPLLPARLDVVNAHA-A 186

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
            + + EG+  +++++F      V  L R   G   L   L AG  R ++
Sbjct: 187 RLTITEGRYHQVRRMFAAVGNHVVALHRERIGGIALPDDLAAGQHRILT 235


>gi|87118320|ref|ZP_01074219.1| hypothetical ribosomal small subunit pseudouridine synthase A
           [Marinomonas sp. MED121]
 gi|86165954|gb|EAQ67220.1| hypothetical ribosomal small subunit pseudouridine synthase A
           [Marinomonas sp. MED121]
          Length = 230

 Score =  135 bits (340), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 47/234 (20%), Positives = 98/234 (41%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I ++   ++ + +  I    VK+N  ++      V + + + +D   L      
Sbjct: 1   MRLDKFICKSTNLNKEQAQAQIQAGIVKINNDIVCDIKAQVHANNQVRLDNRLLYLRPFR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +  +     + +   + +  S            +  VGRLD++T G++L+T+DG  +  
Sbjct: 61  YILFHKPANTICSNLDE-NYPSLFNFLDIEYLDELHIVGRLDVDTTGMVLITDDGHWSFN 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  Q ++ YRV     +D+  +   K G+ +QG     +   L      N  + +  
Sbjct: 120 ITRPEKQCVKEYRVSLSQTLDESAIEQFKYGLKLQGEAELTLPARLTFIDDKNVVLGIT- 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            +GK  ++K++F     +V RL R + G   L  +  G  R +++  +     P
Sbjct: 179 -QGKFHQVKRMFAALGNRVVRLHRQAIGSVTL-DVAEGQWRYLTEAEVASFSAP 230


>gi|315125093|ref|YP_004067097.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni ICDCCJ07001]
 gi|315018815|gb|ADT66908.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni ICDCCJ07001]
          Length = 233

 Score =  135 bits (340), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 68/229 (29%), Positives = 110/229 (48%), Gaps = 17/229 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+     SRRE + +I Q  VK+N  +    +  V   D + V G  ++K  + 
Sbjct: 1   MRINKFISHNTRYSRREADELIKQGLVKINNKIA-LLSDEVKFDDKVFVKGKRVQKRTQF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +YHK  G + +  D  GR T++D LP  FS  +SVGRLD  +EGLLLLT+   +A  
Sbjct: 60  SVIIYHKQKGEIVSKKDDRGRKTIYDTLPRQFSTWLSVGRLDYASEGLLLLTDSPVIADA 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--------------YGDMQVTL 179
           L        R Y ++  G V +  +  ++ G+ I+                    +   +
Sbjct: 120 LMHSD--LEREYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEI 177

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
               G    + V + EGKNRE+++ F  F+ +V  L R+++G   LG L
Sbjct: 178 FGSSGGYTKLRVVINEGKNRELRRFFGHFDLEVMDLKRVAFGALDLGML 226


>gi|322378546|ref|ZP_08052993.1| Pseudouridine synthase [Helicobacter suis HS1]
 gi|321149023|gb|EFX43476.1| Pseudouridine synthase [Helicobacter suis HS1]
          Length = 257

 Score =  135 bits (340), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 63/245 (25%), Positives = 110/245 (44%), Gaps = 13/245 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ IA     SRR+ +++I + +VK+N  L    A      D I V+G  L   E+ 
Sbjct: 6   MRLNQFIAHNLPCSRRQADKLIKEGKVKINRQLA-SFATPFSPYDKIFVEGRMLNSYEKR 64

Query: 74  RL--WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                +YHKP G + +  D  GR T+F++L S F     +GRLD  + GLLLL++   + 
Sbjct: 65  SYTVLVYHKPKGELVSRIDHRGRKTIFESLESKFRHFTPIGRLDFASMGLLLLSDSKQVV 124

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI----------CYGDMQVTLDT 181
             L   S + + + +++ +      +       +                   M   +  
Sbjct: 125 NALMHSSLERVYLVKIQGNITQTMLEAMQTGLELQGLEGAHPKSKYTRMHIAPMACQILK 184

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              + + + + L+EG NREI++ F  F  +V  L R+S+G   L  L  G TR ++ K  
Sbjct: 185 NHRNYSKIKITLQEGHNREIRRFFAHFKKEVLDLRRVSFGFVSLNALPVGKTRYLNPKEY 244

Query: 242 REQLG 246
           ++   
Sbjct: 245 KQLHQ 249


>gi|315498660|ref|YP_004087464.1| pseudouridine synthase [Asticcacaulis excentricus CB 48]
 gi|315416672|gb|ADU13313.1| pseudouridine synthase [Asticcacaulis excentricus CB 48]
          Length = 233

 Score =  135 bits (340), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 52/230 (22%), Positives = 88/230 (38%), Gaps = 7/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVN--GILLERAAVNVMSTDHIEVDGVPLRKAE 71
            R+ K++A  G  SR+EV++ I    V  +  G LL   A        I  +  PL  A 
Sbjct: 1   MRLIKLLANLGYGSRKEVQKYIRMGIVT-DAEGNLLNDDAKTAHED--IRFNERPLDPAH 57

Query: 72  RTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              L L      + +   +       +          + +VGRLD +T GLLL T+DG  
Sbjct: 58  GVVLMLNKPTGYVCSLKDTGKLVYELLPHRFSERKPVLSTVGRLDADTSGLLLFTDDGDY 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P     ++Y V     +   +  +   G ++       ++     Q G      
Sbjct: 118 LHRIISPKNHVAKIYEVTLARPLQGHEAAIFASGELMLESEKTPLKPAAMEQTGEKT-AR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           + L EG+  +++++F      V  L R   G   LG L  G  R ++ + 
Sbjct: 177 LTLYEGRYHQVRRMFAAVGNHVEALHRSQMGDLTLGELRPGKWRLLTTEE 226


>gi|91794227|ref|YP_563878.1| pseudouridine synthase, Rsu [Shewanella denitrificans OS217]
 gi|91716229|gb|ABE56155.1| Pseudouridine synthase, Rsu [Shewanella denitrificans OS217]
          Length = 234

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 52/230 (22%), Positives = 96/230 (41%), Gaps = 8/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A      R+ V  M+   RV V+ ++++   + +     + VDG  L+  +   
Sbjct: 7   RLDQFLAGKLQVPRKSVRFMLLAGRVSVDNMIIKDMDLQLDEFSQVCVDGAALQNNQPCY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L      +V+   D   ++ +          +   GRLD+N+ GLLL+TND   +  L
Sbjct: 67  LMLNKPVG-VVSATKDDIHKTALELLHGIKLEMLHIAGRLDLNSSGLLLITNDARWSEAL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLK--KGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
             P  +  + Y V     +D+  ++          +GI        + ++  +     V 
Sbjct: 126 MSPDNKVSKKYLVTLANPIDETYISAFAGGMYFAFEGITTQAAGFEILSEYQA----RVS 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           L+EGK  +IK++F  F   V  L R + G   L   L  G  R ++   +
Sbjct: 182 LKEGKYHQIKRMFGRFRNPVIGLHREAIGELVLDETLAPGEFRHLTPAEI 231


>gi|227501207|ref|ZP_03931256.1| pseudouridylate synthase [Anaerococcus tetradius ATCC 35098]
 gi|227216608|gb|EEI82012.1| pseudouridylate synthase [Anaerococcus tetradius ATCC 35098]
          Length = 232

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 49/232 (21%), Positives = 105/232 (45%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+I  +G+ +R+ ++R   +  ++VNG +++  ++ V    D +      +   E 
Sbjct: 1   MRLDKMIGNSGLDTRKNIKRNAKKGAIRVNGQVVKDTSIQVDPDLDEVYYMDQFVDYFEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +       ++   D D       +       +   GRLD +T GL+LL+ DG    
Sbjct: 61  IYIMMNKPAG-FLSATEDKDPTVIDILDDFYKGLDLSIAGRLDKDTTGLILLSTDGKFIH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVT 190
            +  P++   + Y+V    ++  D + + ++G+ I          ++ +  +K +   V 
Sbjct: 120 KVTSPNSNIEKTYQVETRDEIKNDLIKIFEEGVYIKEDDYTARPAKLEILEEKKA--LVR 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           V   EGK   +K++F   + +V +L R++ G  +L + L  G  RE+S   +
Sbjct: 178 VT--EGKFHLVKRLFANCDNEVLKLKRLAIGKLKLDSHLAEGEYRELSDDEI 227


>gi|57234401|ref|YP_181521.1| RsuA family pseudouridine synthase [Dehalococcoides ethenogenes
           195]
 gi|57224849|gb|AAW39906.1| pseudouridine synthase, RsuA family [Dehalococcoides ethenogenes
           195]
          Length = 249

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 68/230 (29%), Positives = 110/230 (47%), Gaps = 5/230 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTR 74
           + KV+  A + SRR++   I Q  V +NG   E  +  V +  D +  +G P+  +   R
Sbjct: 11  LVKVLVEARLGSRRKMAEAIKQGLVTLNGQKAESYSQPVNTQQDKVTFEGKPVELSRIRR 70

Query: 75  -LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
              + +KP  +V+T SD  GR TV D L   +       VGRLD  T GLLLLTNDG L 
Sbjct: 71  IYLMLNKPPEIVSTTSDELGRKTVMDLLHRRYEGAGLFPVGRLDETTTGLLLLTNDGELT 130

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  PS +  + Y +     + Q     L+KG+++        +++  T +       +
Sbjct: 131 NRLTHPSYEIEKEYLISIDAALTQADKESLEKGMLLDDGLTSPARLSRVTDEPPYN-YKL 189

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + EGK R ++++F    +++  L R      +LG L  G TRE++   +
Sbjct: 190 IIHEGKKRIVRRMFAHLGYQIKALKRSRIATLRLGKLEEGKTRELTPGEI 239


>gi|171060852|ref|YP_001793201.1| pseudouridine synthase [Leptothrix cholodnii SP-6]
 gi|170778297|gb|ACB36436.1| pseudouridine synthase [Leptothrix cholodnii SP-6]
          Length = 241

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 50/232 (21%), Positives = 94/232 (40%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            ++S+V+   G  +RRE E +I    V V G+++E  +  V        V+G       +
Sbjct: 1   MKLSQVLFSQGFGARRECEGLICAGLVSVGGVVIEEPSHEVAPEGLLFTVEGQTWAYHAK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +        +                     + +VGRLD +T GLLL T+DG L  
Sbjct: 61  ALIVMNKPAGFECSKKPRHHPSIYNLLPAQFKRRDMQTVGRLDEDTTGLLLFTDDGNLIH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----ICYGDMQVTLDTQKGSN-- 186
               P     ++Y       VD+ ++  L  G+V+      +     ++T   +  ++  
Sbjct: 121 RWTSPKHHVPKIYEAGCKHPVDEAQVARLLAGVVLHDDPLPVQALAAEITGAFEHPTHGT 180

Query: 187 -AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
              + + L EGK  ++K++    + +V  L R  +G ++L   L  G  R +
Sbjct: 181 LHGLRLTLAEGKYHQVKRMLAAVSNRVETLHRSGFGAYRLPDDLKLGEWRWL 232


>gi|66768225|ref|YP_242987.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. 8004]
 gi|66573557|gb|AAY48967.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. 8004]
          Length = 542

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 87/359 (24%), Positives = 146/359 (40%), Gaps = 25/359 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG     +  T
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKIELDGRSFVASALT 86

Query: 74  ----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + T        +          SR I++GRLDINT GLLLLT DG 
Sbjct: 87  ESSRVLVYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR      ++      +  L +G++++       ++       
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVPDSMIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV---SKKI 240
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + E+       
Sbjct: 207 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGKVSLPRELLRGQSVELAQEKVDA 266

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRP-----------NIISEVPDDFTRMKKNS 289
           LR +L       + + L   I                      N  +   D+   +++  
Sbjct: 267 LRAELKLEEGAPSALTLQPVIGQRRAAKSTVHVSRDGRSNAYVNGQTSGADEGRELRRFD 326

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           + +     +     P   +   +    A    S       +      RS    +  + R
Sbjct: 327 NLREDRGGRGGRGKPGGFKGGLTVSGEAAAKQSQQRPFKQRGPAKGDRSLPDGNPAAFR 385


>gi|16126081|ref|NP_420645.1| ribosomal small subunit pseudouridine synthase A [Caulobacter
           crescentus CB15]
 gi|13423277|gb|AAK23813.1| ribosomal small subunit pseudouridine synthase A [Caulobacter
           crescentus CB15]
          Length = 241

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 45/229 (19%), Positives = 95/229 (41%), Gaps = 7/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMST--DHIEVDGVPLRKA 70
           R+ +++A  G  SR+EV+ ++A  +V ++G +L+ A     V +T  + + + G P+   
Sbjct: 3   RLDRLLANLGYGSRKEVQALVAGGKVVLDGAILKDAGARIAVDATLPERMTIRGAPVDPP 62

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               L ++     + +           +          + +VGRLD +T GL+L+T+DG 
Sbjct: 63  APLVLIMHKPLGVVCSHKEDGEKIYDLLPRRWRLRDPGLSTVGRLDKDTSGLILITDDGD 122

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
               +  P     + Y       ++  +  +   G ++       +         ++A  
Sbjct: 123 FLHRVISPKRHVPKTYLATLDRPLNGSEGEVFAAGTLMLDSEEKPLLPARLDVVNAHA-A 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
            + + EG+  +++++F      V  L R   G   L   L AG  R ++
Sbjct: 182 RLTITEGRYHQVRRMFAAVGNHVVALHRERIGGIALPDDLAAGQHRILT 230


>gi|149908911|ref|ZP_01897570.1| hypothetical 16S rRNA uridine-516 pseudouridylate synthase
           [Moritella sp. PE36]
 gi|149807922|gb|EDM67865.1| hypothetical 16S rRNA uridine-516 pseudouridylate synthase
           [Moritella sp. PE36]
          Length = 229

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 49/230 (21%), Positives = 100/230 (43%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I ++   +R   +R IA+  VK+NG ++ +A   V +   +   G  L +    
Sbjct: 1   MRLDKFICQSTNLTRTLAKREIARSNVKINGEVVRKADHKVTADMDVWFSGKSLSQRAPR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     ++ +  D +  S +          +   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMMHKPL-DVICSTVDEEHPSVMNLIEADKREELHIAGRLDVDTTGLVLITDDGKWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P     + YRV+    +    +   + GI +  +       ++ + ++K     V +
Sbjct: 120 VTSPKRACNKRYRVQLAEAIAPTAVADFEAGIHLRSEDKPCLPAKLEILSEK----EVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            ++EGK  ++K++F      V  L R   G   L   L  G  R ++ + 
Sbjct: 176 TIQEGKYHQVKRMFASQGNSVVGLHREQIGEIVLDPALELGEWRYLTDEE 225


>gi|313885042|ref|ZP_07818794.1| pseudouridylate synthase [Eremococcus coleocola ACS-139-V-Col8]
 gi|312619733|gb|EFR31170.1| pseudouridylate synthase [Eremococcus coleocola ACS-139-V-Col8]
          Length = 246

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 56/243 (23%), Positives = 98/243 (40%), Gaps = 6/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++      S+ + + +  ++ V V+  ++   ++NV      I+V    +   + 
Sbjct: 1   MRIDRLLQVNDFGSKSDRKHLFQRKIVTVDQRVITDGSINVDPGLQIIKVGNHLITGPQE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +                       + S+GRLD  TEGLL+LT +G L+R
Sbjct: 61  YYWMMNKPAGYVTANKDITKPVVFDLLQAQDRHPDLYSLGRLDRFTEGLLILTTNGPLSR 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V  +G +  D++    +GIVI         Q+ +     S +   V
Sbjct: 121 RLLQPHQHVAKTYAVEVNGFLGYDQVQAFAQGIVIDQSYQCQPAQLQIIQAGSSASRAQV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL---REQLGP 247
            L EGK  ++KK+F     KV +L R+S+    L   L  G  R +    L   +  LGP
Sbjct: 181 TLHEGKFHQVKKMFLSLGVKVTQLKRLSFAGIDLDPDLAPGQYRVLKADELALIKAFLGP 240

Query: 248 HLL 250
              
Sbjct: 241 QKP 243


>gi|21233067|ref|NP_638984.1| ribosomal small subunit pseudouridylate synthase [Xanthomonas
           campestris pv. campestris str. ATCC 33913]
 gi|66770007|ref|YP_244769.1| ribosomal small subunit pseudouridylate synthase [Xanthomonas
           campestris pv. campestris str. 8004]
 gi|188993219|ref|YP_001905229.1| Ribosomal small subunit pseudouridylate synthase [Xanthomonas
           campestris pv. campestris str. B100]
 gi|21114919|gb|AAM42908.1| ribosomal small subunit pseudouridylate synthase [Xanthomonas
           campestris pv. campestris str. ATCC 33913]
 gi|66575339|gb|AAY50749.1| ribosomal small subunit pseudouridylate synthase [Xanthomonas
           campestris pv. campestris str. 8004]
 gi|167734979|emb|CAP53191.1| Ribosomal small subunit pseudouridylate synthase [Xanthomonas
           campestris pv. campestris]
          Length = 237

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 53/232 (22%), Positives = 89/232 (38%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVN--GILLERAAVNVMSTDHIEVDGVPLRKAE 71
            ++ K IA  G  SR++V ++  Q  +  +  G +L  A   V     I +DG PL    
Sbjct: 1   MKLVKHIANLGYGSRKQVTQLFRQGAIT-DAAGEVLY-ADDQVD-HAAIRIDGEPLDPPP 57

Query: 72  RTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              + L+       +   +       +          +  VGRLD  T G+LL+T+DG L
Sbjct: 58  GFSVLLHKPSGYTCSTKDTGRLIYELLPPRFRLRAPVLAPVGRLDRETSGMLLMTDDGAL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P +   +VY V     +  D+  L   G ++       +        G+     
Sbjct: 118 LHRIISPKSALDKVYDVTLAEDLRGDEAALFASGTLLLEGETKPLLPAELEVLGARQ-AR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + L EG+  +++++F      V  L R   G   L  L AG  R +    L 
Sbjct: 177 LTLHEGRYHQVRRMFAAAGNHVVALHRSRIGGLSLDGLDAGHWRPLGPDDLE 228


>gi|319939885|ref|ZP_08014240.1| pseudouridine synthase [Streptococcus anginosus 1_2_62CV]
 gi|319810896|gb|EFW07215.1| pseudouridine synthase [Streptococcus anginosus 1_2_62CV]
          Length = 225

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 57/214 (26%), Positives = 95/214 (44%), Gaps = 3/214 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
              R+ K +   G  SR EV+R++ +++V VNG +   A + +    D I V+   L   
Sbjct: 3   EKMRLDKFLVEMGFGSRTEVKRLLKKKQVLVNGKIETSAKIQIDENQDEISVNNQVLIYK 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                 L      +  T  D         +  +    V  VG LDI+T GLLLLTN+G L
Sbjct: 63  RFVYYLLNKPKGVISATEDDKHRTVLDLLDENARQKEVFPVGWLDIDTHGLLLLTNNGTL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAW 188
           A  +  P     +VYR +  G + +  +   + GI ++       ++T+    ++   + 
Sbjct: 123 AHAMLSPKKHAAKVYRAKVDGIITEKDVEHFEAGIELKDFTCRPAKLTILEVNEEPQTSL 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP 222
           V + + EGK  + K++ +    KV  L R S GP
Sbjct: 183 VEITISEGKFHQEKRMVQACGKKVTDLERFSMGP 216


>gi|171463163|ref|YP_001797276.1| pseudouridine synthase [Polynucleobacter necessarius subsp.
           necessarius STIR1]
 gi|171192701|gb|ACB43662.1| pseudouridine synthase [Polynucleobacter necessarius subsp.
           necessarius STIR1]
          Length = 241

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 49/234 (20%), Positives = 96/234 (41%), Gaps = 4/234 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKA 70
            P  + K++   G  +RR    ++  + VKVNG+L E     +      + V+G      
Sbjct: 3   KPISLEKILFSQGFGTRRYCSDLVYAELVKVNGVLAEDPEERIATENLMLNVEGKDWEYH 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E+  L          +  +            P +   +  VGRLD +T GLLL+++DG  
Sbjct: 63  EKAYLAFNKPANYECSHKTIHHPSVYSLLPSPFVERGLQCVGRLDYDTTGLLLISDDGQF 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P     +VYR+     + Q +++ L  G+V+              ++ S+  + 
Sbjct: 123 IHKMTTPKKNIGKVYRITTSEPITQKQIDHLLNGVVLDDDP-KPC-FATACKQVSDHVLA 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           + + +G+  ++K++       V +L R   G +Q+   L  G  R +    L++
Sbjct: 181 MTIVDGRYHQVKRMMAAVGNHVTQLHRTEIGAYQMPVDLAEGEWRWLYPDDLKQ 234


>gi|57506142|ref|ZP_00372063.1| RNA pseudouridylate synthase family protein [Campylobacter
           upsaliensis RM3195]
 gi|57015537|gb|EAL52330.1| RNA pseudouridylate synthase family protein [Campylobacter
           upsaliensis RM3195]
          Length = 253

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 66/248 (26%), Positives = 115/248 (46%), Gaps = 16/248 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K ++     SRRE + +I Q  VK+N  + +  +  V   D I +    + K  + 
Sbjct: 1   MRINKFLSHNTSYSRREADELIKQGLVKINQKIAQ-LSDEVKDEDKIFLKNKRIYKKTQF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +YHK  G + +  D  GR T+++NLP  FS  +SVGRLD  +EGLLLLT+   +A  
Sbjct: 60  SVIIYHKQKGELVSRKDDRGRKTIYENLPKNFSTWLSVGRLDYASEGLLLLTDSPVIADA 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNL--LKKGIVIQGICYG----------DMQVTLDT 181
           L     +     +++        +     L+     +G               +   +  
Sbjct: 120 LMHSDLEREYYLKIKGQISKKVIEAMQNGLEIQNSTKGAHAKTKINSMKFAPFLDFEIFG 179

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI- 240
             G    + V + EG+NRE+++ F +F+ +V  L R+++G  +LG L  G  R + +   
Sbjct: 180 WSGGYTKLRVVINEGQNRELRRFFGYFDLEVMDLKRVAFGIVELGMLKVGKYRFLERGEY 239

Query: 241 --LREQLG 246
             LR+ L 
Sbjct: 240 EKLRDFLK 247


>gi|238022208|ref|ZP_04602634.1| hypothetical protein GCWU000324_02115 [Kingella oralis ATCC 51147]
 gi|237866822|gb|EEP67864.1| hypothetical protein GCWU000324_02115 [Kingella oralis ATCC 51147]
          Length = 234

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 63/235 (26%), Positives = 108/235 (45%), Gaps = 6/235 (2%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL----WLYHKPIGLVT 86
           +E  I    V+VNG   +     V   D + V G  ++     RL      Y +   +V+
Sbjct: 1   MEEWIGNGWVQVNGKTAQ-LGDKVSPDDQVTVKGSAIKLKWADRLPRILLYYKQEGEIVS 59

Query: 87  THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR 146
                   S       +  SR +++GRLDINT GLL+LT  G L +    P  +  R Y 
Sbjct: 60  RDDPQGRVSVFDRLPQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPKFEVQREYA 119

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
           VR  G+V ++++  L +GI+++       +++    +G+N W  V ++EG+NRE++++FE
Sbjct: 120 VRVLGEVSREQMQQLTQGIMLEDGLAQVERISEQGGEGANKWYNVVIKEGRNREVRRIFE 179

Query: 207 FFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLLEEAQVNLDAP 260
                V+RL+R+ +GP  L   L  G   E++   +   L    +          
Sbjct: 180 HIGLTVSRLVRVGFGPIGLPNRLKRGQFYELNPAEVAAILKWADMALPNSGKRRR 234


>gi|50085470|ref|YP_046980.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter sp. ADP1]
 gi|49531446|emb|CAG69158.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter sp. ADP1]
          Length = 239

 Score =  134 bits (338), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 44/225 (19%), Positives = 87/225 (38%), Gaps = 4/225 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTD-HIEVDGVPLRKAERT 73
           + K++   G  SR+  +++I    V +   + +     +   TD + +V        E+ 
Sbjct: 7   LEKMLQSQGFGSRKYCQQLIKNGAVSIQDEIQKDLKYRIHDLTDFNFQVFDQNYVYREKV 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L        +                 I   + +VGRLD +T GLLLLT+DG     
Sbjct: 67  YIILNKPKGFECSHQPHHHQSVFSLLPDLLIQRNIAAVGRLDQDTTGLLLLTDDGQYLHT 126

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     +VY V     +  D+++ L++G+ +           +         +++ +
Sbjct: 127 LTHPKKHVPKVYHVATIDPITVDQMHQLEQGVELHNEKGVFAATNVTLLN--ETQLSMTI 184

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +G   ++K++      KV  L R   G  +L  L  G    +++
Sbjct: 185 HQGVYHQVKRMIAAVGNKVTALHRHKIGQLELPNLAEGEWMYLTE 229


>gi|145588562|ref|YP_001155159.1| pseudouridine synthase [Polynucleobacter necessarius subsp.
           asymbioticus QLW-P1DMWA-1]
 gi|145046968|gb|ABP33595.1| ribosomal small subunit pseudouridine synthase A [Polynucleobacter
           necessarius subsp. asymbioticus QLW-P1DMWA-1]
          Length = 241

 Score =  134 bits (338), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 45/233 (19%), Positives = 91/233 (39%), Gaps = 4/233 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKA 70
            P  + K++   G  +RR    ++    VKVNG+L E     +      + V+       
Sbjct: 3   KPISLEKILFSQGFGTRRYCSDLVYADLVKVNGVLAEDPEERIATEGLVLTVEDRDWEYH 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E+  +          +  +            P +   +  VGRLD +T GLLL+++DG  
Sbjct: 63  EKAYIAFNKPENYECSHKTTHHPSVYSLLPSPFVERGLQCVGRLDFDTTGLLLISDDGQF 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P     +VY +     + Q +++ L  G+V+           +   + +   + 
Sbjct: 123 IHKMTTPKKNIGKVYEITTPEPITQSQIDHLLNGVVLDDDP-KPC-FAVACNQLTEYTLA 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           + + EG+  ++K++       V +L R   G + +   L  G  R +  + L+
Sbjct: 181 MTIVEGRYHQVKRMMAAVGNHVAKLHRTEIGAYLMPTDLAEGEWRWLYPQDLQ 233


>gi|298369360|ref|ZP_06980678.1| ribosomal small subunit pseudouridine synthase A [Neisseria sp.
           oral taxon 014 str. F0314]
 gi|298283363|gb|EFI24850.1| ribosomal small subunit pseudouridine synthase A [Neisseria sp.
           oral taxon 014 str. F0314]
          Length = 227

 Score =  134 bits (338), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 47/229 (20%), Positives = 90/229 (39%), Gaps = 8/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPL--RK 69
            ++ K I   G+ SR++ + +I    + VNG +   A  ++   +     +DG P+    
Sbjct: 1   MQLLKYIQAQGLGSRKQCQWLIDNGCIAVNGEIRSDAKSSIKPEEVETLAIDGEPIFAVP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 61  LPYFYILLNKPANYETSHKPQQYPSVFSLFPNHMRNIDMQAVGRLDADTTGVLLITNDGQ 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAW 188
               +  P  +  ++YRV      D      LK G+++            +  +      
Sbjct: 121 FNHRVTSPKHKVPKLYRVTLKHAADNRLCETLKNGVLLHDDNETVAADEAVLEK---PTV 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + + EGK  ++K++      +V RL R  +G +    L +GS + + 
Sbjct: 178 LLMTITEGKYHQVKRMVAAAGNRVERLHREKFGDWSADDLPSGSWKFIR 226


>gi|301120326|ref|XP_002907890.1| ribosomal large subunit pseudouridine synthase F, putative
           [Phytophthora infestans T30-4]
 gi|262102921|gb|EEY60973.1| ribosomal large subunit pseudouridine synthase F, putative
           [Phytophthora infestans T30-4]
          Length = 293

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 66/258 (25%), Positives = 109/258 (42%), Gaps = 30/258 (11%)

Query: 8   QENFTP-QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           Q+N     R++K++A+ G+ SRRE E  I    V V+G  ++   + V     + +D   
Sbjct: 37  QDNEKSLVRLAKLMAQKGLCSRREAEAYIQAGDVLVDGERVQADWLKVPVDSDVSLDFRA 96

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------------------FSRV 108
            R   +    + +KP+G V++  + +    V                           ++
Sbjct: 97  QRHQNKKVTLVLNKPLGYVSSQPELNKTPAVRLLTFENECQELSRVKPRQNVEPVALWKM 156

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI- 167
              GRLD+N+ GLLL T DG +A+ L  P     + Y VR    +D     + +K  V+ 
Sbjct: 157 AVCGRLDVNSTGLLLFTQDGTVAKKLLDPKGGIEKEYLVRVDLNLDPLTDKIRRKIEVLQ 216

Query: 168 ------QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
                 +GI Y    V +         + V L EGKNR I+++ E    +V  L R+  G
Sbjct: 217 AGVTSDEGITYRAKSVEILNANQ----LRVVLTEGKNRHIRRMCEHVGLRVMALKRVRIG 272

Query: 222 PFQLGTLLAGSTREVSKK 239
             +LG+L  G  R +   
Sbjct: 273 GVKLGSLPVGQWRYLQPN 290


>gi|86132523|ref|ZP_01051117.1| pseudouridylate synthase [Dokdonia donghaensis MED134]
 gi|85817084|gb|EAQ38268.1| pseudouridylate synthase [Dokdonia donghaensis MED134]
          Length = 296

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 59/240 (24%), Positives = 105/240 (43%), Gaps = 2/240 (0%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K +   +++    R++K IA +G+ SRRE +  I+  +V VNG ++      V   D + 
Sbjct: 53  KKQTQRKKDDGTMRLNKYIANSGVCSRREADMYISIGQVTVNGKVINEMGYQVKIEDDVR 112

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
            DG  +   E     L +KP G  TT S+  G + +     S  SR+  +GRL  N  GL
Sbjct: 113 FDGRRINP-EAKAYVLLNKPKGFATTTSNDKGNTVMDLVAGSTKSRIQPIGRLGRNAMGL 171

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL TND  L +          ++Y +     +       +++G+ I G     ++     
Sbjct: 172 LLFTNDDELVQRFTNSKKGVDKLYHIELSNNLKAADAERIREGLKI-GGKTIMVEEISFV 230

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                  V + ++   N  I+ +FE  N++V R+  ++        L  G  R ++K+ +
Sbjct: 231 DGAPKKEVGLRIKNTGNSIIRTIFEHLNYEVVRVDCVTIAGLTKKDLPRGHWRHLTKQEV 290


>gi|319939632|ref|ZP_08013991.1| pseudouridine synthase [Streptococcus anginosus 1_2_62CV]
 gi|319811221|gb|EFW07527.1| pseudouridine synthase [Streptococcus anginosus 1_2_62CV]
          Length = 241

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 55/232 (23%), Positives = 102/232 (43%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+A   SR+++++ + ++++ V+     + + NV +    I ++  P+     
Sbjct: 1   MRLDVLLAQA-HISRKKMKQALLKKKILVDDCPARKLSQNVDTGLQTITLEEQPVLGKPH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +      +                      ++ SVGRLD +T GLLL+T++G L  
Sbjct: 60  QYFMMNKPLGVVTANSDAKSQTVLDLIKPEDFNDKLYSVGRLDRDTSGLLLITDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V  +G +D   +   +KGIV           +T+ +   + +  TV
Sbjct: 120 QLLHPQYHVTKTYEVEVNGLLDDRAVQSFQKGIVFLDGTSCKPAILTIHSSSSNKSCATV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  +IKK+F     KV  L R  +G F+L     AG  R +++  L 
Sbjct: 180 TISEGKFHQIKKMFLTVGVKVTSLKRTHFGDFELEPNSAAGEYRALNQAELE 231


>gi|69249938|ref|ZP_00605064.1| Pseudouridine synthase, Rsu [Enterococcus faecium DO]
 gi|257878831|ref|ZP_05658484.1| pseudouridine synthase [Enterococcus faecium 1,230,933]
 gi|257881468|ref|ZP_05661121.1| pseudouridine synthase [Enterococcus faecium 1,231,502]
 gi|257890690|ref|ZP_05670343.1| pseudouridine synthase [Enterococcus faecium 1,231,410]
 gi|258615098|ref|ZP_05712868.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecium DO]
 gi|260558396|ref|ZP_05830592.1| pseudouridine synthase [Enterococcus faecium C68]
 gi|261207103|ref|ZP_05921792.1| pseudouridine synthase [Enterococcus faecium TC 6]
 gi|289565895|ref|ZP_06446335.1| pseudouridine synthase [Enterococcus faecium D344SRF]
 gi|293556881|ref|ZP_06675442.1| ribosomal small subunit pseudouridine synthase A, putative
           [Enterococcus faecium E1039]
 gi|293563628|ref|ZP_06678072.1| ribosomal small subunit pseudouridine synthase A, putative
           [Enterococcus faecium E1162]
 gi|293567817|ref|ZP_06679158.1| ribosomal small subunit pseudouridine synthase A, putative
           [Enterococcus faecium E1071]
 gi|294616086|ref|ZP_06695897.1| ribosomal small subunit pseudouridine synthase A, putative
           [Enterococcus faecium E1636]
 gi|294619421|ref|ZP_06698876.1| ribosomal small subunit pseudouridine synthase A, putative
           [Enterococcus faecium E1679]
 gi|294621229|ref|ZP_06700414.1| ribosomal small subunit pseudouridine synthase A, putative
           [Enterococcus faecium U0317]
 gi|314938858|ref|ZP_07846129.1| conserved hypothetical protein [Enterococcus faecium TX0133a04]
 gi|314943663|ref|ZP_07850417.1| conserved hypothetical protein [Enterococcus faecium TX0133C]
 gi|314949098|ref|ZP_07852458.1| conserved hypothetical protein [Enterococcus faecium TX0082]
 gi|314952191|ref|ZP_07855209.1| conserved hypothetical protein [Enterococcus faecium TX0133A]
 gi|314994547|ref|ZP_07859813.1| conserved hypothetical protein [Enterococcus faecium TX0133B]
 gi|314996546|ref|ZP_07861583.1| conserved hypothetical protein [Enterococcus faecium TX0133a01]
 gi|68194054|gb|EAN08603.1| Pseudouridine synthase, Rsu [Enterococcus faecium DO]
 gi|257813059|gb|EEV41817.1| pseudouridine synthase [Enterococcus faecium 1,230,933]
 gi|257817126|gb|EEV44454.1| pseudouridine synthase [Enterococcus faecium 1,231,502]
 gi|257827050|gb|EEV53676.1| pseudouridine synthase [Enterococcus faecium 1,231,410]
 gi|260075570|gb|EEW63876.1| pseudouridine synthase [Enterococcus faecium C68]
 gi|260078731|gb|EEW66433.1| pseudouridine synthase [Enterococcus faecium TC 6]
 gi|289162268|gb|EFD10128.1| pseudouridine synthase [Enterococcus faecium D344SRF]
 gi|291589402|gb|EFF21209.1| ribosomal small subunit pseudouridine synthase A, putative
           [Enterococcus faecium E1071]
 gi|291591049|gb|EFF22747.1| ribosomal small subunit pseudouridine synthase A, putative
           [Enterococcus faecium E1636]
 gi|291594333|gb|EFF25755.1| ribosomal small subunit pseudouridine synthase A, putative
           [Enterococcus faecium E1679]
 gi|291599225|gb|EFF30257.1| ribosomal small subunit pseudouridine synthase A, putative
           [Enterococcus faecium U0317]
 gi|291600965|gb|EFF31256.1| ribosomal small subunit pseudouridine synthase A, putative
           [Enterococcus faecium E1039]
 gi|291604428|gb|EFF33918.1| ribosomal small subunit pseudouridine synthase A, putative
           [Enterococcus faecium E1162]
 gi|313589287|gb|EFR68132.1| conserved hypothetical protein [Enterococcus faecium TX0133a01]
 gi|313591069|gb|EFR69914.1| conserved hypothetical protein [Enterococcus faecium TX0133B]
 gi|313595723|gb|EFR74568.1| conserved hypothetical protein [Enterococcus faecium TX0133A]
 gi|313597700|gb|EFR76545.1| conserved hypothetical protein [Enterococcus faecium TX0133C]
 gi|313641869|gb|EFS06449.1| conserved hypothetical protein [Enterococcus faecium TX0133a04]
 gi|313644514|gb|EFS09094.1| conserved hypothetical protein [Enterococcus faecium TX0082]
          Length = 238

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 102/232 (43%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+I      +R+E++R+ A ++V ++G +  R   NV S    IEV G  L   E 
Sbjct: 1   MRLDKLIEEKLETTRKEMKRLFALKQVMIDGTVEFRQNRNVDSLLHQIEVAGEHLETNES 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                    F  +  VGRLD +T GLLL+T++G L  
Sbjct: 61  -YYLLNKPEKAVTAVSDPEKTTVIDLIASADRFQPLYPVGRLDRDTTGLLLITSNGQLGY 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            + LP  +  + Y+V  + +V    +   + GIV   G       + +       + V +
Sbjct: 120 EMLLPEKKVSKTYQVVVNERVTPADVTAFENGIVFADGYQCKPADLKILKADKHQSTVLL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            ++EGK  ++KK+F     KV  L R+S GP +L   L  G  R ++   ++
Sbjct: 180 TIQEGKFHQVKKMFLAQGKKVTALKRLSMGPLELDEQLGVGEYRSLTLAEMK 231


>gi|294624624|ref|ZP_06703296.1| ribosomal small subunit pseudouridylate synthase [Xanthomonas
           fuscans subsp. aurantifolii str. ICPB 11122]
 gi|294667289|ref|ZP_06732509.1| ribosomal small subunit pseudouridylate synthase [Xanthomonas
           fuscans subsp. aurantifolii str. ICPB 10535]
 gi|292601059|gb|EFF45124.1| ribosomal small subunit pseudouridylate synthase [Xanthomonas
           fuscans subsp. aurantifolii str. ICPB 11122]
 gi|292602961|gb|EFF46392.1| ribosomal small subunit pseudouridylate synthase [Xanthomonas
           fuscans subsp. aurantifolii str. ICPB 10535]
          Length = 237

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 54/232 (23%), Positives = 89/232 (38%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVN--GILLERAAVNVMSTDHIEVDGVPLRKAE 71
            ++ K IA  G  SR++V ++  Q  +  +  G +L  A   V     I VDG PL    
Sbjct: 1   MKLVKHIANLGYGSRKQVTQLFRQGAIT-DAQGEVLY-ADDQVEHGA-IRVDGEPLDPPA 57

Query: 72  RTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              L L+       +   +       +          +  VGRLD  T G+LL+T+DG L
Sbjct: 58  GFSLLLHKPGGYTCSTKDTGRLIYELLPPRFRLRAPVLAPVGRLDRETSGMLLMTDDGAL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P +   +VY V    ++  D+  L   G ++       +        G      
Sbjct: 118 LHRIISPKSALDKVYDVTLAEELRGDEAALFASGSLLLEGETKPLLPAELEVLGPRQT-R 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + L EG+  +++++F      V  L R   G   L  L +G  R +    L 
Sbjct: 177 LTLHEGRYHQVRRMFAAAGNHVVALHRSRIGGLSLDGLPSGQWRALEASDLD 228


>gi|21244403|ref|NP_643985.1| ribosomal small subunit pseudouridylate synthase [Xanthomonas
           axonopodis pv. citri str. 306]
 gi|21110064|gb|AAM38521.1| ribosomal small subunit pseudouridylate synthase [Xanthomonas
           axonopodis pv. citri str. 306]
          Length = 237

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 54/232 (23%), Positives = 89/232 (38%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVN--GILLERAAVNVMSTDHIEVDGVPLRKAE 71
            ++ K IA  G  SR++V ++  Q  +  +  G +L  A   V   D I +DG PL    
Sbjct: 1   MKLVKHIANLGYGSRKQVTQLFRQGAIT-DAQGEVLY-ADDQV-EHDAIRIDGEPLDPPA 57

Query: 72  RTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              L L+       +   +       +          +  VGRLD  T GLLL+T+DG L
Sbjct: 58  GLSLLLHKPSGYTCSTKDTGRLIYELLPPRFRLRAPVLAPVGRLDRETSGLLLMTDDGAL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P +   +VY +     +  D+  L   G ++       +        G      
Sbjct: 118 LHRIISPKSALDKVYDITLAEDLRGDEAALFASGSLLLEGETKPLLPAELEVLGPRQ-AR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + L EG+  +++++F      V  L R   G   L  L +G  R +    L 
Sbjct: 177 LTLHEGRYHQVRRMFAAAGSHVVALHRSRIGGLSLDGLPSGQWRALEASDLE 228


>gi|237749128|ref|ZP_04579608.1| RNA pseudouridine synthase [Oxalobacter formigenes OXCC13]
 gi|229380490|gb|EEO30581.1| RNA pseudouridine synthase [Oxalobacter formigenes OXCC13]
          Length = 242

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 54/234 (23%), Positives = 93/234 (39%), Gaps = 4/234 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++ R G  SR+    ++ Q RV    ++         +   H  VDG      E   
Sbjct: 8   LEKILQRQGFGSRKLCRTLVRQGRVHAGDVVCTDPDRRFETDALHFSVDGEDWVYREHLY 67

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        +                 I   +  VGRLD +T GLLLL++DG      
Sbjct: 68  IVLNKPSGFECSHQPQHHSSVFTLFPTQFIQRGLQCVGRLDQDTTGLLLLSDDGDFIHRY 127

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  +VY +  + ++D+ +L  LK G+ ++      M   L  +      + + + 
Sbjct: 128 TSPKKKVPKVYEISTNAEIDESQLEKLKNGVQLKDETG--MTKALSCESFDEYRMRLVIA 185

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGP 247
           EGK  ++K++      +V +L R + G F L   L AG  R +    L +   P
Sbjct: 186 EGKYHQVKRMVAAAGNRVEKLHRSAIGGFALEESLPAGEWRYLDVNDLNKLDEP 239


>gi|167622881|ref|YP_001673175.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
 gi|167352903|gb|ABZ75516.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
          Length = 234

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 60/246 (24%), Positives = 111/246 (45%), Gaps = 16/246 (6%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+ K          R+ + I+     +++ V  ++A+ +V V+G +     + +    H+
Sbjct: 1   MESKRA--------RLDRFISVKTGINKKYVRLLLAKGQVLVDGEIARDIDLIIDQFSHV 52

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            +DG  L+    + + LY     +V+   D   ++ +          +  VGRLD+NT G
Sbjct: 53  SLDGQVLQANAPSYVMLYKPVG-VVSATIDDKHKTVIDLLDREDKHSLHIVGRLDLNTSG 111

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK--KGIVIQGICYGDMQVT 178
           LLLLTNDG  ++ L  P  +  +VYRV     +D+  +           + I     ++ 
Sbjct: 112 LLLLTNDGRWSKKLMSPQHKVDKVYRVTLKNPIDESYIVAFAAGMYFAFEDITTQPAKLE 171

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
           +      +    V L EG+  +IK++F  F   V  L R+S G  +LG  L  G +R++S
Sbjct: 172 IV----DDHTALVTLVEGRYHQIKRMFGRFRNPVIGLHRLSVGTIELGLQLAVGESRDLS 227

Query: 238 KKILRE 243
           +  ++ 
Sbjct: 228 ESEIQN 233


>gi|54023979|ref|YP_118221.1| putative pseudouridine synthase [Nocardia farcinica IFM 10152]
 gi|54015487|dbj|BAD56857.1| putative pseudouridine synthase [Nocardia farcinica IFM 10152]
          Length = 237

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 73/227 (32%), Positives = 113/227 (49%), Gaps = 5/227 (2%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERTRLWLY 78
           +A+AG+ASRR  E MI Q RV+V+G+++    + +   T  + VDGV +   +       
Sbjct: 2   LAKAGVASRRAAEEMIDQGRVEVDGVIVREQGLRIDPQTAVVRVDGVRVVVRDEQVYVAL 61

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           +KP G  +T SD  GR  V D +        R+  VGRLD +TEGLLLLTNDG LA  L 
Sbjct: 62  NKPKGWQSTMSDDLGRPCVGDIVAERIAAGQRLFHVGRLDADTEGLLLLTNDGDLAHRLM 121

Query: 136 LPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
            PS +  + Y    HG+V    +   L+ GI ++       +  +       + V + L 
Sbjct: 122 HPSFEVSKTYLATVHGEVHHKVIGKRLRDGIELEDGPAKVDRFQVLELGEGRSLVKIVLH 181

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           EG+   ++++ +     V RL+R   GP  LG    G+ R + +  +
Sbjct: 182 EGRKHIVRRLLDAVGHPVTRLVRTHIGPVALGDQRPGTLRVLGRDEI 228


>gi|15606012|ref|NP_213389.1| hypothetical protein aq_554 [Aquifex aeolicus VF5]
 gi|3915394|sp|O66829|Y554_AQUAE RecName: Full=Uncharacterized RNA pseudouridine synthase aq_554;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|2983194|gb|AAC06794.1| hypothetical protein aq_554 [Aquifex aeolicus VF5]
          Length = 238

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 63/236 (26%), Positives = 114/236 (48%), Gaps = 7/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++++   SR+E + +I + RVKV+G ++++A   V   + +EV+G  ++  +  
Sbjct: 1   MRLDKYLSKSLHISRKEAKELIREGRVKVSGKVVKQAEYRVKEGEEVEVEGKSVKPKKNV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLAR 132
            L LY     L TT  D    S +        SR   S GRLD++ EGLLL+T+DG LA 
Sbjct: 61  YLMLYKPKGYLSTTEEDKKYPSFLELIREHFPSRKLFSAGRLDVDAEGLLLITDDGELAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + Y VR    +  ++L  L + + ++      ++    +       V   
Sbjct: 121 RLTHPKWKVEKEYIVRLDRDIGDEELKKLYE-VKLEEKPVQLVKAEKLSGD----TVKAI 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGP 247
           L EG++  +K++F+     V  L R   G  +L   +  G  RE++++ ++E    
Sbjct: 176 LTEGRHHVVKRLFKAVGHNVVYLKRTRVGNLRLDENMEPGEWRELTEEEVKELKRL 231


>gi|260909948|ref|ZP_05916635.1| ribosomal large subunit pseudouridine synthase B [Prevotella sp.
           oral taxon 472 str. F0295]
 gi|260635898|gb|EEX53901.1| ribosomal large subunit pseudouridine synthase B [Prevotella sp.
           oral taxon 472 str. F0295]
          Length = 211

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 51/203 (25%), Positives = 87/203 (42%), Gaps = 1/203 (0%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           VKVNG ++      V+ TD +     P+   ++  + +      + T+      ++ +  
Sbjct: 2   VKVNGNVVTELGTKVLRTDEVIFHEQPVTLEKKVYVLINKPKDYVTTSDDPQQRKTVMDL 61

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
                  R+  VGRLD NT G+LLLTNDG LA  L  P     +VY V    +V +  L 
Sbjct: 62  VKGVCPERIYPVGRLDRNTTGVLLLTNDGDLASKLAHPKFLKKKVYHVFLDKEVTEHDLQ 121

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
            +  G+ +                     V + +  GKNR ++++FE   ++V RL R+ 
Sbjct: 122 QIATGVTLDDGEVH-ADAIEYANDKDKTQVGIEIHSGKNRIVRRIFESLGYRVVRLDRVQ 180

Query: 220 YGPFQLGTLLAGSTREVSKKILR 242
           +       L  G  R +++K + 
Sbjct: 181 FAGLTKKNLKRGDWRFLTEKEVD 203


>gi|186475366|ref|YP_001856836.1| pseudouridine synthase [Burkholderia phymatum STM815]
 gi|184191825|gb|ACC69790.1| pseudouridine synthase [Burkholderia phymatum STM815]
          Length = 234

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 52/225 (23%), Positives = 89/225 (39%), Gaps = 4/225 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  V+   G  SRR+   MIA  RV + G  L+   ++V +   + EVDG      ER  
Sbjct: 3   LESVLFSQGFGSRRQCRAMIADGRVSIGGATLDDPDIDVDAKALVFEVDGTVWPYHERAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        +                     +  VGRLD +T GLLLL++DG      
Sbjct: 63  VLLNKPAGYECSRDPQHHLSVFNLLPAQFATRGIQCVGRLDQDTTGLLLLSDDGQFVHAY 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y       +D  +L  L++G+++ G         +     S   + + + 
Sbjct: 123 TSPKRKVPKRYLATTRHPLDDAQLAALREGVLLHGEAKR--IAAVAAHARSAHELELTVL 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
           EGK  ++K++      +V  L R   G   L   L  G+ + + +
Sbjct: 181 EGKYHQVKRMVAAAGNRVEALHRERIGGLALPAELAEGAWQWLDE 225


>gi|330950091|gb|EGH50351.1| pseudouridine synthase, Rsu [Pseudomonas syringae Cit 7]
          Length = 230

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 59/232 (25%), Positives = 104/232 (44%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R++V   +A  RV+V+G         V     + +D   L+  +  
Sbjct: 1   MRLDRFLSNLPRFNRQQVRLALASGRVQVDGQATRDPHHEVREFSCVALDEEILQAGKAA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V+  SD    + +          +   GRLD NT GL+L+TNDG  +R 
Sbjct: 61  RYFMLHKPEGCVSATSDAQHPTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+       +      + I     Q+TL   + +     +
Sbjct: 121 LTQPQTKMPKVYYVETEQPIDERYAAKFAEGLYFAFENITTQPAQLTLLGPRSA----RL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EG+  ++K++F  F+ KV RL R + G   L   +  GS R ++   + 
Sbjct: 177 SIVEGRYHQVKRMFGHFDNKVLRLHRENIGALALDHDVPPGSYRALNVGEID 228


>gi|90023354|ref|YP_529181.1| pseudouridine synthase, Rsu [Saccharophagus degradans 2-40]
 gi|89952954|gb|ABD82969.1| Pseudouridine synthase, Rsu [Saccharophagus degradans 2-40]
          Length = 249

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 57/234 (24%), Positives = 94/234 (40%), Gaps = 12/234 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I+     +RR+V   IAQ+R+ VNG         V    HI  D   L+      
Sbjct: 7   RLDRFISLNSNLNRRDVRLAIAQKRILVNGKHASTIHQVVSQFCHITFDNQTLQANAPVY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L      + +   D    + V      + + +  VGRLD N+ GL+LLTN+G  +R L
Sbjct: 67  IMLNKPAGRV-SATKDSTHPTVVGCLPQQLQANIHIVGRLDFNSTGLMLLTNNGAWSRHL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLK------KGIVIQGICYGDMQVTLDTQKGSNAW 188
             P  +  ++Y V     ++ D+                + +     ++   T   +   
Sbjct: 126 TSPENKVNKIYEVELERTINDDEWPQYISAFASGMYFAFEDLTTQPAKLERLTATRA--- 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
             V L EG+  +IK++F  F  KV  L R   G   L   L  G  R ++   +
Sbjct: 183 -RVTLVEGRYHQIKRMFGRFRNKVIALHRTQLGALPLDPALQPGEHRLLNDDEI 235


>gi|295689516|ref|YP_003593209.1| pseudouridine synthase [Caulobacter segnis ATCC 21756]
 gi|295431419|gb|ADG10591.1| pseudouridine synthase [Caulobacter segnis ATCC 21756]
          Length = 246

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 44/232 (18%), Positives = 88/232 (37%), Gaps = 7/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMST--DHIEVDGVPLRKA 70
           R+ +++A  G  SR+EV+ ++A  +V ++G  L+ A +   V +T  + + + GV +   
Sbjct: 8   RLDRLLANLGYGSRKEVQALVAAGKVVLDGKPLKDAGLRIAVDATLPERMTIRGVAVDPP 67

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               L ++     + +           +          + +VGRLD  T GL+L+T+DG 
Sbjct: 68  APLVLMMHKPLGVVCSHKEDGEKIYDLLPRRWRLRDPALSTVGRLDKETSGLILITDDGD 127

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
               +  P     + Y  R    +   +      G ++       +              
Sbjct: 128 FLHRVISPKRHVPKTYLARLDRPLSGSEGETFAAGTLMLEGEEKPLLPARLEI-VDERTA 186

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
            + + EG+  +++++F      V  L R   G   L   L  G  R +    
Sbjct: 187 RLTITEGRYHQVRRMFAAVGNHVTDLHRERIGRLVLPDDLEPGQHRILPAGE 238


>gi|87120569|ref|ZP_01076463.1| hypothetical 16S rRNA uridine-516 pseudouridylate synthase
           [Marinomonas sp. MED121]
 gi|86164212|gb|EAQ65483.1| hypothetical 16S rRNA uridine-516 pseudouridylate synthase
           [Marinomonas sp. MED121]
          Length = 230

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 100/231 (43%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+   +A A   SR+E +  IA+ RV VNG    +A   V     + +D  PL   +  
Sbjct: 1   MRLDYYLAHAANLSRKEAKIAIAKGRVLVNGESKLKANSPVTDLCDVILDKSPLSFQQNR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +Y     +V    D +    +      I   +  VGRLD +T GLLLLT DG     
Sbjct: 61  YYMMYKPAG-VVCALQDDEHDVVLDLLPHEIQKELKIVGRLDKDTTGLLLLTTDGQWLHK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V    ++ +D +  L+KG++++G        +V   T+K     +++
Sbjct: 120 ITSPKHDCPKTYLVDLADEITKDAIEALEKGVLLKGEIDLTKPAKVVSHTEKQ----ISL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++K++      KV  L R   G   L   +  G   E+S + +
Sbjct: 176 TISEGKYHQVKRMLAAVGNKVEALHRTQIGEVCLSQDMALGEFTELSPEQV 226


>gi|241758832|ref|ZP_04756945.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           flavescens SK114]
 gi|241321040|gb|EER57253.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           flavescens SK114]
          Length = 227

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 47/228 (20%), Positives = 92/228 (40%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLR--K 69
            ++ K I   G+ SR++ + +I    + +NG +  RA  N+  +    + VDG  +    
Sbjct: 1   MQLLKYIQSQGLGSRKQCQWLIDNDCIAINGEIHNRAKDNIDPSQVHTLSVDGEEIAAVP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L+       +                     + +VGRLD +T G++L+TNDG 
Sbjct: 61  MPHFYILLHKPADYETSHKPQQYPSIFSLFPDHMRNIDMQAVGRLDADTTGIILITNDGQ 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAW 188
               +  P  +  ++YRV      D      LK G+++            + T       
Sbjct: 121 FNHRVTSPKHKVPKLYRVTLKHPADDTLCTTLKNGVLLHDDNETVAAAEAVLT---DPTT 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + + EGK  ++K++      +V +L R  +G + +  L AG  + +
Sbjct: 178 LMMTITEGKYHQVKRMVAAAGNRVEQLHREKFGDWNVDDLAAGEWKFI 225


>gi|331006460|ref|ZP_08329763.1| Ribosomal small subunit pseudouridine synthase A [gamma
           proteobacterium IMCC1989]
 gi|330419760|gb|EGG94123.1| Ribosomal small subunit pseudouridine synthase A [gamma
           proteobacterium IMCC1989]
          Length = 235

 Score =  134 bits (336), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 48/240 (20%), Positives = 99/240 (41%), Gaps = 12/240 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   ++ +  + I    V VNG ++   +  V   + + + GV L   +  
Sbjct: 1   MRLDKFVCKSTQLTKADAVQCIHLGEVGVNGEVITSESTQVHENNTVTLRGVKLIARDFR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + ++     + +   D    S          S +   GRLD++T GL+L+T+DG     
Sbjct: 61  YILMHKPAGTICSN-IDEVYPSLFNSLDVENVSELHIAGRLDVDTTGLVLITDDGRWTFD 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLN----LLKKGIVIQGIC--YGDMQVTLDTQKGSNA 187
           + +PS Q  + YRV     +  D ++        G+ +QG         + +     +  
Sbjct: 120 ITVPSKQCAKTYRVTLSRGIAADGVDDLVSRFAAGVKLQGEQQLTLPATLQVI----TPT 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V + + EGK  ++K++F     +V  L R   G   L  +  G  R ++ + ++  +  
Sbjct: 176 EVLLTITEGKFHQVKRMFAAVGHRVVALHRERIGDICL-DVDVGQWRYLTDEEVKSVVRH 234


>gi|332519089|ref|ZP_08395556.1| RNA-binding S4 domain protein [Lacinutrix algicola 5H-3-7-4]
 gi|332044937|gb|EGI81130.1| RNA-binding S4 domain protein [Lacinutrix algicola 5H-3-7-4]
          Length = 285

 Score =  134 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 48/239 (20%), Positives = 107/239 (44%), Gaps = 3/239 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
            N    R++K +A AGI SRR+ +  IA   V VNG ++      V   D +  DG  + 
Sbjct: 50  SNSNEIRLNKYVANAGICSRRDADVHIATGLVTVNGKVVTEMGYKVKLEDEVRYDGARIN 109

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ++  + L        TT S+  G++ +     +  SR+  +GRL  N+ GLLL TND 
Sbjct: 110 PEKKAYVLLNKPKG-FATTTSEYKGKTVMDLVANATSSRIKPIGRLGRNSTGLLLFTNDD 168

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +       +   +R++ +     +  + L  +++G+ I+G      +  +D        
Sbjct: 169 KVVDRFTNSNKGVVRLFHLELDKNLKLEDLKKIREGLRIEGKQINVEE--IDYVDNRKNE 226

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           + + ++   N  +  +F++F +++ ++  +         +  G+ + ++++ ++  +  
Sbjct: 227 IGIKIKNTGNTILHTIFDYFKYELVKIDCVQIAHLTKKDIPRGNWKILTEQEVQTLMMM 285


>gi|42524638|ref|NP_970018.1| putative pseudouridylate synthase [Bdellovibrio bacteriovorus
           HD100]
 gi|39576848|emb|CAE78077.1| putative pseudouridylate synthase [Bdellovibrio bacteriovorus
           HD100]
          Length = 265

 Score =  134 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 73/258 (28%), Positives = 122/258 (47%), Gaps = 7/258 (2%)

Query: 34  MIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPL-RKAERTRLWLYHKPIGLVTTHSDP 91
           MI +  V VNG  +    + V   +D I VDG PL +   +    + +KP G++TT  DP
Sbjct: 1   MIEEGLVTVNGKRVYELGIKVDPQSDRILVDGKPLRKPLTQKIYAILNKPTGVLTTMDDP 60

Query: 92  DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151
             R TV + L  +  RV  VGRLD ++EG+LLLTNDG  A  +  P  +  + Y V+ +G
Sbjct: 61  HDRPTVAEYLTELPVRVFPVGRLDWDSEGMLLLTNDGDFANKVMHPKAEVTKTYLVKLNG 120

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA-----WVTVGLREGKNREIKKVFE 206
           + +  +L  LKKG+ I G       +    + G N      W  + + EGKNR+I+++F 
Sbjct: 121 KPEPFQLEKLKKGVSIVGGKVSARHIEKIKKTGDNKSEKYEWYKIVITEGKNRQIRQMFA 180

Query: 207 FFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSET 266
              + V RL R++ G  ++G +  G    ++   ++        EE +        ++  
Sbjct: 181 KIGFDVMRLQRVAIGRLRMGAVKTGELVYLNDAAVQRVFLADDPEEIKTKRTYKGRATSE 240

Query: 267 LVRDRPNIISEVPDDFTR 284
               +P    +     ++
Sbjct: 241 KKTAKPASKVKTTKKPSK 258


>gi|217077200|ref|YP_002334918.1| RNA pseudouridine synthase family protein [Thermosipho africanus
           TCF52B]
 gi|217037055|gb|ACJ75577.1| RNA pseudouridine synthase family protein [Thermosipho africanus
           TCF52B]
          Length = 225

 Score =  134 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 50/230 (21%), Positives = 100/230 (43%), Gaps = 9/230 (3%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           ++ A + SR++V+++I ++RVKVNG ++ +   NV   D + VD + +       +    
Sbjct: 1   MSNAKVGSRKQVKKLIKEKRVKVNGSIVTKPEFNVDENDEVFVDDIEIIPHHNVYIVFNK 60

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
                 +       R+            +  VGRLD + EGL+L+TNDG     +  P +
Sbjct: 61  PSGFTSSKS--EYERNIFEFIDHPYLDELHIVGRLDKDVEGLILITNDGNFTHKVISPKS 118

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVGLREGKN 198
              + Y V+  G + ++ + +   GI +     +   ++T    +     +++ + EGK 
Sbjct: 119 NIEKEYIVKIEGILTKEMIEIASNGITLNNGIKFKPAKITKIDDE----TISLVITEGKF 174

Query: 199 REIKKVFEFFNWKVNRLIRISYGP--FQLGTLLAGSTREVSKKILREQLG 246
            E+K +  F   K  ++ R+  G        L  G  +E+     ++ L 
Sbjct: 175 HEVKLIVGFLGLKYKKIKRVRIGKLNLNDFNLNLGEWKEIDYNTAKKALE 224


>gi|163750086|ref|ZP_02157329.1| putative ribosomal small subunit pseudouridine synthase A
           [Shewanella benthica KT99]
 gi|161330143|gb|EDQ01125.1| putative ribosomal small subunit pseudouridine synthase A
           [Shewanella benthica KT99]
          Length = 233

 Score =  134 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 58/244 (23%), Positives = 106/244 (43%), Gaps = 16/244 (6%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+ K          R+ + I+     +R+ V  ++A+  V+V+G +       +     +
Sbjct: 1   MQSKRA--------RLDRFISVKTGINRKNVRLLLAKGLVEVDGDIARNIDQIIDEFSDV 52

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            ++G  L+    + + L+     +V+   D   ++ +          +  VGRLD+NT G
Sbjct: 53  SLEGEVLQSNSPSYVMLHKPVG-VVSATVDDKHKTVIDLLTDKSKHDLHIVGRLDLNTSG 111

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVT 178
           LLLLTNDG  ++ L  P  +  ++YRV     +D   +    +      + I     Q+ 
Sbjct: 112 LLLLTNDGRWSKKLMSPHHKVGKLYRVTLQNPIDDSYVKAFAEGIYFEFEDIITKPAQLA 171

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVS 237
           L      +    V L EG+  +IK++F  F   V  L RIS G   L + L  G +R ++
Sbjct: 172 LV----DSHTALVTLVEGRYHQIKRMFGRFRNPVIGLHRISVGKILLDSQLTPGMSRSLT 227

Query: 238 KKIL 241
            + +
Sbjct: 228 AQEI 231


>gi|221133423|ref|ZP_03559728.1| pseudouridine synthase [Glaciecola sp. HTCC2999]
          Length = 226

 Score =  134 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 50/224 (22%), Positives = 99/224 (44%), Gaps = 4/224 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++++ + +  +V  +IA+  + VN  + +  +  V   + +      L      
Sbjct: 1   MRLDKYVSKSTVLTAAQVLEVIARGEISVNDSVTDDPSYQVHKNNTVHWLDTRLECRPFR 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L   P  + +   +         ++P      I+ GRLD +T GL+L+T+DG  +  
Sbjct: 61  YIMLNKPPNMICSNIDEHYPSVFNLVDIPHQHELHIA-GRLDADTTGLVLITDDGSWSYR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     +VYRV     +  D +  L+KG+++QG     +   +D    +   V + +
Sbjct: 120 LTHPDNHCPKVYRVCLAKPISDDMIMRLEKGVLLQGESAPTLPAAIDVVGAN--EVLLTI 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +GK  ++K++F     +V  L R + G   L  +  G  R +S
Sbjct: 178 TQGKFHQVKRMFAAVGNRVKALHREAIGEINL-DVEVGQWRYIS 220


>gi|256420249|ref|YP_003120902.1| pseudouridine synthase [Chitinophaga pinensis DSM 2588]
 gi|256035157|gb|ACU58701.1| pseudouridine synthase [Chitinophaga pinensis DSM 2588]
          Length = 516

 Score =  134 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 67/229 (29%), Positives = 116/229 (50%), Gaps = 4/229 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           ++K IA +G+ SRR+    + + +V VNG L+   A  V + D + ++   +   +    
Sbjct: 282 LNKYIAHSGLCSRRKAVDFVKEGKVTVNGELITEPAFKVTAKDEVAINNRKINIQKNLVY 341

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            L +KP G +TT  DP+GR TV + +        RV  VGRLD NT GLLLLTNDG LA+
Sbjct: 342 ILLNKPKGYITTTDDPEGRKTVMELIQDATTEEQRVYPVGRLDRNTSGLLLLTNDGELAQ 401

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     ++Y V  +  + +     + +G+ ++        +    + G    V + 
Sbjct: 402 KLAHPKHNIKKIYHVGLNKPLTKAHFENILQGVTLEDGVANVDALGYV-EAGDKTQVGIE 460

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +  GKNR ++++FE   ++V +L R++Y       +  G  R +++K +
Sbjct: 461 IHSGKNRIVRRIFEHLEYEVEKLDRVTYAGLTKKNINRGKWRFLTEKEI 509


>gi|115352585|ref|YP_774424.1| pseudouridine synthase, Rsu [Burkholderia ambifaria AMMD]
 gi|115282573|gb|ABI88090.1| ribosomal small subunit pseudouridine synthase A [Burkholderia
           ambifaria AMMD]
          Length = 238

 Score =  133 bits (335), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 53/234 (22%), Positives = 87/234 (37%), Gaps = 4/234 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV V G        +  +   +  VD        R  
Sbjct: 3   LESILYTQGFGSRRQCRGLIETGRVTVAGASATDPDASFDTDGLVFTVDDTAWPFHARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L        +               P +   V  VGRLD +T GLLLL++DG      
Sbjct: 63  LALNKPAGYECSRDPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFVHAY 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y       +D  +LN L+ G+ + G     +             + + + 
Sbjct: 123 TSPKRKVPKTYVATVRHPLDDTQLNALRAGVQLHGEP-KPIAAVAAHA-RDTHALALTVL 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
           EGK  ++K++    + +V  L R S G F L   L  G+ R + ++ L     P
Sbjct: 181 EGKYHQVKRMVAAASNRVEALHRESIGGFTLPEDLAPGAWRWLGERELSALRDP 234


>gi|332527071|ref|ZP_08403153.1| RNA-binding S4 domain-containing protein [Rubrivivax
           benzoatilyticus JA2]
 gi|332111503|gb|EGJ11486.1| RNA-binding S4 domain-containing protein [Rubrivivax
           benzoatilyticus JA2]
          Length = 255

 Score =  133 bits (335), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 64/248 (25%), Positives = 97/248 (39%), Gaps = 24/248 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG------- 64
              RVSK+I   G+ASRRE +  I    VKV+G +         +   IE+D        
Sbjct: 10  EGVRVSKLITERGLASRREADAWIEAGWVKVDGKMA-VLGQRAAADCRIEIDPRARNEQA 68

Query: 65  --------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
                    P+          Y     LV   +      T     P     +   GRLDI
Sbjct: 69  RRVTVLLHKPMGFVSGQAEDGYKPAATLVIPANRWKDDPTRLAFHPGQLRGLAPAGRLDI 128

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN----LLKKGIVIQGICY 172
           ++ GLL+LT DG +A+ L    T+  + Y VR          +     L+ G+ + G   
Sbjct: 129 DSTGLLVLTQDGRIAKTLIGDETKVEKEYLVRVQYTKPGRLPDADLERLRHGLELDGRPL 188

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
              +V+   +      +   LREG+ R+I+++ E    KV  L R+  G   LG L  G 
Sbjct: 189 RPARVSWQNEDQ----LRFVLREGRKRQIRRMCELVGLKVVGLKRVRIGSVSLGQLPPGQ 244

Query: 233 TREVSKKI 240
            R + +  
Sbjct: 245 WRYLGENE 252


>gi|218682423|ref|ZP_03530024.1| pseudouridine synthase [Rhizobium etli CIAT 894]
          Length = 538

 Score =  133 bits (335), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 59/206 (28%), Positives = 96/206 (46%), Gaps = 1/206 (0%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTRLW 76
           + +++ G  SR + ER+IA+ RV V+G  +   +  V  +T  I VDG+ +    +  L 
Sbjct: 24  RALSKLGYCSRTQAERLIAESRVAVDGRTISDTSAWVDLATAKISVDGLVIAAETKIYLM 83

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L      + T H      +            +  VGRLD  +EGLLL TND   A++L  
Sbjct: 84  LNKPRGLVTTRHDPEGRPTVYDCLRDFDIPHLSPVGRLDKASEGLLLFTNDTEFAQILLD 143

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
           P T   + Y V+    +D + +  +  GI   G            Q   N+W+ V L EG
Sbjct: 144 PVTHVTKTYHVQIDRIMDDEAIAAMTSGIRHDGELLTATAARRLRQGDRNSWIEVELDEG 203

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGP 222
           +NR+I+++ E    +  RL+R++ G 
Sbjct: 204 RNRQIRRMLEALGTECLRLVRVAIGR 229


>gi|188581487|ref|YP_001924932.1| pseudouridine synthase [Methylobacterium populi BJ001]
 gi|179344985|gb|ACB80397.1| pseudouridine synthase [Methylobacterium populi BJ001]
          Length = 242

 Score =  133 bits (335), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 57/241 (23%), Positives = 98/241 (40%), Gaps = 7/241 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV----MSTDHIEVDGVPL 67
              R+ +++A  G  SRREVE +     V+ +G  L  A+  +      +  + V G PL
Sbjct: 2   KAVRLDRLLANLGYGSRREVEGLARAGLVRRDGEALRDASQRIALEPDLSARMTVQGAPL 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                  L L+       +         S + +        + +VGRLD  T GLLL+T+
Sbjct: 62  DPLPGVCLMLHKPLGVTCSHKEAGPLIYSLLPERWRRRDPALSTVGRLDKETSGLLLMTD 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L   +  P  +  + YRV     +  D+  +L  G ++       + + ++ +    
Sbjct: 122 DGALLHRIIAPKAKVAKRYRVTLARPLQGDEAAILASGELMLEGEDKPL-LPVEMEGEDA 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
              TV L EG+  +++++F      V+ L R   G   L   L AG  R +    +    
Sbjct: 181 THCTVTLHEGRYHQVRRMFAALGNHVDALHRDRVGGLALPADLPAGEFRILGPGEIAAVF 240

Query: 246 G 246
           G
Sbjct: 241 G 241


>gi|221064931|ref|ZP_03541036.1| RNA-binding S4 domain protein [Comamonas testosteroni KF-1]
 gi|220709954|gb|EED65322.1| RNA-binding S4 domain protein [Comamonas testosteroni KF-1]
          Length = 700

 Score =  133 bits (335), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 67/251 (26%), Positives = 104/251 (41%), Gaps = 29/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA  G+ SRRE +  +    V VNG +      NV+  D IE+D     + ++ 
Sbjct: 453 VRINKRIADMGLCSRREADEWVENGWVTVNGEVAT-MGQNVVPGDRIEIDQKAQDRQDQQ 511

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---------------ISVGRLDINT 118
              L +KP+G V+  ++      V                             GRLDI++
Sbjct: 512 VTILLNKPMGYVSGQAEDGHEPAVVLITNENRWNEDRSKTRFNFSQLKGLAPCGRLDIDS 571

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQG 169
            GLL+LT DG +AR +    ++  + Y VR               ++KL LL+ G+ +  
Sbjct: 572 VGLLVLTQDGRVARQIIGEDSEVDKEYLVRVTFGDRDVDVQSVFPEEKLALLRHGLSLDE 631

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                 QV     +     +   L EGK R+I+++ E    KV  L RI  G   LG L 
Sbjct: 632 QPLKPAQVDWQNPEQ----LRFVLTEGKKRQIRRMCEQVGLKVVGLKRIRIGGVTLGNLP 687

Query: 230 AGSTREVSKKI 240
            G  R ++   
Sbjct: 688 TGQWRYLAAHE 698


>gi|78067288|ref|YP_370057.1| ribosomal small subunit pseudouridine synthase A [Burkholderia sp.
           383]
 gi|77968033|gb|ABB09413.1| ribosomal small subunit pseudouridine synthase A [Burkholderia sp.
           383]
          Length = 238

 Score =  133 bits (335), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 53/234 (22%), Positives = 85/234 (36%), Gaps = 4/234 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV V G           +   +  VD           
Sbjct: 3   LESILYTQGFGSRRQCRGLIEAGRVTVAGASATDPDATFDTDGLVFSVDDTAWPFHAHAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L        +               P +   V  VGRLD +T GLLLL++DG      
Sbjct: 63  LALNKPAGYECSRDPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFVHAY 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y       +D  +LN L+ G+ + G     +   +         + + + 
Sbjct: 123 TSPKRKVPKTYVATVRHPLDDTQLNTLRTGVQLHGEP-KPI-AAVAADARDTHALALTVL 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
           EGK  ++K++    + +V  L R S G F L G L  G+ R +    L     P
Sbjct: 181 EGKYHQVKRMVAAASNRVEALHRESIGGFTLPGDLAPGAWRWLDDADLSALRNP 234


>gi|213619052|ref|ZP_03372878.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 270

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 75/266 (28%), Positives = 110/266 (41%), Gaps = 10/266 (3%)

Query: 35  IAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE-----RTRLWLYHKPIGLVTTH 88
           I   RV V+G +      V V     I +DG  +   E        L  Y     L T +
Sbjct: 3   IEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKESAEQICRVLAYYKPEGELCTRN 62

Query: 89  SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
                 +          +R I+VGRLD+NT GLLL T DG LA  L  PS +  R Y VR
Sbjct: 63  DPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVR 122

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
             GQVD+ KL  L +G+ ++        +     +G N W  V L EG+NRE+++++E  
Sbjct: 123 VFGQVDESKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAV 182

Query: 209 NWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILREQLGPHLLEEAQVNLDAPIYSS 264
             +V+RLIR+ YG   L   L  G   E+       LR  +       ++V ++      
Sbjct: 183 GVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLRGLVELPPETSSKVAVEKDRRRM 242

Query: 265 ETLVRDRPNIISEVPDDFTRMKKNSS 290
           +     R            R    ++
Sbjct: 243 KANQIRRAVKRHSQIAGGRRSGGRNN 268


>gi|67639490|ref|ZP_00438342.1| RNA pseudouridine synthase family protein [Burkholderia mallei GB8
           horse 4]
 gi|238520037|gb|EEP83501.1| RNA pseudouridine synthase family protein [Burkholderia mallei GB8
           horse 4]
          Length = 475

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 227 VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 286

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 287 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 346

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 347 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDG 406

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 407 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 462

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 463 QGEWRYLGPDE 473


>gi|203284055|ref|YP_002221795.1| pseudouridylate synthase [Borrelia duttonii Ly]
 gi|203287595|ref|YP_002222610.1| pseudouridylate synthase [Borrelia recurrentis A1]
 gi|201083498|gb|ACH93089.1| pseudouridylate synthase [Borrelia duttonii Ly]
 gi|201084815|gb|ACH94389.1| pseudouridylate synthase [Borrelia recurrentis A1]
          Length = 248

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 65/238 (27%), Positives = 98/238 (41%), Gaps = 12/238 (5%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +   N    RV   +A  GI SRR  E +I +  +KVNGI  +     V   D +E  G 
Sbjct: 1   MTNINSKGLRVHVFLAEKGIGSRRFCEELIRKNLIKVNGIFAK-LGDKVFLGDRVEY-GK 58

Query: 66  PL------RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
            +      +   +  + L      L +       +  +    P    R+ S+GRLD  + 
Sbjct: 59  QVFVFQDSKVVNKIYIALNKPINYLCSNFDPMGRKLAISLVQPLFRERLFSIGRLDFKSS 118

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL TNDG  A  +  P  +  + Y +     V +D L   K GI +    +      +
Sbjct: 119 GLLLFTNDGRFANSIVHPKNEIEKEYIIESKRVVSEDLLVNFKNGIKVDNELFKLKSYVM 178

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                 N    + L EGKNREI+KVF   N  + ++ R+  G   L  L  G  + +S
Sbjct: 179 L----GNNTARLILTEGKNREIRKVFLSRNIFLKKVHRVRIGNITLSNLKEGQIKVLS 232


>gi|262370359|ref|ZP_06063685.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter johnsonii
           SH046]
 gi|262314701|gb|EEY95742.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter johnsonii
           SH046]
          Length = 244

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 43/230 (18%), Positives = 95/230 (41%), Gaps = 6/230 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    ++++G ++      +       +V G      E+  
Sbjct: 3   LEKMLQSQGFGSRKHCQQLIKNAAIEIDGQIITDPKYKLKLDALNYKVHGKSFEYREKVY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        +  +          +   +   +  VGRLD +T GLLLLT+DG   + L
Sbjct: 63  IALNKPQGYECSHQATHHFSVFDLFDDVLLNRGIQCVGRLDQDTTGLLLLTDDGQFLQAL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     +VYR++    V  +++  L++G+ ++           D ++ +   + + + 
Sbjct: 123 THPKKHVAKVYRMKTADPVTDEQVQQLEQGVELRNEKGSFAAT--DVKRLAECELQMTVH 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLG---TLLAGSTREVSKKIL 241
           +G   ++K++      KV  L R   G   L     L+ G    ++ + +
Sbjct: 181 QGVYHQVKRMLAAVGNKVESLHRQQIGALDLTGIPDLVEGHWIYLNAEQV 230


>gi|328870986|gb|EGG19358.1| hypothetical protein DFA_02145 [Dictyostelium fasciculatum]
          Length = 534

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 49/282 (17%), Positives = 106/282 (37%), Gaps = 13/282 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R+ K+++  G+ +R +V++ I   +V   G  +      V   D I V G  +   E
Sbjct: 3   ERVRLDKLLSNLGLCTRSKVQQFINANKVTYQGQKV-SPKAKVDVED-IRVMGRKVDHPE 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV----GRLDINTEGLLLLTND 127
              + ++     + +   +      ++D LP  F+         GRLD    GL++++ +
Sbjct: 61  LLTIAVHKPIGYVCSNSREDGDHKIIYDLLPKEFADRSPTLSIAGRLDKWVTGLVVMSQN 120

Query: 128 G----GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           G     +    +    +   V         + D++   +  +  +          +  Q+
Sbjct: 121 GKIVERIITPKDDKMGKVYEVVCESKFNGTEADEMASGRVQLRSEDGPCKPAHFEVVDQE 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
             N    + L EGK  +++++      K   + R   GP QLG L  G  R +SK+ + E
Sbjct: 181 --NKMARLTLYEGKYHQVRRMMSAVGNKAIGIHRTQVGPIQLGDLEVGKWRILSKEEM-E 237

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
            L    + +  +  +     ++   RD   +  ++     + 
Sbjct: 238 LLEAIQVSKPAITKNLYRRKAKEDARDEAELDDKMTMKPGQK 279


>gi|167903268|ref|ZP_02490473.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei NCTC 13177]
          Length = 444

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 196 VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 255

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 256 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 315

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 316 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDG 375

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 376 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 431

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 432 QGEWRYLGPDE 442



 Score = 35.9 bits (81), Expect = 9.6,   Method: Composition-based stats.
 Identities = 12/113 (10%), Positives = 23/113 (20%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R +              A             +     P       +           K  
Sbjct: 39  RGKDRAPREGARPGARGATGAKFGGAAHRSDDADRRTPRATRADSRARDAAPSSFAGKTT 98

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                    A + + A G  +S   +  +R       P+  +  S  R    +
Sbjct: 99  TAGKRAPQRADDRYGAAGKRTSPRPERTERPARFGERPATRASASGERRPTAR 151


>gi|149371928|ref|ZP_01891247.1| pseudouridylate synthase (ribosomal large subunit pseudouridine
           synthase B) [unidentified eubacterium SCB49]
 gi|149355068|gb|EDM43629.1| pseudouridylate synthase (ribosomal large subunit pseudouridine
           synthase B) [unidentified eubacterium SCB49]
          Length = 289

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 52/232 (22%), Positives = 91/232 (39%), Gaps = 4/232 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
                R++K I+ +GI SRRE +  I    V VNG ++      V   D +  DG  +  
Sbjct: 56  KQEGIRLNKYISNSGICSRREADTYIETGLVSVNGKIVNEMGYKVKLEDDVRFDGRRINP 115

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
              T + L        TT S+  G + +     +  SR+  +GRL  N  GLLL TND  
Sbjct: 116 EPMTYVLLNKPKG-FATTTSESKGNTVMDLVANASNSRITPIGRLGRNATGLLLFTNDDK 174

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L       L          +    +  +++G  I G     ++     +  +   +
Sbjct: 175 LKEKLSKKGMSRLFHV--ELDKNLKAADIQKIREGFTIAGKKIE-IEEINYVEGKTKKEI 231

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + ++   N  I+ +F  F + + RL  ++        L  G  + ++ + L
Sbjct: 232 GLKIKNLGNSVIRDIFAHFEYDIVRLDCVALAHLTKKDLPRGKWKILTTQEL 283


>gi|257885740|ref|ZP_05665393.1| pseudouridine synthase [Enterococcus faecium 1,231,501]
 gi|257821596|gb|EEV48726.1| pseudouridine synthase [Enterococcus faecium 1,231,501]
          Length = 238

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 101/232 (43%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+I      +R+E++R+ A ++V ++G +  R   NV S    IEV G  L   E 
Sbjct: 1   MRLDKLIEEKLETTRKEMKRLFALKQVMIDGTVELRQNRNVDSLLHQIEVAGEHLETNES 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                    F  +  VGRLD +T GLLL+T++G L  
Sbjct: 61  -YYLLNKPEKAVTAVSDPEKTTVIDLIASADRFQPLYPVGRLDRDTTGLLLITSNGQLGY 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            + LP  +  + Y+V  + +V    +   + GIV   G       + +       + V +
Sbjct: 120 EMLLPEKKVSKTYQVVVNERVTSADVTAFENGIVFADGYQCKPADLKILKADKHQSTVLL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            ++EGK  ++KK+F     KV  L R+S GP +L   L  G  R  +   ++
Sbjct: 180 TIQEGKFHQVKKMFLAQGKKVTALKRLSMGPLELDEQLGVGEYRSFTLAEMK 231


>gi|110833959|ref|YP_692818.1| ribosomal small subunit pseudouridine synthase A [Alcanivorax
           borkumensis SK2]
 gi|110647070|emb|CAL16546.1| Ribosomal small subunit pseudouridine synthase A [Alcanivorax
           borkumensis SK2]
          Length = 248

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 60/240 (25%), Positives = 104/240 (43%), Gaps = 8/240 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     SR  +  ++A  RV+VNG +       +   D +  DG  L+      
Sbjct: 14  RLDRFLSARLQMSRSNLRLLLAAGRVRVNGQVERDRQRRIGLFDAVVCDGEILQANRPRY 73

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L +      +V+   D    + +          +   GRLD N+ GL+LLTNDG  +R L
Sbjct: 74  LMINKPAG-VVSATRDEHHPTVLELLPRGQREGLHLAGRLDFNSTGLVLLTNDGAWSRRL 132

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTVG 192
            LP T   + YRV     +  + +    + +            ++T+ +   ++ W    
Sbjct: 133 SLPETGLWKHYRVSVDKPLSDEDVVSFSQRMWFDFEQIYTQPARLTIRSSFEADVW---- 188

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLLE 251
           L EGK  +IK++F     KV  L R++ G  QL   L  G +RE+++   +  L P  +E
Sbjct: 189 LHEGKYHQIKRMFGRTGKKVTALHRLAVGRIQLDAYLAPGESRELTQAEQQTALDPEPVE 248


>gi|257893304|ref|ZP_05672957.1| pseudouridine synthase [Enterococcus faecium 1,231,408]
 gi|257829683|gb|EEV56290.1| pseudouridine synthase [Enterococcus faecium 1,231,408]
          Length = 238

 Score =  132 bits (333), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 102/232 (43%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+I      +R+E++R+ A ++V V+G +  R   NV S    IEV G  L   E 
Sbjct: 1   MRLDKLIEEKLETTRKEMKRLFALKQVMVDGTVEFRQNRNVDSLLHRIEVAGEHLETNES 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                    F  +  VGRLD +T GLLL+T++G L  
Sbjct: 61  -YYLLNKPKKAVTAVSDPEKTTVIDLIASADRFQPLYPVGRLDRDTTGLLLITSNGQLGY 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            + LP  +  + Y+   + +V    +   +KGIV   G       + +       + V +
Sbjct: 120 EMLLPEKKVSKTYQAVVNERVTSADVAAFEKGIVFADGYQCQPANLKILKADKHQSTVLL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            ++EGK  ++KK+F     KV  L R+S GP +L   L  G  R ++   ++
Sbjct: 180 TIQEGKFHQVKKMFLAQGKKVIALKRLSMGPLELDEQLAVGEYRSLTLAEMK 231


>gi|225075240|ref|ZP_03718439.1| hypothetical protein NEIFLAOT_00240 [Neisseria flavescens
           NRL30031/H210]
 gi|224953415|gb|EEG34624.1| hypothetical protein NEIFLAOT_00240 [Neisseria flavescens
           NRL30031/H210]
          Length = 227

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 45/228 (19%), Positives = 91/228 (39%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLR--K 69
            ++ K I   G+ SR++ + +I    + +NG +  RA  ++  +    + VDG  +    
Sbjct: 1   MQLLKYIQSQGLGSRKQCQWLIDNDCIAINGEIHNRAKDDIDPSQVHTLSVDGEEIAAVP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L+       +                     + +VGRLD +T G++L+TNDG 
Sbjct: 61  MPHFYILLHKPADYETSHKPQQYPSIFSLFPDHMRNIDMQAVGRLDADTTGIILITNDGQ 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAW 188
               +  P  +  ++YRV      D      LK G+++            +         
Sbjct: 121 FNHRVTSPKHKVPKLYRVTLKHPADDTLCTTLKNGVLLHDDNETVAAAEAVLA---DPTT 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + + EGK  ++K++      +V +L R  +G + +  L AG  + +
Sbjct: 178 LMMTITEGKYHQVKRMIAAAGNRVEQLHREKFGDWNVDDLAAGEWKFI 225


>gi|269963430|ref|ZP_06177757.1| ribosomal small subunit pseudouridine synthase A [Vibrio harveyi
           1DA3]
 gi|269831830|gb|EEZ85962.1| ribosomal small subunit pseudouridine synthase A [Vibrio harveyi
           1DA3]
          Length = 225

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 43/208 (20%), Positives = 83/208 (39%), Gaps = 2/208 (0%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRS 95
               V V+G + +  A  V     +E +G  +       + LY     + +     +  +
Sbjct: 15  KSGEVTVDGEVQKSGAFKVPEGGVVEWEGREVGAPGPRYIMLYKPADFVCSHEDGHNP-T 73

Query: 96  TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
                       +   GRLD++T GL+L+T+DG  +  +  P  +  + YRV     +  
Sbjct: 74  AFVLLDEPKVENLHFAGRLDVDTTGLVLITDDGQWSHRITSPKHKCEKTYRVWLVDAIQP 133

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRL 215
           D +    +GI ++      +   L+    +   V + + EGK  ++K++F     KV  L
Sbjct: 134 DYVEKFAEGIELRNEREATLPAHLEIVNEAENEVLLTIVEGKYHQVKRMFAALGNKVEHL 193

Query: 216 IRISYGPFQLGT-LLAGSTREVSKKILR 242
            R   G   L   L  G  R ++++ + 
Sbjct: 194 HRERIGSIVLDEALEPGDYRFLTEEEVE 221


>gi|312796240|ref|YP_004029162.1| ribosomal large subunit pseudouridine synthase F [Burkholderia
           rhizoxinica HKI 454]
 gi|312168015|emb|CBW75018.1| Ribosomal large subunit pseudouridine synthase F (EC 4.2.1.70)
           [Burkholderia rhizoxinica HKI 454]
          Length = 522

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 103/251 (41%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI------------- 60
            R+SK ++  G+ SRRE +  I +  V+V+G +++     V +  HI             
Sbjct: 274 MRLSKRMSELGLCSRREADEWIEKGWVRVDGQIVDTLGAKVTAAQHIDVLPNARAAQARQ 333

Query: 61  --EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
              V   P+          Y   + L+T  +             +    +   GRLDI++
Sbjct: 334 VTIVLNKPVGYVSGQPEGDYPPAVALITPANRWSDDPAPTRFSATHLRSLAPAGRLDIDS 393

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG---------QVDQDKLNLLKKGIVIQG 169
            GLL+LT DG +A+ L    ++  + Y VR                DKL  L++G+ + G
Sbjct: 394 TGLLVLTQDGRIAKQLIGEQSEVEKEYLVRVRYGTHTQQVERYFPIDKLAQLREGLSLDG 453

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +     QV     +     +   LREG+ R+I+++ E    +V  L R+  G   LG L 
Sbjct: 454 VRLKPAQVDWQNGEQ----LRFVLREGRKRQIRRMCELVGLEVVGLKRVRIGQLVLGALP 509

Query: 230 AGSTREVSKKI 240
           +G  R +    
Sbjct: 510 SGKWRYLRADE 520


>gi|257887896|ref|ZP_05667549.1| pseudouridine synthase [Enterococcus faecium 1,141,733]
 gi|257823950|gb|EEV50882.1| pseudouridine synthase [Enterococcus faecium 1,141,733]
          Length = 238

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 102/232 (43%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+I      +R+E++R+ A ++V V+G +  R   NV S    IEV G  L   E 
Sbjct: 1   MRLDKLIEEKLETTRKEMKRLFALKQVMVDGTVEFRQNRNVDSLLHRIEVAGEHLETKES 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                    F  +  VGRLD +T GLLL+T++G L  
Sbjct: 61  -YYLLNKPKKAVTAVSDPEKTTVIDLIASADRFQPLYPVGRLDRDTTGLLLITSNGQLGY 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            + LP  +  + Y+   + +V    +   +KGIV   G       + +       + V +
Sbjct: 120 EMLLPEKKVSKTYQAVVNERVTSADVAAFEKGIVFADGYQCQPANLKILKADKHQSTVLL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            ++EGK  ++KK+F     KV  L R+S GP +L   L  G  R ++   ++
Sbjct: 180 TIQEGKFHQVKKMFLAQGKKVIALKRLSMGPLELDEQLAVGEYRSLTLAEMK 231


>gi|119775917|ref|YP_928657.1| pseudouridine synthase, Rsu [Shewanella amazonensis SB2B]
 gi|119768417|gb|ABM00988.1| pseudouridine synthase, Rsu [Shewanella amazonensis SB2B]
          Length = 251

 Score =  132 bits (332), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 52/229 (22%), Positives = 98/229 (42%), Gaps = 8/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+   +A+     ++ V  ++  +RV V+G +    A+ +     I +    LR      
Sbjct: 7   RLDSFLAKTLNIPKKAVRELLKAERVTVDGKVALEMALQIGPFSQIYLGDTALRADTPRY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L      +V+   D + ++ +     ++ + +  VGRLD+NT GL+LL+ND   +  +
Sbjct: 67  LMLNKPVG-VVSATKDKEHKTVLDLIPEALRAGLHIVGRLDLNTSGLVLLSNDSRWSESM 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTVG 192
             P     + Y V     + +D +   ++G     +GI     ++ +  ++ +     V 
Sbjct: 126 MQPGAHVPKEYWVTLEHPLTEDYIAAFERGFYFETEGITTLPARLAILGEREA----RVE 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
           L EGK  +IK++F  F   V  L R   G   L   L  G  R ++   
Sbjct: 182 LCEGKYHQIKRMFGRFQNPVVALHRHRIGALMLDPGLAPGQWRPLTDDE 230


>gi|254673145|emb|CBA07952.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis alpha275]
          Length = 256

 Score =  132 bits (332), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 45/228 (19%), Positives = 87/228 (38%), Gaps = 6/228 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPLR--K 69
            ++ K +   GI SR++ + +IA   V +NG  ++    ++ S+      +DG  +    
Sbjct: 27  MKLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTVVP 86

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 87  EPYFYIMLNKPEDYETSHKPKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS +  ++Y V       +     LK G+++              +      +
Sbjct: 147 LNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAADAVLENP--TTL 204

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + EGK  ++K++      +V  L R  +   +   L  G  + + 
Sbjct: 205 LLTITEGKYHQVKRMIAAVGNRVQHLHRRRFAHLETENLKPGEWKFID 252


>gi|134094298|ref|YP_001099373.1| putative ribosomal large subunit pseudouridine synthase
           [Herminiimonas arsenicoxydans]
 gi|133738201|emb|CAL61246.1| putative ribosomal large subunit pseudouridine synthase
           [Herminiimonas arsenicoxydans]
          Length = 237

 Score =  132 bits (332), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 51/238 (21%), Positives = 88/238 (36%), Gaps = 12/238 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRK 69
               R++K +A A   SRRE E+ I    V V+G+++E     V     I +     L  
Sbjct: 2   TDSIRLAKRVADAVPCSRREAEQYIEGGWVTVDGVVIEEPGHRVSPQQAIHLSPDATLVA 61

Query: 70  AERTRLWLYHKPI-------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
                + L+            L+T  +      +    L    S +  V  L+    GL+
Sbjct: 62  INPVTILLHKPAGIDADAALRLITPENLYAEDRSGIRFLKKHTSELKPVDVLETYASGLM 121

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + T D  +AR L   +    + Y     G +  + L LL  G+   G     ++V+   +
Sbjct: 122 VFTQDWHVARKLVDDAATVEQEYIAEVSGDLIPNGLALLNHGLNFNGKPLAPIKVSWQNE 181

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 +   L+ G+  +I  + E    K+  L RI      + +L AG  R +    
Sbjct: 182 ----TRLRFALKAGRRGQIAHMCEMVGLKLLNLKRIRIARLPMASLPAGQWRYLKGYE 235


>gi|121635011|ref|YP_975256.1| putative ribosomal small subunit pseudouridine synthase [Neisseria
           meningitidis FAM18]
 gi|120866717|emb|CAM10469.1| putative ribosomal small subunit pseudouridine synthase [Neisseria
           meningitidis FAM18]
 gi|261392420|emb|CAX49965.1| ribosomal small subunit pseudouridine synthase A (16S
           pseudouridylate 516 synthase; 16S pseudouridine 516
           synthase; rRNA-uridine isomerase A; rRNA pseudouridylate
           synthase A) [Neisseria meningitidis 8013]
 gi|325132500|gb|EGC55193.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis M6190]
 gi|325138274|gb|EGC60843.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis ES14902]
 gi|325142501|gb|EGC64904.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis 961-5945]
 gi|325198451|gb|ADY93907.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis G2136]
          Length = 230

 Score =  132 bits (332), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 45/228 (19%), Positives = 87/228 (38%), Gaps = 6/228 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPLR--K 69
            ++ K +   GI SR++ + +IA   V +NG  ++    ++ S+      +DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTVVP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 61  EPYFYIMLNKPEDYETSHKPKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS +  ++Y V       +     LK G+++              +      +
Sbjct: 121 LNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAADAVLENP--TTL 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + EGK  ++K++      +V  L R  +   +   L  G  + + 
Sbjct: 179 LLTITEGKYHQVKRMIAAVGNRVQHLHRRRFAHLETENLKPGEWKFID 226


>gi|325130337|gb|EGC53103.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis OX99.30304]
          Length = 230

 Score =  132 bits (332), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 45/228 (19%), Positives = 87/228 (38%), Gaps = 6/228 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPLR--K 69
            ++ K +   GI SR++ + +IA   V +NG  ++    ++ S+      +DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTVVP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 61  EPYFYIMLNKPEDYETSHKPKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS +  ++Y V       +     LK G+++              +      +
Sbjct: 121 LNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAADAVLKNP--TTL 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + EGK  ++K++      +V  L R  +   +   L  G  + + 
Sbjct: 179 LLTITEGKYHQVKRMIAAAGNRVLHLHRRRFAHLETENLKPGEWKFID 226


>gi|325204300|gb|ADY99753.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis M01-240355]
          Length = 230

 Score =  132 bits (332), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 44/227 (19%), Positives = 86/227 (37%), Gaps = 6/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPLR--K 69
            ++ K +   GI SR++ + +I    V +NG  ++    ++ S+      +DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSSVETLDIDGEAVTVVP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 61  EPYFYIMLNKPEDYETSHKPKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS +  ++Y V       +     LK G+++              +      +
Sbjct: 121 LNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAADAVLKNP--TTL 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 179 LLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 225


>gi|206560456|ref|YP_002231220.1| putative RNA pseudouridylate synthase [Burkholderia cenocepacia
           J2315]
 gi|198036497|emb|CAR52394.1| putative RNA pseudouridylate synthase [Burkholderia cenocepacia
           J2315]
          Length = 625

 Score =  132 bits (332), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 377 MRLSKRMSELGMCSRREADEWIEKGWVLVDGERIDTLGTKVRADQKIEIDERASAAQAAQ 436

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     L+T  +   G  +     P     +   GRLDI++
Sbjct: 437 VTILLHKPVGYVSGQAEDGYEPAAVLITRANRWSGDHSPVRFSPQHLHALAPAGRLDIDS 496

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 497 TGLLVLTQNGVIAKQLIGEQSDIDKEYLVRVRFGERLIDIDQHFPAESLAKLRHGLELDG 556

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E     V  L R+  G   LG L 
Sbjct: 557 VALKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLDVIGLKRVRMGRVMLGALP 612

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 613 QGQWRYLSADE 623


>gi|304387404|ref|ZP_07369595.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis ATCC 13091]
 gi|304338497|gb|EFM04616.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis ATCC 13091]
          Length = 230

 Score =  132 bits (331), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 44/228 (19%), Positives = 86/228 (37%), Gaps = 6/228 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPLR--K 69
            ++ K +   GI SR++ + +I    V +NG  ++    ++ S+      +DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSSVETLDIDGEAVTVVP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 61  EPYFYIMLNKPEDYETSHKPKHYRSIFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS +  ++Y V       +     LK G+++              +      +
Sbjct: 121 LNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAADAVLENP--TTL 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + EGK  ++K++      +V  L R  +   +   L  G  + + 
Sbjct: 179 LLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPGEWKFID 226


>gi|171058596|ref|YP_001790945.1| RNA-binding S4 domain-containing protein [Leptothrix cholodnii
           SP-6]
 gi|170776041|gb|ACB34180.1| RNA-binding S4 domain protein [Leptothrix cholodnii SP-6]
          Length = 416

 Score =  132 bits (331), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 63/248 (25%), Positives = 100/248 (40%), Gaps = 24/248 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
             +R+SK +A  G+ASRRE +  I    V+V+G +       V     I VD        
Sbjct: 171 EGERLSKRMAALGLASRREADEWIEAGWVRVDGKMA-VLGQRVGPQAKIHVDPAAHKQQA 229

Query: 64  -------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
                    P+          Y     L+   +     S+  +  P     +   GRLDI
Sbjct: 230 QRVTILVNKPVGYVSGQAEDGYEPAAALIRPENRWSEDSSGVNWHPGQLRGLAPAGRLDI 289

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL----LKKGIVIQGICY 172
           ++ GLL+LT DG +A++L    +   + Y VR   Q      +     L  G+ + G   
Sbjct: 290 DSVGLLVLTQDGRVAKLLIGDESLVEKEYLVRVAYQGQGRLPDSALALLNHGLELDGQAL 349

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
              +V+   +      +   LREGK R+I+++ E    +V  L R+  G   LG L AG 
Sbjct: 350 RPAKVSWQNEDQ----LRFVLREGKKRQIRRMCEAVGLQVLGLKRVRIGSVSLGHLPAGQ 405

Query: 233 TREVSKKI 240
            R + +  
Sbjct: 406 WRYLRRDE 413


>gi|291459824|ref|ZP_06599214.1| ribosomal small subunit pseudouridine synthase A [Oribacterium sp.
           oral taxon 078 str. F0262]
 gi|291417614|gb|EFE91333.1| ribosomal small subunit pseudouridine synthase A [Oribacterium sp.
           oral taxon 078 str. F0262]
          Length = 249

 Score =  132 bits (331), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 54/250 (21%), Positives = 108/250 (43%), Gaps = 7/250 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKAE 71
            R+ + ++  GI+SR E+++ I + +V +NG      ++ V   +   +   G       
Sbjct: 1   MRLDRFLSEMGISSRSELKKEIRRGQVLLNGEEARDPSLFVDPENPPVVLYRGREFHYEA 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            +   +      +++   D    + +          +  VGRLD + EGLLL++NDG L+
Sbjct: 61  FSYYMMNKPAG-ILSASRDKKQSTVLDLIQEDRRRDLFPVGRLDKDCEGLLLISNDGPLS 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVT 190
             L  P +   ++Y VR  G++ +    L ++G+           ++T+ + +   +   
Sbjct: 120 HRLLRPKSHVPKLYFVRVSGRLTESDAELFRRGLRYDEDLTALPAELTILSAEDIISEAC 179

Query: 191 VGLREGKNREIKKVFEFF--NWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGP 247
           V + EGK  +IKK+F       +V  L RI+ GP +L   L  G  R++ +  +      
Sbjct: 180 VRITEGKFHQIKKMFLALPKKKEVLFLKRIALGPLRLDEALKPGEYRKLKEAEISALKEI 239

Query: 248 HLLEEAQVNL 257
                 ++  
Sbjct: 240 PSSASEEMRR 249


>gi|296157141|ref|ZP_06839977.1| pseudouridine synthase [Burkholderia sp. Ch1-1]
 gi|295892477|gb|EFG72259.1| pseudouridine synthase [Burkholderia sp. Ch1-1]
          Length = 236

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 53/230 (23%), Positives = 91/230 (39%), Gaps = 6/230 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH---IEVDGVPLRKAER 72
           +  ++   G  SRR+   +IA  RV + G +   A  +  + D      VDGV     E 
Sbjct: 3   LESILFTQGFGSRRQCRALIADARVSIGGAVCTDADADFPTGDTTFSFTVDGVVWPYREH 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L        +                     V  VGRLD +T GLLLL++DG    
Sbjct: 63  AYLLLNKPAGYECSRDPQHHLSVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGKFVH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +   P  +  +VY       +D  +L+ L  G+++ G     +   ++ +   +  + + 
Sbjct: 123 LFTSPKRKVPKVYVATTRHPIDDVQLSALHDGVLLHGES-KPI-AAVNVEARGDHTLALT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           + EGK  ++K++      +   L R   G F L G L  G  + + +  L
Sbjct: 181 VMEGKYHQVKRMIAAAGNRCEALHRERIGGFALPGALAPGGWQWLDETHL 230


>gi|323527102|ref|YP_004229255.1| pseudouridine synthase [Burkholderia sp. CCGE1001]
 gi|323384104|gb|ADX56195.1| pseudouridine synthase [Burkholderia sp. CCGE1001]
          Length = 239

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 53/230 (23%), Positives = 90/230 (39%), Gaps = 6/230 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH---IEVDGVPLRKAER 72
           +  ++   G  SRR+   +I   RV ++G +   A  +  + D      VDGV     ER
Sbjct: 3   LESILFSQGFGSRRQCRALIVDARVSIDGTVCADADADFPAGDAAFCFSVDGVVWPYRER 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L        +                     V  VGRLD +T GLLLL++DG    
Sbjct: 63  AYLLLNKPAGYECSRDPQHHLSVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGKFVH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  +VY       +D  +L LL+ G+++ G         +D +      + + 
Sbjct: 123 TFTSPKRKVPKVYVATTRHPLDDAQLGLLRHGVLLHGESKPVA--AVDAEARGEHSLALT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           + EGK  ++K++      +   L R   G   L  TL  G+ + + +  +
Sbjct: 181 VMEGKYHQVKRMIAAAGNRCEALHRERIGGLALPATLAPGAWQWLDETEI 230


>gi|107028798|ref|YP_625893.1| pseudouridine synthase, Rsu [Burkholderia cenocepacia AU 1054]
 gi|116690043|ref|YP_835666.1| pseudouridine synthase, Rsu [Burkholderia cenocepacia HI2424]
 gi|105897962|gb|ABF80920.1| Pseudouridine synthase, Rsu [Burkholderia cenocepacia AU 1054]
 gi|116648132|gb|ABK08773.1| Pseudouridine synthase, Rsu [Burkholderia cenocepacia HI2424]
          Length = 669

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 421 MRLSKRMSELGMCSRREADEWIEKGWVLVDGARIDTLGTKVRADQKIEIDERASAAQAAQ 480

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     L+T  +   G  +     P     +   GRLDI++
Sbjct: 481 VTILLHKPVGYVSGQAEDGYEPAAVLITRANRWSGDHSPVRFSPQHLHALAPAGRLDIDS 540

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 541 TGLLVLTQNGVIAKQLIGEQSDIDKEYLVRVRFGERLIDIDQHFPAESLAKLRHGLELDG 600

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E     V  L R+  G   LG L 
Sbjct: 601 VALKPALVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLDVIGLKRVRMGRVMLGALP 656

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 657 QGQWRYLSADE 667


>gi|257896486|ref|ZP_05676139.1| pseudouridine synthase [Enterococcus faecium Com12]
 gi|293379264|ref|ZP_06625410.1| pseudouridylate synthase [Enterococcus faecium PC4.1]
 gi|257833051|gb|EEV59472.1| pseudouridine synthase [Enterococcus faecium Com12]
 gi|292642060|gb|EFF60224.1| pseudouridylate synthase [Enterococcus faecium PC4.1]
          Length = 238

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 102/232 (43%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+I      +R+E++R+ A ++V V+G +  R   NV S    IEV G  L   E 
Sbjct: 1   MRLDKLIEEKLETTRKEMKRLFALKQVMVDGTVEFRQNRNVDSLLHRIEVAGEHLETNES 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                    F  +  VGRLD +T GLLL+T++G L  
Sbjct: 61  -YYLLNKPKKAVTAVSDPEKTTVIDLIASADRFQPLYPVGRLDRDTTGLLLITSNGQLGY 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            + LP  +  + Y+   + +V    +   +KGIV   G       + +       + V +
Sbjct: 120 EMLLPEKKVSKTYQAVVNERVTSADVAAFEKGIVFADGYQCQPANLKILKADKHQSTVLL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            ++EGK  ++KK+F     KV  L R+S GP +L   L  G  R ++   ++
Sbjct: 180 TIQEGKFHQVKKMFLAQGKKVIALKRLSMGPLELDERLAVGEYRSLTLAEMK 231


>gi|221199286|ref|ZP_03572330.1| pseudouridine synthase, Rsu [Burkholderia multivorans CGD2M]
 gi|221205812|ref|ZP_03578827.1| pseudouridine synthase, Rsu [Burkholderia multivorans CGD2]
 gi|221174650|gb|EEE07082.1| pseudouridine synthase, Rsu [Burkholderia multivorans CGD2]
 gi|221180571|gb|EEE12974.1| pseudouridine synthase, Rsu [Burkholderia multivorans CGD2M]
          Length = 238

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 51/234 (21%), Positives = 87/234 (37%), Gaps = 4/234 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV + G         + +   +  VDG P     R  
Sbjct: 3   LESILYTQGFGSRRQCRGLIEAGRVAIGGAPATDPDAELDTDGLVFTVDGTPWPFHARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        +               P +   V  VGRLD +T GLLLL++DG      
Sbjct: 63  VVLNKPAGYECSRDPQHHPSVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFVHAY 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y       +D  +L+ L+ G+ + G         +         + + + 
Sbjct: 123 TSPKRKVPKTYVATVRHALDAAQLDALRGGVQLHGEP--KPVAAVAADARDPHTLALTVL 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
           EGK  ++K++    + +V  L R S G   L   L  G+ R + +  L     P
Sbjct: 181 EGKYHQVKRMVAAASNRVEALHRESVGGLALPADLAPGAWRWLGQAELAALRNP 234


>gi|328544686|ref|YP_004304795.1| 16S rRNA uridine-516 pseudouridylate synthase-related
           pseudouridylate synthase [polymorphum gilvum
           SL003B-26A1]
 gi|326414428|gb|ADZ71491.1| 16S rRNA uridine-516 pseudouridylate synthase-related
           pseudouridylate synthase [Polymorphum gilvum
           SL003B-26A1]
          Length = 243

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 52/245 (21%), Positives = 89/245 (36%), Gaps = 7/245 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVN--GILLERAAVNVMSTDHIEVDGVPLRKAE 71
            R+ +++A  G  +R+EV   I    V  +  G  L   A      + I  D  PL  A 
Sbjct: 1   MRLVRLLANLGYGTRKEVALAIRNGWVT-DRAGRPLTADAR--TPHEDILFDDEPLDPAP 57

Query: 72  RTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              L L        +           + D        + +VGRLD +T G LL T+DG L
Sbjct: 58  GMVLLLNKPVGYTCSTKDRGRLVYDLLPDRFRLRKPVLSTVGRLDRDTSGALLFTDDGVL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P ++  +VY       +  D+      G ++       ++       G      
Sbjct: 118 LHRIIAPKSEVPKVYEAELDRPLKGDEAAQFASGTLMLDGEDKPLKPAELEVLGERR-AR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L EG+  +++++F      V  L RI  G   L  L  G+ R + ++ + +   P   
Sbjct: 177 LTLHEGRYHQVRRMFAATGNHVTALARIRIGALTLDGLAEGTWRLLDERDVAKIFAPPSG 236

Query: 251 EEAQV 255
                
Sbjct: 237 NVPPP 241


>gi|115352106|ref|YP_773945.1| pseudouridine synthase, Rsu [Burkholderia ambifaria AMMD]
 gi|115282094|gb|ABI87611.1| Pseudouridine synthase, Rsu [Burkholderia ambifaria AMMD]
          Length = 690

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 60/251 (23%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V     IE+D          
Sbjct: 442 MRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPDQKIEIDERASAAQAAQ 501

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     L+T  +   G  +     P     +   GRLDI++
Sbjct: 502 VTILLHKPVGYVSGQAEDGYEPASVLITRANQWSGDRSPLRFSPQHLHALAPAGRLDIDS 561

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            G+L+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 562 TGMLVLTQNGRIAKQLIGEQSDIDKEYLVRVRFGERLLDIDQHFPAESLAKLRHGLELDG 621

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 622 VALKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 677

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 678 QGQWRYLSPDE 688



 Score = 41.7 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 12/105 (11%), Positives = 28/105 (26%), Gaps = 3/105 (2%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
            E          ++    +          D   R   + ++      +     P   +  
Sbjct: 292 AEGGARAPYRDKATGDAPKRSFGERRAPSDRPARRSDDDTRPRRAGAEGGARAPYRDKAT 351

Query: 311 ASNVWMAKGIHSSFLSDSGQREENH---RRSPSFPSKRSLRRTSA 352
                 + G  S+      +R ++    RR+ +    R+  R  A
Sbjct: 352 GDAPKRSFGERSTSTDRPARRSDDDARPRRAGAEGGARAPYRDKA 396



 Score = 39.8 bits (91), Expect = 0.58,   Method: Composition-based stats.
 Identities = 10/113 (8%), Positives = 26/113 (23%), Gaps = 3/113 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +        E          +     +          D   R   + ++      +    
Sbjct: 102 DARPRRAGAEGGARAPYRDKAEGYGEKRSFGERRTSSDRPARRSDDDTRPRRAGAEGGAR 161

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENH---RRSPSFPSKRSLRRTSA 352
            P   +        +     +      +R ++    RR+ +    R+  R  A
Sbjct: 162 APYRDKATGEGAKRSFDDRRTSSDRPARRSDDDTRPRRAGAEGGARAPYRDKA 214



 Score = 36.3 bits (82), Expect = 6.6,   Method: Composition-based stats.
 Identities = 13/110 (11%), Positives = 25/110 (22%), Gaps = 2/110 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+ + P     A         ++     +R                          ++  
Sbjct: 28  RKAVRPAGPPAADKPPRPKKAAAPAAAGERAFKPRGAERPGADRAPAKRAPRDGGAERGD 87

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
           A P   R   S             ++ G R     ++  +  KRS     
Sbjct: 88  ARPA--RPYRSAEGQPDARPRRAGAEGGARAPYRDKAEGYGEKRSFGERR 135


>gi|221211505|ref|ZP_03584484.1| pseudouridine synthase, Rsu [Burkholderia multivorans CGD1]
 gi|221168866|gb|EEE01334.1| pseudouridine synthase, Rsu [Burkholderia multivorans CGD1]
          Length = 238

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 51/234 (21%), Positives = 88/234 (37%), Gaps = 4/234 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV + G        ++ +   +  VDG P     R  
Sbjct: 3   LESILYTQGFGSRRQCRGLIEAGRVAIGGAPATDPDADLDTDGLVFTVDGTPWPFHARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        +               P +   V  VGRLD +T GLLLL++DG      
Sbjct: 63  VVLNKPAGYECSRDPQHHPSVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFVHAY 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y       +D  +L+ L+ G+ + G         +         + + + 
Sbjct: 123 TSPKRKVPKTYVATVRHALDAAQLDALRGGVQLHGEP--KPVAAVAADARDPHTLALTVL 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
           EGK  ++K++    + +V  L R S G   L   L  G+ R + +  L     P
Sbjct: 181 EGKYHQVKRMVAAASNRVEALHRESVGGLALPADLAPGAWRWLGEAELAALRNP 234


>gi|332527599|ref|ZP_08403646.1| ribosomal small subunit pseudouridine synthase A [Rubrivivax
           benzoatilyticus JA2]
 gi|332112002|gb|EGJ11979.1| ribosomal small subunit pseudouridine synthase A [Rubrivivax
           benzoatilyticus JA2]
          Length = 232

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 51/230 (22%), Positives = 90/230 (39%), Gaps = 4/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            ++ +++   G  +RR    ++    V+V G +++  + +   +    EVDG      + 
Sbjct: 1   MKLEQILFTQGFGTRRVCAGLVDCGAVRVGGQVVDDPSADFDTAGLVFEVDGREWPFRQP 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L+       +               P     V  VGRLD +T GLLL T+DG L  
Sbjct: 61  ALVMLHKPAGYECSQKPRHHPSVMSLLPPPLRTRGVQPVGRLDEDTTGLLLFTDDGKLIH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VY       VD+  +  L  G+V+       ++       G N  + + 
Sbjct: 121 RLTSPKHHVPKVYEATTKHPVDEAVVQRLLAGVVLDDDP-QPVRALQAQCTGPNT-LRLV 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           L EGK  ++K++      +V  L R ++G   L   L  G    V  + +
Sbjct: 179 LAEGKYHQVKRMVAAAGNRVEALHRSAFGALTLPADLAPGRWCWVEPEAI 228


>gi|78357001|ref|YP_388450.1| pseudouridine synthase, Rsu [Desulfovibrio desulfuricans subsp.
           desulfuricans str. G20]
 gi|78219406|gb|ABB38755.1| ribosomal large subunit pseudouridine synthase B [Desulfovibrio
           desulfuricans subsp. desulfuricans str. G20]
          Length = 292

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 69/241 (28%), Positives = 115/241 (47%), Gaps = 8/241 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
           E     R++K +A AG+ SRR  + ++AQ  V VNG++++   V V+   D + V G  +
Sbjct: 43  EAEQSVRINKALADAGVCSRRAADELVAQGVVTVNGVVVDTPGVKVVPDRDELCVRGKKI 102

Query: 68  -----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGL 121
                     T L ++     + T       R+ +    P     R+  VGRLD  +EGL
Sbjct: 103 FLKSSSSRSHTYLMMHKPVEVVTTVSDPEGRRTVIDILPPLHRKKRLFPVGRLDFFSEGL 162

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLD 180
           LLLT+DG L   L  PS    + Y V+  G V  + L  ++KG+ + +G     ++V + 
Sbjct: 163 LLLTDDGVLTHRLTHPSWHLPKTYLVKVRGVVQDNDLQAMRKGMTLAEGEKLAPVEVEVL 222

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++      + + L +G NR+I+++       V  L R+  GP  LG L  G  RE++   
Sbjct: 223 SRHHDWLLLEMTLFQGINRQIRRMCRDAGLTVLSLHRVRQGPLSLGELRTGEVRELTDSE 282

Query: 241 L 241
           +
Sbjct: 283 I 283


>gi|121601596|ref|YP_993376.1| RNA pseudouridine synthase family protein [Burkholderia mallei
           SAVP1]
 gi|121230406|gb|ABM52924.1| RNA pseudouridine synthase family protein [Burkholderia mallei
           SAVP1]
          Length = 559

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 311 VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 370

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 371 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 430

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 431 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDG 490

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 491 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 546

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 547 QGEWRYLGPDE 557


>gi|126449776|ref|YP_001080883.1| RNA pseudouridine synthase family protein [Burkholderia mallei NCTC
           10247]
 gi|126242646|gb|ABO05739.1| RNA pseudouridine synthase family protein [Burkholderia mallei NCTC
           10247]
          Length = 559

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 311 VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 370

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 371 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 430

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 431 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDG 490

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 491 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 546

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 547 QGEWRYLGPDE 557


>gi|302841952|ref|XP_002952520.1| hypothetical protein VOLCADRAFT_93239 [Volvox carteri f.
           nagariensis]
 gi|300262159|gb|EFJ46367.1| hypothetical protein VOLCADRAFT_93239 [Volvox carteri f.
           nagariensis]
          Length = 381

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 64/316 (20%), Positives = 121/316 (38%), Gaps = 30/316 (9%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEV----- 62
            N +  R++KV+A  G+ASRR  E +I++ RV+VNG ++      +   TD +E+     
Sbjct: 71  TNESRPRLAKVLAACGVASRRACEELISEGRVRVNGRVVSEQGTTIDPTTDRVELLVKYS 130

Query: 63  ----DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---------- 108
                G  +R+     ++       + ++             L     +           
Sbjct: 131 VNLHRGHRVRR--HNLIYPEPDKGYICSSSDVSGRGKLAVQLLNPWLEQWRRNSKDTKRL 188

Query: 109 ----ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                +VGRLD+ + GL+ +TNDG  A  +  PS+   + Y V       + +L  L  G
Sbjct: 189 PPRFFTVGRLDVASSGLIFITNDGHWANRVIHPSSGLTKEYVVGLGRDASRPQLQALAAG 248

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
             + G     ++V +    G +  + + ++EGK  E++++ +    ++  L R+  G F+
Sbjct: 249 TEVAGTFVSPVEVEVL---GDSRRLRIVVQEGKKHEVRELVKAAGLELTSLKRVRIGGFR 305

Query: 225 L-GTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
           L   L  G  RE+    LR        E A  + +            R    +       
Sbjct: 306 LPRDLGIGGFRELKPSDLRTVTDLAAQEAASASGETRQAVQRQAAAQRAAAAAASVPRAL 365

Query: 284 RMKKNSSQKNGLSKQK 299
           R       +     ++
Sbjct: 366 RGMGEEVLERLRKARE 381


>gi|293573040|ref|ZP_06683982.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecium E980]
 gi|291606942|gb|EFF36322.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecium E980]
          Length = 238

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 102/232 (43%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+I      +R+E++R+ A ++V ++G +  R   NV S    IEV G  L   E 
Sbjct: 1   MRLDKLIEEKLETTRKEMKRLFALKQVMIDGTVEFRQNRNVDSLLHRIEVAGEHLETNES 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                    F  +  VGRLD +T GLLL+T++G L  
Sbjct: 61  -YYLLNKPKKAVTAVSDPEKTTVIDLIASADRFQPLYPVGRLDRDTTGLLLITSNGQLGY 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            + LP  +  + Y+   + +V    +   +KGIV   G       + +       + V +
Sbjct: 120 EMLLPEKKVSKTYQAVVNERVTSADVAAFEKGIVFADGYQCQPANLKILKADKHQSTVLL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            ++EGK  ++KK+F     KV  L R+S GP +L   L  G  R ++   ++
Sbjct: 180 TIQEGKFHQVKKMFLAQGKKVIALKRLSMGPLELDEHLAVGEYRSLTLAEMK 231


>gi|225164908|ref|ZP_03727125.1| RNA-binding S4 domain protein [Opitutaceae bacterium TAV2]
 gi|224800485|gb|EEG18864.1| RNA-binding S4 domain protein [Opitutaceae bacterium TAV2]
          Length = 253

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 55/251 (21%), Positives = 90/251 (35%), Gaps = 25/251 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVK--------------VN---G-ILLERAAVNVMS 56
           R+ ++++  G  SRRE    +    V               VN   G   L   +  V  
Sbjct: 4   RLDQLLSSLGYCSRREARDFLRAHTVTISPPPPPPPSAGNSVNVSVGLQPLRDPSAKVNP 63

Query: 57  TDH---IEVDGVPLRKAERTRLWLYHKPIGLVTTHSD--PDGRSTVFDNLPSIFSRVISV 111
            D    + VDG  L       L L+     + +      P     +     +   +V S+
Sbjct: 64  LDPARPVFVDGEALDHPGGLLLMLHKPTGFVCSHDEREGPRVYDLLPPRWRARNPQVTSI 123

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD +T GLL+LT+   L      P  +  ++YR      V    ++L   G +     
Sbjct: 124 GRLDKDTSGLLILTDRTELVHTYTSPRHKVPKLYRATLDRDVPASLVDLFAAGTLQLDGE 183

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF-NWKVNRLIRISYGPFQLGTLLA 230
                        +     + L EGK  +++++F       V  L R  +G   LG L  
Sbjct: 184 KAPCAPATLRL-PAPRVAELVLVEGKYHQVRRMFAAAAGATVLTLHRECFGRLTLGDLKP 242

Query: 231 GSTREVSKKIL 241
           G  RE+S+  +
Sbjct: 243 GEYREISESEI 253


>gi|171914565|ref|ZP_02930035.1| putative pseudouridylate synthase [Verrucomicrobium spinosum DSM
           4136]
          Length = 235

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 101/230 (43%), Gaps = 7/230 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           +S++IAR     R    + IA +RVKV   ++      V     + +D   +++ E    
Sbjct: 3   LSRLIARHKGMGRTAAMQAIAGKRVKVEDQVVTDGQHEVDRFSTVWLDDTLVQEGESALY 62

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            + HKP+G ++   DP   + +          +   GRLD ++ GLLLLTNDG  +R L 
Sbjct: 63  IMLHKPVGYLSATRDPQHPTVIDLIDHPARETLHIAGRLDRSSSGLLLLTNDGRWSRRLT 122

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTVGL 193
            P  +  +VY V     +  + + L  KG     + +     ++ +           V L
Sbjct: 123 EPGEKVDKVYLVETAEPIAPEAVELFAKGFYFHTEDLTTLPAELGIL----GERLARVTL 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            EG+  +IK++F     +V  L R S G   L   L  G  RE+ + +LR
Sbjct: 179 HEGRYHQIKRMFHRVGNRVISLHRESIGSLVLPVELFPGQWREIRRDVLR 228


>gi|319638371|ref|ZP_07993133.1| ribosomal small subunit pseudouridine synthase A [Neisseria mucosa
           C102]
 gi|317400120|gb|EFV80779.1| ribosomal small subunit pseudouridine synthase A [Neisseria mucosa
           C102]
          Length = 227

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 43/228 (18%), Positives = 91/228 (39%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAE 71
            ++ K I   G+ SR++ + +I    + +NG +  RA  ++  +    + VDG  +    
Sbjct: 1   MQLLKYIQSQGLGSRKQCQWLIDNDCIAINGEIHNRAKDDIDPSQVHTLSVDGEEIAAVP 60

Query: 72  RTRLWL--YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               ++  +       +                     + +VGRLD +T G++L+TNDG 
Sbjct: 61  MPYFYILLHKPADYETSHKPQQYPSIFSLFPDHMRNIDMQAVGRLDADTTGIILITNDGQ 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAW 188
               +  P  +  ++YRV      +      LK G+++            +         
Sbjct: 121 FNHRVTSPKHKVPKLYRVTLKHPANDTLCATLKNGVLLHDDNETVAAAEAVLA---DPTT 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + + EGK  ++K++      +V +L R  +G + +  L AG  + +
Sbjct: 178 LMMTITEGKYHQVKRMVAAAGNRVEQLHREKFGDWNVDDLAAGEWKFI 225


>gi|170697674|ref|ZP_02888762.1| pseudouridine synthase [Burkholderia ambifaria IOP40-10]
 gi|170137422|gb|EDT05662.1| pseudouridine synthase [Burkholderia ambifaria IOP40-10]
          Length = 238

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 52/228 (22%), Positives = 85/228 (37%), Gaps = 4/228 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV V G        +  +   +  VD        R  
Sbjct: 3   LESILYTQGFGSRRQCRGLIETGRVSVAGASATDPDASFDTDGLVFTVDDTAWPFHARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L        +               P +   V  VGRLD +T GLLLL++DG      
Sbjct: 63  LALNKPAGYECSRDPQHHASVFSLLPTPLVARGVQCVGRLDQDTTGLLLLSDDGQFVHAY 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y       +D  +LN L+ G+ + G     +             + + + 
Sbjct: 123 TSPKRKVPKTYVATVRHPLDDTQLNALRAGVQLHGEP-KPIAAVAAHA-RDTHALALTVL 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           EGK  ++K++    + +V  L R S G F L   L  G+ R + +  L
Sbjct: 181 EGKYHQVKRMVAAASNRVEALHRESIGGFTLPDDLAPGAWRWLGEGEL 228


>gi|315303907|ref|ZP_07874374.1| ribosomal large subunit pseudouridine synthase B [Listeria ivanovii
           FSL F6-596]
 gi|313627724|gb|EFR96390.1| ribosomal large subunit pseudouridine synthase B [Listeria ivanovii
           FSL F6-596]
          Length = 217

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 63/213 (29%), Positives = 102/213 (47%), Gaps = 3/213 (1%)

Query: 39  RVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF 98
           +V VNG ++    V V  ++ IEV+G+ L K E      Y     +     D    +   
Sbjct: 1   KVTVNGKVVTELGVKVSGSERIEVEGIQLTKEEHRYFLFYKPRGTVSAVTDDKGRTTVAD 60

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
                I  R+  VGRLD +T GLLL+TNDG  A +L  P  +  + Y  R  G  +++ +
Sbjct: 61  YF-TDIPERLYPVGRLDYDTSGLLLMTNDGDFANLLMHPKNEVAKTYIARIKGIPEREVI 119

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
             L++G+VI G      +V + +       A V + + EG+NR+++K+FE   ++V +L 
Sbjct: 120 RELERGVVIDGRKTAPAKVKIRSSDKAKDKAIVEITIHEGRNRQVRKMFEAVGFEVQKLS 179

Query: 217 RISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           R  Y    L  L AG  RE+S   +++      
Sbjct: 180 REEYSFLNLRGLNAGERRELSHHEVKQLKTEAR 212


>gi|326802612|ref|YP_004320431.1| pseudouridine synthase Rsu [Sphingobacterium sp. 21]
 gi|326553376|gb|ADZ81761.1| pseudouridine synthase Rsu [Sphingobacterium sp. 21]
          Length = 421

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 112/234 (47%), Gaps = 2/234 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPL 67
           E     R+++ IA +G+ SRR+ + +I    V VNG+++      V  + D I  +G  L
Sbjct: 181 EENGLIRLNRYIANSGVCSRRKADELIQAGVVTVNGVVVTELGTKVDAAKDEIRYNGEKL 240

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +   + L      + TT    + ++ +     +   R+  VGRLD NT GLLLLTND
Sbjct: 241 KREKMVYVLLNKPKDYITTTDDPQERKTVMHLVEKASRERIYPVGRLDRNTTGLLLLTND 300

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P    +++Y V  +  + Q   N +  G+ ++       +V+   Q  S  
Sbjct: 301 GNLAEKLSHPRNNIMKIYHVELNKSLTQGDFNKIGYGVELEDGFIKPDEVSYI-QGASKR 359

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + + +  G+NR ++++FE   + V +L R+ Y       L  G  R + +K +
Sbjct: 360 EIGIQIHSGRNRIVRRIFESLGYDVIKLDRVIYANLTKKDLPRGRWRYLEEKEI 413


>gi|124384572|ref|YP_001029187.1| RNA pseudouridine synthase family protein [Burkholderia mallei NCTC
           10229]
 gi|254178102|ref|ZP_04884757.1| RNA pseudouridine synthase family protein [Burkholderia mallei ATCC
           10399]
 gi|254358102|ref|ZP_04974375.1| RNA pseudouridine synthase family protein [Burkholderia mallei
           2002721280]
 gi|124292592|gb|ABN01861.1| RNA pseudouridine synthase family protein [Burkholderia mallei NCTC
           10229]
 gi|148027229|gb|EDK85250.1| RNA pseudouridine synthase family protein [Burkholderia mallei
           2002721280]
 gi|160699141|gb|EDP89111.1| RNA pseudouridine synthase family protein [Burkholderia mallei ATCC
           10399]
          Length = 563

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 315 VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 374

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 375 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 434

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 435 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDG 494

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 495 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 550

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 551 QGEWRYLGPDE 561


>gi|329118041|ref|ZP_08246754.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           bacilliformis ATCC BAA-1200]
 gi|327465929|gb|EGF12201.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           bacilliformis ATCC BAA-1200]
          Length = 228

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 46/228 (20%), Positives = 85/228 (37%), Gaps = 6/228 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPL--RK 69
            ++ K +   G+ SRR+ ER+     V+VNG  +  A   +       + + G  +    
Sbjct: 1   MQLVKYLQAQGVGSRRQCERLAECGGVEVNGETVSGAKTEIAPDSVRTLRIGGAAVCVVP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 61  LPYFYIVLNKPAGYETSHKPRDWPGVFTLFPANLRNLDMQAVGRLDADTTGVLLITNDGQ 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
               +  P     ++YR       D      L+ G+++            +        +
Sbjct: 121 FNHRMTSPKHHVAKLYRATLKHAADAALCETLQNGVLLHDDNETVAADAAELADP--HTL 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + EGK  ++K++      +V +L R+ +G +    L  G  R VS
Sbjct: 179 LLTIGEGKYHQVKRMVAAAGNRVEKLHRLRFGSWSAEDLAVGEWRFVS 226


>gi|170733378|ref|YP_001765325.1| RNA-binding S4 domain-containing protein [Burkholderia cenocepacia
           MC0-3]
 gi|169816620|gb|ACA91203.1| RNA-binding S4 domain protein [Burkholderia cenocepacia MC0-3]
          Length = 650

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 402 MRLSKRMSELGMCSRREADEWIEKGWVLVDGERIDTLGTKVRADQKIEIDERASAAQAAQ 461

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     L+T  +   G  +     P     +   GRLDI++
Sbjct: 462 VTILLHKPVGYVSGQAEDGYEPAAVLITRANRWSGDHSPVRFSPQHLHALAPAGRLDIDS 521

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 522 TGLLVLTQNGVIAKQLIGEQSDIDKEYLVRVRFGERLIDIDQHFPAESLAKLRHGLELDG 581

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E     V  L R+  G   LG L 
Sbjct: 582 VALKPALVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLDVIGLKRVRMGRVMLGALP 637

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 638 QGQWRYLSADE 648


>gi|325134459|gb|EGC57104.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis M13399]
 gi|325144560|gb|EGC66859.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis M01-240013]
 gi|325205927|gb|ADZ01380.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis M04-240196]
          Length = 230

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 45/228 (19%), Positives = 87/228 (38%), Gaps = 6/228 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPLR--K 69
            ++ K +   GI SR++ + +IA   V +NG  ++    ++ S+      +DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTVVP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 61  EPYFYIMLNKPEDYETSHKPKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS +  ++Y V       +     LK G+++              +      +
Sbjct: 121 LNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAADAVLKNP--TTL 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + EGK  ++K++      +V  L R  +   +   L  G  + + 
Sbjct: 179 LLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPGEWKFID 226


>gi|161523988|ref|YP_001579000.1| pseudouridine synthase [Burkholderia multivorans ATCC 17616]
 gi|189351251|ref|YP_001946879.1| ribosomal small subunit pseudouridine synthase A [Burkholderia
           multivorans ATCC 17616]
 gi|160341417|gb|ABX14503.1| pseudouridine synthase [Burkholderia multivorans ATCC 17616]
 gi|189335273|dbj|BAG44343.1| ribosomal small subunit pseudouridine synthase A [Burkholderia
           multivorans ATCC 17616]
          Length = 238

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 51/234 (21%), Positives = 88/234 (37%), Gaps = 4/234 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV + G        ++ +   +  VDG P     R  
Sbjct: 3   LESILYTQGFGSRRQCRGLIEAGRVAIGGAPATDPDADLDTDGLVFTVDGTPWPFHARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        +               P +   V  VGRLD +T GLLLL++DG      
Sbjct: 63  VALNKPAGYECSRDPQHHPSVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFVHAY 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y       +D  +L+ L+ G+ + G         +         + + + 
Sbjct: 123 TSPKRKVPKTYVATVRHALDAAQLDALRGGVQLHGEP--KPVAAVAADARDPHTLALTVL 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
           EGK  ++K++    + +V  L R S G   L   L  G+ R + +  L     P
Sbjct: 181 EGKYHQVKRMVAAASNRVEALHRESVGGLALPADLAPGAWRWLGEAELAALRNP 234


>gi|289671226|ref|ZP_06492301.1| pseudouridylate synthase [Xanthomonas campestris pv. musacearum
           NCPPB4381]
          Length = 291

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 77/254 (30%), Positives = 123/254 (48%), Gaps = 11/254 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG         
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKIELDGRSFVASALT 86

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L        + T        +          SR I++GRLDINT GLLLLT DG 
Sbjct: 87  EPSRVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR      ++      +  L +G++++       ++       
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + EV+++ +  
Sbjct: 207 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGQSVEVAQEKVDA 266

Query: 244 QLGPHLLEEAQVNL 257
                 LEE   + 
Sbjct: 267 LRAELKLEEGAPSA 280


>gi|319937261|ref|ZP_08011668.1| pseudouridine synthase [Coprobacillus sp. 29_1]
 gi|319807627|gb|EFW04220.1| pseudouridine synthase [Coprobacillus sp. 29_1]
          Length = 241

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 53/213 (24%), Positives = 85/213 (39%), Gaps = 10/213 (4%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHS 89
           E   +I    V+VN  ++      V   D I V G  +         +      +   + 
Sbjct: 27  ECRTLIKHGFVEVNNQVINDHRYVVHDDDKINVFGKAIHSQPFVYYMMNKPKGYICANYD 86

Query: 90  DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
                           +  I VGRLD +T G LLLTND  + + L LP     + Y V  
Sbjct: 87  KNHLCVVD----LIERNDCICVGRLDKDTTGFLLLTNDKSIVKALLLPQNHQPKTYLVTT 142

Query: 150 HGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
              +D++ +   + GIVI   IC    Q+ L     +     + L EGK  ++KK+F   
Sbjct: 143 RFPIDENSIYRFEMGIVIDQDICCLPAQLELI----NTHQCYLTLHEGKYHQVKKMFLSC 198

Query: 209 NWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
             +V  L RI++    L  +L  G  R++++  
Sbjct: 199 QNEVVDLKRIAFAGLVLDASLGYGEYRQLNQDE 231


>gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [Herbaspirillum seropedicae SmR1]
 gi|300074275|gb|ADJ63674.1| RNA pseudouridylate synthase protein [Herbaspirillum seropedicae
           SmR1]
          Length = 248

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 60/249 (24%), Positives = 99/249 (39%), Gaps = 23/249 (9%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------- 63
             P R+SK ++  G+ SRRE +  I +  V+V+G+++      V+    + V+       
Sbjct: 2   TEPVRLSKRMSELGLCSRREADEWIEKGWVRVDGVVVSVLGSKVLPHQKVTVERQASAEQ 61

Query: 64  --------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                     P+          Y   + LV   S      T     P     ++  GRLD
Sbjct: 62  AQRVTILLNKPMGYVSGQAEDGYKPAVVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRLD 121

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL----NLLKKGIVIQGIC 171
           I++ GLL+LT DG +A+ L    +   + Y VR                L  G+++ G  
Sbjct: 122 IDSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKRLNHGLIMDGKP 181

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
               +V    +      +   LREGK R+I+++ +    KV  L R+  G  +LG L  G
Sbjct: 182 LRPAKVVWQNEDQ----LRFTLREGKKRQIRRMCDMVGLKVIGLKRVRIGGVKLGELPTG 237

Query: 232 STREVSKKI 240
             R +    
Sbjct: 238 QWRYLRPDE 246


>gi|83719576|ref|YP_442548.1| pseudouridine synthase family protein [Burkholderia thailandensis
           E264]
 gi|83653401|gb|ABC37464.1| pseudouridine synthase family protein [Burkholderia thailandensis
           E264]
          Length = 557

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 309 VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAEQAAQ 368

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 369 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWGGDRSPLRFSPQHLRALAPAGRLDIDS 428

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 429 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTTDIERHFPAESLAKLRHGLELDG 488

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 489 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 544

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 545 QGQWRYLGPDE 555


>gi|254471903|ref|ZP_05085304.1| ribosomal small subunit pseudouridylate synthase [Pseudovibrio sp.
           JE062]
 gi|211959105|gb|EEA94304.1| ribosomal small subunit pseudouridylate synthase [Pseudovibrio sp.
           JE062]
          Length = 232

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 47/235 (20%), Positives = 93/235 (39%), Gaps = 5/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVK-VNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+E++  I    +   +G  ++ A   +   + I  D  PL   E 
Sbjct: 1   MRLVKLLANLGYGSRKEMQAAIRNGWITDKDGNAIK-ADSKL-PHEEILFDDEPLDPPEG 58

Query: 73  TRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           + + L        +           + D        +  VGRLD +T GLLL T+DG L 
Sbjct: 59  SVILLNKPLGYTCSMKDRGRLVFDLLPDRYRVRKPALSFVGRLDKDTTGLLLFTDDGKLL 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P     ++Y V     +   + +L   G ++       ++          +   +
Sbjct: 119 HRIISPKADVAKIYEVELDRPMTGGEGDLFASGEMMLENETNPLKPAELEVLSETS-ARL 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            L EG+  +++++F      V  L R   G   L  +  G+ + ++++ + +  G
Sbjct: 178 TLHEGRYHQVRRMFAATGNHVTNLHRAQLGGLTLEGVEEGTWKLLAQEEIAKIFG 232


>gi|257138757|ref|ZP_05587019.1| pseudouridine synthase family protein [Burkholderia thailandensis
           E264]
          Length = 547

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 299 VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAEQAAQ 358

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 359 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWGGDRSPLRFSPQHLRALAPAGRLDIDS 418

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 419 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTTDIERHFPAESLAKLRHGLELDG 478

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 479 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 534

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 535 QGQWRYLGPDE 545


>gi|91784948|ref|YP_560154.1| ribosomal small subunit pseudouridine synthase A [Burkholderia
           xenovorans LB400]
 gi|91688902|gb|ABE32102.1| ribosomal small subunit pseudouridine synthase A [Burkholderia
           xenovorans LB400]
          Length = 261

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 52/230 (22%), Positives = 91/230 (39%), Gaps = 6/230 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH---IEVDGVPLRKAER 72
           +  ++   G  SRR+   +IA  RV + G +   A  +  + D      VDGV     E 
Sbjct: 28  LESILFTQGFGSRRQCRALIADARVSIGGAVCTDADADFPTGDTTFSFTVDGVDWPYREH 87

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L        +                     V  VGRLD +T GLLLL++DG    
Sbjct: 88  AYLLLNKPAGYECSRDPQHHLSVFSLLPPQFAGRGVQCVGRLDQDTTGLLLLSDDGKFVH 147

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +   P  +  +VY       +D  +L+ L+ G+++ G     +   +D +   +  + + 
Sbjct: 148 LFTSPKRKVPKVYVATTRHPIDDAQLSALRDGVLLNGE-ARPI-AAVDVEARGDHTLALT 205

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + EGK  ++K++      +   L R   G   L   L  G+ + + +  L
Sbjct: 206 VMEGKYHQVKRMIAAAGNRCEALHRERIGGLALPEALARGAWQWLDETDL 255


>gi|186476099|ref|YP_001857569.1| RNA-binding S4 domain-containing protein [Burkholderia phymatum
           STM815]
 gi|184192558|gb|ACC70523.1| RNA-binding S4 domain protein [Burkholderia phymatum STM815]
          Length = 624

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 61/250 (24%), Positives = 104/250 (41%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---------- 64
           R+SK+++  G+ SRRE +  I +  V V+G+++++    V     I++D           
Sbjct: 377 RLSKLMSELGLCSRREADEWIEKGWVTVDGVVVDKLGTKVRPDADIQIDPAAQAAQQKQV 436

Query: 65  -----VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
                 P+          Y   + LV   +  DG  T          ++   GRLDI++ 
Sbjct: 437 TILVHKPVGYVSGQAEDGYEPAVTLVKPENRWDGDRTDIRFSAVHLRQLAPAGRLDIDST 496

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT DG +A+ L    ++  + Y VR            +   + L  L+ G+ + G+
Sbjct: 497 GLLVLTQDGRIAKQLIGGHSEIDKEYLVRVSYGDIETDVEHEFPAESLAKLRHGLELDGV 556

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E     V  L R+  G   LG L  
Sbjct: 557 PLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLHVVGLKRVRMGHVMLGALPP 612

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 613 GQWRYLGPDE 622



 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 12/122 (9%), Positives = 22/122 (18%), Gaps = 9/122 (7%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R        E A                   +     P                  +   
Sbjct: 166 RSGAASRAGERAPRFSRDDDARVARRTAPDSDDGRRAPRPPRESDDVRRAPRTARTEGTP 225

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF---------PSKRSLRRTSA 352
           +     R    +    +   S     S  R E     P+          P +R     + 
Sbjct: 226 SRERTERRYRDDAPEGRTTRSPRGERSEARGERSYARPARAAYEDRGAAPERRPRGEGAP 285

Query: 353 KK 354
           ++
Sbjct: 286 RR 287


>gi|325128404|gb|EGC51287.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis N1568]
          Length = 230

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 44/228 (19%), Positives = 86/228 (37%), Gaps = 6/228 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLR--K 69
            ++ K +   GI SR++ + +I    V +NG  ++    ++ S+    +D  G  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSSVETLDLDGEAVTVVP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 61  EPYFYILLNKPEDYETSHKPKHYRSIFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS +  ++Y V       +     LK G+++              +      +
Sbjct: 121 LNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAADAVLENP--TTL 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + EGK  ++K++      +V  L R  +   +   L  G  + + 
Sbjct: 179 LLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPGEWKFID 226


>gi|134296660|ref|YP_001120395.1| ribosomal small subunit pseudouridine synthase A [Burkholderia
           vietnamiensis G4]
 gi|134139817|gb|ABO55560.1| ribosomal small subunit pseudouridine synthase A [Burkholderia
           vietnamiensis G4]
          Length = 238

 Score =  131 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 52/234 (22%), Positives = 87/234 (37%), Gaps = 4/234 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV V G           +   +  +DG       R  
Sbjct: 3   LESILYTQGFGSRRQCRGLIESGRVTVAGASATDPDAAFDTDGLVFTLDGTAWPYHARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L        +               P +   V  VGRLD +T GLLLL++DG      
Sbjct: 63  LALNKPAGYECSRDPQHHASVFSLLPAPLLARGVQCVGRLDQDTTGLLLLSDDGQFVHAY 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y       +D+ +LN L+ G+ + G     +   +         + + + 
Sbjct: 123 TSPKRKVPKTYVATVRHPLDETQLNALRSGVQLHGEP-KPI-AAVAAVARDTHTLALTVL 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
           EGK  ++K++    + +V  L R   G F L   L  GS   +++  L     P
Sbjct: 181 EGKYHQVKRMVAAASNRVEALHRERIGGFALPAGLAPGSWCWLAEAELAALRNP 234


>gi|237812812|ref|YP_002897263.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei MSHR346]
 gi|237503454|gb|ACQ95772.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei MSHR346]
          Length = 571

 Score =  131 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 323 VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 382

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 383 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 442

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 443 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDG 502

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 503 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 558

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 559 QGEWRYLGPDE 569


>gi|238028391|ref|YP_002912622.1| Pseudouridine synthase, Rsu [Burkholderia glumae BGR1]
 gi|237877585|gb|ACR29918.1| Pseudouridine synthase, Rsu [Burkholderia glumae BGR1]
          Length = 239

 Score =  131 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 50/226 (22%), Positives = 87/226 (38%), Gaps = 5/226 (2%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTRLWL 77
           ++   G  SRR+   ++A  RV + G + +    +        +VDG      +   L L
Sbjct: 6   ILFSQGFGSRRQCRALVAAGRVAIGGAICDDPEQSFPTDGLEFDVDGTRWLYRQHAYLVL 65

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
                   +                     V  VGRLD +T GLLLL++DG        P
Sbjct: 66  NKPAGYECSREPQHHESVFALLPPQLATRGVQCVGRLDQDTTGLLLLSDDGQFVHAYTSP 125

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGK 197
             +  + Y       +D  +L  L+ G+++ G     +   LD Q      + + ++EGK
Sbjct: 126 KRKVPKTYLATLKHPLDAAQLTALRDGVLLHGEP-KPI-AALDAQARGTHQLEMTVQEGK 183

Query: 198 NREIKKVFEFFNWKVNRLIRISYGPFQL--GTLLAGSTREVSKKIL 241
             ++K++      +  +L R   G F L    L  G+ R + +  L
Sbjct: 184 YHQVKRMIAAAGNRCEQLHRERIGGFALPADALPPGAWRWLDEADL 229


>gi|134277960|ref|ZP_01764675.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 305]
 gi|134251610|gb|EBA51689.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 305]
          Length = 570

 Score =  131 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 322 VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 381

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 382 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 441

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 442 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDG 501

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 502 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 557

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 558 QGEWRYLGPDE 568


>gi|161870172|ref|YP_001599342.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis 053442]
 gi|161595725|gb|ABX73385.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis 053442]
          Length = 256

 Score =  131 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 45/227 (19%), Positives = 87/227 (38%), Gaps = 6/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPLR--K 69
            ++ K +   GI SR++ + +IA   V +NG  ++    ++ S+      +DG  +    
Sbjct: 27  MKLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTVVP 86

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 87  EPYFYIMLNKPEDYETSHKPKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS +  ++Y V       +     LK G+++              +      +
Sbjct: 147 LNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAADAVLKNP--TTL 204

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 205 LLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 251


>gi|254805100|ref|YP_003083321.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis alpha14]
 gi|254668642|emb|CBA06281.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis alpha14]
          Length = 256

 Score =  131 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 45/227 (19%), Positives = 87/227 (38%), Gaps = 6/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPLR--K 69
            ++ K +   GI SR++ + +IA   V +NG  ++    ++ S+      +DG  +    
Sbjct: 27  MKLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTVVP 86

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 87  EPYFYIMLNKPEDYETSHKPKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS +  ++Y V       +     LK G+++              +      +
Sbjct: 147 LNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAADAVLENP--TTL 204

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 205 LLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 251


>gi|254500656|ref|ZP_05112807.1| conserved hypothetical protein [Labrenzia alexandrii DFL-11]
 gi|222436727|gb|EEE43406.1| conserved hypothetical protein [Labrenzia alexandrii DFL-11]
          Length = 232

 Score =  130 bits (327), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 47/229 (20%), Positives = 87/229 (37%), Gaps = 7/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVN--GILLERAAVNVMSTDHIEVDGVPLRKAE 71
            R+ K++A  G  SR+E+++ I    V  +  G  L+ A       D I  D  PL  A+
Sbjct: 1   MRLVKLLANLGYGSRKEMQQAIRHGWVT-DRKGNQLK-ADAKTDHKD-ILFDDEPLDPAQ 57

Query: 72  RTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              + +      + +           + D        + ++GRLD  T G LL T+DG  
Sbjct: 58  GVVILMNKPLGYVCSTKDQGRLVYDLLPDRFRMRKPVLSTIGRLDKETSGALLFTDDGTF 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P +   +VY V     ++  +  L   G ++       ++              
Sbjct: 118 LHQVISPKSNVPKVYEVTLDRPMNGSEAALFASGEMMLENEQKPLKPAELDV-IDETHAR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + L EG+  +++++F      V  L R   G   L  +  G  + +S+ 
Sbjct: 177 LTLHEGRYHQVRRMFAATGNHVTDLARSRIGTLTLEGVDEGQWKILSED 225


>gi|170740346|ref|YP_001769001.1| pseudouridine synthase [Methylobacterium sp. 4-46]
 gi|168194620|gb|ACA16567.1| pseudouridine synthase [Methylobacterium sp. 4-46]
          Length = 244

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 55/235 (23%), Positives = 96/235 (40%), Gaps = 7/235 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD----HIEVDGVPLR 68
             R+ +++A  G  SRRE++ +    R++++G  L  A   + +T      + V G PL 
Sbjct: 6   TIRLDRLLANLGYGSRREIQALARAGRIRLDGEALREADGRIAATADLPARLTVSGEPLD 65

Query: 69  KAERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                 L L+       +           + +        + +VGRLD +T GLLL+T+D
Sbjct: 66  PPAPLALMLHKPTGVTCSHKEAGPLVYGLLPERWRRREPALSTVGRLDKDTSGLLLVTDD 125

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +  P  +  + YRV     +  D+  +L  G ++       +     T +G   
Sbjct: 126 GALLHRIISPKAKIEKQYRVELDRPLRGDEGAILVSGTLMLEGEEAPLLPVGFTAQGPRQ 185

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
              V L EG+  +++++F      V  L R   G   L   L  G+ R +    L
Sbjct: 186 -ARVVLTEGRYHQVRRMFAALGNHVTALHRDRVGGLTLPEDLAPGAYRILDAAAL 239


>gi|145342798|ref|XP_001416276.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144576501|gb|ABO94569.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 249

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 65/252 (25%), Positives = 104/252 (41%), Gaps = 24/252 (9%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--- 65
           E+   +RVSK++AR G  SRRE ER+I   RV V+G  +        +   IE+ G    
Sbjct: 2   EDDELERVSKILARRGTCSRREAERLIEDGRVLVDGETI-ELGFKARANARIEITGEGTR 60

Query: 66  -------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF----------DNLPSIFSRV 108
                   +       +        +          + +             +    S  
Sbjct: 61  WLREKLTVIVNKPPGYVSNLPAEGEIAAAACVEPRNAWMRAMEGTPMDDLKRVTRDVSSF 120

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              GRLD ++ GLL+LT DG LAR +   +   L+ Y V     V +  +  L   + + 
Sbjct: 121 NVCGRLDKDSRGLLILTEDGALARSVIGGN-GVLKKYVVTTDADVRESHMRSLNGRVQLD 179

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           G+    M   +      +  +   LREGKNR+I++V E F  +V  L R+  G  Q+G L
Sbjct: 180 GVELLPM--NVQRLGHGSRTLEFNLREGKNRQIRRVCEKFGLRVVDLHRVQIGDVQIGDL 237

Query: 229 LAGSTREVSKKI 240
             G+ R +S++ 
Sbjct: 238 PEGAWRLMSERE 249


>gi|330840760|ref|XP_003292378.1| hypothetical protein DICPUDRAFT_157085 [Dictyostelium purpureum]
 gi|325077385|gb|EGC31101.1| hypothetical protein DICPUDRAFT_157085 [Dictyostelium purpureum]
          Length = 533

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 51/282 (18%), Positives = 106/282 (37%), Gaps = 7/282 (2%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           ++ +N    R+ ++++  GI  R  V R + ++RV ++G      +      D + +DG 
Sbjct: 1   MIIKNSKKLRIDRLLSNLGIVERSSVPRFLNEKRVTISGKKAT-LSSKASP-DEVRIDGK 58

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTV---FDNLPSIFSRVISVGRLDINTEGLL 122
            +       L L+     + +T +D D +        +  S        GRLD    GL+
Sbjct: 59  LIENPSALHLALHKPSGYICSTVNDGDHKVVYDLLPKDFQSRKPIPSIAGRLDKWVTGLV 118

Query: 123 LLTNDGG--LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           + + DG      +             V  +     +       G++++G         L+
Sbjct: 119 IFSQDGKLVERIITPKDDGCGKDYEVVLKNKLGGDEIGVFESGGLMLRGEEAPCKPAKLE 178

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
               S   V V L EG+  +++++F   + K   + R   GP +LG L  G  R +++K 
Sbjct: 179 ILDESKNKVKVTLFEGRYHQVRRMFAANDNKALEIHRTRIGPVELGDLPVGKWRHLTEKE 238

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDF 282
           +++     + +  +      I   +   +    I+    D  
Sbjct: 239 IQDLYNIQVSQSKKKRDYKEIKKDKEKDKLYKAIVEPDQDKT 280


>gi|308389419|gb|ADO31739.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis alpha710]
          Length = 256

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 45/227 (19%), Positives = 87/227 (38%), Gaps = 6/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPLR--K 69
            ++ K +   GI SR++ + +IA   V +NG  ++    ++ S+      +DG  +    
Sbjct: 27  MKLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTVVP 86

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 87  EPYFYIMLNKPEDYETSHKPKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS +  ++Y V       +     LK G+++              +      +
Sbjct: 147 LNHSLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAADAVLKNP--TTL 204

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 205 LLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 251


>gi|261380161|ref|ZP_05984734.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           subflava NJ9703]
 gi|284796999|gb|EFC52346.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           subflava NJ9703]
          Length = 227

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 44/228 (19%), Positives = 91/228 (39%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLR--K 69
            ++ K I   G+ SR++ + +I    + +NG +  RA  ++  +    + VDG  +    
Sbjct: 1   MQLLKYIQSQGLGSRKQCQWLIDNDCIAINGEIHNRAKDDIDPSQVHTLSVDGEEIAAVP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L+       +                     + +VGRLD +T G++L+TNDG 
Sbjct: 61  MPHFYILLHKPADYETSHKPQQYPSIFSLFPDHMRNIDMQAVGRLDADTTGIILITNDGQ 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAW 188
               +  P  +  ++YRV      D      LK G+++             +    +   
Sbjct: 121 FNHRVTSPKHKVPKLYRVTLKHPADDTLCTTLKNGVLLHDDNET---VAAAEAVLAAPTT 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + + EGK  ++K++      +V +L R  +G + +  L  G  + +
Sbjct: 178 LMMTITEGKYHQVKRMVAAAGNRVEQLHREKFGDWNVDDLATGEWKFI 225


>gi|15677165|ref|NP_274318.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis MC58]
 gi|218768321|ref|YP_002342833.1| putative ribosomal small subunit pseudouridine synthase [Neisseria
           meningitidis Z2491]
 gi|7226539|gb|AAF41674.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis MC58]
 gi|121052329|emb|CAM08659.1| putative ribosomal small subunit pseudouridine synthase [Neisseria
           meningitidis Z2491]
 gi|316984090|gb|EFV63068.1| conserved hypothetical protein [Neisseria meningitidis H44/76]
 gi|319410566|emb|CBY90934.1| ribosomal small subunit pseudouridine synthase A (16S
           pseudouridylate 516 synthase; 16S pseudouridine 516
           synthase; rRNA-uridine isomerase A; rRNA pseudouridylate
           synthase A) [Neisseria meningitidis WUE 2594]
 gi|325140476|gb|EGC62997.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis CU385]
 gi|325200075|gb|ADY95530.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis H44/76]
          Length = 230

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 45/227 (19%), Positives = 87/227 (38%), Gaps = 6/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPLR--K 69
            ++ K +   GI SR++ + +IA   V +NG  ++    ++ S+      +DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTVVP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 61  EPYFYIMLNKPEDYETSHKPKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS +  ++Y V       +     LK G+++              +      +
Sbjct: 121 LNHSLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAADAVLKNP--TTL 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 179 LLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 225


>gi|224418175|ref|ZP_03656181.1| putative ribosomal pseudouridine synthase [Helicobacter canadensis
           MIT 98-5491]
 gi|253827502|ref|ZP_04870387.1| pseudouridine synthase, Rsu [Helicobacter canadensis MIT 98-5491]
 gi|313141710|ref|ZP_07803903.1| RNA pseudouridine synthase [Helicobacter canadensis MIT 98-5491]
 gi|253510908|gb|EES89567.1| pseudouridine synthase, Rsu [Helicobacter canadensis MIT 98-5491]
 gi|313130741|gb|EFR48358.1| RNA pseudouridine synthase [Helicobacter canadensis MIT 98-5491]
          Length = 250

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 66/241 (27%), Positives = 119/241 (49%), Gaps = 16/241 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ IA     SRRE +++I + +V +N  +++  +  V +   + V+G  L++ E  
Sbjct: 1   MRLNQYIAHHSKFSRREADQLIKEGKVSINKEIIKDFSYQVKNHTKVYVNGKCLKEKEEY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +Y+KP G + +  D  GR  ++++LP  F   I +GRLD  +EGLLLLT+   +A  
Sbjct: 61  TVIVYNKPKGELVSKRDDRGRRVIYESLPKRFKDFIPIGRLDFASEGLLLLTDSVKVATK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--------------DMQVTL 179
           L     +  RVY ++  G++ ++    ++ G+ +Q    G               M   +
Sbjct: 121 LMES--KLERVYLLKLSGEIKEEVFEAMENGLSLQDARLGGHQKSKIKAMEFSPFMGYWV 178

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                  + + V + EGKNRE+++ F  FN KV  L R++YG   L  L     R + + 
Sbjct: 179 SKNTAKLSKIKVAINEGKNRELRRFFAHFNLKVLDLKRVAYGFVSLNNLPTQKVRFLERG 238

Query: 240 I 240
            
Sbjct: 239 E 239


>gi|254457376|ref|ZP_05070804.1| ribosomal small subunit pseudouridine synthase A [Campylobacterales
           bacterium GD 1]
 gi|207086168|gb|EDZ63452.1| ribosomal small subunit pseudouridine synthase A [Campylobacterales
           bacterium GD 1]
          Length = 226

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 52/222 (23%), Positives = 93/222 (41%), Gaps = 2/222 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           RV   ++  G  SR E ++ +   +V+VNG  +      V   D I +D + L     T 
Sbjct: 7   RVDAHLSSLGYCSRSEAKKFLKIFQVRVNGERVFDTNKKVYHNDII-IDEIVLDPETLTV 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L      I            S + +       ++ ++GRLD +T G +LLT+DG L   L
Sbjct: 66  LMHKPSGIICSHDDVGVLIYSLLPERWQKRNPKLSTIGRLDGDTTGAILLTDDGALNHRL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P +   ++Y V     +  ++  +   G +I       +         S + V + + 
Sbjct: 126 TSPKSDISKLYEVTLAQPLKGNEAEIFTSGTLILRGEKKPLLPAKMNV-ISESVVHLEIS 184

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           EGK  ++K++F     KV  L R+S+G + +  L  G  + +
Sbjct: 185 EGKYHQVKRMFAAVGNKVTALHRVSFGKYSIENLAIGEYKIL 226


>gi|74316797|ref|YP_314537.1| ribosomal small subunit pseudouridine synthase A [Thiobacillus
           denitrificans ATCC 25259]
 gi|74056292|gb|AAZ96732.1| pseudouridine synthase, Rsu [Thiobacillus denitrificans ATCC 25259]
          Length = 240

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 51/231 (22%), Positives = 89/231 (38%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            ++ + +   G+ SRR    ++    V  NG+        V      + VDG      ++
Sbjct: 1   MKLYRALQSQGLGSRRGCAALVRAGAVLANGLACADPEAEVDPVGLELTVDGTVWAYRDK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L ++       + H             P +   V  VGRLD +T GLLL ++DG    
Sbjct: 61  AYLVMHKPEGYECSHHPRHHPSVFSLLPAPLVQRGVQCVGRLDQDTTGLLLFSDDGQFIH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  +VYR R    V+   L  L+ G+ +           L  +   +  + + 
Sbjct: 121 RMTSPKKRVGKVYRARCAEPVNAATLAALRAGVQLNDEPAPLA--ALACEAVDDRTLRLV 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           L EGK  +++++       V RL R + G + L   L  G  R +    L+
Sbjct: 179 LAEGKYHQVRRMIAAAGNHVARLHREAVGEYPLPDDLPPGGWRWLEAGDLQ 229


>gi|261415072|ref|YP_003248755.1| pseudouridine synthase [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|261371528|gb|ACX74273.1| pseudouridine synthase [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 234

 Score =  130 bits (326), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 48/228 (21%), Positives = 96/228 (42%), Gaps = 5/228 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERTR 74
           + +++A  G  SR++   ++    V+++G +L+   +   +    I V+G      E+  
Sbjct: 6   LERLLASMGFGSRKDARGLVRMGLVELDGKVLDDPFMEFKTRPEFITVNGEEAPTVEKLY 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + LY       + ++                  + SVGRLD ++ GLLLL+N G     +
Sbjct: 66  VMLYKPTDVECSHNARDHKPVYDLLPERFTAMGIQSVGRLDADSSGLLLLSNQGDFIHKV 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           E P     + YRV         +   L  G++++      +   ++    +   V + + 
Sbjct: 126 ESPKKGLWKKYRVTLARPFTDAQKAELLAGVMLKDERRPVLAREIEVSGDA---VDISIG 182

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           EG   +++++F      V  L RI+ GP  L  TL  G  R ++ + +
Sbjct: 183 EGLYHQVRRMFAAVGNHVETLERIAIGPVVLDRTLGEGGWRFLTDEEV 230


>gi|254283917|ref|ZP_04958885.1| ribosomal large subunit pseudouridine synthase B [gamma
           proteobacterium NOR51-B]
 gi|219680120|gb|EED36469.1| ribosomal large subunit pseudouridine synthase B [gamma
           proteobacterium NOR51-B]
          Length = 265

 Score =  130 bits (326), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 67/266 (25%), Positives = 108/266 (40%), Gaps = 5/266 (1%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL---RKAERTRLWLYHKPIGLVTT 87
           +ER I Q R++++G +       +     ++VDG  L   RK E   L  +     + + 
Sbjct: 1   MERWIEQGRIEIDGRVAT-LGDRIYPDQRLKVDGRRLDLERKEEVRCLLYHKPVGEVCSR 59

Query: 88  HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
                 R+           R I +GRLD  T GLLL T DG LA  L  PS++  R Y V
Sbjct: 60  KDPEGRRTVFDSLPALNNGRWIVIGRLDYTTSGLLLFTTDGELANGLMHPSSEIDREYLV 119

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
           R  G+VD   L+ L++G+++         +      G N W  V L EG+NRE+++++E 
Sbjct: 120 RVMGEVDDAMLDRLRQGVLLDDGPARFTDIQEGGGDGINRWFYVVLMEGRNREVRRLWES 179

Query: 208 FNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSET 266
               V+RL R+ +G   +   L  G   E+ +K +        L    V         + 
Sbjct: 180 QGLTVSRLKRVRFGEVFIPSKLKKGQWMELPEKDVEVLYQMAKLPAKPVVPLTAREQEKQ 239

Query: 267 LVRDRPNIISEVPDDFTRMKKNSSQK 292
               + +                 +K
Sbjct: 240 ERLTKKSGRRIQRPGKGGKPWRVRKK 265


>gi|294788264|ref|ZP_06753507.1| ribosomal small subunit pseudouridine synthase A [Simonsiella
           muelleri ATCC 29453]
 gi|294483695|gb|EFG31379.1| ribosomal small subunit pseudouridine synthase A [Simonsiella
           muelleri ATCC 29453]
          Length = 227

 Score =  130 bits (326), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 45/228 (19%), Positives = 90/228 (39%), Gaps = 8/228 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGV--PLRKAE 71
           + K +   GI SR+  + +I    V++NG ++      +   +     +DG    +    
Sbjct: 3   LLKYLQAQGIGSRKMCQTLIRCGLVQINGEIINNEKAEITPENVQTMNIDGEDAVVIPLP 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              + L        +          +        + + ++GRLD +T G+LL+TNDG   
Sbjct: 63  YYYILLNKPENYETSHKPRDYPSVFMLFPDHLRATDIQAIGRLDADTTGVLLITNDGQFN 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             +  P  +  ++YRV      ++     LK G+++         +    T   S   + 
Sbjct: 123 HKMTSPKHKVAKIYRVTLKHSANESICETLKNGVLLHDDNETVSAENAELT---SPTELI 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + + EGK  ++K++      +V  L R+ +G +    L AG  R +  
Sbjct: 180 LTISEGKYHQVKRMVAAAGNRVEALHRLQFGDWGTEDLAAGEWRFIQP 227


>gi|309379227|emb|CBX22184.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 230

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 45/228 (19%), Positives = 89/228 (39%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPLR--K 69
            ++ K +   GI SR++ + +I    V +NGI ++    ++ S+      +DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIRGGYVSINGICMDDTDADIDSSSVETLDIDGKAVTVIP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 61  EPYFYILLNKPTDYETSHKPKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGH 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAW 188
           L   L  P+ +  ++Y V       +     LK G+++            +     S + 
Sbjct: 121 LNHKLTSPNHKIPKLYEVTLKHPAGETLCETLKNGVLLHDENETVYAADAVL---ESPSA 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 178 LLLTITEGKYHQVKRMVAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 225


>gi|114562089|ref|YP_749602.1| pseudouridine synthase, Rsu [Shewanella frigidimarina NCIMB 400]
 gi|114333382|gb|ABI70764.1| Pseudouridine synthase, Rsu [Shewanella frigidimarina NCIMB 400]
          Length = 237

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 62/236 (26%), Positives = 101/236 (42%), Gaps = 8/236 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + IA      ++ V  ++   +V V+G   +   + V    HIE +GV LR+ ++  
Sbjct: 7   RLDQFIAGTLQIPKKAVRLLLVTNKVLVDGQFAKSPDLQVDEFTHIECNGVVLRQYQKQY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             L      +V+   D    + +          +   GRLD+++ GLLLLTND   +  L
Sbjct: 67  YMLNKPDG-VVSATIDDKHATALGLITGVNTDMLHIAGRLDLHSTGLLLLTNDAKWSEAL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTVG 192
             P  +  + Y V     ++Q+ +    KG+    + I     Q+TL     S+    V 
Sbjct: 126 MDPQHKVDKQYLVTLANPLEQEYVEAFSKGMYFGFEDITTLPAQLTLL----SSHRARVV 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGP 247
           LREGK  +IK++F  F   V  L R S G   L   L  G  R ++K  +      
Sbjct: 182 LREGKYHQIKRMFGRFRNPVVALHRESIGKIVLDKQLELGEFRSLTKAEVDSIFQH 237


>gi|268594989|ref|ZP_06129156.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae 35/02]
 gi|291043587|ref|ZP_06569303.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae DGI2]
 gi|293398899|ref|ZP_06643064.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae F62]
 gi|268548378|gb|EEZ43796.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae 35/02]
 gi|291012050|gb|EFE04039.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae DGI2]
 gi|291610313|gb|EFF39423.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae F62]
          Length = 241

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 44/227 (19%), Positives = 88/227 (38%), Gaps = 6/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLR--K 69
            ++ K +   GI SR++ + +I    V +NG  ++    ++ S+  + +++DG  +    
Sbjct: 12  MKLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSYVETLDIDGEAVTVVP 71

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 72  EPYFYILLNKPEDYETSHKPKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 131

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS +  ++Y V       +     LK G+ +              +      +
Sbjct: 132 LNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVPLHDENETVCAADAVLENP--TTL 189

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 190 LLTITEGKYHQVKRMVAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 236


>gi|59801035|ref|YP_207747.1| hypothetical protein NGO0607 [Neisseria gonorrhoeae FA 1090]
 gi|194098870|ref|YP_002001934.1| Ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae NCCP11945]
 gi|254493930|ref|ZP_05107101.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae 1291]
 gi|260440294|ref|ZP_05794110.1| Ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae DGI2]
 gi|268599217|ref|ZP_06133384.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae MS11]
 gi|268601564|ref|ZP_06135731.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae PID18]
 gi|268603903|ref|ZP_06138070.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae PID1]
 gi|268684524|ref|ZP_06151386.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae SK-92-679]
 gi|268686834|ref|ZP_06153696.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae SK-93-1035]
 gi|59717930|gb|AAW89335.1| conserved hypothetical protein [Neisseria gonorrhoeae FA 1090]
 gi|193934160|gb|ACF29984.1| Ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae NCCP11945]
 gi|226512970|gb|EEH62315.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae 1291]
 gi|268583348|gb|EEZ48024.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae MS11]
 gi|268585695|gb|EEZ50371.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae PID18]
 gi|268588034|gb|EEZ52710.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae PID1]
 gi|268624808|gb|EEZ57208.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae SK-92-679]
 gi|268627118|gb|EEZ59518.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae SK-93-1035]
 gi|317164444|gb|ADV07985.1| hypothetical protein NGTW08_1017 [Neisseria gonorrhoeae
           TCDC-NG08107]
          Length = 230

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 44/227 (19%), Positives = 88/227 (38%), Gaps = 6/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLR--K 69
            ++ K +   GI SR++ + +I    V +NG  ++    ++ S+  + +++DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSYVETLDIDGEAVTVVP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 61  EPYFYILLNKPEDYETSHKPKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS +  ++Y V       +     LK G+ +              +      +
Sbjct: 121 LNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVPLHDENETVCAADAVLENP--TTL 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 179 LLTITEGKYHQVKRMVAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 225


>gi|34558267|ref|NP_908082.1| putative ribosomal pseudouridine synthase [Wolinella succinogenes
           DSM 1740]
 gi|34483986|emb|CAE10982.1| PUTATIVE RIBOSOMAL PSEUDOURIDINE SYNTHASE [Wolinella succinogenes]
          Length = 293

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 74/292 (25%), Positives = 130/292 (44%), Gaps = 18/292 (6%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +       R+++ I+     SRRE + +I   RV +    +E  A  V   + + +DG  
Sbjct: 4   IDPKEPTMRLNQYISHHSKYSRREADELIKAGRVNIEKRKIENLATQVKEDERVFIDGKF 63

Query: 67  LRKA--ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
           L++   E   + +YHKP G + T SD  GR T++D+LPS F   I VGRLD  +EGLLLL
Sbjct: 64  LKEKSEENYTVIVYHKPKGELVTKSDDRGRKTIYDSLPSGFKHFIPVGRLDFASEGLLLL 123

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG----------- 173
           T+   +A+ L     +  RVY ++   +V  + +  +++G+V++    G           
Sbjct: 124 TDSPKVAKALMES--ELERVYHLKIDKRVSPEMIKAMEEGLVLEDASAGGHEKSEIKSMS 181

Query: 174 ---DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                   +     +++ + V ++EGKNRE+++ F  F  KV  L R+SYG   L  L  
Sbjct: 182 FSPFAGFEVAKDSPTHSKIKVAIKEGKNRELRRFFAHFGAKVLDLKRVSYGWVSLNALPD 241

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDF 282
           G  R +++    +        +     +     +      + +         
Sbjct: 242 GKNRYLNRSEYNKLHAFMKELQKSEEKEKKPRKASYRSATKSDSARAPRKKG 293


>gi|313668437|ref|YP_004048721.1| ribosomal small subunit pseudouridine synthase [Neisseria lactamica
           ST-640]
 gi|313005899|emb|CBN87355.1| putative ribosomal small subunit pseudouridine synthase [Neisseria
           lactamica 020-06]
          Length = 230

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 44/228 (19%), Positives = 88/228 (38%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPLR--K 69
            ++ K +   GI SR++ + +I    V +NG  ++    ++ S+      +DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSSVETLDIDGEAVTVVP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 61  EPYFYILLNKPEDYETSHKPKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGH 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAW 188
           L   L  P+ +  ++Y V       +     LK G+++            +     S + 
Sbjct: 121 LNHKLTSPNHKIPKLYEVTLKHPAGETLCETLKNGVLLHDENETVYAADAVL---ESPSA 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 178 LLLTITEGKYHQVKRMVAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 225


>gi|221198326|ref|ZP_03571372.1| RNA pseudouridine synthase family protein [Burkholderia multivorans
           CGD2M]
 gi|221182258|gb|EEE14659.1| RNA pseudouridine synthase family protein [Burkholderia multivorans
           CGD2M]
          Length = 512

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 60/251 (23%), Positives = 101/251 (40%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 264 MRLSKRMSELGLCSRREADEWIEKGWVIVDGERIDTLGTKVRADQRIEIDERAQAAQAAQ 323

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     L+T  +   G  +     P     +   GRLDI++
Sbjct: 324 VTILLHKPVGYVSGQAEDGYEPASVLITRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 383

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                ++L  L+ G+ + G
Sbjct: 384 TGLLVLTQNGRIAKQLIGEQSDVDKEYLVRVRFGDRLTDIDQHFPAERLAQLRHGLELDG 443

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREG+ R+I+++ E    +V  L R+  G   LG L 
Sbjct: 444 VALKPAMVSWQNGEQ----LRFVLREGRKRQIRRMCELVGLEVIGLKRVRMGRVTLGALP 499

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 500 QGQWRYLSADE 510



 Score = 37.1 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 14/102 (13%), Positives = 30/102 (29%), Gaps = 4/102 (3%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
                 SSE   R   +         T   K +  ++G +  +            S+   
Sbjct: 134 FGERRASSERPARRNDDDARPRRAGATEGGKRAPYRDGAAGGEGPKRGSFGERRTSSERP 193

Query: 317 AKGIHSSFLSDSGQREENHRRSP----SFPSKRSLRRTSAKK 354
           A+              E  +R+P    +   + + R T+ ++
Sbjct: 194 ARRNDDDARPRRAGAAEGGKRAPYRDGAAGGEGAKRGTAERR 235


>gi|291543398|emb|CBL16507.1| pseudouridine synthase family [Ruminococcus sp. 18P13]
          Length = 255

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 61/242 (25%), Positives = 101/242 (41%), Gaps = 6/242 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K IA     SR+EV+ ++ +  V+VNG   +     V    D I + GV L  A  
Sbjct: 1   MRLDKCIADHSAYSRKEVKELLRRGSVRVNGAPEQDPGRQVDPEGDEIMLAGVILPTALH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      + ++      ++ V    P +   +   GRLD++TEG+LLLTNDG LA 
Sbjct: 61  RTYMLNKPKGCI-SSTRTGKTKTVVEFLPPELRKGIFPAGRLDVDTEGMLLLTNDGDLAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V+    V +  +   + G+V++        +V       + A V  
Sbjct: 120 RILSPRRHIPKYYLVQLAKPVVEKTVETFENGVVLEDGTRCLPARVAALPGVENTALVE- 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLL 250
            L EGK  ++K++F      V +L+R+  G   +   L  G    +  K +         
Sbjct: 179 -LHEGKFHQVKRMFAAVENHVEQLLRVQMGGLPIDVKLGKGDYLLLLHKDIERLFKTPDF 237

Query: 251 EE 252
            E
Sbjct: 238 SE 239


>gi|172060970|ref|YP_001808622.1| RNA-binding S4 domain-containing protein [Burkholderia ambifaria
           MC40-6]
 gi|171993487|gb|ACB64406.1| RNA-binding S4 domain protein [Burkholderia ambifaria MC40-6]
          Length = 646

 Score =  129 bits (325), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 60/251 (23%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V     IE+D          
Sbjct: 398 MRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPDQKIEIDERASAAQAAQ 457

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     L+T  +   G  +     P     +   GRLDI++
Sbjct: 458 VTILLHKPVGYVSGQAEDGYEPASVLITRANQWSGDRSPLRFSPQHLHALAPAGRLDIDS 517

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            G+L+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 518 TGMLVLTQNGRIAKQLIGEQSDIDKEYLVRVRFGERLLDIDQHFPAESLAKLRHGLELDG 577

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 578 VALKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 633

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 634 QGQWRYLSPDE 644



 Score = 41.3 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 11/114 (9%), Positives = 30/114 (26%), Gaps = 3/114 (2%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            +        E          ++    +   +      D   R   + ++      +   
Sbjct: 239 DDTRPRRAGAEGGARAPYRDKTTGDAPKRSFDERRTSSDRPARRSDDDTRPRRAGAEGGA 298

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENH---RRSPSFPSKRSLRRTSA 352
             P   + +      + G   +      +R ++    RR+ +    R+  R  A
Sbjct: 299 RAPYRDKAIGDAPKRSFGERRTSTDRPARRSDDDARPRRAGAEGGARAPYRDKA 352



 Score = 39.8 bits (91), Expect = 0.60,   Method: Composition-based stats.
 Identities = 11/113 (9%), Positives = 29/113 (25%), Gaps = 3/113 (2%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            +        E          ++    +      S   D   R   + ++      +   
Sbjct: 147 DDARPRRAGAEGGARAPYRDKATGYGEKRSFGERSTSSDRPARRSDDDTRPRRAGGEGGA 206

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENH---RRSPSFPSKRSLRRTS 351
             P   +  +     + G   +      +R ++    RR+ +    R+  R  
Sbjct: 207 RAPYRDKATSDAPKRSFGERRTSSDRPARRSDDDTRPRRAGAEGGARAPYRDK 259



 Score = 39.8 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 12/113 (10%), Positives = 27/113 (23%), Gaps = 3/113 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +        E          +     +          D   R   + ++      +    
Sbjct: 102 DARPRRAGAEGGARAPYRDKAEGYGEKRSFGERRTSTDRPARRSDDDARPRRAGAEGGAR 161

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENH---RRSPSFPSKRSLRRTSA 352
            P   +        + G  S+      +R ++    RR+      R+  R  A
Sbjct: 162 APYRDKATGYGEKRSFGERSTSSDRPARRSDDDTRPRRAGGEGGARAPYRDKA 214



 Score = 39.8 bits (91), Expect = 0.74,   Method: Composition-based stats.
 Identities = 10/114 (8%), Positives = 27/114 (23%), Gaps = 3/114 (2%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            +        E          ++    +          D   R   + ++      +   
Sbjct: 193 DDTRPRRAGGEGGARAPYRDKATSDAPKRSFGERRTSSDRPARRSDDDTRPRRAGAEGGA 252

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENH---RRSPSFPSKRSLRRTSA 352
             P   +        +     +      +R ++    RR+ +    R+  R  A
Sbjct: 253 RAPYRDKTTGDAPKRSFDERRTSSDRPARRSDDDTRPRRAGAEGGARAPYRDKA 306



 Score = 37.1 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 11/108 (10%), Positives = 26/108 (24%), Gaps = 3/108 (2%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               E      AP   +                  +   +  ++      +     P   
Sbjct: 61  PRGAERPGADRAPAKRAPRDGGAERGDARPARPYRSAEGQPDARPRRAGAEGGARAPYRD 120

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENH---RRSPSFPSKRSLRRTSA 352
           +        + G   +      +R ++    RR+ +    R+  R  A
Sbjct: 121 KAEGYGEKRSFGERRTSTDRPARRSDDDARPRRAGAEGGARAPYRDKA 168



 Score = 35.9 bits (81), Expect = 9.6,   Method: Composition-based stats.
 Identities = 13/110 (11%), Positives = 25/110 (22%), Gaps = 2/110 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+ + P     A         ++     +R                          ++  
Sbjct: 28  RKAVRPAGPPAADKPPRPKKAAAPAAAGERAFKPRGAERPGADRAPAKRAPRDGGAERGD 87

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
           A P   R   S             ++ G R     ++  +  KRS     
Sbjct: 88  ARPA--RPYRSAEGQPDARPRRAGAEGGARAPYRDKAEGYGEKRSFGERR 135


>gi|254181470|ref|ZP_04888067.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1655]
 gi|184212008|gb|EDU09051.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1655]
          Length = 240

 Score =  129 bits (325), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 51/228 (22%), Positives = 88/228 (38%), Gaps = 4/228 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   ++    V V G     A  +  +T  + EVDG+      R  
Sbjct: 3   LESILFTQGFGSRRQCRALVEAGHVAVGGATCADAHASFDTTQLVFEVDGIAWPYRARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        +                     V  VGRLD +T GLLLL++DG      
Sbjct: 63  VALNKPAGYECSREPQHHSSVFALLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVHAY 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y       +D  +L+ L+ G+++ G         L         + + + 
Sbjct: 123 TSPKRKVPKTYVATVRHPLDDAQLDALRAGVLLHGEPKPVA--ALAAVARGERLLEMTIA 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           EGK  ++K++    + +V  L R   G F L   L  G+ R + ++ L
Sbjct: 181 EGKYHQVKRMVAAASNRVEALHRSRIGGFALPEDLAEGAWRWLDERDL 228


>gi|53718572|ref|YP_107558.1| putative ribosomal small subunit pseudouridine synthase A
           [Burkholderia pseudomallei K96243]
 gi|53725922|ref|YP_103555.1| ribosomal small subunit pseudouridine synthase A [Burkholderia
           mallei ATCC 23344]
 gi|67643830|ref|ZP_00442573.1| RNA pseudouridine synthase family protein [Burkholderia mallei GB8
           horse 4]
 gi|76808867|ref|YP_332565.1| ribosomal small subunit pseudouridine synthase A [Burkholderia
           pseudomallei 1710b]
 gi|121599028|ref|YP_992290.1| RNA pseudouridine synthase family protein [Burkholderia mallei
           SAVP1]
 gi|124385466|ref|YP_001026865.1| RNA pseudouridine synthase family protein [Burkholderia mallei NCTC
           10229]
 gi|126440770|ref|YP_001058044.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 668]
 gi|126450171|ref|YP_001079848.1| RNA pseudouridine synthase family protein [Burkholderia mallei NCTC
           10247]
 gi|126454957|ref|YP_001065281.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1106a]
 gi|134281077|ref|ZP_01767786.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 305]
 gi|166999977|ref|ZP_02265806.1| RNA pseudouridine synthase family protein [Burkholderia mallei
           PRL-20]
 gi|167718484|ref|ZP_02401720.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei DM98]
 gi|167737534|ref|ZP_02410308.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 14]
 gi|167814653|ref|ZP_02446333.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 91]
 gi|167823121|ref|ZP_02454592.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 9]
 gi|167893211|ref|ZP_02480613.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 7894]
 gi|167901665|ref|ZP_02488870.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei NCTC 13177]
 gi|167909915|ref|ZP_02497006.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 112]
 gi|167917937|ref|ZP_02505028.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei BCC215]
 gi|217419721|ref|ZP_03451227.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 576]
 gi|226194533|ref|ZP_03790131.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei Pakistan 9]
 gi|242315027|ref|ZP_04814043.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1106b]
 gi|254175384|ref|ZP_04882044.1| RNA pseudouridine synthase family protein [Burkholderia mallei ATCC
           10399]
 gi|254190858|ref|ZP_04897365.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei Pasteur 52237]
 gi|254197033|ref|ZP_04903457.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei S13]
 gi|254202240|ref|ZP_04908603.1| RNA pseudouridine synthase family protein [Burkholderia mallei FMH]
 gi|254207573|ref|ZP_04913923.1| RNA pseudouridine synthase family protein [Burkholderia mallei JHU]
 gi|254262015|ref|ZP_04953069.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1710a]
 gi|52208986|emb|CAH34925.1| putative ribosomal small subunit pseudouridine synthase A
           [Burkholderia pseudomallei K96243]
 gi|52429345|gb|AAU49938.1| ribosomal small subunit pseudouridine synthase A [Burkholderia
           mallei ATCC 23344]
 gi|76578320|gb|ABA47795.1| ribosomal small subunit pseudouridine synthase A [Burkholderia
           pseudomallei 1710b]
 gi|121227838|gb|ABM50356.1| RNA pseudouridine synthase family protein [Burkholderia mallei
           SAVP1]
 gi|124293486|gb|ABN02755.1| RNA pseudouridine synthase family protein [Burkholderia mallei NCTC
           10229]
 gi|126220263|gb|ABN83769.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 668]
 gi|126228599|gb|ABN92139.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1106a]
 gi|126243041|gb|ABO06134.1| RNA pseudouridine synthase family protein [Burkholderia mallei NCTC
           10247]
 gi|134247383|gb|EBA47468.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 305]
 gi|147746487|gb|EDK53564.1| RNA pseudouridine synthase family protein [Burkholderia mallei FMH]
 gi|147751467|gb|EDK58534.1| RNA pseudouridine synthase family protein [Burkholderia mallei JHU]
 gi|157938533|gb|EDO94203.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei Pasteur 52237]
 gi|160696428|gb|EDP86398.1| RNA pseudouridine synthase family protein [Burkholderia mallei ATCC
           10399]
 gi|169653776|gb|EDS86469.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei S13]
 gi|217397025|gb|EEC37041.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 576]
 gi|225933618|gb|EEH29607.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei Pakistan 9]
 gi|238525270|gb|EEP88698.1| RNA pseudouridine synthase family protein [Burkholderia mallei GB8
           horse 4]
 gi|242138266|gb|EES24668.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1106b]
 gi|243064092|gb|EES46278.1| RNA pseudouridine synthase family protein [Burkholderia mallei
           PRL-20]
 gi|254220704|gb|EET10088.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1710a]
          Length = 240

 Score =  129 bits (325), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 52/228 (22%), Positives = 88/228 (38%), Gaps = 4/228 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   ++    V V G     A  +  +T  + EVDGV      R  
Sbjct: 3   LESILFTQGFGSRRQCRALVEAGHVAVGGATCADAHASFDTTQLVFEVDGVAWPYRARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        +                     V  VGRLD +T GLLLL++DG      
Sbjct: 63  VALNKPAGYECSREPQHHSSVFALLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVHAY 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y       +D  +L+ L+ G+++ G         L         + + + 
Sbjct: 123 TSPKRKVPKTYVATVRHPLDDAQLDALRAGVLLHGEPKPVA--ALAAVARGERLLEMTIA 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           EGK  ++K++    + +V  L R   G F L   L  G+ R + ++ L
Sbjct: 181 EGKYHQVKRMVAAASNRVEALHRSRIGGFALPEDLAEGAWRWLDERDL 228


>gi|76810574|ref|YP_333978.1| pseudouridine synthase family protein [Burkholderia pseudomallei
           1710b]
 gi|76580027|gb|ABA49502.1| pseudouridine synthase family protein [Burkholderia pseudomallei
           1710b]
          Length = 585

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 337 VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 396

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 397 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 456

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 457 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDG 516

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 517 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 572

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 573 QGEWRYLGPDE 583


>gi|312795325|ref|YP_004028247.1| ribosomal small subunit pseudouridine synthase A [Burkholderia
           rhizoxinica HKI 454]
 gi|312167100|emb|CBW74103.1| Ribosomal small subunit pseudouridine synthase A (EC 4.2.1.70)
           [Burkholderia rhizoxinica HKI 454]
          Length = 258

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 50/228 (21%), Positives = 84/228 (36%), Gaps = 4/228 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERTR 74
           +  ++   G  SRRE   ++ +  V +     +              VDGV      +  
Sbjct: 28  LENILFSQGFGSRRECRALVIRGAVTIGEQRCDDPDAVFEPAGLVFHVDGVRWAYRHQAY 87

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L+  P    +                 I   V  VGRLD +T GLLLL++DG     L
Sbjct: 88  LVLHKPPGYECSHAPQHHPSVYSLLPPALITRGVQCVGRLDADTTGLLLLSDDGAFIHRL 147

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y       V   +L+ L++G+ + G     + V    +      + + L 
Sbjct: 148 SSPKHKIPKTYVATTRHPVRDAQLDALRQGVQLHGEPA--VSVARSARLRDEHTIELVLT 205

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           EGK  ++K++      +V +L R + G   L   L  G    +    L
Sbjct: 206 EGKYHQVKRMIAAAGNRVEQLHREAIGALVLPAALAPGQWWWLEADEL 253


>gi|302327988|gb|ADL27189.1| ribosomal small subunit pseudouridine synthase A [Fibrobacter
           succinogenes subsp. succinogenes S85]
          Length = 231

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 48/228 (21%), Positives = 96/228 (42%), Gaps = 5/228 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERTR 74
           + +++A  G  SR++   ++    V+++G +L+   +   +    I V+G      E+  
Sbjct: 3   LERLLASMGFGSRKDARGLVRMGLVELDGKVLDDPFMEFKTRPEFITVNGEEAPTVEKLY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + LY       + ++                  + SVGRLD ++ GLLLL+N G     +
Sbjct: 63  VMLYKPTDVECSHNARDHKPVYDLLPERFTAMGIQSVGRLDADSSGLLLLSNQGDFIHKV 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           E P     + YRV         +   L  G++++      +   ++    +   V + + 
Sbjct: 123 ESPKKGLWKKYRVTLARPFTDAQKAELLAGVMLKDERRPVLAREIEVSGDA---VDISIG 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           EG   +++++F      V  L RI+ GP  L  TL  G  R ++ + +
Sbjct: 180 EGLYHQVRRMFAAVGNHVETLERIAIGPVVLDRTLGEGGWRFLTDEEV 227


>gi|217421322|ref|ZP_03452826.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 576]
 gi|217395064|gb|EEC35082.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 576]
          Length = 574

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 326 VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 385

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 386 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 445

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 446 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDG 505

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 506 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 561

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 562 QGEWRYLGPDE 572



 Score = 36.3 bits (82), Expect = 6.8,   Method: Composition-based stats.
 Identities = 13/113 (11%), Positives = 24/113 (21%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R +              A         R   +     P       +           K  
Sbjct: 169 RGKDRAPREGARPGARGATGAKFGGAARRSDDADRRTPRATRADSRARDAAPSSFAGKTA 228

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                    A + + A G  +S   +  +R       P+  +  S  R    +
Sbjct: 229 TAGKRAPQRADDRYGAAGKRTSPRPERTERPARFGERPATRASASGERRPTAR 281


>gi|115450787|ref|NP_001048994.1| Os03g0152700 [Oryza sativa Japonica Group]
 gi|108706231|gb|ABF94026.1| RNA pseudouridylate synthase family protein, expressed [Oryza
           sativa Japonica Group]
 gi|113547465|dbj|BAF10908.1| Os03g0152700 [Oryza sativa Japonica Group]
          Length = 415

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 61/225 (27%), Positives = 100/225 (44%), Gaps = 16/225 (7%)

Query: 4   KNIVQENF---TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDH 59
           +    EN     PQR++KV+A AG+ASRR  E +I Q +V VNG +       V  S D 
Sbjct: 160 RRFYNENIKEHEPQRLAKVLAAAGVASRRTCEELIFQGKVTVNGSVCTAPQTKVDISKDS 219

Query: 60  IEVDGVPLRKAERTRLWL--YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--------I 109
           I V+G  + K    +L+         + +        S   D L                
Sbjct: 220 IYVNGNRISKKLPPKLYFAVNKPKGYICSCGEPKSIISLFDDYLKGWNKIQPGVPKPRLF 279

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           +VGRLD+ T GL+++TNDG  A+ L  PS+  ++ Y V   G V ++ L  + +G  I G
Sbjct: 280 TVGRLDVATSGLIIITNDGEFAQKLSHPSSNIMKEYVVTIDGPVHRNHLIAISEGTKIDG 339

Query: 170 ICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           +       +            + + + EG+N E++++ +    +V
Sbjct: 340 VKCIPDLVEPLDVQSNTKRTRIRIAVHEGRNHEVRELVQNAGLEV 384


>gi|315453388|ref|YP_004073658.1| putative ribosomal pseudouridine synthase [Helicobacter felis ATCC
           49179]
 gi|315132440|emb|CBY83068.1| putative ribosomal pseudouridine synthase [Helicobacter felis ATCC
           49179]
          Length = 250

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 70/240 (29%), Positives = 113/240 (47%), Gaps = 16/240 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ IAR    SRR+ + +IA+ +VK+N  +           D I ++G  L+  +  
Sbjct: 1   MRLNQFIARYAHCSRRQADTLIAEGKVKINHQVA-SFTTPFNKEDKIFIEGRLLKIPKAP 59

Query: 74  RL--WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R    +YHKP G +    D   R T+F++L   F+  I VGRLD  + GLLLL++  G+A
Sbjct: 60  RYSVVIYHKPKGELVARRDDRARPTIFESLDRKFAHFIPVGRLDFASSGLLLLSDHSGVA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG-----------DMQVTLD 180
             L   +    RVY ++  G +  + L  ++ GI      +                 + 
Sbjct: 120 SALMHSA--LERVYLLKIQGPITPEILEGMQNGICSHKGAHPNNPKQSLELPPFAHCHII 177

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 + + + L EGKNRE+++ F  F+  V  L R+SYG   L  L  G TR ++ K 
Sbjct: 178 KNHPHFSKLKITLTEGKNRELRRFFAHFDRAVLDLQRVSYGFTHLNALPEGKTRYLNPKE 237


>gi|254197891|ref|ZP_04904313.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei S13]
 gi|169654632|gb|EDS87325.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei S13]
          Length = 574

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 326 VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 385

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 386 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 445

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 446 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDG 505

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 506 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 561

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 562 QGEWRYLGPDE 572


>gi|167844683|ref|ZP_02470191.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei B7210]
          Length = 240

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 52/228 (22%), Positives = 87/228 (38%), Gaps = 4/228 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   ++    V V G     A     +T  + EVDGV      R  
Sbjct: 3   LESILFTQGFGSRRQCRALVEAGHVAVGGATCADAHAPFDTTQLVFEVDGVAWPYRARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        +                     V  VGRLD +T GLLLL++DG      
Sbjct: 63  VALNKPAGYECSREPQHHSSVFALLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVHAY 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y       +D  +L+ L+ G+++ G         L         + + + 
Sbjct: 123 TSPKRKVPKTYVATVRHPLDDAQLDALRAGVLLHGEPKPVA--ALAAVARGERLLEMTIA 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           EGK  ++K++    + +V  L R   G F L   L  G+ R + ++ L
Sbjct: 181 EGKYHQVKRMVAAASNRVEALHRSRIGGFALPEDLAEGAWRWLDERDL 228


>gi|171316750|ref|ZP_02905962.1| pseudouridine synthase [Burkholderia ambifaria MEX-5]
 gi|171098100|gb|EDT42915.1| pseudouridine synthase [Burkholderia ambifaria MEX-5]
          Length = 238

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 51/228 (22%), Positives = 83/228 (36%), Gaps = 4/228 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV V G        +  +   +  VD           
Sbjct: 3   LESILYTQGFGSRRQCRGLIETGRVNVAGASATDPDASFDTDGLVFTVDDTAWPFHAHAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L        +               P +   V  VGRLD +T GLLLL++DG      
Sbjct: 63  LALNKPAGYECSRDPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFVHGY 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y       +D  +LN L+ G+ + G     +             + + + 
Sbjct: 123 TSPKRKVPKTYVATVRHPLDDTQLNALRAGVQLHGEP-KPIAAVAAHA-RDTHALALTVL 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           EGK  ++K++    + +V  L R S G F L   L  G+ R +    L
Sbjct: 181 EGKYHQVKRMVAAASNRVEALHRESIGGFTLPDDLAPGAWRWLGASEL 228


>gi|295677418|ref|YP_003605942.1| pseudouridine synthase [Burkholderia sp. CCGE1002]
 gi|295437261|gb|ADG16431.1| pseudouridine synthase [Burkholderia sp. CCGE1002]
          Length = 236

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 52/227 (22%), Positives = 86/227 (37%), Gaps = 6/227 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAA--VNVMSTD-HIEVDGVPLRKAER 72
           +  ++   G  SRR+   +I   RV ++G +   A     V S      VDGV     E 
Sbjct: 3   LESILFTQGFGSRRQCRALIGDGRVGIDGAICTDADADFAVDSGALRFSVDGVEWPYREH 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L        +                     V  VGRLD +T GLLLL++DG    
Sbjct: 63  AYLLLNKPVGYECSRDPQHHLSVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGKFVH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  ++Y       +D  +L  L+ G+++ G         LD +      + + 
Sbjct: 123 QFTSPKRKVPKLYVATTRHPLDDAQLAALRDGVLLHGE-TKP-SAALDAEARDTHTLALT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
           + EGK  ++K++      +   L R   G   L  TL  G+ + + +
Sbjct: 181 VLEGKYHQVKRMIAASGNRCEALHRERIGGLVLPATLAPGAWQWLDE 227


>gi|126451482|ref|YP_001066756.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1106a]
 gi|242315358|ref|ZP_04814374.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1106b]
 gi|126225124|gb|ABN88664.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1106a]
 gi|242138597|gb|EES24999.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1106b]
          Length = 571

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 323 VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 382

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 383 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 442

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 443 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDG 502

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 503 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 558

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 559 QGEWRYLGPDE 569


>gi|261377760|ref|ZP_05982333.1| ribosomal small subunit pseudouridine synthase A [Neisseria cinerea
           ATCC 14685]
 gi|269146049|gb|EEZ72467.1| ribosomal small subunit pseudouridine synthase A [Neisseria cinerea
           ATCC 14685]
          Length = 230

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 49/227 (21%), Positives = 89/227 (39%), Gaps = 6/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLR--K 69
            ++ K +   GI SR++ + +IA   V +NG  +  A  ++ S     +++DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIAGGYVSINGTCMNDADADIDSASVHTLDIDGKAVTIIP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 61  EPYFYILLNKPADYETSHKPKHYRSIFSLFPDNMRNIDMQAVGRLDADTTGVLLVTNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS +  ++Y V      D      LK G+++            D    S   +
Sbjct: 121 LNHNLTSPSRKIPKLYEVTLKHPADGILCETLKNGVLLHDENETVC--AADANLESPTTL 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 179 LLTITEGKYHQVKRMIAAAGNRVQHLHRRQFAHLETKNLKPGEWKFI 225


>gi|326384757|ref|ZP_08206434.1| pseudouridine synthase [Gordonia neofelifaecis NRRL B-59395]
 gi|326196565|gb|EGD53762.1| pseudouridine synthase [Gordonia neofelifaecis NRRL B-59395]
          Length = 362

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 75/235 (31%), Positives = 115/235 (48%), Gaps = 4/235 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R+ KV+A AG+ASRR  E +IA  RV+V+G ++    + +      I+VDG  +  
Sbjct: 119 SDGMRLQKVLAAAGVASRRGAEELIAAGRVEVDGEVVVEQGLRIDPDTAIIKVDGARVVI 178

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTN 126
            E  +    +KP G  +T SD  GR  + D +        R+  VGRLD +TEGLLLLTN
Sbjct: 179 DESKQYLALNKPKGWHSTMSDDQGRPCIGDIIAERVMAGQRLFHVGRLDADTEGLLLLTN 238

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  + Y     G+V++     L++G+ ++          L       
Sbjct: 239 DGELAHRLMHPSYEVPKTYLATVRGEVNRGLGRELRQGVELEDGPVAVDSFALLEVNQGK 298

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + V + L EG+ R ++++     + V  L+R   GP  LG    GS R +  K +
Sbjct: 299 SLVRLTLHEGRKRVVRRLLAEVGFPVVGLVRTDIGPVTLGKQRPGSLRVLDNKEI 353



 Score = 37.9 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 8/84 (9%), Positives = 18/84 (21%)

Query: 260 PIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKG 319
              +S      +        +   R     + +   S  K        +++A       G
Sbjct: 1   MASASRDGTPGKRRDNGRDDNRRGRSSDKQNPRGKSSGGKAAGKSAGGKSVAGKKGAPAG 60

Query: 320 IHSSFLSDSGQREENHRRSPSFPS 343
              +        +    R P    
Sbjct: 61  KRGAGAKRGAPGQHPSSRKPHRKG 84


>gi|237811195|ref|YP_002895646.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei MSHR346]
 gi|237505702|gb|ACQ98020.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei MSHR346]
          Length = 240

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 52/228 (22%), Positives = 88/228 (38%), Gaps = 4/228 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   ++    V V G     A  +  +T  + EVDGV      R  
Sbjct: 3   LESILFTQGFGSRRQCRALVEAGHVAVGGATCADAHASFDTTQLVFEVDGVAWPYRARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        +                     V  VGRLD +T GLLLL++DG      
Sbjct: 63  VALNKPAGYECSREPQHHSSVFALLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVHAY 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y       +D  +L+ L+ G+++ G         L         + + + 
Sbjct: 123 TSPKRKVPKTYVATVRHPLDDAQLDALRAGVLLHGEPKPVA--ALAAVARGERLLEMTIA 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           EGK  ++K++    + +V  L R   G F L   L  G+ R + ++ L
Sbjct: 181 EGKYHQVKRMVAAASNRVEALHRSRIGGFALPENLAEGAWRWLDERDL 228


>gi|302819504|ref|XP_002991422.1| hypothetical protein SELMODRAFT_45109 [Selaginella moellendorffii]
 gi|300140815|gb|EFJ07534.1| hypothetical protein SELMODRAFT_45109 [Selaginella moellendorffii]
          Length = 251

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 66/230 (28%), Positives = 107/230 (46%), Gaps = 16/230 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPL--R 68
             +R+SKV+A AG+ASRR  E +I   +V VNG +      +V    D I +DG P+  R
Sbjct: 18  KAERLSKVMAAAGVASRRACEEIIFAGKVVVNGKVCRTPETHVDPLKDLIYIDGKPIPRR 77

Query: 69  KAERTRLWLYHKPIGLVTTHSDP----------DGRSTVFDNLPSIFSRVISVGRLDINT 118
              +    LY     + +   D             ++   +N      R  +VGRLD+ T
Sbjct: 78  LPPKMVFALYKPKGYICSDAKDDKKTVYLLLEKYLKTWEKNNPGLTKPRFFTVGRLDVAT 137

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQGICYGDMQV 177
            GL+ +TNDG  A+ +  PS+   + Y V    + V + +L  +  G  I G+    + V
Sbjct: 138 TGLIFVTNDGEFAQKVSHPSSGITKEYLVTVDNESVTKRQLKRIASGTEIDGVMCVPISV 197

Query: 178 TLDTQKG--SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            L   +   S   + V + EG+N E++++ E    KV+ L R+  G  +L
Sbjct: 198 ELVKSEPGDSRHRIRVVVTEGRNHEVRQLVESAFLKVHALKRVRVGGLRL 247


>gi|172061447|ref|YP_001809099.1| pseudouridine synthase [Burkholderia ambifaria MC40-6]
 gi|171993964|gb|ACB64883.1| pseudouridine synthase [Burkholderia ambifaria MC40-6]
          Length = 238

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 53/234 (22%), Positives = 87/234 (37%), Gaps = 4/234 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV V G        +  +   +  VD        R  
Sbjct: 3   LESILYTQGFGSRRQCRGLIETGRVSVAGASATDPDASFDTDGLVFTVDDTAWPFHARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L        +               P +   V  VGRLD +T GLLLL++DG      
Sbjct: 63  LALNKPAGYECSRDPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFVHAY 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y       +D  +LN L+ G+ + G     +             + + + 
Sbjct: 123 TSPKRKVPKTYVATVRHPLDDTQLNALRAGVQLHGEP-KPIAAVAAHA-RDTHALALTVL 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGP 247
           EGK  ++K++    + +V  L R S G F L   L  G+ R + ++ L     P
Sbjct: 181 EGKYHQVKRMVAAASNRVEALHRESIGGFTLPVDLAPGAWRWLGERDLSALRDP 234


>gi|207091745|ref|ZP_03239532.1| hypothetical protein HpylHP_01046 [Helicobacter pylori
           HPKX_438_AG0C1]
          Length = 257

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 62/249 (24%), Positives = 117/249 (46%), Gaps = 19/249 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  
Sbjct: 1   MRINQFLAHYTKCSRREAEKLVLEGRVKINHEHAK-LASVVKENDKVFLDKRLIKPLKNK 59

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQV 177
             L        + Y V+  G V ++  N +++G+ ++                    +  
Sbjct: 120 SALMHA--NLEKEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVVINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQLG 246
           ++   E   
Sbjct: 238 RQEYNELHA 246


>gi|302813266|ref|XP_002988319.1| hypothetical protein SELMODRAFT_45172 [Selaginella moellendorffii]
 gi|300144051|gb|EFJ10738.1| hypothetical protein SELMODRAFT_45172 [Selaginella moellendorffii]
          Length = 251

 Score =  129 bits (324), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 66/230 (28%), Positives = 107/230 (46%), Gaps = 16/230 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPL--R 68
             +R+SKV+A AG+ASRR  E +I   +V VNG +      +V    D I +DG P+  R
Sbjct: 18  KAERLSKVMAAAGVASRRACEEIIFAGKVVVNGKVCRTPETHVDPLKDLIYIDGKPIPRR 77

Query: 69  KAERTRLWLYHKPIGLVTTHSDP----------DGRSTVFDNLPSIFSRVISVGRLDINT 118
              +    LY     + +   D             ++   +N      R  +VGRLD+ T
Sbjct: 78  LPPKMVFALYKPKGYICSDAKDDKKTVYLLLEKYLKTWEKNNPGLTKPRFFTVGRLDVAT 137

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQGICYGDMQV 177
            GL+ +TNDG  A+ +  PS+   + Y V    + V + +L  +  G  I G+    + V
Sbjct: 138 TGLIFVTNDGEFAQKVSHPSSGITKEYLVTVDSESVTKRQLKRIASGTEIDGVMCVPISV 197

Query: 178 TLDTQKG--SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            L   +   S   + V + EG+N E++++ E    KV+ L R+  G  +L
Sbjct: 198 ELVKSEPGDSRHRIRVVVTEGRNHEVRQLVESAFLKVHALKRVRVGGLRL 247


>gi|187918008|ref|YP_001883571.1| ribosomal large subunit pseudouridine synthase B [Borrelia hermsii
           DAH]
 gi|119860856|gb|AAX16651.1| ribosomal large subunit pseudouridine synthase B [Borrelia hermsii
           DAH]
          Length = 253

 Score =  129 bits (323), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 67/237 (28%), Positives = 102/237 (43%), Gaps = 10/237 (4%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +   N    R    +A  G+ SRR  E +I +  VK+NG L +     V   D +E    
Sbjct: 1   MTNINSRGLRAHVFLAEKGMGSRRFCEELIRKNLVKINGTLAK-LGDKVFLGDRVEYRRQ 59

Query: 66  P-----LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 L+   +  + L+     L +       +  +    P    R+ S+GRLD  + G
Sbjct: 60  VFVLRDLKIESKIYIALHKPKNYLCSNFDPEGRKLAISLVQPLFKERLFSIGRLDFKSSG 119

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLL TNDG  A  +  P ++  + Y V     V++D L   K GI I+   +      + 
Sbjct: 120 LLLFTNDGQFANSIVHPRSEVEKEYIVESKKDVNEDLLINFKHGIKIEREIFKLKSYEML 179

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                N  V + L EGKNREI+KVF   N  + ++ RI  G  +L  L  G  + +S
Sbjct: 180 ----GNNSVKLVLTEGKNREIRKVFLSKNIFLKKVHRIRIGNIKLDNLKEGQIKVLS 232


>gi|254670490|emb|CBA06210.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis alpha153]
          Length = 256

 Score =  129 bits (323), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 44/227 (19%), Positives = 86/227 (37%), Gaps = 6/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD----GVPLRK 69
            ++ K +   GI SR++ + +I    V +NG  ++    ++ S+    +D     V +  
Sbjct: 27  MKLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSSVETLDIDEEAVTVVP 86

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 87  EPYFYIMLNKPEDYETSHKPKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS +  ++Y V       +     LK G+++              +      +
Sbjct: 147 LNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAADAVLKNP--TTL 204

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 205 LLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 251


>gi|126439492|ref|YP_001059472.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 668]
 gi|126218985|gb|ABN82491.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 668]
          Length = 574

 Score =  129 bits (323), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 326 VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 385

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 386 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 445

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 446 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDG 505

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 506 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 561

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 562 QGEWRYLGPDE 572


>gi|197105762|ref|YP_002131139.1| ribosomal small subunit pseudouridine synthase A [Phenylobacterium
           zucineum HLK1]
 gi|196479182|gb|ACG78710.1| ribosomal small subunit pseudouridine synthase A [Phenylobacterium
           zucineum HLK1]
          Length = 242

 Score =  129 bits (323), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 51/235 (21%), Positives = 91/235 (38%), Gaps = 7/235 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV----MSTDHIEVDGVPLR 68
             R+ K++A  G  SRREV+ +     + ++G  + +A   +         ++VDG PL 
Sbjct: 4   SVRLDKLLANMGYGSRREVQALARAGAITLDGAPVPKADTRIALTPDLPARMQVDGRPLD 63

Query: 69  KAERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                 L L+       +     +   S +          + +VGRLD  T GLLLLT+D
Sbjct: 64  PLPGMALMLHKPTGVTCSHKETGELVYSLLPSRWRMREPPLSTVGRLDKETSGLLLLTDD 123

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +  P     + Y       +  D+  +   G ++       +   +  +  S  
Sbjct: 124 GDLLHRIISPRRHVAKRYVATLARPLRGDEGAIFAAGELMLEGEDKPLAPAVL-EPLSPT 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
              + + EG+  +++++F      V  L R   G   L   L  G  R +  + L
Sbjct: 183 LARLTITEGRYHQVRRMFAAVGNHVEALHRDRIGGLDLPADLAPGRYRLMGAEDL 237


>gi|254261229|ref|ZP_04952283.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1710a]
 gi|254219918|gb|EET09302.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1710a]
          Length = 579

 Score =  129 bits (323), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 331 VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 390

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     LVT  +   G  +     P     +   GRLDI++
Sbjct: 391 VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 450

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 451 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDG 510

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 511 VPLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 566

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 567 QGEWRYLGPDE 577


>gi|119477210|ref|ZP_01617446.1| Hypothetical pseudouridylate synthase [marine gamma proteobacterium
           HTCC2143]
 gi|119449573|gb|EAW30811.1| Hypothetical pseudouridylate synthase [marine gamma proteobacterium
           HTCC2143]
          Length = 233

 Score =  129 bits (323), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 61/235 (25%), Positives = 113/235 (48%), Gaps = 7/235 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
                R+ + I++  + S  +  R++AQQR+ V+G L       V    H+ +DG  L  
Sbjct: 2   TSKTSRLDRFISQNSVYSLSDTRRLLAQQRIFVDGHLAYSIQQQVTQFTHVVLDGNCLND 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +    + L      + +  +DP   + +        + +  VGRLD NT GL+LLTNDG 
Sbjct: 62  STAVYMMLNKPKGFV-SATTDPKHPTVLDLIQHPQKNELHIVGRLDFNTTGLVLLTNDGA 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNA 187
            +R + LP T+  ++Y V     ++ + + + +KGI    + I      + + ++  +  
Sbjct: 121 WSRKISLPETKLAKIYEVTLSKPLNDEYIEVFRKGIYFSYENITTQPAYLEILSEYQA-- 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
              + L EGK  ++K++F FF  +V  L R + GP  L  L  G ++ ++K+ + 
Sbjct: 179 --RLSLIEGKYHQVKRMFGFFQNEVLALHRTAVGPISLDGLTVGHSKLLTKQTIE 231


>gi|261416947|ref|YP_003250630.1| pseudouridine synthase [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|261373403|gb|ACX76148.1| pseudouridine synthase [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|302327155|gb|ADL26356.1| RNA pseudouridine synthase family protein [Fibrobacter succinogenes
           subsp. succinogenes S85]
          Length = 286

 Score =  129 bits (323), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 54/253 (21%), Positives = 99/253 (39%), Gaps = 33/253 (13%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWL 77
           +VI++ G  SR + E ++ + RV + G ++          D I VDG P++ +E     +
Sbjct: 32  RVISKRGFCSRSQAENLVREGRVSLRGKIVRDPDTPARENDEICVDGKPVKASEFVYFMM 91

Query: 78  YHKPIGLVTTHSDPDGRSTVF--------DNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                 + T   +    + +                  +  VGRLD  +EGLLL TND  
Sbjct: 92  NKPRGYVTTASDEKGRATVMDLFREQYAKMFPGKPVPHISPVGRLDAASEGLLLFTNDTQ 151

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG---------------- 173
            A  L     +  +    +   +  +  ++     + + G                    
Sbjct: 152 WADALLKTKDERRKTRDDKCVERESRGPIHTKIYRVQVNGHPTAEELSQMEAGFNVPPRV 211

Query: 174 ---------DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
                     +   L +    N W+ + L EGKNREI+++     ++V RL+RI +  ++
Sbjct: 212 FGEPEEFMHAVSAKLYSAGEKNCWLEITLDEGKNREIRRMLAKLGYEVLRLVRIKFCNYE 271

Query: 225 LGTLLAGSTREVS 237
           LG L  G  R+++
Sbjct: 272 LGDLKQGEIRKIN 284


>gi|257899452|ref|ZP_05679105.1| pseudouridine synthase [Enterococcus faecium Com15]
 gi|257837364|gb|EEV62438.1| pseudouridine synthase [Enterococcus faecium Com15]
          Length = 238

 Score =  129 bits (323), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 102/232 (43%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+I      +R+E++R+ A ++V ++G +  R   NV S    IEV G  L   E 
Sbjct: 1   MRLDKLIEEKLETTRKEMKRLFALKQVMIDGTVEFRQNRNVDSLLHRIEVAGEHLETNES 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                    F  +  VGRLD +T GLLL+T++G L  
Sbjct: 61  -YYLLNKPKKAVTAVSDPEKTTVIDLIASADRFQPLYPVGRLDRDTTGLLLITSNGQLGY 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            + LP  +  + Y+   + +V    +   +KGIV   G       + +       + V +
Sbjct: 120 EMLLPEKKVSKTYQAVVNERVTSADVAAFEKGIVFADGYQCQSANLKILKADKHQSTVLL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            ++EGK  ++KK+F     KV  L R+S GP +L   L  G  R ++   ++
Sbjct: 180 TIQEGKFHQVKKMFLAQGKKVIALKRLSMGPLELDEQLAVGEYRSLTLAEMK 231


>gi|264680454|ref|YP_003280364.1| Pseudouridine synthase, Rsu [Comamonas testosteroni CNB-2]
 gi|262210970|gb|ACY35068.1| Pseudouridine synthase, Rsu [Comamonas testosteroni CNB-2]
          Length = 642

 Score =  128 bits (322), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 67/251 (26%), Positives = 104/251 (41%), Gaps = 29/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA  G+ SRRE +  +    V VNG +      NV+  D IE+D     + ++ 
Sbjct: 395 VRINKRIADMGMCSRREADEWVENGWVTVNGEVAT-MGQNVVPGDRIEIDQKAQERQDQQ 453

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---------------ISVGRLDINT 118
              L +KP+G V+  ++      V                             GRLDI++
Sbjct: 454 VTILLNKPMGYVSGQAEDGHEPAVVLITNENRWNEDRSKTRFNFSQLKGLAPCGRLDIDS 513

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQG 169
            GLL+LT DG +AR +    ++  + Y VR               ++KL LL+ G+ +  
Sbjct: 514 VGLLVLTQDGRVARQIIGEDSEVDKEYLVRVTFGDRDVDVQSVFPEEKLALLRHGLSLDE 573

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                 QV     +     +   L EGK R+I+++ E    KV  L RI  G   LG L 
Sbjct: 574 QPLKPAQVDWQNPEQ----LRFVLTEGKKRQIRRMCEQVGLKVVGLKRIRIGGVTLGNLP 629

Query: 230 AGSTREVSKKI 240
            G  R ++   
Sbjct: 630 TGQWRYLAPHE 640


>gi|330957838|gb|EGH58098.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. maculicola
           str. ES4326]
          Length = 230

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 98/231 (42%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R+ V   +A   VKV+G+        V     +  D   L+  +  
Sbjct: 1   MRLDRFLSNLPRFNRKNVRLALAGGHVKVDGLTSTDPHHEVREFSCVVFDEEILQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G V+   D    + +          +   GRLD NT GL+L+TNDG  +R 
Sbjct: 61  RYFMLHKPQGCVSATVDAQHPTVIDLLDEPDRHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+       +      + I     Q+TL           +
Sbjct: 121 LTQPQTRLAKVYYVETEQIIDERYAARFAEGLYFSFENITTQPAQLTLL----GPRCARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F  F+ KV  L R S G   L  TL  G+ R +    +
Sbjct: 177 SITEGRYHQVKRMFGHFDNKVVTLHRESVGELLLDPTLEPGNYRALHAPEI 227


>gi|226941109|ref|YP_002796183.1| Pseudouridine synthase [Laribacter hongkongensis HLHK9]
 gi|226716036|gb|ACO75174.1| Pseudouridine synthase [Laribacter hongkongensis HLHK9]
          Length = 703

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 67/235 (28%), Positives = 116/235 (49%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A AG+ SRR+++ ++A  RV +NG +       V   D + VD  P+      
Sbjct: 453 MRLQKALALAGLGSRRDMDELVAAGRVSINGAVA-ELGARVRPGDKVRVDSKPVLIRWPD 511

Query: 74  RL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           RL      + +   +VT        +       +  S+ +++GRLD+NT GLL+ T  G 
Sbjct: 512 RLPRVIVYHKQEGEIVTRDDPEGRTTVFDRLPQTRSSKWVAIGRLDVNTSGLLIFTTSGD 571

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY--GDMQVTLDTQKGSNA 187
           LA  +  PS +  R Y VR  G++  +++     G+ +         ++   D +   N 
Sbjct: 572 LANRMTHPSFEVEREYAVRVLGKLTPEQMKETTAGVQLDDGPASFQFIREDDDKEDSVNH 631

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           W  VG+REG+NRE++++FE F   V+RL+R+ +G   L   L  G   E+++  +
Sbjct: 632 WYRVGIREGRNREVRRMFEHFGLTVSRLMRVRFGIVTLPSRLKRGQFYELNELEV 686


>gi|296314515|ref|ZP_06864456.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           polysaccharea ATCC 43768]
 gi|296838827|gb|EFH22765.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           polysaccharea ATCC 43768]
          Length = 230

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 49/227 (21%), Positives = 90/227 (39%), Gaps = 6/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLR--K 69
            ++ K +   GI SR++ + +IA   V +NG  ++ A  ++ S     +++DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCIDDADADIHSASVHTLDIDGKAVTVIP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 61  EPYFYILLNKPADYETSHKPKHYRSIFSLFPDNMRNIDMQAVGRLDADTTGVLLVTNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS +  ++Y V      D      LK G+++            D    S   +
Sbjct: 121 LNHNLTSPSRKIPKLYEVTLKHPADGILCETLKNGVLLHDENETVC--AADANLESPTTL 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 179 LLTITEGKYHQVKRMIAAAGNRVQHLHRRQFAHLETENLKPGEWKFI 225


>gi|167835760|ref|ZP_02462643.1| RNA pseudouridine synthase family protein [Burkholderia
           thailandensis MSMB43]
          Length = 240

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 55/236 (23%), Positives = 91/236 (38%), Gaps = 6/236 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVK-VNGILLERAAVNVMSTDHI-EVDGVPLRKAERT 73
           +  ++   G  SRR+   ++   RV  V G     A  +  +T  + EVDGV      R 
Sbjct: 3   LESILFTQGFGSRRQCRALVEAGRVAAV-GATCTDAHASFDTTQLVFEVDGVAWPYRARA 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L        +                     V  VGRLD +T GLLLL++DG     
Sbjct: 62  YVVLNKPAGYECSREPQHHASVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVHA 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
              P  +  + Y       +D  +L+ L+ G+++ G         L         + + +
Sbjct: 122 YTSPKRKTPKTYVATVRHPLDDAQLDALRAGVLLHGEPKPVA--ALAAVARGERLLEMTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
            EGK  ++K++    + +V+ L R   G F L G L  G+ R + +  L    G  
Sbjct: 180 AEGKYHQVKRMVAAASNRVDALHRSRIGGFALPGDLAEGAWRWLDEHDLAALRGTA 235


>gi|110638234|ref|YP_678444.1| ribosomal large subunit pseudouridine synthase F [Cytophaga
           hutchinsonii ATCC 33406]
 gi|110280915|gb|ABG59101.1| ribosomal large subunit pseudouridine synthase F [Cytophaga
           hutchinsonii ATCC 33406]
          Length = 281

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 109/229 (47%), Gaps = 9/229 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN-VMSTDHIEVDGVPLRKAERTR 74
           +++ + +    S+ +   M+ + +V +NG  ++    N V+ +DHI V+G  L++     
Sbjct: 61  INEFLIKRFHISKDKASNMVLENQVFING--VKALQRNDVLKSDHIVVNGEVLQEGRNFT 118

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            + Y+KP G+  T +     + +          V  VGRLD  +EGLLLLTNDG L + +
Sbjct: 119 YYAYYKPRGIECTLNAAIENNLLHTL--PFGEHVYPVGRLDKESEGLLLLTNDGKLYKDI 176

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y V     +  + +  L  GIVI G      +V++ T+        + L 
Sbjct: 177 AFSDNFKEKEYLVEVDKPLTDEAVEQLSSGIVIMGQKTRPARVSMVTE----HSFRIILT 232

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           +G NR+I+++     ++V  L RI     +LG L  G+ R +++  + +
Sbjct: 233 QGLNRQIRRMCYKLRYEVTMLKRIRITSIELGDLKPGAYRVLTRAEIFD 281


>gi|299148164|ref|ZP_07041226.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           3_1_23]
 gi|298512925|gb|EFI36812.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           3_1_23]
          Length = 211

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 49/202 (24%), Positives = 88/202 (43%), Gaps = 1/202 (0%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           V VNG ++      +  +D ++    P+    +  + L      + T+    + R+ +  
Sbjct: 2   VSVNGEVVTELGTKIKRSDVVKFHDEPVSIERKVYVLLNKPKDTVTTSDDPQERRTVMDL 61

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
              +   R+  VGRLD NT G+LLLTNDG LA  L  P     ++Y V     + +  ++
Sbjct: 62  VKGACNERIYPVGRLDRNTTGVLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADMD 121

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
            +  GI ++            T       V + +  GKNR ++++FE   +KV +L R+ 
Sbjct: 122 QIAAGIQLEDGEIH-ADAISYTDDFKKDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVF 180

Query: 220 YGPFQLGTLLAGSTREVSKKIL 241
           +       L  G  R +S+  +
Sbjct: 181 FAGLTKKGLRRGDWRYLSEAEV 202


>gi|82541066|ref|XP_724803.1| hypothetical protein [Plasmodium yoelii yoelii str. 17XNL]
 gi|23479575|gb|EAA16368.1| 1st euk. member [Plasmodium yoelii yoelii]
          Length = 318

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 56/268 (20%), Positives = 110/268 (41%), Gaps = 34/268 (12%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVP 66
            +N    R++K I+     SRR+ ++ I    +K+N   +     +V  + D I+V+   
Sbjct: 40  NQNENIIRLNKFISINNNISRRKSDKFIQNGNIKINNKTIINPGTHVDITKDQIKVNDKK 99

Query: 67  LRKAE--------------RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVIS 110
           +                     + L+     + T   + D +S             R++S
Sbjct: 100 INIQNIKNILNNYNINNNSYKWIVLHKPKGLICTNQDEKDRKSVFSIFPEDLLQKYRIVS 159

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--- 167
           VGRLD NT G+LL TN+      L  P  + +R Y +   G V  D L +L  G+ +   
Sbjct: 160 VGRLDRNTSGILLFTNEYAWVNKLTHPKYERVRKYMIHIEGPVRMDALKMLANGVYLKDE 219

Query: 168 -----QGICYGDMQVTLDTQKGSN--------AWVTVGLREGKNREIKKVFEFFNWKVNR 214
                +        + +  ++           + + + ++EG+NR+I+K+F+  N  + +
Sbjct: 220 DNDKKKNKKTQPALIEVLREENVKIQNQIKKISVLNISIKEGRNRQIRKMFQQINQPIIK 279

Query: 215 LIRISYGPFQLGTLL-AGSTREVSKKIL 241
           + R ++    L  +      RE++KK +
Sbjct: 280 IKRTAFENITLKNIHLPKQYRELTKKEI 307


>gi|224436886|ref|ZP_03657875.1| hypothetical protein HcinC1_02926 [Helicobacter cinaedi CCUG 18818]
 gi|313143364|ref|ZP_07805557.1| conserved hypothetical protein [Helicobacter cinaedi CCUG 18818]
 gi|313128395|gb|EFR46012.1| conserved hypothetical protein [Helicobacter cinaedi CCUG 18818]
          Length = 269

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 66/243 (27%), Positives = 114/243 (46%), Gaps = 17/243 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ IA     SRRE +++I   RV +           +     + +DG  +   E+ 
Sbjct: 1   MRLNQYIAHHTKYSRREADKLIESGRVNIEKSKA-SLQSVLREGMSVFIDGKRIVPKEQF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +YHK  G + + SD  GR  ++D+L S F   + VGRLD  +EGLL+LT+   +A+ 
Sbjct: 60  TCIVYHKQKGELVSKSDERGRKVIYDSLESRFKHFMYVGRLDFASEGLLILTDSTPVAKA 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQVTL 179
           L        RVY V+ +G++ ++ +  ++KG+V +                        +
Sbjct: 120 LMES--HLERVYLVKINGEITKEIIEAMEKGLVSEDARAGGHIKSNIVAMEFAPFAHYEI 177

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                 ++ + V + EGKNRE+++ F  F  +V  L RI+YG   L  L  G  R  +K+
Sbjct: 178 LKNDKRHSKLKVSITEGKNRELRRFFGVFGREVLDLRRIAYGFVNLNALPCGKKRYFTKE 237

Query: 240 ILR 242
             +
Sbjct: 238 EYK 240


>gi|224531930|ref|ZP_03672562.1| hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Borrelia valaisiana VS116]
 gi|224511395|gb|EEF81801.1| hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Borrelia valaisiana VS116]
          Length = 249

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 63/228 (27%), Positives = 101/228 (44%), Gaps = 10/228 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--- 68
              RV   +A  G+ SRR  E +I ++ V+VNG + +     V   D I           
Sbjct: 5   KTPRVQVFLAEKGVGSRRFCEELIKKKLVRVNGSIAK-LGDKVALGDRITYKKQIYVFTD 63

Query: 69  -KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
            +++       +KP   + ++ D +GR      +      R+ S+GRLD  + GLLL TN
Sbjct: 64  FQSKSKIYLALNKPKNYLCSNFDVNGRKLAISLVQPLFKERIFSIGRLDFKSSGLLLFTN 123

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  A  +  P  +  R Y +     +D++ L   K GI I+   +      +  +  + 
Sbjct: 124 DGKFANYIIHPKGKVEREYIIESKKDIDENLLISFKSGIKIKKEFFKLKSYEILNKNSA- 182

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
               + L EGKNREI+KVF   N  + ++ RI  G   L +L  G  +
Sbjct: 183 ---RLILDEGKNREIRKVFLSKNVFLKKIHRIRIGNINLDSLREGQVK 227


>gi|317181142|dbj|BAJ58928.1| hypothetical protein HPF32_1346 [Helicobacter pylori F32]
          Length = 257

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 62/249 (24%), Positives = 118/249 (47%), Gaps = 19/249 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAK-LASVVKENDKVFLDKRLIKPLKNK 59

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++  + VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKADPLKRCVIYESLEKKYTHFVPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQV 177
             L        + Y V+  G V ++  N +++G+ ++                    +  
Sbjct: 120 SALMHA--NLEKEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLKRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQLG 246
           ++   E   
Sbjct: 238 RQEYNELHA 246


>gi|119952932|ref|YP_945141.1| ribosomal large subunit pseudouridine synthase B [Borrelia
           turicatae 91E135]
 gi|119861703|gb|AAX17471.1| ribosomal large subunit pseudouridine synthase B [Borrelia
           turicatae 91E135]
          Length = 247

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 64/237 (27%), Positives = 99/237 (41%), Gaps = 10/237 (4%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +   N    RV   +A  G+ SRR  E +I +  V++N  L +     V   D +E    
Sbjct: 1   MTNTNSKGLRVHVFLAEKGVGSRRFCEDLIRKNSVRINNTLAK-LGDKVFLGDRVECRKQ 59

Query: 66  PLRKAERT-----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                +        + L+     L +       +  +    P    R+ S+GRLD  + G
Sbjct: 60  VFVFRDCKVESKIYIALHKPKNYLCSNFDPEGRQLAISLVQPLFKERLFSIGRLDFKSSG 119

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLL TNDG  A  +  P ++  + Y V     V+++ L   K GI I    +      + 
Sbjct: 120 LLLFTNDGQFANNIVHPRSKVEKEYIVESKRAVNENLLINFKHGIKIGREIFKLKSYVML 179

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                N  V + L EGKNREI+KVF   N  + ++ RI  G  +L  L  G  + +S
Sbjct: 180 ----GNNSVKLVLTEGKNREIRKVFLSKNIFLKKIHRIRIGNIKLDDLKEGQIKVLS 232


>gi|160882411|ref|ZP_02063414.1| hypothetical protein BACOVA_00362 [Bacteroides ovatus ATCC 8483]
 gi|156112224|gb|EDO13969.1| hypothetical protein BACOVA_00362 [Bacteroides ovatus ATCC 8483]
          Length = 211

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 49/202 (24%), Positives = 87/202 (43%), Gaps = 1/202 (0%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           V VNG ++      +  +D ++    P+    +  + L      + T+    + R+ +  
Sbjct: 2   VSVNGEVVTELGTKIKRSDVVKFHDEPVSIERKVYVLLNKPKDTVTTSDDPQERRTVMDL 61

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
              +   R+  VGRLD NT G+LLLTNDG LA  L  P     ++Y V     + +  + 
Sbjct: 62  VKGACNERIYPVGRLDRNTTGVLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADME 121

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
            +  GI ++            T       V + +  GKNR ++++FE   +KV +L R+ 
Sbjct: 122 QIAAGIQLEDGEIH-ADAISYTDDFKKDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVF 180

Query: 220 YGPFQLGTLLAGSTREVSKKIL 241
           +       L  G  R +S+  +
Sbjct: 181 FAGLTKKGLRRGDWRYLSEAEV 202


>gi|170749852|ref|YP_001756112.1| pseudouridine synthase [Methylobacterium radiotolerans JCM 2831]
 gi|170656374|gb|ACB25429.1| pseudouridine synthase [Methylobacterium radiotolerans JCM 2831]
          Length = 246

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 53/236 (22%), Positives = 93/236 (39%), Gaps = 7/236 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV----MSTDHIEVDGVPL 67
              R+ K++A  G  SRRE++ +     ++++G  L  A   V       + + VDG  L
Sbjct: 5   RSVRLDKLLANLGYGSRREIQALARAGAIRLDGAELADAGDRVALAPDLPERLTVDGESL 64

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                  L L+       +           + +        + +VGRLD  T GLLLLT+
Sbjct: 65  DPLPGLCLMLHKPLGVTCSHKEAGPLVYGLLPERWRRRDPPLSTVGRLDKETSGLLLLTD 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L   +  P  Q  + YRV     +   +  +   G ++       +       + + 
Sbjct: 125 DGALLHRIISPKAQVAKRYRVTLDRPLTGREAEVFAAGTLVLEGEERPLLPVRLDVEDAT 184

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
               V L EG+  +++++F      V  L R   G   L   L AG+ R ++ + +
Sbjct: 185 RCA-VTLTEGRYHQVRRMFAAVGNHVAALHRDRVGGLALPADLPAGAHRVMTAEDV 239


>gi|189350818|ref|YP_001946446.1| ribosomal large subunit pseudouridine synthase F [Burkholderia
           multivorans ATCC 17616]
 gi|189334840|dbj|BAG43910.1| ribosomal large subunit pseudouridine synthase F [Burkholderia
           multivorans ATCC 17616]
          Length = 612

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 60/251 (23%), Positives = 101/251 (40%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 364 MRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDERAQAAQAAQ 423

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     L+T  +   G  +     P     +   GRLDI++
Sbjct: 424 VTILLHKPVGYVSGQAEDGYEPASVLITRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 483

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                ++L  L+ G+ + G
Sbjct: 484 TGLLVLTQNGRIAKQLIGEQSDVDKEYLVRVRFGDRLTDIDQHFPAERLAQLRHGLELDG 543

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREG+ R+I+++ E    +V  L R+  G   LG L 
Sbjct: 544 VALKPAMVSWQNGEQ----LRFVLREGRKRQIRRMCELVGLEVIGLKRVRMGRVTLGALP 599

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 600 QGQWRYLSADE 610


>gi|325136197|gb|EGC58805.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis M0579]
 gi|325201990|gb|ADY97444.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis M01-240149]
 gi|325208259|gb|ADZ03711.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis NZ-05/33]
          Length = 230

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 46/229 (20%), Positives = 89/229 (38%), Gaps = 8/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPLR--K 69
            ++ K +   GI SR++ + +IA   V +NG  ++    ++ S+      +DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTVVP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 61  EPYFYIMLNKPEDYETSHKPKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAW 188
           L   L  PS +  ++Y V       +     LK G+++            +     S + 
Sbjct: 121 LNHNLTSPSRKIPKLYEVTLKHPAGETLCETLKNGVLLHDENETVYAADAVL---ESPSA 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + + EGK  ++K++      +V  L R  +   +   L  G  + + 
Sbjct: 178 LLLTITEGKYHQVKRMVAAAGNRVQHLHRRRFAHLETENLKPGEWKFID 226


>gi|187925109|ref|YP_001896751.1| pseudouridine synthase [Burkholderia phytofirmans PsJN]
 gi|187716303|gb|ACD17527.1| pseudouridine synthase [Burkholderia phytofirmans PsJN]
          Length = 236

 Score =  128 bits (321), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 53/230 (23%), Positives = 91/230 (39%), Gaps = 6/230 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH---IEVDGVPLRKAER 72
           +  ++   G  SRR+   +IA  RV + G+    A  +  + D      VDGV     E 
Sbjct: 3   LESILFTQGFGSRRQCRALIADARVSIGGVACTDADADFPTGDTAFFFSVDGVDWPYREH 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L        +                     V  VGRLD +T GLLLL++DG    
Sbjct: 63  AYLLLNKPAGYECSRDPQHHLSVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGKFVH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +   P  +  +VY       +D  +L+ L+ G+++ G     +       +G+N  + + 
Sbjct: 123 LFTSPKRKVPKVYIATTRHPLDDAQLSALRDGVLLHGEP-KPIAAVDAAARGANT-LALT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + EGK  ++K++      +   L R   G   L   L  G+ + + +  L
Sbjct: 181 VMEGKYHQVKRMIAAAGNRCEALHRERIGGLALPETLAPGAWQWLDETDL 230


>gi|167582947|ref|ZP_02375821.1| ribosomal small subunit pseudouridine synthase A [Burkholderia
           thailandensis TXDOH]
          Length = 240

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 52/228 (22%), Positives = 91/228 (39%), Gaps = 4/228 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   ++   RV V G     A  +  +   + EVDGV      R  
Sbjct: 3   LESILFTQGFGSRRQCRALVEAGRVAVGGATCADAHTSFDTARLVFEVDGVAWPYRARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        +                     V  VGRLD +T GLLLL++DG      
Sbjct: 63  VALNKPAGYECSREPQHHASVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVHAY 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y       +D  +L+ L+ G+++ G     +       +G    + + + 
Sbjct: 123 TSPKRKVPKTYVAAVRHPLDDAQLDALRAGVLLHGEP-KPIAALAAAARGER-LLEMTIA 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           EGK  ++K++    + +V+ L R   G F L   L  G+ R + ++ L
Sbjct: 181 EGKYHQVKRMVAAVSNRVDALHRSRIGGFALPEDLAEGAWRWLDERDL 228


>gi|71280205|ref|YP_271062.1| putative ribosomal small subunit pseudouridine synthase A
           [Colwellia psychrerythraea 34H]
 gi|71145945|gb|AAZ26418.1| putative ribosomal small subunit pseudouridine synthase A
           [Colwellia psychrerythraea 34H]
          Length = 240

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 56/233 (24%), Positives = 99/233 (42%), Gaps = 10/233 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ ++I+ +   +R++V  ++AQ+RV V+G+L    A  V    H+ +D   L+  +   
Sbjct: 7   RLDRLISDSRQINRKKVRLILAQKRVYVDGVLATDIAQLVDQFSHVVMDNEVLQANQTHY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV---FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           + L      +  T                   +   +  VGRLD+NT GL+LLTND   +
Sbjct: 67  IMLNKPIGVVCATKDKKHKTVIDLLAEQFDQDVLDSLHIVGRLDLNTSGLVLLTNDSRWS 126

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWV 189
             L  P  +  + Y+V     +  D ++   K      + I      + + +        
Sbjct: 127 ERLTSPEHKVSKGYQVTLENALTTDYIDAFAKGMYFPYENITTKPAILHIVSL----FEA 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            V L EG+  +IK++F  F   V  L R S G  +L   L  G +R ++   +
Sbjct: 183 QVSLTEGRYHQIKRMFGRFRNPVIALHRYSIGSLRLDESLKDGESRVLNVSEV 235


>gi|261838734|gb|ACX98500.1| pseudouridine synthase B [Helicobacter pylori 51]
          Length = 262

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 59/248 (23%), Positives = 117/248 (47%), Gaps = 19/248 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ +A   + SRRE E+++ + RVK+N    +  +  V   D + +D   ++  +  +
Sbjct: 7   RINQFLAHYTMHSRREAEKLVLEGRVKINHEHAK-LSSVVKENDKVFLDKRLIKPLKNKK 65

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQVT 178
            L        + Y V+    V ++  + +++G+ ++                    +   
Sbjct: 126 ALMHA--NLEKEYLVKIQSFVTKEMESAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 KILREQLG 246
           +   E   
Sbjct: 244 QEYNELHA 251


>gi|182417073|ref|ZP_02948451.1| RNA pseudouridine synthase family protein [Clostridium butyricum
           5521]
 gi|237667148|ref|ZP_04527132.1| RNA pseudouridine synthase family protein [Clostridium butyricum E4
           str. BoNT E BL5262]
 gi|182379082|gb|EDT76586.1| RNA pseudouridine synthase family protein [Clostridium butyricum
           5521]
 gi|237655496|gb|EEP53052.1| RNA pseudouridine synthase family protein [Clostridium butyricum E4
           str. BoNT E BL5262]
          Length = 258

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 60/256 (23%), Positives = 97/256 (37%), Gaps = 28/256 (10%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV-NVMSTDHIEVDGVPLRKAER 72
            R+ K +A++ I +R+ V + +    VK+NGI +  AAV      D IE +G      E+
Sbjct: 1   MRLDKFLAQSQIGTRKIVRQYVKDGLVKINGITIFEAAVEINEIEDIIEYNGQITEYKEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                      + T   D D ++            V  VGRLD +TEGLLL TNDG    
Sbjct: 61  VYYMFNKPSGCI-TARKDADDKTVFDYFKEINMDGVFHVGRLDKDTEGLLLFTNDGDFNN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQK------- 183
            L  P     + Y     G +D+     L+ G+ I          ++             
Sbjct: 120 KLMSPKFHVDKKYFFIALGSIDEKNKKNLESGVSIGENEPITKPAKIENLKNGTYEELKD 179

Query: 184 --------GSNAWV--------TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
                     N+           + + EG+  ++K++ +     V  L R+S G   L  
Sbjct: 180 KLNLKKYYHVNSEYYIQPVVCGHITISEGRRHQVKRMLKSIGCHVIYLKRMSIGNLALDE 239

Query: 228 -LLAGSTREVSKKILR 242
            L  G  R ++K  ++
Sbjct: 240 FLKKGDYRSLTKDEIK 255


>gi|302879744|ref|YP_003848308.1| pseudouridine synthase [Gallionella capsiferriformans ES-2]
 gi|302582533|gb|ADL56544.1| pseudouridine synthase [Gallionella capsiferriformans ES-2]
          Length = 241

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 40/230 (17%), Positives = 79/230 (34%), Gaps = 7/230 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           + +++   G  +R+   ++IA   +++ G  +      +        VD       ER  
Sbjct: 6   LDRILHTQGFGTRKYCRQLIAAGAIRIGGDTITDTNTPIETDGLEFSVDDEHCIYRERIY 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        +                     V  VGRLD +T GLLL+++DG      
Sbjct: 66  VALNKPANIECSRKPSHHPGVLSILPDQFTRRDVQPVGRLDHDTTGLLLMSDDGAFIHTQ 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTVGL 193
             P     +VY    +  V  + +  L  G+ +         +     +   +  + + L
Sbjct: 126 SSPKHHVPKVYVATTYAPVTGELIERLLAGVKLHDEPGTLAAE---ICRMIDDHHLEIVL 182

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTREVSKKIL 241
            +GK  ++K++    +     L R   G  +L    L  G    ++   L
Sbjct: 183 EQGKYHQVKRMLAAADNHCTALNRSQIGNLKLAELALAPGEWCYLNDAQL 232


>gi|167618201|ref|ZP_02386832.1| ribosomal small subunit pseudouridine synthase A [Burkholderia
           thailandensis Bt4]
 gi|257139975|ref|ZP_05588237.1| ribosomal small subunit pseudouridine synthase A [Burkholderia
           thailandensis E264]
          Length = 240

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 52/228 (22%), Positives = 91/228 (39%), Gaps = 4/228 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   ++   RV V G     A  +  +   + EVDGV      R  
Sbjct: 3   LESILFTQGFGSRRQCRALVEAGRVAVGGATCADAHTSFDTARLVFEVDGVAWPYRARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        +                     V  VGRLD +T GLLLL++DG      
Sbjct: 63  VALNKPAGYECSREPQHHASVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVHAY 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y       +D  +L+ L+ G+++ G     +       +G    + + + 
Sbjct: 123 TSPKRKVPKTYVATVRHPLDDAQLDALRAGVLLHGEP-KPIAALAAAARGER-LLEMTIA 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           EGK  ++K++    + +V+ L R   G F L   L  G+ R + ++ L
Sbjct: 181 EGKYHQVKRMVAAASNRVDALHRSRIGGFALPEDLAEGAWRWLDERDL 228


>gi|209517428|ref|ZP_03266269.1| pseudouridine synthase [Burkholderia sp. H160]
 gi|209502082|gb|EEA02097.1| pseudouridine synthase [Burkholderia sp. H160]
          Length = 236

 Score =  127 bits (319), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 53/227 (23%), Positives = 86/227 (37%), Gaps = 6/227 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAA--VNVMSTD-HIEVDGVPLRKAER 72
           +  ++   G  SRR+   +I   RV ++G +   A     V S      VDGV     E 
Sbjct: 3   LESILFTQGFGSRRQCRALIGDARVSIDGAICTDADADFAVESGALRFSVDGVEWPYREH 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L        +                     V  VGRLD +T GLLLL++DG    
Sbjct: 63  AYLLLNKPVGYECSRDPQHHLSVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGKFVH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  ++Y       +D  +L  L+ G+++ G         LD Q      + + 
Sbjct: 123 QFTSPKRKVPKLYVATTRHPLDDAQLTALRHGVLLHGE-TRP-SAALDAQARDTHTLALT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
           + EGK  ++K++      +   L R   G   L  TL  G+ + + +
Sbjct: 181 VLEGKYHQVKRMIAASGNRCEALHRERIGGLALPATLAPGAWQWLDE 227


>gi|221215453|ref|ZP_03588417.1| RNA pseudouridine synthase family protein [Burkholderia multivorans
           CGD1]
 gi|221164637|gb|EED97119.1| RNA pseudouridine synthase family protein [Burkholderia multivorans
           CGD1]
          Length = 610

 Score =  127 bits (319), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 60/251 (23%), Positives = 101/251 (40%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 362 MRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDERAQAAQAAQ 421

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     L+T  +   G  +     P     +   GRLDI++
Sbjct: 422 VTILLHKPVGYVSGQAEDGYEPASVLITRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 481

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                ++L  L+ G+ + G
Sbjct: 482 TGLLVLTQNGRIAKQLIGEQSDVDKEYLVRVRFGDRLTDIDQHFPAERLAQLRHGLELDG 541

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREG+ R+I+++ E    +V  L R+  G   LG L 
Sbjct: 542 VALKPAMVSWQNGEQ----LRFVLREGRKRQIRRMCELVGLEVIGLKRVRMGRVTLGALP 597

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 598 QGQWRYLSADE 608


>gi|21910600|ref|NP_664868.1| putative 16S pseudouridylate synthetase [Streptococcus pyogenes
           MGAS315]
 gi|21904801|gb|AAM79671.1| putative 16S pseudouridylate synthetase [Streptococcus pyogenes
           MGAS315]
          Length = 221

 Score =  127 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 51/212 (24%), Positives = 88/212 (41%), Gaps = 2/212 (0%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHS 89
           ++++I  Q V V+ +       NV      IEV G  +   + + + L      +     
Sbjct: 1   MKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQRVTHPKHSYIILNKPSGVVSAKKD 60

Query: 90  DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
                             +  VGRLD +TEGL+LLT++G L   +  PS    + Y V  
Sbjct: 61  TNYLTVIDQLAEEDKSPDLYPVGRLDRDTEGLVLLTDNGPLGFRMLDPSHHVSKTYLVTV 120

Query: 150 HGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
           +G + +D  +    GI    G      Q+T+       +  ++ + EGK  ++KK+F  +
Sbjct: 121 NGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQSQASLTISEGKFHQVKKMFLTY 180

Query: 209 NWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             KV  L R  +   +LG L +G  R ++   
Sbjct: 181 GLKVTSLKRTHFAGLELGHLASGEYRYLTASE 212


>gi|56807363|ref|ZP_00365352.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Streptococcus pyogenes M49
           591]
          Length = 228

 Score =  127 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 48/212 (22%), Positives = 88/212 (41%), Gaps = 4/212 (1%)

Query: 35  IAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           + ++ + VN  +   A  ++    D +   G PL         L      +  T      
Sbjct: 7   LKKKAIFVNQKVETSAKAHIDEYKDLVTYQGTPLVYESFVYYLLNKPSGYVSATQDRQQA 66

Query: 94  RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
                 +  +    V  VGRLD +T GLLLLTN+G LA  L  P     + Y  +  G +
Sbjct: 67  TVMELLDDTARQKAVFPVGRLDKDTRGLLLLTNNGQLAHDLLSPKKHVTKEYLAKVAGIM 126

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +   +   +GI ++        + +     +   + V + ++EGK  ++K++      +
Sbjct: 127 TEADKDYFARGISLKDHQCLPAHLEVLASDLQQQTSLVKITIQEGKFHQVKRMVAACGKE 186

Query: 212 VNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V  L R+S GP +L  +L  G  R ++ + L+
Sbjct: 187 VLDLQRLSMGPLKLDPSLAEGEFRRLTPEELQ 218


>gi|257461220|ref|ZP_05626318.1| S4 domain protein [Campylobacter gracilis RM3268]
 gi|257441594|gb|EEV16739.1| S4 domain protein [Campylobacter gracilis RM3268]
          Length = 256

 Score =  127 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 65/251 (25%), Positives = 111/251 (44%), Gaps = 16/251 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K I+     SRRE + +I Q +V +NG ++    + V   + I +    ++   
Sbjct: 2   QKMRLNKFISHNTAYSRREADELIKQGKVSINGRVVSD-FIEVSGEEKIRIGSRLIKPKT 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              + +Y+K  G + T  D  GR T++D+LP  FSR +SVGRLD  +EGLLLLT+   +A
Sbjct: 61  EFTMIVYNKRKGELVTKKDDRGRRTIYDSLPEGFSRFVSVGRLDFASEGLLLLTDAPAIA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLL-----------KKGIVIQGICYGD-MQVTL 179
             L     +     +V+   + +                       I+ + +   +   +
Sbjct: 121 TALMNSDIEREYYLKVKGEVKEEVVTAIREGFFAADASKGAHAKSKIKSMEFKPFLGYRI 180

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               G    +   + EG+NRE+++ F +F+  V  L R ++G   LG L  G  R     
Sbjct: 181 MPSSGGYTKIKAIINEGQNRELRRFFGYFDLDVVELKRTAFGRMTLGMLKPGKWRYFDHS 240

Query: 240 I---LREQLGP 247
               LR+ L  
Sbjct: 241 EYEDLRDFLKE 251


>gi|308805586|ref|XP_003080105.1| unnamed protein product [Ostreococcus tauri]
 gi|116058564|emb|CAL53753.1| unnamed protein product [Ostreococcus tauri]
          Length = 405

 Score =  127 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 60/250 (24%), Positives = 104/250 (41%), Gaps = 20/250 (8%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR-----K 69
           ++K +A  G+ASRR  + +I   RVKVNG  +      V    D + VDG  +       
Sbjct: 145 LNKALASLGVASRRGADDLIFGGRVKVNGTTITAPQTKVNLNTDVVMVDGKVVEGGVSFV 204

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------------ISVGRLDIN 117
            E T   L      + +     +   TV D                      +VGRLD+ 
Sbjct: 205 KEHTYFMLNKPKGFVCSARPGSESGKTVLDLFEQWREEFRSEYPGKLPPRLFTVGRLDVA 264

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLL+T DG  ++ +  PS++ ++ Y V  + +  + ++  + KG  + G     ++V
Sbjct: 265 TTGLLLVTTDGDWSQRVSHPSSEVVKQYVVTANAKPTRAQIVAMSKGTEVDGAHVVPVRV 324

Query: 178 TLDTQK-GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTRE 235
            +     G    + V + +G+NRE++ + E    +V  L R   G  ++   L  G    
Sbjct: 325 EVAGADGGPKNRIIVEVVDGRNREVRVLCESAGVEVKNLKRTRVGGLRMPKELPLGKYVR 384

Query: 236 VSKKILREQL 245
           +    +   L
Sbjct: 385 LKPAQIAHVL 394


>gi|75762594|ref|ZP_00742444.1| Ribosomal large subunit pseudouridine synthase F [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
 gi|74489914|gb|EAO53280.1| Ribosomal large subunit pseudouridine synthase F [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
          Length = 192

 Score =  127 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 52/198 (26%), Positives = 89/198 (44%), Gaps = 8/198 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-R 72
            ++++ I+ A   SRRE +R+I   RV +NG +       V   D + +DG  + K E  
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTH-GALVSDGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D    + +         R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAADHIEDNIIDYI--HYPERIFPVGRLDKASEGLILLTNDGTIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT       +      
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVTRVRSINISYH---- 173

Query: 193 LREGKNREIKKVFEFFNW 210
           L +G NR+I+++     +
Sbjct: 174 LTQGMNRQIRRMSRAIGY 191


>gi|68068373|ref|XP_676096.1| pseudouridine synthetase [Plasmodium berghei strain ANKA]
 gi|56495631|emb|CAH95418.1| pseudouridine synthetase, putative [Plasmodium berghei]
          Length = 318

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 52/271 (19%), Positives = 106/271 (39%), Gaps = 37/271 (13%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVP 66
            +N    R++K+I+     SRR+ ++ I    +K+N  ++     +V  + D I+V    
Sbjct: 40  NKNENIIRLNKLISINNNISRRKSDKFIQNANIKINNKVVLNPGTHVDITKDQIKVHDKK 99

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-------------------IFSR 107
           +      ++   +                     + +                      R
Sbjct: 100 IDIENIKKILNNYNISNTNHNSYKWIVMHKPKGLICTNQDEKDRKSIFSIFPDDLLQKYR 159

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           ++SVGRLD NT G+LL TN+      L  P  + +R Y +   G V  D L +L  G+ +
Sbjct: 160 IVSVGRLDRNTSGVLLFTNEYTWVNKLTHPKYERVRKYMIHIEGPVRMDALKMLANGVYL 219

Query: 168 QGI--------CYGDMQVTLDTQKGSN--------AWVTVGLREGKNREIKKVFEFFNWK 211
           +                + +  ++             + + ++EG+NR+I+K+F+  N  
Sbjct: 220 KDEDNNKKKKKKTQPAFIEVLREENVKIQNQIKKITVLNISIKEGRNRQIRKMFQQINQP 279

Query: 212 VNRLIRISYGPFQLGTLL-AGSTREVSKKIL 241
           + ++ R ++    L  +      RE++KK +
Sbjct: 280 IVKIKRTAFENITLKNIHLPKQYRELTKKEI 310


>gi|83719779|ref|YP_441351.1| ribosomal small subunit pseudouridine synthase A [Burkholderia
           thailandensis E264]
 gi|83653604|gb|ABC37667.1| ribosomal small subunit pseudouridine synthase A [Burkholderia
           thailandensis E264]
          Length = 252

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 53/234 (22%), Positives = 92/234 (39%), Gaps = 4/234 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLR 68
           N     +  ++   G  SRR+   ++   RV V G     A  +  +   + EVDGV   
Sbjct: 9   NARAMDLESILFTQGFGSRRQCRALVEAGRVAVGGATCADAHTSFDTARLVFEVDGVAWP 68

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              R  + L        +                     V  VGRLD +T GLLLL++DG
Sbjct: 69  YRARAYVALNKPAGYECSREPQHHASVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDG 128

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
                   P  +  + Y       +D  +L+ L+ G+++ G     +       +G    
Sbjct: 129 QFVHAYTSPKRKVPKTYVATVRHPLDDAQLDALRAGVLLHGEP-KPIAALAAAARGER-L 186

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           + + + EGK  ++K++    + +V+ L R   G F L   L  G+ R + ++ L
Sbjct: 187 LEMTIAEGKYHQVKRMVAAASNRVDALHRSRIGGFALPEDLAEGAWRWLDERDL 240


>gi|291613717|ref|YP_003523874.1| pseudouridine synthase [Sideroxydans lithotrophicus ES-1]
 gi|291583829|gb|ADE11487.1| pseudouridine synthase [Sideroxydans lithotrophicus ES-1]
          Length = 241

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 46/230 (20%), Positives = 78/230 (33%), Gaps = 7/230 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPLRKAERT 73
           + +++   G  +R+    +I    V V G  +     +   TD++E  V G   R  E  
Sbjct: 6   LDRILQSQGFGTRKWCRELIEDGEVLVAGDSITDY-RHAFETDNLEFSVYGESWRFREHV 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L        +                     V  VGRLD +T GLLL+++DG     
Sbjct: 65  YIALNKPADYECSRKPSHHPGVLSLLPEQFALRDVQPVGRLDHDTTGLLLMSDDGAFIHA 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
              P     +VY    H  V    +  L  G+ +         V  +        + + L
Sbjct: 125 QSSPKRHIPKVYVATTHDPVTPQLVRQLMSGVKLHDEPAPLAAVVCNMLD--TCQLKIVL 182

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKIL 241
            +GK  ++K++          L R   G  +L    L  G    + +  L
Sbjct: 183 EQGKYHQVKRMLAAAGNHCTALRRTEIGKLRLEALGLAEGEWCYLGEAEL 232


>gi|21672551|ref|NP_660618.1| hypothetical protein BUsg271 [Buchnera aphidicola str. Sg
           (Schizaphis graminum)]
 gi|22654296|sp|P42395|RLUB_BUCAP RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|21623176|gb|AAM67829.1| hypothetical 30.2 kDa protein [Buchnera aphidicola str. Sg
           (Schizaphis graminum)]
          Length = 257

 Score =  126 bits (317), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 73/255 (28%), Positives = 117/255 (45%), Gaps = 10/255 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV--NVMSTDHIEVDGVPL----R 68
           ++ K+++  G  SRR +E MI   ++ +NG                 I +D   +     
Sbjct: 4   KIQKILSDLGYGSRRFIECMIKCGKISINGEKAIIGQYLNKKNPG-EILIDKKKIIVKRN 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           K     L        + T        +          +R +SVGRLDINT+GLLL TNDG
Sbjct: 63  KNLPKVLIYNKPIGEVCTRDDFQKRLTVFDKLPKLNLNRWVSVGRLDINTKGLLLFTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKGSN 186
            LA  L  P +Q  R Y +R  G+++++K+N+L+KG+ I        ++    D ++G N
Sbjct: 123 TLANKLMHPRSQIEREYNIRIFGEMNKNKINILRKGVKIIHGYVSFKEIVPLYDKKEGKN 182

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
            W    L EGKNREI+ +F+    +VN+LIR+ YG   L   L  G    ++   L++  
Sbjct: 183 KWFKGILCEGKNREIRLMFKSIQCQVNQLIRVRYGNIILPKNLKEGQWMMLNSIFLKKLY 242

Query: 246 GPHLLEEAQVNLDAP 260
                ++  +N    
Sbjct: 243 NLINFDKEIINKKKN 257


>gi|308062723|gb|ADO04611.1| hypothetical protein HPCU_07355 [Helicobacter pylori Cuz20]
          Length = 257

 Score =  126 bits (316), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 62/249 (24%), Positives = 117/249 (46%), Gaps = 19/249 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAK-LASVVKENDKVFLDKRLIKPLKNK 59

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKNDPLKRCVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQV 177
             L        + Y V+  G V ++  N +++G+ ++                    +  
Sbjct: 120 SALMHA--NLEKEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQLG 246
           ++   E   
Sbjct: 238 RQEYNELHA 246


>gi|227486208|ref|ZP_03916524.1| pseudouridylate synthase [Anaerococcus lactolyticus ATCC 51172]
 gi|227235839|gb|EEI85854.1| pseudouridylate synthase [Anaerococcus lactolyticus ATCC 51172]
          Length = 232

 Score =  126 bits (316), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 52/233 (22%), Positives = 100/233 (42%), Gaps = 9/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            RV K+I   G+ +R+ ++R   +  + +NG +++ ++V V    D +   G  +   E 
Sbjct: 1   MRVDKMIGNTGLDTRKNIKRNAKKGALVINGEIVKDSSVKVDPLVDEVFYMGHFVEYIEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L      +++   D +       +       +   GRLD +T GL++L+ DG    
Sbjct: 61  LYLILNKPSG-VLSATQDAEETVIDLLDDFYKNYDLSIAGRLDKDTTGLIILSTDGKFIH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVT 190
            +  P++   + Y V+    + ++     KKG+ I          ++T+  +K +   V 
Sbjct: 120 KITSPNSHITKTYEVKTRDPIAENLKEEFKKGVYIKEDDYTARPAELTITGEKEAIVKV- 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
               EGK   +K++F     +V  L R + G   L   L  G  RE+++  L 
Sbjct: 179 ---TEGKYHLVKRLFSNLGNEVVGLKRTAIGKLVLDPYLKEGDYRELTEAELE 228


>gi|221208265|ref|ZP_03581269.1| RNA pseudouridine synthase family protein [Burkholderia multivorans
           CGD2]
 gi|221171913|gb|EEE04356.1| RNA pseudouridine synthase family protein [Burkholderia multivorans
           CGD2]
          Length = 610

 Score =  126 bits (316), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 60/251 (23%), Positives = 101/251 (40%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 362 MRLSKRMSELGLCSRREADEWIEKGWVIVDGERIDTLGTKVRADQRIEIDERAQAAQAAQ 421

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     L+T  +   G  +     P     +   GRLDI++
Sbjct: 422 VTILLHKPVGYVSGQAEDGYEPASVLITRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 481

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y VR                ++L  L+ G+ + G
Sbjct: 482 TGLLVLTQNGRIAKQLIGEQSDVDKEYLVRVRFGDRLTDIDQHFPAERLAQLRHGLELDG 541

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREG+ R+I+++ E    +V  L R+  G   LG L 
Sbjct: 542 VALKPAMVSWQNGEQ----LRFVLREGRKRQIRRMCELVGLEVIGLKRVRMGRVTLGALP 597

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 598 QGQWRYLSADE 608


>gi|331006786|ref|ZP_08330052.1| Hypothetical pseudouridylate synthase [gamma proteobacterium
           IMCC1989]
 gi|330419404|gb|EGG93804.1| Hypothetical pseudouridylate synthase [gamma proteobacterium
           IMCC1989]
          Length = 239

 Score =  126 bits (316), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 53/235 (22%), Positives = 102/235 (43%), Gaps = 12/235 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I+R    + + V  ++ ++++ V+G +       V     + VDG  +++ +   
Sbjct: 7   RLDRFISRRLSVTNKAVRELLVRKKIIVDGEVASLMNQTVGPFTFVVVDGEVIQQRQPVY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L +      +V+   D      +      +   +   GRLD NT GLLLLTNDG  ++ L
Sbjct: 67  LMMNKPKG-VVSATKDDKHTIVLDLIDHPLKEELHIAGRLDFNTTGLLLLTNDGAWSKQL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAW 188
            LP    ++ YRV     +             +G+ +  + I      +   +       
Sbjct: 126 SLPENNIMKKYRVTLKDHLFSSDVLIYQKKFSEGVFLSSENITTRPATLLALSSNI---- 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           V + + EG+  ++K++F FF  +V  L R+S G  ++ G L  G  R ++ K + 
Sbjct: 182 VELSICEGRYHQVKRMFGFFQNEVLELHRLSVGSLEMEGGLALGRYRVLTPKEID 236


>gi|293394908|ref|ZP_06639198.1| ribosomal large subunit pseudouridine synthase F [Serratia
           odorifera DSM 4582]
 gi|291422659|gb|EFE95898.1| ribosomal large subunit pseudouridine synthase F [Serratia
           odorifera DSM 4582]
          Length = 217

 Score =  126 bits (316), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 42/217 (19%), Positives = 83/217 (38%), Gaps = 4/217 (1%)

Query: 51  AVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
              V   D + V+G P+   +   L L      +    S          +  +   R   
Sbjct: 5   GEQVFVGDSVSVNGQPIAPRKAEDLVLIALNKPVGVITSMGKQVRNNIGDWVNHSQRTFP 64

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
           +GRLD +++GL+ LTN G L   +        + Y V     +  + +  +  G+ I G 
Sbjct: 65  IGRLDKDSQGLIFLTNHGELVNKILRAGNNHQKEYLVSVDRPITDEFIQAMGAGVPILGT 124

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                      +K ++  + + L +G NR+I+++ ++F ++V +L R+      L  L  
Sbjct: 125 VTKPC----LVEKIASQILRITLVQGLNRQIRRMCKYFGYQVTKLERVRIMNINLHGLAL 180

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETL 267
           G  R+ + +  RE         ++ +  A        
Sbjct: 181 GEWRDFTDEERRELFRLIEHSSSEASQPATTSIPPVA 217


>gi|317182664|dbj|BAJ60448.1| hypothetical protein HPF57_1374 [Helicobacter pylori F57]
          Length = 257

 Score =  126 bits (316), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 61/249 (24%), Positives = 117/249 (46%), Gaps = 19/249 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAK-LASVVKENDKVFLDKRLIKPLKNK 59

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQV 177
             L        + Y V+  G V ++  + +++G+ ++                    +  
Sbjct: 120 SALMHA--NLEKEYLVKIQGFVTKEMESAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQLG 246
           ++   E   
Sbjct: 238 RQEYNELHA 246


>gi|294155840|ref|YP_003560224.1| ribosomal small subunit pseudouridine synthase A [Mycoplasma
           crocodyli MP145]
 gi|291600207|gb|ADE19703.1| ribosomal small subunit pseudouridine synthase A [Mycoplasma
           crocodyli MP145]
          Length = 228

 Score =  126 bits (316), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 48/232 (20%), Positives = 105/232 (45%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++     +R E++ ++   RV +NG L +   +     + + +DG+     +  
Sbjct: 1   MRIEKWLSDVTDYTRSEIKNLLKNNRVYINGRLYDET-IKYNEFNSLRIDGIDYATDKYV 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L      + +   +     +VF+ +      +I+ GRLD++TEGLL+L+++  L   
Sbjct: 60  YIMLNKPQGYITSNKDELY--PSVFNLIDVPRKNLIAYGRLDVDTEGLLVLSDNHKLCHE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           L  P     + Y V+   Q++ + +++ K+G  I +       ++ +      N    + 
Sbjct: 118 LLAPKKHVFKKYLVQVDKQLEPNLIDIFKQGFSIGEDKNTLPSKLEII----DNFTCYLT 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
           + EGK  ++K++F+   + V  L R+S+    L   L     R +S   + +
Sbjct: 174 ISEGKFHQVKRMFKTNGYNVIFLKRVSFKNIILDEKLKPSQWRFLSSDEIND 225


>gi|167585734|ref|ZP_02378122.1| Pseudouridine synthase, Rsu [Burkholderia ubonensis Bu]
          Length = 238

 Score =  126 bits (316), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 88/228 (38%), Gaps = 4/228 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTR 74
           +  ++   G  SRR+   ++   RV V G                + VDGV      R  
Sbjct: 3   LESILFTQGFGSRRQCRGLVDAARVAVAGAPCTDPDAEFDTDGLVVSVDGVAWPFHARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L        +               P +   V  VGRLD +T GLLLL++DG      
Sbjct: 63  LALNKPAGYECSRDPQHHASVFSLLPTPLVARGVQCVGRLDQDTTGLLLLSDDGQFVHAY 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y       +D  +L+ L+ G+ + G     +       + +   + + + 
Sbjct: 123 TSPKRKVPKTYVATVRHPLDDAQLHALRTGVQLHGEP-KPIAAVAADARDA-HVLALTVL 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           EGK  ++K++    + +V  L R S G F L   L  G+ R +S+  L
Sbjct: 181 EGKYHQVKRMVAAASNRVEALHRESIGGFALPADLEPGAWRWLSEADL 228


>gi|111114952|ref|YP_709570.1| hypothetical protein BAPKO_0131 [Borrelia afzelii PKo]
 gi|110890226|gb|ABH01394.1| conserved hypothetical protein [Borrelia afzelii PKo]
          Length = 249

 Score =  126 bits (316), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 63/228 (27%), Positives = 97/228 (42%), Gaps = 10/228 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP----- 66
              R+   +A  G+ SRR  E +I ++ V+VNG + +     V   D I           
Sbjct: 5   KTPRIHVFLAEKGVGSRRFCEELIRKKLVRVNGSIAK-LGDKVALGDRIIYKKQIYVFKD 63

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L+   R  L L      L +       +  +    P    R+ S+GRLD  + GLLL TN
Sbjct: 64  LQSKSRVYLALNKPRNYLCSNFDANGRKLAISLVQPLFKERLFSIGRLDFKSSGLLLFTN 123

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  A  +  P  +  R Y +     +D++ L   K GI I+   +      +  +  + 
Sbjct: 124 DGKFANDIIHPRQKVEREYIIESKKDIDENLLISFKSGIKIKKEFFKLKSYEILNKNSA- 182

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
               + L EGKNREI+KVF   N  + ++ RI  G   L +L  G  +
Sbjct: 183 ---RLILDEGKNREIRKVFLSKNVFLKKIHRIRIGNINLDSLKEGQVK 227


>gi|91784123|ref|YP_559329.1| pseudouridine synthase, Rsu [Burkholderia xenovorans LB400]
 gi|91688077|gb|ABE31277.1| Pseudouridine synthase, Rsu [Burkholderia xenovorans LB400]
          Length = 649

 Score =  126 bits (316), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 62/261 (23%), Positives = 107/261 (40%), Gaps = 28/261 (10%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           +   ++     R+SK+++  G+ SRRE +  I +  V V+G  ++     V     IE+D
Sbjct: 391 RRDYEDAPGTLRLSKLMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPDQRIEID 450

Query: 64  G---------------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                             +          Y   I LVT  +  +G  +      +   ++
Sbjct: 451 PAAEAAQASQVTVLIHKTVGFVSGQAEDGYQPAITLVTPENRWEGDRSNIRFSVAHLRQL 510

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLN 159
              GRLDI++ GLL+LT DG +A+ L    ++  + Y VR                + L 
Sbjct: 511 APAGRLDIDSTGLLVLTQDGRIAKRLVGGHSEIDKEYLVRVAFGEHTTDVESHFPPESLA 570

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
           LL+ G+ +  +     QV+    +     +   LREGK R+I+++ E    +V  L R+ 
Sbjct: 571 LLRHGLSLDDVPLKPAQVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVR 626

Query: 220 YGPFQLGTLLAGSTREVSKKI 240
            G   LG L  G  R ++   
Sbjct: 627 MGHVMLGALPPGQWRYLAADE 647


>gi|308064218|gb|ADO06105.1| hypothetical protein HPSAT_07015 [Helicobacter pylori Sat464]
          Length = 257

 Score =  126 bits (316), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 61/259 (23%), Positives = 117/259 (45%), Gaps = 19/259 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAK-LASVVKENDKVFLDKRLIKPLKNK 59

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQV 177
             L        + Y ++  G V ++  N +++G+ ++                    +  
Sbjct: 120 SALMHA--NLEKEYLIKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQLGPHLLEEAQVN 256
           ++   E             
Sbjct: 238 RQEYNELHAFMANAANVKE 256


>gi|261840134|gb|ACX99899.1| pseudouridylate synthase [Helicobacter pylori 52]
          Length = 257

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 62/249 (24%), Positives = 118/249 (47%), Gaps = 19/249 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAK-LASVVKENDKVFLDKRLIKPLKNK 59

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++  + VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKNDPLKRHVIYESLEKKYAHFVPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQV 177
             L        + Y V+  G V ++  N +++G+ ++                    +  
Sbjct: 120 SALMHA--NLEKEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQLG 246
           ++   E   
Sbjct: 238 RQEYNELHA 246


>gi|208435327|ref|YP_002266993.1| ribosomal large subunit pseudouridinesynthase B [Helicobacter
           pylori G27]
 gi|208433256|gb|ACI28127.1| ribosomal large subunit pseudouridinesynthase B [Helicobacter
           pylori G27]
          Length = 257

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 61/249 (24%), Positives = 118/249 (47%), Gaps = 19/249 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAK-LASVVKENDKVFLDKRLIKPLKNK 59

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++  + VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFVPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQV 177
             L        + Y ++  G V ++  N +++G+ ++                    +  
Sbjct: 120 SALMHAD--LEKEYLIKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVVINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQLG 246
           ++   E   
Sbjct: 238 RQEYNELHA 246


>gi|188528230|ref|YP_001910917.1| hypothetical protein HPSH_07470 [Helicobacter pylori Shi470]
 gi|188144470|gb|ACD48887.1| hypothetical protein HPSH_07470 [Helicobacter pylori Shi470]
          Length = 257

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 62/259 (23%), Positives = 117/259 (45%), Gaps = 19/259 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAK-LASVVKENDKVFLDKRLIKPLKNK 59

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQV 177
             L        + Y V+  G V ++  N +++G+ ++                    +  
Sbjct: 120 SALMHA--NLEKEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQLGPHLLEEAQVN 256
           ++   E             
Sbjct: 238 RQEYNELHAFMANAANVKE 256


>gi|51598393|ref|YP_072581.1| hypothetical protein BG0131 [Borrelia garinii PBi]
 gi|51572964|gb|AAU06989.1| conserved hypothetical protein [Borrelia garinii PBi]
          Length = 249

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 61/228 (26%), Positives = 98/228 (42%), Gaps = 10/228 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA- 70
              RV   +A  G+ SRR  E +I ++ ++VNG + +     V   D I           
Sbjct: 5   KSPRVQVFLAEKGVGSRRFCEELIRKKLIRVNGSIAK-LGDKVSPGDRIIYKKQIYVFKD 63

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
              +       +KP   + ++ D +GR      +      R+ S+GRLD  + GLLL TN
Sbjct: 64  FQSKNKIYLALNKPKNYLCSNFDVNGRKLAISLVQPLFKERIFSIGRLDFKSSGLLLFTN 123

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  A  +  P  +  R Y +     +D++ L   K GI ++   +      +  +  + 
Sbjct: 124 DGEFANDIIHPRRKVEREYIIESKKDIDENLLISFKSGIKVKKEFFKLKSYEILNKNSA- 182

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
               + L EGKNREI+KVF   N  + ++ RI  G   L  L  G  +
Sbjct: 183 ---RLILDEGKNREIRKVFLSKNIFLKKIHRIRIGNINLDNLKEGQVK 227


>gi|90415084|ref|ZP_01223042.1| Hypothetical pseudouridylate synthase [Photobacterium profundum
           3TCK]
 gi|90323819|gb|EAS40432.1| Hypothetical pseudouridylate synthase [Photobacterium profundum
           3TCK]
          Length = 223

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 60/227 (26%), Positives = 104/227 (45%), Gaps = 7/227 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R+ + I++    S  +   +IAQ+R+ ++G +       V    ++E+DG  L+ 
Sbjct: 2   KSTTNRLDRFISQNSPFSISDTRLLIAQKRILLDGHVAHSNQQKVTKFTYVELDGNCLQD 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L      +V+   D    + +        + +  VGRLD NT GL+LLTNDG 
Sbjct: 62  NNPLYIMLNKPKG-VVSATKDIKHSTVLDLIQHPQKNELHIVGRLDFNTTGLVLLTNDGA 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNA 187
            +R + LP T+  +VY V     + ++ + + ++GI    + I      + +     S  
Sbjct: 121 WSRKISLPETKLAKVYEVTLSKPLTEEYVAVFREGIYFGYEDITTKPACLEIL----SEY 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              + L EGK  ++K++F FF  +V  L R S G   L  L  G +R
Sbjct: 177 TARLSLVEGKYHQVKRMFGFFQNEVLELHRASVGNISLEGLEEGHSR 223


>gi|66811146|ref|XP_639281.1| hypothetical protein DDB_G0282961 [Dictyostelium discoideum AX4]
 gi|60467911|gb|EAL65924.1| hypothetical protein DDB_G0282961 [Dictyostelium discoideum AX4]
          Length = 571

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 53/266 (19%), Positives = 101/266 (37%), Gaps = 7/266 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ ++++  G+  R  V + +  +RV V G  +   A      D I++DG P+   E   
Sbjct: 10  RIERILSNLGVCERSRVPQFLRDKRVTVLGKKVT-PATKANIKD-IQIDGEPIENGETLH 67

Query: 75  LWLYHKPIGLVTTHSDPDG---RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           + ++     + +T +D D       +          +   GRLD    GL++L+ DG L 
Sbjct: 68  IAVHKPSGYICSTVNDHDHKIIYDILPKEFFKRKPTLSIAGRLDKWVTGLVVLSQDGKLV 127

Query: 132 RVLELPST--QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
             +  P           V     V  +        I+++G         L         V
Sbjct: 128 DRIISPKDDGCGKDYEVVLKDKLVGDEAEVFESGKIMLRGESTPCKPAKLQVLDKEKNKV 187

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            V L EG+  +I+++F     K   + R   GP +LG L  G  R ++++ L+E     +
Sbjct: 188 KVTLYEGRYHQIRRMFASTENKAVEIHRTRIGPVELGDLGLGKWRHLTEQELKELYSIKI 247

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNII 275
            + +       +  +  L + +    
Sbjct: 248 DDNSNKTDKKKVKLNSFLEKKKKLRG 273


>gi|109946748|ref|YP_663976.1| pseudouridylate synthase [Helicobacter acinonychis str. Sheeba]
 gi|109713969|emb|CAJ98977.1| pseudouridylate synthase [Helicobacter acinonychis str. Sheeba]
          Length = 254

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 61/249 (24%), Positives = 119/249 (47%), Gaps = 19/249 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAK-LASVVKENDKVFLDKRLIKPLKNK 59

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++  + VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKNDPLKRRMIYESLERKYAHFVPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQV 177
             L        + Y ++  G V ++  N +++G+ ++                    +  
Sbjct: 120 SALMHA--NLEKEYLIKIQGFVTKEMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN +V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKIRVVINEGKNRELRRFFAFFNARVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQLG 246
           ++   E   
Sbjct: 238 RQEYNELHA 246


>gi|262372211|ref|ZP_06065490.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter junii SH205]
 gi|262312236|gb|EEY93321.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter junii SH205]
          Length = 237

 Score =  126 bits (315), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 46/224 (20%), Positives = 85/224 (37%), Gaps = 5/224 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V +   + +    N        EV G      E   
Sbjct: 3   LEKILQSQGFGSRKYCQQIIKNGSVTIENQICDNPKQNFPTEHLCFEVFGEEYLFRENVY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        +  +              +   +  VGRLD +T GLLLLT+DG   + L
Sbjct: 63  IVLNKPKGYECSHQATHHKSVFSLFPEILLHRGIQCVGRLDQDTTGLLLLTDDGQYLQAL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTVGL 193
             P     +VY V     + Q++   L++G+ ++                 S   +++ +
Sbjct: 123 TNPRKHVPKVYHVTTADPITQEQKQALEQGVELRNEKGIYAATDVHLF---SEHQLSMTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +G   ++K++      KV  L R   G F+L  +  G    +S
Sbjct: 180 HQGIYHQVKRMLAAVGNKVEDLHRHQVGLFELPKIPEGEWLYLS 223


>gi|216264053|ref|ZP_03436047.1| hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Borrelia afzelii ACA-1]
 gi|215980097|gb|EEC20919.1| hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Borrelia afzelii ACA-1]
          Length = 249

 Score =  126 bits (315), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 64/228 (28%), Positives = 97/228 (42%), Gaps = 10/228 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP----- 66
              R+   +A  G+ SRR  E +I ++ V+VNG + +     V   D I           
Sbjct: 5   KTPRIHVFLAEKGVGSRRFCEELIRKKLVRVNGSIAK-LGDKVALGDRIIYKKQIYVFKD 63

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L+   R  L L      L +       +  +    P    RV S+GRLD  + GLLL TN
Sbjct: 64  LQSKSRVYLALNKPRNYLCSNFDANGRKLAISLVQPLFKERVFSIGRLDFKSSGLLLFTN 123

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  A  +  P  +  R Y +     +D++ L   K GI I+   +      +  +  + 
Sbjct: 124 DGKFANDIIHPRQKVEREYIIESKKDIDENLLISFKLGIKIKKEFFKLKSYEILNKNSA- 182

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
               + L EGKNREI+KVF   N  + ++ RI  G   L +L  G  +
Sbjct: 183 ---RLILDEGKNREIRKVFLSKNVFLKKIHRIRIGNINLDSLKEGQVK 227


>gi|268682366|ref|ZP_06149228.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae PID332]
 gi|268622650|gb|EEZ55050.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae PID332]
          Length = 230

 Score =  126 bits (315), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 43/227 (18%), Positives = 87/227 (38%), Gaps = 6/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLR--K 69
            ++ K +   GI SR++ + +I    V +NG  ++    ++ S+  + +++DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSYVETLDIDGEAVTVVP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 61  EPYFYILLNKPEDYETSHKPKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS +  ++Y V       +     LK G+ +              +      +
Sbjct: 121 LNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVPLHDENETVCAADAVLENP--TTL 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + + EGK  ++K++      +   L R  +   +   L  G  + +
Sbjct: 179 LLTITEGKYHQVKRMVAAAGNRAQHLHRRRFAHLETENLKPGEWKFI 225


>gi|268596631|ref|ZP_06130798.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae FA19]
 gi|268550419|gb|EEZ45438.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae FA19]
          Length = 241

 Score =  126 bits (315), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 43/227 (18%), Positives = 87/227 (38%), Gaps = 6/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLR--K 69
            ++ K +   GI SR++ + +I    V +NG  ++    ++ S+  + +++DG  +    
Sbjct: 12  MKLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSYVETLDIDGEAVTVVP 71

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 72  EPYFYILLNKPEDYETSHKPKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 131

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS +  ++Y V       +     LK G+ +              +      +
Sbjct: 132 LNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVPLHDENETVCAADAVLENP--TTL 189

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + + EGK  ++K++      +   L R  +   +   L  G  + +
Sbjct: 190 LLTITEGKYHQVKRMVAAAGNRAQHLHRRRFAHLETENLKPGEWKFI 236


>gi|217033910|ref|ZP_03439334.1| hypothetical protein HP9810_870g42 [Helicobacter pylori 98-10]
 gi|216943673|gb|EEC23118.1| hypothetical protein HP9810_870g42 [Helicobacter pylori 98-10]
          Length = 257

 Score =  126 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 62/249 (24%), Positives = 118/249 (47%), Gaps = 19/249 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +A     SRRE E+++ + RVK+N    +  +V V   D + +D   ++  +  
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLVSV-VKENDKVFLDKRLIKPLKNK 59

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQV 177
             L        + Y V+  G V ++  N +++G+ ++                    +  
Sbjct: 120 STLMHA--NLEKEYLVKIQGFVTKEMENAMQEGLKLENATKGAHQKTSIKSMEFAPFIGY 177

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQLG 246
           ++   E   
Sbjct: 238 RQEYNELHA 246


>gi|317013226|gb|ADU83834.1| ribosomal large subunit pseudouridinesynthase B [Helicobacter
           pylori Lithuania75]
          Length = 257

 Score =  125 bits (314), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 62/249 (24%), Positives = 118/249 (47%), Gaps = 19/249 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAK-LASVVKENDKVFLDKRLIKPLKNK 59

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++  + VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFVPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQV 177
             L        + Y V+  G V ++  N +++G+ ++                    +  
Sbjct: 120 SALMHAD--LEKEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKIRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQLG 246
           ++   E   
Sbjct: 238 RQEYNELHA 246


>gi|255068178|ref|ZP_05320033.1| ribosomal small subunit pseudouridine synthase A [Neisseria sicca
           ATCC 29256]
 gi|255047605|gb|EET43069.1| ribosomal small subunit pseudouridine synthase A [Neisseria sicca
           ATCC 29256]
          Length = 227

 Score =  125 bits (314), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 42/230 (18%), Positives = 88/230 (38%), Gaps = 10/230 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGV--PLRK 69
            ++ K +   GI SR++ + +I    V++N  +      ++       + +DG    +  
Sbjct: 1   MQLIKYLQSQGIGSRKQCQWLIQNDCVEINDTIRNDTKADIDPAEVQTLRIDGEDIVVVP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 61  MPYFYILLNKPADYETSHKPQQYPSVFSLFPDHMRNIDMQAVGRLDADTTGVLLITNDGQ 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNA 187
               +  P  +  ++YRV      D      LK G+++          +  L+    +  
Sbjct: 121 FNHRVTSPKHKVPKIYRVTLKHPADDSLCETLKNGVLLHDDNETVRAAEAVLE----NPT 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + + EGK  ++K++      +V  L R  +    +  L +G  + ++
Sbjct: 177 TLLMTITEGKYHQVKRMVAAAGNRVEHLHRDEFNGRTVENLASGEWKFIT 226


>gi|167561885|ref|ZP_02354801.1| RNA pseudouridine synthase family protein [Burkholderia
           oklahomensis EO147]
          Length = 240

 Score =  125 bits (314), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 90/228 (39%), Gaps = 4/228 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTR 74
           +  ++   G  SRR+   ++   RV V G     A  +  +     EVDGV      R  
Sbjct: 3   LESILFTQGFGSRRQCRALVEAGRVAVGGATCTDAHASFDTARLAFEVDGVAWPYHARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        +                     V  VGRLD +T GLLLL++DG      
Sbjct: 63  VVLNKPAGYECSREPQHHSSVFRLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVHAY 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y       +D  +L+ L+ G+++ G     +       +G    + + + 
Sbjct: 123 TSPKRKVPKTYVATVRHPLDDAQLDALRAGVLLHGEP-KPIAAVAAHARGER-LLEMTVA 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           EGK  ++K++    + +V  L R S G F L   L  G+ R + ++ L
Sbjct: 181 EGKYHQVKRMVAAASNRVEALHRASIGGFTLPADLAEGAWRWLDERDL 228


>gi|319763700|ref|YP_004127637.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
 gi|330824037|ref|YP_004387340.1| pseudouridine synthase Rsu [Alicycliphilus denitrificans K601]
 gi|317118261|gb|ADV00750.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
 gi|329309409|gb|AEB83824.1| pseudouridine synthase Rsu [Alicycliphilus denitrificans K601]
          Length = 245

 Score =  125 bits (314), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 51/243 (20%), Positives = 89/243 (36%), Gaps = 17/243 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKV--NG----ILLERAAVNVMS-TDHIEVDGVP 66
            ++  ++   G  +RR    +I Q  V V   G    ++    A N+      + V G  
Sbjct: 1   MQLQDILYSQGFGTRRICAGLIQQGWVAVHSAGSLEPVVCLEPAQNLKEQGLVLRVQGQD 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGR-------STVFDNLPSIFSRVISVGRLDINTE 119
                +  + L        +                       S  S V +VGRLD +T 
Sbjct: 61  WPYHAKAYVMLNKPAGTECSQKPSAYPSVYTLLPAPLRQRPGKSAVSGVQAVGRLDQDTT 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLL++DG     +  P     +VY+V     VD  ++  L  G+V+       ++  +
Sbjct: 121 GLLLLSDDGQFIHRMSSPKKHVPKVYQVTVRHPVDAAQVECLLAGVVLDDDP-KPVR-AV 178

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
              +     + + L EGK  ++K++      +V  L R   G  +L   +  G  R +  
Sbjct: 179 ACVQRDAHRIDLTLTEGKYHQVKRMIAAVGNRVEALHRARIGGLELPADMAPGQWRWLGL 238

Query: 239 KIL 241
             L
Sbjct: 239 DEL 241


>gi|255084639|ref|XP_002508894.1| predicted protein [Micromonas sp. RCC299]
 gi|226524171|gb|ACO70152.1| predicted protein [Micromonas sp. RCC299]
          Length = 248

 Score =  125 bits (314), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 68/244 (27%), Positives = 101/244 (41%), Gaps = 32/244 (13%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR------------- 74
           RRE +  ++  RV+VNG L++  +  V S D + +DG  L                    
Sbjct: 1   RREADEAVSAGRVRVNGALVK-PSFRVRSGDVVTLDGKALDWEPFAAATEGSIGAHAGSN 59

Query: 75  ---LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                 Y+KP G+  T                  +RV  VGRLD ++ GL+LLT+DG + 
Sbjct: 60  GFFYLKYNKPRGVTCTMESSQRTKPAKGV---GSARVFPVGRLDRDSSGLVLLTDDGRVP 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI----------CYGDMQVTLDT 181
             L  PS +  + Y V        D +  L+ G+VI                   V L  
Sbjct: 117 EALLDPSRKAPKTYEVDVRPAPTPDAIEALRDGVVITTTQQRDGVTTTSPTAPCPVDLIK 176

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTREVSKK 239
           +  ++A +   LREG+NR+I+K+ E    +V RL R+S G   L    L  G  R +S  
Sbjct: 177 KSETSATLRFELREGRNRQIRKMCEAVGVEVVRLHRVSVGGVWLDESALEVGGVRALSGD 236

Query: 240 ILRE 243
            L  
Sbjct: 237 ELDA 240


>gi|308183557|ref|YP_003927684.1| hypothetical protein HPPC_07130 [Helicobacter pylori PeCan4]
 gi|308065742|gb|ADO07634.1| hypothetical protein HPPC_07130 [Helicobacter pylori PeCan4]
          Length = 257

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 57/247 (23%), Positives = 112/247 (45%), Gaps = 15/247 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAK-LASVVKENDKVFLDKRLIKPLKNK 59

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLL------------KKGIVIQGICYGDMQVTL 179
             L   + +   + +++     + +                 +K  +        +   +
Sbjct: 120 SALMHANLEKEYLIKIQGFVTREMENAMQEGLKLKNATKGAHQKTPIKSMEFAPFIGYEI 179

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                  + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++++
Sbjct: 180 IKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNRQ 239

Query: 240 ILREQLG 246
              E   
Sbjct: 240 EYNELHA 246


>gi|317010168|gb|ADU80748.1| ribosomal large subunit pseudouridinesynthase B [Helicobacter
           pylori India7]
          Length = 257

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 61/249 (24%), Positives = 118/249 (47%), Gaps = 19/249 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAK-LASVVKENDRVFLDKRLIKPLKNK 59

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++  + VGRLD  +EG+L+L++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFVPVGRLDFASEGVLILSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQV 177
             L        + Y V+  G V ++  N +++G+ ++                    +  
Sbjct: 120 SALMHA--NLEKEYLVKIQGFVTREIENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVVINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQLG 246
           ++   E   
Sbjct: 238 RQEYNELHA 246


>gi|167752034|ref|ZP_02424161.1| hypothetical protein ALIPUT_00276 [Alistipes putredinis DSM 17216]
 gi|167660275|gb|EDS04405.1| hypothetical protein ALIPUT_00276 [Alistipes putredinis DSM 17216]
          Length = 451

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 58/235 (24%), Positives = 110/235 (46%), Gaps = 2/235 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            +     R+++ IA++GI SRRE +  I    V VNG+++      V  TD ++ +   +
Sbjct: 211 NKPTGEIRLNRFIAQSGICSRREADDFIQAGLVTVNGVVVTTLGTKVQPTDEVKFNDSRV 270

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              ++  L L      + +       ++ +     +   R+  VGRLD N+ GLLL TND
Sbjct: 271 EGEKKVYLVLNKPKGYVTSLDDPHADKTVMELVKDACTERIYPVGRLDKNSVGLLLFTND 330

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L R L  PS Q  ++Y+V     + +  +  + +GI ++       +  +   K    
Sbjct: 331 GDLTRQLTHPSFQKKKIYQVSLDKPLTKADMEQIAQGITLEDGEIYADE--IAYVKEDKT 388

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V + +  G+NR ++++FE   + V +L R+ Y       L  G  R ++++ ++
Sbjct: 389 EVGIEIHSGRNRIVRRIFEHLGYAVKKLDRVYYAGLSKKNLKRGQWRFLTREEVQ 443


>gi|219685350|ref|ZP_03540169.1| hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Borrelia garinii Far04]
 gi|219673123|gb|EED30143.1| hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Borrelia garinii Far04]
          Length = 249

 Score =  125 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 61/228 (26%), Positives = 98/228 (42%), Gaps = 10/228 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA- 70
              RV   +A  G+ SRR  E +I ++ ++VNG + +     V   D I           
Sbjct: 5   KSPRVHVFLAEKGVGSRRFCEELIRKKLIRVNGSIAK-LGDKVSPGDRIIYKKQIYVFKD 63

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
              +       +KP   + ++ D +GR      +      R+ S+GRLD  + GLLL TN
Sbjct: 64  FQSKNKIYLALNKPRNYLCSNFDVNGRKLAISLVQPLFKERIFSIGRLDFKSSGLLLFTN 123

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  A  +  P  +  R Y +     +D++ L   K GI ++   +      +  +  + 
Sbjct: 124 DGEFANDIIHPRGKVEREYIIESKKDIDENLLISFKSGIKVKKEFFKLKSYEILNKNSA- 182

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
               + L EGKNREI+KVF   N  + ++ RI  G   L  L  G  +
Sbjct: 183 ---RLILDEGKNREIRKVFLSKNIFLKKIHRIRIGNINLDNLKEGQVK 227


>gi|108758119|ref|YP_629838.1| RsuA family pseudouridine synthase [Myxococcus xanthus DK 1622]
 gi|108461999|gb|ABF87184.1| pseudouridine synthase, RsuA family [Myxococcus xanthus DK 1622]
          Length = 266

 Score =  125 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 64/245 (26%), Positives = 107/245 (43%), Gaps = 11/245 (4%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           VQ +     +++ + +AG+  R + E  I + RV ++G +       V     + VDG+ 
Sbjct: 22  VQPSGRSDWLARALGKAGVMPRAQAEAAIREGRVTLDGRVEHEPFAPVRPEMEVRVDGLV 81

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEG 120
                     ++HKP GLV   SD +G  TVF+ L             ++VGRLD +T G
Sbjct: 82  RNLEAPVLTLMFHKPAGLVVHGSDAEGVGTVFECLRERLTQPLRDYEWLAVGRLDRDTTG 141

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLL TND  L +    P     + Y     G   +D L  L++G+V++          L 
Sbjct: 142 LLLFTNDERLVQHGTSPERHLPKRYVAGVVGPPPEDALRRLREGLVLEDGPTRPAGARLR 201

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                   V + L EG+N ++K++       V  L R + G   L  +  G+ R ++ + 
Sbjct: 202 APD----VVELTLTEGRNHQVKRMLAAVGHPVRTLHREAVGGVTL-DVPEGAWRLLTDEE 256

Query: 241 LREQL 245
           + + L
Sbjct: 257 VSQGL 261


>gi|261365024|ref|ZP_05977907.1| ribosomal small subunit pseudouridine synthase A [Neisseria mucosa
           ATCC 25996]
 gi|288566613|gb|EFC88173.1| ribosomal small subunit pseudouridine synthase A [Neisseria mucosa
           ATCC 25996]
          Length = 227

 Score =  125 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 42/230 (18%), Positives = 88/230 (38%), Gaps = 10/230 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGV--PLRK 69
            ++ K +   GI SR++ + +I    V++N  +      ++       + +DG    +  
Sbjct: 1   MQLIKYLQSQGIGSRKQCQWLIQNDCVEINDTVRNDTKADIDPAEVQTLRIDGEDIVVVP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 61  MPYFYILLNKPADYETSHKPQQYPSVFSLFPDHMRNIDMQAVGRLDADTTGVLLITNDGQ 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNA 187
               +  P  +  ++YRV      D      LK G+++          +  L+    +  
Sbjct: 121 FNHRVTSPKHKVPKIYRVTLKHPADDSLCETLKNGVLLHDDNETVHAAEAVLE----NPT 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + + EGK  ++K++      +V  L R  +    +  L +G  + ++
Sbjct: 177 TLLMTITEGKYHQVKRMVAAAGNRVEHLHRDEFNGRTVENLASGEWKFIT 226


>gi|325268067|ref|ZP_08134713.1| ribosomal small subunit pseudouridine synthase A [Kingella
           denitrificans ATCC 33394]
 gi|324980452|gb|EGC16118.1| ribosomal small subunit pseudouridine synthase A [Kingella
           denitrificans ATCC 33394]
          Length = 228

 Score =  125 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 44/227 (19%), Positives = 87/227 (38%), Gaps = 8/227 (3%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGV--PLRKAERT 73
           K +   GI +R+  + ++    V++NG  +     ++       + +DG    +      
Sbjct: 5   KYLQAQGIDTRKGCQWLVKHGLVQINGATVPDEKADIAPDSVQTLTIDGEDAVVIPLPYF 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L        +                   + + +VGRLD +T G+LL+TNDG     
Sbjct: 65  YILLNKPAGYETSHKPRDYPSVFSLLPDQVRAADIQAVGRLDADTTGVLLITNDGQFNHR 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           +  P  +  ++YR       D      L+ G+++         Q            + + 
Sbjct: 125 MTSPKHKVDKIYRATLKHAADPSLCAQLQAGVLLHDDNETVSAQAAELH---DAHTLILT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +REGK  ++K++      +V  L R+ +GP+    L AG  R +  +
Sbjct: 182 IREGKYHQVKRMVAAAGNRVEHLHRLQFGPWDTQDLQAGEWRFIRVE 228


>gi|317178163|dbj|BAJ55952.1| hypothetical protein HPF16_1355 [Helicobacter pylori F16]
          Length = 262

 Score =  125 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 61/248 (24%), Positives = 117/248 (47%), Gaps = 19/248 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ +A     SRRE E+++ + RVK+N    +  +V V   D + +D   ++  +  +
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLVSV-VKENDKVFLDKRLIKPLKNKK 65

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQVT 178
            L        + Y ++  G V ++  N +++G+ ++                    +   
Sbjct: 126 ALMHA--NLEKEYLIKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++ 
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNH 243

Query: 239 KILREQLG 246
           +   E   
Sbjct: 244 QEYNELHA 251


>gi|303256317|ref|ZP_07342333.1| ribosomal small subunit pseudouridine synthase A [Burkholderiales
           bacterium 1_1_47]
 gi|330999012|ref|ZP_08322737.1| putative 16S pseudouridylate 516 synthase [Parasutterella
           excrementihominis YIT 11859]
 gi|302861046|gb|EFL84121.1| ribosomal small subunit pseudouridine synthase A [Burkholderiales
           bacterium 1_1_47]
 gi|329575754|gb|EGG57280.1| putative 16S pseudouridylate 516 synthase [Parasutterella
           excrementihominis YIT 11859]
          Length = 231

 Score =  125 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 57/218 (26%), Positives = 93/218 (42%), Gaps = 4/218 (1%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTRLW 76
           +++   G  +R E   +I Q R +VNG  +     ++ + D   EVDGV     E+  + 
Sbjct: 5   QILFSQGFGTRHECTGLIVQGRFRVNGTAVTDPDEDIPTEDLTFEVDGVQWPFFEKAIIL 64

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L        +               P    +V  VGRLD +T GLLLLT+DG L   L  
Sbjct: 65  LNKPEHYECSLKPIHHPSVLSLLPPPLRVRKVQPVGRLDEDTTGLLLLTDDGKLIHRLTH 124

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
           P     ++YRV     V + ++  L KG+ +       +   +   K S   + +G+ +G
Sbjct: 125 PKKHVTKIYRVTLKHPVTEKQIAQLLKGVQLADSPD--IVKAVSCDKVSELVIDLGITQG 182

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
           K  ++K++    + +V  L RI +G   L   L  G  
Sbjct: 183 KYHQVKRMMAAVSNRVVALERIRFGNLSLPEDLKPGEW 220


>gi|169350969|ref|ZP_02867907.1| hypothetical protein CLOSPI_01746 [Clostridium spiroforme DSM 1552]
 gi|169292031|gb|EDS74164.1| hypothetical protein CLOSPI_01746 [Clostridium spiroforme DSM 1552]
          Length = 224

 Score =  125 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 50/215 (23%), Positives = 92/215 (42%), Gaps = 9/215 (4%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHS 89
           + + +I   R++VN  +++     V   D I  DG  +        ++ +KP G +  + 
Sbjct: 10  KCKNLIKSSRIRVNNQIIKDIRYQVDIDDVIVFDG--VELKWPFVYYMLNKPKGYICANH 67

Query: 90  DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
           D                    +GRLDI+T GLLL+TND  L++ L LP     + Y V  
Sbjct: 68  DK---KYKCVIDLIGRDDCYCLGRLDIDTTGLLLITNDKTLSKRLLLPENHIDKKYYVTV 124

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
             ++  D + +   GI+I        + +            + + EG+  +IKK+F   N
Sbjct: 125 KNKLTDDLIEIFNNGIIIDQKV--KCKPSYLEIIDDYHCY-LTINEGRYHQIKKMFLSCN 181

Query: 210 WKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
            KV  L R+ +    L   L   + R+++ + +++
Sbjct: 182 NKVLELKRVMFASINLDNNLSLANYRKLNNQEIKQ 216


>gi|160896616|ref|YP_001562198.1| pseudouridine synthase [Delftia acidovorans SPH-1]
 gi|160362200|gb|ABX33813.1| pseudouridine synthase [Delftia acidovorans SPH-1]
          Length = 591

 Score =  124 bits (312), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 62/252 (24%), Positives = 106/252 (42%), Gaps = 29/252 (11%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++K +A  G+ SRRE +  + +  V+VNG L      NV++ D I V+     + ++
Sbjct: 343 GVRINKRLADMGLCSRREADEWVDKGWVRVNGELA-VMGQNVVAADRITVEREARERQDQ 401

Query: 73  TRLWLYHKPIGLVT---------------THSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
               L HKP+G V+                 +  +  ++      +    +   GRLDI+
Sbjct: 402 QVTILIHKPMGYVSGQAEDGHEPAVVLVTPQNHWNQDTSRTRFNFAQLKGLAPCGRLDID 461

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQ 168
           + GLL++T DG +AR +    ++  + Y VR                ++L  L  G+ + 
Sbjct: 462 SVGLLVMTQDGRVARQIIGEDSEMDKEYLVRVTYGDRDIDVQSVFPAEQLARLCHGLSLD 521

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           G      +V     +     +   L EGK R+I+++ E    +V  L RI  G   LG L
Sbjct: 522 GEALKPAKVDWQNPEQ----LRFVLTEGKKRQIRRMCELVGLRVVGLKRIRIGRVTLGNL 577

Query: 229 LAGSTREVSKKI 240
             G  R +    
Sbjct: 578 PVGQWRYLGAHE 589



 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 17/126 (13%), Positives = 30/126 (23%), Gaps = 5/126 (3%)

Query: 229 LAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
             G  RE      R       + +A+   DA           R     +  +     ++ 
Sbjct: 182 PRGDWREQGGGENRAPREQRDMRDARDTRDARPPRPPRPDDRRDRPYGQRDERPRDGQR- 240

Query: 289 SSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
              +    +      P            A+G          +   +  R P     R  R
Sbjct: 241 -DGQRDGQRDGPRDGPREGGFRDRPRDDARGPRRDDARGPRR---DDARGPRRDDARGPR 296

Query: 349 RTSAKK 354
           R  A +
Sbjct: 297 RDEAPQ 302


>gi|15646068|ref|NP_208250.1| hypothetical protein HP1459 [Helicobacter pylori 26695]
 gi|2501526|sp|P55986|Y1459_HELPY RecName: Full=Uncharacterized RNA pseudouridine synthase HP_1459;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|2314637|gb|AAD08501.1| conserved hypothetical protein [Helicobacter pylori 26695]
          Length = 262

 Score =  124 bits (312), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 61/248 (24%), Positives = 117/248 (47%), Gaps = 19/248 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  +
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAK-LASVVKENDRVFLDKRLIKPLKNKK 65

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQVT 178
            L        + Y ++  G V ++  N +++G+ ++                    +   
Sbjct: 126 ALMHAD--LEKEYLIKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 KILREQLG 246
           +   E   
Sbjct: 244 QEYNELHA 251


>gi|396661|emb|CAA79503.1| unknown open reading frame [Buchnera aphidicola]
          Length = 258

 Score =  124 bits (312), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 72/256 (28%), Positives = 117/256 (45%), Gaps = 11/256 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV--NVMSTDHIEVDGVPLRKAER 72
           ++ K+++  G  SRR +E MI   ++ +NG                 I +D   +     
Sbjct: 4   KIQKILSDLGYGSRRFIECMIKCGKISINGEKAIIGQYLNKKNPG-EILIDKKKIIVKRN 62

Query: 73  TRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             L     +       + T        +          +R +SVGRLDINT+GLLL TND
Sbjct: 63  KNLPKVLIYNNKPIGEVCTRDDFQKRLTVFDKLPKLNLNRWVSVGRLDINTKGLLLFTND 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKGS 185
           G LA  L  P +Q  R Y +R  G+++++K+N+L+KG+ I        ++    D ++G 
Sbjct: 123 GTLANKLMHPRSQIEREYNIRIFGEMNKNKINILRKGVKIIHGYVSFKEIVPLYDKKEGK 182

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           N W    L EGKNREI+ +F+    +VN+LIR+ YG   L   L  G    ++   L++ 
Sbjct: 183 NKWFKGILCEGKNREIRLMFKSIQCQVNQLIRVRYGNIILPKNLKEGQWMMLNSIFLKKL 242

Query: 245 LGPHLLEEAQVNLDAP 260
                 ++  +N    
Sbjct: 243 YNLINFDKEIINKKKN 258


>gi|90420204|ref|ZP_01228112.1| ribosomal small subunit pseudouridine synthase A [Aurantimonas
           manganoxydans SI85-9A1]
 gi|90335538|gb|EAS49288.1| ribosomal small subunit pseudouridine synthase A [Aurantimonas
           manganoxydans SI85-9A1]
          Length = 251

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 55/242 (22%), Positives = 93/242 (38%), Gaps = 10/242 (4%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV----MSTDHIEV 62
           + +  T  R+ +++A  G ASRRE++ +    R++++G     A   +         + V
Sbjct: 1   MTKTPTS-RLDRLLANMGYASRREIQMLARNGRIQLDGAAFHDADKRIALTPDLETRLVV 59

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           DG  L       L L+       +           +          + +VGRLD  T GL
Sbjct: 60  DGEALDPLPGFALMLHKPLGVTCSHKEAGPLVYDLLPQRWRRRDPAISTVGRLDKETSGL 119

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD-MQVTLD 180
           LL+T+DG L   +  P     + YRV     +  D+  L   G ++            L+
Sbjct: 120 LLMTDDGKLLHRIISPKRHVAKRYRVHLARSMTGDEAALFAAGTLMLEGEEKPLAPAELE 179

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
                 A + V   EG+  +++++F      V  L R S G   L   L  G+ R +   
Sbjct: 180 VVGPQEALLEV--HEGRYHQVRRMFAATGNHVEALHRESVGGLSLPADLAPGAIRRLDDA 237

Query: 240 IL 241
            L
Sbjct: 238 DL 239


>gi|317011592|gb|ADU85339.1| hypothetical protein HPSA_06915 [Helicobacter pylori SouthAfrica7]
          Length = 254

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 62/249 (24%), Positives = 116/249 (46%), Gaps = 19/249 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAK-LASVVKENDKVFLDKRLIKPLKNK 59

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   +     VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYVHFAPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQV 177
             L        R Y ++  G V ++  N +++G+ ++                    +  
Sbjct: 120 SALMHA--NLEREYLIKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFVGY 177

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EILKNHAKYSKLKVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQLG 246
           ++   E   
Sbjct: 238 RQEYNELHA 246


>gi|224534191|ref|ZP_03674769.1| hypothetical RNA pseudouridine synthase [Borrelia spielmanii A14S]
 gi|224514293|gb|EEF84609.1| hypothetical RNA pseudouridine synthase [Borrelia spielmanii A14S]
          Length = 249

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 62/228 (27%), Positives = 99/228 (43%), Gaps = 10/228 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R+   +A  G+ SRR  E +I ++ V+VNG + +     V   D I          +
Sbjct: 5   KTPRIHVFLAEKGVGSRRFCEELIRKKLVRVNGSIAK-LGDKVTLGDRIIYKKQVYLFKD 63

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                      +KP   + ++ D +GR      +      RV S+GRLD  + GLLL TN
Sbjct: 64  FQSKDRVYLALNKPKNYLCSNFDANGRKLAISLVQPLFKERVFSIGRLDFKSSGLLLFTN 123

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  A  +  P  +  R Y +     +D++ L   K GI I+   +      +  +  + 
Sbjct: 124 DGKFANDIIHPRLKVEREYIIESKKDIDENLLISFKSGIKIKKEFFKLKSYEILNKNSA- 182

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
               + L EGKNREI+KVF   +  + ++ RI  G   L +L  G  +
Sbjct: 183 ---RLILDEGKNREIRKVFLSKSVFLKKIHRIRIGNINLDSLKEGQVK 227


>gi|221134604|ref|ZP_03560907.1| RNA pseudouridine synthase family protein [Glaciecola sp. HTCC2999]
          Length = 211

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 47/205 (22%), Positives = 86/205 (41%), Gaps = 11/205 (5%)

Query: 41  KVNGILLERAAVNVMSTDHIEVDGVPLRK----AERTRLWLYHKPIGLVTTHSDPDGRST 96
            VNG L       +  +D + + G  +             LYHKP+G+  T       + 
Sbjct: 1   MVNGQLP-LLGTKITPSDTVSIQGKVISAVAADKSDRVYVLYHKPVGITCTTERHIKGNI 59

Query: 97  VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
           +        +R+  VGRLD  +EGL++LT+DG +   +        ++YRV     +   
Sbjct: 60  IDAI--GHKTRIFPVGRLDKPSEGLIILTSDGDIVNKILRAENAHDKLYRVTVDKPITSK 117

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
            + ++  G+ I        +V    ++       + L +G NR+I+++ E+  + V RL+
Sbjct: 118 FIEIMSGGVPILDTVTKPCKV----KQIGKFSFDITLTQGLNRQIRRMCEYCGYDVKRLV 173

Query: 217 RISYGPFQLGTLLAGSTREVSKKIL 241
           R       L  L  G  R ++ + L
Sbjct: 174 RTRIMHLTLAKLPVGQWRNLTNEEL 198


>gi|108563881|ref|YP_628197.1| hypothetical protein HPAG1_1456 [Helicobacter pylori HPAG1]
 gi|107837654|gb|ABF85523.1| ribosomal large subunit pseudouridine synthase B [Helicobacter
           pylori HPAG1]
          Length = 262

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 62/248 (25%), Positives = 117/248 (47%), Gaps = 19/248 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  +
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAK-LASVVKENDKVFLDKRLIKPLKNKK 65

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQVT 178
            L        + Y V+  G V ++  N +++G+ ++                    +   
Sbjct: 126 TLMHA--NLEKEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 KILREQLG 246
           +   E   
Sbjct: 244 QEYNELHA 251


>gi|317179635|dbj|BAJ57423.1| hypothetical protein HPF30_1326 [Helicobacter pylori F30]
          Length = 262

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 62/248 (25%), Positives = 117/248 (47%), Gaps = 19/248 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  +
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAK-LASVVKENDKVFLDKRLIKPLKNKK 65

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQVT 178
            L        + Y V+  G V ++  N +++G+ ++                    +   
Sbjct: 126 ALMHA--NLEKEYLVKIQGFVTREMENAIQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 KILREQLG 246
           +   E   
Sbjct: 244 QEYNELHA 251


>gi|298735573|ref|YP_003728094.1| ribosomal large subunit pseudouridine synthase B [Helicobacter
           pylori B8]
 gi|298354758|emb|CBI65630.1| ribosomal large subunit pseudouridine synthase B [Helicobacter
           pylori B8]
          Length = 262

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 61/248 (24%), Positives = 117/248 (47%), Gaps = 19/248 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  +
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAK-LASVVKENDKVFLDKRLIKPLKNKK 65

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+L+L++   +  
Sbjct: 66  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLILSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQVT 178
            L        + Y V+  G V ++  N +++G+ ++                    +   
Sbjct: 126 ALMHA--NLEKEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVVINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 KILREQLG 246
           +   E   
Sbjct: 244 QEYNELHA 251


>gi|219684864|ref|ZP_03539806.1| hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Borrelia garinii PBr]
 gi|219671809|gb|EED28864.1| hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Borrelia garinii PBr]
          Length = 249

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 62/228 (27%), Positives = 98/228 (42%), Gaps = 10/228 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA- 70
              RV   +A  G+ SRR  E +I ++ ++VNG + +     V   D I           
Sbjct: 5   KSPRVHVFLAEKGVGSRRFCEELIRKKLIRVNGSIAK-LGDKVSPGDRIIYKKQIYVFKG 63

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
              +       +KP   + ++ D +GR      +      R+ S+GRLD  + GLLL TN
Sbjct: 64  FQSKNKIYLALNKPRNYLCSNFDVNGRKLAISLVQPLFKERIFSIGRLDFKSSGLLLFTN 123

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  A  +  P  +  R Y V     +D++ L   K GI ++   +      +  +  + 
Sbjct: 124 DGEFANDIIHPRRKVEREYIVESKKDIDENLLISFKSGIKVKKEFFKLKSYEILNKNSA- 182

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
               + L EGKNREI+KVF   N  + ++ RI  G   L  L  G  +
Sbjct: 183 ---RLILDEGKNREIRKVFLSKNIFLKKIHRIRIGNINLDNLKEGQVK 227


>gi|332674227|gb|AEE71044.1| RNA pseudouridine synthase [Helicobacter pylori 83]
          Length = 262

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 62/248 (25%), Positives = 117/248 (47%), Gaps = 19/248 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  +
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAK-LASVVKENDKVFLDKRLIKSLKNKK 65

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQVT 178
            L        + Y V+  G V ++  N +++G+ ++                    +   
Sbjct: 126 ALMHA--NLEKEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKIRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 KILREQLG 246
           +   E   
Sbjct: 244 QEYNELHA 251


>gi|297380685|gb|ADI35572.1| conserved hypothetical protein [Helicobacter pylori v225d]
          Length = 262

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 61/248 (24%), Positives = 118/248 (47%), Gaps = 19/248 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ +A     SRRE E+++ + RVK+N    +  +V V   D + +D   ++  +  +
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLVSV-VKENDKVFLDKRLIKPLKNKK 65

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQVT 178
            L        + Y ++  G V ++  N +++G+ ++                    +   
Sbjct: 126 ALMHA--NLEKEYLIKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 KILREQLG 246
           +   E   
Sbjct: 244 QEYNELHA 251


>gi|315585848|gb|ADU40229.1| RNA pseudouridine synthase [Helicobacter pylori 35A]
          Length = 262

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 61/248 (24%), Positives = 119/248 (47%), Gaps = 19/248 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ +A     SRRE E+++ + RVK+N    +  +V V   D + +D   ++  +  +
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLVSV-VKENDKVFLDKRLIKPLKNKK 65

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++  + VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFVPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQVT 178
            L        + Y ++  G V ++  N +++G+ ++                    +   
Sbjct: 126 ALMHA--NLEKEYLIKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKIRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 KILREQLG 246
           +   E   
Sbjct: 244 QEYNELHA 251


>gi|296273383|ref|YP_003656014.1| pseudouridine synthase [Arcobacter nitrofigilis DSM 7299]
 gi|296097557|gb|ADG93507.1| pseudouridine synthase [Arcobacter nitrofigilis DSM 7299]
          Length = 229

 Score =  124 bits (310), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 44/222 (19%), Positives = 90/222 (40%), Gaps = 2/222 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+   ++  G  +R + ++ +    + VN   +   +      D I ++G  L     T 
Sbjct: 7   RIDAHLSSLGYCTRGDAKKFLKINELLVNENRVFNPSTKAYHDD-ITINGEKLDPETLTI 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L      +      +     S +         ++ +VGRLD++T G ++LT+DG L   L
Sbjct: 66  LLNKPSGVICSHNDAGVLIYSLLPYRWTQRNPKISTVGRLDVDTTGAIILTDDGTLNHKL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  ++Y       +  D+  +   G ++       +         S   V + + 
Sbjct: 126 ANPKKEISKIYEAHLKVPLKGDEEKIFASGELLLNGEDKPLLPAKLEV-LSPTCVRLEIV 184

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           EGK  ++K++F   + +V +L RIS+  F +  L  G  + +
Sbjct: 185 EGKYHQVKRMFAAVDNRVVKLHRISFDNFTVEDLKEGEYKSI 226


>gi|302879321|ref|YP_003847885.1| RNA-binding S4 domain-containing protein [Gallionella
           capsiferriformans ES-2]
 gi|302582110|gb|ADL56121.1| RNA-binding S4 domain protein [Gallionella capsiferriformans ES-2]
          Length = 232

 Score =  124 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 48/234 (20%), Positives = 82/234 (35%), Gaps = 9/234 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----DGVP 66
             P R++K +      SRRE E  IA   V V+G ++E     V     +E+    D  P
Sbjct: 2   TEPVRLAKRLVELVACSRREAELYIAGGWVMVDGQIVEEPQFMVSE-QLVELHPNADLTP 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +  A      L       +   +      +    L   F ++     L+ N  GL +LT 
Sbjct: 61  IEPATLLFHHLNATNTTAICAGTRSADDLSGIHLLRQHFFKLTPCTPLERNASGLTVLTQ 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           D  + R L+  +    + Y V   G++  D L LL  G+   G      +V+   +    
Sbjct: 121 DFRIIRKLKDEAATIEQEYIVEIAGEIMADGLKLLNHGLKFNGKPLPPAKVSWQNETRLR 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             +   +      +I  + +     V  + RI  G   +  L     R +    
Sbjct: 181 FALKGVI----PGQIAAMCQKVGLDVISMRRIRIGRISMAKLQPDQWRYLMLHE 230


>gi|254779971|ref|YP_003058078.1| Ribosomal large subunit pseudouridine synthase B [Helicobacter
           pylori B38]
 gi|254001884|emb|CAX30134.1| Ribosomal large subunit pseudouridine synthase B [Helicobacter
           pylori B38]
          Length = 257

 Score =  124 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 61/249 (24%), Positives = 117/249 (46%), Gaps = 19/249 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAK-LASVVKENDKVFLDKRLIKPLKNK 59

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQV 177
             L        + Y ++  G V ++  N +++G+ ++                    +  
Sbjct: 120 SALMHA--NLEKEYLIKIQGFVTREIENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQLG 246
           ++   E   
Sbjct: 238 RQEYNELHA 246


>gi|167569105|ref|ZP_02361979.1| RNA pseudouridine synthase family protein [Burkholderia
           oklahomensis C6786]
          Length = 240

 Score =  124 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 52/225 (23%), Positives = 87/225 (38%), Gaps = 4/225 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTR 74
           +  ++   G  SRR+   ++   RV V G     A  +  +     EVDGV      R  
Sbjct: 3   LESILFTQGFGSRRQCRALVEAGRVAVGGATCTDAHASFDTARLAFEVDGVAWPYHARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        +                     V  VGRLD +T GLLLL++DG      
Sbjct: 63  VVLNKPAGYECSREPQHHSSVFRLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVHAY 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y       +D   L+ L+ G+++ G     +       +G    + + + 
Sbjct: 123 TSPKRKVPKTYVATVRHPLDDALLDALRAGVLLHGEP-KPIAAVAAHARGER-LLEMTVA 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
           EGK  ++K++    + +V  L R S G F L   L  G+ R + +
Sbjct: 181 EGKYHQVKRMVAAASNRVEALHRASIGGFTLPADLAEGAWRWLDE 225


>gi|302847122|ref|XP_002955096.1| pseudouridine synthase mitochondrial precursor [Volvox carteri f.
           nagariensis]
 gi|300259624|gb|EFJ43850.1| pseudouridine synthase mitochondrial precursor [Volvox carteri f.
           nagariensis]
          Length = 564

 Score =  123 bits (309), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 58/251 (23%), Positives = 98/251 (39%), Gaps = 19/251 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKV-NGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           RV +++A  G   RRE + ++ + RV   +G  L+     V   D + +D   L      
Sbjct: 80  RVERLLANLGYGKRRECQVLVKKGRVTRRDGGKLKV-GDKVCWGDVV-LDEEDLDPPSPL 137

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-----RVISVGRLDINTEGLLLLTNDG 128
            L L+     +VT+  D +    V  +L           +  VGRLD +T GLLLLT+DG
Sbjct: 138 LLALHKPGGYVVTSPDDENITDPVVYDLLPYRFARRRPFLAPVGRLDKDTSGLLLLTDDG 197

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-------IVIQGICYGDMQVTLDT 181
            L   +  P     +VY       +  ++     +        +          ++ L  
Sbjct: 198 ALLHRINSPRRGIWKVYEATLAEPMSTNQAAAAARRFASGSLVLEGDHTPLLPAKLDLIG 257

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                    V + EGK  +++++F      V  L R+S G   LG+L  G  R +  + L
Sbjct: 258 A----RTARVAICEGKYHQVRRMFAAVGSHVVALHRVSVGGLTLGSLPEGEWRYLQPQEL 313

Query: 242 REQLGPHLLEE 252
           +        E+
Sbjct: 314 QLVFEGPSAED 324


>gi|308185223|ref|YP_003929356.1| ribosomal large subunit pseudouridine synthase B [Helicobacter
           pylori SJM180]
 gi|308061143|gb|ADO03039.1| ribosomal large subunit pseudouridine synthase B [Helicobacter
           pylori SJM180]
          Length = 257

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 60/249 (24%), Positives = 117/249 (46%), Gaps = 19/249 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAQ-LASVVKENDKVFLDKRLIKPLKNK 59

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQV 177
             L        + Y ++  G + ++  N +++G+ ++                    +  
Sbjct: 120 SALMHA--NLEKEYLIKIQGFITREMENAMQEGLKLKNATKGAHQKTPIKSMEFAPFIGY 177

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVVINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQLG 246
           ++   E   
Sbjct: 238 RQEYNELHA 246


>gi|294340758|emb|CAZ89150.1| putative ribosomal large subunit pseudouridine synthase [Thiomonas
           sp. 3As]
          Length = 300

 Score =  123 bits (308), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 59/260 (22%), Positives = 96/260 (36%), Gaps = 38/260 (14%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM---STDHIEVDG------ 64
            R+SK ++  G+ASRRE +  I +  V ++G         V        I +        
Sbjct: 44  VRLSKRMSELGLASRREADDWIERGWVLLDGTPA-VLGTKVAGNLPASRIVIRKAAQHRQ 102

Query: 65  ---------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                     P+          Y   + L+   +            P+    +   GRLD
Sbjct: 103 AAQVTILLHKPVGYVSAQAEHGYTPAVALIKAENRWAECEAPQPFSPAHLRHLAVAGRLD 162

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------------HGQVDQDKLNL 160
           I++ GLL+LT DG +AR L    +   + Y VR                     + +L L
Sbjct: 163 IDSTGLLVLTQDGRIARQLIGEDSAVEKEYLVRVSLTDAPARNGAEEDVQAAFTESRLAL 222

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           L+ G+ +        QV     +     +   LREGK R+I+++ E    +V  L R+  
Sbjct: 223 LRHGLKLDDQPLRPAQVEWINPQQ----LRFVLREGKKRQIRRMCELVGLRVTGLKRVRI 278

Query: 221 GPFQLGTLLAGSTREVSKKI 240
           G  +LG L  G  R + +  
Sbjct: 279 GGLRLGALPLGQWRYLREDE 298


>gi|15612417|ref|NP_224070.1| hypothetical protein jhp1352 [Helicobacter pylori J99]
 gi|11136000|sp|Q9ZJG0|YE59_HELPJ RecName: Full=Uncharacterized RNA pseudouridine synthase jhp_1352;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|4155973|gb|AAD06937.1| putative [Helicobacter pylori J99]
          Length = 262

 Score =  123 bits (308), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 62/248 (25%), Positives = 117/248 (47%), Gaps = 19/248 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  +
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAK-LASVVKENDKVFLDKRLIKPLKNKK 65

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKADPLKRHVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQVT 178
            L        + Y V+  G V ++  N +++G+ ++                    +   
Sbjct: 126 ALMHA--NLEKEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKARFLNR 243

Query: 239 KILREQLG 246
           +   E   
Sbjct: 244 QEYNELHA 251


>gi|307730739|ref|YP_003907963.1| pseudouridine synthase [Burkholderia sp. CCGE1003]
 gi|307585274|gb|ADN58672.1| pseudouridine synthase [Burkholderia sp. CCGE1003]
          Length = 239

 Score =  123 bits (308), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 54/232 (23%), Positives = 91/232 (39%), Gaps = 6/232 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH---IEVDGVPLRKAER 72
           +  ++   G  SRR+   +IA  RV +   +   A  +  + D      VDGV     E 
Sbjct: 3   LESILFTQGFGSRRQCRALIADARVTIGDTVCTDADADFPAEDTSFCFSVDGVTWPYREH 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L        +                     V  VGRLD +T GLLLL++DG    
Sbjct: 63  AYLLLNKPAGYECSRDPQHHLSVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGKFVH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +   P  +  +VY       VD  +L+LL+ G+++ G     +       +G  + + + 
Sbjct: 123 LFTSPKRKVPKVYVASTRHPVDDTQLSLLRNGVLLHGES-KPVAAVDAQLRGERS-LALT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           + EGK  ++K++      +   L R   G   L  TL  G+ + + +  L  
Sbjct: 181 VMEGKYHQVKRMIAAAGNRCEALHRERVGGLALPATLAPGAWQWLDEAALEA 232


>gi|317014873|gb|ADU82309.1| hypothetical protein HPGAM_07680 [Helicobacter pylori Gambia94/24]
          Length = 257

 Score =  123 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 57/247 (23%), Positives = 112/247 (45%), Gaps = 15/247 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAK-LASVVKENDKVFLDKRLIKPLKNK 59

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLIYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLL------------KKGIVIQGICYGDMQVTL 179
             L   + +   + +++     + +                 +K  +        +   +
Sbjct: 120 SALMHANLEKEYLVKIQGFVTREMENAMQEGLKLKNATKGAHQKTPIKSMEFAPFIGYEI 179

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                  + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++++
Sbjct: 180 IKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKARFLNRQ 239

Query: 240 ILREQLG 246
              E   
Sbjct: 240 EYNELHA 246


>gi|212696672|ref|ZP_03304800.1| hypothetical protein ANHYDRO_01213 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212676403|gb|EEB36010.1| hypothetical protein ANHYDRO_01213 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 235

 Score =  123 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 55/229 (24%), Positives = 106/229 (46%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            RV K+I  A + +R+ ++R   +  + +NG +++ ++V V    D +   G  +   + 
Sbjct: 3   MRVDKMIGNANLDTRKNIKRNAKKGELIINGQIVKDSSVKVDPNLDEVIYMGELVDYFDN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +  +   +    ++ DG      +   +   +   GRLD +T GLLLL+ DG    
Sbjct: 63  IYIMMNKREGLI-CQSNELDGTVMSDLDEFYLNLDLAIAGRLDKDTTGLLLLSTDGKFIH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P++   + Y V    ++D   +   K G+ I+   Y      LD      A+V V 
Sbjct: 122 KVISPNSHIWKKYEVETSKKIDPSLVENFKDGVYIKEDDYYARSAKLDIIGEKKAYVYVT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
             EGK   +K++F   + +V +L R++ G  +L  +L  G  RE+S++ 
Sbjct: 182 --EGKFHLVKRLFSNNDNEVIKLKRLAIGDLELDQSLNPGQYRELSEEE 228


>gi|330807854|ref|YP_004352316.1| RNA-binding S4 domain-containing protein [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
 gi|327375962|gb|AEA67312.1| Conserved hypothetical protein; putative RNA-binding S4
           domain-containing protein [Pseudomonas brassicacearum
           subsp. brassicacearum NFM421]
          Length = 236

 Score =  123 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 52/238 (21%), Positives = 87/238 (36%), Gaps = 13/238 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+SK +      SRRE E  I    V V+G +++     V  T  +E+D      A
Sbjct: 2   TDPIRLSKRLIELVGCSRREAELFIEGGWVTVDGEVIDEPQFKVT-TQKVELDPEAKATA 60

Query: 71  ERTRLWLYHKPIGLVTTHSD--------PDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
                 L + P G     +          +        L   F R+ +   L  N  GLL
Sbjct: 61  PEPVTLLLNVPAGTDVDTAMASLGPQTLSEEHRFGKRPLKGHFLRLTASADLQANASGLL 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + T D  + R L   + +  + Y V   G++    LN L  G+  +G     ++ +   +
Sbjct: 121 VFTQDWKILRKLTADAAKIEQEYVVEVEGEMVAHGLNRLNHGLTYKGKELPAVKASWQNE 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 +   ++  +   I    +    KV  + RI  G   +G +  G  R +S K 
Sbjct: 181 NR----LRFAMKNPQPGVIALFCQAVGLKVVAIRRIRIGGVSIGKVPLGQWRYLSAKE 234


>gi|296136628|ref|YP_003643870.1| pseudouridine synthase [Thiomonas intermedia K12]
 gi|295796750|gb|ADG31540.1| pseudouridine synthase [Thiomonas intermedia K12]
          Length = 300

 Score =  122 bits (307), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 57/260 (21%), Positives = 93/260 (35%), Gaps = 38/260 (14%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM---STDHIEVDG------ 64
            R+SK ++  G+ASRRE +  I +  V ++G         V        I +        
Sbjct: 44  VRLSKRMSELGLASRREADDWIERGWVLLDGTPA-VLGTKVAGNLPASRIVIRKAAQHRQ 102

Query: 65  ---------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                     P+          Y   + L+   +            P+    +   GRLD
Sbjct: 103 AAQVTILLHKPVGYVSAQAEHGYTPAVALIKAENRWAECEAPQPFSPAHLRHLAVAGRLD 162

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL--------------- 160
           I++ GLL+LT DG +AR L    +   + Y VR        +                  
Sbjct: 163 IDSTGLLVLTQDGRIARQLIGEDSAVEKEYLVRVSLTDAPARNGAEEDVQAAFPESRLAL 222

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           L+ G+ +        QV     +     +   LREGK R+I+++ E    +V  L R+  
Sbjct: 223 LRHGLKLDDQPLRPAQVEWINPQQ----LRFVLREGKKRQIRRMCELVGLRVTGLKRVRI 278

Query: 221 GPFQLGTLLAGSTREVSKKI 240
           G  +LG L  G  R + +  
Sbjct: 279 GGLRLGALPLGQWRYLREDE 298


>gi|210135626|ref|YP_002302065.1| ribosomal large subunit pseudouridine synthase B [Helicobacter
           pylori P12]
 gi|210133594|gb|ACJ08585.1| ribosomal large subunit pseudouridine synthase B [Helicobacter
           pylori P12]
          Length = 262

 Score =  122 bits (307), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 61/248 (24%), Positives = 118/248 (47%), Gaps = 19/248 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  +
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAQ-LASVVKENDKVFLDKRLIKPLKNKK 65

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++  + VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFVPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQVT 178
            L        + Y ++  G V ++  N +++G+ ++                    +   
Sbjct: 126 ALMHA--NLEKEYLIKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 KILREQLG 246
           +   E   
Sbjct: 244 QEYNELHA 251


>gi|150020316|ref|YP_001305670.1| pseudouridine synthase [Thermosipho melanesiensis BI429]
 gi|149792837|gb|ABR30285.1| pseudouridine synthase [Thermosipho melanesiensis BI429]
          Length = 243

 Score =  122 bits (307), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 104/233 (44%), Gaps = 7/233 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +     ++ +++   G A RR+ + +I  ++VKVNG ++ +   +V   D I V+G    
Sbjct: 2   KGVDNIKLQRILQICGFA-RRKADELIFSKKVKVNGKIVTKPWFDVKVDDEITVEGKKFT 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             +     L+     + + +   +  +                GRLD +  G+L+LTNDG
Sbjct: 61  LPKFEYYVLHKPKGYVTSLYDPKEKNTIKEFFKDKPL---KPAGRLDKDVSGVLILTNDG 117

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L  VL        +VY  +  G+V  + L  LKKGI  +G         +  Q  + + 
Sbjct: 118 DLIDVLTNAKYGVKKVYIAKITGRVKFEDLLSLKKGIYDKGDFLKLEHFDILEQGFNYST 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVSKK 239
           V V + +GK  E+K++FE    KV  L RI +GP  +  L    G  R++  +
Sbjct: 178 VKVEMIKGKKHEVKRLFEKIGHKVLELRRIKHGPVSIS-LAPNPGDMRKIEGE 229


>gi|307638112|gb|ADN80562.1| Ribosomal large subunit pseudo uridine synthase B [Helicobacter
           pylori 908]
          Length = 257

 Score =  122 bits (307), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 56/241 (23%), Positives = 111/241 (46%), Gaps = 15/241 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAK-LASVVKENDKVFLDKRLIKPLKNK 59

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLL------------KKGIVIQGICYGDMQVTL 179
             L   + +   + +++     + +                 +K  +        +   +
Sbjct: 120 SALMHANLEKEYLVKIQGFVTREMESAMQEGLKLKNATKGAHQKTPIKSMEFAPFIGYEI 179

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                  + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++++
Sbjct: 180 IKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNRQ 239

Query: 240 I 240
            
Sbjct: 240 E 240


>gi|329737424|gb|EGG73678.1| S4 domain protein [Staphylococcus epidermidis VCU028]
          Length = 180

 Score =  122 bits (306), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 58/180 (32%), Positives = 95/180 (52%), Gaps = 1/180 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +R+ K IA +G  SRR+ E +I + RVKVNG  +      VM +D +EVDG+ + +
Sbjct: 2   SKEQERLQKRIANSGYTSRRKAEVLITEGRVKVNGQTVTELGSKVMPSDLVEVDGIKIEQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ++  + LY     ++T+ SD  GR  V D    + SR+  VGRLD +T G+LLLTNDG 
Sbjct: 62  EDKIYILLYKPT-QVITSVSDDRGRRVVTDYFDDLESRIYPVGRLDYDTSGVLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
              ++  P     + Y  +  G + ++++  L+KGI ++       QV +  Q      +
Sbjct: 121 FTNLMTHPRYHIKKKYVAKLKGYLMREEIKQLEKGIELEDGYTQPAQVKIKKQDKEKIRL 180


>gi|325996712|gb|ADZ52117.1| Ribosomal large subunit pseudouridine synthase B [Helicobacter
           pylori 2018]
 gi|325998306|gb|ADZ50514.1| Ribosomal large subunit pseudouridine synthase B [Helicobacter
           pylori 2017]
          Length = 262

 Score =  122 bits (306), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 56/240 (23%), Positives = 111/240 (46%), Gaps = 15/240 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  +
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAK-LASVVKENDKVFLDKRLIKPLKNKK 65

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLL------------KKGIVIQGICYGDMQVTLD 180
            L   + +   + +++     + +                 +K  +        +   + 
Sbjct: 126 ALMHANLEKEYLVKIQGFVTREMESAMQEGLKLKNATKGAHQKTPIKSMEFAPFIGYEII 185

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++++ 
Sbjct: 186 KNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNRQE 245


>gi|229588738|ref|YP_002870857.1| hypothetical protein PFLU1201 [Pseudomonas fluorescens SBW25]
 gi|229360604|emb|CAY47461.1| conserved hypothetical protein [Pseudomonas fluorescens SBW25]
          Length = 236

 Score =  122 bits (306), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 52/238 (21%), Positives = 86/238 (36%), Gaps = 13/238 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+SK +      SRRE E  I    V V+G +++     V  T  +E+D       
Sbjct: 2   TDPIRLSKRLIELVGCSRREAELFIEGGWVSVDGEVIDEPQFKVT-TQKVELDPEAKATV 60

Query: 71  ERTRLWLYHKPIGLV--------TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
                 L H P G+         +  +  +        L   F R+ +   L     GLL
Sbjct: 61  PEPVTILMHAPAGMDAETAMASISAETLSEEHRFSKRPLKGHFLRLTASADLQAKASGLL 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + T D  + R L   + +  + Y V   G +    LN L  G+  +G     ++ +   +
Sbjct: 121 VFTQDWKILRKLTADAAKIEQEYVVEVEGDMVAHGLNRLNHGLTYKGKELPAVKASWQNE 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 +   ++  +   I    E    KV  + RI  G   +G +  G  R +S K 
Sbjct: 181 NR----LRFAMKNPQPGVIALFCEAVGLKVIAIRRIRIGGVSIGKVPVGQWRYLSGKE 234


>gi|86147035|ref|ZP_01065352.1| pseudouridine synthase family 1 protein [Vibrio sp. MED222]
 gi|85835100|gb|EAQ53241.1| pseudouridine synthase family 1 protein [Vibrio sp. MED222]
          Length = 305

 Score =  122 bits (305), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 74/301 (24%), Positives = 124/301 (41%), Gaps = 8/301 (2%)

Query: 55  MSTDHIEVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                I +DG  +            L  Y     L T H     R+          SR I
Sbjct: 7   DENSVIRIDGHTITGKASEEVVCRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWI 66

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           SVGRLD NT GLLL T DG LA  L  PS Q  R Y VR  G+V + K+  + +G+ ++ 
Sbjct: 67  SVGRLDANTSGLLLFTTDGELANRLMHPSRQVEREYLVRVFGEVTEQKVKNVTRGVQLED 126

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TL 228
                  V     +G N    V + EG+NRE+++++E     V+RL R+ YG   L   L
Sbjct: 127 GMARFEDVVYAGGEGMNHTFYVAINEGRNREVRRLWESQETTVSRLKRVRYGDIYLDKKL 186

Query: 229 LAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
             G  +E+  + +   L   +  + +      +  + T  +   +   ++     R ++ 
Sbjct: 187 PRGGWKELDLQEV-NYLRELVELQPEKETLLDLDPANTSRKRERSRSQKIRRAVKRHEER 245

Query: 289 SSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           ++   G S Q K   P  R     +   +    ++    + ++ + +   P+ P+K   R
Sbjct: 246 ANAPKGRSNQTKRKKPATRGTTTPDSGRSAPA-TNGKPQATKKPKLNNGRPAKPAKPRSR 304

Query: 349 R 349
           +
Sbjct: 305 K 305


>gi|307297760|ref|ZP_07577566.1| RNA-binding S4 domain protein [Thermotogales bacterium
           mesG1.Ag.4.2]
 gi|306917020|gb|EFN47402.1| RNA-binding S4 domain protein [Thermotogales bacterium
           mesG1.Ag.4.2]
          Length = 231

 Score =  122 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 55/234 (23%), Positives = 103/234 (44%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+   ++R G  SR E  R+I    V +NG+L    +  V  TD + VDG PL      
Sbjct: 1   MRLDAFVSRFGRFSRSESRRIIRSNGVSLNGVLTNNPSEVVDETDTVIVDGRPLEAFWNV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L      + +     +GRS       +  + + + GRLD +  GLL+L+NDG     
Sbjct: 61  YIALNKPEGYVCSRERS-EGRSVFELIDANFSADLSTGGRLDKDATGLLILSNDGKFIHE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V    ++ + +++++ +G+ I    +         ++  +  + + L
Sbjct: 120 VISPRKLVEKEYLVETAKEITKKEISMISQGLFIGNNEFSKPTHV---EQIDHFHMRIVL 176

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
            EG+  E+K++      KV +L R   G + L   L  G  + +S+   ++  G
Sbjct: 177 TEGRYHEVKRLVSASGNKVIQLHRRRIGSYCLSEELRPGDWQLLSENDRKKITG 230


>gi|224536211|ref|ZP_03676750.1| hypothetical protein BACCELL_01078 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|224522154|gb|EEF91259.1| hypothetical protein BACCELL_01078 [Bacteroides cellulosilyticus
           DSM 14838]
          Length = 208

 Score =  122 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 48/200 (24%), Positives = 85/200 (42%), Gaps = 1/200 (0%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
           VNG+++      +   D ++     +    +  + L      + T+      R+ +    
Sbjct: 1   VNGVVVTELGTKIKRADEVKFHDQMVSIERKIYILLNKPKDTVTTSDDPQARRTVMDLVK 60

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
            +   R+  VGRLD NT G+LLLTNDG LA  L  P     ++Y V     V +  ++ +
Sbjct: 61  GACDERIYPVGRLDRNTTGVLLLTNDGDLASKLTHPKFLKKKIYHVHTDKNVTKADMDQI 120

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             GI +             T       V + +  GKNR ++++FE   +KV +L R+ + 
Sbjct: 121 AAGIQLDDGEIH-ADAISYTDDVRRDEVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFA 179

Query: 222 PFQLGTLLAGSTREVSKKIL 241
                 L  G  R +S++ +
Sbjct: 180 GLTKKGLRRGEWRYLSEQEV 199


>gi|299472407|emb|CBN77595.1| conserved unknown protein [Ectocarpus siliculosus]
          Length = 390

 Score =  121 bits (304), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 68/255 (26%), Positives = 105/255 (41%), Gaps = 4/255 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK++A   I +R EV+ ++ + RVKV+G +++     +     IEV+G  +       
Sbjct: 137 RLSKLLADRAIGTRSEVDTLVRRGRVKVDGAVVKSPKTKLPVDCVIEVNGE-VHGPVPLL 195

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +  +     + T   D D          S+  +   VGRLD ++ GLLLL++DG L   L
Sbjct: 196 VAFHKPKGVITTLSDDWDREDLSDVLPKSLLLKHHPVGRLDADSSGLLLLSSDGALTHRL 255

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  R Y        + ++        + +GI   D     D    S   V V +R
Sbjct: 256 LNPRFEVEREYVASVDVPPEGEEPGDSLVTALKEGITTADGVYKADVPAISGRDVGVVVR 315

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL---REQLGPHLLE 251
           EGKNR ++++     + V  L R  YG   LG L  G    VS   L   R  L      
Sbjct: 316 EGKNRMVRRMLANAGYPVLELRRERYGKILLGDLPEGEHVPVSGDALEWARSVLQLQAAT 375

Query: 252 EAQVNLDAPIYSSET 266
            A V+        E 
Sbjct: 376 AAVVDGGGDEKGVEP 390


>gi|218533320|ref|YP_002424135.1| pseudouridine synthase [Methylobacterium chloromethanicum CM4]
 gi|218525623|gb|ACK86207.1| pseudouridine synthase [Methylobacterium chloromethanicum CM4]
          Length = 320

 Score =  121 bits (304), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 69/238 (28%), Positives = 112/238 (47%), Gaps = 1/238 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEV 62
           +     + +P  + +V+++ G  SRR  E +I   RV+V+G ++  A V V      I V
Sbjct: 15  RFAAHSSPSPVSLPRVLSKFGFCSRRSAEVLIESGRVRVDGRVVRNAGVRVDPQRAAICV 74

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG  L  A +  L L      L T       ++            +  VGRLD  +EGLL
Sbjct: 75  DGRRLVSAAKVYLLLNKPRGLLTTYGDPQGRKTVYDCLAGHDLPFLAPVGRLDCASEGLL 134

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L+TND   A  L  P++   +VY V+   + D+  L  L++G+   G       V     
Sbjct: 135 LMTNDTRWAHRLLDPASNVDKVYHVQIDRRPDEALLTGLREGVAHDGERLAAKSVAPLRV 194

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
              NAW+ V L EG+NR+I+++      +V RL+R++ G  +LG +  G+ R ++   
Sbjct: 195 GERNAWLEVVLSEGRNRQIRRMMALNGAEVLRLVRVAVGGVRLGDVRKGAFRHLTDAE 252


>gi|224532779|ref|ZP_03673395.1| hypothetical RNA pseudouridine synthase [Borrelia burgdorferi
           WI91-23]
 gi|224512267|gb|EEF82652.1| hypothetical RNA pseudouridine synthase [Borrelia burgdorferi
           WI91-23]
          Length = 249

 Score =  121 bits (304), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 63/225 (28%), Positives = 95/225 (42%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-----RK 69
           RV   +A  G+ SRR  E +I ++ VKVN  + +     V   D I            + 
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLVKVNNTIAK-LGDKVALGDRIIYKKQIFVFKDFQI 66

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             R  L L      L +       +  +    P    RV S+GRLD  + GLLL TNDG 
Sbjct: 67  NNRIYLALNKPRNYLCSNFDVDGRKLAISLVQPLFKERVFSIGRLDFKSSGLLLFTNDGK 126

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P  +  R Y +     +D++ L   K GI ++   +      +  +  +    
Sbjct: 127 FANDIIHPRQKVEREYIIESKKDIDENLLISFKSGIKVKKEFFKLKSYEILNKNSA---- 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L EGKNREI+KVF   N  + ++ RI  G   L +L  G  +
Sbjct: 183 RLILDEGKNREIRKVFLSKNIFLKKIHRIRIGNINLDSLKEGQVK 227


>gi|256003625|ref|ZP_05428614.1| pseudouridine synthase [Clostridium thermocellum DSM 2360]
 gi|255992416|gb|EEU02509.1| pseudouridine synthase [Clostridium thermocellum DSM 2360]
          Length = 202

 Score =  121 bits (304), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 54/193 (27%), Positives = 87/193 (45%), Gaps = 4/193 (2%)

Query: 52  VNVMS-TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
           + V      IEV G  L+  E   + +      +  T+ +              F  +  
Sbjct: 1   MQVNPKESVIEVAGEILKYREYIYIMMNKPQGVISATYDNRHRTVIDILPDEYKFFNLFP 60

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
           VGRLDI+TEGLLLLTNDG LA  L  P     + Y     G V    +++ ++G+V+   
Sbjct: 61  VGRLDIDTEGLLLLTNDGQLAHELLSPRKHVPKKYYALIDGIVTTKDVDVFREGVVLDDG 120

Query: 171 -CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-L 228
                 ++ +  + G  + V + + EGK  ++K++FE    KV  L RI  G  +L   L
Sbjct: 121 YKTLPSELFIL-KSGPYSEVEIVIYEGKFHQVKRMFEAVGKKVKYLRRIGMGKLKLDETL 179

Query: 229 LAGSTREVSKKIL 241
             G  RE++ + +
Sbjct: 180 EPGDVRELTDEEM 192


>gi|32266216|ref|NP_860248.1| hypothetical protein HH0717 [Helicobacter hepaticus ATCC 51449]
 gi|32262266|gb|AAP77314.1| conserved hypothetical protein [Helicobacter hepaticus ATCC 51449]
          Length = 258

 Score =  121 bits (304), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 62/261 (23%), Positives = 116/261 (44%), Gaps = 17/261 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ IA     SRRE +++I+Q RV +        ++ + +   + +DG  +   E  
Sbjct: 1   MRLNQYIAHHTKYSRREADKLISQGRVNIEKTKATLHSL-LGANQRVFIDGKKIIPKEHF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +YHKP G + +  D  GR  ++++L + F   + VGRLD  +EGLL+LT+   +AR 
Sbjct: 60  TCIVYHKPKGEIVSKRDERGRRVIYESLEAKFKHFVYVGRLDFASEGLLILTDSTPVARA 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQVTL 179
           L         +   + +G + Q+ ++ ++ G++ +                        +
Sbjct: 120 LMESDLLRTYIL--KINGFITQEIISAMENGLISEDTRVGAHSKSHITSMEFAPFNSYKI 177

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                  + + V + +GKNRE+++ F  F  +V  L RISYG   L  L  G  R  + +
Sbjct: 178 LKNDRRYSKIKVSIAQGKNRELRRFFGAFGREVLDLRRISYGFVHLNALPCGKKRFFTHE 237

Query: 240 ILREQLGPHLLEEAQVNLDAP 260
             R+       +  + N    
Sbjct: 238 EYRDLHIFLRDKIDKANNPQM 258


>gi|15594474|ref|NP_212263.1| hypothetical protein BB0129 [Borrelia burgdorferi B31]
 gi|216264234|ref|ZP_03436226.1| hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Borrelia burgdorferi 156a]
 gi|221217438|ref|ZP_03588909.1| hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Borrelia burgdorferi 72a]
 gi|225549328|ref|ZP_03770301.1| hypothetical RNA pseudouridine synthase [Borrelia burgdorferi 94a]
 gi|225549831|ref|ZP_03770793.1| hypothetical RNA pseudouridine synthase [Borrelia burgdorferi 118a]
 gi|3915347|sp|O51155|Y129_BORBU RecName: Full=Uncharacterized RNA pseudouridine synthase BB_0129;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|2688006|gb|AAC66508.1| conserved hypothetical protein [Borrelia burgdorferi B31]
 gi|215980707|gb|EEC21514.1| hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Borrelia burgdorferi 156a]
 gi|221192716|gb|EEE18932.1| hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Borrelia burgdorferi 72a]
 gi|225369522|gb|EEG98973.1| hypothetical RNA pseudouridine synthase [Borrelia burgdorferi 118a]
 gi|225370186|gb|EEG99626.1| hypothetical RNA pseudouridine synthase [Borrelia burgdorferi 94a]
 gi|312149536|gb|ADQ29607.1| hypothetical RNA pseudouridine synthase [Borrelia burgdorferi N40]
          Length = 249

 Score =  121 bits (304), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 62/225 (27%), Positives = 95/225 (42%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-----RK 69
           RV   +A  G+ SRR  E +I ++ V+VN  + +     V   D I            + 
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLVRVNNTIAK-LGDKVTLGDRIIYKKQIFVFKDFQI 66

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             R  L L      L +       +  +    P    RV S+GRLD  + GLLL TNDG 
Sbjct: 67  NNRIYLALNKPRNYLCSNFDVDGRKLAISLVQPLFKERVFSIGRLDFKSSGLLLFTNDGK 126

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P  +  R Y +     +D++ L   K GI ++   +      +  +  +    
Sbjct: 127 FANDIIHPRQKVEREYIIESKKDIDENLLISFKSGIKVKKEFFKLKSYEILNKNSA---- 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L EGKNREI+KVF   N  + ++ RI  G   L +L  G  +
Sbjct: 183 RLILDEGKNREIRKVFLSKNIFLKKIHRIRIGNINLDSLKEGQVK 227


>gi|254515118|ref|ZP_05127179.1| ribosomal small subunit pseudouridine synthase A [gamma
           proteobacterium NOR5-3]
 gi|219677361|gb|EED33726.1| ribosomal small subunit pseudouridine synthase A [gamma
           proteobacterium NOR5-3]
          Length = 205

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 54/208 (25%), Positives = 99/208 (47%), Gaps = 7/208 (3%)

Query: 34  MIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           M+AQ+R+ V+G +    +  +     +++DG    +       + +KP G+V    DP  
Sbjct: 1   MLAQRRIMVDGKVASDMSQTIDKFSRVQLDGE-WTQNHTAHYLMLNKPQGVVCATKDPLH 59

Query: 94  RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
           R+ +         ++  VGRLD N+ GL+LLTNDG  +R L  P ++ ++ YRV     +
Sbjct: 60  RTILDLLELPDKEQLHIVGRLDYNSTGLVLLTNDGQWSRKLSHPDSKLIKRYRVTTEQTI 119

Query: 154 DQDKLNLLK--KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            ++ +   +       +GI      +T+      +    V L EG+  +IK++F  F  K
Sbjct: 120 TEEYVQAFQSGMYFDFEGITTRPAPLTIL----DSKTAQVDLTEGRYHQIKRMFGRFQNK 175

Query: 212 VNRLIRISYGPFQLGTLLAGSTREVSKK 239
           V  + R + G ++LG L  G  + ++  
Sbjct: 176 VLSIHRFAVGSYELGELSPGEYKSIAPD 203


>gi|51244672|ref|YP_064556.1| ribosomal large subunit pseudouridine synthase B [Desulfotalea
           psychrophila LSv54]
 gi|50875709|emb|CAG35549.1| related to ribosomal large subunit pseudouridine synthase B
           [Desulfotalea psychrophila LSv54]
          Length = 229

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 57/129 (44%), Positives = 75/129 (58%), Gaps = 5/129 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DH 59
           +K  NI+     P R+ K +A +GI SRR+ E++I   RV +NG  +      +    D 
Sbjct: 91  IKSYNIMS----PVRLQKFLAASGICSRRKAEQLILDGRVTLNGETVLILGTKITPDIDK 146

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           I VDG  +++ E+   +L +KP G VTT SDP GR  V D L  I  RV  VGRLD +TE
Sbjct: 147 ITVDGKLVKEEEQKVYYLLNKPKGYVTTLSDPQGRPVVTDLLHGINERVFPVGRLDFDTE 206

Query: 120 GLLLLTNDG 128
           G LLLTNDG
Sbjct: 207 GALLLTNDG 215


>gi|256544407|ref|ZP_05471782.1| ribosomal small subunit pseudouridine synthase A [Anaerococcus
           vaginalis ATCC 51170]
 gi|256399939|gb|EEU13541.1| ribosomal small subunit pseudouridine synthase A [Anaerococcus
           vaginalis ATCC 51170]
          Length = 236

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 54/229 (23%), Positives = 109/229 (47%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            RV K+I  A + +R+ +++   +  + +NG +++ ++V V    D +   G  +   E 
Sbjct: 3   MRVDKMIGNANLDTRKNIKKNAKKGGLVINGEIIKDSSVKVDPNIDEVIYMGELVDYFEN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +  +   +    ++ DG      +   +   +   GRLD +T GLLL++ DG    
Sbjct: 63  IYIMMNKREGLI-CQSNELDGTVMSDLDEFYLNLDLAIAGRLDKDTTGLLLMSTDGKFIH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P++   + Y V    ++D D + + K+G+ I+   Y      L+  +   A+V V 
Sbjct: 122 RVISPNSNIWKKYEVETSKKIDPDLVEIFKEGVYIKEDDYYARSAKLEIIEDKKAYVYVT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
             EGK   +K++F   + +V +L R++ G  QL   L  G  RE++++ 
Sbjct: 182 --EGKFHLVKRLFSNNDNEVVKLKRLAIGKLQLDKTLNPGDYRELTQEE 228


>gi|152981630|ref|YP_001352859.1| RNA pseudouridylate synthase [Janthinobacterium sp. Marseille]
 gi|151281707|gb|ABR90117.1| RNA pseudouridylate synthase [Janthinobacterium sp. Marseille]
          Length = 237

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 47/237 (19%), Positives = 81/237 (34%), Gaps = 12/237 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRKA 70
              R+SK +A A   SRRE E+ I    V V+G ++E     V     I +     L   
Sbjct: 3   DSIRLSKRVAEALACSRREAEQYIEGGWVSVDGKVIEEPGHRVDPQQAIVLSPDATLVAV 62

Query: 71  ERTRLWLYHKPIG-------LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           +   + L+             +T  +      +    L      +     L+    GLL+
Sbjct: 63  DPVTILLHKPAGMDAAAALQCITPENLYAEDRSGIRFLKKHTVDLKPTDSLESLASGLLV 122

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T D  +AR L   +    + Y     G +  + L LL  G+ +       ++V+   + 
Sbjct: 123 FTQDWHVARKLVDDAAGIEQEYIAEVSGTLVANGLALLNHGLSMNRKPLAPVKVSWQNET 182

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                   G++ G   +I  + E     +  L RI      +  L  G  R +    
Sbjct: 183 RLRFAGK-GIQRG---QIPYMCEQVGLTLVGLKRIRMARMPMAALPVGQWRYLKGYE 235


>gi|221068469|ref|ZP_03544574.1| pseudouridine synthase [Comamonas testosteroni KF-1]
 gi|220713492|gb|EED68860.1| pseudouridine synthase [Comamonas testosteroni KF-1]
          Length = 248

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 48/244 (19%), Positives = 87/244 (35%), Gaps = 17/244 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG------ILLERAAVNVMS-TDHIEVDGVP 66
            ++  ++   G   RR    ++ Q  V++          +  +   V        V GV 
Sbjct: 1   MQLQDMLYSQGFGIRRVCSGLVQQGWVELWNPQTSDWEKVLDSTQQVDPEGLRFRVQGVE 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGR-------STVFDNLPSIFSRVISVGRLDINTE 119
               E   + L        +                            V +VGRLD +T 
Sbjct: 61  WEYHELGYVLLNKPAGTECSQKPSAYPSIYTLLPAPLRQRPNKGAVQGVQAVGRLDQDTT 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLL++DG     +  P     +VYRV     VD  ++  L  G+V+       ++   
Sbjct: 121 GMLLLSDDGQFIHRMSSPKKHVSKVYRVTCKHPVDAKQIQRLLDGVVLDDDP-KPVK-AA 178

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
             ++  +  + + L EGK  ++K++    + +V  L R   G  +L   L  G  R ++ 
Sbjct: 179 ACEQVDSHVLDLTLTEGKYHQVKRMIAAVSNRVEGLHRRRIGGMELPADLEPGQWRWLTA 238

Query: 239 KILR 242
             L 
Sbjct: 239 HELE 242


>gi|325846912|ref|ZP_08169769.1| putative 16S pseudouridylate 516 synthase [Anaerococcus
           hydrogenalis ACS-025-V-Sch4]
 gi|325481154|gb|EGC84198.1| putative 16S pseudouridylate 516 synthase [Anaerococcus
           hydrogenalis ACS-025-V-Sch4]
          Length = 233

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 55/229 (24%), Positives = 107/229 (46%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            RV K+I  A + +R+ ++R   +  + +NG +++ ++V V    D +   G  +   + 
Sbjct: 1   MRVDKMIGNANLDTRKNIKRNAKKGELIINGQIVKDSSVKVDPNLDEVIYMGELVDYFDN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +  +   +    ++ DG      +   +   +   GRLD +T GLLLL+ DG    
Sbjct: 61  IYIMMNKREGLI-CQSNELDGTVMSDLDEFYLNLDLAIAGRLDKDTTGLLLLSTDGKFIH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P++   + Y V    ++D   + + K G+ I+   Y      LD   G  A+V V 
Sbjct: 120 KVISPNSHIWKKYEVETSKKIDPSLVEIFKDGVYIKEDDYYARSAKLDIIGGKKAYVYVT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
             EGK   +K++F   + +V +L R++ G  +L  +L  G  RE+ ++ 
Sbjct: 180 --EGKFHLVKRLFSNNDNEVIKLKRLAIGDLELDQSLNPGQYRELIEEE 226


>gi|195941866|ref|ZP_03087248.1| hypothetical protein Bbur8_03164 [Borrelia burgdorferi 80a]
 gi|195942365|ref|ZP_03087747.1| hypothetical protein Bbur8_05879 [Borrelia burgdorferi 80a]
 gi|195942740|ref|ZP_03088122.1| hypothetical protein Bbur8_07965 [Borrelia burgdorferi 80a]
 gi|195942847|ref|ZP_03088229.1| hypothetical protein Bbur8_08590 [Borrelia burgdorferi 80a]
 gi|218249574|ref|YP_002374657.1| hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Borrelia burgdorferi ZS7]
 gi|223889072|ref|ZP_03623661.1| hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Borrelia burgdorferi 64b]
 gi|226321960|ref|ZP_03797485.1| hypothetical RNA pseudouridine synthase [Borrelia burgdorferi
           Bol26]
 gi|218164762|gb|ACK74823.1| hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Borrelia burgdorferi ZS7]
 gi|223885321|gb|EEF56422.1| hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Borrelia burgdorferi 64b]
 gi|226232550|gb|EEH31304.1| hypothetical RNA pseudouridine synthase [Borrelia burgdorferi
           Bol26]
          Length = 249

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 63/225 (28%), Positives = 95/225 (42%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-----RK 69
           RV   +A  G+ SRR  E +I ++ VKVN  + +     V   D I            + 
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLVKVNNTIAK-LGDKVALGDRIIYKKQIFVFKDFQI 66

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             R  L L      L +       +  +    P    RV S+GRLD  + GLLL TNDG 
Sbjct: 67  NNRIYLALNKPRNYLCSNFDVDGRKLAISLVQPLFKERVFSIGRLDFKSSGLLLFTNDGK 126

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P  +  R Y +     +D++ L   K GI ++   +      +  +  +    
Sbjct: 127 FANDIIHPRQKVEREYIIESKKDIDENLLISFKSGIKVKKEFFKLKSYEILNKNSA---- 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L EGKNREI+KVF   N  + ++ RI  G   L +L  G  +
Sbjct: 183 RLILDEGKNREIRKVFLSKNIFLKKIHRIRIGNINLDSLKEGQVK 227


>gi|220921089|ref|YP_002496390.1| pseudouridine synthase [Methylobacterium nodulans ORS 2060]
 gi|219945695|gb|ACL56087.1| pseudouridine synthase [Methylobacterium nodulans ORS 2060]
          Length = 247

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 53/235 (22%), Positives = 93/235 (39%), Gaps = 7/235 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV----MSTDHIEVDGVPLRKA 70
           R+ +++A  G  SRRE++ +     + ++G  L  A   +       + + V GV L   
Sbjct: 8   RLDRLLANLGYGSRREIQALARAGAIILDGARLRAADERIPVTRDLPERLTVGGVALDPP 67

Query: 71  ERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               L L+       +           + +        + +VGRLD  T GLLLLT+DG 
Sbjct: 68  PGLVLMLHKPTGVTCSHKEAGPLVYGLLPERWRRRDPPLSTVGRLDKETSGLLLLTDDGA 127

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +  P  +  + YRV     +  D+  L   G ++       +       +G     
Sbjct: 128 LLHRIISPKAKVAKRYRVELARPLAGDEGALFASGTLMLEGEDKPLLPVELVAEGP-TRA 186

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           +V L EG+  +++++F      V  L R   G   L   L  G+ R + +  L +
Sbjct: 187 SVTLTEGRYHQVRRMFAAVGNHVTALHRDRVGRLDLPADLAPGAYRILGEAELAQ 241


>gi|285019273|ref|YP_003376984.1| pseudouridylate synthase [Xanthomonas albilineans GPE PC73]
 gi|283474491|emb|CBA16992.1| putative pseudouridylate synthase protein [Xanthomonas albilineans]
          Length = 236

 Score =  121 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 43/237 (18%), Positives = 84/237 (35%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-------STDHIEVD 63
             P R+ K +A     SR E ++ I    V V+GI++E    N+            + VD
Sbjct: 2   SAPVRLDKYLAAMLHCSRGEAQQYIEGGWVSVDGIVVEEPQANITTQHVTLAPDAQLGVD 61

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                   +       + + L +  +      T    L   F  +     L+    GLL+
Sbjct: 62  DAATLLLHKPIGLTAAQALALASPATRSRLDPTDRRMLKRHFLHLSMPLPLEQEASGLLV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           L+ D  + R L   +    + + V+  G +    L+ L  G+          +V+   + 
Sbjct: 122 LSQDRRVLRRLNEDAATIEQEFVVQVRGDLLPYGLHRLAHGLRHGSRTLPPCKVSWQNED 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   +++ +  ++  +      +V  L R+  G   LG L +G  R +    
Sbjct: 182 R----LRFAIKQVQPGQLHDMCAQVGLEVIGLRRLRIGRIALGKLASGEWRYLPNSE 234


>gi|218192109|gb|EEC74536.1| hypothetical protein OsI_10056 [Oryza sativa Indica Group]
          Length = 279

 Score =  121 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 58/234 (24%), Positives = 97/234 (41%), Gaps = 14/234 (5%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTRLWL--YHKPIGLV 85
           R  E +I Q +V VNG +       V  S D I V+G  + K    +L+         + 
Sbjct: 46  RTCEELIFQGKVTVNGSVCTAPQTKVDISKDSIYVNGNRISKKLPPKLYFAVNKPKGYIC 105

Query: 86  TTHSDPDGRSTVFDNLPSIFSRV--------ISVGRLDINTEGLLLLTNDGGLARVLELP 137
           +        S   D L                +VGRLD+ T GL+++TNDG  A+ L  P
Sbjct: 106 SCGERKSIISLFDDYLKGWNKIQPGVPKPRLFTVGRLDVATSGLIIITNDGEFAQKLSHP 165

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLRE 195
           S+  ++ Y V   G V ++ L  + +G  I G+       +            + + + E
Sbjct: 166 SSNIMKEYVVTIDGPVHRNHLIAISEGTKIDGVKCIPDLVEPLDVQSNTKRTRIRIAVHE 225

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
           G+N E++++ +    +V  L R+  G F+L   L  G   E+ +  L+   G  
Sbjct: 226 GRNHEVRELVQNAGLEVYALKRVRIGRFRLPPDLGIGKFVELKQTDLKSLEGKK 279


>gi|315637055|ref|ZP_07892278.1| ribosomal small subunit pseudouridine synthase A [Arcobacter
           butzleri JV22]
 gi|315478591|gb|EFU69301.1| ribosomal small subunit pseudouridine synthase A [Arcobacter
           butzleri JV22]
          Length = 229

 Score =  121 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 46/225 (20%), Positives = 93/225 (41%), Gaps = 2/225 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           RV   ++  G  +R E ++ +    + +N   +   ++     D I+++G  L       
Sbjct: 7   RVDAHLSSLGYCTRSEAKKFLRMNEICINDNRVYNTSIKAYHDD-IKINGEVLDDETLLI 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L    +        S     S +         ++ ++GRLDI+T G++LLT+DG L   L
Sbjct: 66  LLNKPQGYICSHNDSGKLIYSLLPQRYNRRNPKISTIGRLDIDTTGVILLTDDGVLNHKL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     ++Y       +  D++ +   G ++       +         +  +V + + 
Sbjct: 126 TSPKKDISKIYEATLEKPLKGDEVEIFASGTLMLNGEEKPLLPAKLEI-ITPTFVKIEIV 184

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           EGK  ++K++F   + KV +L R  +  F+L  L  G  + +  K
Sbjct: 185 EGKYHQVKRMFAAVSNKVIKLHRTKFADFELEDLKEGEFKIIKSK 229


>gi|219120673|ref|XP_002181070.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217407786|gb|EEC47722.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 331

 Score =  121 bits (302), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 94/298 (31%), Positives = 143/298 (47%), Gaps = 33/298 (11%)

Query: 10  NFTPQRVSKVIA---RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH----IEV 62
           +    R+SKV++      + SRRE ERMI    V + G +L    + +   D     ++V
Sbjct: 33  STDTVRLSKVLSLHTENLVISRREAERMIRSGDVTLAGNVLTSPMMMLKEEDLNDGALKV 92

Query: 63  DGVPLRKA---------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---- 103
           +G  +                   +TR+W+ HK  G +   +DP  R ++   L      
Sbjct: 93  NGKVVNLRSSKGPRSVAGEENSVHKTRVWIAHKLPGEIVADNDPYDRPSLLQRLIRGGVG 152

Query: 104 ----IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
                   + SVGRLD+NTEGL+L+TNDG  AR +ELPS +  R YRVR HG +   KL 
Sbjct: 153 KVGKTRLHLKSVGRLDMNTEGLILVTNDGKYAREMELPSNKLHRTYRVRVHGLLTDHKLA 212

Query: 160 LLKKGIVIQGICYGDMQVTLD---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
            ++KG+ ++GI Y  M++  +     + +N W+ V   EGKNR+I+ VF++    V RLI
Sbjct: 213 RIRKGVTVEGIRYPPMRIIPESTRQSQSTNKWLKVTCTEGKNRQIRNVFKYLGLTVTRLI 272

Query: 217 RISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNI 274
           RISYG ++L T+  G   EV  K +  Q     L             +E+    +   
Sbjct: 273 RISYGDYRLQTIPPGMAIEVPAKHIENQKHRGRLIRPTKPAPKRSDEAESSKAVQWVR 330


>gi|299533039|ref|ZP_07046425.1| Pseudouridine synthase, Rsu [Comamonas testosteroni S44]
 gi|298718924|gb|EFI59895.1| Pseudouridine synthase, Rsu [Comamonas testosteroni S44]
          Length = 250

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 48/245 (19%), Positives = 87/245 (35%), Gaps = 17/245 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNG------ILLERAAVNVMST-DHIEVDGV 65
             ++  ++   G   RR    ++ Q  V++          +  +   V        V GV
Sbjct: 2   SMQLQDMLYSQGFGIRRVCSGLVQQGWVELWNPQTSDWEKILDSTQQVDPGGLRFRVQGV 61

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGR-------STVFDNLPSIFSRVISVGRLDINT 118
                E   + L        +                            V +VGRLD +T
Sbjct: 62  EWEYHELGYVLLNKPAGTECSQKPSAYPSIYTLLPAPLRQRPNKGAVQGVQAVGRLDQDT 121

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            G+LLL++DG     +  P     +VYRV     VD  ++  L  G+V+       ++  
Sbjct: 122 TGMLLLSDDGQFIHRMSSPKKHVSKVYRVTCKHPVDAKQIQRLLDGVVLDDDP-KPVK-A 179

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
              ++  +  + + L EGK  ++K++    + +V  L R   G  +L   L  G  R ++
Sbjct: 180 AACEQVDSHVLDLTLTEGKYHQVKRMIAAVSNRVEGLHRRRIGGMELPAELEPGQWRWLT 239

Query: 238 KKILR 242
              L 
Sbjct: 240 ADELE 244


>gi|226320679|ref|ZP_03796237.1| hypothetical RNA pseudouridine synthase [Borrelia burgdorferi
           29805]
 gi|226233895|gb|EEH32618.1| hypothetical RNA pseudouridine synthase [Borrelia burgdorferi
           29805]
          Length = 249

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 63/225 (28%), Positives = 95/225 (42%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-----RK 69
           RV   +A  G+ SRR  E +I ++ VKVN  + +     V   D I            + 
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLVKVNNTIAK-LGDKVALGDRIIYKKQIFVFKDFQI 66

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             R  L L      L +       +  +    P    RV S+GRLD  + GLLL TNDG 
Sbjct: 67  NNRIYLALNKPRNYLCSNFDVDGRKLAISLVQPLFKERVFSIGRLDFKSSGLLLFTNDGK 126

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P  +  R Y +     +D++ L   K GI ++   +      +  +  +    
Sbjct: 127 FANDIIHPRKKVEREYIIESKKDIDENLLISFKSGIKVKKEFFKLKSYEILNKNSA---- 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L EGKNREI+KVF   N  + ++ RI  G   L +L  G  +
Sbjct: 183 RLILDEGKNREIRKVFLSKNIFLKKIHRIRIGNINLDSLKEGQVK 227


>gi|238026899|ref|YP_002911130.1| Pseudouridine synthase, Rsu [Burkholderia glumae BGR1]
 gi|237876093|gb|ACR28426.1| Pseudouridine synthase, Rsu [Burkholderia glumae BGR1]
          Length = 543

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 60/251 (23%), Positives = 98/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE------------ 61
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V     IE            
Sbjct: 295 MRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPDQKIEIDDQAIAAQAAQ 354

Query: 62  ---VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
              +   P+          Y   + L+T  +   G  +     P     +   GRLDI++
Sbjct: 355 VTILLHKPVGYVSGQAEDGYEPAVTLITRENHWSGDRSALRLSPLHLRTLAPAGRLDIDS 414

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT DG +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 415 TGLLVLTQDGRIAKQLIGEQSDIDKEYLVRVRFGEHVIDVDQHFPAESLAKLRHGLELDG 474

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 475 VPLKPAMVSWQNSEQ----LRFVLREGKKRQIRRMCELVGLEVVGLKRVRMGRVMLGALP 530

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 531 QGQWRYLGADE 541



 Score = 42.5 bits (98), Expect = 0.097,   Method: Composition-based stats.
 Identities = 10/105 (9%), Positives = 20/105 (19%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G    +       A   +++          +    D     +    ++G    +    P 
Sbjct: 39  GAPKPKSKPSAKGAAPRAAKPAGAGAVKPRAPREADRPSRSEARPARDGERPFRSEGRPA 98

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                                 S  R       P+    R  R  
Sbjct: 99  RDGERPVRSGARPPRDGERPFRSEGRPARDGERPARNGARPPRDG 143



 Score = 40.9 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 11/107 (10%), Positives = 21/107 (19%), Gaps = 1/107 (0%)

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           + P    EA     +    +    R   +      D    ++  +       +  +    
Sbjct: 65  VKPRAPREADRPSRSEARPARDGERPFRSEGRPARDGERPVRSGARPPRDGERPFRSEGR 124

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSG-QREENHRRSPSFPSKRSLRRT 350
             R         A+             R       P     R  R  
Sbjct: 125 PARDGERPARNGARPPRDGERPFRSEGRPARDGERPVRSGARPPRDG 171



 Score = 39.4 bits (90), Expect = 0.76,   Method: Composition-based stats.
 Identities = 13/109 (11%), Positives = 19/109 (17%), Gaps = 1/109 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R +  P    E  V   A                +   +   R       ++G    +  
Sbjct: 92  RSEGRPARDGERPVRSGARPPRDGERPFRSEGRPARDGERPARNGARPP-RDGERPFRSE 150

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
             P                       S  R       P     R  R  
Sbjct: 151 GRPARDGERPVRSGARPPRDGERPFRSEGRPARDGERPVRSGARPPRDG 199



 Score = 39.4 bits (90), Expect = 0.83,   Method: Composition-based stats.
 Identities = 10/118 (8%), Positives = 20/118 (16%), Gaps = 1/118 (0%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R         + G     + +    +    +    R   +      D     +       
Sbjct: 124 RPARDGERPARNGARPPRDGERPFRSEGRPARDGERPVRSGARPPRDGERPFRSEGRPAR 183

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSG-QREENHRRSPSFPSKRSLRRT 350
              +  +      R          +          G  R       P     R  R  
Sbjct: 184 DGERPVRSGARPPRDGERPFRSEGRPARDGERPLRGTARPVRDGERPVRAGTRPPRDG 241



 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 11/106 (10%), Positives = 19/106 (17%), Gaps = 1/106 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G     + +    +    +    R   N      D     +          +  +     
Sbjct: 108 GARPPRDGERPFRSEGRPARDGERPARNGARPPRDGERPFRSEGRPARDGERPVRSGARP 167

Query: 306 HRRNLASNVWMAKGIHSSFLS-DSGQREENHRRSPSFPSKRSLRRT 350
            R          +          SG R       P     R  R  
Sbjct: 168 PRDGERPFRSEGRPARDGERPVRSGARPPRDGERPFRSEGRPARDG 213



 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 13/105 (12%), Positives = 21/105 (20%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P   + A      P    E     R         +     +    ++G    +  A P 
Sbjct: 53  APRAAKPAGAGAVKPRAPREADRPSRSEARPARDGERPFRSEGRPARDGERPVRSGARPP 112

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                               + +G R       P     R  R  
Sbjct: 113 RDGERPFRSEGRPARDGERPARNGARPPRDGERPFRSEGRPARDG 157



 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 12/109 (11%), Positives = 20/109 (18%), Gaps = 1/109 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R +  P    E      A                +   +   R       ++G    +  
Sbjct: 120 RSEGRPARDGERPARNGARPPRDGERPFRSEGRPARDGERPVRSGARPP-RDGERPFRSE 178

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
             P                       S  R       P   + R +R  
Sbjct: 179 GRPARDGERPVRSGARPPRDGERPFRSEGRPARDGERPLRGTARPVRDG 227



 Score = 37.9 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 11/110 (10%), Positives = 25/110 (22%), Gaps = 1/110 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR-MKKNSSQKNGLSKQKKLATP 304
           G     + +    +    +    R   +      D       +    ++G    +  A P
Sbjct: 164 GARPPRDGERPFRSEGRPARDGERPVRSGARPPRDGERPFRSEGRPARDGERPLRGTARP 223

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           V                    S    R       P+   + +  R +  +
Sbjct: 224 VRDGERPVRAGTRPPRDGDRPSRVESRPARDTDRPARKPRVTTERPAPSR 273



 Score = 35.9 bits (81), Expect = 9.6,   Method: Composition-based stats.
 Identities = 9/107 (8%), Positives = 20/107 (18%), Gaps = 1/107 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK-LATP 304
           G   +               +  R   +    V       +          +  +    P
Sbjct: 157 GERPVRSGARPPRDGERPFRSEGRPARDGERPVRSGARPPRDGERPFRSEGRPARDGERP 216

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
           +                 +     G R       P+  + R  R+  
Sbjct: 217 LRGTARPVRDGERPVRAGTRPPRDGDRPSRVESRPARDTDRPARKPR 263


>gi|225552398|ref|ZP_03773338.1| hypothetical RNA pseudouridine synthase [Borrelia sp. SV1]
 gi|225371396|gb|EEH00826.1| hypothetical RNA pseudouridine synthase [Borrelia sp. SV1]
          Length = 249

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 64/225 (28%), Positives = 95/225 (42%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-----RK 69
           RV   +A  G+ SRR  E +I ++ VKVN  + +     V   D I            + 
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLVKVNNTIAK-LGDKVALGDRIIYKKQIFVFKDFQI 66

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             R  L L      L +       R  +    P    RV S+GRLD  + GLLL TNDG 
Sbjct: 67  NNRIYLALNKPRNYLCSNFDINGRRLAISLVQPLFKERVFSIGRLDFKSSGLLLFTNDGK 126

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P  +  R Y +     +D++ L   K GI ++   +      +  +  +    
Sbjct: 127 FANDIIHPRQKVEREYIIESKKDIDENLLISFKSGIKVKKEFFKLKSYEILNKNSA---- 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L EGKNREI+KVF   N  + ++ RI  G   L +L  G  +
Sbjct: 183 RLILDEGKNREIRKVFLTKNIFLKKIHRIRIGNINLDSLKEGQVK 227


>gi|78778204|ref|YP_394519.1| pseudouridine synthase, Rsu [Sulfurimonas denitrificans DSM 1251]
 gi|78498744|gb|ABB45284.1| ribosomal small subunit pseudouridine synthase A [Sulfurimonas
           denitrificans DSM 1251]
          Length = 228

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 52/223 (23%), Positives = 89/223 (39%), Gaps = 2/223 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           RV   ++  G  +R E +R +    V V    +      V     I V+G  L       
Sbjct: 7   RVDAHLSSLGYCTRSEAKRFLTTNNVSVYNERIFDVTKKVH-HSEIRVNGELLDAERLVI 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L      +    + S     S +         +V ++GRLDI+T G +LL++DG L   L
Sbjct: 66  LMNKPHGVVCSHSDSGVLIYSLLPPRWQRRNPKVSTIGRLDIDTTGAILLSDDGALNHKL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P ++  ++Y V     +  D+  +   G ++       +        G    V V + 
Sbjct: 126 TSPKSEVTKIYEVTLAQALRGDEAEIFASGELLLNGEKKPLLPAKMEVIGPIH-VRVEIC 184

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           EG+  ++K++F     +V  L R S+G F +  L     RE+S
Sbjct: 185 EGRYHQVKRMFASVGNRVTALHRASFGDFSVEDLKPSEFREIS 227


>gi|330818049|ref|YP_004361754.1| Pseudouridine synthase, Rsu [Burkholderia gladioli BSR3]
 gi|327370442|gb|AEA61798.1| Pseudouridine synthase, Rsu [Burkholderia gladioli BSR3]
          Length = 238

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 50/221 (22%), Positives = 89/221 (40%), Gaps = 4/221 (1%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTRLWL 77
           ++   G  SRR+   ++   RV ++GI+L+ A  +  + D H +VDG       +  L L
Sbjct: 6   ILYSQGFGSRRQCRALVEAGRVSIDGIVLDDADADFATDDLHFDVDGTRWPYRAQAYLVL 65

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
                   +                     V  VGRLD +T GLLLL++DG        P
Sbjct: 66  NKPAGYECSRDPQHHLSVFSLLPPQFGARGVQCVGRLDQDTTGLLLLSDDGQFVHAYTSP 125

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGK 197
             +  + Y       +D  +L  L++G+++ G     +       +   + + + + EGK
Sbjct: 126 KKKVPKTYLAEVKHALDDRQLAALREGVLLHGEP-KPIAAVAARARELRS-LELTVLEGK 183

Query: 198 NREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
             ++K++      +V  L R   G + L   L  G  R + 
Sbjct: 184 YHQVKRMVAASGNRVEALHRERVGGYTLPADLAPGGWRWLD 224


>gi|145355123|ref|XP_001421818.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144582057|gb|ABP00112.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 238

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 58/239 (24%), Positives = 92/239 (38%), Gaps = 26/239 (10%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER--------------- 72
           RRE +  ++  RV VNG L+   +  V + D + +DG  +                    
Sbjct: 1   RREADAAVSAGRVLVNGELVR-PSQRVKAGDVVTLDGKVMLWEAYARRVEEEIANDATSS 59

Query: 73  -TRLWLYHKPIGLVTTHSDPD---GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              L        + T           +   +       R+  VGRLD ++ GL+LLTNDG
Sbjct: 60  FVYLLYNKPRGVVCTMEPHQRTSLHFALERERARMKKIRIFPVGRLDKDSSGLVLLTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ------GICYGDMQVTLDTQ 182
            ++  L  PS +  + Y V     V    +  L  G+VI                  + +
Sbjct: 120 RVSDALLDPSRKAEKEYDVDVDRDVSAADVERLAAGVVITTLQQRTMTETTAPTQPCEVR 179

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           K     +   L+EG+NR+I+K+ E  ++ V RL R      +LG L  G  R +    L
Sbjct: 180 KIGPRTLRFVLKEGRNRQIRKMCEALSYDVTRLHRTRIAELELGDLEIGGLRPLDVDEL 238


>gi|312148012|gb|ADQ30671.1| hypothetical RNA pseudouridine synthase [Borrelia burgdorferi JD1]
          Length = 249

 Score =  120 bits (300), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 62/225 (27%), Positives = 95/225 (42%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-----RK 69
           RV   +A  G+ SRR  E +I ++ V+VN  + +     V   D I            + 
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLVRVNNTIAK-LGDKVALGDRIIYKKQIFVFKDFQI 66

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             R  L L      L +       +  +    P    RV S+GRLD  + GLLL TNDG 
Sbjct: 67  NNRIYLALNKPRNYLCSNFDVDGRKLAISLVQPLFKERVFSIGRLDFKSSGLLLFTNDGK 126

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P  +  R Y +     +D++ L   K GI ++   +      +  +  +    
Sbjct: 127 FANDIIHPRQKVEREYIIESKKDIDENLLISFKSGIKVKKEFFKLKSYEILNKNSA---- 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L EGKNREI+KVF   N  + ++ RI  G   L +L  G  +
Sbjct: 183 RLILDEGKNREIRKVFLSKNIFLKKIHRIRIGNINLDSLKEGQVK 227


>gi|160897953|ref|YP_001563535.1| pseudouridine synthase [Delftia acidovorans SPH-1]
 gi|160363537|gb|ABX35150.1| pseudouridine synthase [Delftia acidovorans SPH-1]
          Length = 249

 Score =  120 bits (300), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 51/243 (20%), Positives = 89/243 (36%), Gaps = 17/243 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-------EVDGVP 66
            ++  ++   G   RR    ++ Q  V++           + ST  I        V GV 
Sbjct: 3   MQLQDILYSQGFGIRRVCSGLVQQGWVELWDTEANDWVRCLDSTQDIDPEGLRYRVQGVE 62

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-------SVGRLDINTE 119
                   + L+       +              LP              +VGRLD +T 
Sbjct: 63  WAYHALGYVLLHKPAGTECSQKPSTYPSIYSLLPLPLRLRPNKGAVQGVQAVGRLDQDTT 122

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLL++DG     +  P     ++YRV     VD  ++  L  G+V+       ++   
Sbjct: 123 GLLLLSDDGQFIHRMSSPKKHVPKIYRVTTKHPVDASQVQRLLDGVVLDDDP-KPVK-AA 180

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
             ++ S   + + L EGK  ++K++      +V  L R   G  +L   L  G  R ++ 
Sbjct: 181 ACEQVSEHVLDLTLTEGKYHQVKRMIAAVGNRVEGLHRWKIGELELTEDLQPGQWRWLTA 240

Query: 239 KIL 241
           + L
Sbjct: 241 EDL 243


>gi|194364229|ref|YP_002026839.1| pseudouridine synthase [Stenotrophomonas maltophilia R551-3]
 gi|194347033|gb|ACF50156.1| pseudouridine synthase [Stenotrophomonas maltophilia R551-3]
          Length = 233

 Score =  120 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 56/239 (23%), Positives = 101/239 (42%), Gaps = 11/239 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVK-VNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            ++ K+IA  G  SR++V+ M  + RV   +G +L  A   V   + + VDG PL     
Sbjct: 1   MKLVKLIANLGYGSRKQVQWMFREGRVTDADGEVLY-ADDQV-PHEAVRVDGEPLDPPVG 58

Query: 73  TRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             + L+       +           +          + +VGRLD +T GLLLLT+DGGL 
Sbjct: 59  LSIALHKPAGYTCSTKDKGRLIYDLLPPRYRDRDPVLSTVGRLDRDTSGLLLLTDDGGLL 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GIVIQGICY--GDMQVTLDTQKGSNAW 188
             +  P ++  +VY V     +  D++ L     ++++         ++ +   + +   
Sbjct: 119 HRIISPKSKLPKVYEVELSDDLRGDEVALFASGTLMLESEKTPLLPAELEVLDARRA--- 175

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
             + L EG+  +++++F      V  L R   G   L  L  G  R+++   L     P
Sbjct: 176 -RLVLHEGRYHQVRRMFAATGNHVQALHRSRVGGLDLQGLDEGQWRQLTPTDLDTLFAP 233


>gi|224534022|ref|ZP_03674606.1| hypothetical RNA pseudouridine synthase [Borrelia burgdorferi
           CA-11.2a]
 gi|224512858|gb|EEF83225.1| hypothetical RNA pseudouridine synthase [Borrelia burgdorferi
           CA-11.2a]
          Length = 249

 Score =  120 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 61/225 (27%), Positives = 95/225 (42%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-----RK 69
           RV   +A  G+ SRR  E +I ++ ++VN  + +     V   D I            + 
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLIRVNNTIAK-LGDKVTLGDRIIYKKQIFVFKDFQI 66

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             R  L L      L +       +  +    P    RV S+GRLD  + GLLL TNDG 
Sbjct: 67  NNRIYLALNKPRNYLCSNFDVDGRKLAISLVQPLFKERVFSIGRLDFKSSGLLLFTNDGK 126

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P  +  R Y +     +D++ L   K GI ++   +      +  +  +    
Sbjct: 127 FANDIIHPRQKVEREYIIESKKDIDENLLISFKSGIKVKKEFFKLKSYEILNKNSA---- 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L EGKNREI+KVF   N  + ++ RI  G   L +L  G  +
Sbjct: 183 RLILDEGKNREIRKVFLSKNIFLKKIHRIRIGNINLDSLKEGQVK 227


>gi|293363560|ref|ZP_06610316.1| pseudouridylate synthase [Mycoplasma alligatoris A21JP2]
 gi|292552909|gb|EFF41663.1| pseudouridylate synthase [Mycoplasma alligatoris A21JP2]
          Length = 230

 Score =  119 bits (299), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 49/234 (20%), Positives = 102/234 (43%), Gaps = 14/234 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST----DHIEVDGVPLRK 69
            ++ K I+     +R ++++++ +++V +N  L+   ++N        D I  +      
Sbjct: 1   MKLEKFISNVTDLTRSQIKKLLKEKKVFINDNLVTSDSINFKVEKLVIDQIAYN------ 54

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +     + +KP   +T+H D    S       +    +I+ GRLD++TEGLLL+++D  
Sbjct: 55  TDEYVYIMLNKPQNYITSHKDELYPSLFNLVSDAKRKNLIAYGRLDVDTEGLLLISDDTE 114

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            +  L  P     + Y V    ++    + +   G +I       +   L     +    
Sbjct: 115 SSHKLLSPKHHVEKKYYVEVDKKIPTSLVEIFLNGFII-DKNDKVLPSKLLIISDNKC-- 171

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            + ++EGK  ++K++F+     V  L RI +   +L   L  G  R ++KK + 
Sbjct: 172 YLTIKEGKFHQVKRMFKTHYLNVTFLKRIEFNNLKLDETLKPGQWRYLTKKEVE 225


>gi|224008973|ref|XP_002293445.1| pseudouridylate synthase [Thalassiosira pseudonana CCMP1335]
 gi|220970845|gb|EED89181.1| pseudouridylate synthase [Thalassiosira pseudonana CCMP1335]
          Length = 253

 Score =  119 bits (299), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 61/262 (23%), Positives = 112/262 (42%), Gaps = 21/262 (8%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           + +KN+    F P R++KV  +    SRR+ ++++A  R+ +N   +  A   V +    
Sbjct: 3   VSNKNV---TFQPIRINKVFKKT--HSRRQADQLVADGRITINDEPVHSAGQRVSNGGA- 56

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDIN 117
                     +      Y KP+G+  T       + +           SR+  VGRLD  
Sbjct: 57  ----NSESSTQVFEYIKYWKPLGVTCTTDRRIYDNLIDALQQDGCRPKSRIFPVGRLDKE 112

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T G++L+T+DG L         +  + Y V+ +  V  D +  L++G+ +        +V
Sbjct: 113 TSGIILMTSDGRLPNAALRGKYKHPKTYVVKANRPVANDDIKRLREGVPLT-APTLPCKV 171

Query: 178 TLDTQKG---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL-AGST 233
                     S+ ++ + L EG+NR+I+K+ E   ++V  L R S+    L  L   G  
Sbjct: 172 KAVQLSTLDLSSRYLEITLVEGRNRQIRKMLEAIGYRVMELHRKSFMNLTLENLEGEGDW 231

Query: 234 REVSKKI---LREQLGPHLLEE 252
             ++ +    +RE L     E+
Sbjct: 232 AHLTNREMEIVREVLDRAEQED 253


>gi|291320513|ref|YP_003515777.1| 16S rRNA uridine 516 pseudouridylate synthase [Mycoplasma
           agalactiae]
 gi|290752848|emb|CBH40823.1| 16S rRNA uridine 516 pseudouridylate synthaseand related
           pseudouridylate synthase [Mycoplasma agalactiae]
          Length = 232

 Score =  119 bits (299), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 55/231 (23%), Positives = 102/231 (44%), Gaps = 9/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K IA     SR EV+  + ++ +KVNG++L +  + +    D +E+D   L+  + 
Sbjct: 4   IRIEKYIADLTNLSRNEVKNKLKKKAIKVNGVILTKL-IKIDPEKDVVELDNGILKYEKF 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                      +       +   T+FD +     +  S GRLD +TEGLL+L+NDG +  
Sbjct: 63  QYYMFNKPANFICANSDSEEA--TIFDIVGLPAEKFFSFGRLDKDTEGLLILSNDGQMCH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V+   ++D + L       +        +   +       +   + 
Sbjct: 121 RLLSPKNHVPKKYYVKVDKKIDSEILLNNSPIKINDDFV---VSKYILELIDDKSCF-LT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + EGK  +IK++F    + V  L R+ +G  +L   L  G  R++S+  ++
Sbjct: 177 IYEGKFHQIKRMFGSLGFSVLYLKRVEFGKLKLDNNLKLGQVRKLSEDEVK 227


>gi|89901747|ref|YP_524218.1| pseudouridine synthase Rsu [Rhodoferax ferrireducens T118]
 gi|89346484|gb|ABD70687.1| ribosomal small subunit pseudouridine synthase A [Rhodoferax
           ferrireducens T118]
          Length = 247

 Score =  119 bits (299), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 56/249 (22%), Positives = 92/249 (36%), Gaps = 18/249 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKV---NGILL----ERAAVN-VMSTDHIEVDGV 65
            ++  ++   G  +RR    MI Q  V V   N  L      +AA   +     + V GV
Sbjct: 1   MQLQDILYSQGFGTRRVCAGMIQQGLVGVYESNQALAPVIYTQAATEFIAEGLRLRVQGV 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-------SVGRLDINT 118
                E+  + L+       +                              +VGRLD +T
Sbjct: 61  DWPYHEKAYVMLHKPSATECSQKPSTYPSVYTLLPSALRLRPQKGAVQGVQAVGRLDQDT 120

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLLLT+DG     +  P     +VY V     +D  ++  L  G+V+       ++  
Sbjct: 121 TGLLLLTDDGQFIHRMNSPRHHVPKVYEVTVKHPLDDTQVARLLAGVVLDDDP-KPVRAA 179

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
              +  S+  + + L EGK  ++K++    + +V  L R   G  +L   L  G  R +S
Sbjct: 180 AA-EAVSSHHLRLTLTEGKYHQVKRMVAAVSNRVEALHRSQIGGLRLPDDLAPGQWRWLS 238

Query: 238 KKILREQLG 246
              L    G
Sbjct: 239 AADLASIAG 247


>gi|190572631|ref|YP_001970476.1| putative ribosomal small subunit pseudouridine synthase A
           [Stenotrophomonas maltophilia K279a]
 gi|190010553|emb|CAQ44162.1| putative ribosomal small subunit pseudouridine synthase A
           [Stenotrophomonas maltophilia K279a]
          Length = 233

 Score =  119 bits (299), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 57/239 (23%), Positives = 101/239 (42%), Gaps = 11/239 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVK-VNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            ++ K+IA  G  SR++V+ M  + RV   +G +L  A   V   + I VDG PL     
Sbjct: 1   MKLVKLIANLGYGSRKQVQWMFREGRVTDADGEVLY-ADDQV-PHEAIRVDGEPLDPPVG 58

Query: 73  TRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             + L+       +   +       +          + +VGRLD  T GLLLLT+DGGL 
Sbjct: 59  LSIALHKPAGYTCSTKDTGRLIYDLLPPRFRDRDPVLSTVGRLDRETSGLLLLTDDGGLL 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GIVIQGICY--GDMQVTLDTQKGSNAW 188
             +  P ++  +VY V     +  D++ L     ++++         ++ +   + +   
Sbjct: 119 HRIISPKSKLPKVYEVELSDDLRGDEVALFASGTLMLESEKTPLLPAELEVLDARRA--- 175

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
             + L EG+  +++++F      V  L R   G   L  L  G  R+++   L     P
Sbjct: 176 -RLVLHEGRYHQVRRMFAATGNHVQALHRSRVGGLDLQGLDEGQWRQLTSTDLDTLFAP 233


>gi|157737342|ref|YP_001490025.1| ribosomal small subunit pseudouridine synthase A [Arcobacter
           butzleri RM4018]
 gi|157699196|gb|ABV67356.1| ribosomal small subunit pseudouridine synthase A [Arcobacter
           butzleri RM4018]
          Length = 228

 Score =  119 bits (298), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 45/223 (20%), Positives = 93/223 (41%), Gaps = 2/223 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           RV   ++  G  +R E ++ +    + +N   +   ++     D I+++G  L       
Sbjct: 7   RVDAHLSSLGYCTRSEAKKFLRMNEICINDNRVYNTSIKAYHDD-IKINGEVLDDETLLI 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L    +        S     S +         ++ ++GRLDI+T G++LLT+DG L+  L
Sbjct: 66  LLNKPQGYICSHNDSGKLIYSLLPQRYSRRNPKISTIGRLDIDTTGVILLTDDGVLSHRL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     ++Y       +  D++ +   G ++       +         +  +V + + 
Sbjct: 126 TSPKKDISKIYEATLEKPLKGDEVEIFASGTLMLNGEEKPLLPAKLEI-ITPTFVKIEIV 184

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           EGK  ++K++F   + KV +L R  +  F+L  L  G  + + 
Sbjct: 185 EGKYHQVKRMFAAVSNKVIKLHRTKFADFELEDLKEGEFKIIK 227


>gi|254481482|ref|ZP_05094726.1| conserved hypothetical protein, putative [marine gamma
           proteobacterium HTCC2148]
 gi|214038110|gb|EEB78773.1| conserved hypothetical protein, putative [marine gamma
           proteobacterium HTCC2148]
          Length = 238

 Score =  119 bits (298), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 56/243 (23%), Positives = 101/243 (41%), Gaps = 9/243 (3%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW 76
            ++++  G   R+EV  ++AQ R+ ++G   +     V     + +D   L+  +   + 
Sbjct: 2   DRLVSERGGVHRKEVRLLLAQGRIHIDGRPADSINQAVGPFTRVTLDARVLQANKARYVM 61

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L+     +V+   D   ++ +        S +  VGRLD N+ GL+LLTNDG  +R L  
Sbjct: 62  LHKPSG-VVSATRDKQHKTVIDLLSVPYSSELHIVGRLDFNSTGLMLLTNDGRWSRSLSD 120

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLK--KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           P     + YRV     +D   +           +G+     ++ +           V L 
Sbjct: 121 PQNNIAKTYRVLLEKALDDSYVKAFADGMYFDFEGVTTRPAELRIL----GQYEAEVDLI 176

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHLLEEA 253
           EG+  +IK++F  F+ +V  L R S G   +      G  RE++   L + LG      +
Sbjct: 177 EGRYHQIKRMFGRFDNRVKALHRTSVGSLSMAAGPALGQWRELTLSEL-DLLGLEHCCLS 235

Query: 254 QVN 256
              
Sbjct: 236 PTE 238


>gi|330817442|ref|YP_004361147.1| Pseudouridine synthase, Rsu [Burkholderia gladioli BSR3]
 gi|327369835|gb|AEA61191.1| Pseudouridine synthase, Rsu [Burkholderia gladioli BSR3]
          Length = 736

 Score =  119 bits (298), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 62/251 (24%), Positives = 100/251 (39%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V    +IE+D          
Sbjct: 488 VRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPEQNIEIDQRAQAAQAAQ 547

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y   + L+T  +   G  +     P     +   GRLDI++
Sbjct: 548 VTILLHKPVGYVSGQAEDGYEPAVTLITRENHWSGDHSALRFSPQHLRTLAPAGRLDIDS 607

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT DG +A+ L    +   + Y VR                + L  L+ G+ + G
Sbjct: 608 TGLLVLTQDGRIAKQLIGEQSDIDKEYLVRVRFGERLTDIDQHFPAESLAKLRHGLELDG 667

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                  V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 668 APLKPAMVSWQNGEQ----LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGHVMLGALP 723

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 724 QGEWRYLSPDE 734



 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 12/106 (11%), Positives = 27/106 (25%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
             +    +    P   +      +P   ++ P         +++  G    K  A     
Sbjct: 18  APVRSGSLAGRKPTRPAPLDPATKPKPSAKRPAGAKSAAPRAAKPAGAGAVKPRAPRDGE 77

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           R          G   +       R+ +    P+   +R   R   +
Sbjct: 78  RGGFGRPPREGGDRPARDGARFSRDGDRPARPARDGERGAFRGEGR 123



 Score = 37.9 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 11/109 (10%), Positives = 20/109 (18%), Gaps = 2/109 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +   G                      RD        P      +             + 
Sbjct: 47  KRPAGAKSAAPRAAKPAGAGAVKPRAPRDGERGGFGRPPREGGDRPARDGARFSRDGDRP 106

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDS--GQREENHRRSPSFPSKRSLR 348
           A P       +     +   +        G R       P+ P++   R
Sbjct: 107 ARPARDGERGAFRGEGRPARTGGDRPPRDGARFSRDGDRPARPARDGER 155



 Score = 37.5 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 12/111 (10%), Positives = 19/111 (17%), Gaps = 2/111 (1%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P      +                R        D     +            ++ A   
Sbjct: 61  KPAGAGAVKPRAPRDGERGGFGRPPREGGDRPARDGARFSRDGDRPARPARDGERGAFRG 120

Query: 306 HRRNLASNVWMAK--GIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             R   +        G   S   D   R        SF  +    R    +
Sbjct: 121 EGRPARTGGDRPPRDGARFSRDGDRPARPARDGERGSFRGEGRPAREGGDR 171



 Score = 37.5 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 9/105 (8%), Positives = 18/105 (17%)

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
                  + +   +  E                      +   +     ++       R 
Sbjct: 145 RPARPARDGERGSFRGEGRPAREGGDRPPRDGARFSRDGDRPARPARDGERGSFRGEGRP 204

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                     G   S   D   R        SF  +    R   +
Sbjct: 205 ARDGERPPRDGARFSRDGDRPARPARDSERGSFRGEGRPTRDGER 249



 Score = 37.5 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 11/111 (9%), Positives = 24/111 (21%), Gaps = 6/111 (5%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             L P    +      A   S+           +  P      ++    +       + A
Sbjct: 34  APLDPATKPKPSAKRPAGAKSAAPRAAKPAGAGAVKPRAPRDGERGGFGRPPREGGDRPA 93

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               R +   +            +  G+        P+        R  A+
Sbjct: 94  RDGARFSRDGDRPARPARDGERGAFRGEG------RPARTGGDRPPRDGAR 138



 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 10/103 (9%), Positives = 20/103 (19%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           +          +       RP           +     + K    +  +           
Sbjct: 29  KPTRPAPLDPATKPKPSAKRPAGAKSAAPRAAKPAGAGAVKPRAPRDGERGGFGRPPREG 88

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +     G   S   D   R        +F  +    RT   +
Sbjct: 89  GDRPARDGARFSRDGDRPARPARDGERGAFRGEGRPARTGGDR 131



 Score = 37.5 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 14/102 (13%), Positives = 22/102 (21%), Gaps = 1/102 (0%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
           +   D    S     R   +      D     +            ++ A     R     
Sbjct: 344 RPARDGERGSFRGEGRPTRDGERPPRDGARFSRDGDRPARPARDGERSAFRGEGRPTRDG 403

Query: 314 VWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               + G   S   D   R        SF  +    R S  +
Sbjct: 404 ERPPRDGARFSRDGDRPARPARDGERGSFRGEGRPARDSGNR 445



 Score = 36.7 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 14/123 (11%), Positives = 22/123 (17%), Gaps = 3/123 (2%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE   +  R+        +                  RP    E P            + 
Sbjct: 166 REGGDRPPRDGARFSRDGDRPARPARDGERGSFRGEGRPARDGERPPRDGARFSRDGDRP 225

Query: 294 GLSKQKKLATPVHRRNLASNVWMAK---GIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
               +             +         G   S   D   R        SF  +    R 
Sbjct: 226 ARPARDSERGSFRGEGRPTRDGERPPRDGARFSRDGDRPARPARDGERGSFRGEGRPTRD 285

Query: 351 SAK 353
             +
Sbjct: 286 GER 288



 Score = 36.7 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 11/115 (9%), Positives = 19/115 (16%), Gaps = 3/115 (2%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+        +                  RP    E P            +     +   
Sbjct: 291 RDGARFSRDGDRPARPARDGERGSFRGEGRPTRDGERPPRDGARFSRDGDRPARPARDGE 350

Query: 302 ATPVHRRNLASNVWMAK---GIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                     +         G   S   D   R        +F  +    R   +
Sbjct: 351 RGSFRGEGRPTRDGERPPRDGARFSRDGDRPARPARDGERSAFRGEGRPTRDGER 405



 Score = 36.3 bits (82), Expect = 7.1,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 18/112 (16%), Gaps = 2/112 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+   P                                      +     ++G     + 
Sbjct: 101 RDGDRPARPARDGERGAFRGEGRPARTGGDRPPRDGARFSRDGDRPARPARDGERGSFRG 160

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                R           G   S   D   R        SF  +    R   +
Sbjct: 161 EGRPAREGGDRPPRD--GARFSRDGDRPARPARDGERGSFRGEGRPARDGER 210



 Score = 35.9 bits (81), Expect = 8.5,   Method: Composition-based stats.
 Identities = 12/115 (10%), Positives = 19/115 (16%), Gaps = 3/115 (2%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+        +                  RP    E P            +     +   
Sbjct: 252 RDGARFSRDGDRPARPARDGERGSFRGEGRPTRDGERPPRDGARFSRDGDRPARPARDGE 311

Query: 302 ATPVHRRNLASNVWMAK---GIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                     +         G   S   D   R        SF  +    R   +
Sbjct: 312 RGSFRGEGRPTRDGERPPRDGARFSRDGDRPARPARDGERGSFRGEGRPTRDGER 366



 Score = 35.9 bits (81), Expect = 8.6,   Method: Composition-based stats.
 Identities = 12/115 (10%), Positives = 19/115 (16%), Gaps = 3/115 (2%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+        +                  RP    E P            +     +   
Sbjct: 213 RDGARFSRDGDRPARPARDSERGSFRGEGRPTRDGERPPRDGARFSRDGDRPARPARDGE 272

Query: 302 ATPVHRRNLASNVWMAK---GIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                     +         G   S   D   R        SF  +    R   +
Sbjct: 273 RGSFRGEGRPTRDGERPPRDGARFSRDGDRPARPARDGERGSFRGEGRPTRDGER 327



 Score = 35.9 bits (81), Expect = 8.9,   Method: Composition-based stats.
 Identities = 12/107 (11%), Positives = 25/107 (23%), Gaps = 1/107 (0%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              +  +     P               S   D   R  ++  +     + +   T   R
Sbjct: 72  APRDGERGGFGRPPREGGDRPARDGARFSRDGDRPARPARDGERGAFRGEGRPARTGGDR 131

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREE-NHRRSPSFPSKRSLRRTSAK 353
                  +   G   +  +  G+R        P+        R  A+
Sbjct: 132 PPRDGARFSRDGDRPARPARDGERGSFRGEGRPAREGGDRPPRDGAR 178



 Score = 35.9 bits (81), Expect = 10.0,   Method: Composition-based stats.
 Identities = 14/107 (13%), Positives = 22/107 (20%), Gaps = 4/107 (3%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS---KQKKLA 302
           G                      RD             R   +   ++G        + A
Sbjct: 128 GGDRPPRDGARFSRDGDRPARPARDGERGSFRGEGRPAREGGDRPPRDGARFSRDGDRPA 187

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDS-GQREENHRRSPSFPSKRSLR 348
            P       S     +           G R       P+ P++ S R
Sbjct: 188 RPARDGERGSFRGEGRPARDGERPPRDGARFSRDGDRPARPARDSER 234


>gi|171911201|ref|ZP_02926671.1| ribosomal large subunit pseudouridine synthase B [Verrucomicrobium
           spinosum DSM 4136]
          Length = 345

 Score =  119 bits (297), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 68/317 (21%), Positives = 131/317 (41%), Gaps = 7/317 (2%)

Query: 34  MIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           M+   RV +NG +    +  V  +D + VDG  +R  +   + L+     + +   + D 
Sbjct: 1   MVRDGRVILNGKICTNLSTTVTDSDDVVVDGNKVRPHKGVVIVLHKPRGLVCSRRDERDR 60

Query: 94  RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
            +  +  LP  F  +  VGRLD  +EGLLL+TN G +++ L  PS    + Y V    + 
Sbjct: 61  DTI-YSLLPEKFHTLHHVGRLDKESEGLLLMTNRGEVSQRLLHPSQGVEKEYEVILETRF 119

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           D + L  L KG   +       +  +      +  + + L++G  R+I+ +  F  ++V 
Sbjct: 120 DPENLTRLTKGFHTEDGYAKAERAWMI----GDYKIGMVLKQGLKRQIRMMLYFLGYEVK 175

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPN 273
           RL+R+  G   +  +L G+ +E+S K + + L   L ++          S    +     
Sbjct: 176 RLVRVRIGNLAIKGILEGNWKELSDKDVDKMLLNPLAKDRPKMSKPKTASVRKSLEIHRQ 235

Query: 274 IISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREE 333
             ++     T  +K +   +  S     ++    R  ++    A+G      S  G+  +
Sbjct: 236 KEAKRSSRKTGARKRTGGTSPASGAGAGSSFGGDRGQSAGEGAARGPR--GGSIRGRERD 293

Query: 334 NHRRSPSFPSKRSLRRT 350
              +    P   S  R+
Sbjct: 294 GGSKGSRGPKSESGPRS 310


>gi|121593595|ref|YP_985491.1| ribosomal small subunit pseudouridine synthase A [Acidovorax sp.
           JS42]
 gi|120605675|gb|ABM41415.1| ribosomal small subunit pseudouridine synthase A [Acidovorax sp.
           JS42]
          Length = 245

 Score =  119 bits (297), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 51/245 (20%), Positives = 92/245 (37%), Gaps = 21/245 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVN--GI----LLERAAVNVM-STDHIEVDGVP 66
            ++  ++   G  +RR    +I Q RV ++  G     + + A  ++      + V GV 
Sbjct: 1   MQLQDILYSQGFGTRRICAGLIQQGRVAIHATGTLEPTICQDATQDIDVEGLVLRVQGVD 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGR-------STVFDNLPSIFSRVISVGRLDINTE 119
                R  + L+       +                            V +VGRLD +T 
Sbjct: 61  WPYQPRAYVMLHKPAGTECSQKPSAYPSIYTLLPAPLRQRPSKGSVDGVQAVGRLDQDTT 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQV 177
           GLLLL++DG     +  P     +VYRV     V +++++ L +G+V+            
Sbjct: 121 GLLLLSDDGQFIHRMSSPKKHVPKVYRVTAKHPVTKEQIDRLLEGVVLDDDPRPVRAAAC 180

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
            L         + + L EGK  ++K++      +V  L R   G   L   +  G  R +
Sbjct: 181 ALVDA----HVLDLTLTEGKYHQVKRMIAAVGNRVEALHRSHIGRLALPADMQPGEWRWL 236

Query: 237 SKKIL 241
            ++ L
Sbjct: 237 GEEEL 241


>gi|225847909|ref|YP_002728072.1| ribosomal small subunit pseudouridine synthase A
           [Sulfurihydrogenibium azorense Az-Fu1]
 gi|225644186|gb|ACN99236.1| putative ribosomal small subunit pseudouridine synthase A
           [Sulfurihydrogenibium azorense Az-Fu1]
          Length = 200

 Score =  119 bits (297), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 43/190 (22%), Positives = 78/190 (41%), Gaps = 4/190 (2%)

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            D + V+   +   E     L      +  T+ +         +  ++  ++  +GRLD+
Sbjct: 2   KDKVSVEDEDVNYQENFYFMLNKPLGYITATYDENFPTVISLLDDETVKDKLFPIGRLDL 61

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYG 173
           +TEGLL+LT DG LA  L  P     + Y     G V +   +  +K  +          
Sbjct: 62  DTEGLLILTTDGQLAHRLAHPKWNIEKEYYAIVEGDVSKIDFSPFEKEGIYLKKDKYKTK 121

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGS 232
             +V + +     + V + + EGK   +KK+ E     V  L R+  G  +L   L  G 
Sbjct: 122 PFKVKVLSALEEESKVLITVSEGKYHIVKKIMESLGHPVKYLKRVRMGNLKLDENLQPGD 181

Query: 233 TREVSKKILR 242
            R ++++ +R
Sbjct: 182 YRPLTEEEIR 191


>gi|82523723|emb|CAI78504.1| S4 domain protein [uncultured beta proteobacterium]
          Length = 240

 Score =  119 bits (297), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 54/242 (22%), Positives = 97/242 (40%), Gaps = 17/242 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+SK +A     SRRE E++I    V+V+G+++E     V ++  IE+D       
Sbjct: 2   TDSIRLSKRVAELRACSRREAEQIITGGWVRVDGVVIEEPQFRV-ASQRIEIDPQADPSQ 60

Query: 71  ERTRLWLYHKPIGLVTTHSD------------PDGRSTVFDNLPSIFSRVISVGRLDINT 118
                 L HKP G+  +  D             +   T    L + F+++ +   L+ + 
Sbjct: 61  IEPVTLLLHKPAGVRISDDDKTALQLLRADSLWEHDGTGISPLKAHFTQLTACVPLEADA 120

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GL++ T D  + R L   +        V   G++  + L  L KGI   G     ++V+
Sbjct: 121 SGLVVFTQDWRIVRKLTDDAATLEHEVIVEVSGELIPNGLKRLNKGIPYHGHTPAAIKVS 180

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              +      + V L+  +  +I  + E    +V  + RI  G   L  +  G  R + +
Sbjct: 181 WQNE----TRLRVALKGCQIGQIAHLCEAVGLQVVSMKRIRLGGIPLAKVPPGQWRYMRE 236

Query: 239 KI 240
             
Sbjct: 237 DE 238


>gi|264677343|ref|YP_003277249.1| Pseudouridine synthase, Rsu [Comamonas testosteroni CNB-2]
 gi|262207855|gb|ACY31953.1| Pseudouridine synthase, Rsu [Comamonas testosteroni CNB-2]
          Length = 248

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 48/244 (19%), Positives = 87/244 (35%), Gaps = 17/244 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG------ILLERAAVNVMS-TDHIEVDGVP 66
            ++  ++   G   RR    ++ Q  V++          +  +   V        V GV 
Sbjct: 1   MQLQDMLYSQGFGIRRVCSGLVQQGWVELWNPQTSDWEKVLDSTQQVDPEGLRFRVQGVE 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGR-------STVFDNLPSIFSRVISVGRLDINTE 119
               E   + L        +                            V +VGRLD +T 
Sbjct: 61  WEYHELGYVLLNKPAGTECSQKPSAYPSIYTLLPAPLRQRPNKGAVQGVQAVGRLDQDTT 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLL++DG     +  P     +VYRV     VD  ++  L  G+V+       ++   
Sbjct: 121 GMLLLSDDGQFIHRMSSPKKHVSKVYRVTCKHPVDAKQIQRLLDGVVLDDDP-KPVR-AA 178

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
             ++  +  + + L EGK  ++K++    + +V  L R   G  +L   L  G  R ++ 
Sbjct: 179 ACEQVDSHVLDLTLTEGKYHQVKRMIAAVSNRVEGLHRRRIGGMELPAELEPGQWRWLTA 238

Query: 239 KILR 242
             L 
Sbjct: 239 DELE 242


>gi|289677286|ref|ZP_06498176.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. syringae FF5]
          Length = 208

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 70/205 (34%), Positives = 96/205 (46%), Gaps = 8/205 (3%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG         V   D I
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDAT-LGQRVDLHDAI 62

Query: 61  EVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            VDG  +++ E     R  +        + T        +           R I++GRLD
Sbjct: 63  SVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           INT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++       
Sbjct: 123 INTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPARFT 182

Query: 176 QVTLDT-QKGSNAWVTVGLREGKNR 199
            +      +G N W    + EG+NR
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNR 207


>gi|113868037|ref|YP_726526.1| 16S rRNA uridine-516 pseudouridylate synthase [Ralstonia eutropha
           H16]
 gi|113526813|emb|CAJ93158.1| 16S rRNA uridine-516 pseudouridylate synthase [Ralstonia eutropha
           H16]
          Length = 583

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 63/255 (24%), Positives = 100/255 (39%), Gaps = 32/255 (12%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I    V V+G  +      +     IE+           
Sbjct: 331 VRLSKRMSELGLCSRREADEWIPHGWVLVDGKPVTELGSRIRPDAEIEIMQEARSEQGER 390

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     L T  +  +G  T     P     +   GRLDI++
Sbjct: 391 VTVLLNKPVGYVSGQAEDGYEPAAVLFTPENQWEGDPTRKRFAPWQRKSLAPAGRLDIDS 450

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------------DKLNLLKKGI 165
            GLL+LT DG +AR L    +   + Y VR      Q             D L LL+ G+
Sbjct: 451 TGLLVLTQDGRVARALIGEDSTVEKEYLVRVIWHSPQGVVERNISAEFPADDLELLRHGL 510

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G+     +V+   ++     +   LREG+ R+I+++ E    +V  L R+  G   L
Sbjct: 511 SLDGVPLKPAKVSWQNEEQ----LRFVLREGRKRQIRRMCEQVGLQVVGLKRVRMGRVVL 566

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R + +  
Sbjct: 567 GDLPPGKWRFLGQFE 581



 Score = 36.3 bits (82), Expect = 7.8,   Method: Composition-based stats.
 Identities = 9/103 (8%), Positives = 18/103 (17%), Gaps = 1/103 (0%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
             +              R      S  P           +  G   + +       R   
Sbjct: 178 RGEARPRRFEGGEARPPRRFEGGDSRPPRRAGEDNNRPRRFEGAESRPRRVGDDENRPRR 237

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSF-PSKRSLRRTSAK 353
                ++        +  +R E     P          R +  
Sbjct: 238 FEGADSRPRRYGDDENRPRRFEGADSRPRRYGDDDQRPRPAPS 280


>gi|330504052|ref|YP_004380921.1| RNA-binding S4 domain-containing protein [Pseudomonas mendocina
           NK-01]
 gi|328918338|gb|AEB59169.1| RNA-binding S4 domain-containing protein [Pseudomonas mendocina
           NK-01]
          Length = 245

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 47/237 (19%), Positives = 85/237 (35%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+SK +      SRRE +  I    V V+G ++E     V       + G  L   
Sbjct: 11  SEPTRLSKRVIELFGCSRREADLYITGGWVTVDGQVVEAPQFKVKDQRVELLPGASLEPV 70

Query: 71  ERTRLWLYHKPI-------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           E   L ++            L+   +  +        L   F R      L     GL++
Sbjct: 71  EPVTLLVHCPAGSNAAQLQHLLARENHWEEDPHAQRILHGHFLRQEQSLPLQHGASGLVI 130

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           L+ D    R L     +  + Y V   G++       LKKG+  +G  +   + +  +++
Sbjct: 131 LSQDWRAQRKLREDGAKLEQEYLVDVTGELPASTFERLKKGLAHKGTQFPPCKASWQSEQ 190

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   L+      ++++ +    +VN + RI  G   +  L  G  R +  K 
Sbjct: 191 R----LRFALKNPAPDLLQQICKALGLQVNAMKRIRVGGVPMAKLPVGQWRYLGDKE 243


>gi|241662940|ref|YP_002981300.1| RNA-binding S4 domain-containing protein [Ralstonia pickettii 12D]
 gi|240864967|gb|ACS62628.1| RNA-binding S4 domain protein [Ralstonia pickettii 12D]
          Length = 627

 Score =  118 bits (295), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 62/261 (23%), Positives = 100/261 (38%), Gaps = 32/261 (12%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---- 63
            E+    R+SK ++  G+ SRRE +  I +  V V+G  +      V     IE+     
Sbjct: 369 TESSGLVRLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVKPDAIIEIHQSAR 428

Query: 64  -----------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
                        P+          Y   + L    +  +G  T     P     +   G
Sbjct: 429 SEQGERVTVLMHKPVGYVSGQAEDGYQPAVSLFVPENQWEGDPTRKRFAPWQRRALAPAG 488

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-------------VDQDKLN 159
           RLDI++ GLL+LT DG +AR L    +   + Y VR                   ++ + 
Sbjct: 489 RLDIDSTGLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWHSPDGVVEHDISKVFPEELME 548

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
            L+ G+ + G      +V+   ++     +   LREGK R+I+++ E    +V  L RI 
Sbjct: 549 KLRFGLSLDGEALKPAKVSWQNEEQ----LRFVLREGKKRQIRRMCEQVGLEVVGLKRIR 604

Query: 220 YGPFQLGTLLAGSTREVSKKI 240
            G   LG L  G  R +    
Sbjct: 605 MGSIVLGDLPVGQWRFLGPFE 625



 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 10/109 (9%), Positives = 25/109 (22%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P  ++  +               D         D+    +           ++      
Sbjct: 112 KPRRMQGDRPPRRFDDERPPRRFSDEQRSPRRSDDERPPRRFEDRPPRRFDDERPPRRFD 171

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           + R              S      +R ++ R       +R+ RR   ++
Sbjct: 172 NDRPPRRFDDERPPRRFSDDQRPPRRFDDERPRRYGDDQRAPRRDGDQR 220



 Score = 37.9 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 14/119 (11%), Positives = 29/119 (24%), Gaps = 1/119 (0%)

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G TRE   + ++    P   ++ +               D         D   R   +  
Sbjct: 106 GQTREAKPRRMQGDRPPRRFDDERPPRRFSDEQRSPRRSDDERPPRRFEDRPPRRFDDER 165

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                   +        R         +     F  +  +R  + +R+P     +   R
Sbjct: 166 PPRRFDNDRPPRRFDDERPPRRFSDDQRPPR-RFDDERPRRYGDDQRAPRRDGDQRPPR 223



 Score = 36.3 bits (82), Expect = 7.7,   Method: Composition-based stats.
 Identities = 10/115 (8%), Positives = 27/115 (23%), Gaps = 3/115 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS---KQK 299
           +   P    + +              R          DD    +++  Q+       ++ 
Sbjct: 171 DNDRPPRRFDDERPPRRFSDDQRPPRRFDDERPRRYGDDQRAPRRDGDQRPPRRFDEERP 230

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                  +R                     +R ++         +R+ RR   ++
Sbjct: 231 PRRFNDEQRPPRRFDEERPPRKFGDDQRPPRRFDDEGPRRYGDDQRAPRRDGDQR 285


>gi|221052937|ref|XP_002257843.1| pseudouridine synthetase [Plasmodium knowlesi strain H]
 gi|193807675|emb|CAQ38379.1| pseudouridine synthetase, putative [Plasmodium knowlesi strain H]
          Length = 328

 Score =  118 bits (295), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 61/265 (23%), Positives = 110/265 (41%), Gaps = 37/265 (13%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R++K+I+     SRR+ +  I    VK+N  +++    ++  S D I++ G  +     
Sbjct: 56  VRLNKIISMEKKISRRKSDEFIKDGNVKLNNKVVKNPGTHIDVSKDKIKISGKLVNIVRT 115

Query: 73  TRLWL------------YHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINT 118
            ++              +     L T++ + D  S             R++SVGRLD NT
Sbjct: 116 QKMINRNDNNFYKWFVLHKPKGFLCTSNDEKDRASIYSLFPQDIMDNYRLVSVGRLDRNT 175

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------- 169
            G+LLLTN+      L  P  Q +R YRV   G      L  L  GI +Q          
Sbjct: 176 SGVLLLTNEYAWVNKLTHPKYQRIRTYRVHIEGPAQMKVLKQLATGIYLQDDNRGKENKK 235

Query: 170 ----ICYGDMQVTLDTQKGSN--------AWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
                      + +  ++           + + + +REG+NR+I+K+FE  N  V ++ R
Sbjct: 236 IVKKKRTQPAFIEILREETIKVKDQVKKVSVLNISVREGRNRQIRKMFEQINQPVIKIKR 295

Query: 218 ISYGPFQLGTL-LAGSTREVSKKIL 241
            ++    L  +      RE++++ +
Sbjct: 296 TAFENITLKDVFFPKQYRELTQREI 320


>gi|167757241|ref|ZP_02429368.1| hypothetical protein CLORAM_02791 [Clostridium ramosum DSM 1402]
 gi|167703416|gb|EDS17995.1| hypothetical protein CLORAM_02791 [Clostridium ramosum DSM 1402]
          Length = 235

 Score =  118 bits (295), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 47/212 (22%), Positives = 81/212 (38%), Gaps = 8/212 (3%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSD 90
            + +I    ++VN  ++      V + D I    + L         +      L   H  
Sbjct: 24  CKTLIRHGEIRVNDQVITDVRYPVKADDIIMYHHIQLNAQPFVYYMMNKPADYLCANHDK 83

Query: 91  PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
                               +GRLDI+T GLL++TND  L++ L LP     + Y V   
Sbjct: 84  YHQCVID----LIGREDCYCLGRLDIDTTGLLIITNDTSLSKKLLLPQNHVNKKYYVTTK 139

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             +  + +     G+VI          +L         + V + EG+  +IKK+F+    
Sbjct: 140 FPLKDELIKKFFDGVVIDHKV--QCLPSLLEILDEYHCL-VTINEGRYHQIKKMFKSCQN 196

Query: 211 KVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           +V  L RI++   +L   L  G  R+++   L
Sbjct: 197 EVCTLKRIAFAGIELDQKLALGEYRDLTSTEL 228


>gi|309782139|ref|ZP_07676869.1| ribosomal large subunit pseudouridine synthase F [Ralstonia sp.
           5_7_47FAA]
 gi|308919205|gb|EFP64872.1| ribosomal large subunit pseudouridine synthase F [Ralstonia sp.
           5_7_47FAA]
          Length = 613

 Score =  118 bits (295), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 62/261 (23%), Positives = 100/261 (38%), Gaps = 32/261 (12%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---- 63
            E+    R+SK ++  G+ SRRE +  I +  V V+G  +      V     IE+     
Sbjct: 355 TESSGLVRLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVKPDAIIEIHQSAR 414

Query: 64  -----------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
                        P+          Y   + L    +  +G  T     P     +   G
Sbjct: 415 SEQGERVTVLMHKPVGYVSGQAEDGYQPAVSLFVPENQWEGDPTRKRFAPWQRRALAPAG 474

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-------------VDQDKLN 159
           RLDI++ GLL+LT DG +AR L    +   + Y VR                   ++ + 
Sbjct: 475 RLDIDSTGLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWHSPDGVVEHDISKVFPEELME 534

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
            L+ G+ + G      +V+   ++     +   LREGK R+I+++ E    +V  L RI 
Sbjct: 535 KLRFGLSLDGEALKPAKVSWQNEEQ----LRFVLREGKKRQIRRMCEQVGLEVVGLKRIR 590

Query: 220 YGPFQLGTLLAGSTREVSKKI 240
            G   LG L  G  R +    
Sbjct: 591 MGSIVLGDLPVGQWRFLGPFE 611



 Score = 37.9 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 14/119 (11%), Positives = 29/119 (24%), Gaps = 1/119 (0%)

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G TRE   + ++    P   ++ +               D         D   R   +  
Sbjct: 92  GQTREAKPRRMQGDRPPRRFDDERPPRRFNDEQRSPRRSDDERPPRRFEDRPPRRFDDER 151

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                   +        R         +     F  +  +R  + +R+P     +   R
Sbjct: 152 PPRRFDNDRPPRRFDDERPPRRFSDDQRPPR-RFDDERPRRYGDDQRAPRRDGDQRPPR 209



 Score = 37.9 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 10/109 (9%), Positives = 25/109 (22%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P  ++  +               D         D+    +           ++      
Sbjct: 98  KPRRMQGDRPPRRFDDERPPRRFNDEQRSPRRSDDERPPRRFEDRPPRRFDDERPPRRFD 157

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           + R              S      +R ++ R       +R+ RR   ++
Sbjct: 158 NDRPPRRFDDERPPRRFSDDQRPPRRFDDERPRRYGDDQRAPRRDGDQR 206



 Score = 37.5 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 11/115 (9%), Positives = 27/115 (23%), Gaps = 3/115 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS---KQK 299
           +   P    + +              R          DD    +++  Q+       ++ 
Sbjct: 157 DNDRPPRRFDDERPPRRFSDDQRPPRRFDDERPRRYGDDQRAPRRDGDQRPPRRFDEERP 216

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                  RR                     +R ++         +R+ RR   ++
Sbjct: 217 PRRFNDERRPPRRFDEERPPRKFGDDQRPPRRFDDEGPRRYGDDQRAPRRDGDQR 271


>gi|94310374|ref|YP_583584.1| pseudouridine synthase, Rsu [Cupriavidus metallidurans CH34]
 gi|93354226|gb|ABF08315.1| 16S rRNA uridine-516 pseudouridylate synthase [Cupriavidus
           metallidurans CH34]
          Length = 610

 Score =  118 bits (295), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 62/262 (23%), Positives = 101/262 (38%), Gaps = 33/262 (12%)

Query: 4   KNIVQENFTP-QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +  V E+     R+SK ++  G+ SRRE +  I +  V V+G  +      +     IE+
Sbjct: 347 RQPVSEHEDGLVRLSKRMSELGLCSRREADEWIPRGWVLVDGKPVTELGTRIRPEAEIEI 406

Query: 63  ---------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                             P+          Y     L    +  +   T     P     
Sbjct: 407 LQAARSEQGERVTVLLNKPVGYVSGQAEDGYEPAAVLFAPENQWELDPTRKRFAPWQRKN 466

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-------------VD 154
           +   GRLDI++ GLL+LT DG +AR L    +   + Y VR   +               
Sbjct: 467 LAPAGRLDIDSTGLLVLTQDGRVARALIGDDSNVEKEYLVRVEWESPQGLVERNISAVFP 526

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
            D L  L+ G+ + G+     +V+   ++     +   LREG+ R+I+++ E    KV  
Sbjct: 527 DDLLERLRHGLSLDGVALKPAKVSWQNEEQ----LRFVLREGRKRQIRRMCEQVGLKVVG 582

Query: 215 LIRISYGPFQLGTLLAGSTREV 236
           L R+  G   LG L  G  R +
Sbjct: 583 LKRVRMGRVVLGDLPPGQWRFL 604



 Score = 35.9 bits (81), Expect = 9.8,   Method: Composition-based stats.
 Identities = 13/115 (11%), Positives = 25/115 (21%), Gaps = 2/115 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R        ++ +          +   R R     E P    R   ++            
Sbjct: 121 RPAQPRRYGDDNRAERPRRFSDEDRAARPRRFGDEERPQRERRYGDDNRPAQPRRYGDDN 180

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK--RSLRRTSAKK 354
                RR    N   +            +R       P+ P +     R    ++
Sbjct: 181 RAERPRRFSDENRAASPRRFGDEERPQRERRYGDDNRPAQPRRYGDDNRAERPRR 235


>gi|115376490|ref|ZP_01463724.1| ribosomal large subunit pseudouridine synthase B [Stigmatella
           aurantiaca DW4/3-1]
 gi|310819631|ref|YP_003951989.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|115366493|gb|EAU65494.1| ribosomal large subunit pseudouridine synthase B [Stigmatella
           aurantiaca DW4/3-1]
 gi|309392703|gb|ADO70162.1| Pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 264

 Score =  118 bits (295), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 66/241 (27%), Positives = 109/241 (45%), Gaps = 11/241 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           +++ + RAG+  ++E E+ I   RVKV G L       V    ++ VDG   R      +
Sbjct: 29  LARALGRAGVMPQQEAEQAIRDGRVKVEGRLELEPFAPVRLGSNVFVDGWAHRLEAPLHV 88

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLP------SIFSRVISVGRLDINTEGLLLLTNDGG 129
            ++HKP G++   +DP+GR TVF+ L              +VGRLD +T GLLL TND  
Sbjct: 89  LMFHKPEGVIVAGTDPEGRGTVFERLRAVLPPDMRNFEWYAVGRLDRDTTGLLLFTNDER 148

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           + +    P     + Y  +  G+  ++ L  L++GIV++          L   +     V
Sbjct: 149 VVQHGTSPDKHLPKRYVAQVAGKPSEETLARLREGIVLEDGPTRPAGARLLAPE----CV 204

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L EG++ ++K++       V  L R + G   L  +  G  R +S   +   LG   
Sbjct: 205 ELVLTEGRHHQVKRMLAAVGHPVRTLHRQAVGTVSL-DVPVGDWRSLSPGEVTGGLGFQA 263

Query: 250 L 250
            
Sbjct: 264 P 264


>gi|66044638|ref|YP_234479.1| RNA-binding S4 [Pseudomonas syringae pv. syringae B728a]
 gi|63255345|gb|AAY36441.1| RNA-binding S4 [Pseudomonas syringae pv. syringae B728a]
          Length = 236

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 51/238 (21%), Positives = 90/238 (37%), Gaps = 13/238 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLR 68
             P R+SK +      SRRE E  I    V V+G ++E     V  T  IE+  D     
Sbjct: 2   TDPIRLSKRLIELVGCSRREAELFIEGGWVTVDGEVIEEPHFKVS-TQKIELSPDAKADS 60

Query: 69  KAERTRLWLYHKPI------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
               T +              ++T  +     S     L   F R+ ++  L  N  GL+
Sbjct: 61  PEPVTIILHKPASASAEEALQMITPGTLSVEHSYSKRPLKGHFMRLEAISSLQANASGLM 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + + D  + R L    ++  + Y V   G++    LN L  G+  +G     ++ +   +
Sbjct: 121 VFSQDWKILRKLTDDRSKIEQEYVVEISGEMAAHGLNRLNHGLTYKGKELPAVKASWQNE 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
               + +   ++  +   I  + E    K+  + RI  G   +G L  G  R ++ K 
Sbjct: 181 ----SRLRFAMKNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRYMTAKE 234


>gi|237735675|ref|ZP_04566156.1| pseudouridine synthase [Mollicutes bacterium D7]
 gi|229381420|gb|EEO31511.1| pseudouridine synthase [Coprobacillus sp. D7]
          Length = 235

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 47/212 (22%), Positives = 81/212 (38%), Gaps = 8/212 (3%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSD 90
            + +I    ++VN  ++      V + D I    + L         +      L   H  
Sbjct: 24  CKTLIRHGEIRVNDQVITDVRYPVKADDIIMYHHIQLNAQPFVYYMMNKPADYLCANHDK 83

Query: 91  PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
                               +GRLDI+T GLL++TND  L++ L LP     + Y V   
Sbjct: 84  YHQCVID----LIGREDCYCLGRLDIDTTGLLIITNDTSLSKKLLLPQNHVNKKYYVTTK 139

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             +  + +     G+VI          +L         + V + EG+  +IKK+F+    
Sbjct: 140 FPLKDELIKKFSDGVVIDHKV--QCLPSLLEILDEYHCL-VTINEGRYHQIKKMFKSCQN 196

Query: 211 KVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           +V  L RI++   +L   L  G  R+++   L
Sbjct: 197 EVCTLKRIAFAGIELDQKLALGEYRDLTSTEL 228


>gi|222110316|ref|YP_002552580.1| pseudouridine synthase [Acidovorax ebreus TPSY]
 gi|221729760|gb|ACM32580.1| pseudouridine synthase [Acidovorax ebreus TPSY]
          Length = 245

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 49/247 (19%), Positives = 91/247 (36%), Gaps = 21/247 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRV------KVNGILLERAAVNVM-STDHIEVDGVP 66
            ++  ++   G  +RR    +I Q RV       +   + + A  ++   +  + V GV 
Sbjct: 1   MQLQDILYSQGFGTRRICAGLIQQGRVAMHATGTLEPTICQDATQDIDVESLVLRVQGVD 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGR-------STVFDNLPSIFSRVISVGRLDINTE 119
                +  + L+       +                            V +VGRLD +T 
Sbjct: 61  WPYQPKAYVMLHKPAGTECSQKPSAYPSIYTLLPAPLRQRPSKGAVDGVQAVGRLDQDTT 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQV 177
           GLLLL++DG     +  P     +VYRV     V +++++ L  G+V+            
Sbjct: 121 GLLLLSDDGQFIHRMSSPKKHVPKVYRVTAKHPVTKEQVDRLLAGVVLDDDPRPVRAAAC 180

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
            L         + + L EGK  ++K++      +V  L R   G   L   +  G  R +
Sbjct: 181 ALVDA----HVLDLTLTEGKYHQVKRMIAAVGNRVEALHRSHIGRLALPADMQPGEWRWL 236

Query: 237 SKKILRE 243
            ++ L +
Sbjct: 237 GEEELAQ 243


>gi|258420276|ref|ZP_05683224.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9719]
 gi|257843739|gb|EEV68140.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9719]
          Length = 200

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 63/198 (31%), Positives = 105/198 (53%), Gaps = 3/198 (1%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
             +D IEV+G+ +   E     L+HKP  ++T+ SD  GR+ V D    I +R+  VGRL
Sbjct: 2   KPSDTIEVEGIKIEL-EDKIYILFHKPTQVITSVSDDRGRTVVTDYFKDIEARIYPVGRL 60

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D +T GLLLLTNDG    ++  P  Q  + Y  +  G + ++++  L+KGI ++      
Sbjct: 61  DYDTSGLLLLTNDGEFTNLMTHPRYQIKKKYVAKLKGYLMREEVKALEKGIELEDGMTQP 120

Query: 175 MQVTLDTQKG--SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
            +V +  Q    +   V + + EG+NR+++++FE F  +V +L RI YGP  +  L AG 
Sbjct: 121 AEVKVKKQDKDKNTTLVEITITEGRNRQVRRMFEHFGHQVTKLSRIEYGPLNVVGLNAGE 180

Query: 233 TREVSKKILREQLGPHLL 250
            R ++   ++        
Sbjct: 181 GRVLTPHEVKVMRHLAEH 198


>gi|124801447|ref|XP_001349696.1| pseudouridine synthase, putative [Plasmodium falciparum 3D7]
 gi|3845303|gb|AAC71967.1| pseudouridine synthase, putative [Plasmodium falciparum 3D7]
          Length = 338

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 64/293 (21%), Positives = 119/293 (40%), Gaps = 57/293 (19%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
            E+    R++K+I+     SRR+ +  I   +VK+N  ++     +V    D + +    
Sbjct: 40  NEDANIIRLNKLISMKRNISRRKSDEFIKDGKVKINNKIITNPGTHVHIGKDSLRIYDKK 99

Query: 67  LRK-----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVG 112
           ++             +  +  + HKP GL+ T +D   R +++           R+++VG
Sbjct: 100 IKLTNIINMIKQNENKLHKWIVLHKPKGLLCTSNDEKNRKSIYTLFPEEMLQKYRLVTVG 159

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGIC 171
           RLD NT G+LLLTND      L  P  Q +R YRV   G V  + L  L +GI + +   
Sbjct: 160 RLDRNTSGVLLLTNDYAWVNKLTHPKYQRIRTYRVHIEGPVKMNALKELARGIYLEEDEK 219

Query: 172 YGDMQVTLDTQKGSNA----------------------------------------WVTV 191
               ++    +    +                                         + +
Sbjct: 220 TQPKKIYNYKESREKSNIDDKKKKKMSKMKKKTNPAFIEILREEKIKIKEDTKKITVLNI 279

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL-AGSTREVSKKILRE 243
            ++EG+NR+I+K+F+  N  V ++ R S+    L  +      RE+++K + +
Sbjct: 280 SIKEGRNRQIRKMFQQINQPVIKIKRTSFENITLKNIYFPKQYRELNQKEVND 332


>gi|70728627|ref|YP_258376.1| S4 domain-containing protein [Pseudomonas fluorescens Pf-5]
 gi|68342926|gb|AAY90532.1| S4 domain protein [Pseudomonas fluorescens Pf-5]
          Length = 236

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 50/238 (21%), Positives = 85/238 (35%), Gaps = 13/238 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+SK +      SRRE E  I    V V+G +++     V +   + +D      A
Sbjct: 2   TDPIRLSKRLIELVGCSRREAELFIEGGWVTVDGEVIDEPQFKVGA-QTVALDPEAKATA 60

Query: 71  ERTRLWLYHKPIGLVTTHSDP--------DGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
                 L + P G     +          +        L   F R+ +   L  N  GLL
Sbjct: 61  PEPVTILLNVPAGQDLDSAMQSIGADSLSEEHRYGKRPLRGHFLRLTASDDLQPNASGLL 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + T D  + R L     +  + Y V   G++    LN L  G+  +G     ++ +   +
Sbjct: 121 VFTQDWKVLRKLTADVAKIEQEYVVEVEGEMIDHGLNRLNHGLTYKGRELPPVKASWQNE 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 +   ++  +   I    +    KV  + RI  G   +G +  G  R +S K 
Sbjct: 181 NR----LRFAMKNPQPGVIALFCQAVGLKVVAIRRIRVGGVSIGKVPLGQWRYLSAKE 234


>gi|217978386|ref|YP_002362533.1| pseudouridine synthase [Methylocella silvestris BL2]
 gi|217503762|gb|ACK51171.1| pseudouridine synthase [Methylocella silvestris BL2]
          Length = 255

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 50/232 (21%), Positives = 91/232 (39%), Gaps = 7/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST----DHIEVDGVPLRKA 70
           R+ +++A  G  +R +++ M    R+K++G  L   A+ V +T      + ++G  L   
Sbjct: 12  RLDRLLANLGYGTRTQMQAMAHAGRIKLDGAALRDPALRVAATPEFCARLSINGEALDPP 71

Query: 71  ERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               + L        +           +          + +VGRLD +T GLLL+T+DG 
Sbjct: 72  PGMVIALNKPRGVTCSRKEAGPLVFDLLPPRFRLREPALSTVGRLDKDTSGLLLITDDGA 131

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     + Y  +    +  D+  +   G ++       +   +     S    
Sbjct: 132 LLHRLISPKHNIAKRYCAKLARPLRGDEAEIFASGEMMLDDEAKPLLPAVLRV-LSPTEA 190

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            V + EG+  +I+++F      V  L R+S G F L  TL  G    +    
Sbjct: 191 EVSVTEGRYHQIRRMFAATGNHVLELHRMSIGDFALPLTLAPGDFLLLRASE 242


>gi|254522077|ref|ZP_05134132.1| ribosomal small subunit pseudouridylate synthase [Stenotrophomonas
           sp. SKA14]
 gi|219719668|gb|EED38193.1| ribosomal small subunit pseudouridylate synthase [Stenotrophomonas
           sp. SKA14]
          Length = 233

 Score =  117 bits (293), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 57/239 (23%), Positives = 100/239 (41%), Gaps = 11/239 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVK-VNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            ++ K IA  G  SR++V+ M  + RV   +G +L  A   V   + I VDG PL     
Sbjct: 1   MKLVKHIANLGYGSRKQVQWMFREGRVTDADGEVLY-ADDQV-PHEAIRVDGEPLDPPVG 58

Query: 73  TRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             + L+       +   +       +          + +VGRLD  T GLLLLT+DGGL 
Sbjct: 59  LSIALHKPAGYTCSTKDTGRLIYDLLPPRFRDRDPVLSTVGRLDRETSGLLLLTDDGGLL 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GIVIQGICY--GDMQVTLDTQKGSNAW 188
             +  P ++  +VY V     +  D++ L     ++++         ++ +   + +   
Sbjct: 119 HRIISPKSKLPKVYEVELSEDLRGDEVALFASGTLMLESEKTPLLPAELEVLDARRA--- 175

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
             + L EG+  +++++F      V  L R   G   L  L  G  R+++   L     P
Sbjct: 176 -RLVLHEGRYHQVRRMFAATGNHVQALHRSRVGGLDLQGLDEGQWRQLTSTDLDTLFAP 233


>gi|224004838|ref|XP_002296070.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|209586102|gb|ACI64787.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 365

 Score =  117 bits (293), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 92/295 (31%), Positives = 145/295 (49%), Gaps = 16/295 (5%)

Query: 2   KDKNIVQEN----FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS- 56
           K K+I   N        R++ ++ +    SRR+ ERM+   RV + G +++  +    + 
Sbjct: 63  KRKDITNTNLSNGTEGVRITTLLCKHLGLSRRQSERMVLLGRVTLFGKVVDSPSFEFSAS 122

Query: 57  TDH----IEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-----SIFS 106
           TD     I+VDG  +    + TR+WL +K  G + T  DPDGR ++   L       + +
Sbjct: 123 TDEGEIAIKVDGRLIYGAEKTTRVWLANKLKGELITEDDPDGRPSMLQRLKANGTKHLPT 182

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
            +  VGRLD+ TEGL++ +NDG  AR LELPS    R YRVR HG++   KL  ++KG+ 
Sbjct: 183 HLKPVGRLDMMTEGLMIFSNDGQYARNLELPSNHLWRTYRVRVHGRLTLGKLTAMRKGVT 242

Query: 167 IQGICYGDMQVTLDTQKGS-NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           ++G     +Q T     GS N W+ +   EGKNR+++++       V RLIRISYG + L
Sbjct: 243 VRGASGEVVQSTGKDVNGSTNTWLQITCTEGKNRQLRRILGSMGLDVTRLIRISYGDYDL 302

Query: 226 GTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
            ++  G   EV  K L        + + +        +     + R +    V  
Sbjct: 303 NSIPPGLAIEVPVKPLESMKKKGSVGKIEETTRDKGGTRFDRRQKRNDGEEGVRS 357


>gi|289674640|ref|ZP_06495530.1| RNA-binding S4 [Pseudomonas syringae pv. syringae FF5]
          Length = 236

 Score =  117 bits (293), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 51/238 (21%), Positives = 89/238 (37%), Gaps = 13/238 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLR 68
             P R+SK +      SRRE E  I    V V+G ++E     V  T  IE+  D     
Sbjct: 2   TDPIRLSKRLIELVGCSRREAELFIEGGWVTVDGEVIEEPHFKVS-TQKIELSPDAKADS 60

Query: 69  KAERTRLWLYHKPI------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
               T +              ++T  +     S     L   F R+ ++  L  N  GL+
Sbjct: 61  PEPVTIILHKPASASAEEALQMITPGTLSVDHSYSKRPLKGHFMRLEAISSLQANASGLM 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + + D  + R L    ++  + Y V   G++    LN L  G+  +G     ++ +   +
Sbjct: 121 VFSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKGKELPAVKASWQNE 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 +   ++  +   I  + E    K+  + RI  G   +G L  G  R ++ K 
Sbjct: 181 NR----LRFAMKNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRYMTAKE 234


>gi|326316292|ref|YP_004233964.1| pseudouridine synthase Rsu [Acidovorax avenae subsp. avenae ATCC
           19860]
 gi|323373128|gb|ADX45397.1| pseudouridine synthase Rsu [Acidovorax avenae subsp. avenae ATCC
           19860]
          Length = 248

 Score =  117 bits (293), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 53/249 (21%), Positives = 95/249 (38%), Gaps = 18/249 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKV---NGI----LLERAAVNVMS-TDHIEVDGV 65
            ++ +++   G  +RR    +I    V++   N      +   A++++        V G 
Sbjct: 1   MQLQEILYSQGFGTRRVCAGLIQHGHVQLRKKNDTGDAWVCTDASLDIDPEGLTFHVQGK 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDG-------RSTVFDNLPSIFSRVISVGRLDINT 118
             +  ER  + +        +                      P     V ++GRLD +T
Sbjct: 61  VWQWHERAYVMMNKPAAVECSQKPSTYPSVYTLLPDPLRQRPGPGKILGVQTIGRLDQDT 120

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLLL++DG     +  P  Q  + YRV     + Q + + L KG+V+       +   
Sbjct: 121 TGLLLLSDDGSFIHRVSSPKKQIQKTYRVHAKYDLSQQQKDQLLKGVVLNDDPKPVIAAD 180

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
              Q+G  +   + + EGK  +IK++      +V +L RI  G   L   L AG  R + 
Sbjct: 181 CVLQEG--SVFDLTVTEGKYHQIKRMVAAVGNRVEQLHRIRIGGLHLPDDLQAGDWRWLG 238

Query: 238 KKILREQLG 246
              +R    
Sbjct: 239 DDDVRRIFE 247


>gi|213969165|ref|ZP_03397304.1| S4 domain protein [Pseudomonas syringae pv. tomato T1]
 gi|301383941|ref|ZP_07232359.1| S4 domain protein [Pseudomonas syringae pv. tomato Max13]
 gi|302064174|ref|ZP_07255715.1| S4 domain protein [Pseudomonas syringae pv. tomato K40]
 gi|302134741|ref|ZP_07260731.1| S4 domain protein [Pseudomonas syringae pv. tomato NCPPB 1108]
 gi|213926163|gb|EEB59719.1| S4 domain protein [Pseudomonas syringae pv. tomato T1]
          Length = 236

 Score =  117 bits (293), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 51/238 (21%), Positives = 93/238 (39%), Gaps = 13/238 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+SK +      SRRE E  I    V V+G++++     V  T  IE+       +
Sbjct: 2   TDPIRLSKRLIELVGCSRREAELFIEGGWVTVDGVVIDEPHFKVS-TQKIELSPEAKADS 60

Query: 71  ERTRLWLYHKPI--------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
             +   + HKP          ++T  +     S     L   F R+ ++  L  N  GL+
Sbjct: 61  PESVTIILHKPASASAESALQMITPGTLSAEHSYSKRPLKGHFMRLEAISSLQANASGLM 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + + D  + R L    ++  + Y V   G++    LN L  G+  +G     ++ +   +
Sbjct: 121 VFSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKGKELPAVKASWQNE 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 +   ++  +   I  + E    K+  + RI  G   +G L  G  R ++ K 
Sbjct: 181 NR----LRFAMKNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRYMTTKE 234


>gi|241765880|ref|ZP_04763813.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
 gi|241364178|gb|EER59374.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
          Length = 249

 Score =  117 bits (293), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 49/244 (20%), Positives = 88/244 (36%), Gaps = 18/244 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRV-KVNGIL------LERAAVNVMSTD-HIEVDGV 65
            ++  ++   G  +RR    ++ Q  V   +G           A+      D  ++V GV
Sbjct: 1   MQLQDILYSQGFGTRRVCAGLVQQGWVETASGDPDAAFSACTEASAEFDVDDLRLKVQGV 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGR-------STVFDNLPSIFSRVISVGRLDINT 118
                 +  + L+       +                            V +VGRLD +T
Sbjct: 61  LWPYHAKAYIMLHKPAGTECSQKPSTYPSIYTLLPAPLRQRPCKGAIQGVQAVGRLDQDT 120

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLLL++DG     +  P     +VY+V     VD+ ++  L  G+V+       ++  
Sbjct: 121 TGLLLLSDDGQFIHRMSSPKKHVPKVYQVTTKHPVDERQIAALLAGVVLDDDP-KPVR-A 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
                  +  +++ L EGK  ++K++      +V  L R   G   L   L  G    +S
Sbjct: 179 AACSVVDSHRLSLTLTEGKYHQVKRMLAAVGNRVEALHRSRIGTLDLPADLAPGQWLWLS 238

Query: 238 KKIL 241
              L
Sbjct: 239 DADL 242


>gi|330936760|gb|EGH40926.1| RNA-binding S4 [Pseudomonas syringae pv. pisi str. 1704B]
 gi|330968912|gb|EGH68978.1| RNA-binding S4 [Pseudomonas syringae pv. aceris str. M302273PT]
 gi|330975346|gb|EGH75412.1| RNA-binding S4 [Pseudomonas syringae pv. aptata str. DSM 50252]
          Length = 236

 Score =  117 bits (293), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 51/238 (21%), Positives = 89/238 (37%), Gaps = 13/238 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLR 68
             P R+SK +      SRRE E  I    V V+G ++E     V  T  IE+  D     
Sbjct: 2   TDPIRLSKRLIELVGCSRREAELFIEGGWVTVDGEVIEEPHFKVS-TQKIELSPDAKADS 60

Query: 69  KAERTRLWLYHKPI------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
               T +              ++T  +     S     L   F R+ ++  L  N  GL+
Sbjct: 61  PEPVTIILHKPASASAEEALQMITPGTLSVEHSYSKRPLKGHFMRLEAISSLQANASGLM 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + + D  + R L    ++  + Y V   G++    LN L  G+  +G     ++ +   +
Sbjct: 121 VFSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKGKELPAVKASWQNE 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 +   ++  +   I  + E    K+  + RI  G   +G L  G  R ++ K 
Sbjct: 181 NR----LRFAMKNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRYMTAKE 234


>gi|146319594|ref|YP_001199306.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Streptococcus suis 05ZYH33]
 gi|145690400|gb|ABP90906.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           Pseudouridylate synthase [Streptococcus suis 05ZYH33]
          Length = 233

 Score =  117 bits (293), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 52/200 (26%), Positives = 84/200 (42%), Gaps = 4/200 (2%)

Query: 48  ERAAVNVMST-DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
                 +    D I V G  L         L      +  T  D         +  +   
Sbjct: 26  TSPKQQINEKKDQIAVAGQVLSHETFVYYLLNKPKGVISATEDDHHRTVLDLLDNTARQK 85

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
            V  VGRLDI+T GLLLLTN G LA  +  P     ++YR +  G + Q+ +     GI 
Sbjct: 86  EVFPVGRLDIDTHGLLLLTNKGQLAHAMLSPKKHVDKLYRAQVDGIMTQEDVERFAAGIE 145

Query: 167 IQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
           ++       Q+T+ +   +   + V + +REGK  +IK++ +     V  L R++ GP +
Sbjct: 146 LKDFTCQPAQLTILSTDEAKQTSLVDITIREGKFHQIKRMVQACGKTVTDLQRLTMGPLR 205

Query: 225 LG-TLLAGSTREVSKKILRE 243
           L   L  G  R ++   L++
Sbjct: 206 LDPKLALGEYRRLTAAELKQ 225


>gi|116515110|ref|YP_802739.1| YciL [Buchnera aphidicola str. Cc (Cinara cedri)]
 gi|116256964|gb|ABJ90646.1| ribosomal large subunit pseudouridine synthase B [Buchnera
           aphidicola str. Cc (Cinara cedri)]
          Length = 243

 Score =  117 bits (293), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 74/242 (30%), Positives = 119/242 (49%), Gaps = 8/242 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLR 68
           +++ K+++  G+ SRR +E+ I  + +K+NG ++      +     I+        + ++
Sbjct: 3   EKIQKILSNCGVDSRRNIEKHILNKSLKINGKIVHIGERFLKKN--IKSIFLKKKKIFIK 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             +   L  +     + T     +  +         FS+ IS+GRLDINT GLLL TN G
Sbjct: 61  NEKTKILIYHKPVGEICTKKDQYNRITVFKKLPKLFFSKWISIGRLDINTSGLLLFTNFG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  R Y V   G++ + K+ LLKKGI+I        ++    +K  N W
Sbjct: 121 ELAHRLMHPSYRIKREYLVCVLGKILKKKILLLKKGILINNSISKFHEIIFLKKKKKNQW 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGP 247
             V L +GKNRE++ ++   N KVNRLIRI +G   L   L +G   E+S +  +  L  
Sbjct: 181 FKVSLFQGKNREVRLLWNAINIKVNRLIRIKFGIITLPKFLKSGCFFELSYQKTKNILSL 240

Query: 248 HL 249
             
Sbjct: 241 VN 242


>gi|302187180|ref|ZP_07263853.1| RNA-binding S4 [Pseudomonas syringae pv. syringae 642]
          Length = 236

 Score =  117 bits (293), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 51/238 (21%), Positives = 90/238 (37%), Gaps = 13/238 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLR 68
             P R+SK +      SRRE E  I    V V+G ++E     V  T  IE+  D     
Sbjct: 2   TDPIRLSKRLIELVGCSRREAELFIEGGWVTVDGEVIEEPHFKVS-TQKIELSPDAKADS 60

Query: 69  KAERTRLWLYHKPI------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
               T +              ++T  +     S +   L   F R+ ++  L  N  GL+
Sbjct: 61  PEPVTIILHKPASASAEEALQMITPGTLSVEHSYIKRPLKGHFMRLEAISSLQANASGLM 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + + D  + R L    ++  + Y V   G++    LN L  G+  +G     ++ +   +
Sbjct: 121 VFSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKGKELPAVKASWQNE 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 +   ++  +   I  + E    K+  + RI  G   +G L  G  R ++ K 
Sbjct: 181 NR----LRFAMKNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRYMTAKE 234


>gi|330950630|gb|EGH50890.1| RNA-binding S4 [Pseudomonas syringae Cit 7]
          Length = 236

 Score =  117 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 51/238 (21%), Positives = 89/238 (37%), Gaps = 13/238 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLR 68
             P R+SK +      SRRE E  I    V V+G ++E     V  T  IE+  D     
Sbjct: 2   TDPIRLSKRLIELVGCSRREAELFIEGGWVTVDGEVIEEPHFKVS-TQKIELSPDAKADA 60

Query: 69  KAERTRLWLYHKPI------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
               T +              ++T  +     S     L   F R+ ++  L  N  GL+
Sbjct: 61  PEPVTIILHKPASASAEEALQMITPGTLSVEHSYSKRPLKGHFMRLEAISSLQANASGLM 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + + D  + R L    ++  + Y V   G++    LN L  G+  +G     ++ +   +
Sbjct: 121 VFSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKGKELPAVKASWQNE 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 +   ++  +   I  + E    K+  + RI  G   +G L  G  R ++ K 
Sbjct: 181 NR----LRFAMKNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRYMTAKE 234


>gi|330959244|gb|EGH59504.1| S4 domain-containing protein [Pseudomonas syringae pv. maculicola
           str. ES4326]
          Length = 236

 Score =  117 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 50/238 (21%), Positives = 90/238 (37%), Gaps = 13/238 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLR 68
             P R+SK +      SRRE E  I    V V+G+++E     V  T  +E+  D     
Sbjct: 2   TDPIRLSKRLIELVGCSRREAELFIEGGWVTVDGVVIEEPHFKVS-TQKVELSPDAKADS 60

Query: 69  KAERTRLWLYHKPI------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
               T +              ++T  +  +  S     L   F R+  +  L  N  GL+
Sbjct: 61  PEAVTIILHKPASASAESALQMITPGTLSEEHSYSKRPLKGHFMRLEPISSLQANASGLM 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + + D  + R L    ++  + Y V   G +    LN L  G+  +G     ++ +   +
Sbjct: 121 VFSQDWKILRKLTDDRSKIEQEYVVEITGDMVAHGLNRLNHGLTYKGKELPAVKASWQNE 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 +   ++  +   I ++ E    K+  + RI  G   +G L  G  R ++ K 
Sbjct: 181 NR----LRFAMKNPQPGIIAQLCEAVGLKIVSIRRIRIGGVSMGKLPEGQWRYMTSKE 234


>gi|312959321|ref|ZP_07773838.1| ribosomal large subunit pseudouridine synthase F [Pseudomonas
           fluorescens WH6]
 gi|311286038|gb|EFQ64602.1| ribosomal large subunit pseudouridine synthase F [Pseudomonas
           fluorescens WH6]
          Length = 235

 Score =  117 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 52/238 (21%), Positives = 82/238 (34%), Gaps = 14/238 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+SK +      SRRE E  I    V V+G +++     V  T  +E+D       
Sbjct: 2   TDPIRLSKRLIELVGCSRREAELFIEGGWVSVDGEVIDEPQFKVT-TQKVELDPEAKATV 60

Query: 71  ERTRLWLYHKPIGLV--------TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
                 L H P G+         +  +  +        L   F R+ +   L     GLL
Sbjct: 61  PEPVTILLHAPAGVDAETAMASISAETLSEEHRFSKRPLKGHFLRLTASADLQAKASGLL 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + T D  + R L   + +  + Y V   G +    LN L  G+  +G             
Sbjct: 121 VFTQDWKILRKLTADAAKIEQEYVVEVEGDMVAHGLNRLNHGLTYKGKEL-----XXXXX 175

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 +   ++  +   I    E    KV  + RI  G   +G +  G  R +S K 
Sbjct: 176 XXXXNRLRFAMKNPQPGVIALFCEAVGLKVVAIRRIRIGGVSIGKVPVGQWRYLSGKE 233


>gi|126640866|ref|YP_001083850.1| putative ribosomal large subunit pseudouridine synthase B
           [Acinetobacter baumannii ATCC 17978]
          Length = 279

 Score =  117 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 69/281 (24%), Positives = 111/281 (39%), Gaps = 13/281 (4%)

Query: 41  KVNGILLERAAVNVMSTDHIEVDGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRS 95
            VNG + +     +   D + +DG  ++        R  L  Y     + + +      +
Sbjct: 2   SVNGRVAQV-GERIEPGDELRIDGRKVQFQIEDEIRRRVLIYYKPEGEICSRNDPEKRPT 60

Query: 96  TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
                      R + VGRLDIN+ GLLL TNDG LA  L  PS +  R Y VR  G+V  
Sbjct: 61  VFDHLPQIANDRWVMVGRLDINSTGLLLFTNDGELANRLMHPSNEIEREYAVRVMGEVTP 120

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRL 215
                +  G+ ++         +    +G N W  V ++EG+NRE++++FE    KV+RL
Sbjct: 121 QLRQNMVNGVELEDGPAKFESFSEIGGEGINRWYQVVVKEGRNREVRRIFESQGLKVSRL 180

Query: 216 IRISYGPFQL-GTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNI 274
           +R  YG   L   L  G   E+ K  +          ++             + + R   
Sbjct: 181 LRTRYGTVILPRELRTGRWMELDKTDIDNL------AKSVELKPRQGTGLFGMAKRRTER 234

Query: 275 ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW 315
           ++E P    R      Q+    K+    T   R++   N  
Sbjct: 235 MTEKPMAARRGGYLRQQRRDDEKEAPANTGNQRKSTGFNRG 275


>gi|313678357|ref|YP_004056097.1| RNA pseudouridine synthase family protein [Mycoplasma bovis PG45]
 gi|312950302|gb|ADR24897.1| RNA pseudouridine synthase family protein [Mycoplasma bovis PG45]
          Length = 236

 Score =  117 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 106/231 (45%), Gaps = 9/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K IA     SR EV+  + ++ +KVNGI+L +  + +    D++EVD V ++  + 
Sbjct: 4   IRIEKFIADLTGLSRNEVKAKLKKKAIKVNGIVLSKL-IKIDPESDYVEVDNVVVKYEKF 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                      +       +   T+FD +     +  S GRLD +TEGLL+L+NDG +  
Sbjct: 63  QYYMFNKPANFVCANSDPNEA--TIFDIVGLPNKKFFSFGRLDKDTEGLLILSNDGEMCH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V+   +++ D L   +   +         +  L+     + ++   
Sbjct: 121 KLLSPKNHIPKKYYVKVDKKINSDVLLNNRPIKISDDFIVS--KYELEPIDEKSCFL--T 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           + EGK  ++K++F  F   V  L R+ +G  +L   L  G  R++S+  + 
Sbjct: 177 IYEGKFHQVKRMFGAFGISVLYLKRVQFGNLKLDNSLKLGEIRKLSELEVE 227


>gi|315185613|gb|EFU19381.1| pseudouridine synthase [Spirochaeta thermophila DSM 6578]
          Length = 214

 Score =  117 bits (292), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 65/204 (31%), Positives = 95/204 (46%), Gaps = 6/204 (2%)

Query: 41  KVNGILLERAAVNVMS-TDHIEVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVF 98
           +VNG ++   A  V    D + +DG  +    +   L  +  P  L T            
Sbjct: 2   RVNGRVITNPAHRVDPQEDRVTLDGRDVHLVGKFLYLAFHKPPGYLCTRSDPQGRPLVYD 61

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
              P +  +V S+GRLD  + GLLLLTNDG  A ++  P  +  + Y V     + +  L
Sbjct: 62  LIDPVLPYKVFSIGRLDFLSSGLLLLTNDGEFADIVMHPKHRVEKEYLVETKRPIPRALL 121

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
               KGI I+G  Y    V    +  S   V + L EGKNREI+KVF   +  + R+ RI
Sbjct: 122 ESYLKGIRIEGERY----VLKAYKSKSPHKVHLILEEGKNREIRKVFYSSHLPIVRIHRI 177

Query: 219 SYGPFQLGTLLAGSTREVSKKILR 242
             GP +LG L  G  R ++K+ +R
Sbjct: 178 RIGPVRLGRLRPGHFRNLTKEEIR 201


>gi|251792414|ref|YP_003007140.1| hypothetical protein NT05HA_0650 [Aggregatibacter aphrophilus
           NJ8700]
 gi|247533807|gb|ACS97053.1| hypothetical protein NT05HA_0650 [Aggregatibacter aphrophilus
           NJ8700]
          Length = 254

 Score =  117 bits (292), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 74/253 (29%), Positives = 112/253 (44%), Gaps = 10/253 (3%)

Query: 43  NGILLERAA-VNVMSTDHIEVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRST 96
           +G +      +NV S+  + +DG  +   +        L  Y     L T H      + 
Sbjct: 2   DGKIATLGDRINVHSSVKVRIDGNLINLTQAQKEVCRVLMYYKPEGELCTRHDPEGRATV 61

Query: 97  VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
                    +R I+VGRLDINT GLLL T DG LA  L  P+ +  R Y VR  G VD  
Sbjct: 62  FDRLPRLTGARWIAVGRLDINTSGLLLFTTDGELANRLMHPNREVEREYSVRVFGHVDDA 121

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
            LN LKKG+ ++        +      G N W  V L EG+NRE+++++E    +V+RLI
Sbjct: 122 MLNRLKKGVQLEDGPANFKDIKFGGGVGMNQWFDVTLMEGRNREVRRLWESQGIQVSRLI 181

Query: 217 RISYGPFQL-GTLLAGSTREVSKKI---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRP 272
           RI YG  +L  TL  G  +E+       LR+ +G     E +++++     S+     + 
Sbjct: 182 RIRYGNIKLMKTLPRGGWQEMPLDEVNYLRDLVGLAPETETKLDVNKQRRQSKAGQIRKA 241

Query: 273 NIISEVPDDFTRM 285
                      + 
Sbjct: 242 VKRYSELSRRYKK 254


>gi|194289795|ref|YP_002005702.1| 16S rRNA uridine-516 pseudouridylate synthase [Cupriavidus
           taiwanensis LMG 19424]
 gi|193223630|emb|CAQ69637.1| putative 16S rRNA uridine-516 pseudouridylate synthase [Cupriavidus
           taiwanensis LMG 19424]
          Length = 607

 Score =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 58/255 (22%), Positives = 97/255 (38%), Gaps = 32/255 (12%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
            R+SK ++  G+ SRRE +  I +  V V+G  +      +     IE+           
Sbjct: 355 VRLSKRMSELGLCSRREADEWIPRGWVLVDGKPVTELGSRIRPDAEIEILQEARSEQGER 414

Query: 63  ----DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     L    +  +G  T     P     +   GRLDI++
Sbjct: 415 VTVLLNKPVGYVSGQAEDGYEPAAALFAPENQWEGDPTRKRFAPWQRKNLAPAGRLDIDS 474

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL-------------LKKGI 165
            GLL+LT DG +AR L    +   + Y VR         +               L+ G+
Sbjct: 475 TGLLVLTQDGRVARALIGEDSTVEKEYLVRVVWHSPHGPVERNISAEFPADDLELLRHGL 534

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G+     +V+   ++     +   LREG+ R+I+++ E    +V  L R+  G   L
Sbjct: 535 SLDGVPLKPAKVSWQNEEQ----LRFVLREGRKRQIRRMCEQVGLQVVGLKRVRMGRVVL 590

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R + +  
Sbjct: 591 GDLPPGKWRFLGQFE 605



 Score = 37.1 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 7/114 (6%), Positives = 19/114 (16%), Gaps = 1/114 (0%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           + E +             +           +P        +     +         ++  
Sbjct: 45  VSEGIKRAQQRAGGKTGGSAAQGEAPAQPRQPRAPRPADSERQARPRRPDAGEARPRRFG 104

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                 RR                 S   +R  +    P             ++
Sbjct: 105 DDESRPRRYGDDRGEARPRRFEGSESRPPRRFGDDDNRPRRAG-DDRGEARPRR 157



 Score = 35.9 bits (81), Expect = 8.7,   Method: Composition-based stats.
 Identities = 12/111 (10%), Positives = 22/111 (19%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E                         R   +     P  F   +    ++ G    +   
Sbjct: 185 EARPRRFEGSESRPPRRYGDDDNRPRRTGDDRGEARPRRFESSESRPPRRYGDDDNRPRR 244

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           T   R       +           D  +R      + S P +       A+
Sbjct: 245 TGDDRGEPRPRRFEGADTRPRRFGDDDKRPRRFEGADSRPRRHGDDERRAR 295


>gi|289667011|ref|ZP_06488086.1| pseudouridylate synthase [Xanthomonas campestris pv. musacearum
           NCPPB4381]
          Length = 236

 Score =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 46/237 (19%), Positives = 87/237 (36%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+ K +A A   SR E ++ I    V V+G+++E       +      +   L  A
Sbjct: 2   SDPIRLDKCVAAAFGCSRGEAQQYIEGGWVSVDGVVVEEPQALATAGQVTLAEDAVLAPA 61

Query: 71  ERTRLWLYHKPI-------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           E   L L+            L T  +      +    L   F R+ +   L+    GLL+
Sbjct: 62  EPATLLLHKPAGVSAEAALALATPTTRSALYPSDIRVLKRHFLRLTAPLPLEDAASGLLI 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           L+ DG + R L   +    + + V    ++    +  L  G+V Q       +V+   + 
Sbjct: 122 LSQDGRVLRRLSAEARSIEQEFLVEVQCELRPYGMARLAHGLVYQQRSLSPCKVSWQNED 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   ++  +  +++ +      +V  + R+  G   LG L  G  R +    
Sbjct: 182 R----LRFAIKNVQPGQLRYMCGEVGLEVVNIRRLRVGRVSLGKLAIGQWRYLPTGE 234


>gi|160896898|ref|YP_001562480.1| RNA-binding S4 domain-containing protein [Delftia acidovorans
           SPH-1]
 gi|160362482|gb|ABX34095.1| RNA-binding S4 domain protein [Delftia acidovorans SPH-1]
 gi|222832645|gb|EEE71122.1| predicted protein [Populus trichocarpa]
          Length = 247

 Score =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 46/248 (18%), Positives = 77/248 (31%), Gaps = 20/248 (8%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPL 67
                 R++K +A     SRRE E  I    V+V+G +++     V     + +  G   
Sbjct: 2   SESESVRLAKRLAEQEQCSRREAELHITAGNVQVDGKVVQLPETRVRPEQQVTLRSGAQP 61

Query: 68  RKAERTRLWLYHKPIGLVTTH---------------SDPDGRSTVFDNLPSIFSRVISVG 112
                  L +                                      L   F  + S  
Sbjct: 62  EAVPPVTLLMNKPAGYTQGRPYGRVRSAHSLLGEASMAQVDTPMPLLVLAQHFKNLESFL 121

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
            L +   GL++ T D  +AR L        +   V   GQ+ +D L L+K G+ I     
Sbjct: 122 PLPLPASGLIVYTQDKRVARKLGEEGMWLEQECIVGVEGQIHEDGLELMKAGLPIGKRQL 181

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
              +V+   +      +   L+     EI  +      +V  L R+  G   L  +  G 
Sbjct: 182 PPCRVSWQNENH----LRFALKGIAPDEIDAMCTEVGLRVVSLRRLRIGRLSLAKVPEGQ 237

Query: 233 TREVSKKI 240
            R +    
Sbjct: 238 WRYLMPWE 245


>gi|257487032|ref|ZP_05641073.1| S4 domain-containing protein [Pseudomonas syringae pv. tabaci ATCC
           11528]
 gi|330894641|gb|EGH27302.1| S4 domain-containing protein [Pseudomonas syringae pv. mori str.
           301020]
 gi|331009326|gb|EGH89382.1| S4 domain-containing protein [Pseudomonas syringae pv. tabaci ATCC
           11528]
          Length = 236

 Score =  116 bits (290), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 51/238 (21%), Positives = 90/238 (37%), Gaps = 13/238 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLR 68
             P R+SK +      SRRE E  I    V V+G+++E     V  T  IE+  D     
Sbjct: 2   TDPIRLSKRLIELVGCSRREAELFIEGGWVTVDGVVIEEPHFKVS-TQKIELSPDAKANS 60

Query: 69  KAERTRLWLYHKPI------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
               T +              ++T  +     S     L   F R+ ++  L  N  GL+
Sbjct: 61  PEPVTIILHKPASASAEEALQMITPGTLSVEHSYSKRPLKGHFMRLEAISSLQANASGLM 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + + D  + R L    ++  + Y V   G++    LN L  G+  +G     ++ +   +
Sbjct: 121 VFSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKGKELPAVKASWQNE 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 +   ++  +   I  + E    K+  + RI  G   +G L  G  R ++ K 
Sbjct: 181 NR----LRFAMKNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRYMTTKE 234


>gi|237800196|ref|ZP_04588657.1| S4 domain-containing protein [Pseudomonas syringae pv. oryzae str.
           1_6]
 gi|331023053|gb|EGI03110.1| S4 domain-containing protein [Pseudomonas syringae pv. oryzae str.
           1_6]
          Length = 236

 Score =  116 bits (290), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 51/238 (21%), Positives = 92/238 (38%), Gaps = 13/238 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLR 68
             P R+SK +      SRRE E  I    V V+G+++E     V  T  IE+  D     
Sbjct: 2   TDPIRLSKRLIELVGCSRREAELFIEGGWVTVDGVVIEEPHFKVS-TQKIELSPDAKADS 60

Query: 69  KAERTRLWLYHKPI------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
               T +              ++T  +  +  S     L   F R+ ++  L  N  GL+
Sbjct: 61  PEPVTIILHKPASASAESALQMITPGTLSEEHSYSKRPLKGHFMRLEAISSLQANASGLM 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + + D  + R L    ++  + Y V   G++    LN L  G+  +G     ++ +   +
Sbjct: 121 VFSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKGKELPAVKASWQNE 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 +   ++  +   I ++ E    K+  + RI  G   +G L  G  R ++ K 
Sbjct: 181 NR----LRFAMKNPQPGIIAQLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRYMTTKE 234


>gi|289625988|ref|ZP_06458942.1| S4 domain-containing protein [Pseudomonas syringae pv. aesculi str.
           NCPPB3681]
 gi|289651496|ref|ZP_06482839.1| S4 domain-containing protein [Pseudomonas syringae pv. aesculi str.
           2250]
 gi|298488229|ref|ZP_07006264.1| S4 domain protein [Pseudomonas savastanoi pv. savastanoi NCPPB
           3335]
 gi|298157237|gb|EFH98322.1| S4 domain protein [Pseudomonas savastanoi pv. savastanoi NCPPB
           3335]
 gi|320323074|gb|EFW79163.1| S4 domain-containing protein [Pseudomonas syringae pv. glycinea
           str. B076]
 gi|320329654|gb|EFW85643.1| S4 domain-containing protein [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330868588|gb|EGH03297.1| S4 domain-containing protein [Pseudomonas syringae pv. aesculi str.
           0893_23]
 gi|330878026|gb|EGH12175.1| S4 domain-containing protein [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330985156|gb|EGH83259.1| S4 domain-containing protein [Pseudomonas syringae pv. lachrymans
           str. M301315]
          Length = 236

 Score =  116 bits (290), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 51/238 (21%), Positives = 90/238 (37%), Gaps = 13/238 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLR 68
             P R+SK +      SRRE E  I    V V+G+++E     V  T  IE+  D     
Sbjct: 2   TDPIRLSKRLIELVGCSRREAELFIEGGWVTVDGVVIEEPHFKVS-TQKIELSPDAKADS 60

Query: 69  KAERTRLWLYHKPI------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
               T +              ++T  +     S     L   F R+ ++  L  N  GL+
Sbjct: 61  PEPVTIILHKPASASAEEALQMITPGTLSVEHSYSKRPLKGHFMRLEAISSLQANASGLM 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + + D  + R L    ++  + Y V   G++    LN L  G+  +G     ++ +   +
Sbjct: 121 VFSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKGKELPAVKASWQNE 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 +   ++  +   I  + E    K+  + RI  G   +G L  G  R ++ K 
Sbjct: 181 NR----LRFAMKNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRYMTTKE 234


>gi|28871164|ref|NP_793783.1| S4 domain-containing protein [Pseudomonas syringae pv. tomato str.
           DC3000]
 gi|28854414|gb|AAO57478.1| S4 domain protein [Pseudomonas syringae pv. tomato str. DC3000]
 gi|330872678|gb|EGH06827.1| S4 domain-containing protein [Pseudomonas syringae pv. morsprunorum
           str. M302280PT]
 gi|330967892|gb|EGH68152.1| S4 domain-containing protein [Pseudomonas syringae pv. actinidiae
           str. M302091]
 gi|331016415|gb|EGH96471.1| S4 domain protein [Pseudomonas syringae pv. lachrymans str.
           M302278PT]
          Length = 236

 Score =  116 bits (289), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 50/238 (21%), Positives = 90/238 (37%), Gaps = 13/238 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLR 68
             P R+SK +      SRRE E  I    V V+G++++     V  T  IE+  D     
Sbjct: 2   TDPIRLSKRLIELVGCSRREAELFIEGGWVTVDGVVIDEPHFKVS-TQKIELSPDAKADS 60

Query: 69  KAERTRLWLYHKPI------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
               T +              ++T  +     S     L   F R+ ++  L  N  GL+
Sbjct: 61  PESVTIILHKPASASAESALQMITPGTLSAEHSYSKRPLKGHFMRLEAISSLQANASGLM 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + + D  + R L    ++  + Y V   G++    LN L  G+  +G     ++ +   +
Sbjct: 121 VFSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKGKELPAVKASWQNE 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 +   ++  +   I  + E    K+  + RI  G   +G L  G  R ++ K 
Sbjct: 181 NR----LRFAMKNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRYMTTKE 234


>gi|120610123|ref|YP_969801.1| ribosomal small subunit pseudouridine synthase A [Acidovorax
           citrulli AAC00-1]
 gi|120588587|gb|ABM32027.1| ribosomal small subunit pseudouridine synthase A [Acidovorax
           citrulli AAC00-1]
          Length = 253

 Score =  116 bits (289), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 54/247 (21%), Positives = 92/247 (37%), Gaps = 18/247 (7%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGI-------LLERAAVNVMS-TDHIEVDGVPL 67
           +  ++   G  +RR    +I    V++              A ++V        V G   
Sbjct: 8   LQDILYSQGFGTRRVCAGLIQHGHVQLREKGDAGGAWTCTDAGLDVDPEGLTFYVQGTAW 67

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDG-------RSTVFDNLPSIFSRVISVGRLDINTEG 120
           +  ER  + +        +                      P     V ++GRLD +T G
Sbjct: 68  QWHERAYVMMNKPAAVECSQKPSTYPSVYTLLPDPLRQRPGPGKILGVQTIGRLDQDTTG 127

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLLL++DG     +  P  Q  + YRV     + Q + + L KG+V+       + V   
Sbjct: 128 LLLLSDDGSFIHRVSSPKKQIQKTYRVHAKYDLSQQQKDQLLKGVVLNDDPKPVIAVDCV 187

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
            Q+G      + + EGK  +IK++      +V +L RI  G   L   L AG  R + ++
Sbjct: 188 LQEGP--VFDLTVTEGKYHQIKRMVAAVGNRVEQLHRIRIGGLHLPDDLQAGDWRWLREE 245

Query: 240 ILREQLG 246
            +R    
Sbjct: 246 DVRRIFE 252


>gi|145355350|ref|XP_001421926.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144582165|gb|ABP00220.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 287

 Score =  115 bits (288), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 52/223 (23%), Positives = 92/223 (41%), Gaps = 7/223 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG----ILLERAAVNVMSTDHIEVDGV 65
               +R+  +++R G+ SR +  R IA++ V  +G           +   + D + VDG 
Sbjct: 44  TAKAERLDALLSRLGLTSRADAARFIAERVVTTDGARATERATSGKLKARAAD-VRVDGE 102

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDG--RSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
            L   +   + ++     + +            + +        + SVGRLD +T GLLL
Sbjct: 103 TLEDVDGLLIVMHKARGVVCSHDVREGTSVYDALPERWRRRKPSIESVGRLDKDTSGLLL 162

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LT+DG L   L  P  +  + YRV+    + +D + +   G +         +  +    
Sbjct: 163 LTDDGALVHALTTPKKEIGKWYRVKTDRPIPRDAVEVFASGELTLDGETRACKPAVCELM 222

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
                  + L EGK  ++K++F FF   V  L R S+G   L 
Sbjct: 223 DDETEARLRLTEGKFHQVKRMFAFFGCTVIGLHRESFGSLTLE 265


>gi|303286517|ref|XP_003062548.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226456065|gb|EEH53367.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 230

 Score =  115 bits (288), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 53/229 (23%), Positives = 95/229 (41%), Gaps = 19/229 (8%)

Query: 25  IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGL 84
             SRR  +R++A   V VNG ++  A   V   D +E+ G  +R      +  +      
Sbjct: 9   FTSRRNADRLVASGAVTVNGAVVA-AGAMVFPGDVVELRGERVRWETLNYVKYWKPRGVT 67

Query: 85  VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV 144
            TT +     + + D +    +R+  VGRLD ++ GL+LLT+DG L         +  + 
Sbjct: 68  CTTDARDR--TNIVDAVNYPDARLFPVGRLDKDSTGLILLTSDGRLPNAALRSGRKRDKK 125

Query: 145 YRVRFHGQVDQDKLNLLKKGIVI------------QGICYGDMQVTLDTQKGSNAWVTVG 192
           Y V     V  + + +L+ G+VI                    ++ +         + + 
Sbjct: 126 YLVVVDAVVRPEDVRMLRDGVVISTPVQRDRVDRVLTARTLPCEIDVVGA----RTLEIT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           LREG+NR+I+++ +   ++V  L R       L     G   E  ++ L
Sbjct: 182 LREGRNRQIRRMLDAVGYRVINLHRTEIMGIGLRGTREGRWVECDEEEL 230


>gi|303275424|ref|XP_003057006.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226461358|gb|EEH58651.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 305

 Score =  115 bits (288), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 54/235 (22%), Positives = 99/235 (42%), Gaps = 9/235 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P+R+ ++++R G  +R E +R     RV ++G  + RA   V   D + +DG P    + 
Sbjct: 54  PERLDRLLSRLGYCTRAEAKRWARDGRVLLHGEPVARAEAKVTPRD-VLIDGEPAEAPDG 112

Query: 73  TRLWLYHKPIGLVTTH--SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               ++     +        P     + +   +    V ++GRLD +T GLLLLT+DG L
Sbjct: 113 LLALMHKPRGRVCGHDASEGPSVYDLLPERWRARRPGVETIGRLDKDTTGLLLLTDDGDL 172

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG----SN 186
              L  P  +  +VY +     + +D ++L   G +                      + 
Sbjct: 173 LHRLASPKKRVEKVYELVVDAPIPRDAVDLFASGSLTLTGEKKPCLPAKLIVSERADHNR 232

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKK 239
              ++ + EGK  ++K++      +V  L R S+G   L    L  G  R +S++
Sbjct: 233 TRASLSVTEGKFHQVKRMMRAVGCEVTALHRESFGGMALSRMELREGEVRVLSRE 287


>gi|107100561|ref|ZP_01364479.1| hypothetical protein PaerPA_01001586 [Pseudomonas aeruginosa PACS2]
 gi|218892926|ref|YP_002441795.1| hypothetical protein PLES_42111 [Pseudomonas aeruginosa LESB58]
 gi|313106072|ref|ZP_07792330.1| hypothetical protein PA39016_000160009 [Pseudomonas aeruginosa
           39016]
 gi|218773154|emb|CAW28966.1| hypothetical protein PLES_42111 [Pseudomonas aeruginosa LESB58]
 gi|310878832|gb|EFQ37426.1| hypothetical protein PA39016_000160009 [Pseudomonas aeruginosa
           39016]
          Length = 236

 Score =  115 bits (288), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 50/237 (21%), Positives = 85/237 (35%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+SK +A     SRRE E  I    V V+G ++E     V+      + G      
Sbjct: 2   TDPIRLSKRLAELTACSRREAELYIEGGWVSVDGEVIEEPQFKVLDQRVELLPGARAETI 61

Query: 71  ERTRLWLYHKPI-------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           E   L L+           GL+          +    L   F+R      LD    GL++
Sbjct: 62  EPATLLLHKPAGWRHDDFEGLLAAGRRWSDDPSPLRALKKHFARQRPTLALDSEASGLVV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            +   G+ R L     +  + Y V   G +    L  L+ G+  QG      +V+   + 
Sbjct: 122 FSQQHGVLRKLVDDGARLEQEYLVEVAGDLAAGGLERLRHGLAYQGRRLSPCKVSWQNE- 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
              + +   L++    +++ + E    +V  + R+  G   L  L  G  R +    
Sbjct: 181 ---SHLRFALKDVLPGQLRFMCESEGLEVRSIRRLRIGALSLARLPLGEWRYLGLHE 234


>gi|254234244|ref|ZP_04927567.1| hypothetical protein PACG_00081 [Pseudomonas aeruginosa C3719]
 gi|126166175|gb|EAZ51686.1| hypothetical protein PACG_00081 [Pseudomonas aeruginosa C3719]
          Length = 236

 Score =  115 bits (288), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 50/237 (21%), Positives = 85/237 (35%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+SK +A     SRRE E  I    V V+G ++E     V+      + G      
Sbjct: 2   TDPIRLSKRLAELTACSRREAELYIEGGWVSVDGEVIEEPQFKVLDQRVELLPGARAETI 61

Query: 71  ERTRLWLYHKPI-------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           E   L L+           GL+          +    L   F+R      LD    GL++
Sbjct: 62  EPATLLLHKPAGWRHDDLEGLLAAGRRWSDDPSPLRALKKHFARQRPTLALDSEASGLVV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            +   G+ R L     +  + Y V   G +    L  L+ G+  QG      +V+   + 
Sbjct: 122 FSQQHGVLRKLVDDGARLEQEYLVEVAGDLAAGGLERLRHGLAYQGRRLSPCKVSWQNE- 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
              + +   L++    +++ + E    +V  + R+  G   L  L  G  R +    
Sbjct: 181 ---SHLRFALKDVLPGQLRFMCESEGLEVRSIRRLRIGALSLARLPLGEWRYLGLHE 234


>gi|218459923|ref|ZP_03500014.1| RNA-pseudouridine synthase protein, ribosomal large subunit B
           [Rhizobium etli Kim 5]
          Length = 199

 Score =  115 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 55/195 (28%), Positives = 88/195 (45%)

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           I VDG+ +    +  L L      + T H      +            +  VGRLD  +E
Sbjct: 4   IRVDGLVIAAEAKIYLMLNKPRGLVTTRHDPEGRPTVYDCLKDFEIPHLSPVGRLDKASE 63

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL TND   A++L  P T   + Y V+    +D + +  +  GI   G       V  
Sbjct: 64  GLLLFTNDTEFAQILLDPITHVTKTYHVQIDRIMDDEAIAAMTSGIRHDGELLTATAVRR 123

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             Q   N+W+ V L EG+NR+I+++ E    +  RL+R++ G  +LG L  G+ R ++  
Sbjct: 124 LRQGDRNSWIEVELDEGRNRQIRRMLEALGTECLRLVRVAIGGLELGELPKGAVRALTAA 183

Query: 240 ILREQLGPHLLEEAQ 254
            L+       +E A+
Sbjct: 184 ELQALHRSAGMERAR 198


>gi|71737151|ref|YP_275932.1| S4 domain-containing protein [Pseudomonas syringae pv. phaseolicola
           1448A]
 gi|71557704|gb|AAZ36915.1| S4 domain protein [Pseudomonas syringae pv. phaseolicola 1448A]
          Length = 236

 Score =  115 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 51/238 (21%), Positives = 90/238 (37%), Gaps = 13/238 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLR 68
             P R+SK +      SRRE E  I    V V+G+++E     V  T  IE+  D     
Sbjct: 2   TDPIRLSKRLIELVGCSRREAELFIEGGWVTVDGVVIEEPHFKVS-TQKIELSPDAKADS 60

Query: 69  KAERTRLWLYHKPI------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
               T +              ++T  +     S     L   F R+ ++  L  N  GL+
Sbjct: 61  PEPVTIILHKPASASAEEALQMITPGTLSVEHSYSKRPLKGHFMRLEAISSLQANASGLM 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + + D  + R L    ++  + Y V   G++    LN L  G+  +G     ++ +   +
Sbjct: 121 VFSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKGKELPSVKASWQNE 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 +   ++  +   I  + E    K+  + RI  G   +G L  G  R ++ K 
Sbjct: 181 NR----LRFAMKNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRYMTTKE 234


>gi|296188747|ref|ZP_06857134.1| S4 domain protein [Clostridium carboxidivorans P7]
 gi|296046674|gb|EFG86121.1| S4 domain protein [Clostridium carboxidivorans P7]
          Length = 179

 Score =  115 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 54/178 (30%), Positives = 87/178 (48%), Gaps = 2/178 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +A  GIASRR+ E +I Q RVKVNG ++    V +    D + +DG  ++K + 
Sbjct: 3   ERLQKYMAACGIASRRKCEEIILQARVKVNGKIVNELGVKIDEEKDLVTLDGKLIKKEKN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP G V+T  D  GR T   +L  +  R+  +GRLD +T GL+LLTNDG +  
Sbjct: 63  KVYIALNKPKGYVSTVKDERGRKT-ILDLVDVTERIYPIGRLDYDTSGLILLTNDGDIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            +  P  +  ++Y     G   ++ +   + GI I G      +  +         + 
Sbjct: 122 KIIHPKQEKNKIYIALIKGIPTENDIKKFEIGINIDGYVTAPAKFKIIKNLKIIVKLK 179


>gi|254239479|ref|ZP_04932801.1| hypothetical protein PA2G_00092 [Pseudomonas aeruginosa 2192]
 gi|126192857|gb|EAZ56920.1| hypothetical protein PA2G_00092 [Pseudomonas aeruginosa 2192]
          Length = 236

 Score =  115 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 50/237 (21%), Positives = 85/237 (35%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+SK +A     SRRE E  I    V V+G ++E     V+      + G      
Sbjct: 2   TDPIRLSKRLAELTACSRREAELYIEGGWVSVDGEVIEEPQFKVLDQRVELLPGARAETI 61

Query: 71  ERTRLWLYHKPI-------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           E   L L+           GL+          +    L   F+R      LD    GL++
Sbjct: 62  EPATLLLHKPAGWRHDDFEGLLAAGRRWSDDPSPLRALKKHFARQRPTLALDSEASGLVV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            +   G+ R L     +  + Y V   G +    L  L+ G+  QG      +V+   + 
Sbjct: 122 FSQQHGVLRKLVDDGARLEQEYLVEVTGDLAAGGLERLRHGLAYQGRRLSPCKVSWQNE- 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
              + +   L++    +++ + E    +V  + R+  G   L  L  G  R +    
Sbjct: 181 ---SHLRFALKDVLPGQLRFMCESEGLEVRSIRRLRIGALSLARLPLGEWRYLGLHE 234


>gi|291276387|ref|YP_003516159.1| putative ribosomal pseudouridine synthase [Helicobacter mustelae
           12198]
 gi|290963581|emb|CBG39413.1| putative ribosomal pseudouridine synthase [Helicobacter mustelae
           12198]
          Length = 273

 Score =  115 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 69/262 (26%), Positives = 113/262 (43%), Gaps = 19/262 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ IA     SRRE + +IAQ RV V           +     + VDG  LR+ +  
Sbjct: 1   MRLNQYIAHHSKYSRREADGLIAQGRVNVEKKKA-VLGQELKEGQRVFVDGKQLREKKDG 59

Query: 74  --RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              + +YHKP G + T SD  GR ++FD+L   ++    VGRLD  +EGLLLL++D  +A
Sbjct: 60  PSTVIVYHKPKGELVTRSDDRGRRSIFDSLGRRYAHFTPVGRLDFASEGLLLLSDDKKIA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--------------DMQV 177
             L     +   +   +  G V +     ++ G+ ++    G                  
Sbjct: 120 HFLMQSDLEREYIL--KISGAVTEKMKEAMENGLELEDARAGGHEKSKIQKMSFKPFAFY 177

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +     + + + V + EGKNRE+++ F  F  +V  L R+ YG   L  L  G  R +S
Sbjct: 178 QIQKNDRNFSKLKVRITEGKNRELRRFFAHFKAEVLDLRRVGYGFVTLSALPVGKVRFLS 237

Query: 238 KKILREQLGPHLLEEAQVNLDA 259
           K+  ++                
Sbjct: 238 KEEYKKLHQLLKEHAKNPEGRN 259


>gi|255081278|ref|XP_002507861.1| predicted protein [Micromonas sp. RCC299]
 gi|226523137|gb|ACO69119.1| predicted protein [Micromonas sp. RCC299]
          Length = 257

 Score =  114 bits (286), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 58/257 (22%), Positives = 107/257 (41%), Gaps = 30/257 (11%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
              QR+SK +A  G+ASRR  E +I   RV+VNG+ +      V ++ D I VDG  ++ 
Sbjct: 1   DEGQRLSKALAALGVASRRASEELIFAGRVQVNGVTVTMPQHAVSTSRDVIAVDGKVVQG 60

Query: 70  -------AERTRLWLYHKPIGLVTTH------------------SDPDGRSTVFDNLPSI 104
                         L+     L ++                    +         +   +
Sbjct: 61  GLESLGDGGHLYFLLHKPKGYLCSSKPAGAGARASGQDRLVLDLFEDWREGWRKRHPGQL 120

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
             R+ +VGRLD+NT G+LL+T DG   + +  PS+Q  + Y V    +  + ++  + +G
Sbjct: 121 APRLFTVGRLDVNTTGMLLVTTDGQWCQRVAHPSSQIPKSYIVTAATRPTKAQIKKMAEG 180

Query: 165 IVIQGICYGDMQ---VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             + G+    ++   +      G    + V + +G+NRE++ +       V +L R+  G
Sbjct: 181 CEVDGVHVTPLRVESMEGARDGGPAHRILVDVVDGRNREVRVLSASAGVDVKKLKRVRVG 240

Query: 222 PFQL-GTLLAGSTREVS 237
             ++   L  G    + 
Sbjct: 241 GLRMPSELPIGKYMSLK 257


>gi|238021999|ref|ZP_04602425.1| hypothetical protein GCWU000324_01904 [Kingella oralis ATCC 51147]
 gi|237866613|gb|EEP67655.1| hypothetical protein GCWU000324_01904 [Kingella oralis ATCC 51147]
          Length = 230

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 43/227 (18%), Positives = 89/227 (39%), Gaps = 8/227 (3%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGV--PLRKAERT 73
           K +   GI +R+  + ++  Q V++NG  +      V   +   + ++G    +      
Sbjct: 5   KYLQAQGIDTRKGCQWLVKHQLVQINGDTIASDKAEVQPENVRSLSIEGEDALIIPLPHF 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L       V+                   + + ++GRLD +T G+LL+TNDG     
Sbjct: 65  YILLNKPADYEVSHKPRDYPSVFTLLPDQIRAADIQAIGRLDADTTGVLLITNDGQFNHR 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           +  P  +  ++YR+           + LK G+++         Q  +     +   + + 
Sbjct: 125 MTSPKHKVAKIYRITLKHPASDTLCSSLKNGVLLHDDNETVAAQEAIL---QTPTTLLMT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + EGK  ++K++      +V +L R  +G +    L AG  R +   
Sbjct: 182 ISEGKYHQVKRMIAAAGNRVAQLHRQQFGDWDTQDLAAGEWRFIQPD 228


>gi|296390524|ref|ZP_06879999.1| hypothetical protein PaerPAb_20321 [Pseudomonas aeruginosa PAb1]
          Length = 236

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 50/237 (21%), Positives = 87/237 (36%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+SK +A     SRRE E  I    V V+G ++E     V+      + G      
Sbjct: 2   TDPIRLSKRLAELTACSRREAELYIEGGWVSVDGEVIEEPQFKVLDQRVELLPGARAETI 61

Query: 71  ERTRLWLYHKPI-------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           E   L L+           GL+          +    L   F+R      LD    GL++
Sbjct: 62  EPATLLLHKPAGWRHDDFEGLLAAGRRWSDDPSPLRALKKHFARQRPTLALDSEASGLVV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            +   G+ R L     +  + Y V   G++    L  L++G+  QG      +V+   + 
Sbjct: 122 FSQQHGVLRKLVDDGARLEQEYLVEVTGELAAGGLERLRQGLAYQGRRLSPCKVSWQNE- 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
              + +   L++    +++ + E    +V  + R+  G   L  L  G  R +    
Sbjct: 181 ---SHLRFALKDVLPGQLRFMCESEGLEVRSIRRLRIGALSLARLPLGEWRYLGLHE 234


>gi|289661981|ref|ZP_06483562.1| pseudouridylate synthase [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 236

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 47/237 (19%), Positives = 88/237 (37%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+ K +A A   SR E ++ I    V V+G+++E       +      +   L  A
Sbjct: 2   SDPIRLDKCVAAAFGCSRGEAQQYIEGGWVSVDGVVVEEPQALATAGQVTLAEDAVLAPA 61

Query: 71  ERTRLWLYHKPI-------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           E   L L+            L T  +      +    L   F R+ +   L+    GLL+
Sbjct: 62  EPATLLLHKPAGVSAEAALALATPTTRSALDPSDIRVLKRHFLRLTAPLPLEDAASGLLI 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           L+ DG + R L   +    + + V   G++    +  L  G+V Q       +V+   + 
Sbjct: 122 LSQDGRVLRRLSAEARSIEQEFLVEVQGELRPYGMARLAHGLVYQQRRLSPCKVSWQNED 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   ++  +  +++ +      +V  + R+  G   LG L  G  R +    
Sbjct: 182 R----LRFAIKNVQPGQLRYMCGEVGLEVVNIRRLRVGRVSLGKLAIGQWRYLPTGE 234


>gi|51244311|ref|YP_064195.1| pseudouridine synthase [Desulfotalea psychrophila LSv54]
 gi|50875348|emb|CAG35188.1| related to pseudouridine synthase [Desulfotalea psychrophila LSv54]
          Length = 230

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 106/237 (44%), Gaps = 9/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
            R+ K ++  G  SR + E +I ++++ VNG         V   + I ++G  L + +  
Sbjct: 1   MRLQKFLSDIGYCSRGQAEDLIRKRKIMVNGKQAT-LGDKVRGNEKIVIEGRLLERKKGP 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ L+HKP  +  + +      T+ D       RV  VG LD  +EG+LLLTNDG +A
Sbjct: 60  AKKVLLFHKPEAVDCSLAPSKTTKTLLDF-DFGTDRVFPVGYLDQASEGILLLTNDGEIA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L LP  +    Y +    ++D + +  L +            +  +D ++     + +
Sbjct: 119 NKLSLPEFRPEDEYLLTSPEEIDAEMIEKLTQA-----RKAEKNKSVVDIEQIDAKHLRI 173

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + G++++IKK+ E     + +L+R+  G   L  L  G    +  + L+  L   
Sbjct: 174 LQQGGRSKDIKKMCEAVELVIEQLVRVRVGNITLEGLEKGIYIPLDPEQLKRLLKKQ 230


>gi|187928364|ref|YP_001898851.1| RNA-binding S4 domain-containing protein [Ralstonia pickettii 12J]
 gi|187725254|gb|ACD26419.1| RNA-binding S4 domain protein [Ralstonia pickettii 12J]
          Length = 674

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 61/261 (23%), Positives = 99/261 (37%), Gaps = 32/261 (12%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---- 63
            E+    R+SK ++  G+ SRRE +  I +  V V+G  +      V     IE+     
Sbjct: 416 TESSGLVRLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVKPDAIIEIHQAAR 475

Query: 64  -----------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
                        P+          Y   + L    +  +   T     P     +   G
Sbjct: 476 SEQGERVTVLMHKPVGYVSGQAEDGYQPAVSLFVPENQWEADPTRKRFAPWQRRALAPAG 535

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-------------VDQDKLN 159
           RLDI++ GLL+LT DG +AR L    +   + Y VR                   ++ + 
Sbjct: 536 RLDIDSTGLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWHSPDGVVERDISKVFPEELME 595

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
            L+ G+ + G      +V+   ++     +   LREGK R+I+++ E    +V  L RI 
Sbjct: 596 KLRFGLSLDGEALKPAKVSWQNEEQ----LRFVLREGKKRQIRRMCEQVGLEVVGLKRIR 651

Query: 220 YGPFQLGTLLAGSTREVSKKI 240
            G   LG L  G  R +    
Sbjct: 652 MGSIVLGDLPVGQWRFLGPFE 672



 Score = 37.1 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 14/119 (11%), Positives = 29/119 (24%), Gaps = 1/119 (0%)

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G TRE   + ++    P   ++ +               D         D   R   +  
Sbjct: 107 GQTREAKPRRMQGDRPPRRFDDERPPRRFNEEQRPPRRSDDERPPRRFEDRPPRRFDDER 166

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                   +        R         +     F  +  +R  + +R+P     +   R
Sbjct: 167 PPRRFDNDRPPRRFDDERPPRRFSDDQRPPR-RFDEERPRRYGDDQRAPRRDGDQRPPR 224



 Score = 36.7 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 9/109 (8%), Positives = 24/109 (22%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P  ++  +               +         D+    +           ++      
Sbjct: 113 KPRRMQGDRPPRRFDDERPPRRFNEEQRPPRRSDDERPPRRFEDRPPRRFDDERPPRRFD 172

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           + R              S      +R +  R       +R+ RR   ++
Sbjct: 173 NDRPPRRFDDERPPRRFSDDQRPPRRFDEERPRRYGDDQRAPRRDGDQR 221



 Score = 36.3 bits (82), Expect = 7.0,   Method: Composition-based stats.
 Identities = 14/114 (12%), Positives = 31/114 (27%), Gaps = 2/114 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL--SKQKK 300
           +Q  P   +E +               D      +  DD    ++   ++       Q+ 
Sbjct: 219 DQRPPRRFDEERPPRRFNDEQRPPRRFDEERPPRKFGDDQRPPRRFDDERPRRYGDDQRA 278

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                 +R              S      +R ++ R       +R+ RR   ++
Sbjct: 279 PRRDGDQRPPRRLDDERPPRRFSDDQRPPRRFDDERPRRYGDDQRAPRRDGDQR 332



 Score = 36.3 bits (82), Expect = 7.3,   Method: Composition-based stats.
 Identities = 11/115 (9%), Positives = 28/115 (24%), Gaps = 3/115 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS---KQK 299
           +   P    + +              R          DD    +++  Q+       ++ 
Sbjct: 172 DNDRPPRRFDDERPPRRFSDDQRPPRRFDEERPRRYGDDQRAPRRDGDQRPPRRFDEERP 231

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                  +R                     +R ++ R       +R+ RR   ++
Sbjct: 232 PRRFNDEQRPPRRFDEERPPRKFGDDQRPPRRFDDERPRRYGDDQRAPRRDGDQR 286


>gi|319788193|ref|YP_004147668.1| RNA-binding S4 domain protein [Pseudoxanthomonas suwonensis 11-1]
 gi|317466705|gb|ADV28437.1| RNA-binding S4 domain protein [Pseudoxanthomonas suwonensis 11-1]
          Length = 270

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 48/242 (19%), Positives = 95/242 (39%), Gaps = 17/242 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV-PLRK 69
             P R+++ +A     SR E E+ I    VKV+G ++E     V S   +E+D    L+ 
Sbjct: 32  SNPIRLARRVAELAQCSRSEAEQYIEGGWVKVDGQVVELPGHMVTSE-RVEIDPKARLQP 90

Query: 70  AERTRLWLYHKPI-----------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
            E     L+                L+      +G ++    L   F R+ S+  L+   
Sbjct: 91  VEPATFLLHKPAGVDLEAVADTLATLLPPQERWEGDTSNIRTLRKNFQRLASLVPLEPEA 150

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GL++L+ DG + R L        + + V   G ++   L+ L  G+  +G+     +V+
Sbjct: 151 SGLVVLSQDGRVRRRLVEDFATIEQEFVVEVEGSLEPWGLSRLSHGLTFEGLELPPGKVS 210

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              +      +   L+  +  +++ +      +V  + R+  G   L  +  G+ R +  
Sbjct: 211 WQNE----TRLRFALKGPRPGQLRAMCTQVGLEVVSIRRLRIGRIPLAKMPPGAWRYLPV 266

Query: 239 KI 240
             
Sbjct: 267 GE 268


>gi|23007931|ref|ZP_00049587.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Magnetospirillum
           magnetotacticum MS-1]
          Length = 179

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 94/158 (59%), Positives = 113/158 (71%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +R++K IARAGIASRR+ E +I   RV +NG +L   A+NV  +D I VDG PL   E
Sbjct: 20  EGERIAKAIARAGIASRRDAEALIEAGRVTLNGQVLTSPAINVTDSDRITVDGEPLPARE 79

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RTRLWL HKP G+VTT  DP+GR TVFD LP    RV+++GRLDINTEGLLLLTNDGGLA
Sbjct: 80  RTRLWLLHKPRGVVTTARDPEGRQTVFDGLPEELPRVVAIGRLDINTEGLLLLTNDGGLA 139

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           +V+  P T WLR YRVR  G V Q  L+ LKKG+ + G
Sbjct: 140 KVIAHPDTGWLRRYRVRAFGDVTQADLDKLKKGVTVDG 177


>gi|146306738|ref|YP_001187203.1| RNA-binding S4 domain-containing protein [Pseudomonas mendocina
           ymp]
 gi|145574939|gb|ABP84471.1| RNA-binding S4 domain protein [Pseudomonas mendocina ymp]
          Length = 236

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 52/243 (21%), Positives = 84/243 (34%), Gaps = 23/243 (9%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+SK +      SRRE +  I    + V+G ++E     V       + G  L   
Sbjct: 2   SEPTRLSKRVIELLGCSRREADLYITGGWISVDGQVVEAPQFKVGDQRVELLPGANLEPV 61

Query: 71  ERTRLWLYHKPI-------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           E   L ++            L+      +        L   F R      L     GL++
Sbjct: 62  EPVTLLVHCPTGTSAAQLQHLLVHERHWEEDPHARRVLHGHFLRQEQSLPLQNGASGLVV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           L+ D    R L     +  + Y V   G++    L  LKKG+V +G  +   + +  +++
Sbjct: 122 LSQDWRAQRKLREDGAKLEQEYLVDVAGELPASALERLKKGLVHKGTQFPPCKASWQSEQ 181

Query: 184 GSNAWVTVGLREGKN------REIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                +   L   KN      R+I         KV  + RI  G   +  L  G  R + 
Sbjct: 182 R----LRFAL---KNPAPDLLRQI---CAALGLKVLGMKRIRIGGVPMAKLPVGQWRYLG 231

Query: 238 KKI 240
            K 
Sbjct: 232 DKE 234


>gi|329902666|ref|ZP_08273221.1| 16S rRNA pseudouridylate 516 synthase [Oxalobacteraceae bacterium
           IMCC9480]
 gi|327548656|gb|EGF33305.1| 16S rRNA pseudouridylate 516 synthase [Oxalobacteraceae bacterium
           IMCC9480]
          Length = 239

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 36/210 (17%), Positives = 71/210 (33%), Gaps = 3/210 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERTR 74
           + +++   G  +R+   ++I    V V G ++               +        E   
Sbjct: 6   LDRLLQSQGFGTRKWCRQLIDDGEVSVAGTVVTDYRTAFEPDGLTFRLFDEDWDFHEHVF 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L+  P    +                  +  V  VGRLD +T GLLL+++ G      
Sbjct: 66  VALHKPPNFECSRKPSHHPGVLSILPENFTWRDVQPVGRLDHDTTGLLLMSDHGPFIHAQ 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P +   +VY       V  + + LL  G+ +         V        +  + + L 
Sbjct: 126 SSPKSHIPKVYIATTAEAVTPELVALLLAGVQLHDEPAPLAAVRCSMVD--SHRIEIVLE 183

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
           +GK  ++K++          L R++ G   
Sbjct: 184 QGKYHQVKRMLAAAGNHCAALQRVAIGQLT 213


>gi|290954061|ref|ZP_06558682.1| RNA pseudouridine synthase B [Francisella tularensis subsp.
           holarctica URFT1]
 gi|295312554|ref|ZP_06803314.1| RNA pseudouridine synthase B [Francisella tularensis subsp.
           holarctica URFT1]
          Length = 198

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 65/198 (32%), Positives = 91/198 (45%), Gaps = 8/198 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+  N   +   P+R+ K++A+ GI SRR++E  I Q RVKVNG +           D I
Sbjct: 1   MRRANQNNDKN-PERLQKLLAKYGIGSRRKIEEYIEQGRVKVNGKVAT-LGDKASEADKI 58

Query: 61  EVDGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
             D   L            +  + +   + T+  + D ++          SR I VGRLD
Sbjct: 59  SFDSKALHSYGQPMTRPRVVIYHKREGEVCTSKDEKDRQTVFDSLPKLAKSRWIMVGRLD 118

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGD 174
           INT GLLL T DG LA  L  PS Q  R Y VR  GQ    + +N LK+GI ++      
Sbjct: 119 INTTGLLLFTTDGDLANRLMHPSYQIEREYAVRVFGQQLSDETINKLKEGIQLEDGIAKF 178

Query: 175 MQVTLDTQKGSNAWVTVG 192
             +     +G+N W  V 
Sbjct: 179 NSIKFSGGEGANLWYYVT 196


>gi|116049039|ref|YP_792159.1| hypothetical protein PA14_50030 [Pseudomonas aeruginosa UCBPP-PA14]
 gi|115584260|gb|ABJ10275.1| hypothetical protein PA14_50030 [Pseudomonas aeruginosa UCBPP-PA14]
          Length = 236

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 50/237 (21%), Positives = 85/237 (35%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+SK +A     SRRE E  I    V V+G ++E     V+      + G      
Sbjct: 2   TDPIRLSKRLAELTACSRREAELYIEGGWVSVDGEVIEEPQFKVLDQRVELLPGARAETI 61

Query: 71  ERTRLWLYHKPI-------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           E   L L+           GL+          +    L   F+R      LD    GL++
Sbjct: 62  EPATLLLHKPAGWRHDDFEGLLAAGRRWSDDPSPLRALKKHFARQRPTLALDSEASGLVV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            +   G+ R L     +  + Y V   G +    L  L+ G+  QG      +V+   + 
Sbjct: 122 FSQQHGVLRKLVDDGARLEQEYLVEVAGDLAAGGLERLRHGLAYQGRRLSPCKVSWQNE- 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
              + +   L++    +++ + E    +V  + R+  G   L  L  G  R +    
Sbjct: 181 ---SHLRFALKDVLPGQLRFMCESEGLEVRSIRRLRIGALPLARLPLGEWRYLGLHE 234


>gi|145348269|ref|XP_001418577.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144578806|gb|ABO96870.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 230

 Score =  114 bits (284), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 100/230 (43%), Gaps = 19/230 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR----- 68
           R+SK +A  G+ASRR  + +I   RVKVNG  +      V    D + VDG  +      
Sbjct: 1   RLSKALASLGVASRRGADDLIFGGRVKVNGETVTAPQTKVNLNADVVMVDGKIVEGGVNF 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------------ISVGRLDI 116
             E     L      + +T S+     TV+D                      +VGRLD+
Sbjct: 61  VKEHAYFMLNKPKGFVCSTKSNSAQGKTVYDLFEQWRDEFKAAYPGKLPPRLFTVGRLDV 120

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
            T GLLLLT DG  ++ +  PS++ ++ Y V  + +  + ++  + KG  + G     ++
Sbjct: 121 ATTGLLLLTTDGDWSQRVAHPSSEVVKQYVVTANNKPTRAQIAAMAKGTEVDGARVVPVR 180

Query: 177 VTLDTQKGSNA-WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           V      G  A  + V + +G+NRE++ +       V  L R   G  ++
Sbjct: 181 VESMGADGGPANRILVEVVDGRNREVRVLCADAGVDVKNLKRTRVGGLRM 230


>gi|91787026|ref|YP_547978.1| RNA-binding S4 [Polaromonas sp. JS666]
 gi|91696251|gb|ABE43080.1| RNA-binding S4 [Polaromonas sp. JS666]
          Length = 248

 Score =  114 bits (284), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 51/250 (20%), Positives = 87/250 (34%), Gaps = 26/250 (10%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKA 70
            P R++K +A     SRRE E+ I    V V+G+++E     V     IE+     L   
Sbjct: 2   EPVRLAKRLAEMLSCSRREAEQYIEGGWVTVDGVVVEEPQFRV-LDQTIELSKDASLLAL 60

Query: 71  ERTRLWLYHKPIG-----------------LVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
               L L+                      L+   +      +    L   FS    V  
Sbjct: 61  APVTLLLHKPAGHEAGLDAPAGRGVPSAAELLVAANQSPDDRSGIRPLKKHFSAAELVTP 120

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---DKLNLLKKGIVIQGI 170
           L     GL++ T D  +AR L   +        V   G++     ++LN +  G    G+
Sbjct: 121 LATAASGLVVFTQDWRVARKLREDAGVLEHEVIVEVTGEIKPGGLERLNRIDHGFTFNGV 180

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                +V+      S A +   L+  +  +I  + E    +V  + R+  G   +  L +
Sbjct: 181 LLPPAKVSWQ----SEARLRFALKGERPGQIAYMCESVGLRVEAMKRLRIGRVPMSNLQS 236

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 237 GRWRYLLPHE 246


>gi|15596307|ref|NP_249801.1| hypothetical protein PA1110 [Pseudomonas aeruginosa PAO1]
 gi|9947028|gb|AAG04499.1|AE004541_4 hypothetical protein PA1110 [Pseudomonas aeruginosa PAO1]
          Length = 236

 Score =  114 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 50/237 (21%), Positives = 85/237 (35%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+SK +A     SRRE E  I    V V+G ++E     V+      + G      
Sbjct: 2   TDPIRLSKRLAELTACSRREAELYIEGGWVSVDGEVIEEPQFKVLDQRVELLPGARAETI 61

Query: 71  ERTRLWLYHKPI-------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           E   L L+           GL+          +    L   F+R      LD    GL++
Sbjct: 62  EPATLLLHKPAGWRHDDFEGLLAAGRRWSDDPSPLRALKKHFARQRPTLALDSEASGLVV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            +   G+ R L     +  + Y V   G +    L  L+ G+  QG      +V+   + 
Sbjct: 122 FSQQHGVLRKLVDDGARLEQEYLVEVAGDLAAGGLERLRHGLAYQGRRLSPCKVSWQNE- 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
              + +   L++    +++ + E    +V  + R+  G   L  L  G  R +    
Sbjct: 181 ---SHLRFALKDVLPGQLRFMCEREGLEVRSIRRLRIGALSLARLPLGEWRYLGLHE 234


>gi|325181472|emb|CCA15906.1| ribosomal large subunit pseudouridine synthase F put [Albugo
           laibachii Nc14]
          Length = 246

 Score =  114 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 59/235 (25%), Positives = 104/235 (44%), Gaps = 25/235 (10%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           +A   + SRR+ ER I+   V VNG  +++  + +     +E  G  ++  ++    + +
Sbjct: 1   MAERKMCSRRDAERYISAGDVYVNGEQIQQDWIKIPRDSCVEFSGKAVKAEKQKVSVILN 60

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------------VGRLDINTEGLLLL 124
           KP+G V++  +P  +  +         ++ +                GRLDIN+ GLLL 
Sbjct: 61  KPLGYVSSQPEPMRKPAIELLSIQNAFQLTARWYGKEPKSLSKLAVCGRLDINSTGLLLF 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVR------FHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           T DG LA+ +  P+    + Y VR         +  ++ ++ L++G +   ICY    V 
Sbjct: 121 TQDGVLAKQILDPNGGVEKEYLVRVDMDLERDTKQAEEVVDKLREGFIWNDICYRARSVR 180

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
           +         +   L EGK R I+ + E    KV  L R+  G  +LG L  G+ 
Sbjct: 181 VLNANQ----LQFILTEGKKRHIRYMCEAVGIKVIALKRVRIGNIRLGALPVGNF 231


>gi|329891024|ref|ZP_08269367.1| hypothetical protein BDIM_27350 [Brevundimonas diminuta ATCC 11568]
 gi|328846325|gb|EGF95889.1| hypothetical protein BDIM_27350 [Brevundimonas diminuta ATCC 11568]
          Length = 246

 Score =  114 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 50/241 (20%), Positives = 91/241 (37%), Gaps = 7/241 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTD--HIEV 62
           + +     RV +++   G  SR E+ R+     + ++G  L   +    V       +E+
Sbjct: 1   MSKKIPTSRVDQLLGSMGYGSRAEMARLGKAGGIVLDGADLTDVSKRIPVTPDLPGRMEI 60

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           DG PL       + L        +   D       + D        + ++GRLD  T GL
Sbjct: 61  DGEPLDPVAGLVVLLNKPLGMTCSHKEDGALVYDVLPDRWRRRDPAISTIGRLDKQTSGL 120

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLT+DG L   +  P     +VYR      ++  +  L   G ++       +   +  
Sbjct: 121 LLLTDDGDLLHRVISPKRHVAKVYRATLARPLNGTEGALFASGELVLEGEDKPLAPAVLE 180

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
              S     + + EG+  +++++F      V  L R   G   L   L  G  R +++  
Sbjct: 181 V-VSPTEALLTVTEGRYHQVRRMFAAAGNHVEALHRERLGGLVLPDELAPGEWRLLTEDE 239

Query: 241 L 241
           +
Sbjct: 240 I 240


>gi|84517063|ref|ZP_01004419.1| ribosomal small subunit pseudouridine synthase A [Loktanella
           vestfoldensis SKA53]
 gi|84508958|gb|EAQ05419.1| ribosomal small subunit pseudouridine synthase A [Loktanella
           vestfoldensis SKA53]
          Length = 244

 Score =  114 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 45/233 (19%), Positives = 85/233 (36%), Gaps = 7/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMST--DHIEVDGVPLRKA 70
           R+ +++   G  SR ++ RM     + ++   +  A     V       + V   PL   
Sbjct: 8   RIDQLLGSLGYGSRGDIARMAKSGWITLDDARIWDATTRIAVTPDLPARMVVSREPLDPL 67

Query: 71  ERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               + L+       +   D       + D        + +VGRLD  T GLLLLT+DG 
Sbjct: 68  AGMVILLHKPLGMTCSHKEDGPLVYDILPDRWKRRQPVISTVGRLDKQTSGLLLLTDDGP 127

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +  P     + YR      ++ ++  +   G ++       +         S    
Sbjct: 128 LLHRIISPKQHIKKTYRATLARPLEGNEAAIFAAGDLVLQGEDKPLAPAELRV-ISPTEA 186

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            + + EG+  +++++F      V  L R + G   L   L+ G  R +    +
Sbjct: 187 VLTVTEGRYHQVRRMFAATGNHVTALHRDALGGLVLPDDLMPGQWRIIDGAQI 239


>gi|75764639|ref|ZP_00744075.1| Ribosomal small subunit pseudouridine synthase A [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
 gi|74487875|gb|EAO51655.1| Ribosomal small subunit pseudouridine synthase A [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
          Length = 188

 Score =  114 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 46/177 (25%), Positives = 74/177 (41%), Gaps = 3/177 (1%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              E   L ++     +  T  D          L         VGRLDI+TEG LL+TND
Sbjct: 2   EYKEFVYLMMHKPQGVISATEDDNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITND 61

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSN 186
           G L+  L  P     + Y     G V ++ +    KG+++          +T+  +    
Sbjct: 62  GKLSHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGTLTIL-KSDDI 120

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + + + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 121 SEIELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 177


>gi|34499601|ref|NP_903816.1| pseudouridylate synthase [Chromobacterium violaceum ATCC 12472]
 gi|34105452|gb|AAQ61807.1| pseudouridylate synthase [Chromobacterium violaceum ATCC 12472]
          Length = 233

 Score =  113 bits (283), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 50/238 (21%), Positives = 78/238 (32%), Gaps = 15/238 (6%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           + T  R+SK +   G+ SRRE +  I Q  VKV+G ++      V     I + G P   
Sbjct: 2   DETSVRLSKRMVELGLCSRREADACIEQGLVKVDGKVVNTLGARVRPEQQITLAGKPQAM 61

Query: 70  AERTRLWLYH-------KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           A      L +        P  L+   S           L      + +VG +D    GLL
Sbjct: 62  ATLPVTMLLNRPAGEEAPPAQLLGPDSRAPQDGAEQVWLARHRQHLTAVGAVDERCHGLL 121

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           +LT D    + L     +    + ++       D L      I + G      +++  + 
Sbjct: 122 VLTQD----KKLPRHLAECEMEFLLQVEQAPAADALKARVAAIRLDGKPLRQCKISRQSD 177

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 V    R G   EI +        +     I  G   L  L  G  R +    
Sbjct: 178 HQLRCAVY-APRAGFFAEISR---QLGVSLQSARCIRIGRLALAGLQPGQWRYLQPFE 231


>gi|84623215|ref|YP_450587.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|84367155|dbj|BAE68313.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae MAFF
           311018]
          Length = 236

 Score =  113 bits (283), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 49/237 (20%), Positives = 88/237 (37%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+ K +A A   SR E +  I    V V+G+++E       +      D   L  A
Sbjct: 2   SDPIRLDKCVAAAFGCSRGEAQHYIEGGWVSVDGVVVEEPQALATAAQITLADDAVLSPA 61

Query: 71  ERTRLWLYHKPI-------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           E   L L+            L T  +      +    L   F R+ +   L+    GLL+
Sbjct: 62  EPATLLLHKPAGVSVEAALALATPTTRSALDQSDIRVLKRHFLRLTAPLPLENAASGLLI 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           L++DG + R L   ++   + + V   G V    +  L  G+V Q       +V+   + 
Sbjct: 122 LSHDGRVLRRLSADASSIEQEFLVEVQGDVRPYGMARLAHGLVYQQRSLLPCKVSWQNED 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   ++  +  +++ +      +V  + R+  G   LG L  G  R +    
Sbjct: 182 R----LRFAIKNVQPGQLRYMCGEVGLEVVSIRRLRVGRVSLGKLAIGEWRYLPTGE 234


>gi|308812959|ref|XP_003083786.1| pseudouridine synthase family 1 protein (ISS) [Ostreococcus tauri]
 gi|116055668|emb|CAL57753.1| pseudouridine synthase family 1 protein (ISS) [Ostreococcus tauri]
          Length = 391

 Score =  113 bits (282), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 65/287 (22%), Positives = 108/287 (37%), Gaps = 24/287 (8%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER------------TRL 75
           RRE +  ++  RV VNG L+   +  V+  D + +DG  +                    
Sbjct: 106 RREADDAVSAGRVLVNGELVR-PSRRVVHGDVVTLDGKAMDWEPYAQSVESELGDARFVY 164

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGRLDINTEGLLLLTNDGGL 130
             Y+KP G+V T SD +  S                R+  VGRLD ++ GL+LLTNDG +
Sbjct: 165 LKYNKPRGVVCTMSDTERTSMFHALHHERKALGKDVRLFPVGRLDKDSSGLVLLTNDGRV 224

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI------QGICYGDMQVTLDTQKG 184
           +  L  P  +  + Y V     V +     L +G+VI               +  +  K 
Sbjct: 225 SDALLDPERKAEKTYDVDVDRIVSEADARTLARGVVISTTQQRDLKETVAATLPCEVTKT 284

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
               +   L+EG+NR+I+K+ E  ++ V RL R       LG L  G    + +  +   
Sbjct: 285 GEKSLRFVLKEGRNRQIRKMCEVLSYDVERLHRTRIDDVALGDLEVGGVAPLDEDEVNAL 344

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
                   +     +   S     R   +            ++++S 
Sbjct: 345 SARVDARASTPRESSKHTSESRRRRRAIDANPGGWGAKMFKERDASA 391


>gi|89902224|ref|YP_524695.1| RNA-binding S4 [Rhodoferax ferrireducens T118]
 gi|89346961|gb|ABD71164.1| RNA-binding S4 [Rhodoferax ferrireducens T118]
          Length = 262

 Score =  112 bits (281), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 46/248 (18%), Positives = 90/248 (36%), Gaps = 20/248 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--LRK 69
             +R++K +A     SRRE E+ I    V VNG ++E     V     +EVD     L  
Sbjct: 14  EGERLAKRVAEMVPCSRREAEQYIEGGWVSVNGQVVEEPMFRVS-DQRVEVDPDASLLEL 72

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRS-----------------TVFDNLPSIFSRVISVG 112
           +  T L         +      +                    +    L   F+++ +  
Sbjct: 73  SAVTLLLHKPPGFDAMAAPGQANRHVKSAQQLLSAATHATDDASGVRLLKRHFAKLTACV 132

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
            L+    GL++ T D  + R L   +    +   V   G+V    L  + +G+ + G   
Sbjct: 133 PLETAASGLVVFTQDWRVLRKLTEDAQLMEQEVIVEVAGEVPAQSLQRINQGLAVDGQPL 192

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
             ++V+L++   +++ +   L+      I  + E    ++  + R+  G   +  L  G 
Sbjct: 193 PAVKVSLNSTGETSSKLRFALKGSHPGLIAYLCERLGLQIVSMKRLRIGRVSMTQLPLGQ 252

Query: 233 TREVSKKI 240
            R +    
Sbjct: 253 WRYLQAHE 260


>gi|78048815|ref|YP_364990.1| ribosomal small subunit pseudouridylate synthase [Xanthomonas
           campestris pv. vesicatoria str. 85-10]
 gi|78037245|emb|CAJ24990.1| ribosomal small subunit pseudouridylate synthase [Xanthomonas
           campestris pv. vesicatoria str. 85-10]
          Length = 236

 Score =  112 bits (281), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 48/237 (20%), Positives = 88/237 (37%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+ K IA A   SR E ++ I    V V+G+++E       +      +   L  A
Sbjct: 2   SDPIRLDKCIAAAFGCSRGEAQQYIEGGWVSVDGVVVEEPQTLATAAQVTLAENAVLAPA 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLPSIFSRVISVGRLDINTEGLLL 123
           E   L L+      V         +T           L   F R+ +   L+    GLL+
Sbjct: 62  EPATLLLHKPAGICVDAALALATPATRSALDQADVRVLKRHFLRLHAPLPLEDAASGLLI 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           L+ DG + R L   ++   + + V   G++    +  L  G+V Q       +V+   + 
Sbjct: 122 LSQDGRVLRRLSADASAIEQEFLVEVRGELRPYGMARLAHGLVYQHRSLSPCKVSWQNED 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   ++  +  +++ +      +V  + R+  G   LG L  G  R +    
Sbjct: 182 R----LRFAIKHVQPGQLRYMCGEVGPEVVSIRRLRVGRVSLGKLAIGEWRYLPAGE 234


>gi|146282670|ref|YP_001172823.1| pseudouridine synthase [Pseudomonas stutzeri A1501]
 gi|145570875|gb|ABP79981.1| pseudouridine synthase [Pseudomonas stutzeri A1501]
          Length = 297

 Score =  112 bits (281), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 68/296 (22%), Positives = 113/296 (38%), Gaps = 21/296 (7%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L        + T +      +           R I++GRLDINT GLLL T DG LA  L
Sbjct: 2   LIYNKPDGEICTRNDPEGRPTVFDRLPRPKEGRWINIGRLDINTTGLLLFTTDGELANRL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-KGSNAWVTVGL 193
             PS +  R Y VR  G+VD + +  LK G++++        +      +G N W    +
Sbjct: 62  MHPSYEMDREYAVRVRGEVDDEMIERLKTGVMLEDGPARFTDIQEAPGGEGFNHWYHCVV 121

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL----------- 241
            EG+NRE+++++E     V+RL R+ +GP  +   L  G  RE+S+  +           
Sbjct: 122 MEGRNREVRRLWESQGLVVSRLKRVRFGPVFMTSDLPMGRWREMSQAEVDILSEEVGLKP 181

Query: 242 --------REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
                   + +     ++               ++R        V D     + + S++ 
Sbjct: 182 VALPSMKAKTKEKIDRMQRKVAKPLGRGERRSRVLRPAHEADMPVADKPRAARDDKSERK 241

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                K   TPV  R   +     +       S   ++     + P F  +RS R 
Sbjct: 242 PRGSDKPRGTPVAERPGDTRKGGKRHEGGGRSSGPARKPAGEGQRPGFGRERSKRP 297


>gi|325929346|ref|ZP_08190476.1| pseudouridylate synthase, 16S rRNA uridine-516 family [Xanthomonas
           perforans 91-118]
 gi|325540258|gb|EGD11870.1| pseudouridylate synthase, 16S rRNA uridine-516 family [Xanthomonas
           perforans 91-118]
          Length = 236

 Score =  112 bits (281), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 47/237 (19%), Positives = 88/237 (37%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+ K +A A   SR E ++ I    V V+G+++E       +      +   L  A
Sbjct: 2   SDPIRLDKCVAAAFGCSRGEAQQYIEGGWVSVDGVVVEEPQTLATAAQVTLAENAVLAPA 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLPSIFSRVISVGRLDINTEGLLL 123
           E   L L+      V         +T           L   F R+ +   L+    GLL+
Sbjct: 62  EPATLLLHKPAGICVDAALALATPATRSALDQADVRVLKRHFLRLHAPLPLEDAASGLLI 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           L+ DG + R L   ++   + + V   G++    +  L  G+V Q       +V+   + 
Sbjct: 122 LSQDGRVLRRLSADASAIEQEFLVEVRGELRPYGMARLAHGLVYQQRSLSPCKVSWQNED 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   ++  +  +++ +      +V  + R+  G   LG L  G  R +    
Sbjct: 182 R----LRFAIKHVQPGQLRYMCGEVGLEVVSIRRLRVGRVSLGKLAIGEWRYLPAGE 234


>gi|17546120|ref|NP_519522.1| hypothetical protein RSc1401 [Ralstonia solanacearum GMI1000]
 gi|17428416|emb|CAD15103.1| hypothetical protein RSc1401 [Ralstonia solanacearum GMI1000]
          Length = 631

 Score =  112 bits (281), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 63/258 (24%), Positives = 100/258 (38%), Gaps = 32/258 (12%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-- 64
           + E+    R+SK ++  G+ SRRE +  I +  V V+G  +      V     IE+    
Sbjct: 372 LAESSGLVRLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVRPDAEIEILPAA 431

Query: 65  -------------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                         P+          Y     L T  +  +   T           +   
Sbjct: 432 RSEQGERVTVLLHKPVGYVSGQAEDGYEPAAALFTAENQWEEDPTRKHFAAWQHKGLAPA 491

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-------------VDQDKL 158
           GRLDI++ GLL+LT DG +AR L    +   + Y VR                   +D L
Sbjct: 492 GRLDIDSTGLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWNAPQGPVEHDISKVFPEDLL 551

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
            +L+ G+ + G      +V+   ++     +   LREGK R+I+++ E    +V  L RI
Sbjct: 552 EMLRHGLSLDGEALKPAKVSWQNEEQ----LRFVLREGKKRQIRRMCEQVGLEVVGLKRI 607

Query: 219 SYGPFQLGTLLAGSTREV 236
             G   LG L  G  R +
Sbjct: 608 RMGSVVLGDLPVGKWRFL 625



 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 6/111 (5%), Positives = 17/111 (15%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           +                    +     R            R  +    +    +      
Sbjct: 251 RFEDRPPRRFDDERPPRRSGDDQRPPRRFGDERPPRRFEDRPPRRFDDERPPRRSGDDQR 310

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           P  R                   D  +        P+   +      + ++
Sbjct: 311 PPRRFEDRPPRRFDDERPPRRSGDDQRPPRRFEDRPARAPRPERDERAPQR 361



 Score = 35.9 bits (81), Expect = 9.4,   Method: Composition-based stats.
 Identities = 7/98 (7%), Positives = 19/98 (19%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
                        D         DD    ++   ++     + +                
Sbjct: 248 PPRRFEDRPPRRFDDERPPRRSGDDQRPPRRFGDERPPRRFEDRPPRRFDDERPPRRSGD 307

Query: 317 AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +     F     +R ++ R        +   R    +
Sbjct: 308 DQRPPRRFEDRPPRRFDDERPPRRSGDDQRPPRRFEDR 345



 Score = 35.9 bits (81), Expect = 10.0,   Method: Composition-based stats.
 Identities = 10/101 (9%), Positives = 17/101 (16%), Gaps = 2/101 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +   P                     R          D+    +    Q+     + +  
Sbjct: 261 DDERPPRRSGDDQRPPRRFGDERPPRRFEDRPPRRFDDERPPRRSGDDQRPPRRFEDRPP 320

Query: 303 TP--VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF 341
                 R    S                  R E   R+P  
Sbjct: 321 RRFDDERPPRRSGDDQRPPRRFEDRPARAPRPERDERAPQR 361


>gi|239813882|ref|YP_002942792.1| RNA-binding S4 domain protein [Variovorax paradoxus S110]
 gi|239800459|gb|ACS17526.1| RNA-binding S4 domain protein [Variovorax paradoxus S110]
          Length = 237

 Score =  112 bits (280), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 40/232 (17%), Positives = 76/232 (32%), Gaps = 1/232 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
                 R++K +A     SRRE E +I    V+V+G+        V +   +E++     
Sbjct: 5   SEEEGIRLAKRVAAIAGCSRREAELLIENGAVRVDGVPALLPQSRVHAHQKVEIEPGAKP 64

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           +       L HKP G+ T  +     +           R +            L     G
Sbjct: 65  EPVVPVTLLLHKPAGMATDTAHRLLVAANHHEPERAGMRFLPAHAKAQRCMTPLETGASG 124

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +    E    + L+        +V  D    L    +++       +V++  Q      
Sbjct: 125 LVVYTQEWRIERKLQEDAGVLEHEVMVDVSGKLSPEQLVRFER-SPARVSIGRQADEQTG 183

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +   L+  +  +I  + +    ++  + RI  G   L  L  G  R +S   
Sbjct: 184 LRFALKGARPGQIAHLCDEAGLRILAMRRIRIGRVPLAGLEPGQWRYLSPHE 235


>gi|319791604|ref|YP_004153244.1| RNA-binding s4 domain protein [Variovorax paradoxus EPS]
 gi|315594067|gb|ADU35133.1| RNA-binding S4 domain protein [Variovorax paradoxus EPS]
          Length = 241

 Score =  112 bits (280), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 43/250 (17%), Positives = 82/250 (32%), Gaps = 21/250 (8%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           MK+ N    +    R++K +A     SRRE E +I    V+V+G+        V +   +
Sbjct: 1   MKNNN--APDDEGIRLAKRVAALAGVSRREAELLIENGAVRVDGVPAVLPQSRVQAHQQV 58

Query: 61  EV-DGVPLRKAERTRLWLYHKPIGLVTTHS-------DPDGRSTVFDNLPSIFSRVISVG 112
           E+  G          + LY                    +        LP+       + 
Sbjct: 59  EIAAGAKPEPVVPVTMLLYKPAGMPTDNAHRLLVAANHHEPERAGQKFLPAHLKGQHCMT 118

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
            L+    GL+  T +  + R L+  +        V   G V  + L   ++         
Sbjct: 119 PLETGASGLVAYTQEFRIERKLQEDAGILEHEVMVDVAGTVSPEVLMRFERS-------- 170

Query: 173 GDMQVTL--DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
              +V++    + G    +   L+  +  +I  + +     +  + RI  G   L  L  
Sbjct: 171 -PARVSIGRQAEDGKQTGLRFALKGARPGQIAHLCDQMGLTIVAMRRIRIGRVPLAGLQP 229

Query: 231 GSTREVSKKI 240
           G  R ++   
Sbjct: 230 GQWRYLAPHE 239


>gi|325914184|ref|ZP_08176537.1| pseudouridylate synthase, 16S rRNA uridine-516 [Xanthomonas
           vesicatoria ATCC 35937]
 gi|325539687|gb|EGD11330.1| pseudouridylate synthase, 16S rRNA uridine-516 [Xanthomonas
           vesicatoria ATCC 35937]
          Length = 236

 Score =  112 bits (280), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 46/237 (19%), Positives = 87/237 (36%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+ K +A     SR E ++ I    V VNG+++E       +          L  A
Sbjct: 2   SDPIRLDKCVAAQFGCSRGEAQQYIEGGWVSVNGVVVEEPQALATAAQVELAADAVLEPA 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-------LPSIFSRVISVGRLDINTEGLLL 123
           E   L L+                ++  +        L   F R+ +   L+ +  GLL+
Sbjct: 62  EPATLLLHKPAGMTAAAAVALAKPASRSELDNAELRVLKRHFLRLNAPLPLEDDASGLLV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           L+ DG + R L   ++   + + V   G++    +  L  G+V Q       +V+   ++
Sbjct: 122 LSQDGRVLRRLTADASSIEQEFLVEVRGELRPYGMARLAHGLVYQQRSLPPCKVSWQNEE 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   ++  +  +++ +       V  L R+  G   LG L  G  R +    
Sbjct: 182 R----LRFAIKHVQPGQLRYMCGEVGLDVVSLRRLRVGRVSLGKLAIGQWRYLPAGE 234


>gi|148377816|ref|YP_001256692.1| 16S rRNA uridine-516 pseudouridylate synthaseand related
           pseudouridylate synthase [Mycoplasma agalactiae PG2]
 gi|148291862|emb|CAL59253.1| 16S rRNA uridine 516 pseudouridylate synthaseand related
           pseudouridylate synthase [Mycoplasma agalactiae PG2]
          Length = 232

 Score =  112 bits (280), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 55/241 (22%), Positives = 97/241 (40%), Gaps = 29/241 (12%)

Query: 14  QRVSKVIARAGIASRREVE-----------RMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            R+ K IA     SR EV+           R+I  + +K++              D +E+
Sbjct: 4   IRIEKYIADLTNLSRNEVKNKLKKKAIKVNRVILTKLIKID-----------SEKDVVEL 52

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           D   L+  +            +       +   T+FD +     +  S GRLD +TEGLL
Sbjct: 53  DNSILKYEKFQYYMFNKPANFICANSDSEEA--TIFDIVGLPAEKFFSFGRLDKDTEGLL 110

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           +L+NDG +   L  P     + Y V+   ++D + L      I I       +      +
Sbjct: 111 ILSNDGQMCHRLLSPKNHVPKKYYVKVDKKIDSEILLN-HSPIKINDD---FIVSKYILE 166

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
              +    + + EGK  +IK++F    + V  L R+ +G  +L   L  G  R++S+  +
Sbjct: 167 LIDDKGCFLTIYEGKFHQIKRMFGSLGFSVLYLKRVEFGKLKLDNNLKLGQVRKLSEDEV 226

Query: 242 R 242
           +
Sbjct: 227 K 227


>gi|118587632|ref|ZP_01545042.1| ribosomal small subunit pseudouridylate synthase [Stappia aggregata
           IAM 12614]
 gi|118439254|gb|EAV45885.1| ribosomal small subunit pseudouridylate synthase [Stappia aggregata
           IAM 12614]
          Length = 234

 Score =  112 bits (280), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 47/229 (20%), Positives = 85/229 (37%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVK-VNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+E++  I    V  + G  L+  A        I  D  PL  A  
Sbjct: 1   MRLVKLLANLGYGSRKEMQVAIRNGWVTDLKGNRLKADAKTAHED--ILFDDEPLDPAHG 58

Query: 73  TRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             + +        +           + D        + ++GRLD  T G LL T+DG   
Sbjct: 59  VVILMNKPLGYTCSIKDQGRLVYDLLPDRFRMRKPVLSTIGRLDKETSGALLFTDDGTFL 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P ++  ++Y V     +  D+  L   G ++       ++              +
Sbjct: 119 HRVISPKSEVPKIYEVALDRPMKGDEGALFASGDMMLESEDKPLKPAELEV-IDETHARL 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            L EG+  +++++F      V  L R   G   L  L  G  + +S++ 
Sbjct: 178 TLHEGRYHQVRRMFAATGNHVTDLTRSHIGGLGLEGLEEGQWKVLSEEE 226


>gi|257091698|ref|YP_003165339.1| pseudouridine synthase [Candidatus Accumulibacter phosphatis clade
           IIA str. UW-1]
 gi|257044222|gb|ACV33410.1| pseudouridine synthase [Candidatus Accumulibacter phosphatis clade
           IIA str. UW-1]
          Length = 238

 Score =  112 bits (279), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 58/220 (26%), Positives = 84/220 (38%), Gaps = 4/220 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERA-AVNVMSTDHIEVDGVPLRKAERTR 74
           + +++   G  SR E   ++   RV V G +     A          VDG P        
Sbjct: 3   LERLLRSQGFGSRAECRGLVCTGRVSVEGRVCNDPLAQFEPEGLSFAVDGQPWAYRRFVY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L        +              +P +   V +VGRLD +T GLLLLT+DG      
Sbjct: 63  LALNKPAGHECSRRPIHYPSVFSLLPIPLVRRGVQAVGRLDADTTGLLLLTDDGAFIHAC 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     +VY V     VD  ++  L  G+V+       M    D Q   +  +TV L 
Sbjct: 123 TSPRRMVPKVYEVSTRHAVDDGQVAALLSGVVLHDESQAIMAAACDRQGERSLRLTVTL- 181

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
            GK   +K++      +V  L R++ G   L  TL AG  
Sbjct: 182 -GKYHLVKRMVAAAGNRVEALHRVAIGGLALPATLAAGRW 220


>gi|73541573|ref|YP_296093.1| pseudouridine synthase, Rsu [Ralstonia eutropha JMP134]
 gi|72118986|gb|AAZ61249.1| Pseudouridine synthase, Rsu [Ralstonia eutropha JMP134]
          Length = 694

 Score =  112 bits (279), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 63/255 (24%), Positives = 100/255 (39%), Gaps = 32/255 (12%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+SK ++  G+ SRRE +  I +  V V+G  +      V +  +IE+           
Sbjct: 442 IRLSKRMSELGLCSRREADEWIPRGWVIVDGKPVTELGSRVRADANIEIHQAARSEQGER 501

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                  P+          Y     L T  +      T     P     +   GRLDI++
Sbjct: 502 VTVLLHKPMGYVSGQAEDGYEPAAVLFTAENQWSEDPTRKRFAPWQRKSLAPAGRLDIDS 561

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-------------VDQDKLNLLKKGI 165
            GLL+LT DG +AR L    +   + Y VR                    DKL LL+ G+
Sbjct: 562 TGLLVLTQDGRVARALIGEDSNVEKEYLVRVQWHSPDGVVERNVSEVFPADKLELLRHGL 621

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G+     +V+   ++     +   LREG+ R+I+++ E    +V  L R+  G   L
Sbjct: 622 SLDGVVLKPAKVSWQNEEQ----LRFVLREGRKRQIRRMCEQVGLEVVGLKRVRMGRIVL 677

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R +    
Sbjct: 678 GDLPPGQWRFLGPFE 692



 Score = 36.7 bits (83), Expect = 5.9,   Method: Composition-based stats.
 Identities = 8/103 (7%), Positives = 22/103 (21%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           EA+    +     +   R       +        +      +    ++       +R   
Sbjct: 305 EARPRRFSDDNRPQRPRRPEGGEQPQRRFRDDESRPRRFGDDEARPRRFSDDNRPQRPRR 364

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                             +R  +  R    P   + R  +  +
Sbjct: 365 PEGGEQPQRRFRDDESRPRRFGDDDRQRRAPDAGARRGDAPAR 407


>gi|119505843|ref|ZP_01627909.1| Pseudouridine synthase, Rsu [marine gamma proteobacterium HTCC2080]
 gi|119458341|gb|EAW39450.1| Pseudouridine synthase, Rsu [marine gamma proteobacterium HTCC2080]
          Length = 229

 Score =  112 bits (279), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 57/212 (26%), Positives = 97/212 (45%), Gaps = 9/212 (4%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPD 92
           +++AQ R+ ++G+  E  +  V    H+ +D   + +AE+ R  + +KP G+V+   D  
Sbjct: 3   QLLAQGRILLDGLAAESISQVVGPFTHVVLD-QRVLQAEQPRYIMLNKPPGMVSATCDEQ 61

Query: 93  GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152
             + +          +  VGRLD N+ GLLLLTNDG  +R +  P    ++ YRV+    
Sbjct: 62  HSTVLDLVSAPNAKSLHIVGRLDFNSTGLLLLTNDGRWSRGVSSPQKGVVKTYRVQLEQP 121

Query: 153 VDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
              D             + I     ++   +       V     EG+  +IK++F +FN 
Sbjct: 122 FRSDYREAFAAGLYFAFENITTRPAEIRRLSDLSRGRSV-----EGRYHQIKRMFGYFNN 176

Query: 211 KVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           +V  L R+S G   L   L  G+ RE++   L
Sbjct: 177 RVLNLHRLSIGALSLDPKLHQGAWRELTLSEL 208


>gi|325923678|ref|ZP_08185302.1| pseudouridine synthase family protein [Xanthomonas gardneri ATCC
           19865]
 gi|325545844|gb|EGD17074.1| pseudouridine synthase family protein [Xanthomonas gardneri ATCC
           19865]
          Length = 217

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 53/215 (24%), Positives = 89/215 (41%), Gaps = 7/215 (3%)

Query: 47  LERAAVNVMSTDH--IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           +      + +     I VDG PL    R  L L      + T   +    +       + 
Sbjct: 2   VHDPEYPIRADQQSSITVDGQPLAGPARCYLMLNKPRGVVTTVRDEQGRDTVYRCFDGAG 61

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
              +  VGRLD  +EGLLL +ND   A  +  P+T   + Y V+   +   ++L  L+ G
Sbjct: 62  LPWIAPVGRLDKASEGLLLFSNDPQWAAAVTDPATGPDKTYHVQIDCRPSAEQLAQLRAG 121

Query: 165 IVI-----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
           +V       G       V +  +   NAW+ + L EG+NR+I+++       V RL+R++
Sbjct: 122 VVDPDPEGDGALLRAKHVGVLREGERNAWLEIVLDEGRNRQIRRLLAALEIGVLRLVRVA 181

Query: 220 YGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
            G   +G L  G+ R +S + +R            
Sbjct: 182 IGALAMGELGKGAWRMLSAEEVRALTAAPASAPDA 216


>gi|49081944|gb|AAT50372.1| PA1110 [synthetic construct]
          Length = 237

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 50/237 (21%), Positives = 85/237 (35%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+SK +A     SRRE E  I    V V+G ++E     V+      + G      
Sbjct: 2   TDPIRLSKRLAELTACSRREAELHIEGGWVSVDGEVIEEPQFKVLDQRVELLPGARAETI 61

Query: 71  ERTRLWLYHKPI-------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           E   L L+           GL+          +    L   F+R      LD    GL++
Sbjct: 62  EPATLLLHKPAGWRHDDFEGLLAAGRRWSDDPSPLRALKKHFARQRPTLALDSEASGLVV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            +   G+ R L     +  + Y V   G +    L  L+ G+  QG      +V+   + 
Sbjct: 122 FSQQHGVLRKLVDDGARLEQEYLVEVAGDLAAGGLERLRHGLAYQGRRLSPCKVSWQNE- 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
              + +   L++    +++ + E    +V  + R+  G   L  L  G  R +    
Sbjct: 181 ---SHLRFALKDVLPGQLRFMCEREGLEVRSIRRLRIGALSLARLPLGEWRYLGLHE 234


>gi|323253055|gb|EGA36888.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
          Length = 171

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 40/171 (23%), Positives = 76/171 (44%), Gaps = 7/171 (4%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 1   RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     V  D      KG+ +           + +     +   V +
Sbjct: 61  ITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKDLTKPATLEVI----TPVQVRL 116

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 117 TISEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEEEI 167


>gi|254974047|ref|ZP_05270519.1| putative RNA pseudouridine synthase [Clostridium difficile
           QCD-66c26]
 gi|255091448|ref|ZP_05320926.1| putative RNA pseudouridine synthase [Clostridium difficile CIP
           107932]
 gi|255313181|ref|ZP_05354764.1| putative RNA pseudouridine synthase [Clostridium difficile
           QCD-76w55]
 gi|255515866|ref|ZP_05383542.1| putative RNA pseudouridine synthase [Clostridium difficile
           QCD-97b34]
 gi|255648959|ref|ZP_05395861.1| putative RNA pseudouridine synthase [Clostridium difficile
           QCD-37x79]
 gi|306519077|ref|ZP_07405424.1| pseudouridine synthase [Clostridium difficile QCD-32g58]
          Length = 172

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 43/168 (25%), Positives = 77/168 (45%), Gaps = 3/168 (1%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +      +  T    D       +L  +      VGRLD +TEGLL+LTNDG L+  +  
Sbjct: 1   MNKPDGYISATTDKYDPTVLDLIDLSYLAFEPFPVGRLDKDTEGLLVLTNDGKLSHRVLS 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVGLRE 195
           P     + Y  +  G V ++ +    +G+V+         Q+ +  +    + + + + E
Sbjct: 61  PKKHVPKTYYAKIDGVVTEEDVEAFLEGVVLDDGYKTMPSQLNIL-KSDDESEIELTIHE 119

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           GK  ++K++FE    KV  L R+S G  +L   L  G  RE++ + ++
Sbjct: 120 GKFHQVKRMFESVGKKVVYLKRLSMGNLKLDESLELGEYRELTDEEVK 167


>gi|309792033|ref|ZP_07686509.1| pseudouridine synthase [Oscillochloris trichoides DG6]
 gi|308225926|gb|EFO79678.1| pseudouridine synthase [Oscillochloris trichoides DG6]
          Length = 637

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 80/295 (27%), Positives = 122/295 (41%), Gaps = 2/295 (0%)

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           D IEVDG P+RK       + +KP+G V+T  DP GR TV  +L  + +RV  VGRLD++
Sbjct: 6   DVIEVDGQPVRKPTTRTYLVLNKPVGFVSTVDDPQGRPTV-VDLVDVPARVYPVGRLDVD 64

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           +EGLLLLT+DG L   L  P  +  + YR      +D + L   ++G+++ G       V
Sbjct: 65  SEGLLLLTDDGELTHQLTHPRFEIEKEYRALLDRPLDTEALRQWREGVLLNGEPTAPAWV 124

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L        W  V LREG+ R+I++V     ++V RLIR+  G   LG L   + R ++
Sbjct: 125 DLLETTAEGPWFRVVLREGRKRQIREVARLLGYEVLRLIRVREGDLLLGDLPLRAWRPLT 184

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +  +        +              +           E   D +  ++      G  +
Sbjct: 185 EDEVAALRAHVAVRRESGERMDVGGKRQAAAGRGEPRREESRRDDSSPRREDGPPRGRGE 244

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLS-DSGQREENHRRSPSFPSKRSLRRTS 351
            ++   P   R               F   D   R     R    P +R   R S
Sbjct: 245 FRREDGPPRGRGEFRREDGPPRGRGEFRREDGPPRGRGEFRREDGPPRRDEGRGS 299



 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 14/108 (12%), Positives = 24/108 (22%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           RE   P    E +     P    E    D P              +    +      ++ 
Sbjct: 247 REDGPPRGRGEFRREDGPPRGRGEFRREDGPPRGRGEFRREDGPPRRDEGRGSYGAPRRE 306

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
             P  R     +    +         + +RE+   R           R
Sbjct: 307 DGPPRRDEGRGSYGAPRRDEGRGGYGAPRREDGPPRRDEGRGGYGAPR 354


>gi|300691607|ref|YP_003752602.1| pseudouridine synthase [Ralstonia solanacearum PSI07]
 gi|299078667|emb|CBJ51325.1| Pseudouridine synthase [Ralstonia solanacearum PSI07]
          Length = 641

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 62/256 (24%), Positives = 98/256 (38%), Gaps = 32/256 (12%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---- 64
           E+    R+SK ++  G+ SRRE +  I +  V V+G  +      V     IE+      
Sbjct: 384 ESSGLVRLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVRPDAEIEILPAARS 443

Query: 65  -----------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
                       P+          Y     L T  +  +   T           +   GR
Sbjct: 444 EQGERVTVLLHKPVGYVSGQAEDGYEPAAALFTAENQWEEDPTHKRFAAWQHKGLAPAGR 503

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-------------VDQDKLNL 160
           LDI++ GLL+LT DG +AR L    +   + Y VR                   ++ L  
Sbjct: 504 LDIDSTGLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWDAPQGPVEHDVSKVFPEELLEK 563

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           L+ G+ + G      +V+   ++     +   LREGK R+I+++ E    +V  L RI  
Sbjct: 564 LRHGLSLDGEALKPAKVSWQNEEQ----LRFVLREGKKRQIRRMCEQVGLEVVGLKRIRM 619

Query: 221 GPFQLGTLLAGSTREV 236
           G   LG L  G  R +
Sbjct: 620 GRVVLGDLPVGKWRFL 635


>gi|296505025|ref|YP_003666725.1| tRNA pseudouridine synthase A [Bacillus thuringiensis BMB171]
 gi|296326078|gb|ADH09006.1| tRNA pseudouridine synthase A [Bacillus thuringiensis BMB171]
          Length = 169

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 44/168 (26%), Positives = 78/168 (46%), Gaps = 6/168 (3%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
              +HKP+G+  T +D    + +     +   R+  VGRLD  +EGL+LLTNDGG+A  +
Sbjct: 2   YIAFHKPVGITCTAADHIEDNIIDYI--NYPERIFPVGRLDKASEGLILLTNDGGIANQI 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V          ++ + +G+ I+       +VT        +   + L 
Sbjct: 60  LHGDHEHEKEYVVTVDKPFTDWFIDEMSRGVKIKDGMTKPCKVTRV----DQSTFRIVLT 115

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L 
Sbjct: 116 QGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTAEELE 163


>gi|121595983|ref|YP_987879.1| RNA-binding S4 domain-containing protein [Acidovorax sp. JS42]
 gi|120608063|gb|ABM43803.1| RNA-binding S4 domain protein [Acidovorax sp. JS42]
          Length = 266

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 51/268 (19%), Positives = 86/268 (32%), Gaps = 38/268 (14%)

Query: 7   VQENFTP---QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           + E+  P    R+SK +A+    SR   E+ I    V V+G ++E     V S   + + 
Sbjct: 1   MTESSHPTDAVRLSKRVAQQFQCSRTTAEQYIEGGWVSVDGQVVELPGARVASAQSVVLA 60

Query: 63  -DGVPLRKAERTRLWLYHK-----------------------------PIGLVTTHSDPD 92
            D  P+     T L                                   + L+   S   
Sbjct: 61  PDANPMELTPVTLLLHKPPGYEAGLGLVTGATHRAPGAHGSRSQGAPQAVALLNAQSHLP 120

Query: 93  GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152
             +     L   F ++     L     GL++ T D  +AR L+       +   V   GQ
Sbjct: 121 EDAAGTRVLLRHFKQLECFTPLPTEASGLVVYTQDRRVARKLQEDIETLEQECIVEVAGQ 180

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           +    L  L  G+   G     ++V+      S   +   L+  +  +I  + E     V
Sbjct: 181 IADGGLQKLCHGLSFNGRPLPPIKVSWQ----SETRLRFALKGIRPGQIPAMCEAVGLSV 236

Query: 213 NRLIRISYGPFQLGTLLAGSTREVSKKI 240
             + RI  G   L  +  G  R +    
Sbjct: 237 RAIKRIRIGRVPLAKVPEGQWRYLQPWE 264


>gi|146281832|ref|YP_001171985.1| S4 domain-containing protein [Pseudomonas stutzeri A1501]
 gi|145570037|gb|ABP79143.1| S4 domain protein [Pseudomonas stutzeri A1501]
          Length = 241

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 52/242 (21%), Positives = 93/242 (38%), Gaps = 16/242 (6%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRK 69
             P R++K +A     SRRE E  I    V V+G L+E   + V     IE+  G   ++
Sbjct: 2   TDPVRLAKRVAEQFGCSRREAELYIEGGWVTVDGELVEAPFLKVGPQQRIELQPGATAKE 61

Query: 70  AERTRLWLYHKPIGLVTTHS-----------DPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                L L+      + + +                 +  + L     R   +  LD + 
Sbjct: 62  IAPVTLLLHKPAELPIDSDNDGPRRALQASEHWADDPSRTEPLQRHLLRHTLLLPLDADA 121

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GL +L+    + R+L     +  + Y V   G+ ++  L LL KGI  +G      +V+
Sbjct: 122 SGLSVLSQQREVIRLLGDTRNKLEQEYVVEVSGEAEEGGLALLAKGIGHRGRILPKAKVS 181

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
             ++      + V ++E    E++ + E    +V    RI  G   +  L  G  R + +
Sbjct: 182 WQSENR----LRVVVKEPAPGEVRMLCEAIGLRVVASKRIRIGRLSMAKLPVGHWRFLGE 237

Query: 239 KI 240
             
Sbjct: 238 HE 239


>gi|328947358|ref|YP_004364695.1| pseudouridine synthase Rsu [Treponema succinifaciens DSM 2489]
 gi|328447682|gb|AEB13398.1| pseudouridine synthase Rsu [Treponema succinifaciens DSM 2489]
          Length = 255

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 55/238 (23%), Positives = 95/238 (39%), Gaps = 18/238 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+  V  R GI++ R V R++ +  V VNG  +  +   +  +TD + +DG+    A  
Sbjct: 7   ERLDTVFIRRGISTHRRVRRLLQKHNVCVNGTRVLESGFGLNLATDELSIDGIKKNLAPD 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--------VISVGRLDINTEGLLLL 124
             L +  K   + +T  D   ++         F          + +VGRLD +TEGLL+ 
Sbjct: 67  IYLMMNKKSGTICSTKDDGLYKTVYSFIPQKYFYYAKENSLQKIHTVGRLDTDTEGLLIF 126

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T +G  +  L  P     + Y V      + ++     +    +G      +   +    
Sbjct: 127 TTNGDFSHSLANPLFHVKKTYYVELEKS-EPEEQRKFLEKKFSEGFFIPPEKNEREFISR 185

Query: 185 SNAW-------VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
                        + + EGK  ++K++F     KV  L RIS G   L   L  G +R
Sbjct: 186 PAILEWNSANSCRLTITEGKFHQVKRMFSAQGNKVIFLKRISIGSLALDEKLAPGDSR 243


>gi|226943804|ref|YP_002798877.1| 16S rRNA uridine-516 pseudouridylate synthase [Azotobacter
           vinelandii DJ]
 gi|226718731|gb|ACO77902.1| 16S rRNA uridine-516 pseudouridylate synthase [Azotobacter
           vinelandii DJ]
          Length = 236

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 47/236 (19%), Positives = 82/236 (34%), Gaps = 11/236 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E  I    V V+G  +E     V   + +          E
Sbjct: 3   EPIRLSKRLIELYRCSRREAELYIEGGWVSVDGRAVEEPQFKVGDEEVVLHPDAVATPVE 62

Query: 72  RTRLWLYHKPIGLVT-------THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
              L L+      +          +  +        L   F R+ ++  L+    GL + 
Sbjct: 63  PVTLLLHKPAGETLEQALARLGPATRAESDRDPRRPLSRHFHRLTALLPLEPAASGLQVF 122

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           +   G+ R L   S    + + V   G+   D L  L  G+  +G      +V+      
Sbjct: 123 SQQRGVLRRLGEESDAPEQEFVVEIAGEPAADGLARLGHGLDQRGRPLPPCKVSRQ---- 178

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           S   +   L+  +  +I+ +      +V  L RI  G   +  L  G  R + ++ 
Sbjct: 179 SERHLRFALKAPQAGQIEHMCRSLGLEVLALRRIRIGRLAMAGLPVGQWRYLGERE 234


>gi|237751152|ref|ZP_04581632.1| ribosomal large subunit pseudouridine synthase B [Helicobacter
           bilis ATCC 43879]
 gi|229373597|gb|EEO23988.1| ribosomal large subunit pseudouridine synthase B [Helicobacter
           bilis ATCC 43879]
          Length = 267

 Score =  111 bits (276), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 66/267 (24%), Positives = 117/267 (43%), Gaps = 30/267 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV------MSTD-----HIEV 62
            R++  IA     SRRE +R+I +  VK+N  L       V                I +
Sbjct: 1   MRLNHFIALHSKYSRREADRLIIEGAVKINHALATT-KTLVPQIALQNPHAAMKEFKIFI 59

Query: 63  DGVPLRKAERTRL--WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            G  L  A++      +YHKP G + +  D  GR  ++D+L + ++  + VGRLD  +EG
Sbjct: 60  HGKMLHYAKKQNYTAIVYHKPKGELVSKKDSYGRKLIYDSLNARYAHFMPVGRLDFASEG 119

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG------- 173
           LL+L++   +   L   +     +   +    + +  +  +++G+ +Q    G       
Sbjct: 120 LLILSDSKEVVSKLMHSNLPRTYIL--KIDSHITKQMIKAMEEGLTLQNAKAGGHRLSKI 177

Query: 174 ------DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
                  M+  +  +  S + + V + EGKNRE+++ F  FN  V  L R+SYG   L  
Sbjct: 178 KTMEFMPMEYEII-KSASISKLKVRISEGKNRELRRFFAHFNANVLDLRRVSYGFINLNA 236

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQ 254
           L  G TR  +K+   +       +++ 
Sbjct: 237 LPVGKTRFFTKQEYDDLHKFMSEKDSN 263


>gi|166712972|ref|ZP_02244179.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzicola BLS256]
          Length = 236

 Score =  111 bits (276), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 48/237 (20%), Positives = 87/237 (36%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+ K +A A   SR E +R I    V V+G+++E       +      D   L   
Sbjct: 2   SDPIRLDKCVAAAFGCSRGEAQRYIEGGWVSVDGVVVEEPQAPATAAQITLADDAVLSPV 61

Query: 71  ERTRLWLYHKPI-------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           E   L L+            L T  +      +    L   F R+ +   L+    GLL+
Sbjct: 62  EPATLLLHKPAGVSAEAALALATPTTRSALDQSDIRVLKRHFLRLTAPLPLEEAASGLLI 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           L++DG + R L   ++   + + V   G V    +  L  G+V Q       +V+   + 
Sbjct: 122 LSHDGRVLRRLSADASSIEQEFLVEVQGDVRPYGMARLAHGLVYQQRSLSPCKVSWQNED 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   ++  +  +++ +      +V  + R+  G   LG L  G    +    
Sbjct: 182 R----LRFAIKNVQPGQLRYMCGEVGLEVVSIRRLRVGRVSLGKLAIGEWCYLPTGE 234


>gi|222112171|ref|YP_002554435.1| RNA-binding s4 domain-containing protein [Acidovorax ebreus TPSY]
 gi|221731615|gb|ACM34435.1| RNA-binding S4 domain protein [Acidovorax ebreus TPSY]
          Length = 266

 Score =  111 bits (276), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 50/268 (18%), Positives = 85/268 (31%), Gaps = 38/268 (14%)

Query: 7   VQENFTP---QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           + E+  P    R+SK +A+    SR   E+ I    V V+G ++E     V S   + + 
Sbjct: 1   MTESSHPTDAVRLSKRVAQQFQCSRTTAEQYIEGGWVSVDGQVVELPGARVASAQSVVLA 60

Query: 63  -DGVPLRKAERTRLWLYHK-----------------------------PIGLVTTHSDPD 92
            D   +     T L                                   + L+   S   
Sbjct: 61  PDANLMELTPVTLLLHKPPGYEAGLGLVTGATHGAPGAHGSRSQGAPQAVTLLNAQSHLP 120

Query: 93  GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152
             +     L   F ++     L     GL++ T D  +AR L+       +   V   GQ
Sbjct: 121 EDAAGTRVLLRHFKQLECFTPLPTEASGLVVYTQDRRVARKLQEDIETLEQECIVEVAGQ 180

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           +    L  L  G+   G     ++V+      S   +   L+  +  +I  + E     V
Sbjct: 181 IADGGLQKLCHGLSFNGRPLPPIKVSWQ----SETRLRFALKGIRPGQIPAMCEAVGLSV 236

Query: 213 NRLIRISYGPFQLGTLLAGSTREVSKKI 240
             + RI  G   L  +  G  R +    
Sbjct: 237 RAIKRIRIGRVPLAKVPQGQWRYLQPWE 264


>gi|319940718|ref|ZP_08015060.1| pseudouridine synthase [Sutterella wadsworthensis 3_1_45B]
 gi|319805869|gb|EFW02636.1| pseudouridine synthase [Sutterella wadsworthensis 3_1_45B]
          Length = 235

 Score =  111 bits (276), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 41/227 (18%), Positives = 79/227 (34%), Gaps = 4/227 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERTR 74
           ++ ++ + G  +R +   + A   V ++G  L     +       +   G+    ++   
Sbjct: 3   LADILFKQGFGTRYDCRSIAASGAVSIDGRELTDPDEDFDPEGLVLTWRGMQWPVSDNVL 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +        +               P     V  VGRLD +T GLLL T++G L   L
Sbjct: 63  IAMNKPTGYECSLKPSAHPSVMNLLPGPLRTRGVQPVGRLDWDTTGLLLFTDNGALLHRL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     +VYR              L  G+V+       +          +  + + + 
Sbjct: 123 THPKKHVNKVYRATLSHPAANGTCEKLLSGVVLDDDP-KPVFAKAAELMAPD-VLMLTIS 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
           +GK  ++K++      +V  L RI  G ++L   L  G    +    
Sbjct: 181 QGKYHQVKRMVAACGNRVVALHRIKVGAYELPADLKPGEWCWLRGPE 227


>gi|330953605|gb|EGH53865.1| pseudouridine synthase, Rsu [Pseudomonas syringae Cit 7]
          Length = 343

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 60/277 (21%), Positives = 101/277 (36%), Gaps = 9/277 (3%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +        + T        +           R I++GRLDINT GLL+ T DG LA  
Sbjct: 15  VIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLDINTTGLLMFTTDGELANR 74

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-KGSNAWVTVG 192
           L  PS +  R Y VR  G+VD D L  LK G++++        +      +G N W    
Sbjct: 75  LMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPARFTDIQQAPGGEGFNHWYHCV 134

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLLE 251
           + EG+NRE+++++E     V+RL R+ YGP  L   L  G  RE+S+  + + L   +  
Sbjct: 135 VMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRWREMSQYEV-DILAAEVGL 193

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV------ 305
           +          + + + R +      +           +     +  ++           
Sbjct: 194 QPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVRTLRPAAGAPATGGERAPRQPQITGSE 253

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
             R    ++               +       S   P
Sbjct: 254 RDRPRGGDLTQRPSPRKDSGKPGSRAPRPADNSRGTP 290


>gi|308050789|ref|YP_003914355.1| ribosomal small subunit pseudouridine synthase A [Ferrimonas
           balearica DSM 9799]
 gi|307632979|gb|ADN77281.1| ribosomal small subunit pseudouridine synthase A [Ferrimonas
           balearica DSM 9799]
          Length = 230

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 56/231 (24%), Positives = 101/231 (43%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ +++ +    +RR V  ++ Q RV VN +++      V + D +  DG   +  +  
Sbjct: 1   MRLDRLLCQHPKWNRRHVLGLLVQGRVTVNEVVVTNPTHEVSAFDTVHADGELCQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP G+++  SDP   + +     ++   +   GRLD  + GL+LLTNDG  +R 
Sbjct: 61  HYLMLNKPAGILSATSDPVHPTVMQLLPEALAKDLHIGGRLDRASTGLMLLTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
              P  +  +VYRV     +  D   +  +      + I     Q+             +
Sbjct: 121 ATDPDKRSPKVYRVTLANPIHPDTEQVFAEGIYFPFEAITTSPAQLERL----GECECRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EG+  +IK++F  F   V  L R S G   L  TL  G  R ++ + +
Sbjct: 177 TIYEGRYHQIKRMFGRFRNPVVALHRESMGAITLDPTLAPGQYRALTAEEI 227


>gi|290977401|ref|XP_002671426.1| predicted protein [Naegleria gruberi]
 gi|284084995|gb|EFC38682.1| predicted protein [Naegleria gruberi]
          Length = 244

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 94/245 (38%), Gaps = 21/245 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRV--KVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
           R+ +V++  GI SR +V   I +  V   +    +      +       + V+G P    
Sbjct: 3   RIDRVLSGMGICSRSDVIHYIRKNEVMDTIKKQRILSLKHKISEHQLESLMVNGKPFPFP 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISV----GRLDINTEGLLLLT 125
                   +KP   + +          ++D LP  F          GRLD+++ GLL++T
Sbjct: 63  TLNLTIALNKPESYLCSTQRESSNHKIIYDLLPPEFLNRNPTLGNVGRLDLDSCGLLIMT 122

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI------VIQGICYGDMQVTL 179
            DG L   +     +   +       + D +   + +           +      +    
Sbjct: 123 QDGDLHHRILSADVEKTYLVEFVPPIESDVELNQMKELFFSGDLQLRSEDSTLKPITN-- 180

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL---AGSTREV 236
             +  + + +++ + EGK  +++++F   + +V  L RI  G   L  L    +G+   +
Sbjct: 181 -FEYINPSTISISIVEGKYHQVRRMFAACSKRVVGLKRIKIGDLTLEGLNIETSGAWCVL 239

Query: 237 SKKIL 241
           SK++L
Sbjct: 240 SKEVL 244


>gi|219122723|ref|XP_002181690.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217406966|gb|EEC46904.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 217

 Score =  110 bits (274), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 55/221 (24%), Positives = 94/221 (42%), Gaps = 26/221 (11%)

Query: 27  SRREVERMIAQQRVKVNGILLER-AAVNVMS-TDHIEVDGVPL----RKAERTRLWLYHK 80
           SRRE +++I   RV VN I ++      V+   D I +DG+P+              Y K
Sbjct: 1   SRREADKLIEAGRVSVNDIPVKSKGGFKVVPFHDKITLDGIPVTGTSDATINFDYVKYWK 60

Query: 81  PIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           P+G+  T       + +            R+  VGRLD  T GL+LLT+DG +   +   
Sbjct: 61  PVGVTCTTDRKIAGNIIDALEEAGFDSSKRIFPVGRLDKETSGLILLTSDGRVPNAVLRG 120

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-------------CYGDMQVTLDTQKG 184
             +  ++Y+V     V    +  L+ G++I  +                   V +  ++ 
Sbjct: 121 RHKQPKIYQVWVDRPVLAKDVAQLRDGVIITTVAQRDGNRAEPLTARTKSCAVQVLGREK 180

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
               + + L EG+NR+I+K+    N+ V RL R+ +    L
Sbjct: 181 ----LQLTLVEGRNRQIRKMLGALNYTVKRLHRVQFMELTL 217


>gi|254418383|ref|ZP_05032107.1| conserved hypothetical protein, putative [Brevundimonas sp. BAL3]
 gi|196184560|gb|EDX79536.1| conserved hypothetical protein, putative [Brevundimonas sp. BAL3]
          Length = 244

 Score =  110 bits (274), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 49/233 (21%), Positives = 90/233 (38%), Gaps = 7/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV----MSTDHIEVDGVPLRKA 70
           RV +++   G  SR E+ RM     + ++G  L   +  +         +E+DG PL   
Sbjct: 8   RVDRLLGSMGYGSRAEMARMAKAGGIVLDGADLTDVSRRIPVTRDLPTRMEIDGEPLDPV 67

Query: 71  ERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   + L        +   +       +     S    + ++GRLD  T GLLLLT+DG 
Sbjct: 68  QGLVILLNKPLGMTCSHKEEGALVYDILPGRWRSRDPAISTIGRLDKQTTGLLLLTDDGD 127

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +  P     +VYR      +   + +L   G ++       +   +     S    
Sbjct: 128 LLHRVISPKRHVAKVYRAGLARPLMGTEGDLFASGELVLEGEDKPLAPAVLEV-VSPTEA 186

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            + + EG+  +++++F      V  L R   G   L   L  G  R ++ + +
Sbjct: 187 LLTVTEGRYHQVRRMFAAAGNHVETLHRERLGGLVLPADLAPGQWRLLTPEEI 239


>gi|15675319|ref|NP_269493.1| putative 16S pseudouridylate synthetase [Streptococcus pyogenes M1
           GAS]
 gi|13622499|gb|AAK34214.1| putative 16S pseudouridylate synthetase [Streptococcus pyogenes M1
           GAS]
          Length = 194

 Score =  109 bits (273), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 47/194 (24%), Positives = 81/194 (41%), Gaps = 2/194 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +   + 
Sbjct: 1   MRLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQRVTHPKH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + + L      +                       +  VGRLD +TEGL+LLT++G L  
Sbjct: 61  SYIILNKPSGVVSAKKDTNYLTVIDQLAEEDKSPDLYPVGRLDRDTEGLVLLTDNGPLGF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +  PS    + Y V  +G + +D  +    GI    G      Q+T+       +  ++
Sbjct: 121 RMLHPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQSQASL 180

Query: 192 GLREGKNREIKKVF 205
            + EGK  ++KK F
Sbjct: 181 TISEGKFHQVKKCF 194


>gi|299067456|emb|CBJ38655.1| Pseudouridine synthase [Ralstonia solanacearum CMR15]
          Length = 687

 Score =  109 bits (273), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 62/256 (24%), Positives = 99/256 (38%), Gaps = 32/256 (12%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---- 64
           E+    R+SK ++  G+ SRRE +  I +  V V+G  +      V     +E+      
Sbjct: 430 ESSGLVRLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVRPDAEVEILPAARS 489

Query: 65  -----------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
                       P+          Y     L T  +  +   T           +   GR
Sbjct: 490 EQGERVTVLLHKPVGYVSGQAEDGYEPAAALFTAENQWEEDPTRKHFAAWQHKGLAPAGR 549

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-------------VDQDKLNL 160
           LDI++ GLL+LT DG +AR L    +   + Y VR                   +D L +
Sbjct: 550 LDIDSTGLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWNAPQGPVEHDISKVFPEDLLEM 609

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           L+ G+ + G      +V+   ++     +   LREGK R+I+++ E    +V  L RI  
Sbjct: 610 LRHGLSLDGEALKPAKVSWQNEEQ----LRFVLREGKKRQIRRMCEQVGLEVVGLKRIRM 665

Query: 221 GPFQLGTLLAGSTREV 236
           G   LG L  G  R +
Sbjct: 666 GSIVLGDLPVGKWRFL 681



 Score = 35.9 bits (81), Expect = 9.2,   Method: Composition-based stats.
 Identities = 8/112 (7%), Positives = 22/112 (19%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            +   ++  P    + Q               +         +   R   +  +      
Sbjct: 213 PRRFDDERPPRRSGDDQRPPRRFGDERPPRRFEDRPPRRFDDERPPRRSGDDQRPPRRFD 272

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
            ++       R                     +R ++ R    F   +   R
Sbjct: 273 DERPPRRFEDRPPRRFDDERPPRKFGDDQRPPRRFDDERPPRRFGDDQRPPR 324



 Score = 35.9 bits (81), Expect = 9.6,   Method: Composition-based stats.
 Identities = 12/113 (10%), Positives = 22/113 (19%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R             +   P  S +     R         D  R  + S        +   
Sbjct: 305 RRFDDERPPRRFGDDQRPPRRSDDARPPRRFEDRPPRRFDDERPPRRSGDDQRPPHRFGD 364

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             P  R                  SD  +        P+   +      + ++
Sbjct: 365 ERPPRRFEDRPPRRFDDERPPRRFSDDQRPPRRFEDRPARAPRPEREERAPQR 417


>gi|291532977|emb|CBL06090.1| ribosomal large subunit pseudouridine synthase B [Megamonas
           hypermegale ART12/1]
          Length = 173

 Score =  109 bits (273), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 54/167 (32%), Positives = 89/167 (53%), Gaps = 2/167 (1%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           + +KP G +++  D  GR TV D L  +  R+  +GRLD NTEGLLLLTNDG     L  
Sbjct: 1   MLNKPKGYISSVKDEKGRKTVVDILSDVEERIFPIGRLDYNTEGLLLLTNDGEFMNKLLH 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTVGLR 194
           P  +  + Y  R  G ++ + L+ L  G+ ++        V LD+       + V + + 
Sbjct: 61  PKYEIGKTYVARIDGIINMEDLDKLANGVKLEDGKTAPADVYLDSINKTLKESRVEITIY 120

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           EGKNR+++++F+   ++V  L RI++    L  L  G  R++++  L
Sbjct: 121 EGKNRQVRRMFKALGYEVKALKRIAFAGLTLSKLKRGEYRKLTETEL 167


>gi|282876081|ref|ZP_06284948.1| pseudouridylate synthase [Staphylococcus epidermidis SK135]
 gi|281295106|gb|EFA87633.1| pseudouridylate synthase [Staphylococcus epidermidis SK135]
          Length = 194

 Score =  109 bits (272), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 55/175 (31%), Positives = 98/175 (56%), Gaps = 2/175 (1%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +     L++KP  ++T+ SD  GR  V D    + SR+  VGRLD +T G+LLLTNDG 
Sbjct: 10  KKTKIYILFYKPTQVITSVSDDRGRRVVTDYFDDLESRIYPVGRLDYDTSGVLLLTNDGE 69

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNA 187
              ++  P  +  + Y  +  G + ++++  L+KGI ++       QV +    ++ +  
Sbjct: 70  FTNLMTHPRYRIKKKYVAKLKGYLMREEIKQLEKGIELEDGYTQPAQVKIKKQDKEKNTT 129

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V + + EG+NR+++++FE+F  +VN+L RI +GP  L  L AG  R ++   ++
Sbjct: 130 LVEITISEGRNRQVRRMFEYFGHQVNKLTRIQFGPIDLKGLNAGEGRVLTPHEVK 184


>gi|167035218|ref|YP_001670449.1| RNA-binding S4 domain-containing protein [Pseudomonas putida GB-1]
 gi|166861706|gb|ABZ00114.1| RNA-binding S4 domain protein [Pseudomonas putida GB-1]
          Length = 236

 Score =  109 bits (272), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 45/237 (18%), Positives = 81/237 (34%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+SK +      SRRE E+ I    V V+G+++E+    V       + G      
Sbjct: 2   SEPVRLSKRLIEQLGCSRREAEQYIEGGWVTVDGVVVEQPQFKVEQQRVELLPGARAETL 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDG-------RSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           E   L L         T                    L   F+R   V  L+    GL +
Sbjct: 62  EPVTLLLNQPAGVDSETARASMNMASLSEAHREGVRALHGHFARQDCVAPLERGASGLQV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T D  + R +E    +  + + V   G+     L  L +G           + +   + 
Sbjct: 122 FTQDWRVTRKVEADLRRLEQEFIVEVRGETTPQALERLARGATRNDRELPKAKASWQNE- 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                + + L+  +  +I ++  +   ++  + RI  G   +G L  G  R ++   
Sbjct: 181 ---THLRMVLKNPQPGQISELCAYLRLELISMRRIRLGGVSMGKLPLGQWRYLATTE 234


>gi|170723179|ref|YP_001750867.1| RNA-binding S4 domain-containing protein [Pseudomonas putida W619]
 gi|169761182|gb|ACA74498.1| RNA-binding S4 domain protein [Pseudomonas putida W619]
          Length = 252

 Score =  109 bits (272), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 43/237 (18%), Positives = 82/237 (34%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+SK +      SRRE E  I    V V+G+++E+    V       + G      
Sbjct: 18  SEPVRLSKRLIEQLGCSRREAELYIEGGWVTVDGVVVEQPQFKVEHQAVELLPGANAEAL 77

Query: 71  ERTRLWLYHKPIGLVTTHSDPDG-------RSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           +   L L       + T                    L   F+R+     L+    GL +
Sbjct: 78  DPVTLLLNQPAGVDIDTARASMNMASLSEAHREGVRALHGHFTRLTCSAPLERGASGLQV 137

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T D  + R +E    +  + Y +   G+     L  L +G           + +   + 
Sbjct: 138 FTQDWRVTRKIEADLRRLEQEYIIEVRGETTPQALERLARGATRNDRELPKAKASWQNE- 196

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                + + L+  +  +I ++  +   ++  + RI  G   +G L  G+ R ++   
Sbjct: 197 ---THLRLALKNPQPGQISEICAYLRLEILSMRRIRLGGVSMGKLPVGNWRYLAGTE 250


>gi|300704234|ref|YP_003745837.1| pseudouridine synthase [Ralstonia solanacearum CFBP2957]
 gi|299071898|emb|CBJ43227.1| Pseudouridine synthase [Ralstonia solanacearum CFBP2957]
          Length = 677

 Score =  109 bits (272), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 62/256 (24%), Positives = 97/256 (37%), Gaps = 32/256 (12%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           E+    R+SK ++  G+ SRRE +  I +  V V+G  +      V     IE+      
Sbjct: 420 ESSGLVRLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVRPDAEIEILPAARS 479

Query: 63  -DGVPLR--------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
             G  +                  Y     L T  +  +   T           +   GR
Sbjct: 480 EQGERVTVLLHKPMGYVSGQAEDGYEPAATLFTAENQWEEDPTHKRFAAWQHKGLAPAGR 539

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-------------VDQDKLNL 160
           LDI++ GLL+LT DG +AR L    +   + Y VR                   ++ L  
Sbjct: 540 LDIDSTGLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWDAPQGPVEHDISKVFPEELLEK 599

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           L+ G+ + G      +V+   ++     +   LREGK R+I+++ E     V  L RI  
Sbjct: 600 LRHGLSLDGEALKPAKVSWQNEEQ----LRFVLREGKKRQIRRMCEQVGLTVVGLKRIRM 655

Query: 221 GPFQLGTLLAGSTREV 236
           G   LG L  G  R +
Sbjct: 656 GSVVLGDLPVGKWRFL 671


>gi|26987926|ref|NP_743351.1| S4 domain-containing protein [Pseudomonas putida KT2440]
 gi|24982636|gb|AAN66815.1|AE016310_7 S4 domain protein [Pseudomonas putida KT2440]
 gi|313497548|gb|ADR58914.1| RNA-binding S4 domain-containing protein [Pseudomonas putida
           BIRD-1]
          Length = 236

 Score =  109 bits (271), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 43/237 (18%), Positives = 82/237 (34%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+SK +      SRRE E+ I    V V+G+++E+    V       + G      
Sbjct: 2   SEPVRLSKRLIEQLGCSRREAEQYIEGGWVTVDGVVVEQPQFKVEQQRVELLPGARAETL 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDG-------RSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           E   L L                              L   F+R   V  L+    GL +
Sbjct: 62  EPVTLLLNQPAGMDSEDARASMNMGSLSEAHREGVRALHGHFARQACVAPLERGASGLQV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T D  ++R +E    +  + + +   G+     L  L +G +         + +   + 
Sbjct: 122 FTQDWRVSRKIEADLRRLEQEFIIEVRGETTPQALERLARGAMRNDRELPKAKASWQNE- 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                + + L+  +  +I ++  +   ++  + RI  G   +G L  G  R ++   
Sbjct: 181 ---THLRMVLKNPQPGQISELCAYLRLELLGMRRIRLGGVSMGKLPLGQWRYLATSE 234


>gi|83748810|ref|ZP_00945823.1| Ribosomal large subunit pseudouridine synthase F [Ralstonia
           solanacearum UW551]
 gi|207743247|ref|YP_002259639.1| hypothetical protein RSIPO_01416 [Ralstonia solanacearum IPO1609]
 gi|83724502|gb|EAP71667.1| Ribosomal large subunit pseudouridine synthase F [Ralstonia
           solanacearum UW551]
 gi|206594644|emb|CAQ61571.1| hypothetical protein RSIPO_01416 [Ralstonia solanacearum IPO1609]
          Length = 677

 Score =  109 bits (271), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 62/256 (24%), Positives = 97/256 (37%), Gaps = 32/256 (12%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           E+    R+SK ++  G+ SRRE +  I +  V V+G  +      V     IE+      
Sbjct: 420 ESSGLVRLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVRPDAEIEILPAARS 479

Query: 63  -DGVPLR--------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
             G  +                  Y     L T  +  +   T           +   GR
Sbjct: 480 EQGERVTVLLHKPMGYVSGQAEDGYEPAATLFTAENQWEEDPTHKRFAAWQHKGLAPAGR 539

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-------------VDQDKLNL 160
           LDI++ GLL+LT DG +AR L    +   + Y VR                   ++ L  
Sbjct: 540 LDIDSTGLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWDAPQGPVEHDISKVFPEELLEK 599

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           L+ G+ + G      +V+   ++     +   LREGK R+I+++ E     V  L RI  
Sbjct: 600 LRHGLSLDGEALKPAKVSWQNEEQ----LRFVLREGKKRQIRRMCEQVGLTVVGLKRIRM 655

Query: 221 GPFQLGTLLAGSTREV 236
           G   LG L  G  R +
Sbjct: 656 GSVVLGDLPVGKWRFL 671



 Score = 36.3 bits (82), Expect = 7.2,   Method: Composition-based stats.
 Identities = 8/104 (7%), Positives = 20/104 (19%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                 +                           DD    ++   +    S  ++     
Sbjct: 94  AKPRRMQGDRPPRRFDDERPPRRFGDDQRPPRRFDDERPPRRFEDRPPRRSDDERPPRRF 153

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                    +  +     F     +R ++ R    F   +   R
Sbjct: 154 GDDQRPPRRFGDERPPRRFEDRPPRRSDDERPPRKFGDDQRPPR 197


>gi|327480070|gb|AEA83380.1| S4 domain-containing protein [Pseudomonas stutzeri DSM 4166]
          Length = 241

 Score =  109 bits (271), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 52/242 (21%), Positives = 92/242 (38%), Gaps = 16/242 (6%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRK 69
             P R++K +A     SRRE E  I    V V+G L+E   + V     IE+  G   ++
Sbjct: 2   TDPVRLAKRVAEQFGCSRREAELYIEGGWVTVDGELVEAPFLKVGPQQRIEMQPGATAKE 61

Query: 70  AERTRLWLYHKPIGLVTTHS-----------DPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                L L+      + + +                 +  + L     R   +  LD   
Sbjct: 62  IAPVTLLLHKPAELPIDSDNDGPRRALQASEHWADDPSRTEPLQRHLLRHTLLLPLDAGA 121

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GL +L+    + R+L     +  + Y V   G+ ++  L LL KGI  +G      +V+
Sbjct: 122 SGLSVLSQQREVIRLLGDTRNKLEQEYVVEVSGEAEEGGLALLAKGIGHRGRILPKAKVS 181

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
             ++      + V ++E    E++ + E    +V    RI  G   +  L  G  R + +
Sbjct: 182 WQSENR----LRVVVKEPAPGEVRMLCEAIGLRVVASKRIRIGRLSMAKLPVGHWRFLGE 237

Query: 239 KI 240
             
Sbjct: 238 HE 239


>gi|298492438|ref|YP_003722615.1| pseudouridine synthase ['Nostoc azollae' 0708]
 gi|298234356|gb|ADI65492.1| pseudouridine synthase ['Nostoc azollae' 0708]
          Length = 195

 Score =  108 bits (270), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 50/188 (26%), Positives = 78/188 (41%), Gaps = 17/188 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   +  +     L     +     T+ D +      +  VGRLD ++EGL+LLTNDG 
Sbjct: 3   NDFKYIIFHKPYGVLSQFTQESPKHITLKDYID--VPEIYPVGRLDWDSEGLMLLTNDGQ 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------- 180
           L   L  P     R Y V+     D + +N L  G+ IQ       QV L          
Sbjct: 61  LQHRLANPRFGHKRTYWVQLEHIPDGEAINKLCTGVEIQNYQTRPAQVKLFLEEPTVSER 120

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    AW+ + L EGKNR+++++     +   RLIR+S    QL  L  G  R
Sbjct: 121 NPPIRFRKNIPTAWLEMTLTEGKNRQVRRMTAAVGFPTLRLIRVSITNLQLNGLQPGEWR 180

Query: 235 EVSKKILR 242
            ++   ++
Sbjct: 181 YLTAPEIQ 188


>gi|301510575|ref|ZP_07235812.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter baumannii
           AB058]
          Length = 210

 Score =  108 bits (270), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 41/204 (20%), Positives = 77/204 (37%), Gaps = 3/204 (1%)

Query: 38  QRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRST 96
             V ++G ++          +    V G   +  E+  + L        +          
Sbjct: 1   GSVIIDGEVVSDLKKQFSPENFEFSVFGQNYQYREKIYIALRKPQGFECSHQPQHHQSVF 60

Query: 97  VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
                  I   V +VGRLD +T GLLLLT+DG   + L  P     +VY V  +  V  +
Sbjct: 61  SLLPETMIHRGVQAVGRLDQDTTGLLLLTDDGKYLQALTHPRKHVPKVYHVTTYDPVTPE 120

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
           ++ +L +G+ +           +         +T+ + +G   ++K++      KV +L 
Sbjct: 121 QIEMLTQGVNLHQEKGVFAATDVALL--GTHQLTMTIHQGVYHQVKRMIAAVGNKVEKLH 178

Query: 217 RISYGPFQLGTLLAGSTREVSKKI 240
           R   G   L  +  G    +S++ 
Sbjct: 179 RHQIGQLVLPEIEEGGWVYLSEQE 202


>gi|120609486|ref|YP_969164.1| RNA-binding S4 domain-containing protein [Acidovorax citrulli
           AAC00-1]
 gi|120587950|gb|ABM31390.1| RNA-binding S4 domain protein [Acidovorax citrulli AAC00-1]
          Length = 267

 Score =  108 bits (269), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 50/253 (19%), Positives = 79/253 (31%), Gaps = 30/253 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+SK +A     SRRE E +I    V+V+G + E     V     + V      +    
Sbjct: 17  IRLSKRVAEMRGCSRREAEWLIEGGWVQVDGRMTEAPGARVRPDQDVVVAQNAKAEEAPP 76

Query: 74  RLWLYHKPIGLVT--------------------------THSDPDGRSTVFDNLPSIFSR 107
              L HKP G                                   G S     L   F +
Sbjct: 77  VTLLLHKPAGWEAGIGHGPAGDPRQARSGGAPDAGTLLEPGRRYVGDSPPVRVLQRHFRQ 136

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
                 L     GL++ T D  +AR L        +       G++ +  L  L +G+  
Sbjct: 137 QECFTPLADAASGLVVYTQDRRMARRLAEDIELLEQECIATVDGRIAEGGLERLCRGLEF 196

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G      +V+      S   +   L+  +  +I  + E    +V  L R+  G   L  
Sbjct: 197 NGRPLPPAKVSWQ----SETRLRFALKGIRPGQIPAMCEAVGLQVTALKRLRIGRVSLAR 252

Query: 228 LLAGSTREVSKKI 240
           +  G  R +    
Sbjct: 253 VPEGQWRYLLPWE 265


>gi|325919307|ref|ZP_08181345.1| pseudouridylate synthase, 16S rRNA uridine-516 [Xanthomonas
           gardneri ATCC 19865]
 gi|325550205|gb|EGD21021.1| pseudouridylate synthase, 16S rRNA uridine-516 [Xanthomonas
           gardneri ATCC 19865]
          Length = 236

 Score =  108 bits (269), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 45/237 (18%), Positives = 86/237 (36%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+ K +A     SR E ++ I    V V+G+++E       +          L  A
Sbjct: 2   SEPIRLDKCVAALFGCSRGEAQQYIEGGWVSVDGVVVEEPQTLATAPQVTLAADAVLAPA 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRST-------VFDNLPSIFSRVISVGRLDINTEGLLL 123
           E   L L+                +            L   F R+ +   L+    GLL+
Sbjct: 62  EPATLLLHKSAGMTAEAALALAIPAARSSLDQANVRVLKRHFLRLSAPLPLEDEASGLLV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           L+ DG + R L   +T   + + V   G++    +  L  G+V Q       +V+   ++
Sbjct: 122 LSQDGRVLRRLSADATSIEQEFLVEVSGELRPYGMARLAHGLVYQQRSLSPCKVSWQNEE 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   ++  +  +++ + +    +V  + R+  G   LG L  G  R +    
Sbjct: 182 R----LRFAIKHVQPGQLRFMCKEVGLEVVSIRRLRVGRISLGKLAIGEWRYLPAGE 234


>gi|172039623|ref|YP_001806124.1| pseudouridine synthase [Cyanothece sp. ATCC 51142]
 gi|171701077|gb|ACB54058.1| probable pseudouridine synthase [Cyanothece sp. ATCC 51142]
          Length = 206

 Score =  108 bits (269), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 52/196 (26%), Positives = 81/196 (41%), Gaps = 23/196 (11%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             +  R  L++KP G++   +D                 V SVGRLD ++EGLL LTN+G
Sbjct: 2   LNKNYRYLLFNKPYGVLCQFTDNTENPRPTLKDYIPVPDVYSVGRLDRDSEGLLFLTNNG 61

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   L        R Y V+     D+  LN L++G+ I+       +V L         
Sbjct: 62  LLKHRLSHRQFAHPRTYLVQVERIPDETTLNQLRQGVAIKDYKTRPAKVKLLKSPPAIPP 121

Query: 181 -------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG--------PFQL 225
                   +    AW+ + L EG+NR+++++     +   RLIR + G           L
Sbjct: 122 RDPPIRYRKTVPTAWLAMTLTEGRNRQVRRMTAAVGYPTLRLIRTAIGVQTQGKITNLTL 181

Query: 226 GTLLAGSTREVSKKIL 241
             L  G  RE++   L
Sbjct: 182 EGLNPGQWRELTPSEL 197


>gi|148546465|ref|YP_001266567.1| RNA-binding S4 domain-containing protein [Pseudomonas putida F1]
 gi|148510523|gb|ABQ77383.1| RNA-binding S4 domain protein [Pseudomonas putida F1]
          Length = 247

 Score =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 83/238 (34%), Gaps = 13/238 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-VDGVPLRK 69
             P R+SK +      SRRE E+ I    V V+G+++E+    V     +E + G     
Sbjct: 13  SEPVRLSKRLIEQLGCSRREAEQYIEGGWVTVDGVVVEQPQFKV-EQQRVELLPGARAET 71

Query: 70  AERTRLWLYHKPIGLVTTHSDPDG-------RSTVFDNLPSIFSRVISVGRLDINTEGLL 122
            E   L L                              L   F+R   V  L+    GL 
Sbjct: 72  LEPVTLLLNQPAGMDSEDARASMNMGSLSEAHREGVRALHGHFARQACVAPLERGASGLQ 131

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + T D  ++R +E    +  + + +   G+     L  L +G +         + +   +
Sbjct: 132 VFTQDWRVSRKIEADLRRLEQEFIIEVRGETTPQALERLARGAMRNDRELPKAKASWQNE 191

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 + + L+  +  +I ++  +   ++  + RI  G   +G L     R ++   
Sbjct: 192 ----THLRMVLKNPQPGQISELCAYLRLELLGMRRIRLGGVSMGKLPLAQWRYLATSE 245


>gi|317406580|gb|EFV86770.1| RNA pseudouridylate synthase [Achromobacter xylosoxidans C54]
          Length = 241

 Score =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 43/237 (18%), Positives = 84/237 (35%), Gaps = 16/237 (6%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-VDGVPLRK 69
               R++K +A     SR + ER I    V V+G ++E     V     +  + G  L +
Sbjct: 2   SDSVRLAKRLAAEQSCSRGDAERYIEGGWVAVDGKVVEEPGFRVSPGQVVVLLPGARLEE 61

Query: 70  AERTRLWLYHKPIGLVTTHSD-----------PDGRSTVFDNLPSIFSRVISVGRLDINT 118
                + ++       +  +              G  +    L  +F+ +     L+   
Sbjct: 62  MRPVSILVHKPAGLSASDPAHSALGLVVPENLMPGDRSGQRYLKRMFNGLKLATPLERAA 121

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GL++ T +  +AR L        + Y  +  G +D   L  L++G+  +G     M+V+
Sbjct: 122 SGLVVYTQEYAVARKLVEEGRHVEQEYIAQVRGTLDAVGLARLQRGLAYEGRPATPMKVS 181

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              +      +   L+      I+   +    ++  L RI  G   +  L  G  R 
Sbjct: 182 WQNE----THLRFALKTPALGFIEYACDMAGLELQALRRIRIGRLPMAGLAVGQWRY 234


>gi|186681253|ref|YP_001864449.1| pseudouridine synthase [Nostoc punctiforme PCC 73102]
 gi|186463705|gb|ACC79506.1| pseudouridine synthase [Nostoc punctiforme PCC 73102]
          Length = 192

 Score =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 55/188 (29%), Positives = 82/188 (43%), Gaps = 17/188 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                +  Y     L     D    ST+ D +      V  VGRLD ++EGLLLLTNDG 
Sbjct: 3   NHYRYIIFYKPYGVLSQFTKDAPTHSTLKDYID--VPDVYPVGRLDWDSEGLLLLTNDGQ 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG----- 184
           L   L  P     R Y V+     D+D +  L+ G+ IQ       QV L +++      
Sbjct: 61  LQHRLAHPRFGHKRTYWVQVERIPDEDAIKRLQTGVKIQDYRTQPAQVRLLSKEPELPER 120

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       AW+ + L EGKNR+++++     +   RL+R+S    QL  L  G  R
Sbjct: 121 TPPIRFRKNVPTAWLEMTLTEGKNRQVRRMTAAVGFPTLRLVRVSIAHLQLDDLQLGEWR 180

Query: 235 EVSKKILR 242
           +++   L+
Sbjct: 181 DLTTSELQ 188


>gi|163747964|ref|ZP_02155293.1| ribosomal small subunit pseudouridine synthase A [Oceanibulbus
           indolifex HEL-45]
 gi|161378761|gb|EDQ03201.1| ribosomal small subunit pseudouridine synthase A [Oceanibulbus
           indolifex HEL-45]
          Length = 248

 Score =  107 bits (267), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 44/231 (19%), Positives = 90/231 (38%), Gaps = 7/231 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV----MSTDHIEVDGVPLRKA 70
           R+ +++   G  SR E+ ++   +R+ ++G  +   A  +      T+ + V G PL   
Sbjct: 8   RIDRLLGSLGYGSRGEIAQIARARRIVLDGARVANVAKRIPMSPDLTERMTVHGAPLDPL 67

Query: 71  ERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               + +      + +           + D        +  VGRLD  T GLLLLT+ G 
Sbjct: 68  LGMVVMMNKPAGYICSRKDSGPLVYDLLPDRWRHRKPMLSPVGRLDKETSGLLLLTDHGD 127

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +  P+    + YR      ++  ++N+   G ++       +     +   S    
Sbjct: 128 LLHRITSPNLAVEKTYRASLARPLEGHEVNVFASGELMLSGEKKPLHPAKLSV-LSPTEA 186

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
            + + EG+  +++++F      V  L R + G   L   L A +   ++  
Sbjct: 187 RLNITEGRYHQVRRMFAAVGNHVEALHREALGDLTLPDNLQAAAWCLLNAD 237


>gi|153813881|ref|ZP_01966549.1| hypothetical protein RUMTOR_00087 [Ruminococcus torques ATCC 27756]
 gi|145848277|gb|EDK25195.1| hypothetical protein RUMTOR_00087 [Ruminococcus torques ATCC 27756]
          Length = 194

 Score =  107 bits (267), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 42/189 (22%), Positives = 87/189 (46%), Gaps = 6/189 (3%)

Query: 50  AAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
             + V +   ++V    + K +   +   +KP G+V T    +          +   RV 
Sbjct: 1   MGMRVTAGQIVKVGKKTVSKQDEMIVLAVNKPKGIVCTEDQRE--RDSIVRFLNYPVRVT 58

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
             GRLD ++ GLLL+TN+G +   +   + +  + Y+V    ++ +  +  + +G+ I  
Sbjct: 59  YAGRLDKDSRGLLLMTNNGDIINQMMRAANRHEKEYKVTVDKEITEQFIKKMSEGVPILD 118

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                  V    +K      ++ L +G NR+I+++   F ++V  L+RI     +LG+L 
Sbjct: 119 TVTRPCTV----KKIGKYTFSIILTQGLNRQIRRMCAAFGYEVKDLVRIRIMNIRLGSLK 174

Query: 230 AGSTREVSK 238
            G+ R+++ 
Sbjct: 175 EGAYRKLTD 183


>gi|221065112|ref|ZP_03541217.1| RNA-binding S4 domain protein [Comamonas testosteroni KF-1]
 gi|220710135|gb|EED65503.1| RNA-binding S4 domain protein [Comamonas testosteroni KF-1]
          Length = 255

 Score =  107 bits (267), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 45/249 (18%), Positives = 78/249 (31%), Gaps = 18/249 (7%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVP 66
                 R++K +A     SRRE E  I    V+V+G +++     V     + +  D  P
Sbjct: 6   PEQESIRLAKRLAEQEQCSRREAELHIVAGNVQVDGKVVQVPETRVRPDQVVILRKDAKP 65

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDG---------------RSTVFDNLPSIFSRVISV 111
                   + +                                      L   F  + S 
Sbjct: 66  -EAIPPVTILMNKPAGMTQGPAYGRVRSAHSLLSEDTKAKLDTPMPQLVLDHHFRNLESF 124

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
             + +   GL++ T D  +AR L        +   V   GQ+ +D L +L +G+ I G  
Sbjct: 125 LTIPLPASGLIVYTQDKRVARKLAEEGIWLEQEIIVGVEGQIIEDGLEILYEGLPIPGGN 184

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                        S + +   L+     EI+K+       V  + R+  G   L  +  G
Sbjct: 185 GHRRMPPCHVSWQSESHLRFALKGIAPEEIEKMCAAIGLTVVSMRRLRLGRVSLAKVPEG 244

Query: 232 STREVSKKI 240
             R +    
Sbjct: 245 QWRYLMPWE 253


>gi|281202742|gb|EFA76944.1| hypothetical protein PPL_09696 [Polysphondylium pallidum PN500]
          Length = 614

 Score =  107 bits (266), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 48/266 (18%), Positives = 93/266 (34%), Gaps = 22/266 (8%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL------- 75
           +G+ SR +    I   RV V G  +      V   D + + G  L       L       
Sbjct: 116 SGLCSRSKALSYIGINRVTVLGQKV-SPKTKVNVED-VRIMGKKLENTNPYILYYYYYSK 173

Query: 76  ---WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV----GRLDINTEGLLLLTNDG 128
                 HKP G + +++       ++D LP  F++ +      GRLD    GL+L++ DG
Sbjct: 174 RLTIAVHKPNGYICSNAREGDHKIIYDLLPPEFAKRLPTLSVAGRLDKWVTGLVLMSQDG 233

Query: 129 GLARVLELPST----QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
            +   +  P      +   V         + +        +  +       +  +     
Sbjct: 234 KIVERIITPKDDSFGKIYDVVCKAPFKGNEAEAFESGTMMLRSEEEPCKAAKFEVL--DN 291

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
                 + L EG+  +++++    + K   + RI  GP  LG L AG  R ++++ + + 
Sbjct: 292 DRNLARLTLYEGRYHQVRRMMAALDNKAMEIHRIKVGPIDLGDLPAGKWRYLTEEEMEKI 351

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRD 270
               + + A           +    D
Sbjct: 352 KAIQVTKSALTKKKYNKKKLDNSRAD 377


>gi|104783092|ref|YP_609590.1| hypothetical protein PSEEN4116 [Pseudomonas entomophila L48]
 gi|95112079|emb|CAK16806.1| conserved hypothetical protein; RNA-binding protein S4 domain
           [Pseudomonas entomophila L48]
          Length = 236

 Score =  107 bits (266), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 49/237 (20%), Positives = 86/237 (36%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+SK +      SRRE E  I    V V+G+++E+    V       + G      
Sbjct: 2   SEPIRLSKRLIEQLGCSRREAELYIEGGWVTVDGVVVEQPQFKVADQRVELLPGARAETL 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDG-------RSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           E   L L  +                           L   F+R   +  L     GL L
Sbjct: 62  EPVTLLLNQQAGQDTAAAQASMSMASLSEAHREGVRPLHGHFARQACIAPLLPGATGLQL 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T D  + R L+    +  + Y V+  G+     L  L +G+  +G+     + +   ++
Sbjct: 122 FTQDWRVTRKLDADLRRMEQEYIVQVSGEAKPGALERLARGVERKGVELPRAKASWQNEQ 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                + + L+  +   I+++ E    KV  + RI  G   +G L +G  R ++   
Sbjct: 182 H----LRMVLKNPQPGLIEQLCETAGLKVLAMRRIRLGGVSMGKLPSGQWRYLAATE 234


>gi|300867766|ref|ZP_07112410.1| pseudouridine synthase, Rsu [Oscillatoria sp. PCC 6506]
 gi|300334233|emb|CBN57582.1| pseudouridine synthase, Rsu [Oscillatoria sp. PCC 6506]
          Length = 193

 Score =  107 bits (266), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 47/186 (25%), Positives = 75/186 (40%), Gaps = 15/186 (8%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              +  Y     L                     S +  VGRLD ++EGLLLLT+DG + 
Sbjct: 3   YRYILFYKPYDVLTQFTDAESENKRSTLKDYIPISFIYPVGRLDRDSEGLLLLTDDGQMQ 62

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----------- 180
             L  P     R Y V+      +D +  L+ GI IQ       +V L            
Sbjct: 63  HRLSDPKFAHPRTYWVQVEKIPSEDAIAHLRSGITIQNYRTRPTKVQLLSTEPLLPPRNP 122

Query: 181 ----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +    AW+ + L EGKNR+++++     +   RL+R++    +L  L  G  RE+
Sbjct: 123 PIRFRKNIPTAWLEMTLTEGKNRQVRRMTAAVGFPTLRLVRVAIAHLRLDGLEPGQWREL 182

Query: 237 SKKILR 242
           + + L+
Sbjct: 183 NPEELK 188


>gi|315929678|gb|EFV08855.1| conserved hypothetical protein [Campylobacter jejuni subsp. jejuni
           305]
          Length = 204

 Score =  107 bits (266), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 60/206 (29%), Positives = 97/206 (47%), Gaps = 17/206 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+     SRRE + +I Q  VK+N  +    +  V   D + V G  ++K  + 
Sbjct: 1   MRINKFISHNTRYSRREADELIKQGLVKINNKIA-LLSDEVKFDDKVFVKGKRVQKRTQF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +YHK  G + +  D  GR T++D LP  FS  +SVGRLD  +EGLLLLT+   +A  
Sbjct: 60  SVIIYHKQKGEIVSKKDDRGRKTIYDTLPRQFSTWLSVGRLDYASEGLLLLTDSPVIADA 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--------------YGDMQVTL 179
           L        R Y ++  G V +  +  ++ G+ I+                    +   +
Sbjct: 120 LMHSD--LEREYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEI 177

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVF 205
               G    + V + EGKNRE+++ F
Sbjct: 178 FGSSGGYTKLRVVINEGKNRELRRFF 203


>gi|213023264|ref|ZP_03337711.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 244

 Score =  106 bits (265), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 68/241 (28%), Positives = 101/241 (41%), Gaps = 9/241 (3%)

Query: 59  HIEVDGVPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
            I +DG  +   E        L  Y     L T +      +          +R I+VGR
Sbjct: 2   KIRIDGHLISVKESAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGR 61

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LD+NT GLLL T DG LA  L  PS +  R Y VR  GQVD+ KL  L +G+ ++     
Sbjct: 62  LDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDESKLRDLSRGVQLEDGPAA 121

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGS 232
              +     +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G 
Sbjct: 122 FKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGG 181

Query: 233 TREVS---KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
             E+       LR  +       ++V ++      +     R            R    +
Sbjct: 182 WTELDLAQTNYLRGLVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQIAGGRRSGGRN 241

Query: 290 S 290
           +
Sbjct: 242 N 242


>gi|224824940|ref|ZP_03698046.1| RNA-binding S4 domain protein [Lutiella nitroferrum 2002]
 gi|224602611|gb|EEG08788.1| RNA-binding S4 domain protein [Lutiella nitroferrum 2002]
          Length = 244

 Score =  106 bits (265), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 57/245 (23%), Positives = 106/245 (43%), Gaps = 19/245 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+SK +   G+ SRRE +  I    VKV+G+++      V     IE+    +   
Sbjct: 2   SDTVRLSKRMTELGLCSRREADEFIEMGLVKVDGVVVNVLGSRVRPEQTIELTRQAMALQ 61

Query: 71  ERTRLWLYHKPIGLVT---------------THSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                +L +KP+G  +                 +      + +  L    + +   G+LD
Sbjct: 62  AERVTFLLNKPVGYGSGPSEAGERPAWQLIKPETRSPRDRSGYTFLKKHLNYLAPAGKLD 121

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           +++ GLL+LT DG +AR L   +  + + + V   G+V    L  L+ G+ + G     +
Sbjct: 122 VDSSGLLVLTQDGRIARALMAKAADFEQEFLVWVEGEVSDAMLEQLRHGLSLDGEALKPV 181

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           +V+      S++ +   LR+   R+I+++ E    +V  + RI  G   LG L  G  R 
Sbjct: 182 KVSRQ----SDSQLRFVLRDPVRRQIRRMAELVGLRVTAVRRIRIGRIALGDLEQGQWRY 237

Query: 236 VSKKI 240
           +++  
Sbjct: 238 LTEHE 242


>gi|295839696|ref|ZP_06826629.1| RNA pseudouridylate synthase [Streptomyces sp. SPB74]
 gi|295827612|gb|EFG65503.1| RNA pseudouridylate synthase [Streptomyces sp. SPB74]
          Length = 196

 Score =  106 bits (265), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 51/187 (27%), Positives = 84/187 (44%), Gaps = 1/187 (0%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
             +D I+VDG+ +         L      + T       ++   D + +  +R+  VGRL
Sbjct: 2   KPSDEIKVDGLTVATQSYQFFSLNKPAGVVATMEDPEGRQNLG-DYVNNRETRLFHVGRL 60

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D  TEG++LLTN G LA  L  P     + Y     G + +D    LK GI ++      
Sbjct: 61  DTETEGVILLTNHGELAHRLTHPRYGVRKTYLAHIVGPIPRDLGKRLKDGIELEDGWARA 120

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
               +  Q G N  V V L EG+   ++++     + V++L+R ++GP  LG   +G  R
Sbjct: 121 DHFRVVEQTGKNYLVEVTLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPITLGDQKSGWLR 180

Query: 235 EVSKKIL 241
            +S   +
Sbjct: 181 RLSNTEV 187


>gi|226939304|ref|YP_002794375.1| pseudouridine synthase [Laribacter hongkongensis HLHK9]
 gi|226714228|gb|ACO73366.1| Probable pseudouridine synthase [Laribacter hongkongensis HLHK9]
          Length = 224

 Score =  106 bits (265), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 42/217 (19%), Positives = 77/217 (35%), Gaps = 14/217 (6%)

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
                T                   + V   GRLD ++EG++LLT+ G L   +  P+ +
Sbjct: 8   NKPFDTICQFSASPPHATLADWVPVAGVYPAGRLDTDSEGMVLLTDHGPLQHAIAHPAAK 67

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--------------QKGSN 186
             + Y V+  G  + ++L  L++G+ +         V +                +    
Sbjct: 68  APKTYWVQVEGTPEAEQLEQLRQGVDLGDFVTQPASVRILPEPELWPRQPPVRFRKTVPT 127

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            W+ + + EGKNR+++++         RL+R++ G  +LG L  G  RE++K  L     
Sbjct: 128 HWLEIIISEGKNRQVRRMTAKVGLPTLRLVRVAVGSLKLGELQPGEWREIAKGELPAVWQ 187

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
               + A         SS                   
Sbjct: 188 QAWSQTAAPKPHRAPQSSRAPRFKSTGAGRTARQRPK 224


>gi|293605498|ref|ZP_06687880.1| ribosomal large subunit pseudouridine synthase F [Achromobacter
           piechaudii ATCC 43553]
 gi|292816226|gb|EFF75325.1| ribosomal large subunit pseudouridine synthase F [Achromobacter
           piechaudii ATCC 43553]
          Length = 241

 Score =  106 bits (264), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 43/237 (18%), Positives = 87/237 (36%), Gaps = 16/237 (6%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRK 69
               R++K +A     SR + ER I    V V+G  +E     V     +  + G  L  
Sbjct: 2   SESVRLAKRLAADLSCSRGDAERYIEGGWVAVDGKTVEEPGARVSPGQTVALLPGAKLED 61

Query: 70  AERTRLWLYHKPIGL-----------VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
            +   + ++                 +   +   G  +    L  +F+ +  V  L+   
Sbjct: 62  IKPVTILVHKPAGTYADNEPGSALDLIIPKNLMPGDRSGRRYLKRMFNGLKLVTPLERAA 121

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GL++ T +  ++R L        + Y  +  G++ +  L  L++G+  +G     M+V+
Sbjct: 122 SGLVVYTQEYAVSRKLMEEGRLVEQEYVAQVTGKLSEADLARLQRGMAFEGRAATPMKVS 181

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              +      +   L+      I+ V +    ++ +L RI  G   L  +  G  R 
Sbjct: 182 WQNE----THLRFALKTPLPGFIEYVCDTAGLQLQQLRRIRIGRLPLAGMAVGQWRY 234


>gi|75765038|ref|ZP_00744346.1| Ribosomal large subunit pseudouridine synthase B [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
 gi|74487472|gb|EAO51380.1| Ribosomal large subunit pseudouridine synthase B [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
          Length = 100

 Score =  106 bits (264), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 31/87 (35%), Positives = 45/87 (51%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDN 100
              LY     + +   D          
Sbjct: 62  YFLLYKPTGVISSVSDDKGRSVVTDFF 88


>gi|322490748|emb|CBZ26012.1| putative tRNA pseudouridine synthase A [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 694

 Score =  106 bits (264), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 75/221 (33%), Positives = 112/221 (50%), Gaps = 4/221 (1%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-ERTRLWLY 78
           + RAG  SRRE   +IA  +V+VN +        V + D + V G   R      RLW+Y
Sbjct: 338 LPRAGFCSRREAAAIIASGQVRVNNVTERNPFRLVQAQDDVHVAGHRSRLRFAPPRLWMY 397

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-SVGRLDINTEGLLLLTNDGGLARVLELP 137
           HKP  ++ + +D  GR+ +  +   +    +  VG L +   G+LLLTNDG L+R LE P
Sbjct: 398 HKPAHVIVSRNDAAGRTLITKHARILGMDHLVPVGSLPMRAHGILLLTNDGELSRFLENP 457

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
            +   R Y +R     D   ++ L  +GI I G  Y + +  ++    S   V V +R G
Sbjct: 458 KSMVQRTYLLRVRPAFDPVLVHKLNTEGIQINGRLYRNAEFFVNPATKSRYSVKVKVR-G 516

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           ++  I ++ +    KV R  RIS+GPF L  L  GS REV+
Sbjct: 517 ESMPIAQLMQHLGRKVERGGRISFGPFALSNLAVGSVREVT 557


>gi|302384331|ref|YP_003820154.1| pseudouridine synthase [Brevundimonas subvibrioides ATCC 15264]
 gi|302194959|gb|ADL02531.1| pseudouridine synthase [Brevundimonas subvibrioides ATCC 15264]
          Length = 243

 Score =  106 bits (264), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 36/241 (14%), Positives = 70/241 (29%), Gaps = 13/241 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMST--DHIEVDGVPLRKA 70
           RV K++   G  SR E+ R+     + ++G+ L   +    V       ++VDG PL   
Sbjct: 7   RVDKLLGSMGYGSRSEIARLGKVGGIVLDGVDLTDVSKRIAVTPDLPSRMQVDGRPLDPP 66

Query: 71  ERTRLWLYHKPIGLVTTHSD----PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
               L L        +   D     D     +       S +  + +       L    +
Sbjct: 67  AGVVLILNKPLGMTCSHKEDGDLVYDVLPDRWRRRDPAISTIGRLDKQTSGLLLLTDDGD 126

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
                   +    +       R     + D        +  +       ++ +     S 
Sbjct: 127 LLHRVISPKRHVAKVYHATLARPLAGTEGDVFAAGGLVLEGEDKPLAPAELEVL----SP 182

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
               + + EG+   ++++F      V  L R   G   L   L  G  R  +   +    
Sbjct: 183 TEARLTVTEGRYHMVRRMFAAVGNHVEALHRERVGGLVLPADLGPGDWRLATGAEVEAIF 242

Query: 246 G 246
            
Sbjct: 243 A 243


>gi|157876796|ref|XP_001686740.1| tRNA pseudouridine synthase A [Leishmania major strain Friedlin]
 gi|68129815|emb|CAJ09121.1| putative tRNA pseudouridine synthase A [Leishmania major strain
           Friedlin]
          Length = 694

 Score =  106 bits (264), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 66/221 (29%), Positives = 98/221 (44%), Gaps = 4/221 (1%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--PLRKAERTRLWL 77
           + RAG  SRRE   +IA  +V+VN +        V + D + V G    LR A       
Sbjct: 338 LPRAGFCSRREAAAIIASGQVRVNNVTERNPFRLVQAEDDVHVAGHQSRLRFAPPRLWMY 397

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           +     +V+                     ++ VG L +   G+LLLTNDG L+R LE P
Sbjct: 398 HKPAHVIVSRSDTAGRTLITKHARILGMDHLVPVGSLPMRAHGILLLTNDGELSRFLENP 457

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
            +   R Y +R     D   ++ L  +G+ I G  Y + +  ++    S   V V +R G
Sbjct: 458 KSMVQRTYLLRVRPAFDPVLVHKLNTEGVHINGRPYRNAEFFVNPATKSRYSVKVKVR-G 516

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           ++  I  + +     V R  RIS+GPF L  L  GS REV+
Sbjct: 517 ESMPIAHLMQHLGRTVERGGRISFGPFALSNLAVGSVREVT 557


>gi|326315537|ref|YP_004233209.1| RNA-binding S4 domain-containing protein [Acidovorax avenae subsp.
           avenae ATCC 19860]
 gi|323372373|gb|ADX44642.1| RNA-binding S4 domain protein [Acidovorax avenae subsp. avenae ATCC
           19860]
          Length = 267

 Score =  106 bits (264), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 51/263 (19%), Positives = 83/263 (31%), Gaps = 34/263 (12%)

Query: 8   QENFTPQ----RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            +N   +    R+SK +A     SRRE E +I    V+V+G + E     V     + V 
Sbjct: 7   NDNSAGEAGHIRLSKRVAGMRGCSRREAEWLIEGGWVQVDGRMTEAPGARVRPDQDVVVA 66

Query: 64  GVPLRKAERTRLWLYHKPIGLVT--------------------------THSDPDGRSTV 97
                +       L HKP G                               +   G S  
Sbjct: 67  QNAKAEEAPPVTLLLHKPAGWEAGIGHGPAGDPRQARSGGAPDAGTLLEPGNRYVGDSPP 126

Query: 98  FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
              L   F +      L     GL++ T D  +AR L        +       G++ +  
Sbjct: 127 VRVLQRHFRQQECFTPLADAASGLVVYTQDRRMARRLAEDIELLEQECIATVEGRIAEGG 186

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
           L  L +G+   G      +V+      S   +   L+  +  +I  + E    +V  L R
Sbjct: 187 LERLCRGLEFNGRPLPPARVSWQ----SETRLRFALKGIRPGQIPAMCEAVGLQVTALKR 242

Query: 218 ISYGPFQLGTLLAGSTREVSKKI 240
           +  G   L  +  G  R +    
Sbjct: 243 LRIGRVSLAKVPEGQWRYLLPWE 265


>gi|294942120|ref|XP_002783386.1| pseudouridine synthase, putative [Perkinsus marinus ATCC 50983]
 gi|239895841|gb|EER15182.1| pseudouridine synthase, putative [Perkinsus marinus ATCC 50983]
          Length = 267

 Score =  106 bits (263), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 101/231 (43%), Gaps = 20/231 (8%)

Query: 30  EVERMIAQQRVKVNGI-LLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTH 88
           E  R+I + R+ +NG  +++   VNV   D I V+G PL    R  L ++     +V+  
Sbjct: 8   EAGRLIERGRISINGRPIVQNRWVNVH-KDSILVNGTPLEATCRLTLLMHKPAGYVVSRD 66

Query: 89  SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
              +  +  F  LP     + + GRLD +T GLLLLTND  L   L  P  +  +VYRV 
Sbjct: 67  DPLNRDTV-FQLLPDPSVYIGASGRLDKDTTGLLLLTNDTYLQSSLVDPVYKVPKVYRVV 125

Query: 149 FHGQV-DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-------------AWVTVGLR 194
             G   +  +L  L+ G+ ++        V      G                 + + L 
Sbjct: 126 VKGAALNGAQLMALRSGVSLEDGPTLPALVEPLDVNGDPLPLEMSEYDRYKCKQLNITLW 185

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL---GTLLAGSTREVSKKILR 242
           EG+NR+++++ E     V  L RI  GPF L   G    G  R+++   + 
Sbjct: 186 EGRNRQVRRMVEAVGSTVRDLCRIQLGPFSLHAAGVPNPGDVRQLTIDEVE 236


>gi|21232382|ref|NP_638299.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66767486|ref|YP_242248.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. 8004]
 gi|21114159|gb|AAM42223.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66572818|gb|AAY48228.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. 8004]
          Length = 236

 Score =  106 bits (263), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 46/238 (19%), Positives = 87/238 (36%), Gaps = 13/238 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+ K +A     SR E ++ I    V V+G+++E     +     + +    +   
Sbjct: 2   SDPIRLDKHVAAVFGCSRGEAQQYIEGGWVSVDGVVVEEPQAPIT-GQQVSLAADAVLGQ 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRS--------TVFDNLPSIFSRVISVGRLDINTEGLL 122
                 L +KP G+    +              T    L   F R+ +   LD    GLL
Sbjct: 61  AEPATLLLNKPAGMSCEAAVALATPQSRSSLDQTEIRVLKRHFLRLSAPMPLDDEASGLL 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           +L+ DG + R L   +    + Y V   G++    +  L  G+V Q       +V+   +
Sbjct: 121 VLSQDGRILRRLTADAATIEQEYLVEVRGELRPYGMARLASGLVYQQRSLPACKVSWQNE 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +     +   ++  +  +++ +       V  + R+  G   LG L  G  R +    
Sbjct: 181 ER----LRFAIKHVQPGQLRYMCNEVGLDVVTIRRLRVGRISLGKLALGEWRYLPTGE 234


>gi|291545735|emb|CBL18843.1| pseudouridine synthase family [Ruminococcus sp. SR1/5]
          Length = 610

 Score =  106 bits (263), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 41/179 (22%), Positives = 74/179 (41%), Gaps = 4/179 (2%)

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
              R+  +GRLD ++EGLLLLTN+G L   +        + Y+V  +  V ++ +  +  
Sbjct: 9   YPVRIYPIGRLDKDSEGLLLLTNEGDLVNRIMKAGNYHEKEYQVTVNKPVTEEFIRGMGG 68

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
           G+ I        +VT   + G N+   + L +G NR+I+++ E+F +KV  L R+     
Sbjct: 69  GVPILDTVTRPCKVT---KTGKNS-FRIILTQGLNRQIRRMCEYFGYKVVTLKRVRIMNL 124

Query: 224 QLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDF 282
            +  L  G  RE+  +  +E       E+++                            
Sbjct: 125 YIDGLEEGKYREIRPEERKELEEMLSSEKSEKRTGGSHERIIHKKMKELGEKLREASRA 183


>gi|188990595|ref|YP_001902605.1| Ribosomal small subunit pseudouridylate synthase [Xanthomonas
           campestris pv. campestris str. B100]
 gi|167732355|emb|CAP50547.1| Ribosomal small subunit pseudouridylate synthase [Xanthomonas
           campestris pv. campestris]
          Length = 236

 Score =  106 bits (263), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 45/238 (18%), Positives = 88/238 (36%), Gaps = 13/238 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+ K +A     SR E ++ I    V V+G+++E     +     + +    +   
Sbjct: 2   SDPIRLDKHVAAVFGCSRGEAQQYIEGGWVSVDGVVVEEPQAPIT-GQQVSLAADAVLGQ 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRS--------TVFDNLPSIFSRVISVGRLDINTEGLL 122
            +    L +KP G+    +              T    L   F R+ +   LD    GLL
Sbjct: 61  AKPATLLLNKPAGMSCEAAVALATPQSRSSLDQTEIRVLKRHFLRLSAPMPLDDEASGLL 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           +L+ DG + R L   +    + Y V   G++    +  L  G++ Q       +V+   +
Sbjct: 121 VLSQDGRILRRLTADAATIEQEYLVEVRGELRPYGMARLASGLLYQQRSLPACKVSWQNE 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +     +   ++  +  +++ +       V  + R+  G   LG L  G  R +    
Sbjct: 181 ER----LRFAIKHVQPGQLRYMCNEVGLDVVTIRRLRVGRISLGKLALGEWRYLPTGE 234


>gi|329906588|ref|ZP_08274441.1| putative ribosomal large subunit pseudouridine synthase
           [Oxalobacteraceae bacterium IMCC9480]
 gi|327547243|gb|EGF32094.1| putative ribosomal large subunit pseudouridine synthase
           [Oxalobacteraceae bacterium IMCC9480]
          Length = 241

 Score =  105 bits (262), Expect = 9e-21,   Method: Composition-based stats.
 Identities = 53/242 (21%), Positives = 91/242 (37%), Gaps = 16/242 (6%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K +A     SR E E+ I    + V+G+L E A   V     I +    +   
Sbjct: 2   TDTIRLAKRVAEELGCSRTEAEQFIEGGWITVDGVLTEEAGARVAPEQAIVLLPDAVPAP 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD------------NLPSIFSRVISVGRLDINT 118
                 L HKP G+ T  +    +S +               L      +     L+ + 
Sbjct: 62  LDPVTILLHKPAGMRTIDAIDPEQSWITPATLGPDDRSGLRFLRRHTKALTLTNPLEDSA 121

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLL+LT D  + R L   +++  + + V   G +D   L LL+KG+   G     M+V+
Sbjct: 122 SGLLVLTQDWRIERALVQEASRIEQEFVVEVTGTLDAAGLELLQKGLKWNGKPIASMKVS 181

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
                 S   +   ++  +  +I  + E    +V  + RI  G   +  L  G  R +  
Sbjct: 182 WQ----SEHKLRFAIKAAERGQIPYLCEKVGLQVVSIKRIRIGRMSMAALPVGQWRYLLG 237

Query: 239 KI 240
             
Sbjct: 238 YE 239


>gi|17228041|ref|NP_484589.1| hypothetical protein alr0545 [Nostoc sp. PCC 7120]
 gi|17129890|dbj|BAB72503.1| alr0545 [Nostoc sp. PCC 7120]
          Length = 204

 Score =  105 bits (262), Expect = 9e-21,   Method: Composition-based stats.
 Identities = 50/184 (27%), Positives = 85/184 (46%), Gaps = 16/184 (8%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  ++HKP G+++     +    +          V  VGRLD ++EGLLLLTN+G L   
Sbjct: 6   RYIIFHKPYGVLS-QFTQESPKHITLKDYIDVPDVYPVGRLDWDSEGLLLLTNNGRLQHR 64

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT------------ 181
           L  P     R Y V+     D++ ++ L+ G+ I+       +V L              
Sbjct: 65  LSDPRFGHERTYWVQVERIPDEEAISKLQTGVEIRDYRTRPAKVGLLPEYPPVGDRQPPI 124

Query: 182 ---QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              +    AW+ + L EGKNR+++++     +   RL+R+S G  +L  L  G  R+++ 
Sbjct: 125 RFRKNVPTAWLEMTLTEGKNRQVRRMTAAVGFPTLRLVRVSIGHLRLDGLALGEWRDLTS 184

Query: 239 KILR 242
             L+
Sbjct: 185 LELK 188


>gi|254562844|ref|YP_003069939.1| pseudouridine synthase, 1-deoxy-D-xylulose 5-phosphate
           reductoisomerase [Methylobacterium extorquens DM4]
 gi|254270122|emb|CAX26112.1| Putative pseudouridine synthase, putative 1-deoxy-D-xylulose
           5-phosphate reductoisomerase [Methylobacterium
           extorquens DM4]
          Length = 256

 Score =  105 bits (262), Expect = 9e-21,   Method: Composition-based stats.
 Identities = 55/182 (30%), Positives = 83/182 (45%)

Query: 59  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
            I VDG  L  A +  L L      L T       ++            +  VGRLD  +
Sbjct: 7   VICVDGRRLVSAAKVYLLLNKPRGLLTTYGDPQGRKTVYDCLAGHDLPFLAPVGRLDCAS 66

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLLL+TND   A  L  P++   +VY V+     D+  L  L++G V  G       V 
Sbjct: 67  EGLLLMTNDTRWAHRLLDPASNVDKVYHVQIDRTPDEALLTGLREGAVHDGERLAAKSVA 126

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
                  NAW+ V L EG+NR+I+++      +V RL+R++ G  +LG +  G+ R ++ 
Sbjct: 127 PLRVGERNAWLEVVLSEGRNRQIRRMMALNGAEVLRLVRVAVGGLRLGDVRKGAFRHLTD 186

Query: 239 KI 240
             
Sbjct: 187 AE 188


>gi|241765949|ref|ZP_04763876.1| RNA-binding S4 domain protein [Acidovorax delafieldii 2AN]
 gi|241364099|gb|EER59324.1| RNA-binding S4 domain protein [Acidovorax delafieldii 2AN]
          Length = 265

 Score =  105 bits (262), Expect = 9e-21,   Method: Composition-based stats.
 Identities = 47/270 (17%), Positives = 83/270 (30%), Gaps = 37/270 (13%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M DK+   ++    R++K +A     SR   E+ I    V V+G + E     V     +
Sbjct: 1   MTDKHPAPDH---IRLAKRVAEQLNCSRSTAEQFIEGGFVSVDGRVEEAPGARVRPDQAV 57

Query: 61  EVD-GVPLRKAERTRLWLYHKPIG-----------------------------LVTTHSD 90
            V     L       L L+                                  L++  S 
Sbjct: 58  VVAPDASLLALTPVTLLLHKPAGFEAGLGQPGQGGAPHSSQGSRSQGAPSAATLLSAASH 117

Query: 91  PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
               ++    L   F ++     L     GL++ T D  +AR L        +   V   
Sbjct: 118 LPEDASGIRVLQRHFKQLECFTPLPTEASGLVVYTQDKRIARKLAEDIESLEQECIVEVA 177

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           G +  + L  L  G+   G     ++V+   +      +   L+  +  +I  + E    
Sbjct: 178 GDIAPNGLQRLCHGLSFNGRPLPPIKVSWQNE----TRLRFALKGIRPGQIPAMCEAVGL 233

Query: 211 KVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
               + RI  G   L  +  G  R +    
Sbjct: 234 TAVGIKRIRIGRVPLAKVPEGQWRYLQPWE 263


>gi|146104193|ref|XP_001469756.1| tRNA pseudouridine synthase A [Leishmania infantum]
 gi|134074126|emb|CAM72868.1| putative tRNA pseudouridine synthase A [Leishmania infantum JPCM5]
          Length = 877

 Score =  105 bits (262), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 67/221 (30%), Positives = 99/221 (44%), Gaps = 4/221 (1%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--PLRKAERTRLWL 77
           + RAG  SRRE   +IA  +V+VN +        V + D + V G    LR A       
Sbjct: 521 LPRAGFCSRREAAAIIASGQVRVNNVTERNPFRLVQAQDDVHVAGHQSRLRFAPPRLWIY 580

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           +     +V+ +                   ++ VG L +   G+LLLTNDG L+R LE P
Sbjct: 581 HKPAHVIVSRNDAAGRTLITKHARILGMDHLVPVGSLPMRAHGILLLTNDGELSRFLENP 640

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
            +   R Y +R     D   ++ L  +GI I G  Y + +  ++    S   V V +R G
Sbjct: 641 KSMVQRTYLLRVRPAFDPVLVHKLNTEGIHINGRLYRNAEFFVNPATKSRYSVKVKVR-G 699

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           ++  I  + +     V R  RIS+GPF L  L  GS REV+
Sbjct: 700 ESMPIAHLMQHLGRTVERGGRISFGPFALSNLAVGSVREVT 740


>gi|297517087|ref|ZP_06935473.1| 23S rRNA pseudouridine synthase F [Escherichia coli OP50]
          Length = 147

 Score =  105 bits (262), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 39/144 (27%), Positives = 62/144 (43%), Gaps = 1/144 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   
Sbjct: 4   DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 63  EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVD 154
              +        + Y V     + 
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPIT 146


>gi|322503526|emb|CBZ38612.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 877

 Score =  105 bits (261), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 67/221 (30%), Positives = 99/221 (44%), Gaps = 4/221 (1%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--PLRKAERTRLWL 77
           + RAG  SRRE   +IA  +V+VN +        V + D + V G    LR A       
Sbjct: 521 LPRAGFCSRREAAAIIASGQVRVNNVTERNPFRLVQAQDDVHVAGHQSRLRFAPPRLWIY 580

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           +     +V+ +                   ++ VG L +   G+LLLTNDG L+R LE P
Sbjct: 581 HKPAHVIVSRNDAAGRTLITKHARILGMDHLVPVGSLPMRAHGILLLTNDGELSRFLENP 640

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
            +   R Y +R     D   ++ L  +GI I G  Y + +  ++    S   V V +R G
Sbjct: 641 KSMVQRTYLLRVRPAFDPVLVHKLNTEGIQINGRLYRNAEFFVNPATKSRYSVKVKVR-G 699

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           ++  I  + +     V R  RIS+GPF L  L  GS REV+
Sbjct: 700 ESMPIAHLMQHLGRTVERGGRISFGPFALSNLAVGSVREVT 740


>gi|113476033|ref|YP_722094.1| pseudouridine synthase, Rsu [Trichodesmium erythraeum IMS101]
 gi|110167081|gb|ABG51621.1| Pseudouridine synthase, Rsu [Trichodesmium erythraeum IMS101]
          Length = 201

 Score =  105 bits (261), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 49/187 (26%), Positives = 83/187 (44%), Gaps = 17/187 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
            R  L++KP  +++  +D          L    S      VGRLD ++EGLLLLTN G L
Sbjct: 6   YRYILFNKPYNVLSQFTDNRNVKHRSSTLKEYISVDSVYPVGRLDQDSEGLLLLTNHGQL 65

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------ 184
              L  P     R Y V+     D   L  L++G++I+       +V L + +       
Sbjct: 66  QYRLSDPKFAHPRTYWVQVERIPDTIALKQLQEGVMIKNYQTRPAKVKLLSNEPLLPSRH 125

Query: 185 ---------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                      AW+ + L EG+NR+++++     +   RL+RI+    +L  L  G  R+
Sbjct: 126 PPIRFRKTVPTAWLEITLTEGRNRQVRRMTAAVGFPTLRLVRIAIANLRLEGLKPGEWRD 185

Query: 236 VSKKILR 242
           ++   ++
Sbjct: 186 LNLSEIQ 192


>gi|21243856|ref|NP_643438.1| pseudouridylate synthase [Xanthomonas axonopodis pv. citri str.
           306]
 gi|21109456|gb|AAM37974.1| pseudouridylate synthase [Xanthomonas axonopodis pv. citri str.
           306]
          Length = 236

 Score =  104 bits (260), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 46/237 (19%), Positives = 85/237 (35%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+ K +A A   SR E +  I    V V+G+++E                  L  A
Sbjct: 2   SDPIRLDKCVAAAFGCSRGEAQHYIEGGWVSVDGVVVEEPQALATVAQVTLAANAVLAPA 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIFSRVISVGRLDINTEGLLL 123
           E   L L+                +T           L   F R+ +   L+    GLL+
Sbjct: 62  EPATLLLHKPAGICADAALALATPATRSALDQSDLRVLKRHFLRLQAPLPLEDAASGLLI 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           L+ DG + R L   ++   + + V   G++    +  L  G+V Q       +V+  ++ 
Sbjct: 122 LSQDGRVLRRLSADASAIEQEFLVEVQGELRPYGMARLAHGLVYQQRSLSPCKVSWQSED 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   ++  +  +++ +      +V  + R+  G   LG L  G  R +    
Sbjct: 182 R----LRFAIKHVQPGQLRYMCGEVGLEVRSIRRLRVGRVSLGKLAIGEWRYLPAGE 234


>gi|294911634|ref|XP_002778026.1| pseudouridine synthase, putative [Perkinsus marinus ATCC 50983]
 gi|239886147|gb|EER09821.1| pseudouridine synthase, putative [Perkinsus marinus ATCC 50983]
          Length = 267

 Score =  104 bits (260), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 64/237 (27%), Positives = 101/237 (42%), Gaps = 18/237 (7%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPI 82
            GI S  E  R+I + R+ +NG  + +     +  D I V+G PL    R  L ++    
Sbjct: 1   MGIPSGTEAGRLIERGRISINGRPIVQNRWVDVRKDSILVNGTPLEATCRLTLLMHKPAG 60

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL 142
            +V+     +  +  F  LP     + + GRLD +T GLLLLTND  L   L  P  +  
Sbjct: 61  YVVSRDDPLNRDTV-FQLLPDPSVYIGASGRLDKDTTGLLLLTNDTYLQSSLVDPVYKVP 119

Query: 143 RVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-------------AW 188
           +VYRV   G   +  +L  L+ G+ ++        V      G                 
Sbjct: 120 KVYRVVVKGAALNGAQLMALRSGVSLEDGPTLPALVEPLDVNGDPLPLEMSEYDRYKCKQ 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL---GTLLAGSTREVSKKILR 242
           + + L EG+NR+++++ E     V  L RI  GPF L   G    G  R+++   + 
Sbjct: 180 LNITLWEGRNRQVRRMVEAVGSTVRDLCRIQLGPFSLHAAGVPNPGDVRQLTIDEVE 236


>gi|291615279|ref|YP_003525436.1| RNA-binding S4 domain protein [Sideroxydans lithotrophicus ES-1]
 gi|291585391|gb|ADE13049.1| RNA-binding S4 domain protein [Sideroxydans lithotrophicus ES-1]
          Length = 272

 Score =  104 bits (260), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 45/272 (16%), Positives = 82/272 (30%), Gaps = 49/272 (18%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRKAE 71
           P R+++ +A     SRRE E  IA   V V+G ++E     V     +E+     L   E
Sbjct: 4   PVRLARRLAELVHCSRREAELYIAGGWVSVDGQVVEEPQFMVS-QQKVELHPDATLVPVE 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVF--------------------------------- 98
              +  +          +    R                                     
Sbjct: 63  SVTILFHQPSPQPSDGTTSHSTRPPKNGDQVAGYPSGRGSDREGQSLILADSIRQLPSAD 122

Query: 99  ----------DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
                       L   F R+     L ++  GL + T D  + R L   +    + Y V 
Sbjct: 123 TRAADDRSGIRLLKQHFVRLTQCLPLQLHASGLTVFTQDYRVIRKLTEDAATIEQEYVVE 182

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
             G++  D   LL  G+   G     ++V+   +      +   L+  +  ++  +    
Sbjct: 183 VAGELVPDGFKLLNHGLSFNGKPLPPVKVSWQNE----THLRFALKGAQPGQVAHMCLAV 238

Query: 209 NWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             +V  + R+  G   +  L  G  R +    
Sbjct: 239 GLQVQAMKRLRIGRMSMCKLPLGQWRYLMPYE 270


>gi|320161627|ref|YP_004174852.1| pseudouridine synthase [Anaerolinea thermophila UNI-1]
 gi|319995481|dbj|BAJ64252.1| pseudouridine synthase [Anaerolinea thermophila UNI-1]
          Length = 239

 Score =  104 bits (259), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 103/230 (44%), Gaps = 14/230 (6%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            K    R  L++KP G++T  +DP+GR T+ D        V   GRLD+++EGLL L+ND
Sbjct: 6   EKQGTYRYILFYKPYGVLTAFTDPEGRPTLKD--WIPVPDVYPAGRLDMDSEGLLFLSND 63

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----- 182
           G L   +  P  Q  + Y V+  G V  + L  L++G+ ++G      QV +  +     
Sbjct: 64  GDLMHRITDPRYQHPKTYLVQVEGVVSGEALAKLRRGVEVKGRQTQRCQVMVIPEPDLPP 123

Query: 183 -------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                   G   W+ + L EGK R+++ +         RL+R++ GP  L  L  G  R+
Sbjct: 124 RAKPVTPHGPTTWLRMVLTEGKKRQVRHMTAAVGHPTLRLVRVAIGPLSLEGLTPGEWRD 183

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
           ++ + L        L + ++   +   + E+  R+     S      +  
Sbjct: 184 LTPQELALLKRSLRLTDGRIPAMSAGNARESRYRNAARQSSNRGSRPSGA 233


>gi|261414799|ref|YP_003248482.1| pseudouridine synthase [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|261371255|gb|ACX74000.1| pseudouridine synthase [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|302326658|gb|ADL25859.1| ribosomal large subunit pseudouridine synthase E [Fibrobacter
           succinogenes subsp. succinogenes S85]
          Length = 183

 Score =  104 bits (258), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 47/182 (25%), Positives = 84/182 (46%), Gaps = 17/182 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +++KP G+++  +   G   +          V + GRLD ++EG LLLT++G L + L
Sbjct: 4   VIIFNKPFGVLSQFTPEAGHPALDSF--GFPPGVYAAGRLDHDSEGALLLTDNGKLIKKL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  R Y  +  GQ+ ++ +  L KG+ I+G      +  +               
Sbjct: 62  LDPKYEHPRTYLAQVDGQITEEAVCKLAKGVDIKGYHTKPCKAEIVEAPEWIWERNPPVR 121

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                  +WV + L EGKNR+++ +     +   RL+R+  G   LG L  G  R V+ K
Sbjct: 122 FRANIPTSWVKLTLIEGKNRQVRHMTAAVGFPTLRLVRVQIGNIPLGKLKPGEWRIVTDK 181

Query: 240 IL 241
           ++
Sbjct: 182 VI 183


>gi|325272758|ref|ZP_08139106.1| S4 domain-containing protein [Pseudomonas sp. TJI-51]
 gi|324102109|gb|EGB99607.1| S4 domain-containing protein [Pseudomonas sp. TJI-51]
          Length = 236

 Score =  104 bits (258), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 46/237 (19%), Positives = 81/237 (34%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+SK +      SRRE E  I    V V+G+++E+    V       + G      
Sbjct: 2   SEPVRLSKRLIEQLGCSRREAELYIEGGWVTVDGVVVEQPQFKVGQQRVELLPGARAEPL 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDG-------RSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           E   L L         +                    L   F+R   V  L+    GL +
Sbjct: 62  EPVTLLLNQPADMDSESARASINMGSLSETHREGVRALHGHFARQACVAPLERGASGLQV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T D  + R +E    +  + + V   GQ     L  L +G +         + +   + 
Sbjct: 122 FTQDWRVTRKIEADLRRLEQEFIVEVRGQTTPQALERLARGAMRNDRELPKAKASWQNE- 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                + + L+  +  +I ++  +   ++  + RI  G   +G L  G  R V+   
Sbjct: 181 ---THLRMALKNPQPGQIAELCAYLRLELVGMRRIRLGGVSMGKLPLGQWRYVAATE 234


>gi|255654429|ref|ZP_05399838.1| putative RNA pseudouridine synthase [Clostridium difficile
           QCD-23m63]
          Length = 141

 Score =  104 bits (258), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 39/138 (28%), Positives = 59/138 (42%), Gaps = 1/138 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA 70
             QR+ K+++  G  SR E+++   Q  V VNG  +      V    D I  +G  +   
Sbjct: 3   KKQRIDKILSNLGYGSRSEIKKYCKQGSVVVNGSEVSNPGTQVDTENDEILFNGEEVIYR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L +      +  T    D       +L  +      VGRLD +TEGLL+LTNDG L
Sbjct: 63  EYIYLMMNKPDGYVSATTDKYDPTVLDLIDLSYLAFEPFPVGRLDKDTEGLLVLTNDGKL 122

Query: 131 ARVLELPSTQWLRVYRVR 148
           +  +  P     + Y  +
Sbjct: 123 SHRVLSPKKHVPKTYYDK 140


>gi|77457416|ref|YP_346921.1| RNA-binding S4 [Pseudomonas fluorescens Pf0-1]
 gi|77381419|gb|ABA72932.1| conserved hypothetical protein [Pseudomonas fluorescens Pf0-1]
          Length = 236

 Score =  104 bits (258), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 49/238 (20%), Positives = 85/238 (35%), Gaps = 13/238 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P R+SK +      SRRE E  I    V V+G +++     V     +E+D       
Sbjct: 2   TDPIRLSKRLIELVGCSRREAELFIEGGWVTVDGEVIDEPQFKVG-DQKVELDKDAKATA 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPD------GRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
               T L      + + +     +              L   F R+ +   L     GLL
Sbjct: 61  PEPVTILLNVPAGMDVDSAMQSLNAETLSEEHRYGKRPLRGHFLRLTASADLQPKASGLL 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + T D  + R L   + +  + Y V   G +    LN L+ G+  +G     ++ +   +
Sbjct: 121 VFTQDWKVLRKLTADAAKIEQEYVVEVEGDMVAHGLNRLQHGLTHKGKELPPVKASWQNE 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 +   ++  +   I +  E    KV  + RI  G   +G +  G  R +S K 
Sbjct: 181 NR----LRFAMKNPQPGIIAQFCEAVGLKVIGIRRIRIGGVSIGKVPVGQWRYLSGKE 234


>gi|330751986|emb|CBL80499.1| ribosomal large subunit pseudouridine synthase F [uncultured
           Polaribacter sp.]
          Length = 164

 Score =  103 bits (257), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 43/162 (26%), Positives = 72/162 (44%), Gaps = 3/162 (1%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +   N     ++K I+ +G+ SRRE E+ I + R+ +NG    +    V   D ++ DG 
Sbjct: 1   METNNQQSINLNKYISSSGVCSRREAEKFIKEGRITINGKK-TQLGNRVGKKDVVKFDGR 59

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +     T     +KP+G+V+T  D            +   R+  +GRLD  +EGL+ LT
Sbjct: 60  LVEPKNITLYIALNKPVGIVSTTDD--REPNNIVQHVNYPERLFPIGRLDKPSEGLIFLT 117

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           NDG +   +        + Y V     +  D +  +  GI I
Sbjct: 118 NDGDIVNKILRAGNNHEKEYFVSVDKSITDDFIASMGNGIPI 159


>gi|330826621|ref|YP_004389924.1| RNA-binding S4 domain-containing protein [Alicycliphilus
           denitrificans K601]
 gi|329311993|gb|AEB86408.1| RNA-binding S4 domain protein [Alicycliphilus denitrificans K601]
          Length = 241

 Score =  103 bits (257), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 45/235 (19%), Positives = 74/235 (31%), Gaps = 9/235 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRK 69
              R++K +A+    SR   E+ I    V V+G ++E  A  V  T  + +  D   L  
Sbjct: 8   EAVRLAKRVAQQLGCSRATAEQYIEGGWVSVDGRVVEEPAARVAPTQAVALAPDANLLDL 67

Query: 70  AERTRLWL----YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
              T L       +    L       +        L      +     L     GL + T
Sbjct: 68  RPVTLLLHRPANANAQEFLRAERHAAELDRPGTRVLRRHLRALECAAPLPAGASGLTVYT 127

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            +  +AR L        +   V   GQ+  D L  L + +   G         L     +
Sbjct: 128 QERRIARRLAEDMALLEQECTVHVEGQIAPDGLQALGRNLPHHGG---PAAPHLKASWQN 184

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
              + + L+      I ++      +V  + RI  G   L  L  G  R +    
Sbjct: 185 ETHLRLALKGVDMARIPELCAAVGLRVLGVRRIRMGRLPLARLPEGQWRYLQPWE 239


>gi|154345736|ref|XP_001568805.1| tRNA pseudouridine synthase A [Leishmania braziliensis
           MHOM/BR/75/M2904]
 gi|134066147|emb|CAM43937.1| putative tRNA pseudouridine synthase A [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 692

 Score =  103 bits (257), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 72/221 (32%), Positives = 110/221 (49%), Gaps = 4/221 (1%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-ERTRLWLY 78
           + RAG  SRRE   +IA  +V+VN ++       V + D + V G   R      RLW+Y
Sbjct: 336 LPRAGFCSRREAAAIIASGQVRVNNVVERNPFRLVEAQDDVHVAGHQSRLRFAPPRLWMY 395

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-SVGRLDINTEGLLLLTNDGGLARVLELP 137
           +KP  ++ + +D  GR+ +  +   +    +  VG L +   G+LLLTNDG L+R LE P
Sbjct: 396 NKPANVIVSRNDVAGRTLITKHARILGMDHLVPVGSLPMRAHGILLLTNDGELSRFLESP 455

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
            +   R Y +R         ++ L  +GI I G  Y + +  ++    S   V V +R G
Sbjct: 456 KSMVQRTYMLRVRPAFGPVLVHKLNTEGIQINGRRYRNTEFFVNPATKSRYSVKVKVR-G 514

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           ++  I  + +     V R  RIS+GPF L  L  GS REV+
Sbjct: 515 ESMPIAHLMQHLGRTVERGGRISFGPFALSNLAVGSVREVT 555


>gi|75906581|ref|YP_320877.1| pseudouridine synthase, Rsu [Anabaena variabilis ATCC 29413]
 gi|75700306|gb|ABA19982.1| Pseudouridine synthase, Rsu [Anabaena variabilis ATCC 29413]
          Length = 204

 Score =  103 bits (257), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 52/184 (28%), Positives = 85/184 (46%), Gaps = 16/184 (8%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  ++HKP G+++     +    +          V  VGRLD ++EGLLLLTN+G L   
Sbjct: 6   RYIIFHKPYGVLS-QFTQESPKHITLKDYIDVPNVYPVGRLDWDSEGLLLLTNNGRLQHR 64

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT------------ 181
           L  P     R Y V+     D++ +N L+ G+ IQ       +V L              
Sbjct: 65  LSDPRFGHERTYWVQVERIPDEEAINRLQAGVEIQDYRTRPAKVRLLPEYPPVGDRQPPI 124

Query: 182 ---QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              +    AW+ + L EGKNR+++++     +   RL+R+S G  +L  L  G  R+++ 
Sbjct: 125 RFRKNVPTAWLEMTLTEGKNRQVRRMTAAVGFPTLRLLRVSIGHLRLDGLALGEWRDLTS 184

Query: 239 KILR 242
             L+
Sbjct: 185 LELK 188


>gi|330752219|emb|CBL87177.1| ribosomal large subunit pseudouridine synthase B [uncultured
           Sphingobacteria bacterium]
          Length = 230

 Score =  103 bits (257), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 51/237 (21%), Positives = 101/237 (42%), Gaps = 7/237 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA     +RRE  R++A+  +KVN  +++  +  VM  D +     PL++    
Sbjct: 1   MRLNKYIAHTRYCTRREASRLLARGEIKVNNKVVKEESYRVMEGDEVTHLNKPLQEQLLY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  L +KP    T   D D +  +        + +I+V  +   + GLLLLT+D  L   
Sbjct: 61  RYLLINKPKHFTTDIGDKDSKYIMGLIKKEDPTGLIAVDHMGPKSVGLLLLTSDKALVEK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L   + +  RVY +  +  +++  +N L     ++      ++           ++ + +
Sbjct: 121 LNQKNRKVRRVYLIELNKDIEKKDINKL-----LKDRKTIKIESASHVDGYQANYIGLEM 175

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
             G    +K V     +++ R+ R  Y       L  G  R +  + + E++  H +
Sbjct: 176 TIGSENILKGVINRMGFEIERIDRSYYAGLTKKDLKRGWIRPL--QEMEERMMKHFI 230


>gi|152985556|ref|YP_001349615.1| hypothetical protein PSPA7_4261 [Pseudomonas aeruginosa PA7]
 gi|150960714|gb|ABR82739.1| hypothetical protein PSPA7_4261 [Pseudomonas aeruginosa PA7]
          Length = 236

 Score =  103 bits (257), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 47/237 (19%), Positives = 87/237 (36%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+S+ +      SRRE E  I    V V+G ++E     V+      + G      
Sbjct: 2   TEPIRLSRRLVELIACSRREAELYIEGGWVSVDGTVVEEPQFKVLDQRVELLPGARPEPL 61

Query: 71  ERTRLWLYHKPIG-------LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
               L L+            L+      +  ++V   L   F+R  +   LD    GLL+
Sbjct: 62  APVTLLLHKPAGCREDEAARLLVAAHRWEADASVLRPLKKHFARQRATLPLDTEASGLLV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            +   G+ R L     +  + Y V   G++    L  L+ G+  +G      +V+   + 
Sbjct: 122 FSQQHGVLRKLVEDGARIEQEYLVEVAGELPPGGLERLRHGLAYRGRALPPCKVSWQNEN 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   L+  +  +++ + E    +V  + R+  G   L  L +G  R +    
Sbjct: 182 H----LRFALKGAQPGQLRFMCESEGLEVRGIRRLRIGALSLARLPSGEWRYLGVHE 234


>gi|294626845|ref|ZP_06705437.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 11122]
 gi|292598859|gb|EFF43004.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 11122]
          Length = 236

 Score =  103 bits (257), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 47/237 (19%), Positives = 88/237 (37%), Gaps = 11/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+ K +A A   SR E +  I    V V+G+++E       +      +   L  A
Sbjct: 2   SDPIRLDKCVAAAFGCSRGEAQHYIEGGWVSVDGVVVEEPQALATAAQVTLAENAVLAPA 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIFSRVISVGRLDINTEGLLL 123
           E   L L+      V         +T           L   F R+ +   L+    GLL+
Sbjct: 62  EPATLLLHKPAGICVDAALALATPATRSALDQSDLRVLKRHFLRLQAPLPLEDAASGLLI 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           L+ DG + R L   ++   + + V   G++    +  L  G+V Q       +V+  ++ 
Sbjct: 122 LSQDGRVLRRLSADASAIEQEFLVEVQGELRPYGMARLAHGLVYQHRSLSACKVSWQSED 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   ++  +  +++ +      +V  + R+  G   LG L  G  R +    
Sbjct: 182 R----LRFAIKHVQPGQLRYMCGEVGLEVRSIRRLRVGRVSLGRLAIGEWRYLPVGE 234


>gi|282899316|ref|ZP_06307285.1| Pseudouridine synthase, Rsu [Cylindrospermopsis raciborskii CS-505]
 gi|281195773|gb|EFA70701.1| Pseudouridine synthase, Rsu [Cylindrospermopsis raciborskii CS-505]
          Length = 191

 Score =  103 bits (257), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 50/188 (26%), Positives = 77/188 (40%), Gaps = 17/188 (9%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 +  +     L     +     T+ D +      V  VGRLD ++EGLLLLTNDG
Sbjct: 2   AHNFKYIIFHKPYGVLSQFTRELPEHVTLKDYID--VPDVYPVGRLDWDSEGLLLLTNDG 59

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---- 184
            L   +  P     R Y V+     D   +  L +G+ IQ       QV L  ++     
Sbjct: 60  KLQHHIANPRFGHQRTYWVQVERIPDPVAIAKLGQGVEIQNYRTLPAQVKLLLEEPIVGE 119

Query: 185 -----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                        AW+ + L+EGKNR+++++     +   RLIR+     QL  L  G+ 
Sbjct: 120 RYPPIRFRKNVPTAWLEMTLKEGKNRQVRRMTAAVGFPTLRLIRVRIAQLQLDDLPVGTW 179

Query: 234 REVSKKIL 241
           R +S   +
Sbjct: 180 RYLSPVEV 187


>gi|319764400|ref|YP_004128337.1| RNA-binding s4 domain protein [Alicycliphilus denitrificans BC]
 gi|317118961|gb|ADV01450.1| RNA-binding S4 domain protein [Alicycliphilus denitrificans BC]
          Length = 241

 Score =  103 bits (256), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 45/235 (19%), Positives = 74/235 (31%), Gaps = 9/235 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRK 69
              R++K +A+    SR   E+ I    V V+G ++E  A  V  T  + +  D   L  
Sbjct: 8   EAVRLAKRVAQQLGCSRATAEQYIEGGWVSVDGRVVEEPAARVAPTQAVALAPDANLLDL 67

Query: 70  AERTRLWL----YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
              T L       +    L       +        L      +     L     GL + T
Sbjct: 68  RPVTLLLHRPANANAQEFLRAERHAAELDRPGTRVLRRHLRALECAAPLPAGASGLTVYT 127

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            +  +AR L        +   V   GQ+  D L  L + +   G         L     +
Sbjct: 128 QERRIARRLAEDMALLEQECTVHVEGQIAPDGLQALGRNLPHHGGLAAP---HLKASWQN 184

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
              + + L+      I ++      +V  + RI  G   L  L  G  R +    
Sbjct: 185 ETHLRLALKGVDMARIPELCAAVGLRVLGVRRIRMGRLPLARLPEGQWRYLQPWE 239


>gi|326802921|ref|YP_004320739.1| putative 16S pseudouridylate 516 synthase [Aerococcus urinae
           ACS-120-V-Col10a]
 gi|326650345|gb|AEA00528.1| putative 16S pseudouridylate 516 synthase [Aerococcus urinae
           ACS-120-V-Col10a]
          Length = 248

 Score =  103 bits (256), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 55/230 (23%), Positives = 95/230 (41%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  +I      S  + +R+I    V   G  L      +      I+  G  +     
Sbjct: 1   MRLLDLIQAECHLSATKAKRLIHAGEVFYKGHPLVDINQALDPDLMAIDYQGKRIGLGLG 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +Y+K  G V+         T +D+LP  +     VGRLD + EGLLLLT++G L  
Sbjct: 61  HHYLVYNKAAGQVSAK-KDAHWPTPYDHLPECYQGTSIVGRLDRDVEGLLLLTDNGQLHY 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTV 191
            LE       + Y+V  +G +  D +   + G+           Q+ +   + +     +
Sbjct: 120 FLEHARFHIPKTYQVTVNGDLGADLVEKFQAGVTFADGTTCRPAQLEIIGPRQA----YL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + +G   ++KK+F     KV+ L R+S GP +L   L  G  R ++ + 
Sbjct: 176 TIDQGMRHQVKKMFLANGLKVSYLKRLSLGPLRLDPDLKRGHFRPLTGEE 225


>gi|167470950|ref|ZP_02335654.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           FV-1]
          Length = 165

 Score =  103 bits (256), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 40/165 (24%), Positives = 77/165 (46%), Gaps = 2/165 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    
Sbjct: 1   MRLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQMVGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQ 176
           +  P     + Y V     +  D       G+ +          Q
Sbjct: 121 VTSPRHHCEKTYLVTLEHPLSDDTAQQFADGVQLYNEKSLTKPAQ 165


>gi|283770564|ref|ZP_06343456.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus H19]
 gi|283460711|gb|EFC07801.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus H19]
          Length = 156

 Score =  102 bits (255), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 54/143 (37%), Positives = 79/143 (55%), Gaps = 1/143 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R+ K IA +G  SRR+ E +I++ +VKVNG  +      V  +D IEV+G+ +  
Sbjct: 2   TKELERLQKRIANSGYTSRRKAETLISEGKVKVNGTTVTELGTKVKPSDTIEVEGIKIEL 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E     L+HKP  ++T+ SD  GR+ V D    I +R+  VGRLD +T GLLLLTNDG 
Sbjct: 62  -EDKIYILFHKPTQVITSVSDDRGRTVVTDYFKDIEARIYPVGRLDYDTSGLLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQ 152
              ++  P  Q  + Y  +  G 
Sbjct: 121 FTNLMTHPRYQIKKKYVAKLKGY 143


>gi|160901833|ref|YP_001567414.1| pseudouridine synthase [Petrotoga mobilis SJ95]
 gi|160359477|gb|ABX31091.1| pseudouridine synthase [Petrotoga mobilis SJ95]
          Length = 220

 Score =  102 bits (255), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 59/215 (27%), Positives = 101/215 (46%), Gaps = 10/215 (4%)

Query: 41  KVNGILLERAAVNVMSTDHIEVDGVPL-------RKAERTRLWLYHKPIGLVTTHSDPDG 93
           KVNG L++     +   + IE +           +   +    L      L T   D   
Sbjct: 2   KVNGKLVKEPWYELKENNFIEFNNKKYGLSDLQKKAENKVYYLLNKPKGILCTFKDDFGR 61

Query: 94  RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
           ++        I  RV  VGRLD ++ GLLLLTNDG LA  L  P  +  +VY V   G  
Sbjct: 62  KTINDLIKGKIEERVFYVGRLDYDSSGLLLLTNDGDLANYLLRPENKVTKVYEVLVKGSP 121

Query: 154 DQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            + +L +L++GI ++ G      +V +  ++   + + + L EGK R+IK + +   +KV
Sbjct: 122 SKKELQMLEEGITLETGYKTMKSKVKILKKQKDLSLLQISLNEGKKRQIKLMIKALGYKV 181

Query: 213 NRLIRISYGPFQLGTLL-AGSTREV-SKKILREQL 245
             L RI +GP+ +  +   G+ + + S + ++ +L
Sbjct: 182 IELKRIKFGPWSIKEVPKPGNIKSLGSMEEVKNRL 216


>gi|220906656|ref|YP_002481967.1| pseudouridine synthase [Cyanothece sp. PCC 7425]
 gi|219863267|gb|ACL43606.1| pseudouridine synthase [Cyanothece sp. PCC 7425]
          Length = 195

 Score =  102 bits (255), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 54/185 (29%), Positives = 89/185 (48%), Gaps = 17/185 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              R  L+HKP G+++  S  +G  T+ D +    + V  VGRLD ++EGL+LLTN G L
Sbjct: 1   MHYRYLLFHKPYGVLSQFSGGEGPPTLKDYIT--VADVYPVGRLDRDSEGLMLLTNHGEL 58

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------ 184
              L  P     R Y V+  G    + L  L  G+++QG C    QV +   +       
Sbjct: 59  QHRLSDPRFAHPRTYWVQVEGCPTPEALEQLATGVMVQGKCTRPAQVEVLAAEPDLPPRD 118

Query: 185 ---------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                       W+++ LREG+NR+++++     +   RL+R++     LG+L  G  R+
Sbjct: 119 PPIRFRLSIPTTWLSLTLREGRNRQVRRMTAAVGFPTLRLVRVAIAHLNLGSLAPGQWRD 178

Query: 236 VSKKI 240
           ++   
Sbjct: 179 LTPVE 183


>gi|330722223|gb|EGH00111.1| Ribosomal large subunit pseudouridine synthase E [gamma
           proteobacterium IMCC2047]
          Length = 220

 Score =  102 bits (255), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 48/222 (21%), Positives = 95/222 (42%), Gaps = 16/222 (7%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L L++KP  +++  +D  GR T+ D +        + GRLD N+EGLLLLT++G L 
Sbjct: 1   MPTLILFNKPYDVLSQFTDDKGRPTLADFITQKGV--YAAGRLDYNSEGLLLLTDNGQLQ 58

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--------- 182
             +  P  +  + Y V+  G + +  +  L+ GI ++       +V    +         
Sbjct: 59  HHIAHPRHKQEKTYWVQVEGDISEQAVKQLRTGIQLKDGLTRPAKVQKLPEPELWPRNPP 118

Query: 183 -----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                +   +WV + + EG+NR+++++     +   RL+R++ G ++L  L  G  + ++
Sbjct: 119 VRFRAEIPTSWVEIKISEGRNRQVRRMTAAVGFPTLRLVRVAIGNWELENLQPGEYKVLT 178

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVP 279
                E       +     L   +  S+   +         P
Sbjct: 179 VDAPAEPKKHASKKTRIPTLKPTVRYSKKRTKQALKRQKAKP 220


>gi|299533144|ref|ZP_07046529.1| RNA-binding S4 [Comamonas testosteroni S44]
 gi|298718921|gb|EFI59893.1| RNA-binding S4 [Comamonas testosteroni S44]
          Length = 255

 Score =  102 bits (254), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 47/248 (18%), Positives = 78/248 (31%), Gaps = 16/248 (6%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVP 66
                 R++K +A     SRRE E  I    V+V+G +++     V     + +  D  P
Sbjct: 6   PEQESIRLAKRVAEQEQCSRREAELHIVAGNVQVDGKVVQVPETRVRPDQVVILRKDAKP 65

Query: 67  LRKAERTRLWLYHKPIGL--------------VTTHSDPDGRSTVFDNLPSIFSRVISVG 112
                 T L      +                                L   F  + S  
Sbjct: 66  EAIPPVTILMNKPSGMTQGKAYGRVRSAHSLLREDTKAKLDTPMPQLVLDHHFRNLESFL 125

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
            + +   GL++ T D  +AR L        +   V   GQ+ +D L +L +G+ I G   
Sbjct: 126 TIPLPASGLIVYTQDKRVARKLAEEGMWLEQEIIVGVEGQIIEDGLEILYEGLPIPGGNG 185

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                       S   +   L+     EI+K+       V  + R+  G   L  +  G 
Sbjct: 186 HRRMPPCHVSWQSENHLRFALKGIAPEEIEKMCAAIGLTVVSMRRLRLGRVSLAKVPEGQ 245

Query: 233 TREVSKKI 240
            R +    
Sbjct: 246 WRYLMPWE 253


>gi|156093633|ref|XP_001612855.1| pseudouridine synthetase [Plasmodium vivax SaI-1]
 gi|148801729|gb|EDL43128.1| pseudouridine synthetase, putative [Plasmodium vivax]
          Length = 327

 Score =  102 bits (254), Expect = 9e-20,   Method: Composition-based stats.
 Identities = 59/306 (19%), Positives = 110/306 (35%), Gaps = 70/306 (22%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R++K+I+     SRR+ ++ I    VK+N  +++    ++    D I++ G  +   + 
Sbjct: 22  VRLNKIISLEKKMSRRKSDQFIKDGNVKLNNKIVKNPGTHIDVKKDKIKICGKTVNILKT 81

Query: 73  TRLWL------------YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINT 118
            ++              +     L T+  + +  S        I      +SVGRLD NT
Sbjct: 82  QKMISPNDSSMYKWFVLHKPKGLLCTSDDEKERASIYSLFPQDILDNYRLVSVGRLDRNT 141

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----------- 167
            G+LLLTN+      L  P  Q +R YRV   G      L  L  G+ +           
Sbjct: 142 SGVLLLTNEYAWVNKLTHPKYQRIRTYRVHIEGAAQMKVLRELAAGVYLPDDDRGGKVKK 201

Query: 168 -----------------------------------QGICYGDMQVTLDTQKGSN------ 186
                                              +G       + +  Q+         
Sbjct: 202 GMQKGMQKGMQKGMQKGMQKGVPKGIQKGFPTGMQKGFPTQPAFIEILRQETIKVKDQVK 261

Query: 187 --AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL-LAGSTREVSKKILRE 243
             + + + +REG+NR+I+K+FE  N  V ++ R ++    L  +      RE++ + + +
Sbjct: 262 RVSVLNISVREGRNRQIRKMFEQINQPVIKIKRTAFENITLKDVFFPKQYRELTPREVSD 321

Query: 244 QLGPHL 249
                 
Sbjct: 322 LKARRF 327


>gi|255069983|ref|XP_002507073.1| pseudouridylate synthase [Micromonas sp. RCC299]
 gi|226522348|gb|ACO68331.1| pseudouridylate synthase [Micromonas sp. RCC299]
          Length = 334

 Score =  102 bits (254), Expect = 9e-20,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 91/236 (38%), Gaps = 19/236 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA--------VNVMSTDHIEVDGV 65
           QR+SK+IA     SRRE ER+I++ +V VNG+L+ + +              D +     
Sbjct: 90  QRISKIIALREFCSRREAERLISRSQVVVNGVLIHQGSKAECDSEIQLAEIGDQVWFQSK 149

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
                 + R ++ + P             +T      S +S         +N  G L   
Sbjct: 150 STVALNKPRGYVSNLPSHGEVEACSLLITTTGSHIHSSKWSSRTENDNGQLNVCGRLDKN 209

Query: 126 NDGGLARVLELPSTQW-------LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           + G L    +    +         + Y V     V Q+ L+ L             ++V 
Sbjct: 210 SRGLLVLSQDGVLAREVIAGVFVSKTYLVEVDKMVTQNDLDRLNGPCKFLTDVIRPIRVR 269

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           L     +   +   LREGKNR+I+++ E     V  L R+  G  +LG+L  GS R
Sbjct: 270 LL----APTLLEFVLREGKNRQIRRMCEQMGLIVVDLFRVRLGKSELGSLPEGSWR 321


>gi|159486060|ref|XP_001701062.1| pseudouridine synthase [Chlamydomonas reinhardtii]
 gi|158281561|gb|EDP07316.1| pseudouridine synthase [Chlamydomonas reinhardtii]
          Length = 241

 Score =  102 bits (253), Expect = 9e-20,   Method: Composition-based stats.
 Identities = 56/241 (23%), Positives = 90/241 (37%), Gaps = 13/241 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKV-NGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            RV +++A  G   RRE ++M+ +  V   +G  L+     V  +D     G  L     
Sbjct: 1   MRVERLLANLGYGKRRECQQMVKKGHVMRKDGGKLKV-GDKVAWSDLELEGGEELDPPGP 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGRLDINTEGLLLLTN 126
             L +      +VT   D      V  +L            +  VGRLD +T GLLLLT+
Sbjct: 60  LLLAINKPTGYVVTAPDDEKVSDPVVYDLLPYSRFGRRRPFLSCVGRLDKDTSGLLLLTD 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDMQVTLDTQ 182
           DG L   +  P     +VY       +         K            +  +      +
Sbjct: 120 DGTLLHRINSPKRGIWKVYEATLADPLSPKAAEAAAKKFASGTLTLEGDFSPLLPARLER 179

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            G  +   V + EG+  +++++F     KV  L R+S G   LG L     R ++ + L 
Sbjct: 180 TGERS-ARVAICEGRYHQVRRMFAAVGNKVVGLRRVSVGGLALGDLPEAEWRFLTPQDLE 238

Query: 243 E 243
            
Sbjct: 239 A 239


>gi|224543154|ref|ZP_03683693.1| hypothetical protein CATMIT_02354 [Catenibacterium mitsuokai DSM
           15897]
 gi|224523941|gb|EEF93046.1| hypothetical protein CATMIT_02354 [Catenibacterium mitsuokai DSM
           15897]
          Length = 234

 Score =  102 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 49/207 (23%), Positives = 81/207 (39%), Gaps = 17/207 (8%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTV 97
             ++VN  +++   +++     +  D   L         ++     +       D     
Sbjct: 25  GLIQVNNEIVDE-DMDITDE-TVIYDSKILDPHPLKYYIIHKPSGYVCANKDSHD----P 78

Query: 98  FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                     +  VGRLD NT GL++LTND  L + L LP     R Y            
Sbjct: 79  CLISLLPDDNLHYVGRLDRNTTGLVILTNDLKLRKRLTLPEFHIPRTYAFTC--LNPLKD 136

Query: 158 LNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT--VGLREGKNREIKKVFEFFNWKVNR 214
           +   K+GI I   +      V +       +     + L EG+  EIKK+F   N K+  
Sbjct: 137 ITPFKEGITIDGDVKCLPAIVEM------TSEYEGVITLEEGRYHEIKKMFLSLNNKITS 190

Query: 215 LIRISYGPFQLGTLLAGSTREVSKKIL 241
           L RI YG   LG L +G+ R ++++ +
Sbjct: 191 LHRIMYGDISLGDLPSGTYRTLTQEEI 217


>gi|311106376|ref|YP_003979229.1| S4 domain-containing protein [Achromobacter xylosoxidans A8]
 gi|310761065|gb|ADP16514.1| S4 domain protein [Achromobacter xylosoxidans A8]
          Length = 241

 Score =  102 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 45/237 (18%), Positives = 82/237 (34%), Gaps = 16/237 (6%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRK 69
               R++K +A     SR + ER I      V+G  +E     V     +  + G  L  
Sbjct: 2   SASVRLAKRLAEELSCSRGDAERYIEGGWAAVDGKPVEEPGFRVEPGQSVGLLPGARLED 61

Query: 70  AERTRLWLYHKPIGLVT-----------THSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                + L+                     +   G  +    L  +F+ +  V  L+   
Sbjct: 62  VRPVTILLHKPAGIYANDEPGSARDLILPENLMPGDRSGQRYLKRMFNGLKLVTPLERAA 121

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GL++ T +  +AR L        + Y  +  GQ+    L  L++G+   G     M+V+
Sbjct: 122 SGLVVYTQEYPVARKLVEEGRYVEQEYVAQVSGQLSAADLARLQRGMAYDGRAATPMKVS 181

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              +      +   L+      I+ V +    ++  L RI  G   +  L+ G  R 
Sbjct: 182 WQNE----THLRFALKTPAPGFIEYVCDAAGLRLQALRRIRIGRLPMAGLVPGQWRY 234


>gi|302036786|ref|YP_003797108.1| 23S rRNA pseudouridylate synthase E [Candidatus Nitrospira
           defluvii]
 gi|190343202|gb|ACE75590.1| ribosomal large subunit pseudouridine synthase E [Candidatus
           Nitrospira defluvii]
 gi|300604850|emb|CBK41183.1| 23S rRNA pseudouridylate synthase E [Candidatus Nitrospira
           defluvii]
          Length = 195

 Score =  102 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 60/189 (31%), Positives = 93/189 (49%), Gaps = 17/189 (8%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR  ++HKP  ++   +DPDGR T+ D +        + GRLD ++EGLLLLT+DG LA 
Sbjct: 7   TRTLVFHKPYDVLPCFTDPDGRPTLGDYIDVPGV--YAAGRLDRDSEGLLLLTSDGALAH 64

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------ 180
            +  P     ++Y V+     D   +  L++G+V+ G      Q  L             
Sbjct: 65  RITDPEHHLPKIYFVQVERIPDAAAVERLQQGVVVGGRRTKPAQARLLLEAPSIPERPVP 124

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +    AW+ + LREG NR+++++         RL+R++ GP  LG LL G  RE++
Sbjct: 125 IRFRKHVPTAWLELTLREGMNRQVRRMTAAVGHPTLRLVRVAIGPITLGALLPGQWRELT 184

Query: 238 KKILREQLG 246
           K    E  G
Sbjct: 185 KAETAEIYG 193


>gi|119511122|ref|ZP_01630240.1| Pseudouridine synthase, Rsu [Nodularia spumigena CCY9414]
 gi|119464217|gb|EAW45136.1| Pseudouridine synthase, Rsu [Nodularia spumigena CCY9414]
          Length = 208

 Score =  101 bits (252), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 54/189 (28%), Positives = 79/189 (41%), Gaps = 17/189 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 +  Y     L     +    ST+ D +P     V  VGRLD ++EGLLLLTNDG
Sbjct: 2   ANHYRYIIFYKPYGVLSQFTQETPKHSTLKDYIP--VRDVYPVGRLDWDSEGLLLLTNDG 59

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   L  P     R Y V+     D D +N L+ G+ IQG      +V L         
Sbjct: 60  QLQHRLAHPRFGHQRTYWVQVERIPDVDAINKLQTGVEIQGYRTQPAEVRLLLAATQLPE 119

Query: 181 -------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                   +    AW+ + L EGKNR+++++     +   RL+R++     L  L  G  
Sbjct: 120 RNPPIRFRKNVPTAWLEMTLTEGKNRQVRRMTAAVGFPTLRLVRVNIAHLNLDGLDLGEW 179

Query: 234 REVSKKILR 242
           R++    L 
Sbjct: 180 RDLMPSELE 188


>gi|205373780|ref|ZP_03226582.1| ribosomal large subunit pseudouridine synthaseB (pseudouridylate
           synthase) (uracil hydrolyase) [Bacillus coahuilensis
           m4-4]
          Length = 131

 Score =  101 bits (252), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 31/128 (24%), Positives = 61/128 (47%), Gaps = 2/128 (1%)

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           +TNDG  + +L  P  +  + Y  +  G   + +L  L++GI ++       +V   +  
Sbjct: 1   MTNDGEFSNLLTHPKYEIDKTYIAKIKGIPTRQELTKLQRGIKLEDGMTAPAKVKFISAD 60

Query: 184 GSNAW--VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            S     V + + EG+NR+++++FE   + V +L R  +G   L  L AG  RE++   +
Sbjct: 61  RSKNTCIVELTIHEGRNRQVRRMFEALGFPVMKLRRERFGTLTLKGLNAGEARELTPHEV 120

Query: 242 REQLGPHL 249
           ++      
Sbjct: 121 KQLRTLAQ 128


>gi|194367660|ref|YP_002030270.1| pseudouridine synthase [Stenotrophomonas maltophilia R551-3]
 gi|194350464|gb|ACF53587.1| pseudouridine synthase [Stenotrophomonas maltophilia R551-3]
          Length = 189

 Score =  101 bits (252), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 46/177 (25%), Positives = 85/177 (48%), Gaps = 15/177 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP  ++   +D             +  RV + GRLD ++EGLLLLT++G LA  L
Sbjct: 12  LIAFNKPFNVLCQFTDRSVPPRPTLAGFGLPPRVYAAGRLDHDSEGLLLLTDNGTLAHKL 71

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y V+  G    ++L  L+ G+V+        ++                 
Sbjct: 72  TDPKHKADKTYWVQVEGMPSDEQLQQLRTGVVLNDGPTLPAKIERLDPAPSLWTRDPPVR 131

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +   ++W+ + +REG+NR+++++    N    RL+R+S GP++L  L  G  R++
Sbjct: 132 FRKTVPDSWLAITIREGRNRQVRRMTAAVNLPTLRLVRVSMGPYRLDDLQPGQWRQI 188


>gi|121606251|ref|YP_983580.1| RNA-binding S4 domain-containing protein [Polaromonas
           naphthalenivorans CJ2]
 gi|120595220|gb|ABM38659.1| RNA-binding S4 domain protein [Polaromonas naphthalenivorans CJ2]
          Length = 251

 Score =  101 bits (252), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 49/253 (19%), Positives = 84/253 (33%), Gaps = 28/253 (11%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLR 68
             P R++K +A     SRRE E+ I    V V+G+++E     V     I +  D   L 
Sbjct: 2   TEPVRLAKRLAEMLACSRREAEQYIEGGFVTVDGVVVEEPQFRVQ-NQAIALSPDASLLA 60

Query: 69  KAERTRLWLY------------------HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
               T L                          L+T  +      +    L   FS    
Sbjct: 61  LTPVTILLHKPAGYEASDTPGANPASAGKTAAQLLTAANHASDDRSGIRPLKKHFSSSEL 120

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---DKLNLLKKGIVI 167
           +  L     GL++ + D  +AR L   +        V   G++     ++LN +  G   
Sbjct: 121 LTPLATAASGLVVFSGDWRVARKLREDARVLEHEVVVEVSGEIKPGGLERLNRIDHGFTY 180

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
           +G      +V+      S   +   L+     +I  + +    K+  + R+  G   L  
Sbjct: 181 RGALLPPAKVSWQ----SETRLRFALKGEVPGQIAYMCDSVGLKIEAMKRLRVGRMPLSQ 236

Query: 228 LLAGSTREVSKKI 240
           L  G  R +    
Sbjct: 237 LQPGQWRYLMPYE 249


>gi|264680273|ref|YP_003280183.1| RNA-binding S4 [Comamonas testosteroni CNB-2]
 gi|262210789|gb|ACY34887.1| RNA-binding S4 [Comamonas testosteroni CNB-2]
          Length = 255

 Score =  101 bits (252), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 47/248 (18%), Positives = 78/248 (31%), Gaps = 16/248 (6%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVP 66
                 R++K +A     SRRE E  I    V+V+G +++     V     + +  D  P
Sbjct: 6   PEQESIRLAKRVAEQEQCSRREAELHIVAGNVQVDGKVVQVPETRVRPDQVVILRKDAKP 65

Query: 67  LRKAERTRLWLYHKPIGL--------------VTTHSDPDGRSTVFDNLPSIFSRVISVG 112
                 T L      +                                L   F  + S  
Sbjct: 66  EAIPPVTILMNKPAGMTQGPAYGRVRSAHSLLREDTKAKLDTPMPQLVLDHHFRNLESFL 125

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
            + +   GL++ T D  +AR L        +   V   GQ+ +D L +L +G+ I G   
Sbjct: 126 TIPLPASGLIVYTQDKRVARKLAEEGMWLEQEIIVGVEGQIIEDGLEILYEGLPIPGGNG 185

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                       S   +   L+     EI+K+       V  + R+  G   L  +  G 
Sbjct: 186 HRRMPPCHVSWQSENHLRFALKGIAPEEIEKMCAAIGLAVVSMRRLRLGRVSLAKVPEGQ 245

Query: 233 TREVSKKI 240
            R +    
Sbjct: 246 WRYLMPWE 253


>gi|56808584|ref|ZP_00366315.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and
          related pseudouridylate synthases [Streptococcus
          pyogenes M49 591]
          Length = 109

 Score =  101 bits (252), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 27/83 (32%), Positives = 43/83 (51%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R++K IA AGIASRR+ E +I Q  V +NG ++   A  V S D +E++G P+   E+ 
Sbjct: 1  MRINKYIAHAGIASRRKAEELIKQGLVTLNGQVIMDLATTVKSGDVVEIEGSPIYNEEKV 60

Query: 74 RLWLYHKPIGLVTTHSDPDGRST 96
             L      + +   D   ++ 
Sbjct: 61 YYLLNKPRGAISSVSDDKGRKTV 83


>gi|90021328|ref|YP_527155.1| ribosomal large subunit pseudouridine synthase E [Saccharophagus
           degradans 2-40]
 gi|89950928|gb|ABD80943.1| ribosomal large subunit pseudouridine synthase E [Saccharophagus
           degradans 2-40]
          Length = 213

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 46/216 (21%), Positives = 86/216 (39%), Gaps = 22/216 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L +      L          +         +      GRLD+++EGLL+LTN+G L   +
Sbjct: 5   LLINKPYNTLCQFTDGEGRNTLANLLPDGKYKDYYPAGRLDLDSEGLLILTNNGSLQHRI 64

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---------------L 179
             PS +  + Y V+  G + Q+ +  L+ G+ ++       +                  
Sbjct: 65  SHPSQKLEKTYWVQVEGDITQEAIAQLEAGVELKDGKTKPAKAKKIAPPQNLWERNPPVR 124

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + +    +W+ + + EGKNR+++++    N+   RLIR + GP+QL  L  GS +E    
Sbjct: 125 ERKNIPTSWLRLTISEGKNRQVRRMTAAVNYPTLRLIRAAIGPWQLDNLAPGSYKE---- 180

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNII 275
              E +     ++             T   ++PN  
Sbjct: 181 ---ETVHLAPPKQKPRTSTGNYKKRTTKPTNKPNKR 213


>gi|282897768|ref|ZP_06305767.1| Pseudouridine synthase, Rsu [Raphidiopsis brookii D9]
 gi|281197447|gb|EFA72344.1| Pseudouridine synthase, Rsu [Raphidiopsis brookii D9]
          Length = 191

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 50/188 (26%), Positives = 76/188 (40%), Gaps = 17/188 (9%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 +  +     L     +     T+ D +      V  VGRLD ++EGLLLLTNDG
Sbjct: 2   AHNFKYIIFHKPYGVLSQFTRELPEHVTLKDYID--VPDVYPVGRLDWDSEGLLLLTNDG 59

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---- 184
            L   +  P     R Y V+     D   +  L +G+ IQ       QV L  ++     
Sbjct: 60  KLQHHIANPRFGHQRTYWVQVERIPDPVAIAKLGQGVEIQNYRTLPAQVKLLLEEPTVGE 119

Query: 185 -----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                        AW+ + L+EGKNR+++++     +   RLIRI     QL  L  G+ 
Sbjct: 120 RHPPIRYRKNVPTAWLEMTLKEGKNRQVRRMTAAVGFPTLRLIRIRIAQLQLDDLPVGTW 179

Query: 234 REVSKKIL 241
           R +    +
Sbjct: 180 RYLGPVEV 187


>gi|332531387|ref|ZP_08407292.1| RNA-binding S4 domain protein [Hylemonella gracilis ATCC 19624]
 gi|332039171|gb|EGI75592.1| RNA-binding S4 domain protein [Hylemonella gracilis ATCC 19624]
          Length = 245

 Score =  101 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 85/238 (35%), Gaps = 14/238 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV-PLRKA 70
             QR++KV+A     SRRE E+ IAQ  V V+G  ++   V V ++  +++D    L+  
Sbjct: 11  DAQRLAKVVAALVPCSRREAEQYIAQGWVSVDGQCVDAPQVRVTTSQRVQIDPQARLQAV 70

Query: 71  ERTRLWLYHKPIGLVTTHS-------DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                 ++        +            G ++      +    + ++  L +   GL +
Sbjct: 71  VPATFLVHKPAGMETESAMDLLGESAHWSGDASGIRRSKAHQVGLKTLLPLPVQASGLCV 130

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            + D  + R L   +    +       G +  D L  L  G++  G      +V+     
Sbjct: 131 FSQDFRVVRKLTEDAAFVEQELVAEVKGTIAPDGLARLGHGLLRDGRPLPPARVSWQ--- 187

Query: 184 GSNAWVTVGLREGKNREIKKVFEF-FNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            S   +     +G   E           +++ L RI  G   +  L  G  R + +  
Sbjct: 188 -SETRLRFA-TKGIAPEWTAWMCAQVGLELSALRRIRIGRIAMAGLPLGQWRYLPEGE 243


>gi|126659424|ref|ZP_01730558.1| Pseudouridine synthase, Rsu [Cyanothece sp. CCY0110]
 gi|126619260|gb|EAZ89995.1| Pseudouridine synthase, Rsu [Cyanothece sp. CCY0110]
          Length = 208

 Score =  101 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 51/198 (25%), Positives = 79/198 (39%), Gaps = 25/198 (12%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDG--RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
             +     L++KP  ++   +D                   V SVGRLD ++EGLL LTN
Sbjct: 2   AKKNRHYLLFNKPYNVLCQFTDNSNLENPRPTLKDYIKVPDVYSVGRLDKDSEGLLFLTN 61

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------ 180
           +  L   L        R Y V+     DQ  LN L++G+ I+       +V L       
Sbjct: 62  NAQLKHRLSHRQFAHPRTYLVQVERIPDQVALNQLRQGVRIKDYKTRPAKVKLLDSPPSV 121

Query: 181 ---------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG--------PF 223
                     +    AW+ + L EG+NR+++++     +   RLIRI+ G          
Sbjct: 122 PPRDPPIRYRKTVPTAWLEMTLTEGRNRQVRRMTAAVGYPTLRLIRIAIGVQRKGKIINL 181

Query: 224 QLGTLLAGSTREVSKKIL 241
            L  L  G  RE++   L
Sbjct: 182 TLEGLKPGQWRELTPSEL 199


>gi|119484911|ref|ZP_01619393.1| Pseudouridine synthase, Rsu [Lyngbya sp. PCC 8106]
 gi|119457729|gb|EAW38853.1| Pseudouridine synthase, Rsu [Lyngbya sp. PCC 8106]
          Length = 202

 Score =  101 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 48/197 (24%), Positives = 78/197 (39%), Gaps = 15/197 (7%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L+     +    T +DP                V  VGRLD ++EGLLLLTN G +   
Sbjct: 6   ILFYKPYDVLCQFTDNDPTTSPRKTLKDFISIPGVYPVGRLDRDSEGLLLLTNQGKIQHR 65

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------- 184
           L        R Y V+     D+  LN L+ G+ I+       QV L   +          
Sbjct: 66  LSHRKFNHPRTYWVQVEHIPDETALNALRAGVQIKDYQTRSAQVQLLPTEPALPPRDPPI 125

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
                   AW+ + L EG+NR+I+++     +   RL+R++   F+L  L  G  R++++
Sbjct: 126 RFRKTVPTAWLEITLTEGRNRQIRRMTAAVGFPTLRLVRVAIADFRLDGLKPGQWRDLTQ 185

Query: 239 KILREQLGPHLLEEAQV 255
             +            + 
Sbjct: 186 IEVHNLYKLTGFSPPKK 202


>gi|225851129|ref|YP_002731363.1| RNA pseudouridine synthase family protein [Persephonella marina
           EX-H1]
 gi|225645852|gb|ACO04038.1| RNA pseudouridine synthase family protein [Persephonella marina
           EX-H1]
          Length = 180

 Score =  100 bits (249), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 38/171 (22%), Positives = 72/171 (42%), Gaps = 4/171 (2%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
                   +     +       F        ++  VGRLDI+TEGLL++T+DG LA  + 
Sbjct: 1   MFNKPSGYITAVKDERYPTVMDFFADLPFSKKLFPVGRLDIDTEGLLIITDDGQLAHRIA 60

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWVTVG 192
            P  +  + Y     G +    L+  +K  ++   +       ++ + +     + + + 
Sbjct: 61  HPKWEIEKEYYAVVKGDISDLDLSRFEKEGIVLKKEKYRTKPFKINIISTSEERSEIYIT 120

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           +REGK   +K++ E     V  L R+  GP +L   L  G  RE++ + + 
Sbjct: 121 VREGKYHIVKRIMEELGHPVLYLKRVRIGPLRLDEDLEEGDFRELTDEEIE 171


>gi|308125708|ref|ZP_07663491.1| ribosomal large subunit pseudouridine synthase F [Vibrio
           parahaemolyticus K5030]
 gi|308114211|gb|EFO51751.1| ribosomal large subunit pseudouridine synthase F [Vibrio
           parahaemolyticus K5030]
          Length = 163

 Score =  100 bits (249), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 36/134 (26%), Positives = 57/134 (42%), Gaps = 3/134 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRR  +++I + RV +NG         V+  D + VDG P+   E+  
Sbjct: 8   RLNKFISETGFCSRRAADKLIEEGRVTINGKQP-EMGTKVLPGDDVCVDGKPVASKEKPI 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T            +      R+  +GRLD  ++GL+ LTNDG +    
Sbjct: 67  YIALNKPTGITCTTER--DIPGNIVDFIGHKKRIFPIGRLDKPSDGLIFLTNDGDIVTDS 124

Query: 135 ELPSTQWLRVYRVR 148
                        R
Sbjct: 125 ARWYNHEKIRGACR 138


>gi|11967881|emb|CAC19451.1| hypothetical pseudouridine synthase [Streptococcus pneumoniae]
          Length = 75

 Score =  100 bits (248), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 26/75 (34%), Positives = 40/75 (53%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E+ 
Sbjct: 1  MRINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQPIYNEEKV 60

Query: 74 RLWLYHKPIGLVTTH 88
             L      + +  
Sbjct: 61 YYLLNKPRGVISSVT 75


>gi|206603683|gb|EDZ40163.1| Protein of unknown function [Leptospirillum sp. Group II '5-way
           CG']
          Length = 298

 Score =  100 bits (248), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 97/234 (41%), Gaps = 13/234 (5%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKV-NGILLERAAVNV--MSTD--HIEVDGVPLRKAE 71
            + I++ G+ +R      +   R+ + +G L++     V           +D   L    
Sbjct: 23  DRWISKLGLGTRGMAREWVRDGRLSLGDGTLVQHVDQFVQGTPGSEPVFRLDQKILSADP 82

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-------SIFSRVISVGRLDINTEGLLLL 124
                       LVT        +                 SR++ VGRLD  + GL+LL
Sbjct: 83  PAVFAFNKPRGVLVTRTDPGGRETICESIGRSSGQRTGMDMSRLMPVGRLDQASSGLILL 142

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           TN       L  P+ ++ R YRV+       +D    L  G   + +    + V  + + 
Sbjct: 143 TNRSSELTRLLNPALEFPREYRVQVRPSLKKRDWEMGLFGGKWARELGLKPVDVRYEKEN 202

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               W+ VGL+EGKNREI+++FE   ++V  LIR+ +GPF L  L  G   EVS
Sbjct: 203 LRTTWLRVGLKEGKNREIRRLFESGGYEVLHLIRVGFGPFCLKNLPPGGIVEVS 256


>gi|330864071|emb|CBX74147.1| ribosomal large subunit pseudouridine synthase F [Yersinia
           enterocolitica W22703]
          Length = 162

 Score = 99.9 bits (247), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 39/152 (25%), Positives = 68/152 (44%), Gaps = 1/152 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRR+ +R + Q  V +NG         V   D ++V+G  +  
Sbjct: 3   TNSSIRLNKYISESGICSRRDADRYVEQGNVFINGKRAAV-GDQVYVGDVVKVNGQLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + + L L      +    +  DG S    +  +   RV  +GRLD +++GL+ LTN G 
Sbjct: 62  RDESDLILIALNKPVGIISTTEDGESDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
           L   +        + Y V  +  V  + +  L
Sbjct: 122 LVNKILRAGNDHEKEYVVTVNKPVTDEFILGL 153


>gi|237732602|ref|ZP_04563083.1| RNA pseudouridine synthase [Mollicutes bacterium D7]
 gi|229384319|gb|EEO34410.1| RNA pseudouridine synthase [Coprobacillus sp. D7]
          Length = 155

 Score = 99.9 bits (247), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 42/151 (27%), Positives = 71/151 (47%), Gaps = 2/151 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A  GI +R+EV+ +I +  VKVNG+++++    V    D I  D   +     
Sbjct: 3   MRLDKLLANYGIGTRKEVKSLIRKGFVKVNGMIIKKDDFKVDHEIDEIVFDDELIEYRPY 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L      + +   D    + +          +  VGRLD++TEGLLL+TNDG  + 
Sbjct: 63  VYIMLNKPAGYI-SATKDNLHPTVLELIEGYENYDLFPVGRLDLDTEGLLLITNDGDFSH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
            L  PS    ++Y     G +D+  +   K 
Sbjct: 122 KLLAPSRNHSKIYFANIAGVMDEQDIQAFKD 152


>gi|120554678|ref|YP_959029.1| pseudouridine synthase [Marinobacter aquaeolei VT8]
 gi|120324527|gb|ABM18842.1| ribosomal large subunit pseudouridine synthase E [Marinobacter
           aquaeolei VT8]
          Length = 202

 Score = 99.9 bits (247), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 41/177 (23%), Positives = 72/177 (40%), Gaps = 14/177 (7%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +        L     +                 V   GRLD ++EGLLLLT+ G L   +
Sbjct: 5   ILFNKPFHVLSQFTDERASHPRATLADWIDQPGVYPAGRLDYDSEGLLLLTDQGALQHRI 64

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P+ +  + Y V+  G++  + L+ L+KG+V++       +                  
Sbjct: 65  ASPTNKMPKTYWVQVEGELTDEALHKLRKGVVLKDGITRPARAERLETPDLWPRNPPVRF 124

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            Q     W+ + + EGKNR+++++     +   RLIR+  G + L  L  G  R V+
Sbjct: 125 RQNVPTTWLALTITEGKNRQVRRMTAAVGYPTLRLIRVRIGDWTLDNLKPGEYRSVT 181


>gi|117617574|ref|YP_855956.1| ribosomal large subunit pseudouridine synthase E [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
 gi|117558981|gb|ABK35929.1| ribosomal large subunit pseudouridine synthase E [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
          Length = 313

 Score = 99.9 bits (247), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 54/273 (19%), Positives = 93/273 (34%), Gaps = 23/273 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P       +L L +KP  ++   +D  GR T+ D +        + GRLD ++EGLLLL
Sbjct: 49  KPAPAPADRKLLLLNKPYMVLCQFTDEAGRETLKDYITEPGI--YAAGRLDRDSEGLLLL 106

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TNDG L   L  P  +  + Y V+  G   ++KL  L  G+ +                 
Sbjct: 107 TNDGKLQARLTQPGEKTPKTYWVQVEGVPSEEKLAALCAGVELNDGMTLPAGARIMEEPA 166

Query: 176 -----QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + ++    W+ + + EG+NR+++++         RLIR + G + L  L  
Sbjct: 167 VWPRNPPIRERKEIPTCWLEIKIVEGRNRQVRRMTAHIGHPTLRLIRYAIGDWSLDGLAP 226

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G +R +    L                     +S                      +  +
Sbjct: 227 GESRALPAPEL-------APAPRPATTQGKAQTSAKPQGAGQRGAPRAARRPQHQGQEQA 279

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSS 323
              G   ++    P HR               +
Sbjct: 280 PGQGRGSREAEPHPGHRSGGRGTARRPARSKPA 312


>gi|260219993|emb|CBA27086.1| hypothetical protein Csp_A00520 [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 279

 Score = 99.9 bits (247), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 46/263 (17%), Positives = 89/263 (33%), Gaps = 34/263 (12%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP-LRK 69
            T +R+SK +      SR+E E+ I    V+VNG+++E     V     I +D    L +
Sbjct: 16  TTGERLSKRVMALKDCSRKEAEQYIEGGWVQVNGVVVEEPQHRVDRE-TITLDPNASLME 74

Query: 70  AERTRLWLYHKPIGLV--------------------------------TTHSDPDGRSTV 97
                L L                                        T  +  +G    
Sbjct: 75  LTPVTLLLNKPAGHTDGLEELTPVRAGAPARTGAPGHKAPPANARALLTPANHWEGDPAD 134

Query: 98  FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
              L   F+ + +   L+    GL++ T D    R L    +     + V   G+V+ D 
Sbjct: 135 TRVLKRHFNHLEADVELETGATGLVVFTQDWRTTRKLTEDMSTMEHEFLVEVKGEVEPDA 194

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
           L  +   +  + +    ++V++++    ++ +   ++      I  + E     +  + R
Sbjct: 195 LKPIAYALKDERLDLPQVKVSVNSTTPESSRLRFAIKGSHPGLIAFLCEKAGLHILGMKR 254

Query: 218 ISYGPFQLGTLLAGSTREVSKKI 240
           I  G   L  L  G  R ++   
Sbjct: 255 IRLGRVALSDLPVGQWRYLAGWE 277


>gi|318606116|emb|CBY27614.1| ribosomal large subunit pseudouridine synthase E; LSU Psi2457
           [Yersinia enterocolitica subsp. palearctica Y11]
          Length = 208

 Score = 99.9 bits (247), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 55/188 (29%), Positives = 95/188 (50%), Gaps = 17/188 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             ++     R+ L++KP  ++   +D  GRST+ + +P  F+ V + GRLD ++EGLL+L
Sbjct: 21  KQVKPITPRRVLLFNKPFDVLPQFTDEAGRSTLKEFIP--FNDVYAAGRLDRDSEGLLVL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TNDG L   L  P+ +  +VY V+  G  D+D L+ L+ GI ++                
Sbjct: 79  TNDGKLQARLTQPAQKTGKVYFVQVEGLPDEDALSQLRTGITLKDGPTLPAGAELVSEPA 138

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR S G   LG L 
Sbjct: 139 WLWPRHPPIRERKAIPTSWLKITLFEGRNRQVRRMTAHIGFPTLRLIRFSIGNLSLGDLQ 198

Query: 230 AGSTREVS 237
            G  +E++
Sbjct: 199 PGEWKEIN 206


>gi|332162068|ref|YP_004298645.1| putative pseudouridine synthase [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|325666298|gb|ADZ42942.1| putative pseudouridine synthase [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330860065|emb|CBX70391.1| ribosomal large subunit pseudouridine synthase E [Yersinia
           enterocolitica W22703]
          Length = 208

 Score = 99.5 bits (246), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 55/188 (29%), Positives = 95/188 (50%), Gaps = 17/188 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             ++     R+ L++KP  ++   +D  GRST+ + +P  F+ V + GRLD ++EGLL+L
Sbjct: 21  KQVKPITPRRVLLFNKPFDVLPQFTDEAGRSTLKEFIP--FNDVYAAGRLDRDSEGLLVL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TNDG L   L  P+ +  +VY V+  G  D+D L+ L+ GI ++                
Sbjct: 79  TNDGKLQARLTQPAQKTGKVYFVQVEGLPDEDALSQLRTGITLKDGPTLPAGAELVSEPA 138

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR S G   LG L 
Sbjct: 139 WLWPRQSPIRERKAIPTSWLKITLFEGRNRQVRRMTAHIGFPTLRLIRFSIGNLSLGDLQ 198

Query: 230 AGSTREVS 237
            G  +E++
Sbjct: 199 PGEWKEIN 206


>gi|254412396|ref|ZP_05026170.1| conserved hypothetical protein [Microcoleus chthonoplastes PCC
           7420]
 gi|196180706|gb|EDX75696.1| conserved hypothetical protein [Microcoleus chthonoplastes PCC
           7420]
          Length = 189

 Score = 99.5 bits (246), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 50/180 (27%), Positives = 84/180 (46%), Gaps = 15/180 (8%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +++KP  +++  +D +             S V  VGRLD ++EGLLLLTN G L   L  
Sbjct: 1   MFYKPYDVLSQFTDREDSPRRTLKDYIPVSEVYPVGRLDRDSEGLLLLTNHGRLQHRLSN 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS----------- 185
           P  +  R Y V+     D+  LN L++G+VI+       QV   +Q+             
Sbjct: 61  PRFRHPRTYWVQVERIPDEAALNQLRQGVVIKDYQTRKAQVQRLSQEPDLPPRDPPIRFR 120

Query: 186 ----NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                 W+ + L EG+NR+++++     +   RLIR++    +L  L  G  R+++   L
Sbjct: 121 KTVPTCWLEITLTEGRNRQVRRMTAVVGFPTLRLIRVAIAHLRLDGLQPGQWRDLTPPEL 180


>gi|121608853|ref|YP_996660.1| RNA-binding S4 domain-containing protein [Verminephrobacter
           eiseniae EF01-2]
 gi|121553493|gb|ABM57642.1| RNA-binding S4 domain protein [Verminephrobacter eiseniae EF01-2]
          Length = 264

 Score = 99.5 bits (246), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 43/255 (16%), Positives = 85/255 (33%), Gaps = 33/255 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKAERT 73
           R+++ +AR    SR   E++I    V V G +++     V +  ++ V     L      
Sbjct: 12  RLTRRVARQLNCSRSTAEQLIENGCVSVQGQVVQAPGARVSAQQNVTVAQDAALPDPRPV 71

Query: 74  RLWLYHKPIGLVTTHSDPDGRS---------------TVFDNLPSIFSRVISVGRLDINT 118
            L L+       ++ + PDG                 +    LP  F  +  +  L    
Sbjct: 72  TLLLHKPAGFAASSAAPPDGPQASALLHAASHLAEDASGMRVLPRHFLHLACLTPLPTEA 131

Query: 119 EGLLLLTNDG-------------GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
            GL++ T D                 R     +    +   V+  G +  D L  L++G+
Sbjct: 132 SGLVVYTQDRRLARVFAQDFAQDMALRQPAQQTHSPEQECIVQVAGTIAPDGLQRLRQGL 191

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           ++ G+    ++ +   +      +   L+  +  +I  +       V  + RI  G   L
Sbjct: 192 LLDGLRLPPIRASWQNE----TRLRFALKGVRPGQIPAICAAVGLTVEAIKRIRIGRVAL 247

Query: 226 GTLLAGSTREVSKKI 240
                G  R +    
Sbjct: 248 ARQPPGQWRYLLPWE 262


>gi|22298188|ref|NP_681435.1| putative pseudouridylate synthase [Thermosynechococcus elongatus
           BP-1]
 gi|22294367|dbj|BAC08197.1| tll0646 [Thermosynechococcus elongatus BP-1]
          Length = 195

 Score = 99.5 bits (246), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 59/185 (31%), Positives = 88/185 (47%), Gaps = 17/185 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              R  L +KP  ++    D  GRST+ D +P     V   GRLD ++EGL+LLTNDG L
Sbjct: 1   MNYRYILLYKPYRVLCQFQDQKGRSTLKDYVPIP--DVYPAGRLDYDSEGLVLLTNDGWL 58

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK------- 183
              L  P     R Y V+  G+ D   L+ L  G+VIQG      +V +  Q        
Sbjct: 59  QHRLTDPRYGHPRTYWVQVEGKPDTAALSQLAAGVVIQGYRTRPARVEVLDQDPPLPPRY 118

Query: 184 --------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                     + W+++ LREG+NR+++++     +   RL+R++    QLG L  G  RE
Sbjct: 119 PPIRYRRHIPSQWLSLTLREGRNRQVRRMTAAVGFPTLRLVRVAIANLQLGNLAPGQWRE 178

Query: 236 VSKKI 240
           +    
Sbjct: 179 ILPLE 183


>gi|330504976|ref|YP_004381845.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           mendocina NK-01]
 gi|328919262|gb|AEB60093.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           mendocina NK-01]
          Length = 189

 Score = 99.5 bits (246), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 49/182 (26%), Positives = 89/182 (48%), Gaps = 16/182 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              + RL L +KP  ++T  +D  GR+T+ D +          GRLD ++EGLLLLTNDG
Sbjct: 5   PPAQPRLLLLNKPFDVLTQFNDEQGRATLKDFVDVPGV--YPAGRLDRDSEGLLLLTNDG 62

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+  +++L  L+ G+++        +            
Sbjct: 63  RLQARIADPKHKLAKTYWVQVEGEPSEEQLQQLRTGVMLNDGPTLPAEARRLDEPELWER 122

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + +REG+NR+++++         RL+R++ GP++L  L  G  R
Sbjct: 123 NPPVRFRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVAIGPWRLDGLQPGQWR 182

Query: 235 EV 236
           E+
Sbjct: 183 EL 184


>gi|158338459|ref|YP_001519636.1| pseudouridine synthase family 1 protein [Acaryochloris marina
           MBIC11017]
 gi|158308700|gb|ABW30317.1| pseudouridine synthase family [Acaryochloris marina MBIC11017]
          Length = 198

 Score = 99.1 bits (245), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 48/195 (24%), Positives = 78/195 (40%), Gaps = 16/195 (8%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +  Y     +++  +D    S            +  VGRLD ++EGLLLL+N GGL  
Sbjct: 4   QHILFYKPYG-VLSQFTDRQETSHPTLKEFIPIPDIYPVGRLDRDSEGLLLLSNHGGLQH 62

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------V 177
            L  P     R Y V+     DQ  L  LK+G+ I+       Q                
Sbjct: 63  QLCNPKFGHPRTYWVQVENIPDQIALQKLKQGVTIRNYRTRPTQASLLSEPPLLPPRTPP 122

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +    AW+T+ L EG+NR+++++     +   RL+R++    QL  L  G  R +S
Sbjct: 123 VRFRKHIPTAWMTMTLYEGRNRQVRRMTAAVGFPTLRLVRVAIAHLQLQDLQPGQWRHLS 182

Query: 238 KKILREQLGPHLLEE 252
              + +      +  
Sbjct: 183 PAEIEQLQFLTHVSR 197


>gi|330828860|ref|YP_004391812.1| ribosomal large subunit pseudouridine synthase E [Aeromonas veronii
           B565]
 gi|328803996|gb|AEB49195.1| ribosomal large subunit pseudouridine synthase E [Aeromonas veronii
           B565]
          Length = 307

 Score = 99.1 bits (245), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 53/279 (18%), Positives = 99/279 (35%), Gaps = 20/279 (7%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E  +L L +KP  ++   +D  GR T+ D +        + GRLD ++EGLLLL
Sbjct: 35  KPELAPEDRKLLLLNKPYMVLCQFTDEAGRETLKDYIKEPGI--YAAGRLDRDSEGLLLL 92

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TNDG L   L  P  +  + Y V+  G   ++KL  L+ G+ +                 
Sbjct: 93  TNDGKLQARLTQPGEKTPKTYWVQVEGIPSEEKLAALRAGVELNDGMTLPAGARIMDEPA 152

Query: 176 -----QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + ++   +W+ + + EG+NR+++++         RLIR + G + L  L  
Sbjct: 153 VWPRNPPIRERKEIPTSWLEIKIIEGRNRQVRRMTAHIGHPTLRLIRYAIGDWTLDGLAP 212

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G +R +    L     P      +         +    +   +            +  S+
Sbjct: 213 GESRSLPAPEL----TPSSSRSPRPASSRSGAHTAKPAKPAGDAPRRASQPRQDERPRST 268

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSG 329
                +               +    A+  + +      
Sbjct: 269 HPTERAATNPTGGKHRSSGRGTARRPARAGNPNSNDKES 307


>gi|54309135|ref|YP_130155.1| putative pseudouridylate synthase [Photobacterium profundum SS9]
 gi|46913567|emb|CAG20353.1| Hypothetical pseudouridylate synthase [Photobacterium profundum
           SS9]
          Length = 240

 Score = 99.1 bits (245), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 55/201 (27%), Positives = 96/201 (47%), Gaps = 7/201 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R+ + I++    S  +   +IAQ+R+ V+G +       V    ++E+DG  L+ 
Sbjct: 29  KSTTNRLDRFISQNSTFSISDTRLLIAQKRILVDGHVAHSNQQKVTKFTYVELDGNCLQ- 87

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                  + +KP G+V+   D    + +     S  + +  VGRLD NT GL+LLTNDG 
Sbjct: 88  DNNPVYIVLNKPKGVVSATKDIKHSTVLDLIQHSQKNELHIVGRLDFNTTGLVLLTNDGA 147

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNA 187
            +R + LP T+  +VY V     +  + + + ++GI    + I      + +     S  
Sbjct: 148 WSRKISLPETKLAKVYEVTLSKPLSDEYITVFREGIYFGYEDITTKPACLEIL----SEY 203

Query: 188 WVTVGLREGKNREIKKVFEFF 208
              + L EGK  ++K++F FF
Sbjct: 204 TARLSLVEGKYHQVKRMFGFF 224


>gi|108807879|ref|YP_651795.1| putative pseudouridine synthase [Yersinia pestis Antiqua]
 gi|165938447|ref|ZP_02227004.1| ribosomal large subunit pseudouridine synthase E [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|270490347|ref|ZP_06207421.1| pseudouridylate synthase [Yersinia pestis KIM D27]
 gi|108779792|gb|ABG13850.1| ribosomal large subunit pseudouridine synthase E [Yersinia pestis
           Antiqua]
 gi|165913562|gb|EDR32182.1| ribosomal large subunit pseudouridine synthase E [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|270338851|gb|EFA49628.1| pseudouridylate synthase [Yersinia pestis KIM D27]
          Length = 177

 Score = 99.1 bits (245), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 53/178 (29%), Positives = 88/178 (49%), Gaps = 17/178 (9%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L++KP  ++   +D  GR+T+   +P  F  V + GRLD ++EGLL+LTNDG L   L 
Sbjct: 1   MLFNKPFDVLPQFTDESGRTTLQGFIP--FKDVYAAGRLDRDSEGLLVLTNDGKLQARLT 58

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------QVTLD 180
            P+ +  +VY V+  G  D D L  LK+G+ ++                          +
Sbjct: 59  QPAQKTGKVYFVQVEGVPDNDALTQLKRGVTLKDGLTLPAGAELVAEPEWLWPRHPPIRE 118

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +    +W+ + L EG+NR+++++     +   RLIR S G   LG L  G  +E++ 
Sbjct: 119 RKTIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRFSMGNLSLGNLQPGEWKEITD 176


>gi|31747805|gb|AAO38400.1| Lfe193p2 [Leptospirillum ferrooxidans]
          Length = 164

 Score = 99.1 bits (245), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 52/153 (33%), Positives = 79/153 (51%), Gaps = 11/153 (7%)

Query: 3   DKNIVQENFTPQ---------RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN 53
            K         +         R+ K++A  GI SRR  E +IA   V VNG +       
Sbjct: 8   QKKTTSNKSDTEYATTLSGEVRLQKLLAHRGITSRRNAEELIAGGLVTVNGKVETTPGTK 67

Query: 54  VMST-DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
           V    D + V+G  L + + T L+L++KP G+++   DPDG+ T+ D  P+I   ++ +G
Sbjct: 68  VDPQRDVVVVEGRMLPREKETFLFLFYKPKGVISAVFDPDGKPTLKDFFPNIS-PLLHIG 126

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVY 145
           RLD  TEG+LLLTN+G L++ +  P     R Y
Sbjct: 127 RLDFQTEGVLLLTNNGDLSQRILHPRFAIPRTY 159


>gi|149191532|ref|ZP_01869780.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio shilonii AK1]
 gi|148834657|gb|EDL51646.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio shilonii AK1]
          Length = 164

 Score = 99.1 bits (245), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 39/162 (24%), Positives = 71/162 (43%), Gaps = 7/162 (4%)

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
            V +H D    +            +   GRLD++T GL+L+T+DG  +  +  P  +  +
Sbjct: 2   FVCSHEDGFNHTAFVLLDEVKMENLHFAGRLDVDTTGLVLITDDGQWSHRITSPKHKCAK 61

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
            YRV     V  + +   ++GI ++         Q+ +  +K     V + + EGK  ++
Sbjct: 62  TYRVWLADPVQDNYIKAFEEGIELRNEKAPTLPAQLEIIDEK----EVLLTIHEGKYHQV 117

Query: 202 KKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           K++F     KV  L R S G   L   L  G  R ++++ + 
Sbjct: 118 KRMFAALGNKVEGLHRESVGDIVLDEMLEPGEYRYLTQEEID 159


>gi|258626360|ref|ZP_05721207.1| pseudouridine synthase family 1 protein [Vibrio mimicus VM603]
 gi|258581412|gb|EEW06314.1| pseudouridine synthase family 1 protein [Vibrio mimicus VM603]
          Length = 275

 Score = 99.1 bits (245), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 47/187 (25%), Positives = 80/187 (42%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +  +ER  +        L         ++            V + GRLD ++EGLL+L
Sbjct: 91  RAISPSERKVVLFNKPYDTLSQFTDGDGRKTLANYI---QIKDVYAAGRLDRDSEGLLIL 147

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +  L  L++G+ ++       +V +  +  
Sbjct: 148 TNDGILQARLTQPQSKAPKTYWVQVEGVPQESDLEALRQGVTLKDGPTLPAKVEIMPEPE 207

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+T+ L EG+NR+++++     +   RLIR S G + LG L  
Sbjct: 208 LWPRNPPVRFRAAIPTTWLTITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQP 267

Query: 231 GSTREVS 237
           G  REV+
Sbjct: 268 GEWREVT 274


>gi|87122220|ref|ZP_01078103.1| Pseudouridine synthase, Rsu [Marinomonas sp. MED121]
 gi|86162540|gb|EAQ63822.1| Pseudouridine synthase, Rsu [Marinomonas sp. MED121]
          Length = 242

 Score = 99.1 bits (245), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 39/215 (18%), Positives = 84/215 (39%), Gaps = 15/215 (6%)

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
               +     GRLD ++EGLLLLT+ G L  ++  P  +  + Y V+  G++ ++ +  L
Sbjct: 29  FIDKANFYPAGRLDYDSEGLLLLTDHGALQHLIASPQHKMPKTYLVQVEGELTKEAVEQL 88

Query: 162 KKGIVIQGICYGDMQVTL--------------DTQKGSNAWVTVGLREGKNREIKKVFEF 207
           + G+ ++       +  +              + +    +W+ + + EGKNR+++++   
Sbjct: 89  RVGVELKDGLTKPAEAKIASDFEPWPRHPPIRERKNIPTSWLELTITEGKNRQVRRMTAA 148

Query: 208 FNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETL 267
             +   RLIR   GP+ L  +  G   E     +   +     E+ +        SS   
Sbjct: 149 VGFPTLRLIRTQIGPYSLTDIELGHWLEKPIDEM-LAMELEKFEKNRARQKPRGTSSNNR 207

Query: 268 VRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            R             +  ++  + + G    ++  
Sbjct: 208 RRSHSAKNKLSRSPVSNGQRKKTGQAGTQPTRRTR 242


>gi|229894384|ref|ZP_04509567.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           Pestoides A]
 gi|229703782|gb|EEO90798.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           Pestoides A]
          Length = 128

 Score = 99.1 bits (245), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 25/131 (19%), Positives = 50/131 (38%), Gaps = 7/131 (5%)

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVT 178
           ++L+T+DG  +  +  P     + Y V     +  D       G+ +          Q+ 
Sbjct: 1   MVLMTDDGQWSHRVTSPRHHCEKTYLVTLEHPLSDDTAQQFADGVQLYNEKSLTKPAQLD 60

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
           +   +     V + + EG+  ++K++F     +V  L R   G   L   L  G  R ++
Sbjct: 61  VIEPQR----VRLTISEGRYHQVKRMFAAVGNRVIELHRERIGDITLDDDLAPGEYRPLT 116

Query: 238 KKILREQLGPH 248
            + +     PH
Sbjct: 117 TEEIASVGAPH 127


>gi|238796005|ref|ZP_04639517.1| Ribosomal large subunit pseudouridine synthase E [Yersinia
           mollaretii ATCC 43969]
 gi|238720210|gb|EEQ12014.1| Ribosomal large subunit pseudouridine synthase E [Yersinia
           mollaretii ATCC 43969]
          Length = 208

 Score = 99.1 bits (245), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 50/184 (27%), Positives = 92/184 (50%), Gaps = 17/184 (9%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                R+ L++KP  ++   +D  GR T+ + +P  F+ V + GRLD ++EGLL+LTN+G
Sbjct: 25  PVPPQRVLLFNKPFDVLPQFTDESGRRTLKEFIP--FNDVYAAGRLDRDSEGLLVLTNNG 82

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------- 175
            L   L  P+ +  +VY V+  G   ++ L  L++G++++                    
Sbjct: 83  KLQAKLTQPAQKTGKVYFVQVEGVPTEEALTQLQRGVILKDGPTLPAGAELVCEPEWLWP 142

Query: 176 --QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 + +    +W+ + L EG+NR+++++     +   RLIR S G   LG L  G  
Sbjct: 143 RNPPIRERKSIPTSWLKITLFEGRNRQVRRMTAHIGFPTLRLIRFSMGNLSLGDLQPGEW 202

Query: 234 REVS 237
           +E++
Sbjct: 203 KEIN 206


>gi|254521474|ref|ZP_05133529.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
 gi|219719065|gb|EED37590.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
          Length = 179

 Score = 98.7 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 45/177 (25%), Positives = 85/177 (48%), Gaps = 15/177 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP  ++   +D             +  RV + GRLD ++EGLLLLT++G LA  L
Sbjct: 2   LIAFNKPFNVLCQFTDRSVPPRPTLAGFGLPPRVYAAGRLDHDSEGLLLLTDNGTLAHKL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y V+  G    ++L  L+ G+++        ++                 
Sbjct: 62  TDPKHKADKTYWVQVEGTPSDEQLQQLRDGVLLNDGPTLPAKIERLDPAPSLWTRDPPVR 121

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +   +AW+ + +REG+NR+++++    N    RL+R++ GP++L  L  G  R++
Sbjct: 122 FRKTVPDAWLAITIREGRNRQVRRMTAAVNLPTLRLVRVAMGPYRLDDLQPGQWRQI 178


>gi|153947226|ref|YP_001400591.1| ribosomal large subunit pseudouridine synthase E [Yersinia
           pseudotuberculosis IP 31758]
 gi|152958721|gb|ABS46182.1| ribosomal large subunit pseudouridine synthase E [Yersinia
           pseudotuberculosis IP 31758]
          Length = 208

 Score = 98.7 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 55/186 (29%), Positives = 91/186 (48%), Gaps = 17/186 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             A   R+ L++KP  ++   +D  GR+T+   +P  F  V + GRLD ++EGLL+LTND
Sbjct: 24  PPAAPRRVLLFNKPFDVLPQFTDESGRTTLQGFIP--FKDVYAAGRLDRDSEGLLVLTND 81

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P+ +  +VY V+  G  D D L  LK+G+ ++                   
Sbjct: 82  GKLQARLTQPAQKTGKVYFVQVEGVPDNDALTQLKRGVTLKDGLTLPAGAELVAEPEWLW 141

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ + L EG+NR+++++     +   RLIR S G   LG L  G 
Sbjct: 142 PRHPPIRERKTIPTSWLKITLYEGRNRQVRRITAHVGFPTLRLIRFSIGNLSLGNLQPGE 201

Query: 233 TREVSK 238
            +E++ 
Sbjct: 202 WKEITD 207


>gi|85712896|ref|ZP_01043937.1| RNA pseudouridylate synthase-family protein [Idiomarina baltica
           OS145]
 gi|85693276|gb|EAQ31233.1| RNA pseudouridylate synthase-family protein [Idiomarina baltica
           OS145]
          Length = 199

 Score = 98.7 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 51/179 (28%), Positives = 82/179 (45%), Gaps = 17/179 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L L +KP G+++  S      T+ D +P     V   GRLD ++EGL+LLTNDG   
Sbjct: 18  NPKLVLLNKPYGVLSQFSGEPDDVTLKDFVPHS--NVYPAGRLDKDSEGLMLLTNDGVYQ 75

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------------- 176
             L  P  +  + Y V+  G  D+ +L  L+ G  +        Q               
Sbjct: 76  ARLANPKYKVAKTYWVQVEGIPDEAQLTALRNGCELNDGLTKPAQAFAIDAPIGLWPRNP 135

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              + +   ++W+++ + EGKNR+++++         RLIR   GPF+L  L  G  RE
Sbjct: 136 PVRERKTVPDSWLSLSITEGKNRQVRRMTAHVGLPTLRLIRAQIGPFKLAGLQPGEWRE 194


>gi|15641153|ref|NP_230785.1| pseudouridine synthase family 1 protein [Vibrio cholerae O1 biovar
           El Tor str. N16961]
 gi|121587413|ref|ZP_01677182.1| pseudouridine synthase family 1 protein [Vibrio cholerae 2740-80]
 gi|121726313|ref|ZP_01679603.1| pseudouridine synthase family 1 protein [Vibrio cholerae V52]
 gi|147674615|ref|YP_001216660.1| pseudouridine synthase family 1 protein [Vibrio cholerae O395]
 gi|153816936|ref|ZP_01969603.1| pseudouridine synthase family 1 protein [Vibrio cholerae NCTC 8457]
 gi|153821998|ref|ZP_01974665.1| pseudouridine synthase family 1 protein [Vibrio cholerae B33]
 gi|227081313|ref|YP_002809864.1| pseudouridine synthase family 1 protein [Vibrio cholerae M66-2]
 gi|254848268|ref|ZP_05237618.1| pseudouridine synthase family 1 protein [Vibrio cholerae MO10]
 gi|298498755|ref|ZP_07008562.1| pseudouridine synthase family 1 protein [Vibrio cholerae MAK 757]
 gi|9655613|gb|AAF94299.1| pseudouridine synthase family 1 protein [Vibrio cholerae O1 biovar
           El Tor str. N16961]
 gi|121548333|gb|EAX58397.1| pseudouridine synthase family 1 protein [Vibrio cholerae 2740-80]
 gi|121631259|gb|EAX63632.1| pseudouridine synthase family 1 protein [Vibrio cholerae V52]
 gi|126512523|gb|EAZ75117.1| pseudouridine synthase family 1 protein [Vibrio cholerae NCTC 8457]
 gi|126520463|gb|EAZ77686.1| pseudouridine synthase family 1 protein [Vibrio cholerae B33]
 gi|146316498|gb|ABQ21037.1| pseudouridine synthase family 1 protein [Vibrio cholerae O395]
 gi|227009201|gb|ACP05413.1| pseudouridine synthase family 1 protein [Vibrio cholerae M66-2]
 gi|227013007|gb|ACP09217.1| pseudouridine synthase family 1 protein [Vibrio cholerae O395]
 gi|254843973|gb|EET22387.1| pseudouridine synthase family 1 protein [Vibrio cholerae MO10]
 gi|297543088|gb|EFH79138.1| pseudouridine synthase family 1 protein [Vibrio cholerae MAK 757]
          Length = 290

 Score = 98.7 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 49/187 (26%), Positives = 79/187 (42%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER  +        L         ++            V + GRLD ++EGLL+L
Sbjct: 106 RPLSPAERKVILFNKPYDTLSQFTDGDGRKTLADYI---PIKDVYAAGRLDRDSEGLLIL 162

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 163 TNDGILQARLTQPQSKAPKTYWVQVEGSPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 222

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + L EG+NR+++++     +   RLIR S G + LG L  
Sbjct: 223 LWPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQP 282

Query: 231 GSTREVS 237
           G  REV+
Sbjct: 283 GEWREVT 289


>gi|146284031|ref|YP_001174184.1| pseudouridine synthase [Pseudomonas stutzeri A1501]
 gi|145572236|gb|ABP81342.1| probable pseudouridine synthase [Pseudomonas stutzeri A1501]
          Length = 209

 Score = 98.7 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 54/185 (29%), Positives = 90/185 (48%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                RL L +KP  ++T  +D DGR+T+ D +P         GRLD ++EGLLLLTNDG
Sbjct: 26  PPAEPRLLLLNKPFDVLTQFADADGRATLKDFVPVPGV--YPAGRLDRDSEGLLLLTNDG 83

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+VD+ +L  L++G+ +        +            
Sbjct: 84  RLQARIADPKHKLPKTYWVQVEGEVDETQLERLRQGVELNDGMTLPAEARQLDEPELWPR 143

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + +REG+NR+++++         RL+R+  GP+ L  L  G  R
Sbjct: 144 NPPVRFRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGPWALDGLQPGEWR 203

Query: 235 EVSKK 239
           EV  +
Sbjct: 204 EVPAQ 208


>gi|206561035|ref|YP_002231800.1| putative ribosomal small subunit pseudouridine synthase A
           [Burkholderia cenocepacia J2315]
 gi|198037077|emb|CAR52998.1| putative ribosomal small subunit pseudouridine synthase A
           [Burkholderia cenocepacia J2315]
          Length = 238

 Score = 98.7 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 49/243 (20%), Positives = 84/243 (34%), Gaps = 22/243 (9%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGI---------LLERAAVNVMSTDHI-EVDGV 65
           +  ++   G  SRR+   +I                             +   +  VD  
Sbjct: 3   LESILYTQGFGSRRQCRGLI---------EAGRVAVAGAAATDPDAAFDTDGLVFSVDDA 53

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
                 R  L L        +               P +   V  VGRLD +T GLLLL+
Sbjct: 54  AWPFHARAYLALNKPAGYECSRDPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLS 113

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG        P  +  + Y       +D  +L+ L+ G+ + G     +       +  
Sbjct: 114 DDGQFVHAYTSPKRKVPKTYVATVRHPLDDTQLHALRTGVQLHGEP-KPIAAVAADARAP 172

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           +A + + + EGK  ++K++    + +V  L R S G F L   L  G+ R + +  L   
Sbjct: 173 HA-LALTVLEGKYHQVKRMVAAASNRVELLHRESIGGFTLPADLAPGAWRWLDEADLAAL 231

Query: 245 LGP 247
             P
Sbjct: 232 RNP 234


>gi|255745552|ref|ZP_05419500.1| ribosomal large subunit pseudouridine synthase E [Vibrio cholera
           CIRS 101]
 gi|262158374|ref|ZP_06029490.1| ribosomal large subunit pseudouridine synthase E [Vibrio cholerae
           INDRE 91/1]
 gi|262170186|ref|ZP_06037874.1| ribosomal large subunit pseudouridine synthase E [Vibrio cholerae
           RC27]
 gi|255736627|gb|EET92024.1| ribosomal large subunit pseudouridine synthase E [Vibrio cholera
           CIRS 101]
 gi|262021355|gb|EEY40068.1| ribosomal large subunit pseudouridine synthase E [Vibrio cholerae
           RC27]
 gi|262029815|gb|EEY48463.1| ribosomal large subunit pseudouridine synthase E [Vibrio cholerae
           INDRE 91/1]
          Length = 189

 Score = 98.7 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 49/187 (26%), Positives = 79/187 (42%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER  +        L         ++            V + GRLD ++EGLL+L
Sbjct: 5   RPLSPAERKVILFNKPYDTLSQFTDGDGRKTLADYI---PIKDVYAAGRLDRDSEGLLIL 61

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 62  TNDGILQARLTQPQSKAPKTYWVQVEGSPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 121

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + L EG+NR+++++     +   RLIR S G + LG L  
Sbjct: 122 LWPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQP 181

Query: 231 GSTREVS 237
           G  REV+
Sbjct: 182 GEWREVT 188


>gi|37520948|ref|NP_924325.1| pseudouridylate synthase [Gloeobacter violaceus PCC 7421]
 gi|35211943|dbj|BAC89320.1| gll1379 [Gloeobacter violaceus PCC 7421]
          Length = 185

 Score = 98.7 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 49/148 (33%), Positives = 72/148 (48%), Gaps = 14/148 (9%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
             VGRLD ++EGLLLLT+DG LA  L  P     R Y V+  G  D + L  L  G+ IQ
Sbjct: 24  YPVGRLDRDSEGLLLLTDDGALAHRLTDPRFAHPRTYWVQVEGTPDGEALGRLAAGVEIQ 83

Query: 169 GICYGDMQ--------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
           GI                         +    +W+ + L EG+NR+++++     +   R
Sbjct: 84  GIRTRPATAVAIAEPDLPERPVPIRVRKSIPTSWIALTLTEGRNRQVRRMTAAVGYATLR 143

Query: 215 LIRISYGPFQLGTLLAGSTREVSKKILR 242
           L+R++ G   LG L  G  RE+S++ LR
Sbjct: 144 LVRVAIGALSLGDLAPGRWRELSERELR 171


>gi|15599163|ref|NP_252657.1| pseudouridine synthase [Pseudomonas aeruginosa PAO1]
 gi|107103485|ref|ZP_01367403.1| hypothetical protein PaerPA_01004555 [Pseudomonas aeruginosa PACS2]
 gi|116052008|ref|YP_789149.1| putative pseudouridine synthase [Pseudomonas aeruginosa UCBPP-PA14]
 gi|254236861|ref|ZP_04930184.1| hypothetical protein PACG_02881 [Pseudomonas aeruginosa C3719]
 gi|254242653|ref|ZP_04935975.1| hypothetical protein PA2G_03415 [Pseudomonas aeruginosa 2192]
 gi|34098719|sp|Q9HX48|RLUE_PSEAE RecName: Full=Ribosomal large subunit pseudouridine synthase E;
           AltName: Full=rRNA pseudouridylate synthase E; AltName:
           Full=rRNA-uridine isomerase E
 gi|9950157|gb|AAG07355.1|AE004814_10 probable pseudouridine synthase [Pseudomonas aeruginosa PAO1]
 gi|115587229|gb|ABJ13244.1| possible pseudouridylate synthase [Pseudomonas aeruginosa
           UCBPP-PA14]
 gi|126168792|gb|EAZ54303.1| hypothetical protein PACG_02881 [Pseudomonas aeruginosa C3719]
 gi|126196031|gb|EAZ60094.1| hypothetical protein PA2G_03415 [Pseudomonas aeruginosa 2192]
          Length = 189

 Score = 98.7 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 53/185 (28%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  +D  GRST+ D +P         GRLD ++EGLLLLTNDG
Sbjct: 5   PPSEPKLLLFNKPFDVLTQFNDEQGRSTLKDFIPVPGV--YPAGRLDRDSEGLLLLTNDG 62

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G  D+++L  L++G+ +        +  L         
Sbjct: 63  RLQARIADPRHKLPKTYWVQVEGTPDEEQLRRLREGVTLNDGPTLPAEARLLDEPTLWER 122

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +     W+ + +REG+NR+++++         RL+R+  GP+ L  L  G  R
Sbjct: 123 VPPVRFRKSVPTHWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGPWSLDGLGLGEWR 182

Query: 235 EVSKK 239
           EV  +
Sbjct: 183 EVPAR 187


>gi|213028620|ref|ZP_03343067.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 122

 Score = 98.7 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 36/119 (30%), Positives = 58/119 (48%), Gaps = 1/119 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R++K I+ +GI SRRE +R I Q  V +NG         V++ D ++V+G  +  
Sbjct: 3   TDTSTRLNKYISESGICSRREADRFIEQGNVFINGKRAA-IGDQVVAGDVVKVNGRLIEP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            E   L L      +    +  DG      +  +   R+  +GRLD +++GL+ LTN G
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRIFPIGRLDKDSQGLIFLTNHG 120


>gi|107023425|ref|YP_621752.1| pseudouridine synthase, Rsu [Burkholderia cenocepacia AU 1054]
 gi|116690507|ref|YP_836130.1| pseudouridine synthase, Rsu [Burkholderia cenocepacia HI2424]
 gi|105893614|gb|ABF76779.1| ribosomal small subunit pseudouridine synthase A [Burkholderia
           cenocepacia AU 1054]
 gi|116648596|gb|ABK09237.1| ribosomal small subunit pseudouridine synthase A [Burkholderia
           cenocepacia HI2424]
          Length = 238

 Score = 98.3 bits (243), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 47/237 (19%), Positives = 81/237 (34%), Gaps = 22/237 (9%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGI---------LLERAAVNVMSTDHI-EVDGV 65
           +  ++   G  SRR+   +I                             +   +  VD  
Sbjct: 3   LESILYTQGFGSRRQCRGLI---------EAGRVAVAGAAATDPDATFDTDGLVFSVDDT 53

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
                 R  L L        +               P +   V  VGRLD +T GLLLL+
Sbjct: 54  AWPFHARAYLALNKPAGYECSRDPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLS 113

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG        P  +  + Y       +D  +L+ L+ G+ + G     +   +      
Sbjct: 114 DDGQFVHAYTSPKRKVPKTYVATVRHPLDDTQLHALRTGVQLHGEP-KPI-AAVAADARD 171

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
              + + + EGK  ++K++    + +V  L R S G F L   L  G+ R + +  L
Sbjct: 172 THALALTVLEGKYHQVKRMVAAASNRVELLHRESIGGFALPADLAPGAWRWLDEADL 228


>gi|124806269|ref|XP_001350676.1| RNA pseudouridylate synthase, putative [Plasmodium falciparum 3D7]
 gi|23496802|gb|AAN36356.1|AE014848_32 RNA pseudouridylate synthase, putative [Plasmodium falciparum 3D7]
          Length = 564

 Score = 98.3 bits (243), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 47/264 (17%), Positives = 83/264 (31%), Gaps = 40/264 (15%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER-----AAVNVMSTDHIEV 62
                  ++++  +  GI S R V   +     KVN  ++         V     D IE+
Sbjct: 307 NTKKEKIKLNQYCSYNGICSSRFVNNNVQNGLFKVNDKIVYENVEICLGV-----DKIEL 361

Query: 63  --DGVPLRKAERTRLWLYHKPI-----------------------GLVTTHSDPDGRSTV 97
              G  L K + T +    K                           +            
Sbjct: 362 TNRGKDLLKNKITIILNKPKHYLSISNDNKSYKKLLVRNLIRNENKYIQEEHKCMSYFIY 421

Query: 98  FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL-ELPSTQWLRVYRVRFHGQVDQD 156
            +        +   GRLD N+ GLL+ T +      L         + Y ++ +  + Q+
Sbjct: 422 KNVNIEKVPNLYVCGRLDANSSGLLIFTQNTLSNNYLLYRYKYNIEKEYVIKTYNSITQE 481

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
            + LLK+   + G       +        N  +   + +G ++ I+K+    N K+  L 
Sbjct: 482 NMKLLKEHFYVDGKLIYKCHIQYV----DNFTLIFKIYQGFHKIIRKMCMLSNIKIKSLH 537

Query: 217 RISYGPFQLGTLLAGSTREVSKKI 240
           RI  G   L  L  G  R +    
Sbjct: 538 RIRIGNIHLNDLPIGKWRFLMPNE 561


>gi|123442027|ref|YP_001006010.1| putative pseudouridine synthase [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|122088988|emb|CAL11799.1| putative pseudouridine synthase [Yersinia enterocolitica subsp.
           enterocolitica 8081]
          Length = 208

 Score = 98.3 bits (243), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 55/188 (29%), Positives = 95/188 (50%), Gaps = 17/188 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             ++     R+ L++KP  ++   +D  GRST+ + +P  F+ V + GRLD ++EGLL+L
Sbjct: 21  KQVKPITPRRVLLFNKPFDVLPQFTDEAGRSTLKEFIP--FNDVYAAGRLDRDSEGLLVL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TNDG L   L  P+ +  +VY V+  G  D+D L+ L+ GI ++                
Sbjct: 79  TNDGKLQARLTQPAQKTGKVYFVQVEGLPDEDALSQLRIGITLKDGPTLPAGAELVSEPA 138

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR S G   LG L 
Sbjct: 139 WLWPRHPPIRERKAIPTSWLKITLFEGRNRQVRRMTAHIGFPTLRLIRFSMGNLSLGDLQ 198

Query: 230 AGSTREVS 237
            G  +E++
Sbjct: 199 PGEWKEIN 206


>gi|238762227|ref|ZP_04623199.1| Ribosomal large subunit pseudouridine synthase E [Yersinia
           kristensenii ATCC 33638]
 gi|238699574|gb|EEP92319.1| Ribosomal large subunit pseudouridine synthase E [Yersinia
           kristensenii ATCC 33638]
          Length = 208

 Score = 98.3 bits (243), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 54/188 (28%), Positives = 93/188 (49%), Gaps = 17/188 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             ++     R+ L++KP  ++   +D  GRST+ + +P  FS V + GRLD ++EGLL+L
Sbjct: 21  KQVKPIAPRRVLLFNKPFDVLPQFTDESGRSTLKEFIP--FSDVYAAGRLDRDSEGLLVL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TNDG L   L  P+ +  +VY V+  G    D L+ L+ G+ ++                
Sbjct: 79  TNDGKLQARLTQPAQKTGKVYFVQVEGVPGDDTLSQLRTGMTLKDGPTLPAGAELVSEPE 138

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR S G   LG L 
Sbjct: 139 WLWPRNPPIRERKTIPTSWLKITLFEGRNRQVRRMTAHVGFPTLRLIRFSMGNLSLGDLQ 198

Query: 230 AGSTREVS 237
            G  +E++
Sbjct: 199 PGEWKEIN 206


>gi|22125695|ref|NP_669118.1| hypothetical protein y1801 [Yersinia pestis KIM 10]
 gi|45441581|ref|NP_993120.1| putative pseudouridine synthase [Yersinia pestis biovar Microtus
           str. 91001]
 gi|51596750|ref|YP_070941.1| pseudouridine synthase [Yersinia pseudotuberculosis IP 32953]
 gi|108812153|ref|YP_647920.1| pseudouridine synthase [Yersinia pestis Nepal516]
 gi|145599090|ref|YP_001163166.1| pseudouridine synthase [Yersinia pestis Pestoides F]
 gi|149366396|ref|ZP_01888430.1| putative pseudouridine synthase [Yersinia pestis CA88-4125]
 gi|162418698|ref|YP_001607231.1| ribosomal large subunit pseudouridine synthase E [Yersinia pestis
           Angola]
 gi|165925507|ref|ZP_02221339.1| ribosomal large subunit pseudouridine synthase E [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|166008516|ref|ZP_02229414.1| ribosomal large subunit pseudouridine synthase E [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166210805|ref|ZP_02236840.1| ribosomal large subunit pseudouridine synthase E [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|167421894|ref|ZP_02313647.1| ribosomal large subunit pseudouridine synthase E [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167426327|ref|ZP_02318080.1| ribosomal large subunit pseudouridine synthase E [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|167470790|ref|ZP_02335494.1| ribosomal large subunit pseudouridine synthase E [Yersinia pestis
           FV-1]
 gi|186895817|ref|YP_001872929.1| pseudouridine synthase [Yersinia pseudotuberculosis PB1/+]
 gi|218928776|ref|YP_002346651.1| putative pseudouridine synthase [Yersinia pestis CO92]
 gi|229841627|ref|ZP_04461785.1| 23S rRNA pseudouridine synthase [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229843744|ref|ZP_04463887.1| 23S rRNA pseudouridine synthase [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229894488|ref|ZP_04509670.1| 23S rRNA pseudouridine synthase [Yersinia pestis Pestoides A]
 gi|229902474|ref|ZP_04517593.1| 23S rRNA pseudouridine synthase [Yersinia pestis Nepal516]
 gi|294504162|ref|YP_003568224.1| putative pseudouridine synthase [Yersinia pestis Z176003]
 gi|34098646|sp|Q8ZFQ3|RLUE_YERPE RecName: Full=Ribosomal large subunit pseudouridine synthase E;
           AltName: Full=rRNA pseudouridylate synthase E; AltName:
           Full=rRNA-uridine isomerase E
 gi|21958610|gb|AAM85369.1|AE013782_10 hypothetical protein y1801 [Yersinia pestis KIM 10]
 gi|45436442|gb|AAS61997.1| putative pseudouridine synthase [Yersinia pestis biovar Microtus
           str. 91001]
 gi|51590032|emb|CAH21666.1| putative pseudouridine synthase [Yersinia pseudotuberculosis IP
           32953]
 gi|108775801|gb|ABG18320.1| ribosomal large subunit pseudouridine synthase E [Yersinia pestis
           Nepal516]
 gi|115347387|emb|CAL20285.1| putative pseudouridine synthase [Yersinia pestis CO92]
 gi|145210786|gb|ABP40193.1| ribosomal large subunit pseudouridine synthase E [Yersinia pestis
           Pestoides F]
 gi|149290770|gb|EDM40845.1| putative pseudouridine synthase [Yersinia pestis CA88-4125]
 gi|162351513|gb|ABX85461.1| ribosomal large subunit pseudouridine synthase E [Yersinia pestis
           Angola]
 gi|165922616|gb|EDR39767.1| ribosomal large subunit pseudouridine synthase E [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165992898|gb|EDR45199.1| ribosomal large subunit pseudouridine synthase E [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166207985|gb|EDR52465.1| ribosomal large subunit pseudouridine synthase E [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|166960379|gb|EDR56400.1| ribosomal large subunit pseudouridine synthase E [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167054682|gb|EDR64486.1| ribosomal large subunit pseudouridine synthase E [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|186698843|gb|ACC89472.1| pseudouridine synthase [Yersinia pseudotuberculosis PB1/+]
 gi|229680520|gb|EEO76617.1| 23S rRNA pseudouridine synthase [Yersinia pestis Nepal516]
 gi|229689352|gb|EEO81415.1| 23S rRNA pseudouridine synthase [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229694090|gb|EEO84138.1| 23S rRNA pseudouridine synthase [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229703507|gb|EEO90524.1| 23S rRNA pseudouridine synthase [Yersinia pestis Pestoides A]
 gi|262362279|gb|ACY59000.1| putative pseudouridine synthase [Yersinia pestis D106004]
 gi|262366212|gb|ACY62769.1| putative pseudouridine synthase [Yersinia pestis D182038]
 gi|294354621|gb|ADE64962.1| putative pseudouridine synthase [Yersinia pestis Z176003]
 gi|320014783|gb|ADV98354.1| 23S rRNA pseudouridine synthase [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 208

 Score = 97.9 bits (242), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 55/186 (29%), Positives = 91/186 (48%), Gaps = 17/186 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             A   R+ L++KP  ++   +D  GR+T+   +P  F  V + GRLD ++EGLL+LTND
Sbjct: 24  PPAAPRRVLLFNKPFDVLPQFTDESGRTTLQGFIP--FKDVYAAGRLDRDSEGLLVLTND 81

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P+ +  +VY V+  G  D D L  LK+G+ ++                   
Sbjct: 82  GKLQARLTQPAQKTGKVYFVQVEGVPDNDALTQLKRGVTLKDGLTLPAGAELVAEPEWLW 141

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ + L EG+NR+++++     +   RLIR S G   LG L  G 
Sbjct: 142 PRHPPIRERKTIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRFSMGNLSLGNLQPGE 201

Query: 233 TREVSK 238
            +E++ 
Sbjct: 202 WKEITD 207


>gi|170733848|ref|YP_001765795.1| pseudouridine synthase [Burkholderia cenocepacia MC0-3]
 gi|169817090|gb|ACA91673.1| pseudouridine synthase [Burkholderia cenocepacia MC0-3]
          Length = 238

 Score = 97.9 bits (242), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 48/243 (19%), Positives = 81/243 (33%), Gaps = 22/243 (9%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGI---------LLERAAVNVM-STDHIEVDGV 65
           +  ++   G  SRR+   +I                              +     VD  
Sbjct: 3   LESILYTQGFGSRRQCRGLI---------EAGRVAVAGAAATDPDAPFDTAGLVFSVDDT 53

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
                 R  L L        +               P +   V  VGRLD +T GLLLL+
Sbjct: 54  AWPFHARAYLALNKPAGYECSRDPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLS 113

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG        P  +  + Y       +D  +L+ L+ G+ + G     +   +      
Sbjct: 114 DDGQFVHAYTSPKRKVPKTYVATVRHPLDDTQLHALRTGVQLHGEP-KPI-AAVAADARD 171

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
              + + + EGK  ++K++    + +V  L R S G F L   L  G+ R + +  L   
Sbjct: 172 THALALTVLEGKYHQVKRMVAAASNRVELLHRESIGGFALPADLAPGAWRWLDEADLAAL 231

Query: 245 LGP 247
             P
Sbjct: 232 RNP 234


>gi|308125709|ref|ZP_07663492.1| pseudouridine synthase family 1 protein [Vibrio parahaemolyticus
           K5030]
 gi|308114216|gb|EFO51756.1| pseudouridine synthase family 1 protein [Vibrio parahaemolyticus
           K5030]
          Length = 221

 Score = 97.9 bits (242), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 27/197 (13%), Positives = 58/197 (29%), Gaps = 10/197 (5%)

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           +  G+ I        +VT    K +     + L +G NR+I+++ E   ++V +L R+  
Sbjct: 1   MSSGVRILDTVTLPCKVT----KETKFSFRIVLTQGLNRQIRRMCEALGYEVFKLRRVRI 56

Query: 221 GPFQLGTLLAGSTREVSKKILREQLGPHL----LEEAQVNLDAPIYSSETLVRDRPNIIS 276
               L  +  G  R ++   + E L         EEA           +       +   
Sbjct: 57  MNISLDGIPNGKWRYLTDDEVAEILAMCDGSVGTEEASKTDSRGRNIRKATDAKLFDSRE 116

Query: 277 EVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR 336
           E      R  + +    G +  +    P  ++                      + +   
Sbjct: 117 ENQGSTARRNQKTRTFRGNNADEFRHAPNSKKGQQKRRQRDDESSRPAKEHYKAKTQGEH 176

Query: 337 RSPSFPSKRSLRRTSAK 353
             P    +    +   +
Sbjct: 177 AKP--QGEHGRPQNKPQ 191


>gi|159045448|ref|YP_001534242.1| ribosomal large subunit pseudouridine synthase E [Dinoroseobacter
           shibae DFL 12]
 gi|157913208|gb|ABV94641.1| ribosomal large subunit pseudouridine synthase E [Dinoroseobacter
           shibae DFL 12]
          Length = 178

 Score = 97.9 bits (242), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 41/179 (22%), Positives = 78/179 (43%), Gaps = 17/179 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP+ +++  +       + D +        + GRLD ++EGLLLLT+DG L   +
Sbjct: 2   LIAFNKPMNVLSQFTSEGKWRGLKDWIDVPGV--YAAGRLDRDSEGLLLLTDDGRLQARI 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------VTL 179
             P  +  + Y     G+  QD +N L +G+ ++       +                  
Sbjct: 60  TDPRAKMPKTYYALVEGRPSQDAINRLCEGVSLKDGPTRPAKVAAVPAPDWLWPRDPPVR 119

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
             +   +AW+ + + EG+NR+++++         RLIR   G + L  L  G  R ++ 
Sbjct: 120 LRKTVPDAWLRLTITEGRNRQVRRMCAAVGLPCLRLIRTQIGDWTLDGLAPGQWRRIAP 178


>gi|170023963|ref|YP_001720468.1| pseudouridine synthase [Yersinia pseudotuberculosis YPIII]
 gi|169750497|gb|ACA68015.1| pseudouridine synthase [Yersinia pseudotuberculosis YPIII]
          Length = 208

 Score = 97.9 bits (242), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 55/186 (29%), Positives = 91/186 (48%), Gaps = 17/186 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             A   R+ L++KP  ++   +D  GR+T+   +P  F  V + GRLD ++EGLL+LTND
Sbjct: 24  PPAAPRRVLLFNKPFDVLPQFTDESGRTTLQGFIP--FKDVYAAGRLDRDSEGLLVLTND 81

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P+ +  +VY V+  G  D D L  LK+G+ ++                   
Sbjct: 82  GKLQARLTQPAQKTGKVYFVQVEGVPDNDALTQLKRGVTLKDGLTLPAGAELVAEPEWLW 141

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ + L EG+NR+++++     +   RLIR S G   LG L  G 
Sbjct: 142 PRHPPIRERKTIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRFSMGNLSLGNLQPGE 201

Query: 233 TREVSK 238
            +E++ 
Sbjct: 202 WKEITD 207


>gi|332530792|ref|ZP_08406718.1| pseudouridine synthase [Hylemonella gracilis ATCC 19624]
 gi|332039704|gb|EGI76104.1| pseudouridine synthase [Hylemonella gracilis ATCC 19624]
          Length = 261

 Score = 97.6 bits (241), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 59/255 (23%), Positives = 91/255 (35%), Gaps = 37/255 (14%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAE 71
           P ++  ++   G  +RR    ++ Q RV V G               H+ V+G  L    
Sbjct: 3   PMQLQDILFGQGFGARRVCAGLVQQGRVSVAGAACIDPLAEFEPEGLHLRVEG--LEGRT 60

Query: 72  RTR------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----------- 108
             R            L + +KP G   +       S        +  R            
Sbjct: 61  GLREGGLDWVCHLSALIMLNKPAGYECSQKPSAWPSVYTLLPLPLRQRPAQGKKGATAGV 120

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV----DQDKLNLLKKG 164
            +VGRLD +T GLLLLT+DG L   L  P  +  +VY V     V    +   +  L  G
Sbjct: 121 QAVGRLDQDTTGLLLLTDDGQLIHKLASPRHKVSKVYEVGLKHPVPSPAEASFVQRLLDG 180

Query: 165 IVIQG--ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP 222
           +V+             L T +     + + L +GK  ++K++      +V  L R   G 
Sbjct: 181 VVLDDDPHPVRAAACELLTPQH----LRLTLTDGKYHQVKRMVAAVGNRVETLHRSRIGA 236

Query: 223 FQL-GTLLAGSTREV 236
            QL   L  G  R +
Sbjct: 237 LQLPDDLAPGQWRWL 251


>gi|258621694|ref|ZP_05716725.1| pseudouridine synthase family 1 protein [Vibrio mimicus VM573]
 gi|258585925|gb|EEW10643.1| pseudouridine synthase family 1 protein [Vibrio mimicus VM573]
          Length = 280

 Score = 97.6 bits (241), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 47/189 (24%), Positives = 79/189 (41%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +  +ER  +        L         ++            V + GRLD ++EGLL+L
Sbjct: 91  RVISPSERKVVLFNKPYDTLSQFTDGDGRKTLADYI---PIKDVYAAGRLDRDSEGLLIL 147

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 148 TNDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVEIIPEPE 207

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + L EG+NR+++++     +   RLIR S G + LG L  
Sbjct: 208 LWPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQP 267

Query: 231 GSTREVSKK 239
           G  REV+ K
Sbjct: 268 GEWREVTLK 276


>gi|327482354|gb|AEA85664.1| pseudouridine synthase [Pseudomonas stutzeri DSM 4166]
          Length = 177

 Score = 97.6 bits (241), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 41/145 (28%), Positives = 70/145 (48%), Gaps = 14/145 (9%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              GRLD ++EGLLLLTNDG L   +  P  +  + Y V+  G+VD+ +L  L++G+ + 
Sbjct: 32  YPAGRLDRDSEGLLLLTNDGRLQARIADPKHKLPKTYWVQVEGEVDETQLERLRQGVELN 91

Query: 169 GICYGDMQVTLD--------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                  +                   +    +W+ + +REG+NR+++++         R
Sbjct: 92  DGMTLPAEARQLDEPELWPRNPPVRFRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLR 151

Query: 215 LIRISYGPFQLGTLLAGSTREVSKK 239
           L+R+  GP+ L  L  G  REV  +
Sbjct: 152 LVRVRIGPWALDGLQPGEWREVPAQ 176


>gi|218246198|ref|YP_002371569.1| pseudouridine synthase [Cyanothece sp. PCC 8801]
 gi|218166676|gb|ACK65413.1| pseudouridine synthase [Cyanothece sp. PCC 8801]
          Length = 204

 Score = 97.6 bits (241), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 51/194 (26%), Positives = 78/194 (40%), Gaps = 24/194 (12%)

Query: 71  ERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               +        L   T +D                 + SVGRLD ++EGLLLLTN+G 
Sbjct: 1   MYEYILFNKPYGVLCQFTDTDNPNSPRPTLKDYIPLPDIYSVGRLDFDSEGLLLLTNNGR 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------- 180
           L   L        R Y V+     D+  L+ L++G++I+  C    Q+ L          
Sbjct: 61  LKHRLSHREFSHPRTYWVQVERIPDEIALDRLRQGVLIKDYCTRPAQIKLLATEPNLSPR 120

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG--------PFQLG 226
                  +    AW+ + L EG+NR+++++     +   RLIRIS G           LG
Sbjct: 121 NPPIRYRKTVPTAWLEITLTEGRNRQVRRMTAAIGYPTLRLIRISMGFKIGKTLEKLSLG 180

Query: 227 TLLAGSTREVSKKI 240
            L  G  RE ++  
Sbjct: 181 DLKPGEWREATQLE 194


>gi|296387506|ref|ZP_06876981.1| putative pseudouridine synthase [Pseudomonas aeruginosa PAb1]
 gi|313109406|ref|ZP_07795366.1| putative pseudouridylate synthase [Pseudomonas aeruginosa 39016]
 gi|310881868|gb|EFQ40462.1| putative pseudouridylate synthase [Pseudomonas aeruginosa 39016]
          Length = 189

 Score = 97.6 bits (241), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 53/185 (28%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  +D  GRST+ D +P         GRLD ++EGLLLLTNDG
Sbjct: 5   PPSEPKLLLFNKPFDVLTQFNDEQGRSTLKDFIPVPGV--YPAGRLDRDSEGLLLLTNDG 62

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G  D+++L  L++G+ +        +  L         
Sbjct: 63  RLQARIADPRHKLPKTYWVQVEGTPDEEQLRRLREGVTLNDGPTLPAEARLLDEPTLWER 122

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +     W+ + +REG+NR+++++         RL+R+  GP+ L  L  G  R
Sbjct: 123 VPPVRFRKSVPTQWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGPWSLDGLGLGEWR 182

Query: 235 EVSKK 239
           EV  +
Sbjct: 183 EVPAR 187


>gi|226330493|ref|ZP_03806011.1| hypothetical protein PROPEN_04411 [Proteus penneri ATCC 35198]
 gi|225201288|gb|EEG83642.1| hypothetical protein PROPEN_04411 [Proteus penneri ATCC 35198]
          Length = 209

 Score = 97.2 bits (240), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 52/188 (27%), Positives = 89/188 (47%), Gaps = 17/188 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P+R     ++ +++KP  ++   +D +GR T+ D +P     + + GRLD ++EGLL+L
Sbjct: 22  KPVRPRGERKVVIFNKPFDVLVQFTDENGRKTLKDFIPIR--DIYAAGRLDRDSEGLLVL 79

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TNDG L   L  PS    ++Y  +  G      L   + G+ ++       QV +     
Sbjct: 80  TNDGKLQAKLTQPSKNTGKIYYAQVEGVPCTAALQQFRDGLALKDGKTLPAQVEIVEQPE 139

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + Q     W+ + L EGKNR+++++     +   RLIR S G   L  LL
Sbjct: 140 WLWERNPPIRERQTIPTTWLRITLFEGKNRQVRRMTAHIGYPTLRLIRFSMGNITLDNLL 199

Query: 230 AGSTREVS 237
            G  +E++
Sbjct: 200 PGEWKEIN 207


>gi|257059246|ref|YP_003137134.1| pseudouridine synthase [Cyanothece sp. PCC 8802]
 gi|256589412|gb|ACV00299.1| pseudouridine synthase [Cyanothece sp. PCC 8802]
          Length = 204

 Score = 97.2 bits (240), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 52/194 (26%), Positives = 78/194 (40%), Gaps = 24/194 (12%)

Query: 71  ERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               +        L   T +D                 + SVGRLD ++EGLLLLTN+G 
Sbjct: 1   MYEYILFNKPYGVLCQFTDTDNPNAPRPTLKDYIPLPDIYSVGRLDFDSEGLLLLTNNGR 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------- 180
           L   L        R Y V+     D+  L+ L++G++I+  C    QV L          
Sbjct: 61  LKHRLSHREFSHPRTYWVQVERIPDEIALDRLRQGVLIKDYCTRPAQVKLLATEPNLSPR 120

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG--------PFQLG 226
                  +    AW+ + L EG+NR+++++     +   RLIRIS G           LG
Sbjct: 121 NPPIRYRKTVPTAWLEITLTEGRNRQVRRMTAAIGYPTLRLIRISMGFKIGKTLEKLSLG 180

Query: 227 TLLAGSTREVSKKI 240
            L  G  RE ++  
Sbjct: 181 DLKPGEWREATQLE 194


>gi|254247451|ref|ZP_04940772.1| 16S pseudouridylate synthase [Burkholderia cenocepacia PC184]
 gi|124872227|gb|EAY63943.1| 16S pseudouridylate synthase [Burkholderia cenocepacia PC184]
          Length = 238

 Score = 97.2 bits (240), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 47/237 (19%), Positives = 80/237 (33%), Gaps = 22/237 (9%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGI---------LLERAAVNVM-STDHIEVDGV 65
           +  ++   G  SRR+   +I                              +     VD  
Sbjct: 3   LESILYTQGFGSRRQCRGLI---------EAGRVAVAGAAATDPDAPFDTAGLVFSVDDT 53

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
                 R  L L        +               P +   V  VGRLD +T GLLLL+
Sbjct: 54  AWPFHARAYLALNKPAGYECSRDPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLS 113

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG        P  +  + Y       +D  +L+ L+ G+ + G     +   +      
Sbjct: 114 DDGQFVHAYTSPKRKVPKTYVATVRHPLDDTQLHALRTGVQLHGEP-KPI-AAVAADARD 171

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
              + + + EGK  ++K++    + +V  L R S G F L   L  G+ R + +  L
Sbjct: 172 THALALTVLEGKYHQVKRMVAAASNRVELLHRESIGGFALPADLAPGAWRWLDEADL 228


>gi|218889749|ref|YP_002438613.1| putative pseudouridine synthase [Pseudomonas aeruginosa LESB58]
 gi|218769972|emb|CAW25734.1| probable pseudouridine synthase [Pseudomonas aeruginosa LESB58]
          Length = 189

 Score = 97.2 bits (240), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 54/185 (29%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  +D  GRST+ D +P     V   GRLD ++EGLLLLTNDG
Sbjct: 5   PPSEPKLLLFNKPFDVLTQFNDEQGRSTLKDFIP--LPGVYPAGRLDRDSEGLLLLTNDG 62

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G  D+ +L  L++G+ +        +  L         
Sbjct: 63  RLQARIADPRHKLPKTYWVQVEGTPDEKQLRRLREGVTLNDGPTLPAEARLLDEPTLWER 122

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +     W+ + +REG+NR+++++         RL+R+  GP+ L  L  G  R
Sbjct: 123 VPPVRFRKSVPTHWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGPWSLDGLGLGEWR 182

Query: 235 EVSKK 239
           EV  +
Sbjct: 183 EVPAR 187


>gi|304311203|ref|YP_003810801.1| Probable pseudouridine synthase [gamma proteobacterium HdN1]
 gi|301796936|emb|CBL45149.1| Probable pseudouridine synthase [gamma proteobacterium HdN1]
          Length = 254

 Score = 97.2 bits (240), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 45/177 (25%), Positives = 84/177 (47%), Gaps = 16/177 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             T + L+HKP G++   S    R T+ + +      + + GRLD ++EGLL+LTNDG L
Sbjct: 75  TSTTILLFHKPFGVICQFSRDGTRPTLANYIS--LPDIYAAGRLDQDSEGLLVLTNDGKL 132

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------------- 176
            + +  P  +  + Y  +  G + ++ L+ L+ GI ++       +              
Sbjct: 133 QQRITHPKHKLEKTYLAQVEGIISEEALHQLRTGIALKDGKTLPAKAQRIEPPNFAERIP 192

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
              + +    +W+ + + EG+NR+++++     +   RLIR   G +QLG L  G  
Sbjct: 193 PIRERKNIPTSWLELRICEGRNRQVRRMTAATGFPTLRLIRTRIGEWQLGELQPGEW 249


>gi|56808585|ref|ZP_00366316.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Streptococcus pyogenes M49
           591]
          Length = 141

 Score = 97.2 bits (240), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 39/141 (27%), Positives = 68/141 (48%), Gaps = 2/141 (1%)

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           +D +T G+L+LTNDG     +  P  +  +VY  R  G   ++ L  L +GIVI G    
Sbjct: 1   MDWDTSGVLILTNDGDFTDTMIHPRNEIDKVYLARVKGIATKENLRPLTRGIVIDGKKTK 60

Query: 174 DMQVTLDTQ--KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
             +  +       + + V + + EG+N ++KK+FE     V++L R  +G   L  L  G
Sbjct: 61  PARYNIVRVEADKNRSIVELTIHEGRNHQVKKMFESVGLLVDKLSRTRFGTVDLKGLRPG 120

Query: 232 STREVSKKILREQLGPHLLEE 252
             R ++KK + +       ++
Sbjct: 121 EARRLNKKEISQLHNLANTKK 141


>gi|213620819|ref|ZP_03373602.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 165

 Score = 97.2 bits (240), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 45/164 (27%), Positives = 75/164 (45%), Gaps = 2/164 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G +++ AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDM 175
           +  P     + Y V     V  D      KG+ +          
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKDLTKPA 164


>gi|134095624|ref|YP_001100699.1| putative pseudouridylate synthase [Herminiimonas arsenicoxydans]
 gi|133739527|emb|CAL62578.1| Ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Herminiimonas arsenicoxydans]
          Length = 186

 Score = 97.2 bits (240), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 52/185 (28%), Positives = 84/185 (45%), Gaps = 19/185 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L++KP  ++   S    R+++ D L      +   GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LILFNKPFQVMCQFSPHPTRASLADYLDIP--DIYPAGRLDADSEGLLLLTDDGKLQHAI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ------------ 182
             P  +  + Y  +  G    + L  L+  + +        +V    +            
Sbjct: 61  SHPDHKQTKTYLAQVEGIPHTEALARLRAPLNLGDFITQGCEVKRVQEPDWLWPRNPPIR 120

Query: 183 ---KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTREVS 237
              +   +W+ + L EGKNR+++++         RLIRI+ GP  L +  LL G  REVS
Sbjct: 121 ERAQVPTSWLAITLAEGKNRQVRRMTGAVGLPTLRLIRIAIGPISLQSHPLLPGQWREVS 180

Query: 238 KKILR 242
              LR
Sbjct: 181 AAELR 185


>gi|260913461|ref|ZP_05919939.1| ribosomal large subunit pseudouridine synthase E [Pasteurella
           dagmatis ATCC 43325]
 gi|260632401|gb|EEX50574.1| ribosomal large subunit pseudouridine synthase E [Pasteurella
           dagmatis ATCC 43325]
          Length = 241

 Score = 96.8 bits (239), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 42/209 (20%), Positives = 81/209 (38%), Gaps = 18/209 (8%)

Query: 48  ERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           +R  + V  +     +   +  AE   +        L     +    +          S+
Sbjct: 25  KRPNLKVAKSAVNFYEKKVISFAETKVILFNKPYDVLTQFSDENGRATLKDFI---PVSQ 81

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           V   GRLD ++EGL+LLTN+G +   L  P  +  + Y  +      +  L  L++G+V+
Sbjct: 82  VYPAGRLDRDSEGLVLLTNNGEIQHRLAEPKFKTEKTYFAQVEAIPQEVDLEQLRQGVVL 141

Query: 168 QGICYGDMQ---------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                   +                  + +    +W+ + + EG+NR+++++     +  
Sbjct: 142 NDGKTLPAKVRLVSEPNWLWERNPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPT 201

Query: 213 NRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            RLIR     F L  L  G  R++S+  L
Sbjct: 202 LRLIRYQMALFTLDNLPQGQYRQLSEAEL 230


>gi|156973850|ref|YP_001444757.1| hypothetical protein VIBHAR_01560 [Vibrio harveyi ATCC BAA-1116]
 gi|156525444|gb|ABU70530.1| hypothetical protein VIBHAR_01560 [Vibrio harveyi ATCC BAA-1116]
          Length = 176

 Score = 96.8 bits (239), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 37/143 (25%), Positives = 68/143 (47%), Gaps = 14/143 (9%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGL++LTNDG L   L  P ++  + Y V+  G   ++ L  L+KG+ ++
Sbjct: 33  YAAGRLDRDSEGLMVLTNDGILQAKLTQPQSKSPKTYWVQVDGAPTEEDLEKLRKGVELK 92

Query: 169 GICYGDMQVTLDTQ--------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                  ++ +  +                   W+ + + EG+NR+++++     +   R
Sbjct: 93  DGMTLPAKIEVMPEPEIWERTPPVRFRANIPTTWLAITIIEGRNRQVRRMTAHIGFPTLR 152

Query: 215 LIRISYGPFQLGTLLAGSTREVS 237
           L+R S G   L  L  G  RE+ 
Sbjct: 153 LVRYSMGGIALDDLKPGEWREIK 175


>gi|170078980|ref|YP_001735619.1| RNA pseudouridine synthase [Synechococcus sp. PCC 7002]
 gi|169886649|gb|ACB00363.1| probable RNA pseudouridine synthase [Synechococcus sp. PCC 7002]
          Length = 223

 Score = 96.8 bits (239), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 48/222 (21%), Positives = 77/222 (34%), Gaps = 19/222 (8%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L      +    T + P G              + SVGRLD+++EGLLLLTND  
Sbjct: 2   QHSYVLLHKPYNVLCQFTDNSPQGSQRQTLKDFVPVPDIYSVGRLDLDSEGLLLLTNDAP 61

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-------------- 175
           L   L  P     R Y V+     D   L  L++G+++QG                    
Sbjct: 62  LKHYLCEPKFAHSRTYWVQVENIPDGQALEQLRQGVMVQGKKTRPAIANLLTPEPTVPAR 121

Query: 176 -QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG----PFQLGTLLA 230
                  +    AW+ + L EG+NR+++++         RL+R++ G       L  L  
Sbjct: 122 EPPIRFRKNVPTAWLELTLTEGRNRQVRRMTAAVGHPTLRLMRVAIGAGPAKLTLTGLGP 181

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRP 272
           G  R ++   +          +          +S      R 
Sbjct: 182 GEWRHLTTAEIGALQNLVKKAKPNQRSPHKKTASRKPKGKRR 223


>gi|315635284|ref|ZP_07890561.1| pseudouridylate synthase [Aggregatibacter segnis ATCC 33393]
 gi|315476030|gb|EFU66785.1| pseudouridylate synthase [Aggregatibacter segnis ATCC 33393]
          Length = 233

 Score = 96.8 bits (239), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 48/190 (25%), Positives = 92/190 (48%), Gaps = 17/190 (8%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +T++ L++KP  ++   SD +GRST+ D +      V  VGRLD ++EGLLLLTN+G + 
Sbjct: 40  QTQVILFNKPFDVLCQFSDENGRSTLKDFIDIA--EVYPVGRLDRDSEGLLLLTNNGEIQ 97

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------------- 176
             L  P  +  + Y ++  G  D+  L  L++G+ ++       +               
Sbjct: 98  HRLAEPKFKMEKTYWMQVEGVPDETALEQLRRGVQLKDGMTKPAKVRLISEPDCLWQRVP 157

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + + EG+NR+++++     +   RLIR     F L  L   + R +
Sbjct: 158 PIRERKNIPTSWLEIKIYEGRNRQVRRMTAHIGFPTLRLIRCQLAGFTLQNLAPKTYRTL 217

Query: 237 SKKILREQLG 246
           ++  L++   
Sbjct: 218 TQDELKQLYQ 227


>gi|262191472|ref|ZP_06049658.1| ribosomal large subunit pseudouridine synthase E [Vibrio cholerae
           CT 5369-93]
 gi|262032667|gb|EEY51219.1| ribosomal large subunit pseudouridine synthase E [Vibrio cholerae
           CT 5369-93]
          Length = 176

 Score = 96.8 bits (239), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 42/143 (29%), Positives = 69/143 (48%), Gaps = 14/143 (9%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LTNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++
Sbjct: 33  YAAGRLDRDSEGLLILTNDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLK 92

Query: 169 GICYGDMQVTLDTQ--------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                  +V +  +                   W+ + L EG+NR+++++     +   R
Sbjct: 93  DGPTLPAKVDIMPEPTLWPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLR 152

Query: 215 LIRISYGPFQLGTLLAGSTREVS 237
           LIR S G + LG L  G  REV+
Sbjct: 153 LIRYSMGDWNLGDLQPGEWREVT 175


>gi|262165413|ref|ZP_06033150.1| ribosomal large subunit pseudouridine synthase E [Vibrio mimicus
           VM223]
 gi|262025129|gb|EEY43797.1| ribosomal large subunit pseudouridine synthase E [Vibrio mimicus
           VM223]
          Length = 246

 Score = 96.4 bits (238), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 47/189 (24%), Positives = 80/189 (42%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +  +ER  +        L         ++            V + GRLD ++EGLL+L
Sbjct: 57  RAISPSERKVVLFNKPYDTLSQFTDGDGRKTLADYI---PIKDVYAAGRLDRDSEGLLIL 113

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V + ++  
Sbjct: 114 TNDGILQARLTQPQSKAPKTYWVQVEGVPQESDLEALRHGVTLKDGPTLPAKVEIMSEPE 173

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + L EG+NR+++++     +   RLIR S G + LG L  
Sbjct: 174 LWPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQP 233

Query: 231 GSTREVSKK 239
           G  REV+ K
Sbjct: 234 GEWREVTLK 242


>gi|302879449|ref|YP_003848013.1| pseudouridine synthase [Gallionella capsiferriformans ES-2]
 gi|302582238|gb|ADL56249.1| pseudouridine synthase [Gallionella capsiferriformans ES-2]
          Length = 179

 Score = 96.4 bits (238), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 45/176 (25%), Positives = 80/176 (45%), Gaps = 17/176 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP G++   S      T+ D +P         GRLD ++EGLL+LT+DG L   
Sbjct: 3   RILLFNKPFGVICQFSQDGLHPTLADYIP--VPEFYPAGRLDTDSEGLLVLTDDGQLQHR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------QVT 178
           +  P  +  + Y V+  G  D   L+ L+ G++++                         
Sbjct: 61  ITDPKHKLPKTYWVQVEGVPDSAALDALRAGVLLKDGMTQPAGAALIDTPPGLWPRTPPV 120

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              +    +W+ + +REGKNR+++++     +   RLIR   G + L  L  G+ +
Sbjct: 121 RARKAIPTSWLELTIREGKNRQVRRMTAAVGFPTLRLIRYRIGAWTLDGLDQGTWK 176


>gi|145631551|ref|ZP_01787318.1| hypothetical protein CGSHi22421_09850 [Haemophilus influenzae
           R3021]
 gi|148826662|ref|YP_001291415.1| hypothetical protein CGSHiEE_08665 [Haemophilus influenzae PittEE]
 gi|144982820|gb|EDJ90342.1| hypothetical protein CGSHi22421_09850 [Haemophilus influenzae
           R3021]
 gi|148716822|gb|ABQ99032.1| hypothetical protein CGSHiEE_08665 [Haemophilus influenzae PittEE]
 gi|309973807|gb|ADO97008.1| 23S rRNA U2457 pseudouridine synthase [Haemophilus influenzae
           R2846]
          Length = 227

 Score = 96.4 bits (238), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 42/196 (21%), Positives = 78/196 (39%), Gaps = 17/196 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L   E T +                D +             V + GRLD ++EGLL+L
Sbjct: 31  KTLSLDETTVVLFNKP---FDVLTQFTDEQGRATLKDFISIPNVYAAGRLDRDSEGLLIL 87

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TN+G L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +        
Sbjct: 88  TNNGELQHRLSDPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGMTKPAKVRLISEPN 147

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  
Sbjct: 148 LWERNPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSINGLEN 207

Query: 231 GSTREVSKKILREQLG 246
           GS R +S   ++    
Sbjct: 208 GSFRLLSLDEIKALFQ 223


>gi|238789078|ref|ZP_04632867.1| Ribosomal large subunit pseudouridine synthase E [Yersinia
           frederiksenii ATCC 33641]
 gi|238722842|gb|EEQ14493.1| Ribosomal large subunit pseudouridine synthase E [Yersinia
           frederiksenii ATCC 33641]
          Length = 208

 Score = 96.4 bits (238), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 57/189 (30%), Positives = 94/189 (49%), Gaps = 20/189 (10%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G PL      R+ L++KP  ++   +D  GR+T+ + +P  F+ V + GRLD ++EGLL+
Sbjct: 23  GKPLSPR---RVLLFNKPFDVLPQFTDESGRATLKEFIP--FNDVYAAGRLDRDSEGLLV 77

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-------- 175
           LTNDG L   L  P+ +  +VY V+  G    D L  L++GI ++               
Sbjct: 78  LTNDGKLQAKLTQPAQKTGKVYFVQVEGVPGDDALMQLRRGISLKDGPTLPAGAELVDEP 137

Query: 176 -------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                      + +    +WV + L EG+NR+++++     +   RLIR S G   LG L
Sbjct: 138 EWLWPRNPPIRERKNIPTSWVKITLFEGRNRQVRRMTAHVGFPTLRLIRFSMGNLSLGNL 197

Query: 229 LAGSTREVS 237
             G  +E++
Sbjct: 198 QPGEWKEIN 206


>gi|154482916|ref|ZP_02025364.1| hypothetical protein EUBVEN_00613 [Eubacterium ventriosum ATCC
           27560]
 gi|149736200|gb|EDM52086.1| hypothetical protein EUBVEN_00613 [Eubacterium ventriosum ATCC
           27560]
          Length = 175

 Score = 96.4 bits (238), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 45/176 (25%), Positives = 84/176 (47%), Gaps = 5/176 (2%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           + +KP G+++  SD + ++ +     +    +  VGRLD +TEGLLL+TNDG L+  L  
Sbjct: 1   MLNKPAGVLSAVSDNNCKTVIDLLDVTPKKGLFPVGRLDKDTEGLLLITNDGELSHNLLS 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVGLRE 195
           P+    + Y V  +G +    + L +KG+ I          + +  +    +   + + E
Sbjct: 61  PAKHVDKTYYVELNGDLIDSDIELFEKGLDIGEKNLTKPAILKILEK---RSTALITITE 117

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLL 250
           GK  ++K++F+     V  L R++ GP +L   L  G  R+++   +   L     
Sbjct: 118 GKYHQVKRMFQAIGLTVTFLKRLTMGPLKLDENLKPGEYRKLTVSEVEALLNNKPR 173


>gi|154487334|ref|ZP_02028741.1| hypothetical protein BIFADO_01184 [Bifidobacterium adolescentis
           L2-32]
 gi|154083852|gb|EDN82897.1| hypothetical protein BIFADO_01184 [Bifidobacterium adolescentis
           L2-32]
          Length = 164

 Score = 96.4 bits (238), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 41/148 (27%), Positives = 74/148 (50%), Gaps = 1/148 (0%)

Query: 96  TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
           T+ D +   + R+  +GRLD ++EGL+L+TNDG L++ +  P  +  + Y     G++  
Sbjct: 9   TLRDIVGDKYERIFHMGRLDYDSEGLILMTNDGELSQHVMHPKYEVEKTYIATLEGRISG 68

Query: 156 DKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                L    + +        +  +      +  V V L  GKNR ++++F    + V R
Sbjct: 69  QVCRRLVTTGVKLDDGWIKLDRCAILDSSRESTLVKVVLHSGKNRIVRRIFGSIGFPVKR 128

Query: 215 LIRISYGPFQLGTLLAGSTREVSKKILR 242
           L+R   GP +LG L +G+ R +S+  +R
Sbjct: 129 LVRTQIGPIKLGDLKSGTYRVLSQAEVR 156


>gi|303286639|ref|XP_003062609.1| pseudouridylate synthase [Micromonas pusilla CCMP1545]
 gi|226456126|gb|EEH53428.1| pseudouridylate synthase [Micromonas pusilla CCMP1545]
          Length = 386

 Score = 96.4 bits (238), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 66/265 (24%), Positives = 105/265 (39%), Gaps = 41/265 (15%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----DGVPL 67
             QRVSK++++ G+ASRRE E +I +  V VNG  +    + V     I++    DG   
Sbjct: 90  QTQRVSKLMSQRGMASRREAEALIDRGDVIVNGGEVATRGMKVAIDATIDIAGDSDGGAN 149

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----------------- 110
               +    + +KP G V+       R       P       S                 
Sbjct: 150 ALLAKKVTVVLNKPPGYVSNLPSRGEREASELITPRNAIYHHSTGGGVVGGGADADAATR 209

Query: 111 ---------------VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
                           GRLD ++ GLL+LT DG LAR +   + +  +VY V       +
Sbjct: 210 RKLEDVCRDARALNVCGRLDKDSRGLLVLTTDGVLARAIVGGN-EIPKVYEVVVDAIATR 268

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRL 215
           ++L  L   + + G     M+V           +   LR+GK R+I+++ E    +V  L
Sbjct: 269 EQLAALNGPVALDGERLLPMRVETLEG----TTLRFELRQGKKRQIRRLCEGLALRVLDL 324

Query: 216 IRISYGPFQLGTLLAGSTREVSKKI 240
            R+  G   +G L  G  R +S+  
Sbjct: 325 RRVHVGTCDVGDLPEGRWRLMSEAE 349


>gi|190576318|ref|YP_001974163.1| putative pseudouridine synthase [Stenotrophomonas maltophilia
           K279a]
 gi|190014240|emb|CAQ47884.1| putative pseudouridine synthase [Stenotrophomonas maltophilia
           K279a]
          Length = 179

 Score = 96.4 bits (238), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 45/177 (25%), Positives = 85/177 (48%), Gaps = 15/177 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP  ++   +D    +        +  RV + GRLD ++EGLLLLT++G LA  L
Sbjct: 2   LIAFNKPFNVLCQFTDRSVPARPTLAGFGLPPRVYAAGRLDHDSEGLLLLTDNGTLAHKL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y V+  G    ++L  L+ G+ +        ++                 
Sbjct: 62  TDPRHKADKTYWVQVEGTPSDEQLQQLRDGVELNDGPTLPAKIERLDPAPSLWTRDPPVR 121

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +   +AW+ + +REG+NR+++++    N    RL+R++ GP++L  L  G  R++
Sbjct: 122 FRKTVPDAWLAITIREGRNRQVRRMTAAVNLPTLRLVRVAMGPYRLDDLQPGQWRQI 178


>gi|238783800|ref|ZP_04627819.1| Ribosomal large subunit pseudouridine synthase E [Yersinia
           bercovieri ATCC 43970]
 gi|238715351|gb|EEQ07344.1| Ribosomal large subunit pseudouridine synthase E [Yersinia
           bercovieri ATCC 43970]
          Length = 208

 Score = 96.0 bits (237), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 52/188 (27%), Positives = 91/188 (48%), Gaps = 17/188 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                    R+ L++KP  ++   +D  GR T+ + +P  FS V + GRLD ++EGLL+L
Sbjct: 21  KATAPVTPRRVLLFNKPFDVLPQFTDESGRRTLKEFIP--FSDVYAAGRLDRDSEGLLVL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TNDG L   L  P+ +  +VY V+  G   ++ L  L++G+ ++                
Sbjct: 79  TNDGKLQAKLTQPAQKTGKVYFVQVEGVPGEEALTQLQRGVTLKDGPTLPAGAELVAEPE 138

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR S G   LG L 
Sbjct: 139 WLWPRHPPIRERKSIPTSWLKITLFEGRNRQVRRMTAHIGFPTLRLIRFSMGNLSLGDLQ 198

Query: 230 AGSTREVS 237
            G  +E++
Sbjct: 199 PGEWKEIN 206


>gi|152980789|ref|YP_001354207.1| pseudouridylate synthase family protein [Janthinobacterium sp.
           Marseille]
 gi|151280866|gb|ABR89276.1| pseudouridylate synthase family protein [Janthinobacterium sp.
           Marseille]
          Length = 211

 Score = 96.0 bits (237), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 49/192 (25%), Positives = 84/192 (43%), Gaps = 19/192 (9%)

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +       L L++KP   +   S    R ++ D++      +   GRLD ++EGLLLL +
Sbjct: 19  IHAISNMPLILFNKPFQTMCQFSPHPTRKSLADHIDIP--NIYPAGRLDADSEGLLLLND 76

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ---- 182
           DG L   +  P  +  + Y V+  G  D D L  L+  + +      + +V    +    
Sbjct: 77  DGKLQHAISHPDRKHTKTYLVQVEGVPDADALARLRAPLDLGDFVTQECEVKRVAEPDWL 136

Query: 183 -----------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LL 229
                          +W+ + L EGKNR+++++     +   RL+RI+ GP  L +  L 
Sbjct: 137 WPRNPPIRERANAPTSWLAITLSEGKNRQVRRMTGAVGYPTLRLVRIAIGPVSLQSHPLW 196

Query: 230 AGSTREVSKKIL 241
            G  RE+S   L
Sbjct: 197 PGEWREISVAEL 208


>gi|3915395|sp|P72581|Y612_SYNY3 RecName: Full=Uncharacterized RNA pseudouridine synthase slr0612;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
          Length = 261

 Score = 96.0 bits (237), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 41/206 (19%), Positives = 76/206 (36%), Gaps = 31/206 (15%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +   +  +  +++KP G++   +D                 +  VGRLD ++EGLLLLT
Sbjct: 32  LIALNKTPQTIVFYKPYGVLCQFTDNSAHPRPTLKDYINLPDLYPVGRLDQDSEGLLLLT 91

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--- 182
           ++G L   L        R Y  +  G    + L  L++GI             + T+   
Sbjct: 92  SNGKLQHRLAHREFAHQRTYFAQVEGSPTDEDLEPLRRGITFADYPTRPAIAKIITEPDF 151

Query: 183 -----------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY---GP------ 222
                          +W+++ L EG+NR+++++     +   RL+R+     G       
Sbjct: 152 PPRNPPIRYRASIPTSWLSITLTEGRNRQVRRMTAAVGFPTLRLVRVQIQVTGRSPQQGK 211

Query: 223 --------FQLGTLLAGSTREVSKKI 240
                     L  L  G  R ++   
Sbjct: 212 GKSAATWCLTLEGLSPGQWRPLTPWE 237


>gi|254496292|ref|ZP_05109179.1| pseudouridine synthase [Legionella drancourtii LLAP12]
 gi|254354480|gb|EET13128.1| pseudouridine synthase [Legionella drancourtii LLAP12]
          Length = 240

 Score = 96.0 bits (237), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 48/182 (26%), Positives = 73/182 (40%), Gaps = 17/182 (9%)

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +R      +        +     +    +              + GRLD N+EGLLLLTN
Sbjct: 48  IRHFMSELILFNKPFAVVCQFTGEKHEHTLAEFI---DKPDFYAAGRLDKNSEGLLLLTN 104

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------ 180
           DG L   L  P     + Y V+  G      L  LKKG+V++ I +   +V         
Sbjct: 105 DGALQHQLTHPKFNKKKYYWVQVEGIPTAADLEPLKKGLVLKDITFLPAEVRCIEEPALW 164

Query: 181 --------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                    Q    +W+ + LREGKN +++++     +   RL+R   G +QLG L  G 
Sbjct: 165 PRTPPVRFRQSIPTSWLEIILREGKNHQVRRMTAAMGFPTLRLVRHRIGDWQLGDLQPGE 224

Query: 233 TR 234
            R
Sbjct: 225 FR 226


>gi|325181473|emb|CCA15907.1| ribosomal large subunit pseudouridine synthase F put [Albugo
           laibachii Nc14]
          Length = 241

 Score = 96.0 bits (237), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 54/219 (24%), Positives = 96/219 (43%), Gaps = 25/219 (11%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           +A   + SRR+ ER I+   V VNG  +++  + +     +E  G  ++  ++    + +
Sbjct: 1   MAERKMCSRRDAERYISAGDVYVNGEQIQQDWIKIPRDSCVEFSGKAVKAEKQKVSVILN 60

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------------VGRLDINTEGLLLL 124
           KP+G V++  +P  +  +         ++ +                GRLDIN+ GLLL 
Sbjct: 61  KPLGYVSSQPEPMRKPAIELLSIQNAFQLTARWYGKEPKSLSKLAVCGRLDINSTGLLLF 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVR------FHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           T DG LA+ +  P+    + Y VR         +  ++ ++ L++G +   ICY    V 
Sbjct: 121 TQDGVLAKQILDPNGGVEKEYLVRVDMDLERDTKQAEEVVDKLREGFIWNDICYRARSVR 180

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
           +         +   L EGK R I+ + E    KV  L R
Sbjct: 181 VLNANQ----LQFILTEGKKRHIRYMCEAVGIKVIALKR 215


>gi|323969847|gb|EGB65128.1| RNA pseudouridylate synthase [Escherichia coli TA007]
          Length = 191

 Score = 96.0 bits (237), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 37/195 (18%), Positives = 77/195 (39%), Gaps = 4/195 (2%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           +  +GRLD +++GL+ LTN G L   +        + Y V     + ++ +  +  G+ I
Sbjct: 1   MFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPI 60

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G            +K +     + L +G NR+I+++ E F ++V +L R       L  
Sbjct: 61  LGTV----TKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSG 116

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           +  G  R+++   L +         ++V   A        ++     + +  +   R   
Sbjct: 117 IPLGEWRDLTDDELIDLFKLIENSSSEVKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPAS 176

Query: 288 NSSQKNGLSKQKKLA 302
           N  +     ++KK  
Sbjct: 177 NGKRFTSPGRKKKGR 191


>gi|261332662|emb|CBH15657.1| tRNA pseudouridine synthase A, putative [Trypanosoma brucei
           gambiense DAL972]
          Length = 688

 Score = 96.0 bits (237), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 65/225 (28%), Positives = 101/225 (44%), Gaps = 4/225 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--PLRKAERT 73
           + + + RAG  SRRE   +IA  +V+V+ ++       V + ++I V      LR A   
Sbjct: 346 LLRCLPRAGFCSRREALAVIASGQVRVDNVVERNPFRLVRAENNIHVASHSGRLRFAPPR 405

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               +     +V+ +                   ++ VG L +   GLLLLTNDG L+R 
Sbjct: 406 LWMYHKPAHVIVSRNDVAGRALFTKHARILGMDHLVPVGSLPMRAHGLLLLTNDGELSRF 465

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           LE P     + Y +R    VD    + L  +GI I G  Y +M+  ++    S   + V 
Sbjct: 466 LENPKCMIQQTYLLRVRPAVDPVLAHKLNFQGITINGKQYKNMEFFVNPAMKSRFSLKVK 525

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +R G+   +  + +     V R  RIS+GPF L  L  GS REV+
Sbjct: 526 VR-GEVMPVAHLMQHLGRTVERGGRISFGPFSLSGLPVGSLREVT 569


>gi|71747592|ref|XP_822851.1| tRNA pseudouridine synthase A [Trypanosoma brucei TREU927]
 gi|70832519|gb|EAN78023.1| tRNA pseudouridine synthase A, putative [Trypanosoma brucei]
          Length = 688

 Score = 96.0 bits (237), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 65/225 (28%), Positives = 101/225 (44%), Gaps = 4/225 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--PLRKAERT 73
           + + + RAG  SRRE   +IA  +V+V+ ++       V + ++I V      LR A   
Sbjct: 346 LLRCLPRAGFCSRREALAVIASGQVRVDNVVERNPFRLVRAENNIHVASHSGRLRFAPPR 405

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               +     +V+ +                   ++ VG L +   GLLLLTNDG L+R 
Sbjct: 406 LWMYHKPAHVIVSRNDVAGRALFTKHARILGMDHLVPVGSLPMRAHGLLLLTNDGELSRF 465

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           LE P     + Y +R    VD    + L  +GI I G  Y +M+  ++    S   + V 
Sbjct: 466 LENPKCMIQQTYLLRVRPAVDPVLAHKLNFQGITINGKQYKNMEFFVNPAMKSRFSLKVK 525

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +R G+   +  + +     V R  RIS+GPF L  L  GS REV+
Sbjct: 526 VR-GEVMPVAHLMQHLGRTVERGGRISFGPFSLSGLPVGSLREVT 569


>gi|254362527|ref|ZP_04978630.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|261494150|ref|ZP_05990653.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
 gi|153094127|gb|EDN75026.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|261310316|gb|EEY11516.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
          Length = 227

 Score = 96.0 bits (237), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 52/185 (28%), Positives = 87/185 (47%), Gaps = 17/185 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L +KP  ++T  +D  GR T+ D +      +  VGRLD ++EGLLLLTN+G +  
Sbjct: 34  TTLVLLNKPYDVLTQFTDEQGRKTLKDFITMP--NIYPVGRLDRDSEGLLLLTNNGEIQH 91

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------V 177
            L  P     + Y V+  G    + L  L KG+ ++       +                
Sbjct: 92  RLAHPKFDKQKTYWVQVEGVPQPEDLAKLAKGVELKDGLTKPAKVRAIATPDFAWNIAPQ 151

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + + EGKNR+++++     +   RLIR+  G F+LG L  G  + +S
Sbjct: 152 IRERKTIPTSWIELIISEGKNRQVRRMTAHIGFPTLRLIRVGIGQFRLGNLGCGEFQVLS 211

Query: 238 KKILR 242
           +   R
Sbjct: 212 ENEKR 216


>gi|114768970|ref|ZP_01446596.1| ribosomal large subunit pseudouridine synthase E [alpha
           proteobacterium HTCC2255]
 gi|114549887|gb|EAU52768.1| ribosomal large subunit pseudouridine synthase E [alpha
           proteobacterium HTCC2255]
          Length = 184

 Score = 96.0 bits (237), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 36/144 (25%), Positives = 71/144 (49%), Gaps = 15/144 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LTNDG L + +  P  +W + Y V+  G   QD + +L+ G+ ++
Sbjct: 40  YAAGRLDKDSEGLLVLTNDGVLQQEISNPKHKWPKTYVVQVEGTPTQDDIKVLESGVTLK 99

Query: 169 GICYGDMQVTLD---------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +  +                 +   ++W+ + + EG+NR+++++     +   
Sbjct: 100 DGITKPAEAEIIDKPEGLWDRLPPIRYRKAIPDSWLMITITEGRNRQVRRMTAAIGFPTL 159

Query: 214 RLIRISYGPFQLGTLLAGSTREVS 237
           RLIR S G F +  +  G  +++ 
Sbjct: 160 RLIRYSIGNFTIDDIPNGQWKQLD 183


>gi|291456799|ref|ZP_06596189.1| ribosomal large subunit pseudouridine synthase B [Bifidobacterium
           breve DSM 20213]
 gi|291382076|gb|EFE89594.1| ribosomal large subunit pseudouridine synthase B [Bifidobacterium
           breve DSM 20213]
          Length = 141

 Score = 95.6 bits (236), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 39/133 (29%), Positives = 64/133 (48%), Gaps = 1/133 (0%)

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQG 169
           +GRLD ++EGL+L+TNDG L++ +  P  +  + Y     G++       L    + +  
Sbjct: 1   MGRLDYDSEGLILMTNDGELSQHVMHPKYEVEKTYIATLEGRISGTVCRRLVTTGVQLDD 60

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                    +         V V L  GKNR ++++F    + V RL+R   GP +LG L 
Sbjct: 61  GWIKLDHCAIIDSSRDFTMVKVVLHSGKNRIVRRIFGSIGFPVKRLVRTQIGPIKLGELK 120

Query: 230 AGSTREVSKKILR 242
            GS R +S+  +R
Sbjct: 121 PGSYRVLSQAEVR 133


>gi|291613437|ref|YP_003523594.1| pseudouridine synthase [Sideroxydans lithotrophicus ES-1]
 gi|291583549|gb|ADE11207.1| pseudouridine synthase [Sideroxydans lithotrophicus ES-1]
          Length = 180

 Score = 95.6 bits (236), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 46/175 (26%), Positives = 77/175 (44%), Gaps = 17/175 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP G++   S      T+ D +      V   GRLD ++EGLLLLT+DG L   
Sbjct: 3   RILLFNKPYGVICQFSRDGMHPTLADYIA--VPDVYPAGRLDTDSEGLLLLTDDGKLQHR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------VT 178
           +  P  +  + Y V+  G  D   L  L++GI ++       +                 
Sbjct: 61  ITDPKHKQPKTYWVQVEGIPDATALEQLRRGIQLKDGMTLPAEANLMAEPQGLWLRDPPV 120

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
              +     W+ + + EGKNR+++++     +   RLIR S G + +  L  G  
Sbjct: 121 RFRKDIPTCWLWLTIHEGKNRQVRRMTAAVGFPTLRLIRYSIGKWTIDGLAPGKW 175


>gi|261496009|ref|ZP_05992419.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|261308259|gb|EEY09552.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
          Length = 227

 Score = 95.6 bits (236), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 52/185 (28%), Positives = 87/185 (47%), Gaps = 17/185 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L +KP  ++T  +D  GR T+ D +      +  VGRLD ++EGLLLLTN+G +  
Sbjct: 34  TTLVLLNKPYDVLTQFTDEQGRKTLKDFITMP--NIYPVGRLDRDSEGLLLLTNNGEIQH 91

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------V 177
            L  P     + Y V+  G    + L  L KG+ ++       +                
Sbjct: 92  RLAHPKFDKQKTYWVQVEGVPQPEDLAKLAKGVELKDGLTKPAKVRAIATPDFAWHIAPQ 151

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + + EGKNR+++++     +   RLIR+  G F+LG L  G  + +S
Sbjct: 152 IRERKTIPTSWIELIISEGKNRQVRRMTAHIGFPTLRLIRVGIGQFRLGNLGCGEFQVLS 211

Query: 238 KKILR 242
           +   R
Sbjct: 212 ENEKR 216


>gi|76665077|emb|CAJ17986.1| rRNA pseudouridylate synthase [Candidatus Phytoplasma solani]
          Length = 96

 Score = 95.6 bits (236), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 25/88 (28%), Positives = 41/88 (46%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A A + SRR+ E +I Q+RVKVN  ++      V  +D I VD   + K    
Sbjct: 2   ERLQKVLAAANLVSRRKAETLILQKRVKVNNQIVYELGTKVSPSDVITVDNTLITKTPLF 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
              L      L T   +   ++ +   +
Sbjct: 62  YYLLNKPQGYLSTAKDNKTRQTVLDLII 89


>gi|260582971|ref|ZP_05850754.1| ribosomal large subunit pseudouridine synthase E [Haemophilus
           influenzae NT127]
 gi|260093955|gb|EEW77860.1| ribosomal large subunit pseudouridine synthase E [Haemophilus
           influenzae NT127]
          Length = 227

 Score = 95.6 bits (236), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 77/196 (39%), Gaps = 17/196 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L   E   +                D +             V + GRLD ++EGLL+L
Sbjct: 31  KTLSLDETKVVLFNKP---FDVLTQFTDEQGRATLKDFISIPNVYAAGRLDRDSEGLLIL 87

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TN+G L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +        
Sbjct: 88  TNNGELQHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGMTKPAKVRLISEPN 147

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  
Sbjct: 148 LWERNPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSINGLEN 207

Query: 231 GSTREVSKKILREQLG 246
           GS R +S   ++    
Sbjct: 208 GSFRLLSLDEIKALFQ 223


>gi|254474543|ref|ZP_05087929.1| ribosomal large subunit pseudouridine synthase E [Ruegeria sp. R11]
 gi|214028786|gb|EEB69621.1| ribosomal large subunit pseudouridine synthase E [Ruegeria sp. R11]
          Length = 251

 Score = 95.6 bits (236), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 88/240 (36%), Gaps = 17/240 (7%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGG 129
            TRL  ++KP  ++   +D     +    L        V   GRLD ++EGL+LLT+ G 
Sbjct: 1   MTRLIRFNKPYDVLPQFTDRGSTDSPRATLSDWIDLPGVYPAGRLDRDSEGLMLLTDQGR 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------- 180
           L   +  P  +  + Y V+  G  D   +  L +G+ ++       +  L          
Sbjct: 61  LQAWISDPQHKMPKTYWVQVEGTPDAAAITALAEGVELKDGLTRPAKARLIAEPEGLWAR 120

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +   ++W+ + +REG+NR+++++         RLIR + G + L  L  G   
Sbjct: 121 NPPIRVRKSVPDSWIELTIREGRNRQVRRMTAAVGHPTLRLIRAAIGAWTLNGLGQGQWE 180

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           ++    +     P  +   Q              ++      +          ++   + 
Sbjct: 181 DLEVPNIPGPPRPKHVPNRQAIARRHAREEAEAKQEARVSRPKPGKSTGTKAGSAKAGSA 240


>gi|229515523|ref|ZP_04404982.1| ribosomal large subunit pseudouridine synthase E [Vibrio cholerae
           TMA 21]
 gi|229347292|gb|EEO12252.1| ribosomal large subunit pseudouridine synthase E [Vibrio cholerae
           TMA 21]
          Length = 244

 Score = 95.6 bits (236), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 49/187 (26%), Positives = 79/187 (42%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER  +        L         ++            V + GRLD ++EGLL+L
Sbjct: 60  RPLSPAERKVVLFNKPYDTLSQFTDGDGRKTLADYI---PIKDVYAAGRLDRDSEGLLIL 116

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 117 TNDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 176

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + L EG+NR+++++     +   RLIR S G + LG L  
Sbjct: 177 LWPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQP 236

Query: 231 GSTREVS 237
           G  REV+
Sbjct: 237 GEWREVT 243


>gi|197284775|ref|YP_002150647.1| ribosomal large subunit pseudouridine synthase E [Proteus mirabilis
           HI4320]
 gi|227357781|ref|ZP_03842130.1| RluE protein [Proteus mirabilis ATCC 29906]
 gi|194682262|emb|CAR41996.1| ribosomal large subunit pseudouridine synthase E [Proteus mirabilis
           HI4320]
 gi|227162110|gb|EEI47124.1| RluE protein [Proteus mirabilis ATCC 29906]
          Length = 209

 Score = 95.6 bits (236), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 50/188 (26%), Positives = 89/188 (47%), Gaps = 17/188 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P R     ++ +++KP  ++   +D  GR T+ D +P     + + GRLD ++EGLL+L
Sbjct: 22  KPSRPRGERKVIIFNKPFDVLVQFTDDSGRKTLKDFIPIP--DIYAAGRLDRDSEGLLVL 79

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TNDG L   L  P+ +  +VY  +  G   +  L   ++G+ ++       +        
Sbjct: 80  TNDGKLQAKLTQPNKKTGKVYYAQVEGIPTEIALQQFREGLNLKDGKTLPAKIERVEQPT 139

Query: 177 -------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + Q    +W+ + L EGKNR+++++     +   RLIR S G   L  LL
Sbjct: 140 WVWTRFPPIRERQSIPTSWLKITLFEGKNRQVRRMTAHIGYPTLRLIRFSMGNITLDNLL 199

Query: 230 AGSTREVS 237
            G  +E++
Sbjct: 200 PGQWKEIN 207


>gi|229525751|ref|ZP_04415156.1| ribosomal large subunit pseudouridine synthase E [Vibrio cholerae
           bv. albensis VL426]
 gi|229339332|gb|EEO04349.1| ribosomal large subunit pseudouridine synthase E [Vibrio cholerae
           bv. albensis VL426]
          Length = 244

 Score = 95.6 bits (236), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 49/187 (26%), Positives = 79/187 (42%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER  +        L         ++            V + GRLD ++EGLL+L
Sbjct: 60  RPLSPAERKVVLFNKPYDTLSQFTDGDGRKTLADYI---QIKDVYAAGRLDRDSEGLLIL 116

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 117 TNDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 176

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + L EG+NR+++++     +   RLIR S G + LG L  
Sbjct: 177 LWPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQP 236

Query: 231 GSTREVS 237
           G  REV+
Sbjct: 237 GEWREVT 243


>gi|238758424|ref|ZP_04619601.1| Ribosomal large subunit pseudouridine synthase E [Yersinia aldovae
           ATCC 35236]
 gi|238703328|gb|EEP95868.1| Ribosomal large subunit pseudouridine synthase E [Yersinia aldovae
           ATCC 35236]
          Length = 208

 Score = 95.2 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 52/183 (28%), Positives = 91/183 (49%), Gaps = 17/183 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               R+ L++KP  ++   +D  GR+T+ + +P  F+ V + GRLD ++EGLL+LTNDG 
Sbjct: 26  ITPRRVLLFNKPFDVLPQFTDESGRTTLKEFIP--FNDVYAAGRLDRDSEGLLVLTNDGK 83

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-------------- 175
           L   L  P+ +  +VY V+  G    D L  L++G+ ++                     
Sbjct: 84  LQARLTQPAKKTGKVYFVQVEGVPSDDALLQLQRGMTLKDGPTLPAGAELVSEPEWLWPR 143

Query: 176 -QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + +    +W+ + L EG+NR+++++     +   RLIR S G   LG L  G  +
Sbjct: 144 NPPIRERKSIPTSWLKITLFEGRNRQVRRMTAHIGFPTLRLIRFSMGNLSLGDLQPGEWK 203

Query: 235 EVS 237
           E++
Sbjct: 204 EIN 206


>gi|319775460|ref|YP_004137948.1| Pseudouridine synthase [Haemophilus influenzae F3047]
 gi|329122507|ref|ZP_08251092.1| ribosomal large subunit pseudouridine synthase E [Haemophilus
           aegyptius ATCC 11116]
 gi|317450051|emb|CBY86265.1| Pseudouridine synthase [Haemophilus influenzae F3047]
 gi|327473197|gb|EGF18619.1| ribosomal large subunit pseudouridine synthase E [Haemophilus
           aegyptius ATCC 11116]
          Length = 227

 Score = 95.2 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 77/196 (39%), Gaps = 17/196 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L   E   +                D +             V + GRLD ++EGLL+L
Sbjct: 31  QTLSLDETKVVLFNKP---FDVLTQFTDEQGRATLKDFISIPNVYAAGRLDRDSEGLLIL 87

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TN+G L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +        
Sbjct: 88  TNNGELQHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKPAKVRLISEPN 147

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  
Sbjct: 148 LWERNPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSINGLEN 207

Query: 231 GSTREVSKKILREQLG 246
           GS R +S   ++    
Sbjct: 208 GSFRLLSLDEIKALFQ 223


>gi|261856640|ref|YP_003263923.1| pseudouridine synthase [Halothiobacillus neapolitanus c2]
 gi|261837109|gb|ACX96876.1| pseudouridine synthase [Halothiobacillus neapolitanus c2]
          Length = 180

 Score = 95.2 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 43/174 (24%), Positives = 77/174 (44%), Gaps = 15/174 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP  +++  +   G +            V + GRLD ++EGLLLLT+DG L   L
Sbjct: 2   LIAFNKPFDVLSQFTVEPGSAAGTLADYIDQPNVYAAGRLDRDSEGLLLLTDDGRLQAQL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT------------- 181
             P  +  + Y  +  G V    L  L+ G+V++       +  +               
Sbjct: 62  TQPDAKQPKTYLAQVDGDVTAQALAQLRAGVVLKDGKTRPAEAHVVPEPDWLWPRTPPIR 121

Query: 182 --QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
             +    +W+ + + EGKNR+++++     +   RLIR++ G   LG+L  G  
Sbjct: 122 VRKNIPTSWIELTITEGKNRQVRRMTAAVGFPTLRLIRVAVGSHNLGSLQPGQW 175


>gi|126642165|ref|YP_001085149.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter baumannii ATCC
           17978]
          Length = 201

 Score = 95.2 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 41/182 (22%), Positives = 72/182 (39%), Gaps = 2/182 (1%)

Query: 59  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
              V G   +  E+  + L        + H               I   V +VGRLD +T
Sbjct: 14  EFSVFGQNYQYREKIYIALRKPQGFECSHHPQHHQSVFSLLPETMIHRGVQAVGRLDQDT 73

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLLLT+DG   + L  P     +VY V  +  V  +++ +L +G+ +     G     
Sbjct: 74  TGLLLLTDDGKYLQALTHPRKHVPKVYHVTTYDPVTPEQIEMLTQGVNLHQEKGGFAATD 133

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +         +T+ + +G   ++K++      KV +L R   G   L  +  G    +S+
Sbjct: 134 VALL--GTHQLTMTIHQGVYHQVKRMIAAVGNKVEKLHRHQIGQLVLPEIEEGGWVYLSE 191

Query: 239 KI 240
           + 
Sbjct: 192 QE 193


>gi|86607240|ref|YP_476003.1| RNA pseudouridine synthase family protein [Synechococcus sp.
           JA-3-3Ab]
 gi|86555782|gb|ABD00740.1| RNA pseudouridine synthase family protein [Synechococcus sp.
           JA-3-3Ab]
          Length = 208

 Score = 95.2 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 57/183 (31%), Positives = 88/183 (48%), Gaps = 17/183 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R   ++KP G++T  +D  GR T+   +P        VGRLD ++EGLLLLT+DG L   
Sbjct: 2   RYLKFYKPYGVLTQFTDRQGRPTLKSFIPVPKV--YPVGRLDRDSEGLLLLTDDGRLNAR 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------- 184
           L  P     R Y V+  G      L  L++G+VIQG      +V +  ++          
Sbjct: 60  LIDPKFGHERTYWVQVEGIPTPQALQQLQEGVVIQGRKTRPAEVRVLAEEPELPPRDPPI 119

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
                    W+ + LREG+NR+++++         RL+R+  GP  L  L  G  +E+S+
Sbjct: 120 RFRRSIPTTWLELMLREGRNRQVRRMTAAVGIPTLRLVRVGLGPLSLQGLAPGQWQELSE 179

Query: 239 KIL 241
             L
Sbjct: 180 AEL 182


>gi|46143311|ref|ZP_00135512.2| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
          Length = 232

 Score = 95.2 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 56/197 (28%), Positives = 94/197 (47%), Gaps = 17/197 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E T + L++KP  ++T  +D  GR T+ D +P    ++  VGRLD ++EGLLLL
Sbjct: 32  KPQLSFEDTVVVLFNKPFDVLTQFTDEQGRQTLKDFIPIP--QIYPVGRLDRDSEGLLLL 89

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------ 178
           TN+G +   L  P  +  + Y  +  G      L  L+KG+ ++       +        
Sbjct: 90  TNNGEVQHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPN 149

Query: 179 ---------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + + EGKNR+++++     +   RLIRI  G FQLG L 
Sbjct: 150 YEWQTAPKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPTLRLIRIGLGQFQLGELN 209

Query: 230 AGSTREVSKKILREQLG 246
           +G  R + +K  R+   
Sbjct: 210 SGEYRVLDEKEKRQLFQ 226


>gi|146329452|ref|YP_001209494.1| ribosomal large subunit pseudouridine synthase, RluE [Dichelobacter
           nodosus VCS1703A]
 gi|146232922|gb|ABQ13900.1| ribosomal large subunit pseudouridine synthase, RluE [Dichelobacter
           nodosus VCS1703A]
          Length = 189

 Score = 95.2 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 47/185 (25%), Positives = 91/185 (49%), Gaps = 16/185 (8%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +R     +L  ++KP G++   SD  GR T+ D +P   + V   GRLD ++EGL+LLT
Sbjct: 5   IIRPRAGKKLLRFNKPYGVLCQFSDQQGRKTLKDFVP--VADVYPAGRLDYDSEGLVLLT 62

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----- 180
           +DG L   +  P ++  + Y V+  G + ++ +  L  G+ ++       +  +      
Sbjct: 63  DDGRLQARIAQPHSKLPKTYWVQVEGMITENAVRQLAAGVRLKDGMTQPARARILTKPTL 122

Query: 181 ---------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                     +    +W+ + L EG+NR+++++     +   RL+R++ G ++L  L  G
Sbjct: 123 WAREPPVRFRKTIPTSWLELTLYEGRNRQVRRMTAAVGFPTLRLVRVAIGMWRLNDLALG 182

Query: 232 STREV 236
           +  EV
Sbjct: 183 AYEEV 187


>gi|330973498|gb|EGH73564.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. aceris str.
           M302273PT]
          Length = 173

 Score = 95.2 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 49/174 (28%), Positives = 81/174 (46%), Gaps = 7/174 (4%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +  R ++ HKP G V+  SD    + +          +   GRLD NT GL+L+TNDG  
Sbjct: 1   KVPRYFMLHKPEGCVSATSDAQHPTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQW 60

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAW 188
           +R L  P ++  +VY V     +D+       +      +GI     Q+TL   + +   
Sbjct: 61  SRRLTQPQSKMPKVYYVETEQPIDERYAAKFAEGLYFAFEGITTQPAQLTLLGPRRA--- 117

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
             + + EG+  ++K++F  F+ KV RL R + G   L   L  GS R ++   +
Sbjct: 118 -RLSIVEGRYHQVKRMFGHFDNKVLRLHRETIGALLLDPDLRPGSYRALNAGEI 170


>gi|165975545|ref|YP_001651138.1| pseudouridylate synthase [Actinobacillus pleuropneumoniae serovar 3
           str. JL03]
 gi|303250222|ref|ZP_07336423.1| pseudouridylate synthase [Actinobacillus pleuropneumoniae serovar 6
           str. Femo]
 gi|303251911|ref|ZP_07338082.1| ribosomal large subunit pseudouridine synthase E [Actinobacillus
           pleuropneumoniae serovar 2 str. 4226]
 gi|307244890|ref|ZP_07526988.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 1
           str. 4074]
 gi|307247067|ref|ZP_07529120.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 2
           str. S1536]
 gi|307251610|ref|ZP_07533516.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 6
           str. Femo]
 gi|165875646|gb|ABY68694.1| probable pseudouridylate synthase [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|302649341|gb|EFL79526.1| ribosomal large subunit pseudouridine synthase E [Actinobacillus
           pleuropneumoniae serovar 2 str. 4226]
 gi|302650933|gb|EFL81088.1| pseudouridylate synthase [Actinobacillus pleuropneumoniae serovar 6
           str. Femo]
 gi|306854212|gb|EFM86419.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 1
           str. 4074]
 gi|306856436|gb|EFM88586.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 2
           str. S1536]
 gi|306860921|gb|EFM92928.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 6
           str. Femo]
          Length = 231

 Score = 95.2 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 56/197 (28%), Positives = 94/197 (47%), Gaps = 17/197 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E T + L++KP  ++T  +D  GR T+ D +P    ++  VGRLD ++EGLLLL
Sbjct: 31  KPQLSFEDTVVVLFNKPFDVLTQFTDEQGRQTLKDFIPIP--QIYPVGRLDRDSEGLLLL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------ 178
           TN+G +   L  P  +  + Y  +  G      L  L+KG+ ++       +        
Sbjct: 89  TNNGEIQHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPN 148

Query: 179 ---------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + + EGKNR+++++     +   RLIRI  G FQLG L 
Sbjct: 149 YEWQTAPKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPTLRLIRIGLGQFQLGELN 208

Query: 230 AGSTREVSKKILREQLG 246
           +G  R + +K  R+   
Sbjct: 209 SGEYRVLDEKEKRQLFQ 225


>gi|229520430|ref|ZP_04409855.1| ribosomal large subunit pseudouridine synthase E [Vibrio cholerae
           TM 11079-80]
 gi|229342528|gb|EEO07521.1| ribosomal large subunit pseudouridine synthase E [Vibrio cholerae
           TM 11079-80]
          Length = 244

 Score = 95.2 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 49/187 (26%), Positives = 79/187 (42%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER  +        L         ++            V + GRLD ++EGLL+L
Sbjct: 60  RPLSPAERKVILFNKPYDTLSQFTDGDGRKTLADYI---PIKDVYAAGRLDRDSEGLLIL 116

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 117 TNDGILQARLTQPQSKAPKTYWVQVEGSPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 176

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + L EG+NR+++++     +   RLIR S G + LG L  
Sbjct: 177 LWPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQP 236

Query: 231 GSTREVS 237
           G  REV+
Sbjct: 237 GEWREVT 243


>gi|145635545|ref|ZP_01791244.1| hypothetical protein CGSHiAA_01247 [Haemophilus influenzae PittAA]
 gi|229845528|ref|ZP_04465656.1| hypothetical protein CGSHi6P18H1_07818 [Haemophilus influenzae
           6P18H1]
 gi|145267208|gb|EDK07213.1| hypothetical protein CGSHiAA_01247 [Haemophilus influenzae PittAA]
 gi|229811544|gb|EEP47245.1| hypothetical protein CGSHi6P18H1_07818 [Haemophilus influenzae
           6P18H1]
          Length = 227

 Score = 95.2 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 77/196 (39%), Gaps = 17/196 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L   E   +                D +             V + GRLD ++EGLL+L
Sbjct: 31  KTLSLDETKVVLFNKP---FDVLTQFTDEQGRATLKDFISIPNVYAAGRLDRDSEGLLIL 87

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TN+G L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +        
Sbjct: 88  TNNGELQHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKPAKVRLISEPN 147

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  
Sbjct: 148 LWERNPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSINGLEN 207

Query: 231 GSTREVSKKILREQLG 246
           GS R +S   ++    
Sbjct: 208 GSFRLLSLDEIKALFQ 223


>gi|126207576|ref|YP_001052801.1| ribosomal large subunit pseudouridine synthase E [Actinobacillus
           pleuropneumoniae L20]
 gi|126096368|gb|ABN73196.1| ribosomal large subunit pseudouridine synthase E [Actinobacillus
           pleuropneumoniae serovar 5b str. L20]
          Length = 231

 Score = 95.2 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 56/197 (28%), Positives = 94/197 (47%), Gaps = 17/197 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E T + L++KP  ++T  +D  GR T+ D +P    ++  VGRLD ++EGLLLL
Sbjct: 31  KPQLSFEDTVVVLFNKPFDVLTQFTDEQGRQTLKDFIPIP--QIYPVGRLDRDSEGLLLL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------ 178
           TN+G +   L  P  +  + Y  +  G      L  L+KG+ ++       +        
Sbjct: 89  TNNGEVQHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPN 148

Query: 179 ---------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + + EGKNR+++++     +   RLIRI  G FQLG L 
Sbjct: 149 YEWQTAPKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPTLRLIRIGLGQFQLGELN 208

Query: 230 AGSTREVSKKILREQLG 246
           +G  R + +K  R+   
Sbjct: 209 SGEYRVLDEKEKRQLFQ 225


>gi|148827867|ref|YP_001292620.1| hypothetical protein CGSHiGG_06765 [Haemophilus influenzae PittGG]
 gi|148719109|gb|ABR00237.1| hypothetical protein CGSHiGG_06765 [Haemophilus influenzae PittGG]
          Length = 227

 Score = 95.2 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 77/196 (39%), Gaps = 17/196 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L   E   +                D +             V + GRLD ++EGLL+L
Sbjct: 31  KTLSLDETKVVLFNKP---FDVLTQFTDEQGRATLKDFISIPNVYAAGRLDRDSEGLLIL 87

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TN+G L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +        
Sbjct: 88  TNNGELQHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKPAKVRLISEPN 147

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  
Sbjct: 148 LWERNPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSINGLEN 207

Query: 231 GSTREVSKKILREQLG 246
           GS R +S   ++    
Sbjct: 208 GSFRLLSLDEIKALFQ 223


>gi|145641981|ref|ZP_01797554.1| hypothetical protein CGSHiR3021_02808 [Haemophilus influenzae
           R3021]
 gi|145273347|gb|EDK13220.1| hypothetical protein CGSHiR3021_02808 [Haemophilus influenzae
           22.4-21]
          Length = 221

 Score = 95.2 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 77/196 (39%), Gaps = 17/196 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L   E   +                D +             V + GRLD ++EGLL+L
Sbjct: 25  QTLSLDETKVVLFNKP---FDVLTQFTDEQGRATLKDFISIPNVYAAGRLDRDSEGLLIL 81

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TN+G L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +        
Sbjct: 82  TNNGELQHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKPAKVRLISEPN 141

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  
Sbjct: 142 LWERNPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSINGLEN 201

Query: 231 GSTREVSKKILREQLG 246
           GS R +S   ++    
Sbjct: 202 GSFRLLSLDEIKALFQ 217


>gi|229505265|ref|ZP_04394775.1| ribosomal large subunit pseudouridine synthase E [Vibrio cholerae
           BX 330286]
 gi|229511065|ref|ZP_04400544.1| ribosomal large subunit pseudouridine synthase E [Vibrio cholerae
           B33]
 gi|229518185|ref|ZP_04407629.1| ribosomal large subunit pseudouridine synthase E [Vibrio cholerae
           RC9]
 gi|229608284|ref|YP_002878932.1| ribosomal large subunit pseudouridine synthase E [Vibrio cholerae
           MJ-1236]
 gi|34098711|sp|Q9F855|RLUE_VIBCH RecName: Full=Ribosomal large subunit pseudouridine synthase E;
           AltName: Full=rRNA pseudouridylate synthase E; AltName:
           Full=rRNA-uridine isomerase E
 gi|229344900|gb|EEO09874.1| ribosomal large subunit pseudouridine synthase E [Vibrio cholerae
           RC9]
 gi|229351030|gb|EEO15971.1| ribosomal large subunit pseudouridine synthase E [Vibrio cholerae
           B33]
 gi|229357488|gb|EEO22405.1| ribosomal large subunit pseudouridine synthase E [Vibrio cholerae
           BX 330286]
 gi|229370939|gb|ACQ61362.1| ribosomal large subunit pseudouridine synthase E [Vibrio cholerae
           MJ-1236]
          Length = 241

 Score = 95.2 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 49/187 (26%), Positives = 79/187 (42%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER  +        L         ++            V + GRLD ++EGLL+L
Sbjct: 57  RPLSPAERKVILFNKPYDTLSQFTDGDGRKTLADYI---PIKDVYAAGRLDRDSEGLLIL 113

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 114 TNDGILQARLTQPQSKAPKTYWVQVEGSPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 173

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + L EG+NR+++++     +   RLIR S G + LG L  
Sbjct: 174 LWPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQP 233

Query: 231 GSTREVS 237
           G  REV+
Sbjct: 234 GEWREVT 240


>gi|10304093|gb|AAG16128.1|AF261151_1 pseudouridylate synthase-like protein [Vibrio cholerae]
          Length = 241

 Score = 94.9 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 48/187 (25%), Positives = 78/187 (41%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER  +        L         ++              + GRLD ++EGLL+L
Sbjct: 57  RPLSPAERKVILFNKPYDTLSQFTDGDGRKTLADYIPIKDG---YAAGRLDRDSEGLLIL 113

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 114 TNDGILQARLTQPQSKAPKTYWVQVEGSPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 173

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + L EG+NR+++++     +   RLIR S G + LG L  
Sbjct: 174 LWPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQP 233

Query: 231 GSTREVS 237
           G  REV+
Sbjct: 234 GEWREVT 240


>gi|87201125|ref|YP_498382.1| ribosomal large subunit pseudouridine synthase E [Novosphingobium
           aromaticivorans DSM 12444]
 gi|87136806|gb|ABD27548.1| ribosomal large subunit pseudouridine synthase E [Novosphingobium
           aromaticivorans DSM 12444]
          Length = 182

 Score = 94.9 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 42/179 (23%), Positives = 72/179 (40%), Gaps = 14/179 (7%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +        L     +  G              V   GRLD ++EGLLLLT+DG L   +
Sbjct: 4   ILFNKPYGVLCQFTDERTGPPRPTLADHIHRPGVYPAGRLDHDSEGLLLLTDDGRLQARI 63

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y  +  G  D+  L  L+KG+ ++       +  L               
Sbjct: 64  ADPRHKMPKTYLAQVEGVPDEAALASLRKGVRLKDGMTLPAEAALIEDPALWPRDPPIRV 123

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            +   ++W+ + +REG+NR+++++         RL+R   G + L  L  G  REV  +
Sbjct: 124 RKTVPDSWLRLTIREGRNRQVRRMTAAVGHPTLRLVRWQVGDWSLDGLRPGEWREVEVR 182


>gi|190149356|ref|YP_001967881.1| ribosomal large subunit pseudouridine synthase E [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|307262671|ref|ZP_07544300.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 13
           str. N273]
 gi|189914487|gb|ACE60739.1| ribosomal large subunit pseudouridine synthase E [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|306871999|gb|EFN03714.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 13
           str. N273]
          Length = 232

 Score = 94.9 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 55/191 (28%), Positives = 93/191 (48%), Gaps = 17/191 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E T + L++KP  ++T  +D  GR T+ D +P    ++  VGRLD ++EGLLLLTN+G +
Sbjct: 38  EDTVVVLFNKPFDVLTQFTDEQGRQTLKDFIPIP--QIYPVGRLDRDSEGLLLLTNNGEI 95

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------ 178
              L  P  +  + Y  +  G      L  L+KG+ ++       +              
Sbjct: 96  QHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPNYEWQTA 155

Query: 179 ---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + + EGKNR+++++     +   RLIRI  G FQLG L +G  R 
Sbjct: 156 PKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPTLRLIRIGLGQFQLGELNSGEYRV 215

Query: 236 VSKKILREQLG 246
           + +K  R+   
Sbjct: 216 LDEKEKRQLFQ 226


>gi|152989625|ref|YP_001346527.1| putative pseudouridine synthase [Pseudomonas aeruginosa PA7]
 gi|150964783|gb|ABR86808.1| probable pseudouridine synthase [Pseudomonas aeruginosa PA7]
          Length = 189

 Score = 94.9 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 55/188 (29%), Positives = 90/188 (47%), Gaps = 16/188 (8%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P       RL L++KP  ++T  +D  GRST+ D +P         GRLD ++EGLLLLT
Sbjct: 2   PKAPPSEPRLLLFNKPFDVLTQFNDERGRSTLKDFIPVPGV--YPAGRLDRDSEGLLLLT 59

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----- 180
           NDG L   +  P  +  + Y V+  G  ++D+L  L++G+ +        +  L      
Sbjct: 60  NDGRLQARIADPRHKLPKTYWVQVEGTPEEDQLRRLREGVTLNDGPSLPAEARLLDEPAL 119

Query: 181 ---------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                     +     W+ + +REG+NR+++++         RL+R+  GP+ L  L  G
Sbjct: 120 WERVPPVRFRKSVPTHWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGPWSLDGLGLG 179

Query: 232 STREVSKK 239
             REV  +
Sbjct: 180 EWREVPAR 187


>gi|302135159|ref|ZP_07261149.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. tomato NCPPB 1108]
          Length = 222

 Score = 94.9 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 49/185 (26%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  SD +GR+T+ D +          GRLD ++EGLLLLTNDG
Sbjct: 39  PPAEPKLILFNKPFDVLTQFSDEEGRATLKDFIKIPGI--YPAGRLDRDSEGLLLLTNDG 96

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+   ++L  L+ G+ +        +            
Sbjct: 97  QLQARIADPKHKLAKTYWVQVEGEPTPEQLQQLRNGVQLNDGPTLPAEARQLDEPQLWPR 156

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  R
Sbjct: 157 NPPVRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLDQGQYR 216

Query: 235 EVSKK 239
           EV+ K
Sbjct: 217 EVAAK 221


>gi|307260542|ref|ZP_07542235.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 12
           str. 1096]
 gi|306869771|gb|EFN01555.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 12
           str. 1096]
          Length = 231

 Score = 94.9 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 55/197 (27%), Positives = 93/197 (47%), Gaps = 17/197 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E T + L++KP  ++T  +D   R T+ D +P    ++  VGRLD ++EGLLLL
Sbjct: 31  KPQLSFEDTVVVLFNKPFDVLTQFTDEQRRQTLKDFIPIP--QIYPVGRLDRDSEGLLLL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------ 178
           TN+G +   L  P  +  + Y  +  G      L  L+KG+ ++       +        
Sbjct: 89  TNNGEIQHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPN 148

Query: 179 ---------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + + EGKNR+++++     +   RLIRI  G FQLG L 
Sbjct: 149 YEWQTAPKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPTLRLIRIGLGQFQLGELN 208

Query: 230 AGSTREVSKKILREQLG 246
           +G  R + +K  R+   
Sbjct: 209 SGEYRVLDEKEKRQLFQ 225


>gi|301155121|emb|CBW14585.1| 23S rRNA pseudouridine synthase [Haemophilus parainfluenzae T3T1]
          Length = 228

 Score = 94.9 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 41/197 (20%), Positives = 77/197 (39%), Gaps = 18/197 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL   +   +                D               V + GRLD ++EGLL+L
Sbjct: 27  KPLTLEQTIVILFNKP---FDVLTQFTDENGRATLKDFITIPNVYAAGRLDRDSEGLLIL 83

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TN+G +   L  P  +  + Y V+  G  ++  L+ L+KG+ ++       +        
Sbjct: 84  TNNGEVQHRLADPKFKTEKTYFVQVEGIPEETDLDKLRKGVELKDGMTKPAKVRLISEPD 143

Query: 177 -------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + Q  + +W+ + + EG+NR+++++     +   RLIR       L  L 
Sbjct: 144 FLWPRNPPIRERQSITTSWLEIKISEGRNRQVRRMTAHIGFPTLRLIRYQMSHLTLDGLG 203

Query: 230 AGSTREVSKKILREQLG 246
            G  R ++K+ +R    
Sbjct: 204 NGEYRCLNKEEMRALFK 220


>gi|146308760|ref|YP_001189225.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           mendocina ymp]
 gi|145576961|gb|ABP86493.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           mendocina ymp]
          Length = 206

 Score = 94.9 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 50/182 (27%), Positives = 86/182 (47%), Gaps = 16/182 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              + RL L +KP  ++T  +D  GR+T+ D +          GRLD ++EGLLLLTNDG
Sbjct: 22  PPAQPRLILLNKPFDVLTQFNDEQGRATLKDFVEVPGV--YPAGRLDRDSEGLLLLTNDG 79

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+  + +L  L+ G+ +        +  L         
Sbjct: 80  RLQARIADPRHKLAKTYWVQVEGEPSEAQLQQLRDGVTLNDGPTLPAEARLLDEPQLWDR 139

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + +REG+NR+++++         RL+R++ GP+ L  L  G   
Sbjct: 140 HPPVRFRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVAIGPWALNGLQPGQWC 199

Query: 235 EV 236
           EV
Sbjct: 200 EV 201


>gi|325576785|ref|ZP_08147400.1| ribosomal large subunit pseudouridine synthase E [Haemophilus
           parainfluenzae ATCC 33392]
 gi|325160991|gb|EGC73109.1| ribosomal large subunit pseudouridine synthase E [Haemophilus
           parainfluenzae ATCC 33392]
          Length = 230

 Score = 94.9 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 38/197 (19%), Positives = 77/197 (39%), Gaps = 18/197 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L  AE   +        L     +    +     +        + GRLD ++EGLL+L
Sbjct: 29  RALSIAESQVILFNKPFDVLTQFTDENGRATLKDFIIIPNV---YAAGRLDRDSEGLLIL 85

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TN+G +   L  P  +  + Y  +  G  ++  L+ L++G+ ++       +        
Sbjct: 86  TNNGEVQHRLADPKFKTEKTYFAQVEGIPEESDLDKLRQGVELKDGMTKPAKVRLISEPD 145

Query: 177 -------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + Q    +W+ + + EG+NR+++++     +   RLIR       L  L 
Sbjct: 146 FLWPRNPPIRERQSIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLIRYQMSHLTLDGLS 205

Query: 230 AGSTREVSKKILREQLG 246
            G  R ++++ +R    
Sbjct: 206 NGEYRRLNEEEMRALFK 222


>gi|323455461|gb|EGB11329.1| hypothetical protein AURANDRAFT_61729 [Aureococcus anophagefferens]
          Length = 294

 Score = 94.9 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 65/248 (26%), Positives = 108/248 (43%), Gaps = 29/248 (11%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP---------LRKAERTRLWL 77
           SRR  +  +A  RV+VNG   +  ++ + S D + +DG           L        + 
Sbjct: 36  SRRAADAAVAAGRVRVNGETAK-PSLRLRSGDTLALDGKKRDWEALAAKLEGGGGLEYYA 94

Query: 78  YHKPIGLVTTHSDPDGRSTVFDN----LPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           YHKP G+  T    D RS         L +   R+   GRLD+++ GL++LTNDG  A  
Sbjct: 95  YHKPEGVACTTDANDRRSLRRAPALKKLFAGGKRIFPAGRLDVDSCGLVVLTNDGAAADA 154

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----------QGICYGDMQVTLDTQ 182
              PS++  +VY V    +   D +  L  G+ I           +        V     
Sbjct: 155 ALQPSSKLAKVYEVELDRRAADDDVAALAAGVEIATPLQRGSKAEKTGKTLPCDVARGDG 214

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +G    + + L EG+NR+++++ E   ++V  L R+++GP  LG L  G+ R ++   + 
Sbjct: 215 RG----LVITLAEGRNRQLRRMAEALGYEVTGLRRVAFGPVSLGDLRPGTLRPLAAAEVD 270

Query: 243 EQLGPHLL 250
             L     
Sbjct: 271 ALLAHKDK 278


>gi|318042073|ref|ZP_07974029.1| pseudouridine synthase, Rsu [Synechococcus sp. CB0101]
          Length = 232

 Score = 94.9 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 52/192 (27%), Positives = 84/192 (43%), Gaps = 20/192 (10%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L++KP G+++  +   G              V + GRLD ++EGLLLLT +G L + L 
Sbjct: 11  LLFYKPYGVLSQFTPEPGSRWGCLADHIPVPDVYTAGRLDADSEGLLLLTANGRLQQRLT 70

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------------T 181
            P+    R Y V+  G  D  +L  L++G+VIQG      +                   
Sbjct: 71  DPAWGHWRRYWVQVEGIPDAAQLQQLEQGLVIQGQRTLPARANAIADPDLPPRDPPIRSR 130

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY------GPFQLGTLLAGSTRE 235
           Q+   +W+ V LREG+NR+++++         RL+R++        P  L  L  G  R 
Sbjct: 131 QQIPTSWLAVELREGRNRQVRRMTAAVGLPTLRLLRVAIDLMDGGAPLSLDGLEPGQWRA 190

Query: 236 VSKKILREQLGP 247
           V+ +  R     
Sbjct: 191 VTPEEERRLQAL 202


>gi|332667990|ref|YP_004450778.1| pseudouridine synthase Rsu [Haliscomenobacter hydrossis DSM 1100]
 gi|332336804|gb|AEE53905.1| pseudouridine synthase Rsu [Haliscomenobacter hydrossis DSM 1100]
          Length = 197

 Score = 94.9 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 53/196 (27%), Positives = 82/196 (41%), Gaps = 19/196 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                L HKP G ++  +          +L      V  VGRLD ++EGLLLL+ND  L 
Sbjct: 1   MFHYILLHKPFGYLSQFTPETPGQLTLADLGPFPPEVYPVGRLDQDSEGLLLLSNDSRLN 60

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKG--- 184
             L  P     R Y V+  G  D+  L  L+ G+ I    +       +  L   +    
Sbjct: 61  VQLLDPRHAHWRTYWVQVEGIPDEAALAHLRSGVEIRFNKKTYHTLPARAQLLDPQPTVA 120

Query: 185 ------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                          W+ + L+EGKNR+++++     + V RLIR++    QLG L  G+
Sbjct: 121 ERNPPIRYRANIPETWLELSLQEGKNRQVRRMCAKVGYPVLRLIRVNIENLQLGDLAVGA 180

Query: 233 TREVSKKILREQLGPH 248
            R  ++K +   L   
Sbjct: 181 WRACTQKEIYTYLKLK 196


>gi|262402501|ref|ZP_06079062.1| ribosomal large subunit pseudouridine synthase E [Vibrio sp. RC586]
 gi|262351283|gb|EEZ00416.1| ribosomal large subunit pseudouridine synthase E [Vibrio sp. RC586]
          Length = 241

 Score = 94.9 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 45/187 (24%), Positives = 79/187 (42%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +  +ER  +        L         ++            V + GRLD ++EGLL+L
Sbjct: 57  RAISPSERKVVLFNKPYDTLSQFTDGDGRKTLADYI---PIKDVYAAGRLDRDSEGLLIL 113

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V + ++  
Sbjct: 114 TNDGILQARLTQPQSKAPKTYWVQVEGVPQESDLEALRHGVTLKDGPTLPAKVKIMSEPE 173

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + L EG+NR+++++     +   RLIR S G + LG L  
Sbjct: 174 LWPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRHSMGDWNLGDLQP 233

Query: 231 GSTREVS 237
           G  RE++
Sbjct: 234 GEWREMT 240


>gi|254291565|ref|ZP_04962355.1| pseudouridine synthase family 1 protein [Vibrio cholerae AM-19226]
 gi|150422517|gb|EDN14474.1| pseudouridine synthase family 1 protein [Vibrio cholerae AM-19226]
          Length = 241

 Score = 94.9 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 49/187 (26%), Positives = 79/187 (42%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER  +        L         ++            V + GRLD ++EGLL+L
Sbjct: 57  RPLSPAERKVILFNKPYDTLSQFTDGDGRKTLADYI---PIKDVYAAGRLDRDSEGLLIL 113

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 114 TNDGILQARLTRPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 173

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + L EG+NR+++++     +   RLIR S G + LG L  
Sbjct: 174 LWPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQP 233

Query: 231 GSTREVS 237
           G  REV+
Sbjct: 234 GEWREVT 240


>gi|153826036|ref|ZP_01978703.1| pseudouridine synthase family 1 protein [Vibrio cholerae MZO-2]
 gi|149740256|gb|EDM54403.1| pseudouridine synthase family 1 protein [Vibrio cholerae MZO-2]
          Length = 241

 Score = 94.9 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 49/187 (26%), Positives = 79/187 (42%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER  +        L         ++            V + GRLD ++EGLL+L
Sbjct: 57  RPLSPAERKVILFNKPYDTLSQFTDGDGRKTLADYI---PIKDVYAAGRLDRDSEGLLIL 113

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 114 TNDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 173

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + L EG+NR+++++     +   RLIR S G + LG L  
Sbjct: 174 LWPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQP 233

Query: 231 GSTREVS 237
           G  REV+
Sbjct: 234 GEWREVT 240


>gi|153828665|ref|ZP_01981332.1| pseudouridine synthase family 1 protein [Vibrio cholerae 623-39]
 gi|148875818|gb|EDL73953.1| pseudouridine synthase family 1 protein [Vibrio cholerae 623-39]
          Length = 241

 Score = 94.9 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 49/187 (26%), Positives = 79/187 (42%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER  +        L         ++            V + GRLD ++EGLL+L
Sbjct: 57  RPLSPAERKVILFNKPYDTLSQFTDGDGRKTLADYI---PIKDVYAAGRLDRDSEGLLIL 113

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 114 TNDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 173

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + L EG+NR+++++     +   RLIR S G + LG L  
Sbjct: 174 LWPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQP 233

Query: 231 GSTREVS 237
           G  REV+
Sbjct: 234 GEWREVT 240


>gi|153214245|ref|ZP_01949280.1| pseudouridine synthase family 1 protein [Vibrio cholerae 1587]
 gi|124115494|gb|EAY34314.1| pseudouridine synthase family 1 protein [Vibrio cholerae 1587]
          Length = 241

 Score = 94.9 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 49/187 (26%), Positives = 79/187 (42%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER  +        L         ++            V + GRLD ++EGLL+L
Sbjct: 57  RPLSPAERKVILFNKPYDTLSQFTDGDGRKTLADYI---PIKDVYAAGRLDRDSEGLLIL 113

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 114 TNDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 173

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + L EG+NR+++++     +   RLIR S G + LG L  
Sbjct: 174 LWPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQP 233

Query: 231 GSTREVS 237
           G  REV+
Sbjct: 234 GEWREVT 240


>gi|71736265|ref|YP_276494.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. phaseolicola 1448A]
 gi|71556818|gb|AAZ36029.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. phaseolicola 1448A]
          Length = 210

 Score = 94.9 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 48/182 (26%), Positives = 85/182 (46%), Gaps = 16/182 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L+L++KP  ++T  SD  GR+T+ D +          GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPKLFLFNKPFDVLTQFSDEGGRATLKDFIKIPGI--YPAGRLDRDSEGLLLLTNDG 84

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+   ++L  L+ G+ +        +            
Sbjct: 85  QLQARIADPKHKLAKTYWVQVEGEPTDEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPS 144

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  R
Sbjct: 145 NPPVRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLDQGQYR 204

Query: 235 EV 236
           EV
Sbjct: 205 EV 206


>gi|114778386|ref|ZP_01453233.1| ribosomal large subunit pseudouridine synthase E [Mariprofundus
           ferrooxydans PV-1]
 gi|114551349|gb|EAU53906.1| ribosomal large subunit pseudouridine synthase E [Mariprofundus
           ferrooxydans PV-1]
          Length = 221

 Score = 94.5 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 42/187 (22%), Positives = 82/187 (43%), Gaps = 15/187 (8%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLLLLT+DG L   +  P  +  +VY V+  G +  + +  L+ G+ ++
Sbjct: 35  YAAGRLDRDSEGLLLLTDDGPLQNRISHPLHKLKKVYWVQVDGAISDEAVERLRHGVELK 94

Query: 169 GICYGDMQVTLD---------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +V++                  +   +W+++ + EG+NR+++++     +   
Sbjct: 95  DGMTSPARVSVMEAPATLWPRNPPIRTRAQIPTSWISLEISEGRNRQVRRMTAAVGFPTL 154

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPN 273
           RLIR + GP  L  L  G+  EV  + L            +  + A     +  ++ RP 
Sbjct: 155 RLIRYAIGPITLDGLQPGTYDEVDAQQLWNLFPTQGSGVDRPVVSAGNSHKKFDLKHRPI 214

Query: 274 IISEVPD 280
              +   
Sbjct: 215 RKKKQQR 221


>gi|326794629|ref|YP_004312449.1| pseudouridine synthase Rsu [Marinomonas mediterranea MMB-1]
 gi|326545393|gb|ADZ90613.1| pseudouridine synthase Rsu [Marinomonas mediterranea MMB-1]
          Length = 232

 Score = 94.5 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 104/237 (43%), Gaps = 19/237 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              +L + +KP  +++  +  DG+ T+ + +      V + GRLD ++EGLLLLTN+G L
Sbjct: 1   MPEKLIILNKPFHVLSQFTADDGKDTLANYIDDE--NVYAAGRLDYDSEGLLLLTNNGSL 58

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-------- 182
             ++  P  +  + Y V+  G++  D +  L +G+ ++       +     Q        
Sbjct: 59  QHLIASPKFKMPKTYWVQVEGEITDDAIGSLCRGVELKDGMTKPAECRKIDQPNIWDRTP 118

Query: 183 ------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                     +WV + + EGKNR+++++     +   RLIR S GP+ + +L +G ++  
Sbjct: 119 AVRYRANIPTSWVALTITEGKNRQVRRMTAAVGFPTLRLIRYSIGPYTVDSLRSGESK-- 176

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
               L  QL   + E  Q     P   S    + +     +      R  +++ +  
Sbjct: 177 -IAELTSQLREQVSEFEQKKRATPPNRSRHRSKGQSLPDGKGNTRRHRSAQSARRPR 232


>gi|149376381|ref|ZP_01894144.1| Pseudouridine synthase, Rsu [Marinobacter algicola DG893]
 gi|149359395|gb|EDM47856.1| Pseudouridine synthase, Rsu [Marinobacter algicola DG893]
          Length = 213

 Score = 94.5 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 40/179 (22%), Positives = 73/179 (40%), Gaps = 14/179 (7%)

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
                 +   GRLD ++EGLLLLT++G L   +  P  +  + Y V+  G++++  L  L
Sbjct: 35  WLTIPAIYPAGRLDYDSEGLLLLTDNGQLQHRIASPRLKMPKTYWVQVEGEINESALTKL 94

Query: 162 KKGIVIQGICYGDMQ--------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
           ++G+ ++                           +    +WV + + EGKNR+++++   
Sbjct: 95  REGVELKDGKTRPADVATMTPPEIWPRNPPVRYRESIPTSWVRITITEGKNRQVRRMTAA 154

Query: 208 FNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSET 266
             +   RLIR   G + L  L  G  R +S             + A++   AP      
Sbjct: 155 VGFPTLRLIRYGIGDWTLDGLTPGEYRAISVHAPAPPPEKAARKPAKLRKHAPRRRPRP 213


>gi|86138278|ref|ZP_01056852.1| RNA pseudouridylate synthase [Roseobacter sp. MED193]
 gi|85824803|gb|EAQ45004.1| RNA pseudouridylate synthase [Roseobacter sp. MED193]
          Length = 241

 Score = 94.5 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 48/240 (20%), Positives = 96/240 (40%), Gaps = 17/240 (7%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGG 129
            TRL  ++KP  ++   +D   + +    L +  +     + GRLD ++EGL+LLT++G 
Sbjct: 1   MTRLIRFNKPYDVLPQFTDSGSQGSARPTLSAYINCPGVYAAGRLDRDSEGLMLLTDNGR 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------- 180
           L   +  P  +  + Y V+  G+ D   L  L++G+ ++       +  L          
Sbjct: 61  LQAWISDPQHKMAKTYWVQVEGEPDSRALAALQQGVALKDGMTRPAKAHLMEAPAQLWQR 120

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+++ L+EGKNR+++++     +   RLIR S G + L  L  GS  
Sbjct: 121 EPPIRTRKSIPTSWISLTLKEGKNRQVRRMTAAVGFPTLRLIRYSIGVWTLDGLPQGSWE 180

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           ++    +     P  L   +          +          +       + ++ S     
Sbjct: 181 DLEVPSIPGPAKPSQLPNRRAQQKRNKEGQDQEGNPSERNATARQKQRGKPRRRSRSTKP 240


>gi|323447017|gb|EGB02989.1| hypothetical protein AURANDRAFT_34656 [Aureococcus anophagefferens]
          Length = 273

 Score = 94.5 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 108/243 (44%), Gaps = 29/243 (11%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP---------LRKAERTRLWL 77
           SRR  +  +A  RV+VNG   +  ++ + S D + +DG           L        + 
Sbjct: 36  SRRAADAAVAAGRVRVNGETAK-PSLRLRSGDTLALDGKKRDWEALAAKLEGGGGLEYYA 94

Query: 78  YHKPIGLVTTHSDPDGRSTVFDN----LPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           YHKP G+  T    D RS         L +   R+   GRLD+++ GL++LTNDG  A  
Sbjct: 95  YHKPEGVACTTDANDRRSLRRAPALKKLFAGGKRIFPAGRLDVDSCGLVVLTNDGAAADA 154

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----------QGICYGDMQVTLDTQ 182
              PS++  +VY V    +   D +  L  G+ I           +        V     
Sbjct: 155 ALQPSSKLAKVYEVELDRRAADDDVAALAAGVEIATPLQRGSKAEKTGKTLPCDVARGDG 214

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +G    + + L EG+NR+++++ E   ++V  L R+++GP  LG L  G+ R ++   + 
Sbjct: 215 RG----LVITLAEGRNRQLRRMAEALGYEVTGLRRVAFGPVSLGDLRPGTLRPLAAAEVD 270

Query: 243 EQL 245
             L
Sbjct: 271 ALL 273


>gi|46205033|ref|ZP_00209673.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Magnetospirillum
           magnetotacticum MS-1]
          Length = 228

 Score = 94.5 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 46/199 (23%), Positives = 84/199 (42%), Gaps = 6/199 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV----MSTDHIEVDGVP 66
               R+ +++A  G  SRREVE +     V+++G  L  AA  +      +  + + G  
Sbjct: 2   TKAVRLDRLLANLGYGSRREVEGLAWAGLVRLDGETLTDAAQRIPLDPDLSARMTIQGQL 61

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           L       L L+       +         S + +        + +VGRLD  T GLLLLT
Sbjct: 62  LDPLPGLCLMLHKPLGVTCSHKEAGPLVYSLLPERWRRRDPALSTVGRLDKETSGLLLLT 121

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG L   +  P  +  + YRV     +  D+ ++L  G ++       + + ++ +   
Sbjct: 122 DDGALLHRIISPKAKVAKRYRVTLARPLQGDETSILASGELMLDGEDKPL-LPVEMEADD 180

Query: 186 NAWVTVGLREGKNREIKKV 204
               TV L EG+  +++ +
Sbjct: 181 ATHCTVTLHEGRYHKVRAL 199


>gi|262171826|ref|ZP_06039504.1| ribosomal large subunit pseudouridine synthase E [Vibrio mimicus
           MB-451]
 gi|261892902|gb|EEY38888.1| ribosomal large subunit pseudouridine synthase E [Vibrio mimicus
           MB-451]
          Length = 242

 Score = 94.5 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 46/187 (24%), Positives = 78/187 (41%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +  +ER  +        L         ++            V + GRLD ++EGLL+L
Sbjct: 58  RAISPSERKVVLFNKPYDTLSQFTDGDGRKTLADYI---SIKDVYAAGRLDRDSEGLLIL 114

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 115 TNDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 174

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + L EG+NR+++++     +   RLIR S G + LG L  
Sbjct: 175 LWPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRHSMGDWNLGDLQP 234

Query: 231 GSTREVS 237
           G  REV+
Sbjct: 235 GEWREVT 241


>gi|145637609|ref|ZP_01793265.1| ribosomal large subunit pseudouridine synthase E [Haemophilus
           influenzae PittHH]
 gi|145269206|gb|EDK09153.1| ribosomal large subunit pseudouridine synthase E [Haemophilus
           influenzae PittHH]
          Length = 221

 Score = 94.5 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 40/196 (20%), Positives = 76/196 (38%), Gaps = 17/196 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L   E   +                D +             V + GRLD ++EGLL+L
Sbjct: 25  KTLSLDETKVVLFNKP---FDVLTQFTDEQGRATLKDFISIPNVYAAGRLDRDSEGLLIL 81

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TN+G L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +        
Sbjct: 82  TNNGELQHRLSDPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGMTKPAKVRLISEPN 141

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + +    +W+ + + EG+NR+++++     +   RL+R+  G   +  L  
Sbjct: 142 LWERNPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVGMGSLSINGLAN 201

Query: 231 GSTREVSKKILREQLG 246
           GS R +S   ++    
Sbjct: 202 GSFRLLSLDEIKALFQ 217


>gi|188026122|ref|ZP_02960941.2| hypothetical protein PROSTU_02927 [Providencia stuartii ATCC 25827]
 gi|188021695|gb|EDU59735.1| hypothetical protein PROSTU_02927 [Providencia stuartii ATCC 25827]
          Length = 178

 Score = 94.5 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 37/144 (25%), Positives = 64/144 (44%), Gaps = 15/144 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LTNDG L   L  P     +VY  +  G  D   L   ++G+ ++
Sbjct: 33  YAAGRLDRDSEGLLILTNDGKLQARLTQPQKNTNKVYYAQVEGIPDDAALVKFRQGLTLK 92

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +    +W+ + L EG+NR+++++     +   
Sbjct: 93  DGPTRPAGIERVNEPDWLWPRTPPIRERKNIPTSWLKITLSEGRNRQVRRMTAHIGYPTL 152

Query: 214 RLIRISYGPFQLGTLLAGSTREVS 237
           RLIR   G + L  L  G  +E++
Sbjct: 153 RLIRYQIGEYTLNNLAPGEWKEIT 176


>gi|238791828|ref|ZP_04635465.1| Ribosomal large subunit pseudouridine synthase E [Yersinia
           intermedia ATCC 29909]
 gi|238728932|gb|EEQ20449.1| Ribosomal large subunit pseudouridine synthase E [Yersinia
           intermedia ATCC 29909]
          Length = 208

 Score = 94.1 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 51/189 (26%), Positives = 91/189 (48%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             ++     R+ L++KP  ++   +D  GR T+ + +P  F+ V + GRLD ++EGLL+L
Sbjct: 21  KQVKPVGPRRVLLFNKPFDVLPQFTDESGRRTLKEFIP--FNDVYAAGRLDRDSEGLLVL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TNDG L   L  P+ +  ++Y V+  G  + D L+ L+ G+V++                
Sbjct: 79  TNDGKLQAKLTQPTAKTGKIYFVQVEGVPEDDALDKLRHGVVLKDGPTLPAGAELVSEPE 138

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ + L EG+NR+++++     +   RLIR S G   L  L 
Sbjct: 139 WLWPRVPPIRERKNIPTRWLQITLYEGRNRQVRRMTAHIGFPTLRLIRFSVGNLSLADLQ 198

Query: 230 AGSTREVSK 238
            G  +E+  
Sbjct: 199 PGEWKEIRD 207


>gi|288959446|ref|YP_003449787.1| ribosomal large subunit pseudouridine synthase E [Azospirillum sp.
           B510]
 gi|288911754|dbj|BAI73243.1| ribosomal large subunit pseudouridine synthase E [Azospirillum sp.
           B510]
          Length = 261

 Score = 94.1 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 55/247 (22%), Positives = 97/247 (39%), Gaps = 24/247 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              RL L +KP G++   +D  GR T+ + +P       + GRLD ++EGLL L++DG L
Sbjct: 22  PVPRLILLNKPYGVLPQFTDDQGRPTLAELVPVKGV--YAAGRLDRDSEGLLALSDDGPL 79

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-------- 182
              +  P+++  + Y V+  G    + L  L++G+ ++       +V    +        
Sbjct: 80  IARIAAPASKMPKTYWVQVEGVPTDEALEALRRGVTLKDGPTLPAEVRRMEEPDPLWPRD 139

Query: 183 -------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                      +W+ + LREG+NR+++++     +   RLIR S G + L  L  G  RE
Sbjct: 140 PPVRYRAAIPTSWIALTLREGRNRQVRRMTAAVGFPTLRLIRWSIGDWTLDGLAPGQWRE 199

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           V          P      Q +        +   +      +  P       K        
Sbjct: 200 V-------PQPPATPSSRQKSSGQKSTGQKLTGQKLTGPKAPAPTGKRGPIKPRRTVAPR 252

Query: 296 SKQKKLA 302
           S   +  
Sbjct: 253 SAPSRPR 259


>gi|209525302|ref|ZP_03273844.1| pseudouridine synthase [Arthrospira maxima CS-328]
 gi|209494317|gb|EDZ94630.1| pseudouridine synthase [Arthrospira maxima CS-328]
          Length = 193

 Score = 94.1 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 50/187 (26%), Positives = 82/187 (43%), Gaps = 17/187 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
            R  L++KP  +++  +D D  +     L          SVGRLD+++EGLLLLT+D  L
Sbjct: 3   YRYILFYKPYNVLSQFTDRDSHTPSRQTLKDYIPIPSVYSVGRLDLDSEGLLLLTDDRKL 62

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---------- 180
              L  P     R Y V+         L  L++GI IQ       +V L           
Sbjct: 63  KYRLGQPEFAHPRTYWVQVERIPTTQALEQLRRGITIQNYRTRTARVQLLLTEPLLPPRI 122

Query: 181 -----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                 Q    AW+ + L EG+NR+++++     +   RL+R++     L +L  G  R+
Sbjct: 123 PPIRFRQNVPTAWLEITLTEGRNRQVRRMTAAVGFPTLRLVRVAIAHLTLNSLQPGDWRD 182

Query: 236 VSKKILR 242
           +    ++
Sbjct: 183 LHPHEIQ 189


>gi|170718088|ref|YP_001785122.1| pseudouridine synthase [Haemophilus somnus 2336]
 gi|168826217|gb|ACA31588.1| pseudouridine synthase [Haemophilus somnus 2336]
          Length = 227

 Score = 94.1 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 49/194 (25%), Positives = 88/194 (45%), Gaps = 16/194 (8%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +T++ L++KP  ++   +D  GR+T+ D +      +  VGRLD ++EGLLLLTN+G L 
Sbjct: 35  QTKVILFNKPFDVLCQFTDEQGRATLKDFIKIP--HIYPVGRLDRDSEGLLLLTNNGELQ 92

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------------V 177
             L  P  +  + Y V+  G   +  L  L+KGI +        +               
Sbjct: 93  HRLTNPKFKMEKTYWVQIEGIPVETDLAQLRKGIELNDGLTKPAKVRLISEPNIWQRHPP 152

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + + EG+NR+++++     +   RLIR       L  L  G  RE++
Sbjct: 153 IRERKTVPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLIRYETAGLTLTNLANGQFRELT 212

Query: 238 KKILREQLGPHLLE 251
              L++        
Sbjct: 213 LTELQDLYQQVKKS 226


>gi|307253844|ref|ZP_07535697.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 9
           str. CVJ13261]
 gi|307258300|ref|ZP_07540042.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 11
           str. 56153]
 gi|306863204|gb|EFM95145.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 9
           str. CVJ13261]
 gi|306867639|gb|EFM99485.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 11
           str. 56153]
          Length = 232

 Score = 94.1 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 56/197 (28%), Positives = 94/197 (47%), Gaps = 17/197 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E T + L++KP  ++T  +D  GR T+ D +P    ++  VGRLD ++EGLLLL
Sbjct: 32  KPQLSFEDTVVVLFNKPFDVLTQFTDEQGRQTLKDFIPIP--QIYPVGRLDRDSEGLLLL 89

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------ 178
           TN+G +   L  P  +  + Y  +  G      L  L+KG+ ++       +        
Sbjct: 90  TNNGEIQHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPN 149

Query: 179 ---------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + + EGKNR+++++     +   RLIRI  G FQLG L 
Sbjct: 150 YEWQTAPKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPPLRLIRIGLGQFQLGELN 209

Query: 230 AGSTREVSKKILREQLG 246
           +G  R + +K  R+   
Sbjct: 210 SGEYRVLDEKEKRQLFQ 226


>gi|307249289|ref|ZP_07531284.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 4
           str. M62]
 gi|306858688|gb|EFM90749.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 4
           str. M62]
          Length = 232

 Score = 94.1 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 57/197 (28%), Positives = 94/197 (47%), Gaps = 17/197 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E T + L++KP  ++T  +D  GR T+ D +P    +V  VGRLD ++EGLLLL
Sbjct: 32  KPQLSFEDTVVVLFNKPFDVLTQFTDEQGRQTLKDFIPIP--QVYPVGRLDRDSEGLLLL 89

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------ 178
           TN+G +   L  P  +  + Y  +  G      L  L+KG+ ++       +        
Sbjct: 90  TNNGEIQHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPN 149

Query: 179 ---------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + + EGKNR+++++     +   RLIRI  G FQLG L 
Sbjct: 150 YEWQTAPKIRERKIIPTSWIELKIHEGKNRQVRRMTAHIGFPTLRLIRIGLGQFQLGELN 209

Query: 230 AGSTREVSKKILREQLG 246
           +G  R + +K  R+   
Sbjct: 210 SGEYRVLDEKEKRQLFQ 226


>gi|301169411|emb|CBW29011.1| 23S rRNA pseudouridine synthase [Haemophilus influenzae 10810]
          Length = 240

 Score = 94.1 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 76/196 (38%), Gaps = 17/196 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L   E   +                D +             V + GRLD ++EGLL+L
Sbjct: 44  KTLSLDETKVVLFNKP---FDVLTQFTDEQGRATLKDFISIPNVYAAGRLDRDSEGLLIL 100

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TN G L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +        
Sbjct: 101 TNHGELQHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKPAKVRLISEPN 160

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  
Sbjct: 161 LWERNPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGLLSINGLEN 220

Query: 231 GSTREVSKKILREQLG 246
           GS R +S   ++    
Sbjct: 221 GSFRLLSLDEIKALFQ 236


>gi|307256109|ref|ZP_07537896.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 10
           str. D13039]
 gi|306865290|gb|EFM97186.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 10
           str. D13039]
          Length = 231

 Score = 94.1 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 56/197 (28%), Positives = 94/197 (47%), Gaps = 17/197 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E T + L++KP  ++T  +D  GR T+ D +P    ++  VGRLD ++EGLLLL
Sbjct: 31  KPQLSFEDTVVVLFNKPFDVLTQFTDEQGRQTLKDFIPIP--QIYPVGRLDRDSEGLLLL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------ 178
           TN+G +   L  P  +  + Y  +  G      L  L+KG+ ++       +        
Sbjct: 89  TNNGEIQHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPN 148

Query: 179 ---------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + + EGKNR+++++     +   RLIRI  G FQLG L 
Sbjct: 149 YEWQTAPKIRERKIIPTSWIELKIHEGKNRQVRRMTAHIGFPTLRLIRIGLGQFQLGELN 208

Query: 230 AGSTREVSKKILREQLG 246
           +G  R + +K  R+   
Sbjct: 209 SGEYRVLDEKEKRQLFQ 225


>gi|313650387|gb|EFS14794.1| ribosomal large subunit pseudouridine synthase E [Shigella flexneri
           2a str. 2457T]
 gi|332758324|gb|EGJ88647.1| ribosomal large subunit pseudouridine synthase E [Shigella flexneri
           4343-70]
 gi|332759318|gb|EGJ89626.1| ribosomal large subunit pseudouridine synthase E [Shigella flexneri
           2747-71]
 gi|332761102|gb|EGJ91389.1| ribosomal large subunit pseudouridine synthase E [Shigella flexneri
           K-671]
 gi|332767380|gb|EGJ97574.1| 23S rRNA pseudouridine synthase [Shigella flexneri 2930-71]
 gi|333005361|gb|EGK24879.1| ribosomal large subunit pseudouridine synthase E [Shigella flexneri
           K-218]
 gi|333019471|gb|EGK38754.1| ribosomal large subunit pseudouridine synthase E [Shigella flexneri
           K-304]
          Length = 177

 Score = 93.7 bits (231), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 48/179 (26%), Positives = 84/179 (46%), Gaps = 17/179 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+LTN+G L   L
Sbjct: 1   MILFNKPYDVLPQFTDETGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVLTNNGALQARL 58

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------QVTL 179
             P  +  ++Y V+  G   QD L  L+ G+ +                           
Sbjct: 59  TQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIR 118

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  REV+ 
Sbjct: 119 ERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVTD 177


>gi|145629614|ref|ZP_01785411.1| hypothetical protein CGSHi22121_01167 [Haemophilus influenzae
           22.1-21]
 gi|144978125|gb|EDJ87898.1| hypothetical protein CGSHi22121_01167 [Haemophilus influenzae
           22.1-21]
          Length = 221

 Score = 93.7 bits (231), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 76/196 (38%), Gaps = 17/196 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L   E   +                D +             V + GRLD ++EGLL+L
Sbjct: 25  QTLSLDETKVVLFNKP---FDVLTQFTDEQGRATLKDFISIPNVYAAGRLDRDSEGLLIL 81

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TN G L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +        
Sbjct: 82  TNHGELQHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKPAKVRLISEPN 141

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  
Sbjct: 142 LWERNPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGLLSINGLEN 201

Query: 231 GSTREVSKKILREQLG 246
           GS R +S   ++    
Sbjct: 202 GSFRLLSLDEIKALFQ 217


>gi|309751708|gb|ADO81692.1| 23S rRNA U2457 pseudouridine synthase [Haemophilus influenzae
           R2866]
          Length = 227

 Score = 93.7 bits (231), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 76/196 (38%), Gaps = 17/196 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L   E   +                D +             V + GRLD ++EGLL+L
Sbjct: 31  QTLSLDETKVVLFNKP---FDVLTQFTDEQGRATLKDFISIPNVYAAGRLDRDSEGLLIL 87

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TN G L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +        
Sbjct: 88  TNHGELQHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKPAKVRLISEPN 147

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  
Sbjct: 148 LWERNPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGLLSINGLEN 207

Query: 231 GSTREVSKKILREQLG 246
           GS R +S   ++    
Sbjct: 208 GSFRLLSLDEIKALFQ 223


>gi|191168333|ref|ZP_03030125.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           B7A]
 gi|193071705|ref|ZP_03052605.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           E110019]
 gi|194433663|ref|ZP_03065939.1| ribosomal large subunit pseudouridine synthase E [Shigella
           dysenteriae 1012]
 gi|190901628|gb|EDV61385.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           B7A]
 gi|192954967|gb|EDV85470.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           E110019]
 gi|194418092|gb|EDX34185.1| ribosomal large subunit pseudouridine synthase E [Shigella
           dysenteriae 1012]
 gi|320179165|gb|EFW54123.1| 23S rRNA pseudouridine synthase E [Shigella boydii ATCC 9905]
 gi|320201031|gb|EFW75615.1| 23S rRNA pseudouridine synthase E [Escherichia coli EC4100B]
 gi|323153177|gb|EFZ39441.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           EPECa14]
 gi|323163679|gb|EFZ49501.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           E128010]
 gi|323172488|gb|EFZ58125.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           LT-68]
 gi|323179329|gb|EFZ64899.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           1180]
 gi|332092949|gb|EGI98017.1| ribosomal large subunit pseudouridine synthase E [Shigella
           dysenteriae 155-74]
 gi|333004972|gb|EGK24492.1| ribosomal large subunit pseudouridine synthase E [Shigella flexneri
           VA-6]
 gi|333008367|gb|EGK27841.1| ribosomal large subunit pseudouridine synthase E [Shigella flexneri
           K-272]
 gi|333019854|gb|EGK39126.1| ribosomal large subunit pseudouridine synthase E [Shigella flexneri
           K-227]
          Length = 177

 Score = 93.7 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 40/145 (27%), Positives = 67/145 (46%), Gaps = 15/145 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LTN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ + 
Sbjct: 33  YAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLN 92

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +    +W+ + L EG+NR+++++     +   
Sbjct: 93  DGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTL 152

Query: 214 RLIRISYGPFQLGTLLAGSTREVSK 238
           RLIR + G + L  L  G  REV+ 
Sbjct: 153 RLIRYAMGDYSLDNLANGEWREVTD 177


>gi|297578742|ref|ZP_06940670.1| pseudouridine synthase family 1 protein [Vibrio cholerae RC385]
 gi|297536336|gb|EFH75169.1| pseudouridine synthase family 1 protein [Vibrio cholerae RC385]
          Length = 275

 Score = 93.7 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 48/187 (25%), Positives = 79/187 (42%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER  +        L         ++            V + GRLD ++EGLL+L
Sbjct: 91  RPLSPAERKVILFNKPYDTLSQFTDGDGRKTLADYI---PIKDVYAAGRLDRDSEGLLIL 147

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 148 TNDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 207

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + L EG+NR+++++     +   RLIR S G + LG L  
Sbjct: 208 LWPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQP 267

Query: 231 GSTREVS 237
           G  +EV+
Sbjct: 268 GEWQEVT 274


>gi|254225530|ref|ZP_04919140.1| pseudouridine synthase family 1 protein [Vibrio cholerae V51]
 gi|125622000|gb|EAZ50324.1| pseudouridine synthase family 1 protein [Vibrio cholerae V51]
          Length = 275

 Score = 93.7 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 48/187 (25%), Positives = 79/187 (42%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER  +        L         ++            V + GRLD ++EGLL+L
Sbjct: 91  RPLSPAERKVILFNKPYDTLSQFTDGDGRKTLADYI---PIKDVYAAGRLDRDSEGLLIL 147

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 148 TNDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 207

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + L EG+NR+++++     +   RLIR S G + LG L  
Sbjct: 208 LWPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQP 267

Query: 231 GSTREVS 237
           G  +EV+
Sbjct: 268 GEWQEVT 274


>gi|86607580|ref|YP_476342.1| RNA pseudouridine synthase family protein [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86556122|gb|ABD01079.1| RNA pseudouridine synthase family protein [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 226

 Score = 93.7 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 56/188 (29%), Positives = 91/188 (48%), Gaps = 17/188 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R   ++KP G++T  +D +GR T+   +P        VGRLD ++EGLLLLT+DG L   
Sbjct: 29  RYLKFYKPYGVLTQFTDREGRPTLQSFIPVPRV--YPVGRLDRDSEGLLLLTDDGRLNAR 86

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------- 184
           L  P     R+Y V+  G      L  L++G++IQG      QV +  ++          
Sbjct: 87  LIDPKFGHERIYWVQVEGIPTPQALQQLQQGLIIQGRKTRPAQVKVLAEEPTLPPRDPPI 146

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
                    W+ + LREG+NR+++++         RL+R+  GP  L  L  G  +++S+
Sbjct: 147 RFRRSIPTTWLELTLREGRNRQVRRMTAAVGIPTLRLVRVGLGPLSLAGLAPGQWQDLSE 206

Query: 239 KILREQLG 246
             L +   
Sbjct: 207 VELAQLRQ 214


>gi|284052916|ref|ZP_06383126.1| pseudouridine synthase, Rsu [Arthrospira platensis str. Paraca]
 gi|291569841|dbj|BAI92113.1| probable pseudouridine synthase [Arthrospira platensis NIES-39]
          Length = 193

 Score = 93.7 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 50/187 (26%), Positives = 83/187 (44%), Gaps = 17/187 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
            R  L++KP  +++  +D D  +     L          SVGRLD+++EGLLLLT+D  L
Sbjct: 3   YRYILFYKPYNVLSQFTDRDSHAQSRQTLKDYIPIPSVYSVGRLDLDSEGLLLLTDDRKL 62

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---------- 180
              L  P     R Y V+         L  L++GI IQ       +V L           
Sbjct: 63  KYRLGQPEFAHPRTYWVQVERIPTTQALEQLRQGITIQNYRTRTARVQLLLTEPLLPPRI 122

Query: 181 -----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                 Q    AW+ + L EG+NR+++++     +   RL+R++     L +L  G  R+
Sbjct: 123 PPIRFRQNVPTAWLEITLTEGRNRQVRRMTAAVGFPTLRLVRVAIAHLTLNSLEPGHWRD 182

Query: 236 VSKKILR 242
           +  + ++
Sbjct: 183 LHPQEIQ 189


>gi|329577701|gb|EGG59128.1| pseudouridylate synthase [Enterococcus faecalis TX1467]
          Length = 197

 Score = 93.7 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 52/197 (26%), Positives = 86/197 (43%), Gaps = 2/197 (1%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L      +                       +  VGRLD +TEGLLLLT++G L   L 
Sbjct: 1   MLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQLGYQLI 60

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTVGLR 194
            P+ +  + Y V+ +G V  +     K GIV+QG       ++T+     + + V + ++
Sbjct: 61  RPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHVFLTIQ 120

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLLEEA 253
           EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L    +E+ 
Sbjct: 121 EGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYFFIEKQ 180

Query: 254 QVNLDAPIYSSETLVRD 270
           Q +   P        R 
Sbjct: 181 QTSKALPSNLKREEERK 197


>gi|257482196|ref|ZP_05636237.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. tabaci ATCC 11528]
 gi|289625808|ref|ZP_06458762.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. aesculi str. NCPPB3681]
 gi|289648408|ref|ZP_06479751.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. aesculi str. 2250]
 gi|330867203|gb|EGH01912.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. aesculi str. 0893_23]
 gi|330871091|gb|EGH05800.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. aesculi str. 0893_23]
 gi|330887918|gb|EGH20579.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. mori str. 301020]
 gi|331011340|gb|EGH91396.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. tabaci ATCC 11528]
          Length = 210

 Score = 93.7 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 49/185 (26%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L+L++KP  ++T  SD  GR+T+ D +          GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPKLFLFNKPFDVLTQFSDEGGRATLKDFIKIPGI--YPAGRLDRDSEGLLLLTNDG 84

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+   ++L  L+ G+ +        +            
Sbjct: 85  QLQARIADPKHKLAKTYWVQVEGEPTDEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPR 144

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  R
Sbjct: 145 NPPVRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLDQGQYR 204

Query: 235 EVSKK 239
           EV+ K
Sbjct: 205 EVAAK 209


>gi|205373779|ref|ZP_03226581.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           coahuilensis m4-4]
          Length = 125

 Score = 93.7 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 29/95 (30%), Positives = 47/95 (49%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA +GIASRR+ E +I + +VKVNG++++     V   D +EV+GV + + E+ 
Sbjct: 2   ERLQKVIAHSGIASRRKSEELIVEGKVKVNGVIVKELGTKVGPNDTVEVEGVKVEREEKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
              LY     +     D D +              
Sbjct: 62  YFLLYKPRGVISAVRDDKDRKVVTDFFPHIQERIY 96


>gi|269960959|ref|ZP_06175328.1| pseudouridine synthase family 1 protein [Vibrio harveyi 1DA3]
 gi|269834178|gb|EEZ88268.1| pseudouridine synthase family 1 protein [Vibrio harveyi 1DA3]
          Length = 236

 Score = 93.7 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 50/187 (26%), Positives = 90/187 (48%), Gaps = 16/187 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E  ++ +++KP   ++  +D DGR T+ D +P     V + GRLD ++EGL++L
Sbjct: 49  KPRIAPEDRKVIIFNKPYDTLSQFTDGDGRKTLADYIP--VKDVYAAGRLDRDSEGLMVL 106

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   ++ L  L+KG+ ++       +V +  +  
Sbjct: 107 TNDGILQAKLTQPQSKSPKTYWVQVDGAPTEEDLEKLRKGVELKDGMTLPAKVEVMPEPE 166

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + + EG+NR+++++     +   RL+R S G   L  L  
Sbjct: 167 IWDRTPPVRFRANIPTTWLAITITEGRNRQVRRMTAHIGFPTLRLVRYSMGGIVLDDLKP 226

Query: 231 GSTREVS 237
           G  RE+ 
Sbjct: 227 GEWREIK 233


>gi|70732728|ref|YP_262491.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           fluorescens Pf-5]
 gi|68347027|gb|AAY94633.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           fluorescens Pf-5]
          Length = 212

 Score = 93.7 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 37/142 (26%), Positives = 66/142 (46%), Gaps = 14/142 (9%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              GRLD ++EGLLLLTNDG L   +  P  +  + Y V+  G+   ++L  L++G+ + 
Sbjct: 67  YPAGRLDRDSEGLLLLTNDGQLQARIADPKHKLAKTYWVQVEGEPSAEQLQRLREGVQLN 126

Query: 169 GICYGDMQVTLD--------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                  +                   +    +W+ + +REG+NR+++++         R
Sbjct: 127 DGMTLPAEARQLEEPTLWPRNPPVRFRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLR 186

Query: 215 LIRISYGPFQLGTLLAGSTREV 236
           L+R+  G + L  L  G  +EV
Sbjct: 187 LVRVRIGDWTLDGLEQGQWKEV 208


>gi|194437055|ref|ZP_03069154.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           101-1]
 gi|194424038|gb|EDX40026.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           101-1]
          Length = 177

 Score = 93.3 bits (230), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 38/145 (26%), Positives = 67/145 (46%), Gaps = 15/145 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LTN+G L   L  P  +  ++Y V+  G   QD +  L+ G+ + 
Sbjct: 33  YAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGFPTQDAIEALRNGVTLN 92

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +    +W+ + L EG+NR+++++     +   
Sbjct: 93  DGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTL 152

Query: 214 RLIRISYGPFQLGTLLAGSTREVSK 238
           RLIR + G + L  L  G  RE ++
Sbjct: 153 RLIRYAMGDYTLDNLANGEWREATE 177


>gi|170768017|ref|ZP_02902470.1| ribosomal large subunit pseudouridine synthase E [Escherichia
           albertii TW07627]
 gi|170122783|gb|EDS91714.1| ribosomal large subunit pseudouridine synthase E [Escherichia
           albertii TW07627]
          Length = 207

 Score = 93.3 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 49/184 (26%), Positives = 87/184 (47%), Gaps = 17/184 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+LTN+G 
Sbjct: 26  NQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVLTNNGA 83

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-------------- 175
           L   L  P  +  ++Y V+  G   QD L  L+ G+ +                      
Sbjct: 84  LQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGVELVTEPEWLWPR 143

Query: 176 -QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R
Sbjct: 144 NPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGNYTLDNLANGEWR 203

Query: 235 EVSK 238
           E ++
Sbjct: 204 EATE 207


>gi|229529771|ref|ZP_04419161.1| ribosomal large subunit pseudouridine synthase E [Vibrio cholerae
           12129(1)]
 gi|229333545|gb|EEN99031.1| ribosomal large subunit pseudouridine synthase E [Vibrio cholerae
           12129(1)]
          Length = 244

 Score = 93.3 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 48/187 (25%), Positives = 80/187 (42%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER  +        L         ++            V + GRLD ++EGLL+L
Sbjct: 60  RPLSPAERKVILFNKPYDTLSQFTDGDGRKTLADYI---PIKDVYAAGRLDRDSEGLLIL 116

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G++++       +V +  +  
Sbjct: 117 TNDGILQARLTQPQSKAPKTYWVQVEGSPQESDLEALRHGVILKDGPTLPAKVDIMPEPT 176

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + L EG+NR+++++     +   RLIR S G + LG L  
Sbjct: 177 LWPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQP 236

Query: 231 GSTREVS 237
           G  +EV+
Sbjct: 237 GEWQEVT 243


>gi|261210699|ref|ZP_05924991.1| ribosomal large subunit pseudouridine synthase E [Vibrio sp. RC341]
 gi|260840184|gb|EEX66764.1| ribosomal large subunit pseudouridine synthase E [Vibrio sp. RC341]
          Length = 154

 Score = 93.3 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 41/143 (28%), Positives = 69/143 (48%), Gaps = 14/143 (9%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LTNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++
Sbjct: 11  YAAGRLDRDSEGLLILTNDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLK 70

Query: 169 GICYGDMQVTLDTQ--------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                  +V +  +                   W+ + L EG+NR+++++     +   R
Sbjct: 71  DGPTLPAKVEIMPEPTLWPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLR 130

Query: 215 LIRISYGPFQLGTLLAGSTREVS 237
           LIR S G + LG L  G  +EV+
Sbjct: 131 LIRYSMGDWNLGDLQPGEWQEVT 153


>gi|37526692|ref|NP_930036.1| hypothetical protein plu2802 [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|36786124|emb|CAE15176.1| unnamed protein product [Photorhabdus luminescens subsp. laumondii
           TTO1]
          Length = 210

 Score = 93.3 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 53/185 (28%), Positives = 93/185 (50%), Gaps = 17/185 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +  E  R+ +++KP  ++   +D  GR+T+ D +P  F  V + GRLD ++EGLL+LTND
Sbjct: 26  KPIEPRRVLIFNKPYDVLPQFTDEMGRTTLKDFIP--FPNVYAAGRLDRDSEGLLILTND 83

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P  +  +VY V+  G  D+  L+ L+ GI+++                   
Sbjct: 84  GKLQAQLTQPHKKTAKVYYVQVEGVPDEISLDKLRNGIILKDGPTLPAGVELVHEPTWLW 143

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ + L EG+NR+++++     +   RLIR S G   LG +  G 
Sbjct: 144 SRHPPIRERKNIPVSWLKITLYEGRNRQVRRMTAHIGFPTLRLIRFSMGNLPLGKMKPGE 203

Query: 233 TREVS 237
            +E++
Sbjct: 204 WKEIN 208


>gi|325925904|ref|ZP_08187273.1| ribosomal large subunit pseudouridine synthase E [Xanthomonas
           perforans 91-118]
 gi|325543735|gb|EGD15149.1| ribosomal large subunit pseudouridine synthase E [Xanthomonas
           perforans 91-118]
          Length = 190

 Score = 93.3 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 48/175 (27%), Positives = 82/175 (46%), Gaps = 15/175 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L +KP G+++  SD             +   V + GRLD ++EGLLLLT+DG LA  L
Sbjct: 2   LVLLNKPYGVLSQFSDRSQPPKRTLAEFGLPPDVYAAGRLDHDSEGLLLLTDDGALAHRL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y V+  G    ++L  L+ G+V+        QV +               
Sbjct: 62  TDPRHKQPKTYWVQVEGAPQPEQLQALRDGVVLNDGPTRPAQVRMLDQAPQLWPRDPPVR 121

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +   +AW+ + + EG+NR+++++         RL+R++ G ++L  L  G  R
Sbjct: 122 VRKTVPDAWLELQITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLDALAPGQWR 176


>gi|145580106|pdb|2OML|A Chain A, Crystal Structure Of E. Coli Pseudouridine Synthase Rlue
          Length = 189

 Score = 93.3 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 88/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 3   RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 60

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 61  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPA 120

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 121 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 180

Query: 230 AGSTREVSK 238
            G  REV+ 
Sbjct: 181 NGEWREVTD 189


>gi|331004981|ref|ZP_08328391.1| pseudouridine synthase [gamma proteobacterium IMCC1989]
 gi|330421223|gb|EGG95479.1| pseudouridine synthase [gamma proteobacterium IMCC1989]
          Length = 237

 Score = 93.3 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 43/213 (20%), Positives = 79/213 (37%), Gaps = 36/213 (16%)

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
                 V   GRLD ++EGLLLLT+DG L + +  P  +  + Y V+  G+ + + +  L
Sbjct: 47  YIKQKHVYPAGRLDYDSEGLLLLTDDGALQQHISHPQYKLPKTYWVQVEGEQNLEAIIAL 106

Query: 162 KKGIVIQGICYGDM--------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
           +KG+ ++                           Q     W+++ + EGKNR+++++   
Sbjct: 107 RKGVELKDGLTKPALVEAIEEPDLWPRNPPVRFRQSIPTHWLSITISEGKNRQVRRMTAA 166

Query: 208 FNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETL 267
                 RL+R S G + L  L  G  R +                      A        
Sbjct: 167 VGLPTLRLVRASIGDWTLEGLQPGEHRSI----------------------AVPSPPNQP 204

Query: 268 VRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           ++ +            +   N++ K+   K K+
Sbjct: 205 IKTKNKAGKPKAHRTRKSANNTNAKDKKGKHKR 237


>gi|298489014|ref|ZP_07007037.1| tRNA pseudouridine synthase A [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|298156512|gb|EFH97609.1| tRNA pseudouridine synthase A [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
          Length = 210

 Score = 93.3 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 49/185 (26%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L+L++KP  ++T  SD  GR+T+ D +          GRLD ++EGLLLLTNDG
Sbjct: 27  PTAEPKLFLFNKPFDVLTQFSDEGGRATLKDFIKIPGI--YPAGRLDRDSEGLLLLTNDG 84

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+   ++L  L+ G+ +        +            
Sbjct: 85  QLQARIADPKHKLAKTYWVQVEGEPTDEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPR 144

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  R
Sbjct: 145 NPPVRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLDQGQYR 204

Query: 235 EVSKK 239
           EV+ K
Sbjct: 205 EVAAK 209


>gi|112490799|pdb|2GML|A Chain A, Crystal Structure Of Catalytic Domain Of E.Coli Rluf
 gi|112490800|pdb|2GML|B Chain B, Crystal Structure Of Catalytic Domain Of E.Coli Rluf
          Length = 237

 Score = 93.3 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 43/228 (18%), Positives = 83/228 (36%), Gaps = 4/228 (1%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L      +    +  DG      +  +   RV  +GRLD +++GL+ LTN G L   +
Sbjct: 14  LVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKI 73

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y V     + ++ +     G+ I G            +K +     + L 
Sbjct: 74  LRAGNDHEKEYLVTVDKPITEEFIRGXSAGVPILGTV----TKKCKVKKEAPFVFRITLV 129

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I++  E F ++V +L R       L  +  G  R+++   L +         ++
Sbjct: 130 QGLNRQIRRXCEHFGYEVKKLERTRIXNVSLSGIPLGEWRDLTDDELIDLFKLIENSSSE 189

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           V   A        ++       +  +   R   N  +     ++KK  
Sbjct: 190 VKPKAKAKPKTAGIKRPVVKXEKTAEKGGRPASNGKRFTSPGRKKKGR 237


>gi|213966827|ref|ZP_03394978.1| Pseudouridine synthase, Rsu [Pseudomonas syringae pv. tomato T1]
 gi|301381958|ref|ZP_07230376.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. tomato Max13]
 gi|302058781|ref|ZP_07250322.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. tomato K40]
 gi|213928677|gb|EEB62221.1| Pseudouridine synthase, Rsu [Pseudomonas syringae pv. tomato T1]
          Length = 210

 Score = 93.3 bits (230), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 49/185 (26%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  SD +GR+T+ D +          GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPKLILFNKPFDVLTQFSDEEGRATLKDFIKIPGI--YPAGRLDRDSEGLLLLTNDG 84

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+   ++L  L+ G+ +        +            
Sbjct: 85  QLQARIADPKHKLAKTYWVQVEGEPTPEQLQQLRNGVQLNDGPTLPAEARQLDEPQLWPR 144

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  R
Sbjct: 145 NPPVRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLDQGQYR 204

Query: 235 EVSKK 239
           EV+ K
Sbjct: 205 EVAAK 209


>gi|260433638|ref|ZP_05787609.1| ribosomal large subunit pseudouridine synthase E [Silicibacter
           lacuscaerulensis ITI-1157]
 gi|260417466|gb|EEX10725.1| ribosomal large subunit pseudouridine synthase E [Silicibacter
           lacuscaerulensis ITI-1157]
          Length = 205

 Score = 93.3 bits (230), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 35/143 (24%), Positives = 62/143 (43%), Gaps = 15/143 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              GRLD ++EGL+LLT++G L   +  P  +  + Y V+  G  D   +  L+ G+ + 
Sbjct: 44  YPAGRLDRDSEGLMLLTDNGRLQSHISDPKHKMPKTYWVQVEGIPDAAAIRALRDGVELN 103

Query: 169 GICYGDMQ---------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +                  + +   + W+ + LREG+NR+++++         
Sbjct: 104 DGMTRPAKARLIDEPEGLWPRTPPIRERKTVPDCWLELTLREGRNRQVRRMTAAVGHPTL 163

Query: 214 RLIRISYGPFQLGTLLAGSTREV 236
           RLIR   G + L  L  GS   +
Sbjct: 164 RLIRARIGDWTLDDLAPGSWDSL 186


>gi|145639451|ref|ZP_01795056.1| hypothetical protein CGSHiII_04737 [Haemophilus influenzae PittII]
 gi|145271498|gb|EDK11410.1| hypothetical protein CGSHiII_04737 [Haemophilus influenzae PittII]
          Length = 227

 Score = 92.9 bits (229), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 77/196 (39%), Gaps = 17/196 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L   E   +                D +             V + GRLD ++EGLL+L
Sbjct: 31  KTLSLDETKVVLFNKP---FDVLTQFTDEQGRATLKDFISIPNVYAAGRLDRDSEGLLIL 87

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TN+G L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +        
Sbjct: 88  TNNGELQHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKPAKVRLISEPN 147

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  
Sbjct: 148 LWERNPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGLLSINGLEN 207

Query: 231 GSTREVSKKILREQLG 246
           GS R +S   ++    
Sbjct: 208 GSFRLLSLDEIKALFQ 223


>gi|284920961|emb|CBG34024.1| ribosomal large subunit pseudouridine synthase E (rRNA
           pseudouridylate synthase E) [Escherichia coli 042]
          Length = 217

 Score = 92.9 bits (229), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 88/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 31  KRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 89  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGVELVDEPA 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 149 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 208

Query: 230 AGSTREVSK 238
            G  REV+ 
Sbjct: 209 NGEWREVTD 217


>gi|78485444|ref|YP_391369.1| pseudouridine synthase, Rsu [Thiomicrospira crunogena XCL-2]
 gi|78363730|gb|ABB41695.1| ribosomal large subunit pseudouridine synthase E [Thiomicrospira
           crunogena XCL-2]
          Length = 185

 Score = 92.9 bits (229), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 43/175 (24%), Positives = 81/175 (46%), Gaps = 17/175 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
           L L++KP  ++   +D          L    ++    + GRLD ++EGLLLLTNDG L +
Sbjct: 4   LLLFNKPFNVLCQFTDEPEFKDQRQTLADFINQPGFYAAGRLDRDSEGLLLLTNDGKLQQ 63

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------V 177
            +  P  +  + Y V+  G ++++ +  L++G+ ++       +                
Sbjct: 64  HIANPKHKQPKTYLVQVEGDINKEAIKQLQQGVTLKDGLTRPAKARKIPEPKWLWPRNPP 123

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
             + +    +WV + + EGKNR+++++     +   RLIR   G +QL  L  G 
Sbjct: 124 IRERKNIPTSWVELIITEGKNRQVRRMTAAVGFPTLRLIRTQIGDYQLKNLQPGE 178


>gi|330963493|gb|EGH63753.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. actinidiae str. M302091]
          Length = 210

 Score = 92.9 bits (229), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 49/185 (26%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  SD +GR+T+ D +          GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPKLILFNKPFDVLTQFSDEEGRATLKDFIKIPGI--YPAGRLDRDSEGLLLLTNDG 84

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+   ++L  L+ G+ +        +            
Sbjct: 85  QLQARIADPKHKLAKTYWVQVEGEPTPEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPR 144

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  R
Sbjct: 145 NPPVRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLDQGQYR 204

Query: 235 EVSKK 239
           EV+ K
Sbjct: 205 EVAAK 209


>gi|224584255|ref|YP_002638053.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Paratyphi C strain
           RKS4594]
 gi|224468782|gb|ACN46612.1| putative ribosomal large subunit pseudouridine synthase B
           [Salmonella enterica subsp. enterica serovar Paratyphi C
           strain RKS4594]
          Length = 245

 Score = 92.9 bits (229), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 51/187 (27%), Positives = 88/187 (47%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLL+LTND
Sbjct: 58  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIPVQGV--YAAGRLDCDSEGLLVLTND 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P  +  ++Y V+  G  D   L  L+ G+ +                    
Sbjct: 116 GVLQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 175

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G 
Sbjct: 176 PRTPPIRERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQ 235

Query: 233 TREVSKK 239
            RE++++
Sbjct: 236 WREIAQE 242


>gi|238749634|ref|ZP_04611139.1| Ribosomal large subunit pseudouridine synthase E [Yersinia rohdei
           ATCC 43380]
 gi|238712289|gb|EEQ04502.1| Ribosomal large subunit pseudouridine synthase E [Yersinia rohdei
           ATCC 43380]
          Length = 208

 Score = 92.9 bits (229), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 54/185 (29%), Positives = 93/185 (50%), Gaps = 17/185 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           + A   R+ L++KP  ++   +D  GR+T+   +P  F+ V + GRLD ++EGLL+LTND
Sbjct: 24  KPASPRRVLLFNKPFDVLPQFTDESGRTTLKGFIP--FTDVYAAGRLDRDSEGLLVLTND 81

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P+ +  +VY V+  G    D L+ L++G+V++                   
Sbjct: 82  GKLQAKLTQPAQKTGKVYFVQVEGTPGDDALSQLRQGMVLKDGPTLPAGAELVDEPEWLW 141

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +     W+ + L EG+NR+++++     +   RLIR S G   LG L  G 
Sbjct: 142 PRNPPIRERKTIPTCWMKITLFEGRNRQVRRMTAHIGFPTLRLIRFSMGNLSLGDLKPGE 201

Query: 233 TREVS 237
            +E++
Sbjct: 202 WKEIN 206


>gi|52426397|ref|YP_089534.1| RsuA protein [Mannheimia succiniciproducens MBEL55E]
 gi|52308449|gb|AAU38949.1| RsuA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 247

 Score = 92.9 bits (229), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 41/193 (21%), Positives = 75/193 (38%), Gaps = 18/193 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L  +E   +                D               V + GRLD ++EGLL+L
Sbjct: 47  KQLAFSETQVILFNKP---FDVLTQFTDENGRATLKDFIHIPDVYAAGRLDRDSEGLLIL 103

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TN+G +   L  P  +  + Y V+  G+  +  L  L++G+ ++       +        
Sbjct: 104 TNNGEIQHRLADPKFKMEKTYFVQVEGEPTETDLAKLRQGVELKDGMTRPAKVRLIAQPD 163

Query: 177 -------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + + EGKNR+++++     +   RLIR +   F L  L 
Sbjct: 164 FIWQRTPPIRERKSIPTSWLEIKISEGKNRQVRRMTANIGFPTLRLIRYAVSSFTLDNLA 223

Query: 230 AGSTREVSKKILR 242
            GS R ++   L 
Sbjct: 224 NGSYRLLTDNELE 236


>gi|170660219|ref|YP_001740062.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. tomato str. DC3000]
 gi|170652969|gb|ACB22025.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. tomato str. DC3000]
 gi|331014769|gb|EGH94825.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. lachrymans str. M302278PT]
          Length = 210

 Score = 92.9 bits (229), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 49/185 (26%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  SD +GR+T+ D +          GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPKLILFNKPFDVLTQFSDEEGRATLKDFIKIPGI--YPAGRLDRDSEGLLLLTNDG 84

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+   ++L  L+ G+ +        +            
Sbjct: 85  QLQARIADPKHKLAKTYWVQVEGEPTPEQLQQLRNGVQLNDGPTLPAEARQLDEPQLWPR 144

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  R
Sbjct: 145 NPPVRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLDQGQYR 204

Query: 235 EVSKK 239
           EV+ K
Sbjct: 205 EVAAK 209


>gi|21229751|ref|NP_635668.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66766627|ref|YP_241389.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. 8004]
 gi|34098585|sp|Q8PDR2|RLUE_XANCP RecName: Full=Ribosomal large subunit pseudouridine synthase E;
           AltName: Full=rRNA pseudouridylate synthase E; AltName:
           Full=rRNA-uridine isomerase E
 gi|21111241|gb|AAM39592.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66571959|gb|AAY47369.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. 8004]
          Length = 187

 Score = 92.9 bits (229), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 48/183 (26%), Positives = 82/183 (44%), Gaps = 15/183 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L +KP G+++  SD             +  +V + GRLD ++EGLLLLT+DG LA  L
Sbjct: 2   LVLLNKPYGVLSQFSDRSTPPKRTLAEFGLPPQVYAAGRLDHDSEGLLLLTDDGPLAHRL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------QVTL 179
             P  +  + Y V+  G  D  +L  L  G+++                           
Sbjct: 62  TDPRHKQPKTYWVQVEGDPDTSQLQALCDGVLLNDGPTRPANVRRLECAPTLWPRDPPVR 121

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +   +AW+ V + EG+NR+++++         RL+R++ G + L +L  G  R    +
Sbjct: 122 VRKTVPDAWLEVQITEGRNRQVRRMTASVGLPTLRLVRVAIGAWSLASLQPGQWRVDDAR 181

Query: 240 ILR 242
            +R
Sbjct: 182 AVR 184


>gi|327483844|gb|AEA78251.1| Ribosomal large subunit pseudouridine synthase E LSU Psi2457
           [Vibrio cholerae LMA3894-4]
          Length = 241

 Score = 92.9 bits (229), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 48/187 (25%), Positives = 80/187 (42%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER  +        L         ++            V + GRLD ++EGLL+L
Sbjct: 57  RPLSPAERKVILFNKPYDTLSQFTDGDGRKTLADYI---PIKDVYAAGRLDRDSEGLLIL 113

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G++++       +V +  +  
Sbjct: 114 TNDGILQARLTQPQSKAPKTYWVQVEGSPQESDLEALRHGVILKDGPTLPAKVDIMPEPT 173

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + L EG+NR+++++     +   RLIR S G + LG L  
Sbjct: 174 LWPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQP 233

Query: 231 GSTREVS 237
           G  +EV+
Sbjct: 234 GEWQEVT 240


>gi|330873550|gb|EGH07699.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. morsprunorum str. M302280PT]
          Length = 210

 Score = 92.9 bits (229), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 49/185 (26%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  SD +GR+T+ D +          GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPKLILFNKPFDVLTQFSDEEGRATLKDFIKIPGI--YPAGRLDRDSEGLLLLTNDG 84

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+   ++L  L+ G+ +        +            
Sbjct: 85  QLQARIADPKHKLAKTYWVQVEGEPTPEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPR 144

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  R
Sbjct: 145 NPPVRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLDQGQYR 204

Query: 235 EVSKK 239
           EV+ K
Sbjct: 205 EVAAK 209


>gi|113461776|ref|YP_719845.1| ribosomal large subunit pseudouridine synthase E [Haemophilus
           somnus 129PT]
 gi|112823819|gb|ABI25908.1| ribosomal large subunit pseudouridine synthase E [Haemophilus
           somnus 129PT]
          Length = 215

 Score = 92.9 bits (229), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 49/194 (25%), Positives = 88/194 (45%), Gaps = 16/194 (8%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +T++ L++KP  ++   +D  GR+T+ D +      +  VGRLD ++EGLLLLTN+G L 
Sbjct: 23  QTKVILFNKPFDVLCQFTDEQGRATLKDFIKIP--HIYPVGRLDRDSEGLLLLTNNGELQ 80

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------------V 177
             L  P  +  + Y V+  G   +  L  L+KGI +        +               
Sbjct: 81  HRLTNPKFKMEKTYWVQIEGIPVETDLAQLRKGIELNDGLTKPAKVRLISEPNIWQRHPP 140

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + + EG+NR+++++     +   RLIR       L  L+ G  RE++
Sbjct: 141 IRERKTVPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLIRYETAGLTLTNLVNGQFRELT 200

Query: 238 KKILREQLGPHLLE 251
              L+         
Sbjct: 201 LTELQNLYQQVKKS 214


>gi|256822323|ref|YP_003146286.1| pseudouridine synthase [Kangiella koreensis DSM 16069]
 gi|256795862|gb|ACV26518.1| pseudouridine synthase [Kangiella koreensis DSM 16069]
          Length = 203

 Score = 92.9 bits (229), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 40/168 (23%), Positives = 70/168 (41%), Gaps = 14/168 (8%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              GRLD ++EGLLLLT+DG L   +  P  +  + Y V+  G  + ++L  L+ G++IQ
Sbjct: 36  YPAGRLDKDSEGLLLLTDDGQLQNQIASPKHKMEKTYWVQVEGVPEDNELEPLRLGVIIQ 95

Query: 169 GICYGDMQ--------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                  +                 + +    +W+ + + EGKNR+++++     +   R
Sbjct: 96  NYKTKPAKVRLLETPEVWPRNPPIRERKNIPTSWLEITISEGKNRQVRRMTAAVGFPTLR 155

Query: 215 LIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIY 262
           LIR   G +QL  L  G  + +     +   GP               
Sbjct: 156 LIRAQIGQWQLDDLKVGEYKVIEVSTPKAMAGPRNKSTQSKRFSQRHK 203


>gi|255654430|ref|ZP_05399839.1| putative RNA pseudouridine synthase [Clostridium difficile
           QCD-23m63]
          Length = 103

 Score = 92.9 bits (229), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 22/99 (22%), Positives = 47/99 (47%), Gaps = 3/99 (3%)

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
             +  G V ++ +    +G+V+         Q+ +  +    + + + + EGK  ++K++
Sbjct: 1   MTKIDGVVTEEDVEAFLEGVVLDDGYKTMPSQLNIL-KSDDESEIELTIHEGKFHQVKRM 59

Query: 205 FEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           FE    KV  L R+S G  +L   L  G  RE++ + ++
Sbjct: 60  FESVGKKVVYLKRLSMGNLKLDESLELGEYRELTDEEIK 98


>gi|319794805|ref|YP_004156445.1| pseudouridine synthase [Variovorax paradoxus EPS]
 gi|315597268|gb|ADU38334.1| pseudouridine synthase [Variovorax paradoxus EPS]
          Length = 182

 Score = 92.9 bits (229), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 46/177 (25%), Positives = 80/177 (45%), Gaps = 17/177 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL  ++KP G+++  +       + D +      V   GRLD ++EGLLLLTNDG L   
Sbjct: 8   RLIRFNKPYGVLSQFTPEGRWRGLKDFIDIP--DVYVAGRLDADSEGLLLLTNDGQLQAR 65

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------VT 178
           +  P  +  + Y V+  G   ++ L  L++G+ +        +                 
Sbjct: 66  IADPRFKMEKTYWVQVEGVPTEEALAALRQGVQLNDGLTRPARASLLDPPPDVWPRQPPI 125

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
            + +    AW+ + + EG+NR+++++         RLIR + GP  L  L  G+ RE
Sbjct: 126 RERKSIPTAWLELAISEGRNRQVRRMTAAVGLPTLRLIRAAIGPHTLDGLAPGTWRE 182


>gi|254511085|ref|ZP_05123152.1| ribosomal large subunit pseudouridine synthase E [Rhodobacteraceae
           bacterium KLH11]
 gi|221534796|gb|EEE37784.1| ribosomal large subunit pseudouridine synthase E [Rhodobacteraceae
           bacterium KLH11]
          Length = 201

 Score = 92.9 bits (229), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 35/143 (24%), Positives = 62/143 (43%), Gaps = 15/143 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              GRLD ++EGL++LT+ G L   +  P  +  + Y V+  G+ D   L  L+ G+ ++
Sbjct: 40  YPAGRLDRDSEGLMVLTDHGRLQAQISDPRHKMAKTYWVQVEGRPDAAALKALQDGVELK 99

Query: 169 GICYGDMQ---------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +                    Q   ++W+ + LREG+NR+++++         
Sbjct: 100 DGLTRPAKALMINEPKGLWPRNPPIRVRQTIPDSWIELTLREGRNRQVRRMTAAVGHPTL 159

Query: 214 RLIRISYGPFQLGTLLAGSTREV 236
           RLIR   G + L  L  G    +
Sbjct: 160 RLIRARIGDWSLDGLAPGQWESL 182


>gi|71279927|ref|YP_269599.1| ribosomal large subunit pseudouridine synthase E [Colwellia
           psychrerythraea 34H]
 gi|71145667|gb|AAZ26140.1| ribosomal large subunit pseudouridine synthase E [Colwellia
           psychrerythraea 34H]
          Length = 201

 Score = 92.9 bits (229), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 43/184 (23%), Positives = 82/184 (44%), Gaps = 16/184 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                 E+  + L++KP  ++   +D + R T+ D +        + GRLD ++EGLLLL
Sbjct: 17  KVRPLDEKQIVVLFNKPFDVLCQFTDENNRRTLKDFITIPGI--YAAGRLDRDSEGLLLL 74

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   +  P  +  + Y V+  G   +  L  L++G+ ++       +V +  +  
Sbjct: 75  TNDGKLQHQIANPVKKTEKTYWVQIEGAPSEQDLAKLRQGVELKDGMTKPAKVAIMLEPN 134

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + + EG+NR+++++     +   RLIR   G + L  +  
Sbjct: 135 VWPRNPPIRERASIPTTWLEITITEGRNRQVRRMTANIGFPTLRLIRYRIGNWTLDNINN 194

Query: 231 GSTR 234
           G  +
Sbjct: 195 GEYK 198


>gi|68249271|ref|YP_248383.1| pseudouridylate synthase [Haemophilus influenzae 86-028NP]
 gi|68057470|gb|AAX87723.1| ribosomal large subunit pseudouridine synthase E [Haemophilus
           influenzae 86-028NP]
          Length = 227

 Score = 92.9 bits (229), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 42/192 (21%), Positives = 77/192 (40%), Gaps = 17/192 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L   E   +                D +             V + GRLD ++EGLL+L
Sbjct: 31  KTLSLDETKVVLFNKP---FDVLTQFTDEQGRATLKDFISIPNVYAAGRLDRDSEGLLIL 87

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TN+G L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       Q        
Sbjct: 88  TNNGELQHRLSDPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGMTKQAQVRLISEPN 147

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  
Sbjct: 148 LWERNPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSIDGLAN 207

Query: 231 GSTREVSKKILR 242
           GS R +S   ++
Sbjct: 208 GSFRLLSLDEIK 219


>gi|84516902|ref|ZP_01004260.1| RNA pseudouridine synthase family protein [Loktanella vestfoldensis
           SKA53]
 gi|84509370|gb|EAQ05829.1| RNA pseudouridine synthase family protein [Loktanella vestfoldensis
           SKA53]
          Length = 183

 Score = 92.9 bits (229), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 40/178 (22%), Positives = 67/178 (37%), Gaps = 14/178 (7%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               L L      L               +       V   GRLD ++EGLL+LT+DG L
Sbjct: 1   MSRILLLNKPYGVLSQFTDARSPSPRPTLSGFVTVPGVYPAGRLDRDSEGLLVLTDDGAL 60

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---------- 180
              +  P  +  + Y V+  G      L LL+ G+ +        QV             
Sbjct: 61  QARIADPRHKLPKTYLVQVEGAPTDADLALLRHGVTLNDGPTRPAQVQRIAPPALWERDP 120

Query: 181 ----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                +   + W+ + + EG+NR+++++     +   RL+R   G + L  L  G+ R
Sbjct: 121 PVRFRKSVPDQWIEITIHEGRNRQVRRMTAHIGFPTLRLVRWQIGDWTLDGLAPGAWR 178


>gi|229847199|ref|ZP_04467303.1| hypothetical protein CGSHi7P49H1_08845 [Haemophilus influenzae
           7P49H1]
 gi|229809875|gb|EEP45597.1| hypothetical protein CGSHi7P49H1_08845 [Haemophilus influenzae
           7P49H1]
          Length = 227

 Score = 92.9 bits (229), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 43/196 (21%), Positives = 78/196 (39%), Gaps = 17/196 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L   E T +                D +             V + GRLD ++EGLL+L
Sbjct: 31  KTLSLDETTVVLFNKP---FDVLTQFTDEQGRATLKDFISIPNVYAAGRLDRDSEGLLIL 87

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TN+G L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       Q        
Sbjct: 88  TNNGELQHRLSDPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGMTKQAQVRLISEPN 147

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  
Sbjct: 148 LWERNPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSINGLEN 207

Query: 231 GSTREVSKKILREQLG 246
           GS R +S   ++    
Sbjct: 208 GSFRLLSLDEIKALFQ 223


>gi|331652186|ref|ZP_08353205.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Escherichia coli M718]
 gi|331050464|gb|EGI22522.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Escherichia coli M718]
          Length = 217

 Score = 92.5 bits (228), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 88/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 31  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 89  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPA 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 149 WLSPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLA 208

Query: 230 AGSTREVSK 238
            G  REV+ 
Sbjct: 209 NGEWREVTD 217


>gi|309788205|ref|ZP_07682811.1| ribosomal large subunit pseudouridine synthase E [Shigella
           dysenteriae 1617]
 gi|308924057|gb|EFP69558.1| ribosomal large subunit pseudouridine synthase E [Shigella
           dysenteriae 1617]
 gi|320175641|gb|EFW50733.1| 23S rRNA pseudouridine synthase E [Shigella dysenteriae CDC
           74-1112]
 gi|323165643|gb|EFZ51430.1| ribosomal large subunit pseudouridine synthase E [Shigella sonnei
           53G]
 gi|332094422|gb|EGI99471.1| ribosomal large subunit pseudouridine synthase E [Shigella boydii
           3594-74]
          Length = 177

 Score = 92.5 bits (228), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 39/145 (26%), Positives = 67/145 (46%), Gaps = 15/145 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LTN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ + 
Sbjct: 33  YAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLN 92

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +    +W+ + L EG+NR+++++     +   
Sbjct: 93  DGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTL 152

Query: 214 RLIRISYGPFQLGTLLAGSTREVSK 238
           RLIR + G + L  L  G  RE ++
Sbjct: 153 RLIRYAMGDYTLDNLANGEWREATE 177


>gi|163736511|ref|ZP_02143930.1| hypothetical protein RGBS107_15306 [Phaeobacter gallaeciensis
           BS107]
 gi|161390381|gb|EDQ14731.1| hypothetical protein RGBS107_15306 [Phaeobacter gallaeciensis
           BS107]
          Length = 232

 Score = 92.5 bits (228), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 46/220 (20%), Positives = 86/220 (39%), Gaps = 17/220 (7%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGG 129
            TRL  ++KP  ++   +D    S+    L        V   GRLD ++EGL+LLT+ G 
Sbjct: 1   MTRLIRFNKPYDVLPQFTDRGSDSSPRATLSDWIDLPGVYPAGRLDRDSEGLMLLTDHGR 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------- 180
           L   +  P  +  + Y V+  G  D   +  L  G+ ++       +  L          
Sbjct: 61  LQAWISDPQHKMPKTYWVQVEGTPDAAAIQALANGVELKDGMTRPAKAALIEEPEGIWAR 120

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +   ++W+ + +REG+NR+++++         RLIR + G + L  L  G+  
Sbjct: 121 NPPIRVRKSVPDSWIALTIREGRNRQVRRMTAAVGHPTLRLIRAAIGIWTLDGLSPGTWE 180

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNI 274
           ++    +     P      Q        +S+    +    
Sbjct: 181 DLEAPTIPGPPKPKPAPNRQAIARRKAAASKPARPESDAG 220


>gi|325276236|ref|ZP_08142031.1| pseudouridine synthase [Pseudomonas sp. TJI-51]
 gi|324098614|gb|EGB96665.1| pseudouridine synthase [Pseudomonas sp. TJI-51]
          Length = 181

 Score = 92.5 bits (228), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 52/180 (28%), Positives = 87/180 (48%), Gaps = 16/180 (8%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL L++KP  ++T  SD +GR+T+ D +          GRLD ++EGLLLLTNDGGL   
Sbjct: 1   RLILFNKPFDVLTQFSDGEGRATLKDFIDIPGV--YPAGRLDRDSEGLLLLTNDGGLQAR 58

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------- 180
           +  P  +  + Y V+  G+   ++L  L+ G+ +        +                 
Sbjct: 59  IADPKHKLAKTYWVQVEGEPSDEQLQRLRDGVELNDGPTLPAEARRLAEPALWPRNPPVR 118

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +    +W+ + +REG+NR+++++         RL+R+  G + L  L  G  REV  K
Sbjct: 119 FRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWALDGLEQGCWREVPAK 178


>gi|217031798|ref|ZP_03437301.1| hypothetical protein HPB128_199g6 [Helicobacter pylori B128]
 gi|216946450|gb|EEC25052.1| hypothetical protein HPB128_199g6 [Helicobacter pylori B128]
          Length = 208

 Score = 92.5 bits (228), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 49/211 (23%), Positives = 100/211 (47%), Gaps = 19/211 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +A     SRRE E+++ + RVK+N    +  A  V   D + +D   ++  +  
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAK-LASVVKENDKVFLDKRLIKPLKNK 59

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+L+L++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLILSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQV 177
             L        + Y V+  G V ++  N +++G+ ++                    +  
Sbjct: 120 SALMHA--NLEKEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
            +       + + V + EGKNRE+++ F  F
Sbjct: 178 EIIKNHAKYSKLRVVINEGKNRELRRFFVVF 208


>gi|332535580|ref|ZP_08411350.1| ribosomal large subunit pseudouridine synthase E [Pseudoalteromonas
           haloplanktis ANT/505]
 gi|332034998|gb|EGI71518.1| ribosomal large subunit pseudouridine synthase E [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 228

 Score = 92.5 bits (228), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 44/188 (23%), Positives = 84/188 (44%), Gaps = 16/188 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P   ++  ++ L++KP  ++   +D   R T+ + +P     V + GRLD ++EGLLLL
Sbjct: 39  KPQIASKDRKIVLFNKPFDVLCQFTDDADRKTLAEFIPIK--EVYAAGRLDRDSEGLLLL 96

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---- 180
           TN G L   L  P  +  + Y  +  G+   + +N L  G+ ++        V +     
Sbjct: 97  TNCGKLQNSLTAPDKKTNKTYWAQVEGEPTSESINDLCNGVELKDGLTLPANVKIIDEPT 156

Query: 181 ----------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                      +     W+++ + EG+NR+++++         RLIR S G + L  +  
Sbjct: 157 IWARNPPVRERKAIPTTWLSITINEGRNRQVRRMTAHIGHPTLRLIRYSIGNYTLDDINC 216

Query: 231 GSTREVSK 238
           G  + +  
Sbjct: 217 GEYKVIKG 224


>gi|182415617|ref|YP_001820683.1| pseudouridine synthase [Opitutus terrae PB90-1]
 gi|177842831|gb|ACB77083.1| pseudouridine synthase [Opitutus terrae PB90-1]
          Length = 188

 Score = 92.5 bits (228), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 46/181 (25%), Positives = 74/181 (40%), Gaps = 15/181 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   HKP G+++  +   G          +   V  +GRLD ++EGLLLL+++ GL   L
Sbjct: 2   LCALHKPYGVLSQFTPEPGSRWRTLAEFGLPPAVYPLGRLDADSEGLLLLSDEPGLNTRL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------QVTL 179
             P     R Y V+         L  L++G+ I                           
Sbjct: 62  LNPDQAHRREYWVQVERVPTDAALAQLQRGVKIGDYATRPCAARRLDPAPTLPPRDPPIR 121

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +   + W+ + L EGKNR+++++         RL+R+  G F LG L  G  RE++  
Sbjct: 122 ARKNVPDCWLALELIEGKNRQVRRMTAAIGHPTLRLVRVRIGDFALGKLAVGQWRELTAD 181

Query: 240 I 240
            
Sbjct: 182 E 182


>gi|238754415|ref|ZP_04615771.1| Ribosomal large subunit pseudouridine synthase E [Yersinia ruckeri
           ATCC 29473]
 gi|238707448|gb|EEP99809.1| Ribosomal large subunit pseudouridine synthase E [Yersinia ruckeri
           ATCC 29473]
          Length = 208

 Score = 92.5 bits (228), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 44/150 (29%), Positives = 74/150 (49%), Gaps = 15/150 (10%)

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
            F+ V + GRLD ++EGLL+LTNDG L   L  P  +  +VY V+  G+ D++ L  L++
Sbjct: 58  PFNDVYAAGRLDRDSEGLLVLTNDGKLQARLTQPGQKTAKVYYVQVEGEPDEEALRHLRQ 117

Query: 164 GIVIQGICYGDMQ---------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
           G++++                          + +     W+ + L EG+NR+++++    
Sbjct: 118 GVILKDGPTLPADAEKVEQPEWLWPRNPPIRERKSIPTHWLKMTLYEGRNRQVRRMTAHI 177

Query: 209 NWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +   RLIR S G   LG L  G  +E+S 
Sbjct: 178 GFPTLRLIRFSMGNLTLGNLQPGEWKEISD 207


>gi|330987630|gb|EGH85733.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. lachrymans str. M301315]
          Length = 210

 Score = 92.5 bits (228), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 49/185 (26%), Positives = 88/185 (47%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L+L++KP  ++T  SD  GR+T+ D +          GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPKLFLFNKPFDVLTQFSDEGGRATLKDFIKIPGI--YPAGRLDRDSEGLLLLTNDG 84

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+   ++L  L+ G+ +        +            
Sbjct: 85  QLQARIADPKHKLAKTYWVQVEGEPTDEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPR 144

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + ++EG+NR+++++         RL+R+  G + L +L  G  R
Sbjct: 145 NPPVRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLDSLDQGQYR 204

Query: 235 EVSKK 239
           EV+ K
Sbjct: 205 EVAAK 209


>gi|110805163|ref|YP_688683.1| 23S rRNA pseudouridine synthase E [Shigella flexneri 5 str. 8401]
 gi|34098457|sp|Q83LF6|RLUE_SHIFL RecName: Full=Ribosomal large subunit pseudouridine synthase E;
           AltName: Full=rRNA pseudouridylate synthase E; AltName:
           Full=rRNA-uridine isomerase E
 gi|110614711|gb|ABF03378.1| conserved hypothetical protein [Shigella flexneri 5 str. 8401]
 gi|281600568|gb|ADA73552.1| Ribosomal large subunit pseudouridine synthase E [Shigella flexneri
           2002017]
          Length = 217

 Score = 92.5 bits (228), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 88/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 31  RRKHENQPTRVILFNKPYDVLPQFTDETGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 89  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPA 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 149 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 208

Query: 230 AGSTREVSK 238
            G  REV+ 
Sbjct: 209 NGEWREVTD 217


>gi|330960137|gb|EGH60397.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. maculicola
           str. ES4326]
          Length = 210

 Score = 92.5 bits (228), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 48/182 (26%), Positives = 85/182 (46%), Gaps = 16/182 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  SD  GR+T+ D +          GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPKLILFNKPFDVLTQFSDEGGRATLKDFIDIPGI--YPAGRLDRDSEGLLLLTNDG 84

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+  +++L  L+ G+ +        +            
Sbjct: 85  QLQARIADPKHKLAKTYWVQVEGEPSEEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPR 144

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  R
Sbjct: 145 NPPVRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLDQGQYR 204

Query: 235 EV 236
           EV
Sbjct: 205 EV 206


>gi|161503669|ref|YP_001570781.1| hypothetical protein SARI_01753 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160865016|gb|ABX21639.1| hypothetical protein SARI_01753 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 245

 Score = 92.5 bits (228), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 53/190 (27%), Positives = 89/190 (46%), Gaps = 17/190 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P ++ +  R+ L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLL+L
Sbjct: 55  KPRKENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIPVQGV--YAAGRLDRDSEGLLVL 112

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TNDG L   L  P  +  ++Y V+  G  D + L  L+ G+ +                 
Sbjct: 113 TNDGALQARLTQPDKRTGKIYYVQVEGIPDHEALQALRAGVTLNDGPTLPAGIEIVAEPD 172

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ V L EG+NR+I+++         RLIR S G + L  L 
Sbjct: 173 WLWPRTPPIRERKNIPTTWLKVTLYEGRNRQIRRMTAHVGHPTLRLIRYSMGDYMLNGLN 232

Query: 230 AGSTREVSKK 239
            G  RE++++
Sbjct: 233 NGQWREIAQE 242


>gi|42560927|ref|NP_975378.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           mycoides subsp. mycoides SC str. PG1]
 gi|42492424|emb|CAE77020.1| Ribosomal large subunit pseudouridine synthase B [Mycoplasma
           mycoides subsp. mycoides SC str. PG1]
          Length = 113

 Score = 92.5 bits (228), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 38/110 (34%), Positives = 58/110 (52%), Gaps = 2/110 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--RKAE 71
           +R+ KVI+  G  SRR  E++I + RVKVN  ++    V +     I++D   +      
Sbjct: 4   ERLQKVISSRGYCSRRAAEKLILENRVKVNDQIINTLGVKIDPKAEIKIDNRLVLSDSNN 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +   +L++KP  ++TT  DP  R TV D    +  RV  VGRLD +  GL
Sbjct: 64  QKYYYLFYKPRLVLTTMYDPKKRKTVNDYFKDLNHRVYPVGRLDYDVSGL 113


>gi|188989694|ref|YP_001901704.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. B100]
 gi|167731454|emb|CAP49629.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris]
          Length = 223

 Score = 92.5 bits (228), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 48/192 (25%), Positives = 83/192 (43%), Gaps = 15/192 (7%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +       L L +KP G+++  SD             +  +V + GRLD ++EGLLLLT
Sbjct: 29  AICLDGLLMLVLLNKPYGVLSQFSDRSTPPKRTLAEFGLPPQVYAAGRLDHDSEGLLLLT 88

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------- 175
           +DG LA  L  P  +  + Y V+  G  D  +L  L  G+++                  
Sbjct: 89  DDGPLAHRLTDPRHKQPKTYWVQVEGDPDTSQLQALCDGVLLNDGPTRPANVRRLECAPT 148

Query: 176 -----QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                      +   +AW+ V + EG+NR+++++         RL+R++ G + L +L  
Sbjct: 149 LWPRDPPVRVRKTVPDAWLEVQITEGRNRQVRRMTASVGLPTLRLVRVAIGAWSLASLQP 208

Query: 231 GSTREVSKKILR 242
           G  R    + +R
Sbjct: 209 GQWRVDDARAVR 220


>gi|192361547|ref|YP_001983032.1| pseudouridylate synthase [Cellvibrio japonicus Ueda107]
 gi|190687712|gb|ACE85390.1| pseudouridylate synthase [Cellvibrio japonicus Ueda107]
          Length = 258

 Score = 92.5 bits (228), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 48/246 (19%), Positives = 93/246 (37%), Gaps = 25/246 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L++KP G+++  +  + R T+   +      V   GRLD ++EGLLLLT+DG L  ++
Sbjct: 9   LILFNKPYGVLSQFTAKEERPTLAQYIRIP--NVYPAGRLDHDSEGLLLLTDDGDLQHLI 66

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------------VTLD 180
             P+ +  + Y V+  G  +   L  L++G+ +        +                 +
Sbjct: 67  SHPAHKQPKTYWVQVEGAPNSYALTKLRQGVELNDGMTQPAEVRLIPAPKLWERKPPIRE 126

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                  W+ + + EG+NR+++++         RL+R+  GP+ L  +  G  R      
Sbjct: 127 RANIPTQWLEIVITEGRNRQVRRMTAAVGHPTLRLVRVKIGPWTLEGIEPGKYR------ 180

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                  H  +        P  S  +  +      +  P           +    + +  
Sbjct: 181 ---TETVHAPKMGNTTNRRPSGSRPSGAKTGVPHKTPHPKATQERAHAGPRGKPAAPKST 237

Query: 301 LATPVH 306
            A P  
Sbjct: 238 AAKPAK 243


>gi|163743246|ref|ZP_02150627.1| RNA pseudouridylate synthase [Phaeobacter gallaeciensis 2.10]
 gi|161383434|gb|EDQ07822.1| RNA pseudouridylate synthase [Phaeobacter gallaeciensis 2.10]
          Length = 232

 Score = 92.2 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 47/232 (20%), Positives = 90/232 (38%), Gaps = 17/232 (7%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGG 129
            TRL  ++KP  ++   +D    S+    L        V   GRLD ++EGL+LLT+ G 
Sbjct: 1   MTRLIRFNKPYDVLPQFTDRGSDSSPRATLSDWIDLPGVYPAGRLDRDSEGLMLLTDHGR 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------- 180
           L   +  P  +  + Y V+  G  D   +  L  G+ ++       +  L          
Sbjct: 61  LQAWISDPQHKMPKTYWVQVEGTPDAAAIQALANGVELKDGMTRPAKAALIEEPEGIWAR 120

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +   ++W+ + +REG+NR+++++         RLIR + G + L  L  G+  
Sbjct: 121 NPPIRVRKSVPDSWIALTIREGRNRQVRRMTAAVGHPTLRLIRAAIGIWTLDGLSPGTWE 180

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
           ++    +     P      Q        +S++   +    +        R +
Sbjct: 181 DLEAPTIPGPPKPKPAPNRQAIARRKAAASKSARPEPDAGLKLRKPRKPRKR 232


>gi|89092944|ref|ZP_01165896.1| RsuA protein [Oceanospirillum sp. MED92]
 gi|89082969|gb|EAR62189.1| RsuA protein [Oceanospirillum sp. MED92]
          Length = 223

 Score = 92.2 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 39/210 (18%), Positives = 82/210 (39%), Gaps = 29/210 (13%)

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
                   + GRLD ++EGLL+LTNDG     L  P  +  + Y  +  G+V ++ L  L
Sbjct: 29  YIELPDYYAAGRLDYDSEGLLILTNDGPTQHYLANPQFKMEKTYWAQVEGEVTEEALETL 88

Query: 162 KKGIVIQGICYGDMQ--------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
             G+ ++       +                 + +    +W+ + + EGKNR+++++   
Sbjct: 89  SSGVELKDGMTRPAKAKKINEPAIWQRTPPIRERKNIPTSWIELKITEGKNRQVRRMTAA 148

Query: 208 FNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETL 267
             +   RL+R + G + L  L  G                  L E+ + +      + + 
Sbjct: 149 VGFPTLRLVRYAIGEWTLDNLKPGQ---------------SSLIESDIKIPKRKPKNRST 193

Query: 268 VRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
                +   +     +R K+++ +  G ++
Sbjct: 194 TARSLSGKRKERPGESRQKRSAPKNKGYNR 223


>gi|204930693|ref|ZP_03221566.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|205360072|ref|ZP_02834344.2| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|204320152|gb|EDZ05356.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|205341275|gb|EDZ28039.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|320086322|emb|CBY96095.1| ribosomal large subunit pseudouridine synthase [Salmonella enterica
           subsp. enterica serovar Weltevreden str. 2007-60-3289-1]
          Length = 245

 Score = 92.2 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 51/187 (27%), Positives = 89/187 (47%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLL+LTND
Sbjct: 58  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIPVQGV--YAAGRLDRDSEGLLVLTND 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P  +  ++Y V+  G  D + L  L+ G+ +                    
Sbjct: 116 GALQARLTQPGKRTGKIYYVQVEGIPDNEALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 175

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G 
Sbjct: 176 PRTPPIRERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQ 235

Query: 233 TREVSKK 239
            RE++++
Sbjct: 236 WREIAQE 242


>gi|307153241|ref|YP_003888625.1| pseudouridine synthase [Cyanothece sp. PCC 7822]
 gi|306983469|gb|ADN15350.1| pseudouridine synthase [Cyanothece sp. PCC 7822]
          Length = 203

 Score = 92.2 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 50/194 (25%), Positives = 82/194 (42%), Gaps = 25/194 (12%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGG 129
             +  L++KP  ++   +D  G  T    L        V SVGRLD+++EGLLLLT++G 
Sbjct: 1   MYKYILFYKPYNVLCQFTDNSGDKTNRQTLKDFIDIPHVYSVGRLDLDSEGLLLLTDNGP 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-------- 181
           L   L        R Y V+     D+  LN L++G+ I+        V            
Sbjct: 61  LQHRLGHRQFAHPRTYWVQVENIPDEAALNRLREGVKIEDYWTRKASVIKLPTEPVLPPR 120

Query: 182 -------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG--------PFQLG 226
                  +     W+ + L EG+NR+++++     +   RL+R++ G           L 
Sbjct: 121 NPPIRYRKSIPTCWLEITLTEGRNRQVRRMTAAVGYPTLRLVRVAMGIGKGKNEFQLGLE 180

Query: 227 TLLAGSTREVSKKI 240
            L  G  REV++  
Sbjct: 181 GLEPGQWREVTEIE 194


>gi|302185134|ref|ZP_07261807.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. syringae 642]
          Length = 210

 Score = 92.2 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 49/185 (26%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  SD +GR+T+ D +          GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPKLILFNKPFDVLTQFSDEEGRATLKDFIKIPGI--YPAGRLDRDSEGLLLLTNDG 84

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+   ++L  L+ G+ +        +            
Sbjct: 85  QLQARIADPKHKLAKTYWVQVEGEPSDEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPR 144

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  R
Sbjct: 145 NPPVRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLDQGQYR 204

Query: 235 EVSKK 239
           EV+ K
Sbjct: 205 EVAAK 209


>gi|153802567|ref|ZP_01957153.1| pseudouridine synthase family 1 protein [Vibrio cholerae MZO-3]
 gi|124121881|gb|EAY40624.1| pseudouridine synthase family 1 protein [Vibrio cholerae MZO-3]
          Length = 241

 Score = 92.2 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 48/187 (25%), Positives = 78/187 (41%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER  +        L         ++            V + GRLD ++EGLL+L
Sbjct: 57  RPLSPAERKVILFNKPYDTLSQFTDGDGRKTLADYI---PIKDVYAAGRLDRDSEGLLIL 113

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 114 TNDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 173

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + L EG+NR+++++     +   RLIR S G + LG L  
Sbjct: 174 LWPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQP 233

Query: 231 GSTREVS 237
           G   EV+
Sbjct: 234 GEWSEVT 240


>gi|24112554|ref|NP_707064.1| 23S rRNA pseudouridine synthase E [Shigella flexneri 2a str. 301]
 gi|30062682|ref|NP_836853.1| 23S rRNA pseudouridine synthase E [Shigella flexneri 2a str. 2457T]
 gi|24051449|gb|AAN42771.1| orf, conserved hypothetical protein [Shigella flexneri 2a str. 301]
 gi|30040930|gb|AAP16660.1| hypothetical protein S1237 [Shigella flexneri 2a str. 2457T]
          Length = 207

 Score = 92.2 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 88/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 21  RRKHENQPTRVILFNKPYDVLPQFTDETGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 79  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPA 138

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 139 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 198

Query: 230 AGSTREVSK 238
            G  REV+ 
Sbjct: 199 NGEWREVTD 207


>gi|271500470|ref|YP_003333495.1| pseudouridine synthase [Dickeya dadantii Ech586]
 gi|270344025|gb|ACZ76790.1| pseudouridine synthase [Dickeya dadantii Ech586]
          Length = 218

 Score = 92.2 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 51/182 (28%), Positives = 85/182 (46%), Gaps = 17/182 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            + R+ L +KP  +++  +D  GR T+ D +P  F  + + GRLD ++EGLL+LTNDG L
Sbjct: 37  TQRRIVLLNKPFDVLSQFTDEGGRPTLKDYVP--FRDIYAAGRLDRDSEGLLILTNDGKL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------------- 175
              L  P  Q  ++Y  +  G  D+D L   + G+V+                       
Sbjct: 95  QARLTQPGKQTPKIYYAQVEGIPDEDALRAFRTGLVLNDGPTLPAGAECVDEPVWLWPRQ 154

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                 +    +W+ + L EG+NR+++++     +   RLIR S     L  LL G  +E
Sbjct: 155 PPIRQRKNIPVSWLKITLYEGRNRQVRRMTAHIGYPTLRLIRYSMANLTLDGLLPGDWKE 214

Query: 236 VS 237
           + 
Sbjct: 215 ID 216


>gi|260779180|ref|ZP_05888072.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E) [Vibrio
           coralliilyticus ATCC BAA-450]
 gi|260605344|gb|EEX31639.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E) [Vibrio
           coralliilyticus ATCC BAA-450]
          Length = 174

 Score = 92.2 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 39/142 (27%), Positives = 70/142 (49%), Gaps = 14/142 (9%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGL++LTNDG L   L  P ++  + Y V+  G   +  L+ L+KG+ ++
Sbjct: 31  YAAGRLDRDSEGLMVLTNDGILQAKLTQPKSKSPKTYWVQVDGAPSESDLDKLRKGVELK 90

Query: 169 GICYGDMQVTLDTQ--------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                  +V +  +                   W+ + + EG+NR+++++     +   R
Sbjct: 91  DGMTLPAKVEVMAEPNVWERTPPVRFRANIPTTWLAITIIEGRNRQVRRMTANIGFPTLR 150

Query: 215 LIRISYGPFQLGTLLAGSTREV 236
           LIR S G  +LG L  G  +E+
Sbjct: 151 LIRYSMGDIKLGELQPGEWKEI 172


>gi|285019777|ref|YP_003377488.1| ribosomal large subunit pseudouridine synthase e protein
           [Xanthomonas albilineans GPE PC73]
 gi|283474995|emb|CBA17494.1| probable ribosomal large subunit pseudouridine synthase e protein
           [Xanthomonas albilineans]
          Length = 178

 Score = 92.2 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 47/177 (26%), Positives = 80/177 (45%), Gaps = 15/177 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP  ++   +D +           +   V   GRLD ++EGLLLLT+DG LA  L
Sbjct: 2   LIAFNKPFNVLCQFTDRNASPRRTLAGFGLPGGVYVAGRLDYDSEGLLLLTDDGALAHRL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y V+  G    ++L  L  G+ +        QV+                
Sbjct: 62  TDPRHKQPKTYWVQVEGVPQPEQLQRLGDGVALNDGPTAPAQVSRLDAAPALWPRDPPVR 121

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +   +AW+ + LREG+NR+++++         RL+R++ G  +L  L  GS R +
Sbjct: 122 FRKTVPDAWLQIVLREGRNRQVRRMTAAVGLPTLRLVRVAMGTHRLDGLAPGSWRAL 178


>gi|320187862|gb|EFW62532.1| hypothetical protein ECoD_05570 [Escherichia coli O157:H7 str.
           EC1212]
 gi|326339414|gb|EGD63226.1| hypothetical protein ECoA_04444 [Escherichia coli O157:H7 str.
           1044]
 gi|326341463|gb|EGD65254.1| hypothetical protein ECF_03320 [Escherichia coli O157:H7 str. 1125]
          Length = 177

 Score = 92.2 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 39/145 (26%), Positives = 67/145 (46%), Gaps = 15/145 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LTN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ + 
Sbjct: 33  YAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLN 92

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +    +W+ + L EG+NR+++++     +   
Sbjct: 93  DGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTL 152

Query: 214 RLIRISYGPFQLGTLLAGSTREVSK 238
           RLIR + G + L  L  G  RE ++
Sbjct: 153 RLIRYAMGDYSLDNLANGEWREATE 177


>gi|301328490|ref|ZP_07221556.1| conserved hypothetical protein [Escherichia coli MS 78-1]
 gi|300845097|gb|EFK72857.1| conserved hypothetical protein [Escherichia coli MS 78-1]
          Length = 217

 Score = 92.2 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 88/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 31  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 89  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGVELVDEPA 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 149 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 208

Query: 230 AGSTREVSK 238
            G  REV+ 
Sbjct: 209 NGEWREVTD 217


>gi|323209958|gb|EFZ94867.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
          Length = 150

 Score = 92.2 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 55/148 (37%), Positives = 71/148 (47%), Gaps = 6/148 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVD 154
           DG LA  L  PS +  R Y VR  GQVD
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVD 149


>gi|89107981|ref|AP_001761.1| 23S rRNA pseudouridine synthase [Escherichia coli str. K-12 substr.
           W3110]
 gi|157158295|ref|YP_001462404.1| 23S rRNA pseudouridine synthase E [Escherichia coli E24377A]
 gi|162135898|ref|NP_415653.4| 23S rRNA U2457 pseudouridine synthase [Escherichia coli str. K-12
           substr. MG1655]
 gi|170020472|ref|YP_001725426.1| 23S rRNA pseudouridine synthase E [Escherichia coli ATCC 8739]
 gi|170080786|ref|YP_001730106.1| 23S rRNA pseudouridine synthase [Escherichia coli str. K-12 substr.
           DH10B]
 gi|209918392|ref|YP_002292476.1| 23S rRNA pseudouridine synthase E [Escherichia coli SE11]
 gi|218553713|ref|YP_002386626.1| 23S rRNA pseudouridine synthase E [Escherichia coli IAI1]
 gi|218694669|ref|YP_002402336.1| 23S rRNA pseudouridine synthase E [Escherichia coli 55989]
 gi|238900389|ref|YP_002926185.1| 23S rRNA pseudouridine synthase [Escherichia coli BW2952]
 gi|260843451|ref|YP_003221229.1| 23S rRNA pseudouridine synthase [Escherichia coli O103:H2 str.
           12009]
 gi|260854817|ref|YP_003228708.1| 23S rRNA pseudouridine synthase [Escherichia coli O26:H11 str.
           11368]
 gi|260867564|ref|YP_003233966.1| 23S rRNA pseudouridine synthase [Escherichia coli O111:H- str.
           11128]
 gi|293414426|ref|ZP_06657075.1| 23S rRNA pseudouridine synthase E [Escherichia coli B185]
 gi|293433423|ref|ZP_06661851.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           B088]
 gi|300816838|ref|ZP_07097058.1| conserved hypothetical protein [Escherichia coli MS 107-1]
 gi|300821081|ref|ZP_07101230.1| conserved hypothetical protein [Escherichia coli MS 119-7]
 gi|300906946|ref|ZP_07124618.1| hypothetical protein HMPREF9536_04903 [Escherichia coli MS 84-1]
 gi|300917908|ref|ZP_07134541.1| conserved hypothetical protein [Escherichia coli MS 115-1]
 gi|300922665|ref|ZP_07138762.1| hypothetical protein HMPREF9548_00907 [Escherichia coli MS 182-1]
 gi|301306079|ref|ZP_07212157.1| hypothetical protein HMPREF9347_04696 [Escherichia coli MS 124-1]
 gi|301644553|ref|ZP_07244546.1| conserved hypothetical protein [Escherichia coli MS 146-1]
 gi|307137770|ref|ZP_07497126.1| 23S rRNA pseudouridine synthase E [Escherichia coli H736]
 gi|307310088|ref|ZP_07589738.1| pseudouridine synthase [Escherichia coli W]
 gi|309796518|ref|ZP_07690925.1| conserved hypothetical protein [Escherichia coli MS 145-7]
 gi|331641679|ref|ZP_08342814.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Escherichia coli H736]
 gi|331676928|ref|ZP_08377624.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Escherichia coli H591]
 gi|331682641|ref|ZP_08383260.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Escherichia coli H299]
 gi|332279677|ref|ZP_08392090.1| 23S rRNA pseudouridine synthase [Shigella sp. D9]
 gi|3916025|sp|P75966|RLUE_ECOLI RecName: Full=Ribosomal large subunit pseudouridine synthase E;
           AltName: Full=rRNA pseudouridylate synthase E; AltName:
           Full=rRNA-uridine isomerase E
 gi|145580080|pdb|2OLW|A Chain A, Crystal Structure Of E. Coli Pseudouridine Synthase Rlue
 gi|145580081|pdb|2OLW|B Chain B, Crystal Structure Of E. Coli Pseudouridine Synthase Rlue
 gi|4062699|dbj|BAA35957.1| 23S rRNA pseudouridine synthase [Escherichia coli str. K12 substr.
           W3110]
 gi|87081838|gb|AAC74219.2| 23S rRNA U2457 pseudouridine synthase [Escherichia coli str. K-12
           substr. MG1655]
 gi|157080325|gb|ABV20033.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           E24377A]
 gi|169755400|gb|ACA78099.1| pseudouridine synthase [Escherichia coli ATCC 8739]
 gi|169888621|gb|ACB02328.1| 23S rRNA pseudouridine synthase [Escherichia coli str. K-12 substr.
           DH10B]
 gi|209911651|dbj|BAG76725.1| conserved hypothetical protein [Escherichia coli SE11]
 gi|218351401|emb|CAU97107.1| 23S rRNA pseudouridine synthase [Escherichia coli 55989]
 gi|218360481|emb|CAQ98035.1| 23S rRNA pseudouridine synthase [Escherichia coli IAI1]
 gi|238859757|gb|ACR61755.1| 23S rRNA pseudouridine synthase [Escherichia coli BW2952]
 gi|257753466|dbj|BAI24968.1| 23S rRNA pseudouridine synthase [Escherichia coli O26:H11 str.
           11368]
 gi|257758598|dbj|BAI30095.1| 23S rRNA pseudouridine synthase [Escherichia coli O103:H2 str.
           12009]
 gi|257763920|dbj|BAI35415.1| 23S rRNA pseudouridine synthase [Escherichia coli O111:H- str.
           11128]
 gi|260449726|gb|ACX40148.1| pseudouridine synthase [Escherichia coli DH1]
 gi|291324242|gb|EFE63664.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           B088]
 gi|291434484|gb|EFF07457.1| 23S rRNA pseudouridine synthase E [Escherichia coli B185]
 gi|300401293|gb|EFJ84831.1| hypothetical protein HMPREF9536_04903 [Escherichia coli MS 84-1]
 gi|300414898|gb|EFJ98208.1| conserved hypothetical protein [Escherichia coli MS 115-1]
 gi|300421014|gb|EFK04325.1| hypothetical protein HMPREF9548_00907 [Escherichia coli MS 182-1]
 gi|300526380|gb|EFK47449.1| conserved hypothetical protein [Escherichia coli MS 119-7]
 gi|300530612|gb|EFK51674.1| conserved hypothetical protein [Escherichia coli MS 107-1]
 gi|300838651|gb|EFK66411.1| hypothetical protein HMPREF9347_04696 [Escherichia coli MS 124-1]
 gi|301077135|gb|EFK91941.1| conserved hypothetical protein [Escherichia coli MS 146-1]
 gi|306909806|gb|EFN40300.1| pseudouridine synthase [Escherichia coli W]
 gi|308119830|gb|EFO57092.1| conserved hypothetical protein [Escherichia coli MS 145-7]
 gi|309701459|emb|CBJ00763.1| ribosomal large subunit pseudouridine synthase E (rRNA
           pseudouridylate synthase E) [Escherichia coli ETEC
           H10407]
 gi|315060412|gb|ADT74739.1| 23S rRNA pseudouridine synthase [Escherichia coli W]
 gi|315135767|dbj|BAJ42926.1| 23S rRNA pseudouridine synthase [Escherichia coli DH1]
 gi|315254891|gb|EFU34859.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           MS 85-1]
 gi|323379028|gb|ADX51296.1| pseudouridine synthase [Escherichia coli KO11]
 gi|323937875|gb|EGB34139.1| RNA pseudouridylate synthase [Escherichia coli E1520]
 gi|323942605|gb|EGB38772.1| RNA pseudouridylate synthase [Escherichia coli E482]
 gi|323947561|gb|EGB43565.1| RNA pseudouridylate synthase [Escherichia coli H120]
 gi|324017531|gb|EGB86750.1| hypothetical protein HMPREF9542_03832 [Escherichia coli MS 117-3]
 gi|324117294|gb|EGC11201.1| RNA pseudouridylate synthase [Escherichia coli E1167]
 gi|331038477|gb|EGI10697.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Escherichia coli H736]
 gi|331075617|gb|EGI46915.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Escherichia coli H591]
 gi|331080272|gb|EGI51451.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Escherichia coli H299]
 gi|332102029|gb|EGJ05375.1| 23S rRNA pseudouridine synthase [Shigella sp. D9]
          Length = 217

 Score = 92.2 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 88/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 31  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 89  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPA 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 149 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 208

Query: 230 AGSTREVSK 238
            G  REV+ 
Sbjct: 209 NGEWREVTD 217


>gi|331667536|ref|ZP_08368400.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Escherichia coli TA271]
 gi|331065121|gb|EGI37016.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Escherichia coli TA271]
          Length = 217

 Score = 91.8 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 49/189 (25%), Positives = 87/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + T + L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 31  RRKPENQPTHVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 89  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPA 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 149 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 208

Query: 230 AGSTREVSK 238
            G  REV+ 
Sbjct: 209 NGEWREVTD 217


>gi|254441719|ref|ZP_05055212.1| conserved hypothetical protein [Octadecabacter antarcticus 307]
 gi|198251797|gb|EDY76112.1| conserved hypothetical protein [Octadecabacter antarcticus 307]
          Length = 179

 Score = 91.8 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 38/177 (21%), Positives = 70/177 (39%), Gaps = 14/177 (7%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            T +        L               +   +   V + GRLD ++EGLL+LT+DG L 
Sbjct: 1   MTTILFNKPFGVLTQFTDAKCPTERPTLSGFDLPKGVYAAGRLDRDSEGLLVLTDDGKLQ 60

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----------- 180
             L  P  +  + Y V+  G      L+ ++  + ++       +V L            
Sbjct: 61  AQLSSPKFKTPKTYLVQVEGDTTDADLDPMRASLSLKDGPTLPARVHLIDPPDLWLRDPP 120

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
               +   + W+ V + EG+NR+++++     +   RL+R S G + L  +  G  R
Sbjct: 121 VRVRKSIPDTWIKVTITEGRNRQVRRMCAALGFPCLRLVRWSVGSWTLDGISQGQWR 177


>gi|307294620|ref|ZP_07574462.1| pseudouridine synthase [Sphingobium chlorophenolicum L-1]
 gi|306879094|gb|EFN10312.1| pseudouridine synthase [Sphingobium chlorophenolicum L-1]
          Length = 180

 Score = 91.8 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 41/178 (23%), Positives = 71/178 (39%), Gaps = 14/178 (7%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            T +        L     +  G              V   GRLD+++EGLLLLT+DG L 
Sbjct: 1   MTLILFNKPYGVLCQFTDESTGPPRPTLAAFIKRPGVYPAGRLDLDSEGLLLLTDDGRLQ 60

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----------- 180
             +  P  +  + Y  +  G  D+  L  L++G+ ++       QV              
Sbjct: 61  AQIADPRFKTPKTYLAQVEGDPDEAALEALRRGVKLKDGPTLPAQVERIDDPALWPRDPP 120

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               +   + W+ + +REG+NR+++++         RL+R   G + L  +  G  RE
Sbjct: 121 VRFRKSVPDCWLRLTIREGRNRQVRRMTAAVGHPTLRLVRWRIGDWTLDGIAQGQWRE 178


>gi|109898693|ref|YP_661948.1| pseudouridine synthase, Rsu [Pseudoalteromonas atlantica T6c]
 gi|109700974|gb|ABG40894.1| ribosomal large subunit pseudouridine synthase E [Pseudoalteromonas
           atlantica T6c]
          Length = 192

 Score = 91.8 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 50/187 (26%), Positives = 89/187 (47%), Gaps = 16/187 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P   A RT++ L++KP  ++T  +D  GR T+ D +P     + + GRLD ++EGLL+L
Sbjct: 8   KPKTPASRTKIVLFNKPFNVLTQFTDATGRQTLKDFIPIP--DIYASGRLDKDSEGLLVL 65

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TNDG L   L  P  +  + Y V+  G   + +L  L+ G+ ++       +        
Sbjct: 66  TNDGKLQSKLTDPKKKTSKTYWVQVEGIPQERQLQALRDGVELKDGLTRPAKVESMPEPA 125

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                      Q    +W+++ + EGKNR+++++     +   RL+R   G + L  +  
Sbjct: 126 LWPRTPPVRFRQSIPTSWLSITISEGKNRQVRRMTAHIGFPTLRLVRYRIGNWTLDGIDT 185

Query: 231 GSTREVS 237
           G   E+ 
Sbjct: 186 GQYVELD 192


>gi|194735157|ref|YP_002114244.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           CVM19633]
 gi|197301168|ref|ZP_02664202.2| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|194710659|gb|ACF89880.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           CVM19633]
 gi|197288149|gb|EDY27536.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
          Length = 245

 Score = 91.8 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 51/187 (27%), Positives = 89/187 (47%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLL+LTND
Sbjct: 58  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIPVQGV--YAAGRLDRDSEGLLVLTND 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P  +  ++Y V+  G  D + L  L+ G+ +                    
Sbjct: 116 GALQARLTQPGKRTGKIYYVQVEGIPDNEALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 175

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G 
Sbjct: 176 PRTPPIRERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLSGLDNGQ 235

Query: 233 TREVSKK 239
            RE++++
Sbjct: 236 WREIAQE 242


>gi|262365461|gb|ACY62018.1| putative RNA pseudouridylate synthase-family protein [Yersinia
           pestis D182038]
          Length = 194

 Score = 91.8 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 51/201 (25%), Positives = 83/201 (41%), Gaps = 8/201 (3%)

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +A  L  PS +  R Y VR  GQ+D DK+  L +G+ ++        ++    +G N W 
Sbjct: 1   MANRLMHPSREVEREYAVRVFGQIDDDKIKQLSRGVQLEDGPAAFRTISYQGGEGINQWY 60

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
            V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+    L+      
Sbjct: 61  NVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELD---LKATNYLR 117

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
            L E  V       S   + +DR  + +       +     S +    +Q        R+
Sbjct: 118 ELVELDVETV----SKLPVEKDRRRVKANQIRRAVKRHTEVSGRQVAGRQGSARKGSTRQ 173

Query: 309 NLASNVWMAKGIHSSFLSDSG 329
           N+ +    A     S     G
Sbjct: 174 NVGNAAPAATASRRSGPKKRG 194


>gi|157160659|ref|YP_001457977.1| 23S rRNA pseudouridine synthase E [Escherichia coli HS]
 gi|157066339|gb|ABV05594.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           HS]
          Length = 217

 Score = 91.8 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 88/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 31  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 89  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPA 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 149 WLWPRNPSIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 208

Query: 230 AGSTREVSK 238
            G  REV+ 
Sbjct: 209 NGEWREVTD 217


>gi|322515146|ref|ZP_08068149.1| ribosomal large subunit pseudouridine synthase E [Actinobacillus
           ureae ATCC 25976]
 gi|322118860|gb|EFX91050.1| ribosomal large subunit pseudouridine synthase E [Actinobacillus
           ureae ATCC 25976]
          Length = 232

 Score = 91.8 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 55/192 (28%), Positives = 94/192 (48%), Gaps = 20/192 (10%)

Query: 65  VPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
            PL+     E T + L++KP  ++T  +D  GR T+ D +P    +V  VGRLD ++EGL
Sbjct: 29  QPLKPQLSFEDTVVVLFNKPFDVLTQFTDEQGRQTLKDFIPIP--QVYPVGRLDRDSEGL 86

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--- 178
           LLLTN+G +   L  P  +  + Y  +  G      L  L+KG+ ++       +     
Sbjct: 87  LLLTNNGEIQHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAIS 146

Query: 179 ------------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
                        + +    +W+ + + EGKNR+++++     +   RLIR+  G FQLG
Sbjct: 147 APNYEWQTAPKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPTLRLIRVGLGQFQLG 206

Query: 227 TLLAGSTREVSK 238
            L +G  R +++
Sbjct: 207 DLDSGEYRILNE 218


>gi|261252477|ref|ZP_05945050.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E) [Vibrio
           orientalis CIP 102891]
 gi|260935868|gb|EEX91857.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E) [Vibrio
           orientalis CIP 102891]
          Length = 230

 Score = 91.8 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 91/189 (48%), Gaps = 16/189 (8%)

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +   P    E  ++ +++KP   ++  +D DGR T+ D +      V + GRLD ++EGL
Sbjct: 42  IKNKPKVAPEDRKVVVFNKPFDTLSQFTDGDGRKTLADYIT--VKDVYAAGRLDRDSEGL 99

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD- 180
           ++LTNDG L   L  P+++  + Y V+  G    + L+ L+KG+ ++       +V +  
Sbjct: 100 MVLTNDGILQARLTQPNSKSPKTYWVQVDGAPSDEDLDKLRKGVELKDGMTLPAKVEVMD 159

Query: 181 -------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
                               W+ + + EG+NR+++++     +   RLIR S G   LG 
Sbjct: 160 APNVWERNPPVRFRANIPTTWLAITIIEGRNRQVRRMTANIGFPTLRLIRYSMGDVTLGD 219

Query: 228 LLAGSTREV 236
           L  G  +E+
Sbjct: 220 LQPGEWKEI 228


>gi|34499118|ref|NP_903333.1| pseudouridine synthase [Chromobacterium violaceum ATCC 12472]
 gi|34104969|gb|AAQ61325.1| probable pseudouridine synthase [Chromobacterium violaceum ATCC
           12472]
          Length = 248

 Score = 91.8 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 48/230 (20%), Positives = 89/230 (38%), Gaps = 19/230 (8%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L L +KP G++   S+     T+   +P         GRLD ++EGLLLLT DG L 
Sbjct: 24  MPQLILLNKPYGVICQFSEHPTHPTLKSCVPQAGV--YPAGRLDTDSEGLLLLTGDGALQ 81

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----------- 180
             +  P  +  + Y V+  G   +++L +L++G+ +        +V              
Sbjct: 82  HRIADPRWKLPKTYWVQVEGDPKEEQLEMLRRGVDLGDFVTRPAEVRRIETPELWPRNPP 141

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +   + W+ + + EGKNR+++++         RL+R++ GP++L  L  G  R + 
Sbjct: 142 VRFRKTVPDCWLEIIISEGKNRQVRRMTAKAGLPTLRLVRVAIGPWKLDGLQPGEMRAID 201

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
              +R +  P                         +            K 
Sbjct: 202 ---VRTEDLPRGASAGPGGKPGDRAPQSRSAAAAKSGKIPSFRFARNRKG 248


>gi|126737772|ref|ZP_01753502.1| RNA pseudouridylate synthase [Roseobacter sp. SK209-2-6]
 gi|126721165|gb|EBA17869.1| RNA pseudouridylate synthase [Roseobacter sp. SK209-2-6]
          Length = 231

 Score = 91.8 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 51/234 (21%), Positives = 90/234 (38%), Gaps = 20/234 (8%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGG 129
             RL  ++KP  ++   +D   + +    L            GRLD ++EGL+LLT+ G 
Sbjct: 1   MPRLIRFNKPYDVLPQFTDRGSQESSRKTLSDFIDCPGVYPAGRLDRDSEGLMLLTDFGR 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-------------- 175
           L   +  PS +  + Y V+  GQ D+  L  L KG+ ++                     
Sbjct: 61  LQAWISDPSHKMAKTYWVQVEGQPDRAGLEALSKGVELKDGLTLPASAHLMEEPAMLWAR 120

Query: 176 -QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + +    +W+++ ++EGKNR+++++         RLIR S G + L  L  GS  
Sbjct: 121 TPPIRERKNIPTSWISLTIKEGKNRQVRRMTAAIGHPTLRLIRYSIGTWTLEGLSQGSWE 180

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
           ++    +    G         +       S      +     E  D   R +K 
Sbjct: 181 DL---EVPRVPGRPKPSGLPKSRTEKTVPSTKPNSKKRKSPPEKRDSARRKRKT 231


>gi|157370266|ref|YP_001478255.1| pseudouridine synthase [Serratia proteamaculans 568]
 gi|157322030|gb|ABV41127.1| pseudouridine synthase [Serratia proteamaculans 568]
          Length = 178

 Score = 91.8 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 42/151 (27%), Positives = 67/151 (44%), Gaps = 15/151 (9%)

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
              F  V + GRLD ++EGLL+LTNDG L   L  P  +  +VY V+  G    + L  L
Sbjct: 26  FIPFPDVYAAGRLDRDSEGLLVLTNDGKLQAQLTEPGKRTGKVYYVQVEGAPQDNDLVSL 85

Query: 162 KKGIVIQGICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
           + G+ ++                          + +    AW+ + L EG+NR+++++  
Sbjct: 86  RNGVTLKDGPTLPAGVELVAEPQWLWPRNPPIRERKSIPTAWLKITLYEGRNRQVRRMTA 145

Query: 207 FFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              +   RLIR S G   LG L  G  + + 
Sbjct: 146 HIGFPTLRLIRYSMGNISLGELQPGEWKCLD 176


>gi|226943128|ref|YP_002798201.1| Pseudouridine synthase, RluE [Azotobacter vinelandii DJ]
 gi|226718055|gb|ACO77226.1| Pseudouridine synthase, RluE [Azotobacter vinelandii DJ]
          Length = 210

 Score = 91.8 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 53/186 (28%), Positives = 89/186 (47%), Gaps = 16/186 (8%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G P       RL L++KP  ++T     DGR+T+ D +P         GRLD ++EGLLL
Sbjct: 22  GPPEAPQAAPRLILFNKPFDVLTQFRGGDGRATLKDFIPVPGV--YPAGRLDRDSEGLLL 79

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--- 180
           LT+DG L   +  P  +  + Y V+  G+ D+ +L  L++G+ +        +V      
Sbjct: 80  LTDDGRLQARIADPRHKLAKTYWVQVEGEPDEAQLQRLREGVTLNDGPTRPAEVRRLDAP 139

Query: 181 -----------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                       +    AW+ + +REG+NR+++++         RL+R+  GP+ +  L 
Sbjct: 140 ELWPRDPPVRFRKSVPTAWLELTIREGRNRQVRRMTAAVGLPTLRLVRVRIGPWSVDGLA 199

Query: 230 AGSTRE 235
            G  RE
Sbjct: 200 PGEWRE 205


>gi|300949486|ref|ZP_07163483.1| conserved hypothetical protein [Escherichia coli MS 116-1]
 gi|300955541|ref|ZP_07167903.1| hypothetical protein HMPREF9547_01414 [Escherichia coli MS 175-1]
 gi|300317580|gb|EFJ67364.1| hypothetical protein HMPREF9547_01414 [Escherichia coli MS 175-1]
 gi|300451106|gb|EFK14726.1| conserved hypothetical protein [Escherichia coli MS 116-1]
          Length = 217

 Score = 91.8 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 88/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 31  RRKPENQPTRVILFNKPYDILPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 89  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPA 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 149 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 208

Query: 230 AGSTREVSK 238
            G  REV+ 
Sbjct: 209 NGEWREVTD 217


>gi|239999156|ref|ZP_04719080.1| Ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae 35/02]
 gi|240113135|ref|ZP_04727625.1| Ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae MS11]
 gi|240115891|ref|ZP_04729953.1| Ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae PID18]
 gi|240118189|ref|ZP_04732251.1| Ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae PID1]
 gi|240125928|ref|ZP_04738814.1| Ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae SK-92-679]
 gi|240128440|ref|ZP_04741101.1| Ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae SK-93-1035]
          Length = 197

 Score = 91.8 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 34/177 (19%), Positives = 62/177 (35%), Gaps = 4/177 (2%)

Query: 62  VDGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           +DG  +         + L        +                     + +VGRLD +T 
Sbjct: 18  IDGEAVTVVPEPYFYILLNKPEDYETSHKPKHYRSVFSLFPDNMRNIDMQAVGRLDADTT 77

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LL+TNDG L   L  PS +  ++Y V       +     LK G+ +            
Sbjct: 78  GVLLITNDGKLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVPLHDENETVCAADA 137

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +      + + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 138 VLENP--TTLLLTITEGKYHQVKRMVAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 192


>gi|33151571|ref|NP_872924.1| pseudouridylate synthase [Haemophilus ducreyi 35000HP]
 gi|33147791|gb|AAP95313.1| probable pseudouridylate synthase [Haemophilus ducreyi 35000HP]
          Length = 229

 Score = 91.8 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 52/197 (26%), Positives = 92/197 (46%), Gaps = 17/197 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P      T + L++KP  +++  SD  GR+T+ D +P     V  VGRLD ++EGLLLL
Sbjct: 29  KPKVSFAETIVLLFNKPYNVLSQFSDQQGRATLKDFIPIE--NVYPVGRLDRDSEGLLLL 86

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TN+G +   L  P  + ++ Y  +  GQ     L  L  G+ ++       +        
Sbjct: 87  TNNGEIQHRLAHPKFEKVKTYLAQLEGQPQAVDLAKLTCGVELKDGLTRPAKVSVIAPPN 146

Query: 177 -------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + + EGKNR+++++     +   RLIR++   F+LG L 
Sbjct: 147 YNWHTAPNIRERKTIPTSWLELKIYEGKNRQVRRMTAHIGFPTLRLIRVALSGFELGNLA 206

Query: 230 AGSTREVSKKILREQLG 246
            G  R +++   R+   
Sbjct: 207 TGEYRLLTEIEKRQLFA 223


>gi|242239490|ref|YP_002987671.1| pseudouridine synthase [Dickeya dadantii Ech703]
 gi|242131547|gb|ACS85849.1| pseudouridine synthase [Dickeya dadantii Ech703]
          Length = 208

 Score = 91.8 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 47/188 (25%), Positives = 86/188 (45%), Gaps = 17/188 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +   +  R+ L++KP  +++  +D  GR T+ + +P  F  + S GRLD ++EGL+LL
Sbjct: 21  KSIPIGQARRIVLFNKPFDVLSQFTDESGRETLKNYIP--FGDIYSAGRLDRDSEGLMLL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TNDG L   L  P  +  ++Y  +  G  D+  L   + G+ +                 
Sbjct: 79  TNDGKLQARLTQPGKKTPKIYYAQIEGIPDEAALQAFRTGLQLNDGLTQPAGAERVDAPL 138

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + ++   +W+ + L EG+NR+++++     +   RLIR S     L  L 
Sbjct: 139 WLWPRNPPIRERKQIPTSWLKITLYEGRNRQVRRMTAHIGFPTLRLIRYSMANHTLDGLQ 198

Query: 230 AGSTREVS 237
            G  +E+ 
Sbjct: 199 PGEWKEID 206


>gi|300938707|ref|ZP_07153431.1| conserved hypothetical protein [Escherichia coli MS 21-1]
 gi|300456352|gb|EFK19845.1| conserved hypothetical protein [Escherichia coli MS 21-1]
          Length = 212

 Score = 91.8 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 49/189 (25%), Positives = 87/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 26  KRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 83

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 84  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGVELVDEPA 143

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 144 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 203

Query: 230 AGSTREVSK 238
            G  RE + 
Sbjct: 204 NGEWREATD 212


>gi|253773841|ref|YP_003036672.1| 23S rRNA pseudouridine synthase E [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254161242|ref|YP_003044350.1| 23S rRNA pseudouridine synthase E [Escherichia coli B str. REL606]
 gi|297518451|ref|ZP_06936837.1| 23S rRNA pseudouridine synthase E [Escherichia coli OP50]
 gi|253324885|gb|ACT29487.1| pseudouridine synthase [Escherichia coli 'BL21-Gold(DE3)pLysS AG']
 gi|253973143|gb|ACT38814.1| 23S rRNA pseudouridine synthase [Escherichia coli B str. REL606]
 gi|253977357|gb|ACT43027.1| 23S rRNA pseudouridine synthase [Escherichia coli BL21(DE3)]
 gi|313848606|emb|CAQ31658.2| 23S rRNA pseudouridine 2457 synthase [Escherichia coli BL21(DE3)]
 gi|323962734|gb|EGB58312.1| RNA pseudouridylate synthase [Escherichia coli H489]
 gi|323973275|gb|EGB68464.1| RNA pseudouridylate synthase [Escherichia coli TA007]
          Length = 217

 Score = 91.8 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 48/189 (25%), Positives = 88/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 31  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD +  L+ G+ +                 
Sbjct: 89  TNNGALQARLTQPGKRTGKIYYVQVEGFPTQDAIEALRNGVTLNDGPTLPAGAELVDEPA 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 149 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLA 208

Query: 230 AGSTREVSK 238
            G  RE ++
Sbjct: 209 NGEWREATE 217


>gi|193066244|ref|ZP_03047296.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           E22]
 gi|194429525|ref|ZP_03062046.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           B171]
 gi|256018609|ref|ZP_05432474.1| 23S rRNA pseudouridine synthase E [Shigella sp. D9]
 gi|256023167|ref|ZP_05437032.1| 23S rRNA pseudouridine synthase E [Escherichia sp. 4_1_40B]
 gi|301029556|ref|ZP_07192634.1| conserved hypothetical protein [Escherichia coli MS 196-1]
 gi|312971272|ref|ZP_07785450.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           1827-70]
 gi|192926093|gb|EDV80735.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           E22]
 gi|194412399|gb|EDX28700.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           B171]
 gi|299877551|gb|EFI85762.1| conserved hypothetical protein [Escherichia coli MS 196-1]
 gi|310336474|gb|EFQ01660.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           1827-70]
 gi|315616007|gb|EFU96633.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           3431]
 gi|323185681|gb|EFZ71042.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           1357]
 gi|332089263|gb|EGI94369.1| ribosomal large subunit pseudouridine synthase E [Shigella boydii
           5216-82]
          Length = 207

 Score = 91.8 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 88/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 21  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 79  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPA 138

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 139 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 198

Query: 230 AGSTREVSK 238
            G  REV+ 
Sbjct: 199 NGEWREVTD 207


>gi|330952996|gb|EGH53256.1| pseudouridine synthase, Rsu [Pseudomonas syringae Cit 7]
          Length = 210

 Score = 91.8 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 50/185 (27%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                RL L++KP  ++T  SD +GR+T+ D +          GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPRLILFNKPFDVLTQFSDEEGRATLKDFIKIPGI--YPAGRLDRDSEGLLLLTNDG 84

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+   ++L  L+ G+ +        +            
Sbjct: 85  QLQARIADPKHKLAKTYWVQVEGEPSDEQLQQLRDGVQLNDGPTLPAEARRLDEPQLWPR 144

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  R
Sbjct: 145 NPPVRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLEGLDQGQYR 204

Query: 235 EVSKK 239
           EV+ K
Sbjct: 205 EVAAK 209


>gi|237798440|ref|ZP_04586901.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. oryzae str. 1_6]
 gi|331021291|gb|EGI01348.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. oryzae str. 1_6]
          Length = 212

 Score = 91.8 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 40/182 (21%), Positives = 72/182 (39%), Gaps = 14/182 (7%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L+             D               +   GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPKLILFLFNKPFDVLTQFSDEGGRATLKDFIDIPGIYPAGRLDRDSEGLLLLTNDG 86

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+ ++ +L  L+ G+ +        +            
Sbjct: 87  QLQARIADPKHKLAKTYWVQVEGEPNEAQLQQLRDGVQLNDGPTLPAEARQLEEPQLWPR 146

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  R
Sbjct: 147 NPPVRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVKIGNWTLDGLDQGQYR 206

Query: 235 EV 236
           EV
Sbjct: 207 EV 208


>gi|323187623|gb|EFZ72930.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           RN587/1]
          Length = 177

 Score = 91.8 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 39/145 (26%), Positives = 66/145 (45%), Gaps = 15/145 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LTN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ + 
Sbjct: 33  YAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLN 92

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +    +W+ + L EG+NR+++++     +   
Sbjct: 93  DGPTLPAGAELVEEPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTL 152

Query: 214 RLIRISYGPFQLGTLLAGSTREVSK 238
           RLIR + G + L  L  G  RE + 
Sbjct: 153 RLIRYAMGDYSLDNLANGEWREATD 177


>gi|293409501|ref|ZP_06653077.1| 23S rRNA pseudouridine synthase E [Escherichia coli B354]
 gi|291469969|gb|EFF12453.1| 23S rRNA pseudouridine synthase E [Escherichia coli B354]
          Length = 217

 Score = 91.4 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 88/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 31  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 89  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPE 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 149 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 208

Query: 230 AGSTREVSK 238
            G  REV+ 
Sbjct: 209 NGEWREVTD 217


>gi|289810570|ref|ZP_06541199.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 147

 Score = 91.4 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 51/142 (35%), Positives = 67/142 (47%), Gaps = 6/142 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKE 61

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L  Y     L T +      +          +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVR 148
           DG LA  L  PS +  R Y VR
Sbjct: 122 DGELANRLMHPSREVEREYAVR 143


>gi|195874174|ref|ZP_02701041.2| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|205360749|ref|ZP_02686223.2| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|195630337|gb|EDX48963.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|205347204|gb|EDZ33835.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
          Length = 245

 Score = 91.4 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 51/187 (27%), Positives = 88/187 (47%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLL+LTND
Sbjct: 58  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIPVQGV--YAAGRLDRDSEGLLVLTND 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P  +  ++Y V+  G  D   L  L+ G+ +                    
Sbjct: 116 GALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 175

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G 
Sbjct: 176 PRTPPIRERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQ 235

Query: 233 TREVSKK 239
            RE++++
Sbjct: 236 WREIAQE 242


>gi|21241064|ref|NP_640646.1| pseudouridylate synthase [Xanthomonas axonopodis pv. citri str.
           306]
 gi|21106359|gb|AAM35182.1| pseudouridylate synthase [Xanthomonas axonopodis pv. citri str.
           306]
          Length = 192

 Score = 91.4 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 46/175 (26%), Positives = 80/175 (45%), Gaps = 15/175 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L +KP G+++  SD             +   V + GRLD ++EGLL+LT+DG LA  L
Sbjct: 4   LVLLNKPYGVLSQFSDRSQPPKRTLAEFGLPPDVYAAGRLDHDSEGLLVLTDDGALAHRL 63

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y V+  G    + L  L+ G+ +        QV +               
Sbjct: 64  TDPRHKQPKTYWVQVEGAPQAEHLQALRDGVALNDGPTRPAQVRMLDPAPQLWPRDPPVR 123

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +   +AW+ + + EG+NR+++++         RL+R++ G ++L  L  G  R
Sbjct: 124 VRKTVPDAWLELQITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLDALAPGQWR 178


>gi|218439161|ref|YP_002377490.1| pseudouridine synthase [Cyanothece sp. PCC 7424]
 gi|218171889|gb|ACK70622.1| pseudouridine synthase [Cyanothece sp. PCC 7424]
          Length = 203

 Score = 91.4 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 48/195 (24%), Positives = 81/195 (41%), Gaps = 25/195 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDG 128
              R  +++KP  ++   +D    +T    L        V  VGRLD+++EGLLLLT+DG
Sbjct: 1   MSYRYIVFYKPYNVLCQFTDEGNSTTSRQTLKDYINIPNVYPVGRLDLDSEGLLLLTDDG 60

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT------- 181
            L   L        R Y V+     D+  LN L++G+ I+        V +         
Sbjct: 61  QLQHRLAHRKFAHPRTYWVQVENIPDEPALNRLREGVKIKDYQTRKAWVKVFPTEPPLPP 120

Query: 182 --------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG--------PFQL 225
                   +     W+ + L EG+NR+++++     +   RL+R++ G           L
Sbjct: 121 RNPPIRYRKNIPTCWLEITLTEGRNRQVRRMTAAVGYPTLRLVRVAMGIGKGKNGFQLDL 180

Query: 226 GTLLAGSTREVSKKI 240
             L  G  R+V+   
Sbjct: 181 KGLEPGQWRDVTDIE 195


>gi|159028310|emb|CAO87208.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 194

 Score = 91.4 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 54/196 (27%), Positives = 88/196 (44%), Gaps = 22/196 (11%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +  L++KP  ++   +D +GRST+ D +P     + SVGRLD ++EGLLLLT++G L 
Sbjct: 1   MNKYILFYKPYDVLCQFTDENGRSTLKDYIPIP--NIYSVGRLDRDSEGLLLLTDNGQLQ 58

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----------- 180
             L        R Y V+     D + L  L++G+ IQ        V +            
Sbjct: 59  HRLGHRQFAHPRTYWVQVERIPDLNALEKLRQGLAIQDYRTRPAIVNILDFEPDLPPREP 118

Query: 181 ----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY-----GPFQLGTLLAG 231
                +    AW+ + L EG+NR+++++     +   RLIR +          L  L  G
Sbjct: 119 PIRYRKSIPTAWLEITLTEGRNRQVRRMTAAVGYPTLRLIRTAITIDKNNKLCLTGLQPG 178

Query: 232 STREVSKKILREQLGP 247
             REV++K  +     
Sbjct: 179 QWREVTEKERKALERL 194


>gi|103487783|ref|YP_617344.1| pseudouridine synthase, Rsu [Sphingopyxis alaskensis RB2256]
 gi|98977860|gb|ABF54011.1| ribosomal large subunit pseudouridine synthase E [Sphingopyxis
           alaskensis RB2256]
          Length = 185

 Score = 91.4 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 36/143 (25%), Positives = 66/143 (46%), Gaps = 14/143 (9%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              GRLD ++EGLL+LT+DG L   +  P  +  + Y  +  G+ D   L+ L +G+ + 
Sbjct: 43  YPAGRLDKDSEGLLVLTDDGALQARISSPKHKMPKTYLAQVEGEPDDAALDALARGVTLN 102

Query: 169 GICYGDMQVTLD--------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                   V                  +   ++W+ + + EG+NR+++++         R
Sbjct: 103 DGPTRPATVRRIGAPKLWDRDPPVRYRKSVPDSWLELTITEGRNRQVRRMTAAVGHPTLR 162

Query: 215 LIRISYGPFQLGTLLAGSTREVS 237
           L+R   G +++G L  G+ REV 
Sbjct: 163 LVRWRIGGWEIGDLAVGAWREVK 185


>gi|66047563|ref|YP_237404.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. syringae
           B728a]
 gi|63258270|gb|AAY39366.1| Pseudouridine synthase, Rsu [Pseudomonas syringae pv. syringae
           B728a]
 gi|330969466|gb|EGH69532.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. aceris str.
           M302273PT]
          Length = 210

 Score = 91.4 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 50/185 (27%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                RL L++KP  ++T  SD +GR+T+ D +          GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPRLILFNKPFDVLTQFSDEEGRATLKDFIKIPGI--YPAGRLDRDSEGLLLLTNDG 84

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+   ++L  L+ G+ +        +            
Sbjct: 85  QLQARIADPKHKLAKTYWVQVEGEPSDEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPR 144

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  R
Sbjct: 145 NPPVRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLEGLDQGQYR 204

Query: 235 EVSKK 239
           EV+ K
Sbjct: 205 EVAAK 209


>gi|187732570|ref|YP_001879943.1| 23S rRNA pseudouridine synthase E [Shigella boydii CDC 3083-94]
 gi|187429562|gb|ACD08836.1| ribosomal large subunit pseudouridine synthase E [Shigella boydii
           CDC 3083-94]
          Length = 217

 Score = 91.4 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 49/189 (25%), Positives = 88/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 31  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 89  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPA 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 149 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLA 208

Query: 230 AGSTREVSK 238
            G  RE ++
Sbjct: 209 NGEWREATE 217


>gi|88703375|ref|ZP_01101091.1| Ribosomal large subunit pseudouridine synthase E [Congregibacter
           litoralis KT71]
 gi|88702089|gb|EAQ99192.1| Ribosomal large subunit pseudouridine synthase E [Congregibacter
           litoralis KT71]
          Length = 201

 Score = 91.4 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 48/174 (27%), Positives = 87/174 (50%), Gaps = 16/174 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L+HKP  +++  +D +GR T+ D +    +   + GRLD ++EGLLLL NDG L + +
Sbjct: 4   LILFHKPYRVLSQFTDSEGRGTLGDFIT--KAGFYAAGRLDYDSEGLLLLCNDGRLQQRI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT------------- 181
             P  +  + Y V+  G + +  L  L+ G+ ++       + ++               
Sbjct: 62  ADPRFKLWKSYAVQLEGDITEAALCSLRDGVELKDGATLPARASIIRTPAFWPRNPPIRE 121

Query: 182 -QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +  + +WV + +REG+NR+++++     + V RLIR   G + L  L  G  R
Sbjct: 122 RKTQTTSWVEISIREGRNRQVRRMCAKVGFPVLRLIRTRIGDWGLDDLAPGEYR 175


>gi|331672646|ref|ZP_08373435.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Escherichia coli TA280]
 gi|331070289|gb|EGI41655.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Escherichia coli TA280]
          Length = 217

 Score = 91.4 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 88/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 31  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 89  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGRTLPAGVELVDEPT 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 149 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 208

Query: 230 AGSTREVSK 238
            G  REV+ 
Sbjct: 209 NGEWREVTD 217


>gi|332342737|gb|AEE56071.1| ribosomal pseudouridine synthase, large subunit [Escherichia coli
           UMNK88]
          Length = 207

 Score = 91.4 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 48/189 (25%), Positives = 88/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 21  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD +  L+ G+ +                 
Sbjct: 79  TNNGALQARLTQPGKRTGKIYYVQVEGFPTQDAIEALRNGVTLNDGPTLPAGAELVDEPA 138

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 139 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLA 198

Query: 230 AGSTREVSK 238
            G  RE ++
Sbjct: 199 NGEWREATE 207


>gi|77360629|ref|YP_340204.1| ribosomal large subunit pseudouridine synthase E (pseudouridylate
           synthase) (Uracil hydrolyase) [Pseudoalteromonas
           haloplanktis TAC125]
 gi|76875540|emb|CAI86761.1| ribosomal large subunit pseudouridine synthase E (Pseudouridylate
           synthase) (Uracil hydrolyase) [Pseudoalteromonas
           haloplanktis TAC125]
          Length = 227

 Score = 91.4 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 45/190 (23%), Positives = 87/190 (45%), Gaps = 16/190 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P   A+  ++ L++KP  ++   +D   R T+ + +P     V + GRLD ++EGLLLL
Sbjct: 38  KPAIAAQDIKIVLFNKPFDVLCQFTDDANRKTLAEFIPIK--EVYAAGRLDRDSEGLLLL 95

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---- 180
           TN G L   L  P  +  + Y V+  G+   + +  L  G+ ++       +V++     
Sbjct: 96  TNCGKLQNTLTAPGKKTSKTYWVQVEGEPSSESIAALCTGVELKDGLTLPAKVSIISEPT 155

Query: 181 ----------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                      +     W+++ + EG+NR+++++         RLIR S G + L  +  
Sbjct: 156 VWTRNPPVRERKLIPTTWLSITISEGRNRQVRRMTAHIGHPTLRLIRYSIGKYTLDGIKN 215

Query: 231 GSTREVSKKI 240
           G  + ++   
Sbjct: 216 GEYKVMTGIE 225


>gi|291336757|gb|ADD96295.1| hypothetical protein [uncultured organism MedDCM-OCT-S08-C1656]
          Length = 169

 Score = 91.4 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 44/166 (26%), Positives = 78/166 (46%), Gaps = 3/166 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
            N    ++ K +A AG+ SRR+ E  I    V +NG   +     +  +D ++V+G  ++
Sbjct: 4   TNSQRPKLQKFLADAGLCSRRKGEEWIEDGLVTINGENAKLGERVIPDSDIVKVNGKRVQ 63

Query: 69  KAERTRL-WLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLT 125
                 +  L +KP G   ++ D      +F+ L       R+   GRLD+++EG+++LT
Sbjct: 64  VKRIPNITLLVNKPKGYTCSNDDEYADRLIFELLESKYRSVRLFCAGRLDVDSEGMVILT 123

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           N+G LA  L  PS    + Y++      D   L  L  G +++   
Sbjct: 124 NNGTLAHRLTHPSQMVRKKYKIEIDTPFDTKDLPSLINGELVEEEF 169


>gi|325920868|ref|ZP_08182763.1| ribosomal large subunit pseudouridine synthase E [Xanthomonas
           gardneri ATCC 19865]
 gi|325548620|gb|EGD19579.1| ribosomal large subunit pseudouridine synthase E [Xanthomonas
           gardneri ATCC 19865]
          Length = 190

 Score = 91.4 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 48/175 (27%), Positives = 80/175 (45%), Gaps = 15/175 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L +KP G+++  SD             + + V + GRLD ++EGLLLLT+DG LA  L
Sbjct: 2   LVLLNKPYGVLSQFSDRSQPPKRTLAEFGLPADVYAAGRLDHDSEGLLLLTDDGALAHRL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------VTL 179
             P  +  + Y V+  G     +L  L+ G+V+        +                  
Sbjct: 62  TDPRHKQPKTYWVQVEGTPAPSQLQALRDGVVLNDGPTRPAKVRSIDPSPQVWPRDPPVR 121

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +   +AW+ + + EG+NR+++++         RLIR++ G + L TL  G  R
Sbjct: 122 VRKTVPDAWLELQITEGRNRQVRRMTASVGLPTLRLIRVAIGDWTLDTLAPGQWR 176


>gi|294636775|ref|ZP_06715113.1| ribosomal large subunit pseudouridine synthase E [Edwardsiella
           tarda ATCC 23685]
 gi|291089990|gb|EFE22551.1| ribosomal large subunit pseudouridine synthase E [Edwardsiella
           tarda ATCC 23685]
          Length = 178

 Score = 91.4 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 40/144 (27%), Positives = 68/144 (47%), Gaps = 15/144 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LTNDG L   L  P  +  +VY V+  G+  +  L   ++G+ ++
Sbjct: 33  YAAGRLDRDSEGLLVLTNDGQLQAQLTQPGKRTGKVYYVQVEGEPTEHDLARFRQGLTLK 92

Query: 169 GICYGDMQ---------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  Q                  + +    +W+ + L EG+NR+++++     +   
Sbjct: 93  DGPTLPAQAERVAEPEWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHIGYPTL 152

Query: 214 RLIRISYGPFQLGTLLAGSTREVS 237
           RLIR S G   L  L +G  RE+ 
Sbjct: 153 RLIRYSMGSITLEDLASGCWREID 176


>gi|323499463|ref|ZP_08104434.1| ribosomal large subunit pseudouridine synthase E [Vibrio
           sinaloensis DSM 21326]
 gi|323315450|gb|EGA68490.1| ribosomal large subunit pseudouridine synthase E [Vibrio
           sinaloensis DSM 21326]
          Length = 230

 Score = 91.4 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 52/187 (27%), Positives = 96/187 (51%), Gaps = 16/187 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E  ++ +++KP   ++  +D +GR T+ D +P     V + GRLD ++EGL++L
Sbjct: 45  KPKVAPEDRKVIVFNKPFDTLSQFTDGEGRKTLADFIP--VKDVYAAGRLDRDSEGLMVL 102

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   ++ L+ L+KG+ ++       +V +  +  
Sbjct: 103 TNDGVLQAKLTQPQSKSPKTYWVQVDGAPSEEDLDKLRKGVELKDGMTLPAKVEVMDEPS 162

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+++ + EG+NR+++++     +   RLIR S G  +LG L  
Sbjct: 163 VWERNPPVRFRANIPTTWLSITIIEGRNRQVRRMTANIGFPTLRLIRYSMGDIKLGDLQP 222

Query: 231 GSTREVS 237
           G+ +EVS
Sbjct: 223 GAWKEVS 229


>gi|212712843|ref|ZP_03320971.1| hypothetical protein PROVALCAL_03940 [Providencia alcalifaciens DSM
           30120]
 gi|212684535|gb|EEB44063.1| hypothetical protein PROVALCAL_03940 [Providencia alcalifaciens DSM
           30120]
          Length = 178

 Score = 91.0 bits (224), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 40/144 (27%), Positives = 67/144 (46%), Gaps = 15/144 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LTNDG L   L  P  +  +VY  +  G  D+  L   ++G+ + 
Sbjct: 33  YAAGRLDRDSEGLLVLTNDGKLQAELTQPQKKTGKVYYAQVEGVPDETALAKFRQGLTLN 92

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +    +W+ + L EG+NR+++++     +   
Sbjct: 93  DGPTLPAGIERVDEPEWLWVRNPPIRERKNIPTSWLKITLYEGRNRQVRRMTANIGFPTL 152

Query: 214 RLIRISYGPFQLGTLLAGSTREVS 237
           RLIR S G F L  L +G  +EV+
Sbjct: 153 RLIRYSMGSFTLNNLSSGEWKEVT 176


>gi|194470599|ref|ZP_03076583.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|205358660|ref|ZP_02658177.2| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
 gi|194456963|gb|EDX45802.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|205332703|gb|EDZ19467.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
          Length = 245

 Score = 91.0 bits (224), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 51/187 (27%), Positives = 88/187 (47%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLL+LTND
Sbjct: 58  KENQLKRVVLFNKPYDVLPQFTDEAGRRTLKDFIPVQGV--YAAGRLDRDSEGLLVLTND 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P  +  ++Y V+  G  D   L  L+ G+ +                    
Sbjct: 116 GALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 175

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G 
Sbjct: 176 PRTPPIRERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQ 235

Query: 233 TREVSKK 239
            RE++++
Sbjct: 236 WREIAQE 242


>gi|290475825|ref|YP_003468717.1| Ribosomal large subunit pseudouridine synthase E [Xenorhabdus
           bovienii SS-2004]
 gi|289175150|emb|CBJ81953.1| Ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Xenorhabdus bovienii SS-2004]
          Length = 227

 Score = 91.0 bits (224), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 55/181 (30%), Positives = 90/181 (49%), Gaps = 17/181 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             R+ +++KP  ++   +D  GR+T+ D +P  F  V + GRLD ++EGLL+LTNDG L 
Sbjct: 47  PRRVLIFNKPYDVLPQFTDEMGRTTLKDFIP--FPDVYAAGRLDRDSEGLLILTNDGKLQ 104

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------Q 176
             L  P  +  +VY V+  G  D+  LN L+ G+ ++                       
Sbjct: 105 AKLTQPHKKTAKVYYVQVEGIPDESTLNKLRNGVTLKDGPTLSAGAELVEEPEWLWERTP 164

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + L EG+NR+++++     +   RLIR S G  QLG L  G  RE+
Sbjct: 165 PIRERKNIPVSWLKITLFEGRNRQVRRMTAHVGFPTLRLIRFSIGSLQLGQLSPGEWREI 224

Query: 237 S 237
            
Sbjct: 225 D 225


>gi|161614528|ref|YP_001588493.1| hypothetical protein SPAB_02277 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|194442636|ref|YP_002040493.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Newport str. SL254]
 gi|197250532|ref|YP_002146804.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Agona str. SL483]
 gi|197263615|ref|ZP_03163689.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|205357418|ref|ZP_02347541.2| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|161363892|gb|ABX67660.1| hypothetical protein SPAB_02277 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|194401299|gb|ACF61521.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Newport str. SL254]
 gi|197214235|gb|ACH51632.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Agona str. SL483]
 gi|197241870|gb|EDY24490.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|205321847|gb|EDZ09686.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|323129507|gb|ADX16937.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|326628108|gb|EGE34451.1| RNA pseudouridylate synthase [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 9]
          Length = 245

 Score = 91.0 bits (224), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 51/187 (27%), Positives = 88/187 (47%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLL+LTND
Sbjct: 58  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIPVQGV--YAAGRLDRDSEGLLVLTND 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P  +  ++Y V+  G  D   L  L+ G+ +                    
Sbjct: 116 GALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 175

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G 
Sbjct: 176 PRTPPIRERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQ 235

Query: 233 TREVSKK 239
            RE++++
Sbjct: 236 WREIAQE 242


>gi|34098591|sp|Q8PQN3|RLUE_XANAC RecName: Full=Ribosomal large subunit pseudouridine synthase E;
           AltName: Full=rRNA pseudouridylate synthase E; AltName:
           Full=rRNA-uridine isomerase E
          Length = 190

 Score = 91.0 bits (224), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 46/175 (26%), Positives = 80/175 (45%), Gaps = 15/175 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L +KP G+++  SD             +   V + GRLD ++EGLL+LT+DG LA  L
Sbjct: 2   LVLLNKPYGVLSQFSDRSQPPKRTLAEFGLPPDVYAAGRLDHDSEGLLVLTDDGALAHRL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y V+  G    + L  L+ G+ +        QV +               
Sbjct: 62  TDPRHKQPKTYWVQVEGAPQAEHLQALRDGVALNDGPTRPAQVRMLDPAPQLWPRDPPVR 121

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +   +AW+ + + EG+NR+++++         RL+R++ G ++L  L  G  R
Sbjct: 122 VRKTVPDAWLELQITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLDALAPGQWR 176


>gi|224824759|ref|ZP_03697866.1| pseudouridine synthase [Lutiella nitroferrum 2002]
 gi|224603252|gb|EEG09428.1| pseudouridine synthase [Lutiella nitroferrum 2002]
          Length = 225

 Score = 91.0 bits (224), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 47/180 (26%), Positives = 85/180 (47%), Gaps = 17/180 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L L++KP G++   S  +   T+ D++          GRLD ++EGLLLLT DG L 
Sbjct: 1   MPQLILFNKPYGVICQFSQHELHPTLKDHIDIPGV--YPAGRLDTDSEGLLLLTGDGELQ 58

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----------- 180
             +  P  +  + Y V+  G   +++L  L+ G+ +        +V L            
Sbjct: 59  HRISDPRWKQSKTYWVQVEGTPVEEQLEALRAGVNLGDFITQPAEVRLLSEPPQLWERKP 118

Query: 181 ----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +   +AW+ + + EGKNR+++++         RL+R++ GP++L  L  G  R +
Sbjct: 119 PVRFRKTVPDAWLEIIISEGKNRQVRRMTAKVGLPTLRLVRVAVGPWRLDGLQPGEFRRL 178


>gi|320184392|gb|EFW59203.1| 23S rRNA pseudouridine synthase E [Shigella flexneri CDC 796-83]
          Length = 207

 Score = 91.0 bits (224), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 49/189 (25%), Positives = 88/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 21  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 79  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPA 138

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 139 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLA 198

Query: 230 AGSTREVSK 238
            G  RE ++
Sbjct: 199 NGEWREATE 207


>gi|331657199|ref|ZP_08358161.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Escherichia coli TA206]
 gi|315296604|gb|EFU55899.1| conserved hypothetical protein [Escherichia coli MS 16-3]
 gi|331055447|gb|EGI27456.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Escherichia coli TA206]
          Length = 217

 Score = 91.0 bits (224), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 49/184 (26%), Positives = 86/184 (46%), Gaps = 17/184 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+LTN+G 
Sbjct: 36  NQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVLTNNGA 93

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-------------- 175
           L   L  P  +  ++Y V+  G   QD L  L+ G+ +                      
Sbjct: 94  LQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPR 153

Query: 176 -QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R
Sbjct: 154 NPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGNYSLDNLANGEWR 213

Query: 235 EVSK 238
           E + 
Sbjct: 214 EATD 217


>gi|194447665|ref|YP_002045239.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL476]
 gi|205359348|ref|ZP_02669243.2| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|194405969|gb|ACF66188.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL476]
 gi|205336733|gb|EDZ23497.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
          Length = 245

 Score = 91.0 bits (224), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 51/187 (27%), Positives = 88/187 (47%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLL+LTND
Sbjct: 58  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIPVQGV--YAAGRLDRDSEGLLVLTND 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P  +  ++Y V+  G  D   L  L+ G+ +                    
Sbjct: 116 GALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEMVAEPDWLW 175

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G 
Sbjct: 176 PRTPPIRERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQ 235

Query: 233 TREVSKK 239
            RE++++
Sbjct: 236 WREIAQE 242


>gi|82544378|ref|YP_408325.1| 23S rRNA pseudouridine synthase E [Shigella boydii Sb227]
 gi|81245789|gb|ABB66497.1| conserved hypothetical protein [Shigella boydii Sb227]
          Length = 207

 Score = 91.0 bits (224), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 49/189 (25%), Positives = 88/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 21  RRKHENQPTRVILFNKPYDVLPQFTDETGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 79  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPA 138

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 139 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLA 198

Query: 230 AGSTREVSK 238
            G  RE ++
Sbjct: 199 NGEWREATE 207


>gi|223041724|ref|ZP_03611918.1| ribosomal large subunit pseudouridine synthase E [Actinobacillus
           minor 202]
 gi|223017462|gb|EEF15879.1| ribosomal large subunit pseudouridine synthase E [Actinobacillus
           minor 202]
          Length = 224

 Score = 91.0 bits (224), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 53/185 (28%), Positives = 89/185 (48%), Gaps = 17/185 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E T + L++KP  ++T  +D  GR T+ D +         VGRLD ++EGLLLLTN+G +
Sbjct: 29  EETIIVLFNKPYDVLTQFTDEQGRKTLKDFIDIPKI--YPVGRLDRDSEGLLLLTNNGEI 86

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------ 178
              L  P  +  + Y V+  G   Q  L  L+KG+ ++       +              
Sbjct: 87  QHRLAHPKFEKEKTYWVQVEGIPSQADLAKLEKGVELKDGLTQPAKAKQIEAPDFDWQTA 146

Query: 179 ---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + + EGKNR+++++     +   RLIR+  G +QLG L +G  R 
Sbjct: 147 PKIRERKTVPTSWIELKITEGKNRQVRRMTAHIGFPTLRLIRVGLGHYQLGELGSGEYRI 206

Query: 236 VSKKI 240
           +S   
Sbjct: 207 LSLSE 211


>gi|301024579|ref|ZP_07188251.1| conserved hypothetical protein [Escherichia coli MS 69-1]
 gi|300396504|gb|EFJ80042.1| conserved hypothetical protein [Escherichia coli MS 69-1]
          Length = 212

 Score = 91.0 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 49/189 (25%), Positives = 87/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 26  KRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 83

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 84  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGSTLPAGVELVDEPA 143

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 144 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 203

Query: 230 AGSTREVSK 238
            G  RE + 
Sbjct: 204 NGEWREATD 212


>gi|289669952|ref|ZP_06491027.1| pseudouridylate synthase [Xanthomonas campestris pv. musacearum
           NCPPB4381]
          Length = 190

 Score = 91.0 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 48/175 (27%), Positives = 82/175 (46%), Gaps = 15/175 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L +KP G+++  SD             +   V + GRLD ++EGLLLLT+DG LA  L
Sbjct: 2   LVLLNKPYGVLSQFSDRSQPPKRTLAEFGLPPDVYAAGRLDHDSEGLLLLTDDGALAHRL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------VTL 179
             P  +  + Y V+  G+   ++L  L+ G+V+        Q                  
Sbjct: 62  TDPRHKQPKTYWVQVEGEPQAEQLQALRDGVVLNDGPTLPAQVRSLDPVPQLWPRDPPVR 121

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +   +AW+ + + EG+NR+++++         RL+R++ G ++L TL  G  R
Sbjct: 122 VRKTVPDAWLELQITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLDTLAPGQWR 176


>gi|289664922|ref|ZP_06486503.1| pseudouridylate synthase [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 190

 Score = 91.0 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 48/175 (27%), Positives = 82/175 (46%), Gaps = 15/175 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L +KP G+++  SD             +   V + GRLD ++EGLLLLT+DG LA  L
Sbjct: 2   LVLLNKPYGVLSQFSDRSQPPKRTLAEFGLPPDVYAAGRLDHDSEGLLLLTDDGALAHRL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------VTL 179
             P  +  + Y V+  G+   ++L  L+ G+V+        Q                  
Sbjct: 62  TDPRHKQPKTYWVQVEGEPQAEQLQALRDGVVLNDGPTLPAQVRSLDPAPQLWPRDPPVR 121

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +   +AW+ + + EG+NR+++++         RL+R++ G ++L TL  G  R
Sbjct: 122 VRKTVPDAWLELQITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLDTLAPGQWR 176


>gi|218700342|ref|YP_002407971.1| 23S rRNA pseudouridine synthase E [Escherichia coli IAI39]
 gi|218370328|emb|CAR18131.1| 23S rRNA pseudouridine synthase [Escherichia coli IAI39]
          Length = 216

 Score = 91.0 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 49/189 (25%), Positives = 87/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 30  KRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 87

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 88  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGVDLVEEPE 147

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 148 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTANVGFPTLRLIRYAMGDYSLDNLA 207

Query: 230 AGSTREVSK 238
            G  RE + 
Sbjct: 208 NGEWREATD 216


>gi|145298401|ref|YP_001141242.1| ribosomal large subunit pseudouridine synthase E [Aeromonas
           salmonicida subsp. salmonicida A449]
 gi|142851173|gb|ABO89494.1| ribosomal large subunit pseudouridine synthase E [Aeromonas
           salmonicida subsp. salmonicida A449]
          Length = 321

 Score = 91.0 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 56/285 (19%), Positives = 97/285 (34%), Gaps = 31/285 (10%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P       +L L +KP  ++   +D  GR T+ D +        + GRLD ++EGLLLL
Sbjct: 49  KPQVAPADRKLLLLNKPYMVLCQFTDEAGRETLKDYIKEPGI--YAAGRLDRDSEGLLLL 106

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TNDG L   L  P  +  + Y V+  G   +++L  L+ G+ +        +        
Sbjct: 107 TNDGKLQARLTQPGEKTPKTYWVQVEGIPSEEELAALRAGVELNDGLTLPAEARLMDEPN 166

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--- 227
                    + ++    W+ + + EG+NR+++++         RLIR + G + LG    
Sbjct: 167 VWPRNPPIRERKEVPTRWLEIKIVEGRNRQVRRMTAHIGHPTLRLIRYAIGDWTLGNWQE 226

Query: 228 --LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
             L  G +R +    L                      + +      N          R 
Sbjct: 227 DGLAPGESRSLPAPEL----------APVSPARPRKPQTGSSTAKPANDRPRRTAQSNRK 276

Query: 286 KKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ 330
               S       Q     P   +  +S    A+            
Sbjct: 277 NPPRSAGKPAIDQAGSRPPAESKPRSSGRGTARRPARHTTDKESS 321


>gi|229592774|ref|YP_002874893.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           fluorescens SBW25]
 gi|229364640|emb|CAY52558.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           fluorescens SBW25]
          Length = 211

 Score = 91.0 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 48/185 (25%), Positives = 86/185 (46%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  SD  GR+T+ D +          GRLD ++EGLLLLTNDG
Sbjct: 28  PPAEPKLILFNKPFDVLTQFSDEGGRATLKDFIDIPGI--YPAGRLDRDSEGLLLLTNDG 85

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+  +++L  L+ G+ +        +  L         
Sbjct: 86  QLQARIADPKHKLAKTYWVQVEGEPTEEQLQRLRDGVALNDGKTLPAEARLLEEPALWPR 145

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +     W+ + +REG+NR+++++         RL+R+  G + +  L  G  +
Sbjct: 146 NPPVRFRKSVPTHWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWTIDGLDQGQWK 205

Query: 235 EVSKK 239
           EV  +
Sbjct: 206 EVPAR 210


>gi|218506664|ref|ZP_03504542.1| pseudouridylate synthase, subunit B protein [Rhizobium etli Brasil
           5]
          Length = 157

 Score = 91.0 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 72/110 (65%), Positives = 87/110 (79%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R+SKV+ARAG+ASRR++ERMI + RV +NG +LE   VNV   D IEVDGVP+R 
Sbjct: 48  EAKAERISKVMARAGVASRRDIERMIMEGRVTLNGKVLETPVVNVTLADRIEVDGVPIRG 107

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
            ERTRLWLYHKP GLVTT++DP+GR TVFDNLP    RV+S+GRLDINTE
Sbjct: 108 IERTRLWLYHKPAGLVTTNADPEGRPTVFDNLPEELPRVMSIGRLDINTE 157


>gi|299533715|ref|ZP_07047087.1| Pseudouridine synthase, Rsu [Comamonas testosteroni S44]
 gi|298718264|gb|EFI59249.1| Pseudouridine synthase, Rsu [Comamonas testosteroni S44]
          Length = 223

 Score = 90.6 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 50/188 (26%), Positives = 82/188 (43%), Gaps = 17/188 (9%)

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            V   P  + E TRL  +HKP G+++  +                  V   GRLD ++EG
Sbjct: 29  TVVRQPAPRPEVTRLLCFHKPYGVLSQFTPEG--KWQGLKDWIDVPGVYVAGRLDADSEG 86

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLLLTNDG L   +  P  +  + Y V+  G  D+  L  L++G+ +        +  L 
Sbjct: 87  LLLLTNDGQLQARIADPRHKMEKTYWVQVEGIPDEAALQRLREGVELSDGKTLPAKARLI 146

Query: 181 ---------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                           Q   + W+ + +REGKNR+++++         RL+R++ GP+ +
Sbjct: 147 EPQPLMWPRNPPIRVRQNIPDCWIELIIREGKNRQVRRMTAAVGHPTLRLVRMAVGPYSI 206

Query: 226 GTLLAGST 233
             L  G  
Sbjct: 207 EGLEPGQW 214


>gi|51244671|ref|YP_064555.1| ribosomal large subunit pseudouridine synthase B [Desulfotalea
           psychrophila LSv54]
 gi|50875708|emb|CAG35548.1| probable ribosomal large subunit pseudouridine synthase B
           [Desulfotalea psychrophila LSv54]
          Length = 130

 Score = 90.6 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 31/111 (27%), Positives = 55/111 (49%)

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            +    PS +  + Y     G   + KL  L++GI+++G      +V + +QK  +  V 
Sbjct: 12  PKRPCHPSYETFKTYEADLSGTPSRAKLQRLEQGILLEGKPTAPARVKILSQKKHSTKVA 71

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + EG+  ++KK+F      VN L RI+YG  +L TL  G  + +S   +
Sbjct: 72  ITIHEGRKHQVKKMFAAIGHPVNHLKRIAYGKLELQTLATGQFKRLSPTEI 122


>gi|323493242|ref|ZP_08098371.1| ribosomal large subunit pseudouridine synthase E [Vibrio
           brasiliensis LMG 20546]
 gi|323312508|gb|EGA65643.1| ribosomal large subunit pseudouridine synthase E [Vibrio
           brasiliensis LMG 20546]
          Length = 230

 Score = 90.6 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 44/186 (23%), Positives = 80/186 (43%), Gaps = 17/186 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +   +R  +          T     DG              + + GRLD ++EGL++LT
Sbjct: 47  RISAQDRKVVVFNKP---FDTLSQFTDGEGRKTLADYIPIKDIYAAGRLDRDSEGLMVLT 103

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--- 182
           NDG L   L  PS++  + Y V+  G  ++  L+ L+KG+ ++       +V +  +   
Sbjct: 104 NDGILQARLTQPSSKSPKTYWVQVDGAPNEADLDKLRKGVELKDGMTLPAKVEVMAEPSV 163

Query: 183 -----------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + + EG+NR+++++     +   RLIR S G   LG L  G
Sbjct: 164 WERNPPVRFRANIPTTWIAITIVEGRNRQVRRMTANIGFPTLRLIRYSMGDVTLGDLQPG 223

Query: 232 STREVS 237
             +E++
Sbjct: 224 EWKEIT 229


>gi|320540370|ref|ZP_08040020.1| putative 16S RNA U516 pseudouridine synthase [Serratia symbiotica
           str. Tucson]
 gi|320029301|gb|EFW11330.1| putative 16S RNA U516 pseudouridine synthase [Serratia symbiotica
           str. Tucson]
          Length = 203

 Score = 90.6 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 49/188 (26%), Positives = 85/188 (45%), Gaps = 17/188 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +   +  R+ L++KP  ++   +D  GR+T+   +P  F+ V + GRLD ++EGLL+L
Sbjct: 16  KHVAAQDLYRVVLFNKPFDVLPQFTDAAGRTTLKAFIP--FTDVYAAGRLDRDSEGLLVL 73

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
            N+G L   L  P  +  +VY V+  G      L  L+ G+ ++                
Sbjct: 74  NNEGKLQAQLTQPGKRIGKVYFVQVEGVPQDRDLTPLRHGVTLKDGPTLPAIVERVDEPQ 133

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ + L EG+NR+I+++     +   RLIR S G   LG L 
Sbjct: 134 WLWPRNPPIRERKSIPTTWLKITLFEGRNRQIRRMTAHIGFPTLRLIRYSMGNLSLGELQ 193

Query: 230 AGSTREVS 237
            G  + + 
Sbjct: 194 PGEWKNLD 201


>gi|82777254|ref|YP_403603.1| 23S rRNA pseudouridine synthase E [Shigella dysenteriae Sd197]
 gi|81241402|gb|ABB62112.1| conserved hypothetical protein [Shigella dysenteriae Sd197]
          Length = 207

 Score = 90.6 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 49/184 (26%), Positives = 87/184 (47%), Gaps = 17/184 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+LTN+G 
Sbjct: 26  NQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVLTNNGA 83

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-------------- 175
           L   L  P  +  ++Y V+  G   QD L  L+ G+ +                      
Sbjct: 84  LQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPR 143

Query: 176 -QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R
Sbjct: 144 NPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLANGEWR 203

Query: 235 EVSK 238
           E ++
Sbjct: 204 EATE 207


>gi|189405961|ref|ZP_02825460.2| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. EC508]
 gi|189377278|gb|EDU95694.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. EC508]
          Length = 207

 Score = 90.6 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 49/184 (26%), Positives = 87/184 (47%), Gaps = 17/184 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+LTN+G 
Sbjct: 26  NQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVLTNNGA 83

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-------------- 175
           L   L  P  +  ++Y V+  G   QD L  L+ G+ +                      
Sbjct: 84  LQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPR 143

Query: 176 -QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R
Sbjct: 144 NPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWR 203

Query: 235 EVSK 238
           E ++
Sbjct: 204 EATE 207


>gi|74311694|ref|YP_310113.1| 23S rRNA pseudouridine synthase E [Shigella sonnei Ss046]
 gi|73855171|gb|AAZ87878.1| conserved hypothetical protein [Shigella sonnei Ss046]
          Length = 207

 Score = 90.6 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 88/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD +TEGLL+L
Sbjct: 21  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDTEGLLVL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 79  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPA 138

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 139 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLA 198

Query: 230 AGSTREVSK 238
            G  RE ++
Sbjct: 199 NGEWREATE 207


>gi|166364490|ref|YP_001656763.1| ribosomal large subunit pseudouridine synthase E [Microcystis
           aeruginosa NIES-843]
 gi|166086863|dbj|BAG01571.1| ribosomal large subunit pseudouridine synthase E [Microcystis
           aeruginosa NIES-843]
          Length = 194

 Score = 90.6 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 53/196 (27%), Positives = 86/196 (43%), Gaps = 22/196 (11%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +  L++KP  ++   +D +GRST+ D +P     + SVGRLD ++EGLLLLT++G L 
Sbjct: 1   MNKYILFYKPYDVLCQFTDENGRSTLKDYIPIP--NIYSVGRLDRDSEGLLLLTDNGQLQ 58

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------Q 176
             L        R Y V+     D + L  L++G+ IQ                       
Sbjct: 59  HRLGHRQFAHPRTYWVQVERIPDLNALEKLRQGLPIQDYRTRPAIVNLLDFEPDLPPREP 118

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY-----GPFQLGTLLAG 231
                +    AW+ + L EG+NR+++++     +   RLIR +          L  L  G
Sbjct: 119 PIRYRKSVPTAWLEITLTEGRNRQVRRMTAAVGYPTLRLIRTAITIDKNNKLCLTGLQPG 178

Query: 232 STREVSKKILREQLGP 247
             REV++K  +     
Sbjct: 179 QWREVTEKERKALERL 194


>gi|167855378|ref|ZP_02478145.1| ribosomal large subunit pseudouridine synthase E [Haemophilus
           parasuis 29755]
 gi|219871231|ref|YP_002475606.1| pseudouridylate synthase [Haemophilus parasuis SH0165]
 gi|167853526|gb|EDS24773.1| ribosomal large subunit pseudouridine synthase E [Haemophilus
           parasuis 29755]
 gi|219691435|gb|ACL32658.1| pseudouridylate synthase [Haemophilus parasuis SH0165]
          Length = 220

 Score = 90.6 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 41/192 (21%), Positives = 80/192 (41%), Gaps = 18/192 (9%)

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            ++   L   E   + +      L    ++   ++            V  +GRLD ++EG
Sbjct: 14  RINNAKLTFDETIVVLVNKPYGVLSQFTNNQACKTLKEFI---SIPNVYPIGRLDKDSEG 70

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLLLTN+G +   L  P  +  + Y V+  G    + LN L  G++++       +V + 
Sbjct: 71  LLLLTNNGQIQHRLANPKFEKEKTYWVQIEGIPQPEDLNRLASGVILKDGLTKPAKVKII 130

Query: 181 T---------------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                           +    +W+ + + EGKNR+++++     +   RL+R+    F+L
Sbjct: 131 PDPHFKWQSAPKIRERKNIPTSWIELKIVEGKNRQVRRMTAHIGFPTLRLVRVGVSYFKL 190

Query: 226 GTLLAGSTREVS 237
           G+L  G    + 
Sbjct: 191 GSLAPGEYLILD 202


>gi|312966391|ref|ZP_07780613.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           2362-75]
 gi|312288844|gb|EFR16742.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           2362-75]
 gi|325497563|gb|EGC95422.1| 23S rRNA pseudouridine synthase E [Escherichia fergusonii ECD227]
          Length = 177

 Score = 90.6 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 38/145 (26%), Positives = 66/145 (45%), Gaps = 15/145 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LTN+G L   L  P  +  ++Y V+  G   +D L  L+ G+ + 
Sbjct: 33  YAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTEDALEALRNGVTLN 92

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +    +W+ + L EG+NR+++++     +   
Sbjct: 93  DGPTLPAGAEMVEEPEWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTL 152

Query: 214 RLIRISYGPFQLGTLLAGSTREVSK 238
           RLIR + G + L  L  G  RE + 
Sbjct: 153 RLIRYAMGDYSLDNLANGEWREATD 177


>gi|306814015|ref|ZP_07448188.1| 23S rRNA pseudouridine synthase E [Escherichia coli NC101]
 gi|305852652|gb|EFM53100.1| 23S rRNA pseudouridine synthase E [Escherichia coli NC101]
          Length = 207

 Score = 90.6 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 49/184 (26%), Positives = 86/184 (46%), Gaps = 17/184 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+LTN+G 
Sbjct: 26  NQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVLTNNGA 83

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-------------- 175
           L   L  P  +  ++Y V+  G   QD L  L+ G+ +                      
Sbjct: 84  LQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPR 143

Query: 176 -QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R
Sbjct: 144 NPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGNYSLDNLANGEWR 203

Query: 235 EVSK 238
           E + 
Sbjct: 204 EATD 207


>gi|16272636|ref|NP_438854.1| hypothetical protein HI0694 [Haemophilus influenzae Rd KW20]
 gi|1175289|sp|P44827|RLUE_HAEIN RecName: Full=Ribosomal large subunit pseudouridine synthase E;
           AltName: Full=rRNA pseudouridylate synthase E; AltName:
           Full=rRNA-uridine isomerase E
 gi|1573697|gb|AAC22354.1| conserved hypothetical protein [Haemophilus influenzae Rd KW20]
          Length = 240

 Score = 90.6 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 77/196 (39%), Gaps = 17/196 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L   E   +                D +             V + GRLD ++EGLL+L
Sbjct: 44  KTLSLDETKVVLFNKP---FDVLTQFTDEQGRATLKDFISIPNVYAAGRLDRDSEGLLIL 100

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TN+G L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +        
Sbjct: 101 TNNGELQHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKSAKVRLISEPN 160

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  
Sbjct: 161 LWERNPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGLLSINGLEN 220

Query: 231 GSTREVSKKILREQLG 246
           GS R +S   ++    
Sbjct: 221 GSFRLLSLDEIKALFQ 236


>gi|330938238|gb|EGH41915.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. pisi str.
           1704B]
          Length = 210

 Score = 90.6 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 49/185 (26%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  SD +GR+T+ D +          GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPKLILFNKPFDVLTQFSDEEGRATLKDFIKIPGI--YPAGRLDRDSEGLLLLTNDG 84

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+   ++L  L+ G+ +        +            
Sbjct: 85  QLQARIADPKHKLAKTYWVQVEGEPSDEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPR 144

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  R
Sbjct: 145 NPPVRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLEGLDQGQYR 204

Query: 235 EVSKK 239
           EV+ K
Sbjct: 205 EVAAK 209


>gi|119470121|ref|ZP_01612887.1| ribosomal large subunit pseudouridine synthase E [Alteromonadales
           bacterium TW-7]
 gi|119446542|gb|EAW27816.1| ribosomal large subunit pseudouridine synthase E [Alteromonadales
           bacterium TW-7]
          Length = 227

 Score = 90.6 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 46/188 (24%), Positives = 86/188 (45%), Gaps = 16/188 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P   A+  ++ L++KP  ++   +D   R T+ + +P     V + GRLD ++EGLLLL
Sbjct: 38  KPQIDAKDKKIVLFNKPFDVLCQFTDDADRKTLAEFIPIK--DVYAAGRLDRDSEGLLLL 95

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN G L   L  P+ +  + Y V+  G+   + +  L KG+ ++                
Sbjct: 96  TNCGKLQNTLTAPNKKTNKTYWVQVEGEPSTESIQALCKGVELKDGLTLPANVKMIEEPN 155

Query: 176 -----QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + +    +W+++ + EGKNR+++++         RLIR S G + L  +  
Sbjct: 156 IWQRTPPVRERKSIPTSWLSITINEGKNRQVRRMTAHIGHPTLRLIRYSIGNYTLDDINT 215

Query: 231 GSTREVSK 238
           G  + +  
Sbjct: 216 GEYKIIKG 223


>gi|56752508|ref|YP_173209.1| pseudouridine synthase [Synechococcus elongatus PCC 6301]
 gi|81300323|ref|YP_400531.1| pseudouridine synthase, Rsu [Synechococcus elongatus PCC 7942]
 gi|56687467|dbj|BAD80689.1| probable pseudouridine synthase [Synechococcus elongatus PCC 6301]
 gi|81169204|gb|ABB57544.1| Pseudouridine synthase, Rsu [Synechococcus elongatus PCC 7942]
          Length = 199

 Score = 90.6 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 52/190 (27%), Positives = 80/190 (42%), Gaps = 20/190 (10%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R  L+HKP  ++   S  D               V  VGRLD ++EGLLLLTN+G L  
Sbjct: 3   YRYLLFHKPYDVLCQFSPSDRPDQQTLKDYIDVPEVYPVGRLDRDSEGLLLLTNNGALQH 62

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------ 180
            L  P     R Y V+   +  +  L  L++G+ IQ       +V               
Sbjct: 63  RLCHPRFGHDRTYWVQVEREPTEAALQALRQGVQIQDYRTRPAKVQRLDDPQIPERDPPI 122

Query: 181 --TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQLGTLLAGS 232
              +    AW+ + L+EG+NR+++++         RLIR +        P QL  L  G+
Sbjct: 123 RFRKTVPTAWLALTLQEGRNRQVRRMTAAVGHPTLRLIRAAIATHPDQPPLQLQGLAPGT 182

Query: 233 TREVSKKILR 242
            R+++    R
Sbjct: 183 WRDLTAIECR 192


>gi|325914394|ref|ZP_08176741.1| ribosomal large subunit pseudouridine synthase E [Xanthomonas
           vesicatoria ATCC 35937]
 gi|325539402|gb|EGD11051.1| ribosomal large subunit pseudouridine synthase E [Xanthomonas
           vesicatoria ATCC 35937]
          Length = 191

 Score = 90.6 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 46/175 (26%), Positives = 80/175 (45%), Gaps = 15/175 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L +KP G+++  SD             +   V + GRLD ++EGLLLLT+DG LA  L
Sbjct: 2   LVLLNKPYGVLSQFSDRSQPPKRTLAEFGLPPDVYAAGRLDHDSEGLLLLTDDGALAHRL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------QVTL 179
             P  +  + Y V+  G+  + +L  L+ G+V+                           
Sbjct: 62  TDPRHKQPKTYWVQVEGEPQEAQLQALRDGVVLNDGPTRPASVRMLDPAPELWPRTPPVR 121

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +   +AW+ + + EG+NR+++++         RL+R++ G ++L  L  G  R
Sbjct: 122 VRKTVPDAWLELQITEGRNRQVRRMTASVGLPTLRLVRVAIGDWRLDGLAPGQWR 176


>gi|330976863|gb|EGH76892.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. aptata str.
           DSM 50252]
          Length = 210

 Score = 90.6 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 49/185 (26%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  SD +GR+T+ D +          GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPKLILFNKPFDVLTQFSDEEGRATLKDFIKIPGI--YPAGRLDRDSEGLLLLTNDG 84

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+   ++L  L+ G+ +        +            
Sbjct: 85  QLQARIADPKHKLAKTYWVQVEGEPSDEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPR 144

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  R
Sbjct: 145 NPPVRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLEGLDQGQYR 204

Query: 235 EVSKK 239
           EV+ K
Sbjct: 205 EVAAK 209


>gi|254514301|ref|ZP_05126362.1| ribosomal large subunit pseudouridine synthase E [gamma
           proteobacterium NOR5-3]
 gi|219676544|gb|EED32909.1| ribosomal large subunit pseudouridine synthase E [gamma
           proteobacterium NOR5-3]
          Length = 197

 Score = 90.6 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 42/177 (23%), Positives = 82/177 (46%), Gaps = 16/177 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L +KP  +++  +D  GR T+   + +        GRLD ++EGLLLL ++G L + +
Sbjct: 4   LILLNKPYQVLSQFTDSAGRDTLAKFIRTPGF--YPAGRLDYDSEGLLLLCDEGRLQQRI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--------------LD 180
             P  +  + Y V+  G++    L  LK G+ ++       +V                 
Sbjct: 62  ADPHFKLWKTYCVQLEGEITAQALQSLKNGLNLKDGPTRPARVKTLQEPLFWERNPPIRQ 121

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +    +W+ + + EG+NR+++++     + V RL+R   G + +  L  G  R ++
Sbjct: 122 RKHQPTSWIEISINEGRNRQVRRMCAAVGFPVLRLVRTRIGDWAIDGLQPGQHRRMT 178


>gi|322833615|ref|YP_004213642.1| pseudouridine synthase [Rahnella sp. Y9602]
 gi|321168816|gb|ADW74515.1| pseudouridine synthase [Rahnella sp. Y9602]
          Length = 208

 Score = 90.6 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 42/143 (29%), Positives = 69/143 (48%), Gaps = 15/143 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LTNDG L   L  P  +  ++Y V+  G+ D   +  L++GI ++
Sbjct: 63  YAAGRLDRDSEGLLVLTNDGKLQAALTQPGKRTGKIYYVQVEGEPDDAAVKSLREGITLK 122

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +    AW+ + L EG+NR+++++     +   
Sbjct: 123 DGPTLPAGAAIVPEPEWLWARNPPIRERKSIPTAWLKITLYEGRNRQVRRMTAHVGFPTL 182

Query: 214 RLIRISYGPFQLGTLLAGSTREV 236
           RLIR S G F LG L  G  +E+
Sbjct: 183 RLIRYSMGEFTLGDLQPGQWKEI 205


>gi|218704609|ref|YP_002412128.1| 23S rRNA pseudouridine synthase E [Escherichia coli UMN026]
 gi|293404491|ref|ZP_06648485.1| 23S rRNA pseudouridine synthase E [Escherichia coli FVEC1412]
 gi|298380266|ref|ZP_06989871.1| 23S rRNA pseudouridine synthase E [Escherichia coli FVEC1302]
 gi|300896836|ref|ZP_07115331.1| conserved hypothetical protein [Escherichia coli MS 198-1]
 gi|218431706|emb|CAR12588.1| 23S rRNA pseudouridine synthase [Escherichia coli UMN026]
 gi|291429077|gb|EFF02102.1| 23S rRNA pseudouridine synthase E [Escherichia coli FVEC1412]
 gi|298279964|gb|EFI21472.1| 23S rRNA pseudouridine synthase E [Escherichia coli FVEC1302]
 gi|300359318|gb|EFJ75188.1| conserved hypothetical protein [Escherichia coli MS 198-1]
          Length = 217

 Score = 90.2 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 49/184 (26%), Positives = 86/184 (46%), Gaps = 17/184 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+LTN+G 
Sbjct: 36  NQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVLTNNGA 93

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-------------- 175
           L   L  P  +  ++Y V+  G   QD L  L+ G+ +                      
Sbjct: 94  LQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGVELVDEPAWLWPR 153

Query: 176 -QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R
Sbjct: 154 NPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWR 213

Query: 235 EVSK 238
           E + 
Sbjct: 214 EATD 217


>gi|167623648|ref|YP_001673942.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
 gi|167353670|gb|ABZ76283.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
          Length = 239

 Score = 90.2 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 46/186 (24%), Positives = 85/186 (45%), Gaps = 16/186 (8%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +      + L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLLLLTND
Sbjct: 56  KTVANPVIVLFNKPFDVLCQFTDEQGRKTLKDYIPVPGV--YAAGRLDRDSEGLLLLTND 113

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   +  P  +  + Y  +  G  D   L  L++G+ ++       ++++        
Sbjct: 114 GKLQSQITEPKKKTYKTYWAQVEGAPDDSDLEKLRQGVELKDGMTLPAKISIMDNPAIWP 173

Query: 180 ------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 +       W+ + + EG+NR+++++     +   RLIR   G + L  L  G  
Sbjct: 174 RTPPIRERANIPTTWLEIQICEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDDLQNGEY 233

Query: 234 REVSKK 239
           R++  K
Sbjct: 234 RQLDMK 239


>gi|160895691|ref|YP_001561273.1| pseudouridine synthase [Delftia acidovorans SPH-1]
 gi|160361275|gb|ABX32888.1| pseudouridine synthase [Delftia acidovorans SPH-1]
          Length = 211

 Score = 90.2 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 45/180 (25%), Positives = 81/180 (45%), Gaps = 17/180 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL  ++KP G+++  +       + + +        + GRLD ++EGLLLLTNDG L   
Sbjct: 33  RLLCFNKPYGVLSQFTPEGRWRGLKEYIDVPGV--HAAGRLDADSEGLLLLTNDGPLQAR 90

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------VT 178
           +  P  +  + Y V+  G  D+  L  L++G+ +        Q                 
Sbjct: 91  IADPRFKMEKTYWVQVEGLPDEAALQALRQGVQLNDGMTLPAQARRLEPPPVLWQRDPPI 150

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              Q   + W+ + +REG+NR+++++         RL+R + GP+ L  L  G  ++V  
Sbjct: 151 RVRQNIPDCWIELVIREGRNRQVRRMTAAIGHPTLRLVRAAIGPYTLDGLEPGQWKDVEP 210


>gi|260581465|ref|ZP_05849276.1| ribosomal large subunit pseudouridine synthase E [Haemophilus
           influenzae RdAW]
 gi|260091866|gb|EEW75818.1| ribosomal large subunit pseudouridine synthase E [Haemophilus
           influenzae RdAW]
          Length = 238

 Score = 90.2 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 77/196 (39%), Gaps = 17/196 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L   E   +                D +             V + GRLD ++EGLL+L
Sbjct: 42  KTLSLDETKVVLFNKP---FDVLTQFTDEQGRATLKDFISIPNVYAAGRLDRDSEGLLIL 98

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TN+G L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +        
Sbjct: 99  TNNGELQHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKSAKVRLISEPN 158

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  
Sbjct: 159 LWERNPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGLLSINGLEN 218

Query: 231 GSTREVSKKILREQLG 246
           GS R +S   ++    
Sbjct: 219 GSFRLLSLDEIKALFQ 234


>gi|170719828|ref|YP_001747516.1| pseudouridine synthase [Pseudomonas putida W619]
 gi|169757831|gb|ACA71147.1| pseudouridine synthase [Pseudomonas putida W619]
          Length = 209

 Score = 90.2 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 54/189 (28%), Positives = 90/189 (47%), Gaps = 16/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P       RL L++KP  ++T  SD DGR+T+ D +          GRLD ++EGLLLL
Sbjct: 22  QPKAPPAEPRLILFNKPFDVLTQFSDSDGRATLKDYIDIPSI--YPAGRLDRDSEGLLLL 79

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---- 180
           TNDGGL   +  P  +  + Y V+  G+ + ++L  L++G+ +        +        
Sbjct: 80  TNDGGLQARIADPRHKLAKTYWVQVEGEPNDEQLKRLREGVELNDGPTLPAEARRLDEPE 139

Query: 181 ----------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                      +    +W+ + +REG+NR+++++         RL+R+  G + L  L  
Sbjct: 140 LWPRNPPVRFRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWALDGLEQ 199

Query: 231 GSTREVSKK 239
           G  REV  K
Sbjct: 200 GCWREVPAK 208


>gi|195938767|ref|ZP_03084149.1| 23S rRNA pseudouridine synthase E [Escherichia coli O157:H7 str.
           EC4024]
 gi|254792595|ref|YP_003077432.1| 23S rRNA pseudouridine synthase E [Escherichia coli O157:H7 str.
           TW14359]
 gi|261227236|ref|ZP_05941517.1| 23S rRNA pseudouridine synthase [Escherichia coli O157:H7 str.
           FRIK2000]
 gi|261258757|ref|ZP_05951290.1| 23S rRNA pseudouridine synthase [Escherichia coli O157:H7 str.
           FRIK966]
 gi|291282170|ref|YP_003498988.1| Ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O55:H7 str. CB9615]
 gi|34098618|sp|Q8X724|RLUE_ECO57 RecName: Full=Ribosomal large subunit pseudouridine synthase E;
           AltName: Full=rRNA pseudouridylate synthase E; AltName:
           Full=rRNA-uridine isomerase E
 gi|13361071|dbj|BAB35030.1| hypothetical protein [Escherichia coli O157:H7 str. Sakai]
 gi|209772818|gb|ACI84721.1| hypothetical protein ECs1607 [Escherichia coli]
 gi|209772820|gb|ACI84722.1| hypothetical protein ECs1607 [Escherichia coli]
 gi|209772822|gb|ACI84723.1| hypothetical protein ECs1607 [Escherichia coli]
 gi|209772824|gb|ACI84724.1| hypothetical protein ECs1607 [Escherichia coli]
 gi|209772826|gb|ACI84725.1| hypothetical protein ECs1607 [Escherichia coli]
 gi|254591995|gb|ACT71356.1| 23S rRNA pseudouridine synthase [Escherichia coli O157:H7 str.
           TW14359]
 gi|290762043|gb|ADD56004.1| Ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O55:H7 str. CB9615]
 gi|320637603|gb|EFX07403.1| 23S rRNA pseudouridine synthase E [Escherichia coli O157:H7 str.
           G5101]
 gi|320643163|gb|EFX12364.1| 23S rRNA pseudouridine synthase E [Escherichia coli O157:H- str.
           493-89]
 gi|320653933|gb|EFX22007.1| 23S rRNA pseudouridine synthase E [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320659413|gb|EFX26982.1| 23S rRNA pseudouridine synthase E [Escherichia coli O55:H7 str.
           USDA 5905]
          Length = 217

 Score = 90.2 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 49/189 (25%), Positives = 88/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 31  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 89  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPA 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 149 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 208

Query: 230 AGSTREVSK 238
            G  RE ++
Sbjct: 209 NGEWREATE 217


>gi|254521767|ref|ZP_05133822.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
 gi|219719358|gb|EED37883.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
          Length = 232

 Score = 90.2 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 37/232 (15%), Positives = 64/232 (27%), Gaps = 6/232 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+ K ++      R E  R I    V V+G ++E+    V     I V         
Sbjct: 2   EPIRLDKRLSALLGIPRGEARRYIEGGWVTVDGEVVEQPQRPVDDNAVIVVAEQASDDKA 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                L HKP G+          S     L +   R +      +     L   + G + 
Sbjct: 62  ERVSMLLHKPAGVAAETLCALVSSDSRSELDASGIRPLQRHFHGLQLAASLPAADSGLVV 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
              +  +   L+    R   +   +      +                     S   +  
Sbjct: 122 VSQDPATLAHLQRNLGRTEQEYLIEVAEGGPERGPWLLARLQHESGGAKVSWQSEQRLRF 181

Query: 192 GLREGK---NREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
               GK    + ++        +V  + R+  G   LG L  G  R +    
Sbjct: 182 A---GKGLTAKGLRVAVTAAGLQVAAVRRLRIGRVALGPLPPGQWRYLGSDE 230


>gi|307131186|ref|YP_003883202.1| 23S rRNA pseudouridine synthase [Dickeya dadantii 3937]
 gi|306528715|gb|ADM98645.1| 23S rRNA pseudouridine synthase [Dickeya dadantii 3937]
          Length = 208

 Score = 90.2 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 37/144 (25%), Positives = 65/144 (45%), Gaps = 15/144 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            S GRLD ++EGL++LTNDG L   L  P  +  ++Y  +  G  D++ L+  + G+++ 
Sbjct: 63  YSAGRLDRDSEGLMILTNDGKLQARLTQPGKKTPKIYYAQVEGVPDKEALHAFRTGLILS 122

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +    +W+ + L EG+NR+++++     +   
Sbjct: 123 DGPTLPAGVEQVEEPAWLWPRQPPIRERKTIPVSWLKITLYEGRNRQVRRMTAHIGYPTL 182

Query: 214 RLIRISYGPFQLGTLLAGSTREVS 237
           RLIR S     L  L  G  RE+ 
Sbjct: 183 RLIRYSMAGQTLDGLHPGEWREID 206


>gi|251789551|ref|YP_003004272.1| pseudouridine synthase [Dickeya zeae Ech1591]
 gi|247538172|gb|ACT06793.1| pseudouridine synthase [Dickeya zeae Ech1591]
          Length = 218

 Score = 90.2 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 35/144 (24%), Positives = 63/144 (43%), Gaps = 15/144 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGL++LTNDG L   L  P  +  ++Y  +  G  D + L+  + G+ + 
Sbjct: 73  YAAGRLDRDSEGLMILTNDGQLQARLTQPGKKTPKIYYAQVEGIPDDEALHAFRTGLQLN 132

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +    +W+ + L EG+NR+++++     +   
Sbjct: 133 DGTTLPAGAERVEEPAWLWPRQPPIRERKNIPVSWLKITLYEGRNRQVRRMTAHIGYPTL 192

Query: 214 RLIRISYGPFQLGTLLAGSTREVS 237
           RLIR S     L  L  G  +E+ 
Sbjct: 193 RLIRYSMANQTLDGLSPGEWKEID 216


>gi|294627501|ref|ZP_06706084.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 11122]
 gi|292598132|gb|EFF42286.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 11122]
          Length = 190

 Score = 90.2 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 49/175 (28%), Positives = 83/175 (47%), Gaps = 15/175 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L +KP G+++  SD             +   V + GRLD ++EGLLLLT+DG LA  L
Sbjct: 2   LVLLNKPYGVLSQFSDRSQPPKRTLAEFGLPPDVYAAGRLDHDSEGLLLLTDDGALAHRL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y V+  G    ++L  L+ G+V+        QV +               
Sbjct: 62  TDPRHKQPKTYWVQVEGAPQAEQLQALRDGVVLNDGPTRPAQVRMLDPAPQLWPRDPPVR 121

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +   +AW+ + + EG+NR+++++         RL+R++ G ++L TL  G  R
Sbjct: 122 VRKTVPDAWLELQITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLETLAPGQWR 176


>gi|209966489|ref|YP_002299404.1| ribosomal large subunit pseudouridine synthase E [Rhodospirillum
           centenum SW]
 gi|209959955|gb|ACJ00592.1| ribosomal large subunit pseudouridine synthase E [Rhodospirillum
           centenum SW]
          Length = 205

 Score = 90.2 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 50/181 (27%), Positives = 86/181 (47%), Gaps = 17/181 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
              TR+ L +KP  ++   +D DGR+T+ D +P       + GRLD ++EGL++LT+DG 
Sbjct: 4   RAMTRVILLNKPYDVLCQFTDADGRATLKDFVPVPGV--YAAGRLDRDSEGLVVLTDDGA 61

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-------- 181
           L   +  P  +  + Y  +  G  +   L  L++G+V+        +V            
Sbjct: 62  LTARIADPRHKMAKTYWAQVEGIPEDAALEALRRGVVLNDGPTLPAEVRAIPEPPGLWPR 121

Query: 182 -------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    AW+ + LREG+NR+++++         RL+R + GP+ L  L  G  R
Sbjct: 122 TPPVRFRKSIPTAWLELTLREGRNRQVRRMTAAVGLPTLRLVRRAVGPWTLEGLAPGEWR 181

Query: 235 E 235
           E
Sbjct: 182 E 182


>gi|167035821|ref|YP_001671052.1| pseudouridine synthase [Pseudomonas putida GB-1]
 gi|166862309|gb|ABZ00717.1| pseudouridine synthase [Pseudomonas putida GB-1]
          Length = 212

 Score = 90.2 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 52/189 (27%), Positives = 87/189 (46%), Gaps = 16/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                    RL L++KP  ++T  SD +GR+T+ D +          GRLD ++EGLLLL
Sbjct: 23  QAKAPPAEPRLILFNKPFDVLTQFSDCEGRATLKDFIDIAGV--YPAGRLDRDSEGLLLL 80

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---- 180
           TNDGGL   +  P  +  + Y V+  G+   ++L  L+ G+ +        +        
Sbjct: 81  TNDGGLQARIADPKHKLAKTYWVQVEGEPSDEQLQRLRDGVELNDGPTLPAEARRLEEPE 140

Query: 181 ----------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                      +    +W+ + +REG+NR+++++         RL+R+  G + L  L  
Sbjct: 141 LWPRNPPVRFRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWALDGLEQ 200

Query: 231 GSTREVSKK 239
           G  REV  K
Sbjct: 201 GCWREVPAK 209


>gi|92114560|ref|YP_574488.1| ribosomal large subunit pseudouridine synthase E [Chromohalobacter
           salexigens DSM 3043]
 gi|91797650|gb|ABE59789.1| ribosomal large subunit pseudouridine synthase E [Chromohalobacter
           salexigens DSM 3043]
          Length = 257

 Score = 90.2 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 42/154 (27%), Positives = 69/154 (44%), Gaps = 14/154 (9%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              GRLD ++EGLLLLT DG LA  +  P  +  + Y V+  G+ +   L  L++G+ ++
Sbjct: 94  YPAGRLDYDSEGLLLLTGDGALAHRISHPRHKQPKTYWVQVEGEPEPAALQALRQGVTLR 153

Query: 169 GICYGDMQVTLD--------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                  +V                  +    AW+ + L EG+NR+++++         R
Sbjct: 154 DGPTRPAKVRRLESPDVAPRHPPVRHREAVPTAWLELTLSEGRNRQVRRMTAHVGHPTLR 213

Query: 215 LIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           LIR++ G + L  L  G  R  +    R Q  P 
Sbjct: 214 LIRVAIGSWHLAGLAPGEWRRETLHAPRAQAAPA 247


>gi|15603470|ref|NP_246544.1| hypothetical protein PM1605 [Pasteurella multocida subsp. multocida
           str. Pm70]
 gi|34098696|sp|Q9CKK7|RLUE_PASMU RecName: Full=Ribosomal large subunit pseudouridine synthase E;
           AltName: Full=rRNA pseudouridylate synthase E; AltName:
           Full=rRNA-uridine isomerase E
 gi|12722002|gb|AAK03689.1| unknown [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 241

 Score = 90.2 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 40/192 (20%), Positives = 75/192 (39%), Gaps = 18/192 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +  AE   +        L     +    +            V   GRLD ++EGL+LL
Sbjct: 42  KTVNFAETQVILFNKPYDVLTQFSDEEGRATLKAFI---PIPHVYPAGRLDRDSEGLVLL 98

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TN+G +   L +P     + Y  +  G   +  L  L++G+V+        +        
Sbjct: 99  TNNGEIQHRLAVPKFNTEKTYFAQVEGIPQETDLAQLRQGVVLNDGKTLPAKVRLVPEPN 158

Query: 177 -------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + ++   +W+ + + EG+NR+++++     +   RLIR     F L  L 
Sbjct: 159 WLWQRNPPIRERKQIPTSWLEIKIHEGRNRQVRRMTAHIGFPTLRLIRYQMALFNLANLE 218

Query: 230 AGSTREVSKKIL 241
            G  R++S+  L
Sbjct: 219 QGQYRQLSEVEL 230


>gi|239617259|ref|YP_002940581.1| pseudouridine synthase [Kosmotoga olearia TBF 19.5.1]
 gi|239506090|gb|ACR79577.1| pseudouridine synthase [Kosmotoga olearia TBF 19.5.1]
          Length = 205

 Score = 90.2 bits (222), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 51/204 (25%), Positives = 97/204 (47%), Gaps = 5/204 (2%)

Query: 48  ERAAVNVMS-TDHIEVDGVPLRKAERTR--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
                 +    D I +DG  +R  ++ R    L      L +   D   ++        I
Sbjct: 2   TEPWFEIDPVKDSITLDGKKVRPRKQQRVVYALNKPRGYLSSMSDDRGRKTIADLIKGKI 61

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
             +V  VGRLD++TEGL++LTNDG LAR L  PS++  + Y  R  G++   ++  L+ G
Sbjct: 62  PEKVFHVGRLDMDTEGLIILTNDGELARKLSHPSSKIRKTYVARVTGKLSHHEIKRLENG 121

Query: 165 IVIQGI-CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
           +V++         + +      +  V + + EG  REI+++F+ F+  V  L R + G  
Sbjct: 122 VVLRDGFKTSGASIRVIRASLRDTLVEIIIHEGHKREIREMFKVFDKHVLYLKRTAIGSL 181

Query: 224 QLGTL-LAGSTREVSKKILREQLG 246
           ++  +   G  ++++ + +++ L 
Sbjct: 182 KVDIVPNPGDIKKLTGQEIQKLLK 205


>gi|118595184|ref|ZP_01552531.1| hypothetical protein MB2181_05910 [Methylophilales bacterium
           HTCC2181]
 gi|118440962|gb|EAV47589.1| hypothetical protein MB2181_05910 [Methylophilales bacterium
           HTCC2181]
          Length = 176

 Score = 90.2 bits (222), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 47/173 (27%), Positives = 85/173 (49%), Gaps = 16/173 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L +++KP G++T  S+ +   ++ + +      V   GRLD ++EGL++LT++G L   L
Sbjct: 2   LIIFNKPYGVITQFSEHEVYPSLKEFISHK--NVYPAGRLDADSEGLVILTDNGALQNKL 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P++   +VY V+       + L  L+KG++I        +V L               
Sbjct: 60  SDPTSNIEKVYVVQVENIPSSEDLAKLEKGVMISKYITKPAKVRLIEDPMLWERVPPIRK 119

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 AW+ + + EGKNR+++K+     +   RLIR S G +++G L  G+ 
Sbjct: 120 RSSIPTAWLEIRITEGKNRQVRKMTAAVGFPTLRLIRTSVGNYKIGDLEPGNY 172


>gi|330811899|ref|YP_004356361.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
 gi|327380007|gb|AEA71357.1| Ribosomal large subunit pseudouridine synthase E [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
          Length = 211

 Score = 90.2 bits (222), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 48/185 (25%), Positives = 86/185 (46%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  SD +GR+T+ D +          GRLD ++EGLLLLTNDG
Sbjct: 28  PPAEPKLILFNKPFDVLTQFSDGEGRATLKDFIDVPGI--YPAGRLDRDSEGLLLLTNDG 85

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ------------ 176
            L   +  P  +  + Y V+  G+   ++L  L+ G+ +        +            
Sbjct: 86  QLQARIADPKHKLAKTYWVQVEGEPSAEQLQRLRDGVELNDGMTLPAEARSLDEPQLWPR 145

Query: 177 --VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +WV + +REG+NR+++++         RL+R+  G + +  L  G  +
Sbjct: 146 NPPVRFRKSVPTSWVELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWTIEGLDQGQWK 205

Query: 235 EVSKK 239
           EV  +
Sbjct: 206 EVPAR 210


>gi|330824860|ref|YP_004388163.1| pseudouridine synthase Rsu [Alicycliphilus denitrificans K601]
 gi|329310232|gb|AEB84647.1| pseudouridine synthase Rsu [Alicycliphilus denitrificans K601]
          Length = 188

 Score = 90.2 bits (222), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 44/178 (24%), Positives = 81/178 (45%), Gaps = 17/178 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL  ++KP G+++  +       + D +      V   GRLD ++EGLLLLT+ G L   
Sbjct: 6   RLIRFNKPYGVLSQFTPEGRWRGLKDFID--LPGVYVAGRLDADSEGLLLLTDSGPLQAR 63

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------- 180
           +  P  +  + Y V+  G  D   L  L++GI +        +V                
Sbjct: 64  ISDPRHKMEKTYWVQVEGIPDDAALAALQRGITLNDGPTRPARVHRLEPPPALCPRDPPI 123

Query: 181 --TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              +   ++W+ + +REG+NR+++++         RL+R + GP+ L  L  G+  ++
Sbjct: 124 RVRRNIPDSWIELVIREGRNRQVRRMTAAVGHPTLRLVRTAIGPYTLDGLAPGAWDDI 181


>gi|315126735|ref|YP_004068738.1| ribosomal large subunit pseudouridine synthase E [Pseudoalteromonas
           sp. SM9913]
 gi|315015249|gb|ADT68587.1| ribosomal large subunit pseudouridine synthase E [Pseudoalteromonas
           sp. SM9913]
          Length = 225

 Score = 90.2 bits (222), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 47/184 (25%), Positives = 84/184 (45%), Gaps = 16/184 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P       ++ L++KP  ++   +D   R T+ + +P     V + GRLD ++EGLLLL
Sbjct: 36  KPQIAQSDKKVILFNKPYDVLCQFTDEQNRQTLANFIPIK--DVYAAGRLDRDSEGLLLL 93

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---- 180
           TN G L   L  P  +  + Y V+  G   +  ++ L +G+ ++       QV L     
Sbjct: 94  TNCGKLQNTLTAPGKKTNKTYWVQVEGVPTEASIDALSQGVELKDGLTLPAQVKLIDEPA 153

Query: 181 ----------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                      +    +W+++ + EGKNR+++++         RLIR S G + L  +  
Sbjct: 154 LWPRTPPVRERKSIPTSWLSITINEGKNRQVRRMTAHIGHPTLRLIRYSIGKYTLDGIET 213

Query: 231 GSTR 234
           G  +
Sbjct: 214 GQYK 217


>gi|331662548|ref|ZP_08363471.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Escherichia coli TA143]
 gi|331060970|gb|EGI32934.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Escherichia coli TA143]
          Length = 217

 Score = 90.2 bits (222), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 49/189 (25%), Positives = 87/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 31  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 89  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGVELVDEPA 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 149 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 208

Query: 230 AGSTREVSK 238
            G  RE + 
Sbjct: 209 NGEWREATD 217


>gi|149913759|ref|ZP_01902291.1| Pseudouridine synthase, Rsu [Roseobacter sp. AzwK-3b]
 gi|149812043|gb|EDM71874.1| Pseudouridine synthase, Rsu [Roseobacter sp. AzwK-3b]
          Length = 195

 Score = 89.9 bits (221), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 44/191 (23%), Positives = 84/191 (43%), Gaps = 16/191 (8%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RL L++KP G+++  +D     +    L        V   GRLD ++EGLLLLT+DG L 
Sbjct: 3   RLILFNKPYGVLSQFTDKGMADSKRATLSDHIDLPGVYPAGRLDRDSEGLLLLTDDGKLQ 62

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----------- 180
             +  P  +  ++Y V+     D   +  L +G+ ++       +V+             
Sbjct: 63  ERIASPRFKTEKIYLVQVERIPDDAAIEALCRGVTLKDGPTRPARVSRIAPPDLWERDPP 122

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +   + W+++ + EG+NR+++++         RL+R   G + L  L  G+ R+  
Sbjct: 123 VRFRKSVPDCWLSITISEGRNRQVRRMTAHVGHPTLRLVRWRIGAWSLDGLAPGTWRDAP 182

Query: 238 KKILREQLGPH 248
            + L   +   
Sbjct: 183 PETLGTPVKNR 193


>gi|294667800|ref|ZP_06733010.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 10535]
 gi|292602426|gb|EFF45867.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 10535]
          Length = 190

 Score = 89.9 bits (221), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 49/175 (28%), Positives = 83/175 (47%), Gaps = 15/175 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L +KP G+++  SD             +   V + GRLD ++EGLLLLT+DG LA  L
Sbjct: 2   LVLLNKPYGVLSQFSDRSQPPKRTLAEFGLPPDVYAAGRLDHDSEGLLLLTDDGALAHRL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y V+  G    ++L  L+ G+V+        QV +               
Sbjct: 62  TDPRHKQPKTYWVQVEGAPQAEQLQALRDGVVLNDGPTRPAQVRMLDPAPQLWPRDPPVR 121

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +   +AW+ + + EG+NR+++++         RL+R++ G ++L TL  G  R
Sbjct: 122 VRKTVPDAWLELQITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLETLAPGQWR 176


>gi|77461162|ref|YP_350669.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           fluorescens Pf0-1]
 gi|77385165|gb|ABA76678.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           fluorescens Pf0-1]
          Length = 211

 Score = 89.9 bits (221), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 47/185 (25%), Positives = 84/185 (45%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  SD +GR+T+ D +          GRLD ++EGLLLLTNDG
Sbjct: 28  PPAEPKLILFNKPFDVLTQFSDGEGRATLKDYIDIPGI--YPAGRLDRDSEGLLLLTNDG 85

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ------ 182
            L   +  P  +  + Y V+  G    ++L  L+ G+ +        +     +      
Sbjct: 86  QLQARIADPRHKLAKTYWVQVEGLPTAEQLQRLRDGVELNDGMTLPARARQLDEPELWPR 145

Query: 183 --------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                        W+ + +REG+NR+++++         RL+R+  G + +  L  G  +
Sbjct: 146 NPPVRFRATIPTTWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWTIEGLDQGQWK 205

Query: 235 EVSKK 239
           EV  +
Sbjct: 206 EVPAR 210


>gi|313500758|gb|ADR62124.1| Pseudouridine synthase [Pseudomonas putida BIRD-1]
          Length = 210

 Score = 89.9 bits (221), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 52/189 (27%), Positives = 87/189 (46%), Gaps = 16/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                    RL L++KP  ++T  SD +GR+T+ D +          GRLD ++EGLLLL
Sbjct: 23  QAKAPPAEPRLILFNKPFDVLTQFSDGEGRATLKDFIDIPGV--YPAGRLDRDSEGLLLL 80

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---- 180
           TNDGGL   +  P  +  + Y V+  G+   ++L  L+ G+ +        +        
Sbjct: 81  TNDGGLQARIADPKHKLAKTYWVQVEGEPSDEQLQRLRDGVELNDGPTLPAEARRLEEPE 140

Query: 181 ----------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                      +    +W+ + +REG+NR+++++         RL+R+  G + L  L  
Sbjct: 141 LWPRNPPVRFRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWALDGLEQ 200

Query: 231 GSTREVSKK 239
           G  REV  K
Sbjct: 201 GCWREVPAK 209


>gi|15801332|ref|NP_287349.1| 23S rRNA pseudouridine synthase E [Escherichia coli O157:H7 EDL933]
 gi|162139799|ref|NP_309634.2| 23S rRNA pseudouridine synthase E [Escherichia coli O157:H7 str.
           Sakai]
 gi|168749738|ref|ZP_02774760.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. EC4113]
 gi|168756474|ref|ZP_02781481.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. EC4401]
 gi|187776203|ref|ZP_02801059.2| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. EC4196]
 gi|189010504|ref|ZP_02807479.2| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. EC4076]
 gi|189403535|ref|ZP_02796010.2| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. EC4486]
 gi|189404169|ref|ZP_02787559.2| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. EC4501]
 gi|189405017|ref|ZP_02812617.2| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. EC869]
 gi|208809289|ref|ZP_03251626.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. EC4206]
 gi|208815426|ref|ZP_03256605.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. EC4045]
 gi|208822240|ref|ZP_03262559.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. EC4042]
 gi|209396285|ref|YP_002270052.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. EC4115]
 gi|217327988|ref|ZP_03444070.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. TW14588]
 gi|12514789|gb|AAG55961.1|AE005329_5 orf, hypothetical protein [Escherichia coli O157:H7 str. EDL933]
 gi|187768550|gb|EDU32394.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. EC4196]
 gi|188015997|gb|EDU54119.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. EC4113]
 gi|189000066|gb|EDU69052.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. EC4076]
 gi|189356411|gb|EDU74830.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. EC4401]
 gi|189360150|gb|EDU78569.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. EC4486]
 gi|189367183|gb|EDU85599.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. EC4501]
 gi|189372526|gb|EDU90942.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. EC869]
 gi|208729090|gb|EDZ78691.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. EC4206]
 gi|208732074|gb|EDZ80762.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. EC4045]
 gi|208737725|gb|EDZ85408.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. EC4042]
 gi|209157685|gb|ACI35118.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. EC4115]
 gi|217318415|gb|EEC26841.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           O157:H7 str. TW14588]
 gi|320648100|gb|EFX16776.1| 23S rRNA pseudouridine synthase E [Escherichia coli O157:H- str. H
           2687]
 gi|320664550|gb|EFX31701.1| 23S rRNA pseudouridine synthase E [Escherichia coli O157:H7 str.
           LSU-61]
          Length = 207

 Score = 89.9 bits (221), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 49/189 (25%), Positives = 88/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 21  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 79  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPA 138

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 139 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 198

Query: 230 AGSTREVSK 238
            G  RE ++
Sbjct: 199 NGEWREATE 207


>gi|240950257|ref|ZP_04754536.1| pseudouridylate synthase [Actinobacillus minor NM305]
 gi|240295234|gb|EER46035.1| pseudouridylate synthase [Actinobacillus minor NM305]
          Length = 224

 Score = 89.9 bits (221), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 52/185 (28%), Positives = 89/185 (48%), Gaps = 17/185 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E T + L++KP  ++T  +D  GR T+ D +         VGRLD ++EGLLLLTN+G +
Sbjct: 29  EETIIVLFNKPYDVLTQFTDEQGRKTLKDFIDIPKI--YPVGRLDRDSEGLLLLTNNGEI 86

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------ 178
              L  P  +  + Y V+  G   Q  L  L+KG+ ++       +              
Sbjct: 87  QHRLAHPKFEKEKTYWVQVEGIPSQADLAKLEKGVELKDGLTQPAKAKQIEAPDFDWQTA 146

Query: 179 ---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + + EGKNR+++++     +   RLIR+  G +QLG L +G  + 
Sbjct: 147 PKIRERKTIPTSWIELKITEGKNRQVRRMTAHIGFPTLRLIRVGLGHYQLGELGSGEYQV 206

Query: 236 VSKKI 240
           +S   
Sbjct: 207 LSLSE 211


>gi|148549856|ref|YP_001269958.1| pseudouridine synthase [Pseudomonas putida F1]
 gi|148513914|gb|ABQ80774.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           putida F1]
          Length = 210

 Score = 89.9 bits (221), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 52/189 (27%), Positives = 87/189 (46%), Gaps = 16/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                    RL L++KP  ++T  SD +GR+T+ D +          GRLD ++EGLLLL
Sbjct: 23  QAKAPPAEPRLILFNKPFDVLTQFSDGEGRATLKDFIDIPGV--YPAGRLDRDSEGLLLL 80

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---- 180
           TNDGGL   +  P  +  + Y V+  G+   ++L  L+ G+ +        +        
Sbjct: 81  TNDGGLQARIADPKHKLAKTYWVQVEGEPSDEQLQRLRDGVALNDGPTLPAEARRLEEPE 140

Query: 181 ----------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                      +    +W+ + +REG+NR+++++         RL+R+  G + L  L  
Sbjct: 141 LWPRNPPVRFRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWALDGLGQ 200

Query: 231 GSTREVSKK 239
           G  REV  K
Sbjct: 201 GCWREVPAK 209


>gi|223992791|ref|XP_002286079.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220977394|gb|EED95720.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 370

 Score = 89.9 bits (221), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 52/279 (18%), Positives = 93/279 (33%), Gaps = 45/279 (16%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKV---------NGILLERAAVNVMSTDH 59
           +    QR+ KV+A  G+ +R +   +   +R+               ++  +  V S   
Sbjct: 85  KKAALQRIDKVLADRGVGTRSQTFDLAKAKRITWSTSPDATHEERTRIKGPSEKVPSNAS 144

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGR 113
           + +DG  L       L  +     L     D   +     +L  I         +  VGR
Sbjct: 145 LFLDGNLLPAPTPLLLVYHKPKFVLSVMEDDKKYQDQQRKHLGHILEPRYARSGMHPVGR 204

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH-GQVDQDKLNLLKKGIVIQGICY 172
           LD +T GL+L ++DG L + L  P     + Y           +   +L  G+      +
Sbjct: 205 LDYDTTGLILFSSDGKLTQRLLHPRRGVEKEYVATVQGEVNASELREMLANGVETTDGTF 264

Query: 173 GD-----------------------------MQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                                           + T +   G  + V + + EGK R +++
Sbjct: 265 AANLIAVTSSNGPSEVSEEDLNNVPEEDEGGDETTDEPYNGPYSDVRLVVSEGKYRMVRR 324

Query: 204 VFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +       V  L R  +G   L  L  G  R+V+ + L 
Sbjct: 325 ILANSGHPVVELRRERHGEILLDDLPVGKFRDVTPEELE 363


>gi|307297964|ref|ZP_07577768.1| pseudouridine synthase [Thermotogales bacterium mesG1.Ag.4.2]
 gi|306916050|gb|EFN46433.1| pseudouridine synthase [Thermotogales bacterium mesG1.Ag.4.2]
          Length = 228

 Score = 89.9 bits (221), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 51/225 (22%), Positives = 96/225 (42%), Gaps = 5/225 (2%)

Query: 43  NGILLERAAVNV-MSTDHIEVDGVPL--RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           NG +     ++V   +  I +DG  L     E+    +      L     D   ++    
Sbjct: 2   NGRIETYPRLDVFSESSEILLDGNRLIFSSEEKVVYLVNKPIGYLSAMSDDRGRKTLSDL 61

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
               I  RV  VGRLD ++ GL+L+TNDG L+ ++  P+++  + Y V   G++    L 
Sbjct: 62  VSDRIKERVFHVGRLDQDSCGLILMTNDGDLSNLVSHPASEIEKTYVVGIKGKLTDRDLE 121

Query: 160 LLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
            +K G+ +         ++ L    G  +   + + EG  REI+++F   N  V+ L+R+
Sbjct: 122 AVKGGLTLGDGFKTSPAKIRLVRSDGDFSKYAITIHEGHKREIREIFRVLNKSVSSLVRV 181

Query: 219 SYGPFQLGTLL-AGSTREVSKKILREQLGPHLLEEAQVNLDAPIY 262
           S GP  +  +   G  + +S+K +         +  +       +
Sbjct: 182 SIGPLSISLVPSPGDIKRLSRKEIALLENGAHRKAPKKAQRKNNF 226


>gi|262274514|ref|ZP_06052325.1| putative pseudouridine synthase family 1 protein [Grimontia
           hollisae CIP 101886]
 gi|262221077|gb|EEY72391.1| putative pseudouridine synthase family 1 protein [Grimontia
           hollisae CIP 101886]
          Length = 170

 Score = 89.9 bits (221), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 38/144 (26%), Positives = 65/144 (45%), Gaps = 14/144 (9%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              GRLD ++EGLL+LTNDG L   L  P ++  + Y V+  G   ++ L  L+ G+ ++
Sbjct: 23  YPAGRLDKDSEGLLVLTNDGILQARLTQPKSKSAKTYWVQVEGIPSENALKSLRNGVELK 82

Query: 169 GICYGDMQVTLDTQ--------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                   V +  +                   W+++ L EG+NR+++++         R
Sbjct: 83  DGWTLPAIVEIMDEPAIWDRNPPIRHRPSVPTTWLSITLTEGRNRQVRRMTAAVGHPTLR 142

Query: 215 LIRISYGPFQLGTLLAGSTREVSK 238
           L+R   G + +  L  G  REV  
Sbjct: 143 LVRYQMGHWTVDGLQPGEWREVPP 166


>gi|320322675|gb|EFW78768.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. glycinea str. B076]
 gi|320330540|gb|EFW86519.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. glycinea str. race 4]
          Length = 210

 Score = 89.9 bits (221), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 49/185 (26%), Positives = 86/185 (46%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L+L++KP  ++T  SD  GR+T+ D +          GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPKLFLFNKPFDVLTQFSDEGGRATLKDFIKIPGI--YPAGRLDRDSEGLLLLTNDG 84

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+   ++L  L+ G+ +        +            
Sbjct: 85  QLQARIADPKHKLAKTYWVQVEGEPTDEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPR 144

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + ++EG NR+++++         RL+R+  G + L  L  G  R
Sbjct: 145 NPPVRFRKSVPTSWLELVIKEGCNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLDQGQYR 204

Query: 235 EVSKK 239
           EV+ K
Sbjct: 205 EVAAK 209


>gi|71418278|ref|XP_810803.1| tRNA pseudouridine synthase A [Trypanosoma cruzi strain CL Brener]
 gi|70875392|gb|EAN88952.1| tRNA pseudouridine synthase A, putative [Trypanosoma cruzi]
          Length = 687

 Score = 89.9 bits (221), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 60/225 (26%), Positives = 101/225 (44%), Gaps = 4/225 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--PLRKAERT 73
           + + + RAG  SRRE   +IA  +V+V+ ++       V + + I V+     LR A   
Sbjct: 345 LLRCLPRAGFCSRREALSIIASGQVRVDNVVERNPFRLVRAENSIHVESHSGRLRFAPPR 404

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               +     +V+ +                   ++ VG L +   GLLLLTNDG L+R+
Sbjct: 405 LWMYHKPAYVIVSRNDVAGRTLITKHARILGMDHLVPVGSLPMRAHGLLLLTNDGELSRL 464

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           LE P T   + Y +R    +D    + L    ++  G  Y +++  ++    S   + V 
Sbjct: 465 LENPKTMIQQTYLLRVRPAIDPVLAHKLNTEGILVNGKRYNNVEFFVNPAMKSRHSLKVK 524

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +R G+   +  + +     V R  RIS+GPF +  L  GS REV+
Sbjct: 525 VR-GETMPVAHLMQHLGRTVERGGRISFGPFSMSGLPVGSIREVT 568


>gi|320195863|gb|EFW70488.1| Ribosomal large subunit pseudouridine synthase E [Escherichia coli
           WV_060327]
          Length = 177

 Score = 89.9 bits (221), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 38/145 (26%), Positives = 66/145 (45%), Gaps = 15/145 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LTN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ + 
Sbjct: 33  YAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLN 92

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +    +W+ + L EG+NR+++++     +   
Sbjct: 93  DGPTLPAGAELVEEPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTL 152

Query: 214 RLIRISYGPFQLGTLLAGSTREVSK 238
           RLIR + G + L  L  G  R+ + 
Sbjct: 153 RLIRYAMGDYSLDNLANGEWRDATD 177


>gi|259419278|ref|ZP_05743195.1| ribosomal large subunit pseudouridine synthase E [Silicibacter sp.
           TrichCH4B]
 gi|259345500|gb|EEW57354.1| ribosomal large subunit pseudouridine synthase E [Silicibacter sp.
           TrichCH4B]
          Length = 227

 Score = 89.5 bits (220), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 44/225 (19%), Positives = 86/225 (38%), Gaps = 17/225 (7%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
           RL  ++KP  ++   +D     +    L            GRLD ++EGL+LLT++G L 
Sbjct: 3   RLIRFNKPFDVLPQFTDRGSEGSPRATLSDYVDCPGVYPAGRLDRDSEGLMLLTDNGRLQ 62

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------------- 176
             +  P  +  + Y  +  G  D+D LNLL++G+ ++       +               
Sbjct: 63  AWISDPKHKLEKTYWAQVEGIPDEDALNLLRQGVELKDGMTRPAKARLINEPAQLWARTP 122

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    AW+ + + EGKNR+++++         RLIR + G + L  L  G  +++
Sbjct: 123 PIRERKSVPTAWLELKITEGKNRQVRRMTAAVGHPTLRLIRYAIGAWTLDGLAQGKWQDL 182

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD 281
               +     P      +        +  +    +          
Sbjct: 183 DPPRVPGPPKPSQKPPRRKPHAQNTENGASRSPSKRRKPRSKSTR 227


>gi|194366722|ref|YP_002029332.1| RNA-binding S4 domain-containing protein [Stenotrophomonas
           maltophilia R551-3]
 gi|194349526|gb|ACF52649.1| RNA-binding S4 domain protein [Stenotrophomonas maltophilia R551-3]
          Length = 232

 Score = 89.5 bits (220), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 38/232 (16%), Positives = 67/232 (28%), Gaps = 6/232 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+ K ++      R E  R I    V VNG ++E+    V  +  I V         
Sbjct: 2   EPTRLDKRLSALLGIPRGEARRYIEGGWVSVNGEVVEQPQRPVDESAVIVVAEQASDDKA 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                L HKP G+          S     L +  +R +      +     L  ++ G + 
Sbjct: 62  ERVTMLLHKPAGVAAEALCALISSDSRSELDASGTRPLQRHFHGLQLAAALPASDSGLVV 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
              +  +   L+    R   +   +      +                     S   +  
Sbjct: 122 VSQDPATLAHLQRNLGRTEQEYLIEVAEGGPERGPWLMARLQHESGGAKVSWQSEQRLRF 181

Query: 192 GLREGK---NREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
               GK    + ++        +V  + R+  G   LG L  G  R +    
Sbjct: 182 A---GKGLTAKGLRVAVGAAGLQVAAVRRLRIGRVALGPLPPGQWRYLGSDE 230


>gi|254453784|ref|ZP_05067221.1| ribosomal large subunit pseudouridine synthase E [Octadecabacter
           antarcticus 238]
 gi|198268190|gb|EDY92460.1| ribosomal large subunit pseudouridine synthase E [Octadecabacter
           antarcticus 238]
          Length = 206

 Score = 89.5 bits (220), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 41/180 (22%), Positives = 72/180 (40%), Gaps = 14/180 (7%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
               T +        L               +  ++   V + GRLD ++EGLL+LT+DG
Sbjct: 25  PIPMTTILFNKPFGVLTQFTDAKSPTERPTLSGFNLPKGVYAAGRLDRDSEGLLVLTDDG 84

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   L  P+ +  + Y V+  G      L  L+  + ++       QV L         
Sbjct: 85  KLQAQLSKPTFKTPKTYLVQIEGDPTDADLAPLRTRVTLKDGPTLPAQVRLIDPPDVWHR 144

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +   +AW+ V + EG+NR+++++     +   RL+R S G + L  +  G  R
Sbjct: 145 DPPVRVRKSIPDAWIEVTITEGRNRQVRRMCAHIGFPCLRLVRWSVGAWTLDGIDQGQWR 204


>gi|324113926|gb|EGC07900.1| RNA pseudouridylate synthase [Escherichia fergusonii B253]
          Length = 217

 Score = 89.5 bits (220), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 47/189 (24%), Positives = 87/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 31  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   +D L  L+ G+ +                 
Sbjct: 89  TNNGALQARLTQPGKRTGKIYYVQVEGIPTEDALEALRNGVTLNDGPTLPAGAEMVEEPE 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + + EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 149 WLWPRNPPIRERKSIPTSWLKITIYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 208

Query: 230 AGSTREVSK 238
            G  RE + 
Sbjct: 209 NGEWREATD 217


>gi|110679964|ref|YP_682971.1| RNA pseudouridylate synthase [Roseobacter denitrificans OCh 114]
 gi|109456080|gb|ABG32285.1| RNA pseudouridylate synthase [Roseobacter denitrificans OCh 114]
          Length = 187

 Score = 89.5 bits (220), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 34/142 (23%), Positives = 66/142 (46%), Gaps = 15/142 (10%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
               GRLD ++EGL++LT+DG L   +  P  +  + Y  +  G  +   +  L+ G+ +
Sbjct: 39  FYPAGRLDRDSEGLMVLTDDGKLQARISNPKHKMTKTYLAQIEGTPEPQHIEALRAGVRL 98

Query: 168 QGICYGDMQVTLD---------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           +       QV++                 +   +AW+ + + EG+NR+++++        
Sbjct: 99  KDGMTRPAQVSVATPPDTLWERSPPVRFRKTVPDAWLQISISEGRNRQVRRMCAHVGLPC 158

Query: 213 NRLIRISYGPFQLGTLLAGSTR 234
            RLIR+  G + L  L+ G+ R
Sbjct: 159 LRLIRMRIGDWALNDLVPGAWR 180


>gi|300723599|ref|YP_003712904.1| Ribosomal large subunit pseudouridine synthase E [Xenorhabdus
           nematophila ATCC 19061]
 gi|297630121|emb|CBJ90758.1| Ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Xenorhabdus nematophila ATCC 19061]
          Length = 209

 Score = 89.5 bits (220), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 53/190 (27%), Positives = 94/190 (49%), Gaps = 17/190 (8%)

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           + +  +     R+ +++KP  ++   +D  GR+T+ D +P   + V + GRLD ++EGLL
Sbjct: 20  NNITQKPTGPRRVLVFNKPYDVLPQFTDEMGRTTLKDFIP--LTDVYTAGRLDRDSEGLL 77

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------- 175
           +LTNDG L   L  P  +  ++Y V+  G  D+  LN L+ GI ++              
Sbjct: 78  VLTNDGKLQARLTQPHKKTAKIYYVQVEGIPDESALNKLRNGITLKDGPTLPAGAELVKE 137

Query: 176 --------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
                       + +    +W+ + L EG+NR+++++     +   RLIR S G  QL T
Sbjct: 138 PEWLWERTPPIRERKNIPVSWLKITLYEGRNRQVRRMTAHIGFPTLRLIRFSLGSIQLET 197

Query: 228 LLAGSTREVS 237
           L  G  +E++
Sbjct: 198 LSPGEWKEIN 207


>gi|283833487|ref|ZP_06353228.1| ribosomal large subunit pseudouridine synthase E [Citrobacter
           youngae ATCC 29220]
 gi|291071148|gb|EFE09257.1| ribosomal large subunit pseudouridine synthase E [Citrobacter
           youngae ATCC 29220]
          Length = 205

 Score = 89.5 bits (220), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 49/184 (26%), Positives = 86/184 (46%), Gaps = 17/184 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLL+LTND
Sbjct: 24  KENQPKRVVLFNKPYDVLPQFTDEAGRKTLKDFIPVPGI--YAAGRLDRDSEGLLVLTND 81

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P  +  ++Y V+  G+   + L  L+ G+ +                    
Sbjct: 82  GALQARLTQPGKRTGKIYYVQVEGEPTPEALEALRTGVALNDGPTLPAGVEVVEEPAWLW 141

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +     W+ V L EG+NR+++++     +   RLIR + G + L  L  G 
Sbjct: 142 PRNPPIRERKNIPTRWLKVTLYEGRNRQVRRMTAHVGYPTLRLIRYAMGNYTLDNLANGE 201

Query: 233 TREV 236
            RE+
Sbjct: 202 WREL 205


>gi|170681779|ref|YP_001744042.1| 23S rRNA pseudouridine synthase E [Escherichia coli SMS-3-5]
 gi|170519497|gb|ACB17675.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           SMS-3-5]
          Length = 207

 Score = 89.5 bits (220), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 49/189 (25%), Positives = 87/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 21  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 79  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGVDLVEEPE 138

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 139 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 198

Query: 230 AGSTREVSK 238
            G  RE + 
Sbjct: 199 NGEWREATD 207


>gi|325568386|ref|ZP_08144753.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           casseliflavus ATCC 12755]
 gi|325158155|gb|EGC70308.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           casseliflavus ATCC 12755]
          Length = 138

 Score = 89.5 bits (220), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 36/131 (27%), Positives = 66/131 (50%), Gaps = 2/131 (1%)

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY- 172
           +D +TEGL+L+T +G L   L  P+ +  + Y V  +  V  + +     GI   G    
Sbjct: 1   MDRDTEGLVLVTTNGQLGYDLLHPTKKVTKRYEVVVNDLVTPEDVAAFAAGITFHGGVTC 60

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAG 231
               +T+   +  +++V++ + EGK  ++KK+F     KV +L R + G   L   L  G
Sbjct: 61  KPAALTIIDARADHSFVSLEIAEGKFHQVKKMFLARGKKVIQLKRTAMGSLVLPDDLAVG 120

Query: 232 STREVSKKILR 242
           S R ++++ L+
Sbjct: 121 SYRSLTQEELK 131


>gi|323967074|gb|EGB62500.1| RNA pseudouridylate synthase [Escherichia coli M863]
          Length = 217

 Score = 89.5 bits (220), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 49/189 (25%), Positives = 87/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 31  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 89  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAEMVEEPE 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 149 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 208

Query: 230 AGSTREVSK 238
            G  RE + 
Sbjct: 209 NGEWREATD 217


>gi|254506210|ref|ZP_05118354.1| ribosomal large subunit pseudouridine synthase E [Vibrio
           parahaemolyticus 16]
 gi|219551028|gb|EED28009.1| ribosomal large subunit pseudouridine synthase E [Vibrio
           parahaemolyticus 16]
          Length = 231

 Score = 89.5 bits (220), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 54/186 (29%), Positives = 90/186 (48%), Gaps = 16/186 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E  ++  ++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+L
Sbjct: 45  KPKIAPEARKVIAFNKPFDTLSQFTDGDGRKTLADFIP--VKDVYAAGRLDRDSEGLLIL 102

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---- 180
           TNDG L   L  P ++  + Y V+  G   +  L+ L+KG+ ++       QV +     
Sbjct: 103 TNDGVLQAKLTQPKSKSPKTYWVQVDGAPSEADLDKLRKGVELKDGMTLPAQVEVMEAPE 162

Query: 181 ----------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + + EG+NR+++++     +   RLIR S G  +LG L  
Sbjct: 163 IWERNPPVRFRANIPTTWLAITIIEGRNRQVRRMTANIGFPTLRLIRYSMGDIKLGDLQP 222

Query: 231 GSTREV 236
           G  +EV
Sbjct: 223 GEWKEV 228


>gi|237731117|ref|ZP_04561598.1| pseudouridylate synthase [Citrobacter sp. 30_2]
 gi|226906656|gb|EEH92574.1| pseudouridylate synthase [Citrobacter sp. 30_2]
          Length = 207

 Score = 89.5 bits (220), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 49/185 (26%), Positives = 89/185 (48%), Gaps = 17/185 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GRST+ D +P       + GRLD ++EGLL+LTND
Sbjct: 24  KENQPKRVVLFNKPYDVLPQFTDEAGRSTLKDFIPVPGI--YAAGRLDRDSEGLLVLTND 81

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P  +  ++Y V+  G+   + L+ L+ G+ +                    
Sbjct: 82  GALQARLTQPGKRTGKIYYVQVEGEPTAEALDALRNGVTLNDGPTLPAGIEVVEEPVWLW 141

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G 
Sbjct: 142 PRNPPIRERKNIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLENLANGE 201

Query: 233 TREVS 237
            RE+ 
Sbjct: 202 WRELK 206


>gi|321223855|gb|EFX48918.1| Ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           TN061786]
          Length = 181

 Score = 89.5 bits (220), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 41/146 (28%), Positives = 67/146 (45%), Gaps = 15/146 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LTNDG L   L  P  +  ++Y V+  G  D   L  L+ G+ + 
Sbjct: 33  YAAGRLDRDSEGLLVLTNDGALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLN 92

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +    +W+ V L EG+NR+++++         
Sbjct: 93  DGPTLPAGIEIVAEPDWLWPRTPPIRERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTL 152

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKK 239
           RLIR S G + L  L  G  RE++++
Sbjct: 153 RLIRYSMGDYTLNGLDNGQWREIAQE 178


>gi|88798700|ref|ZP_01114283.1| Pseudouridine synthase, Rsu [Reinekea sp. MED297]
 gi|88778463|gb|EAR09655.1| Pseudouridine synthase, Rsu [Reinekea sp. MED297]
          Length = 228

 Score = 89.5 bits (220), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 51/227 (22%), Positives = 101/227 (44%), Gaps = 17/227 (7%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  L++KP  ++T  +DPD R T+ D +      V S GRLD ++EGLLLLT+DG L   
Sbjct: 3   RYLLFNKPFQVLTQFTDPDNRQTLADFID--VPEVYSAGRLDYDSEGLLLLTDDGALIHS 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------VT 178
           +  P  +  + Y  +  G +  + +  L+ G+ ++       +                 
Sbjct: 61  MMNPRFKTPKTYLAQVEGDITDEAIRRLESGLQLKDGPTLPAKARRVSEPAWLWPRQPPI 120

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +      +WV + L EG+NR+++++     +   RLIR++     + +L  G  +EV +
Sbjct: 121 RERATIPASWVELTLVEGRNRQVRRMTAAVGFPTLRLIRVALAELTVESLSVGQYKEVDR 180

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
           +++ +      ++++        + +    +DR    +  P    R 
Sbjct: 181 ELIVDNGIKWQIKKSSPKAAHSKHQTTVKRQDRRRHRNRRPQSRNRK 227


>gi|251793652|ref|YP_003008382.1| RNA pseudouridine synthase family protein [Aggregatibacter
           aphrophilus NJ8700]
 gi|247535049|gb|ACS98295.1| RNA pseudouridine synthase family protein [Aggregatibacter
           aphrophilus NJ8700]
          Length = 182

 Score = 89.5 bits (220), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 37/153 (24%), Positives = 69/153 (45%), Gaps = 15/153 (9%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
             +GRLD ++EGLLLLTN+G +   L  P  +  + Y V+  G  D+  L  L++G+ + 
Sbjct: 24  YPIGRLDRDSEGLLLLTNNGDIQHRLAEPKFKMEKTYWVQVEGVPDEIALERLRRGVELN 83

Query: 169 GICYGDMQ---------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +                  + +    AW+ + + EG+NR+++++     +   
Sbjct: 84  DGMTLPAKVRLISEPNFLWPRVPPIRERKNIPTAWLEIKIYEGRNRQVRRMTAHIGFPTL 143

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           RLIR     F L  L   + R +++  L++   
Sbjct: 144 RLIRYQQAGFSLQHLAPKTYRTLTQDELKQLYQ 176


>gi|269967650|ref|ZP_06181700.1| pseudouridine synthase family 1 protein [Vibrio alginolyticus 40B]
 gi|269827737|gb|EEZ82021.1| pseudouridine synthase family 1 protein [Vibrio alginolyticus 40B]
          Length = 233

 Score = 89.5 bits (220), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 51/187 (27%), Positives = 91/187 (48%), Gaps = 16/187 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    +  ++ +++KP   ++  +D DGR T+ D +P     V + GRLD ++EGL++L
Sbjct: 48  KPKVAPKDRKVIIFNKPYDTLSQFTDGDGRKTLADYIPIK--NVYAAGRLDRDSEGLMVL 105

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +  L  L+KG+ ++       +V +  +  
Sbjct: 106 TNDGILQAKLTQPKSKSPKTYWVQVDGAPQEQDLEKLRKGVELKDGMTLPAEVEVIPEPQ 165

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + + EG+NR+++++     +   RLIR S G   L  L+ 
Sbjct: 166 VWDRTPPVRFRANIPTTWLAITIIEGRNRQVRRMTAHIGFPTLRLIRHSMGDIVLNDLMP 225

Query: 231 GSTREVS 237
           G  RE+S
Sbjct: 226 GEWREIS 232


>gi|218549142|ref|YP_002382933.1| 23S rRNA pseudouridine synthase E [Escherichia fergusonii ATCC
           35469]
 gi|218356683|emb|CAQ89310.1| 23S rRNA pseudouridine synthase [Escherichia fergusonii ATCC 35469]
          Length = 217

 Score = 89.1 bits (219), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 48/189 (25%), Positives = 88/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 31  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPIQGV--YAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   +D L  L+ G+ +                 
Sbjct: 89  TNNGALQARLTQPGKRTGKIYYVQVEGIPTEDALEALRNGVTLNDGPTLPAGAEMVEEPE 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 149 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 208

Query: 230 AGSTREVSK 238
            G  R+V+ 
Sbjct: 209 NGEWRDVTD 217


>gi|253989219|ref|YP_003040575.1| pseudouridine synthase [Photorhabdus asymbiotica subsp. asymbiotica
           ATCC 43949]
 gi|253780669|emb|CAQ83831.1| pseudouridine synthase [Photorhabdus asymbiotica]
          Length = 161

 Score = 89.1 bits (219), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 43/144 (29%), Positives = 73/144 (50%), Gaps = 15/144 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LTNDG L   L  P  +  +VY V+  G  D++ L+ L+KGI+++
Sbjct: 16  YAAGRLDRDSEGLLILTNDGKLQAQLTQPGKKTAKVYYVQVEGVPDEESLDKLRKGIILK 75

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +    +W+ + L EG+NR+++++     +   
Sbjct: 76  DGLTLPAGVELVNEPTWLWVRHPPIRERKSIPVSWLKITLYEGRNRQVRRMTAHIGFPTL 135

Query: 214 RLIRISYGPFQLGTLLAGSTREVS 237
           RLIR S G  QLG +  G  +E++
Sbjct: 136 RLIRFSMGTLQLGEIKPGEWKEIN 159


>gi|83645148|ref|YP_433583.1| 16S rRNA uridine-516 pseudouridylate synthase-like protein [Hahella
           chejuensis KCTC 2396]
 gi|83633191|gb|ABC29158.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Hahella chejuensis KCTC 2396]
          Length = 202

 Score = 89.1 bits (219), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 48/176 (27%), Positives = 86/176 (48%), Gaps = 16/176 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L +++KP+ ++T  +D  GR+T+ D +      V + GRLD ++EGLLLLT+DG +   
Sbjct: 3   ILVVFNKPMNVLTQFNDSQGRATLSDFID--KPGVYAAGRLDYDSEGLLLLTDDGAIQAR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------------VTL 179
           +  P  +  + Y V+  G + +  L  L+KG+++                          
Sbjct: 61  ISQPKFKLPKTYWVQVEGVIGEAALRRLEKGVMLNDGPTRPAHASLISPPEVWERDPPIR 120

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
             +    +W+ + L EG+NR+++++     +   RLIR S GP+ +  L  G  RE
Sbjct: 121 QRKNIPTSWIALTLFEGRNRQVRRMTAAVGFPTLRLIRYSIGPWSINGLQPGEWRE 176


>gi|169795136|ref|YP_001712929.1| putative pseudouridine synthase [Acinetobacter baumannii AYE]
 gi|184159008|ref|YP_001847347.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           baumannii ACICU]
 gi|239501106|ref|ZP_04660416.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           baumannii AB900]
 gi|260556624|ref|ZP_05828842.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           baumannii ATCC 19606]
 gi|301348363|ref|ZP_07229104.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           baumannii AB056]
 gi|301511564|ref|ZP_07236801.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           baumannii AB058]
 gi|301596990|ref|ZP_07241998.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           baumannii AB059]
 gi|332853984|ref|ZP_08435100.1| pseudouridylate synthase [Acinetobacter baumannii 6013150]
 gi|332869736|ref|ZP_08438924.1| pseudouridylate synthase [Acinetobacter baumannii 6013113]
 gi|332874787|ref|ZP_08442657.1| pseudouridylate synthase [Acinetobacter baumannii 6014059]
 gi|169148063|emb|CAM85926.1| putative pseudouridine synthase [Acinetobacter baumannii AYE]
 gi|183210602|gb|ACC58000.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           baumannii ACICU]
 gi|193077980|gb|ABO12894.2| putative pseudouridine synthase [Acinetobacter baumannii ATCC
           17978]
 gi|260409883|gb|EEX03183.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           baumannii ATCC 19606]
 gi|332728266|gb|EGJ59648.1| pseudouridylate synthase [Acinetobacter baumannii 6013150]
 gi|332732638|gb|EGJ63871.1| pseudouridylate synthase [Acinetobacter baumannii 6013113]
 gi|332737048|gb|EGJ68005.1| pseudouridylate synthase [Acinetobacter baumannii 6014059]
          Length = 262

 Score = 89.1 bits (219), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 41/222 (18%), Positives = 87/222 (39%), Gaps = 19/222 (8%)

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD+++EGL+ LT+ GGL + +  P+ +  + Y V+  G V ++ L  L+KG+ +    
Sbjct: 38  GRLDMDSEGLVFLTDHGGLNQFITNPANKKYKTYLVQVDGDVTEEALEQLRKGVELNDGM 97

Query: 172 YGDMQVTLDTQ---------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
               +    ++                   +W+ + + EG+NR+++++     +   RLI
Sbjct: 98  TLPAKAIKVSEPEWLWDRDPPVRYRASIPTSWIEISICEGRNRQVRRMTSAVGFPTLRLI 157

Query: 217 RISYGPFQL--GTLLAGSTREVSKKILREQ--LGPHLLEEAQVNLDAPIYSSETLVRDRP 272
           R   G   L    L  G T+E+   +  +   +       ++  +  P  +    +  + 
Sbjct: 158 RTKIGTIDLVQLGLQPGETKEIEPLLYPDFKDVPAEQPYRSRSYVKKPGGTGGKPMVRKN 217

Query: 273 NIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
              S       R+ +    +    K      P  +     + 
Sbjct: 218 KDGSAKKSGTKRIWQMDESEKPRRKTNGTTRPNTKAPRGRSR 259


>gi|149908393|ref|ZP_01897056.1| pseudouridine synthase family 1 protein [Moritella sp. PE36]
 gi|149808556|gb|EDM68491.1| pseudouridine synthase family 1 protein [Moritella sp. PE36]
          Length = 239

 Score = 89.1 bits (219), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 43/185 (23%), Positives = 74/185 (40%), Gaps = 17/185 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P               + L       +  +            + + GRLD ++EGLLLL
Sbjct: 51  KPKESGPTQVYVFNKPYMVLTQFTDADNRETLKDYI---KVPDIYAAGRLDRDSEGLLLL 107

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TN+G L   L  P  +  + Y V+  G+   +KL+ L+ GI+++       +V +     
Sbjct: 108 TNNGRLQAKLTQPGEKTEKTYWVQVEGEPSPEKLSDLRYGIILKDGPTLPAKVEIMTEPS 167

Query: 180 ---------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + Q     W+ + + EG+NR+I+++         RLIR   GP+ L  +  
Sbjct: 168 VWPRVPPIRERQNIPTTWLAITIIEGRNRQIRRMTAHIGHPTLRLIRYRIGPWTLDNIQP 227

Query: 231 GSTRE 235
           G   E
Sbjct: 228 GELVE 232


>gi|149203717|ref|ZP_01880686.1| RNA pseudouridylate synthase [Roseovarius sp. TM1035]
 gi|149142834|gb|EDM30876.1| RNA pseudouridylate synthase [Roseovarius sp. TM1035]
          Length = 180

 Score = 89.1 bits (219), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 44/177 (24%), Positives = 74/177 (41%), Gaps = 16/177 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RL L++KP  +++  +D     +    L       RV   GRLD ++EGLLLLT+DG L 
Sbjct: 3   RLILFNKPYDVLSQFTDRGSEGSPRATLSDFIDIPRVYPAGRLDRDSEGLLLLTDDGQLQ 62

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------------V 177
             +  P  +  + Y  +  G  D   L  L+ G+ +        +               
Sbjct: 63  ARIANPRFKTEKTYYAQVEGLPDDTALAALRAGVTLSDGPTRPARVERTEPPTLWPRTPP 122

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
               +   + W+ + + EG+NR+++++         RLIR   G + L  L  G  R
Sbjct: 123 VRFRKSVPDCWLKLTISEGRNRQVRRMTAHIGHPTLRLIRWRIGDWTLDGLGPGEWR 179


>gi|114563429|ref|YP_750942.1| pseudouridine synthase, Rsu [Shewanella frigidimarina NCIMB 400]
 gi|114334722|gb|ABI72104.1| ribosomal large subunit pseudouridine synthase E [Shewanella
           frigidimarina NCIMB 400]
          Length = 235

 Score = 89.1 bits (219), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 51/184 (27%), Positives = 88/184 (47%), Gaps = 16/184 (8%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            + E   + L++KP  ++   +D  GR T+ D +P   + V + GRLD ++EGLLLLTND
Sbjct: 51  PRPENPVIVLFNKPFDVLCQFTDEAGRQTLKDFIP--VADVYAAGRLDRDSEGLLLLTND 108

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  PS +  + Y V+  G+   + +N L  G+ ++       +V +        
Sbjct: 109 GQLQAKLTQPSQKTFKTYWVQVEGEPSDEAINALCNGVGLKDGMTLPAKVCVMASPDIWP 168

Query: 180 ------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 + +     W+ V + EG+NR+++++         RLIR   G + L  L  G  
Sbjct: 169 RTPPVRERKAIPTTWLEVQICEGRNRQVRRMTAHVGHPTLRLIRYKIGQWCLDDLPNGEY 228

Query: 234 REVS 237
           + +S
Sbjct: 229 KVIS 232


>gi|262375434|ref|ZP_06068667.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           lwoffii SH145]
 gi|262309688|gb|EEY90818.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           lwoffii SH145]
          Length = 262

 Score = 89.1 bits (219), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 49/255 (19%), Positives = 103/255 (40%), Gaps = 21/255 (8%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ + +KP  +++     +   T+ D +     R+   GRLD+++EGL+ LT+ GGL + 
Sbjct: 2   KIVILNKPYDVLSQFRADEKHPTMADFVNDKDLRL--AGRLDMDSEGLVFLTDHGGLNQY 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----------- 182
           +  P+ +  + Y V+  G V ++ L  L+KG+ ++       +    ++           
Sbjct: 60  ITNPANKKFKTYMVQVEGDVTEEALEQLRKGVELKDGITLPARAEKVSEPEWLWERNPPV 119

Query: 183 ----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL--GTLLAGSTREV 236
                   +WV + + EG+NR+++++     +   RLIR   G   L    L  G TRE+
Sbjct: 120 RFRASVPTSWVEISICEGRNRQVRRMTSAVGFPTLRLIRTKIGEIDLVRMGLQPGETREI 179

Query: 237 SKKILREQLGPHLLE--EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
              +  +       E   ++  +  P  +    +  +    S       R+ +    +  
Sbjct: 180 EPLLYPDFQNVPAEEPYRSRSYVKKPGGTGGKPMVRKNKDGSVKKSGTKRIWQMDESEKP 239

Query: 295 LSKQKKLATPVHRRN 309
             K      P  +  
Sbjct: 240 RRKTNGTTRPNTKAP 254


>gi|215486389|ref|YP_002328820.1| 23S rRNA pseudouridine synthase E [Escherichia coli O127:H6 str.
           E2348/69]
 gi|215264461|emb|CAS08824.1| 23S rRNA pseudouridine synthase [Escherichia coli O127:H6 str.
           E2348/69]
 gi|323976494|gb|EGB71582.1| RNA pseudouridylate synthase [Escherichia coli TW10509]
          Length = 217

 Score = 89.1 bits (219), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 48/189 (25%), Positives = 87/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 31  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   +D L  L+ G+ +                 
Sbjct: 89  TNNGALQARLTQPGKRTGKIYYVQVEGIPTEDALEALRNGVTLNDGPTLPAGAEMVEEPE 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 149 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 208

Query: 230 AGSTREVSK 238
            G  RE + 
Sbjct: 209 NGEWREATD 217


>gi|196233257|ref|ZP_03132103.1| pseudouridine synthase [Chthoniobacter flavus Ellin428]
 gi|196222728|gb|EDY17252.1| pseudouridine synthase [Chthoniobacter flavus Ellin428]
          Length = 188

 Score = 89.1 bits (219), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 51/181 (28%), Positives = 81/181 (44%), Gaps = 16/181 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  +HKP G+++    PDG              V  +GRLD  +EGLLLL+++  L   L
Sbjct: 2   LLAFHKPYGVLS-QFTPDGSRHRPLAEFDFPKGVYPLGRLDAESEGLLLLSDEAALNARL 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---------- 184
             P+    R Y  +      ++ L  L++G+VI G      +V L   +           
Sbjct: 61  LHPTRGHYRTYWAQVERVPTREALTQLERGVVIGGRQTLPCRVWLLDPQPAVSPRVPPIR 120

Query: 185 -----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                   W+ + L EGKN +++++         RL+R+  G F+LG+L AGS RE+   
Sbjct: 121 FRKNVPETWIALELVEGKNHQVRRMTAAVGHPTLRLVRVKIGKFELGSLAAGSWRELDAT 180

Query: 240 I 240
            
Sbjct: 181 E 181


>gi|110641312|ref|YP_669042.1| 23S rRNA pseudouridine synthase E [Escherichia coli 536]
 gi|110342904|gb|ABG69141.1| putative ribosomal large subunit pseudouridine synthase
           [Escherichia coli 536]
          Length = 217

 Score = 89.1 bits (219), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 48/184 (26%), Positives = 86/184 (46%), Gaps = 17/184 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+LTN+G 
Sbjct: 36  NQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVLTNNGA 93

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-------------- 175
           L   L  P  +  ++Y V+  G   QD L  L+ G+ +                      
Sbjct: 94  LQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPR 153

Query: 176 -QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R
Sbjct: 154 NPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGNYSLDNLANGEWR 213

Query: 235 EVSK 238
           + + 
Sbjct: 214 DATD 217


>gi|327253839|gb|EGE65468.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           STEC_7v]
          Length = 207

 Score = 89.1 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 49/189 (25%), Positives = 87/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 21  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 79  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAEMVEEPE 138

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 139 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 198

Query: 230 AGSTREVSK 238
            G  RE + 
Sbjct: 199 NGEWREATD 207


>gi|255264737|ref|ZP_05344079.1| ribosomal large subunit pseudouridine synthase E [Thalassiobium sp.
           R2A62]
 gi|255107072|gb|EET49746.1| ribosomal large subunit pseudouridine synthase E [Thalassiobium sp.
           R2A62]
          Length = 178

 Score = 89.1 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 39/175 (22%), Positives = 70/175 (40%), Gaps = 16/175 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L      L     +     T+ D +        + GRLD ++EGLL+LT+DG L   
Sbjct: 4   VILLNKPFGVLSQFTDEGTNHPTLKDYVKIPGV--YAAGRLDRDSEGLLVLTDDGRLQNR 61

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------- 180
           +  P  +  + Y  +  G  D   L  L+ G+ ++       +  +              
Sbjct: 62  IASPKFKQPKTYWAQVEGTPDDAALEALRAGVKLKDGMTKPARARIIDAPDVWERDPPIR 121

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +   + W+ + L EG+NR+++++         RLIR S G + +  L  G  R
Sbjct: 122 VRKAIPDTWIELVLTEGRNRQVRRMTAAVGHPTLRLIRYSIGDWTIDNLALGQWR 176


>gi|163802088|ref|ZP_02195984.1| pseudouridine synthase family 1 protein [Vibrio sp. AND4]
 gi|159174229|gb|EDP59037.1| pseudouridine synthase family 1 protein [Vibrio sp. AND4]
          Length = 234

 Score = 89.1 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 41/186 (22%), Positives = 76/186 (40%), Gaps = 17/186 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +   +R  +        L         ++            V + GRLD ++EGL++LT
Sbjct: 51  RIAPKDRKVVIFNKPYDTLSQFTDGDGRKTLADYI---PVKDVYAAGRLDRDSEGLMVLT 107

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--- 182
           NDG L   L  P ++  + Y V+  G   ++ L  L+KG+ ++        V +  +   
Sbjct: 108 NDGILQAKLTQPQSKSPKTYWVQVDGAPTEEDLEKLRKGVELKDGITLPAIVEVMPEPEI 167

Query: 183 -----------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + + EG+NR+++++     +   RL+R S G   L  L  G
Sbjct: 168 WERNPPVRFRANIPTTWLAITIIEGRNRQVRRMTAHIGFPTLRLVRYSMGSIVLDNLKPG 227

Query: 232 STREVS 237
             RE++
Sbjct: 228 EWREIN 233


>gi|166714192|ref|ZP_02245399.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzicola BLS256]
          Length = 200

 Score = 89.1 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 46/175 (26%), Positives = 81/175 (46%), Gaps = 15/175 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L +KP G+++  SD             +   V + GRLD ++EGLLLLT+DG LA  +
Sbjct: 12  LVLLNKPYGVLSQFSDRSQPPKRTLAEFGLPPDVYAAGRLDHDSEGLLLLTDDGALAHRV 71

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------VTL 179
             P  +  + Y V+  G+   ++L  L+ G+V+        Q                  
Sbjct: 72  TDPRHKQPKTYWVQVEGEPQAEQLQALRDGVVLNDGPTRPAQVRSLDPAPPLWPRDPPVR 131

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +   +AW+ + + EG+NR+++++         RL+R++ G ++L  L  G  R
Sbjct: 132 VRKTVPDAWLELRITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLDMLAPGQWR 186


>gi|326387279|ref|ZP_08208889.1| pseudouridine synthase [Novosphingobium nitrogenifigens DSM 19370]
 gi|326208460|gb|EGD59267.1| pseudouridine synthase [Novosphingobium nitrogenifigens DSM 19370]
          Length = 180

 Score = 89.1 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 48/177 (27%), Positives = 81/177 (45%), Gaps = 15/177 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
           L  ++KP G++   +D             I    V   GRLD+++EGLLLLT+DG L   
Sbjct: 2   LIAFNKPYGVLCQFTDESTGPARPTLATFIDVPGVYPAGRLDLDSEGLLLLTDDGRLQAR 61

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------- 180
           +  P  +  + Y V+  G+ D+D L  L++G+ ++       QV                
Sbjct: 62  IADPRYKAPKTYLVQVEGEPDEDALAALRRGVRLKDGMTLPAQVERIEAPDLWPRNPPVR 121

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +   + W+ + LREG+NR+++++         RL+R   G + L  +  G  REV
Sbjct: 122 FRKSVPDCWLKLILREGRNRQVRRMTAAVGHPTLRLVRWRIGDWTLEGIAPGEWREV 178


>gi|84499356|ref|ZP_00997644.1| RNA pseudouridylate synthase [Oceanicola batsensis HTCC2597]
 gi|84392500|gb|EAQ04711.1| RNA pseudouridylate synthase [Oceanicola batsensis HTCC2597]
          Length = 182

 Score = 89.1 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 37/141 (26%), Positives = 63/141 (44%), Gaps = 15/141 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              GRLD ++EGL++LT+DG L   +  P  +  + Y  +  G  D   L  L++G+ ++
Sbjct: 40  YPAGRLDRDSEGLMILTDDGRLQARIAHPRYKAAKTYLAQVEGLPDHAALEALRRGVTLK 99

Query: 169 GICYGDMQVTLD---------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +V                   +   + W+ + L EG+NR+++++         
Sbjct: 100 DGPTRPARVRRIDVPEDLWDRDPPVRYRKSVPDCWIELTLTEGRNRQVRRMTAHVGHPTL 159

Query: 214 RLIRISYGPFQLGTLLAGSTR 234
           RLIRI  G +QL  L  G  R
Sbjct: 160 RLIRIRIGDWQLDHLPPGHWR 180


>gi|325982095|ref|YP_004294497.1| pseudouridine synthase Rsu [Nitrosomonas sp. AL212]
 gi|325531614|gb|ADZ26335.1| pseudouridine synthase Rsu [Nitrosomonas sp. AL212]
          Length = 184

 Score = 89.1 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 49/185 (26%), Positives = 88/185 (47%), Gaps = 17/185 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             R+ L++KP G++   +   G  ++ D +P         GRLD ++EGL+LLT++G L 
Sbjct: 1   MPRIILFNKPYGVICQFTPTCGHRSLQDFIPFAGF--YPAGRLDADSEGLVLLTDNGKLQ 58

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT---------- 181
             +  P  +  + Y V+  G+ D   LN +++GIV+        QV+L            
Sbjct: 59  DKICSPKYKLSKTYWVQVEGKPDDVALNAMRRGIVLSDFKTKSAQVSLMNEPSFIWDRQP 118

Query: 182 -----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +     W+++ L+EGKNR+I+++     +   RLIR + G   L  +  G  R +
Sbjct: 119 PIRFRKSIPTTWLSLILKEGKNRQIRRMTAAVFFPTLRLIRYAIGLHTLKGIAPGEWRML 178

Query: 237 SKKIL 241
           +   +
Sbjct: 179 AASDI 183


>gi|253998302|ref|YP_003050365.1| pseudouridine synthase [Methylovorus sp. SIP3-4]
 gi|313200376|ref|YP_004039034.1| pseudouridine synthase [Methylovorus sp. MP688]
 gi|253984981|gb|ACT49838.1| pseudouridine synthase [Methylovorus sp. SIP3-4]
 gi|312439692|gb|ADQ83798.1| pseudouridine synthase [Methylovorus sp. MP688]
          Length = 178

 Score = 89.1 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 46/177 (25%), Positives = 83/177 (46%), Gaps = 17/177 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L++KP G+V   S  +   T+ D +      V + GRLD ++EGLL+LT+DG L   +
Sbjct: 2   LILFNKPFGVVCQFSAHENHPTLKDYIAMP--DVYAAGRLDTDSEGLLILTDDGRLQHRI 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  + +++Y  +  G  D + L+ L++G+ +        QV +               
Sbjct: 60  AHPKHKEIKIYWAQVEGAPDDEALSPLRRGVDLGDFVTQPAQVKIIAEPANLWARVPPIR 119

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +     W+ + + EGKNR+++++     +   RLIR + G   L  L  G  + +
Sbjct: 120 ERKAIPTTWLEIRISEGKNRQVRRMTAKIGFPTLRLIRYAIGAHTLAGLQPGEFKIL 176


>gi|291617070|ref|YP_003519812.1| RluE [Pantoea ananatis LMG 20103]
 gi|291152100|gb|ADD76684.1| RluE [Pantoea ananatis LMG 20103]
          Length = 219

 Score = 89.1 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 49/191 (25%), Positives = 89/191 (46%), Gaps = 17/191 (8%)

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           V    +      R+ L++KP  ++   +D  GR T+ D +    S V + GRLD ++EGL
Sbjct: 28  VQRKAVAPPAVRRVLLFNKPFDVLPQFTDEAGRRTLKDFID--VSEVYAAGRLDRDSEGL 85

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------ 175
           ++LTNDG L   L  P  +  ++Y V+  G  ++  L  L+ G+ ++             
Sbjct: 86  MVLTNDGALQAALTQPGKRTGKIYYVQVEGAPEERDLQPLRDGVNLKDGLTLPAGIEKVA 145

Query: 176 ---------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
                        + +     W+ + L EG+NR+++++     +   RL+R + G F+L 
Sbjct: 146 EPEWLWARQPPIRERKAIPTQWLKITLYEGRNRQVRRMTAHIGFPTLRLVRYAMGDFELD 205

Query: 227 TLLAGSTREVS 237
            L  G  R++S
Sbjct: 206 NLAPGEWRDIS 216


>gi|260768154|ref|ZP_05877088.1| ribosomal large subunit pseudouridine synthase E [Vibrio furnissii
           CIP 102972]
 gi|260616184|gb|EEX41369.1| ribosomal large subunit pseudouridine synthase E [Vibrio furnissii
           CIP 102972]
          Length = 183

 Score = 89.1 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 43/183 (23%), Positives = 73/183 (39%), Gaps = 17/183 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              ER  +          T     DG              V + GRLD ++EGL++LTND
Sbjct: 2   SPQERQVVIFNKP---FDTLSQFTDGDGRKTLADFIPVKEVYAAGRLDRDSEGLMVLTND 58

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----- 182
           G L   L  P ++  + Y V+  G   +  L+ L+ G+ ++        V +  +     
Sbjct: 59  GILQAKLTQPQSKSPKTYWVQVEGAPQEADLDKLRNGVELKDGPTLPAIVEIMPEPEVWE 118

Query: 183 ---------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                         W+ + + EG+NR+++++     +   RLIR S G   LG L  G  
Sbjct: 119 RHPPVRFRAAIPTTWLAITIIEGRNRQVRRMTANIGFPTLRLIRYSMGDIVLGDLQPGEW 178

Query: 234 REV 236
           + +
Sbjct: 179 KHI 181


>gi|169632786|ref|YP_001706522.1| putative pseudouridine synthase [Acinetobacter baumannii SDF]
 gi|169151578|emb|CAP00355.1| putative pseudouridine synthase [Acinetobacter baumannii]
          Length = 262

 Score = 89.1 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 41/222 (18%), Positives = 87/222 (39%), Gaps = 19/222 (8%)

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD+++EGL+ LT+ GGL + +  P+ +  + Y V+  G V ++ L  L+KG+ +    
Sbjct: 38  GRLDMDSEGLVFLTDHGGLNQFITNPANKKYKTYLVQVDGDVTEEALEQLRKGVELNDGM 97

Query: 172 YGDMQVTLDTQ---------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
               +    ++                   +W+ + + EG+NR+++++     +   RLI
Sbjct: 98  TLPAKAIKVSEPEWLWDRDPPVRYRASIPTSWIEISICEGRNRQVRRMTSAVGFPTLRLI 157

Query: 217 RISYGPFQLG--TLLAGSTREVSKKILREQ--LGPHLLEEAQVNLDAPIYSSETLVRDRP 272
           R   G   L    L  G T+E+   +  +   +       ++  +  P  +    +  + 
Sbjct: 158 RTKIGTIDLVQLGLQPGETKEIEPLLYPDFKDVPAEQPYRSRSYVRKPGGTGGKPMVRKN 217

Query: 273 NIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
              S       R+ +    +    K      P  +     + 
Sbjct: 218 KDGSAKKSGTKRIWQMDESEKPRRKTNGTTRPNTKAPRGRSR 259


>gi|281491905|ref|YP_003353885.1| ribosomal large subunit pseudouridine synthase E [Lactococcus
           lactis subsp. lactis KF147]
 gi|281375614|gb|ADA65118.1| Ribosomal large subunit pseudouridine synthase E [Lactococcus
           lactis subsp. lactis KF147]
          Length = 185

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 45/178 (25%), Positives = 78/178 (43%), Gaps = 15/178 (8%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +              DG              V + GRLD ++EGLLLLT+DG L 
Sbjct: 4   CKKIMIILFNKPYDVLTKFTDGEGRKTLKDYIKIPNVYAAGRLDKDSEGLLLLTDDGKLN 63

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----------- 180
            +L  P ++  + Y V+  G+   +    L+KG++++       +V L            
Sbjct: 64  HLLTDPKSKSYKTYLVQVEGEFSSEAAQKLQKGLLLKDGKTLPAKVKLIDEPDWLWERTP 123

Query: 181 ----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                +    +WV + ++EGKNR+I+++     +   RLIR S G + LG L +G  +
Sbjct: 124 PIRERKAIPTSWVEISIKEGKNRQIRRMTAAVGFPTLRLIRWSIGQYSLGNLKSGEYK 181


>gi|6689331|emb|CAB65436.1| hypothetical protein [Synechococcus elongatus PCC 6301]
          Length = 199

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 53/190 (27%), Positives = 79/190 (41%), Gaps = 20/190 (10%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R  L+HKP   V   S  D               V  VGRLD ++EGLLLLTN+G L  
Sbjct: 3   YRYLLFHKPYDAVCQFSPSDRPDQQTLKDYIDVPEVYPVGRLDRDSEGLLLLTNNGALQH 62

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------ 180
            L  P     R Y V+   +  +  L  L++G+ IQ       +V               
Sbjct: 63  RLCHPRFGHDRTYWVQVEREPTEAALQALRQGVQIQDYRTRPAKVQRLDDPQIPERDPPI 122

Query: 181 --TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQLGTLLAGS 232
              +    AW+ + L+EG+NR+++++         RLIR +        P QL  L  G+
Sbjct: 123 RFRKTVPTAWLALTLQEGRNRQVRRMTAAVGHPTLRLIRAAIATHPDQPPLQLQGLAPGT 182

Query: 233 TREVSKKILR 242
            R+++    R
Sbjct: 183 WRDLTAIECR 192


>gi|56475798|ref|YP_157387.1| pseudouridine synthase [Aromatoleum aromaticum EbN1]
 gi|56311841|emb|CAI06486.1| Pseudouridine synthase [Aromatoleum aromaticum EbN1]
          Length = 230

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 45/176 (25%), Positives = 75/176 (42%), Gaps = 17/176 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL L +KP G++   S      T+   +P         GRLD ++EGLLLLT+DG L   
Sbjct: 30  RLILLNKPYGVICQFSGDGVHVTLKAFVPVPGV--YPAGRLDTDSEGLLLLTDDGALQHR 87

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------QVT 178
           +  P  +  + Y  +  G+  +  L  L+ G+ +                          
Sbjct: 88  IADPRHKLPKTYLAQVEGEPGETALTALRGGLDLGDFVTRPCSARRVAEPDWLWPRDPPV 147

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              +    +W+ + L EGKNR+++++     +   RLIR++ G + L  L  G  R
Sbjct: 148 RFRKNVPTSWLEIVLHEGKNRQVRRMTAKAGFPTLRLIRVAIGDWSLAGLAPGQWR 203


>gi|116071100|ref|ZP_01468369.1| Pseudouridine synthase, Rsu [Synechococcus sp. BL107]
 gi|116066505|gb|EAU72262.1| Pseudouridine synthase, Rsu [Synechococcus sp. BL107]
          Length = 210

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 50/188 (26%), Positives = 78/188 (41%), Gaps = 23/188 (12%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L HKP G+++  +  D               V + GRLD ++EGLL+LT++G L + L 
Sbjct: 1   MLLHKPYGVLSQFTPEDNSRWDCLRDFVDIPDVYAAGRLDADSEGLLVLTSNGRLQQQLT 60

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK------------ 183
            P     R Y V+  G     +L  L+ GI IQG      +      +            
Sbjct: 61  NPRFGHWRTYWVQVEGSPQPHQLQQLRDGITIQGYRTRPAKAAWLNAEAIPTIGERIPPI 120

Query: 184 -----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQLGTLLAGS 232
                    W+ + L+EG+NR+++++         RLIR +        PF L  L  G+
Sbjct: 121 RVRAAIPTHWLEISLQEGRNRQVRRMTAAVGLPTLRLIRHTIDLMDGDTPFTLKGLEPGA 180

Query: 233 TREVSKKI 240
            R V+K  
Sbjct: 181 WRTVTKAE 188


>gi|15673334|ref|NP_267508.1| pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403]
 gi|12724335|gb|AAK05450.1|AE006367_6 pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403]
 gi|326406888|gb|ADZ63959.1| ribosomal large subunit pseudouridine synthase E [Lactococcus
           lactis subsp. lactis CV56]
          Length = 185

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 45/178 (25%), Positives = 78/178 (43%), Gaps = 15/178 (8%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +              DG              V + GRLD ++EGLLLLT+DG L 
Sbjct: 4   CKKIMIILFNKPYDVLTKFTDGEGRKTLKDYIKIPNVYAAGRLDKDSEGLLLLTDDGKLN 63

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----------- 180
            +L  P ++  + Y V+  G+   +    L+KG++++       +V L            
Sbjct: 64  HLLTDPKSKSYKTYLVQVEGEFSPEAAQKLQKGLLLKDGKTLPAKVKLIDEPDWLWERTP 123

Query: 181 ----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                +    +WV + ++EGKNR+I+++     +   RLIR S G + LG L +G  +
Sbjct: 124 PIRERKAIPTSWVEISIKEGKNRQIRRMTAAVGFPTLRLIRWSIGQYSLGNLKSGEYK 181


>gi|322616613|gb|EFY13522.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           315996572]
 gi|322619872|gb|EFY16746.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           495297-1]
 gi|322622440|gb|EFY19285.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           495297-3]
 gi|322629442|gb|EFY26219.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           495297-4]
 gi|322632938|gb|EFY29681.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           515920-1]
 gi|322636817|gb|EFY33520.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           515920-2]
 gi|322641383|gb|EFY38022.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str. 531954]
 gi|322645148|gb|EFY41677.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           NC_MB110209-0054]
 gi|322652311|gb|EFY48667.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           OH_2009072675]
 gi|322655663|gb|EFY51965.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           CASC_09SCPH15965]
 gi|322660968|gb|EFY57198.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str. 19N]
 gi|322665446|gb|EFY61634.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           81038-01]
 gi|322667577|gb|EFY63738.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           MD_MDA09249507]
 gi|322673629|gb|EFY69731.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str. 414877]
 gi|322677555|gb|EFY73619.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str. 366867]
 gi|322679780|gb|EFY75819.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str. 413180]
 gi|322687253|gb|EFY83225.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str. 446600]
 gi|323193055|gb|EFZ78277.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           609458-1]
 gi|323199448|gb|EFZ84541.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           556150-1]
 gi|323203636|gb|EFZ88658.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str. 609460]
 gi|323208823|gb|EFZ93761.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           507440-20]
 gi|323214161|gb|EFZ98921.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str. 556152]
 gi|323217797|gb|EGA02512.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           MB101509-0077]
 gi|323218892|gb|EGA03403.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           MB102109-0047]
 gi|323226640|gb|EGA10840.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           MB110209-0055]
 gi|323229600|gb|EGA13723.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           MB111609-0052]
 gi|323232825|gb|EGA16921.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           2009083312]
 gi|323240139|gb|EGA24183.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           2009085258]
 gi|323242874|gb|EGA26895.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           315731156]
 gi|323246790|gb|EGA30760.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           IA_2009159199]
 gi|323254310|gb|EGA38127.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           IA_2010008282]
 gi|323255576|gb|EGA39335.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           IA_2010008283]
 gi|323259410|gb|EGA43046.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           IA_2010008284]
 gi|323267006|gb|EGA50491.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           IA_2010008285]
 gi|323272110|gb|EGA55524.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           IA_2010008287]
          Length = 221

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 51/187 (27%), Positives = 89/187 (47%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLL+LTND
Sbjct: 34  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIPVQGV--YAAGRLDRDSEGLLVLTND 91

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P  +  ++Y V+  G  D + L  L+ G+ +                    
Sbjct: 92  GALQARLTQPGKRTGKIYYVQVEGIPDNEALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 151

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G 
Sbjct: 152 PRTPPIRERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLSGLDNGQ 211

Query: 233 TREVSKK 239
            RE++++
Sbjct: 212 WREIAQE 218


>gi|294146965|ref|YP_003559631.1| ribosomal large subunit pseudouridine synthase E [Sphingobium
           japonicum UT26S]
 gi|292677382|dbj|BAI98899.1| ribosomal large subunit pseudouridine synthase E [Sphingobium
           japonicum UT26S]
          Length = 179

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 39/174 (22%), Positives = 68/174 (39%), Gaps = 14/174 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +        L     +  G                  GRLD+++EGLLLLT+DG L   +
Sbjct: 4   ILFNKPYGVLCQFSDERTGPPRPTLAAYIDRPGFYPAGRLDLDSEGLLLLTDDGRLQARI 63

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y V+  G  D+  L  L+ G+ ++       QV                 
Sbjct: 64  ADPRFKMPKTYLVQVEGDPDEAALAALRHGVRLKDGPTLPAQVERIEAPALWPRDPPVRF 123

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +   + W+ + +REG+NR+++++         RL+R   G + L  +  G  R
Sbjct: 124 RKSVPDRWLRLTIREGRNRQVRRMTAAIGHPTLRLVRWRIGDWTLDGIPQGQWR 177


>gi|52841050|ref|YP_094849.1| pseudouridine synthase [Legionella pneumophila subsp. pneumophila
           str. Philadelphia 1]
 gi|52628161|gb|AAU26902.1| pseudouridine synthase [Legionella pneumophila subsp. pneumophila
           str. Philadelphia 1]
          Length = 222

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 52/199 (26%), Positives = 85/199 (42%), Gaps = 18/199 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R  +  +L L++KP G++T  +      T+   +        + GRLD  +EGLL+LT+D
Sbjct: 19  RNHKMPQLILFNKPYGILTQFTGELPEQTLSAFIK--LPGFYAAGRLDKQSEGLLILTDD 76

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ----------- 176
           G L   L  P  +  + Y V+  G      L  L+KG+VI+ I +   +           
Sbjct: 77  GKLQHRLTHPKFEKKKHYWVQVEGVPTDKDLQPLRKGLVIKDITFLPAEARLISEPKIWP 136

Query: 177 ---VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 + +     W+ + LREGKN +I+K+     +   RLIR   G + L  L  G  
Sbjct: 137 RIPPIRERKHIPTTWLEIILREGKNHQIRKMTAAIGFPTLRLIRYQIGDWHLDQLQPGEY 196

Query: 234 R--EVSKKILREQLGPHLL 250
           +   ++   L E       
Sbjct: 197 KLINLTNDKLNELTRKSNP 215


>gi|198244181|ref|YP_002215898.1| RNA pseudouridine synthase family protein [Salmonella enterica
           subsp. enterica serovar Dublin str. CT_02021853]
 gi|200390314|ref|ZP_03216925.1| RNA pseudouridine synthase family protein [Salmonella enterica
           subsp. enterica serovar Virchow str. SL491]
 gi|197938697|gb|ACH76030.1| RNA pseudouridine synthase family protein [Salmonella enterica
           subsp. enterica serovar Dublin str. CT_02021853]
 gi|199602759|gb|EDZ01305.1| RNA pseudouridine synthase family protein [Salmonella enterica
           subsp. enterica serovar Virchow str. SL491]
          Length = 245

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 50/187 (26%), Positives = 87/187 (46%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLL+LTND
Sbjct: 58  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIPVQGV--YAAGRLDRDSEGLLVLTND 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P  +  ++Y V+  G  D   L  L+ G+ +                    
Sbjct: 116 GALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 175

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G 
Sbjct: 176 PRTPPIRERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQ 235

Query: 233 TREVSKK 239
             E++++
Sbjct: 236 WCEIAQE 242


>gi|264676389|ref|YP_003276295.1| Pseudouridine synthase, Rsu [Comamonas testosteroni CNB-2]
 gi|262206901|gb|ACY30999.1| Pseudouridine synthase, Rsu [Comamonas testosteroni CNB-2]
          Length = 223

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 48/188 (25%), Positives = 81/188 (43%), Gaps = 17/188 (9%)

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            V   P  +   TRL  +HKP G+++  +                  V   GRLD ++EG
Sbjct: 29  TVVRQPAPRPGVTRLLCFHKPYGVLSQFTPEG--KWQGLKDWIDVPGVYVAGRLDADSEG 86

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLLLTNDG L   +  P  +  + Y V+  G  D+  L  L++G+ +        +  L 
Sbjct: 87  LLLLTNDGQLQARIADPRHKMEKTYWVQVEGIPDEAALQRLREGVELSDGKTLPAKARLI 146

Query: 181 ---------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                           Q   + W+ + +REG+NR+++++         RL+R++ GP+ +
Sbjct: 147 EPQPLMWPRNPPIRVRQNIPDCWIELIIREGRNRQVRRMTAAVGHPTLRLVRMAVGPYSI 206

Query: 226 GTLLAGST 233
             L  G  
Sbjct: 207 EGLEPGQW 214


>gi|218461411|ref|ZP_03501502.1| probable RNA-pseudouridine synthase protein, ribosomal large
           subunit B [Rhizobium etli Kim 5]
          Length = 153

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 68/108 (62%), Positives = 86/108 (79%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           + +   +R+SKV+ARAG+ASRR++ERMI + RV +NG +LE   VNV   D IEVDGVP+
Sbjct: 46  ESDAKAERISKVMARAGVASRRDIERMIMEGRVTLNGRVLETPVVNVTLADRIEVDGVPI 105

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
           R  ERTRLWLYHKP GLVTT++DP+GR+TVFDNLP    RV+S+GRLD
Sbjct: 106 RGIERTRLWLYHKPAGLVTTNADPEGRATVFDNLPEELPRVMSIGRLD 153


>gi|54296835|ref|YP_123204.1| hypothetical protein lpp0876 [Legionella pneumophila str. Paris]
 gi|53750620|emb|CAH12027.1| hypothetical protein lpp0876 [Legionella pneumophila str. Paris]
          Length = 200

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 44/186 (23%), Positives = 69/186 (37%), Gaps = 16/186 (8%)

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
                              +         + GRLD  +EGLL+LT+DG L   L  P  +
Sbjct: 8   NKPYGILTQFTGELPEQTLSAFIKLPGFYAAGRLDKQSEGLLILTDDGKLQHRLTHPKFE 67

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------------VTLDTQKGSN 186
             + Y V+  G      L  L+KG+VI+ I +   +                 + +    
Sbjct: 68  KKKHYWVQVEGVPTDKDLQPLRKGLVIKDITFLPAEARLISEPKIWPRIPPIRERKHIPT 127

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR--EVSKKILREQ 244
            W+ + LREGKN +I+K+     +   RLIR   G + L  L  G  +   ++   L E 
Sbjct: 128 TWLEIILREGKNHQIRKMTAAIGFPTLRLIRYQIGDWHLDQLQPGEYKLINLTNDKLNEL 187

Query: 245 LGPHLL 250
                 
Sbjct: 188 TRKSNP 193


>gi|148360539|ref|YP_001251746.1| pseudouridine synthase [Legionella pneumophila str. Corby]
 gi|148282312|gb|ABQ56400.1| pseudouridine synthase [Legionella pneumophila str. Corby]
          Length = 219

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 53/199 (26%), Positives = 86/199 (43%), Gaps = 18/199 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R  +  +L L++KP G++T  +      T+   +        + GRLD  +EGLL+LT+D
Sbjct: 16  RNHKMPQLILFNKPYGVLTQFTGELPEQTLSAFIKFPGF--YAAGRLDKQSEGLLVLTDD 73

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------- 180
           G L   L  P  +  + Y V+  G      L  L+KG+VI+ I +   +  L        
Sbjct: 74  GKLQHRLTHPKFEKKKHYWVQVEGAPTDKDLQPLRKGLVIKDITFLPAEAKLISEPKIWP 133

Query: 181 -------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                   +     W+ + LREGKN +I+K+     +   RLIR   G ++L  L  G  
Sbjct: 134 RIPPIRERKHIPTTWLEIILREGKNHQIRKMTAAIGFPTLRLIRHQIGDWRLDQLQPGEY 193

Query: 234 R--EVSKKILREQLGPHLL 250
           +   ++   L E       
Sbjct: 194 KLINLTNDKLNELTRKSNP 212


>gi|254283622|ref|ZP_04958590.1| ribosomal large subunit pseudouridine synthase E [gamma
           proteobacterium NOR51-B]
 gi|219679825|gb|EED36174.1| ribosomal large subunit pseudouridine synthase E [gamma
           proteobacterium NOR51-B]
          Length = 184

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 44/140 (31%), Positives = 74/140 (52%), Gaps = 14/140 (10%)

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD ++EGLLLLTNDG L + +  P  +  + Y V+  G V+ + L  L KG+ ++   
Sbjct: 44  GRLDYDSEGLLLLTNDGVLQQRIANPRHKQWKTYWVQIEGAVNNEILGQLMKGVELKDGP 103

Query: 172 YGDMQVTLDTQ--------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
               + T  ++                 ++W+ + LREG+NR+I+++     +   RL+R
Sbjct: 104 TQPCKATAISEPALWSRDPPVRYRRNVPDSWIEMSLREGRNRQIRRMTAAVGFPTLRLVR 163

Query: 218 ISYGPFQLGTLLAGSTREVS 237
            + GP+QL TL  G  R ++
Sbjct: 164 RAIGPWQLDTLRPGEHRRLT 183


>gi|221069503|ref|ZP_03545608.1| pseudouridine synthase [Comamonas testosteroni KF-1]
 gi|220714526|gb|EED69894.1| pseudouridine synthase [Comamonas testosteroni KF-1]
          Length = 221

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 49/184 (26%), Positives = 80/184 (43%), Gaps = 17/184 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P  + E TRL  +HKP G+++  +                  V   GRLD ++EGLLLL
Sbjct: 33  QPAPRPEVTRLLCFHKPYGVLSQFTPEG--KWQGLKDWIDAPGVYVAGRLDADSEGLLLL 90

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---- 180
           TNDG L   +  P  +  + Y V+  G  D+  L  L+ G+ +        +  L     
Sbjct: 91  TNDGQLQARIADPRHKMEKTYWVQVEGVPDEAALQRLRDGVELSDGKTLPARARLIEPQP 150

Query: 181 -----------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                       Q   + W+ + +REGKNR+++++         RL+R++ GP+ +  L 
Sbjct: 151 SMWPRNPPIRVRQNIPDCWIELIIREGKNRQVRRMTAAVGHPTLRLVRMAVGPYSIEGLE 210

Query: 230 AGST 233
            G  
Sbjct: 211 PGQW 214


>gi|283784946|ref|YP_003364811.1| ribosomal large subunit pseudouridine synthase E (rRNA
           pseudouridylate synthase E) [Citrobacter rodentium
           ICC168]
 gi|282948400|emb|CBG87988.1| ribosomal large subunit pseudouridine synthase E (rRNA
           pseudouridylate synthase E) [Citrobacter rodentium
           ICC168]
          Length = 218

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 49/190 (25%), Positives = 88/190 (46%), Gaps = 17/190 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
              R+ +  R+ L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLL+L
Sbjct: 31  KRRRENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIPVQGV--YAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TNDG L   L  P  +  ++Y V+  G    + LN L+ G+ +                 
Sbjct: 89  TNDGALQARLTQPGKRTGKIYFVQVEGDPTAEALNALRNGVTLNDGPTLPAGVELVAEPD 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 149 WLWPRNPPIRERKTIPTRWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLA 208

Query: 230 AGSTREVSKK 239
            G  R+++ +
Sbjct: 209 NGEWRDITGE 218


>gi|260549672|ref|ZP_05823889.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter sp.
           RUH2624]
 gi|260407189|gb|EEX00665.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter sp.
           RUH2624]
          Length = 262

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 41/225 (18%), Positives = 87/225 (38%), Gaps = 19/225 (8%)

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD+++EGL+ LT+ GGL + +  P+ +  + Y V+  G V ++ L  L+KG+ +    
Sbjct: 38  GRLDMDSEGLVFLTDHGGLNQFITNPANKKYKTYLVQVDGDVTEEALEQLRKGVELNDGM 97

Query: 172 YGDMQVTLDTQ---------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
               +    ++                   +W+ + + EG+NR+++++     +   RLI
Sbjct: 98  TLPAKAIKVSEPEWLWDRDPPVRYRASIPTSWIEISICEGRNRQVRRMTSAVGFPTLRLI 157

Query: 217 RISYGPFQLG--TLLAGSTREVSKKILREQ--LGPHLLEEAQVNLDAPIYSSETLVRDRP 272
           R   G   L    L  G T+E+   +  +   +       ++  +  P  +    +  + 
Sbjct: 158 RTKIGSIDLVQLGLQPGETKEIEPLLYPDFKDVPAEQPYRSRSYVKKPGGTGGKPMVRKN 217

Query: 273 NIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
              S       R+ +    +    K      P  +     +    
Sbjct: 218 KDGSVKKSGTKRIWQMDESEKPRRKTNGTTRPNTKAPRGRSRNGR 262


>gi|262370314|ref|ZP_06063640.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           johnsonii SH046]
 gi|262314656|gb|EEY95697.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           johnsonii SH046]
          Length = 262

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 44/225 (19%), Positives = 87/225 (38%), Gaps = 19/225 (8%)

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD+++EGL+ LT+ GGL + +  P+ +  + Y V+  G V ++ L  L+KG+ ++   
Sbjct: 38  GRLDMDSEGLVFLTDHGGLNQYITNPANKKFKTYLVQVDGDVTEEALEQLRKGVELKDGM 97

Query: 172 YGDMQVTLDTQ---------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
               + +   Q                   +WV + + EG+NR+++++     +   RLI
Sbjct: 98  TLPAEASKVEQPEWLWERDPPVRFRASVPTSWVEISICEGRNRQVRRMTAAVGFPTLRLI 157

Query: 217 RISYGPFQL--GTLLAGSTREVSKKILREQLGPHLLE--EAQVNLDAPIYSSETLVRDRP 272
           R   G   L    L  G T+E+   +  +       E   ++  +  P  +    +  + 
Sbjct: 158 RTKIGAIDLVQMGLQPGETKEIEPLLYPDFQNIPAEEPYRSRSYVKKPGGTGGKPMVRKN 217

Query: 273 NIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
              S       R+ +    +    K      P  +          
Sbjct: 218 KDGSVKKSGTKRIWQMDDSEKPKRKTNGTTRPNTKAPRGRGRNGR 262


>gi|114798241|ref|YP_760095.1| RNA pseudouridine synthase family protein [Hyphomonas neptunium
           ATCC 15444]
 gi|114738415|gb|ABI76540.1| RNA pseudouridine synthase family protein [Hyphomonas neptunium
           ATCC 15444]
          Length = 178

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 33/141 (23%), Positives = 61/141 (43%), Gaps = 15/141 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              GRLD ++EGLL+LT+DG     +  P  +  + Y  +  G   ++ L  L+KG+ ++
Sbjct: 36  YPAGRLDFDSEGLLILTDDGREQARIADPKHKIPKTYLAQVEGIPSEEALQALRKGVDLK 95

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                       +   + W+ + + EG+NR+++++         
Sbjct: 96  DGRTRPATARLAAEPENLWPRDPPIRYRKSVPDTWIELTITEGRNRQVRRMTAAAGHPTL 155

Query: 214 RLIRISYGPFQLGTLLAGSTR 234
           RLIR+  G + L  L  G+ R
Sbjct: 156 RLIRLRIGDWDLENLPPGAWR 176


>gi|293609786|ref|ZP_06692088.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292828238|gb|EFF86601.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|325123010|gb|ADY82533.1| putative pseudouridine synthase [Acinetobacter calcoaceticus
           PHEA-2]
          Length = 262

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 40/225 (17%), Positives = 85/225 (37%), Gaps = 19/225 (8%)

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD+++EGL+ LT+ GGL + +  P+ +  + Y V+  G V ++ L  L+KG+ +    
Sbjct: 38  GRLDMDSEGLVFLTDHGGLNQFITNPANKKYKTYLVQVDGDVTEEALEQLRKGVELNDGM 97

Query: 172 YGDMQVTLDTQ---------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
               +    ++                   +W+ + + EG+NR+++++     +   RLI
Sbjct: 98  TLPAKAIKVSEPEWLWERNPPVRYRANIPTSWIEISICEGRNRQVRRMTSAVGFPTLRLI 157

Query: 217 RISYGPFQL--GTLLAGSTREVSKKILREQ--LGPHLLEEAQVNLDAPIYSSETLVRDRP 272
           R   G   L    L  G  +E+   +  +   +       ++  +  P  +    +  + 
Sbjct: 158 RTKIGSIDLVQLGLRPGDVKEIEPLLYPDFKDVPAEQPYRSRSYVKKPGGTGGKPMVRKN 217

Query: 273 NIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
              S       R+ +    +    K      P  +          
Sbjct: 218 KDGSAKKSGTKRIWQMDESEKPRRKTNGTTRPNTKAPRGRGRNGR 262


>gi|294649789|ref|ZP_06727191.1| ribosomal large subunit pseudouridine synthase E family protein
           [Acinetobacter haemolyticus ATCC 19194]
 gi|292824272|gb|EFF83073.1| ribosomal large subunit pseudouridine synthase E family protein
           [Acinetobacter haemolyticus ATCC 19194]
          Length = 267

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 44/245 (17%), Positives = 83/245 (33%), Gaps = 30/245 (12%)

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD+++EGL+ LT+ GGL + +  PS +  + Y  +  G V ++ L  L+ G+ +    
Sbjct: 38  GRLDLDSEGLMFLTDHGGLNQFITHPSNKKYKTYLAQVDGDVTEEALEQLRNGVELADGM 97

Query: 172 YGDMQVTLDTQ---------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
               +     +                   +W+ + + EG+NR+++++     +   RLI
Sbjct: 98  TLPAKAMKVDEPEWLWDRDPPVRYRASIPTSWIELQICEGRNRQVRRMTAAVGFPTLRLI 157

Query: 217 RISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIIS 276
           R   G   L               +R  L P    E +  L             R     
Sbjct: 158 RTQIGSINL---------------IRLGLQPGEQTEIEPLLFPDFKDLPEDKPYRSRSYV 202

Query: 277 EVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR 336
           + P        +  +K G  K         +R    +        ++  +    +    R
Sbjct: 203 KKPGGTGGKPMHQKKKEGDKKDPNKKKSGTKRIWQMDESEKPRRKTNGTTRPNTKAPRGR 262

Query: 337 RSPSF 341
              S 
Sbjct: 263 SRNSR 267


>gi|255318391|ref|ZP_05359624.1| putative pseudouridine synthase [Acinetobacter radioresistens SK82]
 gi|262378621|ref|ZP_06071778.1| conserved hypothetical protein [Acinetobacter radioresistens SH164]
 gi|255304383|gb|EET83567.1| putative pseudouridine synthase [Acinetobacter radioresistens SK82]
 gi|262299906|gb|EEY87818.1| conserved hypothetical protein [Acinetobacter radioresistens SH164]
          Length = 274

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 49/281 (17%), Positives = 103/281 (36%), Gaps = 27/281 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ +++KP  +++   +     T+   +     R+   GRLD+++EGL+ LT+ GGL + 
Sbjct: 2   KIIIFNKPYDVLSQFREDSKHLTLSHFIHDPELRL--AGRLDLDSEGLMFLTDHGGLNQF 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----------- 182
           +  P  +  + Y  +  G + ++ L  L++G+ +        +     Q           
Sbjct: 60  ITNPKNKKFKTYLAQVDGDITEEALEQLRRGVELADGMTLPAKARKVEQPEWLWDRDPPV 119

Query: 183 ----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
                    WV + + EG+NR+++++     +   RLIR   G   L    L  G   E+
Sbjct: 120 RFRASIPTTWVELQICEGRNRQVRRMTAAVGFPTLRLIRTQIGTIDLVKLGLQPGEQVEI 179

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
                 E L     ++   +      S+      +P    +    F + +      N   
Sbjct: 180 ------EPLLYPDFKDVPADKPYTGRSAPRSAAKKPFEQKDGKSKFNKEQPKDKGANKAG 233

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
           K+        +R   +    AK    +  +    +     R
Sbjct: 234 KKLPSGG--TKRVWQTEEGEAKPRRKTNGTTRPGKIRRSNR 272


>gi|59712383|ref|YP_205159.1| 23S rRNA pseudouridine synthase [Vibrio fischeri ES114]
 gi|59480484|gb|AAW86271.1| 23S rRNA pseudouridine synthase [Vibrio fischeri ES114]
          Length = 206

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 47/187 (25%), Positives = 93/187 (49%), Gaps = 16/187 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    +  ++ +++KP  +++  +D   R T+ D +      V + GRLD ++EGLL+L
Sbjct: 21  KPRPAPKDRKVIIFNKPFDVLSQFTDDQHRQTLADFIS--VKDVYAAGRLDRDSEGLLIL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +D L+ L++G+ ++       +V +  +  
Sbjct: 79  TNDGVLQARLTQPESKSPKTYWVQVEGAPTEDDLDKLRQGVELKDGMTLPAKVEIIPEPN 138

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+++ + EG+NR+++++     +   RLIR S G + +  +  
Sbjct: 139 VWERNPPVRFRAAIPTTWISITITEGRNRQVRRMTANIGFPTLRLIRYSMGDWTIKDVAH 198

Query: 231 GSTREVS 237
           G+ +EVS
Sbjct: 199 GTWKEVS 205


>gi|315179854|gb|ADT86768.1| pseudouridine synthase family 1 protein [Vibrio furnissii NCTC
           11218]
          Length = 183

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 43/183 (23%), Positives = 73/183 (39%), Gaps = 17/183 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              ER  +          T     DG              V + GRLD ++EGL++LTND
Sbjct: 2   SPHERQVVIFNKP---FDTLSQFTDGDGRKTLADFIPVKDVYAAGRLDRDSEGLMVLTND 58

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----- 182
           G L   L  P ++  + Y V+  G   +  L+ L+ G+ ++        V +  +     
Sbjct: 59  GILQAKLTQPQSKSPKTYWVQVEGAPQEADLDKLRNGVELKDGPTLPAIVEIMPEPEVWE 118

Query: 183 ---------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                         W+ + + EG+NR+++++     +   RLIR S G   LG L  G  
Sbjct: 119 RHPPVRFRAAIPTTWLAITIIEGRNRQVRRMTANIGFPTLRLIRYSMGDIVLGDLQPGEW 178

Query: 234 REV 236
           + +
Sbjct: 179 KHI 181


>gi|3402689|gb|AAC28992.1| unknown protein [Arabidopsis thaliana]
          Length = 303

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 52/149 (34%), Positives = 73/149 (48%), Gaps = 15/149 (10%)

Query: 4   KNIVQENFT--PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHI 60
           +    ENF   PQR+SKV+A AG+ASRR  E +I   +V VNGIL       V  + D I
Sbjct: 148 RRFYNENFKEQPQRLSKVLAAAGVASRRTSEELIFDGKVTVNGILCNTPQTRVDPSRDII 207

Query: 61  EVDGVPLRKA-ERTRLWLYHKPIGLVTTH-----------SDPDGRSTVFDNLPSIFSRV 108
            V+G  + K       +  +KP G + +             D    S    N  +   R+
Sbjct: 208 YVNGNRIPKKLPPKVYFALNKPKGYICSSGEKEIKSAISLFDEYLSSWDKRNPGTPKPRL 267

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELP 137
            +VGRLD+ T GL+++TNDG  A+ L  P
Sbjct: 268 FTVGRLDVATTGLIVVTNDGDFAQKLSHP 296


>gi|294668516|ref|ZP_06733613.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           elongata subsp. glycolytica ATCC 29315]
 gi|291309479|gb|EFE50722.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           elongata subsp. glycolytica ATCC 29315]
          Length = 186

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 45/180 (25%), Positives = 84/180 (46%), Gaps = 21/180 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L +++KP G++   S  +   ++ D++ +        GRLD ++EGLLLLT+DG L   +
Sbjct: 4   LIIFNKPCGVICQFSPHEKHPSLKDHIDAPGF--YPAGRLDTDSEGLLLLTDDGQLQARI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---------- 184
             P  +  + Y  +  G  D DKL LL++ + +        ++ L +++           
Sbjct: 62  TQPRFKVEKTYWAQLEGIPDTDKLQLLQRPMDLGDFTTRPAKIRLLSEEETDGLWPRNPP 121

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTRE 235
                   + W+ + + EGKNR+++++     +   RLIR++ G   L    L  G  R 
Sbjct: 122 VRVRKTVPDFWLEIKISEGKNRQVRRMTAKAGYPCLRLIRVAIGRLNLFDEQLGLGEWRY 181


>gi|126642512|ref|YP_001085496.1| putative pseudouridine synthase [Acinetobacter baumannii ATCC
           17978]
 gi|213158201|ref|YP_002320252.1| pseudouridine synthase, Rsu [Acinetobacter baumannii AB0057]
 gi|215482683|ref|YP_002324879.1| Ribosomal large subunit pseudouridine synthase E [Acinetobacter
           baumannii AB307-0294]
 gi|213057361|gb|ACJ42263.1| pseudouridine synthase, Rsu [Acinetobacter baumannii AB0057]
 gi|213985967|gb|ACJ56266.1| Ribosomal large subunit pseudouridine synthase E [Acinetobacter
           baumannii AB307-0294]
 gi|322508988|gb|ADX04442.1| Pseudouridine synthase [Acinetobacter baumannii 1656-2]
 gi|323518972|gb|ADX93353.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           baumannii TCDC-AB0715]
          Length = 240

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 41/222 (18%), Positives = 87/222 (39%), Gaps = 19/222 (8%)

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD+++EGL+ LT+ GGL + +  P+ +  + Y V+  G V ++ L  L+KG+ +    
Sbjct: 16  GRLDMDSEGLVFLTDHGGLNQFITNPANKKYKTYLVQVDGDVTEEALEQLRKGVELNDGM 75

Query: 172 YGDMQVTLDTQ---------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
               +    ++                   +W+ + + EG+NR+++++     +   RLI
Sbjct: 76  TLPAKAIKVSEPEWLWDRDPPVRYRASIPTSWIEISICEGRNRQVRRMTSAVGFPTLRLI 135

Query: 217 RISYGPFQL--GTLLAGSTREVSKKILREQ--LGPHLLEEAQVNLDAPIYSSETLVRDRP 272
           R   G   L    L  G T+E+   +  +   +       ++  +  P  +    +  + 
Sbjct: 136 RTKIGTIDLVQLGLQPGETKEIEPLLYPDFKDVPAEQPYRSRSYVKKPGGTGGKPMVRKN 195

Query: 273 NIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
              S       R+ +    +    K      P  +     + 
Sbjct: 196 KDGSAKKSGTKRIWQMDESEKPRRKTNGTTRPNTKAPRGRSR 237


>gi|28897784|ref|NP_797389.1| pseudouridine synthase family 1 protein [Vibrio parahaemolyticus
           RIMD 2210633]
 gi|260363791|ref|ZP_05776546.1| RNA pseudouridine synthase family protein [Vibrio parahaemolyticus
           K5030]
 gi|260876948|ref|ZP_05889303.1| RNA pseudouridine synthase family protein [Vibrio parahaemolyticus
           AN-5034]
 gi|260897911|ref|ZP_05906407.1| RNA pseudouridine synthase family protein [Vibrio parahaemolyticus
           Peru-466]
 gi|34098484|sp|Q87QY8|RLUE_VIBPA RecName: Full=Ribosomal large subunit pseudouridine synthase E;
           AltName: Full=rRNA pseudouridylate synthase E; AltName:
           Full=rRNA-uridine isomerase E
 gi|28805997|dbj|BAC59273.1| pseudouridine synthase family 1 protein [Vibrio parahaemolyticus
           RIMD 2210633]
 gi|308085469|gb|EFO35164.1| RNA pseudouridine synthase family protein [Vibrio parahaemolyticus
           Peru-466]
 gi|308093803|gb|EFO43498.1| RNA pseudouridine synthase family protein [Vibrio parahaemolyticus
           AN-5034]
 gi|308113873|gb|EFO51413.1| RNA pseudouridine synthase family protein [Vibrio parahaemolyticus
           K5030]
          Length = 238

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 41/185 (22%), Positives = 74/185 (40%), Gaps = 17/185 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +    R  +        L         ++            V + GRLD ++EGL++LT
Sbjct: 55  RVDLQNRKVIIFNKPYDTLSQFTDGDGRKTLADYI---PVKDVYAAGRLDRDSEGLMVLT 111

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----- 180
           NDG L   L  P ++  + Y V+  G   +  L  L+KG+ ++       +V +      
Sbjct: 112 NDGILQAKLTQPKSKSPKTYWVQVDGAPQEQDLEKLRKGVELKDGMTLPAKVEVIDAPTI 171

Query: 181 ---------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + + EG+NR+++++     +   RL+R S G   LG L  G
Sbjct: 172 WERNPPVRFRANIPTTWLAITIIEGRNRQVRRMTAHIGFPTLRLVRYSMGDITLGDLQPG 231

Query: 232 STREV 236
             +E+
Sbjct: 232 QWKEI 236


>gi|319762719|ref|YP_004126656.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
 gi|317117280|gb|ADU99768.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
          Length = 188

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 44/178 (24%), Positives = 81/178 (45%), Gaps = 17/178 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL  ++KP G+++  +       + D +      V   GRLD ++EGLLLLT+ G L   
Sbjct: 6   RLIRFNKPYGVLSQFTPEGRWRGLKDFID--LPGVYVAGRLDADSEGLLLLTDSGPLQAR 63

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------- 180
           +  P  +  + Y V+  G  D   L  L++GI +        +V                
Sbjct: 64  ISDPRHKMEKTYWVQVEGIPDDAALAALQRGITLNDGPTRPARVHRLEPPPALCPRDPPI 123

Query: 181 --TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              +   ++W+ + +REG+NR+++++         RL+R + GP+ L  L  G+  ++
Sbjct: 124 RVRRNIPDSWIELVIREGRNRQVRRMTAAVGHPTLRLVRAAIGPYTLDGLAPGAWDDI 181


>gi|298710181|emb|CBJ26256.1| pseudouridine synthase [Ectocarpus siliculosus]
          Length = 387

 Score = 88.7 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 28/168 (16%), Positives = 56/168 (33%), Gaps = 1/168 (0%)

Query: 173 GDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
             +         +   W+ V LREGKNR+I+++     +++ RL RIS GP  LG +  G
Sbjct: 139 QPVPWRFKPGTVATITWIEVVLREGKNRQIRRLCRRSEFELTRLHRISVGPIVLGDVEEG 198

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           S RE++++ +       L E+        +         +         +    +  + +
Sbjct: 199 SCRELTRQEVEALYKRCLPEDPLCPTIDAVQDILQSRLSQTARRIRTTAEVGGHRFKARE 258

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
            +      +   P       +    A            +  +   R  
Sbjct: 259 HSSAMDVPQKDMPERPTAEDAEQRRAAKARDGERGCPCRTTQGPGRRR 306


>gi|226952496|ref|ZP_03822960.1| pseudouridine synthase [Acinetobacter sp. ATCC 27244]
 gi|226836767|gb|EEH69150.1| pseudouridine synthase [Acinetobacter sp. ATCC 27244]
          Length = 267

 Score = 88.3 bits (217), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 43/245 (17%), Positives = 82/245 (33%), Gaps = 30/245 (12%)

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD+++EGL+ LT+ GGL + +  PS +  + Y  +  G V ++ L  L+ G+ +    
Sbjct: 38  GRLDLDSEGLMFLTDHGGLNQFITHPSNKKYKTYLAQVDGDVTEEALEQLRNGVELADGM 97

Query: 172 YGDMQVTLDTQ---------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
               +     +                   +W+ + + EG+NR+++++     +   RLI
Sbjct: 98  TLPAKAMKVDEPEWLWDRDPPVRYRASIPTSWIELQICEGRNRQVRRMTAAVGFPTLRLI 157

Query: 217 RISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIIS 276
           R   G   L               +R  L P    E +  L             R     
Sbjct: 158 RTQIGSINL---------------IRLGLQPGEQTEIEPLLFPDFKDLPEDKPYRSRSYV 202

Query: 277 EVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR 336
           + P        +  +K G  K         +R    +        ++  +    +    R
Sbjct: 203 KKPGGTGGKPMHQKKKEGDKKDPNKKKSGTKRIWQMDESEKPRRKTNGTTRPNTKAPRGR 262

Query: 337 RSPSF 341
                
Sbjct: 263 SRNGR 267


>gi|254467319|ref|ZP_05080730.1| ribosomal large subunit pseudouridine synthase E [Rhodobacterales
           bacterium Y4I]
 gi|206688227|gb|EDZ48709.1| ribosomal large subunit pseudouridine synthase E [Rhodobacterales
           bacterium Y4I]
          Length = 217

 Score = 88.3 bits (217), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 50/234 (21%), Positives = 90/234 (38%), Gaps = 34/234 (14%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGG 129
            TRL  ++KP  ++   +D   + +    L          + GRLD ++EGLLLLT++G 
Sbjct: 1   MTRLIRFNKPYDVLPQFTDSGSQDSPRATLSKYIDCPGVYAAGRLDRDSEGLLLLTDNGR 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ------------- 176
           L   +  P  +  + Y V+  G  DQ+ L  L +G+ ++       +             
Sbjct: 61  LQAWITDPKHKMDKTYWVQVEGIPDQEALKNLAEGVELKDGITRPAKVRLMPEPTGLWAR 120

Query: 177 --VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +   ++W+ + LREG+NR+++++         RLIR S G + L  L  G+  
Sbjct: 121 TPPVRVRKTVPDSWIALTLREGRNRQVRRMTAAVGHPTLRLIRYSIGAWTLDGLAQGAW- 179

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
                           E+ +                RP   +  P    R ++ 
Sbjct: 180 ----------------EDVEPPRVPGPPKPSQKPPRRPKPSAARPPKGDRPRRR 217


>gi|331646394|ref|ZP_08347497.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Escherichia coli M605]
 gi|331045146|gb|EGI17273.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Escherichia coli M605]
          Length = 217

 Score = 88.3 bits (217), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 47/184 (25%), Positives = 86/184 (46%), Gaps = 17/184 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+LTN+G 
Sbjct: 36  NQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPIQGV--YAAGRLDRDSEGLLVLTNNGA 93

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-------------- 175
           L   L  P  +  ++Y V+  G   Q+ L  L+ G+ +                      
Sbjct: 94  LQARLTQPGKRTGKIYYVQVEGIPTQEALEALRNGVTLNDGPTLPAGAELVEEPAWLWPR 153

Query: 176 -QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R
Sbjct: 154 NPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWR 213

Query: 235 EVSK 238
           + + 
Sbjct: 214 DATD 217


>gi|299769196|ref|YP_003731222.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter sp.
           DR1]
 gi|298699284|gb|ADI89849.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter sp.
           DR1]
          Length = 262

 Score = 88.3 bits (217), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 42/222 (18%), Positives = 84/222 (37%), Gaps = 19/222 (8%)

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD+++EGL+ LT+ GGL + +  P+ +  + Y V+  G V ++ L  L+KG+ +    
Sbjct: 38  GRLDMDSEGLVFLTDHGGLNQFITNPANKKYKTYLVQVDGDVTEEALEQLRKGVELNDGM 97

Query: 172 YGDMQVTLDTQ---------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
                    ++                   +WV + + EG+NR+++++     +   RLI
Sbjct: 98  TLPATAIKVSEPEWLWERNPPVRYRANIPTSWVEISICEGRNRQVRRMTSAVGFPTLRLI 157

Query: 217 RISYGPFQLG--TLLAGSTREVSKKILREQLGPHLLE--EAQVNLDAPIYSSETLVRDRP 272
           R   G   L    L  G  +E+   +  +       E   ++  +  P  +    +  + 
Sbjct: 158 RTKIGSIDLVQLGLRPGDVKEIEPLLYPDFKDVPAEEPYRSRSYVKKPGGTGGKPMVRKN 217

Query: 273 NIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
              S       R+ +    +    K      P  +       
Sbjct: 218 KDGSAKKSGTKRIWQMDESEKPRRKTNGTTRPNTKAPRGRGR 259


>gi|126735443|ref|ZP_01751189.1| Pseudouridine synthase, Rsu [Roseobacter sp. CCS2]
 gi|126715998|gb|EBA12863.1| Pseudouridine synthase, Rsu [Roseobacter sp. CCS2]
          Length = 180

 Score = 88.3 bits (217), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 36/176 (20%), Positives = 72/176 (40%), Gaps = 14/176 (7%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +        L               +       V   GRLD ++EGLL+LT+DG L   
Sbjct: 4   VILFNKPFGVLSQFTDAKSPTPRPTLSAFIDVPGVYPAGRLDRDSEGLLVLTDDGKLQAR 63

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------- 180
           +  P  +  + Y V+  G+  +  L+LL+ G+ ++       ++ L              
Sbjct: 64  IAAPKNKMSKTYFVQVEGEPTEKDLSLLRDGVTLKDGPTRPAKLRLIDPPQLWDRDPPVR 123

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
             +   + W+ + + EG+NR+++++     +   RL+R   G + L  + +G+  E
Sbjct: 124 FRKSVPDTWIEITISEGRNRQVRRMTAHIGFPTLRLVRWRIGNWTLDGIESGTWIE 179


>gi|296106395|ref|YP_003618095.1| ribosomal large subunit pseudouridine synthase E [Legionella
           pneumophila 2300/99 Alcoy]
 gi|295648296|gb|ADG24143.1| ribosomal large subunit pseudouridine synthase E [Legionella
           pneumophila 2300/99 Alcoy]
 gi|307609608|emb|CBW99110.1| hypothetical protein LPW_08951 [Legionella pneumophila 130b]
          Length = 200

 Score = 88.3 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 46/186 (24%), Positives = 71/186 (38%), Gaps = 16/186 (8%)

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
                              +    F    + GRLD  +EGLL+LT+DG L   L  P  +
Sbjct: 8   NKPYGVLTQFTGELPEQTLSAFIKFPGFYAAGRLDKQSEGLLVLTDDGKLQHRLTHPKFE 67

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------------TQKGSN 186
             + Y V+  G      L  L+KG+VI+ I +   +  L                +    
Sbjct: 68  KKKHYWVQVEGAPTDKDLQPLRKGLVIKDITFLPAEAKLISEPKIWPRIPPIRERKHIPT 127

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR--EVSKKILREQ 244
            W+ + LREGKN +I+K+     +   RLIR   G ++L  L  G  +   ++   L E 
Sbjct: 128 TWLEIILREGKNHQIRKMTAAIGFPTLRLIRHQIGDWRLDQLQPGEYKLINLTNDKLNEL 187

Query: 245 LGPHLL 250
                 
Sbjct: 188 TRKSNP 193


>gi|190575386|ref|YP_001973231.1| putative RNA-binding protein [Stenotrophomonas maltophilia K279a]
 gi|190013308|emb|CAQ46942.1| putative RNA-binding protein [Stenotrophomonas maltophilia K279a]
          Length = 232

 Score = 88.3 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 38/238 (15%), Positives = 71/238 (29%), Gaps = 18/238 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+ K ++      R E  R I    V VNG ++E+    V     I V      +  
Sbjct: 2   EPIRLDKRLSALLGIPRGEARRYIEGGWVTVNGDVVEQPQRPVDDRAVIVVAEQASDEKA 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                L +KP G+          S     L +   R +      +     L  ++ G + 
Sbjct: 62  ERVSMLLNKPAGVAAETLCALVSSDSRSELDASDIRPLQRHFHGLQLAASLPASDSGLVV 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
              +  +   L+    R   +   +           +   +   ++  +   G  +W   
Sbjct: 122 VSQDPATLAHLQRNLGRTEQEYLIE-----VAEGGPERGPWLMARLQQEAGGGKVSW--- 173

Query: 192 GLREGKNRE---------IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
              E + R          ++        +V  + R+  G   LG L  G  R +    
Sbjct: 174 -QSEQRLRFAGKGLTAKGLRAAVTAAGLQVTGVRRLRIGRVALGPLPPGQWRYLGSDE 230


>gi|56413777|ref|YP_150852.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Paratyphi A str. ATCC
           9150]
 gi|197362700|ref|YP_002142337.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Paratyphi A str.
           AKU_12601]
 gi|56128034|gb|AAV77540.1| putative ribosomal large subunit pseudouridine synthase B
           [Salmonella enterica subsp. enterica serovar Paratyphi A
           str. ATCC 9150]
 gi|197094177|emb|CAR59681.1| putative ribosomal large subunit pseudouridine synthase B
           [Salmonella enterica subsp. enterica serovar Paratyphi A
           str. AKU_12601]
          Length = 221

 Score = 88.3 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 50/187 (26%), Positives = 87/187 (46%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLL+LTND
Sbjct: 34  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIPVQGV--YAAGRLDRDSEGLLVLTND 91

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P  +  ++Y V+     D   L  L+ G+ +                    
Sbjct: 92  GALQARLTQPGKRTGKIYYVQVESIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 151

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G 
Sbjct: 152 PRTPPIRERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQ 211

Query: 233 TREVSKK 239
            RE++++
Sbjct: 212 WREIAQE 218


>gi|163731747|ref|ZP_02139194.1| RNA pseudouridylate synthase [Roseobacter litoralis Och 149]
 gi|161395201|gb|EDQ19523.1| RNA pseudouridylate synthase [Roseobacter litoralis Och 149]
          Length = 187

 Score = 88.3 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 42/178 (23%), Positives = 83/178 (46%), Gaps = 17/178 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R+ L++KP G+++  +D     +    L            GRLD ++EGL++LT+DG L 
Sbjct: 3   RVILFNKPYGVLSQFTDKGSEGSPRPTLSAYIDQPGFYPAGRLDRDSEGLMVLTDDGKLQ 62

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT---------- 181
             +  P  +  + Y V+  G  +  +L +L+ G+ ++       + TL            
Sbjct: 63  ARISNPKHKMAKTYLVQVEGTPEPQQLEVLRAGVRLKDGMTKPAKATLACPPENLWERTP 122

Query: 182 -----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                +   ++W+ + + EG+NR+++++         RLIR+  G + L  L+ G+ R
Sbjct: 123 PVRYRKTVPDSWLQISISEGRNRQVRRMTAHVGLPCLRLIRMRVGDWALNDLVPGAWR 180


>gi|327393520|dbj|BAK10942.1| ribosomal large subunit pseudouridine synthase E RluE [Pantoea
           ananatis AJ13355]
          Length = 219

 Score = 88.3 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 48/188 (25%), Positives = 88/188 (46%), Gaps = 17/188 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +      R+ L++KP  ++   +D  GR T+ D +    S V + GRLD ++EGL++L
Sbjct: 31  KAIAPPAVRRVLLFNKPFDVLPQFTDEAGRRTLKDFID--VSEVYAAGRLDRDSEGLMVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TNDG L   L  P  +  ++Y V+  G  ++  L  L+ G+ ++                
Sbjct: 89  TNDGALQAALTQPGKRTGKIYYVQVEGAPEERDLQPLRDGVNLKDGLTLPAGIEKVAEPE 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ + L EG+NR+++++     +   RL+R + G F+L  L 
Sbjct: 149 WLWARQPPIRERKAIPTQWLKITLYEGRNRQVRRMTAHIGFPTLRLVRYAMGDFELDNLA 208

Query: 230 AGSTREVS 237
            G  R++S
Sbjct: 209 PGEWRDIS 216


>gi|153853944|ref|ZP_01995277.1| hypothetical protein DORLON_01268 [Dorea longicatena DSM 13814]
 gi|149753326|gb|EDM63257.1| hypothetical protein DORLON_01268 [Dorea longicatena DSM 13814]
          Length = 216

 Score = 88.3 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 45/195 (23%), Positives = 80/195 (41%), Gaps = 26/195 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                +++HKP G VT   D    + +         R+  VGRLD  T GLLL+T+DG  
Sbjct: 21  TMPHYYMFHKPFGCVTARRDDRYPTVMDYFEELQNDRLSPVGRLDRETTGLLLITDDGIF 80

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTL--------- 179
            + L  PS    + Y     G +  + ++ L+ G++++         ++T+         
Sbjct: 81  NQKLTHPSYHKEKTYEFTLLGDLTPELVHKLETGVILKGADTLTAPAKITVTGHAVMSDI 140

Query: 180 -----------DTQKGSNAWVT---VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                        +   +  +T   + + EGK R+I+++ +  +  V  L RIS G   L
Sbjct: 141 LSTLPEEIQKDIHKNRPDHPITYGIITISEGKKRQIRRMMKSVHCCVIELKRISIGDIVL 200

Query: 226 GT-LLAGSTREVSKK 239
              L  G  +E+   
Sbjct: 201 DKALCPGEWKEIFPH 215


>gi|269102224|ref|ZP_06154921.1| putative pseudouridine synthase family 1protein [Photobacterium
           damselae subsp. damselae CIP 102761]
 gi|268162122|gb|EEZ40618.1| putative pseudouridine synthase family 1protein [Photobacterium
           damselae subsp. damselae CIP 102761]
          Length = 215

 Score = 88.3 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 50/192 (26%), Positives = 87/192 (45%), Gaps = 16/192 (8%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
             P R     ++ L++KP  ++T  S   G  T+ D +P     V   GRLD ++EGLL+
Sbjct: 24  NKPKRPRGPRKIILFNKPFNVLTQFSGEPGDITLADFIP--VKDVYPAGRLDKDSEGLLV 81

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-------- 175
           LTNDG L   L  P ++  + Y V+  G   ++ L  L+KG+ ++               
Sbjct: 82  LTNDGILQARLTQPKSKQPKTYWVQVEGAPSEESLQALRKGVELKDGMTLPAGVEVMSEP 141

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ + L+EG+NR+++++         RLIR     + +  L 
Sbjct: 142 NIWPRNPPIRERKNIPTTWLAITLKEGRNRQVRRMTAHIGHPTLRLIRYKMADWTVDDLE 201

Query: 230 AGSTREVSKKIL 241
            G  RE++ + L
Sbjct: 202 PGQWREITLETL 213


>gi|91793186|ref|YP_562837.1| pseudouridine synthase, Rsu [Shewanella denitrificans OS217]
 gi|91715188|gb|ABE55114.1| ribosomal large subunit pseudouridine synthase E [Shewanella
           denitrificans OS217]
          Length = 242

 Score = 88.3 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 49/189 (25%), Positives = 85/189 (44%), Gaps = 18/189 (9%)

Query: 65  VPLRKA--ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
            P+ K       + L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLL
Sbjct: 34  KPISKPSVANPVMVLFNKPFDVLCQFTDEAGRKTLKDFIPVPGV--YAAGRLDRDSEGLL 91

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ------ 176
           LLTNDG     L  P  +  + Y V+  G+ +Q  ++ L  G+ ++       +      
Sbjct: 92  LLTNDGKFQSKLTEPKQKTFKTYWVQVEGEPNQAAIDALCAGVELKDGMTLPAKVRLMAT 151

Query: 177 --------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                      + Q    AW+ V + EG+NR+++++         RLIR   G + L  L
Sbjct: 152 PDVWPRTPPVRERQSIPTAWLEVQICEGRNRQVRRMTAHVGHPTLRLIRYKIGQWSLDDL 211

Query: 229 LAGSTREVS 237
             G  + ++
Sbjct: 212 NNGDYKLLN 220


>gi|330910949|gb|EGH39459.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           AA86]
          Length = 207

 Score = 87.9 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 47/184 (25%), Positives = 86/184 (46%), Gaps = 17/184 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+LTN+G 
Sbjct: 26  NQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPIQGV--YAAGRLDRDSEGLLVLTNNGA 83

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-------------- 175
           L   L  P  +  ++Y V+  G   Q+ L  L+ G+ +                      
Sbjct: 84  LQARLTQPGKRTGKIYYVQVEGIPTQEALEALRNGVTLNDGPTLPAGAELVEEPAWLWPR 143

Query: 176 -QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R
Sbjct: 144 NPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWR 203

Query: 235 EVSK 238
           + + 
Sbjct: 204 DATD 207


>gi|281178245|dbj|BAI54575.1| conserved hypothetical protein [Escherichia coli SE15]
          Length = 217

 Score = 87.9 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 48/184 (26%), Positives = 86/184 (46%), Gaps = 17/184 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+LTN+G 
Sbjct: 36  NQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVLTNNGA 93

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-------------- 175
           L   L  P  +  ++Y V+  G   QD L  L+ G+ +                      
Sbjct: 94  LQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPR 153

Query: 176 -QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R
Sbjct: 154 NPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWR 213

Query: 235 EVSK 238
           + + 
Sbjct: 214 DATD 217


>gi|300982380|ref|ZP_07176078.1| hypothetical protein HMPREF9553_02183 [Escherichia coli MS 200-1]
 gi|300307217|gb|EFJ61737.1| hypothetical protein HMPREF9553_02183 [Escherichia coli MS 200-1]
 gi|324013228|gb|EGB82447.1| hypothetical protein HMPREF9533_02732 [Escherichia coli MS 60-1]
          Length = 217

 Score = 87.9 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 47/184 (25%), Positives = 85/184 (46%), Gaps = 17/184 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L N+G 
Sbjct: 36  NQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVLANNGA 93

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-------------- 175
           L   L  P  +  ++Y V+  G   QD L  L+ G+ +                      
Sbjct: 94  LQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPR 153

Query: 176 -QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R
Sbjct: 154 NPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGNYSLDNLANGEWR 213

Query: 235 EVSK 238
           + + 
Sbjct: 214 DATD 217


>gi|117623320|ref|YP_852233.1| 23S rRNA pseudouridine synthase E [Escherichia coli APEC O1]
 gi|218558017|ref|YP_002390930.1| 23S rRNA pseudouridine synthase E [Escherichia coli S88]
 gi|218689088|ref|YP_002397300.1| 23S rRNA pseudouridine synthase E [Escherichia coli ED1a]
 gi|227886508|ref|ZP_04004313.1| 23S rRNA pseudouridine synthase E [Escherichia coli 83972]
 gi|237706879|ref|ZP_04537360.1| ribosomal large subunit pseudouridine synthase E [Escherichia sp.
           3_2_53FAA]
 gi|300975601|ref|ZP_07173080.1| conserved hypothetical protein [Escherichia coli MS 45-1]
 gi|301051075|ref|ZP_07197909.1| conserved hypothetical protein [Escherichia coli MS 185-1]
 gi|34098556|sp|Q8FIB6|RLUE_ECOL6 RecName: Full=Ribosomal large subunit pseudouridine synthase E;
           AltName: Full=rRNA pseudouridylate synthase E; AltName:
           Full=rRNA-uridine isomerase E
 gi|91071865|gb|ABE06746.1| 23S rRNA pseudouridine synthase [Escherichia coli UTI89]
 gi|115512444|gb|ABJ00519.1| 23S rRNA pseudouridine synthase [Escherichia coli APEC O1]
 gi|218364786|emb|CAR02476.1| 23S rRNA pseudouridine synthase [Escherichia coli S88]
 gi|218426652|emb|CAR07480.1| 23S rRNA pseudouridine synthase [Escherichia coli ED1a]
 gi|226898089|gb|EEH84348.1| ribosomal large subunit pseudouridine synthase E [Escherichia sp.
           3_2_53FAA]
 gi|227836712|gb|EEJ47178.1| 23S rRNA pseudouridine synthase E [Escherichia coli 83972]
 gi|294491737|gb|ADE90493.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           IHE3034]
 gi|300297247|gb|EFJ53632.1| conserved hypothetical protein [Escherichia coli MS 185-1]
 gi|300410264|gb|EFJ93802.1| conserved hypothetical protein [Escherichia coli MS 45-1]
 gi|307553136|gb|ADN45911.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           ABU 83972]
 gi|307627393|gb|ADN71697.1| 23S rRNA pseudouridine synthase E [Escherichia coli UM146]
 gi|315287468|gb|EFU46879.1| conserved hypothetical protein [Escherichia coli MS 110-3]
 gi|315293097|gb|EFU52449.1| conserved hypothetical protein [Escherichia coli MS 153-1]
 gi|323953178|gb|EGB49044.1| RNA pseudouridylate synthase [Escherichia coli H252]
 gi|323957961|gb|EGB53673.1| RNA pseudouridylate synthase [Escherichia coli H263]
          Length = 217

 Score = 87.9 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 48/189 (25%), Positives = 87/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 31  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 89  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPA 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 149 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 208

Query: 230 AGSTREVSK 238
            G  R+ + 
Sbjct: 209 NGEWRDATD 217


>gi|119775195|ref|YP_927935.1| pseudouridylate synthase [Shewanella amazonensis SB2B]
 gi|119767695|gb|ABM00266.1| ribosomal large subunit pseudouridine synthase E [Shewanella
           amazonensis SB2B]
          Length = 212

 Score = 87.9 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 55/211 (26%), Positives = 100/211 (47%), Gaps = 27/211 (12%)

Query: 45  ILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            + ER +                RK   T+L L++KP  ++   +D  GR T+ D +P  
Sbjct: 4   KIAERPSAKAAP-----------RKPAVTQLVLFNKPFDVLCQFTDEAGRQTLKDFIP-- 50

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
              V + GRLD ++EGLLLLTNDG L   L  P  Q  + Y V+  G  D+  L+ L++G
Sbjct: 51  LPGVYAAGRLDRDSEGLLLLTNDGQLQSRLTEPKKQTYKTYWVQVEGIPDESALDKLREG 110

Query: 165 IVIQGICYGDMQ--------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           + ++       +                 + +   + W+ + + EG+NR+++++     +
Sbjct: 111 VELKDGPTLPARVRRIDAPQIWPRNPPVRERKSIPDCWLEIQICEGRNRQVRRMTAHIGY 170

Query: 211 KVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              RL+R + G  +LG L +G  R++++  +
Sbjct: 171 PTLRLVRAAIGEIRLGHLGSGEYRKLNRDEI 201


>gi|16764592|ref|NP_460207.1| ribosomal large subunit pseudouridine synthase [Salmonella enterica
           subsp. enterica serovar Typhimurium str. LT2]
 gi|205353029|ref|YP_002226830.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Gallinarum str. 287/91]
 gi|205357731|ref|ZP_02573072.2| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|207857256|ref|YP_002243907.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Enteritidis str.
           P125109]
 gi|34098654|sp|Q8ZPZ1|RLUE_SALTY RecName: Full=Ribosomal large subunit pseudouridine synthase E;
           AltName: Full=rRNA pseudouridylate synthase E; AltName:
           Full=rRNA-uridine isomerase E
 gi|16419756|gb|AAL20166.1| putative ribosomal large subunit pseudouridine synthase [Salmonella
           enterica subsp. enterica serovar Typhimurium str. LT2]
 gi|205272810|emb|CAR37736.1| putative ribosomal large subunit pseudouridine synthase B
           [Salmonella enterica subsp. enterica serovar Gallinarum
           str. 287/91]
 gi|205329690|gb|EDZ16454.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|206709059|emb|CAR33392.1| putative ribosomal large subunit pseudouridine synthase B
           [Salmonella enterica subsp. enterica serovar Enteritidis
           str. P125109]
 gi|261246449|emb|CBG24259.1| putative ribosomal large subunit pseudouridine synthase B
           [Salmonella enterica subsp. enterica serovar Typhimurium
           str. D23580]
 gi|267993016|gb|ACY87901.1| putative ribosomal large subunit pseudouridine synthase [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           14028S]
 gi|301157778|emb|CBW17271.1| putative ribosomal large subunit pseudouridine synthase B
           [Salmonella enterica subsp. enterica serovar Typhimurium
           str. SL1344]
 gi|312912225|dbj|BAJ36199.1| 23S rRNA pseudouridine synthase E [Salmonella enterica subsp.
           enterica serovar Typhimurium str. T000240]
 gi|332988128|gb|AEF07111.1| putative ribosomal large subunit pseudouridine synthase [Salmonella
           enterica subsp. enterica serovar Typhimurium str. UK-1]
          Length = 221

 Score = 87.9 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 51/187 (27%), Positives = 88/187 (47%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLL+LTND
Sbjct: 34  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIPVQGV--YAAGRLDRDSEGLLVLTND 91

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P  +  ++Y V+  G  D   L  L+ G+ +                    
Sbjct: 92  GALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 151

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G 
Sbjct: 152 PRTPPIRERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQ 211

Query: 233 TREVSKK 239
            RE++++
Sbjct: 212 WREIAQE 218


>gi|71416087|ref|XP_810087.1| tRNA pseudouridine synthase A [Trypanosoma cruzi strain CL Brener]
 gi|70874568|gb|EAN88236.1| tRNA pseudouridine synthase A, putative [Trypanosoma cruzi]
          Length = 687

 Score = 87.9 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 60/225 (26%), Positives = 101/225 (44%), Gaps = 4/225 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--PLRKAERT 73
           + + + RAG  SRRE   +IA  +V+V+ ++       V + + I V+     LR A   
Sbjct: 345 LLRCLPRAGFCSRREALSIIASGQVRVDNVVERNPFRLVRAENSIHVESHSGRLRFAPPR 404

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               +     +V+ +                   ++ VG L +   GLLLLTNDG L+R+
Sbjct: 405 LWMYHKPAYVIVSRNDVAGRTLMTKHARILGMDHLVPVGSLPMRAHGLLLLTNDGELSRL 464

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           LE P T   + Y +R    +D    + L    ++  G  Y +++  ++    S   + V 
Sbjct: 465 LENPKTMIQQTYLLRVRPAIDPVLAHKLNTEGILVNGNRYNNVEFFVNPAMKSRYSLKVK 524

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +R G+   +  + +     V R  RIS+GPF +  L  GS REV+
Sbjct: 525 VR-GETMPVAHLMQHLGRTVERGGRISFGPFSMSGLPVGSIREVT 568


>gi|54293791|ref|YP_126206.1| hypothetical protein lpl0847 [Legionella pneumophila str. Lens]
 gi|53753623|emb|CAH15081.1| hypothetical protein lpl0847 [Legionella pneumophila str. Lens]
          Length = 200

 Score = 87.9 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 46/190 (24%), Positives = 70/190 (36%), Gaps = 16/190 (8%)

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
                              +    F    + GRLD  +EGLL+LT+DG L   L  P  +
Sbjct: 8   NKPYGVLTQFTGELPEQTLSAFIKFPGFYAAGRLDKQSEGLLILTDDGKLQHRLTHPKFE 67

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------------TQKGSN 186
             + Y V+  G      L  L+KG+VI+ I +   +  L                +    
Sbjct: 68  KKKHYWVQVEGVPTDKDLQPLRKGLVIKDITFLPAEAKLISEPKIWPRIPPIRERKHIPT 127

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR--EVSKKILREQ 244
            W+ + LREGKN +I+K+     +   RLIR   G + L  L  G  +   ++   L E 
Sbjct: 128 TWLGIILREGKNHQIRKMTAAIGFPTLRLIRYQIGDWHLDQLQPGEYKLINLTNDKLNEL 187

Query: 245 LGPHLLEEAQ 254
                     
Sbjct: 188 TRKSNPRPES 197


>gi|85703587|ref|ZP_01034691.1| RNA pseudouridylate synthase [Roseovarius sp. 217]
 gi|85672515|gb|EAQ27372.1| RNA pseudouridylate synthase [Roseovarius sp. 217]
          Length = 180

 Score = 87.9 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 41/177 (23%), Positives = 74/177 (41%), Gaps = 16/177 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RL L++KP  +++  +      +    L       RV   GRLD ++EGLL+LT+DG L 
Sbjct: 3   RLILFNKPYDVLSQFTGRGSADSPRATLSDFIDVPRVYPAGRLDRDSEGLLVLTDDGQLQ 62

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------------V 177
             +  P  +  + Y  +  G  D   L  L++G+ +        +               
Sbjct: 63  ARIANPRFKTEKTYFAQVEGLPDDATLAALRQGVTLNDGPTRPARVDRMEPPTLWPRTPP 122

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
               +   + W+ + + EG+NR+++++         RLIR   G + L  +  G  R
Sbjct: 123 VRFRKSVPDCWLKLTISEGRNRQVRRMTAHIGHPTLRLIRWRIGDWTLDGIGPGQWR 179


>gi|121604242|ref|YP_981571.1| pseudouridine synthase [Polaromonas naphthalenivorans CJ2]
 gi|120593211|gb|ABM36650.1| ribosomal large subunit pseudouridine synthase E [Polaromonas
           naphthalenivorans CJ2]
          Length = 221

 Score = 87.9 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 46/176 (26%), Positives = 80/176 (45%), Gaps = 17/176 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL L++KP G+++  +       + D +          GRLD ++EGLLLL NDG L   
Sbjct: 34  RLILFNKPYGVLSQFTPEGRWRGLKDFIAIPGV--YVAGRLDADSEGLLLLANDGKLQAH 91

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------VT 178
           +  P  +  ++Y V+  G   +  L  L++G+ +        +                 
Sbjct: 92  IADPRFKMEKIYWVQVEGTPGEAALQALREGVALNDGPTRPARARLMDAPAALWQREPPV 151

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              Q    AW+ +G+REG+NR+++++     +   RL+R + G + L  L  GS R
Sbjct: 152 RVRQSIPTAWIELGIREGRNRQVRRMTAAVGFPTLRLVRAAIGNWSLDGLAPGSWR 207


>gi|222032887|emb|CAP75627.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           LF82]
 gi|324005948|gb|EGB75167.1| hypothetical protein HMPREF9532_04391 [Escherichia coli MS 57-2]
          Length = 217

 Score = 87.9 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 47/189 (24%), Positives = 87/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 31  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   +D L  L+ G+ +                 
Sbjct: 89  TNNGALQARLTQPGKRTGKIYYVQVEGIPTEDALEALRNGVTLNDGPTLPAGAEMVEEPE 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 149 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGNYSLDNLA 208

Query: 230 AGSTREVSK 238
            G  R+ + 
Sbjct: 209 NGEWRDATD 217


>gi|191173066|ref|ZP_03034599.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           F11]
 gi|190906611|gb|EDV66217.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           F11]
          Length = 207

 Score = 87.9 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 47/184 (25%), Positives = 85/184 (46%), Gaps = 17/184 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L N+G 
Sbjct: 26  NQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVLANNGA 83

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-------------- 175
           L   L  P  +  ++Y V+  G   QD L  L+ G+ +                      
Sbjct: 84  LQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPR 143

Query: 176 -QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R
Sbjct: 144 NPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGNYSLDNLANGEWR 203

Query: 235 EVSK 238
           + + 
Sbjct: 204 DATD 207


>gi|78045854|ref|YP_362029.1| pseudouridylate synthase [Xanthomonas campestris pv. vesicatoria
           str. 85-10]
 gi|78034284|emb|CAJ21929.1| pseudouridylate synthase [Xanthomonas campestris pv. vesicatoria
           str. 85-10]
          Length = 190

 Score = 87.9 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 48/175 (27%), Positives = 82/175 (46%), Gaps = 15/175 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L +KP G+++  SD             +   V + GRLD ++EGLLLLT+DG LA  L
Sbjct: 2   LVLLNKPYGVLSQFSDRSQPPKRTLAEFGLPPDVYAAGRLDHDSEGLLLLTDDGALAHRL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y V+  G    ++L  L+ G+V+        QV +               
Sbjct: 62  TDPRHKQPKTYWVQVEGAPQPEQLQALRDGVVLNDGPTRSAQVRMLDPAPQLWPRDPPVR 121

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +   +AW+ + + EG+NR+++++         RL+R++ G ++L  L  G  R
Sbjct: 122 VRKTVPDAWLELQITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLDALAPGQWR 176


>gi|269468805|gb|EEZ80409.1| 16S rRNA uridine-516 pseudouridylate synthase [uncultured SUP05
           cluster bacterium]
          Length = 174

 Score = 87.9 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 33/147 (22%), Positives = 63/147 (42%), Gaps = 15/147 (10%)

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
                 +   GRLD ++EGL++LT+DG L   +  P     + Y V+  G +  + +  L
Sbjct: 25  YIDIKNIYPAGRLDKDSEGLIVLTDDGKLQHQISHPKFDKEKTYVVQVEGSITDNAITQL 84

Query: 162 KKGIVIQGICYGDMQVTLDTQ---------------KGSNAWVTVGLREGKNREIKKVFE 206
            +G+ ++       +  + T+                   +W+ + + EGKNR+++++  
Sbjct: 85  CRGVALKDGMTKPAKAKIITKPSWVWDRIPPIRKRQNIPTSWIELSITEGKNRQVRRMSA 144

Query: 207 FFNWKVNRLIRISYGPFQLGTLLAGST 233
              +   RLIR   G + L  L  G  
Sbjct: 145 HVGFPTLRLIRTEIGSWSLKRLPLGKY 171


>gi|237653664|ref|YP_002889978.1| pseudouridine synthase [Thauera sp. MZ1T]
 gi|237624911|gb|ACR01601.1| pseudouridine synthase [Thauera sp. MZ1T]
          Length = 229

 Score = 87.9 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 51/189 (26%), Positives = 89/189 (47%), Gaps = 17/189 (8%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
              TRL L +KP G++   +D  GR T+ D +        + GRLD ++EGL+LLT DG 
Sbjct: 26  RAETRLLLLNKPFGVLCQFTDEAGRRTLKDYVEVPGV--YAAGRLDADSEGLVLLTGDGA 83

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-------------- 175
           L   +  P  +  + Y V+  G++D+  L +L+ G+ +                      
Sbjct: 84  LQHRIADPRHKLAKTYLVQVEGEIDEAALAILRAGVDLGDFRSLPCAARRMPAPDWLWPR 143

Query: 176 -QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + L EGKNR+++++    +    RL+R++ GP+ L  L  G  R
Sbjct: 144 DPPVRFRKSVPTSWIEIVLCEGKNRQVRRMTAKVDHPTLRLVRVAIGPWTLAGLGVGEWR 203

Query: 235 EVSKKILRE 243
           E++   + E
Sbjct: 204 ELAGAEIAE 212


>gi|262278236|ref|ZP_06056021.1| conserved hypothetical protein [Acinetobacter calcoaceticus
           RUH2202]
 gi|262258587|gb|EEY77320.1| conserved hypothetical protein [Acinetobacter calcoaceticus
           RUH2202]
          Length = 262

 Score = 87.9 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 41/222 (18%), Positives = 84/222 (37%), Gaps = 19/222 (8%)

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD+++EGL+ LT+ GGL + +  P+ +  + Y V+  G V ++ L  L+KG+ +    
Sbjct: 38  GRLDMDSEGLVFLTDHGGLNQFITNPANKKYKTYLVQVDGDVTEEALEQLRKGVELNDGM 97

Query: 172 YGDMQVTLDTQ---------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
                    ++                   +W+ + + EG+NR+++++     +   RLI
Sbjct: 98  TLPATAIKVSEPEWLWERNPPVRFRANIPTSWIEISICEGRNRQVRRMTSAVGFPTLRLI 157

Query: 217 RISYGPFQL--GTLLAGSTREVSKKILREQLGPHLLE--EAQVNLDAPIYSSETLVRDRP 272
           R   G   L    L  G  +E+   +  +       E   ++  +  P  +    +  + 
Sbjct: 158 RTKIGSIDLVQLGLKPGDVKEIEPLLYPDFKDVPAEEPYRSRSYVKKPGGTGGKPMVRKN 217

Query: 273 NIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
              S       R+ +    +    K      P  +       
Sbjct: 218 KDGSTKKSGTKRIWQMDEGEKPRRKTNGTTRPNAKAPRGRGR 259


>gi|294142340|ref|YP_003558318.1| ribosomal large subunit pseudouridine synthase family protein
           [Shewanella violacea DSS12]
 gi|293328809|dbj|BAJ03540.1| ribosomal large subunit pseudouridine synthase family protein
           [Shewanella violacea DSS12]
          Length = 210

 Score = 87.9 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 40/187 (21%), Positives = 79/187 (42%), Gaps = 21/187 (11%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                 ++     L     +      +   L      ++++GRLD ++EGLLLLT DG +
Sbjct: 21  PHQDYKIFKPHGFLSQFVPETKKNKKLLGELAQFPVGIMAIGRLDHDSEGLLLLTTDGMV 80

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQ---------- 176
           +  +     +  + Y V+  G +D + +  L++G+ I    +       +          
Sbjct: 81  SHRVRSK--KVEKEYYVQVDGIIDDEAIIRLQQGVEIGIKGEKYLTLPCKVVKLDGEPNL 138

Query: 177 -----VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                   D + G  +WV++ + EGKNR+I+K+     +   RL+R+  G   L  +  G
Sbjct: 139 PDNGRRVRDPRHGPLSWVSITISEGKNRQIRKMTAAAGFPTMRLVRVRIGNIHLSDMQPG 198

Query: 232 STREVSK 238
              E+++
Sbjct: 199 EVFELTQ 205


>gi|56460417|ref|YP_155698.1| RNA pseudouridylate synthase-family protein [Idiomarina loihiensis
           L2TR]
 gi|56179427|gb|AAV82149.1| RNA pseudouridylate synthase-family protein [Idiomarina loihiensis
           L2TR]
          Length = 191

 Score = 87.9 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 50/182 (27%), Positives = 87/182 (47%), Gaps = 17/182 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++    +L L +KP G+++  +  +G  T+   +P     V   GRLD ++EGLLLLTND
Sbjct: 6   KRPANPKLVLLNKPYGVLSQFTGEEGDQTLKPFIPHN--DVYPAGRLDKDSEGLLLLTND 63

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ----------- 176
           G     L  P  +  + Y V+  G   +++L  L+ G+ +        +           
Sbjct: 64  GVYQARLANPKYKVWKTYWVQVEGDPSEEQLEQLRNGVELNDGMTRPAEAFVMPEPMNLW 123

Query: 177 ----VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +   ++W+ + +REGKNR+++++         RLIR + GPFQL T+  G 
Sbjct: 124 PRNPPVRERKSVPDSWLCLKIREGKNRQVRRMTAHVGLPTLRLIRAAVGPFQLKTMQPGE 183

Query: 233 TR 234
            R
Sbjct: 184 WR 185


>gi|289811254|ref|ZP_06541883.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 114

 Score = 87.9 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 20/113 (17%), Positives = 40/113 (35%), Gaps = 7/113 (6%)

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWV 189
             +  P     + Y V     V  D      KG+ +           + +     +   V
Sbjct: 2   HRITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKDLTKPATLEVI----TPVQV 57

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + + EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 58  RLTISEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEEEI 110


>gi|328473240|gb|EGF44088.1| pseudouridine synthase family 1 protein [Vibrio parahaemolyticus
           10329]
          Length = 232

 Score = 87.9 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 49/187 (26%), Positives = 89/187 (47%), Gaps = 16/187 (8%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
             P    +  ++ +++KP   ++  +D DGR T+ D +P     V + GRLD ++EGL++
Sbjct: 46  NKPRVVLQNRKVIVFNKPYDTLSQFTDGDGRKTLADYIP--VKDVYAAGRLDRDSEGLMV 103

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--- 180
           LTNDG L   L  P ++  + Y V+  G   +  L  L+KG+ ++       +V +    
Sbjct: 104 LTNDGILQAKLTQPKSKSPKTYWVQVDGAPQEQDLEKLRKGVELKDGMTLPAKVEVIDAP 163

Query: 181 -----------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                             W+ + + EG+NR+++++     +   RL+R S G   LG L 
Sbjct: 164 TIWERNPPVRFRANIPTTWLAITIIEGRNRQVRRMTAHIGFPTLRLVRYSMGDITLGDLQ 223

Query: 230 AGSTREV 236
            G  +E+
Sbjct: 224 PGQWKEI 230


>gi|99081002|ref|YP_613156.1| ribosomal large subunit pseudouridine synthase E [Ruegeria sp.
           TM1040]
 gi|99037282|gb|ABF63894.1| ribosomal large subunit pseudouridine synthase E [Ruegeria sp.
           TM1040]
          Length = 221

 Score = 87.9 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 42/219 (19%), Positives = 84/219 (38%), Gaps = 17/219 (7%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
           RL  ++KP  ++   +D     +    L            GRLD ++EGL+LLT++G L 
Sbjct: 3   RLIRFNKPFDVLPQFTDRGSEGSPRATLSDYVDCPGVYPAGRLDRDSEGLMLLTDNGRLQ 62

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------------- 176
             +  P  +  + Y V+  G   +D L  L++G+ ++       +               
Sbjct: 63  AWISDPKHKLEKTYWVQVEGIPTEDALKALRQGVDLKDGMTRPAKAELISEPAQLWARTP 122

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    AW+ + + EGKNR+++++     +   RLIR + G + L  L  G   ++
Sbjct: 123 PIRERKSVPTAWLELKISEGKNRQVRRMTAAMGYPTLRLIRYAIGAWTLDGLAQGKWDDL 182

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNII 275
               +     P      +        ++      +    
Sbjct: 183 DPPRVPGPPKPAAKPHRKHAAKRRATATPARKPRQRRDG 221


>gi|304409066|ref|ZP_07390687.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|307303069|ref|ZP_07582824.1| pseudouridine synthase [Shewanella baltica BA175]
 gi|304352887|gb|EFM17284.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|306913429|gb|EFN43851.1| pseudouridine synthase [Shewanella baltica BA175]
          Length = 282

 Score = 87.9 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 49/188 (26%), Positives = 88/188 (46%), Gaps = 17/188 (9%)

Query: 65  VPLRKAE-RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
            P++       + L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLL
Sbjct: 92  KPVQSQTLAPIIVLFNKPFDVLCQFTDEQGRKTLKDYIPIA--DVYAAGRLDRDSEGLLL 149

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
           LTNDG L   L  P  +  + Y V+  G   +D L  L++G+ +        +V +    
Sbjct: 150 LTNDGQLQARLTEPKKKTFKTYWVQVEGVPTEDALTKLRQGVELNDGMTLPAKVKIMDSP 209

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ + + EG+NR+++++     +   RLIR   G + L  L 
Sbjct: 210 DIGPRNPPVRERKNIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDNLP 269

Query: 230 AGSTREVS 237
           +G  + + 
Sbjct: 270 SGEHKCIR 277


>gi|153000988|ref|YP_001366669.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|151365606|gb|ABS08606.1| pseudouridine synthase [Shewanella baltica OS185]
          Length = 282

 Score = 87.9 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 49/188 (26%), Positives = 88/188 (46%), Gaps = 17/188 (9%)

Query: 65  VPLRKAE-RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
            P++       + L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLL
Sbjct: 92  KPVQSQTLAPIIVLFNKPFDVLCQFTDEQGRKTLKDYIPIA--DVYAAGRLDRDSEGLLL 149

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
           LTNDG L   L  P  +  + Y V+  G   +D L  L++G+ +        +V +    
Sbjct: 150 LTNDGQLQARLTEPKKKTFKTYWVQVEGVPTEDALTKLRQGVELNDGMTLPAKVKIMDSP 209

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ + + EG+NR+++++     +   RLIR   G + L  L 
Sbjct: 210 DIWPRNPPVRERKNIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDNLP 269

Query: 230 AGSTREVS 237
           +G  + + 
Sbjct: 270 SGEHKCIR 277


>gi|162138450|ref|YP_540277.2| 23S rRNA pseudouridine synthase E [Escherichia coli UTI89]
          Length = 207

 Score = 87.5 bits (215), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 48/189 (25%), Positives = 87/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 21  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +                 
Sbjct: 79  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPA 138

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 139 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 198

Query: 230 AGSTREVSK 238
            G  R+ + 
Sbjct: 199 NGEWRDATD 207


>gi|238910944|ref|ZP_04654781.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Tennessee str.
           CDC07-0191]
          Length = 211

 Score = 87.5 bits (215), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 51/187 (27%), Positives = 88/187 (47%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLL+LTND
Sbjct: 24  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIPVQGV--YAEGRLDRDSEGLLVLTND 81

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P  +  ++Y V+  G  D   L  L+ G+ +                    
Sbjct: 82  GALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 141

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G 
Sbjct: 142 PRTPPIRERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQ 201

Query: 233 TREVSKK 239
            RE++++
Sbjct: 202 WREIAQE 208


>gi|217973052|ref|YP_002357803.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217498187|gb|ACK46380.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 282

 Score = 87.5 bits (215), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 49/188 (26%), Positives = 88/188 (46%), Gaps = 17/188 (9%)

Query: 65  VPLRKAE-RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
            P++       + L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLL
Sbjct: 92  KPVQSQTLAPIIVLFNKPFDVLCQFTDEQGRKTLKDYIPIA--DVYAAGRLDRDSEGLLL 149

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
           LTNDG L   L  P  +  + Y V+  G   +D L  L++G+ +        +V +    
Sbjct: 150 LTNDGQLQARLTEPKKKTFKTYWVQVEGVPTEDALTKLRQGVELNDGMTLPAKVKIMDSP 209

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ + + EG+NR+++++     +   RLIR   G + L  L 
Sbjct: 210 DIGPRNPPVRERKNIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDNLP 269

Query: 230 AGSTREVS 237
           +G  + + 
Sbjct: 270 SGEHKCIR 277


>gi|160875701|ref|YP_001555017.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|160861223|gb|ABX49757.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|315267890|gb|ADT94743.1| pseudouridine synthase [Shewanella baltica OS678]
          Length = 282

 Score = 87.5 bits (215), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 49/188 (26%), Positives = 88/188 (46%), Gaps = 17/188 (9%)

Query: 65  VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
            P++       + L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLL
Sbjct: 92  KPVQSQTIAPIIVLFNKPFDVLCQFTDEQGRKTLKDYIPIA--DVYAAGRLDRDSEGLLL 149

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
           LTNDG L   L  P  +  + Y V+  G   +D L  L++G+ +        +V +    
Sbjct: 150 LTNDGQLQARLTEPKKKTFKTYWVQVEGVPTEDALTKLRQGVELNDGMTLPAKVKIMDSP 209

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ + + EG+NR+++++     +   RLIR   G + L  L 
Sbjct: 210 DIWPRNPPVRERKNIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDNLP 269

Query: 230 AGSTREVS 237
           +G  + + 
Sbjct: 270 SGEHKCIR 277


>gi|254228993|ref|ZP_04922414.1| conserved hypothetical protein [Vibrio sp. Ex25]
 gi|262394731|ref|YP_003286585.1| ribosomal large subunit pseudouridine synthase E [Vibrio sp. Ex25]
 gi|151938461|gb|EDN57298.1| conserved hypothetical protein [Vibrio sp. Ex25]
 gi|262338325|gb|ACY52120.1| ribosomal large subunit pseudouridine synthase E [Vibrio sp. Ex25]
          Length = 233

 Score = 87.5 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 51/189 (26%), Positives = 92/189 (48%), Gaps = 16/189 (8%)

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           +  P    +  ++ +++KP   ++  +D DGR T+ D +P     V + GRLD ++EGL+
Sbjct: 46  NQKPKVDPKDRKVIIFNKPYDTLSQFTDGDGRKTLADYIP--VKDVYAAGRLDRDSEGLM 103

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           +LTNDG L   L  P ++  + Y V+  G   +  L  L+KG+ ++       +V +  +
Sbjct: 104 VLTNDGILQAKLTQPKSKSPKTYWVQVDGAPLEQDLEKLRKGVELKDGMTLPAEVEVIPE 163

Query: 183 --------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                              W+ + + EG+NR+++++     +   RLIR S G   L  L
Sbjct: 164 PQVWDRTPPVRFRANIPTTWLAITIIEGRNRQVRRMTAHIGFPTLRLIRHSMGDIVLKDL 223

Query: 229 LAGSTREVS 237
           + G  RE+S
Sbjct: 224 MPGEWREIS 232


>gi|269139396|ref|YP_003296097.1| ribosomal large subunit pseudouridine synthase [Edwardsiella tarda
           EIB202]
 gi|267985057|gb|ACY84886.1| ribosomal large subunit pseudouridine synthase [Edwardsiella tarda
           EIB202]
 gi|304559292|gb|ADM41956.1| Ribosomal large subunit pseudouridine synthase E [Edwardsiella
           tarda FL6-60]
          Length = 213

 Score = 87.5 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 39/144 (27%), Positives = 65/144 (45%), Gaps = 15/144 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LTNDG L   L  P  +  +VY V+  G+ D+  L    +G+ ++
Sbjct: 68  YAAGRLDRDSEGLLVLTNDGRLQAQLTQPGKRTGKVYYVQVEGEPDEADLRRFCQGLTLK 127

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +    +W+ + L EG+NR+++++     +   
Sbjct: 128 DGPTLPALAERVAQPEWLWPRNPPIRERKNIPTSWLKITLYEGRNRQVRRMTAHIGYPTL 187

Query: 214 RLIRISYGPFQLGTLLAGSTREVS 237
           RLIR S G   L  L  G  R + 
Sbjct: 188 RLIRYSMGSLTLQDLAPGEWRLID 211


>gi|268318226|ref|YP_003291945.1| pseudouridine synthase [Rhodothermus marinus DSM 4252]
 gi|262335760|gb|ACY49557.1| pseudouridine synthase [Rhodothermus marinus DSM 4252]
          Length = 201

 Score = 87.5 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 55/186 (29%), Positives = 87/186 (46%), Gaps = 17/186 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +  R  L+ KP G+++  +D +GR T+ D +      V  VGRLD+++EGLLLLTNDG 
Sbjct: 2   RKPVRHILFWKPYGVLSQFTDREGRPTLKDYID--VPDVYPVGRLDMDSEGLLLLTNDGL 59

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLD-------- 180
           L   L  P     R Y  +     D + L  L +G+VI G       +V           
Sbjct: 60  LKYRLLHPRYGHWRTYWAQVERIPDDEALRRLAEGVVIAGGYRTRPARVRRIEPPELPPR 119

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +     W+ + +REGKNR+++++         RL+R++ GP +L  L  G  R
Sbjct: 120 PVPIRYRKTVPTYWLEISIREGKNRQVRRMTAAVGHPTLRLVRVAIGPLRLDGLEPGHWR 179

Query: 235 EVSKKI 240
            ++   
Sbjct: 180 PLTPDE 185


>gi|83951841|ref|ZP_00960573.1| RNA pseudouridylate synthase [Roseovarius nubinhibens ISM]
 gi|83836847|gb|EAP76144.1| RNA pseudouridylate synthase [Roseovarius nubinhibens ISM]
          Length = 186

 Score = 87.5 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 44/178 (24%), Positives = 83/178 (46%), Gaps = 16/178 (8%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
           RL L++KP G+++  +D     +    L    +       GRLD ++EGLLLLT+DG L 
Sbjct: 3   RLLLFNKPFGVLSQFTDRGTADSPRATLSDHINIPGVYPAGRLDRDSEGLLLLTDDGRLQ 62

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----------- 180
             +  P  +  + Y V+  G+ D   L  L++G+ ++       Q               
Sbjct: 63  ARISHPKFKAPKTYLVQVEGEPDDAALAALRRGVTLKDGPTRPAQAERIAPPDLWPRDPP 122

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               +   ++W+ + + EG+NR+++++     +   RL+R S G + L  +  G+ +E
Sbjct: 123 VRYRKSVPDSWLRLTITEGRNRQVRRMTAHVGYPTLRLVRWSVGDWTLDGIAPGTWQE 180


>gi|312945697|gb|ADR26524.1| 23S rRNA pseudouridine synthase E [Escherichia coli O83:H1 str. NRG
           857C]
          Length = 207

 Score = 87.5 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 47/189 (24%), Positives = 87/189 (46%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P       + GRLD ++EGLL+L
Sbjct: 21  RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGV--YAAGRLDRDSEGLLVL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN+G L   L  P  +  ++Y V+  G   +D L  L+ G+ +                 
Sbjct: 79  TNNGALQARLTQPGKRTGKIYYVQVEGIPTEDALEALRNGVTLNDGPTLPAGAEMVEEPE 138

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 139 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGNYSLDNLA 198

Query: 230 AGSTREVSK 238
            G  R+ + 
Sbjct: 199 NGEWRDATD 207


>gi|71908867|ref|YP_286454.1| ribosomal large subunit pseudouridine synthase E [Dechloromonas
           aromatica RCB]
 gi|71848488|gb|AAZ47984.1| ribosomal large subunit pseudouridine synthase E [Dechloromonas
           aromatica RCB]
          Length = 191

 Score = 87.5 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 43/179 (24%), Positives = 79/179 (44%), Gaps = 17/179 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP G+++  +       + + +      V   GRLD ++EGLL+LT+DG L   +
Sbjct: 4   LVFFNKPYGVLSQFTPEGKWRALNEFIT--VKDVYVAGRLDADSEGLLILTDDGKLQAKI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ------------ 182
             P  +  + Y  +  G  D+  L+ L+ GI +        +V L  +            
Sbjct: 62  ADPRHKLEKTYWAQVEGVPDEAALDRLRAGIELSDFTAKPAKVRLIDEPAGLWQRDPPIR 121

Query: 183 ---KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
                  +W+ + + EGKNR+++++     +   RLIR + G   L  L  G  R++  
Sbjct: 122 FRAAIPTSWLEIRISEGKNRQVRRMTAAIGYPTLRLIRAAIGAATLDGLALGQWRKIDG 180


>gi|240013936|ref|ZP_04720849.1| Ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae DGI18]
 gi|240016378|ref|ZP_04722918.1| Ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae FA6140]
 gi|240080497|ref|ZP_04725040.1| Ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae FA19]
 gi|240121505|ref|ZP_04734467.1| Ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae PID24-1]
 gi|240123737|ref|ZP_04736693.1| Ribosomal small subunit pseudouridine synthase A [Neisseria
           gonorrhoeae PID332]
          Length = 197

 Score = 87.5 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 33/177 (18%), Positives = 61/177 (34%), Gaps = 4/177 (2%)

Query: 62  VDGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           +DG  +         + L        +                     + +VGRLD +T 
Sbjct: 18  IDGEAVTVVPEPYFYILLNKPEDYETSHKPKHYRSVFSLFPDNMRNIDMQAVGRLDADTT 77

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LL+TNDG L   L  PS +  ++Y V       +     LK G+ +            
Sbjct: 78  GVLLITNDGKLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVPLHDENETVCAADA 137

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +      + + + EGK  ++K++      +   L R  +   +   L  G  + +
Sbjct: 138 VLENP--TTLLLTITEGKYHQVKRMVAAAGNRAQHLHRRRFAHLETENLKPGEWKFI 192


>gi|104783740|ref|YP_610238.1| pseudouridylate synthase [Pseudomonas entomophila L48]
 gi|95112727|emb|CAK17455.1| pseudouridylate synthase [Pseudomonas entomophila L48]
          Length = 209

 Score = 87.5 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 52/186 (27%), Positives = 89/186 (47%), Gaps = 16/186 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P       RL L++KP  ++T  SD +GR+T+ D +          GRLD ++EGLLLL
Sbjct: 22  QPKAPPAEPRLILFNKPFDVLTQFSDGEGRATLKDFIDIPGI--YPAGRLDRDSEGLLLL 79

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---- 180
           TNDG L   +  P  +  + Y V+  G+  +++L  L++G+ +        +  L     
Sbjct: 80  TNDGRLQARIADPKHKLAKTYWVQVEGEPSEEQLKRLREGVELNDGPTLPAEARLLEEPE 139

Query: 181 ----------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                      +    AW+ + +REG+NR+++++         RL+R+  G + +  L  
Sbjct: 140 LWPRNPPVRFRKSVPTAWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWTIEGLEQ 199

Query: 231 GSTREV 236
           G  REV
Sbjct: 200 GCWREV 205


>gi|220936136|ref|YP_002515035.1| pseudouridine synthase [Thioalkalivibrio sp. HL-EbGR7]
 gi|219997446|gb|ACL74048.1| pseudouridine synthase [Thioalkalivibrio sp. HL-EbGR7]
          Length = 180

 Score = 87.5 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 43/176 (24%), Positives = 79/176 (44%), Gaps = 17/176 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             R+ L +KP  ++   +D +GR T+   +P       + GRLD ++EGL++LT+DG L 
Sbjct: 1   MPRIILLNKPFDVLCQFTDREGRRTLAVYVPEPGV--YAAGRLDRDSEGLVVLTDDGRLQ 58

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--------- 182
             +  P  +  + Y V+  G  D   L  L +G+ ++       +V +  +         
Sbjct: 59  ARISDPKHKMSKTYWVQVEGVPDAQALKALAEGVELKDGLTLPARVKIIDEPPGLWPRDP 118

Query: 183 ------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                     +W+ + + EG+NR+++++         RLIR   G + L  L  G 
Sbjct: 119 PIRVRQSIPTSWLELTISEGRNRQVRRMTAAVGHPTLRLIRYRVGSWTLDGLGPGE 174


>gi|253995971|ref|YP_003048035.1| pseudouridine synthase [Methylotenera mobilis JLW8]
 gi|253982650|gb|ACT47508.1| pseudouridine synthase [Methylotenera mobilis JLW8]
          Length = 184

 Score = 87.5 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 36/176 (20%), Positives = 69/176 (39%), Gaps = 15/176 (8%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
            ++         S                  V + GRLD ++EGLL+LT+DG L   L  
Sbjct: 8   PFNVVCQFSPHDSPNPDNRHATLKDFIPIPDVYAAGRLDTDSEGLLILTDDGALQHRLSH 67

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------VTLDT 181
           P  + ++ Y V+  G    + L  L+ G+ +        +                  + 
Sbjct: 68  PKHKEIKTYWVQVEGAPSDEALQPLRVGVDLGDFITQPAEVSVMNEPAGIWLRNPPIRER 127

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +     W+ + + EGKNR+++++     +   RLIR + G + L  +  G  + ++
Sbjct: 128 KAIPTTWLQIKISEGKNRQVRRMTAKVGFPTLRLIRYAIGRYTLDGIANGEYKVLT 183


>gi|125623931|ref|YP_001032414.1| ribosomal large subunit pseudouridine synthase [Lactococcus lactis
           subsp. cremoris MG1363]
 gi|124492739|emb|CAL97694.1| ribosomal large subunit pseudouridine synthase [Lactococcus lactis
           subsp. cremoris MG1363]
 gi|300070705|gb|ADJ60105.1| ribosomal large subunit pseudouridine synthase [Lactococcus lactis
           subsp. cremoris NZ9000]
          Length = 177

 Score = 87.5 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 52/178 (29%), Positives = 92/178 (51%), Gaps = 17/178 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP  ++T  +D +GR T+ D +      V + GRLD ++EGLLLLT+DG L  +L
Sbjct: 2   IILFNKPFDVLTKFTDSEGRKTLKDYIEIP--NVYAAGRLDKDSEGLLLLTDDGKLNHLL 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P ++  + Y V+  G+   +    L+KG++++       +V L               
Sbjct: 60  TDPKSKSFKTYLVQVEGEFSIEAAQKLEKGVLLKDGKTLPAKVKLIDEPEWLWERTPPIR 119

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             +    +WV + ++EGKNR+I+++     +   RLIR S G + LG L +G  + + 
Sbjct: 120 ERKAIPTSWVEISIKEGKNRQIRRMTAAVGFPTLRLIRWSIGQYTLGNLKSGDYKIIK 177


>gi|89069156|ref|ZP_01156529.1| RNA pseudouridine synthase family protein [Oceanicola granulosus
           HTCC2516]
 gi|89045329|gb|EAR51395.1| RNA pseudouridine synthase family protein [Oceanicola granulosus
           HTCC2516]
          Length = 180

 Score = 87.5 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 40/175 (22%), Positives = 68/175 (38%), Gaps = 14/175 (8%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +        L               +       V   GRLD ++EGLL+LT+DG L   
Sbjct: 4   VILFNKPFGVLSQFTDTRSPTERPTLSRYVDVPAVYPAGRLDRDSEGLLVLTDDGRLQAR 63

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------------QVTL 179
           +  P  +  +VY  +  G  D D L  L++G+ ++                         
Sbjct: 64  IASPKARTEKVYLAQVEGDPDDDALAPLRRGLELKDGPTRPAVARLIEPPALWERDPPVR 123

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +   + WV V + EG+NR+++++     + V RL+R   G + L  L  G+ R
Sbjct: 124 FRKSVPDRWVEVTITEGRNRQVRRMCAAIGFPVLRLVRWRVGDWTLEGLAPGAWR 178


>gi|332306350|ref|YP_004434201.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
 gi|332173679|gb|AEE22933.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
          Length = 192

 Score = 87.5 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 48/187 (25%), Positives = 91/187 (48%), Gaps = 16/187 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                  R+++ L++KP  ++T  +D  GR T+ D +P     + + GRLD ++EGLL+L
Sbjct: 8   KRKAPIRRSKIVLFNKPFNVLTQFTDATGRQTLKDFIPIP--DIYAAGRLDKDSEGLLVL 65

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P  +  + Y V+  G+  + +L  L+ G+ ++       +V    +  
Sbjct: 66  TNDGKLQHKLTDPKKKTSKTYWVQVEGEPQEYQLQALRDGVALKDGMTRPAKVERMQEPS 125

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                           +W+ + + EGKNR+++++     +   RL+R   G + L  + +
Sbjct: 126 LWARNPPVRFRQSIPTSWLAITISEGKNRQVRRMTAHIGFPTLRLVRYRVGNWTLDGIAS 185

Query: 231 GSTREVS 237
           G+ RE+ 
Sbjct: 186 GTYRELD 192


>gi|90579123|ref|ZP_01234933.1| putative pseudouridine synthase family 1protein [Vibrio angustum
           S14]
 gi|90439956|gb|EAS65137.1| putative pseudouridine synthase family 1protein [Vibrio angustum
           S14]
          Length = 216

 Score = 87.2 bits (214), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 51/188 (27%), Positives = 84/188 (44%), Gaps = 16/188 (8%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
             P R     ++ L++KP   +T  S   G ST+ D +P     V   GRLD ++EGLL+
Sbjct: 24  NKPKRARGPQKIILFNKPFNTLTQFSGEPGDSTLADFIP--VKDVYPAGRLDKDSEGLLV 81

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-------- 175
           LTNDG L   L  P ++  +VY V+  G   +  L  L+ G+ ++               
Sbjct: 82  LTNDGVLQARLTQPKSKQAKVYWVQVEGTPTEANLQALRDGVELKDGMTLPAGVEVIESP 141

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ + L+EG+NR+++++         RLIR     + +  L 
Sbjct: 142 IVWDRNPPIRERKSIPTTWLAITLKEGRNRQVRRMTAHIGHPTLRLIRYQMAQWTVNDLA 201

Query: 230 AGSTREVS 237
            G  REV+
Sbjct: 202 PGEWREVT 209


>gi|238920207|ref|YP_002933722.1| ribosomal large subunit pseudouridine synthase E [Edwardsiella
           ictaluri 93-146]
 gi|238869776|gb|ACR69487.1| ribosomal large subunit pseudouridine synthase E [Edwardsiella
           ictaluri 93-146]
          Length = 175

 Score = 87.2 bits (214), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 37/144 (25%), Positives = 63/144 (43%), Gaps = 15/144 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LTNDG L   L  P  +  +VY V+  G+  +  L    +G+ ++
Sbjct: 30  YAAGRLDRDSEGLLVLTNDGRLQAQLTQPGKRTGKVYYVQVEGEPSEADLQRFCQGLTLK 89

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +    +W+ + L EG+NR+++++     +   
Sbjct: 90  DGPTLPALAERVAQPDWLWPRNPPIRERKNIPTSWLKITLYEGRNRQVRRMTAHIGYPTL 149

Query: 214 RLIRISYGPFQLGTLLAGSTREVS 237
           RLIR S     L  L  G  R + 
Sbjct: 150 RLIRYSMDSLTLQDLAPGEWRRID 173


>gi|88860124|ref|ZP_01134763.1| ribosomal large subunit pseudouridine synthase E [Pseudoalteromonas
           tunicata D2]
 gi|88818118|gb|EAR27934.1| ribosomal large subunit pseudouridine synthase E [Pseudoalteromonas
           tunicata D2]
          Length = 221

 Score = 87.2 bits (214), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 44/180 (24%), Positives = 82/180 (45%), Gaps = 16/180 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                ++ L++KP  ++   +D  GR T+ D +      + + GRLD ++EGLL+LTNDG
Sbjct: 39  AKSEQKIVLFNKPFDVLCQFTDEAGRQTLADFIDIK--DIYAAGRLDRDSEGLLVLTNDG 96

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT------- 181
            L   L  P  +  + Y V+  G    + +  L +G+ ++       QV L         
Sbjct: 97  QLQNKLASPKHKTSKTYWVQVEGIPSAEAIKSLCQGVELKDGPTLPAQVELMHAPDIWPR 156

Query: 182 -------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+++ L EG+NR+++++         RLIR   G + +  +  G  +
Sbjct: 157 NPPIRERKNIPTSWLSITLTEGRNRQVRRMTAHIGHPTLRLIRYRIGHWTIDGIENGQFK 216


>gi|311694975|gb|ADP97848.1| RNA pseudouridylate synthase [marine bacterium HP15]
          Length = 175

 Score = 87.2 bits (214), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 37/149 (24%), Positives = 66/149 (44%), Gaps = 14/149 (9%)

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
                +   GRLD ++EGLLLLT +G L   +  PS +  + Y V+  G + ++ L  L 
Sbjct: 1   MHIPGIYPAGRLDYDSEGLLLLTAEGSLQHRIASPSLKMPKTYWVQVEGNISEEALRHLA 60

Query: 163 KGIVIQGICYGDMQ--------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
            G+ ++       +                        +W+ + + EGKNR+++++    
Sbjct: 61  SGVQLKDGLTRPAKADRMPAPTVWPRVPPVRHRDNIPTSWIELTITEGKNRQVRRMTAAV 120

Query: 209 NWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +   RLIR   G + L  L +G+ R V+
Sbjct: 121 GFPTLRLIRYRIGDWTLDGLESGAHRTVT 149


>gi|53805209|ref|YP_113067.1| RNA pseudouridine synthase family protein [Methylococcus capsulatus
           str. Bath]
 gi|53758970|gb|AAU93261.1| RNA pseudouridine synthase family protein [Methylococcus capsulatus
           str. Bath]
          Length = 198

 Score = 87.2 bits (214), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 45/180 (25%), Positives = 84/180 (46%), Gaps = 16/180 (8%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ +++KP G++T  +D +       +   I       GRLD ++EGL++LT+DG L   
Sbjct: 3   RIIVFNKPYGVLTQFTDREHGRATLADFIPIPGVR-PAGRLDRDSEGLIVLTDDGRLQAR 61

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----------- 182
           +  P  +  + YRV+  G  D+  LN L++G+ +        +  +  +           
Sbjct: 62  IADPRHKMAKTYRVQVEGLPDEAALNRLRRGVRLNDGLTLPAEANIIPEPAWLWPRDPPV 121

Query: 183 ----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
                    W+ + +REG+NR+++++     +   RLIR + G + L  L  G  RE+  
Sbjct: 122 RFRATIPTTWLELVIREGRNRQVRRMTAAVGFPTLRLIRWAIGAWTLEGLAPGEWRELPP 181


>gi|312963210|ref|ZP_07777694.1| ribosomal large subunit pseudouridine synthase [Pseudomonas
           fluorescens WH6]
 gi|311282476|gb|EFQ61073.1| ribosomal large subunit pseudouridine synthase [Pseudomonas
           fluorescens WH6]
          Length = 211

 Score = 87.2 bits (214), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 46/185 (24%), Positives = 83/185 (44%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  SD  GR+T+ D +          GRLD ++EGLLLLTNDG
Sbjct: 28  PPAEPKLILFNKPFDVLTQFSDEGGRATLKDFIDIPGI--YPAGRLDRDSEGLLLLTNDG 85

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+  ++ L  L+ G+ +        +            
Sbjct: 86  QLQARIADPKHKLAKTYWVQVEGEPTEEHLQRLRDGVELNDGKTLPAEARRLDEPQLWPR 145

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +     W+ + +REG+NR+++++         RL+R+  G + +  L  G  +
Sbjct: 146 NPPVRFRKNIPTYWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWTIDGLDQGQWK 205

Query: 235 EVSKK 239
            V  +
Sbjct: 206 AVPAR 210


>gi|254786016|ref|YP_003073445.1| ribosomal large subunit pseudouridine synthase E [Teredinibacter
           turnerae T7901]
 gi|237684616|gb|ACR11880.1| ribosomal large subunit pseudouridine synthase E [Teredinibacter
           turnerae T7901]
          Length = 206

 Score = 87.2 bits (214), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 40/159 (25%), Positives = 71/159 (44%), Gaps = 18/159 (11%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
               GRLD ++EGLLLLT++G L   +  P  +  + Y V+  G+ D + L  L+ G+ +
Sbjct: 39  FYPAGRLDYDSEGLLLLTDEGSLQHRISEPKMKLAKTYWVQVEGEPDSEALAQLRGGVDL 98

Query: 168 QGICYGDMQVTLD--------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +       QV L                 +   +W+ + + EG+NR+++++         
Sbjct: 99  KDGRTHPAQVKLLETPTLWERTPPVRHRAQIPTSWLELKISEGRNRQVRRMTAAVGHPTL 158

Query: 214 RLIRISYGPFQLGTLLAGSTR----EVSKKILREQLGPH 248
           RLIR + G +QL  L  G  R     + +   ++  G  
Sbjct: 159 RLIRYAIGSWQLAGLQPGEHRWDEVHLPQSERKKPHGMA 197


>gi|254492373|ref|ZP_05105545.1| conserved hypothetical protein [Methylophaga thiooxidans DMS010]
 gi|224462265|gb|EEF78542.1| conserved hypothetical protein [Methylophaga thiooxydans DMS010]
          Length = 237

 Score = 87.2 bits (214), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 49/254 (19%), Positives = 95/254 (37%), Gaps = 31/254 (12%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            T+L L++KP  ++T  +D  GR T+ D++     +V   GRLD ++EGLLLLT+ G L 
Sbjct: 1   MTQLILFNKPYDVLTQFTDSAGRRTLKDHID--LEQVYPAGRLDRDSEGLLLLTDSGPLQ 58

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------------V 177
            ++  P  +  + Y V+     D+  L  L+ G+ ++       +               
Sbjct: 59  HLIANPKFKLEKTYWVQVENIPDETALQQLRDGVELKDGLTLPAKARLIDPPPVWPRTPP 118

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +     W+ + ++EG+NR+++++         RLIR S   + L  L  G      
Sbjct: 119 IRERKSIPTQWLELKIQEGRNRQVRRMTAAIGCPTLRLIRYSIDIWTLDNLSQGQW---- 174

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
                              +           R R +          R     +      +
Sbjct: 175 -----------QAAPDADMIKWRNDLETKNNRRRRDPTQRSVPAGRRRNPRKTDLKPARR 223

Query: 298 QKKLATPVHRRNLA 311
             +    ++R + +
Sbjct: 224 SSRTRRKLNRGSDS 237


>gi|262190430|ref|ZP_06048686.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           CT 5369-93]
 gi|262033696|gb|EEY52180.1| ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           CT 5369-93]
          Length = 99

 Score = 87.2 bits (214), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 21/98 (21%), Positives = 39/98 (39%), Gaps = 7/98 (7%)

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGI--CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
           +     +  D      +GI ++G        Q+ +     S   V + + EGK  ++K++
Sbjct: 1   MWLADPIQADYAEQFNRGIELRGEREMTLPAQLEVI----SETEVLLTIHEGKYHQVKRM 56

Query: 205 FEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           F     KV  L R   G   L   L  G  R ++++ +
Sbjct: 57  FAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEEEV 94


>gi|254487430|ref|ZP_05100635.1| ribosomal large subunit pseudouridine synthase E [Roseobacter sp.
           GAI101]
 gi|214044299|gb|EEB84937.1| ribosomal large subunit pseudouridine synthase E [Roseobacter sp.
           GAI101]
          Length = 187

 Score = 87.2 bits (214), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 36/142 (25%), Positives = 69/142 (48%), Gaps = 15/142 (10%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
               GRLD ++EGL++LT++G L   +  P  +  + Y V+  G  D   +N L++G+ +
Sbjct: 39  FYPAGRLDRDSEGLIVLTDNGALQARISHPKYKLAKTYWVQVEGTPDDAAINALRQGVTL 98

Query: 168 QGICYGDMQVTLD---------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           +       +V+L                 +   +AW+++ + EG+NR+++++        
Sbjct: 99  KDGKTAPAKVSLIDTPAGLWDRDPPVRFRKSVPDAWLSITITEGRNRQVRRMTAHVGLPT 158

Query: 213 NRLIRISYGPFQLGTLLAGSTR 234
            RLIR   G +QL  +  G+ R
Sbjct: 159 LRLIRAQIGDWQLNAMRPGTWR 180


>gi|116512199|ref|YP_809415.1| ribosomal large subunit pseudouridine synthase E [Lactococcus
           lactis subsp. cremoris SK11]
 gi|116107853|gb|ABJ72993.1| ribosomal large subunit pseudouridine synthase E [Lactococcus
           lactis subsp. cremoris SK11]
          Length = 177

 Score = 87.2 bits (214), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 42/144 (29%), Positives = 73/144 (50%), Gaps = 15/144 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLLLLT+DG L  +L  P ++  + Y V+  G+   +    L+KG++++
Sbjct: 34  YAAGRLDKDSEGLLLLTDDGKLNHLLTDPKSKSFKTYLVQVEGEFSIEAAQKLEKGVLLK 93

Query: 169 GICYGDMQVTLD---------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +V L                 +    +WV + ++EGKNR+I+++     +   
Sbjct: 94  DGKTLPAKVKLIDEPEWLWERTPPIRERKAIPTSWVEISIKEGKNRQIRRMTAAVGFPTL 153

Query: 214 RLIRISYGPFQLGTLLAGSTREVS 237
           RLIR S G + LG L +G  + + 
Sbjct: 154 RLIRWSIGQYTLGNLKSGDYKIIK 177


>gi|330446457|ref|ZP_08310109.1| 23S rRNA pseudouridine 2457 synthase [Photobacterium leiognathi
           subsp. mandapamensis svers.1.1.]
 gi|328490648|dbj|GAA04606.1| 23S rRNA pseudouridine 2457 synthase [Photobacterium leiognathi
           subsp. mandapamensis svers.1.1.]
          Length = 216

 Score = 87.2 bits (214), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 51/188 (27%), Positives = 85/188 (45%), Gaps = 16/188 (8%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
             P R     ++ L++KP   +T  S   G ST+ D +P     V   GRLD ++EGLL+
Sbjct: 24  NKPKRARGPQKIILFNKPFNTLTQFSGEPGDSTLADFIP--VKDVYPAGRLDKDSEGLLV 81

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-------- 175
           LTNDG L   L  P ++  +VY V+  G   +  L  L+ G+ ++               
Sbjct: 82  LTNDGVLQARLTQPKSKQAKVYWVQVEGAPTEADLQALRDGVELKDGMTLPAGVEVIESP 141

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ + L+EG+NR+++++     +   RLIR     + +  L 
Sbjct: 142 QIWDRNPPIRERKNIPTTWLAITLKEGRNRQVRRMTAHIGFPTLRLIRYKMAQWTVDDLA 201

Query: 230 AGSTREVS 237
            G  REV+
Sbjct: 202 PGEWREVT 209


>gi|289807291|ref|ZP_06537920.1| putative ribosomal large subunit pseudouridine synthase B
           [Salmonella enterica subsp. enterica serovar Typhi str.
           AG3]
          Length = 153

 Score = 87.2 bits (214), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 39/146 (26%), Positives = 65/146 (44%), Gaps = 15/146 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LTNDG L   L  P  +  ++Y V+  G  D   L  L+ G+ + 
Sbjct: 5   YAAGRLDRDSEGLLVLTNDGALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLN 64

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +    +W+ V L EG+N +++++         
Sbjct: 65  DGPTLPAGIEIVAEPDWLWPRTPPIRERKNIPTSWLKVTLYEGRNHQVRRMTAHVGHPTL 124

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKK 239
           RLIR S G + L  L  G   E++++
Sbjct: 125 RLIRYSMGDYTLNGLDNGQWCEIAQE 150


>gi|126667267|ref|ZP_01738240.1| Pseudouridine synthase, Rsu [Marinobacter sp. ELB17]
 gi|126628212|gb|EAZ98836.1| Pseudouridine synthase, Rsu [Marinobacter sp. ELB17]
          Length = 219

 Score = 87.2 bits (214), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 36/146 (24%), Positives = 63/146 (43%), Gaps = 14/146 (9%)

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
                 +   GRLD ++EGLLLLT+DG L   +  P  +  + Y V+  G ++   L  L
Sbjct: 35  WINQPGIYPAGRLDYDSEGLLLLTSDGQLQHCIASPRGKMEKTYWVQVEGTINPQTLRQL 94

Query: 162 KKGIVIQGICYGDM--------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
           ++G+ ++                           Q    +W+ + + EG+NR+++++   
Sbjct: 95  EQGVQLKDGLTRPALARAMDEPVIWLRTPPVRFRQNIPTSWLELTICEGRNRQVRRMTAA 154

Query: 208 FNWKVNRLIRISYGPFQLGTLLAGST 233
             +   RLIR   G + LG L  G  
Sbjct: 155 LGFPTLRLIRYRIGDWSLGLLEPGQY 180


>gi|153837322|ref|ZP_01989989.1| RNA pseudouridine synthase family protein [Vibrio parahaemolyticus
           AQ3810]
 gi|260901420|ref|ZP_05909815.1| RNA pseudouridine synthase family protein [Vibrio parahaemolyticus
           AQ4037]
 gi|149749353|gb|EDM60126.1| RNA pseudouridine synthase family protein [Vibrio parahaemolyticus
           AQ3810]
 gi|308107510|gb|EFO45050.1| RNA pseudouridine synthase family protein [Vibrio parahaemolyticus
           AQ4037]
          Length = 232

 Score = 87.2 bits (214), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 41/185 (22%), Positives = 74/185 (40%), Gaps = 17/185 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +    R  +        L         ++            V + GRLD ++EGL++LT
Sbjct: 49  RVDLKNRKVIIFNKPYDTLSQFTDGDGRKTLADYI---PVKDVYAAGRLDRDSEGLMVLT 105

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----- 180
           NDG L   L  P ++  + Y V+  G   +  L  L+KG+ ++       +V +      
Sbjct: 106 NDGILQAKLTQPKSKSPKTYWVQVDGAPQEQDLEKLRKGVELKDGMTLPAKVEVIDAPTI 165

Query: 181 ---------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + + EG+NR+++++     +   RL+R S G   LG L  G
Sbjct: 166 WERNPPVRFRANIPTTWLAITIVEGRNRQVRRMTAHIGFPTLRLVRYSMGDITLGGLQPG 225

Query: 232 STREV 236
             +E+
Sbjct: 226 QWKEI 230


>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 = 87.2 bits (214), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 29/240 (12%), Positives = 65/240 (27%), Gaps = 35/240 (14%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP- 66
           ++    +R+   +A     SR  ++++I +  V VNG  ++  +  V   D + V+    
Sbjct: 12  EKEDEGKRIDVFLASELDYSRSYIKKLIEEGLVLVNGKNVK-PSYKVKEDDEVIVNIKEA 70

Query: 67  -------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
                        +   +   + +      +V         + V   L    +     G 
Sbjct: 71  EKIEVVPENIPLDILYEDEDIIVINKPQGMVVHPAPGNYSGTLVNALLYHCKNLSGINGI 130

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------------------ 155
           L       L     G +       +   L                               
Sbjct: 131 LRPGIVHRLDKDTSGVMVVAKNDKAHMSLSNQIKERSVLKKYVAIVEGVIKEEEGKIEAP 190

Query: 156 --DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                   K+  V+Q   Y      +  +  +N +V   ++ G+  +I+    +    V 
Sbjct: 191 IGRHPVDRKRMAVVQDGRYALTLYKVLERFKNNTFVEATIKTGRTHQIRVHLSYIGHPVV 250


>gi|325181474|emb|CCA15908.1| ribosomal large subunit pseudouridine synthase F put [Albugo
           laibachii Nc14]
          Length = 248

 Score = 87.2 bits (214), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 51/213 (23%), Positives = 93/213 (43%), Gaps = 25/213 (11%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           +A   + SRR+ ER I+   V VNG  +++  + +     +E  G  ++  ++    + +
Sbjct: 1   MAERKMCSRRDAERYISAGDVYVNGEQIQQDWIKIPRDSCVEFSGKAVKAEKQKVSVILN 60

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------------VGRLDINTEGLLLL 124
           KP+G V++  +P  +  +         ++ +                GRLDIN+ GLLL 
Sbjct: 61  KPLGYVSSQPEPMRKPAIELLSIQNAFQLTARWYGKEPKSLSKLAVCGRLDINSTGLLLF 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVR------FHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           T DG LA+ +  P+    + Y VR         +  ++ ++ L++G +   ICY    V 
Sbjct: 121 TQDGVLAKQILDPNGGVEKEYLVRVDMDLERDTKQAEEVVDKLREGFIWNDICYRARSVR 180

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +         +   L EGK R I+ + E    K
Sbjct: 181 VLNANQ----LQFILTEGKKRHIRYMCEAVGIK 209


>gi|304397253|ref|ZP_07379132.1| pseudouridine synthase [Pantoea sp. aB]
 gi|304355402|gb|EFM19770.1| pseudouridine synthase [Pantoea sp. aB]
          Length = 184

 Score = 87.2 bits (214), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 40/144 (27%), Positives = 68/144 (47%), Gaps = 15/144 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGL++LTNDG L   L  P  +  +VY V+  G+  +  L  L+ G+ ++
Sbjct: 37  YAAGRLDRDSEGLMVLTNDGALQAALTQPGKRTGKVYYVQVEGEPQEADLQPLRDGVNLK 96

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +     W+ V L EG+NR+++++     +   
Sbjct: 97  DGMTLPAGIEKVPEPQWLWPRQPPIRERKNIPTQWLKVTLYEGRNRQVRRMTAHIGFPTL 156

Query: 214 RLIRISYGPFQLGTLLAGSTREVS 237
           RLIR + G + L  L  G+ RE+S
Sbjct: 157 RLIRYAMGQYSLDDLAPGAWRELS 180


>gi|90413209|ref|ZP_01221204.1| putative pseudouridine synthase family 1 protein [Photobacterium
           profundum 3TCK]
 gi|90325761|gb|EAS42219.1| putative pseudouridine synthase family 1 protein [Photobacterium
           profundum 3TCK]
          Length = 216

 Score = 87.2 bits (214), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 50/187 (26%), Positives = 84/187 (44%), Gaps = 16/187 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P R     ++ L++KP  ++T  S   G  T+ D +      +   GRLD ++EGLL+L
Sbjct: 25  NPKRPRGPQKIILFNKPFNVLTQFSGEPGDKTLADYISIK--DIYPAGRLDKDSEGLLVL 82

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TNDG L   L  P ++  + Y V+  G    D L  L+KG+ ++                
Sbjct: 83  TNDGILQARLTQPQSKQPKTYWVQVEGVPSDDDLEQLRKGVTLKDGLTLPADIERMEQPV 142

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + +     W+ + LREG+NR+++++     +   RLIR     + +  L  
Sbjct: 143 IWDRTPPIRERKNIPTTWLALTLREGRNRQVRRMTAHIGFPTLRLIRYKMADWTVDDLAP 202

Query: 231 GSTREVS 237
           G  REV+
Sbjct: 203 GEWREVT 209


>gi|94495563|ref|ZP_01302143.1| Pseudouridine synthase, Rsu [Sphingomonas sp. SKA58]
 gi|94424951|gb|EAT09972.1| Pseudouridine synthase, Rsu [Sphingomonas sp. SKA58]
          Length = 182

 Score = 86.8 bits (213), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 41/178 (23%), Positives = 72/178 (40%), Gaps = 14/178 (7%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +        L        G      +      RV   GRLD ++EGLLLLT+DG L   +
Sbjct: 5   ILFNKPYDVLSQFTDSSIGADRRTLSDFIDVPRVYPAGRLDRDSEGLLLLTDDGRLQARI 64

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y V+  G V  D L  L+ G+ ++       +                  
Sbjct: 65  SNPRFKTPKTYLVQVEGDVTSDALACLRAGVSLKDGPTLPAEAERIDPPALWPRDPPVRF 124

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +   + W+++ +REG+NR+++++         RL+R   G + L  +  G+ R+ S 
Sbjct: 125 RKTVPDCWISLTIREGRNRQVRRMTAAVGHPTLRLVRWRIGDWTLDGVAPGTWRDASP 182


>gi|83942369|ref|ZP_00954830.1| RNA pseudouridylate synthase [Sulfitobacter sp. EE-36]
 gi|83846462|gb|EAP84338.1| RNA pseudouridylate synthase [Sulfitobacter sp. EE-36]
          Length = 187

 Score = 86.8 bits (213), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 42/180 (23%), Positives = 79/180 (43%), Gaps = 17/180 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGG 129
             R+ L++KP G+++  +D     +    L            GRLD ++EGL++LT+ G 
Sbjct: 1   MNRVILFNKPFGVLSQFTDKGTEGSPRPTLSAYIDEKGFYPAGRLDRDSEGLMVLTDSGP 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------- 180
           L   +  P  +  + Y V+  G  D+  L  L+ G+ ++       +  L          
Sbjct: 61  LQARISHPKYKLAKTYWVQVEGTPDEQALAALRSGVTLKDGKTAPAKARLMDPPEPLWDR 120

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +   +AW+ + + EG+NR+++++         RLIR   G ++L  L  G+ R
Sbjct: 121 DPPVRFRKSVPDAWLEITITEGRNRQVRRMTAHVGLPTLRLIRARVGDWELHKLQPGAWR 180


>gi|16760112|ref|NP_455729.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Typhi str. CT18]
 gi|29142117|ref|NP_805459.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Typhi str. Ty2]
 gi|289828345|ref|ZP_06546258.1| putative ribosomal large subunit pseudouridine synthase B
           [Salmonella enterica subsp. enterica serovar Typhi str.
           E98-3139]
 gi|34098637|sp|Q8Z7G6|RLUE_SALTI RecName: Full=Ribosomal large subunit pseudouridine synthase E;
           AltName: Full=rRNA pseudouridylate synthase E; AltName:
           Full=rRNA-uridine isomerase E
 gi|25324021|pir||AF0647 probable ribosomal large chain pseudouridine synthase B STY1277
           [imported] - Salmonella enterica subsp. enterica serovar
           Typhi (strain CT18)
 gi|16502406|emb|CAD08361.1| putative ribosomal large subunit pseudouridine synthase B
           [Salmonella enterica subsp. enterica serovar Typhi]
 gi|29137746|gb|AAO69308.1| putative ribosomal large subunit pseudouridine synthase B
           [Salmonella enterica subsp. enterica serovar Typhi str.
           Ty2]
          Length = 221

 Score = 86.8 bits (213), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 49/187 (26%), Positives = 86/187 (45%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLL+LTND
Sbjct: 34  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIPVQGV--YAAGRLDRDSEGLLVLTND 91

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P  +  ++Y V+  G  D   L  L+ G+ +                    
Sbjct: 92  GALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 151

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ V L EG+N +++++         RLIR S G + L  L  G 
Sbjct: 152 PRTPPIRERKNIPTSWLKVTLYEGRNHQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQ 211

Query: 233 TREVSKK 239
             E++++
Sbjct: 212 WCEIAQE 218


>gi|324112364|gb|EGC06342.1| ribosomal large subunit pseudouridine synthase F [Escherichia
           fergusonii B253]
          Length = 177

 Score = 86.8 bits (213), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 28/177 (15%), Positives = 62/177 (35%), Gaps = 4/177 (2%)

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
             G L   +        + Y V     +  + +  +  G++I G            +K +
Sbjct: 5   QFGDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVLILGTV----TKKCKVKKEA 60

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +  
Sbjct: 61  PFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLF 120

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
                  ++V   A        ++     + +  +   R   N  +     ++KK  
Sbjct: 121 KLIENSTSEVKPKAKAKPKTAGIKRPVVKMEKTSEKGGRPASNGKRFTSPGRKKKGR 177


>gi|120598595|ref|YP_963169.1| pseudouridylate synthase [Shewanella sp. W3-18-1]
 gi|146293327|ref|YP_001183751.1| pseudouridylate synthase [Shewanella putrefaciens CN-32]
 gi|120558688|gb|ABM24615.1| ribosomal large subunit pseudouridine synthase E [Shewanella sp.
           W3-18-1]
 gi|145565017|gb|ABP75952.1| ribosomal large subunit pseudouridine synthase E [Shewanella
           putrefaciens CN-32]
          Length = 270

 Score = 86.8 bits (213), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 49/188 (26%), Positives = 88/188 (46%), Gaps = 17/188 (9%)

Query: 65  VPLRKAE-RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
            P++       + L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLL
Sbjct: 80  KPVQSQTLAPIIVLFNKPFDVLCQFTDEQGRKTLKDYIPIA--DVYAAGRLDRDSEGLLL 137

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
           LTNDG L   L  P  +  + Y V+  G   +D L  L++G+ +        +V +    
Sbjct: 138 LTNDGQLQARLTEPKKKTFKTYWVQVEGVPTEDALTKLRQGVELNDGITLPAKVKIMDSP 197

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ + + EG+NR+++++     +   RLIR   G + L  L 
Sbjct: 198 DIWPRNPPVRERKNIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDNLP 257

Query: 230 AGSTREVS 237
           +G  + + 
Sbjct: 258 SGEHKCIR 265


>gi|239994883|ref|ZP_04715407.1| ribosomal large subunit pseudouridine synthase E [Alteromonas
           macleodii ATCC 27126]
          Length = 180

 Score = 86.8 bits (213), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 37/139 (26%), Positives = 65/139 (46%), Gaps = 14/139 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LTNDG L   L  P  +  + Y V+  G +D+  +  L+ G+ ++
Sbjct: 39  YAAGRLDRDSEGLLVLTNDGKLQHKLANPKAKTSKTYWVQVEGIMDEKAMQALRDGVELK 98

Query: 169 GICYGDMQVTLD--------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                  +V                  Q    +WV + + EG+NR+++++     +   R
Sbjct: 99  DGMTRPAKVKAMEAPSVWPRNPPVRFRQSIPTSWVEITITEGRNRQVRRMTANVGYPTLR 158

Query: 215 LIRISYGPFQLGTLLAGST 233
           LIR   G + +  +  GS 
Sbjct: 159 LIRYRVGNWTIDGIDNGSY 177


>gi|54308341|ref|YP_129361.1| pseudouridine synthase family 1 protein [Photobacterium profundum
           SS9]
 gi|46912769|emb|CAG19559.1| putative pseudouridine synthase family 1protein [Photobacterium
           profundum SS9]
          Length = 216

 Score = 86.8 bits (213), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 50/187 (26%), Positives = 84/187 (44%), Gaps = 16/187 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P R     ++ L++KP  ++T  S   G  T+ D +      +   GRLD ++EGLL+L
Sbjct: 25  NPKRPRGPQKIILFNKPFNVLTQFSGEPGDKTLADYISIK--DIYPAGRLDKDSEGLLVL 82

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TNDG L   L  P ++  + Y V+  G    D L  L+KG+ ++                
Sbjct: 83  TNDGILQARLTQPQSKQPKTYWVQVEGAPSDDDLEQLRKGVTLKDGLTLPADIERMEQPV 142

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + +     W+ + LREG+NR+++++     +   RLIR     + +  L  
Sbjct: 143 IWDRTPPIRERKNIPTTWLALTLREGRNRQVRRMTAHIGFPTLRLIRYKMADWTVDDLAP 202

Query: 231 GSTREVS 237
           G  REV+
Sbjct: 203 GEWREVT 209


>gi|312881482|ref|ZP_07741274.1| ribosomal large subunit pseudouridine synthase E [Vibrio
           caribbenthicus ATCC BAA-2122]
 gi|309370848|gb|EFP98308.1| ribosomal large subunit pseudouridine synthase E [Vibrio
           caribbenthicus ATCC BAA-2122]
          Length = 226

 Score = 86.8 bits (213), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 48/186 (25%), Positives = 91/186 (48%), Gaps = 16/186 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E  ++ +++KP   ++  +D +GR T+ D +        + GRLD ++EGLL+L
Sbjct: 41  KPKIAPEERKVIIFNKPFDTLSQFTDGEGRKTLADYISIKGV--YAAGRLDRDSEGLLVL 98

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  PS++  + Y V+  G   +  L+ L++G+ ++       +V +  +  
Sbjct: 99  TNDGILQARLTQPSSKSPKTYWVQVDGSPGEVDLDKLRQGVELKDGLTLPARVEIIDEPK 158

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+++ + EG+NR+++++     +   RLIR S G   L +L  
Sbjct: 159 VWPRNPPVRFRANIPTTWLSITIIEGRNRQVRRMTAHIGYPTLRLIRYSVGDIHLDSLKP 218

Query: 231 GSTREV 236
           G  +E+
Sbjct: 219 GEWKEI 224


>gi|212634690|ref|YP_002311215.1| pseudouridine synthase Rsu [Shewanella piezotolerans WP3]
 gi|212556174|gb|ACJ28628.1| Pseudouridine synthase, Rsu [Shewanella piezotolerans WP3]
          Length = 226

 Score = 86.8 bits (213), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 48/184 (26%), Positives = 87/184 (47%), Gaps = 16/184 (8%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +   + L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTND
Sbjct: 39  KEVKDPIIVLFNKPFDVLCQFTDEQGRKTLKDFIPIQ--EVYAAGRLDRDSEGLLLLTND 96

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   +  P  +  + Y V+  G   +  L  L+ G+ ++       +V +        
Sbjct: 97  GKLQAQITEPKKKTFKTYWVQVEGAPSETDLEKLRTGVELKDGLTLPAKVNIMSNPAVWP 156

Query: 180 ------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 +       W+T+ + EG+NR+++++     +   RLIR   G + L  L  G  
Sbjct: 157 RNPPIRERANIPTTWLTIEICEGRNRQVRRMTANIGFPTLRLIRYKIGQWSLDDLPNGQY 216

Query: 234 REVS 237
           R++ 
Sbjct: 217 RKLD 220


>gi|213052785|ref|ZP_03345663.1| putative ribosomal large subunit pseudouridine synthase B
           [Salmonella enterica subsp. enterica serovar Typhi str.
           E00-7866]
 gi|213423671|ref|ZP_03356651.1| putative ribosomal large subunit pseudouridine synthase B
           [Salmonella enterica subsp. enterica serovar Typhi str.
           E01-6750]
 gi|213428087|ref|ZP_03360837.1| putative ribosomal large subunit pseudouridine synthase B
           [Salmonella enterica subsp. enterica serovar Typhi str.
           E02-1180]
 gi|213580467|ref|ZP_03362293.1| putative ribosomal large subunit pseudouridine synthase B
           [Salmonella enterica subsp. enterica serovar Typhi str.
           E98-0664]
 gi|213648218|ref|ZP_03378271.1| putative ribosomal large subunit pseudouridine synthase B
           [Salmonella enterica subsp. enterica serovar Typhi str.
           J185]
 gi|213850125|ref|ZP_03381023.1| putative ribosomal large subunit pseudouridine synthase B
           [Salmonella enterica subsp. enterica serovar Typhi str.
           M223]
          Length = 211

 Score = 86.8 bits (213), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 49/187 (26%), Positives = 86/187 (45%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLL+LTND
Sbjct: 24  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIPVQGV--YAAGRLDRDSEGLLVLTND 81

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P  +  ++Y V+  G  D   L  L+ G+ +                    
Sbjct: 82  GALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 141

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ V L EG+N +++++         RLIR S G + L  L  G 
Sbjct: 142 PRTPPIRERKNIPTSWLKVTLYEGRNHQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQ 201

Query: 233 TREVSKK 239
             E++++
Sbjct: 202 WCEIAQE 208


>gi|284035455|ref|YP_003385385.1| pseudouridine synthase [Spirosoma linguale DSM 74]
 gi|283814748|gb|ADB36586.1| pseudouridine synthase [Spirosoma linguale DSM 74]
          Length = 198

 Score = 86.8 bits (213), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 47/191 (24%), Positives = 80/191 (41%), Gaps = 18/191 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP  +++  S    +ST+ +      + V  VGRLD ++EGLLLLTND  L   L
Sbjct: 7   YFLIYKPYLMLSQFSKEGDKSTLANLDFDFPTDVYPVGRLDADSEGLLLLTNDKQLNHRL 66

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLD---------- 180
             P  +  R Y V+  G +  +    L  G+ I    +       +  L           
Sbjct: 67  LNPKFRHNRTYYVQVDGALTDEACQQLSAGVTISVDGKAYDTLPAKAILIEAPNLPERNP 126

Query: 181 ----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                     +W+++ L EGKNR+++K+     +   RL+R +        +  G  R +
Sbjct: 127 PIRFRASIPTSWLSITLHEGKNRQVRKMTAAVGFPTLRLVRWAIESLTAEEMAPGEVRLL 186

Query: 237 SKKILREQLGP 247
           S+  +   L  
Sbjct: 187 SRAEVLRGLRL 197


>gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum
           seropedicae SmR1]
 gi|300073512|gb|ADJ62911.1| 16S rRNA uridine-516 pseudouridylate synthase protein
           [Herbaspirillum seropedicae SmR1]
          Length = 188

 Score = 86.8 bits (213), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 52/187 (27%), Positives = 85/187 (45%), Gaps = 19/187 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L +KP  +++  S    R T+ D +      V   GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LILLNKPFQVMSQFSAHPERQTLADYIDIP--NVYPAGRLDADSEGLLLLTDDGKLQHAI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ------------ 182
             P  +  + Y  +  GQ   + L+ L++ + +        Q  L  +            
Sbjct: 61  AHPRRKLPKTYLAQVEGQPSPEALDKLRQPLDLGDFVTQGSQARLIQEPGWMWPRNPPIR 120

Query: 183 ---KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTREVS 237
                  +W+ + + EGKNR+++++         RL+RI+ GPF L T  ++ G  REV 
Sbjct: 121 QRQNQPTSWIALTISEGKNRQVRRMTAAVGLPTLRLVRIAIGPFSLATHPVMPGEWREVD 180

Query: 238 KKILREQ 244
              L  Q
Sbjct: 181 PLELERQ 187


>gi|325136481|gb|EGC59087.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M0579]
          Length = 200

 Score = 86.8 bits (213), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 48/181 (26%), Positives = 89/181 (49%), Gaps = 2/181 (1%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              +  Y +   +V+        S       +  SR +++GRLDINT GLL+LT  G L 
Sbjct: 9   PRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTTSGELV 68

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAWVT 190
           +    PS +  R Y VR  G +  +++ +L +  ++++       ++     +G+N W  
Sbjct: 69  QRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGANKWYN 128

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHL 249
           V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   E++   +   +    
Sbjct: 129 VVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFYELNPAEVANIIKWAD 188

Query: 250 L 250
           +
Sbjct: 189 M 189


>gi|255024632|ref|ZP_05296618.1| RNA pseudouridine synthase family protein [Listeria monocytogenes
           FSL J1-208]
          Length = 105

 Score = 86.8 bits (213), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 24/103 (23%), Positives = 41/103 (39%), Gaps = 1/103 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D + V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQVTVHGTPVVYQEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
               L+     +  T  +               +    VGRLD
Sbjct: 61  VYFMLHKPQNVVSATEDNVSETVIDLLAQEDTLTNPFPVGRLD 103


>gi|261346009|ref|ZP_05973653.1| ribosomal large subunit pseudouridine synthase E [Providencia
           rustigianii DSM 4541]
 gi|282565894|gb|EFB71429.1| ribosomal large subunit pseudouridine synthase E [Providencia
           rustigianii DSM 4541]
          Length = 223

 Score = 86.4 bits (212), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 49/185 (26%), Positives = 91/185 (49%), Gaps = 17/185 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           + +   ++ +++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTND
Sbjct: 39  KPSTPRKVIIFNKPFDVLPQFTDEQGRETLKNYIPIS--DVYAAGRLDRDSEGLLVLTND 96

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y  +  G  D+  L   ++G+V+        ++ L        
Sbjct: 97  GKLQARLTQPQKKTGKIYYAQVEGIPDEIALANFRRGLVLNDGPTLPAEIELVEEPDWLW 156

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ + L EG+NR+++++     +   RLIR S G F L  L  G 
Sbjct: 157 ERIPPIRERKNIPTSWLKITLFEGRNRQVRRMTANIGFPTLRLIRYSTGEFSLDNLSPGE 216

Query: 233 TREVS 237
            +EV+
Sbjct: 217 WKEVT 221


>gi|56696990|ref|YP_167352.1| RNA pseudouridylate synthase [Ruegeria pomeroyi DSS-3]
 gi|56678727|gb|AAV95393.1| RNA pseudouridylate synthase [Ruegeria pomeroyi DSS-3]
          Length = 200

 Score = 86.4 bits (212), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 34/143 (23%), Positives = 64/143 (44%), Gaps = 15/143 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              GRLD ++EGL+LLT+ G L   +  P  +  + Y V+  G  D   L  L +G+ ++
Sbjct: 40  YPAGRLDRDSEGLMLLTDVGRLQARIADPRHKLAKTYWVQVEGVPDAAALRALAEGVELK 99

Query: 169 GICYGDMQ---------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +                  + +   ++W+ + +REG+NR+++++         
Sbjct: 100 DGLTRPARARAMPEPPGLWPRNPPIRERKSVPDSWIELTIREGRNRQVRRMTAAVGHPTL 159

Query: 214 RLIRISYGPFQLGTLLAGSTREV 236
           RLIR   G + L  L+ G  + +
Sbjct: 160 RLIRARIGDWTLDGLVPGEWQSL 182


>gi|197335196|ref|YP_002156597.1| ribosomal large subunit pseudouridine synthase E [Vibrio fischeri
           MJ11]
 gi|197316686|gb|ACH66133.1| ribosomal large subunit pseudouridine synthase E [Vibrio fischeri
           MJ11]
          Length = 206

 Score = 86.4 bits (212), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 47/187 (25%), Positives = 93/187 (49%), Gaps = 16/187 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    +  ++ +++KP  +++  +D   R T+ D +      V + GRLD ++EGLL+L
Sbjct: 21  KPRPAPKDRKVIIFNKPFDVLSQFTDDQHRQTLADFIS--VKDVYAAGRLDRDSEGLLIL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +D L+ L++G+ ++       +V +  +  
Sbjct: 79  TNDGVLQARLTQPESKSPKTYWVQVEGAPTEDDLDKLRQGVELKDGMTLPAKVEIIPEPN 138

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+++ + EG+NR+++++     +   RLIR S G + +  +  
Sbjct: 139 VWERNPPVRFRAAIPTTWISITIIEGRNRQVRRMTANIGFPTLRLIRYSMGDWTIKDVAH 198

Query: 231 GSTREVS 237
           G+ +EVS
Sbjct: 199 GTWKEVS 205


>gi|127512491|ref|YP_001093688.1| pseudouridylate synthase [Shewanella loihica PV-4]
 gi|126637786|gb|ABO23429.1| ribosomal large subunit pseudouridine synthase E [Shewanella
           loihica PV-4]
          Length = 264

 Score = 86.4 bits (212), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 43/180 (23%), Positives = 84/180 (46%), Gaps = 16/180 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   + L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTNDG L
Sbjct: 84  QNPIIVLFNKPFDVLCQFTDEQGRQTLKDFIPIQ--DVYAAGRLDRDSEGLLLLTNDGQL 141

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------------- 176
              +  P  +  + Y V+  G    + +  L+ G+ ++       +              
Sbjct: 142 QSRITEPKKKTDKTYWVQVEGIPSDEAIQALRDGVTLKDGPTLPAKVERIAEPDVWPRNP 201

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + ++   +W+ + + EG+NR+++++     +   RLIR   G + L  +  G  + +
Sbjct: 202 PVRERKQIPTSWLAITICEGRNRQVRRMTAHVGYPTLRLIRYKIGQWSLNGVANGEYKVL 261


>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 = 86.4 bits (212), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 35/247 (14%), Positives = 68/247 (27%), Gaps = 37/247 (14%)

Query: 3   DKNIVQ--ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           DK ++Q  +    +R+   +A     +R  ++++I    V VNG  ++  +  V   D +
Sbjct: 5   DKIVLQGEKEDEGKRIDVFLAAELDYTRSYIKKLIVDGLVFVNGKTVK-PSYKVKENDEV 63

Query: 61  EVD------------GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
            V+             +PL     +   + +      +V         + V   L    +
Sbjct: 64  VVNIPEAEKIDVLPENIPLDILYEDDDIIVINKPQGMVVHPAPGNYSGTLVNALLYHCKN 123

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ----------- 155
                G L       L     G +       +   L                        
Sbjct: 124 LSGINGILRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIKERSVFKKYVAIVEGVIKDE 183

Query: 156 ---------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          KK  VI+   Y      +  +   N  V   ++ G+  +I+    
Sbjct: 184 EGKIEAPIGRHPVDRKKMAVIEDGRYALTLYKVLERFKENTLVEAVIKTGRTHQIRVHMA 243

Query: 207 FFNWKVN 213
           F    V 
Sbjct: 244 FIGHPVV 250


>gi|114765384|ref|ZP_01444499.1| Pseudouridine synthase, Rsu [Pelagibaca bermudensis HTCC2601]
 gi|114542227|gb|EAU45257.1| Pseudouridine synthase, Rsu [Roseovarius sp. HTCC2601]
          Length = 179

 Score = 86.4 bits (212), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 36/142 (25%), Positives = 66/142 (46%), Gaps = 14/142 (9%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              GRLD ++EGLLLLT+DG L   +  P  +  + Y V+  G    +++  L++G+ ++
Sbjct: 38  YPAGRLDRDSEGLLLLTDDGRLQARIAHPKFKKPKTYLVQVEGDPSDEQIARLRRGVTLK 97

Query: 169 GICYGDMQVTLDT--------------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                  QV                  +   +AW+ + + EG+NR+++++         R
Sbjct: 98  DGPTRPAQVRRLPPPDLWPRVPPVRFRKSVPDAWLEMTITEGRNRQVRRMTAHVGLPCLR 157

Query: 215 LIRISYGPFQLGTLLAGSTREV 236
           L+R S G + +  L  G  R +
Sbjct: 158 LVRWSIGDWSVEGLAPGEWRNI 179


>gi|467162|gb|AAA50926.1| u0247g [Mycobacterium leprae]
          Length = 186

 Score = 86.4 bits (212), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 49/177 (27%), Positives = 73/177 (41%), Gaps = 3/177 (1%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLLTNDGGL 130
                +KP G+ +T SD  GR  V D +            VGRLD +TEGL+LLTNDG L
Sbjct: 7   VYLALNKPRGMYSTMSDDRGRPCVGDLIERRVRGNKKLFHVGRLDADTEGLILLTNDGEL 66

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS +  + Y     G V +     L  G+ +           +         V 
Sbjct: 67  AHRLMHPSHEVSKTYLATVKGAVPRGLGKKLSVGLELDDGPAHVDDFAVVDAIPGKTLVR 126

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           + L EG+ R ++++     + V  L+R   G   LG    G  R + +  +R+    
Sbjct: 127 LTLHEGRKRIVRRLLTAAGFPVEMLVRTDIGAVSLGDQRPGCLRALLRDEIRQLYKE 183


>gi|121594837|ref|YP_986733.1| ribosomal large subunit pseudouridine synthase E [Acidovorax sp.
           JS42]
 gi|120606917|gb|ABM42657.1| ribosomal large subunit pseudouridine synthase E [Acidovorax sp.
           JS42]
          Length = 216

 Score = 86.4 bits (212), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 43/179 (24%), Positives = 78/179 (43%), Gaps = 17/179 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP G+++  +       + D +          GRLD ++EGLLLLT+DG L   +
Sbjct: 30  LLRFNKPYGVLSQFTPEGRWRGLQDFIDVPGV--YVAGRLDADSEGLLLLTDDGALQARI 87

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y V+  G  D+  L  L+ G+ +        +V                 
Sbjct: 88  SDPRHKMEKTYWVQVEGIPDEAALQALRHGVQLGDGPTLPARVRRLEPPPALWERDPPIR 147

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
             Q   + W+ + +REG+NR+++++         RL+R + GP+ L  L  G  +  + 
Sbjct: 148 VRQNIPDCWIELIIREGRNRQVRRMTAAVGHPTLRLVRAAIGPYALDGLEPGCWQPATP 206


>gi|84625925|ref|YP_453297.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|84369865|dbj|BAE71023.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae MAFF
           311018]
          Length = 190

 Score = 86.4 bits (212), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 46/175 (26%), Positives = 80/175 (45%), Gaps = 15/175 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L +KP G+++  SD             +   V + GRLD ++EGLLLLT+DG LA  +
Sbjct: 2   LVLLNKPYGVLSQFSDRSQPPKRTLAEFGLPPDVYAAGRLDHDSEGLLLLTDDGALAHRV 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------VTL 179
             P  +  + Y V+  G+    +L  L+ G+V+        Q                  
Sbjct: 62  TDPRHKQPKTYWVQVEGEPQAGQLQALRDGVVLNDGPTRTAQVRSLDPAPPLWPREPPVR 121

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +   +AW+ + + EG+NR+++++         RL+R++ G ++L  L  G  R
Sbjct: 122 VRKTVPDAWLELRITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLDMLAPGQWR 176


>gi|320155833|ref|YP_004188212.1| ribosomal large subunit pseudouridine synthase E [Vibrio vulnificus
           MO6-24/O]
 gi|319931145|gb|ADV86009.1| ribosomal large subunit pseudouridine synthase E [Vibrio vulnificus
           MO6-24/O]
          Length = 234

 Score = 86.4 bits (212), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 44/187 (23%), Positives = 76/187 (40%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L  AER  +        L         ++            V + GRLD ++EGL++L
Sbjct: 48  KSLSLAERKIIIFNKPYDTLSQFTDGEGRKTLADFI---PVKEVYAAGRLDRDSEGLMVL 104

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   + +L  L+ G+ ++       QV +     
Sbjct: 105 TNDGILQAKLTQPKSKSPKTYWVQVEGAPTEAQLEPLRSGVELKDGLTLPAQVEIIQDPQ 164

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + + EG+NR+++++     +   RL+R S G   L  L  
Sbjct: 165 LWERNPPVRFRAAIPTTWLAITIIEGRNRQVRRMTAHIGFPTLRLVRYSMGGMTLQDLQP 224

Query: 231 GSTREVS 237
           G  +E+S
Sbjct: 225 GEWKEIS 231


>gi|319426627|gb|ADV54701.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 270

 Score = 86.4 bits (212), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 49/193 (25%), Positives = 89/193 (46%), Gaps = 18/193 (9%)

Query: 65  VPLRKAE-RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
            P++       + L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLL
Sbjct: 80  KPVQSQTLAPIIVLFNKPFDVLCQFTDEQGRKTLKDYIPIA--DVYAAGRLDRDSEGLLL 137

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
           LTNDG L   L  P  +  + Y V+  G   +D L  L++G+ +        +V +    
Sbjct: 138 LTNDGQLQARLTEPKKKTFKTYWVQVEGVPTEDALTKLRQGVELNDGITLPAKVKIMDSP 197

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ + + EG+NR+++++     +   RLIR   G + L  L 
Sbjct: 198 DVWPRNPPVRERKNIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDNLP 257

Query: 230 AGSTREVS-KKIL 241
           +G  + +     +
Sbjct: 258 SGEHKCIRLGDEI 270


>gi|87301078|ref|ZP_01083919.1| Pseudouridine synthase, Rsu [Synechococcus sp. WH 5701]
 gi|87284046|gb|EAQ75999.1| Pseudouridine synthase, Rsu [Synechococcus sp. WH 5701]
          Length = 224

 Score = 86.4 bits (212), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 50/192 (26%), Positives = 78/192 (40%), Gaps = 20/192 (10%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   L HKP G+++  S                  V + GRLD ++EGLLLLT+DG
Sbjct: 10  ARPAPTTLLLHKPYGVLSQFSPEPLSPWSTLAPLVPVPGVYAAGRLDADSEGLLLLTSDG 69

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ------------ 176
            L + L  P     R Y V+  G      L  L++G+++QG      Q            
Sbjct: 70  PLQQRLTDPRWGHWRRYWVQVEGTPSDAALQQLREGVMVQGRRTLSAQAIALADPGLAER 129

Query: 177 --VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQLGTL 228
                  +    +W+ +GLREG+NR+++++         RL+R++        P  L  L
Sbjct: 130 VPPIRQRRSIPTSWLELGLREGRNRQVRRMTAAVGLPTLRLLRVAIDLMDGEPPLSLEGL 189

Query: 229 LAGSTREVSKKI 240
             G  R V+   
Sbjct: 190 APGQWRPVTAAE 201


>gi|119944741|ref|YP_942421.1| pseudouridine synthase [Psychromonas ingrahamii 37]
 gi|119863345|gb|ABM02822.1| ribosomal large subunit pseudouridine synthase E [Psychromonas
           ingrahamii 37]
          Length = 220

 Score = 86.4 bits (212), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 38/207 (18%), Positives = 76/207 (36%), Gaps = 20/207 (9%)

Query: 44  GILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           G   +  +V        +++   L         +              D  +        
Sbjct: 20  GNAAKHPSVKN------KINTQQLPPVSDATRKILLFNKPFNVLSQFTDQDNRQTLKDYI 73

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
               V + GRLD ++EGLLLLTNDG L   +  P+ +  + Y V+  G+  +  L  L+ 
Sbjct: 74  DIPEVYAAGRLDRDSEGLLLLTNDGKLQAKITEPNAKTSKTYWVQVEGRPTEADLQKLRD 133

Query: 164 GIVIQGICYGDM--------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
           G+ ++                         +       W+++ + EG+NR+++++     
Sbjct: 134 GVNLKDGLTLPAGIELMEQPAIWARVPPIRERANIPTTWLSITISEGRNRQVRRMTAHIG 193

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREV 236
           +   RLIR   G + +  +  G  + +
Sbjct: 194 FPTLRLIRYRIGDWTIDDIDNGQYKLL 220


>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 = 86.0 bits (211), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 31/240 (12%), Positives = 67/240 (27%), Gaps = 35/240 (14%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP- 66
           ++    +R+   +A     SR  ++++I +  V VNG  ++  +  V   D I V+    
Sbjct: 12  EKEDEGKRIDVFLASELDYSRSYIKKLIEEGLVLVNGKNVK-PSYKVKEDDEIVVNIKEA 70

Query: 67  -------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
                        +   +   + +      +V   +     + V   L    +     G 
Sbjct: 71  EKIEVVPENIPLDILYEDEDIIVINKPQGMVVHPAAGNYSGTLVNALLYHCKNLSGINGI 130

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------------------ 155
           L       L     G +       +   L                               
Sbjct: 131 LRPGIVHRLDKDTSGVMVVAKNDKAHMSLSNQIKERSVLKKYIAIVEGVIKEEEGKVEAP 190

Query: 156 --DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                   K+  V+Q   Y      +  +  +N +V   ++ G+  +I+  F +    V 
Sbjct: 191 IGRHPVDRKRMAVVQEGRYALTLYKVLERFKNNTFVEATIKTGRTHQIRVHFSYIGHPVV 250


>gi|157962357|ref|YP_001502391.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157847357|gb|ABV87856.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 244

 Score = 86.0 bits (211), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 45/183 (24%), Positives = 86/183 (46%), Gaps = 16/183 (8%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +      + L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLLLLTND
Sbjct: 57  KSVTNPIIVLFNKPFDVLCQFTDEQGRQTLKDFIPIPGV--YAAGRLDRDSEGLLLLTND 114

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   +  P  +  + Y  +  G  ++D L  L++G+ ++       ++++        
Sbjct: 115 GKLQSQITEPKKKTYKTYWAQVEGAPNEDDLEKLRQGVELKDGMSLPAKISIMNNPDIWP 174

Query: 180 ------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 +       W+ + + EG+NR+++++     +   RLIR   G + L  L  G  
Sbjct: 175 RTPPIRERANIPTTWLEIKICEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDDLKNGEY 234

Query: 234 REV 236
           R++
Sbjct: 235 RQL 237


>gi|260425703|ref|ZP_05779683.1| ribosomal large subunit pseudouridine synthase E [Citreicella sp.
           SE45]
 gi|260423643|gb|EEX16893.1| ribosomal large subunit pseudouridine synthase E [Citreicella sp.
           SE45]
          Length = 179

 Score = 86.0 bits (211), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 37/142 (26%), Positives = 64/142 (45%), Gaps = 14/142 (9%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              GRLD ++EGLLLLT+DG L   +  P  +  + Y V+  G    D+L  L++G+ + 
Sbjct: 38  YPAGRLDRDSEGLLLLTDDGALQARIAHPKFRKPKTYLVQVEGDPTDDQLAQLRRGVSLN 97

Query: 169 GICYGDMQVTLDT--------------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                   V                  +   +AW+ + + EG+NR+++++         R
Sbjct: 98  DGPTRPATVRRLPPPDLWPRVPPVRFRKSVPDAWLELTITEGRNRQVRRMTAHVGLPCLR 157

Query: 215 LIRISYGPFQLGTLLAGSTREV 236
           L+R S G + +  L  G  R +
Sbjct: 158 LVRWSIGDWSVAGLAPGEWRGL 179


>gi|229175257|ref|ZP_04302772.1| RNA pseudouridine synthase [Bacillus cereus MM3]
 gi|228608089|gb|EEK65396.1| RNA pseudouridine synthase [Bacillus cereus MM3]
          Length = 84

 Score = 86.0 bits (211), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 19/82 (23%), Positives = 36/82 (43%), Gaps = 4/82 (4%)

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           +  G+ I+       +VT        +   + L +G NR+I+++   F + V +L R+  
Sbjct: 1   MSSGVKIKDGMTKPCKVTRV----DQSTFRIVLTQGMNRQIRRMSRAFGFTVTKLKRVRI 56

Query: 221 GPFQLGTLLAGSTREVSKKILR 242
              +L  L  G  R V+ + L 
Sbjct: 57  LNIELDDLEVGKWRSVTFEELD 78


>gi|89073382|ref|ZP_01159906.1| putative pseudouridine synthase family 1 protein [Photobacterium
           sp. SKA34]
 gi|89050869|gb|EAR56343.1| putative pseudouridine synthase family 1 protein [Photobacterium
           sp. SKA34]
          Length = 216

 Score = 86.0 bits (211), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 51/188 (27%), Positives = 84/188 (44%), Gaps = 16/188 (8%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
             P R     ++ L++KP   +T  S   G ST+ D +P     V   GRLD ++EGLL+
Sbjct: 24  NKPKRSRGPQKIILFNKPFNTLTQFSGEPGDSTLADFIP--VKDVYPAGRLDKDSEGLLV 81

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-------- 175
           LTNDG L   L  P ++  +VY V+  G   +  L  L+ G+ ++               
Sbjct: 82  LTNDGVLQARLTQPKSKQAKVYWVQVEGAPTETNLQALRDGVELKDGMTLPAGVEVIESP 141

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ + L+EG+NR+++++         RLIR     + +  L 
Sbjct: 142 IVWDRNPPIRERKNIPTTWLAITLKEGRNRQVRRMTAHIGHPTLRLIRYQMAQWTVSDLA 201

Query: 230 AGSTREVS 237
            G  REV+
Sbjct: 202 PGEWREVT 209


>gi|326623646|gb|EGE29991.1| RNA pseudouridine synthase family protein [Salmonella enterica
           subsp. enterica serovar Dublin str. 3246]
          Length = 172

 Score = 86.0 bits (211), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 40/146 (27%), Positives = 66/146 (45%), Gaps = 15/146 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LTNDG L   L  P  +  ++Y V+  G  D   L  L+ G+ + 
Sbjct: 24  YAAGRLDRDSEGLLVLTNDGALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLN 83

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +    +W+ V L EG+NR+++++         
Sbjct: 84  DGPTLPAGIEIVAEPDWLWPRTPPIRERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTL 143

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKK 239
           RLIR S G + L  L  G   E++++
Sbjct: 144 RLIRYSMGDYTLNGLDNGQWCEIAQE 169


>gi|254293970|ref|YP_003059993.1| pseudouridine synthase [Hirschia baltica ATCC 49814]
 gi|254042501|gb|ACT59296.1| pseudouridine synthase [Hirschia baltica ATCC 49814]
          Length = 185

 Score = 86.0 bits (211), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 37/148 (25%), Positives = 71/148 (47%), Gaps = 15/148 (10%)

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
                  V + GRLD ++EGLL+LT+DG L   +  PS +  + Y V+  G  D+  L+L
Sbjct: 32  HFIDVPNVYAAGRLDKDSEGLLVLTDDGKLQHRISDPSNKMEKSYWVQVEGIPDETALDL 91

Query: 161 LKKGIVIQGICYGDMQVTLD---------------TQKGSNAWVTVGLREGKNREIKKVF 205
           L+ G++++       +V L                 +   ++W+ + + EG+NR+++++ 
Sbjct: 92  LRAGVLLKDGMTKPAKVKLMDQPVDLWVREPPVRYRKSVPDSWIEITISEGRNRQVRRMT 151

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGST 233
               +   RLIR   G + +  + +G  
Sbjct: 152 ACVGFPTLRLIRYRVGNWTIDGIESGDW 179


>gi|144897678|emb|CAM74542.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Magnetospirillum
           gryphiswaldense MSR-1]
          Length = 195

 Score = 86.0 bits (211), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 45/181 (24%), Positives = 78/181 (43%), Gaps = 16/181 (8%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             RL L++KP  ++T  +D +       +       V   GRLD ++EGLL+L++DG L 
Sbjct: 1   MPRLILFNKPYDVLTQFTDREAGRATLAD-YVDVPGVYPAGRLDRDSEGLLVLSDDGPLI 59

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------Q 176
             +  P  +  + Y  +  G      L  L++G++++                       
Sbjct: 60  ARIAQPRHKLAKTYFAQVEGIPTAAALAQLRQGVMLKDGPTLTAGAELVAEPDWLWPRHP 119

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                     AWV + L EG+NR+++++     +   RLIR + G + L  L  G  REV
Sbjct: 120 PIRWRAAIPTAWVKLTLHEGRNRQVRRMTAAVGFPTLRLIRWAVGDWNLAGLAPGQWREV 179

Query: 237 S 237
           +
Sbjct: 180 T 180


>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 = 86.0 bits (211), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 32/240 (13%), Positives = 68/240 (28%), Gaps = 35/240 (14%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---- 63
           ++    +R+   +A     SR  ++++I +  V VNG  ++  +  V   D + V+    
Sbjct: 12  EKEDEGKRIDVFLASELDYSRSYIKKLIEEGLVLVNGKNVK-PSYKVKEDDEVVVNIPEA 70

Query: 64  --------GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
                    +PL     +   + +      +V         + V   L    +     G 
Sbjct: 71  EKIEVVPENIPLDILYEDEDIIVINKPQGMVVHPAPGNYSGTLVNALLYHCKNLSGINGI 130

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------------------ 155
           L       L     G +       +   L                               
Sbjct: 131 LRPGIVHRLDKDTSGVMVVAKNDKAHMSLSNQIKERSVLKKYVAIVEGVIKEEEGKIEAP 190

Query: 156 --DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                   K+  V+Q   Y      +  +  +N +V   ++ G+  +I+  F +    V 
Sbjct: 191 IGRHPVDRKRMAVVQDGRYALTLYKVLERFKNNTFVEATIKTGRTHQIRVHFSYIGHPVV 250


>gi|329894884|ref|ZP_08270683.1| Ribosomal large subunit pseudouridine synthase E [gamma
           proteobacterium IMCC3088]
 gi|328922613|gb|EGG29948.1| Ribosomal large subunit pseudouridine synthase E [gamma
           proteobacterium IMCC3088]
          Length = 209

 Score = 86.0 bits (211), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 39/139 (28%), Positives = 67/139 (48%), Gaps = 14/139 (10%)

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD ++EGLL+LT+ G L   L  P     + Y V+  GQ+D+  +  L+ G+ ++   
Sbjct: 39  GRLDSDSEGLLVLTSYGRLQAYLTAPKHNTWKYYYVQVEGQIDEQAVCRLQAGVQLKDGP 98

Query: 172 YGDMQVTLD--------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
               +V +                     +W+ +GL+EG+NR+I+++     +   RL+R
Sbjct: 99  TLPARVKVIEPPSLWQRTPPVRYRAHIPTSWLEIGLQEGRNRQIRRMTAHVGYPTLRLVR 158

Query: 218 ISYGPFQLGTLLAGSTREV 236
              GPF+L  L  G    +
Sbjct: 159 FRSGPFKLADLGPGEYVRI 177


>gi|317491859|ref|ZP_07950294.1| RNA pseudouridylate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316920293|gb|EFV41617.1| RNA pseudouridylate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 207

 Score = 86.0 bits (211), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 42/143 (29%), Positives = 66/143 (46%), Gaps = 15/143 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LTNDG L   L  P  +  +VY V+  G  D   L   ++G+ ++
Sbjct: 63  YAAGRLDRDSEGLLVLTNDGKLQAQLTQPGQKTGKVYYVQVEGVPDDAALAQFRQGLELK 122

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +    AW+ V L EG+NR+++++     +   
Sbjct: 123 DGMTLPAGIEIVAEPEWLWPRNPPIRERKSIPTAWIKVILFEGRNRQVRRMTAHIGFPTL 182

Query: 214 RLIRISYGPFQLGTLLAGSTREV 236
           RLIR S G + L  L  G  RE+
Sbjct: 183 RLIRYSMGDYTLDNLANGEWREM 205


>gi|83953590|ref|ZP_00962311.1| RNA pseudouridylate synthase [Sulfitobacter sp. NAS-14.1]
 gi|83841535|gb|EAP80704.1| RNA pseudouridylate synthase [Sulfitobacter sp. NAS-14.1]
          Length = 187

 Score = 86.0 bits (211), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 42/180 (23%), Positives = 79/180 (43%), Gaps = 17/180 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGG 129
             R+ L++KP G+++  +D     +    L            GRLD ++EGL++LT+ G 
Sbjct: 1   MNRVILFNKPFGVLSQFTDKGTEGSPRPTLSAYIDEKGFYPAGRLDRDSEGLMVLTDSGP 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------- 180
           L   +  P  +  + Y V+  G  D+  L  L+ G+ ++       +  L          
Sbjct: 61  LQARISHPKYKLAKTYWVQVEGTPDEQALAALRSGVTLKDGKTAPARARLMDPPDPLWDR 120

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +   +AW+ + + EG+NR+++++         RLIR   G ++L  L  G+ R
Sbjct: 121 DPPVRFRKSVPDAWLEITITEGRNRQVRRMTAHVGLPTLRLIRARVGDWELHKLQPGAWR 180


>gi|163748446|ref|ZP_02155700.1| RNA pseudouridine synthase family protein [Shewanella benthica
           KT99]
 gi|161332024|gb|EDQ02701.1| RNA pseudouridine synthase family protein [Shewanella benthica
           KT99]
          Length = 210

 Score = 85.6 bits (210), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 37/186 (19%), Positives = 73/186 (39%), Gaps = 17/186 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                  ++     L     +      +   L    + ++++GRLD ++EGLLLLT DG 
Sbjct: 20  EPHRHFKIFKPHGFLSQFVPETRKSKKLLGELALFPTGIMAIGRLDHDSEGLLLLTTDGM 79

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQ----------- 176
           ++  +     +     +V      +      L   I I+G        +           
Sbjct: 80  VSHRVRSKKVEKEYYVQVDGDIDDEAIIRLRLGVEIGIKGEKYLTLPCKVFKLDGEPELP 139

Query: 177 ----VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  D + G  +W+++ + EGKNR+I+K+    ++   RL+R+  G   L  +  G 
Sbjct: 140 SNGRKIRDPRHGPMSWISITISEGKNRQIRKMTAAADFPTMRLVRVRIGNIMLDNMQPGK 199

Query: 233 TREVSK 238
             E+++
Sbjct: 200 VIELTE 205


>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 = 85.6 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 33/247 (13%), Positives = 68/247 (27%), Gaps = 37/247 (14%)

Query: 3   DKNIVQ--ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           DK ++Q  +    +R+   +A     +R  ++++I    V VNG  ++  +  V   D +
Sbjct: 5   DKIVLQGEKEDEGKRIDVFLAAELDYTRSYIKKLIVDGLVFVNGKTVK-PSYKVKENDEV 63

Query: 61  EVD------------GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
            V+             +PL     +   + +      +V         + V   L    +
Sbjct: 64  VVNIPEAEKIDVLPENIPLDILYEDDDIIVINKPQGMVVHPAPGNYSGTLVNALLYHCKN 123

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ----------- 155
                G L       L     G +       +   L                        
Sbjct: 124 LSGINGILRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIKERSVFKKYVAIVEGVIKHE 183

Query: 156 ---------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          KK  VI+   Y      +  +   N  +   ++ G+  +I+    
Sbjct: 184 EGKIEALIGRHPVDRKKMAVIEDGRYALTLYKVLERFKENTLIEAVIKTGRTHQIRVHMA 243

Query: 207 FFNWKVN 213
           +    V 
Sbjct: 244 YIGHPVV 250


>gi|146311304|ref|YP_001176378.1| ribosomal large subunit pseudouridine synthase E [Enterobacter sp.
           638]
 gi|145318180|gb|ABP60327.1| ribosomal large subunit pseudouridine synthase E [Enterobacter sp.
           638]
          Length = 217

 Score = 85.6 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 49/184 (26%), Positives = 87/184 (47%), Gaps = 17/184 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               R+ L++KP  ++   +D  GRST+ D +P       + GRLD ++EGLL+LTNDG 
Sbjct: 36  NPPKRVILFNKPYDVLPQFTDEAGRSTLKDFIPVQGV--YAAGRLDRDSEGLLVLTNDGA 93

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-------------- 175
           L   L  P  +  ++Y V+  G+   + L  L+ G+ +                      
Sbjct: 94  LQASLTQPGKRTGKIYYVQVEGEPTDETLAALRHGVELNDGPTLPAGVERVSEPEWLWPR 153

Query: 176 -QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + +    AW+ + L EG+NR+++++     +   RLIR + G + L +L  G  R
Sbjct: 154 NPPIRERKSIPTAWLKITLYEGRNRQVRRMTAHVGYPTLRLIRYAMGHYTLDSLANGEWR 213

Query: 235 EVSK 238
           + ++
Sbjct: 214 DATE 217


>gi|221134863|ref|ZP_03561166.1| pseudouridine synthase, Rsu [Glaciecola sp. HTCC2999]
          Length = 196

 Score = 85.6 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 36/184 (19%), Positives = 70/184 (38%), Gaps = 14/184 (7%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
              +R     +  +              D               + + GRLD ++EGLL+
Sbjct: 10  NKRVRHTNNEKKLVVLFNKPFNVLTQFTDQAGRQTLKDYIDIPNIYAAGRLDRDSEGLLV 69

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ------- 176
           LTNDG L   L  P+ +  + Y V+  G +  + +  L  G+ ++       +       
Sbjct: 70  LTNDGKLQHALAHPTQKTTKTYWVQVEGDITDEAIEQLSNGVNLKDGMTAPAKVEKMAAP 129

Query: 177 -------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     +      +WV++ + EG+NR+++++    N+   RLIR   G + +  + 
Sbjct: 130 AIWPRTPPIRERASIPTSWVSITISEGRNRQVRRMTAHVNYPTLRLIRYRVGQWTIDNIA 189

Query: 230 AGST 233
            G  
Sbjct: 190 NGEF 193


>gi|308049703|ref|YP_003913269.1| ribosomal large subunit pseudouridine synthase E [Ferrimonas
           balearica DSM 9799]
 gi|307631893|gb|ADN76195.1| ribosomal large subunit pseudouridine synthase E [Ferrimonas
           balearica DSM 9799]
          Length = 214

 Score = 85.6 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 49/191 (25%), Positives = 87/191 (45%), Gaps = 17/191 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P R  E  R+ L++KP  +++  +D   R+T+ D +        + GRLD ++EGLLLL
Sbjct: 25  RPDRPREARRIVLFNKPFDVLSQFTDGGNRATLADYIQEPGV--YAAGRLDRDSEGLLLL 82

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TNDG L   L  P  +  + Y V+  G+ D+  L  L+ G+ +        +        
Sbjct: 83  TNDGALQAKLTQPGKKTSKTYYVQVEGEPDEAALQALRDGVTLNDGPTLPAKVERIDEPH 142

Query: 177 -------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+++ + EG+NR+++++     +   RLIR   G + L  L 
Sbjct: 143 WLWPRNPPIRERKAIPTSWLSISIIEGRNRQVRRMTAHIGYPTLRLIRYRIGSWTLDGLA 202

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 203 NGEYRVLHGNE 213


>gi|58584154|ref|YP_203170.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae KACC10331]
 gi|188579145|ref|YP_001916074.1| ribosomal large subunit pseudouridine synthase E [Xanthomonas
           oryzae pv. oryzae PXO99A]
 gi|58428748|gb|AAW77785.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae KACC10331]
 gi|188523597|gb|ACD61542.1| ribosomal large subunit pseudouridine synthase E [Xanthomonas
           oryzae pv. oryzae PXO99A]
          Length = 200

 Score = 85.6 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 46/175 (26%), Positives = 80/175 (45%), Gaps = 15/175 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L +KP G+++  SD             +   V + GRLD ++EGLLLLT+DG LA  +
Sbjct: 12  LVLLNKPYGVLSQFSDRSQPPKRTLAEFGLPPDVYAAGRLDHDSEGLLLLTDDGALAHRV 71

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------VTL 179
             P  +  + Y V+  G+    +L  L+ G+V+        Q                  
Sbjct: 72  TDPRHKQPKTYWVQVEGEPQAGQLQALRDGVVLNDGPTRTAQVRSLDPAPPLWPREPPVR 131

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +   +AW+ + + EG+NR+++++         RL+R++ G ++L  L  G  R
Sbjct: 132 VRKTVPDAWLELRITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLDMLAPGQWR 186


>gi|163746241|ref|ZP_02153599.1| RNA pseudouridylate synthase [Oceanibulbus indolifex HEL-45]
 gi|161380126|gb|EDQ04537.1| RNA pseudouridylate synthase [Oceanibulbus indolifex HEL-45]
          Length = 188

 Score = 85.6 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 45/183 (24%), Positives = 83/183 (45%), Gaps = 17/183 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
           R+ L +KP G+++  +D     +    L +          GRLD ++EGLL+LT+ G L 
Sbjct: 4   RVILLNKPYGVLSQFTDKGTEGSSRPTLSTYIDEKGFYPAGRLDRDSEGLLVLTDHGPLQ 63

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------------- 176
             +  P  +  + Y V+  G  D   L  L+KG+ ++       +               
Sbjct: 64  ARIAHPKYKRPKTYLVQVEGTPDAAALEALRKGVDLKDGLTKPAEVDQIDAPETLWPRDP 123

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +   +AW+ + +REG+NR+++++    +    RLIR S G ++L  L  G+ R  
Sbjct: 124 PVRFRKTVPDAWLRITIREGRNRQVRRMTAHVDLPTLRLIRASVGDWELAGLQPGAWRWS 183

Query: 237 SKK 239
           ++ 
Sbjct: 184 TEN 186


>gi|291550526|emb|CBL26788.1| pseudouridine synthase family [Ruminococcus torques L2-14]
          Length = 194

 Score = 85.6 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 44/193 (22%), Positives = 78/193 (40%), Gaps = 26/193 (13%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               ++++KP G VT   D    + +          +  VGRLD  T GLLL+T+DG   
Sbjct: 1   MFHYYMFNKPFGCVTARRDSLYPTVMDYFSELNNDNLNPVGRLDRETTGLLLITDDGVFN 60

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWV 189
           + L  PS    + Y     G + +D+   L+KGI+++G        ++ +  Q   +  +
Sbjct: 61  QKLTHPSYHKEKTYHFTVLGDLTEDRCQQLEKGILLKGSPVLTSPAKLKVFRQDILSNII 120

Query: 190 -----------------------TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
                                   + + EG+ R+I+++ +  +  V  L RIS     L 
Sbjct: 121 DTLHPEVQNAVCHNLPTHPVTYGEITISEGRKRQIRRMMKAVHCCVIELKRISIEDIILD 180

Query: 227 T-LLAGSTREVSK 238
             L  G  +E+  
Sbjct: 181 ETLSPGEWKEIFP 193


>gi|303285788|ref|XP_003062184.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226456595|gb|EEH53896.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 244

 Score = 85.6 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 50/244 (20%), Positives = 97/244 (39%), Gaps = 33/244 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI------EVDGVPLR 68
           R+ K +A+ G+ASRR  E +I   RV VNG+++     +V+  D +       + G    
Sbjct: 1   RLGKALAQLGVASRRASEDLIFAGRVAVNGVVVTAPQHHVVLADDVVAVDGKVIQGGVEE 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRS------------------------TVFDNLPSI 104
             E     L      +      P+                               +   +
Sbjct: 61  TREHLYFLLNKPKGYICANAKSPNKPPGKGERGGGASGKLVMDLFDEWKAAWRKKHPKRL 120

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
             R+ +VGRLD+NT G+LL+T DG   + +  P ++ ++ Y +    +  + ++  +  G
Sbjct: 121 PPRLFTVGRLDVNTTGMLLVTTDGQWCQRVAHPKSEVVKSYVLTASARPTKAQIRAMAAG 180

Query: 165 IVIQGICYGDM---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             + G     +    +  D   G    V V + +G+NRE++++         +L R+  G
Sbjct: 181 AEVDGAFVKPVNVRSMDNDRDGGPPNRVLVEVVDGRNREVRQLASSAGVDCKKLKRVRVG 240

Query: 222 PFQL 225
             ++
Sbjct: 241 GLRM 244


>gi|157146080|ref|YP_001453399.1| hypothetical protein CKO_01836 [Citrobacter koseri ATCC BAA-895]
 gi|157083285|gb|ABV12963.1| hypothetical protein CKO_01836 [Citrobacter koseri ATCC BAA-895]
          Length = 217

 Score = 85.6 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 49/189 (25%), Positives = 86/189 (45%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
              ++ +  R+ L++KP  ++   +D  GRST+ D +P       + GRLD ++EGLL+L
Sbjct: 31  KRRKENQPKRVVLFNKPYDVLPQFTDEAGRSTLKDYIPVQGV--YAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TNDG L   L  P  +  ++Y V+  G+   + L  L+ G+ +                 
Sbjct: 89  TNDGALQARLTQPGKRTGKIYYVQVEGEPTAEALEALRNGVTLNDGPTLPAGIEVVDEPE 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ V L EG+NR+++++         RLIR + G + L  L 
Sbjct: 149 WLWPRTPPIRERKSIPTRWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYAMGNYTLDNLA 208

Query: 230 AGSTREVSK 238
            G  R+ + 
Sbjct: 209 NGEWRDATD 217


>gi|27365449|ref|NP_760977.1| ribosomal large subunit pseudouridine synthase E [Vibrio vulnificus
           CMCP6]
 gi|37680510|ref|NP_935119.1| pseudouridine synthase family 1 protein [Vibrio vulnificus YJ016]
 gi|34098533|sp|Q8DAS3|RLUE_VIBVU RecName: Full=Ribosomal large subunit pseudouridine synthase E;
           AltName: Full=rRNA pseudouridylate synthase E; AltName:
           Full=rRNA-uridine isomerase E
 gi|27361597|gb|AAO10504.1| Ribosomal large subunit pseudouridine synthase E [Vibrio vulnificus
           CMCP6]
 gi|37199258|dbj|BAC95090.1| pseudouridine synthase family 1 protein [Vibrio vulnificus YJ016]
          Length = 234

 Score = 85.6 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 44/187 (23%), Positives = 77/187 (41%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L  AER  +        L         ++            V + GRLD ++EGL++L
Sbjct: 48  KSLSLAERKIIIFNKPYDTLSQFTDGEGRKTLADFI---PVKEVYAAGRLDRDSEGLMVL 104

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   + +L  L++G+ ++       QV +     
Sbjct: 105 TNDGILQAKLTQPKSKSPKTYWVQVEGAPTEAQLEPLRRGVELKDGLTLPAQVEIIQDPQ 164

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + + EG+NR+++++     +   RL+R S G   L  L  
Sbjct: 165 LWERNPPVRFRAAIPTTWLAITIIEGRNRQVRRMTAHIGFPTLRLVRYSMGGMTLQDLQP 224

Query: 231 GSTREVS 237
           G  +E+S
Sbjct: 225 GEWKEIS 231


>gi|163751229|ref|ZP_02158457.1| ribosomal large subunit pseudouridine synthase E [Shewanella
           benthica KT99]
 gi|161328943|gb|EDQ00017.1| ribosomal large subunit pseudouridine synthase E [Shewanella
           benthica KT99]
          Length = 239

 Score = 85.6 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 49/186 (26%), Positives = 87/186 (46%), Gaps = 16/186 (8%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             A+   + L++KP  ++   +D  GR T+ D +      V + GRLD ++EGLLLLTND
Sbjct: 53  PAAKDPVILLFNKPFDVLCQFTDEQGRKTLKDFIA--VKDVYAAGRLDRDSEGLLLLTND 110

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--------- 178
           G L   +  P+ +  + Y V+  G  DQ  L  L+ G+ ++       ++T         
Sbjct: 111 GKLQSKITEPNKRTFKTYWVQVEGTPDQADLQALRDGVKLKDGMTLPAKITSISEPKVWD 170

Query: 179 -----LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 + +     W+ + + EG+NR+++++     +   RLIR   G + L  +  G  
Sbjct: 171 REPPIRERKNIPTTWLEIQICEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDDIDIGQY 230

Query: 234 REVSKK 239
           R +  K
Sbjct: 231 RILDMK 236


>gi|126661900|ref|ZP_01732899.1| RNA pseudouridine synthase family protein [Flavobacteria bacterium
           BAL38]
 gi|126625279|gb|EAZ95968.1| RNA pseudouridine synthase family protein [Flavobacteria bacterium
           BAL38]
          Length = 188

 Score = 85.6 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 41/187 (21%), Positives = 75/187 (40%), Gaps = 21/187 (11%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                 ++     L     +      +   L       +++GRLD ++EGLLLLT DG +
Sbjct: 1   MHHHFLIHKPYGYLSQFIYELKRPKKLLGELYDFPGNTMAIGRLDEDSEGLLLLTTDGMM 60

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDM----------- 175
           + ++     +  + Y  +  G + ++ +  LK  + I    +                  
Sbjct: 61  SEIVRSK--KVEKEYYAQVDGLITEEAIEKLKNRVEIGFNGKKYLTKKCNAFILETIPNL 118

Query: 176 ----QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
               +   D + G  +WV++ L EGK R+++K+     +   RL+R+  G   L  L AG
Sbjct: 119 GERGKKIRDERHGPTSWVSITLTEGKFRQVRKMTSAVGFPTLRLVRVRVGNIHLNDLKAG 178

Query: 232 STREVSK 238
              EVS 
Sbjct: 179 EVLEVSG 185


>gi|94311828|ref|YP_585038.1| ribosomal large subunit pseudouridine synthase E [Cupriavidus
           metallidurans CH34]
 gi|93355680|gb|ABF09769.1| 23S rRNA pseudouridine synthase [Cupriavidus metallidurans CH34]
          Length = 214

 Score = 85.6 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 44/206 (21%), Positives = 74/206 (35%), Gaps = 17/206 (8%)

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
                T        S            V   GRLD ++EGLLLLT+DG L   +  P  +
Sbjct: 7   NKPYQTMSQFSAHPSRATLADCVDVPGVYPAGRLDADSEGLLLLTDDGALQARIADPRHK 66

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ---------------KGS 185
            ++ Y  +  G  D+  L  L+ G+ +        +  +  +                  
Sbjct: 67  LVKTYLAQVEGVPDEAALATLRTGVDLGDFKTLPAKARVVDEPAWLWERHPPIRYRAAIP 126

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKILRE 243
             W+ + +REGKNR+++++         RL+RIS G  +L    L+ G   E     L  
Sbjct: 127 TTWIELSIREGKNRQVRRMTAAVGLPTLRLVRISIGNLKLPELGLMPGQWCETDVSRLGL 186

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVR 269
             G   +  A+         +    +
Sbjct: 187 SSGNPHVSTARPERAPTSGPARRSYK 212


>gi|156934379|ref|YP_001438295.1| hypothetical protein ESA_02210 [Cronobacter sakazakii ATCC BAA-894]
 gi|156532633|gb|ABU77459.1| hypothetical protein ESA_02210 [Cronobacter sakazakii ATCC BAA-894]
          Length = 218

 Score = 85.2 bits (209), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 50/190 (26%), Positives = 87/190 (45%), Gaps = 17/190 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
              +     RL L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLL+L
Sbjct: 31  KRRKPEGPKRLILFNKPYDVLPQFTDEAGRQTLKDFIPVAGV--YAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TNDG L   L  P  +  ++Y V+  G+  +  L  L+ G+ +                 
Sbjct: 89  TNDGALQAKLTQPGKRTGKIYFVQVEGEPTEAALAQLRSGVTLNDGPTLPAGVERVEEPA 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L +L 
Sbjct: 149 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDSLA 208

Query: 230 AGSTREVSKK 239
            G  R+V  K
Sbjct: 209 CGQWRDVPLK 218


>gi|260597505|ref|YP_003210076.1| ribosomal large subunit pseudouridine synthase E [Cronobacter
           turicensis z3032]
 gi|260216682|emb|CBA30036.1| Ribosomal large subunit pseudouridine synthase E [Cronobacter
           turicensis z3032]
          Length = 218

 Score = 85.2 bits (209), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 53/190 (27%), Positives = 88/190 (46%), Gaps = 17/190 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
              +     RL L++KP  ++   +D  GR T+ D +P   + V + GRLD ++EGLL+L
Sbjct: 31  KRRKPEGPKRLILFNKPYDVLPQFTDEAGRQTLKDFIP--VADVYAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TNDG L   L  P  +  +VY V+  G+   + L  L+ G+ +                 
Sbjct: 89  TNDGALQAKLTQPGKRTGKVYFVQVEGEPTDEALAQLRTGVTLNDGPTLPAGVERVAEPA 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 149 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYATGDYTLDALA 208

Query: 230 AGSTREVSKK 239
            G  REV  K
Sbjct: 209 CGQWREVPLK 218


>gi|222110563|ref|YP_002552827.1| pseudouridine synthase [Acidovorax ebreus TPSY]
 gi|221730007|gb|ACM32827.1| pseudouridine synthase [Acidovorax ebreus TPSY]
          Length = 216

 Score = 85.2 bits (209), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 44/179 (24%), Positives = 79/179 (44%), Gaps = 17/179 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP G+++  +       + D +          GRLD ++EGLLLLT+DG L   +
Sbjct: 30  LLRFNKPYGVLSQFTPEGRWRGLQDFIDVPGV--YVAGRLDADSEGLLLLTDDGALQARI 87

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y V+  G  D+  L  L++G+ +        +V                 
Sbjct: 88  SDPRHKMEKTYWVQVEGIPDEAALQALRQGVQLGDGPTLPARVRRLEPPPALWERDPPIR 147

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
             Q   + W+ + +REG+NR+++++         RL+R + GP+ L  L  G  +  S 
Sbjct: 148 VRQNIPDCWIELIIREGRNRQVRRMTAAVGHPTLRLVRAAIGPYALDGLEPGCWQPASP 206


>gi|332288598|ref|YP_004419450.1| 23S rRNA pseudouridine synthase E [Gallibacterium anatis UMN179]
 gi|330431494|gb|AEC16553.1| 23S rRNA pseudouridine synthase E [Gallibacterium anatis UMN179]
          Length = 223

 Score = 85.2 bits (209), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 45/199 (22%), Positives = 91/199 (45%), Gaps = 20/199 (10%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P  + E+ ++ L++KP  ++T  +D  GR T+ + +      +   GRLD ++EGLLLL
Sbjct: 18  KPKLQLEQIKVVLFNKPYDVLTQFTDEQGRKTLKNFIHIP--DIYPCGRLDRDSEGLLLL 75

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TN G +   L  P+ +  + Y V+  G   +  L  L++G++++                
Sbjct: 76  TNCGEIQHRLTTPAFKSKKTYWVQVEGVPSEQDLEALRQGVILKDGKTLPALVKFIPPPQ 135

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-- 227
                     + +    +W+ + + EG+NR+++++     +   RLIRI+     L    
Sbjct: 136 NLWQRDPPIRERKTIPTSWLEIAIHEGRNRQVRRMTAHIGYPTLRLIRIATAGLNLFDFP 195

Query: 228 -LLAGSTREVSKKILREQL 245
            L  G +  ++   + + L
Sbjct: 196 QLQLGCSYSLNSNEIEQLL 214


>gi|270159867|ref|ZP_06188523.1| ribosomal large subunit pseudouridine synthase E [Legionella
           longbeachae D-4968]
 gi|289165378|ref|YP_003455516.1| 23S rRNA pseudouridine synthase [Legionella longbeachae NSW150]
 gi|269988206|gb|EEZ94461.1| ribosomal large subunit pseudouridine synthase E [Legionella
           longbeachae D-4968]
 gi|288858551|emb|CBJ12432.1| 23S rRNA pseudouridine synthase [Legionella longbeachae NSW150]
          Length = 183

 Score = 85.2 bits (209), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 38/177 (21%), Positives = 65/177 (36%), Gaps = 17/177 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               +        +     +    +              + GRLD N+EGLLLLT+ G L
Sbjct: 1   MPQIVLFNKPYGVVSQFSGEEHEHTLAAFI---DIPNFYAAGRLDKNSEGLLLLTDSGAL 57

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------------Q 176
              L  P     + Y V+  G      L++L+ G+V++ I +                  
Sbjct: 58  QHRLTAPKFNKRKYYWVQVEGTPCNQDLDILRNGLVLKDISFLPAGARLIDEPHLWPRNP 117

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                +    +W+ + L EGKN +I+K+     +   RL+R     ++L  L  G  
Sbjct: 118 PIRFRKNIPTSWLEIILSEGKNHQIRKMTAAIGFPTLRLVRHRISDWRLDNLQPGEY 174


>gi|290510858|ref|ZP_06550228.1| ribosomal large subunit pseudouridine synthase E [Klebsiella sp.
           1_1_55]
 gi|289777574|gb|EFD85572.1| ribosomal large subunit pseudouridine synthase E [Klebsiella sp.
           1_1_55]
          Length = 216

 Score = 85.2 bits (209), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 42/199 (21%), Positives = 75/199 (37%), Gaps = 18/199 (9%)

Query: 52  VNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
             V      +V      +  +T +        L     +    +          + V + 
Sbjct: 19  HRVERFSTQQVTRQRKERQPKTVILFNKPYDVLPQFTDEAGRSTLKDFI---PVAGVYAA 75

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD ++EGLL+LTNDG L   L  P  +  ++Y V+  G+   + L  L+ G+ +    
Sbjct: 76  GRLDRDSEGLLVLTNDGALQAKLTQPGKRTGKIYYVQVEGEPTAEALAALRNGVTLNDGP 135

Query: 172 YGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
                                  + +     W+ + L EG+NR+++++     +   RLI
Sbjct: 136 TLPAGVEVVEEPAWLWPRNPPIRERKSIPTCWLKITLYEGRNRQVRRMTAHVGFPTLRLI 195

Query: 217 RISYGPFQLGTLLAGSTRE 235
           R + G + L  L  G  R 
Sbjct: 196 RYAMGGYTLDGLANGEWRR 214


>gi|119503233|ref|ZP_01625317.1| pseudouridylate synthase [marine gamma proteobacterium HTCC2080]
 gi|119460879|gb|EAW41970.1| pseudouridylate synthase [marine gamma proteobacterium HTCC2080]
          Length = 208

 Score = 85.2 bits (209), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 38/136 (27%), Positives = 65/136 (47%), Gaps = 14/136 (10%)

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD ++EGL LLT+DG L + +  P  +  + Y V+  G   Q  +  L  G+V+    
Sbjct: 64  GRLDYDSEGLTLLTDDGKLQQQIANPKFKVWKTYWVQVEGAPKQQAIEQLTSGVVLNDGL 123

Query: 172 YGDMQVTLDTQ--------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
               +V                      +AW+ + ++EG+NR+I+++    N    RL+R
Sbjct: 124 TKPAKVRAIDPPDLWERSPSVRFRAHIPDAWLEISIQEGRNRQIRRMTAAVNLPTLRLVR 183

Query: 218 ISYGPFQLGTLLAGST 233
           I+ G +++G L  G  
Sbjct: 184 IAIGDWEIGNLQPGEY 199


>gi|171909920|ref|ZP_02925390.1| Pseudouridine synthase, Rsu [Verrucomicrobium spinosum DSM 4136]
          Length = 189

 Score = 84.8 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 37/182 (20%), Positives = 77/182 (42%), Gaps = 19/182 (10%)

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           +     L     +     T+ +    + + V  +GRLD ++EGLLLL+++    + L  P
Sbjct: 6   HKPYGVLSQFTKEHPSHRTLAEF--GLPAGVYPIGRLDSDSEGLLLLSDEARWNQQLLHP 63

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------VTLDTQ 182
           +    R Y V+  G    + +  L +G+ +        +                  + +
Sbjct: 64  TRGHERTYHVQVEGIPTAEAITRLTRGVQLPDFYTLACKVQLLEPAPLYPARVPPIRERK 123

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKI 240
               +W+ + L EGKNR+++++     +   RLIR + G  +L    L  G  +E+++  
Sbjct: 124 SIPTSWLAMKLVEGKNRQVRRMTAAVGYPTLRLIRAAMGRLELARLDLEPGKWQELTEGQ 183

Query: 241 LR 242
           ++
Sbjct: 184 IK 185


>gi|326692342|ref|ZP_08229347.1| ribosomal large subunit pseudouridine synthase E [Leuconostoc
           argentinum KCTC 3773]
          Length = 177

 Score = 84.8 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 44/178 (24%), Positives = 82/178 (46%), Gaps = 17/178 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP  ++T  +D DGR T+ D +        + GRLD+++EGLLLLT+ G L   L
Sbjct: 2   IVLFNKPYNVLTKFTDADGRPTLADYIDIPRV--YAAGRLDMDSEGLLLLTDSGKLNHAL 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT------------- 181
             P  +  + Y V+  G   + +L  L+ G+ ++       +                  
Sbjct: 60  TDPENKAYKTYVVQVEGVPTKAQLKQLENGVELKDGWTLPAKAKRIPYPKWLWPRENPIR 119

Query: 182 --QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             +    +++ + ++EG+NR+++++         RLIR   G + L  L  G  R + 
Sbjct: 120 VRKNQPTSFIQLKIKEGRNRQVRRMTAAVGLPTLRLIRTHIGDYHLADLKPGEYRVIK 177


>gi|262372034|ref|ZP_06065313.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter junii
           SH205]
 gi|262312059|gb|EEY93144.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter junii
           SH205]
          Length = 267

 Score = 84.8 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 51/255 (20%), Positives = 94/255 (36%), Gaps = 41/255 (16%)

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD+++EGL+ LT+ GGL + +  P+ +  + Y  +  G V ++ L  L+KG+ +    
Sbjct: 38  GRLDLDSEGLMFLTDHGGLNQYITNPTNKKFKTYLAQVDGDVTEEALEQLRKGVELADGM 97

Query: 172 YGDMQVTLDTQ---------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
               +     Q                   +W+ + + EG+NR+++++     +   RLI
Sbjct: 98  TLPAKAIKVDQPEWLWDRDPPVRFRANIPTSWIELQICEGRNRQVRRMTAAVGFPTLRLI 157

Query: 217 RISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIIS 276
           R   G   L               +R  L P   +E +  L             R     
Sbjct: 158 RTKIGAIDL---------------VRLGLQPGEQKEIEPLLYPDFKDLPEDKPYRSRSYV 202

Query: 277 EVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR 336
           + P        +  +K G  K      P  +++    +W          S+  +R+ N  
Sbjct: 203 KKPGGTGGKPMHQKKKEGDKKD-----PNKKKSGTKRIWQ------MDESEKPRRKTNGT 251

Query: 337 RSPSFPSKRSLRRTS 351
             P+  + R   R S
Sbjct: 252 TRPNTKAPRGRSRNS 266


>gi|152978114|ref|YP_001343743.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
 gi|150839837|gb|ABR73808.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
          Length = 243

 Score = 84.8 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 49/185 (26%), Positives = 92/185 (49%), Gaps = 16/185 (8%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +T++ L++KP  ++T  +D  GR T+ D +P       + GRLD ++EGLL+LTN+G L 
Sbjct: 52  QTQVVLFNKPFDVLTQFTDESGRKTLKDFIPVPGI--YAAGRLDRDSEGLLILTNNGELQ 109

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------------V 177
             L  P  +  + Y V+  GQ  +  L  L++G+ ++       +               
Sbjct: 110 HRLANPKFKLPKTYWVQVEGQPTEADLERLRRGVELKDGMTKPAKVRSIAEPDLWQRVPP 169

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    AW+ + L EGKNR+++++     +   RL+R +     L  L +G  RE++
Sbjct: 170 IRERKNIPTAWLEIQLGEGKNRQVRRMTAHIGFPTLRLVRAATAGLTLHGLPSGQYRELT 229

Query: 238 KKILR 242
           +  ++
Sbjct: 230 ESEIK 234


>gi|84393764|ref|ZP_00992512.1| pseudouridine synthase family 1 protein [Vibrio splendidus 12B01]
 gi|84375626|gb|EAP92525.1| pseudouridine synthase family 1 protein [Vibrio splendidus 12B01]
          Length = 242

 Score = 84.8 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 49/188 (26%), Positives = 94/188 (50%), Gaps = 16/188 (8%)

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           +  P    E  ++ L++KP   ++  +D +GR T+ D +P     V + GRLD ++EGL+
Sbjct: 57  NMKPKVALEDRKVILFNKPFDTLSQFTDGEGRKTLADFIP--VKDVYAAGRLDRDSEGLM 114

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           +LTNDG     L  P+++  + Y V+  G   ++ L+ L+KG+ ++       Q+ + ++
Sbjct: 115 VLTNDGIFQAKLTQPNSKSPKTYWVQVEGAPSEEDLDKLRKGVELKDGMTLPAQIEVMSE 174

Query: 183 --------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                              W+ + + EG+NR+++++     +   RLIR S G   +G L
Sbjct: 175 PVVWERTPPVRFRAAIPTTWLAITIIEGRNRQVRRMTANIGFPTLRLIRYSMGNMNVGQL 234

Query: 229 LAGSTREV 236
             G  +E+
Sbjct: 235 QPGEWKEI 242


>gi|170727048|ref|YP_001761074.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169812395|gb|ACA86979.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 235

 Score = 84.8 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 49/190 (25%), Positives = 90/190 (47%), Gaps = 20/190 (10%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G  +       + L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLLL
Sbjct: 46  GKTVEP----VIVLFNKPFDVLCQFTDEQGRQTLKDFIPIPGV--YAAGRLDRDSEGLLL 99

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
           LTNDG L   L  P  +  + Y  +  G  D+ +L+LL+KG+ ++       ++++    
Sbjct: 100 LTNDGKLQSKLTEPKKKTFKTYWAQVEGAPDEAQLDLLRKGVELKDGMTLPAKISIMSQP 159

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ + + EG+NR+++++     +   RLIR   G + L  L 
Sbjct: 160 TVWERVPPIRERKAIPTTWLEIQICEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDDLS 219

Query: 230 AGSTREVSKK 239
            G  + +  K
Sbjct: 220 PGQYQSIDMK 229


>gi|157960587|ref|YP_001500621.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157845587|gb|ABV86086.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 197

 Score = 84.8 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 40/185 (21%), Positives = 67/185 (36%), Gaps = 17/185 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                  +Y     L     +      +   L     + +++GRLD ++EGLLLLT DG 
Sbjct: 10  QAHQHFLIYKPYGFLSQFVPETRKSKPLLGQLYDFPDKTMAIGRLDHDSEGLLLLTTDGM 69

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDM------------ 175
            + ++   S +     +V       Q         I I G                    
Sbjct: 70  QSHLIRSKSIEKEYYVQVDGLVSQAQLLQLQQGVEIGISGGKYLTLPCQVELLTTEPNLP 129

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
              +   D + G  +W++V + EGKNR+++K+         RL+R+  G   L  +  G 
Sbjct: 130 ARGKKIRDPRHGPTSWLSVTIAEGKNRQVRKMTAAVGLPTLRLVRVRIGHICLKQMQPGE 189

Query: 233 TREVS 237
              VS
Sbjct: 190 VLPVS 194


>gi|256423976|ref|YP_003124629.1| pseudouridine synthase [Chitinophaga pinensis DSM 2588]
 gi|256038884|gb|ACU62428.1| pseudouridine synthase [Chitinophaga pinensis DSM 2588]
          Length = 212

 Score = 84.8 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 47/186 (25%), Positives = 80/186 (43%), Gaps = 19/186 (10%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R +  +KP  +V+    PD    + D          +VGRLD N+EGLLLLT +  + R
Sbjct: 6   HRYFAINKPYNMVSQFISPDKVRLLGDLDFDFPEGTHAVGRLDNNSEGLLLLTTNKRVTR 65

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-----GICYGDMQVTLDTQKG--- 184
           +L        R Y V     V Q+ +  L+ G+ I+            +  +  +     
Sbjct: 66  LLFESEQPHKRAYLVMVKNIVTQETIEKLRNGVTIRIKGGVDWVTTPCEAEIVEKPAYIA 125

Query: 185 -----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                       ++W+ + L EGK  +++K+    +   +RLIR+S    +LG L  G  
Sbjct: 126 PREHHPVKEFLPHSWLLITLTEGKFHQVRKMTSAIHHHCDRLIRVSIEDMELGDLPPGGV 185

Query: 234 REVSKK 239
           RE+ ++
Sbjct: 186 REIEEE 191


>gi|209695641|ref|YP_002263570.1| ribosomal large subunit pseudouridine synthase E [Aliivibrio
           salmonicida LFI1238]
 gi|208009593|emb|CAQ79889.1| ribosomal large subunit pseudouridine synthase E [Aliivibrio
           salmonicida LFI1238]
          Length = 210

 Score = 84.8 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 48/187 (25%), Positives = 90/187 (48%), Gaps = 16/187 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E  ++ +++KP  +++  +D   R T+ D +      V + GRLD ++EGLL+L
Sbjct: 21  KPRPAPEDRKVLIFNKPFDVLSQFTDDQHRQTLADFIS--VKDVYAAGRLDRDSEGLLIL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +D L  L++G+ ++       +V + T+  
Sbjct: 79  TNDGVLQARLTQPESKSPKTYWVQVEGAPTEDDLEKLRQGVELKDGMTLPAKVEVMTEPE 138

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ V + EG+NR+++++     +   RLIR S G + +  +  
Sbjct: 139 LWERNPPVRFRAAIPTTWIAVTIIEGRNRQVRRMTAHIGFPTLRLIRYSMGDWTIKDVPH 198

Query: 231 GSTREVS 237
              +EV+
Sbjct: 199 REWKEVT 205


>gi|332993406|gb|AEF03461.1| ribosomal large subunit pseudouridine synthase E [Alteromonas sp.
           SN2]
          Length = 180

 Score = 84.8 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 34/139 (24%), Positives = 65/139 (46%), Gaps = 14/139 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LTNDG L   L  P  +  + Y V+  G  ++  L+ L+ G+ ++
Sbjct: 39  YAAGRLDRDSEGLLVLTNDGKLQHKLAHPEAKTSKTYWVQVEGIPNEAALDALRNGVELK 98

Query: 169 GICYGDMQVTLD--------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                  +V                  Q    +W+++ + EG+NR+++++     +   R
Sbjct: 99  DGMTKPAKVVAIDPPELWDRIPPVRFRQAIPTSWLSITISEGRNRQVRRMTAHIGFPTLR 158

Query: 215 LIRISYGPFQLGTLLAGST 233
           L+R   G + +  +  G  
Sbjct: 159 LVRYRVGNWTIDGIDNGKY 177


>gi|149917094|ref|ZP_01905594.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthase [Plesiocystis pacifica SIR-1]
 gi|149822010|gb|EDM81403.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthase [Plesiocystis pacifica SIR-1]
          Length = 210

 Score = 84.5 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 43/178 (24%), Positives = 85/178 (47%), Gaps = 16/178 (8%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ L++KP G+++  +  DG+ T+ + +        + GRLD ++EGLL+LT+DG L   
Sbjct: 3   KVVLFNKPCGVLSQFTAQDGQRTLAEFIDQPGV--YAAGRLDKDSEGLLVLTDDGALQHR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------------QVTL 179
           +  P    ++ Y  +  G      L+ L++G+ ++                         
Sbjct: 61  IASPRHASVKRYWAQVEGTPTNAALDALREGVELKDGWTRPAGARRLDAPPLWPRDPPIR 120

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + +    AW+ + L EG+NR+++++     +   RL+R S GP+ L  L  G  R ++
Sbjct: 121 ERKSIPTAWIELSLSEGRNRQVRRMTAAVGFPTLRLVRWSVGPWDLEGLAPGELRVIT 178


>gi|255037074|ref|YP_003087695.1| pseudouridine synthase [Dyadobacter fermentans DSM 18053]
 gi|254949830|gb|ACT94530.1| pseudouridine synthase [Dyadobacter fermentans DSM 18053]
          Length = 225

 Score = 84.5 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 45/187 (24%), Positives = 78/187 (41%), Gaps = 18/187 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             R ++ +KP  +V+          + +          +VGRLD  +EGLL+LT +  + 
Sbjct: 9   PHRYFIINKPPNMVSQFVSSHDVRLLGELDFDFPEGTHAVGRLDSMSEGLLILTTNKKVT 68

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-----GICYGDMQVTLDTQ---- 182
            +L L      R Y V     V  + + LL+ GI I+            +V +  +    
Sbjct: 69  NLLFLGEVPHTRTYWVNVGHIVPPETVQLLRTGIPIRVKGGGYYTTAPCEVEVIERPAIL 128

Query: 183 ---------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                       N W+++ L EGK  +++K+    N +  RL+R S    +LG L  G  
Sbjct: 129 PWHQSEGQPGVPNTWLSITLTEGKYHQVRKMVREANHRCKRLVRASIEDLELGDLPPGGV 188

Query: 234 REVSKKI 240
           RE+ ++ 
Sbjct: 189 REIGEEE 195


>gi|78213500|ref|YP_382279.1| pseudouridine synthase, Rsu [Synechococcus sp. CC9605]
 gi|78197959|gb|ABB35724.1| Pseudouridine synthase, Rsu [Synechococcus sp. CC9605]
          Length = 230

 Score = 84.5 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 45/196 (22%), Positives = 79/196 (40%), Gaps = 23/196 (11%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +        L +KP G+++  +  +G      +      +V + GRLD ++EGLL+LT++
Sbjct: 11  KTQADLTTLLLNKPYGVLSQFTSEEGSRWRCLSDFVDVPQVYAAGRLDADSEGLLILTSN 70

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--- 184
           G L + L  P     R Y  +  G  + ++L  L  G+V+QG      +      +    
Sbjct: 71  GRLQQRLTDPRFGHWRSYWAQVEGTPNTEQLQQLCDGVVVQGRRTLPAKARWLQGQDLPQ 130

Query: 185 --------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQ 224
                            W+ + L EG+NR+++++         RL+R          P  
Sbjct: 131 LPERTPQIRFRAAIPTNWLQLSLSEGRNRQVRRMTAAVGLPTLRLVRCCIDLMDNGPPLD 190

Query: 225 LGTLLAGSTREVSKKI 240
           L  L  GS R V+   
Sbjct: 191 LTGLQPGSWRTVTAAE 206


>gi|188495586|ref|ZP_03002856.1| RNA pseudouridylate synthase family protein [Escherichia coli
           53638]
 gi|188490785|gb|EDU65888.1| RNA pseudouridylate synthase family protein [Escherichia coli
           53638]
          Length = 127

 Score = 84.5 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 25/110 (22%), Positives = 45/110 (40%), Gaps = 15/110 (13%)

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------QVTLDTQKGSNAW 188
           +Y V+  G   QD L  L+ G+ +                           + +    +W
Sbjct: 18  IYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTSW 77

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + + L EG+NR+++++     +   RLIR + G + L  L  G  REV+ 
Sbjct: 78  LKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVTD 127


>gi|266624513|ref|ZP_06117448.1| ribosomal small subunit pseudouridine synthase A [Clostridium
           hathewayi DSM 13479]
 gi|288863635|gb|EFC95933.1| ribosomal small subunit pseudouridine synthase A [Clostridium
           hathewayi DSM 13479]
          Length = 108

 Score = 84.5 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 20/88 (22%), Positives = 36/88 (40%), Gaps = 3/88 (3%)

Query: 168 QGICYGDMQVTLDTQKG--SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            G       + L  + G    + + + + EGK  ++K++FE     V  L R+S G   L
Sbjct: 21  DGTETLPADLELVRRGGCGELSEIRLTIHEGKFHQVKRMFETLGCHVVYLKRLSMGTLTL 80

Query: 226 GT-LLAGSTREVSKKILREQLGPHLLEE 252
              L  G  R ++++ L         +E
Sbjct: 81  DETLKPGEYRPLTREELELLNKTDQEQE 108


>gi|119476174|ref|ZP_01616526.1| pseudouridine synthase family 1 protein [marine gamma
           proteobacterium HTCC2143]
 gi|119450801|gb|EAW32035.1| pseudouridine synthase family 1 protein [marine gamma
           proteobacterium HTCC2143]
          Length = 199

 Score = 84.5 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 34/143 (23%), Positives = 66/143 (46%), Gaps = 14/143 (9%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              GRLD ++EGLLLLT++G +   +  P T+  + Y V+  G   +  +  L+ G +++
Sbjct: 36  YPAGRLDYDSEGLLLLTDNGTVQHRISHPRTKMPKTYWVQVEGAPTEQDIEPLRVGAILK 95

Query: 169 GICYGDM--------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                                      +     W+ + + EG+NR+++++     +   R
Sbjct: 96  DGPCLPAMVELIPEPNIWKREPPIRARKAIPTTWLQLVITEGRNRQVRRMTASLGFPTLR 155

Query: 215 LIRISYGPFQLGTLLAGSTREVS 237
           LIR+  G + + TL  G TR+++
Sbjct: 156 LIRVKIGEWSIDTLKPGETRQIT 178


>gi|94499667|ref|ZP_01306204.1| Pseudouridine synthase, Rsu [Oceanobacter sp. RED65]
 gi|94428421|gb|EAT13394.1| Pseudouridine synthase, Rsu [Oceanobacter sp. RED65]
          Length = 210

 Score = 84.5 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 51/210 (24%), Positives = 95/210 (45%), Gaps = 16/210 (7%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL L++KP  +++  SD +G+ T+ D + +    V   GRLD ++EGLLLLT+DG L   
Sbjct: 3   RLILFNKPYQVISQFSDSEGKKTLADFIDTK--NVYPAGRLDFDSEGLLLLTDDGLLQHR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----------- 182
           +  P  +  + Y V+  G  D   +  L  G+ ++       +V +  +           
Sbjct: 61  ISDPKHKSYKTYWVQVEGIPDNLAIQHLVNGVDLKDGKTLPAKVNIIDEPNLWDRHPPIR 120

Query: 183 ---KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                  +W+ + + EGKNR+++++         RL+R+S G + L  L  G  +E+S  
Sbjct: 121 QRSNDVTSWLEIQIMEGKNRQVRRMTAAVGHPTLRLVRVSIGQWHLEQLKPGEFKELSVH 180

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVR 269
           + +     +   +    +  P  +     R
Sbjct: 181 MPKASRDKYPKNQHSDKMRNPKSTRRKSRR 210


>gi|227550852|ref|ZP_03980901.1| possible pseudouridylate synthase [Enterococcus faecium TX1330]
 gi|227179950|gb|EEI60922.1| possible pseudouridylate synthase [Enterococcus faecium TX1330]
          Length = 103

 Score = 84.5 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G       + +       + V + ++EGK  ++KK+F     KV  L R+S GP +L  
Sbjct: 21  DGYQCQPANLKILKADKHQSTVLLTIQEGKFHQVKKMFLAQGKKVIALKRLSMGPLELDE 80

Query: 228 -LLAGSTREVSKKILR 242
            L  G  R ++   ++
Sbjct: 81  RLAVGEYRSLTLAEMK 96


>gi|213023878|ref|ZP_03338325.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 165

 Score = 84.5 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 24/166 (14%), Positives = 55/166 (33%), Gaps = 4/166 (2%)

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
                  + Y V     +  + +  +  G+ I G            +K +     + L +
Sbjct: 4   RAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFRITLVQ 59

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQV 255
           G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +         ++ 
Sbjct: 60  GLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEGSSSEA 119

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
              A        ++     I +  +            +   K+K  
Sbjct: 120 KPKAKAKPKTAGIKRPVVAIEKSNEKARPASSGKRFTSPGRKKKGR 165


>gi|83593274|ref|YP_427026.1| ribosomal large subunit pseudouridine synthase E [Rhodospirillum
           rubrum ATCC 11170]
 gi|83576188|gb|ABC22739.1| ribosomal large subunit pseudouridine synthase E [Rhodospirillum
           rubrum ATCC 11170]
          Length = 199

 Score = 84.5 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 47/181 (25%), Positives = 82/181 (45%), Gaps = 16/181 (8%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             RL L +KP  +++  +D         +L  I       GRLD ++EGLLLLT++G L 
Sbjct: 1   MPRLILLNKPYDVLSQFTDRAEGRATLASLVPIPGV-YVCGRLDRDSEGLLLLTDNGPLQ 59

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--------- 182
             +  P ++  + YR +  G  D+  L+ L++G+ ++      + V    +         
Sbjct: 60  HHISHPRSKVPKTYRAQVEGVADKAALDRLRQGVTLRDGPARAVTVEAIDEPAGLWPRDP 119

Query: 183 ------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                     +W+ + + EG+NR ++++         RLIR S G + L  L  GS RE 
Sbjct: 120 PIRWRANIPTSWIELTIDEGRNRMVRRMTAAVGLPTLRLIRWSIGDWTLENLPPGSWREE 179

Query: 237 S 237
           +
Sbjct: 180 T 180


>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 = 84.5 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 82/248 (33%), Gaps = 38/248 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+ K I+       R+ K +A +   SR +++++I + +V VN IL+ +A+  +   D I
Sbjct: 1   MEIKKIIATEIN--RIDKFLANSTDYSRNDIQQLIDEHQVYVNDILVRKASFKIKENDQI 58

Query: 61  EVDGVPLRKAERTR--------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           E+    +++                   L +  +   +V         + V   L    +
Sbjct: 59  EIKKQLIKETNAIAQNINLDIVFENEDFLIINKRSGMVVHPAPGNMQDTLVNALLFHFKN 118

Query: 107 R---------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                        V R+D +T GLLL+           L   +     + +       D 
Sbjct: 119 NLSNINGEIRPGIVHRIDKDTSGLLLVAKTNEAHNYFALLLKKHQIERKYQAIIVGKMDH 178

Query: 158 LN-------------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                           LK  +          ++T      +++ +   L+ G+  +I+  
Sbjct: 179 TITNINLPIGRNTSSRLKMEVTAHNSKEAFTKITSLKASETHSLIQCELKTGRTHQIRVH 238

Query: 205 FEFFNWKV 212
               N  +
Sbjct: 239 LAHINKPI 246


>gi|46203293|ref|ZP_00208890.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Magnetospirillum
           magnetotacticum MS-1]
          Length = 187

 Score = 84.5 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 45/188 (23%), Positives = 88/188 (46%), Gaps = 16/188 (8%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            TRL +++KP  ++T  +D +G      +  ++     + GRLD ++EGLL+LT+ G LA
Sbjct: 1   MTRLIVFNKPYDVLTQFTDREGGRATLKDFINVPGV-YAAGRLDRDSEGLLVLTDSGPLA 59

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------Q 176
             +  P  +  + Y  +  G   +D L+ L++G+V++                       
Sbjct: 60  ARISDPKHKLAKTYWAQVEGIPSEDDLDKLRRGVVLKDGPTLPAGVRTMPEPDNLWPRDP 119

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                     +W+ + +REG+NR+++++     +   RLIR + G + L  L  G  R+ 
Sbjct: 120 PIRYRAAIPTSWIELTIREGRNRQVRRMTAAMGFPTLRLIRWAVGEWTLAGLAPGEWRDE 179

Query: 237 SKKILREQ 244
             + L++ 
Sbjct: 180 PVRALKKP 187


>gi|254480519|ref|ZP_05093766.1| conserved hypothetical protein [marine gamma proteobacterium
           HTCC2148]
 gi|214039102|gb|EEB79762.1| conserved hypothetical protein [marine gamma proteobacterium
           HTCC2148]
          Length = 206

 Score = 84.5 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 44/175 (25%), Positives = 89/175 (50%), Gaps = 16/175 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ L++KP  +++  SD +GR T+ D L +   R  + GRLD ++EGLLLLT++G L + 
Sbjct: 12  KIILFNKPFRVLSQFSDTEGRRTLADFLSAPEFR--AAGRLDYDSEGLLLLTDNGQLQQQ 69

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------------VTL 179
           +  P  +  + Y V+  G++D   +  L   + ++       +                 
Sbjct: 70  IANPRHKQWKTYLVQVEGELDDLSIAALCAPLKLKDGLTLPARARRIEPPALWPRHPPVR 129

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + +   ++W+ + +REG+NR+++++     +   RL+R + G + LG +  G  R
Sbjct: 130 ERKSVPDSWLELSIREGRNRQVRRMTAAVGFPTLRLVRQAVGDWSLGDIAPGEYR 184


>gi|254448522|ref|ZP_05061982.1| ribosomal large subunit pseudouridine synthase E [gamma
           proteobacterium HTCC5015]
 gi|198261905|gb|EDY86190.1| ribosomal large subunit pseudouridine synthase E [gamma
           proteobacterium HTCC5015]
          Length = 187

 Score = 84.5 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 50/182 (27%), Positives = 86/182 (47%), Gaps = 22/182 (12%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP G++    DPDG  T+ D +      V + GRLD ++EGLL+LT+DG L   
Sbjct: 3   RVILFNKPCGVLCQFRDPDGVPTLGDYID--VPDVYAAGRLDKDSEGLLVLTDDGRLQNR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------- 184
           +  P  +  + Y V+  G+   + L  L++G+ ++        V     +          
Sbjct: 61  ITSPENKLPKTYWVQVEGEPSDEALKQLRRGVHLKDGKTRRADVKRMAGEPLSEHGGLWP 120

Query: 185 -----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                         W+++ L+EGKNR+++++         RL+R   GP+QL  L +G  
Sbjct: 121 RNPPVRYRKSVPTCWLSITLKEGKNRQVRRMTAAVGHPTLRLVRWRIGPWQLADLASGDW 180

Query: 234 RE 235
            E
Sbjct: 181 IE 182


>gi|170018060|ref|YP_001728979.1| 16S rRNA uridine-516 pseudouridylate synthase [Leuconostoc citreum
           KM20]
 gi|169804917|gb|ACA83535.1| 16S rRNA uridine-516 pseudouridylate synthase [Leuconostoc citreum
           KM20]
          Length = 177

 Score = 84.5 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 36/144 (25%), Positives = 66/144 (45%), Gaps = 15/144 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD+++EGLLLLT+ G L   L  P  +  + Y V+  G   + +L  L++G+ ++
Sbjct: 34  YAAGRLDMDSEGLLLLTDQGHLNHALTDPDNKAYKTYVVQVEGIPTKAQLKQLEQGVDLK 93

Query: 169 GICYGDMQVTLDT---------------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +V                   Q    +++ + ++EG+NR+++++         
Sbjct: 94  DGLTLPAKVKRIPYPKWLWAREKPIRTRQNQPTSFIQLKIKEGRNRQVRRMTAAVGIPTL 153

Query: 214 RLIRISYGPFQLGTLLAGSTREVS 237
           RLIR   G + L  L  G  R + 
Sbjct: 154 RLIRTHIGDYHLADLQPGQYRIIK 177


>gi|89054176|ref|YP_509627.1| ribosomal large subunit pseudouridine synthase E [Jannaschia sp.
           CCS1]
 gi|88863725|gb|ABD54602.1| ribosomal large subunit pseudouridine synthase E [Jannaschia sp.
           CCS1]
          Length = 188

 Score = 84.5 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 45/185 (24%), Positives = 83/185 (44%), Gaps = 17/185 (9%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 L  ++KP+  ++  +   G   +      +   V + GRLD ++EGLLLLT+DG
Sbjct: 6   PRGHHMLIAFNKPMNTLSQFTSEGGWPALDGF--GLPKGVYAAGRLDRDSEGLLLLTDDG 63

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ------------ 176
           GL   +  P  +  +VY     G  D   L+ L++G+ ++       +            
Sbjct: 64  GLQARISSPKYRSPKVYFALVEGVPDDAALDHLRRGVTLKDGQTAPCEAEAVAAPDWIWD 123

Query: 177 ---VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                   +  ++ W+ + L EG+NR+++++     + V RL+R S GP  +  L  G  
Sbjct: 124 RDPPVRIRKSITDTWLKLTLTEGRNRQVRRMCAGVGFPVIRLVRFSIGPHDIRDLPPGMW 183

Query: 234 REVSK 238
           RE++ 
Sbjct: 184 RELAP 188


>gi|294140594|ref|YP_003556572.1| ribosomal large subunit pseudouridine synthase E [Shewanella
           violacea DSS12]
 gi|293327063|dbj|BAJ01794.1| ribosomal large subunit pseudouridine synthase E [Shewanella
           violacea DSS12]
          Length = 239

 Score = 84.5 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 46/186 (24%), Positives = 88/186 (47%), Gaps = 16/186 (8%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             A+   + L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTND
Sbjct: 53  PAAKDPVILLFNKPFDVLCQFTDEQGRKTLKDFIP--VKDVYAAGRLDRDSEGLLLLTND 110

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   +  P  +  + Y V+  G  ++  L  L+ G+ ++       ++++        
Sbjct: 111 GKLQSKITEPKKKTFKTYWVQVEGAPNEAALQTLRNGVKLKDGMTLPAKISILSEPNIWD 170

Query: 180 ------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 + +     W+ + + EG+NR+++++     +   RLIR   G + L  +  G  
Sbjct: 171 REPPIRERKNIPTTWLEIQICEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDDIDIGQY 230

Query: 234 REVSKK 239
           + +  K
Sbjct: 231 QILDMK 236


>gi|300906321|ref|ZP_07124020.1| hypothetical protein HMPREF9536_04286 [Escherichia coli MS 84-1]
 gi|301302690|ref|ZP_07208819.1| hypothetical protein HMPREF9347_01269 [Escherichia coli MS 124-1]
 gi|300401894|gb|EFJ85432.1| hypothetical protein HMPREF9536_04286 [Escherichia coli MS 84-1]
 gi|300841910|gb|EFK69670.1| hypothetical protein HMPREF9347_01269 [Escherichia coli MS 124-1]
 gi|315254683|gb|EFU34651.1| conserved hypothetical protein [Escherichia coli MS 85-1]
          Length = 168

 Score = 84.5 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 26/172 (15%), Positives = 59/172 (34%), Gaps = 4/172 (2%)

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 1   MNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 56

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 57  ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 116

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++V   A        ++     + +  +   R   N  +     ++KK  
Sbjct: 117 SSSEVKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 168


>gi|300716272|ref|YP_003741075.1| ribosomal large subunit pseudouridine synthase E [Erwinia
           billingiae Eb661]
 gi|299062108|emb|CAX59224.1| Ribosomal large subunit pseudouridine synthase E [Erwinia
           billingiae Eb661]
          Length = 210

 Score = 84.1 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 37/146 (25%), Positives = 67/146 (45%), Gaps = 15/146 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGL++LTNDG L   L  P  +  ++Y V+  G  D   +  L+ G+ ++
Sbjct: 62  YAAGRLDRDSEGLMVLTNDGALQATLTQPGKRTGKIYYVQVEGIPDISHIQALRDGVNLK 121

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +    +W+ + L EG+NR+++++     +   
Sbjct: 122 DGPTLPAGAELVAEPEWLWPRNPPIRERKAIPTSWLKITLYEGRNRQVRRMTAQIGFPTL 181

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKK 239
           RLIR + G   L  L  G  R+V+ +
Sbjct: 182 RLIRFAMGTQMLQDLPPGEWRDVTAE 207


>gi|188534084|ref|YP_001907881.1| Ribosomal large subunit pseudouridine synthase E [Erwinia
           tasmaniensis Et1/99]
 gi|188029126|emb|CAO96996.1| Ribosomal large subunit pseudouridine synthase E [Erwinia
           tasmaniensis Et1/99]
          Length = 238

 Score = 84.1 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 42/146 (28%), Positives = 73/146 (50%), Gaps = 15/146 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGL++LTNDG L   L  P  +  +VY V+  G   ++ L  L+ G+ ++
Sbjct: 92  YAAGRLDRDSEGLMILTNDGTLQARLTQPGKRTGKVYFVQVEGCPHENDLVPLRAGVDLK 151

Query: 169 GICYGDMQVTL---------------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +V +               + +    +W+ + L EG+NR+++++     +   
Sbjct: 152 DGPTLPAEVEIVAAPDWLWDRHPPVRERKAIPTSWLKITLYEGRNRQVRRMTAHIGFPTL 211

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKK 239
           RLIR S G  QL TL  G  R++S +
Sbjct: 212 RLIRFSMGTLQLQTLAPGEWRDISSE 237


>gi|261821431|ref|YP_003259537.1| pseudouridine synthase [Pectobacterium wasabiae WPP163]
 gi|261605444|gb|ACX87930.1| pseudouridine synthase [Pectobacterium wasabiae WPP163]
          Length = 209

 Score = 84.1 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 46/190 (24%), Positives = 84/190 (44%), Gaps = 17/190 (8%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G         R+ L++KP  ++   +D  GR T+ D +P       + GRLD ++EGL++
Sbjct: 21  GKRQPDNAPRRIVLFNKPFDVLPQFTDEAGRRTLKDYIPISGI--YAAGRLDRDSEGLMI 78

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-------- 175
           LTNDG L   L  P+ +  ++Y V+  G  D+  L   + G+ +                
Sbjct: 79  LTNDGKLQARLTQPTEKTAKIYYVQVEGIPDEAALTHFRTGLELNDGKTLPAGAEIVPEP 138

Query: 176 -------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                      + +   + W+ + L EG+NR+++++     +   RLIR       +  L
Sbjct: 139 DWLWPRNPPIRERKSIPDCWLKITLYEGRNRQVRRMTANIGYPTLRLIRYGMANQTVENL 198

Query: 229 LAGSTREVSK 238
           L G  +E++ 
Sbjct: 199 LPGEWKEITD 208


>gi|187925144|ref|YP_001896786.1| pseudouridine synthase [Burkholderia phytofirmans PsJN]
 gi|187716338|gb|ACD17562.1| pseudouridine synthase [Burkholderia phytofirmans PsJN]
          Length = 189

 Score = 84.1 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 39/176 (22%), Positives = 66/176 (37%), Gaps = 17/176 (9%)

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
                T        +            V   GRLD ++EGLLLLT+DG L   +  P  +
Sbjct: 7   NKPFGTICQFSPHETRASLADWVKVPDVYPAGRLDSDSEGLLLLTDDGALQARIAEPRHK 66

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---------------S 185
            ++ Y  +  G VD   L  L +G+ +        +                        
Sbjct: 67  LVKRYWAQVEGAVDAATLKKLARGVDLGDYVTRPCRAEYVEPTDALWTRTPPIRFRAAIP 126

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKK 239
             W+ + + EGKNR+++++     +   RL+R+  G   +    L  G + E+S K
Sbjct: 127 TTWIELSITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFSLGLQPGESVELSPK 182


>gi|300906320|ref|ZP_07124019.1| S4 domain protein [Escherichia coli MS 84-1]
 gi|301302689|ref|ZP_07208818.1| S4 domain protein [Escherichia coli MS 124-1]
 gi|300401893|gb|EFJ85431.1| S4 domain protein [Escherichia coli MS 84-1]
 gi|300841909|gb|EFK69669.1| S4 domain protein [Escherichia coli MS 124-1]
 gi|315254682|gb|EFU34650.1| S4 domain protein [Escherichia coli MS 85-1]
          Length = 59

 Score = 84.1 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 11 FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +
Sbjct: 4  DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDIVKVNGQLI 59


>gi|319944626|ref|ZP_08018893.1| ribosomal large subunit pseudouridine synthase E [Lautropia
           mirabilis ATCC 51599]
 gi|319742065|gb|EFV94485.1| ribosomal large subunit pseudouridine synthase E [Lautropia
           mirabilis ATCC 51599]
          Length = 193

 Score = 84.1 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 48/186 (25%), Positives = 83/186 (44%), Gaps = 21/186 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP G++   S  +   ++ D++ +        GRLD ++EGLLLLTNDG L   +
Sbjct: 7   LIAFNKPCGVICQFSPHETHPSLKDHIDAPGF--YPAGRLDTDSEGLLLLTNDGRLQARI 64

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P     + Y  +  G  D+ KL LL++ + +        +  L               
Sbjct: 65  AEPRHGKEKTYWAQVEGAPDEHKLALLRRPMDLGDFITQPARTRLLAADETERLWPRQPP 124

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL--AGSTRE 235
               +   + W+ + ++EGKNR+++++     +   RL+RI+ G   L  L    G  R 
Sbjct: 125 VRVRKTVPDFWLEIRIQEGKNRQVRRMTAKAGYPCLRLVRIAVGALNLWDLGLAPGEWRF 184

Query: 236 VSKKIL 241
           VS   L
Sbjct: 185 VSPAAL 190


>gi|119897392|ref|YP_932605.1| pseudouridylate synthase [Azoarcus sp. BH72]
 gi|119669805|emb|CAL93718.1| pseudouridylate synthase [Azoarcus sp. BH72]
          Length = 201

 Score = 84.1 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 55/181 (30%), Positives = 89/181 (49%), Gaps = 17/181 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL L +KP G++   S   GR+T+ D++P     V   GRLD ++EGLLLLT+DG L   
Sbjct: 3   RLILLNKPYGVLCQFSGEPGRATLKDHVPIP--EVYPAGRLDTDSEGLLLLTDDGALQAR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------QVT 178
           +  P  +  + Y V+  G+ D   L  L+ G+ +                          
Sbjct: 61  IADPRHKLPKTYLVQVEGEPDDAALAALRAGVDLGDFRTRPCSARRVVEPDWLWPRDPPV 120

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              +    +WV + LREGKNR+++++     +   RL+R++ GP++L  L  G+ REV  
Sbjct: 121 RYRKSVPTSWVEIVLREGKNRQVRRMTAKVGFPTLRLLRVAIGPWRLDGLAPGAWREVEP 180

Query: 239 K 239
           +
Sbjct: 181 R 181


>gi|260772636|ref|ZP_05881552.1| ribosomal large subunit pseudouridine synthase E [Vibrio
           metschnikovii CIP 69.14]
 gi|260611775|gb|EEX36978.1| ribosomal large subunit pseudouridine synthase E [Vibrio
           metschnikovii CIP 69.14]
          Length = 227

 Score = 84.1 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 43/186 (23%), Positives = 75/186 (40%), Gaps = 17/186 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P    ER  +        L         ++            + + GRLD ++EGL++LT
Sbjct: 44  PRSPDERKVIAFNKPYDTLSQFTDGQGRQTLADFI---TIKDIYAAGRLDRDSEGLMILT 100

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----- 180
           NDG L   L  P  +  + Y V+  G+  +  L  L++G+ ++       +V +      
Sbjct: 101 NDGVLQARLTQPKAKAPKTYWVQVEGEPQEADLEQLRRGVTLKDGPTLPAKVEIIKPPQV 160

Query: 181 ---------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + + EG+NR+++++     +   RLIR S G   L TL  G
Sbjct: 161 WERNPPVRFRAAIPTTWLAMTIIEGRNRQVRRMTACIGFPTLRLIRYSIGNTTLETLQPG 220

Query: 232 STREVS 237
             RE+ 
Sbjct: 221 EWREID 226


>gi|206581129|ref|YP_002239231.1| ribosomal large subunit pseudouridine synthase E [Klebsiella
           pneumoniae 342]
 gi|206570187|gb|ACI11963.1| ribosomal large subunit pseudouridine synthase E [Klebsiella
           pneumoniae 342]
          Length = 216

 Score = 84.1 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 43/198 (21%), Positives = 74/198 (37%), Gaps = 18/198 (9%)

Query: 52  VNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
             V      +V         +T +        L     +    +          + V + 
Sbjct: 19  HRVERFSTQQVTRQRKEHQPKTVILFNKPYDVLPQFTDEAGRSTLKDFI---PVAGVYAA 75

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD ++EGLL+LTNDG L   L  P  +  ++Y V+  G+   + L  L+ G+ +    
Sbjct: 76  GRLDRDSEGLLVLTNDGALQAKLTQPGKRTGKIYYVQVEGEPTAEALAALRDGVTLNDGP 135

Query: 172 YGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
                                  + +     W+ V L EG+NR+++++     +   RLI
Sbjct: 136 TLPAGVEVVEEPAWLWPRNPPIRERKSIPTRWLKVTLYEGRNRQVRRMTAHVGFPTLRLI 195

Query: 217 RISYGPFQLGTLLAGSTR 234
           R + G + L  L  G  R
Sbjct: 196 RYAMGGYTLDGLANGEWR 213


>gi|126174689|ref|YP_001050838.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|125997894|gb|ABN61969.1| ribosomal large subunit pseudouridine synthase E [Shewanella
           baltica OS155]
          Length = 270

 Score = 84.1 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 48/188 (25%), Positives = 88/188 (46%), Gaps = 17/188 (9%)

Query: 65  VPLRKAE-RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
            P++       + L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLL
Sbjct: 80  KPVQSQTLAPIIVLFNKPFDVLCQFTDEQGRKTLKDYIPIA--DVYAAGRLDRDSEGLLL 137

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
           LTNDG L   L  P  +  + Y V+  G   +D L  L++G+ +        +V +    
Sbjct: 138 LTNDGQLQARLTEPKKKTFKTYWVQVEGVPTEDALTKLRQGVELNDGMTLPAKVKIMDSP 197

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ + + EG+NR+++++     +   RLIR   G + +  L 
Sbjct: 198 DIWPRNPPVRERKNIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSIDNLP 257

Query: 230 AGSTREVS 237
           +G  + + 
Sbjct: 258 SGEHKCIR 265


>gi|83311571|ref|YP_421835.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthase [Magnetospirillum magneticum
           AMB-1]
 gi|82946412|dbj|BAE51276.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthase [Magnetospirillum magneticum
           AMB-1]
          Length = 196

 Score = 84.1 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 46/180 (25%), Positives = 83/180 (46%), Gaps = 16/180 (8%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TRL +++KP  ++T  +D +G      +   +     + GRLD ++EGLL+LT+ G LA 
Sbjct: 16  TRLIVFNKPYDVLTQFTDREGGRATLKDFIKVPGV-YAAGRLDRDSEGLLVLTDSGPLAA 74

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------QV 177
            +  P  +  + Y  +  G   +  L+ L++GIV++                        
Sbjct: 75  RISDPKHKLAKTYWAQVEGVPTEADLDRLRRGIVLKDGPTLPAGARAMAEPDNLWPRDPP 134

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    +W+ + LREG+NR+++++     +   RLIR + G + L  L  G  R+V 
Sbjct: 135 IRYRAAIPTSWIELTLREGRNRQVRRMTAAMGFPTLRLIRWAVGEWNLEGLAPGEWRDVR 194


>gi|312172141|emb|CBX80398.1| ribosomal large subunit pseudouridine synthase [Erwinia amylovora
           ATCC BAA-2158]
          Length = 218

 Score = 84.1 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 39/153 (25%), Positives = 67/153 (43%), Gaps = 15/153 (9%)

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
                 + + GRLD ++EGL++LTNDG L   L  P  +  +VY V+  G   +  L  L
Sbjct: 65  YIPHPGIYAAGRLDRDSEGLMVLTNDGALQAQLTQPGKRTGKVYFVQVEGCPQESDLQPL 124

Query: 162 KKGIVIQGICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
           + G+ ++                          + +     W+ + L EG+NR+++++  
Sbjct: 125 RDGVNLKDGPTLPAVVERVAAPGWLWDRQPPIRERKAIPTCWLKITLYEGRNRQVRRMTA 184

Query: 207 FFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
              +   RLIR S G   L  L  G  R++S +
Sbjct: 185 HIGYPTLRLIRFSMGNLGLRALAPGEWRDISHE 217


>gi|296102845|ref|YP_003612991.1| ribosomal large subunit pseudouridine synthase E [Enterobacter
           cloacae subsp. cloacae ATCC 13047]
 gi|295057304|gb|ADF62042.1| ribosomal large subunit pseudouridine synthase E [Enterobacter
           cloacae subsp. cloacae ATCC 13047]
          Length = 217

 Score = 83.7 bits (205), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 50/186 (26%), Positives = 93/186 (50%), Gaps = 17/186 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++++  R+ L++KP  ++   +D  GRST+ D +P       + GRLD ++EGLL+LTND
Sbjct: 34  QESQPKRVILFNKPYDVLPQFTDEAGRSTLKDYIPVQGV--YAAGRLDRDSEGLLVLTND 91

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P  +  ++Y V+  G+ D++ L  L+ G+ +                    
Sbjct: 92  GALQAKLTQPGKRTGKIYFVQVEGEPDEEALAALRNGVTLNDGPTLPAGIERVNEPEWLW 151

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ + L EG+NR+++++     +   RLIR + G + L +L  G 
Sbjct: 152 PRNPPIRERKSIPTSWLKITLFEGRNRQVRRMTAHVGFPTLRLIRYAMGSYTLDSLANGE 211

Query: 233 TREVSK 238
            R+V+ 
Sbjct: 212 WRDVAP 217


>gi|288936090|ref|YP_003440149.1| pseudouridine synthase [Klebsiella variicola At-22]
 gi|288890799|gb|ADC59117.1| pseudouridine synthase [Klebsiella variicola At-22]
          Length = 216

 Score = 83.7 bits (205), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 42/198 (21%), Positives = 75/198 (37%), Gaps = 18/198 (9%)

Query: 52  VNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
             V      +V      +  +T +        L     +    +          + V + 
Sbjct: 19  HRVERFSTQQVTRQRKERQPKTVILFNKPYDVLPQFTDEAGRSTLKDFI---PVAGVYAA 75

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD ++EGLL+LTNDG L   L  P  +  ++Y V+  G+   + L  L+ G+ +    
Sbjct: 76  GRLDRDSEGLLVLTNDGALQAKLTQPGKRTGKIYYVQVEGEPTPEALAALRDGVTLNDGP 135

Query: 172 YGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
                                  + +     W+ + L EG+NR+++++     +   RLI
Sbjct: 136 TLPAGVEVVEEPAWLWPRNPPIRERKSIPTRWLKITLYEGRNRQVRRMTAHVGFPTLRLI 195

Query: 217 RISYGPFQLGTLLAGSTR 234
           R + G + L  L  G  R
Sbjct: 196 RYAMGGYTLDGLANGEWR 213


>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 = 83.7 bits (205), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 38/245 (15%), Positives = 85/245 (34%), Gaps = 33/245 (13%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  + ++ ++    R+   +A     SR E++++I  ++V VNG + ++    +   D I
Sbjct: 1   MIYEFLIDDSNQNARLDVFLANVVELSRSEIQKLIDDKKVLVNGKIQKK-NYKLNLNDKI 59

Query: 61  EVD----GVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--- 105
            +D       ++          E   L + +K   ++   ++     T+ + L   F   
Sbjct: 60  TLDYEKPDKTIKAQKQDLDIVYEDDYLAIINKDKDVIVHPTETIYSDTLVNYLMYNFKNL 119

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL------RVYRVRFHGQV 153
                  R   V RLD +T GL+++  D      L+              +   +     
Sbjct: 120 SDVDGDYRRGIVHRLDKDTTGLIIIAKDNDTHLKLKEIIKNHEIIKTYLCIVHGKIDECG 179

Query: 154 DQDKLN-----LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
             ++         KK +V         Q          + V V ++ G+  +I+    + 
Sbjct: 180 TIEEYMSRNPKDRKKMMVSDEGKLSISQYERLDYNDDYSLVKVQIKTGRTHQIRVHMNYI 239

Query: 209 NWKVN 213
           +  + 
Sbjct: 240 HHPIL 244


>gi|292488017|ref|YP_003530894.1| ribosomal large subunit pseudouridine synthase [Erwinia amylovora
           CFBP1430]
 gi|291553441|emb|CBA20486.1| ribosomal large subunit pseudouridine synthase [Erwinia amylovora
           CFBP1430]
          Length = 218

 Score = 83.7 bits (205), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 39/153 (25%), Positives = 67/153 (43%), Gaps = 15/153 (9%)

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
                 + + GRLD ++EGL++LTNDG L   L  P  +  +VY V+  G   +  L  L
Sbjct: 65  YIPHPGIYAAGRLDRDSEGLMVLTNDGALQAQLTQPGKRTGKVYFVQVEGCPQESDLLPL 124

Query: 162 KKGIVIQGICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
           + G+ ++                          + +     W+ + L EG+NR+++++  
Sbjct: 125 RDGVNLKDGPTLPAVVERVAAPGWLWDRQPPIRERKAIPTCWLKITLYEGRNRQVRRMTA 184

Query: 207 FFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
              +   RLIR S G   L  L  G  R++S +
Sbjct: 185 HIGYPTLRLIRFSMGNLGLRALAPGEWRDISHE 217


>gi|113969946|ref|YP_733739.1| ribosomal large subunit pseudouridine synthase E [Shewanella sp.
           MR-4]
 gi|113884630|gb|ABI38682.1| ribosomal large subunit pseudouridine synthase E [Shewanella sp.
           MR-4]
          Length = 261

 Score = 83.7 bits (205), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 46/183 (25%), Positives = 86/183 (46%), Gaps = 16/183 (8%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +      + L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLLLLTND
Sbjct: 78  KPQGDPMIVLFNKPFDVLCQFTDEQGRKTLKDYIPIPGV--YAAGRLDRDSEGLLLLTND 135

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  + Y V+  G+  +  L  L++G+ ++       +V++        
Sbjct: 136 GQLQAKLTEPKKKTFKTYWVQVEGKPTEADLAKLRQGVELKDGMTLPAKVSIMATPNVWP 195

Query: 180 ------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 + +     W+ + + EG+NR+++++     +   RLIR   G + L  L  G  
Sbjct: 196 RNPPIRERKNIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDDLATGEH 255

Query: 234 REV 236
           + +
Sbjct: 256 KCI 258


>gi|152969697|ref|YP_001334806.1| pseudouridine synthase [Klebsiella pneumoniae subsp. pneumoniae MGH
           78578]
 gi|150954546|gb|ABR76576.1| pseudouridine synthase [Klebsiella pneumoniae subsp. pneumoniae MGH
           78578]
          Length = 206

 Score = 83.7 bits (205), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 42/198 (21%), Positives = 75/198 (37%), Gaps = 18/198 (9%)

Query: 52  VNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
             V      +V      +  +T +        L     +    +          + V + 
Sbjct: 9   HRVERFSTQQVTRQRKERQPKTVILFNKPYDVLPQFTDEAGRSTLKDFI---PVAGVYAA 65

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD ++EGLL+LTNDG L   L  P  +  ++Y V+  G+   + L  L+ G+ +    
Sbjct: 66  GRLDRDSEGLLVLTNDGALQAKLTQPGKRTGKIYYVQVEGEPTPEALTALRDGVTLNDGP 125

Query: 172 YGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
                                  + +     W+ + L EG+NR+++++     +   RLI
Sbjct: 126 TLPAGVELVEEPVWLWPRNPPIRERKSIPTRWLKITLYEGRNRQVRRMTAHVGFPTLRLI 185

Query: 217 RISYGPFQLGTLLAGSTR 234
           R + G + L  L  G  R
Sbjct: 186 RYAMGGYTLDGLANGDWR 203


>gi|301046963|ref|ZP_07194075.1| conserved hypothetical protein [Escherichia coli MS 185-1]
 gi|300301121|gb|EFJ57506.1| conserved hypothetical protein [Escherichia coli MS 185-1]
 gi|324007835|gb|EGB77054.1| hypothetical protein HMPREF9532_02485 [Escherichia coli MS 57-2]
          Length = 168

 Score = 83.7 bits (205), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 25/172 (14%), Positives = 58/172 (33%), Gaps = 4/172 (2%)

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 1   MNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTV----TKKCKVKKEAPFVFR 56

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 57  ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 116

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             ++    A        ++     + +  +   R   N  +     ++KK  
Sbjct: 117 SSSEAKPKAKAKPKTVGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 168


>gi|308186451|ref|YP_003930582.1| ribosomal large subunit pseudouridine synthase [Pantoea vagans
           C9-1]
 gi|308056961|gb|ADO09133.1| putative ribosomal large subunit pseudouridine synthase [Pantoea
           vagans C9-1]
          Length = 223

 Score = 83.3 bits (204), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 40/145 (27%), Positives = 68/145 (46%), Gaps = 15/145 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGL++LTNDG L   L  P  +  +VY V+  G   +  L  L+ G+ ++
Sbjct: 76  YAAGRLDRDSEGLMVLTNDGALQAALTQPGKRTGKVYYVQVEGDPQEADLQPLRDGVNLK 135

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +     W+ V L EG+NR+++++     +   
Sbjct: 136 DGMTLPAGVEKVAEPAWLWPRQPPIRERKNIPTQWLKVTLYEGRNRQVRRMTAHIGFPTL 195

Query: 214 RLIRISYGPFQLGTLLAGSTREVSK 238
           RLIR + G + L  L +G  RE+S+
Sbjct: 196 RLIRYAMGSYSLDDLASGMWREISE 220


>gi|114047181|ref|YP_737731.1| ribosomal large subunit pseudouridine synthase E [Shewanella sp.
           MR-7]
 gi|113888623|gb|ABI42674.1| ribosomal large subunit pseudouridine synthase E [Shewanella sp.
           MR-7]
          Length = 265

 Score = 83.3 bits (204), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 45/183 (24%), Positives = 83/183 (45%), Gaps = 16/183 (8%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +      + L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLLLLTND
Sbjct: 78  KPQGDPMIVLFNKPFDVLCQFTDEQGRKTLKDYIPIPGV--YAAGRLDRDSEGLLLLTND 135

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ----------- 176
           G L   L  P  +  + Y V+  G+  +  L  L++G+ ++       +           
Sbjct: 136 GQLQAKLTEPKKKTFKTYWVQVEGEPTEADLAKLRQGVELKDGMTLPAKVSLMATPNVWP 195

Query: 177 ---VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 + +     W+ + + EG+NR+++++     +   RLIR   G + L  L  G  
Sbjct: 196 RNPPIRERKNIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDDLATGEH 255

Query: 234 REV 236
           + +
Sbjct: 256 KCI 258


>gi|218709063|ref|YP_002416684.1| ribosomal large subunit pseudouridine synthase E [Vibrio splendidus
           LGP32]
 gi|218322082|emb|CAV18165.1| Ribosomal large subunit pseudouridine synthase E [Vibrio splendidus
           LGP32]
          Length = 242

 Score = 83.3 bits (204), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 51/186 (27%), Positives = 91/186 (48%), Gaps = 16/186 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E  ++ L++KP   ++  +D +GR T+ D +P     V + GRLD ++EGLL+L
Sbjct: 59  KPKVAPEDRKVILFNKPFDTLSQFTDGEGRKTLADFIP--VKDVYAAGRLDRDSEGLLVL 116

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG     L  P+++  + Y V+  G   +  L+ L+KG+ ++       +V +  +  
Sbjct: 117 TNDGIFQAKLTQPNSKSTKTYWVQVEGAPSEKDLDKLRKGVELKDGMTLPAEVEVMQEPQ 176

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + + EG+NR+++++     +   RLIR S G   +G L  
Sbjct: 177 VWERTPPVRFRAAIPTTWLAITIIEGRNRQVRRMTANIGFPTLRLIRYSMGNMNVGQLQP 236

Query: 231 GSTREV 236
           G  +EV
Sbjct: 237 GEWKEV 242


>gi|117920196|ref|YP_869388.1| ribosomal large subunit pseudouridine synthase E [Shewanella sp.
           ANA-3]
 gi|117612528|gb|ABK47982.1| ribosomal large subunit pseudouridine synthase E [Shewanella sp.
           ANA-3]
          Length = 269

 Score = 83.3 bits (204), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 46/183 (25%), Positives = 85/183 (46%), Gaps = 16/183 (8%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +      + L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLLLLTND
Sbjct: 83  KPQGEPMIVLFNKPFDVLCQFTDEQGRKTLKDYIPIPGV--YAAGRLDRDSEGLLLLTND 140

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  + Y V+  G+     L  L++G+ ++       +V++        
Sbjct: 141 GQLQAKLTEPKKKTFKTYWVQVEGEPTDADLAKLRQGVELKDGITLPAKVSIMATPNVWP 200

Query: 180 ------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 + +     W+ + + EG+NR+++++     +   RLIR   G + L  L  G  
Sbjct: 201 RNPPIRERKNIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDDLATGEH 260

Query: 234 REV 236
           + +
Sbjct: 261 KCI 263


>gi|33863440|ref|NP_895000.1| pseudouridine synthase [Prochlorococcus marinus str. MIT 9313]
 gi|33640889|emb|CAE21345.1| possible pseudouridine synthase [Prochlorococcus marinus str. MIT
           9313]
          Length = 215

 Score = 83.3 bits (204), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 49/205 (23%), Positives = 78/205 (38%), Gaps = 23/205 (11%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L +KP G ++  +   G             RV + GRLD ++EGLL+LT+ G L   L 
Sbjct: 11  LLLNKPYGFLSQFTPEPGSQWRCLADLIPIPRVYAAGRLDADSEGLLVLTSHGRLQHRLT 70

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-----------------QVT 178
            P     RVY V+  G   + +L  L  G++I+G                          
Sbjct: 71  NPHLSHWRVYWVQVEGSPSESQLQKLASGVIIKGKRTRPALASWLKGNVAPIVREREPPI 130

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQLGTLLAGS 232
              Q    +W+ + L+EG+NR+++++         RLIR          P  +  +  G 
Sbjct: 131 RVRQSIPTSWLELKLKEGRNRQVRRMTAAVGLPTLRLIRHRIELMDGEPPLSIEGMDPGQ 190

Query: 233 TREVSKKILREQLGPHLLEEAQVNL 257
            R+VS +     L       A    
Sbjct: 191 WRQVSSRETNLLLSLLNHPAADPQA 215


>gi|319638581|ref|ZP_07993343.1| pseudouridine synthase [Neisseria mucosa C102]
 gi|317400330|gb|EFV80989.1| pseudouridine synthase [Neisseria mucosa C102]
          Length = 186

 Score = 83.3 bits (204), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 45/182 (24%), Positives = 81/182 (44%), Gaps = 21/182 (11%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L + +KP G++   S  +    + D +          GRLD ++EGLLLLTN+G L 
Sbjct: 1   MNDLIILNKPYGVICQFSAHEKHPCLKDFVE--KPGFYPAGRLDTDSEGLLLLTNNGRLQ 58

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------- 184
             +  P  + ++ Y  +  G  D+ KL+LL++G+ +        +V +  +         
Sbjct: 59  AQIADPKFKQVKTYWAQVEGSPDEAKLDLLRRGVDLGDFVTRPAEVRVLEEGEADVLWPR 118

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL--AGS 232
                      + WV + + EGKNR+++++     +   RL+R++ G   L  L    G 
Sbjct: 119 VPPIRVRKSVPDFWVEIKISEGKNRQVRRMTAKAGFPCLRLVRVAIGRLNLFDLNLELGQ 178

Query: 233 TR 234
            R
Sbjct: 179 WR 180


>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 = 83.3 bits (204), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 32/247 (12%), Positives = 68/247 (27%), Gaps = 37/247 (14%)

Query: 3   DKNIVQ--ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           DK ++Q  +    +R+   +A     +R  ++++I    V VNG  ++  +  V   D +
Sbjct: 5   DKIVLQGEKEDEGKRIDVFLAAELDYTRSYIKKLIVDGLVFVNGKTVK-PSYKVKENDEV 63

Query: 61  EVD------------GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
            ++             +PL     +   + +      +V         + V   L    +
Sbjct: 64  VLNVPEAEKIDVLPEDIPLDILYEDDDIIVINKPQGMVVHPAPGNYSGTLVNALLYHCKN 123

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ----------- 155
                G L       L     G +       +   L                        
Sbjct: 124 LSGINGILRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIKERSVFKKYVAIVEGVIKDE 183

Query: 156 ---------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          KK  VI+   Y      +  +   N  V   ++ G+  +I+    
Sbjct: 184 EGKIEAPIGRHPVDRKKMAVIEDGRYALTLYKVLERFKENTLVEAVIKTGRTHQIRVHMA 243

Query: 207 FFNWKVN 213
           +    + 
Sbjct: 244 YIGHPIV 250


>gi|311279960|ref|YP_003942191.1| pseudouridine synthase [Enterobacter cloacae SCF1]
 gi|308749155|gb|ADO48907.1| pseudouridine synthase [Enterobacter cloacae SCF1]
          Length = 215

 Score = 83.3 bits (204), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 48/178 (26%), Positives = 85/178 (47%), Gaps = 17/178 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             R+ L++KP  ++   +D  GRST+ D +P       + GRLD ++EGLL+LTNDG L 
Sbjct: 38  PKRVILFNKPYDVLPQFTDEAGRSTLKDYIPVQGV--YAAGRLDRDSEGLLVLTNDGPLQ 95

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------Q 176
             L  P  +  ++Y V+  G+  ++ L  L+ G+ +                        
Sbjct: 96  ARLTQPGKRTGKIYFVQVEGEPGEEALAALRSGVTLNDGPTLPAGAERVAEPTWLWPRNP 155

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L +G  R
Sbjct: 156 PIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLASGEWR 213


>gi|50121367|ref|YP_050534.1| putative RNA pseudouridylate synthase [Pectobacterium atrosepticum
           SCRI1043]
 gi|49611893|emb|CAG75342.1| putative RNA pseudouridylate synthase [Pectobacterium atrosepticum
           SCRI1043]
          Length = 218

 Score = 83.3 bits (204), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 47/187 (25%), Positives = 83/187 (44%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                    R+ L++KP  ++   +D  GRST+ D +P       + GRLD ++EGL++L
Sbjct: 31  KRQPDNTPRRIVLFNKPFDVLPQFTDEAGRSTLKDYIPISGI--YAAGRLDRDSEGLMIL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TNDG L   L  P+ +  ++Y V+  G  D   L   + G+ +                 
Sbjct: 89  TNDGKLQAQLTQPTKKTAKIYYVQVEGIPDDAILTRFRTGLELNDGKTQPAGAEIVPEPD 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +   + W+ + L EG+NR+++++     +   RLIR S     +  LL
Sbjct: 149 WLWPRNPPIRERKSIPDCWLKITLYEGRNRQVRRMTANIGYPTLRLIRYSMANQTVENLL 208

Query: 230 AGSTREV 236
            G  +E+
Sbjct: 209 PGEWKEI 215


>gi|325205754|gb|ADZ01207.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           meningitidis M04-240196]
          Length = 186

 Score = 83.3 bits (204), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 44/178 (24%), Positives = 79/178 (44%), Gaps = 21/178 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP G++   S  +   ++ D +          GRLD ++EGLLLLT+DG L   +
Sbjct: 4   LIAFNKPYGVICQFSPHEKHKSLKDFINFPGF--YPAGRLDTDSEGLLLLTDDGRLQAQI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y  +  G  D+ +L  L+KGI + G       + +               
Sbjct: 62  TDPKFKHPKTYWAQLEGVPDESRLESLRKGIDLGGFVTRPASIRILKHGEADSLWERIPP 121

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL--AGST 233
               +   + W+ + + EGKNR+++++     +   RLIR++ G  +L  L    G  
Sbjct: 122 IRVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLIRVASGRLKLFDLDLKPGEW 179


>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 = 83.3 bits (204), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 38/245 (15%), Positives = 85/245 (34%), Gaps = 33/245 (13%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  + ++ ++    R+   +A     SR E++++I  ++V VNG + ++    +   D I
Sbjct: 1   MIYEFLIDDSNQNARLDVFLANVVELSRSEIQKLIDDKKVLVNGKIQKK-NYKLNLNDKI 59

Query: 61  EVD----GVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--- 105
            +D       ++          E   L + +K   ++   ++     T+ + L   F   
Sbjct: 60  TLDYEKPDKTIKAQKQDLDIVYEDDYLAIINKDKDVIVHPTETIYSDTLVNYLMYNFKNL 119

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL------RVYRVRFHGQV 153
                  R   V RLD +T GL+++  D      L+              +   +     
Sbjct: 120 SDVDGDYRRGIVHRLDKDTTGLIIIAKDNDTHLKLKEIIKNHEIIKTYLCIVHGKIDECG 179

Query: 154 DQDKLN-----LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
             ++         KK +V         Q          + V V ++ G+  +I+    + 
Sbjct: 180 TIEEYMSRNPKDRKKMMVSDEGKLSISQYERLDYNDDYSLVKVQIKTGRTHQIRVHMNYI 239

Query: 209 NWKVN 213
           +  + 
Sbjct: 240 HHPIL 244


>gi|74316871|ref|YP_314611.1| ribosomal large subunit pseudouridine synthase E [Thiobacillus
           denitrificans ATCC 25259]
 gi|74056366|gb|AAZ96806.1| pseudouridine synthase, Rsu [Thiobacillus denitrificans ATCC 25259]
          Length = 180

 Score = 83.3 bits (204), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 43/178 (24%), Positives = 79/178 (44%), Gaps = 17/178 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL L++KP G+++  +       + D+L      V + GRLD ++EGLL+LT+DG     
Sbjct: 3   RLILFNKPYGVLSQFTPEGRWQGLRDHLA--LPGVYAAGRLDADSEGLLILTDDGPTQAR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----------- 182
           +  P  +  + Y  +  G      L  L++G+ +           +  +           
Sbjct: 61  IADPRHKLPKTYWAQVEGAPADADLEPLRRGVDLGDFVTRPAGARIIAEPPSLWPRNPPI 120

Query: 183 ----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                   AW+ + + EGKNR+++++     +   RLIR + G + L  L  G  +E+
Sbjct: 121 RFRANIPTAWIELVIAEGKNRQVRRMTAKVGFPTLRLIRAAVGEWNLNGLQPGQWKEL 178


>gi|238894184|ref|YP_002918918.1| pseudouridine synthase [Klebsiella pneumoniae NTUH-K2044]
 gi|330016184|ref|ZP_08308414.1| ribosomal large subunit pseudouridine synthase E [Klebsiella sp. MS
           92-3]
 gi|238546500|dbj|BAH62851.1| pseudouridine synthase [Klebsiella pneumoniae subsp. pneumoniae
           NTUH-K2044]
 gi|328529469|gb|EGF56374.1| ribosomal large subunit pseudouridine synthase E [Klebsiella sp. MS
           92-3]
          Length = 216

 Score = 83.3 bits (204), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 42/198 (21%), Positives = 75/198 (37%), Gaps = 18/198 (9%)

Query: 52  VNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
             V      +V      +  +T +        L     +    +          + V + 
Sbjct: 19  HRVERFSTQQVTRQRKERQPKTVILFNKPYDVLPQFTDEAGRSTLKDFI---PVAGVYAA 75

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD ++EGLL+LTNDG L   L  P  +  ++Y V+  G+   + L  L+ G+ +    
Sbjct: 76  GRLDRDSEGLLVLTNDGALQAKLTQPGKRTGKIYYVQVEGEPTPEALTALRDGVTLNDGP 135

Query: 172 YGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
                                  + +     W+ + L EG+NR+++++     +   RLI
Sbjct: 136 TLPAGVELVEEPVWLWPRNPPIRERKSIPTRWLKITLYEGRNRQVRRMTAHVGFPTLRLI 195

Query: 217 RISYGPFQLGTLLAGSTR 234
           R + G + L  L  G  R
Sbjct: 196 RYAMGGYTLDGLANGDWR 213


>gi|110834141|ref|YP_693000.1| pseudouridylate synthase [Alcanivorax borkumensis SK2]
 gi|110647252|emb|CAL16728.1| pseudouridylate synthase [Alcanivorax borkumensis SK2]
          Length = 206

 Score = 82.9 bits (203), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 48/174 (27%), Positives = 84/174 (48%), Gaps = 16/174 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L +KP  +++  SD  GR T+ + +          GRLD ++EGLLLLT+DG L   +
Sbjct: 4   LILLNKPFRVLSQFSDDQGRRTLREFVCVPGV--YPAGRLDWDSEGLLLLTDDGALQARI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y V+  GQ    +L  L++GI ++       +V+L               
Sbjct: 62  SDPRFKLPKTYLVQVEGQPGPQELQKLRQGIRLKDGPTRPAKVSLIDDPCLWPRTPPVRS 121

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +   ++W+++ + EG+NR+++++         RLIR   G + L  L  G +R
Sbjct: 122 RKTVPDSWLSLTIDEGRNRQVRRMTAAIGHPTLRLIRWQIGDWSLADLAPGESR 175


>gi|212637003|ref|YP_002313528.1| RNA pseudouridine synthase family protein [Shewanella piezotolerans
           WP3]
 gi|212558487|gb|ACJ30941.1| RNA pseudouridine synthase family protein [Shewanella piezotolerans
           WP3]
          Length = 210

 Score = 82.9 bits (203), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 45/184 (24%), Positives = 74/184 (40%), Gaps = 17/184 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                +Y     L     +   R  +   L S  S+ +++GRLD ++EGLLLLT DG ++
Sbjct: 18  HQHFKIYKPYGFLSQFLPEARKRKKLLGELFSFPSKTMAIGRLDHDSEGLLLLTTDGMMS 77

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------ 179
             +     +     +V             L   I I G  Y  +   +            
Sbjct: 78  HQIRSKGIEKEYYVQVDGDITASAITALQLGVEIGINGEKYQTLPCNVFRLTEEPQLPVR 137

Query: 180 -----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                D + G  +WV++ L EGKNR+I+K+     +   RL+R+  G   +G + AG   
Sbjct: 138 GRKIRDPRHGPTSWVSITLCEGKNRQIRKMTAAVGFATLRLVRVRIGNIFVGGMQAGDVT 197

Query: 235 EVSK 238
            +S 
Sbjct: 198 PLSD 201


>gi|329119600|ref|ZP_08248281.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           bacilliformis ATCC BAA-1200]
 gi|327464197|gb|EGF10501.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           bacilliformis ATCC BAA-1200]
          Length = 186

 Score = 82.9 bits (203), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 40/179 (22%), Positives = 76/179 (42%), Gaps = 21/179 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L +++KP G+V      +   ++ D + +        GRLD ++EGLLLLT +G +   +
Sbjct: 4   LIVFNKPCGVVCQFGAHEKHRSLKDFIDAPGF--YPAGRLDTDSEGLLLLTCNGRMQARI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------------- 179
             P  +  + Y  +  G    DKL  L++ + +        ++ L               
Sbjct: 62  AHPKFKLEKTYWAQLEGSPQADKLAALQRPMDLGDFVARPAKIRLPDAGETDALWPRVPP 121

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTR 234
               +   + W+ + + EGKNR+++++     +   RL+R+  G   L    L  G  R
Sbjct: 122 VRLRKTVPDFWLEIKIAEGKNRQVRRMTAKAGYPCLRLVRVGIGRLNLSGCALRPGEWR 180


>gi|255030766|ref|ZP_05302717.1| hypothetical protein LmonL_19661 [Listeria monocytogenes LO28]
          Length = 69

 Score = 82.9 bits (203), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 1/69 (1%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D I V G P+   E 
Sbjct: 1  MRLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQITVHGTPVVYQEF 60

Query: 73 TRLWLYHKP 81
              L+   
Sbjct: 61 VYFMLHKPQ 69


>gi|218682180|ref|ZP_03529781.1| RNA-binding S4 domain protein [Rhizobium etli CIAT 894]
          Length = 130

 Score = 82.9 bits (203), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 49/79 (62%), Positives = 61/79 (77%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +R+SKV+ARAG+ASRR++ERMI + RV +NG  L+   VNV   D IEVDGVP+R 
Sbjct: 44  DAKAERISKVMARAGVASRRDIERMIMEGRVTLNGRALDTPVVNVTLADRIEVDGVPIRG 103

Query: 70  AERTRLWLYHKPIGLVTTH 88
            ERTRLWLYHKP GLVTT+
Sbjct: 104 IERTRLWLYHKPAGLVTTN 122


>gi|226330250|ref|ZP_03805768.1| hypothetical protein PROPEN_04163 [Proteus penneri ATCC 35198]
 gi|225201045|gb|EEG83399.1| hypothetical protein PROPEN_04163 [Proteus penneri ATCC 35198]
          Length = 176

 Score = 82.9 bits (203), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 40/171 (23%), Positives = 70/171 (40%), Gaps = 1/171 (0%)

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             PS +  R Y VR  G++D  K+  L +G+ ++        V+    +G N W  V L 
Sbjct: 1   MHPSREVEREYAVRVFGEIDDAKIRQLTRGVQLEDGPASFRSVSYRGGEGINQWYNVSLT 60

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHLLEEA 253
           EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+    +        L + 
Sbjct: 61  EGRNREVRRMWEAVGVQVSRLIRVRYGDIDLPKGLPRGGWVELGLAQINYLRQLVELNDE 120

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
            V   A       +  ++     +     +     S  K   S+++     
Sbjct: 121 TVTKVAVEKDQRRIKANQIRRAVKRHTKISTRTSTSPAKRASSRRQSAGNK 171


>gi|145309058|gb|ABP57738.1| 16S rRNA pseudouridine synthase [Chromobacterium violaceum]
          Length = 150

 Score = 82.9 bits (203), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 36/150 (24%), Positives = 67/150 (44%), Gaps = 3/150 (2%)

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDT 181
           +T  G LA  +  PS +  R Y VR  G++  + +  +  G+ ++       +       
Sbjct: 1   ITTSGELANRMMHPSFEVEREYSVRVLGELTPEIMKQMVAGVELEDGEARFDRVFQKGGP 60

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
           ++ +N W  V ++EG+NRE++++FE F   V+RLIR+ +G   L   L  G   E++   
Sbjct: 61  EEAANQWFNVVIKEGRNREVRRMFEHFGLTVSRLIRVRFGNIGLPPRLKRGQFYELNSAE 120

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRD 270
           +   +    L        AP+  +      
Sbjct: 121 VAAVMKWSNLTVTGGKKAAPVKKASAKAHR 150


>gi|323527142|ref|YP_004229295.1| pseudouridine synthase [Burkholderia sp. CCGE1001]
 gi|323384144|gb|ADX56235.1| pseudouridine synthase [Burkholderia sp. CCGE1001]
          Length = 189

 Score = 82.9 bits (203), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 38/176 (21%), Positives = 64/176 (36%), Gaps = 17/176 (9%)

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
                T        +            V   GRLD ++EGLLLLT+DG L   +  P  +
Sbjct: 7   NKPFGTICQFSPHETRASLADWVKVPGVYPAGRLDSDSEGLLLLTDDGALQARIAEPRHK 66

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---------------S 185
            ++ Y  +  G VD   L  L +G+ +        +                        
Sbjct: 67  LVKRYWAQVEGTVDAAALKKLARGVDLGDYVTKPCRADYVEPGDTLWTRTPPIRYRAAIP 126

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKK 239
            +W+ + + EGKNR+++++     +   RL+R+  G   +    L  G   EV   
Sbjct: 127 TSWIELSITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFSLGLQPGEYVEVPPN 182


>gi|148977560|ref|ZP_01814139.1| pseudouridine synthase family 1 protein [Vibrionales bacterium
           SWAT-3]
 gi|145963211|gb|EDK28478.1| pseudouridine synthase family 1 protein [Vibrionales bacterium
           SWAT-3]
          Length = 242

 Score = 82.9 bits (203), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 50/186 (26%), Positives = 92/186 (49%), Gaps = 16/186 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E  ++ L++KP   ++  +D +GR T+ D +P     V + GRLD ++EGL++L
Sbjct: 59  KPKIALEDRKVILFNKPFDTLSQFTDGEGRKTLADFIP--VKDVYAAGRLDRDSEGLMVL 116

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG     L  P+++  + Y V+  G   ++ L+ L+KG+ ++       +V L  +  
Sbjct: 117 TNDGIFQAKLTQPNSKSPKTYWVQVEGAPSEEDLDKLRKGVELKDGMTLPAKVELMAEPE 176

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + + EG+NR+++++     +   RLIR S G   +G L  
Sbjct: 177 VWDRNPPVRFRAAIPTTWLVITIIEGRNRQVRRMTANIGFPTLRLIRYSMGDMNVGQLQP 236

Query: 231 GSTREV 236
           G  +E+
Sbjct: 237 GEWKEI 242


>gi|262043150|ref|ZP_06016288.1| ribosomal large subunit pseudouridine synthase E [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
 gi|259039538|gb|EEW40671.1| ribosomal large subunit pseudouridine synthase E [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
          Length = 216

 Score = 82.9 bits (203), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 42/198 (21%), Positives = 75/198 (37%), Gaps = 18/198 (9%)

Query: 52  VNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
             V      +V      +  +T +        L     +    +          + V + 
Sbjct: 19  HRVERFSTQQVTRQRKERQPKTVILFNKPYDVLPQFTDEAGRSTLKDFI---PVAGVYAA 75

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD ++EGLL+LTNDG L   L  P  +  ++Y V+  G+   + L  L+ G+ +    
Sbjct: 76  GRLDRDSEGLLVLTNDGALQAKLTQPGKRTGKIYYVQVEGEPTPEALTALRDGVPLNDGP 135

Query: 172 YGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
                                  + +     W+ + L EG+NR+++++     +   RLI
Sbjct: 136 TLPAGVELVEEPVWLWPRNPPIRERKSIPTRWLKITLYEGRNRQVRRMTAHVGFPTLRLI 195

Query: 217 RISYGPFQLGTLLAGSTR 234
           R + G + L  L  G  R
Sbjct: 196 RYAMGGYTLDGLANGDWR 213


>gi|292899235|ref|YP_003538604.1| ribosomal large subunit pseudouridine synthase E [Erwinia amylovora
           ATCC 49946]
 gi|291199083|emb|CBJ46194.1| ribosomal large subunit pseudouridine synthase E [Erwinia amylovora
           ATCC 49946]
          Length = 208

 Score = 82.9 bits (203), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 39/153 (25%), Positives = 67/153 (43%), Gaps = 15/153 (9%)

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
                 + + GRLD ++EGL++LTNDG L   L  P  +  +VY V+  G   +  L  L
Sbjct: 55  YIPHPGIYAAGRLDRDSEGLMVLTNDGALQAQLTQPGKRTGKVYFVQVEGCPQESDLLPL 114

Query: 162 KKGIVIQGICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
           + G+ ++                          + +     W+ + L EG+NR+++++  
Sbjct: 115 RDGVNLKDGPTLPAVVERVAAPGWLWDRQPPIRERKAIPTCWLKITLYEGRNRQVRRMTA 174

Query: 207 FFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
              +   RLIR S G   L  L  G  R++S +
Sbjct: 175 HIGYPTLRLIRFSMGNLGLRALAPGEWRDISHE 207


>gi|261377574|ref|ZP_05982147.1| ribosomal large subunit pseudouridine synthase E [Neisseria cinerea
           ATCC 14685]
 gi|269146318|gb|EEZ72736.1| ribosomal large subunit pseudouridine synthase E [Neisseria cinerea
           ATCC 14685]
          Length = 186

 Score = 82.9 bits (203), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 43/178 (24%), Positives = 79/178 (44%), Gaps = 21/178 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L +++KP G++   S  +   ++ D +          GRLD ++EGLLLLT+DG L   +
Sbjct: 4   LIIFNKPYGVICQFSPHEKHKSLKDFID--LPGFYPAGRLDTDSEGLLLLTDDGWLQAKI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y  +  G  D+ +L  L+KGI +         V +               
Sbjct: 62  TDPKFKHPKTYWAQLEGVPDETRLERLRKGIDLGDFVTRPATVRILKHGETDPLWERIPP 121

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL--AGST 233
               +   + W+ + + EGKNR+++++     +   RL+R++ G  +L  L    G  
Sbjct: 122 IRVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLVRVASGRLKLFDLDLKPGEW 179


>gi|255036743|ref|YP_003087364.1| pseudouridine synthase [Dyadobacter fermentans DSM 18053]
 gi|254949499|gb|ACT94199.1| pseudouridine synthase [Dyadobacter fermentans DSM 18053]
          Length = 201

 Score = 82.9 bits (203), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 80/189 (42%), Gaps = 23/189 (12%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP  +++  S      T+ D   +    +  VGRLD ++EGLLLLTND  L   L
Sbjct: 4   YFLIYKPFNMLSQFSREGDHQTLADLGFTFAKDIYPVGRLDADSEGLLLLTNDNFLKTKL 63

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLD---------- 180
             P  +  R Y V+  G+V  +    L  G+ I    +       ++             
Sbjct: 64  LEPRNRHTRTYYVQVEGEVTDEACRQLSAGVSISINGKQYKTLPAEIAKIAEPELPERNP 123

Query: 181 ----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL-----LAG 231
                +    +W++V LREGKNR+++++     +   RL+R S G   L          G
Sbjct: 124 PIRFRKNIPTSWLSVTLREGKNRQVRRMTAAVGFPTLRLVRWSIGKISLADKKINFPNPG 183

Query: 232 STREVSKKI 240
              EV+ K 
Sbjct: 184 DVWEVTPKE 192


>gi|307102233|gb|EFN50580.1| hypothetical protein CHLNCDRAFT_14498 [Chlorella variabilis]
          Length = 183

 Score = 82.5 bits (202), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 45/181 (24%), Positives = 74/181 (40%), Gaps = 25/181 (13%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLR--KAERTRLW 76
           IA AG+ASRR  + +I   +VKVNG ++      V    D + V G  +     +R   +
Sbjct: 1   IAAAGVASRRGADDLIFGGQVKVNGKVVTEPGTQVDLRKDRVAVSGREISAAAVQRKYYF 60

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----------------------ISVGRL 114
             +KP G + ++            + S+F                          +VGRL
Sbjct: 61  ALNKPKGYICSNKSEHEDGGEGRLVISLFDDWLARWRQRQARPGGGGGGLPPRLFTVGRL 120

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D+ + GL+ +TNDG  A  +  PST   + Y V    +  Q++L  +  G  + G     
Sbjct: 121 DVASIGLIFVTNDGDWAHKVMHPSTGITKEYSVTLDCKPRQEELQAMAAGCDMGGAFVQP 180

Query: 175 M 175
           +
Sbjct: 181 L 181


>gi|82539753|ref|XP_724240.1| hypothetical protein [Plasmodium yoelii yoelii str. 17XNL]
 gi|23478823|gb|EAA15805.1| putative RNA-binding protein [Plasmodium yoelii yoelii]
          Length = 539

 Score = 82.5 bits (202), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 37/256 (14%), Positives = 76/256 (29%), Gaps = 35/256 (13%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM---STDHIEV-------- 62
            ++++  +  G+ S R     + +  +K+N  ++     NV    + D +E+        
Sbjct: 287 IKLNQYCSYKGLCSSRFAYNNLKKGILKINDNIVYE---NVDVSINKDRVELTKVGKILL 343

Query: 63  -DGVPLRKAERTRLWLYHKPIG-----------------LVTTHSDPDGRSTVFDNLPSI 104
            D + +   +                              +             +     
Sbjct: 344 KDRITIIVNKPKHYLSISPDNKLNNKKLLVRNLIRNENKYIEEEHKCMSYFIYKNINIEK 403

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
            + +   GRLD N+ GLL+ T D   +  L       +    +        +    + K 
Sbjct: 404 VNNLYVCGRLDANSSGLLIYTQDSIASSYLLNKYKYQVEKEYIITTFNEINECHLKMLKD 463

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
            +               Q   +  +   L +G ++ I+K+    N K+  L RI  G   
Sbjct: 464 NLFVDGKL---IYKCHIQYVDSFTLIFKLYQGFHKIIRKICLLSNIKIRSLHRIRIGKIH 520

Query: 225 LGTLLAGSTREVSKKI 240
           L  L  G  R +    
Sbjct: 521 LNNLPLGKWRFLMPNE 536


>gi|319788649|ref|YP_004148124.1| pseudouridine synthase [Pseudoxanthomonas suwonensis 11-1]
 gi|317467161|gb|ADV28893.1| pseudouridine synthase [Pseudoxanthomonas suwonensis 11-1]
          Length = 206

 Score = 82.5 bits (202), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 49/188 (26%), Positives = 84/188 (44%), Gaps = 20/188 (10%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 L  ++KP G++   +D             +   V + GRLD ++EGLLLLT+DG
Sbjct: 17  PRNTPMLIAFNKPYGVLCQFTDRSQPPRPTLAGFGLPKDVYAAGRLDHDSEGLLLLTDDG 76

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
           GLA  L  P  +  + Y V+  G   +++L  L+ G+V+        +V           
Sbjct: 77  GLAHRLTDPLHKQPKTYWVQVEGDPREEQLQALRDGVVLNDGPTRPAKVRRLDPVPALWP 136

Query: 181 -------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-----L 228
                   +   ++W+ V + EG+NR+++++         RL+R++ GP +L       L
Sbjct: 137 RDPPVRFRKTVPDSWLEVVIIEGRNRQVRRMTAAAGLPTLRLVRVAMGPHRLHDRDGTPL 196

Query: 229 LAGSTREV 236
             G  REV
Sbjct: 197 APGEWREV 204


>gi|223940798|ref|ZP_03632631.1| pseudouridine synthase [bacterium Ellin514]
 gi|223890528|gb|EEF57056.1| pseudouridine synthase [bacterium Ellin514]
          Length = 192

 Score = 82.5 bits (202), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 47/181 (25%), Positives = 78/181 (43%), Gaps = 16/181 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP G+++     DG              V  +GRLD ++EGLLLL+++  L   L
Sbjct: 2   LIAFNKPYGVLS-QFTRDGSPNRPLAHFGFPKNVYPIGRLDADSEGLLLLSDEAALNERL 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  Q  R+Y  +       + L  L+KG+++Q       +  L               
Sbjct: 61  LHPRQQHGRIYWAQVEHVPSPEVLTRLEKGVIVQARRTLPCKAWLIDPQPAVPPRVPPIR 120

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +     WV + L EGKNR+++++         RL+R+  G FQL  L AG  + ++  
Sbjct: 121 ERKSIPAVWVGLELVEGKNRQVRRMTAAVGHPTLRLMRMQIGKFQLADLPAGKWKVLTPA 180

Query: 240 I 240
            
Sbjct: 181 E 181


>gi|329909999|ref|ZP_08275183.1| putative Pseudouridylate synthase [Oxalobacteraceae bacterium
           IMCC9480]
 gi|327546326|gb|EGF31346.1| putative Pseudouridylate synthase [Oxalobacteraceae bacterium
           IMCC9480]
          Length = 189

 Score = 82.5 bits (202), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 50/185 (27%), Positives = 84/185 (45%), Gaps = 19/185 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L++KP  ++   S   GR T+ D+L      +   GRLD ++EGL+LLT+DG L   
Sbjct: 2   ALILFNKPYLVLCQFSPQAGRRTLADHLAIP--DIYPAGRLDADSEGLMLLTDDGRLQHD 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------VT 178
           +  P+ +  + Y V+  G  D   LN L+ G+ +        +                 
Sbjct: 60  ISDPTHKQPKAYLVQIEGIPDPVALNTLRTGVFLGDFTSKAAKVIEVATPAWLWPRNPPI 119

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTREV 236
                    W+ + + EGKNR+++++         RL+R++ GP+ L +  LL G +R V
Sbjct: 120 RQRAVTPTRWLLLTITEGKNRQVRRMTAAVGLPTLRLVRVAIGPYSLESHPLLPGESRVV 179

Query: 237 SKKIL 241
               L
Sbjct: 180 DAAEL 184


>gi|237749595|ref|ZP_04580075.1| pseudouridine synthase [Helicobacter bilis ATCC 43879]
 gi|229374808|gb|EEO25199.1| pseudouridine synthase [Helicobacter bilis ATCC 43879]
          Length = 92

 Score = 82.5 bits (202), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 19/87 (21%), Positives = 38/87 (43%), Gaps = 2/87 (2%)

Query: 166 VIQGICYGDMQVTLD--TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
            ++       +V L    +K   + V + + EG+NR+++++FE    +V +L R  Y   
Sbjct: 1   RLEDGKTAPAKVKLLSLDKKKQTSIVQITIHEGRNRQVRRMFEAIGHEVLKLKREEYAFL 60

Query: 224 QLGTLLAGSTREVSKKILREQLGPHLL 250
            L  L  G  RE++   ++        
Sbjct: 61  NLAGLKTGEKRELTPHEVKRLRALAEH 87


>gi|50084378|ref|YP_045888.1| putative pseudouridine synthase [Acinetobacter sp. ADP1]
 gi|49530354|emb|CAG68066.1| putative pseudouridine synthase [Acinetobacter sp. ADP1]
          Length = 264

 Score = 82.5 bits (202), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 45/232 (19%), Positives = 80/232 (34%), Gaps = 22/232 (9%)

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD+++EGL+ LT+ GGL + +  PS +  + Y V+  G + +D L  L+KG+ +    
Sbjct: 38  GRLDLDSEGLMFLTDHGGLNQYITHPSNKKYKTYLVQVDGDITEDALEKLRKGVELADGL 97

Query: 172 YGDMQVTLDTQ---------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
               Q T   +                   +WV + + EG+NR+++++     +   RLI
Sbjct: 98  TLPAQATKVEEPEWLWERNPPVRFRASIPTSWVEISICEGRNRQVRRMTATVGFPTLRLI 157

Query: 217 RISYGPFQLG--TLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNI 274
           R   G   L    L  G      +K +   L P   +  +          +         
Sbjct: 158 RTQIGSINLVKLGLQPGE-----QKEIEPLLYPDFKDVPEDKPYRSRSYVKKPGGTGGKP 212

Query: 275 ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLS 326
           I     D  +   +  +       +       RR                  
Sbjct: 213 IHHKNKDGDKKASDKKKSGTKRIWQMDEDEKPRRKTNGTTRPNTKSRGRRAR 264


>gi|15677349|ref|NP_274504.1| hypothetical protein NMB1496 [Neisseria meningitidis MC58]
 gi|7226738|gb|AAF41852.1| conserved hypothetical protein [Neisseria meningitidis MC58]
 gi|254672402|emb|CBA05707.1| probable pseudouridine synthase [Neisseria meningitidis alpha275]
 gi|316984641|gb|EFV63606.1| conserved hypothetical protein [Neisseria meningitidis H44/76]
 gi|325128549|gb|EGC51422.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           meningitidis N1568]
 gi|325134592|gb|EGC57235.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           meningitidis M13399]
 gi|325136615|gb|EGC59216.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           meningitidis M0579]
 gi|325140627|gb|EGC63146.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           meningitidis CU385]
 gi|325144767|gb|EGC67059.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           meningitidis M01-240013]
 gi|325199899|gb|ADY95354.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           meningitidis H44/76]
          Length = 186

 Score = 82.5 bits (202), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 44/178 (24%), Positives = 79/178 (44%), Gaps = 21/178 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP G++   S  +   ++ D +          GRLD ++EGLLLLT+DG L   +
Sbjct: 4   LIAFNKPYGVICQFSPHEKHKSLKDFIN--LPGFYPAGRLDTDSEGLLLLTDDGRLQAQI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y  +  G  D+ +L  L+KGI + G       + +               
Sbjct: 62  TDPKFKHPKTYWAQLEGVPDESRLESLRKGIDLGGFVTRPASIRILKHGEADSLWERIPP 121

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL--AGST 233
               +   + W+ + + EGKNR+++++     +   RLIR++ G  +L  L    G  
Sbjct: 122 IRVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLIRVASGRLKLFDLDLKPGEW 179


>gi|261339436|ref|ZP_05967294.1| ribosomal large subunit pseudouridine synthase E [Enterobacter
           cancerogenus ATCC 35316]
 gi|288318242|gb|EFC57180.1| ribosomal large subunit pseudouridine synthase E [Enterobacter
           cancerogenus ATCC 35316]
          Length = 217

 Score = 82.5 bits (202), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 52/186 (27%), Positives = 94/186 (50%), Gaps = 17/186 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +K + TR+ L++KP  ++   +D  GRST+ D +P       + GRLD ++EGLL+LTND
Sbjct: 34  KKTQPTRVILFNKPYDVLPQFTDEAGRSTLKDYIPVQGV--YAAGRLDRDSEGLLVLTND 91

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P  +  ++Y V+  G+ D+D L  L+ G+ +                    
Sbjct: 92  GALQATLTQPGKRTGKIYFVQVEGEPDEDALAKLRTGVTLNDGPTLSAGVELVSEPEWLW 151

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ + L EG+NR+++++     +   RLIR + G + L +L  G+
Sbjct: 152 PRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGRYTLDSLANGA 211

Query: 233 TREVSK 238
            R+++ 
Sbjct: 212 WRDIAP 217


>gi|149928218|ref|ZP_01916462.1| pseudouridine synthase, Rsu [Limnobacter sp. MED105]
 gi|149823024|gb|EDM82265.1| pseudouridine synthase, Rsu [Limnobacter sp. MED105]
          Length = 214

 Score = 82.5 bits (202), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 36/204 (17%), Positives = 72/204 (35%), Gaps = 22/204 (10%)

Query: 51  AVNVMS-------TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
            + +          D + +DG      +   + ++       +     +           
Sbjct: 5   GIQIDPEIDEISLGDTLLIDGKSFEITQYKYVLMHKPAGYETSHLPSHNPSVFDLLPKHY 64

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARV----LELPSTQWLRVYRVRFHGQVDQDKLN 159
           I   + + GRLD++T GLLL ++DG               +  ++Y V         +L 
Sbjct: 65  IKRGLQAAGRLDVDTTGLLLFSDDGQFIHRLISGKVGTKQEIEKIYEVTGARPFSDLQLQ 124

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAW----VTVGLREGKNREIKKVFEFFNWKVNRL 215
            L +G+ +           +     +       + +G+  GK  ++K++       V+ L
Sbjct: 125 RLLEGVDLDDEP------EIIYASRATLLADGRLELGITTGKYHQVKRMVAAVGNHVDGL 178

Query: 216 IRISYGPFQL-GTLLAGSTREVSK 238
            R S GP++L   L AGS  E+  
Sbjct: 179 HRRSVGPYELPADLAAGSYIEIDP 202


>gi|53803500|ref|YP_114625.1| RNA pseudouridine synthase family protein [Methylococcus capsulatus
           str. Bath]
 gi|53757261|gb|AAU91552.1| RNA pseudouridine synthase family protein [Methylococcus capsulatus
           str. Bath]
          Length = 231

 Score = 82.5 bits (202), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 94/231 (40%), Gaps = 6/231 (2%)

Query: 61  EVDGVPLRKAER-----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            ++G  +   +R       L  +     LV+                    R ++VGRLD
Sbjct: 1   MLNGHLVNLEKRLQAFTRVLLYHKPVGELVSRRDPEGRPLIFSRLPRLELGRWVAVGRLD 60

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           +NT+GL+LLTN+G LA  L  PS    R Y VR  G V +  +  L  G+ ++       
Sbjct: 61  VNTQGLILLTNNGELAHRLMHPSHAVEREYAVRILGTVSEAVIERLLDGVQLEDGPARFE 120

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTR 234
            V     +G+N W  V +REG+NR +++++E  N  V+RLIR+ YG   L   L AG++ 
Sbjct: 121 SVAEAGGEGANRWFHVVVREGRNRLVRRLWESQNLVVSRLIRVRYGDIVLPPRLRAGASI 180

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
           E+  + L   L    L                         +       + 
Sbjct: 181 ELEGEALDGLLRSVGLPPVTPETPQKRRFGGETRGREERRRNRRSALSGKR 231


>gi|313607203|gb|EFR83670.1| ribosomal small subunit pseudouridine synthase A, putative
           [Listeria monocytogenes FSL F2-208]
          Length = 99

 Score = 82.5 bits (202), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 23/95 (24%), Positives = 39/95 (41%), Gaps = 4/95 (4%)

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
           +  G V  + +     GI +        +         N  + V ++EGK  ++K++F  
Sbjct: 2   KIDGDVVAEDVTAFADGITLDDGYT--CKSARLEIINPN-EIKVTIQEGKFHQVKRMFAA 58

Query: 208 FNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
               V+ L RIS G  QL   L  G  R +++  L
Sbjct: 59  RGKTVSYLKRISMGNLQLDESLELGEYRPLTETEL 93


>gi|145633751|ref|ZP_01789476.1| hypothetical protein CGSHi3655_04589 [Haemophilus influenzae 3655]
 gi|144985410|gb|EDJ92237.1| hypothetical protein CGSHi3655_04589 [Haemophilus influenzae 3655]
          Length = 131

 Score = 82.5 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 23/127 (18%), Positives = 53/127 (41%), Gaps = 14/127 (11%)

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------------VTL 179
           +  P  +  + Y V+  G  ++  L  L+KG+ ++       +                 
Sbjct: 1   MADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGMTKPAKVRLISEPNLWERNPPIR 60

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R +S  
Sbjct: 61  ERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSINGLENGSFRLLSLD 120

Query: 240 ILREQLG 246
            ++    
Sbjct: 121 EIKALFQ 127


>gi|261400746|ref|ZP_05986871.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           lactamica ATCC 23970]
 gi|269209518|gb|EEZ75973.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           lactamica ATCC 23970]
          Length = 186

 Score = 82.1 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 42/178 (23%), Positives = 76/178 (42%), Gaps = 21/178 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP G++   S  +   ++ D +          GRLD ++EGLLLLT+DG L   +
Sbjct: 4   LIAFNKPYGVICQFSPHEKHKSLKDFID--LPSFYPAGRLDTDSEGLLLLTDDGWLQAKI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-----------------QV 177
             P  +  + Y  +  G  D+ +L  L+KGI +                           
Sbjct: 62  TDPKFKHPKTYWAQLEGLPDESRLESLRKGIDLGDFVTRPALVRVLNPGEAERLWERVPP 121

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGST 233
               +   + W+ + + EGKNR+++++     +   RL+R++ G  +L    L  G  
Sbjct: 122 IRVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLVRVASGRLKLFDLDLRPGEW 179


>gi|87124863|ref|ZP_01080711.1| Pseudouridine synthase, Rsu [Synechococcus sp. RS9917]
 gi|86167742|gb|EAQ69001.1| Pseudouridine synthase, Rsu [Synechococcus sp. RS9917]
          Length = 212

 Score = 82.1 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 51/188 (27%), Positives = 78/188 (41%), Gaps = 23/188 (12%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L HKP G+++  +   G             +V + GRLD ++EGLLLLT +G L + L 
Sbjct: 8   LLLHKPYGVLSQFTPEPGSRWRCLADLVPVPQVYAAGRLDADSEGLLLLTTEGRLQQRLT 67

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-----------------VT 178
            P     R Y V+  G     +L  L  G+++QG      Q                   
Sbjct: 68  DPRFGHWRTYWVQVEGTATDKQLQQLCDGVLVQGRQTLPAQAQRLRHDQIQPWPDRVPPI 127

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQLGTLLAGS 232
            + +     W+ + LREG+NR+++++         RLIR +        P  L  L  GS
Sbjct: 128 RERRSIPTDWLELSLREGRNRQVRRMTAAVGLPTLRLIRSAIDLMDGGLPLNLNGLAPGS 187

Query: 233 TREVSKKI 240
            R VS + 
Sbjct: 188 WRPVSTEE 195


>gi|62179758|ref|YP_216175.1| putative ribosomal large subunit pseudouridine synthase [Salmonella
           enterica subsp. enterica serovar Choleraesuis str.
           SC-B67]
 gi|62127391|gb|AAX65094.1| putative ribosomal large subunit pseudouridine synthase [Salmonella
           enterica subsp. enterica serovar Choleraesuis str.
           SC-B67]
 gi|322714228|gb|EFZ05799.1| putative ribosomal large subunit pseudouridine synthase [Salmonella
           enterica subsp. enterica serovar Choleraesuis str. A50]
          Length = 219

 Score = 82.1 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 44/172 (25%), Positives = 79/172 (45%), Gaps = 15/172 (8%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLL+LTND
Sbjct: 60  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIPVQGV--YAAGRLDCDSEGLLVLTND 117

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L  +    +               + D L                ++   + +    +
Sbjct: 118 GVLQALRTGVTLNDGPTLPAGIEIVAEPDWLWP----------RTPPIR---ERKNIPTS 164

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           W+ V L EG+NR+++++         RLIR S G + L  L  G  RE++++
Sbjct: 165 WLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQWREIAQE 216


>gi|259908737|ref|YP_002649093.1| Ribosomal large subunit pseudouridine synthase E [Erwinia
           pyrifoliae Ep1/96]
 gi|224964359|emb|CAX55868.1| Ribosomal large subunit pseudouridine synthase E [Erwinia
           pyrifoliae Ep1/96]
 gi|283478710|emb|CAY74626.1| ribosomal large subunit pseudouridine synthase [Erwinia pyrifoliae
           DSM 12163]
          Length = 218

 Score = 82.1 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 39/146 (26%), Positives = 66/146 (45%), Gaps = 15/146 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGL++LTNDG L   L  P  +  +VY V+  G   +  L  L+ G+ ++
Sbjct: 72  YAAGRLDRDSEGLMVLTNDGELQAQLTQPGKRTGKVYYVQVEGCPQEGDLQPLRDGVNLK 131

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +     W+ + L EG+NR+++++     +   
Sbjct: 132 DGPTLPAVVEKVAAPDWLWDRQPPIRERKAIPTCWLKITLYEGRNRQVRRMTAHIGFPTL 191

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKK 239
           RLIR S G   L  L  G  R++S +
Sbjct: 192 RLIRFSMGSLGLRALAPGEWRDISDE 217


>gi|167622752|ref|YP_001673046.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
 gi|167352774|gb|ABZ75387.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
          Length = 203

 Score = 82.1 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 39/186 (20%), Positives = 68/186 (36%), Gaps = 17/186 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +     +Y     L     +      +   L     + +++GRLD ++EGLLLLT DG 
Sbjct: 10  PKHQHFLIYKPYGFLSQFVPETRKSKPLLGQLYEFPEKTMAIGRLDHDSEGLLLLTTDGM 69

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLD------- 180
            + ++   + +     +V       Q         I I G        +V L        
Sbjct: 70  QSHLIRSKTIEKEYYVQVDGEVSQAQLAKLRQGVEIGISGGKYLTLPCKVELLIHEPNLP 129

Query: 181 --------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                    + G   W++V + EGKNR+++K+         RL+R+  G   L  +  G 
Sbjct: 130 ARGKKIRDPRHGPTNWLSVTIDEGKNRQVRKMTAAVGLPTLRLVRVRIGAIHLKQMQPGE 189

Query: 233 TREVSK 238
              V+ 
Sbjct: 190 VIPVTG 195


>gi|310767366|gb|ADP12316.1| Ribosomal large subunit pseudouridine synthase E [Erwinia sp.
           Ejp617]
          Length = 218

 Score = 82.1 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 39/146 (26%), Positives = 66/146 (45%), Gaps = 15/146 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGL++LTNDG L   L  P  +  +VY V+  G   +  L  L+ G+ ++
Sbjct: 72  YAAGRLDRDSEGLMVLTNDGELQAQLTQPGKRTGKVYYVQVEGCPQEGDLQPLRDGVNLK 131

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +     W+ + L EG+NR+++++     +   
Sbjct: 132 DGPTLPAVVEKVAAPDWLWDRQPPIRERKAIPTCWLKITLYEGRNRQVRRMTAHIGFPTL 191

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKK 239
           RLIR S G   L  L  G  R++S +
Sbjct: 192 RLIRFSMGSLGLRALAPGEWRDISNE 217


>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 = 82.1 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 34/247 (13%), Positives = 69/247 (27%), Gaps = 37/247 (14%)

Query: 3   DKNIVQ--ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           DK ++Q  +    +R+   +A     +R  ++++I  + V VNG  ++  +  V   D +
Sbjct: 5   DKIVLQGEKEDEGKRIDVFLAAELDYTRSYIKKLIVDELVFVNGKTVK-PSYKVKENDEV 63

Query: 61  EVD------------GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
            V+             +PL     +   + +      +V         + V   L    +
Sbjct: 64  VVNIPEAEKIDVLPENIPLDILYEDDDIIVINKPQGMVVHPAPGNYSGTLVNALLYHCKN 123

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ----------- 155
                G L       L     G +       +   L                        
Sbjct: 124 LSGINGILRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIKERSVFKKYVAIVEGVIKHE 183

Query: 156 ---------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          KK  VI+   Y      +  +   N  V   ++ G+  +I+    
Sbjct: 184 EGKIEALIGRHPVDRKKMAVIEDGRYALTLYKVLERFKENTLVEAVIKTGRTHQIRVHMA 243

Query: 207 FFNWKVN 213
           +    V 
Sbjct: 244 YIGHPVV 250


>gi|317047747|ref|YP_004115395.1| pseudouridine synthase [Pantoea sp. At-9b]
 gi|316949364|gb|ADU68839.1| pseudouridine synthase [Pantoea sp. At-9b]
          Length = 224

 Score = 82.1 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 51/187 (27%), Positives = 89/187 (47%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R     R+ L++KP  ++   SD  GR T+ D +P   + V + GRLD ++EGL++LTND
Sbjct: 34  RPKGPLRVILFNKPFDVLPQFSDEAGRRTLKDFVP--VTDVYAAGRLDRDSEGLMVLTND 91

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P  +  ++Y V+  G+     L+ L+ G+ +                    
Sbjct: 92  GALQARLTQPGKRTGKIYFVQVEGEPQDSDLSRLRSGVTLNDGPTLPAGVERVAAPEWLW 151

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +     W+ + L EG+NR+++++     +   RLIR + G +QL  L  G 
Sbjct: 152 PRQPPIRERKAIPTCWLKITLYEGRNRQVRRMTAHIGFPTLRLIRYAMGEYQLDHLAPGE 211

Query: 233 TREVSKK 239
            R++S +
Sbjct: 212 WRDISAE 218


>gi|293396525|ref|ZP_06640801.1| ribosomal large subunit pseudouridine synthase E [Serratia
           odorifera DSM 4582]
 gi|291420789|gb|EFE94042.1| ribosomal large subunit pseudouridine synthase E [Serratia
           odorifera DSM 4582]
          Length = 208

 Score = 81.8 bits (200), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 41/148 (27%), Positives = 66/148 (44%), Gaps = 15/148 (10%)

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
              F+ V + GRLD ++EGLL+LTNDG L   L  P  +  +VY V+  G    D +  L
Sbjct: 56  FIPFNDVYAAGRLDRDSEGLLVLTNDGKLQAQLTQPGKRTGKVYYVQVEGAPQDDDVAPL 115

Query: 162 KKGIVIQGICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
           + G+ ++                          + +     W+ + L EG+NR+++++  
Sbjct: 116 RAGVTLKDGPTLPAGVELVDEPTWLWPRHPPIRERKAIPTRWLKITLYEGRNRQVRRMTA 175

Query: 207 FFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              +   RLIR S G   LG L  G  +
Sbjct: 176 HIGFPTLRLIRYSMGELALGELQPGEWK 203


>gi|296314071|ref|ZP_06864012.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           polysaccharea ATCC 43768]
 gi|296839324|gb|EFH23262.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           polysaccharea ATCC 43768]
          Length = 186

 Score = 81.8 bits (200), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 44/178 (24%), Positives = 79/178 (44%), Gaps = 21/178 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L +++KP G++   S  +   ++ D +          GRLD ++EGLLLLT+DG L   +
Sbjct: 4   LIIFNKPYGVICQFSPHEKHKSLKDFIN--LPGFYPAGRLDTDSEGLLLLTDDGRLQAQI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y  +  G  D+ +L  L+KGI +         V L               
Sbjct: 62  TDPKFKHPKTYWAQLEGVPDETRLESLRKGIDLGDFVTRPASVRLLEHGEADSLWERIPP 121

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL--AGST 233
               +   + W+ + + EGKNR+++++     +   RL+R++ G  +L  L    G  
Sbjct: 122 IRVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLVRVASGRLKLFDLDLKPGEW 179


>gi|91776490|ref|YP_546246.1| ribosomal large subunit pseudouridine synthase E [Methylobacillus
           flagellatus KT]
 gi|91710477|gb|ABE50405.1| ribosomal large subunit pseudouridine synthase E [Methylobacillus
           flagellatus KT]
          Length = 176

 Score = 81.8 bits (200), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 43/177 (24%), Positives = 79/177 (44%), Gaps = 17/177 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L++KP G++   S  +   T+ D +        + GRLD ++EGLL+LT+DG L   +
Sbjct: 2   LILFNKPYGVICQFSPHEKHKTLKDYIAVPGV--YAAGRLDTDSEGLLILTDDGRLQHRI 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------VTL 179
             P  +  + Y V+  G    + L  L+ G+ +        +                  
Sbjct: 60  SHPRHKEFKTYWVQVEGDPSDEALEPLRHGMDLGDFVTQPAKVRRIEEPAGLWPRHPPIR 119

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + +    AW+ V + EGKNR+++++     +   RL+R + G   L  +  G  R++
Sbjct: 120 ERKAIPTAWLEVIIAEGKNRQVRRMTAKAGFPTLRLVRYAVGQHTLEGIAPGEWRQL 176


>gi|116073158|ref|ZP_01470420.1| Pseudouridine synthase, Rsu [Synechococcus sp. RS9916]
 gi|116068463|gb|EAU74215.1| Pseudouridine synthase, Rsu [Synechococcus sp. RS9916]
          Length = 229

 Score = 81.8 bits (200), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 49/188 (26%), Positives = 78/188 (41%), Gaps = 23/188 (12%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L +KP G+++  +   G              V + GRLD ++EGLLLLT++G L + L 
Sbjct: 11  LLLNKPYGVLSQFTREQGSRWGCLADWVSVPEVYAAGRLDADSEGLLLLTSNGRLQQRLT 70

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK------------ 183
            P     R Y  +  G+    +L  L++G+ IQG      +      +            
Sbjct: 71  DPRFGHWRTYWAQVEGEATASQLTQLEQGVPIQGKLTLPARAQPLASQLSDALPPRDPPI 130

Query: 184 -----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY------GPFQLGTLLAGS 232
                   +W+T+ LREG+NR+++++         RLIR +        P  L  L AG 
Sbjct: 131 RTRATIPTSWITLSLREGRNRQVRRMTAAVGLPTLRLIRTTIDLMDGEAPLSLEGLSAGE 190

Query: 233 TREVSKKI 240
            R  S   
Sbjct: 191 WRPASTAE 198


>gi|78184255|ref|YP_376690.1| pseudouridine synthase, Rsu [Synechococcus sp. CC9902]
 gi|78168549|gb|ABB25646.1| Pseudouridine synthase, Rsu [Synechococcus sp. CC9902]
          Length = 213

 Score = 81.8 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 48/210 (22%), Positives = 81/210 (38%), Gaps = 23/210 (10%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L HKP G+++  +  +               V + GRLD ++EGLL+LT++G L + L 
Sbjct: 4   LLLHKPYGVLSQFTREENSRWASLQDFVDTPDVYAAGRLDADSEGLLVLTSNGRLQQQLT 63

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK------------ 183
            P     R Y V+  G     +L  L+ GI +QG      +      +            
Sbjct: 64  DPRFGHWRTYWVQVEGTPQPHQLQQLRDGITVQGHRTRPAKAAWLKAEAIPTIGDRVPPI 123

Query: 184 -----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQLGTLLAGS 232
                    W+ + L EG+NR+++++         RL+R +        P  L  L  G+
Sbjct: 124 RYRATIPTHWLEISLTEGRNRQVRRMTAAVGLPTLRLVRHTIDLMDGGTPLTLTGLEPGA 183

Query: 233 TREVSKKILREQLGPHLLEEAQVNLDAPIY 262
           +R VSK+     +        +   D    
Sbjct: 184 SRAVSKEEEARFVQLLKGSNPKNQADRRRG 213


>gi|209517462|ref|ZP_03266303.1| pseudouridine synthase [Burkholderia sp. H160]
 gi|209502116|gb|EEA02131.1| pseudouridine synthase [Burkholderia sp. H160]
          Length = 204

 Score = 81.8 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 39/191 (20%), Positives = 69/191 (36%), Gaps = 17/191 (8%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +     + + L        T        +            V   GRLD ++EGL+LLT
Sbjct: 7   VIALPYHSCMSLLALNKPFGTICQFSPHETRASLADWVKVPGVYPAGRLDSDSEGLVLLT 66

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-- 183
           +DG L   +  P  + ++ Y  +  G VD   L  L +G+ +        Q T       
Sbjct: 67  DDGALQARIAEPRHKLVKRYWAQVEGAVDDAALKKLARGVDLGDYVTRPCQATYVEPDSS 126

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TL 228
                            W+ + + EGKNR+++++     +   RL+R+  G   +    L
Sbjct: 127 LWARTPPIRYRAAIPTTWIELSITEGKNRQVRRMTAAVGFPTLRLVRVGVGALDIFSLGL 186

Query: 229 LAGSTREVSKK 239
             G + E+   
Sbjct: 187 QPGESIELRAN 197


>gi|297521852|ref|ZP_06940238.1| 23S rRNA pseudouridine synthase F [Escherichia coli OP50]
          Length = 142

 Score = 81.8 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 20/119 (16%), Positives = 45/119 (37%)

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            +     + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +
Sbjct: 24  EAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELID 83

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
                    ++V   A        ++     + +  +   R   N  +     ++KK  
Sbjct: 84  LFKLIENSSSEVKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 142


>gi|332971549|gb|EGK10499.1| ribosomal large subunit pseudouridine synthase E [Kingella kingae
           ATCC 23330]
          Length = 203

 Score = 81.8 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 48/186 (25%), Positives = 80/186 (43%), Gaps = 21/186 (11%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           K +   L   +KP G++   S  +   T+ D +      V   GRLD ++EGLLLLT+DG
Sbjct: 15  KKQPAMLIALNKPYGIICQFSPHEKHRTLKDLVN--VPNVYPAGRLDTDSEGLLLLTDDG 72

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---- 184
                +  P  +  + Y  +  G  D DKL  L++ + +        Q+ L  +      
Sbjct: 73  KQQARIADPRNKITKTYWAQLEGSPDADKLARLQQPLDLGDFVAQPAQIRLLNENEIAQI 132

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LL 229
                         + W+ + +REGKNR+++++     +   RLIR+  G   L    L 
Sbjct: 133 WTRNPPIRERKTVPDFWLQIQIREGKNRQVRRMTAKAGYPCLRLIRVGIGRVNLFDLGLE 192

Query: 230 AGSTRE 235
            G  +E
Sbjct: 193 LGQWQE 198


>gi|296110743|ref|YP_003621124.1| pseudouridine synthase [Leuconostoc kimchii IMSNU 11154]
 gi|295832274|gb|ADG40155.1| pseudouridine synthase [Leuconostoc kimchii IMSNU 11154]
          Length = 177

 Score = 81.4 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 35/144 (24%), Positives = 66/144 (45%), Gaps = 15/144 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD+++EGLLLLT++G L   L  P  +  + Y V+  G   + ++  L+ G+ ++
Sbjct: 34  YAAGRLDMDSEGLLLLTDNGQLNHALTDPENKAYKTYIVQVEGVPTKAQIKTLETGVELK 93

Query: 169 GICYGDMQVTLDT---------------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +V                   Q    +++ + ++EG+NR+++++         
Sbjct: 94  DGMTLPAKVKRIPYPKWLWEREKPIRVRQNKPTSFLQIKIKEGRNRQVRRMTAAVGVPTL 153

Query: 214 RLIRISYGPFQLGTLLAGSTREVS 237
           RLIR   G + +  L  G  R V 
Sbjct: 154 RLIRTHIGDYHIADLKPGQYRVVK 177


>gi|261380459|ref|ZP_05985032.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           subflava NJ9703]
 gi|284796701|gb|EFC52048.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           subflava NJ9703]
          Length = 186

 Score = 81.4 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 39/173 (22%), Positives = 68/173 (39%), Gaps = 19/173 (10%)

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
                                          GRLD ++EGLLLLTN+G L   +  P  +
Sbjct: 8   NKPYGVICQFSAHEKHQCLKDFVEKPGFYPAGRLDTDSEGLLLLTNNGRLQAQIADPKFK 67

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---------------- 184
            ++ Y  +  G  D+ KL+LL++G+ +        +V +  +                  
Sbjct: 68  QVKTYWAQVEGSPDEAKLDLLRRGVDLGDFVTRPAEVRVLEEGEADVLWPRVPPIRVRKS 127

Query: 185 -SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL--AGSTR 234
             + WV + + EGKNR+++++     +   RL+R++ G   L  L    G  R
Sbjct: 128 VPDFWVEIKISEGKNRQVRRMTAKAGFPCLRLVRVAIGRLNLFDLNLELGQWR 180


>gi|227327062|ref|ZP_03831086.1| putative RNA pseudouridylate synthase [Pectobacterium carotovorum
           subsp. carotovorum WPP14]
          Length = 208

 Score = 81.4 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 45/189 (23%), Positives = 82/189 (43%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                    R+ L++KP  ++   +D  GR T+ D +P       + GRLD ++EGL++L
Sbjct: 21  KRQPDNTPRRIVLFNKPFDVLPQFTDEAGRRTLKDYIPVSGI--YAAGRLDRDSEGLMIL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TNDG L   L  P+ +  ++Y V+  G  D   L   + G+ +                 
Sbjct: 79  TNDGKLQAQLTQPTKKTAKIYYVQVEGIPDDAALTRFRTGLDLNDGKTLPAGAEIVPEPD 138

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +   + W+ + L EG+NR+++++     +   RLIR       +  LL
Sbjct: 139 WLWPRNPPIRERKSIPDCWLKITLNEGRNRQVRRMTANIGYPTLRLIRYGMANQTVENLL 198

Query: 230 AGSTREVSK 238
            G  +E++ 
Sbjct: 199 PGEWKEITD 207


>gi|124022563|ref|YP_001016870.1| pseudouridine synthase [Prochlorococcus marinus str. MIT 9303]
 gi|123962849|gb|ABM77605.1| possible pseudouridine synthase [Prochlorococcus marinus str. MIT
           9303]
          Length = 203

 Score = 81.4 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 48/186 (25%), Positives = 75/186 (40%), Gaps = 23/186 (12%)

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
            +KP G+++  +   G             RV + GRLD ++EGLL+LT  G L   L  P
Sbjct: 1   MNKPYGVLSQFTPEPGSQWRCLADLIPIPRVYAAGRLDADSEGLLVLTAHGRLQHRLTNP 60

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-----------------QVTLD 180
                RVY V+  G   + +L  L  G++IQG                            
Sbjct: 61  HLSHWRVYWVQVEGSPSESQLQKLASGVIIQGKRTRPALVSWLKGKAAPIVRERDPPIRV 120

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQLGTLLAGSTR 234
            Q    +W+ + L+EG+NR+++++         RLIR          P  +  L  G  R
Sbjct: 121 RQSIPTSWLELKLKEGRNRQVRRMTAAVGLPTLRLIRHRIELMDGEPPLSIEGLDPGQWR 180

Query: 235 EVSKKI 240
           +VS + 
Sbjct: 181 QVSSRE 186


>gi|291519152|emb|CBK74373.1| pseudouridine synthase family [Butyrivibrio fibrisolvens 16/4]
          Length = 117

 Score = 81.4 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 18/119 (15%), Positives = 47/119 (39%), Gaps = 2/119 (1%)

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y V    ++  + +  +  G+ +  +     +  ++    +     + L 
Sbjct: 1   MRAVNAHEKEYIVTVDKEITAEFIKSMSSGVYLDELEVTTRKCQIEKLGSNK--FRIILT 58

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           +G NR+I+++ +   ++V  L R+     QLG L   + R+V+ + L+         + 
Sbjct: 59  QGLNRQIRRMCQALGYRVRTLKRVRIMNIQLGNLKEDTYRDVTPEELKTLNNMLKESKN 117


>gi|90408099|ref|ZP_01216269.1| hypothetical protein PCNPT3_08150 [Psychromonas sp. CNPT3]
 gi|90310785|gb|EAS38900.1| hypothetical protein PCNPT3_08150 [Psychromonas sp. CNPT3]
          Length = 209

 Score = 81.4 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 40/198 (20%), Positives = 77/198 (38%), Gaps = 17/198 (8%)

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           TD   +  +           ++     L     +   + ++   L +    ++++GRLD 
Sbjct: 4   TDQTCLTDIVATLQTHQHFKIFKPYGFLSQFVPEKRKKKSLLGELFNFPENIMAIGRLDH 63

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGD 174
           ++EGLLLLT DG ++  +     +     +V          L      I I G       
Sbjct: 64  DSEGLLLLTTDGMMSYKIRSKGIEKEYYVQVDGEITAQAMSLLQKGVEIAINGATYLTLP 123

Query: 175 MQ---------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
            +                  D + G  +WV++ L EGKNR+I+K+     +   RL+R+ 
Sbjct: 124 CKAFKLDVEPKLPTRGRKIRDPRHGPTSWVSITLCEGKNRQIRKMTAAVGFATLRLVRVR 183

Query: 220 YGPFQLGTLLAGSTREVS 237
            G   + +++AG    ++
Sbjct: 184 IGDIHIDSMIAGDVVTLT 201


>gi|313668119|ref|YP_004048403.1| pseudouridine synthase, Rsu [Neisseria lactamica ST-640]
 gi|313005581|emb|CBN87017.1| putative pseudouridine synthase, Rsu [Neisseria lactamica 020-06]
          Length = 186

 Score = 81.4 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 44/178 (24%), Positives = 79/178 (44%), Gaps = 21/178 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L +++KP G++   S  +   ++ D +          GRLD ++EGLLLLT+DG L   +
Sbjct: 4   LIIFNKPYGVICQFSPHEKHKSLKDFIN--LPGFYPAGRLDTDSEGLLLLTDDGRLQAQI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-------- 186
             P  +  + Y  +  G  D+ +L  L+KGI +         V +     +N        
Sbjct: 62  TDPKFKHPKTYWAQLEGVPDETRLESLRKGIDLGDFVTRPASVRVLEHGETNPLWERIPP 121

Query: 187 ---------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGST 233
                     W+ + + EGKNR+++++     +   RL+R++ G  +L    L  G  
Sbjct: 122 IRVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLVRVASGRLKLFDLDLRPGEW 179


>gi|157373982|ref|YP_001472582.1| RNA pseudouridine synthase family protein [Shewanella sediminis
           HAW-EB3]
 gi|157316356|gb|ABV35454.1| RNA pseudouridine synthase family protein [Shewanella sediminis
           HAW-EB3]
          Length = 218

 Score = 81.4 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 67/188 (35%), Gaps = 17/188 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                  ++     L     +      +   L    +  +++GRLD ++EGLLLLT DG 
Sbjct: 29  QPHHHYKIFKPYGYLSQFVPERRKSKKLLAELALFPAGTMAIGRLDHDSEGLLLLTTDGM 88

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQ----------- 176
           ++  +     +     +V                 I I+G        +           
Sbjct: 89  VSHQVRSKKVEKEYYVQVDGDIDDAAILKLQTGVEIGIKGEKYLTLPCKVFKLENEPELP 148

Query: 177 ----VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  D + G  +WV++ + EGKNR+I+K+     +   RL+R+  G   L  + +G 
Sbjct: 149 SNGRKPRDPKHGPMSWVSITIGEGKNRQIRKMTAAAGFPTLRLVRVRIGNIHLDRMQSGE 208

Query: 233 TREVSKKI 240
              +    
Sbjct: 209 VILLKNPE 216


>gi|255523816|ref|ZP_05390781.1| pseudouridine synthase [Clostridium carboxidivorans P7]
 gi|255512519|gb|EET88794.1| pseudouridine synthase [Clostridium carboxidivorans P7]
          Length = 180

 Score = 81.4 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 39/172 (22%), Positives = 66/172 (38%), Gaps = 26/172 (15%)

Query: 97  VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
           ++       + V  VGRLD +TEGLLLLTNDG     L  P     + Y     G +D++
Sbjct: 1   MYFFDDDKMNGVFHVGRLDKDTEGLLLLTNDGEFEHKLMHPQEHIEKTYFFWALGSLDEE 60

Query: 157 KLNLLKKGIVIQGIC--YGDMQ---VTLDTQKGSNAWV--------------------TV 191
               L++GI I          +         K     +                     +
Sbjct: 61  NRKQLEQGIYIGKGEILTKPAKIEVHRCGMYKDFKHEMPIDNLNNIDSNQYNQPVVSGYL 120

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            + EG+N ++K++ +     V  L R+S G   L   +  G  R +++  ++
Sbjct: 121 TITEGRNHQVKRMLKAAGCYVVYLKRVSIGGLMLDESMEKGRYRLLTEVEIK 172


>gi|309378696|emb|CBX22646.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 186

 Score = 81.4 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 44/178 (24%), Positives = 79/178 (44%), Gaps = 21/178 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L +++KP G++   S  +   ++ D +          GRLD ++EGLLLLT+DG L   +
Sbjct: 4   LIVFNKPYGVICQFSPHEKHKSLKDFIN--LPGFYPAGRLDTDSEGLLLLTDDGRLQAQI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-------- 186
             P  +  + Y  +  G  D+ +L  L+KGI +         V +     +N        
Sbjct: 62  TDPKFKHPKTYWAQLEGVPDETRLESLRKGIDLGDFVTRPASVRVLEHGETNPLWERIPP 121

Query: 187 ---------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL--AGST 233
                     W+ + + EGKNR+++++     +   RL+R++ G  +L  L    G  
Sbjct: 122 IRVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLVRVASGRLKLFDLDLKPGEW 179


>gi|86146446|ref|ZP_01064769.1| pseudouridine synthase family 1 protein [Vibrio sp. MED222]
 gi|85835709|gb|EAQ53844.1| pseudouridine synthase family 1 protein [Vibrio sp. MED222]
          Length = 242

 Score = 81.4 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 49/186 (26%), Positives = 91/186 (48%), Gaps = 16/186 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E  ++ L++KP   ++  +D +GR T+ D +P     V + GRLD ++EGLL+L
Sbjct: 59  KPKVAPEDRKVILFNKPFDTLSQFTDGEGRKTLADFIP--VKDVYAAGRLDRDSEGLLVL 116

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG     L  P+++  + Y V+  G   +  L+ L+KG+ ++       +V +  +  
Sbjct: 117 TNDGIFQAKLTQPNSKSTKTYWVQVEGAPSEKDLDKLRKGVELKDGMTLPAEVEVMQEPQ 176

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + + EG+NR+++++     +   RLIR S G   +G L  
Sbjct: 177 VWERTPPVRFRAAIPTTWLAITIIEGRNRQVRRMTANIGFPTLRLIRYSMGNMDVGQLQP 236

Query: 231 GSTREV 236
           G  +++
Sbjct: 237 GEWKDI 242


>gi|295425099|ref|ZP_06817804.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           amylolyticus DSM 11664]
 gi|295065158|gb|EFG56061.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           amylolyticus DSM 11664]
          Length = 173

 Score = 81.0 bits (198), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 39/171 (22%), Positives = 71/171 (41%), Gaps = 4/171 (2%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +      L  T                 +  +  VG LD +T GLLLLTNDG L   L  
Sbjct: 1   MNKPKDVLSATEDRSQRTVISLLKNTDRYQGISPVGCLDKDTTGLLLLTNDGQLNHELLA 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLD--TQKGSNAWVTVGL 193
           P     ++YR +  G ++++ +     G+ +          + +    +K   + + + +
Sbjct: 61  PGKHVDKIYRAKIAGPINEETVKTFASGMTLGDDTKLKPATLKILSQDEKEDTSQIEIKI 120

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           +EGK  +IK++F     K   L RI+ G  +L   L  G    +S + +++
Sbjct: 121 QEGKYHQIKRIFAAVGMKAIELDRIAMGNLRLPPDLKRGEYCTLSPERIQQ 171


>gi|227111561|ref|ZP_03825217.1| putative RNA pseudouridylate synthase [Pectobacterium carotovorum
           subsp. brasiliensis PBR1692]
          Length = 208

 Score = 81.0 bits (198), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 45/187 (24%), Positives = 81/187 (43%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                    R+ L++KP  ++   +D  GR T+ D +P       + GRLD ++EGL++L
Sbjct: 21  KRQPDNAPRRIVLFNKPFDVLPQFTDEAGRRTLKDYIPISGI--YAAGRLDRDSEGLMIL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TNDG L   L  P+ +  ++Y V+  G  D   L   + G+ +                 
Sbjct: 79  TNDGKLQARLTQPTQKTAKIYYVQVEGIPDAAALTRFRTGLDLNDGKTLPAGAEIVPEPS 138

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +   + W+ + L EG+NR+++++     +   RLIR       +  LL
Sbjct: 139 WLWPRNPPIRERKSIPDCWLKITLHEGRNRQVRRMTANIGYPTLRLIRYGMANQTVENLL 198

Query: 230 AGSTREV 236
            G  +E+
Sbjct: 199 PGEWKEI 205


>gi|253688258|ref|YP_003017448.1| pseudouridine synthase [Pectobacterium carotovorum subsp.
           carotovorum PC1]
 gi|251754836|gb|ACT12912.1| pseudouridine synthase [Pectobacterium carotovorum subsp.
           carotovorum PC1]
          Length = 218

 Score = 81.0 bits (198), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 45/187 (24%), Positives = 81/187 (43%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                    R+ L++KP  ++   +D  GR T+ D +P       + GRLD ++EGL++L
Sbjct: 31  KRQPDNAPRRIVLFNKPFDVLPQFTDEAGRRTLKDYIPVSGI--YAAGRLDRDSEGLMIL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TNDG L   L  P+ +  ++Y V+  G  D   L   + G+ +                 
Sbjct: 89  TNDGKLQARLTQPTQKTAKIYYVQVEGIPDDAALTRFRTGLDLNDGKTLPAGAEIVPEPS 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +   + W+ + L EG+NR+++++     +   RLIR       +  LL
Sbjct: 149 WLWPRNPPIRERKSIPDCWLKITLYEGRNRQVRRMTANIGYPTLRLIRYGMANQTVENLL 208

Query: 230 AGSTREV 236
            G  +E+
Sbjct: 209 PGEWKEI 215


>gi|262037640|ref|ZP_06011085.1| ribosomal small subunit pseudouridine synthase A [Leptotrichia
           goodfellowii F0264]
 gi|261748320|gb|EEY35714.1| ribosomal small subunit pseudouridine synthase A [Leptotrichia
           goodfellowii F0264]
          Length = 72

 Score = 81.0 bits (198), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 1/65 (1%)

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREV 236
            ++  + S   V + + EGK  ++K++F+  N KV  L R+  G  +L   L  G  RE+
Sbjct: 2   KVEVIENSEDKVYITITEGKYHQVKRMFKAVNNKVLYLKRVQMGNLKLDDKLKVGKYREL 61

Query: 237 SKKIL 241
           ++K +
Sbjct: 62  TEKEI 66


>gi|16329172|ref|NP_439900.1| hypothetical protein slr0612 [Synechocystis sp. PCC 6803]
 gi|1651652|dbj|BAA16580.1| slr0612 [Synechocystis sp. PCC 6803]
          Length = 185

 Score = 81.0 bits (198), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/161 (22%), Positives = 62/161 (38%), Gaps = 31/161 (19%)

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
           +GRLD ++EGLLLLT++G L   L        R Y  +  G    + L  L++GI     
Sbjct: 1   MGRLDQDSEGLLLLTSNGKLQHRLAHREFAHQRTYFAQVEGSPTDEDLEPLRRGITFADY 60

Query: 171 CYGDMQVTLDTQ--------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
                   + T+                  +W+++ L EG+NR+++++     +   RL+
Sbjct: 61  PTRPAIAKIITEPDFPPRNPPIRYRASIPTSWLSITLTEGRNRQVRRMTAAVGFPTLRLV 120

Query: 217 RISY---GP--------------FQLGTLLAGSTREVSKKI 240
           R+     G                 L  L  G  R ++   
Sbjct: 121 RVQIQVTGRSPQQGKGKSAATWCLTLEGLSPGQWRPLTPWE 161


>gi|256419723|ref|YP_003120376.1| pseudouridine synthase [Chitinophaga pinensis DSM 2588]
 gi|256034631|gb|ACU58175.1| pseudouridine synthase [Chitinophaga pinensis DSM 2588]
          Length = 194

 Score = 81.0 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 49/194 (25%), Positives = 78/194 (40%), Gaps = 21/194 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                 +Y      V T    +       +   + S V  VGRLD ++EGLL+LTND  L
Sbjct: 2   PFKYYIIYKP--FQVLTRFGKEEGKASLADYFDVPSDVYPVGRLDYDSEGLLILTNDKSL 59

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGSN 186
              L  P     R Y V+  G V+ + +  LK+G+ I    +       Q  +  ++   
Sbjct: 60  NHRLLDPKFSHEREYWVQVDGAVNAEAIQQLKQGVKIAIDGKPYQTRRCQAAIFEEEPPV 119

Query: 187 A---------------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + L EGKNR+++K+     +   RLIR       +  L  G
Sbjct: 120 PERNPPIRFRKLIPAPWIRLTLGEGKNRQVRKMTAAVGFPTLRLIRYRIARITVEGLEPG 179

Query: 232 STREVSKKILREQL 245
             RE+ +K + + L
Sbjct: 180 QMREMDRKEIFDLL 193


>gi|221061561|ref|XP_002262350.1| rna pseudouridylate synthase [Plasmodium knowlesi strain H]
 gi|193811500|emb|CAQ42228.1| rna pseudouridylate synthase, putative [Plasmodium knowlesi strain
           H]
          Length = 469

 Score = 81.0 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 38/263 (14%), Positives = 84/263 (31%), Gaps = 31/263 (11%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVD 63
           N   E     ++++     G+ S R     +++  ++VN  ++    + +    D +E+ 
Sbjct: 207 NKKTEKCREMKITQYCWHEGLCSSRFAFNNLSRGIIQVNDQVVFE-NIIISPGRDKVELT 265

Query: 64  --GVPLRKAERTRLWLYHKPIG------------------------LVTTHSDPDGRSTV 97
             G  L + +   + L                               +            
Sbjct: 266 KVGKELLRNKNITIILNKPKYYLSILNDHKTNKKLLARNLIRNENKFIEEEHKCMSYFIN 325

Query: 98  FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
            +      +++   GRLD N+ GLL+ T +  L   L       +    +    +  ++ 
Sbjct: 326 KNVNIEKVNKLYVCGRLDANSTGLLVFTQNTLLCSYLLNKHKHQVEKEYMIKTAEPIEEV 385

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
              L +  ++              Q   +  ++  L +G ++ I+K+    N K+  L R
Sbjct: 386 HMELLRKNILVDGKL---IYKCRIQYVDSFTLSFTLYQGFHKIIRKLCLLSNIKIKALHR 442

Query: 218 ISYGPFQLGTLLAGSTREVSKKI 240
           +  G   L  L  G  R +    
Sbjct: 443 VRIGGIHLKGLPLGKWRFLMPNE 465


>gi|149184681|ref|ZP_01862999.1| Pseudouridine synthase, Rsu [Erythrobacter sp. SD-21]
 gi|148832001|gb|EDL50434.1| Pseudouridine synthase, Rsu [Erythrobacter sp. SD-21]
          Length = 181

 Score = 81.0 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 41/177 (23%), Positives = 77/177 (43%), Gaps = 14/177 (7%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL L +KP G+++  +                  V   GRLD ++EGLLLLT+DG L   
Sbjct: 3   RLILLNKPFGVLSQFTGGKEGVEDTLAHLVDVPDVYPAGRLDKDSEGLLLLTDDGKLQSR 62

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------- 180
           +  P  +  + Y V+  G+   D L  L +G+ ++       +                 
Sbjct: 63  IAEPRYKIAKAYLVQVEGEPGDDALEKLSRGVELKDGMTRPARAKRIDPPPVWERDPPVR 122

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +   ++W+ + + EG+NR+++++         RLIR   G + +  +  G+ R++
Sbjct: 123 YRKSVPDSWIALEITEGRNRQVRRMTAAVGLPTLRLIRWRIGEWSVDGIAPGTYRKI 179


>gi|332520335|ref|ZP_08396797.1| pseudouridine synthase [Lacinutrix algicola 5H-3-7-4]
 gi|332043688|gb|EGI79883.1| pseudouridine synthase [Lacinutrix algicola 5H-3-7-4]
          Length = 179

 Score = 80.6 bits (197), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 37/154 (24%), Positives = 61/154 (39%), Gaps = 17/154 (11%)

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
           L S     + +GRLD  +EGLLLLT DG L+  +     +      V      ++     
Sbjct: 21  LGSFPQGTMPIGRLDEKSEGLLLLTTDGKLSDYVNSSGIEKEYYALVDGDISQEEISSLK 80

Query: 161 LKKGIVIQGIC--YGDMQ---------------VTLDTQKGSNAWVTVGLREGKNREIKK 203
               I   G        +                  D + G  +W+++ L EGK R+++K
Sbjct: 81  KGVEIGFDGKKYQTKPCKVFKLDNAPLLPERGKKIRDARHGPVSWISITLTEGKFRQVRK 140

Query: 204 VFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +         RL+R+  G  QLG L +G+ + + 
Sbjct: 141 MTSAVGCPTLRLVRVRVGNIQLGNLESGAVKPID 174


>gi|298368975|ref|ZP_06980293.1| ribosomal large subunit pseudouridine synthase E [Neisseria sp.
           oral taxon 014 str. F0314]
 gi|298282978|gb|EFI24465.1| ribosomal large subunit pseudouridine synthase E [Neisseria sp.
           oral taxon 014 str. F0314]
          Length = 186

 Score = 80.6 bits (197), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 44/179 (24%), Positives = 81/179 (45%), Gaps = 21/179 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP G++   S+ +    + D +          GRLD ++EGLLLLT++G L   +
Sbjct: 4   LIAFNKPCGVICQFSEHEKHPCLKDYVDRPGF--YPAGRLDTDSEGLLLLTDNGVLQAQI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y  +  G  D++KL+LL  G+ + G      +V L               
Sbjct: 62  ADPKFKREKTYWAQVEGSPDEEKLDLLCNGMDLGGFVTRPAKVRLLEAGEADILWPRNPP 121

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTR 234
               +   + W+ + + EGKNR+++++     +   RL+R++ G   +    L  G  R
Sbjct: 122 VRMRKTVPDFWLEIRIAEGKNRQVRRMTAKAGYPCLRLVRVAVGRLNVFDLGLGLGEWR 180


>gi|330818088|ref|YP_004361793.1| Pseudouridine synthase [Burkholderia gladioli BSR3]
 gi|327370481|gb|AEA61837.1| Pseudouridine synthase [Burkholderia gladioli BSR3]
          Length = 192

 Score = 80.6 bits (197), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 44/191 (23%), Positives = 77/191 (40%), Gaps = 19/191 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +        GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVRTPGV--YPAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------VTL 179
             P  + ++ Y  +  G  D   L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVEGTPDDAALKALARGVDLGDYVTRPCRADYVEPPETLWPRNPPVR 120

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   L    L  G T  + 
Sbjct: 121 FRAAIPTTWIELSITEGKNRQVRRMTAAVGYPTLRLVRVGIGALDLFALGLAPGDTLALP 180

Query: 238 KKILREQLGPH 248
            +   +   PH
Sbjct: 181 PRAPWDGFAPH 191


>gi|291545734|emb|CBL18842.1| 16S rRNA uridine-516 pseudouridylate synthase and related
          pseudouridylate synthases [Ruminococcus sp. SR1/5]
          Length = 68

 Score = 80.6 bits (197), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 11 FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              R++K ++  G+ SRRE +R+    RV VNG L+    + ++    I +DG P++  
Sbjct: 2  DEKIRINKYLSDIGVCSRREADRLTEAGRVTVNGELVST-GMKILPDAEICIDGKPVKNR 60

Query: 71 E 71
          +
Sbjct: 61 K 61


>gi|254974045|ref|ZP_05270517.1| putative RNA pseudouridine synthase [Clostridium difficile
          QCD-66c26]
 gi|255313091|ref|ZP_05354674.1| putative RNA pseudouridine synthase [Clostridium difficile
          QCD-76w55]
          Length = 70

 Score = 80.6 bits (197), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 1/66 (1%)

Query: 12 TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA 70
            QR+ K+++  G  SR E+++   Q  V VNG  +      V    D I  +G  +   
Sbjct: 3  KKQRIDKILSNLGYGSRSEIKKYCKQGSVVVNGSEVSNPGTQVDTENDEILFNGEEVIYR 62

Query: 71 ERTRLW 76
          E   L 
Sbjct: 63 EYIYLI 68


>gi|71278155|ref|YP_267897.1| RNA pseudouridine synthase family protein [Colwellia
           psychrerythraea 34H]
 gi|71143895|gb|AAZ24368.1| RNA pseudouridine synthase family protein [Colwellia
           psychrerythraea 34H]
          Length = 209

 Score = 80.6 bits (197), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 38/184 (20%), Positives = 69/184 (37%), Gaps = 17/184 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                  ++     L     +   +  +   L +   + +++GRLD ++EGLLLLT DG 
Sbjct: 17  ENHQHFKIFKPYGFLSQFVPESRKKKHLLGELFNFPDKTMAIGRLDHDSEGLLLLTTDGM 76

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQ----------- 176
           ++  +   S       +V      D          I I          +           
Sbjct: 77  MSYKVRDKSIVKEYYVQVDGEITTDAISQLQNGVEIGINSTKYLTMPCKAFKLDCEPQLP 136

Query: 177 ----VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  D + G  +W+++ L EGKNR+I+K+     +   RL+R+  G   +  L+AG 
Sbjct: 137 ARGRKIRDPKHGPTSWISITLCEGKNRQIRKMTAAVGFATLRLVRVRIGNIGIDNLIAGD 196

Query: 233 TREV 236
              +
Sbjct: 197 VVAL 200


>gi|167947963|ref|ZP_02535037.1| hypothetical protein Epers_16024 [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 145

 Score = 80.6 bits (197), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 54/136 (39%), Gaps = 3/136 (2%)

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
             L+T+DG  +  +  P+ +  + Y V     + +     L++GI++        +    
Sbjct: 3   SPLITDDGAWSHRILAPARKCSKRYLVTLAESLSERDAERLRQGILLCSE-ARPTKPVQL 61

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
               SN+   + + E +  ++K++F     +V  L R   G  QL   L  G+ R +++ 
Sbjct: 62  QLVSSNSC-RLTITEDRYHQVKRMFAALGNRVVVLHRERIGALQLDPDLSPGNYRALTED 120

Query: 240 ILREQLGPHLLEEAQV 255
            +       L  +   
Sbjct: 121 EISGIFAEPLNRQRWP 136


>gi|157375021|ref|YP_001473621.1| pseudouridine synthase, Rsu [Shewanella sediminis HAW-EB3]
 gi|157317395|gb|ABV36493.1| pseudouridine synthase, Rsu [Shewanella sediminis HAW-EB3]
          Length = 236

 Score = 80.6 bits (197), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 44/188 (23%), Positives = 89/188 (47%), Gaps = 17/188 (9%)

Query: 65  VPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
             ++   +   + L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLL
Sbjct: 47  KTVKPRAKDPIIVLFNKPFDVLCQFTDEQGRQTLKDYIPIP--DVYAAGRLDRDSEGLLL 104

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
           LTNDG L   +  P  +  + Y  +  G+ ++  ++ L+ G+ ++       +V +    
Sbjct: 105 LTNDGKLQSKITEPKKKTFKTYWAQVEGEPNEADVDKLRHGVELKDGMTLPAKVMIMTQP 164

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ + + EG+NR+++++     +   RLIR   G + L  L 
Sbjct: 165 DVWPRTPPIRERKGIPTTWLEIQICEGRNRQVRRMTANIGFPTLRLIRYKIGQWSLNDLQ 224

Query: 230 AGSTREVS 237
           +G  + + 
Sbjct: 225 SGEYQRID 232


>gi|238028429|ref|YP_002912660.1| Pseudouridine synthase [Burkholderia glumae BGR1]
 gi|237877623|gb|ACR29956.1| Pseudouridine synthase [Burkholderia glumae BGR1]
          Length = 192

 Score = 80.6 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/176 (21%), Positives = 64/176 (36%), Gaps = 17/176 (9%)

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
                T        +            V   GRLD ++EGLLLLT+DG L   +  P  +
Sbjct: 7   NKPFGTICQFSPHETRPSLGDWVRAPGVYPAGRLDADSEGLLLLTDDGALQARIAEPRHK 66

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------VTLDTQKGS 185
            ++ Y  +  G  D   L  L +G+ +        +                        
Sbjct: 67  LVKRYWAQVEGAPDAAALKALARGVDLGDYVTRPCRASLVEPPATLWPRTPPVRFRAAIP 126

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKK 239
             W+ + + EGKNR+++++     +   RL+R+  G   L    L  G T E+  +
Sbjct: 127 TTWIELAISEGKNRQVRRMTAAVGFPTLRLVRVGIGALDLFALGLAPGETIELPPR 182


>gi|325204476|gb|ADY99929.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           meningitidis M01-240355]
          Length = 185

 Score = 80.6 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/178 (20%), Positives = 70/178 (39%), Gaps = 22/178 (12%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP G++   S  +   ++ D +                    LLLT+DG L   +
Sbjct: 4   LIAFNKPYGVICQFSPHEKHKSLKDFINFPG---FYPAGRLDTDSEGLLLTDDGRLQAQI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y  +  G  D+ +L  L+KGI + G       + +               
Sbjct: 61  TDPKFKHPKTYWAQLEGVPDESRLESLRKGIDLGGFVTRPASIRILKHGEADSLWERIPP 120

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL--AGST 233
               +   + W+ + + EGKNR+++++     +   RLIR++ G  +L  L    G  
Sbjct: 121 IRVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLIRVASGRLKLFDLDLKPGEW 178


>gi|149192131|ref|ZP_01870353.1| pseudouridine synthase family 1 protein [Vibrio shilonii AK1]
 gi|148834034|gb|EDL51049.1| pseudouridine synthase family 1 protein [Vibrio shilonii AK1]
          Length = 240

 Score = 80.6 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 46/188 (24%), Positives = 81/188 (43%), Gaps = 17/188 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            L   ER  +        L         ++            V + GRLD ++EGL++LT
Sbjct: 50  RLPIEERKVILFNKPYDTLSQFTDGDGRKTLADYI---PVKDVYAAGRLDRDSEGLMVLT 106

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----- 180
           NDG L   L  P ++  + Y V+  G   +D L+ L++G+V++       +V+L      
Sbjct: 107 NDGILQARLTQPKSKSEKTYWVQVDGAPSEDDLDKLRRGVVLKDGPTLPAKVSLMDTPDV 166

Query: 181 ---------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+++ + EG+NR+++++     +   RLIR S   F++G LL G
Sbjct: 167 WERHPPVRFRANIPTTWLSITIIEGRNRQVRRMTANIGFPTLRLIRASMAGFEIGGLLPG 226

Query: 232 STREVSKK 239
              E+   
Sbjct: 227 DWLEIPTD 234


>gi|194290617|ref|YP_002006524.1| 23S rRNA pseudouridine synthase [Cupriavidus taiwanensis LMG 19424]
 gi|193224452|emb|CAQ70463.1| 23S rRNA pseudouridine synthase [Cupriavidus taiwanensis LMG 19424]
          Length = 220

 Score = 80.2 bits (196), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 44/214 (20%), Positives = 70/214 (32%), Gaps = 17/214 (7%)

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
                T     +  +            V   GRLD ++EGLLLLT+DG L   +  P  +
Sbjct: 7   NKPFGTMSQFSEHPTRPTLASCVSVPGVYPAGRLDADSEGLLLLTDDGVLQARIADPRHK 66

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------VTLDTQKGS 185
             + Y  +  G  D D L  L+ G+ +        +                        
Sbjct: 67  LEKTYLAQVEGIPDADALARLRAGVDLGDFVTRPAKVRAVEAPDWLWPRHPPVRFRAAIP 126

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKILRE 243
            +W+ + +REGKNR+++++         RLIR+  G   L    L  G + EV       
Sbjct: 127 TSWLELKIREGKNRQVRRMTAAVGLPTLRLIRVGIGALDLRSLNLAPGESCEVPLAESGM 186

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISE 277
            L       A         + +     R      
Sbjct: 187 ALATSNGRAAPAPRIHVSKTRQANGTKRRLRYKR 220


>gi|25453489|gb|AAL25966.2| probable pseudouridylate synthase [Azotobacter vinelandii]
          Length = 152

 Score = 80.2 bits (196), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/153 (24%), Positives = 68/153 (44%), Gaps = 7/153 (4%)

Query: 93  GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152
            R+ +          +   GRLD+ T GLLLLTNDG  +R +  P  +  +VY V     
Sbjct: 2   HRTVLDLLDEPDRQGLHLAGRLDLGTTGLLLLTNDGHWSRRITHPRYKLAKVYYVETAEP 61

Query: 153 VDQDKLNLLKK--GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           + ++ +    +      + +      + L      +    + L EG+  ++K++F +F  
Sbjct: 62  IGEEYIETFARGLYFAFEDLVTQPAHLELL----GSHSARLTLFEGRYHQVKRMFGYFRN 117

Query: 211 KVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            V RL R S GP +L   L  G  R ++ + ++
Sbjct: 118 PVLRLHRESMGPLRLESELPPGHYRPLTSEEIQ 150


>gi|295677452|ref|YP_003605976.1| pseudouridine synthase [Burkholderia sp. CCGE1002]
 gi|295437295|gb|ADG16465.1| pseudouridine synthase [Burkholderia sp. CCGE1002]
          Length = 189

 Score = 80.2 bits (196), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/176 (21%), Positives = 64/176 (36%), Gaps = 17/176 (9%)

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
                T        +            V   GRLD ++EGLLLLT+DG L   +  P  +
Sbjct: 7   NKPFGTICQFSPHETRASLADWVKVPGVYPAGRLDSDSEGLLLLTDDGALQARIAEPRHK 66

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---------------GS 185
            ++ Y  +  G +D   L  L +G+ +        Q                        
Sbjct: 67  LVKRYWAQVEGALDDAALKKLARGVDLGDFVTRPCQANYVEPSSSLWTRTPPIRYRAAIP 126

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKK 239
             W+ + + EGKNR+++++     +   RL+R+  G   +    L  G + E+   
Sbjct: 127 TTWIELSITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFSLGLQPGESIELRAN 182


>gi|323969764|gb|EGB65046.1| S4 domain-containing protein [Escherichia coli TA007]
          Length = 56

 Score = 80.2 bits (196), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 11 FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G
Sbjct: 4  DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNG 56


>gi|238021932|ref|ZP_04602358.1| hypothetical protein GCWU000324_01836 [Kingella oralis ATCC 51147]
 gi|237866546|gb|EEP67588.1| hypothetical protein GCWU000324_01836 [Kingella oralis ATCC 51147]
          Length = 184

 Score = 80.2 bits (196), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 35/182 (19%), Positives = 75/182 (41%), Gaps = 21/182 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  +    + + +          GRLD ++EGLLLLT++G     +
Sbjct: 2   LIALNKPYGYICQFSPHEKHPNLKELVNVPRV--YPAGRLDTDSEGLLLLTDNGQQQARI 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  + ++ Y  +  G  + +++  L++ + +        +  L               
Sbjct: 60  ASPKFKLIKTYWAQLEGTPNPEQIAQLEQPMDLGDFIARPAKTRLLTPAETARIWPRNPP 119

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTRE 235
               +   + W+ + + EGKNR+++++    ++   RL+R   G   L    L  G  + 
Sbjct: 120 VRYRKTVPDFWLEIQIAEGKNRQVRRMAAKAHYPCLRLVRTGIGRINLFDLDLPLGQWQP 179

Query: 236 VS 237
           ++
Sbjct: 180 LT 181


>gi|254462214|ref|ZP_05075630.1| ribosomal large subunit pseudouridine synthase E [Rhodobacterales
           bacterium HTCC2083]
 gi|206678803|gb|EDZ43290.1| ribosomal large subunit pseudouridine synthase E [Rhodobacteraceae
           bacterium HTCC2083]
          Length = 181

 Score = 80.2 bits (196), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 47/177 (26%), Positives = 79/177 (44%), Gaps = 16/177 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R+ L +KP G+++  +D     T    L       +V   GRLD ++EGLL+LT+DG L 
Sbjct: 3   RVILLNKPFGVLSQFTDKGLEGTTRPTLSAYVDVPQVYPAGRLDRDSEGLLVLTDDGRLQ 62

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----------- 180
             +  P  +  + Y V       +D L  L+KGI ++       QV              
Sbjct: 63  AQIADPKFKKPKTYLVLVERIPSEDALQSLRKGITLKDGMTRPAQVERVEPPELWERDPP 122

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
               +   + W+   +REG+NR+++++         RL+R S G + L  + +G  R
Sbjct: 123 VRFRKSVPDCWLKFTIREGRNRQVRRMTAAVGHPTLRLVRWSVGEWTLDGIASGVWR 179


>gi|86134787|ref|ZP_01053369.1| RNA pseudouridine synthase family protein [Polaribacter sp. MED152]
 gi|85821650|gb|EAQ42797.1| RNA pseudouridine synthase family protein [Polaribacter sp. MED152]
          Length = 189

 Score = 80.2 bits (196), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 45/188 (23%), Positives = 84/188 (44%), Gaps = 21/188 (11%)

Query: 70  AERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            E     L+     L     +    +  +   L       +++GRLD  +EGLLLLT DG
Sbjct: 2   KEHRHFILHKPYGYLSQFITNQTKRKKKMLGELYDFPEGTMAIGRLDFASEGLLLLTTDG 61

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDT--- 181
            +++ +     ++ + Y V+  G + Q+ +N LKKG+ I    +       + ++     
Sbjct: 62  KVSQEIRSS--KYEKEYYVQVDGLITQEAINQLKKGVEIGFEGKKYITKPGKASIINNPE 119

Query: 182 -----------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                      + G  +W++V +REGK R+++K+     +   RL+RI  G   +  L  
Sbjct: 120 FPLRSQKIRDDRHGPTSWISVIIREGKFRQVRKMTAAVGYPTLRLVRIRIGTITIDDLKN 179

Query: 231 GSTREVSK 238
           G  +EV++
Sbjct: 180 GEVKEVNQ 187


>gi|329297161|ref|ZP_08254497.1| 23S rRNA pseudouridine synthase E [Plautia stali symbiont]
          Length = 222

 Score = 80.2 bits (196), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 39/146 (26%), Positives = 69/146 (47%), Gaps = 15/146 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGL++LTNDG L   L  P  +  ++Y V+  G   +  L+ L++GI + 
Sbjct: 76  YAAGRLDRDSEGLMILTNDGALQAQLTQPGKRTGKIYYVQVEGVPQESDLSRLRRGIPLN 135

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +     W+ + L EG+NR+++++     +   
Sbjct: 136 DGPTLPAGAEVVPEPAWLWPRTPPIRERKAIPTCWLKITLYEGRNRQVRRMTAHIGFPTL 195

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKK 239
           RLIR + G +QL  L  G  R++S +
Sbjct: 196 RLIRFAMGDYQLQDLAPGEWRDISDQ 221


>gi|288575200|ref|ZP_05976507.2| ribosomal large subunit pseudouridine synthase E [Neisseria mucosa
           ATCC 25996]
 gi|288568153|gb|EFC89713.1| ribosomal large subunit pseudouridine synthase E [Neisseria mucosa
           ATCC 25996]
          Length = 188

 Score = 80.2 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/171 (22%), Positives = 66/171 (38%), Gaps = 19/171 (11%)

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
                                         GRLD ++EGLLLLTNDG L   +  P  + 
Sbjct: 11  KPYGVICQFSAHEKYGCLKDYVSLPDFYPAGRLDTDSEGLLLLTNDGRLQARIADPKFKL 70

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-----------------TQKG 184
            + Y  +  G  D+ KL++L++G+ +        +V +                   +  
Sbjct: 71  EKTYWAQVEGSPDEAKLDMLRRGVDLGDFVTRPAKVRVLETGEADVLWQRVPPIRVRKSV 130

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL--AGST 233
            + WV + + EGKNR+++++     +   RL+R++ G   L  L    G  
Sbjct: 131 PDFWVEIRISEGKNRQVRRMTAKAGFPCLRLVRVAIGRLNLFDLGLALGQW 181


>gi|254431844|ref|ZP_05045547.1| ribosomal large subunit pseudouridine synthase E [Cyanobium sp. PCC
           7001]
 gi|197626297|gb|EDY38856.1| ribosomal large subunit pseudouridine synthase E [Cyanobium sp. PCC
           7001]
          Length = 243

 Score = 80.2 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 48/198 (24%), Positives = 79/198 (39%), Gaps = 23/198 (11%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L  +  T L  +     +++  +   G              V + GRLD ++EGLLLL
Sbjct: 6   EELPASRPTTLLFHKPYG-VLSQFTPEPGSRWRCLADFIAVPGVYAAGRLDADSEGLLLL 64

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQ--VDQDKLNLLKKGIVIQGICYGDM------- 175
           T +G L + L  P+    R Y V+  G+     + L  L++G+VIQG             
Sbjct: 65  TANGRLQQRLTDPAFGHWRTYWVQVEGEAGQRPEALQQLRQGVVIQGRLTRPALVRCLSD 124

Query: 176 -------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY------GP 222
                             +W+ + L+EG+NR+++++         RLIR++        P
Sbjct: 125 PKLPERDPPIRQRATIPVSWLELQLQEGRNRQVRRMTARVGLPTLRLIRVAIDLMDGEAP 184

Query: 223 FQLGTLLAGSTREVSKKI 240
             L  L  G  R VS + 
Sbjct: 185 LSLSGLKPGDWRRVSHRE 202


>gi|229016829|ref|ZP_04173757.1| Pseudouridine synthase [Bacillus cereus AH1273]
 gi|228744390|gb|EEL94464.1| Pseudouridine synthase [Bacillus cereus AH1273]
          Length = 96

 Score = 79.8 bits (195), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 21/96 (21%), Positives = 51/96 (53%), Gaps = 2/96 (2%)

Query: 160 LLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
           +L++G++++         ++T   ++   A V + + EG+NR+++++FE  + KV +L R
Sbjct: 1   MLERGVMLEDGKTAPANVKITSWDKRKETAIVQLTIHEGRNRQVRRMFEALDCKVVKLKR 60

Query: 218 ISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
             Y   ++G+L  G  RE++   +++       +  
Sbjct: 61  ERYAFLEVGSLRPGDARELTPHEVKQLRALASTKPR 96


>gi|114332166|ref|YP_748388.1| pseudouridine synthase, Rsu [Nitrosomonas eutropha C91]
 gi|114309180|gb|ABI60423.1| Pseudouridine synthase, Rsu [Nitrosomonas eutropha C91]
          Length = 163

 Score = 79.8 bits (195), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 25/128 (19%), Positives = 52/128 (40%), Gaps = 14/128 (10%)

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ- 182
           +T+DG L   +  P  +  + Y V+  G +    +  L  G++++  C    +     + 
Sbjct: 1   MTDDGFLQHRIASPVQKMPKTYWVQVEGNISASAIAALSAGVMLKDRCTRPAKACAMEEP 60

Query: 183 -------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                            +W+ + + EG+NR+++++     +   RLIR   G + L  L 
Sbjct: 61  ALWPRVPPVRWRDSIPTSWLELIITEGRNRQVRRMTAAVGFPTLRLIRYRIGSWSLEGLE 120

Query: 230 AGSTREVS 237
            G  R + 
Sbjct: 121 PGDYRRIR 128


>gi|294670035|ref|ZP_06734992.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           elongata subsp. glycolytica ATCC 29315]
 gi|291308156|gb|EFE49399.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           elongata subsp. glycolytica ATCC 29315]
          Length = 135

 Score = 79.8 bits (195), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 32/139 (23%), Positives = 62/139 (44%), Gaps = 6/139 (4%)

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
                + +VGRLD +T G+LL+TNDG     +  P  +  ++YR       D+     LK
Sbjct: 1   MRNIDMQAVGRLDADTTGVLLITNDGQFNHRMTSPKYKAAKLYRAGLKHPADETFCQSLK 60

Query: 163 KGIVI--QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
            G+++          +  L+    +   + + + EGK  ++K++      +V  L R+ +
Sbjct: 61  NGVLLHDDDETVQAAEAVLE----NPHTLLLTITEGKYHQVKRMVAAAGNRVETLHRLKF 116

Query: 221 GPFQLGTLLAGSTREVSKK 239
           G +    L  G  + ++ K
Sbjct: 117 GEWSAEHLAPGEWQFITIK 135


>gi|90408077|ref|ZP_01216248.1| ribosomal large subunit pseudouridine synthase E [Psychromonas sp.
           CNPT3]
 gi|90310834|gb|EAS38948.1| ribosomal large subunit pseudouridine synthase E [Psychromonas sp.
           CNPT3]
          Length = 214

 Score = 79.8 bits (195), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 39/184 (21%), Positives = 74/184 (40%), Gaps = 14/184 (7%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +  A R  +        L     D +               V + GRLD ++EGLLLL
Sbjct: 29  KTITSATRKIILFNKPFDVLCQFTDDAEQGQRRTLADYIEEKEVYAAGRLDRDSEGLLLL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           TNDG L   +  P+ +  + Y V+  G      L+ L++G++++       +        
Sbjct: 89  TNDGKLQAQITQPNKKTDKTYWVQVEGAPTDADLDKLRQGVILKDGLTLPAKIEFLKDAK 148

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                      +     W+++ + EG+NR+++++     +   RLIR S G + +  +  
Sbjct: 149 IWPRVPPIRQRENIPTTWLSITICEGRNRQVRRMTANIGFPTLRLIRYSIGQWNIEGIDN 208

Query: 231 GSTR 234
           G  +
Sbjct: 209 GHYK 212


>gi|330864072|emb|CBX74148.1| hypothetical protein YEW_ID35840 [Yersinia enterocolitica W22703]
          Length = 132

 Score = 79.8 bits (195), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 21/136 (15%), Positives = 47/136 (34%), Gaps = 4/136 (2%)

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
           + G      +V    +K +    ++ L +G NR+I+++ + F ++V +L R       L 
Sbjct: 1   MLGTVTKKCKV----RKEAPFVFSITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNVNLK 56

Query: 227 TLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
            L  G  R++    L E         +         +   + +      S+  +      
Sbjct: 57  GLPIGEWRDLRDDELIELFKLIENSSSDEKPQKKPKAKPVVAKKPAISRSKPAEKSETNS 116

Query: 287 KNSSQKNGLSKQKKLA 302
               +     ++KK  
Sbjct: 117 AGRKRFTQPGRKKKGR 132


>gi|213024491|ref|ZP_03338938.1| putative ribosomal large subunit pseudouridine synthase B
           [Salmonella enterica subsp. enterica serovar Typhi str.
           404ty]
          Length = 182

 Score = 79.8 bits (195), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 47/178 (26%), Positives = 81/178 (45%), Gaps = 17/178 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P       + GRLD ++EGLL+LTND
Sbjct: 4   KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIPVQGV--YAAGRLDRDSEGLLVLTND 61

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P  +  ++Y V+  G  D   L  L+ G+ +                    
Sbjct: 62  GALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 121

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                  + +    +W+ V L EG+N +++++         RLIR S G + L  L+ 
Sbjct: 122 PRTPPIRERKNIPTSWLKVTLYEGRNHQVRRMTAHVGHPTLRLIRYSMGDYTLNGLIM 179


>gi|167561838|ref|ZP_02354754.1| pseudouridine synthase family protein [Burkholderia oklahomensis
           EO147]
 gi|167569061|ref|ZP_02361935.1| pseudouridine synthase family protein [Burkholderia oklahomensis
           C6786]
          Length = 192

 Score = 79.8 bits (195), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 41/182 (22%), Positives = 68/182 (37%), Gaps = 17/182 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L        T        +            V   GRLD ++EGLLLLT+DG L   +
Sbjct: 1   MHLIALNKPFGTICQFSPHETRGSLGDWVKTPGVYPAGRLDADSEGLLLLTDDGALQAKI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  + ++ Y  +  G  D   L  L++G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVEGAPDAGALATLERGVDLGDYVTRPCRARFVTPPDTLWPRNPPVR 120

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVS 237
                   W+ + + EGKNR+++++     +   RLIR+  G   L    L  G TRE+ 
Sbjct: 121 YRAAIPTTWIELEIAEGKNRQVRRMTAAVGFPTLRLIRVGIGALDLFALGLAPGETRELP 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>gi|300174214|ref|YP_003773380.1| ribosomal large subunit pseudouridine synthase E [Leuconostoc
           gasicomitatum LMG 18811]
 gi|299888593|emb|CBL92561.1| ribosomal large subunit pseudouridine synthase E [Leuconostoc
           gasicomitatum LMG 18811]
          Length = 177

 Score = 79.8 bits (195), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 47/178 (26%), Positives = 85/178 (47%), Gaps = 17/178 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP  ++T  +DPDGR T+ D +        + GRLD+++EGLLLLT+ G L   L
Sbjct: 2   IILFNKPYNVLTKFTDPDGRPTLADYIDIPRV--YAAGRLDMDSEGLLLLTDSGKLNHDL 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT------------- 181
             P  +  + Y V+  G   + +L  L++GI ++       +V                 
Sbjct: 60  TDPENKAYKTYVVQVEGIPTKAQLKALEQGIELKDGMTLPAKVKRIPYPKWLWEREKPIR 119

Query: 182 --QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             Q    +++ + ++EG+NR+++++         RLIR     + +G L  G  R + 
Sbjct: 120 VRQNQPTSFLQIKIKEGRNRQVRRMTAAVGIPTLRLIRTHIDAYHIGDLKPGMYRVIK 177


>gi|296113684|ref|YP_003627622.1| ribosomal large subunit pseudouridine synthase E [Moraxella
           catarrhalis RH4]
 gi|295921378|gb|ADG61729.1| ribosomal large subunit pseudouridine synthase E [Moraxella
           catarrhalis RH4]
 gi|326562427|gb|EGE12746.1| ribosomal large subunit pseudouridine synthase E [Moraxella
           catarrhalis 7169]
 gi|326563200|gb|EGE13468.1| ribosomal large subunit pseudouridine synthase E [Moraxella
           catarrhalis 12P80B1]
 gi|326563484|gb|EGE13747.1| ribosomal large subunit pseudouridine synthase E [Moraxella
           catarrhalis 103P14B1]
 gi|326569135|gb|EGE19197.1| ribosomal large subunit pseudouridine synthase E [Moraxella
           catarrhalis BC1]
 gi|326570621|gb|EGE20657.1| ribosomal large subunit pseudouridine synthase E [Moraxella
           catarrhalis BC7]
 gi|326571328|gb|EGE21345.1| ribosomal large subunit pseudouridine synthase E [Moraxella
           catarrhalis BC8]
 gi|326572977|gb|EGE22956.1| ribosomal large subunit pseudouridine synthase E [Moraxella
           catarrhalis CO72]
 gi|326573792|gb|EGE23749.1| ribosomal large subunit pseudouridine synthase E [Moraxella
           catarrhalis 101P30B1]
 gi|326574785|gb|EGE24719.1| ribosomal large subunit pseudouridine synthase E [Moraxella
           catarrhalis O35E]
          Length = 250

 Score = 79.8 bits (195), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 47/249 (18%), Positives = 90/249 (36%), Gaps = 29/249 (11%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            T+L L++KP G+ +             +     +  ++ GRLD ++EGLLLLT++G L 
Sbjct: 1   MTKLVLFNKPYGVHSQFKKDHDGMITLADFIDDKTMRVA-GRLDKDSEGLLLLTDNGRLN 59

Query: 132 R---------VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
                       +   T+  + Y V+        ++  L++G++++       +V    +
Sbjct: 60  HAITTPPTAKNAKDKYTKCAKTYLVQVENIATNVQIQALEQGVMLKDGKTLPAKVQKLDE 119

Query: 183 KG------------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
                                  W+ + + EGKNR+I+++         RLIR   G +Q
Sbjct: 120 NELPIRLWQRNPPVRQRVNIPTTWLKITIVEGKNRQIRRMVAHVGLPCLRLIRSQIGIWQ 179

Query: 225 LGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
           L  L  G +R +     +  L   L  +     + P     +  +   N  S       +
Sbjct: 180 LNGLAVGESRVLQLDQ-QTLLKLGLSAQPTPKQNKPTNLISSNTKGAVNPKSGKIHLLKK 238

Query: 285 MKKNSSQKN 293
                    
Sbjct: 239 PSWRVRPPK 247


>gi|84686403|ref|ZP_01014297.1| RNA pseudouridylate synthase [Maritimibacter alkaliphilus HTCC2654]
 gi|84665586|gb|EAQ12062.1| RNA pseudouridylate synthase [Rhodobacterales bacterium HTCC2654]
          Length = 181

 Score = 79.8 bits (195), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 36/174 (20%), Positives = 70/174 (40%), Gaps = 14/174 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +        L               +      +V   GRLD ++EGLLLLT+DG L   +
Sbjct: 5   ILFNKPFDVLSQFTDTKSPSPRATLSDYIDVPKVYPAGRLDRDSEGLLLLTDDGRLQARI 64

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P ++  + Y  +  G      L+ L+KG+ ++       +V L               
Sbjct: 65  SSPKSRTPKTYLAQVEGAPTDADLDPLRKGVTLKDGLTRPAEVHLIDPPDLWERDPPVRY 124

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +   + W+ + + EG+NR+++++     +   RL+R   G + +  +  G+ R
Sbjct: 125 RKSVPDRWIELTITEGRNRQVRRMTAAVGFPTLRLVRWRVGDWSVEGIAPGTWR 178


>gi|326562796|gb|EGE13091.1| ribosomal large subunit pseudouridine synthase E [Moraxella
           catarrhalis 46P47B1]
          Length = 250

 Score = 79.5 bits (194), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 48/254 (18%), Positives = 95/254 (37%), Gaps = 31/254 (12%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            T+L L++KP G+ +             +     +  ++ GRLD ++EGLLLLT++G L 
Sbjct: 1   MTKLVLFNKPYGVHSQFKKDHDGMITLADFIDDKTMRVA-GRLDKDSEGLLLLTDNGRLN 59

Query: 132 R---------VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
                       +   T+  + Y V+        ++  L++G++++       +V    +
Sbjct: 60  HAITTPPTAKNAKDKYTKCAKTYLVQVENIATNVQIQALEQGVMLKDGKTLPAKVQKLDE 119

Query: 183 KG------------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
                                  W+ + + EGKNR+I+++         RLIR   G +Q
Sbjct: 120 NELPIRLWQRNPPVRQRVNIPTTWLKITIVEGKNRQIRRMVAHVGLPCLRLIRSQIGIWQ 179

Query: 225 LGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
           L  L  G +R +    L +Q+   L   AQ        ++      +  +  +       
Sbjct: 180 LNGLAVGESRVL---QLDQQILLKLGLSAQPTPKQNKPTNLISSNTKGAVNPKSGKIHLL 236

Query: 285 MKKNSSQKNGLSKQ 298
            K +   +    + 
Sbjct: 237 KKPSWRVRPPKFRA 250


>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 = 79.5 bits (194), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 33/247 (13%), Positives = 69/247 (27%), Gaps = 37/247 (14%)

Query: 3   DKNIVQ--ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           DK ++Q  +    +R+   +A     +R  ++++I  + V VNG  ++  +  V   D +
Sbjct: 5   DKIVLQGEKEDEGKRIDVFLAAELDYTRSYIKKLIVDELVFVNGKTVK-PSYKVKENDEV 63

Query: 61  EVD------------GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
            V+             +PL     +   + +      +V         + V   L    +
Sbjct: 64  VVNIPEAEKIDVLPENIPLDILYEDDDIIVINKPQGMVVHPAPGNYSGTLVNALLYHCKN 123

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ----------- 155
                G L       L     G +       +   L                        
Sbjct: 124 LSGINGILRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIKERSVFKKYVAIVEGVIKDE 183

Query: 156 ---------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          KK  VI+   Y      +  +   N  V   ++ G+  +I+    
Sbjct: 184 EGKIEAPIGRHPVDRKKMAVIEDGRYALTLYKVLERFKENTLVEAVIKTGRTHQIRVHMA 243

Query: 207 FFNWKVN 213
           +    + 
Sbjct: 244 YIGHPIV 250


>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 = 79.5 bits (194), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 36/245 (14%), Positives = 84/245 (34%), Gaps = 33/245 (13%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  + ++ ++    R+   +A     SR E++++I +++V VN    ++    +   D I
Sbjct: 1   MMYEFLIDDSNQNTRLDVFLANEVELSRSEIQKLIDEKKVLVNEKTQKK-NYKLNLNDKI 59

Query: 61  EVD----GVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--- 105
           + D       ++          E   L + +K   ++   ++     T+ + L S F   
Sbjct: 60  KFDYEKPDKTIKPQQHDLDIVYEDDYLAIINKDKNVIVHPTETIYSDTLVNYLMSNFENL 119

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL------RVYRVRFHGQV 153
                  R   V RLD +T GL+++  D      L+              +   +     
Sbjct: 120 SDVDGDYRRGIVHRLDKDTTGLIIIAKDNNTHLKLKEIIKNHEITKTYLCIVHGKIDECG 179

Query: 154 DQDKLN-----LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
             ++         KK ++                    + V V ++ G+  +I+    + 
Sbjct: 180 TIEEYMTRNPKDRKKMMISDEGKLSISNYERLDYNDDYSLVKVQIKTGRTHQIRVHMNYI 239

Query: 209 NWKVN 213
           +  + 
Sbjct: 240 HHPIL 244


>gi|304387106|ref|ZP_07369355.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           meningitidis ATCC 13091]
 gi|304338806|gb|EFM04911.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           meningitidis ATCC 13091]
          Length = 186

 Score = 79.5 bits (194), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 43/178 (24%), Positives = 78/178 (43%), Gaps = 21/178 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP G++   S  +   ++ D +          GRLD ++EGLLLLT+DG L   +
Sbjct: 4   LIAFNKPYGVICQFSPHEKHKSLKDFINFPGF--YPAGRLDTDSEGLLLLTDDGRLQAQI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y  +  G  D+ +L  L+KGI + G       + +               
Sbjct: 62  TDPKFKHPKTYWAQLEGVPDESRLESLRKGIDLGGFVTRPASIRILKHGEADSLWERIPP 121

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL--AGST 233
               +   + W+ + + EGKNR+++++     +   RLIR++ G  +L  L       
Sbjct: 122 IRVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLIRVASGRLKLFDLDLKPREW 179


>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 = 79.5 bits (194), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 30/240 (12%), Positives = 63/240 (26%), Gaps = 35/240 (14%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---- 63
           ++    +R+   +A     +R  ++++I      VNG  ++  +  V   D + V+    
Sbjct: 12  EKEDEGKRIDVFLAAELDYTRSYIKKLIVDGLAFVNGKTVK-PSYKVKENDKVVVNIPEA 70

Query: 64  --------GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
                    +PL     +   + +      +V         + V   L    +     G 
Sbjct: 71  EKIDVLPENIPLDILYEDDDIIVINKPQGMVVHPAPGNYSGTLVNALLYHCKNLSGINGI 130

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------------------ 155
           L       L     G +       +   L                               
Sbjct: 131 LRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIKERSVFKKYVAIVEGVIKNEEEKIEAP 190

Query: 156 --DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                   KK  VI+   Y      +  +   N  +   ++ G+  +I+    F    V 
Sbjct: 191 IGRHPVDRKKMAVIEDGRYALTLYKVLERFKENTLIEAVIKTGRTHQIRVHMAFIGHPVV 250


>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 = 79.5 bits (194), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 33/245 (13%), Positives = 62/245 (25%), Gaps = 37/245 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           +V      +R+ + IA     SR + + +I    V +NG ++++ +  V   + +     
Sbjct: 5   VVDSEKKGKRLDQFIASIADISRSQAKNLIEDGEVSINGRIVKKPSYKVKEGETVSFEIP 64

Query: 63  -----DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                D  P      +   ++  + +      +V         + V   L          
Sbjct: 65  EPIPLDLQPENIPLDIVYEDKDVIVINKPAGLVVHPAPGHYSGTLVNALLYYCKDFQGIN 124

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKKGIV 166
           G L       L     G L       + Q L     R                     IV
Sbjct: 125 GTLRPGIVHRLDKDTAGLLVVAKNDLAQQSLIEQFKRRTVGRFYRALVLGIFEKQHDRIV 184

Query: 167 IQGICYGDMQVTLDTQKGS------NAWV------------TVGLREGKNREIKKVFEFF 208
           +        +        S      N WV               L  G+  +I+      
Sbjct: 185 VPIGRDKFDRKKFSPNTTSPKEAITNYWVLESFPTHNVSDIKCKLETGRTHQIRVHMSHI 244

Query: 209 NWKVN 213
              + 
Sbjct: 245 GHPLL 249


>gi|319957030|ref|YP_004168293.1| pseudouridine synthase [Nitratifractor salsuginis DSM 16511]
 gi|319419434|gb|ADV46544.1| pseudouridine synthase [Nitratifractor salsuginis DSM 16511]
          Length = 192

 Score = 79.5 bits (194), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 58/186 (31%), Positives = 86/186 (46%), Gaps = 11/186 (5%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTN 126
                +L   HKP G V T SD  GR TV+D LP        + VGRLD++++GLLL T 
Sbjct: 5   LKNSPKLLALHKPKGYVVTRSDELGRKTVYDLLPDWAFENGWMPVGRLDMDSKGLLLFTT 64

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG +   L  P     +VY +   G V  + +   KKG+  +      + V      G+ 
Sbjct: 65  DGKIGDALTRPG-NCKKVYEIWVRGYVTDEHIAAAKKGVESKQGLLKALSVEKLGTGGAK 123

Query: 187 AWVTVGLREGKNREIKKVFEFFN-------WKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             + V + EGKNR I+++F            KV  L R+  G F L  + +G  R ++K+
Sbjct: 124 TKLRVVIDEGKNRHIRRLFGALKDPKFSTPLKVLDLKRVRIGTFDL-DIESGQWRFLTKE 182

Query: 240 ILREQL 245
             +  L
Sbjct: 183 EEKRLL 188


>gi|197302089|ref|ZP_03167150.1| hypothetical protein RUMLAC_00817 [Ruminococcus lactaris ATCC
           29176]
 gi|197298898|gb|EDY33437.1| hypothetical protein RUMLAC_00817 [Ruminococcus lactaris ATCC
           29176]
          Length = 195

 Score = 79.5 bits (194), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 44/190 (23%), Positives = 78/190 (41%), Gaps = 26/190 (13%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +++KP G VT   D    + +         R+  VGRLD  T GLLL+T+DG   + L  
Sbjct: 1   MFNKPFGCVTARRDTLYPTVMDYFSELHNDRLNPVGRLDRETTGLLLITDDGNWNQQLTH 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWV----- 189
           P+    + Y     G + +D+   L+ GI+++G  +     ++TL  +      +     
Sbjct: 61  PAYHKKKTYLFTVLGDLTEDRRQFLENGILLKGSPVPTSPAKITLFKKDTLANILDTLHP 120

Query: 190 ------------------TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLA 230
                              + + EG+ R+I+++ +  +  V  L RIS     L   L  
Sbjct: 121 EVRNAVRTNLPSHPVTYGEITISEGRKRQIRRMMKAVHCCVIELKRISIDDIHLDESLAP 180

Query: 231 GSTREVSKKI 240
           G  +E+    
Sbjct: 181 GKWKEIFPFE 190


>gi|126732067|ref|ZP_01747869.1| RNA pseudouridylate synthase [Sagittula stellata E-37]
 gi|126707356|gb|EBA06420.1| RNA pseudouridylate synthase [Sagittula stellata E-37]
          Length = 181

 Score = 79.5 bits (194), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 34/140 (24%), Positives = 64/140 (45%), Gaps = 14/140 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              GRLD ++EGLL+LT+DG L   +  P  +  + Y V+  G   +D++  L+ G+ + 
Sbjct: 40  YPAGRLDRDSEGLLVLTDDGRLQARIASPKFKRPKTYLVQVEGTPSEDQIRALRAGVDLN 99

Query: 169 GICYGDMQVTLD--------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                  +                   +   +AW+++ + EG+NR+++++         R
Sbjct: 100 DGPTRRAECVAIDPPDLWPRNPPVRFRKSVPDAWLSLTISEGRNRQVRRMTAHVGLPCLR 159

Query: 215 LIRISYGPFQLGTLLAGSTR 234
           L+R S G + +  L  G  R
Sbjct: 160 LVRWSVGDWSVEGLAPGEWR 179


>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 = 79.1 bits (193), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 30/240 (12%), Positives = 65/240 (27%), Gaps = 35/240 (14%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---- 63
           ++    +R+   +A     +R  ++++I  + V VNG  ++  +  V   D + V+    
Sbjct: 12  EKEDEGKRIDVFLAAELDYTRSYIKKLIVDELVFVNGKTVK-PSYKVKENDEVVVNIPEA 70

Query: 64  --------GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
                    +PL     +   + +      +V         + V   L    +     G 
Sbjct: 71  EKIDVLPENIPLDILYEDDDIIVINKPQGMVVHPAPGNYSGTLVNALLYHCKNLSGINGI 130

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------------------ 155
           L       L     G +       +   L                               
Sbjct: 131 LRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIKERSVFKKYVAIVEGVIKDEEGKIEAP 190

Query: 156 --DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                   KK  VI+   Y      +  +   N  V   ++ G+  +I+    +    + 
Sbjct: 191 IGRHPVDRKKMAVIEDGRYALTLYKVLERFKENTLVEAVIKTGRTHQIRVHMAYIGHPIV 250


>gi|325268091|ref|ZP_08134737.1| ribosomal large subunit pseudouridine synthase E [Kingella
           denitrificans ATCC 33394]
 gi|324980476|gb|EGC16142.1| ribosomal large subunit pseudouridine synthase E [Kingella
           denitrificans ATCC 33394]
          Length = 184

 Score = 79.1 bits (193), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 45/180 (25%), Positives = 79/180 (43%), Gaps = 21/180 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G++   S  +   ++ D +P     V   GRLD ++EGLLLLT+DG     +
Sbjct: 2   LIALNKPYGVICQFSPHEKHRSLKDFVP--VPNVYPAGRLDTDSEGLLLLTDDGRQQARI 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---------- 184
             P  +  + Y  +  G  D ++L LL++ + +        ++ L  +            
Sbjct: 60  ANPRFKLTKTYWAQLEGSPDDERLALLQRPLDLGDFVAQPARIRLLDEHETARIWQRDPP 119

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA--GSTRE 235
                   + W+ + + EGKNR+++++     +   RLIR+  G   L  L    G  RE
Sbjct: 120 IRVRKSVPDFWLQIQICEGKNRQVRRMTAKAGYPCLRLIRVGIGRVNLFDLGIELGQWRE 179


>gi|296157175|ref|ZP_06840011.1| pseudouridine synthase [Burkholderia sp. Ch1-1]
 gi|295892511|gb|EFG72293.1| pseudouridine synthase [Burkholderia sp. Ch1-1]
          Length = 189

 Score = 79.1 bits (193), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 38/177 (21%), Positives = 65/177 (36%), Gaps = 19/177 (10%)

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
                T        +            V   GRLD ++EGLLLLT+DG L   +  P  +
Sbjct: 7   NKPFGTICQFSPHETRASLADWVKVPNVYPAGRLDSDSEGLLLLTDDGALQARIAEPRHK 66

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---------------S 185
            ++ Y  +  G VD   L  L +G+ +        +                        
Sbjct: 67  LVKRYWAQVEGAVDAATLKKLARGVDLGDYVTRPCRAEYVEPTDTLWVRTPPIRYRAAIP 126

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF---QLGTLLAGSTREVSKK 239
             W+ + + EGKNR+++++     +   RL+R+  G      LG L  G + ++   
Sbjct: 127 TTWIELSITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDVFSLG-LQPGESVDLPPD 182


>gi|116617531|ref|YP_817902.1| ribosomal large subunit pseudouridine synthase E [Leuconostoc
           mesenteroides subsp. mesenteroides ATCC 8293]
 gi|116096378|gb|ABJ61529.1| ribosomal large subunit pseudouridine synthase E [Leuconostoc
           mesenteroides subsp. mesenteroides ATCC 8293]
          Length = 177

 Score = 79.1 bits (193), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 43/175 (24%), Positives = 83/175 (47%), Gaps = 17/175 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP  ++T  +D +GR T+ D +        + GRLD+++EGLLLLT+ G L   L
Sbjct: 2   IVLFNKPYNVLTKFTDAEGRPTLADYIDIPRV--YAAGRLDMDSEGLLLLTDSGKLNHEL 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT------------- 181
             P  +  + Y V+  G   + +L  L++G+ ++       +V                 
Sbjct: 60  TDPDNKAYKTYVVQVEGVPTKSQLKQLEQGVALKDGLTLPAKVKRIPYPKWLWEREKPIR 119

Query: 182 --QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +    +++ + ++EG+NR+++++         RLIR   G + +  L  G  R
Sbjct: 120 IRKNQPTSFIQLKIKEGRNRQVRRMTAAVGIPTLRLIRTHIGEYHIADLKPGQYR 174


>gi|148263668|ref|YP_001230374.1| pseudouridine synthase [Geobacter uraniireducens Rf4]
 gi|146397168|gb|ABQ25801.1| ribosomal large subunit pseudouridine synthase E [Geobacter
           uraniireducens Rf4]
          Length = 195

 Score = 79.1 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 33/140 (23%), Positives = 60/140 (42%), Gaps = 14/140 (10%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LT+ G + + +  P     + Y V+  G      +  L  G++++
Sbjct: 47  YAAGRLDYDSEGLLVLTDTGRIQQRIADPRADMAKSYWVQVEGVPTLAAIQQLTCGVLLE 106

Query: 169 GICYGDM--------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                                    + ++    W+ + L E +NR I+++         R
Sbjct: 107 DGLTLPAIVEQIKPPSVWLRTPQIRERRQIPTTWLAITLTEDRNRLIRRMTAAVGLPTLR 166

Query: 215 LIRISYGPFQLGTLLAGSTR 234
           LIR + GP+QL  L  G  +
Sbjct: 167 LIRQAVGPWQLNKLQPGDWK 186


>gi|254468338|ref|ZP_05081744.1| ribosomal large subunit pseudouridine synthase E [beta
           proteobacterium KB13]
 gi|207087148|gb|EDZ64431.1| ribosomal large subunit pseudouridine synthase E [beta
           proteobacterium KB13]
          Length = 176

 Score = 79.1 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 45/173 (26%), Positives = 80/173 (46%), Gaps = 16/173 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP G+V   S  +   T+ D L      +   GRLD ++EGLL+LT++G +   +
Sbjct: 2   IVLFNKPFGVVCQFSKHEIHPTLKDYLNIP--NIYPAGRLDTDSEGLLVLTDNGKIQHEI 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT------------- 181
             P++   + Y V+  G +  + +  L+ GI ++       +V                 
Sbjct: 60  SSPNSHKYKGYWVQVEGDIKNEAIQKLQNGIKLKDFTSLPARVEKINEPEIWERSTPIRF 119

Query: 182 -QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
            +    +WV + +REGKNR+++K+     +   RLIR     + L  LL G  
Sbjct: 120 RKNLPTSWVKIQIREGKNRQVRKMTAAVGFPTLRLIRYHVDDYYLNKLLPGDY 172


>gi|91784984|ref|YP_560190.1| pseudouridine synthase, Rsu [Burkholderia xenovorans LB400]
 gi|91688938|gb|ABE32138.1| Pseudouridine synthase, Rsu [Burkholderia xenovorans LB400]
          Length = 189

 Score = 79.1 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 38/177 (21%), Positives = 65/177 (36%), Gaps = 19/177 (10%)

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
                T        +            V   GRLD ++EGLLLLT+DG L   +  P  +
Sbjct: 7   NKPFGTICQFSPHETRASLADWVKVPNVYPAGRLDSDSEGLLLLTDDGALQARIAEPRHK 66

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---------------S 185
            ++ Y  +  G VD   L  L +G+ +        +                        
Sbjct: 67  LVKRYWAQVEGAVDAATLRKLARGVDLGDYVTRPCRAEYVEPTDTLWSRTPPIRYRAAIP 126

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF---QLGTLLAGSTREVSKK 239
             W+ + + EGKNR+++++     +   RL+R+  G      LG L  G + ++   
Sbjct: 127 TTWIELSITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDVFSLG-LQPGESVDLPPD 182


>gi|296273554|ref|YP_003656185.1| pseudouridine synthase [Arcobacter nitrofigilis DSM 7299]
 gi|296097728|gb|ADG93678.1| pseudouridine synthase [Arcobacter nitrofigilis DSM 7299]
          Length = 187

 Score = 79.1 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 53/183 (28%), Positives = 78/183 (42%), Gaps = 12/183 (6%)

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLL 124
           +       L + +KP G + T +D  GR TV+D LP        + +GRLD+ ++GLLL 
Sbjct: 3   ITANNSKILLVLNKPKGYLVTRTDDLGRKTVYDLLPDWAFHEGWMPIGRLDLESKGLLLF 62

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T +G +  +L  P                D+  +   K    I G      +V      G
Sbjct: 63  TTNGKIGDILTKPGNCIKVYEVWVRGFVTDEHIIQASKGVESIYG--LLKAKVVKVGIGG 120

Query: 185 SNAWVTVGLREGKNREIKKVFEFFN-------WKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +   + V L EGKNR I+++F            KV  L RIS G F+L  L  G  R +S
Sbjct: 121 AKTKLLVELEEGKNRHIRRLFGALKDPKFGTPLKVLTLNRISIGNFKL-DLEIGKWRYLS 179

Query: 238 KKI 240
            + 
Sbjct: 180 LEE 182


>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 = 79.1 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 34/250 (13%), Positives = 77/250 (30%), Gaps = 39/250 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  +++ +    +R+ K +       SR  +++++    + VNG  ++ A   +   D 
Sbjct: 1   MEQMSLISKK-KGERIDKFLGENLDDLSRSYIQKLLKDGLILVNGKKVK-ANYKLNEGDQ 58

Query: 60  IEV---DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I+V   D  PL              +   L +      +V         + V   L    
Sbjct: 59  IDVEVPDPEPLDIAAENIPLDILYEDEDILIVNKPKGMVVHPSPGHPDHTLVNAILYHCG 118

Query: 106 SR---------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR---------- 146
                         V R+D+NT G LL+  +    ++L     +     R          
Sbjct: 119 EHLSGINGVIRPGIVHRIDMNTTGSLLICKNDHAHQILAEQLKEHSITRRYHAIVHGSLK 178

Query: 147 ---VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                 +  + +   +  K         +      +  + G+  ++   L  G+  +I+ 
Sbjct: 179 ADTGTVNASIGRHPTDRKKMSTKALNGRHAVTHYRVLERLGNYTYIECELETGRTHQIRV 238

Query: 204 VFEFFNWKVN 213
                   + 
Sbjct: 239 HMASIGHPIL 248


>gi|268611607|ref|ZP_06145334.1| RNA pseudouridine synthase family protein [Ruminococcus
           flavefaciens FD-1]
          Length = 201

 Score = 78.7 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 51/191 (26%), Positives = 79/191 (41%), Gaps = 23/191 (12%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++++KP   VT   D   R+ +      +  R+  VGRLD +T GLLLLT+DG L   +
Sbjct: 6   YYMFNKPQNCVTAKRDAVHRTVMDFFPADLSERLHPVGRLDKDTCGLLLLTDDGDLDFRI 65

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ------------ 182
             P     + Y     G +D +K+  L+KGI + G         L  +            
Sbjct: 66  MQPDRHVSKTYFFYAIGTMDDEKIRSLEKGISMVGFTSRPASFRLIRKYRISQLEEFFPS 125

Query: 183 ----------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAG 231
                      G      + + EGK  E+K++ E  + K+  L RIS G   L   L  G
Sbjct: 126 ERRERYLKNPDGPAFAAELTIHEGKKHEVKRMLEAVHCKIFYLKRISIGGLSLDDSLAEG 185

Query: 232 STREVSKKILR 242
             R ++   L+
Sbjct: 186 QYRPLNDYELQ 196


>gi|225076235|ref|ZP_03719434.1| hypothetical protein NEIFLAOT_01272 [Neisseria flavescens
           NRL30031/H210]
 gi|224952359|gb|EEG33568.1| hypothetical protein NEIFLAOT_01272 [Neisseria flavescens
           NRL30031/H210]
          Length = 186

 Score = 78.7 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 44/181 (24%), Positives = 80/181 (44%), Gaps = 21/181 (11%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L + +KP G++   S  +    + D +          GRLD ++EGLLLLTN+G L 
Sbjct: 1   MNDLIILNKPYGVICQFSAHEKHQCLKDFVE--KPGFYPAGRLDTDSEGLLLLTNNGRLQ 58

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------- 184
             +  P  + ++ Y  +  G  D+ KL+LL++G+ +        +V +  +         
Sbjct: 59  AQIADPKFKQVKTYWAQVEGSPDEAKLDLLRRGVDLGDFVTHPAEVRVLEEGEADVLWPR 118

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL--AGS 232
                      + WV + + EGKNR+++++     +   RL+R++ G   L  L    G 
Sbjct: 119 VPPIRVRKSVPDFWVEIKISEGKNRQVRRMTAKAGFPCLRLVRVAIGRLNLFDLNLELGQ 178

Query: 233 T 233
            
Sbjct: 179 W 179


>gi|294788149|ref|ZP_06753392.1| ribosomal large subunit pseudouridine synthase E [Simonsiella
           muelleri ATCC 29453]
 gi|294483580|gb|EFG31264.1| ribosomal large subunit pseudouridine synthase E [Simonsiella
           muelleri ATCC 29453]
          Length = 184

 Score = 78.7 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 47/180 (26%), Positives = 80/180 (44%), Gaps = 21/180 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G++   S  +   T+ D +      V   GRLD ++EGLLLLT+DG     +
Sbjct: 2   LIALNKPYGVICQFSPHEKYRTLKDFVN--VPNVYPAGRLDTDSEGLLLLTDDGKQQARI 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------------- 179
             P  + ++ Y  +  G  D DKL  L++ + +        Q+ L               
Sbjct: 60  TDPRNKIVKTYWAQLEGSPDADKLARLQQPLDLGDFVAQPAQIRLLETNEIAQIWTRHPP 119

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTRE 235
             + +   + W+ + +REGKNR+++++     +   RLIR+  G   L    L  G  +E
Sbjct: 120 IRERKTVPDFWLQIQIREGKNRQVRRMTAKAGYPCLRLIRVGIGRVNLFDLGLELGQWQE 179


>gi|332968985|gb|EGK08027.1| ribosomal large subunit pseudouridine synthase E [Psychrobacter sp.
           1501(2011)]
          Length = 201

 Score = 78.7 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 44/182 (24%), Positives = 80/182 (43%), Gaps = 23/182 (12%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP G+ +  SD         +       +   GRLD  +EGLLLLT+DG + + +
Sbjct: 4   VILFNKPYGVQSQFSDDANNKFAPLSQFFTDKSLRVAGRLDATSEGLLLLTSDGRVNKAI 63

Query: 135 ELPS-----TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT----------- 178
             P       +  + Y V+  G+   ++L  L +G+V++       +V            
Sbjct: 64  THPPKANAGRKQGKTYLVQVEGEPTAEQLEQLCQGVVLKDGKTLPAEVKHLTEKELPMPL 123

Query: 179 -------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                   + +   ++W+ + + EGKNR+++++         RLIR S   F+LG L  G
Sbjct: 124 WQRDPPIRERKNIPDSWLMMTIYEGKNRQVRRMTAHVGLPCLRLIRWSVAGFELGDLGVG 183

Query: 232 ST 233
             
Sbjct: 184 EF 185


>gi|326317655|ref|YP_004235327.1| pseudouridine synthase Rsu [Acidovorax avenae subsp. avenae ATCC
           19860]
 gi|323374491|gb|ADX46760.1| pseudouridine synthase Rsu [Acidovorax avenae subsp. avenae ATCC
           19860]
          Length = 199

 Score = 78.7 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 49/180 (27%), Positives = 81/180 (45%), Gaps = 17/180 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             RL  +HKP G+++  +       + D +      V   GRLD ++EGLLLLT+DGGL 
Sbjct: 6   PPRLLRFHKPYGVLSQFTPEGRWRGLKDFID--LPGVYVAGRLDADSEGLLLLTDDGGLQ 63

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------------- 176
             +  P  +  + Y V+  G  D   L  L++G+ +        +               
Sbjct: 64  ARIANPRFKMEKTYWVQVEGVPDAAALQALERGVQLNDGPTLPARARRLDAPPPVGEREP 123

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                Q   + W+ + +REG+NR+++++         RL+R + GPF L  L  G+  EV
Sbjct: 124 PIRVRQHIPDTWIELVIREGRNRQVRRMTAAVGHPTLRLVRAAIGPFPLDGLAPGTWAEV 183


>gi|170725304|ref|YP_001759330.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169810651|gb|ACA85235.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 202

 Score = 78.7 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 40/187 (21%), Positives = 73/187 (39%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            K E     ++     L     +   R  +   L       +++GRLD ++EGLLLLT D
Sbjct: 12  NKEEHHHFKIFKPYGFLSQFVPETRKRKKLLAELADFPKGTMAIGRLDHDSEGLLLLTTD 71

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G ++  +     +     ++      D          I I+G  Y  +   +        
Sbjct: 72  GMVSHQVRSKKVEKEYYVQLDGDITADAITQLQNGVEIGIKGDKYLTLPCRVFKLASEPN 131

Query: 180 ---------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    D + G  +W+++ + EGKNR+I+K+     +   RL+R+  G   +  + A
Sbjct: 132 LPANGRKVRDLRHGPMSWISITISEGKNRQIRKMTAAAGFPTLRLVRVRIGNIDINEMQA 191

Query: 231 GSTREVS 237
           G    +S
Sbjct: 192 GDVLPLS 198


>gi|241759766|ref|ZP_04757866.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           flavescens SK114]
 gi|241319774|gb|EER56170.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           flavescens SK114]
          Length = 186

 Score = 78.7 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 44/181 (24%), Positives = 80/181 (44%), Gaps = 21/181 (11%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L + +KP G++   S  +    + D +          GRLD ++EGLLLLTN+G L 
Sbjct: 1   MNDLIILNKPYGVICQFSAHEKHQCLKDFVE--KPGFYPAGRLDTDSEGLLLLTNNGRLQ 58

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------- 184
             +  P  + ++ Y  +  G  D+ KL+LL++G+ +        +V +  +         
Sbjct: 59  AQIADPKFKQIKTYWAQVEGSPDEAKLDLLRRGVDLGDFVTHPAEVRVLEEGEADVLWPR 118

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL--AGS 232
                      + WV + + EGKNR+++++     +   RL+R++ G   L  L    G 
Sbjct: 119 VPPIRVRKSVPDFWVEIKISEGKNRQVRRMTAKAGFPCLRLVRVAIGRLNLFDLNLELGQ 178

Query: 233 T 233
            
Sbjct: 179 W 179


>gi|251773013|gb|EES53569.1| pseudouridine synthase [Leptospirillum ferrodiazotrophum]
          Length = 237

 Score = 78.7 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 53/169 (31%), Positives = 83/169 (49%), Gaps = 6/169 (3%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI------NTEGLLLLTNDGGL 130
             +KP G++ T SDP+GR  V D L        S GR+         + GLLLLTN    
Sbjct: 52  CLNKPRGVLVTLSDPEGRPVVGDFLRRTPWSDGSFGRIRPLGRLDAASAGLLLLTNYQEP 111

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
                 P     R YRV+    +  +   L   G   +G  Y  ++V ++ +   ++W+ 
Sbjct: 112 WSHFLSPEGGVRRRYRVKIRPGLRAEDRKLFLSGKAGEGAGYRRVEVEIEREGPKSSWLL 171

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + L EG+NREI+ V  +  ++V  LIR+++GPF LG L  G    V+++
Sbjct: 172 ISLVEGRNREIRNVLTYHGYEVLHLIRLAFGPFLLGDLKPGEVSSVTEE 220


>gi|187736067|ref|YP_001878179.1| pseudouridine synthase [Akkermansia muciniphila ATCC BAA-835]
 gi|187426119|gb|ACD05398.1| pseudouridine synthase [Akkermansia muciniphila ATCC BAA-835]
          Length = 188

 Score = 78.7 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 48/188 (25%), Positives = 81/188 (43%), Gaps = 18/188 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L        L     +     T+ +        V  VGRLD ++EGLLLL+++ GLA  
Sbjct: 2   ILAFNKPYGILSQFTKEAPHHRTLAEF--GFPPGVYPVGRLDADSEGLLLLSDEKGLADR 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTLDTQKG-------- 184
           L  PS +  R Y  +  G   +  L  L+  G+ I+G C    +  L  ++         
Sbjct: 60  LLNPSGRHPRTYWSQVEGTPSETDLRPLELGGLRIRGHCTLPCRARLMRREPDVPPRIPP 119

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    +W+ + L EGKNR+++++     +   RL+R   G F L  L  G+ +E+ 
Sbjct: 120 VRYRASIPTSWLELTLVEGKNRQVRRMTAAIGFPTLRLLRARIGNFSLAGLKPGAWKELD 179

Query: 238 KKILREQL 245
            +  R+ +
Sbjct: 180 SRERRQLM 187


>gi|120610961|ref|YP_970639.1| ribosomal large subunit pseudouridine synthase E [Acidovorax
           citrulli AAC00-1]
 gi|120589425|gb|ABM32865.1| ribosomal large subunit pseudouridine synthase E [Acidovorax
           citrulli AAC00-1]
          Length = 219

 Score = 78.3 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 50/186 (26%), Positives = 85/186 (45%), Gaps = 17/186 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P+ +A  +RL  +HKP G+++  +       + D +      V   GRLD ++EGLLLL
Sbjct: 19  EPVERAGPSRLLRFHKPYGVLSQFTPEGRWRGLKDFID--LPGVYVAGRLDADSEGLLLL 76

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------- 176
           T+DGGL   +  P  +  + Y V+  G  D   L  L++G+ +        +        
Sbjct: 77  TDDGGLQARIADPRFKMEKTYWVQVEGVPDAAALQALERGVQLNDGPTLPARARRLDVPP 136

Query: 177 -------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                       Q   + W+ + +REG+NR+++++         RL+R + GPF L  L 
Sbjct: 137 PVGEREPPIRVRQHIPDTWIELVIREGRNRQVRRMTAAVGHPTLRLVRAAIGPFALDGLA 196

Query: 230 AGSTRE 235
            G+  E
Sbjct: 197 PGTWAE 202


>gi|170693552|ref|ZP_02884711.1| pseudouridine synthase [Burkholderia graminis C4D1M]
 gi|170141707|gb|EDT09876.1| pseudouridine synthase [Burkholderia graminis C4D1M]
          Length = 189

 Score = 78.3 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 37/173 (21%), Positives = 64/173 (36%), Gaps = 17/173 (9%)

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
                T        +            V   GRLD ++EGLLLLT+DG L   +  P  +
Sbjct: 7   NKPFGTICQFSAHETRASLADWVKVPGVYPAGRLDSDSEGLLLLTDDGALQARIAEPRHK 66

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---------------S 185
            ++ Y  +  G VD   L  L +G+ +        +                        
Sbjct: 67  LVKRYWAQVEGAVDSAALKKLARGVDLGDYVTKPCRAEYVEPGDTLWTRTPPIRYRAAIP 126

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
             W+ + + EGKNR+++++     +   RL+R+  G   +    L  G + E+
Sbjct: 127 TTWIELSITEGKNRQVRRMTAAVGFPTLRLVRVGMGALDIFSLGLQPGESVEL 179


>gi|148239973|ref|YP_001225360.1| pseudouridine synthase [Synechococcus sp. WH 7803]
 gi|147848512|emb|CAK24063.1| Pseudouridine synthase [Synechococcus sp. WH 7803]
          Length = 171

 Score = 78.3 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 44/156 (28%), Positives = 69/156 (44%), Gaps = 23/156 (14%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           + + GRLD ++EGLL+LT +G L + L  P     R Y V+  G  D   L  L++G+VI
Sbjct: 1   MYAAGRLDADSEGLLILTENGRLQQRLTDPRFGHWRTYWVQVEGLADHGHLAALEQGVVI 60

Query: 168 QGICYGDMQ-----------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           +G      +                    + +    +W+++ LREG+NR+I+++      
Sbjct: 61  KGQRTRPARATSLDSSFWFDLPERTPPIRERRTIPTSWLSISLREGRNRQIRRMTAAVGL 120

Query: 211 KVNRLIRISYG------PFQLGTLLAGSTREVSKKI 240
              RLIR S        P  L  L  G  R V+   
Sbjct: 121 PTLRLIRRSIDLMDGGPPLSLEGLAPGQWRPVNSAE 156


>gi|255091431|ref|ZP_05320909.1| putative RNA pseudouridine synthase [Clostridium difficile CIP
          107932]
 gi|255515848|ref|ZP_05383524.1| putative RNA pseudouridine synthase [Clostridium difficile
          QCD-97b34]
 gi|255648941|ref|ZP_05395843.1| putative RNA pseudouridine synthase [Clostridium difficile
          QCD-37x79]
          Length = 65

 Score = 78.3 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 17/62 (27%), Positives = 27/62 (43%), Gaps = 1/62 (1%)

Query: 12 TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA 70
            QR+ K+++  G  SR E+++   Q  V VNG  +      V    D I  +G  +   
Sbjct: 3  KKQRIDKILSNLGYGSRSEIKKYCKQGSVVVNGSEVSNPGTQVDTENDEILFNGEEVIYR 62

Query: 71 ER 72
          E 
Sbjct: 63 EY 64


>gi|90415925|ref|ZP_01223858.1| Pseudouridine synthase, Rsu [marine gamma proteobacterium HTCC2207]
 gi|90332299|gb|EAS47496.1| Pseudouridine synthase, Rsu [marine gamma proteobacterium HTCC2207]
          Length = 208

 Score = 78.3 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 39/175 (22%), Positives = 81/175 (46%), Gaps = 16/175 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +L L++KP  +++  +D + R T+ + +          GRLD ++EGLLLLT+DG L   
Sbjct: 3   KLLLFNKPFHVLSQFTDSEARKTLSEFIEIKGV--YPAGRLDYDSEGLLLLTDDGQLQAQ 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------------- 179
           +  P  +  + Y  +  G   +     L  G+ ++      +   L              
Sbjct: 61  ISNPKFKLNKTYWAQVEGTATETHCLELIAGVSLKDGPAAAVACKLMDPPNLWPRIPPIR 120

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + Q  +++W+ + + EG+NR+++++         RL+R + G +++  +  G  R
Sbjct: 121 ERQNVADSWIELTINEGRNRQVRRMTAAVGLPTLRLVRAAIGDWKVTDIAPGEHR 175


>gi|319955563|ref|YP_004166830.1| pseudouridine synthase rsu [Cellulophaga algicola DSM 14237]
 gi|319424223|gb|ADV51332.1| pseudouridine synthase Rsu [Cellulophaga algicola DSM 14237]
          Length = 191

 Score = 78.3 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 34/172 (19%), Positives = 62/172 (36%), Gaps = 17/172 (9%)

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL 142
             ++       +      L      ++ VGRLD  +EGLLLLT DG L+  +     +  
Sbjct: 18  QFISNDEKEARKKHFLGELYDFPEGIMPVGRLDEKSEGLLLLTTDGKLSDTINQSGIEKE 77

Query: 143 RVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVT---------------LDTQKGS 185
              ++      +          I + G        +V                       
Sbjct: 78  YYAQLDGEIPHEDILQLERGVLIGLSGKKYITKPCRVKALLDPPLLTDPDKKLRIGTHRP 137

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           N+W+++ + EGK R+++K+     +   RLIR+  G   L  L  G+  ++ 
Sbjct: 138 NSWISITITEGKFRQVRKMTAAVGFPTLRLIRVRIGTQILEDLQPGTVAQID 189


>gi|218674542|ref|ZP_03524211.1| RNA-pseudouridine synthase protein, ribosomal large subunit B
           [Rhizobium etli GR56]
          Length = 110

 Score = 78.3 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 28/109 (25%), Positives = 52/109 (47%)

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
             R    +D +++  +  GI   G            Q   N+W+ V L EG+NR+I+++ 
Sbjct: 1   MSRSARLLDDEEIAAMTSGIRHDGEVLTATATRRLRQGDRNSWIEVELDEGRNRQIRRML 60

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           E    +  RL+R++ G  +LG L  G+ R +++  L+       +E A+
Sbjct: 61  EALGAECLRLVRVAIGGLELGELPKGAVRALTEAELQALRRSAGMERAR 109


>gi|227432625|ref|ZP_03914601.1| ribosomal large subunit pseudouridine synthase E [Leuconostoc
           mesenteroides subsp. cremoris ATCC 19254]
 gi|227351595|gb|EEJ41845.1| ribosomal large subunit pseudouridine synthase E [Leuconostoc
           mesenteroides subsp. cremoris ATCC 19254]
          Length = 185

 Score = 78.3 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 43/175 (24%), Positives = 83/175 (47%), Gaps = 17/175 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP  ++T  +D +GR T+ D +        + GRLD+++EGLLLLT+ G L   L
Sbjct: 10  IVLFNKPYNVLTKFTDAEGRPTLADYIDIPRV--YAAGRLDMDSEGLLLLTDSGKLNHGL 67

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT------------- 181
             P  +  + Y V+  G   + +L  L++G+ ++       +V                 
Sbjct: 68  TDPDNKAYKTYVVQVEGVPTKSQLKQLEQGVALKDGLTLPAKVKRIPYPKWLWEREKPIR 127

Query: 182 --QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +    +++ + ++EG+NR+++++         RLIR   G + +  L  G  R
Sbjct: 128 IRKNQPTSFIQLKIKEGRNRQVRRMTAAVGIPTLRLIRTHIGEYHIADLKPGQYR 182


>gi|113869011|ref|YP_727500.1| tRNA pseudouridine synthase A [Ralstonia eutropha H16]
 gi|113527787|emb|CAJ94132.1| tRNA pseudouridine synthase A [Ralstonia eutropha H16]
          Length = 220

 Score = 78.3 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 44/214 (20%), Positives = 74/214 (34%), Gaps = 17/214 (7%)

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
                T     +  +            V   GRLD ++EGLLLLT+DG L   +  P  +
Sbjct: 7   NKPFGTMSQFSEHPTRPTLAACVSVPGVYPAGRLDADSEGLLLLTDDGALQARIADPRHK 66

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---------------TQKGS 185
             + Y  +  G  D   L  L+ G+ +        +V                       
Sbjct: 67  LEKTYLAQVEGIPDAAALARLRAGVDLGDFVTQPARVRAIDAPDWLWPRQPPVRFRAAIP 126

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKILRE 243
            AW+ + +REGKNR+++++     +   RL+R+  GP  L    L  G+  EV    L  
Sbjct: 127 TAWLELKIREGKNRQVRRMTAAVGFPTLRLVRVGIGPLDLRALGLAPGACCEVLPAQLGL 186

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISE 277
                 + +          + +     R +    
Sbjct: 187 APAAPRMRQEPAPRSHVSKTRQANDTKRRSRYKN 220


>gi|150026033|ref|YP_001296859.1| pseudouridylate synthase [Flavobacterium psychrophilum JIP02/86]
 gi|149772574|emb|CAL44057.1| Pseudouridylate synthase [Flavobacterium psychrophilum JIP02/86]
          Length = 206

 Score = 78.3 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 34/181 (18%), Positives = 68/181 (37%), Gaps = 17/181 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                ++     L     +   +  +   L      ++++GRLD ++EGLLLLT DG ++
Sbjct: 11  HQHFIIHKPYGYLSQFKYELKRKKKLLGELYDFPEGIMAIGRLDEDSEGLLLLTTDGKMS 70

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQ------- 182
            ++     +     +V      +  +       I  +G        +  +  +       
Sbjct: 71  EIVRSKKVEKEYYVQVDGLITQEAIEKMKNGVEIGFEGTKYMTKPCKAFIVNEIPNFGER 130

Query: 183 --------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                    G  +W ++ + EGK R+++K+     +   RL+R+  G   LG L A    
Sbjct: 131 GKKIRDERHGPTSWASIVVTEGKFRQVRKMTAAVGFPTLRLVRVRVGNIHLGNLQAREVL 190

Query: 235 E 235
           E
Sbjct: 191 E 191


>gi|88809022|ref|ZP_01124531.1| Pseudouridine synthase, Rsu [Synechococcus sp. WH 7805]
 gi|88786964|gb|EAR18122.1| Pseudouridine synthase, Rsu [Synechococcus sp. WH 7805]
          Length = 171

 Score = 78.3 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 46/156 (29%), Positives = 70/156 (44%), Gaps = 23/156 (14%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           + + GRLD ++EGLL+LT +G L + L  P     R Y V+  G V+  +L  L++G+VI
Sbjct: 1   MYAAGRLDADSEGLLILTENGRLQQRLTDPRFGHWRTYWVQVEGLVEDSQLTALEQGVVI 60

Query: 168 QGICYGDMQVTLD-----------------TQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           +G      Q T                    +    +W+++ LREG+NR+I+++      
Sbjct: 61  KGQSTRPAQATFLDASHWRDLPERTPPIRVRRSIPTSWLSISLREGRNRQIRRMTAAVGL 120

Query: 211 KVNRLIRISYG------PFQLGTLLAGSTREVSKKI 240
              RLIR S        P  L  L  G  R V    
Sbjct: 121 PTLRLIRRSIDLMDSEPPLSLEGLAPGQWRPVKPAE 156


>gi|229023034|ref|ZP_04179549.1| Pseudouridine synthase [Bacillus cereus AH1272]
 gi|228738257|gb|EEL88738.1| Pseudouridine synthase [Bacillus cereus AH1272]
          Length = 90

 Score = 77.9 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 19/90 (21%), Positives = 45/90 (50%), Gaps = 2/90 (2%)

Query: 166 VIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
           +++         ++T   ++   A V + + EG+NR+++++FE  + KV +L R  Y   
Sbjct: 1   MLEDGKTAPANVKITSWDKRKETAIVQLTIHEGRNRQVRRMFEALDCKVVKLKRERYAFL 60

Query: 224 QLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           ++G+L  G  RE++   +++       +  
Sbjct: 61  EVGSLRPGDARELTPHEVKQLRALASTKPR 90


>gi|110637422|ref|YP_677629.1| RNA pseudouridylate synthase small subunit [Cytophaga hutchinsonii
           ATCC 33406]
 gi|110280103|gb|ABG58289.1| RNA pseudouridylate synthase, small subunit [Cytophaga hutchinsonii
           ATCC 33406]
          Length = 224

 Score = 77.9 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 43/184 (23%), Positives = 82/184 (44%), Gaps = 18/184 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP  +V+     D  + + +   +      +VGRLD  +EGLL+LT +  + R+
Sbjct: 29  RYFIINKPFNMVSQFISSDAVNLLGNLDFTFPEGTHAVGRLDNESEGLLILTTNKKVTRL 88

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-----GICYGDMQVTLD-------- 180
           L   + +  R Y V    +V ++ L  L+ GI I+            + ++         
Sbjct: 89  LFQGTKKHTRTYLVLVKNKVSEETLKQLQTGISIRVKGGGNYISSPCEASIVTDAKAIYS 148

Query: 181 -----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                 +   + W+ + L EGK  +++K+    N +  RLIR+S     L  L  G+ +E
Sbjct: 149 YAADTRENYPHTWLLLTLTEGKFHQVRKMVLAVNHRCLRLIRVSIENMLLHDLQPGAVKE 208

Query: 236 VSKK 239
             ++
Sbjct: 209 FEEE 212


>gi|116333694|ref|YP_795221.1| 16S rRNA uridine-516 pseudouridylate synthase related
           pseudouridylate synthase [Lactobacillus brevis ATCC 367]
 gi|116099041|gb|ABJ64190.1| 16S rRNA uridine-516 pseudouridylate synthase related
           pseudouridylate synthase [Lactobacillus brevis ATCC 367]
          Length = 229

 Score = 77.9 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 35/241 (14%), Positives = 75/241 (31%), Gaps = 15/241 (6%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           + + +      +  ++ R++ Q RVKVN  L++     V ++D + VDG+ +       L
Sbjct: 3   IERYLTEHHQGTPGQIFRLLRQGRVKVNDRLIDSPRETVDTSDQVTVDGLAVTGRRPQYL 62

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
                                   N       +  +  L     GL L+T+D      ++
Sbjct: 63  VFNKPVGVQTDLTPVVPHSLGSMLNALDQQQSLQILADLPRTIAGLTLVTDDNTFLTEVQ 122

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
             +       ++     +   +                  +V        + W  + L+ 
Sbjct: 123 GQTWPSTLRVQLTGTTPLTLPQNI--------------AAEVVEQRPDQVHQWTMLTLQT 168

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLLEEAQ 254
                +    E  +     + RI +GP +L   L  G+ R +  + +   L P      +
Sbjct: 169 TALDSVTAWLESLSRVSGAINRIGWGPIKLSPDLAVGTYRGLFPQEIDALLTPATTSSLE 228

Query: 255 V 255
            
Sbjct: 229 K 229


>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 = 77.9 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 32/248 (12%), Positives = 72/248 (29%), Gaps = 38/248 (15%)

Query: 1   MKDKN-IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M++    + E    +R+ K + A+ G  SR +V++ I   +V+VNG    ++   +   D
Sbjct: 1   MEEIQWTILEENKNERIDKFLTAQNGEWSRSQVQQWIKDGQVQVNGK-ATKSNYKMQVED 59

Query: 59  HIEV------------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            + +            + +PL     +   + +      +V         + V   L   
Sbjct: 60  QVTLSIPEPEELDVIAEDIPLDVVYEDADVIVVNKPRGMVVHPAPGHYTGTLVNALLYHC 119

Query: 105 FSRVISVG---------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
                  G                     + D   E L+         R  +      + 
Sbjct: 120 KDLSGINGVIRPGIVHRIDKDTSGLLMVAKNDHAHESLVSQLKAKTTKRHYKAIVHGVIP 179

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                    + +DK +     +            T+        +V   L  G+  +I+ 
Sbjct: 180 HQHGTIEAPIGRDKKDRQSMTVTEDNSRDAVTHFTVLECFKDFTYVQCELETGRTHQIRV 239

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 240 HMKYIGYP 247


>gi|46191229|ref|ZP_00206720.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and
          related pseudouridylate synthases [Bifidobacterium
          longum DJO10A]
          Length = 329

 Score = 77.9 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 1/68 (1%)

Query: 8  QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVP 66
          Q++    R+ K++A+AG  SRR+ E MI + RV+V+G L+      V      + VDG  
Sbjct: 12 QDDSNSIRLQKLLAQAGFGSRRKCEDMITEGRVEVDGELVTELGTRVDPHKQQVRVDGSR 71

Query: 67 LRKAERTR 74
          +R      
Sbjct: 72 VRVNPNHV 79


>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 = 77.9 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 29/242 (11%), Positives = 73/242 (30%), Gaps = 34/242 (14%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            I+    +P+R+ K +      SR  +++M+ Q  V VN  ++ + +  +   D +E+  
Sbjct: 2   KILYSLTSPKRIDKFLVEVTDYSRTSIKKMLEQNLVLVNDNIITKQSYLLQKNDSVEIKN 61

Query: 65  V-----------------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                              +   ++  L +      LV   S  +  +        + + 
Sbjct: 62  EQCVIDSQKELLPFACPLEIVFEDQDLLVINKPSGMLVHPTSFQEQNTLANALKHYLKTD 121

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-- 165
              +          L++      A            V +  +    ++  ++ L   I  
Sbjct: 122 DFYITHRLDKNTSGLIVICKNQKALCCLQQQFMQKTVKKSYYAIVHNRFDMHHLHFMINE 181

Query: 166 ----------VIQGICYGDMQV-----TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      ++     + +       +  Q  + A V V +  G+  +I+      N 
Sbjct: 182 PIGHSYQDKLRMKTGDAKNAKEAISIVKVIEQYQNTALVEVSIITGRTHQIRVHMRHINH 241

Query: 211 KV 212
            +
Sbjct: 242 PI 243


>gi|225023878|ref|ZP_03713070.1| hypothetical protein EIKCOROL_00744 [Eikenella corrodens ATCC
           23834]
 gi|224943352|gb|EEG24561.1| hypothetical protein EIKCOROL_00744 [Eikenella corrodens ATCC
           23834]
          Length = 186

 Score = 77.9 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 43/178 (24%), Positives = 80/178 (44%), Gaps = 21/178 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L +++KP G++   S  +   ++ + +      V   GRLD ++EGLLLLT +G L   +
Sbjct: 4   LIVFNKPYGVICQFSPHEKHRSLKEFIG--LPDVYPAGRLDTDSEGLLLLTANGRLQAKI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------------- 179
             P  + ++ Y  +  G  D+ KL+LL+ G+ +        Q+ L               
Sbjct: 62  ADPRHKTVKTYWAQLEGSPDEAKLDLLRHGVDLGDFVTRPAQIRLPEKSETDRLWSRVPP 121

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGST 233
               +   + W+ + + EGKNR+++++     +   RL+R+  G   L    L  G  
Sbjct: 122 IRVRKSVPDFWLEIRISEGKNRQVRRMTAKAGYPCLRLVRVGIGRLDLWQLDLAPGQW 179


>gi|86143319|ref|ZP_01061721.1| RNA pseudouridine synthase family protein [Leeuwenhoekiella
           blandensis MED217]
 gi|85830224|gb|EAQ48684.1| RNA pseudouridine synthase family protein [Leeuwenhoekiella
           blandensis MED217]
          Length = 192

 Score = 77.5 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 40/185 (21%), Positives = 69/185 (37%), Gaps = 24/185 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTND 127
                 L+     L    S+   +      L    S    ++ +GRLD  +EGLLL+T D
Sbjct: 3   THQHYLLFKPYGYLSQLSSNDLHQKRKKKFLAELYSWPDGIMPIGRLDEKSEGLLLMTTD 62

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDM-------- 175
           G L+  +        + Y     G   + +L  L +GI I    +               
Sbjct: 63  GKLSDHINRS--GIEKEYYALVDGIPTEAQLEQLSQGIEIGINGKKYRTKPCGVKILETS 120

Query: 176 -------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                  +   D + G   W+++ + EGK R+++K+    +    RL+RI  G  +L  +
Sbjct: 121 PALPDRGKKIRDARHGPTTWLSITIIEGKFRQVRKMTSAIDCPTLRLVRIRIGSLKLKAI 180

Query: 229 LAGST 233
             G  
Sbjct: 181 QPGEV 185


>gi|229894383|ref|ZP_04509566.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           Pestoides A]
 gi|229703781|gb|EEO90797.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           Pestoides A]
          Length = 112

 Score = 77.5 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 22/87 (25%), Positives = 45/87 (51%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    
Sbjct: 1   MRLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQMVGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDN 100
           R ++ +KP G V +  DPD  + ++  
Sbjct: 61  RYFMLNKPQGYVCSTEDPDHPTVLYFL 87


>gi|146297843|ref|YP_001192434.1| pseudouridine synthase [Flavobacterium johnsoniae UW101]
 gi|146152261|gb|ABQ03115.1| pseudouridine synthase [Flavobacterium johnsoniae UW101]
          Length = 190

 Score = 77.5 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 41/192 (21%), Positives = 77/192 (40%), Gaps = 21/192 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                 L+     L     +   +  +   L       +++GRLD ++EGLLLLT DG +
Sbjct: 1   MHRHFILFKPYGYLSQFIYELKRKKKLLGELHDFPEGTMAIGRLDEDSEGLLLLTTDGKV 60

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI----CYGDM----------- 175
           +  +     +  + Y V+  G +  + +  L+KG+ I                       
Sbjct: 61  SEQIRSK--KVDKEYYVQVDGIITPEAIEKLQKGVEIGFEGGKYKTKPCTAFIVTEIPDF 118

Query: 176 ----QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
               +   D + G  +W ++ + EGK R+++K+     +   RL+R+  G   L  L AG
Sbjct: 119 GPRAKKIRDERHGPTSWASITVNEGKFRQVRKMTAAVGFPTLRLVRVRIGNVYLQNLKAG 178

Query: 232 STREVSKKILRE 243
              EV+   + +
Sbjct: 179 EVLEVNDFQIND 190


>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 = 77.5 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 47/247 (19%), Positives = 80/247 (32%), Gaps = 38/247 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M + N+        R+ KV+A     SR +VE+++    V VN  ++ + +  V+  D I
Sbjct: 1   MNNFNVETAG----RIDKVLAHELDVSRNQVEKLVKDGLVSVNKKMVTKTSFKVVEGDEI 56

Query: 61  EVDGVPLRKAER-------------TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
             +     K E                L + +KP GLV   +      T+ D L      
Sbjct: 57  TYEFKEAEKREPVEIDFDVEILYEDEYLMVVNKPSGLVVHPAPSVKEPTLVDWLVKKGIS 116

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR------------VYR 146
                   R   V R+D  T G L++  D  +  +L                        
Sbjct: 117 LSTISGEERHGIVHRIDKETTGALVIAKDNKVHEMLSEQLQDKSMGRYYLALIDHFLKED 176

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
           V     + ++  N LK  +V  G         L T +     +   L  G+  +I+    
Sbjct: 177 VVVDKPIGRNPHNRLKMDVVPHGKPAKTAFKKLLTSEYDVELIAAKLFTGRTHQIRVHLN 236

Query: 207 FFNWKVN 213
                + 
Sbjct: 237 TLGRHIL 243


>gi|127511748|ref|YP_001092945.1| pseudouridine synthase [Shewanella loihica PV-4]
 gi|126637043|gb|ABO22686.1| pseudouridine synthase [Shewanella loihica PV-4]
          Length = 182

 Score = 77.5 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 39/178 (21%), Positives = 72/178 (40%), Gaps = 17/178 (9%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            ++     L     +   R  +   L +  + ++++GRLD ++EGLLLLT DG  +  + 
Sbjct: 1   MIFKPYGYLSQFVGERRKRKPLLGELANFPTGIMAIGRLDHDSEGLLLLTTDGKTSHAVR 60

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--DMQVTLDTQ----------- 182
             S +     ++                 I I+G  Y     +     Q           
Sbjct: 61  SKSIEKEYYLQLDGEITEQAISSLCEGVEIGIKGEKYRTLPCRARRLDQAPDLPPRGRKI 120

Query: 183 ----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                G  +W+ + + EGKNR+++K+     +   RL+R+  G  +LGTL  G  + +
Sbjct: 121 RDARHGPTSWLAITITEGKNRQLRKMTAAVGFATLRLVRVRIGDIRLGTLQPGEVKSL 178


>gi|148242785|ref|YP_001227942.1| pseudouridine synthase [Synechococcus sp. RCC307]
 gi|147851095|emb|CAK28589.1| Pseudouridine synthase [Synechococcus sp. RCC307]
          Length = 205

 Score = 77.5 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 49/195 (25%), Positives = 75/195 (38%), Gaps = 23/195 (11%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L HKP G+++  +   G              V + GRLD ++EGLLLLT+DG L   L 
Sbjct: 9   LLLHKPYGVLSQFTPEVGSRWDCLASLVPIKGVYAAGRLDADSEGLLLLTSDGALQHQLT 68

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG----------- 184
            P     R YR +  G   +  L  L++GI ++       +  L                
Sbjct: 69  NPRFGHWRQYRAQVEGAPTEADLEPLRRGIQLKDGPSRPARAQLLDPSVAAGIAERNPPI 128

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQLGTLLAGS 232
                    W+ + L EG+NR+++++     +   RLIR S        P  L  +  G 
Sbjct: 129 RHRLSVPTRWLELELTEGRNRQVRRMTAAIGFPTLRLIRWSLDLMDGQPPLNLDGMEPGQ 188

Query: 233 TREVSKKILREQLGP 247
            R VS    +     
Sbjct: 189 WRWVSAAEEKRLKQL 203


>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 = 77.5 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 30/250 (12%), Positives = 71/250 (28%), Gaps = 39/250 (15%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M+  N  + E  T  R+ K +A A    SR +++  I  + V VNG +++     +   D
Sbjct: 1   METFNFEINEEETGIRIDKFLADANPDWSRSQIQDWIKNEFVLVNGKVIKS-NYKLRLND 59

Query: 59  HIEVDGVPLR--------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            I V   P+                 ++    +Y     +V         + V   + +I
Sbjct: 60  EISVTEKPVEEVDLVAQDLGLEIYYEDKDVAIVYKPKGMVVHPAPGHPDGTLVNGLMHAI 119

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPS---------------------TQWLR 143
                  G +       +     G L       +                        + 
Sbjct: 120 TDLSGINGEIRPGIVHRIDKDTSGLLMIAKNDIAHRGLVDQLVDKSVTRKYTALVHGVIP 179

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                    + +++ +  ++  ++    +      +         V   L  G+  +I+ 
Sbjct: 180 HEFGTIDAPIGRNQKDR-QEMAIVDNGKHAVTHFNVLETFDKYTLVECVLETGRTHQIRV 238

Query: 204 VFEFFNWKVN 213
             +   + + 
Sbjct: 239 HMKHIGFPLV 248


>gi|148653886|ref|YP_001280979.1| pseudouridine synthase [Psychrobacter sp. PRwf-1]
 gi|148572970|gb|ABQ95029.1| ribosomal large subunit pseudouridine synthase E [Psychrobacter sp.
           PRwf-1]
          Length = 203

 Score = 77.5 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 46/194 (23%), Positives = 87/194 (44%), Gaps = 25/194 (12%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP G+ +  SD         +       +   GRLD  +EGLLLLT+DG + + +
Sbjct: 6   VILFNKPYGVQSQFSDDANNKFAPLSQFFTDKSLRVAGRLDATSEGLLLLTSDGQVNKAI 65

Query: 135 ELPS-----TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG----- 184
             P       +  + Y V+  G    ++L  L++G++++       +V   +++      
Sbjct: 66  THPPKANAGRKQGKTYLVQVEGIPSNEQLEQLRQGVLLKDGQTLPAEVKHISEEDLPMPL 125

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                         ++W+ + + EGKNR+++++         RLIR S   F+LG L  G
Sbjct: 126 WQRDPPIRERKSVPDSWLMMTIYEGKNRQVRRMTAHVGLPCLRLIRWSAAGFELGNLAVG 185

Query: 232 ST--REVSKKILRE 243
                 ++ K L+E
Sbjct: 186 EFVRVHLNDKRLKE 199


>gi|255018863|ref|ZP_05290989.1| hypothetical protein LmonF_16091 [Listeria monocytogenes FSL
           F2-515]
          Length = 128

 Score = 77.5 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 30/117 (25%), Positives = 56/117 (47%), Gaps = 2/117 (1%)

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVTVG 192
             P  +  + Y  R  G  +++ +  L++G+VI G      +V +    +    A V + 
Sbjct: 6   MHPKNEVSKTYIARIKGIPEREVIRQLERGVVIDGRKTAPAKVKVRSSDKTKDKAIVEIT 65

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           + EG+NR+++K+FE   ++V +L R  Y    L  L AG  RE+S   +++      
Sbjct: 66  IHEGRNRQVRKMFEAVGFEVQKLSREEYSFLNLRGLNAGERRELSHHEVKQLKTEAR 122


>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 = 77.5 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 35/232 (15%), Positives = 71/232 (30%), Gaps = 33/232 (14%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------DGV 65
            R+   ++     SR    ++I +  V VN   ++  + NV   D I V        D  
Sbjct: 1   MRIDTYLSEVIGKSRSFCSKIIKKGLVLVNNKTVK-PSYNVNLGDEILVKIPQEEKLDLK 59

Query: 66  P------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGR 113
           P      +    +  L +       V         + V   L               V R
Sbjct: 60  PANIPLNIIYENQYYLIINKPAGLCVHPAPGNFDNTLVNALLYHFQINDDNDVRPGIVHR 119

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL------------ 161
           LD +T GL+L+  +  +   +     +     +       +     +L            
Sbjct: 120 LDKDTSGLILVAKNRDVREKMSEMFKEREVDKKYLAICYGNPKWDEILVENSIGRHPVDR 179

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           KK  V++   Y   ++T+  +  +     V +  G+  +I+    +    + 
Sbjct: 180 KKMAVVENGRYAKTKITVLKRYDNIFLADVKIYTGRTHQIRVHCSYLGCPII 231


>gi|305666906|ref|YP_003863193.1| RNA pseudouridine synthase family protein [Maribacter sp. HTCC2170]
 gi|88709133|gb|EAR01367.1| RNA pseudouridine synthase family protein [Maribacter sp. HTCC2170]
          Length = 196

 Score = 77.1 bits (188), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 32/165 (19%), Positives = 58/165 (35%), Gaps = 17/165 (10%)

Query: 86  TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY 145
           +              L       + VGRLD  +EGLLL+T DG L+  +     +     
Sbjct: 23  SNEERQIRSKRFLSELHEFPEGTMPVGRLDEKSEGLLLMTTDGKLSDTINRKGIEKEYYA 82

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICY-----------------GDMQVTLDTQKGSNAW 188
           ++         ++      I  +GI Y                    +     +   N+W
Sbjct: 83  QLDGDISPKAIEILATGVEIGFEGIRYTTKPCTVQKINFKPSLPAPDKRIRLARHRPNSW 142

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
           +++ + EGK R+++K+     +   RL+R+  G   L  L     
Sbjct: 143 ISIVITEGKFRQVRKMTAAVGFPTLRLVRVRIGALILDDLGPEEV 187


>gi|134296698|ref|YP_001120433.1| pseudouridine synthase [Burkholderia vietnamiensis G4]
 gi|134139855|gb|ABO55598.1| pseudouridine synthase [Burkholderia vietnamiensis G4]
          Length = 192

 Score = 77.1 bits (188), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 42/182 (23%), Positives = 76/182 (41%), Gaps = 19/182 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +      + GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKTPGV--YAAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  + ++ Y  +  G  D   L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVDGAPDAADLKALARGVDLGDYVTRPCRAEFIEPPAALWPRTPPIR 120

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L    G T E+ 
Sbjct: 121 YRAAIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGVLDIFALGIAPGETIELP 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>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 = 77.1 bits (188), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 33/242 (13%), Positives = 65/242 (26%), Gaps = 38/242 (15%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E    +R+ K +A   G  SR +V++ I    V VNG  ++     V   D I V  
Sbjct: 8   TVAEEQKSERIDKFVAEINGEWSRSQVQQWIKDDVVTVNGKSVKV-NYKVKENDEITVTI 66

Query: 63  -DGV-----------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
            D              +   +   L +      +V         + V   +         
Sbjct: 67  PDPEELDIQAEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI 126

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRVRF 149
            G +       +     G L       + + L                        +   
Sbjct: 127 NGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTI 186

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +DK    +   V +   +      +  +      V   L  G+  +I+   ++  
Sbjct: 187 DAPIARDKKER-QSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIG 245

Query: 210 WK 211
           + 
Sbjct: 246 YP 247


>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 = 77.1 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 71/246 (28%), Gaps = 36/246 (14%)

Query: 3   DKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           + NI++++   QR+ K+++      SR +++  I +  VKVNG +++     V   D I 
Sbjct: 5   NFNIIEQSQVGQRIDKLVSDLNKDWSRSQLQDWIKEGLVKVNGKVIKS-NYKVKLNDKIV 63

Query: 62  V--------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           V        D  P      +   +     +Y     +V         + V   +  I   
Sbjct: 64  VTEKEVVEADIKPENLNLDIYYEDEDVAIVYKPKGMVVHPSPGHYSGTLVNGLMYQIKDL 123

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------------ 155
               G +       +     G L       + + L    +    +               
Sbjct: 124 SGINGEIRPGIVHRIDKDTSGLLMVAKNDVAHRHLVEQLMSKTVKRKYTALVHGNIPHDY 183

Query: 156 --------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                      N  +   V+           +         +   L  G+  +I+   ++
Sbjct: 184 GTIDAPIGRNKNDRQAMAVVDDGKEAVTHFNVLEHFKDYTLIECQLETGRTHQIRVHMKY 243

Query: 208 FNWKVN 213
             + + 
Sbjct: 244 IGYPLV 249


>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 = 77.1 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 71/246 (28%), Gaps = 36/246 (14%)

Query: 3   DKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           + NI++++   QR+ K+++      SR +++  I +  VKVNG +++     V   D I 
Sbjct: 5   NFNIIEQSQVGQRIDKLVSDLNKDWSRSQLQDWIKEGLVKVNGKVIKS-NYKVKLNDKIV 63

Query: 62  V--------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           V        D  P      +   +     +Y     +V         + V   +  I   
Sbjct: 64  VTEKEVVEADIKPENLNLDIYYEDEDVAVVYKPKGMVVHPSPGHYSGTLVNGLMYQIKDL 123

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------------ 155
               G +       +     G L       + + L    +    +               
Sbjct: 124 SGINGEIRPGIVHRIDKDTSGLLMVAKNDVAHRHLVEQLMSKTVKRKYTALVHGNIPHDY 183

Query: 156 --------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                      N  +   V+           +         +   L  G+  +I+   ++
Sbjct: 184 GTIDAPIGRNKNDRQSMAVVDDGKEAVTHFNVLEHFKDYTLIECQLETGRTHQIRVHMKY 243

Query: 208 FNWKVN 213
             + + 
Sbjct: 244 IGYPLV 249


>gi|289209534|ref|YP_003461600.1| pseudouridine synthase [Thioalkalivibrio sp. K90mix]
 gi|288945165|gb|ADC72864.1| pseudouridine synthase [Thioalkalivibrio sp. K90mix]
          Length = 180

 Score = 77.1 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 45/180 (25%), Positives = 83/180 (46%), Gaps = 16/180 (8%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L+HKP G++   +DP+GR T+ D +          GRLD ++EGL++LT+DG L   
Sbjct: 3   RIVLFHKPWGVLPQFTDPEGRPTLADYIDIPGV--YPAGRLDRDSEGLMVLTDDGRLNAR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------- 180
           L  P  +  + Y V+  G+ D   L  L+ G+ ++       +V                
Sbjct: 61  LTQPRHKTSKTYWVQVEGEPDDAALEALRTGVDLKDGRTQPAKVERMTPPDLPERDPPVR 120

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +     W+ + L EG+NR+++++         RL+R     + L  +  G+   + ++
Sbjct: 121 FRKSVPTTWLALTLHEGRNRQVRRMTAAVGHPTLRLVRYRVASWTLDGVERGAFSVIERE 180


>gi|268680145|ref|YP_003304576.1| pseudouridine synthase [Sulfurospirillum deleyianum DSM 6946]
 gi|268618176|gb|ACZ12541.1| pseudouridine synthase [Sulfurospirillum deleyianum DSM 6946]
          Length = 194

 Score = 77.1 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 54/187 (28%), Positives = 89/187 (47%), Gaps = 11/187 (5%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDG 128
              +L++ +KP G + T SD  GR TV+D LP        + +GRLD++++GLLL T +G
Sbjct: 10  TSKKLFVLNKPKGYLVTRSDDLGRKTVYDLLPDWAFNEGWMPIGRLDLDSKGLLLFTTNG 69

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
                      +  +VY +   G V  + +    KG+         ++V      G+   
Sbjct: 70  -HISNALTTPKKCTKVYEIWVRGHVMDEHIAEALKGVQTSQGLLKALEVKKIGMGGAKTK 128

Query: 189 VTVGLREGKNREIKKVFEFFN-------WKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++V + EGKNR I+++F            KV  L RIS G F+L  +  G+ R +S++  
Sbjct: 129 LSVVIDEGKNRHIRRLFGALKDPKFGTPLKVLELNRISIGDFKL-DIDIGTWRFLSEEEE 187

Query: 242 REQLGPH 248
           +  L  H
Sbjct: 188 KMLLDKH 194


>gi|297537798|ref|YP_003673567.1| pseudouridine synthase [Methylotenera sp. 301]
 gi|297257145|gb|ADI28990.1| pseudouridine synthase [Methylotenera sp. 301]
          Length = 183

 Score = 76.8 bits (187), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 36/175 (20%), Positives = 67/175 (38%), Gaps = 15/175 (8%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
            ++                            V + GRLD ++EGLL+LT+DG L   L  
Sbjct: 8   PFNVVCQFSAHDPGNGKTGHPTLKDFIQIPDVYAAGRLDTDSEGLLILTDDGMLQHRLSD 67

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------VTLDT 181
           P  +  + Y V+  G    + L  L +GI +        Q                  + 
Sbjct: 68  PKRKEFKTYWVQVEGTPSTEDLEPLIRGIDLSDFVAKPAQVRLIPEPESLWLRNPPIRER 127

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           +    +W+ + + EGKNR+++++     +   RLIR + G + +  +  G  + +
Sbjct: 128 KAIPTSWLEIKISEGKNRQVRRMTAKIGFPTLRLIRYAIGQYTIDGIQNGQHKVI 182


>gi|306519054|ref|ZP_07405401.1| putative RNA pseudouridine synthase [Clostridium difficile
          QCD-32g58]
          Length = 63

 Score = 76.8 bits (187), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 12 TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA 70
            QR+ K+++  G  SR E+++   Q  V VNG  +      V    D I  +G  +   
Sbjct: 3  KKQRIDKILSNLGYGSRSEIKKYCKQGSVVVNGSEVSNPGTQVDTENDEILFNGEEVIYR 62

Query: 71 E 71
          E
Sbjct: 63 E 63


>gi|258545633|ref|ZP_05705867.1| ribosomal large subunit pseudouridine synthase E [Cardiobacterium
           hominis ATCC 15826]
 gi|258519100|gb|EEV87959.1| ribosomal large subunit pseudouridine synthase E [Cardiobacterium
           hominis ATCC 15826]
          Length = 189

 Score = 76.8 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 44/182 (24%), Positives = 85/182 (46%), Gaps = 22/182 (12%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L++KP  ++   +D  GR+T+ D +          G LD ++EGL++LT+DG L   +
Sbjct: 8   LILFNKPFNVLCQFTDKSGRATLADFVDVPRV--YPAGLLDYDSEGLVVLTDDGRLQARI 65

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI------CYGDMQVTLDTQ------ 182
             P  + ++ Y V+  G  D+  L  L+ G+ ++              V +  +      
Sbjct: 66  ADPRFKLVKTYWVQVEGVPDEAALVQLRAGVWLKDKGKREAQRTLPAAVRVIAEPPLWPR 125

Query: 183 --------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       AW+ + +REG+NR+++++         RL+R+  G + L  L +G+ +
Sbjct: 126 VPPVRFRLSVPTAWLELSIREGRNRQVRRMTAAVGLPTLRLVRVQVGDWSLRGLQSGAWK 185

Query: 235 EV 236
           +V
Sbjct: 186 KV 187


>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 = 76.8 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 33/247 (13%), Positives = 70/247 (28%), Gaps = 36/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  +  +    T +R+ K ++     SR  V+++     + VNG + +  +  V++ D I
Sbjct: 1   MAKQTWIVSEDTKERLDKYLSSNTELSRTRVQQLADDGMIFVNGKVAKS-SSKVVTGDEI 59

Query: 61  EVD---GVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
             D     P+              +   + +      +V         + V   L     
Sbjct: 60  SCDVPEDRPVDILPENIPLDILYEDHDIIVINKPKGMVVHPAPGNYSNTMVNALLYHCKD 119

Query: 107 RVISVGRLDI---------NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                G +            T  ++   ND     + +    +                 
Sbjct: 120 LSGINGVIRPGIVHRIDKDTTGCIVACKNDKAHEAIAKQLENKTCHRVYKTIVVGNITHD 179

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV------------GLREGKNREIKKVF 205
             L+   I         M+VT +  + +     V             L  G+  +I+   
Sbjct: 180 DGLIDAPIGRDPRDRQRMKVTEENSRDARTHFHVLERFNVATYLECRLETGRTHQIRAHM 239

Query: 206 EFFNWKV 212
           ++ N  V
Sbjct: 240 KYINHPV 246


>gi|312795285|ref|YP_004028207.1| ribosomal large subunit pseudouridine synthase E [Burkholderia
           rhizoxinica HKI 454]
 gi|312167060|emb|CBW74063.1| Ribosomal large subunit pseudouridine synthase E (EC 4.2.1.70)
           [Burkholderia rhizoxinica HKI 454]
          Length = 189

 Score = 76.8 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 37/175 (21%), Positives = 62/175 (35%), Gaps = 17/175 (9%)

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
                T        +            V   GRLD ++EGLLLLT+DG L   +  P  +
Sbjct: 7   NKPYGTICQFSAHETRASLATWVNVPDVYPAGRLDADSEGLLLLTDDGALQARIAEPRHK 66

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---------------TQKGS 185
            ++ Y  +  G      L  L++G+ +        +                        
Sbjct: 67  LVKRYWAQLDGAAPASALAALERGVDLGDYVSRPCRARFIEPPSGLWQRDPPVRYRAAIP 126

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSK 238
             W+ + L EG+NR+++++     +   RLIR+  G   L    L  G  R +  
Sbjct: 127 TTWIELALGEGRNRQVRRMTAAVGFPTLRLIRVGIGALDLFALGLAPGQWRALPP 181


>gi|152992340|ref|YP_001358061.1| ribosomal small subunit pseudouridine synthase A [Sulfurovum sp.
           NBC37-1]
 gi|151424201|dbj|BAF71704.1| ribosomal small subunit pseudouridine synthase A [Sulfurovum sp.
           NBC37-1]
          Length = 188

 Score = 76.8 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 54/177 (30%), Positives = 84/177 (47%), Gaps = 11/177 (6%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
            +L + +KP G V T SD  GR TV+D LP        + +GRLD+ ++GLLL T DG +
Sbjct: 5   KKLLVLNKPKGYVVTRSDELGRKTVYDLLPDWAFHDGWMPIGRLDLESKGLLLFTTDGKI 64

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P      VY +   G V  + +   K+G+  +      + V      G+   + 
Sbjct: 65  GDALTRPGNCIK-VYEIWVRGHVTDEHIAEAKRGVESKHGLLKALVVEKLGTGGAKTKLK 123

Query: 191 VGLREGKNREIKKVFEFFN-------WKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           + + EGKNR I+++F            KV  L RIS G F+L  + +G  R ++ + 
Sbjct: 124 IVIDEGKNRHIRRLFGALKDPKFGTPLKVLELKRISIGSFEL-DIESGKWRYLTVEE 179


>gi|325287743|ref|YP_004263533.1| pseudouridine synthase Rsu [Cellulophaga lytica DSM 7489]
 gi|324323197|gb|ADY30662.1| pseudouridine synthase Rsu [Cellulophaga lytica DSM 7489]
          Length = 191

 Score = 76.8 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 33/186 (17%), Positives = 66/186 (35%), Gaps = 19/186 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDG 128
           +     +Y     L    S+ + +          +    ++ +GRLD  +EGLLLLT DG
Sbjct: 5   QHIHYKMYKPYGVLSQLASNDNNQVKKKFLSEFYNFPQGIMPIGRLDEKSEGLLLLTTDG 64

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--------------- 173
            L+  +     +     ++      +          I + G  Y                
Sbjct: 65  KLSDTINRAGIEKEYYAQLDGIITNEALHKIEKGVVIGLNGTTYTTKTCIVKHIETPKNI 124

Query: 174 --DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                     +   N+W+++ + EGK R+++K+     +   RL+R+      L  L  G
Sbjct: 125 PEPSTKIRLGRHRPNSWISICITEGKFRQVRKMTAAVGFPTLRLVRVRIHNITLDNLTLG 184

Query: 232 STREVS 237
           +   ++
Sbjct: 185 AVTPIN 190


>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 = 76.4 bits (186), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 35/240 (14%), Positives = 76/240 (31%), Gaps = 38/240 (15%)

Query: 12  TPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP---- 66
             +R+ KV+A +    SR  ++ +I    VKVNG  +++    +   D + V+  P    
Sbjct: 35  DGERLDKVLASSLKDISRSRLKTLIEDGLVKVNGKTVDKPKEKMSFGDEVSVEIKPRLED 94

Query: 67  -----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-----S 110
                      +   +   L +      +V   +     + +   L              
Sbjct: 95  MDFIATPMDIDVVYEDDDILVINKPARLVVHPAAGHWDDTLLNGLLAYNPIFRTLPRAGI 154

Query: 111 VGRLDINTEGLLLLTNDGGLA----RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
           V RLD +T GL+++  +        + L+  + +       R     D+     +++   
Sbjct: 155 VHRLDRDTTGLMVVAKNEKAMLDLVQQLQARTVKREYWALTRGKAPADKVIEAAIERDPR 214

Query: 167 I-------QGICYGDMQVTLDTQKGSN------AWVTVGLREGKNREIKKVFEFFNWKVN 213
                   +G         +             +WV   L+ G+  +I+   E     + 
Sbjct: 215 NPLRFTIGKGGRAKPATTHIRCIDQKEVKGKPFSWVACRLKTGRTHQIRVHMESIGLPLI 274


>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 = 76.4 bits (186), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 31/242 (12%), Positives = 72/242 (29%), Gaps = 34/242 (14%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            I+    +P+R+ K +      SR  +++M+ Q  V VN  ++ + +  +   D +E+  
Sbjct: 2   KILYSLTSPKRIDKFLVEVTDYSRTSIKKMLEQNLVLVNDNIITKQSYLLQKNDSVEIKN 61

Query: 65  V-----------------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                              +   ++  L +      LV   S  +  +        + + 
Sbjct: 62  EQCVIDSQKELLPFACPLEIVFEDQDLLVINKPSGMLVHPTSFQEQNTLANALKHYLKTD 121

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
              +          L++      A            V +  +    ++  ++ L   I  
Sbjct: 122 DFYITHRLDKNTSGLIVICKNQKALCCLQQQFMQKTVKKSYYAIVHNRFDMHHLHFMINE 181

Query: 168 QGI---------CYGDMQV--------TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                         GD +          +  Q  + A V V +  G+  +I+      N 
Sbjct: 182 PIGHSYQDKLRMKTGDAKNVKEAISIVKVIEQYQNTALVEVSIITGRTHQIRVHMRHINH 241

Query: 211 KV 212
            +
Sbjct: 242 PI 243


>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 = 76.4 bits (186), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 66/244 (27%), Gaps = 36/244 (14%)

Query: 5   NIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            I  E    QR+ K ++ +  A SR +++  I +  VKVN  +++     V   DHI V 
Sbjct: 7   KITDETQVGQRIDKFLSESNDAWSRSQLQDWIKEDLVKVNDKVIKS-NYKVKLNDHIIVT 65

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   +     +Y     +V         + V   +  I +   
Sbjct: 66  EKEVVEADIQPEDLDLDIYYEDDDVAIVYKPKGMVVHPSPGHYTGTLVNGLMYQIKNLSG 125

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------------- 155
             G +       +     G L       + + L    +    +                 
Sbjct: 126 INGEIRPGIVHRIDKDTSGLLMVAKNDIAHRGLVEQLMAKSVKRKYTALVHDNIPHDYGT 185

Query: 156 ------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                    N  +   V+           +         +   L  G+  +I+   ++  
Sbjct: 186 VDAPIGRNKNDRQAMAVVDDGKEAVTHFNVIEHFKDYTLIECELETGRTHQIRVHMKYIG 245

Query: 210 WKVN 213
           + + 
Sbjct: 246 YPLV 249


>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 = 76.4 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 35/240 (14%), Positives = 76/240 (31%), Gaps = 38/240 (15%)

Query: 12  TPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP---- 66
             +R+ KV+A +    SR  ++ +I    VKVNG  +++    +   D + V+  P    
Sbjct: 50  DGERLDKVLASSLKDISRSRLKTLIEDGLVKVNGKTVDKPKEKMSFGDEVSVEIKPRLED 109

Query: 67  -----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-----S 110
                      +   +   L +      +V   +     + +   L              
Sbjct: 110 MDFIATPMDIDVVYEDDDILVINKPARLVVHPAAGHWDDTLLNGLLAYNPIFRTLPRAGI 169

Query: 111 VGRLDINTEGLLLLTNDGGLA----RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
           V RLD +T GL+++  +        + L+  + +       R     D+     +++   
Sbjct: 170 VHRLDRDTTGLMVVAKNEKAMLDLVQQLQARTVKREYWALTRGKAPADKVIEAAIERDPR 229

Query: 167 I-------QGICYGDMQVTLDTQKGSN------AWVTVGLREGKNREIKKVFEFFNWKVN 213
                   +G         +             +WV   L+ G+  +I+   E     + 
Sbjct: 230 NPLRFTIGKGGRAKPATTHIRCIDQKEVKGKPFSWVACRLKTGRTHQIRVHMESIGLPLI 289


>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 = 76.4 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 33/240 (13%), Positives = 66/240 (27%), Gaps = 37/240 (15%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPL 67
              QR+ + +A A   SR + + +I +  VKVNG  +++ A  V   + +E    +  P+
Sbjct: 6   TQKQRLDQFVAEAAQISRSQAKEIIEKGLVKVNGKTVQKPAYKVKEGERVEFEVPEPEPI 65

Query: 68  R-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-----RVISV 111
                         ++  + +      +V         + V   L            +  
Sbjct: 66  EVKPEAIPLEVIYEDQDVIVINKPAGMVVHPAPGHYSGTLVNALLHHCKDLGGIGGALRP 125

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           G +    +    L          +    Q+      RF+  +           IV+    
Sbjct: 126 GIVHRLDKDTAGLIVVAKNDLAQQSLIEQFKNRSVGRFYRALIYGIPKREHDRIVLPIGR 185

Query: 172 YGDMQVTLDTQKGS------NAWV------------TVGLREGKNREIKKVFEFFNWKVN 213
               +        S      N WV               L  G+  +I+         + 
Sbjct: 186 DKFDRKKFSPNTTSPKEAITNYWVIEKFPEHNVAEIKCKLETGRTHQIRVHMSNLGHPLL 245


>gi|255523817|ref|ZP_05390782.1| RNA-binding S4 domain protein [Clostridium carboxidivorans P7]
 gi|255512520|gb|EET88795.1| RNA-binding S4 domain protein [Clostridium carboxidivorans P7]
          Length = 87

 Score = 76.4 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 14/87 (16%), Positives = 32/87 (36%), Gaps = 1/87 (1%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           R+ K +A + +  R+ V   I +  ++VNG ++   ++++    D I+  G  +    +
Sbjct: 1  MRLDKFLAESSVGRRKIVRIYIKEGLIEVNGEVITEPSMDINENSDVIKYLGKVVSYTGK 60

Query: 73 TRLWLYHKPIGLVTTHSDPDGRSTVFD 99
                     +            VF 
Sbjct: 61 VYYMFNKPAGCITARKDKDHRTVFVFF 87


>gi|332185508|ref|ZP_08387256.1| hypothetical protein SUS17_591 [Sphingomonas sp. S17]
 gi|332014486|gb|EGI56543.1| hypothetical protein SUS17_591 [Sphingomonas sp. S17]
          Length = 182

 Score = 76.4 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 36/177 (20%), Positives = 68/177 (38%), Gaps = 14/177 (7%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L        L               +       V   GRLD ++EGLLLL +DG L   +
Sbjct: 5   LLFNKPFGVLSQFTDRGSPTVRSTLSDFIAVKGVYPAGRLDRDSEGLLLLCDDGRLQARI 64

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------------VTLD 180
             P  +  + Y V+  G   + +L  L++G+ ++                          
Sbjct: 65  ADPRFKMPKTYLVQVEGDPQEPELERLRQGVQLKDGMTLPADVARIDEPDLWLRDPPIRQ 124

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +   + W+ + +REG+NR+++++         RL+R S G + +  +  G   ++S
Sbjct: 125 RKAIPDNWLKLTIREGRNRQVRRMTAAVGLPTLRLVRWSIGDWSVAGIAPGRFEQLS 181


>gi|171320855|ref|ZP_02909856.1| pseudouridine synthase [Burkholderia ambifaria MEX-5]
 gi|171093881|gb|EDT39011.1| pseudouridine synthase [Burkholderia ambifaria MEX-5]
          Length = 192

 Score = 76.4 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 41/182 (22%), Positives = 72/182 (39%), Gaps = 19/182 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D        V   GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGD--WVKTPSVYPAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPHHKLVKRYWAQVDGAPGPADLKALTRGVDLGDYVTRPCRAEFIEPPDALWPRNPPIR 120

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L    G T  + 
Sbjct: 121 YRAAIPTTWIELAITEGKNRQVRRMTAAIGFPTLRLVRVGIGALDIFALGIAPGETIALP 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>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 = 76.4 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 32/241 (13%), Positives = 63/241 (26%), Gaps = 36/241 (14%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E    +R+ K +A      SR +V++ I    V VNG +++     V + D I V  
Sbjct: 8   TVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDAVVTVNGKVVK-GNYKVKANDEITVTI 66

Query: 63  ------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                 D  P      +   +   L +      +V         + V   +         
Sbjct: 67  PEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI 126

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL---------- 160
            G +       +     G L       + + L    V          +            
Sbjct: 127 NGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTI 186

Query: 161 ----------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      +   V +          +  +      V   L  G+  +I+   ++  +
Sbjct: 187 DAPIGRDKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGY 246

Query: 211 K 211
            
Sbjct: 247 P 247


>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 = 76.0 bits (185), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 33/239 (13%), Positives = 64/239 (26%), Gaps = 40/239 (16%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE----VDGVP--- 66
           +R+ K I+     SR +++ +I Q+ V VN I++ +   +V     I     +D      
Sbjct: 10  ERIDKYISNNSEISRNDIKSLIEQKAVLVNDIVVNKPKFSVNEGQVITILKLIDKEIKIE 69

Query: 67  -------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN-- 117
                  +   +   L L      +V         + V   L    + + +   L     
Sbjct: 70  AQNIDLDIAYEDEYLLVLKKPSGMVVHPAPGHHENTLVNALLYHFKNNLSNENGLLRPGI 129

Query: 118 ------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----I 167
                     LLL         +         + R          K   LK  +     I
Sbjct: 130 VHRIDKDTSGLLLIAKNNEVHKILAEGFATKTINRKYVAICDGILKSPKLKLDLPIGRDI 189

Query: 168 QGICYGDMQVT--------------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           +      +                    +    + V   L  G+  +I+    +    V
Sbjct: 190 KNRQLMAITNANSKSAVTHLELLKSFYYENQPKSLVKATLETGRTHQIRVHCAYIKNPV 248


>gi|213419764|ref|ZP_03352830.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 59

 Score = 76.0 bits (185), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 26/54 (48%), Gaps = 1/54 (1%)

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           V + + EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 2   VRLTISEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEEEI 55


>gi|219113879|ref|XP_002176126.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|219121877|ref|XP_002181284.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217402918|gb|EEC42877.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217407270|gb|EEC47207.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 286

 Score = 76.0 bits (185), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 22/115 (19%), Positives = 43/115 (37%), Gaps = 4/115 (3%)

Query: 169 GICYGDMQVTLDTQKG--SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP-FQL 225
           G     +   +        +  V++ + EGKNR+I+++F      V RL R   G    L
Sbjct: 171 GGTTRPVDELIVKTNPTLKSTLVSLTICEGKNRQIRRMFHALGSGVIRLCRTQIGRSLTL 230

Query: 226 GTL-LAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVP 279
            ++ +AG  R +++K +   L        +V+  +    +   V           
Sbjct: 231 SSVPMAGQWRILTEKEVETALDWRPRYIGEVSALSRAGKTTKAVTGTSRRRKRSN 285


>gi|330685506|gb|EGG97159.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU121]
          Length = 305

 Score = 76.0 bits (185), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 30/243 (12%), Positives = 65/243 (26%), Gaps = 36/243 (14%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           I   N   QR+ KV+       SR +++  I +  VKVN  +++     V   D+I V  
Sbjct: 8   ITDSNHVGQRLDKVLPELNSGWSRSQIQDWIKEDLVKVNDKVVK-PNYKVKQNDNIVVTE 66

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                           +   +     +Y     +V         + V   +  I +    
Sbjct: 67  QEVVEADITPENLNLDIFYEDDDVAIVYKPKGMVVHPSPGHYTGTLVNGLMYQIKNLSGI 126

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPST------------QWLRVYRVRFHGQVDQ--- 155
            G +       + +   G L       +             +   +  V  +   D    
Sbjct: 127 NGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMAKSVKRKYIALVHGNIPHDYGTV 186

Query: 156 -----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      +   V+           +         +   L  G+  +I+   ++  +
Sbjct: 187 DAPIGRNKKDRQAMAVVDDGKEAVTHFNVLEHFKDYTLIECELETGRTHQIRVHMKYIGF 246

Query: 211 KVN 213
            + 
Sbjct: 247 PLV 249


>gi|257087008|ref|ZP_05581369.1| pseudouridylate synthase [Enterococcus faecalis D6]
 gi|256995038|gb|EEU82340.1| pseudouridylate synthase [Enterococcus faecalis D6]
          Length = 301

 Score = 76.0 bits (185), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 70/246 (28%), Gaps = 37/246 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 1   MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 58

Query: 60  IEV------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I V            + +P  +   +   + +      +V         + V   L    
Sbjct: 59  IVVTIPEPEVLDMVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSVGHPNGTLVNALLHHAD 118

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                   +       +     G L       + + L                       
Sbjct: 119 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 178

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           K   VI+G        T+  +  +   V + L  G+  +I+   
Sbjct: 179 DKGEINAPIGRSKVDRKMQAVIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRVHM 238

Query: 206 EFFNWK 211
           ++  + 
Sbjct: 239 KYIGYP 244


>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 = 76.0 bits (185), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 36/250 (14%), Positives = 77/250 (30%), Gaps = 39/250 (15%)

Query: 1   MKDKNIVQENF--TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M++K I         +R+ K++ +    +R  +++ +    V VNG +++ A       D
Sbjct: 1   MENKIIELTLSLEKSERLDKILTKELSHTRSVIQQWLKSGFVSVNGEVVK-ANYKAKDGD 59

Query: 59  HIEVDGV--------------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS- 103
           H+ +                  +   +   L +      +V         + V   L   
Sbjct: 60  HVTIQIEEEEELTVLAENIPLEIVFEDEHLLVINKPSGMVVHPSKGHSTGTLVNALLYHV 119

Query: 104 -------IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR------------- 143
                     R   V R+D +T GLL++         L                      
Sbjct: 120 DQLSKGSESYRPGIVHRIDKDTSGLLVVAKTPQAHVGLSNQLMDHSMTRSYVAIVEGSFE 179

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                    + +D  N LK+ +  +G        T+       + + + L  G+  +I+ 
Sbjct: 180 HITGTVDAPLARDPHNRLKRCVQKEGKQA-ITHFTVIQALKETSVLRLNLETGRTHQIRA 238

Query: 204 VFEFFNWKVN 213
             +F +  + 
Sbjct: 239 HMDFIHHPIL 248


>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 = 76.0 bits (185), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 71/246 (28%), Gaps = 37/246 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 1   MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 58

Query: 60  IEV------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I V            + +P  +   +   + +      +V   +     + V   L    
Sbjct: 59  IVVTIPEPEVLDMVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPNGTLVNALLHHAD 118

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                   +       +     G L       + + L                       
Sbjct: 119 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 178

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           K   VI+G        T+  +  +   V + L  G+  +I+   
Sbjct: 179 DKGEINAPIGRSKVDRKMQAVIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRVHM 238

Query: 206 EFFNWK 211
           ++  + 
Sbjct: 239 KYIGYP 244


>gi|330956144|gb|EGH56404.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
          syringae Cit 7]
          Length = 75

 Score = 76.0 bits (185), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 29/71 (40%), Positives = 39/71 (54%), Gaps = 2/71 (2%)

Query: 2  KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
          KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG         V   D I
Sbjct: 4  KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDAT-LGQRVDLHDAI 62

Query: 61 EVDGVPLRKAE 71
           VDG  +++ E
Sbjct: 63 SVDGRVIKREE 73


>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 = 76.0 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 36/248 (14%), Positives = 69/248 (27%), Gaps = 39/248 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K + ++ E    +R+ K IA+     SR  ++ +I    V+VNG   +  ++ + + D 
Sbjct: 3   VKTRRLIAE-SDGERLDKYIAQKETDLSRSFIQALIDSGHVQVNGKTAK-PSLKLKNGDT 60

Query: 60  IEVDGVPLRKAERTR--------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I ++  P    E                 L +   P   V         + +   L    
Sbjct: 61  ITIEISPETPPELKAEDIPLEIIFQDKDLLLINKPPGLTVHPAPGHPDHTLINGVLALEP 120

Query: 106 SRVISVGR---------------------LDINTEGLLLLTNDGGLARVLELPSTQWLRV 144
                                               L     +  + +         L  
Sbjct: 121 KMEDFDDPLRPGIVHRLDKDTSGLLLVAKNRETLANLSAQFKERTVRKYYLTLVKGELHP 180

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                   + +D  N  K  +V  G         L   +G  + + V L  G+  +I+  
Sbjct: 181 AEGFIEAPLGRDPQNRQKIAVVSNGRHARTGYKVLRYIQG-YSLLEVKLETGRTHQIRVH 239

Query: 205 FEFFNWKV 212
           F      V
Sbjct: 240 FAAIGHPV 247


>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 = 76.0 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 31/248 (12%), Positives = 65/248 (26%), Gaps = 37/248 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M +  +  E    +R+   +      SR  ++ +I    V VNG +  +A + + +   I
Sbjct: 1   MNEYKVSLE-QEGKRLDVFLTDVMEGSRSYIQSLIKSGHVLVNGKV-GKANLRLNADSTI 58

Query: 61  EVD------------GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
            VD             +P+     +   + +      +V         + V   L     
Sbjct: 59  SVDIPEPESVEILPEDIPVEYLYEDHDIIIVNKPRGMVVHPAIGNYSGTLVNALLYHCKD 118

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ----------- 155
                G +       L     G +       +   L         +              
Sbjct: 119 LSGINGEIRPGIVHRLDKDTSGVMMAAKNDAAHIGLAEQVKAHSAKRTYLALVQGNIVEE 178

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                        + +K  +V +          +  + G +  V   L  G+  +I+  F
Sbjct: 179 KGIIKAPIGRHPKDRMKMAVVFENSKEAVTHFKVLERYGYHTLVECVLETGRTHQIRVHF 238

Query: 206 EFFNWKVN 213
                 V 
Sbjct: 239 AHIGHPVV 246


>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 = 76.0 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 71/246 (28%), Gaps = 37/246 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 1   MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 58

Query: 60  IEV------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I V            + +P  +   +   + +      +V   +     + V   L    
Sbjct: 59  IVVTIPEPEVLDMVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPNGTLVNALLHHAD 118

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                   +       +     G L       + + L                       
Sbjct: 119 HLSAINDVVRPGIVHRIDKDTSGLLMVAKSDQAHESLAKQLKEKTSLRKYVALVHGVIPH 178

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           K   VI+G        T+  +  +   V + L  G+  +I+   
Sbjct: 179 DKGEINAPIGRSKVDRKMQAVIEGGKEAVTHFTVLERFDTFTLVELQLETGRTHQIRVHM 238

Query: 206 EFFNWK 211
           ++  + 
Sbjct: 239 KYIGYP 244


>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 = 76.0 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 33/248 (13%), Positives = 71/248 (28%), Gaps = 38/248 (15%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M    I VQ     +R+ K +A  G   SR +V++ + +  V VNG  ++ A   +   D
Sbjct: 1   MNQFEITVQPEQKSERIDKFLASTGENWSRTQVQQWVKEGLVSVNGKSVK-ANYKMQPGD 59

Query: 59  HI--------EVD------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            +        E+D       + +   ++  L +      +V         + V   +   
Sbjct: 60  QVNVTIPEPEELDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHVTGTLVNGLMAHC 119

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR--------------------- 143
                  G +       +     G L       + + L                      
Sbjct: 120 NDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKYTAVVHGVIS 179

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                    + +DK +     +  +G         +  +      V   L  G+  +I+ 
Sbjct: 180 HDDGTIDAPIGRDKKDRQSMTVTREGSKNAVTHFHVLERFQDFTLVECRLETGRTHQIRV 239

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 240 HMKYIGFP 247


>gi|317969165|ref|ZP_07970555.1| pseudouridine synthase [Synechococcus sp. CB0205]
          Length = 178

 Score = 76.0 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 39/146 (26%), Positives = 60/146 (41%), Gaps = 20/146 (13%)

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ----- 176
           +LLT++G L + L  PS    R Y  +  G   +D LN L+ G+VIQG      Q     
Sbjct: 1   MLLTSNGRLQQRLTDPSWGHWRRYWSQVEGVPSEDALNALRSGLVIQGQRTLPAQAQALQ 60

Query: 177 ---------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------ 221
                         Q    +W+ + LREG+NR+++++         RL+R++        
Sbjct: 61  DPGWPERDPPIRVRQSIPTSWLQLELREGRNRQVRRMTAAVGLPTLRLLRVAMDLMDGGP 120

Query: 222 PFQLGTLLAGSTREVSKKILREQLGP 247
           P  L  L  G  R V+    R     
Sbjct: 121 PLSLDGLAPGQWRSVNDDEDRRLQSL 146


>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 = 76.0 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 33/243 (13%), Positives = 62/243 (25%), Gaps = 40/243 (16%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            V E    +R+ K +A  G+    SR +V++ I    V VNG  ++     V   D I V
Sbjct: 8   TVTEEQKSERIDKFLA--GVNNEWSRSQVQQWIKDGVVTVNGNAIK-GNYKVKVNDEIAV 64

Query: 63  ---DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
              D   L              +   L +      +V         + V   +       
Sbjct: 65  AIPDPEELDILPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD------------ 156
              G +       +     G L       + + L    V                     
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKG 184

Query: 157 --------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                        +   V +   +      +  +      V   L  G+  +I+   ++ 
Sbjct: 185 TIDAPIGRDKKDRQSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYI 244

Query: 209 NWK 211
            + 
Sbjct: 245 GYP 247


>gi|120436300|ref|YP_861986.1| pseudouridylate synthase [Gramella forsetii KT0803]
 gi|117578450|emb|CAL66919.1| pseudouridylate synthase [Gramella forsetii KT0803]
          Length = 194

 Score = 75.6 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 43/190 (22%), Positives = 73/190 (38%), Gaps = 20/190 (10%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTNDG 128
             R +  +KP G ++              L          +S+GRLD ++EGLLLLT +G
Sbjct: 5   YHRHFKIYKPYGYLSQFITNQKPGGKHKLLGDLYDFPEGTMSIGRLDKDSEGLLLLTTNG 64

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--------------- 173
            L+  +     +     +V      +          I I G  Y                
Sbjct: 65  KLSTKINRGGIEKEYYAQVDGDITDEAMIKLQNGVEISIFGKAYKSLKCKAEKLKNRPSF 124

Query: 174 --DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
               +   D + G  +W+++ L EGK R++KK+     +   RL+R+  G   +  + AG
Sbjct: 125 PERAKKIRDERHGPTSWISISLTEGKFRQVKKMTSAVGFPTLRLVRVRIGNETIKNMDAG 184

Query: 232 STREVSKKIL 241
              E++K  L
Sbjct: 185 EVIELNKVDL 194


>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 = 75.6 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 31/248 (12%), Positives = 65/248 (26%), Gaps = 37/248 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M +  +  E    +R+   +      SR  ++ +I    V VNG +  +A + + +   I
Sbjct: 1   MNEYKVSLE-QEGKRLDVFLTDVMEGSRSYIQSLIKSGHVLVNGKV-GKANLRLNADSTI 58

Query: 61  EVD------------GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
            VD             +P+     +   + +      +V         + V   L     
Sbjct: 59  SVDIPEPESVEILPEDIPVEYLYEDHDIIIVNKPRGMVVHPAIGNYSGTLVNALLYHCKD 118

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ----------- 155
                G +       L     G +       +   L         +              
Sbjct: 119 LSGINGEIRPGIVHRLDKDTSGVMMAAKNDAAHIGLAEQVKAHSAKRTYLALVQGNIVEE 178

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                        + +K  +V +          +  + G +  V   L  G+  +I+  F
Sbjct: 179 KGIIKAPIGRHPKDRMKMAVVFENSKEAVTHFKVLERYGYHTLVECVLETGRTHQIRVHF 238

Query: 206 EFFNWKVN 213
                 V 
Sbjct: 239 AHIGHPVV 246


>gi|260221244|emb|CBA29613.1| Ribosomal large subunit pseudouridine synthase D [Curvibacter
           putative symbiont of Hydra magnipapillata]
          Length = 335

 Score = 75.6 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 33/239 (13%), Positives = 72/239 (30%), Gaps = 38/239 (15%)

Query: 13  PQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP----- 66
            +R+ + +A      SR  ++++I    V+VNG ++ + +  V   + + V+  P     
Sbjct: 33  GERLDRALAFSVQEFSRSYLQQLIESGFVQVNGKVVTKTSGKVKVGEELTVELKPTPQSQ 92

Query: 67  ----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV----- 111
                     +   +   L +      +V         + +   L       +       
Sbjct: 93  AFKPEPMALDVVHEDEHVLVINKPAGLVVHPAPGNWSGTLLNGLLAYSPHAALVPRAGIV 152

Query: 112 GRLDINTEGLLLLTNDGGLA--------------RVLELPSTQWLRVYRVRFHGQVDQDK 157
            RLD +T GL+++                     +   +    W           + +D 
Sbjct: 153 HRLDKDTSGLMVVARSRTAMDALVNAIAAREVSRQYFAIAHKTWPWTRLKEVDAPIGRDP 212

Query: 158 LNLLKKGI---VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            N L+  +   V Q         +L +      WV   L  G+  +I+         + 
Sbjct: 213 RNRLRMAVVDLVHQSGKEARTDFSLISNSQVACWVRCILHTGRTHQIRVHMAHIGHPLV 271


>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 = 75.6 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 32/252 (12%), Positives = 66/252 (26%), Gaps = 39/252 (15%)

Query: 1   MKDKNIVQENFTPQ--RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           MK   +++     +  R+ K +ARA    SR  +++++ +  V VNG  + + +  +   
Sbjct: 1   MKISEVLEFKVEGEEERLDKFLARAYPDFSRSYIKKLVKEGLVYVNGEEVRKPSRKLREG 60

Query: 58  DHIEV---DGVPLRKAERTRLWLY-----------HKPIGLVTTHSDPDGRSTVFDNLPS 103
           + + +   +  PL                           +V         + V   L  
Sbjct: 61  ERVILHVPEPEPLDVKPENIPINIIYEDEDIAVVEKPCGLVVHPSPGYTSGTLVNALLYH 120

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
           I       G         L     G +       + + L         +     L     
Sbjct: 121 IKDLSSIGGVERPGIVHRLDKETAGVMVIAKNNTAHRNLVRQFQERKTEKFYKVLVKGLV 180

Query: 164 GIVIQGICYGDMQVTLD----------------------TQKGSNAWVTVGLREGKNREI 201
                 I     +  +D                       +K     + V +  G+  +I
Sbjct: 181 KKDYGAIDTPIARHPVDRKRFWVRKEGKEALTEYWVLKRYEKYEITLLKVKIHTGRTHQI 240

Query: 202 KKVFEFFNWKVN 213
           +  F      V 
Sbjct: 241 RVHFASIGHPVL 252


>gi|156103349|ref|XP_001617367.1| RNA pseudouridylate synthase [Plasmodium vivax SaI-1]
 gi|148806241|gb|EDL47640.1| RNA pseudouridylate synthase, putative [Plasmodium vivax]
          Length = 483

 Score = 75.6 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 39/247 (15%), Positives = 84/247 (34%), Gaps = 33/247 (13%)

Query: 22  RAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVD--GVPLRKAERTRLWLY 78
             G+ S R     + +  ++VNG ++ +  V++    D +E+   G  L + +   + L 
Sbjct: 238 HEGLCSSRFAFNNLRRGIIQVNGQVVFQ-NVSISPGKDRVELTKAGRELLRNKNVTIILN 296

Query: 79  HKPIG------------------------LVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
                                         +             +      +++   GRL
Sbjct: 297 KPKYYLSILNDHKTNKKLLARNLIRNENKFIEEEHKCMSYFINRNLNIEKVNKLYVCGRL 356

Query: 115 DINTEGLLLLTNDGGLARVL-ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           D N+ GLL+ T +  +   L         + Y V     +++  +  L++  ++ G    
Sbjct: 357 DANSTGLLVFTQNTLICSYLLNRYKYLVEKEYIVEAADPIEEVHMKRLRENALVDGKLIY 416

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
             ++           ++  L +G ++ I+K+    N K+  L R+  G   L  L  G  
Sbjct: 417 KCRIQYV----DCFTLSFTLYQGFHKIIRKLCLLSNIKIRALHRVRIGGIHLKGLPLGKW 472

Query: 234 REVSKKI 240
           R +    
Sbjct: 473 RFLMPNE 479


>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 = 75.6 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 40/245 (16%), Positives = 81/245 (33%), Gaps = 33/245 (13%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  + ++ ++    R+   +A     SR E+++ I  ++V VN    ++    + S D I
Sbjct: 1   MIYEFLIDDSNQNTRLDVFLANEVELSRSEIQKFIEDKKVLVNYKPQKK-NYKLNSNDKI 59

Query: 61  EVD----GVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--- 105
           + D       +R          E   L + +K   ++   ++     T+ + L   F   
Sbjct: 60  KFDYEKEDKTIRAQKHDLDVVYEDDYLAIINKDKDVIVHPTETIYSDTLVNYLMYNFKNL 119

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--- 156
                  R   V RLD +T GL+++  D      L+        +           D   
Sbjct: 120 SDVDGDYRRGIVHRLDKDTTGLIIIAKDNDTHLKLKEIIKNHEIIKTYLCIVHGKIDESG 179

Query: 157 --------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                        KK +V         Q          + V V ++ G+  +I+    + 
Sbjct: 180 TIKEYMTRNPKDRKKMMVSDEGKLSISQYERLDYNDDYSLVKVQIKTGRTHQIRVHMNYI 239

Query: 209 NWKVN 213
           +  + 
Sbjct: 240 HHPIL 244


>gi|284007320|emb|CBA72674.1| ribosomal large subunit pseudouridine synthase E [Arsenophonus
           nasoniae]
          Length = 90

 Score = 75.6 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 17/88 (19%), Positives = 34/88 (38%), Gaps = 15/88 (17%)

Query: 165 IVIQGICYGDMQ---------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
           ++++       +                    +    +W+ + L EG+NR+I+++     
Sbjct: 1   MLLKDGMTKPAKAELVAEPDWLWPRHPPIRIRKNIPTSWLKISLSEGRNRQIRRMTANIG 60

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +   RLI  S   FQL  L  G  +E+ 
Sbjct: 61  FPTLRLILYSIANFQLDNLQPGEWKEID 88


>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 = 75.6 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 71/246 (28%), Gaps = 37/246 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 1   MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 58

Query: 60  IEV------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I V            + +P  +   +   + +      +V   +     + V   L    
Sbjct: 59  IVVTIPEPEALDMVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPKGTLVNALLHHAD 118

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                   +       +     G L       + + L                       
Sbjct: 119 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 178

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           K   VI+G        T+  +  +   V + L  G+  +I+   
Sbjct: 179 DKGEINAPIGRSKVDRKMQAVIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRVHM 238

Query: 206 EFFNWK 211
           ++  + 
Sbjct: 239 KYIGYP 244


>gi|257082401|ref|ZP_05576762.1| pseudouridylate synthase [Enterococcus faecalis E1Sol]
 gi|256990431|gb|EEU77733.1| pseudouridylate synthase [Enterococcus faecalis E1Sol]
          Length = 301

 Score = 75.6 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 71/246 (28%), Gaps = 37/246 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 1   MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 58

Query: 60  IEV------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I V            + +P  +   +   + +      +V   +     + V   L    
Sbjct: 59  IVVTIPEPEVLDMVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPKGTLVNALLHHAD 118

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                   +       +     G L       + + L                       
Sbjct: 119 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 178

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           K   VI+G        T+  +  +   V + L  G+  +I+   
Sbjct: 179 DKGEINTPIGRSKVDRKMQAVIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRVHM 238

Query: 206 EFFNWK 211
           ++  + 
Sbjct: 239 KYIGYP 244


>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 = 75.6 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 71/246 (28%), Gaps = 37/246 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 1   MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 58

Query: 60  IEV------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I V            + +P  +   +   + +      +V   +     + V   L    
Sbjct: 59  IVVTIPEPEVLDMVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPKGTLVNALLHHAD 118

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                   +       +     G L       + + L                       
Sbjct: 119 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 178

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           K   VI+G        T+  +  +   V + L  G+  +I+   
Sbjct: 179 DKGEINAPIGRSKVDRKMQAVIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRVHM 238

Query: 206 EFFNWK 211
           ++  + 
Sbjct: 239 KYIGYP 244


>gi|257090036|ref|ZP_05584397.1| pseudouridylate synthase [Enterococcus faecalis CH188]
 gi|256998848|gb|EEU85368.1| pseudouridylate synthase [Enterococcus faecalis CH188]
          Length = 301

 Score = 75.2 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 71/246 (28%), Gaps = 37/246 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 1   MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 58

Query: 60  IEV------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I V            + +P  +   +   + +      +V   +     + V   L    
Sbjct: 59  IVVTIPEPEVLDMIAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPKGTLVNALLHHAD 118

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                   +       +     G L       + + L                       
Sbjct: 119 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 178

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           K   VI+G        T+  +  +   V + L  G+  +I+   
Sbjct: 179 DKGEINAPIGRSKVDRKMQAVIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRVHM 238

Query: 206 EFFNWK 211
           ++  + 
Sbjct: 239 KYIGYP 244


>gi|206561075|ref|YP_002231840.1| putative pseudouridine synthase [Burkholderia cenocepacia J2315]
 gi|198037117|emb|CAR53038.1| putative pseudouridine synthase [Burkholderia cenocepacia J2315]
          Length = 192

 Score = 75.2 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 41/191 (21%), Positives = 76/191 (39%), Gaps = 19/191 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +      + GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKTPGV--YAAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVDGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPDTLWPRNPPIR 120

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L    G T  + 
Sbjct: 121 YRAAIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFALGIAPGETIALP 180

Query: 238 KKILREQLGPH 248
            +   +   P 
Sbjct: 181 PRAPWDGFAPA 191


>gi|295134129|ref|YP_003584805.1| pseudouridylate synthase [Zunongwangia profunda SM-A87]
 gi|294982144|gb|ADF52609.1| pseudouridylate synthase [Zunongwangia profunda SM-A87]
          Length = 190

 Score = 75.2 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 43/187 (22%), Positives = 75/187 (40%), Gaps = 20/187 (10%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDG 128
             R +  +KP G ++     +        L    +     ++VGRLD ++EGLLLLT +G
Sbjct: 1   MHRYFKIYKPYGYLSQFITNEKPRKKKKLLGELGNFPEETMAVGRLDQDSEGLLLLTTNG 60

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--------------- 173
             +  +   S +     +V      +   L      I I G  Y                
Sbjct: 61  KESARITGSSVEKEYYVQVDGEITEEAIALLKNGVEISINGTKYRSLPCKAFKLYTRPVF 120

Query: 174 --DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
               +   D + G  +W+++ L EGK R++KK+     +   RL+R+  G  +L  + +G
Sbjct: 121 PERAKKIRDERHGPTSWISITLTEGKFRQVKKMTAVVGFPTLRLVRVRIGNEKLEHMNSG 180

Query: 232 STREVSK 238
              E+ K
Sbjct: 181 EVIELEK 187


>gi|298208646|ref|YP_003716825.1| RNA pseudouridine synthase family protein [Croceibacter atlanticus
           HTCC2559]
 gi|83848569|gb|EAP86438.1| RNA pseudouridine synthase family protein [Croceibacter atlanticus
           HTCC2559]
          Length = 195

 Score = 75.2 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 34/154 (22%), Positives = 62/154 (40%), Gaps = 17/154 (11%)

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
           L +     +S+GRLD  +EGLLLLT DG ++  +     +   + +V             
Sbjct: 39  LYNFPEGTMSIGRLDEMSEGLLLLTTDGKVSAAVTSSKYEKEYIVQVSGDITEGAINEMR 98

Query: 161 LKKGIVIQGIC--YGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKK 203
               I I G                       +    ++ G  +W+++ +REGK R+++K
Sbjct: 99  NGLTIPINGKQYDTKPCTAFKLNKTPQFPERQKAIRSSRHGETSWLSISIREGKFRQVRK 158

Query: 204 VFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +     +   RL+RI  G + L  +  G    ++
Sbjct: 159 MTAKVGFPTLRLVRIRIGNYHLEDMQPGQVAPIN 192


>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 = 75.2 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 33/248 (13%), Positives = 73/248 (29%), Gaps = 38/248 (15%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M   NI V E  T +R+ K ++ +    SR +V++ +    ++VNG  ++ A   V + D
Sbjct: 1   MNQVNIAVSEEQTSERLDKFLSTSEPEWSRTQVQQWVKDGLIEVNGKQVK-ANYKVQAGD 59

Query: 59  HIEVD-GVP-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            I+V+   P             +   +   L +      +V         + V   +   
Sbjct: 60  QIKVEIPEPEALDVEAEAMDLDIYYEDADVLVVNKPRGMVVHPAPGHVSGTLVNGLMAHC 119

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------R 143
                  G +       +     G L       + + L                     +
Sbjct: 120 TDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRKYTAVVHGIIQ 179

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                    + +DK +     +  +          +  +      V   L  G+  +I+ 
Sbjct: 180 HDTGTIDAPIGRDKKDRQSMTVTKESSKQAVTHFDVIERFDDFTVVECRLETGRTHQIRV 239

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 240 HMKYIGYP 247


>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 = 75.2 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 30/247 (12%), Positives = 73/247 (29%), Gaps = 36/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M++  ++    T  R+ KV++   IA SR ++++ +    V+VN  +++ A   V   D 
Sbjct: 1   MENIKLIITEKTIGRIDKVLSEELIAYSRSQIQQWLKDSLVRVNNKVVK-ANYKVQPADE 59

Query: 60  IEVD-GVP-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           + +    P             +   ++  + +      +V   +     + V   L  I 
Sbjct: 60  VIIQLPKPKMMVVSPENIPLDIVYEDQDVVVINKPQGMVVHPSAGHFKGTMVHALLYHIK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ------------WLRVYRVRFHGQV 153
                   +       +     G L       + +               +  V      
Sbjct: 120 DLSSINDVIRPGIVHRIDKDTSGLLIVAKNNQAHEALAKQLKDKTILRKYIALVHGEVPH 179

Query: 154 DQ--------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
           +Q              K   +I+          +  +      + + L  G+  +I+   
Sbjct: 180 EQGTIDAPIGRSKTNRKMQAIIKDGRSAVTHFKVLEKFTGYTLIELQLETGRTHQIRVHM 239

Query: 206 EFFNWKV 212
           ++    V
Sbjct: 240 KYIGHPV 246


>gi|170702500|ref|ZP_02893380.1| pseudouridine synthase [Burkholderia ambifaria IOP40-10]
 gi|170132591|gb|EDT01039.1| pseudouridine synthase [Burkholderia ambifaria IOP40-10]
          Length = 192

 Score = 75.2 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 41/182 (22%), Positives = 74/182 (40%), Gaps = 19/182 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +        GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKTPGV--YPAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVDGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPDALWPRNPPIR 120

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   + TL    G T  + 
Sbjct: 121 YRAAIPTTWIELAITEGKNRQVRRMTAAIGFPTLRLVRVGIGALDIFTLGIAPGETIALP 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>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 = 74.8 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 33/249 (13%), Positives = 71/249 (28%), Gaps = 37/249 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK  N   +    QR+   ++      SR +++R+IAQ  V++NG  +  A   +   D+
Sbjct: 1   MKTINHYADPEIGQRLDVYLSNCYPDISRSQLQRLIAQGLVEINGKKVA-AKYKIKPGDY 59

Query: 60  I----------EVDGVPLRK----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I           V+   +       +   + +      +V         + V   L    
Sbjct: 60  INLTIPDPVGVSVEAENIALDIYFEDEDVIVINKPRGMVVHPAEGNYTGTMVNALLYHCR 119

Query: 106 SRVISVGRLDIN---------------------TEGLLLLTNDGGLARVLELPSTQWLRV 144
                 G L                           L        + R         L+ 
Sbjct: 120 DLSGINGVLRPGIVHRLDKDTSGLLMVAKNDLAHNNLAAQLEKRLVNRRYLALVHGNLKQ 179

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                   + +D  +  K  +  +          +  + G    + + L  G+  +I+  
Sbjct: 180 DAGTVDAPIGRDACSRQKMAVTDRNSRSAVTHFKVLKRFGRYTLLELKLETGRTHQIRVH 239

Query: 205 FEFFNWKVN 213
            ++  ++V 
Sbjct: 240 MKYIGYQVV 248


>gi|307730777|ref|YP_003908001.1| pseudouridine synthase [Burkholderia sp. CCGE1003]
 gi|307585312|gb|ADN58710.1| pseudouridine synthase [Burkholderia sp. CCGE1003]
          Length = 189

 Score = 74.8 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 36/173 (20%), Positives = 65/173 (37%), Gaps = 17/173 (9%)

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
                T        +            V   GRLD ++EGLLLLT+DG L   +  P  +
Sbjct: 7   NKPFGTICQFSAHETRASLADWVSVPGVYPAGRLDSDSEGLLLLTDDGALQARIAEPRHK 66

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---------------VTLDTQKGS 185
            ++ Y  +  G VD   L  L +G+ +        +                        
Sbjct: 67  LVKRYWAQVEGAVDAAALKKLARGVDLGDYVTKPCRADYVDPADRLWPRTPPIRYRAAIP 126

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
             W+ + + EGKNR+++++     +   RL+R+  G   +    L+ G + ++
Sbjct: 127 TTWIELSIAEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFALGLMPGESVDL 179


>gi|113460583|ref|YP_718647.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           somnus 129PT]
 gi|112822626|gb|ABI24715.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           somnus 129PT]
          Length = 119

 Score = 74.8 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 32/114 (28%), Positives = 53/114 (46%), Gaps = 2/114 (1%)

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           +DI+T GL+LLT+DG  +  +  P     + Y V     V+      ++KGI+++G    
Sbjct: 1   MDIDTTGLVLLTDDGQWSHRVTSPKHLCDKTYLVTLADPVEDFYQAEIEKGILLRGEKTP 60

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
               TL+     N  V + + EG+  ++K++F     KV  L R   G   L  
Sbjct: 61  TKPATLEILDDYN--VNLTISEGRYHQVKRMFAALGNKVVDLHRWKIGVIMLDD 112


>gi|115352624|ref|YP_774463.1| pseudouridine synthase, Rsu [Burkholderia ambifaria AMMD]
 gi|115282612|gb|ABI88129.1| Pseudouridine synthase, Rsu [Burkholderia ambifaria AMMD]
          Length = 192

 Score = 74.8 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 40/182 (21%), Positives = 73/182 (40%), Gaps = 19/182 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +        GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKTPGV--YPAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVDGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPDALWPRNPPIR 120

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L    G T  + 
Sbjct: 121 YRAAIPTTWIELAITEGKNRQVRRMTAAIGFPTLRLVRVGIGALDIFALGIAPGETIALP 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>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 = 74.8 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 33/247 (13%), Positives = 74/247 (29%), Gaps = 35/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+ K I+  +   +R+ K +       SR  ++ +I++  +KV+G  ++     +  ++ 
Sbjct: 1   METKEIIYASPKSERIDKFLQNELSDLSRTNIQNLISEGYIKVDGNTVKT-NYKLKESNV 59

Query: 60  IEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I +D                 +   +   L +      +V   +     + V   L    
Sbjct: 60  ITIDYKEPEELDVVKQDIPVDIVYEDNDLLIVNKPKGMVVHPSAGHKDGTLVNALLYHCE 119

Query: 106 -------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
                   R   V R+D +T GLL++  +      L           +            
Sbjct: 120 LSSINGTIRPGIVHRIDKDTSGLLIVAKNDKAHVKLSEMIANKEVKRKYYALVHGSIKHD 179

Query: 159 N------------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          K+  VI           +  +      +   L  G+  +I+   +
Sbjct: 180 YGTIDAPIARNPKERKEMAVIDEGKPSITHFKVIDRFEKYTLIECELETGRTHQIRVHMK 239

Query: 207 FFNWKVN 213
           + N  + 
Sbjct: 240 YINHPLV 246


>gi|33865219|ref|NP_896778.1| pseudouridine synthase [Synechococcus sp. WH 8102]
 gi|33638903|emb|CAE07200.1| possible pseudouridine synthase [Synechococcus sp. WH 8102]
          Length = 225

 Score = 74.8 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 46/188 (24%), Positives = 75/188 (39%), Gaps = 23/188 (12%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L++KP G+++  +                  V + GRLD ++EGLLLL++ G L + L 
Sbjct: 12  LLFNKPYGVLSQFTPETASRWRCLAEFINVPGVYAAGRLDADSEGLLLLSDQGRLQQRLT 71

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG----------- 184
            P     R Y V+  G  D  +L  L++GI IQ       +      +            
Sbjct: 72  DPRCGHWRSYWVQVEGHPDDPQLQKLREGIEIQHQRTLPARARWLQGEDIPLLPERDPPI 131

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQLGTLLAGS 232
                   +W+ + LREG+NR+++++         RL+R             L  L AG 
Sbjct: 132 RVRATIPTSWLELSLREGRNRQVRRMTAAVGLPTLRLVRCRIDLMDGGKALDLNDLPAGR 191

Query: 233 TREVSKKI 240
            R V+   
Sbjct: 192 WRSVTNAE 199


>gi|149917083|ref|ZP_01905583.1| ribosomal large subunit pseudouridine synthase B [Plesiocystis
           pacifica SIR-1]
 gi|149821999|gb|EDM81392.1| ribosomal large subunit pseudouridine synthase B [Plesiocystis
           pacifica SIR-1]
          Length = 238

 Score = 74.8 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 48/210 (22%), Positives = 78/210 (37%), Gaps = 13/210 (6%)

Query: 41  KVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
            ++G  ++   + V   + + V G  L   E   L L+     +          +     
Sbjct: 27  TLDGRAMKDPRMPVDVGERVRVRGEELVLREHAHLMLHKPHGVVTARADGRHPTAYALLE 86

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
              +F+ + +VGRLD++  GLLL T DG L   L  P     R Y V      +    + 
Sbjct: 87  GAPLFAELRAVGRLDLDAVGLLLWTTDGQLVHALTHPRRAVPRTYHVALAAPFEAPPRDD 146

Query: 161 LKKGIVIQGICYGD------------MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                +                        L T  G+ A  TV L +G   E+K++F   
Sbjct: 147 DGAVALELRDGLRPRVVALGALDEAAAHPALLTPPGTEALATVTLLDGAYHEVKRIFAAL 206

Query: 209 NWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
              V  L R+ +GP +L  TL AG+ + + 
Sbjct: 207 GSHVLCLARVRHGPVELPRTLEAGAWQLLD 236


>gi|256959131|ref|ZP_05563302.1| pseudouridylate synthase [Enterococcus faecalis DS5]
 gi|256949627|gb|EEU66259.1| pseudouridylate synthase [Enterococcus faecalis DS5]
          Length = 301

 Score = 74.8 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 71/246 (28%), Gaps = 37/246 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 1   MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 58

Query: 60  IEV------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I V            + +P  +   +   + +      +V   +     + V   L    
Sbjct: 59  IVVTIPEPEVLDMVAEDIPLTIVYEDNDVIVVNKPQDMVVHPSAGHPKGTLVNALLHHAD 118

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                   +       +     G L       + + L                       
Sbjct: 119 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 178

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           K   VI+G        T+  +  +   V + L  G+  +I+   
Sbjct: 179 DKGEINAPIGRSKVDRKMQAVIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRVHM 238

Query: 206 EFFNWK 211
           ++  + 
Sbjct: 239 KYIGYP 244


>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 = 74.8 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 28/239 (11%), Positives = 66/239 (27%), Gaps = 35/239 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           V+E     R+ K +A     SR  V++++   +V V+G +++         D +E++   
Sbjct: 8   VKETEKGMRIDKFLAEKASKSRSSVQQLLKDGQVTVDGEVVK-PNYKCQLGDIVEMEERA 66

Query: 67  --------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
                         +   +   L +      +V   +     + V   L          G
Sbjct: 67  PEVIEIEAEDIPLDIYYEDEDLLVVNKPEGMVVHPSAGHYTGTLVNALLYHCKDLSGING 126

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ----------------- 155
           ++       +     G L       + + L           +                  
Sbjct: 127 KIRPGIVHRIDKDTSGLLMVAKNDAAHESLASQLKAKTSHREYVALVHGDIAHQKGTIEA 186

Query: 156 ---DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 +  +K  V+           +  + G    +T  L  G+  +I+   ++    
Sbjct: 187 PIGRAKDDRQKMAVVGDGKEARTHFEVLERFGDFTLITCQLDTGRTHQIRVHLKYIGHP 245


>gi|254251614|ref|ZP_04944932.1| 16S rRNA uridine-516 pseudouridylate synthase [Burkholderia dolosa
           AUO158]
 gi|124894223|gb|EAY68103.1| 16S rRNA uridine-516 pseudouridylate synthase [Burkholderia dolosa
           AUO158]
          Length = 192

 Score = 74.8 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 40/182 (21%), Positives = 73/182 (40%), Gaps = 19/182 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +        GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LLALNKPFGTICQFSAHETRPSLGDWVKTPGV--YPAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVEGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPDTLWPRNPPIR 120

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L    G T  + 
Sbjct: 121 YRAAIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFALGIAPGETIALP 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>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 = 74.4 bits (181), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 33/239 (13%), Positives = 73/239 (30%), Gaps = 40/239 (16%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----DGVP--- 66
           +R+ K I+     SR +++ +I Q+ V VN +++ +    V     I V    D      
Sbjct: 10  ERIDKYISNNSEISRNDIKALIEQKAVFVNDVVVNQPKFIVREGQVISVTKLIDKEIHIE 69

Query: 67  -------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VIS 110
                  +   +   L +      +V         + V   L    +             
Sbjct: 70  AQDIDLDIAYEDEHLLVIKKPSGMVVHPAPGHHENTLVNALLFHFKNNLSNENGLLRPGI 129

Query: 111 VGRLDINTEGLLLLTNDGGLAR-------------VLELPSTQWLRVYRVRFHGQVDQDK 157
           V R+D +T GLL++     + +                      L+  +++    + +D 
Sbjct: 130 VHRIDKDTSGLLIVAKTNEVHQLLSEGFSNKSINRKYFAICDGVLKSKKMKLDLPIGRDV 189

Query: 158 LNLLKKGIVIQGICYGDMQVTLD----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            N  +  +      +    + +             V   L  G+  +I+    + N  +
Sbjct: 190 KNRQQMSVTNSNSKHAITNLEMLKSFYFDNQPKCLVKATLETGRTHQIRVHCAYINNPI 248


>gi|93005144|ref|YP_579581.1| pseudouridine synthase, Rsu [Psychrobacter cryohalolentis K5]
 gi|92392822|gb|ABE74097.1| ribosomal large subunit pseudouridine synthase E [Psychrobacter
           cryohalolentis K5]
          Length = 208

 Score = 74.4 bits (181), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 43/189 (22%), Positives = 75/189 (39%), Gaps = 27/189 (14%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L++KP G+ +   D         +       +   GRLD  +EGLL+LT+DG + + +
Sbjct: 6   LILFNKPYGVQSQFRDESNNDHTTLSEYFTDKSLRIAGRLDATSEGLLILTSDGRINKAI 65

Query: 135 ELPS---------TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------- 175
             P           +  + Y V+  G V   +L  L  G+V++                 
Sbjct: 66  TQPPSAKGFAQNKQKQGKTYLVQVEGMVTSVQLKALASGVVLKDGKTLPASAVLVDEVDL 125

Query: 176 --------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
                       + +    +W+ + + EGKNR+++++         RLIR S   F+LG 
Sbjct: 126 PITLWEREPPIRERKNIPTSWLMLTIYEGKNRQVRRMTAHVGLPCLRLIRWSVAGFELGE 185

Query: 228 LLAGSTREV 236
           L  G    +
Sbjct: 186 LGVGEFVRI 194


>gi|315027878|gb|EFT39810.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2137]
          Length = 310

 Score = 74.4 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 70/246 (28%), Gaps = 37/246 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 10  MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 67

Query: 60  IEV------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I V            + +P  +   +   + +      +V         + V   L    
Sbjct: 68  IVVTIPEPEVLDMVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSVGHPNGTLVNALLHHAD 127

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                   +       +     G L       + + L                       
Sbjct: 128 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 187

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           K   VI+G        T+  +  +   V + L  G+  +I+   
Sbjct: 188 DKGEINAPIGRSKVDRKMQAVIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRVHM 247

Query: 206 EFFNWK 211
           ++  + 
Sbjct: 248 KYIGYP 253


>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 = 74.4 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 32/245 (13%), Positives = 77/245 (31%), Gaps = 36/245 (14%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-- 60
           DK  +  +   +R+   ++     SR   + +I +  V +NG + +  +  V++ DHI  
Sbjct: 17  DKLDITSDSFSERIDIFLSEKLNRSRSYFKNLIDEGLVTLNGKICK-PSSKVVAGDHIIV 75

Query: 61  ------------EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-- 106
                       E+D   +    +    +      +V         + V   L    +  
Sbjct: 76  LIPDDSIDLTPKEIDFEVI-YDSKWYAVINKPAGLVVHPAPGNTTDTLVNGLLAKFKNID 134

Query: 107 -----RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
                R   + RLD +T GLL++  +  + + +     +             +      +
Sbjct: 135 DNDNVRPGIIHRLDKDTSGLLIIAKNRDVRQQMSELFQKREVKKVYLAVCMGEPKNDYYM 194

Query: 162 KKGIV-------------IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               +               G      +V +  +       +V +  G+  +I+    + 
Sbjct: 195 IDNFIGRSLTDRKKMAVLQNGGKRAVSEVKILKRSSGIFLASVAIHTGRTHQIRVHMSYL 254

Query: 209 NWKVN 213
           N+ + 
Sbjct: 255 NYPIL 259


>gi|254423571|ref|ZP_05037289.1| conserved hypothetical protein [Synechococcus sp. PCC 7335]
 gi|196191060|gb|EDX86024.1| conserved hypothetical protein [Synechococcus sp. PCC 7335]
          Length = 219

 Score = 74.4 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 52/218 (23%), Positives = 88/218 (40%), Gaps = 41/218 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              R  L +KP  +++  +D  GR T+ D +      V +VGRLD ++EGLLLLT+DG +
Sbjct: 1   MPYRYLLLYKPYDVLSQFTDESGRRTLKDLVA--VPNVYAVGRLDRDSEGLLLLTDDGPM 58

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKL----NLLKKGIVIQGICYGDMQVTLDT----- 181
              L  P     R Y V+         +    + L+ G+ I+G      QV++       
Sbjct: 59  QHRLSHPRFGHRRQYWVQVECGPKSQPIEAAIDQLRAGVTIRGYRTRPAQVSVIPDPDLP 118

Query: 182 ---------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY------------ 220
                    ++ + AW+ + L EGKNR+++++     +   RL+R +             
Sbjct: 119 PRNPPIRYRKQIATAWLEIALTEGKNRQVRRMTAAVGFPTLRLVRSALFLPTPEKRQKQR 178

Query: 221 ---------GPFQLGTLLAGSTREVSKKILREQLGPHL 249
                        L  L  G  R ++   +R   G   
Sbjct: 179 QTKKRAGAALALTLSGLSPGQWRSLTATEIRSLPGNVH 216


>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 = 74.4 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 32/243 (13%), Positives = 62/243 (25%), Gaps = 40/243 (16%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            V E    +R+ K +A  G+    SR +V++ I    V VNG  ++     V   D I V
Sbjct: 8   TVTEEQKSERIDKFLA--GVNNEWSRSQVQQWIKDGVVTVNGNDIK-GNYKVKVNDEIAV 64

Query: 63  ---DGV-----------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
              D              +   +   L +      +V         + V   +       
Sbjct: 65  AIPDPEELDILPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD------------ 156
              G +       +     G L       + + L    V                     
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKG 184

Query: 157 --------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                        +   V +   +      +  +      V   L  G+  +I+   ++ 
Sbjct: 185 TIDAPIGRDKKDRQSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYI 244

Query: 209 NWK 211
            + 
Sbjct: 245 GYP 247


>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 = 74.4 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 71/246 (28%), Gaps = 37/246 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 10  MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 67

Query: 60  IEV------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I V            + +P  +   +   + +      +V   +     + V   L    
Sbjct: 68  IVVTIPEPEVLDMVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPNGTLVNALLHHAD 127

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                   +       +     G L       + + L                       
Sbjct: 128 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 187

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           K   VI+G        T+  +  +   V + L  G+  +I+   
Sbjct: 188 DKGEINAPIGRSKVDRKMQAVIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRVHM 247

Query: 206 EFFNWK 211
           ++  + 
Sbjct: 248 KYIGYP 253


>gi|83315526|ref|XP_730831.1| pseudouridylate synthase [Plasmodium yoelii yoelii str. 17XNL]
 gi|23490677|gb|EAA22396.1| Predicted pseudouridylate synthase [Plasmodium yoelii yoelii]
          Length = 412

 Score = 74.1 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 23/180 (12%), Positives = 56/180 (31%), Gaps = 7/180 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK+++ + + SR + + +I    VKV+  ++++    +     IEV+G  +     T+
Sbjct: 29  RLSKILSLSSVVSRNKAQELIRSGNVKVDNQIVKQ-NTVIDVNSKIEVNGCEINVDITTK 87

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LW  +KP  +                 P     +++ G   +           G    + 
Sbjct: 88  LWGIYKPKHVFCNTDQNYIYEEKKLINPQKKDILLNDGNDKLQISSEHTKKILGENNMMN 147

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                     Y      +   + +   +             +  +   +       + L 
Sbjct: 148 NKTLIYKSDFYNNNKMSRNYNNNIID-QNIHFPNYTETKMNKRKIQDNEK-----KITLS 201



 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 33/131 (25%), Positives = 60/131 (45%)

Query: 98  FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                 I   +I V  LD + EG++LLTNDG  A  L+  +   L  Y ++   ++  +K
Sbjct: 226 NKIENYIPEHLIIVNSLDSDMEGIILLTNDGDFANKLKDINNNILTTYLIKTQEELTNEK 285

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
           + LL+KG  I  I    +++ +        W+ +   E     +  +F  +N  + +  R
Sbjct: 286 IELLRKGCTIGDIIIRPLELKIIKPNFLYKWLKLTYVEKSQTHLNLLFSKYNMTIRKCKR 345

Query: 218 ISYGPFQLGTL 228
            S+GP++   L
Sbjct: 346 YSFGPYKSSDL 356


>gi|289806402|ref|ZP_06537031.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 100

 Score = 74.1 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 28/100 (28%), Positives = 49/100 (49%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA+    SR    R I   RV V+G +++ AA  ++    +  DG PL +    
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
           R ++ +KP G V +  DPD  + ++     +  ++ + GR
Sbjct: 61  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGR 100


>gi|213616320|ref|ZP_03372146.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 56

 Score = 74.1 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 1   MTISEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEEEI 52


>gi|212703202|ref|ZP_03311330.1| hypothetical protein DESPIG_01244 [Desulfovibrio piger ATCC 29098]
 gi|212673468|gb|EEB33951.1| hypothetical protein DESPIG_01244 [Desulfovibrio piger ATCC 29098]
          Length = 119

 Score = 74.1 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 30/119 (25%), Positives = 51/119 (42%), Gaps = 1/119 (0%)

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGL 193
             P     + Y V   G V    L  +++G+ + +G     ++V    Q   +  + + L
Sbjct: 1   MHPRHHQPKTYDVLVRGIVPASALATMRRGMTLAEGEQLRPVEVESRLQANGHTRLRMVL 60

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
            +G NR+I+++       + RL RIS GP  LG L  GS R +S   +   L    +  
Sbjct: 61  HQGVNRQIRRMCRDLGLTILRLKRISLGPIGLGDLPVGSCRFLSAAEITALLQAAEIRR 119


>gi|71064863|ref|YP_263590.1| ribosomal large subunit pseudouridine synthase E [Psychrobacter
           arcticus 273-4]
 gi|71037848|gb|AAZ18156.1| ribosomal large subunit pseudouridine synthase E [Psychrobacter
           arcticus 273-4]
          Length = 208

 Score = 74.1 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 41/189 (21%), Positives = 73/189 (38%), Gaps = 27/189 (14%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR-- 132
           L L++KP G+ +   D         +       +   GRLD  +EGLL+LT+DG + +  
Sbjct: 6   LILFNKPYGVQSQFRDDSNNDHTTLSEYFTDKSLRIAGRLDATSEGLLILTSDGRINKAI 65

Query: 133 -------VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------- 175
                         +  + Y V+  G V   +L  L  G++++                 
Sbjct: 66  TQPPSAKNFAQNKQKQGKTYLVQVEGVVTAVQLKELASGVILKDGKTLPASATLLDEADL 125

Query: 176 --------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
                       + +    +W+ + + EGKNR+++++         RLIR S   F+LG 
Sbjct: 126 PITLWQRDPPIRERKNIPTSWLMLTIYEGKNRQVRRMTAHVGLPCLRLIRWSVAGFELGE 185

Query: 228 LLAGSTREV 236
           L  G    +
Sbjct: 186 LGVGEFVRI 194


>gi|261867443|ref|YP_003255365.1| RNA pseudouridine synthase family protein [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|293391454|ref|ZP_06635788.1| RNA pseudouridine synthase family protein [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|261412775|gb|ACX82146.1| RNA pseudouridine synthase family protein [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|290951988|gb|EFE02107.1| RNA pseudouridine synthase family protein [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 91

 Score = 74.1 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 18/79 (22%), Positives = 36/79 (45%)

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
              +  +    + +    AW+ V + EG+NR+++++     +   RLIR     F L  L
Sbjct: 8   DFLWQRISPIRERKHIPTAWLEVKIDEGRNRQVRRMTAHIGFPTLRLIRYQLAGFNLQNL 67

Query: 229 LAGSTREVSKKILREQLGP 247
           +  + R +++  LRE    
Sbjct: 68  MPKTYRTLTQNELRELYQL 86


>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 = 74.1 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 33/241 (13%), Positives = 69/241 (28%), Gaps = 37/241 (15%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----- 60
           +++ +  +R+ KVIA      SR +V++ I    V VNG  ++ A     + D +     
Sbjct: 8   IEDEYDGERIDKVIAALNEEWSRSQVQQWIKNGLVTVNGQTVK-ANYKCEAGDSVAVSPP 66

Query: 61  -----EVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                 V+  P+       +   L +      +V         + V   L          
Sbjct: 67  EPEPLHVEPEPIPLDIYYEDEDVLVVNKPRGMVVHPAPGHMRGTLVNALLAHCRDLSGIN 126

Query: 112 GRLDINTEGLLLLTNDGGLA---------------------RVLELPSTQWLRVYRVRFH 150
           G L       +     G L                      R  +      +        
Sbjct: 127 GVLRPGIVHRIDKDTSGLLMVAKNDAAHRSLVEQLVNKTVTRRYKAIVHGVIPHDYGTID 186

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + +DK +  K  +  +          +  +     +V   L  G+  +I+   ++  +
Sbjct: 187 APIGRDKRDRKKMAVTEENGKEAVTHFRVLERFRHYTYVECQLETGRTHQIRVHMKYIGY 246

Query: 211 K 211
            
Sbjct: 247 P 247


>gi|172061486|ref|YP_001809138.1| pseudouridine synthase [Burkholderia ambifaria MC40-6]
 gi|171994003|gb|ACB64922.1| pseudouridine synthase [Burkholderia ambifaria MC40-6]
          Length = 192

 Score = 74.1 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 40/182 (21%), Positives = 73/182 (40%), Gaps = 19/182 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +        GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKTPGV--YPAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVDGAPGPADLKALARGVDLGDCVTRPCRAEFIEPPDALWPRNPPIR 120

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L    G T  + 
Sbjct: 121 YRAAIPTTWIELAITEGKNRQVRRMTAAIGFPTLRLVRVGIGALDIFALGIAPGETIALP 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>gi|221199240|ref|ZP_03572284.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Burkholderia multivorans CGD2M]
 gi|221205858|ref|ZP_03578873.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Burkholderia multivorans CGD2]
 gi|221174696|gb|EEE07128.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Burkholderia multivorans CGD2]
 gi|221180525|gb|EEE12928.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Burkholderia multivorans CGD2M]
          Length = 192

 Score = 74.1 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 40/182 (21%), Positives = 73/182 (40%), Gaps = 19/182 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +        GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKAPGV--YPAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVEGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPETLWPRNPPIR 120

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L    G T  + 
Sbjct: 121 YRAAIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFALGIAPGETIALP 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>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 = 74.1 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 33/248 (13%), Positives = 72/248 (29%), Gaps = 38/248 (15%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M   NI V E  T +R+ K ++      SR +V++ +    ++VNG  ++ A   V + D
Sbjct: 1   MNQVNIAVSEEQTSERLDKFLSTTEPEWSRTQVQQWVKDGLIEVNGKQVK-ANYKVQAGD 59

Query: 59  HIEVD-GVP-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            I+V+   P             +   +   L +      +V         + V   +   
Sbjct: 60  QIKVEIPEPEVLDVEAEPMDLDIYYEDADVLVVNKPRGMVVHPAPGHVSGTLVNGLMAHC 119

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------R 143
                  G +       +     G L       + + L                     +
Sbjct: 120 TDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRKYTAVVHGIIQ 179

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                    + +DK +     +  +          +  +      V   L  G+  +I+ 
Sbjct: 180 HDTGTIDAPIGRDKKDRQSMTVTKESAKQAVTHFDVIERFQDFTVVECRLETGRTHQIRV 239

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 240 HMKYIGYP 247


>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 = 74.1 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 33/242 (13%), Positives = 64/242 (26%), Gaps = 38/242 (15%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E    +R+ K +A      SR +V++ I    V VNG  ++     V   D I V  
Sbjct: 8   TVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDDVVTVNGKSVKV-NYKVKENDEITVTI 66

Query: 63  -DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
            D   L              +   L +      +V         + V   +         
Sbjct: 67  PDPEELDIQAEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI 126

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRVRF 149
            G +       +     G L       + + L                        +   
Sbjct: 127 NGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTI 186

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +DK    +   V +   +      +  +      V   L  G+  +I+   ++  
Sbjct: 187 DAPIARDKKER-QSMTVDENGKHAVTHFQVLDRFKDFTLVECRLETGRTHQIRVHMKYIG 245

Query: 210 WK 211
           + 
Sbjct: 246 YP 247


>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 = 74.1 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 33/242 (13%), Positives = 65/242 (26%), Gaps = 38/242 (15%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E    +R+ K +A      SR +V++ I +  V VNG  ++     V   D I V  
Sbjct: 8   TVAEEQKSERIDKFVAEINSEWSRSQVQQWIKEDVVTVNGKSVKV-NYKVKENDEITVTI 66

Query: 63  -DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
            D   L              +   L +      +V         + V   +         
Sbjct: 67  PDPEELDIQAEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI 126

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRVRF 149
            G +       +     G L       + + L                        +   
Sbjct: 127 NGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTI 186

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +DK    +   V +   +      +  +      V   L  G+  +I+   ++  
Sbjct: 187 DAPIARDKKER-QSMTVDENGKHAVTHFQVIERFKDFTLVECRLETGRTHQIRVHMKYIG 245

Query: 210 WK 211
           + 
Sbjct: 246 YP 247


>gi|262365460|gb|ACY62017.1| RNA pseudouridylate synthase-family protein [Yersinia pestis
           D182038]
          Length = 152

 Score = 74.1 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 40/119 (33%), Positives = 56/119 (47%), Gaps = 8/119 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
            +++ K++ARAG  SRRE+E +I Q RV V+G +  +    V  T    I +DG  L   
Sbjct: 28  GEKLQKILARAGHGSRREIEAIIQQGRVSVDGKV-SKLGDRVEVTQSTKIRLDGHLLSIK 86

Query: 71  E-----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
           E        L  Y     L T +      +          SR ++VGRLD+NT GLLL 
Sbjct: 87  ESEENVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLF 145


>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 = 73.7 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 33/242 (13%), Positives = 64/242 (26%), Gaps = 38/242 (15%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E    +R+ K +A      SR +V++ I    V VNG  ++     V   D I V  
Sbjct: 8   TVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDDVVTVNGKSVKV-NYKVKENDEITVTI 66

Query: 63  -DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
            D   L              +   L +      +V         + V   +         
Sbjct: 67  PDPEELDIQAEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI 126

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRVRF 149
            G +       +     G L       + + L                        +   
Sbjct: 127 NGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTI 186

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +DK    +   V +   +      +  +      V   L  G+  +I+   ++  
Sbjct: 187 DAPIARDKKER-QSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIG 245

Query: 210 WK 211
           + 
Sbjct: 246 YP 247


>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 = 73.7 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 32/242 (13%), Positives = 64/242 (26%), Gaps = 38/242 (15%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E    +R+ K +A      SR +V++ I    V VNG  ++     V   D I V  
Sbjct: 8   TVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDDVVTVNGKSVKV-NYKVKENDEITVTI 66

Query: 63  -DGV-----------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
            D              +   +   L +      +V         + V   +         
Sbjct: 67  PDPEELDIQAEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI 126

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRVRF 149
            G +       +     G L       + + L                        +   
Sbjct: 127 NGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTI 186

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +DK    +   V +   +      +  +      V   L  G+  +I+   ++  
Sbjct: 187 DAPIARDKKER-QSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIG 245

Query: 210 WK 211
           + 
Sbjct: 246 YP 247


>gi|154685962|ref|YP_001421123.1| YlyB [Bacillus amyloliquefaciens FZB42]
 gi|154351813|gb|ABS73892.1| YlyB [Bacillus amyloliquefaciens FZB42]
          Length = 304

 Score = 73.7 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 32/248 (12%), Positives = 70/248 (28%), Gaps = 38/248 (15%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M    I VQ     +R+ K +A  G   SR +V++ + +  V VNG  ++ A   +   D
Sbjct: 1   MNQFEITVQPEQKSERIDKFLASTGENWSRTQVQQWVKEGLVSVNGKSVK-ANYKMQPGD 59

Query: 59  HI--------EVD------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            +        E+D       + +   ++  L +      +V         + V   +   
Sbjct: 60  QVNVTIPEPEELDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHVTGTLVNGLMAHC 119

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR--------------------- 143
                  G +       +     G L       + + L                      
Sbjct: 120 NDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKYTAVVHGVIS 179

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                    + +DK +     +  +          +  +      V   L  G+  +I+ 
Sbjct: 180 HDDGTIDAPIGRDKKDRQSMTVTRESSKNAVTHFHVLERFQDFTLVECRLETGRTHQIRV 239

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 240 HMKYIGFP 247


>gi|88801771|ref|ZP_01117299.1| RNA pseudouridine synthase family protein [Polaribacter irgensii
           23-P]
 gi|88782429|gb|EAR13606.1| RNA pseudouridine synthase family protein [Polaribacter irgensii
           23-P]
          Length = 181

 Score = 73.7 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 37/179 (20%), Positives = 74/179 (41%), Gaps = 16/179 (8%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            ++     +    +    + T+  +L       +++GRLD+ +EGLLLLT DG ++  + 
Sbjct: 1   MVHKPWGMISQFVNPAKRKKTLLGDLYGFPEGTMAIGRLDVPSEGLLLLTTDGKVSAEIR 60

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDT------------ 181
             + +     +V         +       I  +G        +  L              
Sbjct: 61  SNAYEKEYYVQVDGIMTAAALENLKTGVEIGFKGTKYVTKPGKAMLLKDPRFPLRSQKIR 120

Query: 182 --QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
             + G  +W+++ ++EGK R+++K+     +   RL+R+  G  +LG L  G+  EV K
Sbjct: 121 DERHGPTSWISIIIKEGKFRQVRKMTAAVGFPTLRLVRVRIGTMKLGELAIGAVVEVEK 179


>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 = 73.7 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 71/246 (28%), Gaps = 37/246 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 10  MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 67

Query: 60  IEV------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I V            + +P  +   +   + +      +V   +     + V   L    
Sbjct: 68  IVVTIPEPEALDMVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPKGTLVNALLHHAD 127

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                   +       +     G L       + + L                       
Sbjct: 128 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 187

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           K   VI+G        T+  +  +   V + L  G+  +I+   
Sbjct: 188 DKGEINAPIGRSKVDRKMQAVIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRVHM 247

Query: 206 EFFNWK 211
           ++  + 
Sbjct: 248 KYIGYP 253


>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 = 73.7 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 71/246 (28%), Gaps = 37/246 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 10  MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 67

Query: 60  IEV------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I V            + +P  +   +   + +      +V   +     + V   L    
Sbjct: 68  IVVTIPEPEVLDMVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPKGTLVNALLHHAD 127

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                   +       +     G L       + + L                       
Sbjct: 128 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 187

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           K   VI+G        T+  +  +   V + L  G+  +I+   
Sbjct: 188 DKGEINAPIGRSKVDRKMQAVIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRVHM 247

Query: 206 EFFNWK 211
           ++  + 
Sbjct: 248 KYIGYP 253


>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 = 73.7 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 38/236 (16%), Positives = 70/236 (29%), Gaps = 34/236 (14%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP---- 66
            T QR+   +A     SR +V ++I    V VNG  + +    V   D + V+       
Sbjct: 8   TTAQRLDTFLATLLNLSRVKVAKLIVDGLVSVNGKKITKNGWLVQPEDRVHVNWSEELFE 67

Query: 67  --------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISV 111
                         +   +   + +      +    S  +  S +   L     +    V
Sbjct: 68  KVPVEVQPYDFPLDILYEDEQIMVVNKPNGLISHPTSFNESESLLGAALFHCNHQPVFLV 127

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--------------- 156
            RLD +T G+++L  +      L+    Q +             D               
Sbjct: 128 HRLDRDTSGVIMLAKNQSSLLHLQKQLQQRVMKRYYLALVHFPLDSLSGTISAPLERVGN 187

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
              + K G           + T+  Q    A +   L  G+  +I+   +F    V
Sbjct: 188 NKVMWKVGNSSNKAKNAFTKFTVLNQNEKAALIKCELLTGRTHQIRVHLQFIKHPV 243


>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 = 73.7 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 71/246 (28%), Gaps = 37/246 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 10  MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 67

Query: 60  IEV------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I V            + +P  +   +   + +      +V   +     + V   L    
Sbjct: 68  IVVTIPEPEVLDMIAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPKGTLVNALLHHAD 127

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                   +       +     G L       + + L                       
Sbjct: 128 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 187

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           K   VI+G        T+  +  +   V + L  G+  +I+   
Sbjct: 188 DKGEINAPIGRSKVDRKMQAVIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRVHM 247

Query: 206 EFFNWK 211
           ++  + 
Sbjct: 248 KYIGYP 253


>gi|301633483|gb|ADK87037.1| pseudouridine synthase, RluA family [Mycoplasma pneumoniae FH]
          Length = 309

 Score = 73.7 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 38/236 (16%), Positives = 70/236 (29%), Gaps = 34/236 (14%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP---- 66
            T QR+   +A     SR +V ++I    V VNG  + +    V   D + V+       
Sbjct: 8   TTAQRLDTFLATLLNLSRVKVAKLIVDGLVSVNGKKITKNGWLVQPEDRVHVNWSEELFE 67

Query: 67  --------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISV 111
                         +   +   + +      +    S  +  S +   L     +    V
Sbjct: 68  KVPVEVQPYDFPLDILYEDEQIMVVNKPNGLISHPTSFNESESLLGAALFHCNHQPVFLV 127

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--------------- 156
            RLD +T G+++L  +      L+    Q +             D               
Sbjct: 128 HRLDRDTSGVIMLAKNQSSLLHLQKQLQQRVMKRYYLALVHFPLDSLSGTISAPLERVGN 187

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
              + K G           + T+  Q    A +   L  G+  +I+   +F    V
Sbjct: 188 NKVMWKVGNSSNKAKNAFTKFTVLNQNEKAALIKCELLTGRTHQIRVHLQFIKHPV 243


>gi|257453919|ref|ZP_05619196.1| RNA pseudouridine synthase family protein [Enhydrobacter aerosaccus
           SK60]
 gi|257448691|gb|EEV23657.1| RNA pseudouridine synthase family protein [Enhydrobacter aerosaccus
           SK60]
          Length = 234

 Score = 73.7 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 47/234 (20%), Positives = 86/234 (36%), Gaps = 23/234 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L L++KP G+++     D  +    +       +   GRLD  +EGLLLLT DG + 
Sbjct: 1   MPTLILFNKPYGVLSQFRSDDNNNFATLSDYFTDKSLRVAGRLDATSEGLLLLTADGQVN 60

Query: 132 RVLELPST-----QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT----- 181
           + L  P       Q  + Y ++  G     +L  L+ G+ ++       +V   +     
Sbjct: 61  KALTHPPKANAGKQQGKTYWIQVEGDASDAQLQQLQTGVPLKDGITLPAEVVRLSEAQIA 120

Query: 182 -----------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                      ++    W+ + + EGKNR+++++         RLIR++   F LG L  
Sbjct: 121 EHIWQASDKIAKRKVTTWLAITIFEGKNRQVRRMAAHVGLPCLRLIRMASSGFSLGNLEV 180

Query: 231 GST--REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDF 282
           G++    +S   L+      L                T    +    +      
Sbjct: 181 GASTQIPLSPADLKRLGVQPLSTATTTPQSRKKPRVLTPKSLQSKHPTSRRRQP 234


>gi|256828202|ref|YP_003156930.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
 gi|256577378|gb|ACU88514.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
          Length = 281

 Score = 73.7 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 35/253 (13%), Positives = 65/253 (25%), Gaps = 23/253 (9%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M D     E   P R+ +V+A + G   RR    +I   RV V+     +    +    H
Sbjct: 1   MTDSFFYPEGLPPIRLDRVLALQLGFGVRR-CRALIEAGRVLVDDRPCAK-GALIRPGQH 58

Query: 60  IEV-----------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           I V           D   + + E          +  V         S +       +  +
Sbjct: 59  IRVSLPEDAAPDCHDVRLVDRNESFAALAKPDGLHTVAGQEAACLESCLPGLGLEGWELL 118

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-- 166
             +  L            D    +V +           +        +    +       
Sbjct: 119 NRLDCLTSGLVLAAAEKRDAAAYKVWQDAGQVSKWYLALARGEVATLECRGRILDDKRSV 178

Query: 167 -----IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
                 +       +V    Q   N  + V + +G+  +I+         +       YG
Sbjct: 179 VRVTADEDEPLRWTRVRALRQIDGNTLLLVKIFKGRRHQIRAHLAHAGHPLIG--DPVYG 236

Query: 222 PFQLGTLLAGSTR 234
             + G L     R
Sbjct: 237 VCEPGGLYLHHWR 249


>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 = 73.7 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 48/264 (18%), Positives = 87/264 (32%), Gaps = 44/264 (16%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V    TP R+   +A+    A+R +V+  IA+ RV VNG  ++     + S D IEV   
Sbjct: 27  VARTQTPMRIDVYLAQQVENATRNKVQEAIAEHRVLVNGKTIKS-NYRIKSLDSIEVTFL 85

Query: 63  ---------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-----------NL 101
                    + +P+    E   L + +K   +V   +  +   T+ +           +L
Sbjct: 86  RPPAPELAPEDIPIDIIYEDEDLMVVNKASDMVVHPAFGNWTGTLANAILHHIGKEAGDL 145

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
                R   V RLD NT GL+++  +      L           + +       +    L
Sbjct: 146 DCSDMRPGIVHRLDKNTSGLIIIAKNSTALHRLARQFANRQVEKKYQAIVWGVPEPATGL 205

Query: 162 KK----------------GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
            K                    +       +  +       + V V L  G+  +I+   
Sbjct: 206 IKTNIGRSVRNRKVMTSYPFEGKDGKTAITEYRVQQSLCYFSLVEVTLHTGRTHQIRVHM 265

Query: 206 EFFNWKVNRLIRISYGPFQLGTLL 229
           +     +  L   +YG   +  L 
Sbjct: 266 QHLGHPI--LGDETYGGSSIRNLP 287


>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 = 73.7 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 31/251 (12%), Positives = 70/251 (27%), Gaps = 38/251 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M ++  ++      R+ + +A      SR  ++++I Q +V+VNG +     +N+   D 
Sbjct: 1   MLNEFYLEVEENSARIDRYLAEELPDLSRSRIQQLIEQGKVQVNGKVCTSKKINLKVGDR 60

Query: 60  IEV------------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I +            + +PL     +   L L      +V         + V   L    
Sbjct: 61  ITLEVPEAQPLELQAEDIPLDILYEDDQLLILNKPAGLVVHPAPGHSHGTLVNALLAHCP 120

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                 G         L     G +A      + + ++        + +           
Sbjct: 121 HLPGIGGVQRPGIVHRLDKDTTGAIAIAKTDIAYKHIQAQLQTKTARREYLGVVYGAPKT 180

Query: 156 -------------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                             +    V +G         +  + G+   +   L  G+  +I+
Sbjct: 181 SSGKVDLPIGRHPQDRKKMAIVPVEEGGRSAITHWQIQERLGNFTLIHFQLETGRTHQIR 240

Query: 203 KVFEFFNWKVN 213
                    + 
Sbjct: 241 VHSAKIGHPIV 251


>gi|332293351|ref|YP_004431960.1| pseudouridine synthase [Krokinobacter diaphorus 4H-3-7-5]
 gi|332171437|gb|AEE20692.1| pseudouridine synthase [Krokinobacter diaphorus 4H-3-7-5]
          Length = 191

 Score = 73.7 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 36/170 (21%), Positives = 58/170 (34%), Gaps = 17/170 (10%)

Query: 86  TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY 145
           +       +      L       +++GRLD  +EGLLL+T DG L+  +     +     
Sbjct: 20  SNDERQARKKKFLSELHDFPEGTMAIGRLDEKSEGLLLMTTDGKLSDTINRSGIEKEYYV 79

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQK---------------GSNAW 188
           +V      D          I   G        +V    +                G   W
Sbjct: 80  QVDGMITDDAIDQMAAGVEIGFDGKKYQTKPCKVRRLIENPTLPERSKKIRDARHGPTPW 139

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + V + EGK R+++K+     +   RL+RI  G   L  L      EV +
Sbjct: 140 IAVTITEGKFRQVRKMTSAVGFPTLRLVRIRIGSQTLMGLEPRQVIEVKE 189


>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 = 73.7 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 34/245 (13%), Positives = 70/245 (28%), Gaps = 42/245 (17%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V  N   +R+ K + R    A+R +V+  I + RV VNG  ++     V   D I V   
Sbjct: 28  VAPNQARERIDKFLTRQVENATRNKVQEAIEESRVLVNGKPIKS-NYKVCPNDEIFVIFT 86

Query: 63  -----DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                D  P      +   +   L +      +V         +     L    +R+   
Sbjct: 87  HPPAPDLEPENIPLDIVFEDEFLLVINKPAGMVVHPAYANWTGTLAGAVLYHTQNRLSET 146

Query: 112 GRL----------DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ--------- 152
           G+           D +T GL+++  D      L     +                     
Sbjct: 147 GKEALRPGIVHRLDKDTSGLIVVAKDDATHYALAKQFAERTTEKIYTALVWGCPKPPSGT 206

Query: 153 -----VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIKKVF 205
                    +   +      +           + ++  +  + + + L  G+  +I+   
Sbjct: 207 IQTNIWRSKRDRKIMANYPFESETGKPAITDYEVKEDFHWFSLLDLQLHTGRTHQIRAHL 266

Query: 206 EFFNW 210
           +    
Sbjct: 267 QHLGH 271


>gi|148972065|ref|ZP_01811403.1| pseudouridine synthase Rsu [Leptolyngbya valderiana BDU 20041]
 gi|148872769|gb|EDL71127.1| pseudouridine synthase Rsu [Leptolyngbya valderiana BDU 20041]
          Length = 152

 Score = 73.7 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 25/149 (16%), Positives = 49/149 (32%), Gaps = 15/149 (10%)

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---------- 180
              L  P     R Y V+     D+  L  L+ G+ I+       +V             
Sbjct: 2   QHRLLDPKFGKSRAYWVQVERVPDEASLQRLRDGVTIRQYRTRPARVRRLAIAPDLPPRH 61

Query: 181 -----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                 +     W+ + L EG+NR+++++         RL+R++     L  L  G  R+
Sbjct: 62  PPIRFRKNVPTCWLEMSLTEGRNRQVRRMTAAVGHPTLRLVRVAVENLTLDALQPGQWRD 121

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSS 264
           ++   + +      L            + 
Sbjct: 122 LTLAEVSQLQKRCGLSAVASRSGDRNRAR 150


>gi|11967875|emb|CAC19446.1| putative pseudouridine synthase [Streptococcus mitis]
          Length = 46

 Score = 73.7 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 19/46 (41%), Positives = 27/46 (58%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           R++K IA AG+ASRR+ E +I Q  V VN  ++   A  + S D 
Sbjct: 1  MRINKYIAHAGVASRRKAEELIKQGLVTVNSQVVRELATTIKSGDT 46


>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 = 73.3 bits (178), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 29/239 (12%), Positives = 67/239 (28%), Gaps = 39/239 (16%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------DG 64
            +R+ K I+     SR +++ +I ++ V VNG ++++    +     IEV        D 
Sbjct: 9   SERIDKYISDNSAISRNDIKSLILEKAVFVNGKVIQKPNFILKPDAEIEVIKVIDKTIDL 68

Query: 65  VP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
            P      +   +   + +      +V        ++ V   +    +     G L    
Sbjct: 69  KPEKMDLDIVYEDEHLIVINKPSGLVVHPAPGHYSQTLVNGLIYHFKNLSNENGLLRPGI 128

Query: 119 EGLLLLTNDGGLARVLELPST-----QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
              +     G L                      R +  + +         + +      
Sbjct: 129 VHRIDKDTSGLLIIAKTNQVHQLLAKMLKNHEIKRSYIAIVEGFFENKIVHLNLPIGRSQ 188

Query: 174 DMQVTLD--------------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             +  ++                     +K   + V   L  G+  +I+    +F   V
Sbjct: 189 KDRKKMEITNNNSKNAITHVYLIKQFYYEKQPLSLVECQLETGRTHQIRVHLNYFKHPV 247


>gi|255024455|ref|ZP_05296441.1| RNA pseudouridine synthase family protein [Listeria monocytogenes
           FSL J1-208]
          Length = 73

 Score = 73.3 bits (178), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 5/71 (7%)

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLA 230
               ++ +         + V ++EGK  ++K++F      V+ L RIS G   L   L  
Sbjct: 1   CKPARLEIINPN----EIKVTIQEGKFHQVKRMFAARGKTVSYLKRISMGNLPLDESLEL 56

Query: 231 GSTREVSKKIL 241
           G  R +++  L
Sbjct: 57  GEYRPLTETEL 67


>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 = 73.3 bits (178), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 30/243 (12%), Positives = 60/243 (24%), Gaps = 36/243 (14%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           IV       R+   +      SR  ++ +I    V V G +  +A + +     I V   
Sbjct: 5   IVSAEQEGMRLDVFLTEQMEGSRSYIQSLIKGGHVTVGGKV-GKANLRLTPDTVIRVEIP 63

Query: 63  ---------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                    + +PL     +   + +      +V         + V   L          
Sbjct: 64  EPESIEVKPEDIPLDYLYEDHDIVIVNKPRGMVVHPAVGNYSGTLVNALLFHCKDLSGIN 123

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--------------- 156
           G +       L     G +       +   L         +                   
Sbjct: 124 GEIRPGIVHRLDKDTSGVMMVAKNDAAHIGLAEQVKAHSARRTYWALVQGNIVEEKGTIK 183

Query: 157 ------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                   + +K  +V +          +  + G    V   L  G+  +I+  F +   
Sbjct: 184 APIGRHPKDRMKMAVVFENSKDAVTHFKVLARYGHQTLVECNLETGRTHQIRVHFVYIGH 243

Query: 211 KVN 213
            V 
Sbjct: 244 PVV 246


>gi|89891482|ref|ZP_01202987.1| ribosomal pseudouridylate synthase [Flavobacteria bacterium BBFL7]
 gi|89516256|gb|EAS18918.1| ribosomal pseudouridylate synthase [Flavobacteria bacterium BBFL7]
          Length = 200

 Score = 73.3 bits (178), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 46/193 (23%), Positives = 78/193 (40%), Gaps = 23/193 (11%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTNDG 128
             R +L +KP  +++     D        L          ++VGRLD ++EGLLL+T DG
Sbjct: 1   MHRHFLIYKPYRMLSQFMTNDRHQKNKRFLGELYDFPENAMAVGRLDEHSEGLLLITTDG 60

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ----GICYGDMQ-------- 176
            L+  +        + Y     G + +  +  L+ G+ I            Q        
Sbjct: 61  QLSHHINKSGI-VDKEYAALVDGLITEQAIEQLQNGVTISINGSTYDTKPCQVQKPNQIP 119

Query: 177 -------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     D + G  +WV V L EGK R+++K+     +   RL R+  GP+ + +L 
Sbjct: 120 DLPETKQKIRDERHGPTSWVNVTLSEGKFRQVRKMTGVVGFPTLRLARVRIGPYNVLSLR 179

Query: 230 AGSTREVSKKILR 242
                E+S + +R
Sbjct: 180 NQQVIELSDQEIR 192


>gi|223994405|ref|XP_002286886.1| hypothetical protein THAPSDRAFT_261040 [Thalassiosira pseudonana
           CCMP1335]
 gi|220978201|gb|EED96527.1| hypothetical protein THAPSDRAFT_261040 [Thalassiosira pseudonana
           CCMP1335]
          Length = 221

 Score = 73.3 bits (178), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 22/101 (21%), Positives = 38/101 (37%), Gaps = 21/101 (20%)

Query: 169 GICYGDMQV--TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
           G     +     L     S   V++ + EGKNR+I+++F      V +L R+S G   L 
Sbjct: 89  GGHTRPVDRLSVLSHPTRSTTRVSITISEGKNRQIRRMFHAIGSGVMKLHRVSVGDLNLS 148

Query: 227 TLLA-------------------GSTREVSKKILREQLGPH 248
            L+                    G  R + ++ + + LG  
Sbjct: 149 GLMPLEERIQRETSDVARDELKEGEWRVLHEEEVLKGLGWK 189


>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 = 73.3 bits (178), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 29/237 (12%), Positives = 54/237 (22%), Gaps = 35/237 (14%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV---- 65
                R+ K +A     SR +    I    V VNG   ++A   V   D I  +      
Sbjct: 6   KEAGVRLDKALADLTDLSRSQASEQIKAGLVLVNGKT-QKAKYAVKEGDIIHYERPQEEV 64

Query: 66  ----------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                      +   +     +      +V         + V   L  I       G + 
Sbjct: 65  LDCVAQNIPLEIVYEDEDVAVINKPQGMVVHPSVGHPSGTLVNALLFHIKDLSSINGVIR 124

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------------DKLNL 160
                 +     G L       + Q L                            +    
Sbjct: 125 PGIVHRIDKDTSGLLMIAKNDQAHQALAKELKEKKSLRQYIALVHGNLPNDRGVIEAPIG 184

Query: 161 LKKGIVIQGICY---GDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             +    +               +  + G  + V + L  G+  +I+    +    V
Sbjct: 185 RSEKDRKKQTVTAKGKPAVTHFKVLERFGQYSLVELTLETGRTHQIRVHMAYIGHPV 241


>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 = 73.3 bits (178), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 29/247 (11%), Positives = 63/247 (25%), Gaps = 37/247 (14%)

Query: 1   MKDKNIV-QENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M   +I   E    +R+ K +A      SR +V++ +   +V VNG  ++     +   D
Sbjct: 1   MNQIDITASEEQKSERIDKFLASTENDWSRTQVQQWVKDGQVVVNGSPVKS-NYKIQPGD 59

Query: 59  HIEVD-GVP-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            + V    P             +   ++  L +      +V         + V   +   
Sbjct: 60  QVTVTVPEPEALDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHLTGTLVNGLMAHC 119

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------- 155
                  G +       +     G L       + + L    V                 
Sbjct: 120 TDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKYTAVVHGLIS 179

Query: 156 -----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                            +   V +          +  +      V   L  G+  +I+  
Sbjct: 180 HDDGTIDAPIGRDKKDRQSMTVTRDGKNAVTHFHVLERFQDFTLVECQLETGRTHQIRVH 239

Query: 205 FEFFNWK 211
            ++  + 
Sbjct: 240 MKYIGFP 246


>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 = 73.3 bits (178), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 86/247 (34%), Gaps = 34/247 (13%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLE---------RAA 51
           +K+    Q      R+ KV+      SR +++ +I Q  V VNG + +            
Sbjct: 8   IKEIIYFQLEDQSGRLDKVLVEESELSRTQIQSLIKQGLVTVNGQVEKANYKLSGQELIE 67

Query: 52  VNVMSTDHIEVDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           + V   + +E++   +      E   L + +K  G+V   S    R T+ + L   F   
Sbjct: 68  MQVPEEEVLEIEAQAIPLDIIYEDDDLLVINKEAGMVVHPSKGHPRDTLVNALVYHFGNH 127

Query: 109 ISVG----------RLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQD 156
           ++ G          R+D +T GLL++  +    R L          R+Y     GQ++  
Sbjct: 128 LAAGSDSYRPGLVHRIDKDTSGLLVVAKNNESHRYLSQQLMDHTLGRIYYCLVEGQMEVK 187

Query: 157 K--------LNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
           +         +   +                 +     S + +   L+ G+  +I+  FE
Sbjct: 188 QGSIEIPLARDPKNRLKYHADAQGKPAWTDFEVLESYPSASLIQAELKTGRTHQIRAHFE 247

Query: 207 FFNWKVN 213
                + 
Sbjct: 248 HIGHPII 254


>gi|218259522|ref|ZP_03475235.1| hypothetical protein PRABACTJOHN_00893 [Parabacteroides johnsonii
          DSM 18315]
 gi|218225053|gb|EEC97703.1| hypothetical protein PRABACTJOHN_00893 [Parabacteroides johnsonii
          DSM 18315]
          Length = 201

 Score = 73.3 bits (178), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R++K+I+ +G+ SRRE ++ I + RV VNG L +     V   D + +D + ++  + T
Sbjct: 3  VRLNKLISDSGLCSRREADKFIEEGRVTVNGSLPQV-GQKVTEGDIVMLDDIQVKIGKHT 61


>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 = 73.3 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 31/250 (12%), Positives = 76/250 (30%), Gaps = 38/250 (15%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M+ +  IV+E     R+ K ++ A    SR   +++I ++ V+++ + ++  +  V + D
Sbjct: 1   METRILIVEEQDQGVRLDKYLSTAMDDCSRSRAQQLIDEEAVRIDDLPVKN-SYKVKAGD 59

Query: 59  HIEV---DGVPLRKAERT-----------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            IEV   +   L    +             + +      +V         + V   L   
Sbjct: 60  EIEVTLPEEEALEAQPQEMALNVVYEDHDVIVINKPKGLVVHPGPGNPDHTLVNGLLWHC 119

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------R 143
                  G L       +     G +       + Q L                      
Sbjct: 120 HDLSGINGVLRPGIVHRIDKDTSGLIVACKNDNAHQSLAKQLAEKTAGRQYYALVHGVIN 179

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                    + +D+ +  K  +  +          +  +  +   V+  L  G+  +I+ 
Sbjct: 180 HEYGTIDAPIGRDEKDRQKMAVTEKNSRPAITHFKVVERFDNYTLVSCRLETGRTHQIRV 239

Query: 204 VFEFFNWKVN 213
             ++  + + 
Sbjct: 240 HMQYIGFPIV 249


>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 = 73.3 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 34/237 (14%), Positives = 59/237 (24%), Gaps = 35/237 (14%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
             T  R+ K +A     SR +    I +  V VNG +++ A  +V S D I         
Sbjct: 6   KETGLRLDKALANVTDLSRSQANEQIKKGLVLVNGQVVK-AKYSVKSGDEITYQLPEEEI 64

Query: 63  -DGVPLRKAERTRL------WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            D                   +      +V   +     + V   +  I       G + 
Sbjct: 65  LDYKAENLPIDIIYEDSDLAIVNKAQGMVVHPSAGHSSGTLVNALMYHIKDLSSINGVVR 124

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------------------- 155
                 +     G L       + Q L                                 
Sbjct: 125 PGIVHRIDKDTSGLLMVAKNDKAHQVLAEELKAKKSLRKYLAIVHGNLPNDRGMIEAPIG 184

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                 KK  V         + T+  + G    + + L  G+  +I+    +    V
Sbjct: 185 RSEKDRKKQSVTVKGKDAVTRFTVLERFGDYTLLELSLETGRTHQIRVHMAYIGHPV 241


>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 = 73.3 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 31/243 (12%), Positives = 65/243 (26%), Gaps = 36/243 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           I   N   QR+ KV+       SR +++  I +  VKVN  +++     V   D+I V  
Sbjct: 8   ITDSNHVGQRLDKVLPELNSDWSRSQIQDWIKEDLVKVNDKVVK-PNYKVKQNDNIVVTE 66

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                           +   +     +Y     +V         + V   +  I +    
Sbjct: 67  QEVVDADITPENLNLDIYYEDDDVAIVYKPKGMVVHPSPGHYTGTLVNGLMYQIKNLSGI 126

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPST------------QWLRVYRVRFHGQVDQ--- 155
            G +       + +   G L       +             +   V  V  +   D    
Sbjct: 127 NGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMAKSVKRKYVALVHGNIPHDYGTV 186

Query: 156 -----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      +   V+           +         +   L  G+  +I+   ++  +
Sbjct: 187 DAPIGRNKKDRQAMAVVDDGKEAVTHFNVLEHFKDYTLIECELETGRTHQIRVHMKYIGF 246

Query: 211 KVN 213
            + 
Sbjct: 247 PLV 249


>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 = 73.3 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 31/241 (12%), Positives = 61/241 (25%), Gaps = 36/241 (14%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E    +R+ K +A      SR +V++ I    V VNG  ++     V   D I V  
Sbjct: 8   TVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDDVVTVNGKSVKV-NYKVKENDEITVTI 66

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                        G+ +   +   L +      +V         + V   +         
Sbjct: 67  PDPEELDIQAEDMGLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI 126

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL---------- 160
            G +       +     G L       + + L    V          +            
Sbjct: 127 NGVMRPGIVHRIDKDTSGLLMVAKNDVAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTI 186

Query: 161 ----------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      +   V +          +  +      V   L  G+  +I+   ++  +
Sbjct: 187 DAPIGRDKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGY 246

Query: 211 K 211
            
Sbjct: 247 P 247


>gi|182625133|ref|ZP_02952909.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Clostridium perfringens D str. JGS1721]
 gi|177909592|gb|EDT72026.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Clostridium perfringens D str. JGS1721]
          Length = 85

 Score = 73.3 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 16/82 (19%), Positives = 39/82 (47%), Gaps = 4/82 (4%)

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           +++G+ I G      ++    +       ++ L +G NR+I+++ + F + V +L RI  
Sbjct: 1   MERGVEILGQVTKPCKLKRINEN----TYSIILTQGLNRQIRRMSKVFGFNVVKLERIRI 56

Query: 221 GPFQLGTLLAGSTREVSKKILR 242
               L  +  G  R ++++ + 
Sbjct: 57  LNITLEDIEYGKWRYINREEIE 78


>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 = 73.3 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 33/243 (13%), Positives = 64/243 (26%), Gaps = 40/243 (16%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-- 60
            V+E    +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I  
Sbjct: 8   TVKEEQKSERIDKFLA--GINNEWSRSQVQQWIKDGVVTVNGNDIK-GNYKVKENDEIAV 64

Query: 61  ------EVDGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                 E+D         +   +   L +      +V         + V   +       
Sbjct: 65  AIPEPEELDIRAEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMYHCTDLS 124

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL-------- 160
              G +       +     G L       + + L    V          +          
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVEKTVTRRYKAIVHGVIPHDKG 184

Query: 161 ------------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                        +   V +          +  +      V   L  G+  +I+   ++ 
Sbjct: 185 TIDAPIGRDKKERQSMAVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYI 244

Query: 209 NWK 211
            + 
Sbjct: 245 GYP 247


>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 = 72.9 bits (177), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 30/243 (12%), Positives = 59/243 (24%), Gaps = 36/243 (14%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           IV       R+   +      SR  ++ +I    V V G +  +A + +     I V   
Sbjct: 5   IVSAEQEGMRLDVFLTEQMEGSRSYIQSLIKGGHVTVGGKV-GKANLRLTPDTIIRVEIP 63

Query: 63  ---------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                    + +PL     +   + +      +V         + V   L          
Sbjct: 64  EPESIEVKPEDIPLDYLYEDHDIVIVNKPRGMVVHPAVGNYSGTLVNALLFHCKDLSGIN 123

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--------------- 156
           G +       L     G +       +   L         +                   
Sbjct: 124 GEIRPGIVHRLDKDTSGVMMVAKNDAAHIGLAEQVKTHSARRTYWALVQGNIVEEKGTIK 183

Query: 157 ------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                   + +K  +V +          +  + G    V   L  G+  +I+  F     
Sbjct: 184 APIGRHPKDRMKMAVVFENSKDAVTHFKVLERYGHQTLVECNLETGRTHQIRVHFAHIGH 243

Query: 211 KVN 213
            V 
Sbjct: 244 PVV 246


>gi|323210422|gb|EFZ95309.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
          Length = 127

 Score = 72.9 bits (177), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 27/125 (21%), Positives = 47/125 (37%), Gaps = 4/125 (3%)

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTL 228
                  +     +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L
Sbjct: 1   GPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGL 60

Query: 229 LAGSTREVS---KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
             G   E+       LR  +       ++V ++      +     R            R 
Sbjct: 61  PRGGWTELDLAQTNYLRGLVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQIAGGRRS 120

Query: 286 KKNSS 290
              ++
Sbjct: 121 GGRNN 125


>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 = 72.9 bits (177), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 32/191 (16%), Positives = 60/191 (31%), Gaps = 9/191 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R+ K +A     SR +++ +I    V VN I + +    V   D I ++   L K  +
Sbjct: 9   SDRIDKYVANNSEISRNDIKELIENGAVFVNSIKINKPKFVVKEGDEILIE-RLLDKQIK 67

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 H  I           + +     P+      ++    +      L   +G L  
Sbjct: 68  VEPQNIHLDIVYECDDYLIINKPSGLVVHPAPGHHDNTLVNALMYHFKNNLSDVNGLLRM 127

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +      +        +    L K   I+   Y      +   K +N  + + 
Sbjct: 128 GVVHRIDKDTSGLLLIAKNNKAHNYFASLLKTHEIKRSYY-----AIVEGKIANEELHIE 182

Query: 193 LREG---KNRE 200
           L  G   KNR+
Sbjct: 183 LPIGRDTKNRQ 193


>gi|68068209|ref|XP_676014.1| hypothetical protein [Plasmodium berghei strain ANKA]
 gi|56495510|emb|CAH96878.1| conserved hypothetical protein [Plasmodium berghei]
          Length = 360

 Score = 72.9 bits (177), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 22/184 (11%), Positives = 57/184 (30%), Gaps = 10/184 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK+++ + + SR + + +I    VKV+  ++++    +     IEV+G  +     T+
Sbjct: 14  RLSKILSLSSVVSRNKAQELIRSGNVKVDNQIVKQ-NTVIDVNSKIEVNGCEINVDITTK 72

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LW  +KP  +                       +++ G   +      +           
Sbjct: 73  LWGIYKPKNVFCNTDQNYIYEEKKLINKKKKHILLNDGNDKLQISSENMRKLIEENKLKG 132

Query: 135 ELPSTQWLRVYRV----RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           E        +         +     D  N+ +             +  +   + +     
Sbjct: 133 ENNMMNNKTLIYKSDFYNTNKINRNDNTNIYRDMHFPNYTETRMNKRKIQDNEKN----- 187

Query: 191 VGLR 194
           + + 
Sbjct: 188 ITIS 191



 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 34/131 (25%), Positives = 61/131 (46%)

Query: 98  FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                 I   +I V  LD + EG++LLTNDG  A  L+  +   L  Y ++   ++  +K
Sbjct: 216 NKIENYIPEHLIIVNSLDSDMEGIILLTNDGDFANKLKDINNNILTTYLIKTQEELTNEK 275

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
           + LL+KG  I GI    +++ +        W+ +   E     +  +F  +N  + +  R
Sbjct: 276 IELLRKGCTIGGITIRPLELKIIKPNFLYKWIKLTYVEKSQTHLNLLFSKYNMTIRKCKR 335

Query: 218 ISYGPFQLGTL 228
            S+GP++   L
Sbjct: 336 YSFGPYKSSDL 346


>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 = 72.9 bits (177), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 21/227 (9%), Positives = 58/227 (25%), Gaps = 34/227 (14%)

Query: 15  RVSKVIAR-------AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           R+ K +         + I       ++I + +V VNG  +     ++   D +E+     
Sbjct: 13  RLDKFLRNTLKDFPLSTIY------KLIRKGKVYVNGKRVRDPGFDLEEGDTVEIKYVNL 66

Query: 63  -------DGVPLRKAERT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
                  D   L                L L       +         + +   L     
Sbjct: 67  ENLPKRSDKKDLTPVPMKLDIIHENDNYLVLNKPAGIAIHPGKGVHVATLIEGLLYYGQE 126

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
           +      +    +    L           + +  +      + +  + +       K  +
Sbjct: 127 QGFEPFLVHRLDKDTSGLLIVAKNREAARVLTEMFRGRNMEKEYIALVKGVPENNLKITI 186

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                    ++       + + + V +  G+  +I++      + V 
Sbjct: 187 PLDGQEAVSEIVSVKPLKNVSLLRVKIHTGRKHQIRRHLSQIGFPVV 233


>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 = 72.9 bits (177), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 30/251 (11%), Positives = 70/251 (27%), Gaps = 38/251 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M ++  ++      R+ + +A      SR  ++++I Q +V+VNG +     +N+   D 
Sbjct: 1   MLNEFYLEVEEDSARIDRYLAEELPDLSRSRIQQLIEQGKVQVNGKVCTSKKINLKVGDR 60

Query: 60  IEV------------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I +            + +PL     +   L L      +V         + V   L    
Sbjct: 61  ITLEVPEAQPLEIQAEDIPLDILYEDDQLLILNKPAGLVVHPAPGHSHGTLVNALLAHCP 120

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                 G         L     G +A      + + ++        + +           
Sbjct: 121 DLPGIGGVQRPGIVHRLDKDTTGAIAIAKTDIAYKHIQAQLQAKTARREYLGVVYGAPKT 180

Query: 156 -------------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                             +    + +G         +  + G+   +   L  G+  +I+
Sbjct: 181 ASGKVDLPIGRHPQDRKKMAVVPIEEGGRSAITHWQIQERLGNFTLIHFQLETGRTHQIR 240

Query: 203 KVFEFFNWKVN 213
                    + 
Sbjct: 241 VHSAKMGHPIV 251


>gi|315037134|gb|EFT49066.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0027]
          Length = 310

 Score = 72.9 bits (177), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 71/246 (28%), Gaps = 37/246 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 10  MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 67

Query: 60  IEV------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I V            + +P  +   +   + +      +V   +     + V   L    
Sbjct: 68  IVVTIPEPEVLDMVAEDIPLTIVYEDNDVIVVNKPQDMVVHPSAGHPKGTLVNALLHHAD 127

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                   +       +     G L       + + L                       
Sbjct: 128 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 187

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           K   VI+G        T+  +  +   V + L  G+  +I+   
Sbjct: 188 DKGEINAPIGRSKVDRKMQAVIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRVHM 247

Query: 206 EFFNWK 211
           ++  + 
Sbjct: 248 KYIGYP 253


>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 = 72.9 bits (177), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 50/333 (15%), Positives = 93/333 (27%), Gaps = 46/333 (13%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V      +R+   + AR+   SR +V+++I + RV VNG+ ++ A+  + S D I V   
Sbjct: 14  VDVEEKLRRLDVFLSARSPDCSRSQVQKLIREGRVTVNGLPVK-ASYEIRSGDCIAVWLP 72

Query: 63  --------------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
                               D   L   +   + ++        T               
Sbjct: 73  EAVGEDSLQPRPMPLEILFEDDDVLVLNKAPGVIVHPGAGHEEGTLVHGLLAHCSRLASR 132

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR-------------VRF 149
               R   V RLD  T G L++         L                            
Sbjct: 133 GAPRRPGIVHRLDRGTSGALMVAKSERAYLELIRQFKHHEVGKEYLALVYGTMAGASGEI 192

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +  ++  +  ++ +G      Q  +    G  + + V ++ G+  +I+       
Sbjct: 193 RTGMGRHPVDRKRMAVLEKGGREAVSQWKVAVAWGEVSLLRVVIKTGRTHQIRVHLSHMQ 252

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVR 269
             V      +YG            R V   +LRE L     +       A  +       
Sbjct: 253 HPVVG--DETYGG------GKRKARAVKSDVLRELLMEVDRQMLHAVGLAFRHPVSGADL 304

Query: 270 DRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
                +           + S QK G  +     
Sbjct: 305 SFTAPLPPDFAGLLERIRISLQKEGAGRSDPSG 337


>gi|70947937|ref|XP_743537.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56523079|emb|CAH75054.1| conserved hypothetical protein [Plasmodium chabaudi chabaudi]
          Length = 348

 Score = 72.5 bits (176), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 20/118 (16%), Positives = 46/118 (38%), Gaps = 1/118 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK+++ + + SR + + +I    VKV+  ++++    +     IEV+G  +     T+
Sbjct: 14  RLSKILSLSSVVSRNKAQELIRSGNVKVDNQIVKQ-NTVIDVNSKIEVNGCEINVDITTK 72

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           LW  +KP  +                       +++ G   +      +    G   +
Sbjct: 73  LWGIYKPKNVFCNTDQNYIYEEKKLMNKKKNHILLNDGNDRLQICSENMNKLKGENNK 130



 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 33/131 (25%), Positives = 60/131 (45%)

Query: 98  FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                 I   +I V  LD + EG++LLTNDG  A  L+  +   L  Y ++   ++  +K
Sbjct: 206 NKIENYIPEHLIIVNSLDSDMEGIILLTNDGDFANKLKDINNNILTTYLIKTQEELTNEK 265

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
           + LL+KG  I  I    +++ +        W+ +   E     +  +F  +N  + +  R
Sbjct: 266 VELLRKGCTIDDIHIRPLELKIIKPNLLYKWLKLTYVEKSQTHLNLLFSKYNMTIRKCKR 325

Query: 218 ISYGPFQLGTL 228
            S+GP++   L
Sbjct: 326 YSFGPYKSSDL 336


>gi|167944991|ref|ZP_02532065.1| ribosomal large subunit pseudouridine synthase B [Endoriftia
          persephone 'Hot96_1+Hot96_2']
          Length = 88

 Score = 72.5 bits (176), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 28/85 (32%), Positives = 43/85 (50%), Gaps = 6/85 (7%)

Query: 8  QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP- 66
           +    +R+ KV+A AG+ SRRE+E  I++ R++VNG   +     V+ +D I +DG P 
Sbjct: 4  NKPQMGERLQKVLANAGVGSRREIEGWISEGRIEVNGETAK-LGQRVVGSDRIRIDGRPF 62

Query: 67 ----LRKAERTRLWLYHKPIGLVTT 87
              +   ER  L        LVT 
Sbjct: 63 SQKRMEAPERRVLVYNKPEGELVTR 87


>gi|311744891|ref|ZP_07718676.1| ribosomal large subunit pseudouridine synthase E [Algoriphagus sp.
           PR1]
 gi|311302306|gb|EAZ81613.2| ribosomal large subunit pseudouridine synthase E [Algoriphagus sp.
           PR1]
          Length = 209

 Score = 72.5 bits (176), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 45/183 (24%), Positives = 71/183 (38%), Gaps = 19/183 (10%)

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
           L      V  VGRLD ++EGLLL+T+D  L   L  PS    R Y  +  G    + L  
Sbjct: 27  LFDFPKEVYPVGRLDKDSEGLLLITDDKWLNHHLLNPSFGHQRTYWAQVEGIPTPESLKA 86

Query: 161 LKKGIVIQ----GICYGD---------------MQVTLDTQKGSNAWVTVGLREGKNREI 201
           L  G+ I+                                +   ++W+ + L EGKNR++
Sbjct: 87  LGNGVKIKVDGKEYLTKPSIAKLLSESPELPDRDPPIRYRKNVPDSWIELTLIEGKNRQV 146

Query: 202 KKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPI 261
           +K+     +   RL R S     +     G  +E+ ++ +  QLG    +E+  N     
Sbjct: 147 RKMTAAVGFPTLRLARKSMEKINIIGFKVGEVQELDRETVYHQLGLTGFKESAKNFQKRP 206

Query: 262 YSS 264
             S
Sbjct: 207 KRS 209


>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 = 72.5 bits (176), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 26/256 (10%), Positives = 77/256 (30%), Gaps = 44/256 (17%)

Query: 1   MKDKN-----IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNV 54
           M+ K+     IV + +   R+ K+I+      SR  ++++I  ++V  NG +++ A+ +V
Sbjct: 1   MESKSEFFEFIVTDEYDGMRIDKLISELIDSLSRTYIKKLIDDKKVSCNGKVVK-ASFHV 59

Query: 55  MSTDHIEVDGVPLR--------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
              D I ++  P+                 +   + +      +V   +     + V   
Sbjct: 60  SENDEIVMEIPPIEIPQILPQDIPLDIIYEDNDVVVVNKPKDMVVHPAAGHYKDTLVNAI 119

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
           +      +  +  +        +  +  G   + +  +       +++ H          
Sbjct: 120 MYHCKDNLSGINGVMRPGIVHRIDKDTTGSVIICKNDNAHQSIAEQLKEHSINRVYHAIC 179

Query: 161 LKKGIVIQGICYGDM--------QVTLDTQKGSNAW---------------VTVGLREGK 197
                  +G     +        ++ +       +                +   L+ G+
Sbjct: 180 YGVIKEDEGDVTAPIGRSVNDRKKMAVVPGGKYASTHYRVLKRFPEDGFTYIECKLQTGR 239

Query: 198 NREIKKVFEFFNWKVN 213
             +I+         + 
Sbjct: 240 THQIRVHMSHIGHPLL 255


>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 = 72.5 bits (176), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 66/244 (27%), Gaps = 36/244 (14%)

Query: 5   NIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            I  E    QR+ K ++ +  A SR +++  I +  VKVN  +++     V   DHI V 
Sbjct: 7   KITDERRVGQRIDKFLSESNDAWSRSQLQDWIKEDLVKVNDKVIKS-NYKVKLNDHIIVT 65

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   +     +Y     +V         + V   +  I +   
Sbjct: 66  EKEVVEADIQPEDLDLDIYYEDDDVAIVYKPKGMVVHPSPGHYTGTLVNGLMYQIKNLSG 125

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------------- 155
             G +       +     G L       + + L    +    +                 
Sbjct: 126 INGEIRPGIVHRIDKDTSGLLMVAKNDIAHRGLVEQLMNKSVKRKYTALVHGNIPHDYGT 185

Query: 156 ------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                    N  +   V+           +         +   L  G+  +I+   ++  
Sbjct: 186 VDAPIGRNKNDRQAMAVVDDGKEAVTHFNVLEHFKDYTLIECELETGRTHQIRVHMKYIG 245

Query: 210 WKVN 213
           + + 
Sbjct: 246 FPLV 249


>gi|291484098|dbj|BAI85173.1| hypothetical protein BSNT_02552 [Bacillus subtilis subsp. natto
           BEST195]
          Length = 303

 Score = 72.5 bits (176), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 32/249 (12%), Positives = 71/249 (28%), Gaps = 41/249 (16%)

Query: 1   MKDKNIV-QENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M   +I   E    +R+ K +A +    SR +V++ +   +V VNG  ++ A   +   D
Sbjct: 1   MNQIDITASEEQKSERIDKFLASSENDWSRTQVQQWVKDGQVVVNGSAVK-ANYKIQPGD 59

Query: 59  HIEVD-GVP-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            + V    P             +   ++  L +      +V         + V   +   
Sbjct: 60  QVTVTVPEPEALDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHLTGTLVNGLMAHC 119

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                  G +       +     G L       + + L       +  V +    ++   
Sbjct: 120 TDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESL--VNQLVNKTVTRKYTAVVHGL 177

Query: 165 IVIQGICY-------GDMQVTLDTQKGSNAWVT----------VGLRE-----GKNREIK 202
           I                 + ++   +   + VT            L E     G+  +I+
Sbjct: 178 ISHDDGTIDAPIGRDKKDRQSMTVTRDGKSAVTHFHVLERFQDFTLVECQLETGRTHQIR 237

Query: 203 KVFEFFNWK 211
               +  + 
Sbjct: 238 VHMRYIGFP 246


>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 = 72.5 bits (176), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 31/237 (13%), Positives = 67/237 (28%), Gaps = 36/237 (15%)

Query: 10  NFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           N    R+ KV+       +R  +++ I +  V VNG  ++ A   V   D I +      
Sbjct: 10  NEESGRLDKVLTDLLPSITRSHIQQWIKEGNVSVNGEKMK-ANYKVQPGDEIAIVEPELV 68

Query: 63  ------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
                 + +P+     +   + +      +V   +     + V   +  I       G +
Sbjct: 69  SLEVLAEDIPIEIVYQDEDVVVVNKAQGMVVHPSAGHQTGTLVNALMHHITDLSGINGTI 128

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------------------- 155
                  +     G L       + + L           +                    
Sbjct: 129 RPGIVHRIDKDTSGLLMVAKNDAAHEKLAAQLKDKTSLREYIALVHGVIPHEKGTIDAPL 188

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                  KK  +I G        T+  +      V++ L  G+  +I+   ++  + 
Sbjct: 189 GRSKQDRKKQDIIDGGRAAVTHFTVLERFKDFTLVSLKLETGRTHQIRVHMKYIGYP 245


>gi|78067326|ref|YP_370095.1| pseudouridine synthase, Rsu [Burkholderia sp. 383]
 gi|77968071|gb|ABB09451.1| Pseudouridine synthase, Rsu [Burkholderia sp. 383]
          Length = 192

 Score = 72.5 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 41/191 (21%), Positives = 76/191 (39%), Gaps = 19/191 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +      + GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKTPGV--YAAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVEGAPGPTDLKALARGVDLGDYVTRPCRAEFIEPPDTLWPRNPPIR 120

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L    G T  + 
Sbjct: 121 YRAAIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGVGALDIFALGIAPGETIALP 180

Query: 238 KKILREQLGPH 248
            +   +   P 
Sbjct: 181 PRAPWDGFAPA 191


>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 = 72.5 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 34/241 (14%), Positives = 68/241 (28%), Gaps = 37/241 (15%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----- 60
           ++E +  +R+ KVIA      SR +V++ I    V VNG  ++ A       D +     
Sbjct: 8   IEEEYDGERIDKVIAALNDEWSRSQVQQWIKNGLVTVNGRTVK-ANYKSELGDTVAISPP 66

Query: 61  -----EVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                 V+  P+       +   L +      +V         + V   L          
Sbjct: 67  EPEPLHVEPEPIPLDIYYEDEDVLVVNKPRGMVVHPAPGHMRGTLVNALLAHCRDLSGIN 126

Query: 112 GRLDINTEGLLLLTNDGGLA---------------------RVLELPSTQWLRVYRVRFH 150
           G L       +     G L                      R  +      +        
Sbjct: 127 GVLRPGIVHRIDKDTSGLLMVAKNDAAHRSLVEQLVNKTVTRRYKAIVHGVIPHDYGTID 186

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + +DK +  K  +  +          +  +     +V   L  G+  +I+   ++  +
Sbjct: 187 APIGRDKRDRKKMAVTDENGKEAVTHFRVLERFRQYTYVECQLETGRTHQIRVHMKYIGY 246

Query: 211 K 211
            
Sbjct: 247 P 247


>gi|301308929|ref|ZP_07214874.1| putative S4 domain protein [Bacteroides sp. 20_3]
 gi|300832955|gb|EFK63580.1| putative S4 domain protein [Bacteroides sp. 20_3]
          Length = 189

 Score = 72.5 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 23/62 (37%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R++K+I+ AG+ SRRE +  I  +RV VNG         V + D + VDG  L   +  
Sbjct: 3  IRLNKLISEAGVCSRREADNFIEMERVTVNGKQPHV-GQKVTAEDVVLVDGERLNVEKYI 61

Query: 74 RL 75
          RL
Sbjct: 62 RL 63


>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 = 72.1 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 29/244 (11%), Positives = 65/244 (26%), Gaps = 36/244 (14%)

Query: 5   NIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            I  E+   QR+ K+++      SR +++  I +  VKVN  +++     V   DHI V 
Sbjct: 7   KITDESQVGQRIDKLLSEMNDEWSRSQLQDWIKEDLVKVNDKVIKS-NYKVKLNDHIIVT 65

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   +     +Y     +V         + V   +  I     
Sbjct: 66  EKEVVEADIQPEDLNLDIYYEDEDVAIVYKPKGMVVHPSPGHYTGTLVNGLMYQIKDLSG 125

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------------- 155
             G +       +     G L       + + L    +    +                 
Sbjct: 126 INGEIRPGIVHRIDKDTSGLLMVAKNDIAHRGLVEQLMDKTVKRKYTALVHGNIPHDYGT 185

Query: 156 ------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                    N  +   ++           +         +   L  G+  +I+   ++  
Sbjct: 186 VDAPIGRNKNDRQAMAIVDDGKDAVTHFNVLEHFKDYTLIECELETGRTHQIRVHMKYIG 245

Query: 210 WKVN 213
           + + 
Sbjct: 246 FPLV 249


>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 = 72.1 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 25/243 (10%), Positives = 69/243 (28%), Gaps = 36/243 (14%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           IV+ +  P+R+ K ++     SR  +++++ + RV   G+ ++ A+  + + D I VD  
Sbjct: 28  IVEPDAVPERIDKYLSERLSGSRSFLQKLLKENRVSAGGVPVK-ASYRICAGDVIRVDIP 86

Query: 64  ----------GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                      +PL     +   L +      +V   +     + V   +      +  +
Sbjct: 87  AQSEPDILAEDIPLDILYEDDDLLVVNKPKGMVVHPGAGHYSHTLVNALMYHCRDNLSGI 146

Query: 112 G---------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
                                   +  +   +                           +
Sbjct: 147 NGVLRPGIVHRIDQNTTGSLLVCKNDFSHNFIAGQLKEHSITRRYRAIVHGKISSDGTVN 206

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + +  +   K  +  +          +  Q     ++   L  G+  +I+      + 
Sbjct: 207 APIGRHPVERKKMAVNEKNGKPAVTHYRVLEQFEKFTYIECVLETGRTHQIRVHMSSIHH 266

Query: 211 KVN 213
            + 
Sbjct: 267 PIL 269


>gi|224003727|ref|XP_002291535.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220973311|gb|EED91642.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 441

 Score = 72.1 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 1/77 (1%)

Query: 188 WVTVGLREGKNREIKKVFEF-FNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            + + L+EGK R+I+++        V  L+R S GP QL TL  G  R + ++ +RE   
Sbjct: 365 TLRLVLQEGKKRQIRRMCREILGMHVVSLVRKSIGPIQLDTLPEGKWRPLKEQEVREIFA 424

Query: 247 PHLLEEAQVNLDAPIYS 263
               ++ +         
Sbjct: 425 DTPHKKRKKAKRFVGKD 441



 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 14/69 (20%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQR------------VKVNGILLERA-AVNV 54
            +  T  R+SK ++  GI SRRE  R++ +              + V G  +     V V
Sbjct: 66  DDTTTQIRLSKRMSELGICSRREAARILKEANETTSDLKYLKEIIYVRGEPVTEGTGVKV 125

Query: 55  MSTD-HIEV 62
              +  IE+
Sbjct: 126 SPNEKRIEI 134


>gi|225024833|ref|ZP_03714025.1| hypothetical protein EIKCOROL_01720 [Eikenella corrodens ATCC
           23834]
 gi|224942436|gb|EEG23645.1| hypothetical protein EIKCOROL_01720 [Eikenella corrodens ATCC
           23834]
          Length = 98

 Score = 72.1 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 11/56 (19%), Positives = 27/56 (48%)

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            +   + + + +GK  ++K++      +V  L R+ +G ++   LL G  R +  +
Sbjct: 42  ENPHSLLLTITQGKYHQVKRMVAAAGNRVEALHRLRFGDWECEDLLPGQWRFIQPE 97


>gi|163788440|ref|ZP_02182886.1| RNA pseudouridine synthase family protein [Flavobacteriales
           bacterium ALC-1]
 gi|159876760|gb|EDP70818.1| RNA pseudouridine synthase family protein [Flavobacteriales
           bacterium ALC-1]
          Length = 186

 Score = 72.1 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 35/178 (19%), Positives = 69/178 (38%), Gaps = 18/178 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTND 127
                +  +KP G ++   +   +      L    +    V++VGRLD  +EGLLLLT D
Sbjct: 1   MDHHYYKIYKPYGYLSQFINHQNKRRNKKLLSELYTFSDNVMAVGRLDEKSEGLLLLTTD 60

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--CYGDMQVTLDT---- 181
           G  +  +     +      V      +          I ++G      + +  +      
Sbjct: 61  GKFSNYITSSKIEKEYHVMVDGVITEEAVLKLQNGVEISVEGKPYKTKNCKAKILRDTSH 120

Query: 182 ---------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + G  +W+++ L EGK R+++K+     +   RL+R+  G ++L  +  
Sbjct: 121 IVERFVRDERHGITSWLSITLAEGKFRQVRKMTAKVGFPTLRLVRVRIGDYKLEEMKP 178


>gi|167835720|ref|ZP_02462603.1| pseudouridine synthase family protein [Burkholderia thailandensis
           MSMB43]
          Length = 192

 Score = 72.1 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 39/176 (22%), Positives = 66/176 (37%), Gaps = 17/176 (9%)

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
                T        +            V   GRLD ++EGLLLLT+DG L   +  P  +
Sbjct: 7   NKPFGTICQFSPHETRASLGDWVKTPDVYPAGRLDADSEGLLLLTDDGALQAKIAEPRHK 66

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---------------TQKGS 185
            ++ Y  +  G  D   L  L++G+ +        +                        
Sbjct: 67  LVKRYWAQVEGAPDAAALAALERGVDLGDYVSRPCRARFVTPPETLWPRNPPVRYRAAIP 126

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKK 239
             W+ + + EGKNR+++++     +   RLIR+  G   +    L  G TRE+  +
Sbjct: 127 TTWIELEIAEGKNRQVRRMTAAVGFPTLRLIRVGIGALDVFALGLSPGETRELPPR 182


>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 = 72.1 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 32/247 (12%), Positives = 65/247 (26%), Gaps = 40/247 (16%)

Query: 6   IVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           +V      QRV KV+A  G+   SR  +++++A   V +NG +L + +V V   D + V+
Sbjct: 46  MVGTEHHGQRVDKVLA-LGVSEFSRSYLQQLLADGAVTLNGKVLLKPSVKVAVGDRLRVE 104

Query: 64  GVP---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---- 104
             P               +   +   L +      +V         + +   L       
Sbjct: 105 MRPTQQSMAFQPETMDLQVVYEDEDLLVINKPAGLVVHPAPGNWTGTLLNGLLARDEKAR 164

Query: 105 -----------------FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
                               V            ++           L        +   V
Sbjct: 165 QVPRAGIVHRLDKDTSGLMVVARNRSTMDALIKMIAAREVSRQYLALAHKQWGSRKHREV 224

Query: 148 RFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                 D      +    + +           L     +++ V   L  G+  +I+    
Sbjct: 225 DAPIGRDPRNRLRMAVVDLNLHPGKQARTDFDLLDGDAAHSLVRCTLHTGRTHQIRVHMA 284

Query: 207 FFNWKVN 213
                + 
Sbjct: 285 SLGHPLI 291


>gi|154490383|ref|ZP_02030644.1| hypothetical protein PARMER_00616 [Parabacteroides merdae ATCC
          43184]
 gi|154088994|gb|EDN88038.1| hypothetical protein PARMER_00616 [Parabacteroides merdae ATCC
          43184]
          Length = 204

 Score = 72.1 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R++K+I+ +G+ SRRE ++ I + RV VNG L +     V   D + +D + ++  + T
Sbjct: 6  VRLNKLISDSGLCSRREADKFIEEGRVTVNGSLPQV-GQKVTEADIVMLDDIQIKIGKNT 64


>gi|159486376|ref|XP_001701217.1| hypothetical protein CHLREDRAFT_179001 [Chlamydomonas
          reinhardtii]
 gi|158271917|gb|EDO97727.1| predicted protein [Chlamydomonas reinhardtii]
          Length = 235

 Score = 72.1 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 22/49 (44%), Positives = 31/49 (63%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEV 62
          R++KV+A  G+ASRR  E +IA  RV+VNG L++     V    D +EV
Sbjct: 48 RLAKVLAACGVASRRACEGLIADGRVRVNGNLVKEQGTTVDPARDKVEV 96



 Score = 59.4 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 18/118 (15%), Positives = 39/118 (33%), Gaps = 1/118 (0%)

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           G    + + + EGK  E++++ +     +  L R+  G F+L   L  G  + ++   L+
Sbjct: 118 GDPRRLRIVVAEGKKHEVRELVKAAGMNLLSLRRVRIGGFRLPRDLGLGGFKALTPADLK 177

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                   E A V+      + +          S         ++   +       K 
Sbjct: 178 LITDARAQELASVSGATRAAAQQAAQTAATRRASVPRALRDMPEEVLEKFRKARGDKS 235


>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 = 72.1 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 29/243 (11%), Positives = 65/243 (26%), Gaps = 38/243 (15%)

Query: 9   ENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
            +    R+ + +++     SR  ++++I Q  V++N  +     +NV   D I +     
Sbjct: 44  TDTKGDRIDRFLSQELPDLSRSRIQQLIEQGNVQLNDKVCTSKKINVKLGDRITLEIPEA 103

Query: 63  -------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
                  + +PL     +   L L      +V         + V   L    +     G 
Sbjct: 104 QPLELLAEDIPLDILYEDDQLLILNKPAGLVVHPAPGHPDGTLVNALLAHCPNLPGIGGV 163

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------------------ 155
                   L     G +A      +   L+        + +                   
Sbjct: 164 QRPGIVHRLDKDTTGAIAIAKTEVAHHHLQAQLKAKTARREYLGVVYGAPKVESGTIDLP 223

Query: 156 -----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                     +    + QG         +  + G+   +   L  G+  +I+        
Sbjct: 224 IGRHPQDRKKMAIMPIEQGGRSAVTHWQVLERLGNFTLIRFQLETGRTHQIRVHSAKIGH 283

Query: 211 KVN 213
            + 
Sbjct: 284 PIV 286


>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 = 72.1 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 30/250 (12%), Positives = 72/250 (28%), Gaps = 38/250 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+++    E     R+ K ++      SR  ++++I ++ V VNG  ++ A   +   DH
Sbjct: 1   MEERRYTAEKNDLMRIDKFLSEKLPDLSRSYLQKLIKEKEVLVNGQPVK-ANYKLSLEDH 59

Query: 60  IEVD----GVP----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I V       P          +   +   L +      +V   +     + V   +    
Sbjct: 60  ISVTIPELKEPDILPEQIPLDILYEDEDILVVNKPKGMVVHPSAGHYSGTLVNALMFHCK 119

Query: 106 SRVISVG----------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
            ++  +                       + D   + L     D  + R         L+
Sbjct: 120 DQLSGINGVMRPGIVHRIDMDTTGSLIVCKNDFAHQSLAEQLKDHTITRKYHAIVHGVLK 179

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                    + +  +   K  +  +   +      +  +     +V   L  G+  +I+ 
Sbjct: 180 EDNGTIDAPIGRHPVERKKMSVNYKNGKHAVTHYRVLKRFEKFTYVECQLETGRTHQIRV 239

Query: 204 VFEFFNWKVN 213
                   + 
Sbjct: 240 HMASIRHPLL 249


>gi|330752330|emb|CBL87284.1| RNA pseudouridine synthase family protein [uncultured Flavobacteria
           bacterium]
          Length = 195

 Score = 72.1 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 45/189 (23%), Positives = 78/189 (41%), Gaps = 16/189 (8%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +Y     L  +    +       ++  + + V  VGRLD ++EGLLL++ND  +  
Sbjct: 6   KYYIIYKPKGCL--SQFSKEHGKRALGDVFDLPTDVYPVGRLDEDSEGLLLISNDKSINS 63

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVT---------- 178
            L  P     R Y V+  GQ+ +  +  L  G+ I    +       +V           
Sbjct: 64  KLLNPLNGHWRTYWVQVSGQIHKSAIKALVNGVDIVVKGKIHSTLPARVKKGNPPKNILP 123

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           L+  +   +WV + L EGK R+++K+     +   RL+R      +LG L     + + K
Sbjct: 124 LNVSEKETSWVKISLCEGKYRQVRKMTAKVGFPTLRLVRTHIEELELGELKPSEFKSLDK 183

Query: 239 KILREQLGP 247
           K L  +L  
Sbjct: 184 KALFHKLKL 192


>gi|321315311|ref|YP_004207598.1| pseudouridylate synthase [Bacillus subtilis BSn5]
 gi|320021585|gb|ADV96571.1| pseudouridylate synthase [Bacillus subtilis BSn5]
          Length = 303

 Score = 72.1 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 30/247 (12%), Positives = 64/247 (25%), Gaps = 37/247 (14%)

Query: 1   MKDKNIV-QENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M   +I   E    +R+ K +A      SR +V++ +   +V VNG  ++ A   +   D
Sbjct: 1   MNQIDITASEEQKSERIDKFLASTENDWSRTQVQQWVKDGQVVVNGSAVK-ANYKIQPGD 59

Query: 59  HIEVD-GVP-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            + V    P             +   ++  L +      +V         + V   +   
Sbjct: 60  QVTVTVPEPEALDVLAEPLDLDIYYEDQDVLVVNKPRGMVVHPAPGHLTGTLVNGLMAHC 119

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------- 155
                  G +       +     G L       + + L    V                 
Sbjct: 120 TDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKYTAVVHGLIS 179

Query: 156 -----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                            +   V +          +  +      V   L  G+  +I+  
Sbjct: 180 HDDGTIDAPIGRDKKDRQSMTVTRDGKNAVTHFHVLERFQDFTLVECQLETGRTHQIRVH 239

Query: 205 FEFFNWK 211
            ++  + 
Sbjct: 240 MKYIGFP 246


>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 = 72.1 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 35/244 (14%), Positives = 67/244 (27%), Gaps = 42/244 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            V E    +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V
Sbjct: 8   TVAEEQKNERIDKFVA--GINNEWSRTQVQQWIKDNVVTVNGKAVK-GNYKVRENDEITV 64

Query: 63  --------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                   D  P      +   +   L +      +V         + V   +       
Sbjct: 65  TIPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRV 147
              G +       +     G L       + + L                        + 
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKG 184

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                + +DK    +   V +   +      +  +      V   L  G+  +I+   ++
Sbjct: 185 TIDAPIARDKKER-QSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKY 243

Query: 208 FNWK 211
             + 
Sbjct: 244 IGYP 247


>gi|189351290|ref|YP_001946918.1| ribosomal large subunit pseudouridine synthase E [Burkholderia
           multivorans ATCC 17616]
 gi|189335312|dbj|BAG44382.1| ribosomal large subunit pseudouridine synthase E [Burkholderia
           multivorans ATCC 17616]
          Length = 192

 Score = 72.1 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 39/182 (21%), Positives = 72/182 (39%), Gaps = 19/182 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +        GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKTPGV--YPAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVEGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPETLWPRNPPIR 120

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L      T  + 
Sbjct: 121 YRAAIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGSLDIFALGIAPSETIALP 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>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 = 71.7 bits (174), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 28/250 (11%), Positives = 78/250 (31%), Gaps = 38/250 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K +    +  +  R+ + +A      SR  +++++   +V VNG L++ A+  V + DH
Sbjct: 12  LKQEFYPTDLESDVRIDRYLAETCPELSRSYIQKLLKSGQVLVNGRLIK-ASYVVTADDH 70

Query: 60  IEVD--------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           IEVD               + +   ++  + +      +V   +     + V   +    
Sbjct: 71  IEVDVPEAVEPEIEAEPMDLDILYEDQDIILVNKPKGMVVHPAAGHYSHTLVNGLMYHCK 130

Query: 106 SRVISVG----------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
           +++  +                       + D+    +     +  + R  +      ++
Sbjct: 131 NQLSGINGVMRPGIVHRIDMDTTGVLIVCKNDMAHNSIAAQLKEHSITRRYQAIVHGVIK 190

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                    + + +    K  I             +  +     +V   L  G+  +I+ 
Sbjct: 191 EDEGTVDAPIGRHQTERKKMCINYNNGRNAVTHYQVLRRFEQYTYVECRLETGRTHQIRV 250

Query: 204 VFEFFNWKVN 213
                +  + 
Sbjct: 251 HMASLHHPLL 260


>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 = 71.7 bits (174), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 31/251 (12%), Positives = 68/251 (27%), Gaps = 39/251 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK+ N+  +     R+ + +A+     SR  ++++I +  V++N  L       +   D 
Sbjct: 1   MKEINLYNQEN-SDRLDRYLAQQLPDLSRSRIQKLIEEGNVQLNHNLCTSKKATIQPGDS 59

Query: 60  IEV---DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I +   D  PL              +   L +      +V      +  + V   L    
Sbjct: 60  IHLTIPDAKPLDLKPEAIPLDILYEDDQILIVNKPANLVVHPAPGHENGTLVNALLAHCP 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
           +     G         L     G +A      +   L+        + D           
Sbjct: 120 NLAGIGGVQRPGIVHRLDKDTTGAIAIAKTDHAHHHLQAQLKAKTARRDYLGVVYGSPAT 179

Query: 156 -------------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                             +    + +G         +  + G+   +   L  G+  +I+
Sbjct: 180 ETGTINFPIGRHPSDRKKMAVVPLEKGGRSAITHWQIKERLGNYTLIHFQLETGRTHQIR 239

Query: 203 KVFEFFNWKVN 213
                    + 
Sbjct: 240 VHTAHIGHPII 250


>gi|167585691|ref|ZP_02378079.1| Pseudouridine synthase, Rsu [Burkholderia ubonensis Bu]
          Length = 192

 Score = 71.7 bits (174), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 40/182 (21%), Positives = 74/182 (40%), Gaps = 19/182 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +      + GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKTPGV--YAAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVEGAPGPADLKALARGVDLGDYVTRACRAEFIEPPDALWPRNPPIR 120

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L    G T  + 
Sbjct: 121 YRAAKPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGSLDIFALGIAPGETITLP 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>gi|150010511|ref|YP_001305254.1| pseudouridine synthase family 1 protein [Parabacteroides
          distasonis ATCC 8503]
 gi|298377632|ref|ZP_06987583.1| RNA pseudouridine synthase family protein [Bacteroides sp.
          3_1_19]
 gi|149938935|gb|ABR45632.1| putative pseudouridine synthase family 1 protein [Parabacteroides
          distasonis ATCC 8503]
 gi|298265335|gb|EFI06997.1| RNA pseudouridine synthase family protein [Bacteroides sp.
          3_1_19]
          Length = 189

 Score = 71.7 bits (174), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 23/62 (37%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R++K+I+ AG+ SRRE +  I  +RV VNG         V + D + VDG  L   +  
Sbjct: 3  IRLNKLISEAGVCSRREADNFIEMERVTVNGKQPHV-GQKVTAEDVVLVDGERLNVEKYI 61

Query: 74 RL 75
          RL
Sbjct: 62 RL 63


>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 = 71.7 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 30/247 (12%), Positives = 64/247 (25%), Gaps = 37/247 (14%)

Query: 1   MKDKNIV-QENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M   +I   E    +R+ K +A      SR +V++ +   +V VNG  ++ A   +   D
Sbjct: 1   MNQIDITASEEQKSERIDKFLASTENDWSRTQVQQWVKDGQVVVNGSAVK-ANYKIQPGD 59

Query: 59  HIEVD-GVP-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            + V    P             +   ++  L +      +V         + V   +   
Sbjct: 60  QVTVTVPEPEALDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHLTGTLVNGLMAHC 119

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------- 155
                  G +       +     G L       + + L    V                 
Sbjct: 120 TDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKYTAVVHGLIS 179

Query: 156 -----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                            +   V +          +  +      V   L  G+  +I+  
Sbjct: 180 HDDGTIDAPIGRDKKDRQSMTVTRDGKNAVTHFHVLERFQDFTLVECQLETGRTHQIRVH 239

Query: 205 FEFFNWK 211
            ++  + 
Sbjct: 240 MKYIGFP 246


>gi|255016577|ref|ZP_05288703.1| pseudouridine synthase family 1 protein [Bacteroides sp. 2_1_7]
          Length = 189

 Score = 71.7 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 23/62 (37%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R++K+I+ AG+ SRRE +  I  +RV VNG         V + D + VDG  L   +  
Sbjct: 3  IRLNKLISEAGVCSRREADNFIEMERVTVNGKQPHV-GQKVTAEDVVLVDGERLNVEKYI 61

Query: 74 RL 75
          RL
Sbjct: 62 RL 63


>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 = 71.7 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 28/250 (11%), Positives = 74/250 (29%), Gaps = 39/250 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+      +    +R+ + ++      SR  +++++   ++ VN   ++     +   D 
Sbjct: 1   MEQIKFTADRS-GERIDRFLSENLENLSRSYIQKLLKDGKISVNQSSVK-PNYKISENDK 58

Query: 60  IEV---DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           IEV   D   L              +   L +      +V         + V   +    
Sbjct: 59  IEVFIPDPEVLDILPENIPLDILYEDSDILIVNKPKNMVVHPAPGHYEHTLVNAVMYHCK 118

Query: 106 SR---------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-------- 148
                         V R+D++T G LL+  +    +++     +     R          
Sbjct: 119 DNLSGINGILRPGIVHRIDMDTTGSLLICKNDKAHQIIAEQLKEHSITRRYHAIVHGKIK 178

Query: 149 -----FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                 +  + +  ++  K     +   +     T+  +     ++   L  G+  +I+ 
Sbjct: 179 EDNGVVNAPIGRHPIDRKKMSTKAKNGKHAVTHYTVLRRFKDYTYIECELETGRTHQIRV 238

Query: 204 VFEFFNWKVN 213
                   + 
Sbjct: 239 HMASIGHPIL 248


>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 = 71.7 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 35/244 (14%), Positives = 67/244 (27%), Gaps = 42/244 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            V E    +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V
Sbjct: 8   TVAEEQKNERIDKFVA--GINNEWSRTQVQQWIKDNVVTVNGKAVK-GNYKVRENDEITV 64

Query: 63  --------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                   D  P      +   +   L +      +V         + V   +       
Sbjct: 65  TIPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRV 147
              G +       +     G L       + + L                        + 
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKG 184

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                + +DK    +   V +   +      +  +      V   L  G+  +I+   ++
Sbjct: 185 TIDAPIARDKKER-QSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKY 243

Query: 208 FNWK 211
             + 
Sbjct: 244 IGYP 247


>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 = 71.7 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 32/247 (12%), Positives = 66/247 (26%), Gaps = 37/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK + +V E    +R+ K I +     SR  ++ ++    ++VNG   +  ++ + + D 
Sbjct: 1   MKTRKLVAE-SDGERLDKYITQKETDLSRSFIQELVEAGHIQVNGKNAK-PSLKLKNGDT 58

Query: 60  IEVDGVPLRKAERTR--------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I ++  P    E                 L +   P   V         + +   L    
Sbjct: 59  ITIEIPPETPPELKAEDIPLEIIFQDKDLLLINKPPGLTVHPAPGHPDHTLINGVLALEP 118

Query: 106 SRVISVGRLDINTEGLLLLTNDGG-------------LARVLELPSTQWLRVYRVRFHGQ 152
                   L       L     G               A+  E    ++           
Sbjct: 119 EMEDFDDPLRPGIVHRLDKDTSGLLLVAKNREALANLSAQFKERTVRKYYLTLVQGELHP 178

Query: 153 VDQDKLNLLKKGIVIQGICY-----GDMQ--VTLDTQKGSNAWVTVGLREGKNREIKKVF 205
            +      L +    +            +    +       + + V L  G+  +I+  F
Sbjct: 179 AEGFIEAPLGRDPQNRQKIAVVSNGRPARTGYKVLRYIQGYSLLEVKLETGRTHQIRVHF 238

Query: 206 EFFNWKV 212
                 V
Sbjct: 239 AAIGHPV 245


>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 = 71.4 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 32/242 (13%), Positives = 72/242 (29%), Gaps = 37/242 (15%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            + E    +R+ K +   G   SR +V++ I    V +NG  ++     V + D +E+  
Sbjct: 8   TISEQQQGERIDKFLTAQGEEWSRTQVQQWIKDGHVLINGRTIKS-NYKVETGDTLELFV 66

Query: 63  ----------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                     + +P+     +     +      +V         + V   +         
Sbjct: 67  PEPEVLEVVPENIPIEIIYEDEDVAVVNKPRGMVVHPAPGHTTGTLVNALMYHCNDLSSI 126

Query: 111 VG---------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
            G                     + D   E L+         RV +      +       
Sbjct: 127 NGVVRPGIVHRIDKDTSGLLMIAKNDRAHESLVNQLKAKTTERVYQAIVHGNIPHDHGTI 186

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +DK++     +  +         T+  + G   +V   L  G+  +I+  F++  
Sbjct: 187 DAPIGRDKVDRQSMTVTEENSRDAVTHFTVLERFGDFTFVECQLETGRTHQIRVHFKYIG 246

Query: 210 WK 211
           + 
Sbjct: 247 FP 248


>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 = 71.4 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 30/250 (12%), Positives = 72/250 (28%), Gaps = 38/250 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+++    E     R+ K ++      SR  ++++I ++ V VNG  ++ A   +   DH
Sbjct: 1   MEERRYTTEKNDLMRIDKFLSEKLPDLSRSYLQKLIKEKEVLVNGQPVK-ANYKLSLEDH 59

Query: 60  IEVD----GVP----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I V       P          +   +   L +      +V   +     + V   +    
Sbjct: 60  ISVMIPELKEPDILPEQIPLDILYEDEDILVVNKPKGMVVHPSAGHYSGTLVNALMFHCK 119

Query: 106 SRVISVG----------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
            ++  +                       + D   + L     D  + R         L+
Sbjct: 120 DQLSGINGVMRPGIVHRIDMDTTGSLIVCKNDFAHQSLAEQLKDHTITRKYHAIVHGVLK 179

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                    + +  +   K  +  +   +      +  +     +V   L  G+  +I+ 
Sbjct: 180 EDNGTIDAPIGRHPVERKKMSVNYKNGKHAVTHYRVLKRFEKFTYVECQLETGRTHQIRV 239

Query: 204 VFEFFNWKVN 213
                   + 
Sbjct: 240 HMASIRHPLL 249


>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 = 71.4 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 31/243 (12%), Positives = 69/243 (28%), Gaps = 36/243 (14%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            ++E    +R+ K ++      SR ++   I+   +KVNG  ++ A   V + D I +D 
Sbjct: 7   TIEEQQQGERIDKALSSLQSEWSRTQIGNWISDGNIKVNGDAVK-AKYKVKAGDVIAIDV 65

Query: 64  --GVP-----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
               P           +   +   L +      +V         + V   +         
Sbjct: 66  PEAEPLDVIAENLALDIVYEDADVLVVNKPKGMVVHPAPGHMTGTLVNGLMYQCKDLSGI 125

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQ------------WLRVYRVRFHGQVDQ--- 155
            G +       +     G L       + +               +  V  H   D+   
Sbjct: 126 NGIMRPGIVHRIDKDTSGLLMVAKNDVAHESLVDQLVNKTVTRKYIALVHGHIAHDKGTI 185

Query: 156 -----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      +K  ++    +      +  + G    V   L  G+  +I+    +  +
Sbjct: 186 DAPIGRDQKDRQKQAIVDNGKHAVTHFHVVERFGDYTLVECRLETGRTHQIRVHMNYIGF 245

Query: 211 KVN 213
            + 
Sbjct: 246 PLV 248


>gi|221211463|ref|ZP_03584442.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Burkholderia multivorans CGD1]
 gi|221168824|gb|EEE01292.1| ribosomal large subunit pseudouridine synthase E (rRNA-uridine
           isomerase E) (rRNA pseudouridylate synthase E)
           [Burkholderia multivorans CGD1]
          Length = 192

 Score = 71.4 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 41/182 (22%), Positives = 73/182 (40%), Gaps = 19/182 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +        GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKTPGV--YPAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVEGAPGPADLKALARGVDLGDYVSRPCRAEFIEPPETLWPRNPPIR 120

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   WV + + EGKNR+++++     +   RL+R+  G   +  L    G T  + 
Sbjct: 121 YRAAIPTTWVELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFALGIAPGETIALP 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>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 = 71.4 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 33/250 (13%), Positives = 71/250 (28%), Gaps = 38/250 (15%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M++ +I V E+   QR+ K ++      SR  +  +I +  + VNG ++  A   V   D
Sbjct: 1   MREIDIWVAEDADSQRIDKYLSMVVEDLSRSRIASLIEEGSILVNGEVIR-AKYKVKPAD 59

Query: 59  HIE--VDGVP------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           HI    +               +R  +   + +      +V   +     + V   L   
Sbjct: 60  HITAAFEDEMALEAAPEKMELDIRYEDHDVIVINKPKGIVVHPANGNQSGTLVNGLLYHC 119

Query: 105 FSRVISVG---------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
                  G                     + D     L     +  + R+        + 
Sbjct: 120 KDLSGINGVLRPGIVHRIDKDTTGLLIVAKNDKAHASLSKQLQNKSVNRLYYALVHGVIE 179

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                    + +D  +  K  ++            +  +      V   L  G+  +I+ 
Sbjct: 180 HEFGTIDAPIGRDPKDRQKMAVIATNSKPARTHFRVVERFAKYTLVECRLETGRTHQIRV 239

Query: 204 VFEFFNWKVN 213
             ++    V 
Sbjct: 240 HMQYIGHPVV 249


>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 = 71.4 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 28/237 (11%), Positives = 53/237 (22%), Gaps = 35/237 (14%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV---- 65
                R+ K +A     SR +    I    V VNG   ++A   V   D I  +      
Sbjct: 6   KEAGVRLDKALADLTDLSRSQASEQIKAGLVWVNGKT-QKAKYAVKEGDIIHYERPQEEV 64

Query: 66  ----------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                      +   +     +      +V         + V   L  I       G + 
Sbjct: 65  LDCVAQNIPLEIVYEDEDVAVINKPQGMVVHPSVGHPSGTLVNALLFHIKDLSSINGVIR 124

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------------DKLNL 160
                 +     G L       + Q L                            +    
Sbjct: 125 PGIVHRIDKDTSGLLMIAKNDQAHQALAKELKEKKSLRQYIALVHGNLPNDRGVIEAPIG 184

Query: 161 LKKGIVIQGICY---GDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             +    +               +  +    + V + L  G+  +I+    +    V
Sbjct: 185 RSEKDRKKQTVTAKGKPAVTHFKVLERFDQYSLVELTLETGRTHQIRVHMAYIGHPV 241


>gi|291542663|emb|CBL15773.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus
           bromii L2-63]
          Length = 306

 Score = 71.4 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 35/248 (14%), Positives = 75/248 (30%), Gaps = 38/248 (15%)

Query: 3   DKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           ++  +    +  R+ K I+ A I  SR     +I    V VN  ++ +    +   D + 
Sbjct: 2   NEFKLNCETSGVRLDKFISDANIDLSRSAAVNLIENGAVLVNDSVVSK-KYKLSQGDIVV 60

Query: 62  V---DGVP-----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
           V   D  P           +   +   L +      +V   +     + V   L      
Sbjct: 61  VNVPDPTPYEAKAENIPLDIVYEDECLLVVNKPKGMVVHPAAGNYDGTLVNALLYHCGDS 120

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR------------ 146
                   R   V R+D +T GLL++  +    R L     +                  
Sbjct: 121 LSGINGVLRPGIVHRIDKDTSGLLIVAKNDFSHRSLAEQIKEHSFTREYESIVFGNLKND 180

Query: 147 -VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                  + ++  +  K  ++ +         ++ T+      +   L  G+  +I+   
Sbjct: 181 EGTVDAPIGRNPKDRKKMCVIEKNSKNAVTHYSVITRYKGYTHIKCKLETGRTHQIRVHM 240

Query: 206 EFFNWKVN 213
            +    V+
Sbjct: 241 AYIGHPVS 248


>gi|83720677|ref|YP_441314.1| pseudouridine synthase family protein [Burkholderia thailandensis
           E264]
 gi|167580097|ref|ZP_02372971.1| pseudouridine synthase family protein [Burkholderia thailandensis
           TXDOH]
 gi|167618162|ref|ZP_02386793.1| pseudouridine synthase family protein [Burkholderia thailandensis
           Bt4]
 gi|257140011|ref|ZP_05588273.1| pseudouridine synthase family protein [Burkholderia thailandensis
           E264]
 gi|83654502|gb|ABC38565.1| pseudouridine synthase family protein [Burkholderia thailandensis
           E264]
          Length = 192

 Score = 71.4 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 45/183 (24%), Positives = 79/183 (43%), Gaps = 19/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL   +KP G +   S  + R+++ D + +        GRLD ++EGLLLLT+DG L   
Sbjct: 2   RLIALNKPFGTICQFSPHEARASLGDWVKTPGV--YPAGRLDADSEGLLLLTDDGALQAK 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------- 180
           +  P  + ++ Y  +  G  D   L  L++G+ +        +                 
Sbjct: 60  IAEPRHKLVKRYWAQVEGAPDAAALAALERGVDLGDYVSRPCRARFVTPPDTLWPRTPPI 119

Query: 181 --TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
                    W+ + + EGKNR+++++     +   RLIR+  G   +    L  G TRE+
Sbjct: 120 RYRAAIPTTWIELEIAEGKNRQVRRMTAAIGFPTLRLIRVGIGALDVFALGLAPGETREL 179

Query: 237 SKK 239
             +
Sbjct: 180 PPR 182


>gi|254181510|ref|ZP_04888107.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1655]
 gi|184212048|gb|EDU09091.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1655]
          Length = 192

 Score = 71.4 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 41/176 (23%), Positives = 69/176 (39%), Gaps = 17/176 (9%)

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
                T        +            V   GRLD ++EGLLLLT+DG L   +  P  +
Sbjct: 7   NKPFGTICQFSVHETRASLGDWVKTPGVYPAGRLDADSEGLLLLTDDGALQAKIAEPRHK 66

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---------------S 185
            ++ Y  +  G  D   L  L++G+ +        +    T  G                
Sbjct: 67  LVKRYWAQVEGAPDAAALAALERGVDLGDYVSRPCRARFITPPGALWPRNPPIRHRAAIP 126

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKK 239
            AW+ + + EGKNR+++++     +   RL+R+  G   +    L  G TRE+  +
Sbjct: 127 TAWIELEIAEGKNRQVRRMTAAVGFPTLRLVRVGIGALDVFALGLAPGETRELPPR 182


>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 = 71.4 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 31/261 (11%), Positives = 75/261 (28%), Gaps = 49/261 (18%)

Query: 1   MKDKNIVQENF---------TPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERA 50
           M+D+  +  N            +R+ + +  A    SR    ++I +  V+VN  ++E+ 
Sbjct: 1   MRDEIKMNSNQIELFALPLFNKERLDQFLLNATKEESRSYYSKLIKEGLVRVNDKIVEKP 60

Query: 51  AVNVMSTDHIEVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTV 97
           +  V   D I +   P                 E   + + +K   +V      + R+T+
Sbjct: 61  SFIVKPYDKITLFLKPKEPLYIEYDKLNITVLYEDDYIIVINKERNMVVHPGPGNFRNTI 120

Query: 98  FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
            + L +  ++     +        L     G L         + L         +     
Sbjct: 121 LNALINSINKDEFTDQERPGIVHRLDKETTGVLIIAKSEKIMRKLSEQFKNRQVKKTYLA 180

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSN-------------------------AWVTVG 192
           L         +G     ++ +   ++                            + + V 
Sbjct: 181 LVY-GDVNYKEGFISMPIKRSKIHRQKMEVNLSGKVAFTEYSVINKGIFEKQIVSLLKVN 239

Query: 193 LREGKNREIKKVFEFFNWKVN 213
           +  G+  +I+    +    + 
Sbjct: 240 IFTGRTHQIRVHMSYIGHPIV 260


>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 = 71.0 bits (172), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 27/235 (11%), Positives = 58/235 (24%), Gaps = 36/235 (15%)

Query: 12  TPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------- 63
             +R+ K +A      SR +V++ I    + VNG  ++     V   D I V        
Sbjct: 14  KNERIDKFVASVNHEWSRTQVQQWIKDGVITVNGKTVK-GNYKVKENDEITVTVPEPEEL 72

Query: 64  -------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
                   + +   +   L +      +V         + V   +          G +  
Sbjct: 73  DIRAEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMYHCTDLSGINGVMRP 132

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-------------------- 156
                +     G L       + + L    V                             
Sbjct: 133 GIVHRIDKDTSGLLMVAKNDMAHESLVNQLVEKTVTRRYQAIVHGVIPHDKGTIDAPIAR 192

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                +   V +   +      +  +      V   L  G+  +I+   ++  + 
Sbjct: 193 DKKDRQSMAVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYP 247


>gi|237805469|ref|ZP_04592173.1| S4 domain-containing protein [Pseudomonas syringae pv. oryzae
          str. 1_6]
 gi|331026576|gb|EGI06631.1| S4 domain-containing protein [Pseudomonas syringae pv. oryzae
          str. 1_6]
          Length = 114

 Score = 71.0 bits (172), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 21/85 (24%), Positives = 31/85 (36%), Gaps = 1/85 (1%)

Query: 11 FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            P R+SK +      SRRE E  I    V V+G+++E     V  T  IE+       +
Sbjct: 14 TDPIRLSKRLIELVGCSRREAELFIEGGWVTVDGVVIEEPHFKVS-TQKIELSPDAKADS 72

Query: 71 ERTRLWLYHKPIGLVTTHSDPDGRS 95
                + HKP       +      
Sbjct: 73 PEPVTIILHKPASASAESALQMITP 97


>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 = 71.0 bits (172), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 22/248 (8%), Positives = 65/248 (26%), Gaps = 42/248 (16%)

Query: 7   VQENFTPQRVSKVIARAGI-----ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           + +    +R+ K ++          SR  ++++I    V VN     +    +   D I+
Sbjct: 14  IDKTQEGERIDKFLSDMLSSDERTYSRSYIQKLIEAGNVCVNDKN-TKTGYKISYNDLIK 72

Query: 62  V------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           V            + +P  +   +   + +      +V   +     + V   +    + 
Sbjct: 73  VMIPYLEDINIVAENIPLDIVYEDDDIILVNKPKGMVVHPSAGHYTGTLVNALMYHCSNN 132

Query: 108 VISVGRLDIN----------------------TEGLLLLTNDGGLARVLELPSTQWLRVY 145
           +  +  +                            L     +  + R          +  
Sbjct: 133 LSGINGVMRPGIVHRIDKDTTGIIVACKNDAAHISLSEQLKEHNITRYYYAICHNCFKEK 192

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                  + +  +   K  I  +          +     + A++   L  G+  +I+   
Sbjct: 193 EGTVDAPIGRHPVERKKMAINYKNGKKAVTHYEVLENFRNFAYIKCKLETGRTHQIRVHM 252

Query: 206 EFFNWKVN 213
              +  + 
Sbjct: 253 ASISHPLL 260


>gi|262384889|ref|ZP_06078021.1| pseudouridine synthase family 1 protein [Bacteroides sp. 2_1_33B]
 gi|262293605|gb|EEY81541.1| pseudouridine synthase family 1 protein [Bacteroides sp. 2_1_33B]
          Length = 189

 Score = 71.0 bits (172), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 23/62 (37%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R++K+I+ AG+ SRRE +  I  +RV VNG         V + D + VDG  L   +  
Sbjct: 3  IRLNKLISEAGVCSRREADNFIEMERVTVNGKQPHV-GQKVTAEDIVLVDGERLNVEKYI 61

Query: 74 RL 75
          RL
Sbjct: 62 RL 63


>gi|53718535|ref|YP_107521.1| putative pseudouridine synthase [Burkholderia pseudomallei K96243]
 gi|67640945|ref|ZP_00439735.1| ribosomal large subunit pseudouridine synthase E [Burkholderia
           mallei GB8 horse 4]
 gi|121599756|ref|YP_992031.1| RNA pseudouridine synthase family protein [Burkholderia mallei
           SAVP1]
 gi|126439533|ref|YP_001058005.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 668]
 gi|126449425|ref|YP_001079713.1| RNA pseudouridine synthase family protein [Burkholderia mallei NCTC
           10247]
 gi|126453501|ref|YP_001065239.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1106a]
 gi|134281043|ref|ZP_01767752.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 305]
 gi|166998439|ref|ZP_02264299.1| RNA pseudouridine synthase family protein [Burkholderia mallei
           PRL-20]
 gi|167718438|ref|ZP_02401674.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei DM98]
 gi|167737487|ref|ZP_02410261.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 14]
 gi|167814605|ref|ZP_02446285.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 91]
 gi|167823075|ref|ZP_02454546.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 9]
 gi|167844638|ref|ZP_02470146.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei B7210]
 gi|167893169|ref|ZP_02480571.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 7894]
 gi|167901623|ref|ZP_02488828.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei NCTC 13177]
 gi|167909870|ref|ZP_02496961.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 112]
 gi|167917895|ref|ZP_02504986.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei BCC215]
 gi|217420029|ref|ZP_03451535.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 576]
 gi|226193625|ref|ZP_03789229.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei Pakistan 9]
 gi|237811156|ref|YP_002895607.1| ribosomal large subunit pseudouridine synthase E [Burkholderia
           pseudomallei MSHR346]
 gi|242314224|ref|ZP_04813240.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1106b]
 gi|254176988|ref|ZP_04883645.1| RNA pseudouridine synthase family protein [Burkholderia mallei ATCC
           10399]
 gi|254187468|ref|ZP_04893980.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei Pasteur 52237]
 gi|254196524|ref|ZP_04902948.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei S13]
 gi|254261731|ref|ZP_04952785.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1710a]
 gi|254296413|ref|ZP_04963870.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 406e]
 gi|254298237|ref|ZP_04965689.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 406e]
 gi|254359979|ref|ZP_04976249.1| RNA pseudouridine synthase family protein [Burkholderia mallei
           2002721280]
 gi|52208949|emb|CAH34888.1| putative pseudouridine synthase [Burkholderia pseudomallei K96243]
 gi|121228566|gb|ABM51084.1| RNA pseudouridine synthase family protein [Burkholderia mallei
           SAVP1]
 gi|126219026|gb|ABN82532.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 668]
 gi|126227143|gb|ABN90683.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1106a]
 gi|126242295|gb|ABO05388.1| RNA pseudouridine synthase family protein [Burkholderia mallei NCTC
           10247]
 gi|134247349|gb|EBA47434.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 305]
 gi|148029219|gb|EDK87124.1| RNA pseudouridine synthase family protein [Burkholderia mallei
           2002721280]
 gi|157805681|gb|EDO82851.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 406e]
 gi|157808309|gb|EDO85479.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 406e]
 gi|157935148|gb|EDO90818.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei Pasteur 52237]
 gi|160698029|gb|EDP87999.1| RNA pseudouridine synthase family protein [Burkholderia mallei ATCC
           10399]
 gi|169653267|gb|EDS85960.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei S13]
 gi|217397333|gb|EEC37349.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 576]
 gi|225934328|gb|EEH30311.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei Pakistan 9]
 gi|237505123|gb|ACQ97441.1| ribosomal large subunit pseudouridine synthase E [Burkholderia
           pseudomallei MSHR346]
 gi|238521769|gb|EEP85218.1| ribosomal large subunit pseudouridine synthase E [Burkholderia
           mallei GB8 horse 4]
 gi|242137463|gb|EES23865.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1106b]
 gi|243065495|gb|EES47681.1| RNA pseudouridine synthase family protein [Burkholderia mallei
           PRL-20]
 gi|254220420|gb|EET09804.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 1710a]
          Length = 192

 Score = 71.0 bits (172), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 41/176 (23%), Positives = 69/176 (39%), Gaps = 17/176 (9%)

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
                T        +            V   GRLD ++EGLLLLT+DG L   +  P  +
Sbjct: 7   NKPFGTICQFSAHETRASLGDWVKTPGVYPAGRLDADSEGLLLLTDDGALQAKIAEPRHK 66

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---------------S 185
            ++ Y  +  G  D   L  L++G+ +        +    T  G                
Sbjct: 67  LVKRYWAQVEGAPDAAALAALERGVDLGDYVSRPCRARFITPPGALWPRNPPIRHRAAIP 126

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKK 239
            AW+ + + EGKNR+++++     +   RL+R+  G   +    L  G TRE+  +
Sbjct: 127 TAWIELEIAEGKNRQVRRMTAAVGFPTLRLVRVGIGALDVFALGLAPGETRELPPR 182


>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 = 71.0 bits (172), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 63/244 (25%), Gaps = 36/244 (14%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           NI  +  T  RV K++       SR +++  I    V  N  +++     V   DHI V 
Sbjct: 7   NITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKS-NYKVKLNDHIVVT 65

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   +     +Y     +V         + V   +  I     
Sbjct: 66  EKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMYQIKDLSG 125

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPST------------QWLRVYRVRFHGQVDQ-- 155
             G +       + +   G L       +             +   +  V  +   D   
Sbjct: 126 INGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYIALVHGNIPHDYGT 185

Query: 156 ------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                    N  +   V+           +         V   L  G+  +I+   ++  
Sbjct: 186 IDAPIGRNKNDRQSMAVVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIRVHMKYIG 245

Query: 210 WKVN 213
           + + 
Sbjct: 246 FPLV 249


>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 = 71.0 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 44/248 (17%), Positives = 82/248 (33%), Gaps = 37/248 (14%)

Query: 1   MKDKNIVQENFTPQ--RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           MK+K I++     Q  R+ K++A      SR +++++I Q RV VNG  +  A   V   
Sbjct: 5   MKNKQILESTIVNQSGRLDKILATDFSAFSRNQIKKLIDQDRVIVNGKPV-LAKYLVQDG 63

Query: 58  DHIEVDGVPLRKAE--------------RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           DH+ +   P++K E                 + +      +V   +     + V   L  
Sbjct: 64  DHVVIKVPPVKKTELLPEKIPLDIVYEDDDLIVVNKPQGMVVHPSAGHSEHTLVNALLSH 123

Query: 104 IF-------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
                     R   V R+D +T GLL++  +      L L         +       +  
Sbjct: 124 APLSTINGEFRPGIVHRIDKDTSGLLMVAKNNFAHEHLSLDLKSHKTGRKYLAIVHGNFS 183

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV------------GLREGKNREIKKV 204
           +     K  + +       Q  +   + +     V             L  G+  +I+  
Sbjct: 184 EKRGTIKAPIDRDPKNRQKQAVVANGREAITHFKVLESFSNYSLIEAVLETGRTHQIRVH 243

Query: 205 FEFFNWKV 212
             +    V
Sbjct: 244 MAYIGHPV 251


>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 = 71.0 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 40/239 (16%), Positives = 80/239 (33%), Gaps = 38/239 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERM--------IAQQRVKVNGILLERAAVNVMST 57
           IV EN    R+ K +       R++++ M        I + +V VNG  ++  +  +   
Sbjct: 2   IVNENNYYSRLDKFL-------RKQLQNMPLSAIYKIIRKGKVLVNGKRVKEPSFRLEIG 54

Query: 58  DHIEV-----------DGVPLRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           D IE+           +   +          E   L + +KP G+          +T+ +
Sbjct: 55  DEIEIKEETTKYNREKNNQIIPIKMDFEILYEDENLLIINKPAGIPIHPGKGTHIATLIE 114

Query: 100 NLPS----IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
            L             V RLD +T G+ ++  +   AR L    +              + 
Sbjct: 115 GLMYYGKEHNFTPYLVHRLDKHTSGVFVVAKNVNTARELNEIISSRAVEKVYTTLCVGEM 174

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQK-GSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            K  ++K  +  +       +        G  + + V ++ G+  +I+K        V 
Sbjct: 175 KKSEVIKIPLDGKNAVTIYEKQKQFKSGLGYFSLLRVQIKTGRKHQIRKHLSLIGHPVI 233


>gi|330883599|gb|EGH17748.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. glycinea str. race 4]
          Length = 75

 Score = 71.0 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 16/64 (25%), Positives = 31/64 (48%)

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                 +    +W+ + ++EG NR+++++         RL+R+  G + L  L  G  RE
Sbjct: 11  PPVRFRKSVPTSWLELVIKEGCNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLDQGQYRE 70

Query: 236 VSKK 239
           V+ K
Sbjct: 71  VAAK 74


>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 = 71.0 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 38/241 (15%), Positives = 70/241 (29%), Gaps = 36/241 (14%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E    +R+ K +A      SR +V++ I    V VNG  ++     V   D I V  
Sbjct: 8   TVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDAVVTVNGKSVK-GNYKVKGNDEITVTI 66

Query: 63  ------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------ 104
                 D  P      +   +   L +      +V         + V   +         
Sbjct: 67  PEPEELDIQPEDMNLEVYYEDADVLVVNKPRGMVVHPAPGHTKGTLVNGLMHHCTDLSGI 126

Query: 105 --FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
               R   V R+D +T GLL++  +      L     +     R +            + 
Sbjct: 127 NGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVEKTVTRRYKAIVHGVIPHDKGII 186

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNREIKKVFEFFNW 210
              + +           +  K +     V        L E     G+  +I+   ++  +
Sbjct: 187 DAPIGRDKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGY 246

Query: 211 K 211
            
Sbjct: 247 P 247


>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 = 71.0 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 35/244 (14%), Positives = 67/244 (27%), Gaps = 42/244 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            V E    +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V
Sbjct: 8   TVAEEQKNERIDKFVA--GINNEWSRTQVQQWIKDDVVTVNGKAVK-GNYKVKENDEITV 64

Query: 63  --------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                   D  P      +   +   L +      +V         + V   +       
Sbjct: 65  TIPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRV 147
              G +       +     G L       + + L                        + 
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKG 184

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                + +DK    +   V +   +      +  +      V   L  G+  +I+   ++
Sbjct: 185 TIDAPIARDKKER-QSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKY 243

Query: 208 FNWK 211
             + 
Sbjct: 244 IGYP 247


>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 = 71.0 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 44/248 (17%), Positives = 82/248 (33%), Gaps = 37/248 (14%)

Query: 1   MKDKNIVQENFTPQ--RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           MK+K I++     Q  R+ K++A      SR +++++I Q RV VNG  +  A   V   
Sbjct: 1   MKNKQILESTIVNQSGRLDKILATDFSAFSRNQIKKLIDQDRVIVNGKPV-LAKYLVQDG 59

Query: 58  DHIEVDGVPLRKAE--------------RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           DH+ +   P++K E                 + +      +V   +     + V   L  
Sbjct: 60  DHVVIKVPPVKKTELLPEKIPLDIVYEDDDLIVVNKPQGMVVHPSAGHSEHTLVNALLSH 119

Query: 104 IF-------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
                     R   V R+D +T GLL++  +      L L         +       +  
Sbjct: 120 APLSTINGEFRPGIVHRIDKDTSGLLMVAKNNFAHEHLSLDLKSHKTGRKYLAIVHGNFS 179

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV------------GLREGKNREIKKV 204
           +     K  + +       Q  +   + +     V             L  G+  +I+  
Sbjct: 180 EKRGTIKAPIDRDPKNRQKQAVVANGREAITHFKVLESFSNYSLIEAVLETGRTHQIRVH 239

Query: 205 FEFFNWKV 212
             +    V
Sbjct: 240 MAYIGHPV 247


>gi|255066323|ref|ZP_05318178.1| ribosomal large subunit pseudouridine synthase B [Neisseria sicca
           ATCC 29256]
 gi|255049533|gb|EET44997.1| ribosomal large subunit pseudouridine synthase B [Neisseria sicca
           ATCC 29256]
          Length = 106

 Score = 71.0 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 22/90 (24%), Positives = 48/90 (53%), Gaps = 1/90 (1%)

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           ++G++++       ++     +G+N W  V ++EG+NRE++++FE     V+RL+R+ +G
Sbjct: 6   EEGVMLEDGLAKVERIYEQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFG 65

Query: 222 PFQLGT-LLAGSTREVSKKILREQLGPHLL 250
           P  L   L  G   E++   +   +    +
Sbjct: 66  PIGLPNRLKRGQFYELNPAEVANIIKWADM 95


>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 = 71.0 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 38/254 (14%), Positives = 80/254 (31%), Gaps = 42/254 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K+         R+ + +++     SR E+ + I   +VKVN  +++  +  +   D 
Sbjct: 1   MLKKSYEYHGDQSLRLDRYLSQRLDSYSRSEIAQWIKTGQVKVNKQVVK-PSYRLNPMDK 59

Query: 60  IE----------VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I           ++G  L      E   L + +K  G+V   S      T+ + L +   
Sbjct: 60  ISLAIEEEQKLPIEGESLDLDIVYEDKDLLVINKAKGMVVHPSKGHLSGTLVNALLAYAQ 119

Query: 107 RVISV-------------GRLDINTEGLLLLTNDGGLARVLELP-------------STQ 140
           +                  RLD +T GL+++       + L                   
Sbjct: 120 KNHFTLSDLGDYYRPGIVHRLDKDTSGLMVVAKSDPAYQALLEDLANHQLDRKYLALIYG 179

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
            L   +      + +   + ++      G            Q  + A + + L  G+  +
Sbjct: 180 HLPDKQGTIDIPLRRHPKDRMRYVGDPLGKEA-VTHFKQIAQVENYALLRLSLETGRTHQ 238

Query: 201 IKKVFEFFNWKVNR 214
           I+    + +  V  
Sbjct: 239 IRAHLAYLDHPVVD 252


>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 = 70.6 bits (171), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 39/247 (15%), Positives = 69/247 (27%), Gaps = 38/247 (15%)

Query: 4   KNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI- 60
           K +V   ++  R+ K +A       SR  ++++I + +V VNG L  +A+  V   + I 
Sbjct: 6   KVVVNSEYSGLRLDKFLAEQEELELSRSFIKKLIEEGKVTVNG-LHRKASYKVRGGEIIA 64

Query: 61  ---------EVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                     V    +       +   + +  K   +V         + V   L    + 
Sbjct: 65  VLLPPPRELSVKPEEIPLDIVYEDEDLVVVNKKAGMVVHPAEGNWDGTLVNALLYHCQNL 124

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK--LNLLKKGI 165
               G L       L     G L       + Q L           +        LK   
Sbjct: 125 SGIGGVLRPGIVHRLDKDTSGLLVVAKNDLAHQSLAEQIKEKKAVREYWTIVHGYLKNKE 184

Query: 166 VIQGICY----------------GDMQVTLDTQKGSNAWVTVG---LREGKNREIKKVFE 206
            I  +                     Q      +  N   T+    L  G+  +I+  F 
Sbjct: 185 GIIDLPIGRHPRDRQKMAVVSNGKTAQTVYKVLEEFNKGFTLIQAKLLTGRTHQIRVHFS 244

Query: 207 FFNWKVN 213
           +    V 
Sbjct: 245 YLGHPVL 251


>gi|256842186|ref|ZP_05547690.1| pseudouridine synthase family 1 protein [Parabacteroides sp. D13]
 gi|256736070|gb|EEU49400.1| pseudouridine synthase family 1 protein [Parabacteroides sp. D13]
          Length = 189

 Score = 70.6 bits (171), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 23/62 (37%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R++K+I+ AG+ SRRE +  I  +RV VNG         V + D + VDG  L   +  
Sbjct: 3  IRLNKLISEAGVCSRREADNFIEMERVTVNGKQPHV-GQKVTAEDLVLVDGERLNVEKYI 61

Query: 74 RL 75
          RL
Sbjct: 62 RL 63


>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 = 70.6 bits (171), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 31/245 (12%), Positives = 67/245 (27%), Gaps = 38/245 (15%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V   +   R+ K ++     A+R  +E++I    VKVN  ++ +    +   + IEV   
Sbjct: 17  VNSEYEGMRLDKYLSEQIEEATRSYLEKLIDNNFVKVNSKIINKNGRKLKLGEKIEVLIP 76

Query: 63  -----DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                D  P      +       + +      +V         + V   L    +     
Sbjct: 77  EEENIDIEPENIPLNIVYENDDFILINKSYGMVVHPAYGNYTGTLVNALLYYTNNLSSVN 136

Query: 112 GRLDINTE-----------------------GLLLLTNDGGLARVLELPSTQWLRVYRVR 148
           G +                              + +        +  +           R
Sbjct: 137 GNIRPGIIHRLDKDTSGLILVAKNNYAHAKLASMFIDKTIHKTYLCIVKGNFSEENLSGR 196

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +D  +  K  IV +          +  Q    + V V +  G+  +I+   +  
Sbjct: 197 IENLIGRDSKDRKKMTIVKENGKIAISNYKVVEQVEGYSLVEVAIETGRTHQIRVHMKSI 256

Query: 209 NWKVN 213
           N  + 
Sbjct: 257 NHVIL 261


>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 = 70.6 bits (171), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 63/244 (25%), Gaps = 36/244 (14%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           NI  +  T  RV K++       SR +++  I    V  N  +++     V   DHI V 
Sbjct: 7   NITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKS-NYKVKLNDHIVVT 65

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   +     +Y     +V         + V   +  I     
Sbjct: 66  EKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMYQIKDLSG 125

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPST------------QWLRVYRVRFHGQVDQ-- 155
             G +       + +   G L       +             +   +  V  +   D   
Sbjct: 126 INGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYIALVHGNIPHDYGT 185

Query: 156 ------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                    N  +   V+           +         V   L  G+  +I+   ++  
Sbjct: 186 IDAPIGRNKNDRQSMAVVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIRVHMKYIG 245

Query: 210 WKVN 213
           + + 
Sbjct: 246 FPLV 249


>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 = 70.6 bits (171), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 32/241 (13%), Positives = 64/241 (26%), Gaps = 36/241 (14%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--- 61
            ++E    +R+ KVIA      SR +V++ + +  V VNG  ++         D +    
Sbjct: 7   TIEEQHDGERIDKVIAELNEQWSRSQVQQWLKEGHVLVNGKAVK-PNYKCHVDDEVVISI 65

Query: 62  -------VDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                  V   P+       +   L +      +V         + V   L         
Sbjct: 66  PSPEPLDVAPEPIPLDIYYEDADVLVVNKPRGMVVHPAPGHMHGTLVNALLAHCQDLSGI 125

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQ------------WLRVYRVRFHGQVDQ--- 155
            G L       +     G L       + +               V  V      D    
Sbjct: 126 NGVLRPGIVHRIDKDTSGLLMVAKNDLAHESLVNQLVNKTVTRKYVAIVHGVIPHDYGTI 185

Query: 156 -----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      +   V++          +  +     +V   L  G+  +I+   ++  +
Sbjct: 186 DAPIGRDPRDRQSMAVVENGKEAVTHFRVLERFEHYTFVECQLETGRTHQIRVHMKYIGY 245

Query: 211 K 211
            
Sbjct: 246 P 246


>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 = 70.6 bits (171), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 33/260 (12%), Positives = 69/260 (26%), Gaps = 50/260 (19%)

Query: 15  RVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           R+ K +       R +++        ++I + +V VNG  ++  + ++   D +E     
Sbjct: 13  RLDKFL-------RNQLKDVPLSVIYKLIRKGKVYVNGKRVKDPSFDLEEGDVVEFRYVN 65

Query: 63  -----------DGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
                      D  P+        E     + +KP  +          +T+ + L     
Sbjct: 66  LENLPKRSEKKDLTPVPMKLDVLYEGKHYLVLNKPPNIAIHPGKGVHVATLIEGLLHYGQ 125

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
                  L    +            R      T+  +   +                 I 
Sbjct: 126 EKGFSPFLVHRLDKDTSGLLVVAKDREAARILTELFKDRNIEKEYVTLVRGTPENNMKIT 185

Query: 167 I-QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI--------- 216
           I         ++         + + V +  G+  +I++      + V             
Sbjct: 186 IPLDGQEAISEIVSVKSLRDVSLLRVKIHTGRKHQIRRHLSQIGFPVVGDDTYGDRHFNR 245

Query: 217 --RISYGPFQLGTLLAGSTR 234
             R  YG   L  L   S R
Sbjct: 246 EFRKRYG---LKRLFLHSYR 262


>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 = 70.6 bits (171), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 32/247 (12%), Positives = 65/247 (26%), Gaps = 40/247 (16%)

Query: 6   IVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           +V      QRV KV+A  G+   SR  +++++A   V +NG +L + +V V   D + V+
Sbjct: 46  MVGTEHHGQRVDKVLA-LGVSEFSRSYLQQLLADGAVTLNGKVLLKPSVKVAVGDRLRVE 104

Query: 64  GVP---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---- 104
             P               +   +   L +      +V         + +   L       
Sbjct: 105 MRPTQQSMAFQPETMDLQVVYEDEDLLVINKPAGLVVHPAPGNWTGTLLNGLLARDEKAR 164

Query: 105 -----------------FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
                               V            ++           L        +   V
Sbjct: 165 QVPRAGIVHRLDKDTSGLMVVARNRSTMDALIKMIAAREVSRQYLALAHKQWGSRKRREV 224

Query: 148 RFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                 D      +    + +           L     +++ V   L  G+  +I+    
Sbjct: 225 DAPIGRDPRNRLRMAVVDLNLHPGKQARTDFDLLDGDAAHSLVRCTLHTGRTHQIRVHMA 284

Query: 207 FFNWKVN 213
                + 
Sbjct: 285 SLGHPLI 291


>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 = 70.6 bits (171), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 30/237 (12%), Positives = 58/237 (24%), Gaps = 35/237 (14%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
                R+ K +A     SR +    I +  V VNG  ++ A   V   D +         
Sbjct: 6   KEAGVRLDKALADLTELSRSQANDEIKKGTVLVNGKAVK-AKYAVKVGDVVTYEVPKEEV 64

Query: 63  -----DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                + +PL     +     +      +V         + V   +  I       G + 
Sbjct: 65  LEYTAENIPLDIIYEDDDVAVVNKPQGMVVHPSVGHMSGTLVNALMYHIKDLSSINGVIR 124

Query: 116 INTEGLLLLTNDGGLARVLELPSTQ------------WLRVYRVRFHGQVDQDKLNLLKK 163
                 +     G L       +                 V  V  +   D+  +     
Sbjct: 125 PGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHGNIPNDRGVIEAPIG 184

Query: 164 GIVIQGICY------GDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                                  +  + G+   V + L  G+  +I+    +    V
Sbjct: 185 RSEKDRKKQAVTAKGKPAVTHFKVLERFGNYTLVELTLETGRTHQIRVHMAYIGHPV 241


>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 = 70.6 bits (171), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 64/244 (26%), Gaps = 36/244 (14%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           NI  +  T  RV K++       SR +++  I    V  N  +++     V   DHI V 
Sbjct: 7   NITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKS-NYKVKLNDHIVVT 65

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   +     +Y     +V         + V   +  I +   
Sbjct: 66  EKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMYQIKNLSG 125

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPST------------QWLRVYRVRFHGQVDQ-- 155
             G +       + +   G L       +             +   +  V  +   D   
Sbjct: 126 INGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYIALVHGNIPHDYGT 185

Query: 156 ------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                    N  +   V+           +         V   L  G+  +I+   ++  
Sbjct: 186 IDAPIGRNKNDRQSMAVVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIRVHMKYIG 245

Query: 210 WKVN 213
           + + 
Sbjct: 246 FPLV 249


>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 = 70.6 bits (171), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 64/244 (26%), Gaps = 36/244 (14%)

Query: 5   NIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           NI  +  T  RV K++       SR +++  I    V  N  +++     V   DHI V 
Sbjct: 7   NITDKEQTGMRVDKLLPELNNDWSRNQIQDWIKAGLVVANDKVVKS-NYKVKLNDHIVVT 65

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   +     +Y     +V         + V   +  I +   
Sbjct: 66  EKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMYQIKNLSG 125

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPST------------QWLRVYRVRFHGQVDQ-- 155
             G +       + +   G L       +             +   +  V  +   D   
Sbjct: 126 INGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYIALVHGNIPHDYGT 185

Query: 156 ------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                    N  +   V+           +         V   L  G+  +I+   ++  
Sbjct: 186 IDAPIGRNKNDRQSMAVVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIRVHMKYIG 245

Query: 210 WKVN 213
           + + 
Sbjct: 246 FPLV 249


>gi|186475332|ref|YP_001856802.1| pseudouridine synthase [Burkholderia phymatum STM815]
 gi|184191791|gb|ACC69756.1| pseudouridine synthase [Burkholderia phymatum STM815]
          Length = 189

 Score = 70.6 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 35/176 (19%), Positives = 64/176 (36%), Gaps = 17/176 (9%)

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
                T        +            V   GRLD ++EGLLLLT+DG L   +  P  +
Sbjct: 7   NKPFGTICQFSPHETRASLADWVKVPGVYPAGRLDSDSEGLLLLTDDGTLQARIAEPRHK 66

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---------------S 185
            ++ Y  +  G   +  L  L +G+ +        +                        
Sbjct: 67  LVKRYWAQVEGAPTEQHLEALARGVDLGDYVTRPCRAGFVEPGQALWDRTPPIRYRAAIP 126

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKK 239
             W+ + + EGKNR+++++     +   RL+R+  G   +    L  G +  +S +
Sbjct: 127 TTWIELSITEGKNRQVRRMTAAVGFPTLRLVRVGVGALDIFSLGLQPGESIGLSPR 182


>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 = 70.6 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 64/244 (26%), Gaps = 36/244 (14%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           NI  +  T  RV K++       SR +++  I    V  N  +++     V   DHI V 
Sbjct: 7   NITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKS-NYKVKLNDHIVVT 65

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   +     +Y     +V         + V   +  I +   
Sbjct: 66  EKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMYQIKNLSG 125

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPST------------QWLRVYRVRFHGQVDQ-- 155
             G +       + +   G L       +             +   +  V  +   D   
Sbjct: 126 INGEIRPGIVHRIDMDTSGLLMVAKNDIAHRELVEQLMDKSVKRKYIALVHGNIPHDYGT 185

Query: 156 ------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                    N  +   V+           +         V   L  G+  +I+   ++  
Sbjct: 186 IDAPIGRNKNDRQSMAVVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIRVHMKYIG 245

Query: 210 WKVN 213
           + + 
Sbjct: 246 FPLV 249


>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 = 70.6 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 29/237 (12%), Positives = 60/237 (25%), Gaps = 35/237 (14%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
                R+ K +A     SR +    I +  V VNG  ++ A   V   D +         
Sbjct: 6   KEAGIRLDKALADLTELSRSQANDEIKKGTVLVNGKAVK-AKYAVKVGDVVTYEVPKEEV 64

Query: 63  -----DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                + +PL     +     +      +V         + V   +  I       G + 
Sbjct: 65  LEYTAENIPLDIIYEDADVAVVNKPQGMVVHPSVGHTSGTLVNALMYHIKDLSSINGVIR 124

Query: 116 INTEGL---------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
                          ++  ND     +      +      V        +   +++  I 
Sbjct: 125 PGIVHRIDKDTSGLLMIAKNDTAHNALAAELKDKKSLRKYVAIVHGTIPNDRGVIEAPIG 184

Query: 167 IQGI---------CYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                                  +  + G+   V + L  G+  +I+    +    V
Sbjct: 185 RSEKDRKKQAVTAKGKPALTHFKVLERFGNYTLVELTLETGRTHQIRVHMAYIGHPV 241


>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 = 70.6 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 63/244 (25%), Gaps = 36/244 (14%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           NI  +  T  RV K++       SR +++  I    V  N  +++     V   DHI V 
Sbjct: 7   NITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKS-NYKVKLNDHIVVT 65

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   +     +Y     +V         + V   +  I     
Sbjct: 66  EKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMYQIKDLSG 125

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPST------------QWLRVYRVRFHGQVDQ-- 155
             G +       + +   G L       +             +   +  V  +   D   
Sbjct: 126 INGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYIALVHGNIPHDYGT 185

Query: 156 ------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                    N  +   V+           +         V   L  G+  +I+   ++  
Sbjct: 186 IDAPIGRNKNDRQSMAVVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIRVHMKYIG 245

Query: 210 WKVN 213
           + + 
Sbjct: 246 FPLV 249


>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 = 70.6 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 31/245 (12%), Positives = 69/245 (28%), Gaps = 37/245 (15%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +    +R+   +  A G  SR  V+++I    V V+   +++ +  + +   I    
Sbjct: 7   VVDQEAQGKRLDLFLTEAYGEFSRSYVQKLIEDGFVLVDDKEIKKPSRRLKAGQKITFYI 66

Query: 63  ----------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                     + +P  +   +   L L      +V         + V   L  I      
Sbjct: 67  PQVEPLEVLPEDIPFDVVYEDEDILVLIKPCGLVVHPSPGYSSGTLVNALLFRIKELSGI 126

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-------------- 156
            G+        L     G +       + + L    ++                      
Sbjct: 127 GGKERPGIVHRLDKNTAGLMVVAKSDKAHRSLVEEFMQRRVLKRYHALVSGLLREDSGTV 186

Query: 157 ------KLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTVGLREGKNREIKKVFEFF 208
                      KK  V++       +  +    +K    ++ V +  G+  +I+    F 
Sbjct: 187 EKSIGRHPVDRKKFSVVEDGKPAKTEYEVIKRFEKHRITFLDVRIHTGRTHQIRVHLSFI 246

Query: 209 NWKVN 213
              V 
Sbjct: 247 GHPVL 251


>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 = 70.6 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 30/237 (12%), Positives = 59/237 (24%), Gaps = 35/237 (14%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
                R+ K +A     SR +    I +  V VNG  ++ A   V   D +         
Sbjct: 6   KEAGVRLDKALADLTELSRSQANDEIKKGTVLVNGKAVK-AKYAVKVGDVVTYEVPKEEV 64

Query: 63  -----DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                + +PL     +     +      +V         + V   +  I       G + 
Sbjct: 65  LEYTAENIPLDIIYEDDDVAVVNKPQGMVVHPSVGHTSGTLVNALMYHIKDLSSINGVIR 124

Query: 116 INTEGLLLLTNDGGLARVLELPSTQ------------WLRVYRVRFHGQVDQDKLNLLKK 163
                 +     G L       +                 V  V  +   D+  +     
Sbjct: 125 PGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHGNIPNDRGVIEAPIG 184

Query: 164 GIVIQGICY------GDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                                  +  + G+   V + L  G+  +I+    +  + V
Sbjct: 185 RSEKDRKKQAVTAKGKPAVTHFKVLERFGNYTLVELTLETGRTHQIRVHMAYIGYPV 241


>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 = 70.6 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 64/244 (26%), Gaps = 36/244 (14%)

Query: 5   NIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           NI  +  T  RV K++       SR +++  I    V  N  +++     V   DHI V 
Sbjct: 7   NITDKEQTGMRVDKLLPELNNDWSRNQIQDWIKAGLVVANDKVVKS-NYKVKLNDHIVVT 65

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   +     +Y     +V         + V   +  I +   
Sbjct: 66  EKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMYQIKNLSG 125

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPST------------QWLRVYRVRFHGQVDQ-- 155
             G +       + +   G L       +             +   +  V  +   D   
Sbjct: 126 INGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYIALVHGNIPHDYGT 185

Query: 156 ------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                    N  +   V+           +         V   L  G+  +I+   ++  
Sbjct: 186 IDAPIGRNKNDRQSMAVVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIRVHMKYIG 245

Query: 210 WKVN 213
           + + 
Sbjct: 246 FPLV 249


>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 = 70.6 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 31/240 (12%), Positives = 63/240 (26%), Gaps = 40/240 (16%)

Query: 13  PQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP---- 66
            QRV KV+A  G+   SR  +++++A   V +NG +L + +V V   D + V+  P    
Sbjct: 53  GQRVDKVLA-LGVSEFSRSYLQQLLADGAVTLNGKVLLKPSVKVAVGDRLRVEMRPTQQS 111

Query: 67  -----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI----------- 104
                      +   +   L +      +V         + +   L              
Sbjct: 112 MAFQPEAMDLQVVYEDEDLLVINKPAGLVVHPAPGNWTGTLLNGLLARDEKARQVPRAGI 171

Query: 105 ----------FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD 154
                        V            ++           L        +   V      D
Sbjct: 172 VHRLDKDTSGLMVVARNRSTMDALIKMIAAREVSRQYLALAHKQWGSRKRREVDAPIGRD 231

Query: 155 QDKLNLL-KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 +    + +           L     +++ V   L  G+  +I+         + 
Sbjct: 232 PRNRLRMAVVDLNLHPGKQARTDFDLLDGDAAHSLVRCTLHTGRTHQIRVHMASLGHPLI 291


>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 = 70.6 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 35/244 (14%), Positives = 67/244 (27%), Gaps = 42/244 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            V E    +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V
Sbjct: 8   TVAEEQKNERIDKFVA--GINNEWSRTQVQQWIKDDVVTVNGKAVK-GNYKVRENDEITV 64

Query: 63  --------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                   D  P      +   +   L +      +V         + V   +       
Sbjct: 65  TIPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRV 147
              G +       +     G L       + + L                        + 
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKG 184

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                + +DK    +   V +   +      +  +      V   L  G+  +I+   ++
Sbjct: 185 TIDAPIARDKKER-QSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKY 243

Query: 208 FNWK 211
             + 
Sbjct: 244 IGYP 247


>gi|221485770|gb|EEE24040.1| 16S pseudouridylate synthase, putative [Toxoplasma gondii GT1]
 gi|221503852|gb|EEE29536.1| 16S pseudouridylate synthase, putative [Toxoplasma gondii VEG]
          Length = 285

 Score = 70.2 bits (170), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 16/57 (28%), Positives = 29/57 (50%)

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           G    +++ L EG++R+I+++ E    +V ++ RI  G   LG L  G  R +    
Sbjct: 226 GKTTRLSIELLEGRHRQIRRMCELVGLRVLKIHRIRIGKVSLGNLPQGRWRLLLPHE 282


>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 = 70.2 bits (170), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 35/244 (14%), Positives = 67/244 (27%), Gaps = 42/244 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            V E    +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V
Sbjct: 8   TVAEEQKNERIDKFVA--GINNEWSRTQVQQWIKDDVVTVNGKAVK-GNYKVRENDEITV 64

Query: 63  --------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                   D  P      +   +   L +      +V         + V   +       
Sbjct: 65  TIPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRV 147
              G +       +     G L       + + L                        + 
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVIRRYKAIVHGVIPHDKG 184

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                + +DK    +   V +   +      +  +      V   L  G+  +I+   ++
Sbjct: 185 TIDAPIARDKKER-QSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKY 243

Query: 208 FNWK 211
             + 
Sbjct: 244 IGYP 247


>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 = 70.2 bits (170), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 35/244 (14%), Positives = 67/244 (27%), Gaps = 42/244 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            V E    +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V
Sbjct: 8   TVAEEQKNERIDKFVA--GINNEWSRTQVQQWIKDDVVTVNGKAVK-GNYKVREDDEITV 64

Query: 63  --------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                   D  P      +   +   L +      +V         + V   +       
Sbjct: 65  TIPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRV 147
              G +       +     G L       + + L                        + 
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKG 184

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                + +DK    +   V +   +      +  +      V   L  G+  +I+   ++
Sbjct: 185 TIDAPIARDKKER-QSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKY 243

Query: 208 FNWK 211
             + 
Sbjct: 244 IGYP 247


>gi|323435911|ref|ZP_01048953.2| pseudouridylate synthase [Dokdonia donghaensis MED134]
 gi|321496226|gb|EAQ40187.2| pseudouridylate synthase [Dokdonia donghaensis MED134]
          Length = 190

 Score = 70.2 bits (170), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 35/172 (20%), Positives = 66/172 (38%), Gaps = 21/172 (12%)

Query: 86  TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY 145
           T  +    +              ++VGRLD ++EGLL +T DG L+  +   ++   + Y
Sbjct: 19  TNDARQARKKKFLKEFYDFPEGTMAVGRLDEHSEGLLFMTTDGKLSHTI--NTSGVEKEY 76

Query: 146 RVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQK---------------GSN 186
             +  G +  + +  L +G+ I    +       +                      G  
Sbjct: 77  YAQVDGAITDEAILALTQGVEISVEGKKYITKPCKARRIDGDPGFPERSKKIRDLRHGPA 136

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            W+++ + EGK R+++K+     +   RL+RI  G   L  L      EV +
Sbjct: 137 PWISITITEGKFRQVRKMTSAVGFATLRLVRIKIGSQTLKGLEPSQVIEVKE 188


>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 = 70.2 bits (170), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 33/243 (13%), Positives = 70/243 (28%), Gaps = 36/243 (14%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            ++E    +R+ K ++      SR ++   I+   +KVNG  ++ A   V + D I +D 
Sbjct: 7   TIEEQQQGERIDKALSSLQSEWSRTQIGNWISDGVIKVNGDAVK-AKYKVKAGDIIAIDV 65

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                         + +   +   L +      +V       G + V   +         
Sbjct: 66  PEVEELDVVPENLDLDIVYEDADVLVVNKPKGMVVHPAPGHMGGTLVNGLMYHCKDLSGI 125

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQ------------WLRVYRVRFHGQVDQ--- 155
            G L       +     G L       + +               +  V  H   D+   
Sbjct: 126 NGVLRPGIVHRIDKDTSGLLMVAKNDTAHESLVNQLVNKTVTRKYIALVHGHIAHDKGTI 185

Query: 156 -----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      +K  V+    +      +  + G    V   L  G+  +I+    +  +
Sbjct: 186 DAPIGRDQKDRQKQAVVDNGKHAVTHFQVVERFGDYTLVECRLETGRTHQIRVHMNYIGF 245

Query: 211 KVN 213
            + 
Sbjct: 246 PLV 248


>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 = 70.2 bits (170), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 32/241 (13%), Positives = 61/241 (25%), Gaps = 36/241 (14%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E    +R+ K +A      SR +V++ I    V VNG  ++     V   D I V  
Sbjct: 8   TVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDAVVTVNGKSVK-GNYKVKVNDEITVTI 66

Query: 63  ------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                 D  P      +   +   L +      +V         + V   +         
Sbjct: 67  PEPEELDIQPEDMNLEVYYEDADVLVVNKPRGMVVHPAPGHTKGTLVNGLMHHCTDLSGI 126

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL---------- 160
            G +       +     G L       + + L    V          +            
Sbjct: 127 NGVMRPGIVHRIDKDTSGLLMVAKNDVAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTI 186

Query: 161 ----------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      +   V +          +  +      V   L  G+  +I+   ++  +
Sbjct: 187 DAPIGRDKKERQSMTVDENGKNAVTHFQVLDRFKDFTLVECRLETGRTHQIRVHMKYIGY 246

Query: 211 K 211
            
Sbjct: 247 P 247


>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 = 70.2 bits (170), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 32/241 (13%), Positives = 61/241 (25%), Gaps = 36/241 (14%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E    +R+ K +A      SR +V++ I    V VNG  ++     V   D I V  
Sbjct: 8   TVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDAVVTVNGKSVK-GNYKVKGNDEITVTI 66

Query: 63  ------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                 D  P      +   +   L +      +V         + V   +         
Sbjct: 67  PEPEELDIQPEDMNLEVYYEDADVLVVNKPRGMVVHPAPGHTKGTLVNGLMHHCTDLSGI 126

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL---------- 160
            G +       +     G L       + + L    V          +            
Sbjct: 127 NGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGII 186

Query: 161 ----------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      +   V +          +  +      V   L  G+  +I+   ++  +
Sbjct: 187 DAPIGRDKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGY 246

Query: 211 K 211
            
Sbjct: 247 P 247


>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 = 70.2 bits (170), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 32/241 (13%), Positives = 61/241 (25%), Gaps = 36/241 (14%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E    +R+ K +A      SR +V++ I    V VNG  ++     V   D I V  
Sbjct: 8   TVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDAVVTVNGKSVK-GNYKVKGNDEITVTI 66

Query: 63  ------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                 D  P      +   +   L +      +V         + V   +         
Sbjct: 67  PEPEELDIQPEDMNLEVYYEDADVLVVNKPRGMVVHPAPGHTKGTLVNGLMHHCTDLSGI 126

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL---------- 160
            G +       +     G L       + + L    V          +            
Sbjct: 127 NGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGII 186

Query: 161 ----------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      +   V +          +  +      V   L  G+  +I+   ++  +
Sbjct: 187 DAPIGRDKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGY 246

Query: 211 K 211
            
Sbjct: 247 P 247


>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 = 70.2 bits (170), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 85/248 (34%), Gaps = 37/248 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N++ EN    R+ K+IA      SR +++ MI +  V VNG + E+A+      D 
Sbjct: 1   MEKINLLVENNNNYRLDKIIALNMEELSRTQIQEMIGRGLVLVNGKV-EKASYKTKLNDQ 59

Query: 60  IEV------------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           IE+            + +PL     ++  + +      +V         + V   L    
Sbjct: 60  IEITIEDNSDLEIEAEDIPLNVVYEDKDVIVIDKPTGMIVHPSPGITSGTLVNALLFHCK 119

Query: 106 --------SRVISVGRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRV 144
                   +R   V R+D  T GLL++  +    R L                    +  
Sbjct: 120 DLSGINGVNRPGIVHRIDKETSGLLMVAKNDIAHRFLSEQLKDHSVTRRYVALVHGLIPH 179

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
            + +    + ++  +     +            T+  +  + + +   L  G+  +I+  
Sbjct: 180 VQGKIDAPIGRNPNDRQSMCVTKNNSKNAITNFTVLKRYKNMSLIECRLETGRTHQIRVH 239

Query: 205 FEFFNWKV 212
             +  + V
Sbjct: 240 MSYIGYPV 247


>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 = 70.2 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 35/244 (14%), Positives = 67/244 (27%), Gaps = 42/244 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            V E    +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V
Sbjct: 8   TVAEEQKNERIDKFVA--GINNEWSRTQVQQWIKDDVVTVNGKAVK-GNYKVRENDEITV 64

Query: 63  --------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                   D  P      +   +   L +      +V         + V   +       
Sbjct: 65  TIPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRV 147
              G +       +     G L       + + L                        + 
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKG 184

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                + +DK    +   V +   +      +  +      V   L  G+  +I+   ++
Sbjct: 185 TIDAPIARDKKER-QSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKY 243

Query: 208 FNWK 211
             + 
Sbjct: 244 IGYP 247


>gi|329728841|gb|EGG65262.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21193]
          Length = 305

 Score = 70.2 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 64/244 (26%), Gaps = 36/244 (14%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           NI  +  T  RV K++       SR +++  I    V  N  +++     V   DHI V 
Sbjct: 7   NITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKS-NYKVKLNDHIVVT 65

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   +     +Y     +V         + V   +  I +   
Sbjct: 66  EKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMYQIKNLSG 125

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPST------------QWLRVYRVRFHGQVDQ-- 155
             G +       + +   G L       +             +   +  V  +   D   
Sbjct: 126 INGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYIALVHGNIPHDYGT 185

Query: 156 ------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                    N  +   V+           +     +   V   L  G+  +I+    +  
Sbjct: 186 IDAPIGRNKNDRQSMAVVDDGKEAVTHFNVLEHFKNYTLVECQLETGRTHQIRVHMRYIG 245

Query: 210 WKVN 213
           + + 
Sbjct: 246 FPLV 249


>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 = 70.2 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 32/241 (13%), Positives = 61/241 (25%), Gaps = 36/241 (14%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E    +R+ K +A      SR +V++ I    V VNG  ++     V   D I V  
Sbjct: 8   TVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDDVVTVNGKSVKV-NYKVKGNDEITVTI 66

Query: 63  ------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                 D  P      +   +   L +      +V         + V   +         
Sbjct: 67  PDPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI 126

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL---------- 160
            G +       +     G L       + + L    V          +            
Sbjct: 127 NGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTI 186

Query: 161 ----------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      +   V +          +  +      V   L  G+  +I+   ++  +
Sbjct: 187 DAPIGRDKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGY 246

Query: 211 K 211
            
Sbjct: 247 P 247


>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 = 70.2 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 28/247 (11%), Positives = 67/247 (27%), Gaps = 35/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M++   +QE+    R+   +      SR +++ +I    + +NG   + A+V + + D +
Sbjct: 1   MEEIFTLQEDENLIRLDVYLGDKLELSRSKIQSLIESGNISLNGNKAK-ASVKLKTGDTV 59

Query: 61  EVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
            V+                 +   +   L +      +    +     + V   L  +  
Sbjct: 60  YVNYQEENKAEIKAQDIALDIVYEDDDVLVVNKPRGMVTHVANGNHEGTLVNALLYYLKD 119

Query: 107 R------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ----- 155
                  +   G +    +    L             + Q       R +  +       
Sbjct: 120 DISLQNGMYRAGIVHRIDKDTSGLLVVAKNDFSSTELTNQLKDHSMTRVYTLICNGVIDE 179

Query: 156 ---------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                           K  VI+   Y    +          +    L+ G+  +I+    
Sbjct: 180 ETVIEQNIGRNPKDRMKYCVIEDGKYAHTTIIPLEIFEKYTYAKAILKTGRTHQIRVHLR 239

Query: 207 FFNWKVN 213
             N  + 
Sbjct: 240 HINRPIV 246


>gi|261883893|ref|ZP_06007932.1| pseudouridine synthase, Rsu:RNA-binding S4:pseudouridine synthase
           [Campylobacter fetus subsp. venerealis str. Azul-94]
          Length = 163

 Score = 70.2 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 3/76 (3%)

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
            +  T+ +  G    +TV + EG+NRE+++   +++ +V  L R+S+G   L  L  G  
Sbjct: 65  FLAYTIISLSGGYTRLTVIINEGQNRELRRFLGYYDLEVMDLNRVSFGRVSLDQLGEGKW 124

Query: 234 REVSKKI---LREQLG 246
           R  +      LR+ L 
Sbjct: 125 RYFTNSEYDDLRDFLK 140


>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 = 70.2 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 27/230 (11%), Positives = 66/230 (28%), Gaps = 33/230 (14%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R+ K +A     SR ++E++I +  VKVN  ++ ++   +   + +EV  +P++K 
Sbjct: 7   DKNKRLDKFLANKLNVSRNQIEQLIKKGYVKVNEKVITKSGYKLKENEKVEV--LPIKKE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E+           L                +    S   +     +  +G  L T  G  
Sbjct: 65  EKETKKANFDIPILYEDEDLLVINKPPGIVVHPAPSYKEATLVDWLKQKGYSLSTIAGEE 124

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK-------GIVIQGICYGDMQVTLDTQK 183
              +     +      V        + L+   K        +++      + +   +   
Sbjct: 125 RFGIVHRIDKETSGALVIAKNNKTHEFLSNQLKDKSMGRYYLMLLNEPLKEAKCVEEKIG 184

Query: 184 G-SNAWVTVGL-----------------------REGKNREIKKVFEFFN 209
                 + + +                         G+  +I+       
Sbjct: 185 RNPKNRLKMAIVKNGKEAKTLFVPIFDNLTAAKLYTGRTHQIRVHLTKLG 234


>gi|308751621|gb|ADO45104.1| pseudouridine synthase, RluA family [Hydrogenobacter thermophilus
           TK-6]
          Length = 326

 Score = 70.2 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 31/245 (12%), Positives = 69/245 (28%), Gaps = 37/245 (15%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +    +R+   +  A G  SR  V+++I    V V+   +++ +  + +   I    
Sbjct: 15  VVDQEAQGKRLDLFLTEAYGEFSRSYVQKLIEDGFVLVDDKEIKKPSRRLKAGQKITFYI 74

Query: 63  ----------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                     + +P  +   +   L L      +V         + V   L  I      
Sbjct: 75  PQVEPLEVLPEDIPFDVVYEDEDILVLIKPCGLVVHPSPGYSSGTLVNALLFRIKELSGI 134

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-------------- 156
            G+        L     G +       + + L    ++                      
Sbjct: 135 GGKERPGIVHRLDKNTAGLMVVAKSDKAHRSLVEEFMQRRVLKRYHALVSGLLREDSGTV 194

Query: 157 ------KLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTVGLREGKNREIKKVFEFF 208
                      KK  V++       +  +    +K    ++ V +  G+  +I+    F 
Sbjct: 195 EKSIGRHPVDRKKFSVVEDGKPAKTEYEVIKRFEKHRITFLDVRIHTGRTHQIRVHLSFI 254

Query: 209 NWKVN 213
              V 
Sbjct: 255 GHPVL 259


>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 = 69.8 bits (169), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 38/250 (15%), Positives = 81/250 (32%), Gaps = 39/250 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK+   V EN   +R+ + ++      SR  ++++I +  V VN   ++ A   +   D 
Sbjct: 1   MKEFFTV-ENQDGERIDRYLSEELADRSRSYIQKLIKENYVTVNQKPVK-ANYRLSLGDR 58

Query: 60  IEVD------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
           +E+D             +PL    E   + + +KP  +V   +      T+ + L     
Sbjct: 59  VEIDLPEAKEPDIRPEDIPLDILYEDKDIIIVNKPKQMVVHPAPGHYSQTLVNALMYHCG 118

Query: 106 ---------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR------------- 143
                     R   V R+D++T G L+   +    + L     +                
Sbjct: 119 SDLSGINGTMRPGIVHRIDMDTTGSLVACKNDMAHQSLSRQLKEHSIRRIYVAIVHGNIK 178

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                 +  + +      K  I  +          +  + G   ++   L  G+  +I+ 
Sbjct: 179 EEYGTVNAPIGRHPTERKKMSIHSRNGREAVTHYQVLERFGDYTYIRCELETGRTHQIRV 238

Query: 204 VFEFFNWKVN 213
                   + 
Sbjct: 239 HMASLGHPLL 248


>gi|161523949|ref|YP_001578961.1| pseudouridine synthase [Burkholderia multivorans ATCC 17616]
 gi|160341378|gb|ABX14464.1| pseudouridine synthase [Burkholderia multivorans ATCC 17616]
          Length = 228

 Score = 69.8 bits (169), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 39/182 (21%), Positives = 72/182 (39%), Gaps = 19/182 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +        GRLD ++EGLLLLT+DG L   +
Sbjct: 39  LIALNKPFGTICQFSAHETRPSLGDWVKTPGV--YPAGRLDADSEGLLLLTDDGALQARI 96

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 97  AEPRHKLVKRYWAQVEGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPETLWPRNPPIR 156

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L      T  + 
Sbjct: 157 YRAAIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGSLDIFALGIAPSETIALP 216

Query: 238 KK 239
            +
Sbjct: 217 PR 218


>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 = 69.8 bits (169), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 29/245 (11%), Positives = 67/245 (27%), Gaps = 38/245 (15%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V   +   R+ K ++     A+R  +E++I    VK+N  ++ +    +   + IEV   
Sbjct: 12  VNSKYEGMRLDKYLSEQIEEATRSYLEKLIDNNYVKINSKIINKNGRKLKLGEKIEVLIP 71

Query: 63  -----DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                D  P      +       + +      +V         + V   L    +     
Sbjct: 72  EEENIDIEPENIPLDIVYENNDFIVINKNYGMVVHPAYGNYTGTLVNALLYYTNNLSSIN 131

Query: 112 GRLDINTE-----------------------GLLLLTNDGGLARVLELPSTQWLRVYRVR 148
           G +                              + +        +  +           R
Sbjct: 132 GNIRPGIIHRLDKDTSGLILVAKSNYAHAKLASMFIDKTIHKTYLCIVKGNFSEENLSGR 191

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +D  +  K  +V +          +  Q    + V V +  G+  +I+   +  
Sbjct: 192 IENLIGRDSKDRKKMAVVKENGKIAISNYKVVEQVEGYSLVEVAIETGRTHQIRVHMKSI 251

Query: 209 NWKVN 213
           N  + 
Sbjct: 252 NHVIL 256


>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 = 69.8 bits (169), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 33/245 (13%), Positives = 68/245 (27%), Gaps = 43/245 (17%)

Query: 6   IVQENFTPQRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            V E    +R+ K +    A     SR +V++ I + RV VNG  ++ A   V   D + 
Sbjct: 7   TVHEEHKGERIDKYLTAVEADW---SRTQVQQWIKEDRVLVNGNAVK-ANYKVQEGDAVS 62

Query: 62  V---DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           V   +  PL              ++  L +      +V         + V   +      
Sbjct: 63  VQVPEPEPLDVTAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHLTGTLVNGLMAHCDDL 122

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYR 146
               G +       +     G L       + + L                         
Sbjct: 123 SGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKYTALVHGVIPHDH 182

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                 + +DK +     +  +   +      +  +      V   L  G+  +I+   +
Sbjct: 183 GTIDAPIGRDKKDRQSMTVTRENGKHAVTHFEVIERFDDFTVVECQLETGRTHQIRVHMK 242

Query: 207 FFNWK 211
           +  + 
Sbjct: 243 YIGFP 247


>gi|254757932|ref|ZP_05209959.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Australia 94]
          Length = 249

 Score = 69.8 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 35/244 (14%), Positives = 67/244 (27%), Gaps = 42/244 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            V E    +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V
Sbjct: 8   TVAEEQKNERIDKFVA--GINNEWSRTQVQQWIKDDVVTVNGKAVK-GNYKVRENDEITV 64

Query: 63  --------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                   D  P      +   +   L +      +V         + V   +       
Sbjct: 65  TIPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRV 147
              G +       +     G L       + + L                        + 
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKG 184

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                + +DK    +   V +   +      +  +      V   L  G+  +I+   ++
Sbjct: 185 TIDAPIARDKKER-QSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKY 243

Query: 208 FNWK 211
             + 
Sbjct: 244 IGYP 247


>gi|126649705|ref|ZP_01721941.1| YlyB [Bacillus sp. B14905]
 gi|126593424|gb|EAZ87369.1| YlyB [Bacillus sp. B14905]
          Length = 303

 Score = 69.8 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 29/243 (11%), Positives = 68/243 (27%), Gaps = 36/243 (14%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            ++E    +R+ K ++      SR ++   ++   +KVNG  ++     V + D I +D 
Sbjct: 7   TIEEQQQGERIDKALSSLQSEWSRTQIGNWVSDGNIKVNGDAVK-PKYKVKAGDVIAIDV 65

Query: 64  --GVP-----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
               P           +   +   L +      +V         + V   +         
Sbjct: 66  PEAEPLDVIAENLALDIVYEDADVLVVNKPKGMVVHPAPGHLTGTLVNGLMYQCKDLSGI 125

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQ------------WLRVYRVRFHGQVDQ--- 155
            G +       +     G L       + +               +  V  H   D+   
Sbjct: 126 NGIMRPGIVHRIDKDTSGLLMVAKNDVAHESLVDQLVNKTVTRKYIALVHGHIAHDKGTI 185

Query: 156 -----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      +K  ++    +      +  + G    V   L  G+  +I+    +  +
Sbjct: 186 DAPIGRDQKDRQKQAIVDNGKHAVTHFHVVERFGDYTLVECRLETGRTHQIRVHMNYIGF 245

Query: 211 KVN 213
            + 
Sbjct: 246 PLV 248


>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 = 69.8 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 29/246 (11%), Positives = 68/246 (27%), Gaps = 36/246 (14%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            + I+ EN    R+   I+ +    SR  ++++I +  VKVNG   +++   +   D + 
Sbjct: 4   KEFIIHENLVNCRLDLFISNSLEGKSRSYIQKLIQEGHVKVNGKD-KKSNYKLKLHDSVV 62

Query: 62  VDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           V+ +               +   +   + +      +V   +     + V   L    + 
Sbjct: 63  VNNIEKEDKKINPENIEMDILYEDNDIIVINKSQGMVVHPATSNYSGTLVNALLYHCDTL 122

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------------ 155
                         +     G L       + + L         + +             
Sbjct: 123 STLNDDTRPGIVHRIDKDTSGVLVVAKNNKAHEILAEQLKEHSMKREYIAVVEGIVKEEN 182

Query: 156 --------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                          K  V++G         +  +   N  V   L  G+  +I+    +
Sbjct: 183 GLVDEPLGRNPKDRIKMAVVEGGKNAVTHYEVLKRFKKNTLVKCILETGRTHQIRVHMSY 242

Query: 208 FNWKVN 213
               + 
Sbjct: 243 IGHPLV 248


>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 = 69.8 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 29/245 (11%), Positives = 67/245 (27%), Gaps = 38/245 (15%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V   +   R+ K ++     A+R  +E++I    VK+N  ++ +    +   + IEV   
Sbjct: 12  VNSEYEGMRLDKYLSEQIEEATRSYLEKLIDNNYVKINSKIINKNGRKLKLGEKIEVSIP 71

Query: 63  -----DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                D  P      +       + +      +V         + V   L    +     
Sbjct: 72  EEENIDIEPENIPLDIVYENNDFIVINKNYGMVVHPAYGNYTGTLVNALLYYTNNLSSIN 131

Query: 112 GRLDINTE-----------------------GLLLLTNDGGLARVLELPSTQWLRVYRVR 148
           G +                              + +        +  +           R
Sbjct: 132 GNIRPGIIHRLDKDTSGLILVAKSNYAHAKLASMFIDKTIHKTYLCIVKGNFSEENLSGR 191

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +D  +  K  +V +          +  Q    + V V +  G+  +I+   +  
Sbjct: 192 IENLIGRDSKDRKKMAVVKENGKIAISNYKVVEQVEGYSLVEVAIETGRTHQIRVHMKSI 251

Query: 209 NWKVN 213
           N  + 
Sbjct: 252 NHVIL 256


>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 = 69.8 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 27/245 (11%), Positives = 66/245 (26%), Gaps = 38/245 (15%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V   +   R+ K +++    A+R  +E++I    VK+N  ++ +    +   + IEV   
Sbjct: 12  VSSEYEGMRLDKYLSKQIEEATRSYLEKLIDNNYVKINSKVINKNGRKLKLGEKIEVSIP 71

Query: 63  -----DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                D         +       + +      +V         + V   L    +     
Sbjct: 72  KEENIDIEAENISLDIVYENDDFIVINKSYGMVVHPAYGNYSGTLVNALLYYTNNLSSIN 131

Query: 112 GRLDINTE-----------------------GLLLLTNDGGLARVLELPSTQWLRVYRVR 148
           G +                              +          +  +           R
Sbjct: 132 GNIRPGIIHRLDKDTSGLILVAKNNYAHAKLASMFTDKTIHKTYLCIVKGNFSEENLNGR 191

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +D  +  K  +V +          +  Q    + V + +  G+  +I+   +  
Sbjct: 192 IENLIGRDSKDRKKMAVVKENGKTAISNYKVIEQVDGYSLVEIAIETGRTHQIRVHMKSI 251

Query: 209 NWKVN 213
           N  + 
Sbjct: 252 NHVIL 256


>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 = 69.8 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 33/242 (13%), Positives = 67/242 (27%), Gaps = 34/242 (14%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGIL--------------LERA- 50
           IV       R+   +      SR  ++ +I    V V G +              +E   
Sbjct: 5   IVSAEQEGMRLDVFLTEQMEGSRSYIQSLIKGGHVIVGGKVGKANLRLTPNMVIQVEIPE 64

Query: 51  --AVNVMSTDH---IEVDGVPLRKAERTRLWLYHKPIGLVTTH--------------SDP 91
             +V V   D    +  +   +    + R  + H  +G  +                 + 
Sbjct: 65  PESVEVKPEDIPLDVLYEDHDIIIVNKARGMVVHPAVGNYSGTLVNALLFHCKDLSGING 124

Query: 92  DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151
           + R  +   L    S V+   + D    GL     +    R         +   +     
Sbjct: 125 EIRPGIVHRLDKDTSGVMMAAKNDAAHIGLAEQVKEHSAKRTYWALVQGNIVEEKGTIKA 184

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + +   + +K  +V +          +  + G    V   L  G+  +I+  F      
Sbjct: 185 PIGRHPKDRMKMAVVFENSKDAVTHFRVLERYGHQTLVECNLETGRTHQIRVHFAHIGHP 244

Query: 212 VN 213
           V 
Sbjct: 245 VV 246


>gi|237835269|ref|XP_002366932.1| 16S pseudouridylate synthase, putative [Toxoplasma gondii ME49]
 gi|211964596|gb|EEA99791.1| 16S pseudouridylate synthase, putative [Toxoplasma gondii ME49]
          Length = 286

 Score = 69.8 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 16/57 (28%), Positives = 29/57 (50%)

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           G    +++ L EG++R+I+++ E    +V ++ RI  G   LG L  G  R +    
Sbjct: 227 GKTTRLSIELLEGRHRQIRRMCELVGLRVLKIHRIRIGKVSLGNLPQGRWRLLLPHE 283


>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 = 69.8 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 34/247 (13%), Positives = 71/247 (28%), Gaps = 37/247 (14%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M+ +N IV E     R+ KV+  +    SR  ++++I + RV +NG + + A       D
Sbjct: 1   MEQENMIVTEELVGVRLDKVLNESFEDYSRSYLQQLIKEGRVLINGQVAK-ANYKCRLND 59

Query: 59  HIEVD-GVP-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            IE++   P             +   +   + +      +V         + V   +  +
Sbjct: 60  QIEINIPEPEVLDVIPEEMDLDIVYQDDYVIVVNKPENMVVHPAPGSMSGTLVNGLMAQV 119

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------- 155
                  G L       +     G L       + + L    V                 
Sbjct: 120 TDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDVAHESLVNQLVEKTVTRRYVALVHGVIP 179

Query: 156 -----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                            KK  V++   +      +  +      +   L  G+  +I+  
Sbjct: 180 HDNGTIDAPIGRDPKDRKKMAVVESGKHAVTHFKVLQRFKEFTLIECRLETGRTHQIRVH 239

Query: 205 FEFFNWK 211
             +  + 
Sbjct: 240 MRYIGYP 246


>gi|156103361|ref|XP_001617373.1| hypothetical protein [Plasmodium vivax SaI-1]
 gi|148806247|gb|EDL47646.1| hypothetical protein, conserved [Plasmodium vivax]
          Length = 409

 Score = 69.8 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 23/98 (23%), Positives = 45/98 (45%), Gaps = 1/98 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +  T  R+SK+++ + + SR + + +I   +VKVN  ++ +  V V     IE++G P+ 
Sbjct: 8   KRSTLLRLSKILSLSAVTSRGKAQELIKNGKVKVNNQVVRQ-NVAVDINSAIELEGKPIL 66

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
               T+LW  +KP  +  +           + L     
Sbjct: 67  VDVTTKLWGIYKPKHVFCSSERNYEYEEKREALKGRPH 104



 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 32/134 (23%), Positives = 62/134 (46%), Gaps = 1/134 (0%)

Query: 96  TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
           T  +    I   +I V  L  ++EGL+LLTNDG  AR L+      +  Y ++   ++  
Sbjct: 211 TKNNFSNDIPEHLIVVNSLSASSEGLVLLTNDGDFARNLKDAHNNIITTYIIKVKEELTN 270

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQK-GSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
           +K+ L+++G  +  +    + V +      S  W+     E  +  +  +F  +N  + +
Sbjct: 271 EKIKLIERGCHVGDLHIRPLTVHVIKPNCASPKWIKFTYVEKSHTHLDLLFSKYNLTIRK 330

Query: 215 LIRISYGPFQLGTL 228
             R S+GP++   L
Sbjct: 331 CKRFSFGPYKASDL 344


>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 = 69.4 bits (168), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 36/243 (14%), Positives = 75/243 (30%), Gaps = 36/243 (14%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           ++I+ +    +R+ KV++      SR +V++ I    V VNG   +       + D IE+
Sbjct: 2   EHIIPDEQAGERIDKVLSTLNADWSRTQVQQWIKDGNVLVNGQKPKT-NYKCTANDKIEI 60

Query: 63  --------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---- 104
                   D VP      +   ++  L +      +V   +     + V   +       
Sbjct: 61  SIPEPEELDVVPEKMDLDIYYEDKDVLVVNKPKGMVVHPAAGHGTGTLVNGLMAHCTDLS 120

Query: 105 ----FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN- 159
                 R   V R+D +T GLL++  +      L           + R            
Sbjct: 121 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLMNKTVTRKYRAVVHGVIPHDYG 180

Query: 160 -----------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                        +   V+    +      +  +      V   L  G+  +I+   ++ 
Sbjct: 181 TIDAPIARDPKDRQSMTVVDNGKHAVTHFQVLERFRDFTLVECQLETGRTHQIRVHMKYI 240

Query: 209 NWK 211
            + 
Sbjct: 241 GYP 243


>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 = 69.4 bits (168), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 63/246 (25%), Gaps = 36/246 (14%)

Query: 3   DKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +  I +     QR+ K++       SR +++  I +  V VNG  ++ A   V   D IE
Sbjct: 5   NYEITEAEQAGQRIDKLLPEFNSDWSRSQIQDWIKEDLVTVNGKKVK-ANHKVKLNDKIE 63

Query: 62  V--------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           V        D  P      +   +     +Y     +V         + V   +  I   
Sbjct: 64  VTEKETVEADIKPENLNLDIYYEDSDVAIVYKPKGMVVHPSPGHYTGTLVNGLMYQIKDL 123

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------------ 155
               G +       +     G L       + + L    +                    
Sbjct: 124 SGINGEIRPGIVHRIDKDTSGLLMVAKNDIAHRNLVEQLMAKTVTRKYTALVHGNIPHDY 183

Query: 156 --------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                         +   V+           +         V   L  G+  +I+   ++
Sbjct: 184 GTIDAPIGRDKKDRQSMAVVDDGKDAVTHFNVLEHFKDYTLVECELETGRTHQIRVHMKY 243

Query: 208 FNWKVN 213
               + 
Sbjct: 244 IGHPLV 249


>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 = 69.4 bits (168), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 34/236 (14%), Positives = 74/236 (31%), Gaps = 39/236 (16%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++ A   +R  V+++I +  V VN   + + A  V S D I+V            
Sbjct: 9   RLDKYLSEALSKTRSFVQKIIEEGNVWVNQTQVLKPAYKVKSGDIIKVVIPEPKQLSLVA 68

Query: 63  ---DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG------- 112
              D   + + E   +        +V   +     + V   L     R+ S+        
Sbjct: 69  QDIDIEVVYEDEHLAVI-NKPCGMVVHPGTGNFENTLVNALLHKFSGRLSSINGVIRPGI 127

Query: 113 ---------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                          + D     L        + R+        L+      +  + +  
Sbjct: 128 VHRLDKDTSGLLIVAKTDEAHIKLSEALKSHQIKRIYYAICEGVLKEDSGVINAPIGRHP 187

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +N LK  +V  G         +  +     ++ + L+ G+  +I+    +  + + 
Sbjct: 188 VNRLKMAVVPNGKEA-VTYFEVLERFDKYTFIKLRLKTGRTHQIRVHMSYIGYPLL 242


>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 = 69.4 bits (168), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 30/236 (12%), Positives = 62/236 (26%), Gaps = 35/236 (14%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------ 63
                R+ K +A     SR +    I +  V VNG + ++A   V   D I  D      
Sbjct: 6   KVAGVRLDKALADNSELSRSQANEEIKKGIVLVNGQV-KKAKYTVQEGDRITFDIPKKEV 64

Query: 64  ------GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                  +PL     +     +      +V   +     + V   +  I       G + 
Sbjct: 65  LDYQAENIPLDIIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMYHIKDLSSINGVVR 124

Query: 116 INTEGL---------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
                          ++  ND     + E    +      +        +   +++  I 
Sbjct: 125 PGIVHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDQGVIEAPIG 184

Query: 167 IQGI---------CYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                               +  +  + G    V + L  G+  +I+    +    
Sbjct: 185 RSDKDRKKQAVTAKGKPAVTRFHVLERFGDYTLVELSLETGRTHQIRVHMAYIGHP 240


>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 = 69.4 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 44/256 (17%), Positives = 79/256 (30%), Gaps = 46/256 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M    IV E     R+ K +A+   ASR ++E++I ++ VKV+G +  +  + +    ++
Sbjct: 1   MNKNFIVLETN---RLDKFLAQNIDASRNQIEQLIKKEFVKVDGKITNKTGLKLKENQNV 57

Query: 61  EV---------------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           EV                     D       E   + + +KP  L    +     +T+ D
Sbjct: 58  EVFFPEAQLNKRKDEEFLKNSLEDKEVEIIYEDDYILVLNKPYNLTVHDAPSVKDATLVD 117

Query: 100 NLPSIFS---------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR------- 143
            L              R   V RLD  T G++++         L                
Sbjct: 118 WLKLKNISLSTISGEERHGIVHRLDKGTSGVMVIAKTNEAHLNLSKQLEDKSMGRYYLAI 177

Query: 144 -----VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-VGLREGK 197
                   V     + ++  N LK  I   G         +         +    L  G+
Sbjct: 178 LDLALKENVIIEKPIGRNPNNRLKMSIEENGRYAKSAFSKIALSDNEKFELIACKLYTGR 237

Query: 198 NREIKKVFEFFNWKVN 213
             +I+      N  + 
Sbjct: 238 THQIRVHLSSINRHIL 253


>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 = 69.4 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 36/245 (14%), Positives = 72/245 (29%), Gaps = 38/245 (15%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V       R+ + +       SR  ++++++Q  V +NG    +AA  V + D + V+  
Sbjct: 51  VNAAQHGSRLDRALVDLVPEFSRSYLQQLLSQGLVALNGQQATKAAARVKAGDTLTVEMR 110

Query: 66  P---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
           P               +   +   L +      +V       G + +   L       + 
Sbjct: 111 PTLQSQAFRPEALPIDVVYEDAHLLVVNKPAGLVVHPAPGNWGGTLLNGLLARDAKAQLV 170

Query: 111 V-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                  RLD +T GL+++  D      L           +                   
Sbjct: 171 PRAGIVHRLDKDTSGLMVVARDRTTMDALVRMIAARTVHRQYLAIAHRPWTGVPNRAVQA 230

Query: 156 ----DKLNLLKKGIVIQGICY-GDMQVTLDTQKGSN--AWVTVGLREGKNREIKKVFEFF 208
               D  N L+  +V          +  +    G++   WV   L  G+  +I+      
Sbjct: 231 PIGRDPRNRLRMAVVNLDTHAGKPARTDIRWLAGNDLGCWVECTLHTGRTHQIRVHMASL 290

Query: 209 NWKVN 213
              + 
Sbjct: 291 GHPLV 295


>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 = 69.4 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 37/248 (14%), Positives = 76/248 (30%), Gaps = 37/248 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+ + +V E     R+ K ++     SR  ++ +I +Q+V VNG  ++  +  V   D I
Sbjct: 1   MEKRRLVVEKS-GLRLDKYVSDHCELSRSFLQDLIKEQQVLVNGKAVKS-SYKVNLEDII 58

Query: 61  EV---DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-- 104
           E    D   +              +   + +  +   +V         + V   L     
Sbjct: 59  EFAVPDLEEIEVIPQDIPLNVLYEDEDVIVVNKEKGMVVHPSLGHQDGTLVNALLFHCQD 118

Query: 105 ------FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
                   R   V R+D +T G L++  +      L             R     +    
Sbjct: 119 LSGINGKIRPGIVHRIDKDTSGCLVIAKNDVAHIALSKQIETKEAYREYRLIVHGNIQHE 178

Query: 159 NLLKKGIVIQGICY-----------GDMQVTLDTQK--GSNAWVTVGLREGKNREIKKVF 205
           + L    + +                  +      K  G   +++  L  G+  +I+   
Sbjct: 179 DGLIDAPIGRDPKDRQRMAVVAENSRPAKTHFHVLKRFGQYTYLSCLLETGRTHQIRVHM 238

Query: 206 EFFNWKVN 213
           ++    V 
Sbjct: 239 KYIQHPVL 246


>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 = 69.4 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 70/246 (28%), Gaps = 36/246 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  ++         R+ KV+       +R  +++ I +  V VNG  L+ A   V  +D 
Sbjct: 1   MPQEHNFIIKEETGRLDKVLTELLPSITRSHIQQWIKEGNVTVNGENLK-ANYKVQPSDE 59

Query: 60  IEV------------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I +            + +P+     +   + +      +V   +     + V   +  I 
Sbjct: 60  IVIIEPELVSLEVLAEDIPIEIVYQDEDVVVVNKAQGMVVHPSAGHQTGTLVNALMYHIK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                 G +       +     G L       + + L           +           
Sbjct: 120 DLSGINGTIRPGIVHRIDKDTSGLLMVAKNDSAHEKLAAQLKDKTSLREYIALVHGVIPH 179

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           KK  +I G        T+  +      V++ L  G+  +I+   
Sbjct: 180 EKGTIDAPLGRSKVDRKKQDIIDGGREAVTHFTVLERFKDFTLVSLKLETGRTHQIRVHM 239

Query: 206 EFFNWK 211
           ++  + 
Sbjct: 240 KYIGYP 245


>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 = 69.4 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 38/246 (15%), Positives = 72/246 (29%), Gaps = 36/246 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M ++++   +    R+ KV+A A    +R ++ + I    + VNG   ++A   V + D 
Sbjct: 1   MTEESLTITDQEG-RLDKVVAEAFTDYTRTQMSKWIDDGILTVNGET-KKAKYKVHAGDV 58

Query: 60  IEV--------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI- 104
           I          D  P      +   +   L +      +V   +     + V   +    
Sbjct: 59  ISFVVPEPVVLDIKPENLPLDIVYEDDDLLVVNKPQGMVVHPAAGHPNGTLVNALMYHTE 118

Query: 105 ------FSRVISVGRLDINTEGLLLLTNDGGLAR------------VLELPSTQWLRVYR 146
                   R   V R+D +T GLL++  +                               
Sbjct: 119 LSSINGVIRPGIVHRIDKDTSGLLMVAKNDQAHEALSADLKDKKNLRQYYALVHGEFSEN 178

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          KK  VI G         +  +      + V L  G+  +I+    
Sbjct: 179 KGTIKAPLGRSKTDRKKQAVIAGGRDAVTHFEVVKRYVGYTLLRVTLETGRTHQIRVHMA 238

Query: 207 FFNWKV 212
           +    V
Sbjct: 239 YIGHPV 244


>gi|328463102|gb|EGF34868.1| 16S pseudouridylate synthase [Lactobacillus helveticus MTCC 5463]
          Length = 170

 Score = 69.4 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 42/170 (24%), Positives = 72/170 (42%), Gaps = 4/170 (2%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +      L TT +          +    +  ++ VGRLD +T  LLLLTNDG L   L  
Sbjct: 1   MNKPKGVLSTTENRSQRTVISLLDPQDRYQGIVPVGRLDKDTTDLLLLTNDGQLNHELLA 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN--AWVTVGL 193
           P+    ++Y  +  G  D + +     G+ +  G     +   +  Q   N  + + + +
Sbjct: 61  PNKHVAKIYHAKIAGVADSNTVKTFATGMTLGDGTKLKTVTFNVLKQDVENGSSEIEIEI 120

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
            EGK  +IK++F     +V  L R+S G  +L   L  G   E+    ++
Sbjct: 121 SEGKYHQIKRMFSVVGMEVVELERVSMGKLRLPDDLKRGEYVEIDVDEIK 170


>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 = 69.4 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 29/242 (11%), Positives = 65/242 (26%), Gaps = 37/242 (15%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V      +R+ K I       SR +V+  + + RV VNG  ++     + + D + +  
Sbjct: 13  TVDPADKNERIDKFITLQNEDWSRSQVQAWVKEGRVTVNGEPIKN-NYKLQAEDEVTLRV 71

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
            P              +   +   + +      +V         + V   L         
Sbjct: 72  PPPKEMAIQPEEMSLDIVYEDSDVVVVNKPRGLVVHPAPGHYSGTLVNGLLAHCKDLSGI 131

Query: 111 VG---------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
            G                     + D    GL        + R         +       
Sbjct: 132 NGVLRPGIVHRIDKDTSGLLMVAKNDKAHMGLAEQLKAHTVNRKYVALVHGVIPHEMGTI 191

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +D  N  +  +V +          +  +      V + L  G+  +I+   ++ +
Sbjct: 192 EAPIGRDPKNRQQMAVVFENSKPAVTHFIVLERFKEYTMVELKLETGRTHQIRVHMKYID 251

Query: 210 WK 211
           + 
Sbjct: 252 YP 253


>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 = 69.4 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 32/245 (13%), Positives = 69/245 (28%), Gaps = 38/245 (15%)

Query: 6   IVQENFTPQRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
            V  + +  R+ K I  +     SR +V+  I    VKVN   ++     V   DHI + 
Sbjct: 26  TVDADSSKTRLDKYITESLGEEVSRSQVQLWITDGHVKVNEEPVKS-NYKVSQGDHIVLS 84

Query: 63  -----------DGVPLRK--AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                      + +PL     +R  + +      +V         + V   +        
Sbjct: 85  VPQPSVVEIIPEDIPLEIAFEDRDVIVVNKPRGMVVHPAPGHSSGTLVNALMFHCKDLSG 144

Query: 110 SVGR---------------------LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
             G                       D     L     D  + R         +   +  
Sbjct: 145 INGELRPGIVHRIDKDTTGLIMAAKNDKAHASLAAQLKDHSVNRRYLALVHGNISHDQGT 204

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +D  +     +  +   +     T+  + G  + + + L  G+  +I+   ++ 
Sbjct: 205 IDAPIGRDAQDRKLYTVTDRNSKHAVTHFTVVERFGDYSLLELKLETGRTHQIRVHMKYI 264

Query: 209 NWKVN 213
              + 
Sbjct: 265 GHPLV 269


>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 = 69.4 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 33/245 (13%), Positives = 64/245 (26%), Gaps = 37/245 (15%)

Query: 5   NIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--- 60
            I +E     R+ K ++      SR  ++ +I    + VN   ++     + + D I   
Sbjct: 7   KITEEENIGIRIDKYLSNIIEGKSRSFIQGLIDSGAILVNNKEVKS-NYKLRNHDEIIVS 65

Query: 61  -----EVDGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                E+D  P      +   +   + L      +V         + V   L        
Sbjct: 66  MPEPIELDVEPEDIDLNIVYEDEDVIVLNKPQGVVVHPAPGNYSGTLVNGLLYHCKDLSG 125

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV---------------------R 148
             G +       +     G L       +   L                           
Sbjct: 126 INGVIRPGIVHRIDKDTSGILVIAKNDDAHNHLAKQFKNHSIKREYYALVEGKFSKIEGT 185

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + ++K + LK  I+  G         L+      A V   L  G+  +I+      
Sbjct: 186 VDKPIGRNKKDRLKMAIMEDGKRAVTHYNVLEQYNNGTALVKCTLETGRTHQIRVHMASI 245

Query: 209 NWKVN 213
              + 
Sbjct: 246 GHPLV 250


>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 = 69.4 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 30/244 (12%), Positives = 73/244 (29%), Gaps = 36/244 (14%)

Query: 5   NIVQENFT-PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           NI+ E     +R+   +A     +R  ++++I    VKVNG+L++     +   D ++V+
Sbjct: 8   NIIAEKDDVDKRIDSFLASELDYTRSYLKKLILDGLVKVNGLLIK-PNYKLKEGDSVDVN 66

Query: 64  ------------GVPL--RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                        +PL     +   + +      +V         + V   L    +   
Sbjct: 67  IPEAEEIDLSPENIPLDIIYEDDDIIVINKPQGMVVHPAPGNYSGTLVNALLYHCKNLSG 126

Query: 110 SVGRLDI-------NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH------------ 150
             G L              +++      A +      +   + +                
Sbjct: 127 INGELRPGIVHRLDKDTSGVMVVAKNDKAHLDLSNQIKERTILKKYIAIVEGVIKDDEGS 186

Query: 151 -GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                       KK  V +   Y      +  +  +N+ +   ++ G+  +I+    +  
Sbjct: 187 IEAPIGRDHVERKKMAVTEDGRYALTLYKVLERYKNNSLIEATIKTGRTHQIRVHMSYIG 246

Query: 210 WKVN 213
             + 
Sbjct: 247 HPIV 250


>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 = 69.4 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 27/245 (11%), Positives = 66/245 (26%), Gaps = 38/245 (15%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V   +   R+ K +++    A+R  +E++I    VK+N  ++ +    +   + IEV   
Sbjct: 12  VSSEYEGMRLDKYLSKQIEEATRSYLEKLIDNNYVKINSKVINKNGRKLKLGEKIEVSIP 71

Query: 63  -----DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                D         +       + +      +V         + V   L    +     
Sbjct: 72  KEENIDIEAENISLDIVYENDDFIVINKSYGMVVHPAYGNYSGTLVNALLYYTNNLSSIN 131

Query: 112 GRLDINTE-----------------------GLLLLTNDGGLARVLELPSTQWLRVYRVR 148
           G +                              +          +  +           R
Sbjct: 132 GNIRPGIIHRLDKDTSGLILVAKNNYAHAKLASMFTDKTIHKTYLCIVKGNFSEENLNGR 191

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +D  +  K  +V +          +  Q    + V + +  G+  +I+   +  
Sbjct: 192 IENLIGRDSKDRKKMAVVKENGKTAISNYKVIEQVDGYSLVEIAIETGRTHQIRVHMKSI 251

Query: 209 NWKVN 213
           N  + 
Sbjct: 252 NHVIL 256


>gi|291336627|gb|ADD96173.1| hypothetical protein [uncultured organism MedDCM-OCT-S05-C185]
          Length = 59

 Score = 69.4 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 23/55 (41%), Positives = 34/55 (61%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
          +K K +     T +R+SK +ARAG+ SRRE ER I   RV ++  ++  AA+NV 
Sbjct: 2  VKFKTLFNNIDTEERISKRLARAGLCSRREAERWINAGRVSIDNEVINTAAINVS 56


>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 = 69.4 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 31/232 (13%), Positives = 62/232 (26%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K +A     SR +    I    V VNG L + A   V   D I              
Sbjct: 11  RLDKSLADLTELSRSQANEAIKAGTVLVNGKLAK-AKYVVKEGDVITYVLPEEEVLEYKA 69

Query: 63  DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           + +PL     +     +      +V   +     + V   +  +       G +      
Sbjct: 70  EDIPLDIIYEDADVAVVNKPQGIVVHPSAGHTSGTLVNALMYHVKDLSSINGVVRPGIVH 129

Query: 121 L---------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI- 170
                     ++  ND     +      +      V        +   +++  I      
Sbjct: 130 RIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHGNLPNDRGVIEAPIGRSDKD 189

Query: 171 --------CYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                          + T+  + G+   V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFTVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 69.1 bits (167), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 71/246 (28%), Gaps = 35/246 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK+ N   E     R+ KVIA      +R +V+ +I + ++ VN  +       V   D 
Sbjct: 1   MKEINFTIEESAKGRLDKVIAENVADLTRSQVQSLIKKGQILVND-VPTTNRYQVKPNDQ 59

Query: 60  IEV--------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           + +        D  P      +   +   + +      +V      D  + V   L    
Sbjct: 60  VIIKLPDPVAIDVQPEKMDLDIVYEDDDVIVVNKPQGMVVHPAPGHDHGTLVNGLLAHTP 119

Query: 106 SRVISVGRLDINTEGL--------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
              I+          +        ++  ND  L  + +    +  +           ++ 
Sbjct: 120 LATINGELRPGIVHRIDKDTSGLLMVAKNDQALVSLSKQLKDKTNQRKYWAIVHGNIKED 179

Query: 158 LNLLK-----------KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
              +            K  + +          +  + G    +   L  G+  +I+   +
Sbjct: 180 TGTINAPIGRSKKDRKKMAINEEGRPAVTHFKVLERFGEYTLIECQLETGRTHQIRVHLK 239

Query: 207 FFNWKV 212
           +    V
Sbjct: 240 YIGHPV 245


>gi|326692704|ref|ZP_08229709.1| ribosomal large subunit pseudouridine synthase D [Leuconostoc
           argentinum KCTC 3773]
          Length = 308

 Score = 69.1 bits (167), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 34/247 (13%), Positives = 73/247 (29%), Gaps = 35/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M DK  +       R+  ++A   +  SR  +   +    V VNG  ++R +  V + D 
Sbjct: 1   MTDKITINITDQTGRIDAILANQNLPYSRTVLANWVQSGEVLVNGQRVKR-SYKVAAGDV 59

Query: 60  IEVDGVPLRKAERTR--------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I +    ++  E                 L +      +V   +     + V   L    
Sbjct: 60  ISIQPPAVQPTEIVAEAMPLDIVYEDADLLVVNKPQGMVVHPAAGHTSGTLVNGLLHHAP 119

Query: 106 SRVISVGRLDINTEG---------LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
              I+                   ++   +    A   +L + +  R+Y     G+ +++
Sbjct: 120 LSTINGEFRPGIVHRIDRDTSGLLMVAKNDQAHQALSAQLKAHKNDRIYYALVRGEFEEN 179

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          KK  V +G         +  +      + V L  G+  +I+    
Sbjct: 180 TGTINAPIARHAIDRKKQAVQEGGREAVTHFEVIARYVGYTLLKVRLETGRTHQIRVHLT 239

Query: 207 FFNWKVN 213
           +    + 
Sbjct: 240 YIGHPIV 246


>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 = 69.1 bits (167), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 41/237 (17%), Positives = 77/237 (32%), Gaps = 35/237 (14%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVP 66
                R+ K +A     SR +    I +  V VNG  ++ A  NV S D+I     +   
Sbjct: 6   KEAGLRLDKALAETTDLSRSQANEQIKKGLVLVNGQAVK-AKYNVKSGDNITYQLPEEEV 64

Query: 67  LRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV----- 111
           L             E + L + +K  G+V   S      T+ + L      + S+     
Sbjct: 65  LDYQAENLPIDIIYEDSDLAIINKAQGMVVHPSAGHSSGTLVNALMYHIKDLSSINGVVR 124

Query: 112 ----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
                R+D +T GLL++  +    +VL         +         +      + +  + 
Sbjct: 125 PGIVHRIDKDTSGLLMVAKNDKAHQVLAEELKAKKSLRNYLAIVHGNLPNDRGMIEAPIG 184

Query: 168 QGICYGDMQ------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           +       Q             T+  + G    + + L  G+  +I+    +    V
Sbjct: 185 RSEKDRKKQSVTVKGKDAVTRFTVLERFGDYTLLELSLETGRTHQIRVHMAYIGHPV 241


>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 = 69.1 bits (167), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 35/244 (14%), Positives = 67/244 (27%), Gaps = 42/244 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            V E    +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V
Sbjct: 8   TVAEEQKNERIDKFVA--GINNEWSRTQVQQWIKDDVVTVNGKAVK-GNYKVRENDEITV 64

Query: 63  --------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                   D  P      +   +   L +      +V         + V   +       
Sbjct: 65  TIPEPEELDIQPEDMNLEIYYEDADVLVVNKPRSMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRV 147
              G +       +     G L       + + L                        + 
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKG 184

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                + +DK    +   V +   +      +  +      V   L  G+  +I+   ++
Sbjct: 185 TIDAPIARDKKER-QSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKY 243

Query: 208 FNWK 211
             + 
Sbjct: 244 IGYP 247


>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 = 69.1 bits (167), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 37/246 (15%), Positives = 73/246 (29%), Gaps = 37/246 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M D   +       R+ K+I A     +R +V++ +    V VNG  ++ A   V + D 
Sbjct: 1   MSDTFTI--TTESGRIDKIITAHETTHTRSQVQKWLQDGLVTVNGNPVK-ANFKVTAGDV 57

Query: 60  IEV---DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           + V   +  PL+             +   + +      +V         + V   L    
Sbjct: 58  VTVTIPEVKPLKAVAEPIPLEIVYEDDQVIVVNKPQGMVVHPAPGHPDGTLVNGLLYHTK 117

Query: 106 SRVIS-------VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-- 156
              I+       V R+D +T GLL++         L         +              
Sbjct: 118 LPGINGVIRPGIVHRIDKDTSGLLMVAKTEAAQLSLSAQLKAKTSIREYLALVHGTFKED 177

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          K+  V+    +      +  +  +   V   L  G+  +I+    
Sbjct: 178 EGTIDAPLGRDPRDRKRQAVVADGRHAVTHFQVLERFTNYTLVKCILDTGRTHQIRVHMA 237

Query: 207 FFNWKV 212
           + +  V
Sbjct: 238 YIHHPV 243


>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 = 69.1 bits (167), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 34/244 (13%), Positives = 65/244 (26%), Gaps = 42/244 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            V      +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V
Sbjct: 8   TVAAEQKNERIDKFVA--GINNEWSRTQVQQWIKDNVVTVNGKAVK-GNYKVKEEDEITV 64

Query: 63  --------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                   D  P      +   +   L +      +V         + V   +       
Sbjct: 65  TIPEPEELDIQPEDLNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRV 147
              G +       +     G L       + + L                        + 
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKG 184

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                + +DK    +   V +          +  +      V   L  G+  +I+   ++
Sbjct: 185 TIDAPIARDKKER-QSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKY 243

Query: 208 FNWK 211
             + 
Sbjct: 244 IGYP 247


>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 = 69.1 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/248 (17%), Positives = 79/248 (31%), Gaps = 38/248 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M    IV E     R+ K ++     SR ++E++I ++ VKV+  ++ +    +     I
Sbjct: 1   MYKNFIVLEES---RLDKFLSEKLGESRNQIEQLIKKEYVKVDDKIIAKTGYKLKENQEI 57

Query: 61  E-------------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
                         VD       E   + + +KP  LV   +      T+ D L +    
Sbjct: 58  LVELPEVEESISFDVDFDVEIIYEDEHILVINKPYNLVVHPAASVKEPTLVDWLKTKDIS 117

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR------------ 146
                   R   V RLD  T G++++         L                        
Sbjct: 118 LSTISGEERHGIVHRLDKGTSGVMVVAKTNEAHVALSKQLEDKTMGRYYLAIIDLPLKDN 177

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG-LREGKNREIKKVF 205
           +     + ++  N LK GIV +G         +   +     +    L  G+  +I+   
Sbjct: 178 IIIDKPIARNPNNRLKMGIVEKGKNAKTAFAKIALSEDEKYELICCKLFTGRTHQIRVHL 237

Query: 206 EFFNWKVN 213
              N  + 
Sbjct: 238 NSINRHIL 245


>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 = 69.1 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 30/232 (12%), Positives = 61/232 (26%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K +A     SR +    I    V VNG   + A   V   D I              
Sbjct: 11  RLDKALADLTELSRSQANEAIKAGTVLVNGKSAK-AKYAVKEGDVITYELPEEEVLEYKA 69

Query: 63  DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           + +PL     +     +      +V   +     + V   +  +       G +      
Sbjct: 70  EDIPLDIIYEDADVAVVNKPQGMVVHPSAGHTSGTLVNALMYHVKDLSSINGVVRPGIVH 129

Query: 121 L---------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI- 170
                     ++  ND     +      +      V        +   +++  I      
Sbjct: 130 RIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHGNLPNDRGVIEAPIGRSDKD 189

Query: 171 --------CYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                          + T+  + G+   V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFTVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 69.1 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 30/245 (12%), Positives = 66/245 (26%), Gaps = 38/245 (15%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           +Q   T +R+ + ++      SR  ++++I Q  V +N  +     + V + D I ++  
Sbjct: 6   LQVEETGERLDRYLSENLPNLSRSRIQQLIEQGNVHLNEQICTTKKITVKAGDRITLEIP 65

Query: 64  ----------GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--- 108
                      +PL     +   L L      +V         + V   L    +     
Sbjct: 66  EVQPLQVQAQDIPLDILYEDDHLLILNKPAGLVVHPAPGHPDGTLVNALLAHCPNLPGIG 125

Query: 109 ------------------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
                             I++ + DI    L          R          +    +  
Sbjct: 126 GVQRPGIVHRLDKDTTGAIAIAKTDIAYHSLQAQLQAKTARREYLGVVYGAPKTENGKID 185

Query: 151 GQ--VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                       +    + +G         +  + G+   V   L  G+  +I+      
Sbjct: 186 EPIGRHPQDRKKMAVVPIEKGGRNAVTHWQILERLGNQTLVLFQLETGRTHQIRVHSAKI 245

Query: 209 NWKVN 213
              + 
Sbjct: 246 GHPIV 250


>gi|255022986|ref|ZP_05294972.1| hypothetical protein LmonocyFSL_05005 [Listeria monocytogenes FSL
           J1-208]
          Length = 302

 Score = 69.1 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 69/246 (28%), Gaps = 36/246 (14%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+++  I++E+   +RV KVIA     SR  ++ M+    + VNG L +     V   D 
Sbjct: 1   MQNETLIIEESHARERVDKVIAEMMGKSRSAIQLMLKNGDITVNGELAK-PNYKVQVGDE 59

Query: 60  IEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I  +                 +   ++  L +      +V   +     + V   L    
Sbjct: 60  IHYEVREPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCD 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                 G++       +     G L       + + L           +           
Sbjct: 120 DLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVH 179

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           +K  V++          +  +      +   L  G+  +I+   
Sbjct: 180 QKGTIEAPIGRAKEDRQKMAVVRDGKEARTHFEVLERLPGYTLIKCKLDTGRTHQIRVHL 239

Query: 206 EFFNWK 211
           ++    
Sbjct: 240 KYIGHP 245


>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 = 69.1 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 29/244 (11%), Positives = 63/244 (25%), Gaps = 36/244 (14%)

Query: 5   NIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            I  E    QR+ K+++      SR +++  I    V VNG +++     V   D I+V 
Sbjct: 7   KIEDEALVGQRIDKLLSDFNSEWSRSQLQDWIKNDLVTVNGKIIKS-NYKVKLNDEIQVT 65

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   ++    +Y     +V         + V   +  I     
Sbjct: 66  EKEVVEADILPENLNLDIYYEDKDVAIVYKPKGMVVHPSPGHYTGTLVNGLMYQIKDLSG 125

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPST------------QWLRVYRVRFHGQVDQ-- 155
             G +       +     G L       +             +      V  +   D   
Sbjct: 126 INGEIRPGIVHRIDKDTSGLLMVAKNDVAHRGLVEQLMDKTVKRKYTALVHGNIPHDYGT 185

Query: 156 ------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                       +   V+           +         +   L  G+  +I+   ++  
Sbjct: 186 IDAPIGRNKKDRQSMDVVDDGKEAVTHFNVLEHFNDYTLIECQLETGRTHQIRVHMKYIG 245

Query: 210 WKVN 213
           + + 
Sbjct: 246 FPLV 249


>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 = 69.1 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 30/232 (12%), Positives = 61/232 (26%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K +A     SR +    I    V VNG   + A   V   D I              
Sbjct: 11  RLDKALADLTELSRSQANEAIKAGTVLVNGKSAK-AKYAVKEGDVITYVLPEEEVLEYKA 69

Query: 63  DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           + +PL     +     +      +V   +     + V   +  +       G +      
Sbjct: 70  EDIPLDIIYEDADVAVVNKPQGMVVHPSAGHTSGTLVNALMYHVKDLSSINGVVRPGIVH 129

Query: 121 L---------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI- 170
                     ++  ND     +      +      V        +   +++  I      
Sbjct: 130 RIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHGNLPNDRGVIEAPIGRSDKD 189

Query: 171 --------CYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                          + T+  + G+   V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFTVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 69.1 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 34/238 (14%), Positives = 70/238 (29%), Gaps = 39/238 (16%)

Query: 13  PQRVSKVIA--RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------- 63
            +R  K +A    GI +R     +I Q    VNG +  +    + + D + +D       
Sbjct: 11  GERTDKFLALQDTGI-TRSAAAALIEQGCCLVNGKIAAK-NQKLKTGDTVTLDVPEAQPA 68

Query: 64  -----GVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------R 107
                 +P  +   +   L +      +V         + V   +              R
Sbjct: 69  DILPENIPLDIVYEDSDLLVVNKPKGMVVHPAPGHYSGTLVNALMYHCGDSLSGINGVIR 128

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY------------RVRFHGQVDQ 155
              V R+D +T GLL++  +     +L                              + +
Sbjct: 129 PGIVHRIDRDTSGLLIVAKNDTAHNILAEQIKVHSFTREYMAVVQGVIKEDGTVDAPIGR 188

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            K +  K  +  +          ++    +N  V + L  G+  +I+    +    V 
Sbjct: 189 HKTDRKKMCVTTENSREAVTHYFVEQTYRNNTLVRLRLETGRTHQIRVHMAYIGHPVT 246


>gi|45644651|gb|AAS73039.1| predicted pseudouridine synthase D, 23S rRNA-specific [uncultured
           marine gamma proteobacterium EBAC20E09]
          Length = 311

 Score = 69.1 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 34/247 (13%), Positives = 76/247 (30%), Gaps = 38/247 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA----SRREVERMIAQQRVKVNGILLERAAVNVMS 56
           M++K  V +  +  R+ KV   + I     SR ++++ I + RV +N  +       V  
Sbjct: 1   MENKKTVSKEHSKMRLDKV---STIIFEDFSRTQIKKWILEGRVFLNDDIA-SPRDLVHE 56

Query: 57  TDHIEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
            D I++D +               +       L +  +P  ++   +     +     L 
Sbjct: 57  GDSIQIDPIAEEKISWVPEEIDIDVIYENDDYLIINKQPNLIMHPGAGCSSGTLANALLH 116

Query: 103 SIFS-----RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                    R   V RLD +T G++L+  +            +                 
Sbjct: 117 HYPELKNIARAGIVHRLDKDTSGVILVARNDKFRNYFVDLLQKREVTKLYSAIVVGTIIG 176

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQK-----------GSNAWVTVGLREGKNREIKKVFE 206
              +   I         M +  D ++           G+ + + + +  G+  +I+    
Sbjct: 177 SFKVTDPIGRDKKNRVKMSIRSDGKESETFVKLKESLGNYSLLDISIMTGRTHQIRVHLS 236

Query: 207 FFNWKVN 213
                + 
Sbjct: 237 SKKLPII 243


>gi|288871714|ref|ZP_06118719.2| ribosomal small subunit pseudouridine synthase A [Clostridium
          hathewayi DSM 13479]
 gi|288862314|gb|EFC94612.1| ribosomal small subunit pseudouridine synthase A [Clostridium
          hathewayi DSM 13479]
          Length = 74

 Score = 69.1 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 14/66 (21%), Positives = 30/66 (45%), Gaps = 1/66 (1%)

Query: 12 TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
             R+ K +   G  +R +++ M  + R+ VN +  +++   +   +D + VDG  +  A
Sbjct: 8  ELMRLDKYLTEMGQGTRSQIKEMARKGRITVNSVTEKKSDRKISPSSDAVAVDGRIVAYA 67

Query: 71 ERTRLW 76
          E     
Sbjct: 68 EYEYYM 73


>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 = 69.1 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 29/245 (11%), Positives = 67/245 (27%), Gaps = 38/245 (15%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V   +   R+ K ++     A+R  +E++I    VK+N  ++ +    +   + IEV   
Sbjct: 12  VNSEYKGMRLDKYLSEQIEEATRSYLEKLIDNNYVKINSKIINKNGRKLKLGEKIEVSIP 71

Query: 63  -----DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                D  P      +       + +      +V         + V   L    +     
Sbjct: 72  EEENIDIEPENIPLDIVYENNDFIVINKNYGMVVHPAYGNYTGTLVNALLYYTNNLSSIN 131

Query: 112 GRLDINTE-----------------------GLLLLTNDGGLARVLELPSTQWLRVYRVR 148
           G +                              + +        +  +           R
Sbjct: 132 GNIRPGIIHRLDKDTSGLILVAKSNYAHAKLASMFIDKTIHKTYLCIVKGNFSEENISGR 191

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +D  +  K  +V +          +  Q    + V V +  G+  +I+   +  
Sbjct: 192 IENLIGRDSKDRKKMAVVKENGKIAISNYKVVEQVEGYSLVEVAIETGRTHQIRVHMKSI 251

Query: 209 NWKVN 213
           N  + 
Sbjct: 252 NHVIL 256


>gi|226330251|ref|ZP_03805769.1| hypothetical protein PROPEN_04164 [Proteus penneri ATCC 35198]
 gi|225201046|gb|EEG83400.1| hypothetical protein PROPEN_04164 [Proteus penneri ATCC 35198]
          Length = 104

 Score = 69.1 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 23/99 (23%), Positives = 43/99 (43%), Gaps = 6/99 (6%)

Query: 6  IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG 64
          +  ++   +++ K++AR+G  SRRE+E  + + R+ ++G   +    ++V ST  I +DG
Sbjct: 1  MSDKSQRTEKLQKILARSGHGSRREIEGYLQEGRISIDGTKAKLGDRIDVTSTAKIRLDG 60

Query: 65 VPLRKAE-----RTRLWLYHKPIGLVTTHSDPDGRSTVF 98
            L   E        L  Y     L T        +   
Sbjct: 61 RILNIREAQKDVCRVLAYYKPEGELCTRSDPQGRPTVFP 99


>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 = 69.1 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/256 (17%), Positives = 79/256 (30%), Gaps = 46/256 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M    IV E     R+ K +A+   ASR ++E++I ++ VKV+G +  +  + +    ++
Sbjct: 1   MNKNFIVLETN---RLDKFLAQNIDASRNQIEQLIKKEFVKVDGKITNKTGLKLKENQNV 57

Query: 61  EV---------------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           EV                     D       E   + + +KP  L    +     +T+ D
Sbjct: 58  EVFFPETQLNKRKDEEFLKNSLEDKEVEIIYEDDYILVLNKPYNLTVHDAPSVKDATLVD 117

Query: 100 NLPSIFS---------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR------- 143
            L              R   V RLD  T G++++         L                
Sbjct: 118 WLKLKNISLSTISGEERHGIVHRLDKGTSGVMVIAKTNEAHLNLSKQLEDKSMGRYYLAI 177

Query: 144 -----VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-VGLREGK 197
                   V     + ++  N LK  I   G         +         +    L  G+
Sbjct: 178 LDLALKENVIIEKPIRRNPNNRLKMSIEENGRYAKSAFSKIALSDNEKFELIACKLYTGR 237

Query: 198 NREIKKVFEFFNWKVN 213
             +I+      N  + 
Sbjct: 238 THQIRVHLSSINRHIL 253


>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 = 69.1 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 64/244 (26%), Gaps = 36/244 (14%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           NI  +  T  RV K++       SR +++  I    V  N  +++     V   DHI V 
Sbjct: 7   NITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKS-NYKVKLNDHIVVT 65

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   +     +Y     +V         + V   +  I +   
Sbjct: 66  EKEVVEADILPENLNLDIYYEDDDVAVVYKTKGMVVHPSPGHYTNTLVNGLMYQIKNLSG 125

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPST------------QWLRVYRVRFHGQVDQ-- 155
             G +       + +   G L       +             +   +  V  +   D   
Sbjct: 126 INGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYIALVHGNIPHDYGT 185

Query: 156 ------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                    N  +   V+           +         V   L  G+  +I+   ++  
Sbjct: 186 IDAPIGRNKNDRQSMAVVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIRVHMKYIG 245

Query: 210 WKVN 213
           + + 
Sbjct: 246 FPLV 249


>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 = 69.1 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 30/233 (12%), Positives = 62/233 (26%), Gaps = 35/233 (15%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------- 63
             R+ K +A     SR +    I +  V VNG + ++A   V   D I  D         
Sbjct: 9   GVRLDKALADNSELSRSQANEEIKKGIVLVNGQV-KKAKYTVQEGDRITFDIPKEEVLDY 67

Query: 64  ---GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
               +PL     +     +      +V   +     + V   +  I       G +    
Sbjct: 68  QAENIPLDIIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMYHIKDLSSINGVVRPGI 127

Query: 119 EGL---------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
                       ++  ND     + E    +      +        +   +++  I    
Sbjct: 128 VHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDRGVIEAPIGRSD 187

Query: 170 I---------CYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                            +  +  + G    V + L  G+  +I+    +    
Sbjct: 188 KDRKKQAVTAKGKPAITRFHVLERFGDYTLVELSLETGRTHQIRVHMAYIGHP 240


>gi|53725232|ref|YP_102288.1| pseudouridine synthase family protein [Burkholderia mallei ATCC
           23344]
 gi|76811867|ref|YP_332519.1| pseudouridine synthase family protein [Burkholderia pseudomallei
           1710b]
 gi|124383384|ref|YP_001027001.1| RNA pseudouridine synthase family protein [Burkholderia mallei NCTC
           10229]
 gi|254203982|ref|ZP_04910342.1| RNA pseudouridine synthase family protein [Burkholderia mallei FMH]
 gi|254208962|ref|ZP_04915310.1| RNA pseudouridine synthase family protein [Burkholderia mallei JHU]
 gi|52428655|gb|AAU49248.1| pseudouridine synthase family protein [Burkholderia mallei ATCC
           23344]
 gi|76581320|gb|ABA50795.1| pseudouridine synthase family protein [Burkholderia pseudomallei
           1710b]
 gi|124291404|gb|ABN00673.1| RNA pseudouridine synthase family protein [Burkholderia mallei NCTC
           10229]
 gi|147745494|gb|EDK52574.1| RNA pseudouridine synthase family protein [Burkholderia mallei FMH]
 gi|147750838|gb|EDK57907.1| RNA pseudouridine synthase family protein [Burkholderia mallei JHU]
          Length = 235

 Score = 69.1 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/188 (22%), Positives = 72/188 (38%), Gaps = 17/188 (9%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             E   + L        T        +            V   GRLD ++EGLLLLT+DG
Sbjct: 38  PREPCPMRLIALNKPFGTICQFSAHETRASLGDWVKTPGVYPAGRLDADSEGLLLLTDDG 97

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---- 184
            L   +  P  + ++ Y  +  G  D   L  L++G+ +        +    T  G    
Sbjct: 98  ALQAKIAEPRHKLVKRYWAQVEGAPDAAALAALERGVDLGDYVSRPCRARFITPPGALWP 157

Query: 185 -----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAG 231
                        AW+ + + EGKNR+++++     +   RL+R+  G   +    L  G
Sbjct: 158 RNPPIRHRAAIPTAWIELEIAEGKNRQVRRMTAAVGFPTLRLVRVGIGALDVFALGLAPG 217

Query: 232 STREVSKK 239
            TRE+  +
Sbjct: 218 ETRELPPR 225


>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 = 69.1 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 33/240 (13%), Positives = 64/240 (26%), Gaps = 42/240 (17%)

Query: 10  NFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
               +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V    
Sbjct: 12  EQKNERIDKFVA--GINNEWSRTQVQQWIKDNVVTVNGKAVK-GNYKVKEEDEITVTIPE 68

Query: 63  ----DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
               D  P      +   +   L +      +V         + V   +          G
Sbjct: 69  PEELDIQPEDLNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGING 128

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRVRFHG 151
            +       +     G L       + + L                        +     
Sbjct: 129 VMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDA 188

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + +DK    +   V +          +  +      V   L  G+  +I+   ++  + 
Sbjct: 189 PIARDKKER-QSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYP 247


>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 = 69.1 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 30/241 (12%), Positives = 63/241 (26%), Gaps = 42/241 (17%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +R+ K IA     +R +++ +I Q  V VN   + +    V   D IE+    L K + 
Sbjct: 9   SERIDKYIANNSEITRNDIQALIVQGAVFVNSTKINKNKYIVHENDEIEII-KLLDKQQN 67

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                    I           + +     P+      ++    +      L   +G L  
Sbjct: 68  IEAQNLPLEIVYECDDYLVINKPSGLVVHPAPGHSSGTLVNSLMYHFKNNLSDVNGLLRM 127

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ---------- 182
            +     +      +        +    L K   I+   Y  +   ++ +          
Sbjct: 128 GIVHRIDKDTSGLLLVAKNNETHNYFAKLLKNHEIKRTYYAIVDGHIENRLINLDLPIGR 187

Query: 183 -------------------------------KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                                            +   V   L+ G+  +I+    +    
Sbjct: 188 DPNNRQKFAVTEQNSKEAFTALEVIKYLNLAGQNKTLVKCNLKTGRTHQIRVHLAYIKHP 247

Query: 212 V 212
           V
Sbjct: 248 V 248


>gi|325526198|gb|EGD03833.1| pseudouridine synthase [Burkholderia sp. TJI49]
          Length = 192

 Score = 69.1 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 40/182 (21%), Positives = 72/182 (39%), Gaps = 19/182 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +        GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKTPGV--YPAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVDGAPGAADLKALARGVDLGDYVTRPCRAEFIEPPDTLWPRNPPIR 120

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+ +++     +   RL+R+  G   +  L    G T  + 
Sbjct: 121 YRAAIPTTWIELAITEGKNRQGRRMTAAVGFPTLRLVRVGIGALDIFALGIAPGETIALP 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>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 = 69.1 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 28/243 (11%), Positives = 69/243 (28%), Gaps = 39/243 (16%)

Query: 6   IVQENFTPQRVSKVIA--RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           ++ E    +R+ KV++   A   SR +V++ I +   KVN   ++       + D I ++
Sbjct: 7   VINEEQAGERIDKVLSTVNA-EWSRSQVQQWIKEGHAKVNDKTVK-GNYKCKTGDAIIIE 64

Query: 64  --------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                          + +   ++  L +      +V         + V   +        
Sbjct: 65  VPELEELDVVAEEMDLDIYYEDQDVLVVNKPRGMVVHPAPGHHSGTLVNGLMAHCKDLSG 124

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR---------------------VYRVR 148
             G +       +     G L       + + L                           
Sbjct: 125 INGVMRPGIVHRIDKDTSGLLMVAKNDLAHESLVSQLVAKTVTRRYKAIVHGIIAHDHGT 184

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +DK +     +  +         T+  +    + V   L  G+  +I+   ++ 
Sbjct: 185 IDAPIGRDKQDRQSMTVTDENSRDAVTHFTVLQRFKDFSLVECKLETGRTHQIRVHMKYI 244

Query: 209 NWK 211
            + 
Sbjct: 245 GFP 247


>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 = 69.1 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 28/243 (11%), Positives = 69/243 (28%), Gaps = 39/243 (16%)

Query: 6   IVQENFTPQRVSKVIA--RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           ++ E    +R+ KV++   A   SR +V++ I +   KVN   ++       + D I ++
Sbjct: 7   VINEEQAGERIDKVLSTVNA-EWSRSQVQQWIKEGHAKVNDKTVK-GNYKCKTGDAIIIE 64

Query: 64  --------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                          + +   ++  L +      +V         + V   +        
Sbjct: 65  VPELEELDVVAEEMDLDIYYEDQDVLVVNKPRGMVVHPAPGHHSGTLVNGLMAHCKDLSG 124

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR---------------------VYRVR 148
             G +       +     G L       + + L                           
Sbjct: 125 INGVMRPGIVHRIDKDTSGLLMVAKNDLAHESLVSQLVAKTVTRRYKAIVHGVIAHDHGT 184

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +DK +     +  +         T+  +    + V   L  G+  +I+   ++ 
Sbjct: 185 IDAPIGRDKQDRQSMTVTDENSRDAVTHFTVLQRFKDFSLVECKLETGRTHQIRVHMKYI 244

Query: 209 NWK 211
            + 
Sbjct: 245 GFP 247


>gi|291530266|emb|CBK95851.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           siraeum 70/3]
          Length = 304

 Score = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 34/238 (14%), Positives = 70/238 (29%), Gaps = 39/238 (16%)

Query: 13  PQRVSKVIA--RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------- 63
            +R  K +A    GI +R     +I Q    VNG +  +    + + D + +D       
Sbjct: 12  GERTDKFLALQDTGI-TRSAAAALIEQGCCLVNGKIAAK-NQKLKTGDTVTLDVPEAQPA 69

Query: 64  -----GVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------R 107
                 +P  +   +   L +      +V         + V   +              R
Sbjct: 70  DILPENIPLDIVYEDSDLLVVNKPKGMVVHPAPGHYSGTLVNALMYHCGDSLSGINGVIR 129

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY------------RVRFHGQVDQ 155
              V R+D +T GLL++  +     +L                              + +
Sbjct: 130 PGIVHRIDRDTSGLLIVAKNDTAHNILAEQIKVHSFTREYMAVVQGVIKEDGTVDAPIGR 189

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            K +  K  +  +          ++    +N  V + L  G+  +I+    +    V 
Sbjct: 190 HKTDRKKMCVTTENSREAITHYFVEQTYRNNTLVRLRLETGRTHQIRVHMAYIGHPVT 247


>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 = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 26/236 (11%), Positives = 63/236 (26%), Gaps = 25/236 (10%)

Query: 1   MKDKNI---VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERA---- 50
           M++K +   + E  + +R+ K +     A   S  E+ +++    V+VNG  + +     
Sbjct: 1   MENKIVELSINEENSYRRLDKFLRNELKAVPLS--EIYKLLRTGCVQVNGKTVRKPYTEL 58

Query: 51  --AVNVMSTDHIEVDGVP-----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTV 97
                V     + V               +   +   L L  K    +         + +
Sbjct: 59  YVGDKVTIKADLAVYRQKKDLPSIPLKLDILYEDDNLLILNKKAGITIHPSEKTRSTTLI 118

Query: 98  FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                    +      +         +       +     S  +      + +  +   K
Sbjct: 119 QGLHFYGAKKGFKPHLVHRLDRDTSGVLVIAKNVKTARTLSHMFRNRLVKKEYITLVSGK 178

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +                 +  +       + + V L  G+  +I+K F      V 
Sbjct: 179 IFGDGFIDKPLDGSEALTEYKVLENFRDTSLLRVILHTGRTHQIRKHFALIGNPVV 234


>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 = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 30/232 (12%), Positives = 60/232 (25%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K +A     SR +    I +  V VNG  ++ A   V   D +              
Sbjct: 11  RLDKALADLTDLSRSQANDEIKKGTVLVNGKAVK-AKYAVKVGDVVTYEVPEEEVLEYKA 69

Query: 63  DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           + +P  +   +     +Y     +V   +     + V   +  I       G +      
Sbjct: 70  ENIPLDIVYEDEDVAVVYKPQGMVVHPSAGHTSGTLVNALMYHIKDLSSINGVIRPGIVH 129

Query: 121 LLLLTNDGGLARVLELPSTQ------------WLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            +     G L       +                 V  V  +   D+  +          
Sbjct: 130 RIDKDTSGLLMIAKNDTAHNALAAELKDKKSLRKYVAIVHGNIPNDRGVIEAPIGRSEKD 189

Query: 169 GICY------GDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                             +  + G+   V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTHFKVLERFGNYTLVELTLETGRTHQIRVHMAYIGHPV 241


>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 = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 33/239 (13%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I + RV VNG  + +    V+  + I +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKDWILEDRVTVNGKKVTKPKEKVLGGEAIAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  QIEEEARWLPQDIALDIVYEDTDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPAIIDV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L                               
Sbjct: 130 PRCGIVHRLDKDTTGLMVVAKSVPAQTHLVTALQAREITREYEAVAIGTMTAGGTVNEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 ARHSTKRTHMAVHPTGKPATTHYRIMEHFRAHTRLRLRLESGRTHQIRVHMAHINHPLL 248


>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 = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 39/232 (16%), Positives = 73/232 (31%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K +A     SR +    I +  V VNG  ++ A   V   D I              
Sbjct: 11  RLDKALADLTDLSRSQANDEIKKGTVLVNGEPVK-AKYTVKEGDIISYQLPEEEILDYEA 69

Query: 63  DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVG 112
           + +P+    E   L + +K  G+V   S      T+ + L              R   V 
Sbjct: 70  EDIPIEIVYEDEYLAIINKAQGMVVHPSAGHSSGTLVNALLYHIKDLSTINGVVRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           R+D +T GLL++  +     +L         + +       +      + +  + +    
Sbjct: 130 RIDKDTSGLLMIAKNDKAHHILADELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRSEKD 189

Query: 173 GDMQ------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
              Q              +  + G    V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKDAITRFQVVERFGDFTLVELSLETGRTHQIRVHMAYIGHPV 241


>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 = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/270 (15%), Positives = 92/270 (34%), Gaps = 52/270 (19%)

Query: 1   MKDKNIV--QENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M+++     +E  T +R+ K + A+    SR  ++++I    V+VNG  ++     + S 
Sbjct: 1   MREERFFTAEETVTNERIDKFLSAQMPDRSRSYIQKLIKDGLVEVNGKQVKT-NYKLGSE 59

Query: 58  DHIEVD----------GVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           D +++              +      E T L + +KP G+V   +      T+ + L   
Sbjct: 60  DEVKLQIPELEVPDILPEEIPLDILYEDTDLLVVNKPKGMVVHPAPGHYTGTLVNALMYH 119

Query: 105 FSRVIS----------VGRLDINTEGLLLLTNDGGLARVLELP-------------STQW 141
               +S          V R+D++T G LL+  +    ++L                    
Sbjct: 120 CRENLSGINGVMRPGIVHRIDMDTTGSLLVCKNDRAHQILAEQLKDHSITRRYEAIVHGN 179

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
           L+      +  + +   +  K  +             +  + G+   +   L  G+  +I
Sbjct: 180 LKEDSGTVNAPIGRHPTDRKKMSVHAPHGREAVTHYRVLERFGNYTHIECELETGRTHQI 239

Query: 202 KKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           +         +            LG L+ G
Sbjct: 240 RVHMASIGHPI------------LGDLVYG 257


>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 = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 32/242 (13%), Positives = 68/242 (28%), Gaps = 36/242 (14%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---- 60
           +V+   +  R+ K IA      SR  V+ +I Q+ +  NG L  + +  V + D I    
Sbjct: 10  VVKSEESGVRLDKYIATHISTISRTRVQELIKQKLITTNG-LQTKLSYKVNTNDKINIEI 68

Query: 61  ------EVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                  +D   L       +   + +      +V   +     + V   +    +    
Sbjct: 69  PSPQPLSLDPENLNLDIIYEDDDVIVVNKPQGMVVHPSAGHPDHTLVNGLIYHTKNLAKC 128

Query: 111 VGRLDINTEGLLLLTNDGGLA------------RVLELPSTQWLRVYRVRFHGQVDQ--- 155
              L       +     G L             + L     +   +  V  + +      
Sbjct: 129 DEILRPGIVHRIDKDTSGLLMIAKNATARISLEKQLANKINKREYIAIVHANFKHSSGVI 188

Query: 156 -----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      ++  V+          T+  Q    + V   L  G+  +I+    +   
Sbjct: 189 DAPIGRNPYQRQQMAVVASGKKAITHFTVLEQFPGYSLVKCVLETGRTHQIRVHMSYIGH 248

Query: 211 KV 212
            +
Sbjct: 249 PI 250


>gi|319745315|gb|EFV97632.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           agalactiae ATCC 13813]
          Length = 296

 Score = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 30/233 (12%), Positives = 63/233 (27%), Gaps = 35/233 (15%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------- 63
             R+ K +A     SR +    I +  V VNG + ++A   V   D I  D         
Sbjct: 9   GVRLDKALADNSELSRSQANEEIKKGIVLVNGQV-KKAKYTVQEGDRITFDIPKEEVLDY 67

Query: 64  ---GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
               +PL     +     +      +V + +     + V   +  I       G +    
Sbjct: 68  QAENIPLDIIYQDDDVAVVNKPQGMVVHSSAGHSSGTLVNALMYHIKDLSSINGVVRPGI 127

Query: 119 EGL---------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
                       ++  ND     + E    +      +        +   +++  I    
Sbjct: 128 VHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDRGVIEAPIGRSD 187

Query: 170 I---------CYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                            +  +  + G    V + L  G+  +I+    +    
Sbjct: 188 KDRKKQAVTAKGKPAITRFHVLERFGDYTLVELSLETGRTHQIRVHMAYIGHP 240


>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 = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 30/237 (12%), Positives = 61/237 (25%), Gaps = 35/237 (14%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
                R+ K +A     SR +    I    V VNG   + A   V   D I         
Sbjct: 6   KEAGNRLDKALADLTELSRSQANEAIKAGTVLVNGKSAK-AKYAVKEGDVITYELPEEEV 64

Query: 63  -----DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                + +PL     +     +      +V   +     + V   +  +       G + 
Sbjct: 65  LEYKAEDIPLDIIYEDADVAVVNKPQGMVVHPSAGHTSGTLVNALMYHVKDLSSINGVVR 124

Query: 116 INTEGL---------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
                          ++  ND     +      +      V        +   +++  I 
Sbjct: 125 PGIVHRIDKDTSGLLMVAKNDKAHNALAAELKDKKSLRKYVAIVHGNLPNDRGVIEAPIG 184

Query: 167 IQGI---------CYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                               + T+  + G+   V + L  G+  +I+    +    V
Sbjct: 185 RSDKDRKKQAVTAKGKPAVTRFTVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 30/233 (12%), Positives = 62/233 (26%), Gaps = 35/233 (15%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------- 63
             R+ K +A     SR +    I +  V VNG + ++A   V   D I  D         
Sbjct: 9   GVRLDKALADNSELSRSQANEEIKKGIVLVNGQV-KKAKYTVQEGDRITFDIPKEEVLDY 67

Query: 64  ---GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
               +PL     +     +      +V   +     + V   +  I       G +    
Sbjct: 68  QAENIPLDIIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMYHIKDLSSINGVVRPGI 127

Query: 119 EGL---------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
                       ++  ND     + E    +      +        +   +++  I    
Sbjct: 128 VHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDRGVIEAPIGRSD 187

Query: 170 I---------CYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                            +  +  + G    V + L  G+  +I+    +    
Sbjct: 188 KDRKKQAVTAKGKPAITRFHVLERFGDYTLVELSLETGRTHQIRVHMAYIGHP 240


>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 = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 30/235 (12%), Positives = 65/235 (27%), Gaps = 36/235 (15%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
              R+ KV+       SR +++  +    V VNG  ++ A   V   D I V        
Sbjct: 11  ESGRIDKVLTNLFTDYSRSQIQLWLKNGAVSVNGQPVK-ANYKVKQGDEITVLIPEPETL 69

Query: 63  ----DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
               + +P  +   +     +      +V   +     + V   +  I       G +  
Sbjct: 70  DVVPENIPLTIVYEDEDVAVINKPQGMVVHPSAGHTHGTMVNALIYHIKDLSTINGVIRP 129

Query: 117 NTEGLLLLTNDGGLARVLELPSTQ------------WLRVYRVRFHGQVDQDKLNL---- 160
                +     G L       + +               V  V      ++  +N     
Sbjct: 130 GIVHRIDKDTSGLLMVAKNDQAHESLAQQLKDKTSLRKYVALVHGEIPHEKGTINAPIGR 189

Query: 161 ----LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                K   + +         T+  +      V + L  G+  +I+   ++  + 
Sbjct: 190 SKENRKMQAIREDGKPAVTHFTVLERFEGFTLVELKLETGRTHQIRVHMKYIGYP 244


>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 = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 30/235 (12%), Positives = 65/235 (27%), Gaps = 36/235 (15%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
              R+ KV+       SR +++  +    V VNG  ++ A   V   D I V        
Sbjct: 11  ESGRIDKVLTNLFTDYSRSQIQLWLKNGAVSVNGQPVK-ANYKVKQGDEITVLIPEPETL 69

Query: 63  ----DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
               + +P  +   +     +      +V   +     + V   +  I       G +  
Sbjct: 70  DVVPENIPLTIVYEDEDVAVINKPQGMVVHPSAGHTHGTMVNALMYHIKDLSTINGVIRP 129

Query: 117 NTEGLLLLTNDGGLARVLELPSTQ------------WLRVYRVRFHGQVDQDKLNL---- 160
                +     G L       + +               V  V      ++  +N     
Sbjct: 130 GIVHRIDKDTSGLLMVAKNDQAHESLAQQLKDKTSLRKYVALVHGEIPHEKGTINAPIGR 189

Query: 161 ----LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                K   + +         T+  +      V + L  G+  +I+   ++  + 
Sbjct: 190 SKENRKMQAIREDGKSAVTHFTVLERFEGFTLVELKLETGRTHQIRVHMKYIGYP 244


>gi|25011477|ref|NP_735872.1| hypothetical protein gbs1435 [Streptococcus agalactiae NEM316]
 gi|24413015|emb|CAD47094.1| unknown [Streptococcus agalactiae NEM316]
          Length = 296

 Score = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 28/233 (12%), Positives = 60/233 (25%), Gaps = 35/233 (15%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP----- 66
             R+ K +A     SR +    I +  V VNG + ++A   V   D I  D         
Sbjct: 9   GVRLDKALADNSELSRSQANEEIKKGIVLVNGQV-KKAKYTVQEGDRITFDIPKEEVLDY 67

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                   +   +     +      +V   +     + V   +  I       G +    
Sbjct: 68  QAENISLDIIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMYHIKDLSSINGVVRPGI 127

Query: 119 EGL---------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
                       ++  ND     + E    +      +        +   +++  I    
Sbjct: 128 VHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDRGVIEAPIGRSD 187

Query: 170 I---------CYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                            +  +  + G    V + L  G+  +I+    +    
Sbjct: 188 KDRKKQAVTAKGKPAITRFHVLERFGDYTLVELSLETGRTHQIRVHMAYIGHP 240


>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 = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 46/237 (19%), Positives = 78/237 (32%), Gaps = 34/237 (14%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
               R+ KV++ A  ASR +V R+I    V V GI  E+A+  V   + I          
Sbjct: 13  SEGGRLDKVLSAALGASRNQVARLIEAGAVSVEGIPAEKASRKVEPGERIAYRILEAPRR 72

Query: 63  DGVPLR-----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RV 108
           D +P+        E   L + +KP G+V   +      T+   L              R 
Sbjct: 73  DSLPVEFDVEVLYEDEYLMILNKPAGVVVHPAPSVREPTLVHWLVQRGISLSTLAGEERH 132

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR------------VYRVRFHGQVDQD 156
             V RLD  T G L++     + + L                        +     + ++
Sbjct: 133 GIVHRLDKETSGALVIAKTNAVHQALSEELKSREMGRYYLALIDHPLKEDLTVDAPIARN 192

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             N LK  +V  G       + L   +  +  +   L  G+  +I+         + 
Sbjct: 193 PANRLKMAVVEGGREARTDFLKLAEGEEGSELIAARLHTGRTHQIRVHLAKIGRHIL 249


>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 = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 35/247 (14%), Positives = 79/247 (31%), Gaps = 37/247 (14%)

Query: 3   DKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +K IV+E F   R+ + +A A    SR  ++  I    + VNG +++   + +   D +E
Sbjct: 8   NKLIVEEMFDGMRIDQYMALAVTDYSRSVLQTWIKNGNITVNGNVVK-PNLRLKEDDVVE 66

Query: 62  VD-------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR- 107
            +              + +   +   L +      +V        + T+   L +  ++ 
Sbjct: 67  YEITEEQISIVPVPMDLDIVYEDDAILVVNKPKGLIVHPSPSTLNQPTLVHGLLAHTTQL 126

Query: 108 --------VISVGRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVYR 146
                      V R+D +T GLL++        +L                     +   
Sbjct: 127 SDLNGELRPGIVHRIDKDTTGLLVVAKTNEAHEILVEDLKQRLISREYVAIVHHQFKHQS 186

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                 + +D  N  +  +  Q          L  +    + +   L  G+  +I+   +
Sbjct: 187 ATVDAPIGRDPKNRQRMAVTDQNSKQAVTHFYLAERFNDFSVLRCKLDTGRTHQIRVHAQ 246

Query: 207 FFNWKVN 213
           +    + 
Sbjct: 247 YIKHPIV 253


>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 = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 33/234 (14%), Positives = 65/234 (27%), Gaps = 35/234 (14%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
            QR+ K ++     SR      I   +V VNG   ++A   V   D +            
Sbjct: 9   GQRLDKALSELTELSRSLANEQIKAGQVLVNGQ-AKKAKYTVQEGDIVTYHVPEPEVLEY 67

Query: 63  --DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
             + +PL     +     +      +V   +     + V   +  I       G L    
Sbjct: 68  VAEDIPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGI 127

Query: 119 EGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              +     G L       +           + LR Y    HG +  D+  +       +
Sbjct: 128 VHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSE 187

Query: 169 GICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                            +  +  + G  + + + L  G+  +I+    +    V
Sbjct: 188 KDRKKQAVTAKGKPAVTRFQVLERFGDYSLLELQLETGRTHQIRVHMAYIGHPV 241


>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 = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 33/240 (13%), Positives = 65/240 (27%), Gaps = 39/240 (16%)

Query: 13  PQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------- 62
           P+R+ + +A    A SR  V+++I Q  V VNG + +R    V + D+I +         
Sbjct: 12  PERLDRWLADNVEAFSRNRVQQLIEQGAVSVNGEVCDRKKELVTAGDYIILSVPEAQPYE 71

Query: 63  ---DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
              + +PL     +   L +      +V         + V   L     ++  VG +   
Sbjct: 72  LTPEDIPLDILYEDDQLLIVNKPAGMVVHPAPGHATGTLVHALLFYCGEQLTGVGGVQRP 131

Query: 118 ----------------------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ--V 153
                                    L          R          +  +         
Sbjct: 132 GIVHRLDKNTTGAMVVAKTETALCNLQQQIQAKTAKREYLGIVNGAPKAEQGTIDQPIGR 191

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +    V  G            + G+   +   L  G+  +I+    +    + 
Sbjct: 192 HPKHRKKMSILPVESGGRTAITHWKTVERLGNYTLIHFQLETGRTHQIRVHSAYLGLPII 251


>gi|328946167|gb|EGG40312.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK1087]
          Length = 298

 Score = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 35/240 (14%), Positives = 66/240 (27%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GV 65
           ++ +   QR+ K +A     SR      I   R+ VNG   ++A   V   D I  +   
Sbjct: 5   IEASVAGQRLDKAVAELTYLSRSLANEQIKDGRILVNGQ-AKKAKYAVKEGDIIYYELPE 63

Query: 66  P-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
           P             +   +     +      +V   +     + V   +  I       G
Sbjct: 64  PEVVEYVAEDIPLEIVYQDEDVAVINKPQGMVVHPSAGHTSGTLVNALMYHIQDLSGING 123

Query: 113 RLDINTEGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLK 162
            L       +     G L       +           + LR Y    HG +  D+  +  
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 163 KGIVIQGICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                +                    +  + G  + V + L  G+  +I+    +    V
Sbjct: 184 PIGRSEKDRKKQAVTAKGKPALTSFQVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 243


>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 = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 31/245 (12%), Positives = 71/245 (28%), Gaps = 36/245 (14%)

Query: 3   DKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           ++  +  + T  R+ KV+A    + +R +V+++I   +V VNG L      +V   D I 
Sbjct: 20  EQQFMITDQTG-RLDKVLAALQSVWTRSQVDKLIKTDQVTVNGQLEAS-KYHVKPGDEIV 77

Query: 62  VDGVPLR--------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           V    ++                +   L +      +V         + V   L      
Sbjct: 78  VAAQTVQQTTIEPENIPLDIVYEDDDVLVVNKPQGMVVHPAPGHPNHTLVNALLYHSPLS 137

Query: 108 VISVGRLDINTEGL--------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
            I+          +        ++  ND     +      +      V     V ++   
Sbjct: 138 TINGEFRPGIVHRIDKDTSGLLMVAKNDRAHQSLAAQLKAKTNLREYVALVHGVIKEDTG 197

Query: 160 LLK-----------KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
            +            K  +I+          +  +      ++  L  G+  +I+   +  
Sbjct: 198 TINAPLGRSPKDRKKQAIIKTGRPAVTHFKVLKRYQHYTLISCRLETGRTHQIRVHLQSI 257

Query: 209 NWKVN 213
              + 
Sbjct: 258 GHPLV 262


>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 = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 25/244 (10%), Positives = 65/244 (26%), Gaps = 37/244 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--- 61
           I  E    +R+ K ++      SR ++++ I +  + VN   ++     +   D I+   
Sbjct: 15  IAGEEHAGERIDKFVSECLDGVSRTQIQQWIKEGHISVNEKQVK-PNYKLAEGDRIKLNI 73

Query: 62  -----VDGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                VD  P      +   ++  + +      +V         + V   +         
Sbjct: 74  PDPEQVDIRPEPIPLDIYYEDKDVIVVNKPRGMVVHPAPGHSSGTLVNALMYHCKDLSGI 133

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPST---------------------QWLRVYRVRF 149
            G +       +     G +       +                        L   +   
Sbjct: 134 NGEMRPGIVHRIDKDTSGLIMAAKHDKAHASLADQLKEHSVTRKYLALVQGNLAHEQGTV 193

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +D  +     +  +          +  + G      + L  G+  +I+   +F  
Sbjct: 194 EAPIGRDPKDRKLYTVTEKNSKEAVTHFVVMERFGDYTLTELKLETGRTHQIRVHMKFIG 253

Query: 210 WKVN 213
             + 
Sbjct: 254 HPLV 257


>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 = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 29/242 (11%), Positives = 67/242 (27%), Gaps = 38/242 (15%)

Query: 10  NFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
            +   R+ K ++     A+R  +E++I    VKVN  ++++    + S + IEV      
Sbjct: 15  EYEGMRLDKYLSEQIEEATRSYLEKLIDNNFVKVNSKIIKKNGRKLKSGEKIEVLIPEEE 74

Query: 63  --DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
             D         +       + +      +V         + V   L    +     G +
Sbjct: 75  NIDIEAENIPLDVVYENDDFIVINKNYGMVVHPAYGNYTGTLVNALLYYTNNLSSVNGNI 134

Query: 115 DINTE-----------------------GLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151
                                         + +        +  +           R   
Sbjct: 135 RPGIIHRLDKDTSGLILIAKNNFAHAKLASMFIDKTIHKTYLCIVKGNFSEENLSGRIEN 194

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + +D  +  K  +V +          +  Q    + V V +  G+  +I+   +  N  
Sbjct: 195 LIGRDIKDRKKMAVVKENGKIAISNYRVIEQVEGYSLVEVAIETGRTHQIRVHMKSINHV 254

Query: 212 VN 213
           + 
Sbjct: 255 IL 256


>gi|330896110|gb|EGH28331.1| RNA-binding S4 [Pseudomonas syringae pv. japonica str. M301072PT]
          Length = 74

 Score = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 11 FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            P R+SK +      SRRE E  I    V V+G ++E     V  T  IE+
Sbjct: 2  TDPIRLSKRLIELVGCSRREAELFIEGGWVTVDGEVIEEPHFKVS-TQKIEL 52


>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 = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 69/246 (28%), Gaps = 36/246 (14%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+++  I++E+   +RV KVIA     SR  ++ M+    + VNG L +     V   D 
Sbjct: 1   MQNETLIIEESHARERVDKVIAEMMEKSRSAIQLMLKNGDITVNGELAK-PNYKVQVGDE 59

Query: 60  IEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I  +                 +   ++  L +      +V   +     + V   L    
Sbjct: 60  IRYEAREPEELEILAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCD 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                 G++       +     G L       + + L           +           
Sbjct: 120 DLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVH 179

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           +K  V++          +  +      +   L  G+  +I+   
Sbjct: 180 QKGTIEAPIGRAKEDRQKMAVVRDGKEARTHFEVIERLPGYTLINCKLDTGRTHQIRVHL 239

Query: 206 EFFNWK 211
           ++    
Sbjct: 240 KYIGHP 245


>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 = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 31/249 (12%), Positives = 67/249 (26%), Gaps = 37/249 (14%)

Query: 1   MKDKNIVQENFT-PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M++ +I+        R+ K I+     SR  V+ ++ +  + VN    + A   V + DH
Sbjct: 1   MREIDIIAAAEEAGVRIDKYISEQEELSRSRVQSLLQEGLILVNEKPAK-ANYKVKAQDH 59

Query: 60  IE--VDGVP------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I    D               +R  +   + +      +V   +     + V   L    
Sbjct: 60  ITACFDDEMELEARPEAMELDVRYEDEDVIVINKPKNIVVHPAAGNQTGTLVNGLLYHCK 119

Query: 106 SRVISVGRLDIN---------------------TEGLLLLTNDGGLARVLELPSTQWLRV 144
                 G L                           L        + R+        ++ 
Sbjct: 120 DLSGINGTLRPGIIHRIDKDTTGLLIVAKNDLAHASLSKQLQSKTVNRLYYALVHGVIQH 179

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                   + +D  +  K  +             +  +  +   V   L  G+  +I+  
Sbjct: 180 DFGTIDAPIGRDVKDRQKMAVTSTNSKDARTHFQVIERFENYTLVECRLETGRTHQIRVH 239

Query: 205 FEFFNWKVN 213
            ++    V 
Sbjct: 240 MQYIGHPVV 248


>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 = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 28/244 (11%), Positives = 67/244 (27%), Gaps = 35/244 (14%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            +K I++E+   +R+ K +A     SR  ++ M+    + VNG + +     V   D I 
Sbjct: 3   NEKLIIEESHARERIDKAVAELTGKSRSAIQIMLKSGDITVNGEIAK-PNYKVQVGDEIY 61

Query: 62  VDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           ++                 +   ++  L +      +V   +     + V   L      
Sbjct: 62  LEVREPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDL 121

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------------ 155
               G++       +     G L       + + L           +             
Sbjct: 122 SGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQK 181

Query: 156 --------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                         +K  V++          +  +      +   L  G+  +I+   ++
Sbjct: 182 GTIEAPIGRAKEDRQKMAVVRDGKEARTHFEVIERLPGYTLINCKLDTGRTHQIRVHLKY 241

Query: 208 FNWK 211
               
Sbjct: 242 IGHP 245


>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 = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 27/245 (11%), Positives = 69/245 (28%), Gaps = 41/245 (16%)

Query: 6   IVQENFTPQRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +V+ +   +R+ K +    A + + SR +++  I    V VNG   + A   + + D I 
Sbjct: 26  VVEVDEAGERLDKYVTESFADSAV-SRTQIQEWIKSGAVLVNGTEAK-AKHRLEAGDVIT 83

Query: 62  VD---GVP-----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           V+     P           +   +   + +  +   +V         + V   +      
Sbjct: 84  VEVPEPEPAEIIAEPIPLNIVYEDEDVIVINKQRGLVVHPAPGHHSGTVVNALMYHCQDL 143

Query: 108 VISVGRLDIN---------------------TEGLLLLTNDGGLARVLELPSTQWLRVYR 146
               G +                           L     +  + R         L   R
Sbjct: 144 SGINGSIRPGIVHRIDKDTSGLLMAAKNDAAHASLSAQLKEHTVTRKYIALVHGNLPHDR 203

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                 + +D  +     +  +   +     ++  +      + + L  G+  +I+   +
Sbjct: 204 GTVDAPIGRDSRDRKMFAVTDKNSKHAVTHFSVIERLDDYTVLELQLETGRTHQIRVHMK 263

Query: 207 FFNWK 211
           +    
Sbjct: 264 YIGHP 268


>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 = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 30/235 (12%), Positives = 65/235 (27%), Gaps = 36/235 (15%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
              R+ KV+       SR +++  +    V VNG  ++ A   V   D I V        
Sbjct: 11  ESGRIDKVLTNLFTDYSRSQIQLWLKNGAVSVNGQPVK-ANYKVKQGDEITVLIPEPETL 69

Query: 63  ----DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
               + +P  +   +     +      +V   +     + V   +  I       G +  
Sbjct: 70  DVVPENIPLTIVYEDEDVAVINKPQGMVVHPSAGHTHGTMVNALMYHIKDLSTINGVIRP 129

Query: 117 NTEGLLLLTNDGGLARVLELPSTQ------------WLRVYRVRFHGQVDQDKLNL---- 160
                +     G L       + +               V  V      ++  +N     
Sbjct: 130 GIVHRIDKDTSGLLMVAKNDQAHESLAQQLKDKTSLRKYVALVHGEIPHEKGTINAPIGR 189

Query: 161 ----LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                K   + +         T+  +      V + L  G+  +I+   ++  + 
Sbjct: 190 SKENRKMQAIREDGKPAVTHFTVLERFEGFTLVELKLETGRTHQIRVHMKYIGYP 244


>gi|311113288|ref|YP_003984510.1| ribosomal RNA large subunit methyltransferase J [Rothia
          dentocariosa ATCC 17931]
 gi|310944782|gb|ADP41076.1| ribosomal RNA large subunit methyltransferase J [Rothia
          dentocariosa ATCC 17931]
          Length = 244

 Score = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 14 QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+ K +A  G +ASR    ++I    V VNG ++ +A+  V   D + V   PL
Sbjct: 1  MRLDKFLAEHGLVASRTLAAKLIDAGCVSVNGKIVYKASQPVHRDDDVLVQESPL 55


>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 = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 27/237 (11%), Positives = 59/237 (24%), Gaps = 38/237 (16%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R  KV+A      SR  +++++AQ  V +NG +L + A  V + D + ++  P       
Sbjct: 59  RADKVLAECVAEFSRSYLQQLLAQGAVTLNGRVLVKPATKVAAGDRMVLEMRPTQQSMAF 118

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL---- 114
                   +   +   L +      +V         + +   L                 
Sbjct: 119 QPEDMALDVVYEDEHLLVVNKPAGLVVHPAPGNWTGTLLNGLLGRDPKAREVPRAGIVHR 178

Query: 115 -----------------DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                                  ++   +       L   +    +   V      D   
Sbjct: 179 LDKDTSGLMVVARSRAAMDALVAMIAARDVSRQYLALAHKAWGPRKHREVDAPIGRDPRN 238

Query: 158 LNLL-KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +    +           + L       + V   L  G+  +I+         + 
Sbjct: 239 RLRMAVVDLAQHAGKTARTDIDLLAGNEEVSLVRCTLHTGRTHQIRVHMASLGHPLV 295


>gi|113955440|ref|YP_730120.1| pseudouridine synthase [Synechococcus sp. CC9311]
 gi|113882791|gb|ABI47749.1| possible pseudouridine synthase [Synechococcus sp. CC9311]
          Length = 160

 Score = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 39/143 (27%), Positives = 64/143 (44%), Gaps = 23/143 (16%)

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL- 179
           +LLLT++G L + L  P     R Y V+  G  ++ +LN L++G+ IQG      +  + 
Sbjct: 1   MLLLTDNGRLQQRLTDPRFGHWRQYWVQVEGCANEVQLNQLQRGVTIQGRLTRPAKARIL 60

Query: 180 ----------------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY--- 220
                           + +     W+ + LREG+NR+++++         RLIR S    
Sbjct: 61  SDDERQTISDRKPPIRERRSIPTCWLCLELREGRNRQVRRMTAAVGLPTLRLIRHSIDLM 120

Query: 221 -GPFQL--GTLLAGSTREVSKKI 240
            G   L    L AG  REV++  
Sbjct: 121 DGEIVLSIKDLSAGMWREVTRTE 143


>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 = 68.7 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 35/246 (14%), Positives = 71/246 (28%), Gaps = 36/246 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  +  +    + QR+ K +A      SR  ++ ++    V VNG    + +  V   D 
Sbjct: 1   MNREYELTAEESGQRLDKYLAGEMTNLSRSRIKELVQAGEVLVNGKK-SKVSYKVQKGDL 59

Query: 60  IEV------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I+V            + +P  +   +   + +      +V   +     + V   L    
Sbjct: 60  IQVTVLPLEPLKLEAENIPLDIVYEDEDVIVVNKPQGMVVHPAAGHPSHTLVNALLYHTR 119

Query: 106 --------SRVISVGRLDINTEGLLLLTND------------GGLARVLELPSTQWLRVY 145
                    R   V R+D +T GLL++  +                +   L         
Sbjct: 120 DLADSPEGFRPGIVHRIDKDTSGLLMVAKNAAARESLEKQLAAKSNKRQYLAIVHGNFAE 179

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           K+  V++          +  Q    + V   L  G+  +I+   
Sbjct: 180 EEGTIDAPIGRNPKDRKQMAVVEKGKSAVTHFKVLEQYQGYSLVECQLETGRTHQIRVHM 239

Query: 206 EFFNWK 211
            +    
Sbjct: 240 AYIGHP 245


>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 = 68.3 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 30/245 (12%), Positives = 74/245 (30%), Gaps = 34/245 (13%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M    + +ENF  QR+   +A+    SR +++ +I  ++V VN   ++ A   +   D I
Sbjct: 1   MDTFKVDKENF-GQRLDVYLAKLVDLSRSQIKNLIDNEKVLVNNKNVK-AGYKLSEDDVI 58

Query: 61  EV----DGVP--------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
            +    D  P        +   +     +      +V   +     + V   L    +++
Sbjct: 59  SLEYPKDSKPFAEKIDFNVIYEDDYIAVISKPQDLVVHIGAGNSSGTLVNGLLYKFKNQL 118

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPST--------------------QWLRVYRVR 148
            ++  L       L     G +       +                              
Sbjct: 119 SNLDPLRPGIVHRLDKNTSGLMIIAKNNQAHINLVDQFKNSQIKKYYLAIVHGKTPESGI 178

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + ++  +  K  +V +       +     +    + + + L  G+  +I+    + 
Sbjct: 179 IEEPIGRNPNDRKKMAVVYKNSKQAITKYKKLKEFQEYSLLNINLLTGRTHQIRVHMAYI 238

Query: 209 NWKVN 213
            + V 
Sbjct: 239 GYPVL 243


>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 = 68.3 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 42/247 (17%), Positives = 76/247 (30%), Gaps = 36/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K  +       R+ K +A      SR  V+ +I    + VN   +E+A+  V   D 
Sbjct: 1   MTKKYELTVENEKGRLDKYLADKIDDLSRTRVKELIDDGLILVN-QKVEKASYKVKDGDA 59

Query: 60  IEV------------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           IEV            + +PL     +   + +      +V   +     + V   L    
Sbjct: 60  IEVTVPAVKPLDVIPENIPLDIIYEDNDVIVVNKPQGMVVHPAAGHPDHTLVNALLYHTK 119

Query: 106 --------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-- 155
                    R   V R+D +T GLL++  +  +   LE                  +   
Sbjct: 120 DLASSPEGFRPGIVHRIDKDTSGLLMIAKNSQVRESLEDQLAHKTNKRLYLAIVHGNFAE 179

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                        +  KK  V+ G  +      +  Q    + +   L  G+  +I+   
Sbjct: 180 EEGTIDAPIARNPHDRKKMGVVAGGKHAVTHFKVIEQFKGYSLIQCKLETGRTHQIRVHL 239

Query: 206 EFFNWKV 212
            +    V
Sbjct: 240 SYIGHPV 246


>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 = 68.3 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 32/234 (13%), Positives = 64/234 (27%), Gaps = 35/234 (14%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
             R+ K ++     SR      I   +V VNG + ++A   V   D +            
Sbjct: 9   GIRLDKALSDLTELSRSLANEQIKSGQVLVNGQV-KKAKYTVQEGDVVTYQVPEPEVLEY 67

Query: 63  --DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
             + +PL     +     +      +V   +     + V   +  I       G L    
Sbjct: 68  VAEDIPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGI 127

Query: 119 EGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              +     G L       +           + LR Y    HG +  D+  +       +
Sbjct: 128 VHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSE 187

Query: 169 GICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                            +  +  + G    + + L  G+  +I+    +    V
Sbjct: 188 KDRKKQAVTVKGKPAVTRFQVLERFGDYTLLELQLETGRTHQIRVHMAYIGHPV 241


>gi|325116556|emb|CBZ52110.1| putative 16S pseudouridylate synthase [Neospora caninum Liverpool]
          Length = 255

 Score = 68.3 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 15/57 (26%), Positives = 29/57 (50%)

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           G    +++ L EG++R+I+++ E    +V ++ R+  G   LG L  G  R +    
Sbjct: 196 GRTTRLSIELLEGRHRQIRRMCELVGLRVLKIHRVRIGKISLGALPQGRWRLLLPHE 252


>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 = 68.3 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 29/250 (11%), Positives = 69/250 (27%), Gaps = 39/250 (15%)

Query: 2   KDKNIVQENFTPQ-RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
            ++NIV      + R+ K ++     +R  ++++I  + + VN     + A  +   D I
Sbjct: 22  NEENIVVLKEEAESRIDKFLSERLELTRTRIQQLIKDENILVNEKK-TKPAYKIEENDTI 80

Query: 61  EV--------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           +V                + +   +     +  K   +V   +     + V   L  I  
Sbjct: 81  KVVIPELETVEIKPENIDIEIIYEDNDLAVINKKAGIVVHPANGHYSGTLVNAILYYIKD 140

Query: 107 RVISVGRLDI-------NTEGLLLLTNDGGLARVLELPSTQWLRVYRVR----------- 148
                G +              LL+      A +          V +             
Sbjct: 141 LSGINGEIRPGIVHRLDKDTSGLLIIAKNDKAHLKLSQMFHDKTVKKTYLAILKGKLSQK 200

Query: 149 -----FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                     D++    +     +           + +Q      V V +  G+  +I+ 
Sbjct: 201 SGRIVTQIGRDKNDRKKMTVTNDLNSGKTAITNYEVISQTEKFTLVKVHIETGRTHQIRV 260

Query: 204 VFEFFNWKVN 213
             +   + + 
Sbjct: 261 HMKHLGYPIL 270


>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 = 68.3 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 29/246 (11%), Positives = 68/246 (27%), Gaps = 36/246 (14%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            + I+ EN    R+   I+ +    SR  ++++I +  VKVNG   +++   +   D + 
Sbjct: 4   KEFIIHENLVNCRLDVFISNSLEGKSRSYIQKLIQEGHVKVNGKD-KKSNYKLKLHDSVI 62

Query: 62  VDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           V+ +               +   ++  + +      +V   +     + V   L    + 
Sbjct: 63  VNNIENEFQKINPENIDLDILYEDKDIIVINKPQGMVVHPATSNYSGTLVNGLLYHCDTL 122

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------------ 155
                         +     G L       + + L         + +             
Sbjct: 123 STLNDDTRPGIVHRIDKDTSGVLVVAKNNKAHEVLAEQLKEHSMKREYIALVEGILKKDN 182

Query: 156 --------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                          K  V+Q          +  +   N  V   L  G+  +I+    +
Sbjct: 183 GFIDKPLGRNPKDRIKMAVVQEGKNAITHYEVLKRFKKNTLVKCILETGRTHQIRVHMSY 242

Query: 208 FNWKVN 213
               + 
Sbjct: 243 IGHPLV 248


>gi|68075409|ref|XP_679622.1| RNA pseudouridylate synthase [Plasmodium berghei strain ANKA]
 gi|56500415|emb|CAI04773.1| RNA pseudouridylate synthase, putative [Plasmodium berghei]
          Length = 180

 Score = 68.3 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 28/177 (15%), Positives = 50/177 (28%), Gaps = 3/177 (1%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
              L   +     L       +             +      + +   GRLD N+ GLL+
Sbjct: 4   DNKLNNKKLLVRNLIRNENKYIEEEHKCMSYFIYKNINIEKVNNLYVCGRLDANSTGLLI 63

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T D   +  L       +    +        +    + K  +               Q 
Sbjct: 64  YTQDSMASSYLLNKYKYEVEKEYIITTFNEINECHLKMLKDNLFVDGKL---IYKCHIQY 120

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             +  +   L +G ++ I+K+    N K+  L R   G   L  L  G  R +    
Sbjct: 121 VDSFTLIFKLYQGFHKIIRKICLLSNIKIRSLHRTRIGKIHLNNLPLGKWRFLMPNE 177


>gi|332360722|gb|EGJ38531.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK49]
          Length = 298

 Score = 68.3 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 30/234 (12%), Positives = 62/234 (26%), Gaps = 35/234 (14%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP----- 66
            QR+ K +A     SR      I   R+ VNG + ++A   V   D I  +   P     
Sbjct: 11  GQRLDKAVAELTFLSRSLANEQIKDGRILVNGQV-KKAKYVVKEGDVISYELPEPEVVEY 69

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                   +   +     +      +V   +     + V   +  I       G L    
Sbjct: 70  VPEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGI 129

Query: 119 EGL---------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
                       ++  ND     + +    +               +   +++  I    
Sbjct: 130 VHRIDKDTSGLLMIAKNDQAHVALADELKNKKSLRKYWAIVHGNLPNDRGVIEAPIGRSE 189

Query: 170 I---------CYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                            +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 KDRKKQAVTAKGKPALTRFQVLERFGDFSLVELQLETGRTHQIRVHMAYIGHPV 243


>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 = 68.3 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 33/242 (13%), Positives = 71/242 (29%), Gaps = 36/242 (14%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---- 60
           +V+   +  R+ K IA      SR  V+ +I Q+ +  NG L  + +  V + D I    
Sbjct: 10  VVKSEESGVRLDKYIATHISTISRTRVQELIKQKLITTNG-LQTKLSYKVNTNDKINIEI 68

Query: 61  ------EVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
                  +D   L       +   + +      +V   +     + V   +    +    
Sbjct: 69  PSPQPLSLDPENLNLDIIYEDDDVIVVNKPQGMVVHPSAGHPDHTLVNGLIYHTKNLAKC 128

Query: 107 -RVISVGRLDINTEGLLLL-------TNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--- 155
             +   G +    +    L       T    L + L     +   +  V  + +      
Sbjct: 129 DEIFRPGIVHRIDKDTSGLLMIAKNATARISLEKQLANKINKREYIAIVHANFKHSSGVI 188

Query: 156 -----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      ++  V+          T+  Q    + V   L  G+  +I+    +   
Sbjct: 189 DAPIGRNPYQRQQMAVVASGKKAITHFTVLEQFPGYSLVKCVLETGRTHQIRVHMSYIGH 248

Query: 211 KV 212
            +
Sbjct: 249 PI 250


>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 = 68.3 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 33/242 (13%), Positives = 71/242 (29%), Gaps = 36/242 (14%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---- 60
           +V+   +  R+ K IA      SR  V+ +I Q+ +  NG L  + +  V + D I    
Sbjct: 10  VVKSEESGVRLDKYIATHISTISRTRVQELIKQKLITTNG-LQTKLSYKVNTNDKINIEI 68

Query: 61  ------EVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
                  +D   L       +   + +      +V   +     + V   +    +    
Sbjct: 69  PSPQPLSLDPENLNLDIIYEDDDVIVVNKPQGMVVHPSAGHPDHTLVNGLIYHTKNLAEC 128

Query: 107 -RVISVGRLDINTEGLLLL-------TNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--- 155
             +   G +    +    L       T    L + L     +   +  V  + +      
Sbjct: 129 DEIFRPGIVHRIDKDTSGLLMIAKNATARISLEKQLANKINKREYIAIVHANFKHSSGVI 188

Query: 156 -----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      ++  V+          T+  Q    + V   L  G+  +I+    +   
Sbjct: 189 DAPIGRNPYQRQQMAVVASGKKAITHFTVLEQFPGYSLVKCVLETGRTHQIRVHMSYIGH 248

Query: 211 KV 212
            +
Sbjct: 249 PI 250


>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 = 68.3 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 34/244 (13%), Positives = 76/244 (31%), Gaps = 38/244 (15%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V +  +  R+ + ++      SR  +++++ +Q++ VNG  ++ A   V   D I V   
Sbjct: 8   VSDGQSGIRIDRYLSEMNEELSRSYIQKLLKEQKITVNGSAVK-ANYKVQEGDEISVAVP 66

Query: 63  DGVP-----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---- 107
           D              +   +   L +      +V   +     + V   +          
Sbjct: 67  DIKEPDILPEDIPLDILYEDDDVLIVNKPKGMVVHPSAGHTSGTLVNAIMFHCKDNLSGI 126

Query: 108 -----VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-------------F 149
                   V R+D +T G LL+  +    R L     +     R R              
Sbjct: 127 NGVLRPGIVHRIDKDTTGALLVCKNDNAHRNLAEQLKEHSIRRRYRAIVAGVLKEDEGTI 186

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            G + +  ++  K  +  +          +  +  +  +V   L  G+  +I+       
Sbjct: 187 EGPIGRHPIDRKKMAVNYKNGKDAVTHYKVLERFKNATYVECRLETGRTHQIRVHMTSIG 246

Query: 210 WKVN 213
             + 
Sbjct: 247 HPLL 250


>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 = 68.3 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 69/246 (28%), Gaps = 36/246 (14%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+++  I++E+   +RV KVIA     SR  ++ M+    + VNG L +     V   D 
Sbjct: 1   MQNETLIIEESHARERVDKVIAEMMGKSRSAIQLMLKNGDITVNGELAK-PNYKVQVGDE 59

Query: 60  IEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I  +                 +   ++  L +      +V   +     + V   L    
Sbjct: 60  IHYEIREPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCD 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                 G++       +     G L       + + L           +           
Sbjct: 120 DLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVH 179

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           +K  V++          +  +      +   L  G+  +I+   
Sbjct: 180 QKGTIEAPIGRAKEDRQKMAVVRDGKEARTHFEVLERLPGYTLINCKLDTGRTHQIRVHL 239

Query: 206 EFFNWK 211
           ++    
Sbjct: 240 KYIGHP 245


>gi|219124843|ref|XP_002182704.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217406050|gb|EEC45991.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 151

 Score = 68.3 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 2/79 (2%)

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI--LREQ 244
           + V + + EGK+R ++++       V  L R   G   L  L AG  R ++ +     E 
Sbjct: 72  STVRLTVSEGKHRMVRRILANCGHPVVSLHRDRLGAVALNDLPAGEYRPLTTEESPWAET 131

Query: 245 LGPHLLEEAQVNLDAPIYS 263
           L P   +  +         
Sbjct: 132 LVPLEKKHIKPKPKTSRKQ 150


>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 = 68.3 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 28/243 (11%), Positives = 60/243 (24%), Gaps = 36/243 (14%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           IV       R+   +      SR  ++ +I    + V G  + +A + +     + V   
Sbjct: 5   IVNAEQDGMRLDVFLTEHMEGSRSYIQSLIKGGHITV-GAKVGKANLRLTPNAVVRVEIP 63

Query: 63  ---------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                    + +PL     +   + +  +   +V         + V   L          
Sbjct: 64  EPESVEVKPEDIPLDVLYEDHDIIIVNKQRGMVVHPAVGNYSGTLVNALLYHCKDLSGIN 123

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------------- 155
           G +       L     G +       +   L         +                   
Sbjct: 124 GEIRPGIVHRLDKDTSGVMMAAKNDAAHIGLAEQVKEHSAKRTYLALVQGNIVEEKGTIK 183

Query: 156 -----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                   + +K  +V +          +  + G    V   L  G+  +I+  F     
Sbjct: 184 APIGRHPKDRMKMAVVFENSKDAVTHFNVVERFGHQTLVECNLETGRTHQIRVHFAHIGH 243

Query: 211 KVN 213
            V 
Sbjct: 244 PVV 246


>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 = 68.3 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 28/234 (11%), Positives = 61/234 (26%), Gaps = 35/234 (14%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
             R+ K ++     SR      I   +V VNG + ++A   V   D I            
Sbjct: 9   GIRLDKALSDLTELSRSLANEQIKSGQVLVNGHV-KKAKYTVQEGDVITYQIPEPEVLEY 67

Query: 63  --DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
             + +PL     +     +      +V   +     + V   +  I       G L    
Sbjct: 68  VAEDIPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGI 127

Query: 119 EGL---------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
                       ++  ND     + +    +               +   +++  I    
Sbjct: 128 VHRIDKDTSGLLMIAKNDEAHMALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSE 187

Query: 170 I---------CYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                            +  +  + G    + + L  G+  +I+    +    V
Sbjct: 188 KDRKKQAVTAKGKPAVTRFQVLERFGDYTLLELQLETGRTHQIRVHMAYIGHPV 241


>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 = 68.3 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 26/232 (11%), Positives = 60/232 (25%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP------- 66
           R+ K ++     SR      I   +V VNG + ++A   V   D +      P       
Sbjct: 11  RLDKALSDLTELSRSLANEQIKSGQVLVNGQV-KKAKYTVQEGDVVTYHVPEPEVLEYVA 69

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 +   +     +      +V   +     + V   +  I       G L      
Sbjct: 70  ENLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 121 LLLLTNDGGLARVLELPST--------------QWLRVYRV-RFHGQVDQDKLNLLKKGI 165
            +     G L       +               ++  +      + +   +      +  
Sbjct: 130 RIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 166 VIQGICY---GDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             +            +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQGVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>gi|149370420|ref|ZP_01890109.1| RNA pseudouridine synthase family protein [unidentified eubacterium
           SCB49]
 gi|149355971|gb|EDM44528.1| RNA pseudouridine synthase family protein [unidentified eubacterium
           SCB49]
          Length = 172

 Score = 68.3 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 30/148 (20%), Positives = 61/148 (41%), Gaps = 16/148 (10%)

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
           L    + ++++GRLD  +EGL+LLT +G  +  +   + +     +V       + K+  
Sbjct: 16  LADFPNGIMAIGRLDETSEGLILLTTNGAYSYHVNNSNIEKEYYAQVDGIITEKEIKILQ 75

Query: 161 LKKGIVIQG--ICYGDMQVTLDT--------------QKGSNAWVTVGLREGKNREIKKV 204
               I I G        +                   + G  +WV++ + EGK R+++K+
Sbjct: 76  KGLPISINGSIYHTKPCKAKRIDTPLLPPTRQRIRDDRHGPTSWVSITVTEGKFRQVRKM 135

Query: 205 FEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                +   RL R+  G +++  +  G 
Sbjct: 136 TAAVGFPTLRLARVRIGEYKIEQMQPGD 163


>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 = 68.3 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 69/246 (28%), Gaps = 36/246 (14%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+++  I++E+   +RV KVIA     SR  ++ M+    + VNG L +     V   D 
Sbjct: 1   MQNETLIIEESHARERVDKVIAEMMGKSRSAIQLMLKNGDITVNGELAK-PNYKVQVGDE 59

Query: 60  IEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I  +                 +   ++  L +      +V   +     + V   L    
Sbjct: 60  IHYEVREPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCD 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                 G++       +     G L       + + L           +           
Sbjct: 120 DLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVH 179

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           +K  V++          +  +      +   L  G+  +I+   
Sbjct: 180 QKGTIEAPIGRAKEDRQKMAVVRDGKEARTHFEVLERLPGYTLINCKLDTGRTHQIRVHL 239

Query: 206 EFFNWK 211
           ++    
Sbjct: 240 KYIGHP 245


>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 = 68.3 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 33/234 (14%), Positives = 64/234 (27%), Gaps = 35/234 (14%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP----- 66
            QR+ K ++     SR      I   +V VNG + ++A   V   D +      P     
Sbjct: 9   GQRLDKALSDLTELSRSLANEQIKAGQVLVNGQV-KKAKYTVQEGDIVTYHVPEPEVLEY 67

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                   +   +     +      +V   +     + V   +  I       G L    
Sbjct: 68  VAEDIPLDIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGI 127

Query: 119 EGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              +     G L       +           + LR Y    HG +  D+  +       +
Sbjct: 128 VHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSE 187

Query: 169 GICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                            +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 188 KDRKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 35/246 (14%), Positives = 71/246 (28%), Gaps = 36/246 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  +  +    + QR+ K +A      SR  ++ ++    V VNG    + +  V   D 
Sbjct: 1   MNREYELTAEESGQRLDKYLAGEMTDLSRSRIKELVQAGEVLVNGKK-SKVSYKVQKGDL 59

Query: 60  IEV------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I+V            + +P  +   +   + +      +V   +     + V   L    
Sbjct: 60  IQVTVLPLEPLKLEAENIPLDIVYEDEDIIVVNKPQGMVVHPAAGHPSHTLVNALLYHTR 119

Query: 106 --------SRVISVGRLDINTEGLLLLTND------------GGLARVLELPSTQWLRVY 145
                    R   V R+D +T GLL++  +                +   L         
Sbjct: 120 DLADSPEGFRPGIVHRIDKDTSGLLMVAKNAAARESLEKQLAAKSNKRQYLAIVHGNFAE 179

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           K+  V++          +  Q    + V   L  G+  +I+   
Sbjct: 180 EEGTIDAPIGRNPKDRKQMAVVEKGKSAVTHFKVLEQYQGYSLVECQLETGRTHQIRVHM 239

Query: 206 EFFNWK 211
            +    
Sbjct: 240 AYIGHP 245


>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 = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 33/242 (13%), Positives = 71/242 (29%), Gaps = 36/242 (14%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---- 60
           +V+   +  R+ K IA      SR  V+ +I Q+ +  NG L  + +  V + D I    
Sbjct: 10  VVKSEESGVRLDKYIATHISTISRTRVQELIKQKLITTNG-LQTKLSYKVNTNDKINIEI 68

Query: 61  ------EVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
                  +D   L       +   + +      +V   +     + V   +    +    
Sbjct: 69  PSPQPLSLDPENLNLDIIYEDDDVIVVNKPQGMVVHPSAGHPDHTLVNGLIYHTKNLAEC 128

Query: 107 -RVISVGRLDINTEGLLLL-------TNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--- 155
             +   G +    +    L       T    L + L     +   +  V  + +      
Sbjct: 129 DEIFRPGIVHRIDKDTSGLLMIAKNATARISLEKQLANKINKREYIAIVHANFKHSSGVI 188

Query: 156 -----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      ++  V+          T+  Q    + V   L  G+  +I+    +   
Sbjct: 189 DAPIGRNPYQRQQMAVVASGKKAITHFTVLEQFPGYSLVKCILETGRTHQIRVHMSYIGH 248

Query: 211 KV 212
            +
Sbjct: 249 PI 250


>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 = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 69/246 (28%), Gaps = 36/246 (14%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+++  I++E+   +RV KVIA     SR  ++ M+    + VNG L +     V   D 
Sbjct: 1   MQNETLIIEESHARERVDKVIAEMMGKSRSAIQLMLKSGDITVNGELAK-PNYKVQVGDE 59

Query: 60  IEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I  +                 +   ++  L +      +V   +     + V   L    
Sbjct: 60  IHYEVREPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCD 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                 G++       +     G L       + + L           +           
Sbjct: 120 DLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVH 179

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           +K  V++          +  +      +   L  G+  +I+   
Sbjct: 180 QKGTIEAPIGRAKEDRQKMAVVRDGKEARTHFEVLERLPGYTLINCKLDTGRTHQIRVHL 239

Query: 206 EFFNWK 211
           ++    
Sbjct: 240 KYIGHP 245


>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 = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 33/234 (14%), Positives = 63/234 (26%), Gaps = 35/234 (14%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP----- 66
            QR+ K ++     SR      I   +V VNG   ++A   V   D +      P     
Sbjct: 9   GQRLDKALSDLTELSRSLANEQIKAGQVLVNGQ-AKKAKYTVQEGDIVTYHVPEPEVLEY 67

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                   +   +     +      +V   +     + V   +  I       G L    
Sbjct: 68  VAENLPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNSLMYHIKDLSGINGVLRPGI 127

Query: 119 EGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              +     G L       +           + LR Y    HG +  D+  +       +
Sbjct: 128 VHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSE 187

Query: 169 GICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                            +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 188 KDRKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 37/279 (13%), Positives = 81/279 (29%), Gaps = 48/279 (17%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE---- 61
           V   +   R+ K +A     A+R  +E++I    VK+N  ++ +    + S + IE    
Sbjct: 12  VSPEYEGMRLDKYLAEQIEEATRSYLEKLIDNSYVKINSKVINKNGRKLKSGEKIEISIP 71

Query: 62  ----VDGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
               +D         +       + +  K   +V         + V   L    +     
Sbjct: 72  EEENIDIEAENIPLDIVFENDDFILVNKKYNMVVHPAYGNYNGTLVNALLYYTNNLSSVN 131

Query: 112 GRLDI----------------------NTEGLLLLTNDGGLARVLELPSTQWLRVY-RVR 148
           G +                        + +   + T+       L +    +       R
Sbjct: 132 GNIRPGIIHRLDKDTSGLILVAKNNFAHAKLASMFTDKTIHKTYLCIVKGNFSDENLEGR 191

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +D  +  K  +V +          +  Q    + V V +  G+  +I+   +  
Sbjct: 192 IENLIGRDTKDRKKMAVVKENGKLAISNYRVVEQVKDYSLVEVLIETGRTHQIRVHMKSI 251

Query: 209 NWKVN----------RLIRISYGPFQLGTLLAGSTREVS 237
           N  +            + R     F+L  L     +E +
Sbjct: 252 NHPILGDVIYGSEDKNIKRQMLHAFKLEFLNPLDNKEYT 290


>gi|255522642|ref|ZP_05389879.1| hypothetical protein LmonocFSL_15771 [Listeria monocytogenes FSL
           J1-175]
          Length = 279

 Score = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 69/246 (28%), Gaps = 36/246 (14%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+++  I++E+   +RV KVIA     SR  ++ M+    + VNG L +     V   D 
Sbjct: 1   MQNETLIIEESHARERVDKVIAEMMGKSRSAIQLMLKNGDITVNGELAK-PNYKVQVGDE 59

Query: 60  IEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I  +                 +   ++  L +      +V   +     + V   L    
Sbjct: 60  IHYEVREPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCD 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                 G++       +     G L       + + L           +           
Sbjct: 120 DLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVH 179

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           +K  V++          +  +      +   L  G+  +I+   
Sbjct: 180 QKGTIEAPIGRAKEDRQKMAVVRDGKEARTHFEVLERLPGYTLINCKLDTGRTHQIRVHL 239

Query: 206 EFFNWK 211
           ++    
Sbjct: 240 KYIGHP 245


>gi|254994200|ref|ZP_05276390.1| hypothetical protein LmonocytoFSL_15395 [Listeria monocytogenes FSL
           J2-064]
          Length = 296

 Score = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 69/246 (28%), Gaps = 36/246 (14%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+++  I++E+   +RV KVIA     SR  ++ M+    + VNG L +     V   D 
Sbjct: 1   MQNETLIIEESHARERVDKVIAEMMGKSRSAIQLMLKNGDITVNGELAK-PNYKVQVGDE 59

Query: 60  IEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I  +                 +   ++  L +      +V   +     + V   L    
Sbjct: 60  IHYEVREPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCD 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                 G++       +     G L       + + L           +           
Sbjct: 120 DLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVH 179

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           +K  V++          +  +      +   L  G+  +I+   
Sbjct: 180 QKGTIEAPIGRAKEDRQKMAVVRDGKEARTHFEVLERLPGYTLINCKLDTGRTHQIRVHL 239

Query: 206 EFFNWK 211
           ++    
Sbjct: 240 KYIGHP 245


>gi|313623251|gb|EFR93499.1| ribosomal large subunit pseudouridine synthase D [Listeria innocua
           FSL J1-023]
          Length = 297

 Score = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 31/240 (12%), Positives = 65/240 (27%), Gaps = 35/240 (14%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           I++E+   +RV KVIA     SR  ++ M+    + VNG L +     V   D I  +  
Sbjct: 2   IIEESHARERVDKVIAEMMGKSRSAIQLMLKNGDITVNGELAK-PNYKVQVGDEIRYEAR 60

Query: 66  P--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                          +   ++  L +      +V   +     + V   L          
Sbjct: 61  EPEELEILAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGIN 120

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------------- 155
           G++       +     G L       + + L           +                 
Sbjct: 121 GKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIE 180

Query: 156 ----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                     +K  V++          +  +      +   L  G+  +I+   ++    
Sbjct: 181 APIGRAKEDRQKMAVVRDGKEARTHFEVIERLPGYTLINCKLDTGRTHQIRVHLKYIGHP 240


>gi|300741214|ref|ZP_07071235.1| ribosomal RNA large subunit methyltransferase J [Rothia
          dentocariosa M567]
 gi|300380399|gb|EFJ76961.1| ribosomal RNA large subunit methyltransferase J [Rothia
          dentocariosa M567]
          Length = 244

 Score = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+ K +A  G+A SR    ++I    V VNG ++ +A+  V   D + V   PL
Sbjct: 1  MRLDKFLAEHGLAASRTLAAKLIDAGCVSVNGKIVYKASQPVHRDDDVLVQESPL 55


>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 = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 29/245 (11%), Positives = 66/245 (26%), Gaps = 38/245 (15%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-G 64
           V E     R+ K +A      SR   +++I   +V+ NG++ +   + + + D + V+  
Sbjct: 25  VAEGTLGVRLDKWLAEQLPELSRSRCQKLIESGQVQRNGLVCQDKNLILKTGDRLVVNIP 84

Query: 65  VPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
             +                +   + +      +V         + V   L          
Sbjct: 85  ELIPLDVVAQNIPLDILYEDEQLIIINKPAGLVVHPGPGHPDGTVVNALLAHCPDLAGIG 144

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--------------- 156
           G         L     G +       +   L+V       +                   
Sbjct: 145 GVQRPGIVHRLDKDTTGAMVVAKTELALHNLQVQLKEKTARRLYWGIVYGSPKEIQGTVN 204

Query: 157 --------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                       +    V +G         L  + G+++W+   L  G+  +I+   +  
Sbjct: 205 LPVGRHPGDRQKMGIVPVEKGGREAVTHWRLLERIGNHSWLEFQLETGRTHQIRVHSKQM 264

Query: 209 NWKVN 213
              + 
Sbjct: 265 GHPLV 269


>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 = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 25/242 (10%), Positives = 70/242 (28%), Gaps = 44/242 (18%)

Query: 6   IVQENFTPQRVSKVIARAGIASRRE--------VERMIAQQRVKVNGILLERAAVNVMST 57
           IV E     R+ K +       R++        + ++I   ++KVNG  ++  +  +   
Sbjct: 2   IVTEENYYSRLDKFL-------RKKLLNLPLSAIYKLIRTGKIKVNGKKVKNPSYKIEIG 54

Query: 58  DHI-----------EVDGVP--------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF 98
           D I           E++           +   +   L +       +         + + 
Sbjct: 55  DEITIEEDISKYNREINNKVVPIKMDLDIVYEDNDILIINKPAGIPIHPGKGTHIATLIE 114

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLL-------TNDGGLARVLELPSTQWLRVYRVRFHG 151
             +     +  +   +    +    +        +   L  ++   S +   +   +   
Sbjct: 115 GLIYYGQEKNFTPHLVHRLDKHTSGILIIAKNTQSARELGDIIAGRSIKKEYIALCKGKL 174

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +      L+    +       +  T     G  + + V ++ G+  +I+K     N  
Sbjct: 175 SKEGKIDIPLENKQALTTFITQKVYKTHL---GEFSLLNVNIKTGRKHQIRKHLSLINHP 231

Query: 212 VN 213
           + 
Sbjct: 232 II 233


>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 = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 30/247 (12%), Positives = 72/247 (29%), Gaps = 37/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M D  ++ +     R+ KV+       +R ++++MI    +KVNG + ++A   V   D 
Sbjct: 1   MSDYKVLADKTG--RLDKVVTNIFTDYTRSQLKKMIDDGNIKVNGDV-KKANYKVNLGDE 57

Query: 60  IEVDGVPLR--------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I  D   ++                +   + +      +V         + V   L    
Sbjct: 58  ITFDKPEVKKLSLEPENIPLDIVYEDDDVIVVNKPQGMVVHPSPGHFEHTLVNALLYHSP 117

Query: 106 SRVISVGRLDINTEGL--------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
              I+          +        ++  ND     + +    +      +       ++ 
Sbjct: 118 LSTINGTYRPGIVHRIDKDTSGLLMVAKNDMAHQSLAKQLKDKTNTREYIALVHGNIKED 177

Query: 158 LNLLK-----------KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
              +            K  V++          +  + G    V   L  G+  +I+   +
Sbjct: 178 SGTIDAPLGRSKVDRKKQAVVKDGRNAVTHFEVLKRYGDYTLVKCVLETGRTHQIRVHMK 237

Query: 207 FFNWKVN 213
           +    + 
Sbjct: 238 YIGHPLV 244


>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 = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 30/242 (12%), Positives = 73/242 (30%), Gaps = 34/242 (14%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            I+    + QR+ K +      SR  +++M+ Q  + VN   + +A+  +   D+I+++ 
Sbjct: 2   KILYSLMSSQRIDKFLVENTNYSRTLIKKMLDQNLILVNDNFISKASYLLKKNDYIQINN 61

Query: 65  VP-----------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                              +   ++  L +      LV   S  +  +        + + 
Sbjct: 62  ELPIVQEQKKLLPFVYSLEIIFEDQDLLIVNKPSGMLVHPTSFHEQNTLANALKYYLKTD 121

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-- 165
              +          L++     +A            + +  +    ++  +  L   I  
Sbjct: 122 NFYITHRLDKNTSGLIIICKNQIALNSLQQQFMQKTIRKSYYAIVHNRFDMQHLHFMINE 181

Query: 166 -------------VIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                                +    V +  Q  + A V V +  G+  +I+    + N 
Sbjct: 182 PIGHSYQDKLRMKTGNSKNTKEAISIVKVLEQYKNTALVEVSIITGRTHQIRVHMRYINH 241

Query: 211 KV 212
            V
Sbjct: 242 PV 243


>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 = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 37/246 (15%), Positives = 73/246 (29%), Gaps = 37/246 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M D   +       R+ K+I A     +R +V++ +    V VNG  ++ A   V + D 
Sbjct: 1   MSDTFTI--TTESGRIDKIITAHETTHTRSQVQKWLQDGLVTVNGNPVK-ANFKVTAGDV 57

Query: 60  IEV---DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           + V   +  PL+             +   + +      +V         + V   L    
Sbjct: 58  VTVTIPEVKPLKAVAEPIPLEIVYEDDQVIVVNKPQGMVVHPAPGHPDGTLVNGLLYHTK 117

Query: 106 SRVIS-------VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-- 156
              I+       V R+D +T GLL++         L         +              
Sbjct: 118 LPGINGVIRPGIVHRIDKDTSGLLMVAKTEAAQLSLSAQLKAKTSIREYLALVHGTFKED 177

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          K+  V+    +      +  +  +   V   L  G+  +I+    
Sbjct: 178 EGTIDAPLGRDPRDRKRQAVVADGRHAVTHFQVLERFTNYTLVKCILDTGRTHQIRVHMA 237

Query: 207 FFNWKV 212
           + +  V
Sbjct: 238 YTHHPV 243


>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 = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 31/247 (12%), Positives = 72/247 (29%), Gaps = 37/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M D  ++ +     R+ KV+       +R ++++MI    +KVNG + ++A   V   D 
Sbjct: 1   MSDYKVLADKTG--RLDKVVTNIFTDYTRSQLKKMIDDGNIKVNGDV-KKANYKVNLGDE 57

Query: 60  IEVDGVPLR--------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I  D   ++                +   + +      +V         + V   L    
Sbjct: 58  ITFDKPEVKKLSLEPENIPLDIVYEDDDVIVVNKPQGMVVHPSPGHFEHTLVNALLYHSP 117

Query: 106 SRVISVGRLDINTEGL--------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
              I+          +        ++  ND     + +    +      V       ++ 
Sbjct: 118 LSTINGTYRPGIVHRIDKDTSGLLMVAKNDMAHQSLAKQLKDKTNTREYVALVHGNIKED 177

Query: 158 LNLLK-----------KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
              +            K  V++          +  + G    V   L  G+  +I+   +
Sbjct: 178 SGTIDAPLGRSKVDRKKQAVVKDGRNAVTHFEVLKRYGDYTLVKCVLETGRTHQIRVHMK 237

Query: 207 FFNWKVN 213
           +    + 
Sbjct: 238 YIGHPLV 244


>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 = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 33/244 (13%), Positives = 69/244 (28%), Gaps = 36/244 (14%)

Query: 5   NIVQENFT-PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--- 60
           NI+ E     +R+   +A     +R  ++++I  + VKVNG  ++     V   D I   
Sbjct: 8   NIIAEKDDVDKRIDSFLASEVDYTRSYLKKLILDELVKVNGKSVK-PNYKVREGDVINLN 66

Query: 61  -----EVDGVPLRKA------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                E+D  P          +   + +      +V         + V   L    +   
Sbjct: 67  IPEAEEIDLKPENIPLDIIYEDDDIIVVNKPQGMVVHPAPGNLSGTLVNALLYHCTNLSG 126

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPST--------------------QWLRVYRVRF 149
             G L       L     G +       +                     + +       
Sbjct: 127 INGELRPGIVHRLDKDTSGVMVVAKNDKAHLELSNQIKNRTILKKYLAIVEGVIKNDEGA 186

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                       KK  V++   Y      +  +  +N+ V   ++ G+  +I+    +  
Sbjct: 187 VEAPIGRDHIERKKMAVVKDGRYALTLYRVLERYKNNSLVEAIIKTGRTHQIRVHMAYIG 246

Query: 210 WKVN 213
             + 
Sbjct: 247 HPIV 250


>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 = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 29/239 (12%), Positives = 67/239 (28%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I  +RV VNG+++++    V+ ++ I +D 
Sbjct: 10  TVSESQLGQRLDQALAELFPDYSRSRIKEWILDRRVTVNGVIIDKPKEKVLGSEQIAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  EIEEEARWEAQDIPLDIVYEDEDILVINKPRGLVVHPGAGNPDGTVLNALLHHFPAIADV 129

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--- 156
                  R+       +     +        +  L   + ++  V   R       D   
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTHLVESLQLREITREYEAVAIGRMTAGGTVDEPI 189

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+      N  + 
Sbjct: 190 SRHSTKRTHMAVHPTGKPATTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHINHPLV 248


>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 = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 34/236 (14%), Positives = 74/236 (31%), Gaps = 39/236 (16%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++ A   +R  V+++I +  V VN   + + A  V S D I+V            
Sbjct: 9   RLDKYLSEALSKTRSFVQKIIEEGNVWVNQSQVLKPAYKVKSGDIIKVVIPEPKQLSLVA 68

Query: 63  ---DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG------- 112
              D   + + E   +        +V   +     + V   L     R+ S+        
Sbjct: 69  QDIDIEVVYEDEHLAVI-NKPRGMVVHPGAGNFENTLVNALLHKFSGRLSSINGVIRPGI 127

Query: 113 ---------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                          + D     L        + R+        L+      +  + +  
Sbjct: 128 VHRLDKDTSGLLIVAKTDEAHIKLSEALKSHQIKRIYYAICEGVLKEDSGVINAPIGRHP 187

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +N LK  +V  G         +  +     ++ + L+ G+  +I+    +  + + 
Sbjct: 188 VNRLKMAVVPNGKEA-VTYFEVLERFDKYTFIKLRLKTGRTHQIRVHMSYIGYPLL 242


>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 = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 25/245 (10%), Positives = 64/245 (26%), Gaps = 38/245 (15%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V   +   R+ K ++     A+R  +E++I    VK+N  ++ +    +   + IE+   
Sbjct: 12  VSSEYEGMRLDKYLSEQIEEATRSYLEKLIDNNYVKINSKIINKNGRKLKLGEKIEISIP 71

Query: 63  -----DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                D         +       + +      +V         + V   L    +     
Sbjct: 72  EEENIDIEAENISLDIVYENDDFIVINKSYGMVVHPAYGNYSGTLVNALLYYTNNLSSIN 131

Query: 112 GRLDINTE-----------------------GLLLLTNDGGLARVLELPSTQWLRVYRVR 148
           G +                              +          +  +           R
Sbjct: 132 GNIRPGIIHRLDKDTSGLILVAKNNYAHAKLASMFTDKTIHKTYLCIVKGNFSEENLNGR 191

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +   +  K  +V +          +  Q    + V + +  G+  +I+   +  
Sbjct: 192 IENLIGRGSKDRKKMAVVKENGKTAISNYKVIEQVDGYSLVEIAIETGRTHQIRVHMKSI 251

Query: 209 NWKVN 213
           N  + 
Sbjct: 252 NHVIL 256


>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 = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 69/246 (28%), Gaps = 36/246 (14%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+++  I++E+   +RV KVIA     SR  ++ M+    + VNG L +     V   D 
Sbjct: 1   MQNETLIIEESHARERVDKVIAEMMGKSRSAIQLMLKNGDITVNGELAK-PNYKVQVGDE 59

Query: 60  IEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I  +                 +   ++  L +      +V   +     + V   L    
Sbjct: 60  IHYEVREPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCD 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                 G++       +     G L       + + L           +           
Sbjct: 120 DLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVH 179

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           +K  V++          +  +      +   L  G+  +I+   
Sbjct: 180 QKGTIEAPIGRAKEDRQKMAVVRDGKEARTHFEVLERLPGYTLINCKLDTGRTHQIRVHL 239

Query: 206 EFFNWK 211
           ++    
Sbjct: 240 KYIGHP 245


>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 = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 27/249 (10%), Positives = 69/249 (27%), Gaps = 38/249 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           ++  +V +     R+ K ++     +R  ++++I  + + VN     + A  +   D I+
Sbjct: 23  EENIVVLKEEAGSRIDKFLSERLELTRTRIQQLIKDENILVNEKK-TKPAYKIEENDTIK 81

Query: 62  V--------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           V                + +   +     +  K   +V   +     + V   L  I   
Sbjct: 82  VVIPELETVEIKPENIDIEIIYEDNDLAVINKKAGIVVHPANGHYSGTLVNAILYHIKDL 141

Query: 108 VISVGRLDI-------NTEGLLLLTNDGGLARVLELPSTQWLRVYRVR------------ 148
               G +              LL+      A +          V ++             
Sbjct: 142 SGINGEIRPGIVHRLDKDTSGLLIIAKNDKAHLKLSQMFHDKTVKKIYLAILKGKLNQKS 201

Query: 149 ----FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                    D++    +     +           + +Q      V V +  G+  +I+  
Sbjct: 202 GRIVTQIGRDKNDRKKMTVINDLNSGKTAITNYEVISQTEKFTLVKVHIETGRTHQIRVH 261

Query: 205 FEFFNWKVN 213
            +   + + 
Sbjct: 262 MKHLGYPIL 270


>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 = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 30/245 (12%), Positives = 74/245 (30%), Gaps = 34/245 (13%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M +  + +ENF  QR+   +A+    SR +++ +I  ++V VN   ++ A   +   D I
Sbjct: 1   MDNFKVDKENF-GQRLDVYLAKLVDLSRSQIKNLIDNEKVLVNKKNVK-AGYKLSEDDVI 58

Query: 61  EV----DGVP--------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
            +    D  P        +   +     +      +V   +     + V   L    +++
Sbjct: 59  SLEYPKDNKPFAEKIDFNVIYEDEYIAVISKPQDLVVHIGAGNSSGTLVNGLLYKFKNQL 118

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPST--------------------QWLRVYRVR 148
             +  L       L     G +       +                              
Sbjct: 119 SDLDPLRPGIVHRLDKNTSGLMIIAKNNQAHINLVDQFKNSQIKKYYLAIVHGKTPESGI 178

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + ++  +  K  +V +       +     +    + + + L  G+  +I+    + 
Sbjct: 179 IAEPIGRNPNDRKKMAVVYKNSKQAITKYKKLKEFQEYSLLNINLLTGRTHQIRVHMAYI 238

Query: 209 NWKVN 213
            + V 
Sbjct: 239 GYPVL 243


>gi|107023463|ref|YP_621790.1| pseudouridine synthase, Rsu [Burkholderia cenocepacia AU 1054]
 gi|116690545|ref|YP_836168.1| pseudouridine synthase, Rsu [Burkholderia cenocepacia HI2424]
 gi|105893652|gb|ABF76817.1| Pseudouridine synthase, Rsu [Burkholderia cenocepacia AU 1054]
 gi|116648634|gb|ABK09275.1| Pseudouridine synthase, Rsu [Burkholderia cenocepacia HI2424]
          Length = 192

 Score = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 41/182 (22%), Positives = 75/182 (41%), Gaps = 19/182 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +      + GRLD ++EGLLLLT+DGGL   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKTPGV--YAAGRLDADSEGLLLLTDDGGLQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVDGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPDTLWPRNPPIR 120

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL--AGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L    G T  + 
Sbjct: 121 YRAAIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFALGIAPGETIALP 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>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 = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 34/241 (14%), Positives = 71/241 (29%), Gaps = 36/241 (14%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           I+ E    +R+ K ++      SR + ++MI    + VNG    +        D IE+  
Sbjct: 7   IINEEVAGERLDKAVSLLNEELSRSQAQQMIKDGHILVNGQG-TKTNYKCSIDDKIEISF 65

Query: 63  --------------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
                               DG  L   +   + ++  P     T  +         +  
Sbjct: 66  PEPEELDVLPEEMDLDIYYEDGDVLVVNKPKGMVVHPAPGHASGTLVNGLMAHCKDLSGI 125

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN--- 159
           +   R   V R+D +T GLL++  +      L     +     + +              
Sbjct: 126 NGVLRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVEKTVTRKYQAIVHGTIPHDYGTV 185

Query: 160 ---------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      +   V+ G  +      +  +      V   L  G+  +I+   ++  +
Sbjct: 186 DAPLGRDPKDRQSMTVVDGGKHAVTHFHVIHRYKDFTHVECQLETGRTHQIRVHMKYIGY 245

Query: 211 K 211
            
Sbjct: 246 P 246


>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 = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 34/236 (14%), Positives = 74/236 (31%), Gaps = 39/236 (16%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++ A   +R  V+++I +  V VN   + + A  V S D I+V            
Sbjct: 9   RLDKYLSEALSKTRSFVQKIIEEGNVWVNQTQVLKPAYKVKSGDIIKVVIPEPKQLSLVA 68

Query: 63  ---DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG------- 112
              D   + + E   +        +V   +     + V   L     R+ S+        
Sbjct: 69  QDIDIEVVYEDEHLAVI-NKPRGMVVHPGAGNFENTLVNALLHKFRGRLSSINGVIRPGI 127

Query: 113 ---------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                          + D     L        + R+        L+      +  + +  
Sbjct: 128 VHRLDKDTSGLLIVAKTDEAHIKLSEALKSHQIKRIYYAICEGVLKEDSGVINAPIGRHP 187

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +N LK  +V  G         +  +     ++ + L+ G+  +I+    +  + + 
Sbjct: 188 VNRLKMAVVPNGKEA-VTYFEVLERFDKYTFIKLRLKTGRTHQIRVHMSYIGYPLL 242


>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 = 67.9 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 30/235 (12%), Positives = 65/235 (27%), Gaps = 36/235 (15%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
              R+ KV+       SR +++  +    V VNG  ++ A   V   D I V        
Sbjct: 11  ESGRIDKVLTNLFTDYSRSQIQLWLKNGAVSVNGQPVK-ANYKVKQGDDITVLIPEPETL 69

Query: 63  ----DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
               + +P  +   +     +      +V   +     + V   +  I       G +  
Sbjct: 70  DVVPENIPLTIVYEDEDVAVINKPQGMVVHPSAGHTHGTMVNALMYHIKDLSTINGVIRP 129

Query: 117 NTEGLLLLTNDGGLARVLELPSTQ------------WLRVYRVRFHGQVDQDKLNL---- 160
                +     G L       + +               V  V      ++  +N     
Sbjct: 130 GIVHRIDKDTSGLLMVAKNDQAHESLAQQLKDKTSLRKYVALVHGEIPHEKGTINAPIGR 189

Query: 161 ----LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                K   + +         T+  +      V + L  G+  +I+   ++  + 
Sbjct: 190 SKENRKMQAIREDGKPAVTHFTVLERFEGFTLVELKLETGRTHQIRVHMKYIGYP 244


>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 = 67.9 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 32/245 (13%), Positives = 72/245 (29%), Gaps = 38/245 (15%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE---- 61
           V   +   R+ K +A     A+R  +E++I    VK+N  ++ +    + S + IE    
Sbjct: 12  VSPEYEGMRLDKYLAEQIEEATRSYLEKLIDNSYVKINSKVINKNGRKLKSGEKIEISIP 71

Query: 62  ----VDGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
               +D         +       + +  K   +V         + V   L    +     
Sbjct: 72  EEENIDIEAENIPLDIVFENDDFILVNKKYNMVVHPAYGNYTGTLVNALLYYTNNLSSVN 131

Query: 112 GRLDI----------------------NTEGLLLLTNDGGLARVLELPSTQWLRVY-RVR 148
           G +                        + +   + T+       L +    +       R
Sbjct: 132 GNIRPGIIHRLDKDTSGLILVAKNNFAHAKLASMFTDKTIHKTYLCIVKGNFSDENLEGR 191

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +D  +  K  +V +          +  Q    + V V +  G+  +I+   +  
Sbjct: 192 IENLIGRDTKDRKKMAVVKENGKLAISNYRVVEQVKDYSLVEVLIETGRTHQIRVHMKSI 251

Query: 209 NWKVN 213
           N  + 
Sbjct: 252 NHPIL 256


>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 = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 38/284 (13%), Positives = 81/284 (28%), Gaps = 53/284 (18%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE---- 61
           V   +   R+ K +A     A+R  +E++I    VK+N  ++ +    + S + +E    
Sbjct: 12  VNPEYEGMRLDKYLAEQIEEATRSYLEKLIDNSYVKINSKIINKNGRKLKSGEKVEISIP 71

Query: 62  ----VDGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
               +D         +       + +  K   +V         + V   L    +     
Sbjct: 72  EEENIDIEAENIPLDIVFENDDFILVNKKYNMVVHPAYGNYTGTLVNALLYYTNNLSSVN 131

Query: 112 GRLDI----------------------NTEGLLLLTNDGGLARVLELPSTQWLRVY-RVR 148
           G +                        + +   + T+       L +    +       R
Sbjct: 132 GNIRPGIIHRLDKDTSGLILVAKNNFAHAKLASMFTDKTIHKTYLCIVKGNFSDENLEGR 191

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +D  +  K  IV +          +  Q    + V V +  G+  +I+   +  
Sbjct: 192 IENLIGRDTKDRKKMAIVKENGKLAISNYRVVEQVKDYSLVEVLIETGRTHQIRVHMKSI 251

Query: 209 NWKVN----------RLIRISYGPFQLGTLLAGSTREVSKKILR 242
           N  +            + R     F+L  L       +  K  R
Sbjct: 252 NHPILGDVIYGSEDKNVKRQMLHAFKLEFLNP-----LDNKEYR 290


>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 = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 35/248 (14%), Positives = 75/248 (30%), Gaps = 39/248 (15%)

Query: 3   DKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            + +V+E+    R+   +A   +  SR  ++++I  ++V VNG + E+A   V   D I 
Sbjct: 10  REFLVEEDEDGDRLDVYLADQFVDMSRSYIQKIIKDKKVTVNGKV-EKAKYLVKEEDKIV 68

Query: 62  VD--------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           ++               + +   +   + +      +V         + V   L      
Sbjct: 69  IEIPKPKVLEVVPQDIPIEIVYEDDDIIIVNKPQGMVVHPAPGNYEGTLVNAILYHCKGN 128

Query: 108 VISVG----------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVY 145
           + S+                       + +     L     D  + R  E       +  
Sbjct: 129 LSSINGVIRPGIVHRIDKDTSGILMIAKNNNAHNCLAEQLKDHSITREYEFICHSVFKED 188

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
            V     + ++  + LK  IV  G         +  +      V   L  G+  +I+   
Sbjct: 189 NVTVDRPIGRNPKDRLKMAIVPNGKRA-VTHFEVIERFNGYTHVRARLETGRTHQIRVHA 247

Query: 206 EFFNWKVN 213
              N  + 
Sbjct: 248 MSINHPLV 255


>gi|325696405|gb|EGD38295.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK160]
          Length = 298

 Score = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 36/241 (14%), Positives = 68/241 (28%), Gaps = 35/241 (14%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-G 64
           I++ +   QR+ K +A     SR      I   R+ VNG   ++A   V   D I  +  
Sbjct: 4   IIEASVVGQRLDKAVAELTDLSRSLANEQIKDGRILVNGQ-AKKAKYAVKEGDIIYYELP 62

Query: 65  VP-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
            P             +   +     +      +V   +     + V   +  I       
Sbjct: 63  EPEVVEYVPEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGIN 122

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLL 161
           G L       +     G L       +           + LR Y    HG +  D+  + 
Sbjct: 123 GVLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIE 182

Query: 162 KKGIVIQGICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 +                 +  +  + G  + V + L  G+  +I+    +    
Sbjct: 183 APIGRSEKDRKKQAVTAKGKSALTRFQVLERFGDYSLVELQLETGRTHQIRVHMAYIGHP 242

Query: 212 V 212
           V
Sbjct: 243 V 243


>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 = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 69/246 (28%), Gaps = 36/246 (14%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+++  I++E+   +RV KVIA     SR  ++ M+    + VNG L +     V   D 
Sbjct: 1   MQNETLIIEESHARERVDKVIAEMMGKSRSAIQLMLKNGDITVNGELAK-PNYKVQVGDE 59

Query: 60  IEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I  +                 +   ++  L +      +V   +     + V   L    
Sbjct: 60  IHYEAREPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCD 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                 G++       +     G L       + + L           +           
Sbjct: 120 DLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVH 179

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           +K  V++          +  +      +   L  G+  +I+   
Sbjct: 180 QKGTIEAPIGRAKEDRQKMAVVRDGKEARTHFEVLERLPGFTLINCKLDTGRTHQIRVHL 239

Query: 206 EFFNWK 211
           ++    
Sbjct: 240 KYIGHP 245


>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 = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 24/245 (9%), Positives = 72/245 (29%), Gaps = 38/245 (15%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V++ F+  RV K ++      SR  ++++I    V  NG +++ A   + + D + +D 
Sbjct: 6   TVEKEFSGNRVDKFLSEQFPDLSRSYIQKLIKDGHVTANGKIVK-ANYKLNALDTLALDK 64

Query: 65  VPLR--------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
             L+                +   L +      +V   +     + V   +     ++  
Sbjct: 65  PELQEPDIVPENIPIDILYEDEDILIVNKPKGMVVHPSAGHYSGTLVNALMYHCKDQLSG 124

Query: 111 VGRLDIN----------------------TEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
           +  +                          + L     +  + R+        ++     
Sbjct: 125 INGIMRPGIVHRIDMDTTGSLLVCKNDFVHQDLAEQLKEHSIQRIYHAIVHGVIKEDEGT 184

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +  +   K  +  +   +      +  +  +  ++   L  G+  +I+      
Sbjct: 185 IDAPIGRHPIERKKMSVNYKNGKHAVTHYKVIERFKNYTYIKCRLETGRTHQIRVHMAHI 244

Query: 209 NWKVN 213
              + 
Sbjct: 245 RHPLL 249


>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 = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 30/240 (12%), Positives = 68/240 (28%), Gaps = 35/240 (14%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T QR+ + +A      SR  ++  I    V ++G + ++    V+    + V
Sbjct: 8   KSEITATQTGQRLDQTLADLFPDYSRTRIKEWILAGSVFIDGEVSDKPRFKVLEGQVVTV 67

Query: 63  DGVPLR---------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
            G  L                  +   L +  +   +V   +     + +   L      
Sbjct: 68  -GATLEEETKAQAEAIDLDIIYEDDHILIINKQAGLVVHPGAGNQDGTLMNALLHHCPGI 126

Query: 108 VISV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR------------VRFH 150
            +        RLD +T GL+++         L                            
Sbjct: 127 ELVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIVTGTIISGGTID 186

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             +D+         +V  G         +  +  ++  + + L  G+  +I+        
Sbjct: 187 EPIDRHPTKRTHMAVVHNGKPAMT-HYRVAEKFRAHTRLRLRLESGRTHQIRVHMAHIGH 245


>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 = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 37/243 (15%), Positives = 77/243 (31%), Gaps = 37/243 (15%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V      +R+ K +++     SR  ++++I   +V VNG  ++R +  V   DHI +   
Sbjct: 10  VSSEEEGKRIDKYLSKLNKDLSRSYIQKLIDNDKVLVNGESVKR-SFKVNRGDHIRLIIP 68

Query: 63  -------------------DGVPLRKAERTRLWLYHKPIGLVTT-------------HSD 90
                              D   L   +   L ++  P     T                
Sbjct: 69  PPEDSGIKPVEMDLDIIYEDKDILVLNKNAGLVVHPAPGNHENTLVNALIAYCDNLSTIS 128

Query: 91  PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
              R  +   L    S V+ + + DI+   L+         +         L     +  
Sbjct: 129 GVNRPGIVHRLDKDTSGVMVIAKNDISHRKLVEQFKQRKTKKYYRTLLKGELPYKEGKID 188

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + +D  +  K  +  +          +      +++V V L+ G+  +I+  F +  +
Sbjct: 189 APIGRDPHDRKKMAVTRKNSKKAVTYFKVLEFFRDHSYVEVELKTGRTHQIRVHFSYMGF 248

Query: 211 KVN 213
            V 
Sbjct: 249 PVV 251


>gi|255550684|ref|XP_002516391.1| ribosomal large subunit pseudouridine synthase B, putative [Ricinus
           communis]
 gi|223544489|gb|EEF46008.1| ribosomal large subunit pseudouridine synthase B, putative [Ricinus
           communis]
          Length = 315

 Score = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 22/50 (44%), Positives = 30/50 (60%), Gaps = 2/50 (4%)

Query: 4   KNIVQENFT--PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA 51
           +    ENF   PQR+SKV+A +G+ASRR  E +I Q +V VNG +     
Sbjct: 139 RRFYNENFREPPQRLSKVLAASGVASRRNSEELIFQGKVTVNGSVCNTPQ 188



 Score = 59.4 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 19/82 (23%), Positives = 40/82 (48%), Gaps = 2/82 (2%)

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVTVGLREGKNREIKK 203
             +  G V++  L  +  G +IQG+      V L  +K       + + + EG+N E+++
Sbjct: 202 YQKIDGAVNKRHLIAISGGTIIQGVHCTPDSVELLPRKPDLLRPRLRIVVHEGRNHEVRE 261

Query: 204 VFEFFNWKVNRLIRISYGPFQL 225
           + +    +V+ L R+  G ++L
Sbjct: 262 LVKNAGLEVHSLKRVRIGGYRL 283


>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 = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 24/238 (10%), Positives = 61/238 (25%), Gaps = 40/238 (16%)

Query: 15  RVSKV----IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP---- 66
           R+ K     +   GI SR +V+  I     ++NG + ++    +M  + + + G      
Sbjct: 28  RLDKFWGTALEEEGI-SRGKVKDWIKAGFAEINGKICKKPNQKLMGNEELTLKGEAELTS 86

Query: 67  ---------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
                    +   +     +                 + V   +                
Sbjct: 87  LVPEELPLEIIYNDGKIAVINKPAGLTTHPAPSCPTGTLVHRMIHHFPEIRDMDEWRPGI 146

Query: 118 TEGLLLLTN--------------------DGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
              L   T+                    D  + +          +         + +  
Sbjct: 147 VHRLDKFTSGLITVALNEHDRLAMSTAFADREVNKAYLAIVHGVPKREFGEIDQPMGRHP 206

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           ++  K  +V++G      +  +      G  + V V +  G+  +I+         + 
Sbjct: 207 VHKTKMAVVLKGGRDARSEYEVLWSDPAGRASLVKVKIYTGRTHQIRVHMAHIGHPLV 264


>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 = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 33/237 (13%), Positives = 57/237 (24%), Gaps = 35/237 (14%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--- 66
                R+ K IA     SR +    I    V VNG   + A  +V + D I  +      
Sbjct: 6   KEAGSRLDKAIADLTELSRGQANDAIKAGIVLVNGQAAK-AKYSVKAGDIITYEIQEEEV 64

Query: 67  -----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                      +   +     +      +V   +     + V   L  I       G + 
Sbjct: 65  LDYQAEDIPLDVVYEDEDLAIINKPQGMVVHPSAGHSSGTMVNALLYQIKDLSGINGVVR 124

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------------------- 155
                 +     G L       + + L                                 
Sbjct: 125 PGIVHRIDKDTSGLLMVAKNDAAHRALADELKAKKSLRKYLAIVHGNLPNDRGIIEAPIG 184

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                 KK  VI        +  +  + G    V + L  G+  +I+    +    V
Sbjct: 185 RSEKDRKKQAVIARGKEAVTRFQVIERFGDYTLVELTLETGRTHQIRVHMAYIGHPV 241


>gi|255029306|ref|ZP_05301257.1| hypothetical protein LmonL_09598 [Listeria monocytogenes LO28]
          Length = 245

 Score = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 69/246 (28%), Gaps = 36/246 (14%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+++  I++E+   +RV KVIA     SR  ++ M+    + VNG L +     V   D 
Sbjct: 1   MQNETLIIEESHARERVDKVIAEMMGKSRSAIQLMLKNGDITVNGELAK-PNYKVQVGDE 59

Query: 60  IEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I  +                 +   ++  L +      +V   +     + V   L    
Sbjct: 60  IHYEVREPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCD 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                 G++       +     G L       + + L           +           
Sbjct: 120 DLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVH 179

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           +K  V++          +  +      +   L  G+  +I+   
Sbjct: 180 QKGTIEAPIGRAKEDRQKMAVVRDGKEARTHFEVLERLPGYTLINCKLDTGRTHQIRVHL 239

Query: 206 EFFNWK 211
           ++    
Sbjct: 240 KYIGHP 245


>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 = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 34/241 (14%), Positives = 66/241 (27%), Gaps = 37/241 (15%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           +   +  +R+ KVIA      SR +V++ I    V VN   ++ A     + D + V   
Sbjct: 8   IDAEYDNERIDKVIAALNEEWSRSKVQQWIKDGLVTVNDQHVK-ANYKSSAGDVVVVRLP 66

Query: 63  DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
           +  PL              +   L +      +V         + V   L          
Sbjct: 67  EPEPLHVVPENIPLDIYYEDADVLVVNKPRGMVVHPAPGHMRGTLVNALLAHCTDLSGIN 126

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRVRFH 150
           G L       +     G L       + Q L                             
Sbjct: 127 GVLRPGIVHRIDKDTSGLLMVAKNDMAHQSLVDQLVKKTVTRKYKAIVHGVIPHDYGTID 186

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + +DK +  K  +  +          +  +     +V   L  G+  +I+   ++  +
Sbjct: 187 APIGRDKRDRKKMTVTEENGKEAVTHFRVLERFRHYTFVECQLETGRTHQIRVHMKYIGY 246

Query: 211 K 211
            
Sbjct: 247 P 247


>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 = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 34/244 (13%), Positives = 65/244 (26%), Gaps = 42/244 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            V      +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V
Sbjct: 8   TVAAEQKNERIDKFVA--GINNEWSRTQVQQWIKDDVVTVNGKAVK-GNYKVKEEDEITV 64

Query: 63  --------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                   D  P      +   +   L +      +V         + V   +       
Sbjct: 65  TIPEPEELDIQPEDLNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRV 147
              G +       +     G L       + + L                        + 
Sbjct: 125 GINGIMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKG 184

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                + +DK    +   V +          +  +      V   L  G+  +I+   ++
Sbjct: 185 TIDAPIARDKKER-QSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKY 243

Query: 208 FNWK 211
             + 
Sbjct: 244 IGYP 247


>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 = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 30/237 (12%), Positives = 61/237 (25%), Gaps = 35/237 (14%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
                R+ K +A     SR +    I    V VNG   + A   V   D I         
Sbjct: 6   KEAGNRLDKSLADLTELSRSQANEAIKAGTVLVNGKSAK-AKYVVKEGDVITYVLPEEEV 64

Query: 63  -----DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                + +PL     +     +      +V   +     + V   +  +       G + 
Sbjct: 65  LEYKAEDIPLDIIYEDADVAVVNKPQGMVVHPSAGHTSGTLVNALMYHVKDLSSINGVVR 124

Query: 116 INTEGL---------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
                          ++  ND     +      +      V        +   +++  I 
Sbjct: 125 PGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHGNLPNDRGVIEAPIG 184

Query: 167 IQGI---------CYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                               + T+  + G+   V + L  G+  +I+    +    V
Sbjct: 185 RSDKDRKKQAVTAKGKPAVTRFTVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 34/244 (13%), Positives = 65/244 (26%), Gaps = 42/244 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            V      +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V
Sbjct: 8   TVAAEQKNERIDKFVA--GINNEWSRTQVQQWIKDDVVTVNGKAVK-GNYKVKEEDEITV 64

Query: 63  --------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                   D  P      +   +   L +      +V         + V   +       
Sbjct: 65  TIPEPEELDIQPEDLNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRV 147
              G +       +     G L       + + L                        + 
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKG 184

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                + +DK    +   V +          +  +      V   L  G+  +I+   ++
Sbjct: 185 TIDAPIARDKKER-QSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKY 243

Query: 208 FNWK 211
             + 
Sbjct: 244 IGYP 247


>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 = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 34/244 (13%), Positives = 65/244 (26%), Gaps = 42/244 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            V      +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V
Sbjct: 8   TVAAEQKNERIDKFVA--GINNEWSRTQVQQWIKDDVVTVNGKAVK-GNYKVKEEDEITV 64

Query: 63  --------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                   D  P      +   +   L +      +V         + V   +       
Sbjct: 65  TIPEPEELDIQPEDLNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRV 147
              G +       +     G L       + + L                        + 
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKG 184

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                + +DK    +   V +          +  +      V   L  G+  +I+   ++
Sbjct: 185 TIDAPIARDKKER-QSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKY 243

Query: 208 FNWK 211
             + 
Sbjct: 244 IGYP 247


>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 = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 31/247 (12%), Positives = 72/247 (29%), Gaps = 37/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M D  ++ +     R+ KV+       +R ++++MI    +KVNG + ++A   V   D 
Sbjct: 4   MSDYKVLADKTG--RLDKVVTNIFTDYTRSQLKKMIDDGNIKVNGDV-KKANYKVNLGDE 60

Query: 60  IEVDGVPLR--------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I  D   ++                +   + +      +V         + V   L    
Sbjct: 61  ITFDKPEVKKLSLEPENIPLDIVYEDDDVIVVNKPQGMVVHPSPGHFEHTLVNALLYHSP 120

Query: 106 SRVISVGRLDINTEGL--------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
              I+          +        ++  ND     + +    +      V       ++ 
Sbjct: 121 LSTINGTYRPGIVHRIDKDTSGLLMVAKNDMAHQSLAKQLKDKTNTREYVALVHGNIKED 180

Query: 158 LNLLK-----------KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
              +            K  V++          +  + G    V   L  G+  +I+   +
Sbjct: 181 SGTIDAPLGRSKVDRKKQAVVKDGRNAVTHFEVLKRYGDYTLVKCVLETGRTHQIRVHMK 240

Query: 207 FFNWKVN 213
           +    + 
Sbjct: 241 YIGHPLV 247


>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 = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 33/242 (13%), Positives = 71/242 (29%), Gaps = 36/242 (14%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---- 60
           +V+   +  R+ K IA      SR  V+ +I Q+ +  NG L  + +  V + D I    
Sbjct: 10  VVKSEESGVRLDKYIATHISTISRTRVQELIKQKLITTNG-LQTKLSYKVNTNDKINIEI 68

Query: 61  ------EVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
                  +D   L       +   + +      +V   +     + V   +    +    
Sbjct: 69  PYPQPLSLDPENLNLDIIYEDDDVIVVNKPQGMVVHPSAGHPDHTLVNGLIYHTKNLAKC 128

Query: 107 -RVISVGRLDINTEGLLLL-------TNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--- 155
             +   G +    +    L       T    L + L     +   +  V  + +      
Sbjct: 129 DEIFRPGIVHRIDKDTSGLLMIAKNATARISLEKQLANKINKREYIAIVHDNFKHSSGVI 188

Query: 156 -----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      ++  V+          T+  Q    + V   L  G+  +I+    +   
Sbjct: 189 DAPIGRNPYQRQQMAVVASGKKAITHFTVLEQFPGYSLVKCVLETGRTHQIRVHMSYIGH 248

Query: 211 KV 212
            +
Sbjct: 249 PI 250


>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 = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 29/235 (12%), Positives = 71/235 (30%), Gaps = 34/235 (14%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP----- 66
           + QR+ K +      SR  +++M+ Q  + VN   + +A+  +   D+I+++        
Sbjct: 2   SSQRIDKFLVENTNYSRTLIKKMLDQNLILVNDNFISKASYLLKKNDYIQINNELPIVQE 61

Query: 67  ------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
                       +   ++  L +      LV   S  +  +        + +    +   
Sbjct: 62  QKKLLPFVYSLEIIFEDQDLLIVNKPSGMLVHPTSFHEQNTLANALKYYLKTDNFYITHR 121

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--------- 165
                  L++     +A            + +  +    ++  +  L   I         
Sbjct: 122 LDKNTSGLIIICKNQIALNSLQQQFMQKTIRKSYYAIVHNRFDMQHLHFMINEPIGHSYQ 181

Query: 166 ------VIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                         +    V +  Q  + A V V +  G+  +I+    + N  V
Sbjct: 182 DKLRMKTGNSKNTKEAISIVKVLEQYKNTALVEVSIITGRTHQIRVHMRYINHPV 236


>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 = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 34/232 (14%), Positives = 65/232 (28%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++     SR      I   +V VNG + ++A   V   D I              
Sbjct: 11  RLDKALSDLTELSRSLANEQIKSGQVLVNGQV-KKAKYTVQEGDVITYHVPEPEVLEYVA 69

Query: 63  DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           + +PL     +     +      +V   +     + V   +  I       G L      
Sbjct: 70  EDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 121 LLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            +     G L       +           + LR Y    HG +  D+  +       +  
Sbjct: 130 RIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 171 CYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                          +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 35/247 (14%), Positives = 77/247 (31%), Gaps = 40/247 (16%)

Query: 13  PQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----DGVP- 66
            +R+ K +A      SR  +++ +    V VN    + A++ V   D + +    +  P 
Sbjct: 14  GERIDKYLAEVMNDYSRSFLQKQLKDGNVSVNEKTAK-ASLKVAEDDEVRIFIPENKEPD 72

Query: 67  ---------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------V 108
                    +   ++  L +      +V   +    ++ V   +     +          
Sbjct: 73  IVPEDIPLDILYEDQQLLVVNKPKGMVVHPSAGHYSQTLVNALMFHCKDQLSGINGVLRP 132

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVYRVRFHGQVDQ 155
             V R+D++T G L++       + L                    L+       G + +
Sbjct: 133 GIVHRIDMDTTGALVVCKTDLAHQSLAEQLKVHSITRLYRAIVHGRLKEDFGTIEGTIGR 192

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRL 215
              +  K  I ++          +  +     +V   L  G+  +I+         +  L
Sbjct: 193 HPTDRKKMAINVRNGKPATTHYKVLERFDRFTYVECELETGRTHQIRVHMSSIGHPL--L 250

Query: 216 IRISYGP 222
             I YGP
Sbjct: 251 GDIVYGP 257


>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 = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 35/322 (10%), Positives = 88/322 (27%), Gaps = 44/322 (13%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---- 60
           ++ ++   QR+ + +A      SR  ++  I  +RV +NG  + +    VM  + +    
Sbjct: 10  VISDSQLGQRLDQALAECFPDYSRSRIKEWILAERVSLNGKTVAKPREKVMGGEAVLIQA 69

Query: 61  ----EVDGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
               EV   P      +   +   L +      +V   +     + +   L         
Sbjct: 70  EFEEEVAAKPQDIALDIVYEDDDILVINKPADLVVHPGAGNHDGTVLNALLHHCPSIANV 129

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--- 156
                  R+       +     +               + ++  +           D   
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTIPAQTHLVAQLQAREITREYEAIALGVMTAGGHVDEPI 189

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                      V +          +  +  ++  + + L  G+  +I+         +  
Sbjct: 190 GRHPQRRTHMAVTELGKPAVTHYRIREKFRAHTRLRLRLETGRTHQIRVHMAHLGHPLVG 249

Query: 215 LIRISYGPFQLGTLLAGSTREVSK--KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRP 272
                        L +G  R V    + LRE L     +     +    +     +    
Sbjct: 250 -----------DPLYSGRPRPVKGWSEELREFLRRFNRQALHAAMLRLEHPITGEMMQWT 298

Query: 273 NIISEVPDDFTRMKKNSSQKNG 294
             I +     T + +  ++++G
Sbjct: 299 APIPDDMVRLTELLRRDTEEHG 320


>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 = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 32/237 (13%), Positives = 61/237 (25%), Gaps = 40/237 (16%)

Query: 12  TPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
             +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V      
Sbjct: 14  KNERIDKFVA--GINNEWSRSQVQQWIKDDVVTVNGKTVKV-NYKVKEEDEITVTIPEPE 70

Query: 63  --DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
             D  P      +   +   L +      +V         + V   +          G +
Sbjct: 71  ALDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGINGVM 130

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL-------------- 160
                  +     G L       + + L    V          +                
Sbjct: 131 RPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPI 190

Query: 161 ------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                  +   V +          +  +      V   L  G+  +I+   ++  + 
Sbjct: 191 GRDKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYP 247


>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 = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 35/247 (14%), Positives = 73/247 (29%), Gaps = 36/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  +  ++      R+ K ++      SR  V+ ++  Q + VNG + +  +  + + D 
Sbjct: 1   MTKEYSLEVKNEKGRLDKFVSEQIPDLSRTRVKELVKDQNILVNGKVEKV-SYKIQAGDK 59

Query: 60  IEVDGVPLR--------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           IEV+   ++                +   + +      +V         + V   L    
Sbjct: 60  IEVNIPAVKPLDVIPENIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHTK 119

Query: 106 --------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-- 155
                    R   V R+D +T GLL++         LE                  +   
Sbjct: 120 ALAQSPEGFRPGIVHRIDKDTSGLLMIAKTAKARESLEDQLAHKTNKRLYWAIVHGNFAE 179

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           KK  V++          +  Q    + +   L  G+  +I+   
Sbjct: 180 ENGVIDAPIGRNPYDRKKMAVVETGKKAITHFKVLEQFKDYSLIECQLETGRTHQIRVHL 239

Query: 206 EFFNWKV 212
           ++    V
Sbjct: 240 DYIGHPV 246


>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 = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 33/248 (13%), Positives = 72/248 (29%), Gaps = 37/248 (14%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+ + + + E+    R+ KV+A     SR+ ++ ++ +  V VN   + +A+  V   D 
Sbjct: 1   METRILKIDEDTKLDRLDKVLAEKLDFSRKRIKDLLDEGNVLVN-QKVMKASYKVCVNDE 59

Query: 60  IEVD----------GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           IEV             P+       +   + +      +V         + V   L    
Sbjct: 60  IEVSIPELDSTQVLPEPIDLDIVYEDHDIIVINKPKGMVVHPAPGHYSGTLVNALLYHCK 119

Query: 106 SRVISVGRLDIN---------------------TEGLLLLTNDGGLARVLELPSTQWLRV 144
                 G +                         E L     D    R       +    
Sbjct: 120 DLSGINGVMRPGIVHRIDKDTSGLLVVAKNDKAHEALSQQLQDKTCHREYVAIVHKPFTH 179

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                H  + +D+ +  K  +            ++       A++   L  G+  +I+  
Sbjct: 180 EYGTIHAPIGRDEKDRQKMAVTANNSKDAITHFSVLENFSKFAYIKCQLETGRTHQIRVH 239

Query: 205 FEFFNWKV 212
            ++    +
Sbjct: 240 MQYIEHPI 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 = 67.5 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 29/238 (12%), Positives = 63/238 (26%), Gaps = 40/238 (16%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----DGVP---- 66
           R+ K IA     SR +++ +I  + V VN  L+ + +  V     I++    D  P    
Sbjct: 11  RIDKYIASNSSLSRADIQELIKSKAVFVNNGLVCKPSYIVHPPQEIKIIRLLDKTPKIEA 70

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN--- 117
                 +   +   + +      +V         +     L    + +     L      
Sbjct: 71  QNIKLDIIYEDDHLVIIDKPSGLIVHPSPTHYENTLANGLLYHFKNNLSDTNGLLRPGIV 130

Query: 118 -----TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
                    LL+        +      +   + R       +      L+  + I     
Sbjct: 131 HRIDKDTSGLLIVTKTNAVHIKLAEMFKNHSIKRSYIAICDNFLTDKKLRINLPIGLDPK 190

Query: 173 GDMQVTL------------------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
              +  +                    +K   + V   L  G+  +I+      N  +
Sbjct: 191 NPQKRKVTNIKAKEAITNVELIKTFYHEKQPKSLVKCNLETGRTHQIRVHLAHINNPI 248


>gi|332361351|gb|EGJ39155.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK1056]
          Length = 298

 Score = 67.1 bits (162), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 36/240 (15%), Positives = 69/240 (28%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           ++ +   QR+ K +A     SR      I   R+ VNG + ++A   V   D I      
Sbjct: 5   IESSVAGQRLDKAVAELTDLSRSLANEQIKDGRILVNGQV-KKAKYAVKEGDVISYELPE 63

Query: 63  --------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
                   + +PL     +     +      +V   +     + V   +  I       G
Sbjct: 64  PEVVEYVPEDIPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGING 123

Query: 113 RLDINTEGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLK 162
            L       +     G L       +           + LR Y    HG +  D+  +  
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 163 KGIVIQGICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                +                 +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 184 PIGRSEKDRKKQAVTAKGKPALTRFQVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 243


>gi|308190331|ref|YP_003923262.1| pseudouridylate synthase [Mycoplasma fermentans JER]
 gi|307625073|gb|ADN69378.1| pseudouridylate synthase [Mycoplasma fermentans JER]
          Length = 307

 Score = 67.1 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 73/239 (30%), Gaps = 40/239 (16%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGIL-LERAAVNVMSTDHIEV----DGVP-- 66
           +R+ K I +    SR +++ +I Q  V +N  + + +    V     I +    D     
Sbjct: 10  ERIDKYIGQNSELSRNDIKELIEQGAVYINDNVQVHKCNYIVREGQEITIVKLLDKEIKI 69

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VI 109
                   ++  +   + +      +V         + V   L    +            
Sbjct: 70  EPVNIPLDIKYEDDDLVIINKPSNLVVHPSPGHYNDTLVNGLLYHFKNNLSNENGLLRPG 129

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR-------------VRFHGQVDQD 156
            V R+D +T GLL++  +  +   L     +                    + +  + ++
Sbjct: 130 IVHRIDKDTSGLLIIAKNNKMHNSLTDMLKRHEIERSYLAIVRGLIENPLTKINLPIARN 189

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            ++     +  +G         L      K   + V   L+ G+  +I+    +    V
Sbjct: 190 TVDRKMMSVHKEGKEAITFVHLLKHFYLDKEPMSLVRCELKTGRTHQIRVHLSYIKHPV 248


>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 = 67.1 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 35/247 (14%), Positives = 73/247 (29%), Gaps = 36/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  +  ++      R+ K ++      SR  V+ ++  Q + VNG + +  +  + + D 
Sbjct: 1   MTKEYSLEVKNEKGRLDKFVSEQIPDLSRTRVKELVKDQNILVNGKVEKV-SYKIQAGDK 59

Query: 60  IEVDGVPLR--------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           IEV+   ++                +   + +      +V         + V   L    
Sbjct: 60  IEVNIPAVKPLDVIPENIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHSK 119

Query: 106 --------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-- 155
                    R   V R+D +T GLL++         LE                  +   
Sbjct: 120 ALAQSPEGFRPGIVHRIDKDTSGLLMIAKTAKARESLEDQLAHKTNKRLYWAIVHGNFAE 179

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           KK  V++          +  Q    + +   L  G+  +I+   
Sbjct: 180 ENGVIDAPIGRNPYDRKKMAVVETGKKAITHFKVLEQFKDYSLIECQLETGRTHQIRVHL 239

Query: 206 EFFNWKV 212
           ++    V
Sbjct: 240 DYIGHPV 246


>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 = 67.1 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 27/242 (11%), Positives = 70/242 (28%), Gaps = 33/242 (13%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T QR+ + +A      SR  ++  I    V ++G++  +    V+    I +
Sbjct: 8   KSEITATQTGQRLDQTLAELYPDYSRTRIKEWIQAGWVYIDGVVSTKPREKVLEGQEIAI 67

Query: 63  D--------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           +               + +   +   + +  +   +V   +     + +   L       
Sbjct: 68  EATLKEETAAKAQAIDLDIVYEDDHIIVINKQAGLVVHPGAGNQDGTLMNALLHHCPGIE 127

Query: 109 ISV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR------------VRFHG 151
           +        RLD +T GL+++         L                             
Sbjct: 128 LVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVSALQAREITREYEAVVLGTLISGGTVDE 187

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +D+         +V  G         +  +  ++  + + L  G+  +I+         
Sbjct: 188 PIDRHPTKRTHMAVVHNGKPAMT-HYRVAEKFRAHTRLRLRLESGRTHQIRVHMSHIGHT 246

Query: 212 VN 213
           + 
Sbjct: 247 LV 248


>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 = 67.1 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 38/245 (15%), Positives = 75/245 (30%), Gaps = 35/245 (14%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER-----AAVNVM--- 55
           K +  E    QR+ KV+      SR  ++  +    + VNG +++      +   V    
Sbjct: 6   KKLKLELEKTQRLDKVLTGELGLSRTTIQSWLKAGLISVNGEVVKSNYKAQSGDEVTILQ 65

Query: 56  -STDHIEVDGVPLRK----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
              D I +    +       + + + +      +V         + V   L         
Sbjct: 66  KEEDVITIQPENIPLDIVFEDDSLIVVNKPSGMVVHPSKGHYSGTLVNALLYHSNSLSDS 125

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD-- 156
                 R   V R+D +T GLL++  +  + + L       +  R Y     G    +  
Sbjct: 126 TSEEIYRPGLVHRIDKDTSGLLVIAKNNDVHQKLAEQIAENKMNREYIAIVDGHFAHETG 185

Query: 157 --------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                         K +V +G         +       + V+  L  G+  +I+   EF 
Sbjct: 186 VVDAPLSRHQTNRLKRVVEKGGKNAITHFEVLDSFSDYSLVSCRLETGRTHQIRAHMEFI 245

Query: 209 NWKVN 213
              + 
Sbjct: 246 KHPIV 250


>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 = 67.1 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 34/262 (12%), Positives = 74/262 (28%), Gaps = 41/262 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M ++  +       R+ KV+A      SR +++  + +  VK++G++++ A   V   D 
Sbjct: 1   MTEELKISITEEKGRIDKVLAEKLANYSRSQIQLWLKEACVKIDGVVVK-ANYKVQKGDR 59

Query: 60  IEVD-GVP-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I +    P             +   +     +      +V   +     + V   +  + 
Sbjct: 60  ITIQIPEPETLDLIAENLPLEIVYEDADVAVINKPQGMVVHPSAGHPNGTLVNALIYHLN 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ------------WLRVYRVRFHGQV 153
           S     G +       +     G L       + +               V  V      
Sbjct: 120 SLSSINGVIRPGIVHRIDKDTSGLLMVAKNDQAHEDLAKQLKDKTSLRKYVALVHGVIPH 179

Query: 154 DQ--------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
           D+              K   V+           +  +      V + L  G+  +I+   
Sbjct: 180 DKGVIRAPIGRSTVDRKMQAVVDNGKDAVTHFQVLERYEDYTLVELQLETGRTHQIRVHM 239

Query: 206 EFFNW-----KVNRLIRISYGP 222
           ++  +      V  L R   G 
Sbjct: 240 QYIGYPLVGDPVYGLKRTIKGN 261


>gi|268610335|ref|ZP_06144062.1| pseudouridine synthase rRNA-specific [Ruminococcus flavefaciens
           FD-1]
          Length = 108

 Score = 67.1 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 17/104 (16%), Positives = 37/104 (35%), Gaps = 1/104 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K I+     +R +++ + A+  V VNG  ++R+   + +  D + V G  +     
Sbjct: 4   IRLDKFISERTEYTRSQIKSLCAKGSVTVNGSPVKRSDTKIDTGADDVTVCGNAISSERF 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
             + L      + +T                  S +   G   +
Sbjct: 64  RYILLNKPKGYVSSTDDKDGETVISLCVKKREASGMKRAGGRAM 107


>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 = 67.1 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 29/245 (11%), Positives = 65/245 (26%), Gaps = 35/245 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  +  +    + QR+ K +A      SR  ++ ++    + VNG    + +  V   D 
Sbjct: 1   MNREYELTAEESGQRLDKYLAGEMTDLSRSRIKELVQAGEILVNGKK-SKVSYKVQKDDL 59

Query: 60  IEV------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I+V            + +P  +   ++  + +      +V   +     + V   L    
Sbjct: 60  IQVIVLPLEPLKLEAENIPLDIVYEDKDVIVVNKPQGMVVHPAAGHPSHTLVNALLYHTR 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
               S           +     G L       + + L         +             
Sbjct: 120 DLADSPEGFRPGIVHRIDKDTSGLLMVAKNAAARESLEKQLAAKSNKRQYLAIVHGNFAE 179

Query: 156 ---------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          K+  V++          +  Q    + V   L  G+  +I+    
Sbjct: 180 EGTIDAPIGRNPKDRKQMAVVEKGKSAVTHFKVLEQYQGYSLVECQLETGRTHQIRVHMA 239

Query: 207 FFNWK 211
           +    
Sbjct: 240 YIGHP 244


>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 = 67.1 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 32/232 (13%), Positives = 63/232 (27%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP------- 66
           R+ K ++     SR      I   +V VNG + ++A   V   D +      P       
Sbjct: 11  RLDKALSDLTELSRSLANEQIKSGQVLVNGQV-KKAKYTVQEGDVVTYHLPEPEVLEYVA 69

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 +   +     +      +V   +     + V   +  I       G L      
Sbjct: 70  ENLPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 121 LLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            +     G L       +           + LR Y    HG +  D+  +       +  
Sbjct: 130 RIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 171 CYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                          +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 67.1 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 36/232 (15%), Positives = 71/232 (30%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--------EVDGVP 66
           R+ K +A     SR      I + +V VNG  +++A   V   D I        EV    
Sbjct: 11  RLDKALADLTPLSRAVANEQIKEGKVLVNG-TVKKAKYTVKEGDIIQYEVPEVEEVSYEA 69

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISVG 112
                 +   ++  + +      +V   +     + V   L  I          R   V 
Sbjct: 70  EDLPLDIVYEDQDVVVVNKPQGMVVHPSAGHTSGTLVNALLYHIKDLSGINGELRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           R+D +T GLL++  +      L         + +       +      + +  + +    
Sbjct: 130 RIDKDTSGLLMVAKNDQAHVALAEELKDKKSLRKYWAIVHGNLPNDRGMIEAPIGRSEKD 189

Query: 173 GDMQ------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
              Q              +  + G+   V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFQVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 67.1 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 22/228 (9%), Positives = 63/228 (27%), Gaps = 36/228 (15%)

Query: 15  RVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           R+ K +       R +++        ++I + +V VN   ++  +  +   D +E+    
Sbjct: 13  RLDKFL-------RNQLKDVPLSVIYKLIRKGKVYVNKKRVKDPSFELEEGDVVELRYVN 65

Query: 63  -----------DGVPLR------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
                      D  P+         +   L L   P   +         + +   L    
Sbjct: 66  LENLPKRSEKKDLTPVPMKLDVLYEDDHYLVLNKPPNIAIHPGKGVHVATLIEGLLHYGQ 125

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
            +  S   +    +    L           + +  +      + +  + +       K  
Sbjct: 126 EKGFSPFLVHRLDKDTSGLLVVAKNREAARILTELFKGRNIEKEYVTLVRGVPENNMKLT 185

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +         ++         + + V +  G+  +I++      + V 
Sbjct: 186 IPLDGQEAVSEIVSVKPLKDVSLLRVKIHTGRKHQIRRHLSQIGFPVV 233


>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 = 67.1 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 32/234 (13%), Positives = 63/234 (26%), Gaps = 35/234 (14%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP----- 66
            QR+ K ++     SR      I   +V VNG   ++A   V   D +      P     
Sbjct: 9   GQRLDKALSDLTELSRSLANEQIKAGQVLVNGQ-AKKAKYTVQDGDIVTYHVPEPEVLEY 67

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                   +   +     +      +V   +     + V   +  I       G L    
Sbjct: 68  VAENLPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGI 127

Query: 119 EGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              +     G L       +           + LR Y    HG +  D+  +       +
Sbjct: 128 VHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSE 187

Query: 169 GICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                            +  +  + G  + + + L  G+  +I+    +    V
Sbjct: 188 KDRKKQAVTAKGKPAVTRFQVLERFGDYSLLELQLETGRTHQIRVHMAYIGHPV 241


>gi|326575838|gb|EGE25761.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis CO72]
          Length = 355

 Score = 67.1 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 28/242 (11%), Positives = 70/242 (28%), Gaps = 36/242 (14%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           V       R+ K+ A   G  SR  +++ I + ++ VNG +++     V   D + ++  
Sbjct: 48  VSTEQIGIRLDKLCADIFGGFSRANLKKFIDEGQLTVNGKVVK-PKYAVKVGDILTLEAV 106

Query: 64  ------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                        + +   +   + +      +V   +     + V   L     +    
Sbjct: 107 HESHSEDLPENIDIDIIYEDEAVIIINKPAGMVVHPGAGNRTGTLVNALLYHFPKQAHLP 166

Query: 112 -----GRLDINTEGLLLLT---------------NDGGLARVLELPSTQWLRVYRVRFHG 151
                 R+D +T GLL++                                  +   +   
Sbjct: 167 RAGLVHRIDKDTTGLLVIARTKSAQLSLIDQLKDKSVYRHYQCIALGAVHEVLRHAQIDA 226

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + +   +  K  +   G       V         + + + L+ G+  +I+    +    
Sbjct: 227 PIGRHSTHRTKMAVKQTGKPALTHIVNAKYLHERYSLLDIHLKTGRTHQIRVHLSYVGHP 286

Query: 212 VN 213
           + 
Sbjct: 287 LV 288


>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 = 67.1 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 28/242 (11%), Positives = 70/242 (28%), Gaps = 36/242 (14%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           V       R+ K+ A   G  SR  +++ I + ++ VNG +++     V   D + ++  
Sbjct: 48  VSTEQIGIRLDKLCADIFGGFSRANLKKFIDEGQLTVNGKVVK-PKYAVKVGDILTLEAV 106

Query: 64  ------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                        + +   +   + +      +V   +     + V   L     +    
Sbjct: 107 HESHSEDLPENIDIDIIYEDEAVIIINKPAGMVVHPGAGNRTGTLVNALLYHFPKQAHLP 166

Query: 112 -----GRLDINTEGLLLLT---------------NDGGLARVLELPSTQWLRVYRVRFHG 151
                 R+D +T GLL++                                  +   +   
Sbjct: 167 RAGLVHRIDKDTTGLLVIARTKSAQLSLIDQLKDKSVYRHYQCIALGAVHEVLRHAQIDA 226

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + +   +  K  +   G       V         + + + L+ G+  +I+    +    
Sbjct: 227 PIGRHSTHRTKMAVKQTGKPALTHIVNAKYLHERYSLLDIHLKTGRTHQIRVHLSYVGHP 286

Query: 212 VN 213
           + 
Sbjct: 287 LV 288


>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 = 67.1 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 28/242 (11%), Positives = 70/242 (28%), Gaps = 36/242 (14%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           V       R+ K+ A   G  SR  +++ I + ++ VNG +++     V   D + ++  
Sbjct: 48  VSTEQIGIRLDKLCADIFGGFSRANLKKFIDEGQLTVNGKVVK-PKYAVKVGDILTLEAV 106

Query: 64  ------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                        + +   +   + +      +V   +     + V   L     +    
Sbjct: 107 HESHSEDLPENIDIDIIYEDEAVIIINKPAGMVVHPGAGNRTGTLVNALLYHFPKQAHLP 166

Query: 112 -----GRLDINTEGLLLLT---------------NDGGLARVLELPSTQWLRVYRVRFHG 151
                 R+D +T GLL++                                  +   +   
Sbjct: 167 RAGLVHRIDKDTTGLLVIARTKSAQLSLINQLKDKSVYRHYQCIALGAVHEVLRHAQIDA 226

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + +   +  K  +   G       V         + + + L+ G+  +I+    +    
Sbjct: 227 PIGRHSTHRTKMAVKQTGKPALTHIVNAKYLHERYSLLDIHLKTGRTHQIRVHLSYVGHP 286

Query: 212 VN 213
           + 
Sbjct: 287 LV 288


>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 = 67.1 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 36/247 (14%), Positives = 74/247 (29%), Gaps = 36/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K  +Q      R+ K I+      SR  V+ ++ ++ + VN  + +  +  + + D 
Sbjct: 1   MPKKYELQVENEYGRLDKFISEQIPDLSRTRVKELVKEKEILVNHKVEKV-SYKIQAGDK 59

Query: 60  IEVDGVPLR--------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           IE++   ++                +   + +      +V         + V   L    
Sbjct: 60  IEINVPAVKPLDVVPENIPLDIVYEDEVVIVVNKPQGMVVHPAPGHPDHTLVNALLYHTQ 119

Query: 106 --------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-- 155
                    R   V R+D +T GLL++  +      LE                  D   
Sbjct: 120 DLAQSPEGFRPGIVHRIDKDTSGLLMIAKNAKARESLEDQLAHKTNKRIYWAIVHGDFGE 179

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           KK  V++          +  Q    + +   L  G+  +I+   
Sbjct: 180 ENGVIDAPIGRNPYDRKKMAVVENGKKAVTHFKVLKQFKGYSLIECQLETGRTHQIRVHL 239

Query: 206 EFFNWKV 212
           ++    V
Sbjct: 240 DYIGHAV 246


>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 = 67.1 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 35/232 (15%), Positives = 71/232 (30%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--------EVDGVP 66
           R+ K +A     SR      I + +V VNG  +++A   V   D I        EV    
Sbjct: 11  RLDKALADLTPLSRAVANEQIKEGKVLVNG-TVKKAKYTVKEGDIIQYEVPEVEEVSYEA 69

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISVG 112
                 +   ++  + +      +V   +     + V   L  +          R   V 
Sbjct: 70  EDLPLDIVYEDQDVVVVNKPQGMVVHPSAGHTSGTLVNALLYHVKDLSGINGELRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           R+D +T GLL++  +      L         + +       +      + +  + +    
Sbjct: 130 RIDKDTSGLLMIAKNDQAHVALAEELKDKKSLRKYWAIVHGNLPNDRGMIEAPIGRSEKD 189

Query: 173 GDMQ------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
              Q              +  + G+   V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFQVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 67.1 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 33/232 (14%), Positives = 65/232 (28%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++     SR      I   +V VNG + ++A   V   D +              
Sbjct: 11  RLDKALSDLTELSRSLANEQIKSGQVLVNGQV-KKAKYTVQEGDVVTYHVPEPEVLEYVA 69

Query: 63  DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           + +PL     +     +      +V   +     + V   +  I       G L      
Sbjct: 70  ENIPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 121 LLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            +     G L       +           + LR Y    HG +  D+  +       +  
Sbjct: 130 RIDKDTSGLLMIAKNDEAHLALAQDLKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 171 CYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                          +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>gi|326576921|gb|EGE26827.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis O35E]
          Length = 355

 Score = 67.1 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 28/242 (11%), Positives = 70/242 (28%), Gaps = 36/242 (14%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           V       R+ K+ A   G  SR  +++ I + ++ VNG +++     V   D + ++  
Sbjct: 48  VSTEQIGIRLDKLCADIFGGFSRANLKKFIDEGQLTVNGKVVK-PKYAVKVGDILTLEAV 106

Query: 64  ------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                        + +   +   + +      +V   +     + V   L     +    
Sbjct: 107 HESHSEDLPENIDIDIIYEDEAVIIINKPAGMVVHPGAGNRTGTLVNALLYHFPKQAHLP 166

Query: 112 -----GRLDINTEGLLLLT---------------NDGGLARVLELPSTQWLRVYRVRFHG 151
                 R+D +T GLL++                                  +   +   
Sbjct: 167 RAGLVHRIDKDTTGLLVIARTKSAQLSLIDQLKDKSVYRHYQCVALGAVHEVLRHAQIDA 226

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + +   +  K  +   G       V         + + + L+ G+  +I+    +    
Sbjct: 227 PIGRHSTHRTKMAVKQTGKPALTHIVNAKYLHERYSLLDIHLKTGRTHQIRVHLSYVGHP 286

Query: 212 VN 213
           + 
Sbjct: 287 LV 288


>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 = 67.1 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 34/248 (13%), Positives = 71/248 (28%), Gaps = 37/248 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N++ E     R+ KVIA +    SR +++ MI Q  V VN    E+A+      D 
Sbjct: 11  MEKINLIIEEDNNLRLDKVIAMQLQELSRTQIQDMINQGLVLVNQKK-EKASYKTKLNDE 69

Query: 60  IEV--------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           IE+        D  P      +   +   + +      +V   +     + V   L    
Sbjct: 70  IEITILDNVDLDIEPEDISLKIVYEDEDVIVVDKPTGMIVHPSAGIMHGTLVNALLFHCK 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPST---------------------QWLRV 144
                 G         +     G L       +                        +  
Sbjct: 130 DLSGINGVNRPGIVHRIDKETSGLLMVAKNDNAHRLLSKQLKDHTVVRRYVALVHGLIPH 189

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
              +    + ++  +     +            T+  +  + + +   L  G+  +I+  
Sbjct: 190 EHGKVDAPIGRNPKDRQSMAVTRTNSKEAVTNFTVLKRYNAMSLIECRLETGRTHQIRVH 249

Query: 205 FEFFNWKV 212
             +  + V
Sbjct: 250 MSYIGYPV 257


>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 = 67.1 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 40/315 (12%), Positives = 84/315 (26%), Gaps = 49/315 (15%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVN------VMS 56
           ++I  E    +R+   +++     SR  ++  I    VKVN  ++            +  
Sbjct: 9   RHIFDEKVYGKRLDAALSQQFSEYSRSRIQEWIQNGFVKVNDEVITSNKYKMAGFEDIEI 68

Query: 57  TDHIEVDGVP--------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--- 105
              IEV G          +   +   L +      +V   +     + V   L       
Sbjct: 69  NAEIEVAGEWKPEAIDLDIVYEDDALLVINKPAGLVVHPGAGNQDGTMVNALLHHCPDLA 128

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------- 155
              R   + R+D  T GLL++         L                             
Sbjct: 129 NLPRAGIIHRIDKETTGLLVVAKTIAAHTSLVEQLQNRAFTREYDAVVNRVMVSGGTIDK 188

Query: 156 ---DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                        V+           +  +   +  + + L  G+  +I+    +  + +
Sbjct: 189 PIGRHPTKRTSMAVVADGKRAITHYRVVEKFLDHTHLKLRLETGRTHQIRVHMAYLKFPL 248

Query: 213 NRLIRISYGPFQLGTLLAGSTR---EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVR 269
                   G      L +G  R    ++   LR  +     +    +L   +        
Sbjct: 249 -------IG----DPLYSGRYRVPTRITP-ELRNTVDNFKRQALHASL---LGLQHPETD 293

Query: 270 DRPNIISEVPDDFTR 284
           +     + +P D  R
Sbjct: 294 EYIEWRAPMPQDMAR 308


>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 = 67.1 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 35/232 (15%), Positives = 71/232 (30%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--------EVDGVP 66
           R+ K +A     SR      I + +V VNG  +++A   V   D I        EV    
Sbjct: 11  RLDKALADLTPLSRAVANEQIKEGKVLVNG-TVKKAKYTVKEGDIIQYEVPEVEEVSYEA 69

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISVG 112
                 +   ++  + +      +V   +     + V   L  +          R   V 
Sbjct: 70  EDLPLDIVYEDQDVVVVNKPQGMVVHPSAGHTSGTLVNALLYHVKDLSGINGELRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           R+D +T GLL++  +      L         + +       +      + +  + +    
Sbjct: 130 RIDKDTSGLLMVAKNDQAHVALAEELKDKKSLRKYWAIVHGNLPNDRGMIEAPIGRSEKD 189

Query: 173 GDMQ------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
              Q              +  + G+   V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFQVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPV 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 = 66.7 bits (161), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 32/239 (13%), Positives = 67/239 (28%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + +D 
Sbjct: 10  TVSESQLGQRLDQTLAELFPDYSRSRIKEWILNQRVSVNGTVTDKPKEKVLGGERVTIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEQRWEPQNIPLDIVYEDEDIIVINKPRDFVVHPGAGNPDGTVLNALLHHYPAIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTHLVDALQRREITREYEAVAIGTMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 SRHSTKRTHMSVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHINHPLV 248


>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 = 66.7 bits (161), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 34/243 (13%), Positives = 75/243 (30%), Gaps = 42/243 (17%)

Query: 13  PQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
           P R+ + ++R    A+R +V+  I   RV VN  +++     + S D IE+         
Sbjct: 33  PMRIDQYLSRQVENATRNKVQEAIEDGRVLVNDKVVKS-NYRIKSCDLIEMTFLRPPAPE 91

Query: 64  ------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------- 110
                  + +   +   + +  +P  +V         +     L  I     S       
Sbjct: 92  LAPEDIPIAIVYEDSELMVINKEPGMVVHPAFGNWTGTLANAILHHIGENAGSLDESELR 151

Query: 111 ---VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------------ 155
              V RLD +T GL+++  +      L         V   +                   
Sbjct: 152 PGIVHRLDKDTSGLIIIAKNPTALHRLAKQFADRKVVKTYKALVWGVPATPEGTIRTNIG 211

Query: 156 --DKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIKKVFEFFNWK 211
              K   +      +G            ++  +  + +++ L  G+  +I+   +    +
Sbjct: 212 RSRKDRKVMANFPYEGEEGKTAITDYRLEEDLHWFSLLSLTLHTGRTHQIRAHMQHLGHQ 271

Query: 212 VNR 214
           +  
Sbjct: 272 ILS 274


>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 = 66.7 bits (161), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 28/237 (11%), Positives = 69/237 (29%), Gaps = 38/237 (16%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----------EV 62
            R+ K +A A    SR  +++++   +V VNG  ++ A+  V+  D I          E+
Sbjct: 5   VRIDKYLAEACPDLSRSYIQKLLKSGQVLVNGQGIK-ASYIVVEDDRIELEVPEAVEPEI 63

Query: 63  DGVP----LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG------ 112
           D  P    +   ++  + +      +V   +     + V   +     ++  +       
Sbjct: 64  DAEPMDLDILYEDQDLILINKPKGMVVHPAAGHYSHTLVNGLMYHCKDQLSGINGVMRPG 123

Query: 113 ----------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
                           + D+    +     +  + R  +      +          + + 
Sbjct: 124 IVHRIDMDTTGVIIACKNDMAHSSIAAQLKEHSITRRYQAIVHGVIAEDEGTVDAPIGRH 183

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +   K  I  Q          +  +      V   L  G+  +I+         + 
Sbjct: 184 PVERKKMSINYQNGKNAVTHYRVLNRFRQYTHVECRLETGRTHQIRVHMASIRHPLL 240


>gi|270719470|ref|ZP_06223316.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae HK1212]
 gi|270315432|gb|EFA27691.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae HK1212]
          Length = 161

 Score = 66.7 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 50/158 (31%), Positives = 66/158 (41%), Gaps = 6/158 (3%)

Query: 34  MIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE-----RTRLWLYHKPIGLVTT 87
           MIA  RV V G +      ++V S   + +DG  +  +         L  Y     L T 
Sbjct: 1   MIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQIINLSHAQKEICRVLMYYKPEGELCTR 60

Query: 88  HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
                  +          SR I+VGRLDINT GLLL T DG LA  L  PS +  R Y V
Sbjct: 61  SDPEGRATVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSV 120

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           R  GQVD   L  L+KG+ ++       ++        
Sbjct: 121 RVFGQVDDAMLARLRKGVQLEDGPANFKEIKFQLSNED 158


>gi|170733886|ref|YP_001765833.1| pseudouridine synthase [Burkholderia cenocepacia MC0-3]
 gi|169817128|gb|ACA91711.1| pseudouridine synthase [Burkholderia cenocepacia MC0-3]
          Length = 192

 Score = 66.7 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 41/182 (22%), Positives = 76/182 (41%), Gaps = 19/182 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +      + GRLD ++EGLLLLT+DGGL   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKTPGV--YAAGRLDADSEGLLLLTDDGGLQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVDGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPDTLWPRNPPIR 120

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L    G T  ++
Sbjct: 121 YRAAIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFALGIAPGETIALA 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>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 = 66.7 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 33/235 (14%), Positives = 66/235 (28%), Gaps = 37/235 (15%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--------VDGV 65
           R+ K IA      SR +++  I   RV VNG  ++ A   +   DHI         VD +
Sbjct: 36  RIDKYIAEEMKEVSRSQIQLWIGNGRVLVNGTAVK-ANYKLAEGDHIVLSVPEPESVDIM 94

Query: 66  P------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR------ 113
           P      +   +   + +  +   +V         + V   +          G       
Sbjct: 95  PENIPLDVVYEDSDVIVINKQRGLVVHPAPGHSSGTLVNALMYHCHDLSGINGELRPGIV 154

Query: 114 ---------------LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
                           D     L     D  + R         L   +      + +D  
Sbjct: 155 HRIDKDTSGLLMAAKNDQAHASLAAQLKDHSVTRKYIALVHGHLSHDQGTVDAPIGRDSG 214

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +     +  +   +      +  + G    + + L  G+  +I+   +F    + 
Sbjct: 215 DRKMFTVTERNSKHAVTHFLVIERLGDYTLLELQLETGRTHQIRVHMKFIGHPLV 269


>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 = 66.7 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 36/231 (15%), Positives = 70/231 (30%), Gaps = 35/231 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------DGVP 66
           R+ K I+     SR  V+ ++    + VNG   E+ +  V + D I V        +  P
Sbjct: 14  RLDKYISEHSDLSRSRVQELLGSGDILVNGKQ-EKPSYKVANNDQITVHVPKLVPLNVEP 72

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------SRVISVG 112
                 +   +   + +      +V   +     + V   +             R   V 
Sbjct: 73  EDIPLDIVYEDEDVIVVNKPQGMVVHPSAGHPNHTLVNALMNHTKFLAASPEGFRPGIVH 132

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD------------KLNL 160
           R+D +T GLL++  +      LE                  +                  
Sbjct: 133 RIDKDTSGLLMIAKNANARTSLESQLAHKTNKRVYLAIVHGNFKEATGTIDAPIARNPKD 192

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            KK  +++G         +  Q    A V+  L  G+  +I+   ++    
Sbjct: 193 RKKMAIVEGGKEAVTHFHVLEQYPGYALVSCQLETGRTHQIRVHMKYIGHP 243


>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 = 66.7 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 35/238 (14%), Positives = 68/238 (28%), Gaps = 35/238 (14%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGV 65
           +    R    ++      SR  ++++I  + V VNG  ++   V +   D I V   D  
Sbjct: 8   SDKKIRCDVFLSEKISNLSRTSIQKLIKGKLVFVNGKNIK-PNVILEIGDEITVSIPDKK 66

Query: 66  PLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV--- 111
            +              +   + +      +V      +  + V   L      +I+    
Sbjct: 67  EITLVAEDIDLDIVYEDDYIIIINKPRNMVVHPAVGNEKHTLVNALLNHCKLSMINSERP 126

Query: 112 ---GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
               RLD +T GL++   D      L           +          K N L    + +
Sbjct: 127 GIVHRLDKDTTGLIICAKDDETHLKLVEMFANREINKKYLAICNGSFSKENGLIDKPIGR 186

Query: 169 GICYGDM-------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                               +  +       + V V L  G+  +I+  F   N  + 
Sbjct: 187 DEKDRKKMSVKSKSGKAAITEYNVLISNLKYSLVDVTLHTGRTHQIRVHFSSLNHPII 244


>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 = 66.7 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 30/242 (12%), Positives = 69/242 (28%), Gaps = 33/242 (13%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T QR+ + +A      SR  ++  I    V ++G +  +    V+    IEV
Sbjct: 8   KSEITATQTGQRLDQTLAELFPDYSRTRIKEWILDGSVTIDGNVSNKPREKVLEGQEIEV 67

Query: 63  DGVPLR--------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
               +                 +   L +  +   +V   +     + +   L       
Sbjct: 68  GATLVEETTAKAQAIDLNIVYEDDHILVINKQAGLVVHPGAGNSDGTLLNALLHHCPGIE 127

Query: 109 ISV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR------------VRFHG 151
           +        RLD +T GL+++         L                             
Sbjct: 128 LVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVSALQAREITREYEAIVMGSLISGGTVDE 187

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +D+         +V+ G         +  +  ++  + + L  G+  +I+         
Sbjct: 188 PIDRHPTKRTHMAVVLSGKPAMT-HFRVAEKFRAHTRLRLRLESGRTHQIRVHMAHLGHT 246

Query: 212 VN 213
           + 
Sbjct: 247 LV 248


>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 = 66.7 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 34/246 (13%), Positives = 72/246 (29%), Gaps = 36/246 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  +  +    + QR+ K +A      SR  ++ ++    + VNG    + +  V   D 
Sbjct: 1   MNREYELTAEESGQRLDKYLAGEMTDLSRSRIKELVQAGEILVNGKK-SKVSYKVQKDDL 59

Query: 60  IEV------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I+V            + +P  +   ++  + +      +V   +     + V   L    
Sbjct: 60  IQVIVLPLEPLKLEAENIPLDIVYEDKDVIVVNKPQGMVVHPAAGHPSHTLVNALLYHTR 119

Query: 106 --------SRVISVGRLDINTEGLLLLTND------------GGLARVLELPSTQWLRVY 145
                    R   V R+D +T GLL++  +                +   L         
Sbjct: 120 DLADSPEGFRPGIVHRIDKDTSGLLMVAKNAAARESLEKQLAAKSNKRQYLAIVHGNFAE 179

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           K+  V++          +  Q    + V   L  G+  +I+   
Sbjct: 180 EEGTIDAPIGRNPKDRKQMAVVEKGKSAVTHFKVLEQYQGYSLVECQLETGRTHQIRVHM 239

Query: 206 EFFNWK 211
            +    
Sbjct: 240 AYIGHP 245


>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 = 66.7 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 34/248 (13%), Positives = 71/248 (28%), Gaps = 37/248 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N++ E     R+ KVIA +    SR +++ MI Q  V VN    E+A+      D 
Sbjct: 1   MEKINLIIEEDNNLRLDKVIAMQLQELSRTQIQDMINQGLVLVNQKK-EKASYKTKLNDE 59

Query: 60  IEV--------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           IE+        D  P      +   +   + +      +V   +     + V   L    
Sbjct: 60  IEITILDNVDLDIEPEDISLKIVYEDEDVIVVDKPTGMIVHPSAGIMHGTLVNALLFHCK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPST---------------------QWLRV 144
                 G         +     G L       +                        +  
Sbjct: 120 DLSGINGVNRPGIVHRIDKETSGLLMVAKNDNAHRLLSKQLKDHTVVRRYVALVHGLIPH 179

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
              +    + ++  +     +            T+  +  + + +   L  G+  +I+  
Sbjct: 180 EHGKVDAPIGRNPKDRQSMAVTRTNSKEAVTNFTVLKRYNAMSLIECRLETGRTHQIRVH 239

Query: 205 FEFFNWKV 212
             +  + V
Sbjct: 240 MSYIGYPV 247


>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 = 66.7 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 29/265 (10%), Positives = 71/265 (26%), Gaps = 52/265 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M  + I  EN   QR+ + +A+    + SR  ++ +I +  +KV+G L++     + S  
Sbjct: 1   MVTQRITDENALGQRLDQWLAKQYHNVLSRSRLQALIREGYLKVDGQLIKEPKTKLKSNQ 60

Query: 59  HIEVD----------GVPLRK----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            IE+           G  +       +   + +      +V   +     + V   +   
Sbjct: 61  IIELTMPALRDAEPSGEAIALDILFEDDHVIVINKPAGLVVHPGNGNWTGTLVNALIHHC 120

Query: 105 FSRVISVGRL-------------------------------DINTEGLLLLTNDGGLARV 133
              +  +G +                                    G     +    A +
Sbjct: 121 GKSLSGIGGVKRPGIVHRLDKNTSGVMVVAKNDLAHKSLSAQFFDHGRTSALDRRYHALI 180

Query: 134 LELPSTQWLRVYRVRFHGQVDQD-----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
              P+     +         ++          L     +      +   T   +    + 
Sbjct: 181 WGSPNRNVWTIDAPVGRSPHNRTKQAVVYNQCLHARHAVTHFSLLEQYGTCADKTPFASL 240

Query: 189 VTVGLREGKNREIKKVFEFFNWKVN 213
           +   L  G+  +I+         + 
Sbjct: 241 LECRLETGRTHQIRVHMAHIGHPLV 265


>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 = 66.7 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 29/233 (12%), Positives = 66/233 (28%), Gaps = 35/233 (15%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----- 68
           R+ KV+A    + +R +V+++I   +V VNG L      +V   D I V    ++     
Sbjct: 18  RLDKVLAALQSVWTRSQVDKLIKTDQVTVNGQLEAS-KYHVKPGDEIVVAAQTVQQTTIE 76

Query: 69  ---------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
                      +   L +      +V         + V   L       I+         
Sbjct: 77  PENIPLDIVYEDDDVLVVNKPQGMVVHPAPGHPNHTLVNALLYHSPLSTINGEFRPGIVH 136

Query: 120 GL--------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK--------- 162
            +        ++  ND     +      +      V     V ++    +          
Sbjct: 137 RIDKDTSGLLMVAKNDRAHQSLAAQLKAKTNLREYVALVHGVIKEDTGTINAPLGRSPKD 196

Query: 163 --KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             K  +++          +  +      ++  L  G+  +I+   +     + 
Sbjct: 197 RKKQAIVKTGRPAVTHFKVLKRYQHYTLISCRLETGRTHQIRVHLQSIGHPLV 249


>gi|325687371|gb|EGD29392.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK72]
          Length = 298

 Score = 66.7 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 35/234 (14%), Positives = 65/234 (27%), Gaps = 35/234 (14%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP----- 66
            QR+ K +A     SR      I   R+ VNG + ++A   V   D I  +   P     
Sbjct: 11  GQRLDKAVAELTDLSRSLAHEQIKDGRILVNGQV-KKAKYAVKEGDVISYELPEPEVVEY 69

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                   +   +     +      +V   +     + V   +  I       G L    
Sbjct: 70  VAEDIPLEIVYQDEDVAVINKPQGMVVHPSAGHTSGTLVNALMYHIQDLSGINGVLRPGI 129

Query: 119 EGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              +     G L       +           + LR Y    HG +  D+  +       +
Sbjct: 130 VHRIDKDTSGLLMVAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSE 189

Query: 169 GICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                            +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 KDRKKQAVTAKGKPALTRFQVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 243


>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 = 66.7 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 33/249 (13%), Positives = 73/249 (29%), Gaps = 38/249 (15%)

Query: 1   MKDKNI-VQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMST- 57
           M+D  I + E    QR+ K++A      SR +++ +I    V ++   ++ A+  V +  
Sbjct: 1   MEDIKIRIVEEQKGQRIDKILAKELADFSRTQIQSLIQNGYVVIDEKPIK-ASYKVETGE 59

Query: 58  DHIEVDGVP-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           D I     P             +   ++  + +      +V         + V   L   
Sbjct: 60  DVIVYIPKPESTDILPEDIPLDVVYEDQDVIVINKPTGMIVHPSIGIYSGTLVNALLYHC 119

Query: 105 FSRVISVG---------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
                  G                     + D   + L     +  + R         + 
Sbjct: 120 HDLSGINGVTRPGIVHRIDKETSGLLMVAKNDKAHQSLSKQLQEHTVTRRYLALVHGLIP 179

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
               R    + +DK +  K     +          +  +    + V   L  G+  +I+ 
Sbjct: 180 HEFGRIEAPIGRDKNDRQKMTCTDKNAKDAITNFKVIERFRDMSLVECRLETGRTHQIRV 239

Query: 204 VFEFFNWKV 212
             ++  + V
Sbjct: 240 HMQYIGYPV 248


>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 = 66.7 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 29/244 (11%), Positives = 66/244 (27%), Gaps = 36/244 (14%)

Query: 5   NIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           NI       QR+ K++       SR +++  I +  ++VNG  ++     +   D IE+ 
Sbjct: 7   NIEDATHHLQRIDKILPEFNSEWSRSQLQEWIKEGLIEVNGKAVKS-NYKLKLGDRIEIT 65

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   +     +Y     +V         + V   +  I +   
Sbjct: 66  EKEVVEADIQAENLNLDIYYEDDDVAIVYKPKGMVVHPSPGHYTGTLVNGLMYQIKNLSG 125

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPST------------QWLRVYRVRFHGQVDQ-- 155
             G +       +     G L       +             +   +  V  H   +   
Sbjct: 126 INGEIRPGIVHRIDKDTSGLLMVAKNDVAHRSLVEQLMAKTVKRKYIALVHGHIPHEFGT 185

Query: 156 ------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                    N  +   V+           +     +   V   L  G+  +I+   ++  
Sbjct: 186 IDAPIGRNKNDRQSMAVVDDGKEAVTHFNVIETFKNYTLVECELETGRTHQIRVHMKYIG 245

Query: 210 WKVN 213
           + + 
Sbjct: 246 YPLV 249


>gi|157376631|ref|YP_001475231.1| lysozyme [Shewanella sediminis HAW-EB3]
 gi|157319005|gb|ABV38103.1| Lysozyme [Shewanella sediminis HAW-EB3]
          Length = 323

 Score = 66.7 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 29/242 (11%), Positives = 70/242 (28%), Gaps = 33/242 (13%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T QR+ + +A      SR  ++  I    V ++G +  +    V+    I+V
Sbjct: 8   KSEITATQTGQRLDQTLADLFPDYSRTRIKEWIQAGWVYIDGTVSIKPREKVLEGQVIQV 67

Query: 63  DGVPLR--------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           +   +                 +   L +  +   +V   +     + +   L    +  
Sbjct: 68  EATLVEETKAKAQAIDLDIVYEDDHILVINKQAGLVVHPGAGNSDGTLMNALLHHCPNIE 127

Query: 109 ISV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR------------VRFHG 151
           +        RLD +T GL+++         L                             
Sbjct: 128 LVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIVQGSLISGGTVDE 187

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +D+         +V  G         +  +  ++  + + L  G+  +I+         
Sbjct: 188 PIDRHPTKRTHMAVVHNGKPAMT-HYRVAEKFRAHTRLRLRLESGRTHQIRVHMSHIGHT 246

Query: 212 VN 213
           + 
Sbjct: 247 LV 248


>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 = 66.7 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 34/235 (14%), Positives = 73/235 (31%), Gaps = 37/235 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ + ++ A   +R  V+++I +  V VN   + + A  V S D I+V            
Sbjct: 9   RLDRYLSEALSKTRSFVQKIIEEGNVWVNQRQVLKPAYKVKSGDIIKVVIPEPKQLSLVA 68

Query: 63  -D-GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-------- 112
            D  + +   +     +      +V   +     + V   L     R+ S+         
Sbjct: 69  QDIDIEVVYEDEHLSVINKPRGMVVHPGAGNFENTLVNALLHKFKGRLSSINGVIRPGIV 128

Query: 113 --------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
                         + D     L        + R+        L+         + +  +
Sbjct: 129 HRLDKDTSGLLVVAKTDEAHIKLSEALKSHQIKRIYYAICEGVLKEDSGVVDAPIGRHPV 188

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           N LK  IV  G         +  +     +V + L+ G+  +I+    +  + + 
Sbjct: 189 NRLKMAIVPNGKEA-VTYFEVLERFDKYTFVKLRLKTGRTHQIRVHMSYIGYPLL 242


>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 = 66.7 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 32/232 (13%), Positives = 63/232 (27%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP------- 66
           R+ K ++     SR      I   +V VNG + ++A   V   D +      P       
Sbjct: 11  RLDKALSDLTELSRSLANEQIKSGQVLVNGQV-KKAKYTVQEGDVVTYHVPEPEVLEYVA 69

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 +   +     +      +V   +     + V   +  I       G L      
Sbjct: 70  EDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 121 LLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            +     G L       +           + LR Y    HG +  D+  +       +  
Sbjct: 130 RIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 171 CYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                          +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 66.7 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 32/237 (13%), Positives = 59/237 (24%), Gaps = 40/237 (16%)

Query: 12  TPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGV 65
             +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V   D  
Sbjct: 14  KNERIDKFVA--GINNEWSRSQVQQWIKDDVVTVNGKAVKV-NYKVKEEDEITVTIPDPE 70

Query: 66  PLRKAER-----------TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
            L                  L +      +V         + V   +          G +
Sbjct: 71  ALDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGINGVM 130

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL-------------- 160
                  +     G L       + + L    V          +                
Sbjct: 131 RPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPI 190

Query: 161 ------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                  +   V +          +  +      V   L  G+  +I+   ++  + 
Sbjct: 191 GRDKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYP 247


>gi|332366655|gb|EGJ44398.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK1059]
          Length = 298

 Score = 66.7 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 35/240 (14%), Positives = 68/240 (28%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GV 65
           ++ +   QR+ K +A     SR      I   R+ VNG + ++A   V   D I  +   
Sbjct: 5   IEASVVGQRLDKAVAELTDLSRSLAHEQIKDGRILVNGQV-KKAKYAVKEGDVISYELPE 63

Query: 66  P-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
           P             +   +     +      +V   +     + V   +  I       G
Sbjct: 64  PEVVEYVAEDIPLEIVYQDEDVAVINKPQGMVVHPSAGHTSGTLVNALMYHIQDLSGING 123

Query: 113 RLDINTEGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLK 162
            L       +     G L       +           + LR Y    HG +  D+  +  
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKAKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 163 KGIVIQGICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                +                 +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 184 PIGRSEKDRKKQAVTAKGKPALTRFQVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 243


>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 = 66.7 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 37/242 (15%), Positives = 76/242 (31%), Gaps = 42/242 (17%)

Query: 13  PQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------- 62
           P R+ K + +    A+R +V+  I + RV VNG  ++     + S D I++         
Sbjct: 33  PMRIDKYLTQQVENATRNKVQEAITEGRVLVNGKPVKS-NYKIKSCDLIQITFLRPPAPE 91

Query: 63  ---DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRST-----------VFDNLPSIFSR 107
              + +P+    E   L + +K  G+V   +  +   T               L     R
Sbjct: 92  MAPENIPIDIIYEDADLMVVNKEAGMVVHPAFGNWTGTLANAILHHIGNDTGELDCSLQR 151

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK---------- 157
              V RLD +T GL+++  +    + L     Q               +           
Sbjct: 152 PGIVHRLDKDTSGLIIIAKNPLALQRLARQFAQRQVEKIYHALVWGVPEPASGTIKTNIG 211

Query: 158 ----LNLLKKGIVIQ--GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                  +      +     +      +       + V++ L  G+  +I+   +     
Sbjct: 212 RSKKNRKVMTTYPFEGIDGKHAITDYAVIEDLRYFSLVSIKLHTGRTHQIRVHLQHLGHP 271

Query: 212 VN 213
           + 
Sbjct: 272 IL 273


>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 = 66.7 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 33/236 (13%), Positives = 65/236 (27%), Gaps = 37/236 (15%)

Query: 14  QRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--------VDG 64
            R+ K IA      SR +++  I   RV VNG  ++ A   +   D I         VD 
Sbjct: 46  IRIDKYIAEEMKEVSRSQIQMWIGNGRVLVNGTAIK-ANYKLAEGDRIVLSVPEPESVDI 104

Query: 65  VP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR----- 113
           VP      +   +   + +  +   +V         + V   +          G      
Sbjct: 105 VPENIPLDVVYEDSDVIVINKQRGLVVHPAPGHSSGTLVNALMYHCHDLSGINGELRPGI 164

Query: 114 ----------------LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                            D     L     D  + R         L   +      + +D 
Sbjct: 165 VHRIDKDTSGLLMAAKNDQAHASLAAQLKDHSVTRKYIALVHGHLSHDQGTVDAPIGRDS 224

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +     +  +   +      +  + G    + + L  G+  +I+   +F    + 
Sbjct: 225 GDRKLFTVTERNSKHAVTHFLVIERLGDYTLLELQLETGRTHQIRVHMKFIGHPLV 280


>gi|238810211|dbj|BAH70001.1| hypothetical protein [Mycoplasma fermentans PG18]
          Length = 315

 Score = 66.7 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 30/239 (12%), Positives = 73/239 (30%), Gaps = 40/239 (16%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGIL-LERAAVNVMSTDHIEV----DGVP-- 66
           +R+ K I +    SR +++ +I Q  V +N  + + +    V     I +    +     
Sbjct: 18  ERIDKYIGQNSELSRNDIKELIEQGAVYINDNVQVHKCNYIVREGQEITIVKLLNKEIKI 77

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VI 109
                   ++  +   + +      +V         + V   L    +            
Sbjct: 78  EPVNIPLDIKYEDDDLVIINKPSNLVVHPSPGHYNDTLVNGLLYHFKNNLSNENGLLRPG 137

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR-------------VRFHGQVDQD 156
            V R+D +T GLL++  +  +   L     +                    + +  + ++
Sbjct: 138 IVHRIDKDTSGLLIIAKNNKMHNSLTDMLKRHEIERSYLAIVRGLIENPLTKINLPIARN 197

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            ++     +  +G         L      K   + V   L+ G+  +I+    +    V
Sbjct: 198 TVDRKMMSVHKEGKEAITFVHLLKHFYLDKEPMSLVRCELKTGRTHQIRVHLSYIKHPV 256


>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 = 66.4 bits (160), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 32/232 (13%), Positives = 63/232 (27%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP------- 66
           R+ K ++     SR      I   +V VNG + ++A   V   D +      P       
Sbjct: 11  RLDKALSDLSELSRSFANEQIKSGQVLVNGQV-KKAKYTVQEGDVVTYHVPEPEVLEYVA 69

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 +   +     +      +V   +     + V   +  I       G L      
Sbjct: 70  EDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 121 LLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            +     G L       +           + LR Y    HG +  D+  +       +  
Sbjct: 130 RIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 171 CYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                          +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>gi|324991250|gb|EGC23184.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK353]
          Length = 298

 Score = 66.4 bits (160), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 34/240 (14%), Positives = 66/240 (27%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GV 65
           ++ +   QR+ K +A     SR      I    + VNG   ++A   V   D I  +   
Sbjct: 5   IEASVAGQRLDKAVAELTDLSRSLANEQIKDGWILVNGQ-AKKAKYAVKEGDVISYELPE 63

Query: 66  P-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
           P             +   +     +      +V   +     + V   +  I       G
Sbjct: 64  PEVVEYVAEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIQDLSGING 123

Query: 113 RLDINTEGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLK 162
            L       +     G L       +           + LR Y    HG +  D+  +  
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 163 KGIVIQGICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                +                 +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 184 PIGRSEKDRKKQAVTAKGKSALTRFQVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 243


>gi|146318440|ref|YP_001198152.1| YlyB [Streptococcus suis 05ZYH33]
 gi|145689246|gb|ABP89752.1| YlyB [Streptococcus suis 05ZYH33]
          Length = 309

 Score = 66.4 bits (160), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 33/234 (14%), Positives = 64/234 (27%), Gaps = 35/234 (14%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
             R+ K ++     SR      I   +V VNG   ++A  +V   D +            
Sbjct: 9   GIRLDKALSDLTDLSRSVANEQIKAGQVLVNGQP-KKAKYSVQVGDVLTYQIPEVEEIDY 67

Query: 63  --DGVPLRK--AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
             + +PL     +     +      +V   +     + V   L  +       G L    
Sbjct: 68  VAEDIPLEIVFQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALLYHVKDLSGINGVLRPGI 127

Query: 119 EGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              +     G L       +           + LR Y    HG +  D+  +       +
Sbjct: 128 VHRIDKDTSGLLMIAKNDDAHTKLAAELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSE 187

Query: 169 GICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                            +  +  + G    V + L  G+  +I+    +    V
Sbjct: 188 KDRKKQAVTAKGKEAVTRFQVLERFGDYTLVELTLETGRTHQIRVHMAYIGHPV 241


>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 = 66.4 bits (160), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 30/232 (12%), Positives = 61/232 (26%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K +A     SR +    I    V VNG   + A   V   D I              
Sbjct: 11  RLDKSLADLTELSRSQANEAIKAGTVLVNGKSAK-AKYVVKEGDVITYVLPEEEVLEYKA 69

Query: 63  DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           + +PL     +     +      +V   +     + V   +  +       G +      
Sbjct: 70  EDIPLDIIYEDADVAVVNKPQGMVVHPSAGHTSGTLVNALMYHVKDLSSINGVVRPGIVH 129

Query: 121 L---------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI- 170
                     ++  ND     +      +      V        +   +++  I      
Sbjct: 130 RIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHGNLPNDRGVIEAPIGRSDKD 189

Query: 171 --------CYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                          + T+  + G+   V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFTVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 66.4 bits (160), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 35/240 (14%), Positives = 67/240 (27%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GV 65
           ++ +   QR+ K +A     SR      I   R+ VNG   ++A   V   D I  +   
Sbjct: 5   IEASVAGQRLDKAVAELTDLSRSLANEQIKDGRILVNGQ-AKKAKYAVKEGDVISYELPE 63

Query: 66  P-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
           P             +   +     +      +V   +     + V   +  I       G
Sbjct: 64  PEVVEYVAEDIPLEIVYQDEDVAVINKPQGMVVHPSAGHTSGTLVNALMYHIQDLSGING 123

Query: 113 RLDINTEGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLK 162
            L       +     G L       +           + LR Y    HG +  D+  +  
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 163 KGIVIQGICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                +                 +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 184 PIGRSEKDRKKQAVTAKGKPALTRFQVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 243


>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 = 66.4 bits (160), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 32/234 (13%), Positives = 64/234 (27%), Gaps = 35/234 (14%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP----- 66
            QR+ K ++     SR      I   +V VNG + ++A   V   D +      P     
Sbjct: 9   GQRLDKALSDLTELSRSLANEQIKAGQVLVNGQV-KKAKYIVQEGDIVAYHVPEPEVLEY 67

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                   +   +     +      +V   +     + V   +  I       G L    
Sbjct: 68  VAENLPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGI 127

Query: 119 EGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              +     G L       +           + LR Y    HG +  D+  +       +
Sbjct: 128 VHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSE 187

Query: 169 GICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                            +  +  + G  + + + L  G+  +I+    +    V
Sbjct: 188 KDRKKQAVTAKGKPAVTRFQVLERFGDYSLLELQLETGRTHQIRVHMAYIGHPV 241


>gi|311068067|ref|YP_003972990.1| pseudouridylate synthase [Bacillus atrophaeus 1942]
 gi|310868584|gb|ADP32059.1| pseudouridylate synthase [Bacillus atrophaeus 1942]
          Length = 303

 Score = 66.4 bits (160), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 32/238 (13%), Positives = 70/238 (29%), Gaps = 36/238 (15%)

Query: 9   ENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP 66
                +R+ K +A A    SR +V++ +    ++VNG  ++ A   +   D ++V    P
Sbjct: 10  PEQKSERIDKFLASAEKDWSRTQVQQWVKDGHIEVNGSPVK-ANYKMQPGDQVKVTVPEP 68

Query: 67  -------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------- 105
                        +   ++  L +      +V         + V   +            
Sbjct: 69  EALDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHVTGTLVNGLMAHCKDLSGINGV 128

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
            R   V R+D +T GLL++  +      L           +            +      
Sbjct: 129 MRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVHKTVTRKYMAVVHGIISHDDGTIDAP 188

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNREIKKVFEFFNWK 211
           + +          +   K +     V        L E     G+  +I+   ++  + 
Sbjct: 189 IGRDKKDRQSMTVVREGKNAVTHFHVLERFQDFTLVECQLETGRTHQIRVHMKYIGFP 246


>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 = 66.4 bits (160), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 31/250 (12%), Positives = 67/250 (26%), Gaps = 39/250 (15%)

Query: 1   MKDKN--IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN----- 53
           M D    +V +    +R+   ++R    SR +   +I    V+V+G    ++A       
Sbjct: 1   MSDSRTLMVPDGLAGERLDAALSRLFGVSRTKAAELIEAGLVQVDGAPAAKSARVSAGVL 60

Query: 54  ------------------------VMSTDHIEVDGVPL-------RKAERTRLWLYHKPI 82
                                   V   D I V   P+              +  +    
Sbjct: 61  LDVELPAPPGEVTVVPETVENLRIVHDDDEIVVVDKPVGVAAHPSPGWTGPTVIGHLAGA 120

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL 142
           G   + S    R  +   L    S ++ V + + +   L     +  + ++         
Sbjct: 121 GFSISTSGAAERKGIVHRLDVGTSGLMVVAKTEYSYTVLKRAFKERTVKKIYHALVQGHP 180

Query: 143 RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             +       +D+   +   K  V+ G                   + + L  G+  +I+
Sbjct: 181 DPFTGTVDAPIDRHPNHD-YKFGVVAGGKPSITHYETLEAFRYATLLEITLETGRTHQIR 239

Query: 203 KVFEFFNWKV 212
                     
Sbjct: 240 VHMSAIGHPC 249


>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 = 66.4 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 32/232 (13%), Positives = 63/232 (27%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP------- 66
           R+ K ++     SR      I   +V VNG + ++A   V   D +      P       
Sbjct: 11  RLDKALSDLTELSRSLANEQIKSGQVLVNGQV-KKAKYTVQEGDIVTYHVPEPEVLEYVA 69

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 +   +     +      +V   +     + V   +  I       G L      
Sbjct: 70  ENLPLDIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 121 LLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            +     G L       +           + LR Y    HG +  D+  +       +  
Sbjct: 130 RIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 171 CYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                          +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 66.4 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 34/251 (13%), Positives = 67/251 (26%), Gaps = 40/251 (15%)

Query: 3   DKNIVQENFTPQRVSKVIARAG---IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K  +    T  R+ K++         SR  ++++I ++ + VN  ++      V     
Sbjct: 2   NKITLNSLNTTLRLDKLLVELLTSYDYSRSYIQKLIKEECISVNNQIITNNNFLVKPNSQ 61

Query: 60  IEV-------------DGVP---LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           I +             +      +   +   L +  +    V    +    + V   L S
Sbjct: 62  ITITIKDPILDPNLVKNDEIDLDIIYQDDDLLVINKQNNITVHPSLNNTNNTIVNALLAS 121

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------D 156
                   G L       +     G L       + + L           +         
Sbjct: 122 DVELSSINGELRPGIVHRIDKQTTGLLIVAKNDKTHKLLSEMFKNHQIYKEYLAIVTGVI 181

Query: 157 KLNLLKKGIVIQGICY--GDMQVTLDTQKGSNAWVTVG------------LREGKNREIK 202
           K N       I         M VT    K +     V             ++ G+  +I+
Sbjct: 182 KPNKGLIDAPIGRSQTDRKKMSVTAKNSKQAITTFEVVERFFKNTLVKCQIQTGRTHQIR 241

Query: 203 KVFEFFNWKVN 213
             F + N  V 
Sbjct: 242 VHFNYINHPVL 252


>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 = 66.4 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 31/232 (13%), Positives = 63/232 (27%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP------- 66
           R+ K ++     SR      I   +V VNG + ++A   V   D +      P       
Sbjct: 11  RLDKALSDLTELSRSLANEQIKAGQVLVNGQV-KKAKYTVQEGDIVTYHVPEPEVLEYVA 69

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 +   +     +      +V   +     + V   +  I       G L      
Sbjct: 70  EDIPLDIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 121 LLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            +     G L       +           + LR Y    HG +  D+  +       +  
Sbjct: 130 RIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 171 CYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                          +  +  + G  + + + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFQVLERFGDYSLLELQLETGRTHQIRVHMAYIGHPV 241


>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 = 66.4 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 38/235 (16%), Positives = 78/235 (33%), Gaps = 37/235 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ + ++ A   +R  V+++I +  V VN   + + A  V S D I+V            
Sbjct: 9   RLDRYLSEALSKTRSFVQKIIEEGNVLVNQTQVLKPAYKVKSGDIIKVVIPEPKQLSIVA 68

Query: 63  -DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV---------- 111
            D       E   L + +KP G+V      +  +T+ + L   F   +S           
Sbjct: 69  QDINIEVVYEDEHLAVINKPRGMVVHPGAGNFENTLVNALLHKFRGRLSSINGVIRPGIV 128

Query: 112 -------------GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
                         + D     L        + R+        L+      +  + +  +
Sbjct: 129 HRLDKDTSGLLVVAKTDEAHVKLSEALKSHQIKRIYYAICEGVLKEDSGVINAPIGRHPV 188

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           N LK  +V  G         +  +     +V + L+ G+  +I+    +  + + 
Sbjct: 189 NRLKMAVVPNGKEA-VTYFEVLERFDKYTFVKLRLKTGRTHQIRVHMSYIGYPLL 242


>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 = 66.4 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 43/260 (16%), Positives = 78/260 (30%), Gaps = 50/260 (19%)

Query: 13  PQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE---------- 61
           P R+ + + R    A+R +V+  I   RV VNG  ++     V S D IE          
Sbjct: 37  PMRIDQYLTRQVENATRNKVQEAIEDGRVLVNGKSVKS-NYRVKSCDSIEMTFLRPPAPE 95

Query: 62  -------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-------- 106
                  +D   +   +   + +   P  +V         +     L    +        
Sbjct: 96  LAPEDIPID---IVYEDSDLMVVNKAPGMVVHPAFGNWTGTLANAILHHFGTDAEELETD 152

Query: 107 --RVISVGRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVYRVRFHG 151
             R   V RLD +T GL+++  +      L                            H 
Sbjct: 153 ELRPGIVHRLDKDTSGLIIVARNPTALHRLARQFADRKVSKLYTAILWGVPEPQEGTIHT 212

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV---TVGLREGKNREIKKVFEFF 208
            + + + +             G   +T      +  W     + L  G+  +I+   +  
Sbjct: 213 NIGRSRRDRKVMANFPYEGLEGKTAITDYRVTENLHWFSLAELTLHTGRTHQIRAHMQHL 272

Query: 209 NWKVNRLIRISYGPFQLGTL 228
             ++  L   +YG   L TL
Sbjct: 273 GHQI--LGDTTYGGASLRTL 290


>gi|254556664|ref|YP_003063081.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
 gi|254045591|gb|ACT62384.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
          Length = 307

 Score = 66.4 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 29/233 (12%), Positives = 66/233 (28%), Gaps = 35/233 (15%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----- 68
           R+ KV+A    + +R +V+++I   +V VNG L      +V   D I V    ++     
Sbjct: 18  RLDKVLAALQSVWTRSQVDKLIKTDQVTVNGQLEAS-KYHVKPGDEIVVAAQTVQQTTIE 76

Query: 69  ---------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
                      +   L +      +V         + V   L       I+         
Sbjct: 77  PENIPLDIVYEDDDVLVVNKPQGMVVHPAPGHPNHTLVNALLYHSPLSTINGEFRPGIVH 136

Query: 120 GL--------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK--------- 162
            +        ++  ND     +      +      V     V ++    +          
Sbjct: 137 RIDKDTSGLLMVAKNDRAHQSLAAQLKAKTNLREYVALVHGVIKEDTGTINAPLGRSPKD 196

Query: 163 --KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             K  +++          +  +      ++  L  G+  +I+   +     + 
Sbjct: 197 RKKQAIVKTGRPAITHFKVLKRYQHYTLISCRLETGRTHQIRVHLQSIGHPLV 249


>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 = 66.0 bits (159), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 35/240 (14%), Positives = 68/240 (28%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GV 65
           ++ +   QR+ K +A     SR      I   R+ VNG   ++A   V   D I  +   
Sbjct: 5   IEASVASQRLDKAVAELTDLSRSLAHEQIKDGRILVNGQ-AKKAKYAVKEGDVISYELPE 63

Query: 66  P-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
           P             +   +     +      +V   +     + V   +  I       G
Sbjct: 64  PEVVEYVAEDIPLEIVYQDEDVAVINKPQGMVVHPSAGHTSGTLVNALMYHIQDLSGING 123

Query: 113 RLDINTEGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLK 162
            L       +     G L       +           + LR Y    HG +  D+  +  
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 163 KGIVIQGICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                +                 +  +  + G+ + V + L  G+  +I+    +    V
Sbjct: 184 PIGRSEKDRKKQAVTAKGKPALTRFQVLERFGNYSLVELQLETGRTHQIRVHMAYIGHPV 243


>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 = 66.0 bits (159), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 28/245 (11%), Positives = 62/245 (25%), Gaps = 38/245 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
            V    T +RV   ++     +R  ++++I    V VN   ++  +  V   D IE+   
Sbjct: 43  TVSTEKTNKRVDSFLSEKTDLTRSRIQQLIKDGNVSVNNKSVKS-SYKVEENDRIEIIIP 101

Query: 63  -----------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                        + +   ++    +  K   +V        R+ V   L  I       
Sbjct: 102 EAEKVEIIAENIDINIIYEDKDIAVINKKAGMVVHPAHGNYSRTLVNAILYHIKDLSGIN 161

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------------- 155
           G +       L     G +       +   L     +   +                   
Sbjct: 162 GEIRPGIVHRLDKDTSGLIVVAKNDKAHIKLAEMFQKKEVKKTYLAILKGKLNRESGRLE 221

Query: 156 -------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                  D    +                 +         V V +  G+  +I+   ++ 
Sbjct: 222 TQIGRDADDRKKMSVLKENDKGKKAITNYNVILSNELFTLVKVYIETGRTHQIRVHMKYL 281

Query: 209 NWKVN 213
            + + 
Sbjct: 282 GYPIL 286


>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 = 66.0 bits (159), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I   RV VNG  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILDSRVTVNGKKINKPKEKVLGGELVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-- 108
                           +   +   L +      +V   +     + +   L      +  
Sbjct: 70  QIEEDARWAPQEIPLDIVYEDNDILVINKPRGLVVHPGAGNPDGTVLNALLHYYPEIMDV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                V RLD +T GL+++         L                   +           
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNMTAGGRVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHINHPLV 248


>gi|327489656|gb|EGF21448.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK1058]
          Length = 298

 Score = 66.0 bits (159), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 35/240 (14%), Positives = 66/240 (27%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GV 65
           ++ +   QR+ K +A     SR      I   R+ VNG   ++A   V   D I  +   
Sbjct: 5   IEASAAGQRLDKAVAELTDLSRSLANEQIKDGRILVNGQ-AKKAKYAVKEGDVISYEQPE 63

Query: 66  P-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
           P             +   +     +      +V   +     + V   +  I       G
Sbjct: 64  PEVVEYVPEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGING 123

Query: 113 RLDINTEGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLK 162
            L       +     G L       +           + LR Y    HG +  D+  +  
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 163 KGIVIQGICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                +                 +  +  + G    V + L  G+  +I+    +    V
Sbjct: 184 PIGRSEKDRKKQAVTAKGKPALTRFQVLERFGDYTLVELQLETGRTHQIRVHMAYIGHPV 243


>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 = 66.0 bits (159), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 32/244 (13%), Positives = 68/244 (27%), Gaps = 37/244 (15%)

Query: 4   KNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +  + E +  +R+ KVIA      SR +V++ I  Q V VN   ++ A     + D + V
Sbjct: 5   RFHIDEEYDNERIDKVIAALNEDWSRSKVQQWIKNQLVTVNDQHVK-ANYKCSAGDIVVV 63

Query: 63  ---DGVP-----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
              +  P           +   +   L +      +V         + V   L       
Sbjct: 64  RLPEPEPLYVEPENIPLDIYYEDADVLVVNKPRGMVVHPAPGHMRGTLVNALLAHCHDLS 123

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPS---------------------TQWLRVYRV 147
              G L       +     G L       +                        +     
Sbjct: 124 GINGVLRPGIVHRIDKDTSGLLMVAKNDMAHQALVDQLVKKTVTRKYKAIVHGVIPHDYG 183

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                + +DK +  K  +  +          +  +     ++   L  G+  +I+   ++
Sbjct: 184 TIDAPIGRDKRDRKKMAVTEENGKEAVTHFRVLERFRQYTFIECQLETGRTHQIRVHMKY 243

Query: 208 FNWK 211
             + 
Sbjct: 244 IGYP 247


>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 = 66.0 bits (159), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 35/240 (14%), Positives = 66/240 (27%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GV 65
           ++ +   QR+ K +A     SR      I   R+ VNG   ++A   V   D I  +   
Sbjct: 5   IEASVASQRLDKAVAELTDLSRSLAHEQIKDGRILVNGQ-AKKAKYAVKEGDVISYELPE 63

Query: 66  P-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
           P             +   +     +      +V   +     + V   +  I       G
Sbjct: 64  PEVVEYVAEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHINDLSGING 123

Query: 113 RLDINTEGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLK 162
            L       +     G L       +           + LR Y    HG +  D+  +  
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 163 KGIVIQGICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                +                 +  +  + G    V + L  G+  +I+    +    V
Sbjct: 184 PIGRSEKDRKKQAVTAKGKPALTRFQVLERFGDYTLVELQLETGRTHQIRVHMAYIGHPV 243


>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 = 66.0 bits (159), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 66/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I + RV V+G  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILEDRVTVDGKTINKPKEKVLGGELVTIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  QIEEDARWAPQEIPLDIVYEDSDILVINKPRGLVVHPGAGNPDGTVLNALLYYYPEIVDV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L                   +           
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNMTAGGRVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHINHPLV 248


>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 = 66.0 bits (159), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 36/247 (14%), Positives = 75/247 (30%), Gaps = 36/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K  +Q      R+ K I+      SR  V+ ++ ++ + VN  + +  +  + + D 
Sbjct: 4   MPKKYELQVENEYGRLDKFISEQIPDLSRTRVKELVKEKEILVNHKVEKV-SYKIQAGDK 62

Query: 60  IEVDGVPLR--------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           IE++   ++                +   + +      +V         + V   L    
Sbjct: 63  IEINVPAVKPLDVVPENIPLDIVYEDEVVIVVNKPQGMVVHPAPGHPDHTLVNALLYHTQ 122

Query: 106 --------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-- 155
                    R   V R+D +T GLL++  +      LE                  +   
Sbjct: 123 DLAQSPEGFRPGIVHRIDKDTSGLLMIAKNAKARESLEDQLAHKTNKRIYWAIVHGNFGE 182

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                       L   KK  V++          +  Q    + +   L  G+  +I+   
Sbjct: 183 ENGVIDAPIGRNLYDRKKMAVVENGKKAVTHFKVLKQFKGYSLIECQLETGRTHQIRVHL 242

Query: 206 EFFNWKV 212
           ++    V
Sbjct: 243 DYIGHAV 249


>gi|9971939|gb|AAG10501.1|AF279106_63 predicted ribosomal large subunit pseudouridine synthase D
           [uncultured marine gamma proteobacterium EBAC31A08]
          Length = 310

 Score = 66.0 bits (159), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 34/244 (13%), Positives = 73/244 (29%), Gaps = 33/244 (13%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  KN+  +     R+ K  A      SR ++++ I + RV +NG +  +    V   D 
Sbjct: 1   MIVKNVPNDLS-SMRLDKATAEMFTDYSRTQIKKWIEEGRVLINGEV-SQPRDKVYENDQ 58

Query: 60  IEVDGV--------------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           IE+                  +       + +      ++   S     +     +    
Sbjct: 59  IELSPKEEQKVSWEAQDIDFEIHFENEDFIIINKPAGLIMHPGSGCYDGTLANGLIYKFP 118

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
                 R   V RLD +T G+LL+  +            +   V +              
Sbjct: 119 ELINIPRSGIVHRLDKDTSGILLVARNESFRNFFINEMQERRVVKKYTSIVIGSTLGSFS 178

Query: 161 LKKGI-----------VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
           +++ I           + +        V L    G+ + + + +  G+  +I+       
Sbjct: 179 IEEPIGRDKNNRTKMAIREDGKDALTFVKLKENIGNYSVLDIRIETGRTHQIRVHLSSKK 238

Query: 210 WKVN 213
             + 
Sbjct: 239 LPII 242


>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 = 66.0 bits (159), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 35/244 (14%), Positives = 70/244 (28%), Gaps = 33/244 (13%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K+   V +     R+ K +      +R ++++ I    + +N   ++ A  N+   D I 
Sbjct: 3   KNTFNVDKESVGLRLDKFLEEILEINRSQIKKNIVDGNILLNNNKVK-AGYNLKLDDEIT 61

Query: 62  V--------------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
           V                    D      ++   L ++        T  +         + 
Sbjct: 62  VEYEDDFSLSPEKIDFDVLYEDDYLAVISKPQELVVHPGAGNKSGTLVNGLLYKFKELSN 121

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP------------STQWLRVYRVRF 149
           P    R   V RLD +T GL+L+         L                           
Sbjct: 122 PIDNDRPGIVHRLDKDTSGLMLIAKKDEAYYKLVEMFKNRQIDKHYLAICHGNIYEDFDV 181

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +D  N +K  ++ +          +         + V L  G+  +I+    + N
Sbjct: 182 KAPIGRDPNNRIKMRVIDENSKEAYTSFKVLKNFDKYTLLDVHLHTGRTHQIRVHLAYVN 241

Query: 210 WKVN 213
             V 
Sbjct: 242 HPVV 245


>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 = 66.0 bits (159), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 30/242 (12%), Positives = 63/242 (26%), Gaps = 35/242 (14%)

Query: 3   DKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            K  ++E+    R+ K +       SR + + +I +  V VNG  ++     +   D I 
Sbjct: 22  RKCRIEEDIESMRLDKYMGNRFSYYSRNKWQDLIGEGLVLVNGEKIK-YTRTISKGDEIS 80

Query: 62  V-------------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
                               DG  +   +   L +         T               
Sbjct: 81  YYFKDMKEPEVNKDIEIIYDDGDLIIVNKPANLPVIPSGKYYYNTLHTIMQERLGCHLNM 140

Query: 103 SIFSRVISVGRL--------DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD 154
                  + G +              +L   N+  + +           +          
Sbjct: 141 INRIDRETSGCVILSRGSLVASKFCAMLANKNNNNIKKTYIAIVENAKDIEDSFTVEGYM 200

Query: 155 QDKLNLLKKGIVI------QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
           Q+  + L +   I      +   Y   +     + G  A + + L  G+  +I+      
Sbjct: 201 QEVGDKLYRRYQILHKENVEDSKYSKTKFKTVKKIGDYAILKIRLYTGRMHQIRVHLHSK 260

Query: 209 NW 210
           N 
Sbjct: 261 NL 262


>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 = 66.0 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 37/249 (14%), Positives = 72/249 (28%), Gaps = 42/249 (16%)

Query: 4   KNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE- 61
           K  V  N  P R+ K +A +    SR  +++      + VNG  ++     V   D +  
Sbjct: 55  KVQVDANQDPVRIDKYLADKMAYQSRNRIQQAADAGFIHVNGKPVKS-NYKVRPNDLVTL 113

Query: 62  ----------VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                     +    +      E  +L + +K  G+V      +   T+   +      +
Sbjct: 114 MLDRPRHETSIKPEEIAINVVYEDDQLMVVNKEAGMVVHPGAGNFHGTLIQAVAWHLRDM 173

Query: 109 ISV----------GRLDINTEGLLLLTNDG-------------GLARVLELPSTQWLRVY 145
                         R+D +T GLL++                    R         +   
Sbjct: 174 PEFDANDPEVGLVHRIDKDTSGLLVVAKTPTAKNALGKQFFNKTTHRSYNALVWGNIVED 233

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             R  G + +D  N L+  +                +  + G    V   L  G+  +I+
Sbjct: 234 EGRIEGNIGRDPKNRLRMKVFDPDSGIGKTAVTHYKVLERFGYTTLVQCVLETGRTHQIR 293

Query: 203 KVFEFFNWK 211
              +     
Sbjct: 294 AHMKHIGHP 302


>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 = 66.0 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 35/266 (13%), Positives = 73/266 (27%), Gaps = 46/266 (17%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           R+ + +A      SR  ++++I Q  V++N  +       +   D +EV           
Sbjct: 14  RIDRWLANQVDSLSRSHIQKLIEQGHVQINHKICTSKKYALQIGDQVEVHIPAPQPLALE 73

Query: 64  ----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-------- 111
                + +   +   L +      +V         + V   L        S         
Sbjct: 74  PEPMDLEILFEDDHLLIVNKPAGLVVHPAPGHATGTLVHGLLAHCQDGQGSTLSGIGGVE 133

Query: 112 -----GRLDINTEGLLLLTNDGGLARV-------------LELPSTQWLRVYRVRFHGQV 153
                 RLD +T G +++       +                            R    +
Sbjct: 134 RPGIVHRLDKDTTGAIMVAKTNQAHQHLQAQIAAKTALREYVGLVYGRPSALTGRMEFPI 193

Query: 154 DQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + + + +K  +V +  G         +    G+ A V   L  G+  +I+       W 
Sbjct: 194 GRHRSDRIKMAVVPEEQGGKVAVTHWQILQPLGNYALVKFRLETGRTHQIRVHCAQMGWP 253

Query: 212 VNR---LIRISYGPFQLGTLLAGSTR 234
           +       R       L   +  + R
Sbjct: 254 IVGDPLYSRGRSLKVNLSGQVLHAWR 279


>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 = 66.0 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 33/240 (13%), Positives = 67/240 (27%), Gaps = 33/240 (13%)

Query: 3   DKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
             ++V      +R+ +V+ + AG  SR  ++ +I    V+V+G     A+  V +   +E
Sbjct: 17  RSDVVDTARHGERLDRVLVSIAGEFSRSHLQHLIELGHVRVDGQPASTASRRVKAGQRVE 76

Query: 62  V-----------------------DGVPLRKAERTRLWLYHKPIGL--------VTTHSD 90
           V                       D   L   +   L ++  P           +  H+ 
Sbjct: 77  VELVPTDESRAFRPQPMALAILYEDEHLLVLDKPAGLVVHPAPGNWSGTLLNGLLAHHAA 136

Query: 91  PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
                               +           L+ +           +     V   R  
Sbjct: 137 AATLPRAGIVHRLDKDTSGVMMVGKSLPAVTALVRDIAARDVHRRYLALAHGAVATQRID 196

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             V +D ++ ++  +V  G       V    Q    + V   L  G+  +I+        
Sbjct: 197 APVGRDPVSRVRMAVVASGKPART-DVECLAQHDGVSAVRCTLHTGRTHQIRVHLASRGH 255


>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 = 66.0 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 30/247 (12%), Positives = 71/247 (28%), Gaps = 40/247 (16%)

Query: 7   VQENFTPQRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLERAAVN--------- 53
           ++ N    R+ K +    A +   SR  ++ +I    V VNG +  +   N         
Sbjct: 3   IKANVEKVRLDKYLVDALAESTEYSRSYIQTLIKDGNVIVNGNVETKQNFNLIGDIEIEI 62

Query: 54  -------------------VMSTDHIEVDGVP----LRK----AERTRLWLYHKPIGLVT 86
                              V   D I V   P    +       E T +           
Sbjct: 63  NIPEVKTSTINPEKIDLDIVYEDDDILVVNKPNNMVVHPGAGNTEGTMVNALLGRDAEFL 122

Query: 87  THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR 146
           +      R  +   +    + ++ V + D + + L  +  +  + +         ++  +
Sbjct: 123 STIGGVERPGIVHRIDKQTTGLLIVAKNDKSHQVLTEMLKNHEIYKEYVALVWGEIKEDK 182

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                 + + + +  K  +  +   Y      +  +      V   +  G+  +I+  F 
Sbjct: 183 GIIDAPIGRHQNDRKKMMVTSKNSKYAVTNFEVIKRLDKTTLVKCAIETGRTHQIRVHFN 242

Query: 207 FFNWKVN 213
           F    + 
Sbjct: 243 FIKHPIV 249


>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 = 66.0 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 32/243 (13%), Positives = 61/243 (25%), Gaps = 40/243 (16%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            V      +R+ K +   GI    SR +V++ I    V VNG  ++     V   D I V
Sbjct: 8   TVAAEQKNERIDKFV--TGINNEWSRSQVQQWIKDDVVTVNGKAVKV-NYKVKEEDEITV 64

Query: 63  --------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                   D  P      +   +   L +      +V         + V   +       
Sbjct: 65  TIPEPEALDIQPEDLNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL-------- 160
              G +       +     G L       + + L    V          +          
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKG 184

Query: 161 ------------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                        +   V +          +  +      V   L  G+  +I+   ++ 
Sbjct: 185 TIDAPIGRDKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYI 244

Query: 209 NWK 211
            + 
Sbjct: 245 GYP 247


>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 = 66.0 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 26/243 (10%), Positives = 63/243 (25%), Gaps = 35/243 (14%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLE---------RAAVNVM 55
           IV       R+   +A      SR  ++++I    V V+G                + + 
Sbjct: 7   IVDGENAKCRLDVFLANQCQDISRSYIQKLIEDGLVTVDGKPARANHKLRVEETIHMQIP 66

Query: 56  STDHIEVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
             + ++V+   +       +   + +      +V         + V   L          
Sbjct: 67  PAEELKVEPENIPLDIYYEDSHVIVVNKPRGMVVHPAEGNIAGTLVNALLYHCHDLSGIN 126

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY---------------------RVRFH 150
           G +       L     G +       + Q L                            +
Sbjct: 127 GIMRPGIVHRLDKDTSGLIMAAKHDQAHQSLARQLKDRTVTRRYQALVHHNIKGDFGTIN 186

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + +D  +  K  +V +          +  + G    +   L  G+  +I+    +  +
Sbjct: 187 APIGRDPRDRQKMAVVERNSKNAVTHFQVLERFGDYTLIECRLETGRTHQIRVHMAYIGF 246

Query: 211 KVN 213
            + 
Sbjct: 247 PLV 249


>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 = 66.0 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 36/232 (15%), Positives = 66/232 (28%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP------- 66
           R+ K ++     SR      I   +V VNG + ++A   V   D +      P       
Sbjct: 11  RLDKALSDLTELSRSLANEQIKSGQVLVNGQV-KKAKYTVQEGDVVTYHVPEPEVLEYVA 69

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 +   +     +      +V   +     + V   +  I       G L      
Sbjct: 70  EDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 121 LLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDK----------LNL 160
            +     G L       +           + LR Y    HG +  D+             
Sbjct: 130 RIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            KK  VI        +  +  + G  + V + L  G+  +I+    + +  V
Sbjct: 190 RKKQAVIAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIDHPV 241


>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 = 66.0 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 32/244 (13%), Positives = 69/244 (28%), Gaps = 37/244 (15%)

Query: 4   KNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +  + E +  +R+ KVIA      SR +V++ I +Q V VN   ++ A     + D + V
Sbjct: 5   RFHIDEEYDNERIDKVIAALNEDWSRSKVQQWIKKQLVTVNDQHVK-ANYKCSAGDIVVV 63

Query: 63  ---DGVP-----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
              +  P           +   +   L +      +V         + V   L       
Sbjct: 64  RLPEPEPLYVEPENIPLDIYYEDADVLVVNKPRGMVVHPAPGHMRGTLVNALLAHCHDLS 123

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPS---------------------TQWLRVYRV 147
              G L       +     G L       +                        +     
Sbjct: 124 GINGVLRPGIVHRIDKDTSGLLMVAKNDMAHQALVDQLVKKTVTRKYKAIVHGVIPHDYG 183

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                + +DK +  K  +  +          +  +     ++   L  G+  +I+   ++
Sbjct: 184 TIDAPIGRDKRDRKKMAVTEENGKEAVTHFRVLERFRQYTFIECQLETGRTHQIRVHMKY 243

Query: 208 FNWK 211
             + 
Sbjct: 244 IGYP 247


>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 = 66.0 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 29/246 (11%), Positives = 68/246 (27%), Gaps = 36/246 (14%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K I + +   +R+   IA     +R  ++++I    + VN     + +  V   D IE+
Sbjct: 2   EKIIFEISEEGKRLDLYIAERTELTRTRIQQLIKDGNINVNNKK-SKPSYKVEKNDFIEM 60

Query: 63  ---DGVPLRKAERTRLWLY-----------HKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
              D   +                       +   +V      +  + V   +  I    
Sbjct: 61  IIPDEKEIDLVPENINIKILYEDSDIAVIDKEAGIVVHPSHGHESGTLVNAVMYHIKDLS 120

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPST---------------------QWLRVYRV 147
              G +       L     G L       +                        +     
Sbjct: 121 GINGEIRPGIVHRLDKDTSGLLIIAKNDTAHLRLSEMFGSSGIRKTYIAILKGKINKESG 180

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
           +    + +D  +  K  +V            +  +    + V V ++ G+  +I+   ++
Sbjct: 181 KLETLIGRDPKDRKKMAVVKTNGKTAITYFQVLDKNEKFSLVKVNIQTGRTHQIRVHMKY 240

Query: 208 FNWKVN 213
             + V 
Sbjct: 241 LGYPVL 246


>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 = 66.0 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 29/237 (12%), Positives = 61/237 (25%), Gaps = 38/237 (16%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKA 70
           R+   IA+     SR  ++++I Q  V+VN  +       V   D I +   D  PL   
Sbjct: 26  RLDSYIAQQTPDLSRSRIQKLIEQGNVQVNDHVCISKKAKVQLGDRISLTIPDPKPLELQ 85

Query: 71  ERTR-----------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----------- 108
                          + +      +V      +  + V   L                  
Sbjct: 86  PEVIPLDILYEDDVLIIINKPAGLVVHPAPGHESGTLVNALLAHCPKLTGIGGVQRPGIV 145

Query: 109 ----------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
                     I++ + D     L          R                 +  + +  +
Sbjct: 146 HRLDKDTTGAIAIAKTDQAHGHLQAQLQAKTAQRQYLGVVYGAPSAESGTINQPIGRHPV 205

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +  K  +V               ++  G+   +   L  G+  +I+    +    + 
Sbjct: 206 DRKKMAVVPVEKGGRPAITHWQVRERLGNYTLMHFQLETGRTHQIRVHSSYIGHPIV 262


>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 = 66.0 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 31/247 (12%), Positives = 76/247 (30%), Gaps = 35/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  + I+  +   +R+ K + +     SR  ++ +I++  +KV+G  ++     +   + 
Sbjct: 1   MDTQKIIYTSPKSERIDKFLQQELTDVSRTNIQNLISEGYIKVDGNNIKT-NYKLKEGNV 59

Query: 60  IEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I +D                 +   +   + +      +V         + V   L    
Sbjct: 60  ITIDYKEPEELDVVKQDIPVDIVYEDNDLIIVNKAKGMVVHPSVGHKDGTLVNALLFHSE 119

Query: 106 -------SRVISVGRLDINTEGLLLLTNDGGLA----RVLELPSTQWLRVYRVRFHGQVD 154
                   R   V R+D +T GLL++  +         ++     +      V    + D
Sbjct: 120 LSSINGTIRPGIVHRIDKDTSGLLIVAKNDKAHVKLSEMIANKDVKRKYYALVHGSIKHD 179

Query: 155 Q--------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          K+  +I           +  +      +   L  G+  +I+   +
Sbjct: 180 YGTIDAPIARNPKERKEMAIIDEGKPSITHFKVIDRFEKYTLIECELETGRTHQIRVHMK 239

Query: 207 FFNWKVN 213
           + N  + 
Sbjct: 240 YINHPLV 246


>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 = 65.6 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 34/251 (13%), Positives = 67/251 (26%), Gaps = 40/251 (15%)

Query: 3   DKNIVQENFTPQRVSKVIARAG---IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K  +    T  R+ K++         SR  ++++I ++ + VN  ++      V     
Sbjct: 2   NKITLNSLNTTLRLDKLLVELLTSYDYSRSYIQKLIKEECISVNNQIITNNNFVVKPNSQ 61

Query: 60  IEV-------------DGVP---LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           I +             +      +   +   L +  +    V         + V   L S
Sbjct: 62  ITITIKDPILDPNLVKNDEIDLDIIYQDDDLLVINKQNNITVHPSLSNTNNTIVNALLAS 121

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------- 155
                   G L       +     G L       + + L           +         
Sbjct: 122 DVELSSINGELRPGIVHRIDKQTTGLLIVAKNDKTHKLLSEMFKNHQIYKEYLAIVSGVI 181

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG------------LREGKNREIK 202
                L+   I    I    M VT    K +     V             ++ G+  +I+
Sbjct: 182 KPNKGLIDAPIGRSQIDRKKMSVTAKNSKQAITTFEVVERFLKNTLVKCQIQTGRTHQIR 241

Query: 203 KVFEFFNWKVN 213
             F + N  V 
Sbjct: 242 VHFNYINHPVL 252


>gi|156401575|ref|XP_001639366.1| predicted protein [Nematostella vectensis]
 gi|156226494|gb|EDO47303.1| predicted protein [Nematostella vectensis]
          Length = 418

 Score = 65.6 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 51/348 (14%), Positives = 101/348 (29%), Gaps = 41/348 (11%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRKAERTR-LWLYHKP 81
           E+ I   ++ VNG  +      +   D +          V   PL     T  + + +KP
Sbjct: 45  EKAIESGKITVNGEKV-LPTTVLRGNDVLRNRVHRHEPPVTDQPLEIICNTDDIVVLNKP 103

Query: 82  IGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLL----TNDGGLARVLE 135
             +          +TV   L        + ++ R+D  T G+L+     T    L   + 
Sbjct: 104 SSIPVHPCGRYRHNTVVFLLGKEHNLRNLYTIHRIDRLTSGILMFAKTLTRARMLEAQVR 163

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------VTLDTQKGSNA 187
               +   + RV+     +          +  +                 T     G ++
Sbjct: 164 DRQVEKEYLCRVQGEFPSEPVDCEQPIIVVSHKVGICRVSPDGKSCRTVFTKLHSNGKSS 223

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V      G+  +I+   ++  + +         P       A  T+     +  +Q   
Sbjct: 224 VVKCIPYTGRMHQIRVHLQWLGYPIID------DPIY--NHPAWGTKRGRGGVTDDQALE 275

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR------MKKNSSQKNGLSKQKKL 301
            +   AQ              RDR      +P   ++          +   +GL+ ++  
Sbjct: 276 VIKALAQSTTIIEGDDVGYTPRDREAETRPIPTHNSKNINTGMSLAQAHAPSGLTAEQSA 335

Query: 302 AT--PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
               PV  +    N  M  G     +S  G+ E +   S     +R  
Sbjct: 336 HGLTPVPNKCRDDNANMETGAQHDEMSPQGEGERDADCSECRIWRRDP 383


>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 = 65.6 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 28/232 (12%), Positives = 63/232 (27%), Gaps = 37/232 (15%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+ K +A      SR ++++ I    V VNG  ++     ++  D + V           
Sbjct: 16  RIDKELAHHLTDISRSQLQKWIEDGNVTVNGEKVK-PKYKLVVGDRVVVQPKKPQKIDLE 74

Query: 67  -------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI---------- 109
                  +   +   + +      +V         + V   L       I          
Sbjct: 75  PENIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPNHTLVNALLYHSPLSTINGEFRPGIVH 134

Query: 110 ----------SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
                      + + D+    L          R         ++  R      + + K +
Sbjct: 135 RIDKDTSGLLMIAKNDLAHRSLAAQLKAKTNEREYVALVHGVIKEERGTIDAPLGRSKKD 194

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             KK  V++   +      +         V+  L  G+  +I+   ++    
Sbjct: 195 R-KKQAVVEDGRHAVTHFKVLELFQHYTLVSCRLETGRTHQIRVHMKYIGHP 245


>gi|319777728|ref|YP_004137379.1| pseudouridine synthase [Mycoplasma fermentans M64]
 gi|318038803|gb|ADV35002.1| Pseudouridine synthase [Mycoplasma fermentans M64]
          Length = 307

 Score = 65.6 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 30/239 (12%), Positives = 73/239 (30%), Gaps = 40/239 (16%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGIL-LERAAVNVMSTDHIEV----DGVP-- 66
           +R+ K I +    SR +++ +I Q  V +N  + + +    V     I +    +     
Sbjct: 10  ERIDKYIGQNSELSRNDIKELIEQGAVYINDNVQVHKCNYIVREGQEITIVKLLNKEIKI 69

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VI 109
                   ++  +   + +      +V         + V   L    +            
Sbjct: 70  EPVNIPLDIKYEDDDLVIINKPSNLVVHPSPGHYNDTLVNGLLYHFKNNLSNENGLLRPG 129

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR-------------VRFHGQVDQD 156
            V R+D +T GLL++  +  +   L     +                    + +  + ++
Sbjct: 130 IVHRIDKDTSGLLIIAKNNKMHNSLTDMLKRHEIERSYLAIVRGLIENPLTKINLPIARN 189

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            ++     +  +G         L      K   + V   L+ G+  +I+    +    V
Sbjct: 190 TVDRKMMSVHKEGKEAITFVHLLKHFYLDKEPMSLVRCELKTGRTHQIRVHLSYIKHPV 248


>gi|319790681|ref|YP_004152314.1| hemolysin A [Thermovibrio ammonificans HB-1]
 gi|317115183|gb|ADU97673.1| hemolysin A [Thermovibrio ammonificans HB-1]
          Length = 263

 Score = 65.6 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 1/59 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
            +R+ K++   GI  SR   + +I   +V VNG ++++A   V +   +EV G  +  
Sbjct: 2  KKERLDKLLVERGIVKSRERAKALIMAGKVLVNGQVVDKAGTAVPADARVEVKGEDIPY 60


>gi|325689795|gb|EGD31799.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK115]
          Length = 298

 Score = 65.6 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 35/240 (14%), Positives = 67/240 (27%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GV 65
           ++ +   QR+ K +A     SR      I   R+ VNG   ++A   V   D I  +   
Sbjct: 5   IEASVVGQRLDKAVAELTDLSRSLANEQIKDGRILVNGQ-AKKAKYAVKEGDIIYYELPE 63

Query: 66  P-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
           P             +   +     +      +V   +     + V   +  I       G
Sbjct: 64  PEVVEYVPEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGING 123

Query: 113 RLDINTEGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLK 162
            L       +     G L       +           + LR Y    HG +  D+  +  
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 163 KGIVIQGICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                +                 +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 184 PIGRSEKDRKKQAVTAKGKSALTRFQVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 243


>gi|313885861|ref|ZP_07819602.1| S4 domain protein [Porphyromonas asaccharolytica PR426713P-I]
 gi|332300689|ref|YP_004442610.1| RNA-binding S4 domain protein [Porphyromonas asaccharolytica DSM
          20707]
 gi|312924690|gb|EFR35458.1| S4 domain protein [Porphyromonas asaccharolytica PR426713P-I]
 gi|332177752|gb|AEE13442.1| RNA-binding S4 domain protein [Porphyromonas asaccharolytica DSM
          20707]
          Length = 154

 Score = 65.6 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 23/61 (37%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
          R++K+++ AGI SRREVE+ I   RV +NG   E   + V   D + +DG  L   +  R
Sbjct: 4  RINKLLSDAGIGSRREVEKYIVAGRVMLNGERAELTDIVV-EDDIVTLDGEELPVNDILR 62

Query: 75 L 75
           
Sbjct: 63 E 63


>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 = 65.6 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 26/242 (10%), Positives = 67/242 (27%), Gaps = 37/242 (15%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVM----------S 56
           Q +   +R+   +A     +R  V+++I    V+++G     + A+ V            
Sbjct: 26  QGDEEGKRIDAFLAEELGLTRSYVQKLIRLGNVEISGIRRALKPALKVTAEMAIHIVVPP 85

Query: 57  TDHIEVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
            + +E++  P++      +   + +      +V         + V   L           
Sbjct: 86  AETLEIEPEPVKFGIIYEDPYIIVVNKPAGLVVHPAPGNWHGTLVHGLLYKYRDMRKFDE 145

Query: 113 RLDINTEGLLLLTNDG---------------------GLARVLELPSTQWLRVYRVRFHG 151
            +       L     G                      + +     S   LR        
Sbjct: 146 EVRPGIVHRLDSGTSGLLVVARTPKILQNLQNQFRSRSVEKKYLALSCGKLRKAAGFIEE 205

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + + + N L   +   G      +  +       +++   L  G+  +I+   +     
Sbjct: 206 PIGRSQRNRLMMTVTDTGRPALT-EYRILWTHQKYSFIECTLHTGRTHQIRVHLKHRGCP 264

Query: 212 VN 213
           + 
Sbjct: 265 IV 266


>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 = 65.6 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 31/237 (13%), Positives = 62/237 (26%), Gaps = 37/237 (15%)

Query: 14  QRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE------VDGVP 66
           +R+ + +A +    SR  ++++I Q +V VNG L +     V   D I+      V   P
Sbjct: 10  ERLDRYLAAQLPDLSRSRIQQLIEQGQVYVNGQLCQAKKQIVQVGDRIQLELPPPVAAEP 69

Query: 67  LR--------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           L           +   L +      +V       G + V   L          G      
Sbjct: 70  LPEHIPLDILYEDDQLLIVNKPAGLVVHPAPGHSGGTLVNALLAHCGDLPGIGGVQRPGI 129

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD----------------------QD 156
              L     G +A      + + L+        + +                        
Sbjct: 130 VHRLDKDTSGAIAIAKTELAHRHLQAQIKAKTARREYLGVVYGVPKTSSGRIDLPIGRHP 189

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                   +             +  + G+   +   L  G+  +I+         + 
Sbjct: 190 VDRKKMAVVASDKGRSAVTHWQIQERLGNFTLLQFQLETGRTHQIRVHIAQLGHPIV 246


>gi|323464710|gb|ADX76863.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Staphylococcus pseudintermedius ED99]
          Length = 305

 Score = 65.6 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 36/244 (14%), Positives = 75/244 (30%), Gaps = 36/244 (14%)

Query: 5   NIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           NI       QR+ K++       SR +++  I +  ++VNG  ++     +   D IE+ 
Sbjct: 7   NIEDATHHLQRIDKILPEFNSEWSRSQLQEWIKEGLIEVNGKAVKS-NYKLKLGDRIEIT 65

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--- 106
                            +   +     +Y     +V         + V   +  I +   
Sbjct: 66  EKEVVEADIQAENLNLDIYYEDDDVAIVYKPKGMVVHPSPGHYTGTLVNGLMYQIKNLSG 125

Query: 107 -----RVISVGRLDINTEGLLLLTNDGGLARVLELPST----QWLRVYRVRFHGQVDQ-- 155
                R   V R+D +T GLL++  +    R L         +   +  V  H   +   
Sbjct: 126 INSEIRPGIVHRIDKDTSGLLMVAKNDVAHRSLVEQLMAKTVKRKYIALVHGHIPHEFGT 185

Query: 156 ------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                    N  +   V+           +     +   V   L  G+  +I+   ++  
Sbjct: 186 IDAPIGRNKNDRQSMAVVDDGKEAVTHFNVIETFKNYTLVECELETGRTHQIRVHMKYIG 245

Query: 210 WKVN 213
           + + 
Sbjct: 246 YPLV 249


>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 = 65.6 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 32/232 (13%), Positives = 63/232 (27%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP------- 66
           R+ K ++     SR      I   +V VNG + ++A   V   D +      P       
Sbjct: 11  RLDKALSDLSELSRSLANEQIKSGQVLVNGQV-KKAKYTVQEGDVVTYHVPEPEVLEYVA 69

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 +   +     +      +V   +     + V   +  I       G L      
Sbjct: 70  EDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 121 LLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            +     G L       +           + LR Y    HG +  D+  +       +  
Sbjct: 130 RIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 171 CYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                          +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 65.6 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 32/232 (13%), Positives = 63/232 (27%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP------- 66
           R+ K ++     SR      I   +V VNG + ++A   V   D +      P       
Sbjct: 11  RLDKALSDLSELSRSLANEQIKSGQVLVNGQV-KKAKYTVQEGDVVTYHVPEPEVLEYVA 69

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 +   +     +      +V   +     + V   +  I       G L      
Sbjct: 70  EDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 121 LLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            +     G L       +           + LR Y    HG +  D+  +       +  
Sbjct: 130 RIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 171 CYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                          +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 65.6 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 32/232 (13%), Positives = 63/232 (27%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP------- 66
           R+ K ++     SR      I   +V VNG + ++A   V   D +      P       
Sbjct: 11  RLDKALSDLSELSRSLANEQIKSGQVLVNGQV-KKAKYTVQEGDVVTYHVPEPEVLEYVA 69

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 +   +     +      +V   +     + V   +  I       G L      
Sbjct: 70  EDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 121 LLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            +     G L       +           + LR Y    HG +  D+  +       +  
Sbjct: 130 RIDKDTSGLLMIAKNDDAHLVLAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 171 CYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                          +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 65.6 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I   RV VNG  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILDSRVTVNGKKINKPKEKVLGGELVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-- 108
                           +   +   L +      +V   +     + +   L      +  
Sbjct: 70  QIEEDARWAPQEIPLDIVYEDNDILVINKPRGLVVHPGAGNPDGTVLNALLHYYPEIMDV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                V RLD +T GL+++         L                   +           
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNMTAGGRVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHINHPLV 248


>gi|332974183|gb|EGK11117.1| ribosomal large subunit pseudouridine synthase D [Psychrobacter sp.
           1501(2011)]
          Length = 456

 Score = 65.6 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 30/244 (12%), Positives = 66/244 (27%), Gaps = 38/244 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            V ++   QR+ K +A    A  SR +++  +    + VNG + E+    V   D + + 
Sbjct: 149 TVTDDKAGQRIDK-LAAELFADHSRSQLQEWLKSGNLTVNGEV-EKPKYRVRVGDKLLLQ 206

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   + + L +      +V   +     + V   L    ++  
Sbjct: 207 AKLEQHGTDEPEDIALDIMYEDDSVLVINKPVGMVVHPGAGNWTGTLVNGLLYHYPNQAH 266

Query: 110 SV--GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
               G +    +    L   G           Q       R +  +    +  LK+   I
Sbjct: 267 LPRAGLVHRIDKNTSGLLVIGKTKAAQMELQDQLRDKTVYRHYQCIVAGDVASLKRQRTI 326

Query: 168 Q---------------GICYGDMQVTLDTQ---KGSNAWVTVGLREGKNREIKKVFEFFN 209
                                     +        + + + V L  G+  +I+       
Sbjct: 327 DAPIGRHRTQRTKMTVSSVGKPAVTHIMNITALNDNYSLLDVQLETGRTHQIRVHLSHIG 386

Query: 210 WKVN 213
             + 
Sbjct: 387 HPII 390


>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 = 65.6 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 29/239 (12%), Positives = 70/239 (29%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I  +RV VNG++++     V+  + + +D 
Sbjct: 10  TVSESQLGQRLDQTLAELFPDYSRSRIKEWILDRRVTVNGVMVDTPKEKVLGGELVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-- 108
                           +   +   + +      +V   +     + +   L    + +  
Sbjct: 70  EIEEAQRWEPQDLPLDIVYEDEDIIVINKPRDFVVHPGAGNPDGTVLNALLHHYPAIMDV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                V RLD +T GL+++         L     +             +           
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTHLVDSLQRREITREYEAVAIGNMTAGGTVEQPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      +  + 
Sbjct: 190 SRHSTKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHISHPLV 248


>gi|325686216|gb|EGD28262.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 304

 Score = 65.6 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 35/246 (14%), Positives = 70/246 (28%), Gaps = 36/246 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  +  +    + QR+ K +A      SR  ++ ++    V VNG    + +  V   D 
Sbjct: 1   MNREYELTAEESGQRLDKYLAGEMIDLSRSRIKELVQAGEVLVNGKK-SKVSYKVQKGDL 59

Query: 60  IEV------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I+V            + +P  +   +   + +      +V         + V   L    
Sbjct: 60  IQVTVLPLEPLKLEAENIPLDIVYEDEDIIVVNKPQGMVVHPAVGHPSHTLVNALLYHTR 119

Query: 106 --------SRVISVGRLDINTEGLLLLTND------------GGLARVLELPSTQWLRVY 145
                    R   V R+D +T GLL++  +                +   L         
Sbjct: 120 DLADSPEGFRPGIVHRIDKDTSGLLMVAKNAAARESLEKQLAAKSNKRQYLAIVHGNFAE 179

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           K+  V++          +  Q    + V   L  G+  +I+   
Sbjct: 180 EEGTIDAPIGRNPKDRKQMAVVEKGKSAVTHFKVLEQYQGYSLVECQLETGRTHQIRVHM 239

Query: 206 EFFNWK 211
            +    
Sbjct: 240 AYIGHP 245


>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 = 65.6 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 29/239 (12%), Positives = 70/239 (29%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I  +RV VNG++++     V+  + + +D 
Sbjct: 10  TVSESQLGQRLDQTLAELFPDYSRSRIKEWILDRRVTVNGVMVDTPKEKVLGGELVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-- 108
                           +   +   + +      +V   +     + +   L    + +  
Sbjct: 70  EIEEAQRWEPQNLPLDIVYEDEDIIVINKPRDFVVHPGAGNPDGTVLNALLHHYPAIMDV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                V RLD +T GL+++         L     +             +           
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTHLVDSLQRREITREYEAVAIGNMTAGGTVEQPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      +  + 
Sbjct: 190 SRHSTKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHISHPLV 248


>gi|306520956|ref|ZP_07407303.1| putative pseudouridylate synthase [Clostridium difficile QCD-32g58]
          Length = 453

 Score = 65.6 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 35/235 (14%), Positives = 72/235 (30%), Gaps = 37/235 (15%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           R+   +A   G  SR  ++++I   +VKVN  + E+A   V   D+I ++          
Sbjct: 167 RLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKV-EKAKYLVKEEDNIVIEIPEPKVLEVL 225

Query: 64  --GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-------- 111
              +P+     +   L +      +V         + V   L     ++ S+        
Sbjct: 226 PQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGILYHCKDKLSSINGVIRPGI 285

Query: 112 -GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
             R+D +T GLL++  +      L     +        F       +  +     + +  
Sbjct: 286 VHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICYGVVKEDKITVDKPIGRNP 345

Query: 171 CYGDMQVTLDTQKGSNAWVTVG------------LREGKNREIKKVFEFFNWKVN 213
                   +   K +     V             L  G+  +I+      N  + 
Sbjct: 346 KDRLKMAVVKDGKNAITHFEVVERFDKFTHMRARLETGRTHQIRVHALSINHPLL 400


>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 = 65.6 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 36/249 (14%), Positives = 68/249 (27%), Gaps = 37/249 (14%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M+ +  I+ EN    R+   ++      SR  ++ +I + +VKVNG +L+++   +   D
Sbjct: 1   METREFIIDENSVNTRLDLFLSERMEDKSRSYIQGLIEKSQVKVNG-ILKKSNYKLKIKD 59

Query: 59  HIEV--------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            I +        D  P      +   +   + +      +V   S     + V   L   
Sbjct: 60  KILITIPDPVGLDIEPEDIPLDIVYEDSDVIVVNKPQGMVVHPASGVYTGTLVNALLNHC 119

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------- 155
                  G         +     G L       S   L                      
Sbjct: 120 SDLSGINGVTRPGIVHRIDKDTSGILVVAKNDKSHNKLAEQLKDHSMTRAYTALVEGILK 179

Query: 156 -----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                             K  VI+          +  +  SN  V   L  G+  +I+  
Sbjct: 180 EDEGTIDKPLGRHPVERIKISVIKDGKRAVTHYRVLERFKSNTLVECVLETGRTHQIRVH 239

Query: 205 FEFFNWKVN 213
             +    + 
Sbjct: 240 MAYIGHPLV 248


>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 = 65.6 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 22/228 (9%), Positives = 64/228 (28%), Gaps = 36/228 (15%)

Query: 15  RVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           R+ K +       R +++        ++I + +V VN   ++  + ++   D +E+    
Sbjct: 13  RLDKFL-------RNQLKDVPLSVIYKLIRKGKVYVNRKRVKDPSFDLEEGDVVELRYVN 65

Query: 63  -----------DGVPLR------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
                      D  P+         +   L L   P   +         + +   L    
Sbjct: 66  LENLPKRSEKKDLTPVPMKLDVLYEDDHYLVLNKPPNIAIHPGKGVHVATLIEGLLYYGQ 125

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
            +  S   +    +    L           + +  +      + +  + +       K  
Sbjct: 126 EKGFSPFLVHRLDKETSGLLVVAKNREAARILTELFKGRNIEKEYVTLVRGVPENNMKIT 185

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +         ++         + + V +  G+  +I++      + V 
Sbjct: 186 IPLDGQEAVSEIVSVKPLKDVSLLRVKIHTGRKHQIRRHLSQIGFPVV 233


>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 = 65.2 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 33/244 (13%), Positives = 65/244 (26%), Gaps = 42/244 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            V      +R+ K +   GI    SR +V++ I  + V VNG  ++     V   D I V
Sbjct: 8   TVAAEQKNERIDKFV--TGINNEWSRTQVQQWIKDEVVTVNGKAVK-GNYKVKEEDEITV 64

Query: 63  --------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                   D  P      +   +   L +      +V         + V   +       
Sbjct: 65  TIPEPEELDIQPEDLNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRV 147
              G +       +     G L       + + L                        + 
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKG 184

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                + +DK    +   V +          +  +      V   L  G+  +I+   ++
Sbjct: 185 TIDAPIARDKKER-QSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKY 243

Query: 208 FNWK 211
             + 
Sbjct: 244 IGYP 247


>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 = 65.2 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 30/242 (12%), Positives = 61/242 (25%), Gaps = 36/242 (14%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V  +   QR+   +A +    +R  ++ +I    + VNG  ++     +   D I+V   
Sbjct: 8   VTSDKADQRLDTFLAESFEQWTRSHIQNLIKNGNITVNGQHIKS-GYKLKDGDIIKVEVP 66

Query: 63  -----DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                D  P      +   +   + +      +V   +     + V   L          
Sbjct: 67  ELRPIDIQPEDIPLNILYEDEDIIVINKPQGMVVHPAAGNYSATLVNALLAHCKDLSGIN 126

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------------- 155
           G +       +     G L       +   L                             
Sbjct: 127 GEIRPGIVHRIDKDTSGVLVVAKNDMAHVALAQQIKEKTAIRKYVALLEGDIKEDTGVIN 186

Query: 156 ----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                     KK  V+ G         +  + G    +   L  G+  +I+    +    
Sbjct: 187 APIARHPTDRKKMAVVSGGRSAVTHFKVLERFGRYTLIEARLETGRTHQIRVHMAYIGHP 246

Query: 212 VN 213
           V 
Sbjct: 247 VV 248


>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 = 65.2 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 34/234 (14%), Positives = 65/234 (27%), Gaps = 35/234 (14%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
             R+ K ++     SR      I   +V VNG L ++A  +V   D I            
Sbjct: 9   GVRLDKALSDLTELSRSLANEQIKSGQVLVNGQL-KKAKYSVQEGDVITYQVPEPEVLEY 67

Query: 63  --DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
             + +PL     +     +      +V   +     + V   +  I       G L    
Sbjct: 68  VAEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGI 127

Query: 119 EGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              +     G L       +           + LR Y    HG +  D+  +       +
Sbjct: 128 VHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNIPNDRGVIEAPIGRSE 187

Query: 169 GICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                            +  +  + G    + + L  G+  +I+    +    V
Sbjct: 188 KDRKKQAVTAKGKPAVTRFRVLERFGDYTLLELQLETGRTHQIRVHMAYIGHPV 241


>gi|322411546|gb|EFY02454.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           dysgalactiae subsp. dysgalactiae ATCC 27957]
          Length = 297

 Score = 65.2 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 42/240 (17%), Positives = 79/240 (32%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---D 63
           +    + QR+ K +A     SR +    I Q  V VNG   ++A   V + D I+    +
Sbjct: 3   INVLTSGQRLDKALADLSPLSRGQANDQIKQGLVLVNGQQ-KKAKYTVQAGDVIQFELPE 61

Query: 64  GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-- 111
              L             E   L + +KP G+V   S      T+ + L      + S+  
Sbjct: 62  EEVLEYQAQVIPLDIIYEDEALAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSING 121

Query: 112 -------GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   R+D +T GLL++       + L         + +       +      + + 
Sbjct: 122 VVRPGIVHRIDKDTSGLLMVAKTDEAHQALAAELKAKKSLRKYLAIVHGNLPNDRGMIEA 181

Query: 165 IVIQGICYGDMQ------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            + +       Q             T+  + G  + V + L  G+  +I+    +    V
Sbjct: 182 PIGRSEKDRKKQAVTAKGKEAVTRFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>gi|324995685|gb|EGC27597.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK678]
          Length = 298

 Score = 65.2 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 34/240 (14%), Positives = 67/240 (27%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GV 65
           ++ +   QR+ K +A     SR      I   ++ VNG   ++A   V   D I  +   
Sbjct: 5   IESSVAGQRLDKAVAELTDLSRSLANEQIKDGQILVNGQ-AKKAKYAVKEGDVISYELPE 63

Query: 66  P-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
           P             +   +     +      +V   +     + V   +  I       G
Sbjct: 64  PEVVEYVPEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIQDLSGING 123

Query: 113 RLDINTEGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLK 162
            L       +     G L       +           + LR Y    HG +  D+  +  
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHLALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 163 KGIVIQGICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                +                 +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 184 PIGRSEKDRKKQAVTAKGKPALTRFQVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 243


>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 = 65.2 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 32/239 (13%), Positives = 66/239 (27%), Gaps = 38/239 (15%)

Query: 13  PQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP----- 66
             R+ K ++     ASR ++++ I   +V VN +++    V V   D I           
Sbjct: 12  GIRLDKALSSLLENASRNQIQKAIKDSQVLVNDVIISDPDVLVKENDIILFSFKEPEELK 71

Query: 67  ---------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-----RVISVG 112
                    +   +   + +       V   +     + V   L    +          G
Sbjct: 72  IAAANVALDIIYEDDDLIVINKAAGMTVHPGAGHHDDTLVNALLHHTKNLSDIGSSERPG 131

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
            +    +    L       +   L + Q  +   +R +  +    +N L+  I       
Sbjct: 132 IVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRKYKVLVWGVINPLEGVIKNNIGRS 191

Query: 173 GDMQVTL------------------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +  +                     KGS + V   L  G+  +I+         V 
Sbjct: 192 RSDRQKMTILKYGGKEAVTHYKILELFYKGSISMVECKLSTGRTHQIRVQLSHLKHSVV 250


>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 = 65.2 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 30/239 (12%), Positives = 66/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I + RV V+G  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILEDRVTVDGKTINKPKEKVLGGELVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-- 108
                           +   +   L +      +V   +     + +   L      +  
Sbjct: 70  QIEEDARWAPQEIPLDIVYEDNDILVINKPRGLVVHPGAGNPDGTVLNALLYYYPEIMDV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                V RLD +T GL+++         L                   +           
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNMTAGGRVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHINHPLV 248


>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 = 65.2 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 28/238 (11%), Positives = 68/238 (28%), Gaps = 31/238 (13%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T  R+ + IA      SR  ++  I    V V+G+++ +    V+ +  IE+
Sbjct: 8   KSEISATQTGLRLDQAIAELFPDYSRTRLKEWILGGNVYVDGVVVTKPREKVLESQVIEI 67

Query: 63  DGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           +                 +   +   L +  +   +V   +     + +   L       
Sbjct: 68  EATLEEEVAAEAQEIDLDIVYEDDHILVINKQAGLVVHPGAGNADGTLMNALLHHCPEIE 127

Query: 109 ISV-----GRLDINTEGLLLLTNDGGLARV------LELPSTQWLRVYRVRFHGQVDQD- 156
                    RLD +T GL+++                   + ++  +           D 
Sbjct: 128 HVPRAGIIHRLDKDTTGLMVVAKTVEAQTHLVAALQARDITREYEAIVLGTMTAGGTVDA 187

Query: 157 ----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                        V            +  +  ++  + + L  G+  +I+        
Sbjct: 188 PIGRHPTKRTHMAVHHSGRPSVTHYRVAEKFRAHTRLRLRLETGRTHQIRVHMAHIGH 245


>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 = 65.2 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 43/240 (17%), Positives = 79/240 (32%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           +    + QR+ K +A     SR +    I Q  V VNG   ++A   V + D I  +   
Sbjct: 3   INVITSGQRLDKALADLSPLSRGQANDQIKQGLVLVNGQQ-KKAKYTVQAGDVICFELPK 61

Query: 64  GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-- 111
              L             E   L + +KP G+V   S      T+ + L      + S+  
Sbjct: 62  EEVLEYQAQNIPLDIIYEDDALAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSING 121

Query: 112 -------GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   R+D +T GLL++       +VL         + +       +      + + 
Sbjct: 122 VVRPGIVHRIDKDTSGLLMVAKTDAAHQVLTEELKAKKSLRKYLAIVHGNLPNDRGMIEA 181

Query: 165 IVIQGICYGDMQ------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            + +       Q             T+  + G  + V + L  G+  +I+    +    V
Sbjct: 182 PIGRSEKDRKKQAVTAKGKEAVTRFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 65.2 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 28/245 (11%), Positives = 65/245 (26%), Gaps = 38/245 (15%)

Query: 6   IVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
            V  +    R+ K +        SR +V+  IA   V VN   ++     V   D I + 
Sbjct: 27  TVDADAAKTRIDKYLTENLGEDVSRSQVQLWIADGHVSVNDGPIKS-NYKVSQGDRIVLK 85

Query: 63  -----------DGVPLRK--AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                      + +PL     +   + +      +V         + V   +        
Sbjct: 86  VPEPSAVEIIPEDIPLEIAFEDGDVIVVNKPRGMVVHPAPGHSSGTLVNALMFHCKDLSG 145

Query: 110 SVGR---------------------LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
             G                       D     L     +  + R         +   +  
Sbjct: 146 INGELRPGIVHRIDKDTTGLIMAAKNDKAHASLAAQLKEHSVNRRYLALVHGNISHDQGT 205

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +D  +     +  +   +     T+  + G  + + + L  G+  +I+   ++ 
Sbjct: 206 IDAPIGRDAQDRKLYTVTDRNSKHAVTHFTVVERFGDYSLLELKLETGRTHQIRVHMKYI 265

Query: 209 NWKVN 213
              + 
Sbjct: 266 GHPLV 270


>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 = 65.2 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 34/246 (13%), Positives = 68/246 (27%), Gaps = 42/246 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           + QEN    R+   ++  G     SR  ++R+I + +V VN  L  +A   +   D + V
Sbjct: 8   VDQENAKS-RLDVFLS--GQCHDLSRSYIQRLIEEGQVTVND-LPTKANYKLRVGDRVAV 63

Query: 63  D----------GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           +            P+       +   + +      +V         + V   L       
Sbjct: 64  EVPPAEELQVVPEPIPLDIYYEDNDVIVVNKPRGMVVHPAEGNTSGTLVNALLYHCRDLS 123

Query: 109 ISVGRLDIN---------------------TEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
              G L                           L     D  + R         +R    
Sbjct: 124 GINGVLRPGIVHRLDKDTSGLIMVAKNDLAHNSLAQQLKDRTVTRRYRALVHNNIREEVG 183

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
             +  + +D  +  +  +V +          +  + G    V   L  G+  +I+    +
Sbjct: 184 TVNAPIGRDPRDRQRMAVVERNSKPAVTHYRVLERFGQYTLVECRLETGRTHQIRVHMAY 243

Query: 208 FNWKVN 213
               V 
Sbjct: 244 IGHPVV 249


>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 = 65.2 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 31/248 (12%), Positives = 69/248 (27%), Gaps = 41/248 (16%)

Query: 4   KNIVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K +VQE+   +R+   ++  G+    SR  +++ I +  VKVN  +++     +   D I
Sbjct: 6   KILVQEDDAKKRLDVFLS--GVINDLSRSYIQKGIEEGWVKVNERIVK-PHYKLKKGDVI 62

Query: 61  EVD---GVPLRKAERTR-----------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
             D     PL                  + +      +V         + V   L     
Sbjct: 63  VADIPSPKPLSLEPENIPLDIIHEDRDIIVVNKPRGMVVYPAPGNYSGTLVNALLYHTKD 122

Query: 107 RVISVGRLDI-------NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
                G +              +++     +A        +   V +            +
Sbjct: 123 LSGINGVMRPGIVHRLDKDTSGVIVVAKNDMAHRELAMQFKNKLVKKTYLAVVWGNIPED 182

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSN--------------AWVTVGLREGKNREIKKVF 205
                  I       +++ +  + G                 ++ V +  G+  +I+   
Sbjct: 183 RATIEAPIGRHPAKRVEMAVTAKNGKEAITHFKVLERFEDFTFIEVNIETGRTHQIRVHM 242

Query: 206 EFFNWKVN 213
            F    V 
Sbjct: 243 SFIGHPVV 250


>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 = 65.2 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 27/245 (11%), Positives = 65/245 (26%), Gaps = 41/245 (16%)

Query: 7   VQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + +     R+ K ++     A+R +V++ I    V VNG    +A   +   D I+V   
Sbjct: 24  IDKGQKNIRIDKFLSEKLANATRNKVQQAIDAGSVLVNGKP-TKANYKIKPMDDIKVMME 82

Query: 66  P---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                           +   ++  L +      +V         +     +         
Sbjct: 83  KPPRDTEVYPEKIELDIIYEDKYLLIVNKPAGMVVHPAHGNWSGTLANALVYHFQDLPEM 142

Query: 111 ---------VGRLDINTEGLLLLTNDGGLARVLELPSTQW---------------LRVYR 146
                    V R+D +T GLL++         L                           
Sbjct: 143 KGNEGRPGLVHRIDKDTSGLLVIAKQEEAMTHLASQFFHHTIDRTYIALVWGEPKEDEGT 202

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
           +  +         ++      +   +      +  +    + +   L  G+  +I+   +
Sbjct: 203 IEGNVGRSAKNRKVMDVFPDGEQGKHAITHWKVLKRLRYVSLIQCNLETGRTHQIRAHMK 262

Query: 207 FFNWK 211
           +    
Sbjct: 263 YIGHP 267


>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 = 65.2 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 32/239 (13%), Positives = 66/239 (27%), Gaps = 38/239 (15%)

Query: 13  PQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP----- 66
             R+ KV++      SR ++++ I   +V VN +++    V V   D I           
Sbjct: 12  GIRLDKVLSSLLENVSRNQIQKAIKDSQVLVNDVIISDPDVLVKENDIILFSFKEPEELK 71

Query: 67  ---------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-----RVISVG 112
                    +   +   + +       V   +     + V   L    +          G
Sbjct: 72  IAAANVALDIIYEDDDLIVINKAAGMTVHPGAGHHDDTLVNALLHHTKNLSDIGSSERPG 131

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
            +    +    L       +   L + Q  +   +R +  +    +N L+  I       
Sbjct: 132 IVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRKYKVLVWGVINPLEGIIKNNIGRS 191

Query: 173 GDMQVTL------------------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +  +                     KGS + V   L  G+  +I+         V 
Sbjct: 192 RSDRQKMTILKYGGKEAVTHYKTLELFYKGSISMVECKLSTGRTHQIRVQLSHLKHSVV 250


>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 = 65.2 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 28/242 (11%), Positives = 69/242 (28%), Gaps = 36/242 (14%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           V       R+ K+ A   G  SR  ++  I + ++ VNG +++     V   D + ++  
Sbjct: 48  VSTEQIGIRLDKLCADIFGGFSRANLKNFIDEGQLTVNGKVVK-PKYAVKVGDILTLEAV 106

Query: 64  ------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                        + +   +   + +      +V   +     + V   L     +    
Sbjct: 107 HESHSEDLPENIDIDIIYEDEAVIIINKPAGMVVHPGAGNRTGTLVNALLYHFPKQAHLP 166

Query: 112 -----GRLDINTEGLLLLT---------------NDGGLARVLELPSTQWLRVYRVRFHG 151
                 R+D +T GLL++                                  +   +   
Sbjct: 167 RAGLVHRIDKDTTGLLVIARTKSAQLSLIDQLKDKSVYRHYQCIALGAVHEVLRHAQIDA 226

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + +   +  K  +   G       V         + + + L+ G+  +I+    +    
Sbjct: 227 PIGRHSTHRTKMAVKQTGKPALTHIVNAKYLHERYSLLDIHLKTGRTHQIRVHLSYVGHP 286

Query: 212 VN 213
           + 
Sbjct: 287 LV 288


>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 = 65.2 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 30/239 (12%), Positives = 66/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I + +V VNG  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILEDKVTVNGKTINKPKEKVLGGELVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-- 108
                           +   +   L +      +V   +     + +   L      +  
Sbjct: 70  QIEEDARWAPQEIPLDIVYEDNDILVINKPRGLVVHPGAGNPDGTVLNALLYYYPEIMDV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                V RLD +T GL+++         L                   +           
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNMTAGGRVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHINHPLV 248


>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 = 65.2 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 77/250 (30%), Gaps = 39/250 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M++  +V E     R+   I+ R    SR  +++++    V VNG L++     + S+D 
Sbjct: 5   MEEIKLVSEES-GVRIDAWISSRLKEYSRSYIQKLLNDGHVLVNGSLVKS-NYKIKSSDE 62

Query: 60  IEVD--------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I V                +P+   +   L +      +V   +     + V   +    
Sbjct: 63  ITVQIPEPEVLDIVPENIEIPVLYEDEHVLVVNKPKGMVVHPAAGNYSGTLVNALMDYCG 122

Query: 106 SRVISVG----------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
             + S+                       + +   E L L   D  + RV        +R
Sbjct: 123 DSLSSINGVIRPGIVHRIDKDTSGVLVVAKSNEAHEKLSLKLKDHDINRVYVALVHGIIR 182

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
               +    + +  ++  K  +             +  +      V V L  G+  +I+ 
Sbjct: 183 EESGKIDAPIGRHPVDRKKMAVNTNNGRRAVTYFKVLERFKDATLVEVKLETGRTHQIRV 242

Query: 204 VFEFFNWKVN 213
              +  + + 
Sbjct: 243 HMSYIGYPII 252


>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 = 65.2 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 30/239 (12%), Positives = 66/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I + RV V+G  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILEDRVTVDGKTINKPKEKVLGGELVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-- 108
                           +   +   L +      +V   +     + +   L      +  
Sbjct: 70  QIEEDARWAPQDIPLDIVYEDNDILVINKPRGLVVHPGAGNPDGTILNALLYYYPEIMDV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                V RLD +T GL+++         L                   +           
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNMTAGGRVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHINHPLV 248


>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 = 65.2 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 26/239 (10%), Positives = 62/239 (25%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I   RV+VNG  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKDWILDNRVQVNGKTINKPKEKVLGGETVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  QIEEDARWEPQDIALNIVYEDSDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPEIADV 129

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--- 156
                  R+       +     +        A      + ++  V           +   
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQARDITREYEAVAIGTMTAGGTVEEPI 189

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 SRHSTKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHINHPLV 248


>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 = 65.2 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 32/232 (13%), Positives = 64/232 (27%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++     SR      I   +V VN  + ++A   V   D +              
Sbjct: 11  RLDKALSDLTELSRSLANEQIKSGQVLVNDQV-KKAKYTVQEGDVVTYHVPEPEVLEYVA 69

Query: 63  DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           + +PL     +     +      +V   +     + V   +  I       G L      
Sbjct: 70  EDIPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 121 LLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            +     G L       +           + LR Y    HG +  D+  +       +  
Sbjct: 130 RIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 171 CYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                          +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 65.2 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 33/234 (14%), Positives = 64/234 (27%), Gaps = 35/234 (14%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
             R+ K ++     SR      I   +V VNG   ++A  +V   D +            
Sbjct: 9   GIRLDKALSDLTDLSRSVANEQIKAGQVLVNGQP-KKAKYSVQVGDVLTYQIPEVEEIDY 67

Query: 63  --DGVPLRK--AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
             + +PL     +     +      +V   +     + V   L  +       G L    
Sbjct: 68  VAEDIPLEIVFQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALLYHVKDLSGINGVLRPGI 127

Query: 119 EGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              +     G L       +           + LR Y    HG +  D+  +       +
Sbjct: 128 VHRIDKDTSGLLMIAKNDDAHTKLAAELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSE 187

Query: 169 GICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                            +  +  + G    V + L  G+  +I+    +    V
Sbjct: 188 KDRKKQAVTAKGKEAVTRFQVLERFGDYTLVELTLETGRTHQIRVHMAYIGHPV 241


>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 = 65.2 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 33/246 (13%), Positives = 63/246 (25%), Gaps = 36/246 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M    I +EN    R+ K +A     SR  +  +I   +V VN    ++A   V + D I
Sbjct: 1   MPIIKITEENKDL-RLDKALANQTEYSRSLLTELIKNDKVFVNNE-AKKAKYKVKTGDRI 58

Query: 61  EVD--------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           E +               + +   +     +      +V   +     + V   +  I  
Sbjct: 59  EFEIPQAEVLDVAAEDLPLEIIYEDSDVAVVNKPQGMVVHPAAGHASGTLVNAIMYHIKD 118

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPST--------------------QWLRVYR 146
                G +       +     G L       +                            
Sbjct: 119 LSSINGVIRPGIVHRIDKDTSGLLMIAKNDKAHESLAAQLKDKTSKRRYLAIVHGELAND 178

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                      L   KK  V+ G         +  +      + + L  G+  +I+    
Sbjct: 179 KGTIEAPIGRNLKDRKKQAVVSGGKPAVTHFEVLERFVGYTLIALRLETGRTHQIRVHMH 238

Query: 207 FFNWKV 212
           +    V
Sbjct: 239 YIGHPV 244


>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 = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 42/240 (17%), Positives = 79/240 (32%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           +    + QR+ K +A     SR +    I Q  V VNG   ++A   V + D I+ +   
Sbjct: 3   INVLTSGQRLDKALADLSPLSRGQANDQIKQGLVLVNGQQ-KKAKYTVQAGDVIQFELPK 61

Query: 64  GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-- 111
              L             E   L + +KP G+V   S      T+ + L      + S+  
Sbjct: 62  EEVLEYQAQDIPLNIIYEDEALAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSING 121

Query: 112 -------GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   R+D +T GLL++       + L         + +       +      + + 
Sbjct: 122 VVRPGIVHRIDKDTSGLLMVAKTDEAHQALAAELKAKKSLRKYLAIVHGNLPNDRGMIEA 181

Query: 165 IVIQGICYGDMQ------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            + +       Q             T+  + G  + V + L  G+  +I+    +    V
Sbjct: 182 PIGRSEKDRKKQAVTAKGKEAVTRFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 32/244 (13%), Positives = 69/244 (28%), Gaps = 41/244 (16%)

Query: 8   QENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
            +   P RV K +      A+R ++++ I    V+VN  +++     V + DHI V    
Sbjct: 27  SDGQEPLRVDKYLMNFIENATRSKIQQSIKDGAVRVNDEVVKS-NYKVKAGDHIRVLFKH 85

Query: 67  ---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                          +   + T + +      +V         + +   +          
Sbjct: 86  PPHENLLVPEDIPLDIVYEDDTLVVVNKPAGMVVHPGHGNYSGTLINALIHHFDNLPNNS 145

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARV-------------LELPSTQWLRVYRVRFHG 151
            +R   V R+D +T GLL++                                       G
Sbjct: 146 SNRPGLVHRIDKDTSGLLVVAKTEHAMSYLSAQFAAKTSEREYVAIVWGNFDEQSGTVEG 205

Query: 152 QVDQDKLNLLKKGIVIQGI--CYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
            + +   N L+  +                ++    G    ++  L  G+  +I+   + 
Sbjct: 206 NIGRHPKNRLQNYVWSGEEAFKGKPAVTHWSVIEGLGYVTMISCKLETGRTHQIRVHMKH 265

Query: 208 FNWK 211
               
Sbjct: 266 IGHT 269


>gi|323127056|gb|ADX24353.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           dysgalactiae subsp. equisimilis ATCC 12394]
          Length = 297

 Score = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 42/240 (17%), Positives = 79/240 (32%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           +    + QR+ K +A     SR +    I Q  V VNG   ++A   V + D I+ +   
Sbjct: 3   INVLTSGQRLDKALADLSPLSRGQANDQIKQGLVLVNGQQ-KKAKYTVQAGDVIQFELPK 61

Query: 64  GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-- 111
              L             E   L + +KP G+V   S      T+ + L      + S+  
Sbjct: 62  EEVLEYQAQDIPLNIIYEDEALAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSING 121

Query: 112 -------GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   R+D +T GLL++       + L         + +       +      + + 
Sbjct: 122 VVRPGIVHRIDKDTSGLLMVAKTDEAHQALAAELKAKKSLRKYLAIVHGNLPNDRGMIEA 181

Query: 165 IVIQGICYGDMQ------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            + +       Q             T+  + G  + V + L  G+  +I+    +    V
Sbjct: 182 PIGRSEKDRKKQAVTAKGKEAVTRFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 35/233 (15%), Positives = 68/233 (29%), Gaps = 35/233 (15%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV-NVMSTDHIEVDGVPLR--- 68
            +R+   +A+  + SR   +R+I    V V+G    R     V + + +EV   P+    
Sbjct: 15  GERLDLFLAQ-PLGSRARAQRLIDAGLVTVDG--AARPKRHKVSAGERVEVTPEPVVDVE 71

Query: 69  ---------KAERTRLWLYHKPIGLVTTHSDPDGRST-------------------VFDN 100
                      E   L +  KP G+V   +  +   T                   +   
Sbjct: 72  PSGDAPFAVAWEDEHLLIVDKPAGVVVHPAPGNRTGTLSQALAGRAAGGEDPSRAGIVHR 131

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
           L    S ++ V + +     L  +     + R                    + +D+   
Sbjct: 132 LDRDTSGLLIVAKTEEAHRELKRMIEARDVTREYVALVEGTPPARSGTIDAPIGRDRRVR 191

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +                L+     +A + V L  G+  +I+   E     V 
Sbjct: 192 TRMSTETDDPRDARTHFRLERALPDSALLRVTLETGRTHQIRVHLEAIGHPVV 244


>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 = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 30/239 (12%), Positives = 66/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I + +V VNG  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILEDKVTVNGKTINKPKEKVLGGELVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-- 108
                           +   +   L +      +V   +     + +   L      +  
Sbjct: 70  QIEEDARWAPQEIPLDIVYEDSDILVINKPRGLVVHPGAGNPDGTVLNALLYYYPEIMDV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                V RLD +T GL+++         L                   +           
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNMTAGGRVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHINHPLV 248


>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 = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 42/240 (17%), Positives = 78/240 (32%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           +    + QR+ K +A     SR +    I Q  V VNG   ++A   V + D I  +   
Sbjct: 3   INVITSGQRLDKALADLSPLSRGQANDQIKQGLVLVNGQQ-KKAKYTVQAGDVICFELPK 61

Query: 64  GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-- 111
              L             E   L + +KP G+V   S      T+ + L      + S+  
Sbjct: 62  EEVLEYQAQNIPLDIIYEDDALAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSING 121

Query: 112 -------GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   R+D +T GLL++       + L         + +       +      + + 
Sbjct: 122 VVRPGIVHRIDKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMIEA 181

Query: 165 IVIQGICYGDMQ------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            + +       Q             T+  + G  + V + L  G+  +I+    +    V
Sbjct: 182 PIGRSEKDRKKQAVTAKGKEAVTRFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 35/240 (14%), Positives = 61/240 (25%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           +    + QR+ K +A     SR +    I Q  V VNG   ++A   V + D I  +   
Sbjct: 3   INVITSGQRLDKALADLSPLSRGQANDQIKQGLVLVNGQQ-KKAKYTVQAGDVICFELPK 61

Query: 64  GVPLRKAERTRLWLY-----------HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
              L    +                      +V   +     + V   +  I       G
Sbjct: 62  EEVLEYQAQNIPLDIIYEDDALAIINKPQGMVVHPSAGHPSETMVNALMYHIKDLSSING 121

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ----------------- 155
            +       +     G L       + Q L                              
Sbjct: 122 VVRPGIVHRIDKDTSGLLMVAKTDAAHQALTEELKAKKSLRKYLAIVHGNLPNDRGMIEA 181

Query: 156 ---DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                    KK  V         + T+  + G  + V + L  G+  +I+    +    V
Sbjct: 182 PIGRSEKDRKKQAVTAKGKEAVTRFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 76/250 (30%), Gaps = 40/250 (16%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V+E+   +R+ + +A A    SR  ++ ++    V V+G ++ + +  V   + + +   
Sbjct: 14  VEEHQAGKRLDQFLAEAYPDFSRSYIKELVEGGYVLVDGQVVYKPSRKVKGGEVVVLCVP 73

Query: 63  ---------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------- 104
                    + +PL     +     +      +V         + V   L          
Sbjct: 74  KVEPLSLPAEDIPLEILYEDDDLAVVVKPCGLVVHPSPGYTSGTLVNALLFRWRDLPTVG 133

Query: 105 -FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR--------------- 148
            + R   V RLD NT G++++       R L     +   +   R               
Sbjct: 134 EWYRPGIVHRLDRNTMGVMVVAKRELAHRRLAEQFEKRKVLKVYRALVKGLVERDEGTLS 193

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                D             +       +V    +  S + + + +  G+  +I+      
Sbjct: 194 MPLARDPRHRKRFTVSEKGRDAITHY-KVLKRYRSLSVSLLEIRIYTGRTHQIRVHMAGI 252

Query: 209 NWKVNRLIRI 218
              V    RI
Sbjct: 253 GHPVLG-DRI 261


>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 = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 34/246 (13%), Positives = 66/246 (26%), Gaps = 38/246 (15%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +V      QR+ K +A      SR  +++++ Q  V++NG  +++ A  V + D I V+ 
Sbjct: 31  VVGAEQHAQRLDKALAELVPEFSRSYLQQLLLQGCVRLNGREVQKPASRVKAGDRIAVEM 90

Query: 65  VP---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
            P               +   +   L ++     +V         + +   L      + 
Sbjct: 91  RPTQQSQAFRPEQWPLDVVYEDEHILVIHKPAGLVVHPAPGNWSGTLLNALLGRDAQAMQ 150

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   RLD +T GL+++         L           +    G             
Sbjct: 151 VPRAGIVHRLDKDTSGLMVVARSRSAMDALVRMIAAREVSRQYVALGWGGWTGAAHRSVH 210

Query: 165 IVI-----------------QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
             I                            L         V   L  G+  +I+     
Sbjct: 211 APIGRDPRNRLRMAVVDLAQHPGKEARTDFDLIDANEEVCLVRCTLHTGRTHQIRVHMAS 270

Query: 208 FNWKVN 213
               + 
Sbjct: 271 IRHPLV 276


>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 = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 33/246 (13%), Positives = 74/246 (30%), Gaps = 39/246 (15%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E    +R+   +A+A    SR  ++R+I +    V G +  + +  V   D + +  
Sbjct: 11  TVSEEQAGERLDTFLAKAYPELSRSYIKRLIEEGFALVEGKV-RKPSYRVKEGDRVTLSV 69

Query: 63  ----------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
                     + +P+     +R  + +      +V         + V   L  I      
Sbjct: 70  PEPEPLEVKPEDIPIEVVYEDRDVVVIVKPCGLVVHPSPGYTSGTLVNALLYHIKDLSSI 129

Query: 107 ----RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
               R   V RLD  T GL+++  +    R L             R   +    + + + 
Sbjct: 130 GGVERPGIVHRLDKETAGLMVVAKNDTSHRNLVEQFASRRTEKLYRALVKGTVKEEHGIL 189

Query: 163 KGIVIQGICY-----------GDMQVTLDTQKGSN----AWVTVGLREGKNREIKKVFEF 207
           +  + +   +              +      +         + V +  G+  +I+     
Sbjct: 190 ELPIGRHPFHRKKFSTSSPRSKPAKSEFWVLERFPGLELTLLKVKIYTGRTHQIRVHLSS 249

Query: 208 FNWKVN 213
               + 
Sbjct: 250 IGHPIV 255


>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 = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 34/249 (13%), Positives = 70/249 (28%), Gaps = 38/249 (15%)

Query: 1   MKDKNIVQE-NFTPQRVSKV-IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M+ ++I  E      R+ KV +      SR E+++ I   +V VN  + E+A   V   D
Sbjct: 1   MEIQSITPELEEKGLRLDKVILNHMPDRSRTEIQKWIKAGQVIVNDNV-EKANYKVEEED 59

Query: 59  HIEV---DGVP-----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            I+V   D              +   +   + +      +V   +     + V   L   
Sbjct: 60  VIQVTLPDPQSTEIRPEDIPLDIIYEDEDVIVVNKPTGMIVHPSAGIYSGTLVNALLYHC 119

Query: 105 FSRVISVG---------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
                  G                     + D     L     +  + R         + 
Sbjct: 120 HDLSAINGITRPGIVHRIDKETSGLLMVAKNDNAHRSLSKQLEEHSVVRRYVALVHGVIN 179

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
               R    + +D  +  K  +  +          +  +      +   L  G+  +I+ 
Sbjct: 180 HNVGRIEAPIGRDSKDRKKMAVTSKNAKDAITNFKVLERYDDMTLIECRLETGRTHQIRV 239

Query: 204 VFEFFNWKV 212
             ++    V
Sbjct: 240 HMQYIGHPV 248


>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 = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 28/248 (11%), Positives = 66/248 (26%), Gaps = 38/248 (15%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +  V      QR+ K +A      SR  ++++I ++RV VNG  +   +  V     + V
Sbjct: 26  ERAVDAEAAGQRLDKWLATVIPTLSRARLQQLIGEKRVSVNGQTIGEGSRRVKPGQTVRV 85

Query: 63  DGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           +  P              +   +   + +      +V         + V   L      +
Sbjct: 86  EEPPPIAATPQPEAIALTVVYEDDDLIVIDKAAGMVVHPGPGNPDHTLVNALLAHCGPSL 145

Query: 109 ISVGRLDIN--------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
             +G                 L++     LA            + R        + +   
Sbjct: 146 SGIGGERRPGIVHRLDKDTSGLMIAAKTDLAHHGLAEQFACHSLTREYLCLVWGRPRPAA 205

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSN---------------AWVTVGLREGKNREIKKVF 205
                 +        ++ + ++ G                 + V   L  G+  +++   
Sbjct: 206 GSIDAPLGRHPTQRKKMAVVSRGGKRALTHYRVVGDVEGIASIVKCTLSTGRTHQVRVHM 265

Query: 206 EFFNWKVN 213
                 + 
Sbjct: 266 AHIGHPLL 273


>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 = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 35/236 (14%), Positives = 75/236 (31%), Gaps = 39/236 (16%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ + ++ A   +R  V+++I +  V VN I + + A  V S D I+V            
Sbjct: 9   RLDRYLSEALSKTRSFVQKIIEEGNVWVNQIQVLKPAYKVKSGDIIKVVIPEPKQLSLVA 68

Query: 63  ---DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG------- 112
              D   L + E   +        +V   +     + V   L     R+ S+        
Sbjct: 69  QEIDIEVLYEDEHLAVI-NKPRGMVVHPGAGNFENTLVNALLHKFSGRLSSINGVIRPGI 127

Query: 113 ---------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                          + D     L        + R+        L+      +  + +  
Sbjct: 128 VHRLDKDTSGLLVVAKTDEAHIKLSEALKSHQIKRIYYAICEGVLKEDSGVINAPIGRHP 187

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +N LK  +V  G         +  +     ++ + L+ G+  +I+    +  + + 
Sbjct: 188 VNRLKMAVVPNGKEA-VTYFEVLERFDKYTFIKLRLKTGRTHQIRVHISYIGYPLL 242


>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 = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 30/260 (11%), Positives = 82/260 (31%), Gaps = 49/260 (18%)

Query: 1   MKDKNI--VQENFTPQRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           M++     +   +  +R+   +A    GI SR  ++++I    VK+NG +++ A   +  
Sbjct: 1   MENIKTCCIDSEYEDERIDSFLAEFEEGI-SRSYIQKLIKDSLVKINGNVIK-ANYRLKE 58

Query: 57  TDHIEVD-GVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
            D +  +   P+                +   + +      +V   +     + V   L 
Sbjct: 59  GDILTYEVPQPVSLEIAAENIPLDILYEDEDIIVINKPKGLVVHPAAGHYSGTLVNALLY 118

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
               R+  +  +        +  N  G+  V +   +      +++ H    + +  +  
Sbjct: 119 HCKDRLSGINGVMRPGIVHRIDMNTTGVLVVCKNDKSHQSIAEQLKVHSITRKYEALVYN 178

Query: 163 KGIVIQGICYGDM--------QVTLDTQKGSNAW---------------------VTVGL 193
                +G     +        ++ ++ + G NA                      +   L
Sbjct: 179 SFKQTEGTVDAPIGRHPVDRKKMAINHKNGKNAVTNYRVLENFNLGYVHNQGYAHIECTL 238

Query: 194 REGKNREIKKVFEFFNWKVN 213
           + G+  +I+      +  + 
Sbjct: 239 KTGRTHQIRVHMASLHHPLL 258


>gi|328907882|gb|EGG27645.1| ribosomal RNA large subunit methyltransferase J
          [Propionibacterium sp. P08]
          Length = 245

 Score = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 18/64 (28%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ + +  AG+A SR    R++ + RV VNGI++ + A+ V ++D++  D         
Sbjct: 1  MRLDQALVEAGLARSRTLATRLVREGRVTVNGIVVTKPAMKVSASDNLVADEEVWVSRAA 60

Query: 73 TRLW 76
           +L 
Sbjct: 61 YKLL 64


>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 = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 47/249 (18%), Positives = 87/249 (34%), Gaps = 43/249 (17%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           + I   N   +R+ K +A+     R ++E++I Q  V++NG + ++A   + S D +EV 
Sbjct: 2   EKITFTNREKERLDKALAKKLQKPRNQIEQLIKQGYVRINGKIEKKAGSKLKSGDLVEVT 61

Query: 63  --------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-- 106
                         D   +   E   + + +KP GLV   +      T+ D L +     
Sbjct: 62  IPEPKVSQPKDVHFDVERI--YEDEDILVLNKPAGLVVHPAPSVKEPTLVDWLKANDISL 119

Query: 107 -------RVISVGRLDINTEGLLLLTNDGGLAR------------VLELPSTQWLRVYRV 147
                  R   V RLD  T GL+++  +    +               L   +      +
Sbjct: 120 STLSGEERHGIVHRLDKETSGLIVIAKNNETHQALSKQLQDKSMGRYYLAIVEPPLKEDL 179

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG---LREGKNREIKKV 204
                + ++  N LK G+V  G         +      N    +    L  G+  +I+  
Sbjct: 180 IIEKPIARNPKNRLKMGVVEGGRYAKSA--FVKLTTSKNNKYELIGAKLFTGRTHQIRVH 237

Query: 205 FEFFNWKVN 213
               N  + 
Sbjct: 238 LASINRHIL 246


>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 = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 29/235 (12%), Positives = 67/235 (28%), Gaps = 36/235 (15%)

Query: 12  TPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
              R+ KV+       SR +++  + ++ V VNG  ++ A   V   D I V        
Sbjct: 11  ESGRIDKVLTNLFSNYSRSQIQLWLKERAVSVNGEPVK-ANYKVKQGDEITVLIPEPETL 69

Query: 63  ----DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
               + +P  +   +     +      +V   +     + V   +  +       G +  
Sbjct: 70  DVVPENIPLTIVYEDEDVAVINKPQGMVVHPSAGHTHGTMVNALMYHVKDLSTINGVIRP 129

Query: 117 NTEGLLLLTNDGGLARVLELPSTQ------------WLRVYRVRFHGQVDQDKLNL---- 160
                +     G L       + +               V  V      ++  +N     
Sbjct: 130 GIVHRIDKDTSGLLMVAKNDQAHESLAKQLKDKTSLRKYVALVHGEIPHEKGTINAPIGR 189

Query: 161 ----LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                K   + +         T+  +      V + L  G+  +I+   ++  + 
Sbjct: 190 SKENRKMQAIREDGKPAVTHFTVLERFEGFTLVELKLETGRTHQIRVHMKYIGYP 244


>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 = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 32/251 (12%), Positives = 71/251 (28%), Gaps = 39/251 (15%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           MK     V       R+ + +A A    SR  ++ +I +  V +NG + + A+  + + D
Sbjct: 1   MKTSEFRVDAAAAGPRLDQFLASAAAGLSRARIQDLIKEGHVTLNGGVAK-ASARLRAGD 59

Query: 59  HIEVDGVPLRKAERTRL--------------WLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            + +   P    E                   +      +V   +     + V   L   
Sbjct: 60  AVTLHEPPPVPTETVAEEIALDVLFEDDDLIVINKPAGLVVHPAAGNWSGTVVNALLHHC 119

Query: 105 F--------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
                     R   V RLD +T G L++  +    + L                      
Sbjct: 120 QTLSGIGGEQRPGIVHRLDKDTSGCLVVAKNDAAHQSLAKQFAGREVTKIYLALAAGKWA 179

Query: 157 KLNLL------KKGIVIQGICYGDMQVTLDTQKGSNAWVTV--------GLREGKNREIK 202
           + + +      +  +  + +           + G    + +         L  G+  +I+
Sbjct: 180 RKSGVIEAPIGRHPVQRKKMTVLPADKGRAAKTGYRVLLELPVGTLVECTLHTGRTHQIR 239

Query: 203 KVFEFFNWKVN 213
              +     + 
Sbjct: 240 VHLKHLGHPIL 250


>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 = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 42/240 (17%), Positives = 78/240 (32%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           +    + QR+ K +A     SR +    I Q  V VNG   ++A   V + D I  +   
Sbjct: 3   INVITSGQRLDKALADLSPLSRGQANDQIKQGLVLVNGQQ-KKAKYTVQAGDVICFELPK 61

Query: 64  GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-- 111
              L             E   L + +KP G+V   S      T+ + L      + S+  
Sbjct: 62  EEVLEYQAQNIPLDIIYEDDTLAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSING 121

Query: 112 -------GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   R+D +T GLL++       + L         + +       +      + + 
Sbjct: 122 VVRPGIVHRIDKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMIEA 181

Query: 165 IVIQGICYGDMQ------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            + +       Q             T+  + G  + V + L  G+  +I+    +    V
Sbjct: 182 PIGRSEKDRKKQAVTAKGKEAVTRFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 27/235 (11%), Positives = 63/235 (26%), Gaps = 35/235 (14%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
            +R+ K +++    SR +++ +I +  +KVN   ++  +  V   D IEV          
Sbjct: 14  GERIDKYLSQKISLSRSQIQDLIDKGLIKVNEKEVKS-SYKVKVGDKIEVIVPPPEETEI 72

Query: 63  --DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
               +P+     +   + +      +V         + V   L  I       G +    
Sbjct: 73  KPQDIPIEIVYEDDDIVIINKPKGMVVHPAHGHYNDTLVNALLYRIKDLSGIGGEIRPGI 132

Query: 119 EGLLLLTNDGGLARVLELPST------------QWLRVYRVRFHGQVDQDKLNLLKKGIV 166
              L     G L       S             +             ++ ++        
Sbjct: 133 VHRLDKDTTGLLIIAKNDVSHQRLSEQLKNRILKRTYWAICEGEIPWEEKRVEAPLGRHP 192

Query: 167 IQ--------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I                   +  +      ++  L  G+  +I+       + + 
Sbjct: 193 IDRKRMAIVPYGKLAITNFKVLERFKGYTLISADLETGRTHQIRVHISHLGFPIL 247


>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 = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 32/232 (13%), Positives = 63/232 (27%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP------- 66
           R+ K ++     SR      I   +V VNG + ++A   V   D +      P       
Sbjct: 11  RLDKALSDLSELSRSLANEQIKSGQVLVNGQV-KKAKYTVQEGDVVTYHVPEPEVLEYVA 69

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 +   +     +      +V   +     + V   +  I       G L      
Sbjct: 70  EDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 121 LLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            +     G L       +           + LR Y    HG +  D+  +       +  
Sbjct: 130 RIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEASIGRSEKD 189

Query: 171 CYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                          +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHSV 241


>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 = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 24/237 (10%), Positives = 61/237 (25%), Gaps = 31/237 (13%)

Query: 8   QENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           Q++   QR+ + +A      SR  ++  I Q RV ++G +       V++   + VD   
Sbjct: 12  QDHQFGQRLDQALAELFPDYSRTRIKEWILQDRVTLDGQVANTPREKVLAGQQVHVDVEL 71

Query: 67  --------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------- 105
                         +   +   L +      +V   +     + +   L           
Sbjct: 72  EDDTRWDAQDIALNIVYEDEHILVIDKPAGLVVHPGAGTPDGTILNALLHRYPDIAEVPR 131

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD----- 156
                R+       +     +        A      + ++  +           D     
Sbjct: 132 AGIVHRLDKDTTGLMVVAKTVPAQTHLVEALQARQITREYEAIAIGHMTAGGTVDAPIGR 191

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                    V+           +  +   +  + + L  G+  +I+         + 
Sbjct: 192 HPTQRTHMAVVPNGRPSVTHYRVHEKFRGHTRLRLRLETGRTHQIRVHMSHIKHPLV 248


>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 = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 34/248 (13%), Positives = 67/248 (27%), Gaps = 39/248 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           MK   +V E    +R+ K I +  +G+ SR  ++ +++   + VN    +  ++ + + D
Sbjct: 1   MKTFKLVAETA-GERLDKYITQKESGL-SRSFIQELVSSGHILVNNQSAK-PSLRLKTGD 57

Query: 59  HIEVDGVPLRKAERTR--------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            I ++  P   +E                 L +   P   V         + V   L   
Sbjct: 58  TITIEIPPETPSELKAEDIPLEIIFQDKDLLLINKPPGLTVHPAPGHPDHTLVNGVLALE 117

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------- 155
                    L       L     G L       +   L         +            
Sbjct: 118 PEMEDFDDPLRPGIVHRLDKDTSGLLLVAKNRQALANLSAQFKERTIRKYYLALVKGELR 177

Query: 156 -----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                            +K  V+    +      +       + + V L  G+  +I+  
Sbjct: 178 PAEGFIEAPLGRDPQNRQKIAVVSDGRHARTGYKVLRYIQGYSLLEVKLETGRTHQIRVH 237

Query: 205 FEFFNWKV 212
           F      V
Sbjct: 238 FAAIGHPV 245


>gi|329297086|ref|ZP_08254422.1| RluA family pseudouridine synthase [Plautia stali symbiont]
          Length = 326

 Score = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 30/239 (12%), Positives = 66/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V +    QR+ + +A      SR  ++  I ++RV VNG ++++    V+  + + +D 
Sbjct: 10  TVSKAQLGQRLDQTLAELFPDYSRSRIKEWILERRVSVNGTIIDKPKEKVLGGERVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  EIEEEQRWEAQNIPLDIVYEDDHILVINKPRDLVVHPGAGNPDGTVLNVLLYHYPAIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L                               
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTHLVETLQLREITREYEAVAIGTMTAGGTVNEPM 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+         + 
Sbjct: 190 ARHSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMAHIKHPLV 248


>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 = 64.8 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 34/240 (14%), Positives = 75/240 (31%), Gaps = 34/240 (14%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           I+ E    +R+  V+++     SR  ++ ++   R+ V+G   E+ +  V   + + VD 
Sbjct: 11  ILPEEQAGERLDTVLSQLLPETSRSRIQALLRDGRILVDG-TPEKPSARVRGGEQVMVDW 69

Query: 65  VPLRK--------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI- 109
             +                 +   L L+     L    +     + V   L  +      
Sbjct: 70  PQIEPSNWLAEGLPLHILHEDADILVLHKPAGQLTHPGAGHADGTLVNGVLAHVPENAYL 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR------------VRFHGQV 153
                V RLD +T GLL++       + L                         R    +
Sbjct: 130 PRGGIVHRLDKDTTGLLVVAKTEMARQSLIDQLGDHTMHREYLALVTGAMTGGGRVDAPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +   + L+  +   G         L  +   ++++ + L  G+  +I+         + 
Sbjct: 190 GRHAQDRLRMTVRDDGRPAQT-DYRLVERFPRHSYLRLRLATGRTHQIRVHMTHIGHPLV 248


>gi|291519437|emb|CBK74658.1| ribosomal large subunit pseudouridine synthase D [Butyrivibrio
           fibrisolvens 16/4]
          Length = 305

 Score = 64.4 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 29/245 (11%), Positives = 66/245 (26%), Gaps = 39/245 (15%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           I + +    R+ K +A A    SR   ++ I    V VNG  ++         D I V  
Sbjct: 8   IEEPSDEGIRIDKYLAAALPEKSRSYYQKAIDNGFVLVNGKQIKS-KYQTKLGDEIIVSI 66

Query: 65  VPLR--------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
            P++                +   + +      +V         + V   +      +  
Sbjct: 67  EPVKEIDILPEDIPIDILYEDSDVIVVNKPKGMVVHPAPGHYSGTLVNALMYHCKDSLSG 126

Query: 111 VG----------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
           +                       + D     +        + R+ +       +     
Sbjct: 127 INGEIRPGIVHRIDMNTTGSLLVCKNDKAHNDIAAQIKVHSVNRIYKGIVVGNFKEEEGT 186

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
            +  + ++  +  KK  V+          T+  Q    ++V   L  G+  +I+      
Sbjct: 187 INANIGRNPKDR-KKMAVVSDGREAITHYTVLEQYKGFSYVQFKLETGRTHQIRVHMAHI 245

Query: 209 NWKVN 213
              + 
Sbjct: 246 GHPLL 250


>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 = 64.4 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 66/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I + RV V+G  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILEDRVTVDGKTINKPKEKVLGGELVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  QIEEDARWAPQEIPLDIVYEDSDILVINKPRGLVVHPGAGNPDGTVLNALLYYYPEIVDV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L                   +           
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNMTAGGRVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHINHPLV 248


>gi|269926072|ref|YP_003322695.1| hemolysin A [Thermobaculum terrenum ATCC BAA-798]
 gi|269789732|gb|ACZ41873.1| hemolysin A [Thermobaculum terrenum ATCC BAA-798]
          Length = 277

 Score = 64.4 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 1/55 (1%)

Query: 9  ENFTPQRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           N    R+ K++   G+AS RE  + +I+   V VNG     +   V     + V
Sbjct: 5  SNQDSIRLDKLMVELGLASSREKAQALISSGLVTVNGEKARSSDQRVRRGTKVIV 59


>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 = 64.4 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 28/238 (11%), Positives = 72/238 (30%), Gaps = 31/238 (13%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T  R+ + +A      SR  ++  I    V V+G+ +++    V+ +  IE+
Sbjct: 8   KSEITATQTGLRLDQALAELFPDYSRTRIKEWILSGAVYVDGVKVDKPREKVLESQQIEI 67

Query: 63  D--------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           +               + +   +   + +  +   +V   +     + +   L    +  
Sbjct: 68  EATFEEEVKAKAQAIDLNIVYEDDHIIIVNKQAGLVVHPGAGNADGTLMNALLHHCPAIE 127

Query: 109 ISV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------- 155
           +        RLD +T GL+++         L         V                   
Sbjct: 128 MVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREIVREYEAIVLGTMTAGGTVDE 187

Query: 156 ---DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                     +  V  G         +  +  ++  + + L  G+  +I+   ++   
Sbjct: 188 PIERHPTKRTQMSVQHGGRPSVTHYRVSEKFRAHTRLRLRLESGRTHQIRVHMDYIGH 245


>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 = 64.4 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 29/250 (11%), Positives = 63/250 (25%), Gaps = 38/250 (15%)

Query: 1   MKDKNIVQENFT--PQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           MK      EN     QR+ K++       SR +++ +I +  V VN  +++     V   
Sbjct: 1   MKTHEFKIENQELVGQRIDKLLPEFNNEWSRSQIQDLIKEDLVTVNEKVIKS-NYKVKLN 59

Query: 58  DHIEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           D I V                  +   +     +Y     +V         + V   +  
Sbjct: 60  DLIIVTEKEVVEADIQPENLNLDIYYEDEDVAIVYKPKGMVVHPSPGHYSGTLVNGLMYQ 119

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------- 155
           I       G +       +     G L       + + L    +    +           
Sbjct: 120 IKDLSGINGEIRPGIVHRIDKDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYTALVHGNI 179

Query: 156 ------------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                             +   V+           +         +   L  G+  +I+ 
Sbjct: 180 PHDYGTIDAPIGRNEKDRQSMDVVDNGKEAVTHFNVLEHFNDYTLIECQLETGRTHQIRV 239

Query: 204 VFEFFNWKVN 213
             ++  + + 
Sbjct: 240 HMKYIGFPLV 249


>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 = 64.4 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 35/251 (13%), Positives = 68/251 (27%), Gaps = 40/251 (15%)

Query: 3   DKNIVQENFTPQRVSKVIARAG---IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K  +    T  R+ K++         SR  ++++I ++ + VN  ++      V     
Sbjct: 2   NKITLNSLNTILRLDKLLVELLTSYDYSRSYIQKLIKEECISVNNQIITNNNFLVKPNSQ 61

Query: 60  IEV-------DGVPLR---------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           I +       D   ++           +   L +  +    V    +    + V   L S
Sbjct: 62  ITITIKDPILDPNLVKNEDIDLDIVYQDDDLLVINKQNNITVHPSLNNTNNTIVNALLAS 121

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------D 156
                   G L       +     G L       + + L           +         
Sbjct: 122 DVELSSINGELRPGIVHRIDKQTTGLLIVAKNDKTHKLLSEMFKNHQIYKEYLAIVTGVI 181

Query: 157 KLNLLKKGIVIQGICY--GDMQVTLDTQKGSNAWVTVG------------LREGKNREIK 202
           K N       I         M VT    K +     V             ++ G+  +I+
Sbjct: 182 KPNKGLIDAPIGRSQTDRKKMSVTAKNSKQAITTFEVVERFLKNTLVKCQIQTGRTHQIR 241

Query: 203 KVFEFFNWKVN 213
             F + N  V 
Sbjct: 242 VHFNYINHPVL 252


>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 = 64.4 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 39/232 (16%), Positives = 75/232 (32%), Gaps = 35/232 (15%)

Query: 13  PQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------- 62
            +R+ + +A  AG  SR  ++ +I   +V+++G  +   A  V +   IE+         
Sbjct: 32  GERLDRWLATLAGEFSRNHLQTLIEGGQVRIDGQTVTARARRVSAGQQIEITLLPTPESQ 91

Query: 63  --DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRST-------------------VF 98
                P+      E   L +  KP GLV   +  +   T                   + 
Sbjct: 92  AFRPEPVALPVVFEDAHLLVIDKPAGLVVHPAPGNWSGTVLNGLLAHHAGAAALPRAGIV 151

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
             L    S ++ V +       L+       + R         LR         + +D +
Sbjct: 152 HRLDKDTSGLMVVAKTLPAMTSLVRAIAAREVHREYLALVHGVLRQAVFSVDAPIGRDPV 211

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           + + K  V+ G       V L   + + + V   L  G+  +I+        
Sbjct: 212 SRI-KMAVLAGGRTARTDVELIAARDAVSAVRCTLHTGRTHQIRVHMASRGH 262


>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 = 64.4 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 29/236 (12%), Positives = 69/236 (29%), Gaps = 32/236 (13%)

Query: 10  NFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVP 66
                R+ K++       SR  +++ I    +KVN I   +    ++  D I   ++   
Sbjct: 15  KEKSIRLDKILVKHLNSFSRSSIKKWILSGFIKVNNITANKPKKKILFKDRISLIINKKS 74

Query: 67  -------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-- 111
                        +   +   L +      +V         + +   +      ++    
Sbjct: 75  NFIKIKKENIFLNIIFEDSEILIINKPTNFVVHLGYGNTSGTLLNALIFHYPDNLLIPRA 134

Query: 112 ---GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
               RLD NT G+L++         L     +   +           +    ++K I   
Sbjct: 135 GIVHRLDRNTTGILVVAKTISTYYFLINLFKKRKIIKEYDVIVIGRIEVDGKIEKPIKRD 194

Query: 169 -----------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      G        ++ T   ++ ++ + L+ G+  +I+         V 
Sbjct: 195 IYNRTKMTVGIGGKQAITYYSVITIFKNHTYLRIQLKTGRMHQIRVHLSSIFHPVL 250


>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 = 64.4 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 66/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  MVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 64.4 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 27/250 (10%), Positives = 74/250 (29%), Gaps = 38/250 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M +  IV E     R+ + ++      SR  +++++    + +N   ++ A   V  +D 
Sbjct: 1   MNNLFIVDEELFDIRIDRYLSELLPDVSRSFIQKLLKDNEILLNDKPVK-ANYKVQPSDK 59

Query: 60  IEVD-GVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I ++   P+                +   L +      +V         + V   +    
Sbjct: 60  ININIPKPVEANIVAENIPLDIIYEDDDFLIVNKPKDMVVHPAPGHYTGTLVNGLMYHCK 119

Query: 106 SRVISVGRL----------DINTEGLLLLTNDGGLARVLELPSTQWLRVYRV-------- 147
           + + ++  +             T  L++  ND     + E      +    V        
Sbjct: 120 NHLSNINGVLRPGIVHRIDKDTTGALIICKNDYSHNFIAEQLKVHSITRKYVGIVQGVVK 179

Query: 148 ----RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                 +  + +  +N  +  I  +          +  +     ++   L  G+  +I+ 
Sbjct: 180 DESGTINAPIGRHPVNRKEMAINHKNGKEAVTHYKVLKRFDKYTFMEFQLETGRTHQIRV 239

Query: 204 VFEFFNWKVN 213
                +  + 
Sbjct: 240 HMASIHHPLL 249


>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 = 64.4 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 28/246 (11%), Positives = 67/246 (27%), Gaps = 36/246 (14%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK +  I++E    +R+ K +A     SR  ++ M+    + V+G + +     V   D 
Sbjct: 1   MKSETLIIEEKNARERIDKAVAELTGKSRSAIQIMLKNGDITVSGEIAK-PNYKVQVGDE 59

Query: 60  IEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I ++                 +   ++  L +      +V   +     + V   L    
Sbjct: 60  IHLEVREPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASSTLVNALLFHCK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                 G++       +     G L       + + L           +           
Sbjct: 120 DLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVH 179

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           +K  V++          +  +      +   L  G+  +I+   
Sbjct: 180 QKGTIEAPIGRAKEDRQKMAVVRDGKEARTHFEVIERLEGYTLINCKLDTGRTHQIRVHL 239

Query: 206 EFFNWK 211
           ++    
Sbjct: 240 KYIGHP 245


>gi|288560866|ref|YP_003424352.1| rRNA methylase [Methanobrevibacter ruminantium M1]
 gi|288543576|gb|ADC47460.1| rRNA methylase [Methanobrevibacter ruminantium M1]
          Length = 264

 Score = 64.4 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 2/58 (3%)

Query: 14 QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-VDGVPLRK 69
          +R+ K +     IASR + + MI  + VKVN  ++ +A+  V   D +E ++   LR 
Sbjct: 3  ERLDKYLVNNNLIASRTKSKEMIKSKNVKVNDKIITKASYTVRDGDKVEIINDESLRY 60


>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 = 64.4 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 35/240 (14%), Positives = 60/240 (25%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           +    + QR+ K +A     SR +    I Q  V VNG   ++A   V + D I  +   
Sbjct: 3   INVITSGQRLDKALADLSPLSRGQANDQIKQGLVLVNGQQ-KKAKYTVQAGDVICFELPK 61

Query: 64  GVPLRKAERTRLWLY-----------HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
              L    +                      +V         + V   +  I       G
Sbjct: 62  EEVLEYQAQNIPLDIIYEDDTLAIITKPQGMVVHPSGGHPSGTMVNALMYHIKDLSSING 121

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ----------------- 155
            +       +     G L       + Q L                              
Sbjct: 122 VVRPGIVHRIDKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMIEA 181

Query: 156 ---DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                    KK  V         + T+  + G  + V + L  G+  +I+    +    V
Sbjct: 182 PIGRSEKDRKKQAVTAKGKEAVTRFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 64.4 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 33/249 (13%), Positives = 73/249 (29%), Gaps = 33/249 (13%)

Query: 5   NIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           N V+++   QR+ + IA      SR  ++  +   +V+VNG ++ +    VM  + I + 
Sbjct: 9   NTVKDSQLGQRLDQAIAELFADFSRSRLKEWLLDGKVQVNGEVVTKPRTKVMGGEEITLQ 68

Query: 63  ----DGVPLRKAERT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
               D       +            + +      +V   +     + +   L        
Sbjct: 69  AELEDEERWEAQDIPLDIVFEDDDIIVINKPRDFVVHPGAGTPDGTVLNALLHHYPDIAE 128

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   RLD +T GL+++         L     +                    + + 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRMTAGGKVDQP 188

Query: 165 IVIQGIC---------YGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I                        +  +   +  + + L  G+  +I+    +    + 
Sbjct: 189 IGRHSTKRTLMAVAPMGKPAVTHYRVAERFREHTRIRLRLETGRTHQIRVHMSYLQHPL- 247

Query: 214 RLIRISYGP 222
            L  I+YG 
Sbjct: 248 -LGDIAYGG 255


>gi|325295697|ref|YP_004282211.1| hemolysin A [Desulfurobacterium thermolithotrophum DSM 11699]
 gi|325066145|gb|ADY74152.1| hemolysin A [Desulfurobacterium thermolithotrophum DSM 11699]
          Length = 265

 Score = 64.4 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 1/60 (1%)

Query: 11 FTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+ K++   G + SR   + +I   +V VNG ++++A  +V+    IE+ G  +  
Sbjct: 2  SKKERLDKLLVEKGLVKSRERAKALIMAGKVLVNGQVVDKAGASVLPDAVIEIKGDDIPY 61


>gi|325496332|gb|EGC94191.1| 23S rRNA pseudouridine synthase D [Escherichia fergusonii ECD227]
          Length = 326

 Score = 64.4 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 66/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  MVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLYYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 64.4 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 32/249 (12%), Positives = 68/249 (27%), Gaps = 42/249 (16%)

Query: 4   KNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           + +V     P R+ K +      +SR  ++       + VNG  ++     V  +D + +
Sbjct: 27  RTVVDSGQMPVRIDKYLFEKMQHSSRNRIQNAADAGFIHVNGKPVKS-NYKVRPSDVVTL 85

Query: 63  ------DGVPLRKAERTRLWLY---------HKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                     +   E     +Y              +V   +     + V      +   
Sbjct: 86  MLDRPQHDTTIEPEEMPLEVVYEDNDLMVINKPAGLVVHPGAGNFHGTLVNALAWYLKDL 145

Query: 108 VISV---------GRLDINTEGLLLLTNDGG-------------LARVLELPSTQWLRVY 145
                         R+D +T GLLL+                    R             
Sbjct: 146 DTYDPNDPEVGLVHRIDKDTSGLLLIAKTPEAKSKLGVQFLNKTTHRSYVALVWGNFTDE 205

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQG-ICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIK 202
             R  G + +D  + L+  ++               +  + G   W+   L  G+  +I+
Sbjct: 206 EGRIEGNIARDPKDRLRMTVLPSDSEMGKPAVTHYKVLERFGYTTWIECVLETGRTHQIR 265

Query: 203 KVFEFFNWK 211
              ++    
Sbjct: 266 AHMKYIGHP 274


>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 = 64.4 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 30/232 (12%), Positives = 61/232 (26%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD----------- 63
           R+ K +A     SR +    I ++ V VNG  ++ A   V   D +  +           
Sbjct: 11  RLDKALADLTELSRSQANDEIKKETVLVNGKAVK-AKYAVKVGDVVTYEVPEEEVLEYTA 69

Query: 64  -GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
             +PL     +     +      +V         + V   +  I       G +      
Sbjct: 70  ENIPLDIIYEDEDVAVVNKPQGMVVHPSVGHTSGTLVNALMYHIKDLSSINGVIRPGIVH 129

Query: 121 L---------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI- 170
                     ++  ND     +      +      V        +   +++  I      
Sbjct: 130 RIDKDTSGLLMIAKNDAAHNALAAELKDKKSLRKYVAIVHGNIPNDRGVIEAPIGRSDKD 189

Query: 171 --------CYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                             +  + GS   V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTHFKVLERFGSYTLVELTLETGRTHQIRVHMAYIGHPV 241


>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 = 64.4 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 30/242 (12%), Positives = 71/242 (29%), Gaps = 33/242 (13%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K K+ +    T QR+ + +A      SR  ++  I    V ++G + ++    V+    
Sbjct: 10  IKLKSEITSIQTGQRLDQTLADLFPDYSRTRIKEWILSGAVSIDGNVSDKPRTKVLEGQE 69

Query: 60  IEV--------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I V                + +   +   L +  +   +V   +     + +   L    
Sbjct: 70  IIVLATLEEETSAKAEAIDLDIVYEDDHILVINKQAGLVVHPGAGNQDGTLMNALLHHCP 129

Query: 106 SRVISV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR------------VR 148
              +        RLD +T GL+++         L                          
Sbjct: 130 GIELVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVTALQAREITREYEAIVQGGIIAGGT 189

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               +D+         +V  G         +  +  ++  + + L  G+  +I+    + 
Sbjct: 190 VDEPIDRHPTKRTHMAVVHNGKPAMT-HYRVAEKFRAHTRLRLRLESGRTHQIRVHMAYI 248

Query: 209 NW 210
             
Sbjct: 249 GH 250


>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 = 64.4 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 30/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I   RV V+G  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILDDRVTVDGKKINKPKEKVLGGELVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-- 108
                           +   +   L +      +V   +     + +   L      +  
Sbjct: 70  QIEEDARWAPQDIPLDIVYEDNDILVINKPRGLVVHPGAGNPDGTVLNALLHYYPKIMDV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                V RLD +T GL+++         L                   +           
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNMTAGGRVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHINHPLV 248


>gi|51892979|ref|YP_075670.1| putative rRNA methylase [Symbiobacterium thermophilum IAM 14863]
 gi|51856668|dbj|BAD40826.1| putative rRNA methylase [Symbiobacterium thermophilum IAM 14863]
          Length = 257

 Score = 64.4 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 13 PQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +R+   +   G   SR   +  IA   V+VNG ++ + A  V   D IEV G P+  
Sbjct: 3  GERLDVALVSRGHFPSRERAQEAIAAGMVRVNGRVITKPARKVDPGDAIEVTGDPIGY 60


>gi|317122003|ref|YP_004102006.1| hemolysin A [Thermaerobacter marianensis DSM 12885]
 gi|315591983|gb|ADU51279.1| hemolysin A [Thermaerobacter marianensis DSM 12885]
          Length = 301

 Score = 64.4 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 1/59 (1%)

Query: 12 TPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             R+  ++   G   SR      I   RV+V+G ++++A   V     IEV G P+  
Sbjct: 4  KGTRLDVLLVERGWFDSRSRARAAILAGRVRVDGRVVDKAGATVDPGAQIEVAGDPIPY 62


>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 = 64.4 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 24/237 (10%), Positives = 61/237 (25%), Gaps = 31/237 (13%)

Query: 8   QENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           Q++   QR+ + +A      SR  ++  I Q RV ++G +       V++   + VD   
Sbjct: 12  QDHQFGQRLDQALAELFPDYSRTRIKEWILQDRVTLDGQVANTPREKVLAGQKVHVDVEL 71

Query: 67  --------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------- 105
                         +   +   L +      +V   +     + +   L           
Sbjct: 72  ADDTRWDAQNIELNIVYEDEHILVIDKPAGLVVHPGAGTPDGTILNALLHRYPAIAEVPR 131

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD----- 156
                R+       +     +        A      + ++  +           D     
Sbjct: 132 AGIVHRLDKDTTGLMVVAKTIPAQTHLVEALQARQITREYEAIAIGHMTAGGTVDAPIGR 191

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                    V+           +  +   +  + + L  G+  +I+         + 
Sbjct: 192 HPTQRTHMAVVPNGRESVTHYRVHEKFRGHTRLRLRLETGRTHQIRVHMAHIKHPLV 248


>gi|228470101|ref|ZP_04055010.1| S4 domain protein [Porphyromonas uenonis 60-3]
 gi|228308239|gb|EEK17094.1| S4 domain protein [Porphyromonas uenonis 60-3]
          Length = 153

 Score = 64.4 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 23/61 (37%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
          R++K+++ AGI SRREVE+ I   RV +NG   E   + V   D + +DG  L   +  R
Sbjct: 4  RINKLLSDAGIGSRREVEKYIVAGRVMLNGERAELTDIVV-EDDIVTLDGEELPVNDILR 62

Query: 75 L 75
           
Sbjct: 63 E 63


>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 = 64.4 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 31/247 (12%), Positives = 66/247 (26%), Gaps = 42/247 (17%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +N  P R+ K +  R   +SR  +++      V VN   ++     V   D I +  
Sbjct: 26  VVDKNQEPLRIDKYMFERLKHSSRNRIQKAADAGFVHVNDQPVKS-NYKVRPLDVITLML 84

Query: 63  ----DGVPLRKAERT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                   +   E            + +      +V   +     + +      +     
Sbjct: 85  DAPQHDSTIEAEEIPLNIVYEDTEVMVVNKPAGMVVHPGAGNFHGTLINAVAWHLKDLPT 144

Query: 110 SV---------GRLDINTEGLLLLTNDGG-------------LARVLELPSTQWLRVYRV 147
                       R+D +T GLL++                    R               
Sbjct: 145 FDANDPAVGLVHRIDKDTSGLLVIAKTPDAKTKLGLQFFNKTTHRSYHALVWGNFNEEEG 204

Query: 148 RFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
           R  G + +D  + L+  +                +  + G    +   L  G+  +I+  
Sbjct: 205 RIEGNIARDPKDRLRMCVFPPDSAVGKTAITHYRVLERFGYVTLIECILETGRTHQIRAH 264

Query: 205 FEFFNWK 211
            +     
Sbjct: 265 MKHIGHP 271


>gi|327470139|gb|EGF15603.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK330]
          Length = 298

 Score = 64.0 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 35/240 (14%), Positives = 67/240 (27%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           ++ +   QR+ K +A     SR      I    + VNG   ++A   V   D I      
Sbjct: 5   IESSVAGQRLDKAVAELTDLSRSLANEQIKDGLILVNGQ-AKKAKYAVKEGDVISYELPE 63

Query: 63  --------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
                   + +PL     +     +      +V   +     + V   +  I       G
Sbjct: 64  SEVVEYVAEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGING 123

Query: 113 RLDINTEGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLK 162
            L       +     G L       +           + LR Y    HG +  D+  +  
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 163 KGIVIQGICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                +                 +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 184 PIGRSEKDRKKQAVTAKGKPALTRFQVLERFGDFSLVELQLETGRTHQIRVHMAYIGHPV 243


>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 = 64.0 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 25/239 (10%), Positives = 61/239 (25%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--- 156
                  R+       +     +        +      + ++  V           D   
Sbjct: 130 PRAGIVHRLDKDTTGLMAVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>gi|268607871|ref|ZP_06141602.1| pseudouridine synthase [Ruminococcus flavefaciens FD-1]
          Length = 315

 Score = 64.0 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 31/258 (12%), Positives = 72/258 (27%), Gaps = 49/258 (18%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K ++ +N + QRV K I++A     +  + R+I ++ +KVNG      +  +M+ D + V
Sbjct: 3   KFVINDNDSGQRVDKFISKALPDLPKSMMYRLIRKKDIKVNGKRC-EISTKLMTDDVVTV 61

Query: 63  ---------------------------------------------DGVPLRKAERTRLWL 77
                                                        +G         R+ L
Sbjct: 62  YVKQELSGTKQHDMSFLKADTALDTVYEDENVIIVNKPLGLDSHSNGEHNDDTLINRIKL 121

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           Y           +      +   L    S +++  +       +     DG + ++    
Sbjct: 122 YLYNKNEYQPDEESSFAPALCSRLDRNTSGLVTAVKNAAALREINSAIRDGMVHKIYLCI 181

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLRE 195
           +                ++    + +        Y  ++    +       + V V L  
Sbjct: 182 TIAQPPKSADIITAYHKKEDSRNIVRISDHPLDGYKPIKTGYEVLKSHKGLSLVKVTLFT 241

Query: 196 GKNREIKKVFEFFNWKVN 213
           G+  +I+         + 
Sbjct: 242 GRTHQIRAHLSHVGAPLL 259


>gi|224418218|ref|ZP_03656224.1| ribosomal large subunit pseudouridine synthase A [Helicobacter
           canadensis MIT 98-5491]
          Length = 340

 Score = 64.0 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 32/258 (12%), Positives = 78/258 (30%), Gaps = 45/258 (17%)

Query: 1   MKDKN--------IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV 52
           M++K          VQ+  T  R+ K + +    SR ++ ++I ++++ +NG+ +++   
Sbjct: 1   MQEKQRENHSLTFYVQQEETKMRLDKFLTQKLGLSRNQISKIIQEKQITLNGVFIQKNGT 60

Query: 53  NVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           ++   D I +               +P+   +   L L      +V      D + T+ D
Sbjct: 61  SLNFNDQIILTLPNKQEKSKPNHLNIPILYEDEDLLILNKPINLIVHQTHQDDSQYTLQD 120

Query: 100 NLPSIFSRVISVGRL---------------------DINTEGLLLLTNDGGLARVLELPS 138
            L      + ++G                       +     +L             +  
Sbjct: 121 WLQENNFSLSNLGDSYRQGIIHRLDKTTSGAIVIAKNNYAHEILSQQLKSKEMGRYYVCV 180

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG---LRE 195
                   +     + +   N LK     +         T   +  +N  + +    L  
Sbjct: 181 IDSPLKQNILIDAPLIRHPKNRLKYIPTTKDTPLSKEAKTAFFKIINNDKIELIGAKLFS 240

Query: 196 GKNREIKKVFEFFNWKVN 213
           G+  +I+         + 
Sbjct: 241 GRTHQIRAHLSKIQRHIL 258


>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 = 64.0 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 32/232 (13%), Positives = 63/232 (27%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP------- 66
           R+ K ++     SR      I   +V VNG + ++A   V   D +      P       
Sbjct: 11  RLDKALSDLSELSRSLANEQIKSGQVLVNGQV-KKAKYTVQEGDVVTYHVPEPEVLEYVA 69

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 +   +     +      +V   +     + V   +  I       G L      
Sbjct: 70  EDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 121 LLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            +     G L       +           + LR Y    HG +  D+  +       +  
Sbjct: 130 RIDKDTSGLLMIAKNDDAHLVLAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 171 CYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                          +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHSV 241


>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 = 64.0 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 32/232 (13%), Positives = 63/232 (27%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP------- 66
           R+ K ++     SR      I   +V VNG + ++A   V   D +      P       
Sbjct: 11  RLDKALSDLSELSRSLANEQIKSGQVLVNGQV-KKAKYTVQEGDVVTYHVPEPEVLEYVA 69

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 +   +     +      +V   +     + V   +  I       G L      
Sbjct: 70  EDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 121 LLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            +     G L       +           + LR Y    HG +  D+  +       +  
Sbjct: 130 RIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 171 CYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                          +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHSV 241


>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 = 64.0 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 27/238 (11%), Positives = 65/238 (27%), Gaps = 31/238 (13%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T QR+ + +A      SR  ++  I    V V+G++  +    V+    IE+
Sbjct: 8   KSEITATQTGQRLDQTLAELFPDYSRTRIKEWIQAGAVYVDGMVQTKPREKVLEGQEIEI 67

Query: 63  D--------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           +               + +   +   + +  +   +V   +     + +   L       
Sbjct: 68  EATLKEEIKAEAQAIDLDIVYEDDHIIVINKQAGLVVHPGAGNSDGTLMNALLHHCPEIE 127

Query: 109 ISV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------- 155
           +        RLD +T GL+++         L                             
Sbjct: 128 LVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIVSGTMTAGGVVDE 187

Query: 156 ---DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                        V            +  +  ++  + + L  G+  +I+        
Sbjct: 188 PIARHPTKRTHMAVHHSGRPSVTHYRVAEKFRAHTRLRLRLETGRTHQIRVHMAHIGH 245


>gi|332999362|gb|EGK18947.1| ribosomal large subunit pseudouridine synthase D [Shigella flexneri
           VA-6]
          Length = 326

 Score = 64.0 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINS 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>gi|332360785|gb|EGJ38592.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK355]
          Length = 298

 Score = 64.0 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 34/240 (14%), Positives = 67/240 (27%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           ++ +   QR+ K +A     SR      I   ++ VNG   ++A   V   D +      
Sbjct: 5   IEASIAGQRLDKAVAELTDLSRSLANEQIKDGQILVNGQ-AKKAKYAVKEGDVVSYELSE 63

Query: 63  --------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
                   + +PL     +     +      +V   +     + V   +  I       G
Sbjct: 64  PEVVEYVAEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGING 123

Query: 113 RLDINTEGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLK 162
            L       +     G L       +           + LR Y    HG +  D+  +  
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHAALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 163 KGIVIQGICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                +                 +  +  + G    V + L  G+  +I+    +    V
Sbjct: 184 PIGRSEKDRKKQAVTAKGKPALTRFQVLERFGDYTLVELQLETGRTHQIRVHMAYIGHPV 243


>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 = 64.0 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 36/246 (14%), Positives = 72/246 (29%), Gaps = 42/246 (17%)

Query: 7   VQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V +   P R+ K +  R   +SR  +++      + VNG  ++  +  V   D I +   
Sbjct: 35  VDKGQEPVRIDKFLYERMQHSSRNRIQKAADAGFIHVNGAAVKS-SYKVRPEDVITLMLD 93

Query: 63  ---DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                  +           E   L + +KP GLV      +   T+ + +      + + 
Sbjct: 94  RPKHDNTIEAEDIPLDIVYEDDVLMVINKPAGLVVHPGAGNFHGTLINAVAWHLKDMPAF 153

Query: 112 GRLDI----------NTEGLLLLTNDGG-------------LARVLELPSTQWLRVYRVR 148
              D           +T GLL++                    R               R
Sbjct: 154 DPNDPEVGLVHRIDKDTSGLLVVAKTPDAKTDLGRQFFNKTTHRSYNALVWGNFTEEEGR 213

Query: 149 FHGQVDQDKLNLLKKGIVIQGICY-GDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
             G + +D  + L+  +   G            +  + G    +   L  G+  +I+   
Sbjct: 214 IEGNIARDPRDRLRMAVFPPGSETGKPAVTHYRVIERFGYTTLIECVLETGRTHQIRAHM 273

Query: 206 EFFNWK 211
           +     
Sbjct: 274 KHIGHP 279


>gi|294901663|ref|XP_002777463.1| ribosomal large subunit pseudouridine synthase b, putative
           [Perkinsus marinus ATCC 50983]
 gi|239885100|gb|EER09279.1| ribosomal large subunit pseudouridine synthase b, putative
           [Perkinsus marinus ATCC 50983]
          Length = 322

 Score = 64.0 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 47/235 (20%), Positives = 92/235 (39%), Gaps = 38/235 (16%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           + +++ I+ +G  SR + E  I    V V+G ++    V V     +     P+      
Sbjct: 22  EWLARRISLSGQMSRSQAEVAIRNGEVVVDGQVVRH-NVQVSDHCDVICRDQPVEPPGDP 80

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------------------SRVISVGRLD 115
           ++WL +KP G+V + +   G +T+ D                           I +  + 
Sbjct: 81  KVWLINKPRGVVCSATRIRGLTTLPDLFEIWHKRRANELSHNINNVDLIPPHFIVINPIP 140

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           +   GL++LTNDG  A  +  P ++ L V+ VR  G++ +D+    ++    +G+  G++
Sbjct: 141 VMCSGLVILTNDGEFAHNMAHPRSKVLSVFLVRVKGRLPEDRFKSWRRR---EGVKVGNV 197

Query: 176 QVTLDTQKGSN------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
                             W+ V L          V       V ++   S+GP++
Sbjct: 198 DYGQVFVGIDKRPSEDVTWLRVRL----------VMTNEKNLVTKINSSSFGPYR 242


>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 = 64.0 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 32/242 (13%), Positives = 62/242 (25%), Gaps = 38/242 (15%)

Query: 10  NFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           +   QR+   ++      SR  ++++I Q  V +N  +     VNV   D I V      
Sbjct: 29  SQNTQRLDLYLSSELQNLSRSRLQQLIEQGHVLLNDQVCTSKKVNVKVGDRICVEIPSLQ 88

Query: 63  ------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
                 + +PL     +   L L      +V         + V   L    +     G  
Sbjct: 89  PLKLVAEDIPLDILYEDEQLLILNKPAGLVVHPAPGHLDGTLVNALLAHCANLPGIGGVQ 148

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------------------- 155
                  L     G +A      + Q L+        + +                    
Sbjct: 149 RPGIVHRLDKDTTGAIAIAKTDIAYQHLQAQLQAKTARREYLGVVYGVPKTESGIINLPI 208

Query: 156 ----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                    +      QG         +  +  +   +   L  G+  +I+         
Sbjct: 209 SRHPQDRKKMAIVPTEQGGRTAITHWQIRERLSNYTLIHFQLETGRTHQIRVHSAKIGHP 268

Query: 212 VN 213
           + 
Sbjct: 269 IV 270


>gi|291514728|emb|CBK63938.1| ribosomal large subunit pseudouridine synthase D [Alistipes shahii
           WAL 8301]
          Length = 361

 Score = 64.0 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 43/267 (16%), Positives = 74/267 (27%), Gaps = 42/267 (15%)

Query: 8   QENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
            +  TP R+ K +  R    SR  ++       + VNG   +  +  V   D I++    
Sbjct: 36  DKGQTPMRLDKFLTVRMEHCSRNRIQAAADSGNILVNGKAAKS-SYKVKPLDRIQIVMPY 94

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV- 111
                    + +PL    E   L L  KP GLV      +   T+ + L    ++     
Sbjct: 95  PRREVELVAEDIPLDIPYEDQWLLLVDKPAGLVVHPGVGNYSGTLVNALMHHLNKQGIPA 154

Query: 112 ---------GRLDINTEGLLLLTNDGGLARVLELPSTQW---------------LRVYRV 147
                     R+D NT GLL++  D      L                           +
Sbjct: 155 EEQNRAGLVHRIDKNTSGLLVIAKDEQTHARLAKQFFDHTIQRRYVALVWGNFDEDEGTI 214

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
             +          +          +      +  + G    V   L  G+  +I+    +
Sbjct: 215 TGNIGRSPKDRQKMFVFADGSDGKHAVTHWKVLKRYGYVTLVECRLETGRTHQIRVHMAW 274

Query: 208 FNWKVNRLIRISYGPFQLGTLLAGSTR 234
               +    R   G   L        R
Sbjct: 275 IGHPLFNDERYG-GDRILKGTTFAKYR 300


>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 = 64.0 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 34/240 (14%), Positives = 75/240 (31%), Gaps = 34/240 (14%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           I+ E    +R+  V+++     SR  ++ ++   R+ V+G   E+ +  V   + + VD 
Sbjct: 2   ILPEEQAGERLDTVLSQLLPETSRSRIQALLRDGRILVDG-TPEKPSARVRGGEQVMVDW 60

Query: 65  VPLRK--------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI- 109
             +                 +   L L+     L    +     + V   L  +      
Sbjct: 61  PQIEPSNWLAEGLPLHILHEDADILVLHKPAGQLTHPGAGHADGTLVNGVLAHVPENAYL 120

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR------------VRFHGQV 153
                V RLD +T GLL++       + L                         R    +
Sbjct: 121 PRGGIVHRLDKDTTGLLVVAKTEMARQSLIDQLGDHTMHREYLALVTGAMTGGGRVDAPI 180

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +   + L+  +   G         L  +   ++++ + L  G+  +I+         + 
Sbjct: 181 GRHAQDRLRMTVRDDGRPAQT-DYRLVERFPRHSYLRLRLATGRTHQIRVHMTHIGHPLV 239


>gi|239996651|ref|ZP_04717175.1| ribosomal large subunit pseudouridine synthase D [Alteromonas
           macleodii ATCC 27126]
          Length = 327

 Score = 64.0 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 26/230 (11%), Positives = 59/230 (25%), Gaps = 31/230 (13%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVN--------VMSTDHIEVDGV 65
           R+ +V+A      SR +++  I    V VNG ++              V +   ++V   
Sbjct: 22  RLDQVLADLFPEYSRSKLKTWIQDGNVAVNGEVITVPRHKMQMDELVTVQAEMDVQVTSE 81

Query: 66  P------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-----GRL 114
                  +   +   L +      +V   +     + +   L                RL
Sbjct: 82  AQDIALNIVYEDEHILVINKPADLVVHPGAGNPSGTVLNALLNHCPEIDKVPRAGIVHRL 141

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-----------DKLNLLKK 163
           D +T GL+++         L     +                                  
Sbjct: 142 DKDTTGLMVVAKTIPAQTHLVDQLQRREMSREYEAVALGTMVAGGIVDAPIGRHATKRTH 201

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             V +          +  +  +   + + L  G+  +I+         + 
Sbjct: 202 MAVREMGKPAVTHFRVIEKFRAYTHLRLKLETGRTHQIRVHMAHIKHPLL 251


>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 = 64.0 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 64.0 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 30/236 (12%), Positives = 71/236 (30%), Gaps = 39/236 (16%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ + ++     +R  V+++I +  V VN   + + A  V S D I +            
Sbjct: 9   RLDRYLSEVLSKTRSFVQKIIEEGNVWVNQTQVLKPAYKVRSGDIIRIVIPEPKQLSLVA 68

Query: 63  ---DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG------- 112
              D   + + E   +        +V   +     + V   L     ++ S+        
Sbjct: 69  QDIDIEVVYEDEHLAVI-NKPRGMVVHPGAGNFENTLVNALLHKFSGKLSSINGVIRPGI 127

Query: 113 ---------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                          + D     L        + R+        L+         + +  
Sbjct: 128 VHRLDKDTSGLLIVAKTDEAHIKLSEALKSHQIKRIYYAICEGVLKEDSGVVDAPIGRHP 187

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +N LK  ++  G         +  +     +V + L+ G+  +I+    +  + + 
Sbjct: 188 VNRLKMAVIPNGKQA-VTYFEVLERYDKYTFVKLRLKTGRTHQIRVHMSYIGYPLL 242


>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 = 64.0 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 36/246 (14%), Positives = 72/246 (29%), Gaps = 42/246 (17%)

Query: 7   VQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V +   P R+ K +  R   +SR  +++      + VNG  ++  +  V   D I +   
Sbjct: 35  VDKGQEPVRIDKFLYERMQHSSRNRIQKAADAGFIHVNGTAVKS-SYKVRPEDVITLMLD 93

Query: 63  ---DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                  +           E   L + +KP GLV      +   T+ + +      + + 
Sbjct: 94  RPKHDNTIEAEDIPLDIVYEDDVLMVINKPAGLVVHPGAGNFHGTLINAVAWHLKDMPAF 153

Query: 112 GRLDI----------NTEGLLLLTNDGG-------------LARVLELPSTQWLRVYRVR 148
              D           +T GLL++                    R               R
Sbjct: 154 DPNDPEVGLVHRIDKDTSGLLVVAKTPDAKTDLGRQFFNKTTHRSYNALVWGNFTEEEGR 213

Query: 149 FHGQVDQDKLNLLKKGIVIQGICY-GDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
             G + +D  + L+  +   G            +  + G    +   L  G+  +I+   
Sbjct: 214 IEGNIARDPRDRLRMAVFPPGSETGKPAVTHYRVIERFGYTTLIECILETGRTHQIRAHM 273

Query: 206 EFFNWK 211
           +     
Sbjct: 274 KHIGHP 279


>gi|289807462|ref|ZP_06538091.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 74

 Score = 64.0 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 43/74 (58%)

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
           R  GQVD+ KL  L +G+ ++        +     +G N W  V L EG+NRE+++++E 
Sbjct: 1   RVFGQVDESKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEA 60

Query: 208 FNWKVNRLIRISYG 221
              +V+RLIR+ YG
Sbjct: 61  VGVQVSRLIRVRYG 74


>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 = 64.0 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 9   TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 68

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 69  EIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 128

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 129 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 188

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 189 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 247


>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 = 64.0 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 31/247 (12%), Positives = 67/247 (27%), Gaps = 36/247 (14%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K+  IV E    +R+ K +A   +  SR  ++ +I +  +KVN    +     + + D I
Sbjct: 3   KNVFIVDEKDRGERIDKYLAEIFVDKSRSFIQGLIEKDDIKVNNKTPKS-NYKLRALDEI 61

Query: 61  EV---DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           EV   +   LR             ++  + +      +V         + V   L     
Sbjct: 62  EVTFSEPEVLRVEAEEIPINILYEDKDVVVVNKPQGMVVHPAPGNYNGTLVNALLYHCKD 121

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ----------- 155
                G +       +     G L       +   L         + +            
Sbjct: 122 LSSINGIIRPGIVHRIDKDTSGVLVVAKNDEAHNKLSDQLKDHSMKREYYALVEGRLKND 181

Query: 156 ---------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                           K  +++G         +  +      +   L  G+  +I+    
Sbjct: 182 KGIIDKPLARNKRDRLKIGIVEGGKRAVTHYEVLERFNGYTLIKCILETGRTHQIRVHMA 241

Query: 207 FFNWKVN 213
              + + 
Sbjct: 242 SIGFPLV 248


>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 = 64.0 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 29/249 (11%), Positives = 66/249 (26%), Gaps = 37/249 (14%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M+D  I + +    +RV K ++   G  SR ++   + +  VKVNG  ++     V   D
Sbjct: 1   MEDLTIEITKEMAGERVDKAVSSIDGDWSRSQISNWVKEGAVKVNGETVK-PNYKVRLQD 59

Query: 59  HIEVD--------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            I V                + +   +   L +      +V         + V   +   
Sbjct: 60  IIIVTPPELEELDVVPEDLNLEIVYEDEDVLVVNKPKGMVVHPAPGHAKGTLVNGLMHHC 119

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPST--------------------QWLRV 144
                  G +       +     G L       +                          
Sbjct: 120 TDLSGINGVVRPGIVHRIDKDTSGLLMVAKNDAAHTSLVDQLVKKTVTRKYVALVHGHIP 179

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
           +                +   ++    +      +  + G+   V   L  G+  +I+  
Sbjct: 180 HDKGTIQAPIARDPKERQNMAIVDKGKHAVTHFRVLERFGNFTLVECRLETGRTHQIRVH 239

Query: 205 FEFFNWKVN 213
            ++  + + 
Sbjct: 240 MKYIGFPLV 248


>gi|269214548|ref|ZP_06158643.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           lactamica ATCC 23970]
 gi|269209595|gb|EEZ76050.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           lactamica ATCC 23970]
          Length = 246

 Score = 64.0 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 30/144 (20%), Positives = 55/144 (38%), Gaps = 4/144 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPLR--K 69
            ++ K +   GI SR++ + +I    V +NG  ++    ++ S+      +DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSSVETLDIDGKAVTVIP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                + L        +                     + +VGRLD +T G+LL+TNDG 
Sbjct: 61  EPYFYILLNKPTDYETSHKPKHYRSIFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGH 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQV 153
           L   L  P+ +  +  R       
Sbjct: 121 LNHKLTSPNHKNPQTVRSYTQASC 144


>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 = 64.0 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 35/251 (13%), Positives = 73/251 (29%), Gaps = 41/251 (16%)

Query: 1   MKDKNIVQENF-TPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M+ +++V E     +R+ + +A   +   SR +V+ +I +  V V G   ++    +   
Sbjct: 1   METRDVVIEGSHEGERLDRFLAE-TLCDVSRSQVKNLIDEGLVLVGGRP-QKPGYRIRKG 58

Query: 58  DHIEV----------------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRS 95
           D I+V                      D   +   +   L ++        T  +     
Sbjct: 59  DIIQVRIPAARETGLVAQEMPLNIVYEDRDLVVIDKPQGLVVHPAHGHWEGTLVNALLYR 118

Query: 96  TVF-------------DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL 142
                             L    S ++ V + D     L        + R         +
Sbjct: 119 VKDLSGINGELRPGIVHRLDKDTSGLMVVAKNDQAHRDLADQIKARKIRREYVAVVHGVI 178

Query: 143 RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           R         + +   +  K  +V +G        T+  +      V   L  G+  +I+
Sbjct: 179 RENSGTIDAPIGRSPSDRKKMAVVREGRPA-VTHYTVLRRYRDYTLVRARLETGRTHQIR 237

Query: 203 KVFEFFNWKVN 213
             F +    V 
Sbjct: 238 VHFAYIRHPVV 248


>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 = 64.0 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 38/246 (15%), Positives = 72/246 (29%), Gaps = 38/246 (15%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +V      QR+ K +A      SR  +++++ Q  V++NG  +++ A  V   D I V+ 
Sbjct: 31  VVGAEQHAQRLDKALAELVPEFSRSYLQQLLLQGCVRLNGREVQKPASRVKVGDRIAVEM 90

Query: 65  VP---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
            P               +   +   L ++     +V         + +   L      + 
Sbjct: 91  RPTQQSQAFRPEQWPLDVVYEDEHILVIHKPAGLVVHPAPGNWSGTLLNALLGRDAQAMQ 150

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPST--------------QWLRVYRVRFH 150
                   RLD +T GL+++         L                    W        H
Sbjct: 151 VPRAGIVHRLDKDTSGLMVVARSRSAMDALVRMIAAREVSRQYVALGWGGWTGAAHRSVH 210

Query: 151 GQVDQDKLNLLKKGIV---IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
             + +D  N L+  +V               L         V   L  G+  +I+     
Sbjct: 211 APIGRDPRNRLRMAVVDLAQHPGKEARTDFDLIDANEEVCLVRCTLHTGRTHQIRVHMAS 270

Query: 208 FNWKVN 213
               + 
Sbjct: 271 IRHPLV 276


>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 = 64.0 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 29/245 (11%), Positives = 66/245 (26%), Gaps = 38/245 (15%)

Query: 6   IVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
            V+ +    R+ K I        SR +V+  IA   V VN   ++     V   D I + 
Sbjct: 25  TVEADAAKTRIDKYITENLGEDVSRSQVQLWIADGHVSVNDGPIKS-NYKVSQGDRIVLK 83

Query: 63  -----------DGVPLRK--AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                      + +PL     +   + +      +V         + V   +        
Sbjct: 84  VPEPSAVEIIPEDIPLEIAFEDGDVIVVNKPRGMVVHPAPGHSSGTLVNALMFHCKDLSG 143

Query: 110 SVGR---------------------LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
             G                       D     L     +  + R         +   +  
Sbjct: 144 INGELRPGIVHRIDKDTTGLIMAAKNDKAHASLAAQLKEHSVNRRYLALVHGNISHDQGT 203

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +D  +     +  +   +     T+  + G  + + + L  G+  +I+   ++ 
Sbjct: 204 IDAPIGRDAQDRKLYTVTDRNSKHAVTHFTVVERFGDYSLLELKLETGRTHQIRVHMKYI 263

Query: 209 NWKVN 213
              + 
Sbjct: 264 GHPLV 268


>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 = 64.0 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 35/265 (13%), Positives = 81/265 (30%), Gaps = 35/265 (13%)

Query: 5   NIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           N V+++   QR+ + IA      SR  ++  +   +V+VNG ++ +    VM  + I + 
Sbjct: 9   NTVKDSQLGQRLDQAIAELFADFSRSRLKEWLLAGKVQVNGEVVTKPRTKVMGGEEITLQ 68

Query: 63  ----DGVPLRKAERT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
               D       +            + +      +V   +     + +   L        
Sbjct: 69  AELEDEERWEAQDIPLDIVYEDEDIIVINKPRDFVVHPGAGTPDGTVLNALLHHYPDIAE 128

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   RLD +T GL+++         L     +                    + K 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRMTAGGKVDKP 188

Query: 165 IVIQ-----------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I                 +      +      +  + + L  G+  +I+    +    + 
Sbjct: 189 IGRHSTKRTLMAVAPMGKHAVTHYRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPL- 247

Query: 214 RLIRISYGPFQLGTLLAGSTREVSK 238
            L   +YG      +  G+++E+++
Sbjct: 248 -LGDTAYGGRA--RIPTGASQELTE 269


>gi|291546177|emb|CBL19285.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus sp.
           SR1/5]
          Length = 304

 Score = 64.0 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 27/246 (10%), Positives = 70/246 (28%), Gaps = 40/246 (16%)

Query: 6   IVQENFTPQRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            V++  +  R+ + +A   +G+ SR  +++++ + ++ V G    ++   V   D I ++
Sbjct: 7   TVEKEESGIRIDRYLAEKDSGL-SRSFLQKLLKEGQITV-GEKAAKSNYKVRENDRIHLE 64

Query: 64  ------------GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                        +PL     +   L +      +V   +     + V   +      + 
Sbjct: 65  IPDSSEPDIVPEDIPLDILYEDEDVLIVNKPKGMVVHPAAGHYQGTLVNAVMAHCGDSLS 124

Query: 110 SVGRLDIN----------------------TEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
            +  +                            L        + R         L+    
Sbjct: 125 GINGVMRPGIVHRIDKDTTGALLVCKNDIAHRDLAEQLKCHSIRRRYRAVVQGNLKEDEG 184

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
              G + +   +  K  I  +          +  + G   +V   L  G+  +I+     
Sbjct: 185 TIEGPIGRHPTDRKKMAINHKNGKDAITHYKVLERFGEATYVECRLETGRTHQIRVHMAS 244

Query: 208 FNWKVN 213
               + 
Sbjct: 245 IGHPLL 250


>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 = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 40/258 (15%), Positives = 83/258 (32%), Gaps = 44/258 (17%)

Query: 13  PQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------- 62
           P R+ + + +    A+R +V+  I + RV VN   ++     + S D IE+         
Sbjct: 33  PMRIDQYLTQQVENATRNKVQEAIEEGRVLVNENRVKS-NYRIKSCDVIEMTFLRPPAPE 91

Query: 63  ---DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------R 107
              + +P+     +   + +  K   +V         +     L  I            R
Sbjct: 92  LTAENIPIEIIYEDCDLMVVNKKAGMVVHPAFGNWTGTLANAILHHIGMDAEELDQAELR 151

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK---------- 157
              V RLD NT GL+++  +      L     +   +   +       D           
Sbjct: 152 PGIVHRLDKNTSGLIIVAKNPIALHRLARQFAERKVIKVYKAIVWGVPDPAAGTITTNIG 211

Query: 158 ----LNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                  +      +G          ++       + +++ L  G+  +I+   +    +
Sbjct: 212 RSKKDRKVMANFPFEGEYGKTAITDYSVMENLQWFSLLSLRLHTGRTHQIRAHLQHLGHQ 271

Query: 212 VNRLIRISYGPFQLGTLL 229
           +  L  ++YG   L TL 
Sbjct: 272 I--LGDVTYGGTILRTLP 287


>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 = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 28/245 (11%), Positives = 64/245 (26%), Gaps = 39/245 (15%)

Query: 6   IVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-- 61
           I+QE     R+ KV+A       SR   + +I +  V +NG  +++        D +E  
Sbjct: 13  IIQEMEAGIRLDKVLADRYKSNGSRTYFQMLIEKGLVLLNGEPVKK-RFKPNVGDDVELF 71

Query: 62  ------VDGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--- 106
                 +D +P      +   +   L +      +V         + V   L        
Sbjct: 72  FAAAPEIDLIPEQIPLNILYEDEHLLIINKPVGMVVHPAPGNWTGTFVNALLYHCGYSLS 131

Query: 107 ------------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR------VR 148
                         +      +      L      +         +              
Sbjct: 132 DASVDSIRPGIVHRLDKETSGVLVAAKTLSVQQKLMELFAARQVYKEYWAICLGNPGNCE 191

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
            +  + +  ++  +  +   G        TL+          + L  G+  +I+   +  
Sbjct: 192 LNWPIGRHPIHRKQMTVREDGKEALTFCETLEVGNEI-CLAKLILSTGRTHQIRVHLKHK 250

Query: 209 NWKVN 213
              + 
Sbjct: 251 GHPIL 255


>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 = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDDDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 29/246 (11%), Positives = 68/246 (27%), Gaps = 54/246 (21%)

Query: 12  TPQRVSKVI-ARAGIASRR--EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP-- 66
           +  R+ K + A     +R   EV+++I    + VN   ++     +   D +        
Sbjct: 23  SGTRIDKFLIADL---NRSWNEVQKLIRNGEINVNNKKIKDHQFLLKEGDVVTYWDKLKK 79

Query: 67  ---------------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
                                +       + L  K        ++P+    + + L   F
Sbjct: 80  QADTQLRPVPNTQAYEELKKMILYENDQIIILNKKHGYASQGGANPNY--NIPEILNLYF 137

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR-----------------VR 148
                + RLD  T GLL++  +  +A  +     +   + +                  R
Sbjct: 138 KNFYIIHRLDQLTSGLLIIAKNKDIATEISTIIQEKAFITKKYIAVVQGQIKVQKGLIDR 197

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQV------TLDTQKGSNAWVTVGLREGKNREIK 202
                  ++         +    Y   +           Q    + + + + EG+  +I+
Sbjct: 198 PLLFNTNNQKQTCYNEEQLLEGKYLPARTSYEVIEEYQYQDEMYSILDLQIFEGRKHQIR 257

Query: 203 KVFEFF 208
                 
Sbjct: 258 AHLSQV 263


>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 = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 78/248 (31%), Gaps = 42/248 (16%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V +  TP R+ + + +     +R +V+  I + RV VNG  ++     V S DHI +   
Sbjct: 5   VSKVQTPMRIDRYLTQQVENMTRNKVQAAIEEGRVLVNGKPVKS-NYRVKSCDHIHLTFL 63

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------- 105
                    + +P+    E   L +  K  G+V   +  +   T+ + +           
Sbjct: 64  RPPAPELAPEDIPITILYEDDDLMVIDKEAGMVVHPAFGNWTGTLANAILHHLGKDADEL 123

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------ 155
                R   V RLD +T GL+++  +      L             +             
Sbjct: 124 DKTEMRPGIVHRLDKDTSGLIIIAKNPTALHKLARQFANRQVEKVYKAIVWGVPKAESGT 183

Query: 156 --------DKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                    K   +      +G           +    G  + + V L  G+  +I+   
Sbjct: 184 IKTNIGRSHKNRKVMANFPYEGAEGKHAITDYQVVEDLGYFSLMDVTLHTGRTHQIRVHL 243

Query: 206 EFFNWKVN 213
           +     + 
Sbjct: 244 QHLGHSIL 251


>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 = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>gi|312171425|emb|CBX79684.1| ribosomal large subunit pseudouridine synthase D [Erwinia amylovora
           ATCC BAA-2158]
          Length = 325

 Score = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 67/239 (28%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I  +R+ VNG  +++    V+  + I +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILNRRITVNGTTIDKPKEKVLGGEQISIDA 69

Query: 65  V--------------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  EIEEEARWEAQDIPLAIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHHFPAIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPSQTHLVDALQRREITREYEAVAIGRMTAGGTVNEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      +  + 
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHISHPLV 248


>gi|330895553|gb|EGH27863.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. japonica str.
           M301072PT]
          Length = 190

 Score = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 42/165 (25%), Positives = 79/165 (47%), Gaps = 16/165 (9%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  SD +GR+T+ D +          GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPKLILFNKPFDVLTQFSDEEGRATLKDFIKIPGI--YPAGRLDRDSEGLLLLTNDG 84

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+ + ++L  L+ G+ +        +            
Sbjct: 85  QLQARIADPKHKLAKTYGVQVEGEPNDEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPR 144

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
                  +    +W+ + ++EG+NR+++++         RL+R+S
Sbjct: 145 NPPVRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRLS 189


>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 = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 29/239 (12%), Positives = 64/239 (26%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E+   QR+ + +A      SR  ++  I   RV+VNG ++ +    V+  + I VD 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILDDRVQVNGKVINKPKEKVLGGEQILVDA 69

Query: 64  ----GVPLRKAERT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                      +            L +      +V   +     + +   L         
Sbjct: 70  LIEEDNRWEPQDIPLDVVYEDEDILVINKPRGLVVHPGAGNPDGTILNALLHRYPEIVDV 129

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--- 156
                  R+       +     +        +  L   + ++  V   R       +   
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAVGRMTAGGMVEEPI 189

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAITHYRVMEHFRAHTRLRLRLETGRTHQIRVHMAHINHPLI 248


>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 = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 62/246 (25%), Gaps = 36/246 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M    I +EN    R+ K +A     SR  +  +I   +V VN    ++A   V + D I
Sbjct: 1   MPIIKITEENKDL-RLDKALANQTEYSRSLLTELIKNDKVFVNNE-AKKAKYKVKTGDRI 58

Query: 61  EVD--------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           + +               + +   +     +      +V   +     + V   +  I  
Sbjct: 59  QFEIPQAEVLDVVAEDLPLEIIYEDSDVAVVNKPQGMVVHPAAGHASGTLVNAIMYHIKD 118

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPST--------------------QWLRVYR 146
                G +       +     G L       +                            
Sbjct: 119 LSSINGVIRPGIVHRIDKDTSGLLMIAKNDKAHESLAAQLKDKTSKRRYLAIVHGELAND 178

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                      L   KK  V+ G         +         + + L  G+  +I+    
Sbjct: 179 KGTIEAPIGRNLKDRKKQAVVSGGKPAVTHFEVLEGFVGYTLIALRLETGRTHQIRVHMH 238

Query: 207 FFNWKV 212
           +    V
Sbjct: 239 YIGHPV 244


>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 = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 29/235 (12%), Positives = 67/235 (28%), Gaps = 36/235 (15%)

Query: 12  TPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
              R+ KV+       SR +++  + ++ V VNG  ++ A   V   D I V        
Sbjct: 11  ESGRIDKVLTNLFSNYSRSQIQLWLKERAVSVNGEPVK-ANYKVKQGDEITVLIPEPETL 69

Query: 63  ----DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
               + +P  +   +     +      +V   +     + V   +  +       G +  
Sbjct: 70  DVVPENIPLTIVYEDEDVAVINKPQGMVVHPSAGHTHGTMVNALMYHVKDLSTINGVIRP 129

Query: 117 NTEGLLLLTNDGGLARVLELPSTQ------------WLRVYRVRFHGQVDQDKLNL---- 160
                +     G L       + +               V  V      ++  +N     
Sbjct: 130 GIVHRIDKDTSGLLMVAKNDQAHESLAKQLKDKTSLRKYVALVHGEIPHEKGTINAPIGR 189

Query: 161 ----LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                K   + +         T+  +      V + L  G+  +I+   ++  + 
Sbjct: 190 SKENRKMQAIREDGKPAVTHFTVLERFEGFTLVELKLETGRTHQIRVHMKYIGYP 244


>gi|91204218|emb|CAJ71871.1| similar to pseudouridine synthase C [Candidatus Kuenenia
           stuttgartiensis]
          Length = 274

 Score = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 30/201 (14%), Positives = 68/201 (33%), Gaps = 8/201 (3%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKAERTRLWL 77
            IA     S ++ ++++  + V VN   +  A+  +   D IEV  G   +  ++T   L
Sbjct: 18  FIANKLSLSNKKAKQLLDDRLVFVNRKRVWIASYQLKPGDSIEVLSGKTHQPEKKTYDIL 77

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNL-----PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           ++    ++ +       +                R+ +V RLD +T G L+   +     
Sbjct: 78  FNDDCYVIVSKPPGIVTNGQNSIERDLRTQFNRDRIQAVHRLDKDTSGALIFAKNENAFE 137

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            ++    +     +  +   V               G       +TL  +  + +++ V 
Sbjct: 138 EMKKVFKKHD--IQKIYRVIVTGKICEPAFTINSPVGGQTAVTHITLLKKGKNTSYLEVA 195

Query: 193 LREGKNREIKKVFEFFNWKVN 213
              G+  +I+         V 
Sbjct: 196 TETGRRHQIRIHLASIGHPVI 216


>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 = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRSGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 28/232 (12%), Positives = 63/232 (27%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--------EVDGVP 66
           R+ K ++     SR      I + ++ VNG + ++A   V   D I        EV    
Sbjct: 11  RLDKAVSELTELSRGLANEQIKEGKILVNGQV-KKAKYTVKEGDVISYEVPQMEEVTYEA 69

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 +   +   + +      +V   +     + V   +  I       G L      
Sbjct: 70  EDIPLEIVYQDADVVVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGELRPGIVH 129

Query: 121 L---------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI- 170
                     ++  ND     + +    +               +   +++  I      
Sbjct: 130 RIDKDTSGLLMVAKNDAAHVALADELKAKKSLRKYWAIVHGNLPNDRGVIEAPIGRSDKD 189

Query: 171 --------CYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                          +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPALTRFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>gi|3402691|gb|AAC28994.1| unknown protein [Arabidopsis thaliana]
          Length = 86

 Score = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 18/81 (22%), Positives = 40/81 (49%), Gaps = 3/81 (3%)

Query: 166 VIQGICYGDMQVTLDTQK--GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
           +++G+      V L  ++     A + + + EG+N E++++ +    +V+ L R+  G F
Sbjct: 1   MVEGVHCVPDSVELMPKQHDIPRARLRIVVHEGRNHEVRELVKNAGLEVHSLKRVRIGGF 60

Query: 224 QL-GTLLAGSTREVSKKILRE 243
           +L   L  G   E+ +  L+ 
Sbjct: 61  RLPSDLGLGKHVELKQSELKA 81


>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 = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 32/248 (12%), Positives = 70/248 (28%), Gaps = 38/248 (15%)

Query: 1   MKDKN--IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M ++N   V+ N    R+ K +A     SR +V+  +    V+V+G +++     +  T+
Sbjct: 1   MNEQNEWAVKANGATGRIDKWLAEQQDWSRSQVQDWLKAGHVEVDGRIVK-PNYKMSGTE 59

Query: 59  HIEV------------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            I V            + +PL     +   + +      +V   +     + V   L   
Sbjct: 60  EILVRIPEAVELEVLPEDIPLDVVYEDSDVIVINKPKGMVVHPAAGHVSGTLVNALLHHC 119

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------R 143
                  G         +     G L       + + L                      
Sbjct: 120 QDLSGINGVKRPGIVHRIDKDTSGLLMVAKNDLAHESLAQQLKDKTTERLYIALVHGEIP 179

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                    V +DK +  +  +  +          +  +      V   L  G+  +I+ 
Sbjct: 180 HELGTIEAPVGRDKNDRQRMTVTDKNSKAAVTHFRVLERYEGFTVVECKLETGRTHQIRV 239

Query: 204 VFEFFNWK 211
              +  + 
Sbjct: 240 HMRYIGFP 247


>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 = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 30/239 (12%), Positives = 66/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E    QR+ + +A      SR  ++  I ++RV VNG ++++    V+  + + +  
Sbjct: 10  TVSEAQLGQRLDQTLAELFPDYSRSRIKEWILERRVSVNGTVIDKPKEKVLGGEQVSISA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-- 108
                           +   +   + +      +V   +     + +   L      V  
Sbjct: 70  EIEEEQRWEAQNIPLNIVYEDDDIIVINKPRDLVVHPGAGNPDGTVLNALLYHYPPIVDV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                V RLD +T GL+++         L                               
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTHLVETLQLREITREYEAVAIGTMTAGGTVNEPM 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 ARHSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMAHINHPLV 248


>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 = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 69/249 (27%), Gaps = 40/249 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           MK K   Q +    R+   +  +   +R ++  +I    V VNG L  +A   + ++D I
Sbjct: 1   MKFKITEQTDS---RLDHFLVASTELNRSQITTLIKDGLVMVNG-LTTKAGYKLKNSDEI 56

Query: 61  EVDGVP---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-- 103
            ++                  +   +   + +      +V         + V   L    
Sbjct: 57  TLNLEAKEETNPLKPKNIDLNIVYEDDDIMVINKPKGLVVHPSETFSETTLVSGLLHHTD 116

Query: 104 ----IFSRVISVGRLDINTEGLLLL-----TNDGGLARVLELPSTQWLRVYRVRFHGQVD 154
                    +  G L    +    L     TN+       +L S    R Y     G +D
Sbjct: 117 TLSTHNDDPLRPGILHRIDKDTSGLILVAKTNEAHKILAQDLKSHDIKREYIALVEGVLD 176

Query: 155 QDKLNLLKKGIVIQGICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKV 204
            +K  +         I                  +      +  +   L  G+  +I+  
Sbjct: 177 HNKGVIDAPIARHPKIRTKMAVVATGKPAITHFEVMRTFRDHTLLHCKLETGRTHQIRVH 236

Query: 205 FEFFNWKVN 213
             +    V 
Sbjct: 237 LAYIKHPVT 245


>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 = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 32/248 (12%), Positives = 73/248 (29%), Gaps = 40/248 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK+  +  +N    R+ KV +      SR ++++++    + VNG   E+A   V S D 
Sbjct: 1   MKETVVEMQNG---RLDKVCSEIFSDYSRSQIKQLLDGGNITVNGKT-EKAKYKVKSGDV 56

Query: 60  IEVDGVP---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           I ++  P               +   +   + +      +V      D  + V   L   
Sbjct: 57  IRLE-EPETKTLELRPENIPLDIVYEDDDVIVINKPQGMVVHPAPGHDEHTLVNALLYHC 115

Query: 105 FSRVISVGRLDINTEGL--------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
               I+          +        ++  ND     + +    +      V        +
Sbjct: 116 PLSTINGTFRPGIVHRIDKDTSGLLMVAKNDKAHRSLAKQLKDKTNIREYVALVHGRIAE 175

Query: 157 KLNLLKKGI-----------VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
               +   I           V++          +  +     +V   L  G+  +I+   
Sbjct: 176 DEGTINAPIGRSLKDRKKQAVVKDGRNAVTHFEVLKKYRDYTFVKCILETGRTHQIRVHM 235

Query: 206 EFFNWKVN 213
           ++    + 
Sbjct: 236 KYIGHPLV 243


>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 = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 67/239 (28%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I  +R+ VNG  +++    V+  + I +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILNRRITVNGTTIDKPKEKVLGGEQISIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  EIEEEARWEAQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHHFPAIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPSQTHLVDALQRREITREYEAVAIGRMTAGGTVNEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      +  + 
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHISHPLV 248


>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 = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>gi|229495257|ref|ZP_04388992.1| ribosomal large subunit pseudouridine synthase F [Porphyromonas
          endodontalis ATCC 35406]
 gi|229317700|gb|EEN83598.1| ribosomal large subunit pseudouridine synthase F [Porphyromonas
          endodontalis ATCC 35406]
          Length = 168

 Score = 63.7 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R++K+++  G+ SRREVE +I + RV +NG      +  V   D +E+DG  L   +  
Sbjct: 3  VRINKLLSDTGLGSRREVEALIEEGRVWINGDRA-ELSDVVSEDDVVELDGEELPVRDLL 61

Query: 74 R 74
          R
Sbjct: 62 R 62


>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 = 63.7 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 63.7 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 36/239 (15%), Positives = 69/239 (28%), Gaps = 40/239 (16%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGIL-LERAAVNVMSTDHIEV--------DG 64
           +R+ K I+     +R + + +I Q+ V V+    + +    V     I V        + 
Sbjct: 10  ERIDKYISDNSEITRNDAKALIEQEAVYVDDKKFVRKPNYMVREGMVITVLRLLEKESNI 69

Query: 65  VPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL----- 114
             +        E   L + +KP GLV   +      T+ + L   F   +S         
Sbjct: 70  EAVDMPLDIRYEDEYLLILNKPSGLVVHPAPGHLNDTLVNALMYHFKNNLSDTNGLLRLG 129

Query: 115 ------------------DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
                             +     L  +  +  + R         L     + +  + +D
Sbjct: 130 IVHRIDKDTSGLLIIAKDNETHNELAKMLKNHQIKRTYLAICEGILPNKVTKINLPIQRD 189

Query: 157 KLNLLKKGIVIQGI---CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             N     I   G     Y  M  +        + V   L  G+  +I+    +    V
Sbjct: 190 TKNRKLMSIHKDGKSSVTYVHMLKSFYIDNKPYSLVKCELETGRTHQIRVHLTYIKHPV 248


>gi|116740184|gb|ABK20858.1| 23S rRNA pseudouridine synthase [Escherichia coli]
          Length = 38

 Score = 63.7 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 15/35 (42%), Positives = 22/35 (62%)

Query: 11 FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGI 45
           +  R++K I+ +GI SRRE +R I Q  V +NG 
Sbjct: 4  DSSVRLNKYISESGICSRREADRYIEQGNVFLNGK 38


>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 = 63.7 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 32/250 (12%), Positives = 80/250 (32%), Gaps = 38/250 (15%)

Query: 1   MKDKNIVQENFT-PQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           MK+ N+  +     +RV K +A      SR  ++++I   ++KVN   ++  +  +   D
Sbjct: 1   MKEYNLKVDKSEAGKRVDKFLASQFDDFSRNYIQKLIEDSKIKVNSNPVQN-SYLIKEAD 59

Query: 59  HIEV-------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            I+V             D       E   + + +K   +V   +      T+ + L +  
Sbjct: 60  EIKVIIDKAKKSSIKAVDIELDIIYEDQDIIIINKDADMVVHPAPGHYDDTIVNALLAYT 119

Query: 106 SRVISVG----------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
           + + ++                       + D + + L        + +         L 
Sbjct: 120 NDLSAINGVKRPGIVHRLDKDTSGLLLVAKNDKSHKELSRQFKKREVDKYYLALLKGILP 179

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
               +    + +      K  +  +       +  +     ++  V V +  G+  +I+ 
Sbjct: 180 YKTGKIDAPIGRHPNQRKKMAVRKRKSKKAVSRFKILESFKNHTLVEVKIETGRTHQIRV 239

Query: 204 VFEFFNWKVN 213
            F +  + V 
Sbjct: 240 HFAYLGYPVV 249


>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 = 63.7 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>gi|147678153|ref|YP_001212368.1| pseudouridylate synthase [Pelotomaculum thermopropionicum SI]
 gi|146274250|dbj|BAF59999.1| pseudouridylate synthase [Pelotomaculum thermopropionicum SI]
          Length = 312

 Score = 63.7 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 34/257 (13%), Positives = 72/257 (28%), Gaps = 41/257 (15%)

Query: 3   DKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI- 60
           +   V E    +R+   +A      +R  V+++IA+    VNG    RA+  V   D + 
Sbjct: 5   NSFQVGEEDAGKRLDLFLAGEMEGLTRTYVQKLIAEGMASVNGQR-GRASYRVKPGDVVV 63

Query: 61  ---------EVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                    E+   P+       +   + +      +V         + V   L      
Sbjct: 64  LQVPEPEGLEIKKEPIPLEVYYEDADVIVINKPRGMVVHPADGNYSGTLVNALLYHCSDL 123

Query: 108 VISVGRLDIN---------------------TEGLLLLTNDGGLARVLELPSTQWLRVYR 146
               G +                           L     +  + R         L+   
Sbjct: 124 SGINGVMRPGIVHRLDKDTSGLIMVAKNDTAHLSLARQLKERQITRRYLALVHGLLKEQS 183

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                 + +D  +  K  ++ +       +  +  +     ++ + L  G+  +I+    
Sbjct: 184 GMVDAPIGRDPRDRKKMAVLQKNAKQAVTRYRVLERFKGYTYIELMLETGRTHQIRVHMS 243

Query: 207 FFNWKVN-RLIRISYGP 222
           +    V   L    YGP
Sbjct: 244 YIGHPVVGDLK---YGP 257


>gi|58337436|ref|YP_194021.1| pseudouridine synthase [Lactobacillus acidophilus NCFM]
 gi|58254753|gb|AAV42990.1| pseudouridine synthase [Lactobacillus acidophilus NCFM]
          Length = 302

 Score = 63.7 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 38/247 (15%), Positives = 74/247 (29%), Gaps = 36/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K  ++      R+ K I+      SR  V+ +I  Q + VN   +E+ +  +   D 
Sbjct: 1   MPKKYSLEVTNQRGRLDKFISEQLSDLSRTRVKELIQDQNILVN-EKVEKVSYKIQDGDK 59

Query: 60  IEV------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           IE+            + +P  +   +   + +      +V         + V   L    
Sbjct: 60  IEITVPAVKPLDIVAENIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHTQ 119

Query: 106 --------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-- 155
                    R   V R+D +T GLL++  +      LE                  +   
Sbjct: 120 DLAQSPEGFRPGIVHRIDKDTSGLLMIAKNATARESLEQQLANKTNKRIYWAIVHGNFSE 179

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           KK  V++          +  Q    + +   L  G+  +I+   
Sbjct: 180 EQGSIDAPIGRNPYDRKKMAVVENGKKAITHFKVLKQFKGYSLIECQLETGRTHQIRVHL 239

Query: 206 EFFNWKV 212
           ++    V
Sbjct: 240 DYIGHAV 246


>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 = 63.7 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 34/251 (13%), Positives = 66/251 (26%), Gaps = 40/251 (15%)

Query: 3   DKNIVQENFTPQRVSKVIARAG---IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K  +    T  R+ K++         SR  ++++I ++ + VN  ++      V     
Sbjct: 2   NKITLNSLNTTLRLDKLLVELLTSYDYSRSYIQKLIKEKCISVNDQIIINNNFLVKPNSE 61

Query: 60  IE------------VDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           I             V    +       +   L +  +    V    +    + V   L S
Sbjct: 62  IVITIKDPILDTNLVKNKDIDLDIIYQDDDLLVINKQNNITVHPSLNNTNNTIVNALLAS 121

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------D 156
                   G L       +     G L       + + L           +         
Sbjct: 122 DVELSSINGELRPGIVHRIDKQTTGLLIIAKNDKTHKLLSEMFKSHRIYKEYLAIVTGVI 181

Query: 157 KLNLLKKGIVIQGICY--GDMQVTLDTQKGSNAWVTVG------------LREGKNREIK 202
           K N       I         M VT    K +     +             ++ G+  +I+
Sbjct: 182 KPNKGLIDAPIGRSQTDRKKMSVTAKNSKQAITTFELVERFLKNTLVKCQIQTGRTHQIR 241

Query: 203 KVFEFFNWKVN 213
             F + N  V 
Sbjct: 242 VHFNYINHPVL 252


>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 = 63.7 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 33/235 (14%), Positives = 73/235 (31%), Gaps = 37/235 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ + ++ A   +R  ++++I +  V VN   + + A  V + D I+V            
Sbjct: 9   RLDRYLSEALSKTRSFIQKIIEEGNVWVNQTQVFKPAYKVRNGDIIKVVIPEPKQLSLVA 68

Query: 63  ---------DGVPLRKAERTRLWLYHKPIGLVTTH---------------SDPDGRSTVF 98
                    +   L    + R  + H   G                     +   R  + 
Sbjct: 69  QDIDIDVVYEDEHLAVINKPRGMVVHPGAGNFENTLVNALLHKFSGRLSSINGVIRPGIV 128

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
             L    S ++ V + D     L        + R+        L+         + +  +
Sbjct: 129 HRLDKDTSGLLVVAKTDEAHIKLSEALKSHQIKRIYYAICEGVLKEDSGVVDAPIGRHPV 188

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           N LK  +V  G         +  +     +V + L+ G+  +I+    +  + + 
Sbjct: 189 NRLKMAVVPNGKEA-VTYFEVLERFDKYTFVKLRLKTGRTHQIRVHMSYIGYPLL 242


>gi|314927283|gb|EFS91114.1| ribosomal RNA large subunit methyltransferase J
          [Propionibacterium acnes HL044PA1]
          Length = 257

 Score = 63.7 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 18/64 (28%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ + +  AG+A SR    R++ + RV VNGI++ + A+ V ++D++  D         
Sbjct: 13 VRLDQALVEAGLARSRTLATRLVREGRVTVNGIVVTKPAMKVSASDNLVADEEVWVSRAA 72

Query: 73 TRLW 76
           +L 
Sbjct: 73 YKLL 76


>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 = 63.7 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 34/245 (13%), Positives = 74/245 (30%), Gaps = 40/245 (16%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +  +  R+ K +  R   ASR +++  I Q  V VNG  ++  +  +   D I +  
Sbjct: 22  VVDKGQSSIRIDKFLMVRLENASRNKIQNAIEQGNVLVNGKAIK-PSYKIKPLDDISIVL 80

Query: 63  -----------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                      + +P+     +   + +      +V         + V            
Sbjct: 81  PHPPRDTEVYPEDIPIDIIYEDNDVVLVNKVAGMVVHPGYGNWSGTLVNALTHHFSQLPQ 140

Query: 110 SVGR---------LDINTEGLLLLTNDGGLA----RVLELPSTQWLRVYRVRFHGQVDQD 156
             G          +D +T GLL+++ +        +     S +   +  V      D  
Sbjct: 141 LPGNDGRPGLVHRIDKDTSGLLVISKNEKSMASLAKQFFDHSIKRKYLALVWGDLPEDGI 200

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV-----TVGLRE-----GKNREIKKVFE 206
               + + I  + +              ++  V      V L E     G+  +I+   +
Sbjct: 201 ISGYIGRSIKDRKVMDLYDDPEKGKWSVTHYKVVKRLNYVTLIECQLETGRTHQIRAHMK 260

Query: 207 FFNWK 211
                
Sbjct: 261 AIGHP 265


>gi|229817935|ref|ZP_04448217.1| hypothetical protein BIFANG_03222 [Bifidobacterium angulatum DSM
          20098]
 gi|229784539|gb|EEP20653.1| hypothetical protein BIFANG_03222 [Bifidobacterium angulatum DSM
          20098]
          Length = 271

 Score = 63.7 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 3/54 (5%)

Query: 13 PQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMS--TDHIEVD 63
          P R+  ++  AG+  +R + +++I   +V VNG  + + A  V +     I VD
Sbjct: 23 PDRLDLLLVEAGVVGTRTKAQKLIKAGKVTVNGETVTKPAYAVGALGHARIRVD 76


>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 = 63.7 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 66/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               +      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPSKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>gi|147677532|ref|YP_001211747.1| rRNA methylase [Pelotomaculum thermopropionicum SI]
 gi|146273629|dbj|BAF59378.1| predicted rRNA methylase [Pelotomaculum thermopropionicum SI]
          Length = 266

 Score = 63.7 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 1/61 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          +    R+   +AR G   SR + +  I    V V+G    +  + V  +  IEV G PL 
Sbjct: 2  SQKKLRLDVRLARDGYCPSREKAQAAIMAGLVFVDGERACKPGMMVDPSSVIEVRGCPLP 61

Query: 69 K 69
           
Sbjct: 62 Y 62


>gi|85711025|ref|ZP_01042085.1| Pseudouridylate synthase [Idiomarina baltica OS145]
 gi|85694938|gb|EAQ32876.1| Pseudouridylate synthase [Idiomarina baltica OS145]
          Length = 322

 Score = 63.3 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 26/239 (10%), Positives = 68/239 (28%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           IV E+   +R+ +++A      SR  +++ I + +V V+  ++E+    +     + +D 
Sbjct: 10  IVPESLAGKRLDQILAELFPDYSRSRMKKWITEGKVSVDAQVIEKPREKLEFGALVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  ELEREERYQAQPIELDIVYEDEDILIINKPAGLVVHPGAGAPDGTLLNGLLHYDPDIDHV 129

Query: 111 V-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                  RLD +T GL+++  +      L     +                         
Sbjct: 130 PRAGIIHRLDKDTTGLMVVARNIPAQTQLVDMMQKREITREYEAVCNGVMTAGGMVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V+           +  +  ++  + + L  G+  +I+         + 
Sbjct: 190 GRHPTKRTHMAVVSSGKPAVTHYRVVERFRAHTLLRLRLESGRTHQIRVHMAHIRHPLV 248


>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 = 63.3 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 30/252 (11%), Positives = 75/252 (29%), Gaps = 42/252 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMST 57
           MK + IV E  +  R+ K +    I    +R  +++++  + V+VNG  ++  +    + 
Sbjct: 1   MKQEYIVPEKSSGLRIDKFLTE--ICPDYTRSFLQKLLKSELVEVNGKPVKS-SYKTAAG 57

Query: 58  DHIEVD-GVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           D +  +    +                +   + +      +V   +     + V   +  
Sbjct: 58  DTVTFEVPEAVEAEITAQEMPLDILYEDEDVILINKPKGMVVHPAAGHYEGTLVNGLMHH 117

Query: 104 IF---------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR-------- 146
                       R   V R+D++T G+L++  +      +           +        
Sbjct: 118 CREQLSGINGVMRPGIVHRIDMDTTGVLIVCKNDLAHNSIAEQLKVHSITRKYYAVVFGS 177

Query: 147 -----VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
                   H  + +   +  K  I  +          +  +      V   L  G+  +I
Sbjct: 178 LKDDEGTIHAPIGRHPNDRKKMSINSKNGKDAVTHYKVLERFHGYTLVECRLETGRTHQI 237

Query: 202 KKVFEFFNWKVN 213
           +         + 
Sbjct: 238 RVHMASIGHPLL 249


>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 = 63.3 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 28/243 (11%), Positives = 63/243 (25%), Gaps = 36/243 (14%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +     T QR+ K+++      SR +++  I  + V VNG  ++ A   V   D I +  
Sbjct: 8   VTDTRHTGQRIDKLLSDYNHDWSRSQIQDWIKHELVIVNGKAIK-ANYKVKLHDSIVITE 66

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                           +   ++    +Y     +V         + V   +  I      
Sbjct: 67  KEVVDADIQPENLNLDIYYEDKDVAIVYKPKGMVVHPSPGHYSGTLVNGLMYQIKDLSGI 126

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPST------------QWLRVYRVRFHGQVDQ--- 155
            G +       +     G L       +             +      V  +   D    
Sbjct: 127 NGEIRPGIVHRIDKDTSGLLMVAKNDIAHRSLVDQLVAKSVKRKYTALVHGNIPHDYGTV 186

Query: 156 -----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      +   V+           +         +   L  G+  +I+   ++  +
Sbjct: 187 DAPIGRNKKDRQSMDVVDDGKDAVTHFNVLEHFKDYTLIECQLETGRTHQIRVHMKYIGY 246

Query: 211 KVN 213
            + 
Sbjct: 247 PLV 249


>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 = 63.3 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 33/239 (13%), Positives = 72/239 (30%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E+   QR+ + +A      SR  ++  I +QRV++NG ++++    V+  + + +  
Sbjct: 10  TVDESQLGQRLDQALAELFPDYSRSRIKTWILEQRVQINGNVIDKPKEKVLGGESVSITA 69

Query: 63  --------DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                   D  P++      +   L +      +V   +     + +   L         
Sbjct: 70  IIEEDVRWDAQPIQLDIVYEDEDILVINKPRDLVVHPGAGNPDGTVLNALLHHYPAIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++  +      L                               
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKNVPAQTRLVESLQAREITREYEAVANGTMTAGGSVAEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 ARHPTKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMAHINHPLV 248


>gi|20093836|ref|NP_613683.1| RNA-binding protein [Methanopyrus kandleri AV19]
 gi|19886762|gb|AAM01613.1| Predicted RNA-binding protein containing the S4 domain
          [Methanopyrus kandleri AV19]
          Length = 79

 Score = 63.3 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 23/57 (40%), Positives = 34/57 (59%), Gaps = 1/57 (1%)

Query: 13 PQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +R+   +   G+A SRRE +R++   RV+VNG L+ +    V   D IEVDGV +R
Sbjct: 4  GRRLDAFLRDVGLAESRREAKRLVESGRVRVNGKLVRKPWWLVSPGDEIEVDGVTVR 60


>gi|159029548|emb|CAO87700.1| rluD [Microcystis aeruginosa PCC 7806]
          Length = 308

 Score = 63.3 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 29/240 (12%), Positives = 68/240 (28%), Gaps = 38/240 (15%)

Query: 12  TPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPL 67
             +R+   + ++    SR  ++++I Q  +++NG +       V   D +++   D  PL
Sbjct: 11  KKERLDAWMGSQLPDLSRSRLQKLIEQGYIQLNGQICTNKNTKVGQGDRLKITIPDSQPL 70

Query: 68  R----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD-- 115
           +            E   L + +KP  LV   +      T+ + L      +  +G +   
Sbjct: 71  QLSAEAIDLDILYEDEYLIIINKPADLVVHPAPGHESGTLVNALLHHCPNLAGIGGIQRP 130

Query: 116 ----------------------INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
                                        L T       +  +          +      
Sbjct: 131 GIVHRLDKDTTGAIVIAKTDQAHQHLQAQLKTKTARREYMALVHGVPKSETGTIDLPISR 190

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +     +    V +G         +  + G+   +   L  G+  +I+         + 
Sbjct: 191 HRSDRQKMAIIAVEKGGRNAVTHWQVKERLGNYTLMEFRLETGRTHQIRVHSSHIGHPIL 250


>gi|324005834|gb|EGB75053.1| pseudouridine synthase, RluA family [Escherichia coli MS 57-2]
          Length = 326

 Score = 63.3 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-----F 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYSPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>gi|326565266|gb|EGE15451.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis 12P80B1]
          Length = 355

 Score = 63.3 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 28/242 (11%), Positives = 69/242 (28%), Gaps = 36/242 (14%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           V       R+ K+ A   G  SR  ++  I + ++ VNG +++     V   D + ++  
Sbjct: 48  VSTEQIGIRLDKLCADIFGGFSRANLKNFIDEGQLMVNGKVVK-PKYAVKVGDILTLEAV 106

Query: 64  ------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                        + +   +   + +      +V   +     + V   L     +    
Sbjct: 107 HESHSEDLPENIDIDIIYEDEAVIIINKPAGMVVHPGAGNRTGTLVNALLYHFPKQAHLP 166

Query: 112 -----GRLDINTEGLLLLT---------------NDGGLARVLELPSTQWLRVYRVRFHG 151
                 R+D +T GLL++                                  +   +   
Sbjct: 167 RAGLVHRIDKDTTGLLVIARTKSAQLSLIDQLKDKSVYRHYQCIALGAVHEVLRHAQIDA 226

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + +   +  K  +   G       V         + + + L+ G+  +I+    +    
Sbjct: 227 PIGRHSTHRTKMAVKQTGKPALTHIVNAKYLHERYSLLDIHLKTGRTHQIRVHLSYVGHP 286

Query: 212 VN 213
           + 
Sbjct: 287 LV 288


>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 = 63.3 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 34/239 (14%), Positives = 64/239 (26%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG L ++    V+  + + +D 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILNQRVLVNGQLCDKPKEKVLGGERVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  EIDEEIRFEAQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L                               
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVNEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMSVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 63.3 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 65/239 (27%), Gaps = 38/239 (15%)

Query: 13  PQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP----- 66
             R+ K ++      SR ++++ I   +V VN +++    V V   D I           
Sbjct: 12  GIRLDKALSSLLENVSRNQIQKAIKDSQVLVNDVIISDPDVLVKENDIILFSFKEPEELK 71

Query: 67  ---------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-----RVISVG 112
                    +   +   + +       V   +     + V   L    +          G
Sbjct: 72  IAAANVALDIIYEDDDLIVINKAAGMTVHPGAGHHDDTLVNALLHHTKNLSDIGSSERPG 131

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
            +    +    L       +   L + Q  +   +R +  +    +N L+  I       
Sbjct: 132 IVHRLDKDTTGLMVVAKNNKAHMLLANQIEQKQVIRKYKVLVWGVINPLEGVIKNNIGRS 191

Query: 173 GDMQVTL------------------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +  +                     KGS + V   L  G+  +I+         V 
Sbjct: 192 RSDRQKMTILKYGGKEAVTHYKTLELFYKGSISMVECKLSTGRTHQIRVQLSHLKHSVV 250


>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 = 63.3 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 32/249 (12%), Positives = 71/249 (28%), Gaps = 33/249 (13%)

Query: 5   NIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           N V+++   QR+ + IA      SR  ++  +   +V+VNG ++ +    VM  + I + 
Sbjct: 9   NTVKDSQLGQRLDQAIAELFADFSRSRLKEWLLDGKVQVNGEVVTKPRTKVMGGEEITLQ 68

Query: 63  ----DGVPLRKAERT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
               D       +            + +      +V   +     + +   L        
Sbjct: 69  AELEDEERWEAQDIPLDIVYEDDDIIVINKPRDFVVHPGAGTPDGTVLNALLHHYPDIAE 128

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   RLD +T GL+++         L     +                    + + 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRMTAGGKVDQP 188

Query: 165 IVIQGIC---------YGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I                        +      +  + + L  G+  +I+    +    + 
Sbjct: 189 IGRHSTKRTLMAVAPLGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPL- 247

Query: 214 RLIRISYGP 222
            L   +YG 
Sbjct: 248 -LGDTAYGG 255


>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 = 63.3 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 38/247 (15%), Positives = 74/247 (29%), Gaps = 36/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K  ++      R+ K I+      SR  V+ +I  Q + VN   +E+ +  +   D 
Sbjct: 4   MPKKYSLEVTNQRGRLDKFISEQLSDLSRTRVKELIQDQNILVN-EKVEKVSYKIQDGDK 62

Query: 60  IEV------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           IE+            + +P  +   +   + +      +V         + V   L    
Sbjct: 63  IEITVPAVKPLDIVAENIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHTQ 122

Query: 106 --------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-- 155
                    R   V R+D +T GLL++  +      LE                  +   
Sbjct: 123 DLAQSPEGFRPGIVHRIDKDTSGLLMIAKNATARESLEQQLANKTNKRIYWAIVHGNFSE 182

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           KK  V++          +  Q    + +   L  G+  +I+   
Sbjct: 183 EQGSIDAPIGRNPYDRKKMAVVENGKKAITHFKVLKQFKGYSLIECQLETGRTHQIRVHL 242

Query: 206 EFFNWKV 212
           ++    V
Sbjct: 243 DYIGHAV 249


>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 = 63.3 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 52/322 (16%), Positives = 104/322 (32%), Gaps = 48/322 (14%)

Query: 11  FTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
            TP R+ + + R    A+R +V+  I + RV VN   ++     + S D I++       
Sbjct: 31  QTPMRIDQYLTRQVENATRNKVQEAIEEGRVLVNEKRVKS-NYRIKSCDTIQITFLRPPA 89

Query: 63  -----DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------- 106
                + +P+     +   + +  KP  +V         +     L  I           
Sbjct: 90  PELAPEDIPIDIIYEDEDLMVINKKPGMVVHPAFGNWTGTLANAILHHIGIGAEELDKSS 149

Query: 107 -RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ------------- 152
            R   V RLD NT GL+++  +      L         V   +                 
Sbjct: 150 LRPGIVHRLDKNTSGLIIVAKNPVALHRLARQFADRQVVKIYKAIVWGVPAEQSGTITTN 209

Query: 153 ---VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                +D+  +       +         ++       + +++ L  G+  +I+   +   
Sbjct: 210 IGRSKKDRKVMANFPYEGKDGKTAITDYSVTENLHWFSLLSLTLHTGRTHQIRAHMQHLG 269

Query: 210 WKVNRLIRISYGPFQLGTLL----AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSE 265
            ++  L   +YG   L TL      G  R + + + R+ L    L   Q     P+  + 
Sbjct: 270 HQI--LGDETYGGAVLRTLPFSRSEGFVRNLLELLPRQALHAATLSFHQPTTREPLSFTA 327

Query: 266 TLVRDRPNIISEVPDDFTRMKK 287
            L  D  + I ++        +
Sbjct: 328 PLPEDMQSAIEKIRAVVEANSR 349


>gi|73542442|ref|YP_296962.1| pseudouridine synthase, Rsu [Ralstonia eutropha JMP134]
 gi|72119855|gb|AAZ62118.1| Pseudouridine synthase, Rsu [Ralstonia eutropha JMP134]
          Length = 219

 Score = 63.3 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 50/216 (23%), Positives = 88/216 (40%), Gaps = 19/216 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G ++  S+   R T+ + + +        GRLD ++EGLLLLT+DGGL   +
Sbjct: 3   LIALNKPFGTMSQFSEHPSRPTLAEWIATPGV--YPAGRLDADSEGLLLLTDDGGLQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ------------ 182
             P  +  + Y  +  G  D+  L  L++GI +        +V    +            
Sbjct: 61  ADPRHKLAKTYFAQVEGIPDEAALARLRQGIDLGDFHTLPAKVRAVEEPSWLWPRNPPVR 120

Query: 183 ---KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVS 237
                  +W+ + +REGKNR+++++     +   RL+R + G   L    L  G +  V 
Sbjct: 121 FRAAIPTSWLELQIREGKNRQVRRMTAAVGFPTLRLLRATIGRLDLRELGLQPGQSCIVE 180

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPN 273
              L          E +        +  T ++ R  
Sbjct: 181 PDRLGLPPARTPRPEPRTLGSGNAGTRGTGIKGRVR 216


>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 = 63.3 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNLDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 63.3 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 69/244 (28%), Gaps = 37/244 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +V +  T  RV   +ARA   SR     +I   +V +   +L+ A   V   D I ++  
Sbjct: 7   VVTDKDTGIRVDIYVARALDISRSYAGNLIKNGKVSMRNRILK-ANYRVAEGDEIVIEKD 65

Query: 66  P--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                          +   ++  + +      +V   +     + V   L      +  +
Sbjct: 66  EAEDLTVEAENIPLDIVYEDKDIIIVNKARGMVVHPAAGNPNGTLVNALLWHCGGELSGI 125

Query: 112 G----------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
                                  + D   + L          R         +   + R 
Sbjct: 126 NGVIRPGIVHRLDKDTSGLMVAAKTDAAHKSLAEQIKSHTARRTYVALVHGNIVEAKGRI 185

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +   + +K  + ++         T+  + G+   V   L  G+  +I+    +  
Sbjct: 186 DAPLGRHPKDRVKMAVNMKDGKDAITHFTVLERFGNYTLVQCRLETGRTHQIRVHMAYIG 245

Query: 210 WKVN 213
             V 
Sbjct: 246 HPVV 249


>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 = 63.3 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 29/236 (12%), Positives = 70/236 (29%), Gaps = 32/236 (13%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K  + +    +RV K +++    SR ++E++I    V VN   +++  V + + D ++V+
Sbjct: 3   KRFISDKN--ERVDKFLSQKLNVSRNQIEQLIKNSLVSVNSKTIKKGGVKLQAGDTVDVE 60

Query: 64  ---------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                           +P+   +   L +   P  +V         + V       +   
Sbjct: 61  IKEAESSKEDYEVNFDIPVLYEDEDVLVINKPPGIVVHPAPSVKEATLVDWLKTKNYRLS 120

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIV 166
              G         +     G L       + ++L  ++                LK+ + 
Sbjct: 121 TIAGEERFGIVHRIDKETSGALIIAKNNKAHEFLSAQLKDKTMGRYYIMLLNEPLKEAVC 180

Query: 167 IQGICYG----DMQVTLDTQKGSNAWVTV---------GLREGKNREIKKVFEFFN 209
           +           +++           + V          L  G+  +I+       
Sbjct: 181 VDKPIARNPKNRLKMAYVKNGREAKTLFVPVYENVAAAKLFTGRTHQIRVHLSTIG 236


>gi|218506712|ref|ZP_03504590.1| RNA-pseudouridine synthase protein, ribosomal large subunit B
           [Rhizobium etli Brasil 5]
          Length = 102

 Score = 63.3 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 23/102 (22%), Positives = 43/102 (42%), Gaps = 12/102 (11%)

Query: 1   MKDKNIVQENFTPQRVS-----------KVIARAGIASRREVERMIAQQRVKVNGILLER 49
           M+D+   Q+     +++           + +++ G  SR + ER+IA+ RV ++G  +  
Sbjct: 1   MRDRRPRQKTRERPKLTADAAGKRVTLPRALSKLGYCSRTQAERLIAESRVSIDGRTVND 60

Query: 50  AAVNVMS-TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSD 90
            +  V   T  I VDG  +    +  L L      + T H  
Sbjct: 61  PSAWVDLVTAKIRVDGHVIAAEAKIYLILNKPRGLVTTRHDP 102


>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 = 63.3 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 34/239 (14%), Positives = 64/239 (26%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG L ++    V+  + + +D 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILNQRVLVNGQLCDKPKEKVLGGERVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  EIDEEIRFEAQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L                               
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVNEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 GRHPTKRTHMSVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>gi|312880188|ref|ZP_07739988.1| hemolysin A [Aminomonas paucivorans DSM 12260]
 gi|310783479|gb|EFQ23877.1| hemolysin A [Aminomonas paucivorans DSM 12260]
          Length = 270

 Score = 63.3 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 18/50 (36%), Positives = 31/50 (62%), Gaps = 1/50 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          R+ +++A  G+A SR E +R I + RV+V+G ++ + A  V     I+VD
Sbjct: 7  RLDQLLAERGLATSRTEAQRWIEEGRVRVDGFVIVKPASLVDPDQGIQVD 56


>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 = 63.3 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 30/239 (12%), Positives = 67/239 (28%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I  +R+ VN  ++++    V+  + I +D 
Sbjct: 10  TVSESQLGQRLDQALAELFPDYSRSRIKEWILDRRITVNDTIIDKPKEKVLGGEQISIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  EIEEEARWEAQDIPLNIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLYHFPAIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTHLVDALQRREITREYEAVAIGRMTAGGTVDQPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      +  + 
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHISHPLV 248


>gi|91214888|ref|ZP_01251861.1| RNA pseudouridine synthase family protein [Psychroflexus torquis
           ATCC 700755]
 gi|91187315|gb|EAS73685.1| RNA pseudouridine synthase family protein [Psychroflexus torquis
           ATCC 700755]
          Length = 187

 Score = 63.3 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 38/186 (20%), Positives = 68/186 (36%), Gaps = 21/186 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             +   KP G+++       R      L         ++SVGRLD ++EGLL LT DG  
Sbjct: 2   AYYKIFKPYGMLSQFVYNQKRRKNKRLLGELSDFPEGIMSVGRLDQDSEGLLFLTTDGKF 61

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
           +  +     +     +V    + +  +       I I G  Y  +   +           
Sbjct: 62  SHHITSSGMEKEYWVQVDGIAKKEHVEKLSKGLKISIYGKPYQTLACQVKLMEPPQDLPK 121

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  +   G  +W+++ L EGK R+++K+         RL+R   G   +  + A  
Sbjct: 122 RAKDIRNENDHGVTSWLSITLTEGKFRQVRKMTAKIGLPTLRLVRYRIGEQTIEQMQAEE 181

Query: 233 TREVSK 238
             E+  
Sbjct: 182 VIEMHP 187


>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 = 63.3 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 65/239 (27%), Gaps = 38/239 (15%)

Query: 13  PQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP----- 66
             R+ K ++      SR ++++ I   +V VN +++    V V   D I           
Sbjct: 12  GIRLDKALSSLLENVSRNQIQKAIKDSQVLVNDVIISDPDVLVKENDIILFSFKEPEELK 71

Query: 67  ---------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-----RVISVG 112
                    +   +   + +       V   +     + V   L    +          G
Sbjct: 72  IAAANVALDIIYEDDDLIVINKAAGMTVHPGAGHHDDTLVNALLHHTKNLSDIGSSERPG 131

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
            +    +    L       +   L + Q  +   +R +  +    +N L+  I       
Sbjct: 132 IVHRLDKDTTGLMVVAKNNKAHMLLANQIEQKQVIRKYKVLVWGVINPLEGVIKNNIGRS 191

Query: 173 GDMQVTL------------------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +  +                     KGS + V   L  G+  +I+         V 
Sbjct: 192 RSDRQKMTILKYGGKEAVTHYKTIELFYKGSISMVECKLSTGRTHQIRVQLSHLKHSVV 250


>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 = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 75/246 (30%), Gaps = 35/246 (14%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K +  +      +R+ K +++    SR +++ +I ++ +KVN   ++  +  V   D IE
Sbjct: 3   KQRYEIYVEGESERIDKYLSKKVPLSRSQIQDLIEKELIKVNEKPIKN-SYKVKLGDRIE 61

Query: 62  V------------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
           V              +P+     +   + +      +V         + V   L  +   
Sbjct: 62  VIIPPPVETEVKPQDIPIEIVYEDEDMVIINKPKGMVVHPAHGHYNDTLVNALLYRVKDL 121

Query: 107 -------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
                  R   + RLD +T GLL++  +    + L                 + +     
Sbjct: 122 SGIGGELRPGIIHRLDKDTTGLLIIAKNDLSHQKLSEQLKNRTLRRTYWALCEGEIPWEE 181

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV------------GLREGKNREIKKVFEF 207
              +  + +          +   K +     V             L  G+  +I+     
Sbjct: 182 KRIEAPIGRHPINRKKMAIVPYGKIAITNFKVLERFKGYTLISADLETGRTHQIRVHISH 241

Query: 208 FNWKVN 213
             + + 
Sbjct: 242 LGFPIV 247


>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 = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 28/239 (11%), Positives = 62/239 (25%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG L ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKLCDKPKEKVLGGEQVSINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  EIDEEIRFEPQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--- 156
                  R+       +     +        +  L   + ++  V           D   
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVDEPI 189

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMSVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 26/239 (10%), Positives = 61/239 (25%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + +     V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVMVNGKVWDTPKEKVLGGEVVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  EIDEEVRFEAQDIPLTIVYEDDDILVINKPRGLVVHPGAGNPDGTVLNALLHYYPPITDV 129

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--- 156
                  R+       +     +        +  L   + ++  V           +   
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTSGGTVEEPI 189

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMSVHPMGKPAVTHYRIMEHFRIHTRLRLRLETGRTHQIRVHMSHITHPLV 248


>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 = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 29/240 (12%), Positives = 65/240 (27%), Gaps = 37/240 (15%)

Query: 10  NFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVN----------VMSTD 58
           + T +R+   +AR     SR  V+R+I    V+V+G  ++               V   +
Sbjct: 7   DSTGERLDVFLARQMENCSRSYVQRLITDGNVRVDGARVK-PNYKLRSGEEICCTVPPAE 65

Query: 59  HIEVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
            + +    +       +   + +  +   +V   +     + V   L          G L
Sbjct: 66  EVVIAAEDIPLDVLYEDEDIIVINKERGMVVHPAAGNLTGTLVNALLFRCRDLSGINGEL 125

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------------------- 155
                  L     G +       +  +L         + +                    
Sbjct: 126 RPGIVHRLDKDTSGVMVAAKNDMAHHFLAQQIRSKAARREYRALVHGNIAERAGVITGDI 185

Query: 156 --DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                +  +  IV  G         +  + G   +V+  L  G+  +I+         + 
Sbjct: 186 GRHPTDRKRMAIVRSGGKSATTHFEVLERFGDYTFVSCVLETGRTHQIRVHMTSIGHPLV 245


>gi|313114069|ref|ZP_07799621.1| S4 domain protein [Faecalibacterium cf. prausnitzii KLE1255]
 gi|310623478|gb|EFQ06881.1| S4 domain protein [Faecalibacterium cf. prausnitzii KLE1255]
          Length = 272

 Score = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 13/63 (20%), Positives = 26/63 (41%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           ++ +     +  R+  V+A     SR +   +I   RV++N +  ++    V   D   V
Sbjct: 186 EREMHSATVSSLRLDAVLAAMLHCSRGQASELIEAGRVEINHLPADKPHAQVYEGDVFTV 245

Query: 63  DGV 65
            G 
Sbjct: 246 RGK 248


>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 = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 37/246 (15%), Positives = 72/246 (29%), Gaps = 40/246 (16%)

Query: 8   QENFTPQ--RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           Q    PQ  R+ + ++ +    SR  ++ +I+Q  V VN  +     + +   DHIEV  
Sbjct: 16  QTTLEPQNYRLDRWLSESLETLSRSRIQTLISQGHVTVNQKVCVSKKLTLKRGDHIEVKI 75

Query: 64  --GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGR----------------- 94
               PL             E   L + +K  GLV   S                      
Sbjct: 76  PPNEPLELEAVDIPLDILYEDEHLIIINKQAGLVVHPSAGHVNDTLVNALLAHCDTLAGI 135

Query: 95  -----STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
                  +   L    +  I V + D + + L     +    R          +      
Sbjct: 136 GGVERPGIVHRLDKDTTGAIVVAKTDFSLQSLQQQIKNKTAQRQYLGVVYGSHKADFGTI 195

Query: 150 HGQVDQD--KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
              + +       +    + +G         +  + G+ + +   L  G+  +I+    F
Sbjct: 196 EQPIGRHLADRKKMAVVTIERGGRNAITHWQIQERLGNYSLILFTLETGRTHQIRVHSNF 255

Query: 208 FNWKVN 213
               + 
Sbjct: 256 IGHPIV 261


>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 = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 30/243 (12%), Positives = 65/243 (26%), Gaps = 34/243 (13%)

Query: 5   NIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLER-AAVN------VMS 56
            I     T QR+ K++       SR +++  I    VKVN  +++            V  
Sbjct: 7   KIENPEDTGQRIDKLLPEYHSEWSRTQIQDWIKASLVKVNDQVIKSNYKTKMNDHIVVTE 66

Query: 57  TDHIEVDGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
            + +E D  P      +   +     +Y     +V   +     + V   +  + +    
Sbjct: 67  KETVEADIQPENLNLDIYYEDDDVAIVYKPKGMVVHPSAGHYTGTLVNGLMYQMKNLSGI 126

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQ------------WLRVYRVRFHGQVDQ--- 155
            G +       +     G L       + +               V  V      D    
Sbjct: 127 NGEIRPGIVHRIDKDTSGLLMVAKNDVAHRSLVDQLVNKTVTRKYVALVHGKIPHDYGTV 186

Query: 156 -----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                   N  +   V+           +         +   L  G+  +I+   ++  +
Sbjct: 187 DAPIGRNKNDRQSMDVVDDGKEAVTHFNVLEHFNKYTLIECQLETGRTHQIRVHMKYIGY 246

Query: 211 KVN 213
            + 
Sbjct: 247 PLV 249


>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 = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 29/250 (11%), Positives = 74/250 (29%), Gaps = 38/250 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK + IV E  +  R+ K +       +R  +++++  + V+VNG  ++  +    + D 
Sbjct: 1   MKQEYIVPEKSSGLRIDKFLTESCPDYTRSFLQKLLKSELVEVNGKPVKS-SYKTAAGDT 59

Query: 60  IEVD-GVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           +  +    +                +   + +      +V   +     + V   +    
Sbjct: 60  VTFEVPEAVEAEITAQEMPLDILYEDEDVILINKPKGMVVHPAAGHYEGTLVNGLMHHCR 119

Query: 106 ---------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR---------- 146
                     R   V R+D++T G+L++  +      +           +          
Sbjct: 120 EQLSGINGVMRPGIVHRIDMDTTGVLIVCKNDLAHNSIAEQLKVHSITRKYYAVVFGSLK 179

Query: 147 ---VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                 H  + +   +  K  I  +          +  +      V   L  G+  +I+ 
Sbjct: 180 DDEGTIHAPIGRHPNDRKKMSINSKNGKDAVTHYKVLERFHGYTLVECRLETGRTHQIRV 239

Query: 204 VFEFFNWKVN 213
                   + 
Sbjct: 240 HMASIGHPLL 249


>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 = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 39/244 (15%), Positives = 79/244 (32%), Gaps = 39/244 (15%)

Query: 7   VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE---- 61
           V+     QR+ + +       SR  V+++IA   V VNG +  +    +   D +     
Sbjct: 17  VESEQVGQRLDRFLVSVLDGVSRSGVQQLIADALVLVNGKV-SKPGYVLRLKDRVTALRA 75

Query: 62  --------VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                   V    L      E   L + +K  G+V   +  +   T+ + L + +     
Sbjct: 76  TPASQMKQVTPQNLPLEVVFEDDDLLIVNKAAGMVVHPAPGNYEGTLVNALVAHYPELQQ 135

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY-------------RVR 148
                R   + RLD +T GLL++  +      L     Q   +              +  
Sbjct: 136 DEGDMRPGIIHRLDKDTSGLLMVAKNAQSQAALIEQMKQHKIIKRYLALVEGNVELDQGS 195

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +D  +     + +           +  +   +  V V +  G+  +I+  F+  
Sbjct: 196 IDAPIGRDTRHRQMMAVTLTEGRDAVTHFRVLQRFRKHTLVLVQIVTGRTHQIRVHFQAI 255

Query: 209 NWKV 212
              V
Sbjct: 256 KHPV 259


>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 = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 39/244 (15%), Positives = 80/244 (32%), Gaps = 38/244 (15%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           +  +    R+ K +A      SR  +++++    V VN  +++ A       DH+ ++  
Sbjct: 8   IDSSEKNVRIDKYLAECCPDLSRSYLQKLLKDGAVSVNTRIVK-ANYKTQPGDHVILNIP 66

Query: 64  ----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------- 105
                      +PL    E   L + +KP  +V   S      T+ + + +         
Sbjct: 67  DLQTPDIKPENIPLDILYEDQWLMVVNKPKDMVVHPSAGHMEGTLVNAVMAHCGDNLSGI 126

Query: 106 ---SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-------------F 149
               R   V R+D +T G LL+  D  + R L     +     R R              
Sbjct: 127 NGVMRPGIVHRIDKDTTGALLICKDDMVHRNLAEQLKEHSIKRRYRAIVQGNIKEDEGTV 186

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +  ++  K  I  +          +  + G   ++   L  G+  +I+       
Sbjct: 187 DAPIGRHPIDRKKMAINHKNGKEAVTHYKVLERFGQTTYIECRLETGRTHQIRVHMASLG 246

Query: 210 WKVN 213
             + 
Sbjct: 247 HPLL 250


>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 = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 37/243 (15%), Positives = 75/243 (30%), Gaps = 38/243 (15%)

Query: 8   QENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           +E    QR+ K +AR     SR   ++++    V ++G + + A+  +   D I      
Sbjct: 12  EEQDENQRIDKYLARVMPEISRSYFQKLLKDGGVFIDGKVAK-ASDRLQCGDEIYFQMPK 70

Query: 63  ----DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----- 107
               D  P      +   +   L +      +V         + V   L     +     
Sbjct: 71  SREPDIEPEDLSLDILYEDPYLLVINKPKGMVVHPCPGHYSGTLVNGVLFHCKGQLSGIN 130

Query: 108 ----VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-------------FH 150
                  V R+D +T G L++  D    R L +   +     R R               
Sbjct: 131 GVLRPGIVHRIDKDTTGALVVCKDDQTHRNLAVQLAEHTITRRYRAIVTGNLSADEGTVE 190

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           G + +  ++  K  I  +          +  + G   ++   L  G+  +I+        
Sbjct: 191 GPIGRHPVDRKKMSINFKNGKDAVTHYRVLERFGKATYIECRLETGRTHQIRVHLSSIGH 250

Query: 211 KVN 213
            + 
Sbjct: 251 PLL 253


>gi|309389006|gb|ADO76886.1| ribosomal large subunit pseudouridine synthase D [Halanaerobium
           praevalens DSM 2228]
          Length = 303

 Score = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 30/249 (12%), Positives = 83/249 (33%), Gaps = 37/249 (14%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           MK+ +  V++    QR+ K +A+     SR  ++++I ++ +KVN  ++++ +  +++ D
Sbjct: 1   MKEYSLTVKKKDQGQRIDKYLAKYFKDLSRSFIQKLIKEKEIKVNNRVIDK-SYKIINND 59

Query: 59  HIEVDGVP-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            IE+                 +   ++  + +      +V         + V   L  + 
Sbjct: 60  FIELKLKEQESKVKAVAMKLDIVYEDQDIIVINKDADRVVHPAPGHYNDTIVNGLLACVD 119

Query: 106 SRVISVG---------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRV 144
           +     G                     + D + + L        + +         L  
Sbjct: 120 NLSAINGIKRPGIVHRLDKDTSGLLIVAKNDKSHKSLAKQFKARTVDKYYFALIEGNLAY 179

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
            + +    + +D  +  K  +  +       +  +  +      V V +  G+  +I+  
Sbjct: 180 KKGKIEAPIGRDPNHRKKMAVRKRHSKNAISRFKIIEEFNHYTLVEVKIETGRTHQIRVH 239

Query: 205 FEFFNWKVN 213
           F +    + 
Sbjct: 240 FSYLGHPIV 248


>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 = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 24/231 (10%), Positives = 56/231 (24%), Gaps = 35/231 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+ KV+A      SR  +++ I    V+VNG  ++     +   D + ++          
Sbjct: 16  RIDKVLAHQFNQFSRSHLQKWIVDGNVRVNGQPVK-PKYKLAVGDQVVIEPEAPQKVDLT 74

Query: 67  -------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
                  +   +   + +      +V         + V   L       I+         
Sbjct: 75  PEKIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHSPLSTINGEFRPGIVH 134

Query: 120 GL-------------------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
            +                   L         +   +     +                  
Sbjct: 135 RIDKDTSGLLMVAKNDLAHRSLAAQLKAKTNQREYVALVHGVIKQDAGTIDAPIGRSKKD 194

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            KK  V+    +      +  +      V+  L  G+  +I+   +     
Sbjct: 195 RKKQAVVSDGRHAVTHFKVLRRFRHYTLVSCRLETGRTHQIRVHMKSIGHP 245


>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 = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 29/242 (11%), Positives = 67/242 (27%), Gaps = 39/242 (16%)

Query: 10  NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
             +  R+ + +A      SR  ++++I +  V VNG     A+  +   D I V      
Sbjct: 11  EESGLRIDRYLADHLDGQSRNSIQKLIEEGLVLVNGNACR-ASYKLQEKDQIFVSVPDAV 69

Query: 63  ----------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGR------------ 94
                           D   L   +   + ++  P     T  +                
Sbjct: 70  LTELRPERIPLDILYEDDQLLIVNKPKEMVVHPAPGHNTGTLVNAIMYHCGKELSGINGE 129

Query: 95  --STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152
               +   +    +  + V + D     +     +  + RV        L          
Sbjct: 130 IRPGIVHRIDMNTTGSLIVCKTDAAHRFIASQIKEHSVHRVYRAIVYGHLNPTEGTIRTS 189

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWK 211
           + +D  +  K  + ++             +  +N ++V   L  G+  +I+         
Sbjct: 190 IGRDPRDRKKMSVGVKNGRQAITHYRELARLRNNFSYVEFELETGRTHQIRVHMASIGHP 249

Query: 212 VN 213
           + 
Sbjct: 250 IL 251


>gi|323466424|gb|ADX70111.1| Pseudouridine synthase [Lactobacillus helveticus H10]
          Length = 310

 Score = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 34/247 (13%), Positives = 74/247 (29%), Gaps = 36/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K  +Q      R+ K ++      SR  V+ ++ ++ + VN  + +  +  + + D 
Sbjct: 8   MPKKYELQVENEYGRLDKFVSEQIPDLSRTRVKELVKEKEILVNHKVEKV-SYKIQAGDK 66

Query: 60  IEVDGVPLR--------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           IE++   ++                +   + +      +V         + V   L    
Sbjct: 67  IEINVPAVKPLDVVPENIPLDIVYEDEDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHTQ 126

Query: 106 --------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-- 155
                    R   V R+D +T GLL++  +      LE                  +   
Sbjct: 127 DLAQSPEGFRPGIVHRIDKDTSGLLMIAKNAKARESLEDQLAHKTNKRIYWAIVHGNFGE 186

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           KK  V++          +  Q    + +   L  G+  +I+   
Sbjct: 187 ENGVIDAPIGRNPYDRKKMAVVENGKKAVTHFKVLRQFKGYSLIECQLETGRTHQIRVHL 246

Query: 206 EFFNWKV 212
           ++    V
Sbjct: 247 DYIGHAV 253


>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 = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 34/239 (14%), Positives = 64/239 (26%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG L ++    V+  + + +D 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILNQRVLVNGQLCDKPKEKVLGGERVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  EIDEEIRFEAQDIPLDIVYEDDDILVINKPRDLVVHLGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L                               
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVNEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMSVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 35/245 (14%), Positives = 73/245 (29%), Gaps = 38/245 (15%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E     R+ KV+++     SR  +++++    V VNG ++ +    + ++D I V+ 
Sbjct: 8   TVSEENIGDRIDKVLSKQLPEMSRSSLQKLVNDGCVLVNGNIVSK-NYKIKNSDTISVEI 66

Query: 64  -----------GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                       +P+     + + L +      +V   +     + V   L     R+ S
Sbjct: 67  PEAEELKAEPQDIPIDIVYEDDSLLVVNKPQGMVVHPAAGNPDGTLVNALLFHCKGRLSS 126

Query: 111 VG----------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
           +                       + D     L     D    R          +     
Sbjct: 127 INGVIRPGIVHRIDKFTSGLLMVAKTDKAHNFLAQQIKDHNFTREYNAICIGRFKEPTGT 186

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
            +  + + K +  K  +  Q          +    G  + V   L  G+  +I+    F 
Sbjct: 187 VNEPIGRSKFDRKKMCVTYQNCKEAVTHYEVLEDLGQYSLVKFRLETGRTHQIRVHSAFI 246

Query: 209 NWKVN 213
              V 
Sbjct: 247 GHPVL 251


>gi|303272139|ref|XP_003055431.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226463405|gb|EEH60683.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 126

 Score = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 20/72 (27%), Positives = 30/72 (41%), Gaps = 2/72 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDH 59
           KD+        P+R  KV+A  G   R E +  I   RV   G +++       V   D 
Sbjct: 38  KDRKSGPIVEEPERADKVLASHGYCKRSEAKAWIRHGRVTFEGDVVKTCDAKVVVRLYDG 97

Query: 60  IEVDGVPLRKAE 71
           + VDG P+   +
Sbjct: 98  VCVDGKPVPLTK 109


>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 = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 78/248 (31%), Gaps = 42/248 (16%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V +  TP R+ + + +     +R +V+  I + RV VNG  ++     V S DHI +   
Sbjct: 27  VSKVQTPMRIDRYLTQQVENMTRNKVQAAIEEGRVLVNGKPVKS-NYRVKSCDHIHLTFL 85

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------- 105
                    + +P+    E   L +  K  G+V   +  +   T+ + +           
Sbjct: 86  RPPAPELAPEDIPITILYEDDDLMVIDKEAGMVVHPAFGNWTGTLANAILHHLGKDADEL 145

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------ 155
                R   V RLD +T GL+++  +      L             +             
Sbjct: 146 DKTEMRPGIVHRLDKDTSGLIIIAKNPTALHKLARQFANRQVEKVYKAIVWGVPKAESGT 205

Query: 156 --------DKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                    K   +      +G           +    G  + + V L  G+  +I+   
Sbjct: 206 IKTNIGRSHKNRKVMANFPYEGAEGKHAITDYQVVEDLGYFSLMDVTLHTGRTHQIRVHL 265

Query: 206 EFFNWKVN 213
           +     + 
Sbjct: 266 QHLGHSIL 273


>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 = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 31/247 (12%), Positives = 76/247 (30%), Gaps = 35/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  + I+  +   +R+ K + +     SR  ++ +I++  +KV+G  ++     +   + 
Sbjct: 1   MDTQKIIYTSPKSERIDKFLQQELTDVSRTNIQNLISEGYIKVDGNNIKT-NYKLKDGNV 59

Query: 60  IEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I ++                 +   +   + +      +V         + V   L    
Sbjct: 60  ITIEYKEPEELDVVKQDIPIDIVYEDDDLIIVNKAKGMVVHPSVGHKDGTLVNALLFHSE 119

Query: 106 -------SRVISVGRLDINTEGLLLLTNDGGLA----RVLELPSTQWLRVYRVRFHGQVD 154
                   R   V R+D +T GLL++  +         ++     +      V    + D
Sbjct: 120 LSSINGTIRPGIVHRIDKDTSGLLIVAKNDKAHVKLSEMIANKDVKRKYYALVHGSIKHD 179

Query: 155 Q--------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          K+  VI           +  +      +   L  G+  +I+   +
Sbjct: 180 YGTIDAPIARNPKERKEMAVIDEGKLSITHFKVVDRFEKYTLIECELETGRTHQIRVHMK 239

Query: 207 FFNWKVN 213
           + N  + 
Sbjct: 240 YINHPLV 246


>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 = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 26/238 (10%), Positives = 65/238 (27%), Gaps = 40/238 (16%)

Query: 14  QRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           +R+ K  A+  +    SR +++  I    + VNG  ++ A   +   D I +        
Sbjct: 26  ERIDKY-AKTQLGEEFSRSQIQLWIEAGNLVVNGAPVK-ANYKLAEGDRIVLVIPEAEPT 83

Query: 63  ----DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR--- 113
               + +PL     +   + +      +V         + V   +          G    
Sbjct: 84  EIVPEDIPLEIYYEDSDVIVVNKPRGMVVHPAPGHTSGTLVNALMFHCKDLSGINGELRP 143

Query: 114 ------------------LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
                              D     L        + R         +   +      + +
Sbjct: 144 GIVHRIDKDTSGLIMAAKNDKAHASLAAQLKAHTVTRKYYALVHGNVSHDQGTVDAPIGR 203

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           D  +     ++ +   +      +  + G    + + L  G+  +I+   +F    + 
Sbjct: 204 DPHDRKMYTVIERNSKHAVTHFQVVERFGDYTLLELKLETGRTHQIRVHMKFIGHPLV 261


>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 = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 65/239 (27%), Gaps = 38/239 (15%)

Query: 13  PQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP----- 66
             R+ K ++      SR ++++ I   +V VN +++    V V   D I           
Sbjct: 12  GIRLDKALSSLLENVSRNQIQKAIKDSQVLVNDVIISDPDVLVKENDIILFSFKEPEELK 71

Query: 67  ---------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-----RVISVG 112
                    +   +   + +       V   +     + V   L    +          G
Sbjct: 72  IAAANVALDIIYEDDDLIVINKAAGMTVHPGAGHHDDTLVNALLHHTKNLSDIGSSERPG 131

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
            +    +    L       +   L + Q  +   +R +  +    +N L+  I       
Sbjct: 132 IVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRKYKVLVWGVINPLEGVIKNNIGRS 191

Query: 173 GDMQVTL------------------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +  +                     KGS + V   L  G+  +I+         V 
Sbjct: 192 RSDRQKMTILKYGGKEAVTHYKTLELFYKGSISMVECKLSTGRTHQIRVQLSHLKHSVV 250


>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 = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 31/237 (13%), Positives = 67/237 (28%), Gaps = 37/237 (15%)

Query: 11  FTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGV 65
            T +R+ K++A A +A  SR + +  I   ++ V+G  ++           I V   D  
Sbjct: 9   TTTERLDKLVADA-VATVSRSQAKLAIEAGQITVDGATVK-PKDKPKVGATIRVSLPDPE 66

Query: 66  P-----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
           P           +   +   L +      +V         + V   L       I+    
Sbjct: 67  PLDLTPEDIPLEIVYEDADVLVVNKPQGMVVHPAPGHPNHTLVNALLYHSPLSQINGTLR 126

Query: 115 DINTEGL--------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK--------- 157
                 +        ++  ND     +      +      V       +++         
Sbjct: 127 PGIVHRIDKDTSGLLMVAKNDHAHQSLSAQLQAKTNLREYVAIVHGNIKEEDGVIRAPLG 186

Query: 158 --LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                 KK  ++           +  + G+   +   L  G+  +I+    + N  V
Sbjct: 187 RSPKDRKKQAIVADGRPAVTHFRVLERYGTYTLIACRLETGRTHQIRVHMAYINHPV 243


>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 = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 28/242 (11%), Positives = 67/242 (27%), Gaps = 33/242 (13%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T QR+ + +A      SR  ++  I    V ++G +  +    V+    + V
Sbjct: 8   KSEITATQTGQRLDQTLADLFPDYSRTRIKEWILDGSVTIDGDVSNKPREKVLEGQIVVV 67

Query: 63  DGVPLR--------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
               +                 +   L +  +   +V   +     + +   L       
Sbjct: 68  GATLVEETTAKAQAIDLNIVYEDDHILVINKQAGLVVHPGAGNSDGTLLNALLHHCPGIE 127

Query: 109 ISV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR------------VRFHG 151
           +        RLD +T GL+++         L                             
Sbjct: 128 LVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVSALQAREITREYEAIVLGSLISGGTVDE 187

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +D+         +V  G         +  +  ++  + + L  G+  +I+         
Sbjct: 188 PIDRHPTKRTHMAVVYSGKPAMT-HFRVAEKFRAHTRLRLRLESGRTHQIRVHMAHLGHT 246

Query: 212 VN 213
           + 
Sbjct: 247 LV 248


>gi|291279336|ref|YP_003496171.1| hemolysin A [Deferribacter desulfuricans SSM1]
 gi|290754038|dbj|BAI80415.1| hemolysin A [Deferribacter desulfuricans SSM1]
          Length = 268

 Score = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+ K++ + G+A SR + +R+I    V VN   +++    +    HI++
Sbjct: 5  RLDKILFQRGLAESREKAQRLIMAGLVIVNNEKIDKPGTKIDENAHIKL 53


>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 = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 28/234 (11%), Positives = 63/234 (26%), Gaps = 36/234 (15%)

Query: 14  QRVSKVIARA---GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           +R+ + +  A      SR +++R I   +  V+G +    +  + S   +E+        
Sbjct: 26  ERLDRFLGEALSHTDLSREKIKRAIRDGQCTVDGTVCTTPSTRLRSGQRVELAIAPAATA 85

Query: 63  ----DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
               +G          L +  KP GL           T+   L   F  + +        
Sbjct: 86  VEPEEGDLTIIHRDEHLLVIDKPAGLTVHPCPSCPEGTLVHRLVHHFDALRAQEGFRPGI 145

Query: 119 EGLLLLTNDG------------GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
              +     G             L+      + +   +  V        +    + +   
Sbjct: 146 VHRIDKDTSGLLLVALSEGVRLKLSEAFAERTVEKEYLALVHGVPPATGEVDAPIGRHPT 205

Query: 167 IQGICY-----GDMQVTL----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +            +          +G  A V V +  G+  +I+       + 
Sbjct: 206 HKVRMAVVKGGKPARSEWRVLHAAPEGHYALVAVRIHSGRTHQIRVHMAHAGFP 259


>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 = 63.3 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 28/269 (10%), Positives = 70/269 (26%), Gaps = 64/269 (23%)

Query: 3   DKNIVQENFTPQRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
            + I  E+   QR+ + +A+      SR  ++ +I +  +K++G L+      + S   I
Sbjct: 2   TQQITDEDALGQRIDQWLAKHYQNELSRSRLQTLIREGYLKIDGKLVTEPKTKIKSNQTI 61

Query: 61  EV----------DGVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-- 104
           E+          +G  +       +   + +      +V         + V   +     
Sbjct: 62  ELTIPTLNNAYPEGEAIPLHILFEDDHIIVVNKPAGLVVHPGHGNWTGTLVNALIYHCGD 121

Query: 105 ----------------------------------------FSRVISVGRLDINTEGLLLL 124
                                                   FS     G LD     L+  
Sbjct: 122 SLSGIGGVRRPGIVHRLDKNTSGVIVVAKNDLAHKGLSAQFSDHGRTGVLDRRYHALIWG 181

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           + +  +  +            +       +    + +    VI+       ++       
Sbjct: 182 SPNRNIGVITASLGRARYDRTKQAVIHSHNIYARHAVTHFSVIEKYQTCADKIPFA---- 237

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             + +   L  G+  +I+         + 
Sbjct: 238 --SLLECRLETGRTHQIRVHMAHIGHPLV 264


>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 = 62.9 bits (151), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 75/244 (30%), Gaps = 37/244 (15%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---- 60
           I+ +N   QR+ K +A      SR  ++++I    V VN    ++ +  +   D +    
Sbjct: 8   IIDDNDVDQRLDKFLAYQNEELSRSYIQKLIDNGEVTVN-KEEKKNSYRLQVGDEVKLII 66

Query: 61  ----EVDGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
               EV+  P      +   +   + +  +   +V         + V   L    +    
Sbjct: 67  PQPEEVEIKPESIPLEVIAEDEDIVVINKQADLVVHPAPGHKQGTLVNALLYHCDNLSGI 126

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPST---------------------QWLRVYRVRF 149
            G +       L     G +       +                        ++  + + 
Sbjct: 127 NGEIRPGIVHRLDKDTSGAIVAAKNDQAHRNLVKQFKERRTEKIYLALVEGNIKHNKAKI 186

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +D  N  +  +  +       +  +  + G+  WV + L  G+  +I+    + +
Sbjct: 187 DAAIGRDPYNRKRMAVTKRNSKQAVTRFEVLERFGNYTWVKLKLETGRTHQIRVHMSYID 246

Query: 210 WKVN 213
             V 
Sbjct: 247 NPVV 250


>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 = 62.9 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 27/239 (11%), Positives = 63/239 (26%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            + E+   QR+ + +A      SR  ++  I   RV+VNG ++ +    V  ++ I +D 
Sbjct: 10  TIAESQLGQRLDQALAELFPDYSRSRIKEWILADRVQVNGKVINKPKEKVFGSEQILIDA 69

Query: 64  ----GVPLRKAERT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                      +            L +      +V   +     + +   L         
Sbjct: 70  LIEEDNRWEPQDIPLNVIYEDEDILIINKPRDLVVHPGAGNPDGTILNALLYRYPEIADV 129

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--- 156
                  R+       +     +        A      + ++  V   R       +   
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTHLVEALQRREITREYEAVAVGRMTAGGMVEEPI 189

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRVMEHFRAHTRLRLRLETGRTHQIRVHMAHINHPLI 248


>gi|325694604|gb|EGD36513.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK150]
          Length = 298

 Score = 62.9 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 35/240 (14%), Positives = 67/240 (27%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GV 65
           ++ +   QR+ K +A     SR      I   R+ VNG   ++A   V   D I  +   
Sbjct: 5   IEASVAGQRLDKAVAELTDLSRSLANEQIKDGRILVNGQ-AKKAKYAVKEGDVISYELPE 63

Query: 66  P-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
           P             +   +     +      +V   +     + V   +  I       G
Sbjct: 64  PEVVEYVAEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGING 123

Query: 113 RLDINTEGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLK 162
            L       +     G L       +           + LR Y    HG +  D+  +  
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLSNDRGVIEA 183

Query: 163 KGIVIQGICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                +                 +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 184 PIGRSEKDRKKQAVTAKGKPALTRFQVLERFGDYSLVELQLETGRTHQIRVHMAYIEHPV 243


>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 = 62.9 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 28/240 (11%), Positives = 67/240 (27%), Gaps = 35/240 (14%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T QR+ + +A      SR  ++  I    V ++G   ++    V+    + +
Sbjct: 8   KSEITATQTGQRLDQTLADLFPDYSRTRIKEWILSGSVFIDGETSDKPRFKVLEGQVVTI 67

Query: 63  DGVP---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
            G                 +   +   L +  +   +V   +     + +   L      
Sbjct: 68  -GATLEEETKAEAEAIDLDIIYEDDHILVINKQAGLVVHPGAGNQSGTLMNALLHHCPGI 126

Query: 108 VISV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR------------VRFH 150
            +        RLD +T GL+++         L                            
Sbjct: 127 ELVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVTALQAREITREYEAIVTGTIIAGGTVD 186

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             +D+         +V  G         +  +  ++  + + L  G+  +I+        
Sbjct: 187 EPIDRHPTKRTHMAVVHNGKPAMT-HYRVAEKFRAHTRLRLRLESGRTHQIRVHMAHIGH 245


>gi|257898611|ref|ZP_05678264.1| pseudouridylate synthase [Enterococcus faecium Com15]
 gi|257836523|gb|EEV61597.1| pseudouridylate synthase [Enterococcus faecium Com15]
          Length = 303

 Score = 62.9 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 30/235 (12%), Positives = 67/235 (28%), Gaps = 36/235 (15%)

Query: 12  TPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
              R+ KV+       SR +++  + ++ V VNG  ++ A   V   D I V        
Sbjct: 11  ESGRIDKVLTNLFSDYSRSQIQLWLKERAVSVNGQPVK-ANYKVKQGDEITVLIPEPETL 69

Query: 63  ----DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
               + +P  +   +     +      +V   +     + V   +  I       G +  
Sbjct: 70  DVVPENIPLTIVYEDEDVAVINKPQGMVVHPSAGHTHGTMVNALMYHIKDLSTINGVIRP 129

Query: 117 NTEGLLLLTNDGGLARVLELPSTQ------------WLRVYRVRFHGQVDQDKLNL---- 160
                +     G L       + +               V  V      ++  +N     
Sbjct: 130 GIVHRIDKDTSGLLMVAKNDQAHESLAKQLKDKTSLRKYVALVHGEIPHEKGTINAPIGR 189

Query: 161 ----LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                K   + +         T+  +      V + L  G+  +I+   ++  + 
Sbjct: 190 SKENRKMQAIREDGKPAVTHFTVLERFEGFTLVELKLETGRTHQIRVHMKYIGYP 244


>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 = 62.9 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 28/238 (11%), Positives = 66/238 (27%), Gaps = 31/238 (13%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T  R+ + +A      SR  ++  I    V V+G+++ +    V     I +
Sbjct: 8   KSEISATQTGLRLDQALAELFPDYSRTRIKEWILSDAVHVDGVVVNKPREKVYELQQILI 67

Query: 63  D--------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           D               + +   +   + +  +   +V   +     + +   L       
Sbjct: 68  DATLEEEVHAAAQAIDLDIVYEDDDIIVINKQAGLVVHPGAGNADGTLMNALLHHCPDIE 127

Query: 109 ISV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------- 155
                    RLD +T GL+++         L                             
Sbjct: 128 HVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIVMGTMTGGGTVDE 187

Query: 156 ---DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                L       V+           +  +  ++  + + L  G+  +I+   E+   
Sbjct: 188 PIGRHLTKRTHMAVLHSGKPAVTHYRVAEKFRNHTRLRLRLESGRTHQIRVHMEYIGH 245


>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 = 62.9 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 23/201 (11%), Positives = 58/201 (28%), Gaps = 5/201 (2%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--LRKAERTRL 75
           K+++     S ++ +++I   RV + G  L  A          EV      +   E   L
Sbjct: 6   KLLSAQMGISHKQAQKLIDLGRVCLGGRKLTLARQLCPLQSKFEVQNSKAQILYQETDWL 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL- 134
           +L                   +   L    + V+++ +   + +GL            + 
Sbjct: 66  FLNKPAGVNSYALEKQHPPYKLLHRLDLPTTGVLALAQNHAHAQGLEAFKKRAVYKEYIA 125

Query: 135 --ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
             +    +   +       +   +      K ++         ++T   Q  +   + V 
Sbjct: 126 LVQGVIKKPQTLRMPLRVQKSHIEDAKGFVKTLLDPAGRPACTKITPLKQYKNKTLLKVV 185

Query: 193 LREGKNREIKKVFEFFNWKVN 213
           +  G   +I+         + 
Sbjct: 186 ITTGITHQIRAHLSALGCPIV 206


>gi|313678868|ref|YP_004056608.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Mycoplasma bovis PG45]
 gi|312950295|gb|ADR24890.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Mycoplasma bovis PG45]
          Length = 284

 Score = 62.9 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 37/267 (13%), Positives = 83/267 (31%), Gaps = 44/267 (16%)

Query: 4   KNIVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K +  +N   +++ K I+        SR  + +++ Q+ VK+NG  +  +   +   D +
Sbjct: 3   KFVAHKNDGGRKLIKYISSLFKDLPESR--IYKLLRQKCVKINGKRITDSNHIINEGDEV 60

Query: 61  EVDGV-----------------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
            + G+                  +   +   L +  K   +V           +      
Sbjct: 61  VIYGIKEQATIYIYDVGLQLDSKIIYEDDNILIINKKAGKVVHGELLCLDNQVLSYLKFK 120

Query: 104 IFSRVISV--GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
             S       GRLD  T GL++   +    R L      + ++Y ++       + ++  
Sbjct: 121 QNSSFKPSHVGRLDKWTSGLIVYAKNYKALRELNDKIGFFDKIYTLKSDYNGGDNVVSAY 180

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLREGKNREIKKVFEFFNWKVNR 214
                                +     + V        L  G+  +I+   E+  + +  
Sbjct: 181 IHHDEKMQKMIVTKNPAGLNNQIVKTKIYVDSNKLYAQLLTGRKHQIRATMEYLGYPI-- 238

Query: 215 LIRISYGPFQLGTLLAGSTREVSKKIL 241
                YG  + G       R+ + K +
Sbjct: 239 -----YGDIKYG------WRKKTNKRI 254


>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 = 62.9 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 32/269 (11%), Positives = 78/269 (28%), Gaps = 40/269 (14%)

Query: 4   KNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE- 61
           K +  +  +  R+ K +      A+R ++++      + VN I ++     V   D +  
Sbjct: 20  KFVATKGQSILRIDKYLMHLLENATRNKIQQAATSGNIFVNNIPVKS-NYKVKPFDVVTI 78

Query: 62  ----------VDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                     VD   +       +   L +      +V         + V        + 
Sbjct: 79  MLSHPPFENRVDPEDIPLDIVYEDDALLLINKPAGLVVHPGHGNYTGTLVNALAFHFQNL 138

Query: 108 VISV-------GRLDINTEGLLLLTNDGGLARV----LELPSTQWLRVYRVRFHGQVD-- 154
            ++         R+D +T GLL++              E  +++   +  V  + Q D  
Sbjct: 139 PLNSSERPGLVHRIDKDTTGLLVIAKTEQAMTHLAKQFENKTSEREYIAIVWGNVQKDEG 198

Query: 155 -------QDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                  +   + ++  +               +  + G    ++  L  G+  +I+   
Sbjct: 199 TIEGNLARHLKDRMQMAVFADPEIGKPAITHYKVLERFGYITVISCKLETGRTHQIRAHL 258

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +     +    R   G   L        +
Sbjct: 259 KHIGHPLFNDERYG-GHLILKGTTFTKYK 286


>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 = 62.9 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 32/249 (12%), Positives = 73/249 (29%), Gaps = 33/249 (13%)

Query: 5   NIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           N V+++   QR+ + IA      SR  ++  +   +V+V+G ++ +    VM  + I + 
Sbjct: 9   NTVKDSQLGQRLDQAIAELFADFSRSRLKEWLLDGKVQVDGEVVTKPRTKVMGGEEITLQ 68

Query: 63  ----DGVPLRKAERT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
               D       +            + +      +V   +     + +   L        
Sbjct: 69  AELEDEERWEAQDIPLDIVYEDEDIIVINKPRDFVVHPGAGTPDGTVLNALLHHYPDIAE 128

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   RLD +T GL+++         L     +                    + + 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRMTAGGKVDQP 188

Query: 165 IVIQGIC---------YGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I                        +  +   +  + + L  G+  +I+    +    + 
Sbjct: 189 IGRHSTKRTLMAVAPMGKPAVTHYRVAERFREHTRIRLRLETGRTHQIRVHMSYLQHPL- 247

Query: 214 RLIRISYGP 222
            L  I+YG 
Sbjct: 248 -LGDIAYGG 255


>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 = 62.9 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 30/239 (12%), Positives = 64/239 (26%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I   +V V+G  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILDDKVSVDGKTINKPKEKVLGGEIVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  QIEEAARWEPQEIPLDIVYEDSDILVINKPRGLVVHPGAGNPDGTVLNALLYYYPEIVDV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L                               
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGKMTAGGLVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 SRHSTKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHINHPLV 248


>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 = 62.9 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 40/247 (16%), Positives = 72/247 (29%), Gaps = 38/247 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK+  I  +     R+ KVI+      SR   + +I  Q +K+NG  ++     V S D 
Sbjct: 1   MKEYIITNQTG---RLDKVISELDSSISRSRAKNLIDDQHLKINGEPVK-PKYQVKSGDK 56

Query: 60  IEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I+VD V               +   +   + +      +V         + V   L    
Sbjct: 57  IQVDSVQPTPISLEPENMPLDIVYEDDDVIVVNKPQGMVVHPSPGHPDHTLVNALLYHSP 116

Query: 106 -------SRVISVGRLDINTEGLLLLTNDGGLARVLELPST------------QWLRVYR 146
                   R   V R+D +T GLL++  +    + L                        
Sbjct: 117 LSTINGEFRPGIVHRIDKDTSGLLMVAKNDKAHQFLSQQLQAQKNLRKYVALVHGRIKED 176

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          KK  V+           +  +      V   L  G+  +I+   +
Sbjct: 177 SGVVNAPIGRSPKDRKKQAVVSDGRSAVTHFEVLERFADYTLVACRLETGRTHQIRVHMK 236

Query: 207 FFNWKVN 213
           +    + 
Sbjct: 237 YIGHPIV 243


>gi|320449902|ref|YP_004201998.1| ribosomal RNA large subunit methyltransferase J [Thermus
          scotoductus SA-01]
 gi|320150071|gb|ADW21449.1| ribosomal RNA large subunit methyltransferase J [Thermus
          scotoductus SA-01]
          Length = 244

 Score = 62.9 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ + +   G+A SR + +R+I   +VKV G ++ + A  V     +EV
Sbjct: 1  MRLDRYLVERGLAESREKAQRLIQSGQVKVAGQVVTKPAHRVPEGAQVEV 50


>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 = 62.9 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 28/234 (11%), Positives = 63/234 (26%), Gaps = 36/234 (15%)

Query: 14  QRVSKVIARA---GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           +R+ + +  A      SR +++R I   +  V+G +    +  + S   +E+        
Sbjct: 26  ERLDRFLGEALSHTDLSREKIKRAIRDGQCTVDGTVCTTPSTRLRSGQRVELAIAPAATA 85

Query: 63  ----DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
               +G          L +  KP GL           T+   L   F  + +        
Sbjct: 86  VEPEEGDLTIIHRDEHLLVIDKPAGLTVHPCPSCPEGTLVHRLVHHFDALRAQEGFRPGI 145

Query: 119 EGLLLLTNDG------------GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
              +     G             L+      + +   +  V        +    + +   
Sbjct: 146 VHRIDKDTSGLLLVALSEGVRLKLSEAFAERTVEKEYLALVHGVPPATGEVDAPIGRHPT 205

Query: 167 IQGICY-----GDMQVTL----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +            +          +G  A V V +  G+  +I+       + 
Sbjct: 206 HKVRMAVVKGGKPARSEWRVLHAAPEGHYALVAVRIHSGRTHQIRVHMAHAGFP 259


>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 = 62.9 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 37/267 (13%), Positives = 89/267 (33%), Gaps = 49/267 (18%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +V E+   +R+ K ++ +    SR  ++ +I + +V+V G  ++  +  V    +I +  
Sbjct: 27  VVSEDS-GERIDKYLSGKLTEYSRSYLKGLIDEGKVRVEGKPVKS-SFKVTEGINISISI 84

Query: 65  VPLR--------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--- 107
            P++                +   + +      +V   +     + V   +         
Sbjct: 85  PPVKEAEIIPENIPLDILYEDEDVILINKPKGMVVHPAAGHYTGTLVNALMYHCRDNLSG 144

Query: 108 ------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR-------------VR 148
                    V R+D++T G+++   +    R++     +     +              R
Sbjct: 145 INGELRPGIVHRIDMDTTGVIIACKNDVSHRIIAEQLKEHSIKRKYQAIVYGVFKDEEGR 204

Query: 149 FHGQVDQDKLNLLKKGIVIQGIC----YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
             G + + K +  K  ++  G      Y  ++        + A +   L  G+  +I+  
Sbjct: 205 IEGSIGRSKTDRKKMAVIPDGKPAVTHYRVIRNYTSPNGNNFAHIECELETGRTHQIRVH 264

Query: 205 FEFFNWKVNRLIRISYG----PFQLGT 227
                  +  L    YG    PF+L  
Sbjct: 265 MTSIGHPL--LGDEIYGAAKNPFKLDG 289


>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 = 62.9 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 36/242 (14%), Positives = 70/242 (28%), Gaps = 36/242 (14%)

Query: 7   VQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           + E    +R+ K+IA R    SR  V++++ +  + VNG   +  A  V   D +EV   
Sbjct: 15  ISEREHGERLDKLIASRVTGMSRSFVQQLMKRGAILVNGEPCK-PAQRVRYGDRLEVYLP 73

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRS-------TVFDNLPS 103
                         +P+   +   +     P  +       +  +          D    
Sbjct: 74  PVEPPTDLEPEFLPIPVIYEDDDIIVFDKPPGIVTHPAPGHEHGTLVNALKAIRPDLQVQ 133

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
              R   V RLD +T GLL++         L         V +         +  +    
Sbjct: 134 PSHRPGIVHRLDKDTSGLLVVAKTEAARLALLEQWQSRSVVKKYTALVHGVVEPDSGTID 193

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVT------------VGLREGKNREIKKVFEFFNWK 211
             + +          +   + +                 V +  G+  +I+    F    
Sbjct: 194 APISRDPVERTKMAVVSWGRPAITHFRVLERFRCATLLDVTIETGRTHQIRVHCAFIGHP 253

Query: 212 VN 213
           V 
Sbjct: 254 VV 255


>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 = 62.9 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 27/236 (11%), Positives = 61/236 (25%), Gaps = 35/236 (14%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
                R+ K +A     SR +  + I    V VNG   ++A  +V + D I         
Sbjct: 6   KEEGLRLDKALADLSNLSRSQANQAIKDGSVLVNGRP-KKAKYSVKAGDVISFEEPEEEV 64

Query: 63  -DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            D         +   ++    +      +V         + V   L  I       G + 
Sbjct: 65  LDYQAENLPLEIVYEDQDLAVVNKPQGMVVHPSVGHSSGTLVNALLYRIKDLSTINGVVR 124

Query: 116 INTEGL---------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
                          ++  ND     + +    +      +        +    ++  I 
Sbjct: 125 PGIVHRIDKDTSGLLMVAKNDQAHQALADELKAKKSLRKYLAIVHGNLPNDRGKIEAPIG 184

Query: 167 IQGI---------CYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                                  +  + G+ + + + L  G+  +I+    +    
Sbjct: 185 RSEKDRKKQAVTAKGRPAVTHFHVLERFGNYSLLELRLETGRTHQIRVHMAYIGHP 240


>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 = 62.9 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 37/244 (15%), Positives = 77/244 (31%), Gaps = 39/244 (15%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV-- 65
           ++    +R+   I+     SR + +  I ++ VKVN   ++  +  +   D IEV     
Sbjct: 8   EKADEGKRLDIFISDKLNISRAKAQEAIEKKFVKVNN-YVKTKSYKIKFNDLIEVSDEFS 66

Query: 66  --------------PLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------ 104
                         P++   +   L +  KP G+V          T+ + L         
Sbjct: 67  LKLENSEKLIPQNIPIQVIYKDDYLIVLSKPAGMVVYPCAGHPDGTLMNALAYHVKKLAN 126

Query: 105 ---FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
                R   V RLD +T G++++  D      L     +                    +
Sbjct: 127 VGAPFRPGIVHRLDKDTSGVMVVALDDETYYKLVEAFKKREIKKEYLALVYGQLRGSGKI 186

Query: 162 ----------KKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                     +K + I+     +   +  +     +  ++ V +  G+  +I+  F    
Sbjct: 187 TTPVGRAIYDRKKMSIKSKKAKEAITEWEVIKNFKNYTFLKVKILTGRTHQIRVHFSSIG 246

Query: 210 WKVN 213
             V 
Sbjct: 247 HPVI 250


>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 = 62.9 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 35/265 (13%), Positives = 79/265 (29%), Gaps = 35/265 (13%)

Query: 5   NIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           N V+++   QR+ + IA      SR  ++  +   +V+VNG ++ +    VM  + I + 
Sbjct: 9   NTVKDSQLGQRLDQAIAELFADFSRSRLKEWLLAGKVQVNGEVVTKPRTRVMGGEEITLQ 68

Query: 63  ----DGVPLRKAERT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
               D       +            + +      +V   +     + +   L        
Sbjct: 69  AELEDEERWEAQDIPLDIVYEDEDIIVINKPRDFVVHPGAGTPDGTVLNALLHHYPDIAE 128

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   RLD +T GL+++         L     +                    + K 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRMTAGGKVDKP 188

Query: 165 IVIQGIC---------YGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I                        +      +  + + L  G+  +I+    +    + 
Sbjct: 189 IGRHSTKRTLMAVAPMGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPL- 247

Query: 214 RLIRISYGPFQLGTLLAGSTREVSK 238
            L   +YG      +  G++ E+++
Sbjct: 248 -LGDTAYGGRA--RIPTGASEELTE 269


>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 = 62.9 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 31/246 (12%), Positives = 70/246 (28%), Gaps = 43/246 (17%)

Query: 15  RVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTDHIE----- 61
           RV K +       R+ ++        + +   +VK+NG  ++  +  +   D IE     
Sbjct: 29  RVDKFL-------RKMLKNVPLSAIYKFLRTGKVKINGKKVKDPSTKLNIGDVIELIEES 81

Query: 62  VDG--------VPLR-----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           +D          P++       E   +   +KP G+         + ++ + L       
Sbjct: 82  LDNYSREYLELKPVKMDLDIIYEDELIIAINKPAGVSVHPGKNVNKPSIIEGLIHYGKEN 141

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
                L    +            R +    ++ +    V                     
Sbjct: 142 GFEPFLVHRLDKETSGVLIVAKDRSVARELSEIISSRNVEKIYNALVFGKVQKVTINTPI 201

Query: 169 GICYG-----DMQVTLDTQKGSN---AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
                      ++       G +   +++ V +  G+  +I+K     N  +       Y
Sbjct: 202 DGQDAVSHIIPIEYFRVKLNGISVELSFLEVEIETGRKHQIRKHLSSINCPIVGDK--DY 259

Query: 221 GPFQLG 226
           G F+L 
Sbjct: 260 GNFRLN 265


>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 = 62.9 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 32/250 (12%), Positives = 78/250 (31%), Gaps = 38/250 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK + +V+E     R+ K ++ R    SR  +++++  + V V G  ++       + D 
Sbjct: 1   MKQQFVVEEEDKAIRIDKYLSERCPELSRSYLQKLLKAEAVFVGGKPVKS-NYKTAAGDL 59

Query: 60  IE------VDGVPLR--------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           IE      V+   +           +   + +      +V   +     + V   +    
Sbjct: 60  IELEVPEAVEPKIVPEEMDLDILYEDSDIILINKPKGMVVHPAAGHYSGTLVNGLMAHCR 119

Query: 106 ---------SRVISVGRLDINTEGLLLLTNDGGLARVLELP-------------STQWLR 143
                     R   V R+D++T G+L++  +      +                    ++
Sbjct: 120 ADLSGINGVMRPGIVHRIDMDTTGVLIVCKNDMAHNSIAEQLKVHSITRKYYAVVHGVMK 179

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                  G + +  ++  K  I  +          +  +     +V   L  G+  +I+ 
Sbjct: 180 EDEGTVSGPIGRHPVDRKKMCINEKNGRDAVTHYRVLERFRQFTYVECRLETGRTHQIRV 239

Query: 204 VFEFFNWKVN 213
                   + 
Sbjct: 240 HMASIGHPLL 249


>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 = 62.5 bits (150), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 38/246 (15%), Positives = 73/246 (29%), Gaps = 42/246 (17%)

Query: 7   VQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V +   P R+ K +  R   +SR  +++      + VNG  ++     V   D I +   
Sbjct: 38  VDKGQVPVRIDKFLFERMQHSSRNRIQKAADAGFIHVNGSPVKS-NYKVRPEDVITLMLD 96

Query: 63  ---DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                  +           E T L + +KP GLV      +   T+ + +      + + 
Sbjct: 97  RPKHDNTIEAEDIPLDIVYEDTVLMVINKPAGLVVHPGAGNFHGTLINAVAWHLRDMPAF 156

Query: 112 GRLDI----------NTEGLLLLTNDGG-------------LARVLELPSTQWLRVYRVR 148
              D           +T GLL++                    R               R
Sbjct: 157 DPNDPEVGLVHRIDKDTSGLLVVAKTPDAKTALGKQFFNKTTHRSYNALVWGNFTEDEGR 216

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGD---MQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
             G + +D  + L+  +   G   G        +  + G    +   L  G+  +I+   
Sbjct: 217 IEGNIARDPRDRLRMTVFPPGSETGKHAVTHYRVLERFGYTTLIECILETGRTHQIRAHM 276

Query: 206 EFFNWK 211
           +     
Sbjct: 277 KHIGHP 282


>gi|295105659|emb|CBL03203.1| ribosomal large subunit pseudouridine synthase D [Faecalibacterium
           prausnitzii SL3/3]
          Length = 310

 Score = 62.5 bits (150), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 34/255 (13%), Positives = 78/255 (30%), Gaps = 46/255 (18%)

Query: 1   MKDKN-IVQENFTPQRVSKVIA--RAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M+ +  IV++    QR+ + ++    G+ SR  ++ ++A+  V+ NG  + + ++ + + 
Sbjct: 1   MEQREFIVEQETAGQRIDRFLSGEDTGL-SRSALQALVAEGHVQCNGKTVAK-SLKLKAG 58

Query: 58  DHIEV---DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           D + +   D  P+              +   L +      +V         + V   L  
Sbjct: 59  DTVLLEIPDAKPIEAVPQDIPLEIVYEDSHLLVVNKPKGMVVHPAPGNQDGTLVNALLWH 118

Query: 104 IF---------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD 154
                       R   V R+D +T GLL++  D      L             +      
Sbjct: 119 CKGSLSGIGGEIRPGIVHRIDKDTSGLLVVAKDDATHIGLSQQMAVHSVERAYQTVVYGG 178

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV------------TVGLRE-----GK 197
             +     +   +        ++ +      +                  L E     G+
Sbjct: 179 FAQDEGFVEA-NLGRSKTDRKKMAVYPANEPHTKYAYTGYKVLERLGEFTLLECRLKTGR 237

Query: 198 NREIKKVFEFFNWKV 212
             +I+      +  V
Sbjct: 238 THQIRVHMASIHHPV 252


>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 = 62.5 bits (150), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 30/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E    QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSEKQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-- 108
                           +   +   + +      +V   +     + +   L      V  
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIVDV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                V RLD +T GL+++  +      L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKNVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 62.5 bits (150), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 33/248 (13%), Positives = 67/248 (27%), Gaps = 39/248 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M+   +V E    +R+ K I +  +G+ SR  ++ +++   + VN    +  ++ + + D
Sbjct: 1   MRTFKLVAETA-GERLDKYITQKESGL-SRSFIQELVSSGHILVNNQSAK-PSLRLKTGD 57

Query: 59  HIEVDGVPLRKAERTR--------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            I ++  P   +E                 L +   P   V         + V   L   
Sbjct: 58  TITIEIPPETPSELKAENIPLEIIFQDKDLLLINKPPGLTVHPAPGHPDHTLVNGVLALE 117

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------- 155
                    L       L     G L       +   L         +            
Sbjct: 118 PEMEDFDDPLRPGIVHRLDKDTSGLLLVAKNRQALANLSAQFKERTVRKYYLALVKGELR 177

Query: 156 -----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                            +K  V+    +      +       + + V L  G+  +I+  
Sbjct: 178 PAEGFIEAPLGRDPQNRQKIAVVSDGRHARTGYKVLRYIQGYSLLEVKLETGRTHQIRVH 237

Query: 205 FEFFNWKV 212
           F      V
Sbjct: 238 FAAIGHPV 245


>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 = 62.5 bits (150), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 35/243 (14%), Positives = 69/243 (28%), Gaps = 37/243 (15%)

Query: 8   QENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---D 63
            E+   QR+   ++      SR  ++ +I Q  V VN ++ +    NV + D I +   D
Sbjct: 18  TESKLSQRLDLWLSNELPDLSRSRIQNLILQGNVTVNDLICKSKKENVKNGDRIHIAIPD 77

Query: 64  GVPLRKAERTR-----------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--- 109
             PL                  + +      +V   +   G + V   L       I   
Sbjct: 78  AEPLDLKPEAIPLDILYEDESLIIINKPAGLVVHPAAGHPGGTLVNALLAHCPLAEIGGV 137

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN------ 159
                V RLD +T G +++       + L+                       N      
Sbjct: 138 LRPGIVHRLDKDTSGAIVVAKTDFAHQHLQAQLKAKTARREYLGVVYGTLKTENGTIDLP 197

Query: 160 ---------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                     +    + +G         +  + G+   +   L  G+  +I+        
Sbjct: 198 IGRHSVDRKKMAVVTIEKGGRSAVTHWQIQERLGNYTLIHFQLETGRTHQIRVHAAQIGH 257

Query: 211 KVN 213
            + 
Sbjct: 258 PIV 260


>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 = 62.5 bits (150), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 40/249 (16%), Positives = 76/249 (30%), Gaps = 42/249 (16%)

Query: 4   KNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K  V E  TP R+ K +A      SR  ++       ++VNG  ++     V   D I +
Sbjct: 21  KVQVDEGQTPVRIDKYLAEKNPYQSRNRIQNAADAGFIQVNGTPVKS-NYKVRPNDVITL 79

Query: 63  -------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                        + +P+    E   L + +K  G+V      +   T+ + +      +
Sbjct: 80  MLDYPKHDTSIVAENIPIDVVYEDDDLMVINKAAGMVVHPGAGNFTGTLINAIAYYLRDL 139

Query: 109 ISV----------GRLDINTEGLLLLTNDGG-------------LARVLELPSTQWLRVY 145
            S            R+D +T GLL++                    R         +   
Sbjct: 140 ESFDANNPEVGLVHRIDKDTSGLLVVAKTPEAKSALGKQFFNKTTHRSYNALVWGNIVED 199

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             R  G + +D  N L+  +                +  + G    +   L  G+  +I+
Sbjct: 200 EGRIEGNIGRDPKNRLRMKVFEPDSGIGKSAVTHYRVLERFGYTTLIECILETGRTHQIR 259

Query: 203 KVFEFFNWK 211
              +     
Sbjct: 260 AHMKHIGHP 268


>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 = 62.5 bits (150), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 26/240 (10%), Positives = 63/240 (26%), Gaps = 38/240 (15%)

Query: 12  TPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPL 67
             +R+   + +     SR  ++++I Q  +++NG +       V   D +++   D  PL
Sbjct: 11  KKERLDAWMGSHLPDLSRSRLQKLIEQGYIQLNGQICTNKNTKVGQGDRLKITIPDSQPL 70

Query: 68  R-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
                         +   + +      +V      +  + V   L    +     G    
Sbjct: 71  ELTAEAIELDILYEDDYLIIINKPADLVVHPAPGHESGTLVNALLHHCPNLAGIGGIQRP 130

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------------------- 155
                L     G +       + Q L+        + +                      
Sbjct: 131 GIVHRLDKDTTGAIVIAKTDQAHQHLQAQLKTKTARREYIALVHGVPKSETGTIDLPIGR 190

Query: 156 --DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +    V +G         +  + G+   +   L  G+  +I+         + 
Sbjct: 191 HRSDRQKMAIIAVEKGGRNAVTHWQVKERLGNYTLMEFRLETGRTHQIRVHSSHIGHPIL 250


>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 = 62.5 bits (150), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 41/240 (17%), Positives = 77/240 (32%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           +    + QR+ K +A     SR +    I Q  V VN    ++A   V + D I  +   
Sbjct: 3   INVITSGQRLDKALADLSPLSRGQANDQIKQGLVLVNDQQ-KKAKYTVQAGDVICFELPK 61

Query: 64  GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-- 111
              L             E   L + +KP G+V   S      T+ + L      + S+  
Sbjct: 62  EEVLEYQAQNIPLDIIYEDDALAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSING 121

Query: 112 -------GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   R+D +T GLL++       + L         + +       +      + + 
Sbjct: 122 VVRPGIVHRIDKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMIEA 181

Query: 165 IVIQGICYGDMQ------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            + +       Q             T+  + G  + V + L  G+  +I+    +    V
Sbjct: 182 PIGRSEKDRKKQAVTAKGKEAVTRFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 62.5 bits (150), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 29/243 (11%), Positives = 73/243 (30%), Gaps = 38/243 (15%)

Query: 5   NIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           + + E+   +R+ K+++      SR +V++ I    + VNG   E+A   + + D +E+ 
Sbjct: 6   HTILEHEANERLDKMVSSIREEWSRSQVQQWIKDGDITVNGKK-EKANYRLQTGDLVEIE 64

Query: 63  -------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                  D  P      +   +   L +      +V   +     + V   +        
Sbjct: 65  VPEPELPDIEPEDLHLDIYYEDADVLVVNKPKGMVVHPSNGHFTGTLVNGLMYHCKDLSG 124

Query: 110 SVG---------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
             G                     + D   E L    ++  + R         +      
Sbjct: 125 INGVLRPGIVHRIDKDTSGLLMVAKNDYAHEKLAAQLSEKTVTRKYFALVHGNIPHEAGT 184

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +D  +  ++  V+           +  +     ++   L  G+  +I+   ++ 
Sbjct: 185 IDAPIGRDPADR-QRMAVVDNGKDAVTHFHVLERFDRYTFIECRLETGRTHQIRVHMKYI 243

Query: 209 NWK 211
              
Sbjct: 244 GHP 246


>gi|332992387|gb|AEF02442.1| ribosomal large subunit pseudouridine synthase D [Alteromonas sp.
           SN2]
          Length = 327

 Score = 62.5 bits (150), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 24/230 (10%), Positives = 59/230 (25%), Gaps = 31/230 (13%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+ +V+A      SR +++  I    V V+G ++      +   + + V           
Sbjct: 22  RLDQVLADLFPEYSRSKLKTWIQGGNVSVDGQVITVPRHKMQMDEVVTVSAEIEIQVTSQ 81

Query: 67  -------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-----GRL 114
                  +   +   L +      +V   +     + +   L  +             RL
Sbjct: 82  AQDIALDIVYEDEHILVINKSADLVVHPGAGNPSGTVLNALLNHVPDIDKVPRAGIVHRL 141

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-----------DKLNLLKK 163
           D +T GL+++         L       +                                
Sbjct: 142 DKDTTGLMVVAKTLPAQTHLVDQLQTRVMSREYEAVAMGTMVAGGVVDEPIGRHATKRTH 201

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             V +          +  +  +   + + L  G+  +I+         + 
Sbjct: 202 MAVRENGKPAVTHFRVIEKFRAYTHLRLKLETGRTHQIRVHMAHIKHPLL 251


>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 = 62.5 bits (150), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 32/249 (12%), Positives = 72/249 (28%), Gaps = 33/249 (13%)

Query: 5   NIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           N V+++   QR+ + IA      SR  ++  +   +V VNG ++ +    VM  + I + 
Sbjct: 9   NTVKDSQLGQRLDQAIAELFADFSRSRLKEWLLDGKVHVNGEVVTKPRTRVMGGEEITLQ 68

Query: 63  ----DGVPLRKAERT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
               D       +            + +      +V   +     + +   L        
Sbjct: 69  AELEDEERWEAQDIPLDIVYEDEDIIVINKPRDFVVHPGAGTPDCTVLNALLHHYPDIAE 128

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   RLD +T GL+++         L     +                    +++ 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRMTAGGKVEQP 188

Query: 165 IVIQGIC---------YGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I                        +  +   +  + + L  G+  +I+    +    + 
Sbjct: 189 IGRHSTKRTLMAVAPLGKPAVTHYRVAERFREHTRIRLRLETGRTHQIRVHMSYLQHPL- 247

Query: 214 RLIRISYGP 222
            L   +YG 
Sbjct: 248 -LGDTAYGG 255


>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 = 62.5 bits (150), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 26/239 (10%), Positives = 61/239 (25%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  +RV VN  + ++    V+  + + +D 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDRRVLVNDKICDKPKEKVLGGEVVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIDEEIRFEPQDIPLDIVYEDDDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--- 156
                  R+       +     +        A  L   + ++  V           D   
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQLREITREYEAVAIGHMTAGGTVDEPI 189

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMSVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 62.5 bits (150), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 28/238 (11%), Positives = 62/238 (26%), Gaps = 30/238 (12%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRK 69
            QR+ + +A     SRR   R I +  V +NG     A   +   D+I V   +G  L  
Sbjct: 20  GQRLDQGLAEVFTLSRRRSRRAIDEGGVYLNGKRCRTAGRKLSCHDNIRVVMLEGERLIP 79

Query: 70  --------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-----------IFSRVIS 110
                    +     ++ K              +   +                    + 
Sbjct: 80  FTPAQLVWQQPPLYLIHKKSGQYAQEALHRSRGTLPDELARHLELTPAQASELRPVHRLD 139

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
                +              A   +    ++L V          + +L + +        
Sbjct: 140 RDTSGLMLFSASAAMLQHLQAHWHDAVEKRYLAVVSPAPDWDDQRIRLAIDRNRDAHGRY 199

Query: 171 CYGDM------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP 222
                      +  +  ++ + A V +    G++ +++         +  L    YG 
Sbjct: 200 HLSPDGRACDSEAHVVERRDNRALVELVPHTGRSHQLRVHLSALGCPI--LGDSRYGG 255


>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 = 62.5 bits (150), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 30/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV +NG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLINGKVCDKPKEKVLGGEQVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 62.5 bits (150), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 34/249 (13%), Positives = 67/249 (26%), Gaps = 41/249 (16%)

Query: 5   NIVQENFTP-QRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           N+  ++     R+ + +A      SR  ++ +I    V VNG   +     V   D I V
Sbjct: 2   NLTTDDADGKIRLDQYLAAHLPELSRSRIQSLIKSGDVLVNGSPAK-PKNPVSRGDSITV 60

Query: 63  ---DGVP-----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
              +  P           +   +   + +  +   +V   +     + V   L       
Sbjct: 61  RIPEPEPAEAQPQDIPLDILYEDEDVVVINKESGMVVHPAAGNPDGTIVNALLHHCGDLS 120

Query: 109 ISVGRLDI---------NTEGLLLLTNDGGLA------------RVLELPSTQWLRVYRV 147
              G              +  L++  NDG               +               
Sbjct: 121 GIGGVERPGIVHRLDKDTSGCLVIAKNDGAHQSLTAQFAARSTEKRYLAVVQGIPSQSSG 180

Query: 148 RFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIKKV 204
                + +  +N LK  +V  G          L     S   + V   L  G+  +I+  
Sbjct: 181 TVFTHIGRHPVNRLKMAVVNPGSGKAAITDYDLLCADPSTDSSLVLCTLHTGRTHQIRVH 240

Query: 205 FEFFNWKVN 213
             +    + 
Sbjct: 241 MLYLGHPLI 249


>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 = 62.5 bits (150), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 30/246 (12%), Positives = 83/246 (33%), Gaps = 38/246 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +++ I+ +     R+   +++     SR  ++++I ++ + VNG+ ++ A   V + D +
Sbjct: 3   EEQFIINQEENGMRIDVFLSKKMDNVSRSYIQKLIKEKEISVNGMAVK-ANYKVSANDIV 61

Query: 61  EV------------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
           ++            + +PL     +   L +      +V         + V   +     
Sbjct: 62  QLTIPDLSEPDILPENIPLDILYEDADILIVNKPKGMVVHPSPSHYTGTLVNALMYYCKD 121

Query: 106 --------SRVISVGRLDINTEGLLLLTNDGGLAR-------------VLELPSTQWLRV 144
                    R   V R+D++T G LL+  +    +             +        ++ 
Sbjct: 122 DLSGINGVMRPGIVHRIDMDTTGSLLVCKNDFAHQKLAEDLKVHNIKRIYHAIVHGVIKE 181

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                 G + +  ++  K  I  +          +  +  +  ++   L  G+  +I+  
Sbjct: 182 DEGTVEGPIGRHPIDRKKMSINYKNGKPAVTHYRVLKRFSNYTYIECQLETGRTHQIRVH 241

Query: 205 FEFFNW 210
               + 
Sbjct: 242 MASIHH 247


>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 = 62.5 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGELVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 62.5 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 35/240 (14%), Positives = 67/240 (27%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           V+      R+ K +A     SR      I   ++ VNG L+++A   V   D I  +   
Sbjct: 3   VKVEQAGVRLDKAVADLTDLSRSLANEQIKTGKILVNG-LVKKAKYTVKEGDVISYELPE 61

Query: 67  LRKAERTRLWL--------------YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
           + + E     +                    +V   +     + V   +  I       G
Sbjct: 62  IEEIEYVTENIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGING 121

Query: 113 RLDINTEGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLK 162
            L       +     G L       +           + LR Y    HG +  D+  +  
Sbjct: 122 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 181

Query: 163 KGIVIQGICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                +                 +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 182 PIGRSEKDRKKQAVTAKGKPALTRFQVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 62.5 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 29/243 (11%), Positives = 63/243 (25%), Gaps = 36/243 (14%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           I     T QR+ K+++      SR +++  I  + V VNG  ++ A   V   D I +  
Sbjct: 8   ITDTRHTGQRIDKLLSDYNHDWSRSQIQDWIKHELVIVNGKAIK-ANHKVKLHDSIVITE 66

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                           +   ++    +Y     +V         + V   +  I      
Sbjct: 67  KEVVDADIQPENLNLDIYYEDKDVAIVYKPKGMVVHPSPGHYSGTLVNGLMYQIKDLSGI 126

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPST------------QWLRVYRVRFHGQVDQ--- 155
            G +       +     G L       +             +      V  +   D    
Sbjct: 127 NGEIRPGIVHRIDKDTSGLLMVAKNDIAHRSLVDQLVAKSVKRKYTALVHGNIPHDYGTV 186

Query: 156 -----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      +   V+           +         +   L  G+  +I+   ++  +
Sbjct: 187 DAPIGRNKKDRQSMDVVDDGKDAVTHFNVLEHFKDYTLIECQLETGRTHQIRVHMKYIGY 246

Query: 211 KVN 213
            + 
Sbjct: 247 PLV 249


>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 = 62.5 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 35/263 (13%), Positives = 69/263 (26%), Gaps = 51/263 (19%)

Query: 2   KDKNIVQENFTPQRVSKVI--ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
             K +  +     R+   +  A +G  SR  ++ +I Q  V +NG+ +      V   D 
Sbjct: 21  NRKVLTADENAAGRLDAFLTEALSGEFSRNRIKALIEQGAVSINGVTVLEPKRKVHPGDR 80

Query: 60  IEV------DGVP--------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            E+      D  P        +   +   + L      +V   +     + V   +    
Sbjct: 81  FEITLPAPEDPEPKGEDIPIDVLYEDDDLIVLVKPAGLVVHPGAGNWTGTLVNALIHHCG 140

Query: 106 ---------SRVISVGRLDINTEGLLLLTNDGGLARV-----LELPSTQWLRVYRVRFHG 151
                     R   V RLD  T G++++  +    R       +   T  L         
Sbjct: 141 DSLSGIGGVRRPGIVHRLDKETSGVMVVAKNDAAHRHLSDQFADHGRTGPLERAYQAVVW 200

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN---------------------AWVT 190
              +     +   +   G          ++                          A V 
Sbjct: 201 GRPRQLKGTINAALGRAGDRTKRAVKREESDDAREAITHYEVVERYHEKPDGTCLAATVE 260

Query: 191 VGLREGKNREIKKVFEFFNWKVN 213
             L  G+  +I+         + 
Sbjct: 261 CHLETGRTHQIRVHMAHIGNPLI 283


>gi|255326173|ref|ZP_05367259.1| ribosomal RNA large subunit methyltransferase J [Rothia
          mucilaginosa ATCC 25296]
 gi|255296627|gb|EET75958.1| ribosomal RNA large subunit methyltransferase J [Rothia
          mucilaginosa ATCC 25296]
          Length = 242

 Score = 62.5 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  AG  +SR    ++IA   V+VNG +  +A++ V   D + V
Sbjct: 1  MRLDKYLVEAGFVSSRTLAAKLIAAGDVQVNGKVARKASMLVGPEDTLYV 50


>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 = 62.5 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 27/238 (11%), Positives = 61/238 (25%), Gaps = 38/238 (15%)

Query: 13  PQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------D 63
             R+ K +A A    +R  ++++I+   V V G    +A       D I V        D
Sbjct: 14  GIRIDKFLAEAIPDVTRSHIQKLISTGLVTV-GQKAVKANYKTALNDEIAVRIPEPEIPD 72

Query: 64  GVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG----- 112
             P      +   +   L +      +V         + V   +      +  +      
Sbjct: 73  IQPEDIPLDILYEDNDILIVNKPKGMVVHPAPGHYSNTLVNAVMYHCRDNLSGINGVARP 132

Query: 113 -----------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
                            + D   + L     +  + R         L+         + +
Sbjct: 133 GIVHRIDMDTTGSLIICKNDTAHQALAEQLKEHHITRKYHAVVHGNLKEDSQTVDAPIGR 192

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             ++  K                +  + G   ++   L  G+  +I+         + 
Sbjct: 193 HPVDRKKMSTRAPHGRQAVTHYKVLERFGEYTYIECELETGRTHQIRVHMASIGHPIV 250


>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 = 62.5 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 40/250 (16%), Positives = 67/250 (26%), Gaps = 39/250 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVD-- 63
           +       R+   IA     SR   ER++  + VKVNG  + +     V S D I +D  
Sbjct: 10  LNVETGNMRLDAYIADNTDISRSFAERLVTDEFVKVNG--VSKPKKYKVKSGDSIVIDVP 67

Query: 64  ------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                        + +         +       V         + V   L          
Sbjct: 68  REEVPELTPVKMDIEIIYDCDEFAVINKPAGITVHPAPGHADDTIVNAMLAEFDITDDND 127

Query: 107 -RVISVGRLDINTEGLLLLTNDGGLA------------RVLELPSTQWLRVYRVRFHGQV 153
            R   V RLD +T GL+++  +                    L               Q 
Sbjct: 128 LRPGIVHRLDKDTSGLMIVAKNRKSREVLSKVFADRDIDKRYLAVCWGKPKELEFTIEQP 187

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK-- 211
                   K+  V +   Y    V +  Q  +     + +  G+  +I+       +   
Sbjct: 188 IGRHYKDRKRMCVREDGRYSKSGVRVLKQNNNAFLAEIRIFTGRTHQIRVHMSHAGFPLA 247

Query: 212 --VNRLIRIS 219
             V    R S
Sbjct: 248 GDVVYGHRQS 257


>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 = 62.5 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 32/252 (12%), Positives = 70/252 (27%), Gaps = 43/252 (17%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           MK +N  + E+    R+   I++     SR   +++I  + V VNG + +++   + + D
Sbjct: 1   MKTENFLINEDEANSRLDVFISKCFEEKSRSYAQKLIEDKNVLVNGSI-KKSNYKLKTGD 59

Query: 59  HIEV---DGVPLRKAERTRLWLY-----------HKPIGLVTTHSDPDGRSTVFDNLPSI 104
           ++EV   +   +                           +V   +     + V   L   
Sbjct: 60  NVEVTIKEDETINIEPEDIKLNILYEDEDVIVIDKPQGMVVHPGNGNYSGTLVNGLLYHC 119

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
            S     G +       +     G L       +     +   +      + +   L +G
Sbjct: 120 DSLSSINGDVRPGIVHRIDKDTSGVLVVAKNDNAH---IILSEQLKEHSMKREYVALVEG 176

Query: 165 IVIQGICY-----------------------GDMQVTLDTQKGSNAWVTVGLREGKNREI 201
           I+                                   +  +   N  V   L  G+  +I
Sbjct: 177 IIKDDEGTIDEPLGRNPKDRIKRAVVRNGKNAITHYEVIRRFNKNTLVKCILETGRTHQI 236

Query: 202 KKVFEFFNWKVN 213
           +      N  + 
Sbjct: 237 RVHMAHINHPLV 248


>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 = 62.5 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 26/230 (11%), Positives = 60/230 (26%), Gaps = 31/230 (13%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVN--------VMSTDHIEVDGV 65
           R+ +V+A      SR +++  I    V VNG ++              V +   ++V   
Sbjct: 22  RLDQVLADLFPEYSRSKLKTWIQDGNVSVNGEVITVPRHKMQMDELVTVQAEMDVQVTSE 81

Query: 66  P------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-----GRL 114
                  +   +   L +      +V   +     + +   L  +             RL
Sbjct: 82  AQDIALDIVYEDEHILVINKPADLVVHPGAGNPSGTVLNALLNHVPEIDKVPRAGIVHRL 141

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-----------DKLNLLKK 163
           D +T GL+++         L     +                                  
Sbjct: 142 DKDTTGLMVVAKTIPAQTHLVDQLQRREVSREYEAIALGTMVAGGIVDEPIGRHATKRTH 201

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             V +          +  +  +   + + L  G+  +I+         + 
Sbjct: 202 MAVREMGKPAITHFRVIEKFRAYTHLRLKLETGRTHQIRVHMAHIKHPLL 251


>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 = 62.5 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 31/248 (12%), Positives = 70/248 (28%), Gaps = 38/248 (15%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K  +      QR+ + ++      SR  ++ +I Q  V+VNG +     + +   +++EV
Sbjct: 23  KIHLSITQKTQRLDRYLSSVIPDLSRSRIQDLIEQGYVQVNGKVCYSKNITLDGGEYLEV 82

Query: 63  DGVPLR--------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           +  P++                +   L L      +V         + V   L    +  
Sbjct: 83  EIPPVQAAQLVAQDIPLDILYEDEQLLILNKPAGLVVHPAPGHLEGTLVHALLAHCPNLP 142

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------------- 155
              G         L     G +A      + + L++       + +              
Sbjct: 143 GIGGVQRPGIVHRLDKDTTGAIAIAKTDIAYKQLQLQLQSKIARREYLGVVYGAPKSESG 202

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                      +   +    V QG         +  + G+   +   L  G+  +I+   
Sbjct: 203 TIDLPIGRHPQQRKKMAIVPVEQGGRNAITNWHIKERLGNYTLIHFQLETGRTHQIRVHS 262

Query: 206 EFFNWKVN 213
                 + 
Sbjct: 263 AKMGHPIV 270


>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 = 62.5 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 33/264 (12%), Positives = 79/264 (29%), Gaps = 35/264 (13%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
             V+E+   QR+ + +A      SR  ++  + + ++ VNG ++ +    VM  + I V 
Sbjct: 9   QTVKESQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGEVVTKPRTKVMGGEVIVVQ 68

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   +   + +      +V   +     + +   L        
Sbjct: 69  AELEDEQRWEAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADGTVLNALLFHYPPIAE 128

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   RLD +T GL+++         L     +                   ++ K 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAIVIGTMTAGGMIDKP 188

Query: 165 IVIQ-----------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I                 +      +      +  + + L  G+  +I+    +    + 
Sbjct: 189 IGRHSTKRTLMSVSPMGKHAVTHYRVAEHFREHTRLRLRLETGRTHQIRVHMAYLQHPL- 247

Query: 214 RLIRISYGPFQLGTLLAGSTREVS 237
            L   +YG      +  G++ E++
Sbjct: 248 -LGDTAYGGRA--RIPKGASEELT 268


>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 = 62.5 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 31/248 (12%), Positives = 70/248 (28%), Gaps = 38/248 (15%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K  +      QR+ + ++      SR  ++ +I Q  V+VNG +     + +   +++EV
Sbjct: 20  KIHLSITQKTQRLDRYLSSVIPDLSRSRIQDLIEQGYVQVNGKVCYSKNITLDGGEYLEV 79

Query: 63  DGVPLR--------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           +  P++                +   L L      +V         + V   L    +  
Sbjct: 80  EVPPVQAAQLVAQDIPLDILYEDEQLLILNKPAGLVVHPAPGHLEGTLVHALLAHCPNLP 139

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------------- 155
              G         L     G +A      + + L++       + +              
Sbjct: 140 GIGGVQRPGIVHRLDKDTTGAIAIAKTDIAYKQLQLQLQSKTARREYLGVVYGAPKSESG 199

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                      +   +    V QG         +  + G+   +   L  G+  +I+   
Sbjct: 200 TMDLPIGRHPQQRKKMAIVPVEQGGRNAITNWYIKERLGNYTLIHFQLETGRTHQIRVHS 259

Query: 206 EFFNWKVN 213
                 + 
Sbjct: 260 AKMGHPIV 267


>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 = 62.5 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 29/243 (11%), Positives = 73/243 (30%), Gaps = 35/243 (14%)

Query: 4   KNIVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K+ +    T  R+ + +A  G+    SR  ++  I    + ++GI +++    V  +  +
Sbjct: 8   KSEITAIQTGLRLDQALA--GLFPDYSRTRIKEWILSGAITIDGITVDKPREKVFESQLV 65

Query: 61  EVD--------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           EV                + +   +   L +  +   +V   +     + +   L     
Sbjct: 66  EVTATLEEEVSAKAQNIDLNIVYEDDHILVINKQAGLVVHPGAGNADGTLMNALLYHCPD 125

Query: 107 RVISV-----GRLDINTEGLLLLTNDGGLARV------LELPSTQWLRVYRVRFHGQVDQ 155
                      RLD +T GL+++                     ++  +           
Sbjct: 126 IEHVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQARDIVREYEAIVLGTMTAGGTV 185

Query: 156 D-----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           D           +  VI G         +  +  ++  + + L  G+  +I+        
Sbjct: 186 DEPIERHATRRTQMAVIHGGRPSVTHYRVSEKFRAHTRLRLRLESGRTHQIRVHMAHIGH 245

Query: 211 KVN 213
           ++ 
Sbjct: 246 ELV 248


>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 = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 33/264 (12%), Positives = 79/264 (29%), Gaps = 35/264 (13%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
             V+E+   QR+ + +A      SR  ++  + + ++ VNG ++ +    VM  + I V 
Sbjct: 9   QTVKESQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGEVVTKPRTKVMGGEVIVVQ 68

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   +   + +      +V   +     + +   L        
Sbjct: 69  AELEDEQRWEAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADGTVLNALLFHYPPIAE 128

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   RLD +T GL+++         L     +                   ++ K 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAIVIGTMTAGGMIDKP 188

Query: 165 IVIQ-----------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I                 +      +      +  + + L  G+  +I+    +    + 
Sbjct: 189 IGRHSTKRTLMSVSPMGKHAVTHYRVAEHFREHTRLRLRLETGRTHQIRVHMAYLQHPL- 247

Query: 214 RLIRISYGPFQLGTLLAGSTREVS 237
            L   +YG      +  G++ E++
Sbjct: 248 -LGDTAYGGRA--RIPKGASEELT 268


>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 = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 31/240 (12%), Positives = 68/240 (28%), Gaps = 31/240 (12%)

Query: 5   NIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
             V+E+   QR+ + +A   +  SR  ++  +   ++ VNG ++ +    VM  + I V 
Sbjct: 9   QTVKESQLGQRLDQAVAELFVDFSRSRLKEWLLDGKITVNGTVVTKPRTKVMGGECITVL 68

Query: 63  ----DGVPLRKAERT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
               D       +            L +      +V   +    R+ +   L        
Sbjct: 69  AELEDEQRWEAQDIPLNIVYEDDDILVINKPRDFVVHPGAGTPDRTVLNALLFHYPPIAE 128

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   RLD +T GL+++         L     +                   ++ K 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRDLQKRNITREYEAIAIGKMTAGGMIDKP 188

Query: 165 IVIQ---------GICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I                        +      +  + + L  G+  +I+    +    + 
Sbjct: 189 IGRHSTKRTLMAVNQMGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIRVHMAYLQHPLL 248


>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 = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 33/264 (12%), Positives = 79/264 (29%), Gaps = 35/264 (13%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
             V+E+   QR+ + +A      SR  ++  + + ++ VNG ++ +    VM  + I V 
Sbjct: 9   QTVKESQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGEVVTKPRTKVMGGEVIVVQ 68

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   +   + +      +V   +     + +   L        
Sbjct: 69  AELEDEQRWEAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADGTVLNALLFHFPPIAE 128

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   RLD +T GL+++         L     +                   ++ K 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAIVIGTMTAGGMIDKP 188

Query: 165 IVIQ-----------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I                 +      +      +  + + L  G+  +I+    +    + 
Sbjct: 189 IGRHSTKRTLMSVSPMGKHAVTHYRVAEHFREHTRLRLRLETGRTHQIRVHMAYLQHPL- 247

Query: 214 RLIRISYGPFQLGTLLAGSTREVS 237
            L   +YG      +  G++ E++
Sbjct: 248 -LGDTAYGGRA--RIPKGASEELT 268


>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 = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 29/250 (11%), Positives = 77/250 (30%), Gaps = 38/250 (15%)

Query: 1   MKDKNIVQENFT-PQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M    I+ E     +R+   +A+     SR  ++ +I + +V +N  +++ A   +   +
Sbjct: 1   MDTFEIIAEESDVDKRIDLFLAKNLESFSRSYIQDLIKKGKVTINNKIIK-ANYRLKEGE 59

Query: 59  HIEVD---GVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            + +D     PL              +   + +      +V   +     + V   L   
Sbjct: 60  CVVLDIPKPEPLEIVPENIPIDILYEDEDVILVNKPKGMVVHPAAGHYKGTLVNALLYHC 119

Query: 105 FSR---------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
            S             V R+D++T G++++  +    + +           +       + 
Sbjct: 120 KSNLSGINGVLRPGIVHRIDMDTTGVIIICKNDIAHQHIAKQLANHSITRKYVAIVTGNI 179

Query: 156 DKLN------------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
            +                KK  V +          +  +     ++   L  G+  +I+ 
Sbjct: 180 KEDEGVIDAAIARSKSDRKKMAVDKDGKRAVTHYKVLERLNGYTYIECVLETGRTHQIRV 239

Query: 204 VFEFFNWKVN 213
              + +  + 
Sbjct: 240 HMAYIHHPLL 249


>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 = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 36/239 (15%), Positives = 69/239 (28%), Gaps = 40/239 (16%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGIL-LERAAVNVMSTDHIEV--------DG 64
           +R+ K I+     +R + + +I Q+ V V+    + +    V     I V        + 
Sbjct: 10  ERIDKYISDNSEITRNDAKALIEQEAVYVDDRKFVRKPNYMVREGMVITVLRLLEKESNI 69

Query: 65  VPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL----- 114
             +        E   L + +KP GLV   +      T+ + L   F   +S         
Sbjct: 70  EAVDMPLDIRYEDEYLLILNKPSGLVVHPAPGHLNDTLVNALMYHFKNNLSDANGLLRLG 129

Query: 115 ------------------DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
                             +     L  +  +  + R         L     + +  + +D
Sbjct: 130 IVHRIDKDTSGLLIIAKDNETHNELAKMLKNHQIKRTYLAICEGILPNKTTKINLPIQRD 189

Query: 157 KLNLLKKGIVIQGI---CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             N     I   G     Y  M  +        + V   L  G+  +I+    +    V
Sbjct: 190 TKNRKLMSIHKDGKSSVTYVHMLKSFYIDNKPYSLVKCELETGRTHQIRVHLAYIKHPV 248


>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 = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 37/256 (14%), Positives = 74/256 (28%), Gaps = 43/256 (16%)

Query: 1   MKDKN--IVQENFT---PQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNV 54
           M D++  I++ N      QR+   +++  +  SR  ++++I+Q  VKVN  L       V
Sbjct: 1   MSDESPIILEVNSEYEITQRLDIWLSQQMLELSRSHIQKLISQGNVKVNDQLCTSKKAIV 60

Query: 55  MSTDH------------IEVDGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
              D             IE + +PL     +   L +      +V         + V   
Sbjct: 61  HQGDKIILVIPPPIPLAIEANDIPLDILYEDDALLIINKPAGLVVHPAPGHSEGTLVNAL 120

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ----- 155
           L    S     G         L     G +       + Q L+        + +      
Sbjct: 121 LAHCDSLAGIGGVQRPGIVHRLDKDTTGAIMVAKTDHAYQHLQAQLQAKTARREYLGVVY 180

Query: 156 ------------------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGK 197
                                  +    V +G         +  + G+ + +   L  G+
Sbjct: 181 GSPKTDSGIINLPIGRHRVDRKKMAVTPVERGGKIAVTHWEVKERLGNFSMILFRLETGR 240

Query: 198 NREIKKVFEFFNWKVN 213
             +I+       + + 
Sbjct: 241 THQIRVHSAQVGYPIV 256


>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 = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 31/238 (13%), Positives = 65/238 (27%), Gaps = 38/238 (15%)

Query: 14  QRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------ 66
            R+ K ++      SR ++++ I   +V VN +++    V V   D I            
Sbjct: 13  IRLDKALSSLLENVSRNQIQKAIKDSQVLVNDVIISDPDVLVKENDIILFSFKEPEELKI 72

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-----RVISVGR 113
                   +   +   + +       V   +     + V   L    +          G 
Sbjct: 73  AAANVALDIIYEDDDLIVINKAAGMTVHPGAGHHDDTLVNALLHHTKNLSDIGSSERPGI 132

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           +    +    L       +   L + Q  +   +R +  +    +N L+  I        
Sbjct: 133 VHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRKYKVLVWGVINPLEGVIKNNIGRSR 192

Query: 174 DMQVTL------------------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             +  +                     KGS + V   L  G+  +I+         V 
Sbjct: 193 SDRQKMTILKYGGKEAVTHYKTLELFYKGSISMVECKLSTGRTHQIRVQLSHLKHSVV 250


>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 = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 32/250 (12%), Positives = 63/250 (25%), Gaps = 51/250 (20%)

Query: 15  RVSKVI--ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
           R+   +  A AG  SR  ++ +I Q  V +NG  +      V   D   +          
Sbjct: 24  RLDAFLTEALAGEFSRNRIKSLIEQGAVSINGATVTEPKRKVHPGDSFRIALPEPEDPEP 83

Query: 63  DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVI 109
            G  +       +   + L      +V   +     + V   +              R  
Sbjct: 84  KGEAIPLDVLYEDADLIVLVKPAGLVVHPGAGNWTGTLVNALIHHCGDSLSGIGGVKRPG 143

Query: 110 SVGRLDINTEGLLLLTNDGGLARV-----LELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
            V RLD +T G++++  +    R       +      L            +     +   
Sbjct: 144 IVHRLDKDTSGVMVVAKNDAAHRHLSDQFADHGRNGPLERAYRAVVWGRPRQLKGKIDAP 203

Query: 165 IVIQGICYGDMQVTLDTQKGSN---------------------AWVTVGLREGKNREIKK 203
           +   G          D+                          + V   L  G+  +I+ 
Sbjct: 204 LGRAGDRTKRAVKREDSDDAREAITHYEVVERYHEKPDGTSLASTVECHLETGRTHQIRV 263

Query: 204 VFEFFNWKVN 213
                   + 
Sbjct: 264 HMAHIGHPLI 273


>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 = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 27/238 (11%), Positives = 68/238 (28%), Gaps = 31/238 (13%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T  R+ + +A      SR  ++  I    V V+G+++ +    V     IE+
Sbjct: 8   KSEISATQTGLRLDQALAELFPDYSRTRIKEWILSDAVYVDGVIVNKPREKVFELQRIEI 67

Query: 63  DGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           +                 +   +   L +  +   +V   +     + +   L    +  
Sbjct: 68  NATLEEEVHAAAQAIELDIVYEDDDILVINKQAGLVVHPGAGNADGTLMNALLHHCPNIE 127

Query: 109 ISV-----GRLDINTEGLLLLTNDGGLARV------LELPSTQWLRVYRVRFHGQVDQD- 156
                    RLD +T GL+++                   + ++  +           D 
Sbjct: 128 HVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIVLGTMTAGGTVDE 187

Query: 157 ----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                        V            +  +  ++  + + L  G+  +I+    +   
Sbjct: 188 PIGRHPTKRTHMAVHHSGKPAVTHYRVAEKFRNHTRLRLRLESGRTHQIRVHMAYIGH 245


>gi|238917079|ref|YP_002930596.1| lysozyme [Eubacterium eligens ATCC 27750]
 gi|238872439|gb|ACR72149.1| lysozyme [Eubacterium eligens ATCC 27750]
          Length = 310

 Score = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 16/244 (6%), Positives = 57/244 (23%), Gaps = 36/244 (14%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGI--------------LLERA 50
           I +      R+ K +++     SR  +++++    + V+                 +   
Sbjct: 9   IAEPEDKGTRIDKYLSQELEDVSRSRIQKLLDDGDITVDDKCVKSNYKLNGTEHITITIP 68

Query: 51  AVNV--------------MSTDHIEVD---GVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
            + V                 D I +D   G+ +  A           +      +    
Sbjct: 69  ELIVPQILPENIPLNIIYEDDDVILIDKPKGMVVHPAAGHYTGTVVNALMYHCRDNLSGI 128

Query: 94  RSTVFDNLPSIFSRVISVGRLDIN----TEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
              +   +        +   +          +        + R          +      
Sbjct: 129 NGVMRPGIVHRIDMNTTGVIVACKNDKAHNDIAAQLAVHSITRKYYCIVHNRFKEEEGTV 188

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + ++  +     +  +   +      +       +++   L  G+  +I+       
Sbjct: 189 DAPIGRNPKDRKMMAVDRKNGKHAVTHYRVLENFDKYSFIECQLETGRTHQIRVHMASIG 248

Query: 210 WKVN 213
             + 
Sbjct: 249 HPIL 252


>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 = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 33/245 (13%), Positives = 68/245 (27%), Gaps = 38/245 (15%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           I        R+ K++ A+    SR  ++++     V V G  + +    + + D I VD 
Sbjct: 8   IAAPEDAGTRIDKLLSAQLSDMSRSALQKLTEDGSVLVGGKAVSK-NYKLKNGDVITVDI 66

Query: 64  -----------GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                       +P+     +   L +      +V   +     + V   L     R+ S
Sbjct: 67  PEPQELKAEPQDIPIDIVYEDDALLVVNKPKGMVVHPAAGNPDGTLVNALLYHCKGRLSS 126

Query: 111 VG----------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
           +                       + D     L     +    R          +     
Sbjct: 127 INGVIRPGIVHRIDKFTSGLLMVAKTDKAHNSLAAQIKEHSFTREYNAVCVGRFKEPTGT 186

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
            +  + + K +  K  +  Q          +  + G  + V   L  G+  +I+    F 
Sbjct: 187 INEPIGRSKFDRKKMCVTYQNSKEAVTHYEVIEELGQYSLVRFRLETGRTHQIRVHSAFI 246

Query: 209 NWKVN 213
              V 
Sbjct: 247 GHPVL 251


>gi|291550385|emb|CBL26647.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus
           torques L2-14]
          Length = 304

 Score = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 34/243 (13%), Positives = 74/243 (30%), Gaps = 38/243 (15%)

Query: 8   QENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---D 63
             + T +R+ K +  R    SR  ++++I ++++ VN  L  +A   + + D I +   D
Sbjct: 7   NADITGERIDKFLDGRIESLSRSYIQKLIKEKKILVN-QLPVKANYKLTTGDTIILQIPD 65

Query: 64  GVPLRKAERTR-----------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----- 107
             PL                  L +      +V         + V   L           
Sbjct: 66  PEPLDIQPENIPLDILYEDDDILVVNKPKGMVVHPAPGHYSHTLVNAVLYHCGENLSGIN 125

Query: 108 ----VISVGRLDINTEGLLLLTNDGGLARV-------------LELPSTQWLRVYRVRFH 150
                  V R+D+NT G LL+  +    ++                     L+      +
Sbjct: 126 GVIRPGIVHRIDMNTTGSLLICKNDKAHQILAEQLKEHSITRKYHSIVHGNLKEDTGTVN 185

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + +   +  K         +      +  + G+  ++   L  G+  +I+        
Sbjct: 186 APIGRHPTDRKKMSTKAPNGRHAVTHYRVLERFGNFTYIECQLETGRTHQIRVHMSSIGH 245

Query: 211 KVN 213
            + 
Sbjct: 246 PIL 248


>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 = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 34/247 (13%), Positives = 72/247 (29%), Gaps = 36/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K +++      R+ K ++      SR  V+ +I  + + VN    +  +  V + D 
Sbjct: 1   MPKKYLLEVKDEHGRLDKFVSEQVPDLSRTRVKELIQDKNILVNNKSEKV-SYKVQAGDC 59

Query: 60  IEVDGVPLR--------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           + V+   ++                +   + +      +V         + V   L    
Sbjct: 60  VLVNVPAVKPLDVVPENIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHTK 119

Query: 106 --------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-- 155
                    R   V R+D +T GLL++  +      LE                  +   
Sbjct: 120 DLAQSPEGFRPGIVHRIDKDTSGLLMIAKNAKARESLEDQLAHKTNKRIYWAIVHGNFGE 179

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           KK  V++          +  Q    + +   L  G+  +I+   
Sbjct: 180 EGGTIDALIGRNPYDRKKMAVVENGKKAVTHFKVLEQFKGFSLIECQLETGRTHQIRVHL 239

Query: 206 EFFNWKV 212
           ++    V
Sbjct: 240 DYIGHAV 246


>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 = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 32/239 (13%), Positives = 64/239 (26%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I   RV+VNG    +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILDDRVQVNGKTTNKPKEKVLGGETVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  QIEEEARWEPQDIALNIVYEDSDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPEIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L                               
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGTMTAGGTVEEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 SRHSTKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHINHPLV 248


>gi|329118620|ref|ZP_08247324.1| 30S ribosomal protein S4 [Neisseria bacilliformis ATCC BAA-1200]
 gi|327465355|gb|EGF11636.1| 30S ribosomal protein S4 [Neisseria bacilliformis ATCC BAA-1200]
          Length = 118

 Score = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 15 RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          R+  VI R G  S R E  ++++ + V VNG ++   +  V + D + V     ++    
Sbjct: 9  RLDNVIYRMGFGSTRAEARQLVSHKAVTVNGQVVNIPSYQVKAGDVVAVREKAKKQVRIQ 68


>gi|227872363|ref|ZP_03990714.1| pseudouridylate synthase [Oribacterium sinus F0268]
 gi|227841792|gb|EEJ52071.1| pseudouridylate synthase [Oribacterium sinus F0268]
          Length = 303

 Score = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 32/245 (13%), Positives = 73/245 (29%), Gaps = 39/245 (15%)

Query: 7   VQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           V +    QR+ K ++       SR  + + I +  V VNG   + A++ V + D I+ D 
Sbjct: 5   VAKEEEGQRLDKYLSEQKDHDFSRSYLGKCIQEGCVSVNGEKAK-ASLKVKAGDRIDFDI 63

Query: 64  ---------GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                       +       +   L +  +   +V   +     + V   L    S + S
Sbjct: 64  PEQKDPEVLPEAIPLDIVYEDDDLLVVNKERGMVVHPAAGHYSGTLVNAVLAHAGSSLSS 123

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
           +  ++       +  +  GL  + +   +      ++  H    +    +  K     GI
Sbjct: 124 INGVNRPGIVHRIDKDTTGLLLICKNDLSHQSLAKQLEEHSITRRYHALVFGKIKEEDGI 183

Query: 171 CYGDM----------------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               +                         +  +   +  V   L  G+  +I+   +  
Sbjct: 184 ISAPIGRDEKDRKKQAISYKHGKEALTHYKVLERFSDSTLVECRLETGRTHQIRVHMKSI 243

Query: 209 NWKVN 213
              + 
Sbjct: 244 GHPLL 248


>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 = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 72/248 (29%), Gaps = 36/248 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           MK  +         R    +A     +R  V+  I + RV  NG   + A   V   D  
Sbjct: 1   MKTLDPAAPEEKGLRADVFLAARLDCTRSAVQHDIQEGRVTRNGKPAK-ANTKVKEGDVF 59

Query: 61  E------VDGVP--------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           +      VD           +   ++  + +      +V   +     + V   L     
Sbjct: 60  QVQVLPPVDLEARPENIPLDILYEDQDVIVVNKPRGMVVHPAAGNPDGTLVNALLYHCRD 119

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY------------- 145
                   R   V RLD +T G+++   +      L     +                  
Sbjct: 120 LSGINGVIRPGIVHRLDKDTSGVMICAKNDRAHLSLAEQIQKKEAKRTYLAIVRGNIKDD 179

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
           R     Q+D+D  +  K  +V  G  +      +  + G    V   L  G+  +I+   
Sbjct: 180 RGHIETQLDRDPRDRKKMAVVPSGGRWAATDYEVLERYGKFTVVRCRLLTGRTHQIRVHM 239

Query: 206 EFFNWKVN 213
            +    + 
Sbjct: 240 TYIGHPLV 247


>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 = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 35/278 (12%), Positives = 86/278 (30%), Gaps = 36/278 (12%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
             V+++   QR+ + +A      SR  ++  + + ++ VNG ++ +    VM  + I V 
Sbjct: 9   QTVKDSQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGDVITKPRTKVMGGEVITVQ 68

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   +   + +      +V   +    ++ +   L        
Sbjct: 69  AELEDEQRWEAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADKTVLNALLFHYPPIAE 128

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   RLD +T GL+++         L     +                   ++ K 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAIVIGTMTAGGMIDKP 188

Query: 165 IVIQ-----------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I                 +      +      +  + + L  G+  +I+    +    + 
Sbjct: 189 IGRHSTKRTLMSVSPMGKHAVTHYRVAEHFREHTRLRLRLETGRTHQIRVHMAYLQHPL- 247

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L   +YG      +  G+T E++ +++R+     L  
Sbjct: 248 -LGDTAYGGRA--RIPKGATEELT-EMIRDFDRQALHA 281


>gi|325335513|gb|ADZ11787.1| Pseudouridylate synthase, 23S RNA-specific [Riemerella
           anatipestifer RA-GD]
          Length = 354

 Score = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 74/248 (29%), Gaps = 46/248 (18%)

Query: 6   IVQENFTPQRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +V +N  P R+ K +      +   SR ++ +      V VNG  +++    V   D + 
Sbjct: 34  VVDKNQEPLRIDKYLLIFRQNS---SRNKISQTCRAGNVVVNGTPVKQ-NYRVKPGDKVS 89

Query: 62  V-----------------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF 98
           V                       D   L   +   + ++        T  +        
Sbjct: 90  VLLTHPPRENVIVPQDIPINIVYEDDDLLVVDKEAGMVVHPGFGNWDGTLVNALAYHFEK 149

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVY 145
           + L +   RV  V R+D +T GLL++  +      L                    L   
Sbjct: 150 NGLKTDLDRVGLVHRIDKDTSGLLVIAKNEYAMSFLAKQFFERTTKRLYWAFVWGNLAED 209

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                G + +D  N ++  +   G    +      +  +     WV   L  G+  +I+ 
Sbjct: 210 TGTIKGHIGRDLKNRMQMAVYEDGSLGKHAVTHYKVLERFRYMTWVECKLETGRTHQIRA 269

Query: 204 VFEFFNWK 211
            F      
Sbjct: 270 HFRHIGHT 277


>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 = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 28/237 (11%), Positives = 61/237 (25%), Gaps = 37/237 (15%)

Query: 13  PQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVN----------VMSTDHIE 61
            +R+   +AR     SR  V+R+I    V+V+G  ++               V   + + 
Sbjct: 10  GERLDVFLARQIENCSRSYVQRLITDGNVRVDGAPVK-PNYKLRSGEEICCTVPPAEEVV 68

Query: 62  VDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           +    +       +   + +      +V   +     + V   L          G L   
Sbjct: 69  IAAEDIPLDVLYEDEDIIVINKARGMVVHPAAGNLTGTLVNALLFRCRDLSGINGELRPG 128

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------------------D 156
               L     G +       +  +L         + +                       
Sbjct: 129 IVHRLDKDTSGVMVAAKNDMAHHFLAQQIRSKDARREYRALVHGNIAERAGVITGDIGRH 188

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             +  +  IV  G         +  + G    V+  L  G+  +I+         + 
Sbjct: 189 PTDRKRMAIVRSGGKSATTHFEVLERFGDYTLVSCVLETGRTHQIRVHMTSIGHPLV 245


>gi|332638853|ref|ZP_08417716.1| pseudouridine synthase [Weissella cibaria KACC 11862]
          Length = 304

 Score = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 36/246 (14%), Positives = 66/246 (26%), Gaps = 36/246 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M ++ +V  + T  R+ KV+A A    +R +V   I    + VNG + ++A  +V   D 
Sbjct: 1   MSEETLVITDQTG-RLDKVVADAFDDYTRTQVTGWINDGILTVNGAV-KKAKYSVKPNDE 58

Query: 60  I--------EVDGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I        E+D  P      +   +   L +      +V      +  + V   +    
Sbjct: 59  IKFTVPEAVEIDLQPEDIPLDIVYEDDDLLVVNKPQGMVVHPALGHESGTLVNALMFHTP 118

Query: 106 SRVISVGRLD-------------------INTEGLLLLTNDGGLARVLELPSTQWLRVYR 146
              I+                              L                     V  
Sbjct: 119 LSTINGVVRPGIVHRIDKDTSGLLMVAKNDKAHESLSAQLKDKKNLRQYYALVHGEFVEN 178

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          KK  V+ G         +  +      + V L  G+  +I+    
Sbjct: 179 EGTIKAPLGRSSADRKKQAVVAGGRDAVTHFKVVKRFVGYTLLQVTLETGRTHQIRVHMA 238

Query: 207 FFNWKV 212
           +    V
Sbjct: 239 YIGHPV 244


>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 = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 34/256 (13%), Positives = 67/256 (26%), Gaps = 43/256 (16%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAA--VNVMSTDHIEV 62
            V E     R+ + +A      SR  ++++I + RV V     E+    + V     I V
Sbjct: 23  TVMEEQEGMRLDQFLAGELKEHSRSYIQKLIKEGRVTVGDKK-EKPGCRLKVEDNVVICV 81

Query: 63  -------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                        D   + + E   L    K + +        G            +   
Sbjct: 82  PPLKELEVLPEKMDLDIIYEDEDVILINKPKDMVVHPCPGRYTGTLVNGLLYHCRDNLSG 141

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
             G L       +     G L       + + L             + +         +G
Sbjct: 142 INGVLRPGIVHRIDKDTTGVLVVCKNDMAHKSLAEQLKEHSITRKYEAIVY-NNFTQEEG 200

Query: 170 ICYGDM--------QVTLDTQKGSNAW---------------VTVGLREGKNREIKKVFE 206
                +        ++ ++ + G  A                +   L  G+  +I+    
Sbjct: 201 TVDAPIGRSPADRKKMAVEPKNGKRAVTHYKVLSHLNHQFNHIECQLETGRTHQIRVHMA 260

Query: 207 FFNWKVNRLIRISYGP 222
                +  L   +YGP
Sbjct: 261 SIRHPL--LGDTTYGP 274


>gi|327441137|dbj|BAK17502.1| pseudouridylate synthase, 23S RNA-specific [Solibacillus silvestris
           StLB046]
          Length = 300

 Score = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 32/238 (13%), Positives = 65/238 (27%), Gaps = 36/238 (15%)

Query: 9   ENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           E F  +R+ K +++   + SR ++   + ++R+ VNG  ++ A   V   D IEV     
Sbjct: 9   EEFAGERIDKALSQMEESWSRSQISNWLDEERILVNGAAVK-AKYKVKQGDVIEVTVPEV 67

Query: 63  -DGVPLR--------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
            D   +           +   L +      +V         + V   +          G 
Sbjct: 68  EDLEIIPEDLNLEIVYEDADVLVVNKPRGMVVHPAPGHATGTLVNGLMHHCKDLSGINGV 127

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------------------ 155
                   +     G L       + + L    V                          
Sbjct: 128 ARPGIVHRIDKDTSGLLMVAKNDVAHESLVNQLVEKSVTRKYTALVHGHIAHEKGTIDAP 187

Query: 156 --DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                   +K  V+    +      +  + G    V   L  G+  +I+    +  + 
Sbjct: 188 IGRDQKDRQKQAVVDKGKHAVTHFQVIERFGEFTLVECRLETGRTHQIRVHMNYIGFP 245


>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 = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 29/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I   +V V+G  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKDWILDDKVTVDGKKINKPKEKVLGGELVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-- 108
                           +   +   L +      +V   +     + +   L      +  
Sbjct: 70  QIEEDARWAPQEIPLDIVYEDNDILVINKPRGLVVHPGAGNPDGTVLNALLYYYPEIMDV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                V RLD +T GL+++         L                   +           
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNMTAGGRVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHINHPLV 248


>gi|213420845|ref|ZP_03353911.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 278

 Score = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 34/239 (14%), Positives = 64/239 (26%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG L ++    V+  + + +D 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILNQRVLVNGQLCDKPKEKVLGGERVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  EIDEEIRFEAQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L                               
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVNEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMSVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 35/278 (12%), Positives = 86/278 (30%), Gaps = 36/278 (12%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
             V+++   QR+ + +A      SR  ++  + + ++ VNG ++ +    VM  + I V 
Sbjct: 9   QTVKDSQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGDVITKPRTKVMGGEVITVQ 68

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   +   + +      +V   +    ++ +   L        
Sbjct: 69  AELEDEQRWEAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADKTVLNALLFHYPPIAE 128

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   RLD +T GL+++         L     +                   ++ K 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAIVIGTMTAGGMIDKP 188

Query: 165 IVIQ-----------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I                 +      +      +  + + L  G+  +I+    +    + 
Sbjct: 189 IGRHSTKRTLMSVSPMGKHAVTHYRVAEHFREHTRLRLRLETGRTHQIRVHMAYLQHPL- 247

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L   +YG      +  G+T E++ +++R+     L  
Sbjct: 248 -LGDTAYGGRA--RIPKGATEELT-EMIRDFDRQALHA 281


>gi|325292121|ref|YP_004277985.1| hemolysin [Agrobacterium sp. H13-3]
 gi|325059974|gb|ADY63665.1| hemolysin [Agrobacterium sp. H13-3]
          Length = 250

 Score = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 24/57 (42%), Gaps = 1/57 (1%)

Query: 7  VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          + +    +R+ +++   G  ASR      IA+  V VNG    + +  V     I +
Sbjct: 1  MSKTPENERLDQLLVSLGHFASRSRARDAIARGTVSVNGKTATKPSQTVAGNVKIAI 57


>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 = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 31/234 (13%), Positives = 59/234 (25%), Gaps = 35/234 (14%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP----- 66
             R+ K +A     SR      I   ++ VNG + ++A   V + D I  +   P     
Sbjct: 9   GVRLDKAVADLTSLSRSHANEQIKNGQILVNGQV-KKAKYAVKAGDVITYELPEPEALEY 67

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                   +   +     +      +V   +     + V   +  I       G L    
Sbjct: 68  VAENLPLDIVYQDEDVAVVNKAQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGI 127

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL------------------ 160
              +     G L       +   L               +                    
Sbjct: 128 VHRIDKDTSGLLMIAKNDDAHIKLAEELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSE 187

Query: 161 --LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
              KK  V         +  +  + G+   V + L  G+  +I+    +    V
Sbjct: 188 KDRKKQAVTAKGKPAVTRFHVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 74/248 (29%), Gaps = 46/248 (18%)

Query: 6   IVQENFTPQRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +V +N  P R+ K +      +   SR ++ +      V VNG  +++    V   D + 
Sbjct: 32  VVDKNQEPLRIDKYLLIFRQNS---SRNKISQTCRAGNVVVNGTPVKQ-NYRVKPGDKVS 87

Query: 62  V-----------------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF 98
           V                       D   L   +   + ++        T  +        
Sbjct: 88  VLLTHPPRENVIVPQDIPINIVYEDDDLLVVDKEAGMVVHPGFGNWDGTLVNALAYHFEK 147

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVY 145
           + L +   RV  V R+D +T GLL++  +      L                    L   
Sbjct: 148 NGLKTDLDRVGLVHRIDKDTSGLLVIAKNEYAMSFLAKQFFERTTKRLYWAFVWGNLAED 207

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                G + +D  N ++  +   G    +      +  +     WV   L  G+  +I+ 
Sbjct: 208 TGTIKGHIGRDLKNRMQMAVYEDGSLGKHAVTHYKVLERFRYMTWVECKLETGRTHQIRA 267

Query: 204 VFEFFNWK 211
            F      
Sbjct: 268 HFRHIGHT 275


>gi|212715757|ref|ZP_03323885.1| hypothetical protein BIFCAT_00657 [Bifidobacterium catenulatum
          DSM 16992]
 gi|212661124|gb|EEB21699.1| hypothetical protein BIFCAT_00657 [Bifidobacterium catenulatum
          DSM 16992]
          Length = 260

 Score = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 8  QENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           ++    R+   +   G I SR + +R+IA  +V VNG+ + + +  V   D I VD
Sbjct: 11 SDSIQVVRLDVALLERGLIGSRSKAQRLIADGKVSVNGVDITKVSTKVGCDDIITVD 67


>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 = 62.1 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 35/239 (14%), Positives = 69/239 (28%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I + RV VNGI++ +    V+  +HI +D 
Sbjct: 10  TVTESQLGQRLDQALAELFPDYSRSRIKEWILEDRVSVNGIIINKPKEKVLGGEHIAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
           +               +   +   L +      +V   +     + +   L         
Sbjct: 70  LIEEENRWEAQDIALDIVYEDEDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPQIADV 129

Query: 107 -RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L                               
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGTMTAGGTVREPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 ARHPTKRTHMSVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMAHINHPLV 248


>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 = 61.7 bits (148), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 32/244 (13%), Positives = 67/244 (27%), Gaps = 40/244 (16%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V       RV K +  R   ASR  +++      V  NG  ++  +  V   D I V  
Sbjct: 33  VVDRGQEMMRVDKYLFDRLTNASRNRIQKAADAGFVMANGKPVKS-SYKVKPQDVITVMM 91

Query: 63  -----DGVPLR--------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                +   +           +R  + +      +V         + V      +     
Sbjct: 92  DRPRYENEVIPEDIPLNIVYEDRCLMVVNKPAGLVVHPGHGNYHGTLVNAIAWHMKDNPD 151

Query: 110 SV---------GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-- 158
                       R+D +T GLL++         L           R R     + ++   
Sbjct: 152 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTHLGNQFFNKTTKRRYRALVWGNVEQDEG 211

Query: 159 -----------NLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                      + ++  ++      +      +  + G    V   L  G+  +I+   +
Sbjct: 212 TVVGNIGRNPKDRMQMAVLSDDQGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMK 271

Query: 207 FFNW 210
               
Sbjct: 272 HIGH 275


>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 = 61.7 bits (148), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 32/239 (13%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG L ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKLCDKPKEKVLGGEQVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 61.7 bits (148), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHMRLRLRLETGRTHQIRVHMAHITHPLV 248


>gi|293415867|ref|ZP_06658507.1| rluD [Escherichia coli B185]
 gi|291432056|gb|EFF05038.1| rluD [Escherichia coli B185]
          Length = 326

 Score = 61.7 bits (148), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 32/239 (13%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG L ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKLCDKPKEKVLGGEQVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 61.7 bits (148), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 31/232 (13%), Positives = 62/232 (26%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP------- 66
           R+ K ++     SR      I   +V VNG   ++A   V   D +      P       
Sbjct: 11  RLDKALSDLTELSRSLANEQIKVGQVLVNGQ-AKKAKYTVQEGDIVTYHVPEPEVLEYVA 69

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 +   +     +      +V   +     + V   +  I       G L      
Sbjct: 70  EDLPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 121 LLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            +     G L       +           + LR Y    HG +  D+  +       +  
Sbjct: 130 RIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 171 CYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                          +  +  + G  + + + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFQVLERFGDYSLLELQLETGRTHQIRVHMAYIGHPV 241


>gi|284007738|emb|CBA73551.1| 23S rRNA pseudouridine synthase D [Arsenophonus nasoniae]
          Length = 325

 Score = 61.7 bits (148), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 29/236 (12%), Positives = 63/236 (26%), Gaps = 31/236 (13%)

Query: 9   ENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---- 63
           E+   QR+ + +A      SR  ++  I   RV VNG ++ R    V  ++ I +D    
Sbjct: 13  ESQLGQRLDQALAELFPDYSRSRIKEWILDNRVLVNGKIINRPKEKVFGSEQIAIDVLIE 72

Query: 64  ----GVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------- 105
                 P      +   +   L +      +V   +     + +   L            
Sbjct: 73  EDMRWQPQNIPLNIVYEDDEILVINKPRDLVVHPGAGNPDGTVLNALLYRYPEIINVPRA 132

Query: 106 ---SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-----K 157
               R+       +     +        A      + ++  V   R       D      
Sbjct: 133 GIVHRLDKDTTGLMVIAKTIPAQTHLVEALQRREITREYEAVVNGRMTAGGTVDEPIARH 192

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                   +            +     ++  + + L  G+  +I+      N  + 
Sbjct: 193 PTKRTHMAIHPMGKPAITHYRVMEHFRAHTRLRLRLESGRTHQIRVHMAHINHPLV 248


>gi|257869391|ref|ZP_05649044.1| pseudouridylate synthase [Enterococcus gallinarum EG2]
 gi|257803555|gb|EEV32377.1| pseudouridylate synthase [Enterococcus gallinarum EG2]
          Length = 301

 Score = 61.7 bits (148), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 30/245 (12%), Positives = 66/245 (26%), Gaps = 35/245 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M ++  V  +    RV KV+A    ASR ++++ + +  V   G  +  A   V + D +
Sbjct: 1   MNNQIEVVIHEEKGRVDKVLADRLEASRSQIQQWLKEGAVTCQGDPIR-ANYKVKAGDQL 59

Query: 61  EV--------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
            +        D  P      +   ++    +      +V   +     + V   L  +  
Sbjct: 60  VIQVPEPESLDLEPEDIPLTIVYQDQDVAVINKPQGMVVHPSAGHPNGTLVNALLYHMTD 119

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ----------- 155
                  +       +     G L       + + L                        
Sbjct: 120 LSSINDVVRPGIVHRIDKDTSGLLMIAKNDHAHEALAKQLKDKTSLRKYVALVHGNISHE 179

Query: 156 ---------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          K   V +         T+  +      V + L  G+  +I+   +
Sbjct: 180 KGTINAPIGRSKVNRKMQAVQEDGKPAVTHFTVLERFDQFTLVELQLETGRTHQIRVHMQ 239

Query: 207 FFNWK 211
           +  + 
Sbjct: 240 YIGFP 244


>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 = 61.7 bits (148), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 33/232 (14%), Positives = 61/232 (26%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLR--- 68
           R+ K +A     SR      I   ++ VNG   ++A   V   D I     D   +    
Sbjct: 13  RLDKAVADLTELSRGLANEQIKNGQILVNGE-AKKAKYAVKEGDVISYEVPDPEVVEYVA 71

Query: 69  --------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                     +     +      +V   +     + V   +  I       G L      
Sbjct: 72  EDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 131

Query: 121 LLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            +     G L       +           + LR Y    HG +  D+  +       +  
Sbjct: 132 RIDKDTSGLLMIAKNDQAHLALADELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 191

Query: 171 CYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                          +  +  + G    V + L  G+  +I+    +    V
Sbjct: 192 RKKQAVTAKGKPALTRFQVLERFGDYTLVELQLETGRTHQIRVHMAYIGHPV 243


>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 = 61.7 bits (148), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 35/246 (14%), Positives = 70/246 (28%), Gaps = 34/246 (13%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M    +VQ  +   R+   +      SR ++ + I  + V VNG+ ++     +   D I
Sbjct: 9   MNKTLVVQSQYEGMRLDIFLKEVLDYSRSKINKEIKNKSVLVNGVSVKS-GYIIKKNDII 67

Query: 61  E--------------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
                          +D   L + E   +    + + +                  +I  
Sbjct: 68  TLEILEDQVNLEPQKIDFKILFEDEYIMVISKPENLVVHPGAGVFSETLVNGLLDYNINI 127

Query: 107 RVI-------SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
           + I        V RLD +T GL+++  D    + L                     +   
Sbjct: 128 KDIGEEDRPGIVHRLDKDTSGLMIIAKDALAYKKLVNMFKYGEIHKEYIAILTGHLENEI 187

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWV------------TVGLREGKNREIKKVFEF 207
            + + I           V     K + +               V +  G+  +I+    +
Sbjct: 188 RVDEPIGRNPKDRKSFTVIYSNSKNAISTFVPIKYMNGFTLCRVIIETGRTHQIRVHARY 247

Query: 208 FNWKVN 213
            N  V 
Sbjct: 248 LNHPVL 253


>gi|206889218|ref|YP_002248052.1| hemolysin A [Thermodesulfovibrio yellowstonii DSM 11347]
 gi|206741156|gb|ACI20213.1| hemolysin A [Thermodesulfovibrio yellowstonii DSM 11347]
          Length = 246

 Score = 61.7 bits (148), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 1/56 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          R+ +++ + GI  SR +   +I + +V VNG  +E+    V     I + G  L  
Sbjct: 4  RLDQLLFKKGITESREKARALIIEGKVIVNGHKIEKPGTMVDENSEITICGETLPY 59


>gi|307151436|ref|YP_003886820.1| hemolysin A [Cyanothece sp. PCC 7822]
 gi|306981664|gb|ADN13545.1| hemolysin A [Cyanothece sp. PCC 7822]
          Length = 270

 Score = 61.7 bits (148), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 26/54 (48%), Gaps = 1/54 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
          QR+   +    +  SR++ +R+I    VKVN  ++++    V  +  I +   P
Sbjct: 4  QRLDNRLVELNLCDSRQQAQRLIRAGEVKVNQQIIDKPGTEVDPSAEIVLQAKP 57


>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 = 61.7 bits (148), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 34/240 (14%), Positives = 69/240 (28%), Gaps = 31/240 (12%)

Query: 5   NIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           N V+++   QR+ + IA      SR  ++  +   +V V+G ++ +    VM  + I V 
Sbjct: 9   NTVKDSQLGQRLDQAIAELFADFSRSRLKEWLLDGKVTVDGNVVTKPRTKVMGGEVITVL 68

Query: 63  ----DGVPLRKAERT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
               D V     +            L +      +V   +     + +   L        
Sbjct: 69  AELEDEVRWEAQDIPLDIVYEDDDILVINKPRDFVVHPGAGTPDGTVLNALLFHCPEVAE 128

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
             R   V RLD +T GL+++         L     +                    + K 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRHITREYEAIAIGRMTAGGKVDKP 188

Query: 165 IVIQGIC---------YGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I                        +      +  + + L  G+  +I+    +    + 
Sbjct: 189 IGRHATKRTLMAVSPMGKPAVTHFRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPLL 248


>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 = 61.7 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 32/244 (13%), Positives = 69/244 (28%), Gaps = 38/244 (15%)

Query: 7   VQENFTPQRVSKVIA--RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           V    +  R+   +A   +G  SR  ++R+I   RV ++G    RA+  + + D + ++ 
Sbjct: 12  VTATESGLRLDLFLASHESGF-SRARLQRLIESGRVTISGKAAIRASQKLRTGDIVMLEE 70

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
            P              +   +   L L      +V   +     + V   L         
Sbjct: 71  PPATPLELIPQDIPLSILYEDHDLLVLDKPAGLVVHPAAGHVSGTLVNALLFHCRDLAGI 130

Query: 111 VGRLDIN---------------------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
            G +                         +GL L      + +  +       R    + 
Sbjct: 131 GGVMRPGIVHRLDKDTSGLLVVAKTDAAHQGLALQFKKHQVGKTYQALVYGDPREKTGQI 190

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              V +  +   K     +       +  +  + G    + V +  G+  +I+       
Sbjct: 191 DLPVGRHPVERKKMSTKSRRGKEAATRWRIAERFGVATLLNVDIVTGRTHQIRVHLAAIG 250

Query: 210 WKVN 213
             V 
Sbjct: 251 HPVV 254


>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 = 61.7 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 37/237 (15%), Positives = 68/237 (28%), Gaps = 38/237 (16%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+ K +A      SR  +++++AQ  V++NG    + A  V + D + V   P       
Sbjct: 40  RLDKALAELVPEFSRSYLQQLLAQGDVRLNGQPAAKPAHKVRAGDQVAVRMRPTQQSQAF 99

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-----GR 113
                   +   +   L +      +V         + +   L      +         R
Sbjct: 100 KPESLPLDVVHEDEHLLVIDKPAGLVVHPAPGNWSGTLLNALLGRDAQAMQVPRAGIVHR 159

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------------DKLN 159
           LD +T GL+++  +      L           +                       D  N
Sbjct: 160 LDKDTSGLMVVARNRAAMDALVRMIAAREVSRQYLALAWGAWSGSEQRRIRAPIGRDPRN 219

Query: 160 LLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            L+  +V  G   G    T   L         V   L  G+  +I+         + 
Sbjct: 220 RLRMAVVDLGQHAGKEACTDFDLLASGEEVCLVRCTLHTGRTHQIRVHMASIRHPLV 276


>gi|288931952|ref|YP_003436012.1| RNA-binding S4 domain protein [Ferroglobus placidus DSM 10642]
 gi|288894200|gb|ADC65737.1| RNA-binding S4 domain protein [Ferroglobus placidus DSM 10642]
          Length = 208

 Score = 61.7 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 3/65 (4%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRKA 70
           R+ + + ++G   SR + +  I +  VKVNG ++ + +  V  ++ IEV   G P    
Sbjct: 1  MRLDEFLKKSGYFKSRSQAKEAIKRGFVKVNGKVITKPSFQVKGSEKIEVAEKGKPRGYY 60

Query: 71 ERTRL 75
          +   L
Sbjct: 61 KLKEL 65


>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 = 61.7 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 32/228 (14%), Positives = 68/228 (29%), Gaps = 32/228 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD----GVPLRK 69
           R+ K +A      SR  ++  I    VK++ + + R    V +   +EV+       +  
Sbjct: 19  RLDKALAALFPDYSRTRIKEWILDDLVKIDDVTVNRPREKVYTGQQVEVNATLEDEVVFH 78

Query: 70  AER----------TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-----GRL 114
            +             L +      +V   +     + +   L      V         RL
Sbjct: 79  PQNIPLDIIFEDEHILVINKPAGLVVHPGAGNPDGTVLNALLHHYPEIVEVPRAGIVHRL 138

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYR------------VRFHGQVDQDKLNLLK 162
           D +T GL+++         L                         R    + +DK N +K
Sbjct: 139 DKDTTGLMVIAKTVPAQTHLVTSLQAREITREYDAIAMGCFTAGGRVEAPIGRDKANRVK 198

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             +   G  +      +  +  ++  + + L  G+  +I+        
Sbjct: 199 MAVATVGGKHAVTHYRVAEKYRAHTRLRLRLETGRTHQIRVHMSHIGH 246


>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 = 61.7 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 33/239 (13%), Positives = 66/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E+    R+ + +A      SR  ++  I   RVKVNG ++ +    V+  + I +D 
Sbjct: 10  TVTESQLGHRLDQALAELFPDYSRSRIKEWILDDRVKVNGKIINKPKEKVLGGEEIAIDA 69

Query: 64  -------GVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                    P      +   +   L +      +V   +     + +   L         
Sbjct: 70  LIEEEARWEPQNIPLDIVYEDSDILVINKPRDLVVHPGAGNPDGTILNALLYYYPEIVDV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L                               
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGTMTAGGTVEEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      +  + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMAHISHPLV 248


>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 = 61.7 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 34/240 (14%), Positives = 69/240 (28%), Gaps = 31/240 (12%)

Query: 5   NIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           N V+++   QR+ + IA      SR  ++  +   +V V+G ++ +    VM  + I V 
Sbjct: 9   NTVKDSQLGQRLDQAIAELFADFSRSRLKEWLLDGKVTVDGNVVTKPRTKVMGGEVITVL 68

Query: 63  ----DGVPLRKAERT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
               D V     +            L +      +V   +     + +   L        
Sbjct: 69  AELEDEVRWEAQDIPLDIVYEDDDILVINKPRDFVVHPGAGTPDGTVLNALLFHCPEVAE 128

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
             R   V RLD +T GL+++         L     +                    + K 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRMTAGGKVDKP 188

Query: 165 IVIQGIC---------YGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I                        +      +  + + L  G+  +I+    +    + 
Sbjct: 189 IGRHATKRTLMAVSPMGKPAVTHFRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPLL 248


>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 = 61.7 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 28/238 (11%), Positives = 63/238 (26%), Gaps = 31/238 (13%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T  R+ + +A      SR  ++  I    V V+G+++ +    V     IE+
Sbjct: 8   KSEISATQTGLRLDQALAELFPDYSRTRIKEWILSDAVYVDGVIVNKPREKVFELQQIEI 67

Query: 63  DGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                             +   +   L +  +   +V   +     + +   L       
Sbjct: 68  AATLEEEVHAAAQAIELNIVYEDDHILVINKQAGLVVHPGAGNADGTLMNALLHHCPDIE 127

Query: 109 ISV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------- 155
                    RLD +T GL+++         L                             
Sbjct: 128 HVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIVMGTMTGGGTVDE 187

Query: 156 ---DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                        V            +  +  ++  + + L  G+  +I+   E+   
Sbjct: 188 PIGRHPTKRTHMAVHHSGKPAVTHYRVAEKFRNHTRLRLRLESGRTHQIRVHMEYIGH 245


>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 = 61.7 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 37/237 (15%), Positives = 68/237 (28%), Gaps = 38/237 (16%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+ K +A      SR  +++++AQ  V++NG    + A  V + D + V   P       
Sbjct: 44  RLDKALAELVPEFSRSYLQQLLAQGDVRLNGQPAAKPAHKVRAGDQVAVRMRPTQQSQAF 103

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-----GR 113
                   +   +   L +      +V         + +   L      +         R
Sbjct: 104 KPESLPLDVVHEDEHLLVIDKPAGLVVHPAPGNWSGTLLNALLGRDAQAMQVPRAGIVHR 163

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------------DKLN 159
           LD +T GL+++  +      L           +                       D  N
Sbjct: 164 LDKDTSGLMVVARNRAAMDALVRMIAAREVSRQYLALAWGAWSGSEQRRIRAPIGRDPRN 223

Query: 160 LLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            L+  +V  G   G    T   L         V   L  G+  +I+         + 
Sbjct: 224 RLRMAVVDLGQHAGKEACTDFDLLASGEEVCLVRCTLHTGRTHQIRVHMASIRHPLV 280


>gi|218282381|ref|ZP_03488663.1| hypothetical protein EUBIFOR_01245 [Eubacterium biforme DSM 3989]
 gi|218216667|gb|EEC90205.1| hypothetical protein EUBIFOR_01245 [Eubacterium biforme DSM 3989]
          Length = 243

 Score = 61.7 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 1/51 (1%)

Query: 12 TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             R+ K +    I+SR + + MI + ++ VNG ++ +A+  V   D I V
Sbjct: 2  DKIRLDKAL-LKTISSRAKAQDMIKEGKISVNGKVITKASYLVSDEDDIVV 51


>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 = 61.7 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 35/278 (12%), Positives = 86/278 (30%), Gaps = 36/278 (12%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
             V+++   QR+ + +A      SR  ++  + + ++ VNG ++ +    VM  + I V 
Sbjct: 9   QTVKDSQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGDVITKPRTKVMGGEVITVQ 68

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   +   + +      +V   +    ++ +   L        
Sbjct: 69  AELEDEQRWEAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADKTVLNALLFHYSPIAE 128

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   RLD +T GL+++         L     +                   ++ K 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAIVIGTMTAGGMIDKP 188

Query: 165 IVIQ-----------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I                 +      +      +  + + L  G+  +I+    +    + 
Sbjct: 189 IGRHSTKRTLMSVSPMGKHAVTHYRVAEHFREHTRLRLRLETGRTHQIRVHMAYLQHPL- 247

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L   +YG      +  G+T E++ +++R+     L  
Sbjct: 248 -LGDTAYGGRA--RIPKGATEELT-EMIRDFDRQALHA 281


>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 = 61.7 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 33/265 (12%), Positives = 81/265 (30%), Gaps = 35/265 (13%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
             V+E+   QR+ + +A      SR  ++  + + ++ VNG ++ +  + VM  + I V 
Sbjct: 9   QTVKESQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGEVITKPRMKVMGGEVIVVQ 68

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   +   + +      +V   +     + +   L        
Sbjct: 69  AELEDEQRWEAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADSTVLNALLFHYPPIAE 128

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   RLD +T GL+++         L     +                   ++ K 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVRALQKRDVTREYEAIVIGTMTAGGMIDKP 188

Query: 165 IVIQ-----------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I                 +      +      +  + + L  G+  +I+    +    + 
Sbjct: 189 IGRHSTKRTLMSVSPMGKHAVTHYRVAEHFREHTRLRLRLETGRTHQIRVHMAYLQHPL- 247

Query: 214 RLIRISYGPFQLGTLLAGSTREVSK 238
            L   +YG      +  G++ E+++
Sbjct: 248 -LGDTAYGGRA--RIPKGASEELTE 269


>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 = 61.7 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 27/248 (10%), Positives = 71/248 (28%), Gaps = 42/248 (16%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           V    +P R+   + +    A+R +V+  I + RV VNG  ++ A   + S D IEV   
Sbjct: 41  VSRTQSPMRIDVYLTQQVENATRNKVQEAIEEGRVVVNGKCVK-ANYRLKSCDVIEVTFL 99

Query: 64  ------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                        + +   +   + +  +P  +V         +     L  + +   ++
Sbjct: 100 RPPAPELAPEAIPIAIMYEDDDLMVINKEPGMVVHPAFGNWTGTLANAILHHLGNSAEAL 159

Query: 112 GRLDINT--------------------------EGLLLLTNDGGLARVLELPSTQWLRVY 145
              ++                                     G + + L     +     
Sbjct: 160 DASEMRPGIVHRLDKDTSGLIIIAKNPIALHKLARQFAERKVGKIYKALTWGVPKQASGT 219

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                G+  +++  +                  ++      + +++ L  G+  +I+   
Sbjct: 220 ITTNIGRSHKNRKVMANFPFEGLEGKTAITDYCVEENLEWFSVMSLRLHTGRTHQIRVHL 279

Query: 206 EFFNWKVN 213
           +     + 
Sbjct: 280 QHLGLPIV 287


>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 = 61.7 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 36/232 (15%), Positives = 65/232 (28%), Gaps = 35/232 (15%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKA 70
           R+ KVI A     +R +V++ +    V VNG    +A   V S D I +   +  PL   
Sbjct: 13  RIDKVITAHETTHTRSQVQKWLQDGLVTVNGQP-TKANYKVASGDVIAISIPEAKPLEAI 71

Query: 71  ERTRLWLY-----------HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-------VG 112
                                   +V         + V   L       I+       V 
Sbjct: 72  PEPIPLDIVYEDDQVIVVDKPQGMVVHPAPGHPDGTLVNGLLYHTDLPGINGVIRPGIVH 131

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD------------KLNL 160
           R+D +T GLL++         L         +                            
Sbjct: 132 RIDKDTSGLLMVAKTEKAQLSLSAQLKAKTSIREYLALVHGTFKEDEGTIDAPLGRDPRD 191

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            K+  V+    +      +  +     ++   L  G+  +I+    + +  V
Sbjct: 192 RKRQAVVADGRHAVTHFQVLERFEHYTFIKCILETGRTHQIRVHMAYIHHPV 243


>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 = 61.7 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 34/255 (13%), Positives = 77/255 (30%), Gaps = 46/255 (18%)

Query: 1   MKDKN-IVQENFTPQRVSKVIA--RAGIASRREVERMIAQQRVKVNGI-LLERAAVNVMS 56
           M+ +  IV++    QR+ + ++    G+ SR  ++ ++A+  V+ NG  + +     + +
Sbjct: 1   MEQREFIVEQETAGQRIDRFLSGEDTGL-SRSALQALVAEGHVQCNGKAVAKSL--KLKA 57

Query: 57  TDHIEV---DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
            D + +   D  P+              +   L +      +V         + V   L 
Sbjct: 58  GDTVLLEIPDAKPIEAVPQDIPLEIVYEDAHLLVVNKPKGMVVHPAPGNPDGTLVNALLW 117

Query: 103 SIF---------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
                        R   V R+D +T GLL++  D      L             +     
Sbjct: 118 HCKGSLSGIGGEIRPGIVHRIDKDTSGLLVVAKDDATHIGLSQQMAVHSVERAYQTVVYG 177

Query: 154 DQDKLNLLKKGIVIQGICYG------DMQ----------VTLDTQKGSNAWVTVGLREGK 197
              +     +  + +                          +  + G    +   L+ G+
Sbjct: 178 GFAQDEGFVEANLGRSKIDRKKMAVYPATEPHTKYAYTGYKVLERLGEFTLLECRLKTGR 237

Query: 198 NREIKKVFEFFNWKV 212
             +I+      +  V
Sbjct: 238 THQIRVHMASIHHPV 252


>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 = 61.7 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 35/239 (14%), Positives = 70/239 (29%), Gaps = 35/239 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           +  +    R+ K I+     SR  V+ ++    + VN    E+ +  V   D I V    
Sbjct: 6   LNVSAKAGRLDKYISEHSDLSRSRVQELLTSGDILVNSKQ-EKPSYKVAIGDKISVHVPK 64

Query: 63  ----DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------- 105
               +  P      +   +   + +      +V   +     + V   +           
Sbjct: 65  LVPLNVEPEDIPLDIVYEDNDVIVVNKPQGMVVHPSAGHPNHTLVNALMNHTKELAASPE 124

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-------- 156
             R   V R+D +T GLL++  +      LE                  +          
Sbjct: 125 GFRPGIVHRIDKDTSGLLMIAKNTQARESLESQLAHKTNKRVYLAIVHGNFKEASGTIDA 184

Query: 157 ----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                    KK  V++          +  Q  + A V+  L  G+  +I+   ++    
Sbjct: 185 PIARNPKERKKMAVVESGKAAVTHFKVLEQYPNYALVSCQLETGRTHQIRVHMKYIGHP 243


>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 = 61.7 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 39/260 (15%), Positives = 84/260 (32%), Gaps = 41/260 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIA----SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            + + F  +R+    A  G      SR  +   I + +V V+G+++ + ++ V S   + 
Sbjct: 8   TITDEFHNKRLD---AALGGLIDTHSRSTLREYIDEGKVAVDGVVITKPSIKVSSGQIVS 64

Query: 62  V--------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           V        D  P      +   +   L +      +V   +     + +   L      
Sbjct: 65  VTIPDPEDLDAKPQDLPLDIIYQDDDILIINKPINFVVHPGAGIKDGTVMNAVLYHFPQT 124

Query: 108 VI-----SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR------------VRFH 150
                   V RLD +T GL+++       +VL     +   V                  
Sbjct: 125 SSLPRAGIVHRLDKDTSGLMVIALSQLAQQVLTKAIAKHDVVREYEAIAEGQITAGGTID 184

Query: 151 GQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
             + +D     K  ++ +G          +  +  ++  + + L  G+  +I+      +
Sbjct: 185 APIGRDPYVRTKMAVMPEGIGREAVTHYRVMERFRAHTRLRLRLETGRTHQIRVHMASIH 244

Query: 210 WKVNRLIRISYGPFQLGTLL 229
             +  L    YG  +L  L 
Sbjct: 245 HPL--LGDNQYGGKRLKMLP 262


>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 = 61.7 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 31/234 (13%), Positives = 59/234 (25%), Gaps = 35/234 (14%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP----- 66
             R+ K +A     SR      I   ++ VNG + ++A   V + D I  +   P     
Sbjct: 9   GVRLDKAVADLTPLSRSHANEQIKNGQILVNGQV-KKAKYAVKAGDVITYELPEPEALEY 67

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                   +   +     +      +V   +     + V   +  I       G L    
Sbjct: 68  VAENLPLDIVYQDEDVAVVNKAQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGI 127

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL------------------ 160
              +     G L       +   L               +                    
Sbjct: 128 VHRIDKDTSGLLMIAKNDDAHIKLAEELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSE 187

Query: 161 --LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
              KK  V         +  +  + G+   V + L  G+  +I+    +    V
Sbjct: 188 KDRKKQAVTAKGKPAVTRFHVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 84/248 (33%), Gaps = 42/248 (16%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V +   P R+   +A+    A+R +V+  I++ RV+VNG  ++ A   + S D IE+   
Sbjct: 27  VAQTQKPMRIDVYLAQQVENATRNKVQEAISEHRVRVNGKTVK-ANYKIKSLDSIEITFL 85

Query: 63  ---------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------ 106
                    + +P+    E   L + +K  G+V   +  +   T+ + +           
Sbjct: 86  RPPAPELAPEDIPVDIIYEDNDLMVINKAPGMVVHPAFGNWTGTLANAILHHLGTDAEKL 145

Query: 107 -----RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
                R   V RLD NT GL+++         L     +     + +       +    +
Sbjct: 146 DTTELRPGIVHRLDKNTSGLIIVAKHATALHRLAKQFAERQVEKKYQAIVWGVPEPPEGI 205

Query: 162 KK----------------GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
            K                    +       +  +       + V + L  G+  +I+   
Sbjct: 206 VKTNIGRSIRDRKVMTSYDFEGKEGKTAVTEYRVVENLRYFSLVEMILHTGRTHQIRVHL 265

Query: 206 EFFNWKVN 213
           +  N  + 
Sbjct: 266 KHINAPIL 273


>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 = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 32/243 (13%), Positives = 68/243 (27%), Gaps = 37/243 (15%)

Query: 7   VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----- 60
           V +     R+ K ++      SR  ++ +I ++ +KVN  L++     + + D I     
Sbjct: 8   VSKENEGIRIDKYLSEMLNGKSRSFIQGLIEKESIKVNNKLIKS-NYKLKACDEIVITMP 66

Query: 61  -----EVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                +V+   +       ++  + +  +   +V         + V   L          
Sbjct: 67  EAEILKVESEDIDLDILYEDKDVIVVNKEQGMVVHPAPGNYNGTLVNALLFHCTDLSSIN 126

Query: 112 G---------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
           G                     + D +   L     D  + R          +       
Sbjct: 127 GVIRPGIVHRIDKDTSGVLVIAKNDESHNKLAAQLKDHSMNREYYALVEGRFKNDSGVID 186

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + +DK N LK  I   G         L+        +   L  G+  +I+        
Sbjct: 187 KPLGRDKKNRLKIAITEDGRRAITHYEVLERYDTGCTLIKCKLETGRTHQIRVHMASLGH 246

Query: 211 KVN 213
            + 
Sbjct: 247 PLV 249


>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 = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 22/237 (9%), Positives = 61/237 (25%), Gaps = 31/237 (13%)

Query: 8   QENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           Q++   QR+ + +A      SR  ++  I Q RV ++G +       +++   + V+   
Sbjct: 12  QDHQFGQRLDQALAELFPDYSRTRIKEWILQDRVTLDGQVANTPREKILAGQQVHVNVEL 71

Query: 67  --------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------- 105
                         +   +   L +      +V   +     + +   L           
Sbjct: 72  EDDTRWDAQDIELNIVYEDEHILVIDKPAGLVVHPGAGTPDGTILNALLHRYPGIAEVPR 131

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD----- 156
                R+       +     +        A      + ++  +           D     
Sbjct: 132 AGIVHRLDKDTTGLMVVAKTVPAQTHLVEALQARQITREYEAIAIGHMTAGGTVDAPIGR 191

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                    V+           +  +   +  + + L  G+  +I+         + 
Sbjct: 192 HPTQRTHMAVVPNGRPSVTHYRVHEKFRGHTRLRLRLETGRTHQIRVHMAHIKHPLV 248


>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 = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 32/243 (13%), Positives = 68/243 (27%), Gaps = 37/243 (15%)

Query: 7   VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----- 60
           V +     R+ K ++      SR  ++ +I ++ +KVN  L++     + + D I     
Sbjct: 8   VSKENEGIRIDKYLSEMLNGKSRSFIQGLIEKESIKVNDKLIKS-NYKLKACDEIVITMP 66

Query: 61  -----EVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                +V+   +       ++  + +  +   +V         + V   L          
Sbjct: 67  EVETLKVESEDIDLDILYEDKDVIVVNKEQGMVVHPAPGNYNGTLVNALLFHCTDLSSIN 126

Query: 112 G---------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
           G                     + D +   L     D  + R          +       
Sbjct: 127 GVIRPGIVHRIDKDTSGVLVIAKNDESHNKLAAQLKDHSMNREYYALVEGRFKNDSGVID 186

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + +DK N LK  I   G         L+        +   L  G+  +I+        
Sbjct: 187 KPLGRDKKNRLKIAITEDGRRAITHYEVLERYDTGCTLIKCKLETGRTHQIRVHMASLGH 246

Query: 211 KVN 213
            + 
Sbjct: 247 PLV 249


>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 = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 32/251 (12%), Positives = 68/251 (27%), Gaps = 39/251 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M   N+  E     R+ K +++     SR ++++ I   +V VN +++    V V   D 
Sbjct: 1   MLTYNVPNELNN-IRLDKALSQLLEKISRNQIQKAIKNSQVLVNDVIISDPDVLVKENDV 59

Query: 60  IEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I                    +   +   + +       V   +     + V   L    
Sbjct: 60  ILFAFKEPEELKIAAVNIALDIIYEDDDLIVINKAAGMTVHPGAGHHDDTLVNALLYHTK 119

Query: 106 S-----RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
           +          G +    +    L       +   L + Q  +   +R +  +    +N 
Sbjct: 120 NLSDIGSAARPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRKYKALVWGVINP 179

Query: 161 LKKGIVIQGICYGDMQVTL------------------DTQKGSNAWVTVGLREGKNREIK 202
           L   I          +  +                      G+ + V   L  G+  +I+
Sbjct: 180 LAGVIKNNIGRSRVERQKMSILKYGGKEAVTHYKTLELFYGGTISMVECRLNTGRTHQIR 239

Query: 203 KVFEFFNWKVN 213
                    V 
Sbjct: 240 VQLSHVKHSVV 250


>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 = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 34/239 (14%), Positives = 70/239 (29%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            + E+   QR+ + +A      SR  ++  I   RV+VNG ++ +A   V+  + I +D 
Sbjct: 10  TIAESQLGQRLDQALAELFPDYSRSRIKEWILDDRVQVNGKVINKAKEKVLGGEQISIDA 69

Query: 64  -------GVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                    P      +   +   L +      +V   +     + +   L         
Sbjct: 70  LIEEDTRWEPQDIPLDVVYEDEDILVINKPRGLVVHPGAGNPDGTILNALLYRYPEIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-----------FHGQVD 154
            R   V RLD +T GL+++         L     +                      +  
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTHLVDALQRREITREYEAVAVGRMTAGGMVEEPI 189

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMAHINHPLI 248


>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 = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 25/240 (10%), Positives = 53/240 (22%), Gaps = 41/240 (17%)

Query: 13  PQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------ 63
            QR+ K +   G+    SR  V+R I     +++G+ +  A++ + +   + +D      
Sbjct: 19  GQRLDKAL--CGLLPELSRAAVQRAITAGACRIDGMPVATASLKLKAGQAVCLDLPDTAN 76

Query: 64  -----GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG---- 112
                   +     +   L         V         + V   L          G    
Sbjct: 77  ELRAEDEAVDILWQDEHLLLCNKPAGLTVHPCPSCPENTLVQRLLHHFPRLREQEGLRPG 136

Query: 113 -----------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
                                                 L L      +    R       
Sbjct: 137 VVHRLDKDTSGLLLVALDEPTRLRMSEAFARREVHKEYLALVGGVPPQTGTCREPLGRHP 196

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIKKVFEFFNWKVN 213
                +      +G         +         + V V +  G+  +I+         + 
Sbjct: 197 TAKVKMAVVPENRGGKTAHSDWRVLWSSPRKDFSLVAVRIHTGRTHQIRVHMAHVGHPLL 256


>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 = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 24/249 (9%), Positives = 63/249 (25%), Gaps = 45/249 (18%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---GV 65
                R+   ++      SR  ++R+I Q  + +N  +     + V   D ++++     
Sbjct: 8   ENKGNRLDLWLSNQLTDISRSHIQRLIEQGNIILNNEVCTNKKIKVKIGDRLQINLPEPK 67

Query: 66  PLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-- 112
           PL              +   + +      +V      +  + V   L    +     G  
Sbjct: 68  PLELKPEPLPLDILYEDEQLIIINKPANLVVHPAPGHETGTLVHGLLYHCSNLAGIGGVQ 127

Query: 113 -------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
                              + D   + L     +    R         L     + +   
Sbjct: 128 RPGIVHRLDKDTTGAMVVAKTDFAHQNLQAQIKNKTAKREYLGIIYGVLTNQEDKENSHQ 187

Query: 154 ---------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                           +    + +          +  + G+ + V   L  G+  +I+  
Sbjct: 188 GIINLPIGRHPIDRKKMAVVPLEKRGREAITHWEILERLGNYSLVKFTLETGRTHQIRVH 247

Query: 205 FEFFNWKVN 213
             ++   + 
Sbjct: 248 SSYYGNPIV 256


>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 = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 32/243 (13%), Positives = 68/243 (27%), Gaps = 37/243 (15%)

Query: 7   VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----- 60
           V +     R+ K ++      SR  ++ +I ++ +KVN  L++     + + D I     
Sbjct: 8   VSKENEGIRIDKYLSEMLNGKSRSFIQGLIEKESIKVNDKLIKN-NYKLKACDEIVITMP 66

Query: 61  -----EVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                +V+   +       ++  + +  +   +V         + V   L          
Sbjct: 67  EAETLKVESEDIDLDILYEDKDVIVVNKEQGMVVHPAPGNYNGTLVNALLFHCTDLSSIN 126

Query: 112 G---------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
           G                     + D +   L     D  + R          +       
Sbjct: 127 GVIRPGIVHRIDKDTSGVLVIAKNDESHNKLAAQLKDHSMNREYYALVEGRFKNDSGIID 186

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + +DK N LK  I   G         L+        +   L  G+  +I+        
Sbjct: 187 KPLGRDKKNRLKIAITEDGRRAITHYEVLERYDTGCTLIKCKLETGRTHQIRVHMASLGH 246

Query: 211 KVN 213
            + 
Sbjct: 247 PLV 249


>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 = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 32/248 (12%), Positives = 67/248 (27%), Gaps = 36/248 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M++  I+    + +R+ K +A      SR  ++ +I    V VNG   +   + +   D 
Sbjct: 1   MEEIIIIFNELSSKRIDKFLAEQLDGYSRSFIQNIIDGNNVLVNGKPCKS-NLKLKMQDE 59

Query: 60  IEV---DGVP-----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I V   +              +   +   + +      +V   S     + V   L    
Sbjct: 60  ITVIIPEPQEMNVVPENISLNILYEDEDLIVINKPQGMVVHPASGVYNNTLVNALLYHCK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                 G+L       +     G +       S  +L         + +           
Sbjct: 120 DLSGINGKLRPGIVHRIDKDTSGVIVVAKNDKSHNFLAAQLKEHSMKREYIALVEGIIKE 179

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                            K  V++G         +  +   N  V   L  G+  +I+   
Sbjct: 180 EEGTINQPLARDPKERIKIAVVKGGREAITHYKVIERFKENTLVRCILETGRTHQIRVHM 239

Query: 206 EFFNWKVN 213
            +    + 
Sbjct: 240 NYKKHPLV 247


>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 = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 64/239 (26%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I   RV+VNG    +    V+  + + +  
Sbjct: 10  TVAESQLGQRLDQAMAELFPDYSRSRIKEWILDDRVQVNGKTANKPKEKVLGGEIVAIAA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  QIEEDPRWEPQDIALDVVYEDCDILVINKPRDRVVHPGAGNPDGTVLNALLHYYPKIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQEREITREYEAVAIGTMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 SRHSTKRTHMAVYPMGKPAVTHYRILEHFRAHTRLRLRLETGRTHQIRVHMSHINHPLV 248


>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 = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 29/232 (12%), Positives = 64/232 (27%), Gaps = 34/232 (14%)

Query: 14  QRVSKVIARAG---IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
            R+ + +  A      SR +V+R I      V+G +    +  V +   IE+        
Sbjct: 1   MRLDRFLGEALREQDVSREKVKRAIRDGGCLVDGAVCTDVSAKVGAGQSIELRMEAEPTS 60

Query: 63  ----DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
               +G      +   L + +KP G+    +      T+   L + F  + +        
Sbjct: 61  VQPEEGELEILYQDAWLAVLNKPAGMTVHPAPSCPDGTLVHRLVARFPSLRAQEGFRPGI 120

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------------------DKLN 159
              L     G +   L   +   L         + +                        
Sbjct: 121 VHRLDKDTSGLICVALTEEARMRLSEAFAAREIRKEYLALVQGVPAPAGTVDAPLGRHPT 180

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +  K  V +       +  +  +    + + V +  G+  +I+         
Sbjct: 181 VKVKVAVAKNGKEARSEWRVLHKGQGYSLLEVRIFTGRTHQIRVHMAHIGHP 232


>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 = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 32/239 (13%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG L ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKLCDKPKEKVLGGEQVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTXLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 34/239 (14%), Positives = 64/239 (26%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG L ++    V+  + + +D 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILNQRVLVNGQLCDKPKEKVLGGERVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  EIDEEIRFEAQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L                               
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVNEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMSVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 32/250 (12%), Positives = 70/250 (28%), Gaps = 38/250 (15%)

Query: 1   MKDKNIVQENFTP-QRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M++ +++       QR+ K I+      SR  V++++ +  V VNG   + A   +   D
Sbjct: 1   MREIDVIVTEEEAFQRIDKYISEKEDDLSRSRVQQLLQEGIVCVNGNACK-ANYKIKPKD 59

Query: 59  HI------EVDGVP--------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           HI      E++           +R  +   + +      +V         + V   L   
Sbjct: 60  HITAVFCDEIEMEAKPEQMDLDIRYEDHDVIVINKPKGMVVHPAVGNQTGTLVNGLLYHC 119

Query: 105 FSRVISVG---------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
                  G                     + D     L     +  + R+        + 
Sbjct: 120 KDLSGINGVLRPGIVHRIDKDTTGLLIVAKNDKAHTALSKQLQNKTVNRLYYALVHGVIE 179

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                    + +D  +  K  +             +  +      V   L  G+  +I+ 
Sbjct: 180 HDFGTIDAPIGRDVKDRQKMAVTATNAKDARTHFKVIERFAHYTLVECRLETGRTHQIRV 239

Query: 204 VFEFFNWKVN 213
             ++    V 
Sbjct: 240 HMQYIKHPVV 249


>gi|315103776|gb|EFT75752.1| ribosomal RNA large subunit methyltransferase J
          [Propionibacterium acnes HL050PA2]
          Length = 263

 Score = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 1/68 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
             P R+ + +  AG+A SR    R++ + RV VN  ++ + A+ V +TD +  D     
Sbjct: 15 QSVPVRLDQALVEAGLARSRTLATRLVREGRVTVNRAVVTKPAMKVSTTDVLVADEEVWV 74

Query: 69 KAERTRLW 76
               +L 
Sbjct: 75 SRAAHKLL 82


>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 = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 31/248 (12%), Positives = 73/248 (29%), Gaps = 37/248 (14%)

Query: 1   MKDKNIVQE-----NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           M+ K+ + +          R++  +      S R + +   + R+KVNG      +  + 
Sbjct: 1   MESKDNIIKLKVEIETEEIRLNHYLKEVAQCSSRFIRKAAREGRIKVNGNNAR-LSYMLT 59

Query: 56  STDHIEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
           + D +E+                  +   +   + +      +V         +     L
Sbjct: 60  NNDIVELQINRKEEQDIIPEKMDLDIIYEDNDIIVVNKPKGIVVHPTKRHLNGTLSNGVL 119

Query: 102 PSIFSRVISV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRV-YRVRFHGQVDQ 155
                +  +       RLD++T GL+L+  +      L     +   V   +        
Sbjct: 120 YYFNDKNENSIVRLVNRLDMDTSGLVLIAKNAYSHMALSRDMQKDDFVKKYLAIVHGNFN 179

Query: 156 DKLNLLKKGIVIQGICYGD-----------MQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
           +   ++ K I   G                    +  Q  + + V + L  G+  +I+  
Sbjct: 180 EDSGVIDKPIYRVGEGTLKRIIDERGQRSITLFKVIEQYKNASLVELTLETGRTHQIRVH 239

Query: 205 FEFFNWKV 212
                  +
Sbjct: 240 LSSIGHPI 247


>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 = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 36/232 (15%), Positives = 65/232 (28%), Gaps = 35/232 (15%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKA 70
           R+ KVI A     +R +V++ +    V VNG    +A   V S D I +   +  PL   
Sbjct: 13  RIDKVITAHETTHTRSQVQKWLQDGLVTVNGQP-TKANYKVASGDVIAISIPEAKPLEAI 71

Query: 71  ERTRLWLY-----------HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-------VG 112
                                   +V         + V   L       I+       V 
Sbjct: 72  PEPIPLDIVYEDDQVIVVDKPQGMVVHPAPGHPDGTLVNGLLYHTDLPGINGVIRPGIVH 131

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD------------KLNL 160
           R+D +T GLL++         L         +                            
Sbjct: 132 RIDKDTSGLLMVAKTEKAQLSLSAQLKAKTSIREYLALVHGTFKEDEGTIDAPLGRDPRD 191

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            K+  V+    +      +  +     ++   L  G+  +I+    + +  V
Sbjct: 192 RKRQAVVADGRHAVTHFQVLERFEHYTFIKCILETGRTHQIRVHMAYIHHPV 243


>gi|227499078|ref|ZP_03929215.1| hemolysin A [Acidaminococcus sp. D21]
 gi|226904527|gb|EEH90445.1| hemolysin A [Acidaminococcus sp. D21]
          Length = 266

 Score = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 13/69 (18%), Positives = 25/69 (36%), Gaps = 1/69 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +R+   +   G+  SR + + +I    V V+   +++    V     I + G  L   
Sbjct: 2  KKERLDLFLVEQGLFESRSKAQAVIMAGEVLVDDQKIDKPGTMVKPDAKITLLGKKLPFV 61

Query: 71 ERTRLWLYH 79
           R    L  
Sbjct: 62 SRGGYKLNK 70


>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 = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 39/249 (15%), Positives = 78/249 (31%), Gaps = 41/249 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           MK           +R+ + +A   + SR   ++++AQ  V+VNG ++E+A+ ++   D +
Sbjct: 1   MKSSRHELTVDASRRLDQFLAATELFSRSMAQKLVAQGHVQVNGTVIEKASYSLQPGDLV 60

Query: 61  EVD-----------GVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
            V            G  +      E   L + +KP G+V   +  +  +T+ + L     
Sbjct: 61  CVQQPAPVDHATVVGQEIPLNIWYEDESLLVVNKPAGMVVHPAAGNYDATLVNALVHYLG 120

Query: 107 RVIS----------VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
             +           V RLD +T GL+L+       + L                     D
Sbjct: 121 DGLPAIGGVLRPGIVHRLDKDTSGLMLVAKTEVAHQRLVSMFAAKEIDRCYLALCHGSLD 180

Query: 157 K-------------LNLLKKGIVIQGICYGDMQVTLDTQ----KGSNAWVTVGLREGKNR 199
                                +             L  +    +   + +   L  G+  
Sbjct: 181 DSGVIEGNIGRDPKDRKRMAIVEADKGKTARTHYRLLEKFFCHQQWVSLIECRLDTGRTH 240

Query: 200 EIKKVFEFF 208
           +I+      
Sbjct: 241 QIRVHLRSV 249


>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 = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 28/250 (11%), Positives = 69/250 (27%), Gaps = 34/250 (13%)

Query: 5   NIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           N V+++   QR+ + IA      SR  ++  +   +VKVNG ++ +    VM  + I + 
Sbjct: 9   NTVKDSQLGQRLDQAIAELFADFSRSRLKEWLLDGKVKVNGEVISKPRTKVMGGEEIILQ 68

Query: 63  ----DGVPLRKAERT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
               D       +            L +      +V   +     + +   L    +   
Sbjct: 69  AELEDEERWEAQDIPLDIVYEDDDLLVINKPRGFVVHPGAGTPDGTVLNALLHHYPNIAE 128

Query: 110 SVGRLDIN------------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                 ++             + +   T      +       ++  +   R       ++
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKKRNFVREYEAIAIGRMTAGGRVEQ 188

Query: 158 LNLLKKGIVIQGICY---GDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                                     +      +  + + L  G+  +I+    +    +
Sbjct: 189 PIGRHSTKRTLMAVTPTGKPAITHYRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPL 248

Query: 213 NRLIRISYGP 222
             L   +YG 
Sbjct: 249 --LGDTAYGG 256


>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 = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 34/246 (13%), Positives = 67/246 (27%), Gaps = 39/246 (15%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH----- 59
            V+      RV   +A      SR  +++++ Q  V VNG  ++     V   D      
Sbjct: 7   TVETEDEDTRVDAYLASQIDRMSRSYIQKILKQGGVLVNGKAVK-PNYKVCEDDRIEIEI 65

Query: 60  -------IEVDGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                  IE + +PL     +   L +      +V   +     + V   L         
Sbjct: 66  PENEELDIEAEDIPLDILYEDDDVLIVNKPKDMVVHPAAGHYEHTLVNALLFHCRDRLSG 125

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLAR--------------VLELPSTQWLRVYRV 147
                R   V R+D +T G L++  +    +                 + +  +      
Sbjct: 126 INGVMRPGIVHRIDKDTTGALVICKNDAAHQSLAAQLAVHSITRRYRAIVAGNFKDETFT 185

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                            +      +    V +       A+V   L  G+  +I+     
Sbjct: 186 VEGNIGRSANDRKKMAVVSPDKGKHAVTHVKVLQNLKGYAYVECELETGRTHQIRVHMAH 245

Query: 208 FNWKVN 213
               + 
Sbjct: 246 IGHPLL 251


>gi|227115223|ref|ZP_03828879.1| 23S rRNA pseudouridine synthase D [Pectobacterium carotovorum
           subsp. brasiliensis PBR1692]
          Length = 325

 Score = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 68/239 (28%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I + RV++NG ++ +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILENRVQINGNVINKPKEKVLGGESVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
           +               +   +   L +      +V   +     + +   L         
Sbjct: 70  LIEEEARWEAQDIKLDIVYEDEDILVINKPRDLVVHPGAGNPDGTVLNALLHHYPEIVDV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L                               
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGSMTAGGMVEQPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 ARHATKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMAHINHPLV 248


>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 = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 35/282 (12%), Positives = 72/282 (25%), Gaps = 50/282 (17%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V E     R+ K ++      SR  ++ +I ++ VKVN   L+     +   D IE+   
Sbjct: 8   VDEQDEGLRIDKYLSNIFKDKSRSFIQGLIEKENVKVNSKTLKS-NYKLKKADEIEIMIP 66

Query: 63  ---------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                    + +P+     +   + +      +V         + V   L          
Sbjct: 67  EPEILSVEAENIPIDIVYEDEDVIVVNKAQGMVVHPAPGNYNGTLVNALLYHCKDLSSIN 126

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------------- 155
           G +       +     G L       +   L         + +                 
Sbjct: 127 GVIRPGIVHRIDKDTSGILVIAKNDDAHNKLSEQLKDHSMKREYYALIEGRLKNNDGTID 186

Query: 156 ----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                      K  +I+          +  +      V   L  G+  +I+       + 
Sbjct: 187 KPLGRCKKDRLKIGIIEDGKRAVTHYEVVERYNGYTLVKCVLETGRTHQIRVHMASIGFP 246

Query: 212 VN-----RLIRISY---GPF----QLGTLLA--GSTREVSKK 239
           +         R  +   G       LG +    G   E + +
Sbjct: 247 LVGDPLYGFKRQKFKLEGQVLHARTLGFIHPRTGEYMEFTSE 288


>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 = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 39/251 (15%), Positives = 78/251 (31%), Gaps = 42/251 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK++ IV E    +R+ + +A R    SR  ++++I    V VNG   + A   +   D 
Sbjct: 1   MKERLIVDEGAAGERLDRFLAGRELEVSRSHIQKLIESGCVLVNGRTAK-ANAKLREGDA 59

Query: 60  IE-----------------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
           +E                 +D   +   +   + +      +V   +     + V   L 
Sbjct: 60  VETELPEARELEILPEDIPLD---ILYEDSDVIVINKARGMVVHPAAGAADGTLVNALLH 116

Query: 103 SI--------FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD 154
                       R   V RLD +T G+++   +      L     +       R      
Sbjct: 117 HCEDLSGINGVIRPGIVHRLDKDTSGVMVAAKNDRAHVDLAEQIREKTAQRIYRAIVCGT 176

Query: 155 Q------------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                              KK  V+ G         +  +  ++  V   L+ G+  +I+
Sbjct: 177 IAEDRGEIRAPIGRHPTERKKMAVVPGGKEATTLFRVVERFPAHTLVECRLKTGRTHQIR 236

Query: 203 KVFEFFNWKVN 213
               + +  + 
Sbjct: 237 VHMAYIDHPLL 247


>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 = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 32/241 (13%), Positives = 68/241 (28%), Gaps = 32/241 (13%)

Query: 5   NIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           N V+++   QR+ + IA      SR  ++  +   +V+VNG ++ +    VM  + I + 
Sbjct: 9   NTVKDSQLGQRLDQAIAELFADFSRSRLKEWLLAGKVQVNGEVVTKPRTKVMGGEEIILQ 68

Query: 63  ----DGVPLRKAERT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
               D       +            L +      +V   +     + +   L    +   
Sbjct: 69  AELEDEERWEAQDIPLDIVYEDDDILVINKPRGFVVHPGAGTPDGTVLNALLHHYPNIAE 128

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH------------GQ 152
                   RLD +T GL+++         L     +     R                 Q
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKKRNFVREYEAIAIGRMTAGGRIEQ 188

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                        V            +      +  + + L  G+  +I+    +    +
Sbjct: 189 PIGRHSTKRTLMAVSPMGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPL 248

Query: 213 N 213
            
Sbjct: 249 L 249


>gi|147921289|ref|YP_684897.1| putative ribosomal RNA methyltransferase [uncultured methanogenic
          archaeon RC-I]
 gi|110620293|emb|CAJ35571.1| putative ribosomal RNA methyltransferase [uncultured methanogenic
          archaeon RC-I]
          Length = 216

 Score = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ + +   G IASR   +R I +  VK+NG ++ + +  V     IE+
Sbjct: 1  MRLDEYLVSEGLIASRSRAKRYIHRGLVKLNGEVVTKPSKQVKPGAIIEI 50


>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 = 61.3 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 29/242 (11%), Positives = 75/242 (30%), Gaps = 38/242 (15%)

Query: 9   ENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           EN    R+ + +A      SR  ++++I +Q +KVN   ++ A   ++  D +EV     
Sbjct: 8   ENEEGDRIDRYLAEEMPERSRSYLQKLIKEQYIKVNNKPVK-ANYRLVLGDRVEVCIPEA 66

Query: 63  ---DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG- 112
              D  P      +   +   + +      +V         + V   +    + +  +  
Sbjct: 67  KEPDIEPENIPLDILYEDEDVIVVNKPKQMVVHPAPGHYSGTLVNALMYHCGNELSGING 126

Query: 113 ---------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151
                                + D+  + L +   +  + R+ E      ++      + 
Sbjct: 127 TSRPGIVHRIDMDTTGSLIICKNDMAHQSLAVQLEEHSINRIYEAIVHGNIKEEEGTVNA 186

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + +   +  K  I  +          +  + G   ++   L  G+  +I+         
Sbjct: 187 PIGRHPTDRKKMSIHAKNARNAITHYKVLKRFGDYTYIQCKLETGRTHQIRVHMASIGHP 246

Query: 212 VN 213
           + 
Sbjct: 247 LL 248


>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 = 61.0 bits (146), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 30/247 (12%), Positives = 67/247 (27%), Gaps = 42/247 (17%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           IV +   P R+ K +  R   +SR  +++      + VN   ++     V   D I +  
Sbjct: 37  IVDKGQEPVRIDKFLFERMQHSSRNRIQKAADAGYIHVNNAPVKS-NYKVRPEDVITLML 95

Query: 63  -----DGVP--------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                D           +   +   + +      +V   +     + +      +     
Sbjct: 96  DRPKHDNTIEAEDIPLDVVYEDDILMVVNKPAGLVVHPGAGNFHGTLINAIAWHLKDMPS 155

Query: 110 SV---------GRLDINTEGLLLLTNDGG-------------LARVLELPSTQWLRVYRV 147
                       R+D +T GLL++                    R         +     
Sbjct: 156 FDPNDPEVGLVHRIDKDTSGLLVIAKTPDAKTALGKQFFNKTTHRSYNAIVWGNMTEDEG 215

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICY-GDM--QVTLDTQKGSNAWVTVGLREGKNREIKKV 204
           R  G + +D  + L+  +                +  + G    +   L  G+  +I+  
Sbjct: 216 RIEGNIARDPKDRLRMTVFPPDSEVGKPAVTHYRVIERFGYTTLIECILETGRTHQIRAH 275

Query: 205 FEFFNWK 211
            +     
Sbjct: 276 MKHIGHP 282


>gi|119713310|gb|ABL97374.1| putative ribosomal large subunit pseudouridine synthase D
           [uncultured marine bacterium EB80_02D08]
          Length = 310

 Score = 61.0 bits (146), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 35/241 (14%), Positives = 70/241 (29%), Gaps = 33/241 (13%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           KN+   N   +R+ K  A      SR ++++ I   +V VNG +  +    V   D IE+
Sbjct: 4   KNVPN-NLALKRLDKAAAEMFTDYSRTQIKKWIEDGKVLVNGEI-SQPREKVHENDEIEL 61

Query: 63  DGV--------------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--- 105
           +                 +       + +      ++   S     +     +       
Sbjct: 62  NPAEEQKVSWEPEDIQFEVHFENEDFIIINKPAGLIMHPGSGCYDGTLANGLIFKFPELV 121

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR-----------VRFHGQ 152
              R   V RLD +T G+LL+               +   + +                 
Sbjct: 122 NIPRSGIVHRLDKDTSGILLVARTESFRNFFINEMQERRVIKKYSSIVIGSTLGSFSIED 181

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                 N   K  + +        V L    G+ + + V +  G+  +I+         +
Sbjct: 182 PIGRDKNNRTKMAIREDGKDALTFVKLKENIGNYSVLDVRIETGRTHQIRVHLASKKLPI 241

Query: 213 N 213
            
Sbjct: 242 I 242


>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 = 61.0 bits (146), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 27/239 (11%), Positives = 62/239 (25%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG L ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGHLCDKPKEKVLGGEQVSINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  EIDEEVRFEPQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--- 156
                  R+       +     +        +  L   + ++  V           +   
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVEEPI 189

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 61.0 bits (146), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 30/239 (12%), Positives = 65/239 (27%), Gaps = 38/239 (15%)

Query: 13  PQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP----- 66
             R+ K ++      SR ++++ I   +V VN +++    V V   D I           
Sbjct: 12  GIRLDKALSSLLENVSRNQIQKAIKDSQVLVNDVIISDPDVLVKENDIILFSFKEPEELK 71

Query: 67  ---------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-----RVISVG 112
                    +   +   + +       V   +     + V   L    +          G
Sbjct: 72  IATANVALDIIYEDDDLIVINKAAGMTVHPGAGHHDDTLVNALLHHTKNLSDIGSSERPG 131

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
            +    +    L       +   L + Q  +   +R +  +    +N L+  I       
Sbjct: 132 IVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRKYKVLVWGVINPLEGVIKNNIGRS 191

Query: 173 GDMQVTL------------------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +  +                     KGS + V   L  G+  +I+         + 
Sbjct: 192 RSDRQKMTILKYGGKEAVTHYKTLELFYKGSISMVECKLSTGRTHQIRVQLSHLKHSIV 250


>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 = 61.0 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 30/239 (12%), Positives = 68/239 (28%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I   RV++NG ++ +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILDNRVQINGNVINKPKEKVLGGESVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
           +               +   ++  L +      +V   +     + +   L         
Sbjct: 70  LIEEEARWEAQDIKLDIVYEDQDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPEIVDV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L                               
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGSMTAGGMVEQPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      +  + 
Sbjct: 190 ARHATKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHIDHPLV 248


>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 = 61.0 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 36/236 (15%), Positives = 74/236 (31%), Gaps = 40/236 (16%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ K +      ASR +++  I    V VN  +++  +  V   D I V           
Sbjct: 32  RIDKFLMNRVENASRNKIQNAIDAGSVLVNDSVIKS-SYKVKPFDIISVVLPDPPRDTEV 90

Query: 63  --DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-------- 111
             + +PL    E   + + +K  G+V      +   T+ + L   F+++ ++        
Sbjct: 91  YPEDIPLDIIFEDDEVMVVNKVAGMVVHPGFNNYTGTLVNALTHHFNQLPTMPGNAGRPG 150

Query: 112 --GRLDINTEGLLLLTNDGGLARV----LELPSTQWLRVYRVRFHGQVDQ---------- 155
              R+D +T GLL++                 S     V  V      D           
Sbjct: 151 LVHRIDKDTSGLLVIAKSEWAMTYLAKQFFDHSIMRKYVAMVWGDIAEDGTVTGYIGRNL 210

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               ++      +   +      +  + G    +   L  G+  +I+   +     
Sbjct: 211 KDRRVMTMYDDSEKGKWSVTHYRVLERLGYVTLIECQLETGRTHQIRAHMQSIGHP 266


>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 = 61.0 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/235 (14%), Positives = 72/235 (30%), Gaps = 37/235 (15%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           R+   +A   G  SR  ++++I   +VKVN  + E+A   V   D+I ++          
Sbjct: 29  RLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKV-EKAKYLVKEEDNIVIEIPEPKVLEVL 87

Query: 64  --GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-------- 111
              +P+     +   L +      +V         + V   L     ++ S+        
Sbjct: 88  PQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGILYHCKDKLSSINGVIRPGI 147

Query: 112 -GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
             R+D +T GLL++  +      L     +        F       +  +     + +  
Sbjct: 148 VHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICYGVVKEDKITVDKPIGRNP 207

Query: 171 CYGDMQVTLDTQKGSNAWVTVG------------LREGKNREIKKVFEFFNWKVN 213
                   +   K +     V             L  G+  +I+      N  + 
Sbjct: 208 KDRLKMAVVKDGKNAITHFEVVERFDKFTHMRARLETGRTHQIRVHALSINHPLL 262


>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 = 61.0 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 38/304 (12%), Positives = 82/304 (26%), Gaps = 44/304 (14%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V ++   QR+ + +A      SR  ++  I   RV+VN  ++ +    ++  + IE+D 
Sbjct: 10  TVADSQLGQRLDQALAEMFPDYSRSRIKEWILDNRVQVNDKIINKPKEKMLGGEKIEIDA 69

Query: 64  -------GVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                    P      +   +   L +      +V   +     + +   L         
Sbjct: 70  LIEEDVRWEPQNIPLNIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLYRYPEIANV 129

Query: 111 V-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                  RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTHLVEALQRREITREYEAVATGRMTAGGLVNEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                      V            +     ++  + + L  G+  +I+      +  +  
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRVMEHFRAHTRLRLRLETGRTHQIRVHMAHIHHAL-- 247

Query: 215 LIRISYGPFQLGTLLAGSTREVSK--KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRP 272
                 G      L AG  R +      LRE L     +     +    +    +  +  
Sbjct: 248 -----IG----DQLYAGRPRPLKGASDELRETLRLFDRQALHATMLRLYHPITGIEMEWH 298

Query: 273 NIIS 276
             + 
Sbjct: 299 APLP 302


>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 = 61.0 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/235 (14%), Positives = 72/235 (30%), Gaps = 37/235 (15%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           R+   +A   G  SR  ++++I   +VKVN  + E+A   V   D+I ++          
Sbjct: 29  RLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKI-EKAKYLVKEEDNIVIEIPEPKVLEVV 87

Query: 64  --GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-------- 111
              +P+     +   L +      +V         + V   L     ++ S+        
Sbjct: 88  PQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGILYHCKDKLSSINGVIRPGI 147

Query: 112 -GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
             R+D +T GLL++  +      L     +        F       +  +     + +  
Sbjct: 148 VHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICYGVVKENKITVDKPIGRNP 207

Query: 171 CYGDMQVTLDTQKGSNAWVTVG------------LREGKNREIKKVFEFFNWKVN 213
                   +   K +     V             L  G+  +I+      N  + 
Sbjct: 208 KDRLKMAVVKDGKNAITHFEVVERFDKFTHMRAKLETGRTHQIRVHALSINHPLL 262


>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 = 61.0 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 31/270 (11%), Positives = 67/270 (24%), Gaps = 45/270 (16%)

Query: 8   QENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
            ++   QR+ K ++      SR  ++ +I+   V +N          V   D I+V+  P
Sbjct: 9   DKDGENQRLDKWLSERVHQLSRSRLQALISSGHVWINNSPCTSKKATVQIGDRIQVEIPP 68

Query: 67  --------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------- 105
                         +   +   L +      +V      +  + V   L           
Sbjct: 69  AIPLELKATNIPLDILYEDEELLIINKPAGLVVHPAPGHENDTLVNALLAHCETLAGIGG 128

Query: 106 --------------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151
                         +  I++ + D   + L          R          +        
Sbjct: 129 VQRPGIVHRLDKDTTGAIAIAKTDHAHQHLQAQIQAKTARRQYLGIIYGVPKTTSGVIDQ 188

Query: 152 Q--VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                      +      QG         +  + G+   +   L  G+  +I+       
Sbjct: 189 PIGRHPSDRQKMAIVPQHQGGRSAITHWKVKERLGNYTLIEFELETGRTHQIRVHSASMG 248

Query: 210 WKVNRLIRISYG-----PFQLGTLLAGSTR 234
             +    R+ YG        L      + +
Sbjct: 249 HPIVG-DRV-YGKGRSVGVNLPGQALHAWK 276


>gi|268611664|ref|ZP_06145391.1| RluA family pseudouridine synthase [Ruminococcus flavefaciens FD-1]
          Length = 304

 Score = 61.0 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 36/244 (14%), Positives = 76/244 (31%), Gaps = 38/244 (15%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           V ++    R+ K I+      +R  V+ ++ + ++ V+G  + +    +   D +EV+  
Sbjct: 9   VSDSDRGARIDKFISDNVEELTRSAVQGLMEKGKILVSGKSVSK-NYKLRDGDTVEVEIP 67

Query: 64  -GVP-----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
              P           +   +   L +      +V         + V   L          
Sbjct: 68  EPEPMDALPEDIPLDIVYEDSDLLVVNKPKGMVVHPAHGNHSGTLVNALLHHCGDSLSGI 127

Query: 107 ----RVISVGRLDINTEGLLLLTNDGGLARVLELPST-------------QWLRVYRVRF 149
               R   V R+D NT GLL++  +      L                   + +      
Sbjct: 128 NGVIRPGIVHRIDKNTSGLLIVAKNDAAHLHLAEQIKVHSFTREYEAVASGYFKETEGTI 187

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + + K +  K  +  +         ++  Q G  A V + L  G+  +I+    +  
Sbjct: 188 DAPIGRHKTDRKKMCVTTENSRNAVTHYSVIRQYGGYAHVRLRLETGRTHQIRVHLAYIG 247

Query: 210 WKVN 213
             V 
Sbjct: 248 HPVL 251


>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 = 61.0 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 24/241 (9%), Positives = 68/241 (28%), Gaps = 36/241 (14%)

Query: 9   ENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILL--------------ERAAVN 53
           EN   +R+ + +A      SR  ++++I    + VN   +                 +  
Sbjct: 8   ENEEGERIDRYLAEMLSDRSRSYIQKLIKDSHILVNNKPVKANYRLSCGDMLEVTIPSAK 67

Query: 54  ---VMSTD---HIEVDGVPLRKAERTRLWLYHKPIGLVTTH---------------SDPD 92
              ++  D   HI  +   +    + +  + H   G  +                  +  
Sbjct: 68  EPDILPEDIPLHILYEDADIIIVNKPKQMVVHPAPGHYSGTLVNALMFHCGRELSGINGM 127

Query: 93  GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152
            R  +   +    +  + V + D+  + L        + R+ E       +         
Sbjct: 128 MRPGIVHRIDMDTTGSLIVCKNDMAHQALSEQLKKHSIRRIYEAVVHGGFKEEEGTVSAP 187

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           + +   +  +     +          +  + G  +++   L  G+  +I+         +
Sbjct: 188 IGRHPTDRKRMSTHAKNAREAVTHYKVLERFGEYSYIQCELETGRTHQIRVHMSSIGHPI 247

Query: 213 N 213
            
Sbjct: 248 V 248


>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 = 61.0 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/236 (14%), Positives = 74/236 (31%), Gaps = 40/236 (16%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ K +      ASR +++  I    V VN  +++  +  V   D I V           
Sbjct: 32  RIDKFLMNRVENASRNKIQNAIDAGSVLVNDSVIKS-SYKVKPFDIISVVLPDPPRDTEV 90

Query: 63  --DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-------- 111
             + +PL    E   + + +K  G+V      +   T+ + L   F+++ ++        
Sbjct: 91  YPEDIPLDIMFEDDEVMVVNKVAGMVVHPGFNNYTGTLVNALTHHFNQLPTMPGNAGRPG 150

Query: 112 --GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------------- 155
              R+D +T GLL++         L         V +       D               
Sbjct: 151 LVHRIDKDTSGLLVIAKSEWAMTYLAKQFFDHSIVRKYVAMVWGDIAEDGTITGYIGRNL 210

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               ++      +   +      +  + G    +   L  G+  +I+   +     
Sbjct: 211 KDRRVMTMYDDPEKGKWSVTHYRVLERLGYVTLIECQLETGRTHQIRAHMQSIGHP 266


>gi|49066398|gb|AAT49291.1| putative bacteriocin [Prevotella nigrescens]
 gi|242332477|tpg|DAA06525.1| TPA_exp: NigA [Prevotella nigrescens]
          Length = 363

 Score = 61.0 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 30/246 (12%), Positives = 65/246 (26%), Gaps = 42/246 (17%)

Query: 7   VQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V +     R+ K +  R   +SR  +++      + VNG  ++     V   D I +   
Sbjct: 38  VDKGQEAVRIDKFLFERMQHSSRNRIQKAADAGSIYVNGTPVKS-NYKVRPNDVITLMLD 96

Query: 63  ----DGVPLR--------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
               D   +           +   + +      +V   +     + +      +      
Sbjct: 97  RPKHDNTIVAEDMPLNVVYEDNEIMVINKPAGLVVHPGAGNFRGTLINAIAWHLRDLKNF 156

Query: 111 V---------GRLDINTEGLLLLTNDGG-------------LARVLELPSTQWLRVYRVR 148
                      R+D +T GLLL+                    R               R
Sbjct: 157 DPNDPAVGLVHRIDKDTSGLLLIAKTPDAKTFLGKQFFNKTTHRSYVALVWGNFTEDEGR 216

Query: 149 FHGQVDQDKLNLLKKGIVIQG-ICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
             G + +D  + L+  +                +  + G    +   L  G+  +I+   
Sbjct: 217 IEGNIGRDSKDRLRMKVFDTDSGIGKPAVTHYKVLERFGYTTLIECILETGRTHQIRAHM 276

Query: 206 EFFNWK 211
           +     
Sbjct: 277 KHIGHP 282


>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 = 61.0 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 29/245 (11%), Positives = 67/245 (27%), Gaps = 42/245 (17%)

Query: 10  NFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
                R+ K +A  G+    SR  ++++I    V V G+   + +  V + D + ++  P
Sbjct: 44  ESHGCRLDKALA--GLVPEFSRSYLQQLIEDGGVLVKGLKAIKTSAKVKAGDELTIELRP 101

Query: 67  ---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                          +   +R  + +      +V         + +   L          
Sbjct: 102 TPQSQAFKPEEMALDIVYEDRHLIVVNKPAGLVVHPAPGNWSGTLLNGLLAHDPQASFMP 161

Query: 112 -------------------GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152
                               +     + + ++         + L    W      +    
Sbjct: 162 RAGIVHRLDKDTSGLMVVARQRQTMDQLVSMIAARTVSREYIALAHGTWEGAKTRQVEAP 221

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLD---TQKGSNAWVTVGLREGKNREIKKVFEFFN 209
           + +D  N L+  +V      G    T+         +  V   L  G+  +I+    F  
Sbjct: 222 IGRDPRNRLRMAVVDLEKNSGKAASTVISLLDNAEKHCLVKCKLHTGRTHQIRVHMAFLG 281

Query: 210 WKVNR 214
             +  
Sbjct: 282 HPLVS 286


>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 = 61.0 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/242 (14%), Positives = 76/242 (31%), Gaps = 42/242 (17%)

Query: 13  PQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------- 62
           P R+ K + +    A+R +V+  I ++RV VNG  ++     + S D I +         
Sbjct: 37  PMRIDKYLTQQVENATRNKVQEAIEEERVLVNGRPVKS-NYRIKSCDTILITFLRPPAPE 95

Query: 63  ---DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------- 110
              + +P+     +   + +  +P  +V         +     L  I     S       
Sbjct: 96  LAPEDIPIDIVYEDSDLMVVNKEPGMVVHPAFGNWTGTLANAILHHIGRDAESLDASELR 155

Query: 111 ---VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK---------- 157
              V RLD +T GL+++  +      L             +       D           
Sbjct: 156 PGIVHRLDKDTSGLIIIAKNPTALHRLARQFAMRQVQKIYKAIVWGVPDPRSGTILTNIG 215

Query: 158 ----LNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIKKVFEFFNWK 211
                  +      +G+           ++  +  + V++ L  G+  +I+   +     
Sbjct: 216 RSKKNRKIMANYPYEGLDGKHAITDYLVEENLHWFSVVSLTLHTGRTHQIRAHMQHTGNP 275

Query: 212 VN 213
           + 
Sbjct: 276 IL 277


>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 = 61.0 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 33/239 (13%), Positives = 70/239 (29%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I +QRV++NG ++++    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKTWILEQRVQINGKMVDKPKEKVLGGESVAIDA 69

Query: 65  ----------VPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                      P+       +   L +      +V   +     + +   L         
Sbjct: 70  LIEEDARWEAQPISLDIVYEDEDILVINKPRDLVVHPGAGNPDGTVLNALLHHYPEIVDV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L                               
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQAREITREYEAVAIGTMTAGGTVEEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 ARHSTKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMAHINHPLV 248


>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 = 61.0 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 68/244 (27%), Gaps = 40/244 (16%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +     RV K +  R   ASR  +++      V  NG  ++  +  V   D I V  
Sbjct: 32  VVDKGQVMMRVDKYLFDRLTNASRNRIQKAADAGFVMANGKPVKS-SYKVKPQDVITVMM 90

Query: 63  -----DGVPLR--------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                +   +           ++  + +      +V         + V      +     
Sbjct: 91  DRPRYENEVIPEDIPLNIVYEDKHLMVVNKPAGLVVHPGHGNYHGTLVNAIAWHMKDNPD 150

Query: 110 SV---------GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-- 158
                       R+D +T GLL++         L           R R     + ++   
Sbjct: 151 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGNQFFNKTTKRRYRALVWGNVEQDEG 210

Query: 159 -----------NLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                      + ++  ++      +      +  + G    V   L  G+  +I+   +
Sbjct: 211 TVVGNIGRNPKDRMQMTVLPDDQGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMK 270

Query: 207 FFNW 210
               
Sbjct: 271 HIGH 274


>gi|15888079|ref|NP_353760.1| hemolysin [Agrobacterium tumefaciens str. C58]
 gi|15155705|gb|AAK86545.1| hemolysin [Agrobacterium tumefaciens str. C58]
          Length = 250

 Score = 61.0 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 11/57 (19%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 7  VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          + +    +R+ +++   G  ASR      +++  V VNG ++ + +  V +   I +
Sbjct: 1  MSKTSENERLDQLLVSRGHFASRSRARDAVSRGTVSVNGKIVTKPSQTVAANVKIAI 57


>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 = 61.0 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 63/239 (26%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I  QRV VNG + +     V+  + + ++ 
Sbjct: 10  TVSESQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGQMCDTPKEKVLGGERVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L                               
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQLREITREYEAVAIGHMTAGGTVSEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMSVHPMGKPAVTHYRIMEHFRIHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>gi|313679575|ref|YP_004057314.1| hemolysin a [Oceanithermus profundus DSM 14977]
 gi|313152290|gb|ADR36141.1| hemolysin A [Oceanithermus profundus DSM 14977]
          Length = 245

 Score = 61.0 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 1/54 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             R+   +A  G+  SR + + +I   RV+V+G +  + +  V     IEV G
Sbjct: 3  ERVRLDVALAARGLVESRAKAQELIRAGRVRVDGAVATKPSRKVGPEARIEVVG 56


>gi|319408111|emb|CBI81764.1| ribosomal large subunit pseudouridine synthase D [Bartonella
           schoenbuchensis R1]
          Length = 340

 Score = 61.0 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 23/268 (8%), Positives = 65/268 (24%), Gaps = 64/268 (23%)

Query: 4   KNIVQENFTPQRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           + I  E+   QR+ + +A+      SR  ++ +I +  +KV+G L++     +     IE
Sbjct: 3   QQITDESALGQRIDQWLAKKYHNELSRSRLQTLIREGYLKVDGQLIKEPKTKLQPNQTIE 62

Query: 62  ----------VDGVPLRK----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--- 104
                     ++G  +       +   + +      +V   +     + V   +      
Sbjct: 63  LIIPPLKNVHLEGEAIVLDILFEDDHVIVINKPAGLVVHPGNGNWTGTLVNALIHHCGDS 122

Query: 105 ----------------------------FSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
                                                   +  G     +    A +   
Sbjct: 123 LSGIGGVKRPGIVHRLDKNTSGVMVVAKNDFAHKSLSAQFSDHGRTCALDRRYHALIWNA 182

Query: 137 PSTQ-----------WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           P                   +       +    + +    +++              +  
Sbjct: 183 PRRNIGTIDVPLGRSPHNRIKQTVVRHQNVHARHAITHFSLLEKYKT------CADAEPF 236

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVN 213
            + +   L  G+  +I+         + 
Sbjct: 237 ASLLECRLETGRTHQIRVHMAHIGHPLV 264


>gi|294791518|ref|ZP_06756675.1| cytotoxin/hemolysin [Scardovia inopinata F0304]
 gi|294457989|gb|EFG26343.1| cytotoxin/hemolysin [Scardovia inopinata F0304]
          Length = 276

 Score = 61.0 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +   G+  SR   +R++    V +NG +  + +  V   D I +
Sbjct: 1  MRIDKALVSRGLCPSRTRAQRLLEAGLVLLNGHVCTKPSQTVEDKDQISL 50


>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 = 61.0 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 75/249 (30%), Gaps = 42/249 (16%)

Query: 4   KNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K  V +  TP R+ K +A      SR  +++      ++VN   ++     V   D I +
Sbjct: 24  KIEVDKGQTPVRIDKFLAEKNPYQSRNRIQQAADSGCIRVNNQPVKS-NYKVRPGDVITL 82

Query: 63  -------------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                        + +PL    E   L + +KP G+V      +   T+ + +      +
Sbjct: 83  MLDRPKHDTSIIAEDIPLDIVYEDDVLMVVNKPAGMVVHPGAGNFTGTLINAVAWHLKDL 142

Query: 109 ISV----------GRLDINTEGLLLLTNDGG-------------LARVLELPSTQWLRVY 145
                         R+D +T GLL++                    R         L   
Sbjct: 143 KGFDANDPEVGLVHRIDKDTSGLLVVAKTPEAKTVLGKQFFNKTTHRSYNALVWGNLVED 202

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                G V +D  N L+  +                +  + G    V   L  G+  +I+
Sbjct: 203 EGTIEGNVARDPKNRLRMKVFSPESGIGKNAVTHYRVIERYGYTTLVECILETGRTHQIR 262

Query: 203 KVFEFFNWK 211
              +     
Sbjct: 263 VHMKHIGHP 271


>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 = 61.0 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 29/239 (12%), Positives = 66/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            + E+   QR+ + +A      SR  ++  I   RV+VNG ++ +A   V+  + I +D 
Sbjct: 10  TIAESQLGQRLDQALAELFPDYSRSRIKEWILDDRVQVNGKVINKAKEKVLGGEQISIDA 69

Query: 64  -------GVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                    P      +   +   L +      +V   +     + +   L         
Sbjct: 70  LIEEDTRWEPQDIPLDVVYEDEDILIINKPRDLVVHPGAGNPDGTILNALLYRYPEIADV 129

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--- 156
                  R+       +     +        A      + ++  V   R       +   
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTHLVEALQRREITREYEAVAVGRMTAGGMVEEPI 189

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRVMEHFRAHTRLRLRLETGRTHQIRVHMAHINHPLI 248


>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 = 61.0 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 33/244 (13%), Positives = 70/244 (28%), Gaps = 36/244 (14%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K   I++E +  QR+   +A+     SR  ++ +I +++V VNG  ++     + S D++
Sbjct: 3   KYNFIIEEEYENQRIDVYLAQEFENISRSHIQDLIGKKKVFVNGKAVKS-NYKLKSRDNV 61

Query: 61  EV---DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           E    D   L+             +R  + +      +V         + V   L     
Sbjct: 62  EFEIPDNEELKIEAENIPLDIVYEDRDIVVVNKAQGMVVHPAPGNYNGTLVNALLYHCKD 121

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ----------- 155
                G L       +     G L       + + L                        
Sbjct: 122 LSGINGVLRPGIVHRIDKDTSGILVVAKNDAAHKNLANQLKEHSMNRVYRAVVEGIIKED 181

Query: 156 ---------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                           K  V++G         +  +  ++  +   L  G+  +I+    
Sbjct: 182 EGTVDKPLARHPVERVKIAVVKGGRNAVTHYKVLERYRNSTLIECKLETGRTHQIRVHMA 241

Query: 207 FFNW 210
           +   
Sbjct: 242 YIGH 245


>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 = 61.0 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 32/241 (13%), Positives = 69/241 (28%), Gaps = 35/241 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLER-----AAVNVMST-- 57
           I+ +    QR+ KV+    G ASR  V+R I +  V VN   ++          V  T  
Sbjct: 5   IITKEHHEQRIDKVVVDLHGQASRTAVQRWINEGAVLVNEKEVKTNSKVQQGDKVTLTEP 64

Query: 58  --DHIEVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
               +E+ G  +       +   + +      +V      +  + V   L          
Sbjct: 65  AAQEVELLGEDIPLDVVYEDSDVIVVNKPRGLVVHPAPGHESGTLVNALLFHCKDLSGIN 124

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRVRFH 150
           G +       +     G +       + + L                        +    
Sbjct: 125 GEIRPGIVHRIDKDTSGLIMAAKHDAAHEHLAAQLKAKTTERRYKAIVHGVIPHAKGTID 184

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + +D  +  K  +            +L+      ++++  L  G+  +I+  F +   
Sbjct: 185 APIGRDPKDRQKMAVTHVNSRPAVTHFSLEETFKQYSYISCELETGRTHQIRVHFNYIGH 244

Query: 211 K 211
            
Sbjct: 245 P 245


>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 = 60.6 bits (145), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 30/245 (12%), Positives = 64/245 (26%), Gaps = 36/245 (14%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-- 61
           K I        R+ K I+     SR  V+ ++A+  + VN   ++ A   V + D I   
Sbjct: 5   KIIAAAEDAGARIDKYISEQEDLSRSRVQALLAEGSILVNQNAVK-ANYKVKADDCITAV 63

Query: 62  VDGVP------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
            +               +R  +   + +      +V   +     + V   L        
Sbjct: 64  FNDEMEMEARPEKMELDVRYEDEDVIVINKPKNIVVHPAAGNQSGTLVNGLLYHCKDLSG 123

Query: 110 SVGRLDIN---------------------TEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
             G L                           L        + R+        ++     
Sbjct: 124 INGTLRPGIVHRIDKDTTGLLIIAKNDLAHASLSKQLQSKTVNRLYYALVHGVIQHDFGT 183

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +D  +  K  +             +  +  +   V   L  G+  +I+   ++ 
Sbjct: 184 IDAPIGRDVKDRQKMAVTATNSKDARTHFQVIERFENYTLVECRLETGRTHQIRVHMQYI 243

Query: 209 NWKVN 213
              V 
Sbjct: 244 GHPVV 248


>gi|330896109|gb|EGH28330.1| S4 domain-containing protein [Pseudomonas syringae pv. japonica
           str. M301072PT]
          Length = 161

 Score = 60.6 bits (145), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 31/158 (19%), Positives = 62/158 (39%), Gaps = 4/158 (2%)

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL 142
            ++T  +     S     L   F R+ ++  L  N  GL++ + D  + R L    ++  
Sbjct: 6   QMITPGTLSVDHSYSKRPLKGHFMRLEAISSLQANASGLMVFSQDWKILRKLTDDRSKIE 65

Query: 143 RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           + Y V   G++    LN L  G+  +G     ++ +   +      +   ++  +   I 
Sbjct: 66  QEYVVEISGEMVAHGLNRLNHGLTYKGKELPAVKASWQNENR----LRFAMKNPQPSIIA 121

Query: 203 KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + E    K+  + RI  G   +G L  G  R ++ K 
Sbjct: 122 LLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRYMTAKE 159


>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 = 60.6 bits (145), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 25/247 (10%), Positives = 69/247 (27%), Gaps = 36/247 (14%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K    V  +   +R+   +A     SR  +++ I +  +KVNG +++     +   D I 
Sbjct: 4   KYAFTVTRDDEKKRLDIFLADKLQDSRSFLKKGIVEGWIKVNGSIVK-PNYRLRQEDQII 62

Query: 62  V----------DGVPLRK----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           V          D   +       +R  + +      +V         + +   L      
Sbjct: 63  VTVPQALQPLIDPEDIPLDIIFEDRDIVVINKPRGMVVYPAPGNYSGTLINALLNHTKDL 122

Query: 108 VISVGRLDI---------------------NTEGLLLLTNDGGLARVLELPSTQWLRVYR 146
               G +                           L        + +V +      ++  +
Sbjct: 123 SARGGTMRPGIVHRLDKDTSGVIVVAKNDTAHINLSKQLKSREVKKVYQTLVWGKVQEDK 182

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
              +  + +  +   +  +  +          +  +     ++ V +  G+  +I+   +
Sbjct: 183 ATINAPIGRHPIKRKEMAVTTKNSKEAITHFKVLERFDEFTFLEVAIETGRTHQIRVHMK 242

Query: 207 FFNWKVN 213
           F    + 
Sbjct: 243 FIGHPIV 249


>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 = 60.6 bits (145), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 38/245 (15%), Positives = 81/245 (33%), Gaps = 38/245 (15%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           IV ++    R+   IA      SR  ++++I + R++VN  + E+A+  V + D IEV+ 
Sbjct: 23  IVSDDDADSRLDFYIASQYRDISRSYIQKLIKEDRIRVNSKI-EKASYKVKTGDKIEVNM 81

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                        G+ +   +   + +  +   +V        R+ V   L     R+ S
Sbjct: 82  PEPQALEIEPQDIGIDIVYEDDYLMVVNKQQGMVVHPAPGNPDRTLVNAVLFHCGDRLSS 141

Query: 111 VGRL----------------------DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
           +  +                      +   +GL        + R  E+     +      
Sbjct: 142 INGVIRPGIVHRIDKNTSGLLVIAKDNQTHQGLSDQFKVHSITREYEMICIGNVEWQEKT 201

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
             G + ++  + +K  IV            L       + ++  L  G+  +I+      
Sbjct: 202 IDGPIGRNPKDRMKMAIVKTNGKRAVTHFRLVENYDGYSHLSARLETGRTHQIRVHISSI 261

Query: 209 NWKVN 213
           N  + 
Sbjct: 262 NRPIL 266


>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 = 60.6 bits (145), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/265 (13%), Positives = 79/265 (29%), Gaps = 35/265 (13%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
             V+E+   QR+ + +A      SR  ++  + + +V VNG ++ +    VM  + I V 
Sbjct: 9   QTVKESQLGQRLDQAVAELFTDFSRSRLKEWLLEGKVMVNGNVVTKPRTKVMGGEAITVQ 68

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   +   + +      +V   +     + +   L        
Sbjct: 69  AELEDEQRWEAQDIPLNIVYEDDDIIVINKPRDLVVHPGAGTPDGTVLNALLFHFPPIAE 128

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   RLD +T GL+++         L     +                   ++ K 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRELQKRNITREYEAIAIGKMTAGGMIDKP 188

Query: 165 IVIQGIC---------YGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I                        +      +  + + L  G+  +I+    +    + 
Sbjct: 189 IGRHSTKRTLMAVSPLGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIRVHMAYLQHPL- 247

Query: 214 RLIRISYGPFQLGTLLAGSTREVSK 238
            L   +YG      +  G+T+E++ 
Sbjct: 248 -LGDTAYGGRA--RIPKGATQELTD 269


>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 = 60.6 bits (145), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 28/240 (11%), Positives = 68/240 (28%), Gaps = 33/240 (13%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---- 60
           +V E+   QR+ +V+A      SR  ++  I    V +NG ++ +A   +   D I    
Sbjct: 10  VVAEHQVGQRLDQVLAEMFPDYSRTRLKEWILAGFVNLNGNVVVKAREKMQYGDKIILNA 69

Query: 61  EVDGV----------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
           EVD             +   +   L +      +V   +     + +   L         
Sbjct: 70  EVDEEVRYEPQDLPLVIVYEDDDILVINKPAGFVVHPGAGNPDGTVLNALLFHYPDIIDV 129

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF------HGQV 153
                  R+       +     +        A      + ++  V              +
Sbjct: 130 PRAGIVHRLDKDTTGLMVIAKTIPAQTHLVTALQARRITREYEAVVSGTMTAGGFVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +      +  +   G         +  +  +++ + + L  G+  +I+         + 
Sbjct: 190 GRHATKRTQMAVRPLGKPAKT-HYRVAEKYRAHSLLRLRLESGRTHQIRVHMTHIMHPIV 248


>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 = 60.6 bits (145), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 29/239 (12%), Positives = 56/239 (23%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNV---------- 54
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V          
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQMAINA 69

Query: 55  --------MSTDH---IEVDGVPLRKAERTRLWLYHKPIGLVTTHS----DPDGRSTVFD 99
                      D    I  +   +    + R  + H   G                    
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--- 156
               I  R+       +     +        +      + ++  V           D   
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 60.6 bits (145), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 36/248 (14%), Positives = 74/248 (29%), Gaps = 41/248 (16%)

Query: 7   VQENF-----TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           + E       T +R+   +      SR ++ ++I ++ V+V+G ++ R+ V +     + 
Sbjct: 1   MNETQSYICETIERLDTFLTSILGQSRSQIAQLIKKELVQVDGKVVSRSGVKLKKNQVVL 60

Query: 62  V----------------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           V                      D   L   + T L ++  P     T  D      +  
Sbjct: 61  VKFPPAEIKPALDIDFDVEILYEDDDILVINKPTGLTVHPAPSVKEATLVDWLKHKGMRL 120

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR------------V 147
           +  S   R   V RLD  T G +++  +      L                        +
Sbjct: 121 SSLSGEERHGIVHRLDKGTSGAMVIAKNNSTHEFLSDQLQDKSMGRYYLAVINPPLKDEL 180

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTVGLREGKNREIKKVF 205
                      +   K   ++   Y      +   +   +N  +   L  G+  +I+   
Sbjct: 181 TEVIFPIARSSHNRLKMAPLEHGKYAKSAFKVLAYSNDEANQLIACKLYTGRTHQIRVHL 240

Query: 206 EFFNWKVN 213
           E  N  + 
Sbjct: 241 ESLNRHIV 248


>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 = 60.6 bits (145), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 31/270 (11%), Positives = 68/270 (25%), Gaps = 45/270 (16%)

Query: 8   QENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +++   QR+ + ++      SR  ++ +I+   V VN          V   D I+V+  P
Sbjct: 9   EQDGENQRLDRWLSERVQQLSRSRLQALISSGHVWVNNSPCTSKKATVQIGDRIQVEIPP 68

Query: 67  --------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------- 105
                         +   +   L +      +V         + V   L           
Sbjct: 69  AIPLELKATNIPLDILYEDEELLIINKPAGLVVHPAPGHANDTLVNALLAHCETLAGIGG 128

Query: 106 --------------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151
                         +  I++ + D   + L          R          +        
Sbjct: 129 VQRPGIVHRLDKDTTGAIAIAKTDHAHQHLQAQIQAKTARRQYLGIIYGVPKTTSGVIDQ 188

Query: 152 Q--VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                      +      QG      +  +  + G+   +   L  G+  +I+       
Sbjct: 189 PIGRHHSDRKKMAIVPEHQGGRSAITRWQVQERLGNYTLIEFELETGRTHQIRVHSASIG 248

Query: 210 WKVNRLIRISYG-----PFQLGTLLAGSTR 234
             +    R+ YG        L      + +
Sbjct: 249 HPIVG-DRV-YGKGRSVGVNLPGQALHAWK 276


>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 = 60.6 bits (145), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 34/243 (13%), Positives = 67/243 (27%), Gaps = 36/243 (14%)

Query: 4   KNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-- 60
           ++IV+E     R+ KV+ +     SR +V++ I    VKVNG  ++         D I  
Sbjct: 5   EHIVREEEKSVRLDKVLTQLEEKWSRSQVQQWIKDGNVKVNGSQVKT-NYKCAIEDKIII 63

Query: 61  ------EVDGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                 E+D VP      +   +   + +      +V         + V   +       
Sbjct: 64  SIPEPEELDVVPENMDLDIYFEDADVIVVNKPRGMVVHPAPGHPSGTLVNGLMAHCKDLS 123

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD------------ 156
              G L       +     G L       + + L    V                     
Sbjct: 124 GINGVLRPGIVHRIDKDTSGLLMVAKNDLAHEKLVEQLVNKTVTRKYKAIVHGIIPHDHG 183

Query: 157 --------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                        +   V+           +  +     +V   L  G+  +I+   ++ 
Sbjct: 184 TIDAPLGRDPKDRQNMAVVDSGRDAVTHFNVLERFTDFTYVECKLETGRTHQIRVHMKYI 243

Query: 209 NWK 211
            + 
Sbjct: 244 GYP 246


>gi|164688606|ref|ZP_02212634.1| hypothetical protein CLOBAR_02251 [Clostridium bartlettii DSM
           16795]
 gi|164603019|gb|EDQ96484.1| hypothetical protein CLOBAR_02251 [Clostridium bartlettii DSM
           16795]
          Length = 275

 Score = 60.6 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 25/185 (13%), Positives = 53/185 (28%), Gaps = 2/185 (1%)

Query: 7   VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           ++  F  +R+  ++   G   SR + +R I    V V+    ++A   V +   IEV G 
Sbjct: 1   MKGKFMKKRIDVLLVEQGFFESREKAKRSIMAGLVFVDNQKCDKAGTEVKTDAKIEVKGN 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P+    R  L L         T  D                 ++  G   + +  +    
Sbjct: 61  PIPYVSRGGLKLEKAMKNFDITLQDKVCMDIGAST-GGFTDCMLQNGARKVFSIDVGYGQ 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
               L +   +   +   +  V      +      +    +   +        +      
Sbjct: 120 LAWKLRQDDRVVCMERTNIRYVTIEDTKEFADFASIDVSFISLKLVLPVAHNLIIPGGEI 179

Query: 186 NAWVT 190
            A + 
Sbjct: 180 VALIK 184


>gi|319406711|emb|CBI80344.1| ribosomal large subunit pseudouridine synthase D [Bartonella sp.
           1-1C]
          Length = 333

 Score = 60.6 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 26/263 (9%), Positives = 70/263 (26%), Gaps = 52/263 (19%)

Query: 3   DKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
            ++I  EN   QR+ + +A+   G  SR  ++ +I +  +K++G L++     + S   I
Sbjct: 2   TQHITSENACGQRIDQWLAKQYKGELSRSRLQTLIREGYLKIDGQLIKEPKTKLKSNQII 61

Query: 61  EV----------DGVPLRK----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           E+           G  +       +   + +      +V   +     + V   +     
Sbjct: 62  ELTIPTPNDAQPQGEAIALDILFEDNHIIVINKPAGLVVHPGNGNWTGTLVNGLIYHCRD 121

Query: 107 RVISVGRLDIN--------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
            +  +G +               +++      A                           
Sbjct: 122 SLSGIGGIKRPGIVHRLDKDTSGVMVIAKSDFAHRNLNAQFADHGRTSPLDRRYHAVIWG 181

Query: 159 NLLKKGIVIQGICYG----DMQVTLDTQKGSN------------------------AWVT 190
           +  +    I            + T+   + ++                        + + 
Sbjct: 182 SPNRNIATIDTFLARSSRDRTKRTVVHSEHAHARRAITHISLLEKYGTCNDATSLASLLE 241

Query: 191 VGLREGKNREIKKVFEFFNWKVN 213
             L  G+  +I+         + 
Sbjct: 242 CRLETGRTHQIRVHMSHIGHPLI 264


>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 = 60.6 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 30/248 (12%), Positives = 64/248 (25%), Gaps = 38/248 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD- 58
           K+   + E     R  K +A    G+ SR  ++ +    ++ +NG   E+    +   D 
Sbjct: 5   KEVIKITEEEKGIRADKFLALKIDGV-SRNFIQGLFDDGKILINGK-AEKGKYKLSVGDC 62

Query: 59  -----------HIEVDGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
                       +E + +P  +   +   + +      +V         + V   L    
Sbjct: 63  VEVEIPEPEELKVEAEDIPLNIVYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNALLHHCD 122

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                 G +       +     G L       + Q L         + +           
Sbjct: 123 DLSGINGVIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKK 182

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                            K  V++          +     S + V   L  G+  +I+   
Sbjct: 183 EGGTIDAPLGRHHRDRLKYAVVKDGKRAVTHYEVLKVFNSCSLVKCTLETGRTHQIRVHM 242

Query: 206 EFFNWKVN 213
            F    + 
Sbjct: 243 AFIGHPLL 250


>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 = 60.6 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 36/247 (14%), Positives = 72/247 (29%), Gaps = 36/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K +++      R+ K ++      SR  V+ +I    + VN    +  +  V + D 
Sbjct: 1   MPKKYLLEVKDEHGRLDKFVSEQIPDLSRTRVKELIQDDNILVNQKKEKV-SYKVQAGDQ 59

Query: 60  IEVD------------GVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           IEV+             +P  +   +   + +      +V         + V   L    
Sbjct: 60  IEVNVPAVKPLDVVPEDIPLDIVYEDDDVIVVNKPQGMVVHPAPGHSDHTLVNALLYHTK 119

Query: 106 SRVISV--------GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-- 155
               S          R+D +T GLL++  +      LE                  +   
Sbjct: 120 DLAKSPEGFRPGIVHRIDKDTSGLLMIAKNAKARESLEDQLAHKTNKRIYWAIVHGNFSE 179

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           KK  V++          +  Q    + +   L  G+  +I+   
Sbjct: 180 ENGTIDAPIGRNPYDRKKMAVVERGKKAITHFKVLKQFKGYSLIECQLETGRTHQIRVHL 239

Query: 206 EFFNWKV 212
           ++    V
Sbjct: 240 DYIGHAV 246


>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 = 60.6 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 28/243 (11%), Positives = 68/243 (27%), Gaps = 37/243 (15%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           +       R+ K I+      SR  +++ I    ++VNG  ++     V + DHIE+   
Sbjct: 6   ITSEENGVRIDKFISDHFPQWSRTIIQQWIVDNHIQVNGTPIKS-KYKVKAGDHIEIREP 64

Query: 63  DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
           D +PL              +   L +      +V         + V   +          
Sbjct: 65  DPIPLEIPAENLNLDIIYEDGDVLVVNKPRGMVVHPAPGHYTGTLVNGLMYHCHDLSGIN 124

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRVRFH 150
           G +       +     G L       + + L                        +    
Sbjct: 125 GVMRPGIVHRIDKDTSGLLMVAKNDRAHESLVNQLKNKETKRRYYAIVSGIIPHDKGTID 184

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + ++  +     +  +          +  +   +  V+  L  G+  +I+   ++  +
Sbjct: 185 APIGRNPEDRQSMMVTEKNSRDAVTHFQVVERFYRHTLVSCELETGRTHQIRVHLKYIGF 244

Query: 211 KVN 213
            + 
Sbjct: 245 PIV 247


>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 = 60.6 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 32/241 (13%), Positives = 68/241 (28%), Gaps = 32/241 (13%)

Query: 5   NIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           N V+++   QR+ + IA      SR  ++  +   +V+VNG ++ +    VM  + I + 
Sbjct: 9   NTVKDSQLGQRLDQAIAELFADFSRSRLKEWLLDGKVQVNGEVVTKPRTKVMGGEEIILQ 68

Query: 63  ----DGVPLRKAERT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
               D       +            L +      +V   +     + +   L    +   
Sbjct: 69  AELEDEERWEAQDIPLDIVYEDDDILVINKPRGFIVHPGAGTPDGTVLNALLHHYPNIAE 128

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH------------GQ 152
                   RLD +T GL+++         L     +     R                 Q
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKKRNFTREYEAIAIGRMTAGGRIEQ 188

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                        V            +      +  + + L  G+  +I+    +    +
Sbjct: 189 PIGRHSTKRTLMAVSPMGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPL 248

Query: 213 N 213
            
Sbjct: 249 L 249


>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 = 60.6 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 29/247 (11%), Positives = 62/247 (25%), Gaps = 36/247 (14%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTD-- 58
           K+   + E     R  K +A      SR  ++ +    ++ +NG   E+    +   D  
Sbjct: 5   KEVIKITEEEKGIRADKFLALKIEGVSRNFIQGLFDDGKILINGK-AEKGKYKLSVGDCV 63

Query: 59  ----------HIEVDGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
                      +E + +P  +   +   + +      +V         + V   L     
Sbjct: 64  EVEIPEPEELKVEAEDIPLNIVYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNALLYHCDD 123

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ----------- 155
                G +       +     G L       + Q L         + +            
Sbjct: 124 LSGINGVIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKKE 183

Query: 156 ---------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                           K  V++          +     S + V   L  G+  +I+    
Sbjct: 184 GGTIDAPLGRHHRDRLKYAVVKDGKRAVTHYEVLKVFNSCSLVKCTLETGRTHQIRVHMA 243

Query: 207 FFNWKVN 213
           F    + 
Sbjct: 244 FIGHPLL 250


>gi|313901597|ref|ZP_07835036.1| hemolysin A [Thermaerobacter subterraneus DSM 13965]
 gi|313468127|gb|EFR63602.1| hemolysin A [Thermaerobacter subterraneus DSM 13965]
          Length = 308

 Score = 60.6 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 15/61 (24%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          +    R+ +++   G   +R      I   RV+V G ++++A   V     IEV G P+ 
Sbjct: 2  SPRGIRLDQLLVERGYFPTRNRARAAILAGRVRVEGQVVDKAGAAVSPDARIEVAGDPIP 61

Query: 69 K 69
           
Sbjct: 62 Y 62


>gi|291557471|emb|CBL34588.1| hemolysin TlyA family protein [Eubacterium siraeum V10Sc8a]
          Length = 241

 Score = 60.6 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 15 RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          R+   ++    + SR     +I Q  V+VNG +  +A+  V   D+I + G 
Sbjct: 4  RLDVYLSENNTVKSRSLAASLIKQGSVEVNGRICTKASFAVDENDNIRIIGE 55


>gi|167750993|ref|ZP_02423120.1| hypothetical protein EUBSIR_01978 [Eubacterium siraeum DSM 15702]
 gi|167656172|gb|EDS00302.1| hypothetical protein EUBSIR_01978 [Eubacterium siraeum DSM 15702]
          Length = 241

 Score = 60.6 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 15 RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          R+   ++    + SR     +I Q  V+VNG +  +A+  V   D+I + G 
Sbjct: 4  RLDVYLSENNTVKSRSLAASLIKQGSVEVNGRICTKASFAVDENDNIRIIGE 55


>gi|327460457|gb|EGF06794.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK1057]
          Length = 298

 Score = 60.6 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 34/240 (14%), Positives = 66/240 (27%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GV 65
           ++ +   QR+ K +A     SR      I   R+ VNG   ++A   V   D I  +   
Sbjct: 5   IEASVAGQRLDKAVAELTDLSRSLAHEQIKDSRILVNGQ-AKKAKYAVKEGDVISYELPE 63

Query: 66  P-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
           P             +   +     +      +V   +     + V   +  I       G
Sbjct: 64  PEVVEYVAEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGING 123

Query: 113 RLDINTEGLLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLK 162
            L       +     G L       +           + LR Y    HG +  D+  +  
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 163 KGIVIQGICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                +                 +  +  +    + V + L  G+  +I+    +    V
Sbjct: 184 PIGRSEKDRKKQAVTAKGKPALTRFQVLERFADYSLVELQLETGRTHQIRVHMAYIGHPV 243


>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 = 60.6 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 27/237 (11%), Positives = 70/237 (29%), Gaps = 37/237 (15%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+ K + +    SR ++ ++I ++++ +NG+ +++   ++   D I +           
Sbjct: 1   MRLDKFLTQKLGLSRNQISKIIQEKQITLNGVFIQKNGTSLNFNDQIILTLPNKQEKSKP 60

Query: 64  ---GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL------ 114
               +P+   +   L L      +V      D + T+ D L      + ++G        
Sbjct: 61  NHLNIPILYEDEDLLILNKPINLIVHQTHQDDSQYTLQDWLQENNFSLSNLGDSYRQGII 120

Query: 115 ---------------DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
                          +     +L             +          +     + +   N
Sbjct: 121 HRLDKTTSGAIVIAKNNYAHEILSQQLKSKEMGRYYVCVIDSPLKQNILIDAPLIRHPKN 180

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG---LREGKNREIKKVFEFFNWKVN 213
            LK     +         T   +  +N  + +    L  G+  +I+         + 
Sbjct: 181 RLKYIPTTKDTPLSKEAKTAFFKIINNDKIELIGAKLFSGRTHQIRAHLSKIQRHIL 237


>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 = 60.6 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 26/258 (10%), Positives = 67/258 (25%), Gaps = 52/258 (20%)

Query: 8   QENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
            EN   QR+ + +A+   G  SR  ++ +I +  +K++G L++     + S   IE+   
Sbjct: 9   NENACGQRIDQWLAKQYKGEISRSRLQTLIREGHLKIDGQLIKEPKTKLKSNQIIELIIP 68

Query: 63  -------DGVPLRK----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                   G  L       +   + +      +V   +     + V   +      +  +
Sbjct: 69  APNDARPQGEALALDIFFEDDHVIVINKPAGLVVHPGNGNWTGTLVNALIYHCSDSLSGI 128

Query: 112 GRLDIN--------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
           G +               +++     +A                           +  + 
Sbjct: 129 GGIKRPGIVHRLDKDTSGVMVIAKNDIAHRNLNAQFADHGRTSALDRRYHAIIWGSPNRN 188

Query: 164 GIVIQGICYG----DMQVTLDTQKGSN------------------------AWVTVGLRE 195
              I            +  +   + +N                        + +   L  
Sbjct: 189 IATIDTFLARSSHDRTKRAVVHSEHANARHAITHFSLLEKYGTCNDTTPFASLLECRLET 248

Query: 196 GKNREIKKVFEFFNWKVN 213
           G+  +I+         + 
Sbjct: 249 GRTHQIRVHMAHIGHPLI 266


>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 = 60.6 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 29/246 (11%), Positives = 63/246 (25%), Gaps = 43/246 (17%)

Query: 7   VQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V      +R+ ++IA R    SR   + ++    V VNG      A  +   D IE+   
Sbjct: 16  VAAEEDGERLDRLIAARVAEISRSYAQSLVKAGDVYVNGEPAR-PARRIHEGDTIEILLP 74

Query: 63  -----DG-------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                D        VP+   +   +        +       +  + V           + 
Sbjct: 75  PVPEPDDLTPEYIPVPVIYEDDDVIIFDKPAGLVTHPAPGHEHGTLVNVVKALRPDVPLL 134

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
           +G         L     G +       + ++L     +        +   L  G++ +  
Sbjct: 135 MGGKRPGIVHRLDKDTSGLIVVAKNEEARRYLVQQWQQRDV---VKRYIALVHGVIRENE 191

Query: 171 CY---------------------GDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                                          +  +      + V +  G+  +I+    F
Sbjct: 192 GTIDAPISRDPRNRKRMAVVPNGRPAVTHFRVLERFRDATLLNVQIETGRTHQIRVHMLF 251

Query: 208 FNWKVN 213
               + 
Sbjct: 252 IGHPIV 257


>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 = 60.6 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 30/251 (11%), Positives = 66/251 (26%), Gaps = 38/251 (15%)

Query: 3   DKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           ++  V+E     R+   +A +    SR  ++++I+ + V VNG     A+  V   D +E
Sbjct: 5   NRYTVEEEDEQTRLDVFLAGQNPELSRARIQKLISLELVTVNGRPAR-ASHRVRGGDCVE 63

Query: 62  ----------VDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                     ++   +           L +      +V         + V   L      
Sbjct: 64  LKVPDPETPRIEPEAIPLEVCFEDPDVLVVNKPRGLVVHPAVGHYSGTLVNALLHHCRDL 123

Query: 108 VISVG---------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR 146
               G                     + D     L     D  + R          R   
Sbjct: 124 SGINGILRPGIVHRLDRDTSGLLMVAKNDAAHLALAGQLKDRAVLRRYTALVHGRPRRET 183

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                 + +   +  +  +  +          +  +    + + + L  G+  +I+    
Sbjct: 184 GTVDAPIGRHPRDRQRMAVTPRSGRAARTHYRVVRRFDKFSLLELTLDTGRTHQIRVHMA 243

Query: 207 FFNWK-VNRLI 216
                 V  L 
Sbjct: 244 HVGHPLVGDLK 254


>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 = 60.6 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 30/248 (12%), Positives = 64/248 (25%), Gaps = 38/248 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD- 58
           K+   + E     R  K +A    G+ SR  ++ +    ++ +NG   E+    +   D 
Sbjct: 5   KEVIKITEEEKGIRADKFLALKIDGV-SRNFIQGLFDDGKILINGK-AEKGKYKLSVGDC 62

Query: 59  -----------HIEVDGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
                       +E + +P  +   +   + +      +V         + V   L    
Sbjct: 63  VEVEIPEPEELKVEAEDIPLNIVYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNALLHHCD 122

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                 G +       +     G L       + Q L         + +           
Sbjct: 123 DLSGINGVIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKK 182

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                            K  V++          +     S + V   L  G+  +I+   
Sbjct: 183 EGGTIDAPLGRHHRDRLKYAVVKDGKRAVTHYEVLKVFNSCSLVKCTLETGRTHQIRVHM 242

Query: 206 EFFNWKVN 213
            F    + 
Sbjct: 243 AFIGHPLL 250


>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 = 60.6 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 35/235 (14%), Positives = 72/235 (30%), Gaps = 37/235 (15%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           R+   +A   G  SR  ++++I   +VKVN  + E+A   V   D+I ++          
Sbjct: 17  RLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKV-EKAKYLVKEEDNIVIEIPEPKVLEVL 75

Query: 64  --GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-------- 111
              +P+     +   L +      +V         + V   L     ++ S+        
Sbjct: 76  PQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGILYHCKDKLSSINGVIRPGI 135

Query: 112 -GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
             R+D +T GLL++  +      L     +        F       +  +     + +  
Sbjct: 136 VHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICYGVVKEDKITVDKPIGRNP 195

Query: 171 CYGDMQVTLDTQKGSNAWVTVG------------LREGKNREIKKVFEFFNWKVN 213
                   +   K +     V             L  G+  +I+      N  + 
Sbjct: 196 KDRLKMAVVKDGKNAITHFEVVERFDKFTHMRARLETGRTHQIRVHALSINHPLL 250


>gi|325115730|emb|CBZ51285.1| pseudouridine synthase, related [Neospora caninum Liverpool]
          Length = 567

 Score = 60.2 bits (144), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 21/91 (23%), Positives = 42/91 (46%), Gaps = 2/91 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-ER 72
           + +++ ++ AG+ SRRE E+ IA  +V VNG  + +  V V S   +   G  +      
Sbjct: 17  EWLARRLSLAGVLSRREAEKAIAAGQVTVNGETICQ-NVEVCSEAIVCYKGAFVPPPVMT 75

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
            +L+   KP  ++    + +   T+   +  
Sbjct: 76  PQLFGLVKPRRVLCVMEEREDMPTLHTLMRH 106


>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 = 60.2 bits (144), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 34/241 (14%), Positives = 69/241 (28%), Gaps = 32/241 (13%)

Query: 5   NIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           N V+++   QR+ + IA      SR  ++  +   +V+VNG ++ +    VM  + I + 
Sbjct: 9   NTVKDSQLGQRLDQAIAELFADFSRSRLKEWLLAGKVQVNGEVVTKPRTKVMGGEEIILQ 68

Query: 63  ----DGVPLRKAERT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
               D       +            L +      +V   +     + +   L        
Sbjct: 69  AELEDEERWEAQDIPLDIVYEDDDILVINKPRGFVVHPGAGTPDGTVLNALLHHYPSIAE 128

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH------------GQ 152
             R   V RLD +T GL+++         L     +     R                 Q
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKKRNFVREYEAIAIGRMTAGGRVEQ 188

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                        V            +      +  + + L  G+  +I+    +    +
Sbjct: 189 PIGRHSTKRTLMAVSPMGKPAITHYRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPL 248

Query: 213 N 213
            
Sbjct: 249 L 249


>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 = 60.2 bits (144), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 38/242 (15%), Positives = 72/242 (29%), Gaps = 42/242 (17%)

Query: 11  FTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
            TP R+ K +A      SR  +++      + VN   ++     V   D I +       
Sbjct: 53  QTPVRIDKFLAEKNPYQSRNRIQQAADSGFIYVNDKPVKS-NYKVRPGDVITLMLDRPKH 111

Query: 63  ------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV---- 111
                 + +PL    E   L + +K  G+V      +   T+ + +      + S     
Sbjct: 112 DTSIVAEDIPLDIVYEDDALMVINKQAGMVVHPGAGNFTGTLINAVAWHLKDLESFDAND 171

Query: 112 ------GRLDINTEGLLLLTN-------------DGGLARVLELPSTQWLRVYRVRFHGQ 152
                  R+D +T GLL++               +    R         L        G 
Sbjct: 172 PEVGLVHRIDKDTSGLLVVAKTADAKSALGKQFFNKSTHRSYNALVWGNLIDDEGTIEGN 231

Query: 153 VDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
           + +D  N L+  +                +  + G    V   L  G+  +I+   +   
Sbjct: 232 IARDPKNRLRMKVFSPDSGIGKNAVTHYRVIERFGYTTLVECILETGRTHQIRAHMKHIG 291

Query: 210 WK 211
             
Sbjct: 292 HP 293


>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 = 60.2 bits (144), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 45/278 (16%), Positives = 93/278 (33%), Gaps = 36/278 (12%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           + V+ +   QR+ + +A      SR  ++  +   +V+V+G ++ +  V VM  + I + 
Sbjct: 9   DTVKSSQLGQRLDQAVAELFTDFSRSRIKEWLLDGKVQVDGEVITKPRVKVMGGEEIILQ 68

Query: 63  ----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-- 108
               D               E   L + +KP   V          TV + L   + ++  
Sbjct: 69  AELEDEERWEAQDIPLDIVFEDEHLLVINKPRDFVVHPGAGTPDGTVLNALLHHYPQIAE 128

Query: 109 ----ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                 V RLD +T GL+++         L     +                   +++KG
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALAKRRITREYEAIAIGKMTAGGMVEKG 188

Query: 165 IVIQ---------GICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I                        +      +  + + L  G+  +I+    +    + 
Sbjct: 189 ISRHATKRTLMAVNETGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPL- 247

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L  I+YG      +  G++ E++ K++R      L  
Sbjct: 248 -LGDIAYGGRA--RIPKGASEELT-KMIRAFDRQALHA 281


>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 = 60.2 bits (144), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 80/248 (32%), Gaps = 39/248 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNG-------ILLERAAV 52
           M +K          R+ KV+++     SR ++++ + +  V++NG        ++    +
Sbjct: 1   MTEKKEFTITTETGRIDKVLSQLLPDYSRSQIQQWLKKDLVEINGQTSKGNHKVVADEKI 60

Query: 53  NVMSTDHIEVDGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
           +V   D + +D VP      +   +   L +      +V         + V   L     
Sbjct: 61  SVTIPDPVSLDLVPEDIPLDIVYEDDQVLVVNKPQGMVVHPSPGHPNGTLVNALLAHTPL 120

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVYR 146
                  R   V R+D +T GLL++         L                    +    
Sbjct: 121 SEINGVFRPGIVHRIDKDTSGLLMVAKTNEAHESLSEQLKAKSNLREYLALVHGNIEEDE 180

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTVGLREGKNREIKKV 204
                 + + KL+ +K+ IV  G          +  +       +   L  G+  +I+  
Sbjct: 181 GTIDAPIGRSKLDRMKQAIVPDG---RPAVTHFEVVERFTDYTLIRCRLETGRTHQIRVH 237

Query: 205 FEFFNWKV 212
             + N  V
Sbjct: 238 LAYINRPV 245


>gi|329667353|gb|AEB93301.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           johnsonii DPC 6026]
          Length = 304

 Score = 60.2 bits (144), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 34/245 (13%), Positives = 71/245 (28%), Gaps = 37/245 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K+  +V ++    R+ KVIA      SR +++ ++  + + VN    E+ +  V S D I
Sbjct: 3   KNYKLVIDDEKG-RLDKVIAEKITDLSRTKIKELVNDKNILVNNK-AEKVSYKVQSGDVI 60

Query: 61  EVDGVPLR--------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           +V   P++                +   + +      +V   +     + V   L     
Sbjct: 61  DVTIPPVKPLSLEAENLHLDIVYEDSDVIVVNKPQGMVVHPSAGHPDHTLVNGLLYHTRD 120

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ----------- 155
              S           +     G L       + + L         + +            
Sbjct: 121 LADSPEGFRPGIVHRIDKDTSGLLMIAKNDKARESLEKQLAEKINKREYLAIVHGNFEVK 180

Query: 156 ---------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                       N  K+  V           T+  Q  + + V   L  G+  +I+   +
Sbjct: 181 NGVINAPIGRNPNNRKQMAVNPKGKAAVTHFTVLEQFKNYSLVKCVLETGRTHQIRVHMK 240

Query: 207 FFNWK 211
           +    
Sbjct: 241 YIGHP 245


>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 = 60.2 bits (144), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 30/247 (12%), Positives = 67/247 (27%), Gaps = 40/247 (16%)

Query: 4   KNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           + +V +  +  R+ K +      ASR  ++  I    V VN   ++  +  V   D I V
Sbjct: 20  RIVVDKGQSLLRIDKFLMHRVENASRNRIQNAIELGNVLVNDKAIKS-SYKVKPLDVISV 78

Query: 63  -------DGVP--------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                  D           +   +   L +      +V    +    + V   +      
Sbjct: 79  VLPHPPRDTEVYPENIPLDIVYEDDDVLVVNKPAGLVVHPGYNNYTGTLVNGLVYHFQQL 138

Query: 108 VISVGR---------LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-- 156
               G          +D +T GLLL++ +      L     +     +       D +  
Sbjct: 139 PTLPGNDGRPGLVHRIDKDTSGLLLISKNERSMTWLARQFYEHTIARKYLALVWGDLEID 198

Query: 157 ------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                          ++      +   +      +  +      +   L  G+  +I+  
Sbjct: 199 GTVTGYIGRSIKDRRVMSIYDDPEKGKWSVTHYRVLQRMTYVTLIECELETGRTHQIRAH 258

Query: 205 FEFFNWK 211
            +     
Sbjct: 259 MKHIGHP 265


>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 = 60.2 bits (144), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 30/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I + RV+VNG    +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILEDRVQVNGKTTNKPKEKVLGGETVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-- 108
                           +   +   L +      +V   +     + +   L      +  
Sbjct: 70  QIEEEARWEPQDIPLDIVYEDSDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPEIIDV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                V RLD +T GL+++         L                               
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQLREITREYEAVAIGTMTAGGTVEEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      +  + 
Sbjct: 190 ARHSTKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHISHPLV 248


>gi|225872347|ref|YP_002753802.1| hemolysin A [Acidobacterium capsulatum ATCC 51196]
 gi|225791816|gb|ACO31906.1| hemolysin A [Acidobacterium capsulatum ATCC 51196]
          Length = 261

 Score = 60.2 bits (144), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+ K++A  G+A SR   + +I   RV VN   + +    V     + + G  LR 
Sbjct: 3  VRLDKLVAEQGLAASRERAQALILAGRVLVNEQKITKPGHAVDEAATLRLLGEDLRY 59


>gi|284048216|ref|YP_003398555.1| hemolysin A [Acidaminococcus fermentans DSM 20731]
 gi|283952437|gb|ADB47240.1| hemolysin A [Acidaminococcus fermentans DSM 20731]
          Length = 267

 Score = 60.2 bits (144), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 11/56 (19%), Positives = 21/56 (37%), Gaps = 1/56 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
            +R+   +   G   SR + + +I    V VN   +++    V     I + G  
Sbjct: 2  KKERLDVFLTEQGFFESRSKAQAVIMAGEVLVNDQKIDKPGTMVKPDAKITLLGKK 57


>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 = 60.2 bits (144), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 34/239 (14%), Positives = 69/239 (28%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I +QRV++NG  ++R    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKTWILEQRVQINGNTVDRPKEKVLGGESVAIDA 69

Query: 65  ----------VPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                      P+       +   L +      +V   +     + +   L         
Sbjct: 70  LIEEEARWEAQPISLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHHYPAIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L                               
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQAREITREYEAVAIGTMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 ARHSTKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMAHINHPLI 248


>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 = 60.2 bits (144), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 25/241 (10%), Positives = 68/241 (28%), Gaps = 40/241 (16%)

Query: 11  FTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG----- 64
               R+ K I+      +R +++  I  + +KVN   ++  +  +   D I +D      
Sbjct: 6   DEIIRIDKFISDELEEIAREKIKDFIKDKLIKVNNKAVK-PSFKLSEGDEIFIDDSLFAI 64

Query: 65  ----------VPLRKAERTRLWL----------------------YHKPIGLVTTHSDPD 92
                       + + E   +                         +K      +H   +
Sbjct: 65  AEIKAENIDLKVVYENEDYAVIDKDSDLIVHPAGKIVTGTLVNALLYKYGYDGLSHIGGE 124

Query: 93  GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152
            R  +   L    + +I + + + + +    +     + +                    
Sbjct: 125 DRPGIVHRLDKDTTGLILITKNNASYKYFKKMFETRKVDKYYYAIVFGNFDKKTGTIETF 184

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           +D+D  N  K  +   G         +  +    + + + +  G+  +I+      N  +
Sbjct: 185 MDRDPNNRRKMAVRPAGRRA-VSHYEVLREVDGFSLLRIKIETGRTHQIRVHMTHINHPL 243

Query: 213 N 213
            
Sbjct: 244 L 244


>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 = 60.2 bits (144), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 38/320 (11%), Positives = 84/320 (26%), Gaps = 52/320 (16%)

Query: 1   MKDKN-----IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNV 54
           M  K+     +V E +  +R+ + ++      SR   +++I    V  +G  +++ +  V
Sbjct: 1   MNHKDEILSFMVDEEYDRKRLDQFLSSVYPEYSRSYFQKLIKDGYVFEDGKDIKKPSYKV 60

Query: 55  MSTDHIEVDGVPLRKAERTRL-----------------WLYHKPIGLVTTHSDPDGRSTV 97
                I +    +   E   +                  +Y     +V         + V
Sbjct: 61  RKGQEITL---VIPPPETLEIKPENIPVDILFEDEDIAVVYKPAGMVVHPSPGHTSGTLV 117

Query: 98  FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ----- 152
              L    +     G+        L     G +       + + L+              
Sbjct: 118 NALLYHFRNISEYGGKERAGIVHRLDKDTAGLMIIAKSEFAHKELQKQFQERTVDKRYIA 177

Query: 153 ------VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT------------VGLR 194
                  +      L  G  I        + T      +  WV             + L 
Sbjct: 178 VVTGIVQNDHGFIDLPIGRSIYNRKKMGTEATNLRDALTEYWVKNRSEKENLTVVDIKLH 237

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
            G+  +I+  F      +          F+   L +   R +S + L   L  + +    
Sbjct: 238 TGRTHQIRVHFSAIGHPLFNDKVY---GFKKSQLRSEKMRSISDQTLYHALLAYRIAFDH 294

Query: 255 VNLDAPIYSSETLVRDRPNI 274
                 I  +   + +  + 
Sbjct: 295 PRTGEKIDITLQKLPEHISK 314


>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 = 60.2 bits (144), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 1/52 (1%)

Query: 12 TPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             R+   +AR    ASR +++R I + RV VNG+++++ A  V   D I +
Sbjct: 18 EGGRLDAYLARFLAQASRTKIQRGIREGRVTVNGVVVQKPAYTVQPGDVITL 69


>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 = 60.2 bits (144), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 63/239 (26%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V   + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKIWDKPKEKVFGGEAVAINV 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-- 108
                           +   +   L +      +V   +     + +   L      +  
Sbjct: 70  EIEEDVRFEPQDIPLDIVYEDDDILVINKPRGLVVHPGAGNPDGTVLNALLHYYPPIIDV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                V RLD +T GL+++         L                               
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTIPAQTHLVESLQLREITREYEAVAIGHMTSGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMSVHPMGKPAVTHYRIMEHFRIHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 60.2 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 32/232 (13%), Positives = 69/232 (29%), Gaps = 32/232 (13%)

Query: 13  PQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP----- 66
            QR+ +V A+  G  SR  +   I + R+ V+G +       V +   + +D        
Sbjct: 24  GQRLDQVAAQLFGEYSRSRLSTWIKEGRLTVDGAVAR-PRDTVHAGSTLVLDAEQEAQGE 82

Query: 67  ---------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-----G 112
                    +   +   L +      +V   +     + +   L  +   +         
Sbjct: 83  WIAQDIELNIVYEDEHMLVIDKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRAGIVH 142

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQ------WLRVYRVRFHGQVDQDKLN-----LL 161
           RLD +T GL+++         L     +      +  +           D          
Sbjct: 143 RLDKDTTGLMVVAKTLQAQTNLVEQLQKRTVSRIYECICIGVITAGGTIDAPIGRSSSQR 202

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           ++  V  G         +  +  S+  V V L  G+  +I+       + + 
Sbjct: 203 QRMAVTDGGKPAISHYRVLERYRSHTHVRVKLETGRTHQIRVHMTHVGYPLV 254


>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 = 60.2 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 33/247 (13%), Positives = 67/247 (27%), Gaps = 40/247 (16%)

Query: 4   KNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           + +V +  T  R+ K +      ASR  V+  I  + V VN   ++  +  V   D I V
Sbjct: 23  RIVVDKGQTLLRIDKFLMHRVENASRNRVQNAIEAENVLVNNRPVKS-SYKVKPGDLITV 81

Query: 63  -------DGVP--------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                  D           +R  +   L +      +V    +    + V   +      
Sbjct: 82  VLPHPPRDTEIYPENIPLDIRYEDDDLLIVNKPAGMVVHPGYNNYTGTLVNALVYHFNQL 141

Query: 108 VISVGR---------LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
               G          +D +T GLL++  +      L           +       D  + 
Sbjct: 142 PQLPGNDGRPGLVHRIDKDTSGLLVIAKNEWTITNLAKQFFDHTIQRKYLALVWGDLQEN 201

Query: 159 --------------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                          ++          +      +  + G    +   L  G+  +I+  
Sbjct: 202 GTVSGYIGRSLKDRRVMSVYENEDKGKWSVTHYRVLERLGYVTLIECQLETGRTHQIRAH 261

Query: 205 FEFFNWK 211
            +     
Sbjct: 262 MQSIGHP 268


>gi|302392482|ref|YP_003828302.1| hemolysin A [Acetohalobium arabaticum DSM 5501]
 gi|302204559|gb|ADL13237.1| hemolysin A [Acetohalobium arabaticum DSM 5501]
          Length = 270

 Score = 60.2 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 14 QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          +R+ K++ +     SR + +R I    V V+G L+++A   V     IE+ G     
Sbjct: 4  ERLDKLVTQRELYPSRSKAKRAIMAGLVLVDGELVDKAGTQVDVEADIEIKGKVHPY 60


>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 = 60.2 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 32/258 (12%), Positives = 76/258 (29%), Gaps = 46/258 (17%)

Query: 1   MKDKNI-VQENFTPQRVSKVIA--------RAGIASRREVERMIAQQRVKVNGILLERAA 51
           MK +   ++  +  +R+ K ++         +   SR   +++I    VKVN  + + A 
Sbjct: 1   MKQETFEIEAEYEGERLDKYLSVIFEQSKTSSNAPSRSFFQKLIRDGHVKVNDSIAK-AN 59

Query: 52  VNVMSTDHIEV------------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTV 97
             +   D + V            + +PL     +   L +      +V   +     + V
Sbjct: 60  YRLRMDDLVCVEIPDAVETPILPEDIPLDILYEDDDLLVVNKPKGMVVHPSAGHYSGTLV 119

Query: 98  FDNLPSIFS---------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL------ 142
              +              R   V R+D++T G L++  +      +     +        
Sbjct: 120 NAIMFHCKDSLSGINGEIRPGIVHRIDMDTTGSLIVCKNDESHIKIAEQIKEHSVNRRYR 179

Query: 143 -----RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLRE 195
                 V            +    +K + I             +  +  +  ++   L  
Sbjct: 180 GIVYGVVKDDEGTINAPIGRHPTNRKKMAINEKNGKPAITHYKVLERFSNYTYMEFKLET 239

Query: 196 GKNREIKKVFEFFNWKVN 213
           G+  +I+         + 
Sbjct: 240 GRTHQIRVHMASIGHPLL 257


>gi|310766696|gb|ADP11646.1| 23S rRNA pseudouridine synthase D [Erwinia sp. Ejp617]
          Length = 325

 Score = 60.2 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 29/239 (12%), Positives = 67/239 (28%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+    R+ + +A      SR  ++  I  + + VNG+++++    V+  + I +D 
Sbjct: 10  TVAESQLGHRLDQALAELFPDYSRSRIKEWILNRHITVNGVIIDKPKEKVLGGEQISIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  EIEEEARWEAQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHHFPAIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTHLVDSLQRREITREYEAVAIGRMTAGGTVDQPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      +  + 
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHISHPLV 248


>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 = 60.2 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 30/244 (12%), Positives = 77/244 (31%), Gaps = 38/244 (15%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-G 64
           V ++   +R+   IA      SR  V+++I    V VN   +++A+  +   D +E+   
Sbjct: 13  VDQDSAGKRLDVFIADQYQDISRSYVQKLIKDGLVLVN-EEVKKASYKLEEGDRMEIAMP 71

Query: 65  VP-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
            P             +   +   L +      +V         + V   +     ++ S+
Sbjct: 72  EPEVLEVLAQDIDLDIVYEDDDLLIVNKPQGMVVHPAPGNPDGTLVNAIMYHCKDKLSSI 131

Query: 112 G----------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
                                  + + + +GL        + R  E+     +   ++  
Sbjct: 132 NGVIRPGIVHRIDKNTSGLLVVAKNNASHQGLADQFKLHSITREYEMVCIGGVNWDQMTI 191

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + ++  + LK  ++  G  +     T+        ++   L  G+  +I+    +  
Sbjct: 192 DKNIGRNPKDRLKMAVLDTGGRHAVTHFTVIEHLEGYTYMKAKLETGRTHQIRVHSNYLR 251

Query: 210 WKVN 213
             + 
Sbjct: 252 HPIL 255


>gi|218437902|ref|YP_002376231.1| hemolysin A [Cyanothece sp. PCC 7424]
 gi|218170630|gb|ACK69363.1| hemolysin A [Cyanothece sp. PCC 7424]
          Length = 270

 Score = 60.2 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 13/55 (23%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
          QR+  ++    + S R+  +R+I    V+VN  ++++    V     I++   PL
Sbjct: 4  QRLDNLLVTLNLCSSRQLAQRLIRAGEVRVNQQIIDKPGTEVDPGAEIQLQAKPL 58


>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 = 60.2 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 31/248 (12%), Positives = 64/248 (25%), Gaps = 38/248 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD- 58
           K+   + E     R  K +A    G+ SR  ++ +    ++ +NG   E+    +   D 
Sbjct: 5   KEVIKITEEEKGIRADKFLALKIDGV-SRNFIQGLFDDGKILINGK-AEKGKYKLSVGDC 62

Query: 59  -----------HIEVDGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
                       +E + +PL     +   + +      +V         + V   L    
Sbjct: 63  VEVEIPEPEELKVEAEDIPLNIIYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNALLYHCD 122

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                 G +       +     G L       + Q L         + +           
Sbjct: 123 DLSGINGVIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKK 182

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                            K  V++          +     S + V   L  G+  +I+   
Sbjct: 183 EGGTIDAPLGRHHRDRLKYAVVKDGKRAVTHYEVLKVFNSCSLVKCTLETGRTHQIRVHM 242

Query: 206 EFFNWKVN 213
            F    + 
Sbjct: 243 AFIGHPLL 250


>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 = 60.2 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 69/239 (28%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I + RV++NG ++ +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILENRVQINGNVINKPKEKVLGGESVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
           +               +   ++  L +      +V   +     + +   L         
Sbjct: 70  LIEEEARWEAQDIKLDIVYEDQDILVINKSRDLVVHPGAGNPDGTVLNALLHHYPEIVDV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L                               
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGSMTAGGMVEQPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 ARHATKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHINHPLV 248


>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 = 60.2 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 31/245 (12%), Positives = 68/245 (27%), Gaps = 40/245 (16%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +  +  RV K +  R   ASR  ++  I    V VNG  ++  +  V   D I +  
Sbjct: 22  VVDKGQSLLRVDKFLMGRMENASRNRIQNAIDAGNVLVNGKTVKS-SYKVKPADEISIVF 80

Query: 63  -----DGVP--------LRKAERTRLWLYHKPIGLVTTHSDPDGRS------TVFDNLPS 103
                D           +   +   L +      +V    +    +        F+ LP 
Sbjct: 81  PHPPRDTEVYPEDIPLDIVYEDNDLLVVNKPAGMVVHPGYNNYTGTLVNALAFHFEQLPQ 140

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------- 155
           +       G +    +    L         +   + Q+      R +  +          
Sbjct: 141 LPGNEGRPGLVHRIDKDTSGLLLISKNEITMTKLAKQFFDHSITRKYIALAWGDIAENGT 200

Query: 156 ---------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                        ++      +   +     T+  + G    ++  L  G+  +I+   +
Sbjct: 201 VTGFIGRSLKNRIVMDVYDDEEKGKWSVTHYTVLERLGYVTLISCQLETGRTHQIRAHMQ 260

Query: 207 FFNWK 211
                
Sbjct: 261 HIGHP 265


>gi|239618278|ref|YP_002941600.1| hemolysin A [Kosmotoga olearia TBF 19.5.1]
 gi|239507109|gb|ACR80596.1| hemolysin A [Kosmotoga olearia TBF 19.5.1]
          Length = 268

 Score = 60.2 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 13/51 (25%), Positives = 27/51 (52%), Gaps = 1/51 (1%)

Query: 15 RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          R+ +++ AR   +SR     +I Q +V +NG ++++    V     IE++ 
Sbjct: 6  RLDELLVARNFFSSRSRASDIIKQGKVSINGKIVKKPGKKVPLDIKIEIND 56


>gi|313897410|ref|ZP_07830953.1| ribosomal RNA large subunit methyltransferase J [Clostridium sp.
          HGF2]
 gi|312957780|gb|EFR39405.1| ribosomal RNA large subunit methyltransferase J [Clostridium sp.
          HGF2]
          Length = 259

 Score = 60.2 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 12/51 (23%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+   ++  G+  SR   +  I + RV VNG + +++++ V  +  I+++
Sbjct: 1  MRLDVYLSTQGLCDSRARAQDAIQEGRVTVNGRIAKKSSMPVDDSMDIKLE 51


>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 = 60.2 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 29/239 (12%), Positives = 64/239 (26%), Gaps = 40/239 (16%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGIL-LERAAVNVMSTDHIEV----DGVP-- 66
           +R+ K I+     +R + + +I Q+ V ++    + +    V     I +    +     
Sbjct: 10  ERIDKYISDNSEITRNDAKALIEQEAVYIDDKKFVRKPNYMVREGMVITILRLLEKETNI 69

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL---- 114
                   +R  +   L L      +V         + V   +    + +     L    
Sbjct: 70  EAVNMPLDIRYEDDNLLVLNKPSGLVVHPAPGHLNDTLVNALMYHFKNNLSDTNGLLRLG 129

Query: 115 ------------------DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
                             +     L  +  +  + R         L     + +  + +D
Sbjct: 130 IVHRIDKDTSGLLIIAKDNETHNELAKMLKNHQIKRTYIAICKGILPNKVTKINLPIQRD 189

Query: 157 KLNLLKKGIVIQGI---CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             N     I   G     Y  +  T        + V   L  G+  +I+    +    V
Sbjct: 190 AKNRKLMSIHKDGKSSVTYVHLLKTFYIDNKPYSLVKCELETGRTHQIRVHLAYIKHPV 248


>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 = 60.2 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 35/235 (14%), Positives = 72/235 (30%), Gaps = 37/235 (15%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           R+   +A   G  SR  ++++I   +VKVN  + E+A   V   D+I ++          
Sbjct: 29  RLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKV-EKARYLVKEEDNIVIEIPEPKVLEVL 87

Query: 64  --GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-------- 111
              +P+     +   L +      +V         + V   L     ++ S+        
Sbjct: 88  PQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGILYHCKDKLSSINGVIRPGI 147

Query: 112 -GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
             R+D +T GLL++  +      L     +        F       +  +     + +  
Sbjct: 148 VHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICYGVVKEDKITVDKPIGRNP 207

Query: 171 CYGDMQVTLDTQKGSNAWVTVG------------LREGKNREIKKVFEFFNWKVN 213
                   +   K +     V             L  G+  +I+      N  + 
Sbjct: 208 KDRLKMAVVKDGKNAITHFEVVERFDKFTHMRARLETGRTHQIRVHALSINHPLL 262


>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 = 60.2 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 65/239 (27%), Gaps = 38/239 (15%)

Query: 13  PQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP----- 66
            QR+ + +       SR  ++++I    V +NGI++ + +  V + D   ++  P     
Sbjct: 38  GQRLDRALVELVPEFSRSYLQQLIDLGGVTINGIVIHKPSTRVKAADVGTIELRPTPQSQ 97

Query: 67  ----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-----PSIFSRVISV 111
                     +   +   + +      +V         + +   L          R   V
Sbjct: 98  AFKPETMALNVVFEDEHLMVINKPAGLVVHPAPGNWSGTLLNGLLARDAKAMNLPRAGIV 157

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---- 167
            RLD +T GL+++     +   L           +              ++    I    
Sbjct: 158 HRLDKDTSGLMVVARTRPVMDALIRSIAAREVSRQYVALAHGPWTGNRRVEINAPIGRDP 217

Query: 168 -------------QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                 V L        WV   L  G+  +I+         + 
Sbjct: 218 RNRLRMAVVDLARNPGKLARTDVELLQNCDQGCWVLCTLHTGRTHQIRVHMAMIGHPLV 276


>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 = 60.2 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 29/245 (11%), Positives = 74/245 (30%), Gaps = 42/245 (17%)

Query: 8   QENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
            +   P RV K +      A+R ++++   +  + VN  ++++    V + D ++V    
Sbjct: 34  SKGQEPLRVDKFLMNFIENATRNKIQKAAKEGNIYVNDAVVKQ-NYKVKAGDEVKVLFEH 92

Query: 63  ---------DGVPLRKAE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                    + +PL         L +      +V         + +   +    +   + 
Sbjct: 93  PPYEMLLTPEDIPLNIVHEDDDVLVVNKPAGMVVHPGHGNYSGTLINALVFHFDNLPNNS 152

Query: 112 -------GRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVYRVRFHG 151
                   R+D +T GLL++         L                    +   +    G
Sbjct: 153 SNRPGLVHRIDKDTSGLLVVAKTEHAMTHLSKQFFNKTSSREYIALVWGNVEDDQGTIEG 212

Query: 152 QVDQDKLNLLKKGIVIQG---ICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
            + +   N L+  + ++               +  + G    ++  L  G+  +I+   +
Sbjct: 213 HIGRHPKNRLQNTVFLEDDADEKGKPAVTHYKVIERLGYVTLLSCKLETGRTHQIRVHLK 272

Query: 207 FFNWK 211
                
Sbjct: 273 HIGHT 277


>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 = 60.2 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 32/265 (12%), Positives = 81/265 (30%), Gaps = 35/265 (13%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
             V+++   QR+ + +A      SR  ++  + + ++ VNG ++ +    VM  + I V 
Sbjct: 9   QTVKDSQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGDVITKPRTKVMGGEVITVQ 68

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   +   + +      +V   +    ++ +   L        
Sbjct: 69  AELEDEQRWEAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADKTVLNALLFHYPPIAE 128

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   RLD +T GL+++         L     +                   ++ K 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAIVIGTMTAGGMIDKP 188

Query: 165 IVIQ-----------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I                 +      +      +  + + L  G+  +I+    +    + 
Sbjct: 189 IGRHSTKRTLMSVSPMGKHAVTHYRVAEHFREHTRLRLRLETGRTHQIRVHMAYLQHPL- 247

Query: 214 RLIRISYGPFQLGTLLAGSTREVSK 238
            L   +YG      +  G++ E+++
Sbjct: 248 -LGDTAYGGRA--RIPKGASEELTE 269


>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 = 60.2 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 25/239 (10%), Positives = 63/239 (26%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  +++ ++ 
Sbjct: 10  TVSENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKMCDKPKEKVLGGENVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEDVRFEAQDIPLNIVYEDDDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--- 156
                  R+       +     +        +  L   + ++  V           +   
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVEQPI 189

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMSVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 60.2 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 29/249 (11%), Positives = 63/249 (25%), Gaps = 42/249 (16%)

Query: 4   KNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           + +     T  R+ K +  R   A+R  +++      + VNG  ++     +   D + +
Sbjct: 34  RTVADPGQTLIRIDKFLVDRMNNATRSRIQQAAEAGAIFVNGRPVKS-NYRIKPGDVVTL 92

Query: 63  D-------------GVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           +              +P  +   +   L +      +V         + V      +   
Sbjct: 93  ELLRPRRELEIIPEDIPLDIVYEDDVLLVINKPAGLVVHPGHGNYTGTLVNALAYYLRED 152

Query: 108 VISV---------GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
                         R+D +T GLL++         L             R       D  
Sbjct: 153 PEYDPMDPSLGLVHRIDKDTSGLLVVAKRAEAKSDLCKQFYYKTTHRSYRALVWGRFDYP 212

Query: 159 --------------NLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIK 202
                          L        G           +  +    +W+   L  G+  +I+
Sbjct: 213 IGTITGNIGRDLKDRLQMAVFPPDGDIGKPAVTHYQVLEELAYVSWIECRLETGRTHQIR 272

Query: 203 KVFEFFNWK 211
              +     
Sbjct: 273 AHMKHIGHT 281


>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 = 60.2 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 29/239 (12%), Positives = 67/239 (28%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+    R+ + +A      SR  ++  I  + + VNG+++++    V+  + I +D 
Sbjct: 10  TVAESQLGHRLDQALAELFPDYSRSRIKEWILNRHITVNGVIIDKPKEKVLGGEQISIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  EIEEEARWEAQDIPLDIVYEDEDILVVNKPRDLVVHPGAGNPDGTVLNALLHHFPAIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTHLVDALQRREITREYEAVAIGRMTAGGTVDQPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      +  + 
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMSHISHPLV 248


>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 = 59.8 bits (143), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 30/240 (12%), Positives = 70/240 (29%), Gaps = 32/240 (13%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I   +V V+G ++ +  + +M  + I V  
Sbjct: 10  TVNENQLGQRLDQALAELFPDYSRSRIKEWILADKVSVDGEIVNKPRLKMMGGEVIVVQA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEDEQRFEAQDIPLNIVYEDDDIIVINKPRDLVVHPGAGCPDGTVLNGLLYHYPDIAEV 129

Query: 111 V-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR------------FHGQV 153
                  RLD +T GL+++  +      L     +  +  R                 + 
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKNIPTQTRLVRALQKRKKFTREYEAIALGNMTGGGMIEKP 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                       V +          +     ++  + + L  G+  +I+    + N  + 
Sbjct: 190 IGRHSTKRTHMAVQELGKPAITHYRVVEHFRAHTRLRLRLETGRTHQIRVHMAYLNHPLV 249


>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 = 59.8 bits (143), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 31/245 (12%), Positives = 66/245 (26%), Gaps = 41/245 (16%)

Query: 10  NFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
                R+   +++     SR  ++++I Q  + +N  +       V S D ++V      
Sbjct: 16  QDKGDRIDLWLSQNLDQISRSHLQKLIEQGNIYLNNQVCLNKKTKVNSGDRLQVFLPPPE 75

Query: 63  ----------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
                           D   +   +   L ++  P     T                   
Sbjct: 76  PLELQPEPIPLDILYEDDSLIIINKSAGLVVHPAPGHTTGTLVHGLLYHCPNLVGIGGIQ 135

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELP------STQWLRVYRVRFHGQVDQD---- 156
           R   V RLD +T G +++       + L+          ++L V       +        
Sbjct: 136 RPGIVHRLDKDTTGAIVVAKTDYAHQHLQAQLKAKTARREYLGVVYGVPRHEDTHQGTIN 195

Query: 157 --------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                       +    V  G         +  + G+   V   L  G+  +I+    + 
Sbjct: 196 VPIGRHRGDRKKMAVVPVENGGREAITHWQIVERLGNYTLVEFRLETGRTHQIRVHSSYI 255

Query: 209 NWKVN 213
              + 
Sbjct: 256 GHPIV 260


>gi|150016581|ref|YP_001308835.1| hemolysin A [Clostridium beijerinckii NCIMB 8052]
 gi|149903046|gb|ABR33879.1| hemolysin A [Clostridium beijerinckii NCIMB 8052]
          Length = 269

 Score = 59.8 bits (143), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 25/176 (14%), Positives = 52/176 (29%), Gaps = 3/176 (1%)

Query: 11  FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
              +R+  ++   GI  SR + +  I + +V V+G  +++A   V S  +IE  G  L+ 
Sbjct: 3   EKKERLDLLLVEKGIINSREKAKACIMEGKVYVDGQKVDKAGEKVSSNANIEYRGETLKY 62

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             R  L L         +  +                 ++  G   + +  +        
Sbjct: 63  VSRGGLKLEKAMKTYSISLENKVCMDIGAST-GGFTDCMLQNGASKVFSVDVGYGQFAWK 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           L     +   +   +  V      +      +     I         + L    G 
Sbjct: 122 LRTDERVVCMERTNIRYVTLEDIGEHLDFASIDVSF-ISLKKIMPATINLLKDDGE 176


>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 = 59.8 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 33/242 (13%), Positives = 73/242 (30%), Gaps = 38/242 (15%)

Query: 8   QENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
            EN   +R+ K +    I  A+R  V+++I    V++ G  + ++   +  T+ I V+  
Sbjct: 12  NENDKGKRIDKFL-NELIDDATRSYVQKIIDNGLVEIQGKKITKSGNKLKGTEIIVVNIP 70

Query: 64  -GVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
               L              +   + +   P  +V         + V   L  I       
Sbjct: 71  EDEVLDLTPEDIPLDIIYEDSDIVVINKAPNLVVHPAHGNYSGTLVNALLYHIKDLSTIN 130

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRVRFH 150
           G +       L     G +       +   L                     +    R  
Sbjct: 131 GVIRPGIVHRLDKDTSGVIVVAKNDEAHGKLSEMFKEKTLEKIYVCIAKGIFKEKSGRIK 190

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + +D  +  K  +V +          +  +  +++ V V +  G+  +I+   +  N 
Sbjct: 191 TLIGRDSRDRKKMAVVNENGKIAISNYEVIDEGKNHSLVKVRIETGRTHQIRVHMKHLNH 250

Query: 211 KV 212
            +
Sbjct: 251 PI 252


>gi|213620882|ref|ZP_03373665.1| putative ribosomal large subunit pseudouridine synthase B
           [Salmonella enterica subsp. enterica serovar Typhi str.
           E98-2068]
          Length = 153

 Score = 59.8 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 30/121 (24%), Positives = 51/121 (42%), Gaps = 15/121 (12%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            + GRLD ++EGLL+LTNDG L   L  P  +  ++Y V+  G  D   L  L+ G+ + 
Sbjct: 33  YAAGRLDRDSEGLLVLTNDGALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLN 92

Query: 169 GICYGDM---------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                     + +    +W+ V L EG+N +++++         
Sbjct: 93  DGPTLPAGIEIVAEPDWLWPRTPPIRERKNIPTSWLKVTLYEGRNHQVRRMTAHVGHPTL 152

Query: 214 R 214
           R
Sbjct: 153 R 153


>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 = 59.8 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 26/239 (10%), Positives = 61/239 (25%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VN  L ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNDQLCDKPKEKVLGGERVSINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  EIDEEVRFEPQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--- 156
                  R+       +     +        +  L   + ++  V           +   
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVEEPI 189

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>gi|15229266|ref|NP_189920.1| unknown protein [Arabidopsis thaliana]
 gi|7263609|emb|CAB81575.1| putative protein [Arabidopsis thaliana]
 gi|332644266|gb|AEE77787.1| Pseudouridine synthase family protein [Arabidopsis thaliana]
          Length = 74

 Score = 59.8 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 16/69 (23%), Positives = 36/69 (52%), Gaps = 2/69 (2%)

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
             + +G +++GI      V L  ++     AW+ + + EG+N E++++ +    +V+ L 
Sbjct: 1   MAISEGTMVEGIHCVPDLVELMPKQHDIPRAWLRIVVHEGRNHEVRELVKNVGLEVDSLK 60

Query: 217 RISYGPFQL 225
           R+  G  +L
Sbjct: 61  RVRIGGVRL 69


>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 = 59.8 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 26/242 (10%), Positives = 65/242 (26%), Gaps = 40/242 (16%)

Query: 9   ENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
                +R+ K +  +      SR +V+  I    V VN   ++     + S DH+ +   
Sbjct: 19  PEQAGERIDKFVTDSLNEDSISRTQVQEWIKSGAVLVNQNTVK-PNYKLSSGDHVGIRVP 77

Query: 63  ---------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                    + +P  +   +   + +      +V         + V   +          
Sbjct: 78  EPEDAAIVAEDIPLDIVYEDADVIVINKPRGMVVHPAPGHSSGTVVNALMYHCKDLSGIN 137

Query: 112 GRLDI---------------------NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
           G L                           L     D  ++R         L   +    
Sbjct: 138 GVLRPGIVHRIDKDTSGLLMAAKNDLAHVSLAEQLKDHSVSRKYIALVHGNLPHDQGTID 197

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTL-DTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
             + +D+ +     +  +   +      + +        V + L  G+  +I+   ++  
Sbjct: 198 APIGRDQNDRKLFTVTDRNSKHAVTHFAVLERIADDYTIVELQLETGRTHQIRVHMKYIG 257

Query: 210 WK 211
           + 
Sbjct: 258 YP 259


>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 = 59.8 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 34/245 (13%), Positives = 71/245 (28%), Gaps = 37/245 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K+  +V ++    R+ KVIA      SR +++ ++  + + VN    E+ +  V S D I
Sbjct: 3   KNYKLVIDDEKG-RLDKVIAEKITDLSRTKIKELVNDKNILVNNK-AEKVSYKVQSGDVI 60

Query: 61  EVDGVPLR--------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           +V   P++                +   + +      +V   +     + V   L     
Sbjct: 61  DVTIPPVKPLSLEAENLHLDIVYEDSDVIVVNKPQGMVVHPSAGHPDHTLVNGLLYHTRD 120

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ----------- 155
              S           +     G L       + + L         + +            
Sbjct: 121 LADSPEGFRPGIVHRIDKDTSGLLMIAKNDKARESLEKQLAEKINKREYLAIVHGNFEVK 180

Query: 156 ---------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                       N  K+  V           T+  Q  + + V   L  G+  +I+   +
Sbjct: 181 NGVINAPIGRNPNNRKQMAVNPKGKAAVTHFTVLEQFKNYSLVKCVLETGRTHQIRVHMK 240

Query: 207 FFNWK 211
           +    
Sbjct: 241 YIGHP 245


>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 = 59.8 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 27/238 (11%), Positives = 68/238 (28%), Gaps = 31/238 (13%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T  R+ + +A      SR  ++  I    V V+G+++ +    V     IE+
Sbjct: 8   KSEISATQTGLRLDQALAELFPDYSRTRIKEWILSDAVYVDGVMVNKPREKVFELQRIEI 67

Query: 63  DGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           +                 +   +   L +  +   +V   +     + +   L    +  
Sbjct: 68  NATLEEEVHAAAQAIELDIVYEDDDILVINKQAGLVVHPGAGNADGTLMNALLHHCPNIE 127

Query: 109 ISV-----GRLDINTEGLLLLTNDGGLARV------LELPSTQWLRVYRVRFHGQVDQD- 156
                    RLD +T GL+++                   + ++  +           D 
Sbjct: 128 HVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIVLGTMTAGGTVDE 187

Query: 157 ----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                        V            +  +  ++  + + L  G+  +I+    +   
Sbjct: 188 PIGRHPTKRTHMAVHHSGKPAVTHYRVAEKFRNHTRLRLRLESGRTHQIRVHMAYIGH 245


>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 = 59.8 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 34/244 (13%), Positives = 80/244 (32%), Gaps = 39/244 (15%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           I  +   P R+ K +      A+R ++++   +  + VN +++++    V + D I+V  
Sbjct: 58  IASKGQEPLRIDKYLMNFIENATRNKIQQAAKEGHIWVNDLVVKQ-NYKVKAGDQIKVMF 116

Query: 63  -----------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                      + +PL     +   + +   P  +V         + +   L  +    +
Sbjct: 117 THPPYEFLLTPEDIPLDVVYEDSDLMVVNKPPGMVVHPGHGNYSGTLINALLFHVKDLPL 176

Query: 110 S-------VGRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVYRVRF 149
           +       V R+D +T GLL++         L                    +   +   
Sbjct: 177 NADERPGLVHRIDKDTSGLLVVAKTAKAMTHLAKQFFDKTSEREYVAIVWGNVEEEQGTV 236

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
            G + +   N L+  +   G    +      +  + G    V+  L  G+  +I+   + 
Sbjct: 237 RGHIGRHPKNRLQMAVFPDGDQGKEAVTHYKVMERLGYVTLVSCVLETGRTHQIRAHMKH 296

Query: 208 FNWK 211
               
Sbjct: 297 IGHT 300


>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 = 59.8 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 36/235 (15%), Positives = 77/235 (32%), Gaps = 39/235 (16%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--LRK-- 69
           +R+   ++R    SR    ++I  ++V+VNG+++ + +  +   + IE D  P  L+   
Sbjct: 16  ERIDSALSRMLGLSRSAAGKLIDDEKVRVNGVVVAK-SHRLSINEIIEADLEPPALKPAP 74

Query: 70  -------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR--------- 113
                   E   L + +KP+G+           TV DNL +   R+ + G          
Sbjct: 75  IVGMDIVYEDEDLVVVNKPVGVAAHGGPGWDGPTVIDNLEAAGFRISTSGPPERKGIVHR 134

Query: 114 -------------LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
                         ++    L     +  + +      +      +      + +     
Sbjct: 135 LDVGTSGAMAVAKSELAYTKLKHAFKERRVHKTYHALVSGHPDPAKGTIDAPIARHPSKE 194

Query: 161 LKKGIVIQGICYGDMQVTLDTQK--GSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +  +V  G           TQ+     A + + L  G+  +I+  F        
Sbjct: 195 WRMAVVAGG---RPAITHYQTQELLPGAALLDITLETGRTHQIRVHFSAIGHPCV 246


>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 = 59.8 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 34/256 (13%), Positives = 74/256 (28%), Gaps = 43/256 (16%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M + N +V ENF  +R+ +V+A+     SR +V ++I  + +K+NG +L+  +  V S D
Sbjct: 1   MNNYNFVVDENFDQKRIDQVVAKQYPKISRSKVSKIIKTELLKLNGQILKDPSHKVKSGD 60

Query: 59  HIEVDG---VPLRKAERTRLWLY-----------HKPIGLVTTHSDPDGRSTVFDNLPSI 104
            IE +      +    +                      +V   +     + V   L   
Sbjct: 61  QIEFENLIEETINLIPKKMDLNIIFEDQDIIIIDKPIGMVVHPGAGNYEDTMVNGLLYHC 120

Query: 105 FSRVISVGRLDIN-------------------TEGLLLLTNDGGLARVLELPSTQWLRVY 145
            + +  +   D                      +    +        +          + 
Sbjct: 121 KNNLSGMNGEDRPGIVHRIDKDTSGLLVVAKNDQAHAFIAKQFEEHSIKRSYLVFVYGIL 180

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGIC--------YGDMQVTLDTQKGSNAWVTVGLREGK 197
           R            N   +  +   +         Y  ++V    +    + V   L  G+
Sbjct: 181 RPLHGKIETLIGRNKTNRQKMSADVIRGKDAITNYETLEVFKGNKIPDISLVKCILETGR 240

Query: 198 NREIKKVFEFFNWKVN 213
             +I+         + 
Sbjct: 241 THQIRVHMSHKGNPIL 256


>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 = 59.8 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 39/244 (15%), Positives = 75/244 (30%), Gaps = 40/244 (16%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +     RV K +  R   ASR  +++      V  N   ++  +  V   D I V  
Sbjct: 33  VVDKGQEMMRVDKYLFDRLTNASRNRIQKAADAGFVMANDKPVKS-SYKVKPLDVITVMM 91

Query: 63  -----DGVPLR-------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                +   +          E   L + +KP GLV      +   T+ + +         
Sbjct: 92  DRPRYENEVIPEDIPLDIVYEDKYLMVVNKPAGLVVHPGHGNYHGTLVNAIAWHMKDIPD 151

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-- 158
                  V  V R+D +T GLL++         L L         R R     + ++   
Sbjct: 152 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKTTKRRYRALVWGNVEQDEG 211

Query: 159 -----------NLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                      + ++  ++      +      +  + G    V   L  G+  +I+   +
Sbjct: 212 TIIGNVGRNPKDRMQMTVLPDDQGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMK 271

Query: 207 FFNW 210
               
Sbjct: 272 HIGH 275


>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 = 59.8 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 35/255 (13%), Positives = 77/255 (30%), Gaps = 46/255 (18%)

Query: 1   MKDKN-IVQENFTPQRVSKVIA--RAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M+ +  +V++    QR+ + ++    G+ SR  ++ ++A   V  NG L+ + ++ + + 
Sbjct: 1   MEQREFVVEQETAGQRIDRFLSGEDTGL-SRSALQALVADGHVLCNGRLVAK-SLKLKAG 58

Query: 58  DHIEV---DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           D I +   D  P+              +   L +      +V         + V   L  
Sbjct: 59  DTIVLEIPDAKPIEAVPQDIPLEIVYEDEHLLVVNKPKGMVVHPAPGNPDGTLVNALLWH 118

Query: 104 IF---------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD 154
                       R   V R+D +T GLL++  D      L             R      
Sbjct: 119 CKGSLSGIGGEIRPGIVHRIDKDTSGLLVVAKDDATHIGLSQQMAVHSVERAYRTIVYGG 178

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW-----------------VTVGLREGK 197
             +     +   +        ++ +      +                   +   L+ G+
Sbjct: 179 FAQDEGFVES-NLGRSKTDRKKMAVYPASEPHTKYAYTGYQVLERLNNFTMLECRLKTGR 237

Query: 198 NREIKKVFEFFNWKV 212
             +I+         V
Sbjct: 238 THQIRVHMASIQHPV 252


>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 = 59.8 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 29/251 (11%), Positives = 73/251 (29%), Gaps = 41/251 (16%)

Query: 1   MKDKNIVQ-ENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M+ K  +        R+   +++     SR  ++ +I  + V+VNG   +++   + S D
Sbjct: 1   MESKKFLVCSEEENMRLDVFLSKCFQDKSRSYIQNVIEYKLVEVNGK-AKKSNYKIKSGD 59

Query: 59  HIEV------------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           +IE+            + +PL     ++  + +      +V         + V   L   
Sbjct: 60  NIEITIPDPVNLNIQSEDIPLDILYEDKDVIVVNKPQGMIVHPAPGVYEGTLVNALLNHC 119

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                  G         +     G L       S   L   +      + ++ + L++  
Sbjct: 120 RDLSGINGVTRPGIVHRIDKDTSGILVVAKNDNSHNKL--AKQLKDHSMTREYIALVEGV 177

Query: 165 IVIQGICY----------------------GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           + +                                 +  +  +N  +   L  G+  +I+
Sbjct: 178 VKLDEGTVDEPIARHPKDKIKMAVCVNGKRAITHYKVIKRFKNNTLIKCILETGRTHQIR 237

Query: 203 KVFEFFNWKVN 213
               +    + 
Sbjct: 238 VHMAYIGHPLV 248


>gi|154483518|ref|ZP_02025966.1| hypothetical protein EUBVEN_01222 [Eubacterium ventriosum ATCC
           27560]
 gi|149735428|gb|EDM51314.1| hypothetical protein EUBVEN_01222 [Eubacterium ventriosum ATCC
           27560]
          Length = 251

 Score = 59.8 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 16/64 (25%), Positives = 26/64 (40%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            +  I++   +  R+  +IA A   SR  +   I   +V VNG ++          D I 
Sbjct: 163 PEFKIIKGTISNIRLDSLIATAFGTSRSSIISFIESGKVFVNGKMVTSNGHQPKPDDIIS 222

Query: 62  VDGV 65
           V G 
Sbjct: 223 VRGK 226


>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 = 59.8 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 32/232 (13%), Positives = 68/232 (29%), Gaps = 32/232 (13%)

Query: 13  PQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP----- 66
            QR+ +V A+  G  SR  +   I   R+ V+G +       V +   + +D        
Sbjct: 21  GQRLDQVAAQLFGEFSRSRLSTWIKDGRLTVDGAVAR-PRDTVHAGSTLVLDAEQEAQGE 79

Query: 67  ---------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-----G 112
                    +   +   L +      +V   +     + +   L  +   +         
Sbjct: 80  WVAQDIELNIVYEDEHLLVIDKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRAGIVH 139

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQ------WLRVYRVRFHGQVDQDKLN-----LL 161
           RLD +T GL+++         L     +      +  +           D          
Sbjct: 140 RLDKDTTGLMVVAKTLQAQTNLVEQLQKRSVSRIYECICIGVITAGGTIDAPIGRSSSQR 199

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           ++  V  G         +  +  S+  V V L  G+  +I+       + + 
Sbjct: 200 QRMAVTDGGKPAISHYRVLERYRSHTHVRVKLETGRTHQIRVHMSHVGYPLV 251


>gi|254995115|ref|ZP_05277305.1| sfhb-like protein [Anaplasma marginale str. Mississippi]
          Length = 328

 Score = 59.8 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 27/245 (11%), Positives = 68/245 (27%), Gaps = 38/245 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH------- 59
           V +    QR+ K+I+ A   SR   + +IA  +V ++G ++   +    + D        
Sbjct: 9   VTKEDDQQRIDKLISCALEISRNRAQGLIAGGQVTISGRVINNNSYLTKTGDVYTIVTAV 68

Query: 60  ---------------IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDP------------- 91
                          +  +   +   ++      H   G+                    
Sbjct: 69  QKPSTLSPNYDIDLKVVYEDHDVIVIDKDPYIAVHPGNGIEHHTITNALLARFGAGLQSV 128

Query: 92  --DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
               R  +   L    S ++   + +     L     + G  +     +       R   
Sbjct: 129 GSSSRPGIVHRLDKDTSGLMVAAKTENAYYRLSEELANQGFKKEYLAVAWGIPCPKRGVI 188

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFF 208
           H  +   + ++        G      +  ++ + G   + +   L  G+  +I+      
Sbjct: 189 HTNIRVKRSDITMMEAANSGGKPAKTEYEVEQELGEVASLIRCTLHTGRTHQIRVHMSHI 248

Query: 209 NWKVN 213
              + 
Sbjct: 249 GHSIV 253


>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 = 59.8 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 29/245 (11%), Positives = 67/245 (27%), Gaps = 40/245 (16%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +  +  R+ K +  R   ASR  ++  I    V VN   ++ A+  V   D I +  
Sbjct: 22  VVDKGQSLLRIDKFLMHRMENASRNRIQNAIEAGNVLVNQKTVK-ASYKVKPADEISIVF 80

Query: 63  -----DGVP--------LRKAERTRLWLYHKPIGLVTTHSDPDGRS------TVFDNLPS 103
                D           +   +   L +      +V    +    +        F+ LP 
Sbjct: 81  PHPPRDTEVYPEDIPLDIVYEDNDLLVVNKPAGMVVHPGYNNYTGTLVNALAFHFEQLPQ 140

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL--- 160
           +       G +    +    L         +   + Q+      R +  +    +     
Sbjct: 141 LPGNEGRPGLVHRIDKDTSGLLLISKNEITMTRLAKQFFDHTITRKYVALAWGDIEKDGT 200

Query: 161 --------------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                         +      +   +      +  + G    ++  L  G+  +I+   +
Sbjct: 201 VTGYIGRSAKNRIVMDVYDDEEKGKWSVTHYAVLERLGYVTLISCQLETGRTHQIRAHMQ 260

Query: 207 FFNWK 211
                
Sbjct: 261 HIGHP 265


>gi|75764813|ref|ZP_00744194.1| Ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
 gi|74487697|gb|EAO51532.1| Ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
          Length = 192

 Score = 59.8 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 25/146 (17%), Positives = 41/146 (28%), Gaps = 20/146 (13%)

Query: 12  TPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGV 65
             +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V   D  
Sbjct: 14  KNERIDKFVA--GINNEWSRSQVQQWIKDDVVTVNGKAVKV-NYKVKEEDEITVTIPDPE 70

Query: 66  PLRKAER-----------TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
            L                  L +      +V         + V   +          G +
Sbjct: 71  ALDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGINGVM 130

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQ 140
                  +     G L       + +
Sbjct: 131 RPGIVHRIDKDTSGLLMVAKNDMAHE 156


>gi|319403704|emb|CBI77289.1| ribosomal large subunit pseudouridine synthase D [Bartonella
           rochalimae ATCC BAA-1498]
          Length = 333

 Score = 59.4 bits (142), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 33/263 (12%), Positives = 78/263 (29%), Gaps = 52/263 (19%)

Query: 3   DKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
            ++I  EN   QR+ + +A+   G  SR  ++ +I +  +K++G L++     + S   I
Sbjct: 2   TQHITNENACGQRIDQWLAKQYKGELSRSRLQTLIREGYLKIDGQLIKEPKTKLKSNQII 61

Query: 61  EV----------DGVP----LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           E+           G      +   +   + +      +V   +     + V   +     
Sbjct: 62  ELTIPTPNEAQPQGEALVLDILFEDNHIIVINKPAGLVVHPGNGNWTGTLVNGLIYHCRD 121

Query: 107 ---------RVISVGRLDINTEGLLLLTNDGGLARV-----------------LELPSTQ 140
                    R   V RLD +T G++++  +    R                         
Sbjct: 122 SLSGIGGIKRPGIVHRLDKDTSGVMVIAKNDLAHRNLNAQFADHGRTSALDRRYHAVIWG 181

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY--GDMQVTLDTQKGSN--------AWVT 190
                       + +   +  K+ +V     +    +      +K           + + 
Sbjct: 182 SPNRNIATIDTFLARSSRDRTKRTVVHSEYAHARRAITHFSLLEKYGTCNDTTSLASLLE 241

Query: 191 VGLREGKNREIKKVFEFFNWKVN 213
             L  G+  +I+         + 
Sbjct: 242 CRLETGRTHQIRVHMSHIGHPLI 264


>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 = 59.4 bits (142), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 27/237 (11%), Positives = 66/237 (27%), Gaps = 38/237 (16%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--------VDGV 65
           R+ + +A+     SR  ++ +I Q  +++NG +       V S D +         +D  
Sbjct: 13  RLDRWLAQKLPDLSRSRLQTLIEQGNLQLNGTICTDKKTLVKSGDRLHLLIPPVKPLDLQ 72

Query: 66  P------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           P      +   +   + +      +V      +  + V   L    +     G       
Sbjct: 73  PQDIPLDILYEDDQLIIINKPAGLVVHPSPGHEQGTLVNALLSHCSNLAGIGGVQRPGIV 132

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-----------------------D 156
             L     G L       +   L+        + +                         
Sbjct: 133 HRLDKDTTGALVVAKTDYAHHHLQQQLKAKTARREYLGIVYGVPKTTSGKINLSIGRHPI 192

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +   +    + +G         +  + G+ + +   L  G+  +I+   +  N  + 
Sbjct: 193 ERKKMAVVPLEKGGREAITHWEILERLGNYSLIYFRLETGRTHQIRVHCQAMNHPIV 249


>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 = 59.4 bits (142), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 31/243 (12%), Positives = 67/243 (27%), Gaps = 32/243 (13%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILL-ERAAVNVMSTD 58
           +  +  + E     R+   ++R     SR  V+ +I + +V VNG  +       V    
Sbjct: 2   ISKRFQIDEENANNRIDIFLSRKFDSLSRGIVQGLIDEGKVLVNGKTVDRDYKTKVDDQI 61

Query: 59  HIEVDGVP------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
            IE D               +       L +       V   +     + +   L     
Sbjct: 62  EIEFDLETNNADLPQDINLNIVFENNDLLIIDKHAGLTVHPGAGQKDSTLINGLLYMYPD 121

Query: 107 RVISV-----GRLDINTEGLLLLTNDGGLARV------------LELPSTQWLRVYRVRF 149
           +          RLD +T GL+++                               +     
Sbjct: 122 QKKIPRYGVVHRLDKDTSGLMIIARTLESHTNLTDLIQTRKIKRNYYALVHGQPIAGNTI 181

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +   N L   +  +G         +  +  + + + V L  G+  +I+   +   
Sbjct: 182 DKPIGRHPKNRLLFCVK-EGGREAITHFKVHKKFKNFSLLDVSLETGRTHQIRVHMQHIG 240

Query: 210 WKV 212
             +
Sbjct: 241 HPI 243


>gi|291531061|emb|CBK96646.1| hemolysin TlyA family protein [Eubacterium siraeum 70/3]
          Length = 241

 Score = 59.4 bits (142), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 15 RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          R+   ++    + SR     +I Q  V+VNG +  +A+  V   D+I + G 
Sbjct: 4  RLDVYLSENNTVKSRSLAASLIKQGSVEVNGRICTKASFAVDDNDNIRIIGE 55


>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 = 59.4 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 39/274 (14%), Positives = 80/274 (29%), Gaps = 59/274 (21%)

Query: 10  NFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGV 65
           +   QR+ K +       +R  ++R I ++RV V+  + +  +  V    HI +   +  
Sbjct: 17  DDAGQRLDKALCCHFPDLTRSTLQRWIKEERVIVDHEVAKLPSQKVRVGQHIIIYPSEPE 76

Query: 66  P-----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---- 110
           P           +   +   + L      +V   +  +  + V   L    +        
Sbjct: 77  PSTALPEEIALEILFEDEHLIVLNKPAGMVVHPGAGVNHGTLVNALLYHCGTPDNPHGGL 136

Query: 111 -----------VGRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVYR 146
                      V RLD  T G+++          L                +    +  +
Sbjct: 137 SGIGGVIRPGIVHRLDKETSGIMVAAKQDHAHIHLSRQFEQRTIGRRYLALTRGIPQPAQ 196

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
            R  G + +  ++  K  +V QG      +  +    G  A +   L  G+  +I+    
Sbjct: 197 GRIEGAIGRHPIHRTKMAVVEQGGRAAATRYKVLEPLGQFALIRCRLESGRTHQIRVHMT 256

Query: 207 FFNWKVNR----------------LIRISYGPFQ 224
                +                  L R  +  FQ
Sbjct: 257 HIGHPLVGDPLYGAQHKAPSHWPPLHRQRFDQFQ 290


>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 = 59.4 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 32/247 (12%), Positives = 77/247 (31%), Gaps = 35/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+ K I   + T +R+ K +       SR  ++ +I++  +KV+G  ++     +   + 
Sbjct: 1   MEAKIIKYTSQTVERIDKFLQKELSELSRTNIQNLISEGYIKVDGKEIKT-NFKLKDGNE 59

Query: 60  IEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I ++                 +   +   + +      +V   +     + V   L    
Sbjct: 60  ITIEYKEPEELDVVKQDIPVDIVYEDSDLIVVNKAKGMVVHPSAGHRDGTLVNALLFHSE 119

Query: 106 -------SRVISVGRLDINTEGLLLLTNDGGLA----RVLELPSTQWLRVYRVRFHGQVD 154
                   R   V R+D +T GLL++  +         ++     +      V    + D
Sbjct: 120 LSSINGTIRPGIVHRIDKDTSGLLVVAKNDKAHVKLSEMIANKDVKRKYYALVHGSIKHD 179

Query: 155 Q--------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          K+  +I           +  +      +   L  G+  +I+   +
Sbjct: 180 YGTIDAPIARNPKERKEMAIIDEGKPSITHFKVVERFEKYTLIECELETGRTHQIRVHMK 239

Query: 207 FFNWKVN 213
           + N  + 
Sbjct: 240 YINHPLV 246


>gi|291536189|emb|CBL09301.1| ribosomal large subunit pseudouridine synthase D [Roseburia
           intestinalis M50/1]
          Length = 310

 Score = 59.4 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 32/258 (12%), Positives = 76/258 (29%), Gaps = 46/258 (17%)

Query: 1   MKDKNI-VQENFTPQRVSKVIA--------RAGIASRREVERMIAQQRVKVNGILLERAA 51
           MK +   ++  +  +R+ K ++         +   SR   +++I    VKVN  + + A 
Sbjct: 1   MKQETFEIEAEYEGERLDKYLSVIFEQSKTSSNAPSRSFFQKLIRDGHVKVNDSIAK-AN 59

Query: 52  VNVMSTDHIEV------------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTV 97
             +   D + V            + +PL     +   L +      +V   +     + V
Sbjct: 60  YRLRMDDLVCVEIPDAVETPILPEDIPLDILYEDDDLLVVNKPKGMVVHPSAGHYSGTLV 119

Query: 98  FDNLPSIFS---------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL------ 142
              +              R   V R+D++T G L++  +      +     +        
Sbjct: 120 NAIMFHCKDSLSGINGEIRPGIVHRIDMDTTGSLIVCKNDESHVKIAEQIKEHSVNRRYR 179

Query: 143 -----RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLRE 195
                 V            +    +K + I             +  +  +  ++   L  
Sbjct: 180 GIVYGVVKDDEGTINAPIGRHPTNRKKMAINKKNGKPAITHYKVLERFSNYTYMEFKLET 239

Query: 196 GKNREIKKVFEFFNWKVN 213
           G+  +I+         + 
Sbjct: 240 GRTHQIRVHMASIGHPLL 257


>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 = 59.4 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 36/247 (14%), Positives = 71/247 (28%), Gaps = 42/247 (17%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           IV +   P R+ K +  R   +SR  +++      + VN   ++     V   D I +  
Sbjct: 37  IVDKGQEPARIDKFLFERMQHSSRNRIQKAADAGYIHVNNAPVKS-NYKVRPEDVITLML 95

Query: 63  ----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                   +           E   L + +KP GLV      +   T+ + +      + S
Sbjct: 96  DRPKHDNTIEAEDIPLDVVYEDDVLMVVNKPAGLVVHPGAGNFHGTLINAIAWHLKDMPS 155

Query: 111 VGRLDI----------NTEGLLLLTNDGG-------------LARVLELPSTQWLRVYRV 147
               D           +T GLL++                    R         +     
Sbjct: 156 FDPNDPEVGLVHRIDKDTSGLLVIAKTPDAKTALGKQFFNKTTHRSYNAIVWGNMTEDEG 215

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICY-GDM--QVTLDTQKGSNAWVTVGLREGKNREIKKV 204
           R  G + +D  + L+  +                +  + G    +   L  G+  +I+  
Sbjct: 216 RIEGNIARDPKDRLRMTVFPPDSEVGKPAVTHYRVIERFGYTTLIECILETGRTHQIRAH 275

Query: 205 FEFFNWK 211
            +     
Sbjct: 276 MKHIGHP 282


>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 = 59.4 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 30/244 (12%), Positives = 65/244 (26%), Gaps = 38/244 (15%)

Query: 6   IVQENFTPQRVSKVIARA-GI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           +V  +   +R+   +A   G+  +R  ++R+I   RV VNG      +  +   + + ++
Sbjct: 18  VVPGSAAGERLDVFLAEQDGLDLTRSAIQRLIRSHRVWVNGRTAR-PSRRLEPGEEVVIE 76

Query: 64  -------GVP-------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                  GV        +   +   + L      +V         +     L        
Sbjct: 77  LPEPAPSGVVPEALPLDVVYEDPDVVVLNKPRGWVVHPAPGHPQGTLANALLARYPEMEG 136

Query: 110 SVGRLDIN---------------------TEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
             G                             L+    +  + R        W  V    
Sbjct: 137 VGGPGRPGIVHRLDRDTTGLLVVARSPLAYRELVRQIKERRVHREYLALVRGWPEVREGT 196

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +   +  +  ++  G         +  Q G    +   L  G+  +I+    F 
Sbjct: 197 VEAPIGRHPADRTRMTVLTTGGRPARTHFAVVEQVGRYTLLRCWLDTGRTHQIRVHLAFI 256

Query: 209 NWKV 212
              V
Sbjct: 257 GLPV 260


>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 = 59.4 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 27/245 (11%), Positives = 68/245 (27%), Gaps = 38/245 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH------- 59
           V +    QR+ K+I+ A   SR   + +IA  +V ++G ++   +    + D        
Sbjct: 9   VTKEGDQQRIDKLISCALEISRNRAQGLIAGGQVTISGRVINDNSYLTKTGDVYTIVTAV 68

Query: 60  ---------------IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDP------------- 91
                          +  +   +   ++      H   G+                    
Sbjct: 69  QKPSTLSPNYDIDLKVVYEDHDVIVIDKDPYIAVHPGNGIEHHTITNALLARFGAGLQSV 128

Query: 92  --DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
               R  +   L    S ++   + +     L     + G  +     +       R   
Sbjct: 129 GSSSRPGIVHRLDKDTSGLMVAAKTENAYYRLSEELANQGFKKEYLAVAWGIPCPKRGVI 188

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFF 208
           H  +   + ++        G      +  ++ + G   + +   L  G+  +I+      
Sbjct: 189 HTNIRVKRSDITMMEAANSGGKPAKTEYEVEQELGEVASLIRCTLHTGRTHQIRVHMSHI 248

Query: 209 NWKVN 213
              + 
Sbjct: 249 GHSIV 253


>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 = 59.4 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 35/235 (14%), Positives = 72/235 (30%), Gaps = 37/235 (15%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           R+   +A   G  SR  ++++I   +VKVN  + E+A   V   D+I ++          
Sbjct: 17  RLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKV-EKARYLVKEEDNIVIEIPEPKVLEVL 75

Query: 64  --GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-------- 111
              +P+     +   L +      +V         + V   L     ++ S+        
Sbjct: 76  PQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGILYHCKDKLSSINGVIRPGI 135

Query: 112 -GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
             R+D +T GLL++  +      L     +        F       +  +     + +  
Sbjct: 136 VHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICYGVVKEDKITVDKPIGRNP 195

Query: 171 CYGDMQVTLDTQKGSNAWVTVG------------LREGKNREIKKVFEFFNWKVN 213
                   +   K +     V             L  G+  +I+      N  + 
Sbjct: 196 KDRLKMAVVKDGKNAITHFEVVERFDKFTHMRARLETGRTHQIRVHALSINHPLL 250


>gi|257460774|ref|ZP_05625875.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
          gracilis RM3268]
 gi|257442105|gb|EEV17247.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
          gracilis RM3268]
          Length = 495

 Score = 59.4 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 9/51 (17%), Positives = 24/51 (47%)

Query: 13 PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           +R+   ++     SR ++  +I    V+VNG +  +    + + + + +D
Sbjct: 9  SERLDVFLSSQLGISRNQISNLIKSAAVRVNGAVQTKPGYKLSAGELVRID 59


>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 = 59.4 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 34/254 (13%), Positives = 75/254 (29%), Gaps = 46/254 (18%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +V  +   QR+ +V+A R    SR  ++ +I   RV + G  +   A +    + I +D 
Sbjct: 12  VVAGDEGSQRLDRVLAARCPELSRSRLKALILDGRVAIAGTPVRDPAYHASPGETITIDV 71

Query: 64  ---------GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                    G  +       +   + L      +V   +  +  + V   +    + +  
Sbjct: 72  PPPVPAEPAGEAIALDIVYEDADIIVLNKPRGLVVHPAAGHETGTLVNALIAHCGASLSG 131

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
           +G +        L  +  GL    +          +   HG+  + +   L     + G 
Sbjct: 132 IGGVRRPGIVHRLDKDTTGLMVAAKNDKAHQSLSAQFADHGRTGELRRGYLAFVWGVPGR 191

Query: 171 CYGDMQVTLDT--------------QKGSNAW-----------------VTVGLREGKNR 199
            YG +   +D               ++    W                 +   L  G+  
Sbjct: 192 KYGTIDAPIDRHPHAREKMAVRQGGREAITHWEVLENFAGKDGKPVAALIACQLETGRTH 251

Query: 200 EIKKVFEFFNWKVN 213
           +I+         + 
Sbjct: 252 QIRVHLAHLGHPLL 265


>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 = 59.4 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 29/239 (12%), Positives = 69/239 (28%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           IV E+   +R+ + +A      SR  ++  I   +V ++  ++E+    V++   + VD 
Sbjct: 10  IVTESLAGKRLDQALAELFPDYSRSRLKSWITDGKVTIDTKVIEKPREKVVAGALVAVDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                           +   +   L +      +V   +    R+ +   L       + 
Sbjct: 70  EIEGEERHAAQPVELDIVYEDDDILVINKPAGLVVHPGAGAPDRTLLNGLLHYDPQLDLV 129

Query: 111 V-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                  RLD +T GL+++  +      L                               
Sbjct: 130 PRAGIIHRLDKDTTGLMVVARNVPAQTQLVSMMQDRDITREYEAVCNGVMTAGGMVDQPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V+Q          +  +  ++  + + L  G+  +I+         + 
Sbjct: 190 GRHPTKRTHMAVVQSGKPAVTHYRVLDRYRAHTLLRLRLESGRTHQIRVHMAHIRHPLV 248


>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 = 59.4 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 30/251 (11%), Positives = 65/251 (25%), Gaps = 39/251 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M   N+  E     R+ K +++     SR ++++ I    V+VN +++    V V   D 
Sbjct: 1   MLTYNVPNELNN-IRLDKALSQLLENVSRNQIQKSIKSSCVQVNDVIISDPDVLVKENDV 59

Query: 60  IEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I                    +   +   + +       V   +     + V   L    
Sbjct: 60  ILFSFKEPEELKIAAANIALDIIYEDDDLIVINKAAGMTVHPGAGHHDDTLVNALLYHTK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ-----WLRVYRVRFHGQVDQDKLNL 160
           +               L     G +       +         +   +R +  +    +N 
Sbjct: 120 NLSDIGSSERPGIVHRLDKNTTGLMVVAKNNKAHMLLANQIEQRQVIRKYKALVWGVINP 179

Query: 161 LKKGIVIQGICYGDMQVTL------------------DTQKGSNAWVTVGLREGKNREIK 202
           L+  I          +  +                      G+ + V   L  G+  +I+
Sbjct: 180 LEGVIKNNIGRSRSDRQKMTILKYGGKEAVTHYKTLELFYSGTISMVECKLSTGRTHQIR 239

Query: 203 KVFEFFNWKVN 213
                    V 
Sbjct: 240 VQLSHLKHSVV 250


>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 = 59.4 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 22/200 (11%), Positives = 58/200 (29%), Gaps = 6/200 (3%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKAERTRL 75
           KV+A+    S ++ + +I +  V V+   +  A   + +     IE         E   +
Sbjct: 8   KVLAQQQGISNKKAKELIDRGLVFVDDRKVRIARAEINTETTFRIEYPEDIEILYEDEDI 67

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
              +KP  + +             +     +  + +   +       +   +    RV +
Sbjct: 68  IAVNKPAQVDSYEIQDAIEGAELLHRLDRDTSGVLLLGRNREFIERAI--KEFKNRRVEK 125

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTVGL 193
                   V             +   K   +I  +        +  +  +G  + V + +
Sbjct: 126 HYVAWVDGVIYETVEIDEPIFTVKKGKAFSMIDPVRGKKAHTVVHPEEVQGKKSKVKIDI 185

Query: 194 REGKNREIKKVFEFFNWKVN 213
             G+  +I+         + 
Sbjct: 186 TTGRTHQIRVHLAHIGHPIV 205


>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 = 59.4 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 68/244 (27%), Gaps = 40/244 (16%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +     RV K +  R   ASR  +++      V  N   ++  +  V   D I V  
Sbjct: 33  VVDKGQEMMRVDKYLFDRLTNASRNRIQKAADAGFVMANDKPVKS-SYKVKPLDVITVMM 91

Query: 63  -----DGVPLR--------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                +   +           ++  + +      +V         + V      +     
Sbjct: 92  DRPRYENEVIPEDIPLNIVYEDKFLMVVNKPAGLVVHPGHGNYHGTLVNAIAWHMKDIPD 151

Query: 110 SV---------GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-- 158
                       R+D +T GLL++         L L         R R     + ++   
Sbjct: 152 YNANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKTTKRRYRALVWGNVEQDEG 211

Query: 159 -----------NLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                      + ++  ++      +      +  + G    V   L  G+  +I+   +
Sbjct: 212 TIVGNVGRNPKDRMQMTVLPDDQGKHAVTHYRVLERLGYVTLVECVLETGRTHQIRVHMK 271

Query: 207 FFNW 210
               
Sbjct: 272 HIGH 275


>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 = 59.4 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 37/248 (14%), Positives = 75/248 (30%), Gaps = 38/248 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K ++IV       RV K +A      +R  +++ I +  + VN  ++      V + DHI
Sbjct: 4   KIEHIVNSEAKG-RVDKYLAEVFPEYTRSFIQKQIEKGGILVNQKVINS-KYQVKADDHI 61

Query: 61  --------EVDGVPLRKAERTRL------WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
                   EVD +P                +      +V         + V   L     
Sbjct: 62  IMTIPDPIEVDIIPEPIDIEIVYEDDDLMIVNKPQDMVVHPAPGNYSGTLVNGLLYHCKD 121

Query: 107 ---------RVISVGRLDINTEGLLLLTNDGGLAR------VLELPSTQWLRVYRVRFHG 151
                    R   V R+D +T GLL++  +                + ++  +    F  
Sbjct: 122 KLSGINGEIRPGIVHRIDKDTSGLLMIAKNDKAHLGLSELLKDHHITRKYHAIVYGGFKE 181

Query: 152 QVDQ------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           KK  +++   Y      +  +     ++ + L  G+  +I+   
Sbjct: 182 DEGTIEEPIGRSTQDRKKMAIVRDGRYAKTDYKVLERFKQFTYIELTLHTGRTHQIRVHM 241

Query: 206 EFFNWKVN 213
           +     + 
Sbjct: 242 KHIGHPLL 249


>gi|254721426|ref|ZP_05183215.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. A1055]
          Length = 139

 Score = 59.4 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 25/128 (19%), Positives = 40/128 (31%), Gaps = 20/128 (15%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            V E    +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V
Sbjct: 8   TVAEEQKNERIDKFVA--GINNEWSRTQVQQWIKDDVVTVNGKAVK-GNYKVRENDEITV 64

Query: 63  --------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                   D  P      +   +   L +      +V         + V   +       
Sbjct: 65  TIPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 109 ISVGRLDI 116
              G +  
Sbjct: 125 GINGVMRP 132


>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 = 59.4 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 68/244 (27%), Gaps = 40/244 (16%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +     RV K +  R   ASR  +++      V  N   ++  +  V   D I V  
Sbjct: 34  VVDKGQEMMRVDKYLFDRLTNASRNRIQKAADAGFVMANDKPVKS-SYKVKPLDVITVMM 92

Query: 63  -----DGVPLR--------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                +   +           ++  + +      +V         + V      +     
Sbjct: 93  DRPRYENEVIPEDIPLNIVYEDKFLMVVNKPAGLVVHPGHGNYHGTLVNAIAWHMKDIPD 152

Query: 110 SV---------GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-- 158
                       R+D +T GLL++         L L         R R     + ++   
Sbjct: 153 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKTTKRRYRALVWGNVEQDEG 212

Query: 159 -----------NLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                      + ++  ++      +      +  + G    V   L  G+  +I+   +
Sbjct: 213 TIVGNVGRNPKDRMQMTVLPDDQGKHAVTHYRVLERLGYVTLVECVLETGRTHQIRVHMK 272

Query: 207 FFNW 210
               
Sbjct: 273 HIGH 276


>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 = 59.4 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 31/240 (12%), Positives = 69/240 (28%), Gaps = 45/240 (18%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--------------- 57
           P R+ K +A A   SR  V+ +IA+  V++ G  +  A+V V                  
Sbjct: 14  PARLDKALADATELSRARVQALIAEGAVEIAGKAVTSASVKVTENTPFRITVPAVVEAEA 73

Query: 58  --DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
               I +D   +   +   + +      +V   +     + V   L     ++  +G + 
Sbjct: 74  QAQDIALD---VAFEDEDLIVVNKPAGMVVHPAAGNPDGTLVNALLHHCRGQLSGIGGVA 130

Query: 116 IN----------------------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
                                    EGL     +  + R                 + ++
Sbjct: 131 RPGIVHRIDKDTSGLLVVAKSDAAHEGLAAQFAEHSVHRRYLAVCGGHPSPAEGTINERL 190

Query: 154 DQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
            +   N  K  ++ +      +      +    G+ A +   L  G+  +++        
Sbjct: 191 GRSDANRKKMAVLPKNSSRGKHAITHYKVLKPIGAAALIECRLETGRTHQVRVHCASIGH 250


>gi|327385684|gb|AEA57158.1| Hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Lactobacillus casei BD-II]
          Length = 306

 Score = 59.4 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 34/232 (14%), Positives = 64/232 (27%), Gaps = 35/232 (15%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKA 70
           R+ KVI A     +R +V++ +    V VNG    +A   V S D I +   +  PL   
Sbjct: 13  RIDKVITAHETTHTRSQVQKWLQDGLVTVNGQP-TKANYKVASGDVIAISIPEAKPLEAI 71

Query: 71  ERTRLWLY-----------HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-------VG 112
                                   +V         + V   L       I+       V 
Sbjct: 72  PEPIPLDIVYEDDQVIVVDKPQGMVVHPAPGHPDGTLVNGLLYHTDLPGINGVIRPGIVH 131

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--- 169
           R+D +T GLL++         L         +            +        + +    
Sbjct: 132 RIDKDTSGLLMVAKTEKAQLSLSAQLKAKTSIREYLALVHGTFKEDEGTIDAPLGRDPRD 191

Query: 170 ---------ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                      +      +  +     ++   L  G+  +I+    + +  V
Sbjct: 192 RKRQAVVAAGRHAVTHFQVLERFEHYTFIKCILETGRTHQIRVHMAYIHHPV 243


>gi|260220876|emb|CBA28881.1| hypothetical protein Csp_A09350 [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 201

 Score = 59.4 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 43/171 (25%), Positives = 68/171 (39%), Gaps = 15/171 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKV---N-G---ILLERAAVN-VMSTDHIEVDGV 65
            ++ +++   G  +RR    +I Q  V+V   N G   + + +AA   V       V GV
Sbjct: 1   MQLQEILYTQGFGTRRVCAGLIQQGLVQVYMPNEGPAPVTIAQAATEFVAEGLRFRVQGV 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPD-------GRSTVFDNLPSIFSRVISVGRLDINT 118
               AER  L L+       +                       +    V +VGRLD +T
Sbjct: 61  DWPYAERAYLMLHKPAGTECSQKPSTYPSIYTLLPSPLRLRPQKAAVQGVQAVGRLDQDT 120

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
            G+LLLT+DG     +  P     +VY V     +D  ++N L  G+V+  
Sbjct: 121 TGMLLLTDDGKFIHRMSSPKHHVPKVYEVTVKHPLDDKQVNKLLSGVVLDD 171


>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 = 59.4 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 34/232 (14%), Positives = 64/232 (27%), Gaps = 35/232 (15%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKA 70
           R+ KVI A     +R +V++ +    V VNG    +A   V S D I +   +  PL   
Sbjct: 14  RIDKVITAHETTHTRSQVQKWLQDGLVTVNGQP-TKANYKVASGDVIAISIPEAKPLEAI 72

Query: 71  ERTRLWLY-----------HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-------VG 112
                                   +V         + V   L       I+       V 
Sbjct: 73  PEPIPLDIVYEDDQVIVVDKPQGMVVHPAPGHPDGTLVNGLLYHTDLPGINGVIRPGIVH 132

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--- 169
           R+D +T GLL++         L         +            +        + +    
Sbjct: 133 RIDKDTSGLLMVAKTEKAQLSLSAQLKAKTSIREYLALVHGTFKEDEGTIDAPLGRDPRD 192

Query: 170 ---------ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                      +      +  +     ++   L  G+  +I+    + +  V
Sbjct: 193 RKRQAVVAAGRHAVTHFQVLERFEHYTFIKCILETGRTHQIRVHMAYIHHPV 244


>gi|300866710|ref|ZP_07111394.1| hemolysin A [Oscillatoria sp. PCC 6506]
 gi|300335310|emb|CBN56554.1| hemolysin A [Oscillatoria sp. PCC 6506]
          Length = 292

 Score = 59.0 bits (141), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 12/54 (22%), Positives = 26/54 (48%), Gaps = 1/54 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
          QR+  ++    +  SR++ +R+I    V VN  ++++    V     I++   P
Sbjct: 4  QRLDALLVNLDLCASRQQAQRLIRAGEVTVNQQVIDKPGTEVDILAVIKIKERP 57


>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 = 59.0 bits (141), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 81/249 (32%), Gaps = 41/249 (16%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
               I++E    +R+   I+     SR +V+  +    VKVNG + ++ +  +   D IE
Sbjct: 9   NKYFIIEEADAKKRLDVFISEKLNISRSQVKNYLNS--VKVNG-IEKKLSYALKINDKIE 65

Query: 62  VD----GVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           VD       +                E   L + +KP G+    S  +   T+ + L   
Sbjct: 66  VDIKNSDKEIDIENPKAENISLDIIYEDKYLLVINKPAGMSVHCSASEITGTLVNALLYN 125

Query: 105 FSRVISVGR--------LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
                 +G                 +++               +  ++ ++     +   
Sbjct: 126 IKDFDFIGNKSRAGIIHRLDKDTSGIMIIGKNADIVSSIQEQFKNRKIKKIYHAIVIGVL 185

Query: 157 KLNLLKKGIVI-------------QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           K N L+  + I             +        + +  +  ++  + + L+ G+  +I+ 
Sbjct: 186 KDNYLEINLPIGRHQVYRKKMTVREDGKKALTHIKVLKRFKNHTLIEIDLKTGRTHQIRV 245

Query: 204 VFEFFNWKV 212
              + N+ V
Sbjct: 246 HSSYKNFPV 254


>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 = 59.0 bits (141), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 28/273 (10%), Positives = 80/273 (29%), Gaps = 45/273 (16%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--------- 60
                R+ + +      +R ++++ I    + +N  +++ A       D I         
Sbjct: 17  ESDNIRIDRYLVEKLNINRSQIKKYIDFGNILINNSVVK-AGYMTKIGDIIDVSYEDEIL 75

Query: 61  ----EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
               E+D   + + E   +        +V   S     + V   L    +      +L  
Sbjct: 76  LLPEEIDFKIIYEDEHIAVIS-KPQNLVVHPGSGNYNHTLVNGLLFKFKNLSNCGDKLRP 134

Query: 117 NTEGLLLLTNDGGLARVLELPST--------------------QWLRVYRVRFHGQVDQD 156
                L     G +       +                     +         +  + +D
Sbjct: 135 GIVHRLDKDTSGLMIIAKTNLAYLKLVKDFKESKIRKTYIAVVEGKTDEFGIINEPIGRD 194

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
             N  K  ++ +       +     +  + + +++ +  G+  +I+    +    V  L 
Sbjct: 195 PKNRKKMAVIYENSKNAITEYKKIREFNNFSLISINILTGRTHQIRVHLSYIKHPV--LG 252

Query: 217 RISYGP---FQLGTLLAGSTR-----EVSKKIL 241
            ++YG    +++   +  + R      ++ + L
Sbjct: 253 DLTYGNKNKYKIDKQMLHAYRLKFNHPITGEEL 285


>gi|257439837|ref|ZP_05615592.1| putative S4 domain protein [Faecalibacterium prausnitzii A2-165]
 gi|257197746|gb|EEU96030.1| putative S4 domain protein [Faecalibacterium prausnitzii A2-165]
          Length = 273

 Score = 59.0 bits (141), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 25/63 (39%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           ++       +  R+  V+A     SR +    IA  RV++N +  E A   V   D   V
Sbjct: 187 ERKTQTATVSSLRLDAVLAAMLHCSRGQACEWIAAGRVEINHLPAESAHAPVYEGDVFTV 246

Query: 63  DGV 65
            G 
Sbjct: 247 RGK 249


>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 = 59.0 bits (141), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 27/245 (11%), Positives = 68/245 (27%), Gaps = 38/245 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH------- 59
           V +    QR+ K+I+ A   SR   + +IA  +V ++G ++   +    + D        
Sbjct: 3   VTKEDDQQRIDKLISCALEISRNRAQGLIAGGQVTISGRVINNNSYLTKTGDVYTIVTAV 62

Query: 60  ---------------IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDP------------- 91
                          +  +   +   ++      H   G+                    
Sbjct: 63  QKPSTLSPNYDIDLKVVYEDHDVIVIDKDPYIAVHPGNGIEHHTITNALLARFGAGLQSV 122

Query: 92  --DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
               R  +   L    S ++   + +     L     + G  +     +       R   
Sbjct: 123 GSSSRPGIVHRLDKDTSGLMVAAKTENAYYRLSEELANQGFKKEYLAVAWGIPCPKRGVI 182

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFF 208
           H  +   + ++        G      +  ++ + G   + +   L  G+  +I+      
Sbjct: 183 HTNIRVKRSDITMMEAANSGGKPAKTEYEVEQELGEVASLIRCTLHTGRTHQIRVHMSHI 242

Query: 209 NWKVN 213
              + 
Sbjct: 243 GHSIV 247


>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 = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 25/239 (10%), Positives = 63/239 (26%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E    QR+ + +A      SR  ++  I   +V+VNG L+ +    V+  + I +D 
Sbjct: 10  TVAETQLGQRLDQALAELFSDYSRSRIKEWILDNKVQVNGKLINKPKEKVLGGEVISIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
           +               +   +   L +      +V   +     + +   L         
Sbjct: 70  IIEEDARWEPQDIELNIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLYRYPAIADV 129

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--- 156
                  R+       +     +        +  L   + ++  +           +   
Sbjct: 130 PRAGIVHRLDKDTTGLMVIAKTVPAQTRLVESLQLREITREYEAIALGCMTAGGMVEEPI 189

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKSAVTHYRVMEHFRAHTRLRLRLETGRTHQIRVHMAHIKHPLV 248


>gi|34540882|ref|NP_905361.1| S4 domain-containing protein [Porphyromonas gingivalis W83]
 gi|34397197|gb|AAQ66260.1| S4 domain protein [Porphyromonas gingivalis W83]
          Length = 150

 Score = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
          R++K+I+ AG+ SRRE E+ I + RVK+NG +       V   D + +D + +   +  R
Sbjct: 4  RINKLISDAGLGSRREAEKYITEGRVKINGRIAR-LTDLVCEKDIVLLDDIDIPIKDLIR 62

Query: 75 L 75
           
Sbjct: 63 E 63


>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 = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 27/245 (11%), Positives = 68/245 (27%), Gaps = 38/245 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH------- 59
           V +    QR+ K+I+ A   SR   + +IA  +V ++G ++   +    + D        
Sbjct: 9   VTKEDDQQRIDKLISCALEISRNRAQGLIAGGQVTISGRVINNNSYLTKTGDVYTIVTAV 68

Query: 60  ---------------IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDP------------- 91
                          +  +   +   ++      H   G+                    
Sbjct: 69  QKPSTLSPNYDIDLKVVYEDHDVIVIDKDPYIAVHPGNGIEHHTITNALLARFGAGLQSV 128

Query: 92  --DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
               R  +   L    S ++   + +     L     + G  +     +       R   
Sbjct: 129 GSSSRPGIVHRLDKDTSGLMVAAKTENAYYRLSEELANQGFKKEYLAVAWGIPCPKRGVI 188

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFF 208
           H  +   + ++        G      +  ++ + G   + +   L  G+  +I+      
Sbjct: 189 HTNIRVKRSDITMMEAANSGGKPAKTEYEVEQELGEVASLIRCTLHTGRTHQIRVHMSHI 248

Query: 209 NWKVN 213
              + 
Sbjct: 249 GHSIV 253


>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 = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 31/238 (13%), Positives = 64/238 (26%), Gaps = 37/238 (15%)

Query: 12  TPQ-RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP--- 66
            P+ R+   +      SR  +  MI + RV VNG   ++A   + + D I ++   P   
Sbjct: 20  KPEVRLDVCLTEKTGTSRSFIRNMIEEGRVLVNGET-KKANYRIRAEDKIGINLPKPREL 78

Query: 67  ----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG---- 112
                     +   +   L +      +V         + V   L          G    
Sbjct: 79  KVVPQQIPLEIIYEDDDLLVVNKPQGMVVHPAPGVWEGTLVNALLYHCRDLSGINGIIRP 138

Query: 113 -----------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
                            + D +   L     +  + R         L          + +
Sbjct: 139 GIVHRIDKDTSGLLVVAKNDESHNQLAGQLKEHKMQRKYLAVVHGVLSEPSGTIDAPIGR 198

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           D  +  K  +V +          ++ +      +   L  G+  +I+    +    V 
Sbjct: 199 DPKDRKKMAVVFKHSRPAVTHYEVEERFIGYTKIKAVLETGRTHQIRVHMAYIRNPVL 256


>gi|255284126|ref|ZP_05348681.1| hemolysin A [Bryantella formatexigens DSM 14469]
 gi|255265300|gb|EET58505.1| hemolysin A [Bryantella formatexigens DSM 14469]
          Length = 284

 Score = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 25/177 (14%), Positives = 59/177 (33%), Gaps = 2/177 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M++ +  +E    +R+  ++ + G+A SR + + +I    V V+G   ++A      T  
Sbjct: 1   MQNISDYKEKQMKERLDVLVVQKGLAPSREKAKALIMAGCVLVDGEREDKAGTMFAETVQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           I + G  L+   R  L L         T +                  ++  G + +   
Sbjct: 61  ITLKGGTLKYVSRGGLKLEKAMEKFSVTPAGKVCMDIGAST-GGFTDCMLQNGAVKVYAV 119

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
            +     D  L +   +   +   +  V     V++     +    +        ++
Sbjct: 120 DVGYGQLDWKLRQDPRVVCMEKTNIRYVTPEDIVEKAAFASIDVSFISLTKVLLPVR 176


>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 = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 37/252 (14%), Positives = 79/252 (31%), Gaps = 47/252 (18%)

Query: 4   KNIVQENFTPQRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           + +  +  +  R+ K +    A A   SR +++  I  + V+VNG    +A+  V   D 
Sbjct: 20  RIVADKGQSLMRLDKYLNLHVANA---SRTKIQNGIEAEAVRVNGQP-TKASYKVKPFDV 75

Query: 60  IEV-------DGVPLR-------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           + +       D   +          E   L + +K  G+V   +  +   T+ + L   F
Sbjct: 76  VTLSLPQPPRDTEIIPENLPLDIIYEDDVLLIVNKAAGMVVHPAFGNWTGTLINGLVYHF 135

Query: 106 SR----------VISVGRLDINTEGLLLLTNDGGLARV-------------LELPSTQWL 142
            +             V R+D +T GLL++                               
Sbjct: 136 QQLPTGRNGEGRPGLVHRIDKDTSGLLVIAKTEFAMTFLASQFADHSIERTYHALIWGEP 195

Query: 143 RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNRE 200
           +  +    G V +   +     + + G          +  K     + +   L  G+  +
Sbjct: 196 KAEKGTITGHVGRSARDRRVMDVYVDGSQGKHAVTHYEVIKPLRYVSLIKCNLETGRTHQ 255

Query: 201 IKKVFEFFNWKV 212
           I+   +     +
Sbjct: 256 IRAHMKHIGHPI 267


>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 = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 38/257 (14%), Positives = 76/257 (29%), Gaps = 41/257 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           I+ E+   +R+ KV+AR   A  SR   + +I +  + VNGI +++    +   D +EV 
Sbjct: 13  IISEDEVGERLDKVLARRFNAKYSRTYFQFLIDKHLILVNGIAVKK-RTLLQEGDEVEVQ 71

Query: 63  -----------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                      + +PL     +   L +      +V         + V   L       +
Sbjct: 72  FLASPESNLMPENIPLSILYEDEHLLVINKPAGMVVHPAPGNWSGTFVNALLYYCQKLPL 131

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV-----------DQDKL 158
               +       L     G L     L + Q L                      D +  
Sbjct: 132 LPDTIRPGIVHRLDKGTSGLLVAAKTLETQQKLIELFASRKVYKAYLAICIGRPADGEIQ 191

Query: 159 NLLKKGIVIQGICY-----GDMQ--VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             + +  + +                         ++V + +  G+  +I+   ++    
Sbjct: 192 APIGRHPIHRKQMAVIPTGKPAISFCKTLGWSDKLSFVQIEIATGRTHQIRVHMKYRGSP 251

Query: 212 VNR--LIRISYGPFQLG 226
           +    L    YG   L 
Sbjct: 252 ILGDPL----YGQISLN 264


>gi|306822649|ref|ZP_07456027.1| ribosomal RNA large subunit methyltransferase J [Bifidobacterium
          dentium ATCC 27679]
 gi|309800961|ref|ZP_07695093.1| ribosomal RNA large subunit methyltransferase J [Bifidobacterium
          dentium JCVIHMP022]
 gi|304554194|gb|EFM42103.1| ribosomal RNA large subunit methyltransferase J [Bifidobacterium
          dentium ATCC 27679]
 gi|308222497|gb|EFO78777.1| ribosomal RNA large subunit methyltransferase J [Bifidobacterium
          dentium JCVIHMP022]
          Length = 252

 Score = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 8  QENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           ++    R+   +   G++ SR + +R+I Q +V VNG+++ +A+  V   D I  D
Sbjct: 4  NDSQHAVRLDLALLDRGLSDSRSKAQRLIVQGKVSVNGVVVSKASAKVSDDDVIAAD 60


>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 = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 37/238 (15%), Positives = 67/238 (28%), Gaps = 41/238 (17%)

Query: 14  QRVSKVIARAGIA----SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVP 66
           QR+   +A  G+     SR +V+R++    V V+G   + AA  +     I V   D  P
Sbjct: 15  QRLD--VALLGLLGDDFSRAQVQRLLRDGLVLVDGQAAK-AAQKLRPGQAIAVRLPDPEP 71

Query: 67  -----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                      +   +   + +   P  +V         + V   L          G+L 
Sbjct: 72  SELIPMAMDLAILHEDEDLIIINKPPGLVVHPSPGHAEGTLVHGLLHHCGGLAEVGGKLR 131

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------------------DK 157
                 L     G L       + + L         Q +                    +
Sbjct: 132 PGIVHRLDKDTSGALVAAKNDRAHRGLVARFAAGRVQKEYLALVHGRPAKRGRVDSGIGR 191

Query: 158 LNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               +K +  QG        Q  +    G  + + V +  G+  +I+         V 
Sbjct: 192 HPGDRKRMSSQGSRTKPALSQWRVCRSFGEASLLRVNIHTGRTHQIRVHLSEAGHPVL 249


>gi|8575702|gb|AAF78056.1|AF263561_1 23S rRNA pseudouridine synthase [secondary endosymbiont of
           Glycaspis brimblecombei]
          Length = 314

 Score = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 29/236 (12%), Positives = 66/236 (27%), Gaps = 31/236 (13%)

Query: 9   ENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---- 63
           E+   QR+ + +A      SR  ++  I   RV+VNG ++ R    V  ++ I +D    
Sbjct: 2   ESQLGQRLDQTLAELFPDYSRSRIKEWILDNRVQVNGKIINRPKEKVFGSEQIAIDVLIE 61

Query: 64  ----GVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------- 105
                 P      +   +   + +      +V   +     + +   L            
Sbjct: 62  EDMRWQPQNIPLNIVYEDDEIIVINKPRDLVVHPGAGNPDGTVLNALLYRYPEIINVPRA 121

Query: 106 ---SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
               R+       +     +        A  L   + ++  V   R       D+     
Sbjct: 122 GIVHRLDKDTTGLMVIAKTIPAQTHLVEALQLREITREYEAVVNGRMTAGGTVDEPIARH 181

Query: 163 KGIVIQGICY---GDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                    +           +     ++  + + L  G+  +I+      N  + 
Sbjct: 182 PTKRTHMAIHPLGKPAITHYRVMEHFRAHTRLRLRLESGRTHQIRVHMAHINHPLV 237


>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 = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 34/252 (13%), Positives = 80/252 (31%), Gaps = 40/252 (15%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M++ N+   E +T +R+ KV++      SR  ++++     + VN   ++  +  V + D
Sbjct: 1   MEEYNLESSEEWTDRRLDKVLSEYFDGYSRSFIKKLFDDGLILVNSKAVK-PSYKVRAGD 59

Query: 59  HI--------EVDGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            I         +D VP      +   +   + +      +V         + V   +   
Sbjct: 60  MIDISVPDPVSIDIVPEDIPLDIIYEDDDVILVNKPKGMVVHPAPGHYSGTLVNGLMYHF 119

Query: 105 F---------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR--------- 146
                      R   V R+D++T G+L++  +    R L     +     +         
Sbjct: 120 GSSLSGINGEFRPGIVHRIDMDTTGVLVVCKNDNAHRALSEQLHEHSITRKYYAIVYGNI 179

Query: 147 ----VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-KGSNAWVTVGLREGKNREI 201
                     + +   +  K  I  +          +  +  G   ++   L  G+  +I
Sbjct: 180 SSDEGTVDAPIGRSPKDRKKMAINNRNGRRAVTHYRVLERFGGRYTYIECQLETGRTHQI 239

Query: 202 KKVFEFFNWKVN 213
           +         + 
Sbjct: 240 RVHMASIGHPIL 251


>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 = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 41/244 (16%), Positives = 77/244 (31%), Gaps = 40/244 (16%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +     RV K +  R   ASR  +++      V  NG  ++  +  V   D I V  
Sbjct: 33  VVDKGQEMVRVDKYLFDRLTNASRNRIQKAADAGFVMANGKPVKS-SYKVKPLDVITVMM 91

Query: 63  -----DGVPLR-------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                +   +          E   L + +KP GLV      + R T+ + +         
Sbjct: 92  DRPRYENEVIPEDIPLDIVYEDKYLMVVNKPAGLVVHPGHGNYRGTLVNAIAWHMKDIPD 151

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD------ 154
                  V  V R+D +T GLL++         L L         R R     +      
Sbjct: 152 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKTTKRRYRALVWGNVGQDEG 211

Query: 155 -------QDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                  ++  + ++  ++      +      +  + G    V   L  G+  +I+   +
Sbjct: 212 TIVGNVGRNPKDRMQMTVLPDDQGKHAVTHYRVLERLGYVTLVECVLETGRTHQIRVHMK 271

Query: 207 FFNW 210
               
Sbjct: 272 HIGH 275


>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 = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 30/245 (12%), Positives = 65/245 (26%), Gaps = 41/245 (16%)

Query: 10  NFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
                R+   +++     SR  ++++I Q  + +N  +       V   D ++V      
Sbjct: 16  QDKGDRIDLWLSQNLDQISRSHLQKLIEQGNIYLNNQVCLNKKTKVNLGDRLQVFLPPPE 75

Query: 63  ----------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
                           D   +   +   L ++  P     T                   
Sbjct: 76  PLELQPEPIPLDILYEDDSLIIINKSAGLVVHPAPGHTSGTLVHGLLYHCPNLVGIGGVQ 135

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELP------STQWLRVYRVRFHGQVDQD---- 156
           R   V RLD +T G +++       + L+          ++L V       +        
Sbjct: 136 RPGIVHRLDKDTTGAIVVAKTDYAHQHLQAQLKAKTARREYLGVVYGVPRHKDTHQGTIN 195

Query: 157 --------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                       +    V  G         +  + G+   V   L  G+  +I+    + 
Sbjct: 196 VPIGRHRGDRKKMAVVPVENGGREAITHWQIVERLGNYTLVEFRLETGRTHQIRVHSSYI 255

Query: 209 NWKVN 213
              + 
Sbjct: 256 GHPIV 260


>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 = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 44/340 (12%), Positives = 82/340 (24%), Gaps = 52/340 (15%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----- 60
           V+E     R+   +AR     SR  ++R+I +  V+V G  ++  +  V   + I     
Sbjct: 9   VEEEEAGVRLDVYLARNLPENSRSYLQRLINEGYVQVGGRKVK-PSYKVKPGEEILVFLP 67

Query: 61  -----EVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                EV+  P+       +   L +      +V   +     + V   L    S     
Sbjct: 68  PAETLEVEPEPIPLEIIYEDEDLLVVNKPRGMVVHPGAGHKRGTLVNALLYHCRSLSGIN 127

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--------------- 156
           G L       L     G L       +   L           +                 
Sbjct: 128 GVLRPGIVHRLDKDTSGLLMVAKNDAAHLSLSAQLKERRVLKEYWALVYGEVKPAQGRIE 187

Query: 157 -----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                     +K  V+ G         +         + V    G+  +I+    +    
Sbjct: 188 APIGRHPRYRQKMAVVAGGRPAVTHYEVVEYFPGYTLLRVRPETGRTHQIRVHLHYLGHP 247

Query: 212 VNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDR 271
           +             G L  G  R      L  +                           
Sbjct: 248 IV------------GDLKYGPARP----HLGLEGQFLHAGVLGFTHPRTGEFLRFEAPLP 291

Query: 272 PNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           P +   + +   R       +    ++   A P  +R   
Sbjct: 292 PELERVLAELRARQAGRPGSQPLQQEEGVAAQPPSQRGQG 331


>gi|218249068|ref|YP_002374439.1| hemolysin A [Cyanothece sp. PCC 8801]
 gi|218169546|gb|ACK68283.1| hemolysin A [Cyanothece sp. PCC 8801]
          Length = 266

 Score = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 1/56 (1%)

Query: 12 TPQRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
          T QR+  ++    + S R+E + +I    VKVN  ++++    V ST  IE+   P
Sbjct: 2  TKQRLDTLLVERNLCSSRQEAQGLIRAGEVKVNQQVIDKPGTPVESTAEIELQAKP 57


>gi|73670608|ref|YP_306623.1| FtsJ-like methyltransferase [Methanosarcina barkeri str. Fusaro]
 gi|72397770|gb|AAZ72043.1| FtsJ-like methyltransferase [Methanosarcina barkeri str. Fusaro]
          Length = 236

 Score = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   I   G   SR   ++ I    VKVNG ++ +A+ +V + D IEV
Sbjct: 1  MRLDAYIVDMGHFKSRGRAKKAILAGNVKVNGAVITKASRDVSTDDIIEV 50


>gi|301632247|ref|XP_002945202.1| PREDICTED: ribosomal large subunit pseudouridine synthase D-like
           [Xenopus (Silurana) tropicalis]
          Length = 341

 Score = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 35/237 (14%), Positives = 76/237 (32%), Gaps = 38/237 (16%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ K +A      SR  +++++AQ  V ++G    + A  V + D + V+  P ++++  
Sbjct: 39  RLDKALAELVPELSRSYLQQLLAQGLVCLDGAASRKPAHKVKAGDALVVEIRPTQQSQAF 98

Query: 74  R---------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-----SVGR 113
           +               L +      +V         + +   +      ++      V R
Sbjct: 99  KPEPVPVPVVFEDAHLLVVNKPAGLVVHPAPGHWSGTLLNGLMGRDPKAMLLPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------------DKLN 159
           LD +T GL+++  +      L     Q     +    G                  D  N
Sbjct: 159 LDKDTSGLMVVARERTTMDALVRLIAQRQVRRQYLALGHCVWRGGGLRTVDAALGRDPRN 218

Query: 160 LLKKGIVIQGICY-GDMQVTLDTQKGSN--AWVTVGLREGKNREIKKVFEFFNWKVN 213
            L+  +V          +   +   G++    V   L  G+  +I+         + 
Sbjct: 219 RLRMAVVDLAQHAGKPARTDFEYLAGNDLGCLVRCTLHTGRTHQIRVHMLSMGHPLV 275


>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 = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/245 (14%), Positives = 66/245 (26%), Gaps = 41/245 (16%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +     RV K +    + ASR  +++      V  NG  ++  +  V   D I V  
Sbjct: 33  VVDKGQAMVRVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKS-SYKVKPLDVITVMM 91

Query: 63  -----DGVPLR-------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                D   +          E   L + +KP GLV      +   T+ + +         
Sbjct: 92  DRPRYDNEIIPEDIPLNIVYEDKYLMVVNKPAGLVVHPGHGNYHGTLVNAIAWHLKDNSD 151

Query: 111 VGRLDIN----------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-------- 152
               D +          T GLL++         L +         R R            
Sbjct: 152 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGIQFFNKTTKRRYRALVWGIVDQNEG 211

Query: 153 -------VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                   +      +          +      +  + G    V   L  G+  +I+   
Sbjct: 212 TVVGSIARNPKDRMQMAVMPDPAQGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHM 271

Query: 206 EFFNW 210
           +    
Sbjct: 272 KHIGH 276


>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 = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 68/239 (28%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I + RV++NG +  +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILENRVQINGNVTNKPKEKVLGGESVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
           +               +   ++  L +      +V   +     + +   L         
Sbjct: 70  LIEEEARWEAQDIKLDIVYEDQDILVINKPRDLVVHPGAGNPDGTVLNALLHHYPEIVDV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L                               
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGSMTAGGMVDQPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 ARHSTKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMAHINHPLV 248


>gi|227329204|ref|ZP_03833228.1| 23S rRNA pseudouridine synthase D [Pectobacterium carotovorum
           subsp. carotovorum WPP14]
          Length = 325

 Score = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 68/239 (28%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I + RV++NG +  +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILENRVQINGNVTNKPKEKVLGGESVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
           +               +   ++  L +      +V   +     + +   L         
Sbjct: 70  LIEEEARWEAQDIKLDIVYEDQDILVINKPRDLVVHPGAGNPDGTVLNALLHHYPEIVDV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L                               
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGSMTAGGMVEQPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 ARHATKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMAHINHPLV 248


>gi|169838827|ref|ZP_02872015.1| hemolysin A [candidate division TM7 single-cell isolate TM7a]
          Length = 81

 Score = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          QR+ + I    +  SR + E  I   RV VNG ++++    V + D + ++
Sbjct: 3  QRLDRYIVENRLTNSRSQAENYIRLGRVTVNGEVIKKCGFIVSTVDKVVLN 53


>gi|153007893|ref|YP_001369108.1| hemolysin A [Ochrobactrum anthropi ATCC 49188]
 gi|151559781|gb|ABS13279.1| hemolysin A [Ochrobactrum anthropi ATCC 49188]
          Length = 253

 Score = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 8  QENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          + +    R+ +++   G  A+R      I +  VKV+G  + +    V+ T  I VD 
Sbjct: 4  ETSDKNLRLDQLLVELGLFATRSRARDAIQRGTVKVDGKPVTKPGQTVLRTAKIAVDD 61


>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 = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 35/265 (13%), Positives = 81/265 (30%), Gaps = 52/265 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M  + I  E    QR+ + +A+    + SR  ++ +I +  +K++G  ++     +    
Sbjct: 1   MVIQKITDEGALGQRLDQWLAKQYHNVFSRSRLQTLIREGYLKIDGQFIKEPKTKLRPKQ 60

Query: 59  HIEV------DGVP--------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            IE+      D  P        +   +   + +      +V   +     + V   +   
Sbjct: 61  IIELAMPDLRDAEPSAEAIALDILFEDDHIIVINKPAGLVVHPGNGNWTGTLVNALIYHC 120

Query: 105 FS---------RVISVGRLDINTEGLLLLTNDGGLA-----------------RVLELPS 138
            +         R   V RLD NT G++++  +                     R      
Sbjct: 121 GNSLSGIGGVKRPGIVHRLDKNTSGVMIVAKNDLAHKSLSAQFSDHGRTCALDRRYHALI 180

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY---GDMQVTLDTQKGSN-------AW 188
                         + +   N  K+ ++ +   Y        +L  + GS+       + 
Sbjct: 181 WGTPHRNVWTIDASLGRSPHNRTKQAVIHKQNPYARHAVTHFSLLEKYGSHADSTSFASL 240

Query: 189 VTVGLREGKNREIKKVFEFFNWKVN 213
           +   L  G+  +I+         + 
Sbjct: 241 LECRLETGRTHQIRVHMAHIGHPLI 265


>gi|221135103|ref|ZP_03561406.1| RluA family pseudouridine synthase [Glaciecola sp. HTCC2999]
          Length = 330

 Score = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 29/239 (12%), Positives = 63/239 (26%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVN------VMSTD 58
           IV +    +R+ +V+A      SR +++  I    VKV+  ++  A         +    
Sbjct: 16  IVDQTQFDKRLDQVLADLFPEYSRSKLKEWILAGFVKVDDEVVTVARQKMQGDEQIDIHA 75

Query: 59  HIEVD--GVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
            I V     P      +   +   L +      +V   +     + +   L         
Sbjct: 76  VIAVQVLNTPQNIELDIVFEDEHVLVINKPAGLVVHPGAGNADGTVLNALLAHHPEIENI 135

Query: 111 V-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                  RLD +T GL+++         L       +                       
Sbjct: 136 PRAGIVHRLDKDTTGLMVVAKTLIAQTYLVEQLQTRVMSREYEALVMGTMVAGGFVDEPI 195

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +  +  ++  + + L  G+  +I+         + 
Sbjct: 196 GRHPTKRTSMAVRATGKEATTHYRIKEKFRAHTHLRLKLESGRTHQIRVHMAHIRHPLV 254


>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 = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 27/244 (11%), Positives = 65/244 (26%), Gaps = 40/244 (16%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V+E F+ +R+ + +A      SR   + +I    V ++   +++ +  V +     +   
Sbjct: 9   VEEEFSNKRLDQFLALVYPEYSRSFYQNLIENGFVLLDNSPVKKPSTKVKTGQEFTIIIP 68

Query: 66  --------------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                          +   +     +Y  P  +V         + V   L    +     
Sbjct: 69  PPEPLEIEPENIPLEICYEDEDLAVVYKPPGMVVHPSVGHTSGTLVNALLYHFKNVSQYQ 128

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           G+        L     G L       + + L+              +          G+ 
Sbjct: 129 GKERAGIVHRLDKDTAGLLIVAKTEFAHKELQKMFQDREIDKKYKAIVS-GIVKKDHGLI 187

Query: 172 YGDMQVTLDTQKG------------SNAWVT------------VGLREGKNREIKKVFEF 207
              +  ++  ++             +  WV             + L  G+  +I+  F  
Sbjct: 188 DLPIGRSIYNRQKMGTVSTNLKDALTEYWVEKRFEKHNLTLVDIKLHTGRTHQIRVHFSA 247

Query: 208 FNWK 211
               
Sbjct: 248 IGHP 251


>gi|171742791|ref|ZP_02918598.1| hypothetical protein BIFDEN_01905 [Bifidobacterium dentium ATCC
          27678]
 gi|171278405|gb|EDT46066.1| hypothetical protein BIFDEN_01905 [Bifidobacterium dentium ATCC
          27678]
          Length = 252

 Score = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 8  QENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           ++    R+   +   G++ SR + +R+I Q +V VNG+++ +A+  V   D I  D
Sbjct: 4  NDSQHAVRLDLALLDRGLSDSRSKAQRLIVQGKVSVNGVVVSKASAKVSDDDVIAAD 60


>gi|168700598|ref|ZP_02732875.1| ribosomal large subunit pseudouridine synthase [Gemmata
           obscuriglobus UQM 2246]
          Length = 354

 Score = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 40/264 (15%), Positives = 75/264 (28%), Gaps = 44/264 (16%)

Query: 10  NFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
                R+ + +     A  SR  V+R I    V +NG  + + +  V   D + V     
Sbjct: 38  KSEGMRLDQYVQLHLGADWSRSVVQRAIESGGVLLNGRPVLKPSYKVRKNDRLHVTMPEP 97

Query: 63  -------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
                  + +PL    +   L L +KP  +V   +  +   T+ + L   F   +S G  
Sbjct: 98  THEIPVPEDIPLDILYQDEWLALVNKPADMVVHPAKGNWSGTLVNALQWHFREHLSTGAG 157

Query: 115 DIN-----------------------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151
            +                           L +      + +     +   L        G
Sbjct: 158 HLRAGIVHRLDKDTSGVILVAKDDLTHRDLAMQFESRKVFKEYVAIAAGELERDSDYIEG 217

Query: 152 QVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
            +     + LK  +       +      +  +      V V  R G+  +I+        
Sbjct: 218 ALKMHPYDRLKMIVSTDPDAKHALSYYEVLERFRGFTLVKVQPRTGRTHQIRVHLLHVGC 277

Query: 211 KVNRLIRISYGP---FQLGTLLAG 231
            V       YG     +L  +  G
Sbjct: 278 AVLADK--IYGGRAQVKLSEIAPG 299


>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 = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 34/240 (14%), Positives = 74/240 (30%), Gaps = 31/240 (12%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K I+       R+ +V+A+     SR +++  I    VKV+GI   +A   V     IE+
Sbjct: 9   KKIIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEI 68

Query: 63  DGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           +                 +   + T L +      +V   +    ++ +   L    S  
Sbjct: 69  EAQLEPNERWVPQPIPLDVIYEDETLLVINKPVGLIVHPGAGVRDQTLINALLHYDPSLS 128

Query: 109 ISVGRLDIN----TEGLLLLTNDGGLARVLELPSTQWLRVYRV------------RFHGQ 152
           +      I+        LLL      +    + + +  ++ R             R    
Sbjct: 129 VVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEAIVKGVLISGRTIEA 188

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                     +  V++          +  +  ++  + V L  G+  +I+      +  V
Sbjct: 189 PVGRHPIHRTRMAVVEFGRPAITHFRIIKRYRAHTHIRVQLETGRTHQIRVHMAHIHHPV 248


>gi|152990876|ref|YP_001356598.1| hemolysin A [Nitratiruptor sp. SB155-2]
 gi|151422737|dbj|BAF70241.1| hemolysin A [Nitratiruptor sp. SB155-2]
          Length = 234

 Score = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 10/54 (18%), Positives = 24/54 (44%), Gaps = 2/54 (3%)

Query: 14 QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           R+ K + + G  S R +   +I +  V V+G ++ + +  +     + +   P
Sbjct: 1  MRLDKYLYQKGFTSSRNKAAELIREGLVSVDGKVVTKPSFELQKG-EVSIKAKP 53


>gi|291278963|ref|YP_003495798.1| hypothetical protein DEFDS_0560 [Deferribacter desulfuricans SSM1]
 gi|290753665|dbj|BAI80042.1| conserved hypothetical protein [Deferribacter desulfuricans SSM1]
          Length = 278

 Score = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 27/211 (12%), Positives = 73/211 (34%), Gaps = 11/211 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLER-AAVNVMSTDHIE--VDGVPLRKA 70
            ++   +++    S+R  ++ I +++V ++G   +    +  +   HI   +D   +   
Sbjct: 23  MKLVDYLSQQFNISKRLAKKYIKEKKVLIDGKFAKENLEITNIENHHISLNIDIKKIEYN 82

Query: 71  -------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                      +   +KP  + T     +   T+ D +   F     + RLD  T+G++ 
Sbjct: 83  LDEFIISNYENVIFLYKPPFMHTERHKLEDSLTISDIVSEHFKEYKLISRLDFETDGVIA 142

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQ 182
              DG     +       +           ++      KK  V++ I    +    +   
Sbjct: 143 AIKDGYKPENVLKKYLAVVIGNFPEDTIVFNKIVYKKRKKVKVLEEIDLEHLSNIKVINS 202

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             + + + + + +    +I+    F  + + 
Sbjct: 203 DKNYSLLEITIFKATRHQIRAHLSFLGFPIL 233


>gi|237668428|ref|ZP_04528412.1| hemolysin A [Clostridium butyricum E4 str. BoNT E BL5262]
 gi|237656776|gb|EEP54332.1| hemolysin A [Clostridium butyricum E4 str. BoNT E BL5262]
          Length = 270

 Score = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 28/176 (15%), Positives = 48/176 (27%), Gaps = 2/176 (1%)

Query: 11  FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
              +R+  ++   GI  SR + +  I + RV VNG  +++A   V     IE  G  L+ 
Sbjct: 3   EKKERLDILLVEKGIITSREKAKACIMEGRVYVNGQKVDKAGEKVGVDSDIEYRGDTLKY 62

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             R  L L         T  D                 ++  G   +    +        
Sbjct: 63  VSRGGLKLEKAMATWDLTLDDKVCMDIGAST-GGFTDCMLQNGAAKVFAVDVGYGQFAWK 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           L     +   +   +  V      +            I         + L    G 
Sbjct: 122 LRTDERVVCMERTNIRYVTPEDIDNDLLDFASIDVSFISLKKIMPATLGLLKDDGE 177


>gi|257062155|ref|YP_003140043.1| hemolysin A [Cyanothece sp. PCC 8802]
 gi|256592321|gb|ACV03208.1| hemolysin A [Cyanothece sp. PCC 8802]
          Length = 266

 Score = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 1/56 (1%)

Query: 12 TPQRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
          T QR+  ++    + S R+E + +I    VKVN  ++++    V ST  IE+   P
Sbjct: 2  TKQRLDTLLVERNLCSSRQEAQGLIRAGEVKVNQQVIDKPGTPVESTAEIELQAKP 57


>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 = 59.0 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 35/263 (13%), Positives = 67/263 (25%), Gaps = 52/263 (19%)

Query: 3   DKNIVQENFTPQRVSKVIARAG---IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K  +    T  R+ K++         SR  ++++I ++ + VN  ++      V     
Sbjct: 2   NKITLNSVNTTLRLDKLLVELLTSYDYSRSYIQKLIKEECISVNNQIITSNNFLVKPNSQ 61

Query: 60  IEV-------DGVP---------------------LRKAERTRLWLYHKPIGLVTTHSDP 91
           I +       D                        +   +   L +  +    V    + 
Sbjct: 62  IIITIKDPVLDPNITKNKDPVLDPNITKNKDIDLNIIYQDDDLLVINKQNNITVHPSLNN 121

Query: 92  DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151
              + V   L S        G L       +     G L       + + L         
Sbjct: 122 TNNTIVNALLASDVELSSINGELRPGIVHRIDKQTTGLLIVAKNDKTHKLLSEMFKNHQI 181

Query: 152 QVDQ-------DKLNLLKKGIVIQGICY--GDMQVTLDTQKGSNAWVTVG---------- 192
             +         K N       I         M VT    K +     V           
Sbjct: 182 YKEYLAIVTGVIKPNKGLIDAPIGRSQTDRKKMSVTAKNSKHAITTFEVVERFLKNTLIK 241

Query: 193 --LREGKNREIKKVFEFFNWKVN 213
             ++ G+  +I+  F + N  V 
Sbjct: 242 CQIQTGRTHQIRVHFNYINHPVL 264


>gi|167957172|ref|ZP_02544246.1| Hemolysin A [candidate division TM7 single-cell isolate TM7c]
          Length = 199

 Score = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          QR+ + I    +  SR + E  I   RV VNG ++++    V + D + ++
Sbjct: 3  QRLDRYIVENRLTNSRSQAENYIRLGRVTVNGEVIKKCGFIVSTVDKVVLN 53


>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 = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 27/247 (10%), Positives = 66/247 (26%), Gaps = 35/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+ + I+     P+R+   +  R    SR  ++RMI    V+VN  + +  +  + + D 
Sbjct: 1   MQTEFIISAGEQPKRLDVFLVQREPKLSRAALQRMITAGWVRVNSHIAKS-SQRIRAGDV 59

Query: 60  IEVD----------GV----PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I  D          G      +   +   L L      +          + +   L    
Sbjct: 60  IVFDTPQPAPLRIAGETQQLEVLFEDHACLVLNKPAGIVTHPSPGHWSNTLLNALLDHCA 119

Query: 106 SRVISVGRLDIN----TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
               +     ++        +++      A        +   + R      V     +  
Sbjct: 120 RGGGAATPGVVHRLDKDTSGVMVVAKTEEAHRKLSEQFERHSITRQYEALVVGVPAQSEG 179

Query: 162 KKGIVIQGICYGDMQVTLDTQKG-------------SNAWVTVGL--REGKNREIKKVFE 206
           +    +    +   + +  T +                    + L    G+  +I+    
Sbjct: 180 RIEAALGPDRHHPKRTSTQTLQPKPAVTDYRVEEVFDKVAARLVLSPHTGRTHQIRAHLH 239

Query: 207 FFNWKVN 213
                + 
Sbjct: 240 VIGHPIL 246


>gi|295099509|emb|CBK88598.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           cylindroides T2-87]
          Length = 305

 Score = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 30/248 (12%), Positives = 69/248 (27%), Gaps = 37/248 (14%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+ +  I+ +     RV K +A     SR+ V+ ++ +  + VNG   + A+  +   DH
Sbjct: 1   METREFIIDDENAKIRVDKAVASLLDFSRKRVKDILDEGNILVNGSPCK-ASYILQEGDH 59

Query: 60  IEVD------------GVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           + V+             +P  +   +   + +      +V         + V   +    
Sbjct: 60  LLVNIPEVQSLEVLPENIPLNIVYEDDDVIVINKPKGMVVHPAFGHVSGTLVNALMYHCK 119

Query: 106 SRVISVGRLDINTEGLLLLTNDG---------------------GLARVLELPSTQWLRV 144
                 G +       +     G                        R            
Sbjct: 120 DLSGINGVMRPGIVHRIDKDTSGLLVVCKNDKAHLALSEQLSNKTCHREYLAIVHHPFSH 179

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                +  + +D+ +  K  +            T+       A V   L  G+  +I+  
Sbjct: 180 EHGTINAPIGRDEKDRQKMAVTANNSKEAITHFTVLENFKDYALVRCRLETGRTHQIRVH 239

Query: 205 FEFFNWKV 212
            ++    +
Sbjct: 240 MQYIKHPI 247


>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 = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 29/242 (11%), Positives = 68/242 (28%), Gaps = 36/242 (14%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-- 60
           +       +R+ KV+A        SR  ++ +I +  V +N   +++    V + D I  
Sbjct: 10  MTTAEEAGKRLDKVLAER-YPDAYSRSYLQWLIEENHVLLNHKPVKK-RAKVAAGDRIDV 67

Query: 61  ------EVDGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                 E++  P      +   +   + +      +V   +     + V   L       
Sbjct: 68  CFVLAPEIELKPEKIFLDIIHEDEAIIVVNKPAGLVVHPGAGNWTGTFVNGLLYHCKKLP 127

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------------- 155
                       L   T    +A        + + ++  R   +                
Sbjct: 128 EGETLRPGIVHRLDKETTGLLVAAKTAEAQHKLVELFSSRRVYKEYIAVCVGNPGKGTVD 187

Query: 156 ----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                     +K  +++G               S + V + L  G+  +I+   +   + 
Sbjct: 188 APIARHPVHRQKMAIVEGGRRSVTHYETLKYDVSLSLVKLVLETGRTHQIRVHMKQIGFP 247

Query: 212 VN 213
           V 
Sbjct: 248 VL 249


>gi|283458437|ref|YP_003363061.1| putative rRNA methylase [Rothia mucilaginosa DY-18]
 gi|283134476|dbj|BAI65241.1| predicted rRNA methylase [Rothia mucilaginosa DY-18]
          Length = 242

 Score = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  AG  +SR    ++IA + V+VNG +  +A++ V   D + V
Sbjct: 1  MRLDKYLVEAGFVSSRTLAAKLIAARDVQVNGKVARKASMLVGPEDTLYV 50


>gi|329577702|gb|EGG59129.1| S4 domain protein [Enterococcus faecalis TX1467]
          Length = 64

 Score = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 16/60 (26%), Positives = 30/60 (50%), Gaps = 1/60 (1%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +     
Sbjct: 1  MRLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLISHRPM 60


>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 = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/246 (14%), Positives = 72/246 (29%), Gaps = 39/246 (15%)

Query: 4   KNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K +  +   P RV K +      A+R +V++      V VN I ++     V   D + V
Sbjct: 19  KFVAADGQEPLRVDKFLMNFIENATRNKVQQAAKAGNVLVNDIAVKS-NHKVKPKDVVRV 77

Query: 63  -------------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                        + +PL     +   + +      +V         + V   +  I + 
Sbjct: 78  VLAYPPAENLLVAEDIPLDIIYEDDAVIVVNKPAGMVVHPGHGNYSGTLVNGLIHHIENL 137

Query: 108 VISV-------GRLDINTEGLLLLTNDGGLARV-------------LELPSTQWLRVYRV 147
             +         R+D +T GLL++                              +     
Sbjct: 138 PTNSNERPGLVHRIDKDTSGLLVVAKTEFAMAHLSKQFFDRTTERLYYALVWGNIEEDEG 197

Query: 148 RFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
           R  G + +   N L+  +   G    +      +  +      V   L  G+  +I+  F
Sbjct: 198 RIEGNIGRSLKNRLQMAVFPDGDFGKHAVTHFKVLERLTYVTLVQCKLETGRTHQIRAHF 257

Query: 206 EFFNWK 211
           +     
Sbjct: 258 KHIGHT 263


>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 = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 34/237 (14%), Positives = 71/237 (29%), Gaps = 38/237 (16%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ +++A+    SR +V   I    V ++G + ++  V V    ++ V            
Sbjct: 11  RLDQLLAQELNISRSQVLGCIKAGLVSMDGKICQKGGVEVKPGSYVCVQEPPTAEITPLP 70

Query: 63  ----------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
                     D   L   +   L ++  P     +  D         +  +  SR   V 
Sbjct: 71  TTLNIECLYEDEDLLVINKPPHLAVHPAPSLKEESLVDYLVAKGYQLSNLNGTSRCGIVH 130

Query: 113 RLDINTEGLLLLTNDGGLARV----LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           RLD  T G L++  +          L+        V  ++ H +        L +    +
Sbjct: 131 RLDKETSGALVIAKNNACHAHLSAQLQSRQMGRYYVALIQGHLREPLFVECHLGRHPKNR 190

Query: 169 GICYGDMQVTLDTQKGSNAWV---------TVG---LREGKNREIKKVFEFFNWKVN 213
                   + +   K S  +           +    L  G+  +++   E     + 
Sbjct: 191 LKRANLDALKVKGGKPSKTFFVPLFDGLKCQLVGARLYSGRTHQVRAHLESLGRPIL 247


>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 = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 34/239 (14%), Positives = 70/239 (29%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I +QRV++NG +++R    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKTWILEQRVQINGNMVDRPKEKVLGGESVAIDA 69

Query: 65  ----------VPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                      P+       +   L +      +V   +     + +   L         
Sbjct: 70  LIEEDARWEAQPISLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHHYPEIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++         L                               
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQAREITREYEAVAIGTMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 ARHSTKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMAHINHPLV 248


>gi|300869762|ref|YP_003784633.1| hemolysin A [Brachyspira pilosicoli 95/1000]
 gi|300687461|gb|ADK30132.1| hemolysin A [Brachyspira pilosicoli 95/1000]
          Length = 240

 Score = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ + +   G   SR + + +I    V VNG+ +   A  +  TD IEV
Sbjct: 1  MRLDEYVHHNGYTESRSKAQDIILAGCVFVNGVKVTSKAQKIKDTDKIEV 50


>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 = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 34/248 (13%), Positives = 70/248 (28%), Gaps = 35/248 (14%)

Query: 1   MKDKNIVQ----ENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVM 55
           M  K  +     E+   QR+ + +A      SR  ++  I   +V VNGI        V+
Sbjct: 1   MTQKIQLNTTVCESQLGQRLDRALAELFPTYSRSRIKEWILAHQVTVNGITKSIPKEKVL 60

Query: 56  STDHIEV-----DGVPLRKAERT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
             +HIE+     +       +            L +      +V   +     + +   L
Sbjct: 61  GGEHIEIHTYIEENKRWMPQKIPLNIIYEDTDILVINKPSGLVVHPGAGNPDHTILNALL 120

Query: 102 PSIFSRVISV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWL-----------RVY 145
                           RLD +T GL+++         L       L            + 
Sbjct: 121 DYYPDITHVPRAGIVHRLDKDTTGLMVIAKTLRAQTSLVDALQARLVTREYEAIAVGHIT 180

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                 +      +      V            +     ++  + + L  G+  +I+  F
Sbjct: 181 AGGSINEPIARHKSKRTHMAVHPLGKSAVTHYRILQHFRAHTRLRLRLETGRTHQIRVHF 240

Query: 206 EFFNWKVN 213
            + +  + 
Sbjct: 241 SYIHHPLV 248


>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 = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 34/248 (13%), Positives = 76/248 (30%), Gaps = 37/248 (14%)

Query: 1   MKDKN-----IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           M++KN      VQ +    R++  +      S R + +   + R+KVN   +   +  + 
Sbjct: 1   MEEKNNILKIKVQIDEEEIRLNHYLKNHANCSSRFIRKAAREGRIKVNNENVR-LSYMLK 59

Query: 56  STDHIEV-----DGVPLRKAERT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
           + D IE+     +   +   +            + +      +V         +     L
Sbjct: 60  NDDVIELQINREENQDIVPEKMHLDVIYEDKDIVVINKPKGIVVHPTKRHQNGTLSNGVL 119

Query: 102 PSIFSRVISV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY-RVRFHGQVDQ 155
                +  +       RLD++T GL+L+  +      L     +   V   +       +
Sbjct: 120 YYFKEKNENSIVRLVNRLDMDTSGLVLIAKNAYSHMALSRDMQKDDFVKSYLAIVHGNLK 179

Query: 156 DKLNLLKKGIVIQGICYG-----------DMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
           +K  ++ K I   G                 +  +         V + L  G+  +I+  
Sbjct: 180 EKSGVINKPIYRVGEGTLRRVIDERGQRSVTRFKVVESYEDADLVELTLETGRTHQIRVH 239

Query: 205 FEFFNWKV 212
                  +
Sbjct: 240 LSSIGHPI 247


>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 = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 29/234 (12%), Positives = 68/234 (29%), Gaps = 35/234 (14%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----- 68
           +R+   +++    +R  ++ +I    + VNG    +A+  V   D I +D   L+     
Sbjct: 11  ERIDIYLSKKLDETRSRIQELIKSNNILVNGKK-TKASYKVNFGDEIFIDIPLLKEVDII 69

Query: 69  --------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR------- 113
                     E   L + +K  G+V   S      T+ + +      +  +         
Sbjct: 70  PQDIDIDIVYEDKYLAIINKYAGMVVHPSKGHEEDTLVNAIMYKIKDLSGINGDLRPGIV 129

Query: 114 -LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH-------------GQVDQDKLN 159
                    L++               +   + ++ +                +     N
Sbjct: 130 HRLDKNTSGLIIIAKDDKTHFKLSEMFKNKEIKKIYYAIVKGKVNKKSGRIETMIGRNPN 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             KK  V+           +       + + V L  G+  +I+     F + + 
Sbjct: 190 DRKKMAVVDNGKLAITNFEVIDSNEKFSLLKVDLETGRTHQIRVHLSHFFFPIL 243


>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 = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 33/250 (13%), Positives = 73/250 (29%), Gaps = 39/250 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+   +  E+    R+ K + +     SR  +++++   +V V G  ++ A+  V   D 
Sbjct: 1   MERFRVTDEDG-GVRIDKYLTSVCEGLSRSYLQKLLKSGQVLVGGQGVK-ASYAVQEGDL 58

Query: 60  IE------VDGVPLR--------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           IE      V+   L           +   + +      +V   +     + V   L    
Sbjct: 59  IELEVPEAVEPEILAEPMDLDVLYEDEDIILINKPKGMVVHPAAGHYTHTLVNGLLDHCR 118

Query: 106 ---------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR---------- 146
                     R   V R+D++T G+++   +      L     +     R          
Sbjct: 119 GQLSGINGVMRPGIVHRIDMDTTGVIIACKNDLAHSCLAEQLKEHSITRRYQAIVHGVVK 178

Query: 147 ---VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                    + +  +   K  I             +  +      V   L  G+  +I+ 
Sbjct: 179 EDEGTVDAPIGRHPVERKKMSINYNNGREAVTHYKVLRRFRQYTHVECRLETGRTHQIRV 238

Query: 204 VFEFFNWKVN 213
                +  + 
Sbjct: 239 HMASIHHPLL 248


>gi|40889481|pdb|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna
           Pseudouridine Synthase Rlud
          Length = 349

 Score = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 33  TVSENQLGQRLDQALAEXFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 92

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
                           +   +   + +      +V   +     + +   L         
Sbjct: 93  EIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 152

Query: 107 -RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL-----------RVYRVRFHGQVD 154
            R   V RLD +T GL ++         L     +                      +  
Sbjct: 153 PRAGIVHRLDKDTTGLXVVAKTVPAQTRLVESLQRREITREYEAVAIGHXTAGGTVDEPI 212

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 213 SRHPTKRTHXAVHPMGKPAVTHYRIXEHFRVHTRLRLRLETGRTHQIRVHXAHITHPLV 271


>gi|184201185|ref|YP_001855392.1| hypothetical protein KRH_15390 [Kocuria rhizophila DC2201]
 gi|183581415|dbj|BAG29886.1| hypothetical protein [Kocuria rhizophila DC2201]
          Length = 255

 Score = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 13 PQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            R+ + +   G+A SR      I   +V VNG  + +A+  V   D +EV+
Sbjct: 2  STRLDRALTDRGLARSRTVAAGWIRDGKVSVNGAPVTKASTPVSEQDRVEVE 53


>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 = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 39/245 (15%), Positives = 70/245 (28%), Gaps = 41/245 (16%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +     RV K +    + ASR  +++      V  NG  ++  +  V   D I V  
Sbjct: 33  VVDKGQAMVRVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKS-SYKVKPLDVITVMM 91

Query: 63  -----DGVPLR-------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                D   +          E   L + +KP GLV      +   T+ + +         
Sbjct: 92  DRPRYDNEIIPEDIPLHIVYEDKYLMVVNKPAGLVVHPGHGNYHGTLVNAIAWHLKDDPV 151

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-------- 152
                  V  V R+D +T GLL++         L +         R R            
Sbjct: 152 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGVQFFNKTTKRRYRALVWGIVDQDEG 211

Query: 153 -------VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                   +      +          +      +  + G    V   L  G+  +I+   
Sbjct: 212 TIVGSIARNPKDRMQMAVMADPTQGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHM 271

Query: 206 EFFNW 210
           +    
Sbjct: 272 KHIGH 276


>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 = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 32/248 (12%), Positives = 76/248 (30%), Gaps = 37/248 (14%)

Query: 1   MKDKN-----IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           M++KN      VQ N    R++  +      S R + +   + R+KVN   +   +  + 
Sbjct: 1   MEEKNNVLKLKVQINDEEIRLNHYLKNYAKCSSRFIRKAAREGRIKVNNENVR-LSYMLK 59

Query: 56  STDHIEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
           + D IE+                  +   +   + +      +V         +     L
Sbjct: 60  NNDLIEIQINRKEEQDIVPEKMKLDIIYEDEDIIVINKPKAIVVHPTKRHLNGTLSNGVL 119

Query: 102 PSIFSRVISV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
                +  +       RLD++T GL+L+  +      L     +   + R       + +
Sbjct: 120 YYFKEKNENSIVRLVNRLDMDTSGLVLIAKNAYSHMALSRDMQKDDFIKRYLAIVHGNLE 179

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV------------TVGLREGKNREIKKV 204
           + + +    + +       +V  +  + S                 + L  G+  +I+  
Sbjct: 180 EKSGVIDKPIYRVGEGTLKRVIDERGQKSITRFKVIESYENADLIELTLETGRTHQIRVH 239

Query: 205 FEFFNWKV 212
                  +
Sbjct: 240 LSSIGHPI 247


>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 = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 33/232 (14%), Positives = 64/232 (27%), Gaps = 37/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------DGVP 66
           R+ K +A     SR +    I Q+RV VNG   ++A   V   D I          D   
Sbjct: 11  RLDKALADLTPLSRSQANDQIKQKRVLVNGSP-KKAKYIVQVGDCISYHIPEESSLDYQA 69

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 +   +   + +      +V   +     + V   L  +       G +      
Sbjct: 70  QDIPLDIVYQDDVLVIINKPQGMVVHPSAGHSTGTLVNALLYHVKDLSSINGVIRPGIVH 129

Query: 121 LLLLTNDGGLA---------------------RVLELPSTQWLRVYRVRFHGQVDQDKLN 159
            +     G L                      R         L   R      + +   +
Sbjct: 130 RIDKDTSGLLMVAKTDKAHQLLADELKAKKSLRKYVAIVHGNLPKDRGVIEAPIGRSDKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             K+ +  +G      +  +  + G  + V + L  G+  +I+    +    
Sbjct: 190 RKKQTVTAKGKEALT-RFKVLERFGRYSLVELQLETGRTHQIRVHMAYIGHP 240


>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 = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 32/236 (13%), Positives = 64/236 (27%), Gaps = 36/236 (15%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------- 63
               R+ K ++  G  SR +V+  I    + VNG  ++ A   +   D +EV+       
Sbjct: 9   DEKARIDKWVSDRGEWSRSQVQEWIKTGALLVNGSAVK-ANYKLQVGDEVEVNVPEAVEL 67

Query: 64  -----GVPLRK--AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG---- 112
                 +PL     +   + +      +V   +     + V   L          G    
Sbjct: 68  EVLPEDIPLEIVFEDEDVIVVNKARGMVVHPAAGHTSGTLVNALLYHCDDLSGINGVKRP 127

Query: 113 -----------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
                            + D+  E L     D  + R         L          + +
Sbjct: 128 GIVHRIDKDTTGLLMVAKNDLAHESLASQLKDKTIKREYIALVHGELVHELGTIEAPIGR 187

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           D  +  +  +  +          L  +      V   L  G+  +I+    +    
Sbjct: 188 DTNDRQRMTVTDRNAKEAVTHFRLLERYKDFTLVECKLETGRTHQIRVHMRYIGHP 243


>gi|222147750|ref|YP_002548707.1| hemolysin A [Agrobacterium vitis S4]
 gi|221734738|gb|ACM35701.1| hemolysin A [Agrobacterium vitis S4]
          Length = 263

 Score = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 1/57 (1%)

Query: 9  ENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          ++  PQR+ +++ A    ASR      + +  VKVNG  + + ++       IE+D 
Sbjct: 8  QSLEPQRLDQLLVALNLFASRSRARDAVQRGGVKVNGRTVTKPSLTFSPDVTIEIDD 64


>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 = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 32/248 (12%), Positives = 74/248 (29%), Gaps = 40/248 (16%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +VQ  ++ +R+  V++      SR +++R I  ++V +N  +       V+S + IE++ 
Sbjct: 15  VVQIAYSGKRLDWVLSELLPQFSRSQIKRWIINKKVVINNQISVLPKKKVISGEIIEIND 74

Query: 65  V--------------------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           +                     +   +   L +      +V      +  + +   L   
Sbjct: 75  INNDSTSDCNNNILIPQNISLNIVYEDNDILVINKPSNMVVHPGVKNNKDTVLNALLYRY 134

Query: 105 FSRVISV------GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
            S +          RLD +T GL+++         L         +              
Sbjct: 135 PSIMQISKQAGIVQRLDKDTTGLMIIAKTYLAYTNLLQSFKMKQVIKEYDAVVCGTFSYN 194

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGS-------------NAWVTVGLREGKNREIKKVF 205
             +    + +              K +              + + V L  G+  +I+   
Sbjct: 195 AGIISQPIRRHSINRTCMTVHPHGKPAVTRYSVVESFGRTYSRIRVYLETGRTHQIRVHM 254

Query: 206 EFFNWKVN 213
            + N  V 
Sbjct: 255 AYINHPVV 262


>gi|258593870|emb|CBE70211.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [NC10 bacterium 'Dutch sediment']
          Length = 314

 Score = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 25/234 (10%), Positives = 56/234 (23%), Gaps = 36/234 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----------EVDG 64
           R+ + ++ A    R +++R+I   RV V+G    +A+        I           +  
Sbjct: 19  RLDRYLSTATGLPRSQIQRLIKAGRVLVDGR-CPKASAIAHPGQQISLSIPPPQPSTLTP 77

Query: 65  VPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            P+       +   L L      +V         + V   L                   
Sbjct: 78  EPIPLDILYEDTDMLVLNKPAGLVVHPAPGHHSGTLVHAILYHCPDLPGIGEERRPGIVH 137

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------------------DKLN 159
            L     G +       +   L         Q                         + +
Sbjct: 138 RLDKETSGVMVVAKTDTAMASLATQFKGRRVQKTYIALVHGEVKQPQGQIAADIGRHERD 197

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             +  +  +          +  + G    + +  + G+  +I+         V 
Sbjct: 198 RKRMAVRTRKGREAVTNYRVIKRLGGLTLLELQPQTGRTHQIRVHLSAIGHPVV 251


>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 = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/245 (14%), Positives = 66/245 (26%), Gaps = 41/245 (16%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +     RV K +    + ASR  +++      V  NG  ++  +  V   D I V  
Sbjct: 33  VVDKGQAMVRVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKS-SYKVKPLDVITVMM 91

Query: 63  -----DGVPLR-------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                D   +          E   L + +KP GLV      +   T+ + +         
Sbjct: 92  DRPRYDNEIIPEDIPLHIVYEDKYLMVVNKPAGLVVHPGHGNYHGTLVNAIAWHLKDNPD 151

Query: 111 VGRLDIN----------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-------- 152
               D +          T GLL++         L +         R R            
Sbjct: 152 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGVQFFNKTTKRRYRALVWGIVDQDEG 211

Query: 153 -------VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                   +      +          +      +  + G    V   L  G+  +I+   
Sbjct: 212 TIVGSIARNPKDRMQMAVMADPTQGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHM 271

Query: 206 EFFNW 210
           +    
Sbjct: 272 KHIGH 276


>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 = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 32/247 (12%), Positives = 64/247 (25%), Gaps = 35/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K  +       R+  ++A+  +  SR  +   +    + VNG+ ++R A  V + D 
Sbjct: 1   MTKKITINIIDQIGRIDAILAKENLPYSRTTLAEWLQTGHILVNGVQVKR-AYKVTTGDT 59

Query: 60  IEV------------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I +            + +PL     +   L +      +V   +     + V   L    
Sbjct: 60  ITILQPEVITTEIIAEDIPLDIIYEDDDILVVNKPQGMVVHPAAGHSSGTLVNALLFHAP 119

Query: 106 SRVISVGRLD-------------------INTEGLLLLTNDGGLARVLELPSTQWLRVYR 146
              I+                              L           +     +   V  
Sbjct: 120 LSTINGEFRPGIVHRIDRDTSGLLMVAKNDQAHQGLSAQLKAHKNDRIYYALVRGEFVEN 179

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          KK  V +G         +  +      + V L  G+  +I+    
Sbjct: 180 SGTINAPINRHKVDRKKQAVQEGGREAITHFEVIERYVGYTLLKVRLETGRTHQIRVHMT 239

Query: 207 FFNWKVN 213
           +    V 
Sbjct: 240 YIGHPVV 246


>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 = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 81/248 (32%), Gaps = 42/248 (16%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V +  TP R+ + + +    A+R +V++ I +QRV VNG  ++     + S DHI +   
Sbjct: 5   VSKVQTPMRIDRYLTQQVENATRNKVQKAIEEQRVLVNGKPVKS-NYRIKSCDHIHITFL 63

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------- 105
                    + +P+    E   L +  K  G+V   +  +   T+ + +           
Sbjct: 64  RPPAPELAPEDIPISILYEDDDLMVIDKEAGMVVHPAFGNWTGTLANAILHHLGKDADDL 123

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLAR----VLELPSTQWLRVYRVRFHGQVD--- 154
                R   V RLD +T GL+++  +                + +    V          
Sbjct: 124 DKTEMRPGIVHRLDKDTSGLIIVAKNPVALHKLATQFARRQVEKVYKAIVWGVPNPPSGT 183

Query: 155 -------QDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTVGLREGKNREIKKVF 205
                    K   +      +G             +     A + + L  G+  +I+   
Sbjct: 184 IKTNIGRSHKNRKVMANFPFEGAEGKHAITDYLVVEDLAYFALMDMTLHTGRTHQIRVHL 243

Query: 206 EFFNWKVN 213
           +     + 
Sbjct: 244 QHLGHPIL 251


>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 = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 38/245 (15%), Positives = 68/245 (27%), Gaps = 39/245 (15%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V      +R+ K++AR     SR  +++ I    V+V+G +  R    V   + IEV   
Sbjct: 68  VDSASHGERLDKLLARHFSEFSRSRLQQWIESGAVRVDGQV-RRPRDAVQMGNRIEVQPQ 126

Query: 66  P---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   + T L +      +V   +     + +   L         
Sbjct: 127 AAPEASAFAPEDVPLDVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRDPGAASL 186

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL-RVYRVRFHGQVDQDKLNLLKKG 164
            R   V RLD  T GL+++         L         +   +        D+  +    
Sbjct: 187 PRAGIVHRLDKETSGLMVVARTLTAQTDLVRQLQARTVKRTYIALVWGRTYDEGTIDAPI 246

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVT----------------VGLREGKNREIKKVFEFF 208
                       V   + K S                       L  G+  +I+  FE  
Sbjct: 247 GRDPRERTRMAIVQTASGKPSRTHFRTLATVPLGRGFVSMVMCKLETGRTHQIRVHFESI 306

Query: 209 NWKVN 213
              + 
Sbjct: 307 GHPLV 311


>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 = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 30/265 (11%), Positives = 79/265 (29%), Gaps = 52/265 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M  + +  E    QR+ + +A+    + SR  ++ +I +  +K++G  ++     +    
Sbjct: 1   MVIQKVTDEGALDQRLDQWLAKQYHDVLSRSRLQTLIREGCLKIDGQFIKEPKTKLKPNQ 60

Query: 59  HIEV------DGVP--------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            IE+      D  P        +   +   + +      +V   +     + V   +   
Sbjct: 61  IIELEMPNLRDAEPSAEAIALDILYEDDHVIVINKPAGLVVHPGNGNWTGTLVNALIYHC 120

Query: 105 FS---------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ--- 152
            +         R   V RLD NT G++++  +    + L    +   R   +        
Sbjct: 121 GNSLSGIGGVKRPGVVHRLDKNTSGVMVVAKNDLAHKSLSAQFSDHGRTCALDRRYHALI 180

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN------------------------AW 188
                 N+      +    +   +  +  ++  +                        + 
Sbjct: 181 WGTPHRNVWTIDASLGRSPHNRTKQAVVHKQTPHARHAVTHFSLLEKYGTHADSTSFASL 240

Query: 189 VTVGLREGKNREIKKVFEFFNWKVN 213
           +   L  G+  +I+         + 
Sbjct: 241 LECRLETGRTHQIRVHMAHIGHPLI 265


>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 = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 30/245 (12%), Positives = 64/245 (26%), Gaps = 41/245 (16%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +     RV K +    + ASR  +++      V  NG  ++  +  V   D I V  
Sbjct: 33  VVDKGQAMVRVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKS-SYKVKPLDVITVMM 91

Query: 63  -----DGVPLR--------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                +   +           +   + +      +V         + V      +     
Sbjct: 92  DRPRYENEIIPENIPLNIVYEDPYVMVVNKPAGLVVHPGHGNYHGTLVNALAWHMKDIPE 151

Query: 110 SV---------GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK--- 157
                       R+D +T GLL++         L +         R R     + ++   
Sbjct: 152 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGIQFFNKTTKRRYRALVWGNVEQDEG 211

Query: 158 ------------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                          +          +      +  + G    V   L  G+  +I+   
Sbjct: 212 TIVGSIARNPKDRMQMAVMSDPSMGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHM 271

Query: 206 EFFNW 210
           +    
Sbjct: 272 KHIGH 276


>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 = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 30/249 (12%), Positives = 71/249 (28%), Gaps = 33/249 (13%)

Query: 5   NIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           N V++    QR+ + IA      SR  ++  +   +V+V+G ++ +    VM  + I + 
Sbjct: 9   NTVKDAQLGQRLDQAIAELFSDFSRSRLKDWLLDGKVQVDGEVVTKPRTKVMGGEVIVLH 68

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   +   + +      +V   +     + +   L        
Sbjct: 69  AELEDEERWEAQDIPLDIVYEDDDIIVINKPRGFVVHPGAGTPDGTVLNALLHHFPDIAE 128

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   RLD +T GL+++         L     +                    +++ 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRMTAGGRVEQP 188

Query: 165 IVIQGIC---------YGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I                        +      +  + + L  G+  +I+    +    + 
Sbjct: 189 IGRHSTKRTLMAVAPLGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIRVHMAYLQHPL- 247

Query: 214 RLIRISYGP 222
            L   +YG 
Sbjct: 248 -LGDTAYGG 255


>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 = 58.7 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 33/245 (13%), Positives = 65/245 (26%), Gaps = 41/245 (16%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +  TP R+ K +    + ASR  ++       V  NG  ++  +  V   D + V  
Sbjct: 32  VVDKGQTPVRIDKYLFERIVNASRNRIQTAADAGFVMANGKPVKS-SYKVKPLDVLTVMM 90

Query: 63  -----------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                      + +PL    E   L + +KP GLV      +   T+ + +      V S
Sbjct: 91  DRPRYENDIIPEDIPLDIVYEDNDLMVINKPAGLVVHPGCGNYHGTLVNAIAWHLRDVPS 150

Query: 111 VGRLDINTE-------------------------GLLLLTNDGGLARVLELPSTQWLRVY 145
               D                             G+              +         
Sbjct: 151 YDPNDPQVGLVHRIDKDTSGLLVVAKTPDAKTSLGMQFYNKTTKREYNALVWGIVEEDEG 210

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
            +  +   +      +          +      +  + G    V   L  G+  +I+   
Sbjct: 211 TITGNIGRNPKDRMQMAVMSDPTQGKHAVTHYQVLERLGYVTLVKCVLETGRTHQIRVHM 270

Query: 206 EFFNW 210
           +    
Sbjct: 271 KHIGH 275


>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 = 58.7 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/239 (12%), Positives = 63/239 (26%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  +HI +D 
Sbjct: 10  TVTENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGNIGDKPKEKVLGGEHIAIDV 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  EIEEEARFQPQDIPLNIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--- 156
                  R+       +     +        +  L   + ++  V           +   
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTIPAQTRLVESLQLREITREYEAVAIGHMTSGGTVEEPI 189

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRIHTRLRLRLETGRTHQIRVHMSHITHPLV 248


>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 = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 26/245 (10%), Positives = 61/245 (24%), Gaps = 35/245 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M    +  ++    RV K +A      SR ++++ IA   V+VNG  ++ A   +   D 
Sbjct: 1   MDTFKLTVDDTLTGRVDKALAHHFRQFSRSQLQKWIADGNVQVNGEAVK-AKAKLAVGDQ 59

Query: 60  IEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           + +                  +   +   + +      +V         + V   L    
Sbjct: 60  VVIKPEAPQKIDLVPEKIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHCP 119

Query: 106 SRVISVGRLDINTEGL-------------------LLLTNDGGLARVLELPSTQWLRVYR 146
              I+          +                   L         +   +     +    
Sbjct: 120 LSTINGEFRPGIVHRIDKDTSGLLMVAKNDLAHRSLAAQLKAKTNQREYVALVHGVIKQD 179

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          KK  ++    +      +  +      V+  L  G+  +I+   +
Sbjct: 180 AGTVDAPIGRSKKDRKKQAIVSDGRHAVTHFKVLERFRHYTLVSCRLETGRTHQIRVHMK 239

Query: 207 FFNWK 211
                
Sbjct: 240 SIGHP 244


>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 = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 30/240 (12%), Positives = 69/240 (28%), Gaps = 31/240 (12%)

Query: 5   NIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           N V+++   QR+ + +A      SR  ++  +   ++ VNG ++ +    VM  + I V 
Sbjct: 9   NTVKDSQLGQRLDQAVAELFADFSRSRLKEWLLDGKIAVNGEVITKPRTKVMGGELITVQ 68

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
                            +   +   + +      +V   +     + +   L        
Sbjct: 69  AELEDEERFEAQDIPLNIVYEDDDIIVINKPRDFVVHPGAGTPDGTVLNALLHHFPAIAE 128

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
             R   V RLD +T GL+++         L     +                   ++ K 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGKMTAGGMVDKA 188

Query: 165 IVIQ---------GICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I                        +      +  + + L  G+  +I+    +    + 
Sbjct: 189 IGRHSTKRTLMAVNELGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPLL 248


>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 = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/249 (12%), Positives = 68/249 (27%), Gaps = 42/249 (16%)

Query: 4   KNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K  V +    +R+ K +  R   +SR  +++      + VNG  ++     V   D I +
Sbjct: 33  KIEVDKGQEKERIDKFLFERMQHSSRNRIQKAADSGFIHVNGQPVKS-NYKVRPLDVITL 91

Query: 63  ------DGVPLRKAERTRLWLY---------HKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                     +   +     +Y              +V   +     + +      +   
Sbjct: 92  MLDRPKHDNTIEPEDIPLDVIYEDDDLMVIMKPAGLVVHPGAGNFHGTLINAIAWHLKDL 151

Query: 108 VISV---------GRLDINTEGLLLLTNDGG-------------LARVLELPSTQWLRVY 145
                         R+D +T GLLL+                    R             
Sbjct: 152 ASFDANDPEVGLVHRIDKDTSGLLLIAKTPEAKTKLGKQFFNKTTHRSYIALVWGNFVED 211

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             R  G + +D  + L+  +         +      +  + G    +   L  G+  +I+
Sbjct: 212 EGRIEGNIARDPKDRLRMTVFPPDSEIGKHAVTHYKVIERFGYTTLIECILETGRTHQIR 271

Query: 203 KVFEFFNWK 211
              ++    
Sbjct: 272 AHMKYIGHP 280


>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 = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 33/232 (14%), Positives = 64/232 (27%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--------- 65
           R+ K +A     SR      I   ++ VNG L+++A   V   D I  +           
Sbjct: 11  RLDKAVADLTDLSRSLANEQIKTGKILVNG-LVKKAKYTVKEGDVISYELPEVEEVEYVP 69

Query: 66  -----PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 +   +     +      +V   +     + V   +  I       G L      
Sbjct: 70  EDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 121 LLLLTNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            +     G L       +           + LR Y    HG +  D+  +       +  
Sbjct: 130 RIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 171 CYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                          +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKSALTRFQVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 64/239 (26%), Gaps = 39/239 (16%)

Query: 13  PQRVSKV----IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
            QR+       +   G+  R  V+  I   R ++NG +  +AA  +M    + +      
Sbjct: 14  GQRLDVFWQTCLEEEGVG-RSRVQAWIKDGRARINGQVCSKAATRLMPGQTLTLAPEYTD 72

Query: 63  ------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
                 DG          L + +K   +    +      T+   +   F  ++S      
Sbjct: 73  SSVVPDDGPLNVFFADEDLVVVNKTPAMTVHPAPSVAEPTLVHRVAHHFPALLSQSGERP 132

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------------------D 156
                L     G +   L   +   L           +                      
Sbjct: 133 GIVHRLDKDTSGLIVLALSESARLSLTQAFASREVYKEYLALVAGVPDSSGTVSLALGRH 192

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                +  +V +G    + +  L       S + V V +  G+  +I+         + 
Sbjct: 193 PSIKTRMAVVERGGRAAETRFELLWSAADRSASLVRVRIMTGRTHQIRVHMAALGHPLL 251


>gi|183601729|ref|ZP_02963099.1| possible rRNA methyltransferase [Bifidobacterium animalis subsp.
          lactis HN019]
 gi|183219335|gb|EDT89976.1| possible rRNA methyltransferase [Bifidobacterium animalis subsp.
          lactis HN019]
 gi|289178509|gb|ADC85755.1| Putative cell adhesion protein (contact hemolysin TlyA-related)
          [Bifidobacterium animalis subsp. lactis BB-12]
          Length = 262

 Score = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 24/49 (48%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          +R+  V+A A   SR + +R+I   +V VNG    + A  V     I V
Sbjct: 14 ERLDVVVANATGESRSKAQRLIKTGKVHVNGHPQTKPAYAVQPESTISV 62


>gi|323702785|ref|ZP_08114445.1| hemolysin A [Desulfotomaculum nigrificans DSM 574]
 gi|323532302|gb|EGB22181.1| hemolysin A [Desulfotomaculum nigrificans DSM 574]
          Length = 268

 Score = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 14/59 (23%), Positives = 24/59 (40%), Gaps = 1/59 (1%)

Query: 12 TPQRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          T +R+   +   G  S RE     +    V V+   +++    V    H++V G PL  
Sbjct: 4  TKERLDVYLVNHGYFSSREKARAAVMAGLVFVDNRRVDKPGYPVKPDAHVQVQGDPLPY 62


>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 = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/245 (11%), Positives = 75/245 (30%), Gaps = 38/245 (15%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---- 60
           I+  N +  R+   +  +    SR  ++++I    + VNG  ++     +   D I    
Sbjct: 5   ILVSNESGIRIDAWLCGKVKDYSRSYIQKLINDGMILVNGKPVKS-NYKIKQNDEILARI 63

Query: 61  ----EVD------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                +D       VP+   +   + +      +V   +     + V   L    + + +
Sbjct: 64  PEPQVLDVVAEDIDVPILYEDEHIIVVDKPKGMVVHPAAGNYSGTLVNALLKHCGTNLSN 123

Query: 111 VG----------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
           +                       + +   EGL     D  + RV        +R    +
Sbjct: 124 INGIIRPGIVHRIDKDTSGVLVVAKSNAAHEGLSEKLKDHDIERVYIAVVHGIIREDYGK 183

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +  ++  K  +  +       +  +  +     ++   L  G+  +I+    + 
Sbjct: 184 IDAPIGRHPVDRKKMAVNTKNGRRAVTRFKVLERFKDATYIEATLETGRTHQIRVHMSYI 243

Query: 209 NWKVN 213
            + + 
Sbjct: 244 GFPII 248


>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 = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 75/244 (30%), Gaps = 39/244 (15%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVN------VMSTD 58
           IVQE+ + +R+  +++      SR +++  I  ++V VN   +            +   D
Sbjct: 31  IVQESQSGKRLDCILSELLPNYSRSKIKCWILSKKVNVNNQTVIIPKKKMMGGEFIEIKD 90

Query: 59  HIEVDGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
            + +D   +           E   + + +K   +V      +   T+ + L   +  +  
Sbjct: 91  IVNIDNNNIVPQDIPLDIVYEDDDIVVINKAKNMVVHPGAGNHSGTILNALLYKYPAITE 150

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
           V R        L     G +     + +   L     +     + + +  L   +  +G 
Sbjct: 151 VFRSG--IVQRLDKDTTGLMVVAKNMIAYHSLLRLFKKRKIIREYEAVV-LGNFLHNEGT 207

Query: 171 CYGDMQVTLDTQK---------------------GSNAWVTVGLREGKNREIKKVFEFFN 209
               ++     +                      G    + V L  G+  +I+    + N
Sbjct: 208 INQPIRRHAVHRTRMTVNPMGKSAITHYSIIESFGMYTRIRVRLETGRTHQIRVHMAYIN 267

Query: 210 WKVN 213
             + 
Sbjct: 268 HPLL 271


>gi|219683739|ref|YP_002470122.1| hemolysin-like protein [Bifidobacterium animalis subsp. lactis
          AD011]
 gi|219621389|gb|ACL29546.1| hemolysin-like protein with S4 domain found in bacteria and
          plants [Bifidobacterium animalis subsp. lactis AD011]
          Length = 259

 Score = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 24/49 (48%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          +R+  V+A A   SR + +R+I   +V VNG    + A  V     I V
Sbjct: 11 ERLDVVVANATGESRSKAQRLIKTGKVHVNGHPQTKPAYAVQPESTISV 59


>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 = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 32/232 (13%), Positives = 65/232 (28%), Gaps = 36/232 (15%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----- 68
           R+ KVIA      SR +++ ++  + + VN    E+ +  V S D I+V   P++     
Sbjct: 15  RLDKVIAEKITDLSRTKIKELVNDKNILVNNK-AEKVSYKVQSGDVIDVTIPPVKPLSLE 73

Query: 69  ---------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
                      +   + +      +V   +     + V   L        S         
Sbjct: 74  AENLHLDIVYEDSDVIVVNKPQGIVVHPSAGHPDHTLVNGLLYHTRDLADSPEGFRPGIV 133

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------------------DKLN 159
             +     G L       + + L         + +                        N
Sbjct: 134 HRIDKDTSGLLMIAKNDRARESLEKQLAEKINKREYLAIVHGNFEVKNGVINAPIGRNPN 193

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             K+  V           T+  Q  + + V   L  G+  +I+   ++    
Sbjct: 194 NRKQMAVNPKGKAAVTHFTVLEQFKNYSLVKCVLETGRTHQIRVHMKYIGHP 245


>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 = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 32/232 (13%), Positives = 62/232 (26%), Gaps = 31/232 (13%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-----DGVP 66
            QR+ + +A      SR  ++  I Q  V VNG ++      V   + IE+     D   
Sbjct: 16  GQRLDQALAELFPDYSRSRLKTWIEQNLVHVNGDVVNVPRAKVYGGEQIEIVVEIDDDTR 75

Query: 67  ---------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVG 112
                    +   +   L +      +V   +     + +   L          R   V 
Sbjct: 76  FEPENLPLNIVYEDDDILVINKPKDFVVHPGAGNASGTVLNALLYHYPAIAEVPRAGIVH 135

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-----------FHGQVDQDKLNLL 161
           RLD +T GL+++         L     +                      Q         
Sbjct: 136 RLDKDTTGLMVIAKTIPAQTKLVRDLQKRKITREYEAIACGIMTKGGMVDQPMARHPTKR 195

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               V            +  +  +   + + L  G+  +I+         + 
Sbjct: 196 THMAVHPMGKPAVTHYRIMERFRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 247


>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 = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/243 (12%), Positives = 66/243 (27%), Gaps = 37/243 (15%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I   RV VNG  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILDSRVTVNGKKINKPKEKVLGGELVAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-- 108
                           +   +   L +      +V   +     + +   L      +  
Sbjct: 70  QIEEDARWAPQEIPLDIVYEDNDILVINKPRGLVVHPGAGNPDGTVLNALLHYYPEIMDV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
                V RLD +T GL+++         L                   +      + +  
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNMTAGGRVDEP- 188

Query: 166 VIQGICYGDMQVTLD-TQKGSNAWVTVGLR--------------EGKNREIKKVFEFFNW 210
            I         + +    K +     +                  G+  +I+      N 
Sbjct: 189 -ISRHSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLRLETGRTHQIRVHMSHINH 247

Query: 211 KVN 213
            + 
Sbjct: 248 PLV 250


>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 = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/244 (14%), Positives = 71/244 (29%), Gaps = 40/244 (16%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +     RV K +  R   +SR  +++      V  NG  ++  +  V   D I V  
Sbjct: 33  VVDKGQEMMRVDKYLFDRLTNSSRNRIQKAADAGFVMANGKAVKS-SYKVKPMDVITVMM 91

Query: 63  -----DGVPLR-------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                +   +          E   L + +KP GLV      +   T+ + +         
Sbjct: 92  DRPRYENEVIPEDIPLDIVYEDKYLMVVNKPAGLVVHPGHGNYHGTLVNAIAWHMKDNPD 151

Query: 111 VGRLDIN----------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK--- 157
               D +          T GLL++         L           R R     + ++   
Sbjct: 152 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGNQFFNKTTKRRYRALVWGNVEQDEG 211

Query: 158 ----------LNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                      + ++  ++      +      +  + G    V   L  G+  +I+   +
Sbjct: 212 TVVGNIGRNPRDRMQMTVLPDDQGKHAVTHYRVLKRLGYVTLVECILETGRTHQIRVHMK 271

Query: 207 FFNW 210
               
Sbjct: 272 HIGH 275


>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 = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 30/239 (12%), Positives = 62/239 (25%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I  QRV VN  + +     V+  + + ++ 
Sbjct: 12  TVSESQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNDQMCDTPKEKVLGGERVAINA 71

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-- 108
                           +   +   L +      +V   +     + +   L      V  
Sbjct: 72  EIEEEARFEPQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIVDV 131

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                V RLD +T GL+++         L                               
Sbjct: 132 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQLREITREYEAVAIGHMTAGGTVSEPI 191

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 192 SRHPTKRTHMSVHPMGKPAVTHYRIMEHFRIHTRLRLRLETGRTHQIRVHMAHITHPLV 250


>gi|241190773|ref|YP_002968167.1| hemolysin-like protein [Bifidobacterium animalis subsp. lactis
          Bl-04]
 gi|241196179|ref|YP_002969734.1| hemolysin-like protein [Bifidobacterium animalis subsp. lactis
          DSM 10140]
 gi|240249165|gb|ACS46105.1| hemolysin-like protein [Bifidobacterium animalis subsp. lactis
          Bl-04]
 gi|240250733|gb|ACS47672.1| hemolysin-like protein [Bifidobacterium animalis subsp. lactis
          DSM 10140]
 gi|295793762|gb|ADG33297.1| hemolysin-like protein [Bifidobacterium animalis subsp. lactis
          V9]
          Length = 252

 Score = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 24/49 (48%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          +R+  V+A A   SR + +R+I   +V VNG    + A  V     I V
Sbjct: 4  ERLDVVVANATGESRSKAQRLIKTGKVHVNGHPQTKPAYAVQPESTISV 52


>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 = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 34/273 (12%), Positives = 75/273 (27%), Gaps = 41/273 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M ++ IV       R+ K ++       SR  ++R I    V VNG   ++A+  V S D
Sbjct: 1   MPEEQIVTNREDGWRLDKFLSEKAPQWVSRTAIQRHIKDGGVLVNGEK-KKASYRVKSGD 59

Query: 59  HI-----------EVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
            +            V+   +       +   + +   P  +V    +    + V   L  
Sbjct: 60  IVTYTFPEKVEPGTVEPENIPLNIIYEDHDIIVVNKPPDMIVHPVHNKTSGTLVNALLNY 119

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------DK 157
                   G +       L     G +       +   L         +           
Sbjct: 120 CNDLQGIGGIMRPGIVHRLDKETSGVIVVAKNDRAHNSLVQQFKARTTEKYYLAIARGKT 179

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR--------------EGKNREIKK 203
               +    +       +++T+      +  +   +                G+  +I+ 
Sbjct: 180 PLQGEINFSLARHPVNRLKMTVSATGKESHTLFKTITYFGNIASLVLAKPKTGRTHQIRV 239

Query: 204 VFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            F+     +       YG      ++ G+ R +
Sbjct: 240 HFKEIGHPLLGDK--LYGR-HKDDIILGAERHM 269


>gi|188996912|ref|YP_001931163.1| pseudouridine synthase [Sulfurihydrogenibium sp. YO3AOP1]
 gi|188931979|gb|ACD66609.1| pseudouridine synthase [Sulfurihydrogenibium sp. YO3AOP1]
          Length = 270

 Score = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 27/200 (13%), Positives = 60/200 (30%), Gaps = 9/200 (4%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-----KAERT 73
            IA +   S+ + + +I  + V VN   +  A+ N+   D +E+    L+       E  
Sbjct: 16  FIAESLKISKNQAKDIIDSRNVIVNNKRVWIASHNLKPGDVVEIVQSELKNDLKILYEDD 75

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +    KP  +V+          +   L +   + I            +LL         
Sbjct: 76  YIIAIDKPPTIVSDKESSSAEDILRKKLKNDKIKAIH---RLDKETSGVLLFAKDYKIFE 132

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
                 +   V ++      ++           I G       + +  +     +  V +
Sbjct: 133 KFKEIWEDKNVLKIYLAISHNEANFKDFTINQDIDGKQA-ITHLKVLNKGNGFTYFQVRI 191

Query: 194 REGKNREIKKVFEFFNWKVN 213
             G+  +I+K        + 
Sbjct: 192 ETGRKHQIRKHLASIRHPIV 211


>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 = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 26/233 (11%), Positives = 68/233 (29%), Gaps = 32/233 (13%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
            +R+ +V+A+     SR  ++  I   ++ V+G +L      ++  + + V+        
Sbjct: 17  GKRLDQVLAQLFPDYSRSRIKTWILDDKITVDGEILNTPRTKLLGGEVLNVETTIEAPRE 76

Query: 64  ------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-----G 112
                  + +   +   L +      +V   +     + +   L      +         
Sbjct: 77  YLAQNIDLNIVYEDDHILVINKPMGLVVHPGAGNPDGTVLNALLHHYPDIINVPRAGIVH 136

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD------------KLNL 160
           RLD +T GL+++         L     +     R                          
Sbjct: 137 RLDKDTTGLMVVAKTIQAQTHLVKALQKRENFTREYEALCNGTMTAGGMVEKPIGRHATQ 196

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                V +          +  +  ++  + + L  G+  +I+    + N  + 
Sbjct: 197 RTHMAVHEMGKPAITHYRVAEKFRAHTRLRLRLETGRTHQIRVHMAYLNHPLI 249


>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 = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/246 (11%), Positives = 72/246 (29%), Gaps = 33/246 (13%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M     V  +    R+   +      SR +   +I    VKVN  L+ +    +   D +
Sbjct: 1   MPKHTFVNNDSEKIRLDIFLTYNLNLSRNKTSFLILNDLVKVNKKLVNKNNFVLKVGDVV 60

Query: 61  EVDGVP------------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
           E++                     +   +   + +      L    +  +  + +   + 
Sbjct: 61  ELEYEESIFNKVSNEILPFNKKLDIVYEDDDLIIVNKPTNMLSHPTTHNEPDTLLNCLMY 120

Query: 103 SIFSRV-ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
               +      RLD +T GL++ T +      ++   T+ +             ++L  +
Sbjct: 121 HNKKQKVYLAHRLDKDTTGLIVATKNFKALEKIQEQITKRIMKRYYLAIVHYPFNELRAV 180

Query: 162 KK--GIVIQGICYGD------------MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                  ++                   ++ +  Q    A +   L  G+  +I+   +F
Sbjct: 181 IDAPIGYLKDHDLKFGVENTKNPKNAITKIYVLDQNKKYALIKCELLTGRTHQIRVHMDF 240

Query: 208 FNWKVN 213
               + 
Sbjct: 241 IKHNII 246


>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 = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 76/244 (31%), Gaps = 38/244 (15%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           ++ E     R+ KV+A      +R  ++R++ +++V +NG    +      + D + +  
Sbjct: 8   VLSEREEGIRLDKVLAERLPDLTRTAIQRLLEEEQVLINGKPAAK-NRKGRAGDSVALRI 66

Query: 63  -DGVP-----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
            D  P           +   +   L +      +V         + V   L    +    
Sbjct: 67  PDPEPLCLQAENVPLDIVYEDDDLLVVNKPQGMVVHPAPGNYQGTLVNALLAHCGNSLSG 126

Query: 107 -----RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR-------------VR 148
                R   V R+D +T GLL++  +    + L     +                     
Sbjct: 127 INGVIRPGIVHRIDKDTSGLLMVAKNDFAHQGLARQIKEHSFRREYEAVVAGRMKQESGV 186

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
            +  + +  ++  K  +  +          +  +      + + L  G+  +I+    + 
Sbjct: 187 VNAPIGRHPIDRKKMAVTEKNSKEAVTYFRVIAEYPGYTHIRLRLETGRTHQIRVHMAYL 246

Query: 209 NWKV 212
              V
Sbjct: 247 GHPV 250


>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 = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 30/245 (12%), Positives = 63/245 (25%), Gaps = 41/245 (16%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +     RV K +    + ASR  +++      V  NG  ++  +  V   D I V  
Sbjct: 33  VVDKGQAMVRVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKS-SYKVKPLDVITVMM 91

Query: 63  -----DGVPLRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                +   + +        E   L + +KP GLV      +   T+ + L      +  
Sbjct: 92  DRPRYENEIIPENIPLTIVYEDPYLMVVNKPAGLVVHPGHGNYHGTLVNALAWHMKDIPD 151

Query: 111 VGRLDIN-------------------------TEGLLLLTNDGGLARVLELPSTQWLRVY 145
               D +                           G+              +         
Sbjct: 152 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGIQFFNKTTKRKYRALVWGVMEQDEG 211

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
            +  +   +      +          +      +  + G    V   L  G+  +I+   
Sbjct: 212 TIVGNIARNPRDRMQMAVMSDPTVGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHM 271

Query: 206 EFFNW 210
           +    
Sbjct: 272 KHIGH 276


>gi|206901656|ref|YP_002250670.1| RNA-binding protein, putative [Dictyoglomus thermophilum H-6-12]
 gi|206740759|gb|ACI19817.1| RNA-binding protein, putative [Dictyoglomus thermophilum H-6-12]
          Length = 259

 Score = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 14/60 (23%), Positives = 27/60 (45%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            +++   + +R+  V + A   SR +++  I    V VNG  +  A   +   D + V G
Sbjct: 173 RVIRTTESSKRLDSVGSAALGISRSKMQSYIKAGVVTVNGKKVYDAHYELEEGDIVIVQG 232


>gi|188995120|ref|YP_001929372.1| hypothetical protein PGN_1256 [Porphyromonas gingivalis ATCC
          33277]
 gi|188594800|dbj|BAG33775.1| conserved hypothetical protein [Porphyromonas gingivalis ATCC
          33277]
          Length = 150

 Score = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
          R++K+I+ AG+ SRRE E+ I + RVK+NG +       V   D + +D + +   +  R
Sbjct: 4  RINKLISDAGLGSRREAEKYITEGRVKINGRIAR-LTDLVCEKDIVLLDDIDIPIKDLIR 62

Query: 75 L 75
           
Sbjct: 63 E 63


>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 = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 34/295 (11%), Positives = 81/295 (27%), Gaps = 39/295 (13%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            ++ +   +R+ +V+A      SR  ++  I   +V+++G +       VM    +E+  
Sbjct: 10  TIEPHHEGKRLDQVLADLFTDYSRTRLKEWILGGKVQLDGKVCLLPKEKVMGGQQVEIAT 69

Query: 63  ---DGVPLRKAERTRLWLY---------HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
              D    +  +     +Y              +V   +     + +   L         
Sbjct: 70  ELEDDTRWQAQDLPLNIVYEDEHLLVIDKPAGLVVHPGAGTPDGTVLNALLHRYPDIAEV 129

Query: 111 V-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY---------RVRFHGQVDQD 156
                  RLD  T GL+++         L     +                      +  
Sbjct: 130 PRAGIVHRLDKETTGLMVVAKTIPAQIRLVYALQKRRITREYEAIVVGHMTAGGTVDEPI 189

Query: 157 KLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN- 213
             +  ++ ++              +  +  ++  +   L  G+  +I+      N  +  
Sbjct: 190 SRHSTQRTMMAVNPMGKPAITHYRVAERFRAHTRLRCRLETGRTHQIRVHMAHINHALVG 249

Query: 214 ------RLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPI 261
                 RL  I     +L   L     + +   +LR        E    +     
Sbjct: 250 DPVYGGRLRPIRNASVELSDFLRTFRRQALHATMLRLTHPITGEEMEWHSPIPDD 304


>gi|295100789|emb|CBK98334.1| ribosomal large subunit pseudouridine synthase D [Faecalibacterium
           prausnitzii L2-6]
          Length = 310

 Score = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/255 (13%), Positives = 74/255 (29%), Gaps = 46/255 (18%)

Query: 1   MKDKN-IVQENFTPQRVSKVIA--RAGIASRREVERMIAQQRVKVNGI-LLERAAVNVMS 56
           M+ +  IV+     QR+ + ++    G+ SR  ++ ++A+  V  NG  + +     + +
Sbjct: 1   MEQREFIVEAEAAGQRIDRFLSGEDTGL-SRSALQGLVAEGHVLCNGKSIAKSL--KLKA 57

Query: 57  TDHIEV---DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
            D I +   D  P+              +   L +      +V         + V   L 
Sbjct: 58  GDTILLEIPDAKPIEAVPQDIPLDIVYEDDHLLVVNKPKGMVVHPAPGNPDGTLVNALLW 117

Query: 103 SIF---------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
                        R   V R+D +T GLL++  D      L             +     
Sbjct: 118 HCKGSLSGIGGEIRPGIVHRIDKDTSGLLVVAKDDATHIGLSQQMAVHSVERAYQTVVYG 177

Query: 154 DQDKLNLLKKGIVIQGICYG------DMQ----------VTLDTQKGSNAWVTVGLREGK 197
              +     +  + +                          +  + G    +   L+ G+
Sbjct: 178 GFAQDEGFVEANLGRSKTDRKKMAVYPASEPHTKYAYTGYKVLERFGGFTLLECRLKTGR 237

Query: 198 NREIKKVFEFFNWKV 212
             +I+         V
Sbjct: 238 THQIRVHMASIQHPV 252


>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 = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/246 (12%), Positives = 67/246 (27%), Gaps = 42/246 (17%)

Query: 7   VQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V +   P R+ K +  R   +SR  +++      + VNG  ++     V   D I +   
Sbjct: 39  VDKGQVPVRIDKFLFERMQHSSRNRIQKAADAGFIHVNGAPVKS-NYKVRPEDTITLMLD 97

Query: 63  ----DGVP--------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
               D           +   +   + +      +V   +     + +      +      
Sbjct: 98  RPKHDNTIEAEDIPLDIVYEDNALMVVNKPAGLVVHPGAGNFHGTLINAIAWHLKDLPSF 157

Query: 111 V---------GRLDINTEGLLLLTNDGG-------------LARVLELPSTQWLRVYRVR 148
                      R+D +T GLL++                    R         L     R
Sbjct: 158 DPNDPEVGLVHRIDKDTSGLLVIAKTPDAKTILGKQFFNKTTHRSYNALVWGNLTADEGR 217

Query: 149 FHGQVDQDKLNLLKKGIVIQG-ICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
             G + +D  + L+  +                +  + G    +   L  G+  +I+   
Sbjct: 218 IEGNIARDPKDRLRMTVFPPDSEIGKPAVTHYRVLERFGYTTLIECVLETGRTHQIRAHM 277

Query: 206 EFFNWK 211
           +     
Sbjct: 278 KHIGHP 283


>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 = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 34/247 (13%), Positives = 68/247 (27%), Gaps = 41/247 (16%)

Query: 4   KNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           + IV +  +  R+ K +      ASR +V++      VKVNG  ++     V   + I +
Sbjct: 30  RIIVDKGQSLVRIDKFLCDRIENASRNQVQKAAEAGFVKVNGNPVKS-NYKVKPLEEITI 88

Query: 63  -------------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                        + +PL    E   L + +KP GLV      + R T+ + +       
Sbjct: 89  YMDTPPHEIEIIPEDIPLNIVYEDDYLMVVNKPAGLVVHPGHGNYRGTLVNAIAWHMKNN 148

Query: 109 ISVGRLDINTE-------------------------GLLLLTNDGGLARVLELPSTQWLR 143
                 D                             G+              +       
Sbjct: 149 SCYDANDPRVGLVHRIDKDTSGLLVIAKTPEAKSKLGIQFFNKTTKREYRALVWGNIEEE 208

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
             R+  +   +      +      +   +      +  + G    V   L  G+  +I+ 
Sbjct: 209 EGRIEGNIARNPKDRLQMAVFADPEIGKHAVTHYKVLERLGYVTLVACRLETGRTHQIRV 268

Query: 204 VFEFFNW 210
             +    
Sbjct: 269 HMKHIGH 275


>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 = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/225 (13%), Positives = 76/225 (33%), Gaps = 30/225 (13%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG----------VPLR 68
           ++++ G  SR  V+ ++A ++V VN  +  +  + +   D + ++               
Sbjct: 27  LLSKMGGMSRNSVKSLLAHRQVMVNNKITTQFNLALQPEDLVVINNGRGNIELNHPKLKI 86

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGRLDINTEGLL 122
             E   L +  K  GL+T  +     +T F  L +        +R+  V RLD  T G++
Sbjct: 87  IFEDEYLIVVEKKEGLLTVSTGNPDETTAFSILKNHVKKSSPDNRIYVVHRLDRETSGVI 146

Query: 123 LLTNDGGLARVLELPST--------------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           +   +  +  +L+                  +  +         ++ +K   +       
Sbjct: 147 MFAKNKEVQTILQENWHRIITRRIYVALVEGKVEKEQDTIVSWLLENEKSLKIHSSATDN 206

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           G               + + + + L  G+  +I+   +     + 
Sbjct: 207 GGQQAVTHYRCVRSNDNYSLLEIELETGRKNQIRVHMQDIGHPIV 251


>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 = 58.3 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 79/248 (31%), Gaps = 37/248 (14%)

Query: 2   KDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K   IV E     R+   I+ A    SR  ++ +I  ++V VN  + +  +  V   D+I
Sbjct: 5   KKYFIVDEEEEDLRLDVFISSALSDLSRTYIQSLIKDKKVTVNDKIEKS-SYKVAQLDNI 63

Query: 61  EV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
            +            + +P+    E   L + +K  G+V      +   T+ + L   F  
Sbjct: 64  CILIPPAKELVIEAEDIPIEILYEDEDLAVVYKERGMVVHPGAGNANHTLVNALMYHFKG 123

Query: 108 VISV----------GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD- 156
            +S            R+D +T GLL++       R L     +        F    +   
Sbjct: 124 QLSSINGIIRPGIVHRIDKDTSGLLMIAKSDIAHRGLSEQLKEHTVQRTYTFICHGNIKA 183

Query: 157 -----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                            K  V+    +    +T      + ++    L  G+  +I+   
Sbjct: 184 DEFTIDAPIGRNPRDRMKMAVVSDGKHAVTHITKIKSNENYSYAMANLETGRTHQIRVHM 243

Query: 206 EFFNWKVN 213
                 + 
Sbjct: 244 ASKGLPLV 251


>gi|284931618|gb|ADC31556.1| Pseudouridine synthase [Mycoplasma gallisepticum str. F]
          Length = 311

 Score = 57.9 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/246 (11%), Positives = 72/246 (29%), Gaps = 33/246 (13%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M     V  +    R+   +      SR +   +I    VKVN  L+ +    +   D +
Sbjct: 1   MPKHTFVNNDSEKIRLDIFLTYNLNLSRNKTSFLILNDLVKVNKKLVNKNNFVLKVGDVV 60

Query: 61  EVDGVP------------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
           E++                     +   +   + +      L    +  +  + +   + 
Sbjct: 61  ELEYEESIFNKVSNEILPFNKKLDIVYEDDDLIIVNKPTNMLSHPTTHNEPDTLLNCLMY 120

Query: 103 SIFSRV-ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
               +      RLD +T GL++ T +      ++   T+ +             ++L  +
Sbjct: 121 YNKKQKVYLAHRLDKDTTGLIVATKNFKSLEKIQEQITKRIMKRYYLAIVHYPFNELRAV 180

Query: 162 KK--GIVIQGICYGD------------MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                  ++                   ++ +  Q    A +   L  G+  +I+   +F
Sbjct: 181 IDAPIGYLKDHDLKFGVENTKNPKNAITKIYVLDQNKKYALIKCELLTGRTHQIRVHMDF 240

Query: 208 FNWKVN 213
               + 
Sbjct: 241 IKHNII 246


>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 = 57.9 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/239 (12%), Positives = 63/239 (26%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  +HI +D 
Sbjct: 10  TVTENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGSIGDKPKEKVLGGEHIAIDV 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  EIEEEARFQPQDIPLNIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--- 156
                  R+       +     +        +  L   + ++  V           +   
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTIPAQTRLVESLQLREITREYEAVAIGHMTSGGTVEEPI 189

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRIHTRLRLRLETGRTHQIRVHMSHITHPLV 248


>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 = 57.9 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/235 (11%), Positives = 65/235 (27%), Gaps = 35/235 (14%)

Query: 11  FTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
               R+ K +A      SR ++++ I    V VN   ++    ++ + D ++V       
Sbjct: 13  QETGRIDKQLATLLSDVSRSQIKKWIEDGNVTVNKQSVK-PKYHLQAGDIVQVIPEQPQK 71

Query: 63  -DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            D  P      +   +   L +      +V   +     + V   L       I+     
Sbjct: 72  IDLEPENIPLEIVYEDDDVLVVNKPQGMVVHPSAGHPNHTLVNALLYHCPLSHINGEYRP 131

Query: 116 INTEGL--------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK----- 162
                +        ++  ND     +      +  +   V     V ++    +      
Sbjct: 132 GIVHRIDKDTSGLLMVAKNDRAHRSLAAQLKAKTNQREYVALVHGVIKEDQGTIDAPLGR 191

Query: 163 ------KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 K  V+           +  +      V   L  G+  +I+   ++    
Sbjct: 192 SPKDRKKQAVVADGRPAVTHFRVLKRYLHYTLVACKLETGRTHQIRVHMKYIGHP 246


>gi|251780386|ref|ZP_04823306.1| S4 domain protein YaaA [Clostridium botulinum E1 str. 'BoNT E
          Beluga']
 gi|243084701|gb|EES50591.1| S4 domain protein YaaA [Clostridium botulinum E1 str. 'BoNT E
          Beluga']
          Length = 72

 Score = 57.9 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 16/66 (24%), Positives = 31/66 (46%), Gaps = 1/66 (1%)

Query: 2  KDKNIVQENFTPQRVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
          K+ N ++ N    ++   +  +GIAS   E +  I +  +KVNG +  +    + + D I
Sbjct: 3  KNMNKIEINTEIIKLDAFLKWSGIASLGSEAKIYIQEGLIKVNGEICLQRGKKLKAGDII 62

Query: 61 EVDGVP 66
          E +   
Sbjct: 63 EFEDEK 68


>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 = 57.9 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 32/245 (13%), Positives = 66/245 (26%), Gaps = 41/245 (16%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +     RV K +    + ASR  +++      V  NG  ++  +  V   D I V  
Sbjct: 33  VVDKGQAMVRVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKS-SYKVKPLDVITVVM 91

Query: 63  -----DGVPLR--------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
                +   +           ++  + +      +V         + V      +     
Sbjct: 92  DRPRYENEIIPEDIPLNIVYEDKYVMVVNKPAGLVVHPGHGNYHGTLVNALAWHMKDVPD 151

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK--- 157
                  V  V R+D +T GLL++         L L         + R       ++   
Sbjct: 152 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKTTKRKYRALVWGTVEQDEG 211

Query: 158 ------------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                          +          +      +  + G    V   L  G+  +I+   
Sbjct: 212 TIVGNIARNPKDRMQMAVMSDPAVGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHM 271

Query: 206 EFFNW 210
           +    
Sbjct: 272 KHIGH 276


>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 = 57.9 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 32/245 (13%), Positives = 65/245 (26%), Gaps = 41/245 (16%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +  +P R+ K +    + ASR  ++       V  NG  ++  +  V   D + V  
Sbjct: 32  VVDKGQSPVRIDKYLFERIVNASRNRIQTAADAGFVMANGKPVKS-SYKVKPQDVLTVMM 90

Query: 63  -----------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                      + +PL    E   L + +KP GLV      +   T+ + +      V +
Sbjct: 91  DRPRYENDIIPEDIPLDVVYEDEDLMVINKPAGLVVHPGCGNYHGTLVNAIAWHLRDVPT 150

Query: 111 VGRLDIN-------------------------TEGLLLLTNDGGLARVLELPSTQWLRVY 145
               D                             GL              +         
Sbjct: 151 YNPNDPQVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFYNKTTKREYNALVWGIVEEDEG 210

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
            +  +   +      +          +      +  + G    V   L  G+  +I+   
Sbjct: 211 TITGNIGRNPRDRMQMAVISDPTQGKHAVTHYQVLERLGYVTLVKCVLETGRTHQIRVHM 270

Query: 206 EFFNW 210
           +    
Sbjct: 271 KHIGH 275


>gi|330751985|emb|CBL80498.1| protein with similarity to pseudouridine synthase [uncultured
           Polaribacter sp.]
          Length = 105

 Score = 57.9 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 15/104 (14%), Positives = 34/104 (32%)

Query: 204 VFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYS 263
           + E+ +++V +L R      +LG L +G  RE+++  ++E                    
Sbjct: 1   MCEYLDYEVTKLKRTRIMNVELGYLQSGDWRELTEDEMKEINNMISSSSKTEEASVVEEK 60

Query: 264 SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
           S+     R    ++   +        S           ++   R
Sbjct: 61  SKQAKPKRSKAPTKNDFNKKSASFRKSSPKSKRSNSSFSSKKKR 104


>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 = 57.9 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/240 (11%), Positives = 68/240 (28%), Gaps = 31/240 (12%)

Query: 5   NIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           + V+++   QR+ + IA      SR  ++  +   +V+VNG ++ +    VM  + I + 
Sbjct: 9   HTVKDSQLGQRLDQAIAELFADFSRSRLKEWLVDGKVQVNGEVITKPRTKVMGGEIITLQ 68

Query: 63  ----DGVPLRKAERT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
               D       +            + +      +V   +     + +   L        
Sbjct: 69  AELEDEERWEAQDIPLDIVYEDDDIMVINKPRDFVVHPGAGTPDGTVLNALLHHYPDIAE 128

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   RLD +T GL+++         L     +                    +++ 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRMTAGGRVEQP 188

Query: 165 IVIQGIC---------YGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I                        +      +  + + L  G+  +I+    +    + 
Sbjct: 189 IGRHSTKRTLMAVSPMGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPLL 248


>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 = 57.9 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 47/275 (17%), Positives = 83/275 (30%), Gaps = 52/275 (18%)

Query: 1   MKDK-NIVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           MKDK  ++      QR+ K +A   I    SR  +E +I + R+ VN   +++ +  +  
Sbjct: 8   MKDKLKVIYTLQEMQRLDKFLAELKIQELYSRTFIEHLIEEDRILVNLTPVKK-SYLLKE 66

Query: 57  TDHIEVD------------GVPLRKAERTRLWLY--HKPIGLVTTHSDPDGRSTVFDNLP 102
            D + ++             +PL              K   +V         + V   L 
Sbjct: 67  GDEVIINLPEPEPMNVLPQDIPLDVVYEDEYLAIINKKAGMIVHPGFGNPEGTLVNAILY 126

Query: 103 SI---------FSRVISVGRLDINTEGLLLLTNDGGLA----RVLELPSTQWLRVYRVRF 149
                      F+R   V RLD  T GL+++  +         +      +         
Sbjct: 127 RFGENLSSGKEFNRPGIVHRLDRGTSGLIIIAKNDLTHAKLSDMFARREIKKTYFAITTG 186

Query: 150 HGQV---DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE-----GKNREI 201
             +    + +                 + +  L   K    W    L E     G+  +I
Sbjct: 187 IPEPEKGEIETYLARSNKNPRTICVTNEGRYALTHYKTIKTWHYFALVEINPATGRMHQI 246

Query: 202 KKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           +  F    + +            LG LL  S R V
Sbjct: 247 RVHFAHIRYPI------------LGDLLYNSRRYV 269


>gi|254974743|ref|ZP_05271215.1| putative RNA methyltransferase [Clostridium difficile QCD-66c26]
 gi|255092132|ref|ZP_05321610.1| putative RNA methyltransferase [Clostridium difficile CIP 107932]
 gi|255313869|ref|ZP_05355452.1| putative RNA methyltransferase [Clostridium difficile QCD-76w55]
 gi|255516550|ref|ZP_05384226.1| putative RNA methyltransferase [Clostridium difficile QCD-97b34]
 gi|255649650|ref|ZP_05396552.1| putative RNA methyltransferase [Clostridium difficile QCD-37x79]
 gi|260682814|ref|YP_003214099.1| putative RNA methyltransferase [Clostridium difficile CD196]
 gi|260686412|ref|YP_003217545.1| putative RNA methyltransferase [Clostridium difficile R20291]
 gi|306519766|ref|ZP_07406113.1| putative RNA methyltransferase [Clostridium difficile QCD-32g58]
 gi|260208977|emb|CBA62031.1| putative RNA methyltransferase [Clostridium difficile CD196]
 gi|260212428|emb|CBE03297.1| putative RNA methyltransferase [Clostridium difficile R20291]
          Length = 270

 Score = 57.9 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 22/177 (12%), Positives = 47/177 (26%), Gaps = 2/177 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  ++   G   SR   ++ I    V V+    ++A   V     IEV G P+    R 
Sbjct: 4   RIDLLLVEQGYFESRERAKKAIMAGLVFVDNQRCDKAGTEVKEDCSIEVKGNPIPYVSRG 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L         T                    ++  G + + +  +        L + 
Sbjct: 64  GLKLEKAMKNFDLTIDGKVCMDIGAST-GGFTDCMLKNGAIKVFSIDVGYGQLAWKLRQD 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             +   +   +  V             +    +   +     +  +       A + 
Sbjct: 123 DRVVCMERTNIRNVTIEYTKQFADFASIDVSFISLKLVLPKAKELVRHDGEVVALIK 179


>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 = 57.9 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 75/246 (30%), Gaps = 39/246 (15%)

Query: 4   KNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K I  +   P RV K +      A+R ++++      + VN  ++++    V + D ++V
Sbjct: 19  KFIASKGQEPLRVDKFLMNFIENATRNKIQQAAKDGHIWVNEKIVKQ-NYKVKAGDEVKV 77

Query: 63  DGVP---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                              +   +   L +      +V         + +   L      
Sbjct: 78  LFEHPPYELLLTPENIPLDIVYEDDVLLVVNKPAGMVVHPGHGNYTGTLINALLYHSKDL 137

Query: 108 VISV-------GRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVYRV 147
            ++         R+D +T GLL++         L                    +     
Sbjct: 138 PVNSNDRPGLVHRIDKDTSGLLVVAKTEAAMTHLAKQFFDKTSEREYVALVWGNVEDESG 197

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
              G + ++  N L+  +  +G    +      +  + G    V+  L  G+  +I+   
Sbjct: 198 TIEGNIARNPKNRLQMQVFPEGEQGKEAVTHYGVLERLGYVTLVSCKLETGRTHQIRVHM 257

Query: 206 EFFNWK 211
           ++    
Sbjct: 258 KYIGHT 263


>gi|295109999|emb|CBL23952.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus
           obeum A2-162]
          Length = 304

 Score = 57.9 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/244 (11%), Positives = 70/244 (28%), Gaps = 38/244 (15%)

Query: 7   VQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V  +    R+ + +A +    SR  +++++ +++V VNG +++ A     S D+IE    
Sbjct: 8   VDASANNIRIDRYLADQCPEHSRSYIQKLLKEEQVLVNGRVIK-ANYKTQSGDYIEFHIP 66

Query: 63  DGVP-----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
           D              +   +   L +      +V   +     + V   +      +  +
Sbjct: 67  DPEVPDILPENIPLDILYEDDYVLVVNKPKDMVVHPSAGHTSGTLVNAVMAHCGEHLSGI 126

Query: 112 GRLDIN----------------------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
             +                            L     +  + R         L+      
Sbjct: 127 NGVLRPGIVHRIDKDTTGALLICKDDVVHRDLAEQLKEHSIKRRYRAVVQGNLKEDEGTV 186

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
           +  V +   +  K  I  +          +  + G   ++   L  G+  +I+       
Sbjct: 187 NAPVGRHPTDRKKMAINHKNGKEAITHYKVLERFGQATYIECRLETGRTHQIRVHMASLG 246

Query: 210 WKVN 213
             + 
Sbjct: 247 HPLL 250


>gi|168334458|ref|ZP_02692629.1| putative pseudouridylate synthase [Epulopiscium sp. 'N.t.
           morphotype B']
          Length = 304

 Score = 57.9 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 37/251 (14%), Positives = 75/251 (29%), Gaps = 40/251 (15%)

Query: 1   MKDKNIVQ-ENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAA-VNVMST 57
           M DK ++   N    RV K +       +R  +++ I    + +NG +    A   + + 
Sbjct: 1   MNDKLLLTINNIADIRVDKFLTEQLPQYTRSYIQKQIELGLLLINGKVA--PARTRIKTG 58

Query: 58  DHIE--------VDGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           D IE        VD  P      +   +   L +      +V   +     + V   L  
Sbjct: 59  DTIEFTIAPPREVDITPSEIKLDIIYEDSDILIVNKPKNMVVHPSAGHYNDTLVNALLFY 118

Query: 104 IFS---------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY--------- 145
                       R   V R+D +T GLL++  +      L                    
Sbjct: 119 AKDSLSGINGEIRPGIVHRIDKDTTGLLMVAKNDHSHVFLSDLLKDHNIERKYNALVYGN 178

Query: 146 ---RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                    +         KK  +++       +  +  + G+   + + L+ G+  +I+
Sbjct: 179 IKEDFFTIDRPIARNPKDRKKMAIVENGRRAVTECRVLERFGNATHIELSLQTGRTHQIR 238

Query: 203 KVFEFFNWKVN 213
                    + 
Sbjct: 239 VHLTSIGHPLL 249


>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 = 57.9 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 66/244 (27%), Gaps = 40/244 (16%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V       RV K +  R   ASR  +++      V  N   ++  +  V   D I +  
Sbjct: 34  VVDRGQEMMRVDKYLFDRLTNASRNRIQKSAEAGFVMANNKPVKS-SYKVKPMDVITIMM 92

Query: 63  -----------DGVPLRKAERTRLWL--YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                      + +PL      +  +        +V         + V      +     
Sbjct: 93  DRPRYENEVIPEDIPLNIIYEDKYLMVVNKPAGLVVHPGHGNYQGTLVNAIAWHMKDNPD 152

Query: 110 SV---------GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK--- 157
                       R+D +T GLL++         L +         R R       ++   
Sbjct: 153 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGMQFFNKTTKRRYRALVWGTVEQDEG 212

Query: 158 ----------LNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                      + ++  ++      +      +  + G    V   L  G+  +I+   +
Sbjct: 213 TITGNIGRNPRDRMQMTVLPDDQGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMK 272

Query: 207 FFNW 210
               
Sbjct: 273 HIGH 276


>gi|307610038|emb|CBW99572.1| ribosomal large subunit pseudouridine synthase D [Legionella
           pneumophila 130b]
          Length = 321

 Score = 57.9 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 36/236 (15%), Positives = 68/236 (28%), Gaps = 38/236 (16%)

Query: 14  QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------- 63
           QRV +VIAR     SR  +   I    V +N +  +      +  D I ++         
Sbjct: 18  QRVDRVIARLLPEYSRSLISNWIKTGAVTLNNLPCK-PKDKALGGDLITINVDHTMVNTD 76

Query: 64  -------GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI----- 109
                   +P++    +   + +      +V   +     + V   L       +     
Sbjct: 77  FNFCKPENIPIQIIYEDSEVIVVNKPAGLVVHPGAGNKEHTLVNALLHHCPELQLLPRAG 136

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR------------VRFHGQVDQDK 157
            + RLD +T GLL++  +      L                                +  
Sbjct: 137 IIHRLDKDTTGLLIVAKNLISHTSLIRQMQNREIKRHYLTLVHGYVISGGTIDTGFGRHP 196

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            N LK  +   G         ++        + V L  G+  +I+    + N  V 
Sbjct: 197 KNRLKMAVTDFGRQA-VTHYNINKHYKDFTLLNVSLMTGRTHQIRVHMNYINHPVV 251


>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 = 57.9 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 27/239 (11%), Positives = 62/239 (25%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + I +D 
Sbjct: 10  TVTENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGTIGDKPKEKVLGGERIAIDV 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFQPQDIPLNIVYEDDDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--- 156
                  R+       +     +        +  L   + ++  V           +   
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTIPAQTRLVESLQLREITREYEAVAIGHMTAGGTVEEPI 189

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRIHTRLRLRLETGRTHQIRVHMSHITHPLV 248


>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 = 57.9 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 29/241 (12%), Positives = 66/241 (27%), Gaps = 39/241 (16%)

Query: 9   ENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           +   P RV K +      A+R +V++   Q  + VNG  ++ A   V + D ++V     
Sbjct: 32  KGQEPLRVDKFLMNFVENATRNKVQQAAKQGNIFVNGEPVK-ANHRVKANDVVKVLLSHP 90

Query: 63  --------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
                   + +P  +   +   L +      +V         + +   +        +  
Sbjct: 91  PHEDLLVPENIPLNIVYEDDALLVVNKPAGMVVHPGHGNYSGTLINALVYHFEHLPNNSS 150

Query: 113 RLDINTE-----------------GLLLLTNDGGLARVLELPS---TQWLRVYRVRFHGQ 152
                                    +L LT                   +        G 
Sbjct: 151 NRPGLVHRIDKDTSGLLVIAKTEEAMLHLTQQFFYKTTQREYIALVWGNIEEDEGTVRGH 210

Query: 153 VDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           + +   + L+  +   G    +      +  + G    V+  L  G+  +I+   +    
Sbjct: 211 IGRHLKDRLQMDVFPDGSHGKEAVTHYKVLERFGYVTLVSCRLETGRTHQIRVHLKHIGH 270

Query: 211 K 211
            
Sbjct: 271 T 271


>gi|153853144|ref|ZP_01994553.1| hypothetical protein DORLON_00538 [Dorea longicatena DSM 13814]
 gi|149753930|gb|EDM63861.1| hypothetical protein DORLON_00538 [Dorea longicatena DSM 13814]
          Length = 251

 Score = 57.9 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 19/80 (23%), Positives = 29/80 (36%), Gaps = 8/80 (10%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
             +  R+  V+A A   SR ++   I   +V VNG L+      +   D I V       
Sbjct: 171 TVSSIRLDSVLALAYPLSRSKITAQIEAGKVFVNGKLITSNGYRLKDNDIISVRKMGRIA 230

Query: 63  -DGVPLRKAERTRLWLYHKP 81
            DG+     +   L    K 
Sbjct: 231 YDGILSETKKGRYLISVRKY 250


>gi|224373114|ref|YP_002607486.1| hemolysin A [Nautilia profundicola AmH]
 gi|223589777|gb|ACM93513.1| hemolysin A [Nautilia profundicola AmH]
          Length = 236

 Score = 57.9 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ + +       SR + + +I    VKVN  ++++ +  +  TD +EV
Sbjct: 1  MRLDQYLVTNEYTFSRNKAQEIIKSGYVKVNDKIIKKPSFKIAETDSVEV 50


>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 = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 34/246 (13%), Positives = 71/246 (28%), Gaps = 35/246 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  + V  +    R+ KV+       +R +++ +I Q+++ VN          V   D 
Sbjct: 1   MEQFSFVVSDQESGRLDKVVTNHYPDLTRSKIQNLIKQEQILVN-QAPTTNRYKVSENDV 59

Query: 60  IEV---DGVPLRKAERT-----------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I+V   D V +                  + +      +V      +  + V   L    
Sbjct: 60  IDVTLPDPVEVSVKPEKMNLDIVFEDDDVIVVNKPQGMVVHPAPGHENGTLVNGLLDHAP 119

Query: 106 S-------RVISVGRLDINTEGLLLLTNDGGLA------------RVLELPSTQWLRVYR 146
                   R   V R+D +T GLL++  +                +   L          
Sbjct: 120 LATVNGELRPGIVHRIDKDTSGLLMVAKNDQAMLSLSAQLKAKTNQRKYLAIVHGNFKEE 179

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          KK  +++          +  +      +   L  G+  +I+   +
Sbjct: 180 AGTINAPIGRSKKDRKKMAIVEDGRPAVTHFKVLERFTDYTLIECELETGRTHQIRVHLK 239

Query: 207 FFNWKV 212
           +    V
Sbjct: 240 YIGHPV 245


>gi|316971885|gb|EFV55608.1| pseudouridylate synthase 6 [Trichinella spiralis]
          Length = 404

 Score = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 35/263 (13%), Positives = 78/263 (29%), Gaps = 35/263 (13%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE----------VDGVPLRKAERTRLWLYHKP 81
           E  I   RV VNG         V + D I           +D       +   + + +KP
Sbjct: 88  EEAILAGRVTVNGQP-TSVDYVVENGDLIRHMCHRHELPVLDSAVDIVTDTEDILVVNKP 146

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL----ARVLE 135
             +          +++   L  I       +  RLD  T GL++   +  +     + + 
Sbjct: 147 CSIPVHPCGRYHFNSLVLYLKHIGGMDNLKTFHRLDRLTSGLVIFLKNEKIEKKLRQQMI 206

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNL--------LKKGIVIQGICYGDMQVTLDTQKGSNA 187
               +   +  V      ++   +         +    +         +       G  +
Sbjct: 207 ENQIKKEYLCLVDGEFPEEEVVCDKPLDVLSQSMGIMYITADGKPSLTKFYKLFSDGKTS 266

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRL----IRISYGPFQLGTLL-AGSTREVSKKILR 242
            +      G+  +I+   ++  + +          ++GP   G L   G     S   LR
Sbjct: 267 ILKCCPETGRTHQIRVHLQYLGYPIVNDYIYNNSDAFGP-NKGKLCDYGK----SLDELR 321

Query: 243 EQLGPHLLEEAQVNLDAPIYSSE 265
           E +      E  ++  + +  ++
Sbjct: 322 EVVKTCFTAEKWIDRKSTVDPTK 344


>gi|262282736|ref|ZP_06060504.1| S4 domain-containing protein [Streptococcus sp. 2_1_36FAA]
 gi|262262027|gb|EEY80725.1| S4 domain-containing protein [Streptococcus sp. 2_1_36FAA]
          Length = 264

 Score = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 15/51 (29%), Positives = 27/51 (52%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +  R+ K+IA +   SR +  ++I  + VKVN  +++  +  V   D I V
Sbjct: 184 SSMRLDKLIASSFKLSRSDASQLIFGKHVKVNYSIIDNPSYLVGLNDLISV 234


>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 = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 34/232 (14%), Positives = 65/232 (28%), Gaps = 37/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------DGVP 66
           R+ K +A     SR +    I Q+RV VNG L ++A   V   D I          D   
Sbjct: 11  RLDKALADLTPLSRSQANDQIKQKRVLVNG-LPKKAKYIVQVGDCISYHIPEESSLDYQA 69

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 +   +     +      +V   +     + V   L  I       G +      
Sbjct: 70  QDIPLDIVYQDDVLAIINKPQGMVVHPSAGHSTGTLVNALLYHIKDLSSINGVIRPGIVH 129

Query: 121 LLLLTNDGGLARVLELPST---------------------QWLRVYRVRFHGQVDQDKLN 159
            +     G L       +                        L   R      + + + +
Sbjct: 130 RIDKDTSGLLMVAKTDKAHQLLADELKAKKSLRKYVAIVHGNLPKDRGVIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             K+ +  +G     +   +  + G   +V + L  G+  +I+    +    
Sbjct: 190 RKKQTVTAKGKEALTL-FKVLERFGHYTFVELQLETGRTHQIRVHMAYIGHP 240


>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 = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 31/245 (12%), Positives = 63/245 (25%), Gaps = 41/245 (16%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +     RV K +    + ASR  +++      V  NG  ++  +  V   D I V  
Sbjct: 33  VVDKGQAMVRVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKS-SYKVKPLDVITVMM 91

Query: 63  -----DGVPLRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                +   + +        E   L + +KP GLV      +   T+ + L      +  
Sbjct: 92  DRPRYENEIIPENIPLTIVYEDPYLMVVNKPAGLVVHPGHGNYHGTLVNALAWHMKDIPD 151

Query: 111 VGRLDIN-------------------------TEGLLLLTNDGGLARVLELPSTQWLRVY 145
               D +                           GL              +         
Sbjct: 152 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKTTKRRYRALVWGVVEQDEG 211

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
            +  +   +      +          +      +  + G    V   L  G+  +I+   
Sbjct: 212 TIVGNIARNPKDRMQMAVMSDPTVGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHM 271

Query: 206 EFFNW 210
           +    
Sbjct: 272 KHIGH 276


>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 = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 30/244 (12%), Positives = 67/244 (27%), Gaps = 38/244 (15%)

Query: 7   VQE--NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           + E  +    R+ +++A     SR ++  +I    V VN  L+ + +  V+  D I  + 
Sbjct: 1   MNEFISSNSARLDQILASYLSISRNQISELIKSGNVYVNDNLMLKPSFKVLLNDKIGFNL 60

Query: 64  --------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                          V +   +   L L       V         + V     + +    
Sbjct: 61  PKAKFENCEFKADFDVEILYEDDDILVLNKPSNLTVHPAPSVKEATLVEWLKQNGYMLST 120

Query: 110 SVGRL--------------------DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
             G +                    +  +   L           + L    +    ++  
Sbjct: 121 LNGDIRAGIVHRLDKGTSGVIVVAKNNASHSALAAQLSDKSMGRVYLALIDFNLKDKLII 180

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + ++  N LK  +   G         +  +   N  +   L  G+  +I+      N
Sbjct: 181 DRPIGRNPQNRLKNSVAANGRAAKSAFTNIICEDDLN-LIAAKLFTGRTHQIRVHLASIN 239

Query: 210 WKVN 213
             + 
Sbjct: 240 RHIL 243


>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 = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 34/247 (13%), Positives = 75/247 (30%), Gaps = 41/247 (16%)

Query: 6   IVQENFTPQRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI- 60
           +V+     +R+ K +    A  G+ SR  + + I Q+RV+V G L  +    V++   + 
Sbjct: 16  VVEAGEAGKRLDKFLSDRLADLGV-SRSRISQWIRQERVRVAGALCLQGKTKVLNGQKVV 74

Query: 61  ------------EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                       EV  V +  ++   + +       V   +  +  + V           
Sbjct: 75  LLAPSLQSGIKPEVGPVEVVYSDPDVVVVNKAAGVTVHPGTGCESGTLVHHLAALYPELA 134

Query: 109 ISVGRLDI-----------------NTEGLLLLTNDGGLARVLELPST--QWLRVYRVRF 149
              G                     N    L LT       V +   T            
Sbjct: 135 RFDGERPGVVHRLDKDTSGLLTVALNESARLALTRSFARREVDKEYLTLVHGRPEAEGTV 194

Query: 150 HGQVDQDKLNLLKKGIVIQGIC---YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
              + +D  + ++  +V +G         +    +  G  + + V +  G+  +I+    
Sbjct: 195 DHPLGRDPQSKIRMAVVPRGGKEALTRF-KRVWTSPDGRVSLLRVRILTGRTHQIRVHMA 253

Query: 207 FFNWKVN 213
           +  + + 
Sbjct: 254 YLGFPLV 260


>gi|152992058|ref|YP_001357779.1| hemolysin A [Sulfurovum sp. NBC37-1]
 gi|151423919|dbj|BAF71422.1| hemolysin A [Sulfurovum sp. NBC37-1]
          Length = 237

 Score = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +   G   SR      I   +V V+G   +  +V + +  ++EV
Sbjct: 1  MRLDKYLVEEGYFESRNRALEAIKAGQVTVDGKKAK-PSVKIDTNSYVEV 49


>gi|282163383|ref|YP_003355768.1| hypothetical protein MCP_0713 [Methanocella paludicola SANAE]
 gi|282155697|dbj|BAI60785.1| conserved hypothetical protein [Methanocella paludicola SANAE]
          Length = 215

 Score = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 12/53 (22%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+ + +   G+  SR   +R+I + +VKV+G  + + +  V     + ++G 
Sbjct: 1  MRLDEYLVSEGLVPSRSRAKRLIEKGQVKVDGKAVLKPSQKVEYGRKVAIEGE 53


>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 = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 38/247 (15%), Positives = 80/247 (32%), Gaps = 36/247 (14%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K ++IV E     RV K++ +     SR +++  I +  V+VNG+ ++ A    +  D +
Sbjct: 3   KSQHIVTEQQGKTRVDKLLTQLLADQSRSQIQGWIDEGLVEVNGVSVK-ANYKCVEGDAL 61

Query: 61  EV------------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-- 104
                         + +PL     +   + +      +V   +     + V   L     
Sbjct: 62  TWEIPETKPLILEPENIPLDVVYEDSDVIVINKPKGMVVHPSAGHQTGTLVHALLYHCDD 121

Query: 105 ------FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
                   R   V R+D +T GLL++  +    + L     Q     +       +    
Sbjct: 122 LSGINGIERPGIVHRIDKDTSGLLVVAKNDVAHQKLSDQLQQKQLKRKYVAIVHGEIGHD 181

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG------------LREGKNREIKKVFE 206
             L    + +          +D  K +     V             L  G+  +I+   +
Sbjct: 182 TGLIDAPIGRDPKDRQKMAVVDNGKSAITHFRVIERFPDYTFVECQLETGRTHQIRVHMQ 241

Query: 207 FFNWKVN 213
           +  + + 
Sbjct: 242 YIGFPLV 248


>gi|255004408|ref|ZP_05279209.1| sfhb-like protein [Anaplasma marginale str. Virginia]
          Length = 340

 Score = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 27/245 (11%), Positives = 68/245 (27%), Gaps = 38/245 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH------- 59
           V +    QR+ K+I+ A   SR   + +IA  +V ++G ++   +    + D        
Sbjct: 9   VTKEGDQQRIDKLISCALEISRNRAQGLIAGGQVTISGRVINNNSYLTKTGDVYTIVTAV 68

Query: 60  ---------------IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDP------------- 91
                          +  +   +   ++      H   G+                    
Sbjct: 69  QKPSTLSPNYDIDLKVVYEDHDVIVIDKDPYIAVHPGNGIEHHTITNALLARFGAGLQSV 128

Query: 92  --DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
               R  +   L    S ++   + +     L     + G  +     +       R   
Sbjct: 129 GSSSRPGIVHRLDKDTSGLMVAAKTENAYYRLSEELANQGFKKEYLAVAWGIPCPKRGVI 188

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFF 208
           H  +   + ++        G      +  ++ + G   + +   L  G+  +I+      
Sbjct: 189 HTNIRVKRSDITMMEAANSGGKPAKTEYEVEQELGEVASLIRCTLHTGRTHQIRVHMSHI 248

Query: 209 NWKVN 213
              + 
Sbjct: 249 GHSIV 253


>gi|255658173|ref|ZP_05403582.1| hemolysin A [Mitsuokella multacida DSM 20544]
 gi|260849481|gb|EEX69488.1| hemolysin A [Mitsuokella multacida DSM 20544]
          Length = 268

 Score = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 14 QRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          +R+  ++   G+  SR   +RMI    V V+G  +++A   V     I + G  +  
Sbjct: 4  ERLDILLVERGLAGSRERAKRMIMAGEVLVDGQKIDKAGTTVKPEAEIRLLGHDIPY 60


>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 = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 21/250 (8%), Positives = 53/250 (21%), Gaps = 44/250 (17%)

Query: 4   KNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           + +  E   P RV K +      +SR  +++      V VN   ++     +   D + +
Sbjct: 27  RIVADEGQKPLRVDKFMFEKLQHSSRNRIQKAAEAGFVHVNDQPVKS-NYKIRPNDVVTL 85

Query: 63  -------DGVP--------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                  D           +   +   L +      +V         + +      +   
Sbjct: 86  MLDRPRHDNTIEAENIPLDIVYEDAELLVVNKPAGLVVHPGVGNFHGTLINAVAWHMKDD 145

Query: 108 VISVGRLD------------------------INTEGLLLLTNDGGLARVLELPSTQWLR 143
                                               G+         +    +       
Sbjct: 146 KNFDANSPEVGLVHRIDKDTSGLLVVAKTPNAKTKLGVQFFNKTTTRSYKALVWGHIAED 205

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREI 201
             R+  +   D      +                   +  + G    +   L  G+  +I
Sbjct: 206 EGRIEGNIGRDPKDRQRMT-VFSPDSGIGKPAVTHYKVIERFGYTTLIECILETGRTHQI 264

Query: 202 KKVFEFFNWK 211
           +   +     
Sbjct: 265 RAHMKHIGHP 274


>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 = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 28/241 (11%), Positives = 63/241 (26%), Gaps = 41/241 (17%)

Query: 11  FTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
            +P R+ K +       SR  ++       + VNG   +  +  V   D I +       
Sbjct: 36  QSPLRLDKFLTIHMERCSRNRIQTAADAGNILVNGKPAKS-SYKVKPGDRISLVMPYPKR 94

Query: 63  ------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV--- 111
                 + +P  +   +   L +      +V         + V      + +  +     
Sbjct: 95  EIEIIPENIPLEIPYEDDDLLLVNKPAGMVVHPGHGNYSATLVNALTYYLQNLPLFQEGD 154

Query: 112 ------GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--------- 156
                  R+D NT GLL++  +      L           R       + +         
Sbjct: 155 MRAGLVHRIDKNTSGLLVIAKNERAHARLAKQFFDHTITRRYVALVWGNFEEDEGTITGN 214

Query: 157 ------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                     +          +      +  + G    +   L  G+  +I+   ++   
Sbjct: 215 IGRSPKDRQKMWVFEDGSDGKHAVTHYRVLKRYGYVTLIECRLETGRTHQIRVHMQWKGH 274

Query: 211 K 211
            
Sbjct: 275 P 275


>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 = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 28/268 (10%), Positives = 73/268 (27%), Gaps = 54/268 (20%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           MK+  I  +N   QR+ K + +     G   +  + + I  +++KVN          +  
Sbjct: 1   MKEIKI-NQNDANQRLDKFLMKTFPKLG---KSMMYKAIRNKKIKVNRKRCT-FDQKIQE 55

Query: 57  TDHI-------EVDGVPLR-----------KAERTRLWLYHKPI---------------- 82
            D I        ++   +              +   L +                     
Sbjct: 56  NDSILLFLPPDVLEEKKVETNYISSKLDVIYEDENILIVNKPYGLLSQSDQSQNQDCLVN 115

Query: 83  ---------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                         + +     ++   L    + ++   +       +     +  + ++
Sbjct: 116 RVQAYLMEKNEYDPNKEHSFAPSICHRLDRNTTGLVIAAKNANALRKVNEAIANRTIQKM 175

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
                              + ++          ++G     M V ++   G N+  T+ L
Sbjct: 176 YRAHVVGTFEQKDFTMCYYIRKENTIAKVSDKKLEGYQKALMDVHVERDDGENSICTITL 235

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYG 221
             G+  +I+ +       +  L  + YG
Sbjct: 236 HTGRFHQIRALMGHIQHPL--LGDVKYG 261


>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 = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 32/248 (12%), Positives = 62/248 (25%), Gaps = 46/248 (18%)

Query: 6   IVQENFTPQRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            V     P R+ K +      +   SR ++ +      V VNG+ +++    V   D I 
Sbjct: 38  TVDSKQEPLRIDKFLLIYRQNS---SRNKISQTCRAGNVIVNGVAVKQ-NYRVKPGDQIS 93

Query: 62  V-------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           V               +P+    E   L +  K  G+V      +   T+ + L   F +
Sbjct: 94  VLLAHPPRENVIIPQDIPVNIIYEDDDLVVVDKEAGMVVHPGFGNWDGTLVNALAYHFEK 153

Query: 108 V------------------------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
                                    I+     ++                  +       
Sbjct: 154 NGEKSDLDRVGLVHRIDKDTSGLLVIAKNEYALSFLAKQFFNRTTKRLYWAFVWGNLQED 213

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
              +R H          +          +      +  +     WV   L  G+  +I+ 
Sbjct: 214 EGTIRGHIGRHPKNRMQMSVYEDGSQGKHAVTHYKVLERFKYMTWVECKLETGRTHQIRA 273

Query: 204 VFEFFNWK 211
            F      
Sbjct: 274 HFRHIGHT 281


>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 = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 32/239 (13%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VN  L ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNSKLCDKPKEKVLGGEQVAINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   + +      +V   +     + +   L         
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDSTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   V RLD +T GL+++       R L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQRRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +      +  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 248


>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 = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 35/246 (14%), Positives = 73/246 (29%), Gaps = 39/246 (15%)

Query: 4   KNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           + +V +   P R+ K +  R    +R + +  I +  VKVN   ++     V   D I +
Sbjct: 39  RIVVDKGQEPVRIDKFLMDRVPNITRNKTQNAIREGFVKVNDQEVK-PNYKVRPEDIIII 97

Query: 63  -------------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--- 105
                        + +P+    E   L + HK  G+V   +  +   T+ + L   F   
Sbjct: 98  SLPEPPRESEVVPEDIPINIVYEDDDLLVVHKEAGMVVHPAYNNWTGTLVNALAYHFKNL 157

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
             +R    G +    +    L         L+  + Q+      R +  +   +      
Sbjct: 158 PENRDGRPGLVHRIDKDTSGLLVVAKSEHALQHLAKQFFDHTIERTYYALVWGEPKQEAG 217

Query: 164 GIVI------------------QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
            I +                      +      +       + V   L  G+  +I+   
Sbjct: 218 TIDVNLGRSLKDRRVTAAFPEGDFGRHAVTHYKVLKNLRYVSLVQCNLETGRTHQIRAHM 277

Query: 206 EFFNWK 211
           +     
Sbjct: 278 KHLGHP 283


>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 = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 32/243 (13%), Positives = 64/243 (26%), Gaps = 35/243 (14%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRV-KVNGILLERAAVNVMSTDHIEVDG 64
            V    + +R+  V+A A   SR  ++ ++ +  V    G ++ +A+  V   +   +  
Sbjct: 14  TVSTEASGKRLDAVLAAACELSRSRIQTLLREGHVRTAGGSVISQASARVWEGERYLLTL 73

Query: 65  VPLRK--------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
            P++                +   + L      +V      D  + V   L    +    
Sbjct: 74  PPVKPLILEPEDLPLDILFEDEHLIVLNKPAGIVVHPSHGHDHGTLVHALLHHCKTLPGI 133

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            G         L     G L         Q L       +                ++ I
Sbjct: 134 NGVERPGIVHRLDKDTSGSLVIAKSEVVHQRLSEMFAEHNLNRQYIAWCRGVPSWRVKCI 193

Query: 171 CYGDMQVTLDTQK--------------------GSNAWVTVGLREGKNREIKKVFEFFNW 210
                +     QK                    G  + + + L  G+  +I+      N 
Sbjct: 194 ELPIGRHPHQRQKMAVTDSGRESITDAAVEHIFGPFSQMRLTLHTGRTHQIRVHMAHENL 253

Query: 211 KVN 213
            V 
Sbjct: 254 PVL 256


>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 = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 74/244 (30%), Gaps = 44/244 (18%)

Query: 10  NFTPQRVSKVIA----RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
            +  +R+ K ++         SR   +++I    V VN  + ++A   + + D + V   
Sbjct: 11  EYEGERLDKYVSILFPEQ---SRSFFQKLIKDGNVSVNDKV-QKANYRLKTEDLVTVEIP 66

Query: 63  ---------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                    + +PL     +   L +      +V   +     + V   +          
Sbjct: 67  DAVETQILPEDIPLDILYEDDDLLVVNKPKGMVVHPSAGHYSGTLVNAIMYHCKDSLSGI 126

Query: 107 ----RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-------------F 149
               R   V R+D++T G L++  +      +     +     R R              
Sbjct: 127 NGEIRPGIVHRIDMDTTGSLIVCKNDESHVFIAEQIKEHSVNRRYRGIVYGVVRDDEGTI 186

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
           H  + +  ++  K  I  +          +  +     ++   L  G+  +I+       
Sbjct: 187 HAPIGRHPVDRKKMAINEKNGKDAITHYKVLERFDKYTYMEFKLETGRTHQIRVHMASIG 246

Query: 210 WKVN 213
             + 
Sbjct: 247 HPLL 250


>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 = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 30/242 (12%), Positives = 69/242 (28%), Gaps = 42/242 (17%)

Query: 10  NFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---D 63
               +R+ + +AR  +    +R  +++++    V +NG    +    + + D I V   D
Sbjct: 11  EQAGERLDRALAR--LCPDQTRSGLQKLLECGLVTLNGKPAGKHD-RMRAGDEIVVEFPD 67

Query: 64  GVPLRKAERTR-----------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
            VPL    +             L +      +V   +     + V   L      +  +G
Sbjct: 68  PVPLEAKAQDIPIEVVYEDDDLLVVNKPQGMVVHPGAGNPDGTLVNALLFHCGDSLSGIG 127

Query: 113 ----------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
                                 + D   + L          R  E      ++       
Sbjct: 128 GVLRPGIVHRIDKDTSGLLMVAKNDRAHQSLAAQIKAHSFLREYEAVVCGVIKEDSGTVD 187

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             V +   N  +  +  +   +     T+  +      + + L  G+  +I+    +   
Sbjct: 188 APVGRHPTNRKRMAVTQKNSRHAVTHYTVLRRYTHYTHLRLRLETGRTHQIRLHMAYIGH 247

Query: 211 KV 212
            V
Sbjct: 248 PV 249


>gi|91200050|emb|CAJ73092.1| similar to ribosomal large subunit pseudouridine synthase D
           [Candidatus Kuenenia stuttgartiensis]
          Length = 335

 Score = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 18/237 (7%), Positives = 58/237 (24%), Gaps = 35/237 (14%)

Query: 12  TPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERA-----------------AVN 53
             +R+ + I+      SR  +++++ +  + VNG +++ +                    
Sbjct: 24  ESKRIDRFISSRFPDLSRTYIQKLVKEGAIVVNGNVVKSSYFIKKGDVISATVPVPEETK 83

Query: 54  VMSTDH---IEVDGVPLRKAERTRLWLYHKPIGLVT------THSDPDGRSTVFDNLPSI 104
           +   D    I  +   L    +    + H   G  +              S +   L + 
Sbjct: 84  ITPEDIPLNIIYEDDYLMLINKPYDMVVHPAGGHPSGTLVNAVTFYCQNLSQINGPLKAG 143

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
               +      +         +     +  +    +               +    + + 
Sbjct: 144 IVHRLDRDTSGVMLVIKSDAVHSHIAMQFEKRLVKKEYFAVVEGEVAFDSNEINMPIGRH 203

Query: 165 --------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                   +             +  +      V +  + G+  +I+   +     V 
Sbjct: 204 RVDRQKMAVRRDTGKNATSVYEVIERFRGYTLVKIMPKTGRTHQIRVHMQAIGHPVV 260


>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 = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 30/241 (12%), Positives = 60/241 (24%), Gaps = 41/241 (17%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            QR+  +++     SR   +  I    V VNG ++ +    V     I +    +   E 
Sbjct: 4   TQRLDILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKI-VEET 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV---GRLDINTEGLLLLTNDGG 129
             L  + K I +V         +   D +    S  +S      +    +   +  N   
Sbjct: 63  KVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDP 122

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---------------ICYGD 174
           L   +     +      +        +    L     I+                     
Sbjct: 123 LRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAP 182

Query: 175 MQ----------------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           ++                           +  +     V L  G+  +I+   EF    V
Sbjct: 183 IKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIRVHAEFIKNHV 242

Query: 213 N 213
            
Sbjct: 243 I 243


>gi|294495319|ref|YP_003541812.1| RNA-binding S4 domain protein [Methanohalophilus mahii DSM 5219]
 gi|292666318|gb|ADE36167.1| RNA-binding S4 domain protein [Methanohalophilus mahii DSM 5219]
          Length = 218

 Score = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 14/51 (27%), Positives = 27/51 (52%), Gaps = 1/51 (1%)

Query: 14 QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+   +   G  S R   ++ I++  VKV+G ++ +++  V   + IEVD
Sbjct: 1  MRLDVYLIETGFFSSRGRAKKAISEGHVKVDGNVITKSSREVSEFNEIEVD 51


>gi|325680798|ref|ZP_08160336.1| ribosomal RNA large subunit methyltransferase J [Ruminococcus
          albus 8]
 gi|324107578|gb|EGC01856.1| ribosomal RNA large subunit methyltransferase J [Ruminococcus
          albus 8]
          Length = 263

 Score = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+   +   G+A SR   + MI    VKV+G +  + + +V     IEVD 
Sbjct: 1  MRLDIYLTEKGLAKSRERAKTMIKAGCVKVSGTVCTKPSADVADGAEIEVDD 52


>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 = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 20/202 (9%), Positives = 51/202 (25%), Gaps = 6/202 (2%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAERTRL 75
           K++A+    S ++ ++ I    V + G  L  A        H  +          +   L
Sbjct: 6   KILAKNLNISHKQAKKYIDMGLVSLQGKRLTLARQKFPLDTHFHIKECLKTDVLYQDQEL 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            + +K   + +   +   +     +     +  + +          LL      + +   
Sbjct: 66  LVLNKATHIDSYTLERQHKPYKLLHRLDKSTSGLLLLAQATFYTKALLAFKKREVYKEYL 125

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--VIQGICYGDMQVTL--DTQKGSNAWVTV 191
                 L+  +        +       KG       +        L           + V
Sbjct: 126 ALIEGILKRPKTLTQPLSVRTNHMHFNKGFVKTFVDLKGKPAITHLYPIYHTKQQTLLKV 185

Query: 192 GLREGKNREIKKVFEFFNWKVN 213
            +  G   +I+         + 
Sbjct: 186 VIETGITHQIRAHLSHIGHPIV 207


>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 = 57.5 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 33/232 (14%), Positives = 63/232 (27%), Gaps = 37/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------DGVP 66
           R+ K +A     SR +    I Q+RV VNG   ++A   V   D I          D   
Sbjct: 11  RLDKALADLTPLSRSQANDQIKQKRVLVNGSP-KKAKYIVQVGDCISYHIPEESSLDYQA 69

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 +   +     +      +V   +     + V   L  +       G +      
Sbjct: 70  QDIPLDIVYQDDVLAIINKPQGMVVHPSAGHSTGTLVNALLYHVKDLSSINGVIRPGIVH 129

Query: 121 LLLLTNDGGLA---------------------RVLELPSTQWLRVYRVRFHGQVDQDKLN 159
            +     G L                      R         L   R      + +   +
Sbjct: 130 RIDKDTSGLLMVAKTDKAHQLLADELKAKKSLRKYVAIVHGNLPKDRGVIEAPIGRSDKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             K+ +  +G      +  +  + G  + V + L  G+  +I+    +    
Sbjct: 190 RKKQTVTAKGKEALT-RFKVLERFGRYSLVELQLETGRTHQIRVHMAYIGHP 240


>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 = 57.1 bits (136), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 28/202 (13%), Positives = 62/202 (30%), Gaps = 13/202 (6%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------DGVPLRKAE 71
            IA +   S+ + + +I  + V VN   +  A+ N+   D +E+       D   L   E
Sbjct: 16  FIAESLKISKNQAKDIIDSRNVIVNNKRVWIASHNLKPGDVVEIVQSEPKNDLKIL--YE 73

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              +    KP  +V+          +   L +   + I            +LL       
Sbjct: 74  DDYIIAIDKPPTIVSDKESSSAEDLLRKKLKNDKIKAIH---RLDKETSGVLLFAKDYKI 130

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
                   +   V ++      ++           I+G       + + ++     +  V
Sbjct: 131 FEKFKEIWEDKNVLKIYLAISHNEANFKDFTINHDIEGKQA-ITHLKVLSKGNGFTYFQV 189

Query: 192 GLREGKNREIKKVFEFFNWKVN 213
            +  G+  +I+K        + 
Sbjct: 190 RIETGRKHQIRKHLASIRHPIV 211


>gi|126698804|ref|YP_001087701.1| putative RNA methyltransferase [Clostridium difficile 630]
 gi|255100223|ref|ZP_05329200.1| putative RNA methyltransferase [Clostridium difficile QCD-63q42]
 gi|255306112|ref|ZP_05350284.1| putative RNA methyltransferase [Clostridium difficile ATCC 43255]
 gi|115250241|emb|CAJ68062.1| putative RNA-binding S4-domain protein [Clostridium difficile]
          Length = 270

 Score = 57.1 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 22/177 (12%), Positives = 47/177 (26%), Gaps = 2/177 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  ++   G   SR   ++ I    V V+    ++A   V     IEV G P+    R 
Sbjct: 4   RIDLLLVEQGYFESRERAKKAIMAGLVFVDNQRCDKAGTEVKEDCSIEVKGNPIPYVSRG 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L         T                    ++  G + + +  +        L + 
Sbjct: 64  GLKLEKAMKNFDLTIDGKVCMDIGAST-GGFTDCMLKNGAIKVFSIDVGYGQLAWKLRQD 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             +   +   +  V             +    +   +     +  +       A + 
Sbjct: 123 DRVVCMERTNIRNVTIEDTKQFADFASIDVSFISLKLVLPKAKELVRHDGEVVALIK 179


>gi|75910708|ref|YP_325004.1| hemolysin A [Anabaena variabilis ATCC 29413]
 gi|75704433|gb|ABA24109.1| Hemolysin A [Anabaena variabilis ATCC 29413]
          Length = 272

 Score = 57.1 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          QR+  ++    +  SR   +R+I    V VN  ++++    V     I++
Sbjct: 4  QRLDNLLVELNLCNSRTLAQRLIQAGEVTVNEQVIDKPGTEVDVAAQIKI 53


>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 = 57.1 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 35/244 (14%), Positives = 71/244 (29%), Gaps = 40/244 (16%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +     RV K +  R   +SR  +++      V  NG  ++  +  V   D I V  
Sbjct: 33  VVDKGQEMVRVDKYLFDRLTNSSRNRIQKAADAGFVMANGKAVKS-SYKVKPMDVITVMM 91

Query: 63  -----DGVPLR-------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                +   +          E   L + +KP GLV      +   T+ + +         
Sbjct: 92  DRPRYENEVIPEDIPLDIVYEDKYLMVVNKPAGLVVHPGHGNYHGTLVNAIAWHMKDNPD 151

Query: 111 VGRLDIN----------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK--- 157
               D +          T GLL++         L           R R     + ++   
Sbjct: 152 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGNQFFNKTTKRRYRALVWGNVEQDEG 211

Query: 158 ----------LNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                      + ++  ++      +      +  + G    V   L  G+  +I+   +
Sbjct: 212 TVVGNIGRNPRDRMQMTVLPDDQGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMK 271

Query: 207 FFNW 210
               
Sbjct: 272 HIGH 275


>gi|312601410|gb|ADQ90665.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyopneumoniae 168]
          Length = 304

 Score = 57.1 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 30/244 (12%), Positives = 74/244 (30%), Gaps = 43/244 (17%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--------- 60
           +    R+  ++A+    SR+  + +I +++V +N  L+ +    V +   I         
Sbjct: 12  DQEDIRIDILVAKLANLSRKVAQDLILEKKVLINNNLVLKKNQIVKTGQKIKIFNDYKRP 71

Query: 61  -------EVDGVPLRKAERTRLWLYHKPIGLV-------------------TTHSDPDGR 94
                  EVD   + + +   L    K + +                    +       R
Sbjct: 72  KPQLEPAEVDFEIIFQDQNMILINKPKNLVVHPGVGNWKNTLVNGLISHFDSLEQLDHIR 131

Query: 95  STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD 154
             +   L    + ++ V +        +    +  + R  +      +    ++ +  + 
Sbjct: 132 PGIVHRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVIGKVLHKFMKINLPIG 191

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLD------TQKGSNAWVTVGLREGKNREIKKVFEFF 208
           +D  N LKK I             ++       Q    + V   L  G+  +I+      
Sbjct: 192 RDLKNPLKKTISFFNS--KPAITNVELIKHFSYQNQDFSLVKCQLETGRTHQIRLHLAHI 249

Query: 209 NWKV 212
            + +
Sbjct: 250 GYPI 253


>gi|308274565|emb|CBX31164.1| Uncharacterized RNA pseudouridine synthase ylyB [uncultured
           Desulfobacterium sp.]
          Length = 335

 Score = 57.1 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 27/243 (11%), Positives = 56/243 (23%), Gaps = 39/243 (16%)

Query: 8   QENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE---VD 63
            E+ +  R+  V++    + SR     +I + ++ V   + ++    V   D I     D
Sbjct: 28  DESVSGIRLDIVVSSYIPLCSRSIAASLINKGKITVCNQI-KKQGYKVKFGDKITGTIPD 86

Query: 64  GVPLRKAERTRLWLY-----------HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
             P+                        P  +          + V   L          G
Sbjct: 87  PEPVSFLPEPIELNILYEDSDIIVINKPPGIVAHPAPGHYSGTLVNALLFHCPDLTGIGG 146

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
            +       L     G L       S   L +       +       +        G   
Sbjct: 147 EIRPGIVHRLDKDTSGALVVAKNDISHTNLCLQFKERRIRKKY-LALVWGNPEHDSGSIT 205

Query: 173 GDM----------------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             +                         +  +  S +   + L+ G+  +I+        
Sbjct: 206 LPIGRHPSNRKKMSVLTRKPKTAETLWKVIERYKSVSLWEIDLKTGRTHQIRVHCAAIKH 265

Query: 211 KVN 213
            V 
Sbjct: 266 PVI 268


>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 = 57.1 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 30/250 (12%), Positives = 79/250 (31%), Gaps = 38/250 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK + +V       R+ + ++ R    SR  +++++ +Q V V    ++     V + D 
Sbjct: 1   MKQEYVVAPEEAGVRIDRYLSDRCQDISRSYLQKLLKEQSVLVEEKPVKS-NYKVNAGDR 59

Query: 60  IEV------------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I V            + +PL     ++  + +      +V   +     + V   +    
Sbjct: 60  ISVFFPESKEPEIQPEDIPLNIIYEDKDIILINKPKGMVVHPAAGHYSGTLVNGLMSHCR 119

Query: 106 ---------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR---------- 146
                     R   V R+D++T G+L++  +      +     +     +          
Sbjct: 120 SELSGINGVMRPGIVHRIDMDTTGVLIVCKNDMAHSSISEQLKEHSITRKYAAIVHGVLK 179

Query: 147 ---VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                 +  + +  ++  K  I  +          +  +     ++   L  G+  +I+ 
Sbjct: 180 EDEGTVNAPIGRHPVDRKKMSINEKNGREAVTHYRVLERFKQFTYIECQLETGRTHQIRV 239

Query: 204 VFEFFNWKVN 213
                   + 
Sbjct: 240 HMASIGHPLL 249


>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 = 57.1 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 35/263 (13%), Positives = 65/263 (24%), Gaps = 47/263 (17%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           IV +     R+  ++A +G   SR    + I   +V VNG L       V   D I  + 
Sbjct: 8   IVTQADAGMRLDSLLAVSGAYPSRSAAVKQIEAGKVLVNG-LARSKRSIVAPGDTIVYEE 66

Query: 64  ----------GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS------- 103
                     G P+      E   +    K  GL    +      T+ + L         
Sbjct: 67  IPLATHIPLRGEPIPLDVRFEDRWMMAISKQAGLCVHPAPGHEGGTLVNALIYAYGRDSL 126

Query: 104 ------------IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151
                           + + G +    +    +     +           L    + F  
Sbjct: 127 AHVQGDDRPGIVHRLDMDTSGLMMCAKDDTCGMALQDLVRDHKVDRRYLTLVHGNIAFDT 186

Query: 152 QVDQDKLNLLKKGIVIQGICYGDM------------QVTLDTQKGSNAWVTVGLREGKNR 199
               + +  +    +   I Y               +            +   L  G+  
Sbjct: 187 GQIDEPIGRVGDDRLRMKISYRPTARNALTTFTVLERFEAGRADNGYTLLECRLYTGRTH 246

Query: 200 EIKKVFEFFNWKVNRLIRISYGP 222
           +I+   EF            +G 
Sbjct: 247 QIRVHMEFIGHCCVGDPLYRWGN 269


>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 = 57.1 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 28/245 (11%), Positives = 60/245 (24%), Gaps = 41/245 (16%)

Query: 7   VQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V       R+ K +  R    +R +V++ I    V+VNG+ ++     V   D+I +   
Sbjct: 23  VDPKQDLLRIDKFLMDRLPNVTRNKVQKAIKDGFVQVNGVTIK-PNYKVHPDDNIRIALP 81

Query: 63  ----DGVP--------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
               D           +   +   L +  +   +V         + V             
Sbjct: 82  EPPRDTEVKPENIPLDIVYEDSDLLIVNKEAGMVVHPAHQNWEGTLVNALAYHFQQLPEM 141

Query: 111 VGRLDIN------------------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152
            G                       TE  +           +E      +        G 
Sbjct: 142 QGNEGRPGLVHRIDKDTSGLLVIAKTEKSMTALAKQFFDHSIERTYYALVWGELEDEEGT 201

Query: 153 VDQDKLNLLKKGIVIQG------ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
           +D +     K   +                  +  +      +   L  G+  +I+   +
Sbjct: 202 IDVNLGRSFKDRRITDAFPEGDFGRTAITHYKVLERLRYVTLIQCNLETGRTHQIRAHMK 261

Query: 207 FFNWK 211
           +    
Sbjct: 262 YIGHP 266


>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 = 57.1 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 38/304 (12%), Positives = 82/304 (26%), Gaps = 44/304 (14%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V ++   QR+ + +A      SR  ++  I   RV+VN  ++ +    ++  + IEVD 
Sbjct: 10  TVADSQLGQRLDQALAELFPDYSRSRIKEWILDNRVQVNDKIINKPKEKMLGGEKIEVDA 69

Query: 64  -------GVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                    P      +   +   L +      +V   +     + +   L      V  
Sbjct: 70  LIEEDVRWEPQNIPLNIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLYRYPEIVNV 129

Query: 111 V-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                  RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTHLVEALQRREITREYEAVATGRMTAGGLVNEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                      V            +     ++  + + L  G+  +I+      +  +  
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRVMEHFRAHTRLRLRLETGRTHQIRVHMAHIHHPL-- 247

Query: 215 LIRISYGPFQLGTLLAGSTREVSK--KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRP 272
                 G      L  G  R +    +  RE L     +     +    +    +  +  
Sbjct: 248 -----IG----DQLYGGRPRPLKGASEEFRETLRRFDRQALHATMLRLYHPITGIEMEWH 298

Query: 273 NIIS 276
             + 
Sbjct: 299 APLP 302


>gi|157151563|ref|YP_001449982.1| S4 domain-containing protein [Streptococcus gordonii str. Challis
           substr. CH1]
 gi|157076357|gb|ABV11040.1| S4 domain [Streptococcus gordonii str. Challis substr. CH1]
          Length = 275

 Score = 57.1 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 15/51 (29%), Positives = 27/51 (52%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +  R+ K+IA +   SR +  ++I  + VKVN  +++  +  V   D I V
Sbjct: 195 SSMRLDKLIASSFKLSRNDASQLIFGKHVKVNYSIIDNPSYLVELNDLISV 245


>gi|148377981|ref|YP_001256857.1| ribosomal large subunit pseudouridine synthaseC [Mycoplasma
           agalactiae PG2]
 gi|148292027|emb|CAL59419.1| Ribosomal large subunit pseudouridine synthaseC [Mycoplasma
           agalactiae PG2]
          Length = 284

 Score = 57.1 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 37/243 (15%), Positives = 77/243 (31%), Gaps = 41/243 (16%)

Query: 4   KNIVQENFTPQRVSKVIARAGIAS--------RREVERMIAQQRVKVNGILLERAAVNVM 55
           K I Q +   +++ K I      S        R  + R+  Q+ +KVN   +  +   V 
Sbjct: 3   KFIAQSSDNGRKLIKYI-----GSLFKKLPEGR--IYRLFRQKSIKVNNKRITDSNYVVK 55

Query: 56  STDHIEVDGVP-----------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF 98
           + D I + G+                  +   +   L +  K   +V   S+        
Sbjct: 56  TGDEIIIYGIKDEPSFVIYDNSWKLDSEIVYEDDNILLINKKAGTIVHGDSNCLDNQVFS 115

Query: 99  DNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
                     R   VGRLD  T GL++   +      L   +    ++Y ++       +
Sbjct: 116 YFKFRQNSAFRPSHVGRLDKWTSGLIMYAKNYQTLTELNHKTEFLDKIYVLKSDYNPHDE 175

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNA-------WVTVGLREGKNREIKKVFEFFN 209
            +++      +Q        +     K +          +   L  G+  +I+   E+  
Sbjct: 176 IVSVYIHHDELQQKMVATKNMQHPNDKIAKTRFFKKDNKLYAQLFTGRKHQIRATLEYLG 235

Query: 210 WKV 212
           + +
Sbjct: 236 YPI 238


>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 = 57.1 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 31/248 (12%), Positives = 65/248 (26%), Gaps = 38/248 (15%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ V       R+ K ++      SR ++++ +   +V VN I++    V V   D I  
Sbjct: 3   KHSVPHELNGIRLDKALSLLLKNVSRNQIQKAVKDSQVLVNDIIISDPDVLVKENDIILF 62

Query: 63  DGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-- 106
                             +       + +       V         + V   L    +  
Sbjct: 63  SFKEPEELKIEAANIALDIIYENDDLIVINKAAGMTVHPGLGHHNDTLVNALLHYTKNLS 122

Query: 107 ---RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
                   G +    +    L       +   L + Q  +   +R +  +    +N L+ 
Sbjct: 123 DIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRKYKALIWGVINPLEG 182

Query: 164 GIVIQGICYGDMQVTL------------------DTQKGSNAWVTVGLREGKNREIKKVF 205
            I          +  +                      G+ + V   L  G+  +I+   
Sbjct: 183 VIQNNIGRSRSDRQKMTILKYGGKEAVTHYKTLELFYGGTISMVECKLNTGRTHQIRVQL 242

Query: 206 EFFNWKVN 213
                 V 
Sbjct: 243 SHLKHSVV 250


>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 = 57.1 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 35/263 (13%), Positives = 69/263 (26%), Gaps = 51/263 (19%)

Query: 2   KDKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
             K ++       R+   +A +  G  SR  V+ +I Q  V VNG  +      +   D 
Sbjct: 11  PRKELIAGEDAEGRLDAWLAASLGGDLSRNRVKALIEQGAVFVNGTAVTEPKRKIKPGDQ 70

Query: 60  IEV------DGVP--------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           + +      D  P        +   ++  + L      +V   +     + V   +    
Sbjct: 71  LVIAMPEPEDPEPKGEDIPLTVLYEDKDLIVLSKPAGLVVHPGAGNWTGTLVNALIHHCG 130

Query: 106 S---------RVISVGRLDINTEGLLLLTNDGGLARV-----LELPSTQWLRVYRVRFHG 151
                     R   V RLD  T G++++  +    R       +   +  L         
Sbjct: 131 DSLSGIGGVKRPGIVHRLDKETSGVMVVAKNDIAHRHLADQFADHGRSGPLERAYQALVW 190

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN---------------------AWVT 190
              +     +   +   G          DT                          + V 
Sbjct: 191 GRPRGLRGTIDAALGRAGDRTKRTVKREDTDDAREAITHYQVMERYGEKPDATCLASLVE 250

Query: 191 VGLREGKNREIKKVFEFFNWKVN 213
             L  G+  +I+         + 
Sbjct: 251 CRLETGRTHQIRVHMAHIGHPLI 273


>gi|15606155|ref|NP_213532.1| hemolysin [Aquifex aeolicus VF5]
 gi|2983347|gb|AAC06935.1| hemolysin [Aquifex aeolicus VF5]
          Length = 258

 Score = 57.1 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +   GI  SR + + +I   +V VNG ++++    +   + +EV
Sbjct: 1  MRLDKYLTDKGIVPSREKAQAVIMAGQVLVNGKVVDKPGYRLKGNEKVEV 50


>gi|291166433|gb|EFE28479.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Filifactor alocis ATCC 35896]
          Length = 293

 Score = 57.1 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 34/239 (14%), Positives = 81/239 (33%), Gaps = 43/239 (17%)

Query: 14  QRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRK 69
            R+ + I+      SR  ++++I ++RV VNG   ++ +  + S D+IE+   +   +  
Sbjct: 1   MRLDQFISSNLPSISRSYIQKLIDEKRVLVNGKYEKK-SFLLKSFDNIEIYIPEPKSIEI 59

Query: 70  AERT-----------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRVI 109
           +               L +  +   +V         + V   L              R  
Sbjct: 60  SPENIPLNILFEDKDILIVNKEKGMVVHPAPGNYSHTLVNAILYHCKGNLSEINGYIRPG 119

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVYRVRFHGQVDQD 156
            V R+D +T G+L++  +    + L                +   ++   +     + ++
Sbjct: 120 IVHRIDKDTSGILVIAKNNDAHQFLSEQFKEHSIQREYQLITFGNIKTTHLSIEQPIGRN 179

Query: 157 KLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             N L+  +V  G         +T+        ++   L  G+  +I+    +    + 
Sbjct: 180 PKNRLQMAVVPNG---KPAITHLTVIENFKDKTYLKARLETGRTHQIRVHCTYIGHPLL 235


>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 = 57.1 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 28/239 (11%), Positives = 65/239 (27%), Gaps = 39/239 (16%)

Query: 13  PQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
           P+R+   + ++ G  +R ++  +I  + V V+G  + R  V + +   ++V+        
Sbjct: 12  PERLDTFLTSQIGQ-TRSQIAGLIKHECVFVDGKKVPRPGVKLKAGQVVKVEFPEAKQEK 70

Query: 64  ------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
                  V +   +   L +       V         + V              G     
Sbjct: 71  ALDVNFDVEILYEDDDVLVINKPSGVTVHPAPSVKEATLVDWLKHKGIRLSTISGEERHG 130

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------------------HGQVDQD 156
               L     G +       + ++L                               + + 
Sbjct: 131 IVHRLDKGTSGTMVVAKNNEAHEFLSKQLQDKSMGRYYIAVIVPPLKEDITVVESNIGRS 190

Query: 157 KLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             N LK    ++   Y     +    ++      +   L  G+  +I+   E  N  + 
Sbjct: 191 SHNRLKMACGLEHGKYAKTMFKQLALSEDEHTQLIACKLFTGRTHQIRVHLESMNRHIL 249


>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 = 57.1 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 32/241 (13%), Positives = 69/241 (28%), Gaps = 44/241 (18%)

Query: 15  RVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP----- 66
           R+ + +A  GI    SR  ++++I    V++NG  + + +  V + D + ++  P     
Sbjct: 49  RLDRALA--GIVPEFSRSYLQQLIEAAVVQLNGRAVTKPSAKVKAGDELIIELRPTPQSQ 106

Query: 67  ----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-----SV 111
                     +   +   L +      +V         + +   L              V
Sbjct: 107 AFKPEAMALDIVFEDPYLLVIDKPAGLVVHPAPGNWSGTLLNGLLARDPQASFLPRAGIV 166

Query: 112 GRLDINTEGLLLLTNDGGLARV----------------LELPSTQWLRVYRVRFHGQVDQ 155
            RLD +T GL+++                         L   + Q  R   V      D 
Sbjct: 167 HRLDKDTSGLMVVARQRQAMDQLVSMIAARSVSREYIALAHGAWQGARTREVSAAIGRDP 226

Query: 156 DKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                +   + ++          +        +  V   L  G+  +I+         + 
Sbjct: 227 RNRLRMAA-VDLEKNAGKPALTVISLLQNGERHCLVKCKLHTGRTHQIRVHMALLGHPLI 285

Query: 214 R 214
            
Sbjct: 286 S 286


>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 = 57.1 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 33/236 (13%), Positives = 63/236 (26%), Gaps = 35/236 (14%)

Query: 12  TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------- 63
              R+ + +A      SR  ++ +I +  V VNG      A  +   D + V+       
Sbjct: 16  EGWRLDRYLAEKLPDRSRASLQELIREGFVTVNGRPAR-PASPLKPGDRVTVELPPPAPT 74

Query: 64  --------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            L   ++      H   G           S   +   S   R  
Sbjct: 75  TATAEDIPLTVIYEDEDLAVIDKPAGLTTHPAPGHPAGTLLNALLSRFPELRDSGLDRPG 134

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD------------K 157
            V RLD +T GL+++         L                 +   +             
Sbjct: 135 IVHRLDKDTSGLMVVARSRQAHARLSDQFRNREVTKVYLALVRGCVEPAEGIIEAAIGRH 194

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               KK  V +       +  +  +  ++  + V +  G+  +I+         V 
Sbjct: 195 RTQRKKMTVSEQGREARSRFKVIRRFRNHTLLEVRIYTGRTHQIRVHLAAIGHPVI 250


>gi|291543962|emb|CBL17071.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus sp.
           18P13]
          Length = 304

 Score = 57.1 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 35/245 (14%), Positives = 71/245 (28%), Gaps = 39/245 (15%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           ++  + +  R+ K +       SR  V+ +I Q  V  NG    +  + +   D + V  
Sbjct: 5   MLTADGSGMRLDKWLTEQLPELSRSGVQHLIEQGAVLCNGKPAAK-NLKLREGDGLLVQI 63

Query: 63  -------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
                  D  P      +   +   L +      +V   +     + V   L        
Sbjct: 64  PDPAPLEDVQPQNLPLEIVYEDEALLVVNKPKGMVVHPAAGHPDGTLVNALLYHCQGRLS 123

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR-------------V 147
                 R   V R+D NT GLL++       + L                          
Sbjct: 124 TINGVIRPGIVHRIDKNTSGLLMVAKTDFAHQHLAEQIKGHSFTREYEAIACGRFREPSG 183

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                + +   +  K  +  +   +      + TQ   +A +   L  G+  +I+    +
Sbjct: 184 TVDAPIGRSTADRQKMCVTEKNARHAVTHYAVLTQFAKHAHIRCRLETGRTHQIRVHMRY 243

Query: 208 FNWKV 212
               +
Sbjct: 244 IGHPI 248


>gi|260460313|ref|ZP_05808565.1| hemolysin A [Mesorhizobium opportunistum WSM2075]
 gi|259033958|gb|EEW35217.1| hemolysin A [Mesorhizobium opportunistum WSM2075]
          Length = 254

 Score = 57.1 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 14 QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          QR+  ++ + G  ASR      + +  V V+G++  +   NV     + +D 
Sbjct: 11 QRLDDLLVQRGLFASRSRARDAVERGTVTVDGVIARKPGQNVSLQCLVTIDD 62


>gi|288818047|ref|YP_003432394.1| hemolysin [Hydrogenobacter thermophilus TK-6]
 gi|288787446|dbj|BAI69193.1| hemolysin [Hydrogenobacter thermophilus TK-6]
 gi|308751648|gb|ADO45131.1| hemolysin A [Hydrogenobacter thermophilus TK-6]
          Length = 261

 Score = 57.1 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 2/57 (3%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          QR+ K +   G A +R + + +I    V V+G+L+++    V     I+V   P+R 
Sbjct: 4  QRLDKKLVELGFAPTREKAQALIMAGMVTVDGLLVDKPGFLVKEGQKIDVK-EPVRY 59


>gi|255280915|ref|ZP_05345470.1| S4 domain protein [Bryantella formatexigens DSM 14469]
 gi|255268363|gb|EET61568.1| S4 domain protein [Bryantella formatexigens DSM 14469]
          Length = 268

 Score = 57.1 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 15/48 (31%), Positives = 22/48 (45%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             R+  ++A A  ASR  +  +I   +V VNG L+      V   D I
Sbjct: 191 SVRLDSLLALAFGASRSSLVGLIEGGKVFVNGRLITSNGYKVKENDLI 238


>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 = 57.1 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 34/247 (13%), Positives = 76/247 (30%), Gaps = 40/247 (16%)

Query: 4   KNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K +  +   P R+ K +      A+R ++++      + VN +L+++    V + D I V
Sbjct: 19  KVVAAKGQEPLRIDKFLMNFIENATRSQIQKAAKDGHIWVNNVLVKQ-NYKVKAGDDIRV 77

Query: 63  -------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-- 105
                        + +P  +   +   L +      +V         + +   L      
Sbjct: 78  MFSHPPYEFLLQPEDIPLDIVYEDDVLLVVNKPAGMVVHPGHGNYSGTLINALLHHCKVD 137

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVYR 146
                  R   V R+D +T GLL++         L                    +    
Sbjct: 138 LPNNSSDRPGLVHRIDKDTSGLLVVAKTEAAMTFLSKQFFDKTSEREYVAIVWGNVEADE 197

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKV 204
               G + +   N L+  +  +G    +      +  + G    ++  L  G+  +I+  
Sbjct: 198 GTIEGHLGRHPKNRLQMHVFPEGDQGKEAITHYKVLERLGYVTVISCKLETGRTHQIRVH 257

Query: 205 FEFFNWK 211
            +     
Sbjct: 258 MKHIGHT 264


>gi|257439731|ref|ZP_05615486.1| hemolysin A [Faecalibacterium prausnitzii A2-165]
 gi|257197822|gb|EEU96106.1| hemolysin A [Faecalibacterium prausnitzii A2-165]
          Length = 273

 Score = 57.1 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 23/177 (12%), Positives = 52/177 (29%), Gaps = 7/177 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+   I++      R+ + + + G+  SR   + MI    V VN   +++A   +     
Sbjct: 1   MERSRILK-----IRLDQYLVQHGLIQSRERAKAMIMSGVVFVNEQKVDKAGEMIKEDAK 55

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           +EV G  +    R  L L         T                    ++  G + +   
Sbjct: 56  VEVRGHDIGYVSRGGLKLEKAMQCFPLTPKGKVCMDIGAST-GGFTDCMLQNGAVKVYAV 114

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
            +        L     + + +   +  V      +  +   +    +     +   Q
Sbjct: 115 DVGYGQLAWSLRTDERVVNMERTNIRNVTLDQLAEPIEFFSVDVSFISLHHIFPVAQ 171


>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 = 56.7 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 26/233 (11%), Positives = 66/233 (28%), Gaps = 32/233 (13%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------- 62
            +R+ +V+A+     SR  ++  I   ++ V+G +       ++  + + V         
Sbjct: 17  GKRLDQVLAQLFPDYSRSRIKTWILDDKITVDGEIFNTPREKLLGGEVVAVETTIEAPRE 76

Query: 63  ----DGVP-LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-----G 112
               D    +   +   L +      +V   +     + +   L      +         
Sbjct: 77  YEAQDIKLNIVYEDDDILVINKPMGLVVHPGAGNPDGTVLNALLHYYPEIINVPRAGIVH 136

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD------------KLNL 160
           RLD +T GL+++         L     +     R                          
Sbjct: 137 RLDKDTTGLMVVAKTIQAQTHLVKALQKRENFTREYEALCNGTMTAGGMVEKPIGRHATQ 196

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                V +          +  +  ++  + + L  G+  +I+    + N  + 
Sbjct: 197 RTHMAVHEMGKPAITHYRVAEKFRAHTRLRLRLETGRTHQIRVHMAYLNHPLI 249


>gi|311029948|ref|ZP_07708038.1| pseudouridylate synthase [Bacillus sp. m3-13]
          Length = 204

 Score = 56.7 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 2/57 (3%)

Query: 7  VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          + E+    R+ KV++      SR +V++ I + ++ VNG    +        D+I V
Sbjct: 9  IDESQKNDRIDKVLSTQNEEWSRSQVQQWIKEGQILVNGEK-TKPNYKCSVGDNITV 64


>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 = 56.7 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 31/243 (12%), Positives = 65/243 (26%), Gaps = 38/243 (15%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--- 61
            VQ + +  R+ + +A      SR  ++ +I Q  V +N          V S D +    
Sbjct: 12  TVQPDQSAMRLDRWLAEQVADLSRARIQALIDQGLVLLNNRPCR-PRDLVHSGDAVALTI 70

Query: 62  -------VDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                  ++  P+       +   + +      +V         + V   L    +    
Sbjct: 71  PAPEPLAIEARPIALDIVYEDEELIVIDKPRGLVVHPAPGHSDDTLVNALLAHCRNLSGI 130

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQW---------------------LRVYRVRF 149
            G L       L     G L       + Q                              
Sbjct: 131 NGVLRPGIVHRLDKDTTGLLVVAKTDRAHQHLQTQIQAKTARRDYLAIIAGAPAETTGTI 190

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +  ++  K  +  +G         +  + G+   V   L+ G+  +I+       
Sbjct: 191 DAPIGRHPVHRQKMAVHPKGRPART-HWRVLERLGNFTLVEFSLQTGRTHQIRVHCLHKG 249

Query: 210 WKV 212
           W +
Sbjct: 250 WPI 252


>gi|225352189|ref|ZP_03743212.1| hypothetical protein BIFPSEUDO_03805 [Bifidobacterium
          pseudocatenulatum DSM 20438]
 gi|225157436|gb|EEG70775.1| hypothetical protein BIFPSEUDO_03805 [Bifidobacterium
          pseudocatenulatum DSM 20438]
          Length = 253

 Score = 56.7 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 8  QENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           ++    R+   +   G+  SR + +R+IA  +V VNG+ + +A+  V   D I  D
Sbjct: 4  SDSTQVVRLDVALLERGLTDSRSKAQRLIADGKVSVNGVTVTKASAKVGGDDVIAAD 60


>gi|260438388|ref|ZP_05792204.1| S4 domain protein [Butyrivibrio crossotus DSM 2876]
 gi|292808974|gb|EFF68179.1| S4 domain protein [Butyrivibrio crossotus DSM 2876]
          Length = 250

 Score = 56.7 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 2/60 (3%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +++ +    R+  VIA  G   SR  +   I   +V VNG ++   A N+ + D I V G
Sbjct: 166 VIKGSVASLRLDAVIA-LGFNGSRSHITSYIIDGKVSVNGRIITSNAYNLKAGDIISVHG 224


>gi|21226172|ref|NP_632094.1| putative ribosomal RNA methyltransferase [Methanosarcina mazei
          Go1]
 gi|20904401|gb|AAM29766.1| putative ribosomal RNA methyltransferase [Methanosarcina mazei
          Go1]
          Length = 243

 Score = 56.7 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 13 PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          P R+   +   G   SR   +  I   +VKVNGI + + + +V   D IEV
Sbjct: 13 PMRLDAYLVEMGHFKSRGRAKTAILDGKVKVNGIAVTKVSRDVSIDDTIEV 63


>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 = 56.7 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 31/231 (13%), Positives = 65/231 (28%), Gaps = 35/231 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLE-----RAAVNV--MSTDHIEVDGVP 66
           R+ K +       SR +++R I    V VNG  ++     +A   V       +E+D  P
Sbjct: 17  RIDKELGHHFPQFSRSQLKRWIDDGTVTVNGQTVKAKYQLQAGDRVVIEPETPVEIDLEP 76

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI----------- 109
                 +   +   L +      +V         + V   +       I           
Sbjct: 77  ENIPLDIVYEDDDVLVVNKPQGMVVHPAPGHPNHTLVNALMYHAPLSSINGELRPGIVHR 136

Query: 110 ---------SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
                     V + D     L     +    R         ++         + +   + 
Sbjct: 137 IDKDTSGLLMVAKTDRAHRSLTAQLKEKSNLREYVALVHGVIKENEGTIDAPLARSPKDR 196

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            K+ +V+ G  +      +  +      V   L  G+  +I+   ++ N  
Sbjct: 197 KKQAVVV-GGRHAVTHFRVLKRYQHYTLVACRLETGRTHQIRVHMKYINHP 246


>gi|328950029|ref|YP_004367364.1| hemolysin A [Marinithermus hydrothermalis DSM 14884]
 gi|328450353|gb|AEB11254.1| hemolysin A [Marinithermus hydrothermalis DSM 14884]
          Length = 257

 Score = 56.7 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 17/52 (32%), Positives = 30/52 (57%), Gaps = 1/52 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            +R+  ++   G+A SR + + +I   RV+V G ++ +A+  V  TD IEV
Sbjct: 2  ERKRLDVLLVERGMAASRAKAQALIRAGRVRVAGRIVTKASAKVSLTDPIEV 53


>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 = 56.7 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 28/247 (11%), Positives = 64/247 (25%), Gaps = 47/247 (19%)

Query: 11  FTPQRVSKVI-------ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
              +R+ K +        +    +R +++  IA   + VNG   +  +  +   D I VD
Sbjct: 12  SAAERLDKYLISCESVQQQCAGLNRSKLKA-IATG-ITVNGRDAK-LSTKIRPGDSIVVD 68

Query: 64  GVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   +     +  K   +          + V   L       +
Sbjct: 69  WADNIPDHIDPEDIPLDIIYEDGNVAVVNKKQGMVTHPALGNWSGTLVNALLFHWNRESV 128

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR----------------------- 146
           +           L     G +       S +WL+                          
Sbjct: 129 AQTARRPGIVHRLDKDTSGLIITGKNRESEEWLQAQFRDRRVKKEYIAIVAGRPPHASGT 188

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
           ++     D       K     +   +   Q       GS + + + L+ G+  +I+   +
Sbjct: 189 IKTQIIRDPRNRKRFKAETGTENGKFAHTQYRCIACYGSFSLMRLQLKTGRTHQIRVHMK 248

Query: 207 FFNWKVN 213
           +    + 
Sbjct: 249 YLGCPIL 255


>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 = 56.7 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 27/246 (10%), Positives = 73/246 (29%), Gaps = 40/246 (16%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K  ++E    +R+   ++     SR +V+  ++   + VNG + ++ + ++   D +E++
Sbjct: 3   KFSIEEKDLNKRLDIFVSEKLNISRSQVKNYLSS--ILVNGNI-KKLSYSLKLNDIVEIN 59

Query: 64  GVP-----------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
                               +   +   L +       V         + V   L  I  
Sbjct: 60  IKTDDNEEEEDILAENIDLDILYEDEYLLVVNKPCNMSVHCSPSERHGTLVNALLYHIKD 119

Query: 107 RVI-----SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------ 155
                     G +    +    +   G  A ++     Q+      + +  +        
Sbjct: 120 FNFVGDKSRAGIIHRLDKDTSGIMIVGKNADIVSAIQEQFKNRTIKKIYHAIVIGVLREN 179

Query: 156 ---------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          KK  V +        + +  +   +  + V ++ G+  +I+    
Sbjct: 180 FYEINLPIGRHSVYRKKMTVREDGKKALSYIKVLNRFKKHTLIEVNIKTGRTHQIRVHCS 239

Query: 207 FFNWKV 212
           +  + V
Sbjct: 240 YKGFPV 245


>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 = 56.7 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 28/204 (13%), Positives = 61/204 (29%), Gaps = 15/204 (7%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------DGVPLRKAE 71
            IA +   S+ + + +I  + V VN   +  A+  +   D +E+               E
Sbjct: 16  FIAASLNISKNQAKDIIDSRNVLVNNKRVWIASHTLKEGDVVEILQPQQPATKELKIIYE 75

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              +   +KP  L++        S  F       +  I            +LL       
Sbjct: 76  DEYIVAVNKPPTLLSDREK---DSVEFILREKSKNPKIKAIHRLDKETSGILLLAKDYKV 132

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWV 189
                   +   V+++      ++   N L   + +           +   K  N  ++ 
Sbjct: 133 FERFKELWEDKIVFKLYLAISHNEANFNHLTVNLPVDD---KPAVSHIKLVKKGNGFSYF 189

Query: 190 TVGLREGKNREIKKVFEFFNWKVN 213
            V +  G+  +I+K        + 
Sbjct: 190 QVRIETGRKHQIRKHLSSIRHPIV 213


>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 = 56.7 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 30/235 (12%), Positives = 64/235 (27%), Gaps = 42/235 (17%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----------V 62
           QR+ K I      SR  V+R I + +V VN  ++ +    V   D ++           +
Sbjct: 18  QRIPKAI------SRSFVQRAIKEGKVTVND-VIRKPNYRVKFGDVVKISIPSNAQSISI 70

Query: 63  DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           +  P++      +   + +      +V      +  + V   L          G L    
Sbjct: 71  EPEPIQIGVIYEDEDIIVVNKPAGMIVHPIPSHNSGTLVNALLYHCKDLKGIGGELRPGI 130

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
              L     G +       +   L               L   K   +   I     +  
Sbjct: 131 VHRLDKDTSGVMVVAKNDFAHHNLSNQFKDRKVFKMYLALVSGKVEHLEGDIQISIARHP 190

Query: 179 LDTQKGSNAWV-TVGLR-------------------EGKNREIKKVFEFFNWKVN 213
           +   K + + +  + +                     G+  +I+   +  N  + 
Sbjct: 191 VLRTKMAASEIGRIAVTHYKVIKYFEHATLLMAFPKTGRTHQIRVHMKCINHPIL 245


>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 = 56.7 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 28/239 (11%), Positives = 66/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I   RV+VNG L+ +    V+  + I +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKDWILDDRVQVNGKLINKPKEKVLGGEEIAIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
           +               +   +   L +      +V   +     + +   L         
Sbjct: 70  IIEEDARWEPQNIALNIVYEDDDILVINKSRDLVVHPGAGNPDGTVLNALLYHYPEIADV 129

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--- 156
                  R+       +     +        +  L   + ++  V   R       +   
Sbjct: 130 PRAGIVHRLDKDTTGLMVIAKTVPAQTRLVESLQLREITREYEAVATGRMTAGGMVEEPI 189

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      +  + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAITHYRVMEHFRAHTRLRLRLETGRTHQIRVHMAHISHPLV 248


>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 = 56.7 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 30/248 (12%), Positives = 68/248 (27%), Gaps = 36/248 (14%)

Query: 1   MKDKNI---VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           M+ K +   VQ +   QR+ + +A      SR  ++  I    V+V+  ++      V  
Sbjct: 1   MEHKKLTAEVQPHQLGQRLDQTLAELFPEYSRSRIKTWIEAGLVQVDDKIVTVPKEKVFG 60

Query: 57  TDHIEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
           T+ I +                  +   +   L +      +V   +     + +   L 
Sbjct: 61  TEQIIMQAEIEEDTRFTPQNIPLDIVYEDEHILVINKSKDLVVHPGAGNPDNTVLNALLY 120

Query: 103 SIFSRVISV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR----------- 146
                          RLD +T GL+++         L     +                 
Sbjct: 121 HYPPIAEVPRAGIVHRLDKDTTGLMVVAKTIEAQTKLVRALQKRQITREYEAIASGIMTK 180

Query: 147 -VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                  + +         I   G         +  +  +   + + L  G+  +I+   
Sbjct: 181 GGTVDQPMARHPTKRTHMAIHPLGKPA-VTHYRIMERFRNYTRLRLRLETGRTHQIRVHM 239

Query: 206 EFFNWKVN 213
            +    + 
Sbjct: 240 AYIAHPLL 247


>gi|313159132|gb|EFR58507.1| pseudouridine synthase, RluA family [Alistipes sp. HGB5]
          Length = 362

 Score = 56.7 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 33/246 (13%), Positives = 68/246 (27%), Gaps = 41/246 (16%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---- 60
           +  +   P R+ K +  R    SR  ++       + VNG   +  +  V   D I    
Sbjct: 35  VADKGQAPLRLDKFLTVRMEKCSRNRIQAAADSGSILVNGKAAKS-SYKVKPLDRIQIVM 93

Query: 61  -----EVDGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                EV+ +P      +   +   L +      +V         + V      + +  +
Sbjct: 94  PYPRREVEIIPENIPLEIPYEDDDLLIVNKPAGLVVHPGHGNYSGTLVNALTYHLRNLPL 153

Query: 110 SV---------GRLDINTEGLLLLTNDGGLA----RVLELPSTQWLRVYRVRFHGQVD-- 154
                       R+D NT GLL++  +        +     +     V  V  + + D  
Sbjct: 154 FQEGDMRAGLVHRIDKNTSGLLVVAKNEQSHARLAKQFFDHTIGRRYVALVWGNFEEDEG 213

Query: 155 ---------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                          +          +      +  + G    V   L  G+  +I+   
Sbjct: 214 TITGNIGRSPRDRQKMFVFEDGSDGKHAVTHWRVLKRYGYVTLVECRLETGRTHQIRVHM 273

Query: 206 EFFNWK 211
            +    
Sbjct: 274 SWQGHP 279


>gi|210622497|ref|ZP_03293202.1| hypothetical protein CLOHIR_01150 [Clostridium hiranonis DSM 13275]
 gi|210154210|gb|EEA85216.1| hypothetical protein CLOHIR_01150 [Clostridium hiranonis DSM 13275]
          Length = 270

 Score = 56.7 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 21/163 (12%), Positives = 45/163 (27%), Gaps = 2/163 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  ++   G   SR   ++ I    V V+    ++A   V    +IEV G P+    R 
Sbjct: 4   RIDVLLVEQGYFESRERAKKAIMAGLVFVDNQRCDKAGTEVKEDANIEVKGNPIPYVSRG 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L         T                    ++  G + + +  +        L   
Sbjct: 64  GLKLEKAMKNFDLTLEGKICMDIGAST-GGFTDCMLQNGAIKVFSIDVGYGQLAWKLRSD 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
             +   +   +  V      +      +    +   +     +
Sbjct: 123 ERVVCMERTNIRNVTTEDLKEFPDFASIDVSFISLKLVLPVAK 165


>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 = 56.7 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 34/241 (14%), Positives = 71/241 (29%), Gaps = 39/241 (16%)

Query: 9   ENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---- 63
           +   P RV K +      ASR +V++      + VNG +  +A   V + D ++V     
Sbjct: 22  KGQEPLRVDKFLMNFVENASRNKVQQAAKDGNIFVNG-VAVKANHRVKANDEVKVMFAHP 80

Query: 64  -------GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV- 111
                    P+       +   + +      +V         + +   +       ++  
Sbjct: 81  PHEYLLVPEPIPLDIVYEDEELIIINKPAGLVVHPGHGNYQGTLINGLIYHFQHLPMNSS 140

Query: 112 ------GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY-------------RVRFHGQ 152
                  R+D +T GLL++         L                             G 
Sbjct: 141 DRPGLVHRIDKDTSGLLVVAKTEEAMNHLAKQFFNKTSEREYVALVWGNLAQDEGTIIGH 200

Query: 153 VDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           + +   N L+  +   G    +      +  + G    V+  L  G+  +I+  F +   
Sbjct: 201 IGRHPKNRLQMTVFPDGSEGKEAITHYKVLERFGYVTIVSCRLETGRTHQIRAHFTYIGH 260

Query: 211 K 211
            
Sbjct: 261 P 261


>gi|327404068|ref|YP_004344906.1| hemolysin A [Fluviicola taffensis DSM 16823]
 gi|327319576|gb|AEA44068.1| hemolysin A [Fluviicola taffensis DSM 16823]
          Length = 249

 Score = 56.7 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 18/73 (24%), Positives = 28/73 (38%), Gaps = 1/73 (1%)

Query: 14 QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          +R+ K++   G + SR   E +I    V VNGI +E+    +     I +    L    R
Sbjct: 9  ERLDKILFDRGLVTSRTRGEELIKNGDVLVNGISIEKPGKKIPVDAKILLLNEELTWVSR 68

Query: 73 TRLWLYHKPIGLV 85
            L L        
Sbjct: 69 GALKLLKAIEHFE 81


>gi|119511719|ref|ZP_01630823.1| Hemolysin A [Nodularia spumigena CCY9414]
 gi|119463628|gb|EAW44561.1| Hemolysin A [Nodularia spumigena CCY9414]
          Length = 270

 Score = 56.7 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          QR+  ++    + S R   +R+I    V VN  ++++A   V +   I+V
Sbjct: 4  QRLDTLLVDLNLCSSRALAQRLIQAGEVTVNQQVVDKAGTEVDTAAQIKV 53


>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 = 56.7 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 26/236 (11%), Positives = 66/236 (27%), Gaps = 38/236 (16%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMST-------------- 57
            +R+ +V+A+     SR  ++  I   ++ V+G +       ++                
Sbjct: 17  GKRLDQVLAQLFPDYSRSRIKTWILDDKITVDGEIFNTPRTKLLGGEVLNVETTIEAPRE 76

Query: 58  ---DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV--- 111
                I++D   +   +   L +      +V   +     + +   L      +      
Sbjct: 77  YIAQDIKLD---IVYEDDDILVINKPMGLVVHPGAGNPDGTVLNALLHYHPEIINVPRAG 133

Query: 112 --GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD------------K 157
              RLD +T GL+++         L     +     R                       
Sbjct: 134 IVHRLDKDTTGLMVVAKTIPAQTHLVTALQKRENFTREYEALCNGTMTAGGMVEKPIGRH 193

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                   V +          +  +  ++  + + L  G+  +I+    + N  + 
Sbjct: 194 ATQRTHMDVHEQGKPAITHYRVAEKFRAHTRLRLRLETGRTHQIRVHMAYLNHPLI 249


>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 = 56.7 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 31/235 (13%), Positives = 64/235 (27%), Gaps = 37/235 (15%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------D 63
           R+ K + A     SR +++ +I    V+V+G  +++    V +   +E+          +
Sbjct: 17  RLDKFLVAHFPELSRSQIQGLIRDGFVRVSGKTVQKTGFLVEAGKEVEIRIPPPQPTSLE 76

Query: 64  GVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
             P+        +  L +      +V   +  D  + V   L  I       G       
Sbjct: 77  PEPIPLEVIFENQDLLLVNKPAGMVVHPSAGHDRGTLVHAALAHIPELEGIHGEERPGVV 136

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ----------------------DK 157
             L     G +       + +WL+        Q                          K
Sbjct: 137 HRLDKDTSGLILLAKNDRAHRWLQDQFRLRKVQKTYLALVDGRPPTPTGRIEAPIGRDPK 196

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                  +  +       +        S+  + V    G+  +I+    F    V
Sbjct: 197 NRQRMAVVPPEKGREAVSEYFTREVFPSHTLLEVHPLTGRTHQIRVHLAFIGCPV 251


>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 = 56.7 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 30/248 (12%), Positives = 64/248 (25%), Gaps = 38/248 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD- 58
           K+   + E     R  K +A    G+ SR  ++ +    ++ +NG   E+    +   D 
Sbjct: 5   KEVIKITEEEKGIRADKFLALKIDGV-SRNFIQGLFDDGKILINGK-AEKGKYKLSVGDC 62

Query: 59  -----------HIEVDGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
                       +E + +P  +   +   + +      +V         + V   L    
Sbjct: 63  VEVEIPEPEELKVEAEDIPLNIVYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNALLHHCD 122

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                 G +       +     G L       + Q L         + +           
Sbjct: 123 DLSGINGVIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKK 182

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                            K  V++          +     S + V   L  G+  +I+   
Sbjct: 183 EGGTIDAPLGRHHRDRLKYAVVKDGKRAVTHYEVLKVFNSCSLVKCNLETGRTHQIRVHM 242

Query: 206 EFFNWKVN 213
            F    + 
Sbjct: 243 AFIGHPLL 250


>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 = 56.7 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 33/232 (14%), Positives = 71/232 (30%), Gaps = 34/232 (14%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV------ 65
            +R+   +A+     SR  + + +    VKV+G ++      ++  + +EV         
Sbjct: 33  GERLDAALAKLLPDYSRSRLTQWVKDGLVKVDGQVVA-PKTKMLGGEKLEVTLQLTNEEM 91

Query: 66  ---------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISV 111
                    P+   +   L +      +V   +     + +   L          R   V
Sbjct: 92  AFQPEPMDLPIVFEDEHILVINKPAGLVVHPAAGNWSGTLLNGLLHHCPALASVPRAGIV 151

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLN 159
            RLD +T GL+++         L                      +       + +D  N
Sbjct: 152 HRLDKDTSGLMVVAKTLPAQTELVRQLQARTVKRVYRAIADGVVPFDGTIDANIGRDANN 211

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            LK  ++  G       + +  +  S++ V   L  G+  +I+         
Sbjct: 212 RLKMAVLKFGGKPAITHIRVLERFASHSHVECKLETGRTHQIRVHMREAGHP 263


>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 = 56.7 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 30/253 (11%), Positives = 61/253 (24%), Gaps = 46/253 (18%)

Query: 7   VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           V      +R+   +       SR    +++    V VNG         V   D I V+  
Sbjct: 9   VSAADAGERLDSYLGAQSACPSRSACAKLVEAGSVAVNGETCLSKKQAVAEGDRICVELP 68

Query: 64  -----GVPLRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                G  + +        E   L +  K  GLV   +      T+ + L          
Sbjct: 69  EIREPGAIVPQAIPLDIRYEDDYLIVLSKQRGLVCHPAHGHEDGTLANALVHHCGIEHLG 128

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
                +  G++   +      +L     +  R  +     +    +   L  G ++    
Sbjct: 129 TVQGEDRPGIVHRLDRDTSGLMLAAKDDETQRELQNLIRTRTLDRRYITLVHGEIVMDEG 188

Query: 172 Y--------------------GDMQVTL-----------DTQKGSNAWVTVGLREGKNRE 200
                                   +  +                    V   L  G+  +
Sbjct: 189 TINTGIARSTRDRVKMAVSDDPFARQAITTFQVLERFEPARGDEGYTLVECHLYTGRTHQ 248

Query: 201 IKKVFEFFNWKVN 213
           I+      +  + 
Sbjct: 249 IRVHMRHIHHPLV 261


>gi|239831305|ref|ZP_04679634.1| hemolysin A [Ochrobactrum intermedium LMG 3301]
 gi|239823572|gb|EEQ95140.1| hemolysin A [Ochrobactrum intermedium LMG 3301]
          Length = 253

 Score = 56.7 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 13/51 (25%), Positives = 24/51 (47%), Gaps = 1/51 (1%)

Query: 15 RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          R+ +++   G  A+R      I +  VKV+G  + +    V+   +I VD 
Sbjct: 11 RLDQLLVELGLFATRSRARDAIQRGTVKVDGKPVTKPGQTVLRNANIAVDD 61


>gi|310287601|ref|YP_003938859.1| FtsJ-like methyltransferase domain [Bifidobacterium bifidum S17]
 gi|311064517|ref|YP_003971242.1| hemolysinIII-like protein [Bifidobacterium bifidum PRL2010]
 gi|309251537|gb|ADO53285.1| conserved hypothetical protein with FtsJ-like methyltransferase
          domain [Bifidobacterium bifidum S17]
 gi|310866836|gb|ADP36205.1| Hemolysin-like protein with S4 and FtsJ-like methyltransferase
          domains [Bifidobacterium bifidum PRL2010]
          Length = 252

 Score = 56.7 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          +R+  +I   G+  SR + +R+I    V V+G+ + + A NV +   I VD
Sbjct: 2  ERLDALIVGLGLVPSRSKAQRLIRDGHVLVDGVAVTKPAANVATASSITVD 52


>gi|224283243|ref|ZP_03646565.1| Putative rRNA methylase [Bifidobacterium bifidum NCIMB 41171]
          Length = 252

 Score = 56.7 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          +R+  +I   G+  SR + +R+I    V V+G+ + + A NV +   I VD
Sbjct: 2  ERLDALIVGLGLVPSRSKAQRLIRDGHVLVDGVAVTKPAANVATASSITVD 52


>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 = 56.7 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 26/253 (10%), Positives = 58/253 (22%), Gaps = 48/253 (18%)

Query: 9   ENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DG 64
                 R+   +A      SR    +++ + +V +NG  +   +  V+  D + V    G
Sbjct: 12  PEGDGIRIDAFLAAQDELPSRSACAKLVEEGKVFINGTPVSSKSEKVLLGDRLMVVLPKG 71

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
            P              +R  ++  + L  +   +          +     +       + 
Sbjct: 72  EPEAGLLVPNPDIPLDIRFEDQYLIVLSKQAGLVCHPSPGHIDDTLANALVAHCGYEHLG 131

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              G         L +   G +         + L+              L          
Sbjct: 132 LLQGEDRPGIVHRLDMDTSGLMVAAKSDEVQKALQDLIRLRVLDRRYVVLVQGYVAPDEG 191

Query: 169 GICYGDMQVTLD----------------------------TQKGSNAWVTVGLREGKNRE 200
            I  G  +   D                             +    + +   L  G+  +
Sbjct: 192 TIETGIARSIRDRLKMTVTDAPGAREAITTFRTLERFEAGRRGEGYSLLECHLYTGRTHQ 251

Query: 201 IKKVFEFFNWKVN 213
           I+         V 
Sbjct: 252 IRVHMRHVGHPVV 264


>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 = 56.7 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 38/249 (15%), Positives = 78/249 (31%), Gaps = 36/249 (14%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNG-------ILLERAA 51
           MK +N  V ++    R+   I +     SR  ++ +I    V+VN               
Sbjct: 1   MKIRNFLVNDDEENLRLDLFICKHIQDKSRSYIQNLIEDNLVEVNHRMKKSNYKTKTGDN 60

Query: 52  VNVMSTDHIEVD--GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           + V   D +E++  G  ++      +   + +      +V   S     + V   L    
Sbjct: 61  IKVSLPDAVELNIKGEDIKLDILYEDSDVIVVNKPQGMIVHPASGVYTGTLVNALLNHCR 120

Query: 106 S---------RVISVGRLDINTEGLLLLTNDGGLARVLELP-STQWLRVYRVRFHGQVDQ 155
                     R   V R+D +T G+L++  +      L        +    +     + +
Sbjct: 121 EDLSGINGIARPGIVHRIDKDTSGILVIAKNDMSHNKLSEQLKDHSMTREYIALVEGIIK 180

Query: 156 DKLNLLKKGI-----------VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
           ++   L K I           V++G         +  +      V   L  G+  +I+  
Sbjct: 181 EEKGSLDKPIGRHKKDKIKMAVVEGGKRAVTHYEVIKRFKEYTLVKCILETGRTHQIRVH 240

Query: 205 FEFFNWKVN 213
             +    V 
Sbjct: 241 MCYLGHPVV 249


>gi|116754873|ref|YP_843991.1| RNA-binding S4 domain-containing protein [Methanosaeta
          thermophila PT]
 gi|116666324|gb|ABK15351.1| RNA-binding S4 domain protein [Methanosaeta thermophila PT]
          Length = 238

 Score = 56.7 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   +      SR +   +I   +V VNG +  + +  V   D +E+
Sbjct: 3  MRLDIYLVEI-AGSRSKAVHLIKSGKVMVNGAVCRKQSYRVKPGDRVEI 50


>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 = 56.7 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 28/232 (12%), Positives = 60/232 (25%), Gaps = 31/232 (13%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP----- 66
            QR+ + +A      SR  ++  I  + V VNG ++      V   + IE+         
Sbjct: 16  GQRLDQTLAELFPDYSRSRLKTWIEDELVLVNGEVVILPRAKVYGGEQIEITVEIEEDSR 75

Query: 67  ---------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-----G 112
                    +   +   L +      +V   +     + +   L                
Sbjct: 76  FMPENLPLNIVYEDDDILVINKPKDFVVHPGAGNPTGTVLNALLYHYPQIAEVPRAGIVH 135

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-----------FHGQVDQDKLNLL 161
           RLD +T GL+++         L     +                      Q         
Sbjct: 136 RLDKDTTGLMVIAKTIPAQTKLVRDLQKRKITREYEAIASGIMTKGGMVDQPMARHPTKR 195

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +  V            +  +  +   + + L  G+  +I+         + 
Sbjct: 196 TQMAVHPMGKPAITHYRIMERFRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 247


>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 = 56.3 bits (134), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 33/256 (12%), Positives = 77/256 (30%), Gaps = 53/256 (20%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAV 52
           M+ K  + +NF   R+ K I       R+        E+ ++I + R+KVNG  +++   
Sbjct: 1   MEHK--IDKNFHDTRLDKYI-------RKKYEGINLTEIFKLIRKGRIKVNGKKVKQ-NY 50

Query: 53  NVMSTDHIEV---DGVP-------------------LRKAERTRLWLYHKPIGLVTTHSD 90
            +   D ++V    G                     +   +   L     P  ++   S 
Sbjct: 51  RLQDGDIVKVFYMGGETAVKKFIDLSPKETEYIKKGIVYEDEDVLLFNKSPNMVMHKGSG 110

Query: 91  PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR-----VLELPSTQWLRVY 145
            D   +              + R+D  T GL++   +  + R     + +    +   + 
Sbjct: 111 HDYGLSEMLKSYYQREDFTFINRIDKATSGLIIGAKNLPMTRKLSEDMRDGNINKRYYIL 170

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------VTLDTQKGSNAWVTVGLREGK 197
                 + +    + LKK            +          +  +  +   +   L  G+
Sbjct: 171 VEGRVDREEFQIKSYLKKTDTHVVELEKYEKGAKESISYFKVVQRGKNRTILEGTLGTGR 230

Query: 198 NREIKKVFEFFNWKVN 213
             +++         + 
Sbjct: 231 THQLRVHLANLGHPIV 246


>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 = 56.3 bits (134), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 40/247 (16%), Positives = 81/247 (32%), Gaps = 40/247 (16%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           I +E     R+   ++      SR + + +I    V VN   ++ A+ ++ S D ++VD 
Sbjct: 17  IPKEKDEGLRLDLYLSEQIEDLSRSKAKMLINNNSVMVNDNWVK-ASYSITSGDVVKVDT 75

Query: 65  VPLR--------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--- 107
             ++                E   L + +KP  +V      + R T+ + L         
Sbjct: 76  QLIQSEITLIPQSIPLDIVYEDEYLLVVNKPRNMVVHPGAGNYRDTMVNALLYHCQNLSD 135

Query: 108 ------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR-------------VYRVR 148
                    V RLD +T GLL++        +L                        +  
Sbjct: 136 GTSYERPGIVHRLDKDTSGLLVVAKQNETHDILSEEIKNRRVARTYLALVIGDFSKKKAT 195

Query: 149 FHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFE 206
               + +D  N  K  +V  G      +++    Q     +++   L  G+  +I+    
Sbjct: 196 IDLPIGRDPRNRKKMAVVHGGKRAITKVEMLRSFQNPEKISYLKCSLETGRTHQIRVHLS 255

Query: 207 FFNWKVN 213
              + + 
Sbjct: 256 HLGYPLL 262


>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 = 56.3 bits (134), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 36/246 (14%), Positives = 73/246 (29%), Gaps = 39/246 (15%)

Query: 4   KNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K +      P RV K +      A+R ++++      V VN I ++     V   D + +
Sbjct: 19  KFVASAGQEPLRVDKFLMNFIENATRSKLQQAAKAGNVLVNEISVKS-NHKVKPNDVVRI 77

Query: 63  -------------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                        + +PL     + T + +      +V         + V   +  I + 
Sbjct: 78  VLAYPPAESLLVAEDIPLDIIYEDDTVIVVNKPAGMVVHPGHGNYSGTLVNGLIHHIENL 137

Query: 108 VISV-------GRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVYRV 147
             +         R+D +T GLL++         L                    +     
Sbjct: 138 PTNSNERPGLVHRIDKDTSGLLVVAKTEFAMANLSRQFFERTTERLYYALVWGNVAEDEG 197

Query: 148 RFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
           R  G + +   N L+  +   G    +      +  +      V   L  G+  +I+  F
Sbjct: 198 RIEGNIGRSLKNRLQMAVFPDGDFGKHAVSHYKVLERLTYVTLVECKLETGRTHQIRAHF 257

Query: 206 EFFNWK 211
           +     
Sbjct: 258 KHIGHT 263


>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 = 56.3 bits (134), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 33/239 (13%), Positives = 73/239 (30%), Gaps = 31/239 (12%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K I+       R+ +V+A+     SR +++  I    VKV+GI   +A   V     IE+
Sbjct: 9   KKIIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEI 68

Query: 63  DGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           +                 +   + T L +      +V   +    ++ +   L    S  
Sbjct: 69  EAQLEPNERWVPQPIPLDVIYEDETLLVINKPVGLIVHPGAGVRDQTLINALLHYDPSLS 128

Query: 109 ISVGRLDIN----TEGLLLLTNDGGLARVLELPSTQWLRVYRV------------RFHGQ 152
           +      I+        LLL      +    + + +  ++ R             R    
Sbjct: 129 VVPRAGIIHRLDKDTSGLLLIARTLASHHALIKTMKARQIVREYEAIVKGVLISGRTIEA 188

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                     +  V++          +  +  ++  + V L  G+  +I+      +  
Sbjct: 189 PVGRHPIHRTRMAVVEFGRPAITHFRIIKRYRAHTHIRVQLETGRTHQIRVHMAHIHHP 247


>gi|229825482|ref|ZP_04451551.1| hypothetical protein GCWU000182_00842 [Abiotrophia defectiva ATCC
          49176]
 gi|229790045|gb|EEP26159.1| hypothetical protein GCWU000182_00842 [Abiotrophia defectiva ATCC
          49176]
          Length = 275

 Score = 56.3 bits (134), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          +R+  ++   G   SR + + +I    V VNG   ++A         IEV G  L+ 
Sbjct: 3  ERLDVLLTERGFFVSREKAKAVIMAGEVFVNGQREDKAGSKFDREAEIEVKGKVLKY 59


>gi|298492205|ref|YP_003722382.1| hemolysin A ['Nostoc azollae' 0708]
 gi|298234123|gb|ADI65259.1| hemolysin A ['Nostoc azollae' 0708]
          Length = 270

 Score = 56.3 bits (134), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 16/54 (29%), Positives = 31/54 (57%), Gaps = 1/54 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
          QR+  ++   G++ SR++ +R+I    V+VN  ++++A   V  T  I+V   P
Sbjct: 4  QRLDTLLVDLGLSPSRQQAQRLIQAGEVRVNQQVIDKAGTEVDITAQIQVKQRP 57


>gi|313140389|ref|ZP_07802582.1| conserved hypothetical protein [Bifidobacterium bifidum NCIMB
          41171]
 gi|313132899|gb|EFR50516.1| conserved hypothetical protein [Bifidobacterium bifidum NCIMB
          41171]
          Length = 264

 Score = 56.3 bits (134), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          +R+  +I   G+  SR + +R+I    V V+G+ + + A NV +   I VD
Sbjct: 14 ERLDALIVGLGLVPSRSKAQRLIRDGHVLVDGVAVTKPAANVATASSITVD 64


>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 = 56.3 bits (134), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 31/231 (13%), Positives = 65/231 (28%), Gaps = 35/231 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLE-----RAAVNV--MSTDHIEVDGVP 66
           R+ K +       SR +++R I    V VNG  ++     +A   V       +E+D  P
Sbjct: 17  RIDKELGHHFPQFSRSQLKRWIDDGTVTVNGQTVKAKYQLQAGDRVVIEPETPVEIDLEP 76

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI----------- 109
                 +   +   L +      +V         + V   +       I           
Sbjct: 77  ENIPLDIVYEDDDVLVVNKPQGMVVHPAPGHPNHTLVNALMYHAPLSSINGELRPGIVHR 136

Query: 110 ---------SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
                     V + D     L     +    R         ++         + +   + 
Sbjct: 137 IDKDTSGLLMVAKTDRAHRSLTAQLKEKSNLREYVALVHGVIKENEGTIDAPLARSPKDR 196

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            K+ +V+ G  +      +  +      V   L  G+  +I+   ++ N  
Sbjct: 197 KKQAVVV-GGRHAITHFRVLKRYQHYTLVACRLETGRTHQIRVHMKYINHP 246


>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 = 56.3 bits (134), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 33/239 (13%), Positives = 73/239 (30%), Gaps = 31/239 (12%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K I+       R+ +V+A+     SR +++  I    VKV+GI   +A   V     IE+
Sbjct: 13  KKIIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEI 72

Query: 63  DGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           +                 +   + T L +      +V   +    ++ +   L    S  
Sbjct: 73  EAQLEPNERWVPQPIPLDVIYEDETLLVINKPVGLIVHPGAGVRDQTLINALLHYDPSLS 132

Query: 109 ISVGRLDIN----TEGLLLLTNDGGLARVLELPSTQWLRVYRV------------RFHGQ 152
           +      I+        LLL      +    + + +  ++ R             R    
Sbjct: 133 VVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEAIVKGVLISGRTIEA 192

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                     +  V++          +  +  ++  + V L  G+  +I+      +  
Sbjct: 193 PVGRHPIHRTRMAVVEFGRPAITHFRIIKRYRAHTHIRVQLETGRTHQIRVHMAHIHHP 251


>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 = 56.3 bits (134), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 34/245 (13%), Positives = 70/245 (28%), Gaps = 38/245 (15%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V    +  R+ K +++     SR ++++ I    V++N +++  + + V   D I     
Sbjct: 6   VPTELSGLRLDKALSQLLENVSRNQIQKAIKSSCVQINNVIILDSDILVKENDIILFSFK 65

Query: 63  ----------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----- 107
                     D       E   L + +K  G+           T+ + L           
Sbjct: 66  EPEELTIEAADIKLDIVYEDEDLIVINKAAGMTVHPGAGHHDDTLVNALLHHTRNLSDIG 125

Query: 108 -VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
                G +    +    L       +   L + Q  +   VR +  +    +N L+  I 
Sbjct: 126 SSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVVRKYKALVWGVINPLEGTIK 185

Query: 167 IQGICYGDMQVTL------------------DTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                    +  +                      GS + V   L  G+  +I+      
Sbjct: 186 NNIGRSRSDRQKMTILKYGGKEAVTYYKTLELFYGGSISMVECKLATGRTHQIRVQLSHL 245

Query: 209 NWKVN 213
              V 
Sbjct: 246 KHSVV 250


>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 = 56.3 bits (134), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 34/254 (13%), Positives = 75/254 (29%), Gaps = 46/254 (18%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +V  +   QR+ +V+A R    SR  ++ +I   RV + G  +   A +    + I +D 
Sbjct: 85  VVAGDEGSQRLDRVLAARCPELSRSRLKALILDGRVAIAGTPVRDPAYHASPGETITIDV 144

Query: 64  ---------GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                    G  +       +   + L      +V   +  +  + V   +    + +  
Sbjct: 145 PPPVPAEPAGEAIALDIVYEDADIIVLNKPRGLVVHPAAGHETGTLVNALIAHCGASLSG 204

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
           +G +        L  +  GL    +          +   HG+  + +   L     + G 
Sbjct: 205 IGGVRRPGIVHRLDKDTTGLMVAAKNDKAHQSLSAQFADHGRTGELRRGYLAFVWGVPGR 264

Query: 171 CYGDMQVTLDT--------------QKGSNAW-----------------VTVGLREGKNR 199
            YG +   +D               ++    W                 +   L  G+  
Sbjct: 265 KYGTIDAPIDRHPHAREKMAVRQSGREAITHWEVLENFSGKDGKPVAALIACQLETGRTH 324

Query: 200 EIKKVFEFFNWKVN 213
           +I+         + 
Sbjct: 325 QIRVHLAHLGHPLL 338


>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 = 56.3 bits (134), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 38/246 (15%), Positives = 76/246 (30%), Gaps = 40/246 (16%)

Query: 7   VQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           + +    QR+ K ++ AG+   SR  V+ ++ Q  V+ +G  +   +  V      E+  
Sbjct: 46  IPDTAAGQRLDKALS-AGLPDLSRSRVQALLEQGCVRGDGRTITDPSQRVKYGQIFELRM 104

Query: 63  ----------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                       +PL     +   L +      +V   +     + V   L         
Sbjct: 105 PGSAAAEPLPQDIPLDVVYEDADVLVVDKPAGLVVHPAAGNPDGTLVNALLAHCGDSLSG 164

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVYRVR 148
                R   V RLD +T GL+++  +      L                        + R
Sbjct: 165 IGGVRRPGIVHRLDKDTSGLMVVAKNDRAHHGLSDQFSDRTLSRTYLALVWGVPNPTQGR 224

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-SNAWVTVGLREGKNREIKKVFEF 207
             G + +   +  K  +V  G      +  +    G + + V   L  G+  +I+     
Sbjct: 225 IEGNIGRSSADRKKMAVVTGGGKPAGTKYRVVKSFGMAASLVECVLETGRTHQIRVHLTH 284

Query: 208 FNWKVN 213
               + 
Sbjct: 285 IGHPLV 290


>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 = 56.3 bits (134), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 29/241 (12%), Positives = 73/241 (30%), Gaps = 39/241 (16%)

Query: 9   ENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP- 66
           +   P RV K +      A+R ++++      ++VNG ++++    V + D + V     
Sbjct: 26  KGQEPLRVDKFLMNFIEKATRNKIQQAAKNGNIQVNGAVVKQ-NHKVKANDVVRVLFEHP 84

Query: 67  --------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV- 111
                         +   + T L +      +V         + +   +    +   +  
Sbjct: 85  PYEFLLTPEDIPLDIVFEDDTLLVVNKPAGMVVHPGHGNYSGTLINALIYHFDNLPENSS 144

Query: 112 ------GRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVYRVRFHGQ 152
                  R+D +T GLL++         L                    +   +    G 
Sbjct: 145 GRPGLVHRIDKDTSGLLVVAKTEEAMTHLAKQFFDKTSEREYIAIVWGNVEEDQGTVEGH 204

Query: 153 VDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           + +   N ++  +   G    +      +  + G    ++  L  G+  +I+   +    
Sbjct: 205 IGRHPKNRMQNTVYEDGDQGKEAVTHYKVLERLGYVTKISCKLETGRTHQIRVHMKHIGH 264

Query: 211 K 211
            
Sbjct: 265 T 265


>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 = 56.3 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 26/233 (11%), Positives = 65/233 (27%), Gaps = 32/233 (13%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------- 62
            +R+ +V+A+     SR  ++  I   ++ V+G +       ++  + + V         
Sbjct: 17  GKRLDQVLAQLFPDYSRSRIKTWILDDKITVDGEIFNTPREKLLGGEVVSVETTIEAPRE 76

Query: 63  ----DGVP-LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-----G 112
               D    +   +   L +      +V   +     + +   L      +         
Sbjct: 77  YEAQDIKLNIVYEDDDILVINKPMGLVVHPGAGNPNGTVLNALLHYYPEIINVPRAGIVH 136

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD------------KLNL 160
           RLD +T GL+++         L     +     R                          
Sbjct: 137 RLDKDTTGLMVVAKTIPAQTHLVTALQKRENFTREYEALCNGTMTAGGMVEKAIGRHPTQ 196

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                V +          +  +  ++  + + L  G+  +I+      N  + 
Sbjct: 197 RTHMAVHELGKPAITHYRVAEKFRAHTRLRLRLETGRTHQIRVHMAHLNHPLI 249


>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 = 56.3 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 39/247 (15%), Positives = 74/247 (29%), Gaps = 42/247 (17%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +   P R+ K ++     +SR  ++R      V VN   ++     V   D I +  
Sbjct: 26  VVDKGQEPLRIDKYMSEKLQHSSRNRIQRAADAGFVHVNDRPVKS-NYKVRPLDVITLML 84

Query: 63  -----------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                      + +PL    E + L + +KP GLV      +   T+ + +      + S
Sbjct: 85  DRPRHDSTIEAEDIPLDIVFEDSELMVINKPAGLVVHPGVGNFHGTLVNAIAWHLKDLKS 144

Query: 111 VGRLDI----------NTEGLLLLTNDGG-------------LARVLELPSTQWLRVYRV 147
               D           +T GLL++                    R               
Sbjct: 145 FDPNDPEVGLVHRIDKDTSGLLVIAKTPMAKTKLGLQFFNKTTHRSYNALVWGNFTEDEG 204

Query: 148 RFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
           R  G + +D  + L+  +                +  + G    V   L  G+  +I+  
Sbjct: 205 RIEGNIARDPKDRLRMTVFAPDSEIGKSAVTHYRVIERFGYVTLVECILETGRTHQIRAH 264

Query: 205 FEFFNWK 211
            +     
Sbjct: 265 MKHIGHP 271


>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 = 56.3 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 38/245 (15%), Positives = 71/245 (28%), Gaps = 39/245 (15%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + E    +R+ K +A+     SR  +++ I    V++ G ++      +   D IEV   
Sbjct: 55  IPETMHGERLDKALAKLLPDYSRSRLQQWIDAGAVRLRGEVVR-PRAAISGGDRIEVVPQ 113

Query: 66  P---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   + T L +      +V   +     + +   L         
Sbjct: 114 RAADENAFVAEPIDLDVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRYPDAVEL 173

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPST--------------QWLRVYRVRFHG 151
            R   V RLD +T GL+++         L                   +      +    
Sbjct: 174 PRAGIVHRLDKDTSGLMVVARTLPAQTDLVRQLQARTVKRTYLALVWGETPEEATIDAPI 233

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG---LREGKNREIKKVFEFF 208
             D      +       G        TLD      A V++    L  G+  +I+  FE  
Sbjct: 234 GRDPRDRTRMAIIETASGKPARTHFKTLDVVDLGRAQVSLVRCQLETGRTHQIRVHFESE 293

Query: 209 NWKVN 213
              + 
Sbjct: 294 GHPLL 298


>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 = 56.3 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 26/250 (10%), Positives = 67/250 (26%), Gaps = 38/250 (15%)

Query: 1   MKDKNIVQENFT-PQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M +  I+ E     +R+   +++     SR  ++ +I + +  + G  ++ A   +   D
Sbjct: 1   MDNFEIIAEESDINKRIDVFLSKNLESFSRSYIQDLIKKGKATIGGKTIK-ANYRLREGD 59

Query: 59  HIEV---DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            + +      PL              +   + +      +V   +     + V   L   
Sbjct: 60  IVALAIPKPEPLEILPENIPLDIVYEDNDVILVNKPKGMVVHPAAGHYSGTLVNALLYHC 119

Query: 105 FSR-VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------- 155
                   G L       + +   G +       + Q +                     
Sbjct: 120 KDNLSGINGVLRPGIVHRIDMDTTGIIIVCKNDNAHQHIAKQLAEHSITRKYVAIVSGNI 179

Query: 156 ------------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                          N  KK  V +          +  +  +  ++   L  G+  +I+ 
Sbjct: 180 KEDEGVVDAAIARSKNDRKKMTVDKDGKRAVTHFKVLERLNNYTYIECVLETGRTHQIRV 239

Query: 204 VFEFFNWKVN 213
              + +  + 
Sbjct: 240 HMSYLHHPLL 249


>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 = 56.3 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 35/280 (12%), Positives = 76/280 (27%), Gaps = 50/280 (17%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLE---------RAAVNVMS 56
           ++      R+ + +A+A    SR  V+ +IA  +V VN   +            +V V  
Sbjct: 1   MEAQAAGHRLDRFVAQALPDLSRSFVQHLIAAGQVLVNAQAVRPSHALRHGDLVSVTVPP 60

Query: 57  TDHIEVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
              + +    +       +   + +      +V         + V   L       +   
Sbjct: 61  AQPVALVPEAIPLHVVYEDADVVVVEKPAGMVVHPAPGHPNGTLVNALLARYPDMQVGGD 120

Query: 113 RLDINTEGLLLLTN--------------------DGGLARVLELPSTQWLRVYRVRFHGQ 152
                   L   T+                       + ++    +    +         
Sbjct: 121 LRPGIVHRLDAGTSGLLVVARHDQALRHLTALQHARQMRKIYLAVAEGRFKQAEGLIDAP 180

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           V +   + L+  +   G         +  + G+   + + L  G+  +I+   +     +
Sbjct: 181 VGRHPHDRLRMAVTPTGREART-HYRVCEELGNYTLLELRLETGRTHQIRVHLQHLGRPI 239

Query: 213 N--------------RLIRISYGPFQLG-TLLAGSTREVS 237
                           L R       LG  LL GS RE +
Sbjct: 240 LGDPLYGVRKGRPTFGLERQFLHAHCLGFQLLDGSWREFT 279


>gi|295101862|emb|CBK99407.1| Uncharacterized conserved protein [Faecalibacterium prausnitzii
          L2-6]
          Length = 71

 Score = 56.3 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 12/61 (19%), Positives = 26/61 (42%), Gaps = 1/61 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          +    ++  ++  AG+  +  E + ++    VKVNG +           D +E+DG  + 
Sbjct: 7  HTEFIKLDALLKYAGLCETGGEAKELVQGGAVKVNGEVCTMRGKKCRPGDTVELDGQTIE 66

Query: 69 K 69
           
Sbjct: 67 I 67


>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 = 56.3 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 37/247 (14%), Positives = 75/247 (30%), Gaps = 37/247 (14%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           + ++      +R+ K++AR     SR  ++R I Q  V V+G   +     V   + + +
Sbjct: 30  RFVLSLKEGGERLDKIVARHLPDYSRSRIQRWIEQGYVTVDGKAAQGKQTVVGDEEIVVL 89

Query: 63  ------D--------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--- 105
                 D        G P+   +R  L +      +V   +     + +   L  +    
Sbjct: 90  PQLAEEDLAFVPEPVGFPVLFEDRDILVVNKPAGLVVHPAAGNWSGTLLNGLLHHLPKSA 149

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVLELP------STQWLRVYRVRFHGQVDQDK 157
              R   V RLD +T GL+++         L           ++L +           D+
Sbjct: 150 AIPRAGIVHRLDKDTSGLMVVAKTLEAQTHLVRQLQARTVRREYLALVWGETPVAGTVDQ 209

Query: 158 LNLLKKGIVIQGICYGDMQVTL-----------DTQKGSNAWVTVGLREGKNREIKKVFE 206
                    I+                             + V   L  G+  +I+   +
Sbjct: 210 PIGRHPKDRIKMAVLQTASGKPAVTHYRLLETGVCNGSKVSLVKCRLETGRTHQIRVHMQ 269

Query: 207 FFNWKVN 213
           F  + + 
Sbjct: 270 FSGFPLV 276


>gi|254458907|ref|ZP_05072330.1| ribosomal RNA large subunit methyltransferase J
          [Campylobacterales bacterium GD 1]
 gi|207084178|gb|EDZ61467.1| ribosomal RNA large subunit methyltransferase J
          [Campylobacterales bacterium GD 1]
          Length = 235

 Score = 56.3 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 10/50 (20%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   +    ++ SR + + +I    V VNG ++ ++++ +  +D + V
Sbjct: 1  MRLDNYLVENSLSESRTKAQGIIKDGLVSVNGNIITKSSLKIDESDEVNV 50


>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 = 56.3 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 31/269 (11%), Positives = 66/269 (24%), Gaps = 42/269 (15%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +  +  RV K +    + +SR  +++      +  NG  ++  +  V   D + V  
Sbjct: 33  VVDKGQSQVRVDKYLFERLVNSSRNRIQKAADAGLIMANGKPVKS-SYKVKPCDVLTVMM 91

Query: 63  -----DGVPLR-------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                D   +          E   L + +KP GLV      +   T+ + +         
Sbjct: 92  DRPRYDNAIIPEDIPLDIVYEDNDLMVINKPAGLVVHPGCGNYHGTLVNAIAWHLKDNPR 151

Query: 111 VGRLDIN-------------------------TEGLLLLTNDGGLARVLELPSTQWLRVY 145
               D                             GL              +         
Sbjct: 152 YDPNDPQVGLVHRIDKDTSGLLVVAKTPDAKTHLGLQFYNKTTKRKYNALVWGIVENNEG 211

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
            +  +   +      +          +      +  + G    V   L  G+  +I+   
Sbjct: 212 TIEGNIGRNPKDRMQMAVLSDPAQGKHAVTHYRVLERLGYVTLVECVLETGRTHQIRVHM 271

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +     +    R   G   L        +
Sbjct: 272 KHIGHTLFNDERYG-GNEILKGTHFSKYK 299


>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 = 56.3 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 31/231 (13%), Positives = 65/231 (28%), Gaps = 35/231 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLE-----RAAVNV--MSTDHIEVDGVP 66
           R+ K +       SR +++R I    V VNG  ++     +A   V       +E+D  P
Sbjct: 4   RIDKELGHHFPQFSRSQLKRWIDDGTVTVNGQTVKAKYQLQAGDRVVIKPETPVEIDLEP 63

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI----------- 109
                 +   +   L +      +V         + V   +       I           
Sbjct: 64  ENIPLDIVYEDDDVLVVNKPQGMVVHPAPGHPNHTLVNALMYYAPLSSINGELRPGIVHR 123

Query: 110 ---------SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
                     V + D     L     +    R         ++         + +   + 
Sbjct: 124 IDKDTSGLLMVAKTDRAHRSLTAQLKEKSNLREYVALVHGVIKENEGTIDAPLARSPKDR 183

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            K+ +V+ G  +      +  +      V   L  G+  +I+   ++ N  
Sbjct: 184 KKQAVVV-GGRHAVTHFRVLKRYQHYTLVACRLETGRTHQIRVHMKYINHP 233


>gi|220907439|ref|YP_002482750.1| hemolysin A [Cyanothece sp. PCC 7425]
 gi|219864050|gb|ACL44389.1| hemolysin A [Cyanothece sp. PCC 7425]
          Length = 267

 Score = 56.3 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          QR+  ++    +  SR++ +R+I    V+VN  ++++    V     I+V
Sbjct: 4  QRLDTLLVDRQLCDSRQQAQRLIRAGEVRVNQQVIDKPGTEVDVQAQIQV 53


>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 = 56.3 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 34/249 (13%), Positives = 78/249 (31%), Gaps = 42/249 (16%)

Query: 4   KNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           + +  +   P RV K +      A+R ++++   +  + VN ++++     V + D + V
Sbjct: 22  RFVADKGQQPLRVDKYLMNRVENATRSKIQKAAKEGNIFVNNVIVKS-NYKVKANDVVTV 80

Query: 63  --------------D-GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-- 105
                         D  + +   +   L +  +P  +V         + +   +  I   
Sbjct: 81  LFAHPPYELLLTPEDIDIDIVYEDDDLLVVNKQPGMVVHPGHGNYSGTLINALIHHIDNL 140

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVYRV 147
                +R   V R+D +T GLL++         L                    +     
Sbjct: 141 PNNSSNRPGLVHRIDKDTSGLLVVAKTEEAMTHLAKQFFDKTTEREYVALVWGNIEDDEG 200

Query: 148 RFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              G + +   N L+  + +                +  + G    V+  L  G+  +I+
Sbjct: 201 TIEGHIGRHPKNRLQNTVFLDEDAEEKGKAAVTHFKVLERFGYVTLVSCKLETGRTHQIR 260

Query: 203 KVFEFFNWK 211
              +F    
Sbjct: 261 VHMKFIGHT 269


>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 = 56.3 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 30/244 (12%), Positives = 67/244 (27%), Gaps = 37/244 (15%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           I ++    +R+   +  R    SR  ++R+IA   V VNG    +A   +   D++ +  
Sbjct: 12  IAEDVDKGKRLDLFLVERLPELSRTHIQRIIAAGEVTVNGK-AGKANYKLAPADYVTIRL 70

Query: 63  -DGVP-----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
            +  P           +   +   + +      +V   +     + V   L         
Sbjct: 71  PEPKPAEIKAEAISLDILYEDEDIIVINKPRGMVVHPAAGNYEGTLVNALLRHCDRLSGI 130

Query: 111 VG---------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
            G                     + D     L     +    R         ++  +   
Sbjct: 131 NGVSRPGIVHRLDKDTSGVMMVAKTDRAHLDLARQIKERTAGRKYVAIVHGNIKENQGII 190

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
           +  + +   +  K  +V            +  + G    V   L  G+  +I+    +  
Sbjct: 191 NAPIGRHPTDRKKMAVVFTNSKEAITTFQVLERFGDYTLVECRLFTGRTHQIRVHMAYIG 250

Query: 210 WKVN 213
             V 
Sbjct: 251 HPVV 254


>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 = 56.3 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 28/228 (12%), Positives = 68/228 (29%), Gaps = 32/228 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMST----------DHIEVD 63
           R+ + +A      SR  ++  I    VK++G ++ R    V +           D +   
Sbjct: 19  RLDQAVASLFPDYSRTRIKEWILADMVKIDGEVINRPREKVYTGQTVGVQAVLEDEVVFK 78

Query: 64  GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-----GRL 114
              ++      +   L +      +V   +     + +   L      +         RL
Sbjct: 79  AQKIKLEIVYEDDDILVINKPAGLVVHPGAGNPDGTVLNALLHHFPQIIEVPRAGIVHRL 138

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYR------------VRFHGQVDQDKLNLLK 162
           D +T GL+++         L                              + +DK++ +K
Sbjct: 139 DKDTTGLMVVAKTVPAQTHLVTSLQAREITREYEAIAMGGFTAGGFVEAPIGRDKVHRVK 198

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             +   G  +      +  +  ++  + + L  G+  +I+        
Sbjct: 199 MAVNSTGGKHALTHYRVSEKYRAHTRLRLRLETGRTHQIRVHMMHIGH 246


>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 = 56.3 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 28/234 (11%), Positives = 77/234 (32%), Gaps = 31/234 (13%)

Query: 11  FTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGV- 65
           F+ +R+ +++++  +  SR  +++ I    V +NG +  +    ++  + I +   D   
Sbjct: 15  FSGKRLDQILSKLFMQYSRSCLKKWIIMNNVYINGKIENQPDKKILGGEKITIYSTDEKL 74

Query: 66  PLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-----FSRVIS 110
           P+             +   L +   P  +V   +     + +   L          R   
Sbjct: 75  PINLPQNIALNTIYEDSNILIINKPPGLVVHPGAGNQDGTILNALLYRYTNISSIPRCGI 134

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------DKLNLL 161
           + RLD +T GL+++         L     +   + + +   + +             +  
Sbjct: 135 IHRLDKDTSGLMVIAKTIFSYNKLVTLLKKRKIIRKYQGIIKGNMISGGIVNYPIMRHPF 194

Query: 162 KKGIVIQGICYGD--MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           K+  +              +  +   +  V+  L  G+  +I+       + + 
Sbjct: 195 KRICMTTDSLGKKSITHYKIINRFKFHTHVSFRLETGRTHQIRVHMLHIGYPLL 248


>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 = 56.3 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 35/245 (14%), Positives = 66/245 (26%), Gaps = 41/245 (16%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +     RV K +    + ASR  +++      V  NG  ++  +  V   D I V  
Sbjct: 33  VVDKGQAMVRVDKYLFERIVNASRNRIQKAAEGGFVMANGKPVKS-SYKVKPLDVITVMM 91

Query: 63  -----DGVPLR-------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                +   +          E   L + +KP GLV      +   T+ + L         
Sbjct: 92  DRPRYENEIIPEDIPLTIVYEDPYLMVVNKPAGLVVHPGHGNYHGTLVNALAWHMKDNPD 151

Query: 111 VGRLDIN----------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK--- 157
               D +          T GLL++         L           + R       ++   
Sbjct: 152 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGNQFFNKTTKRKYRALVWGIVEQDEG 211

Query: 158 ------------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                          +          +      +  + G    V   L  G+  +I+   
Sbjct: 212 TIIGNIARNPKDRMQMAVMSDPTVGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHM 271

Query: 206 EFFNW 210
           +    
Sbjct: 272 KHIGH 276


>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 = 56.3 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 38/245 (15%), Positives = 72/245 (29%), Gaps = 39/245 (15%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + E    +R+ K +A+     SR  +++ I    V+++G ++      +   D IEV   
Sbjct: 55  IPEAMHGERLDKALAKLLPDYSRSRLQQWIDAGAVRLHGEVVR-PRAAISGGDRIEVVPQ 113

Query: 66  P---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   + T L +      +V   +     + +   L         
Sbjct: 114 RAADENAFVAEPIDLDVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRYPDAVEL 173

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPST--------------QWLRVYRVRFHG 151
            R   V RLD +T GL+++         L                   +      +    
Sbjct: 174 PRAGIVHRLDKDTSGLMVVARTLPAQTDLVRQLQARTVKRTYLALVWGETPEEATIDAPI 233

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG---LREGKNREIKKVFEFF 208
             D      +       G        TLD      A V++    L  G+  +I+  FE  
Sbjct: 234 GRDPRDRTRMAIIETASGKPARTHFKTLDVVDLGRAQVSLVRCQLETGRTHQIRVHFESE 293

Query: 209 NWKVN 213
              + 
Sbjct: 294 GHPLL 298


>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 = 56.3 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 29/244 (11%), Positives = 63/244 (25%), Gaps = 39/244 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-------- 58
           V +    +RV   +AR    SR     +IA   V V+G  + + +  V +          
Sbjct: 13  VPDGLEGERVDAAMARLFGLSRTRAAELIADGLVTVDGSAVAK-SDRVSAGSMLDATIPS 71

Query: 59  -----HIE---VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                 I+   V+G+ +   +   + +       V       G++ V     + F    S
Sbjct: 72  QADPLEIKPEIVEGIKIIYDDDAFVVIDKPVGVAVHPSPGWQGQTVVGHLAAAGFRISTS 131

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
             +        L +   G +       +   L+    +         L        ++G 
Sbjct: 132 GAKEREGIVQRLDVGTSGVMVIAKSEHAYSVLKNAFRQRTVDKTYHALVQ-GHPDPLEGT 190

Query: 171 CYGDM---------------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
               +                                + + + L  G+  +I+       
Sbjct: 191 IDAPIGRNPKYDYKFAVRADGRHSVTHYETLEAHRFASLLKIHLETGRTHQIRVHMSALK 250

Query: 210 WKVN 213
               
Sbjct: 251 HPCV 254


>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 = 56.3 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 33/239 (13%), Positives = 73/239 (30%), Gaps = 31/239 (12%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K I+       R+ +V+A+     SR +++  I    VKV+GI   +A   V     IE+
Sbjct: 13  KKIIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEI 72

Query: 63  DGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           +                 +   + T L +      +V   +    ++ +   L    S  
Sbjct: 73  EAQLEPNERWVPQPIPLDVIYEDETLLVINKPVGLIVHPGAGVRDQTLINALLHYDPSLS 132

Query: 109 ISVGRLDIN----TEGLLLLTNDGGLARVLELPSTQWLRVYRV------------RFHGQ 152
           +      I+        LLL      +    + + +  ++ R             R    
Sbjct: 133 VVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEAIVKGVLISGRTIEA 192

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                     +  V++          +  +  ++  + V L  G+  +I+      +  
Sbjct: 193 PVGRHPIHRTRMAVVEFGRPAITHFRIIKRYRAHTHIRVQLETGRTHQIRVHMAHIHHP 251


>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 = 56.3 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 33/251 (13%), Positives = 75/251 (29%), Gaps = 43/251 (17%)

Query: 1   MKDKNIVQE-----NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           M+ K+ + +          R+S  +      S R   +   + R+KVNG  +   +  + 
Sbjct: 1   MESKDNIIKLKVEIQDEEIRLSHYLKNVAQCSSRFTRKAAREGRIKVNGENVR-LSYMLK 59

Query: 56  STDHIEVDGVPLRKAERTRLWL-----------------YHKPIGLVTTHSDPDGRSTVF 98
           + D +E+    + + E   +                         +V         +   
Sbjct: 60  NDDIVEL---QINRKEEQDIIPEKMDLDIIYEDDDIIVVNKPKGIVVHPTKRHLNGTLSN 116

Query: 99  DNLPSIFSRVISV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRV-YRVRFHGQ 152
             L     +  +       RLD++T GL+L+  +      L     +   V   +     
Sbjct: 117 GVLYYFNDKNENSIVRLVNRLDMDTSGLVLIAKNAYSHMALSRDMQKDDFVKKYLAIVHG 176

Query: 153 VDQDKLNLLKKGIVIQGICYGD-----------MQVTLDTQKGSNAWVTVGLREGKNREI 201
              +   ++ K I   G                 +  +  Q  + + V + L  G+  +I
Sbjct: 177 NLNEDSGVIDKPIYRVGEGTLKRVIDERGQRSITRFKVVEQYKNASLVELTLETGRTHQI 236

Query: 202 KKVFEFFNWKV 212
           +       + +
Sbjct: 237 RVHLSSIGYPI 247


>gi|219847267|ref|YP_002461700.1| hemolysin A [Chloroflexus aggregans DSM 9485]
 gi|219541526|gb|ACL23264.1| hemolysin A [Chloroflexus aggregans DSM 9485]
          Length = 264

 Score = 56.3 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 28/52 (53%), Gaps = 1/52 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          T QR+  ++   G+A +R + + +I   +V VNG +  +A   V +   IEV
Sbjct: 2  TRQRLDTLLVERGLAETRAKAQALIMAGQVLVNGQVQTKAGTQVAADAQIEV 53


>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 = 56.3 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 33/239 (13%), Positives = 73/239 (30%), Gaps = 31/239 (12%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K I+       R+ +V+A+     SR +++  I    VKV+GI   +A   V     IE+
Sbjct: 9   KKIIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEI 68

Query: 63  DGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           +                 +   + T L +      +V   +    ++ +   L    S  
Sbjct: 69  EAQLEPNERWVPQPIPLDVIYEDETLLVINKPVGLIVHPGAGVRDQTLINALLHYDPSLS 128

Query: 109 ISVGRLDIN----TEGLLLLTNDGGLARVLELPSTQWLRVYRV------------RFHGQ 152
           +      I+        LLL      +    + + +  ++ R             R    
Sbjct: 129 VVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEAIVKGVLISGRTIEA 188

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                     +  V++          +  +  ++  + V L  G+  +I+      +  
Sbjct: 189 PVGRHPIHRTRMAVVEFGRPAITHFRIIKRYRAHTHIRVQLETGRTHQIRVHMAHIHHP 247


>gi|296133201|ref|YP_003640448.1| hemolysin A [Thermincola sp. JR]
 gi|296031779|gb|ADG82547.1| hemolysin A [Thermincola potens JR]
          Length = 271

 Score = 56.3 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 1/59 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             R+  ++   G+  SR + +  I    V V+G  +++A   V  +  IEV G P+  
Sbjct: 2  EKMRLDMLLVEKGLFPSREKAKSAIMAGLVFVDGQRVDKAGTTVSVSADIEVQGNPIPY 60


>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 = 56.3 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 33/245 (13%), Positives = 73/245 (29%), Gaps = 35/245 (14%)

Query: 4   KNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERA-------AVNVM 55
           +       T QR+ + + A     SR  ++  I   RV+VNG  ++ +       AV V 
Sbjct: 2   RFTADPADTGQRIDQWLHAHLPDFSRSRIQEWIKSARVRVNGAAVKTSYTLRAADAVEVE 61

Query: 56  STD-------------HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDP----------- 91
             D              I  +   +   ++    + H   G+ +                
Sbjct: 62  PADPPPLNATAEDIPLRILYEDADVVAIDKPAGMVVHAGAGVHSGTLVNALLHRFATLSG 121

Query: 92  ---DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
                R  +   L    S V+ V + D   + L    +   + +V        ++    R
Sbjct: 122 VGGPLRPGIVHRLDRFTSGVLLVAKNDAAHQKLAAQFSGREIEKVYLALVHGTVKPETGR 181

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +D ++  +    +        +  +  +      + V +  G+  +I+      
Sbjct: 182 IERPIARDPVHRARMTARLAEGRAAWSEYRVLRRFPDFTLLEVRIGTGRTHQIRVHLASI 241

Query: 209 NWKVN 213
              V 
Sbjct: 242 RHPVV 246


>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 = 56.3 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 32/241 (13%), Positives = 70/241 (29%), Gaps = 39/241 (16%)

Query: 9   ENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP- 66
           +   P RV K +      ASR +V++      + VNG+ ++     V + D ++V     
Sbjct: 27  KGQEPLRVDKFLMNFVENASRNKVQQAAKDGNIFVNGVAVKS-NHRVKANDEVKVMFAHP 85

Query: 67  --------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV- 111
                         +   +   + +      +V         + +   +        +  
Sbjct: 86  PHEYLLVPELIPLNIVYEDEELIIINKPAGLVVHPGHGNYQGTLINGLIYHFEQLPKNSS 145

Query: 112 ------GRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVYRVRFHGQ 152
                  R+D +T GLL++         L                    +        G 
Sbjct: 146 DRPGLVHRIDKDTSGLLVVAKTEEAMNHLAKQFFNKTSEREYIALVWGNIPEDEGTITGH 205

Query: 153 VDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           + +   N L+  +   G    +      +  + G    V+  L  G+  +I+  F +   
Sbjct: 206 IGRHPKNRLQMTVFPDGSEGKEAITHYKVLERFGYVTLVSCRLETGRTHQIRAHFTYIGH 265

Query: 211 K 211
            
Sbjct: 266 P 266


>gi|297184482|gb|ADI20596.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium EBAC_27G05]
          Length = 311

 Score = 56.3 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 31/241 (12%), Positives = 69/241 (28%), Gaps = 34/241 (14%)

Query: 5   NIVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            I+  +F   R+ +  A A     SR +++R I    + +NG  L      V   D + +
Sbjct: 6   KIISSDFHNIRLDQA-ATALFEDYSRSQIQRWIEAGNLLINGESLR-PKDKVQEGDELSL 63

Query: 63  DGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-- 106
           D +               +   E   L +      ++   +  +  +             
Sbjct: 64  DPILENRVSWEAEDIPLNIHHEEDEFLIINKPYGLVMHPGAGCNNGTLANALAFHYPQLI 123

Query: 107 ---RVISVGRLDINTEGLLLLTNDGGLARVLELPST------QWLRVYRVRFHGQVDQDK 157
              R   V RLD +T GLL++                     ++  +   +  G    ++
Sbjct: 124 QLPRCGIVHRLDKDTSGLLVIAKTEKFRNFFVEKLQNREIFKEYEALVVGQVIGSFSIEQ 183

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQK-----GSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                    I+       +  +            + V + +  G+  +I+         +
Sbjct: 184 AIERDPRNRIKMRTTDFGREAISHISLIKFYNGYSHVAIEIETGRTHQIRVHLSHHKLPI 243

Query: 213 N 213
            
Sbjct: 244 I 244


>gi|56751203|ref|YP_171904.1| hemolysin-like protein [Synechococcus elongatus PCC 6301]
 gi|81299130|ref|YP_399338.1| hemolysin A [Synechococcus elongatus PCC 7942]
 gi|56686162|dbj|BAD79384.1| hemolysin-like protein [Synechococcus elongatus PCC 6301]
 gi|81168011|gb|ABB56351.1| hemolysin A [Synechococcus elongatus PCC 7942]
          Length = 272

 Score = 56.3 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
          R+  ++   G+  SR++ +R+I    V+V   ++++    V     IEV   P
Sbjct: 5  RLDALLVERGLCPSRQQAQRLIRAGEVRVAQAIVDKPGSLVAEDAVIEVAAKP 57


>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 = 56.3 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 41/255 (16%), Positives = 76/255 (29%), Gaps = 49/255 (19%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V E     R+   +A+ G   +R    + +A   V +NG+   ++A  V + D +E    
Sbjct: 10  VDETGDGMRLDAFLAKEGAYTTRSAAAKRVAAGEVSINGVAARKSAT-VKAGDVVEYQVF 68

Query: 63  --------------------DGVPLRKAERTRLWLY----HKPIGLVTTHSDPDGRSTVF 98
                               D   L  +++  L  +    H     +             
Sbjct: 69  IDPRVFDLESADIPLDVRYEDDQVLVISKQAGLVTHPADGHPQQDTLVNALIHHCGRENL 128

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
            N+     R+  V RLD +T GL+L   TN+ G   + ++      R Y    HG +  +
Sbjct: 129 CNVQGEQDRLGIVHRLDRDTSGLMLAAKTNEAGQKLMEDIADRDVDRHYLALVHGWIPLE 188

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG------------------LREGKN 198
              +                   D  + +    +V                   L  G+ 
Sbjct: 189 TGLVDAPIGRSDRDRLRMCVSDRDNARDAMTSFSVVKRFEAGRNDDGYTLIDCKLFTGRT 248

Query: 199 REIKKVFEFFNWKVN 213
            +I+   E+      
Sbjct: 249 HQIRVHMEYIKHPCV 263


>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 = 56.0 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 30/239 (12%), Positives = 59/239 (24%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            VQ     QR+ + +A      SR  ++  I    V VNG++       V   +HIE+  
Sbjct: 9   TVQPQQMGQRLDQTLAELFPDYSRSRLKTWIEDDLVLVNGVVQNVPRTKVYGDEHIEITV 68

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                           +   +   L +      +V   +     + +   L         
Sbjct: 69  EIEDETRFEPENIPLNIVYEDDDILVINKPKDLVVHPGAGNPKGTVLNALLYHYPQIAEV 128

Query: 111 V-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                  RLD +T GL+++         L     +                         
Sbjct: 129 PRAGIVHRLDKDTTGLMVVAKTIPAQTQLVRDLQKRKITREYEAVACGIMTKGGTVDEPM 188

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +  +      + + L  G+  +I+         + 
Sbjct: 189 ARHPTKRTHMAVHPMGKPAVTHYRIMERFRDYTRLRLRLETGRTHQIRVHMAHLAHPLL 247


>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 = 56.0 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 21/50 (42%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          +R+ + IA  G  SR    R I    V V+G   + A   +     + V+
Sbjct: 15 ERIDRFIAARGGISRGLARRAIEAGGVFVDGRRCKVAGRTLTPGQQVVVN 64


>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 = 56.0 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 35/241 (14%), Positives = 75/241 (31%), Gaps = 39/241 (16%)

Query: 9   ENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           +   P RV K +      A+R +V++   Q  + VNG  ++     V + D ++V     
Sbjct: 37  KGQEPLRVDKFLMNFVENATRNKVQQAAKQGNIFVNGQPVKS-NHRVKANDEVKVYFAHP 95

Query: 63  --------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-------F 105
                   + +PL+    + + L +      +V         + +   +           
Sbjct: 96  PHEDLLIPENIPLQIVYEDDSLLVVNKPAGMVVHPGHGNYSGTLINALVYHFENLPNNSS 155

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY-------------RVRFHGQ 152
           +R   V R+D +T GLL++         L                             G 
Sbjct: 156 NRPGLVHRIDKDTSGLLVIAKTEEAMLHLTQQFFHKTTEREYIALVWGNVEADEGTVRGH 215

Query: 153 VDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           + +   + L+  +   G    +      +  + G    V+  L  G+  +I+   +    
Sbjct: 216 IGRHLKDRLQMDVFPDGSHGKEAVTHYKVLERFGYVTLVSCRLETGRTHQIRVHMKHIGH 275

Query: 211 K 211
            
Sbjct: 276 T 276


>gi|144227643|gb|AAZ44541.2| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyopneumoniae J]
          Length = 304

 Score = 56.0 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 29/244 (11%), Positives = 74/244 (30%), Gaps = 43/244 (17%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--------- 60
           +    R+  ++A+    SR+  + +I +++V +N  L+ +    V +   I         
Sbjct: 12  DQEDIRIDILVAKLANLSRKVAQDLILEKKVLINNNLVLKKNQIVKTGQKIKIFNDYKRP 71

Query: 61  -------EVDGVPLRKAERTRLWLYHKPIGLV-------------------TTHSDPDGR 94
                  E+D   + + +   L    K + +                    +       R
Sbjct: 72  KPQLEPAEIDFEIIFQDQNMILINKPKNLVVHPGVGNWKNTLVNGLISHFDSLEQLDHIR 131

Query: 95  STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD 154
             +   L    + ++ V +        +    +  + R  +      +    ++ +  + 
Sbjct: 132 PGIVHRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVIGKVLHKFMKINLPIG 191

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLD------TQKGSNAWVTVGLREGKNREIKKVFEFF 208
           +D  N LKK I             ++       Q    + V   L  G+  +I+      
Sbjct: 192 RDLKNPLKKTISFFNS--KPAITNVELIKHFSYQNQDFSLVKCQLETGRTHQIRLHLAHI 249

Query: 209 NWKV 212
            + +
Sbjct: 250 GYPI 253


>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 = 56.0 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 32/209 (15%), Positives = 61/209 (29%), Gaps = 21/209 (10%)

Query: 24  GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKAERTRL------- 75
            I SR+  ++ I Q  V +N          V   D I +     + K    ++       
Sbjct: 34  TITSRKAFKKAIKQGCVTLNNKQAYTGDY-VNENDLITIYKDKSISKKPSIQIPLKVLFE 92

Query: 76  -----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-----RVISVGRLDINTEGLLLLT 125
                 ++      V+ +      + +   L          R +   RLD  T G LL+ 
Sbjct: 93  DNHLAIIHKPAGVEVSGNKKYTIENALPSLLKKSNQKDALDRPLPAHRLDYPTSGCLLIG 152

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
                 + L     +     +       +Q     + K I  +        +   T K  
Sbjct: 153 KTSETLQALHRMFEKREISKKYIAVTLGNQITEGKIDKPIDDKASLTTFKTLQTITSKKY 212

Query: 186 NA--WVTVGLREGKNREIKKVFEFFNWKV 212
           NA   V +    G+  +++K        +
Sbjct: 213 NALNLVLLTPHTGRRHQLRKHMMQLGNPI 241


>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 = 56.0 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 29/239 (12%), Positives = 65/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I    V VNG  +      V+ ++ + ++ 
Sbjct: 10  TVAESQIGQRLDQALAELFPDYSRSRIKEWILADCVLVNGKKINTPKGRVLGSESVTINA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  EIKENVRSIPQQIPLNIVYEDNDILVINKPRGLVVHPGAGNADGTILNALLHYYPAISNV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
            R   + RLD +T GL+++         L                   +           
Sbjct: 130 PRAGIIHRLDKDTTGLMVVAKTVPAQTHLVEALQARKITREYEAIAIGNMIAGGAVEEPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               +      V            +     ++  + + L  G+  +I+    F    + 
Sbjct: 190 ARHASKRTHMAVHPMGKPAVTHYRIMEHFRAHTHLRLRLETGRTHQIRVHMSFIRHPLV 248


>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 = 56.0 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 33/239 (13%), Positives = 73/239 (30%), Gaps = 31/239 (12%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K I+       R+ +V+A+     SR +++  I    VKV+GI   +A   V     IE+
Sbjct: 9   KKIIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEI 68

Query: 63  DGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           +                 +   + T L +      +V   +    ++ +   L    S  
Sbjct: 69  EAQLEPNERWVPQPIPLDVIYEDETLLVINKPVGLIVHPGAGVRDQTLINALLHYDPSLS 128

Query: 109 ISVGRLDIN----TEGLLLLTNDGGLARVLELPSTQWLRVYRV------------RFHGQ 152
           +      I+        LLL      +    + + +  ++ R             R    
Sbjct: 129 VVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEAIVKGVLISGRTIEA 188

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                     +  V++          +  +  ++  + V L  G+  +I+      +  
Sbjct: 189 PVGRHPIHRTRMAVVEFGRPAITHFRIIKRYRAHTHIRVQLETGRTHQIRVHMAHIHHP 247


>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 = 56.0 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 28/231 (12%), Positives = 65/231 (28%), Gaps = 32/231 (13%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNV----------MSTDHIEVD 63
           R+  V+A      SR  ++  I    V ++G+  ++    V             D +   
Sbjct: 18  RLDAVLAELFSDYSRNRIQDWIRAGLVTLDGVEHKKPNFKVFGDESVVLLAEIEDEVSYQ 77

Query: 64  GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-----GRL 114
              +       +   L L      +V   +     + +   L    +           RL
Sbjct: 78  AQDIPIEVVYEDEDILVLNKPAGLVVHPGAGNPDGTLLNALLFHYETIREVPRAGIVHRL 137

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQW------------LRVYRVRFHGQVDQDKLNLLK 162
           D  T GL+++  +      L     Q               +        + +   +  +
Sbjct: 138 DKETSGLMVVAKNVPAQTHLVEQLQQHDVERVYDAIVVGKMISGGTISKPIGRHPTDRKR 197

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             ++  G         +  +   +  V V L  G+  +I+    +  + + 
Sbjct: 198 MAVLTVGGKPATSHYRVLERFREHTHVRVKLETGRTHQIRVHMAYLGFPLV 248


>gi|302343356|ref|YP_003807885.1| hemolysin A [Desulfarculus baarsii DSM 2075]
 gi|301639969|gb|ADK85291.1| hemolysin A [Desulfarculus baarsii DSM 2075]
          Length = 252

 Score = 56.0 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 11/51 (21%), Positives = 24/51 (47%), Gaps = 1/51 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          R+ + +   G+A SR + + +I     +++G    +   +V     + VDG
Sbjct: 6  RLDQRLVELGLAPSRAKAQALIMAGLARIDGQTARKPGQSVEPEAAVSVDG 56


>gi|291519200|emb|CBK74421.1| hemolysin TlyA family protein [Butyrivibrio fibrisolvens 16/4]
          Length = 265

 Score = 56.0 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 24/164 (14%), Positives = 49/164 (29%), Gaps = 2/164 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  V+   G A SR + + MI +  V V G   ++A   +     IE+ G  L+   R
Sbjct: 3   ERLDIVLVDRGFAPSREKAKTMIMEGYVFVKGNREDKAGTKIDVDADIEIHGQQLKYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L         T                    ++  G   + +  +        L +
Sbjct: 63  GGLKLEKAMTHFDITLDGKVCMDIGAST-GGFTDCMLQNGASKVFSVDVGYGQFAWKLRQ 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
              +   +   +  V      ++     +    +      G  +
Sbjct: 122 DPRVVCMEKTNIRYVTLEDIGEKLDFASVDVSFISLTKVLGPAK 165


>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 = 56.0 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 33/241 (13%), Positives = 75/241 (31%), Gaps = 39/241 (16%)

Query: 9   ENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           +   P RV K +      A+R +V++   Q  + VNG  ++     V + D ++V     
Sbjct: 33  KGQEPLRVDKFLMNFVENATRNKVQQAAKQGNIFVNGEPVKS-NHRVKANDEVKVLFPHP 91

Query: 63  --------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-------F 105
                   + +P  +   + + L +      +V         + +   +           
Sbjct: 92  PHEDLLVPENIPLNIVYEDDSLLVVNKPAGMVVHPGHGNYSGTLINALVYHFENLPNNSS 151

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVYRVRFHGQ 152
           +R   V R+D +T GLL++         L                    +        G 
Sbjct: 152 NRPGLVHRIDKDTSGLLVVAKTEEAMLHLTQQFFNKTTQREYIALVWGNIEEDEGTVCGH 211

Query: 153 VDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           + +   + L+  +   G    +      +  + G    ++  L  G+  +I+   +    
Sbjct: 212 IGRHLKDRLQMDVFPDGSHGKEAVTHYKVLERFGYVTLISCKLETGRTHQIRVHLKHIGH 271

Query: 211 K 211
            
Sbjct: 272 T 272


>gi|15605669|ref|NP_213044.1| 30S ribosomal protein S4 [Aquifex aeolicus VF5]
 gi|6226103|sp|O66484|RS4_AQUAE RecName: Full=30S ribosomal protein S4
 gi|2982819|gb|AAC06442.1| ribosomal protein S04 [Aquifex aeolicus VF5]
          Length = 211

 Score = 56.0 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G AS RR+  +++A   V VNG  +   +  V   D IE+
Sbjct: 99  RLDNVVYRLGFASTRRQARQLVAHGHVLVNGKKVNIPSYLVEPGDVIEI 147


>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 = 56.0 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 30/237 (12%), Positives = 65/237 (27%), Gaps = 38/237 (16%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+ + +       SR  +++++AQ  V +NG  + +AA  V + D + ++  P       
Sbjct: 50  RIDRALVELVPEFSRSYLQQLLAQGGVSLNGRPVRKAASRVNAGDRVVLEMRPTVQSQAF 109

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----------- 107
                   +   +   L L      +V         + +   L    +            
Sbjct: 110 RPQPMDIDVVYEDAHLLVLNKPAGLVVHPAPGHWSATLLNGLLARDANALLLPRAGIVHR 169

Query: 108 --------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
                   ++           +  +       + L L    W           + +D  N
Sbjct: 170 LDKDTSGLMVVARDRATMDALVAQIARRQVQRQYLALAHGAWSGPRSRSVQAPIGRDPRN 229

Query: 160 LLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            L+  +V      G    T            W+   L  G+  +I+         + 
Sbjct: 230 RLRMAVVDLARHAGKCARTDVLCLDATPQGCWLQCRLHTGRTHQIRVHMASLQHPLV 286


>gi|144575467|gb|AAZ53825.2| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyopneumoniae 7448]
          Length = 304

 Score = 56.0 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 29/244 (11%), Positives = 74/244 (30%), Gaps = 43/244 (17%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--------- 60
           +    R+  ++A+    SR+  + +I +++V +N  L+ +    V +   I         
Sbjct: 12  DQEDIRIDILVAKLANLSRKVAQDLILEKKVLINNNLVLKKNQIVKTGQKIKIFNDYKRP 71

Query: 61  -------EVDGVPLRKAERTRLWLYHKPIGLV-------------------TTHSDPDGR 94
                  E+D   + + +   L    K + +                    +       R
Sbjct: 72  KPQLEPAEIDFEIIFQDQNMILINKPKNLVVHPGVGNWKNTLVNGLISHFDSLEQLDHIR 131

Query: 95  STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD 154
             +   L    + ++ V +        +    +  + R  +      +    ++ +  + 
Sbjct: 132 PGIVHRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVIGKVLHKFMKINLPIG 191

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLD------TQKGSNAWVTVGLREGKNREIKKVFEFF 208
           +D  N LKK I             ++       Q    + V   L  G+  +I+      
Sbjct: 192 RDLKNPLKKTISFFNS--KPAITNVELIKHFNYQNQDFSLVKCQLETGRTHQIRLHLAHI 249

Query: 209 NWKV 212
            + +
Sbjct: 250 GYPI 253


>gi|226941139|ref|YP_002796213.1| RluD [Laribacter hongkongensis HLHK9]
 gi|226716066|gb|ACO75204.1| RluD [Laribacter hongkongensis HLHK9]
          Length = 349

 Score = 56.0 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 29/240 (12%), Positives = 60/240 (25%), Gaps = 35/240 (14%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            + +     R+   +A      SR  + + I    V+V+G  +       +    +EVD 
Sbjct: 21  TIPDTLAGDRLDAALAALMPDQSRSRLTQWIKDGHVRVDGSTVTVPRSKTVLGQQVEVDE 80

Query: 65  V---------------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                           P+   +R  L +      +    +     + +   L  +     
Sbjct: 81  QLSLDEMAFAPEDIEIPVIYEDRQILVVNKPAGLVTHPGNGNWSGTLLNGLLYRVPELAH 140

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   RLD +T GL+++         L             R     +      + K 
Sbjct: 141 VPRAGIVHRLDKDTSGLMVVAKTVAAQLDLIRQLQARTVKRHYRAIACGNVAGDITIDKA 200

Query: 165 IVIQGICYGDMQVTLDTQKGS-------------NAWVTVGLREGKNREIKKVFEFFNWK 211
           I  +          +                   +  V   L  G+  +I+         
Sbjct: 201 IG-RDPKTRVKMAVVAFGGKPAITHVRPLEMFEHHTLVECRLETGRTHQIRVHMASIGCP 259


>gi|168186202|ref|ZP_02620837.1| hemolysin A [Clostridium botulinum C str. Eklund]
 gi|169295649|gb|EDS77782.1| hemolysin A [Clostridium botulinum C str. Eklund]
          Length = 270

 Score = 56.0 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 13/62 (20%), Positives = 26/62 (41%), Gaps = 1/62 (1%)

Query: 9  ENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           N   +R+  ++    I  SR + +  I + +V VNG  +++    +     IE  G  +
Sbjct: 2  SNIKSERLDVLLVEKKIFDSREKAKIAIMEGKVFVNGQRVDKCGQKIKVDSEIEFKGEVM 61

Query: 68 RK 69
            
Sbjct: 62 PY 63


>gi|91772977|ref|YP_565669.1| RNA-binding S4 [Methanococcoides burtonii DSM 6242]
 gi|91711992|gb|ABE51919.1| RNA-binding S4 domain protein [Methanococcoides burtonii DSM
          6242]
          Length = 225

 Score = 56.0 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 12/51 (23%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 14 QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+   +   G   SR   ++ I    VK++G ++ + + +V   D ++VD
Sbjct: 1  MRLDAYLVEMGSFKSRGRSKKAIVDGHVKIDGSVVTKPSKDVSIDDDVKVD 51


>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 = 56.0 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 31/249 (12%), Positives = 68/249 (27%), Gaps = 42/249 (16%)

Query: 4   KNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K  V +    +R+ K +  R   +SR  +++      + VNG  ++     V   D I +
Sbjct: 30  KIEVDKGQKAERIDKYLFERMQHSSRNRIQKAAQAGFIHVNGSPVKS-NYKVRPEDVITL 88

Query: 63  ------DGVPLRKAERTRLWLY---------HKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                     +   +     +Y              +V   +     + +      +   
Sbjct: 89  MLDRPKHDNTIEAEDIPLDVVYEDDSLMVVMKPAGLVVHPGAGNFHGTLINAIAWHLRGL 148

Query: 108 VISV---------GRLDINTEGLLLLTNDGG-------------LARVLELPSTQWLRVY 145
                         R+D +T GLLL+                    R         +   
Sbjct: 149 ASFDANDPEVGLVHRIDKDTSGLLLIAKTPEAKSSLGKQFFYKTTHRSYIALVWGNIVDE 208

Query: 146 RVRFHGQVDQDKLNLLKKG-IVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIK 202
           + R  G + +D  + L+      +            +  + G    +   L  G+  +I+
Sbjct: 209 QGRIEGNISRDPKDRLRMTVFPPESDIGKPAVTHYKVIERFGYTTLIECVLETGRTHQIR 268

Query: 203 KVFEFFNWK 211
              +     
Sbjct: 269 AHMKHIGHP 277


>gi|218296418|ref|ZP_03497161.1| hemolysin A [Thermus aquaticus Y51MC23]
 gi|218243212|gb|EED09743.1| hemolysin A [Thermus aquaticus Y51MC23]
          Length = 235

 Score = 56.0 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 28/50 (56%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ + +   G+  SR + +R+IA+ +V+V G ++ + A  V     +E+
Sbjct: 1  MRLDRYLVEKGLVESREKAKRLIAEGKVRVGGRVVTKPAHPVPEGAAVEL 50


>gi|331091119|ref|ZP_08339961.1| hypothetical protein HMPREF9477_00604 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330405341|gb|EGG84877.1| hypothetical protein HMPREF9477_00604 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 251

 Score = 56.0 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 25/50 (50%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             R+  +++    ASR ++  +I   RV VNG L+   + NV   D + V
Sbjct: 174 SVRLDSLLSLVFPASRSKLVPLIEGGRVFVNGKLITTNSYNVKENDIVSV 223


>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 = 56.0 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 30/245 (12%), Positives = 70/245 (28%), Gaps = 39/245 (15%)

Query: 7   VQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           V+     +R+ + +++      SR   ER+I + RV ++G   E+ +  +   + I +  
Sbjct: 9   VEAECAGERLDRYLSKRPELSLSRSYAERLIGEGRVLLDGQ-AEKPSKRLRGGEQISICF 67

Query: 63  -DGVP-----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
            +  P           +   +   L +      +V       G + V   L      + S
Sbjct: 68  PEEKPTEIRAEEIPLDIVYEDSELLLVNKPKGMVVHPAPGHSGGTLVNALLGRPGPELSS 127

Query: 111 VGRL----------------------DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
           +  +                      D     L     +  + R         +R    +
Sbjct: 128 INGVLRPGIVHRIDRDTTGLLLVCKKDRAHRALAEQLKEHTITRRYHAILCGRMREDEGK 187

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + + + +  K+ I  +          +  +      V   L  G+  +I+      
Sbjct: 188 VDAPIGRSRRDRKKQAIDWERGREAVTHYRVLERFSEYTLVECRLETGRTHQIRVHMASI 247

Query: 209 NWKVN 213
              V 
Sbjct: 248 GHPVL 252


>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 = 56.0 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 31/269 (11%), Positives = 66/269 (24%), Gaps = 42/269 (15%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +  +  RV K +    + +SR  +++      +  NG  ++  +  V   D + V  
Sbjct: 33  VVDKGQSQVRVDKYLFERLVNSSRNRIQKAADAGLIMANGKPVKS-SYKVKPCDVLTVMM 91

Query: 63  -----DGVPLR-------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                D   +          E   L + +KP GLV      +   T+ + +         
Sbjct: 92  DRPRYDNDIIPEDIPLDIVYEDNDLMVINKPAGLVVHPGCGNYHGTLVNAIAWHLKDNPR 151

Query: 111 VGRLDIN-------------------------TEGLLLLTNDGGLARVLELPSTQWLRVY 145
               D                             GL              +         
Sbjct: 152 YDPNDPQVGLVHRIDKDTSGLLVVAKTPDAKTHLGLQFYNKTTKRKYNALVWGIVENNEG 211

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
            +  +   +      +          +      +  + G    V   L  G+  +I+   
Sbjct: 212 TIEGNIGRNPKDRMQMAVLSDPAQGKHAVTHYRVLERLGYVTLVECVLETGRTHQIRVHM 271

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +     +    R   G   L        +
Sbjct: 272 KHIGHTLFNDERYG-GNEILKGTHFSKYK 299


>gi|319784706|ref|YP_004144182.1| RNA-binding S4 domain protein [Mesorhizobium ciceri biovar
          biserrulae WSM1271]
 gi|317170594|gb|ADV14132.1| RNA-binding S4 domain protein [Mesorhizobium ciceri biovar
          biserrulae WSM1271]
          Length = 254

 Score = 56.0 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 14 QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          QR+  ++ + G  ASR      + +  V V+G++  +   +V+   H+ +D 
Sbjct: 11 QRLDDLLVQRGLFASRSRARDAVERGTVTVDGVIARKPGQSVLPQCHVAIDD 62


>gi|301154795|emb|CBW14258.1| 23S rRNA pseudouridine synthase [Haemophilus parainfluenzae T3T1]
          Length = 324

 Score = 56.0 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 28/238 (11%), Positives = 62/238 (26%), Gaps = 31/238 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +Q     QR+ + +A      SR  ++  I  ++VK+NG + +     V   + IE+   
Sbjct: 10  IQPEQMGQRLDQTLAELFPEYSRSRLKTWIEAKQVKMNGEIADIPRAKVYGGEQIEISVE 69

Query: 66  P--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                          +   +   + +      +V   +     + +   L          
Sbjct: 70  VEDENRFEPQNIPLNIVYEDDDIIVINKPKDLVVHPGAGNPDGTVLNALLYHYPPIAEVP 129

Query: 112 -----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-----------FHGQVDQ 155
                 RLD +T GL+++         L     +                      Q   
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     V            +     +   + + L  G+  +I+         + 
Sbjct: 190 RHATKRTLMAVHPMGKPAVTHYRIMENFRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 247


>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 = 56.0 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 31/269 (11%), Positives = 66/269 (24%), Gaps = 42/269 (15%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +  +  RV K +    + +SR  +++      +  NG  ++  +  V   D + V  
Sbjct: 34  VVDKGQSQVRVDKYLFERLVNSSRNRIQKAADAGLIMANGKPVKS-SYKVKPCDVLTVMM 92

Query: 63  -----DGVPLR-------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                D   +          E   L + +KP GLV      +   T+ + +         
Sbjct: 93  DRPRYDNDIIPEDIPLDIVYEDNDLMVINKPAGLVVHPGCGNYHGTLVNAIAWHLKDNPR 152

Query: 111 VGRLDIN-------------------------TEGLLLLTNDGGLARVLELPSTQWLRVY 145
               D                             GL              +         
Sbjct: 153 YDPNDPQVGLVHRIDKDTSGLLVVAKTPDAKTHLGLQFYNKTTKRKYNALVWGIVENNEG 212

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
            +  +   +      +          +      +  + G    V   L  G+  +I+   
Sbjct: 213 TIEGNIGRNPKDRMQMAVLSDPAQGKHAVTHYRVLERLGYVTLVECVLETGRTHQIRVHM 272

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +     +    R   G   L        +
Sbjct: 273 KHIGHTLFNDERYG-GNEILKGTHFSKYK 300


>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 = 56.0 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 35/255 (13%), Positives = 73/255 (28%), Gaps = 46/255 (18%)

Query: 1   MKDKN-IVQENFTPQRVSKVIA--RAGIASRREVERMIAQQRVKVNGI-LLERAAVNVMS 56
           M+ +  IV+     QR+ + ++    G+ SR  ++ ++A+  V  NG    +     + +
Sbjct: 1   MEQREYIVEAEGAGQRIDRFLSGEDTGL-SRSALQGLVAEGHVLCNGKAPAKSL--KLKA 57

Query: 57  TDHIEV---DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
            D I +   D  P+              +   L +      +V         + V   L 
Sbjct: 58  GDIILLEIPDAKPIEAVPQEIPLDIIYEDAHLLVVNKPKGMVVHPAPGNPDGTLVNALLW 117

Query: 103 SIF---------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
                        R   V R+D +T GLL++  D      L                   
Sbjct: 118 HCKGSLSGIGGEIRPGIVHRVDKDTSGLLVVAKDDATHIGLSQQMAVHSVERAYNTIVYG 177

Query: 154 DQDKLNLLKKGIVIQGICYG------DMQ----------VTLDTQKGSNAWVTVGLREGK 197
              +     +  + +                          +  + G    +   L+ G+
Sbjct: 178 GFAQDEGFVESNLGRSKTDRKKMAVYPASEPHTKYAYTGYKVLERLGEFTMLECRLKTGR 237

Query: 198 NREIKKVFEFFNWKV 212
             +I+      +  V
Sbjct: 238 THQIRVHMASIHHPV 252


>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 = 56.0 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 31/269 (11%), Positives = 66/269 (24%), Gaps = 42/269 (15%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +  +  RV K +    + +SR  +++      +  NG  ++  +  V   D + V  
Sbjct: 34  VVDKGQSQVRVDKYLFERLVNSSRNRIQKAADAGLIMANGKPVKS-SYKVKPCDVLTVMM 92

Query: 63  -----DGVPLR-------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                D   +          E   L + +KP GLV      +   T+ + +         
Sbjct: 93  DRPRYDNDIIPEDIPLDIVYEDNDLMVINKPAGLVVHPGCGNYHGTLVNAIAWHLKDNPR 152

Query: 111 VGRLDIN-------------------------TEGLLLLTNDGGLARVLELPSTQWLRVY 145
               D                             GL              +         
Sbjct: 153 YDPNDPQVGLVHRIDKDTSGLLVVAKTPDAKTHLGLQFYNKTTKRKYNALVWGIVENNEG 212

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
            +  +   +      +          +      +  + G    V   L  G+  +I+   
Sbjct: 213 TIEGNIGRNPKDRMQMAVLSDPAQGKHAVTHYRVLERLGYVTLVECVLETGRTHQIRVHM 272

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +     +    R   G   L        +
Sbjct: 273 KHIGHTLFNDERYG-GNEILKGTHFSKYK 300


>gi|134298943|ref|YP_001112439.1| hemolysin A [Desulfotomaculum reducens MI-1]
 gi|134051643|gb|ABO49614.1| hemolysin A [Desulfotomaculum reducens MI-1]
          Length = 268

 Score = 56.0 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 13/58 (22%), Positives = 24/58 (41%), Gaps = 1/58 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          T +R+   +   G   SR +    +    V V+G  +++    V +   I+V G  L 
Sbjct: 4  TKERLDVYLVNNGFFPSREKARAAVMAGLVFVDGERVDKPGHQVKAEVSIQVQGKTLP 61


>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 = 56.0 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 21/50 (42%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          +R+ + IA  G  SR    R I    V V+G   + A   +     + V+
Sbjct: 15 ERIDRFIAARGGISRGLARRAIEAGGVFVDGRRCKVAGRTLTPGQQVVVN 64


>gi|325568385|ref|ZP_08144752.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
          casseliflavus ATCC 12755]
 gi|325158154|gb|EGC70307.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
          casseliflavus ATCC 12755]
          Length = 90

 Score = 56.0 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 1/80 (1%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           R+ KVI +    SR+E++R+  Q +V V+  +  R   NV S+   I V G  L   ER
Sbjct: 1  MRLDKVIEQQLNTSRKEMKRLFQQGKVFVDHRIERRPERNVDSSLHQIMVAGRQLETQER 60

Query: 73 TRLWLYHKPIGLVTTHSDPD 92
            +    K +          
Sbjct: 61 YYIVNKPKGVVTANLDQQHQ 80


>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 = 56.0 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 31/245 (12%), Positives = 63/245 (25%), Gaps = 41/245 (16%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +     RV K +    + ASR  +++      V  NG  ++  +  V   D I V  
Sbjct: 33  VVDKGQAMVRVDKYLFERIVNASRNRIQKAAEGGFVMANGKPVKS-SYKVKPLDVITVMM 91

Query: 63  -----DGVPLR--------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                +   +           +   + +      +V         + V      +     
Sbjct: 92  DRPRYENEIIPEDIPLTIVYEDPYVMVVNKPAGLVVHPGHGNYHGTLVNALAWHMKDIPD 151

Query: 110 SV---------GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK--- 157
                       R+D +T GLL++         L L         R R       ++   
Sbjct: 152 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKTTKRRYRALVWGVVEQDEG 211

Query: 158 ------------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                          +          +      +  + G    V   L  G+  +I+   
Sbjct: 212 TIVGNIARNPKDRMQMAVMSDPTVGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHM 271

Query: 206 EFFNW 210
           +    
Sbjct: 272 KHIGH 276


>gi|169334432|ref|ZP_02861625.1| hypothetical protein ANASTE_00832 [Anaerofustis stercorihominis
          DSM 17244]
 gi|169259149|gb|EDS73115.1| hypothetical protein ANASTE_00832 [Anaerofustis stercorihominis
          DSM 17244]
          Length = 267

 Score = 56.0 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 10/66 (15%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          MK K         +R+  ++  +G+A SR + +R+I    V VN   +++A   V    +
Sbjct: 1  MKSK---------ERLDVLLFESGMAESREKAKRLIMAGVVFVNDQRVDKAGTKVDIYSN 51

Query: 60 IEVDGV 65
          I + G 
Sbjct: 52 IIIKGN 57


>gi|160945192|ref|ZP_02092418.1| hypothetical protein FAEPRAM212_02711 [Faecalibacterium prausnitzii
           M21/2]
 gi|158442923|gb|EDP19928.1| hypothetical protein FAEPRAM212_02711 [Faecalibacterium prausnitzii
           M21/2]
          Length = 267

 Score = 56.0 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 20/166 (12%), Positives = 48/166 (28%), Gaps = 2/166 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+ + + + G+  SR   + +I    V VN   +++A   +     +EV G  +    R
Sbjct: 3   IRLDQYLVQNGLVQSRERAKALIMAGVVFVNQQKVDKAGEMIKEDAVVEVRGHDIGYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L         T +                  ++  G + +    +        L  
Sbjct: 63  GGLKLEKAMKCFPLTPNGKVCMDIGAST-GGFTDCMLQNGAVKVYAVDVGYGQLAWSLRT 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
              + + +   +  V      +  +   +    +     +   Q  
Sbjct: 122 DARVVNMERTNIRYVTPEDLAEPIEFFSVDVSFISLHHIFPVAQRI 167


>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 = 56.0 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 45/293 (15%), Positives = 82/293 (27%), Gaps = 72/293 (24%)

Query: 1   MKDKNIVQENFTPQRVSKVI--------ARAGIASRREVERMIAQQRVKVNGILLERA-- 50
           MK K I+ EN   QR+ K +        ++          +M+ ++ VKVNG+ ++    
Sbjct: 1   MK-KLIIDENHANQRIDKYLKKLLCQAPSQLIY-------KMLRKKDVKVNGVKVKENYI 52

Query: 51  -------------------------------AVNVMSTDHIEVDGVP--------LRKAE 71
                                             +   D I V G P        + +  
Sbjct: 53  LQNHDVVELFLYEDKFQEYTRAQTIFDLKIEFQVIYEDDKILVVGKPAGLLVHEDINEDM 112

Query: 72  RT---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            T   ++  Y    G                 L    S ++  G+     + L  +    
Sbjct: 113 NTLSNQVITYLYQKGEYDPQISLGFTPGPVHRLDRNTSGIVIFGKTMRALQDLNEMMKKR 172

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSN 186
                  L   +          G + +D    L K +         M   ++  +     
Sbjct: 173 HCIEKTYLTICKGHM-SSADLVGYMKKDGDQSLVKVVTQNTPGALMMHTLVENIEYHQGF 231

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + + V L  G+  +I+         +       YG F+L        RE+ KK
Sbjct: 232 SLLKVQLVTGRTHQIRVHLASVGHPIIG--DSKYGDFELN-------REMKKK 275


>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 = 56.0 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 30/239 (12%), Positives = 60/239 (25%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            VQ     QR+ + +A      SR  ++  I +  V VNG++       V   +HIE+  
Sbjct: 9   TVQPQQMGQRLDQTLAELFPDYSRSRLKTWIEEDLVLVNGVVQNVPRTKVYGDEHIEITV 68

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                           +   +   L +      +V   +     + +   L         
Sbjct: 69  EIEDETRFEPEAIPLNIVYEDEDILVINKPKDLVVHPGAGNPKGTVLNALLYHYPQIAEV 128

Query: 111 V-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                  RLD +T GL+++         L     +                         
Sbjct: 129 PRAGIVHRLDKDTTGLMVVAKTIPAQTQLVRDLQKRKITREYEAVACGIMTKGGTVDEPM 188

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +  +      + + L  G+  +I+         + 
Sbjct: 189 ARHPTKRTHMAVHPMGKPAVTHYRIMERFRDYTRLRLRLETGRTHQIRVHMAHIAHPLL 247


>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 = 56.0 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 29/244 (11%), Positives = 74/244 (30%), Gaps = 43/244 (17%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--------- 60
           +    R+  ++A+    SR+  + +I +++V +N  L+ +    V +   I         
Sbjct: 12  DQEDIRIDILVAKLANLSRKVAQDLILEKKVLINNNLVLKKNQIVKTGQKIRIFNDYKRP 71

Query: 61  -------EVDGVPLRKAERTRLWLYHKPIGLV-------------------TTHSDPDGR 94
                  E+D   + + +   L    K + +                    +       R
Sbjct: 72  KPQLEPAEIDFEIIFQDQNMILINKPKNLVVHPGVGNWKNTLVNGLISHFDSLEQLDHIR 131

Query: 95  STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD 154
             +   L    + ++ V +        +    +  + R  +      +    ++ +  + 
Sbjct: 132 PGIVHRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVIGKVLHKFMKINLPIG 191

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLD------TQKGSNAWVTVGLREGKNREIKKVFEFF 208
           +D  N LKK I             ++       Q    + V   L  G+  +I+      
Sbjct: 192 RDLKNPLKKTISFFNS--KPAITNVELIKHFSYQNQDFSLVKCQLETGRTHQIRLHLAHI 249

Query: 209 NWKV 212
            + +
Sbjct: 250 GYPI 253


>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 = 56.0 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/240 (10%), Positives = 65/240 (27%), Gaps = 39/240 (16%)

Query: 12  TPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------- 63
           +P+R+ + +       SR +++++I   RV ++G   +     +   + + VD       
Sbjct: 14  SPERLDRFLVEQLPELSRSQLKKLIDDGRVLLDGAAAK-PGSKLKGGETLTVDVPDPSPA 72

Query: 64  -------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
                   + +   +R  + +   P  +V         + V   L          G L  
Sbjct: 73  EAVSEDIPLVILYEDRHLIVIDKPPGMVVHPAPGHYQGTLVNALLHHCQDLSGIGGELRP 132

Query: 117 -------NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
                       +++      A        +   + R            +       I  
Sbjct: 133 GIVHRLDKDTSGVMVATKTDSAHQSLAAQFKAHSITRRYIALIHGVLTGDRGSIDRPIGR 192

Query: 170 ICYGDMQVTLDTQKGSN----------------AWVTVGLREGKNREIKKVFEFFNWKVN 213
                 +++   + G +                  V + L  G+  +I+  F      + 
Sbjct: 193 HPTHRKKMSTTCRTGRHAVTHWRVLRRFDDDRLTLVELALETGRTHQIRVHFSEQQHPLL 252


>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 = 56.0 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 28/236 (11%), Positives = 66/236 (27%), Gaps = 31/236 (13%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I   RV+VNG L+ +    V+  + I +D 
Sbjct: 10  TVAESQLGQRLDQALAEMFPDYSRSRIKEWILGDRVQVNGKLINKPKEKVLGGEEISIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
           +               +   +   L +      +V   +     + +   L         
Sbjct: 70  IIEEDARWEPQNIELNIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLYRYPEIADV 129

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--- 156
                  R+       +     +        +  L   + ++  V   R       +   
Sbjct: 130 PRAGIVHRLDKDTTGLMVIAKTVPAQTRLVESLQLREITREYEAVATGRMTAGGIVEEPI 189

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      V         +  +     ++  + + L  G+  +I+      + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAITRYRVMEHFRAHTRLRLRLETGRTHQIRVHMAHISH 245


>gi|254409976|ref|ZP_05023756.1| hemolysin A [Microcoleus chthonoplastes PCC 7420]
 gi|196183012|gb|EDX77996.1| hemolysin A [Microcoleus chthonoplastes PCC 7420]
          Length = 281

 Score = 56.0 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 12/53 (22%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          QR+  ++    +  SR++ +R+I    V+VN  L+++    + +T  I+++  
Sbjct: 3  QRLDTLLVDLNLCESRQQAQRLILAGEVRVNQQLVDKPGTEIETTAEIKINQK 55


>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 = 56.0 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 29/239 (12%), Positives = 61/239 (25%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            VQ +   QR+ + +A      SR  ++  I +  V VNG++       V   + IE+  
Sbjct: 9   TVQSHQMGQRLDQTLAELFPDYSRSRLKTWIEEDLVLVNGVVQNVPRSKVYGDEQIEITV 68

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                           +   +   L +      +V   +     + +   L         
Sbjct: 69  EIEDETRFEPENIPLNIVYEDDDILVINKPKDLVVHPGAGNPSGTVLNALLYHYPPIAEV 128

Query: 111 V-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                  RLD +T GL+++         L     +   +                     
Sbjct: 129 PRAGIVHRLDKDTTGLMVVAKTIPAQTQLVRDLQKRKIIREYEAVACGIMTKGGTVDEPM 188

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +  +      + + L  G+  +I+         + 
Sbjct: 189 ARHPTKRTHMAVHPMGKPAVTHYRIMERFRDYTRLRLRLETGRTHQIRVHMAHIAHPLL 247


>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 = 56.0 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 39/254 (15%), Positives = 75/254 (29%), Gaps = 42/254 (16%)

Query: 2   KDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K K  V E    +RV + I       SR ++ ++I +  + +N   +E  +  V   D +
Sbjct: 5   KYKFTVSEEQNLKRVDQFIVEELPTFSRTKISKLIKEGALLINNEPIEERSKKVSFGDEV 64

Query: 61  EV--------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           E+        D  P      +   +   L +      +V   +     + V   L     
Sbjct: 65  ELSVPEPVPTDLKPQNIPLDVVYEDDDLLVINKPIGMVVHPGAGNPDGTLVNALLHHCKE 124

Query: 107 R---------VISVGRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRV 144
                        V R+D +T GLL++  +     VL                     + 
Sbjct: 125 NLSGINGELRPGIVHRIDKDTSGLLVVAKNDIAHNVLAKQFEDHSIQRTYLAFVWGMPKP 184

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGIC-----YGDMQVTLDTQKGSNAWVTVGLREGKNR 199
              R    + + K N  K    +         Y  ++V         + +   L  G+  
Sbjct: 185 IHGRIETLIGRSKYNRQKMSAEVGSGKDAITNYKTLEVFKGKTIPDISLIECRLETGRTH 244

Query: 200 EIKKVFEFFNWKVN 213
           +I+         + 
Sbjct: 245 QIRVHLAHQGNPIL 258


>gi|291296964|ref|YP_003508362.1| 30S ribosomal protein S4 [Meiothermus ruber DSM 1279]
 gi|290471923|gb|ADD29342.1| ribosomal protein S4 [Meiothermus ruber DSM 1279]
          Length = 205

 Score = 56.0 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIAS RR+  + +    + VNG  +      V   D I+V
Sbjct: 96  RLDNVVFRMGIASTRRQARQFVRHGHILVNGKRVNIPGYRVRPGDEIKV 144


>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 = 56.0 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 29/240 (12%), Positives = 68/240 (28%), Gaps = 31/240 (12%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVN---------- 53
           N V ++   +R+ +VIA      SR  ++  I   +V V+G ++++  +           
Sbjct: 9   NTVNDSQLGKRLDQVIAELYPDYSRTRIKDWILAGKVAVDGEIIDKPRIKMMGGEQLVIN 68

Query: 54  VMSTDHIEVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
               D +  +   +       +   + +      +V   +     + +   L        
Sbjct: 69  AEIEDEVRWEAQDIPLDIVYEDDDIIVINKPRDFVVHPGAGTPDGTVLNALLWHCPSLAE 128

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------- 155
             R   V RLD +T GL+++         L     +                        
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVQAQTRLVRALQKRNITREYEAIAMGKMTGGGTVEKA 188

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR--EGKNREIKKVFEFFNWKVN 213
              +  K+  +                +       + LR   G+  +I+    +    + 
Sbjct: 189 IGRHSTKRTCMAVHELGKPAITHYRVAEHFREHTRIVLRLETGRTHQIRVHMSYLTHPLV 248


>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 = 56.0 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 29/245 (11%), Positives = 66/245 (26%), Gaps = 41/245 (16%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V +   P R+ K +      A+R +++       + +N   ++     V   D + V   
Sbjct: 22  VDKGQQPLRIDKYLMNFVENATRNKIQSAAKDGCIFINNSPVKS-NYKVKPNDFVTVKFK 80

Query: 66  P---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
                           +   +   L +      +V         + +   +    +    
Sbjct: 81  HPPHENLLIAEDIPIDVVYEDDDLLVVNKPAGMVVHPGHGNYSGTLINALIFHFENLPNN 140

Query: 107 ---RVISVGRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVYRVRFH 150
              R   V R+D +T GLL++         L                    +        
Sbjct: 141 SSDRPGLVHRIDKDTSGLLVVAKTEQAMAHLSNQFAKKTSEREYVALVWGNMTEDEGIIE 200

Query: 151 GQVDQDKLNLLKKGIVIQGI--CYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
           G + +   N L+  + +               +  + G    V+  L  G+  +I+   +
Sbjct: 201 GNIGRHPKNRLQNTVYLDDEADKGKPAITHYKVIERLGYVTLVSCKLETGRTHQIRVHMK 260

Query: 207 FFNWK 211
                
Sbjct: 261 HIGHT 265


>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 = 56.0 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 31/269 (11%), Positives = 66/269 (24%), Gaps = 42/269 (15%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +  +  RV K +    + +SR  +++      +  NG  ++  +  V   D + V  
Sbjct: 34  VVDKGQSQVRVDKYLFERLVNSSRNRIQKAADAGLIMANGKPVKS-SYKVKPCDVLTVMM 92

Query: 63  -----DGVPLR-------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                D   +          E   L + +KP GLV      +   T+ + +         
Sbjct: 93  DRPRYDNDIIPEDIPLDIVYEDNDLMVVNKPAGLVVHPGCGNYHGTLVNAIAWHLKDNPK 152

Query: 111 VGRLDIN-------------------------TEGLLLLTNDGGLARVLELPSTQWLRVY 145
               D                             GL              +         
Sbjct: 153 YDPNDPQVGLVHRIDKDTSGLLVVAKTPDAKTHLGLQFYNKTTKRKYNALVWGVVENNEG 212

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
            +  +   +      +          +      +  + G    V   L  G+  +I+   
Sbjct: 213 TIEGNIGRNPKDRMQMAVLSDPAQGKHAVTHYRVLERLGYVTLVECVLETGRTHQIRVHM 272

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +     +    R   G   L        +
Sbjct: 273 KHIGHTLFNDERYG-GNEILKGTHFSKYK 300


>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 = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 33/253 (13%), Positives = 57/253 (22%), Gaps = 46/253 (18%)

Query: 7   VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           V      +R+   +       SR    +++    V VNG         V   D I ++  
Sbjct: 9   VPSEAAGERLDAYLGAQDACPSRSACAKLVEAGAVAVNGETCLSKKQVVCEGDRISIELP 68

Query: 64  --GVP-----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI- 109
               P           +R  +   L L  +   +       +  +     +       + 
Sbjct: 69  EVREPGAIVPQAIPLDIRYEDDHLLVLSKQRGLVCHPAHGHEDGTLANALVYHCGIEHLG 128

Query: 110 ---------SVGRLDINTEGLLLLTNDGGLAR------------VLELPSTQWLRVYRVR 148
                     V RLD +T GL+L   D    R               +       V    
Sbjct: 129 TVQGEDRPGIVHRLDRDTSGLMLAAKDDETQRALQNLIRTRTLDRRYITLVHGEIVMDEG 188

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------TQKGSNAWVTVGLREGKNRE 200
                         K  V           T                  V   L  G+  +
Sbjct: 189 TINTGIARSTRDRVKMAVSDDPFARQAITTFQVLERFEPARGDEGYTLVECHLYTGRTHQ 248

Query: 201 IKKVFEFFNWKVN 213
           I+      +  + 
Sbjct: 249 IRVHMRHIHHPLV 261


>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 = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 38/245 (15%), Positives = 66/245 (26%), Gaps = 39/245 (15%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V      +R+ K++AR     SR  +++ I    V+V+G    RA  +V     IEV   
Sbjct: 62  VDSASHGERLDKLLARHFSEFSRSRIQQWIEDGAVRVDGEP-SRAKASVQMGQKIEVQPQ 120

Query: 66  P---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 121 AAPESMAFTAEDVPLDVVYEDDAMLVINKPAGLVVHPAAGNWSGTVLNGLLHRDPSAARL 180

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
            R   V RLD  T GL+++         L                   +      +   I
Sbjct: 181 PRAGIVHRLDKETSGLMVVARTLVAQTDLVRQLAARTVKRTYLALVWGETPDDGTIDAPI 240

Query: 166 VIQ-GICYGDMQVTLDTQKGSNAWVT----------------VGLREGKNREIKKVFEFF 208
                       V  ++ K S                       L  G+  +I+  FE  
Sbjct: 241 GRDPRERTRMAIVHTNSGKPSRTHFETLGTVPLGRGKVSMVMCQLETGRTHQIRVHFESI 300

Query: 209 NWKVN 213
              + 
Sbjct: 301 GHPLV 305


>gi|317056623|ref|YP_004105090.1| hemolysin A [Ruminococcus albus 7]
 gi|315448892|gb|ADU22456.1| hemolysin A [Ruminococcus albus 7]
          Length = 263

 Score = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 4/47 (8%)

Query: 18 KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          K +A+    SR   + MI    V++NG +  + A  V  +D IEVD 
Sbjct: 10 KALAK----SRERAKSMIKSGCVRINGKVCTKPAAEVGDSDLIEVDD 52


>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 = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/245 (15%), Positives = 68/245 (27%), Gaps = 39/245 (15%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V      +R+ K++AR     SR  +++ I    V+V+G +  R    V   + IE+   
Sbjct: 49  VDSASHGERLDKLLARHFSEFSRSRLQQWIESGAVRVDGHV-RRPRDAVQMGNRIEIQPQ 107

Query: 66  P---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   + T L +      +V   +     + +   L         
Sbjct: 108 AAPESSAFSPEDVPLDVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRDPGAALL 167

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL-RVYRVRFHGQVDQDKLNLLKKG 164
            R   V RLD  T GL+++         L         +   +        D+  +    
Sbjct: 168 PRAGIVHRLDKETSGLMVVARSLTAQTDLVRQLQARTVKRTYIALVWGRTYDEGTIDAPI 227

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVT----------------VGLREGKNREIKKVFEFF 208
                       V   + K S                       L  G+  +I+  FE  
Sbjct: 228 GRDPRERTRMAVVHTASGKPSRTHFRTLATVPLGRGFVSMVMCKLETGRTHQIRVHFESI 287

Query: 209 NWKVN 213
              + 
Sbjct: 288 GHPLV 292


>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 = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 33/241 (13%), Positives = 75/241 (31%), Gaps = 39/241 (16%)

Query: 9   ENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           +   P RV K +      A+R +V++   Q  + VNG  ++     V + D ++V     
Sbjct: 33  KGQEPLRVDKFLMNFVENATRNKVQQAAKQGNIFVNGEPVKS-NHRVKANDEVKVLFPHP 91

Query: 63  --------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-------F 105
                   + +P  +   + + L +      +V         + +   +           
Sbjct: 92  PHEDLLVPENIPLNIVYEDDSLLVVNKPAGIVVHPGHGNYSGTLINALVYHFENLPNNSS 151

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVYRVRFHGQ 152
           +R   V R+D +T GLL++         L                    +        G 
Sbjct: 152 NRPGLVHRIDKDTSGLLVVAKTEEAMLHLTQQFFNKTTQREYIALVWGNIEEDEGTVCGH 211

Query: 153 VDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           + +   + L+  +   G    +      +  + G    ++  L  G+  +I+   +    
Sbjct: 212 IGRHLKDRLQMDVFPDGSHGKEAVTHYKVLERFGYVTLISCKLETGRTHQIRVHLKHIGH 271

Query: 211 K 211
            
Sbjct: 272 T 272


>gi|253682199|ref|ZP_04862996.1| hemolysin A [Clostridium botulinum D str. 1873]
 gi|253561911|gb|EES91363.1| hemolysin A [Clostridium botulinum D str. 1873]
          Length = 270

 Score = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 20/178 (11%), Positives = 47/178 (26%), Gaps = 3/178 (1%)

Query: 9   ENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            N   +R+  ++       SR + +  I + ++ VNG  +++    V     IE  G  +
Sbjct: 2   SNVKSERLDSLLVEKNLFESREKAKIAIMEGKIFVNGQRVDKCGQKVKVDSDIEFKGEVM 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R    L                              ++  G + + +  +      
Sbjct: 62  PYVSRGGYKLEKSMKSFNIELQGKSCMDIGAST-GGFTDCMLQNGAIKVFSVDVGYGQFA 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
             L     +   +      + F    +      +    +            L ++KG 
Sbjct: 121 WKLRTDPRVVCMERTNARYLTFDDLGEYPDFASIDVSFISLKKII-PAIANLLSEKGE 177


>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 = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 66/244 (27%), Gaps = 40/244 (16%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V       RV K +  R   ASR  +++      V  N   ++  +  V   D I +  
Sbjct: 34  VVDRGQEMMRVDKYLFDRLTNASRNRIQKSAEAGFVMANNKPVKS-SYKVKPMDVITIMM 92

Query: 63  -----------DGVPLRKAERTRLWLY--HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                      + +PL      +  +        +V         + V      +     
Sbjct: 93  DRPRYENEVIPEDIPLNIVYEDKYLMIVNKPAGLVVHPGHGNYHGTLVNAIAWHMKDNPD 152

Query: 110 SV---------GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-- 158
                       R+D +T GLL++         L +         R R       ++   
Sbjct: 153 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGIQFFNKTTKRRYRALVWGIVEQDEG 212

Query: 159 -----------NLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                      + ++  ++      +      +  + G    V   L  G+  +I+   +
Sbjct: 213 TIIGNIGRNPKDRMQMTVLPDDQGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMK 272

Query: 207 FFNW 210
               
Sbjct: 273 HIGH 276


>gi|187934192|ref|YP_001884268.1| S4 domain protein YaaA [Clostridium botulinum B str. Eklund 17B]
 gi|188588344|ref|YP_001919468.1| S4 domain protein YaaA [Clostridium botulinum E3 str. Alaska E43]
 gi|187722345|gb|ACD23566.1| S4 domain protein YaaA [Clostridium botulinum B str. Eklund 17B]
 gi|188498625|gb|ACD51761.1| S4 domain protein YaaA [Clostridium botulinum E3 str. Alaska E43]
          Length = 68

 Score = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 1/63 (1%)

Query: 5  NIVQENFTPQRVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          N ++ N    ++   +  +GIAS   E +  I +  +KVNG +  +    + + D IE +
Sbjct: 2  NKIKINTEIIKLDAFLKWSGIASLGSEAKIYIQEGLIKVNGEICLQRGKKLKAGDIIEFE 61

Query: 64 GVP 66
             
Sbjct: 62 DEK 64


>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 = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 33/267 (12%), Positives = 70/267 (26%), Gaps = 50/267 (18%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVER--------MIAQQRVKVNGILLERAAV 52
           M +K +V ++    R+ K +       R+  +         +I +  VKVNG   +    
Sbjct: 1   MINKYLVDKDHVNIRLDKFM-------RKYSKEESLSIIFSLIRKGFVKVNGKKSKE-NY 52

Query: 53  NVMSTDHIE-------VDGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPD 92
            ++  D I        V    + K              E   +++ +KP  +     D  
Sbjct: 53  RLLLNDEIFFPDAAKIVMDKKIEKEIIDIDLFKNMIVFEDEDVFIINKPNNMPMHKGDKH 112

Query: 93  GRSTVFDNLPSIFSRVISVGRLDINTEG--LLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
                        +  ++            ++   N   L +V E    + +    +   
Sbjct: 113 KFGLSETAKAYYNNPNVNFANRLDLETEGLVIGCKNLQILRKVNEEIRNKKIIKRYIAKV 172

Query: 151 GQVDQDKLNLLKKGIVIQ----------GICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
            Q              I+                    +   K     + + L  G+  +
Sbjct: 173 EQKKLQLDEEFFSDKKIKIFEDRVRVSKDGLEAKTYFKVIEVKDFKVLLDIELITGRKHQ 232

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQLGT 227
           I+         +       YG +Q   
Sbjct: 233 IRVHLSDIGHPIIG--DSKYGNYQKKD 257


>gi|113477291|ref|YP_723352.1| hemolysin A [Trichodesmium erythraeum IMS101]
 gi|110168339|gb|ABG52879.1| hemolysin A [Trichodesmium erythraeum IMS101]
          Length = 284

 Score = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 12/55 (21%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 14 QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
          QR+  ++    + S R++ + +I    V VN  ++++    V    +I+V    L
Sbjct: 4  QRLDVLLVERNLCSSRQKAQVLIRAGEVMVNQQIVDKPGTEVDLESNIKVKQKSL 58


>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 = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 28/238 (11%), Positives = 62/238 (26%), Gaps = 31/238 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +Q     QR+ + +A      SR  ++  I  ++VK+NG + +     V   + IE+   
Sbjct: 10  IQPEQMGQRLDQTLAELFPEYSRSRLKTWIEAKQVKMNGEIADIPRAKVYGGEQIEISVE 69

Query: 66  P--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                          +   +   + +      +V   +     + +   L          
Sbjct: 70  VEDENRFEPQNIPLNIVYEDDDIIVINKPKDLVVHPGAGNPDGTVLNALLYHYPPIAEVP 129

Query: 112 -----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-----------FHGQVDQ 155
                 RLD +T GL+++         L     +                      Q   
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     V            +     +   + + L  G+  +I+         + 
Sbjct: 190 RHATKRTLMAVHPMGKPAVTHYRIMENFRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 247


>gi|11499766|ref|NP_071009.1| hypothetical protein AF2184 [Archaeoglobus fulgidus DSM 4304]
 gi|2648341|gb|AAB89068.1| conserved hypothetical protein [Archaeoglobus fulgidus DSM 4304]
          Length = 208

 Score = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 14/67 (20%), Positives = 25/67 (37%), Gaps = 5/67 (7%)

Query: 14 QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+  ++ R G  S R   +  I +  V V+G  + + +  V     I+V    L+    
Sbjct: 1  MRLDILLVRRGFFSSRSRAKEAIKKGFVLVDGKKVTKPSAEVDFEAEIKV----LQPERP 56

Query: 73 TRLWLYH 79
             W   
Sbjct: 57 RGYWKLK 63


>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 = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 36/263 (13%), Positives = 74/263 (28%), Gaps = 42/263 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           I+      +R+  ++A    + SR +V+R I Q  + VN     + +  +   D I +  
Sbjct: 15  IISPEDVGERLDTLLAHKLESVSRSQVQRAIEQGTILVNDHP-SKPSYKLREGDRILILT 73

Query: 63  -----DGV----------PLRKAERTRLWLYHKPIGLVTTHSDPDGRST-------VFDN 100
                 G            +   +   + +      +V         +          D 
Sbjct: 74  IPRVPQGEVALIPSYVDLRVVYEDDKIIVIDKPAGMVVHPSPGHYDNTLVNALIARYPDL 133

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
           L     R   V RLD +T GL+++  D      L+                    D    
Sbjct: 134 LKQPTDRPGIVHRLDKDTSGLIIVARDLDTLNYLQGQMKARKIFKEYTLLCCGALDPPEG 193

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE-------------GKNREIKKVFEF 207
             +  + + +        +   K +    +  ++              G+  +I+  F  
Sbjct: 194 RIEAPIGRDLRDRTKMSVIAGGKEAVTEYS-TIQSLGKYTLAIARPITGRTHQIRVHFAA 252

Query: 208 FNWKVNRLIRISYGPFQLGTLLA 230
               +       YG  +L  L  
Sbjct: 253 IGHPIAG--DPIYGNCRLEGLNR 273


>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 = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 23/240 (9%), Positives = 59/240 (24%), Gaps = 37/240 (15%)

Query: 10  NFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD----- 63
           +   +R+ K +       SR   +  I +  V VN     +A   +   D + V      
Sbjct: 9   DEQGKRLDKWLTDQSDDWSRSLTQSWIQEGYVTVNDET-SKANYKLKIGDVVRVKVPEVE 67

Query: 64  ---------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
                     + +   ++  + +      +V         + V   +          G  
Sbjct: 68  ELEITAEDLDLDIVYEDQDVIVVNKPAGMVVHPAPGHPSGTLVNGLMYHCQDLSGINGVA 127

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWL---------------------RVYRVRFHGQV 153
                  +     G L       + + L                        +      +
Sbjct: 128 RPGIVHRIDKDTSGLLMVAKHDKAHESLVDQLKNKTTIRQYEALVVGTIPHEKGTVDAPI 187

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +D  +  K  +  +          +  +      V   L  G+  +I+   ++  + + 
Sbjct: 188 GRDPQDRQKMTVTEENARDAVTHFQVIERMNGYTHVLCELETGRTHQIRVHMKYIGYPIV 247


>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 = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 29/244 (11%), Positives = 57/244 (23%), Gaps = 37/244 (15%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V E     R+ + +A      SR  ++++I Q +V +NG         + + D +EV   
Sbjct: 16  VTEKQQGLRLDRGLAEQLPELSRSRLQQLIRQGQVWLNGQPCRDKDRPLQAGDEVEVRIP 75

Query: 63  -------DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                     P+       +   L +      +V         + V   L          
Sbjct: 76  PATPTALQPEPIPLDILYEDDDLLVINKPRGLVVHPAPGHASGTLVHALLAHCPRLSGIN 135

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------------------- 149
           G         L     G L       + Q L+                            
Sbjct: 136 GEQRPGIVHRLDKDTTGALVIAKHDQAHQHLQAQIQAKTARRLYLGVVFGRPAQSQGTVS 195

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                          +             +  + G+   +   L  G+  +I+       
Sbjct: 196 APIGRHPVDRQKMAVLTPGQGRVAVTHWQVLERLGNYTLMQFELETGRTHQIRVHAAHLR 255

Query: 210 WKVN 213
             + 
Sbjct: 256 LPIV 259


>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 = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/247 (10%), Positives = 68/247 (27%), Gaps = 41/247 (16%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V     P R+ K +  R    SR +++  I  Q + VNG +  +A   +   D I++  
Sbjct: 20  TVDPGQKPYRIDKFLIDRLPNTSRNKIQLAIDNQFILVNG-IPTKANYKIRPYDKIQIVL 78

Query: 63  -----DGVPLR--------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                +   +           +   + ++     +V    +    + V   +    +   
Sbjct: 79  PNPPRNNELIPENIPLDIVYEDEALMVVHKPAGMVVHPGYNNWTGTLVNALIYYFDNLPT 138

Query: 110 SVGRLDIN------------------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151
           +   +                     TE  L+          +       +        G
Sbjct: 139 APNNIGRPGLVHRIDKDTSGLLVVAKTEASLIALAKQFYDHSIARTYYALIWGEPETETG 198

Query: 152 QVDQDKLNLLKKGIVI------QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
            +D +    L+   ++      +          +  +    + V   L  G+  +I+   
Sbjct: 199 TIDINLDRSLQDRRIVAPYTNPEKGKRAVTHYQVVERLRYVSLVKCTLETGRTHQIRAHM 258

Query: 206 EFFNWKV 212
           +     +
Sbjct: 259 KHMGHPI 265


>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 = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 28/244 (11%), Positives = 67/244 (27%), Gaps = 38/244 (15%)

Query: 6   IVQENFTPQRVSKVIA--RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           +V  +   +R+   +A   +   +R  ++R+I  Q+++VNG      +  +   + + V+
Sbjct: 18  VVPASAAGERLDVFLAGQDSLELTRSAIQRLIRSQQIRVNGRPAR-PSRRLEPGEEVVVE 76

Query: 64  -------GVP-------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                  GV        +   +   + L      +V         +     L        
Sbjct: 77  LPAPAPSGVVAEPLPLDVVYEDADVVVLNKPRGWVVHPAPGHPQGTLANALLARYPEMEG 136

Query: 110 SVGRLDIN---------------------TEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
             G                             L+    + G+ R           V    
Sbjct: 137 VGGPGRPGIVHRLDRDTTGLLVVARSPLAYRELVRQLKERGVHREYLALVRGSPEVREGT 196

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +  ++  +  ++  G         +  + G    +   L  G+  +I+    F 
Sbjct: 197 VDAPIGRHPVDRKRMAVLPGGGRPARTHFEVVERAGRYTLLRCWLDTGRTHQIRVHLAFI 256

Query: 209 NWKV 212
              V
Sbjct: 257 GLPV 260


>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 = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 28/239 (11%), Positives = 64/239 (26%), Gaps = 41/239 (17%)

Query: 13  PQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------ 63
             R+   +A  GI    SR  ++++I    + VNG  ++ A   + + + + V+      
Sbjct: 32  GTRIDVYLA--GIFDHLSRSFIQKLIGDGYITVNGTRVK-ANYKLKAGELVRVEIPYTEE 88

Query: 64  ----GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                 P+       +R  + +      +V         + V   L          G + 
Sbjct: 89  LEVSAEPIPLEILYEDRDVIVINKPQGMVVHPAPGNYSGTLVNALLWHCKDLSGINGVMR 148

Query: 116 I---------------------NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD 154
                                     L     D  + R         +          + 
Sbjct: 149 PGIVHRLDKDTSGVIMAAKNDETHASLAKQIKDRTVTRRYLALIHGVIPEPAGIIEAPIG 208

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +D  +  K  +  +          +  +     +V   L  G+  +I+    +  + V 
Sbjct: 209 RDPKDRKKMAVTTKNSKPAVTHYKVLERFNKYTFVECKLETGRTHQIRVHMAYLKYPVV 267


>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 = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/232 (15%), Positives = 74/232 (31%), Gaps = 36/232 (15%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----- 68
           R+ KVI       SR +++ ++  + + VN    E+ +  V S D I+V   P++     
Sbjct: 15  RLDKVITEKITDLSRTKIKELVNDKNILVNNK-AEKVSYKVQSGDVIDVTIPPVKPLSLE 73

Query: 69  ---------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------SRVISV 111
                      +   + +      +V   +     + V   L             R   V
Sbjct: 74  AENLHLDIVYEDSDVIVVNKPQGMVVHPSAGHPDHTLVNGLLYHTRDLADSPEGFRPGIV 133

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD------------KLN 159
            R+D +T GLL++  +      LE    + +           + +              N
Sbjct: 134 HRIDKDTSGLLMIAKNDRARESLEKQLAKKINKREYLAIVHGNFEVKNGVINAPIGRNPN 193

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             K+  V           T+  Q  + + V   L  G+  +I+   ++    
Sbjct: 194 SRKQMAVNPKGKAAVTHFTVLEQFKNYSLVKCVLETGRTHQIRVHMKYIGHP 245


>gi|16331005|ref|NP_441733.1| hypothetical protein slr0950 [Synechocystis sp. PCC 6803]
 gi|1653500|dbj|BAA18413.1| slr0950 [Synechocystis sp. PCC 6803]
          Length = 274

 Score = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
              QR+  ++   G+  SR   +R+I    VKVN  L+++    V     +E+   P
Sbjct: 3  KADKQRLDALLVAKGLCESRALAQRLIRAGEVKVNQQLVDKPGTLVTMDVAVELAQRP 60


>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 = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 36/252 (14%), Positives = 83/252 (32%), Gaps = 49/252 (19%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
           + +  R+ + +A     SR + +  I    V V G ++ + +  +   + +EV       
Sbjct: 5   SASGVRLDQALAFEANTSRAKAQEWIEAGLVTVGGKVVTKPSYKLR-GETVEVEPPPPQP 63

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
                + +PL    E   L + +KP G++T  +      T+ + +   F   +S+G  + 
Sbjct: 64  ASVAAEDIPLHILYEDPDLIVINKPAGMITHPAPGVYSGTLVNAILGRFGLDLSLGESEE 123

Query: 117 NTE-------------GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
                           G++   + G    ++        R     F G+    +   L  
Sbjct: 124 EGGLLLQAQKPELIRPGIVHRLDKGTSGVIVVARHEAAHRRLAEAFAGRSVYKRYIALTV 183

Query: 164 GIVIQGICYGDM----------------------QVTLDTQKGSNAWVTVGLREGKNREI 201
           GI  +G+    +                      +  +      +A V+  L  G+  +I
Sbjct: 184 GIPREGLLSAPIGRHPVDRTRMHVGGVAARHAQTEFEVLAVAEPHALVSAILHTGRTHQI 243

Query: 202 KKVFEFFNWKVN 213
           +   +  +  + 
Sbjct: 244 RVHLKHLHAPIL 255


>gi|71894118|ref|YP_278226.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           synoviae 53]
 gi|71850906|gb|AAZ43515.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           synoviae 53]
          Length = 281

 Score = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/235 (13%), Positives = 73/235 (31%), Gaps = 34/235 (14%)

Query: 8   QENFTPQRVSKVIA----RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            +N   + + K+I        IA+   +E++  ++ +KVN   +      V   D +EV 
Sbjct: 7   SKNDENRSLFKLICKYFPNLTIAT---IEKLFRKKEIKVNSKRITDKKFVVSENDLVEVY 63

Query: 64  GV-----------------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           G+                  +   +   L +  K   ++    +      +         
Sbjct: 64  GISESNLNLPQIKKVSFDFQIIYEDANILIIDKKENLVIHGEDNSLDNQVLSYLKHKQID 123

Query: 107 RVISV--GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                  GRLD  T GL++   +    + L   S  + +VY+ +            L   
Sbjct: 124 SFKPSHVGRLDKETSGLIVYAKNYLTLKQLNEKSFNFKKVYQFKSDFLSSSPLELKLY-F 182

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVTVG-------LREGKNREIKKVFEFFNWKV 212
              +       +   +  K +++            +  G+  +I+    + N  +
Sbjct: 183 YKDENNKTKISKTQKENSKLAHSIFYCENNKKFAQIITGRKHQIRLSLAYLNKPI 237


>gi|327401288|ref|YP_004342127.1| RNA-binding S4 domain-containing protein [Archaeoglobus veneficus
          SNP6]
 gi|327316796|gb|AEA47412.1| RNA-binding S4 domain protein [Archaeoglobus veneficus SNP6]
          Length = 218

 Score = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ + +   G  + R++ +  I +  V VNG+ + + +  V     IEV
Sbjct: 1  MRLDQFLVSKGFFTTRQKAKEAIKRGFVFVNGVRVTKPSARVSGDAEIEV 50


>gi|213858018|ref|ZP_03384989.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
          Length = 82

 Score = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 21/82 (25%), Positives = 38/82 (46%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTT 87
           R    R I   RV V+G ++  AA  ++    +  DG PL +    R ++ +KP G V +
Sbjct: 1   RAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGPRYFMLNKPQGYVCS 60

Query: 88  HSDPDGRSTVFDNLPSIFSRVI 109
             DPD  + ++     +  ++ 
Sbjct: 61  TDDPDHPTVLYFLDEPVAWKLH 82


>gi|330955284|gb|EGH55544.1| pseudouridine synthase, Rsu [Pseudomonas syringae Cit 7]
          Length = 132

 Score = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/127 (29%), Positives = 58/127 (45%), Gaps = 3/127 (2%)

Query: 26  ASRREV--ERM-IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPI 82
            +R     + + +A  RV+V+G         V     + +D   L+  +  R ++ HKP 
Sbjct: 6   GTRNHACVDSLALASGRVQVDGQATRDPHHEVREFSCVALDEEILQAGKAARYFMLHKPE 65

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL 142
           G V+  SD    + +          +   GRLD NT GL+L+TNDG  +R L  P T+  
Sbjct: 66  GCVSATSDAQHPTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRRLTQPQTKMP 125

Query: 143 RVYRVRF 149
           +VY V  
Sbjct: 126 KVYYVET 132


>gi|227813198|ref|YP_002813207.1| ribosomal large subunit pseudouridine synthase, RluA family
          [Bacillus anthracis str. CDC 684]
 gi|227007575|gb|ACP17318.1| ribosomal large subunit pseudouridine synthase, RluA family
          [Bacillus anthracis str. CDC 684]
          Length = 88

 Score = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 6/60 (10%)

Query: 6  IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           V E    +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V
Sbjct: 8  TVAEEQKNERIDKFVA--GINNEWSRTQVQQWIKDDVVTVNGKAVK-GNYKVRENDEITV 64


>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 = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 31/245 (12%), Positives = 70/245 (28%), Gaps = 38/245 (15%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            +++E+    R+   I+      SR  ++++I    +KVNG + E+A   +   D IE++
Sbjct: 7   RVLEEDVDN-RLDLYISEQYEELSRSYIQKLIKDHHIKVNGKI-EKAKYMIKLGDEIEIN 64

Query: 64  --------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
                          + +   +   + +      +V         + V   L        
Sbjct: 65  LPQVEEVTIEPENIPLTIVYEDEDVIVVDKPQGMVVHPAPGNYSGTLVNALLFHCKNQLS 124

Query: 106 -----SRVISVGRLDINTEGLLLLTNDG------------GLARVLELPSTQWLRVYRVR 148
                 R   V R+D +T GLL++  +                              +  
Sbjct: 125 DVNGPMRPGIVHRIDKDTSGLLVVAKNNAAHEILAEQFRAHTNTRKYHAIVVGNIREKEA 184

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                         K  V+    +      +        ++   L  G+  +I+    + 
Sbjct: 185 AVDAPIGRHPVDRLKRAVMNDGKHAVTHFKVLEVFRDFTYIEAKLETGRTHQIRVHLSYI 244

Query: 209 NWKVN 213
              + 
Sbjct: 245 GNPLV 249


>gi|13476217|ref|NP_107787.1| hemolysin-like protein [Mesorhizobium loti MAFF303099]
 gi|14026977|dbj|BAB53573.1| hemolysin-like protein [Mesorhizobium loti MAFF303099]
          Length = 254

 Score = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 13/55 (23%), Positives = 25/55 (45%), Gaps = 1/55 (1%)

Query: 11 FTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           T QR+  ++ + G  ASR      + +  V V+G++  +   NV     + +D 
Sbjct: 8  STRQRLDDLLVQRGLFASRSRARDAVERGTVTVDGVMARKPGQNVSPQCLVAIDD 62


>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 = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 34/221 (15%), Positives = 63/221 (28%), Gaps = 30/221 (13%)

Query: 29  REV-ERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT----------RLWL 77
           R+  +  I Q +++V+G  +      + +   +     P  + E             LW 
Sbjct: 14  RQAWQERIEQGQIEVDGKTV-DPTYPLQAGQTLTYWRSPWVEPEVPLQLSVLHRDEDLWA 72

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFS-------RVISVGRLDINTEGLLLLTNDGGL 130
             KP GL           TV + L   +          +  G   +   G   L      
Sbjct: 73  IDKPSGLPVLPGGDFVYHTVLEQLKIQYPQESLFPLHRLGTGTSGLLLLGRSTLGRRELS 132

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GIVIQGICY------GDMQV--TLDT 181
            +  E    +  R            +    + K      G  Y         Q    +  
Sbjct: 133 RQFREHICRKIYRTVIGPCDLPEKFECHQAIGKIPYPQLGYIYAASSHGKPAQSYGRILA 192

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP 222
           +     W+ V +R G+  +I+       + +    R+ YGP
Sbjct: 193 RSPEKTWLEVEIRTGRPHQIRIHLASLGYPLLG-DRL-YGP 231


>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 = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 21/50 (42%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          +R+ + IA  G  SR    R I    V V+G   + A   +     + V+
Sbjct: 15 ERIDRFIAARGGISRGLARRAIEAGGVFVDGRRCKVAGRTLTPGQQVVVN 64


>gi|302039000|ref|YP_003799322.1| hemolysin TlyA-family protein [Candidatus Nitrospira defluvii]
 gi|300607064|emb|CBK43397.1| Hemolysin TlyA-family protein [Candidatus Nitrospira defluvii]
          Length = 251

 Score = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 16/55 (29%), Positives = 34/55 (61%), Gaps = 1/55 (1%)

Query: 11 FTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             +R+ +V+   G +ASR +  R+I    V+V+G+++++AA  ++S   +E+ G
Sbjct: 7  PERERLDRVLVSRGLVASREDAARLILAGLVRVDGVVVDKAAKPILSGAKVELTG 61


>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 = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 80/249 (32%), Gaps = 45/249 (18%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---GV 65
                R+   ++      SR  ++++I Q  + +N  +     + +   D ++V+     
Sbjct: 8   ENQGDRLDIWLSNQLTDISRSRIQKLIEQGNITLNNEVCPNKKIKLKIGDRLQVNIPEPQ 67

Query: 66  PLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------S 106
           PL             E  +L + +K   LV   +      T+   L              
Sbjct: 68  PLELQPEPIPLDILYEDEQLIIINKSANLVVHPAPGHETGTLVHALLYHCSNLAGIGGVQ 127

Query: 107 RVISVGRLDINTEGLLLLTN----DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
           R   V RLD +T G +++         L   ++  + +   +  +      ++D+ N  K
Sbjct: 128 RPGIVHRLDKDTTGAIVVAKTDFAHQNLQFQIKNRTAKREYLGIIYGVLNNEEDENNRDK 187

Query: 163 KGIVIQGICYGDMQ------------------VTLDTQKGSNAWVTVGLREGKNREIKKV 204
             I +    +   +                    +  + G+ + V   L  G+  +I+  
Sbjct: 188 GMINLPIGRHPVDRKRMAVVPREKPGREAVTYWEIIERLGNYSLVKFILETGRTHQIRVH 247

Query: 205 FEFFNWKVN 213
             +F   + 
Sbjct: 248 SSYFGNPIV 256


>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 = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/239 (10%), Positives = 65/239 (27%), Gaps = 36/239 (15%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP---- 66
              +R+ + +      +R EV++ I    V +    +  +  +V   D I          
Sbjct: 12  DEGKRLDQFLKERTGLTRSEVQKWIKAGNVSLLPKKMIHSNYHVSEGDRISFFWEEKKKQ 71

Query: 67  ----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR--- 113
                     +   +   + +  +   +V   +     + V   L     ++ SVG    
Sbjct: 72  ELIGQNIPLDILYEDNDMIVINKRRGVVVHPGAGNTEGTLVNALLFHCGEQLRSVGDPER 131

Query: 114 ------LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD----------- 156
                 LD +T G+++         +L+                    +           
Sbjct: 132 PGIVHRLDKDTSGVMVAAKSERAYGILQKEIASHKAQRCYIALVHGQMEGDTGVIRLPLG 191

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               + +K  ++ +          +       +W+   L  G+  +I+         V 
Sbjct: 192 RSTKDRMKWDVLHETGRPAVTHFHVIEYLPHYSWIECKLETGRTHQIRVHMAHIRHAVV 250


>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 = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 29/217 (13%), Positives = 59/217 (27%), Gaps = 30/217 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--------------LRKAER 72
           SR  ++  I + RV VNG+++ +    V+  +HI +D +               +   + 
Sbjct: 6   SRSRIKEWILEGRVSVNGVIINKPKEKVLGGEHIAIDALIEEENRWEAQDIALDIVYEDE 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-----RVISVGRLDINTEGLLLLTND 127
             L +      +V   +     + +   L          R   V RLD +T GL+++   
Sbjct: 66  DILVINKPRDLVVHPGAGNPDGTVLNALLHHYPQIADVPRAGIVHRLDKDTTGLMVVAKT 125

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQ-----------DKLNLLKKGIVIQGICYGDMQ 176
                 L                                          V          
Sbjct: 126 VPAQTRLVESLQLREITREYEAVAIGTMTAGGTVREPIARHPTKRTHMSVHPMGKPAVTH 185

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             +      +  + + L  G+  +I+      N  + 
Sbjct: 186 YRIMEHFRVHTRLRLRLETGRTHQIRVHMAHINHPLV 222


>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 = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 33/240 (13%), Positives = 66/240 (27%), Gaps = 31/240 (12%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILL----------ERAAVN 53
           N V ++    R+ +VIA      SR  V+  I +  V VNG ++          E   + 
Sbjct: 9   NTVNDSQLGMRLDQVIAELYPDYSRSRVKEWILKNMVSVNGEIVNKPRLKMMGGEELFIK 68

Query: 54  VMSTDHIEVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
               D +      +       +   L +      +V   +    R+ +   L        
Sbjct: 69  AEIEDEVRWVAQDIPLDIVYEDEHILVINKPRDFVVHPGAGTPDRTVLNALLFHCPALAE 128

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------- 155
             R   V RLD +T GL+++         L     +                        
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTIQAQTRLVRALQKRKITREYEAIAMGKMTGGGTVEKP 188

Query: 156 --DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                       V +          +      +  + + L  G+  +I+    + +  + 
Sbjct: 189 IGRHATKRICMAVHELGKPAITHYRVAEHFREHTRLVLRLETGRTHQIRVHMSYMSHPLV 248


>gi|161349358|ref|ZP_02096742.1| ribosomal protein S4 [Coxiella burnetii 'MSU Goat Q177']
 gi|164601574|gb|EDQ95165.1| ribosomal protein S4 [Coxiella burnetii 'MSU Goat Q177']
          Length = 206

 Score = 55.6 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  A+R E  ++I+ + + VNG ++   +  V   D IEV
Sbjct: 97  RLDNVVYRMGFSATRAEARQLISHKAILVNGEVVNIPSYQVKPGDIIEV 145


>gi|149002474|ref|ZP_01827408.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
          pneumoniae SP14-BS69]
 gi|147759411|gb|EDK66403.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
          pneumoniae SP14-BS69]
          Length = 64

 Score = 55.2 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 1/48 (2%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+ K ++     SR      I   +V VNG + ++A   V   D +  
Sbjct: 11 RLDKALSDLTELSRSLANEQIKSGQVLVNGQV-KKAKYTVQEGDVVTY 57


>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 = 55.2 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 29/244 (11%), Positives = 68/244 (27%), Gaps = 41/244 (16%)

Query: 8   QENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
            +   P RV K +      A+R +V++      + VNGI +++    V + D ++V    
Sbjct: 22  SKGQEPLRVDKFLMNFIENATRNKVQQAAKDGNIYVNGIPVKQ-NYKVKAGDEVKVLLAY 80

Query: 63  -------------------DGVPLRKAERTRLWLYHKPIGLV--------TTHSDPDGRS 95
                              D   L   +   + ++                   +    S
Sbjct: 81  PPYENLLTPEDIPLDIVYEDDALLVVNKAAGMVVHPGHGNYSGTLINALVYHFENLPNNS 140

Query: 96  TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS----TQWLRVYRVRFHG 151
           +    L     +  S   +   TE  +   +     +  +          L        G
Sbjct: 141 SDRPGLVHRIDKDTSGLLVVAKTEAAMAYLSRQFFHKTSKREYVAIAWGNLNEEEGTIEG 200

Query: 152 QVDQDKLNLLKKGIVIQG----ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
            + ++  N L+  + +               +  + G    ++  L  G+  +I+   + 
Sbjct: 201 NIGRNPKNRLQNIVYLGDDADQGKPAVTHYKVIERLGYVTLISCQLETGRTHQIRVHLKH 260

Query: 208 FNWK 211
               
Sbjct: 261 IGHT 264


>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 = 55.2 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 33/237 (13%), Positives = 68/237 (28%), Gaps = 38/237 (16%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLR-- 68
           R+ K ++      SR +V++ I    V+VNG+++  + V V   D I     +   L+  
Sbjct: 14  RLDKALSLLLKKVSRNQVQKAIKNYCVQVNGVIISDSDVLVKENDTILFSFKEPEELKIT 73

Query: 69  --------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN--- 117
                     E   L + +K  G+          +T+ + L      +  +G  +     
Sbjct: 74  AANITLDIIYEDDDLIVINKAAGMTVHPGIRHHDNTLVNALLHHTKYLSDIGSAERPGIV 133

Query: 118 -----TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
                    L++        +L     +  +V R                    +     
Sbjct: 134 HRLDKDTTGLMVVAKNNKTHILLANQIKQRQVIRKYKALVWGVINPLEGIIKNNVGRNRN 193

Query: 173 GDMQVTLDTQKGSN----------------AWVTVGLREGKNREIKKVFEFFNWKVN 213
              ++T+    G                  + V   L  G+  +I+         V 
Sbjct: 194 NRKKMTILKYGGKKAVTYYKTLELFYGGTLSMVECKLSTGRTHQIRVQLSNLKHSVV 250


>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 = 55.2 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/241 (11%), Positives = 62/241 (25%), Gaps = 37/241 (15%)

Query: 9   ENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVN----------VMST 57
            +   +R+   + R     SR   +R++A+  V V+G    +A             +   
Sbjct: 6   SDQAGERLDVFLVRQLPTLSRSYAQRLVAEGHVTVDGER-RKANFKLSGGESVACTIPPA 64

Query: 58  DHIEVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
           + +E+    +       +   + +      +V   +     + V   L          G 
Sbjct: 65  EAVEIRAENIPLNVLYEDADIIVINKPRGMVVHPAAGVYTGTLVNALLHHCSDLSGINGD 124

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------------------ 155
           L       L     G +       +  +L         + +                   
Sbjct: 125 LRPGIVHRLDKDTSGVMVAAKNDMAHHFLARQIRDKEARREYRAIVYGNIVERAGVITGD 184

Query: 156 ---DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                 +  K  IV +          +  + G   +V   L  G+  +I+         +
Sbjct: 185 IGRHPTDRKKMAIVRENGKPATTHFEVLERFGDYTFVACRLETGRTHQIRVHMTSIGHPL 244

Query: 213 N 213
            
Sbjct: 245 V 245


>gi|289675786|ref|ZP_06496676.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. syringae FF5]
          Length = 179

 Score = 55.2 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 38/155 (24%), Positives = 72/155 (46%), Gaps = 16/155 (10%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  SD +GR+T+ D +          GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPKLILFNKPFDVLTQFSDEEGRATLKDFIKIPGI--YPAGRLDRDSEGLLLLTNDG 84

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+   ++L  L+ G+ +        +            
Sbjct: 85  QLQSRIADPKHKLAKTYWVQVEGEPSDEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPR 144

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                  +    +W+ + ++EG+NR+++++     
Sbjct: 145 NPPVRFRKSVPTSWLELVIKEGRNRQVRRMTAAVG 179


>gi|313114148|ref|ZP_07799700.1| ribosomal RNA large subunit methyltransferase J [Faecalibacterium
           cf. prausnitzii KLE1255]
 gi|310623557|gb|EFQ06960.1| ribosomal RNA large subunit methyltransferase J [Faecalibacterium
           cf. prausnitzii KLE1255]
          Length = 267

 Score = 55.2 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 21/164 (12%), Positives = 50/164 (30%), Gaps = 2/164 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+ + + + G+  SR   + +I    V VN   +++A   +     +EV G  +    R
Sbjct: 3   IRLDQYLVQHGLTQSRERAKALIMSGIVFVNEQKVDKAGEMIKEDAKVEVRGHDIGYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L         T +                  ++  G + +    +        L  
Sbjct: 63  GGLKLEKAMKCFPLTPNGKVCMDIGAST-GGFTDCMLQNGAVKVYAVDVGYGQLAWSLRT 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
              + + +   +  V+     +Q +   +    +     +   Q
Sbjct: 122 DERVVNMERTNIRNVKPEDLAEQIEFFSVDVSFISLHHIFPVAQ 165


>gi|118579586|ref|YP_900836.1| hemolysin A [Pelobacter propionicus DSM 2379]
 gi|118502296|gb|ABK98778.1| hemolysin A [Pelobacter propionicus DSM 2379]
          Length = 367

 Score = 55.2 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 1/56 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          QR+ K++   G+A SR + + +I   +V V+  + ++A   V     I V G  L 
Sbjct: 5  QRLDKLVLERGLAPSREKAQALIMAGQVIVDDHVADKAGQQVAVDAEIRVRGETLP 60


>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 = 55.2 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 39/249 (15%), Positives = 70/249 (28%), Gaps = 45/249 (18%)

Query: 7   VQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V  N +P R+ K +  R G  SR  V+  I    V VN   ++     +     I +   
Sbjct: 31  VDGNQSPLRIDKFLMDRIGEVSRNRVQNAIKTGSVLVNDQEIK-PNFKIKPGQKITLILP 89

Query: 63  ----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
               D + +           E   L + +KP GLV        + T+ + L         
Sbjct: 90  KSTTDKLRIVPQNIPLNVVYEDEDLLVVNKPPGLVVHPGVGHFKGTLVNALAYHLRLDPN 149

Query: 107 ---------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD- 156
                    RV  V R+D NT GLL++  +      L                   + + 
Sbjct: 150 QISTGNFQERVGLVHRIDKNTSGLLVVAKNEFALSHLAKQFFYHTIERTYNALVWGEPEE 209

Query: 157 --------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                                        +      +  +    + +   L  G+  +I+
Sbjct: 210 DRGTINAHVGRHPRFRKDFTVFPEGDQGKWAVTHYQVLERLYYVSLIKCTLETGRTHQIR 269

Query: 203 KVFEFFNWK 211
              ++    
Sbjct: 270 VHLKYLGHT 278


>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 = 55.2 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 29/246 (11%), Positives = 67/246 (27%), Gaps = 41/246 (16%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           I  +   P R+ K +      A+R +++    +  + VN   ++     V   D I+V  
Sbjct: 22  IADKGQAPLRIDKWLMNKVENATRNKIQAAAKEGNIYVNDQPVKS-NYKVKPLDVIKVLF 80

Query: 65  VP---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                            +   + T L +      +V         + +   +    +   
Sbjct: 81  EHPPFENLLVGEDLPLDIVYEDDTLLVVNKPAGMVVHPGHGNYSGTLINALIYHFDNLPK 140

Query: 110 SV-------GRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVYRVRF 149
           +         R+D +T GLL++         L                    +       
Sbjct: 141 NSSDRPGLVHRIDKDTSGLLVVAKTEHAMAHLSKQFKDKTSEREYVAIVWGNMEEDEGTI 200

Query: 150 HGQVDQDKLNLLKKGIVIQG--ICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
            G + +   N L+  + +               +  +      V+  L  G+  +I+   
Sbjct: 201 EGNIGRHPKNRLQNTVYMDDDADKGKPAVTHYKVLERLTYVTLVSCKLETGRTHQIRVHM 260

Query: 206 EFFNWK 211
           +     
Sbjct: 261 KHIGHT 266


>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 = 55.2 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 40/263 (15%), Positives = 73/263 (27%), Gaps = 39/263 (14%)

Query: 13  PQRVSKVIARA----GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           P R+ K +       G+  R  + + + + ++K+NG   +  +  V + D I +      
Sbjct: 11  PVRLDKYLMEQYPSLGLG-R--LNKALRENKIKLNGKK-QPLSTRVQNGDVIRLFLKDEQ 66

Query: 63  -DGVPLR-----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--VGRL 114
            +  PL        +   L +       V   +       V   L +      +    RL
Sbjct: 67  LEDRPLPSAVFVYEDEDILVVNKPAGIEVDGPAADTLLKRVQTTLAAAGKAGHAVLCHRL 126

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----- 169
           D  T GL+LL  +      L           R              L    +++      
Sbjct: 127 DTGTSGLVLLAKNQATELFLTQAIKARTIEKRYLCVTFGRPQPPAALMHDYLLKDAERGV 186

Query: 170 --ICYGDMQVTLDTQKGSNAW--------VTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
             I         +   G            + V L  G+  +I+         +  L    
Sbjct: 187 VKIITSPASGAKEVITGYETLAVSGRLALLEVELVTGRTHQIRAHLAHIGCPI--LGDSK 244

Query: 220 YGPFQLGTLLAGSTREVSKKILR 242
           YG       L    + +    LR
Sbjct: 245 YGNNAANRELHFKYQALCAWELR 267


>gi|255655213|ref|ZP_05400622.1| putative RNA methyltransferase [Clostridium difficile QCD-23m63]
 gi|296451198|ref|ZP_06892939.1| hemolysin A [Clostridium difficile NAP08]
 gi|296880450|ref|ZP_06904412.1| hemolysin A [Clostridium difficile NAP07]
 gi|296260019|gb|EFH06873.1| hemolysin A [Clostridium difficile NAP08]
 gi|296428404|gb|EFH14289.1| hemolysin A [Clostridium difficile NAP07]
          Length = 270

 Score = 55.2 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 22/177 (12%), Positives = 48/177 (27%), Gaps = 2/177 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  ++   G   SR   ++ I    V V+    ++A   V    +IEV G P+    R 
Sbjct: 4   RIDLLLVEQGHFESRERAKKAIMAGLVFVDNQRCDKAGTEVKEDCNIEVKGNPIPYVSRG 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L         T                    ++  G + + +  +        L + 
Sbjct: 64  GLKLEKAMKNFDLTIDGKVCMDIGAST-GGFTDCMLKNGAIKVFSIDVGYGQLAWKLRQD 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             +   +   +  V             +    +   +     +  +       A + 
Sbjct: 123 DRVVCMERTNIRNVTIEDTKQFADFASIDVSFISLKLVLPKAKELVRHDGEIVALIK 179


>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 = 55.2 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 68/244 (27%), Gaps = 37/244 (15%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           I   +   +R+   + R     SR   +R+I ++RV V+G    +A   +   + +  D 
Sbjct: 4   IFSADCAGERLDVFLVRKMPDLSRSYAQRLIEEKRVTVDG-TPRKANYKLRGGECVACDL 62

Query: 65  VPLR--------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
            P+                 +   + +      +V   +   G + V   L         
Sbjct: 63  PPVEEVSVRAENIPLDILYEDADIIVVNKPRGMVVHPAAGISGGTLVNALLYHCRDLSGI 122

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------------- 155
            G L       L     G +A      + + L     +   + +                
Sbjct: 123 NGALRPGIVHRLDKDTSGVMAAAKNDAAHRSLAEQIQKKEARREYRAIVYGNIAERAGII 182

Query: 156 ------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                    +  +  IV +   +      +  + G   +V   L  G+  +I+       
Sbjct: 183 TGDIGRHPTDRKRMAIVRENGKHATTHFEVLERFGGYTFVACRLETGRTHQIRVHMTSIG 242

Query: 210 WKVN 213
             + 
Sbjct: 243 HPLV 246


>gi|225567966|ref|ZP_03776991.1| hypothetical protein CLOHYLEM_04039 [Clostridium hylemonae DSM
           15053]
 gi|225163254|gb|EEG75873.1| hypothetical protein CLOHYLEM_04039 [Clostridium hylemonae DSM
           15053]
          Length = 251

 Score = 55.2 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 15/58 (25%), Positives = 27/58 (46%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           ++      R+  V++ A   SR ++   I   +V VNG L+     ++  +D I V G
Sbjct: 168 MKGTVPSVRLDTVLSVAWPLSRSKLTAYIEGGKVFVNGKLITSNGYHLKESDRISVRG 225


>gi|291528977|emb|CBK94563.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           rectale M104/1]
          Length = 312

 Score = 55.2 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 33/249 (13%), Positives = 76/249 (30%), Gaps = 38/249 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +D   VQ     +R+ K ++      SR   +R++ + ++ VN    ++A   + + D +
Sbjct: 3   RDTFEVQSEQEGERLDKYLSSIYPDISRSFFQRILKENQILVNDKP-QKANYRLKTDDIV 61

Query: 61  EV------------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           +V              +PL     +   L +      +V   +     + V   +     
Sbjct: 62  DVTIPDAVQTPILPQDIPLDILYEDDDVLVVNKPKGMVVHPSAGHYSDTLVNAIMYHCKD 121

Query: 107 ---------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR-----------VYR 146
                    R   V R+D++T G L++  +      +                    V  
Sbjct: 122 SLSGINGEIRPGIVHRIDMDTTGSLIVCKNDESHIKISEQIKHHSCNRIYVGIVCGNVKN 181

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                +    +    +K + I             +  + G   ++   L  G+  +I+  
Sbjct: 182 DEGTIEGAIGRNPNDRKKMAINEKNGKPAVTHYKVLERFGDYTYMQFKLETGRTHQIRVH 241

Query: 205 FEFFNWKVN 213
               N  + 
Sbjct: 242 MASINHPLL 250


>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 = 55.2 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/251 (14%), Positives = 71/251 (28%), Gaps = 41/251 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIA---RAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M++  I  E   P R+   +A     G+ SR  ++ +I + +V +NG + + A   V   
Sbjct: 1   MREYRITAEEGHP-RIDVFLAGRPEIGL-SRSRIQALIDEGQVTLNGAMPK-ARQAVNPG 57

Query: 58  DHIEV---DGVP-----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           D I V   D  P           +   +   L +  +   +V   +     + V   L  
Sbjct: 58  DVIVVRVPDPEPMELVPEDIPLDIVYEDEDILVVNKQRGLVVHPAAGHWTGTLVHALLDK 117

Query: 104 IFSRVISVGRLDIN---------------------TEGLLLLTNDGGLARVLELPSTQWL 142
           +       G L                           L     D  + RV         
Sbjct: 118 VDDLEGIGGELRPGIVHRLDKDTTGLLVVAKSERAMASLQEQIRDHMVQRVYWALVHGNS 177

Query: 143 RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                R    + +   +  +  +  +          +  +    A +   L  G+  +I+
Sbjct: 178 MPDTGRIEAPIGRHPRDRKRMAVNPKTGRDAVTYFRVLERYRGYALLECRLETGRTHQIR 237

Query: 203 KVFEFFNWKVN 213
               F    V 
Sbjct: 238 VHLSFIGHPVV 248


>gi|171911749|ref|ZP_02927219.1| hemolysin A [Verrucomicrobium spinosum DSM 4136]
          Length = 245

 Score = 55.2 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          QR+  ++   G+  SR + +R+I    V VN + + +A   V     I V
Sbjct: 4  QRLDHLLVARGLCASREQGKRLILAGDVLVNDVPVTKAGQLVPEDSVIRV 53


>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 = 55.2 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/242 (12%), Positives = 64/242 (26%), Gaps = 36/242 (14%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           V E    +R+   +       SR  V+ +I    ++V+    ++ +  + + + I V+  
Sbjct: 9   VDEEMEGERLDAFVTEQLDELSRSLVKTLIENGEIRVDSKQ-QKPSYRLKAGEEIIVEIP 67

Query: 64  ----------GVPLRKAERTRLWLY--HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                      +PL    + +           +          + V   L  +       
Sbjct: 68  AVRELKLKAQDIPLSFIYQDKDIAVIDKPKGMVAHPAHGNWENTLVNALLFHLKDLSGIN 127

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------------- 155
           G L       L     G +       + + L           +                 
Sbjct: 128 GELRPGIVHRLDKDTSGVMVIAKNDMAHRQLAAQIKDHSINREYITLVHGIIKENLGSIE 187

Query: 156 ----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                     KK  VI G         +  + G+   + V L  G+  +I+  F +    
Sbjct: 188 APIGRSKQDRKKMAVIAGGRPAVSNYQVLERLGNYTLLKVKLLTGRTHQIRVHFAYIKHP 247

Query: 212 VN 213
           V 
Sbjct: 248 VV 249


>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 = 55.2 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 46/310 (14%), Positives = 83/310 (26%), Gaps = 52/310 (16%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           + E    +R+ K +A+     SR  +++ I    V+V G  +      V   D IEV   
Sbjct: 38  IPETLHGERLDKALAKLLPDYSRSRLQQWIDAGAVRVGGAAVR-PRAAVCGGDRIEVVPQ 96

Query: 63  --DGVP----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
             D             +   + T L +      +V   +     + +   L         
Sbjct: 97  RADDENAFVAEPIDLDVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRYPQAAGL 156

Query: 107 -RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ------------- 152
            R   V RLD  T GL+++         L                               
Sbjct: 157 PRAGIVHRLDKETSGLMVVARTLPAQTDLVRQLQARTVKRTYLALVWGETPEAGTIDAPI 216

Query: 153 -VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG---LREGKNREIKKVFEFF 208
             D      +       G        TLD      A V++    L  G+  +I+  FE  
Sbjct: 217 GRDPRDRTRMAIIETASGKPARTHFKTLDVVDLGRAQVSLVQCQLETGRTHQIRVHFESE 276

Query: 209 NWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETL 267
              +            LG  +   + R    + ++  L      +A   +   +    + 
Sbjct: 277 GHPL------------LGDPVYTRNFRRGRPQTIKAPLPAPFARQALHAVRLGLVHPASG 324

Query: 268 VRDRPNIISE 277
                +    
Sbjct: 325 HSVHWHAGVP 334


>gi|167766571|ref|ZP_02438624.1| hypothetical protein CLOSS21_01077 [Clostridium sp. SS2/1]
 gi|317498982|ref|ZP_07957264.1| hemolysin TlyA family protein [Lachnospiraceae bacterium 5_1_63FAA]
 gi|167711694|gb|EDS22273.1| hypothetical protein CLOSS21_01077 [Clostridium sp. SS2/1]
 gi|291558607|emb|CBL37407.1| hemolysin TlyA family protein [butyrate-producing bacterium SSC/2]
 gi|316893731|gb|EFV15931.1| hemolysin TlyA family protein [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 273

 Score = 55.2 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/175 (13%), Positives = 50/175 (28%), Gaps = 3/175 (1%)

Query: 12  TPQRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             +R+  ++ + G+AS RE  + +I    V V+G   ++A         I V G  L+  
Sbjct: 2   KKERLDVLLVKKGLASSREKAKAIIMSGIVFVDGQREDKAGSTFDEKQEIIVKGKTLKYV 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            R  L L            D                 ++  G + + +  +     D  L
Sbjct: 62  SRGGLKLEKAMKNFDIVLKDKVCMDVGAST-GGFTDCMLQNGAVKVYSVDVGHGQLDWKL 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
                +   +   +  +      ++     +     I           +    G 
Sbjct: 121 RNDERVVCMERTNMRYMTEDDIDEKASFVSIDVSF-ISLTKILPAVYRILNTGGE 174


>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 = 55.2 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 39/253 (15%), Positives = 82/253 (32%), Gaps = 42/253 (16%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M+  NI   EN+T +RV K +A      SR  +++++    + VN    +  ++ + S D
Sbjct: 1   METYNIEADENWTDKRVDKGLADYFDNYSRSFLKKLLDDGNILVNDKKAK-PSLKIASGD 59

Query: 59  HI----------EVDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            I          E++   +      E   + + +KP G+V   +      T+ + L   F
Sbjct: 60  RIDITIPSIASVEIEPENIPLDIVYEDEDIIIVNKPKGMVVHPAPGHYSGTLVNGLMYHF 119

Query: 106 SRVIS--VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
              +S   G L       + +   G L       +  +L               +     
Sbjct: 120 KDSLSGINGELRPGIVHRIDMDTTGLLVVCKNDAAHNFLSEQLAVHSITRKYYAIC-FNY 178

Query: 164 GIVIQGICYGDM--------QVTLDTQKGSN---------------AWVTVGLREGKNRE 200
               +GI    +        ++ ++ + G N                 +   L  G+  +
Sbjct: 179 FTEDEGIVDLPIGRHPTDRKKMAVNYKNGRNAVTHYKVLKKLKNNFCLIECQLETGRTHQ 238

Query: 201 IKKVFEFFNWKVN 213
           I+    +    + 
Sbjct: 239 IRVHMSYIKHPLL 251


>gi|225619185|ref|YP_002720411.1| hemolysin protein [Brachyspira hyodysenteriae WA1]
 gi|1708222|sp|Q06803|HLYA_TREHY RecName: Full=Hemolysin A
 gi|296626|emb|CAA43858.1| hemolysin [Brachyspira hyodysenteriae]
 gi|225214004|gb|ACN82738.1| hemolysin protein [Brachyspira hyodysenteriae WA1]
          Length = 240

 Score = 55.2 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ + +   G   SR + + +I    V VNG+ +   A  +  TD+IEV
Sbjct: 1  MRLDEYVHSEGYTESRSKAQDIILAGCVFVNGVKVTSKAHKIKDTDNIEV 50


>gi|307243246|ref|ZP_07525417.1| ribosomal RNA large subunit methyltransferase J [Peptostreptococcus
           stomatis DSM 17678]
 gi|306493374|gb|EFM65356.1| ribosomal RNA large subunit methyltransferase J [Peptostreptococcus
           stomatis DSM 17678]
          Length = 280

 Score = 55.2 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 19/162 (11%), Positives = 44/162 (27%), Gaps = 2/162 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  ++   G   SR +  R I    V V+   +++    V     I V G PL    R 
Sbjct: 4   RIDVLLVDMGFFPSREQARRTIMAGNVFVDNQRVDKPGTMVKDDSEILVKGKPLAYVSRG 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L         +                    ++  G + + +  +        L + 
Sbjct: 64  GLKLEKAMKNFDISLEGKVCMDIGAST-GGFTDCMLQNGAVKVYSVDVGYGQLAWKLRQD 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
             +   +   +  +      ++     +    +   +     
Sbjct: 123 ERVVCMERQNIRFLEVDALDERPDFASIDVSFISLKLVLPKA 164


>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 = 55.2 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/217 (14%), Positives = 62/217 (28%), Gaps = 31/217 (14%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--------------LRKAER 72
           SR  ++  I Q  ++VNG  ++     V+  D +E+D                 +   + 
Sbjct: 32  SRSRIQNWIKQGALRVNGKQVK-PKEKVIEGDQVELDVELEAQGDWEAQPIALDVVFEDE 90

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGRLDINTEGLLLLTND 127
             L +  +   +V   +     + V   L          R   V RLD +T GL+++   
Sbjct: 91  HLLVINKQADFVVHPAAGHSDGTVVNAVLHHCPALSELPRAGIVHRLDKDTTGLMVIAKT 150

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVD-----------QDKLNLLKKGIVIQGICYGDMQ 176
                 L                   +                  +K  V +G       
Sbjct: 151 LIAHNSLVEQLQAREMGREYECVVYGELTGGGVVEAAIGRHPQNRQKMAVTRGGKDAVTH 210

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             L  +      + + L  G+  +I+      +  + 
Sbjct: 211 YRLIRRWRGFTHLRLKLETGRTHQIRVHMAHIHHSIL 247


>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 = 55.2 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 30/238 (12%), Positives = 60/238 (25%), Gaps = 31/238 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           VQ +   QR+ + +A      SR  ++  I    V+VNG +       V+  + IE+   
Sbjct: 10  VQSHQMGQRLDQTLAELFPDYSRSRLKTWIEGNLVRVNGNIQNIPRTKVLGGEQIEIRAE 69

Query: 66  P--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                          +   +   L L      +V   +     + +   L          
Sbjct: 70  VEEETHYEPENLPLDIVYEDDHILVLNKPKNFVVHPGAGNPRGTVLNALLYHYPQIAEVP 129

Query: 112 -----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----------VDQ 155
                 RLD +T GL+++         L     +                          
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTQLVRDLQKRKITREYEAVAFGVMTKGGKVDEPMA 189

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     V            +     +   + + L  G+  +I+         + 
Sbjct: 190 RHPTKRTAMAVHPMGKPAVTHYRIMEHFRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 247


>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 = 55.2 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 29/230 (12%), Positives = 63/230 (27%), Gaps = 31/230 (13%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+ + +A+     SR  ++  I    VKVNG ++ +A   V   + IEV           
Sbjct: 19  RLDQALAQLFPYYSRSRLKVWIESDLVKVNGNIVNKAREKVFGGELIEVQAEIEEEVRFE 78

Query: 67  -------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-----GRL 114
                  +   +   L +      +V   +     + +   L                RL
Sbjct: 79  PQDIPLNIVYEDDDILVINKPKDLVVHPGAGNPDGTVLNALLHYYPPIAEVPRAGIVHRL 138

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVY-----------RVRFHGQVDQDKLNLLKK 163
           D +T GL+++  +      L     +                +     +           
Sbjct: 139 DKDTTGLMVVAKNIPAQTHLVTALQKRRITREYEAVTSGVMTQGGKVDEPMARHPTKRTA 198

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             V            +  +  +   + + L  G+  +I+         + 
Sbjct: 199 MAVHPMGKPAVTHYRIMERFRNYTRLRLRLETGRTHQIRVHMTHIAHPLL 248


>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 = 55.2 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/253 (13%), Positives = 62/253 (24%), Gaps = 47/253 (18%)

Query: 6   IVQENFTPQRVSKVIARA--------GIA---SRREVERMIAQQRVKVNGILLERAAVNV 54
            V      QR+ + +  A        G     SR +V+R I      V G         V
Sbjct: 17  TVAPEHAGQRLDRFLGDAMAEQRERDGHGDAVSREKVKRAIRDGAATVQGRACTVPNTRV 76

Query: 55  MSTDHIEV------------DG--------VPLRKAERTRLWLYHKPIGLVTTHSDPDGR 94
                + +            DG          +   ++      H               
Sbjct: 77  EPGQTVTLTLAVPAAKVTPEDGDLAVLYRDAAIAVLDKPAGLTVHPCPSCPEGTLVHRLV 136

Query: 95  STVFDNLPSIFSRVISVGRLDINTEGLLLLTND------------GGLARVLELPSTQWL 142
               +       R   V R+D +T GLLL+                       L     +
Sbjct: 137 RHFPELAAQEGFRPGIVHRIDKDTSGLLLVALTEAVRLELSRAFAERQVHKEYLALVHGV 196

Query: 143 RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----DTQKGSNAWVTVGLREGKN 198
              +      + +  L+ +K  +V +       +           G  A V V +  G+ 
Sbjct: 197 PKAQGELEAPIGRHPLHKVKMAVVPENRGGKPARSAWRVLLADPDGRFALVAVRIFTGRT 256

Query: 199 REIKKVFEFFNWK 211
            +I+         
Sbjct: 257 HQIRVHMAHLGHP 269


>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 = 55.2 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/241 (11%), Positives = 64/241 (26%), Gaps = 45/241 (18%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--------------VMST--- 57
           R+ K +A A   SR  V+ ++    V V+G      +                V      
Sbjct: 24  RLDKALAEASGLSRERVKALMQGGAVLVDGDPATNPSAKGSEGTPYTITLPPTVDPEAQP 83

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG----- 112
             I++D   +   +   L +      +V   +     + V   L     ++  +      
Sbjct: 84  QDIKLD---VVFEDEHLLVVNKPAGMVVHPAAGNPDGTLVNALLHHCRGQLSGINGVARP 140

Query: 113 -----------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
                            + D   EGL     +  + R                  G++ +
Sbjct: 141 GIVHRIDKDTSGLLVVAKTDNAHEGLAAQFAEHTINRRYLALCAGHPNPAEGTIEGRIGR 200

Query: 156 DKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            + +  K   + +      +         +    A +   L  G+  +++   +     +
Sbjct: 201 SERDRKKMAPLPEDSSRGKHAVTHYKTLRRLRDCALIECRLETGRTHQVRVHCQSIGHPL 260

Query: 213 N 213
            
Sbjct: 261 L 261


>gi|162448525|ref|YP_001610892.1| hypothetical protein sce0255 [Sorangium cellulosum 'So ce 56']
 gi|161159107|emb|CAN90412.1| Hypothetical protein sce0255 [Sorangium cellulosum 'So ce 56']
          Length = 753

 Score = 55.2 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 16/125 (12%), Positives = 27/125 (21%), Gaps = 10/125 (8%)

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           +++R+   P     A  +            R         PD   R  +      G   +
Sbjct: 118 RVVRDYRAPRPERPAAASGGPRPDRGPRPDRGPRPDRGPRPDRGPRPDRGPRPDRGPRPE 177

Query: 299 KKLAT----------PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           +                 R       W  +G          +     R        R  R
Sbjct: 178 QGPGAAQVAGAEQGARPDRGPRPDRPWSDRGPRPDRGPRPDRGPRPDRGPRPERGPRPDR 237

Query: 349 RTSAK 353
             SA+
Sbjct: 238 GFSAR 242



 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 12/109 (11%), Positives = 22/109 (20%), Gaps = 9/109 (8%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                 +   P  ++  +VRD      E P   +   +           +    P   R 
Sbjct: 102 PPPTTEDAAPPPAAAPRVVRDYRAPRPERPAAASGGPRPDRGPRPDRGPRPDRGPRPDRG 161

Query: 310 LASNVWMAKGIHSSFLSDSGQRE---------ENHRRSPSFPSKRSLRR 349
              +               G  +          +    P  P      R
Sbjct: 162 PRPDRGPRPDRGPRPEQGPGAAQVAGAEQGARPDRGPRPDRPWSDRGPR 210



 Score = 42.1 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 11/109 (10%), Positives = 22/109 (20%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P    +A               R RP +    P          +    + +  +   P 
Sbjct: 70  APRPSSKAAAKEPQGSLLDVIAPRKRPALADAPPPTTEDAAPPPAAAPRVVRDYRAPRPE 129

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                +      +G          +     R        R  R    ++
Sbjct: 130 RPAAASGGPRPDRGPRPDRGPRPDRGPRPDRGPRPDRGPRPDRGPRPEQ 178



 Score = 40.9 bits (94), Expect = 0.26,   Method: Composition-based stats.
 Identities = 10/103 (9%), Positives = 16/103 (15%), Gaps = 3/103 (2%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P    E      A         R              R  +      G     +   P 
Sbjct: 101 APPPTTEDAAPPPAAAPRVVRDYRAPRPERPAAASGGPRPDRGPRPDRGPRPD-RGPRPD 159

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
             R    +               G  +       + P +    
Sbjct: 160 --RGPRPDRGPRPDRGPRPEQGPGAAQVAGAEQGARPDRGPRP 200



 Score = 40.5 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 9/113 (7%), Positives = 21/113 (18%), Gaps = 5/113 (4%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +            V       +            +  P    R+ ++             
Sbjct: 76  KAAAKEPQGSLLDVIAPRKRPALADAPPPTTEDAAPPPAAAPRVVRDYRAPRPERPAAAS 135

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR-RSPSFPSKRSLRRTSAK 353
             P   R    +    +G          +     R   P    +      +A+
Sbjct: 136 GGPRPDRGPRPD----RGPRPDRGPRPDRGPRPDRGPRPDRGPRPEQGPGAAQ 184


>gi|313896630|ref|ZP_07830179.1| ribosomal RNA large subunit methyltransferase J [Selenomonas sp.
          oral taxon 137 str. F0430]
 gi|312974815|gb|EFR40281.1| ribosomal RNA large subunit methyltransferase J [Selenomonas sp.
          oral taxon 137 str. F0430]
          Length = 268

 Score = 55.2 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 14/59 (23%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
            +R+  ++   G+A SR   +R+I   +V V+   +++A   V +   + V G  L  
Sbjct: 2  KKERLDLLLVAQGLAPSRERAKRLIMAGQVLVDERRVDKAGTTVDADASLRVTGEDLPY 60


>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 = 55.2 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 32/245 (13%), Positives = 68/245 (27%), Gaps = 37/245 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++  +V E     R+ KVIA      SR +++ ++  + + VN    E+ +  V + D I
Sbjct: 3   ENYQLVIEKEKG-RLDKVIAEKIKDLSRTKIKELVNDKNILVNNK-AEKVSYKVQAGDLI 60

Query: 61  EVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           ++   P              +   +   + +      +V   +     + V   L     
Sbjct: 61  DITVPPAKPLSLEAQNLNLDIVYEDADVIVVNKPQGMVVHPSAGHPDHTLVNGLLYHTHK 120

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ----------- 155
              S           +     G L       + + L         + +            
Sbjct: 121 LADSPEGFRPGIVHRIDKDTSGLLMVAKNDKARESLEKQLAEKINKREYLAIVHGNFETK 180

Query: 156 ---------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                       N  K+  V           T+  Q    + V   L  G+  +I+   +
Sbjct: 181 NGVIDAPIGRNPNNRKQMAVNPKGKAAVTHFTVLEQFKDYSLVKCVLETGRTHQIRVHMK 240

Query: 207 FFNWK 211
           +    
Sbjct: 241 YIGHP 245


>gi|254424480|ref|ZP_05038198.1| hemolysin A [Synechococcus sp. PCC 7335]
 gi|196191969|gb|EDX86933.1| hemolysin A [Synechococcus sp. PCC 7335]
          Length = 283

 Score = 55.2 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 28/54 (51%), Gaps = 1/54 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
          QR+  ++   G+  SR++ +R+I    VK+   ++++    V +   IE+   P
Sbjct: 17 QRIDILLVEQGLCPSRQQAQRLIRAGEVKIAQQIIDKPGTLVATDAVIELKQKP 70


>gi|29653614|ref|NP_819306.1| 30S ribosomal protein S4 [Coxiella burnetii RSA 493]
 gi|154706831|ref|YP_001425158.1| 30S ribosomal protein S4 [Coxiella burnetii Dugway 5J108-111]
 gi|161831288|ref|YP_001596209.1| 30S ribosomal protein S4 [Coxiella burnetii RSA 331]
 gi|212213226|ref|YP_002304162.1| 30S ribosomal protein S4 [Coxiella burnetii CbuG_Q212]
 gi|41017834|sp|Q83EQ3|RS4_COXBU RecName: Full=30S ribosomal protein S4
 gi|189045376|sp|A9KD07|RS4_COXBN RecName: Full=30S ribosomal protein S4
 gi|189045377|sp|A9NAZ4|RS4_COXBR RecName: Full=30S ribosomal protein S4
 gi|226697830|sp|B6J239|RS4_COXB2 RecName: Full=30S ribosomal protein S4
 gi|29540876|gb|AAO89820.1| SSU ribosomal protein S4P [Coxiella burnetii RSA 493]
 gi|154356117|gb|ABS77579.1| SSU ribosomal protein S4P [Coxiella burnetii Dugway 5J108-111]
 gi|161763155|gb|ABX78797.1| ribosomal protein S4 [Coxiella burnetii RSA 331]
 gi|212011636|gb|ACJ19017.1| SSU ribosomal protein S4P [Coxiella burnetii CbuG_Q212]
          Length = 206

 Score = 55.2 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R E  ++I+ + + VNG ++   +  V   D IEV
Sbjct: 97  RLDNVVYRMGFAATRAEARQLISHKAILVNGEVVNIPSYQVKPGDIIEV 145


>gi|320451274|ref|YP_004203370.1| 30S ribosomal protein S4 [Thermus scotoductus SA-01]
 gi|320151443|gb|ADW22821.1| 30S ribosomal protein S4 [Thermus scotoductus SA-01]
          Length = 209

 Score = 55.2 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SRR+  +M+    + VNG  ++  A  V   D I +
Sbjct: 100 RLDNVVYRLGFAASRRQARQMVRHGHITVNGRRVDLPAYRVKPGDEIAI 148


>gi|212218098|ref|YP_002304885.1| 30S ribosomal protein S4 [Coxiella burnetii CbuK_Q154]
 gi|226697829|sp|B6J5F6|RS4_COXB1 RecName: Full=30S ribosomal protein S4
 gi|212012360|gb|ACJ19740.1| SSU ribosomal protein S4P [Coxiella burnetii CbuK_Q154]
          Length = 206

 Score = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  A+R E  ++I+ + + VNG ++   +  V   D IEV
Sbjct: 97  RLDNVVYRMGFSATRAEARQLISHKAILVNGEVVNIPSYQVKPGDIIEV 145


>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 = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 32/241 (13%), Positives = 65/241 (26%), Gaps = 43/241 (17%)

Query: 13  PQRVSKVI-ARAGIASRREVERMIAQQRVKVNGIL--LERAAVNVMSTDHIEVD---GVP 66
           P R+ + + ++    SR  +++ I    V+VNGI    +     +   D +E+      P
Sbjct: 27  PMRLDRWLVSQRSEQSRSHIQKFIEAGLVRVNGITGRAKTP---LRQGDEVELWMPPPEP 83

Query: 67  LRK------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--------FS 106
           L               +R  + +       V         + V   L             
Sbjct: 84  LPYLQPEEMPLDVLFEDRHLIVINKPAGLTVHPAPGNRNGTLVNGLLHHCSDLPGISGKL 143

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD------------ 154
           R   V RLD +T G +++         L+    + +                        
Sbjct: 144 RPGIVHRLDKDTTGCIVIAKSQEALVKLQEQIQKRIASRNYLAVVHGAPSGDQGTIVAAI 203

Query: 155 --QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                       +   G  +     TL  +    + +   L  G+  +I+         +
Sbjct: 204 GRHPVDRKKYAVVTEDGGRHACTHWTLVERLADYSLLRFKLDTGRTHQIRVHCAHIGHPI 263

Query: 213 N 213
            
Sbjct: 264 V 264


>gi|158424732|ref|YP_001526024.1| hemolysin A [Azorhizobium caulinodans ORS 571]
 gi|158331621|dbj|BAF89106.1| hemolysin A [Azorhizobium caulinodans ORS 571]
          Length = 274

 Score = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 12/48 (25%), Positives = 22/48 (45%), Gaps = 1/48 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
          R+ K++   G+  SR   +  +   +V VNG + ++    V     IE
Sbjct: 37 RIDKLLVERGLFDSRARAQAAVLAGQVSVNGAVAKKPGQEVDEDAQIE 84


>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 = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 32/240 (13%), Positives = 67/240 (27%), Gaps = 31/240 (12%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERA----------AVN 53
           N V EN    R+ +VIA+     SR  ++  I    V VNG ++++            + 
Sbjct: 9   NTVGENQLGMRLDQVIAQLYPDYSRSRIKDWILNGMVSVNGDVVKKPREKMMGGEELFIQ 68

Query: 54  VMSTDHIEVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
               D +      +       +   L +      +V   +     + +   L        
Sbjct: 69  AEIEDEVRWVAQDIPLDIVYEDDDILVINKPRDFVVHPGAGTPDGTVLNALLHHCPSLAE 128

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------- 155
             R   V RLD +T GL+++         L     +                        
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTIQAQTRLVRALQKRKITREYEALAIGQMTGGGTIEKP 188

Query: 156 --DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                       V +          +  +   +  + + L  G+  +I+    + +  + 
Sbjct: 189 IGRHSTKRICMAVHEMGKDAITHYRVAERFREHTRIVLRLETGRTHQIRVHMSYMSHPLI 248


>gi|20090852|ref|NP_616927.1| FtsJ-like methyltransferase [Methanosarcina acetivorans C2A]
 gi|19915923|gb|AAM05407.1| FtsJ-like methyltransferase [Methanosarcina acetivorans C2A]
          Length = 226

 Score = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   +   G   SR   +  I    VKVNGI + + + +V   D IEV
Sbjct: 1  MRLDAYLVEMGHFKSRGRAKTAILDGNVKVNGITVTKVSRDVSIDDVIEV 50


>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 = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 28/241 (11%), Positives = 66/241 (27%), Gaps = 41/241 (17%)

Query: 11  FTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
               R+ K +  R    SR +++       V VNG  ++     +   D + +       
Sbjct: 27  QESVRIDKYLLDRMPNTSRNKIQSAAKSGSVVVNGSSVKS-NYKIKPKDEVTIVLPYPVR 85

Query: 63  ----------------DGVPLRKAERTRLWLYHKPIGLVTT--HSDPDGRSTVFDNLPSI 104
                           D   +   +   + ++        T  ++       + +     
Sbjct: 86  ELELIAQDIPIDIVYEDDEVIVVNKPPNMVVHPGYGNYTGTLVNALVYHFDNLPERKLDY 145

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL---- 160
           F R   V RLD +T G++++         L           R +     D ++       
Sbjct: 146 FGRPGLVHRLDKHTTGVMVVAKTEDALTNLAKQFYDRTTERRYQALVWGDVEEDMRIEGN 205

Query: 161 ----------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                     +          +    V +  + G    +   L  G+  +I+   ++  +
Sbjct: 206 LGRSLNNRKVMTVFPEGDYGKHAVTHVKVLKRYGLVTLIECKLETGRTHQIRTHLKWKGY 265

Query: 211 K 211
            
Sbjct: 266 P 266


>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 = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 30/250 (12%), Positives = 66/250 (26%), Gaps = 38/250 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGI--------------- 45
           M  ++         R+   + +    +R ++ ++I Q  V V+G                
Sbjct: 1   MTQEDSTFTTDEAVRLDVFLTQQLGQTRNQITQLIEQNCVSVDGKETAKSGLKLKPSQTV 60

Query: 46  ----------LLERAAVNVM---STDHIEVDGVP----LRKAERTRL-----WLYHKPIG 83
                       +    +V      D I V   P    +  A   +      WL HK I 
Sbjct: 61  IIRFPEQKSTPAQEIDFDVDILFEDDDILVINKPSSLTVHPAPSVKEPTLVDWLKHKGIA 120

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
           L T   +         +  +  + VI+          L L     G   +  +       
Sbjct: 121 LSTLSGEERHGIVHRLDRGTSGAMVIAKNNEAHEALSLQLQDKTMGRYYLAIITPAMKET 180

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           +  +        +    +      +       ++     +     +   L  G+  +I+ 
Sbjct: 181 ITVIDRPIGRSANNRLKMAISESGKNAKTAFAKLLPSHDETEE-LIACKLYTGRTHQIRV 239

Query: 204 VFEFFNWKVN 213
             E  +  + 
Sbjct: 240 HLESISRHII 249


>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 = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/236 (14%), Positives = 67/236 (28%), Gaps = 38/236 (16%)

Query: 14  QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------- 63
           QRV  V+AR     SR  +   I    V +N +  +      +  D I ++         
Sbjct: 18  QRVDSVLARLLPEYSRSLICNWIKTGAVTLNNLPCK-PKDKALGGDLITINVNHTIVNTD 76

Query: 64  -------GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI----- 109
                   +P++    +   + +      +V   +     + V   L       +     
Sbjct: 77  FNLCKPENIPIQIIYEDSEVIVVNKPAGLVVHPGAGNKEHTLVNALLHHCPELQLLPRAG 136

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR------------VRFHGQVDQDK 157
            + RLD +T GLL++  +      L                                +  
Sbjct: 137 IIHRLDKDTTGLLIVAKNLISHTSLIRQMQNREIKRHYLTLVHGYVISGGTIDTGFGRHP 196

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            N LK  +   G         ++        + V L  G+  +I+    + N  V 
Sbjct: 197 KNRLKMAVTDFGRQA-VTHYNINKHYKDFTLLNVSLMTGRTHQIRVHMNYINHPVV 251


>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 = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/236 (14%), Positives = 67/236 (28%), Gaps = 38/236 (16%)

Query: 14  QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------- 63
           QRV  V+AR     SR  +   I    V +N +  +      +  D I ++         
Sbjct: 18  QRVDSVLARLLPEYSRSLICNWIKTGAVTLNNLPCK-PKDKALGGDLITINVDHTIVNTD 76

Query: 64  -------GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI----- 109
                   +P++    +   + +      +V   +     + V   L       +     
Sbjct: 77  FNYCKPENIPIQIIYEDSEVIVVNKPAGLVVHPGAGNKEHTLVNALLHHCPELQLLPRAG 136

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR------------VRFHGQVDQDK 157
            + RLD +T GLL++  +      L                                +  
Sbjct: 137 IIHRLDKDTTGLLIVAKNLISHTSLIRQMQNREIKRHYLTLVHGYVISGGTIDTGFGRHP 196

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            N LK  +   G         ++        + V L  G+  +I+    + N  V 
Sbjct: 197 KNRLKMAVTDFGRQA-VTHYNINKHYKDFTLLNVSLMTGRTHQIRVHMNYINHPVV 251


>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 = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/236 (14%), Positives = 67/236 (28%), Gaps = 38/236 (16%)

Query: 14  QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------- 63
           QRV  V+AR     SR  +   I    V +N +  +      +  D I ++         
Sbjct: 18  QRVDSVLARLLPEYSRSLICNWIKTGAVTLNNLPCK-PKDKALGGDLITINVDHTIVNTD 76

Query: 64  -------GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI----- 109
                   +P++    +   + +      +V   +     + V   L       +     
Sbjct: 77  FNLCKPENIPIQIIYEDSEVIVVNKPAGLVVHPGAGNKEHTLVNALLHHCPELQLLPRAG 136

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR------------VRFHGQVDQDK 157
            + RLD +T GLL++  +      L                                +  
Sbjct: 137 IIHRLDKDTTGLLIVAKNLISHTSLIRQMQNREIKRHYLTLVHGYVISGGTIDTGFGRHP 196

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            N LK  +   G         ++        + V L  G+  +I+    + N  V 
Sbjct: 197 KNRLKMAVTDFGRQA-VTHYNINKHYKDFTLLNVSLMTGRTHQIRVHMNYINHPVV 251


>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 = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 21/234 (8%), Positives = 65/234 (27%), Gaps = 33/234 (14%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP----- 66
           PQR+ + IA+     SR +++  I + +VKVN  +       ++  + I++  +      
Sbjct: 18  PQRLDQAIAKLLADYSRSQIKGWILEGKVKVNDQVTILPNKKILGGEIIKISVMIEREHE 77

Query: 67  -----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------- 105
                      +   +   + +      +V + +     + +   L              
Sbjct: 78  QYWKAQNIALNIVYEDDDIIVINKPRDMVVHSGAGNLDGTILNALLYYYPAIANVPRAGI 137

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
             R+       +     L                 ++  +     +     ++       
Sbjct: 138 VHRLDKNTTGLMIVGKTLSAQTKLVELLRTRSIIREYEAITIGIINNDGTVEQPIARHAT 197

Query: 165 IVIQGICY---GDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                             ++  +  ++  + + L  G+  +I+    + N  + 
Sbjct: 198 KRTHMTVNPLGKPAITHYSIIERFRAHTRLRLRLETGRTHQIRVHMAYMNHHLV 251


>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 = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/206 (16%), Positives = 64/206 (31%), Gaps = 20/206 (9%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-VDGVPLRKA----------ERTRL 75
           SR+ V++ I +  V++NG+  E     V   D I  VD                 E    
Sbjct: 31  SRKGVKKAIKKGAVRLNGMPAET-GRWVQPGDIITLVDLEETPPKQYEFTLEVVYEDDHF 89

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFD------NLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + +KP G+  + +       +         LP        V RLD+ T GLL++     
Sbjct: 90  AVINKPAGVKVSGNQYRTIVNMLPGNLKASPLPDALKWAKPVHRLDVPTSGLLMVAKTTQ 149

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKGSNA 187
               L     Q           +        ++  I  Q     +  +Q     +  + +
Sbjct: 150 AHIHLGQQLEQKTIKKAYHAIVKGTPAARGHIRTPINGQSAHSEFEVLQTVPSLRNETLS 209

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVN 213
            V +    G+  +++         + 
Sbjct: 210 LVRLSPHTGRTHQLRVHLASLGHPIT 235


>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 = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/237 (14%), Positives = 71/237 (29%), Gaps = 38/237 (16%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ K +A      SR  +++++ +  V VNG    + +  V + D + V+  P  +++  
Sbjct: 45  RLDKALAELVPEFSRSYLQQLLGEGGVLVNGRAAAKPSARVQAGDVLSVELRPTPQSQAF 104

Query: 74  R---------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
           R                 +      +V         + +   L          R   V R
Sbjct: 105 RPEAMALDTVYEDEHLRIVNKPAGLVVHPAPGNWSGTLLNGLLALDPRAGNVPRAGIVHR 164

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------------DKLN 159
           LD +T GL+++  +  +   L           +    G                  D  N
Sbjct: 165 LDKDTSGLMVVARERSVMDALVRMIAAREVSRQYLALGHRAWQGAQTRVVEEAIGRDPRN 224

Query: 160 LLKKGIVIQGICY-GDMQVTLDTQK--GSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            L+   V   +      +  +       +   V   L  G+  +I+    +    + 
Sbjct: 225 RLRMAAVDLAVHAGKPARTDIAVLDTCENGCLVHCTLHTGRTHQIRVHMAWLRHPLV 281


>gi|10835588|pdb|1FJG|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal
           Subunit In Complex With The Antibiotics Streptomycin,
           Spectinomycin, And Paromomycin
 gi|13096397|pdb|1HR0|D Chain D, Crystal Structure Of Initiation Factor If1 Bound To The
           30s Ribosomal Subunit
 gi|14278013|pdb|1GIX|G Chain G, Crystal Structure Of The Ribosome At 5.5 A Resolution.
           This File, 1gix, Contains The 30s Ribosome Subunit,
           Three Trna, And Mrna Molecules. 50s Ribosome Subunit Is
           In The File 1giy
 gi|15826123|pdb|1JGO|G Chain G, The Path Of Messenger Rna Through The Ribosome. This File,
           1jgo, Contains The 30s Ribosome Subunit, Three Trna, And
           Mrna Molecules. 50s Ribosome Subunit Is In The File 1giy
 gi|15826148|pdb|1JGP|G Chain G, The Path Of Messenger Rna Through The Ribosome. This File,
           1jgp, Contains The 30s Ribosome Subunit, Three Trna, And
           Mrna Molecules. 50s Ribosome Subunit Is In The File 1giy
 gi|15826173|pdb|1JGQ|G Chain G, The Path Of Messenger Rna Through The Ribosome. This File,
           1jgq, Contains The 30s Ribosome Subunit, Three Trna, And
           Mrna Molecules. 50s Ribosome Subunit Is In The File 1giy
 gi|28373702|pdb|1ML5|G Chain G, Structure Of The E. Coli Ribosomal Termination Complex
           With Release Factor 2
 gi|110591326|pdb|2F4V|D Chain D, 30s Ribosome + Designer Antibiotic
          Length = 209

 Score = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SRR+  +++    + VNG  ++  +  V   D I V
Sbjct: 100 RLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAV 148


>gi|46199603|ref|YP_005270.1| 30S ribosomal protein S4 [Thermus thermophilus HB27]
 gi|55981634|ref|YP_144931.1| 30S ribosomal protein S4 [Thermus thermophilus HB8]
 gi|7404455|sp|P80373|RS4_THET8 RecName: Full=30S ribosomal protein S4
 gi|50401228|sp|P62664|RS4_THET2 RecName: Full=30S ribosomal protein S4
 gi|10120567|pdb|1FKA|D Chain D, Structure Of Functionally Activated Small Ribosomal
           Subunit At 3.3 A Resolution
 gi|13399795|pdb|1HNW|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal
           Subunit In Complex With Tetracycline
 gi|13399817|pdb|1HNX|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal
           Subunit In Complex With Pactamycin
 gi|13399839|pdb|1HNZ|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal
           Subunit In Complex With Hygromycin B
 gi|14278059|pdb|1IBK|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal
           Subunit In Complex With The Antibiotic Paromomycin
 gi|14278080|pdb|1IBL|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal
           Subunit In Complex With A Messenger Rna Fragment And
           Cognate Transfer Rna Anticodon Stem-Loop Bound At The A
           Site And With The Antibiotic Paromomycin
 gi|14278104|pdb|1IBM|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal
           Subunit In Complex With A Messenger Rna Fragment And
           Cognate Transfer Rna Anticodon Stem-Loop Bound At The A
           Site
 gi|58177403|pdb|1XMO|D Chain D, Crystal Structure Of Mnm5u34t6a37-Trnalysuuu Complexed
           With Aag-Mrna In The Decoding Center
 gi|58177426|pdb|1XMQ|D Chain D, Crystal Structure Of T6a37-Asllysuuu Aaa-Mrna Bound To The
           Decoding Center
 gi|58177467|pdb|1XNQ|D Chain D, Structure Of An Inosine-Adenine Wobble Base Pair Complex
           In The Context Of The Decoding Center
 gi|58177490|pdb|1XNR|D Chain D, Crystal Structure Of An Inosine-Cytosine Wobble Base Pair
           In The Context Of The Decoding Center
 gi|66361057|pdb|1YL4|G Chain G, Crystal Structure Of 70s Ribosome With Thrs Operator And
           Trnas. 30s Subunit. The Coordinates For The 50s Subunit
           Are In The Pdb Entry 1yl3
 gi|88192239|pdb|2B64|D Chain D, 30s Ribosomal Subunit, Trnas, Mrna And Release Factor Rf1
           From A Crystal Structure Of The Whole Ribosomal Complex.
           This File Contains The 30s Subunit, Trnas, Mrna And
           Release Factor Rf1 From A Crystal Structure Of The Whole
           Ribosomal Complex". The Entire Crystal Structure
           Contains One 70s Ribosome, Trnas, Mrna And Release
           Factor Rf1 And Is Described In Remark 400.
 gi|88192302|pdb|2B9M|D Chain D, 30s Ribosomal Subunit, Trnas, Mrna And Release Factor Rf2
           From A Crystal Structure Of The Whole Ribosomal Complex.
           This File Contains The 30s Ribosomal Subunit, Trnas,
           Mrna And Release Factor Rf2 From A Crystal Structure Of
           The Whole Ribosomal Complex". The Entire Crystal
           Structure Contains One 70s Ribosome, Trnas, Mrna And
           Release Factor Rf2 And Is Described In Remark 400.
 gi|88192358|pdb|2B9O|D Chain D, 30s Ribosomal Subunit, Trnas And Mrna From A Crystal
           Structure Of The Whole Ribosomal Complex With A Stop
           Codon In The A-Site. This File Contains The 30s Subunit,
           Trnas And Mrna From A Crystal Structure Of The Whole
           Ribosomal Complex With A Stop Codon In The A-Site And Is
           Described In Remark 400.
 gi|116667657|pdb|2HHH|D Chain D, Crystal Structure Of Kasugamycin Bound To The 30s
           Ribosomal Subunit
 gi|116668200|pdb|2J00|D Chain D, Structure Of The Thermus Thermophilus 70s Ribosome
           Complexed With Mrna, Trna And Paromomycin (Part 1 Of 4).
           This File Contains The 30s Subunit, Mrna, A-, P- And
           E-Site Trnas And Paromomycin For Molecule I.
 gi|116668261|pdb|2J02|D Chain D, Structure Of The Thermus Thermophilus 70s Ribosome
           Complexed With Mrna, Trna And Paromomycin (Part 3 Of 4)
           This File Contains The 30s Subunit, Mrna, A-, P- And
           E-Site Trnas And Paromomycin For Molecule Ii.
 gi|119389715|pdb|2HGI|G Chain G, Crystal Structure Of The 70s Thermus Thermophilus Ribosome
           Showing How The 16s 3'-End Mimicks Mrna E And P Codons.
           This Entry 2hgi Contains 30s Ribosomal Subunit. The 50s
           Ribosomal Subunit Can Be Found In Pdb Entry 2hgj.
 gi|119389772|pdb|2HGP|G Chain G, Crystal Structure Of The 70s Thermus Thermophilus Ribosome
           With Translocated And Rotated Shine-Dalgarno Duplex.
           This Entry 2hgp Contains 30s Ribosomal Subunit. The 50s
           Ribosomal Subunit Can Be Found In Pdb Entry 2hgq.
 gi|119389828|pdb|2HGR|G Chain G, 70s T.Th. Ribosome Functional Complex With Mrna And E- And
           P-Site Trnas At 4.5a. This Entry 2hgr Contains 30s
           Ribosomal Subunit. The 50s Ribosomal Subunit Can Be
           Found In Pdb Entry 2hgu.
 gi|149242711|pdb|2OW8|EE Chain e, Crystal Structure Of A 70s Ribosome-Trna Complex Reveals
           Functional Interactions And Rearrangements. This File,
           2ow8, Contains The 30s Ribosome Subunit, Two Trna, And
           Mrna Molecules. 50s Ribosome Subunit Is In The File
           1vsa.
 gi|149243621|pdb|2UU9|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal
           Subunit Complexed With A Valine-Asl With Cmo5u In
           Position 34 Bound To An Mrna With A Gug-Codon In The
           A-Site And Paromomycin.
 gi|149243648|pdb|2UUA|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal
           Subunit Complexed With A Valine-Asl With Cmo5u In
           Position 34 Bound To An Mrna With A Guc-Codon In The
           A-Site And Paromomycin.
 gi|149243675|pdb|2UUB|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal
           Subunit Complexed With A Valine-Asl With Cmo5u In
           Position 34 Bound To An Mrna With A Guu-Codon In The
           A-Site And Paromomycin.
 gi|149243702|pdb|2UUC|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal
           Subunit Complexed With A Valine-Asl With Cmo5u In
           Position 34 Bound To An Mrna With A Gua-Codon In The
           A-Site And Paromomycin.
 gi|149243841|pdb|2UXC|D Chain D, Crystal Structure Of An Extended Trna Anticodon Stem Loop
           In Complex With Its Cognate Mrna Ucgu In The Context Of
           The Thermus Thermophilus 30s Subunit.
 gi|157836411|pdb|2UXB|D Chain D, Crystal Structure Of An Extended Trna Anticodon Stem Loop
           In Complex With Its Cognate Mrna Gggu In The Context Of
           The Thermus Thermophilus 30s Subunit.
 gi|157836488|pdb|2V46|D Chain D, Structure Of The Ribosome Recycling Factor Bound To The
           Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe And
           Trna-Fmet (Part 1 Of 4). This File Contains The 30s
           Subunit, Mrna, P-Site Asl, E-Site Trna And Rrf For
           Molecule 1.
 gi|157836544|pdb|2V48|D Chain D, Structure Of The Ribosome Recycling Factor Bound To The
           Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe And
           Trna-Fmet (Part 3 Of 4). This File Contains The 30s
           Subunit, Mrna, P-Site Asl, E-Site Trna And Rrf For
           Molecule 2.
 gi|158430903|pdb|2UXD|D Chain D, Crystal Structure Of An Extended Trna Anticodon Stem Loop
           In Complex With Its Cognate Mrna Cggg In The Context Of
           The Thermus Thermophilus 30s Subunit.
 gi|160285942|pdb|2QNH|EE Chain e, Interactions And Dynamics Of The Shine-Dalgarno Helix In
           The 70s Ribosome. This File, 2qnh, Contains The 30s
           Ribosome Subunit, Two Trna, And Mrna Molecules. 50s
           Ribosome Subunit Is In The File 1vsp.
 gi|186972852|pdb|2VQE|D Chain D, Modified Uridines With C5-Methylene Substituents At The
           First Position Of The Trna Anticodon Stabilize U-G
           Wobble Pairing During Decoding
 gi|186972875|pdb|2VQF|D Chain D, Modified Uridines With C5-Methylene Substituents At The
           First Position Of The Trna Anticodon Stabilize U-G
           Wobble Pairing During Decoding
 gi|187609258|pdb|2ZKQ|DD Chain d, Structure Of A Mammalian Ribosomal 40s Subunit Within An
           80s Complex Obtained By Docking Homology Models Of The
           Rna And Proteins Into An 8.7 A Cryo-Em Map
 gi|209156499|pdb|3D5A|D Chain D, Structural Basis For Translation Termination On The 70s
           Ribosome. This File Contains The 30s Subunit, Release
           Factor 1 (Rf1), Two Trna, And Mrna Molecules Of One 70s
           Ribosome. The Entire Crystal Structure Contains Two 70s
           Ribosomes As Described In Remark 400.
 gi|209156555|pdb|3D5C|D Chain D, Structural Basis For Translation Termination On The 70s
           Ribosome. This File Contains The 30s Subunit, Release
           Factor 1 (Rf1), Two Trna, And Mrna Molecules Of The
           Second 70s Ribosome. The Entire Crystal Structure
           Contains Two 70s Ribosomes As Described In Remark 400.
 gi|211938822|pdb|2JL5|D Chain D, Insights Into Translational Termination From The Structure
           Of Rf2 Bound To The Ribosome (Part 1 Of 4). This File
           Contains The 30s Subunit.
 gi|211938880|pdb|2JL7|D Chain D, Insights Into Translational Termination From The Structure
           Of Rf2 Bound To The Ribosome (Part 3 Of 4). This File
           Contains The 30s Subunit.
 gi|218766776|pdb|3F1E|D Chain D, Crystal Structure Of A Translation Termination Complex
           Formed With Release Factor Rf2. This File Contains The
           30s Subunit, Rf2, Two Trna, And Mrna Molecules Of One
           70s Ribosome. The Entire Crystal Structure Contains Two
           70s Ribosomes As Described In Remark 400.
 gi|218766832|pdb|3F1G|D Chain D, Crystal Structure Of A Translation Termination Complex
           Formed With Release Factor Rf2. This File Contains The
           30s Subunit, Rf2, Two Trna, And Mrna Molecules Of The
           Second 70s Ribosome. The Entire Crystal Structure
           Contains Two 70s Ribosomes As Described In Remark 400.
 gi|226887377|pdb|2WDG|D Chain D, Structure Of The Thermus Thermophilus 70s Ribosome In
           Complex With Mrna, Paromomycin, Acylated A-Site Trna,
           Deacylated P-Site Trna, And E-Site Trna.  This File
           Contains The 30s Subunit A-,P-, And E-Site Trnas And
           Paromomycin For Molecule I.
 gi|226887402|pdb|2WDH|D Chain D, Structure Of The Thermus Thermophilus 70s Ribosome In
           Complex With Mrna, Paromomycin, Acylated A-Site Trna,
           Deacylated P-Site Trna, And E-Site Trna.  This File
           Contains The 30s Subunit A-,P-, And E-Site Trnas And
           Paromomycin For Molecule Ii.
 gi|226887491|pdb|2WDK|D Chain D, Structure Of The Thermus Thermophilus 70s Ribosome In
           Complex With Mrna, Paromomycin, Acylated A- And P-Site
           Trnas, And E-Site Trna.  This File Contains The 30s
           Subunit A-,P-, And E-Site Trnas And Paromomycin For
           Molecule I.
 gi|226887548|pdb|2WDM|D Chain D, Structure Of The Thermus Thermophilus 70s Ribosome In
           Complex With Mrna, Paromomycin, Acylated A- And P-Site
           Trnas, And E-Site Trna.  This File Contains The 30s
           Subunit A-,P-, And E-Site Trnas And Paromomycin For
           Molecule Ii.
 gi|237823532|pdb|2WH1|D Chain D, Insights Into Translational Termination From The Structure
           Of Rf2 Bound To The Ribosome
 gi|237823591|pdb|2WH3|D Chain D, Insights Into Translational Termination From The Structure
           Of Rf2 Bound To The Ribosome). This File Contains The
           30s Subunit.
 gi|260099989|pdb|3HUW|D Chain D, Structure Of Ef-P Bound To The 70s Ribosome; This File
           Contains The 30s Subunit, Mrna, P-Site Trna And Ef-P For
           Molecule I.
 gi|260100045|pdb|3HUY|D Chain D, Structure Of Ef-P Bound To The 70s Ribosome; This File
           Contains The 30s Subunit, Mrna, P-Site Trna And Ef-P For
           Molecule Ii.
 gi|261824487|pdb|2WRI|D Chain D, The Structure Of The Ribosome With Elongation Factor G
           Trapped In The Post-Translocational State (Part 1 Of 4).
 gi|261824549|pdb|2WRK|D Chain D, The Structure Of The Ribosome With Elongation Factor G
           Trapped In The Post-Translocational State (Part 3 Of 4).
 gi|261824611|pdb|2WRN|D Chain D, The Crystal Structure Of The 70s Ribosome Bound To Ef-Tu
           And Trna (Part 1 Of 4).
 gi|261824670|pdb|2WRQ|D Chain D, The Crystal Structure Of The 70s Ribosome Bound To Ef-Tu
           And Trna (Part 3 Of 4).
 gi|281307170|pdb|3KIQ|DD Chain d, Structure Of Rele Nuclease Bound To The 70s Ribosome
           (Precleavage State; Part 1 Of 4)
 gi|281307228|pdb|3KIS|DD Chain d, Structure Of Rele Nuclease Bound To The 70s Ribosome
           (Precleavage State; Part 3 Of 4)
 gi|281307286|pdb|3KIU|DD Chain d, Structure Of Rele Nuclease Bound To The 70s Ribosome
           (Postcleavage State; Part 1 Of 4)
 gi|281307344|pdb|3KIX|DD Chain d, Structure Of Rele Nuclease Bound To The 70s Ribosome
           (Postcleavage State; Part 3 Of 4)
 gi|288965607|pdb|3KNH|D Chain D, The Structures Of Viomycin Bound To The 70s Ribosome. This
           File Contains The 30s Subunit For Molecule I
 gi|289526685|pdb|3KNJ|D Chain D, The Structures Of Viomycin Bound To The 70s Ribosome. This
           File Contains The 30s Subunit For Molecule Ii'
 gi|289526710|pdb|3KNL|D Chain D, The Structures Of Capreomycin Bound To The 70s Ribosome.
           This File Contains The 30s Subunit For Molecule I
 gi|289526735|pdb|3KNN|D Chain D, The Structures Of Capreomycin Bound To The 70s Ribosome.
           This File Contains The 30s Subunit For Molecule Ii
 gi|294979507|pdb|3I8G|G Chain G, Elongation Complex Of The 70s Ribosome With Three Trnas
           And Entry 3i8g Contains 30s Ribosomal Subnit.The 50s
           Ribosomal Can Be Found In Pdb Entry 3i8f. Molecule B In
           The Same Asym Unit Is Deposited As 3i8g (30s) And 3i8f
           (50s).
 gi|294979532|pdb|3I8H|G Chain G, Elongation Complex Of The 70s Ribosome With Three Trnas
           And Entry 3i8h Contains 30s Ribosomal Subnit. The 50s
           Ribosomal Can Be Found In Pdb Entry 3i8i. Molecule A In
           The Same Asym Unit Is Deposited As 3i8f (50s) And 3i8g
           (30s).
 gi|294979591|pdb|3I9B|G Chain G, Initiation Complex Of 70s Ribosome With Two Trnas And
           Mrna. 3i9b Contains 30s Ribosomal Subunit Of Molecule B.
           The 50s Subunit Can Be Found In Pdb Entry 3i9c. Molecule
           A In The S Asymmetric Unit Is Deposited As 3i9d (30s)
           And 3i9e (50s)
 gi|294979645|pdb|3I9D|G Chain G, Initiation Complex Of 70s Ribosome With Two Trnas And
           Mrna. 3i9d Contains 30s Ribosomal Subunit Of Molecule A.
           The 50s Subunit Can Be Found In Pdb Entry 3i9e. Molecule
           B In The S Asymmetric Unit Is Deposited As 3i9b (30s)
           And 3i9c (50s)
 gi|295982078|pdb|2X9R|D Chain D, Structure Of The 70s Ribosome Bound To Release Factor 2
           And A Substrate Analog Provides Insights Into Catalysis
           Of Peptide Release
 gi|295982137|pdb|2X9T|D Chain D, Structure Of The 70s Ribosome Bound To Release Factor 2
           And A Substrate Analog Provides Insights Into Catalysis
           Of Peptide Release
 gi|307567965|pdb|2XFZ|D Chain D, Structure Of Cytotoxic Domain Of Colicin E3 Bound To The
           70s Ribosome (Part 1 Of 4)
 gi|307568023|pdb|2XG1|D Chain D, Structure Of Cytotoxic Domain Of Colicin E3 Bound To The
           70s Ribosome (Part 3 Of 4)
 gi|307776615|pdb|3OTO|D Chain D, Crystal Structure Of The 30s Ribosomal Subunit From A Ksga
           Mutant Of Thermus Thermophilus (Hb8)
 gi|309320238|pdb|3OGE|D Chain D, Structure Of The Thermus Thermophilus Ribosome Complexed
           With Chloramphenicol. This File Contains The 30s Subunit
           Of One 70s Ribosome. The Entire Crystal Structure
           Contains Two 70s Ribosomes.
 gi|309320259|pdb|3OGY|D Chain D, Structure Of The Thermus Thermophilus Ribosome Complexed
           With Chloramphenicol. This File Contains The 30s Subunit
           Of One 70s Ribosome. The Entire Crystal Structure
           Contains Two 70s Ribosomes.
 gi|309320340|pdb|3OHC|D Chain D, Structure Of The Thermus Thermophilus Ribosome Complexed
           With Erythromycin. This File Contains The 30s Subunit Of
           One 70s Ribosome. The Entire Crystal Structure Contains
           Two 70s Ribosomes.
 gi|309320361|pdb|3OHD|D Chain D, Structure Of The Thermus Thermophilus Ribosome Complexed
           With Erythromycin. This File Contains The 30s Subunit Of
           One 70s Ribosome. The Entire Crystal Structure Contains
           Two 70s Ribosomes.
 gi|309320442|pdb|3OHY|D Chain D, Structure Of The Thermus Thermophilus 70s Ribosome
           Complexed With Azithromycin. This File Contains The 30s
           Subunit Of One 70s Ribosome. The Entire Crystal
           Structure Contains Two 70s Ribosomes.
 gi|309320493|pdb|3OI0|D Chain D, Structure Of The Thermus Thermophilus 70s Ribosome
           Complexed With Azithromycin. This File Contains The 30s
           Subunit Of One 70s Ribosome. The Entire Crystal
           Structure Contains Two 70s Ribosomes.
 gi|309320544|pdb|3OI2|D Chain D, Structure Of The Thermus Thermophilus 70s Ribosome
           Complexed With Telithromycin. This File Contains The 30s
           Subunit Of One 70s Ribosome. The Entire Crystal
           Structure Contains Two 70s Ribosomes.
 gi|309320595|pdb|3OI4|D Chain D, Structure Of The Thermus Thermophilus 70s Ribosome
           Complexed With Telithromycin. This File Contains The 30s
           Subunit Of One 70s Ribosome. The Entire Crystal
           Structure Contains Two 70s Ribosomes.
 gi|312207676|pdb|2XQD|D Chain D, The Structure Of Ef-Tu And Aminoacyl-Trna Bound To The 70s
           Ribosome With A Gtp Analog
 gi|313754002|pdb|2XSY|D Chain D, Trna Tranlocation On The 70s Ribosome: The Pre-
           Translocational Translocation Intermediate Ti(Pre)
 gi|313754117|pdb|2XUY|D Chain D, Trna Tranlocation On The 70s Ribosome: The Post-
           Translocational Translocation Intermediate Ti(Post)
 gi|325533405|pdb|2Y0U|D Chain D, The Crystal Structure Of Ef-Tu And A9c-Trna-Trp Bound To A
           Near-Cognate Codon On The 70s Ribosome
 gi|325533464|pdb|2Y0W|D Chain D, The Crystal Structure Of Ef-Tu And A9c-Trna-Trp Bound To A
           Near-Cognate Codon On The 70s Ribosome
 gi|325533523|pdb|2Y0Y|D Chain D, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
           A Near-Cognate Codon On The 70s Ribosome
 gi|325533582|pdb|2Y10|D Chain D, The Crystal Structure Of Ef-Tu And Trp-Trna-Trp Bound To A
           Cognate Codon On The 70s Ribosome.
 gi|325533641|pdb|2Y12|D Chain D, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
           A Near-Cognate Codon On The 70s Ribosome
 gi|325533700|pdb|2Y14|D Chain D, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
           A Cognate Codon On The 70s Ribosome.
 gi|325533759|pdb|2Y16|D Chain D, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
           A Cognate Codon On The 70s Ribosome.
 gi|325533818|pdb|2Y18|D Chain D, The Crystal Structure Of Ef-Tu And Trp-Trna-Trp Bound To A
           Cognate Codon On The 70s Ribosome.
 gi|4519422|dbj|BAA75548.1| ribosomal protein S4 [Thermus thermophilus]
 gi|46197229|gb|AAS81643.1| SSU ribosomal protein S4P [Thermus thermophilus HB27]
 gi|55773047|dbj|BAD71488.1| 30S ribosomal protein S4 [Thermus thermophilus HB8]
          Length = 209

 Score = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SRR+  +++    + VNG  ++  +  V   D I V
Sbjct: 100 RLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAV 148


>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 = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 46/310 (14%), Positives = 82/310 (26%), Gaps = 52/310 (16%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + E    +R+ K +A+     SR  +++ I    V+V G  +      V   D IEV   
Sbjct: 55  IPETLHGERLDKALAKLLPDYSRSRLQQWIDAGAVRVGGAAVR-PRAAVCGGDRIEVVPQ 113

Query: 66  P---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
                           +   + T L +      +V   +     + +   L         
Sbjct: 114 RAADENAFVAEPIDLDVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRYPQAAGL 173

Query: 107 -RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ------------- 152
            R   V RLD  T GL+++         L                               
Sbjct: 174 PRAGIVHRLDKETSGLMVVARTLPAQTDLVRQLQARTVKRTYLALVWGETPEAGTIDAPI 233

Query: 153 -VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG---LREGKNREIKKVFEFF 208
             D      +       G        TLD      A V++    L  G+  +I+  FE  
Sbjct: 234 GRDPRDRTRMAIIETASGKPARTHFKTLDVIDLGRAQVSLVQCQLETGRTHQIRVHFESE 293

Query: 209 NWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETL 267
              +            LG  +   + R    + ++  L      +A   +   I    + 
Sbjct: 294 GHPL------------LGDPVYTRNFRRGRPQTIKAPLPIPFARQALHAVRLGIVHPASG 341

Query: 268 VRDRPNIISE 277
                +    
Sbjct: 342 QSMHWHAGVP 351


>gi|295105662|emb|CBL03206.1| Uncharacterized conserved protein, contains S4-like domain
           [Faecalibacterium prausnitzii SL3/3]
          Length = 272

 Score = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 13/64 (20%), Positives = 27/64 (42%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            ++ ++    +  R+  V++     SR     +I   RV++N + +E+    V   D   
Sbjct: 185 PERQLLTATVSSLRLDAVLSAMLHVSRGTAAELIEAGRVEINHLPVEKPHAPVYEQDVFT 244

Query: 62  VDGV 65
           V G 
Sbjct: 245 VRGK 248


>gi|160945087|ref|ZP_02092313.1| hypothetical protein FAEPRAM212_02606 [Faecalibacterium prausnitzii
           M21/2]
 gi|158442818|gb|EDP19823.1| hypothetical protein FAEPRAM212_02606 [Faecalibacterium prausnitzii
           M21/2]
          Length = 272

 Score = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 13/64 (20%), Positives = 27/64 (42%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            ++ ++    +  R+  V++     SR     +I   RV++N + +E+    V   D   
Sbjct: 185 PERQLLTATVSSLRLDAVLSAMLHVSRGTAAELIEAGRVEINHLPVEKPHAPVYEQDVFT 244

Query: 62  VDGV 65
           V G 
Sbjct: 245 VRGK 248


>gi|119025929|ref|YP_909774.1| hemolysin-like protein [Bifidobacterium adolescentis ATCC 15703]
 gi|118765513|dbj|BAF39692.1| hemolysin-like protein with S4 domain [Bifidobacterium
          adolescentis ATCC 15703]
          Length = 251

 Score = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 13/55 (23%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 7  VQENFTPQ-RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          + ++     R+   +   G+  SR + +R+I   +V+VNG +  +A++ V + D 
Sbjct: 1  MNDDSGAVVRLDIALVERGVTDSRSKAQRLIESGKVRVNGTVASKASLKVTAADT 55


>gi|20807748|ref|NP_622919.1| rRNA methylase [Thermoanaerobacter tengcongensis MB4]
 gi|254478689|ref|ZP_05092060.1| ribosomal RNA large subunit methyltransferase J, putative
          [Carboxydibrachium pacificum DSM 12653]
 gi|20516302|gb|AAM24523.1| predicted rRNA methylase [Thermoanaerobacter tengcongensis MB4]
 gi|214035376|gb|EEB76079.1| ribosomal RNA large subunit methyltransferase J, putative
          [Carboxydibrachium pacificum DSM 12653]
          Length = 265

 Score = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          +R+  ++ + G  S RE  +  I    V V+G   E+A   V     IEV G  L  
Sbjct: 3  ERIDVLLVKRGFFSSREKAKAAIMAGEVYVDGKRAEKAGEMVKEDSKIEVKGNSLPY 59


>gi|296188746|ref|ZP_06857133.1| hypothetical protein CLCAR_4281 [Clostridium carboxidivorans P7]
 gi|296046673|gb|EFG86120.1| hypothetical protein CLCAR_4281 [Clostridium carboxidivorans P7]
          Length = 42

 Score = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 14/40 (35%), Positives = 21/40 (52%)

Query: 204 VFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + +F N +V  L RI  G  +LG L  G  R +S K ++ 
Sbjct: 1   MCDFINHQVLELKRIQIGDIKLGNLPLGKWRYLSNKEVKN 40


>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 = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 22/245 (8%), Positives = 69/245 (28%), Gaps = 38/245 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +V       R+ K ++ A    SR  +++++  + V+V+   ++  +  + + + IE + 
Sbjct: 1   MVPAEAQGVRIDKFLSEACDGLSRSYLQKLLKSELVEVDKRTVKN-SYKLSAGEKIEFEV 59

Query: 64  -----------GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                       +PL     +   + +      +V   +    ++ V   +      +  
Sbjct: 60  PEAAEPEIKAEDIPLDIIYEDSDIILVNKPKGMVVHPAAGHYSQTLVNGLMYHCRDGLSG 119

Query: 111 VG----------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
           +                       + D     +        + R         ++     
Sbjct: 120 INGVLRPGIVHRIDMDTTGVLIVCKNDFAHNAIAEQLKVHSITRKYFAIVHGVIQEDEGT 179

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +  ++  K  I  +          +  +     +V   L  G+  +I+      
Sbjct: 180 VDAPIGRHPVDRKKMSINRKNGKEAVTHYRVLERFRQFTYVECQLETGRTHQIRVHMASI 239

Query: 209 NWKVN 213
              + 
Sbjct: 240 GHPLL 244


>gi|158338042|ref|YP_001519218.1| hemolysin A [Acaryochloris marina MBIC11017]
 gi|158308283|gb|ABW29900.1| hemolysin A, putative [Acaryochloris marina MBIC11017]
          Length = 272

 Score = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          QR+  ++    +  SR++ +R+I    VKVN  ++++    V  T  I+V   
Sbjct: 4  QRLDTLLVSLELCTSRQQAQRVIRAGEVKVNDQIIDKPGTEVQLTAEIQVKQK 56


>gi|14278533|pdb|1I94|D Chain D, Crystal Structures Of The Small Ribosomal Subunit With
           Tetracycline, Edeine And If3
 gi|14278554|pdb|1I95|D Chain D, Crystal Structure Of The 30s Ribosomal Subunit From
           Thermus Thermophilus In Complex With Edeine
 gi|14278575|pdb|1I96|D Chain D, Crystal Structure Of The 30s Ribosomal Subunit From
           Thermus Thermophilus In Complex With The Translation
           Initiation Factor If3 (C-Terminal Domain)
 gi|14278597|pdb|1I97|D Chain D, Crystal Structure Of The 30s Ribosomal Subunit From
           Thermus Thermophilus In Complex With Tetracycline
 gi|20663889|pdb|1J5E|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal
           Subunit
 gi|27065879|pdb|1N32|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal
           Subunit Bound To Codon And Near-Cognate Transfer Rna
           Anticodon Stem-Loop Mismatched At The First Codon
           Position At The A Site With Paromomycin
 gi|27065906|pdb|1N33|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal
           Subunit Bound To Codon And Near-Cognate Transfer Rna
           Anticodon Stem-Loop Mismatched At The Second Codon
           Position At The A Site With Paromomycin
 gi|27065933|pdb|1N34|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal
           Subunit In The Presence Of Codon And
           Crystallographically Disordered Near-Cognate Transfer
           Rna Anticodon Stem-Loop Mismatched At The First Codon
           Position
 gi|27065959|pdb|1N36|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal
           Subunit In The Presence Of Crystallographically
           Disordered Codon And Near-Cognate Transfer Rna Anticodon
           Stem-Loop Mismatched At The Second Codon Position
 gi|34811532|pdb|1PNS|D Chain D, Crystal Structure Of A Streptomycin Dependent Ribosome
           From E. Coli, 30s Subunit Of 70s Ribosome. This File,
           1pns, Contains The 30s Subunit, Two Trnas, And One Mrna
           Molecule. The 50s Ribosomal Subunit Is In File 1pnu.
 gi|34811588|pdb|1PNX|D Chain D, Crystal Structure Of The Wild Type Ribosome From E. Coli,
           30s Subunit Of 70s Ribosome. This File, 1pnx, Contains
           Only Molecules Of The 30s Ribosomal Subunit. The 50s
           Subunit Is In The Pdb File 1pny.
 gi|56966326|pdb|1VOQ|D Chain D, Crystal Structure Of Five 70s Ribosomes From Escherichia
           Coli In Complex With Protein Y. This File Contains The
           30s Subunit Of One 70s Ribosome. The Entire Crystal
           Structure Contains Five 70s Ribosomes And Is Described
           In Remark 400.
 gi|56966379|pdb|1VOS|D Chain D, Crystal Structure Of Five 70s Ribosomes From Escherichia
           Coli In Complex With Protein Y. This File Contains The
           30s Subunit Of One 70s Ribosome. The Entire Crystal
           Structure Contains Five 70s Ribosomes And Is Described
           In Remark 400.
 gi|56966432|pdb|1VOV|D Chain D, Crystal Structure Of Five 70s Ribosomes From Escherichia
           Coli In Complex With Protein Y. This File Contains The
           30s Subunit Of One 70s Ribosome. The Entire Crystal
           Structure Contains Five 70s Ribosomes And Is Described
           In Remark 400.
 gi|56966485|pdb|1VOX|D Chain D, Crystal Structure Of Five 70s Ribosomes From Escherichia
           Coli In Complex With Protein Y. This File Contains The
           30s Subunit Of One 70s Ribosome. The Entire Crystal
           Structure Contains Five 70s Ribosomes And Is Described
           In Remark 400.
 gi|56966538|pdb|1VOZ|D Chain D, Crystal Structure Of Five 70s Ribosomes From Escherichia
           Coli In Complex With Protein Y. This File Contains The
           30s Subunit Of One 70s Ribosome. The Entire Crystal
           Structure Contains Five 70s Ribosomes And Is Described
           In Remark 400.
 gi|149241278|pdb|2E5L|D Chain D, A Snapshot Of The 30s Ribosomal Subunit Capturing Mrna Via
           The Shine- Dalgarno Interaction
 gi|224510686|pdb|3FIC|D Chain D, T. Thermophilus 70s Ribosome In Complex With Mrna, Trnas
           And Ef-Tu.Gdp.Kirromycin Ternary Complex, Fitted To A
           6.4 A Cryo-Em Map. This File Contains The 30s Subunit
           And The Ligands
 gi|226887632|pdb|2ZM6|D Chain D, Crystal Structure Of The Thermus Thermophilus 30s
           Ribosomal Subunit
 gi|300508608|pdb|3MR8|D Chain D, Recognition Of The Amber Stop Codon By Release Factor Rf1.
           This Entry 3mr8 Contains 30s Ribosomal Subunit. The 50s
           Ribosomal Subunit Can Be Found In Pdb Entry 3ms1.
           Molecule B In The Same Asymmetric Unit Is Deposited As
           3mrz (50s) And 3ms0 (30s).
 gi|300508663|pdb|3MS0|D Chain D, Recognition Of The Amber Stop Codon By Release Factor Rf1.
           This Entry 3ms0 Contains 30s Ribosomal Subunit. The 50s
           Ribosomal Subunit Can Be Found In Pdb Entry 3mrz.
           Molecule A In The Same Asymmetric Unit Is Deposited As
           3mr8 (30s) And 3ms1 (50s).
 gi|322812553|pdb|3PYN|D Chain D, Crystal Structure Of A Complex Containing Domain 3 From
           The Psiv Igr Ires Rna Bound To The 70s Ribosome. This
           File Contains The 30s Subunit Of The First 70s Ribosome.
 gi|322812606|pdb|3PYQ|D Chain D, Crystal Structure Of A Complex Containing Domain 3 From
           The Psiv Igr Ires Rna Bound To The 70s Ribosome. This
           File Contains The 30s Subunit Of The Second 70s
           Ribosome.
 gi|322812659|pdb|3PYS|D Chain D, Crystal Structure Of A Complex Containing Domain 3 Of Crpv
           Igr Ires Rna Bound To The 70s Ribosome. This File
           Contains The 30s Subunit Of The First 70s Ribosome.
 gi|322812712|pdb|3PYU|D Chain D, Crystal Structure Of A Complex Containing Domain 3 Of Crpv
           Igr Ires Rna Bound To The 70s Ribosome. This File
           Contains The 30s Subunit Of The Second 70s Ribosome
          Length = 208

 Score = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SRR+  +++    + VNG  ++  +  V   D I V
Sbjct: 99  RLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAV 147


>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 = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/255 (14%), Positives = 71/255 (27%), Gaps = 48/255 (18%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +V  +    R+ +V+A R    SR  ++ +I   RV + G  +   A +    + I +D 
Sbjct: 2   VVAGDEGSSRLDRVLATRCPALSRSRLKVLILDGRVAIAGSAVRDPAYHASPGETITIDV 61

Query: 64  ---------GVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                    G  +           + +      +V   +  +  + V   +         
Sbjct: 62  PPPVAPEPEGEAIALEIVHEDDDIIVINKPRGLVVHPAAGHETGTLVNALIAHCGESLSG 121

Query: 106 ----SRVISVGRLDINTEGLLLLTND-----------------GGLARVLELPSTQWLRV 144
                R   V RLD +T GL++   +                 G L R            
Sbjct: 122 IGGVRRPGIVHRLDKDTTGLMVAAKNDRAHQSLSAQFADHGRTGELRRGYYAFVWGVPNR 181

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG------LREGKN 198
            R      +D+      +K  V  G         +       +   +       L  G+ 
Sbjct: 182 ARGTIEAPIDRHPYAR-EKMAVRDGGREAITHWEVLETFTGRSGGEIVSLIACQLETGRT 240

Query: 199 REIKKVFEFFNWKVN 213
            +I+         + 
Sbjct: 241 HQIRVHLAHLGHPLL 255


>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 = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/272 (12%), Positives = 69/272 (25%), Gaps = 56/272 (20%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--- 65
           E+    R+  V++R    SR    ++I +  V+V        +  V  +  + V G    
Sbjct: 26  EDGEGHRLDFVLSREIGVSRSYASKLIKEGMVQV------SWSPRVKPSLKVRVGGTVTA 79

Query: 66  -----------------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                             +   ++  + +      +V         + V   L      +
Sbjct: 80  QLPPSEELELEPQDVPFRVVYQDQDLVVVDKPAGLVVHPAPGHWRGTLVHGLLYRYPDLM 139

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH------------------ 150
              G         L  T  G +       + + L                          
Sbjct: 140 ELNGVKRPGIVHRLDATTSGLMVVARNGLAMEGLVRAFKDRRVGKVYLAMAAGTLRGEGS 199

Query: 151 ----GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                  D D    +      +          +   +G  + V   ++ G+  +I+    
Sbjct: 200 VSLPIGRDPDNRKRMACVPWGREALTR---YRVIWSRGGYSLVACQIKTGRTHQIRVHMR 256

Query: 207 FFNWKVNRLIRISYGP----FQLGTLLAGSTR 234
                +    RI  GP    F LG +   S R
Sbjct: 257 SLGHPLVG-DRIYGGPCPEGFPLGRVFLHSWR 287


>gi|7440168|pir||JE0399 ribosomal protein S4 - Thermus aquaticus (strain HB8)
          Length = 209

 Score = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SRR+  +++    + VNG  ++  +  V   D I V
Sbjct: 100 RLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAV 148


>gi|148273167|ref|YP_001222728.1| hypothetical protein CMM_1986 [Clavibacter michiganensis subsp.
          michiganensis NCPPB 382]
 gi|147831097|emb|CAN02042.1| unnamed protein product [Clavibacter michiganensis subsp.
          michiganensis NCPPB 382]
          Length = 292

 Score = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          R+   +   G+A SR    R+IA   V V+G  + +A+  VM    +EV G
Sbjct: 27 RLDAALPALGLARSRTHAARLIADGLVTVDGRGVVKASFRVMPGSVVEVAG 77


>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 = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 15 RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          R+ +V+A R    SR  ++ +I   RV + G  +   A +    + I +D
Sbjct: 21 RLDRVLAARCPELSRSRLKALILDGRVAIAGNPVRDPAYHASPGETITID 70


>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 = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 30/240 (12%), Positives = 66/240 (27%), Gaps = 31/240 (12%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERA----------AVN 53
           N V E+    R+ +V+A      SR  ++  I    V VNG ++++            + 
Sbjct: 9   NTVGESQLGMRLDQVVAELYPDYSRSRIKDWILNGMVSVNGKVVKKPREKMMGGEELFIQ 68

Query: 54  VMSTDHIEVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
               D +      +       +   L +      +V   +     + +   L        
Sbjct: 69  AEIEDEVRWVAQDIPLDIVYEDDDILVINKPRDFVVHPGAGTPDGTVLNALLHHCPSLAE 128

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------- 155
             R   V RLD +T GL+++         L     +                        
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTIQAQTRLVRALQKRKITREYEALAIGQMTGGGTVEKP 188

Query: 156 --DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                       V +          +  +   +  + + L  G+  +I+    + +  + 
Sbjct: 189 IGRHSTKRTCMAVHEMGKDAITHYRVAERFREHTRIVLRLETGRTHQIRVHMSYLSHPLI 248


>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 = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/242 (11%), Positives = 73/242 (30%), Gaps = 35/242 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKV-------NGILLE----------- 48
           +       R+   +A+    SR + +R+I  ++VK+       N  +++           
Sbjct: 7   ISSEEKKLRLDTYVAKKCNISRSKAQRLIQNEQVKLLGIPIINNDHIVKPGEEYVVHLIQ 66

Query: 49  -RAAVNVMST-----DHIEVDGVPLRKAERTRLWLYHKPIG-----------LVTTHSDP 91
              + ++        D +  D   +  ++++RL ++                 +      
Sbjct: 67  PDISTSIEPNYDIKLDIVYEDDDIIVLSKQSRLTVHPGAGTNNDTLLNAVIAHLGKIPYT 126

Query: 92  DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151
           + R  +   L    S ++ + + + +   L  L ++  + R         L   +     
Sbjct: 127 NTRPGIVHRLDKDTSGLMVIAKNEQSHSFLSELLSNRKIKREYLAVIWGALPNLQGTVKT 186

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +   + N     +            ++    G  + V   L  G+  +I+         
Sbjct: 187 HIAPKRSNKEMMCVTKTAGKLAITHYSVKKIIGQASLVKCTLETGRTHQIRVHMSHIGHS 246

Query: 212 VN 213
           V 
Sbjct: 247 VV 248


>gi|70726725|ref|YP_253639.1| hypothetical protein SH1724 [Staphylococcus haemolyticus JCSC1435]
 gi|68447449|dbj|BAE05033.1| unnamed protein product [Staphylococcus haemolyticus JCSC1435]
          Length = 275

 Score = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 26/50 (52%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  V+      SR   +++I ++RVKVN  +++     V + D + + G
Sbjct: 199 RLDVVLKEMIHKSRTIAKQLIEKKRVKVNHTIIDSPDFQVQTNDLLSIQG 248


>gi|309789597|ref|ZP_07684178.1| hemolysin A [Oscillochloris trichoides DG6]
 gi|308228333|gb|EFO81980.1| hemolysin A [Oscillochloris trichoides DG6]
          Length = 261

 Score = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ +++   G+A +R + + ++    V+VNG    +    V +   IEV
Sbjct: 4  IRLDQLLVSRGLAETRSKAQALLMAGSVRVNGQPAGKPGAMVDAEVEIEV 53


>gi|257784936|ref|YP_003180153.1| 30S ribosomal protein S4 [Atopobium parvulum DSM 20469]
 gi|257473443|gb|ACV51562.1| ribosomal protein S4 [Atopobium parvulum DSM 20469]
          Length = 197

 Score = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI R G A +R+E  + +    + VNG  ++  +  V S D I V
Sbjct: 88  RLDNVIFRLGFARTRKEARQTVRHGHITVNGQRVDIPSYRVKSGDVIAV 136


>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 = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/238 (11%), Positives = 67/238 (28%), Gaps = 32/238 (13%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLE---------RAAVNVM 55
            V  +   QR+   +A+     SR  +   I    V +NG +              V++ 
Sbjct: 33  TVPTDLAGQRLDAALAKLLPDYSRSRLSTWIKDGNVLLNGQVARPKERLIGGETLEVHIQ 92

Query: 56  -------------STDHIEVDGVPLRKAERTRLWLYHKPIGLVTT--HSDPDGRSTVFDN 100
                          D +  D   +   +   L ++        T  +        + + 
Sbjct: 93  HSHETAAFTPEPMPLDIVFEDDSVIVLNKPAGLVVHPAAGNWSGTLLNGLLAHCPALAEI 152

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR-------VYRVRFHGQV 153
             +     +      +          +  + ++ E    +  R        +  +    +
Sbjct: 153 PRAGIVHRLDKDTSGLMVVAKTPAAQNSLVQQLQERSVKRIYRAVADGIVPFDGKIDTLI 212

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +D  N LK  +V  G       + +  +  S++++   L  G+  +I+         
Sbjct: 213 GRDPHNRLKMAVVGFGGKKAVTHIKVLERYQSHSYIECTLETGRTHQIRVHMREAKHP 270


>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 = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/234 (13%), Positives = 74/234 (31%), Gaps = 35/234 (14%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLE-----RAAVNV-------------- 54
           R+ + +AR+    +R  V+R+I + RV V+G + +     R    +              
Sbjct: 17  RLDQFVARSVEGMTRSTVQRLIDEGRVTVDGKVEKPSLKLRGGERIVVAVPPPAPAVPEA 76

Query: 55  ---------MSTDHIEVD---GVPLRKAERT---RLWLYHKPIGLVTTHSDPDGRSTVFD 99
                      +D + V+   G+ +     T    L           +    + R  +  
Sbjct: 77  EEIPLVILHEDSDLVVVNKSAGMVVHPGAGTPGGTLVNALLAHCTDLSGIGGEIRPGIVH 136

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
            +    + V+ V + D + EGL     +  + R+         +    R  G + +   +
Sbjct: 137 RIDKDTTGVLVVAKNDRSHEGLARQFREHTIKRIYLALVFGSPKTDTGRIEGAIGRHPTD 196

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            L+     +   +      +  +      + + L  G+  +I+         + 
Sbjct: 197 RLRMSGKAKHGKHAVTHWKVLARYPGMTLLRLRLETGRTHQIRVHLAESGHPLV 250


>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 = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/245 (12%), Positives = 70/245 (28%), Gaps = 43/245 (17%)

Query: 8   QENFTPQRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           ++   P RV K +     G A+R ++++      + VNG  ++     V   D I+V   
Sbjct: 25  EKGQQPLRVDKYLMNFIEG-ATRNKIQQAAKDGNIFVNGKPVKS-NYKVKGNDVIKVLFA 82

Query: 63  ----------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                     + +P+     +   L +      +V         + +   +    +   +
Sbjct: 83  HPPYENLLVGEDIPIDIVYEDDDLLVVNKPAGMVVHPGHGNYSGTLINALIYHFDNLPKN 142

Query: 111 V-------GRLDINTEGLLLLTNDGGLARV-------------LELPSTQWLRVYRVRFH 150
                    R+D +T GLL++                              +        
Sbjct: 143 SNERPGLVHRIDKDTSGLLVVAKTEEAMTHLAKQFFDKTSERIYYALVWGNVEEDEGTVE 202

Query: 151 GQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
           G + +   N L+  +                 +  + G    V+  L  G+  +I+   +
Sbjct: 203 GNIGRHPKNRLQNTVFFGEDADKGKPAVTHYKVLERLGYVTLVSCQLETGRTHQIRVHMK 262

Query: 207 FFNWK 211
                
Sbjct: 263 HIGHT 267


>gi|189425760|ref|YP_001952937.1| hemolysin A [Geobacter lovleyi SZ]
 gi|189422019|gb|ACD96417.1| hemolysin A [Geobacter lovleyi SZ]
          Length = 249

 Score = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 1/60 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           + QR+ K++   G+A SR + + +I   +V V     ++A   V     I + G  L  
Sbjct: 2  SSKQRLDKLMVERGLAPSREKAQALIMAGQVVVGDHAAQKAGQQVTDEVEIRIKGELLPY 61


>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 = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 39/245 (15%), Positives = 67/245 (27%), Gaps = 39/245 (15%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + E    +R+ K +A+     SR  +++ I    V+V G  +      V   D +EV   
Sbjct: 43  IPETLHGERLDKALAKLLPDYSRSRLQQWIDAGAVRVGGAAVR-PRAAVCGGDRVEVVPQ 101

Query: 66  P---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   + T L +      +V   +     + +   L         
Sbjct: 102 RAADESAFVAEPIDLDVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRYPEAAEL 161

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ------------- 152
            R   V RLD  T GL+++         L                               
Sbjct: 162 PRAGIVHRLDKETSGLMVVARTLPAQTDLVRQLQARTVKRTYLALVWGETPEAGTIDAPI 221

Query: 153 -VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG---LREGKNREIKKVFEFF 208
             D      +       G        TLD      A V++    L  G+  +I+  FE  
Sbjct: 222 GRDPRDRTRMAIIETASGKPARTHFKTLDVVDLGRAQVSLVRCQLETGRTHQIRVHFESE 281

Query: 209 NWKVN 213
              + 
Sbjct: 282 GHPLL 286


>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 = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 38/247 (15%), Positives = 79/247 (31%), Gaps = 35/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M +K  ++      R+  V+A+  +  SR  +   +    + VN   ++R +  V S D 
Sbjct: 1   MTEKITLEITNETGRIDAVLAKKSLPYSRTVLAEWLQDGHIVVNQTQVKR-SYKVNSGDL 59

Query: 60  IEV------DGVPLRKAERTRLWL--------YHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I +      +   + +     +                +V   +     + V   L    
Sbjct: 60  ITILPPAVQNTEIIAENMPLDIIYEDNDLLVVNKPQGMVVHPAAGHTSGTLVNALLYHAP 119

Query: 106 -------SRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
                   R   V R+D +T GLL++  +    + L     + +  R+Y     G+  +D
Sbjct: 120 LSTINGSFRPGIVHRIDRDTSGLLMVAKNDKAHQALSEQLKAHKNERIYYALVRGEFSED 179

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          KK  V  G         + T+      + + L  G+  +I+    
Sbjct: 180 SGTINAPLARHKVDRKKQAVQAGGREAITHFEVVTRYVGYTLLKIRLETGRTHQIRVHMT 239

Query: 207 FFNWKVN 213
           +    + 
Sbjct: 240 YIGHPII 246


>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 = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/235 (14%), Positives = 65/235 (27%), Gaps = 38/235 (16%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMST-------------- 57
            QR+ +V A+     SR  +   I   R+ V+G +L      V S               
Sbjct: 17  GQRLDQVAAQLFSEYSRSRLSSWIKDGRLTVDGAVLR-PRDTVHSGSILALEAEQEAQGE 75

Query: 58  ---DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV--- 111
                IE+D   +   +   L +      +V   +     + +   L  +   +      
Sbjct: 76  WVAQDIELD---IVYEDDQILVINKPAGLVVHPAAGHPDGTLLNALLHHVPDIINVPRAG 132

Query: 112 --GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
              RLD +T GL+++         L     +                    +   I   G
Sbjct: 133 IVHRLDKDTTGLMVVAKTLQAQTNLVDQLQKRSVSRIYECIVVGVVIAGGKIDAPIGRHG 192

Query: 170 IC---------YGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                               +  +  S+  V V L  G+  +I+       + + 
Sbjct: 193 GERQRMAVTDGGKPAVSHYRVLKRFRSHTHVRVKLETGRTHQIRVHMAHVGYPLV 247


>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 = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 46/310 (14%), Positives = 83/310 (26%), Gaps = 52/310 (16%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           + E    +R+ K +A+     SR  +++ I    V+V G  +      V   D IEV   
Sbjct: 43  IPEALHGERLDKALAKLLPDYSRSRLQQWIDAGAVRVGGAAVR-PRAAVCGGDRIEVVPQ 101

Query: 63  --DGVP----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
             D             +   + T L +      +V   +     + +   L         
Sbjct: 102 RADDENAFVAEPVDLDVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRYPQAAGL 161

Query: 107 -RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ------------- 152
            R   V RLD  T GL+++         L                               
Sbjct: 162 PRAGIVHRLDKETSGLMVVARTLPAQTDLVRQLQARTVKRTYLALVWGETPEAGTIDAPI 221

Query: 153 -VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG---LREGKNREIKKVFEFF 208
             D      +       G        TLD      A V++    L  G+  +I+  FE  
Sbjct: 222 GRDPRDRTRMAIIETASGKPARTHFKTLDVVDLGRAQVSLVQCQLETGRTHQIRVHFESE 281

Query: 209 NWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETL 267
              +            LG  +   + R    + ++  L      +A   +   +    + 
Sbjct: 282 GHPL------------LGDPVYTRNFRRGRPQTIKAPLPAPFARQALHAVRLGLVHPASG 329

Query: 268 VRDRPNIISE 277
                +    
Sbjct: 330 QSVHWHAGVP 339


>gi|167749411|ref|ZP_02421538.1| hypothetical protein EUBSIR_00365 [Eubacterium siraeum DSM 15702]
 gi|167657583|gb|EDS01713.1| hypothetical protein EUBSIR_00365 [Eubacterium siraeum DSM 15702]
 gi|291532117|emb|CBK97702.1| SSU ribosomal protein S4P [Eubacterium siraeum 70/3]
 gi|291558143|emb|CBL35260.1| SSU ribosomal protein S4P [Eubacterium siraeum V10Sc8a]
          Length = 198

 Score = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +RRE  +++      VNG  ++  +  +   D + V
Sbjct: 89  RLDNVVFRMGMAITRREARQLVTHGHFTVNGKKVDVPSYRIKPGDVVAV 137


>gi|260893252|ref|YP_003239349.1| hemolysin A [Ammonifex degensii KC4]
 gi|260865393|gb|ACX52499.1| hemolysin A [Ammonifex degensii KC4]
          Length = 276

 Score = 54.8 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 20/49 (40%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+  ++   G   SR    + I   +V VNG    +    V   D +EV
Sbjct: 7  RLDILLVEQGYFPSRERARQAILAGQVLVNGQRAAKPGRMVGPEDRVEV 55


>gi|320529115|ref|ZP_08030207.1| ribosomal RNA large subunit methyltransferase J [Selenomonas
          artemidis F0399]
 gi|320138745|gb|EFW30635.1| ribosomal RNA large subunit methyltransferase J [Selenomonas
          artemidis F0399]
          Length = 268

 Score = 54.4 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 14/59 (23%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
            +R+  ++   G+A SR   +R+I   +V V+   +++A   V +   + V G  L  
Sbjct: 2  KKERLDLLLVAQGLAPSRERAKRLIMAGQVLVDERRVDKAGTTVDADASLRVTGEDLPY 60


>gi|296127781|ref|YP_003635033.1| hemolysin A [Brachyspira murdochii DSM 12563]
 gi|296019597|gb|ADG72834.1| hemolysin A [Brachyspira murdochii DSM 12563]
          Length = 240

 Score = 54.4 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ + + + G   SR + + +I    V VNG+ +   A  +  TD+IEV
Sbjct: 1  MRLDEYVYKEGYTESRSKAQDIILAGCVFVNGVKVTAKAQKIKDTDNIEV 50


>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 = 54.4 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 42/256 (16%), Positives = 69/256 (26%), Gaps = 38/256 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M ++ I   N    R+ + +A+    SR +VE ++    V V+G    +  V +   + I
Sbjct: 1   MNERKIFH-NTEMARLDQALAKLLGESRNQVEALVRGGNVWVDGEKSSKGGVKLKGGERI 59

Query: 61  EVD--------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           EV+               V +   E   + L      +V         + V        S
Sbjct: 60  EVEIPLLRENPAMEVEFEVEILHEEEHFIVLNKPSGAVVHGAPSVKEATLVDWLKKKGIS 119

Query: 107 RVISVGRLDI--------------------NTEGLLLLTNDGGLARVLELPSTQWLRVYR 146
                G                             L L           L          
Sbjct: 120 LSTLNGEERHGIVHRLDKETSGAIVIAKSNEAHRRLSLQLQEKSMGRYYLAIIDHPLKED 179

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNAWVTVGLREGKNREIKKVF 205
            R    + +   + LK   V  G       V L+    GS   +   L  G+  +I+   
Sbjct: 180 QRVECYLGRHPHHRLKIAKVPVGRYAKSAFVKLEESIDGSKELIAAKLFTGRTHQIRAHL 239

Query: 206 EFFNWKVNRLIRISYG 221
           E     +  L    YG
Sbjct: 240 ELLGRHI--LHDELYG 253


>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 = 54.4 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 32/240 (13%), Positives = 67/240 (27%), Gaps = 31/240 (12%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERA----------AVN 53
           N V EN    R+ +VIA+     SR  ++  I    V VNG ++++            + 
Sbjct: 9   NTVGENQLGMRLDQVIAQLYPDYSRSRIKDWILNGMVSVNGDVVKKPREKMMGGEELFIQ 68

Query: 54  VMSTDHIEVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
               D +      +       +   L +      +V   +     + +   L        
Sbjct: 69  AEIEDEVRWVAQDIPLDIVYEDDDILVINKPRDFVVHPGAGTPDGTILNALLHYCPSLAE 128

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------- 155
             R   V RLD +T GL+++         L     +                        
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTIQAQTRLVRALQKRKITREYEALAIGQMTGGGTIEKP 188

Query: 156 --DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                       V +          +  +   +  + + L  G+  +I+    + +  + 
Sbjct: 189 IGRHSTKRICMAVHEMGKDAITHYRVAERFREHTRIVLRLETGRTHQIRVHMSYMSHPLI 248


>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 = 54.4 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/237 (14%), Positives = 70/237 (29%), Gaps = 38/237 (16%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ K +A      SR  +++++ +  V VNG    + +  V + D + V+  P  +++  
Sbjct: 45  RLDKALAELVPEFSRSYLQQLLGEGGVLVNGRAAAKPSARVQAGDVLSVELRPTPQSQAF 104

Query: 74  R---------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
           R                 +      +V         + +   L          R   V R
Sbjct: 105 RPEAMALDTVYEDEHLRIVNKPAGLVVHPAPGNWSGTLLNGLLSLDPRAGNVPRAGIVHR 164

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------------DKLN 159
           LD +T GL+++  +  +   L           +    G                  D  N
Sbjct: 165 LDKDTSGLMVVARERSVMDALVRMIAAREVSRQYLALGHRAWQGSQTRVVEEAIGRDPRN 224

Query: 160 LLKKGIVIQGICY-GDMQVTLDTQK--GSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            L+   V   +      +  L           V   L  G+  +I+    +    + 
Sbjct: 225 RLRMAAVDLAVHAGKPARTDLAVLDTCEDGCLVHCTLHTGRTHQIRVHMAWLRHPLL 281


>gi|47779342|gb|AAT38571.1| predicted ribosomal large subunit pseudouridine synthase D
           [uncultured gamma proteobacterium eBACHOT4E07]
          Length = 311

 Score = 54.4 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/246 (14%), Positives = 75/246 (30%), Gaps = 36/246 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+    + E+ + +R  K  A      SR ++++ I + RV +N  +       V + D 
Sbjct: 1   MEVTKKITEDLSMERFDKACALIFNDYSRSQLKKWIIEGRVLLNNEIA-SPKEIVTTDDE 59

Query: 60  IEVD---GVPLRKAERTR-----------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I ++      ++                 L +      ++   S  D  +     L    
Sbjct: 60  ISLNPIFKKIIQWEPENIDFEVVHEDENFLIINKPSKLVIHPGSGCDSGTLANGLLFKYP 119

Query: 106 SRVISV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR------------VR 148
                       RLD +T G+LL+               +                   +
Sbjct: 120 ELNKMPRAGIVHRLDKDTSGILLVARTEKFRNYFVSLLQERKVKKIYKAVVVGKIIGSFQ 179

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-GSNAWVTVGLREGKNREIKKVFEF 207
            +  + +DK N +K  I   G     +      +  G+ + V V +  G+  +I+     
Sbjct: 180 INEPIGRDKTNRIKMSIRSDGKEA--ISFVKLHESLGNYSVVDVSIETGRTHQIRVHLAN 237

Query: 208 FNWKVN 213
               + 
Sbjct: 238 KKLPII 243


>gi|323358624|ref|YP_004225020.1| rRNA methylase [Microbacterium testaceum StLB037]
 gi|323274995|dbj|BAJ75140.1| predicted rRNA methylase [Microbacterium testaceum StLB037]
          Length = 265

 Score = 54.4 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+   +A  G+A SR    ++IA   V VNG  + +A+  V +   IEV
Sbjct: 3  RLDAELAARGLARSRSHATQLIAAGEVSVNGRAVVKASAPVDTDSVIEV 51


>gi|323350794|ref|ZP_08086453.1| 30S ribosomal protein S4 [Streptococcus sanguinis VMC66]
 gi|322122968|gb|EFX94671.1| 30S ribosomal protein S4 [Streptococcus sanguinis VMC66]
 gi|325689321|gb|EGD31327.1| 30S ribosomal protein S4 [Streptococcus sanguinis SK115]
 gi|325695727|gb|EGD37626.1| 30S ribosomal protein S4 [Streptococcus sanguinis SK150]
          Length = 245

 Score = 54.4 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V    L+  
Sbjct: 136 RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVTPGQVISVREKSLKVP 192


>gi|309798830|ref|ZP_07693093.1| 30S ribosomal protein S4 [Streptococcus infantis SK1302]
 gi|308117556|gb|EFO54969.1| 30S ribosomal protein S4 [Streptococcus infantis SK1302]
          Length = 133

 Score = 54.4 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 15 RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
          R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V    L+  
Sbjct: 24 RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVTPGQVISVREKSLKVP 80


>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 = 54.4 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/246 (10%), Positives = 63/246 (25%), Gaps = 40/246 (16%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVN--GILLERAAVNVMSTDHIE 61
           + V +    QR+ K+ A      SR +++  +    + VN      +     V   D + 
Sbjct: 107 HTVTQEQAGQRIDKLAADMFTEHSRAQLQDWLKSGNLTVNDHNEKAK---YRVKIGDIVR 163

Query: 62  VDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           ++                 +   + + + +      +V   +     + V   L    ++
Sbjct: 164 LEAKLEQHGSDQPEDIKLDIIYEDDSVIVINKPVGMVVHPGAGNWSGTLVNGLLYHYPNQ 223

Query: 108 VISV--GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
                 G +    +    L   G           Q       R +  V       L +  
Sbjct: 224 AHLPRAGLVHRIDKNTSGLLVIGKTKAAQLELQEQLKDKSVYRHYQCVVAGDAPSLARQR 283

Query: 166 VIQ------------------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
            I                   G       + +     + + + V L  G+  +I+     
Sbjct: 284 TIDAPIGRHRTQRTKMTVTSTGKTAITHIMKITPLSDTYSLLDVRLETGRTHQIRVHLSH 343

Query: 208 FNWKVN 213
               + 
Sbjct: 344 IGHPII 349


>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 = 54.4 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 25/232 (10%), Positives = 63/232 (27%), Gaps = 37/232 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+ K +       SR +++  I    V VNG  ++     ++  DH+++           
Sbjct: 16  RIDKQLGHHFDQFSRSQIQHWIEDGHVLVNGKQVK-PKYKLLVGDHVQIIPEEPQKIDLA 74

Query: 67  -------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI---------- 109
                  +   +   + +      +V         + V   L       I          
Sbjct: 75  PEDIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHSPLSTINGEFRPGIVH 134

Query: 110 ----------SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
                      V + D+    L          R         ++  +      + +   +
Sbjct: 135 RIDKDTSGLLMVAKNDMAHRSLTAQLKAKTNKREYVALVHGVIKEDKGTIDAPLGRSLKD 194

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             K+ +V+    +      +  +  +   V   L  G+  +I+   ++    
Sbjct: 195 RKKQAVVV-DGRHAVTHFNVLERFKNYTLVACQLETGRTHQIRVHMKYIGHP 245


>gi|313112550|ref|ZP_07798214.1| S4 domain protein [Faecalibacterium cf. prausnitzii KLE1255]
 gi|310625132|gb|EFQ08423.1| S4 domain protein [Faecalibacterium cf. prausnitzii KLE1255]
          Length = 71

 Score = 54.4 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 27/60 (45%), Gaps = 1/60 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          +    ++  ++  AG+  +  E + ++    VKVNG +         + D IE+DG  + 
Sbjct: 7  HTEFIKLDALLKYAGLCETGGEAKELVQGGAVKVNGEVCTMRGKKCRAGDVIELDGQTVE 66


>gi|257437732|ref|ZP_05613487.1| S4 domain protein [Faecalibacterium prausnitzii A2-165]
 gi|257200039|gb|EEU98323.1| S4 domain protein [Faecalibacterium prausnitzii A2-165]
          Length = 71

 Score = 54.4 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 12/60 (20%), Positives = 27/60 (45%), Gaps = 1/60 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          +    ++  ++  AG+  +  E + ++    VKVNG +         + D +E+DG  + 
Sbjct: 7  HTEFIKLDALLKYAGLCETGGEAKELVQGGAVKVNGEVCTMRGKKCRAGDVVELDGQTVE 66


>gi|148381393|ref|YP_001255934.1| ribosomal protein S4 [Clostridium botulinum A str. ATCC 3502]
 gi|153933367|ref|YP_001385768.1| 30S ribosomal protein S4 [Clostridium botulinum A str. ATCC 19397]
 gi|153935510|ref|YP_001389175.1| 30S ribosomal protein S4 [Clostridium botulinum A str. Hall]
 gi|153940320|ref|YP_001392806.1| 30S ribosomal protein S4 [Clostridium botulinum F str. Langeland]
 gi|168178860|ref|ZP_02613524.1| ribosomal protein S4 [Clostridium botulinum NCTC 2916]
 gi|168181892|ref|ZP_02616556.1| 30S ribosomal protein S4 [Clostridium botulinum Bf]
 gi|170755638|ref|YP_001783093.1| 30S ribosomal protein S4 [Clostridium botulinum B1 str. Okra]
 gi|226950905|ref|YP_002805996.1| ribosomal protein S4 [Clostridium botulinum A2 str. Kyoto]
 gi|237796914|ref|YP_002864466.1| 30S ribosomal protein S4 [Clostridium botulinum Ba4 str. 657]
 gi|171769230|sp|A7FZ45|RS4A_CLOB1 RecName: Full=30S ribosomal protein S4 A
 gi|171769265|sp|A7GJ46|RS4A_CLOBL RecName: Full=30S ribosomal protein S4 A
 gi|172047868|sp|A5I7H8|RS4A_CLOBH RecName: Full=30S ribosomal protein S4 A
 gi|148290877|emb|CAL85013.1| 30S ribosomal protein S4 [Clostridium botulinum A str. ATCC 3502]
 gi|152929411|gb|ABS34911.1| 30S ribosomal protein S4 [Clostridium botulinum A str. ATCC 19397]
 gi|152931424|gb|ABS36923.1| 30S ribosomal protein S4 [Clostridium botulinum A str. Hall]
 gi|152936216|gb|ABS41714.1| 30S ribosomal protein S4 [Clostridium botulinum F str. Langeland]
 gi|169120850|gb|ACA44686.1| 30S ribosomal protein S4 [Clostridium botulinum B1 str. Okra]
 gi|182669924|gb|EDT81900.1| ribosomal protein S4 [Clostridium botulinum NCTC 2916]
 gi|182674921|gb|EDT86882.1| 30S ribosomal protein S4 [Clostridium botulinum Bf]
 gi|226841883|gb|ACO84549.1| ribosomal protein S4 [Clostridium botulinum A2 str. Kyoto]
 gi|229261759|gb|ACQ52792.1| 30S ribosomal protein S4 [Clostridium botulinum Ba4 str. 657]
 gi|295320786|gb|ADG01164.1| 30S ribosomal protein S4 [Clostridium botulinum F str. 230613]
 gi|322807778|emb|CBZ05353.1| SSU ribosomal protein S4p (S9e) [Clostridium botulinum H04402 065]
          Length = 206

 Score = 54.4 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 15/69 (21%), Positives = 25/69 (36%), Gaps = 1/69 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+  V+ R G   SR E  +++      VNG  ++  +  V + D I V        + 
Sbjct: 98  MRLDNVVYRLGYGNSRTEARQLVTHGHFLVNGKKVDIPSYQVSANDVITVCDKSKATEKF 157

Query: 73  TRLWLYHKP 81
                  K 
Sbjct: 158 KTFAENPKT 166


>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 = 54.4 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/239 (10%), Positives = 69/239 (28%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +V +    +R+ + +A      SR  ++  I   +V ++G ++ +    ++  + IE+D 
Sbjct: 13  VVPQTLLGKRLDQALAEMFPDYSRSRIKDWILADQVSIDGQIVNKPREKLLGEELIEIDA 72

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                         + +   +   L +      +V   +     + +   L  +      
Sbjct: 73  SIEIQERHSAQEIDLNIVYEDEHILVINKPTNLVVHPGAGNANGTILNALLSHVPDIASV 132

Query: 111 V-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD----------- 154
                  RLD +T GL+++         L                   +           
Sbjct: 133 PRAGIVHRLDKDTTGLMVVAKTIPAQTHLVEKLQAREISREYEAVVYGNLIAGGSVDEPI 192

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V+Q          +  +  ++  + + L  G+  +I+         + 
Sbjct: 193 GRHPTKRTNMAVVQSGKPALTHYRVKHKYRAHTHLRLKLESGRTHQIRVHMAHLRHPLV 251


>gi|224436535|ref|ZP_03657544.1| hypothetical protein HcinC1_01225 [Helicobacter cinaedi CCUG 18818]
          Length = 240

 Score = 54.4 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 25/182 (13%), Positives = 54/182 (29%), Gaps = 14/182 (7%)

Query: 14  QRVS---KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            R+    K +      SR + +  I    VKVNG ++++ +  +   D + VD   L  +
Sbjct: 1   MRLDIYVKSLCS----SRTKAKEAIESGCVKVNGAVVKKGSFLLEKDDEVGVDSKDLLLS 56

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE---GLLLLTND 127
                  Y     + +             +  +I     + G   +  E     ++  + 
Sbjct: 57  RA----GYKLRGFIESLVQKGLWDRAYLFHKKAIDIGASTGGFTQVLLESGIDSVVCVDV 112

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G       +   + + V+          ++   L    V     Y  M+           
Sbjct: 113 GKNQLHTSILQDERVSVFEECDIRDFSDEREFDLMVCDVSFISLYKLMESFERLNVKEYI 172

Query: 188 WV 189
           W+
Sbjct: 173 WL 174


>gi|169838496|ref|ZP_02871684.1| pseudouridine synthase [candidate division TM7 single-cell
          isolate TM7a]
          Length = 44

 Score = 54.4 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 22 RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
            G  SRR+ + +I + RV VN        +++   D + +DG  
Sbjct: 1  ETGFCSRRKADELINEGRVTVN-KQEAIIGMDIKPEDVVRIDGKE 44


>gi|311895525|dbj|BAJ27933.1| putative ribosomal large subunit pseudouridine synthase D
           [Kitasatospora setae KM-6054]
          Length = 312

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 23/243 (9%), Positives = 65/243 (26%), Gaps = 37/243 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIE--- 61
           V +    +R+   +AR    SR +   + A+ +V ++G +  + +  V +     +E   
Sbjct: 12  VPDGLEGERLDAALARMFGFSRTKAAELAAEGKVTLDGAVAGK-SDRVTAGSWLEVEIPA 70

Query: 62  -----------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                      V+G+ +   +   + +               G + +     + +    S
Sbjct: 71  PAAPVQIVAEAVEGMRIIHDDDHVVVIDKPVGVAAHPSPGWTGPTVIGGLAAAGYRISTS 130

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPST-----QWLRVYRVRFHGQVDQDKLNLLKKGI 165
                      L +   G +       +      Q+      + +  + Q   + L   +
Sbjct: 131 GAAERQGVVHRLDVGTSGIMVVAKSERAYTDLKRQFHDRVTEKKYNALVQGHPDPLSGTV 190

Query: 166 VIQGICYGDMQVTLDTQKGSN---------------AWVTVGLREGKNREIKKVFEFFNW 210
                 +          +                  + + + L  G+  +I+        
Sbjct: 191 DAPIGRHPSSDWKWAVTRDGKPSVTHYDLIEAYRAASLLDIKLETGRTHQIRVHMSALRH 250

Query: 211 KVN 213
              
Sbjct: 251 PCV 253


>gi|261366958|ref|ZP_05979841.1| hemolysin A [Subdoligranulum variabile DSM 15176]
 gi|282571076|gb|EFB76611.1| hemolysin A [Subdoligranulum variabile DSM 15176]
          Length = 273

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 18/167 (10%), Positives = 50/167 (29%), Gaps = 2/167 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+ + + + G+  SR   + +I    V V+   +++A   +     +EV G  +    R
Sbjct: 4   IRLDQYLCQHGLVQSRERAKALIMSGIVFVDEQKVDKAGEMIAEDAKVEVRGHDIGYVSR 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L    K + +     D      +  +       ++  G + +    +        L  
Sbjct: 64  GGL-KLEKAMQVFPMRPDGKVCMDIGASTGGFTDCMLQNGAVKVYAVDVGYGQLAWSLRT 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
              + + +   +  V+     +      +    +     +       
Sbjct: 123 DSRVVNMERTNIRNVKPEDLTESISFFSVDVSFISLKHIFPVADQIC 169


>gi|114566130|ref|YP_753284.1| hypothetical protein Swol_0583 [Syntrophomonas wolfei subsp.
          wolfei str. Goettingen]
 gi|114337065|gb|ABI67913.1| conserved hypothetical protein [Syntrophomonas wolfei subsp.
          wolfei str. Goettingen]
          Length = 270

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++    +A SR +   MI    V+VNG ++++    V     IE+
Sbjct: 4  IRLDSLLYDKALAPSREKARAMILAGEVRVNGQMVDKPGTTVDEEARIEL 53


>gi|95929505|ref|ZP_01312248.1| hemolysin A [Desulfuromonas acetoxidans DSM 684]
 gi|95134621|gb|EAT16277.1| hemolysin A [Desulfuromonas acetoxidans DSM 684]
          Length = 250

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 1/56 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          + T +R+ K +   G+  SR     +I    V VN  ++++A   V     I V G
Sbjct: 2  SATKERLDKRVVELGLCRSRERARALIMSGNVLVNETVIDKAGTRVAVDAAIRVRG 57


>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 = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 38/245 (15%), Positives = 77/245 (31%), Gaps = 37/245 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K   ++ +     RV KV+A      SR ++++ + +  V + G  +  A   V + DH+
Sbjct: 3   KQIEVIIKEEKG-RVDKVLAERLPNHSRSQIQQWLKEDAVTLKGETVR-ANYKVKAGDHL 60

Query: 61  --------EVDGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
                    VD  P      +   +     +      +V   +     + V   L  +  
Sbjct: 61  IIQVPEPEVVDLQPENIPLTIVYQDADVAVINKPQGMVVHPSAGHPNGTLVNALLYHMDD 120

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
                   R   V R+D +T GLL++  +      L         + +            
Sbjct: 121 LSTINDVVRPGIVHRIDKDTSGLLMIAKNDQAHESLAKQLKDKTSLRKYVALVHGTISHE 180

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNREIKKVFE 206
                  + +      MQ  ++  K +    TV        L E     G+  +I+   +
Sbjct: 181 KGTINAPIGRSKVNRKMQAVIENGKPAVTHFTVLERFEQFTLVELQLETGRTHQIRVHMQ 240

Query: 207 FFNWK 211
           +  + 
Sbjct: 241 YIGFP 245


>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 = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 47/406 (11%), Positives = 110/406 (27%), Gaps = 66/406 (16%)

Query: 6   IVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           IV+E    +R+ K +   G+    SR +V+++I    VKV G  + +    V +   + V
Sbjct: 4   IVEEKHNGERIDKFL--VGVMENVSRTDVQKLIEAGEVKVGGGKVSK-NFRVETGMAVVV 60

Query: 63  DGVP---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           + +                +   +   + +      +V   +     +     L      
Sbjct: 61  EKMIEKESSTLEPEDIPLNIVYEDDDIVVINKPRNLVVHPGNGVSKGTLAAALLYHFKEN 120

Query: 108 ------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
                  +  G +    +    L             + Q       R +  +       L
Sbjct: 121 LSTVNGPLRPGIVHRLDKDTPGLMVVAKNDAAHRHLAHQLETRTLHRTYNALVWGCPRDL 180

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSN---------------AWVTVGLREGKNREIKKVFE 206
           +  I          ++ +   KG                   + + L  G+  +I+    
Sbjct: 181 EGTIDAPIGRNPKNRLKMAVVKGGKESRTHYVAKQFFAIATLLELQLESGRTHQIRVHSR 240

Query: 207 FFNWKVN----------RLIRI------------SYGPFQLGTLLAGSTREVSKKILREQ 244
           +    V            L R+               P QL  L A     +  +  ++ 
Sbjct: 241 YTGHPVVGDPLYDGRDESLNRVPPLMKPVAEKVLEIAPAQL--LQAVKIELIHPRTNKKL 298

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
                +EE   N+   +           +      D   +++ +   +    ++    +P
Sbjct: 299 TFKVPMEEPFANVLKLLKKECPASAPVYDEEEGFRDFDAQIRFDEDDEFDEYEEPLEISP 358

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                +      A+ +     + + +R     R      K + R+ 
Sbjct: 359 DEAAPVKERKTRAQRLAEKKATAAKRRAVAAERKLIKQMKAARRKG 404


>gi|324989545|gb|EGC21491.1| 30S ribosomal protein S4 [Streptococcus sanguinis SK353]
          Length = 245

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V    L+  
Sbjct: 136 RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVNPGQVISVREKSLKVP 192


>gi|170758349|ref|YP_001788793.1| 30S ribosomal protein S4 [Clostridium botulinum A3 str. Loch Maree]
 gi|169405338|gb|ACA53749.1| 30S ribosomal protein S4 [Clostridium botulinum A3 str. Loch Maree]
          Length = 206

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 15/69 (21%), Positives = 25/69 (36%), Gaps = 1/69 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+  V+ R G   SR E  +++      VNG  ++  +  V + D I V        + 
Sbjct: 98  MRLDNVVYRLGYGNSRTEARQLVTHGHFLVNGKKVDIPSYQVSANDVITVCDKSKATEKF 157

Query: 73  TRLWLYHKP 81
                  K 
Sbjct: 158 KTFAENPKT 166


>gi|195952821|ref|YP_002121111.1| hemolysin A [Hydrogenobaculum sp. Y04AAS1]
 gi|195932433|gb|ACG57133.1| hemolysin A [Hydrogenobaculum sp. Y04AAS1]
          Length = 246

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 15 RVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
          R+  ++   G+ S RE  +  I + RV VNG  + +A   V   D IE+ G  
Sbjct: 4  RLDLLLVEKGLVSSREKAQAFIMEGRVFVNGKAVLKAGTLVQEEDGIELLGEE 56


>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 = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 34/236 (14%), Positives = 65/236 (27%), Gaps = 38/236 (16%)

Query: 14  QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------- 63
           QRV  V+AR     SR  +   I    V +N +  +      +  D I ++         
Sbjct: 18  QRVDSVLARLLPEYSRSLICNWIKTGAVTLNNLPCK-PKDKALGGDLITINVDYTIDNTD 76

Query: 64  ---------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI----- 109
                     + +   +   + +      +V   +     + V   L       +     
Sbjct: 77  FNLCKPENIPIQIVYEDSEVIVVNKPASLVVHPGAGNKEHTLVNALLHHCPELQLLPRAG 136

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR------------VRFHGQVDQDK 157
            + RLD +T GLL++  +      L                                +  
Sbjct: 137 IIHRLDKDTTGLLIVAKNLISHTYLIRQMQNREIKRHYLTLVHGYVISGGTIDTGFGRHP 196

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            N LK  +   G         ++        + V L  G+  +I+    + N  V 
Sbjct: 197 KNRLKMAVTDFGRQA-VTHYNINKHYKDFTLLNVSLMTGRTHQIRVHMNYINHPVV 251


>gi|307634844|gb|ADI84260.2| rRNA methyltransferase, YqxC-related, putative [Geobacter
          sulfurreducens KN400]
          Length = 263

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 15/69 (21%), Positives = 30/69 (43%), Gaps = 1/69 (1%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          M   + +    + +R+ K++   G+  SR     +I   +V VN  L ++A + V     
Sbjct: 1  MTASSTLNTAKSRERLDKLLVDRGLVQSRERARALIMAGQVVVNDHLADKAGLQVPVEAE 60

Query: 60 IEVDGVPLR 68
          I + G  + 
Sbjct: 61 IRLKGEDIP 69


>gi|238917013|ref|YP_002930530.1| putative hemolysin [Eubacterium eligens ATCC 27750]
 gi|238872373|gb|ACR72083.1| putative hemolysin [Eubacterium eligens ATCC 27750]
          Length = 267

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/165 (15%), Positives = 53/165 (32%), Gaps = 2/165 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++   G+A SR + + +I    V V+G   ++A  +   T  IEV G  L+   R
Sbjct: 4   ERLDVLLVNKGLATSREKAKAIIMSGNVYVDGQKEDKAGQSFPDTAVIEVRGTTLKYVSR 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L         T                    ++  G + +    +     D  L  
Sbjct: 64  GGLKLEKAMQNFDVTLEGKICMDVGSST-GGFTDCMLQNGAIKVYAVDVGHGQLDWKLRN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
              +   +   +  V      D+ + + +    +        ++ 
Sbjct: 123 DERVVCMEKTNIRYVTPDDVADRIQFSSIDVSFISLTKVLTPVRN 167


>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 = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 26/232 (11%), Positives = 62/232 (26%), Gaps = 37/232 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+ K +       SR +++  I    V VNG  ++     ++  DH+++           
Sbjct: 16  RIDKQLGHHFDQFSRSQIQHWIEDGHVLVNGKQVK-PKYKLLVGDHVQIIPEEPQKIDLA 74

Query: 67  -------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI---------- 109
                  +   +   + +      +V         + V   L       I          
Sbjct: 75  PEDIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHSPLSTINGEFRPGIVH 134

Query: 110 ----------SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
                      V + D+    L          R         ++  +      + +   +
Sbjct: 135 RIDKDTSGLLMVAKNDMAHRSLTAQLKAKTNKREYVALVHGVIKEDKGTIDAPLGRSLKD 194

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             KK  V+    +      +  +  +   V   L  G+  +I+   ++    
Sbjct: 195 R-KKQGVVVDGRHAVTHFNVLERFKNYTLVACQLETGRTHQIRVHMKYIGHP 245


>gi|328724994|ref|XP_001952731.2| PREDICTED: hypothetical protein LOC100168337, partial
           [Acyrthosiphon pisum]
          Length = 1131

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 27/156 (17%), Positives = 49/156 (31%), Gaps = 16/156 (10%)

Query: 5   NIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--- 60
            I  EN    R+ K++       SR +++  I    V+VNG +++ A       D I   
Sbjct: 479 KIETENEIGVRIDKLLPDLNPDWSRNQIQDWIKLGLVEVNGKVIK-ANYKTKLNDVIVAT 537

Query: 61  -----EVD------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                EVD      G+ +   ++    +Y     +V         + V   +  I     
Sbjct: 538 EKVIEEVDIVAEDLGIEVYYEDKDVAVVYKPKGMVVHPAPGHYTGTLVNGLMYVIKDLSG 597

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY 145
             G +       +     G L       + + L   
Sbjct: 598 INGEIRPGIVHRIDKDTSGLLMIAKNDIAHRGLVEQ 633


>gi|261368842|ref|ZP_05981725.1| S4 domain protein [Subdoligranulum variabile DSM 15176]
 gi|282569112|gb|EFB74647.1| S4 domain protein [Subdoligranulum variabile DSM 15176]
          Length = 71

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 30/63 (47%), Gaps = 1/63 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          +    ++  ++  AG+  +  E + +I    VKVNG +         + D +E+DG  ++
Sbjct: 7  HTEYIKLDALLKFAGLCETGGEAKELIQGGAVKVNGEVCTMRGKKCRAGDTVELDGRTVQ 66

Query: 69 KAE 71
           AE
Sbjct: 67 VAE 69


>gi|169836316|ref|ZP_02869504.1| pseudouridine synthase [candidate division TM7 single-cell isolate
           TM7a]
          Length = 42

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 1/40 (2%)

Query: 204 VFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           +F+  N +V  L R+  G   L   L  G  RE++++ L 
Sbjct: 1   MFKAVNNEVLYLKRVKMGNLSLDEKLKLGEYRELTEEELD 40


>gi|125719124|ref|YP_001036257.1| 30S ribosomal protein S4 [Streptococcus sanguinis SK36]
 gi|125499041|gb|ABN45707.1| 30S ribosomal protein S4, putative [Streptococcus sanguinis SK36]
 gi|325686442|gb|EGD28471.1| 30S ribosomal protein S4 [Streptococcus sanguinis SK72]
 gi|325698067|gb|EGD39948.1| 30S ribosomal protein S4 [Streptococcus sanguinis SK160]
 gi|327463801|gb|EGF10117.1| 30S ribosomal protein S4 [Streptococcus sanguinis SK1057]
 gi|327467659|gb|EGF13156.1| 30S ribosomal protein S4 [Streptococcus sanguinis SK330]
 gi|327471574|gb|EGF17017.1| 30S ribosomal protein S4 [Streptococcus sanguinis SK408]
 gi|328945138|gb|EGG39293.1| 30S ribosomal protein S4 [Streptococcus sanguinis SK1087]
 gi|332363571|gb|EGJ41352.1| 30S ribosomal protein S4 [Streptococcus sanguinis SK1059]
 gi|332364129|gb|EGJ41906.1| 30S ribosomal protein S4 [Streptococcus sanguinis SK49]
          Length = 245

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V    L+  
Sbjct: 136 RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVTPGQVISVREKSLKVP 192


>gi|123969198|ref|YP_001010056.1| rRNA methyltransferase [Prochlorococcus marinus str. AS9601]
 gi|123199308|gb|ABM70949.1| FtsJ cell division protein:S4 domain:Hemolysin A [Prochlorococcus
          marinus str. AS9601]
          Length = 270

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 11/54 (20%), Positives = 27/54 (50%), Gaps = 2/54 (3%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVK-VNGILLERAAVNVMSTDHIEVDGVP 66
          R+   +   G+  +R++ + +I   +V+ +NG +L++    V+      +D  P
Sbjct: 6  RLDLYLLNKGLCETRQKAQGLILAGKVRDINGKVLDKPGQQVLIGSEFFIDSEP 59


>gi|78779941|ref|YP_398053.1| hemolysin A [Prochlorococcus marinus str. MIT 9312]
 gi|78713440|gb|ABB50617.1| hemolysin A [Prochlorococcus marinus str. MIT 9312]
          Length = 270

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 11/54 (20%), Positives = 27/54 (50%), Gaps = 2/54 (3%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVK-VNGILLERAAVNVMSTDHIEVDGVP 66
          R+   +   G+  +R++ + +I   +V+ +NG +L++    V+      +D  P
Sbjct: 6  RLDLYLLNKGLCETRQKAQGLILAGKVRDINGKVLDKPGQQVLIGSEFFIDSEP 59


>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 = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 29/247 (11%), Positives = 59/247 (23%), Gaps = 41/247 (16%)

Query: 6   IVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +V      +R  + IA A      SR +++R I+  ++ ++  +       + S  HI  
Sbjct: 44  MVSPQAAGERADRFIAAALAGDAISRGKIQRAISDGQLLIDNTVCTSPKTKLKSGQHIVF 103

Query: 63  ------------DGVP-LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                       +G   +   +   L +       V         + V   L        
Sbjct: 104 SMEAPAACVSPEEGELEVLYRDAHMLVINKPAGLTVHPAPSCPEGTLVHRLLHHFPELEA 163

Query: 110 SVGRLDINTEGL---------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
             G        +         + LT    LA        +  + Y     G  + D   +
Sbjct: 164 QEGFRPGIVHRIDKDTSGLLLIALTEKARLALSDAFAGRRIHKEYLALVKGIPEGDSGEI 223

Query: 161 LKKGIVIQGICYGDM----------QVTLDTQKG------SNAWVTVGLREGKNREIKKV 204
                                       +               V V +  G+  +I+  
Sbjct: 224 DAPVGRHPTHKTRMAVVRGGREALSTWRVLLADPHGGGGTGWTLVAVRIHTGRTHQIRVH 283

Query: 205 FEFFNWK 211
            +     
Sbjct: 284 MQHTGHP 290


>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 = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 33/238 (13%), Positives = 68/238 (28%), Gaps = 42/238 (17%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           RV K + +R   ASR +++       + VNG  ++  +  V   D + V           
Sbjct: 38  RVDKFLMSRLPNASRTKIQEAADAGNILVNGKAVKS-SYKVKPKDIVSVVMAYPRREIEI 96

Query: 63  --DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-------- 110
             + +P  +   +   + +      +V         + V      +    +         
Sbjct: 97  IPENIPLNIVYEDDDLMVVNKPAGMVVHPSYGHYTGTLVNALAWHLKGNPLFKDNNDPRP 156

Query: 111 --VGRLDINTEGLLLLTNDGGLARV-------------LELPSTQWLRVYRVRFHGQVDQ 155
             V R+D +T GLL++                              L        G + +
Sbjct: 157 GLVHRIDKDTSGLLVIAKTEKAKTHLGLQFFNKTSDRKYVAVCWGNLEDETGTITGHIGR 216

Query: 156 DKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +  N         G    +      +  + G    V   L  G+  +I+  F++    
Sbjct: 217 NLTNRKVMACFPDGSHGKHAVTHYRVLERLGYVNVVECILETGRTHQIRAHFKYIKHP 274


>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 = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 37/249 (14%), Positives = 76/249 (30%), Gaps = 37/249 (14%)

Query: 1   MK-DKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           MK +K +V+E F  +R+   I       SR  ++++   + + VN  + ++    V   D
Sbjct: 3   MKIEKFLVKEEFENERLDLFIVENLKDKSRSFIKKLSDDKGIMVNDEI-KKVNYKVKCGD 61

Query: 59  HIEV-----DGVPLR---------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            ++V     +G+ L            +   + +      +V         + V   L   
Sbjct: 62  IVKVLLPKEEGIYLEKENMDLNILYEDEDIIVINKPQGMVVHPGVGNTKGTLVNGLLAHC 121

Query: 105 FSRVISVGRLDINTEGLL----------LLTNDGGLARVLELPSTQWLRVYRVRFHGQVD 154
            S     G         +            TN        +L     LRVY     G + 
Sbjct: 122 KSLSNINGEERPGIVHRIDKDTSGILVIAKTNRAHEHLANQLKDHSMLRVYMALTEGVIK 181

Query: 155 QDK----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
           +D            +   K  V+           +  +  +N+ +   L  G+  +I+  
Sbjct: 182 EDMGTIDKDLGRNPSDRIKFAVVDEGKRAVTHYKVINRYNNNSLIECRLETGRTHQIRVH 241

Query: 205 FEFFNWKVN 213
             +    + 
Sbjct: 242 MSYIGHPIV 250


>gi|186685337|ref|YP_001868533.1| hemolysin A [Nostoc punctiforme PCC 73102]
 gi|186467789|gb|ACC83590.1| hemolysin A [Nostoc punctiforme PCC 73102]
          Length = 272

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          QR+  ++    + S R   +R+I    V VN  L+++    V  +  I +
Sbjct: 4  QRLDTLLVELNLCSSRALAQRLIQAGEVTVNQQLVDKPGTEVDISAQINI 53


>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 = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 29/242 (11%), Positives = 73/242 (30%), Gaps = 38/242 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRRE--------VERMIAQQRVKVNGILLERAAVN 53
           K+  + +ENF  +R+ +V+       R+E        + +++ +  V+VNG  +   +  
Sbjct: 21  KEFKVTKENFY-ERLDRVL-------RKELSDLKLSSIYKLLRRGNVRVNGNKIRDGSWK 72

Query: 54  VMSTDHIEV--DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
           +   D ++V   G P +                +    + D    V             +
Sbjct: 73  MEIGDKVQVVFSGDPSKLKRLEESRELTPKHIPLDILFEDDLIVAVDKPSGISVHPGKGI 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
             + +    +    + G + R +         V       +  ++   L ++  V +G  
Sbjct: 133 QIITLVEGLMAYGNSKGFVPRPVHRLDKHTSGVILFAKSPEAARELSKLFRERGVEKGYF 192

Query: 172 YG----DMQVTLDTQKGSN----------------AWVTVGLREGKNREIKKVFEFFNWK 211
                   +      +                   + + + L  GK  +I++      + 
Sbjct: 193 TLVKGFPEKRGKLVSQREKFVESLAFTVEKSYATTSLLWIDLFTGKKHQIRRQLSEAGYP 252

Query: 212 VN 213
           V 
Sbjct: 253 VV 254


>gi|71893806|ref|YP_279252.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyopneumoniae J]
          Length = 289

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 29/240 (12%), Positives = 73/240 (30%), Gaps = 43/240 (17%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI------------- 60
            R+  ++A+    SR+  + +I +++V +N  L+ +    V +   I             
Sbjct: 1   MRIDILVAKLANLSRKVAQDLILEKKVLINNNLVLKKNQIVKTGQKIKIFNDYKRPKPQL 60

Query: 61  ---EVDGVPLRKAERTRLWLYHKPIGLV-------------------TTHSDPDGRSTVF 98
              E+D   + + +   L    K + +                    +       R  + 
Sbjct: 61  EPAEIDFEIIFQDQNMILINKPKNLVVHPGVGNWKNTLVNGLISHFDSLEQLDHIRPGIV 120

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
             L    + ++ V +        +    +  + R  +      +    ++ +  + +D  
Sbjct: 121 HRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVIGKVLHKFMKINLPIGRDLK 180

Query: 159 NLLKKGIVIQGICYGDMQVTLD------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           N LKK I             ++       Q    + V   L  G+  +I+       + +
Sbjct: 181 NPLKKTISFFNS--KPAITNVELIKHFSYQNQDFSLVKCQLETGRTHQIRLHLAHIGYPI 238


>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 = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 31/264 (11%), Positives = 80/264 (30%), Gaps = 35/264 (13%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           + V+ +   QR+ + +A      SR  ++  +   +++V+G ++ +    V+  + I + 
Sbjct: 9   DTVKSSQLGQRLDQAVAELFTDFSRSRIKEWLLDGKIQVDGEVITKPRTIVLGGEAIILQ 68

Query: 63  ----DGVPLRKAERT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
               D       +            L +      +V   +     + +   L        
Sbjct: 69  AELADEERWEAQDIPLDIVYEDDDLLVINKPRDLVVHPGAGTPDGTILNALLFHYPQIAE 128

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------- 155
                   RLD +T GL+++         L     +                        
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALAKRRITREYEAIAIGKMTAGGVVEKG 188

Query: 156 DKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +  K+ ++              +      +  + + L  G+  +I+    +    + 
Sbjct: 189 ISRHATKRTLMDVNELGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPL- 247

Query: 214 RLIRISYGPFQLGTLLAGSTREVS 237
            L  I+YG      +  G++ E++
Sbjct: 248 -LGDIAYGGRA--RIPKGASEELT 268


>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 = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 29/257 (11%), Positives = 74/257 (28%), Gaps = 50/257 (19%)

Query: 4   KNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K I  +N    R+ K +       SR ++++     ++ VN  ++++    +   D +E+
Sbjct: 11  KIITNKNQKEIRIDKFLKNYIQNISRNQIQKWTTSGKILVNKNIVKK-NYKIKPLDFVEI 69

Query: 63  D--------------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
           +                     + +   +   L +      +V      +  + +     
Sbjct: 70  EISIPSVLDHLEYKNITAEKINLDILYEDEDVLVVNKPAGMVVHPGFGNETGTLIHGIKY 129

Query: 103 S---------IFSRVISVGRLDINTEGLLLLTNDGGLARVLELP---------------- 137
                        R   V RLD +T GLL+   +    + L                   
Sbjct: 130 HLTNSNLNNFNLYRCGLVHRLDKDTSGLLVFAKNEYSQKHLFQQFYSRTIQRKYIALIWG 189

Query: 138 ---STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +      +    +  +    L ++        +      +  +     +V+  ++
Sbjct: 190 NLIEEKGTITGFIGRDPKNRKKMTILKQENQEFNKGKFSVTHYKVLERFKYLTYVSCNIK 249

Query: 195 EGKNREIKKVFEFFNWK 211
            GK  +I+  F+     
Sbjct: 250 TGKTHQIRAHFKHLGHP 266


>gi|218294781|ref|ZP_03495635.1| RNA-binding S4 domain protein [Thermus aquaticus Y51MC23]
 gi|218244689|gb|EED11213.1| RNA-binding S4 domain protein [Thermus aquaticus Y51MC23]
          Length = 209

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SRR+  +M+    + VNG  ++  A  V   D I +
Sbjct: 100 RLDNVVYRLGFAQSRRQARQMVRHGHITVNGRRVDLPAYRVKPGDEIAI 148


>gi|254423526|ref|ZP_05037244.1| photosystem II S4 domain protein [Synechococcus sp. PCC 7335]
 gi|196191015|gb|EDX85979.1| photosystem II S4 domain protein [Synechococcus sp. PCC 7335]
          Length = 259

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 15/65 (23%), Positives = 27/65 (41%), Gaps = 2/65 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             K  +       R+   +A AG   SR ++  MI    V+VN   + +A+  +   D +
Sbjct: 172 PKKKEMTTVEASMRLD-ALASAGFGMSRSKMADMITGGDVRVNWKPVTQASQTLQPGDLV 230

Query: 61  EVDGV 65
            + G 
Sbjct: 231 AIRGK 235


>gi|160932173|ref|ZP_02079564.1| hypothetical protein CLOLEP_01008 [Clostridium leptum DSM 753]
 gi|156868775|gb|EDO62147.1| hypothetical protein CLOLEP_01008 [Clostridium leptum DSM 753]
          Length = 200

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G AS RR+  +++      VNG  +   +  V   D IEV
Sbjct: 90  RLDNVVYRLGFASTRRDARQLVNHGHFTVNGKRVNIPSYLVKPGDVIEV 138


>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 = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 32/249 (12%), Positives = 74/249 (29%), Gaps = 38/249 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +D   VQ     +R+ K ++      SR   +R++ + ++ VN    ++A   + + D +
Sbjct: 3   RDTFEVQSEQEGERLDKYLSSIYPDISRSFFQRILKENQILVNDKP-QKANYRLKTDDIV 61

Query: 61  EV------------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           +V              +PL     +   L +      +V   +     + V   +     
Sbjct: 62  DVTIPDAVQTPILPQDIPLDILYEDDDVLVVNKPKGMVVHPSAGHYSDTLVNAIMYHCKD 121

Query: 107 RVISVGRL----------DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
            +  +                T  L++  ND    ++ E           V       +D
Sbjct: 122 SLSGINGEIRPGIVHRIDMDTTGSLIVCKNDESHIKISEQIKDHSCNRIYVGIVCGNVKD 181

Query: 157 KLNLL----------KKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKV 204
               +          +K + I             +  + G   ++   L  G+  +I+  
Sbjct: 182 DEGTIEGAIGRNPNDRKKMAINEKNGKPAVTHYKVLERFGDYTYMQFKLETGRTHQIRVH 241

Query: 205 FEFFNWKVN 213
               N  + 
Sbjct: 242 MASINHPLL 250


>gi|72080790|ref|YP_287848.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyopneumoniae 7448]
          Length = 289

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 29/240 (12%), Positives = 73/240 (30%), Gaps = 43/240 (17%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI------------- 60
            R+  ++A+    SR+  + +I +++V +N  L+ +    V +   I             
Sbjct: 1   MRIDILVAKLANLSRKVAQDLILEKKVLINNNLVLKKNQIVKTGQKIKIFNDYKRPKPQL 60

Query: 61  ---EVDGVPLRKAERTRLWLYHKPIGLV-------------------TTHSDPDGRSTVF 98
              E+D   + + +   L    K + +                    +       R  + 
Sbjct: 61  EPAEIDFEIIFQDQNMILINKPKNLVVHPGVGNWKNTLVNGLISHFDSLEQLDHIRPGIV 120

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
             L    + ++ V +        +    +  + R  +      +    ++ +  + +D  
Sbjct: 121 HRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVIGKVLHKFMKINLPIGRDLK 180

Query: 159 NLLKKGIVIQGICYGDMQVTLD------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           N LKK I             ++       Q    + V   L  G+  +I+       + +
Sbjct: 181 NPLKKTISFFNS--KPAITNVELIKHFNYQNQDFSLVKCQLETGRTHQIRLHLAHIGYPI 238


>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 = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 36/237 (15%), Positives = 73/237 (30%), Gaps = 36/237 (15%)

Query: 10  NFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP-- 66
                R+ KVIA      SR +++ ++  + + VN    E+ +  V + D I++   P  
Sbjct: 10  EEEKGRLDKVIAEKLKDLSRTKIKELVNDKNILVNHK-AEKVSYKVQAGDSIDITVPPAK 68

Query: 67  ------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------S 106
                       +   +   + +      +V   +     + V   L             
Sbjct: 69  PLSLEAQNLNLDIVYEDADVIVVNKPQGMVVHPSAGHPDHTLVNGLLYHTHELADSPEGF 128

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD---------- 156
           R   V R+D +T GLL++  +      LE    + +           + +          
Sbjct: 129 RPGIVHRIDKDTSGLLMVAKNDKARESLEKQLAEKINKREYLAIVHGNFETKNGVIDAPI 188

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               N  K+  V           T+  Q    + V   L  G+  +I+   ++    
Sbjct: 189 GRNPNNRKQMAVNPKGKAAVTHFTVLEQFKDYSLVKCILETGRTHQIRVHMKYIGHP 245


>gi|258515777|ref|YP_003191999.1| hemolysin A [Desulfotomaculum acetoxidans DSM 771]
 gi|257779482|gb|ACV63376.1| hemolysin A [Desulfotomaculum acetoxidans DSM 771]
          Length = 269

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          +R+   + R G   SR +    I    + VN   +++A   V S   +EV G  L+ 
Sbjct: 6  ERLDNFLVREGFFPSREKARSAIMAGLIYVNDQRMDKAGTQVSSGVQVEVRGNALKY 62


>gi|289548515|ref|YP_003473503.1| ribosomal protein S4 [Thermocrinis albus DSM 14484]
 gi|289182132|gb|ADC89376.1| ribosomal protein S4 [Thermocrinis albus DSM 14484]
          Length = 209

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GI  +RR+  + +A   + VNG  +   +  V   D IEV
Sbjct: 99  RLDNVVYRLGIACTRRQARQFVAHGHILVNGKKVNIPSYLVEPGDVIEV 147


>gi|119486986|ref|ZP_01620858.1| Hemolysin A [Lyngbya sp. PCC 8106]
 gi|119455915|gb|EAW37049.1| Hemolysin A [Lyngbya sp. PCC 8106]
          Length = 300

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          QR+  ++    + S R   +R+I    V VN  ++++    +     I+V
Sbjct: 4  QRLDTLLIDRNLCSSRHIAQRLIRAGEVMVNQQVIDKPGTEIDLEAQIKV 53


>gi|303233180|ref|ZP_07319853.1| ribosomal protein S4 [Atopobium vaginae PB189-T1-4]
 gi|302480765|gb|EFL43852.1| ribosomal protein S4 [Atopobium vaginae PB189-T1-4]
          Length = 176

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           R+  V+ R G A +R+E  + +    + VNG  ++  +  V + D I V+   
Sbjct: 67  RLDNVVFRLGFARTRKEARQTVRHGHITVNGKRVDIPSYQVKAQDVIAVNPKA 119


>gi|225849728|ref|YP_002729962.1| hemolysin A [Persephonella marina EX-H1]
 gi|225646217|gb|ACO04403.1| hemolysin A [Persephonella marina EX-H1]
          Length = 272

 Score = 54.4 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 11/56 (19%), Positives = 25/56 (44%), Gaps = 1/56 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
            +R+ K++   G+  SR + +R+I    V VN   +++    +    +I +    
Sbjct: 3  KKERIDKLLVERGLVESREKAQRLIMAGCVFVNDQRVDKPGTKIPVDANIFLKEKE 58


>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 = 54.0 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 4/57 (7%)

Query: 10 NFTPQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          +  P R+ K +AR    A   SR  + R+I +  V V+G ++      V     +++
Sbjct: 12 DSPPARLDKALARDVPEAANLSRTRLGRLIEEGAVTVDGAVVHDPRAKVAEGQVVQI 68


>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 = 54.0 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 28/245 (11%), Positives = 62/245 (25%), Gaps = 40/245 (16%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           VQ     QR+   +       SR    R+I Q  V V+   +++ +  +   + + V   
Sbjct: 11  VQNKEQGQRLDAFVPVHCKNLSRNACARLIRQGLVTVD-KSVKKPSYVLKPGEMVSVTVP 69

Query: 64  ------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                        + +   +R  + +   P  +V         + V   L          
Sbjct: 70  EPETADIVAQDMDLAILYEDRDIVAVNKPPGMVVHPAPGHSSNTLVNALLAHCKDLSGIG 129

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ------------------- 152
           G         L     G +       +   L     +   +                   
Sbjct: 130 GVQRPGIVHRLDKETSGVILAAKNDAAHAGLSEQLAQRRVEKFYLALAHGVIKEDTGVID 189

Query: 153 ----VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                       +      +G     +  T+  +     +V V ++ G+  +I+      
Sbjct: 190 LPLARHPSDRKRMHVSTPAKGREALSL-WTVKERFLDATYVKVQIKTGRTHQIRVHLAAL 248

Query: 209 NWKVN 213
           +  V 
Sbjct: 249 HHPVI 253


>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 = 54.0 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 31/264 (11%), Positives = 80/264 (30%), Gaps = 35/264 (13%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           + V+ +   QR+ + +A      SR  ++  +   +++V+G ++ +    V+  + I + 
Sbjct: 9   DTVKSSQLGQRLDQAVAELFTDFSRSRIKEWLLDGKIQVDGEVITKPRTIVLGGEAIILQ 68

Query: 63  ----DGVPLRKAERT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
               D       +            L +      +V   +     + +   L        
Sbjct: 69  AELADEERWEAQDIPLDIVYEDDDLLVINKPRDLVVHPGAGTPDGTILNALLFHYPQIAE 128

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------- 155
                   RLD +T GL+++         L     +                        
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALAKRRITREYEAIAIGKMTAGGVVEKG 188

Query: 156 DKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +  K+ ++              +      +  + + L  G+  +I+    +    + 
Sbjct: 189 ISRHATKRTLMDVNELGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPL- 247

Query: 214 RLIRISYGPFQLGTLLAGSTREVS 237
            L  I+YG      +  G++ E++
Sbjct: 248 -LGDIAYGGRA--RIPKGASEELT 268


>gi|297170255|gb|ADI21292.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium HF0010_09F21]
          Length = 305

 Score = 54.0 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 35/243 (14%), Positives = 76/243 (31%), Gaps = 35/243 (14%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K  NI + N    R+   ++      SR  V+++I Q  V VN + +++    +   D I
Sbjct: 4   KTFNIDEANINK-RLDSFLSDILDDISRGLVQQLIEQGNVLVNDLEVKK-NYKLRLNDQI 61

Query: 61  EV--------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---- 102
           +V        +  P      +         +  +    V   +     + +   L     
Sbjct: 62  QVILQFPEVIEDEPQNIPLDIVFENEDFYIINKQAGLTVHPGAGQKDNTLLNGLLHLNKK 121

Query: 103 -SIFSRVISVGRLDINTEGLLLLTNDGGLA------------RVLELPSTQWLRVYRVRF 149
               SR   V RLD  T GL+++  +                            +     
Sbjct: 122 ACELSRCGIVHRLDKETSGLMVVAKNHSSQTILTNLIKDRAIERKYYALVHGNVISGGTI 181

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              +++   N L   +  +G         +  +  + + + V L  G+  +I+   +   
Sbjct: 182 DEPIERHPKNRLIFIVDQEGKESKT-HYLVKERYENFSLLDVKLETGRTHQIRVHLKHIG 240

Query: 210 WKV 212
           + +
Sbjct: 241 FPI 243


>gi|223938948|ref|ZP_03630834.1| hemolysin A [bacterium Ellin514]
 gi|223892375|gb|EEF58850.1| hemolysin A [bacterium Ellin514]
          Length = 252

 Score = 54.0 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+ + +   G+  SR +  R I   +V +N    ++ +  V   D+I +
Sbjct: 5  RLDQALVERGLCESREKARRAIMAGQVTINQQPAKKPSDRVKQGDNIAL 53


>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 = 54.0 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 33/245 (13%), Positives = 70/245 (28%), Gaps = 38/245 (15%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           + +     R+ K ++      SR +V++ I    V++N +++  + V V   D I     
Sbjct: 6   IPKELNNTRLDKALSSLLEKVSRNQVQKAIKNSCVQINDVIISDSDVLVKENDTILFSFK 65

Query: 63  DGVPLRK----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
           +   L+            E   L + +K  G+          +T+ + L      +  +G
Sbjct: 66  EPEELKITSANITLDIIYEDDDLIVINKAAGITVHPGAKHHDNTLVNALLHHTKNLSDIG 125

Query: 113 RLDIN--------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
             +              L++      A +L     +  +V R                  
Sbjct: 126 SAERPGIVHRLDKETTGLMVVAKNNKAHMLLAKQIEQRQVIRKYKALVWGVINPLEGIIN 185

Query: 165 IVIQGICYGDMQVTLDTQKGSN----------------AWVTVGLREGKNREIKKVFEFF 208
             I        ++T+    G                  + V   L  G+  +I+      
Sbjct: 186 NNIGRNRNNRKKMTILKYGGKKAVTHYKTLELFYGGTLSMVECKLSTGRTHQIRVQLSNL 245

Query: 209 NWKVN 213
              V 
Sbjct: 246 KHSVV 250


>gi|52307928|gb|AAU38428.1| RluA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 327

 Score = 54.0 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 27/238 (11%), Positives = 60/238 (25%), Gaps = 31/238 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           VQ +   QR+ + +A      SR  ++  I  + V +NG +       V   + +E+   
Sbjct: 13  VQPHQMGQRLDQTLAELFPDYSRSRLKTWIEDELVLLNGKVANIPREKVYGGEQVEITVE 72

Query: 66  P--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                          +   +   L +      +V   +     + +   L          
Sbjct: 73  IEDENRFEPQNIPLNIVYEDDDILVINKPKDFVVHPGAGNPNGTVLNALLYHYPQITEVP 132

Query: 112 -----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-----------FHGQVDQ 155
                 RLD +T GL+++         L     +                      +   
Sbjct: 133 RAGIVHRLDKDTTGLMVVAKTIPAQTQLVRALQKRKITREYEAIAFGIMTKGGTVDEPMS 192

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     V            +     +   + + L  G+  +I+         + 
Sbjct: 193 RHPTKRTLMAVHPMGKPAVTHYRVMEHFRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 250


>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 = 54.0 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 30/239 (12%), Positives = 69/239 (28%), Gaps = 33/239 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +Q     QR+ + +A      SR  ++  I    VKVNG ++  A   V   + +E+   
Sbjct: 7   IQPQHMGQRLDQTLAELFPDYSRSRLKTWIEGDLVKVNGEIINVARTKVYGGELVELCVE 66

Query: 66  P--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                          +   +   L +      +V   +     + +   L      V   
Sbjct: 67  IEEESRFEPENLPLNIVYEDEHILVINKPKDFVVHPGAGNQRGTVLNALLYHYPKIVEVP 126

Query: 112 -----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR------------VRFHGQVD 154
                 RLD +T GL+++         L     +   +               +    + 
Sbjct: 127 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVQDLQKRKIIREYEAVAFGVMTQGGKVDQPMS 186

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +      +  +   G         +  +  +   + + L  G+  +I+      +  + 
Sbjct: 187 RHPTKRTQMAVHPLGKPA-VTHYRIMERFRNYTRLRLRLETGRTHQIRVHMAHISHPLL 244


>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 = 54.0 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 31/234 (13%), Positives = 57/234 (24%), Gaps = 35/234 (14%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILL----------------ERAAVNV-- 54
            +RV   ++R    SR +   + AQ  V +NG                      AV    
Sbjct: 15  GERVDAALSRMLGMSRSKCADLAAQGAVTLNGRTAGKSDRLGAADIIGIDMPDPAVKAVP 74

Query: 55  --------MSTDHIEVDGVPL-------RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
                      D + VD  P+          E   +       G   T   P  R  +  
Sbjct: 75  VTGMDILYDDEDIVVVD-KPVGVAAHTGPGWEGPTVLGNLAAAGYRITTHGPPERQGIVH 133

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
            L    S  + V + ++    +     +  + +V        L          + +    
Sbjct: 134 RLDVGTSGAMMVAKSELAYSVMKRAFKERTVTKVYHAVVAGHLDPASGTIDAPIGRHPSR 193

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             +  + I G                     + L  G+  +I+           
Sbjct: 194 EWRMAV-IDGGKRAITHYDTLEMMAGACLAEIHLETGRTHQIRVHMAAVGHPCV 246


>gi|227873687|ref|ZP_03991921.1| hemolysin A [Oribacterium sinus F0268]
 gi|227840476|gb|EEJ50872.1| hemolysin A [Oribacterium sinus F0268]
          Length = 275

 Score = 54.0 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 20/157 (12%), Positives = 40/157 (25%), Gaps = 1/157 (0%)

Query: 12  TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             +R+  ++   G+  SR + +R I    V VNG   ++A  +      I V G  L   
Sbjct: 4   KKERLDVLLVERGLMESREKAKRAIMAGLVFVNGEKEDKAGSSFPEEAEILVKGKALPYV 63

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            R  L L         +  +                 + +        +      +    
Sbjct: 64  SRGGLKLEKALKSFPISLENRVCMDIGASTGGFTDCMLQNGAVEVYAVDVGHGQLDWKLR 123

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
                    +    Y          +K +     +  
Sbjct: 124 NDERVHSMEKCNIRYVEEEDILALGEKPSFFSIDVSF 160


>gi|223043737|ref|ZP_03613780.1| YlmH protein [Staphylococcus capitis SK14]
 gi|222442834|gb|EEE48936.1| YlmH protein [Staphylococcus capitis SK14]
          Length = 262

 Score = 54.0 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 27/60 (45%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            I     +  R+  V+      SR   +++I ++RVKVN  +++     +   D + + G
Sbjct: 176 KIQSTTVSAMRLDVVLKDMIHKSRNIAKQLIEKKRVKVNHTIIDTPDFQLEQNDLLSIQG 235


>gi|332359530|gb|EGJ37349.1| 30S ribosomal protein S4 [Streptococcus sanguinis SK1056]
          Length = 226

 Score = 54.0 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V    L+  
Sbjct: 117 RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVTPGQVISVREKSLKVP 173


>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 = 54.0 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 36/248 (14%), Positives = 75/248 (30%), Gaps = 41/248 (16%)

Query: 4   KNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           + +V +  +  R+ + +  R   A+R +++  I  + V+VN     +A+  +  +D I V
Sbjct: 19  RIVVDKGQSLLRIDRFLMDRLQNATRTKIQAGIDAESVRVNDKP-TKASYKIKPSDIITV 77

Query: 63  ---------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                    D  P      +   +   L +      +V         + V   +    + 
Sbjct: 78  SLPHPPRETDLKPENIPINIVFEDDDLLVINKPAGMVVHPAHGNWDGTLVNALVYHFQNL 137

Query: 108 VIS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
             S         V R+D +T GL+++         L     +               +  
Sbjct: 138 PTSRHGEVRPGLVHRIDKDTSGLMVIAKTEFAMTYLARQFFEHTIERTYNALTWGVPNPQ 197

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSN---------------AWVTVGLREGKNREIKK 203
                G + + I    +Q   D +                   A V   L  G+  +I+ 
Sbjct: 198 IGTITGFIGRSIKDRKVQAIYDDESKGKWAVTHYTTLEDLGYVALVECKLETGRTHQIRA 257

Query: 204 VFEFFNWK 211
            F+     
Sbjct: 258 HFKHIGNP 265


>gi|261337851|ref|ZP_05965735.1| cytotoxin/hemolysin [Bifidobacterium gallicum DSM 20093]
 gi|270277318|gb|EFA23172.1| cytotoxin/hemolysin [Bifidobacterium gallicum DSM 20093]
          Length = 285

 Score = 54.0 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          R+ + + R G+  SR   +R+I + RV V+G  + +++  V     I VD
Sbjct: 30 RLDQALVRRGLVQSRSRAQRLIDEGRVFVDGKCVSKSSSKVDGAADIRVD 79


>gi|269114816|ref|YP_003302579.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           hominis]
 gi|268322441|emb|CAX37176.1| Ribosomal large subunit pseudouridine synthaseC [Mycoplasma hominis
           ATCC 23114]
          Length = 278

 Score = 54.0 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 39/246 (15%), Positives = 83/246 (33%), Gaps = 34/246 (13%)

Query: 5   NIVQENFTPQR-VSKVI---ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           N   +     R + K +         SR  +ER+  ++ +KVN I +      V   D I
Sbjct: 3   NFKAKKDDEGRILFKYLVKVCDNVPISR--IERLFREKDIKVNNIRVSDKQYKVKEGDLI 60

Query: 61  EVDG------------------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF-DNL 101
            + G                    + + +   +      I + +  +  D +   + +  
Sbjct: 61  SIYGLIETSKHIDNKANTNINFKVIYEDKNLLIIDKAPNIAMHSEENCLDDQVLKYLNFK 120

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG-----QVDQD 156
                R  S+GR+D  T GL++   +       E    ++ ++Y+           +   
Sbjct: 121 KVSSFRPASIGRIDKKTSGLVVYAKNYKTLVEFENKQNKFDKIYQFVSDFDEDVLDITVR 180

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
               +K   +I    +G    T+  ++G+  +  +    GK  +I+    +    +  L 
Sbjct: 181 LKKDIKNEKMIVDNNFGVKAQTIFYKEGNRKFAKII--TGKKHQIRATLAYLKTPI--LG 236

Query: 217 RISYGP 222
            I YG 
Sbjct: 237 DIKYGG 242


>gi|158320638|ref|YP_001513145.1| hemolysin A [Alkaliphilus oremlandii OhILAs]
 gi|158140837|gb|ABW19149.1| hemolysin A [Alkaliphilus oremlandii OhILAs]
          Length = 268

 Score = 54.0 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 11/57 (19%), Positives = 23/57 (40%), Gaps = 1/57 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          +R+  V+   G   SR + +  I    V V+   +++    V    ++ V G  +  
Sbjct: 5  ERLDVVLVEKGFFDSREKAKGAIMAGIVFVDNEKIDKPGTKVKKNGNVVVKGNLIPY 61


>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 = 54.0 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 37/239 (15%), Positives = 67/239 (28%), Gaps = 39/239 (16%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP----- 66
            +R+ K++AR     SR  +++ I    V+V+G +  R    V   + IEV         
Sbjct: 68  GERLDKLLARHFSEFSRSRLQQWIESGAVRVDGEV-RRPRDAVQMGNRIEVQPQAAPESQ 126

Query: 67  ----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISV 111
                     +   +   L +      +V   +     + +   L          R   V
Sbjct: 127 AFAPEDVALDVVYEDDALLVIDKPAGLVVHPAAGNWSGTVLNGLLHRDPTAAALPRAGIV 186

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GI 170
            RLD  T GL+++         L                      +   +   I      
Sbjct: 187 HRLDKETSGLMVVARTLTAQTDLVRQLQARTVKRTYLALVWGRIYEEGTIDAPIGRDPRE 246

Query: 171 CYGDMQVTLDTQKGSN----------------AWVTVGLREGKNREIKKVFEFFNWKVN 213
                 V  ++ K S                 + V   L  G+  +I+  FE     + 
Sbjct: 247 RTRMAIVHTNSGKPSRTHFRTLATVPLGRSFVSMVRCQLETGRTHQIRVHFESIGHPLV 305


>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 = 54.0 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 28/245 (11%), Positives = 62/245 (25%), Gaps = 42/245 (17%)

Query: 8   QENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI------ 60
                P R+ K +       SR  ++R   Q+ + VNG  ++  +  V   D I      
Sbjct: 39  DSGQKPMRIDKFLMEHLYNTSRNRLQRAAEQEFILVNGRPVKS-SYKVKPLDEIVILLDR 97

Query: 61  -EVDGVPLRKAERTRLWLY--------HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
            + D   + +     +                +V         + V      +       
Sbjct: 98  PKYDNEIIAEDIPLDIVYEDEDLMVVDKPAGLVVHPGCGNYTGTLVNAIAWHLKDNPDYD 157

Query: 112 ---------GRLDINTEGLLLLTNDGGLARV-------------LELPSTQWLRVYRVRF 149
                     R+D +T GLL++  +                            +    R 
Sbjct: 158 PNDPTVGLVHRIDKDTSGLLVVAKNADAKTHLGKQFFNKTTKRLYNALVWGNFQEEEGRI 217

Query: 150 HGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
            G + +   + ++  +         +      +         V   L  G+  +I+   +
Sbjct: 218 EGNIARHPKDRMQMAVFPPDSEIGKHAVTHYRVLENFNYVTLVECRLETGRTHQIRAHMK 277

Query: 207 FFNWK 211
                
Sbjct: 278 HIGHP 282


>gi|302876506|ref|YP_003845139.1| 30S ribosomal protein S4 [Clostridium cellulovorans 743B]
 gi|307687178|ref|ZP_07629624.1| 30S ribosomal protein S4 [Clostridium cellulovorans 743B]
 gi|302579363|gb|ADL53375.1| ribosomal protein S4 [Clostridium cellulovorans 743B]
          Length = 206

 Score = 54.0 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            R+  VI R G   SR E  +++      VNG  ++  +  V + D I V
Sbjct: 98  MRLDNVIYRLGYGNSRNEARQLVTHGHFLVNGKKVDIPSYVVKAGDVITV 147


>gi|205373291|ref|ZP_03226095.1| YlyB [Bacillus coahuilensis m4-4]
          Length = 301

 Score = 54.0 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 33/245 (13%), Positives = 73/245 (29%), Gaps = 36/245 (14%)

Query: 4   KNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           ++ V +    +R+ KV++      SR +V++ I    V VN    +R      ++D I +
Sbjct: 5   EHTVTQEQVGERIDKVVSTINSDWSRSQVQQWIKDGHVLVNMEQ-KRTNYKSQASDVITI 63

Query: 63  --------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--- 105
                   D         +   ++  + +      +V         + V   +       
Sbjct: 64  EVPEAEVLDVEAEDLNLDVYYEDQDVIVVNKPKGMVVHPAPGHYSGTLVNGLMHHCKDLS 123

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
                 R   V R+D +T GLL++  +      L     +     +              
Sbjct: 124 GINGVMRPGIVHRIDKDTSGLLMVAKNDVAHEHLVNQLVEKSVTRKYMALVHGVIQHDYG 183

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNREIKKVFEFF 208
                + +          +D  K +     V        L E     G+  +I+   ++ 
Sbjct: 184 TIDAPIGRDSKDRQSMTIVDQGKHAVTHFEVKDRFEQYTLVECQLETGRTHQIRVHMKYI 243

Query: 209 NWKVN 213
            + + 
Sbjct: 244 GFPLV 248


>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 = 54.0 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 27/203 (13%), Positives = 64/203 (31%), Gaps = 17/203 (8%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV-----PLRKAERTRLWLYHKPI 82
           R + + ++  + V+VNG +    A  +   D +EV         L   +   + +     
Sbjct: 22  RNDCKNLLKYKSVQVNGEVQTYHAFELHPGDEVEVGKKTNLPFELLYEDDDMIVINKPSG 81

Query: 83  GLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
            +     +   ++  +  +        +   V RLD +T G+L+   +  L + L     
Sbjct: 82  LVSEETRNNKYQTAFYMVMEYCRKKRQQCYLVHRLDQDTSGVLMFVKNKKLYQELTHNWN 141

Query: 140 QWL----RVYRVRFHGQVDQDKLNLLKKGIVIQGICYG-----DMQVTLDTQKGSNAWVT 190
           +++     V  +    +      N L +   ++                         + 
Sbjct: 142 KYVKTRGYVAILEGQCRKSGTIKNHLVEDKQLKMRIAKEGQLAITHYKPLEVSKDYTMME 201

Query: 191 VGLREGKNREIKKVFEFFNWKVN 213
           V L  G+  +I+      N  + 
Sbjct: 202 VFLDTGRKNQIRVHMASLNHPII 224


>gi|308176709|ref|YP_003916115.1| S4 domain-containing protein [Arthrobacter arilaitensis Re117]
 gi|307744172|emb|CBT75144.1| S4 domain-containing protein [Arthrobacter arilaitensis Re117]
          Length = 76

 Score = 54.0 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 9/68 (13%)

Query: 11 FTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
              R+ +++     A  GI      + MI+   V VNG +  R    +   D + V+G 
Sbjct: 13 DESIRLGQLLKLASLAEDGI----HAKEMISDGIVTVNGQVDTRRGAQIRPGDVVCVNGE 68

Query: 66 PLRKAERT 73
           ++   + 
Sbjct: 69 CVKVTAQQ 76


>gi|167758166|ref|ZP_02430293.1| hypothetical protein CLOSCI_00504 [Clostridium scindens ATCC 35704]
 gi|167664063|gb|EDS08193.1| hypothetical protein CLOSCI_00504 [Clostridium scindens ATCC 35704]
          Length = 251

 Score = 54.0 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             R+  V++ A   SR ++  +I   RV VNG L+      +   D + V
Sbjct: 174 SVRLDTVLSLAYPLSRSKITGLIEGARVFVNGKLVTSNGYRLKEGDILSV 223


>gi|308235716|ref|ZP_07666453.1| pseudouridylate synthase [Gardnerella vaginalis ATCC 14018]
          Length = 50

 Score = 54.0 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 16/41 (39%), Positives = 25/41 (60%)

Query: 202 KKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +++F    + V RL+R   GP +LG L AGS R +S+  +R
Sbjct: 2   RRIFGAVGYPVKRLVRTQIGPIKLGDLKAGSYRVLSQTEVR 42


>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 = 54.0 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 34/262 (12%), Positives = 70/262 (26%), Gaps = 31/262 (11%)

Query: 25  IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVP-LRKAERTR 74
           +ASR E E  I   ++ VNG  +      +   D I+         V   P L+  E   
Sbjct: 63  VASREEYEEKIRNGKIIVNGRKIPV-DYRIGPLDSIKHICTRIEAPVFNKPLLKLGETDN 121

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL--LLTNDGGLAR 132
              Y KP  +          +++   LP     V  + R+                    
Sbjct: 122 YVAYLKPASVTVNTVGGYFYNSMVKRLPPHLHVVHRLDRVTSGIIVFAKNKAAATNFNQY 181

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD------MQVTLDTQKGSN 186
           ++    ++      +    + +      L     +                 L    G  
Sbjct: 182 LVGEKVSKTYIARVIGRFPKGEIICDQPLGTDFNLHRTVVTPTGKPSKTIFKLLKTNGKE 241

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + V      G+  +I+   ++  + +                + G  REV  K +++ L 
Sbjct: 242 SIVEAHPITGRTHQIRCHLQYLGYPIT------------NDEMYGGKREVYTKEMKDALK 289

Query: 247 PHLLEEAQVNLDAPIYSSETLV 268
                           ++  + 
Sbjct: 290 KAEKLGLWPCDYCQDKTNPRVE 311


>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 = 54.0 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 37/240 (15%), Positives = 76/240 (31%), Gaps = 37/240 (15%)

Query: 9   ENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           E    QR+ +++ A     SR  V+++I    ++VNG   + A++ V   D IE+     
Sbjct: 14  EAEAGQRLDRLVSANMPDLSRTYVQQLITDLHIRVNGRGAK-ASLPVQIGDQIEIFLPLA 72

Query: 63  -------DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
                  + +PL     +   L +      +V         + V   L        S   
Sbjct: 73  KPTDIVAEDLPLDVIYEDADVLLVNKAAGMVVHPAPGHTTGTLVNALLYRYPHLTTSGDL 132

Query: 114 LD-----------------INTEGLLLLTNDGG---LARVLELPSTQWLRVYRVRFHGQV 153
                               + +  ++LT       + +          R         +
Sbjct: 133 RPGIVHRLDKETSGLLVIAKHDQARMMLTEQQMARRMHKKYLALVEGHWREPTGTIDAPI 192

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            ++  N L+  ++ +G  Y      +    G  + V   L  G+  +I+  F + N  + 
Sbjct: 193 GRNPNNRLRMMVMPEG-RYAVTHYQVLEVLGPYSLVRATLETGRTHQIRVHFSYRNRPIL 251


>gi|314933367|ref|ZP_07840732.1| YlmH protein [Staphylococcus caprae C87]
 gi|313653517|gb|EFS17274.1| YlmH protein [Staphylococcus caprae C87]
          Length = 262

 Score = 54.0 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 27/60 (45%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            I     +  R+  V+      SR   +++I ++RVKVN  +++     +   D + + G
Sbjct: 176 KIHSTTVSAMRLDVVLKDMIHKSRNIAKQLIEKKRVKVNHTIIDTPDFQLEQNDLLSIQG 235


>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 = 54.0 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 21/50 (42%), Gaps = 2/50 (4%)

Query: 15 RVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+   +A A     SR  V+ +I    V VNG    +A   +   D I +
Sbjct: 22 RLDAWLAEALAPGLSRSRVKALIEAGAVSVNGTPARQAKHKIKPGDEISL 71


>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 = 54.0 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 29/245 (11%), Positives = 56/245 (22%), Gaps = 37/245 (15%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E     R+ + +A      SR  ++++I Q +V +NG         + + D IEV  
Sbjct: 8   TVTEKQQGLRLDRGLAEQLPELSRSRLQQLIRQGQVWLNGQPCLDKDRPLQAGDQIEVRI 67

Query: 63  --------DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                       +       +   L +      +V         + V   L         
Sbjct: 68  PPATPTPLQPERIPLDILYEDEDLLVINKPRGLVVHPAPGHASGTLVHALLAHCPRLSGI 127

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF--------------------- 149
            G         L     G L       + Q L+                           
Sbjct: 128 NGEQRPGIVHRLDKDTTGALVIAKHDQAHQHLQAQIQAKTARRIYLGVVFGRPAQSQGTI 187

Query: 150 -HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                           +             +  + G+   +   L  G+  +I+      
Sbjct: 188 SAPIGRHPVDRQKMAVVPPGQGRAAVTHWQVLERLGNYTLMQFELETGRTHQIRVHAAHL 247

Query: 209 NWKVN 213
              + 
Sbjct: 248 RLPIV 252


>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 = 54.0 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 40/294 (13%), Positives = 75/294 (25%), Gaps = 65/294 (22%)

Query: 7   VQENFTPQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-- 59
           +      +R+ +V+AR     A   SR  ++R++ + RV V+G ++  AA  V + D   
Sbjct: 35  IAAEDAGERLDRVLARRLALEAPELSRTRIQRLVTEGRVSVSGRVVGDAAGRVNAADVYT 94

Query: 60  -------------------IEVDGVPLRKAERTRLWLYHKPIGLVTTH------------ 88
                              I  +   L   ++    + H   G  +              
Sbjct: 95  LFLPPPEAAEPVAENLPLTIVFEDAHLVVIDKPAGLVVHPAPGHASGTLVNALLYHCGDS 154

Query: 89  ------------SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
                            + T    + +                G         LA V  +
Sbjct: 155 LSGIGGVRRPGIVHRIDKDTSGLLVVAKSDLAHKGLAAQFADHGRTGPLERAYLAFVWGV 214

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------QVTLDT 181
           P         +  H    Q     L     I      +                +  +  
Sbjct: 215 PEAHGSVDAPIDRHPSHRQKMAVRLSGRNAITHWEVQEAFVGHGRTHLRNKGQVKGEVKM 274

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           ++G  + +   L  G+  +I+         +        G     TLL    RE
Sbjct: 275 EEGVASLIECRLETGRTHQIRVHMAHVGHPLLGDEVYGQGFRTKETLLPEDARE 328


>gi|295398656|ref|ZP_06808680.1| 30S ribosomal protein S4 [Aerococcus viridans ATCC 11563]
 gi|294973091|gb|EFG48894.1| 30S ribosomal protein S4 [Aerococcus viridans ATCC 11563]
          Length = 203

 Score = 54.0 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G+A+ RR+  +++    + V+G  ++  +  V     I V
Sbjct: 93  QRLDNVVYRLGLATTRRQARQLVNHGHITVDGKRVDIPSFRVQPGQVISV 142


>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 = 54.0 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 32/244 (13%), Positives = 61/244 (25%), Gaps = 39/244 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHI----- 60
           V E    +RV   +AR    SR R  E +IA   V V+G  + + +  V+    +     
Sbjct: 12  VPEGLAGERVDAALARMFGLSRTRGAE-LIAAGNVLVDGAPVGK-SDRVLPGSTVAVTIP 69

Query: 61  -----------EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                       V+G+ +   +   + +       V       G + V     + F    
Sbjct: 70  VEADPLAVVPEVVEGIKILHDDDDIVVIDKPVGVAVHPSPGWSGPTVVGHLAGAGFRIST 129

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD------------- 156
           S           L +   G +       +   L+    R                     
Sbjct: 130 SGAPERQGIVQRLDVGTSGVMVICKSEHAYSVLKNAFRRRTVDKVYHALVQGHPDPLEGT 189

Query: 157 -------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                        K  V+    +              + + + L  G+  +I+       
Sbjct: 190 IDAPIGRHPKADYKFAVMADGRHSVTHYETLEAHRFASLLEIHLETGRTHQIRVHMAALK 249

Query: 210 WKVN 213
               
Sbjct: 250 HPCV 253


>gi|291521873|emb|CBK80166.1| SSU ribosomal protein S4P [Coprococcus catus GD/7]
          Length = 197

 Score = 54.0 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +I R G A +R+E  +++  + V VNG L+   +  V   D +E+
Sbjct: 88  RLDNIIFRLGFARTRKEARQIVDHKHVSVNGKLVNIPSYQVKPGDVVEI 136


>gi|167951161|ref|ZP_02538235.1| RNA-binding S4 domain protein [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 106

 Score = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 20/106 (18%), Positives = 44/106 (41%), Gaps = 1/106 (0%)

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLLEE 252
            EG+ RE+++++E    +V+RL R+ YG   L + L  G  R ++   + + L    L  
Sbjct: 1   MEGRQREVRRLWEAIGVQVSRLKRVRYGSVILESALKVGRWRALTHTEVNQLLEISGLPP 60

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
            +    A      +  +  P    +      ++++ S      + +
Sbjct: 61  EKRQPPARAKHYRSDRQQAPRKQGQRAKSVGQLREQSMGDAQGNPR 106


>gi|161510965|ref|YP_089013.2| 23S rRNA pseudouridine synthase D [Mannheimia succiniciproducens
           MBEL55E]
          Length = 324

 Score = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 27/238 (11%), Positives = 60/238 (25%), Gaps = 31/238 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           VQ +   QR+ + +A      SR  ++  I  + V +NG +       V   + +E+   
Sbjct: 10  VQPHQMGQRLDQTLAELFPDYSRSRLKTWIEDELVLLNGKVANIPREKVYGGEQVEITVE 69

Query: 66  P--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                          +   +   L +      +V   +     + +   L          
Sbjct: 70  IEDENRFEPQNIPLNIVYEDDDILVINKPKDFVVHPGAGNPNGTVLNALLYHYPQITEVP 129

Query: 112 -----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-----------FHGQVDQ 155
                 RLD +T GL+++         L     +                      +   
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTQLVRALQKRKITREYEAIAFGIMTKGGTVDEPMS 189

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     V            +     +   + + L  G+  +I+         + 
Sbjct: 190 RHPTKRTLMAVHPMGKPAVTHYRVMEHFRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 247


>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 = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 25/232 (10%), Positives = 63/232 (27%), Gaps = 37/232 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+ K +       SR +++  I    V VNG  ++     ++  DH+++           
Sbjct: 16  RIDKQLGHHFDQFSRSQIQHWIEDGHVLVNGEQVK-PKYKLLVGDHVQIIPEEPQKIDLT 74

Query: 67  -------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI---------- 109
                  +   +   + +      +V         + V   L       I          
Sbjct: 75  PEDIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPNHTLVNALLYHSPLSTINGEFRPGIVH 134

Query: 110 ----------SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
                      V + D+    L          R         ++  +      + +   +
Sbjct: 135 RIDKDTSGLLMVAKNDMAHRSLTAQLKAKTNKREYVALVHGVIKEDKGTIDAPLGRSLKD 194

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             K+ +V+    +      +  +  +   V   L  G+  +I+   ++    
Sbjct: 195 RKKQAVVV-DGRHAITHFNVLERFKNYTLVACQLETGRTHQIRVHMKYIGHP 245


>gi|332365060|gb|EGJ42825.1| 30S ribosomal protein S4 [Streptococcus sanguinis SK355]
          Length = 245

 Score = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V    L+  
Sbjct: 136 RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVTPGQVISVREKSLKVP 192


>gi|319935762|ref|ZP_08010192.1| hypothetical protein HMPREF9488_01023 [Coprobacillus sp. 29_1]
 gi|319809311|gb|EFW05752.1| hypothetical protein HMPREF9488_01023 [Coprobacillus sp. 29_1]
          Length = 277

 Score = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 38/237 (16%), Positives = 70/237 (29%), Gaps = 27/237 (11%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQ-QRVKVNGI------LLERAAVNV 54
           K + IV +     R+    A     SR+   ++I Q   + VNG       +L      V
Sbjct: 3   KRELIVTKENHQLRIDDF-AYQHHISRK-ALKVIKQCGDILVNGEHQTVRYVLNEGDYVV 60

Query: 55  ----MSTDHIEVDGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                  + I  + VP  +   +   L +                ++          S  
Sbjct: 61  FIYPPEDNQIIPENVPLYIVYEDDFLLIVDKPKGMACFPTRSHPCQTLANALSYYYHSIE 120

Query: 109 -----ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------D 156
                  V RLD +T GL+++     +  ++        R Y+    GQV+Q        
Sbjct: 121 LDSTVHFVNRLDKDTAGLMMIAKYREIHDMMCQNIQHIYRRYQAHVEGQVEQGVIDLPIH 180

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           K     + I+ +                  + V   L  G+  +I+         + 
Sbjct: 181 KDGQNMRRIIDENGKDSRTYYRCLEYSDGISRVECILETGRTHQIRVHMAAIGHPLI 237


>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 = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 28/229 (12%), Positives = 68/229 (29%), Gaps = 32/229 (13%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLE---------RAAVNVMST------- 57
           R+   +A+     SR  +   I +  V VNG   +         + AV +  +       
Sbjct: 40  RLDAALAKLLPDYSRSRLADWIKEGAVSVNGKPAKPKDKLIGGEKLAVQIRESNETLAFT 99

Query: 58  ------DHIEVDGVPLRKAERTRLWLYHKPIGLVTT--HSDPDGRSTVFDNLPSIFSRVI 109
                 D I  D   +   +   L ++        T  +        + +   +     +
Sbjct: 100 PEAMDLDIIYEDDSVIVLNKPAGLVVHPAAGNWSGTLLNGLLAHCPALQNIPRAGIVHRL 159

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR-------VYRVRFHGQVDQDKLNLLK 162
                 +      L   +  + ++      +  R        +  +   Q+ +D  N +K
Sbjct: 160 DKDTSGLMVVAKTLPAQNHLVQQLQTRTVKRIYRAVADGIVPFDGKIETQIGRDPHNRVK 219

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +V  G       V +  +  +++++   L  G+  +I+         
Sbjct: 220 MAVVKFGGKEAVTHVKVLERYQAHSYIECALETGRTHQIRVHMREAKHP 268


>gi|296140085|ref|YP_003647328.1| hemolysin A [Tsukamurella paurometabola DSM 20162]
 gi|296028219|gb|ADG78989.1| hemolysin A [Tsukamurella paurometabola DSM 20162]
          Length = 271

 Score = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   + R G+A SR +   +I   RV VN  +  +AA  +   D + V
Sbjct: 5  VRLDAELVRRGMARSREQARELIESGRVTVNKQVARKAANQIDPADPVHV 54


>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 = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 23/244 (9%), Positives = 56/244 (22%), Gaps = 39/244 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIE--- 61
           V +    +R+   ++R    SR     +I    V V+G    + +  V +     +    
Sbjct: 9   VPDGLEGERLDAALSRLFGFSRTRAAELIVSGDVLVDGSPAAK-SDRVHAGAWLDVTLPP 67

Query: 62  -----------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                      V G+ +   +   + +           +   G + +   L +      S
Sbjct: 68  PPTAPMPVAEPVPGMKIVYEDDDIVVVNKPIGVAAHPTTGWTGPTVIGGLLGTGHRVATS 127

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
                      L     G +       +   L+              L        ++G 
Sbjct: 128 GAAERQGIVHRLDANTTGAMVVAKSEHAYSHLKRAFKERTVDKRYHALVQ-GHPDPLRGT 186

Query: 171 CYGDMQVTLDTQK---------------------GSNAWVTVGLREGKNREIKKVFEFFN 209
               +                              + + + + L  G+  +I+       
Sbjct: 187 VDAPIDRHPSGDGRFAVVAGGKESVTHYDTIEAFRAASLLDIKLETGRTHQIRVHMSALR 246

Query: 210 WKVN 213
               
Sbjct: 247 HPCV 250


>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 = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 33/239 (13%), Positives = 73/239 (30%), Gaps = 31/239 (12%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K I+       R+ +V+A+     SR +++  I    VKV+GI   +A   V     IE+
Sbjct: 13  KKIIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVWENQFIEI 72

Query: 63  DGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           +                 +   + T L +      +V   +    ++ +   L    S  
Sbjct: 73  EAQLEPNERWVPQPIPLDVIYEDETLLVINKPVGLIVHPGAGVRDQTLINALLHYDPSLS 132

Query: 109 ISVGRLDIN----TEGLLLLTNDGGLARVLELPSTQWLRVYRV------------RFHGQ 152
           +      I+        LLL      +    + + +  ++ R             R    
Sbjct: 133 VVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEAIVKGVLISGRTIEA 192

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                     +  V++          +  +  ++  + V L  G+  +I+      +  
Sbjct: 193 PVGRHPIHRTRMAVVEFGRPAITHFRIIKRYRAHTHIRVQLETGRTHQIRVHMAHIHHP 251


>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 = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 31/245 (12%), Positives = 63/245 (25%), Gaps = 41/245 (16%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V +   P R+ K +    + ASR  ++       V  NG  ++  +  V   D + V  
Sbjct: 36  TVDKGQAPVRIDKYLFERIVNASRNRIQTAADNGYVMANGKPVKS-SYKVKPLDVLTVMM 94

Query: 63  -----------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                      + +PL    E   L + +KP GLV      +   T+ + +      V +
Sbjct: 95  DRPRYENDIIPEDIPLDIVYEDDDLMVVNKPAGLVVHPGCGNYHGTLVNAIAWHLRNVPT 154

Query: 111 VGRLDIN-------------------------TEGLLLLTNDGGLARVLELPSTQWLRVY 145
               D                             G+              +         
Sbjct: 155 YDPNDPQVGLVHRIDKDTSGLLVIAKTPDAKTHLGMQFYNKTTKREYNALVWGIIDEDEG 214

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
            +  +   +      +          +      +  + G    V   L  G+  +I+   
Sbjct: 215 TIEGNIGRNPKDRMQMAVMSDPTQGKHAVTHYQVLERLGYVTLVKCVLETGRTHQIRVHM 274

Query: 206 EFFNW 210
           +    
Sbjct: 275 KHIGH 279


>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 = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 36/258 (13%), Positives = 75/258 (29%), Gaps = 40/258 (15%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ K +      A+R +++       + VN I ++     V   D I +           
Sbjct: 31  RIDKYLMYLIPNATRNKIQNAATDGNIFVNDIPVKS-NYKVKPFDVITIMLSHPPFENHI 89

Query: 63  --DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-------- 111
             + +PL    E   L L +K  G+V      +   T+ + L   F  +           
Sbjct: 90  LPEDIPLNIVYEDDALLLINKEPGMVVHPGHGNYTGTLVNALAHHFDNLPMNSSERPGLV 149

Query: 112 GRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVYRVRFHGQVDQDKL 158
            R+D +T GLL++         L                    +        G + +   
Sbjct: 150 HRIDKDTSGLLVVAKTEAAMTHLAKQFEAKTTEREYIALVWGNVAAESGTIEGNLARHLK 209

Query: 159 NLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
           + ++  +               +  + G    ++  L  G+  +I+   +     +    
Sbjct: 210 DRMQMAVFADPEIGKPAITHYKVLERFGYVTLISCKLETGRTHQIRAHMKHIGHPLFNDE 269

Query: 217 RISYGPFQLGTLLAGSTR 234
           R   G   L        +
Sbjct: 270 RYG-GHLILKGTTFTKYK 286


>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 = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 26/240 (10%), Positives = 61/240 (25%), Gaps = 44/240 (18%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--------------- 58
           R+   +A+     SR  ++ +I Q  +++NG +       V   D               
Sbjct: 13  RLDVWLAQKIPDLSRSRLQNLIEQGNLRLNGKICTDKKTKVQQGDLLYLFIPPVEPLNLQ 72

Query: 59  --HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
              I +D   +   +   + +      +V      +  + V   L    +     G    
Sbjct: 73  PEEIPLD---VLYEDEQLIIINKPAGLVVHPAPGHEKGTLVNALLSHCSNLAGIGGVQRP 129

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------------------- 155
                L     G L       + Q L+        + +                      
Sbjct: 130 GIVHRLDKDTTGALVIAKTDYAHQHLQAQLKAKTARREYLGVVYGVPKTGSGTINLPIGR 189

Query: 156 --DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +   +    + +G         +  + G+   +   L  G+  +I+         + 
Sbjct: 190 HPIERKKMAVVPLEKGGRVAITHWEIRERLGNYTLIHFRLETGRTHQIRVHSTAMGHPIV 249


>gi|315658522|ref|ZP_07911394.1| S4 domain-containing protein YlmH [Staphylococcus lugdunensis
           M23590]
 gi|315496851|gb|EFU85174.1| S4 domain-containing protein YlmH [Staphylococcus lugdunensis
           M23590]
          Length = 264

 Score = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 14/60 (23%), Positives = 28/60 (46%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            I     +  R+  V+      SR   +++I ++RVKVN  ++E +   +   D + + G
Sbjct: 178 KIQHTTVSAMRLDVVLKDMIHKSRSIAKQLIEKKRVKVNHTIVEASDFQLEPNDLLSIQG 237


>gi|154504401|ref|ZP_02041139.1| hypothetical protein RUMGNA_01905 [Ruminococcus gnavus ATCC 29149]
 gi|153795330|gb|EDN77750.1| hypothetical protein RUMGNA_01905 [Ruminococcus gnavus ATCC 29149]
          Length = 262

 Score = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 15/52 (28%), Positives = 26/52 (50%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             R+  +++ A  ASR ++  +I   +V VNG L+   +  +   D I V G
Sbjct: 185 SVRLDSLLSLAFSASRTKLSGLIEGAKVFVNGKLITTNSYQLKENDVISVRG 236


>gi|55980515|ref|YP_143812.1| hemolysin [Thermus thermophilus HB8]
 gi|55771928|dbj|BAD70369.1| hemolysin [Thermus thermophilus HB8]
          Length = 235

 Score = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 28/50 (56%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ + +   G+  SR + +R+I + +V+V G ++++ A  V     +E+
Sbjct: 1  MRLDRYLVERGLVESREKAKRLIQEGKVRVEGKVVQKPAHPVPEGARVEL 50


>gi|328544921|ref|YP_004305030.1| ribosomal RNA large subunit methyltransferase J [polymorphum
          gilvum SL003B-26A1]
 gi|326414663|gb|ADZ71726.1| Ribosomal RNA large subunit methyltransferase J [Polymorphum
          gilvum SL003B-26A1]
          Length = 247

 Score = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 1/55 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             +R+ + +   G+A SR      I +  V V+G + ++  + V  +  I +D 
Sbjct: 2  SDKKRLDQRLVELGLAPSRARARDAILRGTVTVDGRIADKPGLAVGPSAAIAIDD 56


>gi|289551026|ref|YP_003471930.1| S4-like RNA binding domain-containing hypothetical protein
           [Staphylococcus lugdunensis HKU09-01]
 gi|289180558|gb|ADC87803.1| S4-like RNA binding domain-containing hypothetical protein
           [Staphylococcus lugdunensis HKU09-01]
          Length = 264

 Score = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 14/60 (23%), Positives = 28/60 (46%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            I     +  R+  V+      SR   +++I ++RVKVN  ++E +   +   D + + G
Sbjct: 178 KIQHTTVSAMRLDVVLKDMIHKSRSIAKQLIEKKRVKVNHTIVEASDFQLEPNDLLSIQG 237


>gi|218247630|ref|YP_002373001.1| photosystem II S4 domain-containing protein [Cyanothece sp. PCC
           8801]
 gi|257061035|ref|YP_003138923.1| photosystem II S4 domain protein [Cyanothece sp. PCC 8802]
 gi|218168108|gb|ACK66845.1| photosystem II S4 domain protein [Cyanothece sp. PCC 8801]
 gi|256591201|gb|ACV02088.1| photosystem II S4 domain protein [Cyanothece sp. PCC 8802]
          Length = 259

 Score = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 3/65 (4%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K K  +       R+   IA AG   SR ++   I+   V+VN   + +A+ NV S D I
Sbjct: 173 KTKE-MNTVEASMRLD-AIASAGFGISRSKMAEAISAGDVRVNWKEITQASYNVQSGDLI 230

Query: 61  EVDGV 65
              G 
Sbjct: 231 TFRGK 235


>gi|237756998|ref|ZP_04585455.1| hemolysin A [Sulfurihydrogenibium yellowstonense SS-5]
 gi|237690841|gb|EEP59992.1| hemolysin A [Sulfurihydrogenibium yellowstonense SS-5]
          Length = 268

 Score = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 11/57 (19%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
              +R+ K++   G+  SR + + +I    V VN   +++    V +  +I +   
Sbjct: 2  KAQKERIDKLLVDKGLVESREKAQVLIMSGVVFVNNQKIDKPGTKVPTDANIHIKEK 58


>gi|326773128|ref|ZP_08232411.1| cytotoxin/hemolysin [Actinomyces viscosus C505]
 gi|326636358|gb|EGE37261.1| cytotoxin/hemolysin [Actinomyces viscosus C505]
          Length = 290

 Score = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   + R G+A SR     +IA   V ++G ++ + A  V     IE+
Sbjct: 5  IRIDSELVRRGLARSRTHAATLIADGHVTLDGEVVTKPARQVNPAQAIEI 54


>gi|210612739|ref|ZP_03289454.1| hypothetical protein CLONEX_01656 [Clostridium nexile DSM 1787]
 gi|210151432|gb|EEA82440.1| hypothetical protein CLONEX_01656 [Clostridium nexile DSM 1787]
          Length = 264

 Score = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 24/50 (48%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A A  +SR ++   I   +V VNG L+      +   D I V G
Sbjct: 189 RLDSLLALAFSSSRTKLVPYIENGKVFVNGKLITSNGYQIKQDDIISVRG 238


>gi|188996824|ref|YP_001931075.1| hemolysin A [Sulfurihydrogenibium sp. YO3AOP1]
 gi|188931891|gb|ACD66521.1| hemolysin A [Sulfurihydrogenibium sp. YO3AOP1]
          Length = 268

 Score = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 11/54 (20%), Positives = 25/54 (46%), Gaps = 1/54 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
              +R+ K++   G+  SR + + +I    V VN   +++    V +  +I +
Sbjct: 2  KVQKERIDKLLVDKGLVESREKAQALIMSGVVFVNNQKIDKPGTKVPTDANIYI 55


>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 = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 14/59 (23%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 3  DKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
            ++  E   P+R+ +V+ARA    SR  ++ ++    V+ +G ++   A  V +   I
Sbjct: 24 RSHVRDEGSVPERLDRVLARAFDDLSRARLQALVRDGLVQCDGAVVRDPARKVGAGSRI 82


>gi|154488635|ref|ZP_02029484.1| hypothetical protein BIFADO_01942 [Bifidobacterium adolescentis
          L2-32]
 gi|154082772|gb|EDN81817.1| hypothetical protein BIFADO_01942 [Bifidobacterium adolescentis
          L2-32]
          Length = 238

 Score = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 14/37 (37%), Positives = 22/37 (59%)

Query: 27 SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          SR + +R+IA  +V VNG+ + +A+  V   D I  D
Sbjct: 9  SRSKAQRLIADGKVSVNGVTVTKASAKVGGDDVIAAD 45


>gi|284052184|ref|ZP_06382394.1| RNA-binding S4 domain-containing protein [Arthrospira platensis
          str. Paraca]
 gi|291568948|dbj|BAI91220.1| hypothetical protein [Arthrospira platensis NIES-39]
          Length = 72

 Score = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 13/61 (21%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 6  IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          +V+      ++ K + R+G+  S  + +  I    V VNG +  R    ++  D +  +G
Sbjct: 2  VVKVTEQNIKLDKFLKRSGLVQSGGQAKAFIQSGYVMVNGEIETRRGRKLIEGDRVTFNG 61

Query: 65 V 65
           
Sbjct: 62 E 62


>gi|217967342|ref|YP_002352848.1| RNA-binding S4 domain protein [Dictyoglomus turgidum DSM 6724]
 gi|217336441|gb|ACK42234.1| RNA-binding S4 domain protein [Dictyoglomus turgidum DSM 6724]
          Length = 259

 Score = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 13/61 (21%), Positives = 25/61 (40%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K   I++   + +R+  +   A   SR +++  I    V VNG  +      +   D + 
Sbjct: 170 KATRIIRTTESSKRLDSIGGAALGISRSKMQTYIKAGVVTVNGKKVADTHYELEEGDVVI 229

Query: 62  V 62
           V
Sbjct: 230 V 230


>gi|160941043|ref|ZP_02088381.1| hypothetical protein CLOBOL_05936 [Clostridium bolteae ATCC
           BAA-613]
 gi|158435992|gb|EDP13759.1| hypothetical protein CLOBOL_05936 [Clostridium bolteae ATCC
           BAA-613]
          Length = 197

 Score = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 29/73 (39%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G+  +R+E  +++  + + VNG  +   +  V + D IEV           
Sbjct: 88  RLDNVLFRMGLGRTRKEARQIVDHKHILVNGKPVNIPSYRVKAGDVIEVKEKYKSAQRYK 147

Query: 74  RLWLYHKPIGLVT 86
            +        +  
Sbjct: 148 DVLEVTGGRMVPA 160


>gi|24379037|ref|NP_720992.1| hypothetical protein SMU.556 [Streptococcus mutans UA159]
 gi|24376932|gb|AAN58298.1|AE014900_6 conserved hypothetical protein [Streptococcus mutans UA159]
          Length = 263

 Score = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 15/58 (25%), Positives = 30/58 (51%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +    +  R+ K+IA     SRR+  ++I  ++VK+N ++  + +  +   D I V G
Sbjct: 178 MNVLVSSMRLDKIIAAVLKLSRRKANQLIESEKVKLNYLVQPKVSQLIDIGDLISVRG 235


>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 = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 33/237 (13%), Positives = 69/237 (29%), Gaps = 41/237 (17%)

Query: 14  QRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
            R+ K + +R   A+R  ++  I    VKVN     +A+  V   D I +          
Sbjct: 34  MRIDKFLMSRIQYATRSRIQYGIEIDSVKVNDKS-TKASYKVRPGDVITISLPHPPREDV 92

Query: 63  ---DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRS------TVFDNLPSIFSRVISV 111
              + +P  +   +   L +  KP  +V         +        F+NLP+  +  I  
Sbjct: 93  LIPEDIPLDIVYEDDQILIVNKKPGMVVHPAHGNWTGTLVNALAYHFENLPTHVNGKIRP 152

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-KLNLLKKGIVIQGI 170
           G +    +    L         +   + Q+      R +  +                G 
Sbjct: 153 GLIHRIDKDTSGLLVIAKTDYAMTFMAKQFADHSIERTYYAICWGVPDPKSGTIKNYLGR 212

Query: 171 CYGDMQVTLDTQKGSNAWVTVG-----------------LREGKNREIKKVFEFFNW 210
              D ++    +   +  + +                  L  G+  +I+   +    
Sbjct: 213 STKDRKLVTTYENEEDGKLAITHYKTLAAYHYVALIQCNLETGRTHQIRAHMKSIGH 269


>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 = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 70/249 (28%), Gaps = 42/249 (16%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +V    + +R+   +A      SR  ++R+I + R+ +NG  +   +  +   D I ++ 
Sbjct: 12  VVTGGESSKRIDVFLANRDPTFSRSALQRLIGEGRILINGQTIR-PSQKIKPGDRIRLEV 70

Query: 64  --GVPLRKAERTR-----------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------ 104
               PL                  L L+     +V         + V   L         
Sbjct: 71  PRPEPLDLKPEAIPFDILHEDAELLVLHKPAGLVVHPAPGNWSGTLVNALLHHFATSGVT 130

Query: 105 ------FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
                   R   V RLD  T G++++       R L                      K 
Sbjct: 131 PSHIGGKERPGLVHRLDKETSGVMVIAKTDQAHRALAAQFKLHTITRVYEALIWGVPKKG 190

Query: 159 NLLKKGIVIQGIC---------YGDMQVTLDTQKGSNA-----WVTVGLREGKNREIKKV 204
           + L +  + +                    D Q          +V +  R G+  +++  
Sbjct: 191 HGLIELAIGRDTKERKKFSARTTKPKPSATDYQVEERYGKIAAYVRLFPRTGRTHQLRVH 250

Query: 205 FEFFNWKVN 213
               +  + 
Sbjct: 251 LTSIDHPIL 259


>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 = 53.6 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 28/248 (11%), Positives = 60/248 (24%), Gaps = 41/248 (16%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------D 63
           R+ + +    +A SR +V+R+I +  V+V+G  + +    +   + +EV          +
Sbjct: 24  RLDQFLTACELALSRSQVKRLIDEGAVQVDGAEVRKPGFKLQGGEAVEVALPAPQPLAAE 83

Query: 64  GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
              +       +   + +      +V         + V   L          G L     
Sbjct: 84  PQAIPLDICYEDEHIIVVDKPAGLVVHPAPGHPDGTLVNALLAHCHDLSGIGGALRPGIV 143

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY------- 172
             L     G +       +   +         +     +           I         
Sbjct: 144 HRLDKDTSGVMVATKTEIAHHAMVETFQAHRLERAYLAVVAPPPEPPRGTISTLHGRHPV 203

Query: 173 --GDMQVTLDTQKGSNAWVTVG-------------LREGKNREIKKVFEFFNWK----VN 213
                   +   K +     V              L  G+  +I+             V 
Sbjct: 204 HRKKFSGRVSRGKQAITQYRVERVFGRLAAEVRCQLETGRTHQIRVHLSEMGAPLIGDVL 263

Query: 214 RLIRISYG 221
              R   G
Sbjct: 264 YGRRYRDG 271


>gi|298490610|ref|YP_003720787.1| RNA-binding S4 domain-containing protein ['Nostoc azollae' 0708]
 gi|298232528|gb|ADI63664.1| RNA-binding S4 domain protein ['Nostoc azollae' 0708]
          Length = 62

 Score = 53.6 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           ++ + +   GI S   + + MI    VKVNG +  R    +  TD + V G 
Sbjct: 2  IKLDQFLKLLGIGSTGGQAKLMIIDGDVKVNGTVETRRGRKLAPTDIVTVTGK 54


>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 = 53.6 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 40/245 (16%), Positives = 67/245 (27%), Gaps = 39/245 (15%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + E    +R+ K +A+     SR  +++ I    V+V G  +      V   D IEV   
Sbjct: 55  IPETLHGERLDKALAKLLPDYSRSRLQQWIDAGAVRVGGAAVR-PRAAVCGGDRIEVVPQ 113

Query: 66  P---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
                           +   + T L +      +V   +     + +   L         
Sbjct: 114 RAADENAFVAEPIDLDVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRYPQAAGL 173

Query: 107 -RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ------------- 152
            R   V RLD  T GL+++         L                               
Sbjct: 174 PRAGIVHRLDKETSGLMVVARTLPAQTDLVRQLQARTVKRTYLALVWGETPEAGTIDAPI 233

Query: 153 -VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG---LREGKNREIKKVFEFF 208
             D      +       G        TLD      A V++    L  G+  +I+  FE  
Sbjct: 234 GRDPRDRTRMAIIETASGKPARTHFKTLDVIDLGRAQVSLVQCQLETGRTHQIRVHFESE 293

Query: 209 NWKVN 213
              + 
Sbjct: 294 GHPLL 298


>gi|78222437|ref|YP_384184.1| hemolysin A [Geobacter metallireducens GS-15]
 gi|78193692|gb|ABB31459.1| Hemolysin A [Geobacter metallireducens GS-15]
          Length = 260

 Score = 53.6 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 1/56 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          +R+ K++   G+  SR     +I   +V VN  L ++A   V     I + G  + 
Sbjct: 14 ERLDKLLVDRGLVQSRERARALIMAGQVVVNDHLADKAGTQVPLDADIRLKGEDIP 69


>gi|289579115|ref|YP_003477742.1| ribosomal protein S4 [Thermoanaerobacter italicus Ab9]
 gi|297545302|ref|YP_003677604.1| 30S ribosomal protein S4 [Thermoanaerobacter mathranii subsp.
           mathranii str. A3]
 gi|289528828|gb|ADD03180.1| ribosomal protein S4 [Thermoanaerobacter italicus Ab9]
 gi|296843077|gb|ADH61593.1| ribosomal protein S4 [Thermoanaerobacter mathranii subsp. mathranii
           str. A3]
          Length = 206

 Score = 53.6 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SRR+  ++++   ++VNG  ++  +  V   D I V
Sbjct: 99  RLDNVVYRLGFAVSRRQARQLVSHGHIEVNGKKVDIPSFLVKPGDVISV 147


>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 = 53.6 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 40/252 (15%), Positives = 82/252 (32%), Gaps = 51/252 (20%)

Query: 1   MKD---KNIVQENFTPQRVSKVIA-------RAGIASRREVERMIAQQRVKVNGILLERA 50
           MK      ++ ++F   RV + +        ++        E+ + ++ + VN   ++  
Sbjct: 1   MKKPLKSFVINKDFEGSRVDRFLKKQFPNIPQSLF------EKNLRKKNITVNNKKVKNL 54

Query: 51  AVNVMSTDHIEV--------------------DGVPLRKA---ERTRLWLYHKPIGLVTT 87
              +   D + +                    D   L+K    E     + +KP G  + 
Sbjct: 55  -FKLEINDIVNIFTELKIENKINKKKQIFNINDYNELKKNFVFECEDYCVLNKPYGYASQ 113

Query: 88  HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL------ARVLELPSTQW 141
                  S   D L S       V RLD +T GL+LL  +                  ++
Sbjct: 114 DGSKVKLSV-IDILNSTKKNYYIVHRLDKDTSGLMLLAKNRFYAKKFSEMFKSREVKKKY 172

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
           L +   +      +        G  I+   Y      + ++K + +++ + L  G+  +I
Sbjct: 173 LVIINGKIKKNKGEIHSKEKVNGKEIESKLY----FEVISKKNNFSYLEIDLITGRKHQI 228

Query: 202 KKVFEFFNWKVN 213
           +K F      V 
Sbjct: 229 RKQFSDIGHPVV 240


>gi|167464888|ref|ZP_02329977.1| putative cell adhesion protein (contact hemolysin TlyA-related)
          [Paenibacillus larvae subsp. larvae BRL-230010]
 gi|322382771|ref|ZP_08056615.1| methyltransferase-like protein with RNA binding domain
          [Paenibacillus larvae subsp. larvae B-3650]
 gi|321153240|gb|EFX45686.1| methyltransferase-like protein with RNA binding domain
          [Paenibacillus larvae subsp. larvae B-3650]
          Length = 278

 Score = 53.6 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 11/55 (20%), Positives = 22/55 (40%), Gaps = 1/55 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             +R+  ++   G   SR + +  I    V VN   +++  + +     I V G
Sbjct: 2  SDKERIDVLLVEQGYYESREKAKAAIMAGLVFVNEESVDKPGIKICRKADIRVKG 56


>gi|309389907|gb|ADO77787.1| SSU ribosomal protein S4P [Halanaerobium praevalens DSM 2228]
          Length = 208

 Score = 53.6 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 15/66 (22%), Positives = 29/66 (43%), Gaps = 1/66 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G AS R E  + +    + VNG  ++  +  +   D I+V     +     
Sbjct: 99  RLDNVVYRMGFASSRNEARQFVLHGHITVNGRKVDIPSYQIDIDDEIKVKDSSRKSKRFK 158

Query: 74  RLWLYH 79
            ++ Y+
Sbjct: 159 EIFEYN 164


>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 = 53.6 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 31/245 (12%), Positives = 66/245 (26%), Gaps = 42/245 (17%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ + +A A G  SR  V+ +I    V  +G      +  + +     V           
Sbjct: 37  RLDRFLAAAIGTLSRSRVKALIEAGHVTRDGQPAGDPSEAIRTGATYVVAPPAAQPATPQ 96

Query: 63  -----------DGVPLRKAERTRLWLYHKPIGLVT--------------THSDPDGRSTV 97
                      D   +   +   L ++  P                   T    + R  +
Sbjct: 97  AQDIPLTILFEDRHLIVLDKPAGLVVHPAPGNQDGTLVNALLAHAGEELTGIGGEKRPGI 156

Query: 98  FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
              L    S V+ V + ++    L        L R     +              V +  
Sbjct: 157 VHRLDKDTSGVMVVAKSEVAHTALSAAFASRDLERAYLALAWGVPAPASGEVDAPVGRHP 216

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNA-WVTVGLREGKNREIKKVFEFFNWKV---- 212
            +  +  +V +   +   +   +   G++   +   L  G+  +I+         +    
Sbjct: 217 TDRKRMAVVARNGKHALTRYATERAWGTSCALLRCRLATGRTHQIRVHMAHIGHPLVGDP 276

Query: 213 NRLIR 217
             L R
Sbjct: 277 VYLRR 281


>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 = 53.6 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 39/260 (15%), Positives = 75/260 (28%), Gaps = 45/260 (17%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+ K++A      SR  ++  I    V+VNG   +     V   D + V   P       
Sbjct: 34  RLDKILAALLDGHSRSRLQGWIEAGWVQVNGAPAKV-RQVVGPGDVLAVWEQPAPESLAF 92

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-----RVISVGR 113
                   +       + +      +    +     + +   L          R   V R
Sbjct: 93  TPEPIAFAVVAESPDWIVVDKPAGLVTHPGAGNWSGTLLNGLLHRYPELARVARAGIVHR 152

Query: 114 LDINTEGLLLLTNDGGLARVLEL------PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           LD +T GL+++  +      L           +++ +           D+       + +
Sbjct: 153 LDKDTSGLMVVARNELAQTHLVRQLQARSMGREYIALAHGWLPVAGKVDRPIGRDARVPV 212

Query: 168 QGICYGDMQVTLDT-----------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
           +      +                   G    V   L  G+  +I+         +  L 
Sbjct: 213 RMSVERPIAPKPAITHYAPLRRGRAPDGPVTEVACRLETGRTHQIRVHLASLGHPL--LA 270

Query: 217 RISYGPFQLGTLLAGSTREV 236
              YG    G L AG+TR++
Sbjct: 271 DTLYG----GRLTAGATRQM 286


>gi|291544840|emb|CBL17949.1| hemolysin TlyA family protein [Ruminococcus sp. 18P13]
          Length = 261

 Score = 53.6 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 13 PQRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            R+   +   G+AS R   + +I   ++ VNG+   +A+  V  +D I   G
Sbjct: 2  GMRLDSRLVTLGLASSRARAKELICGGQITVNGVPARKASAEVSDSDEILCTG 54


>gi|227821073|ref|YP_002825043.1| hemolysin-like protein [Sinorhizobium fredii NGR234]
 gi|227340072|gb|ACP24290.1| hemolysin-like protein [Sinorhizobium fredii NGR234]
          Length = 251

 Score = 53.6 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 12/60 (20%), Positives = 25/60 (41%), Gaps = 1/60 (1%)

Query: 6  IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          +     +  R+ +++   G +ASR      I +  V V+G  + + A    +   I +D 
Sbjct: 1  MSDNKHSTIRLDQLLLNKGLVASRARARDAIQRGTVMVDGRTVTKPATAFAANATITIDD 60


>gi|157738183|ref|YP_001490867.1| ribosomal large subunit pseudouridine synthase [Arcobacter butzleri
           RM4018]
 gi|315636326|ref|ZP_07891576.1| RNA pseudouridine synthase [Arcobacter butzleri JV22]
 gi|157700037|gb|ABV68197.1| ribosomal large subunit pseudouridine synthase [Arcobacter butzleri
           RM4018]
 gi|315479415|gb|EFU70098.1| RNA pseudouridine synthase [Arcobacter butzleri JV22]
          Length = 251

 Score = 53.6 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 22/206 (10%), Positives = 59/206 (28%), Gaps = 17/206 (8%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILL--------ERAAVNVMSTDHIEVDGVPLRK 69
           K++A     S  + + +I +  VKV    +              +   + ++V       
Sbjct: 10  KLLALQEKISNSKAKELIDKGVVKVGDKKVLIARGEIRTDTKFTIKEINKVKV------I 63

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   + +  KP  L          + +  N     +  + +   +   +   +      
Sbjct: 64  FEDKDILVVDKPAFLTADEVCKKFENAILLNRLDKETSGVMMFAKNEEFQKKAIKEFQAN 123

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNA 187
                 +   +   V  +     +   K   + K   I        + T+     +G+ +
Sbjct: 124 RVYKEYVAIVEGKVVDEIEIDKPILTTKDRGMAKS-KIDVKRGKPAKSTVYPLLVEGNKS 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVN 213
            + V +  G+  +I+         + 
Sbjct: 183 KIKVVIESGRTHQIRVHLNSVGLPII 208


>gi|331269447|ref|YP_004395939.1| hemolysin A [Clostridium botulinum BKT015925]
 gi|329125997|gb|AEB75942.1| hemolysin A [Clostridium botulinum BKT015925]
          Length = 270

 Score = 53.6 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 15/77 (19%), Positives = 28/77 (36%), Gaps = 1/77 (1%)

Query: 9  ENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           N   +R+  ++    I  SR + +  I + ++ VNG  +++    V     IE  G  +
Sbjct: 2  SNVKSERLDVLLVEKNIFESREKAKIAIMEGKIFVNGQRVDKCGQKVKVDSGIEFKGEVM 61

Query: 68 RKAERTRLWLYHKPIGL 84
              R    L       
Sbjct: 62 PYVSRGGYKLEKSMKSF 78


>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 = 53.6 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 32/249 (12%), Positives = 70/249 (28%), Gaps = 33/249 (13%)

Query: 5   NIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           N V+++   QR+ + IA      SR  ++      +V+VNG ++ +    VM  + I + 
Sbjct: 9   NTVKDSQLGQRLDQAIAELFADFSRSRLKDGCWTGKVQVNGEVVTKPRTKVMGGEEITLQ 68

Query: 63  ----DGVPLRKAERT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
               D       +            + +      +V   +     + +   L        
Sbjct: 69  AELEDEERWEAQDIPLDIVYEDDDIIVINKPRDFVVHPGAGTPDGTVLNALLHHYPDIAE 128

Query: 110 SV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                   RLD +T GL+++         L     +                    + + 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRMTAGGKVDQP 188

Query: 165 IVIQGIC---------YGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I                        +      +  + + L  G+  +I+    +    + 
Sbjct: 189 IGRHSTKRTLMAVAPLGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIRVHMSYLQHPL- 247

Query: 214 RLIRISYGP 222
            L   +YG 
Sbjct: 248 -LGDTAYGG 255


>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 = 53.6 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 12/56 (21%), Positives = 26/56 (46%), Gaps = 1/56 (1%)

Query: 8  QENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           E    QR+ + +A +    SR  ++ +I   +V V+G+ +   +  V++     V
Sbjct: 13 TEEDAGQRLDRWLAASVESLSRSRLKALIEAGQVAVDGVAVTDPSAKVLAGSEYTV 68


>gi|78777541|ref|YP_393856.1| hemolysin A [Sulfurimonas denitrificans DSM 1251]
 gi|78498081|gb|ABB44621.1| Hemolysin A [Sulfurimonas denitrificans DSM 1251]
          Length = 236

 Score = 53.6 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+   +   G   SR + + +I +  V VNG  + +++  + S+D + V
Sbjct: 3  RLDNYLVENGQCESRNKAQNIIKEGLVSVNGEQIIKSSYALKSSDKVVV 51


>gi|309810784|ref|ZP_07704590.1| ribosomal RNA large subunit methyltransferase J [Dermacoccus sp.
          Ellin185]
 gi|308435264|gb|EFP59090.1| ribosomal RNA large subunit methyltransferase J [Dermacoccus sp.
          Ellin185]
          Length = 272

 Score = 53.3 bits (126), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 28/54 (51%), Gaps = 1/54 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          +  R+   +   G+  SR + + ++   RV V+G    +A+  V  T ++E++G
Sbjct: 2  SGVRLDAALVARGLVRSRAQAKELLDAGRVLVDGKAEAKASTKVSDTQNVEIEG 55


>gi|126696992|ref|YP_001091878.1| rRNA methyltransferase [Prochlorococcus marinus str. MIT 9301]
 gi|126544035|gb|ABO18277.1| FtsJ cell division protein:S4 domain:Hemolysin A [Prochlorococcus
          marinus str. MIT 9301]
          Length = 270

 Score = 53.3 bits (126), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 10/54 (18%), Positives = 28/54 (51%), Gaps = 2/54 (3%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVK-VNGILLERAAVNVMSTDHIEVDGVP 66
          R+   + ++G+  +R++ + +I   +V+ +NG + ++    V+      +D  P
Sbjct: 6  RLDLYLLKSGLCETRQKAQGLILAGKVRDINGKVWDKPGQQVLIGSEFFIDSEP 59


>gi|253682663|ref|ZP_04863460.1| ribosomal protein S4 [Clostridium botulinum D str. 1873]
 gi|253562375|gb|EES91827.1| ribosomal protein S4 [Clostridium botulinum D str. 1873]
          Length = 206

 Score = 53.3 bits (126), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            R+  V+ R G  S R E  +++      VNG  ++ A+  V + D I V
Sbjct: 98  MRLDNVVYRLGFGSSRSEARQLVTHGHFLVNGKKVDIASFKVSAGDVITV 147


>gi|254526244|ref|ZP_05138296.1| FtsJ cell division protein:S4 domain:Hemolysin A [Prochlorococcus
          marinus str. MIT 9202]
 gi|221537668|gb|EEE40121.1| FtsJ cell division protein:S4 domain:Hemolysin A [Prochlorococcus
          marinus str. MIT 9202]
          Length = 270

 Score = 53.3 bits (126), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 10/54 (18%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVK-VNGILLERAAVNVMSTDHIEVDGVP 66
          R+   +   G+  +R++ + +I   +V+ +NG + ++    V+      +D  P
Sbjct: 6  RLDLYLLNKGLCETRQKAQGLILAGKVRDINGKVFDKPGQQVLIGSEFFIDSEP 59


>gi|157414065|ref|YP_001484931.1| rRNA methylase [Prochlorococcus marinus str. MIT 9215]
 gi|157388640|gb|ABV51345.1| Predicted rRNA methylase [Prochlorococcus marinus str. MIT 9215]
          Length = 270

 Score = 53.3 bits (126), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 10/54 (18%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVK-VNGILLERAAVNVMSTDHIEVDGVP 66
          R+   +   G+  +R++ + +I   +V+ +NG + ++    V+      +D  P
Sbjct: 6  RLDLYLLNKGLCETRQKAQGLILAGKVRDINGKVFDKPGQQVLIGSEFFIDSEP 59


>gi|327399496|ref|YP_004340365.1| 30S ribosomal protein S4 [Hippea maritima DSM 10411]
 gi|327182125|gb|AEA34306.1| ribosomal protein S4 [Hippea maritima DSM 10411]
          Length = 208

 Score = 53.3 bits (126), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R+G+AS RRE  R++    ++VNG  ++  +  V   D I V      K E  
Sbjct: 99  RLDNVVYRSGMASSRREARRLVTHGHIRVNGHKVDIPSYLVRKGDVITVSDKMKAKEEFK 158

Query: 74  RLWLYHKPIG 83
           R +  +    
Sbjct: 159 RRFEENSRRM 168


>gi|296273828|ref|YP_003656459.1| hemolysin A [Arcobacter nitrofigilis DSM 7299]
 gi|296098002|gb|ADG93952.1| hemolysin A [Arcobacter nitrofigilis DSM 7299]
          Length = 240

 Score = 53.3 bits (126), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   + +A    SR +   +I   ++K++G ++ + + NV  T  +E+
Sbjct: 1  MRLDLFLTKAFDIQSRNKAHELIKANKIKIDGAIITKPSFNVEETHKVEI 50


>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 = 53.3 bits (126), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 36/213 (16%), Positives = 68/213 (31%), Gaps = 31/213 (14%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GV-----------PLRKAERTRLW 76
           R+++R   Q +V +NG  ++     V S D I +D G             +   +   L 
Sbjct: 30  RKIKR---QGQVLINGHPVKSFQTPVSSGDEISIDYGDDSCLTPMKMPLHIVYEDDFLLI 86

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLLLLTNDGGLA 131
           +      LV   SDP   +     L  + S+        + RLD NT GL+ +     + 
Sbjct: 87  VNKPAGLLVHPTSDPTEPTLAHGILYYLHSKGALGAFHPIHRLDRNTSGLVAIAKHPHIQ 146

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQ-----------DKLNLLKKGIVIQGICYGDMQVTLD 180
             L     + L+   +     +                N + K +V            + 
Sbjct: 147 HALSGGGAKGLKRLYLAVVTGIPSSLMGRIDAPIGRHPNSIIKRVVRSDGQPAITLYRVL 206

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +     + V + L  G+  +I+         + 
Sbjct: 207 STFSMASLVELELLTGRTHQIRVHLSHIGHPLL 239


>gi|320335497|ref|YP_004172208.1| 30S ribosomal protein S4 [Deinococcus maricopensis DSM 21211]
 gi|319756786|gb|ADV68543.1| ribosomal protein S4 [Deinococcus maricopensis DSM 21211]
          Length = 205

 Score = 53.3 bits (126), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 20/49 (40%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI R GIAS RR+  + +A   + VNG LL+  +  V   D I V
Sbjct: 96  RLDNVIFRLGIASTRRQARQFVAHGHILVNGKLLDVPSYRVKIGDVITV 144


>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 = 53.3 bits (126), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 29/238 (12%), Positives = 67/238 (28%), Gaps = 37/238 (15%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
            +R+ + +A+     SR  ++R+I Q +V++N    +     +   D + +         
Sbjct: 14  GERLDQWLAQQLPELSRSRLQRLIEQGQVQLNEAPCQSKKTKLKVGDRLILKIPAPATMA 73

Query: 64  ------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRV 108
                  + +   +   L +      +V         + V   L              R 
Sbjct: 74  LAPEAMDLDILFEDEHFLIVNKPAGMVVHPAPGNYTGTLVHGLLAHCGENLAGIGGVQRP 133

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLE--------LPSTQWLRVYRVRFHGQVDQDKLNL 160
             V RLD +T G + +       + L+              +     R       +    
Sbjct: 134 GIVHRLDKDTTGAIAIAKTDQAHQHLQAQIKAKTARREYMGIVYGCPRNDAAGTIEAPIA 193

Query: 161 LKKGIVIQ---GICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             KG   +               +  + G+ + +   L  G+  +I+         + 
Sbjct: 194 RHKGDRKKMAVDETGRPAVTHWEIMERLGNYSLLYYKLETGRTHQIRVHSAHMGNPII 251


>gi|167748456|ref|ZP_02420583.1| hypothetical protein ANACAC_03200 [Anaerostipes caccae DSM 14662]
 gi|317472011|ref|ZP_07931343.1| ribosomal protein S4 [Anaerostipes sp. 3_2_56FAA]
 gi|167652448|gb|EDR96577.1| hypothetical protein ANACAC_03200 [Anaerostipes caccae DSM 14662]
 gi|316900415|gb|EFV22397.1| ribosomal protein S4 [Anaerostipes sp. 3_2_56FAA]
          Length = 197

 Score = 53.3 bits (126), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R+E  +++  + V VNG  +   +  V   D IE+
Sbjct: 88  RLDNVLFRLGFGRTRKECRQIVDHKHVLVNGKTVNIPSYRVSVGDVIEI 136


>gi|313496998|gb|ADR58364.1| RluA family pseudouridine synthase [Pseudomonas putida BIRD-1]
          Length = 352

 Score = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 31/231 (13%), Positives = 62/231 (26%), Gaps = 30/231 (12%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLE-----RAAVNVMSTDHIEVDGVP 66
            QR+ +V A+     SR  +   I + R+ V+G ++           +      E  G  
Sbjct: 49  GQRLDQVAAQLFAEYSRSRLTSWIKEGRLTVDGAVVRPRDLVHGGSLLTLEAEQEAQGEW 108

Query: 67  LR--------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-----GR 113
           +           +   L +      +V   +     + +   L  +   V         R
Sbjct: 109 IAEDIELDIVYEDDHILVINKPAGLVVHPAAGHASGTLLNALLHHVPDIVNVPRAGIVHR 168

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-- 171
           LD +T GL+++         L                          +   I   G    
Sbjct: 169 LDKDTTGLMVVAKTLQAQTKLVEQMQARKVSRIYECIVIGVVTAGGKIDAPIGRHGGMRQ 228

Query: 172 -------YGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                           +  +  S+  V V L  G+  +I+       + + 
Sbjct: 229 RMAVTDGGKPAVSHYRVLKRFRSHTHVRVKLETGRTHQIRVHMAHVGFPLV 279


>gi|238924566|ref|YP_002938082.1| putative hemolysin [Eubacterium rectale ATCC 33656]
 gi|238876241|gb|ACR75948.1| probable hemolysin [Eubacterium rectale ATCC 33656]
 gi|291525239|emb|CBK90826.1| hemolysin TlyA family protein [Eubacterium rectale DSM 17629]
 gi|291529302|emb|CBK94888.1| hemolysin TlyA family protein [Eubacterium rectale M104/1]
          Length = 268

 Score = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 25/178 (14%), Positives = 52/178 (29%), Gaps = 2/178 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++   G+A SR + + MI +  V VN    ++A        +IE+ G  L+   R
Sbjct: 3   ERLDVLLVNRGLAPSREKAKTMIMEGNVFVNNNREDKAGSTFPDDCNIEIHGKTLQYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L         T                    ++  G   +    +        L +
Sbjct: 63  GGLKLEKAMKHFDITMDGKVCMDIGAST-GGFTDCMLQNGAKKVYAVDVGYGQFAWKLRQ 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +   +   +  V  +   D+     +    +      G  +  L         + 
Sbjct: 122 DERVVCMEKTNIRYVTPNDIDDELDFASVDVSFISLTKVLGPARALLKDGGEMVCLIK 179


>gi|167945138|ref|ZP_02532212.1| pseudouridine synthase [Endoriftia persephone 'Hot96_1+Hot96_2']
          Length = 55

 Score = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 15/43 (34%), Positives = 26/43 (60%)

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           REG+NR+++++         RL+R   GP++LG L  G  R++
Sbjct: 1   REGRNRQVRRMTAAVGHPTLRLVRTEVGPWRLGNLQPGQWRKL 43


>gi|145631295|ref|ZP_01787067.1| SfhB [Haemophilus influenzae R3021]
 gi|144983080|gb|EDJ90580.1| SfhB [Haemophilus influenzae R3021]
          Length = 324

 Score = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 25/238 (10%), Positives = 56/238 (23%), Gaps = 31/238 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           VQ     +R+ + +A      SR  ++  I    VK+N  +       V+  + IE+   
Sbjct: 10  VQPEQMGERLDQTLAELFPEYSRSRLKTWIEADLVKLNDRIANIPREKVLGGERIEIIVE 69

Query: 63  -------------------DGVPLRKAERTRLWLYHKPIG---LVTTHSDPDGRSTVFDN 100
                              D   +   +   L ++         V           V   
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIVEVP 129

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
              I  R+       +     +               + ++  V           D+   
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 161 LKKGIVIQGICY---GDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 I    +           +     +   + + L  G+  +I+         + 
Sbjct: 190 RHATKRILMAVHPMGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 247


>gi|253577876|ref|ZP_04855148.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251850194|gb|EES78152.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 250

 Score = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 16/59 (27%), Positives = 22/59 (37%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V       R+  +I+ A   SR  +   I   +V VNG L+          D I V G 
Sbjct: 167 VSGTCASVRLDSLISLAFKTSRSSMVSYIEGGQVFVNGKLITSNGYEPKDGDIISVRGK 225


>gi|225848344|ref|YP_002728507.1| hemolysin A [Sulfurihydrogenibium azorense Az-Fu1]
 gi|225644150|gb|ACN99200.1| hemolysin A [Sulfurihydrogenibium azorense Az-Fu1]
          Length = 272

 Score = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 10/60 (16%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 8  QENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
          Q     +R+ K++   G+  +R + + +I    V VN   +++    + +  +I +    
Sbjct: 5  QSTPKKERIDKLLVDKGLVETREKAQALIMSGVVFVNNQKIDKPGTKIPTDANIHIKEKI 64


>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 = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 24/247 (9%), Positives = 73/247 (29%), Gaps = 37/247 (14%)

Query: 3   DKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            + IV E     R  K ++      SR  ++++  +  V +N   ++  +  +++ + ++
Sbjct: 4   KEFIVTEEKQNIRCDKFLSDKLEDFSRESLKKLFKEGEVFLNDEKVK-PSRKLIAGERVK 62

Query: 62  VD-GVP-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           V+   P             +   +   + +      +V   +     + V   +  +   
Sbjct: 63  VNLPEPEVLDVIAENIPINIVYEDEDVVIVDKPQGMVVHPANGNHSGTLVNALMYHVKDL 122

Query: 108 VISVG---------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR 146
               G                     + D     L +   +  + R  +      +    
Sbjct: 123 SSINGVIRPGIVHRIDKDTSGLLIIAKNDNAHNHLAVQFKEHSINRRYKTICHGIIHENS 182

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                 + +DK+   +  +             +  +     ++ V L  G+  +I+   +
Sbjct: 183 GTIDAPIGRDKIKRKEMCVTQSNSKRAVTHFDVIKRYDKYTFLDVHLETGRTHQIRVHLK 242

Query: 207 FFNWKVN 213
           + +  V 
Sbjct: 243 YISHPVI 249


>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 = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 35/214 (16%), Positives = 78/214 (36%), Gaps = 28/214 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTD---------HIEVDGVPLRK-AERTRLW 76
           SR  V+ ++++ ++ VNG +  +    +   D          +E +   LR   E   L 
Sbjct: 42  SRSSVKGLLSRGQISVNGKVTRQFDAALNPNDTVGINYGRGKVEFNNPLLRIVWEDDDLI 101

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGRLDINTEGLLLLTNDG-- 128
           + +K  GL++  +D     T +  L          +++  + RLD +T G+++   +   
Sbjct: 102 VINKREGLLSVSTDRVKERTAYRLLSDYVKQSDPRNKIFVLHRLDRDTSGIMMFAKNQGV 161

Query: 129 --GLARVLELPSTQWLRVYRVRFHGQVDQD-------KLNLLKKGIVIQ-GICYGDMQVT 178
              L        TQ   V  +    + D D       +   ++  + ++        +  
Sbjct: 162 KEQLQSNWSEMITQRTYVAVIEGRPEKDTDLIVSNLVENKNMQVYVTLEGDGKEAITRYR 221

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           L     S + + + L  G+  +I+   +     V
Sbjct: 222 LLQTNNSYSLLELELETGRKNQIRAQMQSIGHPV 255


>gi|260887335|ref|ZP_05898598.1| hemolysin A [Selenomonas sputigena ATCC 35185]
 gi|330838912|ref|YP_004413492.1| hemolysin A [Selenomonas sputigena ATCC 35185]
 gi|260862971|gb|EEX77471.1| hemolysin A [Selenomonas sputigena ATCC 35185]
 gi|329746676|gb|AEC00033.1| hemolysin A [Selenomonas sputigena ATCC 35185]
          Length = 271

 Score = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          +R+  ++   G+A SR     MI + RV V+G  +E+A   V     + + G  +  
Sbjct: 4  ERLDVLLVERGLAASRERARTMIMEGRVLVDGKKVEKAGTGVKPEAELRLLGEEMPY 60


>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 = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 29/244 (11%), Positives = 70/244 (28%), Gaps = 39/244 (15%)

Query: 9   ENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           E    +R+   +      A+R  +E++I +  V  N  ++ +    +   + I++     
Sbjct: 14  EEDQGKRLDLFLKEQLPEATRSYLEKLITEGYVLCNEKVITKNGRKLKGKEVIQLAIPEE 73

Query: 63  -------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
                  + +PL    E   L + +K   +V   +  +   T+ + L       +S    
Sbjct: 74  EKMEIVAENIPLDIVYEDKYLLVVNKQANMVVHPALGNYSGTLVNALLYYCKENLSDMNG 133

Query: 115 DINTE-------------------------GLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
            I                             L+          V  +           R 
Sbjct: 134 VIRPGIVHRLDKDTTGLIIVAKNNQVHSKLALMFQEKTIRKTYVAIVKGRFSEEKKEGRL 193

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +D  +  K  +             +      ++ V V +  G+  +I+   ++ N
Sbjct: 194 ETLITRDSKDRKKMTVSQIQGKKAISNYRVLLDGDKHSLVEVKIETGRTHQIRVHMKYLN 253

Query: 210 WKVN 213
             + 
Sbjct: 254 HPIL 257


>gi|167767777|ref|ZP_02439830.1| hypothetical protein CLOSS21_02312 [Clostridium sp. SS2/1]
 gi|317497068|ref|ZP_07955395.1| ribosomal protein S4 [Lachnospiraceae bacterium 5_1_63FAA]
 gi|167710516|gb|EDS21095.1| hypothetical protein CLOSS21_02312 [Clostridium sp. SS2/1]
 gi|291558882|emb|CBL37682.1| SSU ribosomal protein S4P [butyrate-producing bacterium SSC/2]
 gi|316895613|gb|EFV17768.1| ribosomal protein S4 [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 197

 Score = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 30/73 (41%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R+E  +++  + V VNG  +   +  V + D IE+           
Sbjct: 88  RLDNVLFRLGYGRTRKECRQIVDHKHVLVNGKQVNIPSYQVKAGDVIEIKEKHRTSPRYK 147

Query: 74  RLWLYHKPIGLVT 86
            +    +   + +
Sbjct: 148 EILEVTEGRMIPS 160


>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 = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 32/245 (13%), Positives = 71/245 (28%), Gaps = 41/245 (16%)

Query: 7   VQENFTPQRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           V++     R+ + +        SR  +++ I + +VKVNG + ++ +  +   + +EVD 
Sbjct: 6   VEKREEGWRLDQFLKEKTPSWISRSMIQKAIKEGKVKVNGQI-KKPSYKLKEGEIVEVDL 64

Query: 64  ----------GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                        +       +R  + +      +V         + V   L        
Sbjct: 65  PEKPQEATVQPEEIELKVLYEDRDIIVIDKPGDMIVHPVPSKLSGTLVNALLHHCKDLQG 124

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
             G+L       L     G +       + Q L         +     L    K    +G
Sbjct: 125 VGGKLRPGIVHRLDKETSGVIVVAKNDFAHQSLSKQFKDRKVKKTYILLVK-GKMKNDEG 183

Query: 170 ICYGDMQVT---------LDTQKGSNAWVTV--------GL-----REGKNREIKKVFEF 207
           +    +            ++T K +     V         L     + G+  +I+   + 
Sbjct: 184 VIDLPLARHPVLRIKMAVVETGKEAITEYRVLKRFDDVATLVLAFPKTGRTHQIRVHMKS 243

Query: 208 FNWKV 212
               +
Sbjct: 244 LGHPI 248


>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 = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 34/245 (13%), Positives = 66/245 (26%), Gaps = 45/245 (18%)

Query: 13  PQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE---------- 61
            +R+ KV+A      SR  + ++I    VK+NG +  +        D IE          
Sbjct: 45  GERLDKVLAAHLPDVSRARLAKLIENGSVKLNGAVTTKIRAKATEGDEIELLEPPKLDEA 104

Query: 62  --------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRV 108
                   V+   +   + + + +      +V   +     + +   L          R 
Sbjct: 105 LAFEPQSFVEFEVI-YEDPSIIVVNKPAGLVVHPGAGNPDGTLLNGLLYHFPELKDVPRA 163

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ--------------VD 154
             V RLD +T GL+++         L     +                           D
Sbjct: 164 GIVHRLDRDTTGLMVVARTLAAQTNLVRQLQERTVKREYWALTMGTAAEDFVVDVPIGRD 223

Query: 155 QDKLNLLKKGIVIQGICYGDMQV------TLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                  K      G+     +                +WV   L  G+  +I+      
Sbjct: 224 PKSRIRFKGFPGSTGVRAKPARTRARAVGWSSVDGIPASWVACRLDTGRTHQIRVHLTGE 283

Query: 209 NWKVN 213
           +  + 
Sbjct: 284 DLPLI 288


>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 = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 29/244 (11%), Positives = 70/244 (28%), Gaps = 39/244 (15%)

Query: 9   ENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           E    +R+   +      A+R  +E++I +  V  N  ++ +    +   + I++     
Sbjct: 14  EEDQGKRLDLFLKEQLPEATRSYLEKLITEGYVLCNEKVITKNGKKLKGKEVIQLAIPEE 73

Query: 63  -------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
                  + +PL    E   L + +K   +V   +  +   T+ + L       +S    
Sbjct: 74  EEMEIVAENIPLDIVYEDKYLLVVNKQANMVVHPALGNYSGTLVNALLYYCKENLSDMNG 133

Query: 115 DINTE-------------------------GLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
            I                             L+          V  +           R 
Sbjct: 134 VIRPGIVHRLDKDTTGLIIVAKNNQVHSKLALMFQEKTIRKTYVAIVKGRFSEERKEGRL 193

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +D  +  K  +             +      ++ V V +  G+  +I+   ++ N
Sbjct: 194 ETLITRDPKDRKKMTVSQIQGKKAISNYRVLLDGDKHSLVEVKIETGRTHQIRVHMKYLN 253

Query: 210 WKVN 213
             + 
Sbjct: 254 HPIL 257


>gi|87308396|ref|ZP_01090537.1| probable beta-lactamase regulatory protein [Blastopirellula marina
           DSM 3645]
 gi|87288953|gb|EAQ80846.1| probable beta-lactamase regulatory protein [Blastopirellula marina
           DSM 3645]
          Length = 555

 Score = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 7/104 (6%), Positives = 13/104 (12%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G    +  +                R               +   +      + +   P 
Sbjct: 448 GMRDGDRPRPEGPPRDGGRPRPEGMRDGDRPRPEGPPRDGGRPRPEGMRDGDRPRPEGPP 507

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                     M  G                   P         R
Sbjct: 508 RDGGRPRPEGMRDGDRPRPEGPPRDGGRPRPEGPREGDAAPAPR 551



 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 9/116 (7%), Positives = 21/116 (18%), Gaps = 2/116 (1%)

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL-SK 297
           ++LR  +        ++        +        +     P+   R       +      
Sbjct: 417 QMLRAHMDRIQRRLDELQRPPRRDGNRPRPDGMRDGDRPRPEGPPRDGGRPRPEGMRDGD 476

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           + +   P           M  G                R        R       +
Sbjct: 477 RPRPEGPPRDGGRPRPEGMRDGDRPRPEGPPRDGGRP-RPEGMRDGDRPRPEGPPR 531



 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 9/110 (8%), Positives = 20/110 (18%), Gaps = 1/110 (0%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           ++GP   E   +  +        + R +  +            +          + +   
Sbjct: 400 EVGPPRDEMIDLLREEMQMLRAHMDRIQRRLDELQRPPRRDGNRPRPDGMRDGDRPRPEG 459

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           P           M  G                R        R       +
Sbjct: 460 PPRDGGRPRPEGMRDGDRPRPEGPPRDGGRP-RPEGMRDGDRPRPEGPPR 508



 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/136 (10%), Positives = 28/136 (20%), Gaps = 11/136 (8%)

Query: 227 TLLAGSTREVSKKILR-----EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD 281
            LL    + +   + R     ++L      +        +   +    + P      P  
Sbjct: 410 DLLREEMQMLRAHMDRIQRRLDELQRPPRRDGNRPRPDGMRDGDRPRPEGPPRDGGRPRP 469

Query: 282 FTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAK---GIHSSFLSDS-GQREENHRR 337
                 +  +  G  +      P   R+            G          G R      
Sbjct: 470 EGMRDGDRPRPEGPPRDGGRPRPEGMRDGDRPRPEGPPRDGGRPRPEGMRDGDRPRPEG- 528

Query: 338 SPSFPSKRSLRRTSAK 353
            P     R       +
Sbjct: 529 -PPRDGGRPRPEGPRE 543



 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 9/122 (7%), Positives = 21/122 (17%), Gaps = 7/122 (5%)

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             + + L   +               E     R +     PD      +   +       
Sbjct: 406 DEMIDLLREEMQMLRAHMDRIQRRLDELQRPPRRDGNRPRPDGMRDGDRPRPEGPPRDGG 465

Query: 299 KKLATPVHRRNLASNVWMAK-GIHSSFL------SDSGQREENHRRSPSFPSKRSLRRTS 351
           +     +   +        + G                +        P     R   R  
Sbjct: 466 RPRPEGMRDGDRPRPEGPPRDGGRPRPEGMRDGDRPRPEGPPRDGGRPRPEGMRDGDRPR 525

Query: 352 AK 353
            +
Sbjct: 526 PE 527



 Score = 44.8 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 12/115 (10%), Positives = 24/115 (20%), Gaps = 8/115 (6%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+++   L EE Q+           L   +     +         ++  +       +  
Sbjct: 405 RDEMIDLLREEMQMLRAHMDRIQRRLDELQRPPRRDGNRPRPDGMRDGDRPRPEGPPRDG 464

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDS------GQREENHRRSPSFPSKRSLRRT 350
             P        +    +G               G R       P     R     
Sbjct: 465 GRPRPEGMRDGDRPRPEGPPRDGGRPRPEGMRDGDRPRPEG--PPRDGGRPRPEG 517


>gi|195952670|ref|YP_002120960.1| 30S ribosomal protein S4 [Hydrogenobaculum sp. Y04AAS1]
 gi|195932282|gb|ACG56982.1| RNA-binding S4 domain protein [Hydrogenobaculum sp. Y04AAS1]
          Length = 207

 Score = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           R+  V+ R GI  +RR+  + +    + VNG  ++  +  V   D IEV    + + 
Sbjct: 99  RLDNVVYRLGIACTRRQARQFVVHGHIMVNGKKVDIPSYQVNVGDIIEVYSKDIPQI 155


>gi|331268441|ref|YP_004394933.1| 30S ribosomal protein S4 [Clostridium botulinum BKT015925]
 gi|329124991|gb|AEB74936.1| ribosomal protein S4 [Clostridium botulinum BKT015925]
          Length = 206

 Score = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            R+  V+ R G  S R E  +++      VNG  ++ A+  V + D I V
Sbjct: 98  MRLDNVVYRLGFGSSRSEARQLVTHGHFLVNGKKVDIASFKVSAGDVITV 147


>gi|187776603|ref|ZP_02993076.1| hypothetical protein CLOSPO_00117 [Clostridium sporogenes ATCC
           15579]
 gi|187775262|gb|EDU39064.1| hypothetical protein CLOSPO_00117 [Clostridium sporogenes ATCC
           15579]
          Length = 206

 Score = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 14/69 (20%), Positives = 25/69 (36%), Gaps = 1/69 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+  V+ R G   SR E  +++      +NG  ++  +  V + D I V        + 
Sbjct: 98  MRLDNVVFRLGYGNSRTEARQLVTHGHFLINGKKVDIPSYQVSANDVITVCDKSKATEKF 157

Query: 73  TRLWLYHKP 81
                  K 
Sbjct: 158 KTFAENPKT 166


>gi|302672285|ref|YP_003832245.1| RNA-binding S4 domain-containing protein [Butyrivibrio
           proteoclasticus B316]
 gi|302396758|gb|ADL35663.1| RNA-binding S4 domain-containing protein [Butyrivibrio
           proteoclasticus B316]
          Length = 271

 Score = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 25/59 (42%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +  +   +R+  ++A     SR E +++I  + V ++G        ++     + V G 
Sbjct: 188 ISGSVASERIDAILAFVYHLSRSEAQKLIESESVFIDGRTAYSGGYDLKEGARVSVRGH 246


>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 = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 4/54 (7%)

Query: 13 PQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          P R+ K ++R        SR  + R+I +  V V+G ++      V+    + +
Sbjct: 15 PPRLDKALSRDVPETAALSRTRLARLITEGAVSVDGQVVTDPKARVVEGAQVAI 68


>gi|268679994|ref|YP_003304425.1| hemolysin A [Sulfurospirillum deleyianum DSM 6946]
 gi|268618025|gb|ACZ12390.1| hemolysin A [Sulfurospirillum deleyianum DSM 6946]
          Length = 238

 Score = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 13/51 (25%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+   +   G A SR +   +I +  V VNG +  +++  V   D ++V+
Sbjct: 1  MRLDNYVFEKGFAQSRNKASELIKEGSVWVNGNVERKSSFEVCENDKVDVE 51


>gi|253700204|ref|YP_003021393.1| hemolysin A [Geobacter sp. M21]
 gi|251775054|gb|ACT17635.1| hemolysin A [Geobacter sp. M21]
          Length = 257

 Score = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 1/59 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          T +R+ K++   G+A SR   + +I   +V V+  L ++A + V     I + G PL  
Sbjct: 2  TKERLDKLVLERGLAPSRERAKALIMAGQVVVDDHLADKAGLMVSIEAEIRLKGEPLPY 60


>gi|118444316|ref|YP_878057.1| hemolysin A [Clostridium novyi NT]
 gi|118134772|gb|ABK61816.1| hemolysin A [Clostridium novyi NT]
          Length = 270

 Score = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 11/62 (17%), Positives = 26/62 (41%), Gaps = 1/62 (1%)

Query: 9  ENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           +   +R+  ++    I  SR + +  I + ++ VNG  +++    +     IE  G  +
Sbjct: 2  SSVKSERLDILLVEKNIFDSREKAKIAIMEGKIFVNGQRVDKCGQKIKVDSEIEFKGEVM 61

Query: 68 RK 69
            
Sbjct: 62 PY 63


>gi|170781652|ref|YP_001709984.1| hypothetical protein CMS_1246 [Clavibacter michiganensis subsp.
          sepedonicus]
 gi|169156220|emb|CAQ01362.1| conserved hypothetical protein [Clavibacter michiganensis subsp.
          sepedonicus]
          Length = 290

 Score = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          R+   +   G+A SR    R+I    V V+G  + +A+  VM    +EV G
Sbjct: 25 RLDAALPALGLARSRTHAARLIVDGLVTVDGRGVVKASFRVMPGSVVEVAG 75


>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 = 53.3 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 27/247 (10%), Positives = 66/247 (26%), Gaps = 43/247 (17%)

Query: 7   VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           + +    QR+ KV++  G+    SR  +++ I    V VNG   + A + ++  + +EV 
Sbjct: 46  LDDEVIGQRLDKVLS--GLLPEFSRSRIQQWIEDGHVTVNGAPAK-AKMTMLGDELVEVA 102

Query: 64  GVPLRKAERT---------------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--- 105
              +   +                  + L      +V   +     + +   L       
Sbjct: 103 PQSVPSDQPYGPEPMALDILHEDKALIVLNKPAGLVVHPAAGNWSGTLLNGLLHHCPALA 162

Query: 106 --------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                    R+       +     L    D            Q+L +           + 
Sbjct: 163 KVPRAGIVHRLDKDTSGIMVVAKTLAAQTDLVRQLQARSMKRQYLALVWGLPQLSGTINA 222

Query: 158 LNLLKKGIVIQG-----ICYGDMQVTL------DTQKGSNAWVTVGLREGKNREIKKVFE 206
                    I+      +               +  +   + +   L  G+  +I+   +
Sbjct: 223 PMARHPRDRIKMAVSQSMRAKPAVTHYRRLATGEIDRKPVSLIHCRLETGRTHQIRVHLQ 282

Query: 207 FFNWKVN 213
              + + 
Sbjct: 283 SLGFPLV 289


>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 = 52.9 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 29/252 (11%), Positives = 62/252 (24%), Gaps = 41/252 (16%)

Query: 1   MKDKNIVQ--ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M D   +   +     R+   IAR    SR     +IA+  V V+G    + +  V +  
Sbjct: 1   MSDHRSMPVPDGLEGDRLDTAIARLFGLSRTRAAELIAEGNVLVDGAPAAK-SDRVNAGA 59

Query: 59  --HIEV--------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
              I +               G+ +   +   + +      +        G + V   L 
Sbjct: 60  WLDITLPPPPNPPAPRPEPVPGMRIVYEDADIVVVDKPAGVVAHPTIGWSGPTVVDGLLA 119

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
           +  +   S           L     G +       +   L+        +     L    
Sbjct: 120 AGVAVATSGAAERQGIVHRLDANTTGLMVVAKSEIAYSSLKRAFKERTVEKVYHALVQ-G 178

Query: 163 KGIVIQGICYGDMQ---------------------VTLDTQKGSNAWVTVGLREGKNREI 201
               ++G     +                       T      + + + + L  G+  +I
Sbjct: 179 HPDPLRGTIDAPIDRHPSGDGRFAVVAGGRPSVTHYTTLEAFRAASLLEIDLETGRTHQI 238

Query: 202 KKVFEFFNWKVN 213
           +           
Sbjct: 239 RVHMSAIRHPCV 250


>gi|56460992|ref|YP_156273.1| 30S ribosomal protein S4 [Idiomarina loihiensis L2TR]
 gi|61215388|sp|Q5QXV7|RS4_IDILO RecName: Full=30S ribosomal protein S4
 gi|56180002|gb|AAV82724.1| Ribosomal protein S4 [Idiomarina loihiensis L2TR]
          Length = 206

 Score = 52.9 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G AS R E  ++++ + V VNG ++   +  V   D + V
Sbjct: 96  QRLDNVVYRMGFASTRAEARQLVSHKAVVVNGQVVNIPSFKVRPEDVVSV 145


>gi|163849205|ref|YP_001637249.1| hemolysin A [Chloroflexus aurantiacus J-10-fl]
 gi|222527183|ref|YP_002571654.1| hemolysin A [Chloroflexus sp. Y-400-fl]
 gi|10198134|gb|AAG15202.1|AF288458_1 HlyA [Chloroflexus aurantiacus]
 gi|163670494|gb|ABY36860.1| hemolysin A [Chloroflexus aurantiacus J-10-fl]
 gi|222451062|gb|ACM55328.1| hemolysin A [Chloroflexus sp. Y-400-fl]
          Length = 260

 Score = 52.9 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          QR+ +V+   G+A +R   + +I   +V VNG +  +A   +     +EV
Sbjct: 4  QRLDQVLVSRGLAETRARAQALIMAGQVLVNGQVQTKAGTLIADDASVEV 53


>gi|104779779|ref|YP_606277.1| 30S ribosomal protein S4 [Pseudomonas entomophila L48]
 gi|152112249|sp|Q1IFU2|RS4_PSEE4 RecName: Full=30S ribosomal protein S4
 gi|95108766|emb|CAK13460.1| 30S ribosomal protein S4 [Pseudomonas entomophila L48]
          Length = 206

 Score = 52.9 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 1/56 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V   D + V    L +
Sbjct: 97  RLDNVVYRMGFGSTRSESRQLVSHKAISVNGKTVNIPSYQVRPGDVVSVREKSLNQ 152


>gi|319405172|emb|CBI78777.1| ribosomal large subunit pseudouridine synthase D [Bartonella sp. AR
           15-3]
          Length = 333

 Score = 52.9 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 26/262 (9%), Positives = 72/262 (27%), Gaps = 52/262 (19%)

Query: 4   KNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           ++I  EN   QR+ + +A+      SR  ++ +I +  +K++G L++   + + S   IE
Sbjct: 3   QHITNENACGQRIDQWLAKQYKEELSRSRLQTLIREGYLKIDGQLIKEPKIKLKSNQIIE 62

Query: 62  V----------DGVPLRK----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           +           G  L       +   + +      +V   +     + V   +      
Sbjct: 63  LTIPTPNDARPQGEALALDILFEDNHVIVINKPAGLVVHPGNGNWTGTLVNALIYHCSDS 122

Query: 108 VISVGRLDIN--------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
           +  +G +               +++     LA                           +
Sbjct: 123 LSGIGGIKRPGIVHRLDKDTSGVMVIAKNDLAHRNLNAQFADHGRTSALDRRYHAVIWGS 182

Query: 160 LLKKGIVIQGICYG----DMQVTLDTQKGSN------------------------AWVTV 191
             +  + I            + ++   + ++                        + +  
Sbjct: 183 PNRNIVTIDTFLARSSRDRTKRSVVHSEHAHARRAITHFSLLEKYGACNDATSLASLLEC 242

Query: 192 GLREGKNREIKKVFEFFNWKVN 213
            L  G+  +I+         + 
Sbjct: 243 RLETGRTHQIRVHMAHIGHPLI 264


>gi|313904924|ref|ZP_07838295.1| ribosomal protein S4 [Eubacterium cellulosolvens 6]
 gi|313470181|gb|EFR65512.1| ribosomal protein S4 [Eubacterium cellulosolvens 6]
          Length = 197

 Score = 52.9 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            R+  VI R  +A +R+E  +++  + V VNG ++   +  V   D IE+
Sbjct: 87  MRLDNVIFRLALARTRKEARQIVDHKFVTVNGKVVNIPSYQVKPGDVIEI 136


>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 = 52.9 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 33/255 (12%), Positives = 69/255 (27%), Gaps = 47/255 (18%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V      +R+  V+A      SR  ++ +I    V + G  +      V   D I +  
Sbjct: 19  TVDPEDAGKRIDAVLASHLETLSRNRIQSLIKAGDVSIGGAKIGEPKYRVNEGDEITLHL 78

Query: 64  ---------GVPLRK----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
                    G  +       +   + +      +V   +     + V   +         
Sbjct: 79  PEPEDPDPKGEDIPLSVVFEDAHVIVIDKPAGLVVHPGAGNWTGTLVNALIHHCGDSLSG 138

Query: 107 -----RVISVGRLDINTEGLLLLTN-----------------DGGLARVLELPSTQWLRV 144
                R   V R+D +T GLL++                    G L R            
Sbjct: 139 IGGVKRPGIVHRIDKDTSGLLVVAKTDQAHQGLAAQFADHGRTGPLERAYSALVWGAPSS 198

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS------NAWVTVGLREGKN 198
            +      + + + N  K  +V     +      +  + G+       + +   L  G+ 
Sbjct: 199 LKGTIDANLARSQANRQKMAVVKTSGRHAITHWQVKERFGAADQPPLASLMECRLETGRT 258

Query: 199 REIKKVFEFFNWKVN 213
            +I+         + 
Sbjct: 259 HQIRVHMAHIGHPLL 273


>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 = 52.9 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 31/257 (12%), Positives = 67/257 (26%), Gaps = 45/257 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGI-ASRREVERMIAQQRVKVN---GILLERAAVNVM 55
           M+    V E++   R+   +   AG   SR  V++ I    V  N     ++ +    V 
Sbjct: 1   MQIFVTVSEDYDQSRLDVFLKDNAGDDLSRSTVQKWIDSGFVT-NKTKDQVVHKNGYKVA 59

Query: 56  STDHIEVD--------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
             +   VD               +P+   E   + ++ K      +    D  S V   L
Sbjct: 60  LGEEFVVDVIARPPSRLEPIAMDIPVLYDEDEFMVIHKKAGIACHSGPGDDSPSLVNGLL 119

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDG-------------------------GLARVLEL 136
               +   + G         L    +G                              +  
Sbjct: 120 YQFKNLSGTGGERRPGIVHRLDKPTEGVLIIAKTDRAHAALSKLFQDRLVEKTYYAWVLQ 179

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
              +      +       +     +++   +    Y   ++         + + +GL  G
Sbjct: 180 APVEAEGTINMPIGRHPVERVKMCVREDGRMAITHYKTEKIVQTQTGRKFSLMKLGLETG 239

Query: 197 KNREIKKVFEFFNWKVN 213
           +  +I+         V 
Sbjct: 240 RTHQIRVHMAKVGCPVV 256


>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 = 52.9 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 28/244 (11%), Positives = 69/244 (28%), Gaps = 37/244 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           I  EN   +R+   IAR+    +R   +R+I   ++ V+G   ++ ++ +   + + V  
Sbjct: 7   IFPENSEIERLDSFIARSVNGMTRATAQRLIEAGQITVDGHP-QKPSLKLKGGERLMVTI 65

Query: 65  V--------------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                           +   +R  + +      +V   +   G + V   L         
Sbjct: 66  PPPVAAEPAAETIPLEILFEDRNLVVVNKAAGMVVHPGAGNSGGTLVNALLGHCTDLSGI 125

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV---------------------RF 149
            G L       +     G L       + Q L                          R 
Sbjct: 126 GGELRPGIVHRIDKDTSGVLVVAKSDAAHQSLAEQFKEHTIKRVYLALVYGAPKDDKGRL 185

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +  ++  +     +   +      +  +      + + L  G+  +I+       
Sbjct: 186 ESHIGRHPVDRKRMSGKAKHGKHAVTHWRVVGRYRGITLLRLRLETGRTHQIRVHLSEAG 245

Query: 210 WKVN 213
           + + 
Sbjct: 246 YPLV 249


>gi|291550387|emb|CBL26649.1| Uncharacterized conserved protein, contains S4-like domain
           [Ruminococcus torques L2-14]
          Length = 266

 Score = 52.9 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 28/63 (44%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            D   ++   +  R+  ++  A  +SR ++  +I   +V VNG L+      V   D I 
Sbjct: 178 PDLQQIKGTVSSVRLDSLLPLAFSSSRSKLSGLIEGAKVFVNGKLITSNGYQVKEGDLIS 237

Query: 62  VDG 64
           V G
Sbjct: 238 VRG 240


>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 = 52.9 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 28/240 (11%), Positives = 56/240 (23%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           + E     R+ K +A     SR  +  +I   +V VN    +         D IE +   
Sbjct: 6   INEENKGLRLDKALANQTEYSRSLLTELIKNDKVFVNSEAKKAKYKV-KVGDRIEFEVPE 64

Query: 64  -----------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
                       + +   +     +      +V   +     + V   +  I       G
Sbjct: 65  AEVLDIVAEDLPLEIIYEDSDVAVVNKPQGMVVHPAAGHASGTLVNAIMYHIKDLSSING 124

Query: 113 RLDINTEGLLLLTNDGGLARVLELPST--------------------QWLRVYRVRFHGQ 152
            +       +     G L       +                                  
Sbjct: 125 VIRPGIVHRIDKDTSGLLMIAKNDKAHESLAAQLKDKTSKRRYLAIVHGEIANDKGTIEA 184

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                L   KK  V+ G         +  +      + + L  G+  +I+    +    V
Sbjct: 185 PIGRNLKDRKKQAVVSGGKPAVTHFEVLERFYGYTLIALRLETGRTHQIRVHMNYIGHPV 244


>gi|284161758|ref|YP_003400381.1| RNA-binding S4 domain protein [Archaeoglobus profundus DSM 5631]
 gi|284011755|gb|ADB57708.1| RNA-binding S4 domain protein [Archaeoglobus profundus DSM 5631]
          Length = 209

 Score = 52.9 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 14/67 (20%), Positives = 31/67 (46%), Gaps = 5/67 (7%)

Query: 14 QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ +++   G  S R++ +  I ++ V VNG ++ + + +V     I V    L++ + 
Sbjct: 1  MRLDRLLVIKGYFSSRQKAKEAIRRRFVIVNGKVVTKPSYDVDFDVEIRV----LQEEKP 56

Query: 73 TRLWLYH 79
             W   
Sbjct: 57 KGYWKLK 63


>gi|91070167|gb|ABE11088.1| FtsJ cell division protein:S4 domain:Hemolysin A [uncultured
          Prochlorococcus marinus clone HF10-11D6]
          Length = 270

 Score = 52.9 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 10/54 (18%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVK-VNGILLERAAVNVMSTDHIEVD 63
             R+   +   G+  +R++ + +I   +V+ +NG +L++    V+      +D
Sbjct: 3  KKTRLDLYLLNKGLCETRQKAQGLILAGKVRDINGKVLDKPGQQVLIGSEFFID 56


>gi|269123124|ref|YP_003305701.1| 30S ribosomal protein S4 [Streptobacillus moniliformis DSM 12112]
 gi|268314450|gb|ACZ00824.1| ribosomal protein S4 [Streptobacillus moniliformis DSM 12112]
          Length = 195

 Score = 52.9 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI R G  S RR+  ++++   + +NG  ++ A+  V   D I +
Sbjct: 89  RLDNVIYRLGFGSTRRQARQIVSHGHILINGKRVDIASYRVKQGDVITL 137


>gi|332970080|gb|EGK09077.1| ribosomal large subunit pseudouridine synthase D [Kingella kingae
           ATCC 23330]
          Length = 371

 Score = 52.9 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 28/238 (11%), Positives = 68/238 (28%), Gaps = 32/238 (13%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILL---------ERAAVNVM 55
           IV  +    R+   +A+     SR  +   I    V+ NG            E  +V + 
Sbjct: 31  IVPNDLAGMRLDAALAKLLPDYSRSRITTWIKDGFVQCNGKTASPKEKLIGGEELSVQIQ 90

Query: 56  STDH-------------IEVDGVPLRKAERTRLWLYHKPIGLVTT--HSDPDGRSTVFDN 100
            +D              +  D   +   +   L ++        T  +        +   
Sbjct: 91  QSDENQAYEPEHMDLNIVFEDDTVIVLNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQV 150

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR-------VYRVRFHGQV 153
             +     +      +      L   +  + ++      +  R        +  +    +
Sbjct: 151 PRAGIVHRLDKDTSGLMVVAKTLPAQNSLVQQLQNRTVKRIYRAVADGIVPFDGKIETLI 210

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +D  N LK  +V  G       V +  +  +++++   L  G+  +I+   +     
Sbjct: 211 GRDPHNRLKMAVVKFGGKEAVTHVKVLERYHAHSYIECSLETGRTHQIRVHMKEARHP 268


>gi|225024812|ref|ZP_03714004.1| hypothetical protein EIKCOROL_01699 [Eikenella corrodens ATCC
          23834]
 gi|224942415|gb|EEG23624.1| hypothetical protein EIKCOROL_01699 [Eikenella corrodens ATCC
          23834]
          Length = 140

 Score = 52.9 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 15 RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          R+  V+ R G  S R E  ++++ + + VNG ++   +  V + D + V     ++    
Sbjct: 31 RLDNVVYRMGFGSTRAEARQLVSHKAILVNGEVVNIPSFQVKAGDTVSVREKAKKQVRIQ 90


>gi|171778695|ref|ZP_02919791.1| hypothetical protein STRINF_00643 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171282652|gb|EDT48076.1| hypothetical protein STRINF_00643 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 261

 Score = 52.9 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 18/63 (28%), Positives = 33/63 (52%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K+ + +    +  R+ KV+A     SR +  ++I+ ++VKVN   L+R +  +   D I 
Sbjct: 171 KESHQLDIMVSSMRLDKVLATVLKLSRSQAIQLISAEKVKVNYQTLDRPSEMLQFGDLIS 230

Query: 62  VDG 64
           V G
Sbjct: 231 VRG 233


>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 = 52.9 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 33/239 (13%), Positives = 64/239 (26%), Gaps = 36/239 (15%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
                R+   +A     SR +   +I    V VN     + ++ +   D I V       
Sbjct: 6   QTQSSRLDVALASELKISRNQATNLIKNALVSVNSKPALKPSMQLNQNDEICVKFALPKE 65

Query: 63  -------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG--- 112
                  +       E   + + +KP  +V   +     +T+ + L      + ++    
Sbjct: 66  KTNDYEANFEIPVIYEDEDILVLNKPPQIVVHQAPSVKEATLVEWLNQKGFMLSNLNGDL 125

Query: 113 ------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD 154
                               +      L    +      + L  T             + 
Sbjct: 126 RAGIVHRLDKGTSGAIVVAKNNAAHAALSAQLNDKSMGRIYLALTDLPLKQECIIDKPIG 185

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +   N LK GIV  G       + L      N  +   L  G+  +I+      N  + 
Sbjct: 186 RSPSNRLKMGIVTNGRHAKSAFLNLVQTDEVN-LIAAKLFTGRTHQIRAHLASINRHIL 243


>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 = 52.9 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 32/247 (12%), Positives = 72/247 (29%), Gaps = 35/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M +K I+       R+  ++A+     SR  +   +    + VN   ++R +  V   D 
Sbjct: 1   MMEKTIINITTQVGRIDAILAKEDLQYSRTTLAEWLQNGHILVNNNKVKR-SYKVSVGDT 59

Query: 60  IEV------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I +            + +P  +   +   L +      +V   +     + V   L    
Sbjct: 60  ISIFPPEVASTEIIAEDIPLDIVYEDNDILVVNKPQGMVVHPAAGHSSGTLVNALLHHAP 119

Query: 106 SRVISVGRLDINTEG---------LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
              I+                   ++   +    A   +L + +  R+Y     G+  +D
Sbjct: 120 LSTINGTFRPGIVHRIDRDTSGLLMVAKNDVAHKALSAQLKAHKNDRIYYALVRGEFSED 179

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          K+  V  G         +  +      + V L  G+  +I+    
Sbjct: 180 SGTINAPIGRHPVDRKRQAVQVGGREAITHFEVVHRYVGFTLLKVRLETGRTHQIRVHLT 239

Query: 207 FFNWKVN 213
           +    + 
Sbjct: 240 YIGHPIV 246


>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 = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 24/248 (9%), Positives = 55/248 (22%), Gaps = 41/248 (16%)

Query: 4   KNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-E 61
           + +  +  +  RV K +  R   A+R  ++       + VN   ++     V   D +  
Sbjct: 34  RFVADKGQSLLRVDKFLVDRMMGATRNRIQLAAEAGCILVNDKPVKS-NYRVKPLDVVSV 92

Query: 62  VDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           V   P              +   +   L +      +V         + V      +   
Sbjct: 93  VMDRPRRELEIIPEDIPLNIVYEDDDLLVVNKPAGLVVHPGHGNYTGTLVNALAYYLKDD 152

Query: 108 VISVG------------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
                                            +   L              +       
Sbjct: 153 PYYDPSDPRLGLVHRIDKDTSGLLVVAKRPEAKSNLSLQFFNKTTKRKYRALVWGIVQED 212

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
             R+  +   D      +                T+  + G  + V   L  G+  +I+ 
Sbjct: 213 EGRIEGNIGRDPRDRMQMTVFPEGDQGKTAVTHYTVLERLGYVSLVECRLETGRTHQIRV 272

Query: 204 VFEFFNWK 211
             ++    
Sbjct: 273 HMKYIGHT 280


>gi|289423095|ref|ZP_06424910.1| hemolysin A [Peptostreptococcus anaerobius 653-L]
 gi|289156426|gb|EFD05076.1| hemolysin A [Peptostreptococcus anaerobius 653-L]
          Length = 292

 Score = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 22/56 (39%), Gaps = 1/56 (1%)

Query: 15 RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          R+  ++   G  ASR +  R I    V VN   +++    V     I V G  +  
Sbjct: 4  RIDVLLVDFGYFASREQARRTIMAGNVFVNNQRVDKPGTAVKIDSEILVKGKQIPY 59


>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 = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 29/239 (12%), Positives = 60/239 (25%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            VQ +   QR+ + +A      SR  ++  I +  V VNG++       V   + IE+  
Sbjct: 9   TVQSHQMGQRLDQTLAELFPDYSRSCLKTWIEEDLVLVNGVVQNVPRSKVYGDEQIEITV 68

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                           +   +   L +      +V   +     + +   L         
Sbjct: 69  EIEDETRFEPENIPLNIVYEDDDILVINKPKDLVVHPGAGNPSGTVLNALLYHYPPIAEV 128

Query: 111 V-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                  RLD +T GL+++         L     +                         
Sbjct: 129 PRAGIVHRLDKDTTGLMVVAKTIPAQTQLVRDLQKRKITREYEAVACGIMTKGGMVDEPM 188

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +  +      + + L  G+  +I+         + 
Sbjct: 189 ARHPTKRTHMAVHPMGKPAVTHYRIMERFRDYTRLRLRLETGRTHQIRVHMAHIAHPLL 247


>gi|227550851|ref|ZP_03980900.1| possible pseudouridylate synthase [Enterococcus faecium TX1330]
 gi|227179949|gb|EEI60921.1| possible pseudouridylate synthase [Enterococcus faecium TX1330]
          Length = 135

 Score = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 35/122 (28%), Positives = 53/122 (43%), Gaps = 2/122 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K+I      +R+E++R+ A ++V V+G +  R   NV S    IEV G  L   E 
Sbjct: 1   MRLDKLIEEKLETTRKEMKRLFALKQVMVDGTVEFRQNRNVDSLLHRIEVAGEHLETNES 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L      +                    F  +  VGRLD +T GLLL+T++G L  
Sbjct: 61  -YYLLNKPKKAVTAVSDPEKTTVIDLIASADRFQPLYPVGRLDRDTTGLLLITSNGQLGY 119

Query: 133 VL 134
            +
Sbjct: 120 EM 121


>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 = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 31/241 (12%), Positives = 69/241 (28%), Gaps = 37/241 (15%)

Query: 9   ENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGI--------------LLERAAVN 53
           E     R+   IA      SR  ++++I    V V+G               ++      
Sbjct: 10  EEDEGVRLDIYIAEQYDDLSRSYIQKVIKDNGVTVDGRPEKNRYIVKVGQVIVVSLPEAK 69

Query: 54  -------------VMSTDHIEVDGVP----LRKAERTRLWLYHKPIGLVTT----HSDPD 92
                        V   D + V   P    +  A           +           +  
Sbjct: 70  ELEVTAQNIPLDIVYEDDDLLVVNKPQDMVVHPAPGNYENTMVNALLYHCKGKLSSINGI 129

Query: 93  GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152
            R  +   +    S ++ V + +   + L     D    R     S   ++  R   +  
Sbjct: 130 IRPGIVHRIDKDTSGLLMVAKNNHAHQFLSEQLKDHSTTRKYHGISVGTIKEERATINAP 189

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           + + + + L K  V+ G       + +  + G + ++   L  G+  +I+    +    +
Sbjct: 190 IARHQTDRL-KMAVLAGGRNAVTHIQVLNRFGDHTYMEAQLETGRTHQIRVHLGYIGHPL 248

Query: 213 N 213
            
Sbjct: 249 L 249


>gi|238922856|ref|YP_002936369.1| 30S ribosomal protein S4 [Eubacterium rectale ATCC 33656]
 gi|259495279|sp|C4ZBU5|RS4_EUBR3 RecName: Full=30S ribosomal protein S4
 gi|238874528|gb|ACR74235.1| 30S ribosomal protein S4 [Eubacterium rectale ATCC 33656]
 gi|291523756|emb|CBK89343.1| SSU ribosomal protein S4P [Eubacterium rectale DSM 17629]
 gi|291528778|emb|CBK94364.1| SSU ribosomal protein S4P [Eubacterium rectale M104/1]
          Length = 197

 Score = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI R G A +R+E  +++  + V VNG ++   +  V + D IE+
Sbjct: 88  RIDNVIFRLGFARTRKEARQIVDHKFVTVNGKVVNIPSYLVKAGDVIEI 136


>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 = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 31/236 (13%), Positives = 59/236 (25%), Gaps = 36/236 (15%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE----------- 61
            +RV   +AR    SR +V  + AQ  V+++G +L ++   V +   IE           
Sbjct: 12  GERVDAALARMTGLSRSKVSELCAQGGVRMDGAVLGKSDRLV-AGSLIEVDLPDPRPLGP 70

Query: 62  ----VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
               VDG+ L   +   + +              DG   +            S       
Sbjct: 71  APTPVDGMSLVYEDEDIVVVDKPAGIAAHPSMGWDGPDVLGALKAMHVQVATSGAAERQG 130

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--------------------K 157
               L +   G +       +   L+                                  
Sbjct: 131 IVSRLDVGTSGAMIVAKGERAYSVLKRAFREHEVDKIYHALVQGHLDPSSGTIDAPIGRH 190

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +   K  +I G         +     +     + L  G+  +I+           
Sbjct: 191 PSREWKMAIIDGGRESVTHYDVIESMPAADLAEIHLETGRTHQIRVHMSAVGHPCV 246


>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 = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 33/244 (13%), Positives = 75/244 (30%), Gaps = 38/244 (15%)

Query: 7   VQENFTPQRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           V       R+ K I        SR  ++R I    V VN    ++ +  + + D +    
Sbjct: 6   VTAREKGWRLDKFIQEKAPDWISRTYIQRAIKSGMVTVNNE-EKKPSYKLKNGDVVSFEL 64

Query: 63  --DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
             +   +             E   + + +K  G+VT  +      T+ + L    +    
Sbjct: 65  PEEPKKVEILPENLPLKIIYEDKDIIVVNKDPGVVTHPTPTFLSGTLVNALMYHCNDFQG 124

Query: 111 VG---------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
           +G         RLD +T G++++  +    + L +   +             +  K    
Sbjct: 125 IGGELRPGIVHRLDKDTSGVIVVAKNDKAHQSLSMQFKERKTEKTYIAIVSGEVKKNYGT 184

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GL-----REGKNREIKKVFEFFN 209
               + +          +D  K +  +  V        L     + G+  +I+   ++  
Sbjct: 185 IDVPLGRNPVVRTKIAPVDWGKNAITYFKVIKRFKNATLLLAFPKTGRTHQIRVHMKYIG 244

Query: 210 WKVN 213
             + 
Sbjct: 245 HPLL 248


>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 = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 33/250 (13%), Positives = 78/250 (31%), Gaps = 39/250 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK+  I+  +    R+   +A      SR  ++++     V  NGI ++     V + D+
Sbjct: 1   MKE-FILNCDTDGVRIDSWLAGNLEDYSRSYIQKLCLDGNVWANGIQVKS-NYRVKTDDN 58

Query: 60  IEV--------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I+V        D  P      +   ++  + +      +V         + V   +    
Sbjct: 59  IKVNVPEAEILDVEPEDIPLDIVYEDKHIIVINKPKGMVVHPAVGNYTGTLVNALMKHCG 118

Query: 106 S---------RVISVGRLDINTEGLLLLTNDGGLARVLELP-------------STQWLR 143
                     R   V R+D +T GLL++         L                    + 
Sbjct: 119 DSLSDINGVIRPGIVHRIDKDTSGLLVVAKSNIAHERLSEKLKTHDIKREYIALVDGIIY 178

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
               +    + ++ +   K  +  +          +  +  +  ++ + L  G+  +I+ 
Sbjct: 179 ENSGKIDAPIGRNPVERKKMCVNTENGRNAITHFKVLERFQNATYLELKLETGRTHQIRV 238

Query: 204 VFEFFNWKVN 213
              + N  + 
Sbjct: 239 HMAYINHPII 248


>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 = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 40/245 (16%), Positives = 67/245 (27%), Gaps = 39/245 (15%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + E    +R+ K +A+     SR  +++ I    V+V G  +      V   D IEV   
Sbjct: 55  IPETLHGERLDKALAKLLPDYSRSRLQQWIDAGAVRVGGAAVR-PREAVCGGDRIEVVPQ 113

Query: 66  P---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
                           +   + T L +      +V   +     + +   L         
Sbjct: 114 RAADENAFVAEPIDLDVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRYPQAAGL 173

Query: 107 -RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ------------- 152
            R   V RLD  T GL+++         L                               
Sbjct: 174 PRAGIVHRLDKETSGLMVVARTLPAQTDLVRQLQARTVKRTYLALVWGETPEAGTIDAPI 233

Query: 153 -VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG---LREGKNREIKKVFEFF 208
             D      +       G        TLD      A V++    L  G+  +I+  FE  
Sbjct: 234 GRDPRDRTRMAIIETASGKPARTHFKTLDVIDLGRAQVSLVQCQLETGRTHQIRVHFESE 293

Query: 209 NWKVN 213
              + 
Sbjct: 294 GHPLL 298


>gi|315194077|gb|EFU24470.1| hypothetical protein CGSSa00_05208 [Staphylococcus aureus subsp.
           aureus CGS00]
          Length = 268

 Score = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 16/60 (26%), Positives = 29/60 (48%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            I     +  R+  VI      SR   +++I ++RVKVN  +++ A   + + D I + G
Sbjct: 182 KIESATVSSLRLDVVIKEMIRKSRTIAKQLIEKKRVKVNHTIVDSADFQLQANDLISIQG 241


>gi|313681945|ref|YP_004059683.1| hemolysin a [Sulfuricurvum kujiense DSM 16994]
 gi|313154805|gb|ADR33483.1| hemolysin A [Sulfuricurvum kujiense DSM 16994]
          Length = 236

 Score = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 9/55 (16%), Positives = 25/55 (45%), Gaps = 1/55 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+   +   G   SR + +++I +  V V G ++++ + +V     + +    +
Sbjct: 1  MRLDSYLVEQGFVESRTKAQQLIKEHAVSVEGKIVDKVSFDVAEGMEVVLADTEI 55


>gi|302336354|ref|YP_003801561.1| SSU ribosomal protein S4P [Olsenella uli DSM 7084]
 gi|301320194|gb|ADK68681.1| SSU ribosomal protein S4P [Olsenella uli DSM 7084]
          Length = 197

 Score = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 17/70 (24%), Positives = 30/70 (42%), Gaps = 4/70 (5%)

Query: 1   MKDKNIVQENFTPQ---RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMS 56
           MK   I  +N       R+  V+ R G A +R+E  + +    + VNG  ++  +  V +
Sbjct: 71  MKRDGIAGDNLMSILETRLDNVVFRLGFARTRKEARQTVRHGHITVNGRRVDIPSYQVKA 130

Query: 57  TDHIEVDGVP 66
            D + V    
Sbjct: 131 GDVVAVAPKA 140


>gi|282910764|ref|ZP_06318567.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282325369|gb|EFB55678.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           WBG10049]
          Length = 268

 Score = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 16/60 (26%), Positives = 29/60 (48%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            I     +  R+  VI      SR   +++I ++RVKVN  +++ A   + + D I + G
Sbjct: 182 KIESATVSSLRLDVVIKEMIRKSRTIAKQLIEKKRVKVNHTIVDSADFQLQANDLISIQG 241


>gi|282916441|ref|ZP_06324203.1| hypothetical protein SATG_01276 [Staphylococcus aureus subsp.
           aureus D139]
 gi|283770253|ref|ZP_06343145.1| YlmH [Staphylococcus aureus subsp. aureus H19]
 gi|282319881|gb|EFB50229.1| hypothetical protein SATG_01276 [Staphylococcus aureus subsp.
           aureus D139]
 gi|283460400|gb|EFC07490.1| YlmH [Staphylococcus aureus subsp. aureus H19]
 gi|298694482|gb|ADI97704.1| hypothetical protein SAOV_1192 [Staphylococcus aureus subsp. aureus
           ED133]
 gi|302332796|gb|ADL22989.1| S4 RNA binding domain protein [Staphylococcus aureus subsp. aureus
           JKD6159]
          Length = 268

 Score = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 16/60 (26%), Positives = 29/60 (48%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            I     +  R+  VI      SR   +++I ++RVKVN  +++ A   + + D I + G
Sbjct: 182 KIESATVSSLRLDVVIKEMIRKSRTIAKQLIEKKRVKVNHTIVDSADFQLQANDLISIQG 241


>gi|258423765|ref|ZP_05686651.1| conserved hypothetical protein [Staphylococcus aureus A9635]
 gi|257845997|gb|EEV70025.1| conserved hypothetical protein [Staphylococcus aureus A9635]
          Length = 268

 Score = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 16/60 (26%), Positives = 29/60 (48%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            I     +  R+  VI      SR   +++I ++RVKVN  +++ A   + + D I + G
Sbjct: 182 KIESATVSSLRLDVVIKEMIRKSRTIAKQLIEKKRVKVNHTIVDSADFQLQANDLISIQG 241


>gi|49483354|ref|YP_040578.1| hypothetical protein SAR1167 [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|257427905|ref|ZP_05604303.1| YlmH [Staphylococcus aureus subsp. aureus 65-1322]
 gi|257430538|ref|ZP_05606920.1| YlmH protein [Staphylococcus aureus subsp. aureus 68-397]
 gi|257433299|ref|ZP_05609657.1| YlmH protein [Staphylococcus aureus subsp. aureus E1410]
 gi|257436141|ref|ZP_05612188.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           M876]
 gi|282903743|ref|ZP_06311631.1| YlmH protein [Staphylococcus aureus subsp. aureus C160]
 gi|282905507|ref|ZP_06313362.1| hypothetical protein SDAG_01131 [Staphylococcus aureus subsp.
           aureus Btn1260]
 gi|282913967|ref|ZP_06321754.1| YlmH protein [Staphylococcus aureus subsp. aureus M899]
 gi|282918889|ref|ZP_06326624.1| hypothetical protein SASG_00195 [Staphylococcus aureus subsp.
           aureus C427]
 gi|282924012|ref|ZP_06331688.1| hypothetical protein SARG_01553 [Staphylococcus aureus subsp.
           aureus C101]
 gi|293501000|ref|ZP_06666851.1| hypothetical protein SCAG_01530 [Staphylococcus aureus subsp.
           aureus 58-424]
 gi|293509958|ref|ZP_06668667.1| hypothetical protein SAZG_01859 [Staphylococcus aureus subsp.
           aureus M809]
 gi|293526547|ref|ZP_06671232.1| YlmH protein [Staphylococcus aureus subsp. aureus M1015]
 gi|297591365|ref|ZP_06950003.1| S4 domain-containing protein YlmH [Staphylococcus aureus subsp.
           aureus MN8]
 gi|4009496|gb|AAC95463.1| YlmH [Staphylococcus aureus]
 gi|49241483|emb|CAG40169.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|257274746|gb|EEV06233.1| YlmH [Staphylococcus aureus subsp. aureus 65-1322]
 gi|257278666|gb|EEV09285.1| YlmH protein [Staphylococcus aureus subsp. aureus 68-397]
 gi|257281392|gb|EEV11529.1| YlmH protein [Staphylococcus aureus subsp. aureus E1410]
 gi|257284423|gb|EEV14543.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           M876]
 gi|282313984|gb|EFB44376.1| hypothetical protein SARG_01553 [Staphylococcus aureus subsp.
           aureus C101]
 gi|282316699|gb|EFB47073.1| hypothetical protein SASG_00195 [Staphylococcus aureus subsp.
           aureus C427]
 gi|282322035|gb|EFB52359.1| YlmH protein [Staphylococcus aureus subsp. aureus M899]
 gi|282330799|gb|EFB60313.1| hypothetical protein SDAG_01131 [Staphylococcus aureus subsp.
           aureus Btn1260]
 gi|282595361|gb|EFC00325.1| YlmH protein [Staphylococcus aureus subsp. aureus C160]
 gi|290920619|gb|EFD97682.1| YlmH protein [Staphylococcus aureus subsp. aureus M1015]
 gi|291096005|gb|EFE26266.1| hypothetical protein SCAG_01530 [Staphylococcus aureus subsp.
           aureus 58-424]
 gi|291467408|gb|EFF09925.1| hypothetical protein SAZG_01859 [Staphylococcus aureus subsp.
           aureus M809]
 gi|297576251|gb|EFH94967.1| S4 domain-containing protein YlmH [Staphylococcus aureus subsp.
           aureus MN8]
 gi|312438432|gb|ADQ77503.1| S4 domain-containing protein YlmH [Staphylococcus aureus subsp.
           aureus TCH60]
          Length = 268

 Score = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 16/60 (26%), Positives = 29/60 (48%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            I     +  R+  VI      SR   +++I ++RVKVN  +++ A   + + D I + G
Sbjct: 182 KIESATVSSLRLDVVIKEMIRKSRTIAKQLIEKKRVKVNHTIVDSADFQLQANDLISIQG 241


>gi|289548511|ref|YP_003473499.1| hemolysin A [Thermocrinis albus DSM 14484]
 gi|289182128|gb|ADC89372.1| hemolysin A [Thermocrinis albus DSM 14484]
          Length = 258

 Score = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 10/50 (20%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   +   G+A +R + + +I    V V+G ++++    +  T+ +E+
Sbjct: 1  MRLDVYLVEKGLAPTREKAQALIMAGMVTVDGRVVDKPGFRLKGTEKVEL 50


>gi|46198486|ref|YP_004153.1| hemolysin [Thermus thermophilus HB27]
 gi|46196108|gb|AAS80526.1| hemolysin [Thermus thermophilus HB27]
          Length = 235

 Score = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 28/50 (56%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ + +   G+  SR + +R+I + +V+V G ++++ A  V     +E+
Sbjct: 1  MRLDRYLVERGLVESREKAKRLIQEGKVRVGGKVVQKPAHPVPEGAAVEL 50


>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 = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 33/248 (13%), Positives = 73/248 (29%), Gaps = 41/248 (16%)

Query: 4   KNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K I ++   P RV K +      A+R ++++      + VN + +++    V + D ++V
Sbjct: 24  KFIAEKGQNPLRVDKYLMNYIEKATRNKIQKAAKDGNIYVNDVPVKQ-NYKVKAGDVVQV 82

Query: 63  DGVP---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
                              +   + T L +      +V         + +   +    + 
Sbjct: 83  MFEHPPYEFLLTPENIPLDIVYEDDTLLVVNKPAGMVVHPGHGNYSGTLINALVYHFENL 142

Query: 107 ------RVISVGRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVYRV 147
                 R   V R+D +T GLL++         L                    +     
Sbjct: 143 PNNSSDRPGLVHRIDKDTSGLLVIAKTEHAMAHLSKQFFDKTSEREYIAIVWGNVEEDEG 202

Query: 148 RFHGQVDQDKLNLLKKGIV--IQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKK 203
              G + +   N L+  +               + +  + G    V   L  G+  +I+ 
Sbjct: 203 TVEGNIGRHPKNRLQNTVYEGEDAEKGKPAVTHLKVLERFGYVTLVACKLETGRTHQIRV 262

Query: 204 VFEFFNWK 211
             +     
Sbjct: 263 HMKHIGHT 270


>gi|325272032|ref|ZP_08138475.1| 30S ribosomal protein S4 [Pseudomonas sp. TJI-51]
 gi|324102836|gb|EGC00240.1| 30S ribosomal protein S4 [Pseudomonas sp. TJI-51]
          Length = 206

 Score = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 1/56 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V   D + V    L +
Sbjct: 97  RLDNVVYRMGFGSTRSESRQLVSHKAISVNGKTVNIPSYQVRPGDVVAVREKSLSQ 152


>gi|283470402|emb|CAQ49613.1| RNA-binding S4 domain protein [Staphylococcus aureus subsp. aureus
           ST398]
          Length = 268

 Score = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 16/60 (26%), Positives = 29/60 (48%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            I     +  R+  VI      SR   +++I ++RVKVN  +++ A   + + D I + G
Sbjct: 182 KIESATVSSLRLDVVIKEMIRKSRTIAKQLIEKKRVKVNHTIVDSADFQLQANDLISIQG 241


>gi|238061095|ref|ZP_04605804.1| 30S ribosomal protein S4 [Micromonospora sp. ATCC 39149]
 gi|237882906|gb|EEP71734.1| 30S ribosomal protein S4 [Micromonospora sp. ATCC 39149]
          Length = 208

 Score = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V+ RAG A SR    +++      VNG  ++  +  V   D IEV G 
Sbjct: 99  RLDNVVYRAGYAKSRDMARQLVKHGHFTVNGKKVDIPSYRVKEHDIIEVRGK 150


>gi|194039327|ref|XP_001926827.1| PREDICTED: zinc finger protein 318 [Sus scrofa]
          Length = 2282

 Score = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 19/112 (16%), Positives = 33/112 (29%), Gaps = 5/112 (4%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R  +  H  +E+         SS +                +        ++    + + 
Sbjct: 7   RSSVSSHRPKESGGGGPRTGRSSGSSSGPARRTSPPSSGSSSSRTPARRPRSPSGHRGRR 66

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQR-----EENHRRSPSFPSKRSLR 348
           A+P   R    +    +G  +S     G+R         R SPS P  R  R
Sbjct: 67  ASPSPPRGRRGSPSPPRGRRASPSPPRGRRVSPSPPRARRGSPSSPPPRGRR 118



 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 18/108 (16%), Positives = 31/108 (28%), Gaps = 2/108 (1%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                + V+   P  S     R   +  S           +S   +  +  ++  +P   
Sbjct: 3   RSGARSSVSSHRPKESGGGGPRTGRSSGSSSGPARRTSPPSSGSSSSRTPARRPRSPSGH 62

Query: 308 RNLASNVWMAKGIHSSFLSDSGQR--EENHRRSPSFPSKRSLRRTSAK 353
           R   ++    +G   S     G+R      R     PS    RR S  
Sbjct: 63  RGRRASPSPPRGRRGSPSPPRGRRASPSPPRGRRVSPSPPRARRGSPS 110



 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 15/115 (13%), Positives = 29/115 (25%), Gaps = 2/115 (1%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            +  R                +   SS T  R   +         +       + +    
Sbjct: 23  PRTGRSSGSSSGPARRTSPPSSGSSSSRTPARRPRSPSGHRGRRASPSPPRGRRGSPSPP 82

Query: 298 QKKLATPVHRRNLA--SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
           + + A+P   R      +   A+    S     G+R      +    S R   R+
Sbjct: 83  RGRRASPSPPRGRRVSPSPPRARRGSPSSPPPRGRRLFPPGSAGFRGSSRGDSRS 137



 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 13/112 (11%), Positives = 23/112 (20%), Gaps = 5/112 (4%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN-----GLSKQKKLA 302
                   +         +    R    S  P    R   +  +           ++   
Sbjct: 50  RTPARRPRSPSGHRGRRASPSPPRGRRGSPSPPRGRRASPSPPRGRRVSPSPPRARRGSP 109

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +    R        + G   S   DS        R        S RR+   +
Sbjct: 110 SSPPPRGRRLFPPGSAGFRGSSRGDSRSDFARDGRGDHPGDSGSRRRSPGLR 161


>gi|157363559|ref|YP_001470326.1| hemolysin A [Thermotoga lettingae TMO]
 gi|157314163|gb|ABV33262.1| hemolysin A [Thermotoga lettingae TMO]
          Length = 265

 Score = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 11/37 (29%), Positives = 17/37 (45%)

Query: 26 ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          ASR +   +I   RV VNG +  +        D I++
Sbjct: 16 ASRSQARDLIKLGRVVVNGKICRKPGTICFEEDEIKL 52


>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 = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 24/248 (9%), Positives = 55/248 (22%), Gaps = 41/248 (16%)

Query: 4   KNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE- 61
           + +  +  +  RV K +  R   A+R  ++       + VN   ++     V   D +  
Sbjct: 34  RFVADKGQSLLRVDKFLVDRMMGATRNRIQLAAEAGCILVNDKPVKS-NYRVKPLDVVSI 92

Query: 62  VDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           V   P              +   +   L +      +V         + V      +   
Sbjct: 93  VMDRPRRELEIIPEDIPLNIVYEDDDLLVVNKPAGLVVHPGHGNYTGTLVNALAYYLKDD 152

Query: 108 VISVG------------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
                                            +   L              +       
Sbjct: 153 PYYDPSDPRLGLVHRIDKDTSGLLVVAKRPEAKSNLSLQFFNKTTKRKYRALVWGIVQED 212

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
             R+  +   D      +                T+  + G  + V   L  G+  +I+ 
Sbjct: 213 EGRIEGNIGRDPRDRMQMTVFPEGDQGKTAVTHYTVLERLGYVSLVECRLETGRTHQIRV 272

Query: 204 VFEFFNWK 211
             ++    
Sbjct: 273 HMKYIGHT 280


>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 = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 4/54 (7%)

Query: 13 PQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          PQR+ K + R    A + SR  + R++ +  V+VNG ++  A   V + D IE+
Sbjct: 15 PQRLDKALVRDVPEAAVLSRTRLARLLEEGAVRVNGAVVSEAKARVQAGDLIEI 68


>gi|116620238|ref|YP_822394.1| hemolysin A [Candidatus Solibacter usitatus Ellin6076]
 gi|116223400|gb|ABJ82109.1| hemolysin A [Candidatus Solibacter usitatus Ellin6076]
          Length = 240

 Score = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
          R+ ++I   G+  SR + + +I    V+VNG    +    V S   IE
Sbjct: 4  RLDRLIVDRGLVESREKAQALIMAGEVRVNGQKAAKPGQPVESDCKIE 51


>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 = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 34/250 (13%), Positives = 64/250 (25%), Gaps = 51/250 (20%)

Query: 15  RVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------DGVP 66
           R+   +A    G  SR  ++ +I Q  V +NG  +      V   D +E+      D  P
Sbjct: 24  RIDVWLAGEVGGDLSRSRLKALIEQGAVLLNGTPVTEPKKKVHPHDRVEIVMPEPEDPEP 83

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVI 109
                   +   +   + L      +V   +     + V   +              R  
Sbjct: 84  KGEDIPLDVEYEDDDLIVLVKPAGLVVHPGAGNWTGTLVNALIYHCGDSLSGIGGVKRPG 143

Query: 110 SVGRLDINTEGLLLLTNDGGLARV-----LELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
            V RLD  T G++++  +    R       +   T  L            +     +   
Sbjct: 144 IVHRLDKETSGVMVVAKNDNAHRHLAAQFADHGRTGPLERAYKAVVWGRPRTLRGTIDAA 203

Query: 165 IVIQGICYGDMQVTLDTQKGSN---------------------AWVTVGLREGKNREIKK 203
           +              DT                          + V   L  G+  +I+ 
Sbjct: 204 LGRGADRTKRAVKREDTDDAREAITHYEVMERFHEKADASCLASMVECRLETGRTHQIRV 263

Query: 204 VFEFFNWKVN 213
                   + 
Sbjct: 264 HMAHIGHPLI 273


>gi|258511739|ref|YP_003185173.1| hemolysin A [Alicyclobacillus acidocaldarius subsp.
          acidocaldarius DSM 446]
 gi|257478465|gb|ACV58784.1| hemolysin A [Alicyclobacillus acidocaldarius subsp.
          acidocaldarius DSM 446]
          Length = 279

 Score = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 15 RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          R+  ++ AR   ASR    R I    V+V+G+  ++    V    H+EV+
Sbjct: 5  RLDLLLVARGLYASREAARRAIMAGLVRVDGVRADKPGFKVAEDAHVEVE 54


>gi|304393474|ref|ZP_07375402.1| ribosomal RNA large subunit methyltransferase J [Ahrensia sp.
          R2A130]
 gi|303294481|gb|EFL88853.1| ribosomal RNA large subunit methyltransferase J [Ahrensia sp.
          R2A130]
          Length = 250

 Score = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 14/59 (23%), Positives = 27/59 (45%), Gaps = 1/59 (1%)

Query: 7  VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          + ++ T  R  +++   G+A SR     MI +  V + G  + +   ++     IEVD 
Sbjct: 1  MSQSPTKLRADQLLVERGMAPSRSRAADMIKRGCVMIAGTPITKPGQSLAPDSTIEVDD 59


>gi|296269986|ref|YP_003652618.1| hemolysin A [Thermobispora bispora DSM 43833]
 gi|296092773|gb|ADG88725.1| hemolysin A [Thermobispora bispora DSM 43833]
          Length = 269

 Score = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          T  R+ + + R G+A SR    R+I   RV V G + E+ A  V +   I V
Sbjct: 2  TRVRLDRELVRRGLARSREHAARLIEAGRVYVRGSVAEKPATQVDTGAPIVV 53


>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 = 52.9 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 30/248 (12%), Positives = 66/248 (26%), Gaps = 35/248 (14%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGI------LLERAAV 52
           MK K+  + E+    R+   I++     SR   +++I ++ V VN         L+    
Sbjct: 1   MKIKDFLINESEVNSRLDVFISKCFEEKSRSYAQKLIEEKNVFVNNSSKKSNYKLKIGDY 60

Query: 53  ---NVMSTDHIEVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
               +   + I +    ++      +   + +      +V   +     + V   L    
Sbjct: 61  VEIKIKEDEKINIKPEDIKLNIIYEDEDVIVIDKPQGMVVHPGAGNYSGTLVNGLLYHCD 120

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
           S     G +       +     G L       +   L         + +           
Sbjct: 121 SLSSINGDVRPGIVHRIDKDTSGVLVVAKNDSAHIILSEQLKEHSMKREYIALVEGIIKN 180

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                            K  V++          +  +   N  V   L  G+  +I+   
Sbjct: 181 DEGIIDAPLGRNPKDRIKRAVVRNGKSAVTHYNVLRRFNKNTLVKCILETGRTHQIRVHM 240

Query: 206 EFFNWKVN 213
              N  + 
Sbjct: 241 AHINHPLV 248


>gi|329117696|ref|ZP_08246413.1| ribosomal protein S4 [Streptococcus parauberis NCFD 2020]
 gi|326908101|gb|EGE55015.1| ribosomal protein S4 [Streptococcus parauberis NCFD 2020]
          Length = 203

 Score = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVDPGQVISV 142


>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 = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 30/245 (12%), Positives = 65/245 (26%), Gaps = 37/245 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K   ++ +     RV KV+A      SR +V++ + +  V + G  +  A   V + DH+
Sbjct: 3   KQIEVIIKEEKG-RVDKVLAERLPDHSRSQVQQWLKEDAVTLEGETVR-ANYKVKAGDHL 60

Query: 61  EVD-GVP-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
            +    P             +   +     +      +V   +     + V   L  +  
Sbjct: 61  VIQVPEPEVVGLEPENIPLTIVYQDADVAVINKPQGMVVHPSAGHPNGTLVNALLYHMDD 120

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ----------- 155
                  +       +     G L       + + L                        
Sbjct: 121 LSTINDVVRPGIVHRIDKDTSGLLMIAKNDQAHESLAKQLKDKTSLRKYVALVHGNISHE 180

Query: 156 ---------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          K   VI+         T+  +      V + L  G+  +I+   +
Sbjct: 181 KGTINAPIGRSKVNRKMQAVIENGKPAVTHFTVLERFDQFTLVELQLETGRTHQIRVHMQ 240

Query: 207 FFNWK 211
           +  + 
Sbjct: 241 YIGFP 245


>gi|300857220|ref|YP_003782204.1| 30S ribosomal protein S4 [Clostridium ljungdahlii DSM 13528]
 gi|300437335|gb|ADK17102.1| 30S ribosomal protein S4 [Clostridium ljungdahlii DSM 13528]
          Length = 206

 Score = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 16/68 (23%), Positives = 25/68 (36%), Gaps = 1/68 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  VI R G   SR E  +++      VNG  ++  +  V   D+I V        +  
Sbjct: 99  RLDNVIYRLGYGQSRAEARQLVTHGHFLVNGRKVDIPSFKVSVNDNITVSDKSKSSEKFK 158

Query: 74  RLWLYHKP 81
                 K 
Sbjct: 159 TFAENPKT 166


>gi|255067434|ref|ZP_05319289.1| ribosomal protein S4 [Neisseria sicca ATCC 29256]
 gi|261364879|ref|ZP_05977762.1| ribosomal protein S4 [Neisseria mucosa ATCC 25996]
 gi|255048229|gb|EET43693.1| ribosomal protein S4 [Neisseria sicca ATCC 29256]
 gi|288566927|gb|EFC88487.1| ribosomal protein S4 [Neisseria mucosa ATCC 25996]
          Length = 206

 Score = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNG ++   +  V + D + V     ++    
Sbjct: 97  RLDNVVYRMGFGSTRAEARQLVSHKAITVNGQVVNIPSFQVKAGDVVAVREKAKKQVRIQ 156


>gi|94995345|ref|YP_603443.1| 30S ribosomal protein S4 [Streptococcus pyogenes MGAS10750]
 gi|152112267|sp|Q1J462|RS4_STRPF RecName: Full=30S ribosomal protein S4
 gi|94548853|gb|ABF38899.1| SSU ribosomal protein S4P [Streptococcus pyogenes MGAS10750]
          Length = 203

 Score = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVDPGQVISV 142


>gi|290580942|ref|YP_003485334.1| hypothetical protein SmuNN2025_1416 [Streptococcus mutans NN2025]
 gi|254997841|dbj|BAH88442.1| hypothetical protein [Streptococcus mutans NN2025]
          Length = 262

 Score = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 15/58 (25%), Positives = 30/58 (51%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +    +  R+ K+IA     SRR+  ++I  ++VK+N ++  + +  +   D I V G
Sbjct: 177 MNVLVSSMRLDKIIAAVLKLSRRKANQLIESEKVKLNYLVQPKVSHLIDIGDLISVRG 234


>gi|254495736|ref|ZP_05108651.1| 30S ribosomal protein S4 [Legionella drancourtii LLAP12]
 gi|254355049|gb|EET13669.1| 30S ribosomal protein S4 [Legionella drancourtii LLAP12]
          Length = 206

 Score = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G AS R E  +++  + + VN  ++   +  V   D + V
Sbjct: 97  RLDNVVYRMGFASTRAEARQLVTHKAILVNDKVVNVPSFLVSPGDVVTV 145


>gi|229823967|ref|ZP_04450036.1| hypothetical protein GCWU000282_01271 [Catonella morbi ATCC 51271]
 gi|229786321|gb|EEP22435.1| hypothetical protein GCWU000282_01271 [Catonella morbi ATCC 51271]
          Length = 202

 Score = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 11/47 (23%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  ++ R G A+ RR+  +++    V V+G  ++  +  V     I
Sbjct: 93  RLDNLVYRLGFATTRRQARQLVNHGHVTVDGKRVDIPSYLVTPGQVI 139


>gi|121534494|ref|ZP_01666317.1| hemolysin A [Thermosinus carboxydivorans Nor1]
 gi|121306987|gb|EAX47906.1| hemolysin A [Thermosinus carboxydivorans Nor1]
          Length = 268

 Score = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 1/57 (1%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          +R+  ++ + G+AS RE  +  I    V+V+G  +++A   V     I V G  +  
Sbjct: 4  ERLDVLLVKRGLASSRERAKAWIMAGLVRVDGQRVDKAGAMVPLMADIVVTGDNIGY 60


>gi|296284607|ref|ZP_06862605.1| pseudouridine synthase D large subunit [Citromicrobium
          bathyomarinum JL354]
          Length = 314

 Score = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 13/45 (28%), Positives = 21/45 (46%)

Query: 13 PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
          P R+ K +A A   SR  ++ +IA  +V V G      +  V + 
Sbjct: 14 PARLDKALADATDLSRERIKGLIADGQVSVGGKRATSPSAKVAAG 58


>gi|15675914|ref|NP_270088.1| 30S ribosomal protein S4 [Streptococcus pyogenes M1 GAS]
 gi|19747014|ref|NP_608150.1| 30S ribosomal protein S4 [Streptococcus pyogenes MGAS8232]
 gi|21911369|ref|NP_665637.1| 30S ribosomal protein S4 [Streptococcus pyogenes MGAS315]
 gi|28896741|ref|NP_803091.1| 30S ribosomal protein S4 [Streptococcus pyogenes SSI-1]
 gi|50915197|ref|YP_061169.1| 30S ribosomal protein S4 [Streptococcus pyogenes MGAS10394]
 gi|71904527|ref|YP_281330.1| 30S ribosomal protein S4 [Streptococcus pyogenes MGAS6180]
 gi|71911644|ref|YP_283194.1| 30S ribosomal protein S4 [Streptococcus pyogenes MGAS5005]
 gi|94989474|ref|YP_597575.1| 30S ribosomal protein S4 [Streptococcus pyogenes MGAS9429]
 gi|94991461|ref|YP_599561.1| 30S ribosomal protein S4 [Streptococcus pyogenes MGAS10270]
 gi|94993361|ref|YP_601460.1| 30S ribosomal protein S4 [Streptococcus pyogenes MGAS2096]
 gi|139474603|ref|YP_001129319.1| 30S ribosomal protein S4 [Streptococcus pyogenes str. Manfredo]
 gi|251783531|ref|YP_002997836.1| 30S ribosomal protein S4 [Streptococcus dysgalactiae subsp.
           equisimilis GGS_124]
 gi|306826445|ref|ZP_07459757.1| 30S ribosomal protein S4 [Streptococcus pyogenes ATCC 10782]
 gi|54039513|sp|P66568|RS4_STRP3 RecName: Full=30S ribosomal protein S4
 gi|54039514|sp|P66569|RS4_STRP8 RecName: Full=30S ribosomal protein S4
 gi|54041965|sp|P66567|RS4_STRP1 RecName: Full=30S ribosomal protein S4
 gi|61215413|sp|Q5X9C7|RS4_STRP6 RecName: Full=30S ribosomal protein S4
 gi|90101729|sp|Q48QN5|RS4_STRPM RecName: Full=30S ribosomal protein S4
 gi|152112264|sp|Q1J995|RS4_STRPB RecName: Full=30S ribosomal protein S4
 gi|152112265|sp|Q1JJE2|RS4_STRPC RecName: Full=30S ribosomal protein S4
 gi|152112266|sp|Q1JEE1|RS4_STRPD RecName: Full=30S ribosomal protein S4
 gi|152112268|sp|A2RGZ8|RS4_STRPG RecName: Full=30S ribosomal protein S4
 gi|13623152|gb|AAK34809.1| 30S ribosomal protein S4 [Streptococcus pyogenes M1 GAS]
 gi|19749271|gb|AAL98649.1| 30S ribosomal protein S4 [Streptococcus pyogenes MGAS8232]
 gi|21905585|gb|AAM80440.1| 30S ribosomal protein S4 [Streptococcus pyogenes MGAS315]
 gi|28811995|dbj|BAC64924.1| 30S ribosomal protein S4 [Streptococcus pyogenes SSI-1]
 gi|50904271|gb|AAT87986.1| SSU ribosomal protein S4P [Streptococcus pyogenes MGAS10394]
 gi|71803622|gb|AAX72975.1| SSU ribosomal protein S4P [Streptococcus pyogenes MGAS6180]
 gi|71854426|gb|AAZ52449.1| SSU ribosomal protein S4P [Streptococcus pyogenes MGAS5005]
 gi|94542982|gb|ABF33031.1| SSU ribosomal protein S4P [Streptococcus pyogenes MGAS9429]
 gi|94544969|gb|ABF35017.1| SSU ribosomal protein S4P [Streptococcus pyogenes MGAS10270]
 gi|94546869|gb|ABF36916.1| SSU ribosomal protein S4P [Streptococcus pyogenes MGAS2096]
 gi|134272850|emb|CAM31130.1| 30S ribosomal protein S4 [Streptococcus pyogenes str. Manfredo]
 gi|242392163|dbj|BAH82622.1| 30S ribosomal protein S4 [Streptococcus dysgalactiae subsp.
           equisimilis GGS_124]
 gi|304431375|gb|EFM34372.1| 30S ribosomal protein S4 [Streptococcus pyogenes ATCC 10782]
          Length = 203

 Score = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVDPGQVISV 142


>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 = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 33/235 (14%), Positives = 64/235 (27%), Gaps = 38/235 (16%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTD------------- 58
            QR+ +V A+     SR  +   I + R+ V+G ++      V                 
Sbjct: 49  GQRLDQVAAQLFAEYSRSRLTSWIKEGRLTVDGAVVR-PRDLVHGGSLLALEAEQEAQGE 107

Query: 59  ----HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV--- 111
                IE+D   +   +   L +      +V   +     + +   L  +   V      
Sbjct: 108 WIAEDIELD---IVYEDDHILVINKPAGLVVHPAAGHASGTLLNALLHHVPDIVNVPRAG 164

Query: 112 --GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
              RLD +T GL+++         L                          +   I   G
Sbjct: 165 IVHRLDKDTTGLMVVAKTLQAQTKLVEQMQARKVSRIYECIVIGVVTAGGKIDAPIGRHG 224

Query: 170 IC---------YGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                               +  +  S+  V V L  G+  +I+       + + 
Sbjct: 225 GMRQRMAVTDGGKPAVSHYRVLKRFRSHTHVRVKLETGRTHQIRVHMAHVGFPLV 279


>gi|323456406|gb|EGB12273.1| hypothetical protein AURANDRAFT_61319 [Aureococcus anophagefferens]
          Length = 221

 Score = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 11/48 (22%), Positives = 25/48 (52%)

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
           ++WV + + +GK  +++K+     +   RL+R   G  ++G +  G  
Sbjct: 152 HSWVALTVLDGKYHQVRKMTAAVGFPTLRLVRARIGHLRVGAMRPGDV 199


>gi|254412697|ref|ZP_05026470.1| S4 domain protein [Microcoleus chthonoplastes PCC 7420]
 gi|196180432|gb|EDX75423.1| S4 domain protein [Microcoleus chthonoplastes PCC 7420]
          Length = 68

 Score = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 7  VQENFTPQRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          +       ++ + +   G+AS   E + MI    V VNGI+  R    ++  D + V G 
Sbjct: 1  MTNPIQSIKLDQFLKWVGVASTGGEAKLMIQDGDVTVNGIIETRRGRKLVEGDLVSVQGE 60


>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 = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 32/287 (11%), Positives = 79/287 (27%), Gaps = 53/287 (18%)

Query: 3   DKNIVQENFTPQ-RVSKVI-ARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           ++ ++  + + + R+   + A+ G   SR  ++ +I   +V + G  +      V + D 
Sbjct: 11  NRKVLTADESAEGRLDAWLTAQVGEEFSRSRIKALIKDGQVFLRGEPVTDPQRKVRTGDS 70

Query: 60  IEV----------DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            E+           G  +       +   + +      +V   +     + V   +    
Sbjct: 71  FELTLPEPEDPTPQGEDIPLDILHEDDDVIVISKPSGLVVHPGAGNWTGTLVNALIHHCS 130

Query: 106 SRVISVGRLDIN----------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
           + +  +G +             T  +++  ND     +    +     +   R +  V  
Sbjct: 131 NTLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDIAHRHLSLQFADHGRTMPLERAYQAVVW 190

Query: 156 DKLNLLKKGI-----VIQGICYGDMQVTLDTQKGSN---------------------AWV 189
            +   L   +        G          D+Q                         + V
Sbjct: 191 GRPRSLSGMVDAPLGRATGDRTRRAVKRPDSQDADEAITHYQVVERFHEKPDATAFASLV 250

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              L  G+  +I+         +        G      LL    R++
Sbjct: 251 ECRLETGRTHQIRVHMAHIGHPLLGDTVYGAGFKTKANLLPEEIRKI 297


>gi|160944264|ref|ZP_02091493.1| hypothetical protein FAEPRAM212_01773 [Faecalibacterium
          prausnitzii M21/2]
 gi|158444446|gb|EDP21450.1| hypothetical protein FAEPRAM212_01773 [Faecalibacterium
          prausnitzii M21/2]
          Length = 71

 Score = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 13/65 (20%), Positives = 28/65 (43%), Gaps = 1/65 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          +    ++  ++  AG+  +  E + ++    VKVNG +         + D IE+DG  + 
Sbjct: 7  HTEFIKLDALLKFAGLCETGGEAKELVQGGAVKVNGEVCTMRGKKCRAGDVIELDGQSVE 66

Query: 69 KAERT 73
            +  
Sbjct: 67 IGQGQ 71


>gi|167031523|ref|YP_001666754.1| 30S ribosomal protein S4 [Pseudomonas putida GB-1]
 gi|189045393|sp|B0KK90|RS4_PSEPG RecName: Full=30S ribosomal protein S4
 gi|166858011|gb|ABY96418.1| ribosomal protein S4 [Pseudomonas putida GB-1]
          Length = 206

 Score = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 1/56 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V   D + V    L +
Sbjct: 97  RLDNVVYRMGFGSTRSESRQLVSHKAISVNGKTVNIPSYQVRPGDVVAVREKSLAQ 152


>gi|18308985|ref|NP_560919.1| S4 domain protein [Clostridium perfringens str. 13]
 gi|110799682|ref|YP_694478.1| S4 domain-containing protein [Clostridium perfringens ATCC 13124]
 gi|110802524|ref|YP_697354.1| S4 domain-containing protein [Clostridium perfringens SM101]
 gi|168212006|ref|ZP_02637631.1| S4 domain protein [Clostridium perfringens B str. ATCC 3626]
 gi|168215269|ref|ZP_02640894.1| S4 domain protein [Clostridium perfringens CPE str. F4969]
 gi|168218304|ref|ZP_02643929.1| S4 domain protein [Clostridium perfringens NCTC 8239]
 gi|182627058|ref|ZP_02954783.1| S4 domain protein YaaA [Clostridium perfringens D str. JGS1721]
 gi|18143660|dbj|BAB79709.1| conserved hypothetical protein [Clostridium perfringens str. 13]
 gi|110674329|gb|ABG83316.1| S4 domain protein [Clostridium perfringens ATCC 13124]
 gi|110683025|gb|ABG86395.1| S4 domain protein [Clostridium perfringens SM101]
 gi|170710067|gb|EDT22249.1| S4 domain protein [Clostridium perfringens B str. ATCC 3626]
 gi|170713333|gb|EDT25515.1| S4 domain protein [Clostridium perfringens CPE str. F4969]
 gi|177907584|gb|EDT70223.1| S4 domain protein YaaA [Clostridium perfringens D str. JGS1721]
 gi|182379687|gb|EDT77166.1| S4 domain protein [Clostridium perfringens NCTC 8239]
          Length = 68

 Score = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 27/73 (36%), Gaps = 8/73 (10%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAG---IASRREVERMIAQQRVKVNGILLERAAVNVMST 57
          M++  I   N    ++   +   G   + S  E +  I    V VNG +  +    +   
Sbjct: 1  MQEVKI---NTEFIKLDSFLKWCGAVSLGS--EAKMFIMDGEVLVNGEVCTQRGKKLRVD 55

Query: 58 DHIEVDGVPLRKA 70
          D +E +G   +  
Sbjct: 56 DTVEFNGEIYKLI 68


>gi|322391286|ref|ZP_08064757.1| 30S ribosomal protein S4 [Streptococcus peroris ATCC 700780]
 gi|321145890|gb|EFX41280.1| 30S ribosomal protein S4 [Streptococcus peroris ATCC 700780]
          Length = 203

 Score = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V    L+  
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVTPGQVISVREKSLKVP 150


>gi|77411416|ref|ZP_00787762.1| ylmH protein [Streptococcus agalactiae CJB111]
 gi|77162502|gb|EAO73467.1| ylmH protein [Streptococcus agalactiae CJB111]
          Length = 262

 Score = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 32/63 (50%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +D   +    +  R+ K++A     SR++  ++I   +VKVN  ++ R +  ++  D I 
Sbjct: 172 QDIQKLTVIASSLRLDKILATILKISRKQSTKLIEADKVKVNYAIVNRVSEQLVEGDLIS 231

Query: 62  VDG 64
           V G
Sbjct: 232 VRG 234


>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 = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 21/199 (10%), Positives = 56/199 (28%), Gaps = 4/199 (2%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLRKAERTR 74
           K++A     S ++ + +I +  V V    +  A   +       ++    V +   +   
Sbjct: 6   KLLAAQEGISNKKAKELIDRGLVYVGDQKVRIARAEMPEETKFRIEEPADVKIIYQDEQV 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +            +    + +   L    S V+ + R +   +  +       + +  
Sbjct: 66  VAVNKPAFIDSYEIEEAIEGAQLLHRLDRDTSGVLLLARDEAFAKKAIEAFRQRKVHKEY 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                  +              K     K     G      +V  D  +G  + V + + 
Sbjct: 126 VAWVEGVVVEPFEIDLPIHTIKKGKAFSKIDKKLGKPALT-KVWPDEVQGKKSKVRIEIE 184

Query: 195 EGKNREIKKVFEFFNWKVN 213
            G+  +I+         + 
Sbjct: 185 TGRTHQIRVHLAHVGHPIV 203


>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 = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 13/59 (22%), Positives = 30/59 (50%), Gaps = 3/59 (5%)

Query: 7  VQENFTPQRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          V++     R+ + +        SR  +++ I + +VKVNG + ++ +  +   + +EVD
Sbjct: 6  VEKREEGWRLDQFLKEKTPSWISRSMIQKAIKEGKVKVNGQI-KKPSYKLKEGEIVEVD 63


>gi|16125573|ref|NP_420137.1| hemolysin A [Caulobacter crescentus CB15]
 gi|13422669|gb|AAK23305.1| hemolysin A [Caulobacter crescentus CB15]
          Length = 243

 Score = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 10/47 (21%), Positives = 21/47 (44%), Gaps = 1/47 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
          R+ +++   G+  SR +    I   RV V G ++ + +  V     +
Sbjct: 5  RIDQLLVDRGVFDSRAKARAAIEAGRVSVAGRVVAKPSEQVDDNAEV 51


>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 = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 37/249 (14%), Positives = 75/249 (30%), Gaps = 42/249 (16%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           + +V     P R+ + +      +SR  +++      V VN   ++     V   D I +
Sbjct: 23  RIVVDRGQVPVRIDRFMTERLQHSSRNRIQKAADAGFVHVNERPVKS-NYKVRPGDVITL 81

Query: 63  -------------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                        + +PL    E   L + +KP G+V      +   T+ + +      +
Sbjct: 82  MLDRPHHDTTIEAEDIPLDVVYEDDALMVINKPAGMVVHPGAGNFHGTLINAVAWHLRNM 141

Query: 109 ISV----------GRLDINTEGLLLLTNDGG-------------LARVLELPSTQWLRVY 145
            S            R+D +T GLL++                    R             
Sbjct: 142 PSFDANDPEVGLVHRIDKDTSGLLVVAKTPEAKRKLGLQFFNKTTHRSYNALVWANFAED 201

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICY-GDM--QVTLDTQKGSNAWVTVGLREGKNREIK 202
             R  G + +D  + L+  +                +  + G   +V   L  G+  +I+
Sbjct: 202 EGRIEGNIGRDPRDRLRMAVFPPDSETGKPAVTHYRVLERFGYVTFVECILETGRTHQIR 261

Query: 203 KVFEFFNWK 211
              +     
Sbjct: 262 AHMKHIGHP 270


>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 = 52.5 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 36/251 (14%), Positives = 67/251 (26%), Gaps = 40/251 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             + +V      +R+ KV+A+     SR  ++  I  QRV+V+G   +     V     I
Sbjct: 67  PRRVVVPNELAGERLDKVLAKVFPEFSRSRLQSWIEAQRVRVDGKPAK-IRQPVPLGATI 125

Query: 61  E-----------VDGVP----LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           E               P    +   + T + +      +V   +     + +   L    
Sbjct: 126 ELVPDLLPEQLAFTPEPVPLEIVYEDDTLVVINKPAGMVVHPAAGNWSGTVLNGLLHRYG 185

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
                  R   V RLD  T GL+++         L           R       +     
Sbjct: 186 ETAAGLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLALVWGNMPDEG 245

Query: 160 LLKKGIVIQ-----------GICYGDMQVTL------DTQKGSNAWVTVGLREGKNREIK 202
            +   I              G      +           Q+     +   L  G+  +I+
Sbjct: 246 TIDAPIGRDPRERTRMAVVTGAAGKPARTHFRRVASAIWQRQPVTAIHCDLETGRTHQIR 305

Query: 203 KVFEFFNWKVN 213
                    + 
Sbjct: 306 VHCAHIGHPLL 316


>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 = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 30/239 (12%), Positives = 66/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V+E+   QR+ +  A      SR  ++  +    + VNG ++ +A + VM  + I V  
Sbjct: 10  TVKESQLGQRLDQAAAELFSDFSRSRIKEWLLAGNMTVNGEVVTKARLKVMGGEEITVKA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                           +   +   L +      +V   +     + +   L    +    
Sbjct: 70  ELEDEERWLAQDISLDIVYEDDDLLVINKPRDFVVHPGAGTPDGTVLNALLFHYPNIAEV 129

Query: 111 V-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                  RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRKITREYEAVVVGRMTAGGMIEKPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               N      V +          +      +  + + L  G+  +I+    +    + 
Sbjct: 190 GRHPNKRTLMAVHELGKDAVTHYRVAEHFRIHTRIRLRLETGRTHQIRVHMSYLQHPLV 248


>gi|251796324|ref|YP_003011055.1| hemolysin A [Paenibacillus sp. JDR-2]
 gi|247543950|gb|ACT00969.1| hemolysin A [Paenibacillus sp. JDR-2]
          Length = 278

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 11/57 (19%), Positives = 23/57 (40%), Gaps = 1/57 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          +R+  ++   G   SR + +  +    V VN   +++  + V     I+V G     
Sbjct: 7  ERIDVLLVERGFYESREKAKAAVMAGLVLVNNEPVDKGGMKVPREAEIKVKGAIHPY 63


>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 = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 33/242 (13%), Positives = 65/242 (26%), Gaps = 37/242 (15%)

Query: 5   NIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--- 60
            I +      R+ K +       SR + + +I Q  V +NG  ++     +   D I   
Sbjct: 25  RIEENIDDSIRLDKYMGDRFSYYSRNKWQDLIGQGLVLLNGKKVK-YTRTINKGDEIEYH 83

Query: 61  -------EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
                  EVD       +   L + +KP  L    S     +T+   +  + +  I++  
Sbjct: 84  IIGMKEPEVDKNVTIIYDDGDLIIANKPANLPVIPSGKYYHNTLHTIVKQMLNCNINMLN 143

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV-------------------------R 148
                    ++ + G              +  +                           
Sbjct: 144 RIDRETSGCVVMSRGHETASKFCAMIARRKNTKKKIKKTYIAVVENAKNIEDNFIVEGYM 203

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                +  +         I+G  Y         + G  A V   L  G+  +I+      
Sbjct: 204 LESGHEYYRRFQTLHKENIEGSKYSKTAFKTIKRLGDYAIVMARLYTGRMHQIRVHLYSK 263

Query: 209 NW 210
           N 
Sbjct: 264 NL 265


>gi|169343468|ref|ZP_02864468.1| S4 domain protein [Clostridium perfringens C str. JGS1495]
 gi|169298420|gb|EDS80509.1| S4 domain protein [Clostridium perfringens C str. JGS1495]
          Length = 68

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 27/73 (36%), Gaps = 8/73 (10%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAG---IASRREVERMIAQQRVKVNGILLERAAVNVMST 57
          M++  I   N    ++   +   G   + S  E +  I    V VNG +  +    +   
Sbjct: 1  MQEVKI---NTEFIKLDSFLKWCGAVSLGS--EAKIFIMNGEVLVNGEVCTQRGKKLRVD 55

Query: 58 DHIEVDGVPLRKA 70
          D +E +G   +  
Sbjct: 56 DTVEFNGEIYKLI 68


>gi|94992201|ref|YP_600300.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
          pyogenes MGAS2096]
 gi|94545709|gb|ABF35756.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
          pyogenes MGAS2096]
          Length = 64

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 7  VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          +    + QR+ K +A     SR +    I Q  V VNG   ++A   V + D I  +
Sbjct: 3  INVITSGQRLDKALADLSPLSRGQANDQIKQGLVLVNGQQ-KKAKYTVQAGDVICFE 58


>gi|15900029|ref|NP_344633.1| 30S ribosomal protein S4 [Streptococcus pneumoniae TIGR4]
 gi|15902122|ref|NP_357672.1| 30S ribosomal protein S4 [Streptococcus pneumoniae R6]
 gi|111656925|ref|ZP_01407747.1| hypothetical protein SpneT_02001834 [Streptococcus pneumoniae
           TIGR4]
 gi|116516581|ref|YP_815552.1| 30S ribosomal protein S4 [Streptococcus pneumoniae D39]
 gi|148985431|ref|ZP_01818636.1| ribosomal protein S4 [Streptococcus pneumoniae SP3-BS71]
 gi|148987815|ref|ZP_01819278.1| ribosomal protein S4 [Streptococcus pneumoniae SP6-BS73]
 gi|148993925|ref|ZP_01823308.1| 30S ribosomal protein S4 [Streptococcus pneumoniae SP9-BS68]
 gi|148996492|ref|ZP_01824210.1| ribosomal protein S4 [Streptococcus pneumoniae SP11-BS70]
 gi|149001831|ref|ZP_01826804.1| ribosomal protein S4 [Streptococcus pneumoniae SP14-BS69]
 gi|149007938|ref|ZP_01831516.1| ribosomal protein S4 [Streptococcus pneumoniae SP18-BS74]
 gi|149010947|ref|ZP_01832252.1| ribosomal protein S4 [Streptococcus pneumoniae SP19-BS75]
 gi|149017758|ref|ZP_01834217.1| ribosomal protein S4 [Streptococcus pneumoniae SP23-BS72]
 gi|168483611|ref|ZP_02708563.1| ribosomal protein S4 [Streptococcus pneumoniae CDC1873-00]
 gi|168486664|ref|ZP_02711172.1| ribosomal protein S4 [Streptococcus pneumoniae CDC1087-00]
 gi|168489443|ref|ZP_02713642.1| ribosomal protein S4 [Streptococcus pneumoniae SP195]
 gi|168492605|ref|ZP_02716748.1| ribosomal protein S4 [Streptococcus pneumoniae CDC0288-04]
 gi|168493783|ref|ZP_02717926.1| ribosomal protein S4 [Streptococcus pneumoniae CDC3059-06]
 gi|168577080|ref|ZP_02722909.1| ribosomal protein S4 [Streptococcus pneumoniae MLV-016]
 gi|169832653|ref|YP_001693607.1| 30S ribosomal protein S4 [Streptococcus pneumoniae Hungary19A-6]
 gi|182683053|ref|YP_001834800.1| 30S ribosomal protein S4 [Streptococcus pneumoniae CGSP14]
 gi|194398306|ref|YP_002036801.1| 30S ribosomal protein S4 [Streptococcus pneumoniae G54]
 gi|221231025|ref|YP_002510177.1| 30S ribosomal protein S4 [Streptococcus pneumoniae ATCC 700669]
 gi|225853713|ref|YP_002735225.1| 30S ribosomal protein S4 [Streptococcus pneumoniae JJA]
 gi|225855868|ref|YP_002737379.1| 30S ribosomal protein S4 [Streptococcus pneumoniae P1031]
 gi|225857950|ref|YP_002739460.1| 30S ribosomal protein S4 [Streptococcus pneumoniae 70585]
 gi|225860120|ref|YP_002741629.1| 30S ribosomal protein S4 [Streptococcus pneumoniae Taiwan19F-14]
 gi|237649598|ref|ZP_04523850.1| 30S ribosomal protein S4 [Streptococcus pneumoniae CCRI 1974]
 gi|237821538|ref|ZP_04597383.1| 30S ribosomal protein S4 [Streptococcus pneumoniae CCRI 1974M2]
 gi|270291733|ref|ZP_06197949.1| ribosomal protein S4 [Streptococcus sp. M143]
 gi|289166998|ref|YP_003445265.1| 30S ribosomal protein S4 [Streptococcus mitis B6]
 gi|293364636|ref|ZP_06611357.1| 30S ribosomal protein S4 [Streptococcus oralis ATCC 35037]
 gi|298230010|ref|ZP_06963691.1| 30S ribosomal protein S4 [Streptococcus pneumoniae str. Canada
           MDR_19F]
 gi|298254521|ref|ZP_06978107.1| 30S ribosomal protein S4 [Streptococcus pneumoniae str. Canada
           MDR_19A]
 gi|298501873|ref|YP_003723813.1| 30S ribosomal protein S4 [Streptococcus pneumoniae TCH8431/19A]
 gi|303254819|ref|ZP_07340919.1| 30S ribosomal protein S4 [Streptococcus pneumoniae BS455]
 gi|303259128|ref|ZP_07345106.1| 30S ribosomal protein S4 [Streptococcus pneumoniae SP-BS293]
 gi|303260885|ref|ZP_07346834.1| 30S ribosomal protein S4 [Streptococcus pneumoniae SP14-BS292]
 gi|303263212|ref|ZP_07349135.1| 30S ribosomal protein S4 [Streptococcus pneumoniae BS397]
 gi|303267315|ref|ZP_07353176.1| 30S ribosomal protein S4 [Streptococcus pneumoniae BS457]
 gi|303269590|ref|ZP_07355351.1| 30S ribosomal protein S4 [Streptococcus pneumoniae BS458]
 gi|306826273|ref|ZP_07459607.1| 30S ribosomal protein S4 [Streptococcus sp. oral taxon 071 str.
           73H25AP]
 gi|306828536|ref|ZP_07461731.1| 30S ribosomal protein S4 [Streptococcus mitis ATCC 6249]
 gi|307066759|ref|YP_003875725.1| hypothetical protein SPAP_0129 [Streptococcus pneumoniae AP200]
 gi|307126310|ref|YP_003878341.1| 30S ribosomal protein S4 [Streptococcus pneumoniae 670-6B]
 gi|307702893|ref|ZP_07639841.1| ribosomal protein S4 [Streptococcus oralis ATCC 35037]
 gi|307705409|ref|ZP_07642267.1| ribosomal protein S4 [Streptococcus mitis SK597]
 gi|307707985|ref|ZP_07644460.1| ribosomal protein S4 [Streptococcus mitis NCTC 12261]
 gi|307710135|ref|ZP_07646579.1| ribosomal protein S4 [Streptococcus mitis SK564]
 gi|307711286|ref|ZP_07647707.1| ribosomal protein S4 [Streptococcus mitis SK321]
 gi|315612070|ref|ZP_07886987.1| 30S ribosomal protein S4 [Streptococcus sanguinis ATCC 49296]
 gi|322376030|ref|ZP_08050540.1| ribosomal protein S4 [Streptococcus sp. C300]
 gi|322378050|ref|ZP_08052537.1| ribosomal protein S4 [Streptococcus sp. M334]
 gi|322386473|ref|ZP_08060100.1| 30S ribosomal protein S4 [Streptococcus cristatus ATCC 51100]
 gi|331265518|ref|YP_004325148.1| 30S ribosomal protein S4 [Streptococcus oralis Uo5]
 gi|54039512|sp|P66566|RS4_STRR6 RecName: Full=30S ribosomal protein S4
 gi|54041964|sp|P66565|RS4_STRPN RecName: Full=30S ribosomal protein S4
 gi|122279509|sp|Q04MZ3|RS4_STRP2 RecName: Full=30S ribosomal protein S4
 gi|226695082|sp|B5E5W8|RS4_STRP4 RecName: Full=30S ribosomal protein S4
 gi|226695083|sp|B1I7Y6|RS4_STRPI RecName: Full=30S ribosomal protein S4
 gi|226695084|sp|B2IRG4|RS4_STRPS RecName: Full=30S ribosomal protein S4
 gi|254764612|sp|C1C9Y5|RS4_STRP7 RecName: Full=30S ribosomal protein S4
 gi|254764613|sp|B8ZJX3|RS4_STRPJ RecName: Full=30S ribosomal protein S4
 gi|254764615|sp|C1CBQ4|RS4_STRZJ RecName: Full=30S ribosomal protein S4
 gi|254764616|sp|C1CHZ1|RS4_STRZP RecName: Full=30S ribosomal protein S4
 gi|254764617|sp|C1CNV7|RS4_STRZT RecName: Full=30S ribosomal protein S4
 gi|14971552|gb|AAK74273.1| ribosomal protein S4 [Streptococcus pneumoniae TIGR4]
 gi|15457613|gb|AAK98882.1| 30S Ribosomal protein S4 [Streptococcus pneumoniae R6]
 gi|116077157|gb|ABJ54877.1| ribosomal protein S4 [Streptococcus pneumoniae D39]
 gi|147757067|gb|EDK64106.1| ribosomal protein S4 [Streptococcus pneumoniae SP11-BS70]
 gi|147760289|gb|EDK67278.1| ribosomal protein S4 [Streptococcus pneumoniae SP14-BS69]
 gi|147760561|gb|EDK67536.1| ribosomal protein S4 [Streptococcus pneumoniae SP18-BS74]
 gi|147764583|gb|EDK71513.1| ribosomal protein S4 [Streptococcus pneumoniae SP19-BS75]
 gi|147922389|gb|EDK73509.1| ribosomal protein S4 [Streptococcus pneumoniae SP3-BS71]
 gi|147926279|gb|EDK77352.1| ribosomal protein S4 [Streptococcus pneumoniae SP6-BS73]
 gi|147927632|gb|EDK78658.1| 30S ribosomal protein S4 [Streptococcus pneumoniae SP9-BS68]
 gi|147931322|gb|EDK82300.1| ribosomal protein S4 [Streptococcus pneumoniae SP23-BS72]
 gi|168995155|gb|ACA35767.1| ribosomal protein S4 [Streptococcus pneumoniae Hungary19A-6]
 gi|172043018|gb|EDT51064.1| ribosomal protein S4 [Streptococcus pneumoniae CDC1873-00]
 gi|182628387|gb|ACB89335.1| 30S ribosomal protein S4 [Streptococcus pneumoniae CGSP14]
 gi|183570308|gb|EDT90836.1| ribosomal protein S4 [Streptococcus pneumoniae CDC1087-00]
 gi|183572140|gb|EDT92668.1| ribosomal protein S4 [Streptococcus pneumoniae SP195]
 gi|183573248|gb|EDT93776.1| ribosomal protein S4 [Streptococcus pneumoniae CDC0288-04]
 gi|183576019|gb|EDT96547.1| ribosomal protein S4 [Streptococcus pneumoniae CDC3059-06]
 gi|183577316|gb|EDT97844.1| ribosomal protein S4 [Streptococcus pneumoniae MLV-016]
 gi|194357973|gb|ACF56421.1| 30S ribosomal protein S4 [Streptococcus pneumoniae G54]
 gi|220673485|emb|CAR67956.1| 30S ribosomal protein S4 [Streptococcus pneumoniae ATCC 700669]
 gi|225720035|gb|ACO15889.1| ribosomal protein S4 [Streptococcus pneumoniae 70585]
 gi|225723223|gb|ACO19076.1| ribosomal protein S4 [Streptococcus pneumoniae JJA]
 gi|225724355|gb|ACO20207.1| ribosomal protein S4 [Streptococcus pneumoniae P1031]
 gi|225727282|gb|ACO23133.1| ribosomal protein S4 [Streptococcus pneumoniae Taiwan19F-14]
 gi|270279818|gb|EFA25659.1| ribosomal protein S4 [Streptococcus sp. M143]
 gi|288906563|emb|CBJ21396.1| 30S ribosomal protein S4 [Streptococcus mitis B6]
 gi|291316894|gb|EFE57326.1| 30S ribosomal protein S4 [Streptococcus oralis ATCC 35037]
 gi|298237468|gb|ADI68599.1| 30S ribosomal protein S4 [Streptococcus pneumoniae TCH8431/19A]
 gi|301793388|emb|CBW35753.1| 30S ribosomal protein S4 [Streptococcus pneumoniae INV104]
 gi|301799257|emb|CBW31777.1| 30S ribosomal protein S4 [Streptococcus pneumoniae OXC141]
 gi|301801046|emb|CBW33713.1| 30S ribosomal protein S4 [Streptococcus pneumoniae INV200]
 gi|302598256|gb|EFL65302.1| 30S ribosomal protein S4 [Streptococcus pneumoniae BS455]
 gi|302637722|gb|EFL68208.1| 30S ribosomal protein S4 [Streptococcus pneumoniae SP14-BS292]
 gi|302639546|gb|EFL70003.1| 30S ribosomal protein S4 [Streptococcus pneumoniae SP-BS293]
 gi|302640864|gb|EFL71250.1| 30S ribosomal protein S4 [Streptococcus pneumoniae BS458]
 gi|302643166|gb|EFL73452.1| 30S ribosomal protein S4 [Streptococcus pneumoniae BS457]
 gi|302646985|gb|EFL77209.1| 30S ribosomal protein S4 [Streptococcus pneumoniae BS397]
 gi|304429335|gb|EFM32420.1| 30S ribosomal protein S4 [Streptococcus mitis ATCC 6249]
 gi|304431549|gb|EFM34531.1| 30S ribosomal protein S4 [Streptococcus sp. oral taxon 071 str.
           73H25AP]
 gi|306408296|gb|ADM83723.1| hypothetical protein SPAP_0129 [Streptococcus pneumoniae AP200]
 gi|306483372|gb|ADM90241.1| ribosomal protein S4 [Streptococcus pneumoniae 670-6B]
 gi|307616050|gb|EFN95248.1| ribosomal protein S4 [Streptococcus mitis NCTC 12261]
 gi|307616937|gb|EFN96116.1| ribosomal protein S4 [Streptococcus mitis SK321]
 gi|307619115|gb|EFN98247.1| ribosomal protein S4 [Streptococcus mitis SK564]
 gi|307621040|gb|EFO00119.1| ribosomal protein S4 [Streptococcus mitis SK597]
 gi|307623573|gb|EFO02562.1| ribosomal protein S4 [Streptococcus oralis ATCC 35037]
 gi|315315872|gb|EFU63907.1| 30S ribosomal protein S4 [Streptococcus sanguinis ATCC 49296]
 gi|321269392|gb|EFX52325.1| 30S ribosomal protein S4 [Streptococcus cristatus ATCC 51100]
 gi|321278980|gb|EFX56023.1| ribosomal protein S4 [Streptococcus sp. C300]
 gi|321281032|gb|EFX58045.1| ribosomal protein S4 [Streptococcus sp. M334]
 gi|326682190|emb|CBY99806.1| 30S ribosomal protein S4 [Streptococcus oralis Uo5]
 gi|327390493|gb|EGE88833.1| ribosomal protein S4 [Streptococcus pneumoniae GA04375]
 gi|332075747|gb|EGI86214.1| ribosomal protein S4 [Streptococcus pneumoniae GA17570]
 gi|332076539|gb|EGI87001.1| ribosomal protein S4 [Streptococcus pneumoniae GA17545]
 gi|332077392|gb|EGI87853.1| ribosomal protein S4 [Streptococcus pneumoniae GA41301]
 gi|332202009|gb|EGJ16078.1| ribosomal protein S4 [Streptococcus pneumoniae GA41317]
 gi|332204104|gb|EGJ18169.1| ribosomal protein S4 [Streptococcus pneumoniae GA47901]
 gi|332205115|gb|EGJ19178.1| ribosomal protein S4 [Streptococcus pneumoniae GA47368]
          Length = 203

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V    L+  
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVTPGQVISVREKSLKVP 150


>gi|322387048|ref|ZP_08060660.1| 30S ribosomal protein S4 [Streptococcus infantis ATCC 700779]
 gi|321142132|gb|EFX37625.1| 30S ribosomal protein S4 [Streptococcus infantis ATCC 700779]
          Length = 203

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V    L+  
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVTPGQVISVREKSLKVP 150


>gi|295100786|emb|CBK98331.1| Uncharacterized conserved protein, contains S4-like domain
           [Faecalibacterium prausnitzii L2-6]
          Length = 273

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 14/63 (22%), Positives = 27/63 (42%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           ++ +     +  R+  V+A     SR     ++A  RV++N + +  A   V  +D   V
Sbjct: 187 ERRLQTATVSSLRLDAVLAAMLRCSRGMAAELVAAGRVEINHLPVSSAHAPVYESDVFTV 246

Query: 63  DGV 65
            G 
Sbjct: 247 RGK 249


>gi|295427677|ref|ZP_06820309.1| hypothetical protein SIAG_00197 [Staphylococcus aureus subsp.
           aureus EMRSA16]
 gi|295128035|gb|EFG57669.1| hypothetical protein SIAG_00197 [Staphylococcus aureus subsp.
           aureus EMRSA16]
          Length = 259

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 16/60 (26%), Positives = 29/60 (48%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            I     +  R+  VI      SR   +++I ++RVKVN  +++ A   + + D I + G
Sbjct: 173 KIESATVSSLRLDVVIKEMIRKSRTIAKQLIEKKRVKVNHTIVDSADFQLQANDLISIQG 232


>gi|168207734|ref|ZP_02633739.1| S4 domain protein [Clostridium perfringens E str. JGS1987]
 gi|170660936|gb|EDT13619.1| S4 domain protein [Clostridium perfringens E str. JGS1987]
          Length = 68

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 27/73 (36%), Gaps = 8/73 (10%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAG---IASRREVERMIAQQRVKVNGILLERAAVNVMST 57
          M++  I   N    ++   +   G   + S  E +  I    V VNG +  +    +   
Sbjct: 1  MQEVKI---NTEFIKLDSFLKWCGAVSLGS--EAKMFIMNGEVLVNGEVCTQRGKKLRVD 55

Query: 58 DHIEVDGVPLRKA 70
          D +E +G   +  
Sbjct: 56 DTVEFNGEIYKLI 68


>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 = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 30/268 (11%), Positives = 76/268 (28%), Gaps = 43/268 (16%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVK------VNGI---------LLERAA----VNVM 55
           R+  +I+ +   SR + + +I+   V       +N            +         ++ 
Sbjct: 17  RLDVLISASLNISRSKAQCIISDGGVTLLDTPVLNNSHLTNTGDVYTVTVPDTPQSTSID 76

Query: 56  STD----HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
                  HI  +   +   ++      H   G           +   + L ++ +     
Sbjct: 77  PNHDIPLHIIYEDEHIIVIDKAPNIAVHPGHGTKNDTLAHALLAHCGNALCAVGNSHRPG 136

Query: 111 -VGRLDINTEGLLLLTN-------------DGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
            + RLD +T GL+++               +    +                    +D  
Sbjct: 137 IIHRLDKDTSGLMVIAKTEKAYLVLSQALEEKKFRKEYLALIWGVPTTKHCFIQTNLDVK 196

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWKVNRL 215
           + +     + +    + + +  ++   G+  +     L  G+  +I+         V   
Sbjct: 197 RSDKTMMEVTLSRGKHANTEYIIEKTFGNVASLARCILHTGRTHQIRVHMSHIGHSVVG- 255

Query: 216 IRISYGPFQLGTLLAG--STREVSKKIL 241
               YG     +L  G    R   ++ L
Sbjct: 256 -DQKYGKNNKKSLRCGIPEVRNFKRQAL 282


>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 = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 32/222 (14%), Positives = 60/222 (27%), Gaps = 36/222 (16%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------DGVPLR--KAER 72
           SR  ++ +I +  + VNG    +A   V + D I V            + +PL     + 
Sbjct: 22  SRSFIQGLIEEGHILVNGA-ARKANYKVRAMDQITVVIPPPRELKVEAENIPLEVLYEDE 80

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN--------------- 117
             L +      +V        ++ V   L    +     G L                  
Sbjct: 81  DVLVVNKPQGMVVHPAPGAWTKTMVNALLYHCRNLSGINGVLRPGIVHRIDKDTSGLLVV 140

Query: 118 ------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
                  +GL        +AR         +          V +D  +  K  +V Q   
Sbjct: 141 AKNDLAHQGLAEQIKAHSMARRYLAIVHGVVFEPSGTVDAPVGRDPADRKKMAVVFQNAK 200

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +  +      +   L  G+  +I+    +    V 
Sbjct: 201 EAVTHYEVLERFRDFTLLEARLETGRTHQIRVHMAYLKHPVL 242


>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 = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 28/241 (11%), Positives = 61/241 (25%), Gaps = 38/241 (15%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------- 63
             P+R+   +A     +R ++  +I  + V V+  L+ R  V + S  +I+V+       
Sbjct: 10  DNPERLDIFLASEIGQTRSQIASLIKHKCVFVDEKLVTRPGVKLKSGQNIKVEFPEAKES 69

Query: 64  -------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
                   V +   +   L +       V         + V              G    
Sbjct: 70  PALDIDFNVEILYEDDDVLVINKPSGVTVHPAPSVKEATLVDWLKHKGIRLSNISGEERH 129

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVY---------------RVRFHGQVDQDKLNLL 161
                L     G +       + ++L                            ++    
Sbjct: 130 GIVHRLDKGTSGTMVVAKNNEAHEFLSEQLQDKSMGRYYLAVLNPPLKDEITTIEQNIGR 189

Query: 162 KKGIVIQGICY-----GDMQVTL----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                ++  C         +        +      +V   L  G+  +I+   E  N  +
Sbjct: 190 SAHNRLKMTCTDAGKSKYAKTMFKVLSLSNDEKQQFVACKLFTGRTHQIRVHLESINRHI 249

Query: 213 N 213
            
Sbjct: 250 I 250


>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 = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 31/234 (13%), Positives = 58/234 (24%), Gaps = 35/234 (14%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGI--------------------------L 46
            +RV   +AR    SR     +  +  V VNG+                           
Sbjct: 10  GERVDAALARMLGLSRSRCAELAGEGHVLVNGVAAGKSDRLGALDIIEVTIPEPESKPTP 69

Query: 47  LERAAVNVMSTDHIEVDGVPL-------RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           +   A+     D + VD  P+          E   +    +  G   T   P  R  +  
Sbjct: 70  VTDMAILYDDEDIVVVD-KPVGVAAHTGPGWEGPTVLGNLEAAGYRITSYGPPERQGIVH 128

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
            L    S  + V + ++    +     +  + +V        L          + +    
Sbjct: 129 RLDVGTSGAMMVAKSELAYTVMKRAFKERTIEKVYHAVVAGHLDPASGTIDAPIGRHPSR 188

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             +  + I G                     V L  G+  +I+           
Sbjct: 189 EWRMAV-IDGGKRAVTHYDTLELMAGAQLTEVHLETGRTHQIRVHMAAVGHPCV 241


>gi|312863483|ref|ZP_07723721.1| putative ribosomal protein S4 [Streptococcus vestibularis F0396]
 gi|311101019|gb|EFQ59224.1| putative ribosomal protein S4 [Streptococcus vestibularis F0396]
          Length = 129

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 15 RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
          R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V    L+  
Sbjct: 24 RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYCVTPGQVISVREKSLKVR 80


>gi|187250787|ref|YP_001875269.1| pseudouridine synthase [Elusimicrobium minutum Pei191]
 gi|186970947|gb|ACC97932.1| Pseudouridine synthase [Elusimicrobium minutum Pei191]
          Length = 299

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 16/116 (13%), Positives = 40/116 (34%), Gaps = 2/116 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M +K  +  + T  R+   ++      SR  ++ +I Q +V VNG    + A  +   D+
Sbjct: 1   MSNKETLTFSGTSARLDLFLSENKPDYSRGLIQNLIKQGKVTVNGK-ERKPAWPLAEGDN 59

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
           +E++   +      +  +  +   +   +            +         +G   
Sbjct: 60  VEIEWPSVENKTGLKDLIIFEDKNMFVINKPSGMLVHPQSPVWEENPAAAFIGEET 115


>gi|313637033|gb|EFS02602.1| S4 domain-containing protein [Listeria seeligeri FSL S4-171]
          Length = 259

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 13/55 (23%), Positives = 25/55 (45%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             +  R+  +I+ A   SR++ ++++    VKVN   +E         D + V G
Sbjct: 179 TVSSMRLDVIISNAHHISRQKAKQLVVAGLVKVNWKTVENPDFECEQEDVLSVRG 233


>gi|26987219|ref|NP_742644.1| 30S ribosomal protein S4 [Pseudomonas putida KT2440]
 gi|148545763|ref|YP_001265865.1| 30S ribosomal protein S4 [Pseudomonas putida F1]
 gi|37999419|sp|Q88QL2|RS4_PSEPK RecName: Full=30S ribosomal protein S4
 gi|172048431|sp|A5VXS1|RS4_PSEP1 RecName: Full=30S ribosomal protein S4
 gi|24981858|gb|AAN66108.1|AE016239_3 ribosomal protein S4 [Pseudomonas putida KT2440]
 gi|148509821|gb|ABQ76681.1| SSU ribosomal protein S4P [Pseudomonas putida F1]
 gi|313496843|gb|ADR58209.1| RpsD [Pseudomonas putida BIRD-1]
          Length = 206

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V   D + V
Sbjct: 97  RLDNVVYRMGFGSTRSESRQLVSHKAISVNGKTVNIPSYQVRPGDVVAV 145


>gi|196228479|ref|ZP_03127346.1| ribosomal protein S4 [Chthoniobacter flavus Ellin428]
 gi|196227882|gb|EDY22385.1| ribosomal protein S4 [Chthoniobacter flavus Ellin428]
          Length = 203

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           R+  VI R G A SR    ++++   V+VNG  ++ ++ NV + D I +   P
Sbjct: 94  RLDNVIYRLGFANSRSAARQLVSHGHVQVNGRKVDVSSFNVKAGDAITIKDKP 146


>gi|157150371|ref|YP_001451346.1| 30S ribosomal protein S4 [Streptococcus gordonii str. Challis
           substr. CH1]
 gi|262283690|ref|ZP_06061455.1| ribosomal protein S4 [Streptococcus sp. 2_1_36FAA]
 gi|172045598|sp|A8AZY6|RS4_STRGC RecName: Full=30S ribosomal protein S4
 gi|157075165|gb|ABV09848.1| ribosomal protein S4 [Streptococcus gordonii str. Challis substr.
           CH1]
 gi|262260747|gb|EEY79448.1| ribosomal protein S4 [Streptococcus sp. 2_1_36FAA]
          Length = 203

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V    L+  
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVTPGQVISVREKSLKVP 150


>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 = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 11/56 (19%), Positives = 22/56 (39%), Gaps = 1/56 (1%)

Query: 8  QENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           E    +R+ + +A R    SR  ++ +I    V  +G ++   +  V       V
Sbjct: 17 TEADGGERLDRFLASRLSEMSRSRLKALIEAGTVTCDGAVIRLPSAAVRPGAIYTV 72


>gi|56808368|ref|ZP_00366123.1| COG0522: Ribosomal protein S4 and related proteins [Streptococcus
           pyogenes M49 591]
          Length = 203

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVDPGQVISV 142


>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 = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 36/265 (13%), Positives = 82/265 (30%), Gaps = 52/265 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M  + I  E    QR+ + + +      SR  ++ +I +  +K++G L+      +    
Sbjct: 1   MVTQQITDEGALGQRLDQWLTKQYHSALSRSRLQALIREGYLKIDGQLIHEPKTKLKPNQ 60

Query: 59  HIEVD----------GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            IE+           G  ++     E   + + +K  GLV    + +   T+ + L    
Sbjct: 61  MIELTIPILRDAKPSGEAIKLDILFEDDHVIVINKQAGLVVHPGNGNLTGTLVNALIYHC 120

Query: 106 SRVIS----------VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ--- 152
              +S          V RLD NT G++++  +    + L    +   R   +        
Sbjct: 121 GDSLSGIGGVKRPGIVHRLDKNTSGIMVVAKNDLAHKNLSAQFSDHGRTSALDRRYHALI 180

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN------------------------AW 188
                 N+ K    +    +   +  +   +  +                        + 
Sbjct: 181 WGSPNRNVWKIDAPLGRSPHNRTKQAVIYSQNPHARHAVTHFSLLEKYGICSDKTSFASL 240

Query: 189 VTVGLREGKNREIKKVFEFFNWKVN 213
           +   L  G+  +I+         + 
Sbjct: 241 LECRLETGRTHQIRVHMAHIGHPLV 265


>gi|313632501|gb|EFR99511.1| S4 domain-containing protein [Listeria seeligeri FSL N1-067]
          Length = 258

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 13/55 (23%), Positives = 25/55 (45%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             +  R+  +I+ A   SR++ ++++    VKVN   +E         D + V G
Sbjct: 178 TVSSMRLDVIISNAHHISRQKAKQLVVAGLVKVNWKTVENPDFECEQEDVLSVRG 232


>gi|225850762|ref|YP_002730996.1| 30S ribosomal protein S4 [Persephonella marina EX-H1]
 gi|254764604|sp|C0QQQ0|RS4_PERMH RecName: Full=30S ribosomal protein S4
 gi|225645002|gb|ACO03188.1| ribosomal protein S4 [Persephonella marina EX-H1]
          Length = 205

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+  +++      VNG  ++  +  V   D IE+
Sbjct: 96  RLDNVVYRLGFAKTRRQARQLVRHGHFLVNGRKVDIPSYRVDPGDIIEL 144


>gi|152112269|sp|A3CRA2|RS4_STRSV RecName: Full=30S ribosomal protein S4
 gi|324991900|gb|EGC23823.1| 30S ribosomal protein S4 [Streptococcus sanguinis SK405]
 gi|324996210|gb|EGC28120.1| 30S ribosomal protein S4 [Streptococcus sanguinis SK678]
 gi|327458525|gb|EGF04875.1| 30S ribosomal protein S4 [Streptococcus sanguinis SK1]
 gi|327490386|gb|EGF22172.1| 30S ribosomal protein S4 [Streptococcus sanguinis SK1058]
          Length = 203

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V    L+  
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVTPGQVISVREKSLKVP 150


>gi|258611701|ref|ZP_05711611.1| ribosomal protein S4 [Listeria monocytogenes FSL R2-503]
 gi|258605525|gb|EEW18133.1| ribosomal protein S4 [Listeria monocytogenes FSL R2-503]
          Length = 170

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 62  QRLDNIVYRLGLARTRRAARQLVNHGHITVDGKRVDIPSYQVSVGQVISV 111


>gi|313143038|ref|ZP_07805231.1| hemolysin [Helicobacter cinaedi CCUG 18818]
 gi|313128069|gb|EFR45686.1| hemolysin [Helicobacter cinaedi CCUG 18818]
          Length = 234

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 23/166 (13%), Positives = 50/166 (30%), Gaps = 7/166 (4%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT 86
           SR + +  I    VKVNG ++++ +  +   D + VD   L  +       Y     + +
Sbjct: 7   SRTKAKEAIESGCVKVNGAVVKKGSFLLEKDDEVGVDSKDLLLSRA----GYKLRGFIES 62

Query: 87  THSDPDGRSTVFDNLPSIFSRVISVGRLDINTE---GLLLLTNDGGLARVLELPSTQWLR 143
                        +  +I     + G   +  E     ++  + G       +   + + 
Sbjct: 63  LVQKGLWDRAYLFHKKAIDIGASTGGFTQVLLESGIDSVVCVDVGKNQLHTSILQDERVS 122

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           V+          ++   L    V     Y  M+           W+
Sbjct: 123 VFEECDIRDFSDEREFDLMVCDVSFISLYKLMESFERLNVKEYIWL 168


>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 = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 6/56 (10%)

Query: 13 PQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          P R+ K +AR     A + SR  + R+IA   V+V+GI++      +     I VD
Sbjct: 15 PPRLDKALARDVPEDANL-SRTRLGRLIADGSVQVDGIVVTDPRARIFEGQEITVD 69


>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 = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 33/241 (13%), Positives = 67/241 (27%), Gaps = 40/241 (16%)

Query: 13  PQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
             R+ KV++ A      SR  +  +I Q  V   G  ++ A+  V     +EV       
Sbjct: 56  GDRLDKVLSDALGGAGLSRSRLRSLIDQGCVSSGGETIDDASRRVKPGQIVEVLVPAAEP 115

Query: 63  --------------DGVPLRKAERTRLWLYHK---------------PIGLVTTHSDPDG 93
                         +   L   ++    + H                  G   +      
Sbjct: 116 AVPLPQAIPLAIVHEDEDLLVIDKAAEMVVHPAAGNPDGTLVNALLAHCGDRLSGIGGVR 175

Query: 94  RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
           R  +   L    S ++   + D   +GL     D  L+R                  G +
Sbjct: 176 RPGIVHRLDKGTSGLLVAAKTDRAHQGLTAQFADRSLSRTYLAVVWGVPAAREGVIEGNI 235

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKV 212
            +   +  +  ++ +G      +  +    G   + V   L  G+  +I+         +
Sbjct: 236 GRHPGDRKRMAVLSRGGKPAVTRYRVVRSFGLLASLVECKLLTGRTHQIRVHMAHVGHPL 295

Query: 213 N 213
            
Sbjct: 296 V 296


>gi|13473214|ref|NP_104781.1| pseudouridine synthase [Mesorhizobium loti MAFF303099]
 gi|14023962|dbj|BAB50567.1| pseudouridine synthase [Mesorhizobium loti MAFF303099]
          Length = 329

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 35/259 (13%), Positives = 69/259 (26%), Gaps = 51/259 (19%)

Query: 6   IVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           +V  +   QR+ + +A +     SR  V+ +I Q  V V+G   +     + + + + + 
Sbjct: 3   VVGADAAGQRLDQWLAASLGPDMSRSRVQMLIRQGAVSVDGKPADETKRKMSAGESVSIA 62

Query: 63  ---------DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                     G  +      E   L + +KP GLV      +   T+ + L       +S
Sbjct: 63  MPEPEPAAPQGEAIALDVLYEDDALIVINKPAGLVVHPGAGNWTGTLVNALIHHCGDSLS 122

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN--------- 159
              G         L     G +       + + L           D ++           
Sbjct: 123 GIGGVRRPGIVHRLDKETSGVMVVAKTDRAHKALSEAFADHGRTGDLERAYLALVWGIPQ 182

Query: 160 ------------------LLKKGIVIQGICYGDMQVTLDTQKGSN-------AWVTVGLR 194
                                         +      +  + G N       + V   L 
Sbjct: 183 RPTGTVDAPLGRAADRVRRAVVPEGRDDARHAVTHFAVQERFGENQQEFATASLVECRLE 242

Query: 195 EGKNREIKKVFEFFNWKVN 213
            G+  +I+         V 
Sbjct: 243 TGRTHQIRVHMAHIGHPVI 261


>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 = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 11/56 (19%), Positives = 22/56 (39%), Gaps = 1/56 (1%)

Query: 8  QENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           E    +R+ + +A R    SR  ++ +I    V  +G ++   +  V       V
Sbjct: 17 TEADGGERLDRFLASRLSEMSRSRLKALIEAGTVTCDGAVIRLPSAAVRPGAIYTV 72


>gi|308233884|ref|ZP_07664621.1| 30S ribosomal protein S4 [Atopobium vaginae DSM 15829]
 gi|328943591|ref|ZP_08241056.1| 30S ribosomal protein S4 [Atopobium vaginae DSM 15829]
 gi|327491560|gb|EGF23334.1| 30S ribosomal protein S4 [Atopobium vaginae DSM 15829]
          Length = 197

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 4/66 (6%)

Query: 1   MKDKNIVQENFTP---QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMS 56
           MK + I  +N       R+  V+ R G A +R+E  + I    + VNG  ++  +  V +
Sbjct: 71  MKAEGITGDNLMSLLETRLDNVVFRLGFARTRKESRQTIRHGHITVNGKRVDIPSYQVKA 130

Query: 57  TDHIEV 62
            D I V
Sbjct: 131 DDVIAV 136


>gi|209525207|ref|ZP_03273750.1| RNA-binding S4 domain protein [Arthrospira maxima CS-328]
 gi|209494392|gb|EDZ94704.1| RNA-binding S4 domain protein [Arthrospira maxima CS-328]
          Length = 72

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 12/61 (19%), Positives = 26/61 (42%), Gaps = 1/61 (1%)

Query: 6  IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          +V+      ++ K +  +G+  S  + +  I    V VNG +  R    ++  D +  +G
Sbjct: 2  VVKVTEQNIKLDKFLKLSGLVESGGQAKAFIQSGYVMVNGQIETRRGRKLIEGDRVTFNG 61

Query: 65 V 65
           
Sbjct: 62 E 62


>gi|257875741|ref|ZP_05655394.1| pseudouridylate synthase [Enterococcus casseliflavus EC20]
 gi|257809907|gb|EEV38727.1| pseudouridylate synthase [Enterococcus casseliflavus EC20]
          Length = 302

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 38/245 (15%), Positives = 77/245 (31%), Gaps = 37/245 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K   ++ +     RV KV+A      SR ++++ + +  V + G  +  A   V + DH+
Sbjct: 3   KQIEVIIKEEKG-RVDKVLAERLPNHSRSQIQQWLKEDAVTLMGETVR-ANYKVKAGDHL 60

Query: 61  --------EVDGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
                    VD  P      +   +     +      +V   +     + V   L  +  
Sbjct: 61  IIQVPEPEVVDLQPENIPLTIVYQDADVAVINKPQGMVVHPSAGHPNGTLVNALLYHMDD 120

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
                   R   V R+D +T GLL++  +      L         + +            
Sbjct: 121 LSTINDVVRPGIVHRIDKDTSGLLMIAKNDQAHESLAKQLKDKTSLRKYVALVHGTISHE 180

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNREIKKVFE 206
                  + +      MQ  ++  K +    TV        L E     G+  +I+   +
Sbjct: 181 KGTINAPIGRSKVNRKMQAVIENGKPAVTHFTVLERFEQFTLVELQLETGRTHQIRVHMQ 240

Query: 207 FFNWK 211
           +  + 
Sbjct: 241 YIGFP 245


>gi|209560256|ref|YP_002286728.1| 30S ribosomal protein S4 [Streptococcus pyogenes NZ131]
 gi|226695085|sp|B5XJ99|RS4_STRPZ RecName: Full=30S ribosomal protein S4
 gi|209541457|gb|ACI62033.1| SSU ribosomal protein S4p (S9e) [Streptococcus pyogenes NZ131]
          Length = 203

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVDPGQVISV 142


>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 = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 30/239 (12%), Positives = 66/239 (27%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V+E+   QR+ +  A      SR  ++  +    + VNG ++ +A + VM  + I V  
Sbjct: 10  TVKESQLGQRLDQAAAELFSDFSRSRIKEWLLAGNMTVNGEVVTKARLKVMGGEEITVKA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                           +   +   L +      +V   +     + +   L    +    
Sbjct: 70  ELEDEERWLAQDIPLDIVYEDDDLLVINKPRDFVVHPGAGTPDGTVLNALLFHYPNIAEV 129

Query: 111 V-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------- 155
                  RLD +T GL+++         L     +                         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRKITREYEAVVVGRMTAGGMIEKPI 189

Query: 156 -DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               N      V +          +      +  + + L  G+  +I+    +    + 
Sbjct: 190 GRHPNKRTLMAVHELGKDAVTHYRVAEHFRIHTRIRLRLETGRTHQIRVHMSYLQHPLV 248


>gi|254416092|ref|ZP_05029847.1| photosystem II S4 domain protein [Microcoleus chthonoplastes PCC
           7420]
 gi|196177025|gb|EDX72034.1| photosystem II S4 domain protein [Microcoleus chthonoplastes PCC
           7420]
          Length = 259

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 2/65 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             K  +       R+   IA AG   SR ++  +I    V+VN   + +A+ +V   D I
Sbjct: 172 PKKKEMTTVEASMRLD-AIASAGFGTSRSKMADLIGAGDVRVNWKEVSQASYSVKPGDLI 230

Query: 61  EVDGV 65
            + G 
Sbjct: 231 AIRGK 235


>gi|313885082|ref|ZP_07818834.1| ribosomal protein S4 [Eremococcus coleocola ACS-139-V-Col8]
 gi|312619773|gb|EFR31210.1| ribosomal protein S4 [Eremococcus coleocola ACS-139-V-Col8]
          Length = 201

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 12/47 (25%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  ++ R G AS RR+  +++A   + V+G  ++  +  V     I
Sbjct: 92  RLDNLVYRLGYASTRRQARQLVAHGHITVDGQRVDIPSYLVKPEQVI 138


>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 = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 26/257 (10%), Positives = 64/257 (24%), Gaps = 55/257 (21%)

Query: 10  NFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           +   QR+ + +A +     SR  V+ +I Q  V +NG  ++     ++  + + V     
Sbjct: 12  DAAGQRLDQWLAASLGPDMSRSRVQMLIRQGAVSINGKPVDETKRKMLPGESVSVAMPEP 71

Query: 63  -----DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
                 G  +       +   + +      +V   +     + V   +      +  +G 
Sbjct: 72  EPAEPQGENIALDVLYEDDALIVINKPAGLVVHPGAGNWTGTLVNALIHHCGDSLSGIGG 131

Query: 114 LDIN-------------------------------------TEGLLLLTNDGGLARVLEL 136
           +                                              L    G+ +    
Sbjct: 132 VRRPGIVHRLDKETSGVMVVAKTDRAHKALSEAFADHGLTGDLERAYLALVWGIPQRPTG 191

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
                L     R    V  +  +  +  +    +     +   +      + V   L  G
Sbjct: 192 TVDAPLGRAADRVRRAVVPEGRDDARHAVTHFAVQERFGEKQQEFATA--SLVECRLETG 249

Query: 197 KNREIKKVFEFFNWKVN 213
           +  +I+         V 
Sbjct: 250 RTHQIRVHMAHIGHPVI 266


>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 = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 36/248 (14%), Positives = 67/248 (27%), Gaps = 39/248 (15%)

Query: 4   KNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           + ++      QR+ K++A R    SR  ++R I    + VNG   + A   V+  + I V
Sbjct: 30  RFVLSLKDGGQRLDKLVAGRLSQYSRSRLQRWIEDGHITVNGEKAQ-AKQTVIGDEEICV 88

Query: 63  DGV---------------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-- 105
                             P+   +   L +      +V   +     + +   L      
Sbjct: 89  IPQLAEEDLAFTPEAVDFPVVFEDNAILVVNKPASLVVHPAAGNWSGTLLNGLLYRDPKS 148

Query: 106 ---SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------- 155
               R   V RLD  T G++++         L                   D        
Sbjct: 149 ATVPRAGIVHRLDKETSGVMVVAKTIEAQTDLVRQLQARTVKREYLALVWGDTPQSGTID 208

Query: 156 ----DKLNLLKKGIVIQGICYGDMQVTL------DTQKGSNAWVTVGLREGKNREIKKVF 205
                      K  VI                       + + V   L  G+  +I+   
Sbjct: 209 EPIGRHPRDRVKMAVIHTQSGKPAVTHFRKIAEGVCNNMNVSLVKCRLETGRTHQIRVHL 268

Query: 206 EFFNWKVN 213
           +   + + 
Sbjct: 269 QSIGFPLV 276


>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 = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 33/287 (11%), Positives = 78/287 (27%), Gaps = 53/287 (18%)

Query: 3   DKNIVQENFTPQ-RVSKVI-ARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           ++ ++  + T + R+   + A+ G   SR  ++ +I   +V + G  +      V + D 
Sbjct: 11  NRKVLTADETAEGRLDAWLTAQVGEEFSRSRIKALIKDGQVLLRGEPVTDPQRKVRTGDS 70

Query: 60  IEV----------DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            E+           G  +       +   + +      +V   +     + V   +    
Sbjct: 71  FELTLPEPEDPTPQGEDIPLDILHEDDDVIVISKPSGLVVHPGAGNWTGTLVNALIHHCS 130

Query: 106 SRVISVGRLDIN----------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
             +  +G +             T  +++  ND     +    +     +   R +  +  
Sbjct: 131 DTLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDIAHRHLSLQFADHGRTMPLERAYQAIVW 190

Query: 156 DKLNLLKKGI-----VIQGICYGDMQVTLDTQKGSN---------------------AWV 189
            +   L   +        G          D+Q                         + V
Sbjct: 191 GRPRTLSGTVDAPLGRATGDRTRRAVKRPDSQDADEAITHYQVIERFHEKPDATAFASLV 250

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              L  G+  +I+         +        G      LL    R+V
Sbjct: 251 ECRLETGRTHQIRVHMAHIGHPLLGDTVYGAGFKTKANLLPEEIRKV 297


>gi|94968282|ref|YP_590330.1| SSU ribosomal protein S4P [Candidatus Koribacter versatilis
           Ellin345]
 gi|152060923|sp|Q1IS94|RS4_ACIBL RecName: Full=30S ribosomal protein S4
 gi|94550332|gb|ABF40256.1| SSU ribosomal protein S4P [Candidatus Koribacter versatilis
           Ellin345]
          Length = 209

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G AS RR+  +++    + VNG  +   +  V   D I V
Sbjct: 100 RLDNVVYRLGFASARRQARQLVRHGHIAVNGKKVNIPSYQVSVKDEIAV 148


>gi|15837777|ref|NP_298465.1| 30S ribosomal protein S4 [Xylella fastidiosa 9a5c]
 gi|26399518|sp|Q9PE53|RS4_XYLFA RecName: Full=30S ribosomal protein S4
 gi|9106141|gb|AAF83985.1|AE003951_10 30S ribosomal protein S4 [Xylella fastidiosa 9a5c]
          Length = 208

 Score = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 15/66 (22%), Positives = 28/66 (42%), Gaps = 1/66 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  VI R G A +R    ++++ +RV VNG L+   + +V   D + +     +     
Sbjct: 98  RLDNVIYRMGFAVTRPAARQLVSHRRVLVNGKLVNLPSYHVKPGDVVALSQRAQKYLCVQ 157

Query: 74  RLWLYH 79
                 
Sbjct: 158 ESLTIK 163


>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 = 52.5 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 13/59 (22%), Positives = 30/59 (50%), Gaps = 3/59 (5%)

Query: 7  VQENFTPQRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          V++     R+ + +        SR  +++ I + +VKVNG + ++ +  +   + +EVD
Sbjct: 6  VEKREEGWRLDQFLKEKTPSWISRSLIQKAIKEGKVKVNGQI-KKPSYKLKEGEIVEVD 63


>gi|289435369|ref|YP_003465241.1| S4 domain protein [Listeria seeligeri serovar 1/2b str. SLCC3954]
 gi|289171613|emb|CBH28159.1| S4 domain protein [Listeria seeligeri serovar 1/2b str. SLCC3954]
          Length = 258

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 13/55 (23%), Positives = 25/55 (45%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             +  R+  +I+ A   SR++ ++++    VKVN   +E         D + V G
Sbjct: 178 TVSSMRLDVIISNAHHISRQKAKQLVVAGLVKVNWKTVENPDFECEQEDVLSVRG 232


>gi|170723882|ref|YP_001751570.1| 30S ribosomal protein S4 [Pseudomonas putida W619]
 gi|226699108|sp|B1JAI8|RS4_PSEPW RecName: Full=30S ribosomal protein S4
 gi|169761885|gb|ACA75201.1| ribosomal protein S4 [Pseudomonas putida W619]
          Length = 206

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V   D + V
Sbjct: 97  RLDNVVYRMGFGSTRSESRQLVSHKAISVNGKTVNIPSYQVRPGDVVAV 145


>gi|320531524|ref|ZP_08032476.1| ribosomal RNA large subunit methyltransferase J [Actinomyces sp.
          oral taxon 171 str. F0337]
 gi|320136263|gb|EFW28259.1| ribosomal RNA large subunit methyltransferase J [Actinomyces sp.
          oral taxon 171 str. F0337]
          Length = 290

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   + R G+A SR     +I    V ++G ++ + A  V     IE+
Sbjct: 5  IRIDSELVRRGLARSRTHAATLITDGHVTLDGQVVTKPARQVDPAQAIEI 54


>gi|302539523|ref|ZP_07291865.1| modular polyketide synthase [Streptomyces sp. C]
 gi|302448418|gb|EFL20234.1| modular polyketide synthase [Streptomyces sp. C]
          Length = 4478

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 10/129 (7%), Positives = 16/129 (12%), Gaps = 4/129 (3%)

Query: 230  AGSTREVS--KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
             G  R  +      R+        E           +      R                
Sbjct: 3806 PGRLRPTTALPGTARQSPQWGPWAENAACRRLAPSVARCAQTARTPATRSARPARRGAGP 3865

Query: 288  NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIH--SSFLSDSGQREENHRRSPSFPSKR 345
                + G         P             +                      P     R
Sbjct: 3866 ARRTQPGRRPPGSRPGPDRDGPDRGPAGRTRARRLHPQARRSRRGHPPQAPHRPGAHPDR 3925

Query: 346  SLRRTSAKK 354
               R    +
Sbjct: 3926 LGPRPRHVR 3934



 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 12/132 (9%), Positives = 23/132 (17%), Gaps = 12/132 (9%)

Query: 234  REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
            R ++  + R                          +         P              
Sbjct: 3835 RRLAPSVARCAQTARTPATRSARPARRGAGPARRTQPGRRPPGSRPGPDRDGPDRGPAGR 3894

Query: 294  GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ--REENHRR----------SPSF 341
              +++        RR          G H   L    +  R    R               
Sbjct: 3895 TRARRLHPQARRSRRGHPPQAPHRPGAHPDRLGPRPRHVRPRTGRTLLPGTGTGLAGRHR 3954

Query: 342  PSKRSLRRTSAK 353
             ++ + RR    
Sbjct: 3955 TAQPARRRDRPA 3966



 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 13/109 (11%), Positives = 27/109 (24%), Gaps = 2/109 (1%)

Query: 248  HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            H                           +     +    +N++ +       + A     
Sbjct: 3791 HGQPRPGQLRGRQRLPGRLRPTTALPGTARQSPQWGPWAENAACRRLAPSVARCAQTART 3850

Query: 308  RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF--PSKRSLRRTSAKK 354
                S     +G   +  +  G+R    R  P    P +    RT A++
Sbjct: 3851 PATRSARPARRGAGPARRTQPGRRPPGSRPGPDRDGPDRGPAGRTRARR 3899



 Score = 43.6 bits (101), Expect = 0.041,   Method: Composition-based stats.
 Identities = 12/124 (9%), Positives = 24/124 (19%), Gaps = 19/124 (15%)

Query: 248  HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                                   RP    + PD     +  + + +  +++ +   P   
Sbjct: 3856 ARPARRGAGPARRTQPGRRPPGSRPGPDRDGPDRGPAGRTRARRLHPQARRSRRGHPPQA 3915

Query: 308  RNLASNVWMAKGIHSSFLSDSGQR------------------EENHRRSPSF-PSKRSLR 348
             +         G     +     R                      R  P+  P  R   
Sbjct: 3916 PHRPGAHPDRLGPRPRHVRPRTGRTLLPGTGTGLAGRHRTAQPARRRDRPAALPDARLRP 3975

Query: 349  RTSA 352
               A
Sbjct: 3976 PQPA 3979


>gi|32266018|ref|NP_860050.1| hypothetical protein HH0519 [Helicobacter hepaticus ATCC 51449]
 gi|32262067|gb|AAP77116.1| conserved hypothetical protein [Helicobacter hepaticus ATCC 51449]
          Length = 241

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 21/176 (11%), Positives = 59/176 (33%), Gaps = 2/176 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+   + +  ++SR + +  I    V+VNG ++ ++++ + S+D +++D   L      
Sbjct: 2   QRLDIYL-KTLLSSRTKAQEAIESGCVRVNGKVVYKSSLPLKSSDEVDIDTQGLLLGRAG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                     +     +               +   +   L+     ++ + + G     
Sbjct: 61  YKLRGFFEELVCKGLWEEGYLVGKRALDIGSSTGGFAQVLLNFGVSEIVCV-DVGKNQLH 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
             +   + +RV+      + +  +   +    V     Y  M+           W+
Sbjct: 120 QNMRDDERVRVFEECDVREFEPCEYFDIVVCDVSFISLYKLMESFERLVSAECIWL 175


>gi|317969027|ref|ZP_07970417.1| RNA-binding S4 [Synechococcus sp. CB0205]
          Length = 260

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 2/52 (3%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V A AG+  SR ++   I    V+VN  ++   +  +   D + +DG 
Sbjct: 187 RLDAV-ASAGLGVSRSKMADWIRAGAVRVNWSVITSPSRELKQGDRVRLDGR 237


>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 = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/235 (10%), Positives = 60/235 (25%), Gaps = 38/235 (16%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLE-----RAAVN------------- 53
            QR+ +V A+     SR  +   I + R+ V+G ++                        
Sbjct: 17  GQRLDQVAAQLFAEYSRSRLTSWIKEGRLTVDGAVVRPRDLVHGGSQLALQAEQEAQGEW 76

Query: 54  ---------VMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
                    V   DHI V    + K     +            ++       + +   + 
Sbjct: 77  VAEDIELDIVYEDDHIMV----INKPAGLVVHPAAGHASGTLLNALLHHVPDIVNVPRAG 132

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH------GQVDQDKL 158
               +      +      L      + ++     ++      +                 
Sbjct: 133 IVHRLDKDTTGLMVVAKTLQAQTKLVEQMQARKVSRIYECIVIGVVTAGGKIDAPIGRHG 192

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            + ++  V  G         +  +  S+  V V L  G+  +I+       + + 
Sbjct: 193 GMRQRMAVTDGGKPAVSHYRVLKRFRSHTHVRVKLETGRTHQIRVHMAHVGFPLV 247


>gi|255017199|ref|ZP_05289325.1| 30S ribosomal protein S4 [Listeria monocytogenes FSL F2-515]
          Length = 152

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          QR+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 44 QRLDNIVYRLGLARTRRAARQLVNHGHITVDGKRVDIPSYQVSVGQVISV 93


>gi|308813403|ref|XP_003084008.1| ribosomal small subunit pseudouridine synthase A (ISS)
           [Ostreococcus tauri]
 gi|116055890|emb|CAL57975.1| ribosomal small subunit pseudouridine synthase A (ISS)
           [Ostreococcus tauri]
          Length = 211

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 33/168 (19%), Positives = 66/168 (39%), Gaps = 3/168 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV  +++R G  +R       ++  + V+G  +        ++  + VDG  L   +  
Sbjct: 40  ERVDALLSRLGYCTRSTARAFASRHEIVVDGTRVRGVDAKARAS-TLRVDGEALDHPDGV 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            + ++     + +              +        + ++GRLD +T GLLLLT+DG L 
Sbjct: 99  LVAMHKPRGTVCSHDEREGANVYELLPERWRRRKPSIETIGRLDKDTSGLLLLTDDGALN 158

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
             L  P     + YRVR  G + +  + +   G +         +  +
Sbjct: 159 HALTSPKKDVGKWYRVRTDGPIPRACVEVFASGELTLSGEEKSCKPAM 206


>gi|268608473|ref|ZP_06142200.1| hemolysin A [Ruminococcus flavefaciens FD-1]
          Length = 261

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 1/48 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
          R+   +   GIA SR+  + MI+   V VNGI  ++A+ NV  +D IE
Sbjct: 3  RLDAEMVARGIARSRQTAKEMISAGSVTVNGITAKKASDNVTESDVIE 50


>gi|319939621|ref|ZP_08013980.1| S4 domain-containing protein [Streptococcus anginosus 1_2_62CV]
 gi|319811210|gb|EFW07516.1| S4 domain-containing protein [Streptococcus anginosus 1_2_62CV]
          Length = 263

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 18/53 (33%), Positives = 30/53 (56%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +  R+ KV+A +   SR    R+IA ++VKVN   L+  + +++  D I V G
Sbjct: 183 SSMRLDKVVAASFHLSRSIAARLIATKQVKVNYSTLDNPSHHLLLNDLISVRG 235


>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 = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 31/234 (13%), Positives = 57/234 (24%), Gaps = 35/234 (14%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGI--------------------------L 46
            +RV   +AR    SR     +     V VNG+                           
Sbjct: 10  GERVDAALARMLGLSRSRCAELAGDGHVLVNGVAAGKSDRLGALDIIEVTIPEPESKPTP 69

Query: 47  LERAAVNVMSTDHIEVDGVPL-------RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           +   A+     D + VD  P+          E   +    +  G   T   P  R  +  
Sbjct: 70  VTDMAILYDDEDIVVVD-KPVGVAAHTGPGWEGPTVLGNLEAAGYRITSYGPPERQGIVH 128

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
            L    S  + V + ++    +     +  + +V        L          + +    
Sbjct: 129 RLDVGTSGAMMVAKSELAYTVMKRAFKERTIEKVYHAVVAGHLDPASGTIDAPIGRHPSR 188

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             +  + I G                     V L  G+  +I+           
Sbjct: 189 EWRMAV-IDGGKRAVTHYDTLELMAGAQLTEVHLETGRTHQIRVHMAAVGHPCV 241


>gi|83648828|ref|YP_437263.1| ribosomal protein S4 [Hahella chejuensis KCTC 2396]
 gi|123530606|sp|Q2S936|RS4_HAHCH RecName: Full=30S ribosomal protein S4
 gi|83636871|gb|ABC32838.1| ribosomal protein S4 [Hahella chejuensis KCTC 2396]
          Length = 206

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V   D + +
Sbjct: 97  RLDNVVYRMGFGSTRSEARQLVSHKAILVNGKAVNIPSYQVKPGDVVSI 145


>gi|148264094|ref|YP_001230800.1| hemolysin A [Geobacter uraniireducens Rf4]
 gi|146397594|gb|ABQ26227.1| hemolysin A [Geobacter uraniireducens Rf4]
          Length = 250

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 1/54 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
          +R+ K++   G+A SR   + +I   +V V+  L ++A   V     I + G  
Sbjct: 4  ERLDKILLDRGLAQSRERAKALIMAGQVVVDDHLADKAGQMVALEAEIRLKGEV 57


>gi|237797456|ref|ZP_04585917.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. oryzae str.
          1_6]
 gi|331020306|gb|EGI00363.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. oryzae str.
          1_6]
          Length = 151

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+  V+ R G  S R E  ++++ + V VNG  +   +  V + D + +
Sbjct: 42 RLDNVVYRMGFGSTRAESRQLVSHKSVSVNGKTVNVPSYQVRAGDVVAI 90


>gi|225574732|ref|ZP_03783342.1| hypothetical protein RUMHYD_02809 [Blautia hydrogenotrophica DSM
           10507]
 gi|225038061|gb|EEG48307.1| hypothetical protein RUMHYD_02809 [Blautia hydrogenotrophica DSM
           10507]
          Length = 197

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G A +RRE  +++  + + VNG ++   +  V + D IE+
Sbjct: 88  RLDNIVFRMGFARTRREARQIVDHKHITVNGKVVNIPSYLVKAGDVIEI 136


>gi|206900201|ref|YP_002250765.1| hemolysin A [Dictyoglomus thermophilum H-6-12]
 gi|206739304|gb|ACI18362.1| hemolysin A [Dictyoglomus thermophilum H-6-12]
          Length = 271

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            +R+  ++ + G   SR + +  I    VKVNG ++ +  + +     IE+
Sbjct: 3  EKERLDVLLVKRGFFESREKAKAAIIAGVVKVNGNIVTKPDLKIPVDSLIEI 54


>gi|154249375|ref|YP_001410200.1| hemolysin A [Fervidobacterium nodosum Rt17-B1]
 gi|154153311|gb|ABS60543.1| hemolysin A [Fervidobacterium nodosum Rt17-B1]
          Length = 263

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+ +++   G   SR + ++MI    V ++G +  + +    S   I +
Sbjct: 7  RLDQLLILKGFVESRTKAQQMIENGLVLLDGKVCTKPSKKCHSDSKIII 55


>gi|253731810|ref|ZP_04865975.1| ribosomal protein S4e [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
 gi|253724460|gb|EES93189.1| ribosomal protein S4e [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
          Length = 268

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 2/64 (3%)

Query: 3   DKNIVQENFT--PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++N   E+ T    R+  VI      SR   +++I ++RVKVN  +++ A   + + D I
Sbjct: 178 NENWKNESATVSSLRLDVVIKEMIRKSRTIAKQLIEKKRVKVNHTIVDSADFQLQANDLI 237

Query: 61  EVDG 64
            + G
Sbjct: 238 SIQG 241


>gi|225387211|ref|ZP_03756975.1| hypothetical protein CLOSTASPAR_00963 [Clostridium asparagiforme
           DSM 15981]
 gi|225046690|gb|EEG56936.1| hypothetical protein CLOSTASPAR_00963 [Clostridium asparagiforme
           DSM 15981]
          Length = 159

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 29/73 (39%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G+  +R+E  +++  + V VNG  +   +  V + D IE+           
Sbjct: 50  RLDNVLFRMGLGRTRKETRQIVDHKHVLVNGKPVNIPSYRVKTGDVIEIKEKYKSAQRYK 109

Query: 74  RLWLYHKPIGLVT 86
            +        +  
Sbjct: 110 DILEVTGGRMVPA 122


>gi|221234322|ref|YP_002516758.1| rRNA methylase [Caulobacter crescentus NA1000]
 gi|220963494|gb|ACL94850.1| predicted rRNA methylase [Caulobacter crescentus NA1000]
          Length = 266

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 10/47 (21%), Positives = 21/47 (44%), Gaps = 1/47 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
          R+ +++   G+  SR +    I   RV V G ++ + +  V     +
Sbjct: 28 RIDQLLVDRGVFDSRAKARAAIEAGRVSVAGRVVAKPSEQVDDNAEV 74


>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 = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 30/242 (12%), Positives = 67/242 (27%), Gaps = 39/242 (16%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +  +    R+ KV++      SR  +++ I    V V+G +   A + V   + + +   
Sbjct: 42  LNPDVCGVRLDKVLSTLVPQYSRSRLQQWIDGGHVSVDGEVAR-AKMTVYGDEKVVIYPQ 100

Query: 66  P---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
           P               +   +   L +      +V   +     + +   L  +      
Sbjct: 101 PAPEDEAFKPEAMDLAIVHEDAEMLVINKPAGLVVHPAAGNWSGTLLNGLLHYLPSISGV 160

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK--- 162
            R   V RLD +T GL+++         L                     +    +    
Sbjct: 161 PRAGIVHRLDKDTSGLMVVAKTLIAHTDLVRQLQARTVKREYLALVWGTPNITGKIDASI 220

Query: 163 --------KGIVIQGICYGDMQVTLD-----TQKGSNAWVTVG-LREGKNREIKKVFEFF 208
                   K  V + +                  G    + +  L  G+  +I+   +  
Sbjct: 221 GRHARDRIKMAVSENLTAKPAVTHFQRLATGMLDGRPVSLMLCRLETGRTHQIRVHMQSI 280

Query: 209 NW 210
            +
Sbjct: 281 GF 282


>gi|148267683|ref|YP_001246626.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           subsp. aureus JH9]
 gi|150393741|ref|YP_001316416.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           subsp. aureus JH1]
 gi|253314955|ref|ZP_04838168.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           subsp. aureus str. CF-Marseille]
 gi|255005978|ref|ZP_05144579.2| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           subsp. aureus Mu50-omega]
 gi|257795753|ref|ZP_05644732.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           A9781]
 gi|258415977|ref|ZP_05682247.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           A9763]
 gi|258419724|ref|ZP_05682691.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           A9719]
 gi|258438766|ref|ZP_05689919.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           A9299]
 gi|258444528|ref|ZP_05692857.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           A8115]
 gi|258447639|ref|ZP_05695783.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           A6300]
 gi|258454860|ref|ZP_05702824.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           A5937]
 gi|269202806|ref|YP_003282075.1| RNA-binding S4 domain protein [Staphylococcus aureus subsp. aureus
           ED98]
 gi|282892677|ref|ZP_06300912.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           A8117]
 gi|282929236|ref|ZP_06336811.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           A10102]
 gi|295407129|ref|ZP_06816930.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           A8819]
 gi|296276133|ref|ZP_06858640.1| RNA-binding S4 domain protein [Staphylococcus aureus subsp. aureus
           MR1]
 gi|297245985|ref|ZP_06929844.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           A8796]
 gi|147740752|gb|ABQ49050.1| RNA-binding S4 domain protein [Staphylococcus aureus subsp. aureus
           JH9]
 gi|149946193|gb|ABR52129.1| RNA-binding S4 domain protein [Staphylococcus aureus subsp. aureus
           JH1]
 gi|257789725|gb|EEV28065.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           A9781]
 gi|257839313|gb|EEV63787.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           A9763]
 gi|257844309|gb|EEV68691.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           A9719]
 gi|257848025|gb|EEV72018.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           A9299]
 gi|257850021|gb|EEV73974.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           A8115]
 gi|257853830|gb|EEV76789.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           A6300]
 gi|257863243|gb|EEV86007.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           A5937]
 gi|262075096|gb|ACY11069.1| RNA-binding S4 domain protein [Staphylococcus aureus subsp. aureus
           ED98]
 gi|282589195|gb|EFB94292.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           A10102]
 gi|282764674|gb|EFC04799.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           A8117]
 gi|294967982|gb|EFG44010.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           A8819]
 gi|297177149|gb|EFH36403.1| RNA-binding S4 domain-containing protein [Staphylococcus aureus
           A8796]
 gi|312829585|emb|CBX34427.1| S4 domain protein [Staphylococcus aureus subsp. aureus ECT-R 2]
 gi|315130982|gb|EFT86966.1| RNA-binding S4 domain protein [Staphylococcus aureus subsp. aureus
           CGS03]
 gi|329727412|gb|EGG63868.1| S4 domain protein [Staphylococcus aureus subsp. aureus 21172]
          Length = 268

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 2/64 (3%)

Query: 3   DKNIVQENFT--PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++N   E+ T    R+  VI      SR   +++I ++RVKVN  +++ A   + + D I
Sbjct: 178 NENWKNESATVSSLRLDVVIKEMIRKSRTIAKQLIEKKRVKVNHTIVDSADFQLQANDLI 237

Query: 61  EVDG 64
            + G
Sbjct: 238 SIQG 241


>gi|21282803|ref|NP_645891.1| hypothetical protein MW1074 [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49486031|ref|YP_043252.1| hypothetical protein SAS1125 [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|87159985|ref|YP_493782.1| hypothetical protein SAUSA300_1085 [Staphylococcus aureus subsp.
           aureus USA300_FPR3757]
 gi|88194897|ref|YP_499697.1| hypothetical protein SAOUHSC_01156 [Staphylococcus aureus subsp.
           aureus NCTC 8325]
 gi|161509365|ref|YP_001575024.1| hypothetical protein USA300HOU_1128 [Staphylococcus aureus subsp.
           aureus USA300_TCH1516]
 gi|221140637|ref|ZP_03565130.1| hypothetical protein SauraJ_03241 [Staphylococcus aureus subsp.
           aureus str. JKD6009]
 gi|253733570|ref|ZP_04867735.1| ribosomal protein S4e [Staphylococcus aureus subsp. aureus TCH130]
 gi|258451889|ref|ZP_05699910.1| conserved hypothetical protein [Staphylococcus aureus A5948]
 gi|282919972|ref|ZP_06327701.1| conserved hypothetical protein [Staphylococcus aureus A9765]
 gi|284024115|ref|ZP_06378513.1| hypothetical protein Saura13_05969 [Staphylococcus aureus subsp.
           aureus 132]
 gi|294848184|ref|ZP_06788931.1| hypothetical protein SKAG_00243 [Staphylococcus aureus A9754]
 gi|297208167|ref|ZP_06924597.1| S4 domain-containing protein YlmH [Staphylococcus aureus subsp.
           aureus ATCC 51811]
 gi|300912245|ref|ZP_07129688.1| S4 domain-containing protein YlmH [Staphylococcus aureus subsp.
           aureus TCH70]
 gi|21204241|dbj|BAB94939.1| MW1074 [Staphylococcus aureus subsp. aureus MW2]
 gi|49244474|emb|CAG42902.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|87125959|gb|ABD20473.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           USA300_FPR3757]
 gi|87202455|gb|ABD30265.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           NCTC 8325]
 gi|160368174|gb|ABX29145.1| hypothetical protein USA300HOU_1128 [Staphylococcus aureus subsp.
           aureus USA300_TCH1516]
 gi|253728440|gb|EES97169.1| ribosomal protein S4e [Staphylococcus aureus subsp. aureus TCH130]
 gi|257860497|gb|EEV83324.1| conserved hypothetical protein [Staphylococcus aureus A5948]
 gi|282594688|gb|EFB99672.1| conserved hypothetical protein [Staphylococcus aureus A9765]
 gi|294824984|gb|EFG41406.1| hypothetical protein SKAG_00243 [Staphylococcus aureus A9754]
 gi|296886906|gb|EFH25809.1| S4 domain-containing protein YlmH [Staphylococcus aureus subsp.
           aureus ATCC 51811]
 gi|300886491|gb|EFK81693.1| S4 domain-containing protein YlmH [Staphylococcus aureus subsp.
           aureus TCH70]
 gi|302751014|gb|ADL65191.1| S4 RNA binding domain protein [Staphylococcus aureus subsp. aureus
           str. JKD6008]
 gi|315196921|gb|EFU27264.1| hypothetical protein CGSSa01_04105 [Staphylococcus aureus subsp.
           aureus CGS01]
 gi|320140994|gb|EFW32841.1| S4 domain protein [Staphylococcus aureus subsp. aureus MRSA131]
 gi|320143050|gb|EFW34840.1| S4 domain protein [Staphylococcus aureus subsp. aureus MRSA177]
 gi|329313859|gb|AEB88272.1| MW1074 protein [Staphylococcus aureus subsp. aureus T0131]
 gi|329725026|gb|EGG61522.1| S4 domain protein [Staphylococcus aureus subsp. aureus 21189]
 gi|329728857|gb|EGG65278.1| S4 domain protein [Staphylococcus aureus subsp. aureus 21193]
          Length = 268

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 2/64 (3%)

Query: 3   DKNIVQENFT--PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++N   E+ T    R+  VI      SR   +++I ++RVKVN  +++ A   + + D I
Sbjct: 178 NENWKNESATVSSLRLDVVIKEMIRKSRTIAKQLIEKKRVKVNHTIVDSADFQLQANDLI 237

Query: 61  EVDG 64
            + G
Sbjct: 238 SIQG 241


>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 = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/244 (9%), Positives = 66/244 (27%), Gaps = 39/244 (15%)

Query: 7   VQENFTPQRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           V++     R+ + +        SR  +++ I + +VKVNG + ++ +  +   + +EVD 
Sbjct: 6   VEKREEGWRLDQFLKEKTPSWISRSLIQKAIKEGKVKVNGQI-KKPSYKLKEGEIVEVDL 64

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               +    +       +           +       P       ++    ++    L  
Sbjct: 65  PEKPQEATVQPEEIELKVLYEDRDIVVIDKPGDMIVHPVPSKLSGTLVNALLHHCKDLQG 124

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK------GIVIQGICYGDMQVT 178
                   ++     +   V  V  +    Q      K        I++        +  
Sbjct: 125 VGGKLRPGIVHRLDKETSGVIVVAKNDFAHQSLSKQFKDRKVKKTYILLVKGRVKSDEGV 184

Query: 179 LDTQKGSNAWVTVG----------LRE--------------------GKNREIKKVFEFF 208
           +D     +  + +           + E                    G+  +I+   +  
Sbjct: 185 IDLPLARHPVLRIKMAVVETGKEAITEYRVLKRFDDVATLVLAFPKTGRTHQIRVHMKSL 244

Query: 209 NWKV 212
              +
Sbjct: 245 GHPI 248


>gi|156740575|ref|YP_001430704.1| hemolysin A [Roseiflexus castenholzii DSM 13941]
 gi|156231903|gb|ABU56686.1| hemolysin A [Roseiflexus castenholzii DSM 13941]
          Length = 272

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 1/54 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             R+ +++ + G+A +R   + +I    V+VNG+   +    V     IEV G
Sbjct: 3  KKVRLDQLLVQRGLAETRARAQALILAGEVRVNGVTRHKGGELVPDDAEIEVIG 56


>gi|295103716|emb|CBL01260.1| Uncharacterized conserved protein [Faecalibacterium prausnitzii
          SL3/3]
          Length = 71

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 13/65 (20%), Positives = 28/65 (43%), Gaps = 1/65 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          +    ++  ++  AG+  +  E + ++    VKVNG +         + D IE+DG  + 
Sbjct: 7  HTEFIKLDALLKFAGLCETGGEAKELVQGGAVKVNGEVCTMRGKKCRAGDIIELDGQSVE 66

Query: 69 KAERT 73
            +  
Sbjct: 67 IGQGQ 71


>gi|302382935|ref|YP_003818758.1| hemolysin A [Brevundimonas subvibrioides ATCC 15264]
 gi|302193563|gb|ADL01135.1| hemolysin A [Brevundimonas subvibrioides ATCC 15264]
          Length = 241

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ +++   G+  SR   +  I    V V+GI++  AA        + V
Sbjct: 1  MRLDQLLVSKGLIDSRARAKAAIQAGGVTVDGIVVTNAARAFDDDAIVTV 50


>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 = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 30/243 (12%), Positives = 61/243 (25%), Gaps = 40/243 (16%)

Query: 10  NFTPQRVSKV----IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           +    R+       +A     SR +V   I      V+G +  +  + +   + + +   
Sbjct: 22  DAAGTRLDAFWSARLASE-DISRAKVRAAIEAGLALVDGEICRKPGLKLRGGEALTLRLP 80

Query: 63  ---------DGV-PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
                    DG   L   +   L L       +   S     + V   L          G
Sbjct: 81  ETPSEAKAEDGELKLLYLDGDVLVLNKPAGLTIHPASSQPDGTLVNRLLHHFPDMRAMAG 140

Query: 113 RLDINTEGLLLLTN--------------------DGGLARVLELPSTQWLRVYRVRFHGQ 152
                   L   T+                    +  +A+                    
Sbjct: 141 DRPGIVHRLDKDTSGLLLVAQTESARLALAADFAERRVAKTYLALVHGRPERSDGVIELP 200

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           V +D  +  K  +V +G         L      G+ + + V +  G+  +I+        
Sbjct: 201 VGRDPKHPTKMAVVAKGGREAKSSWKLAWTAPDGTASLLEVAIATGRTHQIRVHMAAMGH 260

Query: 211 KVN 213
            + 
Sbjct: 261 PIV 263


>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 = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 6/55 (10%)

Query: 13 PQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          P R+ K ++R     A + SR  + R+IA+  V VNG  +      +   D I +
Sbjct: 15 PPRLDKALSRDVPEDAAL-SRTRLARLIAEGAVSVNGTPVTDPKSRISEGDSIAI 68


>gi|320458888|dbj|BAJ69509.1| conserved hypothetical protein [Bifidobacterium longum subsp.
          infantis ATCC 15697]
          Length = 257

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 13/63 (20%), Positives = 29/63 (46%), Gaps = 2/63 (3%)

Query: 3  DKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMST-DHI 60
           K  +       R+  ++  +G+  SR + +R+I    V+V+G  + + +  V +    +
Sbjct: 2  TKQHIDSATPLDRLDMMLVASGLVESRAKAQRLIKAGHVRVDGETITKPSFMVKAGHSEL 61

Query: 61 EVD 63
           VD
Sbjct: 62 AVD 64


>gi|297181969|gb|ADI18145.1| predicted rRNA methylase [uncultured Verrucomicrobiales bacterium
           HF0200_39L05]
          Length = 301

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 12/63 (19%), Positives = 27/63 (42%), Gaps = 1/63 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+   +  +     R+   +   G+  SR + +R +   +  VNG    +A+  V  +D 
Sbjct: 45  MEKNQLTPKPKKLARLDLALVERGLCESREKAKRAVMAGQALVNGQRAAKASDKVKPSDE 104

Query: 60  IEV 62
           + +
Sbjct: 105 VTL 107


>gi|298675322|ref|YP_003727072.1| RNA-binding S4 domain-containing protein [Methanohalobium
          evestigatum Z-7303]
 gi|298288310|gb|ADI74276.1| RNA-binding S4 domain protein [Methanohalobium evestigatum
          Z-7303]
          Length = 220

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 12/51 (23%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+   +   G   SR   +  IA  +VK++G ++++A+ +V   + ++V+
Sbjct: 1  MRLDVYLVENGYFTSRGRSKTAIASGKVKIDGRIVKKASKDVKPENKVQVE 51


>gi|213692730|ref|YP_002323316.1| hemolysin A [Bifidobacterium longum subsp. infantis ATCC 15697]
 gi|213524191|gb|ACJ52938.1| hemolysin A [Bifidobacterium longum subsp. infantis ATCC 15697]
          Length = 276

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 13/63 (20%), Positives = 29/63 (46%), Gaps = 2/63 (3%)

Query: 3  DKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMST-DHI 60
           K  +       R+  ++  +G+  SR + +R+I    V+V+G  + + +  V +    +
Sbjct: 21 TKQHIDSATPLDRLDMMLVASGLVESRAKAQRLIKAGHVRVDGETITKPSFMVKAGHSEL 80

Query: 61 EVD 63
           VD
Sbjct: 81 AVD 83


>gi|332653020|ref|ZP_08418765.1| hemolysin A [Ruminococcaceae bacterium D16]
 gi|332518166|gb|EGJ47769.1| hemolysin A [Ruminococcaceae bacterium D16]
          Length = 270

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 18/72 (25%), Positives = 31/72 (43%), Gaps = 1/72 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          R+   +   G+A SR++ + +I   +V V+   +++A   V     I+V G  LR   R 
Sbjct: 6  RLDVAMVERGLAESRQKAQAIIMAGQVYVDDQKVDKAGAPVKEEQVIQVRGKTLRYVSRG 65

Query: 74 RLWLYHKPIGLV 85
           L L        
Sbjct: 66 GLKLEKAMACWP 77


>gi|290968312|ref|ZP_06559854.1| ribosomal RNA large subunit methyltransferase J [Megasphaera
          genomosp. type_1 str. 28L]
 gi|290781671|gb|EFD94257.1| ribosomal RNA large subunit methyltransferase J [Megasphaera
          genomosp. type_1 str. 28L]
          Length = 265

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 1/60 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           + +R+  ++   G+A SR + +  I    V V    +++A         I V G  +  
Sbjct: 2  QSKERLDILLTERGLAESREKAKAAIMAGLVFVENRRVDKAGTKFSEDVRITVKGNAVPY 61


>gi|227499566|ref|ZP_03929673.1| conserved hypothetical protein [Anaerococcus tetradius ATCC 35098]
 gi|227218325|gb|EEI83579.1| conserved hypothetical protein [Anaerococcus tetradius ATCC 35098]
          Length = 255

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 11/48 (22%), Positives = 22/48 (45%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +I++    SR   + +I  + VKV+  ++   +  V     I V
Sbjct: 180 RLDNIISQILNCSRSRAKVLITGRMVKVDHQIIVDPSYQVSEASLISV 227


>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 = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 29/239 (12%), Positives = 63/239 (26%), Gaps = 33/239 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----E 61
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + I    E
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRIANIPREKVLGGERIEIIVE 69

Query: 62  VDGVP----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
           V+             +   +   + +      +V   +     + +   L          
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIAEVP 129

Query: 112 -----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR------------VRFHGQVD 154
                 RLD +T GL+++         L     +                        +D
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMD 189

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +         +   G         +     +   + + L  G+  +I+         + 
Sbjct: 190 RHATKRTLMAVHPMGKPA-VTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 247


>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 = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 37/252 (14%), Positives = 68/252 (26%), Gaps = 42/252 (16%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+ KV+A      SR  ++  I    V VNG   +     V   D + V   P       
Sbjct: 29  RLDKVLAGLMPGHSRSRLQGWIEAGHVLVNGQAAKV-RQPVGPGDVLTVWEQPAPESLAF 87

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-----RVISVGR 113
                   +  +    + +      +    +     + +   L          R   V R
Sbjct: 88  SPEPVDFDVIDSSSDWIVVNKPAGLVTHPGAGNWTGTLLNGLLHRFPELSRVARAGIVHR 147

Query: 114 LDINTEGLLLLTNDGGLARVLEL------PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           LD +T GL+++  +      L           ++L +      G    D+       + +
Sbjct: 148 LDKDTSGLMVVARNELAQTHLVRQLQARSMGREYLALAHGWLAGAGTVDRPIGRDARVPV 207

Query: 168 QGIC-----YGDMQVTLDTQKGSN-------AWVTVGLREGKNREIKKVFEFFNWKVNRL 215
           +                  Q+            V   L  G+  +I+         +  L
Sbjct: 208 RMSVERPIAAKPAITHYLPQRRGEAQEGERVTEVICRLETGRTHQIRVHLASLGHPL--L 265

Query: 216 IRISYGPFQLGT 227
               YG   L  
Sbjct: 266 ADTIYGGRALAG 277


>gi|329737381|gb|EGG73635.1| putative pseudouridine synthase B, ribosomal large subunit
           [Staphylococcus epidermidis VCU028]
          Length = 49

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 15/39 (38%), Positives = 24/39 (61%)

Query: 204 VFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +FE+F  +VN+L RI +GP  L  L AG  R ++   ++
Sbjct: 1   MFEYFGHQVNKLTRIQFGPIDLKGLNAGEGRVLTPHEVK 39


>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 = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 33/258 (12%), Positives = 72/258 (27%), Gaps = 46/258 (17%)

Query: 2   KDKNIVQENFTPQ---RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVM-- 55
           ++K +    +T +   R+ + +       SR  +++ I  + V VNG + + +   V   
Sbjct: 8   EEKTVFNYTYTGEDGLRLDQFVTNQFTDESRTTIKKWIKDKLVTVNGKVAKASQSLVNGD 67

Query: 56  ----------------------------STDHIEVDGVP--------LRKAERTR---LW 76
                                         D I V   P        +     T    L 
Sbjct: 68  LIGVEKPAPAEAEEFKPVAEKMALDIVFEDDDILVVNKPANLVVHPSVNHPTNTLVNGLL 127

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
            + +  G          R  +   L    + ++ V +     E L     +  + R+   
Sbjct: 128 YHVQENGSQLAVGRESFRPGIVHRLDKDTTGLLVVAKSQAALENLTKQVANHQMTRIYAG 187

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
                +          + + + + L K    +   +     T+  +      V   L  G
Sbjct: 188 LVYGEIFEAGGTIDAPIRRHEKDRL-KFETNEAGRHAVTHFTVKHRYVGYTLVNFQLETG 246

Query: 197 KNREIKKVFEFFNWKVNR 214
           +  +I+    F N  +  
Sbjct: 247 RTHQIRVHANFINHPIVD 264


>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 = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/217 (11%), Positives = 56/217 (25%), Gaps = 30/217 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--------------LRKAER 72
           SR  ++  I  QRV VNG + ++    V+  + + ++                 +   + 
Sbjct: 6   SRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDE 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGRLDINTEGLLLLTND 127
             + +      +V   +     + +   L          R   V RLD +T GL+++   
Sbjct: 66  DIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKT 125

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQ-----------DKLNLLKKGIVIQGICYGDMQ 176
                 L     +                                    V          
Sbjct: 126 VPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTH 185

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             +      +  + + L  G+  +I+         + 
Sbjct: 186 YRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 222


>gi|206890097|ref|YP_002249221.1| ribosomal protein S4 [Thermodesulfovibrio yellowstonii DSM 11347]
 gi|226695094|sp|B5YG23|RS4_THEYD RecName: Full=30S ribosomal protein S4
 gi|206742035|gb|ACI21092.1| ribosomal protein S4 [Thermodesulfovibrio yellowstonii DSM 11347]
          Length = 208

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI R G A +RR+  +++      VNG  ++  +  V   D IE+
Sbjct: 99  RLDNVIYRMGFAMNRRQARQLVRHGYFTVNGKKVDIPSYLVRPGDIIEI 147


>gi|160938272|ref|ZP_02085627.1| hypothetical protein CLOBOL_03168 [Clostridium bolteae ATCC
           BAA-613]
 gi|158438645|gb|EDP16402.1| hypothetical protein CLOBOL_03168 [Clostridium bolteae ATCC
           BAA-613]
          Length = 310

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/180 (13%), Positives = 55/180 (30%), Gaps = 2/180 (1%)

Query: 12  TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             +R+  ++ +  +A SR + + +I    V VNG   ++A  +   T  IEV G  L+  
Sbjct: 2   KKERLDVLMVQRNLAESREKAKALIMSGIVYVNGQKEDKAGTSFEETVQIEVRGNTLKYV 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            R  L L           +                  ++  G + +    +        L
Sbjct: 62  SRGGLKLEKAMSRFGVQLAGKVCMDVGAST-GGFTDCMLQNGAVKVYAVDVGHGQLAWKL 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
                +   +   +  V      D+ +   +    +      G ++  L  +      + 
Sbjct: 121 RNDDRVICMEKTNIRYVTPEDIGDRIEFASIDVSFISLTKVLGPVKQLLTDEGQVVCLIK 180


>gi|298370567|ref|ZP_06981882.1| ribosomal protein S4 [Neisseria sp. oral taxon 014 str. F0314]
 gi|298281177|gb|EFI22667.1| ribosomal protein S4 [Neisseria sp. oral taxon 014 str. F0314]
          Length = 206

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 14/60 (23%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNG ++   +  V + D I V     ++    
Sbjct: 97  RLDNVVYRLGFGSTRAEARQLVSHKAITVNGQVVNIPSYQVKAGDIIAVREKAKKQVRIQ 156


>gi|255527584|ref|ZP_05394448.1| S4 domain protein YaaA [Clostridium carboxidivorans P7]
 gi|296186782|ref|ZP_06855183.1| S4 domain protein YaaA [Clostridium carboxidivorans P7]
 gi|255508717|gb|EET85093.1| S4 domain protein YaaA [Clostridium carboxidivorans P7]
 gi|296048496|gb|EFG87929.1| S4 domain protein YaaA [Clostridium carboxidivorans P7]
          Length = 68

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 18/68 (26%), Positives = 26/68 (38%), Gaps = 8/68 (11%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAG---IASRREVERMIAQQRVKVNGILLERAAVNVMST 57
          MK+  I   N    ++   +   G   + S  E +  I    VKVN  +  R    +   
Sbjct: 1  MKEIEI---NTDIIKLDSFLKWCGAVSLGS--EAKMFIQDGLVKVNNEIEVRRGKKLTKG 55

Query: 58 DHIEVDGV 65
          D IE DG 
Sbjct: 56 DIIEFDGE 63


>gi|13357999|ref|NP_078273.1| hemolysin [Ureaplasma parvum serovar 3 str. ATCC 700970]
 gi|168281604|ref|ZP_02689271.1| ribosomal RNA large subunit methyltransferase J [Ureaplasma
          parvum serovar 14 str. ATCC 33697]
 gi|168307749|ref|ZP_02690424.1| ribosomal RNA large subunit methyltransferase J [Ureaplasma
          parvum serovar 1 str. ATCC 27813]
 gi|170762432|ref|YP_001752522.1| ribosomal RNA large subunit methyltransferase J [Ureaplasma
          parvum serovar 3 str. ATCC 27815]
 gi|11279182|pir||C82891 hemolysin UU436 [imported] - Ureaplasma urealyticum
 gi|6899427|gb|AAF30848.1|AE002140_7 hemolysin [Ureaplasma parvum serovar 3 str. ATCC 700970]
 gi|168828009|gb|ACA33271.1| ribosomal RNA large subunit methyltransferase J [Ureaplasma
          parvum serovar 3 str. ATCC 27815]
 gi|171902941|gb|EDT49230.1| ribosomal RNA large subunit methyltransferase J [Ureaplasma
          parvum serovar 1 str. ATCC 27813]
 gi|182676028|gb|EDT87933.1| ribosomal RNA large subunit methyltransferase J [Ureaplasma
          parvum serovar 14 str. ATCC 33697]
          Length = 247

 Score = 52.1 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          QR+   +       +R +   +I + RV VN   + + +  V  TD +E+
Sbjct: 3  QRLDHYLKNTNQCETRSKAIDLIKRGRVFVNNFQVLKPSFLVKQTDSVEI 52


>gi|292670719|ref|ZP_06604145.1| hemolysin A [Selenomonas noxia ATCC 43541]
 gi|292647665|gb|EFF65637.1| hemolysin A [Selenomonas noxia ATCC 43541]
          Length = 269

 Score = 51.7 bits (122), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 14/59 (23%), Positives = 26/59 (44%), Gaps = 1/59 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
            +R+  ++   G A SR   +R+I   +V V+   +++A   V     + V G  L  
Sbjct: 2  KKERLDLLLVARGFAASRERAKRLIMAGQVLVDEQRVDKAGTTVSPLSSLRVVGEDLPY 60


>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 = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 34/250 (13%), Positives = 77/250 (30%), Gaps = 39/250 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK+  I++ +    R+   +A      SR  ++++     + VN  +  ++   V   D+
Sbjct: 1   MKE-FILECDTDGVRIDSWLAGNLEDYSRSYIQKLCLDGNIWVN-EVQAKSNYKVKPGDN 58

Query: 60  IEV--------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I+V        D  P      +   ++  + +      +V         + V   +    
Sbjct: 59  IKVSVPDAEILDVEPEDIPLDIVYEDKHIIVINKPKGMVVHPAVGNYSGTLVNALMKHCG 118

Query: 106 S---------RVISVGRLDINTEGLLLLTNDGGLARVLELP-------------STQWLR 143
                     R   V R+D +T GLL++         L                    + 
Sbjct: 119 DSLSDINGVIRPGIVHRIDKDTSGLLVVAKSNIAHERLSEKLKTHDIKREYIALVDGIIY 178

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
               +    + +  +   K  +  Q          +  +  S  +V + L  G+  +I+ 
Sbjct: 179 ENSGKIDAPIGRHPVERKKMSVNTQNGRNAITHFKVLERFPSATYVQLKLETGRTHQIRV 238

Query: 204 VFEFFNWKVN 213
              + N  + 
Sbjct: 239 HMSYINHPII 248


>gi|163816004|ref|ZP_02207374.1| hypothetical protein COPEUT_02184 [Coprococcus eutactus ATCC 27759]
 gi|158448814|gb|EDP25809.1| hypothetical protein COPEUT_02184 [Coprococcus eutactus ATCC 27759]
          Length = 214

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 1/63 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  +I R G A +RRE  +++  + V VNG  +   + +V   D IE+           
Sbjct: 105 RLDNIIFRLGFARTRREARQIVDHKHVLVNGKCVNIPSYSVKPGDKIEIREKSKSLQRYK 164

Query: 74  RLW 76
            + 
Sbjct: 165 DIM 167


>gi|119773378|ref|YP_926118.1| 30S ribosomal protein S4 [Shewanella amazonensis SB2B]
 gi|152112259|sp|A1S242|RS4_SHEAM RecName: Full=30S ribosomal protein S4
 gi|119765878|gb|ABL98448.1| SSU ribosomal protein S4P [Shewanella amazonensis SB2B]
          Length = 206

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + V VNG ++   +  V + D + +
Sbjct: 97  RLDNVVYRMGFGSTRAEARQLVSHKSVMVNGRVVNIPSFKVSANDVVSI 145


>gi|288906416|ref|YP_003431638.1| Ribosomal protein S4 [Streptococcus gallolyticus UCN34]
 gi|306832453|ref|ZP_07465605.1| 30S ribosomal protein S4 [Streptococcus gallolyticus subsp.
           gallolyticus TX20005]
 gi|325979478|ref|YP_004289194.1| 30S ribosomal protein S4 [Streptococcus gallolyticus subsp.
           gallolyticus ATCC BAA-2069]
 gi|288733142|emb|CBI14723.1| Ribosomal protein S4 [Streptococcus gallolyticus UCN34]
 gi|304425353|gb|EFM28473.1| 30S ribosomal protein S4 [Streptococcus gallolyticus subsp.
           gallolyticus TX20005]
 gi|325179406|emb|CBZ49450.1| 30S ribosomal protein S4 [Streptococcus gallolyticus subsp.
           gallolyticus ATCC BAA-2069]
          Length = 203

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVTPGQVISV 142


>gi|159039806|ref|YP_001539059.1| RNA-binding S4 domain-containing protein [Salinispora arenicola
           CNS-205]
 gi|157918641|gb|ABW00069.1| RNA-binding S4 domain protein [Salinispora arenicola CNS-205]
          Length = 208

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V+ RAG A SR    +++      VNG  ++  +  V   D +EV G 
Sbjct: 99  RLDNVVYRAGYAKSRDMARQLVKHGHFTVNGRKVDIPSYRVKEHDIVEVRGK 150


>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 = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 16/54 (29%), Positives = 29/54 (53%)

Query: 10 NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            TP R+  V+A    +SR +V   I   RV+VNG +  ++++ +   + + VD
Sbjct: 10 TATPGRLDAVLAGLADSSRSQVSAWIDAGRVRVNGQVTTKSSLKLRGGETLIVD 63


>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 = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 33/267 (12%), Positives = 73/267 (27%), Gaps = 42/267 (15%)

Query: 8   QENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
            +   P RV K +      A+R ++++      ++VN  ++++    V + D +      
Sbjct: 25  SKGQEPLRVDKFLMNFVENATRNKIQKAAKNGSIQVNNKVVKQ-NYKVKAGDVVRAMFEH 83

Query: 67  ---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                          +   +   L +      +V         + +   +  I +     
Sbjct: 84  PPHEFLLTPEDIPLDIIYEDDDLLVVNKPAGMVVHPGHGNYSGTLINALIHHIDNLPNNS 143

Query: 107 --RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY-------------RVRFHG 151
             R   V R+D +T GLL++         L                             G
Sbjct: 144 SERPGLVHRIDKDTSGLLVVAKTEHAMTHLSKQFFNKTTEREYVAIVWGNVVDDEGTIEG 203

Query: 152 QVDQDKLNLLKKGIVIQGICY--GDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
            + +   N L+  +                 +  + G    V   L  G+  +I+   ++
Sbjct: 204 NIGRHPKNRLQNTVFKDDEEEQGKPAVTHYKVLERLGYVTQVACKLETGRTHQIRVHMKY 263

Query: 208 FNWKVNRLIRISYGPFQLGTLLAGSTR 234
               +    R   G   L        +
Sbjct: 264 IGHTLFNDERYG-GNAILKGTSFTKYK 289


>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 = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/239 (10%), Positives = 58/239 (24%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E+   QR+ + +A      SR  ++  I    V+VN  +       ++  + +E+  
Sbjct: 10  TVSESQLGQRLDQALAELFPDYSRSRIKAWILDGLVRVNRRVTAVPKEKMLGGESVEIQA 69

Query: 63  --------------------DGVPLRKAERTRLWLYHKPIG---LVTTHSDPDGRSTVFD 99
                               D   L   +   L ++         V           V  
Sbjct: 70  FIEEAPRWEAQAIPLNIVYEDDDILVINKPRDLVVHPGAGNADGTVLNALLHYFPPIVDV 129

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--- 156
               I  R+       +     +        +      + ++  V           +   
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQAREITREYEAVAIGTMTAGGTLEQPI 189

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+      N  + 
Sbjct: 190 ARHATKRTHMAVHPMGKPAVTNYRIMEHFRAHTRLRLRLETGRTHQIRVHMAHINHPLV 248


>gi|163783136|ref|ZP_02178130.1| 30S ribosomal protein S4 [Hydrogenivirga sp. 128-5-R1-1]
 gi|159881470|gb|EDP74980.1| 30S ribosomal protein S4 [Hydrogenivirga sp. 128-5-R1-1]
          Length = 211

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A+ RR+  +++A   + VNG  ++     V   D IEV
Sbjct: 99  RLDNVVYRLGFATTRRQARQLVAHGHILVNGRKVDIPHYEVEPGDIIEV 147


>gi|304321305|ref|YP_003854948.1| Hemolysin HlyA [Parvularcula bermudensis HTCC2503]
 gi|303300207|gb|ADM09806.1| Hemolysin HlyA [Parvularcula bermudensis HTCC2503]
          Length = 243

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+   +  AG   SR   +++I    V VNG+ + +A  ++  TD +E  G 
Sbjct: 1  MRLDSYLVEAGHVRSRERAKKVIGDGYVWVNGVQVRKAGRSLQPTDRVEFRGE 53


>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 = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/239 (10%), Positives = 64/239 (26%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           IV  +   QR+ + +A      SR  ++  I   +V+VNG L+ +    ++  + I +D 
Sbjct: 10  IVAGSQLGQRLDQALAELFPDYSRSRIKEWILDNKVQVNGKLINKPKEKMLGGEDISIDA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
           +               +   +   L +      +V   +     + +   L         
Sbjct: 70  IIEEDARWEPQDIELNVVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLYRYPKIADV 129

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--- 156
                  R+       +     +        +  L   + ++  +           +   
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAIALGCMTAGGMVEEPI 189

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V            +     ++  + + L  G+  +I+         + 
Sbjct: 190 SRHPTKRTHMAVHPMGKPAITHYRVLEHFRAHTRLRLRLETGRTHQIRVHMAHIKHPLV 248


>gi|154483650|ref|ZP_02026098.1| hypothetical protein EUBVEN_01354 [Eubacterium ventriosum ATCC
           27560]
 gi|149735560|gb|EDM51446.1| hypothetical protein EUBVEN_01354 [Eubacterium ventriosum ATCC
           27560]
          Length = 275

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/178 (12%), Positives = 50/178 (28%), Gaps = 2/178 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++ + G+A SR + + +I    V V+    ++A        +IEV G  L+   R
Sbjct: 3   ERLDVLLVKRGLAPSREKAKAIIMSGIVFVDNEREDKAGTTFDEKVNIEVRGKTLKYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L                              ++  G + + +  +        L +
Sbjct: 63  GGLKLEKAMDVFGVKIEGKTCMDVGAST-GGFTDCMLQNGAVKVYSVDVGHGQLAWKLVQ 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +       +  V      D      +    +        ++  L         + 
Sbjct: 122 DDRVICMDRTNIRYVTPDQIDDVLDFASIDVSFISLTKVLLPVKNLLKENGQIVCLIK 179


>gi|169831190|ref|YP_001717172.1| hemolysin A [Candidatus Desulforudis audaxviator MP104C]
 gi|169638034|gb|ACA59540.1| hemolysin A [Candidatus Desulforudis audaxviator MP104C]
          Length = 274

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 13/55 (23%), Positives = 22/55 (40%), Gaps = 1/55 (1%)

Query: 11 FTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             +R+  ++   G   SR      I    V VNG+ +++    +     IEV G
Sbjct: 2  SRKERLDILLHSRGCFPSRERARSAIMAGVVFVNGVRVDKPGTKLDPHADIEVRG 56


>gi|292669832|ref|ZP_06603258.1| 30S ribosomal protein S4 [Selenomonas noxia ATCC 43541]
 gi|292648629|gb|EFF66601.1| 30S ribosomal protein S4 [Selenomonas noxia ATCC 43541]
          Length = 197

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +RR+  +++      VNG  ++  +  V   D IEV
Sbjct: 88  RLDNVVFRLGLANTRRQARQLVRHGHFTVNGKRVDIPSALVREGDVIEV 136


>gi|120553676|ref|YP_958027.1| ribosomal protein S4 [Marinobacter aquaeolei VT8]
 gi|152060959|sp|A1TYM1|RS4_MARAV RecName: Full=30S ribosomal protein S4
 gi|120323525|gb|ABM17840.1| SSU ribosomal protein S4P [Marinobacter aquaeolei VT8]
          Length = 206

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + V VN   +   +  V   D + V
Sbjct: 97  RLDNVVYRMGFGSTRAEARQLVSHKAVLVNDKPVNIPSYQVKPGDVVSV 145


>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 = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 38/242 (15%), Positives = 76/242 (31%), Gaps = 42/242 (17%)

Query: 27  SRREVERMIAQQRVKV-NGILL---------ERAAVNVMSTDHIEVDGVPLR-KAERTRL 75
           SRR+    I    + + NG+           +   V +   D IE + +PL    E   L
Sbjct: 28  SRRK----IKNNGICLQNGVPASMKDLVHQGDSLEVILQPKDTIEAEDIPLSVAYEDDYL 83

Query: 76  WLYHKPIGLVTTHSDPDGRST------VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + +KP G++   +  +   T       +  +         V RLD NT GL L+  +  
Sbjct: 84  IVVNKPPGMLMHQTSSERFGTLANAIMYYYKVHGYDHDYHPVHRLDRNTSGLCLIAKESY 143

Query: 130 LARVLELPSTQW----------LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           +  + +     +               +           + + K    +         T 
Sbjct: 144 VQHLFDKNRLFYARTYTALAQGRFPAMLATVHTPIGRDPDSIIKRNTREDGKEAHSDFTR 203

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                  + + + L  G+  +I+    +    +        G      L  GS R ++++
Sbjct: 204 LAVCDDFSLIRITLHTGRTHQIRVHSAYLGHPL-------IG----DDLYGGSRRFLNRQ 252

Query: 240 IL 241
            L
Sbjct: 253 AL 254


>gi|288818043|ref|YP_003432390.1| ribosomal protein S4 [Hydrogenobacter thermophilus TK-6]
 gi|288787442|dbj|BAI69189.1| ribosomal protein S4 [Hydrogenobacter thermophilus TK-6]
 gi|308751644|gb|ADO45127.1| ribosomal protein S4 [Hydrogenobacter thermophilus TK-6]
          Length = 209

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +RR+  +MIA   + VNG  ++  +  V   D IE+
Sbjct: 99  RLDNVVYRLGMAVTRRQARQMIAHGHILVNGKKVDIPSYRVQVGDIIEL 147


>gi|89093551|ref|ZP_01166499.1| pseudouridine synthase [Oceanospirillum sp. MED92]
 gi|89082241|gb|EAR61465.1| pseudouridine synthase [Oceanospirillum sp. MED92]
          Length = 322

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/238 (11%), Positives = 68/238 (28%), Gaps = 32/238 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVN--------VMST 57
           V ++   +R+ + +A+     SR  ++  I    + VNG + ++            + + 
Sbjct: 11  VTDDLVGKRLDQAVAQLFPDYSRSRLQGWIKDGSLTVNGEV-KKPREKLLGGEAIAIDAN 69

Query: 58  DHIEVDGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
             +  D  P      +   +   L +      +V         + +   L          
Sbjct: 70  LEVIEDHKPQNIPLDIVYEDEHILVINKPAGLVVHPAVGHRDGTLLNALLYHCPDIAQVP 129

Query: 112 -----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----------VDQ 155
                 RLD++T GL+++         L     +                          
Sbjct: 130 RAGIVHRLDMDTTGLMVVAKTIAAQTELVEQLQERSMGREYEAVVNGVMTGGGVVDEPMG 189

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 +K  V+           +  +  S+  + + L  G+  +I+      N+ + 
Sbjct: 190 RHSKNRQKMAVVGVGKEAVTHYRVLKKLRSHTHIRLKLETGRTHQIRVHMSHINYPLV 247


>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 = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 31/236 (13%), Positives = 63/236 (26%), Gaps = 40/236 (16%)

Query: 13  PQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMST------------- 57
            QR+ +V A    A  SR  +   I   R+ V+G ++      V                
Sbjct: 17  GQRLDQV-AAQLFAEHSRSRLSAWIKDGRLTVDGAVIR-PRDIVHGGAILELTAEQEAQG 74

Query: 58  ----DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
                 IE+D   +   +   L +      +V   +     + +   L  I   +     
Sbjct: 75  EWVAQDIELD---IVYEDDDILVINKPAGLVVHPAAGHADGTLLNALLHHIPDIINVPRC 131

Query: 114 LDINTEG----------------LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
             ++                     L+T     +            V             
Sbjct: 132 GIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVVAGGKINAPIGRH 191

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               ++  V++G         +  +  S+  V V L  G+  +I+      N+ + 
Sbjct: 192 GQQRQRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINFPLV 247


>gi|297180028|gb|ADI16253.1| pseudouridylate synthases, 23S RNA-specific [uncultured bacterium
           HF0010_16H03]
          Length = 309

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 38/232 (16%), Positives = 74/232 (31%), Gaps = 34/232 (14%)

Query: 14  QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------G 64
           QR+ K         SR ++++ I + R+ VNG L  +   +V   D IE++         
Sbjct: 12  QRLDKAATELFDEYSRTQIKKWILEGRILVNGDL-SKPRDSVHENDEIEINPTKERKVSW 70

Query: 65  VPLRKAERTR------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
            P      T       + +   P  ++   S     +     +          R   V R
Sbjct: 71  EPQNINFETYHECEDFIIINKPPGLIMHPGSGCYDGTLANGLINKYPDLENLPRCGIVHR 130

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR------------FHGQVDQDKLNLL 161
           LD +T G+LL+  + G          +     +                  + +DK N  
Sbjct: 131 LDKDTSGVLLVARNEGFRNYFIQLMQERRVTKKYTAIVVGSTLGSFSIEDPIGRDKSNRT 190

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           K  +   G        T +   G+ + + + +  G+  +I+         + 
Sbjct: 191 KMSVRPDGKEALTFVKTSERI-GNYSILDIAIETGRTHQIRVHLLSKKLPII 241


>gi|227506077|ref|ZP_03936126.1| S4 domain protein [Corynebacterium striatum ATCC 6940]
 gi|227197359|gb|EEI77407.1| S4 domain protein [Corynebacterium striatum ATCC 6940]
          Length = 95

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 10/35 (28%), Positives = 19/35 (54%)

Query: 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          E + +IAQ  V+VNG ++ +    +   D + + G
Sbjct: 28 EAKELIAQGEVQVNGEVVTQRGATLHPGDEVSIAG 62


>gi|194039345|ref|XP_001926979.1| PREDICTED: zinc finger protein 318 [Sus scrofa]
          Length = 2282

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 19/112 (16%), Positives = 33/112 (29%), Gaps = 5/112 (4%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R  +  H  +E+         SS +                +        ++    + + 
Sbjct: 7   RSSVFSHRPKESGGGGPRTGRSSGSSSGPARRTSPPSSGSSSSRTPARRPRSPSGHRGRR 66

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQR-----EENHRRSPSFPSKRSLR 348
           A+P   R    +    +G  +S     G+R         R SPS P  R  R
Sbjct: 67  ASPSPPRGRRGSPSPPRGRRASPSPPRGRRVSPSPPRARRGSPSSPPPRGRR 118



 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 18/108 (16%), Positives = 30/108 (27%), Gaps = 2/108 (1%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                + V    P  S     R   +  S           +S   +  +  ++  +P   
Sbjct: 3   RSGARSSVFSHRPKESGGGGPRTGRSSGSSSGPARRTSPPSSGSSSSRTPARRPRSPSGH 62

Query: 308 RNLASNVWMAKGIHSSFLSDSGQR--EENHRRSPSFPSKRSLRRTSAK 353
           R   ++    +G   S     G+R      R     PS    RR S  
Sbjct: 63  RGRRASPSPPRGRRGSPSPPRGRRASPSPPRGRRVSPSPPRARRGSPS 110



 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 15/115 (13%), Positives = 29/115 (25%), Gaps = 2/115 (1%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            +  R                +   SS T  R   +         +       + +    
Sbjct: 23  PRTGRSSGSSSGPARRTSPPSSGSSSSRTPARRPRSPSGHRGRRASPSPPRGRRGSPSPP 82

Query: 298 QKKLATPVHRRNLA--SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
           + + A+P   R      +   A+    S     G+R      +    S R   R+
Sbjct: 83  RGRRASPSPPRGRRVSPSPPRARRGSPSSPPPRGRRLFPPGSAGFRGSSRGDSRS 137



 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 13/112 (11%), Positives = 23/112 (20%), Gaps = 5/112 (4%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN-----GLSKQKKLA 302
                   +         +    R    S  P    R   +  +           ++   
Sbjct: 50  RTPARRPRSPSGHRGRRASPSPPRGRRGSPSPPRGRRASPSPPRGRRVSPSPPRARRGSP 109

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +    R        + G   S   DS        R        S RR+   +
Sbjct: 110 SSPPPRGRRLFPPGSAGFRGSSRGDSRSDFARDGRGDHPGDSGSRRRSPGLR 161


>gi|330686325|gb|EGG97930.1| S4 domain protein [Staphylococcus epidermidis VCU121]
          Length = 243

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 27/60 (45%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            I     +  R+  V+      SR   +++I ++RVKVN  +++     +   D + + G
Sbjct: 157 KIQSSTVSALRLDVVLKDMIHKSRSIAKQLIEKKRVKVNHTIIDSPDFQLEMNDLLSIQG 216


>gi|257126747|ref|YP_003164861.1| 30S ribosomal protein S4 [Leptotrichia buccalis C-1013-b]
 gi|260891350|ref|ZP_05902613.1| ribosomal protein S4 [Leptotrichia hofstadii F0254]
 gi|257050686|gb|ACV39870.1| ribosomal protein S4 [Leptotrichia buccalis C-1013-b]
 gi|260858733|gb|EEX73233.1| ribosomal protein S4 [Leptotrichia hofstadii F0254]
          Length = 195

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI R G   +RR+  ++++   + +NG  +  A+  V   D I V
Sbjct: 89  RLDNVIYRLGFGATRRQARQIVSHGHILINGKRVNIASYRVKQGDVITV 137


>gi|331701254|ref|YP_004398213.1| 30S ribosomal protein S4 [Lactobacillus buchneri NRRL B-30929]
 gi|329128597|gb|AEB73150.1| ribosomal protein S4 [Lactobacillus buchneri NRRL B-30929]
          Length = 203

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +R+  ++ R G+A+ RR+  +++    + V+G  ++  +  V     I V
Sbjct: 93  ERLDNMVYRLGLATTRRQARQLVNHGHITVDGKRVDIPSYEVQPGQVISV 142


>gi|297171518|gb|ADI22517.1| predicted rRNA methylase [uncultured verrucomicrobium
          HF0500_08N17]
          Length = 257

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 12/63 (19%), Positives = 27/63 (42%), Gaps = 1/63 (1%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          M+   +  +     R+   +   G+  SR + +R +   +  VNG    +A+  V  +D 
Sbjct: 1  MEKNQLTPKPAKLARLDLALVERGLCESREKAKRAVMAGQALVNGQRAAKASDKVKPSDE 60

Query: 60 IEV 62
          + +
Sbjct: 61 VTL 63


>gi|57651761|ref|YP_186067.1| YlmH protein [Staphylococcus aureus subsp. aureus COL]
 gi|57285947|gb|AAW38041.1| YlmH protein [Staphylococcus aureus subsp. aureus COL]
          Length = 259

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 2/64 (3%)

Query: 3   DKNIVQENFT--PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++N   E+ T    R+  VI      SR   +++I ++RVKVN  +++ A   + + D I
Sbjct: 169 NENWKNESATVSSLRLDVVIKEMIRKSRTIAKQLIEKKRVKVNHTIVDSADFQLQANDLI 228

Query: 61  EVDG 64
            + G
Sbjct: 229 SIQG 232


>gi|317471813|ref|ZP_07931150.1| hemolysin TlyA family protein [Anaerostipes sp. 3_2_56FAA]
 gi|316900704|gb|EFV22681.1| hemolysin TlyA family protein [Anaerostipes sp. 3_2_56FAA]
          Length = 271

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 26/177 (14%), Positives = 54/177 (30%), Gaps = 3/177 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++ + G+A SR + + +I    V V+G   ++A   V     IE+ G  L+   R
Sbjct: 3   ERLDVLLVKKGLAASREKAKAIIMSGVVFVDGQREDKAGTMVKEELPIEIKGKTLKYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L           +D                 ++  G   + +  +     D GL  
Sbjct: 63  GGLKLEKAMKQFNIQLTDRVCMDVGAST-GGFTHCMLLNGAKKVYSVDVGHGQLDWGLRN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
              +   +   +  V      +      +     I           +  + G    +
Sbjct: 122 DERVVCMERTNMRYVTPEDIEEPAGFVSIDVSF-ISLTKILPAVYGILEKGGEVTAL 177


>gi|209548167|ref|YP_002280084.1| hemolysin A [Rhizobium leguminosarum bv. trifolii WSM2304]
 gi|209533923|gb|ACI53858.1| hemolysin A [Rhizobium leguminosarum bv. trifolii WSM2304]
          Length = 248

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 9  ENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +   QR+ +++   G  ASR      + +  V++ G ++ +A   +     IE+D 
Sbjct: 2  SDQNSQRLDQLLVSRGLFASRSRARDAVQRGTVRIAGQVVTKAGALIGDDAAIEIDD 58


>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 = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 39/254 (15%), Positives = 85/254 (33%), Gaps = 43/254 (16%)

Query: 2   KDKN-IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           K+ N IV E+    R+   I  R  + SR  ++ +I ++++K+N  ++   +  V+S D 
Sbjct: 3   KNINLIVGEDENNLRLDVFINKRENLISRSRIKNLILKEKLKINDQIINSPSKKVLSGDE 62

Query: 60  IE-------------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I               +       E   L + +KP G++      +   T+ + L     
Sbjct: 63  INLQIPEPKEASLKPYNFKLQIVYEDDDLLIINKPAGIIMHPGAGNYDETIVNALMHYNK 122

Query: 107 RVISV----------GRLDINTEGLLLLTNDGGLARVLELP-------------STQWLR 143
             +S            R+D +T GL+++  +      L                    LR
Sbjct: 123 DSLSTIGDELRPGIVHRIDKDTSGLIVIAKNNETHENLSHQFSEHTITRVYQLLIWGKLR 182

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGIC-----YGDMQVTLDTQKGSNAWVTVGLREGKN 198
               +    + +   N     +           Y  +++  + +  + + V   L  G+ 
Sbjct: 183 PSSGKIDTFITRSSKNRQMMEVSNSKGKRAITNYKTIEIFENDKTPTLSLVECRLETGRT 242

Query: 199 REIKKVFEFFNWKV 212
            +I+         +
Sbjct: 243 HQIRVHMTHMGNSI 256


>gi|323440963|gb|EGA98670.1| YlmH protein [Staphylococcus aureus O11]
 gi|323442280|gb|EGA99910.1| YlmH protein [Staphylococcus aureus O46]
          Length = 268

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 16/60 (26%), Positives = 29/60 (48%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            I     +  R+  VI      SR   +++I ++RVKVN  +++ A   + + D I + G
Sbjct: 182 KIESATVSSLRLDVVIKEMIRKSRTIAKQLIEKKRVKVNHTIVDSANFQLQANDLISIQG 241


>gi|227496317|ref|ZP_03926613.1| hemolysin A [Actinomyces urogenitalis DSM 15434]
 gi|226834155|gb|EEH66538.1| hemolysin A [Actinomyces urogenitalis DSM 15434]
          Length = 287

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   + R G+A SR    +++    V ++G ++ + A  V     IEV
Sbjct: 5  IRIDSELVRRGLARSRTHAAQLVTDGHVTLDGAVVTKPARQVNPAQAIEV 54


>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 = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/238 (11%), Positives = 65/238 (27%), Gaps = 38/238 (15%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--------IEVD 63
            +RV + ++R     SR   ++++ +  V + G+ +++        D         +EVD
Sbjct: 12  GERVDQFLSRQLPQLSRSAAQKLLEEGAVTLKGLPVKK-NYKTAEGDELVLSLPDPVEVD 70

Query: 64  GVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------- 107
            VP      +   +   + +      +V   +     + V   L                
Sbjct: 71  VVPQDIPLDVVYEDGDVIVINKPVGMVVHPAAGHPDGTLVNALLYHCGKSLSGINGELRP 130

Query: 108 ------------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
                       +I   + D     L     D  L R  E  +    +         + +
Sbjct: 131 GIVHRIDRDTSGLIIAAKSDFAHLALAEQLQDHSLYREYEAVAVGGFKEDEGTVRAPIAR 190

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +  K  +            T+  +      +   L  G+  +I+         + 
Sbjct: 191 HPTDRKKMAVNFLQGREAVTHYTVLERFSGCTHLQCRLETGRTHQIRVHMAHIGHPLL 248


>gi|110004584|emb|CAK98921.1| probable pseudouridine synthase d protein [Spiroplasma citri]
          Length = 306

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/243 (11%), Positives = 70/243 (28%), Gaps = 41/243 (16%)

Query: 11  FTPQRVSKVIA-----RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
            +  R+ K++           SR +++ +I Q++V+VNG ++  A       DH+ ++  
Sbjct: 9   SSSARIDKILTDYFKTNTTPFSRTKIQELIKQEKVQVNGQVVR-ANYVSQIGDHVIIEFP 67

Query: 64  ------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                        + +   +   + +      +V         + V   L        + 
Sbjct: 68  SAKASELTPLAIPLTILYEDSYLMVIDKPNNLVVHPAPGHQNDTLVNALLARGVQWSTAS 127

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLR---------------------VYRVRFH 150
           G         +     G L           L+                       R +  
Sbjct: 128 GEQRPGIVHRIDRQTTGTLIIAKNDVVHHQLQQQIQTKQLQRRYLALVHGQIIENRAKID 187

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + +D  N  K  +  +        + +  +     ++   L  G+  +I+   ++ N 
Sbjct: 188 APIGRDPNNRKKMVVTAKNSKKALTNIVVIERFNDYTYIECELESGRTHQIRAHLKYINH 247

Query: 211 KVN 213
            + 
Sbjct: 248 PIV 250


>gi|126454036|ref|YP_001068009.1| 30S ribosomal protein S4 [Burkholderia pseudomallei 1106a]
 gi|167847640|ref|ZP_02473148.1| 30S ribosomal protein S4 [Burkholderia pseudomallei B7210]
 gi|242314939|ref|ZP_04813955.1| 30S ribosomal protein S4 [Burkholderia pseudomallei 1106b]
 gi|171855208|sp|A3P088|RS4_BURP0 RecName: Full=30S ribosomal protein S4
 gi|126227678|gb|ABN91218.1| 30S ribosomal protein S4 [Burkholderia pseudomallei 1106a]
 gi|242138178|gb|EES24580.1| 30S ribosomal protein S4 [Burkholderia pseudomallei 1106b]
          Length = 207

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 16/73 (21%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + V VNGI+    +  V + D + +     ++A   
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAVTVNGIVANIPSQQVKAGDVVAIREKAKKQARIV 157

Query: 74  RLWLYHKPIGLVT 86
                 +  G+ +
Sbjct: 158 EALSLAEQGGMPS 170


>gi|296875556|ref|ZP_06899628.1| 30S ribosomal protein S4 [Streptococcus parasanguinis ATCC 15912]
 gi|312866896|ref|ZP_07727109.1| ribosomal protein S4 [Streptococcus parasanguinis F0405]
 gi|296433480|gb|EFH19255.1| 30S ribosomal protein S4 [Streptococcus parasanguinis ATCC 15912]
 gi|311097679|gb|EFQ55910.1| ribosomal protein S4 [Streptococcus parasanguinis F0405]
          Length = 203

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVTPGQVISV 142


>gi|290955821|ref|YP_003487003.1| hypothetical protein SCAB_12741 [Streptomyces scabiei 87.22]
 gi|260645347|emb|CBG68433.1| RarA (conservon) homolog [Streptomyces scabiei 87.22]
          Length = 688

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 14/113 (12%), Positives = 28/113 (24%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           +R    P  ++ A     +    ++    DRP           R       +   ++ + 
Sbjct: 388 VRHPDTPRHVQAAPAQRYSGSGPADGPAADRPAADQPDRTATGRPSPAQPARPAGTRPEP 447

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              P      AS         S      G+    H   P   ++      +  
Sbjct: 448 GHRPAPGPARASVPRQQGPGRSGGQQTPGRGGGGHVPLPVRGARGERPNPAEA 500



 Score = 42.9 bits (99), Expect = 0.079,   Method: Composition-based stats.
 Identities = 15/105 (14%), Positives = 25/105 (23%), Gaps = 2/105 (1%)

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           LG    +  Q              R  P    + P             +G +       P
Sbjct: 360 LGNEPGDLPQTRPQTHAQPQPPTGRSTPVRHPDTPRHVQAAPAQRYSGSGPADGPAADRP 419

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
              +   +               +G R E   R    P++ S+ R
Sbjct: 420 AADQPDRTATGRPSPAQP--ARPAGTRPEPGHRPAPGPARASVPR 462


>gi|221195455|ref|ZP_03568510.1| ribosomal protein S4 [Atopobium rimae ATCC 49626]
 gi|221184642|gb|EEE17034.1| ribosomal protein S4 [Atopobium rimae ATCC 49626]
          Length = 197

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R+E  + +    + VNG  ++  +  +   D I V
Sbjct: 88  RLDNVVFRLGFARTRKEARQTVRHGHITVNGQRVDIPSYRIKKGDVIAV 136


>gi|319946013|ref|ZP_08020262.1| 30S ribosomal protein S4 [Streptococcus australis ATCC 700641]
 gi|322390490|ref|ZP_08064008.1| 30S ribosomal protein S4 [Streptococcus parasanguinis ATCC 903]
 gi|319747821|gb|EFW00066.1| 30S ribosomal protein S4 [Streptococcus australis ATCC 700641]
 gi|321142764|gb|EFX38224.1| 30S ribosomal protein S4 [Streptococcus parasanguinis ATCC 903]
          Length = 203

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVTPGQVISV 142


>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 = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 30/248 (12%), Positives = 69/248 (27%), Gaps = 46/248 (18%)

Query: 12  TPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
             QR+ +V+A      SR  ++ +I    V + G  ++  A  V + + I V        
Sbjct: 31  QSQRLDRVLAEQVEDLSRTRLKALIVAGHVSIGGAPVQDPAYQVKADETIIVEVPPAVAP 90

Query: 63  --DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
             +G  +       +   L L      +V   +  +  + V   +    + +  +G +  
Sbjct: 91  EPEGENIPLNIVYEDDDLLVLNKPKGLVVHPAAGHETGTLVNALIAHCGTSLSGIGGVKR 150

Query: 117 N----------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
                      T  +++  ND     +    +         R +        +     I 
Sbjct: 151 PGIVHRLDKDTTGLMVVAKNDRAHQSLTAQFADHGRTGALRRGYMAFVWGAPSRSHGTID 210

Query: 167 IQGICYGDMQVTLDTQKGSNAWVT---------------------VGLREGKNREIKKVF 205
                +   +  +  ++G    VT                       L  G+  +I+   
Sbjct: 211 QPIDRHPFAREKMAVRQGGRHAVTHWEMLESFEGRDGKPLAALLACQLETGRTHQIRVHL 270

Query: 206 EFFNWKVN 213
                 + 
Sbjct: 271 GHAGHPLI 278


>gi|206896167|ref|YP_002246897.1| heat shock protein 15 [Coprothermobacter proteolyticus DSM 5265]
 gi|206738784|gb|ACI17862.1| heat shock protein 15 [Coprothermobacter proteolyticus DSM 5265]
          Length = 82

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 2/51 (3%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+ K +  +GI  RR   +R+I    VK+NG L ++ +  V   D IEVD
Sbjct: 1  MRLDKFLKESGIIKRRTLAQRIIQAGYVKINGKLAKQ-SDPVKVDDMIEVD 50


>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 = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 31/247 (12%), Positives = 71/247 (28%), Gaps = 42/247 (17%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +V    +  R+ K ++      SR  ++  I    VKVNG  ++  +  V   D I +  
Sbjct: 25  VVDSGQSMMRLDKYLSHHLKNISRNRIQNAIDTDSVKVNGSSVKS-SYKVKPFDDISISI 83

Query: 65  VP----------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           V                 +   +   L +      +V         + V   +    +  
Sbjct: 84  VRSSRIPKEVIPQNIPLDIVYEDDDVLLVNKAQEMVVHPGHGNPDGTLVNALVYHFGNLP 143

Query: 109 IS---------VGRLDINTEGLLLLTND-------------GGLARVLELPSTQWLRVYR 146
            +         V R+D  T GLL++  +                 R          +  +
Sbjct: 144 SARDGEIRPGLVHRIDKGTSGLLVIAKNEYALQFLAKQFADHTTERTYYALIWGEPKEPK 203

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIKKV 204
              +  + +   +     +  +G    +     +  K     + +   L  G+  +I+  
Sbjct: 204 GTINAHIGRGFKDRRISDVFPEGEYGKEAITHYEVLKSLRYVSLIKCNLETGRTHQIRAH 263

Query: 205 FEFFNWK 211
            ++    
Sbjct: 264 MKYLGHP 270


>gi|22538271|ref|NP_689122.1| 30S ribosomal protein S4 [Streptococcus agalactiae 2603V/R]
 gi|25012131|ref|NP_736526.1| 30S ribosomal protein S4 [Streptococcus agalactiae NEM316]
 gi|76787020|ref|YP_330685.1| 30S ribosomal protein S4 [Streptococcus agalactiae A909]
 gi|76799096|ref|ZP_00781286.1| ribosomal protein S4 [Streptococcus agalactiae 18RS21]
 gi|77406884|ref|ZP_00783910.1| ribosomal protein S4 [Streptococcus agalactiae H36B]
 gi|77408905|ref|ZP_00785630.1| ribosomal protein S4 [Streptococcus agalactiae COH1]
 gi|77410869|ref|ZP_00787226.1| ribosomal protein S4 [Streptococcus agalactiae CJB111]
 gi|77413207|ref|ZP_00789405.1| ribosomal protein S4 [Streptococcus agalactiae 515]
 gi|41017840|sp|Q8DWS6|RS4_STRA5 RecName: Full=30S ribosomal protein S4
 gi|41017841|sp|Q8E2M6|RS4_STRA3 RecName: Full=30S ribosomal protein S4
 gi|90101728|sp|Q3JYG8|RS4_STRA1 RecName: Full=30S ribosomal protein S4
 gi|22535185|gb|AAN00995.1|AE014288_13 ribosomal protein S4 [Streptococcus agalactiae 2603V/R]
 gi|24413675|emb|CAD47755.1| 30S ribosomal protein S4 [Streptococcus agalactiae NEM316]
 gi|76562077|gb|ABA44661.1| ribosomal protein S4 [Streptococcus agalactiae A909]
 gi|76585564|gb|EAO62132.1| ribosomal protein S4 [Streptococcus agalactiae 18RS21]
 gi|77160747|gb|EAO71860.1| ribosomal protein S4 [Streptococcus agalactiae 515]
 gi|77163087|gb|EAO74041.1| ribosomal protein S4 [Streptococcus agalactiae CJB111]
 gi|77172496|gb|EAO75640.1| ribosomal protein S4 [Streptococcus agalactiae COH1]
 gi|77174516|gb|EAO77359.1| ribosomal protein S4 [Streptococcus agalactiae H36B]
 gi|319746120|gb|EFV98393.1| 30S ribosomal protein S4 [Streptococcus agalactiae ATCC 13813]
          Length = 203

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVTPGQVISV 142


>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 = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 42/248 (16%), Positives = 81/248 (32%), Gaps = 40/248 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M   N++  +    R+  V+A+    SR +   +I    V VN   + + +  +   D I
Sbjct: 1   MVKFNVLNSS----RLDVVVAKELQISRNQALNLIKDSLVSVNLKPVSKPSFLLSENDEI 56

Query: 61  EVDGVPLRKAERTR--------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
            V+  P ++ +                 L + +KP  +V   +     +T+ + L     
Sbjct: 57  CVNFAPKKEVQNEYEVNFDIPIIYEDDDLIVLNKPPQIVVHQAPSVKEATLVEWLNKKGF 116

Query: 107 R---------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR------------VY 145
                        V RLD  T G +++  +      L    +                  
Sbjct: 117 MLSNLNGDVRAGIVHRLDKGTSGAIVVAKNNFAHAKLSEQLSDKSMGRIYLALTDLPLKE 176

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
            +     + ++  N LKK IV          V L ++ G N  +   L  G+  +I+   
Sbjct: 177 DIIIDKPIGRNPNNRLKKAIVADAKFAKSAFVNLLSEGGVN-LIAAKLFTGRTHQIRVHL 235

Query: 206 EFFNWKVN 213
              N  + 
Sbjct: 236 ASINRHIL 243


>gi|313895093|ref|ZP_07828650.1| ribosomal protein S4 [Selenomonas sp. oral taxon 137 str. F0430]
 gi|320529822|ref|ZP_08030899.1| ribosomal protein S4 [Selenomonas artemidis F0399]
 gi|312975988|gb|EFR41446.1| ribosomal protein S4 [Selenomonas sp. oral taxon 137 str. F0430]
 gi|320137840|gb|EFW29745.1| ribosomal protein S4 [Selenomonas artemidis F0399]
          Length = 197

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +RR+  +++      VNG  ++  +  V   D IEV
Sbjct: 88  RIDNVVFRLGLANTRRQARQLVRHGHFTVNGKRVDIPSALVHEGDVIEV 136


>gi|261367775|ref|ZP_05980658.1| ribosomal protein S4 [Subdoligranulum variabile DSM 15176]
 gi|282570573|gb|EFB76108.1| ribosomal protein S4 [Subdoligranulum variabile DSM 15176]
          Length = 200

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+  ++++     VNG  +   +  V   D IEV
Sbjct: 90  RLDNVVYRLGFAKTRRDARQLVSHNHFTVNGKRVNIPSYLVKPGDVIEV 138


>gi|197119031|ref|YP_002139458.1| rRNA methyltransferase, YqxC-like [Geobacter bemidjiensis Bem]
 gi|197088391|gb|ACH39662.1| rRNA methyltransferase, YqxC-related, putative [Geobacter
          bemidjiensis Bem]
          Length = 257

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 1/59 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          T +R+ K++   G+A SR   + +I   +V V+  L ++A + V     I + G PL  
Sbjct: 2  TKERLDKLVLERGLAPSRERAKALIMAGQVVVDDHLADKAGLMVPVEAEIRLKGEPLPY 60


>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 = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/217 (11%), Positives = 56/217 (25%), Gaps = 30/217 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--------------LRKAER 72
           SR  ++  I  QRV VNG + ++    V+  + + ++                 +   + 
Sbjct: 6   SRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDE 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGRLDINTEGLLLLTND 127
             + +      +V   +     + +   L          R   V RLD +T GL+++   
Sbjct: 66  DIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKT 125

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQ-----------DKLNLLKKGIVIQGICYGDMQ 176
                 L     +                                    V          
Sbjct: 126 VPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTH 185

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             +      +  + + L  G+  +I+         + 
Sbjct: 186 YRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 222


>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 = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 4/66 (6%)

Query: 1  MKDKNIVQENFTPQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
          M    +V     PQR+ K +AR    A   SR  + R+IA+  V  +G LL      V  
Sbjct: 1  MDRLRVVIAADPPQRLDKALARDVPEAAALSRTRLGRLIAEGAVTRDGALLTDPKAKVAE 60

Query: 57 TDHIEV 62
           D +E+
Sbjct: 61 GDVLEI 66


>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 = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 34/243 (13%), Positives = 74/243 (30%), Gaps = 37/243 (15%)

Query: 7   VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVM---------- 55
           V      +R+ + +AR+    +R   +R+I + RV V+  L E+ ++ +           
Sbjct: 12  VPTEGEAERLDQFVARSVQGITRSAAQRLIEEGRVTVDDRL-EKPSLKLRGGERVVVTVP 70

Query: 56  -------------------STDHIEVD---GVPLRK---AERTRLWLYHKPIGLVTTHSD 90
                                D + VD   G+ +          L           +   
Sbjct: 71  PPAPAVPEAEEIPLVVLHEDGDVVVVDKPAGMVVHPAAGNPGGTLVNALLAHCTDLSGIG 130

Query: 91  PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
            + R  +   +    S V+ V + D   E L    +D  + RV         R  + R  
Sbjct: 131 GEIRPGIVHRIDKDTSGVLVVAKSDRAHESLSRQFHDHTVKRVYLALVYGSPREDKGRIE 190

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           G + +   +  K     +   +      +  +      + + L  G+  +I+       +
Sbjct: 191 GAIGRHPTDRKKMSGAARHGKHAVTHWRVAARFTGVTLLRLRLETGRTHQIRVHMAEAGF 250

Query: 211 KVN 213
            + 
Sbjct: 251 PLV 253


>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 = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 35/276 (12%), Positives = 77/276 (27%), Gaps = 62/276 (22%)

Query: 10  NFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           N + QR+ K +       R+         + + I +  VK+NG  ++    ++   D +E
Sbjct: 8   NESGQRMDKFL-------RKMLTDVPLGAIYKSIRKGDVKINGKKVKE-KYSLNLGDIVE 59

Query: 62  V-----------DGVPLR--------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
           +           D   +           ++  + +  KP  LV +       +     L 
Sbjct: 60  IRDIKTNAEKHNDFKAIEGANELKVTYEDQNMIIVEKKPGVLVHSDKKNSDPTLTDYVLS 119

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
            ++ +   V   +I          D   A ++             +   +   DK     
Sbjct: 120 YLYDKGDYVPEEEITFTPASCNRLDRNTAGIIIFGKNYESLKDLNQMIRERHVDKYYQAL 179

Query: 163 KGIVIQGICYGD-------------------------MQVTLDTQKGSNAWVTVGLREGK 197
               I+   Y                           M+V      G+ + + + L  G+
Sbjct: 180 VCGKIKDGLYKAHIVKDEKSNKSYIHKEPKKNSKEIEMEVKTIQTCGTYSLLEIQLITGR 239

Query: 198 NREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
           + +I+         +       YG  +L +      
Sbjct: 240 SHQIRAHLSSLGNPIVGDK--KYGSKKLNSFFYNKY 273


>gi|54296389|ref|YP_122758.1| 30S ribosomal protein S4 [Legionella pneumophila str. Paris]
 gi|61215409|sp|Q5X835|RS4_LEGPA RecName: Full=30S ribosomal protein S4
 gi|53750174|emb|CAH11566.1| 30S ribosomal subunit protein S4 [Legionella pneumophila str.
           Paris]
          Length = 206

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G AS R E  +++A + + VN  ++   +  V   D I V
Sbjct: 97  RLDNVVYRMGFASTRAEARQLVAHKAILVNDKVVNVPSFLVNPGDTISV 145


>gi|116511114|ref|YP_808330.1| 30S ribosomal protein S4 [Lactococcus lactis subsp. cremoris SK11]
 gi|125623168|ref|YP_001031651.1| 30S ribosomal protein S4 [Lactococcus lactis subsp. cremoris
           MG1363]
 gi|122940375|sp|Q032G4|RS4_LACLS RecName: Full=30S ribosomal protein S4
 gi|152060956|sp|A2RI10|RS4_LACLM RecName: Full=30S ribosomal protein S4
 gi|116106768|gb|ABJ71908.1| SSU ribosomal protein S4P [Lactococcus lactis subsp. cremoris SK11]
 gi|124491976|emb|CAL96903.1| 30S ribosomal protein S4 [Lactococcus lactis subsp. cremoris
           MG1363]
 gi|300069915|gb|ADJ59315.1| 30S ribosomal protein S4 [Lactococcus lactis subsp. cremoris
           NZ9000]
          Length = 203

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V
Sbjct: 93  QRLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSFRVQPGQVISV 142


>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 = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/217 (11%), Positives = 56/217 (25%), Gaps = 30/217 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--------------LRKAER 72
           SR  ++  I  QRV VNG + ++    V+  + + ++                 +   + 
Sbjct: 6   SRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDE 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGRLDINTEGLLLLTND 127
             + +      +V   +     + +   L          R   V RLD +T GL+++   
Sbjct: 66  DIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKT 125

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQ-----------DKLNLLKKGIVIQGICYGDMQ 176
                 L     +                                    V          
Sbjct: 126 VPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTH 185

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             +      +  + + L  G+  +I+         + 
Sbjct: 186 YRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 222


>gi|320547679|ref|ZP_08041964.1| 30S ribosomal protein S4 [Streptococcus equinus ATCC 9812]
 gi|320447754|gb|EFW88512.1| 30S ribosomal protein S4 [Streptococcus equinus ATCC 9812]
          Length = 203

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVTPGQVISV 142


>gi|306834567|ref|ZP_07467680.1| 30S ribosomal protein S4 [Streptococcus bovis ATCC 700338]
 gi|304423369|gb|EFM26522.1| 30S ribosomal protein S4 [Streptococcus bovis ATCC 700338]
          Length = 203

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVTPGQVISV 142


>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 = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 29/238 (12%), Positives = 60/238 (25%), Gaps = 31/238 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----E 61
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + I    E
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRIANIPREKVLGGERIEIIVE 69

Query: 62  VDGVP----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
           V+             +   +   + +      +V   +     + +   L          
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIAEVP 129

Query: 112 -----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-----------FHGQVDQ 155
                 RLD +T GL+++         L     +                      Q   
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     V            +     +   + + L  G+  +I+         + 
Sbjct: 190 RHATKRTLMAVHPMGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 247


>gi|167746997|ref|ZP_02419124.1| hypothetical protein ANACAC_01709 [Anaerostipes caccae DSM 14662]
 gi|167653957|gb|EDR98086.1| hypothetical protein ANACAC_01709 [Anaerostipes caccae DSM 14662]
          Length = 271

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 26/178 (14%), Positives = 55/178 (30%), Gaps = 2/178 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++ + G+A SR + + +I    V V+G   ++A   V     IE+ G  L+   R
Sbjct: 3   ERLDVLLVKKGLAASREKAKAIIMSGVVFVDGQREDKAGTMVKEELPIEIKGKTLKYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L           +D                 ++  G   + +  +     D GL  
Sbjct: 63  GGLKLEKAMKQFNIQLTDRVCMDVGAST-GGFTHCMLLNGAKKVYSVDVGHGQLDWGLRN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +   +   +  V      +      +    +        +   L+      A + 
Sbjct: 122 DERVVCMERTNMRYVTPEDIEEPAGFVSIDVSFISLTKILPAVYGILENGGEVTALIK 179


>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 = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 29/238 (12%), Positives = 60/238 (25%), Gaps = 31/238 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----E 61
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + I    E
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRIANIPREKVLGGERIEIIVE 69

Query: 62  VDGVP----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
           V+             +   +   + +      +V   +     + +   L          
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIAEVP 129

Query: 112 -----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-----------FHGQVDQ 155
                 RLD +T GL+++         L     +                      Q   
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     V            +     +   + + L  G+  +I+         + 
Sbjct: 190 RHATKRTLMAVHPMGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 247


>gi|296274039|ref|YP_003656670.1| pseudouridine synthase [Arcobacter nitrofigilis DSM 7299]
 gi|296098213|gb|ADG94163.1| pseudouridine synthase [Arcobacter nitrofigilis DSM 7299]
          Length = 249

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/200 (11%), Positives = 64/200 (32%), Gaps = 4/200 (2%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV-PLRKAERTRLW 76
           KV+A+    S  + + +I +  VKV    +  A  ++       V  V P++   +    
Sbjct: 8   KVLAKQENISNSKAKDLIDKGLVKVGDKKVLIARGDISENTKFIVKEVAPIKVIFQDDDI 67

Query: 77  LYHKPIGLVTTHSDPDGRSTV---FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L       +T                        ++     +  T+ +    N+      
Sbjct: 68  LAVDKPAFLTADEVSRKFPNYLLLNRLDKETSGVMLFAKNEEFQTKAIREFKNNNVYKEY 127

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           + +   + +    V       ++   + +  + ++        V     +G+ + + V +
Sbjct: 128 VAVVEGKVIDEIVVDKPILTIKNNKGVARSKVDMKKGKSAKTTVYPMLVEGNKSKIKVVI 187

Query: 194 REGKNREIKKVFEFFNWKVN 213
             G+  +I+    + ++ + 
Sbjct: 188 DTGRTHQIRVHLNYIDYPII 207


>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 = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 30/236 (12%), Positives = 63/236 (26%), Gaps = 40/236 (16%)

Query: 13  PQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMST------------- 57
            QR+ +V A    A  SR  +   I   R+ V+G ++      V                
Sbjct: 17  GQRLDQV-AAQLFAEHSRSRLSAWIKDGRLTVDGAVIR-PRDIVHGGAILELTAEQEAQG 74

Query: 58  ----DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
                 IE+D   +   +   L +      +V   +     + +   L  +   +     
Sbjct: 75  EWVAQDIELD---IVYEDDDILVINKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRC 131

Query: 114 LDINTEG----------------LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
             ++                     L+T     +            V             
Sbjct: 132 GIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVVAGGKINAPIGRH 191

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               ++  V++G         +  +  S+  V V L  G+  +I+      N+ + 
Sbjct: 192 GQQRQRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINFPLV 247


>gi|239618238|ref|YP_002941560.1| ribosomal protein S4 [Kosmotoga olearia TBF 19.5.1]
 gi|259495284|sp|C5CGH5|RS4_KOSOT RecName: Full=30S ribosomal protein S4
 gi|239507069|gb|ACR80556.1| ribosomal protein S4 [Kosmotoga olearia TBF 19.5.1]
          Length = 208

 Score = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G AS R++  ++++   V VNG  + +A+ +V   D IE+
Sbjct: 99  RLDNVVYRMGFASSRKQARQLVSHGHVLVNGRKVNKASYSVRPGDIIEI 147


>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 = 51.7 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 29/238 (12%), Positives = 60/238 (25%), Gaps = 31/238 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----E 61
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + I    E
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRIANIPREKVLGGEKIEITVE 69

Query: 62  VDGVP----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
           V+             +   +   + +      +V   +     + +   L          
Sbjct: 70  VEDETRFEPENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIAEVP 129

Query: 112 -----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-----------FHGQVDQ 155
                 RLD +T GL+++         L     +                      Q   
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     V            +     +   + + L  G+  +I+         + 
Sbjct: 190 RHATKRTLMAVHPMGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 247


>gi|317498471|ref|ZP_07956765.1| S4 domain-containing protein [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316894164|gb|EFV16352.1| S4 domain-containing protein [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 251

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 24/52 (46%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             R+  ++++A   SR   E+++  Q+V  NG +       +   D I V G
Sbjct: 174 SMRLDVLVSQAFSLSRNISEKLLKSQKVFHNGKMCLSGGQKIKQGDIISVRG 225


>gi|167765520|ref|ZP_02437584.1| hypothetical protein CLOSS21_00014 [Clostridium sp. SS2/1]
 gi|167712705|gb|EDS23284.1| hypothetical protein CLOSS21_00014 [Clostridium sp. SS2/1]
 gi|291558988|emb|CBL37788.1| Uncharacterized conserved protein, contains S4-like domain
           [butyrate-producing bacterium SSC/2]
          Length = 251

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 24/52 (46%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             R+  ++++A   SR   E+++  Q+V  NG +       +   D I V G
Sbjct: 174 SMRLDVLVSQAFSLSRNISEKLLKSQKVFHNGKMCLSGGQKIKQGDIISVRG 225


>gi|160894729|ref|ZP_02075504.1| hypothetical protein CLOL250_02280 [Clostridium sp. L2-50]
 gi|156863663|gb|EDO57094.1| hypothetical protein CLOL250_02280 [Clostridium sp. L2-50]
          Length = 197

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI R G A +RRE  +++  + V VNG  +   +  V + D IE+
Sbjct: 88  RLDNVIFRLGFARTRREARQIVDHKHVLVNGKSVNIPSYQVKAGDKIEI 136


>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 = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 32/242 (13%), Positives = 66/242 (27%), Gaps = 35/242 (14%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
            R+ + +A A    SR    ++I    V +NG  + R++  V     +EV          
Sbjct: 1   MRLDQYLASAIPDFSRSFARKIIDLGGVHLNGRRMRRSSFPVPGHAAVEVYLDHRDLDIF 60

Query: 63  --DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
             D   +   +R  + +   P             +     L  +        +  +    
Sbjct: 61  ALDDEHILLRDRYLVVVNKPPGINSQPTPARYKGTLYEALLRLLDDPYNKGRKPSLGMVQ 120

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------------------DKLNL 160
            L     G +   +   + + L         Q                        +   
Sbjct: 121 RLDRDTSGVMIFSIHARAHKSLSDIFAARRVQKHYLALVAGCMQAPQGEFRSLLARQHRT 180

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
                V +G      +  +  + G    + V +  G++ +I+  F      +  L  I Y
Sbjct: 181 NLMKSVARGGKEAVTRYRVIEKFGDAELLEVEIPTGRSHQIRVHFAEAGHPL--LGDIRY 238

Query: 221 GP 222
           G 
Sbjct: 239 GG 240


>gi|323188383|gb|EFZ73674.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           RN587/1]
          Length = 300

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/217 (11%), Positives = 56/217 (25%), Gaps = 30/217 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--------------LRKAER 72
           SR  ++  I  QRV VNG + ++    V+  + + ++                 +   + 
Sbjct: 6   SRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDE 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGRLDINTEGLLLLTND 127
             + +      +V   +     + +   L          R   V RLD +T GL+++   
Sbjct: 66  DIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKT 125

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQ-----------DKLNLLKKGIVIQGICYGDMQ 176
                 L     +                                    V          
Sbjct: 126 VPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTH 185

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             +      +  + + L  G+  +I+         + 
Sbjct: 186 YRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 222


>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 = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 29/232 (12%), Positives = 68/232 (29%), Gaps = 34/232 (14%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV------ 65
            +R+   +A+     SR  + + +    V ++G         ++  +HIEV         
Sbjct: 33  GERLDAALAKLLPDYSRSRLTQWVKDGHVLLDGKPAA-PKTKLLGGEHIEVAVQQTEEQL 91

Query: 66  ---------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV----- 111
                    P+   +   + +      +V   +     + +   L    +          
Sbjct: 92  AYHPEAIELPIVYEDDHIIIINKPAGLVVHPAAGNWTGTLLNGLLHHCPALTHVPRAGIV 151

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLN 159
            RLD  T GL+++         L                      +  +    + +D  N
Sbjct: 152 HRLDKETSGLMVVAKTIPAQTELVRQMQARSVKRIYRAIADGVVPFDGKIETLIGRDPHN 211

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            ++  +V  G       V +     S++++   L  G+  +I+         
Sbjct: 212 RMRMAVVKFGGKQAITHVRVLATFPSHSYIECRLETGRTHQIRVHMREARHP 263


>gi|306820734|ref|ZP_07454361.1| hemolysin A [Eubacterium yurii subsp. margaretiae ATCC 43715]
 gi|304551233|gb|EFM39197.1| hemolysin A [Eubacterium yurii subsp. margaretiae ATCC 43715]
          Length = 266

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 27/212 (12%), Positives = 65/212 (30%), Gaps = 21/212 (9%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  ++   G  ASR + +  I    V ++ IL+++   NV     I +    +    R 
Sbjct: 4   RLDVLLVEKGMFASREKAKSNIMAGNVFIDNILVDKVGTNVDENAVITIKSDAIPYVGRG 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L         +                    ++  G   + +  +     D  L   
Sbjct: 64  GLKLEKALKEFDLSVDCKICMDIGAST-GGFTDCMLQNGASKVYSIDVGYGQLDYKLRIN 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG- 192
            ++   +      ++     D+    ++    +   I +  ++  L      +    V  
Sbjct: 123 EKVVCMERTNFRYLKKEQIFDEIDFAVIDVSFISLKIIFPKLKEFL------SKEFEVVS 176

Query: 193 -L--------RE-GKNREIKKVFEFFNWKVNR 214
            +         E GKN  ++ +    + +V +
Sbjct: 177 LIKPQFESQRHEVGKNGIVRDI--SVHQRVIK 206


>gi|168206128|ref|ZP_02632133.1| hemolysin A [Clostridium perfringens E str. JGS1987]
 gi|170662441|gb|EDT15124.1| hemolysin A [Clostridium perfringens E str. JGS1987]
          Length = 271

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 1/64 (1%)

Query: 6  IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          + ++    +R+  ++   GIA SR + +R I    V +    +++A   V  + +I   G
Sbjct: 1  MAEKKEKKERLDVLLVEQGIAESREKAKRYIMAGMVFIGEKRVDKAGEKVPVSSNIIFRG 60

Query: 65 VPLR 68
            L 
Sbjct: 61 ERLP 64


>gi|167971562|ref|ZP_02553839.1| ribosomal RNA large subunit methyltransferase J [Ureaplasma
          parvum serovar 6 str. ATCC 27818]
 gi|186700951|gb|EDU19233.1| ribosomal RNA large subunit methyltransferase J [Ureaplasma
          parvum serovar 6 str. ATCC 27818]
          Length = 247

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          QR+   +       +R +   +I + RV VN   + + +  V  TD +E+
Sbjct: 3  QRLDHYLKNTNQCETRSKAIDLIKRGRVFVNNFEVLKPSFLVKQTDSVEI 52


>gi|163804148|ref|ZP_02197919.1| 30S ribosomal protein S4 [Vibrio sp. AND4]
 gi|159172034|gb|EDP57005.1| 30S ribosomal protein S4 [Vibrio sp. AND4]
          Length = 143

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+  V+ R G   +R E  ++++ + + VNG ++   +  V + D + +
Sbjct: 34 RLDNVVYRMGFGATRAEARQLVSHKAILVNGKVVNVPSFKVAANDVVSI 82


>gi|52840598|ref|YP_094397.1| 30S ribosomal protein S4 [Legionella pneumophila subsp. pneumophila
           str. Philadelphia 1]
 gi|54293345|ref|YP_125760.1| 30S ribosomal protein S4 [Legionella pneumophila str. Lens]
 gi|148361031|ref|YP_001252238.1| 30S ribosomal protein S4 [Legionella pneumophila str. Corby]
 gi|296105901|ref|YP_003617601.1| small subunit ribosomal protein S4 [Legionella pneumophila 2300/99
           Alcoy]
 gi|61215402|sp|Q5WZI8|RS4_LEGPL RecName: Full=30S ribosomal protein S4
 gi|61215429|sp|Q5ZYL9|RS4_LEGPH RecName: Full=30S ribosomal protein S4
 gi|172047874|sp|A5IHP2|RS4_LEGPC RecName: Full=30S ribosomal protein S4
 gi|52627709|gb|AAU26450.1| 30S ribosomal protein S4 [Legionella pneumophila subsp. pneumophila
           str. Philadelphia 1]
 gi|53753177|emb|CAH14624.1| 30S ribosomal subunit protein S4 [Legionella pneumophila str. Lens]
 gi|148282804|gb|ABQ56892.1| 30S ribosomal protein S4 [Legionella pneumophila str. Corby]
 gi|295647802|gb|ADG23649.1| small subunit ribosomal protein S4 [Legionella pneumophila 2300/99
           Alcoy]
 gi|307609161|emb|CBW98617.1| 30S ribosomal subunit protein S4 [Legionella pneumophila 130b]
          Length = 206

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G AS R E  +++A + + VN  ++   +  V   D + V
Sbjct: 97  RLDNVVYRMGFASTRAEARQLVAHKAILVNDKVVNVPSFLVNPGDTVSV 145


>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 = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 33/271 (12%), Positives = 73/271 (26%), Gaps = 47/271 (17%)

Query: 6   IVQENFTPQRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            V     P R+ K +      +   +R ++ +      V VNG  +++    V   D I 
Sbjct: 33  TVDRGQQPLRIDKFLHIFRQNS---TRNKISQSCRAGNVVVNGTAVKQ-NYRVKPGDRIS 88

Query: 62  V-------------DGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN------ 100
           V               +P  +   +   + +   P  +V         + +         
Sbjct: 89  VLLSRPPRENVIIPQDIPLNIVYEDDDLVVVDKDPGMVVHPGHGNWDGTLINALAFHFEK 148

Query: 101 -----------LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
                      L     +  S   +    E  L         R  +     ++     + 
Sbjct: 149 NGVKSDLDRVGLVHRIDKDTSGLLVIAKNEYALSYLAKQFFDRKTKRLYWAFVWGNLDQE 208

Query: 150 HGQVDQDKLNLLKKGIVI---QGI---CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           +G +  +    LK  + +   +      +      +  +     WV   L  G+  +I+ 
Sbjct: 209 NGTITGNIGRHLKNRMQMAVFEDGSLGKHAVTHYKVVERFKYMTWVECKLETGRTHQIRA 268

Query: 204 VFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            F+     +    R   G   L  +     +
Sbjct: 269 HFKHIGHTLFNDERYE-GNQILKGVNMPKYK 298


>gi|83590353|ref|YP_430362.1| hemolysin A [Moorella thermoacetica ATCC 39073]
 gi|83573267|gb|ABC19819.1| hemolysin A [Moorella thermoacetica ATCC 39073]
          Length = 271

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          +R+  ++ R G+  SR +    I    V VN + +++    V  T  I + G  L  
Sbjct: 4  ERLDLLLVRRGLYPSREQARTAIMAGEVLVNDVPVDKPGAAVPDTATIRLLGQHLPY 60


>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 = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 11/54 (20%), Positives = 23/54 (42%), Gaps = 5/54 (9%)

Query: 15 RVSKVIARA-----GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          R+ + +A          SR  ++ +I   RV + G  +   A  + + D + +D
Sbjct: 28 RLDRFLAERPEIVDAHLSRSRIKALIESGRVSLRGAAIRDPAKKLAAGDAVSLD 81


>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 = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 31/250 (12%), Positives = 71/250 (28%), Gaps = 38/250 (15%)

Query: 1   MKDK-NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M D   +   +   +R+ + + R     SR  V+++IA+ +  V+G +  +A   + + +
Sbjct: 1   MSDSTKVYTADQDGERLDRFLTRMEPTLSRAHVQKVIAEGQALVSGRV-RKANYKLQAGE 59

Query: 59  HIEV---DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            +     +  P+              +   + +      +V   +     + V   L   
Sbjct: 60  KVTFHLPEAKPVEILPEDIPLDILYEDSDIIVINKARGMVVHPATGIYTGTLVNALLYHC 119

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGL---------------------ARVLELPSTQWLR 143
                  G +       L     G +                      R+        +R
Sbjct: 120 KDLSGINGEIRPGIVHRLDKDTSGVMVAAKNDAAHLDLAEQIRTKAAHRIYRAIVCGNIR 179

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                  G + +   +  K  IV +          +  + G+   V   L  G+  +I+ 
Sbjct: 180 EEAGVIKGDIGRHPTDRKKMAIVHEHGKPAVTHFRVLERFGAYTLVECRLETGRTHQIRV 239

Query: 204 VFEFFNWKVN 213
                   V 
Sbjct: 240 HMASIGHPVL 249


>gi|225620833|ref|YP_002722091.1| Pseudouridylate synthase [Brachyspira hyodysenteriae WA1]
 gi|225215653|gb|ACN84387.1| Pseudouridylate synthase [Brachyspira hyodysenteriae WA1]
          Length = 329

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 79/250 (31%), Gaps = 42/250 (16%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K   I+ E+   +R+   I+     +R +V+  +    + VN    ++ + ++   D+I 
Sbjct: 30  KKSFIITEDDIGKRLDTFISEKLNITRSQVKNYLTS--IIVNDA-EKKLSYSLKLNDNII 86

Query: 62  VDG-----------VPLR-------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           +D             P+          E   L + +KP G+    S  +   T+ + L  
Sbjct: 87  IDSDNIFKEKTDTANPIPENIDLDILYEDKYLLVINKPAGMSVHCSPSEMSGTLVNALLY 146

Query: 104 IFSRVISVGR------LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ----- 152
                  VG       +    +    L   G  A ++     Q+      + +       
Sbjct: 147 KIKDFDFVGNKERAGIIHRLDKDTSGLMIIGKNANIVSSIQEQFKNRTIKKIYHAIVVGV 206

Query: 153 ----------VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                              KK  V +        + +  +  S+  + + L+ G+  +I+
Sbjct: 207 LKDNYIEINLPIGRHHVYRKKMTVREDGKEALTHIKVLKRFNSHTLIEINLKTGRTHQIR 266

Query: 203 KVFEFFNWKV 212
               +  + V
Sbjct: 267 VHSSYKGFPV 276


>gi|222153413|ref|YP_002562590.1| hypothetical protein SUB1286 [Streptococcus uberis 0140J]
 gi|222114226|emb|CAR42803.1| conserved hypothetical protein [Streptococcus uberis 0140J]
          Length = 263

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 13/63 (20%), Positives = 36/63 (57%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K+++++    +  R+ ++IA     SR +  +++  ++VKVN  ++ +++ ++   D + 
Sbjct: 173 KEESLIDITLSSLRIDRLIASVLKLSRSQAIKLVESEKVKVNYRIITKSSDSIAIGDLVS 232

Query: 62  VDG 64
           V G
Sbjct: 233 VRG 235


>gi|171778571|ref|ZP_02919698.1| hypothetical protein STRINF_00550 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171282794|gb|EDT48218.1| hypothetical protein STRINF_00550 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 203

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVTPGQVISV 142


>gi|154174170|ref|YP_001409132.1| 30S ribosomal protein S4 [Campylobacter curvus 525.92]
 gi|171769259|sp|A7H0Z0|RS4_CAMC5 RecName: Full=30S ribosomal protein S4
 gi|112802255|gb|EAT99599.1| ribosomal protein S4 [Campylobacter curvus 525.92]
          Length = 208

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G A+ RR   +++    + VNG  ++  +  V     +EV
Sbjct: 98  QRLDNVVYRMGFATTRRFARQLVTHGHILVNGKRVDIPSYRVEPGSKVEV 147


>gi|34558398|ref|NP_908213.1| putative ribosomal pseudouridine synthase [Wolinella succinogenes
           DSM 1740]
 gi|34484117|emb|CAE11113.1| PUTATIVE RIBOSOMAL PSEUDOURIDINE SYNTHASE [Wolinella succinogenes]
          Length = 244

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/204 (11%), Positives = 58/204 (28%), Gaps = 12/204 (5%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLER------AAVNVMSTDHIEVDGVPLRKAE 71
           K+++     S RE + +I +  V V G+ ++                 I+    P    +
Sbjct: 6   KLLSHQQRISHREAKILIDRGMVSVGGMKVKIARGLFPLGTKFS----IQEAPKPKILMQ 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L    KP  + +     + +   +  L  +      V  L                A
Sbjct: 62  DENLLAIDKPPFIASEELLKEHKEKGWTLLHRLDKETSGVILLVQEGSEFQKSAKAEFKA 121

Query: 132 RVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           + +       +   +   R   +          K  + +       ++     +G    +
Sbjct: 122 QKVYKEYVAIVEGMIPEEREITKPILTTKGHFAKSKISKEGESAYTKIEPLAYEGKQTQL 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVN 213
            V ++ G+  +I+      N  + 
Sbjct: 182 KVIIKTGRTHQIRVHLASINHPII 205


>gi|295093660|emb|CBK82751.1| SSU ribosomal protein S4P [Coprococcus sp. ART55/1]
          Length = 197

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 1/63 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  +I R G A +RRE  +++  + V VNG  +   + +V   D IE+           
Sbjct: 88  RLDNIIFRLGFARTRREARQIVDHKHVLVNGKCVNIPSYSVKPGDKIEIREKSKSLQRYK 147

Query: 74  RLW 76
            + 
Sbjct: 148 DIM 150


>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 = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 8/63 (12%)

Query: 5  NIVQENFTPQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           I+ +   P+R+ K IAR     A + SR  + +++A   V +NG +L      V   D 
Sbjct: 9  RIMPDP--PKRLDKAIARDVPADASL-SRSRIAKLLASGDVALNGAVLTDPRAKVAEDDE 65

Query: 60 IEV 62
          I V
Sbjct: 66 ITV 68


>gi|307720212|ref|YP_003891352.1| 30S ribosomal protein S4P [Sulfurimonas autotrophica DSM 16294]
 gi|306978305|gb|ADN08340.1| SSU ribosomal protein S4P [Sulfurimonas autotrophica DSM 16294]
          Length = 208

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G AS RR   +++    + V+G  L+  +  V     IEV
Sbjct: 98  QRLDNVVYRMGFASTRRFARQLVTHGHILVDGKKLDIPSYRVKPGQKIEV 147


>gi|295090871|emb|CBK76978.1| hemolysin TlyA family protein [Clostridium cf. saccharolyticum K10]
          Length = 269

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/164 (14%), Positives = 51/164 (31%), Gaps = 2/164 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++ + G+A SR + + +I    V V+G   ++A      T  +EV G  LR   R
Sbjct: 3   ERLDVLLVKNGLAESREKAKAIIMSGIVYVDGQKEDKAGTTFEETAKLEVRGATLRYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L           S                  ++  G + +    +        L  
Sbjct: 63  GGLKLEKAMTHFGVELSGKVCMDVGAST-GGFTDCMLQNGAVKVYAVDVGHGQLAWKLRN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
              +   +   +  V      +  +   +    +      G ++
Sbjct: 122 DPRVVCMEKTNIRYVTPEDIEEPVEFASIDVSFISLTKVLGPVK 165


>gi|258654197|ref|YP_003203353.1| hemolysin A [Nakamurella multipartita DSM 44233]
 gi|258557422|gb|ACV80364.1| hemolysin A [Nakamurella multipartita DSM 44233]
          Length = 272

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 17/61 (27%), Positives = 24/61 (39%), Gaps = 1/61 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          R+   + R G A SR E    IA  RV V G +  + +  V     + V    L     +
Sbjct: 5  RLDAELVRRGHARSRAEAAEFIAAGRVLVAGQVATKPSTAVDPAVALLVRDADLDPRWAS 64

Query: 74 R 74
          R
Sbjct: 65 R 65


>gi|294931461|ref|XP_002779886.1| Ribosomal large subunit pseudouridine synthase B, putative
           [Perkinsus marinus ATCC 50983]
 gi|239889604|gb|EER11681.1| Ribosomal large subunit pseudouridine synthase B, putative
           [Perkinsus marinus ATCC 50983]
          Length = 182

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 8/38 (21%), Positives = 15/38 (39%)

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
           + V +    G+NR +++        V  L R   G  +
Sbjct: 145 SMVRITTTCGRNRVVRRTLCALGHPVLLLHREEIGGIK 182


>gi|289209305|ref|YP_003461371.1| ribosomal protein S4 [Thioalkalivibrio sp. K90mix]
 gi|288944936|gb|ADC72635.1| ribosomal protein S4 [Thioalkalivibrio sp. K90mix]
          Length = 206

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 16/73 (21%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + V VNG ++  AA  V  +D + +     ++    
Sbjct: 97  RLDNVVYRMGFGSTRSEARQLVSHRAVLVNGQVVNIAAYQVQPSDVVSIREKARKQVRIQ 156

Query: 74  RLWLYHKPIGLVT 86
                 +  G  +
Sbjct: 157 DSMTLAEQSGFPS 169


>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 = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 30/236 (12%), Positives = 64/236 (27%), Gaps = 39/236 (16%)

Query: 13  PQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP----- 66
             R+ KV++      SR  +++ I    V V+G +   A + V   + + +   P     
Sbjct: 24  GVRLDKVLSTLVPQYSRSRLQQWIDAGHVSVDGEIAR-AKMTVYGDEKVVIYPQPAPEDE 82

Query: 67  ----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISV 111
                     +   +   L +      +V   +     + +   L  +       R   V
Sbjct: 83  AFKPEAMDLNIAYEDAAILVIDKPAGLVVHPAAGNWSGTLLNGLLHYLPAIAGVPRAGIV 142

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-----------KLNL 160
            RLD +T GL+++         L                     +               
Sbjct: 143 HRLDKDTSGLMVVAKTLVAHTDLVRQLQARTVKREYLALVWGTPNVSGKVDTSIGRHSRD 202

Query: 161 LKKGIVIQGICYGDMQVTLD-----TQKGSNAWVTVG-LREGKNREIKKVFEFFNW 210
             K  V + +                  G    + +  L  G+  +I+   +   +
Sbjct: 203 RVKMAVSENLTAKPALTHFQRLATGMLDGRPVSLMMCQLETGRTHQIRVHMQSIGF 258


>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 = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/217 (11%), Positives = 56/217 (25%), Gaps = 30/217 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--------------LRKAER 72
           SR  ++  I  QRV VNG + ++    V+  + + ++                 +   + 
Sbjct: 6   SRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDE 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGRLDINTEGLLLLTND 127
             + +      +V   +     + +   L          R   V RLD +T GL+++   
Sbjct: 66  DIIVINKPRDLVVHPGAGNLDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKT 125

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQ-----------DKLNLLKKGIVIQGICYGDMQ 176
                 L     +                                    V          
Sbjct: 126 VPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTH 185

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             +      +  + + L  G+  +I+         + 
Sbjct: 186 YRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 222


>gi|332655117|ref|ZP_08420858.1| ribosomal protein S4 [Ruminococcaceae bacterium D16]
 gi|332515977|gb|EGJ45586.1| ribosomal protein S4 [Ruminococcaceae bacterium D16]
          Length = 200

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 1/63 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G A +RRE  +++      VNG  ++  +  V   D IEV        +  
Sbjct: 90  RLDNVVYRLGFAMTRREARQLVTHGHFTVNGQRVDIPSFLVKVGDVIEVREKSRSSVKFK 149

Query: 74  RLW 76
           RL 
Sbjct: 150 RLL 152


>gi|291545451|emb|CBL18559.1| hemolysin TlyA family protein [Ruminococcus sp. SR1/5]
          Length = 269

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/164 (15%), Positives = 48/164 (29%), Gaps = 2/164 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  ++   G+A SR + +  I    V VNG   ++A      T  +EV G  L    R 
Sbjct: 4   RLDIMMVEQGLAPSREKAKAYIMAGEVYVNGQKEDKAGSMFAETAKLEVRGKTLPYVSRG 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L         T  D                 ++  G + + +  +     D  L   
Sbjct: 64  GLKLEKAMKNFGVTLKDKVCMDVGAST-GGFTDCMLQNGAVKVYSIDVGYGQLDWKLRND 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
             +   +   +  V           + +    +        ++ 
Sbjct: 123 PRVVCMEKTNIRYVVPEDLEGPAAFSSIDVSFISLTKVLLPVRN 166


>gi|225388187|ref|ZP_03757911.1| hypothetical protein CLOSTASPAR_01922 [Clostridium asparagiforme
           DSM 15981]
 gi|225045745|gb|EEG55991.1| hypothetical protein CLOSTASPAR_01922 [Clostridium asparagiforme
           DSM 15981]
          Length = 271

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/164 (14%), Positives = 51/164 (31%), Gaps = 2/164 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++ +  +A SR + + +I    V V+G   ++A         IEV G  L+   R
Sbjct: 3   ERLDVLLVQRNLAPSREKAKALIMSGIVYVDGQKEDKAGTQFDEAAAIEVRGSTLKYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L           +                  ++  G + + +  +     D  L  
Sbjct: 63  GGLKLEKAMTHFGVEPAGKVCMDVGAST-GGFTDCMLQNGAVKVYSVDVGHGQLDWKLRN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
              +   +   +  V      D   L  +    +      G ++
Sbjct: 122 DERVVCMEKTNIRYVTPSDIADPIALASIDVSFISLTKVLGPVR 165


>gi|293400620|ref|ZP_06644765.1| ribosomal RNA large subunit methyltransferase J
          [Erysipelotrichaceae bacterium 5_2_54FAA]
 gi|291305646|gb|EFE46890.1| ribosomal RNA large subunit methyltransferase J
          [Erysipelotrichaceae bacterium 5_2_54FAA]
          Length = 261

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 14 QRVS-KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  K++      SR   + MI +  V+VNG  + +++  +   D I +
Sbjct: 3  MRLDQKIVVMRRDLSRSRAQDMIKEGLVQVNGQTITKSSYAITEEDEIVI 52


>gi|312795803|ref|YP_004028725.1| SSU ribosomal protein S4P [Burkholderia rhizoxinica HKI 454]
 gi|312167578|emb|CBW74581.1| SSU ribosomal protein S4P [Burkholderia rhizoxinica HKI 454]
          Length = 207

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG +    ++ V + D + V
Sbjct: 98  RLDTVVYRMGFGSTRAEARQLVSHKAITVNGQVANIPSLQVKAGDVVAV 146


>gi|283797526|ref|ZP_06346679.1| hemolysin A [Clostridium sp. M62/1]
 gi|291074895|gb|EFE12259.1| hemolysin A [Clostridium sp. M62/1]
          Length = 269

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/164 (14%), Positives = 51/164 (31%), Gaps = 2/164 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++ + G+A SR + + +I    V V+G   ++A      T  +EV G  LR   R
Sbjct: 3   ERLDVLLVKNGLAESREKAKAIIMSGIVYVDGQKEDKAGTTFEETAKLEVRGATLRYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L           S                  ++  G + +    +        L  
Sbjct: 63  GGLKLEKAMTHFGVELSGKVCMDVGAST-GGFTDCMLQNGAVKVYAVDVGHGQLAWKLRN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
              +   +   +  V      +  +   +    +      G ++
Sbjct: 122 DPRVVCMEKTNIRYVTPEDIEEPVEFASIDVSFISLTKVLGPVK 165


>gi|22299000|ref|NP_682247.1| hemolysin-like protein [Thermosynechococcus elongatus BP-1]
 gi|22295182|dbj|BAC09009.1| hemolysin-like protein [Thermosynechococcus elongatus BP-1]
          Length = 262

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 1/58 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
              QR+  ++    +  SR++ +R I    V VN I +++    V     I+V   P
Sbjct: 2  TPRKQRLDSLLVERHLCESRQQAQRWIRAGAVHVNHIPIDKPGTLVAVDATIQVKAKP 59


>gi|157164972|ref|YP_001467696.1| 30S ribosomal protein S4 [Campylobacter concisus 13826]
 gi|171855075|sp|A7ZFY8|RS4_CAMC1 RecName: Full=30S ribosomal protein S4
 gi|112800789|gb|EAT98133.1| ribosomal protein S4 [Campylobacter concisus 13826]
          Length = 208

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G A+ RR   +++    + VNG  ++  +  V     +EV
Sbjct: 98  QRLDNVVYRMGFATTRRFARQLVTHGHILVNGKRVDIPSYRVEPGSKVEV 147


>gi|322688777|ref|YP_004208511.1| hypothetical protein BLIF_0590 [Bifidobacterium longum subsp.
          infantis 157F]
 gi|320460113|dbj|BAJ70733.1| conserved hypothetical protein [Bifidobacterium longum subsp.
          infantis 157F]
          Length = 257

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 12/51 (23%), Positives = 27/51 (52%), Gaps = 2/51 (3%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVD 63
          R+  ++  +G+  SR + +R+I    V+V+G  + + +  V +    + VD
Sbjct: 14 RLDMMLVASGLVESRAKAQRLIKAGHVRVDGETITKPSFMVKAGHSELAVD 64


>gi|296453816|ref|YP_003660959.1| hemolysin A [Bifidobacterium longum subsp. longum JDM301]
 gi|296183247|gb|ADH00129.1| hemolysin A [Bifidobacterium longum subsp. longum JDM301]
          Length = 257

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 12/51 (23%), Positives = 27/51 (52%), Gaps = 2/51 (3%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVD 63
          R+  ++  +G+  SR + +R+I    V+V+G  + + +  V +    + VD
Sbjct: 14 RLDMMLVASGLVESRAKAQRLIKAGHVRVDGETITKPSFMVKAGHSELAVD 64


>gi|227546214|ref|ZP_03976263.1| hemolysin A [Bifidobacterium longum subsp. infantis ATCC 55813]
 gi|239622217|ref|ZP_04665248.1| conserved hypothetical protein [Bifidobacterium longum subsp.
          infantis CCUG 52486]
 gi|312133063|ref|YP_004000402.1| rRNA methylase [Bifidobacterium longum subsp. longum BBMN68]
 gi|317481833|ref|ZP_07940861.1| hemolysin TlyA family protein [Bifidobacterium sp. 12_1_47BFAA]
 gi|322690767|ref|YP_004220337.1| hypothetical protein BLLJ_0577 [Bifidobacterium longum subsp.
          longum JCM 1217]
 gi|227213195|gb|EEI81067.1| hemolysin A [Bifidobacterium longum subsp. infantis ATCC 55813]
 gi|239514214|gb|EEQ54081.1| conserved hypothetical protein [Bifidobacterium longum subsp.
          infantis CCUG 52486]
 gi|291517152|emb|CBK70768.1| hemolysin TlyA family protein [Bifidobacterium longum subsp.
          longum F8]
 gi|311774055|gb|ADQ03543.1| Putative rRNA methylase [Bifidobacterium longum subsp. longum
          BBMN68]
 gi|316916770|gb|EFV38164.1| hemolysin TlyA family protein [Bifidobacterium sp. 12_1_47BFAA]
 gi|320455623|dbj|BAJ66245.1| conserved hypothetical protein [Bifidobacterium longum subsp.
          longum JCM 1217]
          Length = 257

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 12/51 (23%), Positives = 27/51 (52%), Gaps = 2/51 (3%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVD 63
          R+  ++  +G+  SR + +R+I    V+V+G  + + +  V +    + VD
Sbjct: 14 RLDMMLVASGLVESRAKAQRLIKAGHVRVDGETITKPSFMVKAGHSELAVD 64


>gi|172035830|ref|YP_001802331.1| hemolysin A [Cyanothece sp. ATCC 51142]
 gi|171697284|gb|ACB50265.1| hemolysin A [Cyanothece sp. ATCC 51142]
          Length = 270

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 15 RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
          R+  ++    + S R++ +R I    VKVN  ++++    +  T  IE+   P
Sbjct: 5  RLDLLLVERNLCSSRQQAQRCIRAGEVKVNQRIIDKPGTEIEITADIELKQKP 57


>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 = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 30/248 (12%), Positives = 66/248 (26%), Gaps = 47/248 (18%)

Query: 13  PQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------DGV 65
            +R+  V+A    A SR  ++ +I    V V G  +      V   D + +      D  
Sbjct: 26  GKRLDAVLATHLEALSRNRIQSLIKSGDVTVGGAKIVEPKYRVNEGDALTLTLPQAEDPE 85

Query: 66  P--------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG----- 112
           P        +   +   + +      +V   +     + V   +      +  +G     
Sbjct: 86  PKGEDIPVTVVFEDEHLIVVDKPAGLVVHPGAGNWTGTLVNALIHHCGDSLSGIGGVKRP 145

Query: 113 -----------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
                            + D   +GL     D G    LE   +  +        G ++ 
Sbjct: 146 GIVHRIDKDTSGLLVVAKTDQAHKGLAAQFADHGRTGPLERAYSALVWGAPSGLKGTINA 205

Query: 156 DKLNLLKKGIVIQGICY---GDMQVTLDTQKGSN-------AWVTVGLREGKNREIKKVF 205
           +          I  +       +      ++  N       + +   L  G+  +I+   
Sbjct: 206 NLARSQANRQKIAVVKTSGRQAITHWQVKERFGNAEQPALASLLECRLETGRTHQIRVHM 265

Query: 206 EFFNWKVN 213
                 + 
Sbjct: 266 AHIGHPLI 273


>gi|23465615|ref|NP_696218.1| hemolysin-like protein [Bifidobacterium longum NCC2705]
 gi|23326286|gb|AAN24854.1| hemolysin-like protein with S4 domain found in bacteria and
          plants [Bifidobacterium longum NCC2705]
          Length = 280

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 12/51 (23%), Positives = 27/51 (52%), Gaps = 2/51 (3%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVD 63
          R+  ++  +G+  SR + +R+I    V+V+G  + + +  V +    + VD
Sbjct: 37 RLDMMLVASGLVESRAKAQRLIKAGHVRVDGETITKPSFMVKAGHSELAVD 87


>gi|46191091|ref|ZP_00206673.1| COG1189: Predicted rRNA methylase [Bifidobacterium longum DJO10A]
 gi|189439661|ref|YP_001954742.1| putative rRNA methylase [Bifidobacterium longum DJO10A]
 gi|189428096|gb|ACD98244.1| Putative rRNA methylase [Bifidobacterium longum DJO10A]
          Length = 257

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 12/51 (23%), Positives = 27/51 (52%), Gaps = 2/51 (3%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVD 63
          R+  ++  +G+  SR + +R+I    V+V+G  + + +  V +    + VD
Sbjct: 14 RLDMMLVASGLVESRAKAQRLIKAGHVRVDGETITKPSFMVKAGHSELAVD 64


>gi|310779500|ref|YP_003967833.1| hemolysin A [Ilyobacter polytropus DSM 2926]
 gi|309748823|gb|ADO83485.1| hemolysin A [Ilyobacter polytropus DSM 2926]
          Length = 268

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 11/59 (18%), Positives = 24/59 (40%), Gaps = 3/59 (5%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAV--NVMSTDHIEVDGVPLRK 69
          +R+  ++   G   +R + +R I    V V+   +E+      +     I + G  L+ 
Sbjct: 3  ERLDVLLVEQGFFETREKAKRAIMAGIVIVDDKKIEKPGTQIKIDKEPKIRIKGQVLKY 61


>gi|307579486|gb|ADN63455.1| 30S ribosomal protein S4 [Xylella fastidiosa subsp. fastidiosa
          GB514]
          Length = 115

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 13/66 (19%), Positives = 27/66 (40%), Gaps = 1/66 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          R+  VI R G A +R    ++++ + V VNG ++   + +V   D + +     +     
Sbjct: 5  RLDNVIYRMGFAVTRPAARQLVSHRSVLVNGKMVNLPSYHVKPGDVVALSQRAQKYLCVQ 64

Query: 74 RLWLYH 79
                
Sbjct: 65 ESLTIK 70


>gi|227510162|ref|ZP_03940211.1| 30S ribosomal protein S4 [Lactobacillus brevis subsp. gravesensis
           ATCC 27305]
 gi|227190367|gb|EEI70434.1| 30S ribosomal protein S4 [Lactobacillus brevis subsp. gravesensis
           ATCC 27305]
          Length = 231

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A+ RR+  +++    + V+G  ++  +  V     + V
Sbjct: 122 RLDNIVYRLGLATTRRQARQLVNHGHITVDGKRVDIPSYEVKPGQVVSV 170


>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 = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/230 (12%), Positives = 66/230 (28%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 40  RLDAVLAKLLPDYSRSRLTLWIKEGAVIVNDKP-SQPKDKMIGGEQIRVTVRPSEENLAF 98

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL---- 114
                   +   + T + +      +V   +     + +   L                 
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 158

Query: 115 -------------DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
                         +  +  L+        + +       +  +  +   Q+ +D  N L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVWQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIRVHMREANHP 268


>gi|310642769|ref|YP_003947527.1| 30S ribosomal protein s4 [Paenibacillus polymyxa SC2]
 gi|309247719|gb|ADO57286.1| 30S ribosomal protein S4 [Paenibacillus polymyxa SC2]
          Length = 199

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  ++ R G A SR    +++A   V VNG  ++ A+  V   D I
Sbjct: 92  RLDNLVFRLGFANSRAGARQLVAHGHVTVNGKKVDIASYQVSPGDVI 138


>gi|284802475|ref|YP_003414340.1| hypothetical protein LM5578_2231 [Listeria monocytogenes 08-5578]
 gi|284995617|ref|YP_003417385.1| hypothetical protein LM5923_2182 [Listeria monocytogenes 08-5923]
 gi|284058037|gb|ADB68978.1| hypothetical protein LM5578_2231 [Listeria monocytogenes 08-5578]
 gi|284061084|gb|ADB72023.1| hypothetical protein LM5923_2182 [Listeria monocytogenes 08-5923]
          Length = 259

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 22/50 (44%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
             +  R+  +I+ A   SR++ ++++    VKVN   +E         D 
Sbjct: 179 TVSSMRLDVIISNAHHISRQKAKQLVTAGLVKVNWKTVENPDFECEEEDV 228


>gi|290892174|ref|ZP_06555170.1| S4 domain-containing protein [Listeria monocytogenes FSL J2-071]
 gi|290558297|gb|EFD91815.1| S4 domain-containing protein [Listeria monocytogenes FSL J2-071]
          Length = 258

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 22/50 (44%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
             +  R+  +I+ A   SR++ ++++    VKVN   +E         D 
Sbjct: 178 TVSSMRLDVIISNAHHISRQKAKQLVTAGLVKVNWKTVENPDFECEEEDV 227


>gi|217963827|ref|YP_002349505.1| S4 domain protein [Listeria monocytogenes HCC23]
 gi|217333097|gb|ACK38891.1| S4 domain protein [Listeria monocytogenes HCC23]
 gi|307571602|emb|CAR84781.1| RNA-binding S4 domain protein [Listeria monocytogenes L99]
          Length = 259

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 22/50 (44%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
             +  R+  +I+ A   SR++ ++++    VKVN   +E         D 
Sbjct: 179 TVSSMRLDVIISNAHHISRQKAKQLVTAGLVKVNWKTVENPDFECEEEDV 228


>gi|254854035|ref|ZP_05243383.1| S4 domain-containing protein [Listeria monocytogenes FSL R2-503]
 gi|300765463|ref|ZP_07075444.1| hypothetical protein LMHG_12332 [Listeria monocytogenes FSL N1-017]
 gi|258607427|gb|EEW20035.1| S4 domain-containing protein [Listeria monocytogenes FSL R2-503]
 gi|300513774|gb|EFK40840.1| hypothetical protein LMHG_12332 [Listeria monocytogenes FSL N1-017]
          Length = 258

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 22/50 (44%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
             +  R+  +I+ A   SR++ ++++    VKVN   +E         D 
Sbjct: 178 TVSSMRLDVIISNAHHISRQKAKQLVTAGLVKVNWKTVENPDFECEEEDV 227


>gi|116873458|ref|YP_850239.1| S4 domain-containing protein [Listeria welshimeri serovar 6b str.
           SLCC5334]
 gi|116742336|emb|CAK21460.1| S4 domain protein [Listeria welshimeri serovar 6b str. SLCC5334]
          Length = 258

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 22/50 (44%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
             +  R+  +I+ A   SR++ ++++    VKVN   +E         D 
Sbjct: 178 TVSSMRLDVIISNAHHISRQKAKQLVTAGLVKVNWKTVENPDFECEEEDV 227


>gi|16804067|ref|NP_465552.1| hypothetical protein lmo2028 [Listeria monocytogenes EGD-e]
 gi|224501171|ref|ZP_03669478.1| hypothetical protein LmonFR_01400 [Listeria monocytogenes FSL
           R2-561]
 gi|254827084|ref|ZP_05231771.1| S4 domain-containing protein [Listeria monocytogenes FSL N3-165]
 gi|254831730|ref|ZP_05236385.1| hypothetical protein Lmon1_10263 [Listeria monocytogenes 10403S]
 gi|255016669|ref|ZP_05288795.1| hypothetical protein LmonF_00281 [Listeria monocytogenes FSL
           F2-515]
 gi|255026556|ref|ZP_05298542.1| hypothetical protein LmonocytFSL_09855 [Listeria monocytogenes FSL
           J2-003]
 gi|16411498|emb|CAD00106.1| lmo2028 [Listeria monocytogenes EGD-e]
 gi|258599467|gb|EEW12792.1| S4 domain-containing protein [Listeria monocytogenes FSL N3-165]
          Length = 258

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 22/50 (44%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
             +  R+  +I+ A   SR++ ++++    VKVN   +E         D 
Sbjct: 178 TVSSMRLDVIISNAHHISRQKAKQLVTAGLVKVNWKTVENPDFECEEEDV 227


>gi|16801200|ref|NP_471468.1| hypothetical protein lin2134 [Listeria innocua Clip11262]
 gi|16414648|emb|CAC97364.1| lin2134 [Listeria innocua Clip11262]
          Length = 258

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 22/50 (44%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
             +  R+  +I+ A   SR++ ++++    VKVN   +E         D 
Sbjct: 178 TVSSMRLDVIISNAHHISRQKAKQLVTAGLVKVNWKTVENPDFECEEEDV 227


>gi|220931498|ref|YP_002508406.1| hemolysin A [Halothermothrix orenii H 168]
 gi|219992808|gb|ACL69411.1| hemolysin A [Halothermothrix orenii H 168]
          Length = 272

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 20/53 (37%), Gaps = 1/53 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
          R+  ++   G   +R   +R I    V VNG L  +A   V     I V    
Sbjct: 6  RLDILLTDKGFFETRSRAKRAIMAGDVLVNGQLETKAGTRVSEDVKIRVKNKI 58


>gi|47097617|ref|ZP_00235141.1| S4 domain protein [Listeria monocytogenes str. 1/2a F6854]
 gi|254899274|ref|ZP_05259198.1| S4 domain protein [Listeria monocytogenes J0161]
 gi|254912587|ref|ZP_05262599.1| S4 domain-containing protein [Listeria monocytogenes J2818]
 gi|254936913|ref|ZP_05268610.1| S4 domain-containing protein [Listeria monocytogenes F6900]
 gi|47014004|gb|EAL05013.1| S4 domain protein [Listeria monocytogenes str. 1/2a F6854]
 gi|258609513|gb|EEW22121.1| S4 domain-containing protein [Listeria monocytogenes F6900]
 gi|293590578|gb|EFF98912.1| S4 domain-containing protein [Listeria monocytogenes J2818]
          Length = 258

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 22/50 (44%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
             +  R+  +I+ A   SR++ ++++    VKVN   +E         D 
Sbjct: 178 TVSSMRLDVIISNAHHISRQKAKQLVTAGLVKVNWKTVENPDFECEEEDV 227


>gi|46908264|ref|YP_014653.1| S4 domain-containing protein [Listeria monocytogenes serotype 4b
           str. F2365]
 gi|47094010|ref|ZP_00231742.1| S4 domain protein [Listeria monocytogenes str. 4b H7858]
 gi|224498521|ref|ZP_03666870.1| S4 domain protein [Listeria monocytogenes Finland 1988]
 gi|254826216|ref|ZP_05231217.1| S4 domain-containing protein [Listeria monocytogenes FSL J1-194]
 gi|254933456|ref|ZP_05266815.1| S4 domain-containing protein [Listeria monocytogenes HPB2262]
 gi|254992791|ref|ZP_05274981.1| S4 domain protein [Listeria monocytogenes FSL J2-064]
 gi|255522100|ref|ZP_05389337.1| S4 domain protein [Listeria monocytogenes FSL J1-175]
 gi|46881535|gb|AAT04830.1| S4 domain protein [Listeria monocytogenes serotype 4b str. F2365]
 gi|47017615|gb|EAL08416.1| S4 domain protein [Listeria monocytogenes str. 4b H7858]
 gi|293585017|gb|EFF97049.1| S4 domain-containing protein [Listeria monocytogenes HPB2262]
 gi|293595457|gb|EFG03218.1| S4 domain-containing protein [Listeria monocytogenes FSL J1-194]
 gi|328466091|gb|EGF37261.1| S4 domain protein [Listeria monocytogenes 1816]
 gi|328472677|gb|EGF43535.1| S4 domain protein [Listeria monocytogenes 220]
 gi|332312478|gb|EGJ25573.1| S4 domain protein [Listeria monocytogenes str. Scott A]
          Length = 258

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 22/50 (44%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
             +  R+  +I+ A   SR++ ++++    VKVN   +E         D 
Sbjct: 178 TVSSMRLDVIISNAHHISRQKAKQLVTAGLVKVNWKTVENPDFECEEEDV 227


>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 = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/245 (11%), Positives = 63/245 (25%), Gaps = 42/245 (17%)

Query: 8   QENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI------ 60
                P R+ K +       SR  ++R   Q+ + VNG  ++  +  V   D I      
Sbjct: 40  DSGQKPMRIDKFLMEHLYNTSRNRLQRAAEQEFILVNGRPVKS-SYKVKPLDEIVILLDR 98

Query: 61  -EVDGVPLRKAERTRLWLY--------HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
            + +   + +     +                +V         + V      +       
Sbjct: 99  PKYENEIIPEDIPLDIVYEDEDLMVVDKPAGLVVHPGCGNYTGTLVNAIAWHLKDNPDYD 158

Query: 112 ---------GRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVYRVRF 149
                     R+D +T GLL++  +      L                     +    R 
Sbjct: 159 PNDPTVGLVHRIDKDTSGLLVVAKNADAKTHLGRQFFNKTTQRLYNALVWGSFQDEEGRI 218

Query: 150 HGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
            G + +   + ++  +         +      +         V   L  G+  +I+   +
Sbjct: 219 EGNIARHPKDRMQMAVFPPDSGIGKHAVTHYRVLENFNYVTLVECRLETGRTHQIRAHMK 278

Query: 207 FFNWK 211
                
Sbjct: 279 HIGHP 283


>gi|322420039|ref|YP_004199262.1| hemolysin A [Geobacter sp. M18]
 gi|320126426|gb|ADW13986.1| hemolysin A [Geobacter sp. M18]
          Length = 256

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          +R+ K++   G+A SR   + +I   +V V+  L ++A + V     I + G PL  
Sbjct: 4  ERLDKLVLERGLAPSRERAKALIMAGQVVVDDHLADKAGLMVPLEAEIRLKGEPLPY 60


>gi|166031850|ref|ZP_02234679.1| hypothetical protein DORFOR_01551 [Dorea formicigenerans ATCC
           27755]
 gi|166028303|gb|EDR47060.1| hypothetical protein DORFOR_01551 [Dorea formicigenerans ATCC
           27755]
          Length = 251

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 15/52 (28%), Positives = 24/52 (46%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             R+  V++ A   SR ++   I   +V VNG L+     ++   D I V G
Sbjct: 174 SVRLDTVLSVAYPLSRSKLTTYIEAAKVFVNGKLITNNGYHLNEGDLISVRG 225


>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 = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 24/57 (42%), Gaps = 10/57 (17%)

Query: 13 PQRVSKVI-------ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          P R+ K +       A     SR  + ++IA+  V V+G ++      +     +EV
Sbjct: 15 PPRLDKALGRDVPDDASL---SRSRLAKLIAEGAVSVDGAVVTDPRHRIAEGSVVEV 68


>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 = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 31/250 (12%), Positives = 65/250 (26%), Gaps = 51/250 (20%)

Query: 15  RVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
           R+   +  A  G  SR  ++ +I Q  V VN + +  +   V   D  ++          
Sbjct: 24  RLDAFLTEALGGEFSRNRIKGLIEQGAVSVNALTVTESKRKVHPGDTFQIALPEPEDPEP 83

Query: 63  DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVI 109
            G  +       ++  + L      +V   +     + V   +              R  
Sbjct: 84  KGEAITLDVLYEDQDLIVLVKPAGLVVHPGAGNWTGTLVNALIHHCGDSLSGIGGVKRPG 143

Query: 110 SVGRLDINTEGLLLLTNDGGLARV-----LELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
            V RLD +T G++++  +    R       +      L            +     +   
Sbjct: 144 IVHRLDKDTSGVMVVAKNDAAHRHLSDQFADHGRNGPLERAYRAVVWGRPRQLKGTIDAP 203

Query: 165 IVIQGICYGDMQVTLDTQKGSN---------------------AWVTVGLREGKNREIKK 203
           +   G          D+                          + V   L  G+  +I+ 
Sbjct: 204 LGRAGDRTKRAVKRDDSDDAREAITHYEVVDRYHEKPDGTSLASAVECHLETGRTHQIRV 263

Query: 204 VFEFFNWKVN 213
                   + 
Sbjct: 264 HMAHIGHPLI 273


>gi|310828534|ref|YP_003960891.1| hemolysin A [Eubacterium limosum KIST612]
 gi|308740268|gb|ADO37928.1| hemolysin A [Eubacterium limosum KIST612]
          Length = 283

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 4/62 (6%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVN--VMST-DHIEVDGVPL 67
            +R  K +   G   SR + ++ I    V V G + ++A     V      IE+ G P+
Sbjct: 2  KKERFDKYLVDHGFFDSREKAKKAIMAGLVMVGGQVKDKAGDQLAVDLDPSVIEIKGNPI 61

Query: 68 RK 69
            
Sbjct: 62 PY 63


>gi|18310800|ref|NP_562734.1| hemolysin A [Clostridium perfringens str. 13]
 gi|18145481|dbj|BAB81524.1| probable hemolysin [Clostridium perfringens str. 13]
          Length = 271

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 1/64 (1%)

Query: 6  IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          + ++    +R+  ++   GIA SR + +R I    V +    +++A   V  + +I   G
Sbjct: 1  MAEKKEKKERLDVLLVEQGIAESREKAKRYIMAGMVFIGEKRVDKAGEKVPVSSNIIFRG 60

Query: 65 VPLR 68
            L 
Sbjct: 61 EKLP 64


>gi|308069706|ref|YP_003871311.1| 30S ribosomal protein S4 [Paenibacillus polymyxa E681]
 gi|305858985|gb|ADM70773.1| 30S ribosomal protein S4 [Paenibacillus polymyxa E681]
          Length = 199

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  ++ R G A SR    +++A   V VNG  ++ A+  V   D I
Sbjct: 92  RLDNLVFRLGFANSRAGARQLVAHGHVTVNGKKVDIASYQVSPGDVI 138


>gi|301500949|ref|YP_003795414.1| ribosomal protein S4 [Alveolata sp. CCMP3155]
 gi|300069495|gb|ADJ66602.1| ribosomal protein S4 [Chromerida sp. RM11]
          Length = 207

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 20/50 (40%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            R+   + + G A S R   ++I    V VNG ++          D I +
Sbjct: 84  MRLDSFLFQVGFAVSIRSSRQLIRHGHVFVNGRVVSLPGYRCKQGDLICI 133


>gi|312865798|ref|ZP_07726020.1| ribosomal protein S4 [Streptococcus downei F0415]
 gi|311098673|gb|EFQ56895.1| ribosomal protein S4 [Streptococcus downei F0415]
          Length = 203

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVTPGQVISV 142


>gi|306845066|ref|ZP_07477646.1| hemolysin A [Brucella sp. BO1]
 gi|306274481|gb|EFM56276.1| hemolysin A [Brucella sp. BO1]
          Length = 253

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 12/51 (23%), Positives = 22/51 (43%), Gaps = 1/51 (1%)

Query: 15 RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          R+ +++   G  A+R      I +  VKV+G  + +    V     + VD 
Sbjct: 11 RLDQLLVERGFFATRSRARDAIQRGTVKVDGRPITKPGQMVARDATLAVDD 61


>gi|239636332|ref|ZP_04677334.1| YlmH protein [Staphylococcus warneri L37603]
 gi|239597687|gb|EEQ80182.1| YlmH protein [Staphylococcus warneri L37603]
          Length = 243

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 27/60 (45%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            I     +  R+  V+      SR   +++I ++RVKVN  +++     +   D + + G
Sbjct: 157 KIHSSTVSALRLDVVLKDMIHKSRSIAKQLIEKKRVKVNHTIIDSPDFQLEMNDLLSIQG 216


>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 = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 10/36 (27%), Positives = 17/36 (47%)

Query: 27 SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          SR  ++ +I Q  V +NG  +      V   D +E+
Sbjct: 38 SRSRLKALIEQGAVLLNGQPVTEPKKKVHPGDRVEI 73


>gi|320106660|ref|YP_004182250.1| hemolysin A [Terriglobus saanensis SP1PR4]
 gi|319925181|gb|ADV82256.1| hemolysin A [Terriglobus saanensis SP1PR4]
          Length = 266

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 1/56 (1%)

Query: 15 RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          R+ K++  RA + SR   + +I   RV VN   +++    +     I + G  +R 
Sbjct: 6  RLDKLMVDRALVPSRERAQALILAGRVLVNEQKIQKPGTPIAEESVIRLLGEDMRY 61


>gi|304436639|ref|ZP_07396608.1| hemolysin A [Selenomonas sp. oral taxon 149 str. 67H29BP]
 gi|304370335|gb|EFM23991.1| hemolysin A [Selenomonas sp. oral taxon 149 str. 67H29BP]
          Length = 268

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
            +R+  ++   G+A SR   +R+I   +V VN   +++A   V +   + V G  L  
Sbjct: 2  KKERLDVLLTVQGLAPSRERAKRLIMAGQVLVNEQRVDKAGATVPADAVLRVVGEDLPY 60


>gi|268610501|ref|ZP_06144228.1| S4 domain-containing protein [Ruminococcus flavefaciens FD-1]
          Length = 69

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 12/68 (17%), Positives = 27/68 (39%), Gaps = 3/68 (4%)

Query: 1  MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          M +K  +   F   ++  ++   + + +  E +  I    V VNG +       +   D 
Sbjct: 1  MAEKIKISTEF--IKLDALLKFASLVGTGGEAKARIQDGEVLVNGEVCTMRGKKIRPGDT 58

Query: 60 IEVDGVPL 67
          + +DG  +
Sbjct: 59 VSIDGNEV 66


>gi|126666789|ref|ZP_01737766.1| ribosomal protein S4 [Marinobacter sp. ELB17]
 gi|126628834|gb|EAZ99454.1| ribosomal protein S4 [Marinobacter sp. ELB17]
          Length = 206

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V  R G  S R E  ++++ + + VN  ++   +  V   D + V
Sbjct: 97  RLDNVAYRMGFGSTRAECRQLVSHKAILVNDKVVNIPSYQVKPGDVVSV 145


>gi|315651408|ref|ZP_07904433.1| ribosomal protein S4e [Eubacterium saburreum DSM 3986]
 gi|315486367|gb|EFU76724.1| ribosomal protein S4e [Eubacterium saburreum DSM 3986]
          Length = 249

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 16/64 (25%), Positives = 25/64 (39%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +      + N   +R+  VI      SR +V   I   RV +N       ++ V + D I
Sbjct: 160 VNRSEYKKINIPSERLDSVIGSIYNISRSKVNMYIDAGRVFINSKQCLSHSMKVKNGDII 219

Query: 61  EVDG 64
            V G
Sbjct: 220 TVRG 223


>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 = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 6  IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
          ++ E   P+R+ +V+AR     SR  ++ ++ +  V+ +GI++   A  V +   I
Sbjct: 25 VLDEGTVPERLDRVLARVFDDLSRARLQGLVREGLVRCDGIVVRDPARKVGAGCRI 80


>gi|313683416|ref|YP_004061154.1| SSU ribosomal protein s4p [Sulfuricurvum kujiense DSM 16994]
 gi|313156276|gb|ADR34954.1| SSU ribosomal protein S4P [Sulfuricurvum kujiense DSM 16994]
          Length = 208

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           QR+  V+ R G A+ RR   +++    V V+G  ++  +  V     +E+   
Sbjct: 98  QRLDNVVYRMGFATTRRFARQLVNHGHVLVDGKRVDIPSYRVKPGQKVEIHEK 150


>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 = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 11/57 (19%), Positives = 23/57 (40%), Gaps = 1/57 (1%)

Query: 7  VQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          V  +   +R+  V+A +    SR  ++ +I    V V+G  +      V     + +
Sbjct: 20 VDADDHGKRLDAVLAGQIASLSRNRIQTLIKGGEVTVDGRKIVEPKHRVNEGQTLTL 76


>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 = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 27/238 (11%), Positives = 59/238 (24%), Gaps = 37/238 (15%)

Query: 13  PQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
            +R+ +++ A     SR  +++++      V+G+  +R A  +     + +D        
Sbjct: 14  GKRLDRILGATVPELSRAALQKVVQAGCCTVDGLPEKRPAAKMRMGQTVTLDLPEHPDRL 73

Query: 64  ----GVP-LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
               G   L   +   +         V        ++ V   L          G+     
Sbjct: 74  QPEEGHLELLWQDDHLVVCNKPAGLTVHPCPSCPEQTLVQRLLGRFPQLSRLEGQRPGIV 133

Query: 119 EGL---------------------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
             L                                 L L S       + R         
Sbjct: 134 HRLDKDTSGLLVVALTEADCLALAAAFAERQVHKEYLALVSGLPPLEGQCREPLGRHPTA 193

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +      QG      +         GS + + V +  G+  +I+       + + 
Sbjct: 194 KIKMAVVPEDQGGRNAFTEWRRLWNTDDGSVSLLAVRIHTGRTHQIRVHMTHLGYPLL 251


>gi|154249790|ref|YP_001410615.1| 30S ribosomal protein S4 [Fervidobacterium nodosum Rt17-B1]
 gi|171769361|sp|A7HM25|RS4_FERNB RecName: Full=30S ribosomal protein S4
 gi|154153726|gb|ABS60958.1| RNA-binding S4 domain protein [Fervidobacterium nodosum Rt17-B1]
          Length = 209

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR   ++++   V VNG  ++  +  V   D I +
Sbjct: 99  RLDNVVYRLGFAINRRAARQLVSHGHVLVNGKKVDIPSYQVRPGDVISI 147


>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 = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 71/251 (28%), Gaps = 47/251 (18%)

Query: 10  NFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
               +R+  V+A      SR  V+ +I    V V+G  +      V     + +      
Sbjct: 28  EDAGKRLDAVLAAHLADLSRTRVQALIRSGEVTVDGGKIVEPKYRVNEGATLALGLPEPE 87

Query: 63  ----DGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----- 110
                G  +      E   L +  KP GLV      +   T+ + L       +S     
Sbjct: 88  EAEPKGEDIPLVVVYEDDDLIVIDKPAGLVVHPGAGNWTGTLVNALIRHCGDSLSGIGGV 147

Query: 111 -----VGRLDINTEGLLLLTND-----------------GGLARVLELPSTQWLRVYRVR 148
                V RLD  T GLL++                    G L R             R  
Sbjct: 148 RRPGIVHRLDKETSGLLVVAKTDAAHKGLSEQFADHGRSGPLERAYAALVWGAPATLRGT 207

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS------NAWVTVGLREGKNREIK 202
               + +   N  K  +V  G  +      +  + G        + +   L  G+  +I+
Sbjct: 208 VDANLARSDANRQKISVVRNGGRHAVTHWQVLERFGPADQPAVASLLECRLETGRTHQIR 267

Query: 203 KVFEFFNWKVN 213
                    + 
Sbjct: 268 VHMAHIGHPLI 278


>gi|302670348|ref|YP_003830308.1| hemolysin TlyA family protein [Butyrivibrio proteoclasticus B316]
 gi|302394821|gb|ADL33726.1| hemolysin TlyA family protein [Butyrivibrio proteoclasticus B316]
          Length = 300

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/182 (12%), Positives = 47/182 (25%), Gaps = 4/182 (2%)

Query: 12  TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLR 68
             +R+  ++   G+A SR + + +I    V VNG   ++       +    +EV G  L 
Sbjct: 4   DKERLDVLLVNRGLAPSREKAKTLIMAGEVFVNGQREDKPGTTFEESKITSLEVRGDTLP 63

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              R  L L         +  +                 ++  G   + +  +     D 
Sbjct: 64  YVSRGGLKLEKAVNNFGFSLENKICMDIGAST-GGFTDCMLQNGATKVYSVDVGHGQLDW 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L     +   +      +      D           +         +  L         
Sbjct: 123 KLRSDPRVVCMEKTNFRYMVRDDIADDLDFASCDVSFISLTKILLPARRLLKDGGQMVCL 182

Query: 189 VT 190
           + 
Sbjct: 183 IK 184


>gi|15672266|ref|NP_266440.1| 30S ribosomal protein S4 [Lactococcus lactis subsp. lactis Il1403]
 gi|281490826|ref|YP_003352806.1| 50S ribosomal protein S4P [Lactococcus lactis subsp. lactis KF147]
 gi|26399484|sp|Q9CIS2|RS4_LACLA RecName: Full=30S ribosomal protein S4
 gi|12723147|gb|AAK04382.1|AE006266_1 30S ribosomal protein S4 [Lactococcus lactis subsp. lactis Il1403]
 gi|281374584|gb|ADA64104.1| SSU ribosomal protein S4P [Lactococcus lactis subsp. lactis KF147]
 gi|326405863|gb|ADZ62934.1| 30S ribosomal protein S4 [Lactococcus lactis subsp. lactis CV56]
          Length = 203

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V
Sbjct: 93  QRLDNVVFRLGLATTRRQARQFVNHGHILVDGKRVDIPSFRVQPGQVISV 142


>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 = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 6  IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
          ++ E   P+R+ +V+AR     SR  ++ ++ +  V+ +GI++   A  V +   I
Sbjct: 25 VLDEGTVPERLDRVLARVFDDLSRARLQGLVREGLVRCDGIVVRDPARKVGAGCRI 80


>gi|15894757|ref|NP_348106.1| 30S ribosomal protein S4 [Clostridium acetobutylicum ATCC 824]
 gi|26399604|sp|Q97J08|RS4B_CLOAB RecName: Full=Putative 30S ribosomal protein S4 B
 gi|15024424|gb|AAK79446.1|AE007659_1 Ribosomal protein S4 [Clostridium acetobutylicum ATCC 824]
 gi|325508895|gb|ADZ20531.1| 30S ribosomal protein S4 [Clostridium acetobutylicum EA 2018]
          Length = 192

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 14/62 (22%), Positives = 31/62 (50%), Gaps = 2/62 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K ++I+ ++    R+  ++ R G  S  RE  +M++   + VNG  ++  +  V   D +
Sbjct: 72  KSEDILVQSLER-RLDNLVYRLGFGSTLREARQMVSHGHILVNGQKVDIPSYKVNIGDEV 130

Query: 61  EV 62
            +
Sbjct: 131 SL 132


>gi|225849518|ref|YP_002729683.1| 30S ribosomal protein S4 [Sulfurihydrogenibium azorense Az-Fu1]
 gi|225644198|gb|ACN99248.1| ribosomal protein S4 [Sulfurihydrogenibium azorense Az-Fu1]
          Length = 204

 Score = 51.3 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R++  +++      VNG  ++  +  V + D IEV
Sbjct: 95  RLDNVVYRLGFAKTRQQARQLVKHGHFTVNGKKVDIPSYRVDAGDIIEV 143


>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 = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 24/243 (9%), Positives = 58/243 (23%), Gaps = 40/243 (16%)

Query: 9   ENFTPQRVSKVIARA-GIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
            N   +R+   +    G   SR  V+  I      VNG    + ++ +   +++ + G  
Sbjct: 17  PNAAGKRLDVFLGEQVGDGFSRGRVQEWIKIGLASVNGKPWTKPSLRLRGGENVCLLGRA 76

Query: 67  -------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
                        +   +   L L                 + V   L            
Sbjct: 77  EGNCLTPEQGDLAVLYRDDWLLVLNKPAGLTTHPAPSCPEGTLVHRLLHHFPELAALDSE 136

Query: 114 LDINTEGLLLLTN-------------------DGGLARVLELPSTQWLRVYRVRFHGQVD 154
                  L   T+                          + L         R      + 
Sbjct: 137 RPGIVHRLDKDTSGLLVVALTERARLALAEDFAERRVDKVYLALVHGRPQDRGDIDLPMG 196

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDT----QKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           +   +  +  ++ +G      +   +     + G  + + V +  G+  +I+        
Sbjct: 197 RHPTHKTRMAVLKKGG--RPARSAYEMLWSSRDGRFSLLRVRIFTGRTHQIRVHLAAIGH 254

Query: 211 KVN 213
            + 
Sbjct: 255 PII 257


>gi|240145669|ref|ZP_04744270.1| hemolysin A [Roseburia intestinalis L1-82]
 gi|257202227|gb|EEV00512.1| hemolysin A [Roseburia intestinalis L1-82]
          Length = 270

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 24/178 (13%), Positives = 51/178 (28%), Gaps = 2/178 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++   G+A SR + + MI +  V V     ++A     +   IE+ G  L+   R
Sbjct: 3   ERLDLLLVNRGLAPSREKAKTMIMEGNVFVENEREDKAGSMFDTEAKIEIKGNTLKYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L           +D                 ++  G   + +  +        L +
Sbjct: 63  GGLKLEKAMTHFDIELNDKVCMDIRAST-GGFTDCMLQNGAKKVYSVDVGYGQFAWKLRQ 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +   +   +  V      D      +    +      G  +  L         + 
Sbjct: 122 DPRVVCMEKTNIRYVTPQDIDDVLDFASVDVSFISLTKVLGPARELLADGGEMVCLIK 179


>gi|251780039|ref|ZP_04822959.1| hemolysin A [Clostridium botulinum E1 str. 'BoNT E Beluga']
 gi|243084354|gb|EES50244.1| hemolysin A [Clostridium botulinum E1 str. 'BoNT E Beluga']
          Length = 269

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/146 (15%), Positives = 46/146 (31%), Gaps = 2/146 (1%)

Query: 11  FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
              +R+  ++   GI  SR + +  I + +V V+G  +++A   V    +IE  G  L+ 
Sbjct: 3   EKKERLDILLVEKGIITSRDKAKACIMEGKVFVDGQRVDKAGEKVSVIANIEYKGAKLKY 62

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             R  L L         +  D                 ++  G   + +  +        
Sbjct: 63  VSRGGLKLEKAMKSYDISLEDKVCMDIGAST-GGFTDCMLQNGAKKVYSVDVGYGQFAWK 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQ 155
           L     +   +   +  V      + 
Sbjct: 122 LRTDERVVCMERTNIRYVTLEDIGEP 147


>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 = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 28/217 (12%), Positives = 55/217 (25%), Gaps = 30/217 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--------------LRKAER 72
           SR  ++  I  QRV VNG L ++    V+  + + +D                 +   + 
Sbjct: 6   SRSRIKEWILNQRVLVNGQLCDKPKEKVLGGERVAIDAEIDEEIRFEAQDIPLDIVYEDD 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGRLDINTEGLLLLTND 127
             L +      +V   +     + +   L          R   V RLD +T GL+++   
Sbjct: 66  DILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKT 125

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQ-----------DKLNLLKKGIVIQGICYGDMQ 176
                 L                                          V          
Sbjct: 126 VPAQTRLVESLQLREITREYEAVAIGHMTAGGTVNEPISRHPTKRTHMSVHPMGKPAVTH 185

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             +      +  + + L  G+  +I+         + 
Sbjct: 186 YRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 222


>gi|281205328|gb|EFA79520.1| proteasome component region PCI domain-containing protein
            [Polysphondylium pallidum PN500]
          Length = 1051

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 15/112 (13%), Positives = 24/112 (21%), Gaps = 2/112 (1%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            RE       E    +          + R       E        +    ++ G  ++   
Sbjct: 897  REPRRDEPREGGWRDAPRDAPRD--VPRRDEPRREEGGWRDGPRRDEPRREEGGWREGPR 954

Query: 302  ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              P              G       D  +REE   R       R   R   +
Sbjct: 955  DGPRDGPRRDEPRREEGGWRDGPRRDEPKREEGGWRDGPRDGPRDGPRDGQR 1006



 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 12/109 (11%), Positives = 20/109 (18%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P                 +       +        + R  +    + G  +      P 
Sbjct: 859 APRDAPRDAPRDAPRDAPRDAPRDAPRDAPRRDDGPWGREPRRDEPREGGWRDAPRDAPR 918

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                        G       D  +REE   R       R   R    +
Sbjct: 919 DVPRRDEPRREEGGWRDGPRRDEPRREEGGWREGPRDGPRDGPRRDEPR 967



 Score = 45.2 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 8/107 (7%), Positives = 22/107 (20%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              E  +       +        R        D      +++ +       ++   P  R
Sbjct: 838 RREEPRRDEPREGGWRDAPRDAPRDAPRDAPRDAPRDAPRDAPRDAPRDAPRRDDGPWGR 897

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                         +   +       +  R      +   RR   ++
Sbjct: 898 EPRRDEPREGGWRDAPRDAPRDVPRRDEPRREEGGWRDGPRRDEPRR 944



 Score = 44.4 bits (103), Expect = 0.026,   Method: Composition-based stats.
 Identities = 10/119 (8%), Positives = 20/119 (16%), Gaps = 4/119 (3%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           VS K   E            +        E                     +    +   
Sbjct: 776 VSPKE--ENWRGRDEPRRDESWGREPRRDEPREGGWGREPRRDEPREGGWGRRDEPRRDD 833

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               +   P            A     +          +  R     + R   R + ++
Sbjct: 834 GPWGRREEPRRDEPREGGWRDAP--RDAPRDAPRDAPRDAPRDAPRDAPRDAPRDAPRR 890



 Score = 44.0 bits (102), Expect = 0.035,   Method: Composition-based stats.
 Identities = 9/105 (8%), Positives = 16/105 (15%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P                 +                    +    ++ G  +        
Sbjct: 883 APRDAPRRDDGPWGREPRRDEPREGGWRDAPRDAPRDVPRRDEPRREEGGWRDGPRRDEP 942

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
            R           G       D  +REE   R      +      
Sbjct: 943 RREEGGWREGPRDGPRDGPRRDEPRREEGGWRDGPRRDEPKREEG 987



 Score = 42.9 bits (99), Expect = 0.076,   Method: Composition-based stats.
 Identities = 19/131 (14%), Positives = 33/131 (25%), Gaps = 15/131 (11%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNII---------------SEVPDDF 282
           +K +RE      LE+ +    A    S+   R+R                       +  
Sbjct: 731 EKRIREAEEAARLEKERQEALANETYSQRKERERREKAAADAAAGVSPKEENWRGRDEPR 790

Query: 283 TRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
                    +    ++        R       W  +          G+REE  R  P   
Sbjct: 791 RDESWGREPRRDEPREGGWGREPRRDEPREGGWGRRDEPRRDDGPWGRREEPRRDEPREG 850

Query: 343 SKRSLRRTSAK 353
             R   R + +
Sbjct: 851 GWRDAPRDAPR 861



 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 18/124 (14%), Positives = 28/124 (22%), Gaps = 3/124 (2%)

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G  RE  +   RE       E  + +              R     + P D  R      
Sbjct: 808 GWGREPRRDEPREGGWGRRDEPRRDDGPWGRREEPRRDEPREGGWRDAPRDAPRDAPRD- 866

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                 +      P      A               +   RE   R +P    +   RR 
Sbjct: 867 APRDAPRDAPRDAPRDAPRDAPRRDDGPWGREPRRDEP--REGGWRDAPRDAPRDVPRRD 924

Query: 351 SAKK 354
             ++
Sbjct: 925 EPRR 928


>gi|116250744|ref|YP_766582.1| FtsJ cell division/haemolysin-like protein [Rhizobium
          leguminosarum bv. viciae 3841]
 gi|115255392|emb|CAK06467.1| putative FtsJ cell division/haemolysin-like protein [Rhizobium
          leguminosarum bv. viciae 3841]
          Length = 248

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 9  ENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +   QR+ +++   G  ASR      + +  V++ G ++ +A     +   IE+D 
Sbjct: 2  SDQNTQRLDQLLVSLGLFASRSRARDAVQRGTVRIGGQVVTKAGALFSADAAIEIDD 58


>gi|225016757|ref|ZP_03705949.1| hypothetical protein CLOSTMETH_00669 [Clostridium methylpentosum
          DSM 5476]
 gi|224950425|gb|EEG31634.1| hypothetical protein CLOSTMETH_00669 [Clostridium methylpentosum
          DSM 5476]
          Length = 75

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 13/71 (18%), Positives = 28/71 (39%), Gaps = 10/71 (14%)

Query: 1  MKDKNIVQENFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
          MK +++        ++ +++     A+ G       + ++A+  V VNG         + 
Sbjct: 1  MKTESV-TIRTEFIKLDQLLKFTGAAQTGG----HAKELVAEGVVTVNGEPCLMRGKKIR 55

Query: 56 STDHIEVDGVP 66
            D + VDG  
Sbjct: 56 PGDRVSVDGQI 66


>gi|168214392|ref|ZP_02640017.1| hemolysin A [Clostridium perfringens CPE str. F4969]
 gi|169343538|ref|ZP_02864537.1| hemolysin A [Clostridium perfringens C str. JGS1495]
 gi|169298098|gb|EDS80188.1| hemolysin A [Clostridium perfringens C str. JGS1495]
 gi|170714133|gb|EDT26315.1| hemolysin A [Clostridium perfringens CPE str. F4969]
          Length = 271

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 1/64 (1%)

Query: 6  IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          + ++    +R+  ++   GIA SR + +R I    V +    +++A   V  + +I   G
Sbjct: 1  MAEKKEKKERLDVLLVEQGIAESREKAKRYIMAGMVFIGEKRVDKAGEKVPVSSNIIFRG 60

Query: 65 VPLR 68
            L 
Sbjct: 61 EKLP 64


>gi|124806291|ref|XP_001350682.1| RNA pseudouridylate synthase, putative [Plasmodium falciparum 3D7]
 gi|23496808|gb|AAN36362.1| RNA pseudouridylate synthase, putative [Plasmodium falciparum 3D7]
          Length = 409

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 17/89 (19%), Positives = 37/89 (41%), Gaps = 1/89 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK+++ + + SR + + +I    +KVN  ++ +    +     I+V   P++    T+
Sbjct: 14  RLSKILSLSSVTSRNKAQELIKNGDIKVNNQVVNQNVF-IDVNSKIQVKDKPIQVDICTK 72

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           LW  +KP  +                   
Sbjct: 73  LWGIYKPKHIFCNTEKDYTYEEKIHFNKM 101



 Score = 41.7 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 36/161 (22%), Positives = 66/161 (40%), Gaps = 2/161 (1%)

Query: 71  ERTRLWLYHK--PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + T +  Y+K                         I   +I +  L+  +EGLLLLTNDG
Sbjct: 187 KHTNIITYNKLNMNIYDYIKKQNMLYEKKNHVTNYIPEHLIIINSLNSGSEGLLLLTNDG 246

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             A+ L+      L  Y ++    +  DK+ LL+KG  I       + + +   K ++ W
Sbjct: 247 DFAKNLKDIQNNILTTYLIKVQEDLCIDKIKLLRKGCFINNQHIYPVNIEIIKSKHTSKW 306

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +     E  +  +  +F  +N  + +  R S+GP++   + 
Sbjct: 307 IKFTYVEKSHNYLLYLFSKYNITIRKCKRFSFGPYKYTDIN 347


>gi|297625817|ref|YP_003687580.1| 30S ribosomal protein S4 [Propionibacterium freudenreichii subsp.
           shermanii CIRM-BIA1]
 gi|296921582|emb|CBL56136.1| 30S ribosomal protein S4 [Propionibacterium freudenreichii subsp.
           shermanii CIRM-BIA1]
          Length = 201

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG AS RR+  +M++   + VNG  +   +  V   D I+V
Sbjct: 92  RLDNVVYRAGFASTRRQARQMVSHGHILVNGKKVNIPSFRVAPLDIIDV 140


>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 = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 33/230 (14%), Positives = 70/230 (30%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+   +A+     SR  +   I    V  NG         ++  + + V+  P       
Sbjct: 38  RLDAALAKMLPDYSRSRIAGWIKDGEVLCNGQPA-SPKTKLIGGEQLAVNIQPSQETQAY 96

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-----IFSRVISVGR 113
                   +   + + L L      +V   +     + +   L          R   V R
Sbjct: 97  TPEAMPLDIVYEDDSVLVLNKPAGLVVHPAAGNWTGTLLNGLLAHASELSQVPRAGIVHR 156

Query: 114 LDINTEGLLLLTNDGGLARV------------LELPSTQWLRVYRVRFHGQVDQDKLNLL 161
           LD +T GL+++                     +       +  +  +   Q+ +D  N L
Sbjct: 157 LDKDTSGLMVVAKTLPAQNHLVQQLQSRSVKRIYRAIADGIVPFDGKIETQIGRDPHNRL 216

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  +V  G       V +  +  +++++   L  G+  +I+         
Sbjct: 217 KMAVVKFGGKEAITHVKVLERYQAHSYIECSLETGRTHQIRVHLREARHP 266


>gi|110800396|ref|YP_696501.1| hemolysin A [Clostridium perfringens ATCC 13124]
 gi|110803042|ref|YP_699101.1| hemolysin A [Clostridium perfringens SM101]
 gi|168210819|ref|ZP_02636444.1| hemolysin A [Clostridium perfringens B str. ATCC 3626]
 gi|168215446|ref|ZP_02641071.1| hemolysin A [Clostridium perfringens NCTC 8239]
 gi|182625677|ref|ZP_02953446.1| hemolysin A [Clostridium perfringens D str. JGS1721]
 gi|110675043|gb|ABG84030.1| hemolysin A [Clostridium perfringens ATCC 13124]
 gi|110683543|gb|ABG86913.1| hemolysin A [Clostridium perfringens SM101]
 gi|170711111|gb|EDT23293.1| hemolysin A [Clostridium perfringens B str. ATCC 3626]
 gi|177909079|gb|EDT71554.1| hemolysin A [Clostridium perfringens D str. JGS1721]
 gi|182382420|gb|EDT79899.1| hemolysin A [Clostridium perfringens NCTC 8239]
          Length = 271

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 1/64 (1%)

Query: 6  IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          + ++    +R+  ++   GIA SR + +R I    V +    +++A   V  + +I   G
Sbjct: 1  MAEKKEKKERLDVLLVEQGIAESREKAKRYIMAGMVFIGEKRVDKAGEKVPVSSNIIFRG 60

Query: 65 VPLR 68
            L 
Sbjct: 61 EKLP 64


>gi|15617094|ref|NP_240307.1| 30S ribosomal protein S4 [Buchnera aphidicola str. APS
           (Acyrthosiphon pisum)]
 gi|219681846|ref|YP_002468232.1| 30S ribosomal protein S4 [Buchnera aphidicola str. 5A
           (Acyrthosiphon pisum)]
 gi|219682401|ref|YP_002468785.1| 30S ribosomal protein S4 [Buchnera aphidicola str. Tuc7
           (Acyrthosiphon pisum)]
 gi|257471551|ref|ZP_05635550.1| 30S ribosomal protein S4 [Buchnera aphidicola str. LSR1
           (Acyrthosiphon pisum)]
 gi|11387058|sp|P57567|RS4_BUCAI RecName: Full=30S ribosomal protein S4
 gi|254764574|sp|B8D9S3|RS4_BUCA5 RecName: Full=30S ribosomal protein S4
 gi|254764575|sp|B8D825|RS4_BUCAT RecName: Full=30S ribosomal protein S4
 gi|25294492|pir||A84988 30S ribosomal protein S4 [imported] - Buchnera sp. (strain APS)
 gi|10039159|dbj|BAB13193.1| 30S ribosomal protein S4 [Buchnera aphidicola str. APS
           (Acyrthosiphon pisum)]
 gi|219622134|gb|ACL30290.1| 30S ribosomal protein S4 [Buchnera aphidicola str. Tuc7
           (Acyrthosiphon pisum)]
 gi|219624689|gb|ACL30844.1| 30S ribosomal protein S4 [Buchnera aphidicola str. 5A
           (Acyrthosiphon pisum)]
 gi|311086222|gb|ADP66304.1| 30S ribosomal protein S4 [Buchnera aphidicola str. LL01
           (Acyrthosiphon pisum)]
 gi|311086799|gb|ADP66880.1| 30S ribosomal protein S4 [Buchnera aphidicola str. TLW03
           (Acyrthosiphon pisum)]
 gi|311087386|gb|ADP67466.1| 30S ribosomal protein S4 [Buchnera aphidicola str. JF99
           (Acyrthosiphon pisum)]
 gi|311087883|gb|ADP67962.1| 30S ribosomal protein S4 [Buchnera aphidicola str. JF98
           (Acyrthosiphon pisum)]
          Length = 206

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V+ R G   +R E  ++I  + + VN  ++  A+  V   D I +   
Sbjct: 97  RLDNVVYRMGFGCTRSESRQLINHKSIMVNNKVVNIASYQVSPNDQISIRNK 148


>gi|323483273|ref|ZP_08088663.1| hypothetical protein HMPREF9474_00412 [Clostridium symbiosum
           WAL-14163]
 gi|323691228|ref|ZP_08105504.1| ribosomal protein S4 [Clostridium symbiosum WAL-14673]
 gi|323403371|gb|EGA95679.1| hypothetical protein HMPREF9474_00412 [Clostridium symbiosum
           WAL-14163]
 gi|323504747|gb|EGB20533.1| ribosomal protein S4 [Clostridium symbiosum WAL-14673]
          Length = 197

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R+E  +++  + V VNG  +   +  V + D IE+
Sbjct: 88  RLDNVLFRMGFGRTRKETRQIVDHKHVLVNGKPVNIPSYRVKAGDTIEI 136


>gi|262048764|ref|ZP_06021646.1| hypothetical protein SAD30_1594 [Staphylococcus aureus D30]
 gi|262051690|ref|ZP_06023909.1| hypothetical protein SA930_1517 [Staphylococcus aureus 930918-3]
 gi|259160425|gb|EEW45450.1| hypothetical protein SA930_1517 [Staphylococcus aureus 930918-3]
 gi|259163220|gb|EEW47780.1| hypothetical protein SAD30_1594 [Staphylococcus aureus D30]
          Length = 212

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 2/64 (3%)

Query: 3   DKNIVQENFT--PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++N   E+ T    R+  VI      SR   +++I ++RVKVN  +++ A   + + D I
Sbjct: 122 NENWKNESATVSSLRLDVVIKEMIRKSRTIAKQLIEKKRVKVNHTIVDSADFQLQANDLI 181

Query: 61  EVDG 64
            + G
Sbjct: 182 SIQG 185


>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 = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 6  IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
          ++ E   P+R+ +V+AR     SR  ++ ++ +  V+ +GI++   A  V +   I
Sbjct: 12 VLDEGTVPERLDRVLARVFDDLSRARLQGLVREGLVRCDGIVVRDPARKVGAGSRI 67


>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 = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 26/243 (10%), Positives = 63/243 (25%), Gaps = 38/243 (15%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V+E F+ +R+ + +A      SR   + +I  + V ++   + +++  V +     +   
Sbjct: 9   VEEEFSNKRLDQFLALVYPEYSRSFYQNLIENRFVLLDNNPVRKSSTKVKTGQEFTIIIP 68

Query: 66  --------------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                          +   +     +Y  P  +V         + V   L    +     
Sbjct: 69  PPEPLEIEPENIPLEIYYEDEDLAVVYKPPGMVVHPSVGHTSGTLVNALLYHFKNVSQYQ 128

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--------------- 156
           G+        L     G L       + + L+                            
Sbjct: 129 GKERAGIVHRLDKDTAGLLIVAKSEFAHKELQKMFQDREIDKKYKAIVSGIVKKDHGLID 188

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDT------QKGSNAWVTVGLREGKNREIKKVFEFF 208
                 +     +  +         +       +K +   V + L  G+  +I+  F   
Sbjct: 189 LPIGRSIYNRQKMGTVATNPKDALTEYWVEKRFEKHNLTLVDIKLHTGRTHQIRVHFSAI 248

Query: 209 NWK 211
              
Sbjct: 249 GHP 251


>gi|315221952|ref|ZP_07863863.1| S4 domain protein [Streptococcus anginosus F0211]
 gi|315188918|gb|EFU22622.1| S4 domain protein [Streptococcus anginosus F0211]
          Length = 263

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 18/53 (33%), Positives = 31/53 (58%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +  R+ KV+A +   SR    R+IA ++VKVN  +L+  + +++  D I V G
Sbjct: 183 SSMRLDKVVAASFHLSRSIAARLIATKQVKVNYSMLDNPSHHLLLNDLISVRG 235


>gi|291320720|ref|YP_003515985.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           agalactiae]
 gi|290753056|emb|CBH41032.1| Ribosomal large subunit pseudouridine synthaseC [Mycoplasma
           agalactiae]
          Length = 284

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 37/241 (15%), Positives = 79/241 (32%), Gaps = 37/241 (15%)

Query: 4   KNIVQENFTPQRVSKVIARA------GIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           K I Q +   +++ K I+        G   R  + R+  Q+ +KVN   +  +   V + 
Sbjct: 3   KFIAQSSDNGRKLIKYISSLFKKLPEG---R--IYRLFRQKSIKVNNKRIADSNYVVKTG 57

Query: 58  DHIEVDGVP-----------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD- 99
           D I + G+                  +   +   L +  K   +V   S+          
Sbjct: 58  DEIIIYGIKDEPSFVIYDNSWKLDSDIVYEDDNILLINKKAGTIVHGDSNCLDNQVFSYL 117

Query: 100 -NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
               +   R   VGRLD  T GL++   +      L   +    ++Y ++       + +
Sbjct: 118 KFKQNSAFRPSHVGRLDKWTSGLIMYAKNYPALAELNRKTEFLDKIYVLKSDYNPHDEIV 177

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNA-------WVTVGLREGKNREIKKVFEFFNWK 211
           ++      +Q        +     K +          +   L  G+  +I+   E+  + 
Sbjct: 178 SVYVHHDELQQKMVATKNMQHPDDKMAKTRFFKKDNKLYAQLFTGRKHQIRATLEYLEYP 237

Query: 212 V 212
           +
Sbjct: 238 I 238


>gi|85713166|ref|ZP_01044198.1| 30S ribosomal protein S4 [Idiomarina baltica OS145]
 gi|85693036|gb|EAQ31002.1| 30S ribosomal protein S4 [Idiomarina baltica OS145]
          Length = 206

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G AS R E  ++++ + V VNG ++   +  V   D + V
Sbjct: 96  QRLDNVVYRMGFASTRAEARQLVSHKAVVVNGQVVNIPSFMVRPEDVVSV 145


>gi|315221587|ref|ZP_07863507.1| ribosomal protein S4 [Streptococcus anginosus F0211]
 gi|315189421|gb|EFU23116.1| ribosomal protein S4 [Streptococcus anginosus F0211]
          Length = 227

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V    L+  
Sbjct: 118 RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVSVGQVISVREKSLKVP 174


>gi|293376582|ref|ZP_06622810.1| ribosomal RNA large subunit methyltransferase J [Turicibacter
          sanguinis PC909]
 gi|325839398|ref|ZP_08166837.1| ribosomal RNA large subunit methyltransferase J [Turicibacter sp.
          HGF1]
 gi|292644808|gb|EFF62890.1| ribosomal RNA large subunit methyltransferase J [Turicibacter
          sanguinis PC909]
 gi|325490518|gb|EGC92834.1| ribosomal RNA large subunit methyltransferase J [Turicibacter sp.
          HGF1]
          Length = 268

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 12/59 (20%), Positives = 23/59 (38%), Gaps = 1/59 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
            +R+  ++ + G   SR   +R I    V V+   +++    V    +I V G     
Sbjct: 2  KKERIDVLLTQLGYFNSRETAKRAIMAGLVLVDQQRIDKPGEKVPVESNITVKGNVCPY 60


>gi|326382558|ref|ZP_08204249.1| cell division protein FtsW [Gordonia neofelifaecis NRRL B-59395]
 gi|326198677|gb|EGD55860.1| cell division protein FtsW [Gordonia neofelifaecis NRRL B-59395]
          Length = 595

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 12/108 (11%), Positives = 19/108 (17%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G   L                  R         P           ++   S   +  TP 
Sbjct: 480 GLSRLLRLPRPEAYRSARQPDRRRASSATSGRRPAPVRGPSAGGRREAPRSWATRPRTPA 539

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R                    G R     +    P+     R + +
Sbjct: 540 ADRPRRGRWSGESSSGEIHYPARGARPNRSWQESRAPAPHERPRRAGR 587



 Score = 37.1 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 13/88 (14%), Positives = 24/88 (27%), Gaps = 5/88 (5%)

Query: 267 LVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLS 326
             R  P+ ++ +     +      +       +    P  RR  ++              
Sbjct: 462 AARHEPDAVAALAGPAPKGLSRLLRLPRPEAYRSARQPDRRRASSATSGRRPA--PVRGP 519

Query: 327 DSGQREENHR---RSPSFPSKRSLRRTS 351
            +G R E  R     P  P+    RR  
Sbjct: 520 SAGGRREAPRSWATRPRTPAADRPRRGR 547


>gi|15924181|ref|NP_371715.1| YlmH [Staphylococcus aureus subsp. aureus Mu50]
 gi|15926774|ref|NP_374307.1| hypothetical protein SA1034 [Staphylococcus aureus subsp. aureus
           N315]
 gi|156979512|ref|YP_001441771.1| hypothetical protein SAHV_1181 [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|13700990|dbj|BAB42286.1| SA1034 [Staphylococcus aureus subsp. aureus N315]
 gi|14246961|dbj|BAB57353.1| YlmH [Staphylococcus aureus subsp. aureus Mu50]
 gi|156721647|dbj|BAF78064.1| hypothetical protein [Staphylococcus aureus subsp. aureus Mu3]
 gi|285816873|gb|ADC37360.1| hypothetical protein, contains S4-like RNA binding domain
           [Staphylococcus aureus 04-02981]
          Length = 212

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 2/64 (3%)

Query: 3   DKNIVQENFT--PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++N   E+ T    R+  VI      SR   +++I ++RVKVN  +++ A   + + D I
Sbjct: 122 NENWKNESATVSSLRLDVVIKEMIRKSRTIAKQLIEKKRVKVNHTIVDSADFQLQANDLI 181

Query: 61  EVDG 64
            + G
Sbjct: 182 SIQG 185


>gi|331001804|ref|ZP_08325326.1| hypothetical protein HMPREF0491_00188 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330412778|gb|EGG92161.1| hypothetical protein HMPREF0491_00188 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 249

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 3/64 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +++K I   N + +R+  +I      SR +V   I   +V +N       +  +   D I
Sbjct: 163 LENKRI---NISSERLDSIIGSIYNISRSKVNLYIDAGKVFINSKQCFSHSAKIKDGDII 219

Query: 61  EVDG 64
            V G
Sbjct: 220 TVRG 223


>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 = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 72/230 (31%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIREGAVIVNDKP-SQPKDKMIGGEQIRVTVRPSEENLAF 98

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 99  MPEPMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIRVHMREANHP 268


>gi|254670508|emb|CBA06264.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis alpha153]
          Length = 373

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 72/230 (31%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 58  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 116

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 117 VPEPMALDIIYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQVPRAGIVHR 176

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 177 LDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 236

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 237 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIRVHMREANHP 286


>gi|188589502|ref|YP_001921546.1| hemolysin A [Clostridium botulinum E3 str. Alaska E43]
 gi|188499783|gb|ACD52919.1| hemolysin A [Clostridium botulinum E3 str. Alaska E43]
          Length = 269

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/146 (15%), Positives = 46/146 (31%), Gaps = 2/146 (1%)

Query: 11  FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
              +R+  ++   GI  SR + +  I + +V V+G  +++A   V    +IE  G  L+ 
Sbjct: 3   EKKERLDILLVEKGIITSRDKAKACIMEGKVFVDGQRVDKAGEKVSVIANIEYKGAKLKY 62

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             R  L L         +  D                 ++  G   + +  +        
Sbjct: 63  VSRGGLKLEKAMKSYDISLEDKVCMDIGAST-GGFTDCMLQNGAKKVYSVDVGYGQFAWK 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQ 155
           L     +   +   +  V      + 
Sbjct: 122 LRTDERVVCMERTNIRYVTLEDIGEP 147


>gi|109897338|ref|YP_660593.1| 30S ribosomal protein S4 [Pseudoalteromonas atlantica T6c]
 gi|332307746|ref|YP_004435597.1| ribosomal protein S4 [Glaciecola agarilytica 4H-3-7+YE-5]
 gi|122972198|sp|Q15X49|RS4_PSEA6 RecName: Full=30S ribosomal protein S4
 gi|109699619|gb|ABG39539.1| SSU ribosomal protein S4P [Pseudoalteromonas atlantica T6c]
 gi|332175075|gb|AEE24329.1| ribosomal protein S4 [Glaciecola agarilytica 4H-3-7+YE-5]
          Length = 206

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G AS R E  ++++ + + VNG ++   + NV + D + V
Sbjct: 96  QRLDNVVYRIGFASTRSEARQLVSHKAILVNGQVVNVPSFNVSADDVVSV 145


>gi|296132888|ref|YP_003640135.1| translation initiation factor IF-2 [Thermincola sp. JR]
 gi|296031466|gb|ADG82234.1| translation initiation factor IF-2 [Thermincola potens JR]
          Length = 837

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 13/115 (11%), Positives = 29/115 (25%), Gaps = 2/115 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           ++V    ++++      +  Q     P          RP   +  P       +  + + 
Sbjct: 68  KKVDAAAIKDR-ENQGNQRPQPVGQKPAGQGPRPAGQRPPGQAARPAGQRPAGQRPAGQR 126

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
              +  + A                G   +    +GQR       P+    R   
Sbjct: 127 PAGQGPRSAGQRPA-GQRPAGQRPAGQRPAGQRPAGQRPPGQAARPAGQGPRPAG 180



 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 11/115 (9%), Positives = 34/115 (29%), Gaps = 1/115 (0%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           ++ +     LE+ +V       + +    ++ +  +E P           +  G  + + 
Sbjct: 29  IQVKNHMSALEDEEVAKVRAAAAGKKEKNEQTDTAAEAPKKVDAAAIKDRENQGNQRPQP 88

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR-RTSAKK 354
           +      +          G  +         +    + P+    RS   R + ++
Sbjct: 89  VGQKPAGQGPRPAGQRPPGQAARPAGQRPAGQRPAGQRPAGQGPRSAGQRPAGQR 143



 Score = 44.4 bits (103), Expect = 0.027,   Method: Composition-based stats.
 Identities = 11/117 (9%), Positives = 27/117 (23%), Gaps = 4/117 (3%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +E+                    +   +              +  + + Q+      +  
Sbjct: 54  KEKNEQTDTAAEAPKKVDAAAIKDRENQGNQRPQPVGQKPAGQGPRPAGQRPPGQAARPA 113

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS----KRSLRRTSAKK 354
                 +  A      +G  S+    +GQR    R +   P+            A +
Sbjct: 114 GQRPAGQRPAGQRPAGQGPRSAGQRPAGQRPAGQRPAGQRPAGQRPAGQRPPGQAAR 170


>gi|293376356|ref|ZP_06622593.1| ribosomal protein S4 [Turicibacter sanguinis PC909]
 gi|292645045|gb|EFF63118.1| ribosomal protein S4 [Turicibacter sanguinis PC909]
          Length = 169

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR+  +++    + V+G  ++  + +V     I +
Sbjct: 62  RLDNLVYRLGLAATRRQARQLVNHGHITVDGKRVDIPSYSVKPGQTISL 110


>gi|239996313|ref|ZP_04716837.1| 30S ribosomal protein S4 [Alteromonas macleodii ATCC 27126]
 gi|332142182|ref|YP_004427920.1| 30S ribosomal protein S4 [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|226697796|sp|B4RT52|RS4_ALTMD RecName: Full=30S ribosomal protein S4
 gi|327552204|gb|AEA98922.1| 30S ribosomal protein S4 [Alteromonas macleodii str. 'Deep
           ecotype']
          Length = 206

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G AS R E  ++++ + + VNG ++   + NV + D + V
Sbjct: 96  QRLDNVVYRMGFASTRAEARQLVSHKAIMVNGQVVNIPSFNVSAEDVVSV 145


>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 = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 35/247 (14%), Positives = 68/247 (27%), Gaps = 40/247 (16%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--- 61
           +V +    +R+ KV+AR     SR  ++  I  +RV+++G   +     V     IE   
Sbjct: 69  VVPDELAGERLDKVLARVFPEFSRNRLQSWIEAERVRIDGKPAK-IRQPVPLGATIELVP 127

Query: 62  --------VDGVP----LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
                       P    +   + T + +      +V   +     + +   L        
Sbjct: 128 DLLPEQLAFTPEPVPLDIVYEDDTLVVINKPAGMVVHPAAGNWSGTVLNGLLYRYGDAAA 187

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
              R   V RLD  T GL+++         L           R       +  +   +  
Sbjct: 188 GLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLALVWGNMPEEGTIDA 247

Query: 164 GIVIQ-----------GICYGDMQVTL------DTQKGSNAWVTVGLREGKNREIKKVFE 206
            I              G      +           Q+     +   L  G+  +I+    
Sbjct: 248 PIGRDPRERTRMAVVTGASGKPARTHFRRVDTALWQRQPVTAIHCDLETGRTHQIRVHCA 307

Query: 207 FFNWKVN 213
                + 
Sbjct: 308 HIGHPLL 314


>gi|239627500|ref|ZP_04670531.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239517646|gb|EEQ57512.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 278

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 24/165 (14%), Positives = 51/165 (30%), Gaps = 2/165 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++ +  +A SR + + +I    V VNG   ++A  +  +   IEV G  LR   R
Sbjct: 7   ERLDVLMVQKNLAESREKAKALIMSGIVYVNGQKEDKAGTSFDTAAQIEVRGSTLRYVSR 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L                              ++  G + + +  +        L  
Sbjct: 67  GGLKLEKAMSHFGVELEGKVCMDVGAST-GGFTDCMLQNGAVKVYSVDVGHGQLAWKLRN 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
              +   +   +  V      D+     +    +      G ++ 
Sbjct: 126 DERVVCMEKTNIRYVLPGDIGDRIMFASIDVSFISLTKVLGPVKN 170


>gi|218778690|ref|YP_002430008.1| hemolysin A [Desulfatibacillum alkenivorans AK-01]
 gi|218760074|gb|ACL02540.1| hemolysin A [Desulfatibacillum alkenivorans AK-01]
          Length = 245

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
            QR+  +I   G+A SR   + +I   +V V+ +  ++A   +    +I V G 
Sbjct: 3  KKQRLDTLITELGLAPSRTRAQALILSGQVLVDDVPQDKAGAMISPEANITVRGQ 57


>gi|254718615|ref|ZP_05180426.1| Cell division protein FtsJ [Brucella sp. 83/13]
 gi|265983592|ref|ZP_06096327.1| hemolysin A [Brucella sp. 83/13]
 gi|306839867|ref|ZP_07472665.1| hemolysin A [Brucella sp. NF 2653]
 gi|264662184|gb|EEZ32445.1| hemolysin A [Brucella sp. 83/13]
 gi|306405053|gb|EFM61334.1| hemolysin A [Brucella sp. NF 2653]
          Length = 253

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 1/51 (1%)

Query: 15 RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          R+ +++   G  A+R      I +  VKV+G  + +    V S   + VD 
Sbjct: 11 RLDQLLVERGFFATRSRARDAIQRGTVKVDGRPITKPGQMVASDAALAVDD 61


>gi|329907623|ref|ZP_08274693.1| SSU ribosomal protein S4p (S9e) [Oxalobacteraceae bacterium
          IMCC9480]
 gi|327546928|gb|EGF31837.1| SSU ribosomal protein S4p (S9e) [Oxalobacteraceae bacterium
          IMCC9480]
          Length = 139

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+  VI R G  S R E  ++++ +   VNGI++  A+  V + D I V
Sbjct: 30 RLDNVIYRMGFGSTRAEARQLVSHKAFTVNGIVVNIASYQVKAGDVIVV 78


>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 = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 32/258 (12%), Positives = 72/258 (27%), Gaps = 52/258 (20%)

Query: 8   QENFTPQRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
             + T +R+ + +A A     SR  V+ +IA+  V ++G     A   +     I +   
Sbjct: 7   DSDATGKRLDQWLAAALGPELSRSRVQSLIAEGHVTIDGAPAREAKQKLREGMTIAIVLP 66

Query: 63  DGVP-----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
           +  P           +   +   + +      +V   +     + V   +          
Sbjct: 67  EPEPAEPIAENIPLDILYEDDDLIVINKPAGLVVHPGNGNWTGTLVNALIYHCGDSLSGI 126

Query: 106 ---SRVISVGRLDINTEGLLLLTNDGGLARV------LELPSTQWLRVYRVRFHGQVDQD 156
               R   V RLD +T G++++  +    R           +    R Y     G  ++ 
Sbjct: 127 GGIRRPGIVHRLDKDTSGVMVVAKNDRSHRHLSEQFADHGRTGDLERAYLALVWGMTERP 186

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSN---------------------AWVTVGLRE 195
           +  +                V  + +   +                     + V   L  
Sbjct: 187 QGFIDAHLGRSHRDRTKQAVVNEEREDARHAITHYVTVEKFAPLEDATALASLVECRLET 246

Query: 196 GKNREIKKVFEFFNWKVN 213
           G+  +I+         + 
Sbjct: 247 GRTHQIRVHMAHIGHPLV 264


>gi|167957398|ref|ZP_02544472.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [candidate division TM7 single-cell isolate
           TM7c]
          Length = 379

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 31/260 (11%), Positives = 80/260 (30%), Gaps = 42/260 (16%)

Query: 2   KDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           KD  +++     +R+  ++    G  SR   ++MI   +V V+G + + A   V    ++
Sbjct: 101 KDCYLLESKSDKKRLDILLVEKVGKESRSTYQKMITAGQVLVDGKIAKNAKQLVGIESNV 160

Query: 61  EVDGV-----PLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
           +++       P++     E   + + +KP G++T             ++    +   +  
Sbjct: 161 KIESKQQKFTPIKYETIYEDNDIIVINKPAGMLTHAKGAIAEEFTAADIVKPITNYKADT 220

Query: 113 RLD------INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
                          +LL      A            V +  +         +     + 
Sbjct: 221 NRPGIIHRLDRNTSGVLLMVKNSDAASKIQKQFSQRTVKKTYYAIVCGIPYQHKALIDLP 280

Query: 167 IQGICYGDMQVTLD---------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           I+          +                  K + + + +  + G+  +++   ++ N  
Sbjct: 281 IERNPSRPSTFRVGVNGKSAQTSYEVERSIIKKNISLIKLQPKTGRTHQLRVHMQYLNTP 340

Query: 212 VNRLIRISYGPFQLGTLLAG 231
           +            LG L+ G
Sbjct: 341 I------------LGDLVYG 348


>gi|314936647|ref|ZP_07843994.1| YlmH protein [Staphylococcus hominis subsp. hominis C80]
 gi|313655266|gb|EFS19011.1| YlmH protein [Staphylococcus hominis subsp. hominis C80]
          Length = 224

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 15/60 (25%), Positives = 29/60 (48%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           NI     +  R+  V+      SR   +++I ++RVKVN  L++     + + D + + G
Sbjct: 138 NIHHSTVSALRLDVVLKEMIRKSRSIAKQLIEKKRVKVNHTLIDSPDFQLQNNDLLSIQG 197


>gi|228475066|ref|ZP_04059794.1| YlmH protein [Staphylococcus hominis SK119]
 gi|228271051|gb|EEK12439.1| YlmH protein [Staphylococcus hominis SK119]
          Length = 224

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 15/60 (25%), Positives = 29/60 (48%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           NI     +  R+  V+      SR   +++I ++RVKVN  L++     + + D + + G
Sbjct: 138 NIHHSTVSALRLDVVLKEMIRKSRSIAKQLIEKKRVKVNHTLIDSPDFQLQNNDLLSIQG 197


>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 = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 35/247 (14%), Positives = 68/247 (27%), Gaps = 40/247 (16%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--- 61
           +V +    +R+ KV+AR     SR  ++  I  +RV+++G   +     V     IE   
Sbjct: 69  VVPDELAGERLDKVLARLFPEFSRNRLQSWIEAERVRIDGKPAK-IRQPVPLGATIELVP 127

Query: 62  --------VDGVP----LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
                       P    +   + T + +      +V   +     + +   L        
Sbjct: 128 DLLPEQLAFTPEPVPLEIVYEDDTLVVINKPAGMVVHPAAGNWSGTVLNGLLYRYGDAAA 187

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
              R   V RLD  T GL+++         L           R       +  +   +  
Sbjct: 188 GLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLALVWGNMPEEGTIDA 247

Query: 164 GIVIQ-----------GICYGDMQVTL------DTQKGSNAWVTVGLREGKNREIKKVFE 206
            I              G      +           Q+     +   L  G+  +I+    
Sbjct: 248 PIGRDPRERTRMAVVTGASGKPARTHFRRVDTAIWQRQPVTAIHCDLETGRTHQIRVHCA 307

Query: 207 FFNWKVN 213
                + 
Sbjct: 308 HIGHPLL 314


>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 = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 34/261 (13%), Positives = 75/261 (28%), Gaps = 53/261 (20%)

Query: 6   IVQENFTPQRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           IV      +RV K I+       SR  V+ ++ Q  V +NG L    +  + + D +   
Sbjct: 39  IVSHVDDGKRVDKFISANAPDDLSRARVQALVRQGNVTINGELPRGTSTKISNGDVVRFL 98

Query: 63  -----DGVP--------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI----- 104
                D +P        +   +   + L      +V         + V   L        
Sbjct: 99  MPPPEDAIPQPENIPLDILHEDDDLIVLIKPAGMVVHPAPGNWSGTLVNALLHHCDGNLS 158

Query: 105 ----FSRVISVGRLDINTEGLLLLTNDGGLARVLELP-----------------STQWLR 143
                 R   V RLD +T G++++         L+                   +     
Sbjct: 159 GIGGVKRPGIVHRLDKDTSGVMVVAKSYRAHIDLQEQFADHGRTGPLERAYWALAWGAPP 218

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQG-----------ICYGDMQVTLDTQKGSNAWVTVG 192
             + +    + +     +++ +V +G                 +    + +   + +   
Sbjct: 219 RMKGKVDTLIGRHPTRRVQRAVVEEGAPDAKHAITHYEVVKRFEDAERSGEAMASLIECK 278

Query: 193 LREGKNREIKKVFEFFNWKVN 213
           L  G+  +I+         + 
Sbjct: 279 LETGRTHQIRVHLTHLGNPLL 299


>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 = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 72/230 (31%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 99  VPEPMALDIIYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQVPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIRVHMREANHP 268


>gi|73974842|ref|XP_539199.2| PREDICTED: similar to tigger transposable element derived 5 [Canis
           familiaris]
          Length = 847

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 13/113 (11%), Positives = 31/113 (27%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           ++  + P  L E                   P+       D  R +  +   +  S++  
Sbjct: 113 IQRPVQPPRLREPFHVARRYRAHPSEAGLPAPSARHYPRRDPARSEPRAPLAHPTSRRGC 172

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             +    ++        +G      + +G       R+P+ P      R   +
Sbjct: 173 PRSGRRAQDTGKAAGRDQGGRPPAGAAAGSGRPRGPRAPARPGAAQTARGPPR 225


>gi|332199691|gb|EGJ13766.1| hypothetical protein SPAR69_1602 [Streptococcus pneumoniae GA41317]
          Length = 256

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 11/48 (22%), Positives = 26/48 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +++     SR +  ++I ++ V+VN  +++++   V   D I V
Sbjct: 188 RLDVLLSNVLKLSRNQANQLIEKKLVQVNYHVVDKSDYTVQVGDLISV 235


>gi|332073997|gb|EGI84475.1| hypothetical protein SPAR68_1670 [Streptococcus pneumoniae GA41301]
          Length = 252

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 11/48 (22%), Positives = 26/48 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +++     SR +  ++I ++ V+VN  +++++   V   D I V
Sbjct: 184 RLDVLLSNVLKLSRNQANQLIEKKLVQVNYHVVDKSDYTVQVGDLISV 231


>gi|332072491|gb|EGI82974.1| hypothetical protein SPAR50_1662 [Streptococcus pneumoniae GA17570]
 gi|332200221|gb|EGJ14294.1| hypothetical protein SPAR93_1698 [Streptococcus pneumoniae GA47368]
 gi|332201088|gb|EGJ15159.1| hypothetical protein SPAR120_1594 [Streptococcus pneumoniae
           GA47901]
          Length = 252

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 11/48 (22%), Positives = 26/48 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +++     SR +  ++I ++ V+VN  +++++   V   D I V
Sbjct: 184 RLDVLLSNVLKLSRNQANQLIEKKLVQVNYHVVDKSDYTVQVGDLISV 231


>gi|307127872|ref|YP_003879903.1| YlmH protein [Streptococcus pneumoniae 670-6B]
 gi|306484934|gb|ADM91803.1| YlmH protein [Streptococcus pneumoniae 670-6B]
 gi|332072830|gb|EGI83311.1| hypothetical protein SPAR148_1591 [Streptococcus pneumoniae
           GA17545]
          Length = 261

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 11/48 (22%), Positives = 26/48 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +++     SR +  ++I ++ V+VN  +++++   V   D I V
Sbjct: 184 RLDVLLSNVLKLSRNQANQLIEKKLVQVNYHVVDKSDYTVQVGDLISV 231


>gi|303255983|ref|ZP_07342011.1| hypothetical protein CGSSpBS455_10815 [Streptococcus pneumoniae
           BS455]
 gi|302597042|gb|EFL64160.1| hypothetical protein CGSSpBS455_10815 [Streptococcus pneumoniae
           BS455]
          Length = 261

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 11/48 (22%), Positives = 26/48 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +++     SR +  ++I ++ V+VN  +++++   V   D I V
Sbjct: 184 RLDVLLSNVLKLSRNQANQLIEKKLVQVNYHVVDKSDYTVQVGDLISV 231


>gi|237650668|ref|ZP_04524920.1| YlmH protein [Streptococcus pneumoniae CCRI 1974]
 gi|237822427|ref|ZP_04598272.1| YlmH protein [Streptococcus pneumoniae CCRI 1974M2]
          Length = 261

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 11/48 (22%), Positives = 26/48 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +++     SR +  ++I ++ V+VN  +++++   V   D I V
Sbjct: 184 RLDVLLSNVLKLSRNQANQLIEKKLVQVNYHVVDKSDYTVQVGDLISV 231


>gi|225861490|ref|YP_002742999.1| YlmH protein [Streptococcus pneumoniae Taiwan19F-14]
 gi|225726507|gb|ACO22358.1| YlmH protein [Streptococcus pneumoniae Taiwan19F-14]
 gi|327389848|gb|EGE88193.1| hypothetical protein SPAR5_1539 [Streptococcus pneumoniae GA04375]
          Length = 261

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 11/48 (22%), Positives = 26/48 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +++     SR +  ++I ++ V+VN  +++++   V   D I V
Sbjct: 184 RLDVLLSNVLKLSRNQANQLIEKKLVQVNYHVVDKSDYTVQVGDLISV 231


>gi|168491455|ref|ZP_02715598.1| YlmH protein [Streptococcus pneumoniae CDC0288-04]
 gi|225857278|ref|YP_002738789.1| YlmH protein [Streptococcus pneumoniae P1031]
 gi|183574265|gb|EDT94793.1| YlmH protein [Streptococcus pneumoniae CDC0288-04]
 gi|225724661|gb|ACO20513.1| YlmH protein [Streptococcus pneumoniae P1031]
          Length = 261

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 11/48 (22%), Positives = 26/48 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +++     SR +  ++I ++ V+VN  +++++   V   D I V
Sbjct: 184 RLDVLLSNVLKLSRNQANQLIEKKLVQVNYHVVDKSDYTVQVGDLISV 231


>gi|149001946|ref|ZP_01826900.1| YlmH protein [Streptococcus pneumoniae SP14-BS69]
 gi|147759755|gb|EDK66745.1| YlmH protein [Streptococcus pneumoniae SP14-BS69]
          Length = 261

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 11/48 (22%), Positives = 26/48 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +++     SR +  ++I ++ V+VN  +++++   V   D I V
Sbjct: 184 RLDVLLSNVLKLSRNQANQLIEKKLVQVNYHVVDKSDYTVQVGDLISV 231


>gi|116516882|ref|YP_816931.1| YlmH protein [Streptococcus pneumoniae D39]
 gi|149021244|ref|ZP_01835490.1| YlmH protein [Streptococcus pneumoniae SP23-BS72]
 gi|168493563|ref|ZP_02717706.1| YlmH protein [Streptococcus pneumoniae CDC3059-06]
 gi|225855092|ref|YP_002736604.1| YlmH protein [Streptococcus pneumoniae JJA]
 gi|225859417|ref|YP_002740927.1| YlmH protein [Streptococcus pneumoniae 70585]
 gi|116077458|gb|ABJ55178.1| YlmH protein [Streptococcus pneumoniae D39]
 gi|147930345|gb|EDK81329.1| YlmH protein [Streptococcus pneumoniae SP23-BS72]
 gi|183576486|gb|EDT97014.1| YlmH protein [Streptococcus pneumoniae CDC3059-06]
 gi|225720470|gb|ACO16324.1| YlmH protein [Streptococcus pneumoniae 70585]
 gi|225724266|gb|ACO20119.1| YlmH protein [Streptococcus pneumoniae JJA]
          Length = 261

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 11/48 (22%), Positives = 26/48 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +++     SR +  ++I ++ V+VN  +++++   V   D I V
Sbjct: 184 RLDVLLSNVLKLSRNQANQLIEKKLVQVNYHVVDKSDYTVQVGDLISV 231


>gi|15903549|ref|NP_359099.1| hypothetical protein spr1506 [Streptococcus pneumoniae R6]
 gi|15459167|gb|AAL00310.1| Conserved hypothetical protein [Streptococcus pneumoniae R6]
          Length = 283

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 11/48 (22%), Positives = 26/48 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +++     SR +  ++I ++ V+VN  +++++   V   D I V
Sbjct: 206 RLDVLLSNVLKLSRNQANQLIEKKLVQVNYHVVDKSDYTVQVGDLISV 253


>gi|15901497|ref|NP_346101.1| ylmH protein [Streptococcus pneumoniae TIGR4]
 gi|111658558|ref|ZP_01409221.1| hypothetical protein SpneT_02000314 [Streptococcus pneumoniae
           TIGR4]
 gi|148984099|ref|ZP_01817394.1| ylmH protein [Streptococcus pneumoniae SP3-BS71]
 gi|148988709|ref|ZP_01820142.1| ylmH protein [Streptococcus pneumoniae SP6-BS73]
 gi|148993766|ref|ZP_01823193.1| ylmH protein [Streptococcus pneumoniae SP9-BS68]
 gi|148997713|ref|ZP_01825277.1| ylmH protein [Streptococcus pneumoniae SP11-BS70]
 gi|149006731|ref|ZP_01830417.1| ylmH protein [Streptococcus pneumoniae SP18-BS74]
 gi|149011476|ref|ZP_01832723.1| ylmH protein [Streptococcus pneumoniae SP19-BS75]
 gi|168483468|ref|ZP_02708420.1| YlmH protein [Streptococcus pneumoniae CDC1873-00]
 gi|168486969|ref|ZP_02711477.1| YlmH protein [Streptococcus pneumoniae CDC1087-00]
 gi|168488624|ref|ZP_02712823.1| YlmH protein [Streptococcus pneumoniae SP195]
 gi|168575149|ref|ZP_02721112.1| YlmH protein [Streptococcus pneumoniae MLV-016]
 gi|182684604|ref|YP_001836351.1| ylmH protein [Streptococcus pneumoniae CGSP14]
 gi|194398742|ref|YP_002038276.1| YlmH protein [Streptococcus pneumoniae G54]
 gi|221232399|ref|YP_002511552.1| hypothetical protein SPN23F_16630 [Streptococcus pneumoniae ATCC
           700669]
 gi|298230127|ref|ZP_06963808.1| hypothetical protein SpneCMD_05606 [Streptococcus pneumoniae str.
           Canada MDR_19F]
 gi|298254434|ref|ZP_06978020.1| hypothetical protein SpneCM_02315 [Streptococcus pneumoniae str.
           Canada MDR_19A]
 gi|298503406|ref|YP_003725346.1| ribosomal protein S4e [Streptococcus pneumoniae TCH8431/19A]
 gi|303258591|ref|ZP_07344571.1| ylmH protein [Streptococcus pneumoniae SP-BS293]
 gi|303262678|ref|ZP_07348618.1| ylmH protein [Streptococcus pneumoniae SP14-BS292]
 gi|303263618|ref|ZP_07349540.1| ylmH protein [Streptococcus pneumoniae BS397]
 gi|303266379|ref|ZP_07352268.1| ylmH protein [Streptococcus pneumoniae BS457]
 gi|303268252|ref|ZP_07354050.1| ylmH protein [Streptococcus pneumoniae BS458]
 gi|307068287|ref|YP_003877253.1| hypothetical protein SPAP_1667 [Streptococcus pneumoniae AP200]
 gi|4009474|gb|AAC95444.1| YlmH [Streptococcus pneumoniae G54]
 gi|14973153|gb|AAK75741.1| ylmH protein [Streptococcus pneumoniae TIGR4]
 gi|147756212|gb|EDK63254.1| ylmH protein [Streptococcus pneumoniae SP11-BS70]
 gi|147761646|gb|EDK68610.1| ylmH protein [Streptococcus pneumoniae SP18-BS74]
 gi|147764466|gb|EDK71397.1| ylmH protein [Streptococcus pneumoniae SP19-BS75]
 gi|147923388|gb|EDK74501.1| ylmH protein [Streptococcus pneumoniae SP3-BS71]
 gi|147925910|gb|EDK76985.1| ylmH protein [Streptococcus pneumoniae SP6-BS73]
 gi|147927722|gb|EDK78746.1| ylmH protein [Streptococcus pneumoniae SP9-BS68]
 gi|172043115|gb|EDT51161.1| YlmH protein [Streptococcus pneumoniae CDC1873-00]
 gi|182629938|gb|ACB90886.1| ylmH protein [Streptococcus pneumoniae CGSP14]
 gi|183570103|gb|EDT90631.1| YlmH protein [Streptococcus pneumoniae CDC1087-00]
 gi|183572630|gb|EDT93158.1| YlmH protein [Streptococcus pneumoniae SP195]
 gi|183578732|gb|EDT99260.1| YlmH protein [Streptococcus pneumoniae MLV-016]
 gi|194358409|gb|ACF56857.1| YlmH protein [Streptococcus pneumoniae G54]
 gi|220674860|emb|CAR69435.1| conserved hypothetical protein [Streptococcus pneumoniae ATCC
           700669]
 gi|298239001|gb|ADI70132.1| ribosomal protein S4e [Streptococcus pneumoniae TCH8431/19A]
 gi|301794643|emb|CBW37094.1| conserved hypothetical protein [Streptococcus pneumoniae INV104]
 gi|301800473|emb|CBW33112.1| conserved hypothetical protein [Streptococcus pneumoniae OXC141]
 gi|301802364|emb|CBW35118.1| conserved hypothetical protein [Streptococcus pneumoniae INV200]
 gi|302636234|gb|EFL66729.1| ylmH protein [Streptococcus pneumoniae SP14-BS292]
 gi|302640092|gb|EFL70547.1| ylmH protein [Streptococcus pneumoniae SP-BS293]
 gi|302642203|gb|EFL72552.1| ylmH protein [Streptococcus pneumoniae BS458]
 gi|302644079|gb|EFL74337.1| ylmH protein [Streptococcus pneumoniae BS457]
 gi|302646656|gb|EFL76881.1| ylmH protein [Streptococcus pneumoniae BS397]
 gi|306409824|gb|ADM85251.1| hypothetical protein SPAP_1667 [Streptococcus pneumoniae AP200]
          Length = 261

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 11/48 (22%), Positives = 26/48 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +++     SR +  ++I ++ V+VN  +++++   V   D I V
Sbjct: 184 RLDVLLSNVLKLSRNQANQLIEKKLVQVNYHVVDKSDYTVQVGDLISV 231


>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 = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 20/239 (8%), Positives = 59/239 (24%), Gaps = 35/239 (14%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-------------- 55
           +    R+ + +A    ASR + +  IA   V+V+G+ + +    +               
Sbjct: 9   SAEGVRLDQAVAERTGASRAKAQAWIAAGYVRVDGVPVTKPGKRLKGETVEVVAPPDPPP 68

Query: 56  ------STDHIEVDGV-PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                     I  +    +   +   +  +  P     T  +          +       
Sbjct: 69  RVAPEQRDLEILYEDEDMVVVNKPPGMATHPAPGLTSGTLVNALMGRYAQAAVEGEPPEQ 128

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           +  G +         +   G     +   +  +   +  + +  +   +   +     I 
Sbjct: 129 VRPGIVHRLDRDTSGVIVVGRHDAAVRRLADAFKNRFVFKRYVAITVGQPPEMTLVAPIG 188

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGL--------------REGKNREIKKVFEFFNWKVN 213
                  ++ +       A     L                G+  +I+   +     + 
Sbjct: 189 RHPVERHKMHVSGVNARYAETDFSLLATVDGHALVDARPHTGRTHQIRVHLKHLYAPIL 247


>gi|218441671|ref|YP_002380000.1| photosystem II S4 domain protein [Cyanothece sp. PCC 7424]
 gi|218174399|gb|ACK73132.1| photosystem II S4 domain protein [Cyanothece sp. PCC 7424]
          Length = 259

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 18/65 (27%), Positives = 27/65 (41%), Gaps = 2/65 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             K  +       R+   IA AG   SR ++   I+   V+VN   +   + N+ S D I
Sbjct: 172 PKKKEMTTVEASMRLD-AIASAGFGMSRSKMAEAISSGDVRVNWKEITSTSHNIQSGDLI 230

Query: 61  EVDGV 65
            V G 
Sbjct: 231 SVRGK 235


>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 = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 6  IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
          ++ E   P+R+ +V+AR     SR  ++ ++ +  V+ +GI++   A  V +   I
Sbjct: 12 VLDEGTVPERLDRVLARVFDDLSRARLQGLVREGLVRCDGIVVRDPARKVGAGCRI 67


>gi|270292377|ref|ZP_06198588.1| YlmH protein [Streptococcus sp. M143]
 gi|270278356|gb|EFA24202.1| YlmH protein [Streptococcus sp. M143]
          Length = 262

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 13/48 (27%), Positives = 26/48 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +++ A   SR++  ++I ++ V+VN   +E+    V   D I V
Sbjct: 185 RLDALLSSALKLSRKQAGQLIEKKSVQVNYHPIEKLDYLVAVGDLISV 232


>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 = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 34/258 (13%), Positives = 73/258 (28%), Gaps = 52/258 (20%)

Query: 8   QENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
             + T +R+ + +A A     SR  V+ +IA+  V ++G+        +     I V   
Sbjct: 75  DSDATGKRLDQWLAAALGPDLSRSRVQSLIAEGHVTIDGVPARETKQKLREGMTIAVVLP 134

Query: 63  DGVP-----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
           +  P           +   +   + +      +V   +     + V   +          
Sbjct: 135 EPEPAEPIAENIPLDILYEDDDLIVINKPAGLVVHPGNGNWTGTLVNALIYHCGDSLSGI 194

Query: 106 ---SRVISVGRLDINTEGLLLLTNDGGLARVLELP--------------------STQWL 142
               R   V RLD +T G++++  +    R L                        T+  
Sbjct: 195 GGIRRPGIVHRLDKDTSGVMVVAKNDLSHRHLSEQFADHGRTGDLERAYLALVWGMTERP 254

Query: 143 RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-------AWVTVGLRE 195
           + Y     G+  +D+              +         + G         + V   L  
Sbjct: 255 QGYIDAHLGRSHRDRTKQAVVNEERDDARHAITHYATVEKFGPREDATALASLVECRLET 314

Query: 196 GKNREIKKVFEFFNWKVN 213
           G+  +I+         + 
Sbjct: 315 GRTHQIRVHMAHIGHPLV 332


>gi|260587701|ref|ZP_05853614.1| RNA-binding S4 [Blautia hansenii DSM 20583]
 gi|331084008|ref|ZP_08333115.1| hypothetical protein HMPREF0992_02039 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|260541966|gb|EEX22535.1| RNA-binding S4 [Blautia hansenii DSM 20583]
 gi|330402370|gb|EGG81940.1| hypothetical protein HMPREF0992_02039 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 250

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 13/64 (20%), Positives = 22/64 (34%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
             +  +       R+  VI  A   SR  +   I   +V +NG  +      +   D + 
Sbjct: 162 PKREEISGTVASPRLDSVIGLAFRTSRSSMISYIESGKVFINGKSVVSNGYVLKEGDIVS 221

Query: 62  VDGV 65
           V G 
Sbjct: 222 VRGK 225


>gi|254418198|ref|ZP_05031922.1| hemolysin A [Brevundimonas sp. BAL3]
 gi|196184375|gb|EDX79351.1| hemolysin A [Brevundimonas sp. BAL3]
          Length = 241

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 26/73 (35%), Gaps = 2/73 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAE 71
           R+ +++   G+A SR   +  I    V V+G   +  +  V +   I  VD        
Sbjct: 1  MRLDQLLVTRGLAESRARAKAAIEAGGVTVDGTPAKSGSQTVGANAEIGYVDAHRWVGRG 60

Query: 72 RTRLWLYHKPIGL 84
            +L        +
Sbjct: 61 ALKLDHALTVWPV 73


>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 = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 37/247 (14%), Positives = 69/247 (27%), Gaps = 40/247 (16%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--- 61
           +V +    +R+ KV+AR     SR  ++  I  +RV+++G   +     V     IE   
Sbjct: 69  VVPDELAGERLDKVLARVFPEFSRNRLQSWIEAERVRIDGKPAK-IRQPVPLGATIELVP 127

Query: 62  --------VDGVP----LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
                       P    +   + T + +      +V   +     + +   L        
Sbjct: 128 DLLPEQLAFTPEPVPLEIVYEDDTLVVINKPAGMVVHPAAGNWSGTVLNGLLYRYGDAAA 187

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
              R   V RLD  T GL+++         L           R       +  +   +  
Sbjct: 188 GLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLALVWGNMPEEGTIDA 247

Query: 164 GIVIQ-GICYGDMQVTLDTQKGSNAWVT-----------VG-----LREGKNREIKKVFE 206
            I            VT  + K +                V      L  G+  +I+    
Sbjct: 248 PIGRDPRERTRMAVVTSASGKPARTHFRRVDSAIWQRQPVTAIHCDLETGRTHQIRVHCA 307

Query: 207 FFNWKVN 213
                + 
Sbjct: 308 HIGHPLL 314


>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 = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 45/310 (14%), Positives = 92/310 (29%), Gaps = 53/310 (17%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE------------- 61
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I              
Sbjct: 13  RIDEFLAKELQISKNQVLNLIKEGLVFCQKKEVKKGGLALKEGDEITLLTPQITPKPLKK 72

Query: 62  -VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISV 111
            +D       E   L + +KP  LV   +      T+ D L              R   V
Sbjct: 73  GLDLEIEVIFEDEDLLVLNKPPNLVVHKAPSVKEPTLVDWLEFKNYELSNLGLKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR-------VRFHGQVDQDKLNLLKKG 164
            RLD +T G +++  +      L       +                ++  +        
Sbjct: 133 HRLDKDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLARNPN 192

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVTVG-----------LREGKNREIKKVFEFFNWKVN 213
             ++ I     +        S     +            L  G+  +I+           
Sbjct: 193 NRLKMIALKAAKKEKIRYSKSEFTSLLTSQNGMDLIGAKLFTGRTHQIRAHL-------E 245

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPN 273
            L R   G      L  G  + + K+ +R  L  +L+E      +  +     L++D   
Sbjct: 246 YLNRHIIG----DNLY-GLNQALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLE 300

Query: 274 IISEVPDDFT 283
            + +V D  +
Sbjct: 301 YLKKVFDKES 310


>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 = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 72/230 (31%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 159 LDKETSGLMVVAKTLSAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIRVHMREANHP 268


>gi|257067034|ref|YP_003153290.1| 30S ribosomal protein S4 [Anaerococcus prevotii DSM 20548]
 gi|256798914|gb|ACV29569.1| ribosomal protein S4 [Anaerococcus prevotii DSM 20548]
          Length = 197

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +  R+G+A +RRE  +++    + VNG  ++  +  V   D IEV
Sbjct: 88  RLDNIAFRSGLARTRREARQIVTHGHLTVNGKQVDIPSYKVSEGDVIEV 136


>gi|148559255|ref|YP_001258457.1| hemolysin A [Brucella ovis ATCC 25840]
 gi|148370512|gb|ABQ60491.1| hemolysin A [Brucella ovis ATCC 25840]
          Length = 253

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 12/51 (23%), Positives = 23/51 (45%), Gaps = 1/51 (1%)

Query: 15 RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          R+ +++   G  A+R      I +  VKV+G  + +    V+    + VD 
Sbjct: 11 RLDQLLVERGFFATRSRARDAIQRGTVKVDGRPITKPGQMVVRDAALAVDD 61


>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 = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 40/247 (16%), Positives = 73/247 (29%), Gaps = 48/247 (19%)

Query: 14  QRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------- 63
            R+ +V+A RA   SR  ++ +I   RV +    L   A +V + D I +D         
Sbjct: 13  VRLDRVLALRAPELSRSRLKALILAGRVAIGETPLCDPAYHVGAGDTITIDVPPAIAAEP 72

Query: 64  -GVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRVI 109
            G P+           + +      +V   +  +  + V   +              R  
Sbjct: 73  AGEPIALDIVHEDDDIIVIDKPRGLVVHPAAGHETGTLVNALIAHCGASLSGIGGVRRPG 132

Query: 110 SVGRLDINTEGLLLLTND-----------------GGLARVLELPSTQWLRVYRVRFHGQ 152
            V RLD +T GL++   +                 G L R                    
Sbjct: 133 IVHRLDKDTTGLMVAAKNDRAHQSLSAQFADHGRTGALRRGYYAFVWGVPNRPHGTIDAP 192

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDT------QKGSNAWVTVGLREGKNREIKKVFE 206
           +D+   N  +K  V +G         +         K   + +   L  G+  +I+    
Sbjct: 193 IDRHPHNR-EKMAVREGGRDAITHWEVLETFAGRSGKPVASLIACQLETGRTHQIRVHLA 251

Query: 207 FFNWKVN 213
                + 
Sbjct: 252 HIGHPLL 258


>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 = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 32/236 (13%), Positives = 70/236 (29%), Gaps = 39/236 (16%)

Query: 13  PQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP----- 66
             R+ KV+AR     SR  +++ I    V V+G +     + V   +HI V         
Sbjct: 48  GDRLDKVVARLVPQFSRSRMQQWIDDGFVTVDGKVGRT-RMTVYGDEHIVVLPQAAPEDT 106

Query: 67  ----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISV 111
                     +   +   + +      +V   S     + +   L          R   V
Sbjct: 107 AFAPEEMALNIVYEDEAIIVVNKPAGLVVHPGSGNWSGTLLNGLLHYWPALIGVPRAGIV 166

Query: 112 GRLDINTEGLLLLTNDGGLARVLELP------STQWLRVYRVRFHGQVDQD-----KLNL 160
            RLD +T GL+++     +   L           ++  +     +     D         
Sbjct: 167 HRLDKDTSGLMVVAKTLEVHTDLVRQLAARTVKREYFALVWGTPNLSGTIDASMGRHPRD 226

Query: 161 LKKGIVIQGICYGDMQVTLDTQK------GSNAWVTVGLREGKNREIKKVFEFFNW 210
             +  V++ +         +  +         + +   L  G+  +I+   +   +
Sbjct: 227 RIRMAVLESMSAKPAITHFERIESGLLDRRPVSLMRCRLETGRTHQIRVHMQSIGF 282


>gi|325206453|gb|ADZ01906.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis M04-240196]
          Length = 374

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 72/230 (31%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 159 LDKETSGLMVVAKTLSAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIRVHMREANHP 268


>gi|302527747|ref|ZP_07280089.1| predicted protein [Streptomyces sp. AA4]
 gi|302436642|gb|EFL08458.1| predicted protein [Streptomyces sp. AA4]
          Length = 368

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 14/110 (12%), Positives = 30/110 (27%), Gaps = 4/110 (3%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS-SQKNGLSKQKKL 301
           + LG                 +E   ++     +       R  +    +  G    +  
Sbjct: 262 QPLGTGAPRRQNSQPMPQPRPAEAPPQNHAQPPARGAQPPARPVRAPQPRPAGPPHGRAA 321

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
            +P  R +  +       +      D   R       P+ P +R+ RR +
Sbjct: 322 GSPPPRPSNQAPAGPPPEVSPG---DRPSRRTPGASRPTPPGRRNARRNA 368



 Score = 43.6 bits (101), Expect = 0.047,   Method: Composition-based stats.
 Identities = 6/105 (5%), Positives = 13/105 (12%), Gaps = 2/105 (1%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                       P  + +   R       +                 + + +    P   
Sbjct: 230 ARDAVPPARRIGPPEAPDASGRPVRPPRRQNSQPLGTGAPRRQNSQPMPQPRPAEAPPQN 289

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                                  R        +  S        A
Sbjct: 290 HAQPPARGAQPPARPVRAPQP--RPAGPPHGRAAGSPPPRPSNQA 332



 Score = 40.2 bits (92), Expect = 0.57,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 22/112 (19%), Gaps = 2/112 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRP--NIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           E+ G    E           S       R        +             +    +  +
Sbjct: 203 EEPGEARPEPDGAAPRGRAGSLPPRPGARDAVPPARRIGPPEAPDASGRPVRPPRRQNSQ 262

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                  R   S          +   +  Q      + P+ P +    R + 
Sbjct: 263 PLGTGAPRRQNSQPMPQPRPAEAPPQNHAQPPARGAQPPARPVRAPQPRPAG 314


>gi|18311359|ref|NP_563293.1| 30S ribosomal protein S4 [Clostridium perfringens str. 13]
 gi|110801306|ref|YP_697066.1| 30S ribosomal protein S4 [Clostridium perfringens ATCC 13124]
 gi|168215204|ref|ZP_02640829.1| ribosomal protein S4 [Clostridium perfringens CPE str. F4969]
 gi|168216659|ref|ZP_02642284.1| ribosomal protein S4 [Clostridium perfringens NCTC 8239]
 gi|182626935|ref|ZP_02954668.1| ribosomal protein S4 [Clostridium perfringens D str. JGS1721]
 gi|26399584|sp|Q8XHV0|RS4A_CLOPE RecName: Full=30S ribosomal protein S4 A
 gi|123049591|sp|Q0TMS4|RS4A_CLOP1 RecName: Full=30S ribosomal protein S4 A
 gi|18146043|dbj|BAB82083.1| 30S ribosomal protein S4 [Clostridium perfringens str. 13]
 gi|110675953|gb|ABG84940.1| 30S ribosomal protein S4 [Clostridium perfringens ATCC 13124]
 gi|170713408|gb|EDT25590.1| ribosomal protein S4 [Clostridium perfringens CPE str. F4969]
 gi|177907725|gb|EDT70340.1| ribosomal protein S4 [Clostridium perfringens D str. JGS1721]
 gi|182381248|gb|EDT78727.1| ribosomal protein S4 [Clostridium perfringens NCTC 8239]
          Length = 206

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            R+  V+ R G   SR E  +++      VNG  ++ A+  V   D I V
Sbjct: 98  MRLDNVVYRLGYGASRTEARQLVNHGHFLVNGKKVDIASFKVSVNDVITV 147


>gi|302387565|ref|YP_003823387.1| hemolysin A [Clostridium saccharolyticum WM1]
 gi|302198193|gb|ADL05764.1| hemolysin A [Clostridium saccharolyticum WM1]
          Length = 288

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 25/178 (14%), Positives = 54/178 (30%), Gaps = 2/178 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++ + G+A SR + + +I    V V+G   ++A        +IEV G  LR   R
Sbjct: 3   ERLDVLLVKLGLAESREKAKAVIMSGIVYVDGEKEDKAGTTFEENANIEVRGNTLRYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L         +                    ++  G   +    +        L  
Sbjct: 63  GGLKLEKAMTQFGLSLEGRVCMDVGSST-GGFTDCMLQNGAAKVYAVDVGHGQLAWKLRN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +   +   +  V      D  + + +    +      G ++  L  +      + 
Sbjct: 122 DKRVVCMEKTNIRYVTPEDLADPIEFSSIDVSFISLTKVLGPVKALLTDEGEVVCLIK 179


>gi|269124017|ref|YP_003306594.1| RNA-binding S4 domain-containing protein [Streptobacillus
           moniliformis DSM 12112]
 gi|268315343|gb|ACZ01717.1| RNA-binding S4 domain protein [Streptobacillus moniliformis DSM
           12112]
          Length = 245

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 11/76 (14%), Positives = 25/76 (32%), Gaps = 2/76 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRKAER 72
           R+   I+     SR +  ++I    V+++  + +     +   D + +   G  L   E 
Sbjct: 170 RLDNFISAITNLSRNKANQLIESGLVQIDYEICKEKDRKIYQNDILSIRKYGKYLISEEL 229

Query: 73  TRLWLYHKPIGLVTTH 88
                  K   +    
Sbjct: 230 EYSKKGKKRWIIKKYD 245


>gi|110801849|ref|YP_699635.1| 30S ribosomal protein S4 [Clostridium perfringens SM101]
 gi|122956505|sp|Q0SQH2|RS4A_CLOPS RecName: Full=30S ribosomal protein S4 A
 gi|110682350|gb|ABG85720.1| 30S ribosomal protein S4 [Clostridium perfringens SM101]
          Length = 206

 Score = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            R+  V+ R G   SR E  +++      VNG  ++ A+  V   D I V
Sbjct: 98  MRLDNVVYRLGYGASRTEARQLVNHGHFLVNGKKVDIASFKVSVNDVITV 147


>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 = 50.9 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 34/209 (16%), Positives = 69/209 (33%), Gaps = 24/209 (11%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR------KAERTRLWLYHKPI 82
           + V+ ++  ++V VNG ++ +   ++   D I VD  P          E   L + +KP 
Sbjct: 23  KNVKNLLKFKQVSVNGQVISQFDYSLKRDDEIVVDRNPNNNSSLDIIYEDRELIVINKPA 82

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLT------NDGGL 130
           GL++     +   T +  +           RV  V RLD  T G+LL        N    
Sbjct: 83  GLLSMAGGNEKEKTAYHLVGEYLKSKNKNARVFIVHRLDKETSGVLLFAKNEIIKNKLQN 142

Query: 131 ARVLELPSTQWLRVYRVRFHGQVD------QDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
                +    +L +   +   +         +    +                 +  +  
Sbjct: 143 NWNDIVYKRGYLAIIEGKLKKKHGTIKNHLDESKTQMVYIANNGKGKLAITNYKVLKESR 202

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            N+ + V L  G+  +I+   +     + 
Sbjct: 203 YNSLIEVFLETGRKNQIRVHMQSLGHSIV 231


>gi|325069012|ref|ZP_08127685.1| hemolysin A [Actinomyces oris K20]
          Length = 86

 Score = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   + R G+A SR     +IA   V ++G ++ + A  V     IE+
Sbjct: 5  IRIDSELVRRGLARSRTHAATLIADGHVTLDGEVVTKPARQVNPAQAIEI 54


>gi|289644379|ref|ZP_06476461.1| delta-aminolevulinic acid dehydratase [Frankia symbiont of Datisca
           glomerata]
 gi|289505817|gb|EFD26834.1| delta-aminolevulinic acid dehydratase [Frankia symbiont of Datisca
           glomerata]
          Length = 986

 Score = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 17/139 (12%), Positives = 27/139 (19%), Gaps = 18/139 (12%)

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM-- 285
           L  G  R       R+  G       +      +          P+          R   
Sbjct: 485 LAPGRHRH------RDPGGRPEGPRLERRRRHRVPHGTGRAAASPDPGGAQGRPGGRGGV 538

Query: 286 --------KKNSSQKNGLSKQKKLATPVHR--RNLASNVWMAKGIHSSFLSDSGQREENH 335
                        ++       +   P  R  R  A       G                
Sbjct: 539 HLLLDRAQPGRDRRQAARDHGDRGDRPADRGHRGRAGPAGRRPGDRGVDPVAGAGAGRLR 598

Query: 336 RRSPSFPSKRSLRRTSAKK 354
           RR+P    +    R  A +
Sbjct: 599 RRAPGGTGQGRPARGPAAQ 617


>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 = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 28/243 (11%), Positives = 66/243 (27%), Gaps = 38/243 (15%)

Query: 7   VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V+     +R+ K +       +R  ++++I  ++V+  G  L +    + + + I V   
Sbjct: 9   VEPEQAGERLDKFLPTVLPGYTRSALQKLIEGEQVRCEGEPLNK-KHKLRAGETISVTIP 67

Query: 63  DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
           D  PL              +   L +      +V   +     + V   L      +  +
Sbjct: 68  DPEPLDVLPEEIPLDILYEDSDLLVVNKPKHMVVHPAAGNYTGTLVNALLHHCRGSLSGI 127

Query: 112 G----------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
                                  + D    GL     +    R  E              
Sbjct: 128 NGVIRPGIVHRIDKDTSGLLIVAKNDQAHVGLAAQIKEHSFDRTYEAVVYGKFVESTGTV 187

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + + + +  K  +  +          +  + G    + + L  G+  +I+       
Sbjct: 188 DKPIGRSEKDRKKMCVTTKNSKPAVTHYEVLGEYGQFTHLRLRLETGRTHQIRVHMASIG 247

Query: 210 WKV 212
             V
Sbjct: 248 HPV 250


>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 = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 39/254 (15%), Positives = 85/254 (33%), Gaps = 43/254 (16%)

Query: 2   KDKN-IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           K+ N IV E+    R+   I  R  + SR  ++ +I ++++K+N  ++   +  V+S D 
Sbjct: 3   KNINLIVGEDENNLRLDVFINKRENLISRTRIKNLILKEKLKINDQIINSPSKKVLSGDE 62

Query: 60  IE-------------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I               +       E   L + +KP G++      +   T+ + L     
Sbjct: 63  INLQIPEPKEASLKPYNFKLQIVYEDDDLLIINKPAGIIMHPGAGNYDETIVNALMHYNK 122

Query: 107 RVISV----------GRLDINTEGLLLLTNDGGLARVLELP-------------STQWLR 143
             +S            R+D +T GL+++  +      L                    LR
Sbjct: 123 DSLSTIGDELRPGIVHRIDKDTSGLIVIAKNNETHENLSHQFSEHTITRVYQLLIWGKLR 182

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGIC-----YGDMQVTLDTQKGSNAWVTVGLREGKN 198
               +    + +   N     +           Y  +++  + +  + + V   L  G+ 
Sbjct: 183 PSSGKIDTFITRSSKNRQMMEVSNSKGKRAITNYKTIEIFENDKTPTLSLVECRLETGRT 242

Query: 199 REIKKVFEFFNWKV 212
            +I+         +
Sbjct: 243 HQIRVHMTHMGNSI 256


>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 = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 72/230 (31%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQVPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLTHSYIECSLETGRTHQIRVHMREANHP 268


>gi|302874813|ref|YP_003843446.1| hemolysin A [Clostridium cellulovorans 743B]
 gi|302577670|gb|ADL51682.1| hemolysin A [Clostridium cellulovorans 743B]
          Length = 269

 Score = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 16/77 (20%), Positives = 29/77 (37%), Gaps = 1/77 (1%)

Query: 10 NFTPQRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          +   +R+  ++   G+ S RE     I  + + VNG +L++A   +     IE  G  + 
Sbjct: 2  SKEKERLDVLLVEKGLFSSREKARAAIMSRDILVNGQILDKAGEKIDVNSEIEYKGQEMP 61

Query: 69 KAERTRLWLYHKPIGLV 85
             R    L        
Sbjct: 62 YVSRGGYKLEKAMKNFP 78


>gi|257064364|ref|YP_003144036.1| hemolysin A [Slackia heliotrinireducens DSM 20476]
 gi|256792017|gb|ACV22687.1| hemolysin A [Slackia heliotrinireducens DSM 20476]
          Length = 267

 Score = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+   +   G+  SR + +  IA   V VNG  + +A++ V   D IEV G
Sbjct: 1  MRLDVALVERGLEPSRAKAKASIAAGLVFVNGRNVTKASLGVDDGDAIEVQG 52


>gi|222153933|ref|YP_002563110.1| 30S ribosomal protein S4 [Streptococcus uberis 0140J]
 gi|254764614|sp|B9DWC7|RS4_STRU0 RecName: Full=30S ribosomal protein S4
 gi|222114746|emb|CAR43894.1| 30S ribosomal protein S4 [Streptococcus uberis 0140J]
          Length = 203

 Score = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVEPGQVISV 142


>gi|168205206|ref|ZP_02631211.1| ribosomal protein S4 [Clostridium perfringens E str. JGS1987]
 gi|169347013|ref|ZP_02865955.1| ribosomal protein S4 [Clostridium perfringens C str. JGS1495]
 gi|169296696|gb|EDS78825.1| ribosomal protein S4 [Clostridium perfringens C str. JGS1495]
 gi|170663240|gb|EDT15923.1| ribosomal protein S4 [Clostridium perfringens E str. JGS1987]
          Length = 206

 Score = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            R+  V+ R G   SR E  +++      VNG  ++ A+  V   D + V
Sbjct: 98  MRLDNVVYRLGYGASRTEARQLVNHGHFLVNGKKVDIASFKVSVNDVVTV 147


>gi|242373477|ref|ZP_04819051.1| ribosomal protein S4e [Staphylococcus epidermidis M23864:W1]
 gi|242348840|gb|EES40442.1| ribosomal protein S4e [Staphylococcus epidermidis M23864:W1]
          Length = 259

 Score = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 27/60 (45%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            I     +  R+  V+      SR   +++I ++RVKVN  +++     +   D + + G
Sbjct: 173 KIQSATVSALRLDVVLKDMIRKSRNIAKQLIEKKRVKVNHTIVDTPDFQLEKNDLLSIQG 232


>gi|89093809|ref|ZP_01166755.1| hypothetical protein MED92_04904 [Oceanospirillum sp. MED92]
 gi|89081939|gb|EAR61165.1| hypothetical protein MED92_04904 [Oceanospirillum sp. MED92]
          Length = 313

 Score = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 32/217 (14%), Positives = 68/217 (31%), Gaps = 33/217 (15%)

Query: 30  EVERMIAQQRVKVNGILLER---------AAVNVMSTDHIEVDGVPLRKAERTRLWLYHK 80
           +V+R +A   V++NG  +             +++      +VD       E   L   +K
Sbjct: 33  QVDRWLAAGMVRLNGQPIIEDCVCGKGDRLELDIPDHQEAQVDDNWQLVWESDELMAINK 92

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISV--GRLDINTEGLLLLTNDGGLARVLELPS 138
           P  L  + +  +   T+   +        +    RLD  T GL+LL  +    R  +   
Sbjct: 93  PPLLPVSRTTRNLYMTLISLVRRQTPYPDAQLLHRLDTETSGLILLAKNREADRKWKPQL 152

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-----------------GICY---GDMQVT 178
            + +R    +       +  +LL +  + +                    Y      +  
Sbjct: 153 AKLIRRKVYQAWVHGSPNWDHLLMECELSEKAGSDIRSQVYVVEPQSDSQYLKPRPSKTE 212

Query: 179 LDTQK--GSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               +  GS + +   L  G+  +I+         + 
Sbjct: 213 FLVLQRAGSKSLIQCELFTGRKHQIRAQLAHLGHPII 249


>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 = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 29/261 (11%), Positives = 66/261 (25%), Gaps = 55/261 (21%)

Query: 6   IVQENFTPQRVSKVIA-RAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           +   +   QR+ + +A R G   SR  V+ +I Q  V V+G L++     +   + + V 
Sbjct: 20  VADADAAGQRLDQWLAARLGPDMSRSRVQMLIRQGAVSVDGKLIDETKRKMAPGESVSVT 79

Query: 63  ---------DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                     G  +       +   + +      +V   +     + V   +      + 
Sbjct: 80  MPEPEPAEPQGENIALDVLYEDDELIVINKPAGLVVHPGAGNWTGTLVNALIHHCGDSLS 139

Query: 110 SVGRLDIN-------------------------------------TEGLLLLTNDGGLAR 132
            +G +                                              L    G+ +
Sbjct: 140 GIGGVRRPGIVHRLDKETSGVMVVAKTDRAHKSLSEAFADHGLTGDLERAYLALVWGIPQ 199

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
                    L     R    V  +  +  +  +    +     +   +      + V   
Sbjct: 200 RPTGRVDAPLGRAADRVRRAVVPEGRDDARHAVTHFAVQERFGESQQEFATA--SMVECR 257

Query: 193 LREGKNREIKKVFEFFNWKVN 213
           L  G+  +I+         V 
Sbjct: 258 LETGRTHQIRVHMAHIGHPVI 278


>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 = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 35/232 (15%), Positives = 74/232 (31%), Gaps = 32/232 (13%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP----- 66
             R+ +V+A      SR +++  +   RV+VNG+ L+     ++  + I +D        
Sbjct: 14  GMRLDQVLAELFADYSRSKLQSWVKSGRVQVNGLTLK-PRDKLVGGETIALDAEAEIVIT 72

Query: 67  ---------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-----FSRVISVG 112
                    +   + + L +      +V         + +   L          R   V 
Sbjct: 73  AEPEPIPLEIIFEDESLLIVNKPAGLVVHPAIGNWNGTLLNALLNHDSSLETLPRAGIVH 132

Query: 113 RLDINTEGLLLLTNDGGLAR------VLELPSTQWLRVYRVRFHGQVDQD-----KLNLL 161
           R+D  T GLL++                   + ++L + R R       D          
Sbjct: 133 RIDKETSGLLMVAKTLQAHNSLTQQLQDRDITREYLAITRGRMTAGGTVDEPIGRHPTDR 192

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           K+  V +   +      +  +   +  V V L  G+  +I+       + + 
Sbjct: 193 KRYAVRENGKHAVTHYRVGQRFTRHTLVQVKLETGRTHQIRVHMAHIRFPLL 244


>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 = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 72/230 (31%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIREGAVIVNDKP-SQPKDKMIGGEQIRVTVRPSEENLAF 98

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWSGTLLNGLLAHCPELSQVPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 159 LDKETSGLMVVAKTLQAQNSLVQQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIRVHMREANHP 268


>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 = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 72/230 (31%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQVPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLTHSYIECSLETGRTHQIRVHMREANHP 268


>gi|319410076|emb|CBY90410.1| K06180 ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis WUE 2594]
          Length = 392

 Score = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 72/230 (31%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 58  RLDAVLAKLLPDYSRSRLTLWIKEGAVIVNDKP-SQPKDKMIGGEQIRVTVRPSEENLAF 116

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 117 VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 176

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 177 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 236

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 237 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIRVHMREANHP 286


>gi|313889497|ref|ZP_07823143.1| ribosomal protein S4 [Streptococcus pseudoporcinus SPIN 20026]
 gi|332523161|ref|ZP_08399413.1| ribosomal protein S4 [Streptococcus porcinus str. Jelinkova 176]
 gi|313122109|gb|EFR45202.1| ribosomal protein S4 [Streptococcus pseudoporcinus SPIN 20026]
 gi|332314425|gb|EGJ27410.1| ribosomal protein S4 [Streptococcus porcinus str. Jelinkova 176]
          Length = 203

 Score = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVEPGQVISV 142


>gi|134294468|ref|YP_001118203.1| 30S ribosomal protein S4 [Burkholderia vietnamiensis G4]
 gi|134137625|gb|ABO53368.1| SSU ribosomal protein S4P [Burkholderia vietnamiensis G4]
          Length = 213

 Score = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 15/73 (20%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNG++    +  V + D I +     ++A   
Sbjct: 104 RLDNVVYRMGFGSTRAEARQLVSHKSITVNGVVANVPSQQVKAGDVIAIREKAKKQARII 163

Query: 74  RLWLYHKPIGLVT 86
                 +  G+ +
Sbjct: 164 EALSLAEQGGMPS 176


>gi|312863735|ref|ZP_07723973.1| S4 domain protein [Streptococcus vestibularis F0396]
 gi|311101271|gb|EFQ59476.1| S4 domain protein [Streptococcus vestibularis F0396]
          Length = 230

 Score = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 3/67 (4%)

Query: 1   MKDKNIVQENF---TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           + +K    ++F   +  R+  V+A     SR    ++IA  +VK+N   +E+A   +   
Sbjct: 134 ISNKEKYSQSFVLLSSMRLDNVLATVLKISRSNALKLIASGKVKLNYRQIEKADQTISIG 193

Query: 58  DHIEVDG 64
           D I V G
Sbjct: 194 DMISVRG 200


>gi|258543843|ref|ZP_05704077.1| 30S ribosomal protein S4 [Cardiobacterium hominis ATCC 15826]
 gi|258520932|gb|EEV89791.1| 30S ribosomal protein S4 [Cardiobacterium hominis ATCC 15826]
          Length = 159

 Score = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          QR+  V+ R G   +R E  ++++   ++VNG  +  A+  V + D + V
Sbjct: 49 QRLDNVVYRMGYGATRAEARQLVSHGAIEVNGKRVTIASYQVRAEDVVAV 98


>gi|88704352|ref|ZP_01102066.1| 30S ribosomal protein S4 [Congregibacter litoralis KT71]
 gi|88701403|gb|EAQ98508.1| 30S ribosomal protein S4 [Congregibacter litoralis KT71]
          Length = 206

 Score = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  +++A + + VNG ++  A+  V + D + +
Sbjct: 97  RLDNVVYRIGFGSTRSEARQLVAHKAILVNGKVVNIASYKVKAGDVVSL 145


>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 = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 29/229 (12%), Positives = 65/229 (28%), Gaps = 32/229 (13%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILL---------ERAAVNVMST------- 57
           R+  V+A+     SR  +   I +  V VN             E  +V V  +       
Sbjct: 40  RLDAVLAKLMPDYSRSRLTSWIKEGAVIVNDKPAQPKDKMIGGESISVTVRPSEENLAFK 99

Query: 58  ------DHIEVDGVPLRKAERTRLWLYHKPIGLV---------TTHSDPDGRSTVFDNLP 102
                 D +  D   +   +   L ++                              +  
Sbjct: 100 PEAMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHRL 159

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
              +  + V    +  +  L+        + +       +  +  +   Q+ +D  N LK
Sbjct: 160 DKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRLK 219

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 220 MAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIRVHMREANHP 268


>gi|325203791|gb|ADY99244.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis M01-240355]
          Length = 374

 Score = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 72/230 (31%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 159 LDKETSGLMVVAKTLSAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIRVHMREANHP 268


>gi|225076419|ref|ZP_03719618.1| hypothetical protein NEIFLAOT_01464 [Neisseria flavescens
           NRL30031/H210]
 gi|224952267|gb|EEG33476.1| hypothetical protein NEIFLAOT_01464 [Neisseria flavescens
           NRL30031/H210]
          Length = 173

 Score = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNG ++   +  V + D + V     ++    
Sbjct: 64  RLDNVVYRMGFGSTRAEARQLVSHKAIVVNGQVVNIPSFQVKAGDVVAVREKAKKQVRIQ 123


>gi|158320443|ref|YP_001512950.1| RNA-binding S4 domain-containing protein [Alkaliphilus oremlandii
           OhILAs]
 gi|158140642|gb|ABW18954.1| RNA-binding S4 domain protein [Alkaliphilus oremlandii OhILAs]
          Length = 262

 Score = 50.6 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 16/56 (28%), Positives = 30/56 (53%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           N +  R+  +++ A   SR E + +I+++RV VN     ++A +V   + I V G 
Sbjct: 182 NVSSLRLDAILSLAYKISRSEAQELISKERVSVNWKNTTKSAQDVTEGNIISVKGK 237


>gi|322517030|ref|ZP_08069918.1| S4 domain-containing protein YlmH [Streptococcus vestibularis ATCC
           49124]
 gi|322124398|gb|EFX95898.1| S4 domain-containing protein YlmH [Streptococcus vestibularis ATCC
           49124]
          Length = 230

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 16/53 (30%), Positives = 26/53 (49%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +  R+  V+A     SR    ++IA  +VK+N   +E+A   +   D I V G
Sbjct: 148 SSMRLDNVLATVLKISRSNALKLIASGKVKLNYRQIEKADQTISIGDMISVRG 200


>gi|325127790|gb|EGC50698.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis N1568]
          Length = 374

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 72/230 (31%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQVPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLTHSYIECSLETGRTHQIRVHMREANHP 268


>gi|319744574|gb|EFV96927.1| S4 domain-containing protein YlmH [Streptococcus agalactiae ATCC
           13813]
          Length = 262

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 31/63 (49%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +D   +    +  R+ K++A     SR +  ++I   +VKVN  ++ R +  ++  D I 
Sbjct: 172 QDIQKLTVIASSLRLDKILATILKISRTQSTKLIEADKVKVNYAIVNRVSEQLVEGDLIS 231

Query: 62  VDG 64
           V G
Sbjct: 232 VRG 234


>gi|158321656|ref|YP_001514163.1| RNA-binding S4 domain-containing protein [Alkaliphilus oremlandii
          OhILAs]
 gi|158141855|gb|ABW20167.1| RNA-binding S4 domain protein [Alkaliphilus oremlandii OhILAs]
          Length = 80

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   +      RV +NG + +  +  V   D IE+
Sbjct: 1  MRLDKYLKNSRIIKRRTVAKEACEGGRVSINGKVAK-PSTEVALGDIIEI 49


>gi|28212155|ref|NP_783099.1| 30S ribosomal protein S4 [Clostridium tetani E88]
 gi|41017837|sp|Q890Q9|RS4_CLOTE RecName: Full=30S ribosomal protein S4
 gi|28204599|gb|AAO37036.1| SSU ribosomal protein S4P [Clostridium tetani E88]
          Length = 206

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            R+  V+ R G   SR+E  +++      VNG  +   + NV   D I V
Sbjct: 98  MRLDNVVYRLGYGDSRKESRQLVTHGHFLVNGKKVNIPSFNVSVNDVITV 147


>gi|25010599|ref|NP_734994.1| hypothetical protein gbs0530 [Streptococcus agalactiae NEM316]
 gi|77408402|ref|ZP_00785142.1| ylmH protein [Streptococcus agalactiae COH1]
 gi|77414693|ref|ZP_00790826.1| ylmH protein [Streptococcus agalactiae 515]
 gi|23094952|emb|CAD46174.1| Unknown [Streptococcus agalactiae NEM316]
 gi|77159253|gb|EAO70431.1| ylmH protein [Streptococcus agalactiae 515]
 gi|77173005|gb|EAO76134.1| ylmH protein [Streptococcus agalactiae COH1]
          Length = 262

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 31/63 (49%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +D   +    +  R+ K++A     SR +  ++I   +VKVN  ++ R +  ++  D I 
Sbjct: 172 QDIQKLTVIASSLRLDKILATILKISRTQSTKLIEADKVKVNYAIVNRVSEQLVEGDLIS 231

Query: 62  VDG 64
           V G
Sbjct: 232 VRG 234


>gi|315924845|ref|ZP_07921062.1| hemolysin A [Pseudoramibacter alactolyticus ATCC 23263]
 gi|315621744|gb|EFV01708.1| hemolysin A [Pseudoramibacter alactolyticus ATCC 23263]
          Length = 290

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 4/59 (6%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVM---STDHIEVDGVPLR 68
          +R+ K++ + G   +R   ++ I    V+V+G    +A   V        + V G  + 
Sbjct: 6  ERLDKMLVKLGFFDTRERAKKAIMAGLVRVDGRAHTKAGDQVSVTLEKHQVTVKGDAIP 64


>gi|328542021|ref|YP_004302130.1| Helicase conserved C-terminal domain protein [polymorphum gilvum
           SL003B-26A1]
 gi|326411771|gb|ADZ68834.1| Helicase conserved C-terminal domain protein [Polymorphum gilvum
           SL003B-26A1]
          Length = 1004

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 14/117 (11%), Positives = 30/117 (25%), Gaps = 1/117 (0%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
               L     P    + +        +S T+V +            ++       +    
Sbjct: 866 DASELAAADEPTASGQPEPQAQGETEASTTVVIEIWRPGRPERPGRSQGDGEQRGERKGR 925

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR-SPSFPSKRSLRRTSA 352
             K+   P   ++        +       S   +REE      P+    ++ RR   
Sbjct: 926 GDKRPHGPRRGKDTQGGEHRKEADQRHKSSGPDRREERRNAGKPAGQRDKAPRRDKP 982


>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 = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 72/230 (31%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLTHSYIECSLETGRTHQIRVHMREANHP 268


>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 = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 72/230 (31%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 99  VPEPMALDIIYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQVPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVQHLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIRVHMREANHP 268


>gi|83720741|ref|YP_443547.1| 30S ribosomal protein S4 [Burkholderia thailandensis E264]
 gi|167582598|ref|ZP_02375472.1| 30S ribosomal protein S4 [Burkholderia thailandensis TXDOH]
 gi|167620712|ref|ZP_02389343.1| 30S ribosomal protein S4 [Burkholderia thailandensis Bt4]
 gi|257137667|ref|ZP_05585929.1| 30S ribosomal protein S4 [Burkholderia thailandensis E264]
 gi|123536225|sp|Q2SU52|RS4_BURTA RecName: Full=30S ribosomal protein S4
 gi|83654566|gb|ABC38629.1| ribosomal protein S4 [Burkholderia thailandensis E264]
          Length = 207

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 16/73 (21%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNGI+    +  V + D I +     ++A   
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAITVNGIVANIPSQQVKAGDVISIREKAKKQARIV 157

Query: 74  RLWLYHKPIGLVT 86
                 +  G+ +
Sbjct: 158 EALSLAEQGGMPS 170


>gi|308063222|gb|ADO05109.1| hemolysin [Helicobacter pylori Sat464]
          Length = 235

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 10/50 (20%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   +     + SR + + ++ + +V VN +++ + +  V   D IE+
Sbjct: 1  MRLDHALFNQHLVGSREKAKALVLKNQVLVNKMVVSKPSFMVKEGDKIEL 50


>gi|284799892|ref|ZP_05985156.2| ribosomal protein S4 [Neisseria subflava NJ9703]
 gi|284796551|gb|EFC51898.1| ribosomal protein S4 [Neisseria subflava NJ9703]
          Length = 173

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNG ++   +  V + D + V     ++    
Sbjct: 64  RLDNVVYRMGFGSTRAEARQLVSHKAIVVNGQVVNIPSFQVKAGDVVAVREKAKKQVRIQ 123


>gi|255659528|ref|ZP_05404937.1| ribosomal protein S4 [Mitsuokella multacida DSM 20544]
 gi|260848081|gb|EEX68088.1| ribosomal protein S4 [Mitsuokella multacida DSM 20544]
          Length = 197

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +RR+  +++      VNG  ++  +  V + D I V
Sbjct: 88  RLDNVVYRLGLANTRRQARQLVRHGHFTVNGKRVDIPSALVNAGDVIAV 136


>gi|32266901|ref|NP_860933.1| 30S ribosomal protein S4 [Helicobacter hepaticus ATCC 51449]
 gi|41017829|sp|Q7VGC0|RS4_HELHP RecName: Full=30S ribosomal protein S4
 gi|32262953|gb|AAP77999.1| ribosomal protein S4 [Helicobacter hepaticus ATCC 51449]
          Length = 208

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G A+ RR   +++    + VNG  ++  +  V     IEV
Sbjct: 98  QRLDNVVYRMGFATTRRFARQLVTHGHILVNGKRVDIPSYMVKPGQKIEV 147


>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 = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 34/251 (13%), Positives = 69/251 (27%), Gaps = 40/251 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             + +V +    +R+ KV+A+     SR  ++  I  +RV+V+G   +     V     I
Sbjct: 67  PRRVVVPDELAGERLDKVVAKVFPEFSRSRLQSWIEAERVRVDGKPAK-IRQPVPLGATI 125

Query: 61  EVDGVP---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           E++                  +   + T + +      +V   +     + +   L    
Sbjct: 126 ELEPDLLPEQLAFTPEPVPLDIVYEDDTLVVINKPAGMVVHPAAGNWSGTVLNGLLYRYG 185

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
                  R   V RLD  T GL+++         L           R       +     
Sbjct: 186 EAAAGLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLALVWGNMPDEG 245

Query: 160 LLKKGIVIQ-----------GICYGDMQVTL------DTQKGSNAWVTVGLREGKNREIK 202
            +   I              G      +           Q+     +   L  G+  +I+
Sbjct: 246 TIDAPIGRDPRERTRMAVVTGAAGKPARTHFRRVTSAIWQRQPVTAIHCDLETGRTHQIR 305

Query: 203 KVFEFFNWKVN 213
                    + 
Sbjct: 306 VHCAHIGHPLL 316


>gi|241203351|ref|YP_002974447.1| hemolysin A [Rhizobium leguminosarum bv. trifolii WSM1325]
 gi|240857241|gb|ACS54908.1| hemolysin A [Rhizobium leguminosarum bv. trifolii WSM1325]
          Length = 248

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 9  ENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +   QR+ +++   G  ASR      + +  VK+ G ++ +A     +   IE+D 
Sbjct: 2  SDQNTQRLDQLLVSLGLFASRSRARDAVQRGTVKIGGQVVTKAGALFGADAAIEIDD 58


>gi|297583620|ref|YP_003699400.1| 30S ribosomal protein S4 [Bacillus selenitireducens MLS10]
 gi|297142077|gb|ADH98834.1| ribosomal protein S4 [Bacillus selenitireducens MLS10]
          Length = 200

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR+  +++    V V+G  ++  +  V     I +
Sbjct: 93  RLDNLVYRLGLARTRRQARQLVNHGHVTVDGKRVDIPSYRVAPGQSISL 141


>gi|157823950|ref|NP_997554.2| zinc finger protein 318 isoform 1 [Mus musculus]
 gi|168983992|emb|CAQ11965.1| zinc finger protein 318 [Mus musculus]
          Length = 2237

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 14/109 (12%), Positives = 27/109 (24%), Gaps = 2/109 (1%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           GP        +       S        ++        +         +    + +  +P 
Sbjct: 22  GPPPGRPVGASSGPTRRPSSPPPPSCSSLRLPARRHRSPSGHRGRWASPSPPRGRRGSPS 81

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQR--EENHRRSPSFPSKRSLRRTSA 352
             R   ++    +G  +S     G+R      R     PS    RR   
Sbjct: 82  PPRGRRASPSPTRGRRASPSPPRGRRGSPSPPRARRGSPSPPRSRRHYP 130



 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 17/108 (15%), Positives = 29/108 (26%), Gaps = 4/108 (3%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                +      P+ +S    R   +             +     +G     + A+P   
Sbjct: 16  KDGSASGPPPGRPVGASSGPTRRPSSPPPPSCSSLRLPARRHRSPSGHR--GRWASPSPP 73

Query: 308 RNLASNVWMAKGIHSSFLSDSGQR--EENHRRSPSFPSKRSLRRTSAK 353
           R    +    +G  +S     G+R      R     PS    RR S  
Sbjct: 74  RGRRGSPSPPRGRRASPSPTRGRRASPSPPRGRRGSPSPPRARRGSPS 121


>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 = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 72/230 (31%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIREGAVIVNDKP-SQPKDKMIGGEQIRVTVRPSAEYSAF 98

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 99  APEPMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWSGTLLNGLLAHCPELSQVPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIRVHMREANHP 268


>gi|186477562|ref|YP_001859032.1| 30S ribosomal protein S4 [Burkholderia phymatum STM815]
 gi|226697817|sp|B2JI40|RS4_BURP8 RecName: Full=30S ribosomal protein S4
 gi|184194021|gb|ACC71986.1| ribosomal protein S4 [Burkholderia phymatum STM815]
          Length = 207

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG++    ++ V + D I V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAITVNGVVANIPSLQVKAGDVIAV 146


>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 = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 32/245 (13%), Positives = 82/245 (33%), Gaps = 39/245 (15%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           ++     +R+ + + R     +R ++++++    V+VN   ++ A   +   + + V   
Sbjct: 9   IEPGQAAERLDRFLTRQLPELTRSQLKKLVDDGLVRVNDQTVK-AGAKLRGGETVCVTLP 67

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------ 106
                    + +PL    E + L + +K  G+V   +      T+ + L           
Sbjct: 68  QAQSVETLPEDLPLTVLYEDSDLIVINKAAGMVVHPAAGHSSGTLVNALLYHCHDLSGVG 127

Query: 107 ---RVISVGRLDINTEGLLLLTNDGGLARV-------------LELPSTQWLRVYRVRFH 150
              R   V RLD +T G+++ T +                           ++  R    
Sbjct: 128 GELRPGIVHRLDKDTSGVMVATKNDVTHNHLAAQFKDHSIQRRYVALVHGQVQNARGTID 187

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIKKVFEFF 208
             + +   +  K     +G         +  +  ++  + + + L  G+  +I+      
Sbjct: 188 APIGRHPTHRKKMTSKGRGGRRAVTHWKVLRRYDADRLSLLEMRLETGRTHQIRVHLSEM 247

Query: 209 NWKVN 213
           N  + 
Sbjct: 248 NLPLV 252


>gi|125975412|ref|YP_001039322.1| SSU ribosomal protein S4P [Clostridium thermocellum ATCC 27405]
 gi|256005301|ref|ZP_05430267.1| ribosomal protein S4 [Clostridium thermocellum DSM 2360]
 gi|281419374|ref|ZP_06250389.1| ribosomal protein S4 [Clostridium thermocellum JW20]
 gi|152060944|sp|A3DJK0|RS4_CLOTH RecName: Full=30S ribosomal protein S4
 gi|125715637|gb|ABN54129.1| SSU ribosomal protein S4P [Clostridium thermocellum ATCC 27405]
 gi|255990737|gb|EEU00853.1| ribosomal protein S4 [Clostridium thermocellum DSM 2360]
 gi|281406994|gb|EFB37257.1| ribosomal protein S4 [Clostridium thermocellum JW20]
 gi|316939528|gb|ADU73562.1| ribosomal protein S4 [Clostridium thermocellum DSM 1313]
          Length = 208

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A SRRE  +++      VNG  ++  +  V   D I V
Sbjct: 99  RLDNVVYRMGLAVSRREARQLVRHGHFTVNGKRVDIPSYLVKVGDVIAV 147


>gi|329893623|ref|ZP_08269757.1| SSU ribosomal protein S4p (S9e) [gamma proteobacterium IMCC3088]
 gi|328923550|gb|EGG30862.1| SSU ribosomal protein S4p (S9e) [gamma proteobacterium IMCC3088]
          Length = 206

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G AS R E  ++++ + V VNG ++   +  V   D + V
Sbjct: 97  RLDNVVYRMGFASTRAEARQLVSHKGVLVNGSVVNVPSYQVQPGDVVAV 145


>gi|325197923|gb|ADY93379.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis G2136]
          Length = 374

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 71/230 (30%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 40  RLDAVLAKLLPDYSRSRLTLWIKEGAVIVNDKP-SQPKDKMIGGEQIRVTVRPSEENLAF 98

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWRGTLLNGLLAHCPELSQVPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  +V  G       V +  +   ++++   L  G+  +I+      N  
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLPHSYIECSLETGRTHQIRVHMREANHP 268


>gi|322392783|ref|ZP_08066241.1| S4 domain-containing protein YlmH [Streptococcus peroris ATCC
           700780]
 gi|321144361|gb|EFX39764.1| S4 domain-containing protein YlmH [Streptococcus peroris ATCC
           700780]
          Length = 261

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 18/90 (20%), Positives = 37/90 (41%), Gaps = 5/90 (5%)

Query: 1   MKDKNIVQENF---TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           +K K+  QE     +  R+   ++     SR +   ++ ++ V+VN  ++E+    V   
Sbjct: 167 IKSKDGYQEREVLVSSLRLDSFLSSILKLSRSQTSNLVEKKLVQVNYHIVEKLDYQVKVG 226

Query: 58  DHIEVD--GVPLRKAERTRLWLYHKPIGLV 85
           D I V   G  +   E  +     K + + 
Sbjct: 227 DLISVRRFGRIILLKENGQTKKDKKKVTIQ 256


>gi|320160994|ref|YP_004174218.1| putative hemolysin [Anaerolinea thermophila UNI-1]
 gi|319994847|dbj|BAJ63618.1| putative hemolysin [Anaerolinea thermophila UNI-1]
          Length = 272

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 12/58 (20%), Positives = 28/58 (48%), Gaps = 3/58 (5%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMST 57
          M +  I+  +    R+  ++ + G+A SR   +R+I   R++V+  ++   +  V   
Sbjct: 1  MDNDKII--DMAKVRLDILLVQRGLAESRTVAQRLILAGRIRVSNEIVTEPSRRVEED 56


>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 = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 35/332 (10%), Positives = 76/332 (22%), Gaps = 52/332 (15%)

Query: 7   VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           +  +   +R+ +V+  A    SR  +++ +   R  V+G+ + R          + +   
Sbjct: 8   ITADTAGRRLDRVLRDAAPGLSRAALQKAVLAGRCLVDGLPVSRPDAKTRPGQRVLLELP 67

Query: 63  ---------DGVP-LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
                    +G   L   + + +         V         + V   L          G
Sbjct: 68  PTENALSPEEGHLELLWQDESLVVCNKPAGLTVHPCPSCPEHTLVQRLLGRFPQLGRLEG 127

Query: 113 RLDINTEGL---------------------LLLTNDGGLARVLELPSTQWLRVYRVRFHG 151
                   L                                 L L S         R   
Sbjct: 128 LRPGIVHRLDKDTSGLLLVALTEPARLALSAAFARREVHKEYLALVSGLPPEQGECREPL 187

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIKKVFEFFN 209
                    +      +G                   + + V +  G+  +I+       
Sbjct: 188 GRHPTAKIKMAVLPETRGGKPAHTTWKRLWNTPDQRVSLLAVRIHTGRTHQIRVHLAHLG 247

Query: 210 WKVNRLIRISYGPFQLGTLL-AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLV 268
             +               L      RE++    R+ L    L  +  +    ++ +    
Sbjct: 248 HPLLG-----------DKLYAPAPVRELAP---RQMLHAWHLAFSHPDSGEEMHFACPPP 293

Query: 269 RDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
            D P           R+    +  +G S   +
Sbjct: 294 DDLPQAALAACRRMRRLIVTGNPGSGKSALTR 325


>gi|315640101|ref|ZP_07895224.1| 30S ribosomal protein S4 [Enterococcus italicus DSM 15952]
 gi|315484148|gb|EFU74621.1| 30S ribosomal protein S4 [Enterococcus italicus DSM 15952]
          Length = 203

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G+A+ RR+  +++    + V+G  ++  + +V     I V
Sbjct: 93  QRLDNVVYRLGLATTRRQARQLVNHGHITVDGKRVDIPSYHVDLGQVIGV 142


>gi|172044373|sp|A4JAR5|RS4_BURVG RecName: Full=30S ribosomal protein S4
          Length = 207

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 15/73 (20%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNG++    +  V + D I +     ++A   
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKSITVNGVVANVPSQQVKAGDVIAIREKAKKQARII 157

Query: 74  RLWLYHKPIGLVT 86
                 +  G+ +
Sbjct: 158 EALSLAEQGGMPS 170


>gi|34499616|ref|NP_903831.1| 30S ribosomal protein S4 [Chromobacterium violaceum ATCC 12472]
 gi|41017823|sp|Q7NQH6|RS4_CHRVO RecName: Full=30S ribosomal protein S4
 gi|34105467|gb|AAQ61822.1| 30S ribosomal protein S4 [Chromobacterium violaceum ATCC 12472]
          Length = 206

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 15/73 (20%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNG ++   +  V + D + V     ++A   
Sbjct: 97  RLDNVVYRMGFGSTRAEARQLVSHKAIVVNGQVVNIPSYQVKAGDVVSVREKAKKQARIV 156

Query: 74  RLWLYHKPIGLVT 86
                 +  G  +
Sbjct: 157 EGLALAEQGGFPS 169


>gi|330719419|ref|ZP_08314019.1| 30S ribosomal protein S4 [Leuconostoc fallax KCTC 3537]
          Length = 203

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 12/53 (22%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           QR+  ++ R G A SR +  +++    + V+G  ++  + +V+    I V   
Sbjct: 93  QRLDSLVFRLGFATSRAQARQLVNHGHILVDGKRVDIPSYHVVPGQEISVRDK 145


>gi|323156250|gb|EFZ42409.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           EPECa14]
          Length = 300

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 25/217 (11%), Positives = 56/217 (25%), Gaps = 30/217 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--------------LRKAER 72
           SR  ++  I  QRV VNG + ++    V+  + + ++                 +   + 
Sbjct: 6   SRSRIKEWILDQRVLVNGKVCDKPKEKVLGGELVAINAEIEEEARFEPQDIPLDIVYEDE 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGRLDINTEGLLLLTND 127
             + +      +V   +     + +   L          R   V RLD +T GL+++   
Sbjct: 66  DIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKT 125

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQ-----------DKLNLLKKGIVIQGICYGDMQ 176
                 L     +                                    V          
Sbjct: 126 VPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTH 185

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             +      +  + + L  G+  +I+         + 
Sbjct: 186 YRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 222


>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 = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 34/235 (14%), Positives = 77/235 (32%), Gaps = 28/235 (11%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K +V E      V + +   G +SR  + R+    ++ +NG+        +   D IEVD
Sbjct: 2   KFVVDETSQGLTVGEFLKANGFSSRT-IRRLKLGGKILINGVPAYT-NTRISCNDVIEVD 59

Query: 64  -----GVP-------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---- 107
                G+        +   +   + L  +P  +V   +     +     +  +  +    
Sbjct: 60  LTEKSGIVPSPVPINILYEDDHIIVLNKQPGVVVHPTAFHYNDTIANGVIYYLNQKGKKG 119

Query: 108 -VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD---------K 157
               V RLD +T G+L++     +  +++       R   V      + +         +
Sbjct: 120 GFHPVNRLDRDTTGVLIIALSQHMHNLIQTHGRMKKRYIAVVEGVVKENEGVIVEPIARR 179

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
              L +  V +       +  +  +      + +    G+  +I+    F    V
Sbjct: 180 EGSLIERCVSEKGQKAITRFKVVKRLKDLTVLDIEPVTGRTHQIRVHLSFKGHPV 234


>gi|294501546|ref|YP_003565246.1| ribosomal protein S4 [Bacillus megaterium QM B1551]
 gi|295706894|ref|YP_003599969.1| 30S ribosomal protein S4 [Bacillus megaterium DSM 319]
 gi|294351483|gb|ADE71812.1| ribosomal protein S4 [Bacillus megaterium QM B1551]
 gi|294804553|gb|ADF41619.1| 30S ribosomal protein S4 [Bacillus megaterium DSM 319]
          Length = 200

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR+  +++    V V+G  ++  +  V     I V
Sbjct: 93  RLDNLVYRMGLARTRRQARQLVNHGHVLVDGKRVDIPSYRVQPGQVIGV 141


>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 = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 30/229 (13%), Positives = 61/229 (26%), Gaps = 32/229 (13%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILL--------------------ERAAVN 53
           R+  V+A+     SR  +   I +  V VN                        E  A  
Sbjct: 40  RLDAVLAKLMPDYSRSRLTSWIKEGAVIVNDKPAQPKDKMIGGESISVTVLPSEENLAFK 99

Query: 54  --------VMSTDHIEVDGVP---LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
                   V   D + V   P   +                L               +  
Sbjct: 100 PEAMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHRL 159

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
              +  + V    +  +  L+        + +       +  +  +   Q+ +D  N LK
Sbjct: 160 DKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRLK 219

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 220 MAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIRVHMREANHP 268


>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 = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 5/62 (8%)

Query: 6  IVQENFTPQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
          +V      QR+ + +A      A   SR  ++ +I Q  V V+G     A+ +V +   I
Sbjct: 19 VVGAEEAGQRLDRFLAERTETGAAFLSRMRIKTLIEQGHVSVDGEARLTASASVRAGQII 78

Query: 61 EV 62
          E+
Sbjct: 79 EL 80


>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 = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 11/52 (21%), Positives = 21/52 (40%), Gaps = 2/52 (3%)

Query: 8  QENFTPQRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           E     R+ + +A   A   SR  ++ +I +  V +NG  +      V + 
Sbjct: 18 DEKAEGNRLDQWLAARLAPDFSRSRIQALIREGAVTLNGRTVAEPKRKVAAG 69


>gi|78357275|ref|YP_388724.1| 30S ribosomal protein S4 [Desulfovibrio desulfuricans subsp.
           desulfuricans str. G20]
 gi|90101689|sp|Q30Z67|RS4_DESDG RecName: Full=30S ribosomal protein S4
 gi|78219680|gb|ABB39029.1| SSU ribosomal protein S4P [Desulfovibrio desulfuricans subsp.
           desulfuricans str. G20]
          Length = 208

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI R G A SR +  +M+      VNG      ++ V   D IEV
Sbjct: 99  RLDNVIYRLGFANSRSQARQMVRHGIFTVNGRKATIPSIQVKVGDVIEV 147


>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 = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 28/237 (11%), Positives = 75/237 (31%), Gaps = 29/237 (12%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           +K+ +IV +     R+ +  A     I +R  V++ I +Q++ V+G + +     ++   
Sbjct: 3   IKEIHIVPQLSEKIRLQEYAASIFTSITTRSAVKKAIKKQQILVDGEIGQT-GDWILEGQ 61

Query: 59  HIEVDGVPLRKAERTRLWL---------------YHKPIGLVTTHSDPDGRSTVFDNLPS 103
            IE+    L+  ++ +++                        + +     ++ +  NL +
Sbjct: 62  QIEL----LQPQKQQKVFELRLEVIYEDDHIAVINKPAGYPTSGNYHKTIKNALPFNLQA 117

Query: 104 IFSRVI-----SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
                         RLD  T G+LL          L                 +    + 
Sbjct: 118 SKEIDKLEIPQPAHRLDNPTSGILLCAKTNKALIELNRQFQDKEIQKTYIAIVEGCFPEE 177

Query: 159 NLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             +    + +      ++   T+  +    + +      G+  +I+       + + 
Sbjct: 178 QQIFNDEIEEKQATTAVKLLGTIMFKSAKLSLLEAKPLTGRTHQIRIHLAKNGFPIL 234


>gi|195970192|ref|NP_384985.2| hypothetical protein SMc00973 [Sinorhizobium meliloti 1021]
 gi|307304209|ref|ZP_07583961.1| hemolysin A [Sinorhizobium meliloti BL225C]
 gi|307320514|ref|ZP_07599929.1| hemolysin A [Sinorhizobium meliloti AK83]
 gi|187904153|emb|CAC45451.2| Probable hemolysin [Sinorhizobium meliloti 1021]
 gi|306893790|gb|EFN24561.1| hemolysin A [Sinorhizobium meliloti AK83]
 gi|306902677|gb|EFN33270.1| hemolysin A [Sinorhizobium meliloti BL225C]
          Length = 251

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 6  IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          + Q+     R+ +++   G +ASR      I +  VKV+G  + + A        + +D 
Sbjct: 1  MSQDTQMTIRLDQLLLNRGLVASRARARDAIQRGTVKVDGRTVTKPASTFAQGVTLTIDD 60


>gi|172059366|ref|YP_001807018.1| 30S ribosomal protein S4 [Burkholderia ambifaria MC40-6]
 gi|226697813|sp|B1YRQ4|RS4_BURA4 RecName: Full=30S ribosomal protein S4
 gi|171991883|gb|ACB62802.1| ribosomal protein S4 [Burkholderia ambifaria MC40-6]
          Length = 207

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNG++    +  V + D + +     ++A   
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKSITVNGVVANVPSQQVKAGDVVAIREKAKKQARIV 157

Query: 74  RLWLYHKPIGLVT 86
                 +  G+ +
Sbjct: 158 EALSLAEQGGMPS 170


>gi|20808633|ref|NP_623804.1| 30S ribosomal protein S4 [Thermoanaerobacter tengcongensis MB4]
 gi|26399396|sp|Q8R7Y1|RS4_THETN RecName: Full=30S ribosomal protein S4
 gi|20517267|gb|AAM25408.1| Ribosomal protein S4 and related proteins [Thermoanaerobacter
           tengcongensis MB4]
          Length = 206

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SR +  ++++   ++VNG  ++  +  V   D I V
Sbjct: 99  RLDNVVYRLGFAVSRAQARQLVSHGHIEVNGKKVDIPSYLVKPGDVISV 147


>gi|167838187|ref|ZP_02465046.1| 30S ribosomal protein S4 [Burkholderia thailandensis MSMB43]
          Length = 207

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 15/73 (20%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNGI+    +  V + D + +     ++A   
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAITVNGIVANIPSQQVKAGDVVSIREKAKKQARIV 157

Query: 74  RLWLYHKPIGLVT 86
                 +  G+ +
Sbjct: 158 EALSLAEQGGMPS 170


>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 = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 32/240 (13%), Positives = 73/240 (30%), Gaps = 33/240 (13%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--- 61
           IV E+   +R+ +++++   A SR  +++ I  +RV V+    +R    +     I    
Sbjct: 13  IVPEDLAEKRLDQILSQLFPAYSRTRLQQWIHDKRVLVDNE-FKRPRDKIKPGAKITIVA 71

Query: 62  -----VDGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-----IF 105
                +D         +   +   + +      +V   +    ++ V   L         
Sbjct: 72  NLHEAIDWEAENLPLDIIFEDDALVVINKPAGLVVHPGAGNRHKTLVNALLHHLPALKKL 131

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF----------HGQVDQ 155
            R   + RLD +T GLL++         L                               
Sbjct: 132 PRAGIIQRLDKDTSGLLIIPKILNAHTQLVKQLQARTMKREYTAIIQGLLIAGGSINAPI 191

Query: 156 DKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +   L+K + +             +  +   +  + V L  G+  +I+      +  + 
Sbjct: 192 GRHPKLRKKMAVTENHGKPAVSHYRVIERFNHHTLINVQLETGRTHQIRVHMAHIHHPLV 251


>gi|332362883|gb|EGJ40676.1| S4 domain-containing protein YlmH [Streptococcus sanguinis SK49]
          Length = 261

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 14/48 (29%), Positives = 26/48 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K++A     SR +  ++I+ + VKVN  + +  ++ V   D I V
Sbjct: 184 RLDKLVASTFKLSRSQAAQLISGKHVKVNYAVNDNPSLQVGLEDLISV 231


>gi|325694117|gb|EGD36035.1| S4 domain-containing protein YlmH [Streptococcus sanguinis SK150]
          Length = 261

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 14/48 (29%), Positives = 26/48 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K++A     SR +  ++I+ + VKVN  + +  ++ V   D I V
Sbjct: 184 RLDKLVASTFKLSRSQAAQLISGKHVKVNYAVNDNPSLQVGLEDLISV 231


>gi|238926866|ref|ZP_04658626.1| hemolysin A [Selenomonas flueggei ATCC 43531]
 gi|238885398|gb|EEQ49036.1| hemolysin A [Selenomonas flueggei ATCC 43531]
          Length = 268

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
            +R+  ++   G+A SR   +R+I   +V VN   +++A   V +   + V G  L  
Sbjct: 2  KKERLDVLLTVQGLAPSRERAKRLIMAGQVLVNEQRVDKAGATVPADAALRVAGEDLPY 60


>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 = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 26/230 (11%), Positives = 63/230 (27%), Gaps = 31/230 (13%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+ + +A+     SR  ++  I   +V VNG ++ +A   V   + IE+           
Sbjct: 19  RLDQALAQLFPDYSRSRLKVWIENDQVWVNGKIVNKAREKVFGGELIEIQAEVEEEVRFE 78

Query: 67  -------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-----GRL 114
                  +   +   + +      +V   +     + +   L                RL
Sbjct: 79  PQNIPLNIVYEDDDIIVINKPKDLVVHPGAGNPDGTVLNALLYHYPPIAEVPRAGIVHRL 138

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVY-----------RVRFHGQVDQDKLNLLKK 163
           D +T GL+++  +      L     +                +     +           
Sbjct: 139 DKDTTGLMVVAKNIPAQTHLVTALQKRRITREYEAIASGIMTQGGKVDEPMARHPTKRTA 198

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             V            +  +  +   + + L  G+  +I+         + 
Sbjct: 199 MAVHPMGKPAVTHYRIMERFRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 248


>gi|150395716|ref|YP_001326183.1| hemolysin A [Sinorhizobium medicae WSM419]
 gi|150027231|gb|ABR59348.1| hemolysin A [Sinorhizobium medicae WSM419]
          Length = 251

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 12/60 (20%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 6  IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          + Q+     R+ +++   G +ASR      I +  VKV+G  + + +        + +D 
Sbjct: 1  MSQDTQMTIRLDQLLLNRGLVASRARARDAIQRGTVKVDGRTVTKPSSTFAEGVTLAIDD 60


>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 = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 45/247 (18%), Positives = 80/247 (32%), Gaps = 35/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M +K ++       RV  V++      SR  +   +    + VN   ++R +  V+S D 
Sbjct: 1   MANKILIHITDQAGRVDAVLSKENLSYSRTTLSNWLVDGTILVNNHKVKR-SYKVVSGDT 59

Query: 60  IEV------------DGVPLRKAERTRL--WLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I +            + +PL           +      +V   +     + V   L    
Sbjct: 60  ISITPPETQETKIEAENIPLDIIYEDDDIIVVNKPQGMVVHPAAGHSSGTLVNALLHHSP 119

Query: 106 -------SRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
                   R   V R+D +T GLL++  +    R L     S +  RVY     G+  +D
Sbjct: 120 LSTINGEFRPGIVHRIDRDTSGLLMVAKNDKAHRSLSEQLKSHKNQRVYYALVRGEFTED 179

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          KK  VI+G         +  +      + V L  G+  +I+    
Sbjct: 180 SGTIEAPIGRHKIDRKKQAVIEGGREAVTHFRVLKRYVGYTLLKVSLETGRTHQIRVHMS 239

Query: 207 FFNWKVN 213
           +    V 
Sbjct: 240 YIGHPVV 246


>gi|23015589|ref|ZP_00055361.1| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Magnetospirillum magnetotacticum MS-1]
          Length = 327

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 26/246 (10%), Positives = 60/246 (24%), Gaps = 39/246 (15%)

Query: 7   VQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V+      R+ + +A R    SR  ++ +I   RV ++   +  A++ V       V+  
Sbjct: 14  VEPEEAATRLDRWLAARLPELSRTRIKALIEDGRVSLDATTISDASLRVKPGQCFTVEVP 73

Query: 66  P--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
           P              +   +   + +      +V         + V   L          
Sbjct: 74  PDAPAEPEAQDIALSVVYEDEDLIVIDKPAGMVVHPAPGNPDETLVNALLAHCGESLAGI 133

Query: 107 ---------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                      I      +         + G  A+  E    +               + 
Sbjct: 134 GGVKRPGIVHRIDKDTSGLLVAAKTDAAHRGLAAQFAEHSLERAYWALVWGTPSPRQGEI 193

Query: 158 LNLLKKGIVIQGICY------GDM----QVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
              + +    +                 +V      G+ + V   L  G+  +I+     
Sbjct: 194 EGNIGRNPNDRKKMAVVKSGGKPALTRYRVLKSFAGGAVSLVECRLATGRTHQIRVHMTA 253

Query: 208 FNWKVN 213
               + 
Sbjct: 254 QGHPLI 259


>gi|225377098|ref|ZP_03754319.1| hypothetical protein ROSEINA2194_02743 [Roseburia inulinivorans DSM
           16841]
 gi|225211003|gb|EEG93357.1| hypothetical protein ROSEINA2194_02743 [Roseburia inulinivorans DSM
           16841]
          Length = 267

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 25/178 (14%), Positives = 54/178 (30%), Gaps = 2/178 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++   G+A SR + + MI +  V V+    ++A        +IEV G  L+   R
Sbjct: 3   ERLDILLVNKGLAPSREKAKAMIMEGNVFVDNNREDKAGSTFDVNANIEVKGNTLKYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L         T                    ++  G + +    +        L +
Sbjct: 63  GGLKLEKAMTHFGITLEGKVCMDIGAST-GGFTDCMLQNGAVKVYAVDVGYGQFAWKLRQ 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +   +   +  V+     D+     +    +      G  +  L+        + 
Sbjct: 122 DERVVCMEKTNIRYVKPEDIADRLDFASVDVSFISLTKVLGPARELLNDNGEMVCLIK 179


>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 = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 25/232 (10%), Positives = 63/232 (27%), Gaps = 32/232 (13%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------DGV 65
            QR+ +V A+     SR  +   I    + V+G +L      V +   +E+       G 
Sbjct: 21  GQRLDQVAAQLFSEHSRSRLAAWIKDGLLTVDGAVLR-PRDTVHAGAVLELSAEQQAQGE 79

Query: 66  P--------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------R 107
                    +   +   L +      +V   +     + +   L  +             
Sbjct: 80  WVAQDIPLDIVYEDDQILVIDKPAGLVVHPAAGHADGTLLNALLHHVPDLINVPRAGIVH 139

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR------VYRVRFHGQVDQDKLNLL 161
            +      +      L      + ++     ++         +                 
Sbjct: 140 RLDKDTTGLMVVAKTLQAQTRLVEQLQARSVSRIYEAIVIGVIITGGTVDAPIGRHGQQR 199

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           ++  V++G         +  +  S+  V V L  G+  +I+       + + 
Sbjct: 200 QRMAVVEGGKPAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMTHLGYPLV 251


>gi|254253495|ref|ZP_04946813.1| Ribosomal protein S4 [Burkholderia dolosa AUO158]
 gi|124896104|gb|EAY69984.1| Ribosomal protein S4 [Burkholderia dolosa AUO158]
          Length = 207

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 16/73 (21%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNGI+    +  V + D I +     ++A   
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAITVNGIVANIPSQQVKAGDVIAIREKAKKQARIV 157

Query: 74  RLWLYHKPIGLVT 86
                 +  G+ +
Sbjct: 158 ESLSLAEQGGMPS 170


>gi|330722391|gb|EGH00239.1| SSU ribosomal protein S4p (S9e) [gamma proteobacterium IMCC2047]
          Length = 206

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG  +   +  + + D + V
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKSITVNGETVNVPSYKIKAGDVVAV 145


>gi|291456443|ref|ZP_06595833.1| ribosomal RNA large subunit methyltransferase J [Bifidobacterium
          breve DSM 20213]
 gi|291381720|gb|EFE89238.1| ribosomal RNA large subunit methyltransferase J [Bifidobacterium
          breve DSM 20213]
          Length = 248

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 12/51 (23%), Positives = 26/51 (50%), Gaps = 2/51 (3%)

Query: 15 RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVD 63
          R+  ++ A   + SR + +R+I    V+V+G  + + +  V +    + VD
Sbjct: 5  RLDMMLVASDLVESRSKAQRLIKAGHVRVDGETITKPSFMVKAGHCELAVD 55


>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 = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 31/229 (13%), Positives = 65/229 (28%), Gaps = 32/229 (13%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILL---------ERAAVNVMST------- 57
           R+  V+A+     SR  +   I +  V VN             E  AV V  +       
Sbjct: 40  RLDAVLAKLMPDYSRSRLSSWIKEGAVIVNDKPAQPKDKMIGGELIAVTVRPSEENLAFT 99

Query: 58  ------DHIEVDGVPLRKAERTRLWLYHKPIGLV---------TTHSDPDGRSTVFDNLP 102
                 D I  D   +   +   L ++                              +  
Sbjct: 100 PEPMDLDIIYEDDTVIVINKPAGLVVHPAAGNWSGTLLNGLLAHCPELSQVPRAGIVHRL 159

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
              +  + V    +  +  L+        + +       +  +  +   Q+ +D  N LK
Sbjct: 160 DKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAIANGIVPFDGKIETQIGRDPHNRLK 219

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 220 MAVVKFGGKPAITHVKVLERYLAHSYIECSLETGRTHQIRVHMREANHP 268


>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 = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 30/208 (14%), Positives = 59/208 (28%), Gaps = 28/208 (13%)

Query: 29  REVERMIAQQRVKVNGILLERAAVN-------------------VMSTDHIEVDGVPLRK 69
           RE +R I + RV +NG  + + +                     +  TDH  +   P   
Sbjct: 28  REAKRAIDRGRVSINGKRVTQKSFKASGILKCIVFEPNGYGLKPIFETDHFAIFDKPSGV 87

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           A   +     K +         +  + V          VI+       +       N   
Sbjct: 88  AIHPKKLANTKSLLDDVRLLYGNDANLVHRLDKETSGLVIASKNKFAESILKQAFQNKEI 147

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC----YGDMQVTLDTQKGS 185
             + L L      +   ++    V++D+   +K  I  +G         ++       G 
Sbjct: 148 QKKYLALIKGHLDKEITIKKPIAVNKDENIKVKVIISDEGKESITLVKPIKKI-----GK 202

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVN 213
           N  V      G+  +I+         + 
Sbjct: 203 NTLVECIPLTGRQHQIRIHLYSIGHPIV 230


>gi|269303280|gb|ACZ33380.1| RNA pseudouridine synthase family protein [Chlamydophila pneumoniae
           LPCoLN]
          Length = 283

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 31/232 (13%), Positives = 63/232 (27%), Gaps = 15/232 (6%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------DGVPL 67
           R+S  + ++    S++E+   I Q R +VNG +    +  V   D + +         P 
Sbjct: 13  RLSSFLRSQLPNHSKQEILASIRQHRCRVNGFIERFESYKVQPGDRVSLSLIPSTKQQPS 72

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              E     +Y KP  L T       R      L    S  + +G+       L+ L   
Sbjct: 73  ILWEDDYSIIYEKPPHLTTEQMAHMTRFFTVHRLDKGTSGCLLMGKSKQAATELMKLFKQ 132

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL---LKKGIVIQGICYGDMQVTLDTQKG 184
             + +          +                    +              + ++     
Sbjct: 133 RKIHKQYMALVFGHPKKKFGTVKSYTAPVYRRCGAVIFGAASPSQGKLTITEWSVLDSYK 192

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             + +      G+  +I+         +     + YGP           R +
Sbjct: 193 RYSLMLCKPITGRTHQIRLQMGLLGHPIVG--DVDYGP---KEQPPQIFRPL 239


>gi|49079326|gb|AAT49880.1| PA4239 [synthetic construct]
          Length = 207

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V + D + V
Sbjct: 97  RLDNVVYRMGFGSTRSESRQLVSHKAITVNGQTVNIPSYQVKAGDVVAV 145


>gi|15599435|ref|NP_252929.1| 30S ribosomal protein S4 [Pseudomonas aeruginosa PAO1]
 gi|107103755|ref|ZP_01367673.1| hypothetical protein PaerPA_01004826 [Pseudomonas aeruginosa PACS2]
 gi|116052274|ref|YP_788880.1| 30S ribosomal protein S4 [Pseudomonas aeruginosa UCBPP-PA14]
 gi|218889432|ref|YP_002438296.1| 30S ribosomal protein S4 [Pseudomonas aeruginosa LESB58]
 gi|254237103|ref|ZP_04930426.1| 30S ribosomal protein S4 [Pseudomonas aeruginosa C3719]
 gi|254242910|ref|ZP_04936232.1| 30S ribosomal protein S4 [Pseudomonas aeruginosa 2192]
 gi|296387204|ref|ZP_06876703.1| 30S ribosomal protein S4 [Pseudomonas aeruginosa PAb1]
 gi|313111393|ref|ZP_07797198.1| 30S ribosomal protein S4 [Pseudomonas aeruginosa 39016]
 gi|12230936|sp|O52759|RS4_PSEAE RecName: Full=30S ribosomal protein S4
 gi|122261423|sp|Q02T56|RS4_PSEAB RecName: Full=30S ribosomal protein S4
 gi|226699107|sp|B7V667|RS4_PSEA8 RecName: Full=30S ribosomal protein S4
 gi|9950456|gb|AAG07627.1|AE004841_5 30S ribosomal protein S4 [Pseudomonas aeruginosa PAO1]
 gi|115587495|gb|ABJ13510.1| 30S ribosomal protein S4 [Pseudomonas aeruginosa UCBPP-PA14]
 gi|126169034|gb|EAZ54545.1| 30S ribosomal protein S4 [Pseudomonas aeruginosa C3719]
 gi|126196288|gb|EAZ60351.1| 30S ribosomal protein S4 [Pseudomonas aeruginosa 2192]
 gi|218769655|emb|CAW25415.1| 30S ribosomal protein S4 [Pseudomonas aeruginosa LESB58]
 gi|310883700|gb|EFQ42294.1| 30S ribosomal protein S4 [Pseudomonas aeruginosa 39016]
          Length = 206

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V + D + V
Sbjct: 97  RLDNVVYRMGFGSTRSESRQLVSHKAITVNGQTVNIPSYQVKAGDVVAV 145


>gi|296313389|ref|ZP_06863330.1| ribosomal protein S4 [Neisseria polysaccharea ATCC 43768]
 gi|296840099|gb|EFH24037.1| ribosomal protein S4 [Neisseria polysaccharea ATCC 43768]
          Length = 206

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNG ++   +  V + D + V     ++    
Sbjct: 97  RLDNVVYRMGFGSTRAEARQLVSHKAIAVNGQVVNIPSFQVKAGDVVSVREKAKKQVRIQ 156


>gi|221061573|ref|XP_002262356.1| hypothetical protein, conserved in Plasmodium species [Plasmodium
           knowlesi strain H]
 gi|193811506|emb|CAQ42234.1| hypothetical protein, conserved in Plasmodium species [Plasmodium
           knowlesi strain H]
          Length = 414

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 20/102 (19%), Positives = 40/102 (39%), Gaps = 7/102 (6%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH---IEVDGV 65
           +  T  R+SK+++ + + SR + + +I   +V     +  +     +  D    IE+DG 
Sbjct: 8   KRSTLLRLSKILSLSAVTSRGKAQELIKNGKV----KVNNQVVRQNVVVDINSAIELDGK 63

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           P+     T+LW  +KP  +  +             L      
Sbjct: 64  PILVDVTTKLWGIYKPKHVFCSSETNYEYEEKKQALKIAPPH 105



 Score = 42.5 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 34/136 (25%), Positives = 64/136 (47%), Gaps = 1/136 (0%)

Query: 96  TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
           T  +    I   +I V  L  ++EGL+LLTNDG  AR L+      +  Y V+   ++  
Sbjct: 212 TKNNIANDIPEHLIVVNSLSASSEGLVLLTNDGDFARNLKGIENNIITSYIVKVKEELTN 271

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWKVNR 214
           +K+ L++KG  +  +    + V +  Q  S+  W+ +   E  +  +  +F  +   + +
Sbjct: 272 EKIKLIEKGCNVGDVHIRPLDVHVIKQHSSSPKWIKLTYVEKSHTYLNLLFSKYGLTIRK 331

Query: 215 LIRISYGPFQLGTLLA 230
             R S+GP++   L  
Sbjct: 332 CKRFSFGPYKASDLSE 347


>gi|167856725|ref|ZP_02479400.1| putative large adhesin [Haemophilus parasuis 29755]
 gi|167852151|gb|EDS23490.1| putative large adhesin [Haemophilus parasuis 29755]
          Length = 654

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 20/112 (17%), Positives = 30/112 (26%), Gaps = 1/112 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           + + GP   +  Q    A     +     +     E  D   R +   +   G   +   
Sbjct: 463 KGEQGPTGPQGPQGIAGAQGPKGDKGDPGQAGPKGEKGDTGPRGETGPAGPVGPRGETGP 522

Query: 302 ATPVHRRNLASNVWM-AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           A PV  R  A                  G R E     P+ P   +  R  A
Sbjct: 523 AGPVGPRGEAGPAGATGPQGPKGDNGSPGARGEKGEPGPAGPVGPAGPRGPA 574


>gi|156089455|ref|XP_001612134.1| hypothetical protein [Babesia bovis T2Bo]
 gi|154799388|gb|EDO08566.1| hypothetical protein BBOV_III010100 [Babesia bovis]
          Length = 329

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 13/36 (36%), Positives = 21/36 (58%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLER 49
           R+S+  AR GI SR   +R+I +  V +NG  ++ 
Sbjct: 3  IRISQFCARVGICSRGAAKRLIKKGHVLLNGTAVKS 38


>gi|107024278|ref|YP_622605.1| 30S ribosomal protein S4 [Burkholderia cenocepacia AU 1054]
 gi|116688397|ref|YP_834020.1| 30S ribosomal protein S4 [Burkholderia cenocepacia HI2424]
 gi|170731707|ref|YP_001763654.1| 30S ribosomal protein S4 [Burkholderia cenocepacia MC0-3]
 gi|206558666|ref|YP_002229426.1| 30S ribosomal protein S4 [Burkholderia cenocepacia J2315]
 gi|254246578|ref|ZP_04939899.1| Ribosomal protein S4 [Burkholderia cenocepacia PC184]
 gi|123371103|sp|Q1BRX3|RS4_BURCA RecName: Full=30S ribosomal protein S4
 gi|152060938|sp|A0K3Q0|RS4_BURCH RecName: Full=30S ribosomal protein S4
 gi|226697814|sp|B1JU47|RS4_BURCC RecName: Full=30S ribosomal protein S4
 gi|226697815|sp|B4E5E5|RS4_BURCJ RecName: Full=30S ribosomal protein S4
 gi|105894467|gb|ABF77632.1| SSU ribosomal protein S4P [Burkholderia cenocepacia AU 1054]
 gi|116646486|gb|ABK07127.1| SSU ribosomal protein S4P [Burkholderia cenocepacia HI2424]
 gi|124871354|gb|EAY63070.1| Ribosomal protein S4 [Burkholderia cenocepacia PC184]
 gi|169814949|gb|ACA89532.1| ribosomal protein S4 [Burkholderia cenocepacia MC0-3]
 gi|198034703|emb|CAR50570.1| 30S ribosomal protein S4 [Burkholderia cenocepacia J2315]
          Length = 207

 Score = 50.6 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNG++    +  V + D + +     ++A   
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKSITVNGVVANVPSQQVKAGDVVAIREKAKKQARIV 157

Query: 74  RLWLYHKPIGLVT 86
                 +  G+ +
Sbjct: 158 EALSLAEQGGMPS 170


>gi|223984454|ref|ZP_03634588.1| hypothetical protein HOLDEFILI_01882 [Holdemania filiformis DSM
           12042]
 gi|223963578|gb|EEF67956.1| hypothetical protein HOLDEFILI_01882 [Holdemania filiformis DSM
           12042]
          Length = 211

 Score = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G A +RR   +++    + VNG  ++  +  V     +EV
Sbjct: 104 RLDNIVYRMGFARTRRAARQLVNHGHILVNGKKVDIPSFTVKPGSTVEV 152


>gi|182418834|ref|ZP_02950099.1| ribosomal protein S4 [Clostridium butyricum 5521]
 gi|237666637|ref|ZP_04526622.1| ribosomal protein S4 [Clostridium butyricum E4 str. BoNT E BL5262]
 gi|182377331|gb|EDT74892.1| ribosomal protein S4 [Clostridium butyricum 5521]
 gi|237657836|gb|EEP55391.1| ribosomal protein S4 [Clostridium butyricum E4 str. BoNT E BL5262]
          Length = 206

 Score = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            R+  V+ R G   SR E  +++      VNG  ++  + +V + D I V
Sbjct: 98  MRLDNVVYRLGYGASRNEARQLVTHGHFLVNGKKVDICSYSVSANDVITV 147


>gi|163782710|ref|ZP_02177706.1| hemolysin [Hydrogenivirga sp. 128-5-R1-1]
 gi|159881831|gb|EDP75339.1| hemolysin [Hydrogenivirga sp. 128-5-R1-1]
          Length = 256

 Score = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K++   G + SR + + +I   +V V G  +++    +   + +EV
Sbjct: 2  VRLDKLLFERGLVDSREKAQALIMAGQVFVEGRRVDKPGTRLKGDERVEV 51


>gi|332798233|ref|YP_004459732.1| 30S ribosomal protein S4 [Tepidanaerobacter sp. Re1]
 gi|332695968|gb|AEE90425.1| ribosomal protein S4 [Tepidanaerobacter sp. Re1]
          Length = 208

 Score = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G AS R +  +++    V+VNG  +   +  V   D + +
Sbjct: 99  RLDNVVFRMGFASSRPQARQLVRYGHVQVNGKRVTIPSYQVKEKDVVAI 147


>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 = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 32/229 (13%), Positives = 65/229 (28%), Gaps = 32/229 (13%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILL---------ERAAVNVMST------- 57
           R+  V+A+     SR  +   I +  V VN             E  AV V  +       
Sbjct: 40  RLDAVLAKLMPDYSRSRLSSWIKEGAVIVNDKPAQPKDKMIGGELIAVTVRPSEENLAFT 99

Query: 58  ------DHIEVDGVPLRKAERTRLWLYHKPIGLV---------TTHSDPDGRSTVFDNLP 102
                 D I  D   +   +   L ++                              +  
Sbjct: 100 PEPMDLDIIYEDDAVIVINKPAGLVVHPAAGNWSGTLLNGLLAHCPELSQVPRAGIVHRL 159

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
              +  + V    +  +  L+        + +       +  +  +   Q+ +D  N LK
Sbjct: 160 DKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRLK 219

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +V  G       V +  +  S++++   L  G+  +I+      N  
Sbjct: 220 MAVVKFGGKPAITHVKVLERYLSHSYIECSLETGRTHQIRVHMREANHP 268


>gi|146320632|ref|YP_001200343.1| YlyB [Streptococcus suis 98HAH33]
 gi|145691438|gb|ABP91943.1| YlyB [Streptococcus suis 98HAH33]
          Length = 243

 Score = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 20/50 (40%), Gaps = 1/50 (2%)

Query: 13 PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            R+ K ++     SR      I   +V VNG   ++A  +V   D +  
Sbjct: 9  GIRLDKALSDLTDLSRSVANEQIKAGQVLVNGQP-KKAKYSVQVGDVLTY 57


>gi|68537164|ref|YP_251869.1| putative penicillin-binding protein 1 [Corynebacterium jeikeium
           K411]
 gi|68264763|emb|CAI38251.1| putative penicillin-binding protein 1 [Corynebacterium jeikeium
           K411]
          Length = 901

 Score = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 7/108 (6%), Positives = 18/108 (16%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G     +                +      +       +  +    +    K  K A P 
Sbjct: 25  GQRKPGQPGRPRQGQSGKPGQPGQPGRRRAANGNPAHAKPTRGRPAQGQSGKPGKPAKPG 84

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                 +               +  R    +      +K        +
Sbjct: 85  QPGKRRAANGKPAQGRPVQGRSAQGRPAQGKPVQRRGTKPVKSGGPRR 132



 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 8/98 (8%), Positives = 18/98 (18%), Gaps = 2/98 (2%)

Query: 259 APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAK 318
                       R    +       + K     +    +  K   P       +      
Sbjct: 1   MSSDKPSKNPFSRDGAGNSGAGRGGQRKPGQPGRPRQGQSGKPGQPGQPGRRRAANGNPA 60

Query: 319 GIHSSFLSDSGQR--EENHRRSPSFPSKRSLRRTSAKK 354
               +    +  +  +      P  P KR        +
Sbjct: 61  HAKPTRGRPAQGQSGKPGKPAKPGQPGKRRAANGKPAQ 98



 Score = 36.3 bits (82), Expect = 7.8,   Method: Composition-based stats.
 Identities = 8/104 (7%), Positives = 15/104 (14%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P   +  +                          +    +    Q      +     PV
Sbjct: 58  NPAHAKPTRGRPAQGQSGKPGKPAKPGQPGKRRAANGKPAQGRPVQGRSAQGRPAQGKPV 117

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
            RR             ++                  P      R
Sbjct: 118 QRRGTKPVKSGGPRRAAAAAGAGAGAAGAAASQRKRPQNNGQNR 161


>gi|53720796|ref|YP_109782.1| 30S ribosomal protein S4 [Burkholderia pseudomallei K96243]
 gi|53723829|ref|YP_104141.1| 30S ribosomal protein S4 [Burkholderia mallei ATCC 23344]
 gi|67640848|ref|ZP_00439641.1| 30S ribosomal protein S4 [Burkholderia mallei GB8 horse 4]
 gi|76811379|ref|YP_335115.1| 30S ribosomal protein S4 [Burkholderia pseudomallei 1710b]
 gi|121601043|ref|YP_994431.1| 30S ribosomal protein S4 [Burkholderia mallei SAVP1]
 gi|124384949|ref|YP_001027920.1| 30S ribosomal protein S4 [Burkholderia mallei NCTC 10229]
 gi|126439277|ref|YP_001060725.1| 30S ribosomal protein S4 [Burkholderia pseudomallei 668]
 gi|126448998|ref|YP_001083015.1| 30S ribosomal protein S4 [Burkholderia mallei NCTC 10247]
 gi|134283223|ref|ZP_01769924.1| 30S ribosomal protein S4 [Burkholderia pseudomallei 305]
 gi|167001674|ref|ZP_02267466.1| 30S ribosomal protein S4 [Burkholderia mallei PRL-20]
 gi|167721552|ref|ZP_02404788.1| 30S ribosomal protein S4 [Burkholderia pseudomallei DM98]
 gi|167740526|ref|ZP_02413300.1| 30S ribosomal protein S4 [Burkholderia pseudomallei 14]
 gi|167817731|ref|ZP_02449411.1| 30S ribosomal protein S4 [Burkholderia pseudomallei 91]
 gi|167826128|ref|ZP_02457599.1| 30S ribosomal protein S4 [Burkholderia pseudomallei 9]
 gi|167896212|ref|ZP_02483614.1| 30S ribosomal protein S4 [Burkholderia pseudomallei 7894]
 gi|167904594|ref|ZP_02491799.1| 30S ribosomal protein S4 [Burkholderia pseudomallei NCTC 13177]
 gi|167912859|ref|ZP_02499950.1| 30S ribosomal protein S4 [Burkholderia pseudomallei 112]
 gi|167920818|ref|ZP_02507909.1| 30S ribosomal protein S4 [Burkholderia pseudomallei BCC215]
 gi|226198240|ref|ZP_03793811.1| 30S ribosomal protein S4 [Burkholderia pseudomallei Pakistan 9]
 gi|237814120|ref|YP_002898571.1| ribosomal protein S4 [Burkholderia pseudomallei MSHR346]
 gi|254175265|ref|ZP_04881926.1| 30S ribosomal protein S4 [Burkholderia mallei ATCC 10399]
 gi|254180364|ref|ZP_04886962.1| 30S ribosomal protein S4 [Burkholderia pseudomallei 1655]
 gi|254190327|ref|ZP_04896835.1| 30S ribosomal protein S4 [Burkholderia pseudomallei Pasteur 52237]
 gi|254198547|ref|ZP_04904968.1| 30S ribosomal protein S4 [Burkholderia pseudomallei S13]
 gi|254201214|ref|ZP_04907578.1| 30S ribosomal protein S4 [Burkholderia mallei FMH]
 gi|254206555|ref|ZP_04912906.1| 30S ribosomal protein S4 [Burkholderia mallei JHU]
 gi|254260076|ref|ZP_04951130.1| 30S ribosomal protein S4 [Burkholderia pseudomallei 1710a]
 gi|254300601|ref|ZP_04968046.1| 30S ribosomal protein S4 [Burkholderia pseudomallei 406e]
 gi|61215450|sp|Q62GN0|RS4_BURMA RecName: Full=30S ribosomal protein S4
 gi|61215463|sp|Q63Q36|RS4_BURPS RecName: Full=30S ribosomal protein S4
 gi|90101678|sp|Q3JMT8|RS4_BURP1 RecName: Full=30S ribosomal protein S4
 gi|171769469|sp|A1V878|RS4_BURMS RecName: Full=30S ribosomal protein S4
 gi|171769829|sp|A2S7K1|RS4_BURM9 RecName: Full=30S ribosomal protein S4
 gi|171855085|sp|A3MRX9|RS4_BURM7 RecName: Full=30S ribosomal protein S4
 gi|171855116|sp|A3NEF4|RS4_BURP6 RecName: Full=30S ribosomal protein S4
 gi|52211210|emb|CAH37199.1| 30S ribosomal protein S4 [Burkholderia pseudomallei K96243]
 gi|52427252|gb|AAU47845.1| ribosomal protein S4 [Burkholderia mallei ATCC 23344]
 gi|76580832|gb|ABA50307.1| ribosomal protein S4 [Burkholderia pseudomallei 1710b]
 gi|121229853|gb|ABM52371.1| 30S ribosomal protein S4 [Burkholderia mallei SAVP1]
 gi|124292969|gb|ABN02238.1| 30S ribosomal protein S4 [Burkholderia mallei NCTC 10229]
 gi|126218770|gb|ABN82276.1| 30S ribosomal protein S4 [Burkholderia pseudomallei 668]
 gi|126241868|gb|ABO04961.1| 30S ribosomal protein S4 [Burkholderia mallei NCTC 10247]
 gi|134245418|gb|EBA45511.1| 30S ribosomal protein S4 [Burkholderia pseudomallei 305]
 gi|147747108|gb|EDK54184.1| 30S ribosomal protein S4 [Burkholderia mallei FMH]
 gi|147752097|gb|EDK59163.1| 30S ribosomal protein S4 [Burkholderia mallei JHU]
 gi|157810528|gb|EDO87698.1| 30S ribosomal protein S4 [Burkholderia pseudomallei 406e]
 gi|157938003|gb|EDO93673.1| 30S ribosomal protein S4 [Burkholderia pseudomallei Pasteur 52237]
 gi|160696310|gb|EDP86280.1| 30S ribosomal protein S4 [Burkholderia mallei ATCC 10399]
 gi|169655287|gb|EDS87980.1| 30S ribosomal protein S4 [Burkholderia pseudomallei S13]
 gi|184210903|gb|EDU07946.1| 30S ribosomal protein S4 [Burkholderia pseudomallei 1655]
 gi|225929760|gb|EEH25776.1| 30S ribosomal protein S4 [Burkholderia pseudomallei Pakistan 9]
 gi|237504346|gb|ACQ96664.1| ribosomal protein S4 [Burkholderia pseudomallei MSHR346]
 gi|238521643|gb|EEP85093.1| 30S ribosomal protein S4 [Burkholderia mallei GB8 horse 4]
 gi|243062571|gb|EES44757.1| 30S ribosomal protein S4 [Burkholderia mallei PRL-20]
 gi|254218765|gb|EET08149.1| 30S ribosomal protein S4 [Burkholderia pseudomallei 1710a]
          Length = 207

 Score = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 15/73 (20%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNGI+    +  V + D + +     ++A   
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAITVNGIVANIPSQQVKAGDVVAIREKAKKQARIV 157

Query: 74  RLWLYHKPIGLVT 86
                 +  G+ +
Sbjct: 158 EALSLAEQGGMPS 170


>gi|329946512|ref|ZP_08294028.1| ribosomal RNA large subunit methyltransferase J [Actinomyces sp.
          oral taxon 170 str. F0386]
 gi|328527143|gb|EGF54148.1| ribosomal RNA large subunit methyltransferase J [Actinomyces sp.
          oral taxon 170 str. F0386]
          Length = 290

 Score = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   + R G+A SR     +I    V ++G+++ + A  V     IE+
Sbjct: 5  IRIDSELVRRGLARSRTHAATLITDGHVTLDGVVVTKPARQVNPAQAIEI 54


>gi|315283065|ref|ZP_07871338.1| S4 domain-containing protein [Listeria marthii FSL S4-120]
 gi|313613292|gb|EFR87163.1| S4 domain-containing protein [Listeria marthii FSL S4-120]
          Length = 163

 Score = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 22/50 (44%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
             +  R+  +I+ A   SR++ ++++    VKVN   +E         D 
Sbjct: 83  TVSSMRLDVIISNAHHISRQKAKQLVVAGLVKVNWKTVENPDFECEEEDV 132


>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 = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 24/237 (10%), Positives = 65/237 (27%), Gaps = 38/237 (16%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN---------------- 53
               +R+ + +ARA   SR   +  I+   V+V G ++ + A                  
Sbjct: 8   EAEGERLDQALARALGVSRARAQAWISAGHVRVAGEVVTKPARRLAGERVEVEVPPEPPA 67

Query: 54  -VMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VI 109
            V + D + V+   +   +   + +      +          + V   L          +
Sbjct: 68  RVEAED-LTVE---ILYEDEDMVVVNKPAGMVTHPAPGVTRGTLVNALLGRWVEPGGEPV 123

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD--------------Q 155
             G +    +    +         L   +  + + +  + +  +               +
Sbjct: 124 RPGIVHRLDKETSGVIVVARHEAALRRLADAFKQRFVFKRYVALTEGVPANTTVIAPIGR 183

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             ++  K         Y +    +       A V      G+  +I+   +  +  +
Sbjct: 184 HPVHRFKMHTGGIKARYAETDFEVVATAEGRALVEARPHTGRTHQIRVHLKHLHTPI 240


>gi|289578295|ref|YP_003476922.1| hemolysin A [Thermoanaerobacter italicus Ab9]
 gi|289528008|gb|ADD02360.1| hemolysin A [Thermoanaerobacter italicus Ab9]
          Length = 266

 Score = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 11 FTPQRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             +R+  ++ + G  S RE  +  I    V V+G  +E+A   V     IEV
Sbjct: 3  SKKERLDVLLVQKGFFSSREKAKASIMAGEVYVDGKKIEKAGEFVNIDSSIEV 55


>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 = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 27/224 (12%), Positives = 58/224 (25%), Gaps = 35/224 (15%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--------- 66
           + +++      SR  ++  I    V V+G     A   V   + + VD            
Sbjct: 30  LQRLLPEH---SRSRLQSWIKSGLVTVDGK-ASTAKTKVWGGEKVSVDVQVKPESRAFIA 85

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-----ISVGRLD 115
                 +   +   L +      +V   +     + +   L              V RLD
Sbjct: 86  QDIPLDIVYEDDHILVVNKPAGMVVHPAAGNWDGTLLNALLFHAPQLHDVPRAGIVHRLD 145

Query: 116 INTEGLLLLTNDGGLARVLELPST----QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
             T GLL++         L         +      V      +      L +    +   
Sbjct: 146 KETSGLLVVAKTLNAQTHLVRQLQARTVKREYRAIVWGQLWRNGVVDQPLGRDPRSRTKM 205

Query: 172 Y-----GDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                      +  +  +     ++   L  G+  +I+   +  
Sbjct: 206 AINRMGKPAITRYEILERFSVQTYLRCNLETGRTHQIRVHMQHL 249


>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 = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 12/63 (19%), Positives = 29/63 (46%), Gaps = 3/63 (4%)

Query: 3  DKNIVQENFTPQ-RVSKVI-ARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          ++ ++  + T + R+   + A+ G   SR  ++ +I   +V + G  +      V + D 
Sbjct: 11 NRKVLTADETAEGRLDAWLTAQVGEEFSRSRIKALIKDGQVSLRGEPVTDPQRKVRNGDS 70

Query: 60 IEV 62
           E+
Sbjct: 71 FEI 73


>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 = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 31/243 (12%), Positives = 68/243 (27%), Gaps = 36/243 (14%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +V      +R+ + +A R    SR +++  I + RV+V G    +A+  V   + + V+ 
Sbjct: 14  VVDPEEAGERLDRFLAERLADTSRSQIQGWIDEGRVRV-GERPVKASHRVRPGEDVLVEP 72

Query: 65  V--------------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                           +   +   + +      +V         + V   L         
Sbjct: 73  PEPEPLELVPEPIPLKIVFEDEDVVVVDKPRGLVVHPAPGHSRGTLVHGLLAHCGRLSRL 132

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------------- 155
            G L       +     G L       +   L           +                
Sbjct: 133 GGSLRPGIVHRIDRDTSGLLVAAKTDLAYMGLAKQFHDHTVDREYLALVHGVVPHDHGTV 192

Query: 156 -----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                   +L ++  V++G         +  +      + + L  G+  +I+   EF  +
Sbjct: 193 DAPVGRHPHLRQQMAVVRGGRPAVTHFIVIERFARATLLRLRLETGRTHQIRVHMEFIGF 252

Query: 211 KVN 213
            V 
Sbjct: 253 PVI 255


>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 = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 35/228 (15%), Positives = 68/228 (29%), Gaps = 33/228 (14%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVD-------GVPLR 68
           SK +      S R+++ M  ++RVKVN  +       V    D + ++       GV + 
Sbjct: 17  SKYVKERFSLSSRDIQMMFRKKRVKVNSRVAHS--QRVLKKGDVLTLELPQDKDYGVDVE 74

Query: 69  KAERTRLWL--------------YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
           +   T L+                H      +                    R +     
Sbjct: 75  QGPITVLYEDAHTLVVNKAPFMLVHPAGQTKSCTLSNYVAGYYAKKNVVHKVRPVHRLDR 134

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL-------LKKGIVI 167
           D +   L   T +       EL + +  R+Y     G++D D +         +     +
Sbjct: 135 DTSGCILFGKTKEAQQYYTDELQAGRIDRIYTGLVEGRIDADGMVDAPIGVDPVFDNRRV 194

Query: 168 QGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     + T+   +G N  +   L  G+  +I+   E     + 
Sbjct: 195 IDEFGQPAQTEYTVLGYEGDNTLLRFKLLTGRTHQIRVHMEHIGHPIV 242


>gi|297544575|ref|YP_003676877.1| hemolysin A [Thermoanaerobacter mathranii subsp. mathranii str.
          A3]
 gi|296842350|gb|ADH60866.1| hemolysin A [Thermoanaerobacter mathranii subsp. mathranii str.
          A3]
          Length = 266

 Score = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 11 FTPQRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             +R+  ++ + G  S RE  +  I    V V+G  +E+A   V     IEV
Sbjct: 3  SKKERLDVLLVQKGFFSSREKAKASIMAGEVYVDGKKIEKAGEFVNIDSSIEV 55


>gi|254693218|ref|ZP_05155046.1| Cell division protein FtsJ [Brucella abortus bv. 3 str. Tulya]
 gi|261213461|ref|ZP_05927742.1| hemolysin A [Brucella abortus bv. 3 str. Tulya]
 gi|260915068|gb|EEX81929.1| hemolysin A [Brucella abortus bv. 3 str. Tulya]
          Length = 253

 Score = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 12/51 (23%), Positives = 23/51 (45%), Gaps = 1/51 (1%)

Query: 15 RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          R+ +++   G  A+R      I +  VKV+G  + +    V+    + VD 
Sbjct: 11 RLDQLLVERGFFATRSRARDAIQRGTVKVDGRPITKPGQMVVRDAALAVDD 61


>gi|224373704|ref|YP_002608076.1| 30S ribosomal protein S4 [Nautilia profundicola AmH]
 gi|254764602|sp|B9L6T8|RS4_NAUPA RecName: Full=30S ribosomal protein S4
 gi|223590010|gb|ACM93746.1| ribosomal protein S4 [Nautilia profundicola AmH]
          Length = 208

 Score = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G AS RR   +++    + VNG  +   +  V   D IE+
Sbjct: 99  RLDNVVYRMGFASTRRFARQLVTHGHILVNGKKVNIPSYLVKEGDRIEI 147


>gi|306842278|ref|ZP_07474940.1| hemolysin A [Brucella sp. BO2]
 gi|306287586|gb|EFM59037.1| hemolysin A [Brucella sp. BO2]
          Length = 253

 Score = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 12/51 (23%), Positives = 22/51 (43%), Gaps = 1/51 (1%)

Query: 15 RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          R+ +++   G  A+R      I +  VKV+G  + +    V     + VD 
Sbjct: 11 RLDQLLVERGFFATRSRARDAIQRGTVKVDGRPITKPGQMVARDAALAVDD 61


>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 = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 29/251 (11%), Positives = 66/251 (26%), Gaps = 43/251 (17%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-----------------VPLRK 69
           SR  +E++  ++ +KVNGI   +    +   D IE+ G                   + +
Sbjct: 29  SR--IEKLFRKKDIKVNGIRTNQKDYTIAFNDQIEIYGLIDIKKEEAPLISSFSFKKIYE 86

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                +      I + ++ +  D +   +     + S   S           ++L     
Sbjct: 87  DNNILIIDKPNGIEVHSSPNCLDNQVLAYLKFKQVDSFKPSHVGRLDKETSGIMLYAKNY 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A      + + +           ++ K   L                 +   K S    
Sbjct: 147 QALKYLNDNMENIIKTYTFKSDFNEESKDVELYLYKDEDKKRMAASFTKVPYSKLSKTHF 206

Query: 190 TV-------GLREGKNREIKKVFEFFNWKV-------------NRLIRISYGPFQLGTLL 229
            +        L  G+  +I+         +               L  +     QL    
Sbjct: 207 YLESNKKYATLSSGRKHQIRVSLMKLGKPIYGDFKYGGKKAGRLMLHCLQIKFQQL---- 262

Query: 230 AGSTREVSKKI 240
            G  + +++  
Sbjct: 263 EGEFKYLNELE 273


>gi|154498042|ref|ZP_02036420.1| hypothetical protein BACCAP_02023 [Bacteroides capillosus ATCC
          29799]
 gi|150273032|gb|EDN00189.1| hypothetical protein BACCAP_02023 [Bacteroides capillosus ATCC
          29799]
          Length = 268

 Score = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 1/56 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          R+  ++   G+  SR++ + +I   +V V G  +++A      T  IEV G  L  
Sbjct: 5  RLDVLLCERGLMESRQKAQAVIMAGQVYVGGQKVDKAGAQTEETAEIEVRGKTLAY 60


>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 = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 30/236 (12%), Positives = 62/236 (26%), Gaps = 40/236 (16%)

Query: 13  PQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMST------------- 57
            QR+ +V A    A  SR  +   I   R+ V+G ++      V                
Sbjct: 50  GQRLDQV-AAQLFAEHSRSRLSAWIKDGRLTVDGAVIR-PRDIVHGGSILELTAEQEAQG 107

Query: 58  ----DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
                 IE+D   +   +   L +      +V   +     + +   L  I   +     
Sbjct: 108 EWIAQDIELD---IVYEDDDILVINKPAGLVVHPAAGHADGTLLNALLHHIPDIINVPRA 164

Query: 114 LDINTEG----------------LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
             ++                     L+      +            V             
Sbjct: 165 GIVHRLDKDTTGLMVVAKTIQAQTQLVAQLQSRSVSRIYECIVIGVVTAGGKINAPIGRH 224

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               ++  V++G         +  +  S+  V V L  G+  +I+      N+ + 
Sbjct: 225 GQQRQRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINFPLV 280


>gi|121997625|ref|YP_001002412.1| ribosomal protein S4 [Halorhodospira halophila SL1]
 gi|152060952|sp|A1WV98|RS4_HALHL RecName: Full=30S ribosomal protein S4
 gi|121589030|gb|ABM61610.1| SSU ribosomal protein S4P [Halorhodospira halophila SL1]
          Length = 207

 Score = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 15/73 (20%), Positives = 27/73 (36%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V  R G  S R E  +++  + V VNG ++   +  V   D + V      +    
Sbjct: 98  RLDNVCYRMGFGSTRAEARQLVNHRGVLVNGRVVNIPSYQVQPGDTVSVKEKAKSQLRIQ 157

Query: 74  RLWLYHKPIGLVT 86
                 +  G  +
Sbjct: 158 AALELAQQNGWAS 170


>gi|315639612|ref|ZP_07894752.1| S4 domain-containing protein YlmH [Enterococcus italicus DSM 15952]
 gi|315484573|gb|EFU75029.1| S4 domain-containing protein YlmH [Enterococcus italicus DSM 15952]
          Length = 260

 Score = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 26/56 (46%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
              +  R+  VIA     SR+  +++I   +VKVN  + +R    +   D + + G
Sbjct: 178 TTVSSMRLDTVIANVFSISRQRSKQLIEAGKVKVNWRVAQRPDFMLELLDIVSIRG 233


>gi|284051997|ref|ZP_06382207.1| hemolysin A [Arthrospira platensis str. Paraca]
 gi|291568827|dbj|BAI91099.1| hemolysin-like protein [Arthrospira platensis NIES-39]
          Length = 278

 Score = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 12/54 (22%), Positives = 26/54 (48%), Gaps = 9/54 (16%)

Query: 14 QRVS-----KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          QR+      + ++     SR++ +R+I    V VN  ++++    V  +  I+V
Sbjct: 3  QRLDTLLVDRHLSE----SRQQAQRLIRAGEVMVNRQVVDKPGTEVDISATIDV 52


>gi|227891072|ref|ZP_04008877.1| 30S ribosomal protein S4 [Lactobacillus salivarius ATCC 11741]
 gi|227866946|gb|EEJ74367.1| 30S ribosomal protein S4 [Lactobacillus salivarius ATCC 11741]
          Length = 201

 Score = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+AS RR+  +++    + V+G  ++  +  V     I +
Sbjct: 94  RLDNVVYRLGLASTRRQARQLVNHGHITVDGKRVDIPSYEVEPGQVISL 142


>gi|118474712|ref|YP_891268.1| 30S ribosomal protein S4 [Campylobacter fetus subsp. fetus 82-40]
 gi|152060940|sp|A0RM35|RS4_CAMFF RecName: Full=30S ribosomal protein S4
 gi|118413938|gb|ABK82358.1| ribosomal protein S4 [Campylobacter fetus subsp. fetus 82-40]
          Length = 208

 Score = 50.2 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G A+ RR   +++    + VNG  ++  +  V + + IEV
Sbjct: 98  QRLDNVVYRMGFATTRRFARQLVTHGHILVNGKKVDIPSYRVTAGEKIEV 147


>gi|261400076|ref|ZP_05986201.1| ribosomal protein S4 [Neisseria lactamica ATCC 23970]
 gi|313667465|ref|YP_004047749.1| 30S ribosomal protein S4 [Neisseria lactamica ST-640]
 gi|269210301|gb|EEZ76756.1| ribosomal protein S4 [Neisseria lactamica ATCC 23970]
 gi|309379135|emb|CBX22266.1| 30S ribosomal protein S4 [Neisseria lactamica Y92-1009]
 gi|313004927|emb|CBN86353.1| 30S ribosomal protein S4 [Neisseria lactamica 020-06]
          Length = 206

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNG ++   +  V + D + V     ++    
Sbjct: 97  RLDNVVYRMGFGSTRAEARQLVSHKAIAVNGQVVNIPSFQVKAGDVVAVREKAKKQVRIQ 156


>gi|127511116|ref|YP_001092313.1| 30S ribosomal protein S4 [Shewanella loihica PV-4]
 gi|152112260|sp|A3Q9A6|RS4_SHELP RecName: Full=30S ribosomal protein S4
 gi|126636411|gb|ABO22054.1| SSU ribosomal protein S4P [Shewanella loihica PV-4]
          Length = 206

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V + D I V
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKSIMVNGRVVNIPSFKVSANDVISV 145


>gi|115443574|ref|YP_778593.1| 30S ribosomal protein S4 [Bigelowiella natans]
 gi|122233787|sp|Q06J34|RR4_BIGNA RecName: Full=30S ribosomal protein S4, chloroplastic
 gi|110810219|gb|ABG91425.1| 30S ribosomal protein S4 [Bigelowiella natans]
          Length = 194

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 13/59 (22%), Positives = 26/59 (44%), Gaps = 7/59 (11%)

Query: 14  QRVSKVIARAGI----ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
            R+  ++ R G     AS     ++I+   + VNG  ++    N   +D I ++   L+
Sbjct: 84  MRLDTLLYRTGFVPTVAS---ARQLISHGHINVNGKKVDIPGFNCSISDKIVINKEILK 139


>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 = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 31/229 (13%), Positives = 65/229 (28%), Gaps = 32/229 (13%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILL---------ERAAVNVMST------- 57
           R+  V+A+     SR  +   I +  V VN             E  AV V  +       
Sbjct: 40  RLDAVLAKLMPDYSRSRLSSWIKEGAVIVNDKPAQPKDKMIGGELIAVTVRPSEENLAFT 99

Query: 58  ------DHIEVDGVPLRKAERTRLWLYHKPIGLV---------TTHSDPDGRSTVFDNLP 102
                 D I  D   +   +   L ++                              +  
Sbjct: 100 PEPMDLDIIYEDDTVIVINKPAGLVVHPAAGNWSGTLLNGLLAHCSELSQVPRAGIVHRL 159

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
              +  + V    +  +  L+        + +       +  +  +   Q+ +D  N LK
Sbjct: 160 DKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRLK 219

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 220 MAVVKFGGKPAITHVKVLERYLAHSYIECSLETGRTHQIRVHMREANHP 268


>gi|166030419|ref|ZP_02233248.1| hypothetical protein DORFOR_00080 [Dorea formicigenerans ATCC
           27755]
 gi|166029777|gb|EDR48534.1| hypothetical protein DORFOR_00080 [Dorea formicigenerans ATCC
           27755]
          Length = 270

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 21/178 (11%), Positives = 51/178 (28%), Gaps = 2/178 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++ +  +A SR + + +I    V V+    ++          IEV G  L    R
Sbjct: 3   ERLDVLLVKRNLAASREKAKAIIMSGNVYVDNQKEDKPGTTFPEESKIEVRGHTLPYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L         +                    ++  G + +    +     D  L +
Sbjct: 63  GGLKLEKAMKEFQVSVEGKVCTDVGSST-GGFTDCMLQNGAVKVFAIDVGHGQLDWKLRQ 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +   +   +  V      +    + +    +        ++  L  +    A + 
Sbjct: 122 DERVVCMEKTNIRYVTPEDIGEPVDFSSIDVSFISLTKVLMPIRDYLTDKGQIVALIK 179


>gi|145596407|ref|YP_001160704.1| ribosomal protein S4 [Salinispora tropica CNB-440]
 gi|145305744|gb|ABP56326.1| SSU ribosomal protein S4P [Salinispora tropica CNB-440]
          Length = 208

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V+ RAG A SR    +++      VNG  ++  +  V   D +EV G 
Sbjct: 99  RLDNVVYRAGYAKSRDMARQLVKHGHFVVNGKKVDIPSYRVKEHDIVEVRGK 150


>gi|78064949|ref|YP_367718.1| 30S ribosomal protein S4 [Burkholderia sp. 383]
 gi|90101679|sp|Q39KE2|RS4_BURS3 RecName: Full=30S ribosomal protein S4
 gi|77965694|gb|ABB07074.1| SSU ribosomal protein S4P [Burkholderia sp. 383]
          Length = 207

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 15/73 (20%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNG++    +  V S D + +     ++A   
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKSITVNGVVANVPSQQVKSGDVVAIREKAKKQARIV 157

Query: 74  RLWLYHKPIGLVT 86
                 +  G+ +
Sbjct: 158 EALSLAEQGGMPS 170


>gi|218135254|ref|ZP_03464058.1| hypothetical protein BACPEC_03159 [Bacteroides pectinophilus ATCC
           43243]
 gi|217990639|gb|EEC56650.1| hypothetical protein BACPEC_03159 [Bacteroides pectinophilus ATCC
           43243]
          Length = 197

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI R G A +R+E  +++  + V VNG  +   +  V + D IE+
Sbjct: 88  RLDNVIFRMGFARTRKEARQIVDHKHVLVNGKRVNIPSYLVKAGDVIEI 136


>gi|154505142|ref|ZP_02041880.1| hypothetical protein RUMGNA_02655 [Ruminococcus gnavus ATCC 29149]
 gi|153794621|gb|EDN77041.1| hypothetical protein RUMGNA_02655 [Ruminococcus gnavus ATCC 29149]
          Length = 181

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 1/65 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G A +R+E  +++  + V VNG  +   +  V + D IE+           
Sbjct: 72  RLDNVMFRMGFARTRKEARQIVDHKHVLVNGKQVNIPSYLVKAGDVIEIKEKHKDCQRYK 131

Query: 74  RLWLY 78
            +   
Sbjct: 132 DILEV 136


>gi|115350347|ref|YP_772186.1| 30S ribosomal protein S4 [Burkholderia ambifaria AMMD]
 gi|115280335|gb|ABI85852.1| SSU ribosomal protein S4P [Burkholderia ambifaria AMMD]
          Length = 213

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNG++    +  V + D + +     ++A   
Sbjct: 104 RLDNVVYRMGFGSTRAEARQLVSHKSITVNGVVANVPSQQVKAGDIVAIREKAKKQARIV 163

Query: 74  RLWLYHKPIGLVT 86
                 +  G+ +
Sbjct: 164 EALSLAEQGGMPS 176


>gi|307705383|ref|ZP_07642242.1| S4 domain protein [Streptococcus mitis SK597]
 gi|307621046|gb|EFO00124.1| S4 domain protein [Streptococcus mitis SK597]
          Length = 261

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 11/48 (22%), Positives = 26/48 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +++     SR +  ++I ++ V+VN  +++++   V   D I V
Sbjct: 184 RLDVLLSNVLKLSRNQANQLIEKKLVQVNYHVVDKSDYIVQVGDLISV 231


>gi|299137850|ref|ZP_07031031.1| hemolysin A [Acidobacterium sp. MP5ACTX8]
 gi|298600491|gb|EFI56648.1| hemolysin A [Acidobacterium sp. MP5ACTX8]
          Length = 252

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 11/48 (22%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
          R+ K++   G+A SR   + +I   RV V    +++   +V +   + 
Sbjct: 4  RLDKLLVDRGLAASRERAQALILAGRVLVEEQRVDKPGTSVEAEAVVR 51


>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 = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 26/237 (10%), Positives = 61/237 (25%), Gaps = 40/237 (16%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------- 63
            +R    +A+    SR +   ++A    +V G  +++AAV +   D IE+D         
Sbjct: 14  GKRFDVALAKMTGLSRAKAAELVASGSARVLGRDVDKAAVLL-EGDMIEIDEHDPEPVAE 72

Query: 64  ----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
                + +   +   + +               G + +   L                  
Sbjct: 73  PIATDMAIVYEDDDVVVVDKPVGVAAHASVGWTGPTVLGSLLDRGVHITSYGAAGRQGIV 132

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY------- 172
             L +   G +       + + +R            +    L +G + +           
Sbjct: 133 SRLDVGTSGLMLVCKSELAYKEMRRQFSEHEVVKTYE---ALVQGNLQEDKATIDAPIGR 189

Query: 173 --------------GDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                 +  + G      + L  G+  +I+  F      + 
Sbjct: 190 AKVSDFRFCITPAGKPAITHWDVLERFGEATLARINLETGRTHQIRVHFSSIGHPLV 246


>gi|254468445|ref|ZP_05081851.1| ribosomal protein S4 [beta proteobacterium KB13]
 gi|207087255|gb|EDZ64538.1| ribosomal protein S4 [beta proteobacterium KB13]
          Length = 209

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GI  SR E  +++    + VNG  +   +  V   D + V
Sbjct: 100 RLDNVVYRMGIGVSRSESRQLVRHNSITVNGNRVNIPSYQVKPGDQVAV 148


>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 = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 6/59 (10%)

Query: 10 NFTPQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          +  P R+ K +AR     A + SR  + R++ Q  V+V+G ++        +   I VD
Sbjct: 12 DSPPPRLDKALARDVPEDANL-SRTRLGRLLEQGAVQVDGTVVTDPRSRAEAGQQITVD 69


>gi|326201959|ref|ZP_08191829.1| hemolysin A [Clostridium papyrosolvens DSM 2782]
 gi|325987754|gb|EGD48580.1| hemolysin A [Clostridium papyrosolvens DSM 2782]
          Length = 270

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 1/52 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            +R+  ++   G+  SR + +  I    V +NGI  ++    V     IE+
Sbjct: 2  EKERLDVLLVNKGLFESREKCKSAIMAGLVWINGIREDKPGTKVPVECEIEI 53


>gi|254673628|emb|CBA09173.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis alpha275]
          Length = 374

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 71/230 (30%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQVPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  +V  G       V +  +   ++++   L  G+  +I+      N  
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLIHSYIECSLETGRTHQIRVHMREANHP 268


>gi|187250461|ref|YP_001874943.1| putative rRNA methylase [Elusimicrobium minutum Pei191]
 gi|186970621|gb|ACC97606.1| putative rRNA methylase [Elusimicrobium minutum Pei191]
          Length = 258

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 1/58 (1%)

Query: 6  IVQENFTPQRVS-KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          ++  N    R+  ++IA+    SR   +  I    V VNG +   A   +   D I +
Sbjct: 1  MMTSNPKKPRLDMELIAQGFFKSRTRAQASIMAGEVLVNGTVEYGADRKIKPEDIITL 58


>gi|86141165|ref|ZP_01059711.1| 30S ribosomal protein S4 [Leeuwenhoekiella blandensis MED217]
 gi|85831724|gb|EAQ50179.1| 30S ribosomal protein S4 [Leeuwenhoekiella blandensis MED217]
          Length = 201

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA SRR   ++++ + + VNG L+   +  + + D + V
Sbjct: 94  RLDNVVFRMGIAPSRRAARQLVSHRHITVNGELVNIPSYQLKAGDVVAV 142


>gi|90962052|ref|YP_535968.1| 30S ribosomal protein S4 [Lactobacillus salivarius UCC118]
 gi|301300890|ref|ZP_07207062.1| ribosomal protein S4 [Lactobacillus salivarius ACS-116-V-Col5a]
 gi|122448841|sp|Q1WT66|RS4_LACS1 RecName: Full=30S ribosomal protein S4
 gi|90821246|gb|ABD99885.1| SSU ribosomal protein S4P [Lactobacillus salivarius UCC118]
 gi|300214749|gb|ADJ79165.1| 30S ribosomal protein S4 [Lactobacillus salivarius CECT 5713]
 gi|300851489|gb|EFK79201.1| ribosomal protein S4 [Lactobacillus salivarius ACS-116-V-Col5a]
          Length = 201

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+AS RR+  +++    + V+G  ++  +  V     I +
Sbjct: 94  RLDNVVYRLGLASTRRQARQLVNHGHITVDGKRVDIPSYEVEPGQVISL 142


>gi|222823138|ref|YP_002574711.1| 30S ribosomal protein S4 [Campylobacter lari RM2100]
 gi|254764576|sp|B9KEH5|RS4_CAMLR RecName: Full=30S ribosomal protein S4
 gi|222538359|gb|ACM63460.1| 30S ribosomal protein S4 [Campylobacter lari RM2100]
          Length = 208

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G A+ RR   +++    + VNG  ++  +  V +   IEV
Sbjct: 98  QRLDNVVYRMGFATTRRFARQLVTHGHILVNGKRVDIPSYRVEAGQKIEV 147


>gi|296331117|ref|ZP_06873591.1| factor involved in shape determination, RNA-binding fold protein
           [Bacillus subtilis subsp. spizizenii ATCC 6633]
 gi|305674272|ref|YP_003865944.1| shape determination protein [Bacillus subtilis subsp. spizizenii
           str. W23]
 gi|296151761|gb|EFG92636.1| factor involved in shape determination, RNA-binding fold protein
           [Bacillus subtilis subsp. spizizenii ATCC 6633]
 gi|305412516|gb|ADM37635.1| factor involved in shape determination, RNA-binding fold protein
           [Bacillus subtilis subsp. spizizenii str. W23]
          Length = 257

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 16/62 (25%), Positives = 28/62 (45%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           D  I  +  +  R+  V A     SR++ + ++    VKVN  ++E  +  V   D + V
Sbjct: 170 DVEIRDDTVSSLRLDAVCASMSRQSRQKSQTLVKNGLVKVNWKVVEDPSYMVAEGDMLSV 229

Query: 63  DG 64
            G
Sbjct: 230 RG 231


>gi|259503648|ref|ZP_05746550.1| 30S ribosomal protein S4 [Lactobacillus antri DSM 16041]
 gi|259168367|gb|EEW52862.1| 30S ribosomal protein S4 [Lactobacillus antri DSM 16041]
          Length = 142

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+  ++ R G+A+ RR+  +++    + V+G  ++  +  V     I V
Sbjct: 35 RLDNMVYRLGLATTRRQARQLVNHGHITVDGKRVDIPSYEVDVNQVIAV 83


>gi|255076295|ref|XP_002501822.1| predicted protein [Micromonas sp. RCC299]
 gi|226517086|gb|ACO63080.1| predicted protein [Micromonas sp. RCC299]
          Length = 246

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15 RVSKV-IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+ ++ IA     SR  V+  IAQ +V VNG  + +A   +     I +
Sbjct: 9  RLDELTIAEYPEYSRNVVQSWIAQGKVLVNGQPVTKAGTKLRPDVKIVI 57


>gi|146329810|ref|YP_001210128.1| 30S ribosomal protein S4 [Dichelobacter nodosus VCS1703A]
 gi|172047329|sp|A5EX95|RS4_DICNV RecName: Full=30S ribosomal protein S4
 gi|146233280|gb|ABQ14258.1| 30S ribosomal protein S4 [Dichelobacter nodosus VCS1703A]
          Length = 206

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G  S R E  ++++   ++VNG  +  A+  V + D + V
Sbjct: 96  QRLDNVVYRMGYGSTRAEARQLVSHGAIEVNGQRVTIASYQVQAEDIVSV 145


>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 = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 6/59 (10%)

Query: 10 NFTPQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          +  P R+ K +AR     A + SR  + R++ Q  V+V+G ++        +   I VD
Sbjct: 12 DSPPPRLDKALARDVPEDANL-SRTRLGRLLEQGAVQVDGTVVTDPRSRAEAGQQITVD 69


>gi|331268344|ref|YP_004394836.1| S4 domain-containing protein [Clostridium botulinum BKT015925]
 gi|329124894|gb|AEB74839.1| S4 domain protein [Clostridium botulinum BKT015925]
          Length = 93

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   +      RV +NG + +  +  +   D IEV
Sbjct: 5  MRLDKYLKVSRIIKRRTVAKEACESGRVFINGKVAK-PSSEINEDDIIEV 53


>gi|110004829|emb|CAK99162.1| probable ribosomal 23s rrna methyltransferase protein
          [Spiroplasma citri]
          Length = 269

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 12/57 (21%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+ +++    +A SR + + MI    V V+ +   +    V     I++ G  L+ 
Sbjct: 3  IRLDQLMVNNNLAPSREKAKAMILANNVLVDNVPALKPGELVKLDSIIKLRGERLKY 59


>gi|325203287|gb|ADY98740.1| ribosomal protein S4 [Neisseria meningitidis M01-240355]
          Length = 206

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNG ++   +  V + D + V     ++    
Sbjct: 97  RLDNVVYRMGFGSTRAEARQLVSHKAIVVNGQVVNIPSFQVKAGDVVSVREKAKKQVRIQ 156


>gi|256090913|ref|XP_002581414.1| ribosomal pseudouridine synthase [Schistosoma mansoni]
 gi|238667306|emb|CAZ37653.1| ribosomal pseudouridine synthase, putative [Schistosoma mansoni]
          Length = 165

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 24/140 (17%), Positives = 40/140 (28%), Gaps = 15/140 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------DGVP 66
           R+ K +A     SR +    I Q+RV VNG   ++A   V   D I          D   
Sbjct: 7   RLDKALADLTPLSRSQANDQIKQKRVLVNGSP-KKAKYIVQVGDCISYHIPEESSLDYQA 65

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                 +   +     +      +V   +     + V   L  +       G +      
Sbjct: 66  QDIPLDIVYQDDVLAIINKPQGMVVHPSAGHSTGTLVNALLYHVKDLSSINGVIRPGIVH 125

Query: 121 LLLLTNDGGLARVLELPSTQ 140
            +     G L       + Q
Sbjct: 126 RIDKDTSGLLMVAKTDKAHQ 145


>gi|167587747|ref|ZP_02380135.1| 30S ribosomal protein S4 [Burkholderia ubonensis Bu]
          Length = 207

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNGI+    +  V + D I +
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAITVNGIVANVPSQQVKAGDVIAI 146


>gi|118444469|ref|YP_877122.1| S4 domain-containing protein [Clostridium novyi NT]
 gi|118134925|gb|ABK61969.1| S4 domain protein [Clostridium novyi NT]
          Length = 89

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   +      RV +N  + +  +  V   D IEV
Sbjct: 1  MRLDKYLKVSRIIKRRTIAKEACESGRVFINDKVAK-PSTEVNENDIIEV 49


>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 = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 26/198 (13%), Positives = 59/198 (29%), Gaps = 3/198 (1%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K++A+    S  E + +I    V   G  +  A   +       ++    P    E   L
Sbjct: 8   KILAKQKNISNNEAKELIDSGLVYAKGQKVMIARALMSENTKFSIEEMPKPSVIFEDENL 67

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
              +KP  + +       +  +   L    S V+ + + D      +       + ++  
Sbjct: 68  IAINKPAAITSEKISQIYKFPLLHRLDKDTSGVLLLVKNDEFASLAINEFKKMKVEKIYV 127

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
                 +    V     +     N     I  +       +++     G    V V ++ 
Sbjct: 128 AAVRGIMSEEVVVNEPILTIKNKNGAFSKIS-KDGKEAISEISPLMVVGKKTLVKVVIKT 186

Query: 196 GKNREIKKVFEFFNWKVN 213
           G+  +I+      N  + 
Sbjct: 187 GRTHQIRVHLASLNLPIV 204


>gi|17987780|ref|NP_540414.1| hemolysin [Brucella melitensis bv. 1 str. 16M]
 gi|225851973|ref|YP_002732206.1| hemolysin A [Brucella melitensis ATCC 23457]
 gi|256044154|ref|ZP_05447061.1| hemolysin A [Brucella melitensis bv. 1 str. Rev.1]
 gi|256112957|ref|ZP_05453865.1| hemolysin A [Brucella melitensis bv. 3 str. Ether]
 gi|256264519|ref|ZP_05467051.1| cell division protein FtsJ [Brucella melitensis bv. 2 str. 63/9]
 gi|260563511|ref|ZP_05833997.1| cell division protein FtsJ [Brucella melitensis bv. 1 str. 16M]
 gi|265990566|ref|ZP_06103123.1| hemolysin A [Brucella melitensis bv. 1 str. Rev.1]
 gi|265994396|ref|ZP_06106953.1| hemolysin A [Brucella melitensis bv. 3 str. Ether]
 gi|17983504|gb|AAL52678.1| hemolysin [Brucella melitensis bv. 1 str. 16M]
 gi|225640338|gb|ACO00252.1| hemolysin A [Brucella melitensis ATCC 23457]
 gi|260153527|gb|EEW88619.1| cell division protein FtsJ [Brucella melitensis bv. 1 str. 16M]
 gi|262765509|gb|EEZ11298.1| hemolysin A [Brucella melitensis bv. 3 str. Ether]
 gi|263001350|gb|EEZ13925.1| hemolysin A [Brucella melitensis bv. 1 str. Rev.1]
 gi|263094852|gb|EEZ18590.1| cell division protein FtsJ [Brucella melitensis bv. 2 str. 63/9]
 gi|326408469|gb|ADZ65534.1| hemolysin A [Brucella melitensis M28]
 gi|326538186|gb|ADZ86401.1| hemolysin A [Brucella melitensis M5-90]
          Length = 253

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 12/51 (23%), Positives = 23/51 (45%), Gaps = 1/51 (1%)

Query: 15 RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          R+ +++   G  A+R      I +  VKV+G  + +    V+    + VD 
Sbjct: 11 RLDQLLVERGFFATRSRARDAIQRGTVKVDGRPITKPGQMVVRDAALAVDD 61


>gi|332982681|ref|YP_004464122.1| 30S ribosomal protein S4P [Mahella australiensis 50-1 BON]
 gi|332700359|gb|AEE97300.1| SSU ribosomal protein S4P [Mahella australiensis 50-1 BON]
          Length = 206

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 1/51 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+   + R G A SR +  +++    + VNG  +   + +V   D I V G
Sbjct: 98  RLDNTVYRIGFADSRAQARQLVRHGHITVNGRKVNIPSYSVKPGDIIAVKG 148


>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 = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 25/245 (10%), Positives = 66/245 (26%), Gaps = 40/245 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQ-RVKVNGILLERAAVNVMSTDHIEVDGV 65
           V E     R+ + +      +R EV++ I +   + +   ++     ++   + I+    
Sbjct: 8   VDEKQDGMRLDQFLKEVSGLTRSEVQKWIKEGYAISLPNRMVRS-NYHISDKEKIQFSWE 66

Query: 66  P--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                          +   +   + +      +V   +     + V   L      ++ V
Sbjct: 67  EKKEIELIPQKIKLDILYEDEHIIVINKSRGMVVHPGAGNIDNTLVNALLYHCGESLLKV 126

Query: 112 G-RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
           G +        L     G +  V    + + ++        +     L    +     G 
Sbjct: 127 GEKTRPGIVHRLDKDTSGVMVAVKSDIAYEKVKNEIATHEAKRTYLTLVH-GQMEGPDGK 185

Query: 171 CYGD--------MQVTLDTQKGSN--------------AWVTVGLREGKNREIKKVFEFF 208
                       M+  +  + G N              + +   L  G+  +I+    + 
Sbjct: 186 IDLPLGRSLKDRMKWDVQPKTGKNAITHFHVLEFMTKYSLLECKLETGRTHQIRVHMSYI 245

Query: 209 NWKVN 213
              V 
Sbjct: 246 GHPVI 250


>gi|187933335|ref|YP_001886589.1| hemolysin A [Clostridium botulinum B str. Eklund 17B]
 gi|187721488|gb|ACD22709.1| hemolysin A [Clostridium botulinum B str. Eklund 17B]
          Length = 269

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 22/146 (15%), Positives = 45/146 (30%), Gaps = 2/146 (1%)

Query: 11  FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
              +R+  ++   GI  SR   +  I + +V V+G  +++A   V    +IE  G  L+ 
Sbjct: 3   EKKERLDILLVEKGIITSRDRAKACIMEGKVFVDGQRVDKAGEKVSIIANIEYKGAKLKY 62

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             R  L L         +  D                 ++  G   + +  +        
Sbjct: 63  VSRGGLKLEKAMKSYDISLEDKVCMDIGAST-GGFTDCMLQNGAQKVYSVDVGYGQFAWK 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQ 155
           L     +   +   +  V      + 
Sbjct: 122 LRTDERVVCMERTNIRYVTLEDIGEP 147


>gi|325133782|gb|EGC56438.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis M13399]
          Length = 356

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 72/230 (31%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 22  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 80

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 81  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 140

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 141 LDKETSGLMVVAKTLSAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 200

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 201 KMAVVKFGGKPAVTHVKVLERYLTHSYIECSLETGRTHQIRVHMREANHP 250


>gi|295099742|emb|CBK88831.1| SSU ribosomal protein S4P [Eubacterium cylindroides T2-87]
          Length = 202

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G A +RR   +++    + VNG  ++  +  V     IEV
Sbjct: 93  RLDNLVYRMGFARTRRGARQLVNHGHILVNGKKVDIPSYQVKPGTVIEV 141


>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 = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 31/229 (13%), Positives = 65/229 (28%), Gaps = 32/229 (13%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILL---------ERAAVNVMST------- 57
           R+  V+A+     SR  +   I +  V VN             E  AV V  +       
Sbjct: 40  RLDAVLAKLMPDYSRSRLSSWIKEGAVIVNDKPAQPKDKMIGGELIAVTVRPSEENLAFT 99

Query: 58  ------DHIEVDGVPLRKAERTRLWLYHKPIGLV---------TTHSDPDGRSTVFDNLP 102
                 D I  D   +   +   L ++                              +  
Sbjct: 100 PEPMDLDIIYEDDTVIVINKPAGLVVHPASGNWSGTLLNGLLAHCPELSQVPRAGIVHRL 159

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
              +  + V    +  +  L+        + +       +  +  +   Q+ +D  N LK
Sbjct: 160 DKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAIANGIVPFDGKIETQIGRDPHNRLK 219

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 220 MAVVKFGGKPAITHVKVLERYLAHSYIECSLETGRTHQIRVHMREANHP 268


>gi|315303380|ref|ZP_07873992.1| ribosomal protein S4 [Listeria ivanovii FSL F6-596]
 gi|313628248|gb|EFR96769.1| ribosomal protein S4 [Listeria ivanovii FSL F6-596]
          Length = 200

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 92  QRLDNIVYRLGLARTRRAARQLVNHGHITVDGKRVDIPSYQVSVGQVISV 141


>gi|295098920|emb|CBK88009.1| tyrosyl-tRNA synthetase [Eubacterium cylindroides T2-87]
          Length = 412

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 13/61 (21%), Positives = 24/61 (39%), Gaps = 2/61 (3%)

Query: 20  IARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERTRLWL 77
           +  +GIAS RRE    I    + VNG  +      +   +H + V    + +  +   + 
Sbjct: 349 LVESGIASSRREAREWIKGNSIMVNGTKITDPDYMMTPDNHCVCVKNYSIIRRGKKNYYC 408

Query: 78  Y 78
            
Sbjct: 409 L 409


>gi|160915114|ref|ZP_02077327.1| hypothetical protein EUBDOL_01122 [Eubacterium dolichum DSM 3991]
 gi|158432913|gb|EDP11202.1| hypothetical protein EUBDOL_01122 [Eubacterium dolichum DSM 3991]
          Length = 260

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 9/55 (16%), Positives = 21/55 (38%), Gaps = 1/55 (1%)

Query: 14 QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+ + +   G  + R   +  I +  V V+G  + + +  +     + V    L
Sbjct: 1  MRIDQYLVEKGYFTTRTRAQDAIKKGCVSVDGKTIMKNSFVIEEGKEVTVFQEEL 55


>gi|150015071|ref|YP_001307325.1| 30S ribosomal protein S4 [Clostridium beijerinckii NCIMB 8052]
 gi|189045374|sp|A6LPT9|RS4_CLOB8 RecName: Full=30S ribosomal protein S4
 gi|149901536|gb|ABR32369.1| ribosomal protein S4 [Clostridium beijerinckii NCIMB 8052]
          Length = 206

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 14/69 (20%), Positives = 25/69 (36%), Gaps = 1/69 (1%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+  ++ R G  S R E  +++      VNG  ++  + +V   D I V        + 
Sbjct: 98  MRLDNIVYRLGYGSSRNEARQLVTHGHFLVNGKKVDICSYHVSVNDVITVCEKSRSSEKF 157

Query: 73  TRLWLYHKP 81
                  K 
Sbjct: 158 KTFVENPKT 166


>gi|303287646|ref|XP_003063112.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226455748|gb|EEH53051.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 417

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 26/136 (19%), Positives = 41/136 (30%), Gaps = 21/136 (15%)

Query: 9   ENFTPQRVSKVIARA-------GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
              TP R+   IA         G  +R  V   I    V VNG++  +A+  V   D I 
Sbjct: 81  PKPTPARLDAYIATHAPPSEGGGGITRARVVASIKAGLVDVNGVVARKASERVSPGDVIR 140

Query: 62  VDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           V   P              ++  +   L +      +V         + V   L      
Sbjct: 141 VALKPTPPTEAAPEDIPLDVKYEDEHVLVVNKPAGMVVHPAPGHSSGTLVNAVLFRCGCP 200

Query: 108 VISVGRLDINTEGLLL 123
            + V   + NT   + 
Sbjct: 201 AMRVASGNANTADGVA 216


>gi|295658597|ref|XP_002789859.1| conserved hypothetical protein [Paracoccidioides brasiliensis Pb01]
 gi|226283003|gb|EEH38569.1| conserved hypothetical protein [Paracoccidioides brasiliensis Pb01]
          Length = 453

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 23/54 (42%), Gaps = 1/54 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+   I RA  AS  R+  + +    V VNG  ++     +   D  +VD   +
Sbjct: 168 RLDVAIFRAMFASSTRQARQFVLHGSVTVNGKKMKHPGYLLNPGDLFQVDPERV 221


>gi|194099938|ref|YP_002003076.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae NCCP11945]
 gi|193935228|gb|ACF31052.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae NCCP11945]
 gi|316985689|gb|EFV64635.1| ribosomal protein S4 [Neisseria meningitidis H44/76]
 gi|317165390|gb|ADV08931.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae TCDC-NG08107]
          Length = 196

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNG ++   +  V + D + V     ++    
Sbjct: 87  RLDNVVYRMGFGSTRAEARQLVSHKAIVVNGQVVNIPSFQVKAGDVVSVREKAKKQVRIQ 146


>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 = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 72/230 (31%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 58  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 116

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 117 VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQVPRAGIVHR 176

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 177 LDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 236

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 237 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIRVHMREANHP 286


>gi|320168624|gb|EFW45523.1| RNA pseudouridylate synthase domain-containing protein 2
           [Capsaspora owczarzaki ATCC 30864]
          Length = 515

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 25/210 (11%), Positives = 61/210 (29%), Gaps = 33/210 (15%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDH----------------IEVDGVPLRKAERTRL 75
           ++ I   RV VNG ++   +  +  +D                 I V    + + +   +
Sbjct: 144 DQAIRDGRVTVNGKVVA-PSYIIQDSDVLVHTAHRHEPPVTAAPIRV----IAETDDLVV 198

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
                 I +                    +S ++   RLD  T G+L++  +   A  + 
Sbjct: 199 IDKPASIPVHVAGRFNVHTVISIMKSEMGYSNLLGCHRLDRLTSGVLVMAKNRAAAAAVT 258

Query: 136 LPSTQWLRVYRVRF--------HGQVDQDKLNLLKKGIVIQGICY--GDMQVTLDTQK-- 183
              T+                       + L        + G+       +     ++  
Sbjct: 259 RLITEREVEKFYICRVTGVFPQEQVTCTEPLLSFCPKFGLNGVDPSGKPAETVFVREQTN 318

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           G  + V    + G+  +I+   ++  + + 
Sbjct: 319 GVISIVKCFPKTGRAHQIRVHLQYLGYPIE 348


>gi|168187044|ref|ZP_02621679.1| S4 domain protein [Clostridium botulinum C str. Eklund]
 gi|169295080|gb|EDS77213.1| S4 domain protein [Clostridium botulinum C str. Eklund]
          Length = 88

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   +      RV +N  + +  +  V   D IEV
Sbjct: 1  MRLDKYLKVSRIIKRRTIAKEACESGRVFINDKVAK-PSTEVNENDIIEV 49


>gi|309378792|emb|CBX22618.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 374

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 37/230 (16%), Positives = 73/230 (31%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  +HI V   P       
Sbjct: 40  RLDAVLAKLLPDYSRSRLTLWIKEGAVIVNDKP-SQPKDKMIGGEHIRVSIRPSAEYSAF 98

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 99  APEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQVPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIRVHMREANHP 268


>gi|240047580|ref|YP_002960968.1| Pseudouridine synthase [Mycoplasma conjunctivae HRC/581]
 gi|239985152|emb|CAT05162.1| Pseudouridine synthase [Mycoplasma conjunctivae]
          Length = 306

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 31/243 (12%), Positives = 66/243 (27%), Gaps = 43/243 (17%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----------- 60
              R+  V+A+    SR+    +I    VKV+  ++ +    +     I           
Sbjct: 14  EKTRIDLVVAKHLNVSRKISRYLIEANSVKVDNKVVNKVNFLLREGQFISILNNYQEPQL 73

Query: 61  -----EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---------FS 106
                +VD   +   +   + +      +V   +    ++ V   L              
Sbjct: 74  KVEAQKVDFEIV-YQDNDIIVINKPKNLVVHPGNGNWDKTLVNGLLHEFATNLSDVNGEI 132

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
           R   V RLD +T GLLL+  +    + L           +             +     +
Sbjct: 133 RPGIVHRLDKDTSGLLLVAKNNQAHKYLAKQLENHEIERKYIAIVVGKIPHTKMRINLPI 192

Query: 167 IQGICYGDMQ-----------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            +       +                  T   +    + V   L  G+  +I+       
Sbjct: 193 GRDNQNRTKKVVSSFNSKNAITNVELINTFVYKNEHFSIVKCILETGRTHQIRVHLSHIG 252

Query: 210 WKV 212
           + +
Sbjct: 253 YPI 255


>gi|206895668|ref|YP_002247308.1| ribosomal protein S4 [Coprothermobacter proteolyticus DSM 5265]
 gi|206738285|gb|ACI17363.1| ribosomal protein S4 [Coprothermobacter proteolyticus DSM 5265]
          Length = 210

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 1/50 (2%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+  V+ R G AS  +     +    V VNG  ++  +  V   D I +D
Sbjct: 101 RLDAVVQRMGFASSIKMARNWVRHGHVMVNGKRVDIPSYLVKPGDRITLD 150


>gi|170700719|ref|ZP_02891714.1| ribosomal protein S4 [Burkholderia ambifaria IOP40-10]
 gi|171318373|ref|ZP_02907531.1| ribosomal protein S4 [Burkholderia ambifaria MEX-5]
 gi|152060939|sp|Q0BJ21|RS4_BURCM RecName: Full=30S ribosomal protein S4
 gi|170134389|gb|EDT02722.1| ribosomal protein S4 [Burkholderia ambifaria IOP40-10]
 gi|171096451|gb|EDT41350.1| ribosomal protein S4 [Burkholderia ambifaria MEX-5]
          Length = 207

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNG++    +  V + D + +     ++A   
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKSITVNGVVANVPSQQVKAGDIVAIREKAKKQARIV 157

Query: 74  RLWLYHKPIGLVT 86
                 +  G+ +
Sbjct: 158 EALSLAEQGGMPS 170


>gi|258511645|ref|YP_003185079.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|257478371|gb|ACV58690.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 333

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 36/241 (14%), Positives = 68/241 (28%), Gaps = 34/241 (14%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +V  +   +R+S V++     SRR + R+I      VNG  +   +V V   D +  +  
Sbjct: 1   MVPSDLAGRRLSAVLSGRLGMSRRMLRRIIQAGGFYVNGEPVY-LSVTVQDGDRVTWERP 59

Query: 66  -------------PLRKAERTRLWLYHKPIGLVTTHSDPDGRS---TVFDNLPSIFSRVI 109
                         +   +   + +      L          S        L        
Sbjct: 60  EEEVAVEPENIPLEICYEDDDVIVVNKPAGMLTHPSPHERRGSLLAAAAHYLRDRGGVPH 119

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           +V RLD  T G +L+         L+    Q    R Y    +     +    L     +
Sbjct: 120 AVHRLDKYTSGAVLIAKHAHAHHQLDRALRQGLVDRRYVAIVYAPEGCETGRWLTFVDGL 179

Query: 168 QGICYGDMQVTLDTQKGSNAWVT---------------VGLREGKNREIKKVFEFFNWKV 212
               +   +  +      +  VT               + L  G+  +I+    F    +
Sbjct: 180 APNPHRPSRRIVVPPDRGDRAVTHALPLVQAGPLALVALVLETGRTHQIRAQMAFHGMPL 239

Query: 213 N 213
            
Sbjct: 240 V 240


>gi|297567257|ref|YP_003686229.1| 30S ribosomal protein S4 [Meiothermus silvanus DSM 9946]
 gi|296851706|gb|ADH64721.1| ribosomal protein S4 [Meiothermus silvanus DSM 9946]
          Length = 205

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           R+  V+ R GIAS RR+  + +    + VNG  +  A   V   D I V    
Sbjct: 96  RLDNVVFRLGIASTRRQARQFVRHGHILVNGKRVNIAGYRVKQGDTIAVSKKA 148


>gi|227494617|ref|ZP_03924933.1| hemolysin A [Actinomyces coleocanis DSM 15436]
 gi|226831799|gb|EEH64182.1| hemolysin A [Actinomyces coleocanis DSM 15436]
          Length = 306

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 11/37 (29%), Positives = 19/37 (51%)

Query: 27 SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          SR + + MI    VK++G ++ + A  +     I VD
Sbjct: 19 SRTKAQEMIQAGYVKLDGEVVYKPARQMDPAQAIVVD 55


>gi|225873051|ref|YP_002754510.1| ribosomal protein S4 [Acidobacterium capsulatum ATCC 51196]
 gi|254764560|sp|C1F615|RS4_ACIC5 RecName: Full=30S ribosomal protein S4
 gi|225792033|gb|ACO32123.1| ribosomal protein S4 [Acidobacterium capsulatum ATCC 51196]
          Length = 209

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +  R G A SRR+  +++    V+VNG  +   +  V   D I++
Sbjct: 100 RLDNIAFRLGFATSRRQARQIVRHGHVEVNGRKVNIPSFQVKVGDEIKI 148


>gi|170016575|ref|YP_001727494.1| ribosomal protein S4 [Leuconostoc citreum KM20]
 gi|226699084|sp|B1MWZ8|RS4_LEUCK RecName: Full=30S ribosomal protein S4
 gi|169803432|gb|ACA82050.1| Ribosomal protein S4 [Leuconostoc citreum KM20]
          Length = 203

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 11/53 (20%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           QR+  ++ R G A+ R++  +++    + V+G  ++  + NV     + V   
Sbjct: 93  QRLDSLVYRLGFATTRQQARQLVNHGHIMVDGKRVDIPSYNVTPGQVVSVRDK 145


>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 = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 32/240 (13%), Positives = 68/240 (28%), Gaps = 34/240 (14%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           I+      +R+  VI       SR ++++ + +  + VNG    +    V+  + +E++ 
Sbjct: 15  IMHPKDAGKRIDVVINEQFEQFSRAQIQKWLKEGSITVNGR-ATKPKHIVLGDEEVEINI 73

Query: 65  VPLRKAERTRLWLY--------------HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI- 109
             L   E     +                    +V   +     +     L     +   
Sbjct: 74  ELLPTNEWIAEDINLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNALLHRYKDQDKL 133

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVLELP------------STQWLRVYRVRFHGQV 153
                V RLD +T GL++          L                 +     +   +  +
Sbjct: 134 PRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGEIYQQGTINQPI 193

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +D  N  K  I  +G        T          +   L  G+  +I+   +     + 
Sbjct: 194 GRDPTNRTKMAINYRGKEA-ITHYTPIEVYDGFTLIECQLETGRTHQIRVHMKSIKHPLV 252


>gi|16800706|ref|NP_470974.1| 30S ribosomal protein S4 [Listeria innocua Clip11262]
 gi|226224197|ref|YP_002758304.1| ribosomal protein S4 [Listeria monocytogenes Clip81459]
 gi|26399441|sp|Q92BB2|RS4_LISIN RecName: Full=30S ribosomal protein S4
 gi|259495285|sp|C1KVP3|RS4_LISMC RecName: Full=30S ribosomal protein S4
 gi|16414125|emb|CAC96869.1| ribosomal protein S4 [Listeria innocua Clip11262]
 gi|225876659|emb|CAS05368.1| ribosomal protein S4 [Listeria monocytogenes serotype 4b str. CLIP
           80459]
 gi|313618704|gb|EFR90630.1| ribosomal protein S4 [Listeria innocua FSL S4-378]
          Length = 200

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 92  QRLDNIVYRLGLARTRRAARQLVNHGHITVDGKRVDIPSYQVSVGQVISV 141


>gi|293363350|ref|ZP_06610172.1| pseudouridine synthase, RluA family [Mycoplasma alligatoris A21JP2]
 gi|292553019|gb|EFF41770.1| pseudouridine synthase, RluA family [Mycoplasma alligatoris A21JP2]
          Length = 280

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 30/260 (11%), Positives = 70/260 (26%), Gaps = 44/260 (16%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG------------- 64
           K +      SR  VE++  ++ +K+NG    +    +   D IE+ G             
Sbjct: 21  KYL-NNVPLSR--VEKLFRKKDIKINGQRTNQKDYIIAFNDVIEIYGLIDTKKEEAPLLT 77

Query: 65  ----VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF-DNLPSIFSRVISVGRLDINTE 119
                 + +     +      I + +  +  D +   +         +   +GRLD  T 
Sbjct: 78  SFSFKKIYEDANVLIIDKPNGIEVHSAPNCLDNQVLAYLKYKQVDSFKPSHIGRLDKETS 137

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G++L   +    + L        + Y  +     +  ++ L       +           
Sbjct: 138 GIMLYAKNYQALKYLNDYMENIKKTYTFKSDFNDESKEVELFLYKDEEKKRMAASFTKVP 197

Query: 180 DTQKGSNAWV------TVGLREGKNREIKKVFEFFNWKV-------------NRLIRISY 220
            ++                L  G+  +I+         +               L  +  
Sbjct: 198 YSKLSKTHLYTESNKKYATLFSGRKHQIRVTLMKLGKPIYGDFKYGGKKAARLMLHCLQI 257

Query: 221 GPFQLGTLLAGSTREVSKKI 240
               L     G  + ++   
Sbjct: 258 KFVGL----EGEYKYLNDLE 273


>gi|254563644|ref|YP_003070739.1| hemolysin [Methylobacterium extorquens DM4]
 gi|254270922|emb|CAX26927.1| hemolysin [Methylobacterium extorquens DM4]
          Length = 250

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 3/53 (5%)

Query: 12 TPQRV--SKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
          T +R+   + +   G   SR +    I    V  +G L+ R +  V  +  IE
Sbjct: 2  TGERLRADRFLVERGHFRSRAQARAAIEAGLVSADGRLVTRPSDLVEPSARIE 54


>gi|240141133|ref|YP_002965613.1| hemolysin [Methylobacterium extorquens AM1]
 gi|240011110|gb|ACS42336.1| hemolysin [Methylobacterium extorquens AM1]
          Length = 250

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 3/53 (5%)

Query: 12 TPQRV--SKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
          T +R+   + +   G   SR +    I    V  +G L+ R +  V  +  IE
Sbjct: 2  TGERLRADRFLVERGHFRSRAQARAAIEAGLVSADGRLVTRPSDLVEPSARIE 54


>gi|225025927|ref|ZP_03715119.1| hypothetical protein EUBHAL_00163 [Eubacterium hallii DSM 3353]
 gi|224956713|gb|EEG37922.1| hypothetical protein EUBHAL_00163 [Eubacterium hallii DSM 3353]
          Length = 274

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 27/180 (15%), Positives = 52/180 (28%), Gaps = 4/180 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRKA 70
           QR+  ++   G A SR + + MI    V VNG   ++A           IE+ G  LR  
Sbjct: 3   QRLDVLLVEQGHAASREKAKAMIMSGVVFVNGQREDKAGSTFDEKAAATIEIHGSTLRYV 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            R  L L         +  D                 ++  G + + +  +     D  L
Sbjct: 63  SRGGLKLEKAVEQFGFSLKDKTCMDVGAST-GGFTDCMLQNGAVKVFSVDVGRGQLDWKL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
                +   +   +  V+     +      +    +        ++  L         + 
Sbjct: 122 RNDERVVCMEKTNMRYVKPEDIGELADFISIDVSFISLTKILPPVKACLKEDGQVVCLIK 181


>gi|218281549|ref|ZP_03487978.1| hypothetical protein EUBIFOR_00543 [Eubacterium biforme DSM 3989]
 gi|218217338|gb|EEC90876.1| hypothetical protein EUBIFOR_00543 [Eubacterium biforme DSM 3989]
          Length = 202

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G A +RR   +++    V V+G  ++  +  V     IE+
Sbjct: 93  RLDNIVYRMGFARTRRASRQLVNHGHVLVDGKKVDIPSFQVKPGQVIEI 141


>gi|254518736|ref|ZP_05130792.1| hemolysin A [Clostridium sp. 7_2_43FAA]
 gi|226912485|gb|EEH97686.1| hemolysin A [Clostridium sp. 7_2_43FAA]
          Length = 269

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 19/175 (10%), Positives = 47/175 (26%), Gaps = 3/175 (1%)

Query: 12  TPQRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             +R+  ++   GI + RE  +  I   ++ V+G  +++A   +     I   G  +   
Sbjct: 4   KKERLDILLVEKGIFTSRERAKTSIMAGKIFVDGQRVDKAGEKINVDADIIFKGQEIPYV 63

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            R  L L            D                 ++      + +  +        L
Sbjct: 64  SRGGLKLEKAIKEFGVNLKDKVCMDIGAST-GGFTDCMLQNDAKKVFSIDVGYGQFAWKL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
                +   +   +  V      +      +    +          ++L  + G 
Sbjct: 123 RTDSRVVCMERTNIRYVTPEDLGELTDFASIDVSFISL-KKIMPATLSLLNESGE 176


>gi|160942871|ref|ZP_02090110.1| hypothetical protein FAEPRAM212_00347 [Faecalibacterium prausnitzii
           M21/2]
 gi|158445772|gb|EDP22775.1| hypothetical protein FAEPRAM212_00347 [Faecalibacterium prausnitzii
           M21/2]
 gi|295103949|emb|CBL01493.1| SSU ribosomal protein S4P [Faecalibacterium prausnitzii SL3/3]
          Length = 200

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+  ++++     VNG  +   +  V + D IEV
Sbjct: 90  RLDNVVFRLGFAQTRRDARQLVSHAHFTVNGKKVNIPSYQVKAGDVIEV 138


>gi|116873025|ref|YP_849806.1| 30S ribosomal protein S4 [Listeria welshimeri serovar 6b str.
           SLCC5334]
 gi|289434877|ref|YP_003464749.1| ribosomal protein S4 [Listeria seeligeri serovar 1/2b str.
           SLCC3954]
 gi|123466377|sp|A0AJ45|RS4_LISW6 RecName: Full=30S ribosomal protein S4
 gi|116741903|emb|CAK21027.1| 30S ribosomal protein S4 [Listeria welshimeri serovar 6b str.
           SLCC5334]
 gi|289171121|emb|CBH27663.1| ribosomal protein S4 [Listeria seeligeri serovar 1/2b str.
           SLCC3954]
 gi|313633056|gb|EFR99970.1| ribosomal protein S4 [Listeria seeligeri FSL N1-067]
 gi|313638010|gb|EFS03298.1| ribosomal protein S4 [Listeria seeligeri FSL S4-171]
          Length = 200

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 92  QRLDNIVYRLGLARTRRAARQLVNHGHITVDGKRVDIPSYQVSVGQVISV 141


>gi|332671318|ref|YP_004454326.1| transcription termination factor Rho [Cellulomonas fimi ATCC 484]
 gi|332340356|gb|AEE46939.1| transcription termination factor Rho [Cellulomonas fimi ATCC 484]
          Length = 724

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 13/117 (11%), Positives = 35/117 (29%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           + +  R    P    E + + +    S     R+         +   R ++         
Sbjct: 135 TDREPRADREPRAEREPRADSEPRTDSEPRAGRESRTDREPRTEREPRAEREPRADREPR 194

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             ++      +R     +   +    + L+ +  R++   R  +   +RS R    +
Sbjct: 195 ADREPRRDEEQRPRQDALAGLEAALDARLAPAEARDDRAARGDAQAERRSRRAGRGQ 251



 Score = 42.1 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 7/115 (6%), Positives = 27/115 (23%), Gaps = 1/115 (0%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISE-VPDDFTRMKKNSSQKNGL 295
           + +  R +  P    E + + +           ++          +     + +  +   
Sbjct: 171 TDREPRTEREPRAEREPRADREPRADREPRRDEEQRPRQDALAGLEAALDARLAPAEARD 230

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
            +  +      RR+  +              +  QR +  +      +       
Sbjct: 231 DRAARGDAQAERRSRRAGRGQGAPEEPRRGDEPVQRPQPEQAGRGQGAPAPQAEG 285


>gi|325529703|gb|EGD06566.1| 30S ribosomal protein S4 [Burkholderia sp. TJI49]
          Length = 207

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 16/73 (21%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNGI+    +  V + D I +     ++A   
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKSITVNGIVANVPSQQVKAGDVIAIREKAKKQARIV 157

Query: 74  RLWLYHKPIGLVT 86
                 +  G+ +
Sbjct: 158 EALSLAEQGGMPS 170


>gi|302144209|emb|CBI23336.3| unnamed protein product [Vitis vinifera]
          Length = 300

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 14/62 (22%), Positives = 27/62 (43%), Gaps = 8/62 (12%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K K  + E    +R  +        SR  ++  I Q +V V+G ++ +A   V     +
Sbjct: 56  LKKKRRLDEVC-LERFQQY-------SRTFIQSWILQGKVFVDGKVVNKAGTPVSDKAVV 107

Query: 61  EV 62
           E+
Sbjct: 108 EI 109


>gi|15676094|ref|NP_273225.1| 30S ribosomal protein S4 [Neisseria meningitidis MC58]
 gi|59802136|ref|YP_208848.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae FA 1090]
 gi|121634041|ref|YP_974286.1| 30S ribosomal protein S4 [Neisseria meningitidis FAM18]
 gi|161870895|ref|YP_001600070.1| 30S ribosomal protein S4 [Neisseria meningitidis 053442]
 gi|218767143|ref|YP_002341655.1| 30S ribosomal protein S4 [Neisseria meningitidis Z2491]
 gi|239997950|ref|ZP_04717874.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae 35/02]
 gi|240015072|ref|ZP_04721985.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae DGI18]
 gi|240017521|ref|ZP_04724061.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae FA6140]
 gi|240081664|ref|ZP_04726207.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae FA19]
 gi|240113942|ref|ZP_04728432.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae MS11]
 gi|240116676|ref|ZP_04730738.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae PID18]
 gi|240118898|ref|ZP_04732960.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae PID1]
 gi|240122144|ref|ZP_04735106.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae PID24-1]
 gi|240124436|ref|ZP_04737392.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae PID332]
 gi|240124695|ref|ZP_04737581.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae SK-92-679]
 gi|240129112|ref|ZP_04741773.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae SK-93-1035]
 gi|254494697|ref|ZP_05107868.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae 1291]
 gi|254805789|ref|YP_003084010.1| 30S ribosomal protein S4 [Neisseria meningitidis alpha14]
 gi|260439565|ref|ZP_05793381.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae DGI2]
 gi|268593800|ref|ZP_06127967.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae 35/02]
 gi|268597761|ref|ZP_06131928.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae FA19]
 gi|268600006|ref|ZP_06134173.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae MS11]
 gi|268602343|ref|ZP_06136510.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae PID18]
 gi|268604607|ref|ZP_06138774.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae PID1]
 gi|268683064|ref|ZP_06149926.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae PID332]
 gi|268683269|ref|ZP_06150131.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae SK-92-679]
 gi|268687494|ref|ZP_06154356.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae SK-93-1035]
 gi|291042801|ref|ZP_06568542.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae DGI2]
 gi|293398178|ref|ZP_06642383.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae F62]
 gi|304388967|ref|ZP_07371014.1| 30S ribosomal protein S4 [Neisseria meningitidis ATCC 13091]
 gi|54039509|sp|P66561|RS4_NEIMB RecName: Full=30S ribosomal protein S4
 gi|54041962|sp|P66560|RS4_NEIMA RecName: Full=30S ribosomal protein S4
 gi|75507306|sp|Q5F5V1|RS4_NEIG1 RecName: Full=30S ribosomal protein S4
 gi|152112237|sp|A1KRJ8|RS4_NEIMF RecName: Full=30S ribosomal protein S4
 gi|189045388|sp|A9M3U1|RS4_NEIM0 RecName: Full=30S ribosomal protein S4
 gi|7225385|gb|AAF40624.1| 30S ribosomal protein S4 [Neisseria meningitidis MC58]
 gi|59719031|gb|AAW90436.1| putative 30S ribosomal protein S4 [Neisseria gonorrhoeae FA 1090]
 gi|120865747|emb|CAM09476.1| 30S ribosomal protein S4 [Neisseria meningitidis FAM18]
 gi|121051151|emb|CAM07422.1| 30S ribosomal protein S4 [Neisseria meningitidis Z2491]
 gi|161596448|gb|ABX74108.1| 30S ribosomal protein S4 [Neisseria meningitidis 053442]
 gi|226513737|gb|EEH63082.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae 1291]
 gi|254669331|emb|CBA08372.1| 30S ribosomal protein S4 [Neisseria meningitidis alpha14]
 gi|254670762|emb|CBA07036.1| 30S ribosomal protein S4 [Neisseria meningitidis alpha153]
 gi|254672692|emb|CBA06587.1| 30S ribosomal protein S4 [Neisseria meningitidis alpha275]
 gi|261391703|emb|CAX49152.1| 30S ribosomal protein S4 [Neisseria meningitidis 8013]
 gi|268547189|gb|EEZ42607.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae 35/02]
 gi|268551549|gb|EEZ46568.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae FA19]
 gi|268584137|gb|EEZ48813.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae MS11]
 gi|268586474|gb|EEZ51150.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae PID18]
 gi|268588738|gb|EEZ53414.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae PID1]
 gi|268623348|gb|EEZ55748.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae PID332]
 gi|268623553|gb|EEZ55953.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae SK-92-679]
 gi|268627778|gb|EEZ60178.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae SK-93-1035]
 gi|291013235|gb|EFE05201.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae DGI2]
 gi|291611441|gb|EFF40511.1| 30S ribosomal protein S4 [Neisseria gonorrhoeae F62]
 gi|304337101|gb|EFM03288.1| 30S ribosomal protein S4 [Neisseria meningitidis ATCC 13091]
 gi|308388383|gb|ADO30703.1| 30S ribosomal protein S4 [Neisseria meningitidis alpha710]
 gi|319411349|emb|CBY91760.1| 30S ribosomal protein S4 [Neisseria meningitidis WUE 2594]
 gi|325129086|gb|EGC51935.1| ribosomal protein S4 [Neisseria meningitidis N1568]
 gi|325131057|gb|EGC53781.1| ribosomal protein S4 [Neisseria meningitidis OX99.30304]
 gi|325133079|gb|EGC55751.1| ribosomal protein S4 [Neisseria meningitidis M6190]
 gi|325135173|gb|EGC57799.1| ribosomal protein S4 [Neisseria meningitidis M13399]
 gi|325137225|gb|EGC59820.1| ribosomal protein S4 [Neisseria meningitidis M0579]
 gi|325139057|gb|EGC61603.1| ribosomal protein S4 [Neisseria meningitidis ES14902]
 gi|325141180|gb|EGC63680.1| ribosomal protein S4 [Neisseria meningitidis CU385]
 gi|325143257|gb|EGC65596.1| ribosomal protein S4 [Neisseria meningitidis 961-5945]
 gi|325145364|gb|EGC67641.1| ribosomal protein S4 [Neisseria meningitidis M01-240013]
 gi|325197454|gb|ADY92910.1| ribosomal protein S4 [Neisseria meningitidis G2136]
 gi|325199380|gb|ADY94835.1| ribosomal protein S4 [Neisseria meningitidis H44/76]
 gi|325202998|gb|ADY98452.1| ribosomal protein S4 [Neisseria meningitidis M01-240149]
 gi|325205260|gb|ADZ00713.1| ribosomal protein S4 [Neisseria meningitidis M04-240196]
 gi|325207204|gb|ADZ02656.1| ribosomal protein S4 [Neisseria meningitidis NZ-05/33]
          Length = 206

 Score = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNG ++   +  V + D + V     ++    
Sbjct: 97  RLDNVVYRMGFGSTRAEARQLVSHKAIVVNGQVVNIPSFQVKAGDVVSVREKAKKQVRIQ 156


>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 = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
             R+   +A+A    SR  V+ +I   +VKV+G + + A   +   + IE++G P
Sbjct: 58  GMRLDAYLAQALPDISRARVQILIEAGQVKVDGAVPK-AKAKLKGGETIEIEGQP 111


>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 = 50.2 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 34/209 (16%), Positives = 69/209 (33%), Gaps = 24/209 (11%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR------KAERTRLWLYHKPI 82
           + V+ ++  ++V VNG ++ +   ++   D I VD  P          E   L + +KP 
Sbjct: 38  KNVKNLLKFKQVSVNGQVISQFDYSLKRDDEIVVDRNPNNNSSLDIIYEDRELIVINKPA 97

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLT------NDGGL 130
           GL++     +   T +  +           RV  V RLD  T G+LL        N    
Sbjct: 98  GLLSMAGGNEKEKTAYHLVGEYLKSKNKNARVFIVHRLDKETSGVLLFAKNEIIKNKLQN 157

Query: 131 ARVLELPSTQWLRVYRVRFHGQVD------QDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
                +    +L +   +   +         +    +                 +  +  
Sbjct: 158 NWNDIVYKRGYLAIIEGKLKKKHGTIKNHLDESKTQMVYIANNGKGKLAITNYKVLKESR 217

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            N+ + V L  G+  +I+   +     + 
Sbjct: 218 YNSLIEVFLETGRKNQIRVHMQSLGHSIV 246


>gi|326790852|ref|YP_004308673.1| hemolysin A [Clostridium lentocellum DSM 5427]
 gi|326541616|gb|ADZ83475.1| hemolysin A [Clostridium lentocellum DSM 5427]
          Length = 295

 Score = 50.2 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           + +R+  +IA   +A SR   +  I    V VNG   ++  + V  +  IEV
Sbjct: 30 DSKERLDVLIAERQLAESRERAKAYIMAGVVFVNGQREDKPGLKVKRSSTIEV 82


>gi|239623374|ref|ZP_04666405.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239522340|gb|EEQ62206.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 197

 Score = 50.2 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+  +R+E  +++  + + VNG  +   +  V + D IEV
Sbjct: 88  RLDNVLFRMGLGRTRKETRQIVDHKHILVNGKPVNIPSYQVKAGDVIEV 136


>gi|56964109|ref|YP_175840.1| hypothetical protein ABC2344 [Bacillus clausii KSM-K16]
 gi|56910352|dbj|BAD64879.1| conserved hypothetical protein [Bacillus clausii KSM-K16]
          Length = 253

 Score = 50.2 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 24/50 (48%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  +++     SR +   +I +  VKVN  ++E  +  V   D + V G
Sbjct: 178 RLDALLSALYGLSRAKAADLIGKGLVKVNWKVVEHPSFRVAIGDDLSVRG 227


>gi|15896457|ref|NP_349806.1| hypothetical protein CA_C3210 [Clostridium acetobutylicum ATCC
          824]
 gi|15026281|gb|AAK81146.1|AE007816_10 Predicted RNA-binding protein, YABO B.subtilis ortholog
          [Clostridium acetobutylicum ATCC 824]
 gi|325510615|gb|ADZ22251.1| RNA-binding protein [Clostridium acetobutylicum EA 2018]
          Length = 84

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   +      RV +NG + +    +V   D IE+
Sbjct: 1  MRLDKYLKVSRIIKRRTVAKEACESGRVSINGKVAK-PGTDVEEDDIIEI 49


>gi|296269405|ref|YP_003652037.1| peptidoglycan glycosyltransferase [Thermobispora bispora DSM 43833]
 gi|296092192|gb|ADG88144.1| Peptidoglycan glycosyltransferase [Thermobispora bispora DSM 43833]
          Length = 1057

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 9/107 (8%), Positives = 23/107 (21%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                                  RP+     P      +   ++      +         
Sbjct: 848 RPARSRDARSQPARSRDPRSRPARPHGTRSKPARSQDARSQPARSRDPRSRPARPHGTRS 907

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +   S    ++   S        R ++ R   +   + +  R   K+
Sbjct: 908 KPARSQDARSQPARSRDPRSRPARPQDTRSRQARAPRTTGPRAGTKR 954



 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 8/97 (8%), Positives = 21/97 (21%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
                         R       P      +   ++ +G   +   +     +   S    
Sbjct: 837 AHPARSHDTRSRPARSRDARSQPARSRDPRSRPARPHGTRSKPARSQDARSQPARSRDPR 896

Query: 317 AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           ++            R ++ R  P+       R    +
Sbjct: 897 SRPARPHGTRSKPARSQDARSQPARSRDPRSRPARPQ 933



 Score = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 9/114 (7%), Positives = 22/114 (19%), Gaps = 7/114 (6%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                                  R +     P      +   ++      +         
Sbjct: 818 RRAVPRSTAAPRAGSHGTRAHPARSHDTRSRPARSRDARSQPARSRDPRSRPARPHGTRS 877

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF-------PSKRSLRRTSAKK 354
           +   S    ++   S        R    R  P+        P++    R+   +
Sbjct: 878 KPARSQDARSQPARSRDPRSRPARPHGTRSKPARSQDARSQPARSRDPRSRPAR 931



 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 11/113 (9%), Positives = 25/113 (22%), Gaps = 2/113 (1%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
             G         +  +    S                        S        + + A 
Sbjct: 872 PHGTRSKPARSQDARSQPARSRDPRSRPARPHGTRSKPARSQDARSQPARSRDPRSRPAR 931

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSG--QREENHRRSPSFPSKRSLRRTSAKK 354
           P   R+  +      G  +          R ++ R   +   + +  RT + +
Sbjct: 932 PQDTRSRQARAPRTTGPRAGTKRTRPQHGRSQHARSQRARSQRAAAPRTPSPR 984



 Score = 42.9 bits (99), Expect = 0.082,   Method: Composition-based stats.
 Identities = 16/113 (14%), Positives = 30/113 (26%), Gaps = 4/113 (3%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R        + A    DA         R R            R +   +     S++   
Sbjct: 763 RTPQRAERPQRAGAASDARRGGPSATARPRHAAGRPAHRASGRQRALWTAPPAASRRAVP 822

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +    R  +         H +   D+  R    R + S P++    R+   +
Sbjct: 823 RSTAAPRAGSHGTR----AHPARSHDTRSRPARSRDARSQPARSRDPRSRPAR 871



 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 10/113 (8%), Positives = 24/113 (21%), Gaps = 2/113 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R +                ++++      R    S            +        + + 
Sbjct: 790 RPRHAAGRPAHRASGRQRALWTAPPAASRRAVPRSTAAPRAGSHGTRAHPARSHDTRSRP 849

Query: 302 ATPVHRRNL--ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           A     R+    S    ++            R ++ R  P+       R    
Sbjct: 850 ARSRDARSQPARSRDPRSRPARPHGTRSKPARSQDARSQPARSRDPRSRPARP 902



 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 15/112 (13%), Positives = 26/112 (23%), Gaps = 10/112 (8%)

Query: 248  HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                       +    S+      P      P D    +  + +  G     K   P H 
Sbjct: 901  RPHGTRSKPARSQDARSQPARSRDPRSRPARPQDTRSRQARAPRTTGPRAGTKRTRPQHG 960

Query: 308  RNLASNVWMAKGIHSSFLSDSGQREENHR----------RSPSFPSKRSLRR 349
            R+  +    A+   ++       R                 P+ PS     R
Sbjct: 961  RSQHARSQRARSQRAAAPRTPSPRPTASPGGHRATGAPAPGPAVPSGARPPR 1012



 Score = 40.9 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 14/117 (11%), Positives = 26/117 (22%), Gaps = 12/117 (10%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR-- 307
                    A    +      +  + +  P    R    S+           A P     
Sbjct: 785 PSATARPRHAAGRPAHRASGRQRALWTAPPAASRRAVPRSTAAPRAGSHGTRAHPARSHD 844

Query: 308 ---RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF-------PSKRSLRRTSAKK 354
              R   S    ++   S        R    R  P+        P++    R+   +
Sbjct: 845 TRSRPARSRDARSQPARSRDPRSRPARPHGTRSKPARSQDARSQPARSRDPRSRPAR 901



 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 8/108 (7%), Positives = 24/108 (22%), Gaps = 1/108 (0%)

Query: 246  GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
             P   ++ +        ++      +            R ++  SQ+    +        
Sbjct: 928  RPARPQDTRSRQARAPRTTGPRAGTKRTRPQHGRSQHARSQRARSQRAAAPRTPSPRPTA 987

Query: 306  HRRNLASNVWMAKGIHSSFLSDSGQREEN-HRRSPSFPSKRSLRRTSA 352
                  +    A G      +   +R       +P+          + 
Sbjct: 988  SPGGHRATGAPAPGPAVPSGARPPRRTGGAGDGTPAARPGDPAPAGTP 1035


>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 = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 72/230 (31%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIREGAVIVNDKP-SQPKDKMIGGEQIRVTVRPSEENLAF 98

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWSGTLLNGLLAHCPELSQVPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIRVHMREANHP 268


>gi|23501338|ref|NP_697465.1| hemolysin A [Brucella suis 1330]
 gi|62289422|ref|YP_221215.1| hemolysin A [Brucella abortus bv. 1 str. 9-941]
 gi|82699349|ref|YP_413923.1| cell division protein FtsJ [Brucella melitensis biovar Abortus
          2308]
 gi|161618409|ref|YP_001592296.1| hemolysin A [Brucella canis ATCC 23365]
 gi|189023673|ref|YP_001934441.1| Cell division protein FtsJ [Brucella abortus S19]
 gi|225626945|ref|ZP_03784984.1| hemolysin A [Brucella ceti str. Cudo]
 gi|237814910|ref|ZP_04593908.1| hemolysin A [Brucella abortus str. 2308 A]
 gi|254688735|ref|ZP_05151989.1| Cell division protein FtsJ [Brucella abortus bv. 6 str. 870]
 gi|254696863|ref|ZP_05158691.1| Cell division protein FtsJ [Brucella abortus bv. 2 str. 86/8/59]
 gi|254701242|ref|ZP_05163070.1| Cell division protein FtsJ [Brucella suis bv. 5 str. 513]
 gi|254703789|ref|ZP_05165617.1| Cell division protein FtsJ [Brucella suis bv. 3 str. 686]
 gi|254707834|ref|ZP_05169662.1| Cell division protein FtsJ [Brucella pinnipedialis M163/99/10]
 gi|254709585|ref|ZP_05171396.1| Cell division protein FtsJ [Brucella pinnipedialis B2/94]
 gi|254729768|ref|ZP_05188346.1| Cell division protein FtsJ [Brucella abortus bv. 4 str. 292]
 gi|256031077|ref|ZP_05444691.1| Cell division protein FtsJ [Brucella pinnipedialis M292/94/1]
 gi|256060571|ref|ZP_05450739.1| Cell division protein FtsJ [Brucella neotomae 5K33]
 gi|256159141|ref|ZP_05456962.1| Cell division protein FtsJ [Brucella ceti M490/95/1]
 gi|256254480|ref|ZP_05460016.1| Cell division protein FtsJ [Brucella ceti B1/94]
 gi|256256982|ref|ZP_05462518.1| Cell division protein FtsJ [Brucella abortus bv. 9 str. C68]
 gi|256368892|ref|YP_003106398.1| hemolysin A [Brucella microti CCM 4915]
 gi|260168208|ref|ZP_05755019.1| hemolysin A [Brucella sp. F5/99]
 gi|260545826|ref|ZP_05821567.1| cell division protein FtsJ [Brucella abortus NCTC 8038]
 gi|260566958|ref|ZP_05837428.1| cell division protein FtsJ [Brucella suis bv. 4 str. 40]
 gi|260754214|ref|ZP_05866562.1| hemolysin A [Brucella abortus bv. 6 str. 870]
 gi|260757434|ref|ZP_05869782.1| hemolysin A [Brucella abortus bv. 4 str. 292]
 gi|260761259|ref|ZP_05873602.1| hemolysin A [Brucella abortus bv. 2 str. 86/8/59]
 gi|260883239|ref|ZP_05894853.1| hemolysin A [Brucella abortus bv. 9 str. C68]
 gi|261221653|ref|ZP_05935934.1| hemolysin A [Brucella ceti B1/94]
 gi|261315321|ref|ZP_05954518.1| hemolysin A [Brucella pinnipedialis M163/99/10]
 gi|261317113|ref|ZP_05956310.1| hemolysin A [Brucella pinnipedialis B2/94]
 gi|261324566|ref|ZP_05963763.1| hemolysin A [Brucella neotomae 5K33]
 gi|261751781|ref|ZP_05995490.1| hemolysin A [Brucella suis bv. 5 str. 513]
 gi|261754436|ref|ZP_05998145.1| hemolysin A [Brucella suis bv. 3 str. 686]
 gi|261757669|ref|ZP_06001378.1| cell division protein FtsJ [Brucella sp. F5/99]
 gi|265988150|ref|ZP_06100707.1| hemolysin A [Brucella pinnipedialis M292/94/1]
 gi|265997615|ref|ZP_06110172.1| hemolysin A [Brucella ceti M490/95/1]
 gi|294851815|ref|ZP_06792488.1| hemolysin [Brucella sp. NVSL 07-0026]
 gi|297247835|ref|ZP_06931553.1| hemolysin [Brucella abortus bv. 5 str. B3196]
 gi|23347229|gb|AAN29380.1| hemolysin A [Brucella suis 1330]
 gi|62195554|gb|AAX73854.1| TlyA, hemolysin A [Brucella abortus bv. 1 str. 9-941]
 gi|82615450|emb|CAJ10419.1| Cell division protein FtsJ:RNA-binding S4:Hemolysin A [Brucella
          melitensis biovar Abortus 2308]
 gi|161335220|gb|ABX61525.1| hemolysin A [Brucella canis ATCC 23365]
 gi|189019245|gb|ACD71967.1| Cell division protein FtsJ [Brucella abortus S19]
 gi|225618602|gb|EEH15645.1| hemolysin A [Brucella ceti str. Cudo]
 gi|237789747|gb|EEP63957.1| hemolysin A [Brucella abortus str. 2308 A]
 gi|255999050|gb|ACU47449.1| hemolysin A [Brucella microti CCM 4915]
 gi|260097233|gb|EEW81108.1| cell division protein FtsJ [Brucella abortus NCTC 8038]
 gi|260156476|gb|EEW91556.1| cell division protein FtsJ [Brucella suis bv. 4 str. 40]
 gi|260667752|gb|EEX54692.1| hemolysin A [Brucella abortus bv. 4 str. 292]
 gi|260671691|gb|EEX58512.1| hemolysin A [Brucella abortus bv. 2 str. 86/8/59]
 gi|260674322|gb|EEX61143.1| hemolysin A [Brucella abortus bv. 6 str. 870]
 gi|260872767|gb|EEX79836.1| hemolysin A [Brucella abortus bv. 9 str. C68]
 gi|260920237|gb|EEX86890.1| hemolysin A [Brucella ceti B1/94]
 gi|261296336|gb|EEX99832.1| hemolysin A [Brucella pinnipedialis B2/94]
 gi|261300546|gb|EEY04043.1| hemolysin A [Brucella neotomae 5K33]
 gi|261304347|gb|EEY07844.1| hemolysin A [Brucella pinnipedialis M163/99/10]
 gi|261737653|gb|EEY25649.1| cell division protein FtsJ [Brucella sp. F5/99]
 gi|261741534|gb|EEY29460.1| hemolysin A [Brucella suis bv. 5 str. 513]
 gi|261744189|gb|EEY32115.1| hemolysin A [Brucella suis bv. 3 str. 686]
 gi|262552083|gb|EEZ08073.1| hemolysin A [Brucella ceti M490/95/1]
 gi|264660347|gb|EEZ30608.1| hemolysin A [Brucella pinnipedialis M292/94/1]
 gi|294820404|gb|EFG37403.1| hemolysin [Brucella sp. NVSL 07-0026]
 gi|297175004|gb|EFH34351.1| hemolysin [Brucella abortus bv. 5 str. B3196]
          Length = 253

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 12/51 (23%), Positives = 23/51 (45%), Gaps = 1/51 (1%)

Query: 15 RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          R+ +++   G  A+R      I +  VKV+G  + +    V+    + VD 
Sbjct: 11 RLDQLLVERGFFATRSRARDAIQRGTVKVDGRPITKPGQMVVRDAALAVDD 61


>gi|332977573|gb|EGK14343.1| hemolysin A [Desmospora sp. 8437]
          Length = 64

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 11/52 (21%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          +R+  V+   G   +R++ +R +    V+V+G   ++    +     +EV G
Sbjct: 4  ERLDLVLVNKGYFPTRQQAQRAVMAGLVRVDGERADKPGTRIPPEATVEVAG 55


>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 = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 25/245 (10%), Positives = 66/245 (26%), Gaps = 40/245 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQ-RVKVNGILLERAAVNVMSTDHIEVDGV 65
           V E     R+ + +      +R EV++ I +   + +   ++     ++   + I+    
Sbjct: 8   VDEKQDGMRLDQFLKEVSGLTRSEVQKWIKEGYAISLPNRMVRS-NYHISDKEKIQFSWE 66

Query: 66  P--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                          +   +   + +      +V   +     + V   L      ++ V
Sbjct: 67  EKKEIELIPQKIKLDILYEDEHIIVINKSRGMVVHPGAGNIDNTLVNALLYHCGESLLKV 126

Query: 112 G-RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
           G +        L     G +  V    + + ++        +     L    +     G 
Sbjct: 127 GEKTRPGIVHRLDKDTSGVMVAVKSDIAYEKVKNEIATHEAKRTYLTLVH-GQMEGPDGK 185

Query: 171 CYGD--------MQVTLDTQKGSN--------------AWVTVGLREGKNREIKKVFEFF 208
                       M+  +  + G N              + +   L  G+  +I+    + 
Sbjct: 186 IDLPLGRSLKDRMKWDVQPKTGKNAITHFHVLEFMPKYSLLECKLETGRTHQIRVHMSYI 245

Query: 209 NWKVN 213
              V 
Sbjct: 246 GHPVI 250


>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 = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 72/230 (31%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 40  RLDAVLAKLLPDYSRSRLTLWIKEGAVIVNDKP-SQPKDKMIGGEQIRVTVRPSEENLAF 98

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWRGTLLNGLLAHCPELSQVPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLTHSYIECSLETGRTHQIRVHMREANHP 268


>gi|92112578|ref|YP_572506.1| SSU ribosomal protein S4P [Chromohalobacter salexigens DSM 3043]
 gi|122420778|sp|Q1R0F1|RS4_CHRSD RecName: Full=30S ribosomal protein S4
 gi|91795668|gb|ABE57807.1| SSU ribosomal protein S4P [Chromohalobacter salexigens DSM 3043]
          Length = 206

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +  A+  V   D + V
Sbjct: 97  RLDNVVYRMGFGSTRSEARQLVSHKAIAVNGRTVNVASYQVKPGDVVSV 145


>gi|150390272|ref|YP_001320321.1| hemolysin A [Alkaliphilus metalliredigens QYMF]
 gi|149950134|gb|ABR48662.1| hemolysin A [Alkaliphilus metalliredigens QYMF]
          Length = 267

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 11/59 (18%), Positives = 22/59 (37%), Gaps = 1/59 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             R+   +   G   SR   +  I    V V+  ++++    V     I++ G P+  
Sbjct: 3  KKVRIDLRLVEEGYFDSRERAKSSIMAGVVLVDQQVIDKPGTKVDEDLPIKIKGNPIPY 61


>gi|297562525|ref|YP_003681499.1| translation initiation factor IF-2 [Nocardiopsis dassonvillei
           subsp. dassonvillei DSM 43111]
 gi|296846973|gb|ADH68993.1| translation initiation factor IF-2 [Nocardiopsis dassonvillei
           subsp. dassonvillei DSM 43111]
          Length = 1012

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 11/118 (9%), Positives = 24/118 (20%), Gaps = 6/118 (5%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK- 300
           R+   P        +  A                +  P   +     ++      K  + 
Sbjct: 58  RKGSAPRPGPRPAADNGAAPKPGPAPKPGPRPSPAPKPSPQSEAAPRANAPKPGPKAPRG 117

Query: 301 -----LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                          A     ++G         G R +  +R    P +        +
Sbjct: 118 EAGARPGGAPKPGAPAGPGGRSEGGRPEGGRPEGGRPDRAQRGGDRPERGERPERGDR 175



 Score = 42.9 bits (99), Expect = 0.070,   Method: Composition-based stats.
 Identities = 6/107 (5%), Positives = 14/107 (13%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           +L       +                       +         + S       + +    
Sbjct: 45  RLQEAFNNGSDGGRKGSAPRPGPRPAADNGAAPKPGPAPKPGPRPSPAPKPSPQSEAAPR 104

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
               +          G         G       RS     +      
Sbjct: 105 ANAPKPGPKAPRGEAGARPGGAPKPGAPAGPGGRSEGGRPEGGRPEG 151



 Score = 39.4 bits (90), Expect = 0.79,   Method: Composition-based stats.
 Identities = 10/83 (12%), Positives = 17/83 (20%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P    EA    +AP    +    +        P            + G  +  +     
Sbjct: 94  KPSPQSEAAPRANAPKPGPKAPRGEAGARPGGAPKPGAPAGPGGRSEGGRPEGGRPEGGR 153

Query: 306 HRRNLASNVWMAKGIHSSFLSDS 328
             R         +G        S
Sbjct: 154 PDRAQRGGDRPERGERPERGDRS 176


>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 = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 32/240 (13%), Positives = 68/240 (28%), Gaps = 34/240 (14%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           I+      +R+  VI       SR ++++ + +  + VNG    +    V+  + +E++ 
Sbjct: 15  IMHPKDAGKRIDVVINEQFEQFSRAQIQKWLKEGSITVNGR-ATKPKHIVLGDEEVEINI 73

Query: 65  VPLRKAERTRLWLY--------------HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI- 109
             L   E     +                    +V   +     +     L     +   
Sbjct: 74  ELLPTNEWIAEDINLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNALLHRYKDQDKL 133

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVLELP------------STQWLRVYRVRFHGQV 153
                V RLD +T GL++          L                 +     +   +  +
Sbjct: 134 PRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGEIYQQGTINQPI 193

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +D  N  K  I  +G        T          +   L  G+  +I+   +     + 
Sbjct: 194 GRDPTNRTKMAINYRGKEA-ITHYTPIEVYDGFTLIECQLETGRTHQIRVHMKSIKHPLV 252


>gi|312899123|ref|ZP_07758501.1| ribosomal RNA large subunit methyltransferase J [Megasphaera
          micronuciformis F0359]
 gi|310619790|gb|EFQ03372.1| ribosomal RNA large subunit methyltransferase J [Megasphaera
          micronuciformis F0359]
          Length = 267

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 12/59 (20%), Positives = 24/59 (40%), Gaps = 1/59 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
            +R+  ++   G   SR + +  +    V V    +++A   +   + I V G PL  
Sbjct: 3  EKERLDVLLTERGFFESREKAKAAVMAGLVFVKDRRVDKAGTKIEIHEEITVKGNPLPY 61


>gi|307265157|ref|ZP_07546716.1| hemolysin A [Thermoanaerobacter wiegelii Rt8.B1]
 gi|326390209|ref|ZP_08211770.1| hemolysin A [Thermoanaerobacter ethanolicus JW 200]
 gi|306919779|gb|EFN49994.1| hemolysin A [Thermoanaerobacter wiegelii Rt8.B1]
 gi|325993857|gb|EGD52288.1| hemolysin A [Thermoanaerobacter ethanolicus JW 200]
          Length = 264

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 11 FTPQRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             +R+  ++ + G  S RE  +  I    V V+G  +E+A   V     IEV
Sbjct: 3  SKKERLDVLLVQKGFFSSREKAKASIMAGEVYVDGKRIEKAGEFVNIDSSIEV 55


>gi|241759655|ref|ZP_04757756.1| ribosomal protein S4 [Neisseria flavescens SK114]
 gi|241320027|gb|EER56408.1| ribosomal protein S4 [Neisseria flavescens SK114]
          Length = 206

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNG ++   +  V + D + V     ++    
Sbjct: 97  RLDNVVYRMGFGSTRAEARQLVSHKAIIVNGQVVNIPSFQVKAGDVVAVREKAKKQVRIQ 156


>gi|332088103|gb|EGI93228.1| ribosomal large subunit pseudouridine synthase D [Shigella boydii
           5216-82]
          Length = 300

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 25/217 (11%), Positives = 56/217 (25%), Gaps = 30/217 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--------------LRKAER 72
           SR  ++  I  QRV VNG + ++    V+  + + ++                 +   + 
Sbjct: 6   SRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDE 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGRLDINTEGLLLLTND 127
             + +      +V   +     + +   L          R   V RLD +T GL+++   
Sbjct: 66  DIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKT 125

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQ-----------DKLNLLKKGIVIQGICYGDMQ 176
                 L     +                                    V          
Sbjct: 126 VPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTH 185

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             +      +  + + L  G+  +I+         + 
Sbjct: 186 YRIMEHFRVHMRLRLRLETGRTHQIRVHMAHITHPLV 222


>gi|302869943|ref|YP_003838580.1| 30S ribosomal protein S4 [Micromonospora aurantiaca ATCC 27029]
 gi|315501404|ref|YP_004080291.1| ribosomal protein s4 [Micromonospora sp. L5]
 gi|302572802|gb|ADL49004.1| ribosomal protein S4 [Micromonospora aurantiaca ATCC 27029]
 gi|315408023|gb|ADU06140.1| ribosomal protein S4 [Micromonospora sp. L5]
          Length = 208

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG A SR    +++      VNG  ++  +  V   D IEV
Sbjct: 99  RLDNVVYRAGYAKSRDMARQLVKHGHFTVNGKKVDIPSYRVKEHDIIEV 147


>gi|325143909|gb|EGC66219.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis M01-240013]
          Length = 356

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 72/230 (31%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 22  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 80

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 81  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 140

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 141 LDKETSGLMVVAKTLSAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 200

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  +V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 201 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIRVHMREANHP 250


>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 = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 38/265 (14%), Positives = 77/265 (29%), Gaps = 41/265 (15%)

Query: 1   MKDKNI----VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVM 55
           M++K I    + E+   QR+   + +      +  + ++I    V+VN   ++     + 
Sbjct: 1   MQNKQIQHIDIDESSEDQRIDNFLFKTFKDVPKNHIFKIIRNGEVRVNKKRVKTL-YKLK 59

Query: 56  STDHIEV---------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
             D + +               +  P    E   L + +KP GL            +   
Sbjct: 60  INDVVRIPPIEFIEKKEKKPSDNFKPHIIYEDEWLLVVNKPSGLAVHGGSGIDFGLIEHM 119

Query: 101 LPSIFSRVISV--GRLDINTEGLLLLTNDG-----GLARVLELPSTQWLRVYRVRFHGQV 153
                         R+D NT G++++                    +   V         
Sbjct: 120 RHIKPEYKFLELVHRIDKNTSGVIVIAKKRSALRSMQELFRNKKIKKNYLVAVKGNWDSK 179

Query: 154 DQDKLNLLKKGIVIQG-----------ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            ++    L+K    +G                    L  Q    + ++  +  G+  +I+
Sbjct: 180 KKEVSLRLEKKQTSEGHHVNVVEDPLRGKLSKSIFYLVKQMQKQSLLSAQIITGRTHQIR 239

Query: 203 KVFEFFNWKVNRLIRISYGPFQLGT 227
               F  + V  L    YG F L  
Sbjct: 240 VQLAFLGFPV--LGDDKYGDFALNK 262


>gi|187935054|ref|YP_001884501.1| 30S ribosomal protein S4 [Clostridium botulinum B str. Eklund 17B]
 gi|188590506|ref|YP_001919700.1| 30S ribosomal protein S4 [Clostridium botulinum E3 str. Alaska E43]
 gi|251777686|ref|ZP_04820606.1| 30S ribosomal protein S4 [Clostridium botulinum E1 str. 'BoNT E
           Beluga']
 gi|226697826|sp|B2UYD8|RS4_CLOBA RecName: Full=30S ribosomal protein S4
 gi|226697827|sp|B2TIK3|RS4_CLOBB RecName: Full=30S ribosomal protein S4
 gi|187723207|gb|ACD24428.1| 30S ribosomal protein S4 [Clostridium botulinum B str. Eklund 17B]
 gi|188500787|gb|ACD53923.1| 30S ribosomal protein S4 [Clostridium botulinum E3 str. Alaska E43]
 gi|243082001|gb|EES47891.1| 30S ribosomal protein S4 [Clostridium botulinum E1 str. 'BoNT E
           Beluga']
          Length = 206

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 15/69 (21%), Positives = 25/69 (36%), Gaps = 1/69 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+  V+ R G   SR E  +++      VNG  ++  + +V   D I V        + 
Sbjct: 98  MRLDNVVYRLGYGASRNEARQLVTHGHFLVNGKKVDICSYHVSMNDVITVCEKSRSSEKF 157

Query: 73  TRLWLYHKP 81
                  K 
Sbjct: 158 KTFVENPKT 166


>gi|87302222|ref|ZP_01085047.1| tRNA/rRNA methyltransferase (SpoU):RNA methyltransferase TrmH
           [Synechococcus sp. WH 5701]
 gi|87283147|gb|EAQ75103.1| tRNA/rRNA methyltransferase (SpoU):RNA methyltransferase TrmH
           [Synechococcus sp. WH 5701]
          Length = 547

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 12/119 (10%), Positives = 26/119 (21%), Gaps = 4/119 (3%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK--KNS 289
             R       R+        E+          +    R      +    D  R    +  
Sbjct: 37  EWR--GSSEGRDGREDRPRRESVQRPQGEGRPAGRPTRVIGARPAARRFDDQRPGAGRRP 94

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
             +     +++       R+        +G   SF +    R +  R         +  
Sbjct: 95  EGRFEGRPERRPEGRPEGRSEGRPEGRDQGRRPSFGAPRFSRPDGDRPRFQPGRPPARP 153



 Score = 42.9 bits (99), Expect = 0.080,   Method: Composition-based stats.
 Identities = 11/108 (10%), Positives = 24/108 (22%), Gaps = 1/108 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P     ++             V+               +    + +    ++       
Sbjct: 35  RPEWRGSSEGRDGREDRPRRESVQRPQGEGRPAGRPTRVIGARPAARRFDDQRPGAGRRP 94

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R         +G      S+      +  R PSF + R  R    +
Sbjct: 95  EGRFEGRPERRPEG-RPEGRSEGRPEGRDQGRRPSFGAPRFSRPDGDR 141



 Score = 40.2 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 12/109 (11%), Positives = 26/109 (23%)

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           +             +    S      +P+       ++    +    +    +++ +  P
Sbjct: 1   MSQRFERRKPKGAGSGDRPSGGARGGKPSRFGGPRPEWRGSSEGRDGREDRPRRESVQRP 60

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                 A       G   +      QR    RR       R  RR   +
Sbjct: 61  QGEGRPAGRPTRVIGARPAARRFDDQRPGAGRRPEGRFEGRPERRPEGR 109



 Score = 39.8 bits (91), Expect = 0.63,   Method: Composition-based stats.
 Identities = 14/122 (11%), Positives = 26/122 (21%), Gaps = 4/122 (3%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM--KKNSSQ 291
           RE   +  RE +     E         +  +    R   +               +   +
Sbjct: 48  REDRPR--RESVQRPQGEGRPAGRPTRVIGARPAARRFDDQRPGAGRRPEGRFEGRPERR 105

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
             G  + +    P  R       + A             +       PS  S+       
Sbjct: 106 PEGRPEGRSEGRPEGRDQGRRPSFGAPRFSRPDGDRPRFQPGRPPARPSRFSEPEAPGPE 165

Query: 352 AK 353
           A 
Sbjct: 166 AS 167



 Score = 38.2 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 12/114 (10%), Positives = 22/114 (19%), Gaps = 4/114 (3%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
             R+  G    +           S     R      SE  D      +  S +    + +
Sbjct: 6   ERRKPKGAGSGDRPSGGARGGKPSRFGGPRPEWRGSSEGRDGREDRPRRESVQRPQGEGR 65

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               P                       +G+R E                  ++
Sbjct: 66  PAGRPTRVIGARPAARRFDDQRPG----AGRRPEGRFEGRPERRPEGRPEGRSE 115



 Score = 37.9 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 11/80 (13%), Positives = 19/80 (23%), Gaps = 5/80 (6%)

Query: 280 DDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR-----EEN 334
             F R K   +                R       W           D  +R      + 
Sbjct: 3   QRFERRKPKGAGSGDRPSGGARGGKPSRFGGPRPEWRGSSEGRDGREDRPRRESVQRPQG 62

Query: 335 HRRSPSFPSKRSLRRTSAKK 354
             R    P++    R +A++
Sbjct: 63  EGRPAGRPTRVIGARPAARR 82



 Score = 36.7 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 3/104 (2%), Positives = 16/104 (15%), Gaps = 2/104 (1%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
                +                            +   + +   +  +   P        
Sbjct: 1   MSQRFERRKPKGAGSGDRPSGGARGGKPSRFGGPRPEWRGSSEGRDGREDRPRRESVQRP 60

Query: 313 NVWMAKGIHSSF--LSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                     +    +    R  + +R  +            ++
Sbjct: 61  QGEGRPAGRPTRVIGARPAARRFDDQRPGAGRRPEGRFEGRPER 104


>gi|322389018|ref|ZP_08062588.1| S4 domain-containing protein YlmH [Streptococcus parasanguinis ATCC
           903]
 gi|321144323|gb|EFX39731.1| S4 domain-containing protein YlmH [Streptococcus parasanguinis ATCC
           903]
          Length = 263

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 15/48 (31%), Positives = 22/48 (45%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ KVIA     SR +  ++I+   VKVN       +  V   D + V
Sbjct: 185 RLDKVIAGTFKLSRSQASQLISSGLVKVNYATTSNVSYAVGLNDLVSV 232


>gi|312867091|ref|ZP_07727301.1| S4 domain protein [Streptococcus parasanguinis F0405]
 gi|311097220|gb|EFQ55454.1| S4 domain protein [Streptococcus parasanguinis F0405]
          Length = 263

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 15/48 (31%), Positives = 22/48 (45%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ KVIA     SR +  ++I+   VKVN       +  V   D + V
Sbjct: 185 RLDKVIAGTFKLSRSQASQLISSGLVKVNYATTSNVSYAVGLNDLVSV 232


>gi|296876953|ref|ZP_06900997.1| S4 domain-containing protein YlmH [Streptococcus parasanguinis ATCC
           15912]
 gi|296431988|gb|EFH17791.1| S4 domain-containing protein YlmH [Streptococcus parasanguinis ATCC
           15912]
          Length = 263

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 15/48 (31%), Positives = 22/48 (45%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ KVIA     SR +  ++I+   VKVN       +  V   D + V
Sbjct: 185 RLDKVIAGTFKLSRSQASQLISSGLVKVNYATTSNVSYAVGLNDLVSV 232


>gi|325977748|ref|YP_004287464.1| hypothetical protein SGGBAA2069_c05480 [Streptococcus gallolyticus
           subsp. gallolyticus ATCC BAA-2069]
 gi|325177676|emb|CBZ47720.1| conserved hypothetical protein [Streptococcus gallolyticus subsp.
           gallolyticus ATCC BAA-2069]
          Length = 263

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 18/63 (28%), Positives = 32/63 (50%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           KD   +    +  R+ KV+A     SR +  ++I   +VK+N  +++RA+  +   D I 
Sbjct: 173 KDSRQLDIMVSSMRMDKVLATVLKLSRSQAVQLIETDKVKLNYQIVDRASEMLQVGDLIS 232

Query: 62  VDG 64
           V G
Sbjct: 233 VRG 235


>gi|324998566|ref|ZP_08119678.1| hemolysin A [Pseudonocardia sp. P1]
          Length = 274

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 19/61 (31%), Positives = 27/61 (44%), Gaps = 13/61 (21%)

Query: 15 RVS-----KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----DGV 65
          R+      + +AR    SR +   +IA  RV VNG+   +AA  V     + V    DG 
Sbjct: 7  RLDAELVRRRLAR----SRGQAAELIAAGRVSVNGMPAGKAATVVDRDAPVVVRPDDDGE 62

Query: 66 P 66
          P
Sbjct: 63 P 63


>gi|311693294|gb|ADP96167.1| 30S ribosomal protein S4 [marine bacterium HP15]
          Length = 167

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VN   +   +  V   D + V
Sbjct: 58  RLDNVVYRMGFGSTRAEARQLVSHKAILVNDKTVNIPSYQVRPGDVVSV 106


>gi|308048015|ref|YP_003911581.1| 30S ribosomal protein S4P [Ferrimonas balearica DSM 9799]
 gi|307630205|gb|ADN74507.1| SSU ribosomal protein S4P [Ferrimonas balearica DSM 9799]
          Length = 206

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 29/56 (51%), Gaps = 1/56 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+  V+ R G   +R E  ++++ + +KVNG ++   + +V   D I V     ++
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAIKVNGRVVNIPSFSVSPNDVIAVREKAQKQ 152


>gi|306830850|ref|ZP_07464012.1| S4 domain-containing protein YlmH [Streptococcus gallolyticus
           subsp. gallolyticus TX20005]
 gi|304426873|gb|EFM29983.1| S4 domain-containing protein YlmH [Streptococcus gallolyticus
           subsp. gallolyticus TX20005]
          Length = 263

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 18/63 (28%), Positives = 32/63 (50%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           KD   +    +  R+ KV+A     SR +  ++I   +VK+N  +++RA+  +   D I 
Sbjct: 173 KDSRQLDIMVSSMRMDKVLATVLKLSRSQAVQLIETDKVKLNYQIVDRASEMLQVGDLIS 232

Query: 62  VDG 64
           V G
Sbjct: 233 VRG 235


>gi|288904818|ref|YP_003430040.1| hypothetical protein GALLO_0607 [Streptococcus gallolyticus UCN34]
 gi|288731544|emb|CBI13099.1| conserved hypothetical protein [Streptococcus gallolyticus UCN34]
          Length = 261

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 18/63 (28%), Positives = 32/63 (50%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           KD   +    +  R+ KV+A     SR +  ++I   +VK+N  +++RA+  +   D I 
Sbjct: 171 KDSRQLDIMVSSMRMDKVLATVLKLSRSQAVQLIETDKVKLNYQIVDRASEMLQVGDLIS 230

Query: 62  VDG 64
           V G
Sbjct: 231 VRG 233


>gi|161523454|ref|YP_001578466.1| 30S ribosomal protein S4 [Burkholderia multivorans ATCC 17616]
 gi|189351773|ref|YP_001947401.1| 30S ribosomal protein S4 [Burkholderia multivorans ATCC 17616]
 gi|221201590|ref|ZP_03574628.1| 30S ribosomal protein S4 [Burkholderia multivorans CGD2M]
 gi|221207335|ref|ZP_03580345.1| 30S ribosomal protein S4 [Burkholderia multivorans CGD2]
 gi|221213473|ref|ZP_03586448.1| 30S ribosomal protein S4 [Burkholderia multivorans CGD1]
 gi|226697816|sp|A9ADL8|RS4_BURM1 RecName: Full=30S ribosomal protein S4
 gi|160340883|gb|ABX13969.1| ribosomal protein S4 [Burkholderia multivorans ATCC 17616]
 gi|189335795|dbj|BAG44865.1| small subunit ribosomal protein S4 [Burkholderia multivorans ATCC
           17616]
 gi|221166925|gb|EED99396.1| 30S ribosomal protein S4 [Burkholderia multivorans CGD1]
 gi|221172923|gb|EEE05360.1| 30S ribosomal protein S4 [Burkholderia multivorans CGD2]
 gi|221178406|gb|EEE10815.1| 30S ribosomal protein S4 [Burkholderia multivorans CGD2M]
          Length = 207

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 16/73 (21%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNGI+    +  V + D I +     ++A   
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKSITVNGIVANVPSQQVKAGDVIAIREKAKKQARII 157

Query: 74  RLWLYHKPIGLVT 86
                 +  G+ +
Sbjct: 158 EALSLAEQGGMPS 170


>gi|126697569|ref|YP_001086466.1| putative RNA-binding mediating protein [Clostridium difficile
          630]
 gi|255102902|ref|ZP_05331879.1| putative RNA-binding mediating protein [Clostridium difficile
          QCD-63q42]
 gi|255308722|ref|ZP_05352893.1| putative RNA-binding mediating protein [Clostridium difficile
          ATCC 43255]
 gi|255657641|ref|ZP_05403050.1| putative RNA-binding mediating protein [Clostridium difficile
          QCD-23m63]
 gi|296452678|ref|ZP_06894369.1| S4 domain protein YaaA [Clostridium difficile NAP08]
 gi|296880069|ref|ZP_06904038.1| S4 domain protein YaaA [Clostridium difficile NAP07]
 gi|115249006|emb|CAJ66817.1| putative RNA-binding mediating protein [Clostridium difficile]
 gi|296258460|gb|EFH05364.1| S4 domain protein YaaA [Clostridium difficile NAP08]
 gi|296428936|gb|EFH14814.1| S4 domain protein YaaA [Clostridium difficile NAP07]
          Length = 68

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 11/64 (17%), Positives = 25/64 (39%), Gaps = 9/64 (14%)

Query: 10 NFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
               ++ + +     A  G       + +I +  V VN  +  R    + S D +E++G
Sbjct: 7  ESEYIKLDQFLKLAEIASTGG----HAKFLIQEGLVTVNDEIELRRGKKIKSGDIVEIEG 62

Query: 65 VPLR 68
            ++
Sbjct: 63 TKIK 66


>gi|73662889|ref|YP_301670.1| hypothetical protein SSP1580 [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
 gi|72495404|dbj|BAE18725.1| conserved hypothetical protein [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
          Length = 212

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 29/57 (50%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +   +  R+  V+      SR   +++I ++RVKVN  +++ A   + S D + + G
Sbjct: 129 ETTVSGLRLDVVLKEMVRKSRSIAKQLIDKKRVKVNHTVIDAADFQLDSGDLLSIQG 185


>gi|319639573|ref|ZP_07994320.1| 30S ribosomal protein S4 [Neisseria mucosa C102]
 gi|317399144|gb|EFV79818.1| 30S ribosomal protein S4 [Neisseria mucosa C102]
          Length = 206

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNG ++   +  V + D + V     ++    
Sbjct: 97  RLDNVVYRMGFGSTRAEARQLVSHKAIVVNGQVVNIPSFQVKAGDVVAVREKAKKQVRIQ 156


>gi|81428454|ref|YP_395454.1| 30S ribosomal protein S4 [Lactobacillus sakei subsp. sakei 23K]
 gi|90101691|sp|Q38XD6|RS4_LACSS RecName: Full=30S ribosomal protein S4
 gi|78610096|emb|CAI55145.1| 30S Ribosomal protein S4 [Lactobacillus sakei subsp. sakei 23K]
          Length = 201

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  ++ R G+AS R +  +++    V V+G  ++  +  V     I +
Sbjct: 93  QRLDNIVYRLGLASTRAQARQLVNHGHVTVDGKRVDIPSYEVKPGQEISI 142


>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 = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 26/232 (11%), Positives = 62/232 (26%), Gaps = 31/232 (13%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----------E 61
             R+ + +A+     SR  ++  I    VKVNGI++ +A   V   + +           
Sbjct: 17  GCRLDQALAQLFPDYSRSRIKVWIESDLVKVNGIVVNKAREKVFGGEQVEIQAEIEEEIR 76

Query: 62  VDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-----G 112
            +   +       +   + +      +V   +     + +   L                
Sbjct: 77  FEPQDIPLNIVYEDDDIIVINKPKDLVVHPGAGNPDGTVLNALLHYYPPIAEVPRAGIVH 136

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-----------FHGQVDQDKLNLL 161
           RLD +T GL+++  +      L     +                      +         
Sbjct: 137 RLDKDTTGLMVVAKNIPAQTHLVTALQKRRITREYEAVASGVMTQGGKVDEPMARHPTKR 196

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               V            +  +  +   + + L  G+  +I+         + 
Sbjct: 197 TAMAVHPMGKPAVTHYRIMERFRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 248


>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 = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 34/227 (14%), Positives = 67/227 (29%), Gaps = 31/227 (13%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------GVPLRK 69
           SK +      S R+++ M  ++RVKVN  +       +   D + ++       GV + K
Sbjct: 29  SKYVKERFSLSSRDIQMMFRKKRVKVNSRVAHS-QRALKKGDVLTLELPQDKDYGVDVEK 87

Query: 70  AERTRLWL--------------YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
              T L+                H      +                    R +     D
Sbjct: 88  GPITVLYEDAHTLVVNKDPFMLVHPAGQTKSCTLSNYVAGYYAKKNVVHKVRPVHRLDRD 147

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL-------LKKGIVIQ 168
            +   L   T +       EL + +  R+Y     G++D D +         +     + 
Sbjct: 148 TSGCILFGKTKEAQQYYTDELQAGRIDRIYTGLVEGRIDADGMVDAPIGVDPVFDNRRVI 207

Query: 169 GICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                    +  +   +G N  +   L  G+  +I+   E     + 
Sbjct: 208 DEFGQPAQTEYIVLNHEGDNTLLRFKLLTGRTHQIRVHMEHIGHPIV 254


>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 = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 26/244 (10%), Positives = 58/244 (23%), Gaps = 39/244 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIE--- 61
           V E    +RV   +AR    SR     +IA   V V+G  + + +  +       +    
Sbjct: 9   VPEGLDGERVDAALARLFGLSRSRAAELIAAGDVLVDGRTVVK-SDRLHGGGWLEVTLPP 67

Query: 62  -----------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                      V G+ +   +   + +              +G + +   L +  +   S
Sbjct: 68  PPAPPRPVAEPVPGMTILYEDEHIVVVSKPVGVAAHPTIGWNGPTVLGGLLGAGHTVATS 127

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
                      L     G +       +   L+              L        ++G 
Sbjct: 128 GAAERQGIVHRLDANTTGAMVVAKSEIAYSRLKRAFKERRVDKRYHALVQ-GHPDPLRGT 186

Query: 171 CYGDMQVTLDTQK---------------------GSNAWVTVGLREGKNREIKKVFEFFN 209
               +                              + + + + L  G+  +I+       
Sbjct: 187 IDAPIDRHPSGDGRFAVVAGGRPSITHYDTLEAFRAASLLEIDLETGRTHQIRVHMSAVR 246

Query: 210 WKVN 213
               
Sbjct: 247 HPCV 250


>gi|224827041|ref|ZP_03700138.1| ribosomal protein S4 [Lutiella nitroferrum 2002]
 gi|224600707|gb|EEG06893.1| ribosomal protein S4 [Lutiella nitroferrum 2002]
          Length = 206

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNG ++   +  V + D + +     ++A   
Sbjct: 97  RLDNVVYRMGFGSTRAEARQLVSHKAIVVNGQVVNIPSFQVKAGDVVAIREKAKKQARIV 156

Query: 74  RLWLYHKPIGLVT 86
                 +  G  +
Sbjct: 157 EGLALAEQGGFPS 169


>gi|206900643|ref|YP_002251260.1| hypothetical protein DICTH_1441 [Dictyoglomus thermophilum
          H-6-12]
 gi|206739746|gb|ACI18804.1| conserved domain protein [Dictyoglomus thermophilum H-6-12]
          Length = 71

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 12/37 (32%), Positives = 20/37 (54%)

Query: 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
          + + +I   RVKVNG +    +  + + D +EVDG  
Sbjct: 28 QAKNLILAGRVKVNGEIELHRSRKLKNGDVVEVDGEK 64


>gi|300780071|ref|ZP_07089927.1| S4 domain protein [Corynebacterium genitalium ATCC 33030]
 gi|300534181|gb|EFK55240.1| S4 domain protein [Corynebacterium genitalium ATCC 33030]
          Length = 90

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 9/38 (23%), Positives = 18/38 (47%)

Query: 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
          E + +IA   V VNG ++     ++   D + + G  +
Sbjct: 22 EAKELIATGEVAVNGEVVTSRGFSLDDGDEVSLPGHTI 59


>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 = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 71/230 (30%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 58  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 116

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 117 VPEPMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 176

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 177 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 236

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K   V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 237 KMAAVKFGGKPAVTHVKVLERYLAHSYIECSLGTGRTHQIRVHMREANHP 286


>gi|254712999|ref|ZP_05174810.1| Cell division protein FtsJ [Brucella ceti M644/93/1]
 gi|254716647|ref|ZP_05178458.1| Cell division protein FtsJ [Brucella ceti M13/05/1]
 gi|261218448|ref|ZP_05932729.1| hemolysin A [Brucella ceti M13/05/1]
 gi|261320702|ref|ZP_05959899.1| hemolysin A [Brucella ceti M644/93/1]
 gi|260923537|gb|EEX90105.1| hemolysin A [Brucella ceti M13/05/1]
 gi|261293392|gb|EEX96888.1| hemolysin A [Brucella ceti M644/93/1]
          Length = 240

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 12/51 (23%), Positives = 23/51 (45%), Gaps = 1/51 (1%)

Query: 15 RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          R+ +++   G  A+R      I +  VKV+G  + +    V+    + VD 
Sbjct: 11 RLDQLLVERGFFATRSRARDAIQRGTVKVDGRPITKPGQMVVRDAALAVDD 61


>gi|217424827|ref|ZP_03456324.1| 30S ribosomal protein S4 [Burkholderia pseudomallei 576]
 gi|217392283|gb|EEC32308.1| 30S ribosomal protein S4 [Burkholderia pseudomallei 576]
          Length = 207

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 15/73 (20%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNGI+    +  V + D + +     ++A   
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAITVNGIVANIPSQQVRAGDVVAIREKAKKQARIV 157

Query: 74  RLWLYHKPIGLVT 86
                 +  G+ +
Sbjct: 158 EALSLAEQGGMPS 170


>gi|170077101|ref|YP_001733739.1| hemolysin A [Synechococcus sp. PCC 7002]
 gi|169884770|gb|ACA98483.1| hemolysin A [Synechococcus sp. PCC 7002]
          Length = 285

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 1/54 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
          QR+  ++    +  SR++ +R+I    VKV   ++++    V +   IEV   P
Sbjct: 4  QRLDLLLVERKLCESRQQAQRVIRAGEVKVKQQIVDKPGTLVPADVDIEVQAKP 57


>gi|307543849|ref|YP_003896328.1| 30S ribosomal protein S4 [Halomonas elongata DSM 2581]
 gi|307215873|emb|CBV41143.1| 30S ribosomal protein S4 [Halomonas elongata DSM 2581]
          Length = 206

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +  A+  V   D + V
Sbjct: 97  RLDNVVYRMGFGSTRSEARQLVSHKAIAVNGRTVNVASYQVKPGDVVSV 145


>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 = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 13/63 (20%), Positives = 26/63 (41%), Gaps = 7/63 (11%)

Query: 12  TPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE------VDG 64
             QR+ +++A      SR  ++ +I    V +   ++   A  V + + I       VD 
Sbjct: 50  KSQRLDRLLAEQIDDLSRTRLKALILAGHVSLGDTVVRDPAYQVKAGEAITIEVPPAVDP 109

Query: 65  VPL 67
            P+
Sbjct: 110 EPV 112


>gi|332995248|gb|AEF05303.1| 30S ribosomal protein S4 [Alteromonas sp. SN2]
          Length = 206

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G AS R E  ++++ + + VNG ++   + NV + D + V
Sbjct: 97  RLDNVVYRMGFASTRAEARQLVSHKAIMVNGQVVNIPSFNVSAEDVVSV 145


>gi|295109996|emb|CBL23949.1| Uncharacterized conserved protein, contains S4-like domain
           [Ruminococcus obeum A2-162]
          Length = 250

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 14/60 (23%), Positives = 22/60 (36%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
            +       R+  +I  A  +SR  +   I   +V VNG L+          D + V G 
Sbjct: 166 TISGTCASVRLDTLIGLAFQSSRSSMVSFIEGGQVFVNGKLITSNGYEPKDGDIVSVRGK 225


>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 = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 28/243 (11%), Positives = 62/243 (25%), Gaps = 37/243 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+   +V E    +RV   ++R    SR     M     V+V+G+ + + ++ V +   I
Sbjct: 1   MERSILVPEGLEGERVDTALSRLLGLSRSVAAGMAESGDVEVDGVKVPK-SMRVTTGARI 59

Query: 61  EVD----------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           +V                 G+ +   +   + +           +   G + +     + 
Sbjct: 60  DVTMPKPKEPLSIVAEPVPGMNVIYDDDAFVVVDKPVGVAAHAAAGWSGPTVIGGLAAAG 119

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-------- 156
           +    S           L +   G +       +   L+                     
Sbjct: 120 YQIATSGAAERQGIVHRLDVGTSGVMVVAKGEHAYSVLKRAFKNRTVDKTYHALVQGLPD 179

Query: 157 ------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                                V     +      +     S + V V L  G+  +I+  
Sbjct: 180 PVVGTIEAPIGRHPRKDGLYAVRTDGKHAVTHYEVLEAYRSASLVEVKLETGRTHQIRVH 239

Query: 205 FEF 207
              
Sbjct: 240 MSA 242


>gi|261838022|gb|ACX97788.1| pseudouridine synthase D [Helicobacter pylori 51]
          Length = 327

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 42/293 (14%), Positives = 83/293 (28%), Gaps = 53/293 (18%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-------------- 60
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I              
Sbjct: 13  RIDEFLAKELQISKNQVLNLIKEGLVFCQKKEVKKGGLALKEGDEITLLTPKIAPKPLKK 72

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISV 111
           E+D       E   L + +KP  LV   +      T+ D L              R   V
Sbjct: 73  ELDLEIEVIFEDKDLLVLNKPPNLVVHKAPSVKEPTLVDWLEFKNYELSNLGLKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR-------VRFHGQVDQDKLNLLKKG 164
            RLD +T G +++  +      L                        ++  +        
Sbjct: 133 HRLDKDTSGGIVIAKNNFTHVHLSEQLKTKTMGRYYIALLSTPLKEEKMSVECYLTRNPN 192

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVTVG-----------LREGKNREIKKVFEFFNWKVN 213
             ++ I     +        S     +            L  G+  +I+           
Sbjct: 193 NRLKMIALKAAKKEKSRYSKSEFTSLLTSQNHLNLIGAKLFTGRTHQIRAHL-------E 245

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSET 266
            L R   G      L  G  + + K+ +R  L  +L+E      +  +     
Sbjct: 246 YLNRHIIG----DNLY-GLNQALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVP 293


>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 = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 71/230 (30%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 99  VPEPMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K   V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 219 KMAAVKFGGKPAVTHVKVLERYLAHSYIECSLGTGRTHQIRVHMREANHP 268


>gi|269128486|ref|YP_003301856.1| 30S ribosomal protein S4 [Thermomonospora curvata DSM 43183]
 gi|268313444|gb|ACY99818.1| ribosomal protein S4 [Thermomonospora curvata DSM 43183]
          Length = 209

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V+ RAG A SR    ++I     KVNG  ++  +  V   D IEV   
Sbjct: 99  RLDNVVYRAGFAKSRDMARQLIRHGHFKVNGRKVDIPSFLVSENDVIEVKPK 150


>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 = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 33/246 (13%), Positives = 75/246 (30%), Gaps = 41/246 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRR---EVE-----RMIAQQRVKVNGILLERAAV 52
           M+ +  V E     R+   I       R+   E++      +I +  VKVN   +++   
Sbjct: 1   MEKETTVNEKNYYSRLDTFI-------RKNYPEIKLGAIYGLIRKGFVKVNEKRVKKNNY 53

Query: 53  NVMSTD--HIEVDGVPLR-------------------KAERTRLWLYHKPIGLVTTHSDP 91
            +   D   I +D   L                      E   L + +KP  +       
Sbjct: 54  ILEIGDNVKIILDENKLEELSRPTQPSLKARPVSFDIIYEDKDLLVINKPAKVSVHPGSK 113

Query: 92  DGRSTVFDNLPSIFSRVISVGRLDINTE----GLLLLTNDGGLARVLELPSTQWLRVYRV 147
           +  +T+ + +            +    +     +++  N      + +L  ++  R Y +
Sbjct: 114 EEMATIIEGVMHYSRGEFEPHLVHRLDKLTSGVMVVAKNKQTARELTQLIKSRETRKYYL 173

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGD-MQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                    K   L   +  +       ++   D      + V + L  G+  +I+  F 
Sbjct: 174 TLLVGNLNKKSGELVSTVYGKTAQLKFNLKKKFDLFGELYSLVEIELYTGRKHQIRVQFA 233

Query: 207 FFNWKV 212
              + +
Sbjct: 234 DLGFPI 239


>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 = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 32/236 (13%), Positives = 63/236 (26%), Gaps = 40/236 (16%)

Query: 13  PQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMST------------- 57
            QR+ +V A    A  SR  +   I   R+ V+G +L      V                
Sbjct: 17  GQRLDQV-AAQLFAEHSRSRLSAWIKDGRLTVDGGVLR-PRDIVHGGAVLELIAEQEAQG 74

Query: 58  ----DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
                 IE+D   +   +   L +      +V   +     + +   L  +   V     
Sbjct: 75  EWVAQDIELD---IIYEDDQILVINKPAGLVVHPAAGHADGTLLNALLHHVPDIVNVPRA 131

Query: 114 LDINTEGL----------------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
             ++                     L+T     +            V             
Sbjct: 132 GIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVTAGGKIDAPIGRH 191

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               ++  V++G         +  +  S+  V V L  G+  +I+      N+ + 
Sbjct: 192 GQQRQRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHVNYPLV 247


>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 = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 71/230 (30%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 99  VPEPMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K   V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 219 KMAAVKFGGKPAVTHVKVLERYLAHSYIECSLGTGRTHQIRVHMREANHP 268


>gi|320093495|ref|ZP_08025392.1| cytotoxin/hemolysin [Actinomyces sp. oral taxon 178 str. F0338]
 gi|319979540|gb|EFW11005.1| cytotoxin/hemolysin [Actinomyces sp. oral taxon 178 str. F0338]
          Length = 277

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+   + R GIA SR   + +I   RV+++G ++ + A  +     + V
Sbjct: 5  RLDSELVRRGIARSRGHAQELIESGRVRLDGEVVLKPARQMNPAQAVVV 53


>gi|319957378|ref|YP_004168641.1| hemolysin a [Nitratifractor salsuginis DSM 16511]
 gi|319419782|gb|ADV46892.1| hemolysin A [Nitratifractor salsuginis DSM 16511]
          Length = 239

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 25/54 (46%), Gaps = 1/54 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
          R+   +   G+  SR +    I + RV ++G + ++ A  V     I + G P+
Sbjct: 3  RLDTALVERGLFESRNKAAEAIRKGRVFLDGHVQKKPAFKVGEETEITLQGGPV 56


>gi|88857987|ref|ZP_01132629.1| pseudouridine synthase [Pseudoalteromonas tunicata D2]
 gi|88819604|gb|EAR29417.1| pseudouridine synthase [Pseudoalteromonas tunicata D2]
          Length = 325

 Score = 49.8 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 19/233 (8%), Positives = 60/233 (25%), Gaps = 32/233 (13%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----EVDGVP- 66
            +R+ +++A      SR  ++  I    V++NG +       +   + +     ++    
Sbjct: 17  GKRLDQILADLFPEYSRSRIKTWILDDMVQINGEIKNIPKEKLFGEEQVVISATIEPQRE 76

Query: 67  ---------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------R 107
                    +   +   L +      +V   +     + +   L                
Sbjct: 77  YEAQNIALNIVYEDDDILVINKPAGLVVHPGAGNADGTVLNALLHHCPEIANVPRAGIVH 136

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH----GQVDQDKLNLLKK 163
            +      +      +      +A +    +                G +D+       K
Sbjct: 137 RLDKDTTGLMVVAKTIPAQTRLVANLQARYNFTREYEAICTGTMTAGGMIDKPIGRHATK 196

Query: 164 GIVIQGICY-GDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +              +  +  S+  + + L  G+  +I+    +    + 
Sbjct: 197 RTHMDVTITGKPAVTHFRVAEKFRSHTRLRLRLETGRTHQIRVHMSYLTHPLV 249


>gi|322372692|ref|ZP_08047228.1| YlmH protein [Streptococcus sp. C150]
 gi|321277734|gb|EFX54803.1| YlmH protein [Streptococcus sp. C150]
          Length = 267

 Score = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 15/53 (28%), Positives = 26/53 (49%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +  R+  V+A     SR    ++I+  +VK+N   +E+A   +   D I V G
Sbjct: 184 SSMRLDNVLATVLNLSRSRALKLISSGKVKLNYRQVEKADQLITIGDMISVRG 236


>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 = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 18/55 (32%), Positives = 31/55 (56%), Gaps = 6/55 (10%)

Query: 13 PQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          PQR+ K ++R     A + SR  + R++ +  V+VNG ++  A   V + D IE+
Sbjct: 15 PQRLDKALSRDVPEEATL-SRTRLARLLEEGAVQVNGAVMRDAKARVTAGDLIEI 68


>gi|257792535|ref|YP_003183141.1| 30S ribosomal protein S4 [Eggerthella lenta DSM 2243]
 gi|257476432|gb|ACV56752.1| ribosomal protein S4 [Eggerthella lenta DSM 2243]
          Length = 208

 Score = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 1/53 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           R+  V+ R G A SR E  + +    + VNG  ++  +  V   D + V    
Sbjct: 99  RLDNVVYRLGFAKSRAEARQQVRHGHITVNGRRVDIPSFRVKPGDLVAVAPKA 151


>gi|317490401|ref|ZP_07948885.1| ribosomal protein S4 [Eggerthella sp. 1_3_56FAA]
 gi|325833388|ref|ZP_08165837.1| ribosomal protein S4 [Eggerthella sp. HGA1]
 gi|316910536|gb|EFV32161.1| ribosomal protein S4 [Eggerthella sp. 1_3_56FAA]
 gi|325485312|gb|EGC87781.1| ribosomal protein S4 [Eggerthella sp. HGA1]
          Length = 208

 Score = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 1/53 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           R+  V+ R G A SR E  + +    + VNG  ++  +  V   D + V    
Sbjct: 99  RLDNVVYRLGFAKSRAEARQQVRHGHITVNGRRVDIPSFRVKPGDLVAVAPKA 151


>gi|226356866|ref|YP_002786606.1| 30S ribosomal protein S4 [Deinococcus deserti VCD115]
 gi|259495272|sp|C1CXD5|RS4_DEIDV RecName: Full=30S ribosomal protein S4
 gi|226318856|gb|ACO46852.1| putative 30S ribosomal protein S4 [Deinococcus deserti VCD115]
          Length = 206

 Score = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G AS RR+  + +    + VNG  ++  +  V   D I V
Sbjct: 97  RLDNVVFRMGFASTRRQARQFVGHGHILVNGKKVDIPSYRVKIGDEISV 145


>gi|88861470|ref|ZP_01136096.1| 30S ribosomal protein S4 [Pseudoalteromonas tunicata D2]
 gi|88816518|gb|EAR26347.1| 30S ribosomal protein S4 [Pseudoalteromonas tunicata D2]
          Length = 206

 Score = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 28/50 (56%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G AS R E  ++++ + V VNG ++   +  + + D + +
Sbjct: 96  QRLDNVVYRMGFASTRAEARQLVSHKSVMVNGSVVNIPSYRITADDVVVI 145


>gi|47093459|ref|ZP_00231223.1| ribosomal protein S4 [Listeria monocytogenes str. 4b H7858]
 gi|47096809|ref|ZP_00234391.1| ribosomal protein S4 [Listeria monocytogenes str. 1/2a F6854]
 gi|217964250|ref|YP_002349928.1| ribosomal protein S4 [Listeria monocytogenes HCC23]
 gi|224499177|ref|ZP_03667526.1| 30S ribosomal protein S4 [Listeria monocytogenes Finland 1988]
 gi|224501464|ref|ZP_03669771.1| 30S ribosomal protein S4 [Listeria monocytogenes FSL R2-561]
 gi|254824345|ref|ZP_05229346.1| ribosomal protein S4 [Listeria monocytogenes FSL J1-194]
 gi|254828169|ref|ZP_05232856.1| ribosomal protein S4 [Listeria monocytogenes FSL N3-165]
 gi|254831997|ref|ZP_05236652.1| 30S ribosomal protein S4 [Listeria monocytogenes 10403S]
 gi|254898237|ref|ZP_05258161.1| 30S ribosomal protein S4 [Listeria monocytogenes J0161]
 gi|254912270|ref|ZP_05262282.1| ribosomal protein S4 [Listeria monocytogenes J2818]
 gi|254931536|ref|ZP_05264895.1| ribosomal protein S4 [Listeria monocytogenes HPB2262]
 gi|254936597|ref|ZP_05268294.1| ribosomal protein S4 [Listeria monocytogenes F6900]
 gi|254993888|ref|ZP_05276078.1| 30S ribosomal protein S4 [Listeria monocytogenes FSL J2-064]
 gi|255026363|ref|ZP_05298349.1| 30S ribosomal protein S4 [Listeria monocytogenes FSL J2-003]
 gi|255522552|ref|ZP_05389789.1| 30S ribosomal protein S4 [Listeria monocytogenes FSL J1-175]
 gi|284801988|ref|YP_003413853.1| 30S ribosomal protein S4 [Listeria monocytogenes 08-5578]
 gi|284995130|ref|YP_003416898.1| 30S ribosomal protein S4 [Listeria monocytogenes 08-5923]
 gi|290893191|ref|ZP_06556178.1| ribosomal protein S4 [Listeria monocytogenes FSL J2-071]
 gi|300765979|ref|ZP_07075950.1| ribosomal protein S4 [Listeria monocytogenes FSL N1-017]
 gi|315282534|ref|ZP_07870925.1| ribosomal protein S4 [Listeria marthii FSL S4-120]
 gi|254764594|sp|B8DHE5|RS4_LISMH RecName: Full=30S ribosomal protein S4
 gi|47014842|gb|EAL05793.1| ribosomal protein S4 [Listeria monocytogenes str. 1/2a F6854]
 gi|47018187|gb|EAL08956.1| ribosomal protein S4 [Listeria monocytogenes str. 4b H7858]
 gi|217333520|gb|ACK39314.1| ribosomal protein S4 [Listeria monocytogenes HCC23]
 gi|258600556|gb|EEW13881.1| ribosomal protein S4 [Listeria monocytogenes FSL N3-165]
 gi|258609194|gb|EEW21802.1| ribosomal protein S4 [Listeria monocytogenes F6900]
 gi|284057550|gb|ADB68491.1| 30S ribosomal protein S4 [Listeria monocytogenes 08-5578]
 gi|284060597|gb|ADB71536.1| 30S ribosomal protein S4 [Listeria monocytogenes 08-5923]
 gi|290557173|gb|EFD90700.1| ribosomal protein S4 [Listeria monocytogenes FSL J2-071]
 gi|293583091|gb|EFF95123.1| ribosomal protein S4 [Listeria monocytogenes HPB2262]
 gi|293590249|gb|EFF98583.1| ribosomal protein S4 [Listeria monocytogenes J2818]
 gi|293593579|gb|EFG01340.1| ribosomal protein S4 [Listeria monocytogenes FSL J1-194]
 gi|300513297|gb|EFK40373.1| ribosomal protein S4 [Listeria monocytogenes FSL N1-017]
 gi|307571182|emb|CAR84361.1| ribosomal protein S4 [Listeria monocytogenes L99]
 gi|313608550|gb|EFR84435.1| ribosomal protein S4 [Listeria monocytogenes FSL F2-208]
 gi|313613822|gb|EFR87575.1| ribosomal protein S4 [Listeria marthii FSL S4-120]
 gi|313623582|gb|EFR93757.1| ribosomal protein S4 [Listeria innocua FSL J1-023]
 gi|328464963|gb|EGF36242.1| 30S ribosomal protein S4 [Listeria monocytogenes 1816]
 gi|328474830|gb|EGF45634.1| 30S ribosomal protein S4 [Listeria monocytogenes 220]
 gi|332312038|gb|EGJ25133.1| 30S ribosomal protein S4 [Listeria monocytogenes str. Scott A]
          Length = 200

 Score = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 92  QRLDNIVYRLGLARTRRAARQLVNHGHITVDGKRVDIPSYQVSVGQVISV 141


>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 = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 26/232 (11%), Positives = 62/232 (26%), Gaps = 31/232 (13%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----------E 61
             R+ + +A+     SR  ++  I    VKVNGI++ +A   V   + +           
Sbjct: 17  GCRLDQALAQLFPDYSRSRIKVWIESDLVKVNGIVVNKAREKVFGGEQVEIQAEIEEEIR 76

Query: 62  VDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-----G 112
            +   +       +   + +      +V   +     + +   L                
Sbjct: 77  FEPQDIPLNIVYEDDDIIVINKPKDLVVHPGAGNPDGTVLNALLHYYPPIAEVPRAGIVH 136

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-----------FHGQVDQDKLNLL 161
           RLD +T GL+++  +      L     +                      +         
Sbjct: 137 RLDKDTTGLMVVAKNIPAQTHLVTALQKRRITREYEAVASGVMTQGGKVDEPMARHPTKR 196

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               V            +  +  +   + + L  G+  +I+         + 
Sbjct: 197 TAMAVHPMGKPAVTHYRIMERFRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 248


>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 = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 33/252 (13%), Positives = 76/252 (30%), Gaps = 34/252 (13%)

Query: 1   MKDK--NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M+DK   +V ++  P  ++ ++A  G  ++ +V+  +  + +KVNG ++ +    +   D
Sbjct: 9   MQDKYDRMVVKDEKPL-LAWLLANVGE-TKSKVKATLKNRGIKVNGKIVTQFDHQLKIGD 66

Query: 59  HIEVDG------------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
            I +                + + +   +   +  I  +           V D+      
Sbjct: 67  KIAISKSKKNDQFKSRYVKLVYEDKYLVVVEKNVGILSMGAGHASLNVKKVLDDYFHKTK 126

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF----------------H 150
           +  +   +         L       +  +L    W  +   R                  
Sbjct: 127 QNCTAHVVHRLDRDTSGLMIYAKDMQTEQLLEHDWHNIVYDRRYIAVLSGEMADDEGTIA 186

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             +  +K  +     V  G  Y         +  +++ V   L  G+  +I+        
Sbjct: 187 NWLKDNKSYITYSSPVDNGGKYAVTHFFTIDRTVNHSLVEFKLETGRKNQIRVHAADMGH 246

Query: 211 KVNRLIRISYGP 222
            V     I YG 
Sbjct: 247 PVCG--DIKYGN 256


>gi|295689031|ref|YP_003592724.1| hemolysin A [Caulobacter segnis ATCC 21756]
 gi|295430934|gb|ADG10106.1| hemolysin A [Caulobacter segnis ATCC 21756]
          Length = 243

 Score = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 14/78 (17%), Positives = 28/78 (35%), Gaps = 8/78 (10%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-------VDGVP 66
          R+ +++   G+  SR +    I   RV V G ++ + + ++     I        V    
Sbjct: 5  RIDQLLVERGVFDSRAKARAAIEAGRVAVAGRVVAKPSESIDEDAEIVAAAAHPWVGRGA 64

Query: 67 LRKAERTRLWLYHKPIGL 84
          L+      LW       +
Sbjct: 65 LKLVHALDLWPIPVEGRI 82


>gi|257440241|ref|ZP_05615996.1| ribosomal protein S4 [Faecalibacterium prausnitzii A2-165]
 gi|257197275|gb|EEU95559.1| ribosomal protein S4 [Faecalibacterium prausnitzii A2-165]
          Length = 200

 Score = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+  ++++     VNG  +   +  V + D IEV
Sbjct: 90  RLDNVVFRLGFAQTRRDARQLVSHAHFTVNGKKVNIPSYQVKAGDVIEV 138


>gi|254517498|ref|ZP_05129554.1| ribosomal protein S4 [Clostridium sp. 7_2_43FAA]
 gi|226911247|gb|EEH96448.1| ribosomal protein S4 [Clostridium sp. 7_2_43FAA]
          Length = 206

 Score = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 14/69 (20%), Positives = 23/69 (33%), Gaps = 1/69 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+  V+ R G   SR E  +++      VN   ++  +  V   D I V        + 
Sbjct: 98  MRLDNVVYRLGYGASRAEARQLVNHGHFLVNDKKVDIPSYRVSVNDEITVTEKSRGTEKF 157

Query: 73  TRLWLYHKP 81
                  K 
Sbjct: 158 KTFIENPKT 166


>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 = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 22/238 (9%), Positives = 64/238 (26%), Gaps = 41/238 (17%)

Query: 14  QRVS---KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVP- 66
            R+    K I      +R  ++++I +  V VN IL+++    V   D IE+   +G   
Sbjct: 38  IRIDTYLKFILHKK--NRNFIQKIIEKGFVYVNNILIKK-NYIVKINDVIEIFLPEGKKN 94

Query: 67  ---------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD-- 115
                    +   +   + +  +   +V      +  + +         +     ++   
Sbjct: 95  IIPENLKINIFYEDEYVIIINKQSGLVVHPGKGNESMTLINGLHFYFLKKKNIYNKIPIL 154

Query: 116 -INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----- 169
               +            + +     +   +  ++              KG +I       
Sbjct: 155 VHRIDKGTSGLILVAKDKNILEKIYKQFYINHIKRKYITLVWGYIKNNKGTIICNIGRSL 214

Query: 170 --------------ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                           +      +  +      +   L  G+  +I+   ++    + 
Sbjct: 215 KNRIYMNVFPNGIYGKFSITHYKVLERFKYVTLLKCTLETGRTHQIRVHLKYIGHPIL 272


>gi|224542365|ref|ZP_03682904.1| hypothetical protein CATMIT_01544 [Catenibacterium mitsuokai DSM
          15897]
 gi|224524747|gb|EEF93852.1| hypothetical protein CATMIT_01544 [Catenibacterium mitsuokai DSM
          15897]
          Length = 90

 Score = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRREVERMI-AQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR + + I    RVKVNG + +  A  V   D IEV
Sbjct: 1  MRLDKFLKLSRIIKRRTLSKEISEASRVKVNGKVAK-PATKVKIGDEIEV 49


>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 = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 22/238 (9%), Positives = 64/238 (26%), Gaps = 41/238 (17%)

Query: 14  QRVS---KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVP- 66
            R+    K I      +R  ++++I +  V VN IL+++    V   D IE+   +G   
Sbjct: 37  IRIDTYLKFILHKK--NRNFIQKIIEKGFVYVNNILIKK-NYIVKINDVIEIFLPEGKKN 93

Query: 67  ---------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD-- 115
                    +   +   + +  +   +V      +  + +         +     ++   
Sbjct: 94  IIPENLKINIFYEDEYVIIINKQSGLVVHPGKGNESMTLINGLHFYFLKKKNIYNKIPIL 153

Query: 116 -INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----- 169
               +            + +     +   +  ++              KG +I       
Sbjct: 154 VHRIDKGTSGLILVAKDKNILEKIYKQFYINHIKRKYITLVWGYIKNNKGTIICNIGRSL 213

Query: 170 --------------ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                           +      +  +      +   L  G+  +I+   ++    + 
Sbjct: 214 KNRIYMNVFPNGIYGKFSITHYKVLERFKYVTLLKCTLETGRTHQIRVHLKYIGHPIL 271


>gi|86605518|ref|YP_474281.1| S4 domain-containing protein [Synechococcus sp. JA-3-3Ab]
 gi|86554060|gb|ABC99018.1| S4 domain protein [Synechococcus sp. JA-3-3Ab]
          Length = 93

 Score = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 25/59 (42%), Gaps = 7/59 (11%)

Query: 14 QRVSKVIARAGI----ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           ++ + +   G+        + +++I   +V+VNG +  R    +   D + V G   +
Sbjct: 18 IKLDQFLKLTGVVPTGG---QAKQLIQAGQVRVNGEVETRRGRKLRLGDEVAVAGQVWQ 73


>gi|126173882|ref|YP_001050031.1| RNA-binding S4 domain-containing protein [Shewanella baltica
          OS155]
 gi|153000162|ref|YP_001365843.1| RNA-binding S4 domain-containing protein [Shewanella baltica
          OS185]
 gi|160874789|ref|YP_001554105.1| RNA-binding S4 domain-containing protein [Shewanella baltica
          OS195]
 gi|217973870|ref|YP_002358621.1| RNA-binding S4 domain-containing protein [Shewanella baltica
          OS223]
 gi|304409753|ref|ZP_07391373.1| RNA-binding S4 domain-containing protein [Shewanella baltica
          OS183]
 gi|307304109|ref|ZP_07583862.1| RNA-binding S4 domain-containing protein [Shewanella baltica
          BA175]
 gi|125997087|gb|ABN61162.1| RNA-binding S4 domain protein [Shewanella baltica OS155]
 gi|151364780|gb|ABS07780.1| RNA-binding S4 domain protein [Shewanella baltica OS185]
 gi|160860311|gb|ABX48845.1| RNA-binding S4 domain protein [Shewanella baltica OS195]
 gi|217499005|gb|ACK47198.1| RNA-binding S4 domain protein [Shewanella baltica OS223]
 gi|304352271|gb|EFM16669.1| RNA-binding S4 domain-containing protein [Shewanella baltica
          OS183]
 gi|306913007|gb|EFN43430.1| RNA-binding S4 domain-containing protein [Shewanella baltica
          BA175]
 gi|315267027|gb|ADT93880.1| RNA-binding S4 domain-containing protein [Shewanella baltica
          OS678]
          Length = 76

 Score = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 11/51 (21%), Positives = 24/51 (47%), Gaps = 4/51 (7%)

Query: 20 IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
          ++ AG     E +  I + +V VNG +  R    +++ D +  +G  ++  
Sbjct: 27 MSNAGG----EAKHFIEEGQVTVNGEVETRKRKKIIAGDIVSFNGESVQII 73


>gi|309389171|gb|ADO77051.1| hemolysin A [Halanaerobium praevalens DSM 2228]
          Length = 275

 Score = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 12/38 (31%), Positives = 17/38 (44%)

Query: 27 SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          SR + +R I    V VNG   ++A   +     IE  G
Sbjct: 19 SRSQAKRAIMAGLVFVNGQREDKAGTQIDPAAEIEYKG 56


>gi|260654973|ref|ZP_05860461.1| hemolysin A [Jonquetella anthropi E3_33 E1]
 gi|260630288|gb|EEX48482.1| hemolysin A [Jonquetella anthropi E3_33 E1]
          Length = 269

 Score = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 1/60 (1%)

Query: 7  VQENFTPQRVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          + +   P R+ + + R   AS   E   +I+   V V G  ++     V  T  ++V G 
Sbjct: 1  MSKADRPVRLDRRLVREHFASTDEEARLLISSGLVLVEGRAVDSPDCQVKPTASVKVIGQ 60


>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 = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 36/243 (14%), Positives = 70/243 (28%), Gaps = 41/243 (16%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ KVIA      SR  ++  + ++RV VNG+   +    V   D IE+           
Sbjct: 30  RLDKVIAELFPQYSRSRLQGWLKEERVLVNGVAAAKGNQKVQGMDRIELSPGVLAHMQAL 89

Query: 63  ---DGVP-LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-----GR 113
              D    +         +  +   +V         + +          +         R
Sbjct: 90  IPEDMNLDIVARTNEYTVVNKQAGLVVHPAPGHWTGTLMNGLYHLDPELIHVPRAGIVHR 149

Query: 114 LDINTEGLLLLTNDGGLARVLELP------------STQWLRVYRVRFHGQVDQDKLNLL 161
           LD +T GL+++         L                        +  +  + +D  N L
Sbjct: 150 LDADTTGLMVVARTQETQVKLVQMLQARIVKRVYLAMVWGRISSPLTVNNPLGRDPRNRL 209

Query: 162 KKGIVIQGIC--YGDMQVTLDTQKGSNAWVTVG-LREGKNREIKKVFEFFNW-----KVN 213
           +  +V  G         V           + V  L  G+  +I+   +   +      V 
Sbjct: 210 RMAVVDHGKPAVTHFTPVAFGELLEVPVTLMVCRLETGRTHQIRVHAQHAGFALVADPVY 269

Query: 214 RLI 216
           ++ 
Sbjct: 270 KIK 272


>gi|254516934|ref|ZP_05128992.1| ribosomal protein S4 [gamma proteobacterium NOR5-3]
 gi|219674439|gb|EED30807.1| ribosomal protein S4 [gamma proteobacterium NOR5-3]
          Length = 154

 Score = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+  V+ R G  S R E  +++A + + VNG ++  A+  V + D + +
Sbjct: 45 RLDNVVYRIGFGSTRSESRQLVAHKAILVNGKVVNIASYKVKAGDVVSL 93


>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 = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 6/53 (11%)

Query: 13 PQRVSKVIARA-GIASRREVERMIAQQRVKVNGIL--LERAAVNVMSTDHIEV 62
          P+R+ KVIAR     SR  ++  I    V VNG    +++ A      D + V
Sbjct: 27 PERLDKVIARLIPEHSRSRLQGWIEAGHVLVNGQPGRVKQMA---NPGDKLVV 76


>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 = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 30/242 (12%), Positives = 58/242 (23%), Gaps = 36/242 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           V + F  +RV   +AR    SR  VE +     V+  G  L + +  + + + +EVD   
Sbjct: 8   VPDGFDGERVDAALARMTGLSRSRVEDLCEAGEVRRGGETLAK-SSRLRAGELLEVDLPD 66

Query: 64  ------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                       G+ L   +   + +              DG   +            S 
Sbjct: 67  PRPVEPVATPVEGMELLYEDEDIVVVDKPAGVAAHPSMGWDGPDVLGALKAMHVQVATSG 126

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--------------- 156
                     L +   G +       +   L+                            
Sbjct: 127 AAERQGIVSRLDVGTSGVMIVAKGERAYSVLKRAFREHTVDKVYHALVQGHLDPSSGTID 186

Query: 157 -----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                  +   K  +I+G         +           + L  G+  +I+         
Sbjct: 187 APIGRHPSREWKMAIIEGGRESITHYDVIEAMPGACLAEIHLETGRTHQIRVHMAAVGHP 246

Query: 212 VN 213
             
Sbjct: 247 CV 248


>gi|268608720|ref|ZP_06142447.1| hypothetical protein RflaF_04377 [Ruminococcus flavefaciens FD-1]
          Length = 446

 Score = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 26/234 (11%), Positives = 53/234 (22%), Gaps = 26/234 (11%)

Query: 1   MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERM--IAQQRVKVNGILLERAAVNVMST 57
           MK+  +  E   P  +   +    G+ S+R + ++  I    +  +G  +      V   
Sbjct: 1   MKELKLTVETDAPVTLQNFLIGEKGV-SKRLLTKLKRIDGG-ITRDGKTVRSIDT-VNKG 57

Query: 58  DHIEV---DGVPLRKAERT----------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           D I +   D   L                 +         V       G +         
Sbjct: 58  DVIVLRFGDDSFLEPNPDLDVPAVYESDGVIVFNKPSGMPVHPSIKHQGDTLGNKFAAMF 117

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------DK 157
                            L +     LA        + +    V                +
Sbjct: 118 PDLTFRAVNRLDRDTSGLCVVAKNALAANALQGRCEKVYYAAVTGEIPETGTIDAPIARE 177

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +    V +               G  +   + L  G+  +I+  F +    
Sbjct: 178 RESIIIRCVREDGQRAVTHYRRIAYNGRYSLAEIHLETGRTHQIRVHFSYIGHP 231


>gi|227549559|ref|ZP_03979608.1| RNA-binding S4 domain protein [Corynebacterium lipophiloflavum
          DSM 44291]
 gi|227078323|gb|EEI16286.1| RNA-binding S4 domain protein [Corynebacterium lipophiloflavum
          DSM 44291]
          Length = 95

 Score = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 11/60 (18%), Positives = 25/60 (41%), Gaps = 9/60 (15%)

Query: 10 NFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          +    ++ + +     A +G     + + +IA   V VNG ++     ++   D + V G
Sbjct: 8  SSDSIKLGQFLKLANLAESGG----QAKELIASGEVAVNGEVVTSRGHSLGDADVVSVAG 63


>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 = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 37/247 (14%), Positives = 68/247 (27%), Gaps = 40/247 (16%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--- 61
           +V +    +R+ KV+AR     SR  ++  I  +RV+++G   +     V     IE   
Sbjct: 69  VVPDELAGERLDKVLARVFPEFSRNRLQSWIEAERVRIDGKPAK-IRQPVPLGATIELVP 127

Query: 62  --------VDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
                       P+       + T + +      +V   +     + +   L        
Sbjct: 128 DLLPEQLAFTPEPVPLEIIYEDDTLVVINKPAGMVVHPAAGNWSGTLLNGLLYRYGDAAA 187

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
              R   V RLD  T GL+++         L           R       +  +   +  
Sbjct: 188 GLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLALVWGNMPEEGTIDA 247

Query: 164 GIVIQ-GICYGDMQVTLDTQKGSNAWVT-----------VG-----LREGKNREIKKVFE 206
            I            VT    K +                V      L  G+  +I+    
Sbjct: 248 PIGRDPRERTRMAVVTSAAGKPARTHFRRVDSAIWERQPVTAIHCDLETGRTHQIRVHCA 307

Query: 207 FFNWKVN 213
                + 
Sbjct: 308 HIGHPLL 314


>gi|15615110|ref|NP_243413.1| hypothetical protein BH2547 [Bacillus halodurans C-125]
 gi|10175167|dbj|BAB06266.1| BH2547 [Bacillus halodurans C-125]
          Length = 258

 Score = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 18/50 (36%), Positives = 27/50 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  VI      SR +   ++ + RVKVN  L+E  A+ + + DHI V G
Sbjct: 182 RLDAVIGEMLSLSRAKAAELVEKGRVKVNWKLVESGALTLQAGDHISVRG 231


>gi|293192340|ref|ZP_06609451.1| S4 domain protein [Actinomyces odontolyticus F0309]
 gi|292820255|gb|EFF79249.1| S4 domain protein [Actinomyces odontolyticus F0309]
          Length = 76

 Score = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 10/34 (29%), Positives = 17/34 (50%)

Query: 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          +   +I    V VNG +  R   ++ + D +EVD
Sbjct: 29 QARELIQAGDVTVNGEVETRRGHHLSAGDIVEVD 62


>gi|293400755|ref|ZP_06644900.1| ribosomal protein S4 [Erysipelotrichaceae bacterium 5_2_54FAA]
 gi|291305781|gb|EFE47025.1| ribosomal protein S4 [Erysipelotrichaceae bacterium 5_2_54FAA]
          Length = 200

 Score = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G A +RR   +++    + VNG  ++  +  V     IEV
Sbjct: 93  RLDNLVYRLGFARTRRAARQLVNHGHILVNGKKVDIPSFIVKPGTTIEV 141


>gi|209525994|ref|ZP_03274527.1| hemolysin A [Arthrospira maxima CS-328]
 gi|209493520|gb|EDZ93842.1| hemolysin A [Arthrospira maxima CS-328]
          Length = 278

 Score = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 12/54 (22%), Positives = 26/54 (48%), Gaps = 9/54 (16%)

Query: 14 QRVS-----KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          QR+      + ++     SR++ +R+I    V VN  ++++    V  +  I+V
Sbjct: 3  QRLDTLLVDRHLSD----SRQQAQRLIRAGEVMVNRQVVDKPGTEVDISATIDV 52


>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 = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 37/247 (14%), Positives = 69/247 (27%), Gaps = 40/247 (16%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--- 61
           +V +    +R+ KV+AR     SR  ++  I  +RV+++G   +     V     IE   
Sbjct: 69  VVPDELAGERLDKVLARVFPEFSRNRLQSWIEAERVRIDGKPAK-IRQPVPLGATIELVP 127

Query: 62  --------VDGVP----LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
                       P    +   + T + +      +V   +     + +   L        
Sbjct: 128 DLLPEQLAFTPEPVPLAIVYEDDTLVVINKPAGMVVHPAAGNWSGTLLNGLLYRYGDAAA 187

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
              R   V RLD  T GL+++         L           R       +  +   +  
Sbjct: 188 GLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLALVWGNMPEEGTIDA 247

Query: 164 GIVIQ-GICYGDMQVTLDTQKGSNAWVT-----------VG-----LREGKNREIKKVFE 206
            I            VT  + K +                V      L  G+  +I+    
Sbjct: 248 PIGRDPRERTRMAVVTSASGKPARTHFRRVDSAIWERQPVTAIHCDLETGRTHQIRVHCA 307

Query: 207 FFNWKVN 213
                + 
Sbjct: 308 HIGHPLL 314


>gi|257866598|ref|ZP_05646251.1| ribosomal protein S4 [Enterococcus casseliflavus EC30]
 gi|257872886|ref|ZP_05652539.1| ribosomal protein S4 [Enterococcus casseliflavus EC10]
 gi|257876202|ref|ZP_05655855.1| ribosomal protein S4 [Enterococcus casseliflavus EC20]
 gi|325567299|ref|ZP_08143966.1| 30S ribosomal protein S4 [Enterococcus casseliflavus ATCC 12755]
 gi|257800556|gb|EEV29584.1| ribosomal protein S4 [Enterococcus casseliflavus EC30]
 gi|257807050|gb|EEV35872.1| ribosomal protein S4 [Enterococcus casseliflavus EC10]
 gi|257810368|gb|EEV39188.1| ribosomal protein S4 [Enterococcus casseliflavus EC20]
 gi|325158732|gb|EGC70878.1| 30S ribosomal protein S4 [Enterococcus casseliflavus ATCC 12755]
          Length = 203

 Score = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G+A+ RR+  +++    V V+G  ++  + +V     I V
Sbjct: 93  QRLDNVVYRLGLATTRRQARQLVNHGHVLVDGKRVDIPSYHVEVGQVISV 142


>gi|154498912|ref|ZP_02037290.1| hypothetical protein BACCAP_02904 [Bacteroides capillosus ATCC
           29799]
 gi|150271752|gb|EDM98978.1| hypothetical protein BACCAP_02904 [Bacteroides capillosus ATCC
           29799]
          Length = 200

 Score = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   + R G A +RRE  +++      VNG  ++  +  V + D IEV
Sbjct: 90  RLDNAVYRLGFANTRREARQLVNHGHFTVNGQRVDIPSYLVKAGDVIEV 138


>gi|295108285|emb|CBL22238.1| hemolysin TlyA family protein [Ruminococcus obeum A2-162]
          Length = 269

 Score = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 22/164 (13%), Positives = 47/164 (28%), Gaps = 2/164 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  ++    +A SR + +  I    V V+G   ++A      T  IEV G  L    R 
Sbjct: 4   RLDLLMMERALAPSREKAKAYIMAGNVYVDGQKEDKAGTMFQETVKIEVRGNTLPYVSRG 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L                              ++  G + + +  +     D  L   
Sbjct: 64  GLKLEKAMNHFGVELDGKVCMDVGAST-GGFTDCMLQNGAVKVYSIDVGYGQLDWKLRND 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
             +   +   +  V      +  + + +    +        ++ 
Sbjct: 123 PRVVCMEKTNIRYVLPEDIQEPAQFSSIDVSFISLTKVLLPVRN 166


>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 = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 28/246 (11%), Positives = 71/246 (28%), Gaps = 36/246 (14%)

Query: 1   MKDKNIVQ--ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M++K      +     ++ + +      S R        + +  N  +++     + + D
Sbjct: 1   MENKITFNITKEDEGMKIKEFLKLKNNFSSRFCRASALAKNIFANNKVIK-LNYVLKAGD 59

Query: 59  HIEV--------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            IEV        D  P      +   +   + L   P  +V    +    +     L   
Sbjct: 60  VIEVKLNKEESQDIEPENIPLKVAYEDSDIIVLNKPPFIVVHPTKNYPYGTLANGLLYYF 119

Query: 105 FSRVISV-----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
             +  +       RLD+NT GL+++  +      L+    +     +         +   
Sbjct: 120 KEKGENCIVRLVSRLDMNTSGLIIVAKNQFSHMSLQRDMNKEEFKKQYLAIVHGKMEADF 179

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAW-------------VTVGLREGKNREIKKVFE 206
                + I       ++  +D +   +               + + L  G+  +I+    
Sbjct: 180 G-TIDLPIYKEEDEPIKRIIDDRGQRSITHYKVIETYSNAQLLKLTLETGRTHQIRVHLS 238

Query: 207 FFNWKV 212
                +
Sbjct: 239 HLGCPI 244


>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 = 49.8 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 39/238 (16%), Positives = 70/238 (29%), Gaps = 32/238 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V E    QR+ +V+A      SR  +++ I    + V+G +  R    V + + I VD  
Sbjct: 10  VPEGLAGQRLDRVLAALFPDYSRSRLQQWIRAGWITVDGAV-RRPRDPVHAGEQISVDAE 68

Query: 66  P--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----S 106
           P              L   +   L +      +V   +   G + V   L          
Sbjct: 69  PEPETPLAPEPIPLRLLYEDDHLLVVDKPAGLVVHPGAGNPGGTLVNALLHYDPGLEALP 128

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL-----------RVYRVRFHGQVDQ 155
           R   V RLD  T G+L++         L                   R            
Sbjct: 129 RAGIVHRLDKETSGVLVVARTYAAHHALVAQLQARTVGRGYQAVVVGRPTAGGRVDAPIA 188

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 K+  V++          +  +  ++  + V L  G+  +I+         + 
Sbjct: 189 RHPRDRKRMAVVETGRPAVTHYRVAERFTAHTLLDVELETGRTHQIRVHMAHCRLPLV 246


>gi|313112851|ref|ZP_07798497.1| ribosomal protein S4 [Faecalibacterium cf. prausnitzii KLE1255]
 gi|310624756|gb|EFQ08065.1| ribosomal protein S4 [Faecalibacterium cf. prausnitzii KLE1255]
          Length = 200

 Score = 49.4 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+  ++++     VNG  +   +  V + D IEV
Sbjct: 90  RLDNVVFRLGFAQTRRDARQLVSHAHFTVNGKKVNIPSYQVKAGDVIEV 138


>gi|289425824|ref|ZP_06427578.1| S4 domain protein [Propionibacterium acnes SK187]
 gi|289426790|ref|ZP_06428518.1| S4 domain protein [Propionibacterium acnes J165]
 gi|289153767|gb|EFD02474.1| S4 domain protein [Propionibacterium acnes SK187]
 gi|289160116|gb|EFD08292.1| S4 domain protein [Propionibacterium acnes J165]
 gi|332675009|gb|AEE71825.1| RNA-binding S4 domain-containing protein [Propionibacterium acnes
          266]
          Length = 76

 Score = 49.4 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 12/58 (20%), Positives = 21/58 (36%), Gaps = 9/58 (15%)

Query: 10 NFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          +    R+ + +     A  G     +   +IA   V VNG +  R    +   D + V
Sbjct: 3  DDQMIRLGQYLKFANLAETGG----QARELIASGMVSVNGEVETRRGRQLHPGDEVTV 56


>gi|153810471|ref|ZP_01963139.1| hypothetical protein RUMOBE_00852 [Ruminococcus obeum ATCC 29174]
 gi|149833650|gb|EDM88731.1| hypothetical protein RUMOBE_00852 [Ruminococcus obeum ATCC 29174]
          Length = 269

 Score = 49.4 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 22/164 (13%), Positives = 48/164 (29%), Gaps = 2/164 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  ++    +A SR + +  I    V V+G   ++A      T  IEV G  L    R 
Sbjct: 4   RLDLLMVERALAPSREKAKAYIMSGDVYVDGQKEDKAGTMFKETVKIEVRGNTLPYVSRG 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L         +                    ++  G + + +  +     D  L   
Sbjct: 64  GLKLEKAMNNFGVSLDGKVCMDVGAST-GGFTDCMLQNGAVKVYSIDVGYGQLDWKLRND 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
             +   +   +  V      +  + + +    +        ++ 
Sbjct: 123 PRVVCMEKTNIRYVLPENLQEPAQFSSIDVSFISLTKVLLPVRN 166


>gi|332678564|gb|AEE87693.1| Ribosomal large subunit pseudouridine synthase D [Francisella cf.
           novicida Fx1]
          Length = 332

 Score = 49.4 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 29/239 (12%), Positives = 67/239 (28%), Gaps = 32/239 (13%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           I+      +R+  VI       SR ++++ + +  + VNG    +    V+  + +E++ 
Sbjct: 15  IMHPKDAGKRIDVVINEQFEQFSRAQIQKWLKEGSITVNGR-ATKPKHIVLGDEEVEINI 73

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L   E     +  K I         D    +  +  +          L    +    L
Sbjct: 74  ELLPTNEWIAEDINLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNALLHRYKDQDKL 133

Query: 125 TNDGGLA---------RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
              G +           V    S  +  + +     +V +  L +++  I  +G     +
Sbjct: 134 PRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGEIYQEGTINQPI 193

Query: 176 ---------------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                  T          +   L  G+  +I+   +     + 
Sbjct: 194 GRDPTNRTKMAINYRGKEAITHYTPIEVYDGFTLIECQLETGRTHQIRVHMKSIKHPLV 252


>gi|315125002|ref|YP_004067006.1| ribosomal protein S4 [Campylobacter jejuni subsp. jejuni
           ICDCCJ07001]
 gi|315018724|gb|ADT66817.1| ribosomal protein S4 [Campylobacter jejuni subsp. jejuni
           ICDCCJ07001]
          Length = 208

 Score = 49.4 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G A+ RR   +++    V VNG  ++  +  V +   IE+
Sbjct: 98  QRLDNVVYRMGFATTRRFARQLVTHGHVLVNGKRVDIPSFRVEAGAKIEI 147


>gi|302390984|ref|YP_003826804.1| 30S ribosomal protein S4P [Acetohalobium arabaticum DSM 5501]
 gi|302203061|gb|ADL11739.1| SSU ribosomal protein S4P [Acetohalobium arabaticum DSM 5501]
          Length = 208

 Score = 49.4 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 1/51 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++ R G A SR E  +++      VNG  ++  +  V   D +EV  
Sbjct: 99  RLDNIVYRLGFAASRNEARQLVRHGHFLVNGERVDIPSYLVEEGDEVEVKD 149


>gi|226323202|ref|ZP_03798720.1| hypothetical protein COPCOM_00974 [Coprococcus comes ATCC 27758]
 gi|225208392|gb|EEG90746.1| hypothetical protein COPCOM_00974 [Coprococcus comes ATCC 27758]
          Length = 277

 Score = 49.4 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 25/178 (14%), Positives = 57/178 (32%), Gaps = 2/178 (1%)

Query: 14  QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++ +  +AS RE  + +I    V V+G   ++A  +      IEV G  L    R
Sbjct: 3   ERLDVLLVKRNLASSREKAKAIIMSGNVFVDGQREDKAGTSFSEEVQIEVRGHALPYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L            +    + V  +       ++  G + +    +     D  L +
Sbjct: 63  GGLKLEKAMKNFDV-SMEGKVCTDVGSSTGGFTDCMLQNGAVKVFAIDVGHGQLDWKLRQ 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +   +   +  V+     +    + +    +        ++  L       A + 
Sbjct: 122 DERVVCMEKTNIRYVQPEDLGEPIDFSSIDVSFISLTKVLLPIRNYLKENGEIVALIK 179


>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 = 49.4 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 36/230 (15%), Positives = 71/230 (30%), Gaps = 34/230 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P       
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGR 113
                   +   + T + +      +V   +     + +   L          R   V R
Sbjct: 99  VPEPMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRV------------YRVRFHGQVDQDKLNLL 161
           LD  T GL+++         L     +                +  +   Q+ +D  N L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K   V  G       V +  +  +++++   L  G+  +I+      N  
Sbjct: 219 KMAAVKFGGKPAVTHVKVLERYLAHSYIECSLGTGRTHQIRVHMREANHP 268


>gi|134103275|ref|YP_001108936.1| PE-PGRS family protein [Saccharopolyspora erythraea NRRL 2338]
 gi|133915898|emb|CAM06011.1| PE-PGRS family protein [Saccharopolyspora erythraea NRRL 2338]
          Length = 1984

 Score = 49.4 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 9/106 (8%), Positives = 16/106 (15%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                      AP      + R                     +      Q     P   
Sbjct: 721 AQRPHPPRRGGAPEAPGVPVQRGDAPGRRPAGPGRGPEAPEGPRAEAPRPQTPGHRPDGP 780

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           R                 +        +   P  P   + R  + +
Sbjct: 781 RPDFHRPGGPVPNSPRPDAPRPNTPHPNGPRPDAPRPEASRPGAPR 826



 Score = 47.1 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 13/110 (11%), Positives = 25/110 (22%), Gaps = 3/110 (2%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P      +    A   +  T  R +    ++ P    R     +    + +         
Sbjct: 692 PRGRGPERPGAPAGPRAGATPSRPQAGPDAQRPHPPRRGGAPEAPGVPVQRGDAPGRRPA 751

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRR---SPSFPSKRSLRRTSAK 353
                          +      G R +  R     P  P   S R  + +
Sbjct: 752 GPGRGPEAPEGPRAEAPRPQTPGHRPDGPRPDFHRPGGPVPNSPRPDAPR 801



 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 7/112 (6%), Positives = 22/112 (19%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +   P          ++P   +       PN            +  + + +G   +    
Sbjct: 778 DGPRPDFHRPGGPVPNSPRPDAPRPNTPHPNGPRPDAPRPEASRPGAPRPDGTRPEALRP 837

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                     +                 R +    +     +    R+   +
Sbjct: 838 GTPQANAPRPDAPRPDAPRPGAPRTDASRPDGPHPNRPEGLRPDGPRSDGPR 889



 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 8/86 (9%), Positives = 19/86 (22%), Gaps = 4/86 (4%)

Query: 272 PNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ- 330
           P      P      +    ++ G     +      R     +             ++   
Sbjct: 679 PGAAGRAPAGPDSPRGRGPERPGAPAGPRAGATPSRPQAGPDAQRPHPPRRGGAPEAPGV 738

Query: 331 ---REENHRRSPSFPSKRSLRRTSAK 353
              R +   R P+ P +        +
Sbjct: 739 PVQRGDAPGRRPAGPGRGPEAPEGPR 764



 Score = 44.8 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 12/109 (11%), Positives = 21/109 (19%), Gaps = 2/109 (1%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                                   RP      P+     +  + +      +     P  
Sbjct: 725 HPPRRGGAPEAPGVPVQRGDAPGRRPAGPGRGPEAPEGPRAEAPRPQTPGHRPDGPRPDF 784

Query: 307 RRNLAS--NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            R      N         +    +G R +  R   S P       T  +
Sbjct: 785 HRPGGPVPNSPRPDAPRPNTPHPNGPRPDAPRPEASRPGAPRPDGTRPE 833



 Score = 44.0 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 14/94 (14%), Positives = 21/94 (22%), Gaps = 3/94 (3%)

Query: 263 SSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHS 322
           S     R      S       R    +  + G +  +  A P  +R        A     
Sbjct: 678 SPGAAGRAPAGPDSPRGRGPERPGAPAGPRAGATPSRPQAGPDAQRPHPPRRGGAPEAPG 737

Query: 323 ---SFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                    G+R     R P  P          +
Sbjct: 738 VPVQRGDAPGRRPAGPGRGPEAPEGPRAEAPRPQ 771



 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 11/114 (9%), Positives = 19/114 (16%), Gaps = 4/114 (3%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E       E  +                RP             + N+   NG        
Sbjct: 758 EAPEGPRAEAPRPQTPGHRPDGPRPDFHRPGGPVPNSPRPDAPRPNTPHPNGPRPDAPRP 817

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR----SLRRTSA 352
                     +    + +       +  R +  R     P       S      
Sbjct: 818 EASRPGAPRPDGTRPEALRPGTPQANAPRPDAPRPDAPRPGAPRTDASRPDGPH 871



 Score = 41.7 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 10/107 (9%), Positives = 18/107 (16%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           GP                 +    +     +   +               + +   + P 
Sbjct: 809 GPRPDAPRPEASRPGAPRPDGTRPEALRPGTPQANAPRPDAPRPDAPRPGAPRTDASRPD 868

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                        G  S        R +  R   S P    L     
Sbjct: 869 GPHPNRPEGLRPDGPRSDGPRPEVIRPDGPRPDASRPDAPRLDGPRP 915



 Score = 40.9 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 11/111 (9%), Positives = 16/111 (14%), Gaps = 5/111 (4%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              +        P    E     R                                P   
Sbjct: 741 QRGDAPGRRPAGPGRGPEAPEGPRAEAPRPQTPGHRPDGPRPDFHRPGGPVPNSPRPDAP 800

Query: 308 RN--LASNVWMAKGIHSSFLSDSGQREENHRR---SPSFPSKRSLRRTSAK 353
           R      N                 R +  R     P  P   + R  + +
Sbjct: 801 RPNTPHPNGPRPDAPRPEASRPGAPRPDGTRPEALRPGTPQANAPRPDAPR 851



 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 5/106 (4%), Positives = 11/106 (10%), Gaps = 4/106 (3%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
             + LR                                                      
Sbjct: 831 RPEALRPGTPQANAPRPDAPRPDAPRPGAPRTDASRPDGPHPNRPEGLRPDGPRSDGPRP 890

Query: 297 KQKKLATPVHRRNLASNVW----MAKGIHSSFLSDSGQREENHRRS 338
           +  +   P    +                      +  R +   R 
Sbjct: 891 EVIRPDGPRPDASRPDAPRLDGPRPDAPRPDGPHPAVSRPDAPNRR 936


>gi|22299704|ref|NP_682951.1| hypothetical protein tlr2161 [Thermosynechococcus elongatus BP-1]
 gi|22295888|dbj|BAC09713.1| tlr2161 [Thermosynechococcus elongatus BP-1]
          Length = 243

 Score = 49.4 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 2/65 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             +  +       R+  V A AG   SR ++   I+Q  V+VN  ++++    +   D I
Sbjct: 156 PQRKSLSTVEASLRLDAV-ASAGFGVSRSKMSEWISQGLVRVNWQVVQQPRYLLKVNDLI 214

Query: 61  EVDGV 65
            + G 
Sbjct: 215 AIRGK 219


>gi|86152218|ref|ZP_01070429.1| ribosomal protein S4 [Campylobacter jejuni subsp. jejuni 260.94]
 gi|86153129|ref|ZP_01071334.1| ribosomal protein S4 [Campylobacter jejuni subsp. jejuni HB93-13]
 gi|121612243|ref|YP_001001237.1| 30S ribosomal protein S4 [Campylobacter jejuni subsp. jejuni
           81-176]
 gi|153952009|ref|YP_001398874.1| 30S ribosomal protein S4 [Campylobacter jejuni subsp. doylei
           269.97]
 gi|157415814|ref|YP_001483070.1| 30S ribosomal protein S4 [Campylobacter jejuni subsp. jejuni 81116]
 gi|167006130|ref|ZP_02271888.1| 30S ribosomal protein S4 [Campylobacter jejuni subsp. jejuni
           81-176]
 gi|283956978|ref|ZP_06374450.1| ribosomal protein S4 [Campylobacter jejuni subsp. jejuni 1336]
 gi|152060941|sp|A1W1J6|RS4_CAMJJ RecName: Full=30S ribosomal protein S4
 gi|171769457|sp|A7H5U4|RS4_CAMJD RecName: Full=30S ribosomal protein S4
 gi|172047193|sp|A8FNQ6|RS4_CAMJ8 RecName: Full=30S ribosomal protein S4
 gi|85840707|gb|EAQ57958.1| ribosomal protein S4 [Campylobacter jejuni subsp. jejuni 260.94]
 gi|85844014|gb|EAQ61224.1| ribosomal protein S4 [Campylobacter jejuni subsp. jejuni HB93-13]
 gi|87249805|gb|EAQ72764.1| ribosomal protein S4 [Campylobacter jejuni subsp. jejuni 81-176]
 gi|152939455|gb|ABS44196.1| ribosomal protein S4 [Campylobacter jejuni subsp. doylei 269.97]
 gi|157386778|gb|ABV53093.1| 30S ribosomal protein S4 [Campylobacter jejuni subsp. jejuni 81116]
 gi|283791479|gb|EFC30276.1| ribosomal protein S4 [Campylobacter jejuni subsp. jejuni 1336]
 gi|307748451|gb|ADN91721.1| 30S ribosomal protein S4 [Campylobacter jejuni subsp. jejuni M1]
 gi|315931273|gb|EFV10243.1| ribosomal protein S4 [Campylobacter jejuni subsp. jejuni 327]
          Length = 208

 Score = 49.4 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G A+ RR   +++    V VNG  ++  +  V +   IE+
Sbjct: 98  QRLDNVVYRMGFATTRRFARQLVTHGHVLVNGKRVDIPSFRVEAGAKIEI 147


>gi|323144988|ref|ZP_08079548.1| ribosomal protein S4 [Succinatimonas hippei YIT 12066]
 gi|322415267|gb|EFY06041.1| ribosomal protein S4 [Succinatimonas hippei YIT 12066]
          Length = 207

 Score = 49.4 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VN  ++   +  V  +D I V
Sbjct: 97  RLDNVVYRMGFGSTRMEARQLVSHKAITVNDHVVNIPSYQVQPSDVIAV 145


>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 = 49.4 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 34/248 (13%), Positives = 66/248 (26%), Gaps = 44/248 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           I  +   P RV K +       +R ++++      V VN   ++     V + D I V  
Sbjct: 28  IADKGQEPLRVDKFLMNRVEGATRNKIQQACDNGMVIVNDKPVKS-NYKVKAHDRIVVYS 86

Query: 63  -----DGVPLR-------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                +   +          E   L + +K  G+V      +   T+ + L        +
Sbjct: 87  NKNPENTQVIPEELPLNIIYEDEDLMIINKLPGMVVHPGCGNYTGTLVNGLAWYLGDHTT 146

Query: 111 V-------------GRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRV 144
                          R+D NT GLL++         L                       
Sbjct: 147 TPAPEPSIPRFGLVHRIDKNTSGLLVVAKSEKAMNDLAKQFFDHTVQRRYLALVWGDFEE 206

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIK 202
                   V + +          +G    +        +  N    +   L  G+  +I+
Sbjct: 207 DEGTIEAHVGRHQRFRKIMDAYPEGEYGKEAITHYKVLERFNYVTLIECRLETGRTHQIR 266

Query: 203 KVFEFFNW 210
              +    
Sbjct: 267 VHMQHIGH 274


>gi|89076300|ref|ZP_01162641.1| 30S ribosomal protein S4 [Photobacterium sp. SKA34]
 gi|90581702|ref|ZP_01237490.1| 30S ribosomal protein S4 [Vibrio angustum S14]
 gi|330447013|ref|ZP_08310663.1| ribosomal protein S4 [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|89048004|gb|EAR53593.1| 30S ribosomal protein S4 [Photobacterium sp. SKA34]
 gi|90437117|gb|EAS62320.1| 30S ribosomal protein S4 [Vibrio angustum S14]
 gi|328491204|dbj|GAA05160.1| ribosomal protein S4 [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 206

 Score = 49.4 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V + D + +
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAILVNGQVVNVPSFKVAANDVVSI 145


>gi|330977498|gb|EGH77444.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. aptata str. DSM 50252]
          Length = 320

 Score = 49.4 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 31/236 (13%), Positives = 63/236 (26%), Gaps = 40/236 (16%)

Query: 13  PQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMST------------- 57
            QR+ +V A    A  SR  +   I   R+ V+G +L      V                
Sbjct: 17  GQRLDQV-AAQLFAEHSRSRLSAWIKDGRLTVDGGVLR-PRDIVHGGAVLELIAEQEAQG 74

Query: 58  ----DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
                 IE+D   +   +   L +      +V   +     + +   L  +   +     
Sbjct: 75  EWVAQDIELD---IIYEDDQILVINKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRA 131

Query: 114 LDINTEGL----------------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
             ++                     L+T     +            V             
Sbjct: 132 GIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVTAGGKIDAPIGRH 191

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               ++  V++G         +  +  S+  V V L  G+  +I+      N+ + 
Sbjct: 192 GQQRQRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINYPLV 247


>gi|309778473|ref|ZP_07673375.1| ribosomal protein S4 [Erysipelotrichaceae bacterium 3_1_53]
 gi|308913769|gb|EFP59607.1| ribosomal protein S4 [Erysipelotrichaceae bacterium 3_1_53]
          Length = 200

 Score = 49.4 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +I R G A +RR   +++    + VNG  ++  +        +EV
Sbjct: 93  RLDNLIYRMGFARTRRAARQLVNHGHILVNGKKVDIPSFIAKPGMVVEV 141


>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 = 49.4 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 79/247 (31%), Gaps = 35/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M +K ++       RV  V++      SR  +   +    + VN   ++R +  V+S D 
Sbjct: 1   MANKILIHITDQAGRVDAVLSKENLSYSRTTLSNWLVDGTILVNNHKVKR-SYKVVSGDT 59

Query: 60  IEV------------DGVPLRKAERTRL--WLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I +            + +PL           +      +V   +     + V   L    
Sbjct: 60  ISITPPETQETKIEAENIPLDIIYEDDDIIVVNKPQGMVVHPAAGHSSGTLVNALLHHSP 119

Query: 106 -------SRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
                   R   V R+D +T GLL++  +      L     S +  RVY     G+  +D
Sbjct: 120 LSTINGEFRPGIVHRIDRDTSGLLMVAKNDKAHHSLSEQLKSHKNQRVYYALVRGEFTED 179

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                          KK  VI+G         +  +      + V L  G+  +I+    
Sbjct: 180 SGTIEAPIGRHKIDRKKQAVIEGGREAVTHFRVLKRYVGYTLLKVNLETGRTHQIRVHMS 239

Query: 207 FFNWKVN 213
           +    V 
Sbjct: 240 YIGHPVV 246


>gi|227824343|ref|ZP_03989175.1| pseudouridine synthase [Acidaminococcus sp. D21]
 gi|226904842|gb|EEH90760.1| pseudouridine synthase [Acidaminococcus sp. D21]
          Length = 311

 Score = 49.4 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 33/240 (13%), Positives = 68/240 (28%), Gaps = 36/240 (15%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           E     R    +A     SR  ++  + +  V   G  ++ A+  V   D   V      
Sbjct: 15  EKDQGLRADCYLADVLDLSRSSLQHDMEKGLVTKEGKPVK-ASYKVKLGDVFTVVIPPAV 73

Query: 63  ----DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-------- 106
               +  P+       +   + +      +V   +     + V   L             
Sbjct: 74  SLEAEPEPIPLAILYEDEDVIVVNKPRGMVVHPAAGNYTGTLVNALLYHCKDLSGINGVV 133

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY-------------RVRFHGQV 153
           R   V RLD +T G+++   +      L                        R      +
Sbjct: 134 RPGIVHRLDKDTSGVMVCAKNDRAHLSLSQQIKDKEAKRTYIAVVRGNIKDDRGHIETLI 193

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           D+D  + ++  +V  G         +  + G    V   L+ G+  +I+    +    + 
Sbjct: 194 DRDPKDRMRMAVVPSGGRLAVTDYEVLERYGRFTVVRCRLQTGRTHQIRVHMTYLGHPLV 253


>gi|171060594|ref|YP_001792943.1| 30S ribosomal protein S4 [Leptothrix cholodnii SP-6]
 gi|226699083|sp|B1Y7N0|RS4_LEPCP RecName: Full=30S ribosomal protein S4
 gi|170778039|gb|ACB36178.1| ribosomal protein S4 [Leptothrix cholodnii SP-6]
          Length = 207

 Score = 49.4 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + V VNG  +   +  V + D I V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAVTVNGQSVNIPSYLVKAGDVISV 146


>gi|315304053|ref|ZP_07874473.1| S4 domain-containing protein [Listeria ivanovii FSL F6-596]
 gi|313627577|gb|EFR96290.1| S4 domain-containing protein [Listeria ivanovii FSL F6-596]
          Length = 258

 Score = 49.4 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 22/50 (44%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
             +  R+  +I+ A   SR++ ++++    VKVN   +E         D 
Sbjct: 178 TVSSMRLDVIISSAHHISRQKAKQLVVAGLVKVNWKTVENPDFECEEEDV 227


>gi|149193898|ref|ZP_01870996.1| Hemolysin A [Caminibacter mediatlanticus TB-2]
 gi|149135851|gb|EDM24329.1| Hemolysin A [Caminibacter mediatlanticus TB-2]
          Length = 238

 Score = 49.4 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 16/183 (8%), Positives = 58/183 (31%), Gaps = 5/183 (2%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+ + + +   + +R + + +I  ++VKVN  ++++ +  +   D IE+     +    
Sbjct: 1   MRLDEALVKRDLVETRSKAKELIKNEKVKVNDKIIKKPSFEIKDNDKIEI---LQKVYVS 57

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              W     +              V  +        +  G   +    +        +  
Sbjct: 58  RAAWKLKNYLNKYNISFKEKSVLDVGASTGGFSEVSLEKGAKKVVCVDVGSNQLHPKIKE 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDK-LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
            +++ + +   +   +++ + D           + I  +     +  +         V +
Sbjct: 118 NMKVENFENTDIRDFKYNEKFDIVVSDVSFISLLKIIDVIDKFAKSDIILLFKPQFEVGI 177

Query: 192 GLR 194
            ++
Sbjct: 178 EVK 180


>gi|94968074|ref|YP_590122.1| hemolysin A [Candidatus Koribacter versatilis Ellin345]
 gi|94550124|gb|ABF40048.1| hemolysin A [Candidatus Koribacter versatilis Ellin345]
          Length = 252

 Score = 49.4 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 1/57 (1%)

Query: 14 QRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+ K++  RA + SR   + MI   RV VN   +E+A  NV     I + G  LR 
Sbjct: 3  VRLDKLLVERALVPSRERAQAMILAGRVLVNEQKVEKAGANVEDDSAIRLLGDDLRY 59


>gi|302185255|ref|ZP_07261928.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           syringae 642]
          Length = 320

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 31/236 (13%), Positives = 63/236 (26%), Gaps = 40/236 (16%)

Query: 13  PQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMST------------- 57
            QR+ +V A    A  SR  +   I   R+ V+G +L      V                
Sbjct: 17  GQRLDQV-AAQLFAEHSRSRLSAWIKDGRLTVDGGVLR-PRDIVHGGAVLELVAEQEAQG 74

Query: 58  ----DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
                 IE+D   +   +   L +      +V   +     + +   L  +   +     
Sbjct: 75  EWVAQDIELD---IIYEDDQILVINKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRA 131

Query: 114 LDINTEGL----------------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
             ++                     L+T     +            V             
Sbjct: 132 GIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVTAGGKIDAPIGRH 191

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               ++  V++G         +  +  S+  V V L  G+  +I+      N+ + 
Sbjct: 192 GQQRQRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINYPLV 247


>gi|255994615|ref|ZP_05427750.1| hemolysin A [Eubacterium saphenum ATCC 49989]
 gi|255993328|gb|EEU03417.1| hemolysin A [Eubacterium saphenum ATCC 49989]
          Length = 272

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+ K++   G   SR + ++ I+   V+V G +  ++A  V S   I +    L  
Sbjct: 1  MRIDKLLVEEGYYESREKAQQAISAGEVEVEGKICLKSASQVSSKARINIRNDRLPY 57


>gi|156310431|ref|XP_001617741.1| hypothetical protein NEMVEDRAFT_v1g156832 [Nematostella vectensis]
 gi|156195585|gb|EDO25641.1| predicted protein [Nematostella vectensis]
          Length = 207

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V   D + V
Sbjct: 98  RLDNVVYRMGFGSTRSEARQLVSHKAITVNGQSVNIPSYMVKVGDVVAV 146


>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 = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 31/236 (13%), Positives = 63/236 (26%), Gaps = 40/236 (16%)

Query: 13  PQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMST------------- 57
            QR+ +V A    A  SR  +   I   R+ V+G +L      V                
Sbjct: 17  GQRLDQV-AAQLFAEHSRSRLSAWIKDGRLTVDGGVLR-PRDIVHGGAVLELIAEQEAQG 74

Query: 58  ----DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
                 IE+D   +   +   L +      +V   +     + +   L  +   +     
Sbjct: 75  EWVAQDIELD---IIYEDDQILVINKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRA 131

Query: 114 LDINTEGL----------------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
             ++                     L+T     +            V             
Sbjct: 132 GIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVTAGGKIDAPIGRH 191

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               ++  V++G         +  +  S+  V V L  G+  +I+      N+ + 
Sbjct: 192 GQQRQRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINYPLV 247


>gi|297170431|gb|ADI21463.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium HF0070_10G19]
          Length = 312

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 33/251 (13%), Positives = 65/251 (25%), Gaps = 45/251 (17%)

Query: 1   MKDKNIVQENFTPQRVS----KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           +KDK  V E     R+     K + R    SR +++  I    V++N    +     ++S
Sbjct: 2   IKDKFFVDETMHGTRLDIAITKYLGRK--YSRNQIKNFILGGCVQINDENCK-PKDKLVS 58

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            D IE +            W+  K    V   ++         NL          G L  
Sbjct: 59  GDEIEFNFN----DYHDSSWMPEKIDFNVIDETNDYIIVEKSPNLIMHPGAGNEQGTLAN 114

Query: 117 NTEGLLLLTNDGGLARVLEL------------PSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                           ++               + ++       F  +  +     L KG
Sbjct: 115 GLLFRFPELAKLPRCGIVHRLDKDTSGLLVVAKTNEFRNHIVSEFQNRNVKKYYYALIKG 174

Query: 165 IVIQ----GICYGDMQVTLDTQKGSN------------------AWVTVGLREGKNREIK 202
            ++            +                            + V V +  G+  +I+
Sbjct: 175 NILGQIIINEPILRDKSNRIRMTVDQAGREATSIVKNIETFDFYSLVEVEILTGRTHQIR 234

Query: 203 KVFEFFNWKVN 213
              +F    + 
Sbjct: 235 VHMDFNKTPII 245


>gi|312884679|ref|ZP_07744380.1| 30S ribosomal protein S4 [Vibrio caribbenthicus ATCC BAA-2122]
 gi|309367592|gb|EFP95143.1| 30S ribosomal protein S4 [Vibrio caribbenthicus ATCC BAA-2122]
          Length = 206

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V + D + +
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAILVNGKVVNVPSFKVAANDVVSI 145


>gi|257468836|ref|ZP_05632930.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           ulcerans ATCC 49185]
          Length = 342

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 26/242 (10%), Positives = 72/242 (29%), Gaps = 36/242 (14%)

Query: 8   QENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
            EN   +R+   +      A+R  ++++I    V++ G  + ++   +  T+ I V+   
Sbjct: 42  DENDKGKRIDSFLNEVIDDATRSYIQKIIDGGYVEITGKKVTKSGNKLKGTETITVNIPE 101

Query: 64  GVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
              L              ++  + +   P  +V         + V   L  I       G
Sbjct: 102 DEILDVIPENIPLNIIYEDKDIVVINKAPDMVVHPAHGNYNGTLVNALLYHIKDLSTING 161

Query: 113 RLDINTEGLLLLTNDGGLA------------RVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
            +       L     G +              + +  + +   +   +   +    ++  
Sbjct: 162 VIRPGIVHRLDKDTSGVIVVAKNDEAHSTLSDMFKEKTLEKTYICIAKGIFKDKSGRIET 221

Query: 161 LKKGIVIQGICYGDMQ---------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           L             +            +  ++ + + V V +  G+  +I+   ++ N  
Sbjct: 222 LIGRDSRDRKKMAVVDINGKNAISNYEILDEEKNFSLVKVRIETGRTHQIRVHMKYLNHP 281

Query: 212 VN 213
           + 
Sbjct: 282 IL 283


>gi|227501160|ref|ZP_03931209.1| ribosomal protein S4 [Anaerococcus tetradius ATCC 35098]
 gi|227216745|gb|EEI82146.1| ribosomal protein S4 [Anaerococcus tetradius ATCC 35098]
          Length = 197

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V  R+G+A +RRE  +++    + VNG+ ++  +  V   D IEV
Sbjct: 88  RLDNVAFRSGLARTRREARQIVTHGHLTVNGVQVDIPSYKVSEGDVIEV 136


>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 = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 27/243 (11%), Positives = 65/243 (26%), Gaps = 37/243 (15%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V+      R+ + +A      SR   +R+I   +V +N       +  V + D + V  
Sbjct: 9   VVEAANEGDRLDRYVADHVPDLSRTYAQRLIEAAQVLLNNRQAR-PSTPVHAGDTVTVHL 67

Query: 63  --------------------DGVPLRKAERTRLWLYHKPIG------------LVTTHSD 90
                               D   +   +   + ++  P                    +
Sbjct: 68  PAPQPVGLVAEPLPLQIVYEDRDVVVIDKPASMVVHPAPGHDRGTLVNALIARYPEMAIN 127

Query: 91  PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
            D R  +   L    S ++   R +     L        + ++        +        
Sbjct: 128 GDMRPGIVHRLDRDTSGLLVAARNERALRSLQAQQQARTMLKIYLAVVEGRMPELEGVID 187

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + +   + ++  +V  G         +    G    +   L  G+  +I+      N 
Sbjct: 188 APIARHPTDRVRMAVVAGGRPART-HWRVLEDLGEYTLIEARLETGRTHQIRVHCASRNR 246

Query: 211 KVN 213
            + 
Sbjct: 247 PIL 249


>gi|39995572|ref|NP_951523.1| S4 domain-containing protein [Geobacter sulfurreducens PCA]
 gi|39982335|gb|AAR33796.1| S4 domain protein [Geobacter sulfurreducens PCA]
          Length = 71

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 16/66 (24%), Positives = 29/66 (43%), Gaps = 1/66 (1%)

Query: 1  MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          M     ++ +    ++   + A   +AS  E + +IA+  V+VNG    R    +   D 
Sbjct: 1  MPRGEPMKIDTDHIKLDSFLKAANLVASGGEAKIIIAEGAVRVNGETELRRGRKLRPGDQ 60

Query: 60 IEVDGV 65
          +EV G 
Sbjct: 61 VEVAGE 66


>gi|79835462|gb|ABB52091.1| rRNA methylase [Arthrospira platensis]
          Length = 222

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 12/54 (22%), Positives = 26/54 (48%), Gaps = 9/54 (16%)

Query: 14 QRVS-----KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          QR+      + ++     SR++ +R+I    V VN  ++++    V  +  I+V
Sbjct: 3  QRLDTLLVDRHLSE----SRQQAQRLIRAGEVMVNRQVVDKPGTEVDISATIDV 52


>gi|330470145|ref|YP_004407888.1| 30S ribosomal protein S4 [Verrucosispora maris AB-18-032]
 gi|328813116|gb|AEB47288.1| 30S ribosomal protein S4 [Verrucosispora maris AB-18-032]
          Length = 208

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG A SR    +++      VNG  ++  +  V + D IEV
Sbjct: 99  RLDNVVYRAGYAKSRDMARQLVKHGHFTVNGKKVDIPSYRVSAHDIIEV 147


>gi|317051101|ref|YP_004112217.1| hemolysin A [Desulfurispirillum indicum S5]
 gi|316946185|gb|ADU65661.1| hemolysin A [Desulfurispirillum indicum S5]
          Length = 253

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 11/64 (17%), Positives = 24/64 (37%), Gaps = 1/64 (1%)

Query: 7  VQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          + +     R+ K++  R  + SR   + +I    V VN   +++    V     I +   
Sbjct: 1  MNQKTPRTRLDKLLVDRELVKSRERAKALIMAGAVIVNDHRIDKPGTTVPDDATIRLKVK 60

Query: 66 PLRK 69
           +  
Sbjct: 61 DIPY 64


>gi|160896494|ref|YP_001562076.1| 30S ribosomal protein S4 [Delftia acidovorans SPH-1]
 gi|226697834|sp|A9BRX4|RS4_DELAS RecName: Full=30S ribosomal protein S4
 gi|160362078|gb|ABX33691.1| ribosomal protein S4 [Delftia acidovorans SPH-1]
          Length = 207

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V   D + V
Sbjct: 98  RLDNVVYRMGFGSTRSEARQLVSHKAITVNGQSVNIPSYMVKVGDVVAV 146


>gi|330988806|gb|EGH86909.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           lachrymans str. M301315]
          Length = 320

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 31/236 (13%), Positives = 63/236 (26%), Gaps = 40/236 (16%)

Query: 13  PQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMST------------- 57
            QR+ +V A    A  SR  +   I   R+ V+G +L      V                
Sbjct: 17  GQRLDQV-AAQLFAEHSRSRLSAWIKDGRLTVDGGVLR-PRDIVHGGAVLELIAEQEAQG 74

Query: 58  ----DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
                 IE+D   +   +   L +      +V   +     + +   L  +   +     
Sbjct: 75  EWVAQDIELD---IIYEDDQILVINKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRA 131

Query: 114 LDINTEG----------------LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
             ++                     L+T     +            V             
Sbjct: 132 GIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVTAGGKIDAPIGRH 191

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               ++  V++G         +  +  S+  V V L  G+  +I+      N+ + 
Sbjct: 192 GQQRQRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINYPLV 247


>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 = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 31/236 (13%), Positives = 63/236 (26%), Gaps = 40/236 (16%)

Query: 13  PQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMST------------- 57
            QR+ +V A    A  SR  +   I   R+ V+G +L      V                
Sbjct: 17  GQRLDQV-AAQLFAEHSRSRLSAWIKDGRLTVDGGVLR-PRDIVHGGAVLELIAEQEAQG 74

Query: 58  ----DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
                 IE+D   +   +   L +      +V   +     + +   L  +   +     
Sbjct: 75  EWVAQDIELD---IIYEDDQILVINKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRA 131

Query: 114 LDINTEGL----------------LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
             ++                     L+T     +            V             
Sbjct: 132 GIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVTAGGKIDAPIGRH 191

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               ++  V++G         +  +  S+  V V L  G+  +I+      N+ + 
Sbjct: 192 GQQRQRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINYPLV 247


>gi|164686444|ref|ZP_02210472.1| hypothetical protein CLOBAR_00009 [Clostridium bartlettii DSM
          16795]
 gi|164604455|gb|EDQ97920.1| hypothetical protein CLOBAR_00009 [Clostridium bartlettii DSM
          16795]
          Length = 68

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 13/64 (20%), Positives = 27/64 (42%), Gaps = 9/64 (14%)

Query: 10 NFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
               ++ + +     A  G       + +I +  VKVNG +  R    ++  D +EV+G
Sbjct: 7  ESEYIKLDQFLKLADIASTGG----HAKYLIQEGVVKVNGEVEMRRGKKLVPGDIVEVEG 62

Query: 65 VPLR 68
            ++
Sbjct: 63 NQIK 66


>gi|50842085|ref|YP_055312.1| hypothetical protein PPA0599 [Propionibacterium acnes KPA171202]
 gi|50839687|gb|AAT82354.1| conserved protein [Propionibacterium acnes KPA171202]
          Length = 76

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 12/58 (20%), Positives = 21/58 (36%), Gaps = 9/58 (15%)

Query: 10 NFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          +    R+ + +     A  G     +   +IA   V VNG +  R    +   D + V
Sbjct: 3  DDQMIRLGQYLKFANLAETGG----QARELIASGMVSVNGKVETRRGRQLHPGDEVTV 56


>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 = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 35/245 (14%), Positives = 77/245 (31%), Gaps = 33/245 (13%)

Query: 2   KDKNIVQEN---FTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           K K  +++       +R+ K IA      SR ++++ I   +VKVN I +     N+   
Sbjct: 3   KYKFFIKKTCISQNGKRLDKSIAEIFPEYSRNKIKKFIINNQVKVNDICIINPKKNIKGG 62

Query: 58  DHIEV----DGVPLRKAERTRLWLYHKPIGLVTTHSD----PDGRSTVFDNLPSIFSRVI 109
           + I++        + K  +T   +Y     LV           G     + L        
Sbjct: 63  ECIKIKISKKNNLISKKRKTYKLIYEDDDILVINKYKDVIVHPGCDKHENTLLHDILFNY 122

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
              +       +  L  D     ++   S    ++ ++     ++++   +L   I+  G
Sbjct: 123 PDSKNLYRAGIVHRLDKDTTGLMLIARNSFSQKKLIKLLKLRLINREYRAVLLGKIICDG 182

Query: 170 ICYGDM---------------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                +                        +       ++V + L  G+  +I+    + 
Sbjct: 183 TVSAPIIRNSKNRTRMKVHISGKESITHYKIIKNFNDFSYVKINLESGRTHQIRLHMSYI 242

Query: 209 NWKVN 213
           N  V 
Sbjct: 243 NHPVL 247


>gi|86149496|ref|ZP_01067727.1| ribosomal protein S4 [Campylobacter jejuni subsp. jejuni CF93-6]
 gi|88596172|ref|ZP_01099409.1| ribosomal protein S4 [Campylobacter jejuni subsp. jejuni 84-25]
 gi|218563183|ref|YP_002344963.1| 30S ribosomal protein S4 [Campylobacter jejuni subsp. jejuni NCTC
           11168]
 gi|26399526|sp|Q9PM81|RS4_CAMJE RecName: Full=30S ribosomal protein S4
 gi|85840278|gb|EAQ57536.1| ribosomal protein S4 [Campylobacter jejuni subsp. jejuni CF93-6]
 gi|88191013|gb|EAQ94985.1| ribosomal protein S4 [Campylobacter jejuni subsp. jejuni 84-25]
 gi|112360890|emb|CAL35691.1| 30S ribosomal protein S4 [Campylobacter jejuni subsp. jejuni NCTC
           11168]
 gi|284926789|gb|ADC29141.1| 30S ribosomal protein S4 [Campylobacter jejuni subsp. jejuni
           IA3902]
 gi|315927660|gb|EFV06991.1| ribosomal protein S4 [Campylobacter jejuni subsp. jejuni DFVF1099]
 gi|315929465|gb|EFV08662.1| ribosomal protein S4 [Campylobacter jejuni subsp. jejuni 305]
          Length = 208

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  ++ R G A+ RR   +++    V VNG  ++  +  V +   IE+
Sbjct: 98  QRLDNIVYRMGFATTRRFARQLVTHGHVLVNGKRVDIPSFRVEAGAKIEI 147


>gi|328881776|emb|CCA55015.1| Ribosomal large subunit pseudouridine synthase D [Streptomyces
           venezuelae ATCC 10712]
          Length = 313

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 26/243 (10%), Positives = 61/243 (25%), Gaps = 37/243 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIE--- 61
           V +    +RV   IAR    SR +   + A  +V+V+G ++ + +  V       +E   
Sbjct: 12  VPDGLEGERVDAAIARMFGFSRTKAAELAAAGKVQVDGSVVGK-SERVSGGAWLEVEMPG 70

Query: 62  -----------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                      V+G+ +   +   + +               G + +     + +    S
Sbjct: 71  AAAPVQIVAEPVEGMEIVHDDDDIVVIMKPIGVAAHPSPGWTGTTVIGGLAAAGYRISTS 130

Query: 111 VGRLDINTEGLLLLTNDGGL-------------ARVLELPSTQWLRVYRVRFHGQVDQDK 157
                      L +   G +              +  E    +            +    
Sbjct: 131 GAAERQGIVHRLDVGTSGLMVVAKSEYAYTSLKRQFKERTVDKRYHALVQGHPDPMSGTI 190

Query: 158 LNLLKKGIVIQ-------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
              + +                      L     S + + + L  G+  +I+        
Sbjct: 191 DAPIGRHPNHDYKWAVTADGKPSVTHYDLIEAYRSASLLDIKLETGRTHQIRVHMSAHRH 250

Query: 211 KVN 213
              
Sbjct: 251 PCV 253


>gi|270157887|ref|ZP_06186544.1| ribosomal protein S4 [Legionella longbeachae D-4968]
 gi|289163854|ref|YP_003453992.1| 30S ribosomal subunit protein S4 [Legionella longbeachae NSW150]
 gi|269989912|gb|EEZ96166.1| ribosomal protein S4 [Legionella longbeachae D-4968]
 gi|288857027|emb|CBJ10841.1| 30S ribosomal subunit protein S4 [Legionella longbeachae NSW150]
          Length = 206

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G AS R E  +++  + + VN  ++   +  +   D I V
Sbjct: 97  RLDNVVYRMGFASTRAEARQLVTHKAILVNDKIVNVPSYLIKPGDVISV 145


>gi|296129503|ref|YP_003636753.1| hemolysin A [Cellulomonas flavigena DSM 20109]
 gi|296021318|gb|ADG74554.1| hemolysin A [Cellulomonas flavigena DSM 20109]
          Length = 286

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 20/58 (34%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 7  VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          +    T  R+   + R G+A SR     +IA  RV+V+G    RAA  V  T  I V+
Sbjct: 1  MTTTMTTGRLDAELVRRGLARSRGHAADLIAAGRVRVDGTPAHRAATQVDETREIGVE 58


>gi|67926067|ref|ZP_00519319.1| Hemolysin A [Crocosphaera watsonii WH 8501]
 gi|67852087|gb|EAM47594.1| Hemolysin A [Crocosphaera watsonii WH 8501]
          Length = 270

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 15 RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
          R+  ++ +  + S R++ +R I    VKVN  ++++    V  T  IE+   P
Sbjct: 5  RLDLLLVKRDLCSSRQQAQRCIRAGEVKVNQRIIDKPGTEVEITADIELKAKP 57


>gi|228476829|ref|ZP_04061474.1| RNA binding protein [Streptococcus salivarius SK126]
 gi|228251403|gb|EEK10548.1| RNA binding protein [Streptococcus salivarius SK126]
          Length = 267

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 18/53 (33%), Positives = 27/53 (50%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +  R+  V+A     SR    ++IA  +VK+N   +E+A   VM  D I V G
Sbjct: 184 SSMRLDNVLATVLNLSRSNALKLIASGKVKLNYRQIEKANQTVMIGDMISVRG 236


>gi|307297368|ref|ZP_07577174.1| ribosomal protein S4 [Thermotogales bacterium mesG1.Ag.4.2]
 gi|306916628|gb|EFN47010.1| ribosomal protein S4 [Thermotogales bacterium mesG1.Ag.4.2]
          Length = 208

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  ++ R G AS RR+  +++    V VNG  + + + N+   D +E+   
Sbjct: 99  RLDNIVFRMGFASSRRQARQLVNHGHVLVNGRRVNKPSFNLRVGDIVEIKEK 150


>gi|297616625|ref|YP_003701784.1| hemolysin A [Syntrophothermus lipocalidus DSM 12680]
 gi|297144462|gb|ADI01219.1| hemolysin A [Syntrophothermus lipocalidus DSM 12680]
          Length = 270

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 11/52 (21%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             R+  ++   G+A +R +   +I   +V VNG  +++    V    ++ V
Sbjct: 2  EKSRLDTLVHDRGLAPTREKARALILAGKVVVNGNRVDKPGTKVPVDANVAV 53


>gi|253681337|ref|ZP_04862135.1| S4 domain protein [Clostridium botulinum D str. 1873]
 gi|253562575|gb|EES92026.1| S4 domain protein [Clostridium botulinum D str. 1873]
          Length = 88

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   +      RV +NG + +  +  V+  D IEV
Sbjct: 1  MRLDKYLKVSRIIKRRTVAKEACESGRVFINGKVAK-PSSEVIENDIIEV 49


>gi|225174878|ref|ZP_03728875.1| hemolysin A [Dethiobacter alkaliphilus AHT 1]
 gi|225169518|gb|EEG78315.1| hemolysin A [Dethiobacter alkaliphilus AHT 1]
          Length = 273

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 10/53 (18%), Positives = 21/53 (39%), Gaps = 1/53 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             +R+   +  AG+  SR      +    V V+G  +++    V     ++V
Sbjct: 3  TERKRIDVYLTDAGLFPSRSAARAAVMAGLVTVDGQRVDKPGTAVSVDAAVDV 55


>gi|46907827|ref|YP_014216.1| 30S ribosomal protein S4 [Listeria monocytogenes serotype 4b str.
           F2365]
 gi|61215605|sp|Q71Z71|RS4_LISMF RecName: Full=30S ribosomal protein S4
 gi|46881096|gb|AAT04393.1| ribosomal protein S4 [Listeria monocytogenes serotype 4b str.
           F2365]
          Length = 200

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 92  QRLDNIVYRLGLARTRRAARQLVNHGHITVDGKRVDIPSYQVSVGQVISV 141


>gi|152976258|ref|YP_001375775.1| RNA-binding S4 domain-containing protein [Bacillus cereus subsp.
           cytotoxis NVH 391-98]
 gi|152025010|gb|ABS22780.1| RNA-binding S4 domain protein [Bacillus cytotoxicus NVH 391-98]
          Length = 257

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 14/51 (27%), Positives = 27/51 (52%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V+A     SR++V+ +I    VKVN  ++++ +   +  D + V G 
Sbjct: 182 RLDVVLAEILHLSRQKVQPLIKNGLVKVNWKVVDQTSYECLPGDILSVRGH 232


>gi|304440182|ref|ZP_07400072.1| S4 RNA-binding domain protein [Peptoniphilus duerdenii ATCC
          BAA-1640]
 gi|304371231|gb|EFM24847.1| S4 RNA-binding domain protein [Peptoniphilus duerdenii ATCC
          BAA-1640]
          Length = 81

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 24/50 (48%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR   +      R+ VNG + + A+  V + D +E+
Sbjct: 1  MRLDKFLKNSRVIKRRTLAKEACDAGRITVNGRVAK-ASTEVNTGDILEI 49


>gi|289551172|ref|YP_003472076.1| Putative ribosomal large subunit pseudouridine synthase D
           [Staphylococcus lugdunensis HKU09-01]
 gi|289180704|gb|ADC87949.1| Putative ribosomal large subunit pseudouridine synthase D
           [Staphylococcus lugdunensis HKU09-01]
          Length = 284

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 31/223 (13%), Positives = 62/223 (27%), Gaps = 31/223 (13%)

Query: 19  VIARAGIASRREVERMIAQ-QRVKVNGILLERAAVNVMSTDHIEV--------------- 62
            + + G  S ++    I Q   + VN   +      +   D + +               
Sbjct: 16  FLQQQGF-S-KKTTSAIKQNGALLVNHEPVTV-RYQLQPGDKLTIILPTEIPSANLQAFH 72

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGRLDIN 117
             + +   +   L +    +       +    S +   L              V RLD N
Sbjct: 73  HPLDIVYEDDYLLIVCKPSLQNCAPSREHPHESLIEQVLAYCHENDNDFTPHIVTRLDRN 132

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------DKLNLLKKGIVIQGI 170
           T GL+LL   G +  +L         +       Q +           + +    V    
Sbjct: 133 TTGLVLLAKHGHIHHLLSHIKINKRYIALCHGATQPEGIIEAPIARANDSIITRQVSSTG 192

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            Y          K + +   V L  G+  +I+  F++    + 
Sbjct: 193 KYAKSTYRTLNSKQNVSLCEVTLHTGRTHQIRVHFQYIGHPLI 235


>gi|146298136|ref|YP_001192727.1| 30S ribosomal protein S4 [Flavobacterium johnsoniae UW101]
 gi|189045380|sp|A5FN16|RS4_FLAJO RecName: Full=30S ribosomal protein S4
 gi|146152554|gb|ABQ03408.1| 30S ribosomal protein S4 [Flavobacterium johnsoniae UW101]
          Length = 201

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA SRR   ++++ + + VNG ++   + ++   D + V
Sbjct: 94  RLDNVVFRMGIAPSRRGARQIVSHRHITVNGEVVNIPSYHLKPGDKVAV 142


>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 = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 31/260 (11%), Positives = 71/260 (27%), Gaps = 52/260 (20%)

Query: 6   IVQENFTPQRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           I   +   +R+ + +A A     SR  V+ +IA   V ++G         +    +I + 
Sbjct: 5   IADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMNIAIV 64

Query: 63  ---------DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
                     G  +       +   + +      +V   +     + V   +        
Sbjct: 65  LSEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNGNWTGTLVNALIYHCGDSLS 124

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLELP-----------------STQWLR 143
                 R   V RLD +T G++++  +    R L                          
Sbjct: 125 GIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFADHGRTGDLERAYLALVWGMTE 184

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSN---------AWVTVGL 193
             +      + +   +  K+ +V +             T +  +         + V   L
Sbjct: 185 RPQGTVDAYLGRSHRDRTKQAVVHEEREDARHAITHYATVEKFSPREDATALASLVECRL 244

Query: 194 REGKNREIKKVFEFFNWKVN 213
             G+  +I+         + 
Sbjct: 245 ETGRTHQIRVHMAHIGHPLV 264


>gi|167747373|ref|ZP_02419500.1| hypothetical protein ANACAC_02092 [Anaerostipes caccae DSM 14662]
 gi|167653351|gb|EDR97480.1| hypothetical protein ANACAC_02092 [Anaerostipes caccae DSM 14662]
          Length = 91

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 13/51 (25%), Positives = 21/51 (41%), Gaps = 2/51 (3%)

Query: 13 PQRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            R+ K +  + +  RR       +  RV VNG   + A  +V   D I +
Sbjct: 12 GMRLDKFLKVSRLIKRRTVANEACSAGRVTVNGKTAK-AGTDVKPGDEIRI 61


>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 = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 26/235 (11%), Positives = 68/235 (28%), Gaps = 33/235 (14%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN----------------VM 55
              R+ + +A A   SR + +  I   RV+V   ++ + A                  V+
Sbjct: 7   EGVRLDQAVAEALSVSRAKAQAWIQAGRVRVGDRVVLKPAYRLKGEEVAVEPVEEAPMVL 66

Query: 56  STDH---IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
             D    I  +   +    +    L H   G+ +        +  +  +      ++  G
Sbjct: 67  PEDLPIPILYEDEDVLALNKPPGLLTHPAPGVYSGTVVNLLLARYYGPVEKGPPELVRPG 126

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK------------LNL 160
            +    +    +        VLE  +  +     ++ +  + +                 
Sbjct: 127 IVHRLDKDTSGVLVVAKHGGVLEGLARAFRDRLVMKRYLAITEGHPREGVLIAPIGRHPR 186

Query: 161 LKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +  + + G+       +  +    G  A V      G+  +I+   ++    + 
Sbjct: 187 ERHKMHVGGLAARYAETEFQVLATAGPYALVEARPHTGRTHQIRVHLKYLGAPIL 241


>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 = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 18/224 (8%), Positives = 58/224 (25%), Gaps = 30/224 (13%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------------GVP 66
           +++     SR  V+ ++ + +V V+G ++++    ++    + +             G+ 
Sbjct: 30  LLSIMSHTSRNSVKSILTRGQVTVDGKVIKKHNHPLLPNQVVAIQSNKAAIKETALVGMT 89

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR--LDINTEGLLLL 124
           +   +   + +  +   L          +     +  +     +     +         +
Sbjct: 90  ILYEDDAIIVIDKEAGLLSIAAKFAQELTAHRQLINYVKQENHNNRIYVVHRLDRDTSGV 149

Query: 125 TNDGGLARVLELPSTQWLRVYRVR----------------FHGQVDQDKLNLLKKGIVIQ 168
                  +V +     W  + + R                    + + K   +       
Sbjct: 150 MVFAKTEQVKQEMQENWKDIVKERIYSVLVEGIVSEDEGSIKTWLTESKAMKVHSATYDN 209

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           G                   +   L  G+  +I+   E     V
Sbjct: 210 GGKLAITHYKKIRNNDEFTLLEARLETGRKNQIRVHMETLGHPV 253


>gi|284928717|ref|YP_003421239.1| hemolysin A [cyanobacterium UCYN-A]
 gi|284809176|gb|ADB94881.1| hemolysin A [cyanobacterium UCYN-A]
          Length = 264

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 12/53 (22%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 15 RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
          R+  ++       SR++ +R I    VK+N  ++++    +     IEV   P
Sbjct: 4  RLDILLVEKNLYTSRQQAQRCIRAGEVKINQRIIDKPGTEINIKAEIEVKIKP 56


>gi|251787995|ref|YP_003002716.1| 30S ribosomal protein S4 [Dickeya zeae Ech1591]
 gi|247536616|gb|ACT05237.1| ribosomal protein S4 [Dickeya zeae Ech1591]
          Length = 206

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + V VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAVMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|256825074|ref|YP_003149034.1| rRNA methylase [Kytococcus sedentarius DSM 20547]
 gi|256688467|gb|ACV06269.1| predicted rRNA methylase [Kytococcus sedentarius DSM 20547]
          Length = 281

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+ K + + G+  SR   + +I Q +V V G  + + +V+V        DG
Sbjct: 1  MRLDKAVVQRGLTRSRTRAQGLIRQGQVLVEGEPVTKGSVDVDPESISLKDG 52


>gi|223038545|ref|ZP_03608839.1| ribosomal protein S4 [Campylobacter rectus RM3267]
 gi|255321747|ref|ZP_05362902.1| ribosomal protein S4 [Campylobacter showae RM3277]
 gi|222880402|gb|EEF15489.1| ribosomal protein S4 [Campylobacter rectus RM3267]
 gi|255301227|gb|EET80489.1| ribosomal protein S4 [Campylobacter showae RM3277]
          Length = 208

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G A+ RR   +++    + VNG  ++  +  V +   +EV
Sbjct: 98  QRLDNVVYRMGFATTRRFARQLVTHGHILVNGKRVDIPSYRVQAGAKVEV 147


>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 = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 32/222 (14%), Positives = 60/222 (27%), Gaps = 36/222 (16%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------DGVPLR--KAER 72
           SR  ++ +I +  V VNG    +A   V + D I V            + +PL     + 
Sbjct: 56  SRSFIQGLIEEGHVLVNGA-ARKANYKVRAMDQIAVVIPPPRELKVEAENIPLEILYEDE 114

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI---------------- 116
             L +      +V        ++ V   L    +     G L                  
Sbjct: 115 DVLVVNKSQGMVVHPAPGAWTKTLVNALLYHCRNLSGINGVLRPGIVHRIDKDTSGLLVV 174

Query: 117 -----NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
                  +GL        +AR         +          + +D  +  K  +V Q   
Sbjct: 175 AKNDLAHQGLAEQIKAHSMARRYLAIVHGVVFEPSGTVEAPIGRDPADRKKMAVVFQNAK 234

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +  +      +   L  G+  +I+    +    V 
Sbjct: 235 EAVTHYEVLERFRDFTLLEARLETGRTHQIRVHMAYLKHPVL 276


>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 = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 67/239 (28%), Gaps = 31/239 (12%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V+++   QR+ +  A      SR  ++  +    + VNG ++ +A V +M  + I V  
Sbjct: 10  TVKDSQLGQRLDQAAAELFSDFSRSRIKEWVLAGSISVNGEVITKARVKMMGGEEIVVKA 69

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                           +   +   L +      +V   +     + +   L         
Sbjct: 70  ELEDEERWLAQDIPLEIVYEDDDILVINKPRDLVVHPGAGTPDGTILNALLFHYPSIAEV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-----------FHGQVD 154
            R   V RLD +T GL+++         L     +                      +  
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRKITREYEAIVLGRMTAGGMIEKPI 189

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V +          +      +  + + L  G+  +I+    F    + 
Sbjct: 190 GRHPQKRTLMAVHELGKDAVTHYRVAEHFRIHTRLRLRLETGRTHQIRVHMSFLQHPLV 248


>gi|188586310|ref|YP_001917855.1| hemolysin A [Natranaerobius thermophilus JW/NM-WN-LF]
 gi|179350997|gb|ACB85267.1| hemolysin A [Natranaerobius thermophilus JW/NM-WN-LF]
          Length = 276

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 24/57 (42%), Gaps = 10/57 (17%)

Query: 2  KDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMST 57
          KDKN         R+ +++   G  ASR + +R I    V V+   +++    V   
Sbjct: 3  KDKN---------RLDQLLVDKGYFASREQAKRNIMAGLVFVDNQKIDKPGKKVHLD 50


>gi|22536662|ref|NP_687513.1| ylmH protein [Streptococcus agalactiae 2603V/R]
 gi|22533501|gb|AAM99385.1|AE014213_24 ylmH protein [Streptococcus agalactiae 2603V/R]
          Length = 262

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 30/63 (47%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +D   +    +  R+ K++A     SR +  ++I   +VKVN   + R +  ++  D I 
Sbjct: 172 QDIQKLTVIASSLRLDKILATILKISRTQSTKLIEADKVKVNYATVNRVSEQLVEGDLIS 231

Query: 62  VDG 64
           V G
Sbjct: 232 VRG 234


>gi|27364191|ref|NP_759719.1| 30S ribosomal protein S4 [Vibrio vulnificus CMCP6]
 gi|37678582|ref|NP_933191.1| 30S ribosomal protein S4 [Vibrio vulnificus YJ016]
 gi|320157577|ref|YP_004189956.1| 30S ribosomal protein S4p (S9e) [Vibrio vulnificus MO6-24/O]
 gi|31340392|sp|Q8DE62|RS4_VIBVU RecName: Full=30S ribosomal protein S4
 gi|41017818|sp|Q7MPG5|RS4_VIBVY RecName: Full=30S ribosomal protein S4
 gi|27360309|gb|AAO09246.1| ribosomal protein S4 [Vibrio vulnificus CMCP6]
 gi|37197322|dbj|BAC93162.1| ribosomal protein S4 [Vibrio vulnificus YJ016]
 gi|319932889|gb|ADV87753.1| SSU ribosomal protein S4p (S9e) [Vibrio vulnificus MO6-24/O]
          Length = 206

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V + D + +
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAILVNGKVVNVPSFKVAANDVVSI 145


>gi|76798282|ref|ZP_00780529.1| ylmH protein [Streptococcus agalactiae 18RS21]
 gi|76586354|gb|EAO62865.1| ylmH protein [Streptococcus agalactiae 18RS21]
          Length = 179

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 30/63 (47%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +D   +    +  R+ K++A     SR +  ++I   +VKVN   + R +  ++  D I 
Sbjct: 89  QDIQKLTVIASSLRLDKILATILKISRTQSTKLIEADKVKVNYATVNRVSEQLVEGDLIS 148

Query: 62  VDG 64
           V G
Sbjct: 149 VRG 151


>gi|76787217|ref|YP_329217.1| S4 domain-containing protein [Streptococcus agalactiae A909]
 gi|77405577|ref|ZP_00782667.1| ylmH protein [Streptococcus agalactiae H36B]
 gi|76562274|gb|ABA44858.1| S4 domain protein [Streptococcus agalactiae A909]
 gi|77175799|gb|EAO78578.1| ylmH protein [Streptococcus agalactiae H36B]
          Length = 262

 Score = 49.4 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 30/63 (47%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +D   +    +  R+ K++A     SR +  ++I   +VKVN   + R +  ++  D I 
Sbjct: 172 QDIQKLTVIASSLRLDKILATILKISRTQSTKLIEADKVKVNYATVNRVSEQLVEGDLIS 231

Query: 62  VDG 64
           V G
Sbjct: 232 VRG 234


>gi|312143723|ref|YP_003995169.1| hemolysin A [Halanaerobium sp. 'sapolanicus']
 gi|311904374|gb|ADQ14815.1| hemolysin A [Halanaerobium sp. 'sapolanicus']
          Length = 277

 Score = 49.4 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 1/54 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            +R+  V+   G+  SR   +R I    + V+G   ++A   +     IE+ G
Sbjct: 3  QKERLDIVLTERGLFRSRSRAKRAIMAGLIFVDGQREDKAGTQIAKDAEIEIRG 56


>gi|71276503|ref|ZP_00652778.1| Ribosomal protein S4, bacterial and organelle form [Xylella
           fastidiosa Dixon]
 gi|71900586|ref|ZP_00682713.1| Ribosomal protein S4, bacterial and organelle form [Xylella
           fastidiosa Ann-1]
 gi|170729723|ref|YP_001775156.1| 30S ribosomal protein S4 [Xylella fastidiosa M12]
 gi|226703312|sp|B0U5M2|RS4_XYLFM RecName: Full=30S ribosomal protein S4
 gi|71162680|gb|EAO12407.1| Ribosomal protein S4, bacterial and organelle form [Xylella
           fastidiosa Dixon]
 gi|71729643|gb|EAO31747.1| Ribosomal protein S4, bacterial and organelle form [Xylella
           fastidiosa Ann-1]
 gi|167964516|gb|ACA11526.1| 30S ribosomal protein S4 [Xylella fastidiosa M12]
          Length = 208

 Score = 49.4 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 13/66 (19%), Positives = 27/66 (40%), Gaps = 1/66 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  VI R G A +R    ++++ + V VNG ++   + +V   D + +     +     
Sbjct: 98  RLDNVIYRMGFAVTRPAARQLVSHRGVLVNGKIVNLPSYHVKPGDIVALSQRAQKYLCVQ 157

Query: 74  RLWLYH 79
                 
Sbjct: 158 ESLTIK 163


>gi|313763970|gb|EFS35334.1| S4 domain protein [Propionibacterium acnes HL013PA1]
 gi|313791626|gb|EFS39744.1| S4 domain protein [Propionibacterium acnes HL110PA1]
 gi|313802289|gb|EFS43515.1| S4 domain protein [Propionibacterium acnes HL110PA2]
 gi|313808159|gb|EFS46633.1| S4 domain protein [Propionibacterium acnes HL087PA2]
 gi|313812557|gb|EFS50271.1| S4 domain protein [Propionibacterium acnes HL025PA1]
 gi|313814903|gb|EFS52617.1| S4 domain protein [Propionibacterium acnes HL059PA1]
 gi|313818926|gb|EFS56640.1| S4 domain protein [Propionibacterium acnes HL046PA2]
 gi|313820755|gb|EFS58469.1| S4 domain protein [Propionibacterium acnes HL036PA1]
 gi|313822480|gb|EFS60194.1| S4 domain protein [Propionibacterium acnes HL036PA2]
 gi|313825724|gb|EFS63438.1| S4 domain protein [Propionibacterium acnes HL063PA1]
 gi|313828068|gb|EFS65782.1| S4 domain protein [Propionibacterium acnes HL063PA2]
 gi|313839055|gb|EFS76769.1| S4 domain protein [Propionibacterium acnes HL086PA1]
 gi|314915000|gb|EFS78831.1| S4 domain protein [Propionibacterium acnes HL005PA4]
 gi|314918670|gb|EFS82501.1| S4 domain protein [Propionibacterium acnes HL050PA1]
 gi|314920475|gb|EFS84306.1| S4 domain protein [Propionibacterium acnes HL050PA3]
 gi|314925670|gb|EFS89501.1| S4 domain protein [Propionibacterium acnes HL036PA3]
 gi|314932149|gb|EFS95980.1| S4 domain protein [Propionibacterium acnes HL067PA1]
 gi|314954585|gb|EFS98991.1| S4 domain protein [Propionibacterium acnes HL027PA1]
 gi|314958616|gb|EFT02718.1| S4 domain protein [Propionibacterium acnes HL002PA1]
 gi|314959777|gb|EFT03879.1| S4 domain protein [Propionibacterium acnes HL002PA2]
 gi|314962352|gb|EFT06453.1| S4 domain protein [Propionibacterium acnes HL082PA1]
 gi|314968218|gb|EFT12317.1| S4 domain protein [Propionibacterium acnes HL037PA1]
 gi|314979161|gb|EFT23255.1| S4 domain protein [Propionibacterium acnes HL072PA2]
 gi|314986715|gb|EFT30807.1| S4 domain protein [Propionibacterium acnes HL005PA2]
 gi|314989458|gb|EFT33549.1| S4 domain protein [Propionibacterium acnes HL005PA3]
 gi|315077438|gb|EFT49498.1| S4 domain protein [Propionibacterium acnes HL053PA2]
 gi|315080182|gb|EFT52158.1| S4 domain protein [Propionibacterium acnes HL078PA1]
 gi|315084063|gb|EFT56039.1| S4 domain protein [Propionibacterium acnes HL027PA2]
 gi|315089118|gb|EFT61094.1| S4 domain protein [Propionibacterium acnes HL072PA1]
 gi|315098941|gb|EFT70917.1| S4 domain protein [Propionibacterium acnes HL059PA2]
 gi|315100818|gb|EFT72794.1| S4 domain protein [Propionibacterium acnes HL046PA1]
 gi|315108036|gb|EFT80012.1| S4 domain protein [Propionibacterium acnes HL030PA2]
 gi|327330519|gb|EGE72266.1| S4 domain protein [Propionibacterium acnes HL096PA3]
 gi|327446856|gb|EGE93510.1| S4 domain protein [Propionibacterium acnes HL013PA2]
 gi|327450119|gb|EGE96773.1| S4 domain protein [Propionibacterium acnes HL087PA3]
 gi|327455154|gb|EGF01809.1| S4 domain protein [Propionibacterium acnes HL092PA1]
 gi|327455327|gb|EGF01982.1| S4 domain protein [Propionibacterium acnes HL083PA2]
 gi|328752532|gb|EGF66148.1| S4 domain protein [Propionibacterium acnes HL020PA1]
 gi|328752784|gb|EGF66400.1| S4 domain protein [Propionibacterium acnes HL087PA1]
 gi|328759294|gb|EGF72910.1| S4 domain protein [Propionibacterium acnes HL025PA2]
          Length = 71

 Score = 49.4 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 12/54 (22%), Positives = 20/54 (37%), Gaps = 9/54 (16%)

Query: 14 QRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ + +     A  G     +   +IA   V VNG +  R    +   D + V
Sbjct: 2  IRLGQYLKFANLAETGG----QARELIASGMVSVNGEVETRRGRQLHPGDEVTV 51


>gi|307720806|ref|YP_003891946.1| hemolysin A [Sulfurimonas autotrophica DSM 16294]
 gi|306978899|gb|ADN08934.1| hemolysin A [Sulfurimonas autotrophica DSM 16294]
          Length = 235

 Score = 49.4 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   +     + SR + + ++ +  V VN +L+++ A  V  +D + V
Sbjct: 1  MRLDNYLVENDFVESRNKAQTIVKEGLVYVNNMLVKKPAFQVQQSDEVRV 50


>gi|302560761|ref|ZP_07313103.1| nitrite reductase [NAD(P)H], large subunit [Streptomyces
           griseoflavus Tu4000]
 gi|302478379|gb|EFL41472.1| nitrite reductase [NAD(P)H], large subunit [Streptomyces
           griseoflavus Tu4000]
          Length = 926

 Score = 49.4 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 18/108 (16%), Positives = 28/108 (25%), Gaps = 3/108 (2%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           GP                 +   R   +    +P    R + +     G     + A P 
Sbjct: 47  GPCSTCSPLTEAPDVHGHPDHRARRPRHGRPALPRGARRARPDRHPPRGRPV--RGAAPG 104

Query: 306 HRRNLASNVWMAKGIHSSFLSDSG-QREENHRRSPSFPSKRSLRRTSA 352
            R   A  V + +          G  R   HR +P  P      R + 
Sbjct: 105 VRPRPAHLVLLGEHARGPVADGPGVPRAARHRTAPRRPGGDHRPRGAP 152


>gi|302332618|gb|ADL22811.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus JKD6159]
          Length = 284

 Score = 49.4 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 26/199 (13%), Positives = 54/199 (27%), Gaps = 28/199 (14%)

Query: 42  VNGILLERAAVNVMSTDHIEVD---------------GVPLRKAERTRLWLYHKPIGLVT 86
           VN   +      +M  D +E+                 V +   +   + +        T
Sbjct: 38  VNDEPVTV-RKQLMPNDILEIHLPQEIPSVNLIPYARKVEVLYEDAFIIIVTKPNNQNCT 96

Query: 87  THSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
              +    S +   L              V RLD NT G+++    G +  +    + + 
Sbjct: 97  PSREHPHESLIEQVLYHCQEHGENINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKGNLKK 156

Query: 142 LRVYRVRFHGQVD-------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           +    V              +   + +    V     Y      +  Q    +   V L 
Sbjct: 157 IYTCLVYGKTHTSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLH 216

Query: 195 EGKNREIKKVFEFFNWKVN 213
            G+  +I+  F+     + 
Sbjct: 217 TGRTHQIRVHFQHIGHPIV 235


>gi|269104036|ref|ZP_06156733.1| SSU ribosomal protein S4p (S9e) [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268163934|gb|EEZ42430.1| SSU ribosomal protein S4p (S9e) [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 206

 Score = 49.4 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V + D + +
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAILVNGQVVNVPSYKVAANDVVSI 145


>gi|307152717|ref|YP_003888101.1| photosystem II S4 domain-containing protein [Cyanothece sp. PCC
           7822]
 gi|306982945|gb|ADN14826.1| photosystem II S4 domain protein [Cyanothece sp. PCC 7822]
          Length = 259

 Score = 49.4 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 2/65 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             K  +       R+   IA AG   SR ++   I+   V+VN   + +A+ NV S D I
Sbjct: 172 PQKKEMTTVEASMRLD-AIASAGFGMSRSKMAEAISSGDVRVNWKEITQASHNVSSGDLI 230

Query: 61  EVDGV 65
            + G 
Sbjct: 231 SMRGK 235


>gi|153853046|ref|ZP_01994455.1| hypothetical protein DORLON_00440 [Dorea longicatena DSM 13814]
 gi|149753832|gb|EDM63763.1| hypothetical protein DORLON_00440 [Dorea longicatena DSM 13814]
          Length = 269

 Score = 49.4 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 27/221 (12%), Positives = 61/221 (27%), Gaps = 20/221 (9%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++ +  +A SR + + +I    V V+G   ++A         IEV G  L    R
Sbjct: 3   ERLDVLLVKRNLAASREKAKAIIMSGIVYVDGQKEDKAGTTFPEEATIEVRGHTLPYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L         +                    ++  G + +    +     D  L +
Sbjct: 63  GGLKLEKAIKNFDVSVEGKVCTDVGSST-GGFTDCMLQNGAVKVFAIDVGRGQLDWKLRQ 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV--- 189
              +   +   +  V      +  + + +    +        ++  L       A +   
Sbjct: 122 DPRVVCMEKTNIRYVTPEDIGEPVQFSSIDVSFISLTKVLLPIRNYLTEDGQIVALIKPQ 181

Query: 190 ----------TVGLREGKNRE-----IKKVFEFFNWKVNRL 215
                        +RE          +        ++V  L
Sbjct: 182 FEAGREKVGKKGVVREKSTHIEVIHKVIDYAMSIGFEVLNL 222


>gi|227513091|ref|ZP_03943140.1| 30S ribosomal protein S4 [Lactobacillus buchneri ATCC 11577]
 gi|227083666|gb|EEI18978.1| 30S ribosomal protein S4 [Lactobacillus buchneri ATCC 11577]
          Length = 231

 Score = 49.4 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A+ RR+  +++    + V+G  ++  +  V +   + V
Sbjct: 122 RLDNIVYRLGLATTRRQARQLVNHGHITVDGKRVDIPSYEVKTGQVVSV 170


>gi|163814985|ref|ZP_02206372.1| hypothetical protein COPEUT_01138 [Coprococcus eutactus ATCC
          27759]
 gi|158449668|gb|EDP26663.1| hypothetical protein COPEUT_01138 [Coprococcus eutactus ATCC
          27759]
          Length = 69

 Score = 49.4 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 4/52 (7%)

Query: 20 IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
          +  +G+    E +  I Q  V VNG +  R    +   D +E DG  +   +
Sbjct: 22 LVESGV----EAKEFIVQGLVVVNGEVETRRGRKLYDGDEVEFDGDKISIQK 69


>gi|237785442|ref|YP_002906147.1| hypothetical protein ckrop_0850 [Corynebacterium kroppenstedtii
          DSM 44385]
 gi|237758354|gb|ACR17604.1| hypothetical protein ckrop_0850 [Corynebacterium kroppenstedtii
          DSM 44385]
          Length = 276

 Score = 49.4 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 7  VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          + +  + +R+   +    +A SR +   MI   RV VNG    + A  V     I+V+
Sbjct: 1  MTKQPSRRRLDAELVNRKVARSRDQAVEMIRSGRVMVNGFQATKPATRVEPGISIKVE 58


>gi|227524306|ref|ZP_03954355.1| 30S ribosomal protein S4 [Lactobacillus hilgardii ATCC 8290]
 gi|227088537|gb|EEI23849.1| 30S ribosomal protein S4 [Lactobacillus hilgardii ATCC 8290]
          Length = 231

 Score = 49.4 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A+ RR+  +++    + V+G  ++  +  V +   + V
Sbjct: 122 RLDNIVYRLGLATTRRQARQLVNHGHITVDGKRVDIPSYEVKTGQVVSV 170


>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 = 49.4 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 30/256 (11%), Positives = 70/256 (27%), Gaps = 50/256 (19%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVD 63
           +   +   QR+  ++A  G+  SR    R +    V VNG  + ++    V   D I   
Sbjct: 8   VAAPDDAGQRLDALLAARGLYPSRSAAARAVDDGLVFVNGAEVAKK--HPVAPGDTIVYQ 65

Query: 64  -----------GVP----LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                      G P    +R  +   + L  +   +     D D  + V   +    +  
Sbjct: 66  VEEPVEPGPLRGQPIDLDIRFEDEDLIVLSKQVGLVCHPSVDHDDGTLVNALIYHCGAEN 125

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           +   + + +  G++   +      +L   + +           +    +   L  G++  
Sbjct: 126 LCNVQGEDDRLGIVHRLDRDTSGLMLAAKNDETGYALMSDIRDRAVDRRYLALVHGVIAH 185

Query: 169 G-------------ICYGDMQVTLDTQKGSNAWVTV------------------GLREGK 197
                                    + + +     V                   L  G+
Sbjct: 186 DTGMIDAPIARAEKERTRMAVRDTPSAREAITTFRVLERFEHGARDDGYTLIDCKLFTGR 245

Query: 198 NREIKKVFEFFNWKVN 213
             +I+   E+    + 
Sbjct: 246 THQIRVHLEYAKHPLV 261


>gi|323484858|ref|ZP_08090214.1| hypothetical protein HMPREF9474_01965 [Clostridium symbiosum
           WAL-14163]
 gi|323693772|ref|ZP_08107967.1| hemolysin A [Clostridium symbiosum WAL-14673]
 gi|323401854|gb|EGA94196.1| hypothetical protein HMPREF9474_01965 [Clostridium symbiosum
           WAL-14163]
 gi|323502158|gb|EGB18025.1| hemolysin A [Clostridium symbiosum WAL-14673]
          Length = 269

 Score = 49.4 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 25/178 (14%), Positives = 55/178 (30%), Gaps = 2/178 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++ + G+A SR + + +I    V V+    ++A  +   T  IEV G  LR   R
Sbjct: 3   ERLDVLLVKKGLAESREKAKAIIMSGIVYVDDQKEDKAGTSFEETAKIEVRGATLRYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L    I                         ++  G + + +  +        L  
Sbjct: 63  GGLKLEKAMIHFGVVTDKKVCMDVGAST-GGFTDCMLQNGAVKVYSVDVGHGQLAWKLRN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +   +   +  V      D+ +L  +    +        ++  +         + 
Sbjct: 122 DPRVVCMEKTNIRYVTPEDINDKIELVSIDVSFISLTKVLVPVKKLMAEDGQIVCLIK 179


>gi|258420636|ref|ZP_05683575.1| SSU ribosomal protein S4 [Staphylococcus aureus A9719]
 gi|257843240|gb|EEV67650.1| SSU ribosomal protein S4 [Staphylococcus aureus A9719]
          Length = 200

 Score = 49.4 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+   G+A +RR+  +++    + V+G  ++  + +V     I V
Sbjct: 93  RLDAVVYSLGLARTRRQARQLVNHGHILVDGKRVDIPSYSVKPGQTISV 141


>gi|146319810|ref|YP_001199522.1| 30S ribosomal protein S4 [Streptococcus suis 05ZYH33]
 gi|146322003|ref|YP_001201714.1| 30S ribosomal protein S4 [Streptococcus suis 98HAH33]
 gi|223933695|ref|ZP_03625671.1| ribosomal protein S4 [Streptococcus suis 89/1591]
 gi|253752788|ref|YP_003025929.1| 30S ribosomal protein S4 [Streptococcus suis SC84]
 gi|253754613|ref|YP_003027754.1| 30S ribosomal protein S4 [Streptococcus suis P1/7]
 gi|253756546|ref|YP_003029686.1| 30S ribosomal protein S4 [Streptococcus suis BM407]
 gi|172045576|sp|A4W4M5|RS4_STRS2 RecName: Full=30S ribosomal protein S4
 gi|172045584|sp|A4VYD3|RS4_STRSY RecName: Full=30S ribosomal protein S4
 gi|145690616|gb|ABP91122.1| 30S ribosomal protein S4 [Streptococcus suis 05ZYH33]
 gi|145692809|gb|ABP93314.1| 30S ribosomal protein S4 [Streptococcus suis 98HAH33]
 gi|223897648|gb|EEF64033.1| ribosomal protein S4 [Streptococcus suis 89/1591]
 gi|251817077|emb|CAZ52729.1| 30S ribosomal protein S4 [Streptococcus suis SC84]
 gi|251819010|emb|CAZ56857.1| 30S ribosomal protein S4 [Streptococcus suis BM407]
 gi|251820859|emb|CAR47625.1| 30S ribosomal protein S4 [Streptococcus suis P1/7]
 gi|319759206|gb|ADV71148.1| 30S ribosomal protein S4 [Streptococcus suis JS14]
          Length = 203

 Score = 49.4 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V    ++  
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVEVGQVISVREKSIKVP 150


>gi|114561360|ref|YP_748873.1| 30S ribosomal protein S4 [Shewanella frigidimarina NCIMB 400]
 gi|122301094|sp|Q089N0|RS4_SHEFN RecName: Full=30S ribosomal protein S4
 gi|114332653|gb|ABI70035.1| SSU ribosomal protein S4P [Shewanella frigidimarina NCIMB 400]
          Length = 206

 Score = 49.4 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            R+  V+ R G  S R E  ++++ + V VNG ++   +  V + D + +
Sbjct: 96  VRLDNVVYRMGFGSTRAESRQLVSHKSVMVNGRVVNIPSFKVSANDVVSI 145


>gi|16803636|ref|NP_465121.1| 30S ribosomal protein S4 [Listeria monocytogenes EGD-e]
 gi|26399430|sp|Q8Y6T6|RS4_LISMO RecName: Full=30S ribosomal protein S4
 gi|16411025|emb|CAC99674.1| ribosomal protein S4 [Listeria monocytogenes EGD-e]
          Length = 200

 Score = 49.4 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 92  QRLDNIVYRLGLARTRRAARQLVNHGHITVDGKRVDIPSYQVSVGQVISV 141


>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 = 49.4 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 34/236 (14%), Positives = 65/236 (27%), Gaps = 35/236 (14%)

Query: 13  PQRVSKVIARAGIA-SRREVERMIAQQRVKVNGI--------------LLERA---AVNV 54
            +R+   + R   A SR   +R+IA   V V+G               +          +
Sbjct: 9   GERLDVFLVRQMPALSRSYAQRLIAGGNVAVDGERRKANFKLSGAEMVVCTLPPAEETEI 68

Query: 55  MSTDH---IEVDGVPLRKAERTRLWLYHKPIGLVTTH--------------SDPDGRSTV 97
            + D    I  +   +    + R  + H   G+ T                 +   R  +
Sbjct: 69  CAEDIPLDILYEDADIIVINKRRGMVVHPAAGVHTGTLVNALLHHCSDLSGINGALRPGI 128

Query: 98  FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
              L    S V+   + D+    L     D    R         +        G + +  
Sbjct: 129 VHRLDKDTSGVMVAAKNDMAHHYLARQIRDKEARREYRAIVYGNIVERAGVITGDIGRHP 188

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +  K  IV +          +  + G   +V   L  G+  +I+         + 
Sbjct: 189 TDRKKMAIVRENGRPATTHFEVLERFGDYTFVACRLETGRTHQIRVHMTSIGHPLV 244


>gi|117927542|ref|YP_872093.1| SSU ribosomal protein S4P [Acidothermus cellulolyticus 11B]
 gi|152060925|sp|A0LRP7|RS4_ACIC1 RecName: Full=30S ribosomal protein S4
 gi|117648005|gb|ABK52107.1| SSU ribosomal protein S4P [Acidothermus cellulolyticus 11B]
          Length = 208

 Score = 49.4 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG A SR +  +++      VNG  ++  +  V   D IEV
Sbjct: 99  RLDNVVYRAGFAASRDQARQLVRHGHFLVNGRRVDIPSYRVSENDVIEV 147


>gi|57504894|ref|ZP_00370869.1| ribosomal protein S4 [Campylobacter coli RM2228]
 gi|305432399|ref|ZP_07401561.1| 30S ribosomal protein S4 [Campylobacter coli JV20]
 gi|57019322|gb|EAL56024.1| ribosomal protein S4 [Campylobacter coli RM2228]
 gi|304444438|gb|EFM37089.1| 30S ribosomal protein S4 [Campylobacter coli JV20]
          Length = 208

 Score = 49.4 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G A+ RR   +++    + VNG  ++  +  V +   IEV
Sbjct: 98  QRLDNVVYRMGFATTRRFARQLVTHGHILVNGKRVDIPSFRVEAGAKIEV 147


>gi|56692649|ref|YP_164107.1| hypothetical protein ORF012L [Singapore grouper iridovirus]
 gi|42517361|gb|AAS18027.1| unknown [Singapore grouper iridovirus]
          Length = 1024

 Score = 49.4 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/132 (9%), Positives = 32/132 (24%), Gaps = 3/132 (2%)

Query: 226 GTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
             L       + K  L + +  H    ++                 P    +      R 
Sbjct: 12  KALGIRGYSSMRKAELEDVIKQHQAGVSKQKKSPDKRPDSLRKSASPERSRDKRPASPRR 71

Query: 286 KKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK- 344
            ++S +++   +      P      + +   A         +  + +          S  
Sbjct: 72  PRDSPERSRDKRPASPRRPRDSPERSRDKRPASPRRPRDSPERSRDKRPASPRRPRDSPE 131

Query: 345 --RSLRRTSAKK 354
             R  R  S ++
Sbjct: 132 RSRDKRPASPRR 143



 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 15/116 (12%), Positives = 36/116 (31%), Gaps = 3/116 (2%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG---LSKQ 298
           +++  P    ++     +P  S +                  +   +  +       S+ 
Sbjct: 40  KQKKSPDKRPDSLRKSASPERSRDKRPASPRRPRDSPERSRDKRPASPRRPRDSPERSRD 99

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           K+ A+P   R+        +        DS +R  + R +     + S  R+  K+
Sbjct: 100 KRPASPRRPRDSPERSRDKRPASPRRPRDSPERSRDKRPASPRRPRDSPERSRDKR 155



 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 16/108 (14%), Positives = 30/108 (27%), Gaps = 3/108 (2%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              E ++    A             +     P       + S  K   S ++   +P   
Sbjct: 56  ASPERSRDKRPASPRRPRDSPERSRDKRPASPRRPRDSPERSRDKRPASPRRPRDSP--E 113

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK-RSLRRTSAKK 354
           R+        +    S      +R  + RR    P + R  R  S ++
Sbjct: 114 RSRDKRPASPRRPRDSPERSRDKRPASPRRPRDSPERSRDKRPASPRR 161



 Score = 44.8 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 13/117 (11%), Positives = 28/117 (23%), Gaps = 5/117 (4%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK-----NSSQ 291
               LR+   P    + +         S    RD+       P D     +     +  +
Sbjct: 48  RPDSLRKSASPERSRDKRPASPRRPRDSPERSRDKRPASPRRPRDSPERSRDKRPASPRR 107

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                ++ +   P   R    +   ++    +         E  R       +R   
Sbjct: 108 PRDSPERSRDKRPASPRRPRDSPERSRDKRPASPRRPRDSPERSRDKRPASPRRPRG 164



 Score = 44.4 bits (103), Expect = 0.029,   Method: Composition-based stats.
 Identities = 10/102 (9%), Positives = 26/102 (25%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +    P    ++         +S    RD P    +      R  ++S +++   +    
Sbjct: 64  KRPASPRRPRDSPERSRDKRPASPRRPRDSPERSRDKRPASPRRPRDSPERSRDKRPASP 123

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
             P      + +   A         +  + +          S
Sbjct: 124 RRPRDSPERSRDKRPASPRRPRDSPERSRDKRPASPRRPRGS 165



 Score = 39.4 bits (90), Expect = 0.89,   Method: Composition-based stats.
 Identities = 22/121 (18%), Positives = 41/121 (33%), Gaps = 5/121 (4%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           V+ K L+ Q     +        A +       +   +   + PD      + S+     
Sbjct: 2   VTVKELQAQAKALGIRGYSSMRKAELEDVIKQHQAGVSKQKKSPDKRPDSLRKSASPE-R 60

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP--SKRSLRRTSAK 353
           S+ K+ A+P  RR   S         +S        E +  + P+ P   + S  R+  K
Sbjct: 61  SRDKRPASP--RRPRDSPERSRDKRPASPRRPRDSPERSRDKRPASPRRPRDSPERSRDK 118

Query: 354 K 354
           +
Sbjct: 119 R 119


>gi|30019042|ref|NP_830673.1| collagen adhesion protein [Bacillus cereus ATCC 14579]
 gi|29894584|gb|AAP07874.1| Collagen adhesion protein [Bacillus cereus ATCC 14579]
          Length = 1324

 Score = 49.4 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 18/130 (13%), Positives = 34/130 (26%), Gaps = 5/130 (3%)

Query: 221  GPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
            G + L  + A     +S K ++        +   V L            ++P   +E PD
Sbjct: 1131 GDYTLKEIQAPEGYTLSDKEMK--FTISNEKIEVVKLQITNKKDTDKDPEKPGEGTEKPD 1188

Query: 281  DFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSG---QREENHRR 337
            + T      + K G   +K                   G         G    +      
Sbjct: 1189 EGTGKPGEGTGKPGEGTEKPDEGTGKPGEGTGKPGEGTGKPGEGTGKPGEGTGKPGEGTE 1248

Query: 338  SPSFPSKRSL 347
             P   +++  
Sbjct: 1249 KPGEGTEKPG 1258


>gi|34557002|ref|NP_906817.1| putative hemolysin [Wolinella succinogenes DSM 1740]
 gi|34482717|emb|CAE09717.1| PUTATIVE HEMOLYSIN [Wolinella succinogenes]
          Length = 236

 Score = 49.4 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   +A  + + SR +   +I + ++ V+G    + ++ VM    IE+
Sbjct: 1  MRLDAYLAKESLVPSREKARALILEGQILVDGKAASKPSMEVMEGVSIEL 50


>gi|283783153|ref|YP_003373907.1| ribosomal RNA large subunit methyltransferase J [Gardnerella
          vaginalis 409-05]
 gi|283441504|gb|ADB13970.1| ribosomal RNA large subunit methyltransferase J [Gardnerella
          vaginalis 409-05]
          Length = 267

 Score = 49.4 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/63 (22%), Positives = 31/63 (49%), Gaps = 1/63 (1%)

Query: 2  KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
          +D + +  +   QR+   +   G+A SR   +R+I    V V+   + +++  V ++  I
Sbjct: 5  EDLSKLSNSNISQRLDCALVNRGLAESRTTAQRLIRAGVVSVDNRNITKSSFLVNNSHTI 64

Query: 61 EVD 63
           +D
Sbjct: 65 TID 67


>gi|271502222|ref|YP_003335248.1| 30S ribosomal protein S4 [Dickeya dadantii Ech586]
 gi|270345777|gb|ACZ78542.1| ribosomal protein S4 [Dickeya dadantii Ech586]
          Length = 206

 Score = 49.4 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + V VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAVLVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>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 = 49.4 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 30/256 (11%), Positives = 70/256 (27%), Gaps = 50/256 (19%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVD 63
           +   +   QR+  ++A  G+  SR    R +    V VNG  + ++    V   D I   
Sbjct: 8   VAAPDDAGQRLDALLAARGLYPSRSAAARAVDDGLVFVNGAEVAKK--HPVAPGDTIVYQ 65

Query: 64  -----------GVP----LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                      G P    +R  +   + L  +   +     D D  + V   +    +  
Sbjct: 66  VEEPVEPGPLRGQPIDLDIRFEDEDLIVLSKQVGLVCHPSVDHDDGTLVNALIYHCGAEN 125

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           +   + + +  G++   +      +L   + +           +    +   L  G++  
Sbjct: 126 LCNVQGEDDRLGIVHRLDRDTSGLMLAAKNDETGYALMSDIRDRAVDRRYLALVHGVIAH 185

Query: 169 G-------------ICYGDMQVTLDTQKGSNAWVTV------------------GLREGK 197
                                    + + +     V                   L  G+
Sbjct: 186 DTGMIDAPIARAEKERTRMAVRDTPSAREAITTFRVLERFEHGARDDGYTLIDCKLFTGR 245

Query: 198 NREIKKVFEFFNWKVN 213
             +I+   E+    + 
Sbjct: 246 THQIRVHLEYAKHPLV 261


>gi|226224634|ref|YP_002758741.1| hypothetical protein Lm4b_02049 [Listeria monocytogenes Clip81459]
 gi|225877096|emb|CAS05808.1| Hypothetical protein of unknown function [Listeria monocytogenes
           serotype 4b str. CLIP 80459]
          Length = 258

 Score = 49.4 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 10/50 (20%), Positives = 21/50 (42%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
             +  R+  +I+     SR++ ++++    VKVN   +E         D 
Sbjct: 178 TVSSMRLDVIISNVHHISRQKAKQLVTAGLVKVNWKTVENPDFECEEEDV 227


>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 = 49.4 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 31/260 (11%), Positives = 71/260 (27%), Gaps = 52/260 (20%)

Query: 6   IVQENFTPQRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           I   +   +R+ + +A A     SR  V+ +IA   V ++G         +    +I + 
Sbjct: 5   IADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMNIAIV 64

Query: 63  ---------DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
                     G  +       +   + +      +V   +     + V   +        
Sbjct: 65  LPEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNGNWTGTLVNALIYHCGDSLS 124

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLELP-----------------STQWLR 143
                 R   V RLD +T G++++  +    R L                          
Sbjct: 125 GIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFADHGRTGDLERAYLALVWGMTE 184

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSN---------AWVTVGL 193
             +      + +   +  K+ +V +             T +  +         + V   L
Sbjct: 185 RPQGTVDAYLGRSHRDRTKQAVVHEEREDARHAITHYATVEKFSPREDATALASLVECRL 244

Query: 194 REGKNREIKKVFEFFNWKVN 213
             G+  +I+         + 
Sbjct: 245 ETGRTHQIRVHMAHIGHPLV 264


>gi|332530055|ref|ZP_08406005.1| 30S ribosomal protein S4 [Hylemonella gracilis ATCC 19624]
 gi|332040528|gb|EGI76904.1| 30S ribosomal protein S4 [Hylemonella gracilis ATCC 19624]
          Length = 207

 Score = 49.4 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V + D I V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAITVNGQAVNIPSYMVQAGDVIAV 146


>gi|331006743|ref|ZP_08330012.1| hypothetical protein IMCC1989_694 [gamma proteobacterium
          IMCC1989]
 gi|330419432|gb|EGG93829.1| hypothetical protein IMCC1989_694 [gamma proteobacterium
          IMCC1989]
          Length = 74

 Score = 49.4 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 3  DKNIVQENFTPQRVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
          +K +V+ N  P  + K++   G+AS   E + +I Q  V++NG    +    VMS D I 
Sbjct: 4  NKTVVEINQEPVELYKILKFEGLASSGAEAKMVIDQGHVQLNGKTETQKRKKVMSGDTIT 63

Query: 62 VDGVPLRKA 70
           +G  L   
Sbjct: 64 FNGDTLHIQ 72


>gi|327479347|gb|AEA82657.1| 30S ribosomal protein S4 [Pseudomonas stutzeri DSM 4166]
          Length = 167

 Score = 49.4 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V + D + V
Sbjct: 58  RLDNVVYRMGFGSTRAESRQLVSHKSITVNGQTVNIPSYQVKAGDVVAV 106


>gi|323339475|ref|ZP_08079754.1| 30S ribosomal protein S4 [Lactobacillus ruminis ATCC 25644]
 gi|323093089|gb|EFZ35682.1| 30S ribosomal protein S4 [Lactobacillus ruminis ATCC 25644]
          Length = 202

 Score = 49.4 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A+ RR+  +++    + V+G  ++  +  V     I +
Sbjct: 94  RLDNVVYRLGLATTRRQARQLVNHGHITVDGKRVDIPSYEVKPGQVISL 142


>gi|260905245|ref|ZP_05913567.1| hypothetical protein BlinB_07935 [Brevibacterium linens BL2]
          Length = 267

 Score = 49.4 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+ + +     IA+R    R IA  RV VNG  + + +  V  +D + V
Sbjct: 3  RLDRELVERELIATRSRAAREIAAGRVSVNGHTVSKPSQVVSDSDELSV 51


>gi|70936161|ref|XP_739065.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56515775|emb|CAH84527.1| hypothetical protein PC301089.00.0 [Plasmodium chabaudi chabaudi]
          Length = 189

 Score = 49.4 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 33/131 (25%), Positives = 60/131 (45%)

Query: 98  FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                 I   +I V  LD + EG++LLTNDG  A  L+  +   L  Y ++   ++  +K
Sbjct: 3   NKIENYIPEHLIIVNSLDSDMEGIILLTNDGDFANKLKDINNNILTTYLIKTQEELTNEK 62

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
           + LL+KG  I  I    +++ +        W+ +   E     +  +F  +N  + +  R
Sbjct: 63  VELLRKGCTIDDIHIRPLELKIIKPNLLYKWLKLTYVEKSQTHLNLLFSKYNMTIRKCKR 122

Query: 218 ISYGPFQLGTL 228
            S+GP++   L
Sbjct: 123 YSFGPYKSSDL 133


>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 = 49.4 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 34/227 (14%), Positives = 67/227 (29%), Gaps = 31/227 (13%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------GVPLRK 69
           SK +      S R+++ M  ++RVKVN  +       +   D + ++       GV + K
Sbjct: 29  SKYVKERFSLSSRDIQMMFRKKRVKVNSRVAHS-QRALKKGDVLTLELPQDKDYGVDVEK 87

Query: 70  AERTRLWL--------------YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
              T L+                H      +                    R +     +
Sbjct: 88  GPITVLYEDAHTLVVNKAPFMLVHPAGQTKSCTLSNYIAGYYAKKGVVHKVRPVHRLDRE 147

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL-------LKKGIVIQ 168
            +   L   T +       EL + +  R+Y     G +D D +         +     + 
Sbjct: 148 TSGCILFGKTKEAQQYYTDELQAGRIDRIYTGLVEGHIDADGMVDEPIGVDPVFDNRRVI 207

Query: 169 GICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                    + T+   +G N  +   L  G+  +I+   E     + 
Sbjct: 208 DEFGQPAQTEYTVLGYEGDNTLLRFKLLTGRTHQIRVHMEHIGHPII 254


>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 = 49.4 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 40/258 (15%), Positives = 73/258 (28%), Gaps = 43/258 (16%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRRE--------VERMIAQQRVKVNGILLERAAVNV 54
           D+ +V  +   +R+ KVI       R++        + +   +++V+++G         +
Sbjct: 2   DRFVVSRHDDGRRLDKVI-------RKKWPSLPLGAMMKAFRKKQVRIDGARA-SFDQRL 53

Query: 55  MSTDHIEV--------------DGVPLRKAERTRLWLY-HKPIGLVTTHSDPDGRSTVFD 99
           +    I V               G  +       LW+       L               
Sbjct: 54  VEGQEILVPWESAPTDVGAKRTGGHLVTVYRDESLWVVSKPAGLLSQPDKKGGDSVVTRA 113

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
            LP    +  +V RLD NT G+++L   G   R L                   D  +  
Sbjct: 114 FLPGSSFQPQAVNRLDRNTSGIMVLALTGESLRDLSSRWRDGEMEKVYLALVVGDLPEEG 173

Query: 160 LLKKGIVIQGICYGD----------MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            +   +   G                        G  +   V L  G++ +I+       
Sbjct: 174 SIDAPLSKDGSSNKVFVDSKGQSSLTLYRRLASGGGLSLCLVTLITGRSHQIRVHMSHIG 233

Query: 210 WKVNRLIRISYGPFQLGT 227
             V  L  + YG   L  
Sbjct: 234 HPV--LGDVKYGDRALNG 249


>gi|225868958|ref|YP_002744906.1| hypothetical protein SZO_13920 [Streptococcus equi subsp.
           zooepidemicus]
 gi|225702234|emb|CAW99980.1| conserved hypothetical protein [Streptococcus equi subsp.
           zooepidemicus]
          Length = 264

 Score = 49.4 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 17/50 (34%), Positives = 27/50 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           RV ++IA     SR +  R++   +VKVN  L+ +A+  V   D I + G
Sbjct: 187 RVDRLIATVLKQSRNQAIRLVEAGKVKVNYQLVTKASQPVAIGDLISIRG 236


>gi|254449317|ref|ZP_05062762.1| ribosomal protein S4 [gamma proteobacterium HTCC5015]
 gi|198261076|gb|EDY85376.1| ribosomal protein S4 [gamma proteobacterium HTCC5015]
          Length = 173

 Score = 49.4 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG ++  A+  V + D ++V
Sbjct: 64  RLDNVVYRMGYGSTRAEARQLVSHKAILVNGAVVNVASYQVKAGDEVKV 112


>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 = 49.4 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 32/243 (13%), Positives = 67/243 (27%), Gaps = 37/243 (15%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           IV+      R+ + IA +    SR     +I   RV +N   +   A  V   D + V  
Sbjct: 10  IVEAADEGHRLDRYIAGKVPDLSRTYARHLIEDARVLLNNRQVR-PASPVRVGDVVTVQL 68

Query: 63  -DGVP-----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
            +  P           +   +   + +      +V      +  + V   +       IS
Sbjct: 69  PEPQPVGLVAEALPLQIVYEDDDVVVIDKPAGIVVHPAPGHNRGTLVNALIARYPEMAIS 128

Query: 111 VG--------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
                                 R D     L        + ++  +     +        
Sbjct: 129 GDLRPGIVHRLDRDTSGLLVAARNDRALHSLQAQQQARRMLKIYLVVVEGRMNESGGVID 188

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + +   + ++  ++  G         +  + G  A +   L  G+  +I+  F   N 
Sbjct: 189 APIARHPTDRVRMAVMAGGRPART-HWRVLEELGEYALIEARLETGRTHQIRVHFASRNR 247

Query: 211 KVN 213
            V 
Sbjct: 248 PVL 250


>gi|306832984|ref|ZP_07466116.1| S4 domain-containing protein YlmH [Streptococcus bovis ATCC 700338]
 gi|304424883|gb|EFM28017.1| S4 domain-containing protein YlmH [Streptococcus bovis ATCC 700338]
          Length = 263

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 18/63 (28%), Positives = 32/63 (50%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           KD   +    +  R+ KV+A     SR +  ++I   +VK+N  +++RA+  +   D I 
Sbjct: 173 KDSRQLDIIVSSMRMDKVLATVLKLSRSQAVQLIETDKVKLNYQIVDRASEMLQVGDLIS 232

Query: 62  VDG 64
           V G
Sbjct: 233 VRG 235


>gi|282901320|ref|ZP_06309246.1| Hemolysin A [Cylindrospermopsis raciborskii CS-505]
 gi|281193815|gb|EFA68786.1| Hemolysin A [Cylindrospermopsis raciborskii CS-505]
          Length = 279

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 10/41 (24%), Positives = 23/41 (56%)

Query: 27 SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
          SR++ +R+I    V VN  ++++    + ++  I++   PL
Sbjct: 25 SRQQAQRLIQAGEVMVNQQIIDKPGTEIDTSAEIQIKERPL 65


>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 = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 44/318 (13%), Positives = 90/318 (28%), Gaps = 41/318 (12%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLE-----------------RAAVNVMS 56
           R+   ++R     SR   +R I + +V VNG+ ++                      V  
Sbjct: 27  RIDHYLSRLYPNFSRVAFQRTIEEGKVLVNGLPVKISRRLRVNDVIEFSLPAEPDQRVQP 86

Query: 57  TDH---IEVDGVPLRKAERTRLWLYHK-PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
            D    I  D   L    +T   + H        T +          +  +   R   V 
Sbjct: 87  EDIPLDILYDDEYLCVINKTANMIVHPGRGNYRGTLAGALQFHFDSLSDVAGQYRAGIVH 146

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK--------------- 157
           RLD +T G+L++  D  + + L     +             +                  
Sbjct: 147 RLDRDTSGVLVVAKDNTVHQHLSRQFEERSVEKEYHAIVWGEMQFDADYVETYVRVSFRN 206

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
              +                 +  +     +V +  + G+  +++         +    R
Sbjct: 207 RERMMVCPPGDNARQAATFYEVQQRFRGFTYVKLQPQTGRTHQLRVHMHHLGHPIIA-DR 265

Query: 218 ISYGP--FQLGTLLAGSTREVSKKIL-REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNI 274
           +  G    +L  +L  +  E  + ++ R+ L    L          +     L  D    
Sbjct: 266 LYEGKTCVKLSDILPETPEEADETLIDRQALHARRLAFNHPVTKKRMVFEAPLPADFQKT 325

Query: 275 ISEVPDDFTRMKKNSSQK 292
           +  +     + KK+ S K
Sbjct: 326 LDTLKTHAIKPKKSPSSK 343


>gi|94985941|ref|YP_605305.1| 30S ribosomal protein S4 [Deinococcus geothermalis DSM 11300]
 gi|152060945|sp|Q1IX98|RS4_DEIGD RecName: Full=30S ribosomal protein S4
 gi|94556222|gb|ABF46136.1| ribosomal protein S4 [Deinococcus geothermalis DSM 11300]
          Length = 206

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G AS RR+  + +    + VNG  ++  +  V   D I V
Sbjct: 97  RLDNVVFRMGFASTRRQARQFVGHGHILVNGKRVDIPSYRVRIGDEISV 145


>gi|257066413|ref|YP_003152669.1| RNA-binding S4 domain-containing protein [Anaerococcus prevotii DSM
           20548]
 gi|256798293|gb|ACV28948.1| RNA-binding S4 domain protein [Anaerococcus prevotii DSM 20548]
          Length = 255

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 9/48 (18%), Positives = 22/48 (45%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +++     SR + + +I  + VKV+   +   + NV     + +
Sbjct: 180 RLDNIVSSLVNTSRSKAKDLINNRLVKVDHQTITDPSYNVDEGAILSI 227


>gi|228472245|ref|ZP_04057011.1| ribosomal protein S4 [Capnocytophaga gingivalis ATCC 33624]
 gi|228276448|gb|EEK15172.1| ribosomal protein S4 [Capnocytophaga gingivalis ATCC 33624]
          Length = 201

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA SRR   ++++ + + VNG ++   + ++   D + V
Sbjct: 94  RLDNVVYRMGIAPSRRAARQLVSHRHITVNGEVVNIPSYSLKPGDIVGV 142


>gi|154685957|ref|YP_001421118.1| YlmH [Bacillus amyloliquefaciens FZB42]
 gi|154351808|gb|ABS73887.1| YlmH [Bacillus amyloliquefaciens FZB42]
          Length = 256

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/62 (24%), Positives = 27/62 (43%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           D  I  +  +  R+  V A     SR++ + ++    VKVN   +E  +  V   D + +
Sbjct: 169 DVEIRDDTVSSLRLDAVCASMSRQSRQKAQALVKNGLVKVNWKAIEDPSYQVAEGDMLSI 228

Query: 63  DG 64
            G
Sbjct: 229 RG 230


>gi|260886902|ref|ZP_05898165.1| ribosomal protein S4 [Selenomonas sputigena ATCC 35185]
 gi|330839300|ref|YP_004413880.1| ribosomal protein S4 [Selenomonas sputigena ATCC 35185]
 gi|260863501|gb|EEX78001.1| ribosomal protein S4 [Selenomonas sputigena ATCC 35185]
 gi|329747064|gb|AEC00421.1| ribosomal protein S4 [Selenomonas sputigena ATCC 35185]
          Length = 197

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 1/68 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G+A +RR+  +++    ++VNG  L+  +  V + D I +D      A   
Sbjct: 88  RIDNVVYRLGLAQTRRQARQLVTHGHIRVNGKRLDIPSALVRAEDEITIDEKSRSNAFFK 147

Query: 74  RLWLYHKP 81
            L   +KP
Sbjct: 148 ALAENYKP 155


>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 = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 32/247 (12%), Positives = 74/247 (29%), Gaps = 37/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K  + +     R+ K++++     SR   ++MI    V VN    ++       +D 
Sbjct: 1   MPKKFKITD--ELGRLDKIVSKLDPEISRSRAKKMIEDGDVIVNDSK-KKPKYETKVSDT 57

Query: 60  IEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           I +  V               +   +   + +      +V   +     + V   L    
Sbjct: 58  ILIKDVKPETVSIKPENMPLDIVYEDEDVIVVNKPQGMVVHPSAGHPNHTLVNALLFHSP 117

Query: 106 -------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
                   R   V R+D +T GLL++  +    + L         + +          + 
Sbjct: 118 LSSINGEYRPGIVHRIDKDTSGLLMVAKNDMAHKALSKQLKAKKNLRKYVALVHGRIKED 177

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV------------GLREGKNREIKKVFE 206
           + + K  + +       Q  +   + +     V             L  G+  +I+   +
Sbjct: 178 SGVIKAPIGRSPKDRKKQAIVADGRPAITHFEVMERFEDYTLIDCRLETGRTHQIRVHMQ 237

Query: 207 FFNWKVN 213
           +    + 
Sbjct: 238 YIGHPIV 244


>gi|218289979|ref|ZP_03494156.1| ribosomal protein S4 [Alicyclobacillus acidocaldarius LAA1]
 gi|218239964|gb|EED07151.1| ribosomal protein S4 [Alicyclobacillus acidocaldarius LAA1]
          Length = 208

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SR E  +++    ++VNG  ++  +  V   D + V
Sbjct: 99  RLDNVVYRLGFAASRAEARQLVRHGHIQVNGRRVDIPSFLVKEGDVVSV 147


>gi|158319571|ref|YP_001512078.1| ribosomal protein S4 [Alkaliphilus oremlandii OhILAs]
 gi|172048249|sp|A8MLG8|RS4A_ALKOO RecName: Full=30S ribosomal protein S4 A
 gi|158139770|gb|ABW18082.1| ribosomal protein S4 [Alkaliphilus oremlandii OhILAs]
          Length = 207

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 17/67 (25%), Positives = 26/67 (38%), Gaps = 1/67 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V  R G  S R E  +++      VNG  ++  +  V + D I V       A+  
Sbjct: 99  RLDNVAYRLGFGSSRAEARQLVVHGHFTVNGKKVDIPSYLVSAGDTIAVAEKSKSSAKFK 158

Query: 74  RLWLYHK 80
            L    K
Sbjct: 159 ALAENAK 165


>gi|315107243|gb|EFT79219.1| S4 domain protein [Propionibacterium acnes HL030PA1]
 gi|327331109|gb|EGE72849.1| S4 domain protein [Propionibacterium acnes HL097PA1]
          Length = 71

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 12/54 (22%), Positives = 20/54 (37%), Gaps = 9/54 (16%)

Query: 14 QRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ + +     A  G     +   +IA   V VNG +  R    +   D + V
Sbjct: 2  IRLGQYLKFANLAETGG----QARELIASGMVSVNGKVETRRGRQLHPGDEVTV 51


>gi|224437308|ref|ZP_03658280.1| 30S ribosomal protein S4 [Helicobacter cinaedi CCUG 18818]
 gi|313143763|ref|ZP_07805956.1| 30S ribosomal protein S4 [Helicobacter cinaedi CCUG 18818]
 gi|313128794|gb|EFR46411.1| 30S ribosomal protein S4 [Helicobacter cinaedi CCUG 18818]
          Length = 208

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G A+ RR   +++    + VNG  ++  +  V     IEV
Sbjct: 98  QRLDNVVYRMGFATTRRFARQLVTHGHILVNGKHVDIPSYMVKPGQKIEV 147


>gi|149192393|ref|ZP_01870594.1| 30S ribosomal protein S4 [Vibrio shilonii AK1]
 gi|148833784|gb|EDL50820.1| 30S ribosomal protein S4 [Vibrio shilonii AK1]
          Length = 172

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V + D + +
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAILVNGKVVNVPSFKVAANDVVSI 145


>gi|258512643|ref|YP_003186077.1| 30S ribosomal protein S4 [Alicyclobacillus acidocaldarius subsp.
           acidocaldarius DSM 446]
 gi|257479369|gb|ACV59688.1| ribosomal protein S4 [Alicyclobacillus acidocaldarius subsp.
           acidocaldarius DSM 446]
          Length = 208

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SR E  +++    ++VNG  ++  +  V   D + V
Sbjct: 99  RLDNVVYRLGFAASRAEARQLVRHGHIQVNGRRVDIPSFLVKEGDVVSV 147


>gi|218289628|ref|ZP_03493848.1| hemolysin A [Alicyclobacillus acidocaldarius LAA1]
 gi|218240278|gb|EED07461.1| hemolysin A [Alicyclobacillus acidocaldarius LAA1]
          Length = 279

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 15 RVSKVIARAGIASRREV-ERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          R+  ++   G+ S RE   R I    V+V+G+  ++    V     I+V+
Sbjct: 5  RLDLLLVARGLYSSREAARRAIMAGLVRVDGVRADKPGFKVAEDVEIDVE 54


>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 = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 28/260 (10%), Positives = 64/260 (24%), Gaps = 42/260 (16%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           RV K +       +R  ++       +  NG  ++     V   D + +           
Sbjct: 45  RVDKFLVDRMFGATRNRIQSAADAGCIMANGKPVKS-NYRVKPEDVVTIMMTRPPRTFEI 103

Query: 63  --DGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV------- 111
             + +P++    +   L +      +V         + V      +              
Sbjct: 104 LPENIPIKIVYEDDDLLVVDKPAGLVVHPGHGNYTGTLVNALAWYLKDDPTYDPNDPALG 163

Query: 112 --GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ---------------VD 154
              R+D +T GLL++         L +           R                    +
Sbjct: 164 LVHRIDKDTSGLLVVAKKPEAKAHLSMQFFHKTTKREYRALVWGIVREDEGRIEGNIGRN 223

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                 +                ++  + G    V   L  G+  +I+   ++    +  
Sbjct: 224 PRDRMQMTVFPEGDQGKTAVTHYSVLERLGYVTLVKCRLETGRTHQIRVHMKYIGHTLFN 283

Query: 215 LIRISYGPFQLGTLLAGSTR 234
             R   G   L    +   +
Sbjct: 284 DERYG-GNEILKGTTSSKYK 302


>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 = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 39/318 (12%), Positives = 92/318 (28%), Gaps = 45/318 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M  + +V E+    R+   + ++  G  SR ++   +     +V+G ++   +  V +  
Sbjct: 1   MMREFVVPESANGFRIDLFLTQSCDGY-SRSQIRDAVQNDGAEVDGRIIR-PSYKVKAGQ 58

Query: 59  HIEV----------------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRST 96
            +                        D   +   +   + ++        T +       
Sbjct: 59  KVRFRVPPPASDDTVPENIPLDILYEDDGLVVINKPAGMVVHPARGNWTGTLTSALAFRF 118

Query: 97  VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA------RVLELPSTQWLRVYRVRFH 150
              +     +R   V RLD +T G++++  +  +           L   ++  +   R  
Sbjct: 119 QSLSDVGGPTRPGIVHRLDRDTSGVIVVAKNNAVHLNLAAQWHDRLVQKEYTAITFGRLD 178

Query: 151 GQVDQ------DKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
              D              K  + +G            +  + G    V V  + G+  +I
Sbjct: 179 RDRDWIHASIGRHPYQRDKQAIREGHATSKTASTFYEVVERHGRVTRVDVRPKTGRTHQI 238

Query: 202 KKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPI 261
           +         +    R+ YG      L     R ++   +         E  ++ L    
Sbjct: 239 RVHLAHIGCPIL-CDRL-YGGHS--ELSRSQIRRLAGTEVATPGVKPTPEGEEILLSRQA 294

Query: 262 YSSETLVRDRPNIISEVP 279
             ++ L    P    E+ 
Sbjct: 295 LHAKALTFTNPQTGKEMT 312


>gi|325067131|ref|ZP_08125804.1| pseudouridine synthase, RluA family protein [Actinomyces oris K20]
          Length = 306

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 30/242 (12%), Positives = 58/242 (23%), Gaps = 36/242 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           V + F  +RV   +AR    SR  VE +     V+  G  L + +  + + + +EVD   
Sbjct: 8   VPDGFDGERVDAALARMTGLSRSRVEDLCEAGEVRRGGETLAK-SSRLRAGELLEVDLPD 66

Query: 64  ------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                       G+ L   +   + +              DG   +            S 
Sbjct: 67  PRPVEPVATPVEGMELLYEDEDIVVVDKPAGVAAHPSMGWDGPDVLGALKAMHVRVATSG 126

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--------------- 156
                     L +   G +       +   L+                            
Sbjct: 127 AAERQGIVSRLDVGTSGVMIVAKGERAYSVLKRAFREHTVDKVYHALVQGHLDPSSGTID 186

Query: 157 -----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                  +   K  +I+G         +           + L  G+  +I+         
Sbjct: 187 APIGRHPSREWKMAIIEGGRESITHYDVIEAMPGACLAEIHLETGRTHQIRVHMAAVGHP 246

Query: 212 VN 213
             
Sbjct: 247 CV 248


>gi|205374494|ref|ZP_03227290.1| 30S ribosomal protein S4 [Bacillus coahuilensis m4-4]
          Length = 200

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +RR+  +++    V VNG  ++  +  V     I V
Sbjct: 93  RLDNVVYRLGLARTRRQARQLVNHGHVLVNGSRVDIPSFRVQPGQVIGV 141


>gi|157363469|ref|YP_001470236.1| 30S ribosomal protein S4 [Thermotoga lettingae TMO]
 gi|172045985|sp|A8F4T8|RS4_THELT RecName: Full=30S ribosomal protein S4
 gi|157314073|gb|ABV33172.1| RNA-binding S4 domain protein [Thermotoga lettingae TMO]
          Length = 209

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           RV  ++ R G A SRR+  +++      VNG+ ++  +  +   D +EV
Sbjct: 99  RVDNIVYRLGFAISRRQARQLVTHGHFSVNGVKIDIPSYKLRPGDIVEV 147


>gi|326789142|ref|YP_004306963.1| RNA-binding S4 domain protein [Clostridium lentocellum DSM 5427]
 gi|326539906|gb|ADZ81765.1| RNA-binding S4 domain protein [Clostridium lentocellum DSM 5427]
          Length = 68

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 29/72 (40%), Gaps = 6/72 (8%)

Query: 1  MKDKNIVQENFTPQRVSKV--IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
          MK+  I  E     ++ K   + + G     E + +IA + V VNG +  +    +   D
Sbjct: 1  MKEIKIDTEFIKLDQLMKYASMVQTGG----EAKMLIAGELVLVNGEICTQRGKKIRPGD 56

Query: 59 HIEVDGVPLRKA 70
           +  DG   +  
Sbjct: 57 EVLFDGETYKVK 68


>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 = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 22/244 (9%), Positives = 67/244 (27%), Gaps = 41/244 (16%)

Query: 8   QENFTPQRVS---KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           ++     R+    K I      +R  ++++I +  V VN IL+++    V   D IE+  
Sbjct: 8   KKKENLIRIDTYIKFILHKK--NRNFIQKIIEKGFVYVNNILIKK-NYIVKINDVIEIFL 64

Query: 63  -DGVP----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
            +G            +   +   + +  +   +V      +  + +         +    
Sbjct: 65  PEGKKNIIPENLKINIFYEDEYVIIINKQSGLVVHPGKGNESMTLINGLHFYFLKKKNIY 124

Query: 112 GRLD---INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            ++       +            + +    ++   +  ++              KG +I 
Sbjct: 125 NKIPILVHRIDKGTSGLILVAKDKNILEKISKQFYINHIKRKYITLVWGYIKNNKGTIIC 184

Query: 169 G-------------------ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                                 +      +  +      +   L  G+  +I+   ++  
Sbjct: 185 NIGRSLKNRIYMNVFPNGIYGKFSITHYKVLERFKYVTLLKCTLETGRTHQIRVHLKYIG 244

Query: 210 WKVN 213
             + 
Sbjct: 245 HPIL 248


>gi|293192941|ref|ZP_06609785.1| cytotoxin/hemolysin [Actinomyces odontolyticus F0309]
 gi|292819997|gb|EFF78996.1| cytotoxin/hemolysin [Actinomyces odontolyticus F0309]
          Length = 275

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          R+   + R G+A SR    +MI   RVK++G ++ + A  +     I V+
Sbjct: 5  RIDSELVRRGLAKSRAAAAQMIEDGRVKLDGQIVLKPARQMDPAQAIVVE 54


>gi|209693947|ref|YP_002261875.1| 30S ribosomal protein S4 [Aliivibrio salmonicida LFI1238]
 gi|226697795|sp|B6EPU8|RS4_ALISL RecName: Full=30S ribosomal protein S4
 gi|208007898|emb|CAQ78028.1| 30S ribosomal protein S4 [Aliivibrio salmonicida LFI1238]
          Length = 206

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG ++   +  V + D + +
Sbjct: 97  RLDNVVYRMGFGSTRAESRQLVSHKSILVNGKVVNVPSFKVSANDVVSI 145


>gi|153952888|ref|YP_001393653.1| 30S ribosomal protein S4 [Clostridium kluyveri DSM 555]
 gi|219853553|ref|YP_002470675.1| hypothetical protein CKR_0210 [Clostridium kluyveri NBRC 12016]
 gi|146345769|gb|EDK32305.1| RpsD1 [Clostridium kluyveri DSM 555]
 gi|219567277|dbj|BAH05261.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 206

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 2/52 (3%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DG 64
           R+  V+ + G   SR E  +++     KVNG  +   +  V   D I V DG
Sbjct: 99  RLDNVVYKLGYGQSRTEARQLVTHGHFKVNGRKVNIPSFKVSVNDTISVKDG 150


>gi|163942386|ref|YP_001647270.1| 30S ribosomal protein S4 [Bacillus weihenstephanensis KBAB4]
 gi|229013860|ref|ZP_04170988.1| 30S ribosomal protein S4 [Bacillus mycoides DSM 2048]
 gi|229062341|ref|ZP_04199659.1| 30S ribosomal protein S4 [Bacillus cereus AH603]
 gi|229135493|ref|ZP_04264279.1| 30S ribosomal protein S4 [Bacillus cereus BDRD-ST196]
 gi|229169382|ref|ZP_04297092.1| 30S ribosomal protein S4 [Bacillus cereus AH621]
 gi|226697804|sp|A9VKG5|RS4_BACWK RecName: Full=30S ribosomal protein S4
 gi|163864583|gb|ABY45642.1| ribosomal protein S4 [Bacillus weihenstephanensis KBAB4]
 gi|228614145|gb|EEK71260.1| 30S ribosomal protein S4 [Bacillus cereus AH621]
 gi|228647958|gb|EEL04007.1| 30S ribosomal protein S4 [Bacillus cereus BDRD-ST196]
 gi|228716946|gb|EEL68630.1| 30S ribosomal protein S4 [Bacillus cereus AH603]
 gi|228747529|gb|EEL97404.1| 30S ribosomal protein S4 [Bacillus mycoides DSM 2048]
          Length = 200

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 93  RLDNLVYRMGLARTRRAARQLVNHGHITVDGARVDIPSYRVKPNQTISV 141


>gi|291562667|emb|CBL41483.1| hemolysin TlyA family protein [butyrate-producing bacterium SS3/4]
          Length = 269

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 23/178 (12%), Positives = 56/178 (31%), Gaps = 2/178 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++ +  +A SR + + +I    V V+G   ++A      T ++EV G  L+   R
Sbjct: 3   ERLDVLLVKRNLAESREKAKAVIMSGIVYVDGQKEDKAGSMFDETANVEVRGTTLKYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L         T                    ++  G + + +  +        L  
Sbjct: 63  GGLKLEKAMTHFGVTLEGKICMDVGAST-GGFTDCMLQNGAVKVYSVDVGHGQLAWKLRN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +   +   +  V      D+ +   +    +      G ++  ++        + 
Sbjct: 122 DERVVCMEKTNIRYVTPEEIPDRIQFVSIDVSFISLTKVLGPVKALMEPDGEVVCLIK 179


>gi|294669849|ref|ZP_06734908.1| hypothetical protein NEIELOOT_01742 [Neisseria elongata subsp.
          glycolytica ATCC 29315]
 gi|291308242|gb|EFE49485.1| hypothetical protein NEIELOOT_01742 [Neisseria elongata subsp.
          glycolytica ATCC 29315]
          Length = 102

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/52 (21%), Positives = 22/52 (42%), Gaps = 1/52 (1%)

Query: 23 AGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           G  S R E  +++A + + VNG ++   +  V   D + V     ++    
Sbjct: 1  MGFGSTRAEARQLVAHKAIVVNGHVVNIPSFQVQPGDVVAVREKAKKQVRIQ 52


>gi|255321407|ref|ZP_05362567.1| ribosomal RNA large subunit methyltransferase J [Campylobacter
          showae RM3277]
 gi|255301560|gb|EET80817.1| ribosomal RNA large subunit methyltransferase J [Campylobacter
          showae RM3277]
          Length = 380

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/51 (21%), Positives = 19/51 (37%), Gaps = 2/51 (3%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R     A     SR +   +I   ++ +NG +  + +  V   D    DG
Sbjct: 1  MRFDLFTASRLNISRNKAAELIKSGKILLNGKICSKPSFEVGEFDK--FDG 49


>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 = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/100 (13%), Positives = 27/100 (27%), Gaps = 1/100 (1%)

Query: 9   ENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
              T  R+ K +A      SR   ++ I    V +NG +  + +  +   D + +     
Sbjct: 18  TEPTLMRLDKYLAMMYPEYSRAFYQKHIVNHNVFINGEVQTKVSSRLSEGDVVTIHIQEK 77

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
            +                 +      +       PS    
Sbjct: 78  EELSELLPEEIPLHKVYEDSMIIVVNKPRDMVVHPSPGHH 117


>gi|302389863|ref|YP_003825684.1| hemolysin A [Thermosediminibacter oceani DSM 16646]
 gi|302200491|gb|ADL08061.1| hemolysin A [Thermosediminibacter oceani DSM 16646]
          Length = 264

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/59 (22%), Positives = 23/59 (38%), Gaps = 1/59 (1%)

Query: 12 TPQRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
            +R+  ++ + G+ S RE  +  I    V VN   +++    V     I V    L  
Sbjct: 2  QKERLDVLLVQRGLFSSRERAKSEIMMGNVFVNNKKIDKPGTMVDINSDIIVKERSLPY 60


>gi|322435971|ref|YP_004218183.1| hemolysin A [Acidobacterium sp. MP5ACTX9]
 gi|321163698|gb|ADW69403.1| hemolysin A [Acidobacterium sp. MP5ACTX9]
          Length = 259

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 1/49 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           R+ K+I   G A SR   + +I   RV V    +++    V     + 
Sbjct: 3  IRLDKLIVDRGHAASRERAQALILAGRVLVQDQRIDKPGTPVDDASILR 51


>gi|237806899|ref|YP_002891339.1| 30S ribosomal protein S4 [Tolumonas auensis DSM 9187]
 gi|259495302|sp|C4L7V4|RS4_TOLAT RecName: Full=30S ribosomal protein S4
 gi|237499160|gb|ACQ91753.1| ribosomal protein S4 [Tolumonas auensis DSM 9187]
          Length = 206

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A+ R E  ++++ + + VNG ++   +  V   D + V
Sbjct: 97  RLDNVVYRMGFATTRAEARQLVSHKAIVVNGKVVNIPSSQVSPEDVVTV 145


>gi|168187786|ref|ZP_02622421.1| ribosomal protein S4 [Clostridium botulinum C str. Eklund]
 gi|169294366|gb|EDS76499.1| ribosomal protein S4 [Clostridium botulinum C str. Eklund]
          Length = 206

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            R+  V+ + G  S R E  +++      VNG  ++  +  V + D I V
Sbjct: 98  MRLDNVVYKLGFGSSRAEARQLVTHGHFLVNGKKVDIISYQVSAGDVISV 147


>gi|146281194|ref|YP_001171347.1| 30S ribosomal protein S4 [Pseudomonas stutzeri A1501]
 gi|172045574|sp|A4VHQ4|RS4_PSEU5 RecName: Full=30S ribosomal protein S4
 gi|145569399|gb|ABP78505.1| ribosomal protein S4 [Pseudomonas stutzeri A1501]
          Length = 206

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V + D + V
Sbjct: 97  RLDNVVYRMGFGSTRAESRQLVSHKSITVNGQTVNIPSYQVKAGDVVAV 145


>gi|118444508|ref|YP_877226.1| 30S ribosomal protein S4 [Clostridium novyi NT]
 gi|152060917|sp|A0PXX4|RS4A_CLONN RecName: Full=30S ribosomal protein S4 A
 gi|118134964|gb|ABK62008.1| ribosomal protein S4 [Clostridium novyi NT]
          Length = 206

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            R+  V+ + G  S R E  +++      VNG  ++  +  V + D I V
Sbjct: 98  MRLDNVVYKLGFGSSRAEARQLVTHGHFLVNGKKVDIISYQVSAGDVISV 147


>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 = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 30/256 (11%), Positives = 70/256 (27%), Gaps = 50/256 (19%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVD 63
           +   +   QR+  ++A  G+  SR    R +    V VNG  + ++    V   D I   
Sbjct: 8   VAAPDDAGQRLDALLAARGLYPSRSAAARAVDDGLVFVNGAEVAKK--HPVAPGDTIVYQ 65

Query: 64  -----------GVP----LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                      G P    +R  +   + L  +   +     D D  + V   +    +  
Sbjct: 66  VEEPVEPGPLRGQPIDLDIRFEDEDLIVLSKQVGLVCHPSVDHDDGTLVNALIYHCGAEN 125

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           +   + + +  G++   +      +L   + +           +    +   L  G++  
Sbjct: 126 LCNVQGEDDRLGIVHRLDRDTSGLMLAAKNDETGYALMSDIRDRAVDRRYLALVHGVIAH 185

Query: 169 G-------------ICYGDMQVTLDTQKGSNAWVTV------------------GLREGK 197
                                    + + +     V                   L  G+
Sbjct: 186 DTGMIDAPIARAEKERTRMAVRDTPSAREAITTFRVLERFEHGGRDDGYTLIDCKLFTGR 245

Query: 198 NREIKKVFEFFNWKVN 213
             +I+   E+    + 
Sbjct: 246 THQIRVHLEYAKHPLV 261


>gi|309356679|emb|CAP36772.2| hypothetical protein CBG_19546 [Caenorhabditis briggsae AF16]
          Length = 438

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 28/207 (13%), Positives = 59/207 (28%), Gaps = 24/207 (11%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRKAERTR---LWLY 78
            +      R+ VNG  +      + + D +E         V  +P+R    T    +   
Sbjct: 109 AKVACKMGRIYVNGEQMTDVDYVMKNGDRVEHWVHRHEHPVRDLPIRIISETDDLLVIEK 168

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
              + + T                   + +  + RLD  T G+LL   +       +   
Sbjct: 169 PPSLPVHTCGQYAIHTVLGQLRENEEKTGLRVLHRLDRATSGVLLFAKNYETDLEFKTTL 228

Query: 139 TQWLR--VYRVRFHGQVDQDKLNL----------LKKGIVIQGICYGDMQVTLDTQKGSN 186
            Q      Y  +  G    ++             +    V                 G++
Sbjct: 229 KQGEWSKEYVCKVDGVFPDEEQVCEQPIGPLVISMGIQCVRPDGKEAKSTFRKLWSDGTH 288

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVN 213
           + V V +  G+  +I+   +F  + + 
Sbjct: 289 SVVQVHIETGRTHQIRVHSQFLGYPIV 315


>gi|242067965|ref|XP_002449259.1| hypothetical protein SORBIDRAFT_05g006893 [Sorghum bicolor]
 gi|241935102|gb|EES08247.1| hypothetical protein SORBIDRAFT_05g006893 [Sorghum bicolor]
          Length = 260

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 7/49 (14%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          +R  +        SR  ++  I Q +V V+G ++ +A   V     IE+
Sbjct: 17 ERFQQY-------SRTYIQSWILQGKVIVDGRVVNKAGTQVSDKSVIEI 58


>gi|225469571|ref|XP_002271057.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 316

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 22/49 (44%), Gaps = 7/49 (14%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +R  +        SR  ++  I Q +V V+G ++ +A   V     +E+
Sbjct: 84  ERFQQY-------SRTFIQSWILQGKVFVDGKVVNKAGTPVSDKAVVEI 125


>gi|169830294|ref|YP_001716276.1| RNA-binding S4 domain-containing protein [Candidatus Desulforudis
          audaxviator MP104C]
 gi|169637138|gb|ACA58644.1| RNA-binding S4 domain protein [Candidatus Desulforudis
          audaxviator MP104C]
          Length = 88

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 18/71 (25%), Positives = 27/71 (38%), Gaps = 3/71 (4%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRKAE 71
           R+ K +  + +  RR   + +  Q  V VNG L + A   V   D + V  G      E
Sbjct: 1  MRLDKFLKVSRLIKRRALAKEVCDQGLVTVNGRLAK-AGTPVNPGDIVRVQLGSRNLYFE 59

Query: 72 RTRLWLYHKPI 82
            RL  +    
Sbjct: 60 VLRLDEHVPAG 70


>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 = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 35/238 (14%), Positives = 62/238 (26%), Gaps = 43/238 (18%)

Query: 15  RVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------- 63
           R+ K +        SR  ++R I    V VNG   ++ +  V S D I ++         
Sbjct: 13  RLDKFVMEKTPEWISRTFIQRAIKNGEVLVNGTS-KKPSYKVKSGDIITLNAPEAPEIPE 71

Query: 64  ----GVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
                +PL     +R  L +  +P  +          + V   L          G L   
Sbjct: 72  ILPEDIPLDIIYEDRDILVINKQPGIITHPIPSHTSGTIVNGVLYHCKDLQGIGGVLRPG 131

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
               L     G +       + Q L         +     L           I     + 
Sbjct: 132 IVHRLDKDTSGVMVIAKNDLAHQSLTKQFKDRLTEKLYICLVKGVPKRKEGDIEINIARN 191

Query: 178 TL----------DTQKGSNAWVTVGLRE--------------GKNREIKKVFEFFNWK 211
            +          +  K +     V  RE              G+  +I+   ++    
Sbjct: 192 PVLRVKMTVTNSEYGKPALTHYKVV-REFGDIAALVFAYPKTGRTHQIRVHMKYIGHP 248


>gi|17534965|ref|NP_493778.1| hypothetical protein K07E8.7 [Caenorhabditis elegans]
 gi|3915497|sp|O16686|YK27_CAEEL RecName: Full=Uncharacterized protein K07E8.7
 gi|2315726|gb|AAB66153.1| Hypothetical protein K07E8.7 [Caenorhabditis elegans]
          Length = 432

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 28/209 (13%), Positives = 60/209 (28%), Gaps = 24/209 (11%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRKAERTR---L 75
           R   +      R+ VNG  +      + + D +E         +  +P+R    T    +
Sbjct: 100 RNYAKIACKMGRIYVNGEQMTDVDYVMRNGDRVEHWAHRHEHPIRDLPIRVISETDDLFV 159

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
                 + + T              +    + +  + RLD  T G+LL   +       +
Sbjct: 160 VEKPPSLPVHTCGQYAIHTVLGQLRVNEGRTGLRVLHRLDRATSGVLLFAKNYETDLEFK 219

Query: 136 LPSTQWLR--VYRVRFHGQVDQDKLNL----------LKKGIVIQGICYGDMQVTLDTQK 183
               Q      Y  +  G    ++             +    V         +       
Sbjct: 220 TTLKQGEWSKEYICKVDGVFPDEEQVCEQPIGPLVISMGIQCVRPDGKDAKSRFRKLWSD 279

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           G+ + V V +  G+  +I+   +F    +
Sbjct: 280 GTQSVVQVHIETGRTHQIRVHSQFLGHPI 308


>gi|319940172|ref|ZP_08014525.1| 30S ribosomal protein S4 [Streptococcus anginosus 1_2_62CV]
 gi|319810643|gb|EFW06973.1| 30S ribosomal protein S4 [Streptococcus anginosus 1_2_62CV]
          Length = 203

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V    L+  
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVSVGQVISVREKSLKVP 150


>gi|260779479|ref|ZP_05888369.1| SSU ribosomal protein S4p (S9e) [Vibrio coralliilyticus ATCC
           BAA-450]
 gi|260604288|gb|EEX30592.1| SSU ribosomal protein S4p (S9e) [Vibrio coralliilyticus ATCC
           BAA-450]
          Length = 206

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V + D + +
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAILVNGKVVNVPSFKVAANDVVSI 145


>gi|260582391|ref|ZP_05850183.1| pseudouridylate synthase [Haemophilus influenzae NT127]
 gi|260094542|gb|EEW78438.1| pseudouridylate synthase [Haemophilus influenzae NT127]
          Length = 324

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 29/238 (12%), Positives = 60/238 (25%), Gaps = 31/238 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----E 61
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + I    E
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVE 69

Query: 62  VDGVP----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
           V+             +   +   + +      +V   +     + +   L          
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPISEVP 129

Query: 112 -----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-----------FHGQVDQ 155
                 RLD +T GL+++         L     +                      Q   
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     V            +     +   + + L  G+  +I+         + 
Sbjct: 190 RHATKRTLMAVHPMGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 247


>gi|227832272|ref|YP_002833979.1| 30S ribosomal protein S4 [Corynebacterium aurimucosum ATCC 700975]
 gi|262183872|ref|ZP_06043293.1| 30S ribosomal protein S4 [Corynebacterium aurimucosum ATCC 700975]
 gi|254764581|sp|C3PL37|RS4_CORA7 RecName: Full=30S ribosomal protein S4
 gi|227453288|gb|ACP32041.1| 30S ribosomal protein S4 [Corynebacterium aurimucosum ATCC 700975]
          Length = 201

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI RAG+A +RR+  ++++     VNG  +   +  V   D I+V
Sbjct: 92  RLDNVIYRAGLANTRRQARQLVSHGHFTVNGKKINVPSFRVTQYDIIDV 140


>gi|254509448|ref|ZP_05121526.1| ribosomal protein S4 [Vibrio parahaemolyticus 16]
 gi|323495528|ref|ZP_08100602.1| 30S ribosomal protein S4 [Vibrio sinaloensis DSM 21326]
 gi|219547621|gb|EED24668.1| ribosomal protein S4 [Vibrio parahaemolyticus 16]
 gi|323319409|gb|EGA72346.1| 30S ribosomal protein S4 [Vibrio sinaloensis DSM 21326]
          Length = 206

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/61 (18%), Positives = 29/61 (47%), Gaps = 1/61 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V + D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAILVNGKVVNVPSFKVAANDVVAIREKAQKQSRIK 156

Query: 74  R 74
            
Sbjct: 157 A 157


>gi|172040040|ref|YP_001799754.1| 30S ribosomal protein S4 [Corynebacterium urealyticum DSM 7109]
 gi|226697828|sp|B1VEY1|RS4_CORU7 RecName: Full=30S ribosomal protein S4
 gi|171851344|emb|CAQ04320.1| 30S ribosomal protein S4 [Corynebacterium urealyticum DSM 7109]
          Length = 201

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  VI RAG+A +RR+  ++++     VNG  +   +  V   D I+V   
Sbjct: 92  RLDNVIYRAGLARTRRQARQLVSHGHFTVNGKKINVPSFRVSQYDIIDVRDR 143


>gi|159465535|ref|XP_001690978.1| hypothetical protein CHLREDRAFT_128015 [Chlamydomonas reinhardtii]
 gi|158279664|gb|EDP05424.1| predicted protein [Chlamydomonas reinhardtii]
          Length = 291

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 19/70 (27%), Positives = 30/70 (42%), Gaps = 5/70 (7%)

Query: 13  PQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV---PLR 68
             R+   IA AG   SR ++  MI    V++N   + + +V V   D I   G     ++
Sbjct: 215 SMRLD-AIASAGFRMSRTKIGDMIKAGDVRLNWRPVTKPSVEVKEGDVISCSGKGRVEIK 273

Query: 69  KAERTRLWLY 78
             E T+   Y
Sbjct: 274 ACEMTKKEKY 283


>gi|167040179|ref|YP_001663164.1| hemolysin A [Thermoanaerobacter sp. X514]
 gi|256752077|ref|ZP_05492945.1| hemolysin A [Thermoanaerobacter ethanolicus CCSD1]
 gi|300914262|ref|ZP_07131578.1| hemolysin A [Thermoanaerobacter sp. X561]
 gi|307724502|ref|YP_003904253.1| hemolysin A [Thermoanaerobacter sp. X513]
 gi|166854419|gb|ABY92828.1| hemolysin A [Thermoanaerobacter sp. X514]
 gi|256749087|gb|EEU62123.1| hemolysin A [Thermoanaerobacter ethanolicus CCSD1]
 gi|300889197|gb|EFK84343.1| hemolysin A [Thermoanaerobacter sp. X561]
 gi|307581563|gb|ADN54962.1| hemolysin A [Thermoanaerobacter sp. X513]
          Length = 266

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 11 FTPQRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             +R+  ++ + G  S RE  +  I    V V+G  +E+A   V     IE+
Sbjct: 3  SKKERLDVLLVQKGFFSSREKAKASIMAGEVYVDGKKIEKAGEFVNIDSSIEI 55


>gi|108757719|ref|YP_632808.1| hemolysin A [Myxococcus xanthus DK 1622]
 gi|108461599|gb|ABF86784.1| hemolysin A [Myxococcus xanthus DK 1622]
          Length = 246

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 10/61 (16%), Positives = 25/61 (40%), Gaps = 1/61 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
              +R+  ++   G+A SR + + +I   +V V    +++    +     + + G  L 
Sbjct: 2  KPRKERLDVLVVERGLAESRTKAQALILAGQVVVGDQRVDKPGTLIPQEAELRLKGEVLP 61

Query: 69 K 69
           
Sbjct: 62 Y 62


>gi|332524579|ref|ZP_08400783.1| 30S ribosomal protein S4 [Rubrivivax benzoatilyticus JA2]
 gi|332107892|gb|EGJ09116.1| 30S ribosomal protein S4 [Rubrivivax benzoatilyticus JA2]
          Length = 207

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG ++   +  V + D + V
Sbjct: 98  RLDNVVYRMGFGSTRAESRQLVSHKAITVNGQVVNIPSYMVKAGDVVAV 146


>gi|315658673|ref|ZP_07911543.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           lugdunensis M23590]
 gi|315496304|gb|EFU84629.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           lugdunensis M23590]
          Length = 284

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 30/223 (13%), Positives = 62/223 (27%), Gaps = 31/223 (13%)

Query: 19  VIARAGIASRREVERMIAQ-QRVKVNGILLERAAVNVMSTDHIEV--------------- 62
            + + G  S ++    I Q   + VN   +      +   D + +               
Sbjct: 16  FLQQQGF-S-KKTTSAIKQNGALLVNHEPVTV-RYQLQPGDKLTIILPTEIPSANLQAFH 72

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDG-----RSTVFDNLPSIFSRVISVGRLDIN 117
             + +   +   L +    I       +        +   + +          V RLD N
Sbjct: 73  HPLDIVYEDDYLLIVCKPSIQNCAPSREHPHESLIEQVIAYCHENDNDFTPHIVTRLDRN 132

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------DKLNLLKKGIVIQGI 170
           T GL+LL   G +  +L         +       Q +           + +    V    
Sbjct: 133 TTGLVLLAKHGHIHHLLSHIKINKRYIALCHGATQPEGIIEAPIARANDSIITRQVSSTG 192

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            Y          K + +   V L  G+  +I+  F++    + 
Sbjct: 193 KYAKSTYRTLNSKQNVSLCEVTLHTGRTHQIRVHFQYIGHPLI 235


>gi|256383853|gb|ACU78423.1| ribosomal RNA large subunit methyltransferase J [Mycoplasma
           mycoides subsp. capri str. GM12]
 gi|256384684|gb|ACU79253.1| ribosomal RNA large subunit methyltransferase J [Mycoplasma
           mycoides subsp. capri str. GM12]
 gi|296455958|gb|ADH22193.1| ribosomal RNA large subunit methyltransferase J [synthetic
           Mycoplasma mycoides JCVI-syn1.0]
          Length = 268

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 23/177 (12%), Positives = 53/177 (29%), Gaps = 2/177 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ + I +  +  SR + +  I  + V VN I + + +  V S D IE+    L    R 
Sbjct: 4   RLDEYIYKNNLTQSRNKAKEHILNKEVYVNNIAIIKPSFLVDSNDLIEIRSTKLEYVSRA 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L           ++                 + +   L    +      +   L  +
Sbjct: 64  YEKLKKAINKWNIDLTNKICLDIGASTGGFTQCCLDNNASLVYAVDVGTDQLHSSLLNNL 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             +  +Q+      +       D +      I ++   +  ++  L+        + 
Sbjct: 124 KVINMSQYNFRNAKKQDFLKSIDFVCCDVSFISLE-KIFLPLKDILEFNTSGVFLIK 179


>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 = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 30/238 (12%), Positives = 61/238 (25%), Gaps = 31/238 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----E 61
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + I    E
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVE 69

Query: 62  VDGVP----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
           V+             +   +   + +      +V   +     + +   L      V   
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIVEVP 129

Query: 112 -----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-----------FHGQVDQ 155
                 RLD +T GL+++         L     +                      Q   
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     V            +     +   + + L  G+  +I+         + 
Sbjct: 190 RHATKRTLMAVHPMGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 247


>gi|315127932|ref|YP_004069935.1| 30S ribosomal protein S4 [Pseudoalteromonas sp. SM9913]
 gi|332533190|ref|ZP_08409057.1| 30S ribosomal protein S4 [Pseudoalteromonas haloplanktis ANT/505]
 gi|315016446|gb|ADT69784.1| 30S ribosomal protein S4 [Pseudoalteromonas sp. SM9913]
 gi|332037269|gb|EGI73724.1| 30S ribosomal protein S4 [Pseudoalteromonas haloplanktis ANT/505]
          Length = 206

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G AS R E  ++++ + + VNG ++   +  +   D + +
Sbjct: 96  QRLDNVVYRMGFASTRAEARQLVSHKAILVNGRVVNIPSYVITPEDTVVI 145


>gi|311898675|dbj|BAJ31083.1| putative translation initiation factor IF-2 [Kitasatospora setae
           KM-6054]
          Length = 1035

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 7/77 (9%), Positives = 11/77 (14%)

Query: 277 EVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR 336
                        S             P            A G         G+R     
Sbjct: 181 PFTSGGASGMARPSAPRPGGAPSGERGPRPGGERGPRPAGAPGAGERGPRPGGERGPRPA 240

Query: 337 RSPSFPSKRSLRRTSAK 353
            +P    +      +  
Sbjct: 241 GAPGAGDRGPRPGGAPS 257



 Score = 39.4 bits (90), Expect = 0.81,   Method: Composition-based stats.
 Identities = 11/116 (9%), Positives = 20/116 (17%), Gaps = 9/116 (7%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G       +               +R    +  P    R  +   ++         A   
Sbjct: 189 GMARPSAPRPGGAPSGERGPRPGGERGPRPAGAPGAGERGPRPGGERGPRPAGAPGAGDR 248

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQR---------EENHRRSPSFPSKRSLRRTSA 352
             R   +                G                  P  PS   + R + 
Sbjct: 249 GPRPGGAPSGERGPRPGGAPRPGGPGAGAPRPDGMPRPAAPRPGAPSPSGMPRPNP 304


>gi|85859632|ref|YP_461834.1| rRNA methylase [Syntrophus aciditrophicus SB]
 gi|85722723|gb|ABC77666.1| rRNA methylase [Syntrophus aciditrophicus SB]
          Length = 277

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/60 (18%), Positives = 22/60 (36%), Gaps = 1/60 (1%)

Query: 7  VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          +       R+  ++   G+ ASR     +I    V V+    ++A   V     + + G 
Sbjct: 1  MGSREEKIRLDLLLVNRGLSASRERARALILSGAVLVDEKPADKAGALVSCAASVRIKGK 60


>gi|56752497|ref|YP_173198.1| hypothetical protein syc2488_d [Synechococcus elongatus PCC 6301]
 gi|56687456|dbj|BAD80678.1| hypothetical protein [Synechococcus elongatus PCC 6301]
          Length = 259

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 2/52 (3%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+   IA AG   SR ++  +I++  V+VN     + +  + + D + V G 
Sbjct: 185 RLD-AIASAGFGLSRSKMVDLISRGEVRVNWKAATQPSTQLKTGDLVAVRGK 235


>gi|309972703|gb|ADO95904.1| 23S rRNA pseudouridine synthase [Haemophilus influenzae R2846]
          Length = 324

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 29/238 (12%), Positives = 60/238 (25%), Gaps = 31/238 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----E 61
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + I    E
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVE 69

Query: 62  VDGVP----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
           V+             +   +   + +      +V   +     + +   L          
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPISEVP 129

Query: 112 -----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-----------FHGQVDQ 155
                 RLD +T GL+++         L     +                      Q   
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     V            +     +   + + L  G+  +I+         + 
Sbjct: 190 RHATKRTLMAVHPMGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 247


>gi|312134570|ref|YP_004001908.1| RNA-binding S4 domain-containing protein [Caldicellulosiruptor
          owensensis OL]
 gi|311774621|gb|ADQ04108.1| RNA-binding S4 domain protein [Caldicellulosiruptor owensensis
          OL]
          Length = 80

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   +      RV VNG + +  + +V   D IEV
Sbjct: 1  MRIDKYLKVSRIIKRRTLAQEACEAGRVFVNGKVAK-PSTDVKVGDVIEV 49


>gi|239818004|ref|YP_002946914.1| 30S ribosomal protein S4 [Variovorax paradoxus S110]
 gi|319796381|ref|YP_004158021.1| ribosomal protein s4 [Variovorax paradoxus EPS]
 gi|259495303|sp|C5CQ76|RS4_VARPS RecName: Full=30S ribosomal protein S4
 gi|239804581|gb|ACS21648.1| ribosomal protein S4 [Variovorax paradoxus S110]
 gi|315598844|gb|ADU39910.1| ribosomal protein S4 [Variovorax paradoxus EPS]
          Length = 207

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V + D I V   
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAITVNGQSVNIPSYLVKTGDVIAVRDK 149


>gi|154508712|ref|ZP_02044354.1| hypothetical protein ACTODO_01220 [Actinomyces odontolyticus ATCC
          17982]
 gi|153798346|gb|EDN80766.1| hypothetical protein ACTODO_01220 [Actinomyces odontolyticus ATCC
          17982]
          Length = 275

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          R+   + R G+A SR    +MI   RVK++G ++ + A  +     I V+
Sbjct: 5  RIDSELVRRGLAKSRAAAAQMIEDGRVKLDGQIVLKPARQMDPAQAIVVE 54


>gi|119718096|ref|YP_925061.1| 30S ribosomal protein S4 [Nocardioides sp. JS614]
 gi|152112238|sp|A1SNI9|RS4_NOCSJ RecName: Full=30S ribosomal protein S4
 gi|119538757|gb|ABL83374.1| SSU ribosomal protein S4P [Nocardioides sp. JS614]
          Length = 202

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ RAG A +RR   +++     KVNG  ++  +  V + D I+V    L      
Sbjct: 92  RLDNVVYRAGFARTRRHARQLVTHGHFKVNGKKVDIPSFQVTAHDVIDVREKSLEMTPFI 151

Query: 74  R 74
            
Sbjct: 152 V 152


>gi|317401792|gb|EFV82407.1| pseudouridine synthase [Achromobacter xylosoxidans C54]
          Length = 336

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 33/240 (13%), Positives = 57/240 (23%), Gaps = 44/240 (18%)

Query: 15  RVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV------ 65
           R+ KV+A  G+    SR  ++  I    V+VNG   +     V   D I V         
Sbjct: 45  RLDKVLA--GLLPDHSRSRLQGWIEAGNVQVNGAPGKVRQT-VGPGDEIAVWAQPAPEAL 101

Query: 66  ---------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRL 114
                    P+       + +      +V   +     + +   L       +V   G +
Sbjct: 102 AFAPEAIDFPVVDESPDWIVVNKPAGLVVHPGAGNWSGTLLNGLLHRYPELAQVARAGIV 161

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----- 169
               +    L               Q       R +  +    L    K     G     
Sbjct: 162 HRLDKDTSGLMVVARNEIAQTHLVRQLQARSMGREYVALAHGWLAAAGKVDRPIGRDPRV 221

Query: 170 ----------------ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                             Y   +       G    V   L  G+  +I+         + 
Sbjct: 222 PVRMSVERPVAPKPAVTHYAPARRGQIDPGGRATEVVCRLETGRTHQIRVHLASLGHPLL 281


>gi|317494318|ref|ZP_07952732.1| ribosomal protein S4 [Enterobacteriaceae bacterium 9_2_54FAA]
 gi|316917568|gb|EFV38913.1| ribosomal protein S4 [Enterobacteriaceae bacterium 9_2_54FAA]
          Length = 206

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/73 (20%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + V VNG ++  A+  V   D + V     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAVVVNGRVVNIASYQVSPNDVVSVREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|304438388|ref|ZP_07398329.1| 30S ribosomal protein S4 [Selenomonas sp. oral taxon 149 str.
           67H29BP]
 gi|304368754|gb|EFM22438.1| 30S ribosomal protein S4 [Selenomonas sp. oral taxon 149 str.
           67H29BP]
          Length = 197

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +RR+  +++      VNG  ++  +  V   D IEV
Sbjct: 88  RMDNVVFRLGLANTRRQARQLVRHGHFTVNGKRVDIPSALVHEGDVIEV 136


>gi|261854973|ref|YP_003262256.1| ribosomal protein S4 [Halothiobacillus neapolitanus c2]
 gi|261835442|gb|ACX95209.1| ribosomal protein S4 [Halothiobacillus neapolitanus c2]
          Length = 207

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG ++  A+  V + D + V
Sbjct: 98  RLDNVVYRMGFGSTRSESRQLVSHRAITVNGEVVNIASYQVAANDVVAV 146


>gi|219854472|ref|YP_002471594.1| hypothetical protein CKR_1129 [Clostridium kluyveri NBRC 12016]
 gi|219568196|dbj|BAH06180.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 280

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/69 (23%), Positives = 31/69 (44%), Gaps = 3/69 (4%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDH 59
          M  + ++ E    +R+  ++   GI S RE     I    + V+G  +++   N+  + +
Sbjct: 1  MTKEFVMSEPK--ERIDVLLVDKGIFSSRERARASIMAGEIFVDGRRVDKCGQNIKRSSN 58

Query: 60 IEVDGVPLR 68
          IE  G  L 
Sbjct: 59 IEFRGEKLP 67


>gi|123966876|ref|YP_001011957.1| rRNA methyltransferase [Prochlorococcus marinus str. MIT 9515]
 gi|123201242|gb|ABM72850.1| FtsJ cell division protein:S4 domain:Hemolysin A [Prochlorococcus
          marinus str. MIT 9515]
          Length = 270

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 9/54 (16%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVK-VNGILLERAAVNVMSTDHIEVDGVP 66
          R+   +   G+  +R++ + +I   +VK +NG + ++    V++     ++   
Sbjct: 6  RLDLYLLSQGLCETRQKAQGLILAGKVKDINGKIFDKPGQQVITGTEFIIESEA 59


>gi|37519794|ref|NP_923171.1| hypothetical protein gsl0225 [Gloeobacter violaceus PCC 7421]
 gi|35210785|dbj|BAC88166.1| gsl0225 [Gloeobacter violaceus PCC 7421]
          Length = 71

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/61 (18%), Positives = 27/61 (44%), Gaps = 9/61 (14%)

Query: 7  VQENFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
          + E  T  ++ + +     A+ G     + + +I +  V VNG +  R    +++ D + 
Sbjct: 1  MSEERTFIKLDQFLKLVGAAQTGG----QAKILIQEGEVLVNGAVETRRGRKLLAGDQVT 56

Query: 62 V 62
          +
Sbjct: 57 L 57


>gi|269469225|gb|EEZ80756.1| ribosomal protein S4 [uncultured SUP05 cluster bacterium]
          Length = 208

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V + D I V
Sbjct: 99  RLDNVVYRMGFGATRAEARQLVSHKSILVNGSIVNIPSYQVSANDEISV 147


>gi|15615771|ref|NP_244075.1| 30S ribosomal protein S4 [Bacillus halodurans C-125]
 gi|26399508|sp|Q9K7Z8|RS4_BACHD RecName: Full=30S ribosomal protein S4
 gi|10175832|dbj|BAB06928.1| 30S ribosomal protein S4 [Bacillus halodurans C-125]
          Length = 200

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 93  RLDNLVYRMGLARTRRAARQLVNHGHITVDGQRVDIPSYRVKPGQVIGV 141


>gi|312128212|ref|YP_003993086.1| RNA-binding S4 domain-containing protein [Caldicellulosiruptor
          hydrothermalis 108]
 gi|311778231|gb|ADQ07717.1| RNA-binding S4 domain protein [Caldicellulosiruptor
          hydrothermalis 108]
          Length = 80

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   ++     RV VNG + +  + +V   D IEV
Sbjct: 1  MRIDKYLKVSRIIKRRTLAQQACEAGRVFVNGKVAK-PSTDVKVGDVIEV 49


>gi|226323041|ref|ZP_03798559.1| hypothetical protein COPCOM_00813 [Coprococcus comes ATCC 27758]
 gi|225208608|gb|EEG90962.1| hypothetical protein COPCOM_00813 [Coprococcus comes ATCC 27758]
          Length = 90

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 17/66 (25%), Positives = 33/66 (50%), Gaps = 2/66 (3%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKAER 72
          R+  V+ R G A +RRE  +++  ++V VNG  +   +  + + D IE+ +G  +    +
Sbjct: 16 RLDNVVFRLGFARTRREARQIVDHKQVLVNGKQVNIPSYLIKAGDVIEIKEGKKIFTEIQ 75

Query: 73 TRLWLY 78
               Y
Sbjct: 76 RYRRSY 81


>gi|302023694|ref|ZP_07248905.1| RNA pseudouridylate synthase [Streptococcus suis 05HAS68]
          Length = 54

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 1/47 (2%)

Query: 13 PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
            R+ K ++     SR      I   +V VNG   ++A  +V   D 
Sbjct: 9  GIRLDKALSDLTDLSRSFANEQIKAGQVLVNGQP-KKAKYSVQVGDV 54


>gi|291533845|emb|CBL06958.1| ribosomal large subunit pseudouridine synthase D [Megamonas
           hypermegale ART12/1]
          Length = 304

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 33/242 (13%), Positives = 71/242 (29%), Gaps = 46/242 (19%)

Query: 13  PQRVSKVIARAGIA-----SRREVERMIAQQRVKVNGILLERAAVNVMSTD--------- 58
             R+   +A          SR  +++MI    + VN  + +RA   + + D         
Sbjct: 12  GTRLDVFLA----GQEDNPSRASIQKMITDGAITVNNQV-KRANYKLKANDQITMVFEPP 66

Query: 59  -HIEVDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---- 110
             IEV    +      E   + + +K  G+V   +      T+ + L       +S    
Sbjct: 67  TEIEVKPENIPLDILYEDNDIIVINKARGMVVHPAAGVYSGTLVNALLYHCHDELSGING 126

Query: 111 -------------------VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151
                              V + D     L L        +         +   +   +G
Sbjct: 127 KIRPGIVHRLDKDTSGVMVVAKNDFAHNDLALQIGSKTAIKEYVALVHGNITEEKGIING 186

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + +  ++  K  +V  G         +  +  +  +V   L  G+  +I+    +    
Sbjct: 187 NIGRHPIDRKKMAVVTNGGKPATTVFHVLERYKNCTFVQCRLLTGRTHQIRVHMAYIGHP 246

Query: 212 VN 213
           + 
Sbjct: 247 LI 248


>gi|322412877|gb|EFY03785.1| 30S ribosomal protein S4 [Streptococcus dysgalactiae subsp.
           dysgalactiae ATCC 27957]
 gi|323128282|gb|ADX25579.1| 30S ribosomal protein S4 [Streptococcus dysgalactiae subsp.
           equisimilis ATCC 12394]
          Length = 203

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V +   I V
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVEAGQVISV 142


>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 = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 31/243 (12%), Positives = 65/243 (26%), Gaps = 38/243 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           V +    +RV    AR    SR  +  +I +  V ++G  + RA+V V +   ++VD   
Sbjct: 6   VPDGLDGERVDVAAARMSGVSRSRIGNLIEEGGVFLDGQQVSRASVRVTAGQMLDVDLSD 65

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                        G+ +   +   + +              +G S V     + F+   S
Sbjct: 66  PVSTPSITPQIVEGMRIVHDDSDIVVVDKPAGVAAHPSLGWEGPSVVEHLAAAGFAISTS 125

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPST---------------------QWLRVYRVRF 149
                      L +   G +       +                           +    
Sbjct: 126 GLLERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRAVDKVYLALVQGHPDPFAGTI 185

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +D  +   K  ++ G  +                + V L  G+  +I+       
Sbjct: 186 DAPIGRDHRHDW-KMAIVDGGRHSVTHYETVEAFRHATLLKVHLETGRTHQIRVHMAAVK 244

Query: 210 WKV 212
              
Sbjct: 245 HPC 247


>gi|254500931|ref|ZP_05113082.1| hemolysin A [Labrenzia alexandrii DFL-11]
 gi|222437002|gb|EEE43681.1| hemolysin A [Labrenzia alexandrii DFL-11]
          Length = 246

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 1/52 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          QR+ + +   G   SR      I +  V VNG +  + A  V +   I V+ 
Sbjct: 4  QRLDQHLVDTGHFPSRARARDAILRGTVSVNGAVCGKPAQKVAANAAIAVED 55


>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 = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 30/244 (12%), Positives = 71/244 (29%), Gaps = 41/244 (16%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKV-NGILLERAAVNVMSTDHIEVDGVP- 66
           E    QR+   ++     SR ++++ I    +++ NG +L   +  +   + IE+ G   
Sbjct: 19  EKGVGQRLDLFLSSLLNVSRNKIKKKILSGDLRLKNGAVL-EPSHRIRGIEEIEIRGGLT 77

Query: 67  ---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                          +   +   L +  +   +V         + V   L          
Sbjct: 78  EEIPSLPKAEEIALEILYEDEEILIVNKQRGMVVHPSCGHWSGTLVNSLLFHYGESLPGS 137

Query: 107 ---RVISVGRLDINTEGLLLLTN--------------DGGLARVLELPSTQWLRVYRVRF 149
              R   V RLD +T G++++                       L L   ++  +     
Sbjct: 138 SLLRPGIVHRLDKDTSGVMVIAKTERSLKSLLLQFSQRTVQKVYLCLCKNRFPYLRYSFE 197

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                            ++G    + + TL       +++      G+  +I+       
Sbjct: 198 ANIHRHASDRKKMAVHRLKG-KTAETRFTLLFASSQASFLKCEPVSGRTHQIRVHLSHLG 256

Query: 210 WKVN 213
           + + 
Sbjct: 257 FPII 260


>gi|261250393|ref|ZP_05942968.1| SSU ribosomal protein S4p (S9e) [Vibrio orientalis CIP 102891]
 gi|260938962|gb|EEX94949.1| SSU ribosomal protein S4p (S9e) [Vibrio orientalis CIP 102891]
          Length = 206

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V + D + +
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAILVNGKVVNIPSFKVAANDVVSI 145


>gi|229019885|ref|ZP_04176683.1| 30S ribosomal protein S4 [Bacillus cereus AH1273]
 gi|229026111|ref|ZP_04182488.1| 30S ribosomal protein S4 [Bacillus cereus AH1272]
 gi|229032307|ref|ZP_04188280.1| 30S ribosomal protein S4 [Bacillus cereus AH1271]
 gi|229175366|ref|ZP_04302881.1| 30S ribosomal protein S4 [Bacillus cereus MM3]
 gi|228608198|gb|EEK65505.1| 30S ribosomal protein S4 [Bacillus cereus MM3]
 gi|228729087|gb|EEL80090.1| 30S ribosomal protein S4 [Bacillus cereus AH1271]
 gi|228735189|gb|EEL85807.1| 30S ribosomal protein S4 [Bacillus cereus AH1272]
 gi|228741405|gb|EEL91607.1| 30S ribosomal protein S4 [Bacillus cereus AH1273]
          Length = 200

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 93  RLDNLVYRMGLARTRRAARQLVNHGHITVDGSRVDIPSYRVKPGQTISV 141


>gi|227871775|ref|ZP_03990180.1| ribosomal protein S4 [Oribacterium sinus F0268]
 gi|227842376|gb|EEJ52601.1| ribosomal protein S4 [Oribacterium sinus F0268]
          Length = 197

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI R G+A +RRE  +++  + V VNG ++   +  V + D I++
Sbjct: 88  RLDNVIFRMGMARTRREARQVVGHRHVTVNGKIVNIPSYLVSAGDVIQI 136


>gi|313891858|ref|ZP_07825463.1| ribosomal RNA large subunit methyltransferase J [Dialister
          microaerophilus UPII 345-E]
 gi|313119852|gb|EFR43039.1| ribosomal RNA large subunit methyltransferase J [Dialister
          microaerophilus UPII 345-E]
          Length = 278

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 9/57 (15%), Positives = 23/57 (40%), Gaps = 1/57 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          +R+  ++   G   SR   +R I    + V+ + +++    V     + + G  +  
Sbjct: 13 ERLDVLLVERGFFNSRENAKRHIMAGIILVDNMPVDKPGTKVCIDSELRIKGKIMPY 69


>gi|294678313|ref|YP_003578928.1| heat shock protein [Rhodobacter capsulatus SB 1003]
 gi|294477133|gb|ADE86521.1| heat shock protein [Rhodobacter capsulatus SB 1003]
          Length = 92

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 1/55 (1%)

Query: 9  ENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
                R+ K + +A  A SR     ++   RV+VNG  LE+    V   D + +
Sbjct: 2  SEGDRIRIDKWLWQARFAKSRALAVDLVTAGRVRVNGQKLEKPGRAVGPGDVLTL 56


>gi|283788068|ref|YP_003367933.1| 30S ribosomal subunit protein S4 [Citrobacter rodentium ICC168]
 gi|282951522|emb|CBG91221.1| 30S ribosomal subunit protein S4 [Citrobacter rodentium ICC168]
          Length = 206

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + V VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAVMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|224132002|ref|XP_002321231.1| predicted protein [Populus trichocarpa]
 gi|222862004|gb|EEE99546.1| predicted protein [Populus trichocarpa]
          Length = 255

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 12/55 (21%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 9  ENFTPQRVSKV-IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          +    +R+ ++ + R    SR  ++  I Q +V V+G +  +A   V     +E+
Sbjct: 6  KKGRKRRLDEICLERFQQYSRTFIQSWILQGKVFVDGKVANKAGTPVSEKSVVEI 60


>gi|28897055|ref|NP_796660.1| 30S ribosomal protein S4 [Vibrio parahaemolyticus RIMD 2210633]
 gi|153840228|ref|ZP_01992895.1| ribosomal protein S4 [Vibrio parahaemolyticus AQ3810]
 gi|156973074|ref|YP_001443981.1| 30S ribosomal protein S4 [Vibrio harveyi ATCC BAA-1116]
 gi|260877973|ref|ZP_05890328.1| ribosomal protein S4 [Vibrio parahaemolyticus AN-5034]
 gi|260895673|ref|ZP_05904169.1| ribosomal protein S4 [Vibrio parahaemolyticus Peru-466]
 gi|260903551|ref|ZP_05911946.1| ribosomal protein S4 [Vibrio parahaemolyticus AQ4037]
 gi|262392492|ref|YP_003284346.1| 30S ribosomal protein S4p [Vibrio sp. Ex25]
 gi|269964713|ref|ZP_06178951.1| 30S ribosomal protein S4 [Vibrio alginolyticus 40B]
 gi|31340377|sp|Q87SZ1|RS4_VIBPA RecName: Full=30S ribosomal protein S4
 gi|171769916|sp|A7N0H7|RS4_VIBHB RecName: Full=30S ribosomal protein S4
 gi|28805263|dbj|BAC58544.1| ribosomal protein S4 [Vibrio parahaemolyticus RIMD 2210633]
 gi|149746105|gb|EDM57235.1| ribosomal protein S4 [Vibrio parahaemolyticus AQ3810]
 gi|156524668|gb|ABU69754.1| hypothetical protein VIBHAR_00753 [Vibrio harveyi ATCC BAA-1116]
 gi|262336086|gb|ACY49881.1| SSU ribosomal protein S4p (S9e) [Vibrio sp. Ex25]
 gi|269830612|gb|EEZ84833.1| 30S ribosomal protein S4 [Vibrio alginolyticus 40B]
 gi|308089501|gb|EFO39196.1| ribosomal protein S4 [Vibrio parahaemolyticus Peru-466]
 gi|308090096|gb|EFO39791.1| ribosomal protein S4 [Vibrio parahaemolyticus AN-5034]
 gi|308109051|gb|EFO46591.1| ribosomal protein S4 [Vibrio parahaemolyticus AQ4037]
 gi|328471858|gb|EGF42735.1| 30S ribosomal protein S4 [Vibrio parahaemolyticus 10329]
          Length = 206

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V + D + +
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAILVNGKVVNVPSFKVAANDVVSI 145


>gi|88799195|ref|ZP_01114775.1| ribosomal protein S4 [Reinekea sp. MED297]
 gi|88778178|gb|EAR09373.1| ribosomal protein S4 [Reinekea sp. MED297]
          Length = 206

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG  +   +  V   D + V
Sbjct: 97  RLDNVVYRMGFGVTRAEARQLVSHKAILVNGQSVNIPSFQVKPGDVVSV 145


>gi|257483209|ref|ZP_05637250.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. tabaci ATCC
           11528]
 gi|331012437|gb|EGH92493.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. tabaci ATCC
           11528]
          Length = 206

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + V VNG  +   +  V + D + +
Sbjct: 97  RLDNVVYRMGFGSTRAESRQLVSHKSVSVNGKTVNVPSYQVRAGDVVAI 145


>gi|242089543|ref|XP_002440604.1| hypothetical protein SORBIDRAFT_09g003890 [Sorghum bicolor]
 gi|241945889|gb|EES19034.1| hypothetical protein SORBIDRAFT_09g003890 [Sorghum bicolor]
          Length = 299

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 5  NIVQENFTPQRVSKV-IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            +Q     +R+ +V + R    SR  ++  I Q +V V+G ++ +A   V     IE+
Sbjct: 34 QKIQLPKKKRRLDEVCLGRFQQYSRTYIQSWILQGKVIVDGRVVNKAGTQVSDKSVIEI 92


>gi|167037517|ref|YP_001665095.1| hemolysin A [Thermoanaerobacter pseudethanolicus ATCC 33223]
 gi|320115931|ref|YP_004186090.1| hemolysin A [Thermoanaerobacter brockii subsp. finnii Ako-1]
 gi|166856351|gb|ABY94759.1| hemolysin A [Thermoanaerobacter pseudethanolicus ATCC 33223]
 gi|319929022|gb|ADV79707.1| hemolysin A [Thermoanaerobacter brockii subsp. finnii Ako-1]
          Length = 264

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 11 FTPQRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             +R+  ++ + G  S RE  +  I    V V+G  +E+A   V     IE+
Sbjct: 3  SKKERLDVLLVQKGFFSSREKAKASIMAGEVYVDGKKIEKAGEFVNIDSSIEI 55


>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 = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 26/242 (10%), Positives = 72/242 (29%), Gaps = 36/242 (14%)

Query: 8   QENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
            EN   +R+   +      A+R  ++++I    V++ G  + ++   +  T+ I V+   
Sbjct: 13  DENDKGKRIDSFLNEVIDDATRSYIQKIIDGGYVEITGKKVTKSGNKLKGTETITVNIPE 72

Query: 64  GVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
              L              ++  + +   P  +V         + V   L  I       G
Sbjct: 73  DEILDVIPENIPLNIIYEDKDIVVINKAPDMVVHPAHGNYNGTLVNALLYHIKDLSTING 132

Query: 113 RLDINTEGLLLLTNDGGLA------------RVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
            +       L     G +              + +  + +   +   +   +    ++  
Sbjct: 133 VIRPGIVHRLDKDTSGVIVVAKNDEAHSTLSDMFKEKTLEKTYICIAKGIFKDKSGRIET 192

Query: 161 LKKGIVIQGICYGDMQ---------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           L             +            +  ++ + + V V +  G+  +I+   ++ N  
Sbjct: 193 LIGRDSRDRKKMAVVDINGKNAISNYEILDEEKNFSLVKVRIETGRTHQIRVHMKYLNHP 252

Query: 212 VN 213
           + 
Sbjct: 253 IL 254


>gi|291562745|emb|CBL41561.1| SSU ribosomal protein S4P [butyrate-producing bacterium SS3/4]
          Length = 197

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI R G A +R+E  +++  + V VNG  +   +  V + D +E+
Sbjct: 88  RLDNVIFRLGFARTRKEARQIVDHKHVLVNGKCVNIPSYLVKAGDVVEI 136


>gi|187777365|ref|ZP_02993838.1| hypothetical protein CLOSPO_00921 [Clostridium sporogenes ATCC
          15579]
 gi|187774293|gb|EDU38095.1| hypothetical protein CLOSPO_00921 [Clostridium sporogenes ATCC
          15579]
          Length = 68

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/59 (23%), Positives = 24/59 (40%), Gaps = 5/59 (8%)

Query: 10 NFTPQRVSKVIARAG---IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          N    ++   +  +G   + S  E +  I    VKVNG + +R    +   D IE +  
Sbjct: 7  NSEIIKLDSFLKWSGATTLGS--EAKFFIQNGEVKVNGEIEKRRGRKLKIGDLIEFNNE 63


>gi|170758477|ref|YP_001785338.1| S4 domain-containing protein [Clostridium botulinum A3 str. Loch
          Maree]
 gi|169405466|gb|ACA53877.1| S4 domain protein [Clostridium botulinum A3 str. Loch Maree]
          Length = 68

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/59 (23%), Positives = 24/59 (40%), Gaps = 5/59 (8%)

Query: 10 NFTPQRVSKVIARAG---IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          N    ++   +  +G   + S  E +  I    VKVNG + +R    +   D IE +  
Sbjct: 7  NSEIIKLDSFLKWSGATTLGS--EAKFFIQNGEVKVNGEIEKRRGRKLKIGDLIEFNNE 63


>gi|150025382|ref|YP_001296208.1| 30S ribosomal protein S4 [Flavobacterium psychrophilum JIP02/86]
 gi|172048611|sp|A6GZ74|RS4_FLAPJ RecName: Full=30S ribosomal protein S4
 gi|149771923|emb|CAL43397.1| 30S ribosomal protein S4 [Flavobacterium psychrophilum JIP02/86]
          Length = 201

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA +RR   ++++ + V VNG L+   + ++   D + V
Sbjct: 94  RLDNVVYRMGIAPTRRAARQIVSHRHVTVNGELVNVPSYHLKPGDKVAV 142


>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 = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 34/247 (13%), Positives = 73/247 (29%), Gaps = 36/247 (14%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           + + I+ E    QR    +A     +R  +++++ + R  V G  + ++   +   D I+
Sbjct: 11  QQRLIITEQEAGQRADVGLAAMLELTRSNMQKLLEEGR-AVRGSKVLKSNYKLRLGDEID 69

Query: 62  V--------DGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           V        D  P      +   +   + +      +V   +     + V   L    + 
Sbjct: 70  VTLPEPQPLDVQPENIPLDIIYEDEDVVVVNKARGMVVHPAAGNLNGTLVNALLYHCKNL 129

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------------ 155
               G +       L     G +       +   L         Q               
Sbjct: 130 SGINGVIRPGIVHRLDKDTSGIMICAKNDAAHLSLSQQIQAKTAQRTYLAVVRGNIKTDS 189

Query: 156 ---------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                    DK +  K  +V +G      +  +  + G    V   LR G+  +I+   E
Sbjct: 190 GVIETLIARDKNDRKKMAVVKEGGRDAVTEYEVLERFGKYTIVRCRLRTGRTHQIRVHME 249

Query: 207 FFNWKVN 213
           +  + + 
Sbjct: 250 YLGYPLV 256


>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 = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 30/238 (12%), Positives = 61/238 (25%), Gaps = 31/238 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----E 61
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + I    E
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVE 69

Query: 62  VDGVP----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
           V+             +   +   + +      +V   +     + +   L      V   
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIVEVP 129

Query: 112 -----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-----------FHGQVDQ 155
                 RLD +T GL+++         L     +                      Q   
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     V            +     +   + + L  G+  +I+         + 
Sbjct: 190 RHATKRTLMAVHPMGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 247


>gi|315103148|gb|EFT75124.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL050PA2]
          Length = 306

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 32/243 (13%), Positives = 65/243 (26%), Gaps = 38/243 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           V +    +RV    AR    SR  +  +I    V ++G L+ RA+V V +   ++VD   
Sbjct: 6   VPDGLDGERVDVAAARMSGVSRSRISSLIEDGGVFLDGQLVSRASVRVATGQMLDVDLCD 65

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                        G+ +   +   + +              +G S V     + F+   S
Sbjct: 66  PVATPSITPQIVEGMRIIHDDSDIVVVDKPAGVAAHPSLGWEGPSVVEHLAAAGFAISTS 125

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPST---------------------QWLRVYRVRF 149
                      L +   G +       +                           +    
Sbjct: 126 GAPERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTGTI 185

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +D  +   K  ++ G  +                + V L  G+  +I+       
Sbjct: 186 DAPIGRDHRHDW-KMAIVDGGRHSVTHYETVEAFRHATLLKVHLETGRTHQIRVHMAAIK 244

Query: 210 WKV 212
              
Sbjct: 245 HPC 247


>gi|292492445|ref|YP_003527884.1| ribosomal protein S4 [Nitrosococcus halophilus Nc4]
 gi|291581040|gb|ADE15497.1| ribosomal protein S4 [Nitrosococcus halophilus Nc4]
          Length = 208

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++I+ + + VNG ++   +  + + D + V
Sbjct: 99  RLDNVVYRMGFGSTRAEARQLISHKGILVNGKVINVPSYQIRAEDVVSV 147


>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 = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 24/230 (10%), Positives = 54/230 (23%), Gaps = 31/230 (13%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNV------------------M 55
           R+ + +A+     SR  ++  I    VKVNG ++ +A   V                   
Sbjct: 19  RLDQALAQLFPDYSRSRIKVWIESDLVKVNGNIVNKAREKVFGGETVEITAEIEEEIRFE 78

Query: 56  STD----HIEVDGVPLRKAERTRLWLYHKPIG---LVTTHSDPDGRSTVFDNLPSIFSRV 108
             D     +  D   +   +   L ++         V                  I  R+
Sbjct: 79  PQDIPLNIVYEDDDIIVINKPKDLVVHPGAGNPDGTVLNALLHYYPPIAEVPRAGIVHRL 138

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKK 163
                  +     +        A      + ++  +           D            
Sbjct: 139 DKDTTGLMVVAKNIPAQTHLVTALQKRRITREYEAIASGIMTQGGKVDEPMARHPTKRTA 198

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             V            +  +  +   + + L  G+  +I+         + 
Sbjct: 199 MAVHPMGKPAVTHYRIMERFRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 248


>gi|260589250|ref|ZP_05855163.1| ribosomal protein S4 [Blautia hansenii DSM 20583]
 gi|331082658|ref|ZP_08331781.1| 30S ribosomal protein S4 [Lachnospiraceae bacterium 6_1_63FAA]
 gi|260540331|gb|EEX20900.1| ribosomal protein S4 [Blautia hansenii DSM 20583]
 gi|330400277|gb|EGG79919.1| 30S ribosomal protein S4 [Lachnospiraceae bacterium 6_1_63FAA]
          Length = 197

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI R G+A +R+E  +++  + V VNG  +   +  V + D IE+
Sbjct: 88  RLDNVIFRMGLARTRKEARQIVDHKHVMVNGKQVNIPSYLVKAGDVIEI 136


>gi|323492143|ref|ZP_08097305.1| 30S ribosomal protein S4 [Vibrio brasiliensis LMG 20546]
 gi|323313704|gb|EGA66806.1| 30S ribosomal protein S4 [Vibrio brasiliensis LMG 20546]
          Length = 206

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V + D + +
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAILVNGKVVNIPSFKVAANDVVSI 145


>gi|222528664|ref|YP_002572546.1| RNA-binding S4 domain-containing protein [Caldicellulosiruptor
          bescii DSM 6725]
 gi|222455511|gb|ACM59773.1| RNA-binding S4 domain protein [Caldicellulosiruptor bescii DSM
          6725]
          Length = 80

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   ++     RV VNG + +  + +V   D IEV
Sbjct: 1  MRIDKYLKVSRIIKRRTLAQQACEAGRVFVNGKVAK-PSTDVKVGDVIEV 49


>gi|162447341|ref|YP_001620473.1| rRNA methyltransferase [Acholeplasma laidlawii PG-8A]
 gi|161985448|gb|ABX81097.1| rRNA methyltransferase, putative [Acholeplasma laidlawii PG-8A]
          Length = 232

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 6/51 (11%), Positives = 22/51 (43%), Gaps = 1/51 (1%)

Query: 14 QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+ K +       +R +    I +  V ++  ++ + + +V+    ++ +
Sbjct: 1  MRLDKYLTDHYKDITRSQFSDFIKRGFVTIDDKVITKPSFDVLEHHVVKFN 51


>gi|154509029|ref|ZP_02044671.1| hypothetical protein ACTODO_01546 [Actinomyces odontolyticus ATCC
          17982]
 gi|153798663|gb|EDN81083.1| hypothetical protein ACTODO_01546 [Actinomyces odontolyticus ATCC
          17982]
          Length = 76

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 10/34 (29%), Positives = 17/34 (50%)

Query: 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          +   +I    V VNG +  R   ++ + D +EVD
Sbjct: 29 QARELIQAGDVTVNGEVETRRGHHLSAGDLVEVD 62


>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 = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 28/238 (11%), Positives = 56/238 (23%), Gaps = 45/238 (18%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST----------------- 57
           R+ K +A A   SR  V+ +IA   V++ G     A+  V                    
Sbjct: 16  RLDKALADATGLSRERVKGLIADGVVEIAGKAARSASAKVAEGERYFIALPPPEPLETVA 75

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISV 111
             I +D   +   +   L +      +V   +     + V   L          + V   
Sbjct: 76  QDIPLD---VVFEDAYLLVVNKPAGMVVHPAAGNPDGTLVNALLHHCAGRLSGINGVARP 132

Query: 112 GRLDINTEGLLL-----------------LTNDGGLARVLELPSTQWLRVYRVRFHGQVD 154
           G +    +                       +     R L   +                
Sbjct: 133 GIVHRIDKDTSGLLVVAKSDAAHEGLAKQFADHSITRRYLAACAGHPNPPSGTVSGRIGR 192

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA--WVTVGLREGKNREIKKVFEFFNW 210
            D+       +              +T +  N    +   L  G+  +++        
Sbjct: 193 SDRDRKKMAVLPDDSTRGKHAVTHYETVRRLNHAALIECRLETGRTHQVRVHCASIGH 250


>gi|148378014|ref|YP_001252555.1| S4 domain protein [Clostridium botulinum A str. ATCC 3502]
 gi|153932828|ref|YP_001382413.1| S4 domain-containing protein [Clostridium botulinum A str. ATCC
          19397]
 gi|153936289|ref|YP_001385965.1| S4 domain-containing protein [Clostridium botulinum A str. Hall]
 gi|153938642|ref|YP_001389372.1| S4 domain-containing protein [Clostridium botulinum F str.
          Langeland]
 gi|168181118|ref|ZP_02615782.1| S4 domain protein [Clostridium botulinum NCTC 2916]
 gi|170757697|ref|YP_001779629.1| S4 domain-containing protein [Clostridium botulinum B1 str. Okra]
 gi|226947225|ref|YP_002802316.1| S4 domain protein [Clostridium botulinum A2 str. Kyoto]
 gi|148287498|emb|CAL81557.1| putative RNA-binding mediating protein [Clostridium botulinum A
          str. ATCC 3502]
 gi|152928872|gb|ABS34372.1| S4 domain protein [Clostridium botulinum A str. ATCC 19397]
 gi|152932203|gb|ABS37702.1| S4 domain protein [Clostridium botulinum A str. Hall]
 gi|152934538|gb|ABS40036.1| S4 domain protein [Clostridium botulinum F str. Langeland]
 gi|169122909|gb|ACA46745.1| S4 domain protein [Clostridium botulinum B1 str. Okra]
 gi|182668110|gb|EDT80089.1| S4 domain protein [Clostridium botulinum NCTC 2916]
 gi|226841527|gb|ACO84193.1| S4 domain protein [Clostridium botulinum A2 str. Kyoto]
 gi|295317479|gb|ADF97856.1| S4 domain protein [Clostridium botulinum F str. 230613]
 gi|322804281|emb|CBZ01831.1| hypothetical protein H04402_00003 [Clostridium botulinum H04402
          065]
          Length = 68

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/59 (23%), Positives = 24/59 (40%), Gaps = 5/59 (8%)

Query: 10 NFTPQRVSKVIARAG---IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          N    ++   +  +G   + S  E +  I    VKVNG + +R    +   D IE +  
Sbjct: 7  NSEIIKLDSFLKWSGATTLGS--EAKFFIQNGEVKVNGEIEKRRGRKLKIDDLIEFNNE 63


>gi|118474954|ref|YP_892206.1| pseudouridine synthase [Campylobacter fetus subsp. fetus 82-40]
 gi|118414180|gb|ABK82600.1| pseudouridine synthase [Campylobacter fetus subsp. fetus 82-40]
          Length = 254

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 26/198 (13%), Positives = 61/198 (30%), Gaps = 2/198 (1%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAERTRL 75
           K++A     S  E + +I    V   G  L  A   +      +V     P+   E   +
Sbjct: 8   KLLALQEGISNNEAKELIDSGLVSAGGKRLVLARGLLNENTSFKVTKLAKPVMIYEDDNI 67

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
              +KP  + +       +  + + L    S VI + + +   +  +    +  + +   
Sbjct: 68  VAVNKPPFITSEKVAEIFKFPLLNRLDKETSGVILLYKNEEFQKAAIKEFANNKVKKTYL 127

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
                 +                +     I +         V+    +G  + + VG+  
Sbjct: 128 AIVRGIVVDEFSVELPISTVKTKSGAFSKIDLSRGKTAITHVSPLMVEGKKSLIKVGIET 187

Query: 196 GKNREIKKVFEFFNWKVN 213
           G+  +I+    +  + V 
Sbjct: 188 GRTHQIRCHLAYSGYGVI 205


>gi|325843404|ref|ZP_08167962.1| ribosomal protein S4 [Turicibacter sp. HGF1]
 gi|325489326|gb|EGC91700.1| ribosomal protein S4 [Turicibacter sp. HGF1]
          Length = 199

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR+  +++    + V+G  ++  + +V     I +
Sbjct: 92  RLDNLVYRLGLAATRRQARQLVNHGHITVDGKRVDIPSYSVKPGQTISL 140


>gi|167564391|ref|ZP_02357307.1| 30S ribosomal protein S4 [Burkholderia oklahomensis EO147]
 gi|167571538|ref|ZP_02364412.1| 30S ribosomal protein S4 [Burkholderia oklahomensis C6786]
          Length = 207

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + +NG++    +  V + D I +
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAITLNGVVANVPSQQVKAGDVISI 146


>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 = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 26/233 (11%), Positives = 68/233 (29%), Gaps = 33/233 (14%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN----------------VMST 57
            R+ + +A A   SR + +  I   RV+V   ++ + A                  V+  
Sbjct: 1   MRLDQAVAEALSVSRAKAQAWIQAGRVRVGDRVVLKPAYRLKGEEVAVEPVEEAPMVLPE 60

Query: 58  DH---IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
           D    I  +   +    +    L H   G+ +        +  +  +      ++  G +
Sbjct: 61  DLPIPILYEDEDVLALNKPPGLLTHPAPGVYSGTVVNLLLARYYGPVEKGPPELVRPGIV 120

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK------------LNLLK 162
               +    +        VLE  +  +     ++ +  + +                  +
Sbjct: 121 HRLDKDTSGVLVVAKHGGVLEGLARAFRDRLVMKRYLAITEGHPREGVLIAPIGRHPRER 180

Query: 163 KGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             + + G+       +  +    G  A V      G+  +I+   ++    + 
Sbjct: 181 HKMHVGGLAARYAETEFQVLATAGPYALVEARPHTGRTHQIRVHLKYLGAPIL 233


>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 = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 36/249 (14%), Positives = 67/249 (26%), Gaps = 38/249 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K +  +   +  QR+   +A      SR ++   I    + +N    +     V   D 
Sbjct: 5   IKKQLTIPREYHNQRIDTALAHLLSDYSRSQISNWIKCGSIMLNHQSCK-PKDKVEDGDL 63

Query: 60  IEVD---GVP---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
           I+++                     +   +   L L      +V   +     + V   L
Sbjct: 64  IDINVNFNKTDTNLEHCIPEEIPLNIIYEDDDVLVLNKPANMVVHPGAGNKEHTLVNALL 123

Query: 102 PS-----IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR---------- 146
                     R   V RLD +T GLL++         L                      
Sbjct: 124 HHSPSLIHLPRAGIVHRLDKDTTGLLIIAKTLPAHTSLIRQMQAREIKRHYITLVQGHII 183

Query: 147 --VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                     +   N LK  +   G         +  Q      + V L  G+  +I+  
Sbjct: 184 SGGTIDTGFGRHPRNRLKMAVQEHGRQA-ITHYAVKKQYHDFTLLDVNLMTGRTHQIRVH 242

Query: 205 FEFFNWKVN 213
             + +  V 
Sbjct: 243 LAYIHHPVV 251


>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 = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 23/231 (9%), Positives = 52/231 (22%), Gaps = 33/231 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           R+ + + +     SR  ++  + Q  V VNG         V   +HI V           
Sbjct: 33  RLDQALVKLFPEYSRSRLQDWVEQGLVTVNGK-AGSVKQKVWGGEHISVSPQIHPSEQPY 91

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----------SR 107
                   +   +   L +      +V   S     + +   L                R
Sbjct: 92  HAEDIPLDIVYEDDAMLIINKPVGLVVHPGSGNWQGTLLNALLHHAPQLADVPRAGIVHR 151

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           +       +     L+                ++L +           +          +
Sbjct: 152 LDKDTSGLMVVAKSLVAQTALVRQMQARSVKREYLALVWGELDRDYTINVPIGRHPSQRV 211

Query: 168 QGICYGDMQVTLDTQKGSN-----AWVTVGLREGKNREIKKVFEFFNWKVN 213
           +       +  +              V   L  G+  +I+         + 
Sbjct: 212 KMATTESGKEAITHVGIEERFPYCTLVRCRLETGRTHQIRVHMTHIGHPLI 262


>gi|183600728|ref|ZP_02962221.1| hypothetical protein PROSTU_04324 [Providencia stuartii ATCC 25827]
 gi|212709003|ref|ZP_03317131.1| hypothetical protein PROVALCAL_00035 [Providencia alcalifaciens DSM
           30120]
 gi|268593565|ref|ZP_06127786.1| ribosomal protein S4 [Providencia rettgeri DSM 1131]
 gi|188019708|gb|EDU57748.1| hypothetical protein PROSTU_04324 [Providencia stuartii ATCC 25827]
 gi|212688369|gb|EEB47897.1| hypothetical protein PROVALCAL_00035 [Providencia alcalifaciens DSM
           30120]
 gi|291310842|gb|EFE51295.1| ribosomal protein S4 [Providencia rettgeri DSM 1131]
          Length = 206

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/73 (21%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  +M++ + + VNG ++  A+  V   D I V     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQMVSHKAIMVNGRVVNIASYQVSPNDVISVREKAKKQSRIK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|329298510|ref|ZP_08255846.1| 30S ribosomal protein S4 [Plautia stali symbiont]
          Length = 206

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + V VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKSVMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|291484092|dbj|BAI85167.1| hypothetical protein BSNT_02544 [Bacillus subtilis subsp. natto
           BEST195]
          Length = 257

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/62 (24%), Positives = 28/62 (45%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           D  I  +  +  R+  V A     SR++ + ++    VKVN  ++E  +  V   D + +
Sbjct: 170 DVEIRDDTVSSLRLDAVCASMSRQSRQKSQTLVKNGLVKVNWKVVEDPSYIVAEGDMLSI 229

Query: 63  DG 64
            G
Sbjct: 230 RG 231


>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 = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 26/199 (13%), Positives = 56/199 (28%), Gaps = 28/199 (14%)

Query: 42  VNGILLERAAVNVMSTDHIEVD---------------GVPLRKAERTRLWLYHKPIGLVT 86
           VN   +      +M  D +E+                 + +   +   + +        T
Sbjct: 38  VNDEPVTV-RKQLMPNDILEIHLPREIPSVNLIPYARKLEVLYEDAFVIIVTKPNNQNCT 96

Query: 87  THSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLLLLTNDGGLARVLELPSTQ- 140
              +    S +   L              V RLD NT G+++    G +  +    + + 
Sbjct: 97  PSREHPHESLIEQVLYHCQEHGENINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKVNLKK 156

Query: 141 -WLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNAWVTVGLR 194
            +  +   + H     +      K  +I         Y      +  Q    +   V L 
Sbjct: 157 IYTCLVYGKTHTFGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLH 216

Query: 195 EGKNREIKKVFEFFNWKVN 213
            G+  +I+  F+     + 
Sbjct: 217 TGRTHQIRVHFQHIGHPIV 235


>gi|269959712|ref|ZP_06174092.1| 30S ribosomal protein S4 [Vibrio harveyi 1DA3]
 gi|269835635|gb|EEZ89714.1| 30S ribosomal protein S4 [Vibrio harveyi 1DA3]
          Length = 202

 Score = 49.0 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V + D + +
Sbjct: 93  RLDNVVYRMGFGATRAEARQLVSHKAILVNGKVVNVPSFKVAANDVVSI 141


>gi|327395480|dbj|BAK12902.1| 30S ribosomal protein S4 RpsD [Pantoea ananatis AJ13355]
          Length = 176

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + V VNG ++  A+  V   D + +     +++   
Sbjct: 67  RLDNVVYRMGFGATRAEARQLVSHKSVLVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 126

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 127 AALELAEQREKPT 139


>gi|326516230|dbj|BAJ88138.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 318

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 12/36 (33%), Positives = 19/36 (52%)

Query: 27 SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          SR  ++  I Q +V VNG ++ +A   V     IE+
Sbjct: 56 SRTYIQSWILQGKVHVNGRVVNKAGTQVSDKSVIEI 91


>gi|291336629|gb|ADD96175.1| hypothetical protein [uncultured organism MedDCM-OCT-S05-C185]
          Length = 74

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 23/73 (31%), Positives = 38/73 (52%)

Query: 205 FEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSS 264
            +  + +VNRLIR+++GPFQLG L AG+  EV +  L+EQL      + +        ++
Sbjct: 1   MDSIDLQVNRLIRVAFGPFQLGNLSAGAVEEVPENKLKEQLSVFNESQNKNIKVMRGKNA 60

Query: 265 ETLVRDRPNIISE 277
             + R   +  S 
Sbjct: 61  HYIRRKARSKASN 73


>gi|227503700|ref|ZP_03933749.1| possible hemolysin A [Corynebacterium accolens ATCC 49725]
 gi|227075736|gb|EEI13699.1| possible hemolysin A [Corynebacterium accolens ATCC 49725]
          Length = 268

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          R+   + R  IA SR +   MI   RV V G   E+ A  V     I+V+
Sbjct: 7  RLDAELVRRKIARSREQAREMIKSGRVTVGGFKAEKPATVVDPEVSIKVE 56


>gi|163853708|ref|YP_001641751.1| hemolysin A [Methylobacterium extorquens PA1]
 gi|163665313|gb|ABY32680.1| hemolysin A [Methylobacterium extorquens PA1]
          Length = 250

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 3/53 (5%)

Query: 12 TPQRV--SKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
          T +R+   + +   G   SR +    I    V  +G L+ R +  V +   IE
Sbjct: 2  TGERLRADRFLVERGHFRSRAQARAAIEAGLVSADGRLVTRPSDLVEAGARIE 54


>gi|91786410|ref|YP_547362.1| 30S ribosomal protein S4 [Polaromonas sp. JS666]
 gi|123060350|sp|Q12G78|RS4_POLSJ RecName: Full=30S ribosomal protein S4
 gi|91695635|gb|ABE42464.1| SSU ribosomal protein S4P [Polaromonas sp. JS666]
          Length = 207

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 1/69 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V + D I V     ++   T
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAITVNGNSVNIPSYMVKTGDVIAVRDKSKKQTRVT 157

Query: 74  RLWLYHKPI 82
                 K +
Sbjct: 158 EALELAKQV 166


>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 = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 29/238 (12%), Positives = 59/238 (24%), Gaps = 31/238 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----E 61
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V   + I    E
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVFGGERIEIIVE 69

Query: 62  VDGVP----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
           V+             +   +   + +      +V   +     + +   L          
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPISEVP 129

Query: 112 -----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-----------FHGQVDQ 155
                 RLD +T GL+++         L     +                      Q   
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     V            +     +   + + L  G+  +I+         + 
Sbjct: 190 RHATKRTLMAVHPMGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 247


>gi|115484941|ref|NP_001067614.1| Os11g0247400 [Oryza sativa Japonica Group]
 gi|62734664|gb|AAX96773.1| hemolysin A, putative [Oryza sativa Japonica Group]
 gi|77549558|gb|ABA92355.1| hemolysin A family protein, expressed [Oryza sativa Japonica
          Group]
 gi|113644836|dbj|BAF27977.1| Os11g0247400 [Oryza sativa Japonica Group]
          Length = 295

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 8/61 (13%)

Query: 2  KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
          K K  + E    +R  +        SR  ++  I Q +V V+G ++ +A   V     IE
Sbjct: 41 KKKRRLDEVC-LERFQQY-------SRTYIQSWILQGKVLVDGRVVNKAGTQVSDKSIIE 92

Query: 62 V 62
          +
Sbjct: 93 I 93


>gi|261346911|ref|ZP_05974555.1| ribosomal protein S4 [Providencia rustigianii DSM 4541]
 gi|282564977|gb|EFB70512.1| ribosomal protein S4 [Providencia rustigianii DSM 4541]
          Length = 206

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/73 (21%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  +M++ + + VNG ++  A+  V   D I V     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQMVSHKAIMVNGRVVNIASYQVSPNDVISVREKAKKQSRIK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|167770733|ref|ZP_02442786.1| hypothetical protein ANACOL_02079 [Anaerotruncus colihominis DSM
           17241]
 gi|167667328|gb|EDS11458.1| hypothetical protein ANACOL_02079 [Anaerotruncus colihominis DSM
           17241]
          Length = 270

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 25/183 (13%), Positives = 52/183 (28%), Gaps = 2/183 (1%)

Query: 9   ENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           E    +R+  ++       SR + + +I   +V +NG   ++  ++V     IEV G  L
Sbjct: 2   EGAVKKRLDILLTEKEFFPSREKAKAVIMAGQVYINGQKADKPGMDVAEDADIEVRGDTL 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R   R  L L            D                 ++  G   +    +      
Sbjct: 62  RYVSRGGLKLEKAMQVWPIVLQDQICMDIGAST-GGFTDCMLQNGAAKVYAVDVGYGQLA 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
             L     + + +   +  +      D+     +    +   +        L T   +  
Sbjct: 121 WKLRNDPRVVNLERTNIRNITREQLPDRIDFISIDVSFISLRLVLPVAAQLLCTGGKAVC 180

Query: 188 WVT 190
            V 
Sbjct: 181 LVK 183


>gi|323140952|ref|ZP_08075864.1| ribosomal RNA large subunit methyltransferase J
          [Phascolarctobacterium sp. YIT 12067]
 gi|322414555|gb|EFY05362.1| ribosomal RNA large subunit methyltransferase J
          [Phascolarctobacterium sp. YIT 12067]
          Length = 274

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/59 (18%), Positives = 24/59 (40%), Gaps = 1/59 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
            +R+  ++   G+  SR + +  +   +V VN   +++    V     I + G  L  
Sbjct: 2  KKERLDVLLVNRGMFESRAKAQAAVMAGQVLVNEQKIDKPGTPVAPEVTIRLLGNKLPY 60


>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 = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 20/234 (8%), Positives = 56/234 (23%), Gaps = 39/234 (16%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVN-------------------- 53
           R+ + +A+     SR  ++  I    V VNG ++ +A                       
Sbjct: 19  RLDQALAQLFPDYSRSRIKVWIESDLVSVNGKIVNKAREKVFGGELIEIQAEIEEEIRFE 78

Query: 54  --------VMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
                   V   D I V    + K +   +            ++       + +   +  
Sbjct: 79  PQNIPLNIVYEDDDILV----INKPKDLVVHPGAGNPDGTVLNALLHHYPQIAEVPRAGI 134

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL------RVYRVRFHGQVDQDKLN 159
              +      +      +      +  +     T+         + +     +       
Sbjct: 135 VHRLDKDTTGLMVVAKTVPAQTHLVTALQRREITREYEAVASGIMTQGGKVDEPMARHPT 194

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 V            +  +  + + + + L  G+  +I+         + 
Sbjct: 195 KRTAMAVHPMGKPAVTHYRIMERFRNYSRLRLRLETGRTHQIRVHMAHIAHPLL 248


>gi|27807135|ref|NP_777057.1| voltage-dependent N-type calcium channel subunit alpha-1B [Bos
           taurus]
 gi|6690638|gb|AAF24229.1|AF173882_1 N-type calcium channel alpha1B subunit [Bos taurus]
          Length = 2331

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 9/106 (8%), Positives = 23/106 (21%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                     +          R   +  +  P +    +      +G  +  +  +P   
Sbjct: 871 RADAPKAEGGEPGAREERARPRRSRSKEAAGPREARSERGRGLGPDGGRRHHRRGSPEEA 930

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                    A         +     +  RR+      R+  R +  
Sbjct: 931 AEREPRRHRAHRHAPEPSREGAPGSKGERRARHRGGSRAGPREAES 976



 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 10/88 (11%), Positives = 19/88 (21%), Gaps = 2/88 (2%)

Query: 266 TLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFL 325
                        PD   R  +  S +    ++ +           S    A G      
Sbjct: 902 PREARSERGRGLGPDGGRRHHRRGSPEEAAEREPRRHRAHRHAPEPSREG-APGSKGE-R 959

Query: 326 SDSGQREENHRRSPSFPSKRSLRRTSAK 353
               +         +   +   RR  A+
Sbjct: 960 RARHRGGSRAGPREAESGEEPSRRHRAR 987



 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 23/168 (13%), Positives = 42/168 (25%), Gaps = 36/168 (21%)

Query: 223 FQLGTL---LAGSTREVSKKI-LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEV 278
            +L  L         E+  +  LR     HL  + + +LD P+         R     + 
Sbjct: 775 LRLQNLRASCEALYSEMDPEERLRFATSRHLRPDMKTHLDRPLVVEPGRDGARGPAGGKA 834

Query: 279 PDDFTRMKKNSSQK---------------NGLSKQKKLATPVHRRNLA------------ 311
             +     + +                      +  +   P                   
Sbjct: 835 RPEGGEAGEGADPPRRHHRHRDRDRDKAAAPAGEPDRADAPKAEGGEPGAREERARPRRS 894

Query: 312 -----SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                +    A+      L   G R  + R SP   ++R  RR  A +
Sbjct: 895 RSKEAAGPREARSERGRGLGPDGGRRHHRRGSPEEAAEREPRRHRAHR 942



 Score = 36.3 bits (82), Expect = 6.7,   Method: Composition-based stats.
 Identities = 14/117 (11%), Positives = 30/117 (25%), Gaps = 9/117 (7%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G         + D     +     +     +   +      +    +   S+ K+ A P 
Sbjct: 844 GADPPRRHHRHRDRDRDKAAAPAGEPDRADAPKAEGGEPGAREERARPRRSRSKEAAGPR 903

Query: 306 HRRNLASNVWMAKGIHSSFLS--------DSGQREENHRRSPSFPSKRSLRRTSAKK 354
             R+         G                  +R   HR +P  PS+     +  ++
Sbjct: 904 EARSERGRGLGPDGGRRHHRRGSPEEAAEREPRRHRAHRHAP-EPSREGAPGSKGER 959


>gi|326692258|ref|ZP_08229263.1| 30S ribosomal protein S4 [Leuconostoc argentinum KCTC 3773]
          Length = 203

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/53 (20%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           QR+  ++ R G+A+ R++  +++    + V+G  ++  +  V     I V   
Sbjct: 93  QRLDSLVYRLGLATTRQQARQLVNHGHILVDGQRVDIPSYQVTPGQVISVRDK 145


>gi|283850591|ref|ZP_06367879.1| PSP1 domain protein [Desulfovibrio sp. FW1012B]
 gi|283574162|gb|EFC22134.1| PSP1 domain protein [Desulfovibrio sp. FW1012B]
          Length = 443

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/119 (11%), Positives = 24/119 (20%), Gaps = 7/119 (5%)

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G  RE++ +     +   L  E Q                RP             +    
Sbjct: 252 GEERELTVEEWGTVVEARLPSEGQA-------QPRPAEPGRPETARPEGGRPEGGRPEGG 304

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           + +    +         R    +     G      S S         S    +     R
Sbjct: 305 RSDSRRGEGSSHGRPEGRGEGRDRSRPSGAGGPQASPSPAPSRPAGPSAGPEAGPQAER 363


>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 = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 4/54 (7%)

Query: 13 PQRVSKVIARAGIA----SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          P R+ K +AR   A    SR  + R+I +  V V+G +++     V     I +
Sbjct: 15 PPRLDKALARDVPAEESLSRTRLARLIGEGAVTVDGAVVDDPKAKVAEDAQIAI 68


>gi|254283192|ref|ZP_04958160.1| ribosomal protein S4 [gamma proteobacterium NOR51-B]
 gi|219679395|gb|EED35744.1| ribosomal protein S4 [gamma proteobacterium NOR51-B]
          Length = 154

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+  V+ R G  S R E  +++A + + +N  ++   +  V   D + +
Sbjct: 45 RLDNVVYRMGFGSTRAEARQLVAHKGILINNAVVNIPSYQVKPGDVVSI 93


>gi|168183729|ref|ZP_02618393.1| S4 domain protein [Clostridium botulinum Bf]
 gi|237793323|ref|YP_002860875.1| S4 domain-containing protein [Clostridium botulinum Ba4 str. 657]
 gi|182673254|gb|EDT85215.1| S4 domain protein [Clostridium botulinum Bf]
 gi|229263875|gb|ACQ54908.1| S4 domain protein [Clostridium botulinum Ba4 str. 657]
          Length = 68

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/59 (23%), Positives = 24/59 (40%), Gaps = 5/59 (8%)

Query: 10 NFTPQRVSKVIARAG---IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          N    ++   +  +G   + S  E +  I    VKVNG + +R    +   D IE +  
Sbjct: 7  NSEIIKLDSFLKWSGATTLGS--EAKFFIQNGEVKVNGEIEKRRGRKLKIGDLIEFNNE 63


>gi|307266987|ref|ZP_07548503.1| ribosomal protein S4 [Thermoanaerobacter wiegelii Rt8.B1]
 gi|326390634|ref|ZP_08212189.1| ribosomal protein S4 [Thermoanaerobacter ethanolicus JW 200]
 gi|306917972|gb|EFN48230.1| ribosomal protein S4 [Thermoanaerobacter wiegelii Rt8.B1]
 gi|325993312|gb|EGD51749.1| ribosomal protein S4 [Thermoanaerobacter ethanolicus JW 200]
          Length = 206

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SR +  ++++   ++VNG  ++  +  V   D I V
Sbjct: 99  RLDNVVYRLGFAASRPQARQLVSHGHIEVNGKKVDIPSFLVKPGDVISV 147


>gi|257463990|ref|ZP_05628375.1| 30S ribosomal protein S4 [Fusobacterium sp. D12]
 gi|317061512|ref|ZP_07925997.1| SSU ribosomal protein S4P [Fusobacterium sp. D12]
 gi|313687188|gb|EFS24023.1| SSU ribosomal protein S4P [Fusobacterium sp. D12]
          Length = 195

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+  ++++   V VNG  +  A+  V   D I V
Sbjct: 89  RLENVVYRLGFAKTRRQARQIVSHGHVTVNGRRVNIASYRVKVGDVIAV 137


>gi|224438280|ref|ZP_03659207.1| ribosomal pseudouridine synthase [Helicobacter cinaedi CCUG 18818]
 gi|313144719|ref|ZP_07806912.1| ribosomal pseudouridine synthase [Helicobacter cinaedi CCUG 18818]
 gi|313129750|gb|EFR47367.1| ribosomal pseudouridine synthase [Helicobacter cinaedi CCUG 18818]
          Length = 245

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 25/198 (12%), Positives = 58/198 (29%), Gaps = 2/198 (1%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K++A+A   S    + +I +  V  NG  +  A + +  + + EV     P    E  ++
Sbjct: 8   KLLAKAKCISHNLAKSLIDKGLVSSNGKKITIARLELPLSANFEVAEIKKPKVIFEDKQI 67

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
               KP  + +             +     +  + +   + +   L         A   E
Sbjct: 68  LALDKPPFIESYDLSDMFEGWSLLHRLDKQTSGVILLIQENSPFHLKAKEAFKKQAVYKE 127

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
                   +       +          K  + +       Q+T  +  G        +  
Sbjct: 128 YICLLHGILADSITINKPISTIKKGFAKSRIDKNGLSAHTQLTPLSIVGKKTQAQAIITT 187

Query: 196 GKNREIKKVFEFFNWKVN 213
           G+  +I+   +  N  + 
Sbjct: 188 GRTHQIRVHCQSINHPIV 205


>gi|15828588|ref|NP_325948.1| ribosomal large subunit pseudouridine synthase C (pseudouridylate
           synthase) (uracil hydrolyase) [Mycoplasma pulmonis UAB
           CTIP]
 gi|14089530|emb|CAC13290.1| RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE C (PSEUDOURIDYLATE
           SYNTHASE) (URACIL HYDROLYASE) [Mycoplasma pulmonis]
          Length = 282

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 24/253 (9%), Positives = 64/253 (25%), Gaps = 45/253 (17%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG----------VPLRKA-----E 71
           SR  ++++  ++ +KVNG         V   D I++ G            + +      E
Sbjct: 29  SR--IQKLFREKDIKVNGKRNIDKNFIVSKDDLIQIYGLTNVKQKLVFKKIEQKFNVIFE 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              + + +K  G+     +      V   L            +    +    +       
Sbjct: 87  DQNILVINKQAGVSMHSDENSLDKQVLSYLNFKQVDSFVPSSIGRLDKVTSGVVVYAKNY 146

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM----QVTLDTQKGSNA 187
            +L+   +         F   +  +    ++     +           +  ++  K +  
Sbjct: 147 SILKTLKSNEHLRKTYVFMSNITLEPNQKIEHVFYHKYNPIKKKAELFKENVEESKITKT 206

Query: 188 WVTVG-------LREGKNREIKKVFEFFNWKV-------------NRLIRISYGPFQLGT 227
            +          L  G+  +I+       + +               L         L  
Sbjct: 207 LLYKVKNNNYAELITGRKHQIRATLSKLGFPIFGDVKYGGKKDKRVYLHSYKIKFHSLK- 265

Query: 228 LLAGSTREVSKKI 240
              G    ++ + 
Sbjct: 266 ---GEFEYLNNQE 275


>gi|222056129|ref|YP_002538491.1| hemolysin A [Geobacter sp. FRC-32]
 gi|221565418|gb|ACM21390.1| hemolysin A [Geobacter sp. FRC-32]
          Length = 247

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 1/56 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          +R+ K++    +A SR   + +I   +V V+  L ++A   V     I + G  L 
Sbjct: 4  ERLDKILLDRRLAPSRERAKALIMAGQVVVDDHLADKAGQMVAVDAEIRLKGEVLP 59


>gi|304407040|ref|ZP_07388694.1| hemolysin A [Paenibacillus curdlanolyticus YK9]
 gi|304344027|gb|EFM09867.1| hemolysin A [Paenibacillus curdlanolyticus YK9]
          Length = 277

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          +R+  ++   G   SR + +  +    V V+G  +E++ + V     I V G P   
Sbjct: 6  ERIDVLLVEQGFYESREKAKAAVMAGLVLVDGDRMEKSGMKVPRAATITVKGAPHPY 62


>gi|254520694|ref|ZP_05132750.1| S4 domain-containing protein [Clostridium sp. 7_2_43FAA]
 gi|226914443|gb|EEH99644.1| S4 domain-containing protein [Clostridium sp. 7_2_43FAA]
          Length = 68

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/62 (20%), Positives = 24/62 (38%), Gaps = 1/62 (1%)

Query: 10 NFTPQRVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          N    ++   +   G AS   E +  I  + VKVN  +  +    +   D +E +G   +
Sbjct: 7  NTEFIKLDSFLKWCGAASLGSEAKMYILDEMVKVNDEVCTQRGKKLKQGDIVEFNGEKYK 66

Query: 69 KA 70
            
Sbjct: 67 II 68


>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 = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 28/238 (11%), Positives = 58/238 (24%), Gaps = 31/238 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           VQ     QR+ + +A      SR  ++  I    V +N  +       V   + IE+   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVNLNDRIANIPREKVFGGERIEIIVE 69

Query: 63  --DGVP---------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
             D            +   +   + +      +V   +     + +   L          
Sbjct: 70  VEDDTRFEPENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIAEVP 129

Query: 112 -----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-----------FHGQVDQ 155
                 RLD +T GL+++         L     +                      Q   
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     V            +     +   + + L  G+  +I+         + 
Sbjct: 190 RHATKRTLMAVHPMGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 247


>gi|220930992|ref|YP_002507900.1| ribosomal protein S4 [Halothermothrix orenii H 168]
 gi|254764592|sp|B8D0T6|RS4_HALOH RecName: Full=30S ribosomal protein S4
 gi|219992302|gb|ACL68905.1| ribosomal protein S4 [Halothermothrix orenii H 168]
          Length = 208

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/66 (22%), Positives = 28/66 (42%), Gaps = 1/66 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G+A SR E  + +    + VNG  +   +  V   D I V     +     
Sbjct: 99  RLDNVVYRLGLATSRNEARQFVLHGHILVNGRKVNIPSYLVDEGDVISVKDSSRKSKRFK 158

Query: 74  RLWLYH 79
            ++ ++
Sbjct: 159 EVFEFN 164


>gi|89069368|ref|ZP_01156727.1| S4 domain protein [Oceanicola granulosus HTCC2516]
 gi|89045135|gb|EAR51206.1| S4 domain protein [Oceanicola granulosus HTCC2516]
          Length = 128

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 2/71 (2%)

Query: 7  VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DG 64
          + E  +  R+ K + +A    SR     ++   RV+V+G  + + A  V + D +    G
Sbjct: 1  MNEPRSTIRLDKWLWQARFFKSRSLAAEIVGNGRVRVDGQPVSKPARAVGAGDVLTFPQG 60

Query: 65 VPLRKAERTRL 75
            +R      L
Sbjct: 61 QAVRVVRILAL 71


>gi|238916291|ref|YP_002929808.1| small subunit ribosomal protein S4 [Eubacterium eligens ATCC 27750]
 gi|259495278|sp|C4Z2V6|RS4_EUBE2 RecName: Full=30S ribosomal protein S4
 gi|238871651|gb|ACR71361.1| small subunit ribosomal protein S4 [Eubacterium eligens ATCC 27750]
          Length = 197

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R+E  +++  + V VNG  +   +  V + D IE+
Sbjct: 88  RLDNVLFRLGFARTRKEARQIVDHKHVLVNGKCVNIPSYLVKAGDVIEI 136


>gi|225870034|ref|YP_002745981.1| hypothetical protein SEQ_0625 [Streptococcus equi subsp. equi 4047]
 gi|225699438|emb|CAW92932.1| conserved hypothetical protein [Streptococcus equi subsp. equi
           4047]
          Length = 264

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 17/50 (34%), Positives = 27/50 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           RV ++IA     SR +  R++   +VKVN  L+ +A+  V   D I + G
Sbjct: 187 RVDRLIATVLKQSRNQAIRLVEAGKVKVNYQLVTKASQPVAVGDLISIRG 236


>gi|222098129|ref|YP_002532186.1| 30S ribosomal protein s4 [Bacillus cereus Q1]
 gi|254764569|sp|B9J159|RS4_BACCQ RecName: Full=30S ribosomal protein S4
 gi|221242187|gb|ACM14897.1| ribosomal protein S4 (30S ribosomal protein S4) [Bacillus cereus
           Q1]
          Length = 200

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 93  RLDNLVYRMGLARTRRAARQLVNHGHITVDGSRVDIPSYRVKPGQTISV 141


>gi|72162433|ref|YP_290090.1| hemolysin A [Thermobifida fusca YX]
 gi|71916165|gb|AAZ56067.1| hemolysin A [Thermobifida fusca YX]
          Length = 266

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 20/57 (35%), Positives = 26/57 (45%), Gaps = 4/57 (7%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPL 67
          R+   + R G A SR     +IA  RV+V G L  +AA  V     I V   D  P+
Sbjct: 6  RLDAELVRRGHARSRAHAAELIAAGRVRVAGTLATKAATQVGVDQAIVVEQADDEPV 62


>gi|15924709|ref|NP_372243.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus Mu50]
 gi|15927296|ref|NP_374829.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus N315]
 gi|21283391|ref|NP_646479.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus MW2]
 gi|49486544|ref|YP_043765.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|57652018|ref|YP_186603.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus COL]
 gi|82751307|ref|YP_417048.1| 30S ribosomal protein S4 [Staphylococcus aureus RF122]
 gi|87159914|ref|YP_494360.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           USA300_FPR3757]
 gi|88195529|ref|YP_500334.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus NCTC
           8325]
 gi|148268198|ref|YP_001247141.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus JH9]
 gi|150394266|ref|YP_001316941.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus JH1]
 gi|151221825|ref|YP_001332647.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus str.
           Newman]
 gi|156980036|ref|YP_001442295.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus Mu3]
 gi|161509934|ref|YP_001575593.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|253315106|ref|ZP_04838319.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus str.
           CF-Marseille]
 gi|253732369|ref|ZP_04866534.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
 gi|255006504|ref|ZP_05145105.2| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           Mu50-omega]
 gi|257794103|ref|ZP_05643082.1| 30S ribosomal protein S4 [Staphylococcus aureus A9781]
 gi|258415807|ref|ZP_05682078.1| 30S ribosomal protein S4 [Staphylococcus aureus A9763]
 gi|258424134|ref|ZP_05687016.1| SSU ribosomal protein S4 [Staphylococcus aureus A9635]
 gi|258438286|ref|ZP_05689570.1| ribosomal protein S4 [Staphylococcus aureus A9299]
 gi|258443744|ref|ZP_05692083.1| ribosomal protein S4 [Staphylococcus aureus A8115]
 gi|258445955|ref|ZP_05694131.1| 30S ribosomal protein S4 [Staphylococcus aureus A6300]
 gi|258448365|ref|ZP_05696482.1| ribosomal protein S4 [Staphylococcus aureus A6224]
 gi|258450886|ref|ZP_05698939.1| 30S ribosomal protein S4 [Staphylococcus aureus A5948]
 gi|258454155|ref|ZP_05702126.1| SSU ribosomal protein S4P [Staphylococcus aureus A5937]
 gi|262049033|ref|ZP_06021911.1| 30S ribosomal protein S4 [Staphylococcus aureus D30]
 gi|262051784|ref|ZP_06024001.1| 30S ribosomal protein S4 [Staphylococcus aureus 930918-3]
 gi|269203358|ref|YP_003282627.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus ED98]
 gi|282893214|ref|ZP_06301448.1| 30S ribosomal protein S4 [Staphylococcus aureus A8117]
 gi|282916980|ref|ZP_06324738.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus D139]
 gi|282924410|ref|ZP_06332083.1| 30S ribosomal protein S4 [Staphylococcus aureus A9765]
 gi|282927849|ref|ZP_06335460.1| 30S ribosomal protein S4 [Staphylococcus aureus A10102]
 gi|283770798|ref|ZP_06343690.1| small subunit ribosomal protein S4 [Staphylococcus aureus subsp.
           aureus H19]
 gi|284024766|ref|ZP_06379164.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus 132]
 gi|294849881|ref|ZP_06790620.1| 30S ribosomal protein S4 [Staphylococcus aureus A9754]
 gi|295406030|ref|ZP_06815838.1| 30S ribosomal protein S4 [Staphylococcus aureus A8819]
 gi|296276442|ref|ZP_06858949.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus MR1]
 gi|297207568|ref|ZP_06924003.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus ATCC
           51811]
 gi|297245044|ref|ZP_06928921.1| 30S ribosomal protein S4 [Staphylococcus aureus A8796]
 gi|300911649|ref|ZP_07129093.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           TCH70]
 gi|304380688|ref|ZP_07363359.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus ATCC
           BAA-39]
 gi|54039510|sp|P66563|RS4_STAAN RecName: Full=30S ribosomal protein S4
 gi|54039511|sp|P66564|RS4_STAAW RecName: Full=30S ribosomal protein S4
 gi|54041963|sp|P66562|RS4_STAAM RecName: Full=30S ribosomal protein S4
 gi|56749380|sp|Q6G8K8|RS4_STAAS RecName: Full=30S ribosomal protein S4
 gi|62287184|sp|Q5HF54|RS4_STAAC RecName: Full=30S ribosomal protein S4
 gi|90101727|sp|Q2YTH0|RS4_STAAB RecName: Full=30S ribosomal protein S4
 gi|122539301|sp|Q2FXK6|RS4_STAA8 RecName: Full=30S ribosomal protein S4
 gi|123485448|sp|Q2FG18|RS4_STAA3 RecName: Full=30S ribosomal protein S4
 gi|171769945|sp|A7X3F0|RS4_STAA1 RecName: Full=30S ribosomal protein S4
 gi|172048947|sp|A6QHQ3|RS4_STAAE RecName: Full=30S ribosomal protein S4
 gi|189045401|sp|A6U2I6|RS4_STAA2 RecName: Full=30S ribosomal protein S4
 gi|189045402|sp|A5ITP2|RS4_STAA9 RecName: Full=30S ribosomal protein S4
 gi|189045403|sp|A8Z2N6|RS4_STAAT RecName: Full=30S ribosomal protein S4
 gi|13701514|dbj|BAB42808.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus N315]
 gi|14247491|dbj|BAB57881.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus Mu50]
 gi|21204831|dbj|BAB95527.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus MW2]
 gi|49244987|emb|CAG43448.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|57286204|gb|AAW38298.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus COL]
 gi|82656838|emb|CAI81267.1| 30S ribosomal protein S4 [Staphylococcus aureus RF122]
 gi|87125888|gb|ABD20402.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           USA300_FPR3757]
 gi|87203087|gb|ABD30897.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus NCTC
           8325]
 gi|147741267|gb|ABQ49565.1| SSU ribosomal protein S4P [Staphylococcus aureus subsp. aureus JH9]
 gi|149946718|gb|ABR52654.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus JH1]
 gi|150374625|dbj|BAF67885.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus str.
           Newman]
 gi|156722171|dbj|BAF78588.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus Mu3]
 gi|160368743|gb|ABX29714.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|253723891|gb|EES92620.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
 gi|257788075|gb|EEV26415.1| 30S ribosomal protein S4 [Staphylococcus aureus A9781]
 gi|257839400|gb|EEV63873.1| 30S ribosomal protein S4 [Staphylococcus aureus A9763]
 gi|257845755|gb|EEV69787.1| SSU ribosomal protein S4 [Staphylococcus aureus A9635]
 gi|257848330|gb|EEV72321.1| ribosomal protein S4 [Staphylococcus aureus A9299]
 gi|257851150|gb|EEV75093.1| ribosomal protein S4 [Staphylococcus aureus A8115]
 gi|257855197|gb|EEV78136.1| 30S ribosomal protein S4 [Staphylococcus aureus A6300]
 gi|257858333|gb|EEV81218.1| ribosomal protein S4 [Staphylococcus aureus A6224]
 gi|257861422|gb|EEV84230.1| 30S ribosomal protein S4 [Staphylococcus aureus A5948]
 gi|257863607|gb|EEV86364.1| SSU ribosomal protein S4P [Staphylococcus aureus A5937]
 gi|259160278|gb|EEW45305.1| 30S ribosomal protein S4 [Staphylococcus aureus 930918-3]
 gi|259162850|gb|EEW47414.1| 30S ribosomal protein S4 [Staphylococcus aureus D30]
 gi|262075648|gb|ACY11621.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus ED98]
 gi|269941198|emb|CBI49586.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus TW20]
 gi|282319467|gb|EFB49819.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus D139]
 gi|282590359|gb|EFB95438.1| 30S ribosomal protein S4 [Staphylococcus aureus A10102]
 gi|282592911|gb|EFB97914.1| 30S ribosomal protein S4 [Staphylococcus aureus A9765]
 gi|282764532|gb|EFC04658.1| 30S ribosomal protein S4 [Staphylococcus aureus A8117]
 gi|283460945|gb|EFC08035.1| small subunit ribosomal protein S4 [Staphylococcus aureus subsp.
           aureus H19]
 gi|283470985|emb|CAQ50196.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus ST398]
 gi|285817402|gb|ADC37889.1| 30S ribosomal protein S4 [Staphylococcus aureus 04-02981]
 gi|294823220|gb|EFG39650.1| 30S ribosomal protein S4 [Staphylococcus aureus A9754]
 gi|294969027|gb|EFG45048.1| 30S ribosomal protein S4 [Staphylococcus aureus A8819]
 gi|296887585|gb|EFH26483.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus ATCC
           51811]
 gi|297178124|gb|EFH37372.1| 30S ribosomal protein S4 [Staphylococcus aureus A8796]
 gi|298694988|gb|ADI98210.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           ED133]
 gi|300887070|gb|EFK82271.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           TCH70]
 gi|302333384|gb|ADL23577.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           JKD6159]
 gi|304340795|gb|EFM06724.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus ATCC
           BAA-39]
 gi|312830098|emb|CBX34940.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus ECT-R 2]
 gi|315130645|gb|EFT86631.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           CGS03]
 gi|315197186|gb|EFU27525.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           CGS01]
 gi|320141663|gb|EFW33498.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus MRSA131]
 gi|320143817|gb|EFW35590.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus MRSA177]
 gi|323440736|gb|EGA98445.1| 30S ribosomal protein S4 [Staphylococcus aureus O11]
 gi|323442976|gb|EGB00598.1| 30S ribosomal protein S4 [Staphylococcus aureus O46]
 gi|329314393|gb|AEB88806.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           T0131]
 gi|329726987|gb|EGG63444.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus 21189]
 gi|329727555|gb|EGG64011.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus 21172]
 gi|329733129|gb|EGG69466.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus 21193]
          Length = 200

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+   G+A +RR+  +++    + V+G  ++  + +V     I V
Sbjct: 93  RLDAVVYSLGLARTRRQARQLVNHGHILVDGKRVDIPSYSVKPGQTISV 141


>gi|291533602|emb|CBL06715.1| Ribosomal protein S4 and related proteins [Megamonas hypermegale
          ART12/1]
          Length = 125

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+  V+ R G+AS RR+  ++++   + VNG  L+  +  +   D I V
Sbjct: 16 RIDNVVFRLGLASTRRQARQLVSHGHITVNGKRLDIPSALIKVGDVIGV 64


>gi|253578522|ref|ZP_04855794.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251850840|gb|EES78798.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 269

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 24/177 (13%), Positives = 50/177 (28%), Gaps = 2/177 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  ++    +A SR + +  I    V V+G   ++A      T  IEV G  L    R 
Sbjct: 4   RLDMLMMERALAPSREKAKAFIMAGDVYVDGQKEDKAGTMFPETVKIEVRGNTLPYVSRG 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L         T                    ++  G + + +  +     D  L   
Sbjct: 64  GLKLEKAMKNFDVTLDSKVCMDVGAST-GGFTDCMLQNGAVKVYSIDVGYGQLDWKLRND 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             +   +   +  V      +    + +    +        ++  L  +      + 
Sbjct: 123 PRVVCMEKTNIRYVVPEDLGEPADFSSIDVSFISLTKVLLPVRNLLTDEGEIVCLIK 179


>gi|225175647|ref|ZP_03729641.1| ribosomal protein S4 [Dethiobacter alkaliphilus AHT 1]
 gi|225168976|gb|EEG77776.1| ribosomal protein S4 [Dethiobacter alkaliphilus AHT 1]
          Length = 209

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SR E  +++      VNG  ++  +  V   D + V
Sbjct: 100 RLDNVVYRMGFALSRPEARQLVKHGHFTVNGRKVDIPSYQVRPDDVVAV 148


>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 = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 24/225 (10%), Positives = 58/225 (25%), Gaps = 22/225 (9%)

Query: 11  FTPQRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
            +  ++   I +   G  S R+++R I    V VNG +    +  +   D +E D   L 
Sbjct: 8   ESGIKLVDFIHQKLQGKHSLRKIKRAIENNHVCVNGAVERFYSFQLSKGDLVEFDDSVLE 67

Query: 69  KAERTR---------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRV 108
           K+E  +               L                    +                 
Sbjct: 68  KSESEKPVPERDAILFEDDHLLIYNKPSGMNSDEFGLGKFFPSFPLIHRLDKETTGCIMF 127

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
               ++      L            +              F GQ+  +  ++    +  +
Sbjct: 128 AKYPKVKNRMIELFKGKKISKHYLAVVDGVPNKREGVEESFIGQISSNPGSIKWGNVSPK 187

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +   Q  ++ +    A + +    G+  +++         + 
Sbjct: 188 QGQHAKTQWMIEKRGKEAALLKMQPITGRTHQLRVHAAQMGHPIL 232


>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 = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 24/201 (11%), Positives = 62/201 (30%), Gaps = 8/201 (3%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLY 78
            I+     ++ + + +I  + V VN   +  A+  +   D +E+  +    + +    + 
Sbjct: 15  FISEVLGLTKNKAKEIIDSKNVFVNSKRVWIASHTLKKGDIVEIADIDNSFSWKPEKSVI 74

Query: 79  HKPIGLVTTHSDPD------GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           ++   ++     P         S  +     +  R+ ++ RLD  T G+LL   +  +  
Sbjct: 75  YEDQFILAVQKPPFLESEGRKGSVEYQLRKVLDRRLKAIHRLDRETSGVLLFAKNEKIFH 134

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
             +    +   V         +      +    V     Y                  V 
Sbjct: 135 RFKDLWHRKEVVKVYLSISYGEAKFKKKVVNMPV--DKKYAKSIFFTKKISKGFTLFEVE 192

Query: 193 LREGKNREIKKVFEFFNWKVN 213
           ++ G+  +I+         + 
Sbjct: 193 IKTGRKHQIRIHSSKIRHPIV 213


>gi|253734496|ref|ZP_04868661.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|253727550|gb|EES96279.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           TCH130]
          Length = 200

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+   G+A +RR+  +++    + V+G  ++  + +V     I V
Sbjct: 93  RLDAVVYSLGLARTRRQARQLVNHGHILVDGKRVDIPSYSVKPGQTISV 141


>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 = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 20/234 (8%), Positives = 56/234 (23%), Gaps = 39/234 (16%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVN-------------------- 53
           R+ + +A+     SR  ++  I    V VNG ++ +A                       
Sbjct: 19  RLDQALAQLFPDYSRSRIKVWIESDLVSVNGKIVNKAREKVFGGELIEIQAEIEEEIRFE 78

Query: 54  --------VMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
                   V   D I V    + K +   +            ++       + +   +  
Sbjct: 79  PQNIPLNIVYEDDDILV----INKPKDLVVHPGAGNPDGTVLNALLHHYPQIAEVPRAGI 134

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL------RVYRVRFHGQVDQDKLN 159
              +      +      +      +  + +   T+         + +     +       
Sbjct: 135 VHRLDKDTTGLMVVAKTVPAQTHLVTALQKREITREYEAVASGIMTQGGKVDEPMARHPT 194

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 V            +  +  +   + + L  G+  +I+         + 
Sbjct: 195 KRTAMAVHPMGKPAVTHYRIMERFRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 248


>gi|156932259|ref|YP_001436175.1| 30S ribosomal protein S4 [Cronobacter sakazakii ATCC BAA-894]
 gi|260599616|ref|YP_003212187.1| 30S ribosomal protein S4 [Cronobacter turicensis z3032]
 gi|171769807|sp|A7MPF7|RS4_ENTS8 RecName: Full=30S ribosomal protein S4
 gi|156530513|gb|ABU75339.1| hypothetical protein ESA_00030 [Cronobacter sakazakii ATCC BAA-894]
 gi|260218793|emb|CBA34141.1| 30S ribosomal protein S4 [Cronobacter turicensis z3032]
          Length = 206

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + V     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSVREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|325267152|ref|ZP_08133820.1| 30S ribosomal protein S4 [Kingella denitrificans ATCC 33394]
 gi|324981390|gb|EGC17034.1| 30S ribosomal protein S4 [Kingella denitrificans ATCC 33394]
          Length = 206

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/60 (23%), Positives = 29/60 (48%), Gaps = 1/60 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G AS R E  ++++ + + VNG ++   +  V + D + V     ++    
Sbjct: 97  RLDNVVYRMGFASTRAEARQLVSHKALTVNGQVVNIPSFQVKAGDVVAVREKAKKQVRIQ 156


>gi|304399266|ref|ZP_07381132.1| ribosomal protein S4 [Pantoea sp. aB]
 gi|308188332|ref|YP_003932463.1| 30S ribosomal protein S4 [Pantoea vagans C9-1]
 gi|304353192|gb|EFM17573.1| ribosomal protein S4 [Pantoea sp. aB]
 gi|308058842|gb|ADO11014.1| 30S ribosomal protein S4 [Pantoea vagans C9-1]
          Length = 206

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + V VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKSVLVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>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 = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 24/240 (10%), Positives = 54/240 (22%), Gaps = 38/240 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER-AAVNVMSTDHIEVDGV 65
           V E  +  R+   +A     SR     +I    V  +G + +   A  +       V+  
Sbjct: 44  VPEEDSGARLDLFLAGELSLSRSRARSLIDGGAVS-SGQVKKIRPAFKIQPGQIYRVEIP 102

Query: 66  P--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                          +   +   + +      +V   +     + V   +          
Sbjct: 103 EAAPAEIAAQDMPFDVVYEDDDVIVVNKPAGVVVHPGAGRPDGTLVNGLMFRYPEIGRIG 162

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------------- 155
             +       L +   G +       + + L           +                 
Sbjct: 163 DSVRPGIVHRLDVGTSGLMVVARSDAAFRGLTEAFQAHEVLKEYLGLGVGALKAPEGTVD 222

Query: 156 -----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                D  N LK  +             +   +     + V L  G+  +I+        
Sbjct: 223 APIGRDPRNRLKMCVSW-DGRDAVTDYKVLWTRARCNLIRVRLHTGRTHQIRVHMRALGC 281


>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 = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 33/227 (14%), Positives = 67/227 (29%), Gaps = 31/227 (13%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------GVPLRK 69
           SK +      S R+++ M  ++RVKVN  +       +   D + ++       GV + K
Sbjct: 17  SKYVKERFSLSSRDIQMMFRKKRVKVNSRVAHS-QRALKKGDVLTLELPQDKDYGVDVEK 75

Query: 70  AERTRLWL--------------YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
              T L+                H      +                    R +     D
Sbjct: 76  GPITVLYEDAHTLVVNKDPFMLVHPAGQTKSCTLSNYVAGYYAKKNVVHKVRPVHRLDRD 135

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL-------LKKGIVIQ 168
            +   L   T +       EL + +  R+Y     G++D + +         +     + 
Sbjct: 136 TSGCILFGKTKEAQQYYTDELQAGRIDRIYTGLVEGRIDANGMVDAPIGVDPVFDNRRVI 195

Query: 169 GICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                    +  +   +G N  +   L  G+  +I+   E     + 
Sbjct: 196 DELGQPAQTEYIVLDHEGDNTLLRFKLLTGRTHQIRVHMEHIGHPIV 242


>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 = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 31/260 (11%), Positives = 71/260 (27%), Gaps = 52/260 (20%)

Query: 6   IVQENFTPQRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           I   +   +R+ + +A A     SR  V+ +IA   V ++G         +    +I + 
Sbjct: 5   IADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMNIAIV 64

Query: 63  ---------DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
                     G  +       +   + +      +V   +     + V   +        
Sbjct: 65  LPEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNGNWTGTLVNALIYQCGDSLS 124

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLELP-----------------STQWLR 143
                 R   V RLD +T G++++  +    R L                          
Sbjct: 125 GIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFADHGRTGDLERAYLALVWGMTE 184

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSN---------AWVTVGL 193
             +      + +   +  K+ +V +             T +  +         + V   L
Sbjct: 185 RPQGTVDAYLGRSHRDRTKQAVVHEEREDARHAITHYATVEKFSPREDATALASLVECRL 244

Query: 194 REGKNREIKKVFEFFNWKVN 213
             G+  +I+         + 
Sbjct: 245 ETGRTHQIRVHMAHIGHPLV 264


>gi|255283706|ref|ZP_05348261.1| ribosomal protein S4 [Bryantella formatexigens DSM 14469]
 gi|255265771|gb|EET58976.1| ribosomal protein S4 [Bryantella formatexigens DSM 14469]
          Length = 197

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI R G A +R+E  +++  + V VNG  +   +  V + D +E+
Sbjct: 88  RLDNVIFRLGFARTRKEARQIVDHKHVLVNGKQVNIPSYLVKAGDTVEI 136


>gi|160915194|ref|ZP_02077407.1| hypothetical protein EUBDOL_01202 [Eubacterium dolichum DSM 3991]
 gi|158432993|gb|EDP11282.1| hypothetical protein EUBDOL_01202 [Eubacterium dolichum DSM 3991]
          Length = 200

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  ++ R G A +RR   +++    + VNG  ++  +        IEV   
Sbjct: 93  RLDNLVYRMGFARTRRAARQLVNHGHILVNGKKVDIPSYIAKPGAVIEVKEK 144


>gi|84494745|ref|ZP_00993864.1| 30S ribosomal protein S4 [Janibacter sp. HTCC2649]
 gi|84384238|gb|EAQ00118.1| 30S ribosomal protein S4 [Janibacter sp. HTCC2649]
          Length = 202

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 1/60 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  VI RAG+A +RR   +++     +VNG  ++  +  V   D I V    +      
Sbjct: 92  RLDNVIYRAGLARTRRAARQLVTHGHFEVNGKRVDVPSYRVEQYDIITVRKQSVETFPLQ 151


>gi|332968427|gb|EGK07494.1| 30S ribosomal protein S4 [Kingella kingae ATCC 23330]
          Length = 206

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/60 (23%), Positives = 29/60 (48%), Gaps = 1/60 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G AS R E  ++++ + + VNG ++   +  V + D + V     ++    
Sbjct: 97  RLDNVVYRMGFASTRAEARQLVSHKALTVNGQVVNIPSFQVKAGDVVAVREKAKKQVRIQ 156


>gi|291619151|ref|YP_003521893.1| RpsD [Pantoea ananatis LMG 20103]
 gi|291154181|gb|ADD78765.1| RpsD [Pantoea ananatis LMG 20103]
          Length = 206

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + V VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKSVLVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|144143|gb|AAC05398.1| ribosomal protein S4 [Buchnera aphidicola]
 gi|448400|prf||1917188A ribosomal protein S4
          Length = 206

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V+ R G   +R E  ++I+ + +KVN  ++  A+  +   D I V   
Sbjct: 97  RLDNVVYRMGFGCTRSESRQLISHKSIKVNNNIVNIASYQISPNDRISVRDK 148


>gi|15642567|ref|NP_232200.1| 30S ribosomal protein S4 [Vibrio cholerae O1 biovar El Tor str.
           N16961]
 gi|147675276|ref|YP_001218066.1| 30S ribosomal protein S4 [Vibrio cholerae O395]
 gi|153820465|ref|ZP_01973132.1| ribosomal protein S4 [Vibrio cholerae NCTC 8457]
 gi|227082689|ref|YP_002811240.1| ribosomal protein S4 [Vibrio cholerae M66-2]
 gi|229507376|ref|ZP_04396881.1| SSU ribosomal protein S4p (S9e) [Vibrio cholerae BX 330286]
 gi|229509700|ref|ZP_04399181.1| SSU ribosomal protein S4p (S9e) [Vibrio cholerae B33]
 gi|229513495|ref|ZP_04402959.1| SSU ribosomal protein S4p (S9e) [Vibrio cholerae TMA 21]
 gi|229516825|ref|ZP_04406271.1| SSU ribosomal protein S4p (S9e) [Vibrio cholerae RC9]
 gi|229521638|ref|ZP_04411056.1| SSU ribosomal protein S4p (S9e) [Vibrio cholerae TM 11079-80]
 gi|229527498|ref|ZP_04416890.1| SSU ribosomal protein S4p (S9e) [Vibrio cholerae 12129(1)]
 gi|229606882|ref|YP_002877530.1| 30S ribosomal protein S4 [Vibrio cholerae MJ-1236]
 gi|254292241|ref|ZP_04963004.1| ribosomal protein S4 [Vibrio cholerae AM-19226]
 gi|254851112|ref|ZP_05240462.1| ribosomal protein S4 [Vibrio cholerae MO10]
 gi|255744459|ref|ZP_05418411.1| SSU ribosomal protein S4p (S9e) [Vibrio cholera CIRS 101]
 gi|297581414|ref|ZP_06943337.1| ribosomal protein S4 [Vibrio cholerae RC385]
 gi|26399513|sp|Q9KP07|RS4_VIBCH RecName: Full=30S ribosomal protein S4
 gi|172047566|sp|A5F573|RS4_VIBC3 RecName: Full=30S ribosomal protein S4
 gi|254764621|sp|C3LRN4|RS4_VIBCM RecName: Full=30S ribosomal protein S4
 gi|9657158|gb|AAF95713.1| ribosomal protein S4 [Vibrio cholerae O1 biovar El Tor str. N16961]
 gi|126508992|gb|EAZ71586.1| ribosomal protein S4 [Vibrio cholerae NCTC 8457]
 gi|146317159|gb|ABQ21698.1| ribosomal protein S4 [Vibrio cholerae O395]
 gi|150421843|gb|EDN13827.1| ribosomal protein S4 [Vibrio cholerae AM-19226]
 gi|227010577|gb|ACP06789.1| ribosomal protein S4 [Vibrio cholerae M66-2]
 gi|227014461|gb|ACP10671.1| ribosomal protein S4 [Vibrio cholerae O395]
 gi|229335130|gb|EEO00615.1| SSU ribosomal protein S4p (S9e) [Vibrio cholerae 12129(1)]
 gi|229341232|gb|EEO06236.1| SSU ribosomal protein S4p (S9e) [Vibrio cholerae TM 11079-80]
 gi|229345888|gb|EEO10860.1| SSU ribosomal protein S4p (S9e) [Vibrio cholerae RC9]
 gi|229349372|gb|EEO14328.1| SSU ribosomal protein S4p (S9e) [Vibrio cholerae TMA 21]
 gi|229353174|gb|EEO18113.1| SSU ribosomal protein S4p (S9e) [Vibrio cholerae B33]
 gi|229354881|gb|EEO19802.1| SSU ribosomal protein S4p (S9e) [Vibrio cholerae BX 330286]
 gi|229369537|gb|ACQ59960.1| SSU ribosomal protein S4p (S9e) [Vibrio cholerae MJ-1236]
 gi|254846817|gb|EET25231.1| ribosomal protein S4 [Vibrio cholerae MO10]
 gi|255737984|gb|EET93377.1| SSU ribosomal protein S4p (S9e) [Vibrio cholera CIRS 101]
 gi|297534252|gb|EFH73090.1| ribosomal protein S4 [Vibrio cholerae RC385]
 gi|327485054|gb|AEA79461.1| SSU ribosomal protein S4p (S9e) [Vibrio cholerae LMA3894-4]
          Length = 206

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   + NV + D + V
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAILVNGKVVNVPSFNVAANDVVAV 145


>gi|306836026|ref|ZP_07469016.1| cytotoxin/hemolysin [Corynebacterium accolens ATCC 49726]
 gi|304568053|gb|EFM43628.1| cytotoxin/hemolysin [Corynebacterium accolens ATCC 49726]
          Length = 268

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          R+   + R  IA SR +   MI   RV V G   E+ A  V     I+V+
Sbjct: 7  RLDAELVRRKIARSREQAREMIKSGRVTVGGFKAEKPATVVDPEVSIKVE 56


>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 = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 63/244 (25%), Gaps = 37/244 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-G 64
           +V E     RV   +A+A   SR     +I    V ++G  + + +  V +   +EV   
Sbjct: 8   VVPEGLDSMRVDAAVAKAFGLSRTVAAELIEAGEVLIDGSRVTK-SDRVSTGHSLEVTLP 66

Query: 65  VPLRKAERTRLW--------------LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
            P +                      +  KP+G+    +      TV   L ++  ++  
Sbjct: 67  EPKQAPMPKEEIVEGLTVLYDDDDVIVVDKPVGVAAHPTLGWDGPTVVGGLQAMGYQLPD 126

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            G  +       L     G+  V        +     +           +      I G 
Sbjct: 127 AGPPERKGIVQRLDVGTSGVMVVANSIPGYSVLKRAFKERTVEKTYHAVVQGLPDPIVGT 186

Query: 171 CYGDM---------------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
               +                        +       + + V L  G+  +I+       
Sbjct: 187 IDAPIGRHPSSGWKFAVTADGRHSVTHYEVLEAFREASLLEVHLETGRTHQIRVHMSSVG 246

Query: 210 WKVN 213
               
Sbjct: 247 HPCV 250


>gi|28867878|ref|NP_790497.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. tomato str.
           DC3000]
 gi|66047752|ref|YP_237593.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. syringae B728a]
 gi|71734874|ref|YP_276682.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. phaseolicola
           1448A]
 gi|213969238|ref|ZP_03397376.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. tomato T1]
 gi|289623825|ref|ZP_06456779.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. aesculi str.
           NCPPB3681]
 gi|289648918|ref|ZP_06480261.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. aesculi str.
           2250]
 gi|289675512|ref|ZP_06496402.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. syringae FF5]
 gi|298489072|ref|ZP_07007094.1| SSU ribosomal protein S4p (S9e) [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|301381745|ref|ZP_07230163.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. tomato Max13]
 gi|302061055|ref|ZP_07252596.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. tomato K40]
 gi|302130804|ref|ZP_07256794.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. tomato NCPPB
           1108]
 gi|302189301|ref|ZP_07265974.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. syringae 642]
 gi|37999395|sp|Q889U7|RS4_PSESM RecName: Full=30S ribosomal protein S4
 gi|81307873|sp|Q4ZMR7|RS4_PSEU2 RecName: Full=30S ribosomal protein S4
 gi|90101706|sp|Q48D60|RS4_PSE14 RecName: Full=30S ribosomal protein S4
 gi|28851114|gb|AAO54192.1| ribosomal protein S4 [Pseudomonas syringae pv. tomato str. DC3000]
 gi|63258459|gb|AAY39555.1| Ribosomal protein S4, bacterial and organelle form [Pseudomonas
           syringae pv. syringae B728a]
 gi|71555427|gb|AAZ34638.1| ribosomal protein S4 [Pseudomonas syringae pv. phaseolicola 1448A]
 gi|213925916|gb|EEB59473.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. tomato T1]
 gi|298156384|gb|EFH97482.1| SSU ribosomal protein S4p (S9e) [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|320322298|gb|EFW78392.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. glycinea str.
           B076]
 gi|320331956|gb|EFW87892.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. glycinea str.
           race 4]
 gi|330869407|gb|EGH04116.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. aesculi str.
           0893_23]
 gi|330879399|gb|EGH13548.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. glycinea str.
           race 4]
 gi|330879418|gb|EGH13567.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. morsprunorum
           str. M302280PT]
 gi|330891908|gb|EGH24569.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. mori str.
           301020]
 gi|330899712|gb|EGH31131.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. japonica str.
           M301072PT]
 gi|330940914|gb|EGH43865.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. pisi str. 1704B]
 gi|330953173|gb|EGH53433.1| 30S ribosomal protein S4 [Pseudomonas syringae Cit 7]
 gi|330962501|gb|EGH62761.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. maculicola str.
           ES4326]
 gi|330966887|gb|EGH67147.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. actinidiae str.
           M302091]
 gi|330969797|gb|EGH69863.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. aceris str.
           M302273PT]
 gi|330988258|gb|EGH86361.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. lachrymans str.
           M301315]
 gi|331018184|gb|EGH98240.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. lachrymans str.
           M302278PT]
          Length = 206

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + V VNG  +   +  V + D + +
Sbjct: 97  RLDNVVYRMGFGSTRAESRQLVSHKSVSVNGKTVNVPSYQVRAGDVVAI 145


>gi|331703116|ref|YP_004399803.1| Hemolysin A [Mycoplasma mycoides subsp. capri LC str. 95010]
 gi|328801671|emb|CBW53824.1| Hemolysin A [Mycoplasma mycoides subsp. capri LC str. 95010]
          Length = 272

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 22/177 (12%), Positives = 54/177 (30%), Gaps = 2/177 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ + I +  +  SR + +  I  + V VN I + + +  V S D IE+    L    R 
Sbjct: 4   RLDEYIYKNNLTQSRNKAKEHILNKEVYVNNIAIIKPSFLVDSNDLIEIRSTKLEHVSRA 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L           ++                 + +   L    +      +   L  +
Sbjct: 64  YEKLKKAINKWNIDLTNKICLDIGASTGGFTQCCLDNNASLVYAVDVGTNQLHSSLLNNL 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             +  +Q+      +     + D +      I ++   +  ++  ++        + 
Sbjct: 124 KVINMSQYNFRNAKKQDFLKNIDFVCCDVSFISLE-KIFLPLKDVVEFNTSGVFLIK 179


>gi|326332226|ref|ZP_08198506.1| ribosomal protein S4 [Nocardioidaceae bacterium Broad-1]
 gi|325949932|gb|EGD41992.1| ribosomal protein S4 [Nocardioidaceae bacterium Broad-1]
          Length = 202

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ RAG A +RR+  +++      VNG  +   +  V + D I+V    L      
Sbjct: 92  RLDNVVYRAGFARTRRQARQLVVHGHFLVNGKKVNVPSFQVSAHDVIDVREKSLEMTPFI 151

Query: 74  R 74
            
Sbjct: 152 V 152


>gi|283953794|ref|ZP_06371325.1| 30S ribosomal protein S4 [Campylobacter jejuni subsp. jejuni 414]
 gi|283794835|gb|EFC33573.1| 30S ribosomal protein S4 [Campylobacter jejuni subsp. jejuni 414]
          Length = 208

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G A+ RR   +++    V V+G  ++  +  V +   IE+
Sbjct: 98  QRLDNVVYRMGFATTRRFARQLVTHGHVLVDGKRVDIPSFRVKAGAKIEI 147


>gi|262273355|ref|ZP_06051169.1| SSU ribosomal protein S4p (S9e) [Grimontia hollisae CIP 101886]
 gi|262222333|gb|EEY73644.1| SSU ribosomal protein S4p (S9e) [Grimontia hollisae CIP 101886]
          Length = 206

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V + D I +
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKAILVNGKVVNVPSFKVTANDVISI 145


>gi|260893899|ref|YP_003239996.1| RNA-binding S4 domain protein [Ammonifex degensii KC4]
 gi|260866040|gb|ACX53146.1| RNA-binding S4 domain protein [Ammonifex degensii KC4]
          Length = 81

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 4/60 (6%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKA 70
           R+ K +  A + +RR    + + +  V +NG   +  A  V   D I ++  G  LR  
Sbjct: 1  MRIDKFLKEARLITRRTVANQALREGLVTINGRTAK-PATRVKKGDIITLNLGGKLLRLE 59


>gi|156354206|ref|XP_001623291.1| predicted protein [Nematostella vectensis]
 gi|156209974|gb|EDO31191.1| predicted protein [Nematostella vectensis]
          Length = 1300

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 9/109 (8%), Positives = 15/109 (13%)

Query: 243  EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            E            +               P      P            + G    +   
Sbjct: 1001 EPDRLQHEARIPPHDQGRPPYEPGRPPHEPGRPPHEPGRPPHEPGRPPHEPGRPPHEPGR 1060

Query: 303  TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
             P                      + G+      R P  P +       
Sbjct: 1061 PPHEPGRPPHEPGRPPYEPGRPPHEPGRPPHELGRPPHEPGRPPHEPGR 1109



 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/114 (11%), Positives = 21/114 (18%), Gaps = 2/114 (1%)

Query: 243  EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            +Q  P        +               P      P            + G    +   
Sbjct: 1015 DQGRPPYEPGRPPHEPGRPPHEPGRPPHEPGRPPHEPGRPPHEPGRPPHEPGRPPHEPGR 1074

Query: 303  TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS--LRRTSAKK 354
             P                      + G+      R P  P +     RR   +K
Sbjct: 1075 PPYEPGRPPHEPGRPPHELGRPPHEPGRPPHEPGRLPHEPGRPPYEQRRPPHEK 1128



 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 9/112 (8%), Positives = 17/112 (15%), Gaps = 1/112 (0%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            RE          +   +      E  +                 +             + 
Sbjct: 985  REYYDQKPGPPGRPPFEPDRLQHEARIPPHDQGRPPYEPGRPPHEPGRPPHEPGRPPHEP 1044

Query: 302  ATPVHRRNLAS-NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
              P H                     + G+      R P  P +        
Sbjct: 1045 GRPPHEPGRPPHEPGRPPHEPGRPPHEPGRPPYEPGRPPHEPGRPPHELGRP 1096



 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 8/122 (6%), Positives = 21/122 (17%), Gaps = 5/122 (4%)

Query: 238  KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
               L+ +      ++ +   +      E                    +           
Sbjct: 1002 PDRLQHEARIPPHDQGRPPYEPGRPPHEPGRPPHEPGRPPHEPGRPPHEPGRPPHEPGRP 1061

Query: 298  QKKLATPVHRRNLAS-NVWMAKGIHSSFLSDSGQREENHRRSPSFPSK----RSLRRTSA 352
              +   P H                     + G+      R P  P +            
Sbjct: 1062 PHEPGRPPHEPGRPPYEPGRPPHEPGRPPHELGRPPHEPGRPPHEPGRLPHEPGRPPYEQ 1121

Query: 353  KK 354
            ++
Sbjct: 1122 RR 1123



 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 15/126 (11%), Positives = 27/126 (21%), Gaps = 2/126 (1%)

Query: 229  LAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISE--VPDDFTRMK 286
              G++RE     +     P L E   +++       E   +           PD      
Sbjct: 950  HEGASREERPPGIPYPDNPRLGERPPIDVRRQEPGREYYDQKPGPPGRPPFEPDRLQHEA 1009

Query: 287  KNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
            +      G    +    P                      + G+      R P  P +  
Sbjct: 1010 RIPPHDQGRPPYEPGRPPHEPGRPPHEPGRPPHEPGRPPHEPGRPPHEPGRPPHEPGRPP 1069

Query: 347  LRRTSA 352
                  
Sbjct: 1070 HEPGRP 1075



 Score = 44.8 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 10/110 (9%), Positives = 16/110 (14%), Gaps = 1/110 (0%)

Query: 244  QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +  P      Q          E         I          +             +   
Sbjct: 980  RQEPGREYYDQKPGPPGRPPFEPDRLQHEARIPPHDQGRPPYEPGRPPHEPGRPPHEPGR 1039

Query: 304  PVHRRNLAS-NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            P H                     + G+      R P  P +        
Sbjct: 1040 PPHEPGRPPHEPGRPPHEPGRPPHEPGRPPHEPGRPPYEPGRPPHEPGRP 1089



 Score = 36.3 bits (82), Expect = 8.2,   Method: Composition-based stats.
 Identities = 11/107 (10%), Positives = 21/107 (19%)

Query: 246  GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            GP           +       +       + E P    R ++   +            P 
Sbjct: 941  GPEGYRRPSHEGASREERPPGIPYPDNPRLGERPPIDVRRQEPGREYYDQKPGPPGRPPF 1000

Query: 306  HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                L     +          + G+      R P  P +        
Sbjct: 1001 EPDRLQHEARIPPHDQGRPPYEPGRPPHEPGRPPHEPGRPPHEPGRP 1047


>gi|294789218|ref|ZP_06754457.1| ribosomal protein S4 [Simonsiella muelleri ATCC 29453]
 gi|294482959|gb|EFG30647.1| ribosomal protein S4 [Simonsiella muelleri ATCC 29453]
          Length = 206

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/60 (23%), Positives = 29/60 (48%), Gaps = 1/60 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G AS R E  ++++ + + VNG ++   +  V + D + V     ++    
Sbjct: 97  RLDNVVYRMGFASTRAEARQLVSHKALTVNGQVVNIPSFQVKAGDVVAVREKAKKQVRIQ 156


>gi|197287092|ref|YP_002152964.1| 30S ribosomal protein S4 [Proteus mirabilis HI4320]
 gi|227354912|ref|ZP_03839326.1| 30S ribosomal protein S4 [Proteus mirabilis ATCC 29906]
 gi|226699106|sp|B4F1K8|RS4_PROMH RecName: Full=30S ribosomal protein S4
 gi|194684579|emb|CAR46428.1| 30S ribosomal protein S4 [Proteus mirabilis HI4320]
 gi|227164994|gb|EEI49833.1| 30S ribosomal protein S4 [Proteus mirabilis ATCC 29906]
          Length = 206

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  +M++ + + VNG ++  A+  V   D + V
Sbjct: 97  RLDNVVYRMGFGATRAEARQMVSHKAIMVNGRVVNIASYQVSPNDVVSV 145


>gi|21672746|ref|NP_660813.1| 30S ribosomal protein S4 [Buchnera aphidicola str. Sg (Schizaphis
           graminum)]
 gi|22654271|sp|P41186|RS4_BUCAP RecName: Full=30S ribosomal protein S4
 gi|21623392|gb|AAM68024.1| 30S ribosomal protein S4 [Buchnera aphidicola str. Sg (Schizaphis
           graminum)]
          Length = 206

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V+ R G   +R E  ++I+ + +KVN  ++  A+  +   D I V   
Sbjct: 97  RLDNVVYRMGFGCTRSESRQLISHKSIKVNNNIVNIASYQISPNDRISVRDK 148


>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 = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 25/227 (11%), Positives = 59/227 (25%), Gaps = 14/227 (6%)

Query: 1   MKDKNIVQENFTPQRV-----------SKVIARAGIASRREVERMIAQQRVKVNGILLER 49
           MK K         Q +            K+++     S  E + +I +  V + G  L+ 
Sbjct: 1   MKTKQTKNSPKKNQHIPTKIPNNAQKAYKLLSAQEGISHNEAKNLIDRGLVTIQGKKLKI 60

Query: 50  AAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
           A   +    H ++  +P  K       +         T  +       +  L  +     
Sbjct: 61  ARALLSPNTHFKIQQLPPIKIIFQDENILALSKPAFLTSEEIVKLYPQWALLHRLDKETS 120

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-- 167
            V  L        L   +      +       +           +   +       VI  
Sbjct: 121 GVLLLIKENSPFHLKAKEEFKKEQIFKQYVAIVEGIIDEEQEITEPLIIQKGHFAKVIVA 180

Query: 168 -QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +       ++T    +     + + ++ G+  +I+         + 
Sbjct: 181 KKNGIKAYTKITPIEIESKKTKLEILIKTGRTHQIRAHLAHIKHPII 227


>gi|325282667|ref|YP_004255208.1| ribosomal protein S4 [Deinococcus proteolyticus MRP]
 gi|324314476|gb|ADY25591.1| ribosomal protein S4 [Deinococcus proteolyticus MRP]
          Length = 206

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G AS RR+  + +    + VNG  ++ A+  V   D I V
Sbjct: 97  RLDNVVFRMGFASTRRQARQFVGHGHILVNGKKVDIASYRVKIGDEITV 145


>gi|116327250|ref|YP_796970.1| 30S ribosomal protein S4 [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116327290|ref|YP_797010.1| 30S ribosomal protein S4 [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116332096|ref|YP_801814.1| 30S ribosomal protein S4 [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
 gi|122280174|sp|Q04PW4|RS4_LEPBJ RecName: Full=30S ribosomal protein S4
 gi|122284903|sp|Q055B8|RS4_LEPBL RecName: Full=30S ribosomal protein S4
 gi|116119994|gb|ABJ78037.1| 30S Ribosomal protein S4 [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116120034|gb|ABJ78077.1| 30S Ribosomal protein S4 [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116125785|gb|ABJ77056.1| 30S Ribosomal protein S4 [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
          Length = 207

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+    IA + V VNG  ++  +  +   D +E+
Sbjct: 97  RLDNVVYRLGFAVTRRQARNFIAHRHVLVNGERVDIPSYRLNVGDKVEI 145


>gi|308804930|ref|XP_003079777.1| hemolysin A, putative (ISS) [Ostreococcus tauri]
 gi|116058234|emb|CAL53423.1| hemolysin A, putative (ISS) [Ostreococcus tauri]
          Length = 290

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 12/36 (33%), Positives = 18/36 (50%)

Query: 27 SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          SR   +  IAQ +V V+G  + +A      +  IEV
Sbjct: 46 SRNVAQSWIAQGKVLVDGQPVTKAGTKFKPSVKIEV 81


>gi|113970789|ref|YP_734582.1| RNA-binding S4 domain-containing protein [Shewanella sp. MR-4]
 gi|114048016|ref|YP_738566.1| RNA-binding S4 domain-containing protein [Shewanella sp. MR-7]
 gi|117921057|ref|YP_870249.1| RNA-binding S4 domain-containing protein [Shewanella sp. ANA-3]
 gi|113885473|gb|ABI39525.1| RNA-binding S4 domain protein [Shewanella sp. MR-4]
 gi|113889458|gb|ABI43509.1| RNA-binding S4 domain protein [Shewanella sp. MR-7]
 gi|117613389|gb|ABK48843.1| RNA-binding S4 domain protein [Shewanella sp. ANA-3]
          Length = 76

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 12/51 (23%), Positives = 24/51 (47%), Gaps = 4/51 (7%)

Query: 20 IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
          ++ AG     E + +I +  V VNG +  R    V++ D +  +G  ++  
Sbjct: 27 MSNAGG----EAKHVIDEGLVTVNGEVETRKRKKVVAGDIVSFNGESVQII 73


>gi|312829403|emb|CBX34245.1| RNA pseudouridylate synthase family protein [Staphylococcus aureus
           subsp. aureus ECT-R 2]
          Length = 284

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 25/199 (12%), Positives = 54/199 (27%), Gaps = 28/199 (14%)

Query: 42  VNGILLERAAVNVMSTDHIEVD---------------GVPLRKAERTRLWLYHKPIGLVT 86
           VN   +      +M  D +E+                 + +   +   + +        T
Sbjct: 38  VNDEPVTV-RKQLMPNDILEIHLPREIPSVNLIPYARKLEVLYEDAFIIIVTKPNNQNCT 96

Query: 87  THSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
              +    S +   L              V RLD NT G+++    G +  +    + + 
Sbjct: 97  PSREHLHESLIEQVLYHCQEHGENINPHIVTRLDHNTTGIVIFAKYGHIHHLFSKVNLKK 156

Query: 142 LRVYRVRFHGQVD-------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           +    V              +   + +    V     Y      +  Q    +   V L 
Sbjct: 157 IYTCLVYGKTHTSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLH 216

Query: 195 EGKNREIKKVFEFFNWKVN 213
            G+  +I+  F+     + 
Sbjct: 217 TGRTHQIRVHFQHIGHPIV 235


>gi|295425098|ref|ZP_06817803.1| pseudouridylate synthase [Lactobacillus amylolyticus DSM 11664]
 gi|295065157|gb|EFG56060.1| pseudouridylate synthase [Lactobacillus amylolyticus DSM 11664]
          Length = 50

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/40 (27%), Positives = 19/40 (47%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN 53
           R+ K +A   + SR++V ++I    V VNG  +      
Sbjct: 1  MRIDKYLANMNVGSRKDVHKLIKSVIVSVNGHPVTTPKEK 40


>gi|168211877|ref|ZP_02637502.1| ribosomal protein S4 [Clostridium perfringens B str. ATCC 3626]
 gi|170710184|gb|EDT22366.1| ribosomal protein S4 [Clostridium perfringens B str. ATCC 3626]
          Length = 206

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            R+  V+ R G   SR E  +++      VNG  ++ A+  V   D I V
Sbjct: 98  MRLDNVVYRLGYGASRTEARQLVNHGHFLVNGKKVDIASFKVSVNDFITV 147


>gi|116491377|ref|YP_810921.1| SSU ribosomal protein S4P [Oenococcus oeni PSU-1]
 gi|116092102|gb|ABJ57256.1| SSU ribosomal protein S4P [Oenococcus oeni PSU-1]
          Length = 262

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+AS R +  +++    + V+G  +   +  V     I V
Sbjct: 153 RLDSVVFRLGLASTRPQARQLVNHGHILVDGKRVTIPSYEVKPGQIISV 201


>gi|318042231|ref|ZP_07974187.1| hypothetical protein SCB01_11007 [Synechococcus sp. CB0101]
          Length = 263

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 2/52 (3%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V A AG+  SR  +  +I Q  V+VN  ++   +  +   D + +DG 
Sbjct: 190 RLDAV-ASAGLGLSRSRMADLIRQGSVRVNWQVITSPSKELRCGDRVRLDGR 240


>gi|294787547|ref|ZP_06752800.1| ribosomal RNA large subunit methyltransferase J [Parascardovia
          denticolens F0305]
 gi|315226867|ref|ZP_07868655.1| cytotoxin/hemolysin [Parascardovia denticolens DSM 10105]
 gi|294484903|gb|EFG32538.1| ribosomal RNA large subunit methyltransferase J [Parascardovia
          denticolens F0305]
 gi|315120999|gb|EFT84131.1| cytotoxin/hemolysin [Parascardovia denticolens DSM 10105]
          Length = 260

 Score = 48.6 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/58 (24%), Positives = 33/58 (56%), Gaps = 2/58 (3%)

Query: 7  VQENFTPQ-RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          ++ ++T Q R+ + +   G+A SR + + +I++  V VN +   +A+  +   D ++V
Sbjct: 1  MKTDYTSQIRLDRALVEQGLAPSRTKAQELISRGDVFVNHLPAGKASRLIGPEDRLQV 58


>gi|326803755|ref|YP_004321573.1| ribosomal protein S4 [Aerococcus urinae ACS-120-V-Col10a]
 gi|326650742|gb|AEA00925.1| ribosomal protein S4 [Aerococcus urinae ACS-120-V-Col10a]
          Length = 203

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  ++ R G+AS RR+  ++++   + V+G  ++  +  V     I V
Sbjct: 94  QRLDNMVYRLGLASTRRQARQLVSHGHITVDGKRVDIPSYIVEVGQVIGV 143


>gi|284049231|ref|YP_003399570.1| ribosomal protein S4 [Acidaminococcus fermentans DSM 20731]
 gi|283953452|gb|ADB48255.1| ribosomal protein S4 [Acidaminococcus fermentans DSM 20731]
          Length = 197

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +RR+  +++    + VNG  L+  +  V + D + V
Sbjct: 88  RLDNVVYRMGLAHTRRQARQLVTHGHIAVNGKRLDIPSALVKAGDVVSV 136


>gi|229524553|ref|ZP_04413958.1| SSU ribosomal protein S4p (S9e) [Vibrio cholerae bv. albensis
           VL426]
 gi|229338134|gb|EEO03151.1| SSU ribosomal protein S4p (S9e) [Vibrio cholerae bv. albensis
           VL426]
          Length = 206

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   + NV + D + V
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAILVNGKVVNVPSFNVAANDVVAV 145


>gi|328957152|ref|YP_004374538.1| 30S ribosomal protein S4 [Carnobacterium sp. 17-4]
 gi|328673476|gb|AEB29522.1| 30S ribosomal protein S4 [Carnobacterium sp. 17-4]
          Length = 201

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G+A+ RR+  +++    + V+G  ++  + +V     I V
Sbjct: 93  QRLDNVVYRLGLATTRRQARQLVNHGHILVDGKRVDIPSYSVSVGQVITV 142


>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 = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 30/238 (12%), Positives = 61/238 (25%), Gaps = 31/238 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----E 61
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + I    E
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVE 69

Query: 62  VDGVP----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
           V+             +   +   + +      +V   +     + +   L      V   
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIVEVP 129

Query: 112 -----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-----------FHGQVDQ 155
                 RLD +T GL+++         L     +                      Q   
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     V            +     +   + + L  G+  +I+         + 
Sbjct: 190 RHATKRTLMAVHPMGKPAVTHYRIMENYRNYTRLRLRLETGRMHQIRVHMAHIAHPLL 247


>gi|312792842|ref|YP_004025765.1| RNA-binding S4 domain-containing protein [Caldicellulosiruptor
          kristjanssonii 177R1B]
 gi|312876108|ref|ZP_07736096.1| RNA-binding S4 domain protein [Caldicellulosiruptor lactoaceticus
          6A]
 gi|311797094|gb|EFR13435.1| RNA-binding S4 domain protein [Caldicellulosiruptor lactoaceticus
          6A]
 gi|312179982|gb|ADQ40152.1| RNA-binding S4 domain protein [Caldicellulosiruptor
          kristjanssonii 177R1B]
          Length = 80

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   +      RV VNG + +  + +V   D IEV
Sbjct: 1  MRIDKYLKVSRIIKRRTLAQEACEAGRVFVNGKVAK-PSTDVKVGDIIEV 49


>gi|293400557|ref|ZP_06644702.1| tyrosine--tRNA ligase [Erysipelotrichaceae bacterium 5_2_54FAA]
 gi|291305583|gb|EFE46827.1| tyrosine--tRNA ligase [Erysipelotrichaceae bacterium 5_2_54FAA]
          Length = 407

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 2/61 (3%)

Query: 16  VSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           +  V+ +A IAS +RE    I Q  +++NG  ++     V ST  I  +   +++ +R  
Sbjct: 344 LD-VLVQAKIASSKREAREWIKQGSIQINGERIKDCEFIVSSTHAITTNKTIIKRGKRNY 402

Query: 75  L 75
            
Sbjct: 403 Y 403


>gi|227550803|ref|ZP_03980852.1| 30S ribosomal protein S4 [Enterococcus faecium TX1330]
 gi|257878795|ref|ZP_05658448.1| ribosomal protein S4 [Enterococcus faecium 1,230,933]
 gi|257881433|ref|ZP_05661086.1| ribosomal protein S4 [Enterococcus faecium 1,231,502]
 gi|257885703|ref|ZP_05665356.1| ribosomal protein S4 [Enterococcus faecium 1,231,501]
 gi|257887941|ref|ZP_05667594.1| ribosomal protein S4 [Enterococcus faecium 1,141,733]
 gi|257890654|ref|ZP_05670307.1| ribosomal protein S4 [Enterococcus faecium 1,231,410]
 gi|257893257|ref|ZP_05672910.1| ribosomal protein S4 [Enterococcus faecium 1,231,408]
 gi|257896441|ref|ZP_05676094.1| ribosomal protein S4 [Enterococcus faecium Com12]
 gi|257899415|ref|ZP_05679068.1| ribosomal protein S4 [Enterococcus faecium Com15]
 gi|258615136|ref|ZP_05712906.1| 30S ribosomal protein S4 [Enterococcus faecium DO]
 gi|260558361|ref|ZP_05830557.1| ribosomal protein S4 [Enterococcus faecium C68]
 gi|261207068|ref|ZP_05921757.1| ribosomal protein S4 [Enterococcus faecium TC 6]
 gi|289565930|ref|ZP_06446370.1| 30S ribosomal protein S4 [Enterococcus faecium D344SRF]
 gi|293379587|ref|ZP_06625726.1| ribosomal protein S4 [Enterococcus faecium PC4.1]
 gi|293556844|ref|ZP_06675405.1| ribosomal protein S4 [Enterococcus faecium E1039]
 gi|293563783|ref|ZP_06678222.1| ribosomal protein S4 [Enterococcus faecium E1162]
 gi|293567853|ref|ZP_06679194.1| ribosomal protein S4 [Enterococcus faecium E1071]
 gi|294614629|ref|ZP_06694533.1| ribosomal protein S4 [Enterococcus faecium E1636]
 gi|294618566|ref|ZP_06698125.1| ribosomal protein S4 [Enterococcus faecium E1679]
 gi|294622064|ref|ZP_06701197.1| ribosomal protein S4 [Enterococcus faecium U0317]
 gi|314938819|ref|ZP_07846090.1| ribosomal protein S4 [Enterococcus faecium TX0133a04]
 gi|314943624|ref|ZP_07850378.1| ribosomal protein S4 [Enterococcus faecium TX0133C]
 gi|314948703|ref|ZP_07852076.1| ribosomal protein S4 [Enterococcus faecium TX0082]
 gi|314952153|ref|ZP_07855171.1| ribosomal protein S4 [Enterococcus faecium TX0133A]
 gi|314991873|ref|ZP_07857330.1| ribosomal protein S4 [Enterococcus faecium TX0133B]
 gi|314996586|ref|ZP_07861621.1| ribosomal protein S4 [Enterococcus faecium TX0133a01]
 gi|227180040|gb|EEI61012.1| 30S ribosomal protein S4 [Enterococcus faecium TX1330]
 gi|257813023|gb|EEV41781.1| ribosomal protein S4 [Enterococcus faecium 1,230,933]
 gi|257817091|gb|EEV44419.1| ribosomal protein S4 [Enterococcus faecium 1,231,502]
 gi|257821559|gb|EEV48689.1| ribosomal protein S4 [Enterococcus faecium 1,231,501]
 gi|257823995|gb|EEV50927.1| ribosomal protein S4 [Enterococcus faecium 1,141,733]
 gi|257827014|gb|EEV53640.1| ribosomal protein S4 [Enterococcus faecium 1,231,410]
 gi|257829636|gb|EEV56243.1| ribosomal protein S4 [Enterococcus faecium 1,231,408]
 gi|257833006|gb|EEV59427.1| ribosomal protein S4 [Enterococcus faecium Com12]
 gi|257837327|gb|EEV62401.1| ribosomal protein S4 [Enterococcus faecium Com15]
 gi|260075535|gb|EEW63841.1| ribosomal protein S4 [Enterococcus faecium C68]
 gi|260078696|gb|EEW66398.1| ribosomal protein S4 [Enterococcus faecium TC 6]
 gi|289162303|gb|EFD10163.1| 30S ribosomal protein S4 [Enterococcus faecium D344SRF]
 gi|291589438|gb|EFF21245.1| ribosomal protein S4 [Enterococcus faecium E1071]
 gi|291592531|gb|EFF24136.1| ribosomal protein S4 [Enterococcus faecium E1636]
 gi|291595179|gb|EFF26513.1| ribosomal protein S4 [Enterococcus faecium E1679]
 gi|291598362|gb|EFF29446.1| ribosomal protein S4 [Enterococcus faecium U0317]
 gi|291600928|gb|EFF31219.1| ribosomal protein S4 [Enterococcus faecium E1039]
 gi|291604264|gb|EFF33759.1| ribosomal protein S4 [Enterococcus faecium E1162]
 gi|292641803|gb|EFF59974.1| ribosomal protein S4 [Enterococcus faecium PC4.1]
 gi|313589275|gb|EFR68120.1| ribosomal protein S4 [Enterococcus faecium TX0133a01]
 gi|313593578|gb|EFR72423.1| ribosomal protein S4 [Enterococcus faecium TX0133B]
 gi|313595685|gb|EFR74530.1| ribosomal protein S4 [Enterococcus faecium TX0133A]
 gi|313597661|gb|EFR76506.1| ribosomal protein S4 [Enterococcus faecium TX0133C]
 gi|313641830|gb|EFS06410.1| ribosomal protein S4 [Enterococcus faecium TX0133a04]
 gi|313644875|gb|EFS09455.1| ribosomal protein S4 [Enterococcus faecium TX0082]
          Length = 203

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G+A+ RR+  +++    + V+G  ++  + +V     I V
Sbjct: 93  QRLDNVVYRLGLATTRRQARQLVNHGHILVDGKRVDIPSYHVEVGQVISV 142


>gi|239828057|ref|YP_002950681.1| 30S ribosomal protein S4 [Geobacillus sp. WCH70]
 gi|259495282|sp|C5D699|RS4_GEOSW RecName: Full=30S ribosomal protein S4
 gi|239808350|gb|ACS25415.1| ribosomal protein S4 [Geobacillus sp. WCH70]
          Length = 200

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G A +RR+  +++    + V+G  +   +  V     I V
Sbjct: 93  RLDNLVYRLGFARTRRQARQLVTHGHILVDGNRVNIPSYRVKPGQTISV 141


>gi|153831469|ref|ZP_01984136.1| ribosomal protein S4 [Vibrio cholerae 623-39]
 gi|148873050|gb|EDL71185.1| ribosomal protein S4 [Vibrio cholerae 623-39]
          Length = 166

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   + NV + D + V
Sbjct: 57  RLDNVVYRMGFGATRAEARQLVSHKAILVNGKVVNVPSFNVAANDVVAV 105


>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 = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 28/198 (14%), Positives = 60/198 (30%), Gaps = 7/198 (3%)

Query: 5   NIVQENFTPQRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            +V       R+   I+   +GI SR  V+  I    V VNG ++++ + NV   D +  
Sbjct: 63  QVVHAKSVKLRLDSWISSRISGI-SRARVQSSIKSGLVSVNGRVVDKVSHNVKFGDKVTC 121

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
               L+        +    +         +    +  +          V  +  +     
Sbjct: 122 TISELQPLRAEPEDMPLDIVYEDEHLLVVNKPPHMVVHPAPGNPTGTLVNGILHHCNLPT 181

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG----DMQVT 178
           +  +   +    E  S    R Y       +    ++ L KG     +          ++
Sbjct: 182 VAISSQEVLSDAEDRSDDDERSYSSSCESSIRPGIVHRLDKGTSGLLVVAKDEHAHAHLS 241

Query: 179 LDTQKGSNAWVTVGLREG 196
              ++ +   V + L  G
Sbjct: 242 EQFKQHTIQRVYISLTSG 259


>gi|33862020|ref|NP_893581.1| rRNA methyltransferase [Prochlorococcus marinus subsp. pastoris
          str. CCMP1986]
 gi|33634238|emb|CAE19923.1| FtsJ cell division protein:S4 domain:Hemolysin A [Prochlorococcus
          marinus subsp. pastoris str. CCMP1986]
          Length = 270

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 10/54 (18%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVK-VNGILLERAAVNVMSTDHIEVDGVP 66
          R+   +   G+  +R++ + +I   +VK +NG + ++    V+      ++  P
Sbjct: 6  RLDLYLIYKGLCETRQKAQGLILAGKVKDINGKIFDKPGQQVLIGTEFIIESEP 59


>gi|330976664|gb|EGH76707.1| 30S ribosomal protein S4 [Pseudomonas syringae pv. aptata str. DSM
           50252]
          Length = 206

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + V VNG  +   +  V + D + +
Sbjct: 97  RLDNVVYRMGFGSTRAESRQLVSHKSVSVNGKTVNVPSYQVRAGDVVAI 145


>gi|238928129|ref|ZP_04659889.1| ribosomal protein S4 [Selenomonas flueggei ATCC 43531]
 gi|238884089|gb|EEQ47727.1| ribosomal protein S4 [Selenomonas flueggei ATCC 43531]
          Length = 197

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +RR+  +++      VNG  ++  +  V   D IEV
Sbjct: 88  RMDNVVFRLGLANTRRQARQLVRHGHFTVNGKRVDIPSALVREGDVIEV 136


>gi|167036828|ref|YP_001664406.1| 30S ribosomal protein S4 [Thermoanaerobacter pseudethanolicus ATCC
           33223]
 gi|167039547|ref|YP_001662532.1| 30S ribosomal protein S4 [Thermoanaerobacter sp. X514]
 gi|256752659|ref|ZP_05493511.1| ribosomal protein S4 [Thermoanaerobacter ethanolicus CCSD1]
 gi|300915202|ref|ZP_07132517.1| ribosomal protein S4 [Thermoanaerobacter sp. X561]
 gi|307725126|ref|YP_003904877.1| 30S ribosomal protein S4 [Thermoanaerobacter sp. X513]
 gi|320115250|ref|YP_004185409.1| 30S ribosomal protein S4 [Thermoanaerobacter brockii subsp. finnii
           Ako-1]
 gi|226695091|sp|B0KCM7|RS4_THEP3 RecName: Full=30S ribosomal protein S4
 gi|226695092|sp|B0K5S0|RS4_THEPX RecName: Full=30S ribosomal protein S4
 gi|166853787|gb|ABY92196.1| RNA-binding S4 domain protein [Thermoanaerobacter sp. X514]
 gi|166855662|gb|ABY94070.1| RNA-binding S4 domain protein [Thermoanaerobacter pseudethanolicus
           ATCC 33223]
 gi|256748479|gb|EEU61531.1| ribosomal protein S4 [Thermoanaerobacter ethanolicus CCSD1]
 gi|300888926|gb|EFK84073.1| ribosomal protein S4 [Thermoanaerobacter sp. X561]
 gi|307582187|gb|ADN55586.1| ribosomal protein S4 [Thermoanaerobacter sp. X513]
 gi|319928341|gb|ADV79026.1| ribosomal protein S4 [Thermoanaerobacter brockii subsp. finnii
           Ako-1]
          Length = 206

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SR +  ++++   ++VNG  ++  +  V   D I V
Sbjct: 99  RLDNVVFRLGFAASRPQARQLVSHGHIEVNGKKVDIPSFLVKPGDVISV 147


>gi|291538949|emb|CBL12060.1| Uncharacterized conserved protein, contains S4-like domain
           [Roseburia intestinalis XB6B4]
          Length = 250

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 21/66 (31%), Positives = 28/66 (42%), Gaps = 5/66 (7%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M DK+ I+  N    R+  VIA     SR +   +I   RV VNG  ++         D 
Sbjct: 163 MIDKDGIITSN----RLDSVIACVYRLSRSQSLELIRADRVFVNGKNIQTPTYICKPDDI 218

Query: 60  IEVDGV 65
           I V G 
Sbjct: 219 ISVRGH 224


>gi|240146312|ref|ZP_04744913.1| putative S4 domain protein [Roseburia intestinalis L1-82]
 gi|257201553|gb|EEU99837.1| putative S4 domain protein [Roseburia intestinalis L1-82]
          Length = 250

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 21/66 (31%), Positives = 28/66 (42%), Gaps = 5/66 (7%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M DK+ I+  N    R+  VIA     SR +   +I   RV VNG  ++         D 
Sbjct: 163 MIDKDGIITSN----RLDSVIACVYRLSRSQSLELIRADRVFVNGKNIQTPTYICKPDDI 218

Query: 60  IEVDGV 65
           I V G 
Sbjct: 219 ISVRGH 224


>gi|225376437|ref|ZP_03753658.1| hypothetical protein ROSEINA2194_02079 [Roseburia inulinivorans DSM
           16841]
 gi|225211813|gb|EEG94167.1| hypothetical protein ROSEINA2194_02079 [Roseburia inulinivorans DSM
           16841]
          Length = 197

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V+ R G A +R+E  +++  + V VNG  +   +  V + D IE+   
Sbjct: 88  RLDNVVFRLGFARTRKEARQIVDHKFVTVNGKQVNIPSYLVKAGDVIEIKEK 139


>gi|189219451|ref|YP_001940092.1| ribosomal protein S4 [Methylacidiphilum infernorum V4]
 gi|189186309|gb|ACD83494.1| Ribosomal protein S4 [Methylacidiphilum infernorum V4]
          Length = 228

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 17/73 (23%), Positives = 29/73 (39%), Gaps = 1/73 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  V+ R   A SR E  +++    + VNG  +   +      D IEV   P  +   
Sbjct: 118 ERLDNVVYRLCFATSRMEARQLVNHGHIYVNGKKVNIPSYRTKPGDVIEVCPKPQSRKLA 177

Query: 73  TRLWLYHKPIGLV 85
            R     K + + 
Sbjct: 178 LRNLEAMKGVKIP 190


>gi|254977345|ref|ZP_05273817.1| putative RNA-binding mediating protein [Clostridium difficile
          QCD-66c26]
 gi|255094675|ref|ZP_05324153.1| putative RNA-binding mediating protein [Clostridium difficile CIP
          107932]
 gi|255316429|ref|ZP_05358012.1| putative RNA-binding mediating protein [Clostridium difficile
          QCD-76w55]
 gi|255519089|ref|ZP_05386765.1| putative RNA-binding mediating protein [Clostridium difficile
          QCD-97b34]
 gi|255652272|ref|ZP_05399174.1| putative RNA-binding mediating protein [Clostridium difficile
          QCD-37x79]
 gi|260681772|ref|YP_003213057.1| putative RNA-binding mediating protein [Clostridium difficile
          CD196]
 gi|306521986|ref|ZP_07408333.1| putative RNA-binding mediating protein [Clostridium difficile
          QCD-32g58]
 gi|260207935|emb|CBA60045.1| putative RNA-binding mediating protein [Clostridium difficile
          CD196]
          Length = 68

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 10/64 (15%), Positives = 25/64 (39%), Gaps = 9/64 (14%)

Query: 10 NFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
               ++ + +     A  G       + +I +  V VN  +  R    + S D ++++G
Sbjct: 7  ESEYIKLDQFLKLAEIASTGG----HAKFLIQEGLVTVNDEIELRRGKKIKSGDIVKIEG 62

Query: 65 VPLR 68
            ++
Sbjct: 63 TKIK 66


>gi|148657960|ref|YP_001278165.1| hemolysin A [Roseiflexus sp. RS-1]
 gi|148570070|gb|ABQ92215.1| hemolysin A [Roseiflexus sp. RS-1]
          Length = 267

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/56 (23%), Positives = 27/56 (48%), Gaps = 1/56 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
             R+  ++ + G+A +R   + +I    V+V+G++  +A   V     IE+ G  
Sbjct: 3  KKVRLDHLLVQRGLAETRARAQALILAGEVRVDGVVRLKAGELVPEDAGIELAGKL 58


>gi|125973345|ref|YP_001037255.1| hemolysin A [Clostridium thermocellum ATCC 27405]
 gi|256005451|ref|ZP_05430414.1| hemolysin A [Clostridium thermocellum DSM 2360]
 gi|281417545|ref|ZP_06248565.1| hemolysin A [Clostridium thermocellum JW20]
 gi|125713570|gb|ABN52062.1| hemolysin A [Clostridium thermocellum ATCC 27405]
 gi|255990591|gb|EEU00710.1| hemolysin A [Clostridium thermocellum DSM 2360]
 gi|281408947|gb|EFB39205.1| hemolysin A [Clostridium thermocellum JW20]
 gi|316940423|gb|ADU74457.1| hemolysin A [Clostridium thermocellum DSM 1313]
          Length = 270

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 11/52 (21%), Positives = 20/52 (38%), Gaps = 1/52 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            +R+  ++   G   SR + +  I    V VN    ++  V V     I +
Sbjct: 2  KKERLDVLLVNRGFFQSREKAKSSIMAGVVFVNDKKEDKPGVKVDVDSIITI 53


>gi|295399544|ref|ZP_06809526.1| ribosomal protein S4 [Geobacillus thermoglucosidasius C56-YS93]
 gi|312109901|ref|YP_003988217.1| ribosomal protein S4 [Geobacillus sp. Y4.1MC1]
 gi|294979010|gb|EFG54606.1| ribosomal protein S4 [Geobacillus thermoglucosidasius C56-YS93]
 gi|311215002|gb|ADP73606.1| ribosomal protein S4 [Geobacillus sp. Y4.1MC1]
          Length = 200

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G A +RR+  +++    + V+G  +   +  V     I V
Sbjct: 93  RLDNLVYRLGFARTRRQARQLVTHGHILVDGNRVNIPSYRVKPGQTISV 141


>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 = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 18/62 (29%), Positives = 27/62 (43%), Gaps = 4/62 (6%)

Query: 5  NIVQENFTPQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           I+     P R+ K +AR    A   SR  + ++IA+  V   G +L    V V   D I
Sbjct: 6  RIIIGEAPPARLDKALARDVPEAAALSRTRLAKLIAEGAVTRGGEVLSDPKVKVAEGDEI 65

Query: 61 EV 62
           +
Sbjct: 66 VI 67


>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 = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 35/243 (14%), Positives = 71/243 (29%), Gaps = 39/243 (16%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGI-----------------LL 47
           I+ ++    R+ + +A+     SR  ++  I ++RV V+G                    
Sbjct: 4   IIPDHCAGLRLDQALAQLLAEWSRSRLQSWILEKRVSVDGACSLPRQKVWGGEKIVLSPA 63

Query: 48  ERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
              A      + I +D   +   +   + +      +V   S     + +   L      
Sbjct: 64  RDPAETAHEPEAIALD---IVHEDHAIIIIDKPAGLVVHPGSGNWQGTLLNALLHHSPQL 120

Query: 107 ----RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY------------RVRFH 150
               R   V RLD  T GLL++         L     +                   R  
Sbjct: 121 SGIPRSGIVHRLDKETSGLLVVAKTLEAQTSLVRQLQKRTVKREYLALVWGSVSSHGRVD 180

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             V +  +   +  +V  G      +  +  Q      +  GL  G+  +I+   +    
Sbjct: 181 APVGRHPVQRTRMAVVASGKEART-RYEVLEQFTDCTLLRCGLETGRTHQIRVHMQSLGH 239

Query: 211 KVN 213
            + 
Sbjct: 240 PLV 242


>gi|293365886|ref|ZP_06612589.1| S4 domain-containing protein YlmH [Streptococcus oralis ATCC 35037]
 gi|307702291|ref|ZP_07639249.1| S4 domain protein [Streptococcus oralis ATCC 35037]
 gi|291315564|gb|EFE56014.1| S4 domain-containing protein YlmH [Streptococcus oralis ATCC 35037]
 gi|307624094|gb|EFO03073.1| S4 domain protein [Streptococcus oralis ATCC 35037]
          Length = 263

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/48 (27%), Positives = 27/48 (56%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +++ A   SR +  ++I ++ V+VN  ++E++   V   D I V
Sbjct: 186 RLDALLSSALKLSRNQTSQLIEKKSVQVNYHVVEKSDYQVAVGDLISV 233


>gi|260944778|ref|XP_002616687.1| hypothetical protein CLUG_03928 [Clavispora lusitaniae ATCC 42720]
 gi|238850336|gb|EEQ39800.1| hypothetical protein CLUG_03928 [Clavispora lusitaniae ATCC 42720]
          Length = 468

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 1/54 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+   + R+  AS  R+    I    VKVNG+ ++  A  + S D   V+   +
Sbjct: 104 RLEFALFRSMFASSVRQAREFIKNGHVKVNGVTIKHPAFPLKSGDIFSVNPEKV 157


>gi|229006180|ref|ZP_04163866.1| RNA-binding S4 domain protein [Bacillus mycoides Rock1-4]
 gi|228755021|gb|EEM04380.1| RNA-binding S4 domain protein [Bacillus mycoides Rock1-4]
          Length = 246

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+ +I    VKVN   +E+ A      D   + G
Sbjct: 171 RLDVLLAEMLHLSRQKVQPLIKNGLVKVNWKTVEQTAYECFPGDVFSIRG 220


>gi|120609325|ref|YP_969003.1| 30S ribosomal protein S4 [Acidovorax citrulli AAC00-1]
 gi|152060922|sp|A1TJU1|RS4_ACIAC RecName: Full=30S ribosomal protein S4
 gi|120587789|gb|ABM31229.1| SSU ribosomal protein S4P [Acidovorax citrulli AAC00-1]
          Length = 207

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +  A+  V   D + V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAITVNGQSVNIASYLVKPGDVVAV 146


>gi|68535941|ref|YP_250646.1| hypothetical protein jk0864 [Corynebacterium jeikeium K411]
 gi|68263540|emb|CAI37028.1| hypothetical protein jk0864 [Corynebacterium jeikeium K411]
          Length = 283

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 6  IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          + +     QR+   +    IA SR   + MI   RV VNG+L ++ A  V     I+V
Sbjct: 1  MAKRGPKLQRLDAELVARKIARSREHAQEMIKAGRVTVNGMLAKKPASGVDGNVSIKV 58


>gi|194014420|ref|ZP_03053037.1| RNA-binding protein [Bacillus pumilus ATCC 7061]
 gi|194013446|gb|EDW23011.1| RNA-binding protein [Bacillus pumilus ATCC 7061]
          Length = 258

 Score = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 16/65 (24%), Positives = 31/65 (47%), Gaps = 1/65 (1%)

Query: 1   MKDK-NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K K +I ++  +  R+  V A     SR++ + ++    VKVN  + E  +  +   D 
Sbjct: 168 VKSKTDIKEDTISSLRLDAVCAAISRQSRQKAQLLVKNGLVKVNWKVTEDPSFTIGEGDQ 227

Query: 60  IEVDG 64
           + V G
Sbjct: 228 LSVRG 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 = 48.6 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 16/65 (24%), Positives = 23/65 (35%), Gaps = 2/65 (3%)

Query: 1  MKDKNIVQENFT-PQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
          M    I  E     QR+   + ARA   SR   + +I +  V V G +       V    
Sbjct: 1  MNQIVITSEAADAGQRLDAFLGARAEGISRSRAKTLIEEGAVTVGGAVETNPRAPVKKGL 60

Query: 59 HIEVD 63
             V+
Sbjct: 61 VYAVN 65


>gi|298504578|gb|ADI83301.1| S4 domain protein [Geobacter sulfurreducens KN400]
          Length = 65

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 7  VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          ++ +    ++   + A   +AS  E + +IA+  V+VNG    R    +   D +EV G 
Sbjct: 1  MKIDTDHIKLDSFLKAANLVASGGEAKIIIAEGAVRVNGETELRRGRKLRPGDQVEVAGE 60


>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 = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 41/268 (15%), Positives = 76/268 (28%), Gaps = 40/268 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIA----RAGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           M     V E+   +R+ KVI        +     + R I +  V+V+G      +V +  
Sbjct: 1   MSYTFKVSEHHAGRRLDKVIRTLWPNLPLG---AMMRGIRKGLVRVDGRK-TSCSVRLED 56

Query: 57  TDHIEVDGVP-----------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
              + V                     +   +   + L  +   ++      +       
Sbjct: 57  GQSVYVPWEEPELIEKSVKTKRTGALSIVYKDHYIMVLNKEAGLIIQPDQSGEESLIERV 116

Query: 100 NLPSIFSRVI---SVGRLDINTEGLLLLTNDGGL----ARVLELPSTQWLRVYRVRFHGQ 152
            L           +V RLD NT GL+++   G       R           +  VR    
Sbjct: 117 WLEVEPEGDFRACAVHRLDRNTTGLVVVALHGQSLRELQRAFRDNDVDKTYLVAVRGQTP 176

Query: 153 VDQDKLNLLKKGIVIQGICYGDM------QVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
           ++ D    L+K      +                      + + V L  G++ +I+    
Sbjct: 177 LEGDITAPLQKDRDHNIVTASPDGLPAHTHYEKIAGDDECSLLKVSLLTGRSHQIRVHLA 236

Query: 207 FFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              + V     + YG F L        R
Sbjct: 237 ISGYPVIG--DVKYGDFALNKQWYHRIR 262


>gi|293570759|ref|ZP_06681809.1| ribosomal protein S4 [Enterococcus faecium E980]
 gi|291609231|gb|EFF38503.1| ribosomal protein S4 [Enterococcus faecium E980]
          Length = 203

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G+A+ RR+  +++    + V+G  ++  + +V     I V
Sbjct: 93  QRLDNVVYRLGLATTRRQARQLVNHGHILVDGKRVDIPSYHVEVGQVISV 142


>gi|157377427|ref|YP_001476027.1| 30S ribosomal protein S4 [Shewanella sediminis HAW-EB3]
 gi|189045400|sp|A8G1C6|RS4_SHESH RecName: Full=30S ribosomal protein S4
 gi|157319801|gb|ABV38899.1| ribosomal protein S4 [Shewanella sediminis HAW-EB3]
          Length = 206

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V + D I +
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKSIMVNGSVVNIPSFKVSANDVISI 145


>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 = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 39/243 (16%), Positives = 73/243 (30%), Gaps = 37/243 (15%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +V      QR+   + R     SR  + ++I    V VNG  ++ A   +   + I V  
Sbjct: 1   MVTSGDQGQRLDHYLIRQLPEQSRSAIGKLIGAAHVLVNGQQVK-AGYRLHQDEIITVSF 59

Query: 65  VP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
            P              +   +   L +   P  +V       G + V   L         
Sbjct: 60  PPTPSLDLAPEKIDFSILFEDEHLLVIGKPPGLVVHPACGHGGGTLVHGLLYHCQDLPAL 119

Query: 107 ---RVISVGRLDINTEGLLLLT-------------NDGGLARVLELPSTQWLRVYRVRFH 150
              R   V RLD +T G++L+               +  + +       +  R    R  
Sbjct: 120 DAGRPGIVHRLDKDTSGVMLVAKSERSLRSLMADFKNRKIHKTYHALLLRSPREREGRLV 179

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS-NAWVTVGLREGKNREIKKVFEFFN 209
             + +  ++  K  I      Y      +     +    V +G+  G+  +I+       
Sbjct: 180 APIGRHPVDRKKMAIRPDQGKYAATHWRVLESFINGWCLVEIGIETGRTHQIRVHMASLR 239

Query: 210 WKV 212
             V
Sbjct: 240 APV 242


>gi|291087195|ref|ZP_06345679.2| ribosomal protein S4 [Clostridium sp. M62/1]
 gi|291075940|gb|EFE13304.1| ribosomal protein S4 [Clostridium sp. M62/1]
 gi|295092573|emb|CBK78680.1| SSU ribosomal protein S4P [Clostridium cf. saccharolyticum K10]
          Length = 197

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R+E  +++  + V VNG  +   +  V + D IE+
Sbjct: 88  RLDNVLFRMGFGRTRKETRQIVDHKHVLVNGKCVNIPSYLVKAGDVIEI 136


>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 = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 26/231 (11%), Positives = 64/231 (27%), Gaps = 32/231 (13%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILL---------ERAAVNVMSTDH--- 59
             R+   +A+     SR  +   I    V+ NG            E   V +  +D    
Sbjct: 33  GTRLDAALAKLLPDYSRSRITSWIKDGLVQCNGQTASPKHKLIGGELLRVQIQPSDENQA 92

Query: 60  ----------IEVDGVPLRKAERTRLWLYHKPIGLVTT--HSDPDGRSTVFDNLPSIFSR 107
                     +  D   +   +   L ++        T  +        +     +    
Sbjct: 93  FEPEAMDLDIVYEDDSVIVLNKPAGLVVHPAAGNWTGTLLNGLLAHCPELGQVPRAGIVH 152

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR-------VYRVRFHGQVDQDKLNL 160
            +      +      L   +  + ++      +  R        +  +    + +D  N 
Sbjct: 153 RLDKDTSGLMVVAKTLPAQNHLVQQLQNRSVKRIYRAVADGIVPFDGKIETLIGRDPHNR 212

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           LK  +V  G       V++  +  +++++   L  G+  +I+         
Sbjct: 213 LKMAVVKFGGKEAVTHVSVLERYQAHSYIECRLETGRTHQIRVHMREARHP 263


>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 = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 25/199 (12%), Positives = 53/199 (26%), Gaps = 28/199 (14%)

Query: 42  VNGILLERAAVNVMSTDHIEVD-GVPLR--------------KAERTRLWLYHKPIGLVT 86
           VN   +      +M  D +E+     +                 +   + +        T
Sbjct: 38  VNDEPVTV-RKQLMPNDILEIHLPQEIPSVNLIPYARKLEVLYEDAFIIIVTKPNNQNCT 96

Query: 87  THSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
              +    S +   L              V RLD NT G+++    G +  +    + + 
Sbjct: 97  PSREHPHESLIEQVLYHCQEHGENINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKVNLKK 156

Query: 142 LRVYRVRFHGQVD-------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           +    V              +   + +    V     Y      +  Q    +   V L 
Sbjct: 157 IYTCLVYGKTHTSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLH 216

Query: 195 EGKNREIKKVFEFFNWKVN 213
            G+  +I+  F+     + 
Sbjct: 217 TGRTHQIRVHFQHIGHPIV 235


>gi|302913178|ref|XP_003050861.1| predicted protein [Nectria haematococca mpVI 77-13-4]
 gi|256731799|gb|EEU45148.1| predicted protein [Nectria haematococca mpVI 77-13-4]
          Length = 4743

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/122 (10%), Positives = 35/122 (28%), Gaps = 4/122 (3%)

Query: 237  SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
                +R++      EE+     AP      +        +          +  ++++   
Sbjct: 4596 RPDDIRDRPSTAEREESVAPAPAPRRRFFGIKTSDNPPPAREEPAVAEPIRERAKESPPV 4655

Query: 297  KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK----RSLRRTSA 352
            ++ K     +RR   S          +    + +   +    PS   +     S R+   
Sbjct: 4656 EEPKRTRSKYRRPRESMDEARPRSRRTRDEPAPESPRDRDARPSRHVRMDTEDSRRKARH 4715

Query: 353  KK 354
            ++
Sbjct: 4716 EE 4717



 Score = 37.1 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 18/120 (15%), Positives = 37/120 (30%), Gaps = 5/120 (4%)

Query: 239  KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK- 297
            + ++E  G     E +         S +  R RP+ I + P    R +  +       + 
Sbjct: 4565 QEVKEAKGKEPEAEPERRHRRSRRHSHS-GRPRPDDIRDRPSTAEREESVAPAPAPRRRF 4623

Query: 298  ---QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               +     P  R   A    + +    S   +  +R  +  R P      +  R+   +
Sbjct: 4624 FGIKTSDNPPPAREEPAVAEPIRERAKESPPVEEPKRTRSKYRRPRESMDEARPRSRRTR 4683


>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 = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 60/244 (24%), Gaps = 45/244 (18%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLER------AAVNVM------STDHIEV 62
           R+  V+A    ASR +V   IA   VKV G  + +          +           +E 
Sbjct: 13  RLDAVLAALSGASRSQVAAWIAGGHVKVEGQPVTKVSLKLRGGERIDVSPPALPDARVEA 72

Query: 63  DGVPLRKAERTRLWL--YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE- 119
           + +PL         +     P  +          + V   L  +          +     
Sbjct: 73  EDLPLDVIYEDDYLIAVNKPPGMVTHPAPGVLSGTLVNALLGRMPLPEQPDYDSEAGYRP 132

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG------ 173
           G++   +      ++   +          F  +  +     +  G               
Sbjct: 133 GIVHRLDKDTSGVIVVAKTVGAHARLAAAFKDRETRKTYLAIAAGQWRADGPARVEAPIG 192

Query: 174 --DMQVTLDTQKGSN----------------------AWVTVGLREGKNREIKKVFEFFN 209
              +Q    T  G+N                      A V    R G+  +I+       
Sbjct: 193 RHPVQRQRMTVGGANPREAQTLFTPLAAHPDGHGRTLALVRAQPRTGRTHQIRVHLAHLG 252

Query: 210 WKVN 213
             + 
Sbjct: 253 SPIL 256


>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 = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 35/286 (12%), Positives = 79/286 (27%), Gaps = 53/286 (18%)

Query: 4   KNIVQENFTPQ-RVSKVI-ARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           + ++  + T + R+   + A+ G   SR  ++ +I   +V + G L+      V + D  
Sbjct: 25  RKVLTADETAEGRLDAWLTAQLGEEFSRSRIKVLIKDGQVSMRGQLITDPQRKVRAGDSF 84

Query: 61  EV----------DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           E+           G  +       +   + +      +V   S     + V   +    +
Sbjct: 85  EITLPEPEDPTPQGEDIPLDILYEDDDLIVISKPAGLVVHPGSGNWTGTLVNALIHHCGA 144

Query: 107 RVISVGRLDIN----------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
            +  +G +             T  +++  ND     +    +     +   R +  +   
Sbjct: 145 TLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDVAHRHLSLQFADHGRTMPLERAYRAIVWG 204

Query: 157 KLNLLKKGI-----VIQGICYGDMQVTLDTQKGSN---------------------AWVT 190
           +   L   +        G          D+Q                         + V 
Sbjct: 205 RPRSLTGTVDAPLGRATGDRTRRAVKRPDSQDADEAITHYEVIERFHETPDATALASLVE 264

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             L  G+  +I+         +        G      LL    R+V
Sbjct: 265 CRLETGRTHQIRVHMAHIGHPLLGDTVYGAGFRTKANLLPEDIRKV 310


>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 = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 30/244 (12%), Positives = 65/244 (26%), Gaps = 37/244 (15%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M+  N+ V++ F   R+   +++     SR  ++ +I +  V VN    ++    +   D
Sbjct: 1   MEKINLQVEKEFDNVRLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNK-EKKRNYKLKVGD 59

Query: 59  HIEVD-GVP-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           +IEV+   P             +   ++  + +      +V         + V   L   
Sbjct: 60  NIEVNIPEPKLLQIEPEDIKLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNALLHHC 119

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-------- 156
                  G         +     G L       S   L                      
Sbjct: 120 KDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGIIK 179

Query: 157 ------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                             K  V++   +      +  +  ++  V   L  G+  +I+  
Sbjct: 180 YEQGTIEAPIGRHPVDRIKMAVVKDGRHAVTHYKVIERFKNHTLVECRLETGRTHQIRVH 239

Query: 205 FEFF 208
               
Sbjct: 240 MSHI 243


>gi|170728985|ref|YP_001763011.1| 30S ribosomal protein S4 [Shewanella woodyi ATCC 51908]
 gi|226695076|sp|B1KM36|RS4_SHEWM RecName: Full=30S ribosomal protein S4
 gi|169814332|gb|ACA88916.1| ribosomal protein S4 [Shewanella woodyi ATCC 51908]
          Length = 206

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V + D I +
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKSIMVNGSVVNIPSFKVSANDVISI 145


>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 = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 29/238 (12%), Positives = 65/238 (27%), Gaps = 31/238 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE---- 61
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + IE    
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVE 69

Query: 62  VDGVP----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
           V+             +   +   + +      +V   +     + +   L      V   
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIVEVP 129

Query: 112 -----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY---------RVRFHGQVDQDK 157
                 RLD +T GL+++         L     +                +         
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 158 LNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +  K+ ++              +     +   + + L  G+  +I+         + 
Sbjct: 190 RHATKRTLMAVHPIGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 247


>gi|312623027|ref|YP_004024640.1| RNA-binding S4 domain-containing protein [Caldicellulosiruptor
          kronotskyensis 2002]
 gi|312203494|gb|ADQ46821.1| RNA-binding S4 domain protein [Caldicellulosiruptor
          kronotskyensis 2002]
          Length = 80

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   ++     RV VNG + +  + +V   D IEV
Sbjct: 1  MRIDKYLKVSRIIKRRTLAQQACEAGRVFVNGKVAK-PSTDVKVGDVIEV 49


>gi|218134379|ref|ZP_03463183.1| hypothetical protein BACPEC_02273 [Bacteroides pectinophilus ATCC
          43243]
 gi|217989764|gb|EEC55775.1| hypothetical protein BACPEC_02273 [Bacteroides pectinophilus ATCC
          43243]
          Length = 69

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 11/51 (21%), Positives = 22/51 (43%), Gaps = 4/51 (7%)

Query: 20 IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
          +  +G+    E + +I    V VNG +  +    +   D +E DG  ++  
Sbjct: 22 LVESGV----EAKIVITDGEVTVNGQVETQRGKKLHGGDIVEFDGEQIKIE 68


>gi|16078605|ref|NP_389424.1| factor involved in shape determination, RNA-binding fold [Bacillus
           subtilis subsp. subtilis str. 168]
 gi|221309415|ref|ZP_03591262.1| hypothetical protein Bsubs1_08521 [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|221313740|ref|ZP_03595545.1| hypothetical protein BsubsN3_08457 [Bacillus subtilis subsp.
           subtilis str. NCIB 3610]
 gi|221318664|ref|ZP_03599958.1| hypothetical protein BsubsJ_08391 [Bacillus subtilis subsp.
           subtilis str. JH642]
 gi|221322937|ref|ZP_03604231.1| hypothetical protein BsubsS_08497 [Bacillus subtilis subsp.
           subtilis str. SMY]
 gi|81345679|sp|P71020|YLMH_BACSU RecName: Full=Putative RNA-binding protein ylmH
 gi|1518679|gb|AAB49278.1| orf [Bacillus subtilis subsp. subtilis str. 168]
 gi|2633914|emb|CAB13415.1| factor involved in shape determination, RNA-binding fold [Bacillus
           subtilis subsp. subtilis str. 168]
          Length = 257

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/62 (24%), Positives = 28/62 (45%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           D  I  +  +  R+  V A     SR++ + ++    VKVN  ++E  +  V   D + +
Sbjct: 170 DVEIRDDTVSSLRLDAVCASMSRQSRQKSQTLVKNGLVKVNWKVVEDPSYIVAEGDMLSI 229

Query: 63  DG 64
            G
Sbjct: 230 RG 231


>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 = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 23/243 (9%), Positives = 60/243 (24%), Gaps = 37/243 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVN------------GILLE----RA 50
           + E     R    +A+    SR    ++ A+  V V+            G ++       
Sbjct: 10  IPEGLEGMRADAALAKLLGLSRSATAQLCAEGGVTVDSQELGKSERLASGQVVSVLLPEP 69

Query: 51  AVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
              ++  + + V+G+ +  ++   + ++             DG + +     + ++    
Sbjct: 70  EKPLLPREEL-VEGMDVLYSDADIICVHKPVGVAAHPSVGWDGPTVIGGLRAAGYNVASL 128

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-------------- 156
                      L +   G +       +   L+        +                  
Sbjct: 129 GPTERQGIVHRLDVGTSGVMVVASSGRAYSALKHAFKHRTVKKTYHAVVQGLPDPIEGTI 188

Query: 157 ------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                       K  V+           L       + + V L  G+  +I+        
Sbjct: 189 DAPIGRHPKSGWKFAVLDDGKAAVTHYRLIEAFREASLIEVHLETGRTHQIRVHMSATGH 248

Query: 211 KVN 213
              
Sbjct: 249 PCV 251


>gi|226507814|ref|NP_001152354.1| hemolysin A [Zea mays]
 gi|195655423|gb|ACG47179.1| hemolysin A [Zea mays]
          Length = 297

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 8/61 (13%)

Query: 2  KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
          K K  + E    +R  +        SR  ++  I Q +V V+G ++ +A   V     IE
Sbjct: 40 KKKRRLDEVC-LERFQQY-------SRTYIQSWILQGKVIVDGRVVNKAGTQVSDKSVIE 91

Query: 62 V 62
          +
Sbjct: 92 I 92


>gi|145641509|ref|ZP_01797087.1| SfhB [Haemophilus influenzae R3021]
 gi|145273800|gb|EDK13668.1| SfhB [Haemophilus influenzae 22.4-21]
          Length = 324

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 28/238 (11%), Positives = 64/238 (26%), Gaps = 31/238 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE---- 61
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + IE    
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVE 69

Query: 62  VDGVP----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
           V+             +   +   + +      +V   +     + +   L          
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPISEVP 129

Query: 112 -----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY---------RVRFHGQVDQDK 157
                 RLD +T GL+++         L     +                +         
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 158 LNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +  K+ ++              +     +   + + L  G+  +I+         + 
Sbjct: 190 RHATKRTLMAVHPIGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 247


>gi|319774855|ref|YP_004134124.1| RNA polymerase sigma factor, sigma-70 family [Thermovibrio
           ammonificans HB-1]
 gi|317115203|gb|ADU97692.1| RNA polymerase sigma factor, sigma-70 family [Thermovibrio
           ammonificans HB-1]
          Length = 289

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 10/36 (27%), Positives = 17/36 (47%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
              ++ Q  V+VNG ++ + +  V  TD I V    
Sbjct: 171 ASELLEQGLVRVNGRVVRKPSWKVSLTDEILVGDER 206


>gi|212638314|ref|YP_002314834.1| 30S ribosomal protein S4 [Anoxybacillus flavithermus WK1]
 gi|212559794|gb|ACJ32849.1| Ribosomal protein S4 [Anoxybacillus flavithermus WK1]
          Length = 219

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G A +RR+  +++    + V+G  ++  +  V     I V
Sbjct: 112 RLDNLVYRLGFARTRRQARQLVNHGHILVDGSRVDIPSYRVKPGQTISV 160


>gi|291436587|ref|ZP_06575977.1| type I polyketide synthase [Streptomyces ghanaensis ATCC 14672]
 gi|291339482|gb|EFE66438.1| type I polyketide synthase [Streptomyces ghanaensis ATCC 14672]
          Length = 2626

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 12/99 (12%), Positives = 20/99 (20%)

Query: 253  AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
              +   AP        R      + +P      +             +   P   R    
Sbjct: 2044 RHLPAPAPHGLPRRPHRGGLPPPAALPAHREGRRHLRPPGRTRPGGTRTRNPPPGRRGHL 2103

Query: 313  NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                           S  R       P+ PS+    R +
Sbjct: 2104 PGHRRTERTRGRHRPSAGRPRGPAPGPALPSRTRRPRGA 2142



 Score = 41.7 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 12/108 (11%), Positives = 24/108 (22%)

Query: 246  GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                  E + +L  P  +     R R              +   ++        +   P 
Sbjct: 2068 ALPAHREGRRHLRPPGRTRPGGTRTRNPPPGRRGHLPGHRRTERTRGRHRPSAGRPRGPA 2127

Query: 306  HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                L S     +G   +  +    R  +  R       R       +
Sbjct: 2128 PGPALPSRTRRPRGARPAAGTRRPGRARHRPRRRRHRGSRGAPGHRGR 2175



 Score = 40.9 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 11/111 (9%), Positives = 19/111 (17%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            R +           +          L    P+ +   P         +   +   ++   
Sbjct: 2021 RRRHRLPGTRRPPPHGLRGGGRLRHLPAPAPHGLPRRPHRGGLPPPAALPAHREGRRHLR 2080

Query: 302  ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                 R           G                R  PS    R      A
Sbjct: 2081 PPGRTRPGGTRTRNPPPGRRGHLPGHRRTERTRGRHRPSAGRPRGPAPGPA 2131



 Score = 40.2 bits (92), Expect = 0.49,   Method: Composition-based stats.
 Identities = 8/94 (8%), Positives = 16/94 (17%), Gaps = 2/94 (2%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            R      L   A +                    +   +     + +        + +  
Sbjct: 2056 RRPHRGGLPPPAALPAHREGRRHLRPPGRTRPGGTRTRNPPPGRRGHLPGHRRTERTRGR 2115

Query: 302  ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENH 335
              P   R           + S      G R    
Sbjct: 2116 HRPSAGRPRGPAPG--PALPSRTRRPRGARPAAG 2147



 Score = 39.8 bits (91), Expect = 0.59,   Method: Composition-based stats.
 Identities = 19/145 (13%), Positives = 32/145 (22%), Gaps = 17/145 (11%)

Query: 226  GTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
            G     S R + +      L       A +     ++  +   R R       P    R 
Sbjct: 1980 GDRSPASQRPLRRTRQEGHLPQQPDHAAPLRPQPHLHRFQPRRRHRLPGTRRPPPHGLRG 2039

Query: 286  KKN------------SSQKNGLSKQKKLATPVHRRNLA---SNVWMAKGIHSSFLSDSGQ 330
                             + +        A P HR              G   +     G+
Sbjct: 2040 GGRLRHLPAPAPHGLPRRPHRGGLPPPAALPAHREGRRHLRPPGRTRPGGTRTRNPPPGR 2099

Query: 331  RE--ENHRRSPSFPSKRSLRRTSAK 353
            R     HRR+     +        +
Sbjct: 2100 RGHLPGHRRTERTRGRHRPSAGRPR 2124



 Score = 35.9 bits (81), Expect = 9.1,   Method: Composition-based stats.
 Identities = 9/126 (7%), Positives = 19/126 (15%)

Query: 227  TLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
                G     S++ LR       L +   +                              
Sbjct: 1976 GHHPGDRSPASQRPLRRTRQEGHLPQQPDHAAPLRPQPHLHRFQPRRRHRLPGTRRPPPH 2035

Query: 287  KNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
                              + RR     +     + +        R     R     ++  
Sbjct: 2036 GLRGGGRLRHLPAPAPHGLPRRPHRGGLPPPAALPAHREGRRHLRPPGRTRPGGTRTRNP 2095

Query: 347  LRRTSA 352
                  
Sbjct: 2096 PPGRRG 2101


>gi|239928258|ref|ZP_04685211.1| putative type I polyketide synthase WcbR [Streptomyces ghanaensis
            ATCC 14672]
          Length = 2617

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 12/99 (12%), Positives = 20/99 (20%)

Query: 253  AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
              +   AP        R      + +P      +             +   P   R    
Sbjct: 2035 RHLPAPAPHGLPRRPHRGGLPPPAALPAHREGRRHLRPPGRTRPGGTRTRNPPPGRRGHL 2094

Query: 313  NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                           S  R       P+ PS+    R +
Sbjct: 2095 PGHRRTERTRGRHRPSAGRPRGPAPGPALPSRTRRPRGA 2133



 Score = 41.7 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 12/108 (11%), Positives = 24/108 (22%)

Query: 246  GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                  E + +L  P  +     R R              +   ++        +   P 
Sbjct: 2059 ALPAHREGRRHLRPPGRTRPGGTRTRNPPPGRRGHLPGHRRTERTRGRHRPSAGRPRGPA 2118

Query: 306  HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                L S     +G   +  +    R  +  R       R       +
Sbjct: 2119 PGPALPSRTRRPRGARPAAGTRRPGRARHRPRRRRHRGSRGAPGHRGR 2166



 Score = 40.9 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 11/111 (9%), Positives = 19/111 (17%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            R +           +          L    P+ +   P         +   +   ++   
Sbjct: 2012 RRRHRLPGTRRPPPHGLRGGGRLRHLPAPAPHGLPRRPHRGGLPPPAALPAHREGRRHLR 2071

Query: 302  ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                 R           G                R  PS    R      A
Sbjct: 2072 PPGRTRPGGTRTRNPPPGRRGHLPGHRRTERTRGRHRPSAGRPRGPAPGPA 2122



 Score = 40.2 bits (92), Expect = 0.48,   Method: Composition-based stats.
 Identities = 8/94 (8%), Positives = 16/94 (17%), Gaps = 2/94 (2%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            R      L   A +                    +   +     + +        + +  
Sbjct: 2047 RRPHRGGLPPPAALPAHREGRRHLRPPGRTRPGGTRTRNPPPGRRGHLPGHRRTERTRGR 2106

Query: 302  ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENH 335
              P   R           + S      G R    
Sbjct: 2107 HRPSAGRPRGPAPG--PALPSRTRRPRGARPAAG 2138



 Score = 39.8 bits (91), Expect = 0.58,   Method: Composition-based stats.
 Identities = 19/145 (13%), Positives = 32/145 (22%), Gaps = 17/145 (11%)

Query: 226  GTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
            G     S R + +      L       A +     ++  +   R R       P    R 
Sbjct: 1971 GDRSPASQRPLRRTRQEGHLPQQPDHAAPLRPQPHLHRFQPRRRHRLPGTRRPPPHGLRG 2030

Query: 286  KKN------------SSQKNGLSKQKKLATPVHRRNLA---SNVWMAKGIHSSFLSDSGQ 330
                             + +        A P HR              G   +     G+
Sbjct: 2031 GGRLRHLPAPAPHGLPRRPHRGGLPPPAALPAHREGRRHLRPPGRTRPGGTRTRNPPPGR 2090

Query: 331  RE--ENHRRSPSFPSKRSLRRTSAK 353
            R     HRR+     +        +
Sbjct: 2091 RGHLPGHRRTERTRGRHRPSAGRPR 2115



 Score = 35.9 bits (81), Expect = 9.0,   Method: Composition-based stats.
 Identities = 9/126 (7%), Positives = 19/126 (15%)

Query: 227  TLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
                G     S++ LR       L +   +                              
Sbjct: 1967 GHHPGDRSPASQRPLRRTRQEGHLPQQPDHAAPLRPQPHLHRFQPRRRHRLPGTRRPPPH 2026

Query: 287  KNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
                              + RR     +     + +        R     R     ++  
Sbjct: 2027 GLRGGGRLRHLPAPAPHGLPRRPHRGGLPPPAALPAHREGRRHLRPPGRTRPGGTRTRNP 2086

Query: 347  LRRTSA 352
                  
Sbjct: 2087 PPGRRG 2092


>gi|256390172|ref|YP_003111736.1| 30S ribosomal protein S4 [Catenulispora acidiphila DSM 44928]
 gi|256356398|gb|ACU69895.1| ribosomal protein S4 [Catenulispora acidiphila DSM 44928]
          Length = 208

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 1/61 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ RAG A SR    +++    + +NG      ++ V  +D +EV    L      
Sbjct: 99  RLDNVVYRAGFAKSRDHARQLVRHGHILINGHKANIPSMRVTPSDIVEVRKESLELTPFV 158

Query: 74  R 74
            
Sbjct: 159 V 159


>gi|300854303|ref|YP_003779287.1| putative rRNA methylase [Clostridium ljungdahlii DSM 13528]
 gi|300434418|gb|ADK14185.1| predicted rRNA methylase [Clostridium ljungdahlii DSM 13528]
          Length = 274

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 12/56 (21%), Positives = 25/56 (44%), Gaps = 1/56 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          +R+  ++   GI  SR   +  I    V ++G  +++    +  + +IE  G  L 
Sbjct: 6  ERLDVLLVEKGIFQSRERAKASIMAGEVFIDGQRVDKCGQKIKKSSNIEFRGEKLP 61


>gi|296482012|gb|DAA24127.1| calcium channel, voltage-dependent, L type, alpha 1B subunit [Bos
           taurus]
          Length = 1242

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 9/106 (8%), Positives = 23/106 (21%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                     +          R   +  +  P +    +      +G  +  +  +P   
Sbjct: 871 RADAPKAEGGEPGAREERARPRRSRSKEAAGPREARSERGRGLGPDGGRRHHRRGSPEEA 930

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                    A         +     +  RR+      R+  R +  
Sbjct: 931 AEREPRRHRAHRHAPEPSREGAPGSKGERRARHRGGSRAGPREAES 976



 Score = 45.9 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 10/88 (11%), Positives = 19/88 (21%), Gaps = 2/88 (2%)

Query: 266 TLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFL 325
                        PD   R  +  S +    ++ +           S    A G      
Sbjct: 902 PREARSERGRGLGPDGGRRHHRRGSPEEAAEREPRRHRAHRHAPEPSREG-APGSKGE-R 959

Query: 326 SDSGQREENHRRSPSFPSKRSLRRTSAK 353
               +         +   +   RR  A+
Sbjct: 960 RARHRGGSRAGPREAESGEEPSRRHRAR 987



 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 23/168 (13%), Positives = 42/168 (25%), Gaps = 36/168 (21%)

Query: 223 FQLGTL---LAGSTREVSKKI-LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEV 278
            +L  L         E+  +  LR     HL  + + +LD P+         R     + 
Sbjct: 775 LRLQNLRASCEALYSEMDPEERLRFATSRHLRPDMKTHLDRPLVVEPGRDGARGPAGGKA 834

Query: 279 PDDFTRMKKNSSQK---------------NGLSKQKKLATPVHRRNLA------------ 311
             +     + +                      +  +   P                   
Sbjct: 835 RPEGGEAGEGADPPRRHHRHRDRDRDKAAAPAGEPDRADAPKAEGGEPGAREERARPRRS 894

Query: 312 -----SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                +    A+      L   G R  + R SP   ++R  RR  A +
Sbjct: 895 RSKEAAGPREARSERGRGLGPDGGRRHHRRGSPEEAAEREPRRHRAHR 942



 Score = 35.9 bits (81), Expect = 8.4,   Method: Composition-based stats.
 Identities = 14/117 (11%), Positives = 30/117 (25%), Gaps = 9/117 (7%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G         + D     +     +     +   +      +    +   S+ K+ A P 
Sbjct: 844 GADPPRRHHRHRDRDRDKAAAPAGEPDRADAPKAEGGEPGAREERARPRRSRSKEAAGPR 903

Query: 306 HRRNLASNVWMAKGIHSSFLS--------DSGQREENHRRSPSFPSKRSLRRTSAKK 354
             R+         G                  +R   HR +P  PS+     +  ++
Sbjct: 904 EARSERGRGLGPDGGRRHHRRGSPEEAAEREPRRHRAHRHAP-EPSREGAPGSKGER 959


>gi|321315306|ref|YP_004207593.1| shape determination protein [Bacillus subtilis BSn5]
 gi|320021580|gb|ADV96566.1| factor involved in shape determination, RNA-binding fold protein
           [Bacillus subtilis BSn5]
          Length = 257

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/62 (24%), Positives = 28/62 (45%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           D  I  +  +  R+  V A     SR++ + ++    VKVN  ++E  +  V   D + +
Sbjct: 170 DVEIRDDTVSSLRLDAVCASMSRQSRQKSQTLVKNGLVKVNWKVVEDPSYIVAEGDMLSI 229

Query: 63  DG 64
            G
Sbjct: 230 RG 231


>gi|308173503|ref|YP_003920208.1| shape determination protein [Bacillus amyloliquefaciens DSM 7]
 gi|307606367|emb|CBI42738.1| factor involved in shape determination, RNA-binding fold [Bacillus
           amyloliquefaciens DSM 7]
 gi|328553566|gb|AEB24058.1| factor involved in shape determination, RNA-binding fold protein
           [Bacillus amyloliquefaciens TA208]
 gi|328911642|gb|AEB63238.1| factor involved in shape determination, RNA-binding fold [Bacillus
           amyloliquefaciens LL3]
          Length = 256

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/62 (24%), Positives = 28/62 (45%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           D  I ++  +  R+  V A     SR++ + ++    VKVN   +E  +  V   D + +
Sbjct: 169 DVEIREDTVSSLRLDAVCALMSRQSRQKAQALVKNGLVKVNWKAVEDPSYQVAEGDMLSI 228

Query: 63  DG 64
            G
Sbjct: 229 RG 230


>gi|298704938|emb|CBJ28441.1| RNA-binding S4 [Ectocarpus siliculosus]
          Length = 158

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 18/65 (27%), Positives = 25/65 (38%), Gaps = 3/65 (4%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K K++        R+  V A AG+  SR ++   I    V VN         NV   D +
Sbjct: 72  KTKDVSTVEA-SLRLDSV-ASAGMGMSRSKMSAAIKSGLVLVNWKAASSGTTNVREGDIV 129

Query: 61  EVDGV 65
            V G 
Sbjct: 130 TVRGK 134


>gi|296129454|ref|YP_003636704.1| RNA-binding S4 domain protein [Cellulomonas flavigena DSM 20109]
 gi|296021269|gb|ADG74505.1| RNA-binding S4 domain protein [Cellulomonas flavigena DSM 20109]
          Length = 76

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/68 (22%), Positives = 24/68 (35%), Gaps = 9/68 (13%)

Query: 1  MKDKNIVQENFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
          M     V  +  P R+ + +     A +G         ++    V VNG    R    + 
Sbjct: 1  MPHTGHVTRSDDPIRLGQFLKLVNLAESGG----HARALLDDGAVTVNGEPETRRGRQLR 56

Query: 56 STDHIEVD 63
            D +EVD
Sbjct: 57 PGDVVEVD 64


>gi|238021615|ref|ZP_04602041.1| hypothetical protein GCWU000324_01515 [Kingella oralis ATCC
          51147]
 gi|237866229|gb|EEP67271.1| hypothetical protein GCWU000324_01515 [Kingella oralis ATCC
          51147]
          Length = 102

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 10/52 (19%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 23 AGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           G AS R E  ++++ + + VNG ++   +  V + D + +     ++    
Sbjct: 1  MGFASTRAEARQLVSHKAIMVNGQVVNIPSFQVKAGDVVAIREKAKKQVRIQ 52


>gi|228992632|ref|ZP_04152558.1| RNA-binding S4 domain protein [Bacillus pseudomycoides DSM 12442]
 gi|228766964|gb|EEM15601.1| RNA-binding S4 domain protein [Bacillus pseudomycoides DSM 12442]
          Length = 257

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+ +I    VKVN   +E+ A      D   + G
Sbjct: 182 RLDVLLAEMLHLSRQKVQPLIKNGLVKVNWKTVEQTAYECFPGDVFSIRG 231


>gi|153816224|ref|ZP_01968892.1| hypothetical protein RUMTOR_02473 [Ruminococcus torques ATCC 27756]
 gi|145846407|gb|EDK23325.1| hypothetical protein RUMTOR_02473 [Ruminococcus torques ATCC 27756]
          Length = 181

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI R G+A +R+E  +++  + V VNG  +   +  V + D IE+
Sbjct: 72  RLDNVIFRMGLARTRKEARQIVDHKHVLVNGKQVNIPSYLVKAGDTIEI 120


>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 = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 35/247 (14%), Positives = 68/247 (27%), Gaps = 40/247 (16%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--- 61
           +V +    +R+ KV+AR     SR  ++  I  +RV+++G   +     V     IE   
Sbjct: 69  VVPDELAGERLDKVLARVFPEFSRNRLQSWIEAERVRIDGKPAK-IRQPVPLGASIELVP 127

Query: 62  --------VDGVPLRK----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
                       P+       + T + +      +V   +     + +   L        
Sbjct: 128 DLLPEQLAFTPEPVPLEIVFEDDTLVVINKPAGMVVHPAAGNWSGTVLNGLLYRYGDAAA 187

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
              R   V RLD  T GL+++         L           R       +  +   +  
Sbjct: 188 GLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLALVWGNMPEEGTIDA 247

Query: 164 GIVIQ-----------GICYGDMQVTL------DTQKGSNAWVTVGLREGKNREIKKVFE 206
            I              G      +           Q+     +   L  G+  +I+    
Sbjct: 248 PIGRDPRERTRMAVVTGASGKPARTHFRRVDTAIWQRQPVTAIHCDLETGRTHQIRVHCA 307

Query: 207 FFNWKVN 213
                + 
Sbjct: 308 HIGHPLL 314


>gi|256826599|ref|YP_003150558.1| 30S ribosomal protein S4P [Cryptobacterium curtum DSM 15641]
 gi|256582742|gb|ACU93876.1| SSU ribosomal protein S4P [Cryptobacterium curtum DSM 15641]
          Length = 197

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           R+  ++ R G A +RRE  + +    + VNG  ++  +  V   D I V    
Sbjct: 88  RLDNIVFRLGFARTRREARQTVTHGHITVNGNRVDIPSYRVRPGDLIAVAPKA 140


>gi|169824335|ref|YP_001691946.1| putative RNA binding protein [Finegoldia magna ATCC 29328]
 gi|167831140|dbj|BAG08056.1| putative RNA binding protein [Finegoldia magna ATCC 29328]
          Length = 258

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 11/71 (15%), Positives = 33/71 (46%), Gaps = 9/71 (12%)

Query: 3   DKNIVQENFT---------PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN 53
           +KNI ++             +R+  +++     SR++ + +I  +++K+N  ++   + +
Sbjct: 162 EKNIEKDEEKYKPFTGIINSERLDCLVSEMANISRKDAQILIKNKKIKLNYEVVSNTSKS 221

Query: 54  VMSTDHIEVDG 64
           V     + + G
Sbjct: 222 VEENSLVSIRG 232


>gi|81300312|ref|YP_400520.1| RNA-binding S4 [Synechococcus elongatus PCC 7942]
 gi|81169193|gb|ABB57533.1| RNA-binding S4 [Synechococcus elongatus PCC 7942]
          Length = 259

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 2/52 (3%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+   IA AG   SR ++  +I +  V+VN     + +  + + D + V G 
Sbjct: 185 RLD-AIASAGFGLSRSKMVDLINRGEVRVNWKAATQPSTQLKTGDLVAVRGK 235


>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 = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 31/239 (12%), Positives = 69/239 (28%), Gaps = 33/239 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMST-------- 57
           +Q     QR+ + +A      SR  ++  I    VKVNG ++  A   V           
Sbjct: 10  IQPQHMGQRLDQTLAELFPDYSRSRLKTWIEGDLVKVNGEIINVARTKVYGGELVEICVE 69

Query: 58  ----DHIEVDGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                  E + +P  +   +   L +      +V   +     + +   L      V   
Sbjct: 70  IEEESRFEPENLPLNIVYEDEHILVINKPKDFVVHPGAGNQRGTVLNALLYHYPKIVEVP 129

Query: 112 -----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR------------VRFHGQVD 154
                 RLD +T GL+++         L     +   +               +    + 
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVQDLQKRKIIREYEAVAFGVMTQGGKVDQPMS 189

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +      +  +   G         +  +  +   + + L  G+  +I+      +  + 
Sbjct: 190 RHPTKRTQMAVHPLGKPA-VTHYRIMERFRNYTRLRLRLETGRTHQIRVHMAHISHPLL 247


>gi|225571162|ref|ZP_03780160.1| hypothetical protein CLOHYLEM_07250 [Clostridium hylemonae DSM
          15053]
 gi|225159993|gb|EEG72612.1| hypothetical protein CLOHYLEM_07250 [Clostridium hylemonae DSM
          15053]
          Length = 79

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR          RV VNG + + A+V V   D IE+
Sbjct: 1  MRLDKFLKVSRLIKRRTVANEACDAGRVTVNGSVAK-ASVKVKPGDIIEI 49


>gi|57238607|ref|YP_179738.1| 30S ribosomal protein S4 [Campylobacter jejuni RM1221]
 gi|148925738|ref|ZP_01809426.1| 30S ribosomal protein S4 [Campylobacter jejuni subsp. jejuni
           CG8486]
 gi|205355608|ref|ZP_03222378.1| 30S ribosomal protein S4 [Campylobacter jejuni subsp. jejuni
           CG8421]
 gi|81675536|sp|Q5HSJ7|RS4_CAMJR RecName: Full=30S ribosomal protein S4
 gi|57167411|gb|AAW36190.1| ribosomal protein S4 [Campylobacter jejuni RM1221]
 gi|145845748|gb|EDK22839.1| 30S ribosomal protein S4 [Campylobacter jejuni subsp. jejuni
           CG8486]
 gi|205346385|gb|EDZ33018.1| 30S ribosomal protein S4 [Campylobacter jejuni subsp. jejuni
           CG8421]
 gi|315059045|gb|ADT73374.1| SSU ribosomal protein S4p [Campylobacter jejuni subsp. jejuni S3]
          Length = 208

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G A+ RR   +++    + VNG  ++  +  V +   IE+
Sbjct: 98  QRLDNVVYRMGFATTRRFARQLVTHGHILVNGKRVDIPSFRVEAGAKIEI 147


>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 = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 27/240 (11%), Positives = 61/240 (25%), Gaps = 40/240 (16%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIA----QQRVKVNGILLERAAVNV-MSTDHI 60
           IV EN     +   +   G       +R+I     Q  + VNG  ++     +    D I
Sbjct: 4   IVGENEKGVILENFLRNKGF-----SKRLIRIYKWQGEILVNG--VKENVQRILQPGDVI 56

Query: 61  -----EVD--------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                EVD        G+ +   +   L +      +V         +           +
Sbjct: 57  DLILPEVDSDIAPEKMGLDIYYEDEDVLIVDKPAGVVVHPTKRYQSGTLANGVAWYFKDK 116

Query: 108 VISVGRLDINTEG--------------LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
            I      +N                 +            L     +       R    +
Sbjct: 117 GIKALIRPVNRLDKGTSGLVVFAKRPFMQYYLQIVKPMSKLYFAVVEGKMEGEGRIDLPI 176

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +   + +++ +  +G         +       + + V +  G+  +I+         + 
Sbjct: 177 SRKPQSGIERMVSEEGDRA-ITNYKVIKSSERFSLLKVKIETGRTHQIRVHLSHIGHPIV 235


>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 = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 29/238 (12%), Positives = 63/238 (26%), Gaps = 35/238 (14%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--------EVDGVP 66
           R+   ++R    SR    ++I   +V V+     + ++ V+    +        E+D VP
Sbjct: 48  RLDYFLSRELGTSRAFSTKLIRDGQVSVSWCPRVKPSMKVLPGGSVTAVVPPPEELDLVP 107

Query: 67  LRKAERTRLWLY------HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
                R                 +V         + V   L          G        
Sbjct: 108 EDVPFRVVYEDADLIVVDKPAGLVVHPAPGHWRGTLVHGLLFRYPDMEALNGVRRPGIVH 167

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------------------DKLNL 160
            L  T  G L       + + L     +   + +                          
Sbjct: 168 RLDATTSGLLVVARNGLAMEELVRCFKQRTLRKEYLALAHGRPQLPEGEIRLPIGRDPKN 227

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
            K+  +++G      +      +G  + +   L  G+  +I+   +     +    R+
Sbjct: 228 RKRMTILEGGRDSLTRYRTLWTRGRISLLLCQLCTGRTHQIRVHLKALGCPLVG-DRV 284


>gi|325678657|ref|ZP_08158267.1| ribosomal protein S4 [Ruminococcus albus 8]
 gi|324109707|gb|EGC03913.1| ribosomal protein S4 [Ruminococcus albus 8]
          Length = 198

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+  +RRE  +++      VNG  ++  +  V + D I +
Sbjct: 89  RLDSVVFRMGLSMTRREARQLVVHGHFLVNGKRVDIPSYRVKAGDVISL 137


>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 = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 35/247 (14%), Positives = 73/247 (29%), Gaps = 36/247 (14%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKV-NGILLE---------RAA 51
           +++ +V  +    R+   ++     SR  ++R+I    VKV  G  ++            
Sbjct: 32  EEEILVPPDMDGVRLDAFLSDFLGVSRTFIQRVIRDGYVKVFQGKRVKPSRSVLAGESLR 91

Query: 52  VNVMS-------------------TDHIEVD---GVPLRKAERTR---LWLYHKPIGLVT 86
             +                      D I VD   GV +  A       L           
Sbjct: 92  FKLPPPQRMDLVPEPVDFSVVYEDEDIIVVDKPAGVVVHPAPGHWRGTLVHGLLYRYPDI 151

Query: 87  THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR 146
              +   R  +   L S  S +++V R   +   L     D  + +     S   +    
Sbjct: 152 GTINDVVRPGIVHRLDSTTSGLLAVARNTESLNELQSSFRDRKVGKFYLALSDGRVVGEE 211

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
           +     + +D+ N  +  +   G       V     +G  +++   L  G+  +I+    
Sbjct: 212 ISLDAPIGRDRNNRYRMTVTDDGKNART-DVYPLWNRGRYSFLICELHSGRTHQIRVHLR 270

Query: 207 FFNWKVN 213
                + 
Sbjct: 271 HLGAPLV 277


>gi|225018820|ref|ZP_03708012.1| hypothetical protein CLOSTMETH_02770 [Clostridium methylpentosum
          DSM 5476]
 gi|224948380|gb|EEG29589.1| hypothetical protein CLOSTMETH_02770 [Clostridium methylpentosum
          DSM 5476]
          Length = 266

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++   G+A SR + +  I    V V G   ++A   V     I V
Sbjct: 4  IRLDVLLTERGLAPSREKAKAFIMAGEVLVGGERCDKAGQLVQQDAEITV 53


>gi|217077261|ref|YP_002334979.1| hemolysin A [Thermosipho africanus TCF52B]
 gi|217037116|gb|ACJ75638.1| hemolysin A [Thermosipho africanus TCF52B]
          Length = 260

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            +R+  ++   G+  SR + +R+I    V VN  L+++    V     I +
Sbjct: 2  KKERLDVLLVERGLIESREKAKRIIMSGNVFVNEQLVDKPGKLVDVESKIRI 53


>gi|152989997|ref|YP_001355719.1| 30S ribosomal protein S4 [Nitratiruptor sp. SB155-2]
 gi|172048726|sp|A6Q1K3|RS4_NITSB RecName: Full=30S ribosomal protein S4
 gi|151421858|dbj|BAF69362.1| 30S ribosomal protein S4 [Nitratiruptor sp. SB155-2]
          Length = 208

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A+ RR   +++    V V+G  +   +  V     IE+
Sbjct: 99  RLDNVVYRMGFATTRRFARQLVNHGHVLVDGKRVNIPSFRVKPGQKIEI 147


>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 = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 30/244 (12%), Positives = 65/244 (26%), Gaps = 37/244 (15%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M+  N+ V++ F   R+   +++     SR  ++ +I +  V VN    ++    +   D
Sbjct: 1   MEKINLQVEKEFDNVRLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNK-EKKRNYKLKVGD 59

Query: 59  HIEVD-GVP-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           +IEV+   P             +   ++  + +      +V         + V   L   
Sbjct: 60  NIEVNIPEPKLLQIEPEDIKLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNALLHHC 119

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-------- 156
                  G         +     G L       S   L                      
Sbjct: 120 KDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGIIK 179

Query: 157 ------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                             K  V++   +      +  +  ++  V   L  G+  +I+  
Sbjct: 180 DEQGTIEAPIGRHPVDRIKMAVVKDGRHAVTHYKVIERFKNHTLVECRLETGRTHQIRVH 239

Query: 205 FEFF 208
               
Sbjct: 240 MSHI 243


>gi|298500604|ref|ZP_07010408.1| SSU ribosomal protein S4 [Vibrio cholerae MAK 757]
 gi|297540773|gb|EFH76830.1| SSU ribosomal protein S4 [Vibrio cholerae MAK 757]
          Length = 206

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/61 (21%), Positives = 30/61 (49%), Gaps = 1/61 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++   + NV + D + V     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAILVNGKVVNVPSFNVAANDVVAVREKAKKQSRIK 156

Query: 74  R 74
            
Sbjct: 157 A 157


>gi|228998678|ref|ZP_04158265.1| RNA-binding S4 domain protein [Bacillus mycoides Rock3-17]
 gi|228761146|gb|EEM10105.1| RNA-binding S4 domain protein [Bacillus mycoides Rock3-17]
          Length = 257

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+ +I    VKVN   +E+ A      D   + G
Sbjct: 182 RLDVLLAEMLHLSRQKVQPLIKNGLVKVNWKTVEQTAYECFPGDVFSIRG 231


>gi|145637336|ref|ZP_01792996.1| SfhB [Haemophilus influenzae PittHH]
 gi|145269428|gb|EDK09371.1| SfhB [Haemophilus influenzae PittHH]
          Length = 324

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 29/238 (12%), Positives = 60/238 (25%), Gaps = 31/238 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----E 61
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + I    E
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVE 69

Query: 62  VDGVP----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
           V+             +   +   + +      +V   +     + +   L          
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPISEVP 129

Query: 112 -----GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR-----------FHGQVDQ 155
                 RLD +T GL+++         L     +                      Q   
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     V            +     +   + + L  G+  +I+         + 
Sbjct: 190 RHATKRTLMAVHPMGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 247


>gi|260770937|ref|ZP_05879866.1| SSU ribosomal protein S4p (S9e) [Vibrio furnissii CIP 102972]
 gi|260614174|gb|EEX39364.1| SSU ribosomal protein S4p (S9e) [Vibrio furnissii CIP 102972]
          Length = 188

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   + NV + D + +
Sbjct: 79  RLDNVVYRMGFGATRAEARQLVSHKAILVNGKVVNVPSFNVAANDVVAI 127


>gi|257870579|ref|ZP_05650232.1| ribosomal protein S4 [Enterococcus gallinarum EG2]
 gi|257804743|gb|EEV33565.1| ribosomal protein S4 [Enterococcus gallinarum EG2]
          Length = 203

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G+A+ RR+  +++    + V+G  ++  + +V     I V
Sbjct: 93  QRLDNVVYRLGLATTRRQARQLVNHGHILVDGKRVDIPSYHVEVGQVISV 142


>gi|255970731|ref|ZP_05421317.1| 30S ribosomal protein S4 [Enterococcus faecalis T1]
 gi|255974305|ref|ZP_05424891.1| 30S ribosomal protein S4 [Enterococcus faecalis T2]
 gi|256761099|ref|ZP_05501679.1| 30S ribosomal protein S4 [Enterococcus faecalis T3]
 gi|255961749|gb|EET94225.1| 30S ribosomal protein S4 [Enterococcus faecalis T1]
 gi|255967177|gb|EET97799.1| 30S ribosomal protein S4 [Enterococcus faecalis T2]
 gi|256682350|gb|EEU22045.1| 30S ribosomal protein S4 [Enterococcus faecalis T3]
          Length = 208

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G+A+ RR+  +++    + V+G  ++  + +V     I V
Sbjct: 98  QRLDNVVYRLGLATTRRQARQLVNHGHITVDGKRVDIPSYHVEVGQVIGV 147


>gi|167771240|ref|ZP_02443293.1| hypothetical protein ANACOL_02598 [Anaerotruncus colihominis DSM
           17241]
 gi|167666491|gb|EDS10621.1| hypothetical protein ANACOL_02598 [Anaerotruncus colihominis DSM
           17241]
          Length = 206

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SR+E  +++      VNG      ++ + + D + V
Sbjct: 100 RLDNVVYRLGFAASRKEARQLVRHGHFTVNGKKANIPSILLKAGDVVAV 148


>gi|160893235|ref|ZP_02074023.1| hypothetical protein CLOL250_00781 [Clostridium sp. L2-50]
 gi|156865318|gb|EDO58749.1| hypothetical protein CLOL250_00781 [Clostridium sp. L2-50]
          Length = 264

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 22/164 (13%), Positives = 51/164 (31%), Gaps = 2/164 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++   G+A SR + + +I    V V+ I  ++A         IEV G  L+   R
Sbjct: 3   ERLDVMMVNRGLAESREKAKAIIMSGIVYVDNIKEDKAGSTFDEKAQIEVRGNTLKYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L         + +                  ++  G + + +  +        L  
Sbjct: 63  GGLKLEKAMDCFGVSLAGKVAMDVGSST-GGFTDCMLQNGAVKVYSVDVGHGQLAWKLRN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
              +   +   +  V      D+ +   +    +        ++
Sbjct: 122 DERVVCMEKTNIRYVTPDDIEDRIEFASIDVSFISLTKVLPPVK 165


>gi|74316447|ref|YP_314187.1| 30S ribosomal protein S4 [Thiobacillus denitrificans ATCC 25259]
 gi|90101734|sp|Q3SLM5|RS4_THIDA RecName: Full=30S ribosomal protein S4
 gi|74055942|gb|AAZ96382.1| ribosomal protein S4 [Thiobacillus denitrificans ATCC 25259]
          Length = 209

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V  R G   SR E  +++    + VNG  +   +  V   D +EV
Sbjct: 100 RLDSVCYRMGFGASRTEARQIVRHNGIVVNGRRVNIPSYQVRPGDVVEV 148


>gi|81298892|ref|YP_399100.1| RNA-binding S4 [Synechococcus elongatus PCC 7942]
 gi|81167773|gb|ABB56113.1| RNA-binding S4 [Synechococcus elongatus PCC 7942]
          Length = 69

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 12/65 (18%), Positives = 24/65 (36%), Gaps = 9/65 (13%)

Query: 7  VQENFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
          +       R+ + +     A+ G     E +  I   +V+VNG++  R    +   D + 
Sbjct: 1  MGTETATIRLDQFLKWMGAAQTGG----EAKLYIQDGQVEVNGMVETRRGRQLREGDRVN 56

Query: 62 VDGVP 66
            G  
Sbjct: 57 FAGQV 61


>gi|71901055|ref|ZP_00683165.1| Ribosomal protein S4, bacterial and organelle form [Xylella
           fastidiosa Ann-1]
 gi|71729182|gb|EAO31303.1| Ribosomal protein S4, bacterial and organelle form [Xylella
           fastidiosa Ann-1]
          Length = 208

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/66 (19%), Positives = 27/66 (40%), Gaps = 1/66 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  VI R G A +R    ++++ + V VNG ++   + +V   D + +     +     
Sbjct: 98  RLDNVIYRMGFAVTRPAARQLVSHRSVLVNGKMVNLPSYHVKPGDVVALSQRAQKYLCVQ 157

Query: 74  RLWLYH 79
                 
Sbjct: 158 ESLTIK 163


>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 = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 31/247 (12%), Positives = 75/247 (30%), Gaps = 37/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K  + +     R+ K+++      SR   ++MI    + VN    ++      ++D 
Sbjct: 1   MPKKFKITD--ELGRLDKIVSMLDPEISRSRAKKMIEDGDIIVNDSK-KKPKYETKASDT 57

Query: 60  IEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           + +  V               +   +   + +      +V   +     + V   L    
Sbjct: 58  LLIKDVKPETVSIKPENMPLDIVYEDEDVIVVNKPQGMVVHPSAGHPNHTLVNALLFHSP 117

Query: 106 -------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
                   R   V R+D +T GLL++  +    + L         + +          + 
Sbjct: 118 LSSINGEYRPGIVHRIDKDTSGLLMVAKNDMAHKALSKQLKAKKNLRKYVALVHGRIKED 177

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNREIKKVFE 206
           + + K  + +       Q  +   + +     V        L E     G+  +I+   +
Sbjct: 178 SGVIKAPIARSPKDRKKQAIVADGRPAITHFEVMERFQDYTLIECRLETGRTHQIRVHMQ 237

Query: 207 FFNWKVN 213
           +    + 
Sbjct: 238 YIGHPIV 244


>gi|157164345|ref|YP_001467145.1| ribosomal RNA large subunit methyltransferase J [Campylobacter
          concisus 13826]
 gi|112801416|gb|EAT98760.1| ribosomal RNA large subunit methyltransferase J [Campylobacter
          concisus 13826]
          Length = 237

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 12/54 (22%), Positives = 20/54 (37%), Gaps = 5/54 (9%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-----DHIEV 62
           R    +A     SR +   +I   +V +NG +  + +  V        D I V
Sbjct: 1  MRFDNYVASVLNISRNKASELIKGGKVLINGEICTKVSSEVSEAKISLLDEIYV 54


>gi|307823465|ref|ZP_07653694.1| ribosomal protein S4 [Methylobacter tundripaludum SV96]
 gi|307735450|gb|EFO06298.1| ribosomal protein S4 [Methylobacter tundripaludum SV96]
          Length = 206

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           R+  V+ R G AS R E  ++++ + ++VN +L+   +  V   D + V     ++ 
Sbjct: 97  RLDNVVYRMGFASTRAEARQLVSHKSIQVNNVLINVPSYQVSPGDVLTVREKAKKQQ 153


>gi|301168827|emb|CBW28418.1| 23S rRNA pseudouridine synthase [Haemophilus influenzae 10810]
          Length = 324

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 25/238 (10%), Positives = 55/238 (23%), Gaps = 31/238 (13%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + IE+   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVE 69

Query: 63  -------------------DGVPLRKAERTRLWLYHKPIG---LVTTHSDPDGRSTVFDN 100
                              D   +   +   L ++         V           V   
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKSKDLVVHPGAGNPNGTVLNALLYHYPPIVEVP 129

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
              I  R+       +     +               + ++  V           D+   
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 161 LKKGIVIQGICY---GDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      +           +     +   + + L  G+  +I+         + 
Sbjct: 190 RHATKRTLMAVHPMGKPAVTHYRIMENYRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 247


>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 = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 30/243 (12%), Positives = 71/243 (29%), Gaps = 32/243 (13%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M++K I+ E F  +R    +A      SR   +++  +QRV VN  ++   +  +   D 
Sbjct: 1   MQEK-IIYEKFERERADSYLASIYKDYSRSYFQKLTDRQRVFVNDKIIPV-SHKLKRGDI 58

Query: 60  IEVDGVPLRKAERT--------------RLWLYHKPIGLVTTHSDP-------------- 91
           I ++     K +                 + +  +   +V                    
Sbjct: 59  ITIEFEKEEKFQIKPEKIKIDIIYEDDDIVVVNKRSGIVVHPSYGHLSGTLLNALMGYSA 118

Query: 92  -DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
                 +   L    S VI   + +     +        + ++        +   R    
Sbjct: 119 GKYNPYLIHRLDKDTSGVIVFAKTEKAKISISKQLQKRVVKKIYYAAVKGVIAENRGIIK 178

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + +   N     +          +  +  +K     + V +  G+  +I+   ++ N 
Sbjct: 179 APLGRSPKNRKLVSVNPLAKKVAITEFKVIERKDDYTLLKVRIITGRTHQIRSHMKYINH 238

Query: 211 KVN 213
            V 
Sbjct: 239 PVI 241


>gi|68536849|ref|YP_251554.1| 30S ribosomal protein S4 [Corynebacterium jeikeium K411]
 gi|260579207|ref|ZP_05847097.1| 30S ribosomal protein S4 [Corynebacterium jeikeium ATCC 43734]
 gi|90101685|sp|Q4JTC1|RS4_CORJK RecName: Full=30S ribosomal protein S4
 gi|68264448|emb|CAI37936.1| 30S ribosomal protein S4 [Corynebacterium jeikeium K411]
 gi|258602693|gb|EEW15980.1| 30S ribosomal protein S4 [Corynebacterium jeikeium ATCC 43734]
          Length = 201

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR+  ++++     VNG  +   +  V   D I+V
Sbjct: 92  RLDNVVYRAGLARTRRQARQLVSHGHFTVNGKKVNVPSFKVSQYDIIDV 140


>gi|315604117|ref|ZP_07879183.1| cytotoxin/hemolysin [Actinomyces sp. oral taxon 180 str. F0310]
 gi|315313823|gb|EFU61874.1| cytotoxin/hemolysin [Actinomyces sp. oral taxon 180 str. F0310]
          Length = 275

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 18/49 (36%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+   + R GIA SR    RMI + RVK++G ++ +AA  +     I V
Sbjct: 5  RIDSELVRRGIAPSRSSAARMIEEGRVKLDGQVVLKAARQMDPAQAIVV 53


>gi|227529662|ref|ZP_03959711.1| 30S ribosomal protein S4 [Lactobacillus vaginalis ATCC 49540]
 gi|227350452|gb|EEJ40743.1| 30S ribosomal protein S4 [Lactobacillus vaginalis ATCC 49540]
          Length = 220

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 11/52 (21%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  ++ R G+A+ RR+  +++    + V+G  ++  +  V     I V   
Sbjct: 113 RLDNMVYRLGLATTRRQARQLVNHGHITVDGKRVDIPSYEVSVGQVIAVRDK 164


>gi|261378065|ref|ZP_05982638.1| ribosomal protein S4 [Neisseria cinerea ATCC 14685]
 gi|269145515|gb|EEZ71933.1| ribosomal protein S4 [Neisseria cinerea ATCC 14685]
          Length = 206

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 12/60 (20%), Positives = 27/60 (45%), Gaps = 1/60 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNG ++   +  V   D + +     ++    
Sbjct: 97  RLDNVVYRMGFGSTRAEARQLVSHKAIAVNGQVVNIPSFQVKVGDVVSIREKAKKQVRIQ 156


>gi|330827906|ref|YP_004390858.1| 30S ribosomal protein S4 [Aeromonas veronii B565]
 gi|328803042|gb|AEB48241.1| 30S ribosomal protein S4 [Aeromonas veronii B565]
          Length = 206

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V   D I V
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKAIMVNGRVVNIPSFQVSPEDVICV 145


>gi|254483410|ref|ZP_05096639.1| ribosomal protein S4 [marine gamma proteobacterium HTCC2148]
 gi|214036284|gb|EEB76962.1| ribosomal protein S4 [marine gamma proteobacterium HTCC2148]
          Length = 206

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  +++A + + VNG ++  A+  V + D + +
Sbjct: 97  RLDNVVYRMGFGSTRSESRQLVAHKSIMVNGQVVNIASYQVKAGDVVAL 145


>gi|196035794|ref|ZP_03103196.1| S4 domain protein [Bacillus cereus W]
 gi|218905027|ref|YP_002452861.1| S4 domain protein [Bacillus cereus AH820]
 gi|195991443|gb|EDX55409.1| S4 domain protein [Bacillus cereus W]
 gi|218535821|gb|ACK88219.1| S4 domain protein [Bacillus cereus AH820]
          Length = 255

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+ +I    VKVN   +E+ +      D   V G
Sbjct: 180 RLDVMLAEMLHISRQKVQPLIKNGLVKVNWKTVEQTSYECYPGDVFSVRG 229


>gi|117618638|ref|YP_854866.1| ribosomal protein S4 [Aeromonas hydrophila subsp. hydrophila ATCC
           7966]
 gi|152060928|sp|A0KF44|RS4_AERHH RecName: Full=30S ribosomal protein S4
 gi|117560045|gb|ABK36993.1| ribosomal protein S4 [Aeromonas hydrophila subsp. hydrophila ATCC
           7966]
          Length = 206

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V   D I V
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKAIMVNGRVVNIPSFQVSPEDVICV 145


>gi|6137687|pdb|1QD7|C Chain C, Partial Model For 30s Ribosomal Subunit
 gi|7245451|pdb|1EG0|A Chain A, Fitting Of Components With Known Structure Into An 11.5 A
           Cryo-Em Map Of The E.Coli 70s Ribosome
 gi|253722760|pdb|1C05|A Chain A, Solution Structure Of Ribosomal Protein S4 Delta 41,
           Refined With Dipolar Couplings (Minimized Average
           Structure)
 gi|253722761|pdb|1C06|A Chain A, Solution Structure Of Ribosomal Protein S4 Delta 41,
           Refined With Dipolar Couplings (Ensemble Of 16
           Structures)
          Length = 159

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR+  +++    + V+G  +   +  V     I V
Sbjct: 52  RLDNLVYRLGLARTRRQARQLVTHGHILVDGSRVNIPSYRVKPGQTIAV 100


>gi|57242510|ref|ZP_00370448.1| ribosomal protein S4 [Campylobacter upsaliensis RM3195]
 gi|315639080|ref|ZP_07894248.1| 30S ribosomal protein S4 [Campylobacter upsaliensis JV21]
 gi|57016795|gb|EAL53578.1| ribosomal protein S4 [Campylobacter upsaliensis RM3195]
 gi|315480856|gb|EFU71492.1| 30S ribosomal protein S4 [Campylobacter upsaliensis JV21]
          Length = 208

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G A+ RR   +++    + VNG  ++  +  V +   IEV
Sbjct: 98  QRLDNVVYRMGFATTRRFARQLVTHGHILVNGRRVDIPSFRVEAGAKIEV 147


>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 = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 31/260 (11%), Positives = 70/260 (26%), Gaps = 52/260 (20%)

Query: 6   IVQENFTPQRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           I   +   +R+ + +A A     SR  V+ +IA   V ++G         +    +I + 
Sbjct: 5   IADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMNIAIV 64

Query: 63  ---------DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
                     G  +       +   + +      +V   +     + V   +        
Sbjct: 65  LPEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNGNWTGTLVNALIYHCGDSLS 124

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARV------LELPSTQWLRVYRVRFHGQVD 154
                 R   V RLD +T G++++  +    R           +    R Y     G  +
Sbjct: 125 GIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFADHGRTGDLERAYLALVWGMTE 184

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN---------------------AWVTVGL 193
           + +  +                V  + +   +                     + V   L
Sbjct: 185 RPQGTVDAYLGRSHRDRTKQAVVREEREDARHAITHYATVEKFSPREDATALASLVECRL 244

Query: 194 REGKNREIKKVFEFFNWKVN 213
             G+  +I+         + 
Sbjct: 245 ETGRTHQIRVHMAHIGHPLV 264


>gi|145300911|ref|YP_001143752.1| ribosomal protein S4 [Aeromonas salmonicida subsp. salmonicida
           A449]
 gi|152060929|sp|A4SSY2|RS4_AERS4 RecName: Full=30S ribosomal protein S4
 gi|142853683|gb|ABO92004.1| ribosomal protein S4 [Aeromonas salmonicida subsp. salmonicida
           A449]
          Length = 206

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V   D + V
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKAIMVNGRVVNIPSFQVSPEDVVCV 145


>gi|313680488|ref|YP_004058227.1| SSU ribosomal protein s4p [Oceanithermus profundus DSM 14977]
 gi|313153203|gb|ADR37054.1| SSU ribosomal protein S4P [Oceanithermus profundus DSM 14977]
          Length = 209

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIAS R++  +++    + V G  +   +  V   D I V
Sbjct: 100 RLDNVVYRLGIASSRKQARQLVRHGHIAVGGRKVTVPSYRVRPGDVIAV 148


>gi|239906434|ref|YP_002953175.1| hypothetical protein DMR_17980 [Desulfovibrio magneticus RS-1]
 gi|239796300|dbj|BAH75289.1| hypothetical protein [Desulfovibrio magneticus RS-1]
          Length = 490

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/114 (11%), Positives = 24/114 (21%), Gaps = 4/114 (3%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK- 299
           L  + G   +  A                  P    +      R   ++    G  ++K 
Sbjct: 376 LDAKSGAPRVMLAPDPSGVGSAEPRAATGRAPVPGDKAARGQERRSGSTKAGAGSREEKG 435

Query: 300 --KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
             +   P      +           S  S    R     +S          R+ 
Sbjct: 436 GKRRPRPGGAPGASGPAGAPGSSRQSPGSKPP-RPAGKGQSSGSGKPGRPPRSR 488



 Score = 35.9 bits (81), Expect = 8.9,   Method: Composition-based stats.
 Identities = 7/81 (8%), Positives = 14/81 (17%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P           +    +    R+                   +   G S+Q   + P  
Sbjct: 409 PGDKAARGQERRSGSTKAGAGSREEKGGKRRPRPGGAPGASGPAGAPGSSRQSPGSKPPR 468

Query: 307 RRNLASNVWMAKGIHSSFLSD 327
                 +    K         
Sbjct: 469 PAGKGQSSGSGKPGRPPRSRR 489


>gi|212696529|ref|ZP_03304657.1| hypothetical protein ANHYDRO_01067 [Anaerococcus hydrogenalis DSM
          7454]
 gi|325849680|ref|ZP_08170883.1| S4 domain protein [Anaerococcus hydrogenalis ACS-025-V-Sch4]
 gi|212676465|gb|EEB36072.1| hypothetical protein ANHYDRO_01067 [Anaerococcus hydrogenalis DSM
          7454]
 gi|325480021|gb|EGC83099.1| S4 domain protein [Anaerococcus hydrogenalis ACS-025-V-Sch4]
          Length = 81

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR+  +     +RVK+NG + + A  NV   D IEV
Sbjct: 1  MRIDKFLKNSRIIKRRQVAKDACLNERVKINGDIAK-AGTNVNPGDIIEV 49


>gi|62260278|gb|AAX77894.1| unknown protein [synthetic construct]
          Length = 367

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 31/240 (12%), Positives = 67/240 (27%), Gaps = 34/240 (14%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           I+      +R+   I       SR ++++ + +  + VNG    +    V+  + +E++ 
Sbjct: 41  IMHPKDAGKRIDVAINEQFEQFSRAQIQKWLKEGSITVNGR-ATKPKHIVLGDEEVEINI 99

Query: 65  VPLRKAERTRLWLY--------------HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI- 109
             L   E     +                    +V   +     +     L     +   
Sbjct: 100 ELLPTNEWIAEDINLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNALLHRYKDQDKL 159

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVLELP------------STQWLRVYRVRFHGQV 153
                V RLD +T GL++          L                 +     +   +  +
Sbjct: 160 PRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGEIYKQGTINQPI 219

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +D  N  K  I  +G        T          +   L  G+  +I+   +     + 
Sbjct: 220 GRDPTNRTKMAINYRGKEA-ITHYTSIEVYDGFTLIECQLETGRTHQIRVHMKSIKHPLV 278


>gi|28198376|ref|NP_778690.1| 30S ribosomal protein S4 [Xylella fastidiosa Temecula1]
 gi|182681017|ref|YP_001829177.1| 30S ribosomal protein S4 [Xylella fastidiosa M23]
 gi|32129992|sp|Q87E60|RS4_XYLFT RecName: Full=30S ribosomal protein S4
 gi|226703311|sp|B2I8J2|RS4_XYLF2 RecName: Full=30S ribosomal protein S4
 gi|28056446|gb|AAO28339.1| 30S ribosomal protein S4 [Xylella fastidiosa Temecula1]
 gi|182631127|gb|ACB91903.1| ribosomal protein S4 [Xylella fastidiosa M23]
          Length = 208

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/66 (19%), Positives = 27/66 (40%), Gaps = 1/66 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  VI R G A +R    ++++ + V VNG ++   + +V   D + +     +     
Sbjct: 98  RLDNVIYRMGFAVTRPAARQLVSHRSVLVNGKMVNLPSYHVKPGDVVALSQRAQKYLCVQ 157

Query: 74  RLWLYH 79
                 
Sbjct: 158 ESLTIK 163


>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 = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 31/236 (13%), Positives = 59/236 (25%), Gaps = 37/236 (15%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------DGV 65
           R+   +A+     SR   +++I Q  V++NG + +R    +   + +EV        D V
Sbjct: 15  RLDTFLAQQHPEFSRSRWQQLIQQGHVRLNGQVCDRKNQPLSGGEVLEVVLPTPEPLDLV 74

Query: 66  P------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           P      +   +   L L      +V         + V   L          G       
Sbjct: 75  PEPLPLSILYEDEELLILNKPVDLVVHPAPGHSHGTLVHGLLAHCPDLTGIGGVQRPGIV 134

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD----------------------QDK 157
             L     G +       +   L+        Q                           
Sbjct: 135 HRLDKDTSGVMVVAKTEFALHHLQQQLKTRQMQRHYLGVVYGQPREDRGTVITPLGRHPV 194

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +  +          +  +    A V   L  G+  +I+       W + 
Sbjct: 195 DRKKMAVVPPEKGRTAITHWYVKERFRHCALVEFRLETGRTHQIRVHAAHLGWPLL 250


>gi|297584553|ref|YP_003700333.1| hemolysin A [Bacillus selenitireducens MLS10]
 gi|297143010|gb|ADH99767.1| hemolysin A [Bacillus selenitireducens MLS10]
          Length = 268

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/59 (22%), Positives = 25/59 (42%), Gaps = 1/59 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
            +R+  ++   G+A SR   +R I    V  +G  +++A   V     + + G  L  
Sbjct: 2  KKERIDILLVEQGLAESRERAKRSIMAGLVLADGERIDKAGAKVNIDAKLSIKGEVLPY 60


>gi|218532566|ref|YP_002423382.1| hemolysin A [Methylobacterium chloromethanicum CM4]
 gi|218524869|gb|ACK85454.1| hemolysin A [Methylobacterium chloromethanicum CM4]
          Length = 250

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 3/53 (5%)

Query: 12 TPQRV--SKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
          T +R+   + +   G   SR +    I    V  +G L+ R A  V S+  IE
Sbjct: 2  TGERLRADRFLVERGHFRSRAQARAAIEAGLVSADGRLVTRPADLVESSARIE 54


>gi|121592837|ref|YP_984733.1| 30S ribosomal protein S4 [Acidovorax sp. JS42]
 gi|152060926|sp|A1W332|RS4_ACISJ RecName: Full=30S ribosomal protein S4
 gi|120604917|gb|ABM40657.1| SSU ribosomal protein S4P [Acidovorax sp. JS42]
          Length = 207

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V+ R G  S R E  ++++ + + VNG  +  A+  V + D + V   
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAITVNGQSVNIASYLVKAGDVVAVRDK 149


>gi|327538476|gb|EGF25140.1| ribosomal large subunit pseudouridine synthase D [Rhodopirellula
          baltica WH47]
          Length = 321

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 18/73 (24%), Positives = 25/73 (34%), Gaps = 2/73 (2%)

Query: 6  IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DG 64
           V E     RV  ++      SR +   MI    V +NG   +     V   D + V   
Sbjct: 9  TVDETNEG-RVDIIVRELSETSRSQARGMIDHGCVMINGSPCKSVGTTVKPGDLVAVRYD 67

Query: 65 VPLRKAERTRLWL 77
             R  E+ R W 
Sbjct: 68 KHQRYREKKRQWD 80


>gi|309785618|ref|ZP_07680249.1| ribosomal protein S4 [Shigella dysenteriae 1617]
 gi|308926738|gb|EFP72214.1| ribosomal protein S4 [Shigella dysenteriae 1617]
 gi|313647394|gb|EFS11846.1| ribosomal protein S4 [Shigella flexneri 2a str. 2457T]
 gi|323164860|gb|EFZ50651.1| ribosomal protein S4 [Shigella sonnei 53G]
 gi|332086274|gb|EGI91430.1| ribosomal protein S4 [Shigella dysenteriae 155-74]
 gi|332749596|gb|EGJ80013.1| ribosomal protein S4 [Shigella flexneri K-671]
 gi|332749738|gb|EGJ80153.1| ribosomal protein S4 [Shigella flexneri 4343-70]
 gi|332763708|gb|EGJ93947.1| ribosomal protein S4 [Shigella flexneri 2930-71]
 gi|332996506|gb|EGK16133.1| ribosomal protein S4 [Shigella flexneri VA-6]
          Length = 154

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 45  RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 104

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 105 AALELAEQREKPT 117


>gi|45644720|gb|AAS73108.1| predicted ribosomal protein S4 [uncultured marine gamma
           proteobacterium EBAC20E09]
          Length = 211

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  +M++ +   VNG  +   +  V   D IEV
Sbjct: 102 RLDNVVYRMGFGCTRAEARQMVSHKAFMVNGSTVNIPSYQVQPGDEIEV 150


>gi|165936370|ref|ZP_02224938.1| 30S ribosomal protein S4 (BS4) [Yersinia pestis biovar Orientalis
          str. IP275]
 gi|165915486|gb|EDR34095.1| 30S ribosomal protein S4 (BS4) [Yersinia pestis biovar Orientalis
          str. IP275]
          Length = 131

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 22 RLDNVVYRMGFGATRAESRQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 81

Query: 74 RLWLYHKPIGLVT 86
                +     T
Sbjct: 82 AALELAEQREKPT 94


>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 = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 18/73 (24%), Positives = 25/73 (34%), Gaps = 2/73 (2%)

Query: 6  IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DG 64
           V E     RV  ++      SR +   MI    V +NG   +     V   D + V   
Sbjct: 9  TVDETNEG-RVDIIVRELSETSRSQARGMIDHGCVMINGSPCKSVGTTVKPGDLVAVRYD 67

Query: 65 VPLRKAERTRLWL 77
             R  E+ R W 
Sbjct: 68 KHQRYREKKRQWD 80


>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 = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 35/235 (14%), Positives = 73/235 (31%), Gaps = 33/235 (14%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV------ 65
              R+ + +A A   SR   +  IAQ RV+V   ++E+ +  +   + + V         
Sbjct: 10  EGVRLDQAVAEACGVSRSRAQEWIAQGRVQVGEKVVEKPSYRLKGEEVLVVPPEEKPFVA 69

Query: 66  ------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-------- 111
                 P+   +   L L      L          + V   L   F    +         
Sbjct: 70  PQDLAIPVLYEDEDLLVLNKPAGLLTHPAPGVYTGTVVNALLGRYFPLQEAERPEEVRPG 129

Query: 112 --GRLDINTEGLLLLTNDG--------GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
              RLD +T G+L++   G             L +     +     +    +     + +
Sbjct: 130 IVHRLDKDTSGVLVVAKHGGALEALARAFRDRLVMKRYLAITEGHPKEGTLIAPIGRHPV 189

Query: 162 KKGIVIQGI---CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           ++  +  G     Y + +  +    G  A V      G+  +I+   ++    + 
Sbjct: 190 ERHKMHVGGIAPRYAETEFRILATAGPYALVEARPHTGRTHQIRVHLKYLRAPIL 244


>gi|325973258|ref|YP_004250322.1| 30S ribosomal protein S4 [Mycoplasma suis str. Illinois]
 gi|325989693|ref|YP_004249392.1| 30S ribosomal protein S4 [Mycoplasma suis KI3806]
 gi|323574778|emb|CBZ40438.1| 30S ribosomal protein S4 [Mycoplasma suis]
 gi|323651860|gb|ADX97942.1| 30S ribosomal protein S4 [Mycoplasma suis str. Illinois]
          Length = 202

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           ++  ++ RAG+A +RR   ++I    +++NG  ++  +  V  +  IEV
Sbjct: 96  KLDNLVFRAGMANTRRAARQLIVHGHIRLNGKKVDIPSYVVPPSSVIEV 144


>gi|254444170|ref|ZP_05057646.1| S4 domain protein [Verrucomicrobiae bacterium DG1235]
 gi|198258478|gb|EDY82786.1| S4 domain protein [Verrucomicrobiae bacterium DG1235]
          Length = 144

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/72 (18%), Positives = 28/72 (38%), Gaps = 1/72 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  ++   G   +R+   + +    + VNG  ++  +  V   D IEV      +   T
Sbjct: 34  RLDSIVYDLGFTKTRKAARQFVNHGHISVNGQKVDIPSYQVKVGDEIEVRNTTSSRQLAT 93

Query: 74  RLWLYHKPIGLV 85
           R    ++   + 
Sbjct: 94  RNMEANRLRNVP 105


>gi|154496129|ref|ZP_02034825.1| hypothetical protein BACCAP_00413 [Bacteroides capillosus ATCC
          29799]
 gi|150274684|gb|EDN01748.1| hypothetical protein BACCAP_00413 [Bacteroides capillosus ATCC
          29799]
          Length = 70

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 8/35 (22%), Positives = 14/35 (40%)

Query: 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          E + +I    V VNG +       +   D + + G
Sbjct: 30 EAKNIIQAGDVSVNGEVCTMRGKKIRPGDVVTLPG 64


>gi|220929318|ref|YP_002506227.1| hemolysin A [Clostridium cellulolyticum H10]
 gi|219999646|gb|ACL76247.1| hemolysin A [Clostridium cellulolyticum H10]
          Length = 270

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 1/52 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            +R+  ++   G+  SR + +  I    V ++GI  ++    V     IE+
Sbjct: 2  EKERLDVLLVNKGLFESREKCKSAIMAGLVWIDGIREDKPGTKVPVECTIEI 53


>gi|195979012|ref|YP_002124256.1| 30S ribosomal protein S4 [Streptococcus equi subsp. zooepidemicus
           MGCS10565]
 gi|225869452|ref|YP_002745400.1| 30S ribosomal protein S4 [Streptococcus equi subsp. zooepidemicus]
 gi|225871455|ref|YP_002747402.1| 30S ribosomal protein S4 [Streptococcus equi subsp. equi 4047]
 gi|226695078|sp|B4U0N4|RS4_STREM RecName: Full=30S ribosomal protein S4
 gi|254764611|sp|C0MB46|RS4_STRE4 RecName: Full=30S ribosomal protein S4
 gi|259495292|sp|C0MGP5|RS4_STRS7 RecName: Full=30S ribosomal protein S4
 gi|195975717|gb|ACG63243.1| 30S ribosomal protein S4 RpsD [Streptococcus equi subsp.
           zooepidemicus MGCS10565]
 gi|225700859|emb|CAW95600.1| 30S ribosomal protein S4 [Streptococcus equi subsp. equi 4047]
 gi|225702728|emb|CAX00869.1| 30S ribosomal protein S4 [Streptococcus equi subsp. zooepidemicus]
          Length = 203

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSFRVEIGQVISV 142


>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 = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 33/245 (13%), Positives = 79/245 (32%), Gaps = 37/245 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG- 64
           +V    +  R+   +A     SR ++ +M+  +++ +N I   +  + +   D I +   
Sbjct: 1   MVTSQESGMRLDIFLATKLNLSRNKINKMLHNKQITLNQIQASKNGIILKEQDQIHIFPS 60

Query: 65  ------------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------- 105
                       +P+   +   L L      +V   +  D + T+ + L           
Sbjct: 61  LLETAKPTPKIHIPILYEDEDLLVLNKPINLVVHKTNQEDTQYTLHEWLKEQNFKLSNLG 120

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVLELP----STQWLRVYRVRFHGQVDQDKLN 159
              R   + RLD  T G +++  +    ++L             +  +    + D    +
Sbjct: 121 DSYREGIIHRLDKTTSGAIVIAKNNHSHQILSQQLKTKEMGRYYLCVINQPLKQDIIIDS 180

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG-----------LREGKNREIKKVFEFF 208
            L +    +       + T D++    A+  +            L  G+  +I+      
Sbjct: 181 PLIRHPKNRLKYITTSKQTPDSKDAKTAFFKIIDNGKTELIGAKLFSGRTHQIRAHLSKI 240

Query: 209 NWKVN 213
           N  + 
Sbjct: 241 NRHIL 245


>gi|218671119|ref|ZP_03520790.1| hemolysin A [Rhizobium etli GR56]
          Length = 172

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 11/57 (19%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 9  ENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +   QR+ +++   G  ASR      + +  V++ G ++ +A     +   I +D 
Sbjct: 15 SDQNSQRLDQLLVSRGLFASRSRARDAVQRGTVRIAGQVVTKAGALFGADADIAIDD 71


>gi|52081461|ref|YP_080252.1| 30S ribosomal protein S4 [Bacillus licheniformis ATCC 14580]
 gi|52786836|ref|YP_092665.1| 30S ribosomal protein S4 [Bacillus licheniformis ATCC 14580]
 gi|319647367|ref|ZP_08001589.1| 30S ribosomal protein S4 [Bacillus sp. BT1B_CT2]
 gi|81690928|sp|Q65G42|RS4_BACLD RecName: Full=30S ribosomal protein S4
 gi|52004672|gb|AAU24614.1| ribosomal protein S4 [Bacillus licheniformis ATCC 14580]
 gi|52349338|gb|AAU41972.1| RpsD [Bacillus licheniformis ATCC 14580]
 gi|317390714|gb|EFV71519.1| 30S ribosomal protein S4 [Bacillus sp. BT1B_CT2]
          Length = 200

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR+  +++    V V+G  ++  +  V     I +
Sbjct: 93  RLDNIVYRLGLARTRRQARQLVNHGHVLVDGSRVDIPSYQVKPGQTISL 141


>gi|330821053|ref|YP_004349915.1| nonribosomal peptide synthetase [Burkholderia gladioli BSR3]
 gi|327373048|gb|AEA64403.1| nonribosomal peptide synthetase [Burkholderia gladioli BSR3]
          Length = 4527

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/110 (13%), Positives = 23/110 (20%), Gaps = 3/110 (2%)

Query: 246  GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ---KKLA 302
            G            A           R            R  +     +   +     +  
Sbjct: 4292 GHPPATLGPPGSAAGDARQRAAGPRRNRASPRRGQHPRRGGERLRAGHARGRPHHAGRAH 4351

Query: 303  TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                RR        A     +     G R+   R  P     R+L R +A
Sbjct: 4352 ARPGRRAGLPGDRQAARGGGAPARHHGARDAPSRGDPGRLPARALHRRAA 4401



 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 15/124 (12%), Positives = 26/124 (20%), Gaps = 6/124 (4%)

Query: 236  VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
            +    LR  L       A     A + ++   +R              R        +  
Sbjct: 4213 LPAAELRPGLVLRRPAAAGAGHAADLRAAVAGLRQAGRAARLQRRGPGRAASGGDPAHPA 4272

Query: 296  SKQKKLATPVHRRNLASNVW------MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
              +   A  V RR   +            G  +            +R SP          
Sbjct: 4273 GGRLPPAGLVLRRRPGARAGHPPATLGPPGSAAGDARQRAAGPRRNRASPRRGQHPRRGG 4332

Query: 350  TSAK 353
               +
Sbjct: 4333 ERLR 4336



 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 13/122 (10%), Positives = 24/122 (19%), Gaps = 9/122 (7%)

Query: 241  LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNII----SEVPDDFTRMKKNSSQKNGLS 296
            LR+      L+       A           R           P         +    G +
Sbjct: 4245 LRQAGRAARLQRRGPGRAASGGDPAHPAGGRLPPAGLVLRRRPGARAGHPPATLGPPGSA 4304

Query: 297  KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ----REENHRRSPSFPSKR-SLRRTS 351
                       R   ++    +                R  +  R+ + P +R  L    
Sbjct: 4305 AGDARQRAAGPRRNRASPRRGQHPRRGGERLRAGHARGRPHHAGRAHARPGRRAGLPGDR 4364

Query: 352  AK 353
              
Sbjct: 4365 QA 4366



 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 10/107 (9%), Positives = 19/107 (17%), Gaps = 3/107 (2%)

Query: 247  PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS-KQKKLATPV 305
            P      ++     +       R      +  P                  +        
Sbjct: 4268 PAHPAGGRLPPAGLVLRRRPGARAGHPPATLGPPGSAAGDARQRAAGPRRNRASPRRGQH 4327

Query: 306  HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             RR        A                  RR+     +++ R   A
Sbjct: 4328 PRRGGERL--RAGHARGRPHHAGRAHARPGRRAGLPGDRQAARGGGA 4372


>gi|317014156|gb|ADU81592.1| hypothetical protein HPGAM_03855 [Helicobacter pylori Gambia94/24]
          Length = 327

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 44/293 (15%), Positives = 85/293 (29%), Gaps = 53/293 (18%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-------------- 60
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I              
Sbjct: 13  RLDEFLAKELRISKNQVLNLIKEGLVFCQKKEVKKGGLALKEGDEITLLTPKIAPKPLKK 72

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISV 111
           E+D       E   L + +KP  LV   +      T+ D L S            R   V
Sbjct: 73  ELDLEIEVIFEDEDLLVLNKPPNLVVHKAPSVKEPTLVDWLKSQNYELSNLGLKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR-------VRFHGQVDQDKLNLLKKG 164
            RLD +T G +++  +      L       +                ++  +        
Sbjct: 133 HRLDKDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPN 192

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVTVG-----------LREGKNREIKKVFEFFNWKVN 213
             ++ I     +        S     +            L  G+  +I+           
Sbjct: 193 NRLKMIALKAAKKEKSRYSKSEFISLLTSQNGMDLIGAKLFTGRTHQIRAHL-------E 245

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSET 266
            L R   G      L  G    +SK+ +R  L  +L+E      +  +     
Sbjct: 246 YLNRHIIG----DNLY-GLNGALSKEEIRIMLHAYLIEFKHPRSEQKLRFKVP 293


>gi|296133619|ref|YP_003640866.1| RNA-binding S4 domain protein [Thermincola sp. JR]
 gi|296032197|gb|ADG82965.1| RNA-binding S4 domain protein [Thermincola potens JR]
          Length = 260

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 2/59 (3%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +  I+    +  R+  V A AG   SR ++ + I  ++VKVN   +  A   +   D +
Sbjct: 173 NTKIIDTTVSSLRLDAV-AGAGFGISRSKIVKYINSEKVKVNFETITDADYRINEGDVV 230


>gi|77361711|ref|YP_341286.1| 30S ribosomal protein S4 [Pseudoalteromonas haloplanktis TAC125]
 gi|90101708|sp|Q3IJJ5|RS4_PSEHT RecName: Full=30S ribosomal protein S4
 gi|76876622|emb|CAI87844.1| 30S ribosomal subunit protein S4 [Pseudoalteromonas haloplanktis
           TAC125]
          Length = 206

 Score = 48.3 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G AS R E  ++++ + + VNG ++   +  +   D + +
Sbjct: 96  QRLDNVVYRMGFASTRAEARQLVSHKAILVNGRVVNVPSYVIAPEDTVVI 145


>gi|318041724|ref|ZP_07973680.1| RNA-binding S4 domain-containing protein [Synechococcus sp.
          CB0101]
          Length = 74

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/55 (23%), Positives = 25/55 (45%), Gaps = 1/55 (1%)

Query: 12 TPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           P R+ + +   G + +  E ++ I    V+VNG    +    +   D +E+DG 
Sbjct: 8  EPIRLDQFLKWQGLVFTGGEAKQRIQGGEVRVNGFQETQRGRKLKPGDRVEIDGQ 62


>gi|317501800|ref|ZP_07959986.1| ribosomal protein S4 [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331088679|ref|ZP_08337589.1| 30S ribosomal protein S4 [Lachnospiraceae bacterium 3_1_46FAA]
 gi|316896833|gb|EFV18918.1| ribosomal protein S4 [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330407202|gb|EGG86705.1| 30S ribosomal protein S4 [Lachnospiraceae bacterium 3_1_46FAA]
          Length = 197

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI R G+A +R+E  +++  + V VNG  +   +  V + D IE+
Sbjct: 88  RLDNVIFRMGLARTRKEARQIVDHKHVLVNGKQVNIPSYLVKAGDTIEI 136


>gi|302388739|ref|YP_003824560.1| SSU ribosomal protein S4P [Thermosediminibacter oceani DSM 16646]
 gi|302199367|gb|ADL06937.1| SSU ribosomal protein S4P [Thermosediminibacter oceani DSM 16646]
          Length = 208

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SR +  +++    ++VNG  +   +  V   D I V
Sbjct: 99  RLDNVVYRLGFAKSRAQARQIVRHGHIEVNGRKVTIPSYQVREKDVIAV 147


>gi|77461277|ref|YP_350784.1| 30S ribosomal protein S4 [Pseudomonas fluorescens Pf0-1]
 gi|90101709|sp|Q3K611|RS4_PSEPF RecName: Full=30S ribosomal protein S4
 gi|77385280|gb|ABA76793.1| 30S ribosomal protein S4 [Pseudomonas fluorescens Pf0-1]
          Length = 206

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V + D + V
Sbjct: 97  RLDNVVYRMGFGSTRAESRQLVSHKSISVNGQTVNVPSYQVRAGDVVAV 145


>gi|326315414|ref|YP_004233086.1| 30S ribosomal protein S4 [Acidovorax avenae subsp. avenae ATCC
           19860]
 gi|323372250|gb|ADX44519.1| ribosomal protein S4 [Acidovorax avenae subsp. avenae ATCC 19860]
          Length = 207

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +  A+  V   D + V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAITVNGQSVNIASYLVKPGDIVAV 146


>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 = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 27/240 (11%), Positives = 61/240 (25%), Gaps = 40/240 (16%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIA----QQRVKVNGILLERAAVNV-MSTDHI 60
           IV EN     +   +   G       +R+I     Q  + VNG  ++     +    D I
Sbjct: 4   IVGENEKGVILENFLRNKGF-----SKRLIRIYKWQGEILVNG--VKENVQRILQPGDVI 56

Query: 61  -----EVD--------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                EVD        G+ +   +   L +      +V         +           +
Sbjct: 57  DLILPEVDSDIAPEKMGLDIYYEDEDVLIVDKPAGVVVHPTKRYQSGTLANGVAWYFKDK 116

Query: 108 VISVGRLDINTEG--------------LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
            I      +N                 +            L     +       R    +
Sbjct: 117 GIKALIRPVNRLDKGTSGLVVFAKRPFMQYYLQIVKPMSKLYFAVVEGKMEGEGRIDLPI 176

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +   + +++ +  +G         +       + + V +  G+  +I+         + 
Sbjct: 177 SRKPQSGIERMVSEEGDRA-ITNYKVIKSSERFSLLKVKIETGRTHQIRVHLSHIGHPIV 235


>gi|223948145|gb|ACN28156.1| unknown [Zea mays]
          Length = 293

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 8/61 (13%)

Query: 2  KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
          K K  + E    +R  +        SR  ++  I Q +V V+G ++ +A   V     IE
Sbjct: 40 KKKRRLDEVC-LERFQQY-------SRTYIQSWILQGKVIVDGRVVNKAGTQVSDKSVIE 91

Query: 62 V 62
          +
Sbjct: 92 I 92


>gi|157692221|ref|YP_001486683.1| hypothetical protein BPUM_1440 [Bacillus pumilus SAFR-032]
 gi|157680979|gb|ABV62123.1| hypothetical protein BPUM_1440 [Bacillus pumilus SAFR-032]
          Length = 258

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/60 (23%), Positives = 28/60 (46%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +I ++  +  R+  V A     SR++ + ++    VKVN  + E  +  +   D + V G
Sbjct: 173 DIKEDTISSLRLDAVCAAISRQSRQKAQLLVKNGLVKVNWKVTEDPSFTIGEGDQLSVRG 232


>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 = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 48/300 (16%), Positives = 94/300 (31%), Gaps = 54/300 (18%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+   I  +N+   R+ + +A+    S+ +   +I +  V      +++  + +   D I
Sbjct: 1   MQKVFIAPKNYK--RIDEFLAKELQISKNQALSLIKEGLVFCQKKEVKKGGLALKEGDEI 58

Query: 61  --------------EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
                         E+D       E   L + +KP  LV   +      T+ D L +   
Sbjct: 59  ALLTPKIAPKPLKRELDLEIEVIFEDDDLLVLNKPPNLVVHKAPSVKEPTLVDWLEAKNY 118

Query: 107 R---------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR-------------- 143
           +            V RLD +T G +++  +      L                       
Sbjct: 119 QLSNLGSKERYGIVHRLDKDTSGGIVIAKNNFTHVYLSEQLKTKTMGRYYIALLSTPLSR 178

Query: 144 -VYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNRE 200
              ++     + ++  N LK   I  +   Y   + T      +N   +   L  G+  +
Sbjct: 179 KEEKISVECYLTRNPNNRLKMMAIKKEKSRYSKSEFTSLLTSQNNLNLIGAKLYTGRTHQ 238

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAP 260
           I+            L R   G      L  G    + K+ +R  L  +L+E      +  
Sbjct: 239 IRVHL-------EYLNRHIIG----DNLY-GLNEALPKEEIRIMLHAYLIEFKHPKSEQK 286


>gi|77408476|ref|ZP_00785214.1| conserved hypothetical protein TIGR00281 [Streptococcus agalactiae
           COH1]
 gi|77172918|gb|EAO76049.1| conserved hypothetical protein TIGR00281 [Streptococcus agalactiae
           COH1]
          Length = 217

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 12/27 (44%), Positives = 15/27 (55%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERM 34
            E+    R+ K IA AGI SRR+ E  
Sbjct: 186 TEDRKTMRIXKYIAHAGICSRRKAEEF 212


>gi|319949193|ref|ZP_08023282.1| hemolysin A [Dietzia cinnamea P4]
 gi|319437179|gb|EFV92210.1| hemolysin A [Dietzia cinnamea P4]
          Length = 273

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 21/50 (42%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   + R  +  SR     +I   RV VNG+   + A  V  T  I +
Sbjct: 6  MRLDAELVRRKMCDSRERARDLIDSGRVVVNGVAATKPATQVEPTTSIAL 55


>gi|308061712|gb|ADO03600.1| hemolysin [Helicobacter pylori Cuz20]
          Length = 235

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 10/50 (20%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   +     + SR + + ++ + +V VN +++ + +  V   D IE+
Sbjct: 1  MRLDYALFNRHLVGSREKAKALVLKNQVLVNKMVVSKPSFIVKEDDKIEL 50


>gi|55821964|ref|YP_140406.1| 30S ribosomal protein S4 [Streptococcus thermophilus LMG 18311]
 gi|55823881|ref|YP_142322.1| 30S ribosomal protein S4 [Streptococcus thermophilus CNRZ1066]
 gi|55737949|gb|AAV61591.1| 30S ribosomal protein S4 [Streptococcus thermophilus LMG 18311]
 gi|55739866|gb|AAV63507.1| 30S ribosomal protein S4 [Streptococcus thermophilus CNRZ1066]
          Length = 217

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V
Sbjct: 108 RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVEVGQVISV 156


>gi|325261520|ref|ZP_08128258.1| ribosomal protein S4 [Clostridium sp. D5]
 gi|324032974|gb|EGB94251.1| ribosomal protein S4 [Clostridium sp. D5]
          Length = 197

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +R+E  +++  + V VNG  +   +  V + D IE+
Sbjct: 88  RLDNVMFRMGLARTRKEARQIVDHKHVMVNGKQVNIPSYLVKAGDTIEI 136


>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 = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 30/258 (11%), Positives = 76/258 (29%), Gaps = 52/258 (20%)

Query: 7   VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           + +N   QR+ K + +A  A  +  + + I  +R+K+NG      +  +   D +++   
Sbjct: 6   INKNDAGQRMDKFLTKAVPALPKNLMYKYIRLKRIKLNGKRC-EISTKLSEGDSVQLYIN 64

Query: 63  ------------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
                               + +   +   +        +V      +  + +   L  +
Sbjct: 65  DEFFPEKRDEAHRFLNSPKDIEIVYEDENIILCDKPCGLVVHEDESGEADTLIDRVLHYL 124

Query: 105 FSRVIS------------VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152
           + +                 R+D NT G+++   +    RVL                  
Sbjct: 125 YDKGEYDPDTENSFTPALCNRIDRNTSGIVICAKNAESLRVLNQKVKDRELEKLYLCVTV 184

Query: 153 VDQDKLNLLKKGIVIQGICYGDM-----------------QVTLDTQKGSNAWVTVGLRE 195
              +K +   K    +      +                 +V  + ++   A + V L  
Sbjct: 185 GIPNKKSAELKAFHRRDEKTKVVRVEDKSFPGSKTMITRYKVLAENKQSGLALLEVDLVT 244

Query: 196 GKNREIKKVFEFFNWKVN 213
           G+  +I+       + + 
Sbjct: 245 GRTHQIRAHLAHIGYPLL 262


>gi|283470219|emb|CAQ49430.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus ST398]
          Length = 284

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 25/199 (12%), Positives = 54/199 (27%), Gaps = 28/199 (14%)

Query: 42  VNGILLERAAVNVMSTDHIEVD---------------GVPLRKAERTRLWLYHKPIGLVT 86
           VN   +      +M  D +E+                 + +   +   + +        T
Sbjct: 38  VNDEPVTV-RKQLMPNDILEIHLPREIPSVNLIPYARKLEVLYEDAFIIIVTKPNNQNCT 96

Query: 87  THSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
              +    S +   L              V RLD NT G+++    G +  +    + + 
Sbjct: 97  PSREHPHESLIEQVLYHCQVHGENINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKVNLKK 156

Query: 142 LRVYRVRFHGQVD-------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           +    V              +   + +    V     Y      +  Q    +   V L 
Sbjct: 157 IYTCLVYGKTHTSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLH 216

Query: 195 EGKNREIKKVFEFFNWKVN 213
            G+  +I+  F+     + 
Sbjct: 217 TGRTHQIRVHFQHIGHPIV 235


>gi|257425833|ref|ZP_05602257.1| SSU ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257428499|ref|ZP_05604897.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257431133|ref|ZP_05607510.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257433815|ref|ZP_05610173.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus E1410]
 gi|257436732|ref|ZP_05612776.1| SSU ribosomal protein S4 [Staphylococcus aureus subsp. aureus M876]
 gi|282911345|ref|ZP_06319147.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus WBG10049]
 gi|282914514|ref|ZP_06322300.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus M899]
 gi|282924860|ref|ZP_06332526.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus C101]
 gi|293503592|ref|ZP_06667439.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           58-424]
 gi|293510608|ref|ZP_06669313.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus M809]
 gi|293537149|ref|ZP_06671829.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus M1015]
 gi|257271527|gb|EEV03673.1| SSU ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257275340|gb|EEV06827.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257278081|gb|EEV08729.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257281908|gb|EEV12045.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus E1410]
 gi|257284083|gb|EEV14206.1| SSU ribosomal protein S4 [Staphylococcus aureus subsp. aureus M876]
 gi|282313226|gb|EFB43622.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus C101]
 gi|282321695|gb|EFB52020.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus M899]
 gi|282325040|gb|EFB55350.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus WBG10049]
 gi|290919994|gb|EFD97062.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus M1015]
 gi|291095258|gb|EFE25523.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           58-424]
 gi|291466499|gb|EFF09020.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus M809]
 gi|312437824|gb|ADQ76895.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           TCH60]
          Length = 200

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+   G+A +RR+  +++    + V+G  ++  + +V  +  I V
Sbjct: 93  RLDAVVYSLGLARTRRQARQLVNHGHILVDGKRVDIPSYSVKPSQTISV 141


>gi|153810900|ref|ZP_01963568.1| hypothetical protein RUMOBE_01284 [Ruminococcus obeum ATCC 29174]
 gi|149833296|gb|EDM88378.1| hypothetical protein RUMOBE_01284 [Ruminococcus obeum ATCC 29174]
          Length = 206

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/59 (25%), Positives = 21/59 (35%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +       R+  +I  A   SR  +   I   +V VNG L+          D I V G 
Sbjct: 123 INGTCASVRLDALIGLAFQTSRNSMVPFIEGGQVFVNGKLITSNGYEPKDGDIISVRGK 181


>gi|49483960|ref|YP_041184.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|282904289|ref|ZP_06312177.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus C160]
 gi|282906114|ref|ZP_06313969.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           Btn1260]
 gi|282909029|ref|ZP_06316847.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282919482|ref|ZP_06327217.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus C427]
 gi|283958469|ref|ZP_06375920.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           A017934/97]
 gi|295428289|ref|ZP_06820918.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           EMRSA16]
 gi|297590748|ref|ZP_06949386.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus MN8]
 gi|56749409|sp|Q6GFY8|RS4_STAAR RecName: Full=30S ribosomal protein S4
 gi|49242089|emb|CAG40788.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|282317292|gb|EFB47666.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus C427]
 gi|282327293|gb|EFB57588.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282331406|gb|EFB60920.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           Btn1260]
 gi|282595907|gb|EFC00871.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus C160]
 gi|283790618|gb|EFC29435.1| ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           A017934/97]
 gi|295127689|gb|EFG57326.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           EMRSA16]
 gi|297575634|gb|EFH94350.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus MN8]
 gi|315195623|gb|EFU26010.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus
           CGS00]
          Length = 200

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+   G+A +RR+  +++    + V+G  ++  + +V  +  I V
Sbjct: 93  RLDAVVYSLGLARTRRQARQLVNHGHILVDGKRVDIPSYSVKPSQTISV 141


>gi|228987042|ref|ZP_04147167.1| RNA-binding S4 domain protein [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228772636|gb|EEM21077.1| RNA-binding S4 domain protein [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
          Length = 241

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+ +I    VKVN   +E+ +      D   V G
Sbjct: 166 RLDVMLAEMLHISRQKVQPLIKNGLVKVNWKTVEQTSYECYPGDVFSVRG 215


>gi|229157476|ref|ZP_04285553.1| RNA-binding S4 domain protein [Bacillus cereus ATCC 4342]
 gi|228625926|gb|EEK82676.1| RNA-binding S4 domain protein [Bacillus cereus ATCC 4342]
          Length = 241

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+ +I    VKVN   +E+ +      D   V G
Sbjct: 166 RLDVMLAEMLHISRQKVQPLIKNGLVKVNWKTVEQTSYECYPGDVFSVRG 215


>gi|168186165|ref|ZP_02620800.1| RNA binding protein [Clostridium botulinum C str. Eklund]
 gi|169295830|gb|EDS77963.1| RNA binding protein [Clostridium botulinum C str. Eklund]
          Length = 148

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/64 (23%), Positives = 29/64 (45%), Gaps = 5/64 (7%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHI 60
           ++KN+V    +  R+  ++A     SR   E +I +  V +N   +++R    V     I
Sbjct: 63  QEKNVV---ISSMRLDSIVAALSGLSRSNSENLIKKGLVLINYDKVIKR-NTAVKPNSII 118

Query: 61  EVDG 64
            + G
Sbjct: 119 TIRG 122


>gi|75907235|ref|YP_321531.1| RNA-binding S4 [Anabaena variabilis ATCC 29413]
 gi|75700960|gb|ABA20636.1| RNA-binding S4 [Anabaena variabilis ATCC 29413]
          Length = 259

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 2/65 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             K  +       R+   IA AG   SR ++  +I    V+VN   + +A+  V S D I
Sbjct: 172 PKKKELTTVEASLRLD-AIASAGFGMSRSKMVDLIDSGDVRVNWKEVTQASSQVKSGDLI 230

Query: 61  EVDGV 65
            + G 
Sbjct: 231 AIRGK 235


>gi|331091640|ref|ZP_08340474.1| 30S ribosomal protein S4 [Lachnospiraceae bacterium 2_1_46FAA]
 gi|330403397|gb|EGG82956.1| 30S ribosomal protein S4 [Lachnospiraceae bacterium 2_1_46FAA]
          Length = 197

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +RRE  +++  + V VNG  +   +  V + D IE+
Sbjct: 88  RLDNVVFRMGLARTRREARQIVDHKHVLVNGKQVNIPSYLVKAGDTIEI 136


>gi|296111082|ref|YP_003621463.1| 30S ribosomal protein S4 [Leuconostoc kimchii IMSNU 11154]
 gi|295832613|gb|ADG40494.1| 30S ribosomal protein S4 [Leuconostoc kimchii IMSNU 11154]
          Length = 203

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 11/53 (20%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           QR+  ++ R G+A+ R++  +++    + V+G  ++  + +V     I V   
Sbjct: 93  QRLDSLVYRLGLATTRQQARQLVNHGHILVDGKRVDIPSFSVTPGQVISVRDK 145


>gi|228928946|ref|ZP_04091978.1| RNA-binding S4 domain protein [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228947617|ref|ZP_04109907.1| RNA-binding S4 domain protein [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228812137|gb|EEM58468.1| RNA-binding S4 domain protein [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228830753|gb|EEM76358.1| RNA-binding S4 domain protein [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
          Length = 241

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+ +I    VKVN   +E+ +      D   V G
Sbjct: 166 RLDVMLAEMLHISRQKVQPLIKNGLVKVNWKTVEQTSYECYPGDVFSVRG 215


>gi|210611153|ref|ZP_03288767.1| hypothetical protein CLONEX_00957 [Clostridium nexile DSM 1787]
 gi|210152140|gb|EEA83147.1| hypothetical protein CLONEX_00957 [Clostridium nexile DSM 1787]
          Length = 197

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R+E  +++  + V VNG  +   +  V + D IE+
Sbjct: 88  RLDNVVFRMGFARTRKEARQIVDHKHVLVNGKQVNIPSYLVKAGDVIEI 136


>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 = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 7/62 (11%)

Query: 6  IVQENFTPQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
          ++ EN  P+R+ K ++R     A + SR  + R+I   +++VNG ++  A   V     I
Sbjct: 9  VIAENP-PKRLDKAVSRDVPEEATL-SRTRLARLIEAGQLQVNGTVVSDAKAKVDEGALI 66

Query: 61 EV 62
          E+
Sbjct: 67 EI 68


>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 = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 31/214 (14%), Positives = 76/214 (35%), Gaps = 28/214 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTD---------HIEVDGVPLRK-AERTRLW 76
           SR  V+ ++++ ++ VNG +  +    +   D          +E +   LR   E   L 
Sbjct: 42  SRSSVKGLLSRGQISVNGKVTRQFDAPLNPNDTVGINYGRGKVEFNNPLLRIVWEDDDLI 101

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + +K  GL++  +D     T +  L          +++  + RLD +T G+++   +  +
Sbjct: 102 VINKREGLLSVSTDRIKERTAYRILSDYLKECDPRNKIFVLHRLDRDTSGIMMFAKNQKV 161

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ------------GICYGDMQVT 178
              L+   ++ +         +   +K   L    +++                   +  
Sbjct: 162 KEQLQSNWSEAITQRTYVAVIEGRPEKDTDLIVSNLVENKHMQVYVTQDGDGKEAITRYR 221

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           L       + V + L  G+  +I+   +     +
Sbjct: 222 LLQTNNRYSLVELDLETGRKNQIRAQMQSIGHPI 255


>gi|167036434|ref|YP_001664012.1| RNA-binding S4 domain-containing protein [Thermoanaerobacter
          pseudethanolicus ATCC 33223]
 gi|167038678|ref|YP_001661663.1| RNA-binding S4 domain-containing protein [Thermoanaerobacter sp.
          X514]
 gi|256751453|ref|ZP_05492331.1| S4 domain protein YaaA [Thermoanaerobacter ethanolicus CCSD1]
 gi|300913762|ref|ZP_07131079.1| S4 domain protein YaaA [Thermoanaerobacter sp. X561]
 gi|307723221|ref|YP_003902972.1| S4 domain-containing protein YaaA [Thermoanaerobacter sp. X513]
 gi|320114860|ref|YP_004185019.1| S4 domain-containing protein YaaA [Thermoanaerobacter brockii
          subsp. finnii Ako-1]
 gi|166852918|gb|ABY91327.1| RNA-binding S4 domain protein [Thermoanaerobacter sp. X514]
 gi|166855268|gb|ABY93676.1| RNA-binding S4 domain protein [Thermoanaerobacter
          pseudethanolicus ATCC 33223]
 gi|256749672|gb|EEU62698.1| S4 domain protein YaaA [Thermoanaerobacter ethanolicus CCSD1]
 gi|300890447|gb|EFK85592.1| S4 domain protein YaaA [Thermoanaerobacter sp. X561]
 gi|307580282|gb|ADN53681.1| S4 domain protein YaaA [Thermoanaerobacter sp. X513]
 gi|319927951|gb|ADV78636.1| S4 domain protein YaaA [Thermoanaerobacter brockii subsp. finnii
          Ako-1]
          Length = 68

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 12/36 (33%), Positives = 20/36 (55%)

Query: 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          + ++ I + +VKVNG +  +    +   D IEVDG 
Sbjct: 28 QAKQFILEGKVKVNGAIELKRGKKLHKNDIIEVDGK 63


>gi|320581194|gb|EFW95415.1| Mitochondrial ribosomal component of the small subunit [Pichia
           angusta DL-1]
          Length = 476

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 19/111 (17%), Positives = 38/111 (34%), Gaps = 4/111 (3%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---A 70
           R+   + RA  AS  R+  + I    VKVNG+ ++  +  +   D   V+   + +    
Sbjct: 104 RLDVAVFRAMFASSVRQARQFILAGDVKVNGVPIKHPSYPLSPGDVFSVEPDRVLQALGE 163

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           ++  L   +K                  D L    ++     ++      L
Sbjct: 164 KKPSLKEAYKVDREQVIQWQKFVNRARSDPLNVWQNQRSKQKKMRQTYGDL 214


>gi|282854430|ref|ZP_06263767.1| S4 domain protein [Propionibacterium acnes J139]
 gi|282583883|gb|EFB89263.1| S4 domain protein [Propionibacterium acnes J139]
          Length = 76

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 12/58 (20%), Positives = 21/58 (36%), Gaps = 9/58 (15%)

Query: 10 NFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          +    R+ + +     A  G     +   +IA   V VNG +  R    +   D + V
Sbjct: 3  DDQMIRLGQYLKFANLAETGG----QARELIASGMVSVNGEVETRRGRQLHPGDEVRV 56


>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 = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 25/199 (12%), Positives = 54/199 (27%), Gaps = 28/199 (14%)

Query: 42  VNGILLERAAVNVMSTDHIEVD---------------GVPLRKAERTRLWLYHKPIGLVT 86
           VN   +      +M  D +E+                 + +   +   + +        T
Sbjct: 38  VNDEPVTV-RKQLMPNDILEIHLPREIPSVNLIPYARKLEVLYEDAFIIIVTKPNNQNCT 96

Query: 87  THSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
              +    S +   L              V RLD NT G+++    G +  +    + + 
Sbjct: 97  PSREHPHESLIEQVLYHCQEHGENINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKVNLKK 156

Query: 142 LRVYRVRFHGQVD-------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           +    V              +   + +    V     Y      +  Q    +   V L 
Sbjct: 157 IYTCLVYGKTHTSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLH 216

Query: 195 EGKNREIKKVFEFFNWKVN 213
            G+  +I+  F+     + 
Sbjct: 217 TGRTHQIRVHFQHIGHPIV 235


>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 = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 25/199 (12%), Positives = 54/199 (27%), Gaps = 28/199 (14%)

Query: 42  VNGILLERAAVNVMSTDHIEVD---------------GVPLRKAERTRLWLYHKPIGLVT 86
           VN   +      +M  D +E+                 + +   +   + +        T
Sbjct: 38  VNDEPVTV-RKQLMPNDILEIHLPREIPSVNLIPYARKLEVLYEDAFIIIVTKPNNQNCT 96

Query: 87  THSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
              +    S +   L              V RLD NT G+++    G +  +    + + 
Sbjct: 97  PSREHPHESLIEQVLYHCQEHGENINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKVNLKK 156

Query: 142 LRVYRVRFHGQVD-------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           +    V              +   + +    V     Y      +  Q    +   V L 
Sbjct: 157 IYTCLVYGKTHTSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLH 216

Query: 195 EGKNREIKKVFEFFNWKVN 213
            G+  +I+  F+     + 
Sbjct: 217 TGRTHQIRVHFQHIGHPIV 235


>gi|333012800|gb|EGK32178.1| ribosomal protein S4 [Shigella flexneri K-227]
          Length = 152

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 43  RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 102

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 103 AALELAEQREKPT 115


>gi|332997104|gb|EGK16720.1| ribosomal protein S4 [Shigella flexneri K-218]
          Length = 152

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 43  RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 102

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 103 AALELAEQREKPT 115


>gi|295694865|ref|YP_003588103.1| ribosomal protein S4 [Bacillus tusciae DSM 2912]
 gi|295410467|gb|ADG04959.1| ribosomal protein S4 [Bacillus tusciae DSM 2912]
          Length = 208

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 1/62 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G A SR E  +++      VNG  ++  +  +   D + V    L      
Sbjct: 99  RLDNVVYRLGYAASRAEARQLVRHGHFTVNGRRVDIPSYQLKEGDVVAVREKSLESPRLK 158

Query: 74  RL 75
            L
Sbjct: 159 EL 160


>gi|295396795|ref|ZP_06806930.1| ribosomal RNA large subunit methyltransferase J [Brevibacterium
          mcbrellneri ATCC 49030]
 gi|294970379|gb|EFG46319.1| ribosomal RNA large subunit methyltransferase J [Brevibacterium
          mcbrellneri ATCC 49030]
          Length = 250

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15 RVS-KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+  +++AR  + SR    R I    V VNG    + +  V   DH+ +
Sbjct: 3  RLDTELVARGLVTSRNRAAREIMAGNVTVNGHKATKPSHTVGPDDHVAL 51


>gi|291542058|emb|CBL15168.1| SSU ribosomal protein S4P [Ruminococcus bromii L2-63]
          Length = 200

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI R G+A +RRE  ++++     VNG  +   +  V   D IEV
Sbjct: 90  RLDNVIFRLGLAATRREARQLVSHSHFTVNGKKVNIPSYLVKVGDVIEV 138


>gi|182416753|ref|ZP_02948150.1| S4 domain protein YaaA [Clostridium butyricum 5521]
 gi|237669610|ref|ZP_04529588.1| S4 domain protein YaaA [Clostridium butyricum E4 str. BoNT E
          BL5262]
 gi|182379410|gb|EDT76905.1| S4 domain protein YaaA [Clostridium butyricum 5521]
 gi|237654844|gb|EEP52406.1| S4 domain protein YaaA [Clostridium butyricum E4 str. BoNT E
          BL5262]
          Length = 68

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 1/61 (1%)

Query: 5  NIVQENFTPQRVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          N ++      ++   +  A IAS   E +  I  + VKVN  +  +    + + D +  D
Sbjct: 2  NKIKIETEIIKLDAFLKWAAIASSGSEAKFYIQDEMVKVNNEICTQRGKKLKAGDIVNFD 61

Query: 64 G 64
          G
Sbjct: 62 G 62


>gi|166365176|ref|YP_001657449.1| RNA-binding S4 [Microcystis aeruginosa NIES-843]
 gi|166087549|dbj|BAG02257.1| RNA-binding S4 [Microcystis aeruginosa NIES-843]
          Length = 259

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 2/65 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             K  +       R+   IA AG   SR ++   I+   V+VN   + +++ NV + D I
Sbjct: 172 PQKKEINTVEASLRLD-AIASAGFGISRSKMAEAISAGDVRVNWKDISQSSYNVKTGDLI 230

Query: 61  EVDGV 65
              G 
Sbjct: 231 SFRGK 235


>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 = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 31/260 (11%), Positives = 70/260 (26%), Gaps = 52/260 (20%)

Query: 6   IVQENFTPQRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           I   +   +R+ + +A A     SR  V+ +IA   V ++G         +    +I + 
Sbjct: 5   IADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMNIAIV 64

Query: 63  ---------DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
                     G  +       +   + +      +V   +     + V   +        
Sbjct: 65  LPEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNGNWTGTLVNALIYHCGDSLS 124

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARV------LELPSTQWLRVYRVRFHGQVD 154
                 R   V RLD +T G++++  +    R           +    R Y     G  +
Sbjct: 125 GIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFADHGRTGDLERAYLALVWGMTE 184

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN---------------------AWVTVGL 193
           + +  +                V  + +   +                     + V   L
Sbjct: 185 RPQGTVDAYLGRSHRDRTKQAVVREEREDARHAITHYATVEKFSPREDATALASLVECRL 244

Query: 194 REGKNREIKKVFEFFNWKVN 213
             G+  +I+         + 
Sbjct: 245 ETGRTHQIRVHMAHIGHPLV 264


>gi|226939211|ref|YP_002794282.1| 30S ribosomal protein S4 [Laribacter hongkongensis HLHK9]
 gi|254764593|sp|C1DAU2|RS4_LARHH RecName: Full=30S ribosomal protein S4
 gi|226714135|gb|ACO73273.1| RpsD [Laribacter hongkongensis HLHK9]
          Length = 206

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG ++   +  V + D + V
Sbjct: 97  RLDNVVYRMGYGSTRAESRQLVSHKAIVVNGEVVNIPSYQVKAGDVVSV 145


>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 = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 7/62 (11%)

Query: 6  IVQENFTPQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
          ++ EN  P+R+ K ++R     A + SR  + R+I   +++VNG ++  A   V     I
Sbjct: 9  VIAENP-PKRLDKAVSRDVPEEATL-SRTRLARLIEAGQLQVNGTVVSDAKAKVDEGALI 66

Query: 61 EV 62
          E+
Sbjct: 67 EI 68


>gi|169833614|ref|YP_001695043.1| YlmH protein [Streptococcus pneumoniae Hungary19A-6]
 gi|168996116|gb|ACA36728.1| YlmH protein [Streptococcus pneumoniae Hungary19A-6]
          Length = 261

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 11/48 (22%), Positives = 26/48 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +++     SR +  ++I ++ V+VN  +++++   V   D I V
Sbjct: 184 RLDVLLSNVLKLSRNQANQLIEKKLVQVNYHMVDKSDYTVQVGDLISV 231


>gi|70732860|ref|YP_262627.1| 30S ribosomal protein S4 [Pseudomonas fluorescens Pf-5]
 gi|90101707|sp|Q4K556|RS4_PSEF5 RecName: Full=30S ribosomal protein S4
 gi|68347159|gb|AAY94765.1| ribosomal protein S4 [Pseudomonas fluorescens Pf-5]
          Length = 206

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V + D + V
Sbjct: 97  RLDNVVYRMGFGSTRAESRQLVSHKSISVNGQTVNVPSYQVRAGDVVAV 145


>gi|29377528|ref|NP_816682.1| 30S ribosomal protein S4 [Enterococcus faecalis V583]
 gi|227517321|ref|ZP_03947370.1| 30S ribosomal protein S4 [Enterococcus faecalis TX0104]
 gi|227554493|ref|ZP_03984540.1| 30S ribosomal protein S4 [Enterococcus faecalis HH22]
 gi|229547500|ref|ZP_04436225.1| 30S ribosomal protein S4 [Enterococcus faecalis TX1322]
 gi|229548076|ref|ZP_04436801.1| 30S ribosomal protein S4 [Enterococcus faecalis ATCC 29200]
 gi|256618170|ref|ZP_05475016.1| 30S ribosomal protein S4 [Enterococcus faecalis ATCC 4200]
 gi|256854748|ref|ZP_05560112.1| ribosomal protein S4 [Enterococcus faecalis T8]
 gi|256958352|ref|ZP_05562523.1| 30S ribosomal protein S4 [Enterococcus faecalis DS5]
 gi|256960421|ref|ZP_05564592.1| 30S ribosomal protein S4 [Enterococcus faecalis Merz96]
 gi|256962912|ref|ZP_05567083.1| 30S ribosomal protein S4 [Enterococcus faecalis HIP11704]
 gi|257078338|ref|ZP_05572699.1| 30S ribosomal protein S4 [Enterococcus faecalis JH1]
 gi|257080522|ref|ZP_05574883.1| 30S ribosomal protein S4 [Enterococcus faecalis E1Sol]
 gi|257083258|ref|ZP_05577619.1| 30S ribosomal protein S4 [Enterococcus faecalis Fly1]
 gi|257088187|ref|ZP_05582548.1| 30S ribosomal protein S4 [Enterococcus faecalis D6]
 gi|257091313|ref|ZP_05585674.1| 30S ribosomal protein S4 [Enterococcus faecalis CH188]
 gi|257417921|ref|ZP_05594915.1| 30S ribosomal protein S4 [Enterococcus faecalis T11]
 gi|257420473|ref|ZP_05597463.1| 30S ribosomal protein S4 [Enterococcus faecalis X98]
 gi|293383922|ref|ZP_06629824.1| ribosomal protein S4 [Enterococcus faecalis R712]
 gi|293388316|ref|ZP_06632830.1| ribosomal protein S4 [Enterococcus faecalis S613]
 gi|294780202|ref|ZP_06745574.1| ribosomal protein S4 [Enterococcus faecalis PC1.1]
 gi|300861437|ref|ZP_07107521.1| ribosomal protein S4 [Enterococcus faecalis TUSoD Ef11]
 gi|307270423|ref|ZP_07551724.1| ribosomal protein S4 [Enterococcus faecalis TX4248]
 gi|307273936|ref|ZP_07555148.1| ribosomal protein S4 [Enterococcus faecalis TX0855]
 gi|307276703|ref|ZP_07557820.1| ribosomal protein S4 [Enterococcus faecalis TX2134]
 gi|307278207|ref|ZP_07559289.1| ribosomal protein S4 [Enterococcus faecalis TX0860]
 gi|307286409|ref|ZP_07566515.1| ribosomal protein S4 [Enterococcus faecalis TX0109]
 gi|307292091|ref|ZP_07571958.1| ribosomal protein S4 [Enterococcus faecalis TX0411]
 gi|312901910|ref|ZP_07761173.1| ribosomal protein S4 [Enterococcus faecalis TX0470]
 gi|312905372|ref|ZP_07764487.1| ribosomal protein S4 [Enterococcus faecalis TX0635]
 gi|312906737|ref|ZP_07765737.1| ribosomal protein S4 [Enterococcus faecalis DAPTO 512]
 gi|312910725|ref|ZP_07769564.1| ribosomal protein S4 [Enterococcus faecalis DAPTO 516]
 gi|312953171|ref|ZP_07772018.1| ribosomal protein S4 [Enterococcus faecalis TX0102]
 gi|41017833|sp|Q82ZI6|RS4_ENTFA RecName: Full=30S ribosomal protein S4
 gi|29344995|gb|AAO82752.1| ribosomal protein S4 [Enterococcus faecalis V583]
 gi|227075191|gb|EEI13154.1| 30S ribosomal protein S4 [Enterococcus faecalis TX0104]
 gi|227176403|gb|EEI57375.1| 30S ribosomal protein S4 [Enterococcus faecalis HH22]
 gi|229306762|gb|EEN72758.1| 30S ribosomal protein S4 [Enterococcus faecalis ATCC 29200]
 gi|229307342|gb|EEN73329.1| 30S ribosomal protein S4 [Enterococcus faecalis TX1322]
 gi|256597697|gb|EEU16873.1| 30S ribosomal protein S4 [Enterococcus faecalis ATCC 4200]
 gi|256710308|gb|EEU25352.1| ribosomal protein S4 [Enterococcus faecalis T8]
 gi|256948848|gb|EEU65480.1| 30S ribosomal protein S4 [Enterococcus faecalis DS5]
 gi|256950917|gb|EEU67549.1| 30S ribosomal protein S4 [Enterococcus faecalis Merz96]
 gi|256953408|gb|EEU70040.1| 30S ribosomal protein S4 [Enterococcus faecalis HIP11704]
 gi|256986368|gb|EEU73670.1| 30S ribosomal protein S4 [Enterococcus faecalis JH1]
 gi|256988552|gb|EEU75854.1| 30S ribosomal protein S4 [Enterococcus faecalis E1Sol]
 gi|256991288|gb|EEU78590.1| 30S ribosomal protein S4 [Enterococcus faecalis Fly1]
 gi|256996217|gb|EEU83519.1| 30S ribosomal protein S4 [Enterococcus faecalis D6]
 gi|257000125|gb|EEU86645.1| 30S ribosomal protein S4 [Enterococcus faecalis CH188]
 gi|257159749|gb|EEU89709.1| 30S ribosomal protein S4 [Enterococcus faecalis T11]
 gi|257162297|gb|EEU92257.1| 30S ribosomal protein S4 [Enterococcus faecalis X98]
 gi|291078749|gb|EFE16113.1| ribosomal protein S4 [Enterococcus faecalis R712]
 gi|291082326|gb|EFE19289.1| ribosomal protein S4 [Enterococcus faecalis S613]
 gi|294452745|gb|EFG21175.1| ribosomal protein S4 [Enterococcus faecalis PC1.1]
 gi|295114399|emb|CBL33036.1| SSU ribosomal protein S4P [Enterococcus sp. 7L76]
 gi|300848898|gb|EFK76651.1| ribosomal protein S4 [Enterococcus faecalis TUSoD Ef11]
 gi|306496873|gb|EFM66423.1| ribosomal protein S4 [Enterococcus faecalis TX0411]
 gi|306502422|gb|EFM71695.1| ribosomal protein S4 [Enterococcus faecalis TX0109]
 gi|306505196|gb|EFM74384.1| ribosomal protein S4 [Enterococcus faecalis TX0860]
 gi|306506602|gb|EFM75755.1| ribosomal protein S4 [Enterococcus faecalis TX2134]
 gi|306509415|gb|EFM78473.1| ribosomal protein S4 [Enterococcus faecalis TX0855]
 gi|306513201|gb|EFM81832.1| ribosomal protein S4 [Enterococcus faecalis TX4248]
 gi|310627385|gb|EFQ10668.1| ribosomal protein S4 [Enterococcus faecalis DAPTO 512]
 gi|310628914|gb|EFQ12197.1| ribosomal protein S4 [Enterococcus faecalis TX0102]
 gi|310631396|gb|EFQ14679.1| ribosomal protein S4 [Enterococcus faecalis TX0635]
 gi|311288988|gb|EFQ67544.1| ribosomal protein S4 [Enterococcus faecalis DAPTO 516]
 gi|311290977|gb|EFQ69533.1| ribosomal protein S4 [Enterococcus faecalis TX0470]
 gi|315027687|gb|EFT39619.1| ribosomal protein S4 [Enterococcus faecalis TX2137]
 gi|315028229|gb|EFT40161.1| ribosomal protein S4 [Enterococcus faecalis TX4000]
 gi|315031243|gb|EFT43175.1| ribosomal protein S4 [Enterococcus faecalis TX0017]
 gi|315036538|gb|EFT48470.1| ribosomal protein S4 [Enterococcus faecalis TX0027]
 gi|315143294|gb|EFT87310.1| ribosomal protein S4 [Enterococcus faecalis TX2141]
 gi|315148889|gb|EFT92905.1| ribosomal protein S4 [Enterococcus faecalis TX4244]
 gi|315149065|gb|EFT93081.1| ribosomal protein S4 [Enterococcus faecalis TX0012]
 gi|315152920|gb|EFT96936.1| ribosomal protein S4 [Enterococcus faecalis TX0031]
 gi|315154776|gb|EFT98792.1| ribosomal protein S4 [Enterococcus faecalis TX0043]
 gi|315157493|gb|EFU01510.1| ribosomal protein S4 [Enterococcus faecalis TX0312]
 gi|315162550|gb|EFU06567.1| ribosomal protein S4 [Enterococcus faecalis TX0645]
 gi|315164504|gb|EFU08521.1| ribosomal protein S4 [Enterococcus faecalis TX1302]
 gi|315167181|gb|EFU11198.1| ribosomal protein S4 [Enterococcus faecalis TX1341]
 gi|315171025|gb|EFU15042.1| ribosomal protein S4 [Enterococcus faecalis TX1342]
 gi|315173453|gb|EFU17470.1| ribosomal protein S4 [Enterococcus faecalis TX1346]
 gi|315573361|gb|EFU85552.1| ribosomal protein S4 [Enterococcus faecalis TX0309B]
 gi|315578558|gb|EFU90749.1| ribosomal protein S4 [Enterococcus faecalis TX0630]
 gi|315581207|gb|EFU93398.1| ribosomal protein S4 [Enterococcus faecalis TX0309A]
 gi|323479004|gb|ADX78443.1| ribosomal protein S4 [Enterococcus faecalis 62]
 gi|327536193|gb|AEA95027.1| 30S ribosomal protein S4 [Enterococcus faecalis OG1RF]
 gi|329571122|gb|EGG52828.1| ribosomal protein S4 [Enterococcus faecalis TX1467]
          Length = 203

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G+A+ RR+  +++    + V+G  ++  + +V     I V
Sbjct: 93  QRLDNVVYRLGLATTRRQARQLVNHGHITVDGKRVDIPSYHVEVGQVIGV 142


>gi|253575746|ref|ZP_04853081.1| 30S ribosomal protein S4 [Paenibacillus sp. oral taxon 786 str.
           D14]
 gi|251844789|gb|EES72802.1| 30S ribosomal protein S4 [Paenibacillus sp. oral taxon 786 str.
           D14]
          Length = 199

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  ++ R G A SR    ++++   V VNG  ++ A+  V   D I
Sbjct: 92  RLDNLVYRLGFANSRAGARQLVSHGHVTVNGKKVDIASYRVNVGDVI 138


>gi|229592879|ref|YP_002874998.1| 30S ribosomal protein S4 [Pseudomonas fluorescens SBW25]
 gi|312963346|ref|ZP_07777829.1| 30S ribosomal protein S4 [Pseudomonas fluorescens WH6]
 gi|330812052|ref|YP_004356514.1| 30S ribosomal protein S4 [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
 gi|259495288|sp|C3K2V2|RS4_PSEFS RecName: Full=30S ribosomal protein S4
 gi|229364745|emb|CAY52725.1| 30S ribosomal protein S4 [Pseudomonas fluorescens SBW25]
 gi|311282426|gb|EFQ61024.1| 30S ribosomal protein S4 [Pseudomonas fluorescens WH6]
 gi|327380160|gb|AEA71510.1| 30S ribosomal protein S4 [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
          Length = 206

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V + D + V
Sbjct: 97  RLDNVVYRMGFGSTRAESRQLVSHKSISVNGQTVNVPSYQVRAGDVVAV 145


>gi|225571581|ref|ZP_03780577.1| hypothetical protein CLOHYLEM_07679 [Clostridium hylemonae DSM
           15053]
 gi|225159658|gb|EEG72277.1| hypothetical protein CLOHYLEM_07679 [Clostridium hylemonae DSM
           15053]
          Length = 181

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +RRE  +++  + V VNG  +   +  V + D +E+
Sbjct: 72  RLDNVVFRMGLARTRREARQIVDHKHVMVNGKQINIPSYIVKAGDVVEI 120


>gi|218290916|ref|ZP_03494973.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius LAA1]
 gi|218239081|gb|EED06284.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius LAA1]
          Length = 333

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 35/241 (14%), Positives = 68/241 (28%), Gaps = 34/241 (14%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +V  +   +R+S V++     SRR + R+I      +NG  +   +V V   D +  +  
Sbjct: 1   MVPSDLAGRRLSAVLSGRLGMSRRMLRRIIQAGGFYLNGEPVY-LSVTVQDGDRVTWERP 59

Query: 66  -------------PLRKAERTRLWLYHKPIGLVTTHSDPDGRS---TVFDNLPSIFSRVI 109
                         +   +   + +      L          S        L        
Sbjct: 60  EEEVAVEPEDIPLEICYEDDDVIVVNKPAGMLTHPSPHERRGSLLAAAAHYLRDRGGVPH 119

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           +V RLD  T G +L+         L+    Q    R Y    +     +    L     +
Sbjct: 120 AVHRLDKYTSGAVLIAKHAHAHHQLDRALRQGLVDRRYVAIVYAPEGCETGRWLTFVDGL 179

Query: 168 QGICYGDMQVTLDTQKGSNAWVT---------------VGLREGKNREIKKVFEFFNWKV 212
               +   +  +      +  VT               + L  G+  +I+    F    +
Sbjct: 180 APNPHRPSRRIVVPPDRGDRAVTHALPLVQAGPLALVALVLETGRTHQIRAQMAFHGMPL 239

Query: 213 N 213
            
Sbjct: 240 V 240


>gi|189485330|ref|YP_001956271.1| putative rRNA methylase [uncultured Termite group 1 bacterium
          phylotype Rs-D17]
 gi|170287289|dbj|BAG13810.1| putative rRNA methylase [uncultured Termite group 1 bacterium
          phylotype Rs-D17]
          Length = 250

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+  ++   G A +R + +  I    + VN  +  R    V   D IEV
Sbjct: 9  RLDVLLFEKGFAETRTKAQAFIMSGNIFVNNQIQYRPGTLVGKEDSIEV 57


>gi|162456220|ref|YP_001618587.1| 30S ribosomal protein S4 [Sorangium cellulosum 'So ce 56']
 gi|161166802|emb|CAN98107.1| 30S ribosomal protein S4 [Sorangium cellulosum 'So ce 56']
          Length = 209

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  +++    V VNG  L+  +  V + D +E+
Sbjct: 99  RLDNVVHRMGFGSSRAEARQLVRHGHVHVNGKRLDIPSYVVRAGDRVEL 147


>gi|163816792|ref|ZP_02208155.1| hypothetical protein COPEUT_02982 [Coprococcus eutactus ATCC 27759]
 gi|158448049|gb|EDP25044.1| hypothetical protein COPEUT_02982 [Coprococcus eutactus ATCC 27759]
          Length = 266

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 23/141 (16%), Positives = 43/141 (30%), Gaps = 2/141 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  ++   G+A SR + + +I    V V+    ++A      T  IEV G  L+   R 
Sbjct: 4   RLDVLLVEQGLADSREKAKAIIMSGIVYVDNNKEDKAGTTFEETARIEVRGNTLKYVSRG 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L         T                    ++  G + + +  +        L   
Sbjct: 64  GLKLEKAMNNFGVTLEGKVCMDVGAST-GGFTDCMLQNGAVKVYSVDVGHGQLAWKLRND 122

Query: 134 LELPSTQWLRVYRVRFHGQVD 154
             +   +   +  V      D
Sbjct: 123 ERVVCMEKTNIRYVTPDDIDD 143


>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 = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 37/238 (15%), Positives = 70/238 (29%), Gaps = 37/238 (15%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN---------------- 53
             + QR+ K +A     SR  V+ +I +  V V G  L + +                  
Sbjct: 13  EESGQRLDKALAEGSGLSRERVKALIEEGAVTVAGTPLRQPSAKSVAGTEWTIAVPVPAA 72

Query: 54  ------------VMST-DHIEVD---GVPLRK----AERTRLWLYHKPIGLVTTHSDPDG 93
                       V    D I VD   G+ +       + T +           +      
Sbjct: 73  AEAVAQDIPLTVVYEDADLIVVDKPAGMVVHPAAGNPDGTLVNALLHHCRGQLSGIGGVA 132

Query: 94  RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
           R  +   +    S ++ V + D+  EGL     D  + R     +            G +
Sbjct: 133 RPGIVHRIDKDTSGLLVVAKTDVAHEGLARQFADHSIVRAYRAVTGGAPTPPAGTIRGAI 192

Query: 154 DQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
            +   +  K  +V +G   +         +  S+A V   L  G+  +++        
Sbjct: 193 ARSSHDRKKMALVEEGRGKHAVTHYRTLERLDSSALVECRLETGRTHQVRVHLASIGH 250


>gi|325479161|gb|EGC82258.1| ribosomal protein S4 [Anaerococcus prevotii ACS-065-V-Col13]
          Length = 197

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V  R+G+A +RRE  +++    + VNG  ++  +  +   D IEV
Sbjct: 88  RLDNVAFRSGLARTRREARQIVTHGHLTVNGKQVDIPSYQIEEGDVIEV 136


>gi|257417204|ref|ZP_05594198.1| 30S ribosomal protein S4 [Enterococcus faecalis AR01/DG]
 gi|257159032|gb|EEU88992.1| 30S ribosomal protein S4 [Enterococcus faecalis ARO1/DG]
          Length = 203

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G+A+ RR+  +++    + V+G  ++  + +V     I V
Sbjct: 93  QRLDNVVYRLGLATTRRQARQLVNHGHITVDGKRVDIPSYHVEVGQVIGV 142


>gi|262199925|ref|YP_003271134.1| hemolysin A [Haliangium ochraceum DSM 14365]
 gi|262083272|gb|ACY19241.1| hemolysin A [Haliangium ochraceum DSM 14365]
          Length = 282

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          +R+  ++ R G +ASR     +I    V+V GI++ +A   V     I +
Sbjct: 4  ERLDTMLVRRGLVASRERARALILAGEVEVGGIIVSKAGTRVAEEAEIAL 53


>gi|284992847|ref|YP_003411401.1| 30S ribosomal protein S4 [Geodermatophilus obscurus DSM 43160]
 gi|284066092|gb|ADB77030.1| ribosomal protein S4 [Geodermatophilus obscurus DSM 43160]
          Length = 208

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG A SR    +++    ++VNG  ++  +  V S D IEV
Sbjct: 99  RLDNVVYRAGFAESRDMARQLVRHGHIRVNGRKVDIPSYRVASNDIIEV 147


>gi|119964199|ref|YP_947328.1| translation initiation factor IF-2 [Arthrobacter aurescens TC1]
 gi|189028279|sp|A1R516|IF2_ARTAT RecName: Full=Translation initiation factor IF-2
 gi|119951058|gb|ABM09969.1| translation initiation factor IF-2 [Arthrobacter aurescens TC1]
          Length = 958

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 8/109 (7%), Positives = 20/109 (18%), Gaps = 1/109 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P     A                      +       R           +     +  +
Sbjct: 134 APKAETPAPARQGGQAPRPGGPRPGNNPFATSQGMPRGRGGDGDRPPRPGNNPFAPSQGM 193

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREEN-HRRSPSFPSKRSLRRTSAK 353
            R    ++     G   +  +   +         P  P   + R  + +
Sbjct: 194 PRGERRNDGERPGGPRPAAGAGGPRPAAGTGGPRPGAPRPGAPRPGAPR 242



 Score = 43.6 bits (101), Expect = 0.051,   Method: Composition-based stats.
 Identities = 5/91 (5%), Positives = 15/91 (16%)

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
                          N          R ++ +  +     +        R    +     
Sbjct: 169 PRGRGGDGDRPPRPGNNPFAPSQGMPRGERRNDGERPGGPRPAAGAGGPRPAAGTGGPRP 228

Query: 318 KGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                        R      + + P+   + 
Sbjct: 229 GAPRPGAPRPGAPRPAGGPGAGNRPTPGMMP 259



 Score = 42.1 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 15/110 (13%), Positives = 24/110 (21%), Gaps = 6/110 (5%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P      +    AP        R         P   ++        +G    +    P 
Sbjct: 128 KPGARPAPKAETPAPARQGGQAPRPGGPRPGNNPFATSQGMPRGRGGDGDRPPRPGNNPF 187

Query: 306 HRRNLASNVWMAKGIHS-SFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                A +  M +G          G R       P   +     R  A +
Sbjct: 188 -----APSQGMPRGERRNDGERPGGPRPAAGAGGPRPAAGTGGPRPGAPR 232



 Score = 39.8 bits (91), Expect = 0.58,   Method: Composition-based stats.
 Identities = 4/91 (4%), Positives = 14/91 (15%)

Query: 262 YSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIH 321
            +  +                 R    + +  G                       +   
Sbjct: 122 STPVSAKPGARPAPKAETPAPARQGGQAPRPGGPRPGNNPFATSQGMPRGRGGDGDRPPR 181

Query: 322 SSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                 +  +        +   +    R +A
Sbjct: 182 PGNNPFAPSQGMPRGERRNDGERPGGPRPAA 212


>gi|124268602|ref|YP_001022606.1| 30S ribosomal protein S4 [Methylibium petroleiphilum PM1]
 gi|152112230|sp|A2SLD2|RS4_METPP RecName: Full=30S ribosomal protein S4
 gi|124261377|gb|ABM96371.1| SSU ribosomal protein S4P [Methylibium petroleiphilum PM1]
          Length = 207

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG ++  A+  V + D + V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKGITVNGEVVNIASYLVKTGDVVAV 146


>gi|254820179|ref|ZP_05225180.1| ferredoxin, 4Fe-4S [Mycobacterium intracellulare ATCC 13950]
          Length = 991

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 11/121 (9%), Positives = 24/121 (19%), Gaps = 12/121 (9%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G     +     +          R       +      R ++      G    ++     
Sbjct: 822 GHRRRRQETRGQEGGTGQGRGTCRSGRARGRDRGQGARRAREGPGPGRGRQATRRQEGGP 881

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRS------------PSFPSKRSLRRTSAK 353
             R         +    S     G R                       S+ +  R+ A+
Sbjct: 882 EGRGPQGRSTRGRSGAGSRTRGQGARRAGEGPGHRRGRQTTRRQEGGPESRGAESRSRAR 941

Query: 354 K 354
           +
Sbjct: 942 R 942



 Score = 36.3 bits (82), Expect = 7.2,   Method: Composition-based stats.
 Identities = 15/123 (12%), Positives = 26/123 (21%), Gaps = 21/123 (17%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS----- 296
           R + GP      Q              + R           TR +       G       
Sbjct: 860 RAREGPGPGRGRQATRRQEGGPEGRGPQGRSTRGRSGAGSRTRGQGARRAGEGPGHRRGR 919

Query: 297 ------KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSG----------QREENHRRSPS 340
                 +    +     R+ A      +    S +  +G           +   HR   +
Sbjct: 920 QTTRRQEGGPESRGAESRSRARRTGAGRAGTESGVGKAGRRRRRTVAAAGQRPGHRPRGA 979

Query: 341 FPS 343
            P 
Sbjct: 980 TPG 982


>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 = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 25/199 (12%), Positives = 54/199 (27%), Gaps = 28/199 (14%)

Query: 42  VNGILLERAAVNVMSTDHIEVD---------------GVPLRKAERTRLWLYHKPIGLVT 86
           VN   +      +M  D +E+                 + +   +   + +        T
Sbjct: 38  VNDEPVTV-RKQLMPNDILEIHLPREIPSVNLIPYARKLEVLYEDAFIIIVTKPNNQNCT 96

Query: 87  THSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
              +    S +   L              V RLD NT G+++    G +  +    + + 
Sbjct: 97  PSREHPHESLIEQVLYHCQEHGENINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKGNLKK 156

Query: 142 LRVYRVRFHGQVD-------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           +    V              +   + +    V     Y      +  Q    +   V L 
Sbjct: 157 IYTCLVYGKTHTSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLH 216

Query: 195 EGKNREIKKVFEFFNWKVN 213
            G+  +I+  F+     + 
Sbjct: 217 TGRTHQIRVHFQHIGHPIV 235


>gi|56477513|ref|YP_159102.1| ATP-dependent RNA helicase [Aromatoleum aromaticum EbN1]
 gi|56313556|emb|CAI08201.1| ATP-dependent RNA helicase [Aromatoleum aromaticum EbN1]
          Length = 508

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 10/99 (10%), Positives = 27/99 (27%)

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
                    S+     +P   S   +     +  + +  G        +    R+  ++ 
Sbjct: 381 AIAPVDPNESDARPPRQPRQPSRHNNANAPRQARTDRPAGRQATPPSPSRAPVRSRDADN 440

Query: 315 WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +  +   S   +  G  + +  R+          R+S  
Sbjct: 441 FGNRAPRSEVEAKRGHPDADGNRALRNAGPNGAPRSSDS 479


>gi|226942802|ref|YP_002797875.1| 30S ribosomal protein S4 [Azotobacter vinelandii DJ]
 gi|259495268|sp|C1DKN7|RS4_AZOVD RecName: Full=30S ribosomal protein S4
 gi|226717729|gb|ACO76900.1| 30S ribosomal protein S4 [Azotobacter vinelandii DJ]
          Length = 206

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++I+ + + VNG  +   +  V   D + +
Sbjct: 97  RLDNVVYRMGFGATRAESRQLISHKAITVNGQTVNIPSYQVKVGDVVAI 145


>gi|331002438|ref|ZP_08325956.1| hypothetical protein HMPREF0491_00818 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330410254|gb|EGG89688.1| hypothetical protein HMPREF0491_00818 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 263

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 25/172 (14%), Positives = 52/172 (30%), Gaps = 3/172 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  ++ + G+A SR + + +I    V V+G   ++A        +IEV G  L+   R 
Sbjct: 4   RLDILLVKRGLAESREKAKAVIMSGIVYVDGQKEDKAGQTFSENVNIEVRGNTLKYVSRG 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L            +         +       ++  G + +    +        L   
Sbjct: 64  GLKLEKAMECFDVNVENKICMDIGASS-GGFTDCMLQNGAIKVYAVDVGHGQLAWKLRND 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
             +   +   +  V+     +Q     +     I           L  + G 
Sbjct: 123 ERVTVMEKTNIRYVKPEDIGEQIDFASIDVSF-ISLSKVLPAAYNLLKENGE 173


>gi|291563464|emb|CBL42280.1| Uncharacterized conserved protein, contains S4-like domain
           [butyrate-producing bacterium SS3/4]
          Length = 251

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/58 (24%), Positives = 26/58 (44%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +    +  R+  VIA  G  SR      I  ++V VNG +    ++N+   + + + G
Sbjct: 168 ISGTVSSVRLDSVIALCGRLSRTRAASYIEDEKVSVNGAVCTNVSLNLRGGEILSIRG 225


>gi|260578649|ref|ZP_05846557.1| cytotoxin/hemolysin [Corynebacterium jeikeium ATCC 43734]
 gi|258603146|gb|EEW16415.1| cytotoxin/hemolysin [Corynebacterium jeikeium ATCC 43734]
          Length = 283

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 6  IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          + +     QR+   +    IA SR   + MI   RV VNG+L ++ A  V     I+V
Sbjct: 1  MAKRGPKLQRLDAELVARKIARSREHAQEMIKSGRVTVNGMLAKKPASGVDGNVSIKV 58


>gi|257066127|ref|YP_003152383.1| RNA-binding S4 domain-containing protein [Anaerococcus prevotii
          DSM 20548]
 gi|256798007|gb|ACV28662.1| RNA-binding S4 domain protein [Anaerococcus prevotii DSM 20548]
          Length = 81

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  A +  RR+  +      RVK+N    +     V   D +EV
Sbjct: 1  MRIDKFLKNARVIKRRQVAKEACENGRVKINEKEAK-PGSLVEEGDIVEV 49


>gi|58584920|ref|YP_198493.1| 30S ribosomal protein S4 [Wolbachia endosymbiont strain TRS of
           Brugia malayi]
 gi|75497678|sp|Q5GRX3|RS4_WOLTR RecName: Full=30S ribosomal protein S4
 gi|58419236|gb|AAW71251.1| Ribosomal protein S4 [Wolbachia endosymbiont strain TRS of Brugia
           malayi]
          Length = 204

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 26/52 (50%), Gaps = 7/52 (13%)

Query: 15  RVSKVIARAG----IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+S V+  +G    I S    +++I+ + V VN  ++   +  V   D +++
Sbjct: 94  RLSSVLYHSGLVPTIYS---AKQLISHKHVTVNDKIVNIPSYRVKPGDIVKI 142


>gi|34558005|ref|NP_907820.1| 30S ribosomal protein S4 [Wolinella succinogenes DSM 1740]
 gi|41017817|sp|Q7M8F6|RS4_WOLSU RecName: Full=30S ribosomal protein S4
 gi|34483723|emb|CAE10720.1| 30S RIBOSOMAL PROTEIN S4 [Wolinella succinogenes]
          Length = 208

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 1/68 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G A+ RR   +M++   V V+G  +   +  V+    +E+        +  
Sbjct: 99  RLDNVVYRMGFATTRRFARQMVSHGHVLVDGKRVNIPSYMVLPGQKVEIREKSKNNPQVQ 158

Query: 74  RLWLYHKP 81
           R     K 
Sbjct: 159 RSIELTKQ 166


>gi|315178982|gb|ADT85896.1| 30S ribosomal protein S4 [Vibrio furnissii NCTC 11218]
          Length = 206

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   + NV + D + +
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAILVNGKVVNVPSFNVAANDVVAI 145


>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 = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 27/240 (11%), Positives = 61/240 (25%), Gaps = 40/240 (16%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIA----QQRVKVNGILLERAAVNV-MSTDHI 60
           IV EN     +   +   G       +R+I     Q  + VNG  ++     +    D I
Sbjct: 4   IVGENEKGVILENFLRNKGF-----SKRLIRIYKWQGEILVNG--VKENVQRILQPGDVI 56

Query: 61  -----EVD--------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                EVD        G+ +   +   L +      +V         +           +
Sbjct: 57  DLILPEVDSDIAPEKMGLDIYYEDEDVLIVDKPAGVVVHPTKRYQSGTLANGVAWYFKDK 116

Query: 108 VISVGRLDINTEG--------------LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
            I      +N                 +            L     +       R    +
Sbjct: 117 GIKALIRPVNRLDKGTSGLVVFAKRPFMQYYLQIVKPMSKLYFAVVEGKMEGEGRIDLPI 176

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +   + +++ +  +G         +       + + V +  G+  +I+         + 
Sbjct: 177 SRKPQSGIERMVSEEGDRA-ITNYKVVKSSERFSLLKVKIETGRTHQIRVHLSHIGHPIV 235


>gi|300721390|ref|YP_003710661.1| 30S ribosomal subunit protein S4 [Xenorhabdus nematophila ATCC
           19061]
 gi|297627878|emb|CBJ88424.1| 30S ribosomal subunit protein S4 [Xenorhabdus nematophila ATCC
           19061]
          Length = 206

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 16/73 (21%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  +M++ + + VNG ++  A+  V   D + V     ++A   
Sbjct: 97  RLDNVVYRMGFGATRAESRQMVSHKAITVNGRVVNIASYQVSPNDVVSVREKAKKQARIK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|228993388|ref|ZP_04153304.1| 30S ribosomal protein S4 [Bacillus pseudomycoides DSM 12442]
 gi|228766456|gb|EEM15099.1| 30S ribosomal protein S4 [Bacillus pseudomycoides DSM 12442]
          Length = 200

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 93  RLDNLVYRMGLARTRRAARQLVNHGHIMVDGARVDIPSYRVKPGQTISV 141


>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 = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 29/236 (12%), Positives = 60/236 (25%), Gaps = 37/236 (15%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----- 68
           R+ K +       SR   +  I    V++NG +  R A  +   D + +D          
Sbjct: 16  RLDKYLTEVHPKYSRAFYQEHILSGLVQINGQINTRVATRLNCGDIVTIDIQEKEELLEL 75

Query: 69  ----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN- 117
                       +   L +      +V         + V   L  I  R+      +   
Sbjct: 76  LPEAIPLDKVYEDGMILVINKPRDMVVHPAPGHFHGTLVHALLHEIGERLKEEFPEEPWR 135

Query: 118 ---------TEGLLLLTNDGGLARVLELPSTQWLRVY-----------RVRFHGQVDQDK 157
                        L++T     A+ +        R+            R           
Sbjct: 136 PGIVHRLDKDTSGLIITAKTRQAKKVFSELFSTKRLKKSYLAVCIGKPRSTTIHTHISRH 195

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            N  K+  V            +    G  ++V +    G+  +++   +     + 
Sbjct: 196 QNKRKEMTVSSQGKEAVTHCQVLAFNGKLSFVALSPETGRTHQLRVHMKHLGTPIL 251


>gi|258625764|ref|ZP_05720643.1| 30S ribosomal protein S4 [Vibrio mimicus VM603]
 gi|261211127|ref|ZP_05925416.1| SSU ribosomal protein S4p (S9e) [Vibrio sp. RC341]
 gi|262170491|ref|ZP_06038169.1| SSU ribosomal protein S4p (S9e) [Vibrio mimicus MB-451]
 gi|262401859|ref|ZP_06078424.1| SSU ribosomal protein S4p (S9e) [Vibrio sp. RC586]
 gi|258582002|gb|EEW06872.1| 30S ribosomal protein S4 [Vibrio mimicus VM603]
 gi|260839628|gb|EEX66239.1| SSU ribosomal protein S4p (S9e) [Vibrio sp. RC341]
 gi|261891567|gb|EEY37553.1| SSU ribosomal protein S4p (S9e) [Vibrio mimicus MB-451]
 gi|262351831|gb|EEZ00962.1| SSU ribosomal protein S4p (S9e) [Vibrio sp. RC586]
          Length = 206

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   + NV + D + +
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAILVNGKVVNVPSFNVAANDVVAI 145


>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 = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 25/199 (12%), Positives = 54/199 (27%), Gaps = 28/199 (14%)

Query: 42  VNGILLERAAVNVMSTDHIEVD---------------GVPLRKAERTRLWLYHKPIGLVT 86
           VN   +      +M  D +E+                 + +   +   + +        T
Sbjct: 38  VNDEPVTV-RKQLMPNDILEIHLPREIPSVNLIPYARKLEVLYEDAFIIIVTKPNNQNCT 96

Query: 87  THSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
              +    S +   L              V RLD NT G+++    G +  +    + + 
Sbjct: 97  PSREHPHESLIEQVLYHCQEHGENINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKVNLKK 156

Query: 142 LRVYRVRFHGQVD-------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           +    V              +   + +    V     Y      +  Q    +   V L 
Sbjct: 157 IYTCLVYGKTHTSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLH 216

Query: 195 EGKNREIKKVFEFFNWKVN 213
            G+  +I+  F+     + 
Sbjct: 217 TGRTHQIRVHFQHIGHPIV 235


>gi|241763534|ref|ZP_04761586.1| ribosomal protein S4 [Acidovorax delafieldii 2AN]
 gi|241367265|gb|EER61605.1| ribosomal protein S4 [Acidovorax delafieldii 2AN]
          Length = 207

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V   D + V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAITVNGQSVNIPSYLVKVGDVVAV 146


>gi|227499299|ref|ZP_03929411.1| S4 RNA-binding domain protein [Anaerococcus tetradius ATCC 35098]
 gi|227218650|gb|EEI83884.1| S4 RNA-binding domain protein [Anaerococcus tetradius ATCC 35098]
          Length = 81

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  A I  RR+  +      +V +N  L +     V   D +EV
Sbjct: 1  MRIDKFLKNARIIKRRQVAKEACENGKVSINEKLAK-PGSLVEEGDLVEV 49


>gi|221064828|ref|ZP_03540933.1| ribosomal protein S4 [Comamonas testosteroni KF-1]
 gi|220709851|gb|EED65219.1| ribosomal protein S4 [Comamonas testosteroni KF-1]
          Length = 207

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +   + +V   D + +
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAITVNGQSVNIPSYSVKEGDVVAL 146


>gi|299138173|ref|ZP_07031353.1| ribosomal protein S4 [Acidobacterium sp. MP5ACTX8]
 gi|298600103|gb|EFI56261.1| ribosomal protein S4 [Acidobacterium sp. MP5ACTX8]
          Length = 210

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V  R G A SRR+  +++    V+VNG  +   +      D I +
Sbjct: 101 RLDNVCYRLGFALSRRQARQVVRHGHVQVNGRKVNIPSFQCKIGDEIAI 149


>gi|291460744|ref|ZP_06600134.1| ribosomal protein S4 [Oribacterium sp. oral taxon 078 str. F0262]
 gi|291416703|gb|EFE90422.1| ribosomal protein S4 [Oribacterium sp. oral taxon 078 str. F0262]
          Length = 212

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI R G+A +RRE  +++  + V VNG L+   +  V + D I +
Sbjct: 103 RLDSVIFRMGLARTRREARQVVGHRHVTVNGKLVNIPSYLVSAGDVIAI 151


>gi|260438189|ref|ZP_05792005.1| ribosomal protein S4 [Butyrivibrio crossotus DSM 2876]
 gi|292809379|gb|EFF68584.1| ribosomal protein S4 [Butyrivibrio crossotus DSM 2876]
          Length = 197

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 16/65 (24%), Positives = 28/65 (43%), Gaps = 1/65 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  VI R G+A +R+E  +++  + V VNG  +   +  V   D IE+           
Sbjct: 88  RLDNVIFRLGLARTRKEARQIVDHKHVLVNGKCVNIPSYLVNVGDSIEIKEKAKSSQRYK 147

Query: 74  RLWLY 78
            +   
Sbjct: 148 DILEV 152


>gi|210631179|ref|ZP_03296790.1| hypothetical protein COLSTE_00675 [Collinsella stercoris DSM 13279]
 gi|210160146|gb|EEA91117.1| hypothetical protein COLSTE_00675 [Collinsella stercoris DSM 13279]
          Length = 198

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R+E  + +      VNG  ++  +  V + D + V
Sbjct: 89  RLDNVVFRLGFARTRKEARQSVRHGHFTVNGKRVDIPSYRVKAGDVVAV 137


>gi|229543523|ref|ZP_04432583.1| ribosomal protein S4 [Bacillus coagulans 36D1]
 gi|229327943|gb|EEN93618.1| ribosomal protein S4 [Bacillus coagulans 36D1]
          Length = 200

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR+  +++    + V+G  ++  +  V     I V
Sbjct: 93  RLDNLVYRLGLARTRRQARQLVNHGHILVDGKRVDIPSYRVEPGQTIGV 141


>gi|302561675|ref|ZP_07314017.1| serine/threonine protein kinase [Streptomyces griseoflavus Tu4000]
 gi|302479293|gb|EFL42386.1| serine/threonine protein kinase [Streptomyces griseoflavus Tu4000]
          Length = 444

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/131 (11%), Positives = 32/131 (24%), Gaps = 2/131 (1%)

Query: 223 FQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDF 282
            +L  + A   + ++   +R         E      A  Y      R + +         
Sbjct: 263 MRLKEIAAREAQGLTD--VRPPAPRGAETEQPTGRLADTYPDGAQRRRQGDPGGNGTPPP 320

Query: 283 TRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
              +  + + NG + ++   +    R  + N                         P  P
Sbjct: 321 RGGRGTAPKANGSTPRRGNRSVPASRGGSRNSGSRNNASRRGGPRDTSSRSGTPSRPGTP 380

Query: 343 SKRSLRRTSAK 353
                 R S +
Sbjct: 381 RPTPASRNSTR 391


>gi|297623301|ref|YP_003704735.1| 30S ribosomal protein S4 [Truepera radiovictrix DSM 17093]
 gi|297164481|gb|ADI14192.1| ribosomal protein S4 [Truepera radiovictrix DSM 17093]
          Length = 205

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA +RR+  + +  + + VNG +++  +  V   D I V
Sbjct: 96  RLDNVVFRLGIAHTRRQARQFVTHRHILVNGKVVDVPSYRVRPGDEIAV 144


>gi|228902403|ref|ZP_04066557.1| RNA-binding S4 domain protein [Bacillus thuringiensis IBL 4222]
 gi|228966851|ref|ZP_04127895.1| RNA-binding S4 domain protein [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228792950|gb|EEM40508.1| RNA-binding S4 domain protein [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228857147|gb|EEN01653.1| RNA-binding S4 domain protein [Bacillus thuringiensis IBL 4222]
          Length = 255

 Score = 47.9 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+  I    VKVN  ++E+ +      D   V G
Sbjct: 180 RLDVMLAEMLHLSRQKVQPFIKNGLVKVNWKIVEQTSYECYPGDVFSVRG 229


>gi|228909724|ref|ZP_04073547.1| RNA-binding S4 domain protein [Bacillus thuringiensis IBL 200]
 gi|228850013|gb|EEM94844.1| RNA-binding S4 domain protein [Bacillus thuringiensis IBL 200]
          Length = 255

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+  I    VKVN  ++E+ +      D   V G
Sbjct: 180 RLDVMLAEMLHLSRQKVQPFIKNGLVKVNWKIVEQTSYECYPGDVFSVRG 229


>gi|289804412|ref|ZP_06535041.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Typhi str. AG3]
          Length = 175

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 66  RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 125

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 126 AALELAEQREKPT 138


>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 = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 31/222 (13%), Positives = 62/222 (27%), Gaps = 11/222 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M   + + EN  P+R+S  + AR    S+  V R I  Q  ++NG +    +  V   D 
Sbjct: 1   MHTFSWIAEN--PERLSSFLCARLPNHSKLTVLRSIRYQHCRINGSIERFESYKVQPGDR 58

Query: 60  IEV-----DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
           + +        P    E     +Y KP  L T          +   L    +  +   + 
Sbjct: 59  VAISIVHNQQQPSLLWEDAHSCIYDKPPYLTTEEIAKTLGRNLVHRLDRDTTGCLLFAKT 118

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL---LKKGIVIQGIC 171
               + L  L     + +          +                    L          
Sbjct: 119 QDAMQKLSDLFKQRNIHKQYITLVFGLPKQCSGTLTTFTAPKYKRCGAVLFGTTTPSQGK 178

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               + T+  +    + +      G+  +I+   +     + 
Sbjct: 179 LTITKWTVLQRYKHYSLLLCEPITGRTHQIRLHMKHLGHPIV 220


>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 = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 31/243 (12%), Positives = 64/243 (26%), Gaps = 38/243 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           V +    +RV    AR    SR  +  +I    V ++G  + RA+V V +   ++VD   
Sbjct: 6   VPDGLDGERVDVAAARMSGVSRSRISSLIEDGGVFLDGQQVSRASVRVAAGQMLDVDLCD 65

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                        G+ +   +   + +              +G S V     + F+   S
Sbjct: 66  PVATPSITPQIVEGMRIIHDDSDIVVVDKPAGVAAHPSLGWEGPSVVEHLAAAGFAISTS 125

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPST---------------------QWLRVYRVRF 149
                      L +   G +       +                           +    
Sbjct: 126 GAPERQGIVQRLDVGTSGLMVVAKSEHAYILLKQAFRDRTVDKVYLALVQGHPDPFTGTI 185

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +D  +   K  ++ G  +                + V L  G+  +I+       
Sbjct: 186 DAPIGRDHRHDW-KMAIVDGGRHSVTHYETVEAFRHATLLKVHLETGRTHQIRVHMAAIK 244

Query: 210 WKV 212
              
Sbjct: 245 HPC 247


>gi|240141242|ref|YP_002965722.1| hypothetical protein MexAM1_META1p4834 [Methylobacterium extorquens
            AM1]
 gi|240011219|gb|ACS42445.1| conserved hypothetical protein with putative ATP-dependent RNA and
            DNA helicase (N-terminal) and conserved C-terminal
            DEAD/DEAH box domain protein (C-terminal)
            [Methylobacterium extorquens AM1]
          Length = 1131

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/109 (11%), Positives = 24/109 (22%), Gaps = 1/109 (0%)

Query: 247  PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
             HL    +     P          +        D     ++N   +     + +   P  
Sbjct: 999  WHLHRPQRHTGPRPGRGQGRPEGRQDGRQEGRQDGRQDGRRNDGPRRPREDRPEGGRPAR 1058

Query: 307  RRNLASNVWMAKGIHSSFLSDSGQREENHRRS-PSFPSKRSLRRTSAKK 354
                  +    +G         G R    RR     P+         ++
Sbjct: 1059 ADGRGDSRREGQGEGGPRREHQGGRNRPDRRDENRRPNPEQRPPRRERQ 1107



 Score = 42.9 bits (99), Expect = 0.077,   Method: Composition-based stats.
 Identities = 15/103 (14%), Positives = 22/103 (21%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            R   G    E  Q              R          D     +   +   G S+++  
Sbjct: 1011 RPGRGQGRPEGRQDGRQEGRQDGRQDGRRNDGPRRPREDRPEGGRPARADGRGDSRREGQ 1070

Query: 302  ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
                 RR              +   +  QR     R P   S 
Sbjct: 1071 GEGGPRREHQGGRNRPDRRDENRRPNPEQRPPRRERQPDPDSP 1113



 Score = 37.1 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 9/103 (8%), Positives = 22/103 (21%), Gaps = 3/103 (2%)

Query: 252  EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
            E     DA    +     +  ++         R  +   +  G    ++      R++  
Sbjct: 979  EPSTEADAAAEPAAPETVEVWHLHRPQRHTGPRPGRGQGRPEGRQDGRQEGRQDGRQDGR 1038

Query: 312  SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             N               G R            +        ++
Sbjct: 1039 RNDG---PRRPREDRPEGGRPARADGRGDSRREGQGEGGPRRE 1078


>gi|119946251|ref|YP_943931.1| ribosomal protein S4 [Psychromonas ingrahamii 37]
 gi|152060918|sp|A1SXW7|RS4A_PSYIN RecName: Full=30S ribosomal protein S4 A
 gi|119864855|gb|ABM04332.1| SSU ribosomal protein S4P [Psychromonas ingrahamii 37]
          Length = 206

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 15/73 (20%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + V VNG ++   + NV ++D I +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKAVLVNGKVVNIPSFNVKASDVIAIREKAKKQSRIG 156

Query: 74  RLWLYHKPIGLVT 86
                     + T
Sbjct: 157 AALEIAGQREVPT 169


>gi|152986119|ref|YP_001346247.1| 30S ribosomal protein S4 [Pseudomonas aeruginosa PA7]
 gi|171460894|sp|A6UZL2|RS4_PSEA7 RecName: Full=30S ribosomal protein S4
 gi|150961277|gb|ABR83302.1| ribosomal protein S4 [Pseudomonas aeruginosa PA7]
          Length = 206

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V + D + +
Sbjct: 97  RLDNVVYRMGFGSTRAESRQLVSHKAITVNGQTVNIPSYQVKAGDVVAI 145


>gi|325104842|ref|YP_004274496.1| SSU ribosomal protein S4P [Pedobacter saltans DSM 12145]
 gi|324973690|gb|ADY52674.1| SSU ribosomal protein S4P [Pedobacter saltans DSM 12145]
          Length = 202

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA+ R    ++++ + + VNG L+   + +V   D IEV
Sbjct: 94  RLDNVVYRLGIATTRSAARQLVSHRHILVNGELVNIPSFSVRPGDVIEV 142


>gi|294851390|ref|ZP_06792063.1| translation initiation factor IF-2 [Brucella sp. NVSL 07-0026]
 gi|294819979|gb|EFG36978.1| translation initiation factor IF-2 [Brucella sp. NVSL 07-0026]
          Length = 814

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/116 (12%), Positives = 29/116 (25%), Gaps = 2/116 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R + +  +RE +        +    A   +     R+         +   + +  + +K 
Sbjct: 16  RALEEAQIRE-VEERARAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKA 74

Query: 294 GLSKQKKLATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                K++  P  R     +   A  G                   P   S R   
Sbjct: 75  EEEAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAP 130



 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 11/121 (9%), Positives = 28/121 (23%), Gaps = 1/121 (0%)

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           L     REV ++  R         E           S     +    +    +   + ++
Sbjct: 18  LEEAQIREVEERA-RAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKAEE 76

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            ++++    + +       R           G           R +     P+     + 
Sbjct: 77  EAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAPIIADAA 136

Query: 348 R 348
            
Sbjct: 137 P 137


>gi|264680561|ref|YP_003280471.1| ribosomal protein S4 [Comamonas testosteroni CNB-2]
 gi|299532875|ref|ZP_07046262.1| 30S ribosomal protein S4 [Comamonas testosteroni S44]
 gi|262211077|gb|ACY35175.1| ribosomal protein S4 [Comamonas testosteroni CNB-2]
 gi|298719099|gb|EFI60069.1| 30S ribosomal protein S4 [Comamonas testosteroni S44]
          Length = 207

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +   + +V   D + +
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAITVNGQSVNIPSFSVKEGDVVAL 146


>gi|118586622|ref|ZP_01544062.1| 30S ribosomal protein S4 [Oenococcus oeni ATCC BAA-1163]
 gi|118432937|gb|EAV39663.1| 30S ribosomal protein S4 [Oenococcus oeni ATCC BAA-1163]
          Length = 250

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+AS R +  +++    + V+G  +   +  V     I V
Sbjct: 141 RLDSVVFRLGLASTRPQARQLVNHGHILVDGKRVTIPSYEVKPGQIISV 189


>gi|290890943|ref|ZP_06554007.1| hypothetical protein AWRIB429_1397 [Oenococcus oeni AWRIB429]
 gi|290479342|gb|EFD88002.1| hypothetical protein AWRIB429_1397 [Oenococcus oeni AWRIB429]
          Length = 250

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+AS R +  +++    + V+G  +   +  V     I V
Sbjct: 141 RLDSVVFRLGLASTRPQARQLVNHGHILVDGKRVTIPSYEVKPGQIISV 189


>gi|242237883|ref|YP_002986064.1| 30S ribosomal protein S4 [Dickeya dadantii Ech703]
 gi|242129940|gb|ACS84242.1| ribosomal protein S4 [Dickeya dadantii Ech703]
          Length = 206

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 30/73 (41%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  +++  + V VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVGHKAVMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>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 = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 33/240 (13%), Positives = 62/240 (25%), Gaps = 40/240 (16%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE---------- 61
            +R+ K +A+     SR  ++  I  QRV+V+G   +     V     IE          
Sbjct: 67  GERLDKALAQLFPEFSRSRLQSWIEAQRVRVDGEPAKV-RQPVPLGATIELVPDLLPEQL 125

Query: 62  -VDGVP----LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVIS 110
                P    +   +   + +      +V   +     + +   L           R   
Sbjct: 126 AFTPEPVPLAIVYEDEALVVIDKPAGLVVHPAAGNWNGTLLNGLLHRYGEAAAGLPRAGI 185

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-- 168
           V RLD  T GL+++         L           R              +   I     
Sbjct: 186 VHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGRTPASGTIDAPIGRDPR 245

Query: 169 ---------GICYGDMQVT------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                    G      +        +  Q    + +   L  G+  +I+         + 
Sbjct: 246 ERTRMAVVTGASGKPARTHFRTVDSVLWQNQPVSAIQCDLETGRTHQIRVHCAHLGHPLL 305


>gi|259909976|ref|YP_002650332.1| 30S ribosomal protein S4 [Erwinia pyrifoliae Ep1/96]
 gi|292489825|ref|YP_003532715.1| 30S ribosomal protein S4 [Erwinia amylovora CFBP1430]
 gi|292900867|ref|YP_003540236.1| 30S ribosomal protein S4 [Erwinia amylovora ATCC 49946]
 gi|224965598|emb|CAX57130.1| 30S ribosomal protein S4 [Erwinia pyrifoliae Ep1/96]
 gi|283480075|emb|CAY75991.1| 30S ribosomal protein S4 [Erwinia pyrifoliae DSM 12163]
 gi|291200715|emb|CBJ47848.1| 30S ribosomal subunit protein S4 [Erwinia amylovora ATCC 49946]
 gi|291555262|emb|CBA23541.1| 30S ribosomal protein S4 [Erwinia amylovora CFBP1430]
 gi|312174007|emb|CBX82260.1| 30S ribosomal protein S4 [Erwinia amylovora ATCC BAA-2158]
          Length = 206

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKSIMVNGRVVSIASYQVTPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|119947102|ref|YP_944782.1| ribosomal protein S4 [Psychromonas ingrahamii 37]
 gi|152060920|sp|A1T0B8|RS4B_PSYIN RecName: Full=30S ribosomal protein S4 B
 gi|119865706|gb|ABM05183.1| SSU ribosomal protein S4P [Psychromonas ingrahamii 37]
          Length = 206

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 15/73 (20%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + V VNG ++   + NV ++D I +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKAVLVNGKVVNIPSFNVKASDVIAIREKAKKQSRIG 156

Query: 74  RLWLYHKPIGLVT 86
                     + T
Sbjct: 157 AALEIAGQREVPT 169


>gi|116628655|ref|YP_821274.1| 30S ribosomal protein S4 [Streptococcus thermophilus LMD-9]
 gi|90101730|sp|Q5LXK5|RS4_STRT1 RecName: Full=30S ribosomal protein S4
 gi|90101731|sp|Q5M255|RS4_STRT2 RecName: Full=30S ribosomal protein S4
 gi|122266751|sp|Q03I94|RS4_STRTD RecName: Full=30S ribosomal protein S4
 gi|116101932|gb|ABJ67078.1| SSU ribosomal protein S4P [Streptococcus thermophilus LMD-9]
 gi|312279309|gb|ADQ63966.1| 30S ribosomal protein S4 [Streptococcus thermophilus ND03]
          Length = 203

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVEVGQVISV 142


>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 = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 28/252 (11%), Positives = 59/252 (23%), Gaps = 41/252 (16%)

Query: 1   MKDKN----IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILL--------- 47
           M ++      V E     RV   +++    SR     +     V V+G ++         
Sbjct: 1   MNNRQSRTLPVPEGLAGMRVDAALSKLLGISRTVAAELATAGDVSVDGAVVGKSERLVAD 60

Query: 48  -------ERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
                     A  +M  + I V G+ +  ++   + +              +G + V   
Sbjct: 61  SMLDVLLPEPAAPLMPKEEI-VPGLDILYSDDDVIAVNKPVGVAAHPTVGWEGPTVVGGL 119

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD---- 156
             + F    S           L +   G +           L+                 
Sbjct: 120 AAAGFRISTSGPPERKGIVQRLDVGTSGVMVVAASERGYTVLKRAFRDRTVDKTYHALVQ 179

Query: 157 -KLNLLKKGIVIQGICYGDMQVTLDTQKGSNA---------------WVTVGLREGKNRE 200
              + L   I      +                               + + L  G+  +
Sbjct: 180 GHPDPLTGTIEAPIGRHPSAGWRFAVTTEGKHAVTHYETLEAFQEATLLKIHLETGRTHQ 239

Query: 201 IKKVFEFFNWKV 212
           I+  F   +   
Sbjct: 240 IRVHFSALHHPC 251


>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 = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 23/221 (10%), Positives = 62/221 (28%), Gaps = 28/221 (12%)

Query: 33  RMIAQQRVKVNGILLERAAV------------------------NVMSTDHIEVDGVPLR 68
           +++ + R++VN  + ++  +                         V   D+I V   P  
Sbjct: 34  KLLRKGRIRVNFEVAQKGQILQFGDLISFDIEEKYLDQKKVEISKVYEDDNIIVIDKPYG 93

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                     +  +  +  +   +    +   L    S ++ + +       +L   +  
Sbjct: 94  IPSHPDTNNEYSVVNWIEDNYSGNQLPALCHRLDRNTSGLMIIAKNRQVLNEMLKYMSRR 153

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSN 186
            + +     + +            + +D          +    Y ++  +  +   K   
Sbjct: 154 AIKKKYLCITKKVDLPKSGVLVHYLKKDSKKSKVYISDLPAEGYSEIVTRYKIIRGKDDL 213

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
             V V +  GK  +I+         +  L    YG + L  
Sbjct: 214 LLVDVEIETGKTHQIRSQLAHVGLCI--LGDSKYGDWALNK 252


>gi|75763514|ref|ZP_00743226.1| RNA binding protein [Bacillus thuringiensis serovar israelensis
           ATCC 35646]
 gi|74488996|gb|EAO52500.1| RNA binding protein [Bacillus thuringiensis serovar israelensis
           ATCC 35646]
          Length = 255

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+  I    VKVN  ++E+ +      D   V G
Sbjct: 180 RLDVMLAEMLHLSRQKVQPFIKNGLVKVNWKIVEQTSYECYPGDVFSVRG 229


>gi|329728300|gb|EGG64739.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21172]
          Length = 258

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 25/199 (12%), Positives = 54/199 (27%), Gaps = 28/199 (14%)

Query: 42  VNGILLERAAVNVMSTDHIEVD---------------GVPLRKAERTRLWLYHKPIGLVT 86
           VN   +      +M  D +E+                 + +   +   + +        T
Sbjct: 12  VNDEPVTV-RKQLMPNDILEIHLPREIPSVNLIPYARKLEVLYEDAFIIIVTKPNNQNCT 70

Query: 87  THSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
              +    S +   L              V RLD NT G+++    G +  +    + + 
Sbjct: 71  PSREHLHESLIEQVLYHCQEHGENINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKVNLKK 130

Query: 142 LRVYRVRFHGQVD-------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           +    V              +   + +    V     Y      +  Q    +   V L 
Sbjct: 131 IYTCLVYGKTHTSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLH 190

Query: 195 EGKNREIKKVFEFFNWKVN 213
            G+  +I+  F+     + 
Sbjct: 191 TGRTHQIRVHFQHIGHPIV 209


>gi|296163296|ref|ZP_06846057.1| ribosomal protein S4 [Burkholderia sp. Ch1-1]
 gi|295886435|gb|EFG66292.1| ribosomal protein S4 [Burkholderia sp. Ch1-1]
          Length = 207

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG++    ++ V + D + V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAITVNGVVSNIPSMQVKAGDVVAV 146


>gi|256832356|ref|YP_003161083.1| hemolysin A [Jonesia denitrificans DSM 20603]
 gi|256685887|gb|ACV08780.1| hemolysin A [Jonesia denitrificans DSM 20603]
          Length = 310

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 1/59 (1%)

Query: 7  VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          +      +R+   +   G+A SR    R+I+   V VNG  + + A  V + D I + G
Sbjct: 1  MTSEQKSRRLDVTVVMRGLAPSRNRAARIISDGAVFVNGRSITKPAWPVHNADTITLKG 59


>gi|218899051|ref|YP_002447462.1| S4 domain protein [Bacillus cereus G9842]
 gi|218545304|gb|ACK97698.1| S4 domain protein [Bacillus cereus G9842]
          Length = 255

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+  I    VKVN  ++E+ +      D   V G
Sbjct: 180 RLDVMLAEMLHLSRQKVQPFIKNGLVKVNWKIVEQTSYECYPGDVFSVRG 229


>gi|153008083|ref|YP_001369298.1| translation initiation factor IF-2 [Ochrobactrum anthropi ATCC
           49188]
 gi|166232567|sp|A6WWW5|IF2_OCHA4 RecName: Full=Translation initiation factor IF-2
 gi|151559971|gb|ABS13469.1| translation initiation factor IF-2 [Ochrobactrum anthropi ATCC
           49188]
          Length = 964

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 16/116 (13%), Positives = 31/116 (26%), Gaps = 1/116 (0%)

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           L     REV ++  R         E           S     +    +    D   + ++
Sbjct: 165 LEEAQVREVEERA-RAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEADARRKAEE 223

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
            ++++    + +       R     N     G         G R +     P+ PS
Sbjct: 224 EAAKRMPQPEARTERRDDARPAPQGNRPQQAGRPQGNRPPQGGRPQQGGPRPAAPS 279



 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 13/118 (11%), Positives = 30/118 (25%), Gaps = 2/118 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R + +  +RE +        +    A   +     R+         +   + + ++ +K 
Sbjct: 163 RALEEAQVRE-VEERARAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEADARRKA 221

Query: 294 GLSKQKKLATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                K++  P  R     +   A  G                   P     R    +
Sbjct: 222 EEEAAKRMPQPEARTERRDDARPAPQGNRPQQAGRPQGNRPPQGGRPQQGGPRPAAPS 279



 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 8/123 (6%), Positives = 27/123 (21%), Gaps = 2/123 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R   +   R +                   ++   +        +P    R ++    + 
Sbjct: 185 RRAEEDARRAKEREESARRQAEEEARLKAEADARRKAEEEAAKRMPQPEARTERRDDARP 244

Query: 294 GLSKQKKLATPVHRRNLASNVWMA--KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                +       + N           G   +  S +       +  P    ++++    
Sbjct: 245 APQGNRPQQAGRPQGNRPPQGGRPQQGGPRPAAPSLADAAPIPGKPLPQSQLRKTVASDD 304

Query: 352 AKK 354
             +
Sbjct: 305 DDR 307


>gi|144900834|emb|CAM77698.1| Hemolysin A [Magnetospirillum gryphiswaldense MSR-1]
          Length = 251

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+ +++   G+A SR   + ++    V V G  +++A   V     IE+ G 
Sbjct: 5  VRIDQLLVDRGLAESRARAQALVMAGLVIVGGKKIDKAGTQVAEDAGIELKGQ 57


>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 = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 31/240 (12%), Positives = 67/240 (27%), Gaps = 34/240 (14%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           I+      +R+   I       SR ++++ + +  + VNG    +    V+  + +E++ 
Sbjct: 15  IMHPKDAGKRIDVAINEQFEQFSRAQIQKWLKEGSITVNGR-ATKPKHIVLGDEEVEINI 73

Query: 65  VPLRKAERTRLWLY--------------HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI- 109
             L   E     +                    +V   +     +     L     +   
Sbjct: 74  ELLPTNEWIAEDINLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNALLHRYKDQDKL 133

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVLELP------------STQWLRVYRVRFHGQV 153
                V RLD +T GL++          L                 +     +   +  +
Sbjct: 134 PRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGEIYKQGTINQPI 193

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +D  N  K  I  +G        T          +   L  G+  +I+   +     + 
Sbjct: 194 GRDPTNRTKMAINYRGKEA-ITHYTSIEVYDGFTLIECQLETGRTHQIRVHMKSIKHPLV 252


>gi|302871273|ref|YP_003839909.1| RNA-binding S4 domain protein [Caldicellulosiruptor obsidiansis
          OB47]
 gi|302574132|gb|ADL41923.1| RNA-binding S4 domain protein [Caldicellulosiruptor obsidiansis
          OB47]
          Length = 80

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   +      RV VNG + +  + ++   D IEV
Sbjct: 1  MRIDKYLKVSRIIKRRTLAQEACEAGRVFVNGKVAK-PSTDIKVGDVIEV 49


>gi|258622736|ref|ZP_05717754.1| 30S ribosomal protein S4 [Vibrio mimicus VM573]
 gi|262166593|ref|ZP_06034330.1| SSU ribosomal protein S4p (S9e) [Vibrio mimicus VM223]
 gi|258584924|gb|EEW09655.1| 30S ribosomal protein S4 [Vibrio mimicus VM573]
 gi|262026309|gb|EEY44977.1| SSU ribosomal protein S4p (S9e) [Vibrio mimicus VM223]
          Length = 202

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   + NV + D + +
Sbjct: 93  RLDNVVYRMGFGATRAEARQLVSHKAILVNGKVVNVPSFNVAANDVVAI 141


>gi|256371920|ref|YP_003109744.1| hemolysin A [Acidimicrobium ferrooxidans DSM 10331]
 gi|256008504|gb|ACU54071.1| hemolysin A [Acidimicrobium ferrooxidans DSM 10331]
          Length = 249

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ + +   G+A SR    R+IA+ RV VN      AA  V  +D + V
Sbjct: 4  VRLDRALVAGGLARSRSHAARLIAEGRVLVNRAPALSAARLVAPSDVLSV 53


>gi|228478099|ref|ZP_04062710.1| ribosomal protein S4 [Streptococcus salivarius SK126]
 gi|312864106|ref|ZP_07724341.1| ribosomal protein S4 [Streptococcus vestibularis F0396]
 gi|322374008|ref|ZP_08048542.1| ribosomal protein S4 [Streptococcus sp. C150]
 gi|322515823|ref|ZP_08068767.1| 30S ribosomal protein S4 [Streptococcus vestibularis ATCC 49124]
 gi|228250279|gb|EEK09532.1| ribosomal protein S4 [Streptococcus salivarius SK126]
 gi|311100338|gb|EFQ58546.1| ribosomal protein S4 [Streptococcus vestibularis F0396]
 gi|321276974|gb|EFX54045.1| ribosomal protein S4 [Streptococcus sp. C150]
 gi|322125709|gb|EFX97031.1| 30S ribosomal protein S4 [Streptococcus vestibularis ATCC 49124]
          Length = 203

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVEVGQVISV 142


>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 = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 25/199 (12%), Positives = 54/199 (27%), Gaps = 28/199 (14%)

Query: 42  VNGILLERAAVNVMSTDHIEVD---------------GVPLRKAERTRLWLYHKPIGLVT 86
           VN   +      +M  D +E+                 + +   +   + +        T
Sbjct: 38  VNDEPVTV-RKQLMPNDILEIHLPREIPSVNLIPYARKLEVLYEDAFIIIVTKPNNQNCT 96

Query: 87  THSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
              +    S +   L              V RLD NT G+++    G +  +    + + 
Sbjct: 97  PSREHLHESLIEQVLYHCQEHGENINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKVNLKK 156

Query: 142 LRVYRVRFHGQVD-------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           +    V              +   + +    V     Y      +  Q    +   V L 
Sbjct: 157 IYTCLVYGKTHTSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLH 216

Query: 195 EGKNREIKKVFEFFNWKVN 213
            G+  +I+  F+     + 
Sbjct: 217 TGRTHQIRVHFQHIGHPIV 235


>gi|120597013|ref|YP_961587.1| 30S ribosomal protein S4 [Shewanella sp. W3-18-1]
 gi|146294817|ref|YP_001185241.1| 30S ribosomal protein S4 [Shewanella putrefaciens CN-32]
 gi|152112262|sp|A1RED8|RS4_SHESW RecName: Full=30S ribosomal protein S4
 gi|172046874|sp|A4YBV9|RS4_SHEPC RecName: Full=30S ribosomal protein S4
 gi|110812360|gb|ABG91716.1| ribosomal protein S4 [Shewanella putrefaciens 200]
 gi|120557106|gb|ABM23033.1| SSU ribosomal protein S4P [Shewanella sp. W3-18-1]
 gi|145566507|gb|ABP77442.1| SSU ribosomal protein S4P [Shewanella putrefaciens CN-32]
 gi|319424604|gb|ADV52678.1| ribosomal protein S4 [Shewanella putrefaciens 200]
          Length = 206

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + V VNG ++   +  V + D + +
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKSVMVNGRVVNIPSFKVSANDVVSI 145


>gi|238921420|ref|YP_002934935.1| 30S ribosomal protein S4 [Edwardsiella ictaluri 93-146]
 gi|269140550|ref|YP_003297251.1| 30S ribosomal protein S4 [Edwardsiella tarda EIB202]
 gi|294638030|ref|ZP_06716290.1| ribosomal protein S4 [Edwardsiella tarda ATCC 23685]
 gi|259495277|sp|C5BF28|RS4_EDWI9 RecName: Full=30S ribosomal protein S4
 gi|238870989|gb|ACR70700.1| 30S ribosomal protein S4 (BS4) [Edwardsiella ictaluri 93-146]
 gi|267986211|gb|ACY86040.1| 30S ribosomal protein S4 [Edwardsiella tarda EIB202]
 gi|291088822|gb|EFE21383.1| ribosomal protein S4 [Edwardsiella tarda ATCC 23685]
 gi|304560335|gb|ADM42999.1| SSU ribosomal protein S4p (S9e) [Edwardsiella tarda FL6-60]
          Length = 206

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + V     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAIVVNGRVVNIASYQVSPNDVVSVREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|217967932|ref|YP_002353438.1| S4 domain protein YaaA [Dictyoglomus turgidum DSM 6724]
 gi|217337031|gb|ACK42824.1| S4 domain protein YaaA [Dictyoglomus turgidum DSM 6724]
          Length = 71

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 10/37 (27%), Positives = 19/37 (51%)

Query: 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
          + + +I   +VKVNG +    +  +   D +E+DG  
Sbjct: 28 QAKNLILAGKVKVNGEIELHRSRKLKHGDVVEIDGEK 64


>gi|84394604|ref|ZP_00993306.1| 30S ribosomal protein S4 [Vibrio splendidus 12B01]
 gi|84374778|gb|EAP91723.1| 30S ribosomal protein S4 [Vibrio splendidus 12B01]
          Length = 206

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + V VNG ++   +  V + D + +
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKSVLVNGKVVNVPSFKVAANDVVSI 145


>gi|15803823|ref|NP_289857.1| 30S ribosomal protein S4 [Escherichia coli O157:H7 EDL933]
 gi|15833415|ref|NP_312188.1| 30S ribosomal protein S4 [Escherichia coli O157:H7 str. Sakai]
 gi|16131175|ref|NP_417755.1| 30S ribosomal subunit protein S4 [Escherichia coli str. K-12
           substr. MG1655]
 gi|26249881|ref|NP_755921.1| 30S ribosomal protein S4 [Escherichia coli CFT073]
 gi|74313815|ref|YP_312234.1| 30S ribosomal protein S4 [Shigella sonnei Ss046]
 gi|82545659|ref|YP_409606.1| 30S ribosomal protein S4 [Shigella boydii Sb227]
 gi|82778592|ref|YP_404941.1| 30S ribosomal protein S4 [Shigella dysenteriae Sd197]
 gi|89110714|ref|AP_004494.1| 30S ribosomal subunit protein S4 [Escherichia coli str. K-12
           substr. W3110]
 gi|91212723|ref|YP_542709.1| 30S ribosomal protein S4 [Escherichia coli UTI89]
 gi|110643535|ref|YP_671265.1| 30S ribosomal protein S4 [Escherichia coli 536]
 gi|110807144|ref|YP_690664.1| 30S ribosomal protein S4 [Shigella flexneri 5 str. 8401]
 gi|117625578|ref|YP_858901.1| 30S ribosomal protein S4 [Escherichia coli APEC O1]
 gi|157148871|ref|YP_001456190.1| 30S ribosomal protein S4 [Citrobacter koseri ATCC BAA-895]
 gi|157156792|ref|YP_001464764.1| 30S ribosomal protein S4 [Escherichia coli E24377A]
 gi|157162770|ref|YP_001460088.1| 30S ribosomal protein S4 [Escherichia coli HS]
 gi|161486375|ref|NP_839574.2| 30S ribosomal protein S4 [Shigella flexneri 2a str. 2457T]
 gi|168752255|ref|ZP_02777277.1| ribosomal protein S4 [Escherichia coli O157:H7 str. EC4113]
 gi|168758524|ref|ZP_02783531.1| ribosomal protein S4 [Escherichia coli O157:H7 str. EC4401]
 gi|168764979|ref|ZP_02789986.1| ribosomal protein S4 [Escherichia coli O157:H7 str. EC4501]
 gi|168769158|ref|ZP_02794165.1| ribosomal protein S4 [Escherichia coli O157:H7 str. EC4486]
 gi|168777846|ref|ZP_02802853.1| ribosomal protein S4 [Escherichia coli O157:H7 str. EC4196]
 gi|168783864|ref|ZP_02808871.1| ribosomal protein S4 [Escherichia coli O157:H7 str. EC4076]
 gi|168786186|ref|ZP_02811193.1| ribosomal protein S4 [Escherichia coli O157:H7 str. EC869]
 gi|168802725|ref|ZP_02827732.1| ribosomal protein S4 [Escherichia coli O157:H7 str. EC508]
 gi|170018468|ref|YP_001723422.1| 30S ribosomal protein S4 [Escherichia coli ATCC 8739]
 gi|170082816|ref|YP_001732136.1| 30S ribosomal subunit protein S4 [Escherichia coli str. K-12
           substr. DH10B]
 gi|170683332|ref|YP_001745558.1| 30S ribosomal protein S4 [Escherichia coli SMS-3-5]
 gi|170769606|ref|ZP_02904059.1| ribosomal protein S4 [Escherichia albertii TW07627]
 gi|187732648|ref|YP_001881981.1| 30S ribosomal protein S4 [Shigella boydii CDC 3083-94]
 gi|188495865|ref|ZP_03003135.1| ribosomal protein S4 [Escherichia coli 53638]
 gi|191174447|ref|ZP_03035948.1| ribosomal protein S4 [Escherichia coli F11]
 gi|193066487|ref|ZP_03047531.1| ribosomal protein S4 [Escherichia coli E22]
 gi|193071545|ref|ZP_03052454.1| ribosomal protein S4 [Escherichia coli E110019]
 gi|194430280|ref|ZP_03062775.1| ribosomal protein S4 [Escherichia coli B171]
 gi|194435081|ref|ZP_03067319.1| ribosomal protein S4 [Shigella dysenteriae 1012]
 gi|194439993|ref|ZP_03072051.1| ribosomal protein S4 [Escherichia coli 101-1]
 gi|195939844|ref|ZP_03085226.1| 30S ribosomal protein S4 [Escherichia coli O157:H7 str. EC4024]
 gi|208806540|ref|ZP_03248877.1| ribosomal protein S4 [Escherichia coli O157:H7 str. EC4206]
 gi|208812921|ref|ZP_03254250.1| ribosomal protein S4 [Escherichia coli O157:H7 str. EC4045]
 gi|208819506|ref|ZP_03259826.1| ribosomal protein S4 [Escherichia coli O157:H7 str. EC4042]
 gi|209396300|ref|YP_002272752.1| ribosomal protein S4 [Escherichia coli O157:H7 str. EC4115]
 gi|209920762|ref|YP_002294846.1| 30S ribosomal protein S4 [Escherichia coli SE11]
 gi|215488596|ref|YP_002331027.1| 30S ribosomal protein S4 [Escherichia coli O127:H6 str. E2348/69]
 gi|217325090|ref|ZP_03441174.1| ribosomal protein S4 [Escherichia coli O157:H7 str. TW14588]
 gi|218550572|ref|YP_002384363.1| 30S ribosomal protein S4 [Escherichia fergusonii ATCC 35469]
 gi|218555854|ref|YP_002388767.1| 30S ribosomal protein S4 [Escherichia coli IAI1]
 gi|218560358|ref|YP_002393271.1| 30S ribosomal protein S4 [Escherichia coli S88]
 gi|218691583|ref|YP_002399795.1| 30S ribosomal protein S4 [Escherichia coli ED1a]
 gi|218696989|ref|YP_002404656.1| 30S ribosomal protein S4 [Escherichia coli 55989]
 gi|218702059|ref|YP_002409688.1| 30S ribosomal protein S4 [Escherichia coli IAI39]
 gi|218706904|ref|YP_002414423.1| 30S ribosomal protein S4 [Escherichia coli UMN026]
 gi|227883428|ref|ZP_04001233.1| 30S ribosomal protein S4 [Escherichia coli 83972]
 gi|237703026|ref|ZP_04533507.1| 30S ribosomal subunit protein S4 [Escherichia sp. 3_2_53FAA]
 gi|238902387|ref|YP_002928183.1| 30S ribosomal subunit protein S4 [Escherichia coli BW2952]
 gi|253771880|ref|YP_003034711.1| 30S ribosomal protein S4 [Escherichia coli 'BL21-Gold(DE3)pLysS
           AG']
 gi|254038457|ref|ZP_04872513.1| ribosomal protein S4 [Escherichia sp. 1_1_43]
 gi|254163224|ref|YP_003046332.1| 30S ribosomal protein S4 [Escherichia coli B str. REL606]
 gi|254795233|ref|YP_003080070.1| 30S ribosomal protein S4 [Escherichia coli O157:H7 str. TW14359]
 gi|256020655|ref|ZP_05434520.1| 30S ribosomal protein S4 [Shigella sp. D9]
 gi|256025976|ref|ZP_05439841.1| 30S ribosomal protein S4 [Escherichia sp. 4_1_40B]
 gi|260846094|ref|YP_003223872.1| 30S ribosomal subunit protein S4 [Escherichia coli O103:H2 str.
           12009]
 gi|260857417|ref|YP_003231308.1| 30S ribosomal subunit protein S4 [Escherichia coli O26:H11 str.
           11368]
 gi|260870039|ref|YP_003236441.1| 30S ribosomal subunit protein S4 [Escherichia coli O111:H- str.
           11128]
 gi|261224601|ref|ZP_05938882.1| 30S ribosomal subunit protein S4 [Escherichia coli O157:H7 str.
           FRIK2000]
 gi|261254505|ref|ZP_05947038.1| 30S ribosomal subunit protein S4 [Escherichia coli O157:H7 str.
           FRIK966]
 gi|291284654|ref|YP_003501472.1| 30S ribosomal protein S4 [Escherichia coli O55:H7 str. CB9615]
 gi|293406893|ref|ZP_06650817.1| rpsD [Escherichia coli FVEC1412]
 gi|293412715|ref|ZP_06655383.1| 30S ribosomal protein S4 [Escherichia coli B354]
 gi|293416715|ref|ZP_06659352.1| 30S ribosomal protein S4 [Escherichia coli B185]
 gi|293453615|ref|ZP_06664034.1| 30S ribosomal protein S4 [Escherichia coli B088]
 gi|297517820|ref|ZP_06936206.1| 30S ribosomal protein S4 [Escherichia coli OP50]
 gi|298382634|ref|ZP_06992229.1| small subunit ribosomal protein S4 [Escherichia coli FVEC1302]
 gi|300815493|ref|ZP_07095718.1| ribosomal protein S4 [Escherichia coli MS 107-1]
 gi|300822900|ref|ZP_07103036.1| ribosomal protein S4 [Escherichia coli MS 119-7]
 gi|300896645|ref|ZP_07115161.1| ribosomal protein S4 [Escherichia coli MS 198-1]
 gi|300903545|ref|ZP_07121467.1| ribosomal protein S4 [Escherichia coli MS 84-1]
 gi|300918271|ref|ZP_07134875.1| ribosomal protein S4 [Escherichia coli MS 115-1]
 gi|300921894|ref|ZP_07138050.1| ribosomal protein S4 [Escherichia coli MS 182-1]
 gi|300932190|ref|ZP_07147469.1| ribosomal protein S4 [Escherichia coli MS 187-1]
 gi|300935295|ref|ZP_07150305.1| ribosomal protein S4 [Escherichia coli MS 21-1]
 gi|300946519|ref|ZP_07160784.1| ribosomal protein S4 [Escherichia coli MS 116-1]
 gi|300954829|ref|ZP_07167255.1| ribosomal protein S4 [Escherichia coli MS 175-1]
 gi|300973976|ref|ZP_07172383.1| ribosomal protein S4 [Escherichia coli MS 200-1]
 gi|300979869|ref|ZP_07174745.1| ribosomal protein S4 [Escherichia coli MS 45-1]
 gi|301018838|ref|ZP_07183082.1| ribosomal protein S4 [Escherichia coli MS 69-1]
 gi|301046068|ref|ZP_07193246.1| ribosomal protein S4 [Escherichia coli MS 185-1]
 gi|301305506|ref|ZP_07211598.1| ribosomal protein S4 [Escherichia coli MS 124-1]
 gi|301325136|ref|ZP_07218670.1| ribosomal protein S4 [Escherichia coli MS 78-1]
 gi|301643883|ref|ZP_07243914.1| ribosomal protein S4 [Escherichia coli MS 146-1]
 gi|306816361|ref|ZP_07450499.1| 30S ribosomal protein S4 [Escherichia coli NC101]
 gi|307139979|ref|ZP_07499335.1| 30S ribosomal protein S4 [Escherichia coli H736]
 gi|307315125|ref|ZP_07594708.1| ribosomal protein S4 [Escherichia coli W]
 gi|309794572|ref|ZP_07688994.1| ribosomal protein S4 [Escherichia coli MS 145-7]
 gi|331643992|ref|ZP_08345121.1| ribosomal protein S4 [Escherichia coli H736]
 gi|331649093|ref|ZP_08350179.1| ribosomal protein S4 [Escherichia coli M605]
 gi|331654889|ref|ZP_08355888.1| ribosomal protein S4 [Escherichia coli M718]
 gi|331659586|ref|ZP_08360524.1| ribosomal protein S4 [Escherichia coli TA206]
 gi|331664909|ref|ZP_08365810.1| ribosomal protein S4 [Escherichia coli TA143]
 gi|331670125|ref|ZP_08370964.1| ribosomal protein S4 [Escherichia coli TA271]
 gi|331674802|ref|ZP_08375559.1| ribosomal protein S4 [Escherichia coli TA280]
 gi|331679365|ref|ZP_08380035.1| ribosomal protein S4 [Escherichia coli H591]
 gi|331684938|ref|ZP_08385524.1| ribosomal protein S4 [Escherichia coli H299]
 gi|332281851|ref|ZP_08394264.1| 30S ribosomal subunit protein S4 [Shigella sp. D9]
 gi|62288978|sp|P0A7V8|RS4_ECOLI RecName: Full=30S ribosomal protein S4
 gi|62288979|sp|P0A7V9|RS4_ECOL6 RecName: Full=30S ribosomal protein S4
 gi|62288980|sp|P0A7W0|RS4_ECO57 RecName: Full=30S ribosomal protein S4
 gi|90101715|sp|Q31VY0|RS4_SHIBS RecName: Full=30S ribosomal protein S4
 gi|90101716|sp|Q32B55|RS4_SHIDS RecName: Full=30S ribosomal protein S4
 gi|90101726|sp|Q3YWW3|RS4_SHISS RecName: Full=30S ribosomal protein S4
 gi|122957945|sp|Q0TCG5|RS4_ECOL5 RecName: Full=30S ribosomal protein S4
 gi|123047859|sp|Q0T006|RS4_SHIF8 RecName: Full=30S ribosomal protein S4
 gi|123387796|sp|Q1R636|RS4_ECOUT RecName: Full=30S ribosomal protein S4
 gi|152060947|sp|A1AGI7|RS4_ECOK1 RecName: Full=30S ribosomal protein S4
 gi|171855222|sp|A7ZSI5|RS4_ECO24 RecName: Full=30S ribosomal protein S4
 gi|172044361|sp|A8A5A1|RS4_ECOHS RecName: Full=30S ribosomal protein S4
 gi|172045593|sp|A8AQJ1|RS4_CITK8 RecName: Full=30S ribosomal protein S4
 gi|189045379|sp|B1IQ03|RS4_ECOLC RecName: Full=30S ribosomal protein S4
 gi|226695077|sp|B2U2R5|RS4_SHIB3 RecName: Full=30S ribosomal protein S4
 gi|226699056|sp|B7NLL6|RS4_ECO7I RecName: Full=30S ribosomal protein S4
 gi|226699057|sp|B7M102|RS4_ECO8A RecName: Full=30S ribosomal protein S4
 gi|226699058|sp|B1X6E8|RS4_ECODH RecName: Full=30S ribosomal protein S4
 gi|226699059|sp|B7NDR8|RS4_ECOLU RecName: Full=30S ribosomal protein S4
 gi|226699060|sp|B6I210|RS4_ECOSE RecName: Full=30S ribosomal protein S4
 gi|226699061|sp|B1LHB0|RS4_ECOSM RecName: Full=30S ribosomal protein S4
 gi|226699064|sp|B7LRR3|RS4_ESCF3 RecName: Full=30S ribosomal protein S4
 gi|226732180|sp|B7MCR2|RS4_ECO45 RecName: Full=30S ribosomal protein S4
 gi|226732181|sp|B5YT15|RS4_ECO5E RecName: Full=30S ribosomal protein S4
 gi|254764587|sp|B7UK20|RS4_ECO27 RecName: Full=30S ribosomal protein S4
 gi|254764588|sp|B7LHZ8|RS4_ECO55 RecName: Full=30S ribosomal protein S4
 gi|254764589|sp|B7N181|RS4_ECO81 RecName: Full=30S ribosomal protein S4
 gi|259495276|sp|C4ZUF1|RS4_ECOBW RecName: Full=30S ribosomal protein S4
 gi|116666551|pdb|1VS5|D Chain D, Crystal Structure Of The Bacterial Ribosome From
           Escherichia Coli In Complex With The Antibiotic
           Kasugamyin At 3.5a Resolution. This File Contains The
           30s Subunit Of One 70s Ribosome. The Entire Crystal
           Structure Contains Two 70s Ribosomes And Is Described In
           Remark 400.
 gi|116666603|pdb|1VS7|D Chain D, Crystal Structure Of The Bacterial Ribosome From
           Escherichia Coli In Complex With The Antibiotic
           Kasugamyin At 3.5a Resolution. This File Contains The
           30s Subunit Of One 70s Ribosome. The Entire Crystal
           Structure Contains Two 70s Ribosomes And Is Described In
           Remark 400.
 gi|256032366|pdb|3E1A|R Chain R, Structure Of The 30s Subunit And The Trnas Of E. Coli
           Ribosome In Pre-Accommodation State
 gi|256032423|pdb|3E1C|R Chain R, Structure Of The 30s Subunit And The Trnas Of E. Coli
           Ribosome In Post-Accommodation State
 gi|257097325|pdb|3I1M|D Chain D, Crystal Structure Of The E. Coli 70s Ribosome In An
           Intermediate State Of Ratcheting
 gi|257097377|pdb|3I1O|D Chain D, Crystal Structure Of The E. Coli 70s Ribosome In An
           Intermediate State Of Ratcheting
 gi|257097429|pdb|3I1Q|D Chain D, Crystal Structure Of The E. Coli 70s Ribosome In An
           Intermediate State Of Ratcheting
 gi|257097483|pdb|3I1S|D Chain D, Crystal Structure Of The E. Coli 70s Ribosome In An
           Intermediate State Of Ratcheting
 gi|257097537|pdb|3I1Z|D Chain D, Crystal Structure Of The E. Coli 70s Ribosome In An
           Intermediate State Of Ratcheting
 gi|257097592|pdb|3I21|D Chain D, Crystal Structure Of The E. Coli 70s Ribosome In An
           Intermediate State Of Ratcheting
 gi|290560310|pdb|3KC4|D Chain D, Ribosome-Secy Complex. This Entry 3kc4 Contains 30s
           Ribosomal Subnit. The 50s Ribosomal Subunit Can Be Found
           In Pdb Entry 3kcr
 gi|308198690|pdb|3OR9|D Chain D, Crystal Structure Of The E. Coli Ribosome Bound To
           Cem-101. This File Contains The 30s Subunit Of The First
           70s Ribosome.
 gi|308198711|pdb|3ORA|D Chain D, Crystal Structure Of The E. Coli Ribosome Bound To
           Cem-101. This File Contains The 30s Subunit Of The
           Second 70s Ribosome.
 gi|326634282|pdb|3IZV|H Chain H, Structural Insights Into Cognate Vs. Near-Cognate
           Discrimination During Decoding. This Entry Contains The
           Small Subunit Of A Ribosome Programmed With A
           Near-Cognate Codon, AT-Site Trna, P-Site Trna, Mrna And
           Ef-Tu
 gi|326634307|pdb|3IZW|H Chain H, Structural Insights Into Cognate Vs. Near-Cognate
           Discrimination During Decoding.This Entry Contains The
           Small Subunit Of A Ribosome Programmed With A Cognate
           Codon, AT-Site Trna, P-Site Trna, Mrna And Ef-Tu
 gi|12517925|gb|AAG58417.1|AE005556_10 30S ribosomal subunit protein S4 [Escherichia coli O157:H7 str.
           EDL933]
 gi|26110309|gb|AAN82495.1|AE016767_255 30S ribosomal protein S4 [Escherichia coli CFT073]
 gi|42798|emb|CAA26394.1| unnamed protein product [Escherichia coli]
 gi|606231|gb|AAA58094.1| 30S ribosomal subunit protein S4 [Escherichia coli str. K-12
           substr. MG1655]
 gi|1789691|gb|AAC76321.1| 30S ribosomal subunit protein S4 [Escherichia coli str. K-12
           substr. MG1655]
 gi|13363634|dbj|BAB37584.1| 30S ribosomal subunit protein S4 [Escherichia coli O157:H7 str.
           Sakai]
 gi|73857292|gb|AAZ89999.1| 30S ribosomal subunit protein S4 [Shigella sonnei Ss046]
 gi|81242740|gb|ABB63450.1| 30S ribosomal subunit protein S4 [Shigella dysenteriae Sd197]
 gi|81247070|gb|ABB67778.1| 30S ribosomal subunit protein S4 [Shigella boydii Sb227]
 gi|85676745|dbj|BAE77995.1| 30S ribosomal subunit protein S4 [Escherichia coli str. K12 substr.
           W3110]
 gi|91074297|gb|ABE09178.1| 30S ribosomal subunit protein S4 [Escherichia coli UTI89]
 gi|110345127|gb|ABG71364.1| 30S ribosomal protein S4 [Escherichia coli 536]
 gi|110616692|gb|ABF05359.1| 30S ribosomal subunit protein S4 [Shigella flexneri 5 str. 8401]
 gi|115514702|gb|ABJ02777.1| 30S ribosomal subunit protein S4 [Escherichia coli APEC O1]
 gi|157068450|gb|ABV07705.1| ribosomal protein S4 [Escherichia coli HS]
 gi|157078822|gb|ABV18530.1| ribosomal protein S4 [Escherichia coli E24377A]
 gi|157086076|gb|ABV15754.1| hypothetical protein CKO_04709 [Citrobacter koseri ATCC BAA-895]
 gi|169753396|gb|ACA76095.1| ribosomal protein S4 [Escherichia coli ATCC 8739]
 gi|169890651|gb|ACB04358.1| 30S ribosomal subunit protein S4 [Escherichia coli str. K-12
           substr. DH10B]
 gi|170121663|gb|EDS90594.1| ribosomal protein S4 [Escherichia albertii TW07627]
 gi|170521050|gb|ACB19228.1| ribosomal protein S4 [Escherichia coli SMS-3-5]
 gi|187429640|gb|ACD08914.1| ribosomal protein S4 [Shigella boydii CDC 3083-94]
 gi|187767007|gb|EDU30851.1| ribosomal protein S4 [Escherichia coli O157:H7 str. EC4196]
 gi|188013855|gb|EDU51977.1| ribosomal protein S4 [Escherichia coli O157:H7 str. EC4113]
 gi|188491064|gb|EDU66167.1| ribosomal protein S4 [Escherichia coli 53638]
 gi|188998873|gb|EDU67859.1| ribosomal protein S4 [Escherichia coli O157:H7 str. EC4076]
 gi|189354671|gb|EDU73090.1| ribosomal protein S4 [Escherichia coli O157:H7 str. EC4401]
 gi|189361855|gb|EDU80274.1| ribosomal protein S4 [Escherichia coli O157:H7 str. EC4486]
 gi|189365129|gb|EDU83545.1| ribosomal protein S4 [Escherichia coli O157:H7 str. EC4501]
 gi|189374088|gb|EDU92504.1| ribosomal protein S4 [Escherichia coli O157:H7 str. EC869]
 gi|189375351|gb|EDU93767.1| ribosomal protein S4 [Escherichia coli O157:H7 str. EC508]
 gi|190905255|gb|EDV64893.1| ribosomal protein S4 [Escherichia coli F11]
 gi|192925868|gb|EDV80518.1| ribosomal protein S4 [Escherichia coli E22]
 gi|192955133|gb|EDV85627.1| ribosomal protein S4 [Escherichia coli E110019]
 gi|194411669|gb|EDX27996.1| ribosomal protein S4 [Escherichia coli B171]
 gi|194416688|gb|EDX32819.1| ribosomal protein S4 [Shigella dysenteriae 1012]
 gi|194421045|gb|EDX37074.1| ribosomal protein S4 [Escherichia coli 101-1]
 gi|208726341|gb|EDZ75942.1| ribosomal protein S4 [Escherichia coli O157:H7 str. EC4206]
 gi|208734198|gb|EDZ82885.1| ribosomal protein S4 [Escherichia coli O157:H7 str. EC4045]
 gi|208739629|gb|EDZ87311.1| ribosomal protein S4 [Escherichia coli O157:H7 str. EC4042]
 gi|209157700|gb|ACI35133.1| ribosomal protein S4 [Escherichia coli O157:H7 str. EC4115]
 gi|209757278|gb|ACI76951.1| 30S ribosomal subunit protein S4 [Escherichia coli]
 gi|209757280|gb|ACI76952.1| 30S ribosomal subunit protein S4 [Escherichia coli]
 gi|209757282|gb|ACI76953.1| 30S ribosomal subunit protein S4 [Escherichia coli]
 gi|209757284|gb|ACI76954.1| 30S ribosomal subunit protein S4 [Escherichia coli]
 gi|209757286|gb|ACI76955.1| 30S ribosomal subunit protein S4 [Escherichia coli]
 gi|209914021|dbj|BAG79095.1| 30S ribosomal protein S4 [Escherichia coli SE11]
 gi|215266668|emb|CAS11107.1| 30S ribosomal subunit protein S4 [Escherichia coli O127:H6 str.
           E2348/69]
 gi|217321311|gb|EEC29735.1| ribosomal protein S4 [Escherichia coli O157:H7 str. TW14588]
 gi|218353721|emb|CAU99998.1| 30S ribosomal subunit protein S4 [Escherichia coli 55989]
 gi|218358113|emb|CAQ90760.1| 30S ribosomal subunit protein S4 [Escherichia fergusonii ATCC
           35469]
 gi|218362622|emb|CAR00248.1| 30S ribosomal subunit protein S4 [Escherichia coli IAI1]
 gi|218367127|emb|CAR04901.1| 30S ribosomal subunit protein S4 [Escherichia coli S88]
 gi|218372045|emb|CAR19905.1| 30S ribosomal subunit protein S4 [Escherichia coli IAI39]
 gi|218429147|emb|CAR10099.2| 30S ribosomal subunit protein S4 [Escherichia coli ED1a]
 gi|218434001|emb|CAR14918.1| 30S ribosomal subunit protein S4 [Escherichia coli UMN026]
 gi|222035005|emb|CAP77748.1| 30S ribosomal protein S4 [Escherichia coli LF82]
 gi|226838963|gb|EEH70986.1| ribosomal protein S4 [Escherichia sp. 1_1_43]
 gi|226902290|gb|EEH88549.1| 30S ribosomal subunit protein S4 [Escherichia sp. 3_2_53FAA]
 gi|227839572|gb|EEJ50038.1| 30S ribosomal protein S4 [Escherichia coli 83972]
 gi|238859799|gb|ACR61797.1| 30S ribosomal subunit protein S4 [Escherichia coli BW2952]
 gi|242378823|emb|CAQ33615.1| 30S ribosomal subunit protein S4, subunit of 30S ribosomal subunit
           and ribosome [Escherichia coli BL21(DE3)]
 gi|253322924|gb|ACT27526.1| ribosomal protein S4 [Escherichia coli 'BL21-Gold(DE3)pLysS AG']
 gi|253975125|gb|ACT40796.1| 30S ribosomal protein S4 [Escherichia coli B str. REL606]
 gi|253979281|gb|ACT44951.1| 30S ribosomal protein S4 [Escherichia coli BL21(DE3)]
 gi|254594633|gb|ACT73994.1| 30S ribosomal subunit protein S4 [Escherichia coli O157:H7 str.
           TW14359]
 gi|257756066|dbj|BAI27568.1| 30S ribosomal subunit protein S4 [Escherichia coli O26:H11 str.
           11368]
 gi|257761241|dbj|BAI32738.1| 30S ribosomal subunit protein S4 [Escherichia coli O103:H2 str.
           12009]
 gi|257766395|dbj|BAI37890.1| 30S ribosomal subunit protein S4 [Escherichia coli O111:H- str.
           11128]
 gi|260447685|gb|ACX38107.1| ribosomal protein S4 [Escherichia coli DH1]
 gi|281180331|dbj|BAI56661.1| 30S ribosomal protein S4 [Escherichia coli SE15]
 gi|281602661|gb|ADA75645.1| 30S ribosomal protein S4 [Shigella flexneri 2002017]
 gi|284923302|emb|CBG36396.1| 30S ribosomal subunit protein S4 [Escherichia coli 042]
 gi|290764527|gb|ADD58488.1| 30S ribosomal protein S4 [Escherichia coli O55:H7 str. CB9615]
 gi|291321741|gb|EFE61172.1| 30S ribosomal protein S4 [Escherichia coli B088]
 gi|291425704|gb|EFE98738.1| rpsD [Escherichia coli FVEC1412]
 gi|291431291|gb|EFF04276.1| 30S ribosomal protein S4 [Escherichia coli B185]
 gi|291468362|gb|EFF10855.1| 30S ribosomal protein S4 [Escherichia coli B354]
 gi|294491877|gb|ADE90633.1| ribosomal protein S4 [Escherichia coli IHE3034]
 gi|298276470|gb|EFI17988.1| small subunit ribosomal protein S4 [Escherichia coli FVEC1302]
 gi|300301894|gb|EFJ58279.1| ribosomal protein S4 [Escherichia coli MS 185-1]
 gi|300308986|gb|EFJ63506.1| ribosomal protein S4 [Escherichia coli MS 200-1]
 gi|300318229|gb|EFJ68013.1| ribosomal protein S4 [Escherichia coli MS 175-1]
 gi|300359476|gb|EFJ75346.1| ribosomal protein S4 [Escherichia coli MS 198-1]
 gi|300399548|gb|EFJ83086.1| ribosomal protein S4 [Escherichia coli MS 69-1]
 gi|300404418|gb|EFJ87956.1| ribosomal protein S4 [Escherichia coli MS 84-1]
 gi|300409380|gb|EFJ92918.1| ribosomal protein S4 [Escherichia coli MS 45-1]
 gi|300414532|gb|EFJ97842.1| ribosomal protein S4 [Escherichia coli MS 115-1]
 gi|300421742|gb|EFK05053.1| ribosomal protein S4 [Escherichia coli MS 182-1]
 gi|300453765|gb|EFK17385.1| ribosomal protein S4 [Escherichia coli MS 116-1]
 gi|300459451|gb|EFK22944.1| ribosomal protein S4 [Escherichia coli MS 21-1]
 gi|300460014|gb|EFK23507.1| ribosomal protein S4 [Escherichia coli MS 187-1]
 gi|300524666|gb|EFK45735.1| ribosomal protein S4 [Escherichia coli MS 119-7]
 gi|300532385|gb|EFK53447.1| ribosomal protein S4 [Escherichia coli MS 107-1]
 gi|300839201|gb|EFK66961.1| ribosomal protein S4 [Escherichia coli MS 124-1]
 gi|300848015|gb|EFK75775.1| ribosomal protein S4 [Escherichia coli MS 78-1]
 gi|301077786|gb|EFK92592.1| ribosomal protein S4 [Escherichia coli MS 146-1]
 gi|305850757|gb|EFM51214.1| 30S ribosomal protein S4 [Escherichia coli NC101]
 gi|306905474|gb|EFN36009.1| ribosomal protein S4 [Escherichia coli W]
 gi|307555384|gb|ADN48159.1| 30S ribosomal subunit protein S4 [Escherichia coli ABU 83972]
 gi|307628331|gb|ADN72635.1| 30S ribosomal protein S4 [Escherichia coli UM146]
 gi|308121622|gb|EFO58884.1| ribosomal protein S4 [Escherichia coli MS 145-7]
 gi|309703708|emb|CBJ03049.1| 30S ribosomal subunit protein S4 [Escherichia coli ETEC H10407]
 gi|312947847|gb|ADR28674.1| 30S ribosomal protein S4 [Escherichia coli O83:H1 str. NRG 857C]
 gi|315062588|gb|ADT76915.1| 30S ribosomal subunit protein S4 [Escherichia coli W]
 gi|315137871|dbj|BAJ45030.1| 30S ribosomal protein S4 [Escherichia coli DH1]
 gi|315255880|gb|EFU35848.1| ribosomal protein S4 [Escherichia coli MS 85-1]
 gi|315284628|gb|EFU44073.1| ribosomal protein S4 [Escherichia coli MS 110-3]
 gi|315292386|gb|EFU51738.1| ribosomal protein S4 [Escherichia coli MS 153-1]
 gi|315298595|gb|EFU57850.1| ribosomal protein S4 [Escherichia coli MS 16-3]
 gi|320182706|gb|EFW57592.1| SSU ribosomal protein S4p (S9e) [Shigella boydii ATCC 9905]
 gi|320639601|gb|EFX09195.1| 30S ribosomal protein S4 [Escherichia coli O157:H7 str. G5101]
 gi|320645099|gb|EFX14115.1| 30S ribosomal protein S4 [Escherichia coli O157:H- str. 493-89]
 gi|320650410|gb|EFX18876.1| 30S ribosomal protein S4 [Escherichia coli O157:H- str. H 2687]
 gi|320655935|gb|EFX23855.1| 30S ribosomal protein S4 [Escherichia coli O55:H7 str. 3256-97 TW
           07815]
 gi|320661387|gb|EFX28802.1| 30S ribosomal protein S4 [Escherichia coli O55:H7 str. USDA 5905]
 gi|320666409|gb|EFX33392.1| 30S ribosomal protein S4 [Escherichia coli O157:H7 str. LSU-61]
 gi|323162975|gb|EFZ48810.1| ribosomal protein S4 [Escherichia coli E128010]
 gi|323173932|gb|EFZ59560.1| ribosomal protein S4 [Escherichia coli LT-68]
 gi|323189099|gb|EFZ74383.1| ribosomal protein S4 [Escherichia coli RN587/1]
 gi|323376825|gb|ADX49093.1| ribosomal protein S4 [Escherichia coli KO11]
 gi|323934505|gb|EGB30913.1| ribosomal protein S4 [Escherichia coli E1520]
 gi|323939282|gb|EGB35494.1| ribosomal protein S4 [Escherichia coli E482]
 gi|323944283|gb|EGB40359.1| ribosomal protein S4 [Escherichia coli H120]
 gi|323950210|gb|EGB46092.1| ribosomal protein S4 [Escherichia coli H252]
 gi|323954581|gb|EGB50364.1| ribosomal protein S4 [Escherichia coli H263]
 gi|323959553|gb|EGB55206.1| ribosomal protein S4 [Escherichia coli H489]
 gi|323966258|gb|EGB61693.1| ribosomal protein S4 [Escherichia coli M863]
 gi|323970100|gb|EGB65374.1| ribosomal protein S4 [Escherichia coli TA007]
 gi|323974751|gb|EGB69864.1| ribosomal protein S4 [Escherichia coli TW10509]
 gi|324009031|gb|EGB78250.1| ribosomal protein S4 [Escherichia coli MS 57-2]
 gi|324014913|gb|EGB84132.1| ribosomal protein S4 [Escherichia coli MS 60-1]
 gi|324017885|gb|EGB87104.1| ribosomal protein S4 [Escherichia coli MS 117-3]
 gi|324111975|gb|EGC05954.1| ribosomal protein S4 [Escherichia fergusonii B253]
 gi|324116314|gb|EGC10234.1| ribosomal protein S4 [Escherichia coli E1167]
 gi|327250944|gb|EGE62637.1| ribosomal protein S4 [Escherichia coli STEC_7v]
 gi|331036286|gb|EGI08512.1| ribosomal protein S4 [Escherichia coli H736]
 gi|331041591|gb|EGI13735.1| ribosomal protein S4 [Escherichia coli M605]
 gi|331046904|gb|EGI18982.1| ribosomal protein S4 [Escherichia coli M718]
 gi|331052801|gb|EGI24834.1| ribosomal protein S4 [Escherichia coli TA206]
 gi|331057419|gb|EGI29405.1| ribosomal protein S4 [Escherichia coli TA143]
 gi|331062187|gb|EGI34107.1| ribosomal protein S4 [Escherichia coli TA271]
 gi|331067711|gb|EGI39109.1| ribosomal protein S4 [Escherichia coli TA280]
 gi|331072537|gb|EGI43862.1| ribosomal protein S4 [Escherichia coli H591]
 gi|331077309|gb|EGI48521.1| ribosomal protein S4 [Escherichia coli H299]
 gi|332090406|gb|EGI95504.1| ribosomal protein S4 [Shigella boydii 3594-74]
 gi|332104203|gb|EGJ07549.1| 30S ribosomal subunit protein S4 [Shigella sp. D9]
          Length = 206

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|310765574|gb|ADP10524.1| 30S ribosomal protein S4 [Erwinia sp. Ejp617]
          Length = 202

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 93  RLDNVVYRMGFGATRAEARQLVSHKSIMVNGRVVSIASYQVTPNDVVSIREKAKKQSRVK 152

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 153 AALELAEQREKPT 165


>gi|220912135|ref|YP_002487444.1| RNA-binding S4 domain protein [Arthrobacter chlorophenolicus A6]
 gi|219859013|gb|ACL39355.1| RNA-binding S4 domain protein [Arthrobacter chlorophenolicus A6]
          Length = 77

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/39 (30%), Positives = 20/39 (51%)

Query: 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          E   +I    VKVNG + +R    + + D + V+G  +R
Sbjct: 32 EAAELIKNGLVKVNGEIDDRRGRQLHNGDTVTVNGQTVR 70


>gi|134097931|ref|YP_001103592.1| PE-PGRS family protein [Saccharopolyspora erythraea NRRL 2338]
 gi|133910554|emb|CAM00667.1| PE-PGRS family protein [Saccharopolyspora erythraea NRRL 2338]
          Length = 1638

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/112 (11%), Positives = 24/112 (21%)

Query: 243  EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            +  GP     A                D P    + P              G        
Sbjct: 896  DTPGPRPHPSAPDGTSQRPQGPAGQRPDAPGQRPDGPAQRPDGVSPRPDAAGPRPDTAGP 955

Query: 303  TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             P        +             ++  R +   + P+ P +R    T  ++
Sbjct: 956  RPDTAGPRPDSAGPRPDGAGPRPDNAAPRPDATGQRPAGPGQRPDGSTPPRQ 1007



 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 13/102 (12%), Positives = 27/102 (26%), Gaps = 8/102 (7%)

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
                + +      P      PD  ++  +  + +   +  ++   P  R +  S    A
Sbjct: 886 RPDGPAGQRPDTPGPRPHPSAPDGTSQRPQGPAGQRPDAPGQRPDGPAQRPDGVSPRPDA 945

Query: 318 KGIHSSFLSDSGQREENHRRSPSFPSKR-----SLRRTSAKK 354
            G         G R +     P     R          +A +
Sbjct: 946 AGPRPDTA---GPRPDTAGPRPDSAGPRPDGAGPRPDNAAPR 984



 Score = 44.8 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 11/114 (9%), Positives = 24/114 (21%), Gaps = 6/114 (5%)

Query: 246  GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
             P    +        +         RP+     PD     + +S+         +     
Sbjct: 924  APGQRPDGPAQRPDGVSPRPDAAGPRPDTAGPRPD-TAGPRPDSAGPRPDGAGPRPDNAA 982

Query: 306  HRRNLASNVWMAKGIHSSFLSDS-----GQREENHRRSPSFPSKRSLRRTSAKK 354
             R +         G      +         R +  +  P         R +  +
Sbjct: 983  PRPDATGQRPAGPGQRPDGSTPPRQDAPSSRPDGQQPRPDGTRPDGGDRPANAR 1036



 Score = 44.8 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 13/107 (12%), Positives = 23/107 (21%), Gaps = 4/107 (3%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              +        P  S+      RP   +    D    + +   +       +      R
Sbjct: 890 PAGQRPDTPGPRPHPSAPDGTSQRPQGPAGQRPDAPGQRPDGPAQRPDGVSPRPDAAGPR 949

Query: 308 RNLASNVWMAKGIHSSFLSDS----GQREENHRRSPSFPSKRSLRRT 350
            + A       G             G R +N    P    +R     
Sbjct: 950 PDTAGPRPDTAGPRPDSAGPRPDGAGPRPDNAAPRPDATGQRPAGPG 996



 Score = 40.5 bits (93), Expect = 0.43,   Method: Composition-based stats.
 Identities = 15/122 (12%), Positives = 28/122 (22%), Gaps = 10/122 (8%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+  G             P          RP+  +    D    + + S  +G + Q+  
Sbjct: 857 RQHGGDGPPNRPPQGPGGPQRPGGPGGNTRPDGPAGQRPDTPGPRPHPSAPDG-TSQRPQ 915

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDS----GQREENHRRSPSFPSKR-----SLRRTSA 352
                R +               +S      G R +     P     R          + 
Sbjct: 916 GPAGQRPDAPGQRPDGPAQRPDGVSPRPDAAGPRPDTAGPRPDTAGPRPDSAGPRPDGAG 975

Query: 353 KK 354
            +
Sbjct: 976 PR 977



 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 17/125 (13%), Positives = 30/125 (24%), Gaps = 19/125 (15%)

Query: 249  LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
               +                  RP+     PD+       + Q+     Q+   +   R+
Sbjct: 948  PRPDTAGPRPDTAGPRPDSAGPRPDGAGPRPDNAAPRPDATGQRPAGPGQRPDGSTPPRQ 1007

Query: 309  NLASNVWMAKGIHSSF-LSDSGQREENHRR------------------SPSFPSKRSLRR 349
            +  S+    +         D G R  N R                    P      S  +
Sbjct: 1008 DAPSSRPDGQQPRPDGTRPDGGDRPANARPDGTNPQSQHPDGSRPDGTRPDQNQPDSRPK 1067

Query: 350  TSAKK 354
             SA +
Sbjct: 1068 DSADQ 1072


>gi|16762867|ref|NP_458484.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Typhi str. CT18]
 gi|29144354|ref|NP_807696.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|213027591|ref|ZP_03342038.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Typhi str. 404ty]
 gi|213052884|ref|ZP_03345762.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Typhi str. E00-7866]
 gi|213425775|ref|ZP_03358525.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Typhi str. E02-1180]
 gi|213580697|ref|ZP_03362523.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-0664]
 gi|213612395|ref|ZP_03370221.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-2068]
 gi|213647330|ref|ZP_03377383.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Typhi str. J185]
 gi|289824201|ref|ZP_06543796.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-3139]
 gi|25009212|sp|Q8Z1X4|RS4_SALTI RecName: Full=30S ribosomal protein S4
 gi|25294504|pir||AI1008 30S ribosomal chain protein S4 [imported] - Salmonella enterica
           subsp. enterica serovar Typhi (strain CT18)
 gi|16505174|emb|CAD09170.1| 30S ribosomal subunit protein S4 [Salmonella enterica subsp.
           enterica serovar Typhi]
 gi|29139992|gb|AAO71556.1| 30S ribosomal subunit protein S4 [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
          Length = 206

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|332298889|ref|YP_004440811.1| ribosomal protein S4 [Treponema brennaborense DSM 12168]
 gi|332181992|gb|AEE17680.1| ribosomal protein S4 [Treponema brennaborense DSM 12168]
          Length = 211

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R   AS R +  +++    + VNG  +   +  V   D +EV
Sbjct: 100 RLDNVVFRMHFASSRTQARQLVLHGHILVNGKSVNIPSYEVRPGDVVEV 148


>gi|228999440|ref|ZP_04159019.1| 30S ribosomal protein S4 [Bacillus mycoides Rock3-17]
 gi|229006996|ref|ZP_04164624.1| 30S ribosomal protein S4 [Bacillus mycoides Rock1-4]
 gi|228754235|gb|EEM03652.1| 30S ribosomal protein S4 [Bacillus mycoides Rock1-4]
 gi|228760385|gb|EEM09352.1| 30S ribosomal protein S4 [Bacillus mycoides Rock3-17]
          Length = 200

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 93  RLDNLVYRMGLARTRRAARQLVNHGHIMVDGARVDIPSYRVKPGQTISV 141


>gi|226324966|ref|ZP_03800484.1| hypothetical protein COPCOM_02758 [Coprococcus comes ATCC 27758]
 gi|225206314|gb|EEG88668.1| hypothetical protein COPCOM_02758 [Coprococcus comes ATCC 27758]
          Length = 258

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 11/29 (37%), Positives = 14/29 (48%)

Query: 34  MIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +I   RV VNG L+     +V   D I V
Sbjct: 202 LIEAGRVYVNGKLITSNGYHVKDNDIISV 230


>gi|170695706|ref|ZP_02886848.1| ribosomal protein S4 [Burkholderia graminis C4D1M]
 gi|170139311|gb|EDT07497.1| ribosomal protein S4 [Burkholderia graminis C4D1M]
          Length = 207

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG++    ++ V + D + V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAITVNGVVSNIPSMQVKAGDVVAV 146


>gi|134097538|ref|YP_001103199.1| hypothetical protein SACE_0940 [Saccharopolyspora erythraea NRRL
           2338]
 gi|133910161|emb|CAM00274.1| hypothetical protein SACE_0940 [Saccharopolyspora erythraea NRRL
           2338]
          Length = 289

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/117 (11%), Positives = 30/117 (25%), Gaps = 2/117 (1%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
             R +             DA + +    + +R              +++  +       +
Sbjct: 149 EGRAKRSADRDARRDARRDAKLAAGSAKMAEREAKRPPEGGAKRPPERDPRRGAAKRGDE 208

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQR--EENHRRSPSFPSKRSLRRTSAKK 354
           + A    R         A G  +      G+       R   + P  R  +R +  +
Sbjct: 209 RGAGRPARDGDPRARGQAPGRGARGADPRGRAGDPRAEREGRAVPPGRGAQRPAPGR 265



 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 13/104 (12%), Positives = 22/104 (21%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           L          EA+   +            R            R  ++   +       +
Sbjct: 170 LAAGSAKMAEREAKRPPEGGAKRPPERDPRRGAAKRGDERGAGRPARDGDPRARGQAPGR 229

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
            A     R  A +    +   +       QR    R  P  P  
Sbjct: 230 GARGADPRGRAGDPRAEREGRAVPPGRGAQRPAPGRGRPPEPKA 273



 Score = 44.8 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 7/106 (6%), Positives = 22/106 (20%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P    +      A    ++          +             +++      +  A    
Sbjct: 135 PPEDGDTPTRKQAAEGRAKRSADRDARRDARRDAKLAAGSAKMAEREAKRPPEGGAKRPP 194

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            R+             +             ++P   ++ +  R  A
Sbjct: 195 ERDPRRGAAKRGDERGAGRPARDGDPRARGQAPGRGARGADPRGRA 240



 Score = 40.9 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 12/105 (11%), Positives = 26/105 (24%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
               Q        S++   R      +++     +M +  +++      K+      RR 
Sbjct: 142 PTRKQAAEGRAKRSADRDARRDARRDAKLAAGSAKMAEREAKRPPEGGAKRPPERDPRRG 201

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            A           +   D   R +   R       R        +
Sbjct: 202 AAKRGDERGAGRPARDGDPRARGQAPGRGARGADPRGRAGDPRAE 246


>gi|24371853|ref|NP_715895.1| 30S ribosomal protein S4 [Shewanella oneidensis MR-1]
 gi|113968568|ref|YP_732361.1| 30S ribosomal protein S4 [Shewanella sp. MR-4]
 gi|114045731|ref|YP_736281.1| 30S ribosomal protein S4 [Shewanella sp. MR-7]
 gi|26399362|sp|P59131|RS4_SHEON RecName: Full=30S ribosomal protein S4
 gi|123030061|sp|Q0HNR3|RS4_SHESM RecName: Full=30S ribosomal protein S4
 gi|123326989|sp|Q0I081|RS4_SHESR RecName: Full=30S ribosomal protein S4
 gi|24345670|gb|AAN53340.1|AE015474_3 ribosomal protein S4 [Shewanella oneidensis MR-1]
 gi|113883252|gb|ABI37304.1| SSU ribosomal protein S4P [Shewanella sp. MR-4]
 gi|113887173|gb|ABI41224.1| SSU ribosomal protein S4P [Shewanella sp. MR-7]
          Length = 206

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + V VNG ++   +  V + D + +
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKSVMVNGRVVNIPSFKVSANDVVSI 145


>gi|229086462|ref|ZP_04218634.1| RNA-binding S4 domain protein [Bacillus cereus Rock3-44]
 gi|228696779|gb|EEL49592.1| RNA-binding S4 domain protein [Bacillus cereus Rock3-44]
          Length = 257

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 24/50 (48%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  VIA     SR++V+ +I    VKVN   +E+ A      D   + G
Sbjct: 182 RLDVVIAEMLHLSRQKVQPLIKNGLVKVNWKTVEQTAYECFPGDVFSIRG 231


>gi|227499169|ref|ZP_03929304.1| conserved hypothetical protein [Acidaminococcus sp. D21]
 gi|226904616|gb|EEH90534.1| conserved hypothetical protein [Acidaminococcus sp. D21]
          Length = 197

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +RR+  +++    + VNG  L+  +  V + D + V
Sbjct: 88  RLDNVVYRLGLARTRRQARQLVTHGHIAVNGKRLDIPSALVKAGDVVSV 136


>gi|319892767|ref|YP_004149642.1| SSU ribosomal protein S4p (S9e) [Staphylococcus pseudintermedius
           HKU10-03]
 gi|317162463|gb|ADV06006.1| SSU ribosomal protein S4p (S9e) [Staphylococcus pseudintermedius
           HKU10-03]
 gi|323464199|gb|ADX76352.1| ribosomal protein S4 [Staphylococcus pseudintermedius ED99]
          Length = 200

 Score = 47.9 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 9/49 (18%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++   G+A +RR+  +++    V+V+G  ++  +  +     + V
Sbjct: 93  RLDAIVYALGLARTRRQARQLVGHGHVEVDGKRVDIPSYTLKPGQVVTV 141


>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 = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 28/237 (11%), Positives = 61/237 (25%), Gaps = 36/237 (15%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-G 64
           V++ F   R+   +++     SR  ++ +I +  V VN    ++    +   D+I+V+  
Sbjct: 8   VEKEFDNVRLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNK-EKKRNYKLKVGDNIKVNIP 66

Query: 65  VP-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
            P             +   ++  + +      +V         + V   L          
Sbjct: 67  EPKLLQIEPEDIKLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNALLSHCKDLSGIN 126

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--------------- 156
           G         +     G L       S   L                             
Sbjct: 127 GVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGIIKDGQGTIE 186

Query: 157 -----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                      K  V++   Y      +  +  ++  V   L  G+  +I+      
Sbjct: 187 APIGRHPVDRIKMAVVKDGRYAVTHYKVIERFKNHTLVECKLETGRTHQIRVHMSHI 243


>gi|90414980|ref|ZP_01222942.1| 30S ribosomal protein S4 [Photobacterium profundum 3TCK]
 gi|161936335|ref|YP_128585.2| 30S ribosomal protein S4 [Photobacterium profundum SS9]
 gi|152031675|sp|Q6LV92|RS4_PHOPR RecName: Full=30S ribosomal protein S4
 gi|90323919|gb|EAS40519.1| 30S ribosomal protein S4 [Photobacterium profundum 3TCK]
          Length = 206

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG ++   +  V + D + +
Sbjct: 97  RLDNVVYRMGFGSTRAESRQLVSHKAILVNGTVVNVPSFKVAANDVVSI 145


>gi|50122927|ref|YP_052094.1| 30S ribosomal protein S4 [Pectobacterium atrosepticum SCRI1043]
 gi|227115248|ref|ZP_03828904.1| 30S ribosomal protein S4 [Pectobacterium carotovorum subsp.
           brasiliensis PBR1692]
 gi|227328925|ref|ZP_03832949.1| 30S ribosomal protein S4 [Pectobacterium carotovorum subsp.
           carotovorum WPP14]
 gi|253690159|ref|YP_003019349.1| ribosomal protein S4 [Pectobacterium carotovorum subsp. carotovorum
           PC1]
 gi|61215522|sp|Q6CZZ4|RS4_ERWCT RecName: Full=30S ribosomal protein S4
 gi|259495287|sp|C6DFS4|RS4_PECCP RecName: Full=30S ribosomal protein S4
 gi|49613453|emb|CAG76904.1| 30S ribosomal subunit protein S4 [Pectobacterium atrosepticum
           SCRI1043]
 gi|251756737|gb|ACT14813.1| ribosomal protein S4 [Pectobacterium carotovorum subsp. carotovorum
           PC1]
          Length = 206

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  +M++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQMVSHKAIMVNGRVVSIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|330505183|ref|YP_004382052.1| 30S ribosomal protein S4 [Pseudomonas mendocina NK-01]
 gi|328919469|gb|AEB60300.1| 30S ribosomal protein S4 [Pseudomonas mendocina NK-01]
          Length = 206

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG  +   +  V + D + V
Sbjct: 97  RLDNVVYRMGYGATRAESRQLVSHKAISVNGQTVNVPSYQVKAGDVVAV 145


>gi|257459219|ref|ZP_05624338.1| ribosomal protein S4 [Campylobacter gracilis RM3268]
 gi|257443604|gb|EEV18728.1| ribosomal protein S4 [Campylobacter gracilis RM3268]
          Length = 208

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G A+ RR   +++    + V+G  ++  + +V +   IEV
Sbjct: 98  QRLDNVVYRMGFATTRRFARQLVTHGHILVDGKRVDIPSYSVRAGQKIEV 147


>gi|157823982|ref|NP_067321.2| zinc finger protein 318 isoform 2 [Mus musculus]
 gi|220941757|emb|CAX15747.1| zinc finger protein 318 [Mus musculus]
          Length = 1154

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/109 (12%), Positives = 27/109 (24%), Gaps = 2/109 (1%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           GP        +       S        ++        +         +    + +  +P 
Sbjct: 22  GPPPGRPVGASSGPTRRPSSPPPPSCSSLRLPARRHRSPSGHRGRWASPSPPRGRRGSPS 81

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQR--EENHRRSPSFPSKRSLRRTSA 352
             R   ++    +G  +S     G+R      R     PS    RR   
Sbjct: 82  PPRGRRASPSPTRGRRASPSPPRGRRGSPSPPRARRGSPSPPRSRRHYP 130



 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 17/108 (15%), Positives = 29/108 (26%), Gaps = 4/108 (3%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                +      P+ +S    R   +             +     +G     + A+P   
Sbjct: 16  KDGSASGPPPGRPVGASSGPTRRPSSPPPPSCSSLRLPARRHRSPSGHR--GRWASPSPP 73

Query: 308 RNLASNVWMAKGIHSSFLSDSGQR--EENHRRSPSFPSKRSLRRTSAK 353
           R    +    +G  +S     G+R      R     PS    RR S  
Sbjct: 74  RGRRGSPSPPRGRRASPSPTRGRRASPSPPRGRRGSPSPPRARRGSPS 121


>gi|149195169|ref|ZP_01872260.1| 30S ribosomal protein S4 [Caminibacter mediatlanticus TB-2]
 gi|149134721|gb|EDM23206.1| 30S ribosomal protein S4 [Caminibacter mediatlanticus TB-2]
          Length = 208

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A+ RR   +++    + VNG  +   +  V   D IE+
Sbjct: 99  RLDNVVYRMGFATTRRFARQLVTHGHILVNGKRVNIPSYIVKEGDRIEI 147


>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 = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 11/58 (18%), Positives = 24/58 (41%)

Query: 6  IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          +V      +R+ + IA  G  SR    R +    V ++G   + +   + +   + V+
Sbjct: 7  VVASADGGERLDRFIAARGGVSRGAARRALDSGGVFLDGRRCKVSGRLLQAGQKVVVN 64


>gi|46911985|emb|CAG18783.1| putative ribosomal protein S4 [Photobacterium profundum SS9]
          Length = 202

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG ++   +  V + D + +
Sbjct: 93  RLDNVVYRMGFGSTRAESRQLVSHKAILVNGTVVNVPSFKVAANDVVSI 141


>gi|33357881|pdb|1P6G|D Chain D, Real Space Refined Coordinates Of The 30s Subunit Fitted
           Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp
           State Of E. Coli 70s Ribosome
 gi|33357958|pdb|1P87|D Chain D, Real Space Refined Coordinates Of The 30s Subunit Fitted
           Into The Low Resolution Cryo-Em Map Of The
           Initiation-Like State Of E. Coli 70s Ribosome
 gi|83754042|pdb|2AVY|D Chain D, Crystal Structure Of The Bacterial Ribosome From
           Escherichia Coli At 3.5 A Resolution. This File Contains
           The 30s Subunit Of One 70s Ribosome. The Entire Crystal
           Structure Contains Two 70s Ribosomes And Is Described In
           Remark 400.
 gi|83754098|pdb|2AW7|D Chain D, Crystal Structure Of The Bacterial Ribosome From
           Escherichia Coli At 3.5 A Resolution. This File Contains
           The 30s Subunit Of The Second 70s Ribosome. The Entire
           Crystal Structure Contains Two 70s Ribosomes And Is
           Described In Remark 400.
 gi|118138056|pdb|2I2P|D Chain D, Crystal Structure Of Ribosome With Messenger Rna And The
           Anticodon Stem-Loop Of P-Site Trna. This File Contains
           The 30s Subunit Of One 70s Ribosome. The Entire Crystal
           Structure Contains Two 70s Ribosomes And Is Described In
           Remark 400.
 gi|118138127|pdb|2I2U|D Chain D, Crystal Structure Of Ribosome With Messenger Rna And The
           Anticodon Stem-Loop Of P-Site Trna. This File Contains
           The 30s Subunit Of One 70s Ribosome. The Entire Crystal
           Structure Contains Two 70s Ribosomes And Is Described In
           Remark 400.
 gi|157836026|pdb|2QOU|D Chain D, Crystal Structure Of The Bacterial Ribosome From
           Escherichia Coli In Complex With Spectinomycin. This
           File Contains The 30s Subunit Of The First 70s Ribosome,
           With Spectinomycin Bound. The Entire Crystal Structure
           Contains Two 70s Ribosomes.
 gi|157836077|pdb|2QOW|D Chain D, Crystal Structure Of The Bacterial Ribosome From
           Escherichia Coli In Complex With Spectinomycin. This
           File Contains The 30s Subunit Of The Second 70s
           Ribosome, With Spectinomycin Bound. The Entire Crystal
           Structure Contains Two 70s Ribosomes.
 gi|157836130|pdb|2QOY|D Chain D, Crystal Structure Of The Bacterial Ribosome From
           Escherichia Coli In Complex With Spectinomycin And
           Neomycin. This File Contains The 30s Subunit Of The
           First 70s Ribosome, With Spectinomycin And Neomycin
           Bound. The Entire Crystal Structure Contains Two 70s
           Ribosomes.
 gi|157836181|pdb|2QP0|D Chain D, Crystal Structure Of The Bacterial Ribosome From
           Escherichia Coli In Complex With Spectinomycin And
           Neomycin. This File Contains The 30s Subunit Of The
           Second 70s Ribosome, With Spectinomycin And Neomycin
           Bound. The Entire Crystal Structure Contains Two 70s
           Ribosomes.
 gi|158429701|pdb|2QAL|D Chain D, Crystal Structure Of The Bacterial Ribosome From
           Escherichia Coli In Complex With Neomycin. This File
           Contains The 30s Subunit Of The First 70s Ribosome, With
           Neomycin Bound. The Entire Crystal Structure Contains
           Two 70s Ribosomes And Is Described In Remark 400.
 gi|158429753|pdb|2QAN|D Chain D, Crystal Structure Of The Bacterial Ribosome From
           Escherichia Coli In Complex With Neomycin. This File
           Contains The 30s Subunit Of The Second 70s Ribosome,
           With Neomycin Bound. The Entire Crystal Structure
           Contains Two 70s Ribosomes And Is Described In Remark
           400.
 gi|158429811|pdb|2QB9|D Chain D, Crystal Structure Of The Bacterial Ribosome From
           Escherichia Coli In Complex With Gentamicin. This File
           Contains The 30s Subunit Of The First 70s Ribosome, With
           Gentamicin Bound. The Entire Crystal Structure Contains
           Two 70s Ribosomes And Is Described In Remark 400.
 gi|158429863|pdb|2QBB|D Chain D, Crystal Structure Of The Bacterial Ribosome From
           Escherichia Coli In Complex With Gentamicin. This File
           Contains The 30s Subunit Of The Second 70s Ribosome,
           With Gentamicin Bound. The Entire Crystal Structure
           Contains Two 70s Ribosomes And Is Described In Remark
           400.
 gi|158429915|pdb|2QBD|D Chain D, Crystal Structure Of The Bacterial Ribosome From
           Escherichia Coli In Complex With Ribosome Recycling
           Factor (Rrf). This File Contains The 30s Subunit Of The
           First 70s Ribosome. The Entire Crystal Structure
           Contains Two 70s Ribosomes And Is Described In Remark
           400.
 gi|158429967|pdb|2QBF|D Chain D, Crystal Structure Of The Bacterial Ribosome From
           Escherichia Coli In Complex With Ribosome Recycling
           Factor (Rrf). This File Contains The 30s Subunit Of The
           Second 70s Ribosome. The Entire Crystal Structure
           Contains Two 70s Ribosomes And Is Described In Remark
           400.
 gi|158430021|pdb|2QBH|D Chain D, Crystal Structure Of The Bacterial Ribosome From
           Escherichia Coli In Complex With Gentamicin And Ribosome
           Recycling Factor (Rrf). This File Contains The 30s
           Subunit Of The First 70s Ribosome, With Gentamicin
           Bound. The Entire Crystal Structure Contains Two 70s
           Ribosomes And Is Described In Remark 400.
 gi|158430074|pdb|2QBJ|D Chain D, Crystal Structure Of The Bacterial Ribosome From
           Escherichia Coli In Complex With Gentamicin And Ribosome
           Recycling Factor (Rrf). This File Contains The 30s
           Subunit Of The Second 70s Ribosome, With Gentamicin
           Bound. The Entire Crystal Structure Contains Two 70s
           Ribosomes And Is Described In Remark 400.
 gi|158431374|pdb|2Z4K|D Chain D, Crystal Structure Of The Bacterial Ribosome From
           Escherichia Coli In Complex With Paromomycin And
           Ribosome Recycling Factor (Rrf). This File Contains The
           30s Subunit Of The First 70s Ribosome, With Paromomycin
           Bound. The Entire Crystal Structure Contains Two 70s
           Ribosomes And Is Described In Remark 400.
 gi|158431427|pdb|2Z4M|D Chain D, Crystal Structure Of The Bacterial Ribosome From
           Escherichia Coli In Complex With Paromomycin And
           Ribosome Recycling Factor (Rrf). This File Contains The
           30s Subunit Of The Second 70s Ribosome, With Paromomycin
           Bound. The Entire Crystal Structure Contains Two 70s
           Ribosomes And Is Described In Remark 400.
 gi|168988791|pdb|2VHO|D Chain D, Structure Of Pdf Binding Helix In Complex With The
           Ribosome (Part 3 Of 4)
 gi|168988812|pdb|2VHP|D Chain D, Structure Of Pdf Binding Helix In Complex With The
           Ribosome (Part 4 Of 4)
 gi|197107281|pdb|3DF1|D Chain D, Crystal Structure Of The Bacterial Ribosome From
           Escherichia Coli In Complex With Hygromycin B. This File
           Contains The 30s Subunit Of The First 70s Ribosome, With
           Hygromycin B Bound. The Entire Crystal Structure
           Contains Two 70s Ribosomes.
 gi|197107333|pdb|3DF3|D Chain D, Crystal Structure Of The Bacterial Ribosome From
           Escherichia Coli In Complex With Hygromycin B. This File
           Contains The 30s Subunit Of The Second 70s Ribosome,
           With Hygromycin B Bound. The Entire Crystal Structure
           Contains Two 70s Ribosomes.
 gi|224510725|pdb|3FIH|D Chain D, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry
           Consists Of The 30s Subunit, Trnas And The Ternary
           Complex.
 gi|294662220|pdb|2WWL|D Chain D, E.Coli 70s Ribosome Stalled During Translation Of Tnac
           Leader Peptide. This File Contains The 30s, The P-Site
           Trna And The Tnac Leader Peptide (Part 1 Of 2).
 gi|308387968|pdb|3OFO|D Chain D, Crystal Structure Of The E. Coli Ribosome Bound To
           Erythromycin. This File Contains The 30s Subunit Of The
           First 70s Ribosome.
 gi|308387989|pdb|3OFP|D Chain D, Crystal Structure Of The E. Coli Ribosome Bound To
           Erythromycin. This File Contains The 30s Subunit Of The
           Second 70s Ribosome.
 gi|309320026|pdb|3OFA|D Chain D, Crystal Structure Of The E. Coli Ribosome Bound To
           Chloramphenicol. This File Contains The 30s Subunit Of
           The First 70s Ribosome.
 gi|309320047|pdb|3OFB|D Chain D, Crystal Structure Of The E. Coli Ribosome Bound To
           Chloramphenicol. This File Contains The 30s Subunit Of
           The Second 70s Ribosome.
 gi|309320130|pdb|3OFX|D Chain D, Crystal Structure Of The E. Coli Ribosome Bound To
           Clindamycin. This File Contains The 30s Subunit Of The
           First 70s Ribosome.
 gi|309320151|pdb|3OFY|D Chain D, Crystal Structure Of The E. Coli Ribosome Bound To
           Clindamycin. This File Contains The 30s Subunit Of The
           Second 70s Ribosome
 gi|315113615|pdb|3OAQ|D Chain D, Crystal Structure Of The E. Coli Ribosome Bound To
           Telithromycin. This File Contains The 30s Subunit Of The
           First 70s Ribosome.
 gi|315113636|pdb|3OAR|D Chain D, Crystal Structure Of The E. Coli Ribosome Bound To
           Telithromycin. This File Contains The 30s Subunit Of The
           Second 70s Ribosome.
 gi|329665995|pdb|3J00|D Chain D, Structure Of The Ribosome-Secye Complex In The Membrane
           Environment
          Length = 205

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 96  RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 155

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 156 AALELAEQREKPT 168


>gi|16766705|ref|NP_462320.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. LT2]
 gi|56415335|ref|YP_152410.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|62181921|ref|YP_218338.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. SC-B67]
 gi|161506031|ref|YP_001573143.1| 30S ribosomal protein S4 [Salmonella enterica subsp. arizonae
           serovar 62:z4,z23:-- str. RSK2980]
 gi|168264703|ref|ZP_02686676.1| ribosomal protein S4 [Salmonella enterica subsp. enterica serovar
           Hadar str. RI_05P066]
 gi|168468027|ref|ZP_02701864.1| ribosomal protein S4 [Salmonella enterica subsp. enterica serovar
           Newport str. SL317]
 gi|194445278|ref|YP_002042667.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|194447938|ref|YP_002047440.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|194472917|ref|ZP_03078901.1| ribosomal protein S4 [Salmonella enterica subsp. enterica serovar
           Kentucky str. CVM29188]
 gi|194734012|ref|YP_002116359.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|197247634|ref|YP_002148336.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
 gi|197262156|ref|ZP_03162230.1| ribosomal protein S4 [Salmonella enterica subsp. enterica serovar
           Saintpaul str. SARA23]
 gi|198244329|ref|YP_002217379.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|200387686|ref|ZP_03214298.1| ribosomal protein S4 [Salmonella enterica subsp. enterica serovar
           Virchow str. SL491]
 gi|204931411|ref|ZP_03222080.1| ribosomal protein S4 [Salmonella enterica subsp. enterica serovar
           Javiana str. GA_MM04042433]
 gi|205354956|ref|YP_002228757.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|207858658|ref|YP_002245309.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|238913869|ref|ZP_04657706.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Tennessee str. CDC07-0191]
 gi|3914907|sp|O54297|RS4_SALTY RecName: Full=30S ribosomal protein S4
 gi|62287196|sp|Q5PK09|RS4_SALPA RecName: Full=30S ribosomal protein S4
 gi|75505522|sp|Q57J55|RS4_SALCH RecName: Full=30S ribosomal protein S4
 gi|189045396|sp|A9MN71|RS4_SALAR RecName: Full=30S ribosomal protein S4
 gi|226695074|sp|B4TXB9|RS4_SALSV RecName: Full=30S ribosomal protein S4
 gi|226699114|sp|B5F7S2|RS4_SALA4 RecName: Full=30S ribosomal protein S4
 gi|226699115|sp|B5FJJ1|RS4_SALDC RecName: Full=30S ribosomal protein S4
 gi|226699116|sp|B5R1F3|RS4_SALEP RecName: Full=30S ribosomal protein S4
 gi|226699117|sp|B5RH39|RS4_SALG2 RecName: Full=30S ribosomal protein S4
 gi|226699118|sp|B4TJY6|RS4_SALHS RecName: Full=30S ribosomal protein S4
 gi|226699119|sp|B4SUR7|RS4_SALNS RecName: Full=30S ribosomal protein S4
 gi|2780215|emb|CAA11203.1| ribosomal protein S4 [Salmonella typhimurium]
 gi|16421972|gb|AAL22279.1| 30S ribosomal subunit protein S4 [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|56129592|gb|AAV79098.1| 30S ribosomal subunit protein S4 [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|62129554|gb|AAX67257.1| 30S ribosomal subunit protein S4 [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|160867378|gb|ABX24001.1| hypothetical protein SARI_04212 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
 gi|194403941|gb|ACF64163.1| ribosomal protein S4 [Salmonella enterica subsp. enterica serovar
           Newport str. SL254]
 gi|194406242|gb|ACF66461.1| ribosomal protein S4 [Salmonella enterica subsp. enterica serovar
           Heidelberg str. SL476]
 gi|194459281|gb|EDX48120.1| ribosomal protein S4 [Salmonella enterica subsp. enterica serovar
           Kentucky str. CVM29188]
 gi|194709514|gb|ACF88735.1| ribosomal protein S4 [Salmonella enterica subsp. enterica serovar
           Schwarzengrund str. CVM19633]
 gi|195628917|gb|EDX48327.1| ribosomal protein S4 [Salmonella enterica subsp. enterica serovar
           Newport str. SL317]
 gi|197211337|gb|ACH48734.1| ribosomal protein S4 [Salmonella enterica subsp. enterica serovar
           Agona str. SL483]
 gi|197240411|gb|EDY23031.1| ribosomal protein S4 [Salmonella enterica subsp. enterica serovar
           Saintpaul str. SARA23]
 gi|197938845|gb|ACH76178.1| ribosomal protein S4 [Salmonella enterica subsp. enterica serovar
           Dublin str. CT_02021853]
 gi|199604784|gb|EDZ03329.1| ribosomal protein S4 [Salmonella enterica subsp. enterica serovar
           Virchow str. SL491]
 gi|204319839|gb|EDZ05049.1| ribosomal protein S4 [Salmonella enterica subsp. enterica serovar
           Javiana str. GA_MM04042433]
 gi|205274737|emb|CAR39793.1| 30S ribosomal subunit protein S4 [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205346870|gb|EDZ33501.1| ribosomal protein S4 [Salmonella enterica subsp. enterica serovar
           Hadar str. RI_05P066]
 gi|206710461|emb|CAR34819.1| 30S ribosomal subunit protein S4 [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|261248573|emb|CBG26411.1| 30S ribosomal subunit protein S4 [Salmonella enterica subsp.
           enterica serovar Typhimurium str. D23580]
 gi|267995625|gb|ACY90510.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 14028S]
 gi|301159959|emb|CBW19478.1| 30S ribosomal subunit protein S4 [Salmonella enterica subsp.
           enterica serovar Typhimurium str. SL1344]
 gi|312914439|dbj|BAJ38413.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. T000240]
 gi|320087861|emb|CBY97624.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Weltevreden str. 2007-60-3289-1]
 gi|322615043|gb|EFY11967.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315996572]
 gi|322617330|gb|EFY14231.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-1]
 gi|322625552|gb|EFY22377.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-3]
 gi|322626394|gb|EFY23203.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-4]
 gi|322632094|gb|EFY28847.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-1]
 gi|322635027|gb|EFY31750.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-2]
 gi|322643272|gb|EFY39839.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 531954]
 gi|322646644|gb|EFY43151.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. NC_MB110209-0054]
 gi|322649990|gb|EFY46409.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. OH_2009072675]
 gi|322652707|gb|EFY49047.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. CASC_09SCPH15965]
 gi|322659536|gb|EFY55780.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 19N]
 gi|322665522|gb|EFY61709.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 81038-01]
 gi|322670416|gb|EFY66555.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MD_MDA09249507]
 gi|322670489|gb|EFY66623.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 414877]
 gi|322675065|gb|EFY71148.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 366867]
 gi|322681602|gb|EFY77631.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 413180]
 gi|322685946|gb|EFY81935.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 446600]
 gi|322716407|gb|EFZ07978.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. A50]
 gi|323131774|gb|ADX19204.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 4/74]
 gi|323195816|gb|EFZ80989.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609458-1]
 gi|323196428|gb|EFZ81579.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556150-1]
 gi|323202333|gb|EFZ87378.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609460]
 gi|323207318|gb|EFZ92268.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 507440-20]
 gi|323211246|gb|EFZ96091.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556152]
 gi|323216045|gb|EGA00776.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB101509-0077]
 gi|323223464|gb|EGA07792.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB102109-0047]
 gi|323226806|gb|EGA10996.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB110209-0055]
 gi|323231832|gb|EGA15942.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB111609-0052]
 gi|323233215|gb|EGA17310.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009083312]
 gi|323237282|gb|EGA21347.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009085258]
 gi|323245517|gb|EGA29516.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315731156]
 gi|323249023|gb|EGA32945.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2009159199]
 gi|323250646|gb|EGA34527.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008282]
 gi|323256875|gb|EGA40589.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008283]
 gi|323263024|gb|EGA46571.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008284]
 gi|323266024|gb|EGA49519.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008285]
 gi|323272781|gb|EGA56184.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008287]
 gi|326625160|gb|EGE31505.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Dublin str. 3246]
 gi|326630105|gb|EGE36448.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 9]
 gi|332990268|gb|AEF09251.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. UK-1]
          Length = 206

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|237728631|ref|ZP_04559112.1| ribosomal protein S4 [Citrobacter sp. 30_2]
 gi|283835713|ref|ZP_06355454.1| hypothetical protein CIT292_10106 [Citrobacter youngae ATCC 29220]
 gi|226909253|gb|EEH95171.1| ribosomal protein S4 [Citrobacter sp. 30_2]
 gi|291068393|gb|EFE06502.1| ribosomal protein S4 [Citrobacter youngae ATCC 29220]
          Length = 206

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>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 = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 26/212 (12%), Positives = 64/212 (30%), Gaps = 26/212 (12%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLRK-------AERTRLW 76
           SR  +++++    ++ N   +   +  + + D +E++   G+  +         E   + 
Sbjct: 58  SRTRIKKLLRHGNIRCNNKPVTLHSHKLSAGDVVEINTYGGIAAKAGLPFPVLFEDQHVI 117

Query: 77  LYHKPIGLVT-----THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              KP+G+ T     + S     +              +V RLD    G+LL        
Sbjct: 118 AVEKPVGIATFSADGSASVQWIVAQALKEHSRGKIHAFAVHRLDKEVSGVLLFAKSKMAM 177

Query: 132 RVLELPSTQWLRVYRV-----------RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
             ++    +  + Y                  + +D    +          +      + 
Sbjct: 178 DHIKEKWKEAEKRYYALVEGKPESPDGTIESWLVEDHAQKVHSTRESSKAKFSVTHYRII 237

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            Q      + V L+ G+  +I+         +
Sbjct: 238 KQVNQYTLLDVKLQTGRKNQIRVHLSDIGCPI 269


>gi|332996752|gb|EGK16377.1| ribosomal protein S4 [Shigella flexneri K-272]
          Length = 202

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 93  RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 152

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 153 AALELAEQREKPT 165


>gi|306829909|ref|ZP_07463096.1| S4 domain-containing protein YlmH [Streptococcus mitis ATCC 6249]
 gi|304427920|gb|EFM31013.1| S4 domain-containing protein YlmH [Streptococcus mitis ATCC 6249]
          Length = 263

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/48 (27%), Positives = 26/48 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +++ A   SR +  ++I ++ V+VN  ++E+    V   D I V
Sbjct: 186 RLDALLSSALKLSRNQTSQLIEKKSVQVNYHVVEKTDYQVAVGDLISV 233


>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 = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 31/214 (14%), Positives = 76/214 (35%), Gaps = 28/214 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTD---------HIEVDGVPLRK-AERTRLW 76
           SR  V+ ++++ ++ VNG +  +    +   D          +E +   LR   E   L 
Sbjct: 42  SRSSVKGLLSRGQISVNGKVTRQFDAPLNPNDTVGINYGRGKVEFNNPLLRIVWEDDDLI 101

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + +K  GL++  +D     T +  L          +++  + RLD +T G+++   +  +
Sbjct: 102 VINKREGLLSVSTDRIKERTAYRILSDYLKECDPRNKIFVLHRLDRDTSGIMMFAKNQKV 161

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ------------GICYGDMQVT 178
              L+   ++ +         +   +K   L    +++                   +  
Sbjct: 162 KEQLQSNWSEAITQRTYVAVIEGRPEKDTDLIVSNLVENKHMQVYVTQDGDGKEAITRYR 221

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           L       + V + L  G+  +I+   +     +
Sbjct: 222 LLQTNNRYSLVELDLETGRKNQIRAQMQSIGHPI 255


>gi|296481995|gb|DAA24110.1| calcium channel, voltage-dependent, L type, alpha 1B subunit [Bos
           taurus]
          Length = 1089

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 9/106 (8%), Positives = 23/106 (21%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                     +          R   +  +  P +    +      +G  +  +  +P   
Sbjct: 871 RADAPKAEGGEPGAREERARPRRSRSKEAAGPREARSERGRGLGPDGGRRHHRRGSPEEA 930

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                    A         +     +  RR+      R+  R +  
Sbjct: 931 AEREPRRHRAHRHAPEPSREGAPGSKGERRARHRGGSRAGPREAES 976



 Score = 45.2 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 10/88 (11%), Positives = 19/88 (21%), Gaps = 2/88 (2%)

Query: 266 TLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFL 325
                        PD   R  +  S +    ++ +           S    A G      
Sbjct: 902 PREARSERGRGLGPDGGRRHHRRGSPEEAAEREPRRHRAHRHAPEPSREG-APGSKGE-R 959

Query: 326 SDSGQREENHRRSPSFPSKRSLRRTSAK 353
               +         +   +   RR  A+
Sbjct: 960 RARHRGGSRAGPREAESGEEPSRRHRAR 987



 Score = 38.2 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 23/168 (13%), Positives = 42/168 (25%), Gaps = 36/168 (21%)

Query: 223 FQLGTL---LAGSTREVSKKI-LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEV 278
            +L  L         E+  +  LR     HL  + + +LD P+         R     + 
Sbjct: 775 LRLQNLRASCEALYSEMDPEERLRFATSRHLRPDMKTHLDRPLVVEPGRDGARGPAGGKA 834

Query: 279 PDDFTRMKKNSSQKN---------------GLSKQKKLATPVHRRNLA------------ 311
             +     + +                      +  +   P                   
Sbjct: 835 RPEGGEAGEGADPPRRHHRHLDSVSVKAAAPAGEPDRADAPKAEGGEPGAREERARPRRS 894

Query: 312 -----SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                +    A+      L   G R  + R SP   ++R  RR  A +
Sbjct: 895 RSKEAAGPREARSERGRGLGPDGGRRHHRRGSPEEAAEREPRRHRAHR 942



 Score = 36.7 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 17/118 (14%), Positives = 33/118 (27%), Gaps = 4/118 (3%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
              +    H      V++ A   + E    D P      P       +    ++  +   
Sbjct: 843 EGADPPRRHHRHLDSVSVKAAAPAGEPDRADAPKAEGGEPGAREERARPRRSRSKEAAGP 902

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLS---DSGQREENHRRSPSFPSKRSLRRTSAKK 354
           + A     R L  +         S         +R   HR +P  PS+     +  ++
Sbjct: 903 REARSERGRGLGPDGGRRHHRRGSPEEAAEREPRRHRAHRHAP-EPSREGAPGSKGER 959


>gi|322421437|ref|YP_004200660.1| RNA-binding S4 domain-containing protein [Geobacter sp. M18]
 gi|320127824|gb|ADW15384.1| RNA-binding S4 domain protein [Geobacter sp. M18]
          Length = 65

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 27/60 (45%), Gaps = 1/60 (1%)

Query: 7  VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          ++ +    ++   + A   + S  E + +I++  V VNG +  R    +   D +EV G 
Sbjct: 1  MKIDTEFIKLDSFLKAVDAVCSGGEAKIIISEGMVSVNGEVELRRGRKLRPGDRVEVGGK 60


>gi|301021164|ref|ZP_07185202.1| ribosomal protein S4 [Escherichia coli MS 196-1]
 gi|312972443|ref|ZP_07786617.1| ribosomal protein S4 [Escherichia coli 1827-70]
 gi|30043665|gb|AAP19385.1| 30S ribosomal subunit protein S4 [Shigella flexneri 2a str. 2457T]
 gi|299881640|gb|EFI89851.1| ribosomal protein S4 [Escherichia coli MS 196-1]
 gi|310334820|gb|EFQ01025.1| ribosomal protein S4 [Escherichia coli 1827-70]
 gi|315617098|gb|EFU97708.1| ribosomal protein S4 [Escherichia coli 3431]
 gi|320187017|gb|EFW61729.1| SSU ribosomal protein S4p (S9e) [Shigella flexneri CDC 796-83]
 gi|320191670|gb|EFW66320.1| SSU ribosomal protein S4p (S9e) [Escherichia coli O157:H7 str.
           EC1212]
 gi|320195388|gb|EFW70015.1| SSU ribosomal protein S4p (S9e) [Escherichia coli WV_060327]
 gi|320199483|gb|EFW74073.1| SSU ribosomal protein S4p (S9e) [Escherichia coli EC4100B]
 gi|323154134|gb|EFZ40337.1| ribosomal protein S4 [Escherichia coli EPECa14]
 gi|323179168|gb|EFZ64742.1| ribosomal protein S4 [Escherichia coli 1180]
 gi|323182774|gb|EFZ68175.1| ribosomal protein S4 [Escherichia coli 1357]
 gi|325498865|gb|EGC96724.1| ribosomal protein S4 [Escherichia fergusonii ECD227]
 gi|326342544|gb|EGD66318.1| SSU ribosomal protein S4p (S9e) [Escherichia coli O157:H7 str.
           1044]
 gi|326344531|gb|EGD68280.1| SSU ribosomal protein S4p (S9e) [Escherichia coli O157:H7 str.
           1125]
 gi|330909340|gb|EGH37854.1| SSU ribosomal protein S4p (S9e) [Escherichia coli AA86]
 gi|332085445|gb|EGI90611.1| ribosomal protein S4 [Shigella boydii 5216-82]
 gi|332345243|gb|AEE58577.1| ribosomal protein RpsD [Escherichia coli UMNK88]
 gi|332750806|gb|EGJ81213.1| ribosomal protein S4 [Shigella flexneri 2747-71]
 gi|333012395|gb|EGK31776.1| ribosomal protein S4 [Shigella flexneri K-304]
          Length = 202

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 93  RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 152

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 153 AALELAEQREKPT 165


>gi|42560658|ref|NP_975109.1| hemolysin A [Mycoplasma mycoides subsp. mycoides SC str. PG1]
 gi|42492154|emb|CAE76751.1| hemolysin A [Mycoplasma mycoides subsp. mycoides SC str. PG1]
 gi|301320463|gb|ADK69106.1| S4 domain protein [Mycoplasma mycoides subsp. mycoides SC str.
          Gladysdale]
          Length = 149

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 1/71 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          R+ + I +  +  SR + +  I  + V VN I + + +  V S D IE+    L    R 
Sbjct: 4  RLDEYIYKNNLTQSRNKAKEHILNKEVYVNNIAIMKPSFLVDSNDLIEIRSTKLEYVSRA 63

Query: 74 RLWLYHKPIGL 84
             L       
Sbjct: 64 YEKLKKAINKW 74


>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 = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 37/255 (14%), Positives = 72/255 (28%), Gaps = 48/255 (18%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +V  +    R+ +V+A R    SR  ++ +I   RV + G  +   A +  S + I +D 
Sbjct: 104 VVAGDEGSPRLDRVLATRCPALSRSRLKALILDGRVAIRGAPVRDPAYHAASGETITIDV 163

Query: 64  ---------GVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                    G  +           + +      +V   +  +  + V   +         
Sbjct: 164 PPPVAPEPAGEAIALEIVHEDDDIIVIDKPRGLVVHPAAGHETGTLVNALIAHCGESLSG 223

Query: 106 ----SRVISVGRLDINTEGLLLLTND-----------------GGLARVLELPSTQWLRV 144
                R   V RLD +T GL++   +                 G L R            
Sbjct: 224 IGGVRRPGIVHRLDKDTTGLMVAAKNDRAHQSLSAQFADHGRTGELRRGYYAFVWGAPNR 283

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG------LREGKN 198
            R      +D+      +K  V  G         +       +   +       L  G+ 
Sbjct: 284 IRGTIDAPIDRHPHAR-EKMAVRDGGREAITHWEVLETFTGRSGGEIVSLIACQLETGRT 342

Query: 199 REIKKVFEFFNWKVN 213
            +I+         + 
Sbjct: 343 HQIRVHLAHIGHPLL 357


>gi|314922834|gb|EFS86665.1| S4 domain protein [Propionibacterium acnes HL001PA1]
 gi|314966265|gb|EFT10364.1| S4 domain protein [Propionibacterium acnes HL082PA2]
 gi|314980791|gb|EFT24885.1| S4 domain protein [Propionibacterium acnes HL110PA3]
 gi|315090236|gb|EFT62212.1| S4 domain protein [Propionibacterium acnes HL110PA4]
 gi|315093429|gb|EFT65405.1| S4 domain protein [Propionibacterium acnes HL060PA1]
 gi|315102986|gb|EFT74962.1| S4 domain protein [Propionibacterium acnes HL050PA2]
 gi|327327046|gb|EGE68827.1| S4 domain protein [Propionibacterium acnes HL103PA1]
          Length = 71

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/54 (22%), Positives = 20/54 (37%), Gaps = 9/54 (16%)

Query: 14 QRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ + +     A  G     +   +IA   V VNG +  R    +   D + V
Sbjct: 2  IRLGQYLKFANLAETGG----QARELIASGMVSVNGEVETRRGRQLHPGDEVRV 51


>gi|300088170|ref|YP_003758692.1| 30S ribosomal protein S4 [Dehalogenimonas lykanthroporepellens
           BL-DC-9]
 gi|299527903|gb|ADJ26371.1| ribosomal protein S4 [Dehalogenimonas lykanthroporepellens BL-DC-9]
          Length = 207

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A SR +  +++    + VNG  L+  +  V  +D I  
Sbjct: 98  RLDNVVYRLGLADSRAQARQLVRHGHITVNGRKLDIPSYLVKESDEITF 146


>gi|258645384|ref|ZP_05732853.1| hemolysin A [Dialister invisus DSM 15470]
 gi|260402734|gb|EEW96281.1| hemolysin A [Dialister invisus DSM 15470]
          Length = 275

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 9/61 (14%), Positives = 24/61 (39%), Gaps = 1/61 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
              +R+  ++   G   +R   +R I    + VN + +++    + S   + + G  + 
Sbjct: 3  KVKKERLDVLLVERGFFETRENAKRHIMAGIILVNDVPVDKPGTKIPSDVRLRIKGHVMP 62

Query: 69 K 69
           
Sbjct: 63 Y 63


>gi|229076157|ref|ZP_04209125.1| 30S ribosomal protein S4 [Bacillus cereus Rock4-18]
 gi|229099115|ref|ZP_04230049.1| 30S ribosomal protein S4 [Bacillus cereus Rock3-29]
 gi|229105283|ref|ZP_04235932.1| 30S ribosomal protein S4 [Bacillus cereus Rock3-28]
 gi|229118145|ref|ZP_04247504.1| 30S ribosomal protein S4 [Bacillus cereus Rock1-3]
 gi|228665368|gb|EEL20851.1| 30S ribosomal protein S4 [Bacillus cereus Rock1-3]
 gi|228678209|gb|EEL32437.1| 30S ribosomal protein S4 [Bacillus cereus Rock3-28]
 gi|228684343|gb|EEL38287.1| 30S ribosomal protein S4 [Bacillus cereus Rock3-29]
 gi|228707020|gb|EEL59225.1| 30S ribosomal protein S4 [Bacillus cereus Rock4-18]
          Length = 200

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 93  RLDNLVYRMGLARTRRAARQLVNHGHIMVDGARVDIPSYRVKPGQTISV 141


>gi|220907729|ref|YP_002483040.1| photosystem II S4 domain-containing protein [Cyanothece sp. PCC
           7425]
 gi|219864340|gb|ACL44679.1| photosystem II S4 domain protein [Cyanothece sp. PCC 7425]
          Length = 259

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 2/65 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             K  +       R+   IA AG   SR ++  +IA   V+VN   + + +  + + D +
Sbjct: 172 PQKKELTTVEASLRLD-AIASAGFGMSRSKMADLIAAGDVRVNWKDISQPSFTLKAGDLV 230

Query: 61  EVDGV 65
            + G 
Sbjct: 231 AIRGK 235


>gi|125973307|ref|YP_001037217.1| RNA-binding S4 [Clostridium thermocellum ATCC 27405]
 gi|256003788|ref|ZP_05428776.1| RNA-binding S4 domain protein [Clostridium thermocellum DSM 2360]
 gi|281417510|ref|ZP_06248530.1| RNA-binding S4 domain protein [Clostridium thermocellum JW20]
 gi|125713532|gb|ABN52024.1| RNA-binding S4 [Clostridium thermocellum ATCC 27405]
 gi|255992349|gb|EEU02443.1| RNA-binding S4 domain protein [Clostridium thermocellum DSM 2360]
 gi|281408912|gb|EFB39170.1| RNA-binding S4 domain protein [Clostridium thermocellum JW20]
 gi|316940460|gb|ADU74494.1| RNA-binding S4 domain protein [Clostridium thermocellum DSM 1313]
          Length = 263

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 16/60 (26%), Positives = 23/60 (38%), Gaps = 2/60 (3%)

Query: 7   VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +       R+  V A AG   SR +   +I  ++V VN       A  V   D I + G 
Sbjct: 180 ISSTVASLRLDSV-ASAGFGISRSKTADLIRGEKVAVNWETATNPARLVKEGDTISIRGK 238


>gi|322831096|ref|YP_004211123.1| ribosomal protein S4 [Rahnella sp. Y9602]
 gi|321166297|gb|ADW71996.1| ribosomal protein S4 [Rahnella sp. Y9602]
          Length = 206

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  VI R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVIYRMGFGATRAESRQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|217033347|ref|ZP_03438778.1| hypothetical protein HP9810_9g100 [Helicobacter pylori 98-10]
 gi|216944288|gb|EEC23713.1| hypothetical protein HP9810_9g100 [Helicobacter pylori 98-10]
          Length = 235

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   +    +A SR + + ++ + +V VN +++ + +  V  +D IE+
Sbjct: 1  MRLDYALFNQHLANSREKAKALVLKNQVLVNNMVVSKPSFMVKESDKIEL 50


>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 = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 23/243 (9%), Positives = 61/243 (25%), Gaps = 37/243 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIE--- 61
           V +    +RV   I+R    SR +   + A  +V+V+G +  + +  V       +E   
Sbjct: 12  VPDGLEGERVDAAISRMFGFSRTKAAELAAAGKVQVDGSVAGK-SERVHGGAWLEVEMPG 70

Query: 62  -----------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                      V+G+ +   +   + +               G + +     + +    S
Sbjct: 71  APAPVQIVAEPVEGMEIVHDDDDIVVIMKPVGVAAHPSPGWTGTTVIGGLAAAGYRISTS 130

Query: 111 VGRLDINTEGLLLLTNDGGLA-------------RVLELPSTQWLRVYRVRFHGQVDQDK 157
                      L +   G +              +  +    +            +    
Sbjct: 131 GAAERQGIVHRLDVGTSGLMVVAKSERAYTLLKAQFRDRVVDKKYHALVQGHPDPMSGTI 190

Query: 158 LNLLKKGIVIQGICYGDMQVT-------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
              + +            +         L     + + + + L  G+  +I+        
Sbjct: 191 DAPIGRHPNHDYKWAVTAEGKPSVTHYDLIEAYRAASLLDIKLETGRTHQIRVHMSAHRH 250

Query: 211 KVN 213
              
Sbjct: 251 PCV 253


>gi|161616441|ref|YP_001590406.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Paratyphi B str. SPB7]
 gi|224585211|ref|YP_002639010.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|161365805|gb|ABX69573.1| hypothetical protein SPAB_04256 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|224469739|gb|ACN47569.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|321226467|gb|EFX51517.1| SSU ribosomal protein S4p (S9e) [Salmonella enterica subsp.
           enterica serovar Typhimurium str. TN061786]
          Length = 202

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 93  RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 152

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 153 AALELAEQREKPT 165


>gi|116667413|pdb|2GY9|D Chain D, Structure Of The 30s Subunit Of A Pre-Translocational E.
           Coli Ribosome Obtained By Fitting Atomic Models For Rna
           And Protein Components Into Cryo-Em Map Emd-1056
 gi|116667465|pdb|2GYB|D Chain D, Structure Of The 30s Subunit Of A Secm-Stalled E. Coli
           Ribosome Complex Obtained By Fitting Atomic Models For
           Rna And Protein Components Into Cryo-Em Map Emd-1143
          Length = 204

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 95  RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 154

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 155 AALELAEQREKPT 167


>gi|121609261|ref|YP_997068.1| 30S ribosomal protein S4 [Verminephrobacter eiseniae EF01-2]
 gi|152112272|sp|A1WK93|RS4_VEREI RecName: Full=30S ribosomal protein S4
 gi|121553901|gb|ABM58050.1| SSU ribosomal protein S4P [Verminephrobacter eiseniae EF01-2]
          Length = 207

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V + D + V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAITVNGQSVNIPSYLVKTGDLVAV 146


>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 = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 31/243 (12%), Positives = 64/243 (26%), Gaps = 38/243 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           V +    +RV    AR    SR  +  +I    V ++G  + RA+V V +   ++VD   
Sbjct: 6   VPDGLDGERVDVAAARMSGVSRSRISSLIEDGGVFLDGQQVSRASVRVATGQMLDVDLCD 65

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                        G+ +   +   + +              +G S V     + F+   S
Sbjct: 66  PVVTPSITPQIVEGMRIIHDDSDIVVVDKPAGVAAHPSLGWEGPSVVEHLAAAGFAISTS 125

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPST---------------------QWLRVYRVRF 149
                      L +   G +       +                           +    
Sbjct: 126 GAPERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTGTI 185

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +D  +   K  ++ G  +                + V L  G+  +I+       
Sbjct: 186 DAPIGRDHRHDW-KMAIVDGGRHSVTHYETVEAFRHATLLKVHLETGRTHQIRVHMAAIK 244

Query: 210 WKV 212
              
Sbjct: 245 HPC 247


>gi|262038727|ref|ZP_06012087.1| ribosomal protein S4 [Leptotrichia goodfellowii F0264]
 gi|261747279|gb|EEY34758.1| ribosomal protein S4 [Leptotrichia goodfellowii F0264]
          Length = 195

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +RR+  ++++   + +NG  +  A+  V   D I +
Sbjct: 89  RLDNVVYRLGFGATRRQARQIVSHGHILINGKRVNIASYRVKQGDVISI 137


>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 = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 31/243 (12%), Positives = 64/243 (26%), Gaps = 38/243 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           V +    +RV    AR    SR  +  +I    V ++G  + RA+V V +   ++VD   
Sbjct: 6   VPDGLDGERVDVAAARMSGVSRSRISSLIEDGGVFLDGQQVSRASVRVATGQMLDVDLCD 65

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                        G+ +   +   + +              +G S V     + F+   S
Sbjct: 66  PVATPSITPQIVEGMRIIHDDSDIVVVDKPAGVAAHPSLGWEGPSVVEHLAAAGFAISTS 125

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPST---------------------QWLRVYRVRF 149
                      L +   G +       +                           +    
Sbjct: 126 GAPERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTGTI 185

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +D  +   K  ++ G  +                + V L  G+  +I+       
Sbjct: 186 DAPIGRDHRHDW-KMAIVDGGRHSVTHYETVEAFRHATLLKVHLETGRTHQIRVHMAAIK 244

Query: 210 WKV 212
              
Sbjct: 245 HPC 247


>gi|330444360|ref|YP_004377346.1| hypothetical protein G5S_0690 [Chlamydophila pecorum E58]
 gi|197091904|gb|ACH42159.1| hypothetical protein [Chlamydophila pecorum E58]
 gi|328807470|gb|AEB41643.1| hypothetical protein G5S_0690 [Chlamydophila pecorum E58]
          Length = 388

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 23/125 (18%), Positives = 40/125 (32%), Gaps = 1/125 (0%)

Query: 224 QLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
           +L  L   S++E+S K       P   E +   L     SS+ L     +     P + +
Sbjct: 143 ELKDLETSSSKELSPKE-PSPKEPSPKEPSPKELSPKEPSSKELSPKELSPKEPSPKEPS 201

Query: 284 RMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
             + +  + +      K  +P        +         S    S +   +   S   PS
Sbjct: 202 SKELSPKEPSPKEPSSKELSPKEPSPKEPSSKELSPKEPSPKEPSPKEPSSKEPSSKEPS 261

Query: 344 KRSLR 348
           K S R
Sbjct: 262 KFSFR 266


>gi|153812444|ref|ZP_01965112.1| hypothetical protein RUMOBE_02843 [Ruminococcus obeum ATCC 29174]
 gi|149831369|gb|EDM86457.1| hypothetical protein RUMOBE_02843 [Ruminococcus obeum ATCC 29174]
          Length = 197

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +RRE  +++  + V VNG  +   +  V + D IE+
Sbjct: 88  RLDNVVFRMGLARTRREARQIVDHKHVLVNGKCVNIPSYLVKAGDTIEI 136


>gi|139438877|ref|ZP_01772337.1| Hypothetical protein COLAER_01341 [Collinsella aerofaciens ATCC
           25986]
 gi|133775588|gb|EBA39408.1| Hypothetical protein COLAER_01341 [Collinsella aerofaciens ATCC
           25986]
          Length = 198

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R+E  + +      VNG  ++  +  V + D + V
Sbjct: 89  RLDNVVFRLGFARTRKEARQSVRHGHFTVNGKRVDIPSYRVKAGDVVAV 137


>gi|110833282|ref|YP_692141.1| 30S ribosomal protein S4 [Alcanivorax borkumensis SK2]
 gi|123149715|sp|Q0VSH9|RS4_ALCBS RecName: Full=30S ribosomal protein S4
 gi|110646393|emb|CAL15869.1| 30S ribosomal protein S4 [Alcanivorax borkumensis SK2]
          Length = 210

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +  A+  V   D I V
Sbjct: 101 RLDNVVYRMGFGSTRSEARQLVSHRAILVNGQSVNVASYQVKPGDQINV 149


>gi|24380465|ref|NP_722420.1| 30S ribosomal protein S4 [Streptococcus mutans UA159]
 gi|290581395|ref|YP_003485787.1| 30S ribosomal protein S4 [Streptococcus mutans NN2025]
 gi|26399366|sp|P59133|RS4_STRMU RecName: Full=30S ribosomal protein S4
 gi|24378494|gb|AAN59726.1|AE015034_7 30S ribosomal protein S4 [Streptococcus mutans UA159]
 gi|254998294|dbj|BAH88895.1| 30S ribosomal protein S4 [Streptococcus mutans NN2025]
          Length = 203

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A+ RR+  + +    + V+G  ++  +  V     I V
Sbjct: 94  RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVEVGQVISV 142


>gi|323136857|ref|ZP_08071938.1| hemolysin A [Methylocystis sp. ATCC 49242]
 gi|322398174|gb|EFY00695.1| hemolysin A [Methylocystis sp. ATCC 49242]
          Length = 242

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 10/47 (21%), Positives = 17/47 (36%), Gaps = 1/47 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
          R    +   G   SR +    I    V VNG ++ + +  +     I
Sbjct: 5  RADAALHERGFFESRAKAREAIEAGLVTVNGRVVTKPSAPIADDAEI 51


>gi|310829557|ref|YP_003961914.1| ribosomal protein S4 [Eubacterium limosum KIST612]
 gi|308741291|gb|ADO38951.1| ribosomal protein S4 [Eubacterium limosum KIST612]
          Length = 209

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 1/71 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G+A SR+E  +++      VNG  +   +  V   D IEV     +  +  
Sbjct: 100 RLDNVVYRLGLATSRKEARQLVQHAHFLVNGKKVNVPSYLVKEGDTIEVKAKSKKSPKFK 159

Query: 74  RLWLYHKPIGL 84
            +    +   +
Sbjct: 160 EILEATENRAV 170


>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 = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 31/214 (14%), Positives = 76/214 (35%), Gaps = 28/214 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTD---------HIEVDGVPLRK-AERTRLW 76
           SR  V+ ++++ ++ VNG +  +    +   D          +E +   LR   E   L 
Sbjct: 42  SRSSVKGLLSRGQISVNGKVTRQFDAPLNPNDTVGINYGRGKVEFNNPLLRIVWEDDDLI 101

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + +K  GL++  +D     T +  L          +++  + RLD +T G+++   +  +
Sbjct: 102 VINKREGLLSVSTDRIKERTAYRILSDYVKECDPRNKIFVLHRLDRDTSGIMMFAKNQKV 161

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ------------GICYGDMQVT 178
              L+   ++ +         +   +K   L    +++                   +  
Sbjct: 162 KEQLQSNWSEAITQRTYVAVIEGRPEKDTDLIVSNLVENKHMQVYVTQDGDGKEAITRYR 221

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           L       + V + L  G+  +I+   +     +
Sbjct: 222 LLQTNNRYSLVELDLETGRKNQIRAQMQSIGHPI 255


>gi|300857808|ref|YP_003782791.1| 30S ribosomal protein S4 [Corynebacterium pseudotuberculosis FRC41]
 gi|300685262|gb|ADK28184.1| 30S ribosomal protein S4 [Corynebacterium pseudotuberculosis FRC41]
 gi|302205543|gb|ADL09885.1| 30S ribosomal protein S4 [Corynebacterium pseudotuberculosis C231]
 gi|302330098|gb|ADL20292.1| 30S ribosomal protein S4 [Corynebacterium pseudotuberculosis 1002]
 gi|308275779|gb|ADO25678.1| 30S ribosomal protein S4 [Corynebacterium pseudotuberculosis I19]
          Length = 201

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR+  ++++     VNG  +   +  V   D I+V
Sbjct: 92  RLDNVVYRAGLARTRRQARQLVSHGHFTVNGKKINVPSYKVSQYDIIDV 140


>gi|295109501|emb|CBL23454.1| SSU ribosomal protein S4P [Ruminococcus obeum A2-162]
          Length = 197

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +RRE  +++  + V VNG  +   +  V + D IE+
Sbjct: 88  RLDNVVFRMGLARTRREARQIVDHKHVLVNGKCVNIPSYLVKAGDTIEI 136


>gi|217967433|ref|YP_002352939.1| hemolysin A [Dictyoglomus turgidum DSM 6724]
 gi|217336532|gb|ACK42325.1| hemolysin A [Dictyoglomus turgidum DSM 6724]
          Length = 271

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 11/52 (21%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            +R+  ++ + G   SR +    +    VKVNG ++ +  + +     IE+
Sbjct: 3  EKERLDVLLVKRGFFESREKARAAVIAGIVKVNGNVVIKPDLKIPIDSLIEI 54


>gi|15829187|ref|NP_326547.1| 30S ribosomal protein S4 [Mycoplasma pulmonis UAB CTIP]
 gi|26399464|sp|Q98PK6|RS4_MYCPU RecName: Full=30S ribosomal protein S4
 gi|14090131|emb|CAC13889.1| 30S RIBOSOMAL PROTEIN S4 [Mycoplasma pulmonis]
          Length = 199

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           QR+  ++ RAG A +RR+  + +    V V+G  ++  +  V     IE+     + A+ 
Sbjct: 94  QRLDNLVYRAGFAETRRQARQFVNHGHVLVDGKKVDIPSYRVAVGKVIEIKEKLQKNAQV 153

Query: 73  TR 74
            R
Sbjct: 154 LR 155


>gi|218675156|ref|ZP_03524825.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
          [Rhizobium etli GR56]
          Length = 199

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/65 (20%), Positives = 28/65 (43%), Gaps = 3/65 (4%)

Query: 1  MKDKNIVQENFTPQ-RVSKVI-ARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMST 57
          M  + ++  + T + R+   + A+ G   SR  ++ +I   +V + G  +      V   
Sbjct: 1  MGIRKVLTADETAEGRLDAWLTAQVGEDFSRSRIKALIKDGQVSMRGEPVTDPQRKVRVG 60

Query: 58 DHIEV 62
          D  E+
Sbjct: 61 DSFEI 65


>gi|52080143|ref|YP_078934.1| RNA-binding protein [Bacillus licheniformis ATCC 14580]
 gi|52785519|ref|YP_091348.1| YlmH [Bacillus licheniformis ATCC 14580]
 gi|319646078|ref|ZP_08000308.1| YlmH protein [Bacillus sp. BT1B_CT2]
 gi|52003354|gb|AAU23296.1| RNA-binding protein [Bacillus licheniformis ATCC 14580]
 gi|52348021|gb|AAU40655.1| YlmH [Bacillus licheniformis ATCC 14580]
 gi|317391828|gb|EFV72625.1| YlmH protein [Bacillus sp. BT1B_CT2]
          Length = 258

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/63 (19%), Positives = 29/63 (46%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +D  I  +  +  R+  + +     SR++ + ++    VKVN  ++E  +  +   D + 
Sbjct: 170 QDVEIRDDTVSSLRLDAICSAMSRQSRQKAQVLVKNGLVKVNWKVIEDPSYALAEGDMVS 229

Query: 62  VDG 64
           + G
Sbjct: 230 IRG 232


>gi|47565070|ref|ZP_00236113.1| ribosomal protein S4 [Bacillus cereus G9241]
 gi|47557856|gb|EAL16181.1| ribosomal protein S4 [Bacillus cereus G9241]
          Length = 200

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 93  RLDNLVYRMGLARTRRAARQLVNHGHIMVDGARVDIPSYRVKPGQTISV 141


>gi|332366081|gb|EGJ43837.1| S4 domain-containing protein YlmH [Streptococcus sanguinis SK1059]
          Length = 261

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/48 (27%), Positives = 25/48 (52%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K++A     SR +  ++I+ + VK+N  + +  +  V   D I V
Sbjct: 184 RLDKLVASTFKLSRSQAAQLISGKHVKMNYAVNDNPSQQVGLEDLISV 231


>gi|332361764|gb|EGJ39568.1| S4 domain-containing protein YlmH [Streptococcus sanguinis SK1056]
          Length = 261

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/48 (27%), Positives = 25/48 (52%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K++A     SR +  ++I+ + VK+N  + +  +  V   D I V
Sbjct: 184 RLDKLVASTFKLSRSQAAQLISGKHVKMNYAVNDNPSQQVGLEDLISV 231


>gi|329313677|gb|AEB88090.1| Pseudouridine synthase [Staphylococcus aureus subsp. aureus T0131]
          Length = 258

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 20/160 (12%), Positives = 44/160 (27%), Gaps = 12/160 (7%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEG 120
            +   +   + +        T   +    S +   L              V RLD NT G
Sbjct: 50  EVLYEDAFIIIVTKPNNQNCTPSREHPHESLIEQVLYHCQEHGENINPHIVTRLDRNTTG 109

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD-------QDKLNLLKKGIVIQGICYG 173
           +++    G +  +    + + +    V              +   + +    V     Y 
Sbjct: 110 IVIFAKYGHIHHLFSKVNLKKIYTCLVYGKTHTSGIIEANIRRSKDRIITREVASDGKYA 169

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                +  Q    +   V L  G+  +I+  F+     + 
Sbjct: 170 KTSYEVINQNDKYSLCKVHLHTGRTHQIRVHFQHIGHPIV 209


>gi|328945575|gb|EGG39726.1| S4 domain-containing protein YlmH [Streptococcus sanguinis SK1087]
          Length = 261

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/48 (27%), Positives = 25/48 (52%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K++A     SR +  ++I+ + VK+N  + +  +  V   D I V
Sbjct: 184 RLDKLVASTFKLSRSQAAQLISGKHVKMNYAVNDNPSQQVGLEDLISV 231


>gi|327473397|gb|EGF18817.1| S4 domain-containing protein YlmH [Streptococcus sanguinis SK408]
          Length = 261

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/48 (27%), Positives = 25/48 (52%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K++A     SR +  ++I+ + VK+N  + +  +  V   D I V
Sbjct: 184 RLDKLVASTFKLSRSQAAQLISGKHVKMNYAVNDNPSQQVGLEDLISV 231


>gi|327469022|gb|EGF14494.1| S4 domain-containing protein YlmH [Streptococcus sanguinis SK330]
          Length = 261

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/48 (27%), Positives = 25/48 (52%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K++A     SR +  ++I+ + VK+N  + +  +  V   D I V
Sbjct: 184 RLDKLVASTFKLSRSQAAQLISGKHVKMNYAVNDNPSQQVGLEDLISV 231


>gi|327458760|gb|EGF05108.1| S4 domain-containing protein YlmH [Streptococcus sanguinis SK1057]
          Length = 261

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/48 (27%), Positives = 25/48 (52%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K++A     SR +  ++I+ + VK+N  + +  +  V   D I V
Sbjct: 184 RLDKLVASTFKLSRSQAAQLISGKHVKMNYAVNDNPSQQVGLEDLISV 231


>gi|325663703|ref|ZP_08152107.1| hypothetical protein HMPREF0490_02848 [Lachnospiraceae bacterium
          4_1_37FAA]
 gi|331087224|ref|ZP_08336294.1| hypothetical protein HMPREF0987_02597 [Lachnospiraceae bacterium
          9_1_43BFAA]
 gi|325470196|gb|EGC73429.1| hypothetical protein HMPREF0490_02848 [Lachnospiraceae bacterium
          4_1_37FAA]
 gi|330408910|gb|EGG88371.1| hypothetical protein HMPREF0987_02597 [Lachnospiraceae bacterium
          9_1_43BFAA]
          Length = 79

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR          RV VNG + + A+V V   D IE+
Sbjct: 1  MRLDKFLKVSRLIKRRTVANEACDAGRVLVNGTVAK-ASVKVKPGDVIEI 49


>gi|324990664|gb|EGC22600.1| S4 domain-containing protein YlmH [Streptococcus sanguinis SK353]
          Length = 261

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/48 (27%), Positives = 25/48 (52%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K++A     SR +  ++I+ + VK+N  + +  +  V   D I V
Sbjct: 184 RLDKLVASTFKLSRSQAAQLISGKHVKMNYAVNDNPSQQVGLEDLISV 231


>gi|323352734|ref|ZP_08087704.1| S4 domain-containing protein YlmH [Streptococcus sanguinis VMC66]
 gi|322121770|gb|EFX93516.1| S4 domain-containing protein YlmH [Streptococcus sanguinis VMC66]
          Length = 260

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/48 (27%), Positives = 25/48 (52%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K++A     SR +  ++I+ + VK+N  + +  +  V   D I V
Sbjct: 183 RLDKLVASTFKLSRSQAAQLISGKHVKMNYAVNDNPSQQVGLEDLISV 230


>gi|210613798|ref|ZP_03289912.1| hypothetical protein CLONEX_02123 [Clostridium nexile DSM 1787]
 gi|210151007|gb|EEA82015.1| hypothetical protein CLONEX_02123 [Clostridium nexile DSM 1787]
          Length = 79

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR          RV VNG + + A+V V   D IE+
Sbjct: 1  MRLDKFLKVSRLIKRRTVANEACDAGRVLVNGNVAK-ASVKVKPGDVIEI 49


>gi|307709599|ref|ZP_07646052.1| S4 domain protein [Streptococcus mitis SK564]
 gi|307619635|gb|EFN98758.1| S4 domain protein [Streptococcus mitis SK564]
          Length = 261

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 10/48 (20%), Positives = 26/48 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +++     SR +  +++ ++ V+VN  +++++   V   D I V
Sbjct: 184 RLDVLLSSVLKLSRSQANQLVEKKLVQVNYHIVDKSDYTVQVGDLISV 231


>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 = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 31/242 (12%), Positives = 74/242 (30%), Gaps = 37/242 (15%)

Query: 8   QENFTPQRVSKVIARA--GIASRREVERMIAQQRVKV-------NGI-------LLERAA 51
           +E+    R  + +A A  G+ +R  ++++   + V+V       N         +++   
Sbjct: 9   EESDAGVRADRWLASAAEGLLTRSAIQKLCDCKAVRVGEKPVSKNDRLRGGETFIIDVPD 68

Query: 52  VN---VMSTDH-IEV---DGVPLRKAERTRLWLY----HKPIGLVTTHSDPDG------- 93
                ++  D  IE+   DG  L   +   + ++    H    LV               
Sbjct: 69  AQPLDIVPQDIPIEIVYEDGDLLVVNKPKGMVVHPAPGHPNGTLVNALLYHCQGRLSSIN 128

Query: 94  ---RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
              R  +   +    S ++ V + D     L     +    R+                 
Sbjct: 129 GVIRPGIVHRIDKDTSGLLIVAKNDAAHGTLAEQIKNHSFTRIYNAVVYGGFSTDEGTVD 188

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + + + +  K  +  +          +  + G   W+ + L  G+  +I+    +   
Sbjct: 189 APIGRSQNDRKKMCVTDRNARGAVTHYRVLERLGRFTWLKLCLETGRTHQIRVHMAYIGH 248

Query: 211 KV 212
            V
Sbjct: 249 PV 250


>gi|315085265|gb|EFT57241.1| S4 domain protein [Propionibacterium acnes HL002PA3]
          Length = 71

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/54 (22%), Positives = 20/54 (37%), Gaps = 9/54 (16%)

Query: 14 QRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ + +     A  G     +   +IA   V VNG +  R    +   D + V
Sbjct: 2  IRLGQYLKFANLAETGG----QAPELIASGMVSVNGEVETRRGRQLHPGDEVTV 51


>gi|313892596|ref|ZP_07826183.1| ribosomal protein S4 [Dialister microaerophilus UPII 345-E]
 gi|329121298|ref|ZP_08249925.1| 30S ribosomal protein S4 [Dialister micraerophilus DSM 19965]
 gi|313118993|gb|EFR42198.1| ribosomal protein S4 [Dialister microaerophilus UPII 345-E]
 gi|327470232|gb|EGF15695.1| 30S ribosomal protein S4 [Dialister micraerophilus DSM 19965]
          Length = 197

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ RAG A S R+  +M+    + VNG  ++  + +V     + +
Sbjct: 87  RLDNIVYRAGFARSIRQARQMVNHGLISVNGKKVDIPSYSVQPGQVVSL 135


>gi|224065743|ref|XP_002301949.1| predicted protein [Populus trichocarpa]
 gi|222843675|gb|EEE81222.1| predicted protein [Populus trichocarpa]
          Length = 444

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 3/62 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           +K +  V       R+   I+   +GI SR  V+  I    V VNG ++++ + NV + D
Sbjct: 81  VKLEESVDSKSGKSRLDSWISSRISGI-SRARVQSSIKSGLVSVNGKVIDKVSHNVKAGD 139

Query: 59  HI 60
            +
Sbjct: 140 KV 141


>gi|91791563|ref|YP_561214.1| 30S ribosomal protein S4 [Shewanella denitrificans OS217]
 gi|123166579|sp|Q12ST5|RS4_SHEDO RecName: Full=30S ribosomal protein S4
 gi|91713565|gb|ABE53491.1| SSU ribosomal protein S4P [Shewanella denitrificans OS217]
          Length = 206

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + V VNG ++   +  V + D + +
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKTVLVNGRVVNIPSFKVSANDVVSI 145


>gi|75764761|ref|ZP_00744159.1| SSU ribosomal protein S4P [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|74487751|gb|EAO51569.1| SSU ribosomal protein S4P [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
          Length = 212

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 93  RLDNLVYRMGLARTRRAARQLVNHGHIMVDGARVDIPSYRVKPNQTISV 141


>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 = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 31/243 (12%), Positives = 63/243 (25%), Gaps = 38/243 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           V +    +RV    AR    SR  +  +I    V ++G  + RA+V V +   ++VD   
Sbjct: 6   VPDGLDGERVDVAAARMSGVSRSRISSLIEDGGVFLDGQQVSRASVRVATGQMLDVDLCD 65

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                        G  +   +   + +              +G S V     + F+   S
Sbjct: 66  PVATPSITPQIVEGTRIIHDDSDIVVVDKPAGVAAHPSLGWEGPSVVEHLAAAGFAISTS 125

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPST---------------------QWLRVYRVRF 149
                      L +   G +       +                           +    
Sbjct: 126 GAPERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTGTI 185

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +D  +   K  ++ G  +                + V L  G+  +I+       
Sbjct: 186 DAPIGRDHRHDW-KMAIVDGGRHSVTHYETVEAFRHATLLKVHLETGRTHQIRVHMAAIK 244

Query: 210 WKV 212
              
Sbjct: 245 HPC 247


>gi|271967338|ref|YP_003341534.1| hemolysin A [Streptosporangium roseum DSM 43021]
 gi|270510513|gb|ACZ88791.1| hemolysin A [Streptosporangium roseum DSM 43021]
          Length = 272

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+   + R  +A SR +  ++I   RV V G L  + A  V +   I V
Sbjct: 6  RLDSELVRRKLARSREQAAQLIEAGRVSVGGQLAAKPATQVDTASAIVV 54


>gi|261759096|ref|ZP_06002805.1| translation initiation factor IF-2 [Brucella sp. F5/99]
 gi|261739080|gb|EEY27076.1| translation initiation factor IF-2 [Brucella sp. F5/99]
          Length = 834

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/116 (12%), Positives = 29/116 (25%), Gaps = 2/116 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R + +  +RE +        +    A   +     R+         +   + +  + +K 
Sbjct: 36  RALEEAQIRE-VEERARAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKA 94

Query: 294 GLSKQKKLATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                K++  P  R     +   A  G                   P   S R   
Sbjct: 95  EEEAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAP 150



 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 11/121 (9%), Positives = 28/121 (23%), Gaps = 1/121 (0%)

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           L     REV ++  R         E           S     +    +    +   + ++
Sbjct: 38  LEEAQIREVEERA-RAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKAEE 96

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            ++++    + +       R           G           R +     P+     + 
Sbjct: 97  EAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAPIIADAA 156

Query: 348 R 348
            
Sbjct: 157 P 157


>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 = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 23/243 (9%), Positives = 61/243 (25%), Gaps = 37/243 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIE--- 61
           V +    +RV   I+R    SR +   + A  +V+V+G +  + +  V       +E   
Sbjct: 12  VPDGLEGERVDAAISRMFGFSRTKAAELAAAGKVQVDGSVAGK-SERVHGGAWLEVEMPG 70

Query: 62  -----------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                      V+G+ +   +   + +               G + +     + +    S
Sbjct: 71  APAPVQIVAEPVEGMEIVHDDDDIVVIMKPVGVAAHPSPGWTGTTVIGGLAAAGYRISTS 130

Query: 111 VGRLDINTEGLLLLTNDGGLA-------------RVLELPSTQWLRVYRVRFHGQVDQDK 157
                      L +   G +              +  +    +            +    
Sbjct: 131 GAAERQGIVHRLDVGTSGLMVVAKSERAYTLLKAQFRDRVVDKRYHALVQGHPDPMSGTI 190

Query: 158 LNLLKKGIVIQGICYGDMQVT-------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
              + +            +         L     + + + + L  G+  +I+        
Sbjct: 191 DAPIGRHPNHDYKWAVTAEGKPSVTHYDLIEAYRAASLLDIKLETGRTHQIRVHMSAHRH 250

Query: 211 KVN 213
              
Sbjct: 251 PCV 253


>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 = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 38/286 (13%), Positives = 77/286 (26%), Gaps = 53/286 (18%)

Query: 4   KNIVQENFTPQ-RVSKVI-ARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           + ++  + T + R+   + A+ G   SR  ++ +I   +V + G  +      V   D  
Sbjct: 25  RKVLTADETAEGRLDAWLTAQVGEDFSRSRIKALIKDGQVSLRGEQVTDPQRKVRVGDSF 84

Query: 61  EV----------DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           E+           G  +      E   L +  KP GLV      +   T+ + L      
Sbjct: 85  EITLPEPEDPTPKGEDIPLEILHEDDDLIVISKPAGLVVHPGSGNWTGTLVNALIHHCGD 144

Query: 108 VIS--VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL---LK 162
            +S   G         L     G +       + + L +        +  ++        
Sbjct: 145 TLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDVAHRHLSLQFADHGRTMPLERAYRAVVWG 204

Query: 163 KGIVIQGICYGDM-------------------------QVTLDTQKGSN-------AWVT 190
           +   + G     +                            +  +   N       + V 
Sbjct: 205 RPRTLSGTIDAPLGRATGDRTRRAVKRPDSQDADAAITHYEVIERFQENPDATALASLVE 264

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             L  G+  +I+         +        G      LL    R+V
Sbjct: 265 CHLETGRTHQIRVHMAHIGHPLVGDTVYGAGFRTKANLLPEEIRKV 310


>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 = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 31/243 (12%), Positives = 64/243 (26%), Gaps = 38/243 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           V +    +RV    AR    SR  +  +I    V ++G  + RA+V V +   ++VD   
Sbjct: 6   VPDGLDGERVDVAAARMSGVSRSRISSLIEDGGVFLDGQQVSRASVRVATGQMLDVDLCD 65

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                        G+ +   +   + +              +G S V     + F+   S
Sbjct: 66  PVATPSITPRIVEGMRIIHDDSDIVVVDKPAGVAAHPSLGWEGPSVVEHLAAAGFAISTS 125

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPST---------------------QWLRVYRVRF 149
                      L +   G +       +                           +    
Sbjct: 126 GAPERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTGTI 185

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +D  +   K  ++ G  +                + V L  G+  +I+       
Sbjct: 186 DAPIGRDHRHDW-KMAIVDGGRHSVTHYETVEAFRHATLLKVHLETGRTHQIRVHMAAIK 244

Query: 210 WKV 212
              
Sbjct: 245 HPC 247


>gi|187251795|ref|YP_001876277.1| RNA-binding S4 domain-containing protein [Elusimicrobium minutum
           Pei191]
 gi|226699062|sp|B2KEJ4|RS4_ELUMP RecName: Full=30S ribosomal protein S4
 gi|186971955|gb|ACC98940.1| RNA-binding S4 domain protein [Elusimicrobium minutum Pei191]
          Length = 201

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +R    +++  + + V+G +++  + +V     I V
Sbjct: 94  RLDNIVYRMGLARTRAAARQLVTHRHITVDGEIVKTPSYSVKPGQVISV 142


>gi|320173940|gb|EFW49116.1| SSU ribosomal protein S4p (S9e) [Shigella dysenteriae CDC 74-1112]
          Length = 152

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 43  RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRIVNIASYQVSPNDVVSIREKAKKQSRVK 102

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 103 AALELAEQREKPT 115


>gi|15807121|ref|NP_295850.1| 30S ribosomal protein S4 [Deinococcus radiodurans R1]
 gi|26399534|sp|Q9RSJ7|RS4_DEIRA RecName: Full=30S ribosomal protein S4
 gi|6459925|gb|AAF11677.1|AE002047_10 ribosomal protein S4 [Deinococcus radiodurans R1]
          Length = 205

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G AS RR+  + +    + VNG  ++ A+  V   D I V
Sbjct: 96  RLDNVVFRMGFASTRRQARQFVGHGHILVNGKKVDIASYRVKIGDEISV 144


>gi|89093591|ref|ZP_01166539.1| 30S ribosomal protein S4 [Oceanospirillum sp. MED92]
 gi|89082281|gb|EAR61505.1| 30S ribosomal protein S4 [Oceanospirillum sp. MED92]
          Length = 206

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG ++  A+  V + D + V
Sbjct: 97  RLDNVVYRMGFGSTRAEARQIVSHRSITVNGQVVNIASYQVKAGDVVAV 145


>gi|307328948|ref|ZP_07608117.1| hemolysin A [Streptomyces violaceusniger Tu 4113]
 gi|306885458|gb|EFN16475.1| hemolysin A [Streptomyces violaceusniger Tu 4113]
          Length = 303

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   + R  +A SR    ++IA  RV V G +  + A  V ++  + V
Sbjct: 9  VRLDAELVRRKLARSREHASQLIAAGRVTVGGAVATKPATQVETSAAVVV 58


>gi|228941836|ref|ZP_04104383.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar berliner
           ATCC 10792]
 gi|228960923|ref|ZP_04122556.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar pakistani
           str. T13001]
 gi|228974761|ref|ZP_04135327.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228981356|ref|ZP_04141656.1| 30S ribosomal protein S4 [Bacillus thuringiensis Bt407]
 gi|229048362|ref|ZP_04193930.1| 30S ribosomal protein S4 [Bacillus cereus AH676]
 gi|229087217|ref|ZP_04219364.1| 30S ribosomal protein S4 [Bacillus cereus Rock3-44]
 gi|229112121|ref|ZP_04241664.1| 30S ribosomal protein S4 [Bacillus cereus Rock1-15]
 gi|229147216|ref|ZP_04275574.1| 30S ribosomal protein S4 [Bacillus cereus BDRD-ST24]
 gi|228636326|gb|EEK92798.1| 30S ribosomal protein S4 [Bacillus cereus BDRD-ST24]
 gi|228671444|gb|EEL26745.1| 30S ribosomal protein S4 [Bacillus cereus Rock1-15]
 gi|228696098|gb|EEL48936.1| 30S ribosomal protein S4 [Bacillus cereus Rock3-44]
 gi|228723087|gb|EEL74464.1| 30S ribosomal protein S4 [Bacillus cereus AH676]
 gi|228778556|gb|EEM26823.1| 30S ribosomal protein S4 [Bacillus thuringiensis Bt407]
 gi|228785164|gb|EEM33177.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228798819|gb|EEM45799.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar pakistani
           str. T13001]
 gi|228818048|gb|EEM64126.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar berliner
           ATCC 10792]
 gi|326942441|gb|AEA18337.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar chinensis
           CT-43]
          Length = 200

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 93  RLDNLVYRMGLARTRRAARQLVNHGHIMVDGARVDIPSYRVKPGQTISV 141


>gi|254426804|ref|ZP_05040511.1| ribosomal protein S4 [Alcanivorax sp. DG881]
 gi|196192973|gb|EDX87932.1| ribosomal protein S4 [Alcanivorax sp. DG881]
          Length = 210

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +  A+  V   D I V
Sbjct: 101 RLDNVVYRMGFGSTRSEARQLVSHRAILVNGQSVNVASYQVKPGDQINV 149


>gi|206977164|ref|ZP_03238063.1| 30S ribosomal protein S4 [Bacillus cereus H3081.97]
 gi|217962143|ref|YP_002340713.1| 30S ribosomal protein S4 [Bacillus cereus AH187]
 gi|229141392|ref|ZP_04269930.1| 30S ribosomal protein S4 [Bacillus cereus BDRD-ST26]
 gi|229198816|ref|ZP_04325510.1| 30S ribosomal protein S4 [Bacillus cereus m1293]
 gi|226697803|sp|B7HSJ2|RS4_BACC7 RecName: Full=30S ribosomal protein S4
 gi|206744649|gb|EDZ56057.1| 30S ribosomal protein S4 [Bacillus cereus H3081.97]
 gi|217062938|gb|ACJ77188.1| ribosomal protein S4 [Bacillus cereus AH187]
 gi|228584652|gb|EEK42776.1| 30S ribosomal protein S4 [Bacillus cereus m1293]
 gi|228642173|gb|EEK98466.1| 30S ribosomal protein S4 [Bacillus cereus BDRD-ST26]
          Length = 200

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 93  RLDNLVYRMGLARTRRAARQLVNHGHIMVDGARVDIPSYRVKPGQTISV 141


>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 = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 29/224 (12%), Positives = 61/224 (27%), Gaps = 35/224 (15%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD----HIE-VDGVPL------ 67
            + R    S+RE++R IA  RV VNG  +      V  +D     +E +   P+      
Sbjct: 19  FLKRELELSQREIQRYIAIGRVLVNGAPI------VKPSDYLQGEVEYIYFEPISKGLAP 72

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              E   +        L+   +     S + +             R+D  T GL+L   D
Sbjct: 73  HFIEERFVVFDKPSGMLIHPQNRFTEYSLIDELKAQFGMNANIAHRIDQETSGLVLCAKD 132

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--- 184
                 +++   +     +       +  +   +   ++        +   +        
Sbjct: 133 KKSEVDIKMMFQERDMKKKYLAMVHGELKEELRIDAPLLRYDDEKSALVRMVVKVDPTGK 192

Query: 185 ---------------SNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                              V      G+  +I+         + 
Sbjct: 193 ESLTFVRPLKYFPITDTTLVECSPHTGRQHQIRVHMFHMKHPIV 236


>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 = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 25/214 (11%), Positives = 59/214 (27%), Gaps = 3/214 (1%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K + +       +R+ + +AR    S++  +R+I +  V VNG     A   +   + + 
Sbjct: 5   KTERVELRAKGGERLVECVARR-AGSKKRAKRLIDEGLVSVNGQKELLARRRLKGGEVVR 63

Query: 62  V--DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
                 P +      L+                                 ++  +    +
Sbjct: 64  FPLTEAPFKPPNVKLLFRERGVWVFEKPPFITTNEGEKSLEETVRKLFNPNLKVVHRLDK 123

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
                       ++ E    Q+ R    + +  + + KL   +              VT 
Sbjct: 124 QTTGPVIAVESEKLFEAFKKQFKRREVKKEYLCLVKGKLRSRQTVRRPIDGKSAVSLVTP 183

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      V +  G+  +I++      + V 
Sbjct: 184 LEHFKRATLCRVEIETGRKHQIRRHLASVGYPVV 217


>gi|317010964|gb|ADU84711.1| pseudouridine synthase [Helicobacter pylori SouthAfrica7]
          Length = 326

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 48/306 (15%), Positives = 103/306 (33%), Gaps = 54/306 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+   I  +N+   R+ + +A+    S+ +   +I +  V      +++  + +   D I
Sbjct: 1   MQKVFIAPKNYK--RIDEFLAKELQISKNQALSLIKEGLVLCQKKEVKKGGLALKEGDAI 58

Query: 61  -----EVDGVPLRKA---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
                ++   PL+K          E   L + +KP  L+   +      T+ D L S   
Sbjct: 59  ALLTLKITPKPLKKELDLEIGVIFEDDDLLVLNKPPNLIVHKAPSVKEPTLVDWLESKNY 118

Query: 107 RVISVGRLDIN----------TEGLLLLTNDGGLARVLELPSTQWLRVYRVR-------- 148
           ++ ++G  +            + G+++  N+     + E   T+ +  Y +         
Sbjct: 119 QLSNLGSKERYGIVHRLDKDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLSR 178

Query: 149 ------FHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNRE 200
                     + ++  N LK   I  +   Y   + T      +N   +   L  G+  +
Sbjct: 179 KGEKVSVECYLTRNPNNRLKMMAIKNEKGRYSKSEFTSLLTSQNNLNLIGAKLYTGRTHQ 238

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAP 260
           I+            L R   G      L  G    + K+ +R  L  +L+E      +  
Sbjct: 239 IRTHL-------EYLNRHIIG----DNLY-GLNEALPKEEIRIMLHAYLIEFKHPRSEQK 286

Query: 261 IYSSET 266
           +     
Sbjct: 287 LRFKVP 292


>gi|291301899|ref|YP_003513177.1| hemolysin A [Stackebrandtia nassauensis DSM 44728]
 gi|290571119|gb|ADD44084.1| hemolysin A [Stackebrandtia nassauensis DSM 44728]
          Length = 272

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 1/51 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          R+   + R G+A SR     +IA  RV+V G    + A  V   D + + G
Sbjct: 6  RLDAELVRRGLARSRAHAAELIAAGRVRVRGFTATKPAAGVDPADPVLLAG 56


>gi|218899810|ref|YP_002448221.1| ribosomal protein S4 [Bacillus cereus G9842]
 gi|228903174|ref|ZP_04067308.1| 30S ribosomal protein S4 [Bacillus thuringiensis IBL 4222]
 gi|228967755|ref|ZP_04128771.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar sotto str.
           T04001]
 gi|229163648|ref|ZP_04291596.1| 30S ribosomal protein S4 [Bacillus cereus R309803]
 gi|226697801|sp|B7IKS0|RS4_BACC2 RecName: Full=30S ribosomal protein S4
 gi|218544223|gb|ACK96617.1| ribosomal protein S4 [Bacillus cereus G9842]
 gi|228619785|gb|EEK76663.1| 30S ribosomal protein S4 [Bacillus cereus R309803]
 gi|228791909|gb|EEM39495.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar sotto str.
           T04001]
 gi|228856456|gb|EEN00982.1| 30S ribosomal protein S4 [Bacillus thuringiensis IBL 4222]
          Length = 200

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 93  RLDNLVYRMGLARTRRAARQLVNHGHIMVDGARVDIPSYRVKPNQTISV 141


>gi|149376660|ref|ZP_01894419.1| ribosomal protein S4 [Marinobacter algicola DG893]
 gi|149359033|gb|EDM47498.1| ribosomal protein S4 [Marinobacter algicola DG893]
          Length = 206

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VN  L+   +  V   D + V
Sbjct: 97  RLDNVVYRMGFGSTRAESRQLVSHKAILVNDKLVNIPSYQVRPGDVVSV 145


>gi|30022730|ref|NP_834361.1| 30S ribosomal protein S4 [Bacillus cereus ATCC 14579]
 gi|206969984|ref|ZP_03230938.1| 30S ribosomal protein S4 [Bacillus cereus AH1134]
 gi|218235372|ref|YP_002369450.1| 30S ribosomal protein S4 [Bacillus cereus B4264]
 gi|228923404|ref|ZP_04086692.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228954925|ref|ZP_04116943.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar kurstaki
           str. T03a001]
 gi|229072158|ref|ZP_04205367.1| 30S ribosomal protein S4 [Bacillus cereus F65185]
 gi|229081908|ref|ZP_04214400.1| 30S ribosomal protein S4 [Bacillus cereus Rock4-2]
 gi|229129939|ref|ZP_04258905.1| 30S ribosomal protein S4 [Bacillus cereus BDRD-Cer4]
 gi|229152850|ref|ZP_04281033.1| 30S ribosomal protein S4 [Bacillus cereus m1550]
 gi|229180974|ref|ZP_04308309.1| 30S ribosomal protein S4 [Bacillus cereus 172560W]
 gi|229192859|ref|ZP_04319817.1| 30S ribosomal protein S4 [Bacillus cereus ATCC 10876]
 gi|296505124|ref|YP_003666824.1| 30S ribosomal protein S4 [Bacillus thuringiensis BMB171]
 gi|38372409|sp|Q817A4|RS4_BACCR RecName: Full=30S ribosomal protein S4
 gi|226697802|sp|B7H711|RS4_BACC4 RecName: Full=30S ribosomal protein S4
 gi|29898289|gb|AAP11562.1| SSU ribosomal protein S4P [Bacillus cereus ATCC 14579]
 gi|206735672|gb|EDZ52840.1| 30S ribosomal protein S4 [Bacillus cereus AH1134]
 gi|218163329|gb|ACK63321.1| ribosomal protein S4 [Bacillus cereus B4264]
 gi|228590698|gb|EEK48559.1| 30S ribosomal protein S4 [Bacillus cereus ATCC 10876]
 gi|228602531|gb|EEK60017.1| 30S ribosomal protein S4 [Bacillus cereus 172560W]
 gi|228630670|gb|EEK87316.1| 30S ribosomal protein S4 [Bacillus cereus m1550]
 gi|228653630|gb|EEL09502.1| 30S ribosomal protein S4 [Bacillus cereus BDRD-Cer4]
 gi|228701496|gb|EEL53990.1| 30S ribosomal protein S4 [Bacillus cereus Rock4-2]
 gi|228711092|gb|EEL63058.1| 30S ribosomal protein S4 [Bacillus cereus F65185]
 gi|228804746|gb|EEM51347.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar kurstaki
           str. T03a001]
 gi|228836358|gb|EEM81711.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|296326176|gb|ADH09104.1| 30S ribosomal protein S4 [Bacillus thuringiensis BMB171]
          Length = 200

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 93  RLDNLVYRMGLARTRRAARQLVNHGHIMVDGARVDIPSYRVKPGQTISV 141


>gi|332798026|ref|YP_004459525.1| RNA-binding S4 domain-containing protein [Tepidanaerobacter sp.
          Re1]
 gi|332695761|gb|AEE90218.1| RNA-binding S4 domain protein [Tepidanaerobacter sp. Re1]
          Length = 73

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 10 NFTPQRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
          N     + + +  +GI S   E +  I +  VKVNG +  + +  +  +D +EV+G  L
Sbjct: 10 NTETINLDQFLKWSGIFSTGGEAKIAITEGNVKVNGEIETKRSRKLKVSDMVEVNGNRL 68


>gi|148244353|ref|YP_001219047.1| 30S ribosomal protein S4 [Candidatus Vesicomyosocius okutanii HA]
 gi|172047241|sp|A5CXI8|RS4_VESOH RecName: Full=30S ribosomal protein S4
 gi|146326180|dbj|BAF61323.1| 30S ribosomal protein S4 [Candidatus Vesicomyosocius okutanii HA]
          Length = 208

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/60 (23%), Positives = 30/60 (50%), Gaps = 1/60 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G AS R E  ++++ + + VNG+++   +  V   D I +     +++   
Sbjct: 99  RLDNVVYRMGFASTRAEARQLVSHKSIMVNGLVVNIPSYQVSVNDKISIREKAKKQSRIQ 158


>gi|317507355|ref|ZP_07965091.1| hemolysin TlyA family protein [Segniliparus rugosus ATCC BAA-974]
 gi|316254352|gb|EFV13686.1| hemolysin TlyA family protein [Segniliparus rugosus ATCC BAA-974]
          Length = 275

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 1/65 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           T  R+ + + R G+A SR +   +IAQ RV   G L ++ A  V +   + VD  P   
Sbjct: 3  DTTTRLDRELVRRGLARSREQAGSLIAQGRVFAGGKLAKKPAFAVSAETDVRVDADPEEP 62

Query: 70 AERTR 74
             +R
Sbjct: 63 DWASR 67


>gi|260169569|ref|ZP_05756380.1| translation initiation factor IF-2 [Brucella sp. F5/99]
          Length = 861

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/116 (12%), Positives = 29/116 (25%), Gaps = 2/116 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R + +  +RE +        +    A   +     R+         +   + +  + +K 
Sbjct: 63  RALEEAQIRE-VEERARAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKA 121

Query: 294 GLSKQKKLATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                K++  P  R     +   A  G                   P   S R   
Sbjct: 122 EEEAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAP 177



 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 11/121 (9%), Positives = 28/121 (23%), Gaps = 1/121 (0%)

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           L     REV ++  R         E           S     +    +    +   + ++
Sbjct: 65  LEEAQIREVEERA-RAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKAEE 123

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            ++++    + +       R           G           R +     P+     + 
Sbjct: 124 EAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAPIIADAA 183

Query: 348 R 348
            
Sbjct: 184 P 184


>gi|228910481|ref|ZP_04074296.1| 30S ribosomal protein S4 [Bacillus thuringiensis IBL 200]
 gi|228849247|gb|EEM94086.1| 30S ribosomal protein S4 [Bacillus thuringiensis IBL 200]
          Length = 200

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 93  RLDNLVYRMGLARTRRAARQLVNHGHIMVDGARVDIPSYRVKPGQTISV 141


>gi|196044058|ref|ZP_03111295.1| ribosomal protein S4 [Bacillus cereus 03BB108]
 gi|196025394|gb|EDX64064.1| ribosomal protein S4 [Bacillus cereus 03BB108]
 gi|324328549|gb|ADY23809.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar finitimus
           YBT-020]
          Length = 200

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 93  RLDNLVYRMGLARTRRAARQLVNHGHIMVDGARVDIPSYRVKPGQTISV 141


>gi|50365403|ref|YP_053828.1| 30S ribosomal protein S4 [Mesoplasma florum L1]
 gi|61215527|sp|Q6F0M9|RS4_MESFL RecName: Full=30S ribosomal protein S4
 gi|50363959|gb|AAT75944.1| 30S ribosomal protein S4 [Mesoplasma florum L1]
          Length = 208

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G A +R+   +++    + VNG  L+  +  V   D IEV
Sbjct: 98  RLDNIVFRLGFAMTRQAARQLVNHGHILVNGKKLDIPSYQVKPGDSIEV 146


>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 = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 25/199 (12%), Positives = 54/199 (27%), Gaps = 28/199 (14%)

Query: 42  VNGILLERAAVNVMSTDHIEVD---------------GVPLRKAERTRLWLYHKPIGLVT 86
           VN   +      +M  D +E+                 + +   +   + +        T
Sbjct: 38  VNDEPVTV-RKQLMPNDILEIHLPREIPSVNLIPYARKLEVLYEDAFIIIVTKPNNQNCT 96

Query: 87  THSDPDGRSTVFDNLPSIF-----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
              +    S +   L              V RLD NT G+++    G +  +    + + 
Sbjct: 97  PSREHPHESLIEQVLYHCQENGENINPHIVTRLDRNTTGIVIFAKYGYIHHLFSKVNLKK 156

Query: 142 LRVYRVRFHGQVD-------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           +    V              +   + +    V     Y      +  Q    +   V L 
Sbjct: 157 IYTCLVYGKTHTSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLH 216

Query: 195 EGKNREIKKVFEFFNWKVN 213
            G+  +I+  F+     + 
Sbjct: 217 TGRTHQIRVHFQHIGHPIV 235


>gi|30264729|ref|NP_847106.1| 30S ribosomal protein S4 [Bacillus anthracis str. Ames]
 gi|42783839|ref|NP_981086.1| 30S ribosomal protein S4 [Bacillus cereus ATCC 10987]
 gi|47530203|ref|YP_021552.1| 30S ribosomal protein S4 [Bacillus anthracis str. 'Ames Ancestor']
 gi|49187548|ref|YP_030801.1| 30S ribosomal protein S4 [Bacillus anthracis str. Sterne]
 gi|49481409|ref|YP_038704.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar konkukian
           str. 97-27]
 gi|52140852|ref|YP_085977.1| 30S ribosomal protein S4 [Bacillus cereus E33L]
 gi|65322027|ref|ZP_00394986.1| COG0522: Ribosomal protein S4 and related proteins [Bacillus
           anthracis str. A2012]
 gi|118479796|ref|YP_896947.1| 30S ribosomal protein S4 [Bacillus thuringiensis str. Al Hakam]
 gi|165869836|ref|ZP_02214494.1| ribosomal protein S4 [Bacillus anthracis str. A0488]
 gi|167633851|ref|ZP_02392174.1| ribosomal protein S4 [Bacillus anthracis str. A0442]
 gi|167638038|ref|ZP_02396316.1| ribosomal protein S4 [Bacillus anthracis str. A0193]
 gi|170685670|ref|ZP_02876893.1| ribosomal protein S4 [Bacillus anthracis str. A0465]
 gi|170705531|ref|ZP_02895995.1| ribosomal protein S4 [Bacillus anthracis str. A0389]
 gi|177651189|ref|ZP_02934020.1| ribosomal protein S4 [Bacillus anthracis str. A0174]
 gi|190568368|ref|ZP_03021276.1| ribosomal protein S4 [Bacillus anthracis Tsiankovskii-I]
 gi|196032907|ref|ZP_03100320.1| ribosomal protein S4 [Bacillus cereus W]
 gi|196040797|ref|ZP_03108095.1| ribosomal protein S4 [Bacillus cereus NVH0597-99]
 gi|218905885|ref|YP_002453719.1| ribosomal protein S4 [Bacillus cereus AH820]
 gi|225866636|ref|YP_002752014.1| 30S ribosomal protein S4 [Bacillus cereus 03BB102]
 gi|227817448|ref|YP_002817457.1| 30S ribosomal protein S4 [Bacillus anthracis str. CDC 684]
 gi|228917301|ref|ZP_04080856.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar pulsiensis
           BGSC 4CC1]
 gi|228929709|ref|ZP_04092726.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228935965|ref|ZP_04098775.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228948386|ref|ZP_04110669.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar monterrey
           BGSC 4AJ1]
 gi|228987906|ref|ZP_04148014.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229093753|ref|ZP_04224852.1| 30S ribosomal protein S4 [Bacillus cereus Rock3-42]
 gi|229124225|ref|ZP_04253417.1| 30S ribosomal protein S4 [Bacillus cereus 95/8201]
 gi|229158263|ref|ZP_04286330.1| 30S ribosomal protein S4 [Bacillus cereus ATCC 4342]
 gi|229186914|ref|ZP_04314069.1| 30S ribosomal protein S4 [Bacillus cereus BGSC 6E1]
 gi|229602554|ref|YP_002868937.1| 30S ribosomal protein S4 [Bacillus anthracis str. A0248]
 gi|254687468|ref|ZP_05151324.1| 30S ribosomal protein S4 [Bacillus anthracis str. CNEVA-9066]
 gi|254725030|ref|ZP_05186813.1| 30S ribosomal protein S4 [Bacillus anthracis str. A1055]
 gi|254736768|ref|ZP_05194474.1| 30S ribosomal protein S4 [Bacillus anthracis str. Western North
           America USA6153]
 gi|254741805|ref|ZP_05199492.1| 30S ribosomal protein S4 [Bacillus anthracis str. Kruger B]
 gi|254754597|ref|ZP_05206632.1| 30S ribosomal protein S4 [Bacillus anthracis str. Vollum]
 gi|254757429|ref|ZP_05209456.1| 30S ribosomal protein S4 [Bacillus anthracis str. Australia 94]
 gi|300118469|ref|ZP_07056212.1| 30S ribosomal protein S4 [Bacillus cereus SJ1]
 gi|301056163|ref|YP_003794374.1| 30S ribosomal protein S4 [Bacillus anthracis CI]
 gi|38372415|sp|Q81KT2|RS4_BACAN RecName: Full=30S ribosomal protein S4
 gi|61215457|sp|Q633E0|RS4_BACCZ RecName: Full=30S ribosomal protein S4
 gi|61215551|sp|Q6HCM2|RS4_BACHK RecName: Full=30S ribosomal protein S4
 gi|61215626|sp|Q72Z76|RS4_BACC1 RecName: Full=30S ribosomal protein S4
 gi|152060934|sp|A0RJP7|RS4_BACAH RecName: Full=30S ribosomal protein S4
 gi|226697800|sp|B7JS31|RS4_BACC0 RecName: Full=30S ribosomal protein S4
 gi|254764566|sp|C3PBC1|RS4_BACAA RecName: Full=30S ribosomal protein S4
 gi|254764567|sp|C3L9W4|RS4_BACAC RecName: Full=30S ribosomal protein S4
 gi|254764568|sp|C1EV03|RS4_BACC3 RecName: Full=30S ribosomal protein S4
 gi|30259404|gb|AAP28592.1| 30S ribosomal protein S4 [Bacillus anthracis str. Ames]
 gi|42739769|gb|AAS43694.1| ribosomal protein S4 [Bacillus cereus ATCC 10987]
 gi|47505351|gb|AAT34027.1| ribosomal protein S4 [Bacillus anthracis str. 'Ames Ancestor']
 gi|49181475|gb|AAT56851.1| ribosomal protein S4 [Bacillus anthracis str. Sterne]
 gi|49332965|gb|AAT63611.1| ribosomal protein S4 (30S ribosomal protein S4) [Bacillus
           thuringiensis serovar konkukian str. 97-27]
 gi|51974321|gb|AAU15871.1| ribosomal protein S4 (30S ribosomal protein S4) [Bacillus cereus
           E33L]
 gi|118419021|gb|ABK87440.1| SSU ribosomal protein S4P [Bacillus thuringiensis str. Al Hakam]
 gi|164714665|gb|EDR20184.1| ribosomal protein S4 [Bacillus anthracis str. A0488]
 gi|167513855|gb|EDR89223.1| ribosomal protein S4 [Bacillus anthracis str. A0193]
 gi|167530652|gb|EDR93354.1| ribosomal protein S4 [Bacillus anthracis str. A0442]
 gi|170129656|gb|EDS98519.1| ribosomal protein S4 [Bacillus anthracis str. A0389]
 gi|170670134|gb|EDT20874.1| ribosomal protein S4 [Bacillus anthracis str. A0465]
 gi|172083015|gb|EDT68077.1| ribosomal protein S4 [Bacillus anthracis str. A0174]
 gi|190560624|gb|EDV14601.1| ribosomal protein S4 [Bacillus anthracis Tsiankovskii-I]
 gi|195994336|gb|EDX58291.1| ribosomal protein S4 [Bacillus cereus W]
 gi|196028251|gb|EDX66860.1| ribosomal protein S4 [Bacillus cereus NVH0597-99]
 gi|218535551|gb|ACK87949.1| ribosomal protein S4 [Bacillus cereus AH820]
 gi|225790794|gb|ACO31011.1| 30S ribosomal protein S4 [Bacillus cereus 03BB102]
 gi|227006605|gb|ACP16348.1| 30S ribosomal protein S4 [Bacillus anthracis str. CDC 684]
 gi|228596651|gb|EEK54316.1| 30S ribosomal protein S4 [Bacillus cereus BGSC 6E1]
 gi|228625221|gb|EEK81981.1| 30S ribosomal protein S4 [Bacillus cereus ATCC 4342]
 gi|228659527|gb|EEL15175.1| 30S ribosomal protein S4 [Bacillus cereus 95/8201]
 gi|228689638|gb|EEL43446.1| 30S ribosomal protein S4 [Bacillus cereus Rock3-42]
 gi|228771829|gb|EEM20287.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228811373|gb|EEM57711.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar monterrey
           BGSC 4AJ1]
 gi|228823733|gb|EEM69555.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228829888|gb|EEM75508.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228842342|gb|EEM87435.1| 30S ribosomal protein S4 [Bacillus thuringiensis serovar pulsiensis
           BGSC 4CC1]
 gi|229266962|gb|ACQ48599.1| 30S ribosomal protein S4 [Bacillus anthracis str. A0248]
 gi|298724141|gb|EFI64840.1| 30S ribosomal protein S4 [Bacillus cereus SJ1]
 gi|300378332|gb|ADK07236.1| 30S ribosomal protein S4 [Bacillus cereus biovar anthracis str. CI]
          Length = 200

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 93  RLDNLVYRMGLARTRRAARQLVNHGHIMVDGARVDIPSYRVKPGQTISV 141


>gi|302390800|ref|YP_003826620.1| RNA-binding S4 domain protein [Acetohalobium arabaticum DSM 5501]
 gi|302202877|gb|ADL11555.1| RNA-binding S4 domain protein [Acetohalobium arabaticum DSM 5501]
          Length = 69

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 10/37 (27%), Positives = 19/37 (51%)

Query: 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
          E + +I + +V VNG + +R    +   D I++D   
Sbjct: 28 EAKLLIKKGKVMVNGEVEKRRGFTLHPGDVIKIDNEE 64


>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 = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 23/243 (9%), Positives = 61/243 (25%), Gaps = 37/243 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVN------------GILLE----RA 50
           + E     R    +A+    SR    ++ A+  V ++            G ++       
Sbjct: 10  IPEGLEGMRADAALAKLLGLSRSATAQLCAEGSVTIDSQELGKSERLTSGNVVSVLLPEP 69

Query: 51  AVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
              ++  + + V+G+ +   +   + ++             DG + +     + ++   S
Sbjct: 70  EKPLLPREEL-VEGMDVLYNDADIICVHKPVGVAAHPSVGWDGPTVIGGLRAAGYTVASS 128

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-------------- 156
                      L +   G +       +   L+        +                  
Sbjct: 129 GPTERKGIVHRLDVGTSGVMVVASSERAYSALKHAFKYRSVKKTYHAVVQGLPDPIEGTV 188

Query: 157 ------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                       K  V+          +L       + + V L  G+  +I+        
Sbjct: 189 DAPIGRHPKSGWKFAVLDDGKAAVTHYSLIEAFREASLIEVHLETGRTHQIRVHMSATGH 248

Query: 211 KVN 213
              
Sbjct: 249 PCV 251


>gi|169335053|ref|ZP_02862246.1| hypothetical protein ANASTE_01459 [Anaerofustis stercorihominis DSM
           17244]
 gi|169257791|gb|EDS71757.1| hypothetical protein ANASTE_01459 [Anaerofustis stercorihominis DSM
           17244]
          Length = 247

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 15/57 (26%), Positives = 23/57 (40%), Gaps = 2/57 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPL 67
             R+  VI      SR E    +   +VK+N   + + A+ V   D I V   G  +
Sbjct: 170 SMRLDAVIGNIFKLSRNEANMFVKGGKVKINHNQVSKPAMTVKVGDMISVRTKGRAI 226


>gi|119502947|ref|ZP_01625032.1| 30S ribosomal protein S4 [marine gamma proteobacterium HTCC2080]
 gi|119461293|gb|EAW42383.1| 30S ribosomal protein S4 [marine gamma proteobacterium HTCC2080]
          Length = 206

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/65 (20%), Positives = 27/65 (41%), Gaps = 1/65 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + VNG ++   +  V   D + V     ++    
Sbjct: 97  RLDNVVYRMGFGSTRAESRQLVSHKGILVNGTVVNIPSYQVRPGDIVSVREKAKKQLRIQ 156

Query: 74  RLWLY 78
                
Sbjct: 157 AAMSI 161


>gi|54022572|ref|YP_116814.1| putative transcriptional regulator [Nocardia farcinica IFM 10152]
 gi|54014080|dbj|BAD55450.1| putative transcriptional regulator [Nocardia farcinica IFM 10152]
          Length = 837

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/101 (11%), Positives = 25/101 (24%), Gaps = 1/101 (0%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                   +  A   ++     D        P      +         +   + A P   
Sbjct: 149 PATPPRSADPRAASPATPPRSADPRAASPATPPRSADPRIAPPATAPGATDPRTAAPAT- 207

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
            + A++   A        + S +R      +   P +RS  
Sbjct: 208 PSRATDPRAASPAAPRQEAPSARRPAQPPTARPEPGRRSKS 248



 Score = 42.5 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 13/112 (11%), Positives = 24/112 (21%), Gaps = 4/112 (3%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P   +    +  A   ++     D        P      +  S      S   + A+P  
Sbjct: 120 PRATDPRAADPRATSAATPPRSADPRAASPATPPRSADPRAASPATPPRSADPRAASPAT 179

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRR----SPSFPSKRSLRRTSAKK 354
               A                         R      + P+       SA++
Sbjct: 180 PPRSADPRIAPPATAPGATDPRTAAPATPSRATDPRAASPAAPRQEAPSARR 231


>gi|150014984|ref|YP_001307238.1| RNA-binding S4 domain-containing protein [Clostridium
          beijerinckii NCIMB 8052]
 gi|149901449|gb|ABR32282.1| RNA-binding S4 domain protein [Clostridium beijerinckii NCIMB
          8052]
          Length = 86

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   + +    R+ +NG + +  +  +   D IE+
Sbjct: 1  MRLDKYLKVSRIIKRRTVAKEICESGRILINGKVAK-PSTKIKEGDIIEI 49


>gi|308062067|gb|ADO03955.1| hypothetical protein HPCU_03975 [Helicobacter pylori Cuz20]
          Length = 327

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 49/323 (15%), Positives = 96/323 (29%), Gaps = 55/323 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+   I   N    R+ + +A+    S+ +V  +I +  V      +++  + +   D I
Sbjct: 1   MQKIFIALTNHK--RLDEFLAKELQISKNQVLHLIKEGLVFCQKKGVKKGGLALKKGDEI 58

Query: 61  E-----VDGVPLR---------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
                 +   PL+           E   L + +KP  LV   +      T+ D L     
Sbjct: 59  TLLTPKITPKPLKRGLDLEIGVIFEDEDLLVLNKPPNLVIHKAPSVKEPTLVDWLEFKNY 118

Query: 107 ---------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR-------VRFH 150
                    R   V RLD +T G +++  +      L       +               
Sbjct: 119 ELSNLGSKERYGIVHRLDKDTSGGIVIAKNNFTHAHLSEQLKTKMMGRYYIALLSTPLKE 178

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG-----------LREGKNR 199
            ++  +          ++ I     +        S     +            L  G+  
Sbjct: 179 EKMSVECYLTRNPNNRLKMIALKAAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTH 238

Query: 200 EIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDA 259
           +I+            L R   G      L  G  + + K+ +R  L  +L+E      + 
Sbjct: 239 QIRAHL-------EYLNRHIIG----DNLY-GLNQALPKEEIRIMLHAYLIEFKHPRSEQ 286

Query: 260 PIYSSETLVRDRPNIISEVPDDF 282
            +     L++D      +V D  
Sbjct: 287 KLRFKVPLLKDMLEYFKKVFDKE 309


>gi|302687690|ref|XP_003033525.1| hypothetical protein SCHCODRAFT_67657 [Schizophyllum commune H4-8]
 gi|300107219|gb|EFI98622.1| hypothetical protein SCHCODRAFT_67657 [Schizophyllum commune H4-8]
          Length = 1428

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 18/118 (15%), Positives = 38/118 (32%), Gaps = 2/118 (1%)

Query: 237  SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
             K+ L+E        + Q   D  ++ +    R R    +         K+   ++ G  
Sbjct: 1297 DKRSLKEIQEE--ERDLQAEADFLVWWTAEEERLRVEAEAVSAALVKSKKEGGKKRRGPG 1354

Query: 297  KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               +   P  + N ++      G         G R+E+  + P+  +  S  +    K
Sbjct: 1355 PDGQRRRPSGQDNPSAGQQRQMGRPQDGERSEGARQESQGQRPANATPPSKPQGRRPK 1412



 Score = 42.5 bits (98), Expect = 0.090,   Method: Composition-based stats.
 Identities = 13/115 (11%), Positives = 26/115 (22%), Gaps = 2/115 (1%)

Query: 237  SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            S K ++E+      E   +           +  +  +            K+     +G  
Sbjct: 1300 SLKEIQEEERDLQAEADFLVWWTAEEERLRVEAEAVSAALVKSKKEGGKKRRGPGPDGQR 1359

Query: 297  KQKKLATPVHRRNLASNVWMAKGIHSSFLSD--SGQREENHRRSPSFPSKRSLRR 349
            ++                    G  S        GQR  N         +R   +
Sbjct: 1360 RRPSGQDNPSAGQQRQMGRPQDGERSEGARQESQGQRPANATPPSKPQGRRPKSK 1414


>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 = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 27/249 (10%), Positives = 61/249 (24%), Gaps = 40/249 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M    +V E+    R    ++R    SR +   +I Q ++ + G      +  + S D I
Sbjct: 1   MNKVTMVPEDLVGVRFDLAVSRMMGLSRSKAANLIDQGQISLIGR-CGLKSEKLQSGDSI 59

Query: 61  EV-------DGVPLRKAERTRL------WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
            V          P+               +               G + +          
Sbjct: 60  RVSLTTSEKAPEPIDYDMGIVYEDGDLVVVDKPVGMAAHQSVGWTGSTVLGSLKARGVHI 119

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
                +        L +   G +       + + +R    +   +        L +G + 
Sbjct: 120 TDYGPQGRQGIVSRLDVGTSGLMLVCKSQMAYKEMRRQFSQHEVKKT---YYALAQGNLK 176

Query: 168 QGICY---------------------GDMQVTLDTQK--GSNAWVTVGLREGKNREIKKV 204
           +                                D  +  G   +++V L  G+  +I+  
Sbjct: 177 EDKATVDAPIGRDSAADFRFTITPAGKPAITHWDVIERFGQATYISVNLETGRTHQIRVH 236

Query: 205 FEFFNWKVN 213
                  + 
Sbjct: 237 MSSLGHPLV 245


>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 = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 35/206 (16%), Positives = 62/206 (30%), Gaps = 31/206 (15%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHIEV-------DGVPLRK--------AERTRLWLYHKP 81
           ++++ VNG  L      V   D IE+       D  P            E   + + +KP
Sbjct: 39  EKKILVNGKYLP-LNFLVKPGDKIEIQLDHIESDQQPYPASGKLPKVVYEDNDILVINKP 97

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL--------------TND 127
            G  T  +  +  + + D    +      V RLD+ T GLLL+              T+ 
Sbjct: 98  AGQKTHPNLNEEDTALNDCATYLGYSPFIVHRLDMLTSGLLLVAKNPAVVPILNRQLTDK 157

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
                 L   S              +  D  +  K+ +   G         +  +     
Sbjct: 158 TLHREYLAWISNSPQIKNTGIIDLPIGHDPHDQRKRMVRQDGQKA-VTHYEVIKRDKDRI 216

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVN 213
            V + L  G+  +I+         + 
Sbjct: 217 LVKLTLETGRTHQIRVHLAALGAPII 242


>gi|217077309|ref|YP_002335027.1| 30S ribosomal protein S4 [Thermosipho africanus TCF52B]
 gi|226695088|sp|B7IHX2|RS4_THEAB RecName: Full=30S ribosomal protein S4
 gi|217037164|gb|ACJ75686.1| ribosomal protein S4 [Thermosipho africanus TCF52B]
          Length = 209

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R    +++    V VNG  +   +  V   D IE+
Sbjct: 99  RLDNVVYRLGFAVNRTTARQLVNHGHVLVNGRKVTIPSYQVRPGDVIEI 147


>gi|311249257|ref|XP_003123544.1| PREDICTED: microtubule-associated protein 1S-like [Sus scrofa]
          Length = 1065

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 18/145 (12%), Positives = 39/145 (26%), Gaps = 16/145 (11%)

Query: 225 LGTL----LAGSTRE--VSKKIL----REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNI 274
           L  L      G  RE  V+ + L    R +    +     +  +          ++RP +
Sbjct: 441 LDGLVRLQHLGFLREPVVTPQDLAGPRRAESKESVGSRDSLRREGRATVPSRPAQERPGV 500

Query: 275 ISEVPDDFTRMKKNSSQKNGLSKQKK------LATPVHRRNLASNVWMAKGIHSSFLSDS 328
             + P      ++   +     + KK            R    +   +     +   +  
Sbjct: 501 TRKEPPRAEAPRRAEKEARPPREVKKDPKLSAPRAREPREVRRTASAVVSSKKAGAQAAP 560

Query: 329 GQREENHRRSPSFPSKRSLRRTSAK 353
             R   +   P  P   +  R+   
Sbjct: 561 KPRRAPNTPRPGVPPAENGPRSPPS 585


>gi|317049816|ref|YP_004117464.1| 30S ribosomal protein S4 [Pantoea sp. At-9b]
 gi|316951433|gb|ADU70908.1| ribosomal protein S4 [Pantoea sp. At-9b]
          Length = 206

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKSILVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|257453243|ref|ZP_05618542.1| 30S ribosomal protein S4 [Fusobacterium sp. 3_1_5R]
 gi|257467162|ref|ZP_05631473.1| 30S ribosomal protein S4 [Fusobacterium gonidiaformans ATCC 25563]
 gi|315918293|ref|ZP_07914533.1| SSU ribosomal protein S4P [Fusobacterium gonidiaformans ATCC 25563]
 gi|317059777|ref|ZP_07924262.1| SSU ribosomal protein S4P [Fusobacterium sp. 3_1_5R]
 gi|313685453|gb|EFS22288.1| SSU ribosomal protein S4P [Fusobacterium sp. 3_1_5R]
 gi|313692168|gb|EFS29003.1| SSU ribosomal protein S4P [Fusobacterium gonidiaformans ATCC 25563]
          Length = 195

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+  ++++   + VNG  +  A+  V   D I V
Sbjct: 89  RLENVVYRLGFAKTRRQARQIVSHGHITVNGRRVNIASYRVKVGDVIAV 137


>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 = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 27/243 (11%), Positives = 59/243 (24%), Gaps = 35/243 (14%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-----RAAVNV-----M 55
           +V +    +RV   I+R    SR     ++    V V+G            V V      
Sbjct: 8   MVPDGLAGERVDVGISRMLGLSRTRAADLVTAGHVLVDGRAPARSTRLEPGVMVHVELPD 67

Query: 56  STDHIEV-----DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
               +EV     +G+ L   +   + +           +   G + +     +      S
Sbjct: 68  EKPAVEVRPQIAEGMSLIHQDDDIVVIDKPVGVAAHPSAGWSGPTVLGHLAAAGVEIRTS 127

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL---------- 160
                      L +   G +       +   L+              +            
Sbjct: 128 GDPERQGIVSRLDVGTSGLMVVARTERAYTTLKDAFRAREVGKVYHAICQGTPDQPRGTI 187

Query: 161 ----------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                       K  V +   +         +      + +GL  G+  +I+      + 
Sbjct: 188 EAPIGRSPQHDYKFAVREDGKHSVTHYETLEELQGATLLRIGLETGRTHQIRVHMSALHH 247

Query: 211 KVN 213
            + 
Sbjct: 248 PLV 250


>gi|119509093|ref|ZP_01628244.1| RNA-binding S4 [Nodularia spumigena CCY9414]
 gi|119466259|gb|EAW47145.1| RNA-binding S4 [Nodularia spumigena CCY9414]
          Length = 60

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           ++ + +   G+AS   + + +I    VKVNG +  R    ++  D + V+G 
Sbjct: 2  IKLDQFLKFMGVASTGGQAKLIIIDGGVKVNGEVETRRGRKLVLGDKVTVEGK 54


>gi|146308899|ref|YP_001189364.1| 30S ribosomal protein S4 [Pseudomonas mendocina ymp]
 gi|172046040|sp|A4XZ66|RS4_PSEMY RecName: Full=30S ribosomal protein S4
 gi|145577100|gb|ABP86632.1| SSU ribosomal protein S4P [Pseudomonas mendocina ymp]
          Length = 206

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG  +   +  V + D + V
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKAISVNGQTVNVPSYQVKAGDVVAV 145


>gi|299822736|ref|ZP_07054622.1| 30S ribosomal protein S4 [Listeria grayi DSM 20601]
 gi|299816265|gb|EFI83503.1| 30S ribosomal protein S4 [Listeria grayi DSM 20601]
          Length = 200

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G+A +RR   +++    ++V+G  ++  +  V     I V
Sbjct: 92  QRLDNVVYRFGLARTRRAARQLVNHGHIQVDGKRVDIPSYQVSVGQVITV 141


>gi|153854997|ref|ZP_01996210.1| hypothetical protein DORLON_02216 [Dorea longicatena DSM 13814]
 gi|149752494|gb|EDM62425.1| hypothetical protein DORLON_02216 [Dorea longicatena DSM 13814]
          Length = 197

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +RRE  +++  + V VNG  +   +  V + D +E+
Sbjct: 88  RLDNVVFRLGLARTRREARQIVDHKHVLVNGKQINIPSYLVKAGDVVEI 136


>gi|108804292|ref|YP_644229.1| hemolysin A [Rubrobacter xylanophilus DSM 9941]
 gi|108765535|gb|ABG04417.1| hemolysin A [Rubrobacter xylanophilus DSM 9941]
          Length = 265

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 10/51 (19%), Positives = 24/51 (47%), Gaps = 1/51 (1%)

Query: 13 PQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +R+  ++   G+A +R   + MI   RV+V   ++ +A       + + +
Sbjct: 4  GRRLDAILVERGLAETRSRAQAMILAGRVRVGDRVVTKAGFRPAPGEEVRL 54


>gi|78057951|gb|ABB17342.1| RNA-binding protein S4 [Microcoleus chthonoplastes IPPAS B-270]
          Length = 71

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/61 (19%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 6  IVQENFTPQRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          ++ E+    ++ + +   G+ S   E + +I    V+VNG +  R    ++  D +   G
Sbjct: 1  MMIEDSVMIKLDQFLKWVGVVSTGGEAKLLIQDGEVQVNGTVETRRGRKLVPGDVVLARG 60

Query: 65 V 65
           
Sbjct: 61 Q 61


>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 = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 22/237 (9%), Positives = 57/237 (24%), Gaps = 40/237 (16%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIA----QQRVKVNG-----ILLERAAVNVM---- 55
           EN     +   +   G       +R+I     Q  + VNG       + +    +     
Sbjct: 7   ENEKGIILENFLRNKGF-----SKRLIRIYKWQGEILVNGIKSNVKRILQPGDVIDLILP 61

Query: 56  STD----------HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
             D           I  +   +    +    + H   G  +           +       
Sbjct: 62  ENDSNIAPEKLDLDICYEDEEILIVNKPANMVVHPTKGYQSGTLAN---GIAWYFKDKGL 118

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL---- 161
             +I            L++       +          ++Y     G+++ +    L    
Sbjct: 119 KALIRPVNRLDRGTSGLVVFAKLPFMQYYLQIVKPMSKLYFAVVEGKMEGEGRINLPISR 178

Query: 162 -----KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 + +V +          +       + + V +  G+  +I+         + 
Sbjct: 179 KPQSGIERMVSEEGEIAITNYKVVKSSERFSLLKVKIETGRTHQIRVHLSHIGHPIV 235


>gi|305679764|ref|ZP_07402574.1| ribosomal protein S4 [Corynebacterium matruchotii ATCC 14266]
 gi|305660384|gb|EFM49881.1| ribosomal protein S4 [Corynebacterium matruchotii ATCC 14266]
          Length = 203

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V+ RAG+A +RR+  ++++     VNG  +   +  V   D I+V   
Sbjct: 92  RLDNVVYRAGLARTRRQARQLVSHGHFLVNGKKVNVPSYRVSQYDIIDVRDK 143


>gi|229061503|ref|ZP_04198847.1| RNA-binding S4 domain protein [Bacillus cereus AH603]
 gi|229134707|ref|ZP_04263516.1| RNA-binding S4 domain protein [Bacillus cereus BDRD-ST196]
 gi|228648753|gb|EEL04779.1| RNA-binding S4 domain protein [Bacillus cereus BDRD-ST196]
 gi|228717737|gb|EEL69387.1| RNA-binding S4 domain protein [Bacillus cereus AH603]
          Length = 255

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+ +I    VKVN   +E+ +      D   V G
Sbjct: 180 RLDVLLAEMLHISRQKVQPLIKGGLVKVNWKTVEQTSYECFPGDVFSVRG 229


>gi|163941637|ref|YP_001646521.1| RNA-binding S4 domain-containing protein [Bacillus
           weihenstephanensis KBAB4]
 gi|163863834|gb|ABY44893.1| RNA-binding S4 domain protein [Bacillus weihenstephanensis KBAB4]
          Length = 255

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+ +I    VKVN   +E+ +      D   V G
Sbjct: 180 RLDVLLAEMLHISRQKVQPLIKGGLVKVNWKTVEQTSYECFPGDVFSVRG 229


>gi|172058242|ref|YP_001814702.1| ribosomal protein S4 [Exiguobacterium sibiricum 255-15]
 gi|226699065|sp|B1YKD2|RS4_EXIS2 RecName: Full=30S ribosomal protein S4
 gi|171990763|gb|ACB61685.1| ribosomal protein S4 [Exiguobacterium sibiricum 255-15]
          Length = 199

 Score = 47.5 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +RR   +++    ++V+G  ++  +  V     I V
Sbjct: 92  RLDNVVYRMGMARTRRAARQLVNHGHIQVDGARVDIPSFRVKPGQTISV 140


>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 = 47.5 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 21/200 (10%), Positives = 53/200 (26%), Gaps = 6/200 (3%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAERTRL 75
           KV+A+    S ++ + +I +  V V    +  A   + +     +     P    E  ++
Sbjct: 7   KVLAQQLGISNKKAKELIDRGLVYVGDKKVVIARGLIDTDTKFRIKRIEKPEILFEDEKI 66

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
              +KP  + +     D    +   L         +  +         +          E
Sbjct: 67  LAINKPAHITSEEIKEDSGYELLHRL--DKETSGVLLLVKNEAFRKKAIEEFRKSRVYKE 124

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTVGL 193
             +     V                 K    +        +  ++     G  + V   +
Sbjct: 125 YVAWVEGIVAEPYEIDYPILTIKKDGKAKSRLSASKGKPAKTYVEPLEIHGKKSKVKAVI 184

Query: 194 REGKNREIKKVFEFFNWKVN 213
             G+  +I+      +  + 
Sbjct: 185 ETGRTHQIRVHLARTDHPIL 204


>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 = 47.5 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 20/160 (12%), Positives = 44/160 (27%), Gaps = 12/160 (7%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEG 120
            +   +   + +        T   +    S +   L              V RLD NT G
Sbjct: 76  EVLYEDAFIIIVTKPNNQNCTPSREHPHESLIEQVLYHCQEHGENINPHIVTRLDRNTTG 135

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD-------QDKLNLLKKGIVIQGICYG 173
           +++    G +  +    + + +    V              +   + +    V     Y 
Sbjct: 136 IVIFAKYGHIHHLFSKVNLKKIYTCLVYGKTHTSGIIEANIRRSKDRIITREVASDGKYA 195

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                +  Q    +   V L  G+  +I+  F+     + 
Sbjct: 196 KTSYEVINQNDKYSLCKVHLHTGRTHQIRVHFQHIGHPIV 235


>gi|5163230|gb|AAD40609.1|AF115283_28 ribosomal protein S4 [Leptospira interrogans]
          Length = 207

 Score = 47.5 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+    IA + + VNG  ++  +  +   D +E+
Sbjct: 97  RLDNVVYRLGFAITRRQARNFIAHRHILVNGERVDIPSYRLNVGDKVEI 145


>gi|254700796|ref|ZP_05162624.1| translation initiation factor IF-2 [Brucella suis bv. 5 str. 513]
 gi|261751304|ref|ZP_05995013.1| translation initiation factor IF-2 [Brucella suis bv. 5 str. 513]
 gi|261741057|gb|EEY28983.1| translation initiation factor IF-2 [Brucella suis bv. 5 str. 513]
          Length = 959

 Score = 47.5 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/116 (12%), Positives = 29/116 (25%), Gaps = 2/116 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R + +  +RE +        +    A   +     R+         +   + +  + +K 
Sbjct: 161 RALEEAQIRE-VEERARAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKA 219

Query: 294 GLSKQKKLATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                K++  P  R     +   A  G                   P   S R   
Sbjct: 220 EEEAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAP 275



 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 11/121 (9%), Positives = 28/121 (23%), Gaps = 1/121 (0%)

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           L     REV ++  R         E           S     +    +    +   + ++
Sbjct: 163 LEEAQIREVEERA-RAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKAEE 221

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            ++++    + +       R           G           R +     P+     + 
Sbjct: 222 EAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAPIIADAA 281

Query: 348 R 348
            
Sbjct: 282 P 282


>gi|189028462|sp|A5VTB2|IF2_BRUO2 RecName: Full=Translation initiation factor IF-2
          Length = 959

 Score = 47.5 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/116 (12%), Positives = 29/116 (25%), Gaps = 2/116 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R + +  +RE +        +    A   +     R+         +   + +  + +K 
Sbjct: 161 RALEEAQIRE-VEERARAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKA 219

Query: 294 GLSKQKKLATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                K++  P  R     +   A  G                   P   S R   
Sbjct: 220 EEEAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAP 275



 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 11/121 (9%), Positives = 28/121 (23%), Gaps = 1/121 (0%)

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           L     REV ++  R         E           S     +    +    +   + ++
Sbjct: 163 LEEAQIREVEERA-RAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKAEE 221

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            ++++    + +       R           G           R +     P+     + 
Sbjct: 222 EAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAPIIADAA 281

Query: 348 R 348
            
Sbjct: 282 P 282


>gi|57234752|ref|YP_181245.1| 30S ribosomal protein S4 [Dehalococcoides ethenogenes 195]
 gi|90101687|sp|Q3Z954|RS4_DEHE1 RecName: Full=30S ribosomal protein S4
 gi|57225200|gb|AAW40257.1| ribosomal protein S4 [Dehalococcoides ethenogenes 195]
          Length = 207

 Score = 47.5 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   SR +  +++    + VNG   +  +  V     I V
Sbjct: 98  RLDNVLFRLGFGTSRAQARQIVMHGHILVNGQKTDIPSYLVKEGQEITV 146


>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 = 47.5 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 27/254 (10%), Positives = 65/254 (25%), Gaps = 42/254 (16%)

Query: 1   MKDKN----IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           MK KN    IV E     R+ K + ++    SR   ++ I  +RV VN  +  + A  ++
Sbjct: 1   MKSKNTLLFIVNETNR-DRLDKFLVSQNPEYSRAFYQQHILDERVTVNEQVQTKVATQLV 59

Query: 56  STDHI----------------------EVDGVPLRKAERTRLWLYHKPIGLVTTHSDP-- 91
             D +                        +   +    + R  + H   G +        
Sbjct: 60  PGDSVSIIIEEKEELLELLPEAIPLDKVYEDEMILVINKPRDMVVHPAPGHIRGTVVHAL 119

Query: 92  ------------DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
                                +  +      +       +   + +      ++ +    
Sbjct: 120 LHEIGERLKQEFPEEPWRPGIIHRLDKDTSGLLITAKTRQAKTIYSELFATKQLKKSYLA 179

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
             +                +  K+  V            +    G  + V +    G+  
Sbjct: 180 ICVGKPTATLIHTKLARHHSKRKEMAVSLTGKEAITHCEVLAYNGKLSLVLLRPETGRTH 239

Query: 200 EIKKVFEFFNWKVN 213
           +++   +  N  + 
Sbjct: 240 QLRVHMKHLNTPIL 253


>gi|23503013|ref|NP_699140.1| translation initiation factor IF-2 [Brucella suis 1330]
 gi|39931291|sp|Q8FXT2|IF2_BRUSU RecName: Full=Translation initiation factor IF-2
 gi|23349054|gb|AAN31055.1| translation initiation factor IF-2 [Brucella suis 1330]
          Length = 959

 Score = 47.5 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/116 (12%), Positives = 29/116 (25%), Gaps = 2/116 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R + +  +RE +        +    A   +     R+         +   + +  + +K 
Sbjct: 161 RALEEAQIRE-VEERARAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKA 219

Query: 294 GLSKQKKLATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                K++  P  R     +   A  G                   P   S R   
Sbjct: 220 EEEAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAP 275



 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 11/121 (9%), Positives = 28/121 (23%), Gaps = 1/121 (0%)

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           L     REV ++  R         E           S     +    +    +   + ++
Sbjct: 163 LEEAQIREVEERA-RAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKAEE 221

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            ++++    + +       R           G           R +     P+     + 
Sbjct: 222 EAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAPIIADAA 281

Query: 348 R 348
            
Sbjct: 282 P 282


>gi|328767205|gb|EGF77256.1| hypothetical protein BATDEDRAFT_36120 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 693

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 10/101 (9%), Positives = 21/101 (20%), Gaps = 2/101 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R       +     +   P   +           +    +  +      ++ G  K K+ 
Sbjct: 577 RNHQNDFSVPAECKDGAVPSSPAPVPAPAPIPSKTTANPNPRKTTNPGPKRTGRPKPKRT 636

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQ--REENHRRSPS 340
             P  +R                     +  R    R  P 
Sbjct: 637 GRPKPKRTGRPKPKRTGRPKPKRTRKPKRTNRPRPGRPEPG 677



 Score = 43.2 bits (100), Expect = 0.066,   Method: Composition-based stats.
 Identities = 10/81 (12%), Positives = 17/81 (20%), Gaps = 9/81 (11%)

Query: 259 APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAK 318
               +        P           R  +   ++ G  K K+   P  +R          
Sbjct: 610 KTTANPNPRKTTNPGPKRTGRPKPKRTGRPKPKRTGRPKPKRTGRPKPKRTR-------- 661

Query: 319 GIHSSFLSDSGQREENHRRSP 339
                       R E  +  P
Sbjct: 662 -KPKRTNRPRPGRPEPGQCDP 681



 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 9/117 (7%), Positives = 18/117 (15%), Gaps = 2/117 (1%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
            +        +     N                            +   ++      K  
Sbjct: 562 EIWRGFSKRGMGPNARNHQNDFSVPAECKDGAVPSSPAPVPAPAPIPSKTTANPNPRKTT 621

Query: 300 KLATPVHRRNLASNVWMAKGIH-SSFLSDSGQREENHR-RSPSFPSKRSLRRTSAKK 354
                   R         K             R +  R R P   ++    R    +
Sbjct: 622 NPGPKRTGRPKPKRTGRPKPKRTGRPKPKRTGRPKPKRTRKPKRTNRPRPGRPEPGQ 678


>gi|311068062|ref|YP_003972985.1| factor involved in shape determination, RNA-binding fold protein
           [Bacillus atrophaeus 1942]
 gi|310868579|gb|ADP32054.1| factor involved in shape determination, RNA-binding fold protein
           [Bacillus atrophaeus 1942]
          Length = 258

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/63 (22%), Positives = 28/63 (44%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +D  I  +  +  R+  V A     SR++   ++    VKVN  ++E  +  +   D + 
Sbjct: 170 RDVEIRDDTVSSLRLDAVCASMSRQSRQKALTLVKNGLVKVNWKVVEDPSYQLAEGDMLS 229

Query: 62  VDG 64
           + G
Sbjct: 230 IRG 232


>gi|294781812|ref|ZP_06747145.1| S4 domain protein YaaA [Fusobacterium sp. 1_1_41FAA]
 gi|294481922|gb|EFG29690.1| S4 domain protein YaaA [Fusobacterium sp. 1_1_41FAA]
          Length = 71

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 12/70 (17%), Positives = 27/70 (38%), Gaps = 9/70 (12%)

Query: 1  MKDKNIVQENFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
          MK+   V+ +    ++ + +       +G     E + +I   +VKVN  +  R    + 
Sbjct: 1  MKNIEKVKISTEFIKLDQFLKWLAVVDSG----SEAKEIILDGKVKVNDEVETRRGRKIY 56

Query: 56 STDHIEVDGV 65
              +E+   
Sbjct: 57 PEYKVEIFDK 66


>gi|255530540|ref|YP_003090912.1| 30S ribosomal protein S4 [Pedobacter heparinus DSM 2366]
 gi|255343524|gb|ACU02850.1| ribosomal protein S4 [Pedobacter heparinus DSM 2366]
          Length = 202

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   + R GIA+ R    ++++ + V VNG ++   +  + + D I V
Sbjct: 94  RLDNTVYRLGIATTRSAARQLVSHKHVTVNGEVVNIPSYQLKAGDVIAV 142


>gi|241958516|ref|XP_002421977.1| mitochondrial ribosome protein precursor, small subunit [Candida
           dubliniensis CD36]
 gi|223645322|emb|CAX39978.1| mitochondrial ribosome protein precursor, small subunit [Candida
           dubliniensis CD36]
          Length = 461

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 1/54 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+   + R+  AS  R+  + I    VKVNG++++  +  + S D   VD   +
Sbjct: 105 RLEIALFRSMFASSVRQARQFILGGYVKVNGVVIKHPSFPLQSGDVFSVDPEKV 158


>gi|124026568|ref|YP_001015683.1| rRNA methyltransferase [Prochlorococcus marinus str. NATL1A]
 gi|123961636|gb|ABM76419.1| FtsJ cell division protein:S4 domain:Hemolysin A [Prochlorococcus
          marinus str. NATL1A]
          Length = 264

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 12/54 (22%), Positives = 27/54 (50%), Gaps = 2/54 (3%)

Query: 11 FTPQRVS-KVIARAGIASRREVERMIAQQRV-KVNGILLERAAVNVMSTDHIEV 62
              R+   ++ +  + +R+E + +I   +V  +NG +L++    V+    IEV
Sbjct: 2  TKKSRLDLHLLTKGLVKTRQEAQNLIRAGKVKTINGQILDKPGQEVLKDLEIEV 55


>gi|94500968|ref|ZP_01307493.1| ribosomal protein S4 [Oceanobacter sp. RED65]
 gi|94426908|gb|EAT11891.1| ribosomal protein S4 [Oceanobacter sp. RED65]
          Length = 206

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +   + N+ + D + +
Sbjct: 97  RLDNVVYRMGFGSTRAEARQLVSHKAIAVNGQTVNIPSYNIKAGDVVSI 145


>gi|322384358|ref|ZP_08058056.1| 30S ribosomal protein S4-like protein [Paenibacillus larvae subsp.
           larvae B-3650]
 gi|321150860|gb|EFX44297.1| 30S ribosomal protein S4-like protein [Paenibacillus larvae subsp.
           larvae B-3650]
          Length = 199

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  ++ R G A SR    ++++   V VNG  ++ A+  V   D I
Sbjct: 92  RLDNLVFRLGFANSRAGARQLVSHGHVTVNGKKVDIASYQVSVGDVI 138


>gi|306820916|ref|ZP_07454536.1| S4 domain protein [Eubacterium yurii subsp. margaretiae ATCC
          43715]
 gi|304551030|gb|EFM39001.1| S4 domain protein [Eubacterium yurii subsp. margaretiae ATCC
          43715]
          Length = 72

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/61 (22%), Positives = 28/61 (45%), Gaps = 3/61 (4%)

Query: 10 NFTPQRVSKVIARAGIASRREVE--RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
          N    ++ +++  A I S    E   +I   +VKVNG +  +    +   D +EV+   +
Sbjct: 6  NTEFIKLDQLLKLADITS-SGAESHALITDGKVKVNGQVELQKRKKIRENDIVEVNKKVI 64

Query: 68 R 68
          +
Sbjct: 65 Q 65


>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 = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 37/264 (14%), Positives = 79/264 (29%), Gaps = 54/264 (20%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRRE--------VERMIAQQRVKVNGILLERAAV 52
           MK+  + +E +   R+ + +       R+E        + + +   ++KVNG  ++    
Sbjct: 1   MKEYQV-EEKYVGVRIDRYL-------RKEFPDLSLGDIFKTLRTGKIKVNGKKVKE-NY 51

Query: 53  NVMSTDHIE----VDGVP------------------LRKAERTRLWLYHKPIGLVTTHSD 90
             +  D I+    V+                     +   +   L  Y K   L+   S 
Sbjct: 52  RFLEEDRIQNYLQVEEKEKMTFIHLSQEEKKRLEDGIFYQDTDILVFYKKAGELMHKGSS 111

Query: 91  PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
            D                  V RLD  T GL+L      + R L     +   + +    
Sbjct: 112 HDYGLAEQFQAYFQNEDFHFVNRLDKETSGLVLGGKCLKIVRELAEAIKKRTIIKKYYII 171

Query: 151 GQVDQDKLNL-------------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGK 197
            +   +K +              L+     +         ++  +    + +   L  G+
Sbjct: 172 IEGSPEKNHFSLKTYLKKGENKVLESQTAKEEYKECSASFSVIRKNKEYSLLEAVLETGR 231

Query: 198 NREIKKVFEFFNWKVNRLIRISYG 221
             +++       + +  L  I YG
Sbjct: 232 THQLRVQLAGIGFPI--LGDIKYG 253


>gi|229815744|ref|ZP_04446069.1| hypothetical protein COLINT_02793 [Collinsella intestinalis DSM
           13280]
 gi|229808660|gb|EEP44437.1| hypothetical protein COLINT_02793 [Collinsella intestinalis DSM
           13280]
          Length = 198

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R+E  + +      VNG  ++  +  V + D I V
Sbjct: 89  RLDNVVFRLGFARTRKEARQTVRHGHFTVNGKRVDIPSYRVKAGDVIAV 137


>gi|172040777|ref|YP_001800491.1| hypothetical protein cur_1097 [Corynebacterium urealyticum DSM
          7109]
 gi|171852081|emb|CAQ05057.1| hypothetical protein cu1097 [Corynebacterium urealyticum DSM
          7109]
          Length = 262

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/36 (38%), Positives = 23/36 (63%)

Query: 27 SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          SR + ++MI + RV+VNG+L ++ A  V +   I V
Sbjct: 8  SREQAQKMIKEGRVQVNGMLAQKPATGVNAEVSIRV 43


>gi|126657190|ref|ZP_01728356.1| hypothetical protein CY0110_24716 [Cyanothece sp. CCY0110]
 gi|126621461|gb|EAZ92172.1| hypothetical protein CY0110_24716 [Cyanothece sp. CCY0110]
          Length = 260

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 13/40 (32%), Positives = 21/40 (52%)

Query: 27 SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
          SR++ +R I    VKVN  ++++    V  T  IE+   P
Sbjct: 8  SRQQAQRCIRAGEVKVNQRIIDKPGTEVKITADIELKQKP 47


>gi|37523141|ref|NP_926518.1| 30S ribosomal protein S4 [Gloeobacter violaceus PCC 7421]
 gi|41017822|sp|Q7NFF4|RS4_GLOVI RecName: Full=30S ribosomal protein S4
 gi|35214144|dbj|BAC91513.1| 30S ribosomal protein S4 [Gloeobacter violaceus PCC 7421]
          Length = 206

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SR +  + +      VNG  +   +  V   D I V
Sbjct: 99  RLDNVVYRLGFATSRAQARQWVNHGHFAVNGRRVSIPSYRVRPGDAITV 147


>gi|326384768|ref|ZP_08206445.1| hemolysin A [Gordonia neofelifaecis NRRL B-59395]
 gi|326196576|gb|EGD53773.1| hemolysin A [Gordonia neofelifaecis NRRL B-59395]
          Length = 300

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 1/41 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNV 54
          R+   + R G+A SR +   +I    VKVNG    +A+ NV
Sbjct: 6  RLDAELVRRGLARSREQARELIEAGSVKVNGTPATKASTNV 46


>gi|322436519|ref|YP_004218731.1| ribosomal protein S4 [Acidobacterium sp. MP5ACTX9]
 gi|321164246|gb|ADW69951.1| ribosomal protein S4 [Acidobacterium sp. MP5ACTX9]
          Length = 210

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V  R G+A SRR+  +++    ++VNG  +   +      D I V
Sbjct: 101 RLDNVCYRLGLATSRRQARQVVRHGHIQVNGRKVNIPSFQCKVGDEIAV 149


>gi|291550232|emb|CBL26494.1| bacterial translation initiation factor 2 (bIF-2) [Ruminococcus
           torques L2-14]
          Length = 884

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/114 (12%), Positives = 31/114 (27%), Gaps = 5/114 (4%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P   E+     + P+ ++E          +          + + + +G  +Q +   P 
Sbjct: 104 KPARTEKPAAKSERPVRAAEDRPARPAQNGARSERPQGSRTERTGRPSGEGRQVRSDRPG 163

Query: 306 H-----RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                 RR+   N    +G          + +   R        R  R     +
Sbjct: 164 QKPFGDRRSNGENRGENRGPRQDRDGRGQRSDRGGRDGFQGRDNRDGRENRDGR 217



 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 14/113 (12%), Positives = 29/113 (25%), Gaps = 1/113 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           ++ L   +  +   N            R   N      D   R     S+ NG  K  + 
Sbjct: 50  KKNLAFVVRPQNSKNSSRLQGKRPGQGRQGQNQGRPNGDG-KRPAAGQSRSNGEGKPART 108

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             P  +          +    +      +R +  R   +       R+  + +
Sbjct: 109 EKPAAKSERPVRAAEDRPARPAQNGARSERPQGSRTERTGRPSGEGRQVRSDR 161


>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 = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 4/54 (7%)

Query: 13 PQRVSKVIARAGIA----SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          P R+ K ++R   A    SR  + R+I +  V V+G L+  A   V     + +
Sbjct: 15 PPRLDKALSRDVPADESLSRTRLARLIEEGAVAVDGKLVTDAKAKVAEGAAVCI 68


>gi|159028854|emb|CAO90659.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 259

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 2/65 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             K  +       R+   IA AG   SR ++   I+   V+VN   + +++ NV + D I
Sbjct: 172 PQKKEINTVEASLRLD-AIASAGFGISRSKMAEAISSGDVRVNWKDISQSSYNVKTGDLI 230

Query: 61  EVDGV 65
              G 
Sbjct: 231 SFRGK 235


>gi|20808026|ref|NP_623197.1| hypothetical protein TTE1597 [Thermoanaerobacter tengcongensis MB4]
 gi|20516604|gb|AAM24801.1| conserved hypothetical protein [Thermoanaerobacter tengcongensis
           MB4]
          Length = 248

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 3/65 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K K+I        RV  V A +G   SR +   +I    ++VN   +E  + +V   D 
Sbjct: 160 IKYKDIFS-TVASLRVDSV-AASGFGISRTKASELIKSGLLRVNWEAVEDPSFHVGEGDV 217

Query: 60  IEVDG 64
           I + G
Sbjct: 218 ISLRG 222


>gi|295101438|emb|CBK98983.1| SSU ribosomal protein S4P [Faecalibacterium prausnitzii L2-6]
          Length = 200

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+  ++++     VNG  +   +  + + D IEV
Sbjct: 90  RLDNVVFRLGFAQTRRDARQLVSHAHFTVNGKKVNIPSYLIKAGDVIEV 138


>gi|253580647|ref|ZP_04857911.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251848018|gb|EES75984.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 197

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R+E  +++  + V VNG  +   +  V + D IE+
Sbjct: 88  RLDNVVFRMGFARTRKEARQIVDHKHVLVNGKCVNIPSYLVKAGDQIEI 136


>gi|169629445|ref|YP_001703094.1| cytotoxin/hemolysin TlyA [Mycobacterium abscessus ATCC 19977]
 gi|169241412|emb|CAM62440.1| Cytotoxin/haemolysin homologue TlyA [Mycobacterium abscessus]
          Length = 268

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
          RV   + R G+A SR++   +I   RV+++GI   +AA  V +T  + V G  
Sbjct: 6  RVDAELVRRGLARSRQQAAELIEAGRVRIDGIPAVKAATAVPATASLVVQGEA 58


>gi|149279638|ref|ZP_01885767.1| 30S ribosomal protein S4 [Pedobacter sp. BAL39]
 gi|149229674|gb|EDM35064.1| 30S ribosomal protein S4 [Pedobacter sp. BAL39]
          Length = 202

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   + R GIA+ R    ++++ + V VNG ++   +  + + D I V
Sbjct: 94  RLDNTVYRLGIATTRSAARQLVSHKHVTVNGEVVNIPSYQLKAGDVIAV 142


>gi|157372753|ref|YP_001480742.1| 30S ribosomal protein S4 [Serratia proteamaculans 568]
 gi|172047788|sp|A8GKH4|RS4_SERP5 RecName: Full=30S ribosomal protein S4
 gi|157324517|gb|ABV43614.1| ribosomal protein S4 [Serratia proteamaculans 568]
          Length = 206

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRSESRQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 ASLELAEQREKPT 169


>gi|326334520|ref|ZP_08200731.1| 30S ribosomal protein S4 [Capnocytophaga sp. oral taxon 338 str.
           F0234]
 gi|325693289|gb|EGD35217.1| 30S ribosomal protein S4 [Capnocytophaga sp. oral taxon 338 str.
           F0234]
          Length = 201

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 29/49 (59%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA SRR   ++++ + + VNG ++   + ++ + D + V
Sbjct: 94  RLDNVVYRMGIAPSRRAARQLVSHRHITVNGEVVNIPSYSLKAGDIVGV 142


>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 = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 40/232 (17%), Positives = 75/232 (32%), Gaps = 26/232 (11%)

Query: 7   VQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           V +    +R+ +++A R    SRR    ++    V V+   ++ A+  +     +EV   
Sbjct: 12  VADEDVGKRLDQLLAARVPELSRRMARTLLDIGGVFVDRTRVKVASRKLRPGQSVEVHLG 71

Query: 64  ----------GVPLRKA------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
                     G   RK             E   L +  KP GL++  +       +   L
Sbjct: 72  GALERATKEVGKEARKRDSRALPRFKIVFEDRDLVVVDKPAGLLSAPTPESDLGNLAALL 131

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
                RV  V R+D+ T GLL+        + L     +  ++ R            +  
Sbjct: 132 RERRERVYVVHRIDLQTSGLLVFAKTRRANQHLSERFREH-QIERAYTAVVAGAPVEDTF 190

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              + ++G         L       A +   L  G+  +I+       + V 
Sbjct: 191 TIDLPLRGRRATTHLQVLQRIGERAAVLDARLETGRTHQIRLHCLQRGYPVL 242


>gi|37522750|ref|NP_926127.1| hypothetical protein gll3181 [Gloeobacter violaceus PCC 7421]
 gi|35213752|dbj|BAC91122.1| gll3181 [Gloeobacter violaceus PCC 7421]
          Length = 272

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 11/57 (19%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 7  VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          + E     R+ +++   G+A SR++ + +I   +V+V G   ++          + V
Sbjct: 1  MAERPARLRLDQILVERGLAESRQKAQALIRAGQVRVGGERFDKPGSLCPVDSEVSV 57


>gi|304316676|ref|YP_003851821.1| RNA-binding S4 domain protein [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302778178|gb|ADL68737.1| RNA-binding S4 domain protein [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 246

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 10/61 (16%), Positives = 21/61 (34%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           + +       R+  +IA     SR +   +I     +VN       +  +   D + + G
Sbjct: 161 DDINTTVASIRLDSIIASGFKLSRTKASELIKAGLAEVNWETKLEPSFEIKEGDIVSLRG 220

Query: 65  V 65
            
Sbjct: 221 R 221


>gi|229013082|ref|ZP_04170247.1| RNA-binding S4 domain protein [Bacillus mycoides DSM 2048]
 gi|228748336|gb|EEL98196.1| RNA-binding S4 domain protein [Bacillus mycoides DSM 2048]
          Length = 241

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+ +I    VKVN   +E+ +      D   V G
Sbjct: 166 RLDVLLAEMLHISRQKVQPLIKGGLVKVNWKTVEQTSYECFPGDVFSVRG 215


>gi|167759630|ref|ZP_02431757.1| hypothetical protein CLOSCI_01988 [Clostridium scindens ATCC
          35704]
 gi|167662756|gb|EDS06886.1| hypothetical protein CLOSCI_01988 [Clostridium scindens ATCC
          35704]
          Length = 79

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR          RV VNG + + A+V V   D IE+
Sbjct: 1  MRLDKFLKVSRLIKRRTVANEACDAGRVTVNGSVAK-ASVKVKPGDIIEI 49


>gi|87301271|ref|ZP_01084112.1| Hemolysin A [Synechococcus sp. WH 5701]
 gi|87284239|gb|EAQ76192.1| Hemolysin A [Synechococcus sp. WH 5701]
          Length = 273

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 11/45 (24%), Positives = 24/45 (53%), Gaps = 1/45 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMST 57
          QR+ + +   G+A SR++ +++I   RV+    +L++    V   
Sbjct: 5  QRLDQHLVALGLAASRQQAQQLIRAGRVRSGDRVLDKPGQEVAPE 49


>gi|68476945|ref|XP_717450.1| likely mitochondrial ribosomal protein S4 [Candida albicans SC5314]
 gi|68477136|ref|XP_717361.1| likely mitochondrial ribosomal protein S4 [Candida albicans SC5314]
 gi|46439070|gb|EAK98392.1| likely mitochondrial ribosomal protein S4 [Candida albicans SC5314]
 gi|46439163|gb|EAK98484.1| likely mitochondrial ribosomal protein S4 [Candida albicans SC5314]
          Length = 461

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 1/54 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+   + R+  AS  R+  + I    VKVNG++++  +  + S D   VD   +
Sbjct: 105 RLEIALFRSMFASSVRQARQFILGGYVKVNGVVIKHPSFPLQSGDVFSVDPEKV 158


>gi|291613261|ref|YP_003523418.1| ribosomal protein S4 [Sideroxydans lithotrophicus ES-1]
 gi|291583373|gb|ADE11031.1| ribosomal protein S4 [Sideroxydans lithotrophicus ES-1]
          Length = 209

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V  R G   SR E  +++    + VNG  +   +  V   D +EV
Sbjct: 100 RLDNVSYRMGFGASRSEARQVVRHNSILVNGKRVNIPSYQVRPGDVVEV 148


>gi|257064663|ref|YP_003144335.1| SSU ribosomal protein S4P [Slackia heliotrinireducens DSM 20476]
 gi|256792316|gb|ACV22986.1| SSU ribosomal protein S4P [Slackia heliotrinireducens DSM 20476]
          Length = 198

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           R+  V+ R G A +R+E  + ++   + VNG  +   +  V   D + V    
Sbjct: 89  RLDNVVFRLGFARTRKEARQTVSHGHIYVNGKRVNIPSYRVRPGDLVSVAPKA 141


>gi|222151637|ref|YP_002560793.1| 30S ribosomal protein S4 [Macrococcus caseolyticus JCSC5402]
 gi|254764595|sp|B9E7C9|RS4_MACCJ RecName: Full=30S ribosomal protein S4
 gi|222120762|dbj|BAH18097.1| 30S ribosomal protein S4 [Macrococcus caseolyticus JCSC5402]
          Length = 200

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ + G+A +RR+  +++    + V+G  ++  +  +     I V
Sbjct: 93  RLDAVVYQLGLARTRRQARQLVNHGHIMVDGARVDIPSYQLKPGQVISV 141


>gi|117928454|ref|YP_873005.1| hemolysin A [Acidothermus cellulolyticus 11B]
 gi|117648917|gb|ABK53019.1| hemolysin A [Acidothermus cellulolyticus 11B]
          Length = 267

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+ + + R G+A SR E   ++A   V V G    + A  V   D + +
Sbjct: 6  RLDRELVRRGLARSRSEAADLVASGAVLVAGRPAMKPATAVSPQDSLTL 54


>gi|298694246|gb|ADI97468.1| probable RNA pseudoridylate synthase [Staphylococcus aureus subsp.
           aureus ED133]
          Length = 284

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 24/199 (12%), Positives = 52/199 (26%), Gaps = 28/199 (14%)

Query: 42  VNGILLERAAVNVMSTDHIEVD-GVPLR--------------KAERTRLWLYHKPIGLVT 86
           VN   +      +M  D +E+     +                 +   + +         
Sbjct: 38  VNDEPVTV-RKQLMPNDILEIHLPQEIPSVNLIPYARKLEVLYEDAFIIIVTKPNNQNCI 96

Query: 87  THSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
              +    S +   L              V RLD NT G+++    G +  +    + + 
Sbjct: 97  PSREHPHESLIEQVLYHCQVHGENINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKGNLKK 156

Query: 142 LRVYRVRFHGQVD-------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           +    V              +   + +    V     Y      +  Q    +   V L 
Sbjct: 157 IYTCLVYGKTHSSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLH 216

Query: 195 EGKNREIKKVFEFFNWKVN 213
            G+  +I+  F+     + 
Sbjct: 217 TGRTHQIRVHFQHIGHPIV 235


>gi|229168638|ref|ZP_04296360.1| RNA-binding S4 domain protein [Bacillus cereus AH621]
 gi|228614794|gb|EEK71897.1| RNA-binding S4 domain protein [Bacillus cereus AH621]
          Length = 241

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+ +I    VKVN   +E+ +      D   V G
Sbjct: 166 RLDVLLAEMLHISRQKVQPLIKGGLVKVNWKTVEQTSYECFPGDVFSVRG 215


>gi|161620073|ref|YP_001593960.1| translation initiation factor IF-2 [Brucella canis ATCC 23365]
 gi|260567368|ref|ZP_05837838.1| translation initiation factor IF-2 [Brucella suis bv. 4 str. 40]
 gi|189028302|sp|A9M9Z4|IF2_BRUC2 RecName: Full=Translation initiation factor IF-2
 gi|161336884|gb|ABX63189.1| translation initiation factor IF-2 [Brucella canis ATCC 23365]
 gi|260156886|gb|EEW91966.1| translation initiation factor IF-2 [Brucella suis bv. 4 str. 40]
          Length = 959

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/116 (12%), Positives = 29/116 (25%), Gaps = 2/116 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R + +  +RE +        +    A   +     R+         +   + +  + +K 
Sbjct: 161 RALEEAQIRE-VEERARAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKA 219

Query: 294 GLSKQKKLATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                K++  P  R     +   A  G                   P   S R   
Sbjct: 220 EEEAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAP 275



 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 11/121 (9%), Positives = 28/121 (23%), Gaps = 1/121 (0%)

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           L     REV ++  R         E           S     +    +    +   + ++
Sbjct: 163 LEEAQIREVEERA-RAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKAEE 221

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            ++++    + +       R           G           R +     P+     + 
Sbjct: 222 EAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAPIIADAA 281

Query: 348 R 348
            
Sbjct: 282 P 282


>gi|126662239|ref|ZP_01733238.1| 30S ribosomal protein S4 [Flavobacteria bacterium BAL38]
 gi|126625618|gb|EAZ96307.1| 30S ribosomal protein S4 [Flavobacteria bacterium BAL38]
          Length = 201

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 29/49 (59%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A SRR   ++++ + + VNG L+   + ++ + D + V
Sbjct: 94  RLDNVVYRMGVAPSRRAARQIVSHRHITVNGELVNVPSYHLKAGDKVAV 142


>gi|319778700|ref|YP_004129613.1| SSU ribosomal protein S4p (S9e) [Taylorella equigenitalis MCE9]
 gi|317108724|gb|ADU91470.1| SSU ribosomal protein S4p (S9e) [Taylorella equigenitalis MCE9]
          Length = 207

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++   +++NG   +  ++ V + D + V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHGAIELNGKKADIPSMIVNAGDVVSV 146


>gi|256060125|ref|ZP_05450307.1| translation initiation factor IF-2 [Brucella neotomae 5K33]
 gi|261324102|ref|ZP_05963299.1| translation initiation factor IF-2 [Brucella neotomae 5K33]
 gi|261300082|gb|EEY03579.1| translation initiation factor IF-2 [Brucella neotomae 5K33]
          Length = 959

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/116 (12%), Positives = 29/116 (25%), Gaps = 2/116 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R + +  +RE +        +    A   +     R+         +   + +  + +K 
Sbjct: 161 RALEEAQIRE-VEERARAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKA 219

Query: 294 GLSKQKKLATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                K++  P  R     +   A  G                   P   S R   
Sbjct: 220 EEEAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAP 275



 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 11/121 (9%), Positives = 28/121 (23%), Gaps = 1/121 (0%)

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           L     REV ++  R         E           S     +    +    +   + ++
Sbjct: 163 LEEAQIREVEERA-RAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKAEE 221

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            ++++    + +       R           G           R +     P+     + 
Sbjct: 222 EAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAPIIADAA 281

Query: 348 R 348
            
Sbjct: 282 P 282


>gi|254694784|ref|ZP_05156612.1| translation initiation factor IF-2 [Brucella abortus bv. 3 str.
           Tulya]
 gi|261215111|ref|ZP_05929392.1| translation initiation factor IF-2 [Brucella abortus bv. 3 str.
           Tulya]
 gi|260916718|gb|EEX83579.1| translation initiation factor IF-2 [Brucella abortus bv. 3 str.
           Tulya]
          Length = 959

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/116 (12%), Positives = 29/116 (25%), Gaps = 2/116 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R + +  +RE +        +    A   +     R+         +   + +  + +K 
Sbjct: 161 RALEEAQIRE-VEERARAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKA 219

Query: 294 GLSKQKKLATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                K++  P  R     +   A  G                   P   S R   
Sbjct: 220 EEEAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAP 275



 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 11/121 (9%), Positives = 28/121 (23%), Gaps = 1/121 (0%)

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           L     REV ++  R         E           S     +    +    +   + ++
Sbjct: 163 LEEAQIREVEERA-RAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKAEE 221

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            ++++    + +       R           G           R +     P+     + 
Sbjct: 222 EAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAPIIADAA 281

Query: 348 R 348
            
Sbjct: 282 P 282


>gi|238879875|gb|EEQ43513.1| conserved hypothetical protein [Candida albicans WO-1]
          Length = 461

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 1/54 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+   + R+  AS  R+  + I    VKVNG++++  +  + S D   VD   +
Sbjct: 105 RLEIALFRSMFASSVRQARQFILGGYVKVNGVVIKHPSFPLQSGDVFSVDPEKV 158


>gi|258569883|ref|XP_002543745.1| conserved hypothetical protein [Uncinocarpus reesii 1704]
 gi|237904015|gb|EEP78416.1| conserved hypothetical protein [Uncinocarpus reesii 1704]
          Length = 467

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 1/56 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+   I RA  AS  R+  + +    V VNG  ++     +   D  +VD   +  
Sbjct: 132 RLDVAIFRALFASSTRQARQFVVHGWVTVNGKKMQYPGYLLNPGDLFQVDPERVMY 187


>gi|213856915|ref|ZP_03384155.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Typhi str. M223]
          Length = 167

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 93  RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 152

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 153 AALELAEQREKPT 165


>gi|109947356|ref|YP_664584.1| hemolysin [Helicobacter acinonychis str. Sheeba]
 gi|109714577|emb|CAJ99585.1| hemolysin [Helicobacter acinonychis str. Sheeba]
          Length = 235

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   +  +  ++SR + + +I + +V VN I++ + +  V   D IE+
Sbjct: 1  MRLDYALFDQHLVSSREKAKVLILKNQVLVNKIVISKPSFMVKENDKIEL 50


>gi|62291002|ref|YP_222795.1| translation initiation factor IF-2 [Brucella abortus bv. 1 str.
           9-941]
 gi|82700911|ref|YP_415485.1| translation initiation factor IF-2 [Brucella melitensis biovar
           Abortus 2308]
 gi|163844178|ref|YP_001628583.1| translation initiation factor IF-2 [Brucella suis ATCC 23445]
 gi|189025214|ref|YP_001935982.1| translation initiation factor IF-2 [Brucella abortus S19]
 gi|254690296|ref|ZP_05153550.1| translation initiation factor IF-2 [Brucella abortus bv. 6 str.
           870]
 gi|254696412|ref|ZP_05158240.1| translation initiation factor IF-2 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|254709140|ref|ZP_05170951.1| translation initiation factor IF-2 [Brucella pinnipedialis B2/94]
 gi|254731325|ref|ZP_05189903.1| translation initiation factor IF-2 [Brucella abortus bv. 4 str.
           292]
 gi|256030665|ref|ZP_05444279.1| translation initiation factor IF-2 [Brucella pinnipedialis
           M292/94/1]
 gi|256258549|ref|ZP_05464085.1| translation initiation factor IF-2 [Brucella abortus bv. 9 str.
           C68]
 gi|260546265|ref|ZP_05822005.1| translation initiation factor IF-2 [Brucella abortus NCTC 8038]
 gi|260755836|ref|ZP_05868184.1| translation initiation factor IF-2 [Brucella abortus bv. 6 str.
           870]
 gi|260759059|ref|ZP_05871407.1| translation initiation factor IF-2 [Brucella abortus bv. 4 str.
           292]
 gi|260760784|ref|ZP_05873127.1| translation initiation factor IF-2 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260884861|ref|ZP_05896475.1| translation initiation factor IF-2 [Brucella abortus bv. 9 str.
           C68]
 gi|261316639|ref|ZP_05955836.1| translation initiation factor IF-2 [Brucella pinnipedialis B2/94]
 gi|265987711|ref|ZP_06100268.1| translation initiation factor IF-2 [Brucella pinnipedialis
           M292/94/1]
 gi|306842726|ref|ZP_07475369.1| translation initiation factor IF-2 [Brucella sp. BO2]
 gi|306843582|ref|ZP_07476183.1| translation initiation factor IF-2 [Brucella sp. BO1]
 gi|81309341|sp|Q57AA0|IF2_BRUAB RecName: Full=Translation initiation factor IF-2
 gi|90101348|sp|Q2YQR7|IF2_BRUA2 RecName: Full=Translation initiation factor IF-2
 gi|189028303|sp|B0CK11|IF2_BRUSI RecName: Full=Translation initiation factor IF-2
 gi|62197134|gb|AAX75434.1| InfB, translation initiation factor IF-2 [Brucella abortus bv. 1
           str. 9-941]
 gi|82617012|emb|CAJ12121.1| Initiation factor 2:Elongation factor, GTP-binding:ATP/GTP-binding
           site motif A (P-loop):Ras GTPase
           superfamily:Proline-rich [Brucella melitensis biovar
           Abortus 2308]
 gi|163674901|gb|ABY39012.1| translation initiation factor IF-2 [Brucella suis ATCC 23445]
 gi|189020786|gb|ACD73508.1| translation initiation factor IF-2 [Brucella abortus S19]
 gi|260096372|gb|EEW80248.1| translation initiation factor IF-2 [Brucella abortus NCTC 8038]
 gi|260669377|gb|EEX56317.1| translation initiation factor IF-2 [Brucella abortus bv. 4 str.
           292]
 gi|260671216|gb|EEX58037.1| translation initiation factor IF-2 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260675944|gb|EEX62765.1| translation initiation factor IF-2 [Brucella abortus bv. 6 str.
           870]
 gi|260874389|gb|EEX81458.1| translation initiation factor IF-2 [Brucella abortus bv. 9 str.
           C68]
 gi|261295862|gb|EEX99358.1| translation initiation factor IF-2 [Brucella pinnipedialis B2/94]
 gi|264659908|gb|EEZ30169.1| translation initiation factor IF-2 [Brucella pinnipedialis
           M292/94/1]
 gi|306276273|gb|EFM57973.1| translation initiation factor IF-2 [Brucella sp. BO1]
 gi|306287172|gb|EFM58674.1| translation initiation factor IF-2 [Brucella sp. BO2]
          Length = 959

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/116 (12%), Positives = 29/116 (25%), Gaps = 2/116 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R + +  +RE +        +    A   +     R+         +   + +  + +K 
Sbjct: 161 RALEEAQIRE-VEERARAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKA 219

Query: 294 GLSKQKKLATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                K++  P  R     +   A  G                   P   S R   
Sbjct: 220 EEEAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAP 275



 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 11/121 (9%), Positives = 28/121 (23%), Gaps = 1/121 (0%)

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           L     REV ++  R         E           S     +    +    +   + ++
Sbjct: 163 LEEAQIREVEERA-RAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKAEE 221

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            ++++    + +       R           G           R +     P+     + 
Sbjct: 222 EAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAPIIADAA 281

Query: 348 R 348
            
Sbjct: 282 P 282


>gi|24213464|ref|NP_710945.1| 30S ribosomal protein S4 [Leptospira interrogans serovar Lai str.
           56601]
 gi|45658677|ref|YP_002763.1| 30S ribosomal protein S4 [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
 gi|26454650|sp|Q9XD10|RS4_LEPIN RecName: Full=30S ribosomal protein S4
 gi|61215619|sp|Q72NI7|RS4_LEPIC RecName: Full=30S ribosomal protein S4
 gi|24194236|gb|AAN47963.1| 30S ribosomal protein S4 [Leptospira interrogans serovar Lai str.
           56601]
 gi|45601921|gb|AAS71400.1| 30S ribosomal protein S4 [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
          Length = 207

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+    IA + + VNG  ++  +  +   D +E+
Sbjct: 97  RLDNVVYRLGFAITRRQARNFIAHRHILVNGERVDIPSYRLNVGDKVEI 145


>gi|260588128|ref|ZP_05854041.1| hemolysin A [Blautia hansenii DSM 20583]
 gi|331082304|ref|ZP_08331430.1| hypothetical protein HMPREF0992_00354 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|260541655|gb|EEX22224.1| hemolysin A [Blautia hansenii DSM 20583]
 gi|330400790|gb|EGG80391.1| hypothetical protein HMPREF0992_00354 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 268

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 21/162 (12%), Positives = 49/162 (30%), Gaps = 2/162 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++ + G+A SR + + +I    V V+    ++A      T +IE+ G  L+   R
Sbjct: 3   ERLDVLLVKRGLAVSREKAKAVIMAGNVYVDNQKEDKAGTMFQETVNIEIRGNTLKYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L            +                 ++  G + +    +     D  L  
Sbjct: 63  GGLKLEKAMSHFGVALENKVCMDVGSST-GGFTDCMLQNGAVKVYAIDVGHGQLDWKLRN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
              +   +   +  V      +    + +    +        
Sbjct: 122 DPRVVCMEKTNIRYVVPEDLQEAADFSSIDVSFISLTKVLLP 163


>gi|254458831|ref|ZP_05072255.1| ribosomal protein S4 [Campylobacterales bacterium GD 1]
 gi|207084597|gb|EDZ61885.1| ribosomal protein S4 [Campylobacterales bacterium GD 1]
          Length = 208

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G AS RR   +++    + V+G  L+  +  V     IEV
Sbjct: 99  RLDNVVYRMGFASTRRFARQLVTHGHLLVDGKKLDIPSYRVKPGQKIEV 147


>gi|296269380|ref|YP_003652012.1| peptidoglycan glycosyltransferase [Thermobispora bispora DSM 43833]
 gi|296092167|gb|ADG88119.1| Peptidoglycan glycosyltransferase [Thermobispora bispora DSM 43833]
          Length = 727

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 9/116 (7%), Positives = 18/116 (15%), Gaps = 2/116 (1%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           +R+                                    +   R  +             
Sbjct: 1   MRDGGRNPGPGRGGPGSRGGRGPGGGRRHPGTPGRPARSEGPPRPHRPDRAAPPHPPSAG 60

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQR--EENHRRSPSFPSKRSLRRTSAKK 354
                 RR                  + G R       R P   ++ +  R    +
Sbjct: 61  RDDLAGRRGGTPPRPGEPTPRRGPRPEPGGRVPPGRGARQPGSGARAAGPRRPVAR 116



 Score = 44.8 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 11/86 (12%), Positives = 22/86 (25%)

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
                 SE   R      +  P   +  + + + + G +  +       R          
Sbjct: 33  PGRPARSEGPPRPHRPDRAAPPHPPSAGRDDLAGRRGGTPPRPGEPTPRRGPRPEPGGRV 92

Query: 318 KGIHSSFLSDSGQREENHRRSPSFPS 343
                +    SG R    RR  +  +
Sbjct: 93  PPGRGARQPGSGARAAGPRRPVARTA 118



 Score = 42.9 bits (99), Expect = 0.078,   Method: Composition-based stats.
 Identities = 9/104 (8%), Positives = 15/104 (14%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
              P                +       P      P    R +       G   ++  + 
Sbjct: 45  PHRPDRAAPPHPPSAGRDDLAGRRGGTPPRPGEPTPRRGPRPEPGGRVPPGRGARQPGSG 104

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
                        A G                 R  S   +   
Sbjct: 105 ARAAGPRRPVARTASGGRPPERRPRWPWPAGPDRRRSRAPEPPR 148



 Score = 42.9 bits (99), Expect = 0.081,   Method: Composition-based stats.
 Identities = 9/89 (10%), Positives = 15/89 (16%)

Query: 264 SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSS 323
           +                D        S        ++  TP                   
Sbjct: 32  TPGRPARSEGPPRPHRPDRAAPPHPPSAGRDDLAGRRGGTPPRPGEPTPRRGPRPEPGGR 91

Query: 324 FLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                G R+       + P +   R  S 
Sbjct: 92  VPPGRGARQPGSGARAAGPRRPVARTASG 120


>gi|227831921|ref|YP_002833628.1| hypothetical protein cauri_0091 [Corynebacterium aurimucosum ATCC
          700975]
 gi|262183175|ref|ZP_06042596.1| hypothetical protein CaurA7_04220 [Corynebacterium aurimucosum
          ATCC 700975]
 gi|227452937|gb|ACP31690.1| hypothetical protein cauri_0091 [Corynebacterium aurimucosum ATCC
          700975]
          Length = 102

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 10/33 (30%), Positives = 17/33 (51%)

Query: 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          E + +I Q +V VNG + ++    +   D I V
Sbjct: 38 EAKELIEQGQVTVNGEVTKQRGATLALGDVICV 70


>gi|119920305|ref|XP_001254621.1| PREDICTED: GK22061-like [Bos taurus]
 gi|297493144|ref|XP_002700157.1| PREDICTED: GK22061-like [Bos taurus]
 gi|296470778|gb|DAA12893.1| GK22061-like [Bos taurus]
          Length = 892

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 17/111 (15%), Positives = 27/111 (24%), Gaps = 8/111 (7%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                   D            RP      PD     +  S+      +    A    RR 
Sbjct: 417 RPALAPGPDPRGAPGSAAGPTRPRRGGSAPDPARHGRPASAPGPDHRRDGGSAPGPVRRG 476

Query: 310 LASNVWMA--------KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            +++                +     +   +   R  P+F     LRR SA
Sbjct: 477 RSASTRGPNPRGGRVSAPGPARRGGPASAADAARRGRPAFEPGGDLRRGSA 527



 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 10/104 (9%), Positives = 20/104 (19%), Gaps = 3/104 (2%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
                             P          TR ++  S  +     +  + P         
Sbjct: 408 SAPGPVRQGRPALAPGPDPRGAPGSAAGPTRPRRGGSAPDPARHGRPASAPGPDHRRDGG 467

Query: 314 VWMAKGIHSSFLSDSGQREENHR---RSPSFPSKRSLRRTSAKK 354
                       S  G      R     P+     +    +A++
Sbjct: 468 SAPGPVRRGRSASTRGPNPRGGRVSAPGPARRGGPASAADAARR 511



 Score = 40.9 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 13/102 (12%), Positives = 25/102 (24%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
           +   L     S+   VR     ++  PD        +                H R  ++
Sbjct: 398 SGPELRRRGGSAPGPVRQGRPALAPGPDPRGAPGSAAGPTRPRRGGSAPDPARHGRPASA 457

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                +    S      +      R P+    R      A++
Sbjct: 458 PGPDHRRDGGSAPGPVRRGRSASTRGPNPRGGRVSAPGPARR 499



 Score = 39.8 bits (91), Expect = 0.62,   Method: Composition-based stats.
 Identities = 11/107 (10%), Positives = 20/107 (18%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                A         +S      R    S    +       +      S     + P  R
Sbjct: 344 RRSASAPGPDGRGSPTSVPGPARRGRSASAPGPNHCGSPALAPGPGPSSGPTSTSGPELR 403

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           R   S     +    +       R      +     +R        +
Sbjct: 404 RRGGSAPGPVRQGRPALAPGPDPRGAPGSAAGPTRPRRGGSAPDPAR 450



 Score = 38.2 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 16/104 (15%), Positives = 22/104 (21%), Gaps = 4/104 (3%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P L  +A     A   S           I E    F R   ++   +G      +  P  
Sbjct: 307 PALGRQASAPGPAQRGSRAPKPGPTGGGIPEAGPAFRRRSASAPGPDGRGSPTSVPGPA- 365

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                     A G +                  S       RR 
Sbjct: 366 ---RRGRSASAPGPNHCGSPALAPGPGPSSGPTSTSGPELRRRG 406



 Score = 37.9 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 15/106 (14%), Positives = 24/106 (22%), Gaps = 1/106 (0%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
           H    A     A      +                 R  + +S      + +  +TP   
Sbjct: 572 HPGRPASTPGPARRRRLGSTPGPDNRGRPASVSGPARRSRPASTPGPDLRGRPASTPGPA 631

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRS-PSFPSKRSLRRTSA 352
           R          G        S       RR   S P      R+++
Sbjct: 632 RRRRRRPASTPGPDHRGCPASTSGPARRRRRLASTPGPDHRGRSAS 677



 Score = 37.9 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 10/103 (9%), Positives = 18/103 (17%), Gaps = 3/103 (2%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                A         S        P+            ++  S    + + +    P   
Sbjct: 366 RRGRSASAPGPNHCGSPALAPGPGPSSGPTSTSGPELRRRGGSAPGPVRQGRPALAPGPD 425

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
              A              S     +      P+       RR 
Sbjct: 426 PRGAPGSAAGPTRPRRGGSAP---DPARHGRPASAPGPDHRRD 465


>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 = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 24/263 (9%), Positives = 71/263 (26%), Gaps = 61/263 (23%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVM 55
           K  +  N   QR+ K +       R+         + + + ++ ++VNG         + 
Sbjct: 2   KIEIGPNEAGQRLDKFL-------RKLLKDVPLSAIFKALRKKDIRVNGTKQNE-KYFLQ 53

Query: 56  STDHIE-----------------VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRS 95
             D +E                 VD   ++     E   +      + + +  ++ +  +
Sbjct: 54  EGDVVEIKYIQSNKEDKKEKFIKVDPKRIKIAYEDENVVVIEKWPDVLVHSDSNNSEEPT 113

Query: 96  TVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
                L         I    +         L  +     +          +       ++
Sbjct: 114 LTDYVLSYLNDKGDYIPENEITFTPAACNRLDRNTSGMVMFGKTFEGLKAINEAIREDEI 173

Query: 154 DQDKLNL--------LKKGIVIQGICYGD---------------MQVTLDTQKGSNAWVT 190
            +    L        L +  +++                     M++++    G+ + + 
Sbjct: 174 RKYYYALAKGKIRAGLYEAYILKNPETNTSKIYDTEVKNSKKISMEISIVESNGAYSLLE 233

Query: 191 VGLREGKNREIKKVFEFFNWKVN 213
           + L  G++ +I+         + 
Sbjct: 234 IHLITGRSHQIRAHLAHLGNPII 256


>gi|313673260|ref|YP_004051371.1| translation initiation factor if-2 [Calditerrivibrio nitroreducens
           DSM 19672]
 gi|312940016|gb|ADR19208.1| translation initiation factor IF-2 [Calditerrivibrio nitroreducens
           DSM 19672]
          Length = 1043

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 8/108 (7%), Positives = 23/108 (21%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            E        +            +           +         ++ ++K    +  + 
Sbjct: 227 EEHHKKPYQGKKPWEKRPHQDRKDASSPQGQQREDQGRQQNRPDNRSEARKGDHQRGGRP 286

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                +R+  S      G         G R +  R       +   ++
Sbjct: 287 PYQGQQRDGGSYRDRPSGGRPQGDRPQGGRPQGDRAGFDKGKRTDFKK 334



 Score = 41.7 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 12/123 (9%), Positives = 25/123 (20%), Gaps = 11/123 (8%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           + +     E      +          +       +   D +  +    +  G  + +   
Sbjct: 212 QVVKQKSEEPKTHKKEEHHKKPYQGKKPWEKRPHQDRKDASSPQGQQREDQGRQQNRPDN 271

Query: 303 TPVHRRNLASNVWMAK-----------GIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
               R+                         S     G R +  R           +RT 
Sbjct: 272 RSEARKGDHQRGGRPPYQGQQRDGGSYRDRPSGGRPQGDRPQGGRPQGDRAGFDKGKRTD 331

Query: 352 AKK 354
            KK
Sbjct: 332 FKK 334



 Score = 35.9 bits (81), Expect = 8.6,   Method: Composition-based stats.
 Identities = 8/95 (8%), Positives = 17/95 (17%)

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW 315
                   SE     +     + P    +  +    ++              +    N  
Sbjct: 210 ESQVVKQKSEEPKTHKKEEHHKKPYQGKKPWEKRPHQDRKDASSPQGQQREDQGRQQNRP 269

Query: 316 MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
             +          G R     +     S R     
Sbjct: 270 DNRSEARKGDHQRGGRPPYQGQQRDGGSYRDRPSG 304


>gi|300934039|ref|ZP_07149295.1| hypothetical protein CresD4_08212 [Corynebacterium resistens DSM
          45100]
          Length = 281

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+   + +  IA SR   + MI   RV VNG+   + A  V     I+V
Sbjct: 14 RLDAELVKRKIARSREHAQEMIKAGRVTVNGMRATKPATGVTGEVSIKV 62


>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 = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 31/260 (11%), Positives = 71/260 (27%), Gaps = 52/260 (20%)

Query: 6   IVQENFTPQRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           I   +   +R+ + +A A     SR  V+ +IA   V ++G         +    +I + 
Sbjct: 18  IADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMNIAIV 77

Query: 63  ---------DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
                     G  +       +   + +      +V   +     + V   +        
Sbjct: 78  LSEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNGNWTGTLVNALIYHCGDSLS 137

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLELP-----------------STQWLR 143
                 R   V RLD +T G++++  +    R L                          
Sbjct: 138 GIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFADHGRTGDLERAYLALVWGMTE 197

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSN---------AWVTVGL 193
             +      + +   +  K+ +V +             T +  +         + V   L
Sbjct: 198 RPQGTVDAYLGRSHRDRTKQAVVHEEREDARHAITHYATVEKFSPREDATALASLVECRL 257

Query: 194 REGKNREIKKVFEFFNWKVN 213
             G+  +I+         + 
Sbjct: 258 ETGRTHQIRVHMAHIGHPLV 277


>gi|38233157|ref|NP_938924.1| 30S ribosomal protein S4 [Corynebacterium diphtheriae NCTC 13129]
 gi|61215596|sp|Q6NJ64|RS4_CORDI RecName: Full=30S ribosomal protein S4
 gi|38199416|emb|CAE49059.1| 30S ribosomal protein S4 [Corynebacterium diphtheriae]
          Length = 201

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR+  ++++     VNG  +   +  V   D I+V
Sbjct: 92  RLDNVVYRAGLARTRRQARQLVSHGHFTVNGKKINVPSYRVSQYDIIDV 140


>gi|319651867|ref|ZP_08005992.1| 30S ribosomal protein S4 [Bacillus sp. 2_A_57_CT2]
 gi|317396519|gb|EFV77232.1| 30S ribosomal protein S4 [Bacillus sp. 2_A_57_CT2]
          Length = 200

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +RR+  +++    + V+G  ++  +  V     I +
Sbjct: 93  RLDNVVYRLGLARTRRQARQLVNHGHIMVDGSRVDIPSYRVAPGQTITL 141


>gi|260890883|ref|ZP_05902146.1| S4 domain protein YaaA [Leptotrichia hofstadii F0254]
 gi|260859436|gb|EEX73936.1| S4 domain protein YaaA [Leptotrichia hofstadii F0254]
          Length = 78

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 17/76 (22%), Positives = 30/76 (39%), Gaps = 13/76 (17%)

Query: 1  MKDKNIVQE----NFTPQRVSKVI--AR---AGIASRREVERMIAQQRVKVNGILLERAA 51
          MK+ N   E    N    ++ +++  A    +G+    E +  I    VKVN  +  R  
Sbjct: 1  MKNINNEIEEVVINTEFIKLDQLLKWANFTGSGV----EAKMFIQNGEVKVNNAVETRRG 56

Query: 52 VNVMSTDHIEVDGVPL 67
            +   D +E  G  +
Sbjct: 57 KKIYDGDIVEFAGEKV 72


>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 = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 36/240 (15%), Positives = 65/240 (27%), Gaps = 42/240 (17%)

Query: 13  PQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLE-----RAA--VNVMST------- 57
            +R+ KV+       SR  ++  +    V V+G + +     R    + V          
Sbjct: 31  GERLDKVLVGTLPDYSRNRLKTWVEAGAVMVDGKVTKARYLLRGGESIKVFPQEMPEQFA 90

Query: 58  --------DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                   D +  DG  +   +   L ++        T  +             +F R  
Sbjct: 91  FNPEDIPLDVVYEDGDIIVINKPPGLVVHPAAGNWSGTLLNGLLFRYPEL---KMFPRAG 147

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
            V RLD +T GL+++         L           R       D      +   +    
Sbjct: 148 IVHRLDKDTSGLMVVARTSQAQTSLVRQLQDRTVGRRYLAWVWGDAPSQGKVLASVGRDQ 207

Query: 170 ICYGDMQVTLDTQKGSNAWVT-----------VGLRE-----GKNREIKKVFEFFNWKVN 213
                M       K +                V L E     G+  +I+  FE   + + 
Sbjct: 208 RDRLKMAAGSPQGKPAATLFRRLSKGLVQETPVTLLECRLETGRTHQIRVHFESLGFPLV 267


>gi|317970196|ref|ZP_07971586.1| RNA-binding S4 [Synechococcus sp. CB0205]
          Length = 74

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 13/68 (19%), Positives = 29/68 (42%), Gaps = 1/68 (1%)

Query: 10 NFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
             P R+ + +   G + +  E ++ I    V+VNG    +    + + D +E+ G  + 
Sbjct: 7  TSEPIRLDQFLKWQGLVFTGGEAKQRIQGGEVRVNGFQETQRGRKLKAGDRVELAGQTVL 66

Query: 69 KAERTRLW 76
            ++  L 
Sbjct: 67 VPQQLDLH 74


>gi|315636413|ref|ZP_07891657.1| hemolysin A [Arcobacter butzleri JV22]
 gi|315479279|gb|EFU69968.1| hemolysin A [Arcobacter butzleri JV22]
          Length = 236

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   +     I SR +   +I   +VK +G ++ + + NV+    IE+
Sbjct: 1  MRLDMYLTTNFNIQSRNKATELIKSNKVKCDGEIITKPSFNVLDFHKIEL 50


>gi|300782638|ref|YP_003762929.1| 30S ribosomal protein S4 [Amycolatopsis mediterranei U32]
 gi|299792152|gb|ADJ42527.1| small subunit ribosomal protein S4 [Amycolatopsis mediterranei U32]
          Length = 201

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI RAGIA +RR+  ++++     VNG+ +   +  V   D I+V
Sbjct: 92  RLDNVIYRAGIARTRRQARQLVSHGHFLVNGVKVNVPSYQVTKWDIIDV 140


>gi|258645943|ref|ZP_05733412.1| ribosomal protein S4 [Dialister invisus DSM 15470]
 gi|260403312|gb|EEW96859.1| ribosomal protein S4 [Dialister invisus DSM 15470]
          Length = 197

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ RAG A S R+  +M++   + V+G  ++  +  V     I +
Sbjct: 87  RLDNLVYRAGFARSIRQARQMVSHGLIAVDGKKVDIPSYPVRPGQVITL 135


>gi|225020483|ref|ZP_03709675.1| hypothetical protein CORMATOL_00490 [Corynebacterium matruchotii
           ATCC 33806]
 gi|224946872|gb|EEG28081.1| hypothetical protein CORMATOL_00490 [Corynebacterium matruchotii
           ATCC 33806]
          Length = 203

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V+ RAG+A +RR+  ++++     VNG  +   +  V   D I+V   
Sbjct: 92  RLDNVVYRAGLARTRRQARQLVSHGHFLVNGKKVNVPSYRVSQYDIIDVRDK 143


>gi|125974858|ref|YP_001038768.1| RNA-binding S4 [Clostridium thermocellum ATCC 27405]
 gi|256003886|ref|ZP_05428873.1| S4 domain protein YaaA [Clostridium thermocellum DSM 2360]
 gi|281418687|ref|ZP_06249706.1| S4 domain protein YaaA [Clostridium thermocellum JW20]
 gi|125715083|gb|ABN53575.1| RNA-binding S4 [Clostridium thermocellum ATCC 27405]
 gi|255992224|gb|EEU02319.1| S4 domain protein YaaA [Clostridium thermocellum DSM 2360]
 gi|281407771|gb|EFB38030.1| S4 domain protein YaaA [Clostridium thermocellum JW20]
 gi|316939069|gb|ADU73103.1| S4 domain protein YaaA [Clostridium thermocellum DSM 1313]
          Length = 68

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 12/71 (16%)

Query: 1  MKDKNIVQENFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
          M++  I   N    ++ + +        G     E + MI    VKVNG +  R    + 
Sbjct: 1  MENIKI---NTEFIKLDQFLKWTKTVSMG----SEAKLMIRSGLVKVNGEVELRRGRKLR 53

Query: 56 STDHIEVDGVP 66
          + D +E++   
Sbjct: 54 TGDIVEINDKK 64


>gi|317054794|ref|YP_004103261.1| 30S ribosomal protein S4 [Ruminococcus albus 7]
 gi|315447063|gb|ADU20627.1| ribosomal protein S4 [Ruminococcus albus 7]
          Length = 198

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+  +RRE  +++      VNG  ++  +  + + D I +
Sbjct: 89  RLDSVVFRMGLSMTRREARQLVVHGHFLVNGKRVDIPSYRIKAGDVISL 137


>gi|222109617|ref|YP_002551881.1| 30S ribosomal protein s4 [Acidovorax ebreus TPSY]
 gi|254764586|sp|B9MBW1|RS4_DIAST RecName: Full=30S ribosomal protein S4
 gi|221729061|gb|ACM31881.1| ribosomal protein S4 [Acidovorax ebreus TPSY]
          Length = 207

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +  A+  V + D + V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAITVNGQSVNIASYLVKAGDVVAV 146


>gi|260914657|ref|ZP_05921123.1| 30S ribosomal protein S4 [Pasteurella dagmatis ATCC 43325]
 gi|260631256|gb|EEX49441.1| 30S ribosomal protein S4 [Pasteurella dagmatis ATCC 43325]
          Length = 206

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R E  ++++ + + VNG ++   +  V   D + V
Sbjct: 97  RLDNVVYRMGFAATRSEARQLVSHKAIVVNGRVVNIPSFQVSVNDVVAV 145


>gi|213419635|ref|ZP_03352701.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Typhi str. E01-6750]
          Length = 184

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|54778757|gb|AAV39591.1| ribosomal protein S4 [synthetic construct]
          Length = 233

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 121 RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 180

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 181 AALELAEQREKPT 193


>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 = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 28/263 (10%), Positives = 71/263 (26%), Gaps = 43/263 (16%)

Query: 5   NIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
             + E    QR+   + R+     RR + +++   +V+VN   +  A+  +   D + + 
Sbjct: 27  RQIDETAESQRIDNFLIRSLKGIPRRHIYQLLRSGQVRVNSKRI-DASYRLQLGDKVRIP 85

Query: 63  -----------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
                            D   +   +   L +       V   S                
Sbjct: 86  PVIRSVKPVSSQGVYRTDRFNILYQDDHLLVIDKPAGIAVHGGSGISHGVIEQLRGQHPD 145

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
            + + +          +LL      + +      +   V +        + K ++    +
Sbjct: 146 WKFLELVHRLDRETSGILLLARKRQSLLELHRQIREGTVEKHYLTLVRGKWKNSVQNVRL 205

Query: 166 VIQGICYGDMQVTL---------DTQKGSNAWVTV------------GLREGKNREIKKV 204
            +        +  +         D  + ++   T+             L+ G+  +I+  
Sbjct: 206 PLNKYLTAAGERRVAVAAGRNDQDKAQQAHTLFTLQKAWEDFSLLDAELKTGRTHQIRVH 265

Query: 205 FEFFNWKVNRLIRISYGPFQLGT 227
                + +       YG F L  
Sbjct: 266 LAHLGFPIAGDD--KYGDFGLNK 286


>gi|332363499|gb|EGJ41281.1| S4 domain-containing protein YlmH [Streptococcus sanguinis SK355]
          Length = 261

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 13/48 (27%), Positives = 24/48 (50%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K++A     SR +  ++I+ + VK+N  +    +  V   D I V
Sbjct: 184 RLDKLVASTFKLSRSQAAQLISGKHVKMNYAVNNNPSQQVGLEDLISV 231


>gi|325955022|ref|YP_004238682.1| ribosomal protein S4 [Weeksella virosa DSM 16922]
 gi|323437640|gb|ADX68104.1| ribosomal protein S4 [Weeksella virosa DSM 16922]
          Length = 200

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA +R    ++++ + + VNG ++   +  +   D + V
Sbjct: 94  RLDNVVYRLGIAPTRSAARQLVSHKHITVNGNIVNIPSYQLKEGDVVAV 142


>gi|288870170|ref|ZP_06113170.2| ribosomal protein S4 [Clostridium hathewayi DSM 13479]
 gi|288868139|gb|EFD00438.1| ribosomal protein S4 [Clostridium hathewayi DSM 13479]
          Length = 197

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V+ R G   +RRE  +M+  + + VNG  +   +  V + D IEV   
Sbjct: 88  RLDNVVFRMGFGRTRRETRQMVDHKSILVNGKCVNIPSYLVKAGDVIEVKEK 139


>gi|149918794|ref|ZP_01907281.1| rRNA methylase-like protein [Plesiocystis pacifica SIR-1]
 gi|149820395|gb|EDM79811.1| rRNA methylase-like protein [Plesiocystis pacifica SIR-1]
          Length = 267

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+ K++   GI  SR   + +I    V V    +++A   V     I +
Sbjct: 10 RIDKLLVERGICDSRSRAQALILAGEVVVGDHAVDKAGAMVDVEAPIRL 58


>gi|331269808|ref|YP_004396300.1| 30S ribosomal protein S4 [Clostridium botulinum BKT015925]
 gi|329126358|gb|AEB76303.1| ribosomal protein S4 [Clostridium botulinum BKT015925]
          Length = 197

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 4/69 (5%)

Query: 1   MKDKNIVQE---NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMS 56
           MK K +  E        R+  ++ R G A S R+  +M+    + VNG  ++  +  V  
Sbjct: 72  MKSKEVTGEVLLKLLECRLDNIVYRIGFANSIRQARQMVNHGYILVNGKKVDIPSYQVKV 131

Query: 57  TDHIEVDGV 65
            D +++   
Sbjct: 132 GDIVKLKDK 140


>gi|325688225|gb|EGD30244.1| S4 domain-containing protein YlmH [Streptococcus sanguinis SK72]
          Length = 261

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 13/48 (27%), Positives = 25/48 (52%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K++A     SR +  ++I+ + VK+N  + +  +  V   D I V
Sbjct: 184 RLDKLVASTFKLSRSQATQLISGKHVKMNYAVNDNPSQQVGLEDLISV 231


>gi|319955881|ref|YP_004167144.1| SSU ribosomal protein s4p [Nitratifractor salsuginis DSM 16511]
 gi|319418285|gb|ADV45395.1| SSU ribosomal protein S4P [Nitratifractor salsuginis DSM 16511]
          Length = 208

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G A+ R    +++    V V+G  ++  +  V     IE+
Sbjct: 98  QRLDNVVYRMGFATTRAFARQLVNHGHVLVDGKRVDIPSYRVKPGQKIEI 147


>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 = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 28/57 (49%), Gaps = 2/57 (3%)

Query: 7  VQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          V+ +F   R+   +A  A   +R    R +    V+VNG+++ + +  V  +D +E 
Sbjct: 6  VEGSFDGMRIDAFLAAVAAFPTRSAAARRVDAGEVRVNGVVVRK-SFTVRISDVVEY 61


>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 = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 31/260 (11%), Positives = 71/260 (27%), Gaps = 52/260 (20%)

Query: 6   IVQENFTPQRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           I   +   +R+ + +A A     SR  V+ +IA   V ++G         +    +I + 
Sbjct: 18  IADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMNIAIV 77

Query: 63  ---------DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
                     G  +       +   + +      +V   +     + V   +        
Sbjct: 78  LPEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNGNWTGTLVNALIYHCGDSLS 137

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLELP-----------------STQWLR 143
                 R   V RLD +T G++++  +    R L                          
Sbjct: 138 GIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFADHGRTGDLERAYLALVWGMTE 197

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSN---------AWVTVGL 193
             +      + +   +  K+ +V +             T +  +         + V   L
Sbjct: 198 RPQGTVDAYLGRSHRDRTKQAVVHEEREDARHAITHYATVEKFSPREDATALASLVECRL 257

Query: 194 REGKNREIKKVFEFFNWKVN 213
             G+  +I+         + 
Sbjct: 258 ETGRTHQIRVHMAHIGHPLV 277


>gi|307132815|ref|YP_003884831.1| 30S ribosomal subunit protein S4 [Dickeya dadantii 3937]
 gi|306530344|gb|ADN00275.1| 30S ribosomal subunit protein S4 [Dickeya dadantii 3937]
          Length = 206

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + V VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKAVMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>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 = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 22/133 (16%), Positives = 47/133 (35%), Gaps = 17/133 (12%)

Query: 14  QRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----------- 60
            R+   I+    G+ SR  V+  I    V VNG ++++ + NV + D +           
Sbjct: 584 IRLDSWISSRVNGV-SRARVQSSIRLGLVTVNGRVVDKVSHNVKAGDEVNCTISELQPLK 642

Query: 61  -EVDGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
            E + +P  +   ++  L +      +V         + V   L       +S    + +
Sbjct: 643 AEAEDIPLDIVYEDKHVLVVNKPAHMVVHPAPGNPTGTLVNGILHHCSLPCVSYSNAEDD 702

Query: 118 TEGLLLLTNDGGL 130
                  ++D  +
Sbjct: 703 DSDEETFSDDEEM 715


>gi|294631702|ref|ZP_06710262.1| AAA family ATPase [Streptomyces sp. e14]
 gi|292835035|gb|EFF93384.1| AAA family ATPase [Streptomyces sp. e14]
          Length = 585

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 10/120 (8%), Positives = 26/120 (21%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R      L  +         +    A   +    +R      +         ++    ++
Sbjct: 143 RRSPAHRLPAREPRGRRTLLRRLRPAHRRTPGPALRRTRGPGARPAARGPAERRRDRPRH 202

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                    T V     A        +    +   G+R      +P+   + +       
Sbjct: 203 AARGTGSAGTGVGGLRRARADHRHPAVRPPVVRPRGRRPAGAGGAPARHGRGARLGGRPS 262



 Score = 37.9 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 12/112 (10%), Positives = 24/112 (21%), Gaps = 3/112 (2%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R           +    +   +           +  +     R     S  + L  ++  
Sbjct: 97  RGASARRRHPRPRARRTSAPAAGTAPDGRLRRRVRPLHRPAGRPAHRRSPAHRLPAREPR 156

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                 R L        G         G R      +     +R   R +A+
Sbjct: 157 GRRTLLRRLRPAHRRTPGPALRRTRGPGARPAARGPAER---RRDRPRHAAR 205



 Score = 37.5 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 17/100 (17%), Positives = 24/100 (24%), Gaps = 1/100 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R   GP L                   RDRP   +              +     +   +
Sbjct: 170 RRTPGPALRRTRGPGARPAARGPAERRRDRPRHAARGTGSAGTGVGGLRRARADHRHPAV 229

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF 341
             PV R         A G  +     +        RSP+F
Sbjct: 230 RPPVVRPRGRRPAG-AGGAPARHGRGARLGGRPSGRSPAF 268



 Score = 37.1 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 8/100 (8%), Positives = 18/100 (18%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
                           +                  +  + +  G     +   P HRR  
Sbjct: 114 SAPAAGTAPDGRLRRRVRPLHRPAGRPAHRRSPAHRLPAREPRGRRTLLRRLRPAHRRTP 173

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
              +   +G  +   +         R   +     S    
Sbjct: 174 GPALRRTRGPGARPAARGPAERRRDRPRHAARGTGSAGTG 213


>gi|170578286|ref|XP_001894351.1| Hypothetical 50.0 kDa protein K07E8.7 in chromosome IV, putative
           [Brugia malayi]
 gi|158599118|gb|EDP36813.1| Hypothetical 50.0 kDa protein K07E8.7 in chromosome IV, putative
           [Brugia malayi]
          Length = 430

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 31/268 (11%), Positives = 66/268 (24%), Gaps = 30/268 (11%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEVDG------------VPLRKAERTRLWLYHKPIGLV 85
            R+ VN   +      V   D IE  G              +       +      + + 
Sbjct: 86  GRIWVNCNQMTNVNYIVQQNDSIEHIGHRHEHPILDHYIKVIDNDNDMLVVDKPPSMPVH 145

Query: 86  TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL-----TNDGGLARVLELPSTQ 140
                                 +  V RLD  T G+LL      T+      +       
Sbjct: 146 PCGRYSVHTVLGMLREQRGLRGLRVVHRLDRTTSGVLLFARNAETDTKLKKMLRVGEIWH 205

Query: 141 WLRVYRVRFHGQVDQDKLNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
              + +V      D++ +           +    +         +       G  + V  
Sbjct: 206 KEYICKVEGVFPGDKEIVCDRPIGPLVVSMGIQCIRDDGKSARSRFWRLWTDGQTSIVRC 265

Query: 192 GLREGKNREIKKVFEFFNWKVNR---LIRISYGPFQLGTLLAGSTRE-VSKKILREQLGP 247
            L  G+  +I+   ++  + +         ++G  +      G + E + K +L E    
Sbjct: 266 MLETGRTHQIRVHLQYLGYPIVDDYIYNTTAWGEKKGKDGNYGKSLEQLRKDVLEEHKAS 325

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNII 275
           +  E      +  +              
Sbjct: 326 NWHERVNSEYEIRVKRIAEGKVQPEPEG 353


>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 = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 35/246 (14%), Positives = 77/246 (31%), Gaps = 39/246 (15%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           I+ E   P R+ + + ++    SR  ++ +I    V +N    + A   + + D+I++  
Sbjct: 19  IIYELPLPMRLDRWLVSKRPEQSRARIQNLINAGLVLINYKTAK-AKTPLKTGDNIQIWM 77

Query: 65  VP---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
            P               +   +   + +  +   +V         + V   L        
Sbjct: 78  PPPEPLVYLKPEKMHLNILYEDEHIIVINKQSGLIVHPAPGHKSGTLVNGLLFHCKDLPG 137

Query: 110 SVGRLDINT---------------------EGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
             G+L                           L +   D   +R               +
Sbjct: 138 INGKLRPGIVHRLDKDTSGCMVVAKSQESLVNLQIQIRDKIASRNYIAVIHGVPNTSEGK 197

Query: 149 FHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
             G + +DK+N LK  +V +    Y      L  + G+ + ++  L  G+  +I+    +
Sbjct: 198 IVGHIGRDKINRLKYAVVDENSGRYACTYWKLLERFGNYSLMSFKLDTGRTHQIRVHCAY 257

Query: 208 FNWKVN 213
            N  + 
Sbjct: 258 INHPIL 263


>gi|118595311|ref|ZP_01552658.1| 30S ribosomal protein S4 [Methylophilales bacterium HTCC2181]
 gi|118441089|gb|EAV47716.1| 30S ribosomal protein S4 [Methylophilales bacterium HTCC2181]
          Length = 209

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ + G+  SR E  +++    + VNG  +   +  V   D + V
Sbjct: 100 RLDNVVYKMGLGASRTESRQIVKHNAILVNGKRVNIPSFQVSPGDEVSV 148


>gi|115719136|ref|XP_001204073.1| PREDICTED: similar to coiled-coil domain containing 40, partial
           [Strongylocentrotus purpuratus]
 gi|115786722|ref|XP_795411.2| PREDICTED: similar to coiled-coil domain containing 40, partial
           [Strongylocentrotus purpuratus]
          Length = 1079

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 15/114 (13%), Positives = 34/114 (29%), Gaps = 5/114 (4%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G   L   +                RP+  S+ P   ++   + +++   + Q+  +   
Sbjct: 2   GEEDLAVEEAAPSPQAEERPASGTQRPSSGSQRPPSASQRTPSGTERPPSASQRPPSATR 61

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS-----LRRTSAKK 354
                      +    S+    S  R  +    P+  S+RS        +  K+
Sbjct: 62  TPSAGRPPSAGSGRPPSAGRPSSAARPPSAGARPASGSRRSGSGAQRPPSGEKR 115



 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 12/103 (11%), Positives = 20/103 (19%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
             R   G            +    + +     P+     P              G  +  
Sbjct: 18  EERPASGTQRPSSGSQRPPSASQRTPSGTERPPSASQRPPSATRTPSAGRPPSAGSGRPP 77

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
               P       S             S + +     +RSP  P
Sbjct: 78  SAGRPSSAARPPSAGARPASGSRRSGSGAQRPPSGEKRSPVPP 120


>gi|72382832|ref|YP_292187.1| hemolysin A [Prochlorococcus marinus str. NATL2A]
 gi|72002682|gb|AAZ58484.1| hemolysin A [Prochlorococcus marinus str. NATL2A]
          Length = 264

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 12/54 (22%), Positives = 27/54 (50%), Gaps = 2/54 (3%)

Query: 11 FTPQRVS-KVIARAGIASRREVERMIAQQRV-KVNGILLERAAVNVMSTDHIEV 62
              R+   ++ +  + +R+E + +I   +V  +NG +L++    V+    IEV
Sbjct: 2  TKKSRLDLHLLTKGLVKTRQEAQNLIRAGKVKTINGQILDKPGQEVLRDLEIEV 55


>gi|331270704|ref|YP_004397196.1| S4 domain-containing protein [Clostridium botulinum BKT015925]
 gi|329127254|gb|AEB77199.1| S4 domain protein [Clostridium botulinum BKT015925]
          Length = 68

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 16/73 (21%), Positives = 29/73 (39%), Gaps = 8/73 (10%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMST 57
          M++  I   N    ++   +  +GI    S  E +  I    VKVNG + +R    ++  
Sbjct: 1  MQEIKI---NTEFIKLDAFLKWSGIATMGS--EAKFYIQNGEVKVNGEIEDRRGRKLIYG 55

Query: 58 DHIEVDGVPLRKA 70
          D +E      +  
Sbjct: 56 DIVEFQDEIYKII 68


>gi|326383231|ref|ZP_08204919.1| 30S ribosomal protein S4 [Gordonia neofelifaecis NRRL B-59395]
 gi|326197981|gb|EGD55167.1| 30S ribosomal protein S4 [Gordonia neofelifaecis NRRL B-59395]
          Length = 201

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ RAG+A +RR+  +M++   + VNG+ ++  +  V   D I+V    L+     
Sbjct: 92  RLDNVVYRAGLARTRRQARQMVSHGHLTVNGVRVDVPSYRVSQYDIIDVRPKSLQTTPFQ 151

Query: 74  R 74
            
Sbjct: 152 I 152


>gi|268680562|ref|YP_003304993.1| ribosomal protein S4 [Sulfurospirillum deleyianum DSM 6946]
 gi|268618593|gb|ACZ12958.1| ribosomal protein S4 [Sulfurospirillum deleyianum DSM 6946]
          Length = 208

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A+ RR   +++    + VNG  ++  +  V + D +EV
Sbjct: 99  RLDNVVYRMGFATTRRFARQLVTHGHILVNGNKVDIPSYIVRAGDKVEV 147


>gi|255590875|ref|XP_002535387.1| Cardiolipin synthetase, putative [Ricinus communis]
 gi|223523280|gb|EEF26998.1| Cardiolipin synthetase, putative [Ricinus communis]
          Length = 501

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 2/62 (3%)

Query: 4   KNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K I  E     R+ K + A     +R      + + RV VNG   +  A NV   D +E+
Sbjct: 363 KRIGYEVADGVRLDKWLWAARFFKTRSLACDAVDRGRVIVNGDRAK-PARNVKVGDVLEI 421

Query: 63  DG 64
           D 
Sbjct: 422 DN 423


>gi|163761046|ref|ZP_02168124.1| hemolysin-like protein [Hoeflea phototrophica DFL-43]
 gi|162281827|gb|EDQ32120.1| hemolysin-like protein [Hoeflea phototrophica DFL-43]
          Length = 259

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
          R+ +++ R G   SR      I++  + V+G +L +A V V  T  I
Sbjct: 18 RLDQILVRLGHYESRARARDAISRGAITVDGKVLMKAGVLVSPTAAI 64


>gi|134297884|ref|YP_001111380.1| RNA-binding S4 domain-containing protein [Desulfotomaculum
          reducens MI-1]
 gi|134050584|gb|ABO48555.1| RNA-binding S4 domain protein [Desulfotomaculum reducens MI-1]
          Length = 70

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 11 FTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
              R+ + +  A I  S  E + +I    VKVNGI   R    + S D +EVDG
Sbjct: 8  NKDIRLDQFLKWANITGSGGESKILIQSGHVKVNGITEIRRGKKLQSNDIVEVDG 62


>gi|169836999|ref|ZP_02870187.1| hypothetical protein cdivTM_07828 [candidate division TM7
          single-cell isolate TM7a]
          Length = 74

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 11/42 (26%), Positives = 21/42 (50%)

Query: 8  QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER 49
                +R++K +A     SRR+ + +IA+Q+V +N      
Sbjct: 9  NRTEKIERLNKFLAFQLGVSRRQADNLIAKQKVYINNQPATS 50


>gi|148560135|ref|YP_001259959.1| translation initiation factor IF-2 [Brucella ovis ATCC 25840]
 gi|148371392|gb|ABQ61371.1| translation initiation factor IF-2 [Brucella ovis ATCC 25840]
          Length = 990

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/116 (12%), Positives = 29/116 (25%), Gaps = 2/116 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R + +  +RE +        +    A   +     R+         +   + +  + +K 
Sbjct: 192 RALEEAQIRE-VEERARAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKA 250

Query: 294 GLSKQKKLATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                K++  P  R     +   A  G                   P   S R   
Sbjct: 251 EEEAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAP 306



 Score = 45.2 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 11/121 (9%), Positives = 28/121 (23%), Gaps = 1/121 (0%)

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           L     REV ++  R         E           S     +    +    +   + ++
Sbjct: 194 LEEAQIREVEERA-RAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKAEE 252

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            ++++    + +       R           G           R +     P+     + 
Sbjct: 253 EAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAPIIADAA 312

Query: 348 R 348
            
Sbjct: 313 P 313


>gi|38233770|ref|NP_939537.1| putative cytotoxin/hemolysin [Corynebacterium diphtheriae NCTC
          13129]
 gi|38200031|emb|CAE49703.1| Putative cytotoxin/hemolysin [Corynebacterium diphtheriae]
          Length = 273

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 1/51 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          R+   + R  IA SR +   MI   RV V G + ++ A  V     I V+ 
Sbjct: 6  RLDAELVRRKIARSREQAVEMIKDGRVHVQGFVAKKPATQVTPEASIRVED 56


>gi|152977022|ref|YP_001376539.1| 30S ribosomal protein S4 [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|171769250|sp|A7GTT6|RS4_BACCN RecName: Full=30S ribosomal protein S4
 gi|152025774|gb|ABS23544.1| ribosomal protein S4 [Bacillus cytotoxicus NVH 391-98]
          Length = 200

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 93  RLDNLVYRMGLARTRRAARQLVNHGHIMVDGARVDIPSYRVKPGQTISV 141


>gi|327539710|gb|EGF26317.1| ribosomal large subunit pseudouridine synthase D [Rhodopirellula
           baltica WH47]
          Length = 333

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 38/316 (12%), Positives = 91/316 (28%), Gaps = 45/316 (14%)

Query: 3   DKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
            + +V E+    R+   + ++  G  SR ++   +     +V+G ++   +  V +   +
Sbjct: 2   REFVVPESANGFRIDLFLTQSCDGY-SRSQIRDAVQNDGAEVDGRIIR-PSYKVKAGQKV 59

Query: 61  EV----------------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF 98
                                   D   +   +   + ++        T +         
Sbjct: 60  RFRVPPPASDDTVPENIPLDILYEDDGLVVINKPAGMVVHPARGNWTGTLTSALAFRFQS 119

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA------RVLELPSTQWLRVYRVRFHGQ 152
            +     +R   V RLD +T G++++  +  +           L   ++  +   R    
Sbjct: 120 LSDVGGPTRPGIVHRLDRDTSGVIVVAKNNAVHLNLAAQWHDRLVQKEYTAITFGRLDRD 179

Query: 153 VDQ------DKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
            D              K  + +G            +  + G    V V  + G+  +I+ 
Sbjct: 180 RDWIHASIGRHPYQRDKQAIREGHATSKTASTFYEVVERHGRVTRVDVRPKTGRTHQIRV 239

Query: 204 VFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYS 263
                   +    R+ YG      L     R ++   +         E  ++ L      
Sbjct: 240 HLAHIGCPIL-CDRL-YGGHS--ELSRSQIRRLAGTEVATPGVKPTPEGEEILLSRQALH 295

Query: 264 SETLVRDRPNIISEVP 279
           ++ L    P    E+ 
Sbjct: 296 AKALTFTNPQTGKEMT 311


>gi|224543759|ref|ZP_03684298.1| hypothetical protein CATMIT_02975 [Catenibacterium mitsuokai DSM
           15897]
 gi|224523327|gb|EEF92432.1| hypothetical protein CATMIT_02975 [Catenibacterium mitsuokai DSM
           15897]
          Length = 201

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A+ RR   +++    + +NGI  +  +  V   D I V
Sbjct: 92  RLDNVVYRMGFATTRRAARQLVNHGHILLNGIKTDIPSCRVNPGDVITV 140


>gi|77552905|gb|ABA95701.1| retrotransposon protein, putative, unclassified [Oryza sativa
           Japonica Group]
          Length = 1054

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 13/102 (12%), Positives = 23/102 (22%), Gaps = 1/102 (0%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
            E +                             R   +S   +   K+K+  TP   R  
Sbjct: 305 SEERAPKGHDGAGGSRRGEQSTPRGGRASGSRDRGPGSSRPADARGKRKQGGTPPPSRPR 364

Query: 311 ASNVWMAKGIHSSFLSD-SGQREENHRRSPSFPSKRSLRRTS 351
                 A        +  S    E  ++ P    +    R +
Sbjct: 365 GGGAARASNRRPEGAAPTSQPEGERKKKRPRKIGETEPSRGN 406


>gi|150387856|ref|YP_001317905.1| RNA-binding S4 domain-containing protein [Alkaliphilus
          metalliredigens QYMF]
 gi|149947718|gb|ABR46246.1| RNA-binding S4 domain protein [Alkaliphilus metalliredigens QYMF]
          Length = 69

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 28/59 (47%), Gaps = 3/59 (5%)

Query: 12 TPQRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
             ++ +++ + G  + S  + + +I    VKVNG ++ +    +   D +E+    ++
Sbjct: 10 EYIKLDQIL-KLGELVGSGGQAKLLILNGEVKVNGNIVIQRGKKIRPGDIVELFDDKVK 67


>gi|291415789|ref|XP_002724132.1| PREDICTED: vaccinia related kinase 3-like [Oryctolagus cuniculus]
          Length = 649

 Score = 47.1 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 7/98 (7%), Positives = 12/98 (12%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           +       P                  P       +        +  +            
Sbjct: 80  QTPALGQTPALGQTPAPGRPRPRTDPGPGQTPASDRPRPSDRPRASDRPRPRADPGPRTD 139

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                  G  +             R      S R   R
Sbjct: 140 PGPRTDPGPRTDPGPGQTPASGRPRPRADPASGRPRPR 177



 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 11/93 (11%), Positives = 17/93 (18%), Gaps = 4/93 (4%)

Query: 264 SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIH-- 321
               +   P      P       +  +        +  A+   R           G    
Sbjct: 86  QTPALGQTPAPGRPRPRTDPGPGQTPASDRPRPSDRPRASDRPRPRADPGPRTDPGPRTD 145

Query: 322 --SSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                    GQ   + R  P         R  A
Sbjct: 146 PGPRTDPGPGQTPASGRPRPRADPASGRPRPRA 178



 Score = 36.7 bits (83), Expect = 5.0,   Method: Composition-based stats.
 Identities = 12/127 (9%), Positives = 22/127 (17%), Gaps = 8/127 (6%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
            V  ++ RE        E     +    +      D     +          +   + + 
Sbjct: 17  RVEGEVPREPRATQPGPETTAVANPGPRTDPGPRTDPGPGQTPASGRPRPSGRPRPRADP 76

Query: 295 LSKQKKL--------ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
              Q            TP   R             +S       R     R         
Sbjct: 77  GLGQTPALGQTPALGQTPAPGRPRPRTDPGPGQTPASDRPRPSDRPRASDRPRPRADPGP 136

Query: 347 LRRTSAK 353
                 +
Sbjct: 137 RTDPGPR 143


>gi|312084667|ref|XP_003144368.1| hypothetical protein LOAG_08790 [Loa loa]
 gi|307760466|gb|EFO19700.1| hypothetical protein LOAG_08790 [Loa loa]
          Length = 379

 Score = 47.1 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 24/203 (11%), Positives = 50/203 (24%), Gaps = 26/203 (12%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEVDG------------VPLRKAERTRLWLYHKPIGLV 85
            R+ VN   +      V   D IE  G              +       +      + + 
Sbjct: 35  GRIWVNCNQMTNVNYIVQHNDSIEHIGHRHEHPILDHYIRVIDNDNNIIVVDKPASMPVH 94

Query: 86  TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL-----TNDGGLARVLELPSTQ 140
                                 +  V RLD  T G+LL      T+      +       
Sbjct: 95  PCGRYCVHTVLGMLREQRGLRDLRVVHRLDRTTSGVLLFARNSETDTKLKKMLRVGEVWH 154

Query: 141 WLRVYRVRFHGQVDQDKLNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
              + +V      D++ +           +    +         +       G  + V  
Sbjct: 155 KEYLCKVEGVFPADKEIICDRPIGPLVLSMGIQCIRDDGKCARSRFWRLWTDGQTSIVRC 214

Query: 192 GLREGKNREIKKVFEFFNWKVNR 214
            L  G+  +I+   ++  + +  
Sbjct: 215 MLETGRTHQIRVHLQYLGYPIVD 237


>gi|291280122|ref|YP_003496957.1| 30S ribosomal protein S4 [Deferribacter desulfuricans SSM1]
 gi|290754824|dbj|BAI81201.1| 30S ribosomal protein S4 [Deferribacter desulfuricans SSM1]
          Length = 208

 Score = 47.1 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R+G A SR+E  ++I      VNG  +   +      D +EV
Sbjct: 99  RLDNVVYRSGFARSRKEARQLIRHNHFLVNGRKVNIPSFLCKEGDVVEV 147


>gi|317129954|ref|YP_004096236.1| ribosomal protein S4 [Bacillus cellulosilyticus DSM 2522]
 gi|315474902|gb|ADU31505.1| ribosomal protein S4 [Bacillus cellulosilyticus DSM 2522]
          Length = 200

 Score = 47.1 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 12/47 (25%), Positives = 25/47 (53%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  ++ R G+A +RR+  +++    V V+G  ++ A+  V     I
Sbjct: 93  RLDNLVYRLGLARTRRQARQLVNHGHVTVDGGRVDIASYRVKPGQVI 139


>gi|119491309|ref|ZP_01623363.1| RNA-binding S4 [Lyngbya sp. PCC 8106]
 gi|119453473|gb|EAW34635.1| RNA-binding S4 [Lyngbya sp. PCC 8106]
          Length = 259

 Score = 47.1 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 2/65 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             K  +       R+  V A AG   SR ++  +I    V+VN   + +A+  V S D I
Sbjct: 172 PKKKEMTTVEASMRLDAV-ASAGFGMSRSKMVSLIDGGDVRVNWKDISQASYQVKSGDLI 230

Query: 61  EVDGV 65
            + G 
Sbjct: 231 AIRGK 235


>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 = 47.1 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 35/217 (16%), Positives = 72/217 (33%), Gaps = 23/217 (10%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------DGVPLRKAE 71
           ++A+    SRRE+ R      + +N +        V + D + V       +  P+   E
Sbjct: 21  ILAKQMGFSRREISRSHVSGSIYLNDVKCR-LTQEVHTNDIVTVRTEEPILESKPIILYE 79

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV----GRLDINTEGLLLLTND 127
            T + + +KP G+ +  S       +   L   +          GRLD    G+++    
Sbjct: 80  DTDIVVVNKPAGIPSHASAEHFDDDMGSILKRYYQDDAFTVRTVGRLDKGVSGIVVYAKT 139

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLN-----LLKKGIVIQGICY----GDMQVT 178
             +A +L     + L         +   ++        L K   I+G             
Sbjct: 140 KQMAALLASACEEQLLHKEYLAIVKGKFEEKWGKLIYTLGKEKGIRGRSVTADGQKCITN 199

Query: 179 LDTQKGSN--AWVTVGLREGKNREIKKVFEFFNWKVN 213
            +     N  + + V +  G+  +I+    +F   + 
Sbjct: 200 YEVITEGNFFSLIKVHIETGRLHQIRAGMAYFGHPLI 236


>gi|290960065|ref|YP_003491247.1| antigen penicillin-binding protein [Streptomyces scabiei 87.22]
 gi|260649591|emb|CBG72706.1| putative antigen penicillin-binding protein [Streptomyces scabiei
           87.22]
          Length = 1299

 Score = 47.1 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 14/116 (12%), Positives = 32/116 (27%), Gaps = 6/116 (5%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS----- 296
           +++ G  + +E Q   + P ++     R  P       D   R   +             
Sbjct: 43  KQEYGSTMSDEPQPKRNGPGWTPRDPERRTPGTTPGSGDTAARANADGRPGPTPGDGPNP 102

Query: 297 -KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                 A    RR   +      G             ++ R++      ++  R++
Sbjct: 103 TPDGPPAKASPRRPDTAPPGTPPGGERGGRPAGTAGGQSGRQAGERSGGQAGERSA 158


>gi|110225704|ref|YP_665709.1| ribosomal protein S4 [Mesostigma viride]
 gi|17222575|gb|AAL36748.1|AF353999_28 ribosomal protein S4 [Mesostigma viride]
          Length = 270

 Score = 47.1 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 16/70 (22%), Positives = 30/70 (42%), Gaps = 11/70 (15%)

Query: 4   KNIVQENFTPQ----------RVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAV 52
           KNI+ +   P+          R+ +VI +A  AS      + I  +++ VN  L+     
Sbjct: 67  KNIISKKNKPKVTSFFLNLERRLDRVICQARFASSSNMARQWILHEKIFVNNQLVTYPGT 126

Query: 53  NVMSTDHIEV 62
            + + D I +
Sbjct: 127 ILKNGDIISL 136


>gi|323703940|ref|ZP_08115570.1| RNA-binding S4 domain protein [Desulfotomaculum nigrificans DSM
          574]
 gi|323531098|gb|EGB21007.1| RNA-binding S4 domain protein [Desulfotomaculum nigrificans DSM
          574]
          Length = 69

 Score = 47.1 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 20/66 (30%), Positives = 29/66 (43%), Gaps = 7/66 (10%)

Query: 1  MKDKNIVQENFTPQRVSKVI--ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
          M+   I      P R+ + +  A     S  + + MI    VKVNGI   R    + + D
Sbjct: 1  MEKIKINN----PIRLDQFLKWANVT-GSGGQSKIMIQSGMVKVNGITETRRGKVLKAND 55

Query: 59 HIEVDG 64
           +EVDG
Sbjct: 56 TVEVDG 61


>gi|294628390|ref|ZP_06706950.1| serine/threonine protein kinase AfsK [Streptomyces sp. e14]
 gi|292831723|gb|EFF90072.1| serine/threonine protein kinase AfsK [Streptomyces sp. e14]
          Length = 480

 Score = 47.1 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 11/131 (8%), Positives = 28/131 (21%), Gaps = 4/131 (3%)

Query: 225 LGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
           LG L   + R         +L     ++ +        +            S+      +
Sbjct: 273 LGDLRPPAPRAAEADRPTGRLADTYPDQQRATYPEQQRAGRPEQSRSGYAESQRGRRRPQ 332

Query: 285 MKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSD----SGQREENHRRSPS 340
               ++     +     +    R   +     A    +          G    +    P+
Sbjct: 333 GSSQATPAPRGTVPPSRSGTPPRTGGSPRSGGAPRARNGNGRPIPASRGGSRPSGGARPA 392

Query: 341 FPSKRSLRRTS 351
                +  R  
Sbjct: 393 QRGGAARPRPR 403



 Score = 41.7 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 10/123 (8%), Positives = 22/123 (17%), Gaps = 4/123 (3%)

Query: 224 QLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
           +L        R    +  R             +         +         +  P    
Sbjct: 292 RLADTYPDQQRATYPEQQRAGRPEQSRSGYAESQRGRRRPQGSSQATPAPRGTVPPSRSG 351

Query: 284 RMKKNSSQKNGLSKQKKLATPVH----RRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
              +           +            R  +     A+       +    R  +  R P
Sbjct: 352 TPPRTGGSPRSGGAPRARNGNGRPIPASRGGSRPSGGARPAQRGGAARPRPRNTSTGRRP 411

Query: 340 SFP 342
           + P
Sbjct: 412 ANP 414



 Score = 36.7 bits (83), Expect = 5.0,   Method: Composition-based stats.
 Identities = 13/125 (10%), Positives = 26/125 (20%), Gaps = 6/125 (4%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD---DFTRMKKNSSQ 291
           E     L+  L    +   +      +        +       + D   D  R      Q
Sbjct: 250 EERPSTLQLSLRLKEIAAREAQGLGDLRPPAPRAAEADRPTGRLADTYPDQQRATYPEQQ 309

Query: 292 KNGLSKQKKLATPVHRRNLASNVW---MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           + G  +Q +      +R                 +              SP        R
Sbjct: 310 RAGRPEQSRSGYAESQRGRRRPQGSSQATPAPRGTVPPSRSGTPPRTGGSPRSGGAPRAR 369

Query: 349 RTSAK 353
             + +
Sbjct: 370 NGNGR 374


>gi|302876597|ref|YP_003845230.1| RNA-binding S4 domain-containing protein [Clostridium
          cellulovorans 743B]
 gi|307687271|ref|ZP_07629717.1| RNA-binding S4 domain-containing protein [Clostridium
          cellulovorans 743B]
 gi|302579454|gb|ADL53466.1| RNA-binding S4 domain protein [Clostridium cellulovorans 743B]
          Length = 92

 Score = 47.1 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   +      RV +NG + +  +  V   D IE+
Sbjct: 1  MRLDKYLKVSRIIKRRTVAKEACESGRVIINGKVAK-PSSEVKEDDVIEI 49


>gi|206900118|ref|YP_002250727.1| ribosomal protein S4 [Dictyoglomus thermophilum H-6-12]
 gi|226732178|sp|B5YDW9|RS4_DICT6 RecName: Full=30S ribosomal protein S4
 gi|206739221|gb|ACI18279.1| ribosomal protein S4 [Dictyoglomus thermophilum H-6-12]
          Length = 206

 Score = 47.1 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 15/84 (17%), Positives = 34/84 (40%), Gaps = 2/84 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-VDGVPLRKAER 72
           R+  V+ R G A SR +  ++++  ++ VNG  +   + N+   D +E +D   +   E 
Sbjct: 99  RLDNVVYRLGWALSRDQARQLVSHGKIAVNGKRVNIPSYNLKPGDVVELLDKDLIPVQEA 158

Query: 73  TRLWLYHKPIGLVTTHSDPDGRST 96
             ++        +    +      
Sbjct: 159 ISVFGNKNVPAWLELDRENFRGRV 182


>gi|78189781|ref|YP_380119.1| 30S ribosomal protein S4 [Chlorobium chlorochromatii CaD3]
 gi|90101681|sp|Q3APJ9|RS4_CHLCH RecName: Full=30S ribosomal protein S4
 gi|78171980|gb|ABB29076.1| SSU ribosomal protein S4P [Chlorobium chlorochromatii CaD3]
          Length = 203

 Score = 47.1 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ RAG + SR    ++++   V VNG  ++  +  V   D +E 
Sbjct: 94  RLDNIVFRAGFSPSRAGARQLVSHGHVTVNGKKVDIPSYLVSPADVMEF 142


>gi|293393288|ref|ZP_06637602.1| 30S ribosomal protein S4 [Serratia odorifera DSM 4582]
 gi|291424198|gb|EFE97413.1| 30S ribosomal protein S4 [Serratia odorifera DSM 4582]
          Length = 206

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKGIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|221632952|ref|YP_002522175.1| 30S ribosomal protein S4 [Thermomicrobium roseum DSM 5159]
 gi|254764619|sp|B9KZW1|RS4_THERP RecName: Full=30S ribosomal protein S4
 gi|221156886|gb|ACM06013.1| ribosomal protein S4 [Thermomicrobium roseum DSM 5159]
          Length = 217

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 18/73 (24%), Positives = 28/73 (38%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G A SRR+  +++      VNG   +  +  V   D I V     R+    
Sbjct: 106 RLDNVVYRLGFADSRRQARQLVRHGHFLVNGRKTDIPSYQVRPGDIIAVRPESRRREYFK 165

Query: 74  RLWLYHKPIGLVT 86
            L    K   +  
Sbjct: 166 VLEETAKNKAVPA 178


>gi|254361951|ref|ZP_04978082.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|153093498|gb|EDN74478.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
          Length = 266

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 24/230 (10%), Positives = 54/230 (23%), Gaps = 31/230 (13%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNV------------------M 55
           R+ + +A+     SR  ++  I    VKVNG ++ +A   V                   
Sbjct: 19  RLDQALAQLFPDYSRSRIKVWIESDLVKVNGNIVNKAREKVFGGETVEITAEIEEEIRFE 78

Query: 56  STD----HIEVDGVPLRKAERTRLWLYHKPIG---LVTTHSDPDGRSTVFDNLPSIFSRV 108
             D     +  D   +   +   L ++         V                  I  R+
Sbjct: 79  PQDIPLNIVYEDDDIIVINKPKDLVVHPGAGNPDGTVLNALLHYYPPIAEVPRAGIVHRL 138

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKK 163
                  +     +        A      + ++  +           D            
Sbjct: 139 DKDTTGLMVVAKNIPAQTHLVTALQKRRITREYEAIASGIMTQGGKVDEPMARHPTKRTA 198

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             V            +  +  +   + + L  G+  +I+         + 
Sbjct: 199 MAVHPMGKPAVTHYRIMERFRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 248


>gi|218462484|ref|ZP_03502575.1| hemolysin A [Rhizobium etli Kim 5]
          Length = 261

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 11/57 (19%), Positives = 24/57 (42%), Gaps = 1/57 (1%)

Query: 9  ENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +   QR+ +++   G  ASR      + +  V++ G ++ +A         I +D 
Sbjct: 15 SDQNSQRLDQLLVSRGLFASRSRARDALQRGTVRIAGQVVTKAGALFGVNADIAIDD 71


>gi|46579739|ref|YP_010547.1| 30S ribosomal protein S4 [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|120602784|ref|YP_967184.1| 30S ribosomal protein S4 [Desulfovibrio vulgaris DP4]
 gi|61215610|sp|Q72CF5|RS4_DESVH RecName: Full=30S ribosomal protein S4
 gi|152060946|sp|A1VE91|RS4_DESVV RecName: Full=30S ribosomal protein S4
 gi|46449154|gb|AAS95806.1| ribosomal protein S4 [Desulfovibrio vulgaris str. Hildenborough]
 gi|120563013|gb|ABM28757.1| SSU ribosomal protein S4P [Desulfovibrio vulgaris DP4]
 gi|311233530|gb|ADP86384.1| ribosomal protein S4 [Desulfovibrio vulgaris RCH1]
          Length = 208

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI R G A SR +  +++      +NG  +   ++ V   D IEV
Sbjct: 99  RLDNVIYRLGFANSRNQARQLVRHGIFTLNGRKVNIPSLQVRIGDTIEV 147


>gi|311277749|ref|YP_003939980.1| ribosomal protein S4 [Enterobacter cloacae SCF1]
 gi|308746944|gb|ADO46696.1| ribosomal protein S4 [Enterobacter cloacae SCF1]
          Length = 206

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V + D + V     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVKANDVVSVREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|254293557|ref|YP_003059580.1| hemolysin A [Hirschia baltica ATCC 49814]
 gi|254042088|gb|ACT58883.1| hemolysin A [Hirschia baltica ATCC 49814]
          Length = 256

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 11/59 (18%), Positives = 29/59 (49%), Gaps = 4/59 (6%)

Query: 7  VQENFTP---QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
          + ++ +P   QR+   +   G+  +R + +  I   +V ++G + ++A+  V +   I 
Sbjct: 1  MSDDTSPDGLQRLDLALVTRGLMDTRAQGQAAIKAGKVTIDGDVCKKASTKVSAEQVIT 59


>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 = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 23/243 (9%), Positives = 61/243 (25%), Gaps = 37/243 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVN------------GILLE----RA 50
           + E     R    +A+    SR    ++ A+  V ++            G ++       
Sbjct: 10  IPEGLEGMRADAALAKLLGLSRSATAQLCAEGSVTIDSQELGKSERLTSGNVVSVLLPEP 69

Query: 51  AVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
              ++  + + V+G+ +   +   + ++             DG + +     + ++   S
Sbjct: 70  EKPLLPREEL-VEGMDVLYNDADIICVHKPVGVAAHPSVGWDGPTVIGGLRAAGYTVASS 128

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-------------- 156
                      L +   G +       +   L+        +                  
Sbjct: 129 GPTERKGIVHRLDVGTSGVMVVASSERAYSALKHAFKYRSVKKTYHAVVQGLPDPIEGTV 188

Query: 157 ------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                       K  V+          +L       + + V L  G+  +I+        
Sbjct: 189 DAPIGRHPKSGWKFAVLDDGKAAITHYSLIEAFREASLIEVHLETGRTHQIRVHMSATGH 248

Query: 211 KVN 213
              
Sbjct: 249 PCV 251


>gi|167628427|ref|YP_001678926.1| hemolysin a, putative [Heliobacterium modesticaldum Ice1]
 gi|167591167|gb|ABZ82915.1| hemolysin a, putative [Heliobacterium modesticaldum Ice1]
          Length = 274

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 10/56 (17%), Positives = 24/56 (42%), Gaps = 1/56 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          R+   +   G++ +R +    I    V+V+G  +++A   +  +  + V G     
Sbjct: 6  RLDVRLVDEGLSPTREKARAAILAGLVQVDGKRVDKAGTLIADSARVTVTGEACPY 61


>gi|90020630|ref|YP_526457.1| 30S ribosomal protein S4P [Saccharophagus degradans 2-40]
 gi|123277582|sp|Q21M34|RS4_SACD2 RecName: Full=30S ribosomal protein S4
 gi|89950230|gb|ABD80245.1| SSU ribosomal protein S4P [Saccharophagus degradans 2-40]
          Length = 206

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V   D I V
Sbjct: 97  RLDNVVYRMGFGSTRAESRQLVSHKAILVNGKTVNIPSFQVNVGDVISV 145


>gi|225626530|ref|ZP_03784569.1| translation initiation factor IF-2 [Brucella ceti str. Cudo]
 gi|225618187|gb|EEH15230.1| translation initiation factor IF-2 [Brucella ceti str. Cudo]
          Length = 990

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 14/116 (12%), Positives = 29/116 (25%), Gaps = 2/116 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R + +  +RE +        +    A   +     R+         +   + +  + +K 
Sbjct: 192 RALEEAQIRE-VEERARAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKA 250

Query: 294 GLSKQKKLATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                K++  P  R     +   A  G                   P   S R   
Sbjct: 251 EEEAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAP 306



 Score = 45.2 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 11/121 (9%), Positives = 28/121 (23%), Gaps = 1/121 (0%)

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           L     REV ++  R         E           S     +    +    +   + ++
Sbjct: 194 LEEAQIREVEERA-RAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKAEE 252

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            ++++    + +       R           G           R +     P+     + 
Sbjct: 253 EAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAPIIADAA 312

Query: 348 R 348
            
Sbjct: 313 P 313


>gi|28378911|ref|NP_785803.1| 30S ribosomal protein S4 [Lactobacillus plantarum WCFS1]
 gi|254557116|ref|YP_003063533.1| 30S ribosomal protein S4 [Lactobacillus plantarum JDM1]
 gi|300769694|ref|ZP_07079577.1| 30S ribosomal protein S4 [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|308181113|ref|YP_003925241.1| 30S ribosomal protein S4 [Lactobacillus plantarum subsp. plantarum
           ST-III]
 gi|38258326|sp|Q88UX0|RS4_LACPL RecName: Full=30S ribosomal protein S4
 gi|28271748|emb|CAD64654.1| ribosomal protein S4 [Lactobacillus plantarum WCFS1]
 gi|254046043|gb|ACT62836.1| 30S ribosomal protein S4 [Lactobacillus plantarum JDM1]
 gi|300492737|gb|EFK27922.1| 30S ribosomal protein S4 [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|308046604|gb|ADN99147.1| 30S ribosomal protein S4 [Lactobacillus plantarum subsp. plantarum
           ST-III]
          Length = 202

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A+ RR+  +++    + V+G  ++  +  V     + V
Sbjct: 94  RLDNMVYRLGLATTRRQARQLVNHGHITVDGKRVDIPSYEVSVGQVVSV 142


>gi|313681623|ref|YP_004059361.1| pseudouridine synthase [Sulfuricurvum kujiense DSM 16994]
 gi|313154483|gb|ADR33161.1| pseudouridine synthase [Sulfuricurvum kujiense DSM 16994]
          Length = 245

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 23/198 (11%), Positives = 55/198 (27%), Gaps = 2/198 (1%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAERTRL 75
           K++A     S  E + +I +  V V    +  A   +       V          E   L
Sbjct: 8   KLLAEQEGISNSEAKSLIDRGLVYVGNSKVMIARGEISPKTVFIVQKVEKVRPIFENDDL 67

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            +  KP  + +   +   + +   +     +  + +   +       +            
Sbjct: 68  IVVDKPAFVNSDEIERQFKGSQLLHRLDRETSGVLMLVKNEEFRLKAIQEFKKDNVYKEY 127

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
           +   + L          +  +K        V +       +VT     G    V + +  
Sbjct: 128 VAWVEGLVSEPFVVDQPLITEKKGNKAYTKVAKKGKPAITEVTPLEVSGKKTKVQLIIHH 187

Query: 196 GKNREIKKVFEFFNWKVN 213
           G+  +I+   +F    + 
Sbjct: 188 GRTHQIRAHMKFAQHPII 205


>gi|295135677|ref|YP_003586353.1| 30S ribosomal protein S4 [Zunongwangia profunda SM-A87]
 gi|294983692|gb|ADF54157.1| 30S ribosomal protein S4 [Zunongwangia profunda SM-A87]
          Length = 201

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A SRR   ++++ + + VNG L+   +  + + D + V
Sbjct: 94  RLDNVVFRLGVAPSRRAARQLVSHRHITVNGELVNIPSYQLKAGDVVGV 142


>gi|308235815|ref|ZP_07666552.1| ribosomal RNA large subunit methyltransferase J [Gardnerella
          vaginalis ATCC 14018]
 gi|311114477|ref|YP_003985698.1| ribosomal RNA large subunit methyltransferase J [Gardnerella
          vaginalis ATCC 14019]
 gi|310945971|gb|ADP38675.1| ribosomal RNA large subunit methyltransferase J [Gardnerella
          vaginalis ATCC 14019]
          Length = 259

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 13/51 (25%), Positives = 24/51 (47%), Gaps = 1/51 (1%)

Query: 14 QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          QR+   +   G + SR   +R+I    VKV+  ++ +++  V     I  D
Sbjct: 9  QRLDCELVNRGLVKSRTTAQRLIKSGLVKVDNRIVYKSSFLVEKAQEISFD 59


>gi|152112239|sp|Q04E66|RS4_OENOB RecName: Full=30S ribosomal protein S4
          Length = 204

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+AS R +  +++    + V+G  +   +  V     I V
Sbjct: 95  RLDSVVFRLGLASTRPQARQLVNHGHILVDGKRVTIPSYEVKPGQIISV 143


>gi|294055197|ref|YP_003548855.1| ribosomal protein S4 [Coraliomargarita akajimensis DSM 45221]
 gi|293614530|gb|ADE54685.1| ribosomal protein S4 [Coraliomargarita akajimensis DSM 45221]
          Length = 202

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SR    + ++   V VNG   + A+  V   D IEV
Sbjct: 93  RLDSVVYRLGFAKSRSAARQFVSHGHVCVNGKKTDIASFMVKEGDEIEV 141


>gi|254718203|ref|ZP_05180014.1| translation initiation factor IF-2 [Brucella sp. 83/13]
 gi|265983160|ref|ZP_06095895.1| translation initiation factor IF-2 [Brucella sp. 83/13]
 gi|264661752|gb|EEZ32013.1| translation initiation factor IF-2 [Brucella sp. 83/13]
          Length = 959

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 14/116 (12%), Positives = 29/116 (25%), Gaps = 2/116 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R + +  +RE +        +    A   +     R+         +   + +  + +K 
Sbjct: 161 RALEEAQIRE-VEERARAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAETRRKA 219

Query: 294 GLSKQKKLATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                K++  P  R     +   A  G                   P   S R   
Sbjct: 220 EEEAAKRMPQPEARSERRDDARPAPYGARPQQTGRPQGGRPQPAGRPQQGSPRPAP 275



 Score = 44.4 bits (103), Expect = 0.027,   Method: Composition-based stats.
 Identities = 11/121 (9%), Positives = 28/121 (23%), Gaps = 1/121 (0%)

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           L     REV ++  R         E           S     +    +    +   + ++
Sbjct: 163 LEEAQIREVEERA-RAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAETRRKAEE 221

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            ++++    + +       R           G           R +     P+     + 
Sbjct: 222 EAAKRMPQPEARSERRDDARPAPYGARPQQTGRPQGGRPQPAGRPQQGSPRPAPIIADAA 281

Query: 348 R 348
            
Sbjct: 282 P 282


>gi|160871805|ref|ZP_02061937.1| ribosomal protein S4 [Rickettsiella grylli]
 gi|159120604|gb|EDP45942.1| ribosomal protein S4 [Rickettsiella grylli]
          Length = 206

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G AS R E  ++++ + VKVN  ++   +  V   D IE+
Sbjct: 97  RLDNVVYRMGFASTRAEARQLVSHRAVKVNSTIVNIPSYQVKVGDVIEI 145


>gi|296501602|ref|YP_003663302.1| collagen adhesion protein [Bacillus thuringiensis BMB171]
 gi|296322654|gb|ADH05582.1| collagen adhesion protein [Bacillus thuringiensis BMB171]
          Length = 1284

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 12/128 (9%), Positives = 32/128 (25%), Gaps = 1/128 (0%)

Query: 221  GPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
            G + L  + A     +S K ++  +    +E  ++ +     + +   +           
Sbjct: 1105 GDYTLKEIQAPEGYTLSNKEMKFTISNEKIEVVKLQITNKKDTDKDPEKPGEGTGKPGEG 1164

Query: 281  DFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSG-QREENHRRSP 339
                 +       G  K  +                 K    +   D G  +       P
Sbjct: 1165 TGKPGEGTGKPGEGTGKPGEGTGKPGEGTGKPGEGTGKPGEGTEKPDEGTGKPGEGTGKP 1224

Query: 340  SFPSKRSL 347
               +++  
Sbjct: 1225 GEGTEKPG 1232


>gi|149912288|ref|ZP_01900859.1| 30S ribosomal protein S4 [Moritella sp. PE36]
 gi|149804633|gb|EDM64692.1| 30S ribosomal protein S4 [Moritella sp. PE36]
          Length = 206

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG ++   +  V   D + +
Sbjct: 97  RLDNVVYRMGFGSTRAESRQLVSHKAIVVNGKVVNIPSYKVKVNDTVSI 145


>gi|283953926|ref|ZP_06371455.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 414]
 gi|283794531|gb|EFC33271.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 414]
          Length = 250

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 20/200 (10%), Positives = 52/200 (26%), Gaps = 7/200 (3%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILL----ERAAVNVMSTDHIEVDGVPLRKAERT 73
           K++A     S RE + +I +  V  +G  +       +  V   + I+     +   +  
Sbjct: 7   KILALQEKISNREAKDLIDKGCVFSHGKKVVVARALMSDKVK-FNVIKTKNPQIIFEDDK 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +      +            +          ++     D     +            
Sbjct: 66  IIAINKPYSCVSEDLEKKINAKLLNRLDKETSGVILLCKDEDFRKLCIEEFKKHRVYKSY 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           + +          V       + K   L K    +        +T    +       + +
Sbjct: 126 IAVLDGVLAEEIEVNEPIFTIKAKGGALSKVS--KDGLNASSIITPIMMQSKKTLAKIVI 183

Query: 194 REGKNREIKKVFEFFNWKVN 213
           + G+  +I+   +F    V 
Sbjct: 184 QTGRTHQIRVHTKFIKHGVV 203


>gi|302524021|ref|ZP_07276363.1| ribosomal protein S4 [Streptomyces sp. AA4]
 gi|302432916|gb|EFL04732.1| ribosomal protein S4 [Streptomyces sp. AA4]
          Length = 201

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI RAGIA +RR+  ++++     VNG+ +   +  V   D I+V
Sbjct: 92  RLDNVIYRAGIARTRRQARQLVSHGHFLVNGVKVNVPSYQVTKWDIIDV 140


>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 = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 45/258 (17%), Positives = 76/258 (29%), Gaps = 46/258 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M +K I        R    +A     +R +   +I    V +NG  L + +  +   D +
Sbjct: 17  MTEKEIKICESAQARADAFLAAELNVARNQALNLIKSGLVSLNGKPLTKPSAKLNLGDVL 76

Query: 61  EVDGV---------------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            +                  P+   E   L + +KP  LV   +      T+ D L +  
Sbjct: 77  RIKFEQSEQNAAKFEAEFEVPIIY-EDEDLLVLNKPANLVVHPAPSVKEPTLVDWLGAKG 135

Query: 106 S---------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR------------V 144
                     R   V RLD  T G +++  +      L    +                 
Sbjct: 136 FLLSNLSGQSRAGIVHRLDKGTSGAIVVAKNNAAHAALSSQLSDKSMGRIYLALTDLPLK 195

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ------KGSNAWVTVG---LRE 195
                   + ++  N LKK IV  G         L         +  NA V +    L  
Sbjct: 196 QNCTVWRAIGRNPANRLKKAIVPDGRAAKSAFANLLFSEFDGPAQSKNAGVNLIAAKLFT 255

Query: 196 GKNREIKKVFEFFNWKVN 213
           G+  +I+      N  + 
Sbjct: 256 GRTHQIRVHLASLNRHIL 273


>gi|222086840|ref|YP_002545374.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
 gi|221724288|gb|ACM27444.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
          Length = 343

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 13/63 (20%), Positives = 26/63 (41%), Gaps = 3/63 (4%)

Query: 3  DKNIVQENFTPQ-RVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          ++ ++  + T + R+   +        SR  V+ +I    V +NG  +  A   V   D 
Sbjct: 13 NRKVLTADETAEGRLDAWLTAQMDEELSRSRVQALIKANAVLLNGTPVTDAKRKVRPGDI 72

Query: 60 IEV 62
           E+
Sbjct: 73 YEI 75


>gi|253998040|ref|YP_003050103.1| 30S ribosomal protein S4 [Methylovorus sp. SIP3-4]
 gi|313200105|ref|YP_004038763.1| 30S ribosomal protein S4 [Methylovorus sp. MP688]
 gi|253984719|gb|ACT49576.1| ribosomal protein S4 [Methylovorus sp. SIP3-4]
 gi|312439421|gb|ADQ83527.1| ribosomal protein S4 [Methylovorus sp. MP688]
          Length = 209

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V  R G+ S R E  +++    + VNG  +   +  V   D ++V
Sbjct: 100 RLDNVAYRMGLGSSRTEARQIVRHNSILVNGKRVNIPSYQVRPGDVVQV 148


>gi|228940986|ref|ZP_04103544.1| RNA-binding S4 domain protein [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228973917|ref|ZP_04134492.1| RNA-binding S4 domain protein [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228980506|ref|ZP_04140816.1| RNA-binding S4 domain protein [Bacillus thuringiensis Bt407]
 gi|228779326|gb|EEM27583.1| RNA-binding S4 domain protein [Bacillus thuringiensis Bt407]
 gi|228785783|gb|EEM33787.1| RNA-binding S4 domain protein [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228818665|gb|EEM64732.1| RNA-binding S4 domain protein [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|326941667|gb|AEA17563.1| RNA binding protein [Bacillus thuringiensis serovar chinensis
           CT-43]
          Length = 255

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+  I    VKVN   +E+ +      D   V G
Sbjct: 180 RLDVMLAEMLHLSRQKVQPFIKNGLVKVNWKTVEQTSYECYPGDVFSVRG 229


>gi|160893409|ref|ZP_02074194.1| hypothetical protein CLOL250_00958 [Clostridium sp. L2-50]
 gi|156864804|gb|EDO58235.1| hypothetical protein CLOL250_00958 [Clostridium sp. L2-50]
          Length = 69

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 12/42 (28%), Positives = 20/42 (47%)

Query: 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
          E + +I+Q  V VNG +  R    +   D +E DG  +   +
Sbjct: 28 EAKEVISQGLVIVNGEIETRRGKKLYDGDEVEFDGDKISIQK 69


>gi|225026390|ref|ZP_03715582.1| hypothetical protein EUBHAL_00639 [Eubacterium hallii DSM 3353]
 gi|224956279|gb|EEG37488.1| hypothetical protein EUBHAL_00639 [Eubacterium hallii DSM 3353]
          Length = 197

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R+E  +++  + V VNG  +   +  + + D +E+
Sbjct: 88  RLDNVVFRMGFARTRKEARQIVGHKHVLVNGKCVNIPSYRIKAGDVVEI 136


>gi|166031631|ref|ZP_02234460.1| hypothetical protein DORFOR_01331 [Dorea formicigenerans ATCC
           27755]
 gi|166028608|gb|EDR47365.1| hypothetical protein DORFOR_01331 [Dorea formicigenerans ATCC
           27755]
          Length = 197

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RRE  +++  + V VNG  +   +  + + D +E+
Sbjct: 88  RLDNVVFRMGFARTRREARQIVDHKHVLVNGKQVNIPSYLIKAGDTVEI 136


>gi|138896341|ref|YP_001126794.1| 30S ribosomal protein S4 [Geobacillus thermodenitrificans NG80-2]
 gi|196249964|ref|ZP_03148659.1| ribosomal protein S4 [Geobacillus sp. G11MC16]
 gi|172044188|sp|A4IRU5|RS4_GEOTN RecName: Full=30S ribosomal protein S4
 gi|134267854|gb|ABO68049.1| Ribosomal protein S4 (BS4) [Geobacillus thermodenitrificans NG80-2]
 gi|196210478|gb|EDY05242.1| ribosomal protein S4 [Geobacillus sp. G11MC16]
          Length = 200

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR+  +++    + V+G  +   +  V     I V
Sbjct: 93  RLDNLVYRLGLARTRRQARQLVTHGHILVDGSRVNIPSYRVKPGQTIAV 141


>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 = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 26/216 (12%), Positives = 64/216 (29%), Gaps = 36/216 (16%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-----VPLRKA---------ERTRLWLY 78
           +MI ++ + +NG+ +      +   D +E  G      P++           E   L + 
Sbjct: 35  KMIRKKNITINGLKISDIRHRLKEGDVVEFYGCETPTKPIKWEGLKPLRVVFESENLIIV 94

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSI-------FSRVISVGRLDINTEGLLLLTNDGGLA 131
            K   +     D    + + + L            + + + RLD+NT GLL+   +    
Sbjct: 95  DKEAKMPVQEDDKHPFNHMNNRLLKHLNYSNREGWKPVFIHRLDLNTTGLLIGAKNYKTF 154

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----------ICYGDMQVT-- 178
             L             +   Q +           +++                + +    
Sbjct: 155 LKLNKSQKSLKIKKSYKALVQGNVSFKKREISCFLLKKDGRVSISREQVEGAKEAKTIAN 214

Query: 179 --LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                   ++  + + L  G+  +I+    +    +
Sbjct: 215 FLHFFPSINSTLLELTLITGRTHQIRAHMSYIKHPI 250


>gi|284006139|emb|CBA71381.1| 30S ribosomal protein S4 [Arsenophonus nasoniae]
          Length = 206

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 30/73 (41%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+   + R G   +R E  +M++ + + VNG ++  A+  V   D I V     +++   
Sbjct: 97  RLDNTVYRMGFGATRAEARQMVSHKAIMVNGQVVNIASYQVSPNDVISVREKAKKQSRIK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     +
Sbjct: 157 AALELAEQREKPS 169


>gi|304315968|ref|YP_003851113.1| ribosomal protein S4 [Thermoanaerobacterium thermosaccharolyticum
           DSM 571]
 gi|302777470|gb|ADL68029.1| ribosomal protein S4 [Thermoanaerobacterium thermosaccharolyticum
           DSM 571]
          Length = 206

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  V+ R  IAS R +  + +A   + VNG  ++  +  V + D I V  
Sbjct: 99  RLDNVVYRLSIASSRAQARQFVAHGHILVNGKKVDIPSYLVKAGDVISVKD 149


>gi|255324778|ref|ZP_05365892.1| ribosomal protein S4 [Corynebacterium tuberculostearicum SK141]
 gi|311740031|ref|ZP_07713865.1| 30S ribosomal protein S4 [Corynebacterium pseudogenitalium ATCC
           33035]
 gi|255298253|gb|EET77556.1| ribosomal protein S4 [Corynebacterium tuberculostearicum SK141]
 gi|311305104|gb|EFQ81173.1| 30S ribosomal protein S4 [Corynebacterium pseudogenitalium ATCC
           33035]
          Length = 201

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V+ RAG+A +RR+  ++++     VNG  +   +  V   D I+V   
Sbjct: 92  RLDNVVYRAGLARTRRQARQLVSHGHFTVNGKNINVPSYKVTQYDIIDVRDR 143


>gi|56964521|ref|YP_176252.1| 30S ribosomal protein S4 [Bacillus clausii KSM-K16]
 gi|61215394|sp|Q5WEB9|RS4_BACSK RecName: Full=30S ribosomal protein S4
 gi|56910764|dbj|BAD65291.1| 30S ribosomal protein S4 [Bacillus clausii KSM-K16]
          Length = 200

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 11/47 (23%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  ++ R G+A +RR   +++    V V+G  ++  +  V     I
Sbjct: 93  RLDNLVYRMGLARTRRAARQLVNHGHVLVDGSRVDIPSYRVKPGQTI 139


>gi|300857294|ref|YP_003782278.1| putative S4 domain-containing protein [Clostridium ljungdahlii
          DSM 13528]
 gi|300437409|gb|ADK17176.1| predicted S4 domain protein [Clostridium ljungdahlii DSM 13528]
          Length = 82

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   +      RV +NG + +  +V V   D IE+
Sbjct: 1  MRLDKYLKVSRIIKRRTVAKEACEGGRVAINGKVAK-PSVEVKEGDIIEI 49


>gi|239909011|ref|YP_002955753.1| ATP-dependent RNA helicase [Desulfovibrio magneticus RS-1]
 gi|239798878|dbj|BAH77867.1| ATP-dependent RNA helicase [Desulfovibrio magneticus RS-1]
          Length = 496

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 11/121 (9%), Positives = 26/121 (21%)

Query: 230 AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
            G  R +   + +     ++        +    +       RP      P       +  
Sbjct: 350 MGMVRAIESHMKKPLPRRNVEGFEPEPGEFRRSAPAPRSAARPRQGYGAPRQGGYGDRQR 409

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                   + +   P   R  ++     +         +  R  + R           R 
Sbjct: 410 QGDRPYGDRPRGPRPEGARADSARDDRPRSDRPRSDRPAADRPRSDRPRTERQPSDERRS 469

Query: 350 T 350
           T
Sbjct: 470 T 470



 Score = 44.8 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 7/115 (6%), Positives = 18/115 (15%)

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           + +   +   L        +              +            +     +     +
Sbjct: 354 RAIESHMKKPLPRRNVEGFEPEPGEFRRSAPAPRSAARPRQGYGAPRQGGYGDRQRQGDR 413

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                P   R   +    A+            R    R     P          +
Sbjct: 414 PYGDRPRGPRPEGARADSARDDRPRSDRPRSDRPAADRPRSDRPRTERQPSDERR 468



 Score = 42.5 bits (98), Expect = 0.096,   Method: Composition-based stats.
 Identities = 11/91 (12%), Positives = 20/91 (21%)

Query: 264 SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSS 323
            + L R         P +F R            +           +         G    
Sbjct: 361 KKPLPRRNVEGFEPEPGEFRRSAPAPRSAARPRQGYGAPRQGGYGDRQRQGDRPYGDRPR 420

Query: 324 FLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                G R ++ R       +    R +A +
Sbjct: 421 GPRPEGARADSARDDRPRSDRPRSDRPAADR 451


>gi|183234131|ref|XP_648993.2| hypothetical protein [Entamoeba histolytica HM-1:IMSS]
 gi|169801245|gb|EAL43600.2| hypothetical protein, conserved [Entamoeba histolytica HM-1:IMSS]
          Length = 402

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 25/205 (12%), Positives = 50/205 (24%), Gaps = 27/205 (13%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE----------VDGVPLRKAERTRLWLYHKPIGL 84
           I +  +K+N  ++   +  +   D IE                   E        KP  +
Sbjct: 106 IEKGLIKINNKII-EPSTIIHHHDEIEHQVHRHEPPVYCDKLTIVKETNDFIAIDKPSSI 164

Query: 85  VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG---------------LLLLTNDGG 129
                     +TV   L       +                             +T    
Sbjct: 165 PVHPCGRYRHNTVIFILAHEGYTNLRPVHRLDRMTSGILLLAKTIQAAREFQSYMTIKKK 224

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
                     +   V       ++D  K+++    I   G         L   + +N  V
Sbjct: 225 EYLCRVRGRLEKTTVTSKIGRKRIDDKKIHVSVNEIEEDGKECHSEFNPLFYDEKTNTTV 284

Query: 190 TVG-LREGKNREIKKVFEFFNWKVN 213
            V  L  G+  +I+   +  +  + 
Sbjct: 285 AVALLGSGRTHQIRVHLQSIHHPIV 309


>gi|88803725|ref|ZP_01119249.1| 30S ribosomal protein S4 [Polaribacter irgensii 23-P]
 gi|88780458|gb|EAR11639.1| 30S ribosomal protein S4 [Polaribacter irgensii 23-P]
          Length = 201

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+  SR    ++++ + + VNG ++   + N++  D + V
Sbjct: 94  RLDNVVYRMGVSTSRSGARQLVSHRHITVNGEIVNVPSYNLLEGDVVAV 142


>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 = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 4/54 (7%)

Query: 13 PQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          P R+ K ++R        SR  + R++ +  V VNG         V   D + +
Sbjct: 15 PPRLDKALSRDVPEEAHLSRTRLARLVEEGAVSVNGAEARDVKSRVAEGDEVVI 68


>gi|325663035|ref|ZP_08151485.1| 30S ribosomal protein S4 [Lachnospiraceae bacterium 4_1_37FAA]
 gi|331086642|ref|ZP_08335719.1| 30S ribosomal protein S4 [Lachnospiraceae bacterium 9_1_43BFAA]
 gi|325470489|gb|EGC73719.1| 30S ribosomal protein S4 [Lachnospiraceae bacterium 4_1_37FAA]
 gi|330409808|gb|EGG89243.1| 30S ribosomal protein S4 [Lachnospiraceae bacterium 9_1_43BFAA]
          Length = 197

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +R+E  +++  + V VNG  +   +  V + D IE+
Sbjct: 88  RLDNVVFRLGLARTRKEARQIVDHKHVLVNGKQVNIPSYLVKAGDVIEI 136


>gi|323697656|ref|ZP_08109568.1| pseudouridine synthase [Desulfovibrio sp. ND132]
 gi|323457588|gb|EGB13453.1| pseudouridine synthase [Desulfovibrio desulfuricans ND132]
          Length = 275

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 36/238 (15%), Positives = 68/238 (28%), Gaps = 36/238 (15%)

Query: 7   VQENFTPQRVSKVIARAGIAS----RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +  +    R+ + +      S    RR   R+  + R+ V+G    +    V +   +EV
Sbjct: 9   IDASGDGLRLDRALEAVMPGSGLRLRR---RLCDEGRILVDGR-ARKPGYRVRTGQLVEV 64

Query: 63  D-----------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                       GV + K E       +KP G+ +          V   LP++F  +  V
Sbjct: 65  KEGREMTTPGELGVRIVKWEDG-FAAVNKPGGVHSAIISGRDEPCVEAVLPALFPGMEPV 123

Query: 112 --GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
              RLD  T GLLL+               Q           +   D +  ++  +    
Sbjct: 124 LLNRLDRLTSGLLLVALTPEARDAYLEYEDQGAIKKFYLARVRGRLDGIVSVRNRLDTDD 183

Query: 170 ICYG-----DMQVTLDTQK---------GSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      +                   + V   + +G   +I+         + 
Sbjct: 184 RKTTRVLAEPDEDARRWTGVTALSHDNAADTSLVRCLITKGARHQIRAHLASIGHPIV 241


>gi|254716208|ref|ZP_05178019.1| translation initiation factor IF-2 [Brucella ceti M13/05/1]
 gi|261217982|ref|ZP_05932263.1| translation initiation factor IF-2 [Brucella ceti M13/05/1]
 gi|260923071|gb|EEX89639.1| translation initiation factor IF-2 [Brucella ceti M13/05/1]
          Length = 959

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 14/119 (11%), Positives = 34/119 (28%), Gaps = 4/119 (3%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R + +  +RE +        +    A   +     R+         +   + +  + +K 
Sbjct: 161 RALEEAQIRE-VEERARAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKA 219

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                K++  P  R     +   A             R +  R  P+   ++   R + 
Sbjct: 220 EEEAAKRMPQPEARSERRDD---APPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAP 275


>gi|145294734|ref|YP_001137555.1| 30S ribosomal protein S4 [Corynebacterium glutamicum R]
 gi|172044394|sp|A4QBQ6|RS4_CORGB RecName: Full=30S ribosomal protein S4
 gi|140844654|dbj|BAF53653.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 201

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR+  ++++     VNG  ++  +  V   D I V
Sbjct: 92  RLDNVVYRAGLANTRRQARQLVSHGHFTVNGKAIDVPSFRVSQYDIINV 140


>gi|317125841|ref|YP_004099953.1| 30S ribosomal protein S4P [Intrasporangium calvum DSM 43043]
 gi|315589929|gb|ADU49226.1| SSU ribosomal protein S4P [Intrasporangium calvum DSM 43043]
          Length = 202

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           R+  V+ RAG+A +RR   +++     +VNG+ ++  +  V   D + V    + 
Sbjct: 92  RLDNVVYRAGLARTRRHARQLVTHGHFEVNGVRVDVPSYRVEQFDVVTVRKQSVE 146


>gi|293400080|ref|ZP_06644226.1| S4 domain protein [Erysipelotrichaceae bacterium 5_2_54FAA]
 gi|291306480|gb|EFE47723.1| S4 domain protein [Erysipelotrichaceae bacterium 5_2_54FAA]
          Length = 92

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRREV-ERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  A I  RR V + +  QQRV VNG + +  + +V   D I V
Sbjct: 1  MRLDKYLKTARILKRRTVSKELADQQRVYVNGKVAK-PSTDVKIGDEIRV 49


>gi|220921712|ref|YP_002497013.1| RNA-binding S4 domain-containing protein [Methylobacterium
          nodulans ORS 2060]
 gi|219946318|gb|ACL56710.1| RNA-binding S4 domain protein [Methylobacterium nodulans ORS
          2060]
          Length = 93

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 19/52 (36%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            QR+ K +  A  A +R    R+IA   V+VNG   E A+  V   D I V
Sbjct: 4  DRQRLDKWLWFARFAKTRSLAARLIADGHVRVNGQRAEAASKAVAVGDVITV 55


>gi|159043402|ref|YP_001532196.1| DEAD/DEAH box helicase domain-containing protein [Dinoroseobacter
           shibae DFL 12]
 gi|157911162|gb|ABV92595.1| DEAD/DEAH box helicase domain protein [Dinoroseobacter shibae DFL
           12]
          Length = 730

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 16/113 (14%), Positives = 30/113 (26%), Gaps = 1/113 (0%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           L +      L EA               R+    +S         K  + +    + + +
Sbjct: 512 LEDGAVLSRLAEAPDLSQRDGSGPARKPREGRGPVSSTRPSAAGRKPRAPRPAPEATRPE 571

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            A P    + A++   A+         + +        P     RS  R   K
Sbjct: 572 PA-PAPASSQANDAPPARKPRHKDKPPASKGATPDGPKPPKAKPRSADRDRPK 623



 Score = 40.5 bits (93), Expect = 0.41,   Method: Composition-based stats.
 Identities = 10/104 (9%), Positives = 21/104 (20%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P           A   +++     +P    + P                 +      P 
Sbjct: 564 APEATRPEPAPAPASSQANDAPPARKPRHKDKPPASKGATPDGPKPPKAKPRSADRDRPK 623

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
            R   +     A G          +  +  R   +   +    R
Sbjct: 624 DRAPYSPKGGKAGGPRDDKGKPRVKDRKPPRPDAAAAVEEVAPR 667



 Score = 39.4 bits (90), Expect = 0.95,   Method: Composition-based stats.
 Identities = 11/114 (9%), Positives = 28/114 (24%), Gaps = 4/114 (3%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           L ++ G     + +        +  +    +P      P+        +   +  +    
Sbjct: 527 LSQRDGSGPARKPREGRGPVSSTRPSAAGRKPRAPRPAPEATRPEPAPAPASSQANDAPP 586

Query: 301 LATPVHRRNLASNVWM----AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
              P H+    ++        K   +   S    R ++         K    R 
Sbjct: 587 ARKPRHKDKPPASKGATPDGPKPPKAKPRSADRDRPKDRAPYSPKGGKAGGPRD 640



 Score = 36.3 bits (82), Expect = 6.9,   Method: Composition-based stats.
 Identities = 9/102 (8%), Positives = 27/102 (26%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
           +     A     +       +     PD    +++ + +++  +           + L +
Sbjct: 629 SPKGGKAGGPRDDKGKPRVKDRKPPRPDAAAAVEEVAPRRSNAASDPSQRLGPDGKPLRA 688

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               A        +  G +    +   S     + R    K+
Sbjct: 689 RGKGAAKPAGKPGAKPGGKPGRRKTFASKGPDATPRWKKPKR 730


>gi|19551798|ref|NP_599800.1| 30S ribosomal protein S4 [Corynebacterium glutamicum ATCC 13032]
 gi|62389453|ref|YP_224855.1| 30S ribosomal protein S4 [Corynebacterium glutamicum ATCC 13032]
 gi|26399381|sp|Q8NSV4|RS4_CORGL RecName: Full=30S ribosomal protein S4
 gi|21323328|dbj|BAB97956.1| Ribosomal protein S4 and related proteins [Corynebacterium
           glutamicum ATCC 13032]
 gi|41324787|emb|CAF19269.1| RIBOSOMAL PROTEIN S4 [Corynebacterium glutamicum ATCC 13032]
          Length = 201

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR+  ++++     VNG  ++  +  V   D I V
Sbjct: 92  RLDNVVYRAGLANTRRQARQLVSHGHFTVNGKAIDVPSFRVSQYDIINV 140


>gi|116669889|ref|YP_830822.1| RNA-binding S4 domain-containing protein [Arthrobacter sp. FB24]
 gi|116609998|gb|ABK02722.1| RNA-binding S4 domain protein [Arthrobacter sp. FB24]
          Length = 92

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 12/40 (30%), Positives = 19/40 (47%)

Query: 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          E   +I    VKVNG + +R    +   D + V+G  +R 
Sbjct: 47 EATELIRNGLVKVNGEIDDRRGRQLHHGDTVTVNGRTVRI 86


>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 = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 16/62 (25%), Positives = 32/62 (51%), Gaps = 7/62 (11%)

Query: 6  IVQENFTPQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
          ++ EN  P+R+ K ++R     A + SR  + R+I   +++V+G ++  A   V     I
Sbjct: 9  VIAENP-PKRLDKAVSRDVPEEATL-SRTRLARLIEAGQLEVDGKIVTDAKARVEEGATI 66

Query: 61 EV 62
           +
Sbjct: 67 SI 68


>gi|148242945|ref|YP_001228102.1| hypothetical protein SynRCC307_1846 [Synechococcus sp. RCC307]
 gi|147851255|emb|CAK28749.1| Conserved hypothetical protein, contains S4-like domain
           [Synechococcus sp. RCC307]
          Length = 261

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 28/52 (53%), Gaps = 2/52 (3%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+   IA AG   SR ++   I Q R++V+  ++   +  + + + ++++G 
Sbjct: 187 RLD-AIASAGFGVSRSKMATWIRQGRIRVDWAVVTTPSRELQNGERVQLEGR 237


>gi|42782990|ref|NP_980237.1| S4 domain-containing protein [Bacillus cereus ATCC 10987]
 gi|42738917|gb|AAS42845.1| S4 domain protein [Bacillus cereus ATCC 10987]
          Length = 255

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 14/51 (27%), Positives = 23/51 (45%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  ++A     SR++V+  I    VKVN   +E+ +      D   V G 
Sbjct: 180 RLDVMLAEMLHISRQKVQPFIKNGLVKVNWKTVEQTSYECYPGDVFSVRGH 230


>gi|291544483|emb|CBL17592.1| SSU ribosomal protein S4P [Ruminococcus sp. 18P13]
          Length = 198

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V  R G+A +RRE  +++  +   VNG  +   +  V   D I +
Sbjct: 89  RLDNVAYRMGMALTRREARQLVTHRHFTVNGQRVNIPSYRVKEGDVIAL 137


>gi|237816505|ref|ZP_04595498.1| translation initiation factor IF-2 [Brucella abortus str. 2308 A]
 gi|237788572|gb|EEP62787.1| translation initiation factor IF-2 [Brucella abortus str. 2308 A]
          Length = 976

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 14/116 (12%), Positives = 29/116 (25%), Gaps = 2/116 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R + +  +RE +        +    A   +     R+         +   + +  + +K 
Sbjct: 178 RALEEAQIRE-VEERARAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKA 236

Query: 294 GLSKQKKLATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                K++  P  R     +   A  G                   P   S R   
Sbjct: 237 EEEAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAP 292



 Score = 44.8 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 11/121 (9%), Positives = 28/121 (23%), Gaps = 1/121 (0%)

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           L     REV ++  R         E           S     +    +    +   + ++
Sbjct: 180 LEEAQIREVEERA-RAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKAEE 238

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            ++++    + +       R           G           R +     P+     + 
Sbjct: 239 EAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAPIIADAA 298

Query: 348 R 348
            
Sbjct: 299 P 299


>gi|190570680|ref|YP_001975038.1| ribosomal protein S4 [Wolbachia endosymbiont of Culex
           quinquefasciatus Pel]
 gi|213019072|ref|ZP_03334879.1| ribosomal protein S4 [Wolbachia endosymbiont of Culex
           quinquefasciatus JHB]
 gi|226695099|sp|B3CP11|RS4_WOLPP RecName: Full=30S ribosomal protein S4
 gi|190356952|emb|CAQ54338.1| ribosomal protein S4 [Wolbachia endosymbiont of Culex
           quinquefasciatus Pel]
 gi|212995181|gb|EEB55822.1| ribosomal protein S4 [Wolbachia endosymbiont of Culex
           quinquefasciatus JHB]
          Length = 204

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 11/52 (21%), Positives = 26/52 (50%), Gaps = 7/52 (13%)

Query: 15  RVSKVIARAGI----ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+S V+  +G      S    +++I+ + V VN  ++  ++  V   D +++
Sbjct: 94  RLSSVLYHSGFVPTIYS---AKQLISHKHVTVNDKVVNISSYRVKPGDIVKI 142


>gi|108799917|ref|YP_640114.1| hemolysin A [Mycobacterium sp. MCS]
 gi|119869027|ref|YP_938979.1| hemolysin A [Mycobacterium sp. KMS]
 gi|126435545|ref|YP_001071236.1| hemolysin A [Mycobacterium sp. JLS]
 gi|108770336|gb|ABG09058.1| hemolysin A [Mycobacterium sp. MCS]
 gi|119695116|gb|ABL92189.1| hemolysin A [Mycobacterium sp. KMS]
 gi|126235345|gb|ABN98745.1| hemolysin A [Mycobacterium sp. JLS]
          Length = 269

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 19/50 (38%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          RV   + R G+A SR++   +I   RV V+G+   + A  V  T HI VD
Sbjct: 6  RVDAELVRRGLARSRQQAAELIGAGRVTVDGMPAAKPATAVAVTAHIAVD 55


>gi|49478438|ref|YP_037959.1| S4 domain-containing protein [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|49329994|gb|AAT60640.1| S4 domain protein [Bacillus thuringiensis serovar konkukian str.
           97-27]
          Length = 255

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+  I    VKVN   +E+ +      D   V G
Sbjct: 180 RLDVMLAEMLHISRQKVQPFIKNGLVKVNWKTVEQTSYECYPGDVFSVRG 229


>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 = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 8/56 (14%), Positives = 23/56 (41%), Gaps = 4/56 (7%)

Query: 9  ENFTPQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
          +   P R+ K ++R    +   SR  + +++    + +NG +       + +   +
Sbjct: 11 QEDPPARLDKALSRDVPESASLSRTRIAKLLDAGAITINGAVQTDPKAKITAGAQV 66


>gi|68536219|ref|YP_250924.1| translation initiation factor IF-2 [Corynebacterium jeikeium K411]
 gi|90101355|sp|Q4JV51|IF2_CORJK RecName: Full=Translation initiation factor IF-2
 gi|68263818|emb|CAI37306.1| translation initiation factor IF-2 [Corynebacterium jeikeium K411]
          Length = 922

 Score = 46.7 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 9/105 (8%), Positives = 15/105 (14%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                 +                +P                SS         +       
Sbjct: 136 AAKPTPKPGAKPGPKPGGAKPGAKPGPKPGGRAPRVANNPFSSGAPAERPAPRPRGGQAG 195

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                      G         G  ++   R PS     S    + 
Sbjct: 196 PGDMPRPGSRPGGAKKAGPKPGGAKQGGGRRPSPAMMPSHPNPAQ 240



 Score = 44.8 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 13/105 (12%), Positives = 21/105 (20%), Gaps = 1/105 (0%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
             A     + +   E          +         K  +         K  A P  +   
Sbjct: 107 AGAGTRPTSTVKPGEKPAPKPGAKPAPKTAAKPTPKPGAKPGPKPGGAKPGAKPGPKPGG 166

Query: 311 A-SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               V        +       R    +  P    +   R   AKK
Sbjct: 167 RAPRVANNPFSSGAPAERPAPRPRGGQAGPGDMPRPGSRPGGAKK 211



 Score = 44.8 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 8/104 (7%), Positives = 16/104 (15%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           +  +     P          +P                   K G     +     +    
Sbjct: 118 KPGEKPAPKPGAKPAPKTAAKPTPKPGAKPGPKPGGAKPGAKPGPKPGGRAPRVANNPFS 177

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +                           P    K   +   AK+
Sbjct: 178 SGAPAERPAPRPRGGQAGPGDMPRPGSRPGGAKKAGPKPGGAKQ 221



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 4/70 (5%), Positives = 12/70 (17%)

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
              +                +K    P  +    +         +      G  +   + 
Sbjct: 101 KNTNPVAGAGTRPTSTVKPGEKPAPKPGAKPAPKTAAKPTPKPGAKPGPKPGGAKPGAKP 160

Query: 338 SPSFPSKRSL 347
            P    +   
Sbjct: 161 GPKPGGRAPR 170


>gi|325294423|ref|YP_004280937.1| ribosomal protein S4 [Desulfurobacterium thermolithotrophum DSM
           11699]
 gi|325064871|gb|ADY72878.1| ribosomal protein S4 [Desulfurobacterium thermolithotrophum DSM
           11699]
          Length = 208

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 15/73 (20%), Positives = 29/73 (39%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   S R   +++    + VNG  ++R +  V   D +EV        +  
Sbjct: 99  RLDNVVYRLGFGKSHRHARQLVVHGHILVNGKKVDRPSYLVKPGDIVEVKEKSREIPQIK 158

Query: 74  RLWLYHKPIGLVT 86
                 +  G+ +
Sbjct: 159 EGIELAQRRGIPS 171


>gi|317181704|dbj|BAJ59488.1| hemolysin [Helicobacter pylori F57]
          Length = 235

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 21/169 (12%), Positives = 51/169 (30%), Gaps = 13/169 (7%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------D 63
            R+   +    +A SR + + ++ + +V VN +++ + +  V  +D IE+          
Sbjct: 1   MRLDYALFNQHLANSREKAKALVLKNQVLVNKMVVSKPSFMVKESDKIELIATNLFVSRA 60

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G  L          + K + L    S           L     +V+ V    +  +  L 
Sbjct: 61  GEKLAAFLENHFIDFKKKVVLDVGASKGGFSEVA---LLKGAKKVLCVDVGKMQLDESLK 117

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
                      ++   +      +            +L+  + +     
Sbjct: 118 QDKRIECYEECDIRGFKTPEKIDLTLCDVSFISLYCILEAILPLSDEFL 166


>gi|319789265|ref|YP_004150898.1| ribosomal protein S4 [Thermovibrio ammonificans HB-1]
 gi|317113767|gb|ADU96257.1| ribosomal protein S4 [Thermovibrio ammonificans HB-1]
          Length = 208

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 16/73 (21%), Positives = 29/73 (39%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   S R   +++    + VNG  ++R +  V   D IEV        +  
Sbjct: 99  RLDNVVYRLGFGKSHRHARQLVVHGHILVNGKKVDRPSYLVKPGDVIEVKEKSRDIPQIK 158

Query: 74  RLWLYHKPIGLVT 86
                 +  G+ +
Sbjct: 159 EGMELAQRRGIPS 171


>gi|282897035|ref|ZP_06305037.1| Hemolysin A [Raphidiopsis brookii D9]
 gi|281197687|gb|EFA72581.1| Hemolysin A [Raphidiopsis brookii D9]
          Length = 317

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 9/41 (21%), Positives = 20/41 (48%)

Query: 26  ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
            SR++ +R+I    V VN   +++    +  +  I++   P
Sbjct: 62  GSRQQAQRLIQAGEVMVNQQTIDKPGAEIDISAEIQIKERP 102


>gi|260438377|ref|ZP_05792193.1| hemolysin A [Butyrivibrio crossotus DSM 2876]
 gi|292808963|gb|EFF68168.1| hemolysin A [Butyrivibrio crossotus DSM 2876]
          Length = 270

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 22/165 (13%), Positives = 50/165 (30%), Gaps = 2/165 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++    +A SR + + +I    V VNG   ++A         IEV G  L+   R
Sbjct: 3   ERLDVLLVNRKLADSREKAKAIIMSGIVYVNGQKEDKAGSMFDVYAGIEVRGSTLKYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L           ++                 ++  G   + +  +        L +
Sbjct: 63  GGLKLEKAMENFPIELNNKICMDVGSST-GGFTDCMLMNGASKVYSVDVGHGQLAWKLRQ 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
              +   +   +  V      D+   + +    +        ++ 
Sbjct: 122 DERVVVMEKTNIRYVTPDDIPDRIDFSSIDVSFISLTKVLLPVKN 166


>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 = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 1/52 (1%)

Query: 9  ENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
                R  + +A R    SR  +++++A  RV V G ++   A  V + D 
Sbjct: 37 PEDAGLRADRFLAARLPDLSRTRLQKLVADGRVSVGGRVVGDPAERVNAGDE 88


>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 = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 33/233 (14%), Positives = 82/233 (35%), Gaps = 21/233 (9%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M     + +   P ++  ++ R+   S+ + ++MI  +++  NG LL   +  V     +
Sbjct: 1   MPFIRKIIKTNKPIKLFLLLMRSFNISQSQAQKMIDTKKIYQNGKLLTDKSAVVEGEIEV 60

Query: 61  EV-----DG-VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
            V      G  P+ + +   L+       +V   +     + + +       +   V R+
Sbjct: 61  IVFEPITKGLKPIFETKDFVLYD-KPSGIMVHPRNRNTHYTLIDEIRYRYGPQANIVHRI 119

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG- 173
           D  T GL+L + +    + L+          R     + + +K  ++++ I +       
Sbjct: 120 DKETSGLVLASTNKEAEKALKQMFEHKQIQKRYLALVRGNIEKQLVIEEPIALNRDYSKI 179

Query: 174 DMQVTLDTQKGSNAWV--------TVGLRE-----GKNREIKKVFEFFNWKVN 213
            ++V +D        +        +  L E     G+  +I+         + 
Sbjct: 180 KLKVKIDPSGKYAKTIINPLKQFGSFTLVEAIPITGRQHQIRIHLFHVKHPIL 232


>gi|157960037|ref|YP_001500071.1| 30S ribosomal protein S4 [Shewanella pealeana ATCC 700345]
 gi|167626016|ref|YP_001676310.1| 30S ribosomal protein S4 [Shewanella halifaxensis HAW-EB4]
 gi|212634853|ref|YP_002311378.1| 30S ribosomal protein S4 [Shewanella piezotolerans WP3]
 gi|189045398|sp|B0TLY9|RS4_SHEHH RecName: Full=30S ribosomal protein S4
 gi|189045399|sp|A8GYZ9|RS4_SHEPA RecName: Full=30S ribosomal protein S4
 gi|226695075|sp|B8CNF7|RS4_SHEPW RecName: Full=30S ribosomal protein S4
 gi|157845037|gb|ABV85536.1| ribosomal protein S4 [Shewanella pealeana ATCC 700345]
 gi|167356038|gb|ABZ78651.1| ribosomal protein S4 [Shewanella halifaxensis HAW-EB4]
 gi|212556337|gb|ACJ28791.1| Ribosomal protein S4 [Shewanella piezotolerans WP3]
          Length = 206

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V + D + V
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKSIMVNGSVVNIPSFKVSANDVVSV 145


>gi|30021986|ref|NP_833617.1| RNA binding protein [Bacillus cereus ATCC 14579]
 gi|296504392|ref|YP_003666092.1| RNA binding protein [Bacillus thuringiensis BMB171]
 gi|29897542|gb|AAP10818.1| RNA binding protein [Bacillus cereus ATCC 14579]
 gi|296325444|gb|ADH08372.1| RNA binding protein [Bacillus thuringiensis BMB171]
          Length = 255

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+  I    VKVN   +E+ +      D   V G
Sbjct: 180 RLDVMLAEMLHLSRQKVQPFIKNGLVKVNWKTVEQTSYECYPGDVFSVRG 229


>gi|332975023|gb|EGK11933.1| 30S ribosomal protein S4 [Desmospora sp. 8437]
          Length = 199

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  ++ R G A +R +  +++    + VNG  ++R A  V   D I
Sbjct: 92  RLDNLVYRLGFARTRAQSRQLVVHGHITVNGKKVDRPAYRVKPGDVI 138


>gi|229542673|ref|ZP_04431733.1| RNA-binding S4 domain protein [Bacillus coagulans 36D1]
 gi|229327093|gb|EEN92768.1| RNA-binding S4 domain protein [Bacillus coagulans 36D1]
          Length = 168

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 12/53 (22%), Positives = 25/53 (47%), Gaps = 2/53 (3%)

Query: 11  FTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             P R+ K++    I  SR ++  +I + ++ +N   ++     V   D IE+
Sbjct: 115 DEPVRIDKLLGNQLIDISRNQICSLIKEGKILLNKNTIKN-HTAVKEKDTIEI 166


>gi|184153141|ref|YP_001841482.1| 30S ribosomal protein S4 [Lactobacillus reuteri JCM 1112]
 gi|226699080|sp|B2G6C0|RS4_LACRJ RecName: Full=30S ribosomal protein S4
 gi|183224485|dbj|BAG25002.1| 30S ribosomal protein S4 [Lactobacillus reuteri JCM 1112]
          Length = 201

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 11/52 (21%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  ++ R G+A+ RR+  +++    + V+G  ++  +  V     I V   
Sbjct: 94  RLDNMVYRLGLATTRRQARQLVNHGHITVDGKRVDIPSYEVKVGQIIAVRDK 145


>gi|226290430|gb|EEH45914.1| conserved hypothetical protein [Paracoccidioides brasiliensis Pb18]
          Length = 512

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 23/54 (42%), Gaps = 1/54 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+   I RA  AS  R+  + +    V VNG  ++     +   D  +VD   +
Sbjct: 126 RLDVAIFRAMFASSTRQARQFVLHGSVTVNGKKMKYPGYLLNPGDLFQVDPERV 179


>gi|196233367|ref|ZP_03132211.1| hemolysin A [Chthoniobacter flavus Ellin428]
 gi|196222507|gb|EDY17033.1| hemolysin A [Chthoniobacter flavus Ellin428]
          Length = 248

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 11/53 (20%), Positives = 21/53 (39%), Gaps = 1/53 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             QR+ +++   G   SR + +R I    V +     ++    V     I+V
Sbjct: 3  SAKQRLDQLLVARGYFESREKAQRAIMAGTVSIGEQRADKPGTRVPEDAAIQV 55


>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 = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 25/241 (10%), Positives = 75/241 (31%), Gaps = 36/241 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQ--QRVKVNG---------------ILL-- 47
           + E     R+ + + R G + +   E  I +  + + VNG                ++  
Sbjct: 9   ITEKEDGLRIEQFLRRKGYSGQNLAE--IKRMPKSILVNGVHYYMRQTLTAGDILKVIIC 66

Query: 48  -ERAAVNVMS-----------TDHIEVD---GVPLRKAERTRLWLYHKPIGLVTTHSDPD 92
             + +  +              D I ++   G+P+  +           +       D  
Sbjct: 67  ETKCSEKIPPVEIPLDIIYEDEDIIVINKPAGMPIHPSMNNYYNSLANALAWYYQKQDKP 126

Query: 93  GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152
                 + L    S +  V +  ++   L  +T +  + R         +          
Sbjct: 127 FIFRCCNRLDRDTSGLTVVSKHLVSGSILSTMTKNREVHREYLAVVKGRVTPSSGTICAP 186

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           + + +  ++++ +  +          L  +   ++ V++ L  G+  +I+   ++  + +
Sbjct: 187 LARKEGTIIERMVDFEHGEEAITHYKLIREANGHSLVSLKLETGRTHQIRIHMKYLGFPL 246

Query: 213 N 213
            
Sbjct: 247 I 247


>gi|154483162|ref|ZP_02025610.1| hypothetical protein EUBVEN_00863 [Eubacterium ventriosum ATCC
           27560]
 gi|149735970|gb|EDM51856.1| hypothetical protein EUBVEN_00863 [Eubacterium ventriosum ATCC
           27560]
          Length = 197

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  VI R G A +R+E  +++  + V VNG  +   +  +   D IE+   
Sbjct: 88  RLDNVIFRMGFARTRKEARQIVDHKHVLVNGKQVNIPSYLIKVGDVIEIKEK 139


>gi|295677907|ref|YP_003606431.1| ribosomal protein S4 [Burkholderia sp. CCGE1002]
 gi|295437750|gb|ADG16920.1| ribosomal protein S4 [Burkholderia sp. CCGE1002]
          Length = 207

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  +++  + + VNG++    ++ V + D + V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVGHKAITVNGVVTNIPSMQVKAGDVVAV 146


>gi|332291713|ref|YP_004430322.1| PSP1 domain protein [Krokinobacter diaphorus 4H-3-7-5]
 gi|332169799|gb|AEE19054.1| PSP1 domain protein [Krokinobacter diaphorus 4H-3-7-5]
          Length = 495

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 11/115 (9%), Positives = 27/115 (23%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
            L E+           +        +T  + R +   +   +  + + +  +    + +K
Sbjct: 340 ELIEETVIDFGNVVGQDSLTRFDKPKTTNKRRNSRKRKPAGNGNKPQGDRPKAKDRTPRK 399

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                      A+                G + +     P     R   R    K
Sbjct: 400 PNQDGAKGPRPAAKKGPKPQAKGPRPEGKGPKPQAKGPRPEGKGPRPKSRGPKPK 454



 Score = 44.8 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 16/113 (14%), Positives = 29/113 (25%), Gaps = 1/113 (0%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E+    L+EE  ++    +        D+P   ++  +   R    +  K    + K   
Sbjct: 335 EEFAAELIEETVIDFGNVVGQDSLTRFDKPKTTNKRRNSRKRKPAGNGNKPQGDRPKAKD 394

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSD-SGQREENHRRSPSFPSKRSLRRTSAKK 354
               + N                    G R E     P     R   +    K
Sbjct: 395 RTPRKPNQDGAKGPRPAAKKGPKPQAKGPRPEGKGPKPQAKGPRPEGKGPRPK 447



 Score = 44.4 bits (103), Expect = 0.025,   Method: Composition-based stats.
 Identities = 10/99 (10%), Positives = 19/99 (19%)

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW 315
                     +  R      ++   D  + K  + +K      K       +        
Sbjct: 363 KPKTTNKRRNSRKRKPAGNGNKPQGDRPKAKDRTPRKPNQDGAKGPRPAAKKGPKPQAKG 422

Query: 316 MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                        G R E     P     +   +    K
Sbjct: 423 PRPEGKGPKPQAKGPRPEGKGPRPKSRGPKPKAQGGKAK 461


>gi|227549334|ref|ZP_03979383.1| possible hemolysin A [Corynebacterium lipophiloflavum DSM 44291]
 gi|227078653|gb|EEI16616.1| possible hemolysin A [Corynebacterium lipophiloflavum DSM 44291]
          Length = 273

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 9/54 (16%)

Query: 15 RVS-----KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          R+      + +AR    SR + +  I Q RV+V G + ++ A  V     I+++
Sbjct: 7  RLDAEIVRRKLAR----SREQAQDWIKQGRVEVAGFVAKKPATVVEPEVSIKIN 56


>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 = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 11/51 (21%), Positives = 23/51 (45%), Gaps = 5/51 (9%)

Query: 13 PQRVSKVIARAGI-----ASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           +R+ + +A          SR  ++ +I    V VNG+++  A+  V +  
Sbjct: 26 GERLDRFLAAETAAAGADLSRTRLKTLIEGGHVSVNGVIVTEASFAVRAGQ 76


>gi|148379841|ref|YP_001254382.1| hemolysin A [Clostridium botulinum A str. ATCC 3502]
 gi|153933292|ref|YP_001384139.1| hemolysin A [Clostridium botulinum A str. ATCC 19397]
 gi|153936268|ref|YP_001387679.1| hemolysin A [Clostridium botulinum A str. Hall]
 gi|168180468|ref|ZP_02615132.1| hemolysin A [Clostridium botulinum NCTC 2916]
 gi|226949178|ref|YP_002804269.1| putative hemolysin A [Clostridium botulinum A2 str. Kyoto]
 gi|148289325|emb|CAL83421.1| putative methyltransferase [Clostridium botulinum A str. ATCC
          3502]
 gi|152929336|gb|ABS34836.1| hemolysin A [Clostridium botulinum A str. ATCC 19397]
 gi|152932182|gb|ABS37681.1| hemolysin A [Clostridium botulinum A str. Hall]
 gi|182668775|gb|EDT80753.1| hemolysin A [Clostridium botulinum NCTC 2916]
 gi|226841870|gb|ACO84536.1| putative hemolysin A [Clostridium botulinum A2 str. Kyoto]
          Length = 273

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 11/60 (18%), Positives = 25/60 (41%), Gaps = 1/60 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+  ++   GI  SR   +  I    + ++G  +++    +  + +IE  G  L  
Sbjct: 3  EKKERLDLLLVEKGIFQSRERAKASIMAGEIFIDGNRIDKCGEKIKESANIEFRGEKLPY 62


>gi|50546507|ref|XP_500723.1| YALI0B10494p [Yarrowia lipolytica]
 gi|49646589|emb|CAG82968.1| YALI0B10494p [Yarrowia lipolytica]
          Length = 571

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 13/42 (30%), Positives = 21/42 (50%)

Query: 26  ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           AS R+  + I Q  V VNG+ ++ A+  +   D I V    +
Sbjct: 136 ASIRQAGQFIRQGNVTVNGVKIKHASYTLKPGDLISVKPEKV 177


>gi|332685835|ref|YP_004455609.1| 30S ribosomal protein S4p (S9e) [Melissococcus plutonius ATCC
           35311]
 gi|332369844|dbj|BAK20800.1| SSU ribosomal protein S4p (S9e) [Melissococcus plutonius ATCC
           35311]
          Length = 201

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  ++ R G+A+ RR+  +++    + V+   ++  + +V     I V
Sbjct: 93  QRLDNIVYRLGLATTRRQARQLVNHGHILVDNKRVDIPSYHVEVGQVISV 142


>gi|291551160|emb|CBL27422.1| Ribosome-associated heat shock protein implicated in the
          recycling of the 50S subunit (S4 paralog) [Ruminococcus
          torques L2-14]
          Length = 79

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR          RV VNG   + A+V V   D IE+
Sbjct: 1  MRLDKFLKVSRLIKRRTVANEACDAGRVLVNGKTAK-ASVKVKPGDVIEI 49


>gi|298711322|emb|CBJ32469.1| hypothetical protein Esi_0341_0019 [Ectocarpus siliculosus]
          Length = 338

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 11/41 (26%), Positives = 19/41 (46%), Gaps = 1/41 (2%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA 70
            E ++   RV VNG++     + V   TD +  +GV +   
Sbjct: 269 CEILVEMGRVTVNGVVARDPGIKVDLLTDIVVANGVAVTFP 309


>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 = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 22/199 (11%), Positives = 56/199 (28%), Gaps = 3/199 (1%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP---LRKAERTR 74
           K++A     S  E + +I +  V + G  L+ A   +       +  +P   +   +   
Sbjct: 21  KLLALQENISNNEAKSLIDRGLVSIQGKKLKIARALLSPHTKFNIQKIPEIKILFQDDNI 80

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L           +       +   L    S ++ + + +                   
Sbjct: 81  LALSKPAFLTSEEIAKLYPNWALLHRLDKETSGILLLIKENSPFHLKAKEAFKKEQVFKQ 140

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
            +   + +          +   K N  K  +  +       ++T     G    + + ++
Sbjct: 141 YIAIVEGIIEEEQEITAPLIIQKGNFAKVLVSKKEGIRAYTKITPIEIIGKKTKLEIIIK 200

Query: 195 EGKNREIKKVFEFFNWKVN 213
            GK  +I+         + 
Sbjct: 201 TGKTHQIRAHLAHIKHPII 219


>gi|206976717|ref|ZP_03237621.1| S4 domain protein [Bacillus cereus H3081.97]
 gi|217961318|ref|YP_002339886.1| S4 domain protein [Bacillus cereus AH187]
 gi|222097343|ref|YP_002531400.1| s4 domain protein [Bacillus cereus Q1]
 gi|206745027|gb|EDZ56430.1| S4 domain protein [Bacillus cereus H3081.97]
 gi|217063822|gb|ACJ78072.1| S4 domain protein [Bacillus cereus AH187]
 gi|221241401|gb|ACM14111.1| S4 domain protein [Bacillus cereus Q1]
          Length = 255

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+  I    VKVN   +E+ +      D   V G
Sbjct: 180 RLDVMLAEMLHISRQKVQPFIKNGLVKVNWKTVEQTSYECYPGDVFSVRG 229


>gi|317131685|ref|YP_004090999.1| RNA-binding S4 domain protein [Ethanoligenens harbinense YUAN-3]
 gi|315469664|gb|ADU26268.1| RNA-binding S4 domain protein [Ethanoligenens harbinense YUAN-3]
          Length = 248

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 21/52 (40%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            +R+  V+A     SR + E  I   RV ++   +   A  V     + + G
Sbjct: 171 SERLDCVVAALTGCSRTQAEDGITAGRVALDFRTVTDRACRVPPGASLSIRG 222


>gi|296141063|ref|YP_003648306.1| ribosomal protein S4 [Tsukamurella paurometabola DSM 20162]
 gi|296029197|gb|ADG79967.1| ribosomal protein S4 [Tsukamurella paurometabola DSM 20162]
          Length = 201

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+  V+ RAG+A +RR+  +++      VNG+ ++  +  V   D I+V    L
Sbjct: 92  RLDNVVYRAGLARTRRQARQLVTHGHFTVNGVRVDVPSYRVSQYDIIDVRPKSL 145


>gi|206970953|ref|ZP_03231904.1| S4 domain protein [Bacillus cereus AH1134]
 gi|218235237|ref|YP_002368697.1| S4 domain protein [Bacillus cereus B4264]
 gi|228960115|ref|ZP_04121779.1| RNA-binding S4 domain protein [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|229047582|ref|ZP_04193172.1| RNA-binding S4 domain protein [Bacillus cereus AH676]
 gi|229111367|ref|ZP_04240920.1| RNA-binding S4 domain protein [Bacillus cereus Rock1-15]
 gi|229129175|ref|ZP_04258148.1| RNA-binding S4 domain protein [Bacillus cereus BDRD-Cer4]
 gi|229146469|ref|ZP_04274840.1| RNA-binding S4 domain protein [Bacillus cereus BDRD-ST24]
 gi|229152095|ref|ZP_04280290.1| RNA-binding S4 domain protein [Bacillus cereus m1550]
 gi|206733725|gb|EDZ50896.1| S4 domain protein [Bacillus cereus AH1134]
 gi|218163194|gb|ACK63186.1| S4 domain protein [Bacillus cereus B4264]
 gi|228631444|gb|EEK88078.1| RNA-binding S4 domain protein [Bacillus cereus m1550]
 gi|228637102|gb|EEK93561.1| RNA-binding S4 domain protein [Bacillus cereus BDRD-ST24]
 gi|228654412|gb|EEL10277.1| RNA-binding S4 domain protein [Bacillus cereus BDRD-Cer4]
 gi|228672143|gb|EEL27434.1| RNA-binding S4 domain protein [Bacillus cereus Rock1-15]
 gi|228723829|gb|EEL75184.1| RNA-binding S4 domain protein [Bacillus cereus AH676]
 gi|228799631|gb|EEM46584.1| RNA-binding S4 domain protein [Bacillus thuringiensis serovar
           pakistani str. T13001]
          Length = 241

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+  I    VKVN   +E+ +      D   V G
Sbjct: 166 RLDVMLAEMLHLSRQKVQPFIKNGLVKVNWKTVEQTSYECYPGDVFSVRG 215


>gi|153938144|ref|YP_001391202.1| hemolysin A [Clostridium botulinum F str. Langeland]
 gi|152934040|gb|ABS39538.1| hemolysin A [Clostridium botulinum F str. Langeland]
 gi|295319238|gb|ADF99615.1| hemolysin A [Clostridium botulinum F str. 230613]
          Length = 273

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 11/60 (18%), Positives = 25/60 (41%), Gaps = 1/60 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+  ++   GI  SR   +  I    + ++G  +++    +  + +IE  G  L  
Sbjct: 3  EKKERLDLLLVEKGIFQSRERAKASIMAGEIFIDGNRIDKCGEKIKESANIEFRGEKLPY 62


>gi|86609348|ref|YP_478110.1| S4 domain-containing protein [Synechococcus sp. JA-2-3B'a(2-13)]
 gi|86557890|gb|ABD02847.1| S4 domain protein [Synechococcus sp. JA-2-3B'a(2-13)]
          Length = 87

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 14/58 (24%), Positives = 29/58 (50%), Gaps = 1/58 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           ++ + +  AG+A +  + +++I   +V+VNG +  R    + S D + V G   R  
Sbjct: 21 IKLDQFLKLAGVAPTGGQAKQLIQAGQVRVNGEVETRRGRKLRSGDEVAVGGGVWRVR 78


>gi|311031300|ref|ZP_07709390.1| 30S ribosomal protein S4 [Bacillus sp. m3-13]
          Length = 200

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR   +++    + V+G  ++  +  V     I V
Sbjct: 93  RLDNLVYRLGLARTRRGARQLVNHGHITVDGSRVDIPSFRVKPGQVIGV 141


>gi|239613660|gb|EEQ90647.1| 30S ribosomal subunit S4 [Ajellomyces dermatitidis ER-3]
          Length = 498

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 1/54 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+   I RA  AS  R+  + +    V VNG  +      +   D  +VD   +
Sbjct: 126 RLDVAIFRAMFASSTRQARQFVVHGFVTVNGTKMRHPGYLLNPGDLFQVDPERV 179


>gi|261193076|ref|XP_002622944.1| 30S ribosomal subunit S4 [Ajellomyces dermatitidis SLH14081]
 gi|239589079|gb|EEQ71722.1| 30S ribosomal subunit S4 [Ajellomyces dermatitidis SLH14081]
 gi|327352581|gb|EGE81438.1| 30S ribosomal subunit S4 [Ajellomyces dermatitidis ATCC 18188]
          Length = 498

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 1/54 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+   I RA  AS  R+  + +    V VNG  +      +   D  +VD   +
Sbjct: 126 RLDVAIFRAMFASSTRQARQFVVHGFVTVNGTKMRHPGYLLNPGDLFQVDPERV 179


>gi|229075655|ref|ZP_04208637.1| RNA-binding S4 domain protein [Bacillus cereus Rock4-18]
 gi|229098368|ref|ZP_04229313.1| RNA-binding S4 domain protein [Bacillus cereus Rock3-29]
 gi|229104461|ref|ZP_04235128.1| RNA-binding S4 domain protein [Bacillus cereus Rock3-28]
 gi|229117394|ref|ZP_04246770.1| RNA-binding S4 domain protein [Bacillus cereus Rock1-3]
 gi|228666004|gb|EEL21470.1| RNA-binding S4 domain protein [Bacillus cereus Rock1-3]
 gi|228678903|gb|EEL33113.1| RNA-binding S4 domain protein [Bacillus cereus Rock3-28]
 gi|228684985|gb|EEL38918.1| RNA-binding S4 domain protein [Bacillus cereus Rock3-29]
 gi|228707431|gb|EEL59622.1| RNA-binding S4 domain protein [Bacillus cereus Rock4-18]
          Length = 255

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+  I    VKVN   +E+ +      D   V G
Sbjct: 180 RLDVMLAEMLHISRQKVQPFIKNGLVKVNWKTVEQTSYECYPGDVFSVRG 229


>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 = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 33/247 (13%), Positives = 77/247 (31%), Gaps = 35/247 (14%)

Query: 1   MKDK-NIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVN--GI----------- 45
           M  K + V E     R+  + A+     SR+ ++ +I    ++V+               
Sbjct: 1   MNQKEHYVHEEEKNMRLDVLCAQICPNLSRQYLKELIVDGDIQVDFANKKPAYRLKADER 60

Query: 46  -LLERAA---VNVMST----DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTV 97
            +++        VM      D +  DG  +   + + + ++        T  +     T 
Sbjct: 61  IVIKIPDPVPCQVMPESIDLDIVYEDGDVIVVNKPSGMVVHPASGTQSGTLVNALMAHTK 120

Query: 98  FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR----------- 146
             +  +  +R   V R+D +T G+L++  +    R L     +   V +           
Sbjct: 121 DLSGINGVNRPGIVHRIDKDTSGILVVAKNDLAHRHLARQLAEHSMVRQYVALVKGNIVE 180

Query: 147 -VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                            +  V++          +  + G   +V   L  G+  +I+   
Sbjct: 181 NSGTVDMPVGRHPVDRVRMAVVENGKSAVTHFEVIERLGDFTYVAFRLETGRTHQIRVHM 240

Query: 206 EFFNWKV 212
           +     +
Sbjct: 241 QAIGHPI 247


>gi|299144086|ref|ZP_07037166.1| putative YlmH protein [Peptoniphilus sp. oral taxon 386 str. F0131]
 gi|298518571|gb|EFI42310.1| putative YlmH protein [Peptoniphilus sp. oral taxon 386 str. F0131]
          Length = 257

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 20/50 (40%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+   ++     SR     +I   +VKVN     + +  V   D I V G
Sbjct: 182 RLDTFLSSVLKLSRTAASNLIESDKVKVNFRKESKGSNKVNIGDLISVRG 231


>gi|148543735|ref|YP_001271105.1| 30S ribosomal protein S4 [Lactobacillus reuteri DSM 20016]
 gi|194468296|ref|ZP_03074282.1| ribosomal protein S4 [Lactobacillus reuteri 100-23]
 gi|227363285|ref|ZP_03847417.1| 30S ribosomal protein S4 [Lactobacillus reuteri MM2-3]
 gi|227544238|ref|ZP_03974287.1| 30S ribosomal protein S4 [Lactobacillus reuteri CF48-3A]
 gi|300908234|ref|ZP_07125700.1| 30S ribosomal protein S4 [Lactobacillus reuteri SD2112]
 gi|325682107|ref|ZP_08161625.1| 30S ribosomal protein S4 [Lactobacillus reuteri MM4-1A]
 gi|172048234|sp|A5VIU4|RS4_LACRD RecName: Full=30S ribosomal protein S4
 gi|148530769|gb|ABQ82768.1| SSU ribosomal protein S4P [Lactobacillus reuteri DSM 20016]
 gi|194453149|gb|EDX42047.1| ribosomal protein S4 [Lactobacillus reuteri 100-23]
 gi|227071741|gb|EEI10032.1| 30S ribosomal protein S4 [Lactobacillus reuteri MM2-3]
 gi|227185791|gb|EEI65862.1| 30S ribosomal protein S4 [Lactobacillus reuteri CF48-3A]
 gi|300894661|gb|EFK88017.1| 30S ribosomal protein S4 [Lactobacillus reuteri SD2112]
 gi|324978751|gb|EGC15700.1| 30S ribosomal protein S4 [Lactobacillus reuteri MM4-1A]
          Length = 201

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 11/52 (21%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  ++ R G+A+ RR+  +++    + V+G  ++  +  V     I V   
Sbjct: 94  RLDNMVYRLGLATTRRQARQLVNHGHITVDGKRVDIPSYEVKVGQIIAVRDK 145


>gi|222056680|ref|YP_002539042.1| ribosomal protein S4 [Geobacter sp. FRC-32]
 gi|254764590|sp|B9M6F3|RS4_GEOSF RecName: Full=30S ribosomal protein S4
 gi|221565969|gb|ACM21941.1| ribosomal protein S4 [Geobacter sp. FRC-32]
          Length = 208

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G AS R E  +++      +NG  +   ++ V + D +E+
Sbjct: 99  RLDNIVYRLGFASSRIEARQLVRHGHFTLNGKKVTIPSIQVKTGDTVEL 147


>gi|70726207|ref|YP_253121.1| 30S ribosomal protein S4 [Staphylococcus haemolyticus JCSC1435]
 gi|82581621|sp|Q4L760|RS4_STAHJ RecName: Full=30S ribosomal protein S4
 gi|68446931|dbj|BAE04515.1| 30S ribosomal protein S4 [Staphylococcus haemolyticus JCSC1435]
          Length = 200

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+   G+A +RR+  +++    V+V+G  ++  + ++     I V
Sbjct: 93  RLDAVVYSLGLARTRRQARQLVGHGHVEVDGRRVDIPSYSLKPGQVITV 141


>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 = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 4/54 (7%)

Query: 13 PQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          P R+ K +AR    A   SR  + ++IA+  V   G +L  A   V   + IE+
Sbjct: 15 PNRLDKALARDVPEAANLSRSRLAKLIAEGAVMRAGEVLTDAKAKVTEGEVIEI 68


>gi|332295377|ref|YP_004437300.1| ribosomal protein S4 [Thermodesulfobium narugense DSM 14796]
 gi|332178480|gb|AEE14169.1| ribosomal protein S4 [Thermodesulfobium narugense DSM 14796]
          Length = 208

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R+G AS R+E  +MI+     VN   +   + +V   D I V
Sbjct: 100 RLDNVLYRSGFASSRQEARQMISHGHFNVNSRRVSIPSYSVKPGDVISV 148


>gi|228954174|ref|ZP_04116202.1| RNA-binding S4 domain protein [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|229071397|ref|ZP_04204619.1| RNA-binding S4 domain protein [Bacillus cereus F65185]
 gi|229081150|ref|ZP_04213660.1| RNA-binding S4 domain protein [Bacillus cereus Rock4-2]
 gi|229180173|ref|ZP_04307517.1| RNA-binding S4 domain protein [Bacillus cereus 172560W]
 gi|228603382|gb|EEK60859.1| RNA-binding S4 domain protein [Bacillus cereus 172560W]
 gi|228702194|gb|EEL54670.1| RNA-binding S4 domain protein [Bacillus cereus Rock4-2]
 gi|228711688|gb|EEL63641.1| RNA-binding S4 domain protein [Bacillus cereus F65185]
 gi|228805494|gb|EEM52085.1| RNA-binding S4 domain protein [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
          Length = 241

 Score = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+  I    VKVN   +E+ +      D   V G
Sbjct: 166 RLDVMLAEMLHLSRQKVQPFIKNGLVKVNWKTVEQTSYECYPGDVFSVRG 215


>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 = 46.7 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 27/226 (11%), Positives = 58/226 (25%), Gaps = 41/226 (18%)

Query: 22  RAGIASRREVERMIA----QQRVKVNGILLERAAVNVMSTDHIEVD-------------- 63
             G++SR     +I      +R+KV+G +  +    V + + I+++              
Sbjct: 24  ELGLSSR-----LIRSAAIDKRIKVDG-VAVKMNYVVKTGEEIKIELSKKESQNIEPEKM 77

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
            + +   +   L L  KP  +V         +     L              ++   +  
Sbjct: 78  DIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYFKESNQDCIVRLVSRLDMNT 137

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
                                        +     NL +K   I    Y   + T+    
Sbjct: 138 SGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLEEKEGTINRPIYRPAEDTIKRVV 197

Query: 180 -DTQKGSNAWVTVG------------LREGKNREIKKVFEFFNWKV 212
            +  + S     V             L  G+  +I+         +
Sbjct: 198 DERGQESITHYKVIESYNGADLVECLLETGRTHQIRVHLSSLGHPI 243


>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 = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 15/53 (28%), Positives = 30/53 (56%), Gaps = 2/53 (3%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           R+   +A+A    SR  V+ +I Q +V+V+G   +   + ++  + IE++G P
Sbjct: 88  RLDAYLAKAMPDISRGRVQLLIEQGQVRVDGKTAKN-KLKLLGGERIEIEGEP 139


>gi|229192067|ref|ZP_04319036.1| RNA-binding S4 domain protein [Bacillus cereus ATCC 10876]
 gi|228591393|gb|EEK49243.1| RNA-binding S4 domain protein [Bacillus cereus ATCC 10876]
          Length = 241

 Score = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+  I    VKVN   +E+ +      D   V G
Sbjct: 166 RLDVMLAEMLHLSRQKVQPFIKNGLVKVNWKTVEQTSYECYPGDVFSVRG 215


>gi|226348837|gb|ACO50741.1| ribosomal protein S4 [Micromonas pusilla CCMP1545]
          Length = 261

 Score = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 13/71 (18%), Positives = 28/71 (39%), Gaps = 5/71 (7%)

Query: 14  QRVSKVIARAGIASRREVE--RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            R+  ++ RA  A+   ++  + IA  +V VNG ++      +   D + +    +   E
Sbjct: 101 MRLDVILYRARFAT-SYLQLHQWIAHGKVCVNGQVVTTKGRLLSPGDVVSIHPQAVSSVE 159

Query: 72  --RTRLWLYHK 80
                 W +  
Sbjct: 160 ESMRTFWAHAP 170


>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 = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 27/226 (11%), Positives = 58/226 (25%), Gaps = 41/226 (18%)

Query: 22  RAGIASRREVERMIA----QQRVKVNGILLERAAVNVMSTDHIEVD-------------- 63
             G++SR     +I      +R+KV+G +  +    V + + I+++              
Sbjct: 24  ELGLSSR-----LIRSAAIDKRIKVDG-VAVKMNYVVKTGEEIKIELSKKESQNIEPEKM 77

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
            + +   +   L L  KP  +V         +     L              ++   +  
Sbjct: 78  DIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYFKESNQDCIVRLVSRLDMNT 137

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
                                        +     NL +K   I    Y   + T+    
Sbjct: 138 SGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLAEKEGTINRPIYRPAEDTIKRVV 197

Query: 180 -DTQKGSNAWVTVG------------LREGKNREIKKVFEFFNWKV 212
            +  + S     V             L  G+  +I+         +
Sbjct: 198 DERGQESITHYKVIESYNGADLVECLLETGRTHQIRVHLSSLGHPI 243


>gi|306824771|ref|ZP_07458115.1| S4 domain-containing protein YlmH [Streptococcus sp. oral taxon 071
           str. 73H25AP]
 gi|304432982|gb|EFM35954.1| S4 domain-containing protein YlmH [Streptococcus sp. oral taxon 071
           str. 73H25AP]
          Length = 263

 Score = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 14/48 (29%), Positives = 27/48 (56%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +++ A   SR +  ++I ++ V+VN  L+E++   V   D I V
Sbjct: 186 RLDALLSSALKLSRNQTSQLIEKKSVQVNYHLVEKSDYQVAVGDLISV 233


>gi|269839290|ref|YP_003323982.1| ribosomal protein S4 [Thermobaculum terrenum ATCC BAA-798]
 gi|269791020|gb|ACZ43160.1| ribosomal protein S4 [Thermobaculum terrenum ATCC BAA-798]
          Length = 201

 Score = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 15/70 (21%), Positives = 30/70 (42%), Gaps = 1/70 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G A +R    +++    V+VNG  ++R +  V   + I +    L+     
Sbjct: 95  RLDNVVYRLGFARTRPMARQLVVHGHVRVNGQKVDRPSYQVKPGEVITLTEKALQIPVVI 154

Query: 74  RLWLYHKPIG 83
                H+ + 
Sbjct: 155 EEMESHRIVP 164


>gi|197364265|ref|YP_002143902.1| 30S ribosomal protein S4 [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|226695073|sp|B5BGW2|RS4_SALPK RecName: Full=30S ribosomal protein S4
 gi|197095742|emb|CAR61312.1| 30S ribosomal subunit protein S4 [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
          Length = 206

 Score = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 12/73 (16%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  +   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQISPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|313901168|ref|ZP_07834656.1| ribosomal protein S4 [Clostridium sp. HGF2]
 gi|312954126|gb|EFR35806.1| ribosomal protein S4 [Clostridium sp. HGF2]
          Length = 200

 Score = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G A +RR   +++    + VNG  ++  +        +E+
Sbjct: 93  RLDNLVYRMGFARTRRAARQLVNHGHILVNGKKVDIPSFIAKPGMVVEI 141


>gi|261418186|ref|YP_003251868.1| 30S ribosomal protein S4 [Geobacillus sp. Y412MC61]
 gi|297529040|ref|YP_003670315.1| ribosomal protein S4 [Geobacillus sp. C56-T3]
 gi|319767854|ref|YP_004133355.1| ribosomal protein S4 [Geobacillus sp. Y412MC52]
 gi|261374643|gb|ACX77386.1| ribosomal protein S4 [Geobacillus sp. Y412MC61]
 gi|297252292|gb|ADI25738.1| ribosomal protein S4 [Geobacillus sp. C56-T3]
 gi|317112720|gb|ADU95212.1| ribosomal protein S4 [Geobacillus sp. Y412MC52]
          Length = 200

 Score = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR+  +++    + V+G  +   +  V     I V
Sbjct: 93  RLDNLVYRLGLARTRRQARQLVTHGHILVDGSRVNIPSYRVKPGQTIAV 141


>gi|118479118|ref|YP_896269.1| S4 domain-containing protein [Bacillus thuringiensis str. Al Hakam]
 gi|167636417|ref|ZP_02394716.1| S4 domain protein [Bacillus anthracis str. A0442]
 gi|170688819|ref|ZP_02880022.1| S4 domain protein [Bacillus anthracis str. A0465]
 gi|196038619|ref|ZP_03105927.1| S4 domain protein [Bacillus cereus NVH0597-99]
 gi|196045924|ref|ZP_03113153.1| S4 domain protein [Bacillus cereus 03BB108]
 gi|225865879|ref|YP_002751257.1| S4 domain protein [Bacillus cereus 03BB102]
 gi|254683393|ref|ZP_05147253.1| S4 domain protein [Bacillus anthracis str. CNEVA-9066]
 gi|254721431|ref|ZP_05183220.1| S4 domain protein [Bacillus anthracis str. A1055]
 gi|254739815|ref|ZP_05197508.1| S4 domain protein [Bacillus anthracis str. Kruger B]
 gi|301055388|ref|YP_003793599.1| RNA-binding S4 domain-containing protein [Bacillus anthracis CI]
 gi|118418343|gb|ABK86762.1| S4 domain protein [Bacillus thuringiensis str. Al Hakam]
 gi|167528159|gb|EDR90946.1| S4 domain protein [Bacillus anthracis str. A0442]
 gi|170667174|gb|EDT17934.1| S4 domain protein [Bacillus anthracis str. A0465]
 gi|196023364|gb|EDX62042.1| S4 domain protein [Bacillus cereus 03BB108]
 gi|196030342|gb|EDX68941.1| S4 domain protein [Bacillus cereus NVH0597-99]
 gi|225787031|gb|ACO27248.1| S4 domain protein [Bacillus cereus 03BB102]
 gi|300377557|gb|ADK06461.1| RNA-binding S4 domain protein [Bacillus cereus biovar anthracis
           str. CI]
          Length = 255

 Score = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+  I    VKVN   +E+ +      D   V G
Sbjct: 180 RLDVMLAEMLHISRQKVQPFIKNGLVKVNWKTVEQTSYECYPGDVFSVRG 229


>gi|17230382|ref|NP_486930.1| hypothetical protein alr2890 [Nostoc sp. PCC 7120]
 gi|17131984|dbj|BAB74589.1| alr2890 [Nostoc sp. PCC 7120]
          Length = 259

 Score = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 18/65 (27%), Positives = 27/65 (41%), Gaps = 2/65 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             K  +       R+   IA AG   SR ++   I    V+VN   + +A+  V S D I
Sbjct: 172 PKKKELTTVEASLRLD-AIASAGFGMSRSKMVDFIDSGDVRVNWKEVTQASSQVKSGDLI 230

Query: 61  EVDGV 65
            + G 
Sbjct: 231 AIRGK 235


>gi|307328057|ref|ZP_07607238.1| ribosomal protein S4 [Streptomyces violaceusniger Tu 4113]
 gi|306886362|gb|EFN17367.1| ribosomal protein S4 [Streptomyces violaceusniger Tu 4113]
          Length = 208

 Score = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG A SR    +++    + VNG   +  +  V   D IEV
Sbjct: 99  RLDNVVYRAGFAKSRDHARQLVRHGHITVNGRKTDIPSARVTVNDIIEV 147


>gi|319764615|ref|YP_004128552.1| ribosomal protein s4 [Alicycliphilus denitrificans BC]
 gi|330826872|ref|YP_004390175.1| 30S ribosomal protein S4 [Alicycliphilus denitrificans K601]
 gi|317119176|gb|ADV01665.1| ribosomal protein S4 [Alicycliphilus denitrificans BC]
 gi|329312244|gb|AEB86659.1| ribosomal protein S4 [Alicycliphilus denitrificans K601]
          Length = 224

 Score = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +  A+  V + D + V
Sbjct: 115 RLDNVVYRMGFGSTRAEARQLVSHKAITVNGQSVNIASYLVKTGDVVAV 163


>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 = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 27/226 (11%), Positives = 58/226 (25%), Gaps = 41/226 (18%)

Query: 22  RAGIASRREVERMIA----QQRVKVNGILLERAAVNVMSTDHIEVD-------------- 63
             G++SR     +I      +R+KV+G +  +    V + + I+++              
Sbjct: 24  ELGLSSR-----LIRSAAIDKRIKVDG-VAVKMNYVVKTGEEIKIELSKKESQNIEPEKM 77

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
            + +   +   L L  KP  +V         +     L              ++   +  
Sbjct: 78  DIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYFKESNQDCIVRLVSRLDMNT 137

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
                                        +     NL +K   I    Y   + T+    
Sbjct: 138 SGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLEEKEGTINRPIYRPAEDTIKRVV 197

Query: 180 -DTQKGSNAWVTVG------------LREGKNREIKKVFEFFNWKV 212
            +  + S     V             L  G+  +I+         +
Sbjct: 198 DERGQESITHYKVIESYEGADLVECLLETGRTHQIRVHLSSLGHPI 243


>gi|293361544|ref|XP_001062211.2| PREDICTED: zinc finger protein 318, partial [Rattus norvegicus]
          Length = 2148

 Score = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 11/97 (11%), Positives = 21/97 (21%)

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW 315
                  S       R +         +       + +    + +  +P   R+      
Sbjct: 1   PPRGRRGSPSPPRGRRASPSPPRGRRASPSPPRGRRVSPSPPRARRGSPSPPRSRRHYPP 60

Query: 316 MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
              G   S   +S        R        S RR+  
Sbjct: 61  GLGGFRGSIRGESRADFARDGRGDHPGDSGSRRRSPG 97



 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 15/50 (30%), Gaps = 2/50 (4%)

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQR--EENHRRSPSFPSKRSLRRTSAK 353
             R    +    +G  +S     G+R      R     PS    RR S  
Sbjct: 1   PPRGRRGSPSPPRGRRASPSPPRGRRASPSPPRGRRVSPSPPRARRGSPS 50


>gi|254563753|ref|YP_003070848.1| hypothetical protein METDI5429 [Methylobacterium extorquens DM4]
 gi|254271031|emb|CAX27038.1| conserved hypothetical protein; putative ATP-dependent RNA and DNA
            helicase (N-terminal) and conserved C-terminal DEAD/DEAH
            box domain protein (C-terminal) [Methylobacterium
            extorquens DM4]
          Length = 1135

 Score = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 16/111 (14%), Positives = 29/111 (26%), Gaps = 2/111 (1%)

Query: 244  QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
              GP                 E     R +   +   +    +    +  G    +    
Sbjct: 1007 HTGPRPGRGQGRPEGRQDGRQEGRQDGRQDGRQDGRRNDGPRRPREDRPEGGRPARADGR 1066

Query: 304  PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP-SFPSKRSLRRTSAK 353
            P  RR         +  H    +   +R+EN R +P   P +R  +     
Sbjct: 1067 PDSRREGQGEGG-PRREHQGGRNRPDRRDENRRPNPEQRPPRRERQPDPDS 1116



 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 10/112 (8%), Positives = 21/112 (18%), Gaps = 1/112 (0%)

Query: 244  QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
             L                         +        D     ++N   +     + +   
Sbjct: 1000 HLHRPQRHTGPRPGRGQGRPEGRQDGRQEGRQDGRQDGRQDGRRNDGPRRPREDRPEGGR 1059

Query: 304  PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS-PSFPSKRSLRRTSAKK 354
            P        +    +G         G R    RR     P+         ++
Sbjct: 1060 PARADGRPDSRREGQGEGGPRREHQGGRNRPDRRDENRRPNPEQRPPRRERQ 1111



 Score = 40.2 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 11/92 (11%), Positives = 18/92 (19%)

Query: 253  AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
             Q              R          D     +   +     S+++       RR    
Sbjct: 1026 RQEGRQDGRQDGRQDGRRNDGPRRPREDRPEGGRPARADGRPDSRREGQGEGGPRREHQG 1085

Query: 313  NVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
                      +   +  QR     R P   S 
Sbjct: 1086 GRNRPDRRDENRRPNPEQRPPRRERQPDPDSP 1117


>gi|237786335|ref|YP_002907040.1| 30S ribosomal protein S4 [Corynebacterium kroppenstedtii DSM 44385]
 gi|259495271|sp|C4LKZ2|RS4_CORK4 RecName: Full=30S ribosomal protein S4
 gi|237759247|gb|ACR18497.1| 30S ribosomal protein S4 [Corynebacterium kroppenstedtii DSM 44385]
          Length = 201

 Score = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR+  ++++     VNG  +   +  V   D I+V
Sbjct: 92  RLDNVVYRAGLARTRRQARQLVSHGHFTVNGKKVNVPSFQVSQYDIIDV 140


>gi|228922650|ref|ZP_04085950.1| RNA-binding S4 domain protein [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228837079|gb|EEM82420.1| RNA-binding S4 domain protein [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 241

 Score = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+  I    VKVN   +E+ +      D   V G
Sbjct: 166 RLDVMLAEMLHLSRQKVQPFIKNGLVKVNWKTVEQTSYECYPGDVFSVRG 215


>gi|197303838|ref|ZP_03168874.1| hypothetical protein RUMLAC_02577 [Ruminococcus lactaris ATCC
           29176]
 gi|197297131|gb|EDY31695.1| hypothetical protein RUMLAC_02577 [Ruminococcus lactaris ATCC
           29176]
          Length = 181

 Score = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +R+E  +++  + V VNG  +   +  V + D IE+
Sbjct: 72  RLDNVVFRLGLARTRKEARQIVDHKHVLVNGKQVNIPSYLVKAGDTIEI 120


>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 = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 27/226 (11%), Positives = 58/226 (25%), Gaps = 41/226 (18%)

Query: 22  RAGIASRREVERMIA----QQRVKVNGILLERAAVNVMSTDHIEVD-------------- 63
             G++SR     +I      +R+KV+G +  +    V + + I+++              
Sbjct: 24  ELGLSSR-----LIRSAAIDKRIKVDG-VAVKMNYVVKTGEEIKIELSKKESQNIEPEKM 77

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
            + +   +   L L  KP  +V         +     L              ++   +  
Sbjct: 78  DIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYFKESNQDCIVRLVSRLDMNT 137

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
                                        +     NL +K   I    Y   + T+    
Sbjct: 138 SGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLEEKEGTINRPIYRPAEDTIKRVV 197

Query: 180 -DTQKGSNAWVTVG------------LREGKNREIKKVFEFFNWKV 212
            +  + S     V             L  G+  +I+         +
Sbjct: 198 DERGQESITHYKVIESYNGADLVECLLETGRTHQIRVHLSSLGHPI 243


>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 = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 31/260 (11%), Positives = 71/260 (27%), Gaps = 52/260 (20%)

Query: 6   IVQENFTPQRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           I   +   +R+ + +A A     SR  V+ +IA   V ++G         +    +I + 
Sbjct: 18  IADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMNIAIV 77

Query: 63  ---------DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
                     G  +       +   + +      +V   +     + V   +        
Sbjct: 78  LPEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNGNWTGTLVNALIYQCGDSLS 137

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLELP-----------------STQWLR 143
                 R   V RLD +T G++++  +    R L                          
Sbjct: 138 GIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFADHGRTGDLERAYLALVWGMTE 197

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSN---------AWVTVGL 193
             +      + +   +  K+ +V +             T +  +         + V   L
Sbjct: 198 RPQGTVDAYLGRSHRDRTKQAVVHEEREDARHAITHYATVEKFSPREDATALASLVECRL 257

Query: 194 REGKNREIKKVFEFFNWKVN 213
             G+  +I+         + 
Sbjct: 258 ETGRTHQIRVHMAHIGHPLV 277


>gi|56421337|ref|YP_148655.1| 30S ribosomal protein S4 [Geobacillus kaustophilus HTA426]
 gi|61215360|sp|Q5KW49|RS4_GEOKA RecName: Full=30S ribosomal protein S4
 gi|56381179|dbj|BAD77087.1| 30S ribosomal protein S4 [Geobacillus kaustophilus HTA426]
          Length = 200

 Score = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR+  +++    + V+G  +   +  V     I V
Sbjct: 93  RLDNLVYRLGLARTRRQARQLVTHGHILVDGSRVNIPSYRVKPGQTIAV 141


>gi|312198709|ref|YP_004018770.1| acyltransferase [Frankia sp. EuI1c]
 gi|311230045|gb|ADP82900.1| acyltransferase 3 [Frankia sp. EuI1c]
          Length = 902

 Score = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 9/102 (8%), Positives = 24/102 (23%), Gaps = 4/102 (3%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
            D      +           +  D     ++ S+     +               +    
Sbjct: 8   RDGEAEGEDRFAGRATGPARDEGDPAGPDRRGSAGLRDRADGTGPGRAARGPGDRARPGY 67

Query: 317 AKGIHSSFLSD--SGQREENHRRSPSFPS--KRSLRRTSAKK 354
                +         + +   RR+P +    +R  RR +  +
Sbjct: 68  GPAARTGRDQQEERAREDRPGRRAPGWDGEERRDPRRDAIAR 109



 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 10/95 (10%), Positives = 23/95 (24%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           ++ G   L +          +     R RP           + ++ + +     +     
Sbjct: 36  DRRGSAGLRDRADGTGPGRAARGPGDRARPGYGPAARTGRDQQEERAREDRPGRRAPGWD 95

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
               R      +    G          +R +  RR
Sbjct: 96  GEERRDPRRDAIARPGGGRRDDEWPPARRPDGDRR 130



 Score = 44.0 bits (102), Expect = 0.036,   Method: Composition-based stats.
 Identities = 13/110 (11%), Positives = 20/110 (18%), Gaps = 4/110 (3%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           GP   E      D    +      D             R +          + ++     
Sbjct: 24  GPARDEGDPAGPDRRGSAGLRDRADGTGPGRAARGPGDRARPGYGPAARTGRDQQEERAR 83

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRS----PSFPSKRSLRRTS 351
             R                  D+  R    RR     P+       R   
Sbjct: 84  EDRPGRRAPGWDGEERRDPRRDAIARPGGGRRDDEWPPARRPDGDRRPVR 133



 Score = 41.3 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 11/115 (9%), Positives = 21/115 (18%), Gaps = 6/115 (5%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA-TP 304
           G    E+            E          S    D            G   + +    P
Sbjct: 10  GEAEGEDRFAGRATGPARDEGDPAGPDRRGSAGLRDRADGTGPGRAARGPGDRARPGYGP 69

Query: 305 VHRRNLASNVWMAKGIHSSFLSDS-----GQREENHRRSPSFPSKRSLRRTSAKK 354
             R         A+       +        +       +     +R      A++
Sbjct: 70  AARTGRDQQEERAREDRPGRRAPGWDGEERRDPRRDAIARPGGGRRDDEWPPARR 124



 Score = 39.8 bits (91), Expect = 0.60,   Method: Composition-based stats.
 Identities = 17/112 (15%), Positives = 30/112 (26%), Gaps = 7/112 (6%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R   GP           A     +   R R +        +   ++   +++ +++    
Sbjct: 54  RAARGPGDRARPGYGPAARTGRDQQEERAREDRPGRRAPGWDGEERRDPRRDAIARPGGG 113

Query: 302 AT----PVHRRN---LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
                 P  RR         W  +       S          RS + PS RS
Sbjct: 114 RRDDEWPPARRPDGDRRPVRWSDEPEGDDGFSPPTTPVPRGPRSRTGPSDRS 165


>gi|238898903|ref|YP_002924585.1| 30S ribosomal subunit protein S4 [Candidatus Hamiltonella defensa
           5AT (Acyrthosiphon pisum)]
 gi|259495283|sp|C4K794|RS4_HAMD5 RecName: Full=30S ribosomal protein S4
 gi|229466663|gb|ACQ68437.1| 30S ribosomal subunit protein S4 [Candidatus Hamiltonella defensa
           5AT (Acyrthosiphon pisum)]
          Length = 206

 Score = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 11/60 (18%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  +++  + + VN  ++   +  V   D + V     +++   
Sbjct: 97  RLDNVVYRIGFGATRAEARQLVTHKAILVNDRVVNIPSFLVSPNDRVSVRRKAQKQSRIK 156


>gi|225682980|gb|EEH21264.1| conserved hypothetical protein [Paracoccidioides brasiliensis Pb03]
          Length = 513

 Score = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 23/54 (42%), Gaps = 1/54 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+   I RA  AS  R+  + +    V VNG  ++     +   D  +VD   +
Sbjct: 126 RLDVAIFRAMFASSTRQARQFVLHGSVTVNGKKMKYPGYLLNPGDLFQVDPERV 179


>gi|261419331|ref|YP_003253013.1| RNA-binding S4 domain protein [Geobacillus sp. Y412MC61]
 gi|319766147|ref|YP_004131648.1| RNA-binding S4 domain protein [Geobacillus sp. Y412MC52]
 gi|261375788|gb|ACX78531.1| RNA-binding S4 domain protein [Geobacillus sp. Y412MC61]
 gi|317111013|gb|ADU93505.1| RNA-binding S4 domain protein [Geobacillus sp. Y412MC52]
          Length = 257

 Score = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 10/45 (22%), Positives = 21/45 (46%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           R+  V+A+A   +R +   ++    VKVN  ++++        D 
Sbjct: 182 RLDAVLAQAFRLAREKARALVESGLVKVNWKVVDKPDFLCGPGDV 226


>gi|251797775|ref|YP_003012506.1| ribosomal protein S4 [Paenibacillus sp. JDR-2]
 gi|247545401|gb|ACT02420.1| ribosomal protein S4 [Paenibacillus sp. JDR-2]
          Length = 199

 Score = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  ++ R G A SR    ++++   V VNG  ++ A+  V + D I
Sbjct: 92  RLDNLVFRLGFANSRAGARQLVSHGHVTVNGKKVDIASYTVSTGDVI 138


>gi|82701924|ref|YP_411490.1| 30S ribosomal protein S4 [Nitrosospira multiformis ATCC 25196]
 gi|90101698|sp|Q2YAX3|RS4_NITMU RecName: Full=30S ribosomal protein S4
 gi|82409989|gb|ABB74098.1| SSU ribosomal protein S4P [Nitrosospira multiformis ATCC 25196]
          Length = 208

 Score = 46.3 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V  R G   SR E  +++    + VNG  +   +  V   D IEV
Sbjct: 99  RLDTVSYRMGFGASRSEARQIVRHNGILVNGRRINIPSYQVKPGDVIEV 147


>gi|324993402|gb|EGC25322.1| S4 domain-containing protein YlmH [Streptococcus sanguinis SK405]
 gi|324995286|gb|EGC27198.1| S4 domain-containing protein YlmH [Streptococcus sanguinis SK678]
          Length = 261

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 13/48 (27%), Positives = 25/48 (52%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K++A     SR +  ++I+ + VK+N  + +  +  V   D I V
Sbjct: 184 RLDKLVASTFKLSRNQAAQLISGKHVKMNYAVNDNPSQQVGLEDLISV 231


>gi|317471103|ref|ZP_07930475.1| S4 domain-containing protein [Anaerostipes sp. 3_2_56FAA]
 gi|316901417|gb|EFV23359.1| S4 domain-containing protein [Anaerostipes sp. 3_2_56FAA]
          Length = 79

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR       +  RV VNG   + A  +V   D I +
Sbjct: 1  MRLDKFLKVSRLIKRRTVANEACSAGRVTVNGKTAK-AGTDVKPGDEIRI 49


>gi|170758649|ref|YP_001787208.1| hemolysin A [Clostridium botulinum A3 str. Loch Maree]
 gi|169405638|gb|ACA54049.1| hemolysin A [Clostridium botulinum A3 str. Loch Maree]
          Length = 273

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 11/60 (18%), Positives = 25/60 (41%), Gaps = 1/60 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+  ++   GI  SR   +  I    + ++G  +++    +  + +IE  G  L  
Sbjct: 3  EKKERLDLLLVEKGIFQSRERAKASIMAGEIFIDGNRIDKCGEKIKESANIEFRGEKLPY 62


>gi|170754365|ref|YP_001781431.1| hemolysin A [Clostridium botulinum B1 str. Okra]
 gi|169119577|gb|ACA43413.1| hemolysin A [Clostridium botulinum B1 str. Okra]
          Length = 273

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 11/60 (18%), Positives = 25/60 (41%), Gaps = 1/60 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+  ++   GI  SR   +  I    + ++G  +++    +  + +IE  G  L  
Sbjct: 3  EKKERLDLLLVEKGIFQSRERAKASIMAGEIFIDGNRIDKCGEKIKESANIEFRGEKLPY 62


>gi|125717514|ref|YP_001034647.1| hypothetical protein SSA_0659 [Streptococcus sanguinis SK36]
 gi|125497431|gb|ABN44097.1| Conserved hypothetical protein [Streptococcus sanguinis SK36]
 gi|325697073|gb|EGD38960.1| S4 domain-containing protein YlmH [Streptococcus sanguinis SK160]
 gi|327461676|gb|EGF08007.1| S4 domain-containing protein YlmH [Streptococcus sanguinis SK1]
 gi|327489529|gb|EGF21322.1| S4 domain-containing protein YlmH [Streptococcus sanguinis SK1058]
          Length = 261

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 13/48 (27%), Positives = 25/48 (52%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K++A     SR +  ++I+ + VK+N  + +  +  V   D I V
Sbjct: 184 RLDKLVASTFKLSRNQAAQLISGKHVKMNYAVNDNPSQQVGLEDLISV 231


>gi|115376377|ref|ZP_01463614.1| hemolysin A [Stigmatella aurantiaca DW4/3-1]
 gi|310822663|ref|YP_003955021.1| hemolysin a [Stigmatella aurantiaca DW4/3-1]
 gi|115366584|gb|EAU65582.1| hemolysin A [Stigmatella aurantiaca DW4/3-1]
 gi|309395735|gb|ADO73194.1| Hemolysin A [Stigmatella aurantiaca DW4/3-1]
          Length = 246

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 11/61 (18%), Positives = 25/61 (40%), Gaps = 1/61 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
              +R+  ++   G+A SR + + +I   +V V    +++    V     + + G  L 
Sbjct: 2  KPRKERLDILVVERGLAESRTKAQALILAGQVVVGDQRVDKPGALVPVEAEMRLKGEVLP 61

Query: 69 K 69
           
Sbjct: 62 Y 62


>gi|228916535|ref|ZP_04080101.1| RNA-binding S4 domain protein [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228935213|ref|ZP_04098039.1| RNA-binding S4 domain protein [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228824378|gb|EEM70184.1| RNA-binding S4 domain protein [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228843114|gb|EEM88196.1| RNA-binding S4 domain protein [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
          Length = 241

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+  I    VKVN   +E+ +      D   V G
Sbjct: 166 RLDVMLAEMLHISRQKVQPFIKNGLVKVNWKTVEQTSYECYPGDVFSVRG 215


>gi|229140546|ref|ZP_04269101.1| RNA-binding S4 domain protein [Bacillus cereus BDRD-ST26]
 gi|229198009|ref|ZP_04324723.1| RNA-binding S4 domain protein [Bacillus cereus m1293]
 gi|228585488|gb|EEK43592.1| RNA-binding S4 domain protein [Bacillus cereus m1293]
 gi|228643107|gb|EEK99383.1| RNA-binding S4 domain protein [Bacillus cereus BDRD-ST26]
          Length = 241

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+  I    VKVN   +E+ +      D   V G
Sbjct: 166 RLDVMLAEMLHISRQKVQPFIKNGLVKVNWKTVEQTSYECYPGDVFSVRG 215


>gi|195728815|gb|ACG50728.1| VtaA12 precursor [Haemophilus parasuis]
          Length = 1681

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 14/108 (12%), Positives = 24/108 (22%), Gaps = 1/108 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           GP   +  + +         T                 +       + G +       P 
Sbjct: 817 GPRGEKGLKGDKGEQGDRGPTGEAGPKGEAGPAGAKGDQGPPGERGERGPAGATGQTGPA 876

Query: 306 HRRNLASNVWMAKGIH-SSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             R    +              + G+R E   R P+ P      R  A
Sbjct: 877 GPRGPKGDPGQKGDAGLQGPAGERGERGETGERGPAGPVGPVGPRGPA 924


>gi|170079381|ref|YP_001736019.1| S4 domain-containing protein [Synechococcus sp. PCC 7002]
 gi|169887050|gb|ACB00764.1| S4 domain protein [Synechococcus sp. PCC 7002]
          Length = 253

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 2/65 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             K  +       R+   I  AG+  SR ++   IA   V+VN   + +++ NV + D I
Sbjct: 166 PKKKELTTVEASLRLD-AIGSAGLGMSRTKMAEAIASGNVRVNWKTITQSSYNVKAGDLI 224

Query: 61  EVDGV 65
            + G 
Sbjct: 225 SLRGK 229


>gi|126643072|ref|YP_001086056.1| 30S ribosomal protein S4 [Acinetobacter baumannii ATCC 17978]
          Length = 140

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+  V+ R G  S R E  ++++ + + +NG  +  A++ V + D I V
Sbjct: 31 RLDNVVYRMGFGSTRAEARQLVSHRSITLNGRRVNIASIQVKAGDVIAV 79


>gi|115376109|ref|ZP_01463354.1| ribosomal protein S4 [Stigmatella aurantiaca DW4/3-1]
 gi|310821021|ref|YP_003953379.1| 30S ribosomal protein S4 [Stigmatella aurantiaca DW4/3-1]
 gi|115366924|gb|EAU65914.1| ribosomal protein S4 [Stigmatella aurantiaca DW4/3-1]
 gi|309394093|gb|ADO71552.1| 30S ribosomal protein S4 [Stigmatella aurantiaca DW4/3-1]
          Length = 208

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R E  +++      VNG  +   +  V     +EV
Sbjct: 99  RLDNVVFRMGFADTRNEARQLVRHGHFSVNGKKVNIPSFAVKPGSSVEV 147


>gi|28377426|ref|NP_784318.1| hypothetical protein lp_0541 [Lactobacillus plantarum WCFS1]
 gi|254555609|ref|YP_003062026.1| hypothetical protein JDM1_0440 [Lactobacillus plantarum JDM1]
 gi|300768959|ref|ZP_07078850.1| S4 domain protein [Lactobacillus plantarum subsp. plantarum ATCC
          14917]
 gi|308179639|ref|YP_003923767.1| hypothetical protein LPST_C0450 [Lactobacillus plantarum subsp.
          plantarum ST-III]
 gi|28270258|emb|CAD63159.1| unknown [Lactobacillus plantarum WCFS1]
 gi|254044536|gb|ACT61329.1| conserved hypothetical protein [Lactobacillus plantarum JDM1]
 gi|300493480|gb|EFK28657.1| S4 domain protein [Lactobacillus plantarum subsp. plantarum ATCC
          14917]
 gi|308045130|gb|ADN97673.1| hypothetical protein LPST_C0450 [Lactobacillus plantarum subsp.
          plantarum ST-III]
          Length = 95

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 18/89 (20%), Positives = 33/89 (37%), Gaps = 2/89 (2%)

Query: 13 PQRVSKVIARAGIASRREVERMIAQ-QRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKA 70
            R+ K +  + I  RR V + IA   R+++NG + + ++ V+V     I      L   
Sbjct: 2  SMRLDKFLKVSRIIKRRSVAKEIADKGRIQINGKVAKSSSNVSVDDELIISFGNKTLTVK 61

Query: 71 ERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
              L    K    +      +   T + 
Sbjct: 62 VTQLLETTKKNDAELMYDIISEDYKTDYR 90


>gi|313836059|gb|EFS73773.1| ribosomal protein S4 [Propionibacterium acnes HL037PA2]
 gi|314929595|gb|EFS93426.1| ribosomal protein S4 [Propionibacterium acnes HL044PA1]
 gi|314970518|gb|EFT14616.1| ribosomal protein S4 [Propionibacterium acnes HL037PA3]
 gi|328906196|gb|EGG25971.1| 30S ribosomal protein S4 [Propionibacterium sp. P08]
          Length = 201

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR+  ++++     VNG  +   +  V + D I+V
Sbjct: 92  RLDNVVYRAGLAATRRQARQLVSHGHFLVNGKKVNIPSYRVSTHDIIDV 140


>gi|300309481|ref|YP_003773573.1| 30S ribosomal protein S4 [Herbaspirillum seropedicae SmR1]
 gi|300072266|gb|ADJ61665.1| 30S ribosomal subunit S4 protein [Herbaspirillum seropedicae SmR1]
          Length = 207

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG ++  A+ +V + D I V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKALTVNGQVVNIASYSVKAGDVIAV 146


>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 = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 5/61 (8%)

Query: 6  IVQENFTPQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
          ++ +N  P+R+ K IAR        SR  + R+I    V+V+G +   A   V+    I 
Sbjct: 9  VIADNP-PKRLDKAIARDVPEEANLSRTRLARLIESGGVEVDGAVASDAKARVLEGAQIV 67

Query: 62 V 62
          +
Sbjct: 68 I 68


>gi|168184566|ref|ZP_02619230.1| hemolysin A [Clostridium botulinum Bf]
 gi|237795295|ref|YP_002862847.1| putative hemolysin A [Clostridium botulinum Ba4 str. 657]
 gi|182672367|gb|EDT84328.1| hemolysin A [Clostridium botulinum Bf]
 gi|229261315|gb|ACQ52348.1| putative hemolysin A [Clostridium botulinum Ba4 str. 657]
          Length = 273

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 11/60 (18%), Positives = 25/60 (41%), Gaps = 1/60 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+  ++   GI  SR   +  I    + ++G  +++    +  + +IE  G  L  
Sbjct: 3  EKKERLDLLLVEKGIFQSRERAKASIMAGEIFIDGNRIDKCGEKIKESANIEFRGEKLPY 62


>gi|149926591|ref|ZP_01914851.1| 30S ribosomal protein S4 [Limnobacter sp. MED105]
 gi|149824520|gb|EDM83736.1| 30S ribosomal protein S4 [Limnobacter sp. MED105]
          Length = 207

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +   + +V   D I +
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAILVNGKAVNIPSYSVKLNDVISI 146


>gi|117918681|ref|YP_867873.1| 30S ribosomal protein S4 [Shewanella sp. ANA-3]
 gi|152112261|sp|A0KRP8|RS4_SHESA RecName: Full=30S ribosomal protein S4
 gi|117611013|gb|ABK46467.1| SSU ribosomal protein S4P [Shewanella sp. ANA-3]
          Length = 206

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V + D + +
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKSIMVNGRVVNIPSFKVSANDVVSI 145


>gi|260597188|ref|YP_003209759.1| ATP-dependent RNA helicase RhlE [Cronobacter turicensis z3032]
 gi|260216365|emb|CBA29399.1| Putative ATP-dependent RNA helicase rhlE [Cronobacter turicensis
           z3032]
          Length = 500

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 10/80 (12%), Positives = 22/80 (27%)

Query: 273 NIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQRE 332
                  +   R     ++  G   +++           S     +G   S         
Sbjct: 419 EGSRSSGERARRPAGEGNRPAGERSRRQDGEGNRPSGERSRRPAGEGNRPSGERSRRPAG 478

Query: 333 ENHRRSPSFPSKRSLRRTSA 352
           E +R + + P  R   R ++
Sbjct: 479 EGNRPASAKPRARRAPRKAS 498



 Score = 40.2 bits (92), Expect = 0.45,   Method: Composition-based stats.
 Identities = 16/125 (12%), Positives = 29/125 (23%), Gaps = 4/125 (3%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE+ +  +        +    +                       P         SS + 
Sbjct: 368 REIPRMAIAGYEPDPSIPAEPIVNGRQGRGGRGGQGGGGGRGQGQPRRQDGEGSRSSGER 427

Query: 294 GLSKQKKLATPVHRRNLA--SNVWMAKGIHSSFLSDSGQREENHR-RSPSFPSKRSLR-R 349
                 +   P   R+           G  S   +  G R    R R P+    R    +
Sbjct: 428 ARRPAGEGNRPAGERSRRQDGEGNRPSGERSRRPAGEGNRPSGERSRRPAGEGNRPASAK 487

Query: 350 TSAKK 354
             A++
Sbjct: 488 PRARR 492



 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 5/117 (4%), Positives = 24/117 (20%), Gaps = 1/117 (0%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           ++ +          +  +  +  +   +                    +++        +
Sbjct: 367 QREIPRMAIAGYEPDPSIPAEPIVNGRQGRGGRGGQGGGGGRGQGQPRRQDGEGSRSSGE 426

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           + +       R          G  +    +  +R       PS   +         +
Sbjct: 427 RARRPAGEGNRPAGERSRRQDGEGNRPSGERSRRPAGEGNRPS-GERSRRPAGEGNR 482


>gi|288942048|ref|YP_003444288.1| 30S ribosomal protein S4 [Allochromatium vinosum DSM 180]
 gi|288897420|gb|ADC63256.1| ribosomal protein S4 [Allochromatium vinosum DSM 180]
          Length = 206

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 29/49 (59%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V + DH+EV
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKGILVNGRIVNIASYQVNADDHVEV 145


>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 = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 27/226 (11%), Positives = 58/226 (25%), Gaps = 41/226 (18%)

Query: 22  RAGIASRREVERMIA----QQRVKVNGILLERAAVNVMSTDHIEVD-------------- 63
             G++SR     +I      +R+KV+G +  +    V + + I+++              
Sbjct: 24  ELGLSSR-----LIRSAAIDKRIKVDG-VAVKMNYVVKTGEEIKIELSKKESQNIEPEKM 77

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
            + +   +   L L  KP  +V         +     L              ++   +  
Sbjct: 78  DIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYFKESNQDCIVRLVSRLDMNT 137

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
                                        +     NL +K   I    Y   + T+    
Sbjct: 138 SGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLEEKEGTINRPIYRPAEDTIKRVV 197

Query: 180 -DTQKGSNAWVTVG------------LREGKNREIKKVFEFFNWKV 212
            +  + S     V             L  G+  +I+         +
Sbjct: 198 DERGQESITHYKVIESYNGADLVECLLETGRTHQIRVHLSSLGHPI 243


>gi|59710868|ref|YP_203644.1| 30S ribosomal protein S4 [Vibrio fischeri ES114]
 gi|197334188|ref|YP_002155020.1| ribosomal protein S4 [Vibrio fischeri MJ11]
 gi|75507103|sp|Q5E890|RS4_VIBF1 RecName: Full=30S ribosomal protein S4
 gi|226695098|sp|B5FGE0|RS4_VIBFM RecName: Full=30S ribosomal protein S4
 gi|59478969|gb|AAW84756.1| 30S ribosomal subunit protein S4 [Vibrio fischeri ES114]
 gi|197315678|gb|ACH65125.1| ribosomal protein S4 [Vibrio fischeri MJ11]
          Length = 206

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V + D + +
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKSILVNGKVVNVPSFKVAANDVVSI 145


>gi|30263899|ref|NP_846276.1| S4 domain-containing protein [Bacillus anthracis str. Ames]
 gi|47529329|ref|YP_020678.1| s4 domain-containing protein [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49186747|ref|YP_029999.1| S4 domain-containing protein [Bacillus anthracis str. Sterne]
 gi|65321226|ref|ZP_00394185.1| COG2302: Uncharacterized conserved protein, contains S4-like domain
           [Bacillus anthracis str. A2012]
 gi|165872308|ref|ZP_02216945.1| S4 domain protein [Bacillus anthracis str. A0488]
 gi|167641130|ref|ZP_02399385.1| S4 domain protein [Bacillus anthracis str. A0193]
 gi|170708812|ref|ZP_02899248.1| S4 domain protein [Bacillus anthracis str. A0389]
 gi|177654925|ref|ZP_02936642.1| S4 domain protein [Bacillus anthracis str. A0174]
 gi|190566209|ref|ZP_03019128.1| S4 domain protein [Bacillus anthracis Tsiankovskii-I]
 gi|227813193|ref|YP_002813202.1| S4 domain protein [Bacillus anthracis str. CDC 684]
 gi|229601099|ref|YP_002868133.1| S4 domain protein [Bacillus anthracis str. A0248]
 gi|254735937|ref|ZP_05193643.1| S4 domain protein [Bacillus anthracis str. Western North America
           USA6153]
 gi|254751005|ref|ZP_05203044.1| S4 domain protein [Bacillus anthracis str. Vollum]
 gi|254757937|ref|ZP_05209964.1| S4 domain protein [Bacillus anthracis str. Australia 94]
 gi|30258543|gb|AAP27762.1| S4 domain protein [Bacillus anthracis str. Ames]
 gi|47504477|gb|AAT33153.1| S4 domain protein [Bacillus anthracis str. 'Ames Ancestor']
 gi|49180674|gb|AAT56050.1| S4 domain protein [Bacillus anthracis str. Sterne]
 gi|164711984|gb|EDR17524.1| S4 domain protein [Bacillus anthracis str. A0488]
 gi|167510910|gb|EDR86301.1| S4 domain protein [Bacillus anthracis str. A0193]
 gi|170126297|gb|EDS95188.1| S4 domain protein [Bacillus anthracis str. A0389]
 gi|172080436|gb|EDT65523.1| S4 domain protein [Bacillus anthracis str. A0174]
 gi|190563128|gb|EDV17094.1| S4 domain protein [Bacillus anthracis Tsiankovskii-I]
 gi|227003302|gb|ACP13045.1| S4 domain protein [Bacillus anthracis str. CDC 684]
 gi|229265507|gb|ACQ47144.1| S4 domain protein [Bacillus anthracis str. A0248]
          Length = 255

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+  I    VKVN   +E+ +      D   V G
Sbjct: 180 RLDVMLAEMLHISRQKVQPFIKNGLVKVNWKTVEQTSYECYPGDVFSVRG 229


>gi|324327796|gb|ADY23056.1| S4 domain protein [Bacillus thuringiensis serovar finitimus
           YBT-020]
          Length = 255

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+  I    VKVN   +E+ +      D   V G
Sbjct: 180 RLDVMLAEMLHISRQKVQPFIKNGLVKVNWKTVEQTSYECYPGDVFSVRG 229


>gi|296393973|ref|YP_003658857.1| hemolysin A [Segniliparus rotundus DSM 44985]
 gi|296181120|gb|ADG98026.1| hemolysin A [Segniliparus rotundus DSM 44985]
          Length = 269

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 1/61 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          R+ + + R G+A SR +   +IAQ RV   G L ++ A  V     + V+  P      +
Sbjct: 7  RLDRELVRRGLARSREQAGSLIAQGRVFAGGKLAKKPACAVSEGTEVRVESDPAEPDWAS 66

Query: 74 R 74
          R
Sbjct: 67 R 67


>gi|229019100|ref|ZP_04175935.1| RNA-binding S4 domain protein [Bacillus cereus AH1273]
 gi|229025344|ref|ZP_04181762.1| RNA-binding S4 domain protein [Bacillus cereus AH1272]
 gi|228735929|gb|EEL86506.1| RNA-binding S4 domain protein [Bacillus cereus AH1272]
 gi|228742200|gb|EEL92365.1| RNA-binding S4 domain protein [Bacillus cereus AH1273]
          Length = 241

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+ +I    VKVN   +E+ A      D   + G
Sbjct: 166 RLDVLLAEMLHISRQKVQPLIKGGLVKVNWKTVEQTAYECFPGDVFSIRG 215


>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 = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 30/244 (12%), Positives = 65/244 (26%), Gaps = 37/244 (15%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M+  N+ V++ F   R+   +++     SR  ++ +I +  V VN    ++    +   D
Sbjct: 1   MEKINLQVEKEFDNVRLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNK-EKKRNYKLKVRD 59

Query: 59  HIEVD-GVP-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           +IEV+   P             +   ++  + +      +V         + V   L   
Sbjct: 60  NIEVNIPEPKLLQIEPEDINLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNALLHHC 119

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-------- 156
                  G         +     G L       S   L                      
Sbjct: 120 KDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGIIK 179

Query: 157 ------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                             K  V++   +      +  +  ++  V   L  G+  +I+  
Sbjct: 180 DEQGTIEAPIGRHPVDRIKMAVVKDGRHAVTHYKVIERFKNHTLVECRLETGRTHQIRVH 239

Query: 205 FEFF 208
               
Sbjct: 240 MSHI 243


>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 = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 22/113 (19%), Positives = 38/113 (33%), Gaps = 18/113 (15%)

Query: 10  NFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--EVDG 64
           + T  R+   +A + +   ASR  V R I    VKVNG    + A  V   D +  E++G
Sbjct: 63  DDTSPRLDAYVASSVVDASASRARVARAIKASMVKVNGKTERKPARGVKPGDIVEGELEG 122

Query: 65  VP-------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
                          +   + + L +      +    +     + V   L   
Sbjct: 123 ERRSEAIPEPSIELDIVYEDESVLVVCKPAGMVTHPSAGHARGTLVNAVLGHC 175


>gi|52141591|ref|YP_085238.1| S4 domain-containing protein [Bacillus cereus E33L]
 gi|51975060|gb|AAU16610.1| S4 domain protein [Bacillus cereus E33L]
          Length = 255

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+  I    VKVN   +E+ +      D   V G
Sbjct: 180 RLDVMLAEMLHISRQKVQPFIKNGLVKVNWKTVEQTSYECYPGDVFSVRG 229


>gi|238763710|ref|ZP_04624669.1| 30S ribosomal protein S4 [Yersinia kristensenii ATCC 33638]
 gi|238698012|gb|EEP90770.1| 30S ribosomal protein S4 [Yersinia kristensenii ATCC 33638]
          Length = 154

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 45  RLDNVVYRMGFGATRAESRQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 104

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 105 AALELAEQREKPT 117


>gi|229162833|ref|ZP_04290790.1| RNA-binding S4 domain protein [Bacillus cereus R309803]
 gi|228620715|gb|EEK77584.1| RNA-binding S4 domain protein [Bacillus cereus R309803]
          Length = 241

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+ +I    VKVN   +E+ +      D   V G
Sbjct: 166 RLDVMLAEMLHVSRQKVQPLIRNGLVKVNWKTVEQTSYECYPGDVFSVRG 215


>gi|42520265|ref|NP_966180.1| 30S ribosomal protein S4 [Wolbachia endosymbiont of Drosophila
           melanogaster]
 gi|225630200|ref|YP_002726991.1| ribosomal protein S4 [Wolbachia sp. wRi]
 gi|81652701|sp|Q73HZ8|RS4_WOLPM RecName: Full=30S ribosomal protein S4
 gi|254764623|sp|C0R2Q8|RS4_WOLWR RecName: Full=30S ribosomal protein S4
 gi|42410003|gb|AAS14114.1| ribosomal protein S4 [Wolbachia endosymbiont of Drosophila
           melanogaster]
 gi|225592181|gb|ACN95200.1| ribosomal protein S4 [Wolbachia sp. wRi]
          Length = 204

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 27/52 (51%), Gaps = 7/52 (13%)

Query: 15  RVSKVIARAG----IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+S V+  +G    I S    +++I+ + V VN  ++  ++  V   D I++
Sbjct: 94  RLSSVLYHSGLVPTIYS---AKQLISHKHVTVNDKVVNISSYRVKPGDIIKI 142


>gi|86148804|ref|ZP_01067071.1| 30S ribosomal protein S4 [Vibrio sp. MED222]
 gi|148982227|ref|ZP_01816653.1| 30S ribosomal protein S4 [Vibrionales bacterium SWAT-3]
 gi|218710725|ref|YP_002418346.1| 30S ribosomal protein S4 [Vibrio splendidus LGP32]
 gi|254764622|sp|B7VLD3|RS4_VIBSL RecName: Full=30S ribosomal protein S4
 gi|85833394|gb|EAQ51585.1| 30S ribosomal protein S4 [Vibrio sp. MED222]
 gi|145960589|gb|EDK25942.1| 30S ribosomal protein S4 [Vibrionales bacterium SWAT-3]
 gi|218323744|emb|CAV20098.1| ribosomal protein S4 [Vibrio splendidus LGP32]
          Length = 206

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V + D + +
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKSILVNGKVVNVPSFKVAANDVVSI 145


>gi|302036692|ref|YP_003797014.1| 30S ribosomal protein S4 [Candidatus Nitrospira defluvii]
 gi|300604756|emb|CBK41088.1| 30S ribosomal protein S4 [Candidatus Nitrospira defluvii]
          Length = 208

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   SR+E  +++    + +NG  ++     V + D +EV
Sbjct: 99  RLDNVVYRLGFGASRKEARQLVNHGHMMINGRKVKAPGALVKAGDSVEV 147


>gi|296131553|ref|YP_003638800.1| RNA-binding S4 domain protein [Thermincola sp. JR]
 gi|296030131|gb|ADG80899.1| RNA-binding S4 domain protein [Thermincola potens JR]
          Length = 74

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 2/65 (3%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          M+ KNI  E     ++ + +  A I S   E + MIA   +KVNG +  R    +   D 
Sbjct: 1  MQVKNIFIET-ETIKLDQFLKWATIVSTGGEAKNMIAGGSIKVNGEIELRRGRQLRHEDI 59

Query: 60 IEVDG 64
          +EV G
Sbjct: 60 VEVTG 64


>gi|282883330|ref|ZP_06291924.1| ribosomal protein S4 [Peptoniphilus lacrimalis 315-B]
 gi|300813858|ref|ZP_07094163.1| ribosomal protein S4 [Peptoniphilus sp. oral taxon 836 str. F0141]
 gi|281296834|gb|EFA89336.1| ribosomal protein S4 [Peptoniphilus lacrimalis 315-B]
 gi|300512045|gb|EFK39240.1| ribosomal protein S4 [Peptoniphilus sp. oral taxon 836 str. F0141]
          Length = 198

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 14/80 (17%), Positives = 31/80 (38%), Gaps = 3/80 (3%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRKAE 71
           R+  +  R G AS  R+  +M+    + VNG  ++  +     +D I +   G  +   +
Sbjct: 89  RLDNLCYRLGFASSIRQARQMVLHGHILVNGKKVDIPSYRCDVSDEISLSRKGKKVELFK 148

Query: 72  RTRLWLYHKPIGLVTTHSDP 91
                 +      ++ + D 
Sbjct: 149 ENFNTNFPVSYPYLSKNEDF 168


>gi|229031529|ref|ZP_04187529.1| RNA-binding S4 domain protein [Bacillus cereus AH1271]
 gi|228729818|gb|EEL80798.1| RNA-binding S4 domain protein [Bacillus cereus AH1271]
          Length = 241

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+  I    VKVN   +E+ +      D   V G
Sbjct: 166 RLDVMLAEMLHISRQKVQPFIKNGLVKVNWKTVEQTSYECYPGDVFSVRG 215


>gi|291520799|emb|CBK79092.1| hemolysin TlyA family protein [Coprococcus catus GD/7]
          Length = 271

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 22/179 (12%), Positives = 49/179 (27%), Gaps = 3/179 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE 71
           +R+  ++ +  +A SR + + +I    V VNG   ++A          IE+ G  L    
Sbjct: 3   ERLDVLLVKRNLAESREKAKAIIMSGNVFVNGNREDKAGTTFDEEKAQIEIKGHTLPYVS 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R  L L                              ++  G   + +  +        L 
Sbjct: 63  RGGLKLEKAIEVFGVDVKGKVCMDIGAST-GGFTDCMLQNGADHVYSIDVGRGQLAWKLR 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +   +   +   +  V      ++     +    +      G  +  L         + 
Sbjct: 122 QDPRVICMEKTNIRYVTSEQIPEKIDFASVDVSFISLKKVLGPARELLQDDARMVCLIK 180


>gi|265999712|ref|ZP_05467499.2| translation initiation factor IF-2 [Brucella melitensis bv. 2 str.
           63/9]
 gi|263095450|gb|EEZ19051.1| translation initiation factor IF-2 [Brucella melitensis bv. 2 str.
           63/9]
          Length = 834

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 13/116 (11%), Positives = 28/116 (24%), Gaps = 2/116 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R + +  +RE +        +    A   +      +         +   + +  + +K 
Sbjct: 36  RALEEAQIRE-VEERARAVEEAKRRAEEDARRAKEHEESARRQAEEEARLKAEAEARRKA 94

Query: 294 GLSKQKKLATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                K++  P  R     +   A  G                   P   S R   
Sbjct: 95  EEEAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAP 150



 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 11/121 (9%), Positives = 28/121 (23%), Gaps = 1/121 (0%)

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           L     REV ++  R         E           S     +    +    +   + ++
Sbjct: 38  LEEAQIREVEERA-RAVEEAKRRAEEDARRAKEHEESARRQAEEEARLKAEAEARRKAEE 96

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            ++++    + +       R           G           R +     P+     + 
Sbjct: 97  EAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAPIIADAA 156

Query: 348 R 348
            
Sbjct: 157 P 157


>gi|257054497|ref|YP_003132329.1| 30S ribosomal protein S4 [Saccharomonospora viridis DSM 43017]
 gi|256584369|gb|ACU95502.1| SSU ribosomal protein S4P [Saccharomonospora viridis DSM 43017]
          Length = 202

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 1/55 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           R+  V+ RAG+A +RR+  ++++     VNG  +   +  V   D I+V    L+
Sbjct: 92  RLDNVVYRAGLARTRRQARQLVSHGHFLVNGEKVNIPSYRVSKFDIIDVRPKSLK 146


>gi|229174564|ref|ZP_04302094.1| RNA-binding S4 domain protein [Bacillus cereus MM3]
 gi|228608869|gb|EEK66161.1| RNA-binding S4 domain protein [Bacillus cereus MM3]
          Length = 241

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+  I    VKVN   +E+ +      D   V G
Sbjct: 166 RLDVMLAEMLHISRQKVQPFIKNGLVKVNWKTVEQTSYECYPGDVFSVRG 215


>gi|326324004|gb|ADZ54068.1| virulence-associated trimeric autotransporter [Haemophilus parasuis
           SH0165]
          Length = 1047

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 11/109 (10%), Positives = 23/109 (21%), Gaps = 4/109 (3%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G       + +      +                +   + +       G +     A P 
Sbjct: 616 GKDGKNGEKGDRGEQGPAGPRGEAGPKGEAGPKGEAGPKGEAGPVGPAGPTGPAGAAGPK 675

Query: 306 HRRNLASNVWMA----KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
             +        A        +    D GQ      R P+ P   +  + 
Sbjct: 676 GEKGDPGPKGEAGSTGPTGPAGPKGDPGQAGPAGPRGPAGPKGDAGPKG 724


>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 = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 31/243 (12%), Positives = 58/243 (23%), Gaps = 38/243 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGI-LLERAAVNVMSTDHIEVD-- 63
           V + F  +RV   +AR    SR  V  +     V+ NG  L + A   + + + +EVD  
Sbjct: 8   VPDGFDGERVDAALARMTGLSRSRVGDLCEAGGVRRNGEDLAKSA--RLHAGELLEVDLP 65

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                        G+ L   +   + +              DG   +            S
Sbjct: 66  DPRPVEPVATPVEGMELLYEDEDIVVVDKPAGVAAHPSMGWDGPDVLGALKAMRVRVATS 125

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-------------- 156
                      L +   G +       +   L+                           
Sbjct: 126 GAAERQGIVSRLDVGTSGVMIVAKGERAYSVLKRAFREHTVDKVYHALVQGHLDPSSGTI 185

Query: 157 ------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                   +   K  +I+G         +           + L  G+  +I+        
Sbjct: 186 EAPIGRHPSREWKMAIIEGGRESITHYDVIEAMPGACLAEIHLETGRTHQIRVHMAAVGH 245

Query: 211 KVN 213
              
Sbjct: 246 PCV 248


>gi|307731230|ref|YP_003908454.1| 30S ribosomal protein S4 [Burkholderia sp. CCGE1003]
 gi|307585765|gb|ADN59163.1| ribosomal protein S4 [Burkholderia sp. CCGE1003]
          Length = 207

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG++    ++ V + D + V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAIMVNGVVSNIPSMQVKAGDVVAV 146


>gi|229092943|ref|ZP_04224076.1| RNA-binding S4 domain protein [Bacillus cereus Rock3-42]
 gi|229123411|ref|ZP_04252615.1| RNA-binding S4 domain protein [Bacillus cereus 95/8201]
 gi|229186138|ref|ZP_04313307.1| RNA-binding S4 domain protein [Bacillus cereus BGSC 6E1]
 gi|228597314|gb|EEK54965.1| RNA-binding S4 domain protein [Bacillus cereus BGSC 6E1]
 gi|228660187|gb|EEL15823.1| RNA-binding S4 domain protein [Bacillus cereus 95/8201]
 gi|228690447|gb|EEL44231.1| RNA-binding S4 domain protein [Bacillus cereus Rock3-42]
          Length = 241

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  ++A     SR++V+  I    VKVN   +E+ +      D   V G
Sbjct: 166 RLDVMLAEMLHISRQKVQPFIKNGLVKVNWKTVEQTSYECYPGDVFSVRG 215


>gi|147676683|ref|YP_001210898.1| 30S ribosomal protein S4 [Pelotomaculum thermopropionicum SI]
 gi|189045389|sp|A5D5E8|RS4_PELTS RecName: Full=30S ribosomal protein S4
 gi|146272780|dbj|BAF58529.1| ribosomal protein S4 and related proteins [Pelotomaculum
           thermopropionicum SI]
          Length = 208

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 20/50 (40%), Gaps = 1/50 (2%)

Query: 17  SKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
             VI R G+  SR E  +++      VNG  +   +  V   D I V   
Sbjct: 101 DNVIYRLGLGASRNEARQLVRHGHFTVNGRRVNIPSYLVKPGDVIAVRDQ 150


>gi|33152930|ref|NP_874283.1| 30S ribosomal protein S4 [Haemophilus ducreyi 35000HP]
 gi|41017830|sp|Q7VKF7|RS4_HAEDU RecName: Full=30S ribosomal protein S4
 gi|33149155|gb|AAP96672.1| 30S ribosomal protein S4 [Haemophilus ducreyi 35000HP]
          Length = 208

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R E  ++++ + + VNG ++   +  V   D + V
Sbjct: 99  RLDNVVYRMGFAATRAEARQLVSHKSIVVNGRVVNIPSYQVSVDDVVTV 147


>gi|308494100|ref|XP_003109239.1| hypothetical protein CRE_08252 [Caenorhabditis remanei]
 gi|308246652|gb|EFO90604.1| hypothetical protein CRE_08252 [Caenorhabditis remanei]
          Length = 447

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 10/75 (13%), Positives = 20/75 (26%), Gaps = 3/75 (4%)

Query: 280 DDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
                 K           ++  A P   R   +    A+   +        R    R+ P
Sbjct: 33  SPARPGKARQGPARPGKARQGPARPGKARQGPARPGKARQGPARPEG--PARPGKARQGP 90

Query: 340 SFPSKRSLRRTSAKK 354
           + P   +     A++
Sbjct: 91  ARPEGPARP-GKARQ 104



 Score = 43.2 bits (100), Expect = 0.064,   Method: Composition-based stats.
 Identities = 7/75 (9%), Positives = 19/75 (25%), Gaps = 3/75 (4%)

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
            P    + ++  ++     +         +                  +  G+  +   R
Sbjct: 33  SPARPGKARQGPARPGKARQGPARPGKARQGPARPGKARQGPARPEGPARPGKARQGPAR 92

Query: 338 --SPSFPSK-RSLRR 349
              P+ P K R   +
Sbjct: 93  PEGPARPGKARQGPK 107



 Score = 41.7 bits (96), Expect = 0.15,   Method: Composition-based stats.
 Identities = 8/104 (7%), Positives = 21/104 (20%), Gaps = 3/104 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
                   ++ +V  +  +  +  ++                 K           ++  A
Sbjct: 6   NFRRLRAAKKVRVMFNTFLVMAAMVLVSPARPGKARQGPARPGKARQGPARPGKARQGPA 65

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREE-NHRRSPSFPSKR 345
            P   R   +                  R E   R   +    +
Sbjct: 66  RPGKARQGPARPEGP--ARPGKARQGPARPEGPARPGKARQGPK 107


>gi|302337501|ref|YP_003802707.1| ribosomal protein S4 [Spirochaeta smaragdinae DSM 11293]
 gi|301634686|gb|ADK80113.1| ribosomal protein S4 [Spirochaeta smaragdinae DSM 11293]
          Length = 211

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R   A SR++  ++++   + VNG  +   +  V   D IE+
Sbjct: 100 RLDNVVYRLRFANSRKQARQLVSHGHILVNGKRVTIPSYVVRQGDEIEI 148


>gi|291549394|emb|CBL25656.1| SSU ribosomal protein S4P [Ruminococcus torques L2-14]
          Length = 197

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +R+E  +++  + V VNG  +   +  V + D IE+
Sbjct: 88  RLDNVVFRLGLARTRKEARQIVDHKHVLVNGKQVNIPSYLVKAGDVIEI 136


>gi|195729273|gb|ACG50756.1| VtaA7 [Haemophilus parasuis]
          Length = 1024

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 12/115 (10%), Positives = 33/115 (28%), Gaps = 2/115 (1%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           ++   + + +     ++  + +     +S+T+ + +     E  D   +       + G 
Sbjct: 583 ITISTIGKLIEKTEWKDGGLKITYTDGTSDTIAKGKDGKNGEKGDRGEQGPAGPRGEAGP 642

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
             +     P   R                  + GQ      R P+ P   +  + 
Sbjct: 643 RGEAGPVGPAGPRGPQGTTGAQGPK--GDKGEPGQAGPAGPRGPAGPKGDAGPKG 695


>gi|77918663|ref|YP_356478.1| rRNA methylase [Pelobacter carbinolicus DSM 2380]
 gi|77544746|gb|ABA88308.1| predicted rRNA methylase [Pelobacter carbinolicus DSM 2380]
          Length = 252

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 12/63 (19%), Positives = 28/63 (44%), Gaps = 1/63 (1%)

Query: 8  QENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
          + +   +R+ K++   G+A SR     +I   +V V    +++A   V +   + + G  
Sbjct: 3  KSSVQKERLDKLLVVRGLAQSRERARALILAGQVVVGHHTVDKAGAQVATDVSLRLKGED 62

Query: 67 LRK 69
          +  
Sbjct: 63 IPY 65


>gi|227505245|ref|ZP_03935294.1| ribosomal protein S4 [Corynebacterium striatum ATCC 6940]
 gi|227198144|gb|EEI78192.1| ribosomal protein S4 [Corynebacterium striatum ATCC 6940]
          Length = 201

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR+  ++++     VNG  +   +  V   D I+V
Sbjct: 92  RLDNVVYRAGLANTRRQARQLVSHGHFTVNGKKINVPSFQVSQYDIIDV 140


>gi|99034786|ref|ZP_01314708.1| hypothetical protein Wendoof_01000474 [Wolbachia endosymbiont of
           Drosophila willistoni TSC#14030-0811.24]
          Length = 200

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 27/52 (51%), Gaps = 7/52 (13%)

Query: 15  RVSKVIARAG----IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+S V+  +G    I S    +++I+ + V VN  ++  ++  V   D I++
Sbjct: 94  RLSSVLYHSGLVPTIYS---AKQLISHKHVTVNDKVVNISSYRVKPGDIIKI 142


>gi|187779515|ref|ZP_02995988.1| hypothetical protein CLOSPO_03111 [Clostridium sporogenes ATCC
          15579]
 gi|187773140|gb|EDU36942.1| hypothetical protein CLOSPO_03111 [Clostridium sporogenes ATCC
          15579]
          Length = 273

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 11/60 (18%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+  ++ + GI  SR   +  I    + ++G  +++    +  + +IE  G  L  
Sbjct: 3  DKKERLDLLLIKKGIFQSRERAKASIMAGEIFIDGNRVDKCGEKIKESANIEFRGEKLPY 62


>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 = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 22/230 (9%), Positives = 54/230 (23%), Gaps = 31/230 (13%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVM------------------ 55
           R+ + +A+     SR  ++  I   +V VNG ++ +A   V                   
Sbjct: 19  RLDQALAQLFPDYSRSRLKVWIENDQVWVNGKIVNKAREKVFGGELIEVQAEVEEEVRFE 78

Query: 56  ----STDHIEVDGVPLRKAERTRLWLYHKPIG---LVTTHSDPDGRSTVFDNLPSIFSRV 108
                 + +  D   +   +   L ++         V                  I  R+
Sbjct: 79  PQNIPLNIVYEDDDIIVINKPKDLVVHPGAGNPDGTVLNALLYHYPPIAEVPRAGIVHRL 138

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKK 163
                  +     +        A      + ++  +           D            
Sbjct: 139 DKDTTGLMVVAKNIPAQTHLVTALQKRHITREYEAIASGIMTQGGKVDEPMARHPTKRTA 198

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             V            +  +  +   + + L  G+  +I+         + 
Sbjct: 199 MAVHPMGKPAVTHYRIMERFRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 248


>gi|32267201|ref|NP_861233.1| hypothetical protein HH1702 [Helicobacter hepaticus ATCC 51449]
 gi|32263254|gb|AAP78299.1| conserved hypothetical protein [Helicobacter hepaticus ATCC
          51449]
          Length = 83

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 13/81 (16%), Positives = 30/81 (37%), Gaps = 4/81 (4%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ K ++   I  RR+  + M     + +N I+ +  +  V   D I +    L   + 
Sbjct: 1  MRIDKFLSSVNILKRRKLAQDMCENGVITINNIIAK-PSKEVRIGDIIHL--RYLEYTKI 57

Query: 73 TRLWLYHKPIGLVTTHSDPDG 93
           ++        +  + S+   
Sbjct: 58 YKVLAIPTTKTIPKSQSNEYF 78


>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 = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 23/206 (11%), Positives = 52/206 (25%), Gaps = 32/206 (15%)

Query: 39  RVKVNGILLERAAVNVMSTDHIEVD-GVP-------------LRKAERTRLWLYHKPIGL 84
           R+ VNG  +   +  V+  D IEVD   P             +   +   + L      +
Sbjct: 42  RLFVNGKTVR-LSYRVLEGDKIEVDVNKPESQNVDPEKMDLNIVYEDSDIIVLNKPANMI 100

Query: 85  VTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
           V    +    +     L        + ++ +          L+L      + +      +
Sbjct: 101 VHPTKNYQHGTLSNGLLYYFREKGENCIVRLVNRLDMDTSGLVLVAKNQFSHMALARDMK 160

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW------------ 188
                +                    I       ++ T+D +   +              
Sbjct: 161 LDTFKKEYIAVVRGNLSSLKGTIDKPIYKEEEEPIRRTIDDRGQESITHFEVVERYKNAD 220

Query: 189 -VTVGLREGKNREIKKVFEFFNWKVN 213
            V + L  G+  +I+         + 
Sbjct: 221 KVKLVLETGRTHQIRVHLSSIGNPII 246


>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 = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 22/240 (9%), Positives = 58/240 (24%), Gaps = 40/240 (16%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIA----QQRVKVNG-----ILLERAAVNVM- 55
           +V EN     +   +   G       +R+I     Q  + VNG       + +    +  
Sbjct: 4   VVGENEKGVILENFLRNKGF-----SKRLIRIYKWQGEILVNGIKSNVKRILQPGDVIDL 58

Query: 56  ---STD----------HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
                D           I  +   +    +    + H      +           +    
Sbjct: 59  ILPENDSNIAPEKLDLDICYEDEEILIVNKPANMVVHPTKRYQSGTLAN---GVAWYFKE 115

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL- 161
                +I            L++       +          ++Y     G+++ +    L 
Sbjct: 116 KGLKALIRPVNRLDRGTSGLVVFAKRPFMQYYLQIIKPMTKLYFAVVEGKMEGEGRIDLP 175

Query: 162 --------KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                    + +V +          +       + + V +  G+  +I+         + 
Sbjct: 176 ISRKPQSGIERMVSEEGDRAITNYKVVKSSKRFSLLKVKIETGRTHQIRVHLSHIGHPIV 235


>gi|326793582|ref|YP_004311402.1| ribosomal protein S4 [Marinomonas mediterranea MMB-1]
 gi|326544346|gb|ADZ89566.1| ribosomal protein S4 [Marinomonas mediterranea MMB-1]
          Length = 206

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG  S R E  +++  + + VNG  +  A+  V + D + +
Sbjct: 97  RLDNVVYRAGFGSTRAEARQLVGHKGILVNGETVNVASYQVKAGDVVSI 145


>gi|163853790|ref|YP_001641833.1| helicase domain-containing protein [Methylobacterium extorquens PA1]
 gi|163665395|gb|ABY32762.1| helicase domain protein [Methylobacterium extorquens PA1]
          Length = 1140

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 16/111 (14%), Positives = 29/111 (26%), Gaps = 2/111 (1%)

Query: 244  QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
              GP                 E     R +   +   +    +    +  G    +    
Sbjct: 1012 HTGPRPGRGQGRPEGRQDGRQEGRQDGRQDGRQDGRRNDGPRRPREDRPEGGRPARADGR 1071

Query: 304  PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP-SFPSKRSLRRTSAK 353
            P  RR         +  H    +   +R+EN R +P   P +R  +     
Sbjct: 1072 PDSRREGQGEGG-PRREHQGGRNRPDRRDENRRPNPEQRPPRRERQPDPDS 1121



 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 10/112 (8%), Positives = 21/112 (18%), Gaps = 1/112 (0%)

Query: 244  QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
             L                         +        D     ++N   +     + +   
Sbjct: 1005 HLHRPQRHTGPRPGRGQGRPEGRQDGRQEGRQDGRQDGRQDGRRNDGPRRPREDRPEGGR 1064

Query: 304  PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS-PSFPSKRSLRRTSAKK 354
            P        +    +G         G R    RR     P+         ++
Sbjct: 1065 PARADGRPDSRREGQGEGGPRREHQGGRNRPDRRDENRRPNPEQRPPRRERQ 1116



 Score = 40.2 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 11/92 (11%), Positives = 18/92 (19%)

Query: 253  AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
             Q              R          D     +   +     S+++       RR    
Sbjct: 1031 RQEGRQDGRQDGRQDGRRNDGPRRPREDRPEGGRPARADGRPDSRREGQGEGGPRREHQG 1090

Query: 313  NVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
                      +   +  QR     R P   S 
Sbjct: 1091 GRNRPDRRDENRRPNPEQRPPRRERQPDPDSP 1122


>gi|126176331|ref|YP_001052480.1| 30S ribosomal protein S4 [Shewanella baltica OS155]
 gi|152998773|ref|YP_001364454.1| 30S ribosomal protein S4 [Shewanella baltica OS185]
 gi|160873349|ref|YP_001552665.1| 30S ribosomal protein S4 [Shewanella baltica OS195]
 gi|217975177|ref|YP_002359928.1| 30S ribosomal protein S4 [Shewanella baltica OS223]
 gi|304412788|ref|ZP_07394390.1| ribosomal protein S4 [Shewanella baltica OS183]
 gi|307307452|ref|ZP_07587187.1| ribosomal protein S4 [Shewanella baltica BA175]
 gi|171704521|sp|A6WHV2|RS4_SHEB8 RecName: Full=30S ribosomal protein S4
 gi|171769980|sp|A3DA48|RS4_SHEB5 RecName: Full=30S ribosomal protein S4
 gi|189045397|sp|A9KWC5|RS4_SHEB9 RecName: Full=30S ribosomal protein S4
 gi|254764609|sp|B8EBI1|RS4_SHEB2 RecName: Full=30S ribosomal protein S4
 gi|125999536|gb|ABN63611.1| SSU ribosomal protein S4P [Shewanella baltica OS155]
 gi|151363391|gb|ABS06391.1| ribosomal protein S4 [Shewanella baltica OS185]
 gi|160858871|gb|ABX47405.1| ribosomal protein S4 [Shewanella baltica OS195]
 gi|217500312|gb|ACK48505.1| ribosomal protein S4 [Shewanella baltica OS223]
 gi|304348868|gb|EFM13284.1| ribosomal protein S4 [Shewanella baltica OS183]
 gi|306910240|gb|EFN40673.1| ribosomal protein S4 [Shewanella baltica BA175]
 gi|315265577|gb|ADT92430.1| ribosomal protein S4 [Shewanella baltica OS678]
          Length = 206

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V + D + +
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKSIMVNGRVVNIPSFKVSANDVVSI 145


>gi|315652327|ref|ZP_07905319.1| 30S ribosomal protein S4 [Eubacterium saburreum DSM 3986]
 gi|315485450|gb|EFU75840.1| 30S ribosomal protein S4 [Eubacterium saburreum DSM 3986]
          Length = 197

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           R+  V+ R G+  +R+E  +++  + V VNG  +   +  V   D IE+    
Sbjct: 88  RLDNVVFRMGLGRTRKETRQIVDHKHVLVNGKCVNIPSYLVKPGDVIEIKEKA 140


>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 = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 30/255 (11%), Positives = 78/255 (30%), Gaps = 57/255 (22%)

Query: 13  PQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD----- 63
           P R+ K +AR        SR  + +++ +  ++++G +++ A   V     +E+      
Sbjct: 15  PPRLDKALARDVPEEASLSRSRLAKLLDEGAIRIDGTVVQDAKARVTEGALVEITIAEAN 74

Query: 64  -----GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------- 108
                G  +      E   L +  KP G+V   +      T+ + L              
Sbjct: 75  ESHIVGQDIPLNVVYEDDDLIVIDKPAGMVVHPAPGSPDGTLVNALIHHCGESLSGVGGM 134

Query: 109 --------------------------------ISVGRLDINTEGLLLLTNDGGLARVLEL 136
                                                ++     L          RV  L
Sbjct: 135 KRPGIVHRIDKDTSGLLVAAKTDRAHHGLAALFEAHDIERRYLALCYGVLSAADPRVRGL 194

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-KGSNAWVTVGLRE 195
               +     ++   ++D+ + +  ++ ++ +G  +   +  +  +  G+ + +   L  
Sbjct: 195 KGVNFELGNILKIQTRLDRHRTDRQRQAVIWEGGRHAVTRARVVEEYNGAASLIECWLET 254

Query: 196 GKNREIKKVFEFFNW 210
           G+  +I+    +   
Sbjct: 255 GRTHQIRVHMSYVGH 269


>gi|323527577|ref|YP_004229730.1| 30S ribosomal protein S4 [Burkholderia sp. CCGE1001]
 gi|323384579|gb|ADX56670.1| ribosomal protein S4 [Burkholderia sp. CCGE1001]
          Length = 207

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG++    ++ V + D + V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAIMVNGVVSNIPSMQVKAGDVVAV 146


>gi|255994833|ref|ZP_05427968.1| ribosomal protein S4 [Eubacterium saphenum ATCC 49989]
 gi|255993546|gb|EEU03635.1| ribosomal protein S4 [Eubacterium saphenum ATCC 49989]
          Length = 195

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 1/63 (1%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+  ++ R G A+ RRE  +++      VNG  L   +  +   D I+V    +   + 
Sbjct: 87  MRLDSIVYRMGFATTRREARQLVTHGHFLVNGKKLNIPSAELKVGDVIKVKNKSVSSPKF 146

Query: 73  TRL 75
             +
Sbjct: 147 EEI 149


>gi|169335656|ref|ZP_02862849.1| hypothetical protein ANASTE_02076 [Anaerofustis stercorihominis DSM
           17244]
 gi|169258394|gb|EDS72360.1| hypothetical protein ANASTE_02076 [Anaerofustis stercorihominis DSM
           17244]
          Length = 208

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 13/51 (25%), Positives = 24/51 (47%), Gaps = 1/51 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  V+ R G AS R+E  +++      V+G  +   + +V     I+V  
Sbjct: 99  RLDNVVYRMGFASSRKEARQLVRHNHFLVDGKKVNIPSFSVKEGQVIKVKD 149


>gi|152986388|ref|YP_001350515.1| pseudouridine synthase [Pseudomonas aeruginosa PA7]
 gi|150961546|gb|ABR83571.1| pseudouridine synthase [Pseudomonas aeruginosa PA7]
          Length = 320

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 32/234 (13%), Positives = 67/234 (28%), Gaps = 36/234 (15%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGI------LLERAAVNVMST-------- 57
            QR+ ++ A+     SR  +   I   R+ V+G       ++   A  V+          
Sbjct: 17  GQRLDQIAAQLFPEHSRSRLAGWIKDGRLTVDGAAARPRDIVHSGAQLVLEAEQEAQGEW 76

Query: 58  --DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVIS 110
               IE+D   +   +   L +      +V   +     + +   L  +       R   
Sbjct: 77  VAQDIELD---IVHEDEHILVIDKPAGLVVHPAAGHQDGTLLNALLYHVPGIANVPRAGI 133

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLR-----------VYRVRFHGQVDQDKLN 159
           V RLD +T GL+++         L                    +               
Sbjct: 134 VHRLDKDTTGLMVVAKTLEAHTKLVAQLQARSVSRIYEAIVIGVITSGGTIDAPIGRHGV 193

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             +K  V+           +  +  ++    V L  G+  +I+       + + 
Sbjct: 194 QRQKMAVVDAGKVAVSHYRVLERFRAHTHTRVKLETGRTHQIRVHMSHIGYPLV 247


>gi|221133739|ref|ZP_03560044.1| 30S ribosomal protein S4 [Glaciecola sp. HTCC2999]
          Length = 206

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 28/50 (56%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G AS R E  ++++ + + VNG ++   +  V +  ++ V
Sbjct: 96  QRLDNVVYRMGFASTRAEARQLVSHKAICVNGQVVNIPSFKVSAETNVSV 145


>gi|218133259|ref|ZP_03462063.1| hypothetical protein BACPEC_01124 [Bacteroides pectinophilus ATCC
           43243]
 gi|217992132|gb|EEC58136.1| hypothetical protein BACPEC_01124 [Bacteroides pectinophilus ATCC
           43243]
          Length = 251

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 15/53 (28%), Positives = 25/53 (47%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           + +R+  VI++    SR +   M   ++V VNG   E  +  V   D + V G
Sbjct: 173 SSERLDAVISKLYNMSRSQSIEMFRDKKVFVNGRQYENNSGVVKPGDVVAVRG 225


>gi|209551387|ref|YP_002283304.1| RNA-binding S4 domain protein [Rhizobium leguminosarum bv.
          trifolii WSM2304]
 gi|209537143|gb|ACI57078.1| RNA-binding S4 domain protein [Rhizobium leguminosarum bv.
          trifolii WSM2304]
          Length = 134

 Score = 46.3 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 3/51 (5%)

Query: 14 QRVSKVI--ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          QR+ K +  AR  + SR   +  +    V+VNG   +  +  V   D IE+
Sbjct: 13 QRIDKWLFFARM-VKSRSLAQSHVQSGHVRVNGERCKHPSQMVKPGDRIEL 62


>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 = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 12/58 (20%), Positives = 26/58 (44%), Gaps = 2/58 (3%)

Query: 6  IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          IV E     R+ K + ++    SR   ++ I  +RV +N  +  + +  +   D + +
Sbjct: 10 IVNETNR-DRLDKFLVSQNPKYSRAFYQQHILDKRVTINEQIQTKVSTQLAPGDIVSI 66


>gi|126697668|ref|YP_001086565.1| 30S ribosomal protein S4 [Clostridium difficile 630]
 gi|254973759|ref|ZP_05270231.1| 30S ribosomal protein S4 [Clostridium difficile QCD-66c26]
 gi|255091149|ref|ZP_05320627.1| 30S ribosomal protein S4 [Clostridium difficile CIP 107932]
 gi|255099260|ref|ZP_05328237.1| 30S ribosomal protein S4 [Clostridium difficile QCD-63q42]
 gi|255305043|ref|ZP_05349215.1| 30S ribosomal protein S4 [Clostridium difficile ATCC 43255]
 gi|255312803|ref|ZP_05354386.1| 30S ribosomal protein S4 [Clostridium difficile QCD-76w55]
 gi|255515562|ref|ZP_05383238.1| 30S ribosomal protein S4 [Clostridium difficile QCD-97b34]
 gi|255648657|ref|ZP_05395559.1| 30S ribosomal protein S4 [Clostridium difficile QCD-37x79]
 gi|255654190|ref|ZP_05399599.1| 30S ribosomal protein S4 [Clostridium difficile QCD-23m63]
 gi|260681874|ref|YP_003213159.1| 30S ribosomal protein S4 [Clostridium difficile CD196]
 gi|260685472|ref|YP_003216605.1| 30S ribosomal protein S4 [Clostridium difficile R20291]
 gi|296449771|ref|ZP_06891540.1| 30S ribosomal protein S4 [Clostridium difficile NAP08]
 gi|296877835|ref|ZP_06901857.1| 30S ribosomal protein S4 [Clostridium difficile NAP07]
 gi|122974220|sp|Q18CI6|RS4_CLOD6 RecName: Full=30S ribosomal protein S4
 gi|115249105|emb|CAJ66916.1| 30S ribosomal protein S4 [Clostridium difficile]
 gi|260208037|emb|CBA60237.1| 30S ribosomal protein S4 [Clostridium difficile CD196]
 gi|260211488|emb|CBE01627.1| 30S ribosomal protein S4 [Clostridium difficile R20291]
 gi|296261369|gb|EFH08195.1| 30S ribosomal protein S4 [Clostridium difficile NAP08]
 gi|296431135|gb|EFH16960.1| 30S ribosomal protein S4 [Clostridium difficile NAP07]
          Length = 207

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+AS R+E  +++      +NG  ++  ++ V   D IEV
Sbjct: 99  RLDNVVYRMGLASSRKEARQLVTHGHFTLNGNKVDIPSLIVKVGDVIEV 147


>gi|56477618|ref|YP_159207.1| 30S ribosomal protein S4 [Aromatoleum aromaticum EbN1]
 gi|81357334|sp|Q5P308|RS4_AZOSE RecName: Full=30S ribosomal protein S4
 gi|56313661|emb|CAI08306.1| 30S Ribosomal protein S4 [Aromatoleum aromaticum EbN1]
          Length = 209

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   SR E  +++    + VNG  +   +  V   D +E+
Sbjct: 100 RLDSVVYRMGFGGSRAESRQLVRHNGILVNGKRVNIPSYVVRPGDVVEL 148


>gi|37528520|ref|NP_931865.1| 30S ribosomal protein S4 [Photorhabdus luminescens subsp. laumondii
           TTO1]
 gi|41017820|sp|Q7MYH4|RS4_PHOLL RecName: Full=30S ribosomal protein S4
 gi|36787958|emb|CAE17075.1| 30S ribosomal protein S4 [Photorhabdus luminescens subsp. laumondii
           TTO1]
          Length = 206

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  +M++ + + VNG ++  A+  V   D + V
Sbjct: 97  RLDNVVYRMGFGATRAESRQMVSHKAIMVNGRVVNIASYQVSPNDVVSV 145


>gi|296124262|ref|YP_003632040.1| hypothetical protein Plim_4030 [Planctomyces limnophilus DSM 3776]
 gi|296016602|gb|ADG69841.1| protein of unknown function Met10 [Planctomyces limnophilus DSM
           3776]
          Length = 552

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 10/87 (11%), Positives = 21/87 (24%)

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
                +       RP      P    R   N     G   + +  +  +RR   +     
Sbjct: 1   MENSPNPRRSAAKRPAQGQSYPKSSRRPATNRPPAGGEGSETRGESARNRRGDNTPQGDN 60

Query: 318 KGIHSSFLSDSGQREENHRRSPSFPSK 344
           +           +  +   R P+  + 
Sbjct: 61  RAAGGRRYGTPSRGPDARSRGPAPRNP 87


>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 = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 17/161 (10%), Positives = 52/161 (32%), Gaps = 3/161 (1%)

Query: 56  STDHIEVD---GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
             D I ++   G+P+  ++          +                + L    S +  V 
Sbjct: 96  DEDIIVINKPAGMPIHPSQNNYRNSLANALAWYYQEQGKAFVFRCANRLDRDTSGLTVVS 155

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           +  ++   L  +  D  L R         +       H  + +   +++++ +  +    
Sbjct: 156 KHMLSGNVLSSMAADRMLHREYLAICRGHITPSAGTIHAPLSRKPGSIIERTVDWEQGET 215

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 +  +K  ++ V++ L  G+  +I+   +   + + 
Sbjct: 216 AITHYCVVDEKNGHSLVSLRLETGRTHQIRIHMKHLGYPLI 256


>gi|116333868|ref|YP_795395.1| 30S ribosomal protein S4 [Lactobacillus brevis ATCC 367]
 gi|122269445|sp|Q03R08|RS4_LACBA RecName: Full=30S ribosomal protein S4
 gi|116099215|gb|ABJ64364.1| SSU ribosomal protein S4P [Lactobacillus brevis ATCC 367]
          Length = 201

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A+ RR+  +++    + V+G  ++  +  V     I V
Sbjct: 94  RLDNMVYRLGLATTRRQARQLVNHGHITVDGQRVDIPSYEVKIGQVISV 142


>gi|13508185|ref|NP_110134.1| 30S ribosomal protein S4 [Mycoplasma pneumoniae M129]
 gi|1173262|sp|P46775|RS4_MYCPN RecName: Full=30S ribosomal protein S4
 gi|639791|gb|AAA61698.1| ribosomal protein S4 [Mycoplasma pneumoniae]
 gi|1674077|gb|AAB96043.1| ribosomal protein S4 [Mycoplasma pneumoniae M129]
 gi|301633685|gb|ADK87239.1| ribosomal protein S4 [Mycoplasma pneumoniae FH]
          Length = 205

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 9/57 (15%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           R+  ++ R G A +RR   +++    V +N   ++  ++ +   D + +    ++  
Sbjct: 96  RLDNIVYRMGFAPTRRSARQLVNHGHVLLNDRTVDTPSIILNPGDKVRLKAKTIKIP 152


>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 = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 43/346 (12%), Positives = 87/346 (25%), Gaps = 56/346 (16%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V+     +R+   + +R    SR  ++++I    V VNG     A+  V   D + +  
Sbjct: 99  VVKSKLEGRRLDTYLTSRFPDYSRSVIQKVIDANAVMVNGKPAR-ASQKVREGDFVSLRL 157

Query: 63  ----DGVP--------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
               DG          +   ++    +      +          + V        +    
Sbjct: 158 PELWDGTIPAQDIPLTVIYEDQWLSIIDKPAGMVTHPGKGNWSGTVVNALQHRYDTLSQL 217

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--DKLNLLKKGIVIQ 168
            G         L     G L    +      L         + +       + ++     
Sbjct: 218 AGSTRPGVVHRLDRDTTGLLIVARDDTIHGKLAQLFETRTIEKEYLAICSGIPERDRDWI 277

Query: 169 GICYGD---------MQVTLDTQKGSNAWVTVG-------------LREGKNREIKKVFE 206
               G          ++   D  + +  +  V              L  G+  +I+    
Sbjct: 278 DQPLGPHPTVREKMAIRGEADGGRPARTFYEVVERFDRFALVRCQPLT-GRTHQIRVHLT 336

Query: 207 FFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL----REQLGPHLLEEAQVNLDAPIY 262
                +               L +G  R     +L    R     H+L   Q      + 
Sbjct: 337 HVGLPILA-----------DKLYSGRDRITRGDLLGWQARGDDHDHVLLTRQALHAHRLK 385

Query: 263 SSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
                  +   I S +P D     +   Q+   S        + RR
Sbjct: 386 FLHPATGEPLEIRSPLPPDMAETLETLRQRPAASSTNPTRFSITRR 431


>gi|255524166|ref|ZP_05391126.1| hemolysin A [Clostridium carboxidivorans P7]
 gi|296186624|ref|ZP_06855026.1| ribosomal RNA large subunit methyltransferase J [Clostridium
          carboxidivorans P7]
 gi|255512151|gb|EET88431.1| hemolysin A [Clostridium carboxidivorans P7]
 gi|296048661|gb|EFG88093.1| ribosomal RNA large subunit methyltransferase J [Clostridium
          carboxidivorans P7]
          Length = 274

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 11/60 (18%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          +   +R+  ++ + G+  SR +    I    + V+   +++    V  + +IE  G  L 
Sbjct: 2  SEAKERLDVLLVKKGLFPSREKARASIMAGEIFVDNQRVDKCGEKVKESSNIEFRGEKLP 61


>gi|240145850|ref|ZP_04744451.1| ribosomal protein S4 [Roseburia intestinalis L1-82]
 gi|257201998|gb|EEV00283.1| ribosomal protein S4 [Roseburia intestinalis L1-82]
 gi|291535455|emb|CBL08567.1| SSU ribosomal protein S4P [Roseburia intestinalis M50/1]
 gi|291537904|emb|CBL11015.1| SSU ribosomal protein S4P [Roseburia intestinalis XB6B4]
          Length = 197

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R+E  +++  + + VNG  +   +  V + D IE+
Sbjct: 88  RLDNVVFRMGFARTRKEARQIVDHKFILVNGKQVNIPSYLVKAGDVIEI 136


>gi|184154963|ref|YP_001843303.1| 30S ribosomal protein S4 [Lactobacillus fermentum IFO 3956]
 gi|227514502|ref|ZP_03944551.1| ribosomal protein S4 [Lactobacillus fermentum ATCC 14931]
 gi|226699079|sp|B2GAZ1|RS4_LACF3 RecName: Full=30S ribosomal protein S4
 gi|183226307|dbj|BAG26823.1| 30S ribosomal protein S4 [Lactobacillus fermentum IFO 3956]
 gi|227087129|gb|EEI22441.1| ribosomal protein S4 [Lactobacillus fermentum ATCC 14931]
          Length = 201

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A+ RR+  +++    + V+G  ++  +  V     I V
Sbjct: 94  RLDNMVYRLGLATTRRQARQLVNHGHITVDGKRVDIPSYEVKVGQVIAV 142


>gi|270307867|ref|YP_003329925.1| ribosomal protein S4 [Dehalococcoides sp. VS]
 gi|270153759|gb|ACZ61597.1| ribosomal protein S4 [Dehalococcoides sp. VS]
          Length = 207

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   SR +  +++    + VNG   +  +  +     I V
Sbjct: 98  RLDNVLFRLGFGTSRAQARQIVMHGHILVNGQKTDIPSYLIKEGQVITV 146


>gi|309812264|ref|ZP_07706019.1| ribosomal protein S4 [Dermacoccus sp. Ellin185]
 gi|308433569|gb|EFP57446.1| ribosomal protein S4 [Dermacoccus sp. Ellin185]
          Length = 202

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI RAG+A +RR   +++     +VNG+ ++  +  V   D I V
Sbjct: 92  RLDNVIYRAGLARTRRAARQLVTHGHFEVNGVRVDVPSYRVEQYDIITV 140


>gi|15644324|ref|NP_229376.1| hemolysin [Thermotoga maritima MSB8]
 gi|148270346|ref|YP_001244806.1| hemolysin A [Thermotoga petrophila RKU-1]
 gi|170289028|ref|YP_001739266.1| hemolysin A [Thermotoga sp. RQ2]
 gi|281412652|ref|YP_003346731.1| hemolysin A [Thermotoga naphthophila RKU-10]
 gi|4982145|gb|AAD36643.1|AE001802_12 hemolysin [Thermotoga maritima MSB8]
 gi|147735890|gb|ABQ47230.1| hemolysin A [Thermotoga petrophila RKU-1]
 gi|170176531|gb|ACB09583.1| hemolysin A [Thermotoga sp. RQ2]
 gi|281373755|gb|ADA67317.1| hemolysin A [Thermotoga naphthophila RKU-10]
          Length = 267

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 28/52 (53%), Gaps = 1/52 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            +R+ +++   G+  SR + + +I   +V VNG  + +A+  V    ++E+
Sbjct: 3  DKKRLDQLVLERGLVESREKAKVLILAGKVLVNGERVTKASKLVPEDANVEL 54


>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 = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 25/199 (12%), Positives = 53/199 (26%), Gaps = 28/199 (14%)

Query: 42  VNGILLERAAVNVMSTDHIEVD-GVPLR--------------KAERTRLWLYHKPIGLVT 86
           VN   +      +M  D +E+     +                 +   + +        T
Sbjct: 38  VNDEPVTV-RKQLMPNDILEIHLPQEIPSVNLIPYARKLEVLYEDAFIIIVTKLNNQNCT 96

Query: 87  THSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
              +    S +   L              V RLD NT G+++    G +  +    + + 
Sbjct: 97  PSREHPHESLIEQVLYHCQEHGENINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKVNLKK 156

Query: 142 LRVYRVRFHGQVD-------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           +    V              +   + +    V     Y      +  Q    +   V L 
Sbjct: 157 IYTCLVYGKTHTSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLH 216

Query: 195 EGKNREIKKVFEFFNWKVN 213
            G+  +I+  F+     + 
Sbjct: 217 TGRTHQIRVHFQHIGHPIV 235


>gi|306835269|ref|ZP_07468301.1| 30S ribosomal protein S4 [Corynebacterium accolens ATCC 49726]
 gi|304568862|gb|EFM44395.1| 30S ribosomal protein S4 [Corynebacterium accolens ATCC 49726]
          Length = 178

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR+  ++++     VNG  +   +  V   D I+V
Sbjct: 69  RLDNVVYRAGLARTRRQARQLVSHGHFTVNGKNINIPSYRVTQYDIIDV 117


>gi|227431364|ref|ZP_03913416.1| ribosomal protein S4 [Leuconostoc mesenteroides subsp. cremoris
           ATCC 19254]
 gi|227352874|gb|EEJ43048.1| ribosomal protein S4 [Leuconostoc mesenteroides subsp. cremoris
           ATCC 19254]
          Length = 203

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G+A+ R++  +++    + V+G  ++  + +V     + V
Sbjct: 93  QRLDSVVYRLGLATTRQQARQLVNHGHILVDGKRVDIPSYSVQPGQVVSV 142


>gi|56419669|ref|YP_146987.1| hypothetical protein GK1134 [Geobacillus kaustophilus HTA426]
 gi|56379511|dbj|BAD75419.1| hypothetical conserved protein [Geobacillus kaustophilus HTA426]
          Length = 257

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 10/45 (22%), Positives = 21/45 (46%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           R+  V+A+A   +R +   ++    VKVN  ++++        D 
Sbjct: 182 RLDAVLAQAFRLAREKARALVESGLVKVNWKVVDKPDFLCGPGDV 226


>gi|260061922|ref|YP_003195002.1| 30S ribosomal protein S4 [Robiginitalea biformata HTCC2501]
 gi|88786055|gb|EAR17224.1| 30S ribosomal protein S4 [Robiginitalea biformata HTCC2501]
          Length = 201

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 16/70 (22%), Positives = 31/70 (44%), Gaps = 1/70 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R GIA SRR   ++++ + + VNG L+   + ++ + D + V           
Sbjct: 94  RLDNVVYRMGIAPSRRAARQLVSHRHITVNGELVNIPSYSLSAGDVVGVREKSKSLQAIE 153

Query: 74  RLWLYHKPIG 83
                H  + 
Sbjct: 154 DSLSNHSNVY 163


>gi|116618921|ref|YP_819292.1| SSU ribosomal protein S4P [Leuconostoc mesenteroides subsp.
           mesenteroides ATCC 8293]
 gi|122270879|sp|Q03V53|RS4_LEUMM RecName: Full=30S ribosomal protein S4
 gi|116097768|gb|ABJ62919.1| SSU ribosomal protein S4P [Leuconostoc mesenteroides subsp.
           mesenteroides ATCC 8293]
          Length = 203

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G+A+ R++  +++    + V+G  ++  + +V     + V
Sbjct: 93  QRLDSVVYRLGLATTRQQARQLVNHGHILVDGKRVDIPSYSVQPGQVVSV 142


>gi|325690194|gb|EGD32198.1| S4 domain-containing protein YlmH [Streptococcus sanguinis SK115]
          Length = 261

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 30/63 (47%), Gaps = 2/63 (3%)

Query: 2   KDKNIVQEN--FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           + K  V +    +  R+ K++A     SR +  ++I+ + VK+N  + +  +  V   D 
Sbjct: 169 EQKQAVTKEILASSLRLDKLVASTFKLSRSQAVQLISGKHVKMNYAVNDNPSQQVGLEDL 228

Query: 60  IEV 62
           I V
Sbjct: 229 ISV 231


>gi|322375671|ref|ZP_08050183.1| YlmH protein [Streptococcus sp. C300]
 gi|321279379|gb|EFX56420.1| YlmH protein [Streptococcus sp. C300]
          Length = 263

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 14/48 (29%), Positives = 27/48 (56%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +++ A   SR +  ++I ++ V+VN  L+E++   V   D I V
Sbjct: 186 RLDALLSSALKLSRNQTSQLIEKKSVQVNYHLVEKSDYQVAVGDLISV 233


>gi|262066869|ref|ZP_06026481.1| S4 domain protein YaaA [Fusobacterium periodonticum ATCC 33693]
 gi|291379420|gb|EFE86938.1| S4 domain protein YaaA [Fusobacterium periodonticum ATCC 33693]
          Length = 71

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 14/71 (19%), Positives = 28/71 (39%), Gaps = 9/71 (12%)

Query: 1  MKDKNIVQENFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
          MK+   V+ +    ++ + +       +G     E + +I    VKVNG + +R    + 
Sbjct: 1  MKNIEKVKISTEFIKLDQFLKWLAVVDSG----SEAKEVILNGEVKVNGDVEKRRGRKIY 56

Query: 56 STDHIEVDGVP 66
              +EV    
Sbjct: 57 PEYKVEVFDKI 67


>gi|255020792|ref|ZP_05292850.1| SSU ribosomal protein S4p (S9e) [Acidithiobacillus caldus ATCC
          51756]
 gi|254969788|gb|EET27292.1| SSU ribosomal protein S4p (S9e) [Acidithiobacillus caldus ATCC
          51756]
          Length = 159

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 1/42 (2%)

Query: 22 RAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R G  S R E  +++    + VNG  ++  +  V + D + V
Sbjct: 57 RLGYGSSRAEARQVVRHGHITVNGRRVDIPSYQVRAGDVVAV 98


>gi|319442996|ref|ZP_07992152.1| 30S ribosomal protein S4 [Corynebacterium variabile DSM 44702]
          Length = 201

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V+ RAG+A +RR+  ++++     VNG  +   +  V   D I+V   
Sbjct: 92  RLDNVVYRAGLARTRRQARQLVSHGHFTVNGKKINVPSFQVSQYDIIDVRDR 143


>gi|302669990|ref|YP_003829950.1| ribosomal protein S4 RpsD [Butyrivibrio proteoclasticus B316]
 gi|302394463|gb|ADL33368.1| ribosomal protein S4 RpsD [Butyrivibrio proteoclasticus B316]
          Length = 208

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RRE  +++  + V VNG  +   +  V + D IE+
Sbjct: 99  RLDNVVFRMGFARTRREARQVVLHKFVLVNGKQINVPSYLVKAGDTIEI 147


>gi|261837797|gb|ACX97563.1| pore-forming cytolysin [Helicobacter pylori 51]
          Length = 235

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 21/184 (11%), Positives = 55/184 (29%), Gaps = 13/184 (7%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------D 63
            R+   +     + SR + + ++ + +V VN +++ + +  V  +D IE+          
Sbjct: 1   MRLDYALFNQHLVNSREKAKALVLKNQVLVNKMVVSKPSFMVKESDKIELIATNLFVSRA 60

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G  L     T    + K + L    S           L     +V+ V    +  +  L 
Sbjct: 61  GEKLAAFLETHFVDFKKKVVLDVGASKGGFSEVA---LLKGAKKVLCVDVGKMQLDESLK 117

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
                      ++   +      +            +L+  + +        +   +  +
Sbjct: 118 QDKRIECYEECDIRGFKTPEKIDLTLCDVSFISLYCILEAILPLSDEFLALFKPQFEVGR 177

Query: 184 GSNA 187
            +  
Sbjct: 178 VAKR 181


>gi|253991665|ref|YP_003043021.1| 30S ribosomal protein S4 [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 gi|253783115|emb|CAQ86280.1| 30s ribosomal subunit protein s4 [Photorhabdus asymbiotica]
          Length = 206

 Score = 46.3 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  +M++ + + VNG ++  A+  V   D + V
Sbjct: 97  RLDNVVYRMGFGATRAESRQMVSHKAIMVNGRVVNIASYQVSPNDVVSV 145


>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 = 45.9 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 12/51 (23%), Positives = 22/51 (43%), Gaps = 2/51 (3%)

Query: 13 PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +R+ KV+AR     SR  ++  I   RV ++G        +V     + +
Sbjct: 39 GERLDKVLARLFPTFSRSRLQTWIDAGRVTLDGAPAR-LRQSVPLGATVRL 88


>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 = 45.9 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 24/246 (9%), Positives = 60/246 (24%), Gaps = 45/246 (18%)

Query: 13  PQRVSKVIARAGI-------ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
             R+ + +AR           SR  ++ +I   R+ VNG  +   +  V       +D  
Sbjct: 35  SDRIDRWLARCLEDRETDPPLSRNRLKTLILDGRLFVNGATITDPSSPVKPGATYRIDVP 94

Query: 64  ------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                        + +   +   + +       V         + V   +      +  +
Sbjct: 95  EATPAIPEAQDLPLTVVYEDAALIVIDKPAGMTVHPAPGAPKDTLVNALIAHCGDSLSGI 154

Query: 112 GRLDIN----------------------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
           G +                            L     D  + R               R 
Sbjct: 155 GGVKRPGIVHRIDKDTSGLLVVAKTDAAHHALAARFADHSIDRAYRALCWGRPIPPAGRI 214

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTVGLREGKNREIKKVFEF 207
            G + +   + ++  +  +G     +      +    +   +   L  G+  +I+     
Sbjct: 215 EGAIGRHPRDRIRMAVRPEGSGKAAVTHFRTVRAFNEAATLLECRLETGRTHQIRVHLTH 274

Query: 208 FNWKVN 213
               + 
Sbjct: 275 IGHPLV 280


>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 = 45.9 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 6  IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          IV  +    R+ +V+A R    SR  ++ +I   +V ++   +   A +V S D I +D
Sbjct: 4  IVAGDEGSPRLDRVLAARLPELSRSRLKALILAGQVSLSTGAVRDPAYHVASGDTITID 62


>gi|91785440|ref|YP_560646.1| 30S ribosomal protein S4 [Burkholderia xenovorans LB400]
 gi|123358404|sp|Q13TJ5|RS4_BURXL RecName: Full=30S ribosomal protein S4
 gi|91689394|gb|ABE32594.1| SSU ribosomal protein S4P [Burkholderia xenovorans LB400]
          Length = 207

 Score = 45.9 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG++    ++ V + D + V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAIMVNGVVSNIPSMQVKAGDVVAV 146


>gi|74206304|dbj|BAE24898.1| unnamed protein product [Mus musculus]
          Length = 555

 Score = 45.9 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 23/150 (15%), Positives = 37/150 (24%), Gaps = 16/150 (10%)

Query: 221 GPFQLGTLLAGSTREVSKKILREQLGP------HLLEEAQVNLDAPIYSSETLVRDRPNI 274
             F L   L      V   +  E+            E            +    R     
Sbjct: 1   MSFALEETLESDWVAVRPHVFDEREKHKFVFIVAWNEIEGKFAITCHNRTAQRHRSGSRE 60

Query: 275 ISEVPDDFTRMKKNSSQKNGLSKQKKL-----ATPVHRRNLASNVWMAKGIHSSFLSDSG 329
            +  P    R    S    G S+          +P  R++ A     +     S   D  
Sbjct: 61  QAGTPASDGRRGPGSPAARGRSEAAASATAALRSPGPRKSQAWAEGGSPRSARSLKGDPP 120

Query: 330 QREENHR-----RSPSFPSKRSLRRTSAKK 354
           +           RSP+      LRR++  +
Sbjct: 121 RGPAGRGPESPLRSPARAKASPLRRSAESR 150


>gi|118579057|ref|YP_900307.1| RNA-binding S4 domain-containing protein [Pelobacter propionicus
          DSM 2379]
 gi|118501767|gb|ABK98249.1| RNA-binding S4 domain protein [Pelobacter propionicus DSM 2379]
          Length = 70

 Score = 45.9 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 11/58 (18%), Positives = 22/58 (37%), Gaps = 1/58 (1%)

Query: 10 NFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
          +    ++   +     + S  E + MI    V VNG + +R    +   D + + G  
Sbjct: 6  STEYIKLDSFLKCVNLVGSGGEAKEMIVAGEVLVNGQVEQRRGRKLYPGDRVALQGRE 63


>gi|331092114|ref|ZP_08340945.1| hypothetical protein HMPREF9477_01588 [Lachnospiraceae bacterium
          2_1_46FAA]
 gi|330402315|gb|EGG81886.1| hypothetical protein HMPREF9477_01588 [Lachnospiraceae bacterium
          2_1_46FAA]
          Length = 69

 Score = 45.9 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 4/52 (7%)

Query: 20 IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
          +  +G+    E + +I    V+VNG +  R    +   D +  DG  ++  +
Sbjct: 22 LVESGV----EAKEVIQDGLVQVNGEIDTRRGRKLYDGDVVFFDGEEIQIEK 69


>gi|297530699|ref|YP_003671974.1| RNA-binding S4 domain protein [Geobacillus sp. C56-T3]
 gi|297253951|gb|ADI27397.1| RNA-binding S4 domain protein [Geobacillus sp. C56-T3]
          Length = 257

 Score = 45.9 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 10/45 (22%), Positives = 21/45 (46%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           R+  V+A+A   +R +   ++    VKVN  ++++        D 
Sbjct: 182 RLDAVLAQAFRLAREKARALVESGLVKVNWKVVDKPDFLCGPGDV 226


>gi|291568923|dbj|BAI91195.1| hypothetical protein [Arthrospira platensis NIES-39]
          Length = 259

 Score = 45.9 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 16/65 (24%), Positives = 30/65 (46%), Gaps = 2/65 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             K  +       R+   IA AG   SR ++  +I    V+VN   +++A++ + + D I
Sbjct: 172 PKKKAMTTVEASLRLD-AIASAGFGMSRSKMVTLIDGGDVRVNWKEVKQASIAIKTGDLI 230

Query: 61  EVDGV 65
            + G 
Sbjct: 231 AIRGK 235


>gi|78484663|ref|YP_390588.1| ribosomal protein S4 [Thiomicrospira crunogena XCL-2]
 gi|90101733|sp|Q31IV9|RS4_THICR RecName: Full=30S ribosomal protein S4
 gi|78362949|gb|ABB40914.1| SSU ribosomal protein S4P [Thiomicrospira crunogena XCL-2]
          Length = 206

 Score = 45.9 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G AS R E  ++++ + ++VNG  +   +  V + D I +
Sbjct: 97  RLDNVVYRMGFASTRAEARQLVSHKSIQVNGQSVNIPSYEVSAGDVISI 145


>gi|325661583|ref|ZP_08150207.1| hypothetical protein HMPREF0490_00941 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|331084857|ref|ZP_08333945.1| hypothetical protein HMPREF0987_00248 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|325472110|gb|EGC75324.1| hypothetical protein HMPREF0490_00941 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|330410951|gb|EGG90373.1| hypothetical protein HMPREF0987_00248 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 256

 Score = 45.9 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 12/30 (40%), Positives = 14/30 (46%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           I   +V VNG L+     NV   D I V G
Sbjct: 201 IEAGKVFVNGKLISSNGYNVKEDDVISVRG 230


>gi|284053625|ref|ZP_06383835.1| RNA-binding S4 [Arthrospira platensis str. Paraca]
          Length = 259

 Score = 45.9 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 16/65 (24%), Positives = 30/65 (46%), Gaps = 2/65 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             K  +       R+   IA AG   SR ++  +I    V+VN   +++A++ + + D I
Sbjct: 172 PKKKAMTTVEASLRLD-AIASAGFGMSRSKMVTLIDGGDVRVNWKEVKQASIAIKTGDLI 230

Query: 61  EVDGV 65
            + G 
Sbjct: 231 AIRGK 235


>gi|269217219|ref|ZP_06161073.1| ribosomal protein S4 [Slackia exigua ATCC 700122]
 gi|269129356|gb|EEZ60441.1| ribosomal protein S4 [Slackia exigua ATCC 700122]
          Length = 198

 Score = 45.9 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           R+  V+ R G A +R+E  + +    + VNG  ++  +  V   D + V    
Sbjct: 89  RLDNVVFRLGFARTRKEARQTVTHGHILVNGRRVDVPSFRVRPGDLVSVAPKA 141


>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 = 45.9 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 24/254 (9%), Positives = 61/254 (24%), Gaps = 47/254 (18%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           IV       R+ + + +     S  ++ + + +  VK+NG   +     +   D I V  
Sbjct: 7   IVDSESEGMRLDRYLKKTFKNESLSKIFQALRKGDVKINGKKSKE-NYRLCLGDKITVKY 65

Query: 63  ---------------DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
                          D    +     E    ++ +KP  +                    
Sbjct: 66  LYSEKEEKTKKTFDFDEKKYKNMIIFENNDFFIINKPGNVPMHKGTGHKHGLSEIFKKIY 125

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
            +  I+           L++               +   V +        + + +     
Sbjct: 126 ENDNINFANRLDYETSGLVIGCKNLKFLRYISEKIRNNEVQKKYVAAVDGEIEKDKFIIE 185

Query: 165 IVIQGICYGDMQVTLDTQKGSNA-------------------------WVTVGLREGKNR 199
             ++    G +Q  +  +    +                          + + L  G+  
Sbjct: 186 NYLKITENGVIQSYVSDKDAKRSITKYKKINNRFFDKILNNIKKEKVTLLDIDLVTGRKH 245

Query: 200 EIKKVFEFFNWKVN 213
           +I+         V 
Sbjct: 246 QIRVQLSSIGNPVI 259


>gi|327449339|gb|EGE95993.1| ribosomal protein S4 [Propionibacterium acnes HL013PA2]
          Length = 201

 Score = 45.9 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR+  +M++     VNG  +   +  V + D I+V
Sbjct: 92  RLDNVVYRAGLAATRRQARQMVSHGHFLVNGKKVNIPSYRVSTHDIIDV 140


>gi|327325138|gb|EGE66944.1| ribosomal protein S4 [Propionibacterium acnes HL096PA3]
          Length = 201

 Score = 45.9 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR+  +M++     VNG  +   +  V + D I+V
Sbjct: 92  RLDNVVYRAGLAATRRQARQMVSHGHFLVNGKKVNIPSYRVSTHDIIDV 140


>gi|317485797|ref|ZP_07944661.1| ribosomal protein S4 [Bilophila wadsworthia 3_1_6]
 gi|316922903|gb|EFV44125.1| ribosomal protein S4 [Bilophila wadsworthia 3_1_6]
          Length = 208

 Score = 45.9 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SR +  +++      +NG  +   ++ V   D +EV
Sbjct: 99  RLDNVVYRLGFANSRTQARQLVRHGVFTLNGHKVTIPSLQVKVGDSVEV 147


>gi|289613974|emb|CBI59208.1| unnamed protein product [Sordaria macrospora]
          Length = 912

 Score = 45.9 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 15/118 (12%), Positives = 32/118 (27%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           E+SKK  R +         +    +P    +   R R    +  P       +    ++ 
Sbjct: 509 EISKKQDRARKEHSDHGRERERERSPDRRPQRDTRIRDRYEARDPGWRRDDYRPGPGRSP 568

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             ++        R +   +         S     G+  +N  R       R +  +  
Sbjct: 569 SPRRGSRDGRYARDSRDRDFGPGYDSRRSRSPPPGRYYDNGYRRRDESPHRRVPSSEE 626


>gi|160902229|ref|YP_001567810.1| RNA-binding S4 domain-containing protein [Petrotoga mobilis SJ95]
 gi|189045390|sp|A9BFZ1|RS4_PETMO RecName: Full=30S ribosomal protein S4
 gi|160359873|gb|ABX31487.1| RNA-binding S4 domain protein [Petrotoga mobilis SJ95]
          Length = 211

 Score = 45.9 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ + G A +RR   +++    + VNG  +   +  V   D IEV
Sbjct: 100 RLDSVVYQMGFAPNRRTARQIVTHGHILVNGKKVNIPSYRVKVGDVIEV 148


>gi|152998247|ref|YP_001343082.1| 30S ribosomal protein S4 [Marinomonas sp. MWYL1]
 gi|189045385|sp|A6W368|RS4_MARMS RecName: Full=30S ribosomal protein S4
 gi|150839171|gb|ABR73147.1| ribosomal protein S4 [Marinomonas sp. MWYL1]
          Length = 206

 Score = 45.9 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG  S R E  +++  + + VNG  +   +  V + D + +
Sbjct: 97  RLDNVVYRAGFGSTRAEARQLVGHKGILVNGATVNIPSYQVKAGDVVSI 145


>gi|147669123|ref|YP_001213941.1| 30S ribosomal protein S4 [Dehalococcoides sp. BAV1]
 gi|146270071|gb|ABQ17063.1| SSU ribosomal protein S4P [Dehalococcoides sp. BAV1]
          Length = 197

 Score = 45.9 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   SR +  +++    + VNG   +  +  +     I V
Sbjct: 88  RLDNVLFRLGFGTSRAQARQIVMHGHILVNGQKTDIPSYLIKEGQEITV 136


>gi|37912838|gb|AAR05178.1| putative ATP-dependent RNA helicase [uncultured marine
           proteobacterium ANT8C10]
          Length = 635

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 14/103 (13%), Positives = 21/103 (20%), Gaps = 1/103 (0%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
           +           E     RPN            + NS                  R   S
Sbjct: 421 SSSRPGNAEGRPERSGAGRPNSGGAGRPSNGGGRPNSGAGRPERSGAGRPNSGAGRPERS 480

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR-TSAKK 354
                    +   S+ G R  +    PS    R        ++
Sbjct: 481 GAGRPSSGGAGRPSNGGGRPNSGAGRPSNGGGRPNSGAGRPER 523



 Score = 44.8 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 9/115 (7%), Positives = 18/115 (15%), Gaps = 2/115 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R   G    E +     +   +                      + NS            
Sbjct: 469 RPNSGAGRPERSGAGRPSSGGAGRPSNGGGRPNSGAGRPSNGGGRPNSGAGRPERSGAGR 528

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREE--NHRRSPSFPSKRSLRRTSAKK 354
                 R   S                  R       R  +   + +      ++
Sbjct: 529 PNSGAGRPERSGAGRPNSGAGRPERSGAGRPSSGGAGRPSNGGGRPNSGAGRPER 583



 Score = 43.6 bits (101), Expect = 0.044,   Method: Composition-based stats.
 Identities = 14/113 (12%), Positives = 28/113 (24%), Gaps = 4/113 (3%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R   G      A    +     +    R   +          R +++     G       
Sbjct: 434 RSGAGRPNSGGAGRPSNGGGRPNSGAGRPERSGAGRPNSGAGRPERSG---AGRPSSGGA 490

Query: 302 ATPVHRRNL-ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             P +      S             S +G+ E +    P+  + R  R  + +
Sbjct: 491 GRPSNGGGRPNSGAGRPSNGGGRPNSGAGRPERSGAGRPNSGAGRPERSGAGR 543



 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 9/126 (7%), Positives = 24/126 (19%), Gaps = 4/126 (3%)

Query: 230 AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
            G +R  S +  +     +       + ++      +  R              R     
Sbjct: 385 RGDSRSRSPRGRKPAFSRNNRSSDGKSGNSYSKPGGSSSRPGNAEGRPERSGAGRPNSGG 444

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREE--NHRRSPSFPSKRSL 347
           + +      +  +     R   S                  R       R  +   + + 
Sbjct: 445 AGRPSNGGGRPNSGAG--RPERSGAGRPNSGAGRPERSGAGRPSSGGAGRPSNGGGRPNS 502

Query: 348 RRTSAK 353
                 
Sbjct: 503 GAGRPS 508



 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 9/115 (7%), Positives = 22/115 (19%), Gaps = 2/115 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ--KNGLSKQK 299
            E      +E                  D+P+            +       +N  S   
Sbjct: 350 DEHKFLRGIEGLLKIKIDQTSHEAFKPNDKPSGGGRGDSRSRSPRGRKPAFSRNNRSSDG 409

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           K      +   +S+                       R  +   + +      ++
Sbjct: 410 KSGNSYSKPGGSSSRPGNAEGRPERSGAGRPNSGGAGRPSNGGGRPNSGAGRPER 464



 Score = 37.1 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 11/101 (10%), Positives = 26/101 (25%), Gaps = 1/101 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G       +         +    R   +          R +++ + +       + +   
Sbjct: 512 GRPNSGAGRPERSGAGRPNSGAGRPERSGAGRPNSGAGRPERSGAGRPSSGGAGRPSNGG 571

Query: 306 HRRNLASNVWMAKGI-HSSFLSDSGQREENHRRSPSFPSKR 345
            R N  +      G    S  S +   ++   +S     KR
Sbjct: 572 GRPNSGAGRPERSGAGRPSGNSANKPYDKKQDQSQKLAGKR 612


>gi|78043160|ref|YP_360803.1| hemolysin A [Carboxydothermus hydrogenoformans Z-2901]
 gi|77995275|gb|ABB14174.1| hemolysin A [Carboxydothermus hydrogenoformans Z-2901]
          Length = 266

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 11/56 (19%), Positives = 21/56 (37%), Gaps = 1/56 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          R+  ++   G+  SR +   +I    V V    + +    V     I + G  L+ 
Sbjct: 4  RLDVLMVEKGLVQSREKARALIMAGEVLVGEQKVTKPGTMVTEDSPIRILGQGLKY 59


>gi|260663356|ref|ZP_05864247.1| 30S ribosomal protein S4 [Lactobacillus fermentum 28-3-CHN]
 gi|260552208|gb|EEX25260.1| 30S ribosomal protein S4 [Lactobacillus fermentum 28-3-CHN]
          Length = 197

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A+ RR+  +++    + V+G  ++  +  V     I V
Sbjct: 94  RLDNMVYRLGLATTRRQARQLVNHGHITVDGKRVDIPSYEVKVGQVIAV 142


>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 = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 27/226 (11%), Positives = 58/226 (25%), Gaps = 41/226 (18%)

Query: 22  RAGIASRREVERMIA----QQRVKVNGILLERAAVNVMSTDHIEVD-------------- 63
             G++SR     +I      +R+KV+G +  +    V + + I+++              
Sbjct: 24  ELGLSSR-----LIRSAAIDKRIKVDG-VAVKMNYVVKTGEEIKIELSKKESQNIEPEKM 77

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
            + +   +   L L  KP  +V         +     L              ++   +  
Sbjct: 78  DIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYFKESNQDCIVRLVSRLDMNT 137

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
                                        +     NL +K   I    Y   + T+    
Sbjct: 138 SGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLEEKEGTINRPIYRPAEDTIKRVV 197

Query: 180 -DTQKGSNAWVTVG------------LREGKNREIKKVFEFFNWKV 212
            +  + S     V             L  G+  +I+         +
Sbjct: 198 DERGQESITHYKVIESYKGADLVECLLETGRTHQIRVHLSSLGHPI 243


>gi|27228510|ref|NP_758560.1| hypothetical protein pCAR1_p019 [Pseudomonas resinovorans]
 gi|219856932|ref|YP_002473963.1| hypothetical protein pCAR12_p019 [Pseudomonas sp. CA10]
 gi|26106098|dbj|BAC41538.1| hypothetical protein [Pseudomonas resinovorans]
 gi|219688859|dbj|BAH09950.1| hypothetical protein [Pseudomonas putida]
          Length = 479

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 10/104 (9%), Positives = 20/104 (19%), Gaps = 10/104 (9%)

Query: 260 PIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKG 319
               +      R         +    ++ S ++ G     +   P   R           
Sbjct: 1   MDRRANPHPGQRRRHPPGHRPNPAPAQRPSHRRPGRRATGRRHRPGPDRQRRGGGHPGAT 60

Query: 320 IHSSF----------LSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                             SG     H  +P    +R       +
Sbjct: 61  ERHPPQRPRRPEDHLDRGSGTNGRGHHPAPGRGGRRQPDPGRRQ 104


>gi|254495366|ref|ZP_05108290.1| 30S ribosomal protein S4 [Polaribacter sp. MED152]
 gi|85819720|gb|EAQ40877.1| 30S ribosomal protein S4 [Polaribacter sp. MED152]
          Length = 201

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G++ SR    ++++ + + VNG ++   + ++   D + V
Sbjct: 94  RLDNVVYRMGVSNSRSGARQLVSHRHITVNGEIVNIPSYSLKEGDVVAV 142


>gi|325479239|gb|EGC82335.1| pseudouridine synthase, RluA family [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 303

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 34/254 (13%), Positives = 66/254 (25%), Gaps = 66/254 (25%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRV--------------KVNGILLERAAVNVMS 56
               R+ K I+        E+E       +              KVN  +++  +  +  
Sbjct: 4   DEIIRIDKFISD-------ELEE------IPREKIKDFIKDKKIKVNDKIVK-PSFKLSE 49

Query: 57  TDHIEVDGV--------------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
            D IE+D                 +         +      +V         + V   L 
Sbjct: 50  GDEIEIDDSLFHVPTIDPEAMDLKIVYENDDYAIIDKDSNVIVHPAGKIVTGTLVNGLLD 109

Query: 103 SIFSRVIS----------VGRLDINTEGLLLLTNDGGLARVLELP-------------ST 139
                 +S          V RLD +T GL+ +T +    +  +                 
Sbjct: 110 RYGYDGLSHIGGDDRPGIVHRLDKDTTGLIAITKNNTSYKYFKKMFETRKVDKIYYAIVF 169

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
                        +D+D  N  K  +   G         +  +    + V V +  G+  
Sbjct: 170 GTFDKKSDTIETFMDRDPHNRRKMAVTSSGRKA-ISHYEVVAETNDYSLVKVKIVTGRTH 228

Query: 200 EIKKVFEFFNWKVN 213
           +I+      N  + 
Sbjct: 229 QIRVHMTHLNHPIL 242


>gi|288553144|ref|YP_003425079.1| putative RNA-binding S4 domain-containing protein [Bacillus
           pseudofirmus OF4]
 gi|288544304|gb|ADC48187.1| putative RNA-binding S4 domain protein [Bacillus pseudofirmus OF4]
          Length = 257

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 25/57 (43%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
              +  R+  +++     SR +V+  I +  VKVN  + +     V   D+I V G 
Sbjct: 176 TTVSSMRLDVILSEIYNLSRAKVKPYIERGFVKVNWRVTDHVDFLVKEGDYISVRGH 232


>gi|262201793|ref|YP_003273001.1| cell envelope-like function transcriptional attenuator [Gordonia
           bronchialis DSM 43247]
 gi|262085140|gb|ACY21108.1| cell envelope-related function transcriptional attenuator,
           LytR/CpsA family [Gordonia bronchialis DSM 43247]
          Length = 676

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 8/90 (8%), Positives = 19/90 (21%)

Query: 262 YSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIH 321
                   D P       D     ++   ++       +       R   +     +G  
Sbjct: 35  GQPRGAGTDHPERGPRRADATEPERRTQPRRAPRDPSDRAREQQTPRRRPARGTAPQGGA 94

Query: 322 SSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
           +   +     + +  R P         R  
Sbjct: 95  APRDAAPRTEQRDPERRPRRADPADPSRPR 124



 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 10/104 (9%), Positives = 29/104 (27%), Gaps = 5/104 (4%)

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW 315
                   ++   R      +  P+  T+ ++     +  +++++       R  A    
Sbjct: 34  TGQPRGAGTDHPERGPRRADATEPERRTQPRRAPRDPSDRAREQQTPRRRPARGTAPQGG 93

Query: 316 MAKGIHS-----SFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            A    +            +R +    S      +  R  + K+
Sbjct: 94  AAPRDAAPRTEQRDPERRPRRADPADPSRPRRPAKPTRTDAEKR 137



 Score = 41.7 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 13/99 (13%), Positives = 22/99 (22%), Gaps = 3/99 (3%)

Query: 259 APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAK 318
            P  +       R                 + Q  G         P              
Sbjct: 4   PPDGTRGRPRPHRDAPPEPRRRRPAPGGARTGQPRGAGTDHPERGPRRADATEPERRTQP 63

Query: 319 GIHSSFLSDSGQREENHRRSPSF---PSKRSLRRTSAKK 354
                  SD  + ++  RR P+    P   +  R +A +
Sbjct: 64  RRAPRDPSDRAREQQTPRRRPARGTAPQGGAAPRDAAPR 102



 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 12/113 (10%), Positives = 24/113 (21%), Gaps = 7/113 (6%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
             L  +       P   +    R R            R       + G  +         
Sbjct: 1   MDLPPDGTRGRPRPHRDAPPEPRRRRPAPGGARTGQPRGAGTDHPERGPRRADATE--PE 58

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREEN-----HRRSPSFPSKRSLRRTSAKK 354
           RR             +       +R           +P   + R+ +R   ++
Sbjct: 59  RRTQPRRAPRDPSDRAREQQTPRRRPARGTAPQGGAAPRDAAPRTEQRDPERR 111



 Score = 37.5 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 9/116 (7%), Positives = 24/116 (20%), Gaps = 4/116 (3%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           ++   R Q      + +    +             P   +   D   R ++   ++    
Sbjct: 55  TEPERRTQPRRAPRDPSDRAREQQTPRRRPARGTAPQGGAAPRDAAPRTEQRDPERRPRR 114

Query: 297 KQK----KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                  +   P       +      G   +    + +             K S  
Sbjct: 115 ADPADPSRPRRPAKPTRTDAEKRRTSGEIHTRTRPAAEGSRTGPPPTRRRRKPSAP 170


>gi|50843284|ref|YP_056511.1| 30S ribosomal protein S4 [Propionibacterium acnes KPA171202]
 gi|282855171|ref|ZP_06264503.1| ribosomal protein S4 [Propionibacterium acnes J139]
 gi|289424812|ref|ZP_06426594.1| ribosomal protein S4 [Propionibacterium acnes SK187]
 gi|289427659|ref|ZP_06429371.1| ribosomal protein S4 [Propionibacterium acnes J165]
 gi|295131353|ref|YP_003582016.1| ribosomal protein S4 [Propionibacterium acnes SK137]
 gi|61215507|sp|Q6A6R0|RS4_PROAC RecName: Full=30S ribosomal protein S4
 gi|50840886|gb|AAT83553.1| 30S ribosomal protein S4 [Propionibacterium acnes KPA171202]
 gi|282581759|gb|EFB87144.1| ribosomal protein S4 [Propionibacterium acnes J139]
 gi|289154775|gb|EFD03458.1| ribosomal protein S4 [Propionibacterium acnes SK187]
 gi|289159150|gb|EFD07342.1| ribosomal protein S4 [Propionibacterium acnes J165]
 gi|291375309|gb|ADD99163.1| ribosomal protein S4 [Propionibacterium acnes SK137]
 gi|313763204|gb|EFS34568.1| ribosomal protein S4 [Propionibacterium acnes HL013PA1]
 gi|313773119|gb|EFS39085.1| ribosomal protein S4 [Propionibacterium acnes HL074PA1]
 gi|313793291|gb|EFS41349.1| ribosomal protein S4 [Propionibacterium acnes HL110PA1]
 gi|313801065|gb|EFS42333.1| ribosomal protein S4 [Propionibacterium acnes HL110PA2]
 gi|313808806|gb|EFS47260.1| ribosomal protein S4 [Propionibacterium acnes HL087PA2]
 gi|313810400|gb|EFS48114.1| ribosomal protein S4 [Propionibacterium acnes HL083PA1]
 gi|313812264|gb|EFS49978.1| ribosomal protein S4 [Propionibacterium acnes HL025PA1]
 gi|313816541|gb|EFS54255.1| ribosomal protein S4 [Propionibacterium acnes HL059PA1]
 gi|313817985|gb|EFS55699.1| ribosomal protein S4 [Propionibacterium acnes HL046PA2]
 gi|313819898|gb|EFS57612.1| ribosomal protein S4 [Propionibacterium acnes HL036PA1]
 gi|313823389|gb|EFS61103.1| ribosomal protein S4 [Propionibacterium acnes HL036PA2]
 gi|313824860|gb|EFS62574.1| ribosomal protein S4 [Propionibacterium acnes HL063PA1]
 gi|313828398|gb|EFS66112.1| ribosomal protein S4 [Propionibacterium acnes HL063PA2]
 gi|313830102|gb|EFS67816.1| ribosomal protein S4 [Propionibacterium acnes HL007PA1]
 gi|313832626|gb|EFS70340.1| ribosomal protein S4 [Propionibacterium acnes HL056PA1]
 gi|313837982|gb|EFS75696.1| ribosomal protein S4 [Propionibacterium acnes HL086PA1]
 gi|314914365|gb|EFS78196.1| ribosomal protein S4 [Propionibacterium acnes HL005PA4]
 gi|314917685|gb|EFS81516.1| ribosomal protein S4 [Propionibacterium acnes HL050PA1]
 gi|314919583|gb|EFS83414.1| ribosomal protein S4 [Propionibacterium acnes HL050PA3]
 gi|314925755|gb|EFS89586.1| ribosomal protein S4 [Propionibacterium acnes HL036PA3]
 gi|314930173|gb|EFS94004.1| ribosomal protein S4 [Propionibacterium acnes HL067PA1]
 gi|314957154|gb|EFT01258.1| ribosomal protein S4 [Propionibacterium acnes HL027PA1]
 gi|314957795|gb|EFT01898.1| ribosomal protein S4 [Propionibacterium acnes HL002PA1]
 gi|314960835|gb|EFT04936.1| ribosomal protein S4 [Propionibacterium acnes HL002PA2]
 gi|314963509|gb|EFT07609.1| ribosomal protein S4 [Propionibacterium acnes HL082PA1]
 gi|314964877|gb|EFT08976.1| ribosomal protein S4 [Propionibacterium acnes HL082PA2]
 gi|314969908|gb|EFT14006.1| ribosomal protein S4 [Propionibacterium acnes HL037PA1]
 gi|314973049|gb|EFT17145.1| ribosomal protein S4 [Propionibacterium acnes HL053PA1]
 gi|314975545|gb|EFT19640.1| ribosomal protein S4 [Propionibacterium acnes HL045PA1]
 gi|314979766|gb|EFT23860.1| ribosomal protein S4 [Propionibacterium acnes HL072PA2]
 gi|314984828|gb|EFT28920.1| ribosomal protein S4 [Propionibacterium acnes HL005PA1]
 gi|314986087|gb|EFT30179.1| ribosomal protein S4 [Propionibacterium acnes HL005PA2]
 gi|314988702|gb|EFT32793.1| ribosomal protein S4 [Propionibacterium acnes HL005PA3]
 gi|315077130|gb|EFT49197.1| ribosomal protein S4 [Propionibacterium acnes HL053PA2]
 gi|315079817|gb|EFT51793.1| ribosomal protein S4 [Propionibacterium acnes HL078PA1]
 gi|315083184|gb|EFT55160.1| ribosomal protein S4 [Propionibacterium acnes HL027PA2]
 gi|315086862|gb|EFT58838.1| ribosomal protein S4 [Propionibacterium acnes HL002PA3]
 gi|315089954|gb|EFT61930.1| ribosomal protein S4 [Propionibacterium acnes HL072PA1]
 gi|315090476|gb|EFT62452.1| ribosomal protein S4 [Propionibacterium acnes HL110PA4]
 gi|315093709|gb|EFT65685.1| ribosomal protein S4 [Propionibacterium acnes HL060PA1]
 gi|315096724|gb|EFT68700.1| ribosomal protein S4 [Propionibacterium acnes HL038PA1]
 gi|315097952|gb|EFT69928.1| ribosomal protein S4 [Propionibacterium acnes HL059PA2]
 gi|315100595|gb|EFT72571.1| ribosomal protein S4 [Propionibacterium acnes HL046PA1]
 gi|315104001|gb|EFT75977.1| ribosomal protein S4 [Propionibacterium acnes HL050PA2]
 gi|315106038|gb|EFT78014.1| ribosomal protein S4 [Propionibacterium acnes HL030PA1]
 gi|315109198|gb|EFT81174.1| ribosomal protein S4 [Propionibacterium acnes HL030PA2]
 gi|327325233|gb|EGE67038.1| ribosomal protein S4 [Propionibacterium acnes HL096PA2]
 gi|327325529|gb|EGE67328.1| ribosomal protein S4 [Propionibacterium acnes HL103PA1]
 gi|327332742|gb|EGE74476.1| ribosomal protein S4 [Propionibacterium acnes HL097PA1]
 gi|327451455|gb|EGE98109.1| ribosomal protein S4 [Propionibacterium acnes HL087PA3]
 gi|327451570|gb|EGE98224.1| ribosomal protein S4 [Propionibacterium acnes HL092PA1]
 gi|327451857|gb|EGE98511.1| ribosomal protein S4 [Propionibacterium acnes HL083PA2]
 gi|328752071|gb|EGF65687.1| ribosomal protein S4 [Propionibacterium acnes HL087PA1]
 gi|328755531|gb|EGF69147.1| ribosomal protein S4 [Propionibacterium acnes HL025PA2]
 gi|328756316|gb|EGF69932.1| ribosomal protein S4 [Propionibacterium acnes HL020PA1]
 gi|328761350|gb|EGF74877.1| ribosomal protein S4 [Propionibacterium acnes HL099PA1]
 gi|332676223|gb|AEE73039.1| 30S ribosomal protein S4 [Propionibacterium acnes 266]
          Length = 201

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR+  +M++     VNG  +   +  V + D I+V
Sbjct: 92  RLDNVVYRAGLAATRRQARQMVSHGHFLVNGKKVNIPSYRVSTHDIIDV 140


>gi|319942197|ref|ZP_08016513.1| 30S ribosomal protein S4 [Sutterella wadsworthensis 3_1_45B]
 gi|319804250|gb|EFW01142.1| 30S ribosomal protein S4 [Sutterella wadsworthensis 3_1_45B]
          Length = 208

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 13/56 (23%), Positives = 28/56 (50%), Gaps = 1/56 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+  V+ R G  S R E  ++++   ++VNG  +   + +V + D I +     ++
Sbjct: 99  RLDNVVYRMGFGSTRAESRQLVSHGAIEVNGRKVNIPSYSVRAGDVITIREKAQKQ 154


>gi|310777807|ref|YP_003966140.1| S4 domain protein YaaA [Ilyobacter polytropus DSM 2926]
 gi|309747130|gb|ADO81792.1| S4 domain protein YaaA [Ilyobacter polytropus DSM 2926]
          Length = 68

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 16/71 (22%), Positives = 26/71 (36%), Gaps = 12/71 (16%)

Query: 1  MKDKNIVQENFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
          MK   I        ++ + +       +G+    E + M+    V VNG   ER    + 
Sbjct: 1  MKKVKI---TSEFIKLDQFLKWADVTSSGV----EAKYMVQDGEVTVNGEPEERRGRKLY 53

Query: 56 STDHIEVDGVP 66
            D +EV G  
Sbjct: 54 PGDTVEVMGKK 64


>gi|261405769|ref|YP_003242010.1| 30S ribosomal protein S4 [Paenibacillus sp. Y412MC10]
 gi|329922609|ref|ZP_08278161.1| ribosomal protein S4 [Paenibacillus sp. HGF5]
 gi|261282232|gb|ACX64203.1| ribosomal protein S4 [Paenibacillus sp. Y412MC10]
 gi|328941951|gb|EGG38234.1| ribosomal protein S4 [Paenibacillus sp. HGF5]
          Length = 200

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  ++ R G + SR    +++A   V VNG  ++ A+  V + D I
Sbjct: 93  RLDNLVYRLGFSNSRAGARQLVAHGHVTVNGKKVDIASYAVSTGDVI 139


>gi|1938255|gb|AAB52231.1| extracellular lipase [Aeromonas hydrophila]
          Length = 751

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 12/135 (8%), Positives = 31/135 (22%), Gaps = 10/135 (7%)

Query: 230 AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLV---RDRPNIISEVPDDFTRMK 286
               RE+  +  ++ +     +     +   +  S                 P    R  
Sbjct: 284 PAGCRELPAQEQKDAIAAAFGDALHSTIWPWVPPSTAAPSSCPTSSPRPPPAPGTRRRPS 343

Query: 287 KNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGI-------HSSFLSDSGQREENHRRSP 339
             +     L  +++   P  R +                   ++       R +   R  
Sbjct: 344 PGTVPSQPLRHRERPEGPGCRSDRRPGGGGYGSRDEHRALQPAAGTGRGAVRPDADLRRR 403

Query: 340 SFPSKRSLRRTSAKK 354
           +          SA++
Sbjct: 404 TAGEHHRRDHLSARR 418


>gi|315646149|ref|ZP_07899269.1| ribosomal protein S4 [Paenibacillus vortex V453]
 gi|315278348|gb|EFU41664.1| ribosomal protein S4 [Paenibacillus vortex V453]
          Length = 200

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  ++ R G + SR    +++A   V VNG  ++ A+  V + D I
Sbjct: 93  RLDNLVYRLGFSNSRAGARQLVAHGHVTVNGKKVDIASYAVSTGDVI 139


>gi|294811611|ref|ZP_06770254.1| Serine/threonine protein kinase [Streptomyces clavuligerus ATCC
           27064]
 gi|326440201|ref|ZP_08214935.1| putative serine/threonine protein kinase [Streptomyces clavuligerus
           ATCC 27064]
 gi|294324210|gb|EFG05853.1| Serine/threonine protein kinase [Streptomyces clavuligerus ATCC
           27064]
          Length = 400

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 16/109 (14%), Positives = 33/109 (30%), Gaps = 1/109 (0%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           +E++ +   + L        +  +DA   ++    R      +   +   R ++      
Sbjct: 266 KEIAARE-AQGLVEVRPPAPRERIDADRPTTRYPERPGRAAAAARTERLDRGERTERLDR 324

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
              ++   A P   R   S         S      G R  +  R P+ P
Sbjct: 325 AGERRTGPARPKPARTGGSRPRPYPPARSGARPGPGGRTTSTGRRPANP 373



 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 6/110 (5%), Positives = 23/110 (20%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           E     L+  +    +   +      +       R   +  +    +       +++   
Sbjct: 253 EDRPSTLQLSMRLKEIAAREAQGLVEVRPPAPRERIDADRPTTRYPERPGRAAAAARTER 312

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           L + ++           +     K   +                P    +
Sbjct: 313 LDRGERTERLDRAGERRTGPARPKPARTGGSRPRPYPPARSGARPGPGGR 362



 Score = 41.7 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 13/116 (11%), Positives = 28/116 (24%), Gaps = 6/116 (5%)

Query: 236 VSKKIL--REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           +  K +  RE  G           +       T         +       R+ +    + 
Sbjct: 263 MRLKEIAAREAQGLV-EVRPPAPRERIDADRPTTRYPERPGRAAAAARTERLDRGERTER 321

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                ++   P   +   +             + SG R     R+ S   + +  R
Sbjct: 322 LDRAGERRTGPARPKPARTGGSRP---RPYPPARSGARPGPGGRTTSTGRRPANPR 374


>gi|161511118|ref|NP_540882.2| translation initiation factor IF-2 [Brucella melitensis bv. 1 str.
           16M]
 gi|225853590|ref|YP_002733823.1| translation initiation factor IF-2 [Brucella melitensis ATCC 23457]
 gi|256045768|ref|ZP_05448646.1| translation initiation factor IF-2 [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|260563064|ref|ZP_05833550.1| translation initiation factor IF-2 [Brucella melitensis bv. 1 str.
           16M]
 gi|265992185|ref|ZP_06104742.1| translation initiation factor IF-2 [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|39931298|sp|Q8YEB3|IF2_BRUME RecName: Full=Translation initiation factor IF-2
 gi|225641955|gb|ACO01869.1| translation initiation factor IF-2 [Brucella melitensis ATCC 23457]
 gi|260153080|gb|EEW88172.1| translation initiation factor IF-2 [Brucella melitensis bv. 1 str.
           16M]
 gi|263003251|gb|EEZ15544.1| translation initiation factor IF-2 [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|326410163|gb|ADZ67228.1| translation initiation factor IF-2 [Brucella melitensis M28]
 gi|326539881|gb|ADZ88096.1| translation initiation factor IF-2 [Brucella melitensis M5-90]
          Length = 959

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 13/116 (11%), Positives = 28/116 (24%), Gaps = 2/116 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R + +  +RE +        +    A   +      +         +   + +  + +K 
Sbjct: 161 RALEEAQIRE-VEERARAVEEAKRRAEEDARRAKEHEESARRQAEEEARLKAEAEARRKA 219

Query: 294 GLSKQKKLATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                K++  P  R     +   A  G                   P   S R   
Sbjct: 220 EEEAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAP 275



 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 11/121 (9%), Positives = 28/121 (23%), Gaps = 1/121 (0%)

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           L     REV ++  R         E           S     +    +    +   + ++
Sbjct: 163 LEEAQIREVEERA-RAVEEAKRRAEEDARRAKEHEESARRQAEEEARLKAEAEARRKAEE 221

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            ++++    + +       R           G           R +     P+     + 
Sbjct: 222 EAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAPIIADAA 281

Query: 348 R 348
            
Sbjct: 282 P 282


>gi|329962292|ref|ZP_08300298.1| ribosomal protein S4 [Bacteroides fluxus YIT 12057]
 gi|328530400|gb|EGF57277.1| ribosomal protein S4 [Bacteroides fluxus YIT 12057]
          Length = 201

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R GIA +R    ++++ + + VNG ++   +  V     I V
Sbjct: 93  RLDNIVFRLGIAPTRAAARQLVSHKHITVNGEVVNVPSYAVKPGQVIGV 141


>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 = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 34/254 (13%), Positives = 78/254 (30%), Gaps = 41/254 (16%)

Query: 1   MKDKN----IVQENF-TPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNV 54
           MK+      I  EN    +R+   +  +    +R  ++++I Q+ + + G    ++   +
Sbjct: 1   MKNYKEQDTIYAENSDKGKRLDAFVNESFDYLTRSYIQKLIEQRDIIIEGKEKNKSGNKL 60

Query: 55  MSTDHIEV----------------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPD 92
              + I V                      D   +   +   + ++  P     T  +  
Sbjct: 61  KGNEKILVRIPEDEMLDIEPQDIPIEKVYEDKDLVVINKAPDMVVHPAPGNYSGTLVNAL 120

Query: 93  GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP-------------ST 139
             +    +  +   R   V RLD NT GL+++  +      L                  
Sbjct: 121 MHNIKDLSNINGVIRPGIVHRLDKNTSGLIVIAKNDFSHLKLSDMFKNKDISKTYICICK 180

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
                   R    + ++  N     +V +          +  + G  + V V +  G+  
Sbjct: 181 GIFSEKTGRIENLIGRNPKNRKTMTVVQKNGKNAISNYKILDEAGDFSLVEVKIETGRTH 240

Query: 200 EIKKVFEFFNWKVN 213
           +I+   +  N  + 
Sbjct: 241 QIRVHMKSINHPIL 254


>gi|78044748|ref|YP_361490.1| S4 domain-containing protein [Carboxydothermus hydrogenoformans
          Z-2901]
 gi|77996863|gb|ABB15762.1| S4 domain protein [Carboxydothermus hydrogenoformans Z-2901]
          Length = 73

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 12/42 (28%), Positives = 21/42 (50%)

Query: 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
          + ++MI    V VNG++  R    +   D +E+ G P+   E
Sbjct: 28 QAKQMIKSGMVLVNGVVETRRKKKIYPGDRVEIAGGPVLIVE 69


>gi|312868744|ref|ZP_07728936.1| ribosomal protein S4 [Lactobacillus oris PB013-T2-3]
 gi|311095730|gb|EFQ53982.1| ribosomal protein S4 [Lactobacillus oris PB013-T2-3]
          Length = 201

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A+ RR+  +++    + V+G  ++  +  V     I V
Sbjct: 94  RLDNMVYRLGLATTRRQARQLVNHGHITVDGKRVDIPSYEVDVNQVIGV 142


>gi|284033972|ref|YP_003383903.1| 30S ribosomal protein S4 [Kribbella flavida DSM 17836]
 gi|283813265|gb|ADB35104.1| ribosomal protein S4 [Kribbella flavida DSM 17836]
          Length = 202

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR+  +++      VNGI +   +  V + D I+V
Sbjct: 92  RLDNVVYRAGLARTRRQARQLVVHGHFTVNGIKVNIPSYRVAAHDVIDV 140


>gi|312199993|ref|YP_004020054.1| ribosomal protein S4 [Frankia sp. EuI1c]
 gi|311231329|gb|ADP84184.1| ribosomal protein S4 [Frankia sp. EuI1c]
          Length = 208

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG A SR    + +    V+VNG  ++  +  V   D +E+
Sbjct: 99  RLDNVVYRAGFAPSRDAARQAVRHGHVQVNGGKVDIPSYRVSDNDIVEI 147


>gi|266620368|ref|ZP_06113303.1| hemolysin A [Clostridium hathewayi DSM 13479]
 gi|288868042|gb|EFD00341.1| hemolysin A [Clostridium hathewayi DSM 13479]
          Length = 271

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 21/178 (11%), Positives = 52/178 (29%), Gaps = 2/178 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++ +  +A SR + + +I    V V G   ++A      + +IEV G  L+   R
Sbjct: 3   ERLDVLLVKRNLAESREKAKAVIMSGIVYVEGQKEDKAGTTFDESVNIEVRGHTLKYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L                              ++  G + +    +        L  
Sbjct: 63  GGLKLEKAMSHFGVMLEGKTCMDVGSST-GGFTDCMLQNGAVKVYAVDVGHGQLAWKLRN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +   +   +  V      ++   + +    +        ++  L  +      + 
Sbjct: 122 DERVVCMEKTNIRYVTPDEIQEKIDFSSIDVSFISLTKVLEPVKRLLKEEGEIVCLIK 179


>gi|303247017|ref|ZP_07333293.1| ribosomal protein S4 [Desulfovibrio fructosovorans JJ]
 gi|302491724|gb|EFL51607.1| ribosomal protein S4 [Desulfovibrio fructosovorans JJ]
          Length = 208

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI R G A SR +  +++      VNG  +   ++ V   D IEV
Sbjct: 99  RMDNVIYRLGFANSRNQARQLVRHGIFTVNGRRVTIPSLQVKVGDVIEV 147


>gi|315633478|ref|ZP_07888768.1| 30S ribosomal protein S4 [Aggregatibacter segnis ATCC 33393]
 gi|315477520|gb|EFU68262.1| 30S ribosomal protein S4 [Aggregatibacter segnis ATCC 33393]
          Length = 206

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R E  ++++ + + VNG ++   +  V   D I V
Sbjct: 97  RLDNVVYRMGFAATRAEARQLVSHKAIVVNGRVVNIPSFQVSVDDVISV 145


>gi|218132230|ref|ZP_03461034.1| hypothetical protein BACPEC_00087 [Bacteroides pectinophilus ATCC
           43243]
 gi|217992889|gb|EEC58889.1| hypothetical protein BACPEC_00087 [Bacteroides pectinophilus ATCC
           43243]
          Length = 266

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 21/162 (12%), Positives = 49/162 (30%), Gaps = 2/162 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++   G++ +R + + +I    V V+G   ++       +  IEV G  LR   R
Sbjct: 3   ERLDVLMVNRGLSETRSKAQAIIMSGIVYVDGSKEDKCGQKFDESVSIEVRGSTLRYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L         T                    ++  G + + +  +        L +
Sbjct: 63  GGLKLEKAMNNFDVTLEGKVCMDVGSST-GGFTDCMLQNGAVKVYSVDVGNGQLAWKLRQ 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
              +   +   +  V      D+ +   +    +        
Sbjct: 122 DERVVVMEKTNIRYVTPDDIADRIRFASIDVSFISLTKVLVP 163


>gi|254302377|ref|ZP_04969735.1| hypothetical protein FNP_2433 [Fusobacterium nucleatum subsp.
          polymorphum ATCC 10953]
 gi|148322569|gb|EDK87819.1| hypothetical protein FNP_2433 [Fusobacterium nucleatum subsp.
          polymorphum ATCC 10953]
          Length = 71

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 14/71 (19%), Positives = 29/71 (40%), Gaps = 9/71 (12%)

Query: 1  MKDKNIVQENFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
          MK+   V+ +    ++ + +       +G     E +++I    VKVNG + +R    + 
Sbjct: 1  MKNIEKVKISTEFIKLDQFLKWLAVVDSG----SEAKQVILDGMVKVNGDVEKRRGRKIY 56

Query: 56 STDHIEVDGVP 66
              +EV    
Sbjct: 57 PEYKVEVFDKI 67


>gi|243180|gb|AAB21091.1| ribosomal protein S4 [Bacillus stearothermophilus, Peptide, 198 aa]
          Length = 198

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR+  +++    + V+G  +   +  V     I V
Sbjct: 91  RLDNLVYRLGLARTRRQARQLVTHGHIIVDGSRVNIPSYRVKPGQTIAV 139


>gi|213964948|ref|ZP_03393147.1| ribosomal protein S4 [Corynebacterium amycolatum SK46]
 gi|213952484|gb|EEB63867.1| ribosomal protein S4 [Corynebacterium amycolatum SK46]
          Length = 201

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR+  ++++     VNG  +   +  V   D I+V
Sbjct: 92  RLDNVVYRAGLARTRRQARQLVSHGHFTVNGKKINVPSFQVSQYDIIDV 140


>gi|256380568|ref|YP_003104228.1| 30S ribosomal protein S4 [Actinosynnema mirum DSM 43827]
 gi|255924871|gb|ACU40382.1| ribosomal protein S4 [Actinosynnema mirum DSM 43827]
          Length = 201

 Score = 45.9 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 1/56 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+  V+ RAG+A +RR+  ++++     VNG  +   +  V   D I+V    L  
Sbjct: 92  RLDNVVYRAGLARTRRQARQLVSHGHFLVNGHKVNIPSYQVSKFDIIDVKPKSLPL 147


>gi|320540587|ref|ZP_08040237.1| 30S ribosomal subunit protein S4 [Serratia symbiotica str. Tucson]
 gi|320029518|gb|EFW11547.1| 30S ribosomal subunit protein S4 [Serratia symbiotica str. Tucson]
          Length = 206

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 ASLELAEQREKPT 169


>gi|303256474|ref|ZP_07342488.1| ribosomal protein S4 [Burkholderiales bacterium 1_1_47]
 gi|331000668|ref|ZP_08324321.1| ribosomal protein S4 [Parasutterella excrementihominis YIT 11859]
 gi|302859965|gb|EFL83042.1| ribosomal protein S4 [Burkholderiales bacterium 1_1_47]
 gi|329570880|gb|EGG52591.1| ribosomal protein S4 [Parasutterella excrementihominis YIT 11859]
          Length = 207

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++   + VNG  +   + +V + D I V
Sbjct: 98  RLDNVVYRMGFGCTRAEARQLVSHCAISVNGNKVNIPSYSVKAGDVIAV 146


>gi|297571513|ref|YP_003697287.1| hemolysin A [Arcanobacterium haemolyticum DSM 20595]
 gi|296931860|gb|ADH92668.1| hemolysin A [Arcanobacterium haemolyticum DSM 20595]
          Length = 274

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 12/55 (21%), Positives = 24/55 (43%), Gaps = 1/55 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
             RV   + R G+A SR E   +I   RV ++  ++ + +  +     + V+  
Sbjct: 3  KLIRVDAELVRRGLARSRSEAAELINAGRVLLDKNVVVKPSRQMDPAQALIVNDQ 57


>gi|288919689|ref|ZP_06414016.1| ribosomal protein S4 [Frankia sp. EUN1f]
 gi|288348878|gb|EFC83128.1| ribosomal protein S4 [Frankia sp. EUN1f]
          Length = 209

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SR    + +    V+VNG  ++  +  V   D +E+
Sbjct: 99  RLDNVVYRGGFAPSRDAARQAVRHGHVQVNGRKVDIPSYRVTENDIVEI 147


>gi|328906823|gb|EGG26589.1| S4 domain protein [Propionibacterium sp. P08]
          Length = 73

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 11/58 (18%), Positives = 20/58 (34%), Gaps = 9/58 (15%)

Query: 10 NFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          +    R+ + +     A  G     +   +IA   V VN  +  R    +   D + V
Sbjct: 3  DDQMIRLGQYLKFANLAETGG----QARELIASGMVSVNDEVETRRGRQLHPGDEVRV 56


>gi|209525233|ref|ZP_03273776.1| photosystem II S4 domain protein [Arthrospira maxima CS-328]
 gi|209494418|gb|EDZ94730.1| photosystem II S4 domain protein [Arthrospira maxima CS-328]
          Length = 259

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 16/65 (24%), Positives = 30/65 (46%), Gaps = 2/65 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             K  +       R+   IA AG   SR ++  +I    V+VN   +++A++ + + D I
Sbjct: 172 PKKKAMTTVEASLRLD-AIASAGFGMSRSKMVNLIDGGDVRVNWKEVKQASIAIKTGDLI 230

Query: 61  EVDGV 65
            + G 
Sbjct: 231 AIRGK 235


>gi|158317765|ref|YP_001510273.1| RNA-binding S4 domain-containing protein [Frankia sp. EAN1pec]
 gi|158113170|gb|ABW15367.1| RNA-binding S4 domain protein [Frankia sp. EAN1pec]
          Length = 209

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SR    + +    V+VNG  ++  +  V   D +E+
Sbjct: 99  RLDNVVYRGGFAPSRDAARQAVRHGHVQVNGRKVDIPSYRVTENDIVEI 147


>gi|227535269|ref|ZP_03965318.1| ribosomal protein S4 [Lactobacillus paracasei subsp. paracasei ATCC
           25302]
 gi|227187153|gb|EEI67220.1| ribosomal protein S4 [Lactobacillus paracasei subsp. paracasei ATCC
           25302]
          Length = 239

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+AS R +  +++    + V+G  ++  +  V     I +
Sbjct: 130 RLDNLVFRLGLASSRPQARQLVNHGHITVDGKRVDIPSYEVEPGQVIAL 178


>gi|163752126|ref|ZP_02159331.1| 30S ribosomal protein S4 [Shewanella benthica KT99]
 gi|161327961|gb|EDP99136.1| 30S ribosomal protein S4 [Shewanella benthica KT99]
          Length = 206

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V ++D I +
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKSIMVNGSVVNIPSFKVSASDVICI 145


>gi|289641139|ref|ZP_06473307.1| ribosomal protein S4 [Frankia symbiont of Datisca glomerata]
 gi|289509080|gb|EFD30011.1| ribosomal protein S4 [Frankia symbiont of Datisca glomerata]
          Length = 208

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           R+  V+ RAG A SR    + +    V VNG  ++  +  V   D +E+    
Sbjct: 99  RLDNVVYRAGFAPSRDAARQAVRHGHVVVNGGKVDIPSYRVSENDIVEIAPKA 151


>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 = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 38/264 (14%), Positives = 80/264 (30%), Gaps = 54/264 (20%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRRE--------VERMIAQQRVKVNGILLERAAV 52
           MK+  + +E +   R+ + +       R+E        + + +   ++KVNG  ++    
Sbjct: 1   MKEYRV-EEKYIGVRIDRYL-------RKEFPNLSLGDIFKTLRTGKIKVNGKKVKE-NY 51

Query: 53  NVMSTDHIE----VDGVP------------------LRKAERTRLWLYHKPIGLVTTHSD 90
             +  D I+    V+                     +   +   L  Y K   L+   S 
Sbjct: 52  RFLEEDRIQNYLQVEEKEKMTFIHLSQEEKKRLEDGIFYQDTDILVFYKKAGELMHKGSS 111

Query: 91  PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
            D                  V RLD  T GL+L      + R L     +   + +    
Sbjct: 112 HDYGLAEQFQAYFQNEDFHFVNRLDKETSGLVLGGKCLKIVRELAEAIKKRTIIKKYYII 171

Query: 151 GQVDQDKLNLLKKGIVIQGI------CYGD-------MQVTLDTQKGSNAWVTVGLREGK 197
            +   +K +   K  + +G                     ++  +    + +   L  G+
Sbjct: 172 IEGIPEKNHFSLKTYLKKGENKVLESKTAKEEYKECSASFSVIRKNKEYSLLEAVLETGR 231

Query: 198 NREIKKVFEFFNWKVNRLIRISYG 221
             +++       + +  L  I YG
Sbjct: 232 THQLRVQLAGIGFPI--LGDIKYG 253


>gi|294893083|ref|XP_002774330.1| hypothetical protein Pmar_PMAR007911 [Perkinsus marinus ATCC
          50983]
 gi|239879652|gb|EER06146.1| hypothetical protein Pmar_PMAR007911 [Perkinsus marinus ATCC
          50983]
          Length = 96

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 11/46 (23%), Positives = 23/46 (50%), Gaps = 1/46 (2%)

Query: 5  NIVQENFTP-QRVSKVIARAGIASRREVERMIAQQRVKVNGILLER 49
            +Q+  T  + +++ I+ +G  SR + E  I    V V+G ++  
Sbjct: 43 RTLQKMTTSFEWLARRISLSGQMSRSQAEVAIRNGEVVVDGQVVRH 88


>gi|227833157|ref|YP_002834864.1| hypothetical protein cauri_1333 [Corynebacterium aurimucosum ATCC
          700975]
 gi|262182352|ref|ZP_06041773.1| hypothetical protein CaurA7_00025 [Corynebacterium aurimucosum
          ATCC 700975]
 gi|227454173|gb|ACP32926.1| hypothetical protein cauri_1333 [Corynebacterium aurimucosum ATCC
          700975]
          Length = 269

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 22/50 (44%), Gaps = 1/50 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          R+   + R  IA SR +   MI   RV V G    + A  V     I+V+
Sbjct: 7  RLDAELVRRKIARSREQAVEMIKAGRVTVGGFKATKPATVVEPEVSIKVE 56


>gi|73748343|ref|YP_307582.1| 30S ribosomal protein S4 [Dehalococcoides sp. CBDB1]
 gi|289432391|ref|YP_003462264.1| ribosomal protein S4 [Dehalococcoides sp. GT]
 gi|90101688|sp|Q3ZZP7|RS4_DEHSC RecName: Full=30S ribosomal protein S4
 gi|73660059|emb|CAI82666.1| ribosomal protein S4 [Dehalococcoides sp. CBDB1]
 gi|288946111|gb|ADC73808.1| ribosomal protein S4 [Dehalococcoides sp. GT]
          Length = 207

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   SR +  +++    + VNG   +  +  +     I V
Sbjct: 98  RLDNVLFRLGFGTSRAQARQIVMHGHILVNGQKTDIPSYLIKEGQEITV 146


>gi|15644222|ref|NP_229273.1| 30S ribosomal protein S4 [Thermotoga maritima MSB8]
 gi|7388196|sp|Q9X1I3|RS4_THEMA RecName: Full=30S ribosomal protein S4
 gi|4982039|gb|AAD36541.1|AE001798_6 ribosomal protein S4 [Thermotoga maritima MSB8]
          Length = 209

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 14/71 (19%), Positives = 28/71 (39%), Gaps = 1/71 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G A +RR+  +++      VNG  +   +  +   D +EV           
Sbjct: 99  RLDNVVYRMGFAINRRQARQLVNHGHFLVNGKKVNIPSYLLRPNDVVEVREKSRDLEVIK 158

Query: 74  RLWLYHKPIGL 84
           +    +K   +
Sbjct: 159 KAIEANKERSI 169


>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 = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 31/227 (13%), Positives = 68/227 (29%), Gaps = 32/227 (14%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------------G 64
            +      SR+ + +M  + R+++N   ++   V + S D IE +               
Sbjct: 33  FLKNRLKMSRKFIRKMGREYRIRLNCRYVKFTEVKLNSGDLIEFNLNFKEKTYYDPAPLD 92

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-----SVGRLDINTE 119
           + +   +R  L +      LV         + V   L  + ++        + RLD NT 
Sbjct: 93  LDIIYEDRHLLVINKPANMLVHPTPVEKSNTIVNGVLYHMRNQGNYNLVRPIHRLDRNTT 152

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL-------------LKKGIV 166
           GLLL+  +      +                   + +                 +K+ + 
Sbjct: 153 GLLLIAKNQYAHNYITHQFQNNNIHREYLAFVHGNVEFKKESINAPIGKTRDSLIKRKVD 212

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     + +    G  + + V L  G+  +I+         + 
Sbjct: 213 HTLGKRAVTHIKVVKPGGLISLIRVKLETGRTHQIRVHLSHLGHPLL 259


>gi|327290601|ref|XP_003230011.1| PREDICTED: general transcription factor 3C polypeptide 2-like,
           partial [Anolis carolinensis]
          Length = 925

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 16/116 (13%), Positives = 28/116 (24%), Gaps = 3/116 (2%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD---DFTRMKKNSSQKNGLSKQ 298
           ++  GP   EE   +   P    +    +      E PD             ++   +  
Sbjct: 70  KKTRGPEDEEEEAPHGALPAQPEDKKEEEEVTPQEEQPDELHGAAAPVLGHPEEAPSAVA 129

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                    R         +G        +          PS P+K   +R    K
Sbjct: 130 PPRPKGPRGRKPRKGAPGRRGGRPKSSGGAATSPGPSLNGPSLPAKVPKKRGRKSK 185


>gi|226326148|ref|ZP_03801666.1| hypothetical protein COPCOM_03967 [Coprococcus comes ATCC 27758]
 gi|225205690|gb|EEG88044.1| hypothetical protein COPCOM_03967 [Coprococcus comes ATCC 27758]
          Length = 81

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 10/42 (23%), Positives = 20/42 (47%)

Query: 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
          E + +I +  VKVNG +  R    +   D +  +G  ++  +
Sbjct: 40 EAKEVITEGLVKVNGEVDTRRGKKLYDGDVVTFNGEEIKIEK 81


>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 = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 28/198 (14%), Positives = 59/198 (29%), Gaps = 3/198 (1%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAA--VNVMSTDHIEVDGVPLRKAERTRL 75
           K++A     S  E + +I    V   G  +  A   +NV +   ++    P    E   L
Sbjct: 8   KILAMQLNISNNEAKDLIDSGLVFAKGQKVAIARALMNVNTKFSVQETSKPSVIFEDENL 67

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
              +KP  + +       +  +   L    S V+ + + +   +  +       + ++  
Sbjct: 68  LAINKPAFITSEKISQMYKFPLLHRLDKETSGVLLLVKNEEFAKRAIEEFKHMRVEKIYI 127

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
                 L          +           I  +        VT     G    V V ++ 
Sbjct: 128 AAVRGILSEETRVSEPILTIKSKGAAISKIS-KDGKEAVSDVTPLMVVGKKTLVKVAIKT 186

Query: 196 GKNREIKKVFEFFNWKVN 213
           G+  +I+      N  + 
Sbjct: 187 GRTHQIRLHLASINAPII 204


>gi|332670186|ref|YP_004453194.1| hemolysin A [Cellulomonas fimi ATCC 484]
 gi|332339224|gb|AEE45807.1| hemolysin A [Cellulomonas fimi ATCC 484]
          Length = 335

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 20/51 (39%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          R+   + R G+A SR     +IA  RV V G    RAA+ V   D +EV G
Sbjct: 4  RLDSELVRRGLARSRGHAGELIAAGRVSVRGTAARRAALQVDGGDAVEVVG 54


>gi|220905097|ref|YP_002480409.1| hypothetical protein Ddes_1834 [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
 gi|219869396|gb|ACL49731.1| hypothetical protein Ddes_1834 [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
          Length = 659

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 14/110 (12%), Positives = 29/110 (26%), Gaps = 4/110 (3%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               +       P  +       R     +      +     +  NG S+  + A P   
Sbjct: 21  RGRGDRPSRPGKPAGAGADKAERRRPGKDKTGGRSDQGSHGDTAGNGRSRGGRPAGPEMG 80

Query: 308 R-NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK---RSLRRTSAK 353
             +  +     +    +     G+   + R  P        RS  R +A+
Sbjct: 81  GTSRGAGADKKRAERPAPGGKPGEAGRDGRGRPGHKGPDDNRSGGRGAAR 130



 Score = 42.5 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 7/118 (5%), Positives = 19/118 (16%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            K   R          +          +      RP                   +    
Sbjct: 39  DKAERRRPGKDKTGGRSDQGSHGDTAGNGRSRGGRPAGPEMGGTSRGAGADKKRAERPAP 98

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             K        R    +            +     +     +P    + +    + ++
Sbjct: 99  GGKPGEAGRDGRGRPGHKGPDDNRSGGRGAARPSGKSRQEHTPGRGLRDAREIRAPRR 156



 Score = 40.9 bits (94), Expect = 0.28,   Method: Composition-based stats.
 Identities = 11/90 (12%), Positives = 19/90 (21%), Gaps = 2/90 (2%)

Query: 264 SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSS 323
                +          D+ TR + +   + G            RR             S 
Sbjct: 1   MSDQSKKDSRPPRPQQDEKTRGRGDRPSRPGKPAGAGADKAERRRPGKDKTGGRSDQGSH 60

Query: 324 FLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             +    R       P+ P      R +  
Sbjct: 61  GDTAGNGRSRGG--RPAGPEMGGTSRGAGA 88


>gi|197302368|ref|ZP_03167425.1| hypothetical protein RUMLAC_01097 [Ruminococcus lactaris ATCC
          29176]
 gi|197298547|gb|EDY33090.1| hypothetical protein RUMLAC_01097 [Ruminococcus lactaris ATCC
          29176]
          Length = 79

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR          RV VNG   + A+V V   D IE+
Sbjct: 1  MRLDKFLKVSRLIKRRTVANEACDAGRVLVNGKTAK-ASVKVKPGDVIEI 49


>gi|90962330|ref|YP_536246.1| heat shock protein 15 [Lactobacillus salivarius UCC118]
 gi|90821524|gb|ABE00163.1| Heat shock protein 15 [Lactobacillus salivarius UCC118]
          Length = 89

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 2/51 (3%)

Query: 14 QRVSKVIARAGIASRREVERMIA-QQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+ K +  + I  RR V + I+ Q R+ +NG + +  + NV   D I ++
Sbjct: 1  MRLDKFLKISRIIKRRTVAKEISSQGRITINGKVAKS-SSNVNVGDEIVIN 50


>gi|154244366|ref|YP_001415324.1| hypothetical protein Xaut_0409 [Xanthobacter autotrophicus Py2]
 gi|154158451|gb|ABS65667.1| conserved hypothetical protein [Xanthobacter autotrophicus Py2]
          Length = 527

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 5/107 (4%), Positives = 15/107 (14%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                 +                                     + G+  +         
Sbjct: 339 RPGGPNRPGFPDRPGGPNRPGFPDRPGAGPNRPGVPDRPGAGPNRPGVPDRPGAGPNRPD 398

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           R         +            R +   R  + P++         +
Sbjct: 399 RPDRPGAGPNRPDRPDRPGAGPNRPDRPDRPGAGPNRPDRPGAGQNR 445



 Score = 44.8 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 9/97 (9%), Positives = 16/97 (16%)

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
                    +   RP   +           N                V  R  A      
Sbjct: 326 QPGQPDRPVVGPGRPGGPNRPGFPDRPGGPNRPGFPDRPGAGPNRPGVPDRPGAGPNRPG 385

Query: 318 KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                    +   R +     P+ P +         +
Sbjct: 386 VPDRPGAGPNRPDRPDRPGAGPNRPDRPDRPGAGPNR 422



 Score = 36.3 bits (82), Expect = 6.7,   Method: Composition-based stats.
 Identities = 7/111 (6%), Positives = 18/111 (16%), Gaps = 8/111 (7%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK----LATPVH 306
            +            +                    + +   + G    +           
Sbjct: 374 PDRPGAGPNRPGVPDRPGAGPNRPDRPDRPGAGPNRPDRPDRPGAGPNRPDRPDRPGAGP 433

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK----RSLRRTSAK 353
            R         +           QR    +  P         R   + +A+
Sbjct: 434 NRPDRPGAGQNRPQQRPNAHRPSQRPNAGQNRPQQSRPQHNARPRPQHNAR 484



 Score = 36.3 bits (82), Expect = 8.0,   Method: Composition-based stats.
 Identities = 10/107 (9%), Positives = 25/107 (23%), Gaps = 3/107 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           ++         + +      +      +             R +++  Q N   + +  A
Sbjct: 424 DRPDRPGAGPNRPDRPGAGQNRPQQRPNAHRPSQRPNAGQNRPQQSRPQHNARPRPQHNA 483

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
            P  +R    +    +    +       R     R          RR
Sbjct: 484 RPPQQRARPQHNARPQH---NARPQHNARPPQQHRPRPQGGGGERRR 527



 Score = 36.3 bits (82), Expect = 8.2,   Method: Composition-based stats.
 Identities = 7/108 (6%), Positives = 23/108 (21%), Gaps = 1/108 (0%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           ++ G       + +      +         N   + P+   R  +  +      +Q +  
Sbjct: 414 DRPGAGPNRPDRPDRPGAGPNRPDRPGAGQNRPQQRPNAH-RPSQRPNAGQNRPQQSRPQ 472

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                R   +     +       +           +      R   + 
Sbjct: 473 HNARPRPQHNARPPQQRARPQHNARPQHNARPQHNARPPQQHRPRPQG 520


>gi|296332057|ref|ZP_06874521.1| 30S ribosomal protein S4 [Bacillus subtilis subsp. spizizenii ATCC
           6633]
 gi|305675548|ref|YP_003867220.1| 30S ribosomal protein S4 [Bacillus subtilis subsp. spizizenii str.
           W23]
 gi|296150828|gb|EFG91713.1| 30S ribosomal protein S4 [Bacillus subtilis subsp. spizizenii ATCC
           6633]
 gi|305413792|gb|ADM38911.1| 30S ribosomal protein S4 [Bacillus subtilis subsp. spizizenii str.
           W23]
          Length = 200

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ + G+A +RR+  +++    + V+G  ++  +  V     I V
Sbjct: 93  RLDNVVYKLGLARTRRQARQLVNHGHILVDGSRVDIPSYQVKPGQTIGV 141


>gi|296137040|ref|YP_003644282.1| ribosomal protein S4 [Thiomonas intermedia K12]
 gi|294341217|emb|CAZ89618.1| 30S ribosomal subunit protein S4 [Thiomonas sp. 3As]
 gi|295797162|gb|ADG31952.1| ribosomal protein S4 [Thiomonas intermedia K12]
          Length = 207

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG +L   +  V + D + V
Sbjct: 98  RLDNVVYRMGYGSTRAEARQLVSHRSITVNGKVLNIPSALVKTGDVVAV 146


>gi|152972204|ref|YP_001337350.1| 30S ribosomal protein S4 [Klebsiella pneumoniae subsp. pneumoniae
           MGH 78578]
 gi|206575742|ref|YP_002236302.1| ribosomal protein S4 [Klebsiella pneumoniae 342]
 gi|238896793|ref|YP_002921538.1| 30S ribosomal protein S4 [Klebsiella pneumoniae NTUH-K2044]
 gi|262045155|ref|ZP_06018182.1| 30S ribosomal protein S4 [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|288933290|ref|YP_003437349.1| ribosomal protein S4 [Klebsiella variicola At-22]
 gi|290512092|ref|ZP_06551460.1| 30S ribosomal protein S4 [Klebsiella sp. 1_1_55]
 gi|330002271|ref|ZP_08304265.1| ribosomal protein S4 [Klebsiella sp. MS 92-3]
 gi|172052444|sp|A6TEU9|RS4_KLEP7 RecName: Full=30S ribosomal protein S4
 gi|226699076|sp|B5XNB5|RS4_KLEP3 RecName: Full=30S ribosomal protein S4
 gi|150957053|gb|ABR79083.1| 30S ribosomal protein S4 [Klebsiella pneumoniae subsp. pneumoniae
           MGH 78578]
 gi|206564800|gb|ACI06576.1| ribosomal protein S4 [Klebsiella pneumoniae 342]
 gi|238549120|dbj|BAH65471.1| 30S ribosomal protein S4 [Klebsiella pneumoniae subsp. pneumoniae
           NTUH-K2044]
 gi|259037475|gb|EEW38719.1| 30S ribosomal protein S4 [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|288888019|gb|ADC56337.1| ribosomal protein S4 [Klebsiella variicola At-22]
 gi|289775882|gb|EFD83882.1| 30S ribosomal protein S4 [Klebsiella sp. 1_1_55]
 gi|328537344|gb|EGF63594.1| ribosomal protein S4 [Klebsiella sp. MS 92-3]
          Length = 206

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V + D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVKANDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|91216885|ref|ZP_01253849.1| 30S ribosomal protein S4 [Psychroflexus torquis ATCC 700755]
 gi|91185046|gb|EAS71425.1| 30S ribosomal protein S4 [Psychroflexus torquis ATCC 700755]
          Length = 201

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 13/70 (18%), Positives = 28/70 (40%), Gaps = 1/70 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V  R GIA +R    ++++ + + VNG L+   +  +   D + +           
Sbjct: 94  RLDNVTYRLGIAPTRSGARQLVSHKHITVNGQLVNIPSYQIKPNDVVSIREKSKSLNVVQ 153

Query: 74  RLWLYHKPIG 83
                +K + 
Sbjct: 154 ESLSNNKSVN 163


>gi|32892104|gb|AAP88991.1| ribosomal protein S4 [Passiflora edmundoi]
          Length = 183

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 13/82 (15%), Positives = 29/82 (35%), Gaps = 1/82 (1%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+  ++ R G+AS   +  +++  + + VNG +++  +      D I V      K   
Sbjct: 71  MRLDNILFRLGMASTIPQARQLVNHRHILVNGRIVDIPSYRCKPQDLITVKDEQKSKDMI 130

Query: 73  TRLWLYHKPIGLVTTHSDPDGR 94
                      L    +    +
Sbjct: 131 QNYLDSFPQEKLPKHLTLHPFQ 152


>gi|114319643|ref|YP_741326.1| SSU ribosomal protein S4P [Alkalilimnicola ehrlichii MLHE-1]
 gi|122312435|sp|Q0ABF1|RS4_ALHEH RecName: Full=30S ribosomal protein S4
 gi|114226037|gb|ABI55836.1| SSU ribosomal protein S4P [Alkalilimnicola ehrlichii MLHE-1]
          Length = 206

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 13/47 (27%), Positives = 27/47 (57%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  V+ R G A+ R E  ++++ + V+VNG ++   ++ V   D +
Sbjct: 97  RLDNVVYRMGFATTRAEARQLVSHRGVQVNGRVVNVPSMQVSPGDLV 143


>gi|314924148|gb|EFS87979.1| ribosomal protein S4 [Propionibacterium acnes HL001PA1]
          Length = 201

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR+  +M++     VNG  +   +  V + D I+V
Sbjct: 92  RLDNVVYRAGLAATRRQARQMVSHGHFLVNGKKVNIPSYRVSTHDIIDV 140


>gi|194290998|ref|YP_002006905.1| 30S ribosomal protein s4 [Cupriavidus taiwanensis LMG 19424]
 gi|226697831|sp|B3R7E4|RS4_CUPTR RecName: Full=30S ribosomal protein S4
 gi|193224833|emb|CAQ70844.1| 30S ribosomal subunit protein S4 [Cupriavidus taiwanensis LMG
           19424]
          Length = 207

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  L   +  + S D I +
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAILVNGQTLNVPSAQIKSGDVITI 146


>gi|154687087|ref|YP_001422248.1| 30S ribosomal protein S4 [Bacillus amyloliquefaciens FZB42]
 gi|308174649|ref|YP_003921354.1| 30S ribosomal protein S4 (BS4) [Bacillus amyloliquefaciens DSM 7]
 gi|171855002|sp|A7Z7P1|RS4_BACA2 RecName: Full=30S ribosomal protein S4
 gi|154352938|gb|ABS75017.1| RpsD [Bacillus amyloliquefaciens FZB42]
 gi|307607513|emb|CBI43884.1| ribosomal protein S4 (BS4) [Bacillus amyloliquefaciens DSM 7]
 gi|328554576|gb|AEB25068.1| 30S ribosomal protein S4 [Bacillus amyloliquefaciens TA208]
 gi|328912981|gb|AEB64577.1| 30S ribosomal protein S4 [Bacillus amyloliquefaciens LL3]
          Length = 200

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ + G+A +RR+  +++    + V+G  ++  +  V     I V
Sbjct: 93  RLDNVVYKLGLARTRRQARQLVNHGHILVDGSRVDIPSYQVKPGQTIGV 141


>gi|120402446|ref|YP_952275.1| 30S ribosomal protein S4 [Mycobacterium vanbaalenii PYR-1]
 gi|145225547|ref|YP_001136225.1| 30S ribosomal protein S4 [Mycobacterium gilvum PYR-GCK]
 gi|315445899|ref|YP_004078778.1| 30S ribosomal protein S4P [Mycobacterium sp. Spyr1]
 gi|152112236|sp|A1T519|RS4_MYCVP RecName: Full=30S ribosomal protein S4
 gi|189045387|sp|A4TEJ4|RS4_MYCGI RecName: Full=30S ribosomal protein S4
 gi|119955264|gb|ABM12269.1| SSU ribosomal protein S4P [Mycobacterium vanbaalenii PYR-1]
 gi|145218033|gb|ABP47437.1| SSU ribosomal protein S4P [Mycobacterium gilvum PYR-GCK]
 gi|315264202|gb|ADU00944.1| SSU ribosomal protein S4P [Mycobacterium sp. Spyr1]
          Length = 201

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 1/61 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ RAG+A +RR   ++++     VNG+ ++  +  V   D I+V    +      
Sbjct: 92  RLDNVVYRAGLARTRRMARQLVSHGHFTVNGVKVDVPSYRVSQYDIIDVKDKSINTLPFE 151

Query: 74  R 74
            
Sbjct: 152 V 152


>gi|110635705|ref|YP_675913.1| RNA-binding S4 [Mesorhizobium sp. BNC1]
 gi|110286689|gb|ABG64748.1| RNA-binding S4 [Chelativorans sp. BNC1]
          Length = 95

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 17/65 (26%), Positives = 26/65 (40%), Gaps = 5/65 (7%)

Query: 10 NFTPQRVSKVI--ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGV 65
              QR+ K +  AR  + SR    ++    RV+VN   +  A+  V   D   I +D  
Sbjct: 3  TDERQRIDKWLFFARV-VKSRSLAAKLAQAGRVRVNREKINEASQLVRPGDVLTITLDRR 61

Query: 66 PLRKA 70
           L   
Sbjct: 62 ILVYR 66


>gi|271962663|ref|YP_003336859.1| 30S ribosomal protein S4 [Streptosporangium roseum DSM 43021]
 gi|270505838|gb|ACZ84116.1| 30S ribosomal protein S4 [Streptosporangium roseum DSM 43021]
          Length = 208

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG A SR    + +    + VNG  ++  +  V   D +EV
Sbjct: 99  RLDNVVYRAGFAESRDAARQQVRHGHILVNGKKVDIPSYRVREHDIVEV 147


>gi|153854752|ref|ZP_01995986.1| hypothetical protein DORLON_01984 [Dorea longicatena DSM 13814]
 gi|149752659|gb|EDM62590.1| hypothetical protein DORLON_01984 [Dorea longicatena DSM 13814]
          Length = 85

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 3/57 (5%)

Query: 7  VQENFTPQRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          +QEN    R+ K +  + +  RR          RV VN    + A+V V   D IE+
Sbjct: 1  MQENKD-MRLDKFLKVSRLIKRRTVANEACDAGRVLVNDKPAK-ASVKVKPGDIIEI 55


>gi|170742911|ref|YP_001771566.1| helicase domain-containing protein [Methylobacterium sp. 4-46]
 gi|168197185|gb|ACA19132.1| helicase domain protein [Methylobacterium sp. 4-46]
          Length = 1154

 Score = 45.9 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 10/114 (8%), Positives = 26/114 (22%), Gaps = 1/114 (0%)

Query: 241  LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
            L E    H     Q N        +   + +     +         +   +     +   
Sbjct: 999  LIEVWRLHRHPRGQANRHQGRGRPQNGPQAQGRSHQDGRPPRRDENQTGDRPRPQGRPGP 1058

Query: 301  LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                     + ++   A+          G+     +     P +R  R    ++
Sbjct: 1059 RWGERPADGVRADQGRAEHGRQEGARAEGRPPRGAQNGRG-PDERGGRPPQERR 1111



 Score = 41.7 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 7/105 (6%), Positives = 18/105 (17%), Gaps = 2/105 (1%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            R           +                     ++         ++  Q+   ++ +  
Sbjct: 1031 RSHQDGRPPRRDENQTGDRPRPQGRPGPRWGERPADGVRADQGRAEHGRQEGARAEGRPP 1090

Query: 302  ATPVHRRNLASNVWMAKGIHSSF--LSDSGQREENHRRSPSFPSK 344
                + R                        R     R+P   S 
Sbjct: 1091 RGAQNGRGPDERGGRPPQERRDGGYRGQGDSRPPRRERAPDPDSP 1135


>gi|218961407|ref|YP_001741182.1| 30S ribosomal subunit protein S4 [Candidatus Cloacamonas
           acidaminovorans]
 gi|167730064|emb|CAO80976.1| 30S ribosomal subunit protein S4 [Candidatus Cloacamonas
           acidaminovorans]
          Length = 205

 Score = 45.6 bits (106), Expect = 0.010,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R +  + I      VNG  ++  +  V + D IEV
Sbjct: 96  RLDNVVYRMGFAVTRMQARQFINHGHFLVNGRKVDIPSYLVKAGDIIEV 144


>gi|167758092|ref|ZP_02430219.1| hypothetical protein CLOSCI_00430 [Clostridium scindens ATCC 35704]
 gi|167663989|gb|EDS08119.1| hypothetical protein CLOSCI_00430 [Clostridium scindens ATCC 35704]
          Length = 269

 Score = 45.6 bits (106), Expect = 0.010,   Method: Composition-based stats.
 Identities = 24/178 (13%), Positives = 51/178 (28%), Gaps = 2/178 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++ +  +A SR + + +I    V V+G   ++A         IEV G  L    R
Sbjct: 3   ERLDILLVKRNLAASREKAKAIIMSGSVFVDGQREDKAGATFPEKAAIEVRGHTLPYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L         T                    ++  G   +    +     D  L +
Sbjct: 63  GGLKLEKALRNFDVTVDGKVCTDVGSST-GGFTDCMLQNGARKVYAIDVGRGQLDWKLRQ 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +   +   +  V      +    + +    +        +   L  +    A + 
Sbjct: 122 DERVVCMEKTNIRYVTPEDIGEPVDFSSIDVSFISLTKVLLPIHNYLKDKGQIVALIK 179


>gi|77557010|gb|ABA99806.1| retrotransposon protein, putative, unclassified [Oryza sativa
           Japonica Group]
          Length = 1070

 Score = 45.6 bits (106), Expect = 0.010,   Method: Composition-based stats.
 Identities = 10/94 (10%), Positives = 17/94 (18%)

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW 315
            +   + +SE       N                              P   R       
Sbjct: 274 TIMQAVGASEERAPRGHNGAGGSRRGERSTPGGGRASGPRDGGPGSGRPADARGKRKQEG 333

Query: 316 MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                       S +R E    +     +R  +R
Sbjct: 334 TPPPSPHRAARASSRRPEGATPTSQPEGERKKKR 367



 Score = 40.2 bits (92), Expect = 0.56,   Method: Composition-based stats.
 Identities = 6/64 (9%), Positives = 11/64 (17%)

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                + +        RR   S     +            R  + R              
Sbjct: 281 ASEERAPRGHNGAGGSRRGERSTPGGGRASGPRDGGPGSGRPADARGKRKQEGTPPPSPH 340

Query: 351 SAKK 354
            A +
Sbjct: 341 RAAR 344


>gi|323706478|ref|ZP_08118039.1| ribosomal protein S4 [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323534198|gb|EGB23988.1| ribosomal protein S4 [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 206

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 13/51 (25%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  V+ R  IAS R +  + ++   + VNG  ++  +  V + D + V  
Sbjct: 99  RLDNVVYRLSIASSRAQARQFVSHGHILVNGKKVDIPSYLVKAGDVVSVKD 149


>gi|310779569|ref|YP_003967902.1| SSU ribosomal protein S4P [Ilyobacter polytropus DSM 2926]
 gi|309748892|gb|ADO83554.1| SSU ribosomal protein S4P [Ilyobacter polytropus DSM 2926]
          Length = 195

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 3/71 (4%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRKAE 71
           R+  V+ R GIA +RR+  ++++   + VNG  +  A+  V   D I V  +   +   +
Sbjct: 89  RLDNVVYRLGIAKTRRQARQVVSHGHIAVNGRKVNIASYRVKVGDVISVIENSKNVEIIK 148

Query: 72  RTRLWLYHKPI 82
                      
Sbjct: 149 SAVEASNAPSW 159


>gi|304439715|ref|ZP_07399614.1| 30S ribosomal protein S4 [Peptoniphilus duerdenii ATCC BAA-1640]
 gi|304371790|gb|EFM25397.1| 30S ribosomal protein S4 [Peptoniphilus duerdenii ATCC BAA-1640]
          Length = 203

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            R+  +  R G A S R+  ++++   V VNG  L   +      D I +
Sbjct: 93  MRLDNLAYRMGFANSIRQARQLVSHGHVHVNGKKLNIPSYRCKPGDVISL 142


>gi|302388060|ref|YP_003823882.1| ribosomal protein S4 [Clostridium saccharolyticum WM1]
 gi|302198688|gb|ADL06259.1| ribosomal protein S4 [Clostridium saccharolyticum WM1]
          Length = 197

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +RRE  +M+  + + VNG  +   +  + + D IEV
Sbjct: 88  RLDNVVFRMGFGRTRRETRQMVDHKSILVNGKCVNIPSYLIKAGDVIEV 136


>gi|256544532|ref|ZP_05471905.1| 30S ribosomal protein S4 [Anaerococcus vaginalis ATCC 51170]
 gi|256399857|gb|EEU13461.1| 30S ribosomal protein S4 [Anaerococcus vaginalis ATCC 51170]
          Length = 197

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +  R+G+A +RRE  +++    + VNG  ++  ++ V   D IEV
Sbjct: 88  RLDNIAFRSGLARTRREARQIVTHGHLLVNGKSVDIPSILVNEGDVIEV 136


>gi|188589050|ref|YP_001919604.1| S4 domain protein [Clostridium botulinum E3 str. Alaska E43]
 gi|251781016|ref|ZP_04823936.1| S4 domain protein [Clostridium botulinum E1 str. 'BoNT E Beluga']
 gi|188499331|gb|ACD52467.1| S4 domain protein [Clostridium botulinum E3 str. Alaska E43]
 gi|243085331|gb|EES51221.1| S4 domain protein [Clostridium botulinum E1 str. 'BoNT E Beluga']
          Length = 86

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   +      RV +NG + +  + ++   D IE+
Sbjct: 1  MRLDKYLKVSRIIKRRTVAKEACESGRVSINGKVAK-PSTDIKEDDVIEI 49


>gi|113869406|ref|YP_727895.1| 30S ribosomal protein S4 [Ralstonia eutropha H16]
 gi|123032616|sp|Q0K644|RS4_RALEH RecName: Full=30S ribosomal protein S4
 gi|113528182|emb|CAJ94527.1| SSU ribosomal protein S4 [Ralstonia eutropha H16]
          Length = 207

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  L   +  + S D + +
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAILVNGQTLNVPSAQIKSGDVVTI 146


>gi|325264326|ref|ZP_08131057.1| S4 RNA-binding domain protein [Clostridium sp. D5]
 gi|324030397|gb|EGB91681.1| S4 RNA-binding domain protein [Clostridium sp. D5]
          Length = 79

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR          RV VNG + + A+++V   D IE+
Sbjct: 1  MRLDKFLKVSRLIKRRTVANEACDAGRVLVNGTVAK-ASLHVKPGDIIEI 49


>gi|30248442|ref|NP_840512.1| 30S ribosomal protein S4 [Nitrosomonas europaea ATCC 19718]
 gi|41017978|sp|Q82X70|RS4A_NITEU RecName: Full=30S ribosomal protein S4 A
 gi|30138328|emb|CAD84336.1| Ribosomal protein S4:S4 domain [Nitrosomonas europaea ATCC 19718]
          Length = 208

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 23/73 (31%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V    G  S R E  +++    V +NG      +  V   D IE+           
Sbjct: 99  RLDNVAYNMGFGSSRSEARQIVRHNCVLLNGKRANIPSHLVEPGDLIEIAEHAKSYLRIK 158

Query: 74  RLWLYHKPIGLVT 86
                 K   + +
Sbjct: 159 ASIEAAKRRSIPS 171


>gi|218888069|ref|YP_002437390.1| radical SAM protein [Desulfovibrio vulgaris str. 'Miyazaki F']
 gi|218759023|gb|ACL09922.1| Radical SAM domain protein [Desulfovibrio vulgaris str. 'Miyazaki
           F']
          Length = 771

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 11/105 (10%), Positives = 26/105 (24%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P      +        S     R+             + + + + +N     ++     
Sbjct: 654 APGNRAGGKSGGRPNERSGGQDHRNHQGRGDRQGRGDRQERGSDADRNRRGHGERSGGKA 713

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
             R          G  ++  +++   +    R  S P  R   R 
Sbjct: 714 DGRPGGMPDGPGNGDRNANRNETRNDKRPDSRPGSRPGSRPDPRN 758



 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 18/106 (16%), Positives = 30/106 (28%), Gaps = 1/106 (0%)

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
                     AP   +      RPN  S   D      +   Q  G  +++      +RR
Sbjct: 644 PPAAGGHAPGAPGNRAGGKSGGRPNERSGGQDHRNHQGRGDRQGRGDRQERGSDADRNRR 703

Query: 309 NLASNVWMAKGIHSSFLSD-SGQREENHRRSPSFPSKRSLRRTSAK 353
                           + D  G  + N  R+ +   KR   R  ++
Sbjct: 704 GHGERSGGKADGRPGGMPDGPGNGDRNANRNETRNDKRPDSRPGSR 749


>gi|167855575|ref|ZP_02478336.1| possible large adhesin [Haemophilus parasuis 29755]
 gi|167853321|gb|EDS24574.1| possible large adhesin [Haemophilus parasuis 29755]
          Length = 1579

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 12/111 (10%), Positives = 26/111 (23%), Gaps = 5/111 (4%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R  +GP      +          E   +          +      +  +   G   ++  
Sbjct: 863 RGPVGPQGPRGDKGEQGDQGLRGEAGPKGDAGPEGPRGEQGLVGPQGPTGPRGERGEQGP 922

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             P        ++ +        +  +G R E     P+ P      R   
Sbjct: 923 EGPKGEPGPKGDIGL-----PGPMGPAGARGEKGDTGPAGPEGPQGPRGEQ 968



 Score = 41.7 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 11/118 (9%), Positives = 24/118 (20%), Gaps = 7/118 (5%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            R + G    +                 +  P    ++          +  + G +     
Sbjct: 899  RGEQGLVGPQGPTGPRGERGEQGPEGPKGEPGPKGDIGLPGPMGPAGARGEKGDTGPAGP 958

Query: 302  ATPVHRRNLASNVWMAKGIHSSF-------LSDSGQREENHRRSPSFPSKRSLRRTSA 352
              P   R       +A                ++G +     R P   +     R   
Sbjct: 959  EGPQGPRGEQGTPGVAGPKGDRGDKGEQGDRGETGAQGAPGERGPKGDAGPEGPRGEQ 1016


>gi|116515235|ref|YP_802864.1| 30S ribosomal protein S4 [Buchnera aphidicola str. Cc (Cinara
           cedri)]
 gi|122285369|sp|Q057C8|RS4_BUCCC RecName: Full=30S ribosomal protein S4
 gi|58384668|gb|AAW72683.1| ribosomal protein S4 [Buchnera aphidicola (Cinara cedri)]
 gi|116257089|gb|ABJ90771.1| 30S ribosomal protein S4 [Buchnera aphidicola str. Cc (Cinara
           cedri)]
          Length = 206

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G  + R E  ++I  + + VN  ++   +  V   D I V
Sbjct: 97  RLDNIVYRLGFGTTRLEARQLINHKSICVNNKIVSFPSFQVSIDDKISV 145


>gi|51245003|ref|YP_064887.1| 30S ribosomal protein S4 [Desulfotalea psychrophila LSv54]
 gi|61215518|sp|Q6AP44|RS4_DESPS RecName: Full=30S ribosomal protein S4
 gi|50876040|emb|CAG35880.1| probable 30S ribosomal protein S4 [Desulfotalea psychrophila LSv54]
          Length = 210

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   + RAG AS R +  +++  + + +NG  ++  +  V   D I +
Sbjct: 100 RLDNAVFRAGFASSRTQARQIVRHKHILINGKRVDIPSYQVSEGDVISL 148


>gi|164686553|ref|ZP_02210581.1| hypothetical protein CLOBAR_00120 [Clostridium bartlettii DSM
           16795]
 gi|164604422|gb|EDQ97887.1| hypothetical protein CLOBAR_00120 [Clostridium bartlettii DSM
           16795]
          Length = 206

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +R+  V+ R G+A SR+E  +++      +NG  ++  ++ V   D I V
Sbjct: 98  ERLDNVVFRMGLANSRKEARQLVTHAHFTLNGKKVDIPSLTVKVGDVIAV 147


>gi|332521607|ref|ZP_08398060.1| ribosomal protein S4 [Lacinutrix algicola 5H-3-7-4]
 gi|332042696|gb|EGI78896.1| ribosomal protein S4 [Lacinutrix algicola 5H-3-7-4]
          Length = 201

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA +R    ++++ + + VNG L+   +  + + D + V
Sbjct: 94  RLDNVVFRMGIAPTRSAARQLVSHRHITVNGELVNVPSYQLKAGDVVAV 142


>gi|270264349|ref|ZP_06192615.1| 30S ribosomal protein S4 [Serratia odorifera 4Rx13]
 gi|270041485|gb|EFA14583.1| 30S ribosomal protein S4 [Serratia odorifera 4Rx13]
          Length = 206

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 ASLELAEQREKPT 169


>gi|209521361|ref|ZP_03270074.1| ribosomal protein S4 [Burkholderia sp. H160]
 gi|209498181|gb|EDZ98323.1| ribosomal protein S4 [Burkholderia sp. H160]
          Length = 207

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  +++  + + VNG++    ++ V + D + V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVGHKAITVNGVVSNIPSMQVKAGDVVAV 146


>gi|72058953|ref|XP_781802.1| PREDICTED: hypothetical protein [Strongylocentrotus purpuratus]
 gi|115955042|ref|XP_001182766.1| PREDICTED: hypothetical protein [Strongylocentrotus purpuratus]
          Length = 613

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 39/301 (12%), Positives = 92/301 (30%), Gaps = 40/301 (13%)

Query: 32  ERMIAQQRVKVN-GILLERAAVNVMSTD----HIE-----VDGVPLRKA-ERTRLWLYHK 80
           E  I +  ++VN G       + + + D     +      V G P++   +     + +K
Sbjct: 75  ETAIHEGLIRVNKGK--ASPDLILKNNDFMQSKVHRHEPPVSGEPIQIIADTQDYLVINK 132

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           P  +          +T+   L   +      ++ RLD  T GLLL      ++  L+   
Sbjct: 133 PSSIPVHPCGKYRHNTIVFILGKDYGFKGLHTIHRLDRLTSGLLLFARTLQVSHRLDAYV 192

Query: 139 TQWLRVYRVRFHGQVDQDKL------------NLLKKGIVIQGICYGDMQVTLDTQKGSN 186
            +             +                + +    V +       +    +  G  
Sbjct: 193 RERKLEKTYVCKAHGEFPSTPVVCEEPIFIVSHKIGVCRVKEDGKPCKTRFERLSYDGET 252

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNR--L--------IRISYGPFQLGTLLAGSTREV 236
           + +      G+  +I+   ++  + +    L         R   G  QL     G  R++
Sbjct: 253 SIIKCHPHTGRMHQIRVHLQYLGFPIINDPLYNNTVWGQHRGRGGNNQLTDEQVG-IRQL 311

Query: 237 --SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
                +L++ +  H ++       A + +     +   +I + +P+D      +      
Sbjct: 312 INYPFLLKDLIDQHDIDIDSALEKARLQALINKPKVTSHIDTAIPEDAPLTPGSQEPSKD 371

Query: 295 L 295
            
Sbjct: 372 A 372


>gi|20806545|ref|NP_621716.1| hypothetical protein TTE0003 [Thermoanaerobacter tengcongensis
          MB4]
 gi|20514982|gb|AAM23320.1| conserved hypothetical protein [Thermoanaerobacter tengcongensis
          MB4]
          Length = 68

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 12/36 (33%), Positives = 21/36 (58%)

Query: 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          + +R I + +VKVNG++  +    +   D IEV+G 
Sbjct: 28 QAKRFIQEGKVKVNGVIELKRGRKLYKNDIIEVEGK 63


>gi|332289204|ref|YP_004420056.1| 30S ribosomal protein S4 [Gallibacterium anatis UMN179]
 gi|330432100|gb|AEC17159.1| 30S ribosomal protein S4 [Gallibacterium anatis UMN179]
          Length = 206

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R E  ++++ + + VNG ++   +  V   D I V
Sbjct: 97  RLDNVVYRMGFAATRAEARQLVSHKAIIVNGRVVNIPSFQVSVDDVIAV 145


>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 = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 29/237 (12%), Positives = 64/237 (27%), Gaps = 43/237 (18%)

Query: 15  RVSKVIA---RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRK 69
           R+ + +A   R+   SR  + ++I    V VNG  + + +  +   D IE+  D  PL  
Sbjct: 10  RLDQWLATTDRS--LSRTVIRKVIDLGGVHVNGRRVRKCSQALKRGDKIELYRDQQPLTP 67

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
                      +   L +                 +     L  +      + + ++   
Sbjct: 68  FRLSEEDVLFRDDFLLVVNKPSGVESQPTPSRYKGTLYEALLVFLKDPYRPLDKPELGMV 127

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--------- 170
             L     G +   +     + L            +   + L +   +            
Sbjct: 128 QRLDRETSGAMIFSIHSRCHKPLTEAWQSHRV---RKVYHALVRDPGLDDEGEFISLLAR 184

Query: 171 --CYGDMQVTLDTQKGSNA------------WVTVGLREGKNREIKKVFEFFNWKVN 213
                 M+      K ++              V + L  G+  +I+  F      + 
Sbjct: 185 NRRTNRMKSVARGGKSAHTRYRVLKRLSGFALVEIQLLTGRMHQIRVHFSEAGAPLL 241


>gi|22127884|ref|NP_671307.1| 30S ribosomal protein S4 [Yersinia pestis KIM 10]
 gi|45440091|ref|NP_991630.1| 30S ribosomal protein S4 [Yersinia pestis biovar Microtus str.
           91001]
 gi|51597964|ref|YP_072155.1| 30S ribosomal protein S4 [Yersinia pseudotuberculosis IP 32953]
 gi|108809231|ref|YP_653147.1| 30S ribosomal protein S4 [Yersinia pestis Antiqua]
 gi|108813996|ref|YP_649763.1| 30S ribosomal protein S4 [Yersinia pestis Nepal516]
 gi|123444074|ref|YP_001008044.1| 30S ribosomal protein S4 [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|145597474|ref|YP_001161549.1| 30S ribosomal protein S4 [Yersinia pestis Pestoides F]
 gi|150260719|ref|ZP_01917447.1| 30S ribosomal protein S4 [Yersinia pestis CA88-4125]
 gi|153947510|ref|YP_001402839.1| 30S ribosomal protein S4 [Yersinia pseudotuberculosis IP 31758]
 gi|162420100|ref|YP_001605196.1| 30S ribosomal protein S4 [Yersinia pestis Angola]
 gi|165927897|ref|ZP_02223729.1| ribosomal protein S4 [Yersinia pestis biovar Orientalis str.
           F1991016]
 gi|166010539|ref|ZP_02231437.1| ribosomal protein S4 [Yersinia pestis biovar Antiqua str. E1979001]
 gi|166213178|ref|ZP_02239213.1| ribosomal protein S4 [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|167398630|ref|ZP_02304154.1| ribosomal protein S4 [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167419283|ref|ZP_02311036.1| ribosomal protein S4 [Yersinia pestis biovar Orientalis str.
           MG05-1020]
 gi|167425684|ref|ZP_02317437.1| ribosomal protein S4 [Yersinia pestis biovar Mediaevalis str.
           K1973002]
 gi|170022568|ref|YP_001719073.1| 30S ribosomal protein S4 [Yersinia pseudotuberculosis YPIII]
 gi|186897160|ref|YP_001874272.1| 30S ribosomal protein S4 [Yersinia pseudotuberculosis PB1/+]
 gi|218927439|ref|YP_002345314.1| 30S ribosomal protein S4 [Yersinia pestis CO92]
 gi|229836285|ref|ZP_04456452.1| 30S ribosomal subunit protein S4 [Yersinia pestis Pestoides A]
 gi|229840091|ref|ZP_04460250.1| 30S ribosomal subunit protein S4 [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229842173|ref|ZP_04462328.1| 30S ribosomal subunit protein S4 [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229904527|ref|ZP_04519638.1| 30S ribosomal subunit protein S4 [Yersinia pestis Nepal516]
 gi|238752667|ref|ZP_04614138.1| 30S ribosomal protein S4 [Yersinia rohdei ATCC 43380]
 gi|238754196|ref|ZP_04615554.1| 30S ribosomal protein S4 [Yersinia ruckeri ATCC 29473]
 gi|238758784|ref|ZP_04619958.1| 30S ribosomal protein S4 [Yersinia aldovae ATCC 35236]
 gi|238783187|ref|ZP_04627213.1| 30S ribosomal protein S4 [Yersinia bercovieri ATCC 43970]
 gi|238797220|ref|ZP_04640721.1| 30S ribosomal protein S4 [Yersinia mollaretii ATCC 43969]
 gi|270488255|ref|ZP_06205329.1| ribosomal protein S4 [Yersinia pestis KIM D27]
 gi|294502308|ref|YP_003566370.1| 30S ribosomal protein S4 [Yersinia pestis Z176003]
 gi|332163237|ref|YP_004299814.1| 30S ribosomal protein S4 [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|26399435|sp|Q8ZJ88|RS4_YERPE RecName: Full=30S ribosomal protein S4
 gi|61215490|sp|Q664U5|RS4_YERPS RecName: Full=30S ribosomal protein S4
 gi|123245525|sp|Q1C2X0|RS4_YERPA RecName: Full=30S ribosomal protein S4
 gi|123372820|sp|Q1CCW7|RS4_YERPN RecName: Full=30S ribosomal protein S4
 gi|152112273|sp|A1JS02|RS4_YERE8 RecName: Full=30S ribosomal protein S4
 gi|171769160|sp|A7FNL1|RS4_YERP3 RecName: Full=30S ribosomal protein S4
 gi|172044482|sp|A4TH14|RS4_YERPP RecName: Full=30S ribosomal protein S4
 gi|226703313|sp|B2K513|RS4_YERPB RecName: Full=30S ribosomal protein S4
 gi|226703314|sp|A9R917|RS4_YERPG RecName: Full=30S ribosomal protein S4
 gi|226703315|sp|B1JJG9|RS4_YERPY RecName: Full=30S ribosomal protein S4
 gi|21961020|gb|AAM87558.1|AE014003_16 30S ribosomal subunit protein S4 [Yersinia pestis KIM 10]
 gi|45434946|gb|AAS60507.1| 30S ribosomal protein S4 [Yersinia pestis biovar Microtus str.
           91001]
 gi|51591246|emb|CAH22912.1| 30S ribosomal protein S4 [Yersinia pseudotuberculosis IP 32953]
 gi|108777644|gb|ABG20163.1| SSU ribosomal protein S4P [Yersinia pestis Nepal516]
 gi|108781144|gb|ABG15202.1| SSU ribosomal protein S4P [Yersinia pestis Antiqua]
 gi|115346050|emb|CAL18916.1| 30S ribosomal protein S4 [Yersinia pestis CO92]
 gi|122091035|emb|CAL13918.1| 30S ribosomal protein S4 [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|145209170|gb|ABP38577.1| SSU ribosomal protein S4P [Yersinia pestis Pestoides F]
 gi|149290127|gb|EDM40204.1| 30S ribosomal protein S4 [Yersinia pestis CA88-4125]
 gi|152959005|gb|ABS46466.1| ribosomal protein S4 [Yersinia pseudotuberculosis IP 31758]
 gi|162352915|gb|ABX86863.1| ribosomal protein S4 [Yersinia pestis Angola]
 gi|165920173|gb|EDR37474.1| ribosomal protein S4 [Yersinia pestis biovar Orientalis str.
           F1991016]
 gi|165990629|gb|EDR42930.1| ribosomal protein S4 [Yersinia pestis biovar Antiqua str. E1979001]
 gi|166205476|gb|EDR49956.1| ribosomal protein S4 [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|166963277|gb|EDR59298.1| ribosomal protein S4 [Yersinia pestis biovar Orientalis str.
           MG05-1020]
 gi|167051134|gb|EDR62542.1| ribosomal protein S4 [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167055374|gb|EDR65168.1| ribosomal protein S4 [Yersinia pestis biovar Mediaevalis str.
           K1973002]
 gi|169749102|gb|ACA66620.1| ribosomal protein S4 [Yersinia pseudotuberculosis YPIII]
 gi|186700186|gb|ACC90815.1| ribosomal protein S4 [Yersinia pseudotuberculosis PB1/+]
 gi|229678645|gb|EEO74750.1| 30S ribosomal subunit protein S4 [Yersinia pestis Nepal516]
 gi|229690483|gb|EEO82537.1| 30S ribosomal subunit protein S4 [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229696457|gb|EEO86504.1| 30S ribosomal subunit protein S4 [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229706353|gb|EEO92360.1| 30S ribosomal subunit protein S4 [Yersinia pestis Pestoides A]
 gi|238703081|gb|EEP95624.1| 30S ribosomal protein S4 [Yersinia aldovae ATCC 35236]
 gi|238707692|gb|EEQ00052.1| 30S ribosomal protein S4 [Yersinia ruckeri ATCC 29473]
 gi|238709094|gb|EEQ01341.1| 30S ribosomal protein S4 [Yersinia rohdei ATCC 43380]
 gi|238715983|gb|EEQ07969.1| 30S ribosomal protein S4 [Yersinia bercovieri ATCC 43970]
 gi|238718857|gb|EEQ10672.1| 30S ribosomal protein S4 [Yersinia mollaretii ATCC 43969]
 gi|262360388|gb|ACY57109.1| 30S ribosomal protein S4 [Yersinia pestis D106004]
 gi|262364338|gb|ACY60895.1| 30S ribosomal protein S4 [Yersinia pestis D182038]
 gi|270336759|gb|EFA47536.1| ribosomal protein S4 [Yersinia pestis KIM D27]
 gi|294352767|gb|ADE63108.1| 30S ribosomal protein S4 [Yersinia pestis Z176003]
 gi|320013366|gb|ADV96937.1| 30S ribosomal subunit protein S4 [Yersinia pestis biovar Medievalis
           str. Harbin 35]
 gi|325667467|gb|ADZ44111.1| 30S ribosomal protein S4 [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330861830|emb|CBX72001.1| 30S ribosomal protein S4 [Yersinia enterocolitica W22703]
          Length = 206

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|325288452|ref|YP_004264633.1| tyrosyl-tRNA synthetase [Syntrophobotulus glycolicus DSM 8271]
 gi|324963853|gb|ADY54632.1| tyrosyl-tRNA synthetase [Syntrophobotulus glycolicus DSM 8271]
          Length = 413

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 4/51 (7%)

Query: 19  VIARAGIA-SRREVERMIAQQRVKVNGILLERAAV--NVMSTDHIEVDGVP 66
           ++  AG+  SR E  R+I Q  V++N   + +A     +   D I+V G  
Sbjct: 357 ILVSAGLVPSRGEARRLIEQGGVRINDEKVSQAQSSPRINPGDVIKV-GKR 406


>gi|318607721|emb|CBY29219.1| SSU ribosomal protein S4p (S9e) [Yersinia enterocolitica subsp.
           palearctica Y11]
          Length = 206

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|260583938|ref|ZP_05851686.1| 30S ribosomal protein S4 [Granulicatella elegans ATCC 700633]
 gi|260158564|gb|EEW93632.1| 30S ribosomal protein S4 [Granulicatella elegans ATCC 700633]
          Length = 203

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 1/40 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAV 52
           QR+  V+ R G+AS RR+  +++    V VNG  ++  + 
Sbjct: 93  QRLDNVVYRLGLASTRRQARQLVNHGHVTVNGKRVDIPSF 132


>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 = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 42/322 (13%), Positives = 80/322 (24%), Gaps = 71/322 (22%)

Query: 5   NIVQENFTPQRVSKVIARA----GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH- 59
            +V     P R+ K +AR        SR  + +MIA   V + G+ +      V      
Sbjct: 21  RVVIGEDPPDRLDKALARQVPEDAALSRSRLMKMIADGDVTLEGVAVTNPKARVAEGQEY 80

Query: 60  -------IEVDGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
                  +++D  P      +   +   + +      +V         + V   L     
Sbjct: 81  LLRLAPAVDIDAQPEDIPLTVVWEDADLIVVDKPVGMVVHPAPGSYTGTLVNALLHHCGD 140

Query: 107 RVISVG----------------------RLDINTEGLLLLTNDGGLARVLELPSTQWLRV 144
            +  VG                      + D    GL        + R            
Sbjct: 141 TLSGVGGAKRPGIVHRIDKDTSGLLVVAKTDRAHHGLAAQFEAHSVTRHYIALVHGAPNA 200

Query: 145 YRVRFHGQV--DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE------- 195
              R  G      +   ++     +        +  +    G +A   V + E       
Sbjct: 201 ADPRLRGIRGVSFEPGGIVCIATNLARHKTDRQRQAVLFDSGRHAVTRVRVLESYGTPPV 260

Query: 196 ----------GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                     G+  +I+         +            LG    G  R+V+ K + E +
Sbjct: 261 AALVECWLETGRTHQIRVHMSHAGHAL------------LGDQTYGGRRKVAPKAVGEAV 308

Query: 246 GPHLLEEAQVNLDAPIYSSETL 267
                +  +  L A        
Sbjct: 309 AQAANDFPRQALHAASLGFVHP 330


>gi|325962741|ref|YP_004240647.1| hypothetical protein Asphe3_13360 [Arthrobacter
          phenanthrenivorans Sphe3]
 gi|323468828|gb|ADX72513.1| uncharacterized conserved protein [Arthrobacter
          phenanthrenivorans Sphe3]
          Length = 75

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 11/39 (28%), Positives = 19/39 (48%)

Query: 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          E   +I    VKVNG + +R    + + D + V+   +R
Sbjct: 31 EAAELIKNGLVKVNGEIDDRRGRQLHNGDTVTVNNQTVR 69


>gi|300782185|ref|YP_003762476.1| RNA-binding S4 domain-containing protein [Amycolatopsis
          mediterranei U32]
 gi|299791699|gb|ADJ42074.1| RNA-binding S4 domain-containing protein [Amycolatopsis
          mediterranei U32]
          Length = 74

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 5/54 (9%)

Query: 12 TPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           P R+ + +  AG+    S    + +I  + V VNG +  R    +   D + V
Sbjct: 12 EPIRLGQFLKLAGLAEDGS--HAKDLIDAEEVTVNGEVETRRGRQLTDGDVVAV 63


>gi|291519999|emb|CBK75220.1| cell envelope-related function transcriptional attenuator common
           domain [Butyrivibrio fibrisolvens 16/4]
          Length = 514

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 9/82 (10%), Positives = 16/82 (19%)

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW 315
           +          + R RP             + + S++                   S   
Sbjct: 25  DELDMYDYEPEVRRRRPEGARPAGSRPAASRSSQSRQGTRRPAGSRPAGSRPSGSRSAGS 84

Query: 316 MAKGIHSSFLSDSGQREENHRR 337
              G   S    +  R    R 
Sbjct: 85  RPAGSRPSGSRSASGRPTGTRP 106


>gi|26454648|sp|P81288|RS4_BACST RecName: Full=30S ribosomal protein S4; AltName: Full=BS5
          Length = 200

 Score = 45.6 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR+  +++    + V+G  +   +  V     I V
Sbjct: 93  RLDNLVYRLGLARTRRQARQLVTHGHIIVDGSRVNIPSYRVKPGQTIAV 141


>gi|312968379|ref|ZP_07782589.1| ribosomal protein S4 [Escherichia coli 2362-75]
 gi|312287204|gb|EFR15114.1| ribosomal protein S4 [Escherichia coli 2362-75]
          Length = 206

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 12/73 (16%), Positives = 30/73 (41%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VN  ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAIMVNDRVVNIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|312978410|ref|ZP_07790152.1| S4 domain protein [Lactobacillus crispatus CTV-05]
 gi|310894753|gb|EFQ43825.1| S4 domain protein [Lactobacillus crispatus CTV-05]
          Length = 90

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR   + M  Q R+KVNG +++  + +V   D IEV
Sbjct: 1  MRIDKFLKVSRLVKRRTVAKEMADQGRIKVNGRVVKS-SYDVKIDDIIEV 49


>gi|299138192|ref|ZP_07031372.1| conserved hypothetical protein [Acidobacterium sp. MP5ACTX8]
 gi|298600122|gb|EFI56280.1| conserved hypothetical protein [Acidobacterium sp. MP5ACTX8]
          Length = 731

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 24/111 (21%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            E  G       +    A   S  T    +     +  D   R  +   +        K 
Sbjct: 598 DEGAGSSYGGGDRPERPAYGGSDSTPRAPKRPFPRKEGDLADRPVRPWPEHKPERSDSKS 657

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             P                     S  G+R    + +  F  +   R   A
Sbjct: 658 RKPGGFGKRPFTPREGGSGDRPRPSFGGKRPFGSKPAGGFSKRPDSRGGKA 708



 Score = 37.5 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 11/125 (8%), Positives = 29/125 (23%), Gaps = 7/125 (5%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
                R                   +S +   R      +   +  +   K    +   +
Sbjct: 375 RPDRERRPFNRDGASAGSKPSFTRPWSEDRKPRPERAGFTPRAEGDSAAPKRPYVRREGA 434

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR-------EENHRRSPSFPSKRSLRR 349
                A      +       + G   +F  D G+         ++  R P    + +   
Sbjct: 435 APGGFAKREGGFSDRGPARKSFGDKPAFRKDRGEGFAAKPRFAQDGERKPYVRREGAAPS 494

Query: 350 TSAKK 354
            + ++
Sbjct: 495 DAPRR 499


>gi|149202304|ref|ZP_01879277.1| RNA-binding S4 [Roseovarius sp. TM1035]
 gi|149144402|gb|EDM32433.1| RNA-binding S4 [Roseovarius sp. TM1035]
          Length = 126

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 12/57 (21%), Positives = 22/57 (38%), Gaps = 1/57 (1%)

Query: 7  VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          +       R+ K +  A    +R    + I+   V+VNG  + + A  V   D +  
Sbjct: 1  MDAPAAKIRLDKWLWHARFFKTRTLSAKEISAGHVRVNGARVTKPAQAVGPGDVLTF 57


>gi|50425337|ref|XP_461262.1| DEHA2F20988p [Debaryomyces hansenii CBS767]
 gi|49656931|emb|CAG89651.1| DEHA2F20988p [Debaryomyces hansenii]
          Length = 467

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 1/54 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+   + RA  AS  R+  + I    VKVNG++++  +  + S D   V    +
Sbjct: 104 RLEFALFRAMFASSVRQARQFILGGHVKVNGVVVKHPSFPLQSGDVFNVKPEKV 157


>gi|297290906|ref|XP_002803802.1| PREDICTED: zinc finger protein 318-like [Macaca mulatta]
          Length = 2259

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 10/87 (11%), Positives = 20/87 (22%)

Query: 268 VRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSD 327
            R   +         +       + +    + +  +P   R          G   S   +
Sbjct: 54  ARRPRSPSGHRGRRASPSPPRGRRVSPSPPRARRGSPSPPRGRRLFPPGPAGFRGSSRGE 113

Query: 328 SGQREENHRRSPSFPSKRSLRRTSAKK 354
           S        R        S RR+   +
Sbjct: 114 SRADYARDGRGDHPGDSGSRRRSPGLR 140


>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 = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 21/238 (8%), Positives = 55/238 (23%), Gaps = 36/238 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIA----QQRVKVNG-----ILLERAAVNVM- 55
           +V EN     +   +   G       +R+I     Q  + VNG       + +    +  
Sbjct: 4   VVGENEKGVILENFLRNRGF-----SKRLIRIYKWQGEILVNGIKSNVKRILQPGDVIDL 58

Query: 56  ---STD----------HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDP---DGRSTVFD 99
                D           I  +   +    +    + H   G  +                
Sbjct: 59  ILPENDSNIAPEKLDLDICYEDEEILIVNKPANMVVHPTKGYQSGTLANGVAWYFKDKGL 118

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST----QWLRVYRVRFHGQVDQ 155
                    +  G   +     L                     +       R +  + +
Sbjct: 119 KALIRPVNRLDRGTSGLVVFAKLPFMQYYLQIVKPMSKLYFAVVEGKMEGEGRINLPISR 178

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              + +++ +  +G         +       + + V +  G+  +I+         + 
Sbjct: 179 KPQSGIERMVSEEGDRA-ITNYKVVKSSERFSLLKVKIETGRTHQIRVHLSHIGHPIV 235


>gi|256027568|ref|ZP_05441402.1| putative cytoplasmic protein [Fusobacterium sp. D11]
 gi|289765527|ref|ZP_06524905.1| conserved hypothetical protein [Fusobacterium sp. D11]
 gi|289717082|gb|EFD81094.1| conserved hypothetical protein [Fusobacterium sp. D11]
          Length = 71

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 11/71 (15%), Positives = 28/71 (39%), Gaps = 9/71 (12%)

Query: 1  MKDKNIVQENFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
          MK+   V+ +    ++ + +       +G     + +++I   +VKVN  +  R    + 
Sbjct: 1  MKNIEKVKISTEFIKLDQFLKWLAVVDSG----SQAKQVILDGKVKVNDEVETRRGRKIY 56

Query: 56 STDHIEVDGVP 66
              +E+    
Sbjct: 57 PEYKVEIFDKI 67


>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 = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 33/253 (13%), Positives = 74/253 (29%), Gaps = 45/253 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M+   I     T  R+   +A  G     SR  ++ +I Q+RV  +G  + +    V   
Sbjct: 1   MEPIEITAGPQTAGRLDAWLA--GQCEGISRNALQTLIEQERVTKDGRPVNK-KEKVCPG 57

Query: 58  DHIEV---DGVPLRKAERTR-----------LWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
               +   D  P+    +             + +      +V         + V   L  
Sbjct: 58  AVYLLQLPDPKPIEAVPQDIPLSIVYEDNDLIVVNKPKGMVVHPAPGNPDGTLVNALLYH 117

Query: 104 IFSRVISVG----------------------RLDINTEGLLLLTNDGGLARVLELPSTQW 141
              ++  +G                      + D+  + L    +   + RV        
Sbjct: 118 CAGQLSGIGGAIRPGIVHRIDKDTSGLLVVAKNDVAHQALSSQMSVHSIHRVYHAIVYGN 177

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQ---GICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
           L+         + +D  +  K  ++ +   G  Y      +  + G+  ++   L+ G+ 
Sbjct: 178 LKEDEGFVEAWLGRDPRDRKKMAVLSENTTGARYAYTGWRVLERFGNFTYIACKLKTGRT 237

Query: 199 REIKKVFEFFNWK 211
            +I+         
Sbjct: 238 HQIRVHMASIGHP 250


>gi|328951209|ref|YP_004368544.1| ribosomal protein S4 [Marinithermus hydrothermalis DSM 14884]
 gi|328451533|gb|AEB12434.1| ribosomal protein S4 [Marinithermus hydrothermalis DSM 14884]
          Length = 205

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA+ RR+  + +  + + VNG  ++R +  V   D I V
Sbjct: 96  RLDNVVFRLGIATTRRQARQFVVHRHILVNGKRVDRPSYRVKPGDVISV 144


>gi|311069452|ref|YP_003974375.1| 30S ribosomal protein S4 [Bacillus atrophaeus 1942]
 gi|310869969|gb|ADP33444.1| 30S ribosomal protein S4 [Bacillus atrophaeus 1942]
          Length = 200

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ + G+A +RR+  +++    + V+G  ++  +  V     I V
Sbjct: 93  RLDNLVYKLGLARTRRQARQLVNHGHILVDGSRVDIPSYQVKPGQTIGV 141


>gi|295692139|ref|YP_003600749.1| RNA-binding s4 domain protein [Lactobacillus crispatus ST1]
 gi|295030245|emb|CBL49724.1| RNA-binding S4 domain protein [Lactobacillus crispatus ST1]
          Length = 90

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR   + M  Q R+KVNG +++  + +V   D IEV
Sbjct: 1  MRIDKFLKVSRLVKRRTVAKEMADQGRIKVNGRVVKS-SYDVKIDDIIEV 49


>gi|291166546|gb|EFE28592.1| hemolysin A [Filifactor alocis ATCC 35896]
          Length = 272

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 14 QRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          QR+  ++  R    SR   +R I   +V V+  ++++A + + +   I V    +  
Sbjct: 5  QRLDILLVERNFFTSRERAKRNIMAGKVLVDNRVIDKAGMMIDADAEIRVKEDVIPY 61


>gi|291277243|ref|YP_003517015.1| 30S ribosomal protein S4 [Helicobacter mustelae 12198]
 gi|290964437|emb|CBG40287.1| 30S ribosomal protein S4 [Helicobacter mustelae 12198]
          Length = 208

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A+ RR   ++++   + V+G  +   +  V     IEV
Sbjct: 99  RLDNVVYRMGFATTRRFARQLVSHGHILVDGKRVNIPSFFVKQGQKIEV 147


>gi|172036251|ref|YP_001802752.1| putative RNA-binding S4 protein [Cyanothece sp. ATCC 51142]
 gi|171697705|gb|ACB50686.1| putative RNA-binding S4 protein [Cyanothece sp. ATCC 51142]
          Length = 259

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 19/60 (31%), Positives = 28/60 (46%), Gaps = 2/60 (3%)

Query: 7   VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +       R+   IA AG   SR ++   I +  V+VN   + +A+ NV S D I V G 
Sbjct: 177 MTTVEASMRLD-AIASAGFGMSRSKMVDAINKGDVRVNWKEITQASHNVESGDLIAVRGK 235


>gi|238788888|ref|ZP_04632678.1| 30S ribosomal protein S4 [Yersinia frederiksenii ATCC 33641]
 gi|238792959|ref|ZP_04636589.1| 30S ribosomal protein S4 [Yersinia intermedia ATCC 29909]
 gi|238722915|gb|EEQ14565.1| 30S ribosomal protein S4 [Yersinia frederiksenii ATCC 33641]
 gi|238727813|gb|EEQ19337.1| 30S ribosomal protein S4 [Yersinia intermedia ATCC 29909]
          Length = 202

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 93  RLDNVVYRMGFGATRAESRQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVK 152

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 153 AALELAEQREKPT 165


>gi|192359460|ref|YP_001981232.1| 30S ribosomal protein S4 [Cellvibrio japonicus Ueda107]
 gi|226697819|sp|B3PK61|RS4_CELJU RecName: Full=30S ribosomal protein S4
 gi|190685625|gb|ACE83303.1| ribosomal protein S4 [Cellvibrio japonicus Ueda107]
          Length = 206

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG  +  A+  V + D + V
Sbjct: 97  RLDNVVYRMGFGATRSESRQLVSHKAISVNGKTVNVASFQVAAGDVVAV 145


>gi|23015528|ref|ZP_00055301.1| COG1188: Ribosome-associated heat shock protein implicated in the
          recycling of the 50S subunit (S4 paralog)
          [Magnetospirillum magnetotacticum MS-1]
          Length = 61

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 12/60 (20%), Positives = 21/60 (35%), Gaps = 7/60 (11%)

Query: 11 FTPQRVSKVIARAGIA----SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           T  R+ K +          SR     ++    V++NG  + + A  V   D +     P
Sbjct: 2  ETSIRLDKWL---FFCRFFKSRALAANVVESGAVRLNGAPVTKPAHGVRPGDRVAFQTEP 58


>gi|325577150|ref|ZP_08147634.1| 30S ribosomal protein S4 [Haemophilus parainfluenzae ATCC 33392]
 gi|325160732|gb|EGC72853.1| 30S ribosomal protein S4 [Haemophilus parainfluenzae ATCC 33392]
          Length = 206

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R E  ++++ + + VNG ++   +  V   D + V
Sbjct: 97  RLDNVVYRMGFAATRAEARQLVSHKAIVVNGRVVNIPSFQVSVNDVVAV 145


>gi|301155354|emb|CBW14820.1| 30S ribosomal subunit protein S4 [Haemophilus parainfluenzae T3T1]
          Length = 206

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R E  ++++ + + VNG ++   +  V   D + V
Sbjct: 97  RLDNVVYRMGFAATRAEARQLVSHKAIVVNGRVVNIPSFQVSVNDVVAV 145


>gi|77165764|ref|YP_344289.1| ribosomal protein S4 [Nitrosococcus oceani ATCC 19707]
 gi|254433943|ref|ZP_05047451.1| ribosomal protein S4 [Nitrosococcus oceani AFC27]
 gi|90101699|sp|Q3J8T7|RS4_NITOC RecName: Full=30S ribosomal protein S4
 gi|76884078|gb|ABA58759.1| SSU ribosomal protein S4P [Nitrosococcus oceani ATCC 19707]
 gi|207090276|gb|EDZ67547.1| ribosomal protein S4 [Nitrosococcus oceani AFC27]
          Length = 208

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++I  + V VNG  +   +  V + D + V
Sbjct: 99  RLDNVVYRMGFGSTRAEARQLINHKGVLVNGQGINIPSYQVRAEDVVAV 147


>gi|148262425|ref|YP_001229131.1| RNA-binding S4 domain-containing protein [Geobacter
          uraniireducens Rf4]
 gi|146395925|gb|ABQ24558.1| RNA-binding S4 domain protein [Geobacter uraniireducens Rf4]
          Length = 65

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 11/60 (18%), Positives = 25/60 (41%), Gaps = 1/60 (1%)

Query: 7  VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          ++ +    ++   + A   + S  E + +I +  V VNG +  R    +   D + + G 
Sbjct: 1  MKIDTEYIKLDSFLKAVNAVCSGGEAKMIIGEGLVAVNGEVELRRGRKLRPGDRVTLGGE 60


>gi|327402758|ref|YP_004343596.1| 30S ribosomal protein S4P [Fluviicola taffensis DSM 16823]
 gi|327318266|gb|AEA42758.1| SSU ribosomal protein S4P [Fluviicola taffensis DSM 16823]
          Length = 203

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            R+   + R GIA SRR   ++++ + + VNG ++   +  +   D + V
Sbjct: 94  MRLDNTVYRLGIANSRRAARQLVSHKHIVVNGEVVNIPSYTLRIGDVVSV 143


>gi|313900788|ref|ZP_07834278.1| S4 domain protein [Clostridium sp. HGF2]
 gi|312954208|gb|EFR35886.1| S4 domain protein [Clostridium sp. HGF2]
          Length = 96

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRREV-ERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  A I  RR V + +  Q+RV VNG + +  + +V   D I+V
Sbjct: 1  MRLDKYLKTARILKRRTVSKELADQERVYVNGKIAK-PSTDVKVGDTIKV 49


>gi|183221323|ref|YP_001839319.1| 30S ribosomal protein S4 [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Paris)']
 gi|189911414|ref|YP_001962969.1| 30S ribosomal protein S4 [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|226699081|sp|B0SA21|RS4_LEPBA RecName: Full=30S ribosomal protein S4
 gi|226699082|sp|B0SSF3|RS4_LEPBP RecName: Full=30S ribosomal protein S4
 gi|167776090|gb|ABZ94391.1| 30S Ribosomal protein S4 [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|167779745|gb|ABZ98043.1| 30S ribosomal protein S4 [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Paris)']
          Length = 210

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+    +A + + VNG  ++  +  V   D IE+
Sbjct: 100 RLDNVLYRMGFAVTRRQARNFVAHRHILVNGHRVDICSYRVNIGDKIEI 148


>gi|240273798|gb|EER37317.1| NAM9+ protein [Ajellomyces capsulatus H143]
 gi|325094771|gb|EGC48081.1| NAM9+ protein [Ajellomyces capsulatus H88]
          Length = 490

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 1/54 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+   I RA  AS  R+  + +    V VNG  +      +   D  +VD   +
Sbjct: 126 RLDVAIFRAMFASSTRQARQFVIHGSVTVNGKKMRYPGYLLNPGDLFQVDPERV 179


>gi|73542839|ref|YP_297359.1| 30S ribosomal protein S4 [Ralstonia eutropha JMP134]
 gi|90101711|sp|Q46WG8|RS4_RALEJ RecName: Full=30S ribosomal protein S4
 gi|72120252|gb|AAZ62515.1| SSU ribosomal protein S4P [Ralstonia eutropha JMP134]
          Length = 207

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  L   +  + S D I +
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAILVNGQTLNVPSAQIKSGDVITI 146


>gi|217967395|ref|YP_002352901.1| ribosomal protein S4 [Dictyoglomus turgidum DSM 6724]
 gi|226732179|sp|B8E1F9|RS4_DICTD RecName: Full=30S ribosomal protein S4
 gi|217336494|gb|ACK42287.1| ribosomal protein S4 [Dictyoglomus turgidum DSM 6724]
          Length = 206

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 15/70 (21%), Positives = 32/70 (45%), Gaps = 1/70 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G A SR +  ++++  ++ VNG  +   + N+   D +E+    L   +  
Sbjct: 99  RLDNVVYRLGWALSRAQARQIVSHGKIAVNGKRVNIPSYNLKPGDVVELLDKDLIPVQEA 158

Query: 74  RLWLYHKPIG 83
                +K + 
Sbjct: 159 ISVFGNKSVP 168


>gi|220935468|ref|YP_002514367.1| 30S ribosomal protein S4 [Thioalkalivibrio sp. HL-EbGR7]
 gi|254764620|sp|B8GV34|RS4_THISH RecName: Full=30S ribosomal protein S4
 gi|219996778|gb|ACL73380.1| 30S ribosomal protein S4 [Thioalkalivibrio sp. HL-EbGR7]
          Length = 206

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 29/60 (48%), Gaps = 1/60 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + ++VNG  +  A+  V  +D + V     ++    
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAIQVNGQAVNIASYQVQPSDVVAVREKAKKQVRIQ 156


>gi|170718273|ref|YP_001785291.1| 30S ribosomal protein S4 [Haemophilus somnus 2336]
 gi|189045384|sp|B0UX38|RS4_HAES2 RecName: Full=30S ribosomal protein S4
 gi|168826402|gb|ACA31773.1| ribosomal protein S4 [Haemophilus somnus 2336]
          Length = 206

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R E  ++++ + + VNG ++   +  V   D + V
Sbjct: 97  RLDNVVYRMGFAATRAEARQLVSHKAIVVNGRVVNIPSFQVSVNDVVAV 145


>gi|313836989|gb|EFS74703.1| S4 domain protein [Propionibacterium acnes HL037PA2]
 gi|314929421|gb|EFS93252.1| S4 domain protein [Propionibacterium acnes HL044PA1]
 gi|314971495|gb|EFT15593.1| S4 domain protein [Propionibacterium acnes HL037PA3]
          Length = 68

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 11/54 (20%), Positives = 19/54 (35%), Gaps = 9/54 (16%)

Query: 14 QRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ + +     A  G     +   +IA   V VN  +  R    +   D + V
Sbjct: 2  IRLGQYLKFANLAETGG----QARELIASGMVSVNDEVETRRGRQLHPGDEVRV 51


>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 = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 26/232 (11%), Positives = 63/232 (27%), Gaps = 31/232 (13%)

Query: 13  PQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----------E 61
             R+ + +A+     SR  ++  I    VKVNGI++ +A   V   + +           
Sbjct: 17  GCRLDQALAQLFPDYSRSRIKVWIESDLVKVNGIVVNKAREKVFGGEQVEIQAEIEEEIR 76

Query: 62  VDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-----G 112
            +   +       +   + +      +V   +     + +   L                
Sbjct: 77  FEPQDIPLNIVYEDDDIIVINKPKDLVVHPGAGNPDGTVLNALLHYYPPIAEVPRAGIVH 136

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVY-----------RVRFHGQVDQDKLNLL 161
           RLD +T GL+++  +      L     +                +     +         
Sbjct: 137 RLDKDTTGLMVVAKNIPAQTHLVTALQKRRITREYEAVASGVMTQGGKVDEPMARHPTKR 196

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               V            +  +  +   + + L  G+  +I+         + 
Sbjct: 197 TAMAVHPMGKPAVTHYRIMERFRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 248


>gi|15895346|ref|NP_348695.1| rRNA methylase [Clostridium acetobutylicum ATCC 824]
 gi|15025064|gb|AAK80035.1|AE007710_5 Predicted rRNA methylase, YQXC B.subtilis ortholog [Clostridium
          acetobutylicum ATCC 824]
 gi|325509491|gb|ADZ21127.1| rRNA methylase [Clostridium acetobutylicum EA 2018]
          Length = 267

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 12/64 (18%), Positives = 27/64 (42%), Gaps = 3/64 (4%)

Query: 7  VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          + EN   +R+  ++   GI  SR +    I    + V+ + +++    V  +  +E  G 
Sbjct: 1  MSENK--ERLDVLLVEKGIFESREKARASIMAGEIYVDDLRIDKCGQKVKVSSKVEFRGE 58

Query: 66 PLRK 69
           +  
Sbjct: 59 KMPY 62


>gi|52426079|ref|YP_089216.1| 30S ribosomal protein S4 [Mannheimia succiniciproducens MBEL55E]
 gi|61215476|sp|Q65QX9|RS4_MANSM RecName: Full=30S ribosomal protein S4
 gi|52308131|gb|AAU38631.1| RpsD protein [Mannheimia succiniciproducens MBEL55E]
          Length = 206

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R E  ++++ + + VNG ++   +  V   D + V
Sbjct: 97  RLDNVVYRMGFAATRAEARQLVSHKAIVVNGRVVNIPSFQVSVDDVVAV 145


>gi|42524353|ref|NP_969733.1| 30S ribosomal protein S4 [Bdellovibrio bacteriovorus HD100]
 gi|61215581|sp|Q6MJ35|RS4A_BDEBA RecName: Full=30S ribosomal protein S4 A
 gi|39576562|emb|CAE80726.1| 30S ribosomal protein S4 [Bdellovibrio bacteriovorus HD100]
          Length = 208

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+   G A SRRE  +++      +NG      ++ V   D I+V
Sbjct: 99  RLDNVVYTLGYANSRREARQLVKHNHFLLNGKRANIPSILVNKGDVIQV 147


>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 = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 19/49 (38%), Gaps = 4/49 (8%)

Query: 13 PQRVSKVIA----RAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
          P R+ K +          SR  + R+IA   V V+G ++      +   
Sbjct: 21 PPRLDKALGRDVPNDAALSRSRLARLIADGAVAVDGQVVTDPRFRIAEG 69


>gi|237751463|ref|ZP_04581943.1| 30S ribosomal protein S4 [Helicobacter bilis ATCC 43879]
 gi|229372829|gb|EEO23220.1| 30S ribosomal protein S4 [Helicobacter bilis ATCC 43879]
          Length = 208

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A+ RR   +++    + V+G  ++  +  +     +EV
Sbjct: 99  RLDNVVYRMGFATTRRFARQLVTHGHILVDGKRVDIPSFQIKQGQKVEV 147


>gi|50303139|ref|XP_451507.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|49640638|emb|CAH03095.1| KLLA0A11660p [Kluyveromyces lactis]
          Length = 482

 Score = 45.6 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 1/54 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+   + RA  AS  R+  + I    V VNG+ +      + + D   V    +
Sbjct: 104 RLDFALFRAMFASSVRQARQFILHGNVHVNGVKITSPGYALKAGDVFNVRPEKV 157


>gi|302871648|ref|YP_003840284.1| pseudouridine synthase [Caldicellulosiruptor obsidiansis OB47]
 gi|302574507|gb|ADL42298.1| pseudouridine synthase [Caldicellulosiruptor obsidiansis OB47]
          Length = 311

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 22/198 (11%), Positives = 56/198 (28%), Gaps = 13/198 (6%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDP 91
           +R +  ++V++         + V   D+I V   P            +  +  +  +   
Sbjct: 66  DRFLEHKKVEI---------IKVYEDDNIVVIDKPYGIPSHPDSNNEYSVVSWIEDNYSK 116

Query: 92  DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151
                +   L    + ++ + +       +L   +   + +     + +           
Sbjct: 117 GELPQLCHRLDRNTAGLMIIAKNRQVLSEMLKYMSRRTIIKKYLCITKKADLPESGVLVH 176

Query: 152 QVDQDKLNL--LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            + +D              G         +  QK     V V ++ GK  +I+       
Sbjct: 177 YLKKDSKKSKVYISDFPQDGYLEVVTAYKIVRQKDDLQLVDVEIKTGKTHQIRAQLAHVG 236

Query: 210 WKVNRLIRISYGPFQLGT 227
             +  L    YG ++L  
Sbjct: 237 LCI--LGDSKYGDWELNK 252


>gi|94987423|ref|YP_595356.1| 30S ribosomal protein S4 [Lawsonia intracellularis PHE/MN1-00]
 gi|152060957|sp|Q1MPP2|RS4_LAWIP RecName: Full=30S ribosomal protein S4
 gi|94731672|emb|CAJ55035.1| ribosomal protein S4 [Lawsonia intracellularis PHE/MN1-00]
          Length = 208

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A SR +  ++I      +NG  +   ++ V   D IEV
Sbjct: 99  RLDNVVYRLGLANSRVQARQLIRHGIFTLNGHKVTIPSLQVNVGDSIEV 147


>gi|15603256|ref|NP_246330.1| 30S ribosomal protein S4 [Pasteurella multocida subsp. multocida
           str. Pm70]
 gi|26399488|sp|Q9CL53|RS4_PASMU RecName: Full=30S ribosomal protein S4
 gi|12721766|gb|AAK03475.1| RpS4 [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 206

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R E  ++++ + + VNG ++   +  V   D + V
Sbjct: 97  RLDNVVYRMGFAATRAEARQLVSHKAIVVNGRVVNIPSFQVSVNDVVAV 145


>gi|239787587|emb|CAX84055.1| 30S ribosomal protein S4 [uncultured bacterium]
          Length = 208

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+  V+ R G +S R E  ++++ +++ VNG  +   +  V   D I V+
Sbjct: 99  RLDNVVYRLGFSSSRSEARQVVSHKQILVNGKPINICSYLVKPGDKIAVN 148


>gi|312135354|ref|YP_004002692.1| pseudouridine synthase [Caldicellulosiruptor owensensis OL]
 gi|311775405|gb|ADQ04892.1| pseudouridine synthase [Caldicellulosiruptor owensensis OL]
          Length = 311

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 22/198 (11%), Positives = 57/198 (28%), Gaps = 13/198 (6%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDP 91
           +R +  ++V++         + V   D+I V   P            +  +  +  +   
Sbjct: 66  DRFLEHKKVEI---------IKVYEDDNIVVIDKPYGIPSHPDSNNEYSVVSWIEDNYSK 116

Query: 92  DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151
           D    +   L    + ++ + +       +L   +   + +     + +           
Sbjct: 117 DELPQLCHRLDRNTAGLMIIAKNRQVLSEMLKYMSRRAIIKKYLCITKKADLPESGVLVH 176

Query: 152 QVDQDKLNL--LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            + +D              G         +  QK     + V ++ GK  +I+       
Sbjct: 177 YLKKDSKKSKVYISDFPQDGYSEVVTAYKIVRQKDDLQLLDVEIKSGKTHQIRAQLAHVG 236

Query: 210 WKVNRLIRISYGPFQLGT 227
             +  L    YG ++L  
Sbjct: 237 LCI--LGDSKYGDWELNK 252


>gi|240170143|ref|ZP_04748802.1| hypothetical protein MkanA1_12573 [Mycobacterium kansasii ATCC
          12478]
          Length = 269

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 3/53 (5%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDG 64
          RV   + R G+A SR +   +I   +V+++G+ + + A  V  +    + VDG
Sbjct: 6  RVDVELVRRGLARSRHQAAELIEAGKVRIDGLPVVKPATAVAPSAALTVAVDG 58


>gi|255711504|ref|XP_002552035.1| KLTH0B05698p [Lachancea thermotolerans]
 gi|238933413|emb|CAR21597.1| KLTH0B05698p [Lachancea thermotolerans]
          Length = 480

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 23/54 (42%), Gaps = 1/54 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+   + RA  AS  R+  + I    V VNGI + +    + + D   V    +
Sbjct: 104 RLDFALFRAMFASSVRQARQFILHGNVFVNGIKITQPGYPLKAGDVFNVKPEKV 157


>gi|13899137|gb|AAG12403.1| Ybc5 [Chlorobaculum tepidum]
          Length = 101

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 2/57 (3%)

Query: 7  VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          V +  TP R+ + + +    A+R +V++ I +QRV VNG  ++     + S DHI +
Sbjct: 39 VSKVQTPMRIDRYLTQQVENATRNKVQKAIEEQRVLVNGKPVKS-NYRIKSCDHIHI 94


>gi|261867278|ref|YP_003255200.1| 30S ribosomal protein S4 [Aggregatibacter actinomycetemcomitans
           D11S-1]
 gi|261412610|gb|ACX81981.1| hypothetical protein D11S_0571 [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 206

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G A +R E  ++++ + + VNG ++   +  V   D + V
Sbjct: 97  RLDNIVYRMGFAATRAEARQLVSHKAIVVNGRVVNIPSFQVSVDDVVAV 145


>gi|256379171|ref|YP_003102831.1| hypothetical protein Amir_5164 [Actinosynnema mirum DSM 43827]
 gi|255923474|gb|ACU38985.1| hypothetical protein Amir_5164 [Actinosynnema mirum DSM 43827]
          Length = 276

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 10/121 (8%), Positives = 30/121 (24%), Gaps = 3/121 (2%)

Query: 236 VSKKILR---EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
           +++++L    E  G    E   V  +    + +      P   +       +      + 
Sbjct: 96  LTEQVLETQAELFGMSKEELRAVTAEEATTAPQQGPPAPPARPTPPSPGQPQGGPVPGRP 155

Query: 293 NGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                +     P    +        +            R ++ +  P      + +   A
Sbjct: 156 EPGQARTGGPQPGRPHSGRQQSGQPQPGRPQSGQPQPGRPQSGQPQPGKSQPGTSQPGQA 215

Query: 353 K 353
           +
Sbjct: 216 R 216


>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 = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 9/44 (20%), Positives = 19/44 (43%)

Query: 10 NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN 53
               R+ + +A     SR + +  I    V+V+G  + +A+  
Sbjct: 5  TAQGVRLDQALAYEAKTSRVKAQEWIEMGIVRVDGKPVTKASYR 48


>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 = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 27/226 (11%), Positives = 59/226 (26%), Gaps = 41/226 (18%)

Query: 22  RAGIASRREVERMIA----QQRVKVNGILLERAAVNVMSTDHIEVD-------------- 63
             G++SR     +I      +R+KV+G+ ++     V + + I+++              
Sbjct: 24  ELGLSSR-----LIRSAAIDKRIKVDGVSVK-MNYVVKTGEEIKIELSKKESQNIEPEKM 77

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
            + +   +   L L  KP  +V         +     L              ++   +  
Sbjct: 78  DIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYFKESNQDCIVRLVSRLDMNT 137

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
                                        +     NL +K   I    Y   + T+    
Sbjct: 138 SGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLEEKEGTINRPIYRPAEDTIKRVV 197

Query: 180 -DTQKGSNAWVTVG------------LREGKNREIKKVFEFFNWKV 212
            +  + S     V             L  G+  +I+         +
Sbjct: 198 DERGQESITHYKVIESYNGADLVECLLETGRTHQIRVHLSSLGHPI 243


>gi|113477614|ref|YP_723675.1| RNA-binding S4 [Trichodesmium erythraeum IMS101]
 gi|110168662|gb|ABG53202.1| RNA-binding S4 [Trichodesmium erythraeum IMS101]
          Length = 259

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 2/65 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             K  +       R+  V A AG   SR ++  +I    V+VN   + +A+  V + D I
Sbjct: 172 PKKKELTTVEASMRLDAV-ASAGFGMSRSKMVDLIDGGDVRVNWKEISQASYTVKTGDLI 230

Query: 61  EVDGV 65
            + G 
Sbjct: 231 AIRGK 235


>gi|256273838|gb|EEU08760.1| Nam9p [Saccharomyces cerevisiae JAY291]
          Length = 486

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 3/58 (5%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           R+   + RA  AS  R+  + I    V+VNG+ ++  +  +   D   V   P++  E
Sbjct: 104 RLDFALFRAMFASSVRQARQFILHGNVRVNGVKIKHPSYTLKPGDMFSV--KPVKVLE 159


>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 = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 20/199 (10%), Positives = 49/199 (24%), Gaps = 5/199 (2%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP---LRKAERTR 74
           K++A+    S  E + +I    V   G +L+ A   +       V  V    +       
Sbjct: 6   KLLAKQENISNNEAKDLIDAGLVSAKGQILKVARAEMSENTKFSVQKVAKPAIVFENDDI 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L +   P  +            +          V+     +     +    N       +
Sbjct: 66  LVVNKPPFFVSEKLEKIFKFKLLNRLDKETSGIVLLYKNEEFKERAIKEFKNMRVKKTYI 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
            +                  + K     +            ++      G  + V + + 
Sbjct: 126 AIVQGIVSEEMEFDEPILTIKGKTGAFSRISPH--GKSAITRIFPLMISGKKSLVKIEID 183

Query: 195 EGKNREIKKVFEFFNWKVN 213
            G+  +I+       + + 
Sbjct: 184 TGRTHQIRVHLSNAGFGII 202


>gi|269792512|ref|YP_003317416.1| hemolysin A [Thermanaerovibrio acidaminovorans DSM 6589]
 gi|269100147|gb|ACZ19134.1| hemolysin A [Thermanaerovibrio acidaminovorans DSM 6589]
          Length = 269

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ + G+A SR E   +I    V+++G++  + +  V +  ++ V
Sbjct: 2  VRLDALLVKRGLARSRDEARELIETGLVRIDGLVASKGSTMVGTEVNVSV 51


>gi|251793850|ref|YP_003008582.1| 30S ribosomal protein S4 [Aggregatibacter aphrophilus NJ8700]
 gi|247535249|gb|ACS98495.1| ribosomal protein S4 [Aggregatibacter aphrophilus NJ8700]
          Length = 206

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R E  ++++ + + VNG ++   +  V   D + V
Sbjct: 97  RLDNVVYRMGFAATRAEARQLVSHKAIVVNGRVVNIPSFQVSVDDVVAV 145


>gi|225555459|gb|EEH03751.1| NAM9+ protein [Ajellomyces capsulatus G186AR]
          Length = 490

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 1/54 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+   I RA  AS  R+  + +    V VNG  +      +   D  +VD   +
Sbjct: 126 RLDVAIFRAMFASSTRQARQFVIHGSVTVNGKKMRYPGYLLNPGDLFQVDPERV 179


>gi|89100095|ref|ZP_01172964.1| 30S ribosomal protein S4 [Bacillus sp. NRRL B-14911]
 gi|89085185|gb|EAR64317.1| 30S ribosomal protein S4 [Bacillus sp. NRRL B-14911]
          Length = 200

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +RR+  +++    + V+G  ++  +  V     I +
Sbjct: 93  RLDNVVYRLGLARTRRQARQLVNHGHIIVDGGRVDIPSYRVQPGQTITL 141


>gi|312793770|ref|YP_004026693.1| pseudouridine synthase [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|312180910|gb|ADQ41080.1| pseudouridine synthase [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 311

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 23/198 (11%), Positives = 57/198 (28%), Gaps = 13/198 (6%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDP 91
           +R +  ++V++         + V   D+I V   P            +  +  +  +   
Sbjct: 66  DRFLEHKKVEI---------LKVYEDDNIVVIDKPYGIPSHPDSNNEYSVVSWIEDNYSK 116

Query: 92  DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151
           D    +   L    + ++ + +       +L   +   + +     + +           
Sbjct: 117 DELPQLCHRLDRNTAGLMIIAKNRQVLSEMLKYMSRRAIKKRYLCITKKAELPKSGVLVH 176

Query: 152 QVDQDKLNL--LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            + +D              G         +  QK     V V ++ GK  +I+       
Sbjct: 177 YLKKDPKKSKVYISDFPQDGYSEVVTAYKIVRQKDDLQLVDVEIKTGKTHQIRAQLAHVG 236

Query: 210 WKVNRLIRISYGPFQLGT 227
             +  L    YG ++L  
Sbjct: 237 LCI--LGDSKYGDWELNK 252


>gi|304404108|ref|ZP_07385770.1| ribosomal protein S4 [Paenibacillus curdlanolyticus YK9]
 gi|304347086|gb|EFM12918.1| ribosomal protein S4 [Paenibacillus curdlanolyticus YK9]
          Length = 200

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  ++ R G A SR    ++++   V VNG  ++ A+  V   D I
Sbjct: 93  RLDNLVYRLGFANSRAGARQLVSHGHVTVNGKKVDIASYTVALGDVI 139


>gi|260772120|ref|ZP_05881037.1| SSU ribosomal protein S4p (S9e) [Vibrio metschnikovii CIP 69.14]
 gi|260612987|gb|EEX38189.1| SSU ribosomal protein S4p (S9e) [Vibrio metschnikovii CIP 69.14]
          Length = 202

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   + NV + D + +
Sbjct: 93  RLDNVVYRMGFGATRAEARQLVSHKAILVNGSVVNVPSFNVAANDVVAI 141


>gi|154338640|ref|XP_001565542.1| hypothetical protein [Leishmania braziliensis MHOM/BR/75/M2904]
          Length = 1770

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 11/111 (9%), Positives = 22/111 (19%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            L      +      +P                       +  K   +K     QK    
Sbjct: 763 PLAASFAAKTTPPYSSPPKQLVAKGEAETPKGEAQRGRGPQKGKRRPRKGKRRPQKGKRR 822

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           P   +                     +R +  +R P    +R  +     +
Sbjct: 823 PQKGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPQ 873



 Score = 44.4 bits (103), Expect = 0.026,   Method: Composition-based stats.
 Identities = 10/131 (7%), Positives = 26/131 (19%), Gaps = 25/131 (19%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV-- 305
               +                + RP      P    R  +   ++    K++        
Sbjct: 820 KRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRP 879

Query: 306 ---------------------HRRNLASNVWMAKGIHSSFLSDSG-QREENHRRSPSFPS 343
                                 +          +          G +R +  +R P    
Sbjct: 880 RKGKRRPQKGKRRPRKGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPQKGK 939

Query: 344 KRSLRRTSAKK 354
           +R   +   ++
Sbjct: 940 RRPQ-KGKRRR 949



 Score = 43.2 bits (100), Expect = 0.065,   Method: Composition-based stats.
 Identities = 13/148 (8%), Positives = 25/148 (16%), Gaps = 35/148 (23%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK--NGLSKQK 299
           R                          + RP      P    R  +   ++   G  + +
Sbjct: 800 RGPQKGKRRPRKGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPQ 859

Query: 300 KLATPVHRRNLASN-----------------------------VWMAKGIHSSFLSDSGQ 330
           K      +                                                   +
Sbjct: 860 KGKRRPQKGKRRPQKGKRRPRKGKRRPQKGKRRPRKGKRRPQKGKRRPQKGKRRPQKGKR 919

Query: 331 REENHRRSPSFPSKRS----LRRTSAKK 354
           R +  +R P    +R      R    K+
Sbjct: 920 RPQKGKRRPQKGKRRPQKGKRRPQKGKR 947



 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 13/148 (8%), Positives = 29/148 (19%), Gaps = 35/148 (23%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK--NGLSKQK 299
           + +      E  +              + RP      P    R  +   ++   G  + +
Sbjct: 786 KGEAETPKGEAQRGRGPQKGKRRPRKGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPQ 845

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLS-----------------------------DSGQ 330
           K      +          +                                        +
Sbjct: 846 KGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPRKGKRRPQKGKRRPRKGKRRPQKGKR 905

Query: 331 REENHRRSPSFPSKRS----LRRTSAKK 354
           R +  +R P    +R      R    K+
Sbjct: 906 RPQKGKRRPQKGKRRPQKGKRRPQKGKR 933



 Score = 40.5 bits (93), Expect = 0.43,   Method: Composition-based stats.
 Identities = 10/133 (7%), Positives = 22/133 (16%), Gaps = 31/133 (23%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK--------- 292
           R         +                + RP      P    R  +   ++         
Sbjct: 821 RRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPR 880

Query: 293 ---------------------NGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSG-Q 330
                                 G  + +K      +          +          G +
Sbjct: 881 KGKRRPQKGKRRPRKGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKR 940

Query: 331 REENHRRSPSFPS 343
           R +  +R      
Sbjct: 941 RPQKGKRRRMKTG 953



 Score = 39.8 bits (91), Expect = 0.71,   Method: Composition-based stats.
 Identities = 13/146 (8%), Positives = 28/146 (19%), Gaps = 33/146 (22%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           ++ +     E  +          +   R R              K     + G  + +K 
Sbjct: 781 KQLVAKGEAETPKGEAQRGRGPQKGKRRPRKGKRRPQKGKRRPQKGKRRPQKGKRRPQKG 840

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQRE----------------------------- 332
                +          +          G+R                              
Sbjct: 841 KRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPRKGKRRPQKGKRRPRKGKRRP 900

Query: 333 ENHRRSPSFPSKRS----LRRTSAKK 354
           +  +R P    +R      R    K+
Sbjct: 901 QKGKRRPQKGKRRPQKGKRRPQKGKR 926



 Score = 39.4 bits (90), Expect = 0.81,   Method: Composition-based stats.
 Identities = 10/106 (9%), Positives = 23/106 (21%), Gaps = 4/106 (3%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
            + +       +        +   ++             + G   QK    P   +    
Sbjct: 758 RKTDKPLAASFAAKTTPPYSSPPKQLVAKGEAETPKGEAQRGRGPQKGKRRPRKGKRRPQ 817

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS----LRRTSAKK 354
                            +R +  +R P    +R      R    K+
Sbjct: 818 KGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKRRPQKGKR 863



 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 29/111 (26%), Gaps = 3/111 (2%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R Q G    ++ +          +   R              R +K   +     K K+ 
Sbjct: 864 RPQKGKRRPQKGKRRPRKGKRRPQKGKRRPRKGKRRPQKGKRRPQKGKRRPQ---KGKRR 920

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                RR         KG          + +     + +  + R+  R +A
Sbjct: 921 PQKGKRRPQKGKRRPQKGKRRPQKGKRRRMKTGVSGAAASITPRAANRPTA 971



 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 15/119 (12%), Positives = 27/119 (22%), Gaps = 6/119 (5%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
           +L         +  Q                +       P      K  +    G +++ 
Sbjct: 740 MLSAATPKQQAQPPQPLPRKTDKPLAASFAAKTTPPYSSPPKQLVAKGEAETPKGEAQRG 799

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS----LRRTSAKK 354
           +      RR         KG           R +  +R P    +R      R    K+
Sbjct: 800 RGPQKGKRRPRKGKRRPQKGKRRPQKGKR--RPQKGKRRPQKGKRRPQKGKRRPQKGKR 856


>gi|299144486|ref|ZP_07037565.1| ribosomal protein S4 [Peptoniphilus sp. oral taxon 386 str. F0131]
 gi|298517574|gb|EFI41314.1| ribosomal protein S4 [Peptoniphilus sp. oral taxon 386 str. F0131]
          Length = 198

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +  R G AS  R+  +M+    + VNG  +   +    + D I +
Sbjct: 89  RLDNLAYRMGFASSIRQARQMVTHGHITVNGKKVNIPSYRCSAGDVIAL 137


>gi|32892090|gb|AAP88984.1| ribosomal protein S4 [Passiflora setacea]
          Length = 183

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 14/82 (17%), Positives = 30/82 (36%), Gaps = 1/82 (1%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+  ++ R G+AS   +  +++  + + VNG +++  +      D I V   P  K   
Sbjct: 71  MRLDNILFRLGMASTIPQARQLVNHRHILVNGRIVDIPSYRCKPQDLITVKDEPKSKDMI 130

Query: 73  TRLWLYHKPIGLVTTHSDPDGR 94
                      L    +    +
Sbjct: 131 QNSLDSFPQEKLPKHLTLHPFQ 152


>gi|313206370|ref|YP_004045547.1| SSU ribosomal protein s4p [Riemerella anatipestifer DSM 15868]
 gi|312445686|gb|ADQ82041.1| SSU ribosomal protein S4P [Riemerella anatipestifer DSM 15868]
 gi|315023689|gb|EFT36693.1| 30S ribosomal protein S4 [Riemerella anatipestifer RA-YM]
 gi|325336184|gb|ADZ12458.1| Ribosomal protein S4 related protein [Riemerella anatipestifer
           RA-GD]
          Length = 202

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R    ++++ + + VNG ++   + ++   D + V
Sbjct: 96  RLDNVVYRLGFAKTRAAARQLVSHRHITVNGEVVNIPSYSLKPGDKVAV 144


>gi|188535254|ref|YP_001909051.1| 30S ribosomal protein S4 [Erwinia tasmaniensis Et1/99]
 gi|300718681|ref|YP_003743484.1| 30S ribosomal protein S4 [Erwinia billingiae Eb661]
 gi|226699063|sp|B2VK72|RS4_ERWT9 RecName: Full=30S ribosomal protein S4
 gi|188030296|emb|CAO98185.1| 30S ribosomal protein S4 [Erwinia tasmaniensis Et1/99]
 gi|299064517|emb|CAX61637.1| 30S ribosomal protein S4 [Erwinia billingiae Eb661]
          Length = 206

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKSIMVNGRVVSIASYQVTPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|169824696|ref|YP_001692307.1| S4 RNA-binding domain-containing protein [Finegoldia magna ATCC
          29328]
 gi|302380241|ref|ZP_07268713.1| S4 domain protein [Finegoldia magna ACS-171-V-Col3]
 gi|167831501|dbj|BAG08417.1| putative S4 RNA-binding domain protein [Finegoldia magna ATCC
          29328]
 gi|302312024|gb|EFK94033.1| S4 domain protein [Finegoldia magna ACS-171-V-Col3]
          Length = 81

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   +     QRVK+N  + +    NV   D IE+
Sbjct: 1  MRLDKFLKNSRIIKRRTVAKTACESQRVKINDKIAK-PGDNVKVGDIIEI 49


>gi|85060232|ref|YP_455934.1| 30S ribosomal protein S4 [Sodalis glossinidius str. 'morsitans']
 gi|123518718|sp|Q2NQP6|RS4_SODGM RecName: Full=30S ribosomal protein S4
 gi|84780752|dbj|BAE75529.1| 30S ribosomal protein S4 [Sodalis glossinidius str. 'morsitans']
          Length = 206

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V   D + +
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKAIMVNGRVVNIASYQVTPNDVVSI 145


>gi|67923764|ref|ZP_00517228.1| RNA-binding S4 [Crocosphaera watsonii WH 8501]
 gi|67854391|gb|EAM49686.1| RNA-binding S4 [Crocosphaera watsonii WH 8501]
          Length = 275

 Score = 45.6 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 3/65 (4%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K K  +       R+   IA AG   SR ++   I +  V+VN     +++ NV S D I
Sbjct: 189 KTKE-MTTVEASMRLD-AIASAGFGMSRSKMSDAINRGDVRVNWKETSQSSYNVKSGDLI 246

Query: 61  EVDGV 65
            V G 
Sbjct: 247 TVRGK 251


>gi|222099994|ref|YP_002534562.1| 30S ribosomal protein S4 [Thermotoga neapolitana DSM 4359]
 gi|254764618|sp|B9K8B3|RS4_THENN RecName: Full=30S ribosomal protein S4
 gi|221572384|gb|ACM23196.1| 30S ribosomal protein S4 [Thermotoga neapolitana DSM 4359]
          Length = 209

 Score = 45.6 bits (106), Expect = 0.014,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+  +++      VNG  ++  +  +   D +EV
Sbjct: 99  RLDNVVYRMGFAINRRQARQLVNHGHFLVNGKKVDIPSYLLRPNDVVEV 147


>gi|154148523|ref|YP_001405813.1| 30S ribosomal protein S4 [Campylobacter hominis ATCC BAA-381]
 gi|171769700|sp|A7HZX2|RS4_CAMHC RecName: Full=30S ribosomal protein S4
 gi|153804532|gb|ABS51539.1| ribosomal protein S4 [Campylobacter hominis ATCC BAA-381]
          Length = 208

 Score = 45.6 bits (106), Expect = 0.014,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  ++ R G A+ RR   +++    + V+G  ++  + +V     IE+
Sbjct: 98  QRLDNLVYRMGFATTRRFARQLVTHGHILVDGKRVDIPSYSVKVGQKIEI 147


>gi|83591248|ref|YP_431257.1| 30S ribosomal protein S4 [Moorella thermoacetica ATCC 39073]
 gi|123725621|sp|Q2RFS5|RS4_MOOTA RecName: Full=30S ribosomal protein S4
 gi|83574162|gb|ABC20714.1| SSU ribosomal protein S4P [Moorella thermoacetica ATCC 39073]
          Length = 208

 Score = 45.6 bits (106), Expect = 0.014,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SR E   ++      VNG  +   +  V   D I V
Sbjct: 99  RLDNVVYRLGFADSRAEARTLVRHGHFLVNGRKVNIPSYLVRPGDTISV 147


>gi|23099660|ref|NP_693126.1| 30S ribosomal protein S4 [Oceanobacillus iheyensis HTE831]
 gi|26399359|sp|P59130|RS4_OCEIH RecName: Full=30S ribosomal protein S4
 gi|22777890|dbj|BAC14161.1| 30S ribosomal protein S4 [Oceanobacillus iheyensis HTE831]
          Length = 200

 Score = 45.6 bits (106), Expect = 0.014,   Method: Composition-based stats.
 Identities = 10/47 (21%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  ++ R G+A +RR+  +++    V V+G  ++  +  +     I
Sbjct: 93  RLDNLVYRLGLARTRRQARQLVNHGHVTVDGGRVDIPSYAIKPGQVI 139


>gi|189347677|ref|YP_001944206.1| 30S ribosomal protein S4 [Chlorobium limicola DSM 245]
 gi|226697820|sp|B3EGW4|RS4_CHLL2 RecName: Full=30S ribosomal protein S4
 gi|189341824|gb|ACD91227.1| ribosomal protein S4 [Chlorobium limicola DSM 245]
          Length = 203

 Score = 45.6 bits (106), Expect = 0.014,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R+G  ASR    ++++   + VNG  +   +  V   D IE 
Sbjct: 94  RLDNVVFRSGFSASRAGARQLVSHGHLVVNGKKVNIPSFQVSPGDLIEF 142


>gi|291520350|emb|CBK75571.1| Uncharacterized conserved protein [Butyrivibrio fibrisolvens
          16/4]
          Length = 71

 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 9/37 (24%), Positives = 16/37 (43%)

Query: 31 VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           + +I    VKV G +  R    +   D +E +G  +
Sbjct: 29 AKEVIEDGLVKVGGEVETRRGKKIYPGDIVEFNGESV 65


>gi|262203541|ref|YP_003274749.1| 30S ribosomal protein S4 [Gordonia bronchialis DSM 43247]
 gi|262086888|gb|ACY22856.1| ribosomal protein S4 [Gordonia bronchialis DSM 43247]
          Length = 201

 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 1/61 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ RAG+A +RR+  +M++     VNG+ ++  +  V   D I+V    L+     
Sbjct: 92  RLDNVVYRAGLARTRRQARQMVSHGHFTVNGVKVDVPSYRVGQYDIIDVRPKSLQTVPFQ 151

Query: 74  R 74
            
Sbjct: 152 I 152


>gi|153815230|ref|ZP_01967898.1| hypothetical protein RUMTOR_01464 [Ruminococcus torques ATCC
          27756]
 gi|317502313|ref|ZP_07960482.1| S4 RNA-binding domain-containing protein [Lachnospiraceae
          bacterium 8_1_57FAA]
 gi|331089917|ref|ZP_08338809.1| hypothetical protein HMPREF1025_02392 [Lachnospiraceae bacterium
          3_1_46FAA]
 gi|145847489|gb|EDK24407.1| hypothetical protein RUMTOR_01464 [Ruminococcus torques ATCC
          27756]
 gi|316896269|gb|EFV18371.1| S4 RNA-binding domain-containing protein [Lachnospiraceae
          bacterium 8_1_57FAA]
 gi|330403149|gb|EGG82710.1| hypothetical protein HMPREF1025_02392 [Lachnospiraceae bacterium
          3_1_46FAA]
          Length = 79

 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR          RV VNG   + A+V V   D IE+
Sbjct: 1  MRLDKFLKVSRLIKRRTVANEACDAGRVSVNGKPAK-ASVQVKPGDVIEI 49


>gi|94312223|ref|YP_585433.1| 30S ribosomal protein S4 [Cupriavidus metallidurans CH34]
 gi|152112253|sp|Q1LI62|RS4_RALME RecName: Full=30S ribosomal protein S4
 gi|93356075|gb|ABF10164.1| 30S ribosomal subunit protein S4 [Cupriavidus metallidurans CH34]
          Length = 207

 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  L   +  + S D + V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAILVNGETLNVPSAQIKSGDIVSV 146


>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 = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 33/240 (13%), Positives = 69/240 (28%), Gaps = 36/240 (15%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQ----QRVKVNGILLERAAVNVMSTDH 59
           K I  +      + +++   G +S      +I +     R+ VN  +       +   D 
Sbjct: 2   KIIASKEDENLPLKEILINRGFSS-----TLIRKYKHSGRILVNNEI-SIVNRIIKKGDI 55

Query: 60  IEV----DGVPLRKAERTRLWLY---------HKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           IE+    D V ++  +      Y              +V   +     +           
Sbjct: 56  IELYLDDDNVSVKPEKMDLHICYEDDDILVVNKDAGVVVHPTAGHPDGTLANGVAWYYEK 115

Query: 107 RVI-----SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR---VYRVRFHGQVDQDKL 158
             I      V RLD +T GL++   +  +   L++          + R     +   D  
Sbjct: 116 NNINAPIRPVNRLDRDTSGLIIFAKNPFMQNYLQIVCPMKKFYIAIVRGDLEDRGTIDLP 175

Query: 159 NLLKKGIVI-----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              K G  I                +  +    + V + L+ G+  +I+         + 
Sbjct: 176 IKRKPGSTIERMVDDDGDKAVTDFYVLKRGEKLSLVKLELKTGRTHQIRVHLSHIGHPII 235


>gi|187933977|ref|YP_001884412.1| S4 domain protein [Clostridium botulinum B str. Eklund 17B]
 gi|187722130|gb|ACD23351.1| S4 domain protein [Clostridium botulinum B str. Eklund 17B]
          Length = 86

 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   +      RV +NG + +  + ++   D IE+
Sbjct: 1  MRLDKYLKVSRIIKRRTVAKEACESGRVSINGKVAK-PSTDIKEDDIIEI 49


>gi|320160440|ref|YP_004173664.1| 30S ribosomal protein S4 [Anaerolinea thermophila UNI-1]
 gi|319994293|dbj|BAJ63064.1| 30S ribosomal protein S4 [Anaerolinea thermophila UNI-1]
          Length = 212

 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            R+  V+ R G AS R +  +++    ++VN    +  ++ V   D I V
Sbjct: 102 MRLDNVVFRMGFASSRAQARQLVNHGHIQVNNHRADIPSMLVKPGDIISV 151


>gi|307265436|ref|ZP_07546992.1| S4 domain protein YaaA [Thermoanaerobacter wiegelii Rt8.B1]
 gi|306919550|gb|EFN49768.1| S4 domain protein YaaA [Thermoanaerobacter wiegelii Rt8.B1]
          Length = 68

 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 20/36 (55%)

Query: 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          + ++ I + +VKVNG +  +    +   D IEV+G 
Sbjct: 28 QAKKFILEGKVKVNGAIELKRGKKLHKNDIIEVEGK 63


>gi|301300313|ref|ZP_07206520.1| S4 domain protein [Lactobacillus salivarius ACS-116-V-Col5a]
 gi|300852086|gb|EFK79763.1| S4 domain protein [Lactobacillus salivarius ACS-116-V-Col5a]
          Length = 89

 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 2/51 (3%)

Query: 14 QRVSKVIARAGIASRREVERMIA-QQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+ K +  + I  RR V + I+ Q R+ +NG + +  + NV   D I ++
Sbjct: 1  MRLDKFLKISRIIKRRTVAKEISSQGRITINGKVAKS-SSNVNVGDEIVIN 50


>gi|113460232|ref|YP_718290.1| 30S ribosomal protein S4 [Haemophilus somnus 129PT]
 gi|123327085|sp|Q0I138|RS4_HAES1 RecName: Full=30S ribosomal protein S4
 gi|112822275|gb|ABI24364.1| SSU ribosomal protein S4P [Haemophilus somnus 129PT]
          Length = 206

 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R E  ++++ + + VNG ++   +  V   D + V
Sbjct: 97  RLDNVVYRMGFAATRAEARQLVSHKAIVVNGRVVNIPSFQVSVNDVVAV 145


>gi|86158343|ref|YP_465128.1| 30S ribosomal protein S4 [Anaeromyxobacter dehalogenans 2CP-C]
 gi|197122365|ref|YP_002134316.1| 30S ribosomal protein S4 [Anaeromyxobacter sp. K]
 gi|220917147|ref|YP_002492451.1| RNA-binding S4 domain protein [Anaeromyxobacter dehalogenans 2CP-1]
 gi|123497980|sp|Q2IJ65|RS4_ANADE RecName: Full=30S ribosomal protein S4
 gi|226697798|sp|B4UBC5|RS4_ANASK RecName: Full=30S ribosomal protein S4
 gi|254764563|sp|B8J886|RS4_ANAD2 RecName: Full=30S ribosomal protein S4
 gi|85774854|gb|ABC81691.1| SSU ribosomal protein S4P [Anaeromyxobacter dehalogenans 2CP-C]
 gi|196172214|gb|ACG73187.1| RNA-binding S4 domain protein [Anaeromyxobacter sp. K]
 gi|219955001|gb|ACL65385.1| RNA-binding S4 domain protein [Anaeromyxobacter dehalogenans 2CP-1]
          Length = 208

 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V+ R G A +R E  +++     KVNG  +   +      D +E+   
Sbjct: 99  RLDNVVFRLGFADTRNEARQLVRHGHFKVNGRKVNIPSYLCRPGDKVELKDR 150


>gi|19705419|ref|NP_602914.1| putative cytoplasmic protein [Fusobacterium nucleatum subsp.
          nucleatum ATCC 25586]
 gi|296328803|ref|ZP_06871317.1| S4 domain protein YaaA [Fusobacterium nucleatum subsp. nucleatum
          ATCC 23726]
 gi|19713412|gb|AAL94213.1| Hypothetical cytosolic protein [Fusobacterium nucleatum subsp.
          nucleatum ATCC 25586]
 gi|296154138|gb|EFG94942.1| S4 domain protein YaaA [Fusobacterium nucleatum subsp. nucleatum
          ATCC 23726]
          Length = 71

 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 11/71 (15%), Positives = 28/71 (39%), Gaps = 9/71 (12%)

Query: 1  MKDKNIVQENFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
          MK+   V+ +    ++ + +       +G     + +++I   +VKVN  +  R    + 
Sbjct: 1  MKNIEKVKISTEFIKLDQFLKWLAVVDSG----SDAKQVILDGKVKVNDEVETRRGRKIY 56

Query: 56 STDHIEVDGVP 66
              +E+    
Sbjct: 57 PEYKVEIFDKI 67


>gi|325265406|ref|ZP_08132130.1| hemolysin A [Clostridium sp. D5]
 gi|324029407|gb|EGB90698.1| hemolysin A [Clostridium sp. D5]
          Length = 267

 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 23/167 (13%), Positives = 55/167 (32%), Gaps = 2/167 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++ +  +A SR + + +I    V V+G   ++A  +      IEV G  L    R
Sbjct: 3   ERLDVLLVKRNLAESREKAKAIIMAGSVFVDGQREDKAGSSFQEDVQIEVKGHTLPYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L    K +       +    + V  +       ++  G + +    +     D  L +
Sbjct: 63  GGL-KLEKALAEFDVTVEGKVCTDVGSSTGGFTDCMLQNGAVKVYAIDVGRGQLDWKLRQ 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
              +   +   +  V      +    + +    +        ++  L
Sbjct: 122 DDRVVCMEKTNIRYVTPEDIGEPVDFSSIDVSFISLTKVLEPIRRYL 168


>gi|261823208|ref|YP_003261314.1| 30S ribosomal protein S4 [Pectobacterium wasabiae WPP163]
 gi|261607221|gb|ACX89707.1| ribosomal protein S4 [Pectobacterium wasabiae WPP163]
          Length = 206

 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  +M++ + + VNG ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAESRQMVSHKAIMVNGRVVSIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|328865094|gb|EGG13480.1| proteasome component region PCI domain-containing protein
            [Dictyostelium fasciculatum]
          Length = 1066

 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 9/85 (10%), Positives = 16/85 (18%)

Query: 265  ETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSF 324
                R+      + P            ++G  +         RR+     W         
Sbjct: 937  RDAPRNDGGFGGDAPRRDGFGGPRDGPRDGPRRDGGFGGDAPRRDDDGGRWGRDAPRDGP 996

Query: 325  LSDSGQREENHRRSPSFPSKRSLRR 349
                     +  R       R   R
Sbjct: 997  RDGPRDGPRDGPRDGPRDGPRDGPR 1021



 Score = 44.4 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 9/118 (7%), Positives = 19/118 (16%), Gaps = 5/118 (4%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            R+  G       +                R    +   D             G  +    
Sbjct: 905  RDGFGGPRDGPRRDGGFGGDAPRRDDDGGRWGRDAPRNDGGFGGDAPRRDGFGGPRDGPR 964

Query: 302  ATPVHRRNLASNVWM-----AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              P        +         +    +          +  R       R   R   ++
Sbjct: 965  DGPRRDGGFGGDAPRRDDDGGRWGRDAPRDGPRDGPRDGPRDGPRDGPRDGPRDGPRR 1022



 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 11/130 (8%), Positives = 16/130 (12%), Gaps = 1/130 (0%)

Query: 221 GPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
           G F                            +                RD          
Sbjct: 787 GGFGDDDKWNREITRNDGDKWGRDAPRRDDGDRFPPRRDDGGDRFPPRRDNGFGGDAPRR 846

Query: 281 DFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR-EENHRRSP 339
           D    +          +      P +            G               +  R  
Sbjct: 847 DDDGGRWGRDAPRDGPRDGPRDGPRNDGGDRYVPPRRDGGFGGDAPRRDGGFGGDAPRRD 906

Query: 340 SFPSKRSLRR 349
            F   R   R
Sbjct: 907 GFGGPRDGPR 916



 Score = 41.7 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 10/115 (8%), Positives = 25/115 (21%), Gaps = 2/115 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+       +  +              R       + P        ++ +++G    +  
Sbjct: 855 RDAPRDGPRDGPRDGPRNDGGDRYVPPRRDGGFGGDAPRRDGGFGGDAPRRDGFGGPRDG 914

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDS--GQREENHRRSPSFPSKRSLRRTSAKK 354
                     +      G      +    G    +  R   F   R   R   ++
Sbjct: 915 PRRDGGFGGDAPRRDDDGGRWGRDAPRNDGGFGGDAPRRDGFGGPRDGPRDGPRR 969



 Score = 39.8 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 9/98 (9%), Positives = 15/98 (15%)

Query: 253  AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
                 +   +  +   RD      + P D  R                            
Sbjct: 937  RDAPRNDGGFGGDAPRRDGFGGPRDGPRDGPRRDGGFGGDAPRRDDDGGRWGRDAPRDGP 996

Query: 313  NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                  G              +  R        + RR 
Sbjct: 997  RDGPRDGPRDGPRDGPRDGPRDGPRRDGGFGGDAPRRD 1034



 Score = 37.5 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 10/98 (10%), Positives = 20/98 (20%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
                +  I  ++     R     +  D F   + +   +    +         RR+   
Sbjct: 791 DDDKWNREITRNDGDKWGRDAPRRDDGDRFPPRRDDGGDRFPPRRDNGFGGDAPRRDDDG 850

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
             W                  N       P +R     
Sbjct: 851 GRWGRDAPRDGPRDGPRDGPRNDGGDRYVPPRRDGGFG 888



 Score = 37.5 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 8/113 (7%), Positives = 20/113 (17%), Gaps = 2/113 (1%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVR--DRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
            R+  G     +A  N       +          +   + P        ++ +++    + 
Sbjct: 928  RDDDGGRWGRDAPRNDGGFGGDAPRRDGFGGPRDGPRDGPRRDGGFGGDAPRRDDDGGRW 987

Query: 300  KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                P              G                        +R       
Sbjct: 988  GRDAPRDGPRDGPRDGPRDGPRDGPRDGPRDGPRRDGGFGGDAPRRDFGAPRD 1040


>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 = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 1/61 (1%)

Query: 6  IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V+     QRV   +  A   SR +++R+  +  V+VNG  +++  + V +  HI V+  
Sbjct: 10 TVEPTKAGQRVDLFVGEALGLSRAKLKRLFEEGAVRVNGRAVKK-GLLVSAGQHILVEWE 68

Query: 66 P 66
           
Sbjct: 69 E 69


>gi|125975140|ref|YP_001039050.1| RNA-binding S4 [Clostridium thermocellum ATCC 27405]
 gi|256003204|ref|ZP_05428196.1| RNA-binding S4 domain protein [Clostridium thermocellum DSM 2360]
 gi|281418439|ref|ZP_06249458.1| RNA-binding S4 domain protein [Clostridium thermocellum JW20]
 gi|125715365|gb|ABN53857.1| RNA-binding S4 [Clostridium thermocellum ATCC 27405]
 gi|255992895|gb|EEU02985.1| RNA-binding S4 domain protein [Clostridium thermocellum DSM 2360]
 gi|281407523|gb|EFB37782.1| RNA-binding S4 domain protein [Clostridium thermocellum JW20]
 gi|316939307|gb|ADU73341.1| RNA-binding S4 domain protein [Clostridium thermocellum DSM 1313]
          Length = 79

 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR        Q RV +NG + +     V   D IE+
Sbjct: 1  MRIDKYLKVSRLIKRRTLANEACEQGRVLINGKVAK-PGTEVKVGDIIEI 49


>gi|67537988|ref|XP_662768.1| hypothetical protein AN5164.2 [Aspergillus nidulans FGSC A4]
 gi|40743155|gb|EAA62345.1| hypothetical protein AN5164.2 [Aspergillus nidulans FGSC A4]
 gi|259484618|tpe|CBF80996.1| TPA: 30S ribosomal subunit S4, putative (AFU_orthologue;
           AFUA_1G06980) [Aspergillus nidulans FGSC A4]
          Length = 457

 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 22/56 (39%), Gaps = 1/56 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+   I RA  AS  R+  + +    V VNG  +      +   D  +VD   +  
Sbjct: 126 RLDVAIFRALFASSARQARQFVLHGAVTVNGKKMRYPGYLLNPGDMFQVDPERVMY 181


>gi|332292498|ref|YP_004431107.1| ribosomal protein S4 [Krokinobacter diaphorus 4H-3-7-5]
 gi|332170584|gb|AEE19839.1| ribosomal protein S4 [Krokinobacter diaphorus 4H-3-7-5]
          Length = 201

 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G++ SR    +++  + + VNG ++   +  V   D + V
Sbjct: 94  RLDNVVHRMGMSPSRSGARQLVGHRHITVNGSIVNIPSFQVKPGDVVAV 142


>gi|293400860|ref|ZP_06645005.1| YlmH protein [Erysipelotrichaceae bacterium 5_2_54FAA]
 gi|291305886|gb|EFE47130.1| YlmH protein [Erysipelotrichaceae bacterium 5_2_54FAA]
          Length = 251

 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 12/51 (23%), Positives = 25/51 (49%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  +++     SR++ + +I    VKVN ++LE  +    +   I + G 
Sbjct: 176 RLDVLVSSFANISRKKAQELIRAGLVKVNHVILEETSYLCNNNSAISIRGH 226


>gi|320011585|gb|ADW06435.1| hemolysin A [Streptomyces flavogriseus ATCC 33331]
          Length = 271

 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+   + R  +A SR    ++IA  RV V G    + A  V ++  + V
Sbjct: 8  RLDAELVRRKLARSREHASQLIAAGRVTVGGNTATKPATQVETSAAVVV 56


>gi|295094326|emb|CBK83417.1| Uncharacterized conserved protein [Coprococcus sp. ART55/1]
          Length = 69

 Score = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 4/52 (7%)

Query: 20 IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
          +  +G+    + + +I Q  V VNG +  R    +   D +E DG  +   +
Sbjct: 22 LVESGV----DAKEVIVQGLVVVNGEIETRRGRKLYDGDEVEFDGDKISIQK 69


>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 = 45.2 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 30/240 (12%), Positives = 67/240 (27%), Gaps = 40/240 (16%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIA----QQRVKVNGILLERAAVNV-MSTDHI 60
           IV EN     +   +   G       +R+I     Q  + VNG  ++     +    D I
Sbjct: 4   IVGENEKGVILENFLRNKGF-----SKRLIRIYKWQGEILVNG--VKENVQRILQPGDVI 56

Query: 61  EV-------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           ++              G+ +   +   L +      +V         +           +
Sbjct: 57  DLILPENDSNIAPEKMGLDIYYEDEEILIVNKPANMVVHPTKRYQSGTLANGVAWYFKDK 116

Query: 108 VI-----SVGRLDINTEGLLLLTNDGGLARVL---------ELPSTQWLRVYRVRFHGQV 153
            I      V RLD  T GL++      +   L              +       R    +
Sbjct: 117 GIKALIRPVNRLDKGTSGLVVFAKRPFMQYYLQILKPMSKLYFAVVEGKMEGEGRIDLPI 176

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +   + +++ +  +G         +       + + V +  G+  +I+         + 
Sbjct: 177 SRKPQSGIERMVSEEGDRA-ITNYKVVKSSKRFSLLKVKIETGRTHQIRVHLSHIGHPIV 235


>gi|323488432|ref|ZP_08093679.1| 30S ribosomal protein S4 [Planococcus donghaensis MPA1U2]
 gi|323397939|gb|EGA90738.1| 30S ribosomal protein S4 [Planococcus donghaensis MPA1U2]
          Length = 200

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +RR+  +++    + V+G  ++  + +V     I  
Sbjct: 93  RLDNVVYRLGLARTRRQARQIVNHGHILVDGKRVDIPSFSVKPGQTIAF 141


>gi|323303395|gb|EGA57191.1| Nam9p [Saccharomyces cerevisiae FostersB]
          Length = 486

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   + RA  AS  R+  + I    V+VNG+ ++  +  +   D   V
Sbjct: 104 RLDFALFRAMFASSVRQARQFILHGNVRVNGVKIKHPSYTLKPGDMFSV 152


>gi|302388602|ref|YP_003824423.1| RNA-binding S4 domain protein [Thermosediminibacter oceani DSM
          16646]
 gi|302199230|gb|ADL06800.1| RNA-binding S4 domain protein [Thermosediminibacter oceani DSM
          16646]
          Length = 72

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 24/57 (42%), Gaps = 1/57 (1%)

Query: 10 NFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
                + + +  AG + +  E +  I Q  VKVNG +  R +  +   D +E  G 
Sbjct: 7  KTESINLDQFLKWAGAVFTGGEAKIKIRQGLVKVNGQVETRRSRKLFPGDTVEFHGE 63


>gi|151944400|gb|EDN62678.1| nuclear accommodation of mitochondria [Saccharomyces cerevisiae
           YJM789]
          Length = 486

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   + RA  AS  R+  + I    V+VNG+ ++  +  +   D   V
Sbjct: 104 RLDFALFRAMFASSVRQARQFILHGNVRVNGVKIKHPSYTLKPGDMFSV 152


>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 = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 23/121 (19%), Positives = 42/121 (34%), Gaps = 17/121 (14%)

Query: 4   KNIVQENFTPQRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI- 60
           + IV       R+   I+    G+ SR  V+  I    V VNG ++++ + NV S D + 
Sbjct: 72  EEIVDAAKGKIRLDSWISSRINGV-SRARVQSSIRLGLVTVNGRVVDKVSHNVKSGDEVN 130

Query: 61  -----------EVDGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                      E + +P  +   ++  L +      +V         + V   L      
Sbjct: 131 CTISELQPLKAEAEDIPLDIVYEDKHVLVVNKPAHMVVHPAPGNPTGTLVNGILHHCSLP 190

Query: 108 V 108
            
Sbjct: 191 C 191


>gi|23098937|ref|NP_692403.1| hypothetical protein OB1482 [Oceanobacillus iheyensis HTE831]
 gi|22777165|dbj|BAC13438.1| hypothetical conserved protein [Oceanobacillus iheyensis HTE831]
          Length = 258

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 15/58 (25%), Positives = 24/58 (41%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
            +  +  R+  VI      SR+E    I +  VKVN  L++     +   D I + G 
Sbjct: 176 DKTVSSLRLDTVIKEIYPLSRKEATVFIQKGLVKVNYKLVDDNKFQLQEKDMISIRGH 233


>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 = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 26/54 (48%), Gaps = 4/54 (7%)

Query: 13 PQRVSKVIARAG----IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          P+R+ K +AR        SR  + ++IA+  V++ G+ +      V+     E+
Sbjct: 20 PERLDKALAREAPEEAALSRSRLMKLIAEGAVRLKGVPVTDPKARVLEGQVYEI 73


>gi|307106329|gb|EFN54575.1| hypothetical protein CHLNCDRAFT_35967 [Chlorella variabilis]
          Length = 332

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 2/52 (3%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V A AG   SR ++  +I    V+VN     +A+  V + D + V G 
Sbjct: 258 RLDAV-ASAGFRMSRSKMADLIKAGDVRVNWRAAGKASAEVQAGDVVSVAGK 308


>gi|288920312|ref|ZP_06414624.1| hypothetical protein FrEUN1fDRAFT_4322 [Frankia sp. EUN1f]
 gi|288348260|gb|EFC82525.1| hypothetical protein FrEUN1fDRAFT_4322 [Frankia sp. EUN1f]
          Length = 539

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 6/89 (6%), Positives = 18/89 (20%)

Query: 265 ETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSF 324
             + R   +   +        +   ++                    S+         S 
Sbjct: 16  PQVGRGDAHRGGDAHRRGDAYRGGDAKPRWERPSGSRPDANRSGPRRSDGGRPASRGGSS 75

Query: 325 LSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +    +R  +       P   ++ R    
Sbjct: 76  VGRPARRPTDSPSRSGGPGDGTVPRRRPA 104



 Score = 39.4 bits (90), Expect = 0.95,   Method: Composition-based stats.
 Identities = 7/98 (7%), Positives = 21/98 (21%), Gaps = 3/98 (3%)

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
             +             R +            + + S+ +      + +      +   + 
Sbjct: 16  PQVGRGDAHRGGDAHRRGDAYRGGDAKPRWERPSGSRPDANRSGPRRSDGGRPASRGGSS 75

Query: 315 WMAKGIHSSFLSDSGQREENH---RRSPSFPSKRSLRR 349
                   +          +    RR P+ P+     R
Sbjct: 76  VGRPARRPTDSPSRSGGPGDGTVPRRRPAAPALPDEAR 113



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 9/102 (8%), Positives = 22/102 (21%), Gaps = 2/102 (1%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
            QV         +   R       +    + R   +    N    ++        R  +S
Sbjct: 16  PQVGRGDAHRGGDAHRRGDAYRGGDAKPRWERPSGSRPDANRSGPRRSDGGRPASRGGSS 75

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                     +          +       P+  +L   +  +
Sbjct: 76  VGR--PARRPTDSPSRSGGPGDGTVPRRRPAAPALPDEARAE 115


>gi|237741009|ref|ZP_04571490.1| conserved hypothetical protein [Fusobacterium sp. 4_1_13]
 gi|256846677|ref|ZP_05552133.1| conserved hypothetical protein [Fusobacterium sp. 3_1_36A2]
 gi|294784384|ref|ZP_06749675.1| S4 domain protein YaaA [Fusobacterium sp. 3_1_27]
 gi|229431053|gb|EEO41265.1| conserved hypothetical protein [Fusobacterium sp. 4_1_13]
 gi|256717897|gb|EEU31454.1| conserved hypothetical protein [Fusobacterium sp. 3_1_36A2]
 gi|294487956|gb|EFG35311.1| S4 domain protein YaaA [Fusobacterium sp. 3_1_27]
          Length = 71

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 11/71 (15%), Positives = 27/71 (38%), Gaps = 9/71 (12%)

Query: 1  MKDKNIVQENFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
          MK+   V+ +    ++ + +       +G     + +++I    VKVN  +  R    + 
Sbjct: 1  MKNIEKVKISTEFIKLDQFLKWLAVVDSG----SQAKQVILDGEVKVNDEVETRRGRKIY 56

Query: 56 STDHIEVDGVP 66
              +E+    
Sbjct: 57 PEYKVEIFDKI 67


>gi|226953895|ref|ZP_03824359.1| 30S ribosomal protein S4 [Acinetobacter sp. ATCC 27244]
 gi|294651610|ref|ZP_06728914.1| 30S ribosomal protein S4 [Acinetobacter haemolyticus ATCC 19194]
 gi|226835378|gb|EEH67761.1| 30S ribosomal protein S4 [Acinetobacter sp. ATCC 27244]
 gi|292822459|gb|EFF81358.1| 30S ribosomal protein S4 [Acinetobacter haemolyticus ATCC 19194]
          Length = 208

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + +NG  +  A++ V + D I V
Sbjct: 99  RLDNVVYRMGFGSTRSEARQLVSHRSITLNGRRVNIASIQVKAGDVIAV 147


>gi|190409124|gb|EDV12389.1| mitochondrial S4 ribosomal protein [Saccharomyces cerevisiae
           RM11-1a]
 gi|207341770|gb|EDZ69735.1| YNL137Cp-like protein [Saccharomyces cerevisiae AWRI1631]
 gi|259149224|emb|CAY82466.1| Nam9p [Saccharomyces cerevisiae EC1118]
 gi|323307464|gb|EGA60737.1| Nam9p [Saccharomyces cerevisiae FostersO]
 gi|323331931|gb|EGA73343.1| Nam9p [Saccharomyces cerevisiae AWRI796]
 gi|323335936|gb|EGA77214.1| Nam9p [Saccharomyces cerevisiae Vin13]
 gi|323346867|gb|EGA81146.1| Nam9p [Saccharomyces cerevisiae Lalvin QA23]
          Length = 486

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   + RA  AS  R+  + I    V+VNG+ ++  +  +   D   V
Sbjct: 104 RLDFALFRAMFASSVRQARQFILHGNVRVNGVKIKHPSYTLKPGDMFSV 152


>gi|120437150|ref|YP_862836.1| 30S ribosomal protein S4 [Gramella forsetii KT0803]
 gi|152060951|sp|A0M574|RS4_GRAFK RecName: Full=30S ribosomal protein S4
 gi|117579300|emb|CAL67769.1| 30S ribosomal protein S4 [Gramella forsetii KT0803]
          Length = 201

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A SRR   +++  + + VNG L+   + ++ + D + V
Sbjct: 94  RLDNVVYRMGVAPSRRAARQLVGHRHITVNGELVNIPSYHLKAGDVVGV 142


>gi|32892116|gb|AAP88997.1| ribosomal protein S4 [Mitostemma brevifilis]
 gi|74273239|gb|ABA01319.1| ribosomal protein S4 [Dilkea johannesii]
          Length = 186

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 14/84 (16%), Positives = 29/84 (34%), Gaps = 5/84 (5%)

Query: 14  QRVSKVIARAGIAS---RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            R+  ++ R G+AS   R    +++  + + VNG +++  +      D I V      K 
Sbjct: 74  MRLDNILFRLGMASTIPR--ARQLVNHRHILVNGRIVDIPSYRCKPRDLITVKDEQKSKD 131

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGR 94
                        L    +    +
Sbjct: 132 MIQNSLDSFPQEKLPKHLTLHPFQ 155


>gi|313677145|ref|YP_004055141.1| SSU ribosomal protein s4p [Marivirga tractuosa DSM 4126]
 gi|312943843|gb|ADR23033.1| SSU ribosomal protein S4P [Marivirga tractuosa DSM 4126]
          Length = 201

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA +RR   +++  + + VNG +L   +  V  +D I V
Sbjct: 93  RLDNVVFRLGIAPTRRAARQLVGHKHILVNGEILNIPSYQVKESDVIGV 141


>gi|323352538|gb|EGA85037.1| Nam9p [Saccharomyces cerevisiae VL3]
          Length = 486

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   + RA  AS  R+  + I    V+VNG+ ++  +  +   D   V
Sbjct: 104 RLDFALFRAMFASSVRQARQFILHGNVRVNGVKIKHPSYTLKPGDMFSV 152


>gi|153953857|ref|YP_001394622.1| rRNA methylase [Clostridium kluyveri DSM 555]
 gi|146346738|gb|EDK33274.1| Predicted rRNA methylase [Clostridium kluyveri DSM 555]
          Length = 274

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 1/56 (1%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          +R+  ++   GI S RE     I    + V+G  +++   N+  + +IE  G  L 
Sbjct: 6  ERIDVLLVDKGIFSSRERARASIMAGEIFVDGRRVDKCGQNIKRSSNIEFRGEKLP 61


>gi|104773518|ref|YP_618498.1| putative ribosome-associated heat shock protein [Lactobacillus
          delbrueckii subsp. bulgaricus ATCC 11842]
 gi|116513513|ref|YP_812419.1| ribosome-associated heat shock protein implicated in the
          recycling of the 50S subunit S4-like protein
          [Lactobacillus delbrueckii subsp. bulgaricus ATCC
          BAA-365]
 gi|300812083|ref|ZP_07092531.1| S4 domain protein [Lactobacillus delbrueckii subsp. bulgaricus
          PB2003/044-T3-4]
 gi|313123081|ref|YP_004033340.1| ribosome-associated heat shock protein implicated in the
          recycling of the 50S subunit [Lactobacillus delbrueckii
          subsp. bulgaricus ND02]
 gi|103422599|emb|CAI97202.1| Putative ribosome-associated heat shock protein [Lactobacillus
          delbrueckii subsp. bulgaricus ATCC 11842]
 gi|116092828|gb|ABJ57981.1| Ribosome-associated heat shock protein implicated in the
          recycling of the 50S subunit (S4 paralog)
          [Lactobacillus delbrueckii subsp. bulgaricus ATCC
          BAA-365]
 gi|300496922|gb|EFK31996.1| S4 domain protein [Lactobacillus delbrueckii subsp. bulgaricus
          PB2003/044-T3-4]
 gi|312279644|gb|ADQ60363.1| Ribosome-associated heat shock protein implicated in the
          recycling of the 50S subunit [Lactobacillus delbrueckii
          subsp. bulgaricus ND02]
 gi|325125149|gb|ADY84479.1| Hypothetical conserved protein [Lactobacillus delbrueckii subsp.
          bulgaricus 2038]
 gi|325684692|gb|EGD26846.1| S4 RNA-binding domain protein [Lactobacillus delbrueckii subsp.
          lactis DSM 20072]
          Length = 80

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR   + M  Q RV VNG  ++  + NV+  D I V
Sbjct: 1  MRIDKFLKISRLVKRRTVAKEMADQGRVSVNGKTVKS-SYNVVVGDVIAV 49


>gi|228474508|ref|ZP_04059241.1| ribosomal protein S4 [Staphylococcus hominis SK119]
 gi|314936181|ref|ZP_07843528.1| ribosomal protein S4 [Staphylococcus hominis subsp. hominis C80]
 gi|228271537|gb|EEK12899.1| ribosomal protein S4 [Staphylococcus hominis SK119]
 gi|313654800|gb|EFS18545.1| ribosomal protein S4 [Staphylococcus hominis subsp. hominis C80]
          Length = 200

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+   G+A +RR+  +++    ++V+G  ++  +  +     I V
Sbjct: 93  RLDAVVYSLGLARTRRQARQLVGHGHIEVDGKRVDIPSYALKPGQVISV 141


>gi|282855416|ref|ZP_06264737.1| ribosomal protein S4 [Pyramidobacter piscolens W5455]
 gi|282586712|gb|EFB91959.1| ribosomal protein S4 [Pyramidobacter piscolens W5455]
          Length = 206

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R   V+ R G   +R +  +++      VNG  ++   V +   D + V
Sbjct: 99  RFDNVVYRLGYCVTRPQARQLVRHGHFLVNGRKVDMPGVRLNPGDVVTV 147


>gi|253995743|ref|YP_003047807.1| 30S ribosomal protein S4 [Methylotenera mobilis JLW8]
 gi|253982422|gb|ACT47280.1| ribosomal protein S4 [Methylotenera mobilis JLW8]
          Length = 209

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V  R G+  SR E  +++    + VNG  +   +  V + D I V
Sbjct: 100 RLDNVTYRMGLGGSRTEARQIVRHNSILVNGKRVNIPSYQVKAGDVISV 148


>gi|238025957|ref|YP_002910188.1| 30S ribosomal protein S4 [Burkholderia glumae BGR1]
 gi|237875151|gb|ACR27484.1| 30S ribosomal protein S4 [Burkholderia glumae BGR1]
          Length = 207

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG+     ++ V   D I +
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAITVNGVASNIPSLQVKPGDVIAI 146


>gi|315186307|gb|EFU20068.1| SSU ribosomal protein S4P [Spirochaeta thermophila DSM 6578]
          Length = 211

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R   AS R++  +++    V VNG  +   +  V   D +E+
Sbjct: 100 RLDNIVYRMHFASSRKQARQIVDHGHVLVNGRKVNIPSYIVREGDRVEI 148


>gi|238763827|ref|ZP_04624785.1| ATP-dependent RNA helicase rhlE [Yersinia kristensenii ATCC 33638]
 gi|238697957|gb|EEP90716.1| ATP-dependent RNA helicase rhlE [Yersinia kristensenii ATCC 33638]
          Length = 452

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 12/76 (15%), Positives = 23/76 (30%)

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
            PD   +     + + G   Q+             N   A        +   + + + +R
Sbjct: 377 EPDPSIKADPIQNGRQGRGAQRPGMGRGSSAGRPQNGGGATAGRGDSRTSRPRSQADGQR 436

Query: 338 SPSFPSKRSLRRTSAK 353
            P+ PS R   R   +
Sbjct: 437 RPAGPSSRGRSRKPGE 452



 Score = 36.3 bits (82), Expect = 8.2,   Method: Composition-based stats.
 Identities = 6/75 (8%), Positives = 19/75 (25%)

Query: 271 RPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ 330
            P+   +        +   +Q+ G+ +      P +     +    ++       +D  +
Sbjct: 377 EPDPSIKADPIQNGRQGRGAQRPGMGRGSSAGRPQNGGGATAGRGDSRTSRPRSQADGQR 436

Query: 331 REENHRRSPSFPSKR 345
           R              
Sbjct: 437 RPAGPSSRGRSRKPG 451


>gi|6324192|ref|NP_014262.1| Nam9p [Saccharomyces cerevisiae S288c]
 gi|1346661|sp|P27929|NAM9_YEAST RecName: Full=37S ribosomal protein NAM9, mitochondrial; AltName:
           Full=Nuclear accommodation of mitochondria protein 9;
           Flags: Precursor
 gi|507139|gb|AAA19439.1| NAM9+ protein [Saccharomyces cerevisiae]
 gi|854500|emb|CAA86888.1| mitochondrial ribosomal protein (putative) [Saccharomyces
           cerevisiae]
 gi|1302082|emb|CAA96019.1| NAM9 [Saccharomyces cerevisiae]
 gi|285814517|tpg|DAA10411.1| TPA: Nam9p [Saccharomyces cerevisiae S288c]
          Length = 486

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   + RA  AS  R+  + I    V+VNG+ ++  +  +   D   V
Sbjct: 104 RLDFALFRAMFASSVRQARQFILHGNVRVNGVKIKHPSYTLKPGDMFSV 152


>gi|291241720|ref|XP_002740759.1| PREDICTED: probable ATP-dependent RNA helicase DDX46-like
           [Saccoglossus kowalevskii]
          Length = 1091

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 12/89 (13%), Positives = 25/89 (28%)

Query: 266 TLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFL 325
              + R              +++ S++    + K       R                  
Sbjct: 116 RRSKSRERDHRRSKSKERDHRRSKSKERDHRRSKSKEHVHRRSKSRERDHKRSRSRDREN 175

Query: 326 SDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             S  R +  RRS S   +R   R+ +++
Sbjct: 176 KRSETRPQERRRSRSKSKERRKSRSKSRE 204



 Score = 36.7 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 10/104 (9%), Positives = 27/104 (25%), Gaps = 6/104 (5%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
             +     +                  R  + S  K  + ++ K     H+R+ + +   
Sbjct: 116 RRSKSRERDHRRSKSKERDHRRSKSKERDHRRSKSKEHVHRRSKSRERDHKRSRSRDREN 175

Query: 317 AKGIHSSFLSDSGQREENHRRSP------SFPSKRSLRRTSAKK 354
            +           + +   RR            ++S  R   ++
Sbjct: 176 KRSETRPQERRRSRSKSKERRKSRSKSRERRQDRKSPSRIKERE 219


>gi|119478108|ref|ZP_01618187.1| ribosomal protein S4 [marine gamma proteobacterium HTCC2143]
 gi|119448814|gb|EAW30057.1| ribosomal protein S4 [marine gamma proteobacterium HTCC2143]
          Length = 206

 Score = 45.2 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  +++A + + +N  ++  A+  V + D + V
Sbjct: 97  RLDNVVYRMGFGSTRAESRQLVAHKSILINDKVVNIASYQVKAGDKVSV 145


>gi|313676880|ref|YP_004054876.1| transcription termination factor rho [Marivirga tractuosa DSM 4126]
 gi|312943578|gb|ADR22768.1| transcription termination factor Rho [Marivirga tractuosa DSM 4126]
          Length = 526

 Score = 45.2 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 15/137 (10%), Positives = 31/137 (22%), Gaps = 14/137 (10%)

Query: 226 GTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
             L     +++ KK L            Q  L       +          +      +  
Sbjct: 20  EKLGVSQYKKLPKKEL------IYKILDQQALLPESDLPKKGEEKSTPKSAPASKKESAP 73

Query: 286 KKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR-------- 337
           +  + +K   ++ K         +        K       +   +R    R         
Sbjct: 74  RAKAPKKEEKAETKPDKKAEEAPSKPQAEGDDKQERKPRPAPKDKRPRPERAERSNDKGD 133

Query: 338 SPSFPSKRSLRRTSAKK 354
            P  P +       +KK
Sbjct: 134 RPPRPERSDRNDNRSKK 150



 Score = 37.1 bits (84), Expect = 3.7,   Method: Composition-based stats.
 Identities = 13/115 (11%), Positives = 30/115 (26%), Gaps = 3/115 (2%)

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           K + E+LG    ++            +  +    ++  +  +  T     +S+K    + 
Sbjct: 16  KEIAEKLGVSQYKKLPKKELIYKILDQQALLPESDLPKKGEEKSTPKSAPASKKESAPRA 75

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           K                           D  Q  +     P+   KR     + +
Sbjct: 76  KAPKKEEKAETKPDKKAEEAPSKPQAEGDDKQERKP---RPAPKDKRPRPERAER 127


>gi|261855960|ref|YP_003263243.1| DEAD/DEAH box helicase [Halothiobacillus neapolitanus c2]
 gi|261836429|gb|ACX96196.1| DEAD/DEAH box helicase domain protein [Halothiobacillus
           neapolitanus c2]
          Length = 469

 Score = 45.2 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 11/114 (9%), Positives = 28/114 (24%), Gaps = 7/114 (6%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           ++ +R++L   ++   + + +A           R       P                  
Sbjct: 362 ERTIRQKLERVIVPGFEPDPNARPEPLRKPQAARQPRRDFPPRSAQGHGGQGHNAQAPRS 421

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                    R   ++                G R+  +R  P+   +R     +
Sbjct: 422 AGSQRDGQPRSAGSAAAGNRP-------QRDGGRDTGNRSRPAGSGQRRRPSGN 468



 Score = 37.1 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 11/113 (9%), Positives = 27/113 (23%), Gaps = 2/113 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ--KK 300
           E +    ++E ++  D      + L R         P+      +         +    +
Sbjct: 345 EAVSLVCVDEHKLLADIERTIRQKLERVIVPGFEPDPNARPEPLRKPQAARQPRRDFPPR 404

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            A     +   +    + G        S        R      + +  R+   
Sbjct: 405 SAQGHGGQGHNAQAPRSAGSQRDGQPRSAGSAAAGNRPQRDGGRDTGNRSRPA 457


>gi|210614350|ref|ZP_03290169.1| hypothetical protein CLONEX_02383 [Clostridium nexile DSM 1787]
 gi|210150694|gb|EEA81703.1| hypothetical protein CLONEX_02383 [Clostridium nexile DSM 1787]
          Length = 69

 Score = 45.2 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 4/52 (7%)

Query: 20 IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
          +  +G+    E + +I    VKVNG +  R    +   D +  DG  ++  +
Sbjct: 22 LVESGV----EAKEVIQDGLVKVNGEVDTRRGKKLYDGDIVSFDGTDIKIEK 69


>gi|210615784|ref|ZP_03290765.1| hypothetical protein CLONEX_02983 [Clostridium nexile DSM 1787]
 gi|210150120|gb|EEA81129.1| hypothetical protein CLONEX_02983 [Clostridium nexile DSM 1787]
          Length = 269

 Score = 45.2 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 21/178 (11%), Positives = 49/178 (27%), Gaps = 2/178 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++ +  +A SR + + +I    V V G   ++A         IE+ G  L    R
Sbjct: 3   ERLDVLLVKRNLAESREKAKAIIMSGNVFVEGQREDKAGTTFSDEVQIEIKGHTLPYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L                              ++  G   +    +        L +
Sbjct: 63  GGLKLEKAVANFDVCLEGKVCTDVGAST-GGFTDCMLQNGARKVFAIDVGKGQLAWKLRQ 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +   +   +  V      ++   + +    +        ++  L       A + 
Sbjct: 122 DDRVICMEKTNIRYVTPEDLGEEIDFSSIDVSFISLTKVLLPIRNYLKEDGQIVALIK 179


>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 = 45.2 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 13/51 (25%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 13 PQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          P+R+ + +AR     SR  ++ +I +  V+++G  +   AV V     + V
Sbjct: 16 PERLDRALARLWPDLSRNRLQGLIREGGVRLDGAEIRDGAVKVAGGQRVAV 66


>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 = 45.2 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 34/267 (12%), Positives = 72/267 (26%), Gaps = 68/267 (25%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVE---------RMIAQQRVKVNGILLERAAVNVMS 56
            + E+   +R+ KV+        RE           +   ++ +KVNG+ ++     V  
Sbjct: 5   TITEDKANKRIDKVL--------RETFPRLPNGALFKAFRKKDIKVNGVRVKE-DHIVKL 55

Query: 57  TDHI-------EVDGVP------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTV 97
            D +        +DGVP            +   +   L +  K    V         + +
Sbjct: 56  NDRVDIYIIDEILDGVPKAGELNYETAFSVAYEDSNLLIVNKKQGIPVHPDRTQTENTLI 115

Query: 98  FD----------NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
                          +         RLD NT GL+++  +     ++             
Sbjct: 116 DFVKEYLKLKGEFEENSGFTPSLCHRLDRNTGGLVMIAKNSSTLHMVLKKMKSGEISKYY 175

Query: 148 RFHGQVDQDKLNLLKKGIVIQGIC--------------------YGDMQVTLDT-QKGSN 186
           +   +   +K   + K  + +                       Y  +            
Sbjct: 176 QCLVKGKMEKKEDILKAYLEKDEKKSRVFIKDTKSKNAVEIITGYKVLSYKELPDIGEGI 235

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVN 213
           + + V L  G+  +I+         V 
Sbjct: 236 SNLEVTLYTGRTHQIRAHLAHIGHPVV 262


>gi|291336628|gb|ADD96174.1| hypothetical protein [uncultured organism MedDCM-OCT-S05-C185]
          Length = 109

 Score = 45.2 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 45/89 (50%), Positives = 65/89 (73%)

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           SVGRLD+++EGL+LLTN+G LA +LE PST WLR Y+VR +G+      + L+ G+ ++G
Sbjct: 6   SVGRLDLDSEGLILLTNNGELANLLEAPSTNWLRQYKVRVYGRPQISGFDKLRLGVTLEG 65

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
           I Y  +++ L+ Q GSNAW+ + LREGK 
Sbjct: 66  IKYKPIRIELERQTGSNAWLNIALREGKK 94


>gi|253581085|ref|ZP_04858345.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251847621|gb|EES75591.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 69

 Score = 45.2 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 12/39 (30%), Positives = 19/39 (48%)

Query: 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          E + +I    VKVNG + +R    V   D +  DG  ++
Sbjct: 28 EAKYVITDGLVKVNGEVDDRRGRKVYEGDIVSYDGKEIK 66


>gi|240141603|ref|YP_002966083.1| hypothetical protein MexAM1_META1p5204 [Methylobacterium extorquens
           AM1]
 gi|240011580|gb|ACS42806.1| Conserved hypothetical protein; putative OmpA family member
           [Methylobacterium extorquens AM1]
          Length = 729

 Score = 45.2 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 15/113 (13%), Positives = 27/113 (23%), Gaps = 4/113 (3%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                   +        + E   R       E PD   R ++   Q+      +      
Sbjct: 99  RERPEAAERPARPERPAAQERQERPERPERQERPDRQERQERPDRQERPDRPDRPERATP 158

Query: 306 HRRNLASNVWMAKGI---HSSFLSDSGQREENHRRSPSFPSKRSLR-RTSAKK 354
            +R   S    A       +       +RE   R +P+         R    +
Sbjct: 159 PQRPDRSEERPAAPASRERTQDRDAPARREAPEREAPARRETPDRPDRDGQDR 211



 Score = 42.1 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 11/108 (10%), Positives = 23/108 (21%), Gaps = 1/108 (0%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P      +          +          +E P    R      Q+     +++      
Sbjct: 76  PARERPDRSESPERPEPRQAPAARERPEAAERPARPERPAAQERQERPERPERQERPDRQ 135

Query: 307 RRNLASNVWMAKGIHSSFLSD-SGQREENHRRSPSFPSKRSLRRTSAK 353
            R    +                 QR +     P+ P+ R   +    
Sbjct: 136 ERQERPDRQERPDRPDRPERATPPQRPDRSEERPAAPASRERTQDRDA 183



 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 9/110 (8%), Positives = 22/110 (20%), Gaps = 1/110 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                         P  +     R         P+     ++    +    +++      
Sbjct: 78  RERPDRSESPERPEPRQAPAARERPEAAERPARPERPAAQERQERPERPERQERPDRQER 137

Query: 306 HRRNLASNVWMAKGIHSSFLSD-SGQREENHRRSPSFPSKRSLRRTSAKK 354
             R                       R E    +P+   +   R   A++
Sbjct: 138 QERPDRQERPDRPDRPERATPPQRPDRSEERPAAPASRERTQDRDAPARR 187


>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 = 45.2 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 23/121 (19%), Positives = 42/121 (34%), Gaps = 17/121 (14%)

Query: 4   KNIVQENFTPQRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI- 60
           + IV       R+   I+    G+ SR  V+  I    V VNG ++++ + NV S D + 
Sbjct: 72  EEIVDAAKGKIRLDSWISSRINGV-SRARVQSSIRLGLVTVNGRVVDKVSHNVKSGDEVN 130

Query: 61  -----------EVDGVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                      E + +P  +   ++  L +      +V         + V   L      
Sbjct: 131 CTISELQPLKAEAEDIPLDIVYEDKHVLVVNKPAHMVVHPAPGNPTGTLVNGILHHCSLP 190

Query: 108 V 108
            
Sbjct: 191 C 191


>gi|269956101|ref|YP_003325890.1| RNA-binding S4 domain-containing protein [Xylanimonas
          cellulosilytica DSM 15894]
 gi|269304782|gb|ACZ30332.1| RNA-binding S4 domain protein [Xylanimonas cellulosilytica DSM
          15894]
          Length = 77

 Score = 45.2 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 1/53 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
              R+ + +  AG+A S  E   +IA   V VNG +  R    +   D + V
Sbjct: 13 DDMIRLGQFLKLAGLADSGNEARDLIADGEVSVNGEVETRRGRQLGRGDVVAV 65


>gi|212721294|ref|NP_001132288.1| hypothetical protein LOC100193728 [Zea mays]
 gi|195624280|gb|ACG33970.1| protein RCC2 [Zea mays]
          Length = 549

 Score = 45.2 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 20/165 (12%), Positives = 44/165 (26%), Gaps = 5/165 (3%)

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            V + EG    +  V   F   +  + R + G  +LG L        +   + +      
Sbjct: 390 KVDILEGM--HVTSVGCGFGLSLIVVDRANVGD-RLGQLEI--YDGDTGAEVEKVEVQVT 444

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
            + +           +T          +  DD      + +     SK ++   P +R  
Sbjct: 445 KKASASTNSRANKRKKTKDVSESESEEDDDDDEDESGDDENGGVEESKGRRGRKPANRGR 504

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                        S       ++       +  +    +R   +K
Sbjct: 505 GRGGKKATPEAKPSGRGRGRPKKTESSAQKAGGTSGRGKRGRPRK 549


>gi|167855326|ref|ZP_02478094.1| 30S ribosomal protein S4 [Haemophilus parasuis 29755]
 gi|219871572|ref|YP_002475947.1| 30S ribosomal protein S4 [Haemophilus parasuis SH0165]
 gi|254764591|sp|B8F6P7|RS4_HAEPS RecName: Full=30S ribosomal protein S4
 gi|167853584|gb|EDS24830.1| 30S ribosomal protein S4 [Haemophilus parasuis 29755]
 gi|219691776|gb|ACL32999.1| 30S ribosomal protein S4 [Haemophilus parasuis SH0165]
          Length = 206

 Score = 45.2 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R E  ++++ + + VNG ++   +  V   D I V
Sbjct: 97  RLDNVVYRMGFAATRAEARQLVSHKSIVVNGRVVNIPSYQVSVDDVIAV 145


>gi|332708243|ref|ZP_08428225.1| uncharacterized S4-like domain protein [Lyngbya majuscula 3L]
 gi|332352967|gb|EGJ32525.1| uncharacterized S4-like domain protein [Lyngbya majuscula 3L]
          Length = 182

 Score = 45.2 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 2/65 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             K +        R+   IA AG   SR ++   I    V+VN   +++++  V S D I
Sbjct: 95  PKKKLRTTTEASMRLD-AIASAGFGMSRSKMVDFITTGDVRVNWKEVKQSSYTVKSGDLI 153

Query: 61  EVDGV 65
            + G 
Sbjct: 154 AIRGK 158


>gi|327439214|dbj|BAK15579.1| ribosomal protein S4 [Solibacillus silvestris StLB046]
          Length = 200

 Score = 45.2 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR   +++    + V+G  ++  + +V     I +
Sbjct: 93  RLDNLVYRLGLARTRRAARQLVNHGHILVDGNRVDIPSYSVKPGQTISL 141


>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 = 45.2 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 31/258 (12%), Positives = 62/258 (24%), Gaps = 45/258 (17%)

Query: 7   VQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           V +    Q++ + + R   G   R  + R I +  V+V+    +     V     + +  
Sbjct: 8   VTKAEAGQKLVRFLERRVDGAVPRSAIMRWIRKGNVRVDKGRCK-PFDLVKEGQTVRIPP 66

Query: 63  -------DGVPLRKAERTR----LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                      L +              KP GL T        S     L          
Sbjct: 67  YKAEETAQHKKLPELPIIYEDDNYLAVCKPAGLPTQGGTGHDDSVADRLLSMFADAHYKP 126

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHGQVDQDKLNLLKKGI 165
                       +   G   +  +  S  +         Y     G+  ++    L   +
Sbjct: 127 APAHRLDRDTSGVILAGKSHQGQKDLSDFFAEHGEGGKFYLAEVEGRWPEEDWVELHDKM 186

Query: 166 VIQG-----------ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV-- 212
              G                  V   T    ++ + V L  G+  +I+       + +  
Sbjct: 187 EKSGSKGREKVVVGSGKDASSSVCPVTIGEKSSLLIVKLHTGRTHQIRVQLSSRGFPIAG 246

Query: 213 ----------NRLIRISY 220
                      +L  +  
Sbjct: 247 DVKYGGQNGKMKLHCLRI 264


>gi|50292421|ref|XP_448643.1| hypothetical protein [Candida glabrata CBS 138]
 gi|49527955|emb|CAG61606.1| unnamed protein product [Candida glabrata]
          Length = 484

 Score = 45.2 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 1/54 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+   + RA  AS  R+  + I    V VNG+ ++     +   D   V    +
Sbjct: 104 RLDFAVFRAMFASSVRQARQFILHGNVYVNGVKIKHPGYTLKPGDTFNVKPEKV 157


>gi|73662353|ref|YP_301134.1| 30S ribosomal protein S4 [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
 gi|82581622|sp|Q49YF2|RS4_STAS1 RecName: Full=30S ribosomal protein S4
 gi|72494868|dbj|BAE18189.1| 30S ribosomal protein S4 [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
          Length = 200

 Score = 45.2 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 11/56 (19%), Positives = 27/56 (48%), Gaps = 1/56 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+  V+   G+A +RR+  +++    ++V+G  ++  +  +     I V    L+ 
Sbjct: 93  RLDAVVYSLGLARTRRQARQIVNHGHIEVDGKRVDIPSYTLKPGQEISVREKSLKL 148


>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 = 45.2 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 37/257 (14%), Positives = 68/257 (26%), Gaps = 59/257 (22%)

Query: 13  PQRVSKVIARA----GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE------V 62
           P R+ K +AR        SR  + R++    V++NG+++      +   D +E      V
Sbjct: 15  PPRLDKALARDVPEDAALSRSRLARLVPDGAVRINGVVVTDVKARLGEGDAVEIALDIPV 74

Query: 63  D----GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------- 105
           D    G P+       +   + +      +V         + V   +             
Sbjct: 75  DSDMGGEPIPLDVVYEDDELIVINKPAGMVVHPAPGSPDGTLVNALIHHCGESLSGVGGL 134

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLAR--------VLELPSTQWLRVYRVRFHGQVDQDK 157
            R   V R+D +T GLL+                        Q L            +  
Sbjct: 135 RRPGIVHRIDKDTSGLLVAAKTDRAHHGLAAQFEAHDVERHYQALCFGLPDAADPRLRGI 194

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAW------------------------VTVGL 193
                +   I  I     +   D Q+ +  W                        +   L
Sbjct: 195 RGTSFEPGNILKIQTQLARHKTDRQRQAVVWSNGRHAVTRARRVETFGGPPVVARIECWL 254

Query: 194 REGKNREIKKVFEFFNW 210
             G+  +I+        
Sbjct: 255 ETGRTHQIRVHMAHAGH 271


>gi|218885212|ref|YP_002434533.1| 30S ribosomal protein S4 [Desulfovibrio vulgaris str. 'Miyazaki F']
 gi|226732177|sp|B8DNK8|RS4_DESVM RecName: Full=30S ribosomal protein S4
 gi|218756166|gb|ACL07065.1| ribosomal protein S4 [Desulfovibrio vulgaris str. 'Miyazaki F']
          Length = 208

 Score = 45.2 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI R G A SR++  +++      +NG      ++ V   D IEV
Sbjct: 99  RLDNVIYRLGFANSRQQARQLVRHGIFTLNGRKANIPSMQVRVGDIIEV 147


>gi|126654802|ref|ZP_01726336.1| RNA-binding S4 [Cyanothece sp. CCY0110]
 gi|126623537|gb|EAZ94241.1| RNA-binding S4 [Cyanothece sp. CCY0110]
          Length = 259

 Score = 45.2 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 3/65 (4%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K K  +       R+   IA AG   SR ++   I +  V+VN   + +A+ N+ S D I
Sbjct: 173 KTKE-MTTVEASMRLD-AIASAGFGMSRSKMVDAINKGDVRVNWKEITQASHNIESGDLI 230

Query: 61  EVDGV 65
            V G 
Sbjct: 231 AVRGK 235


>gi|120587019|ref|NP_055160.2| zinc finger protein 318 [Homo sapiens]
 gi|166215018|sp|Q5VUA4|ZN318_HUMAN RecName: Full=Zinc finger protein 318; AltName: Full=Endocrine
           regulatory protein
 gi|150041741|emb|CAI14459.2| zinc finger protein 318 [Homo sapiens]
 gi|150178422|emb|CAH71374.2| zinc finger protein 318 [Homo sapiens]
          Length = 2279

 Score = 45.2 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 10/85 (11%), Positives = 19/85 (22%)

Query: 268 VRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSD 327
            R   +         +       + +    + +  +P   R          G   S   +
Sbjct: 54  ARRPRSPSGHRGRRASPSPPRGRRVSPSPPRARRGSPSPPRGRRLFPPGPAGFRGSSRGE 113

Query: 328 SGQREENHRRSPSFPSKRSLRRTSA 352
           S        R        S RR+  
Sbjct: 114 SRADYARDGRGDHPGDSGSRRRSPG 138


>gi|119624584|gb|EAX04179.1| zinc finger protein 318 [Homo sapiens]
          Length = 2279

 Score = 45.2 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 10/85 (11%), Positives = 19/85 (22%)

Query: 268 VRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSD 327
            R   +         +       + +    + +  +P   R          G   S   +
Sbjct: 54  ARRPRSPSGHRGRRASPSPPRGRRVSPSPPRARRGSPSPPRGRRLFPPGPAGFRGSSRGE 113

Query: 328 SGQREENHRRSPSFPSKRSLRRTSA 352
           S        R        S RR+  
Sbjct: 114 SRADYARDGRGDHPGDSGSRRRSPG 138


>gi|289523341|ref|ZP_06440195.1| ribosomal protein S4 [Anaerobaculum hydrogeniformans ATCC
          BAA-1850]
 gi|289503033|gb|EFD24197.1| ribosomal protein S4 [Anaerobaculum hydrogeniformans ATCC
          BAA-1850]
          Length = 140

 Score = 45.2 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          RV  V+ R GIAS R +  +++    + VNG  L+  +  V   D I V
Sbjct: 31 RVDSVVYRLGIASSRAQARQLVTHGHITVNGKKLDIPSALVKVGDVIAV 79


>gi|255526606|ref|ZP_05393513.1| ribosomal protein S4 [Clostridium carboxidivorans P7]
 gi|296187295|ref|ZP_06855691.1| ribosomal protein S4 [Clostridium carboxidivorans P7]
 gi|255509714|gb|EET86047.1| ribosomal protein S4 [Clostridium carboxidivorans P7]
 gi|296048166|gb|EFG87604.1| ribosomal protein S4 [Clostridium carboxidivorans P7]
          Length = 206

 Score = 45.2 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            R+  V  + G   SR E  +++      +NG  ++ A+  V + D I V
Sbjct: 98  MRLDNVAYKFGYGNSRAEARQLVTHGHFLINGKKVDIASYQVSAGDVITV 147


>gi|134103232|ref|YP_001108893.1| 30S ribosomal protein S4 [Saccharopolyspora erythraea NRRL 2338]
 gi|291007976|ref|ZP_06565949.1| 30S ribosomal protein S4 [Saccharopolyspora erythraea NRRL 2338]
 gi|152112258|sp|A4FPJ3|RS4_SACEN RecName: Full=30S ribosomal protein S4
 gi|133915855|emb|CAM05968.1| 30S ribosomal protein S4 [Saccharopolyspora erythraea NRRL 2338]
          Length = 201

 Score = 45.2 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 1/54 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+  V+ RAG+A +RR   ++++     VNG  +   +  V   D I+V    L
Sbjct: 92  RLDNVVYRAGLARTRRMARQLVSHGHFTVNGKKVNIPSYQVSKWDIIDVKQKSL 145


>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 = 45.2 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 19/198 (9%), Positives = 53/198 (26%), Gaps = 2/198 (1%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAERTRL 75
           K++A+    S    + MI +  V V    +  A   +       +          E   +
Sbjct: 8   KLLAQQEGISNSNAKSMIDRGLVYVGNKKVMIARGEIDERTVFRIQKVEKVKPIFENDDI 67

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            +  KP  + +   +   +  V  +     +  + +   + +     +            
Sbjct: 68  IVVDKPAHVNSDEIERQFKPAVLLHRLDRETSGVLMLVKNEDFRQRAIKEFRDDKVYKEY 127

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
           +   + +    +     +   K N      V         +   D        V   +  
Sbjct: 128 IAWVEGIMTEPIEVDKAITTQKKNNKAYSNVSPKGKPARTEFFPDIVSAKKTKVKCIIHN 187

Query: 196 GKNREIKKVFEFFNWKVN 213
           G+  +I+    + +  + 
Sbjct: 188 GRTHQIRVHARYIDHPIV 205


>gi|224000277|ref|XP_002289811.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220975019|gb|EED93348.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 703

 Score = 45.2 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 14/111 (12%), Positives = 30/111 (27%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           + +    + E   +    +      V      +        R +      +   ++K+  
Sbjct: 286 DPVARKEVSEVAWHDLNSLPKHTYAVLPFLGQLRRWIKRDNRKRGREDYADAGGREKRAN 345

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +    R+ + +     G  S   S         R SP   + R   R   K
Sbjct: 346 SRAASRSNSRSKNQTPGPRSDTPSSRKGSAPKQRSSPQKNNNRDRSRGKQK 396


>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 = 45.2 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 26/240 (10%), Positives = 57/240 (23%), Gaps = 32/240 (13%)

Query: 3   DKNIVQENFTPQRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLER-----AAVN 53
           D+ I  ++    R+ K +      +G+   RE  R+I    V VNG              
Sbjct: 31  DRIIAGDSDDGLRLDKFLLKLLPDSGL---RERRRLIENGLVMVNGRSCRSGLKMFPGAE 87

Query: 54  V------MSTDHIEVDGVP-LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           V        +  +E+     + K       +Y          +     S           
Sbjct: 88  VVLLEAEDRSCAVEILSQVKVVKQGEGFGTVYKPEGLHSAAIAGSAESSVEECLSGIFPG 147

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPS---------TQWLRVYRVRFHGQVDQDK 157
           +   +          +LL   G                                 V    
Sbjct: 148 KEPILANRLDFLTSGMLLIAFGVERENEFRECEDSGTVDKVYHAKVHGIPEGPFVVKNSL 207

Query: 158 LNLLKKGIVIQGICYGDMQV----TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               +K   +      + +      ++      + + V + +G   +I+       + + 
Sbjct: 208 DTADRKRTKVLDDQAPEERWSSAEVVERYDDGTSLLEVRIAKGARHQIRAHLAHAGFPIV 267


>gi|108758783|ref|YP_632385.1| ribonuclease R [Myxococcus xanthus DK 1622]
 gi|108462663|gb|ABF87848.1| ribonuclease R [Myxococcus xanthus DK 1622]
          Length = 1182

 Score = 45.2 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 14/135 (10%), Positives = 35/135 (25%), Gaps = 3/135 (2%)

Query: 223 FQLGTLLAGSTREVSK--KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
            +L  L  G   E+ +  + L  Q       +  V        ++   R++   ++    
Sbjct: 25  LRLAGLHPGQQTELKRALRELVRQGDILKDGKRFVPRQPSRREADVRAREQGAPMAWRQR 84

Query: 281 DFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENH-RRSP 339
           D    ++    +      ++ A P                        G+      +   
Sbjct: 85  DAAGPREGGPDRGPRHAGQRAAGPGGFAARRHEPGARGKSAGWQERGPGRERRGASKHGG 144

Query: 340 SFPSKRSLRRTSAKK 354
            F  +R+       +
Sbjct: 145 GFRQERAEWPGRRGR 159


>gi|262039511|ref|ZP_06012813.1| S4 domain protein YaaA [Leptotrichia goodfellowii F0264]
 gi|261746492|gb|EEY34029.1| S4 domain protein YaaA [Leptotrichia goodfellowii F0264]
          Length = 73

 Score = 45.2 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 14/62 (22%), Positives = 26/62 (41%), Gaps = 1/62 (1%)

Query: 10 NFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          N    ++ + +     + S  E +  I + +VKVNG    R    + S D +E  G  ++
Sbjct: 12 NTEFIKLDQFLKWTNFVISGAEAKLFIQEGQVKVNGDTETRRGKKLYSGDIVEFKGEKVK 71

Query: 69 KA 70
            
Sbjct: 72 IK 73


>gi|237736197|ref|ZP_04566678.1| SSU ribosomal protein S4P [Fusobacterium mortiferum ATCC 9817]
 gi|229421750|gb|EEO36797.1| SSU ribosomal protein S4P [Fusobacterium mortiferum ATCC 9817]
          Length = 195

 Score = 45.2 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+  ++++   V VNG  +  A+  V   D I +
Sbjct: 89  RLENVVYRLGFAKTRRQARQIVSHGHVAVNGRRVNIASYRVKVGDVISI 137


>gi|220934111|ref|YP_002513010.1| glutamyl-tRNA synthetase [Thioalkalivibrio sp. HL-EbGR7]
 gi|219995421|gb|ACL72023.1| glutamyl-tRNA synthetase [Thioalkalivibrio sp. HL-EbGR7]
          Length = 468

 Score = 45.2 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 18/125 (14%), Positives = 28/125 (22%)

Query: 225 LGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
           L  ++    RE   K+LR+ +                       R R +     P    R
Sbjct: 343 LADVVPEGAREAFLKVLRDNIRFPGEARDWARRLFGHPPEVDAPRARRHGTGRAPVLHRR 402

Query: 285 MKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
            +                   HRR  ++ V           S  G              +
Sbjct: 403 ARGPGPCAGRFPGTGPAGGGGHRRQGSAPVHAPARGTDGSESRPGDARPLAPAGSRAGGR 462

Query: 345 RSLRR 349
              RR
Sbjct: 463 AFHRR 467


>gi|294142909|ref|YP_003558887.1| 30S ribosomal protein S4 [Shewanella violacea DSS12]
 gi|293329378|dbj|BAJ04109.1| ribosomal protein S4 [Shewanella violacea DSS12]
          Length = 206

 Score = 45.2 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V ++D I +
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKSILVNGSVVNIPSFKVSASDVISI 145


>gi|237747389|ref|ZP_04577869.1| small subunit ribosomal protein S4 [Oxalobacter formigenes HOxBLS]
 gi|229378740|gb|EEO28831.1| small subunit ribosomal protein S4 [Oxalobacter formigenes HOxBLS]
          Length = 207

 Score = 45.2 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           R+  V+ R G  S R E  ++++ Q + VNG ++   +  V   D I +     ++ 
Sbjct: 98  RLDNVVYRMGFGSTRAESRQLVSHQALMVNGKVVNIPSYLVKPEDVITIREKAKKQN 154


>gi|171914054|ref|ZP_02929524.1| 30S ribosomal protein S4 [Verrucomicrobium spinosum DSM 4136]
          Length = 203

 Score = 45.2 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G A SR    +M+    V VNG     A+  + + D + V
Sbjct: 93  QRLDNVVYRMGFANSRFAARQMVGHGHVTVNGKRCNIASAQIKAGDVVAV 142


>gi|187925591|ref|YP_001897233.1| 30S ribosomal protein S4 [Burkholderia phytofirmans PsJN]
 gi|226697818|sp|B2T726|RS4_BURPP RecName: Full=30S ribosomal protein S4
 gi|187716785|gb|ACD18009.1| ribosomal protein S4 [Burkholderia phytofirmans PsJN]
          Length = 207

 Score = 45.2 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG++    ++ V + D + V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAIVVNGVVSNIPSMQVKAGDVVAV 146


>gi|150398309|ref|YP_001328776.1| helicase domain-containing protein [Sinorhizobium medicae WSM419]
 gi|150029824|gb|ABR61941.1| helicase domain protein [Sinorhizobium medicae WSM419]
          Length = 1026

 Score = 45.2 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 14/118 (11%), Positives = 26/118 (22%), Gaps = 4/118 (3%)

Query: 237  SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            +         P    E++  L             R            +    +  + G  
Sbjct: 892  TSDETPAPAEPETPAESKPVLLW--RPGTRQDNQRQGGRQGEQRRGGQRHAQTEGREGGR 949

Query: 297  KQKKLATPVHR-RNLASNVWMAKGIHSSFLSD-SGQREENHRRSPSFPSKRSLRRTSA 352
            +Q     P  + R                     G R +  + SP+    R  R+   
Sbjct: 950  RQGAQGKPPGKPREGKPQEGKGSEGRPGGQRKERGDRYDRSKPSPAKFEGRPPRKEKP 1007



 Score = 40.2 bits (92), Expect = 0.56,   Method: Composition-based stats.
 Identities = 10/112 (8%), Positives = 23/112 (20%), Gaps = 4/112 (3%)

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
                  +       P   +E+         +   +     ++   ++ G    +     
Sbjct: 887 QEVAPTSDETPAPAEPETPAESKPVLLWRPGTRQDNQRQGGRQGEQRRGGQRHAQTEGRE 946

Query: 305 VHRRNLASNVWMAKGIHSSFLSD--SGQREENHRRSPSFPSKRSLRRTSAKK 354
             RR  A       G           G       +      +    + S  K
Sbjct: 947 GGRRQGAQ--GKPPGKPREGKPQEGKGSEGRPGGQRKERGDRYDRSKPSPAK 996


>gi|332967966|gb|EGK07053.1| cell wall surface anchor family protein [Desmospora sp. 8437]
          Length = 523

 Score = 45.2 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 22/176 (12%), Positives = 44/176 (25%), Gaps = 30/176 (17%)

Query: 191 VGLREGKNREIKKVFEFFN---WKVNRLIRISYGPFQLGTLLAGSTREVSKK-------- 239
           + L+E   +E+ K+ +       KVN   RI               RE+++K        
Sbjct: 159 LTLQE--KQEVTKLVKDVGKYENKVNN-KRI---------------RELTEKAKTKGLTK 200

Query: 240 -ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
               E +    ++     L       E   +  P               +   K     +
Sbjct: 201 DERMELINLQPIKNPGSVLKPDKGIEEPEKQQPPKDQPSKEQPPAEQPGDKPGKEQPPAE 260

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +    P   +  A       G         G +    +     P  +  +     +
Sbjct: 261 QPGDKPGKEQPPAEQPGDKPGKEQPPAEQPGDKPGKAQPPAEQPGDKPGKEQPPAE 316


>gi|312127395|ref|YP_003992269.1| pseudouridine synthase [Caldicellulosiruptor hydrothermalis 108]
 gi|311777414|gb|ADQ06900.1| pseudouridine synthase [Caldicellulosiruptor hydrothermalis 108]
          Length = 311

 Score = 45.2 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 23/198 (11%), Positives = 57/198 (28%), Gaps = 13/198 (6%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDP 91
           +R +  ++V++         + V   D+I V   P            +  +  +  +   
Sbjct: 66  DRFLEHKKVEI---------LKVYEDDNIVVIDKPYGIPSHPDSNNEYSVVSWIEDNYSK 116

Query: 92  DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151
           +    +   L    + ++ V +       +L   +   + +     + +           
Sbjct: 117 NELPQLCHRLDRNTAGLMIVAKNRQVLSEMLKYMSRRAIIKKYLCITKKADLPESGVLVH 176

Query: 152 QVDQDKLNL--LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            + +D              G         +  QK     V V ++ GK  +I+       
Sbjct: 177 YLKKDSKKSKVYISDFPQDGYSEVVTAYKIVRQKDDLQLVDVEIKTGKTHQIRAQLAHVG 236

Query: 210 WKVNRLIRISYGPFQLGT 227
             +  L    YG ++L  
Sbjct: 237 LCI--LGDSKYGDWKLNK 252


>gi|332653672|ref|ZP_08419416.1| S4 domain protein [Ruminococcaceae bacterium D16]
 gi|332516758|gb|EGJ46363.1| S4 domain protein [Ruminococcaceae bacterium D16]
          Length = 265

 Score = 45.2 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 22/50 (44%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  V+A     SR +  ++++  RV VN     ++   V   D +   G
Sbjct: 190 RLDAVLASGFSTSRSKAAQLVSAGRVSVNHRECMKSDRTVEQGDVLSCRG 239


>gi|188584014|ref|YP_001927459.1| hemolysin A [Methylobacterium populi BJ001]
 gi|179347512|gb|ACB82924.1| hemolysin A [Methylobacterium populi BJ001]
          Length = 249

 Score = 45.2 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 3/53 (5%)

Query: 12 TPQRV--SKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
          T +R+   + +   G   SR +    I    V+ +G L+ R +  + +   IE
Sbjct: 2  TGERLRADRFLVEHGHFRSRAQARAAIEAGLVRADGSLVTRPSDLIGAGARIE 54


>gi|120602217|ref|YP_966617.1| PSP1 domain-containing protein [Desulfovibrio vulgaris DP4]
 gi|120562446|gb|ABM28190.1| PSP1 domain protein [Desulfovibrio vulgaris DP4]
          Length = 487

 Score = 45.2 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 13/114 (11%), Positives = 29/114 (25%)

Query: 229 LAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
             G  + +   + R  L        ++ +    +      R         P    R +  
Sbjct: 229 NRGPVKVLRANMFRNSLMAFTDTGEEIEISLDEWQQLDPRRPDQQPQQARPPRRDRPEGG 288

Query: 289 SSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
           S++     +    ++               G  +   SD G R +   R+    
Sbjct: 289 SARDGNGDRAPAPSSDRAAGATGGEAARHGGGRAGERSDRGGRPDRAERADRRG 342



 Score = 37.1 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 11/109 (10%), Positives = 21/109 (19%), Gaps = 2/109 (1%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             +++  +   +Q                           P+             ++   
Sbjct: 261 EWQQLDPRRPDQQPQQARPPRRDRPEGGSARDGNGDRAPAPSSDRAAGATGGEAARHGGG 320

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
           + G            R   A    M  G  S          E    +PS
Sbjct: 321 RAGERSD--RGGRPDRAERADRRGMPYGDVSGSGETPPAGGEAEADAPS 367


>gi|116494737|ref|YP_806471.1| ribosomal protein S4 [Lactobacillus casei ATCC 334]
 gi|191638248|ref|YP_001987414.1| 30S ribosomal protein S4 [Lactobacillus casei BL23]
 gi|239631669|ref|ZP_04674700.1| 30S ribosomal protein S4 [Lactobacillus paracasei subsp. paracasei
           8700:2]
 gi|301066295|ref|YP_003788318.1| 30S ribosomal protein L4 [Lactobacillus casei str. Zhang]
 gi|122263845|sp|Q039U3|RS4_LACC3 RecName: Full=30S ribosomal protein S4
 gi|226699078|sp|B3WDV5|RS4_LACCB RecName: Full=30S ribosomal protein S4
 gi|116104887|gb|ABJ70029.1| SSU ribosomal protein S4P [Lactobacillus casei ATCC 334]
 gi|190712550|emb|CAQ66556.1| 30S ribosomal protein S4 [Lactobacillus casei BL23]
 gi|239526134|gb|EEQ65135.1| 30S ribosomal protein S4 [Lactobacillus paracasei subsp. paracasei
           8700:2]
 gi|300438702|gb|ADK18468.1| Ribosomal protein S4 [Lactobacillus casei str. Zhang]
 gi|327382278|gb|AEA53754.1| 30S ribosomal protein S4 [Lactobacillus casei LC2W]
 gi|327385474|gb|AEA56948.1| 30S ribosomal protein S4 [Lactobacillus casei BD-II]
          Length = 203

 Score = 45.2 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+AS R +  +++    + V+G  ++  +  V     I +
Sbjct: 94  RLDNLVFRLGLASSRPQARQLVNHGHITVDGKRVDIPSYEVEPGQVIAL 142


>gi|329956728|ref|ZP_08297301.1| ribosomal protein S4 [Bacteroides clarus YIT 12056]
 gi|328524100|gb|EGF51176.1| ribosomal protein S4 [Bacteroides clarus YIT 12056]
          Length = 201

 Score = 45.2 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA +R    ++++ + + V+G ++   +  V     I V
Sbjct: 93  RLDNVVFRLGIAPTRAAARQLVSHKHITVDGEVVNVPSYAVKPGQVIGV 141


>gi|158423990|ref|YP_001525282.1| helicase [Azorhizobium caulinodans ORS 571]
 gi|158330879|dbj|BAF88364.1| helicase [Azorhizobium caulinodans ORS 571]
          Length = 540

 Score = 45.2 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 8/109 (7%), Positives = 20/109 (18%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R    P    + +         +     +RP       D     +    +        + 
Sbjct: 392 RANAQPRGERQERREPRGERKEARPPRAERPQGERVQGDRPRGERPRGERTGAERNGAER 451

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                      +     G      +            P+   +    R+
Sbjct: 452 NGAERHGAERVHSERPAGARQRSAAGPHGEGRKADARPAHGGRAEQPRS 500



 Score = 44.4 bits (103), Expect = 0.026,   Method: Composition-based stats.
 Identities = 9/107 (8%), Positives = 22/107 (20%), Gaps = 2/107 (1%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                 +                      P    +  +    +    ++ +   P   R 
Sbjct: 378 RPAEAADAVGEDRPRANAQPRGERQERREPRGERKEARPPRAERPQGERVQGDRPRGERP 437

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL--RRTSAKK 354
                   +       ++    E  H   P+   +RS        +K
Sbjct: 438 RGERTGAERNGAERNGAERHGAERVHSERPAGARQRSAAGPHGEGRK 484



 Score = 35.9 bits (81), Expect = 9.2,   Method: Composition-based stats.
 Identities = 7/76 (9%), Positives = 16/76 (21%), Gaps = 6/76 (7%)

Query: 279 PDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS 338
           P    R +   ++      + +       R         +G          +R +  R  
Sbjct: 369 PTTDRRGEARPAEAADAVGEDRPRANAQPRGERQERREPRGERKEARPPRAERPQGERVQ 428

Query: 339 PSFPSKRSLRRTSAKK 354
                     R    +
Sbjct: 429 ------GDRPRGERPR 438


>gi|32034695|ref|ZP_00134833.1| COG0522: Ribosomal protein S4 and related proteins [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|126209247|ref|YP_001054472.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae L20]
 gi|165977220|ref|YP_001652813.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar 3
           str. JL03]
 gi|190151138|ref|YP_001969663.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar 7
           str. AP76]
 gi|303250036|ref|ZP_07336238.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar 6
           str. Femo]
 gi|303253210|ref|ZP_07339359.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar 2
           str. 4226]
 gi|307246713|ref|ZP_07528783.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar 1
           str. 4074]
 gi|307251082|ref|ZP_07533006.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar 4
           str. M62]
 gi|307253468|ref|ZP_07535339.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar 6
           str. Femo]
 gi|307255698|ref|ZP_07537502.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar 9
           str. CVJ13261]
 gi|307257882|ref|ZP_07539638.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar
           10 str. D13039]
 gi|307260150|ref|ZP_07541860.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar
           11 str. 56153]
 gi|307264487|ref|ZP_07546072.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar
           13 str. N273]
 gi|322515611|ref|ZP_08068590.1| 30S ribosomal protein S4 [Actinobacillus ureae ATCC 25976]
 gi|152060927|sp|A3N381|RS4_ACTP2 RecName: Full=30S ribosomal protein S4
 gi|226697792|sp|B3GZ35|RS4_ACTP7 RecName: Full=30S ribosomal protein S4
 gi|226697793|sp|B0BSV5|RS4_ACTPJ RecName: Full=30S ribosomal protein S4
 gi|126098039|gb|ABN74867.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar
           5b str. L20]
 gi|165877321|gb|ABY70369.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar 3
           str. JL03]
 gi|189916269|gb|ACE62521.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar 7
           str. AP76]
 gi|302647892|gb|EFL78099.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar 2
           str. 4226]
 gi|302651099|gb|EFL81253.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar 6
           str. Femo]
 gi|306852413|gb|EFM84648.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar 1
           str. 4074]
 gi|306856912|gb|EFM89044.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar 4
           str. M62]
 gi|306859147|gb|EFM91189.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar 6
           str. Femo]
 gi|306861375|gb|EFM93365.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar 9
           str. CVJ13261]
 gi|306863612|gb|EFM95539.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar
           10 str. D13039]
 gi|306865796|gb|EFM97674.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar
           11 str. 56153]
 gi|306870184|gb|EFN01943.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar
           13 str. N273]
 gi|322118321|gb|EFX90596.1| 30S ribosomal protein S4 [Actinobacillus ureae ATCC 25976]
          Length = 208

 Score = 45.2 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R E  ++++ + + VNG ++   +  V   D + V
Sbjct: 99  RLDNVVYRMGFAATRAEARQLVSHKSIVVNGRVVNIPSYQVSVDDVVAV 147


>gi|290477169|ref|YP_003470084.1| 30S ribosomal subunit protein S4 [Xenorhabdus bovienii SS-2004]
 gi|289176517|emb|CBJ83326.1| 30S ribosomal subunit protein S4 [Xenorhabdus bovienii SS-2004]
          Length = 206

 Score = 44.8 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 16/73 (21%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  +M++ + + VNG ++  A+  V   D + V     ++A   
Sbjct: 97  RLDNVVYRMGFGATRAESRQMVSHKAIMVNGCVVNIASYQVSPNDVVSVREKAKKQARIK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|218509234|ref|ZP_03507112.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Rhizobium etli Brasil 5]
          Length = 274

 Score = 44.8 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 29/251 (11%), Positives = 66/251 (26%), Gaps = 52/251 (20%)

Query: 15  RVSKVI-ARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
           R+   + A+ G   SR  ++ +I   +V + G L+      V   D  E+          
Sbjct: 5   RLDAWLTAQLGEEFSRSRIKVLIKDGQVSMRGQLITDPQRKVRVGDSFEITLPEPEDPTP 64

Query: 63  DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN- 117
            G  +       +   + +      +V   S     + V   +    + +  +G +    
Sbjct: 65  RGEDIPLDILYEDDDLIVISKPAGLVVHPGSGNWTGTLVNALIHHCGATLSGIGGVRRPG 124

Query: 118 ---------TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--- 165
                    T  +++  ND     +    +     +   R +  +   +   L   +   
Sbjct: 125 IVHRLDKDTTGVMVVAKNDVAHRHLSLQFADHGRTMPLERAYQAIVWGRPRSLTGTVDAP 184

Query: 166 --VIQGICYGDMQVTLDTQKGSN---------------------AWVTVGLREGKNREIK 202
                G          D+Q                         + V   L  G+  +I+
Sbjct: 185 LGRATGDRTRRAVKRPDSQDADQAITHYEVIERFHETPDATALASLVECRLETGRTHQIR 244

Query: 203 KVFEFFNWKVN 213
                    + 
Sbjct: 245 VHMAHIGHPLL 255


>gi|162456743|ref|YP_001619110.1| hypothetical protein sce8460 [Sorangium cellulosum 'So ce 56']
 gi|161167325|emb|CAN98630.1| unnamed protein product [Sorangium cellulosum 'So ce 56']
          Length = 691

 Score = 44.8 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 12/128 (9%), Positives = 33/128 (25%), Gaps = 8/128 (6%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK------- 286
           RE  +++ R+ LGP      +        +S            +        +       
Sbjct: 542 REDVQRVARDHLGPTRRTIVETYPPGLPGASSPPRASAGAPRPKGGARAAAPEQDAEVAA 601

Query: 287 KNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
                +     +       ++R   +    A     +  +  G+     + +P   + ++
Sbjct: 602 PGKGAEKAAPGKGAGKAAPNKRADKAGPGKAAPGKGADKAAPGKA-APGKAAPGKGAGKA 660

Query: 347 LRRTSAKK 354
                  K
Sbjct: 661 APGERPAK 668



 Score = 42.5 bits (98), Expect = 0.091,   Method: Composition-based stats.
 Identities = 13/102 (12%), Positives = 23/102 (22%), Gaps = 2/102 (1%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                ++A+V             +           D     K +  K         A P 
Sbjct: 590 AAAPEQDAEVAAPGKGAEKAAPGKGAGKAAPNKRADKAGPGKAAPGKGADKAAPGKAAPG 649

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQR--EENHRRSPSFPSKR 345
                      A G   +       R   +     P+ P+K+
Sbjct: 650 KAAPGKGAGKAAPGERPAKAHGGASRPAPDPAPTKPAKPTKK 691


>gi|154503047|ref|ZP_02040107.1| hypothetical protein RUMGNA_00869 [Ruminococcus gnavus ATCC
          29149]
 gi|153796288|gb|EDN78708.1| hypothetical protein RUMGNA_00869 [Ruminococcus gnavus ATCC
          29149]
          Length = 71

 Score = 44.8 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 11/52 (21%), Positives = 21/52 (40%), Gaps = 4/52 (7%)

Query: 20 IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
          +  +G+    E + +I    V VNG +  R    +   D    DG  ++  +
Sbjct: 24 LVESGV----EAKEVIQDGMVTVNGEVDTRRGRKLYPGDTASFDGQEIKIEK 71


>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 = 44.8 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 35/251 (13%), Positives = 68/251 (27%), Gaps = 46/251 (18%)

Query: 6   IVQENFTPQRVSKVIARAGIAS----RREVERMIAQQRVKVNGILLE----RAAVNVMST 57
           +V  +   +R+  V+A     S    R  ++ +I Q RV+V    +E    +  + + + 
Sbjct: 12  VVAPHEAGRRLDLVLATRAAGSAELTRSRLQSLIRQGRVRVESAGVEAGPLKPGMLLKAG 71

Query: 58  DHI---------------EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
           D +               EV+  PL   +   L L   P  +V         + V   L 
Sbjct: 72  DRVDLQVPPPEATELVAEEVEFTPL-YEDEDILVLVKPPGLVVHPADGHRQGTLVHGLLH 130

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------- 155
              +     G+L       L     G L       +   L         +          
Sbjct: 131 HCRNLSGISGQLRPGIVHRLDKDTSGCLVVAKNDLAHHNLVQQFKGREVEKTYQALLRGI 190

Query: 156 --------------DKLNLLKKGIVIQGICYGDMQVTLDTQ-KGSNAWVTVGLREGKNRE 200
                           ++  K  +  +G         +  +       V + L  G+  +
Sbjct: 191 LAEDTGQVVLPIGRHPVHRKKMAVRREGGREAVTHWRVRQRFSAGYTLVELLLETGRTHQ 250

Query: 201 IKKVFEFFNWK 211
           I+         
Sbjct: 251 IRVHMAALGHP 261


>gi|119899681|ref|YP_934894.1| 30S ribosomal protein S4 [Azoarcus sp. BH72]
 gi|152060933|sp|A1KB02|RS4_AZOSB RecName: Full=30S ribosomal protein S4
 gi|119672094|emb|CAL96008.1| 30S ribosomal protein S4 [Azoarcus sp. BH72]
          Length = 209

 Score = 44.8 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V  R G   SR E  +++    V VNG  +   +  V   D IE+
Sbjct: 100 RLDSVAYRMGFGASRAEARQVVRHNGVLVNGKRVNIPSYTVRPGDVIEL 148


>gi|54025642|ref|YP_119884.1| hypothetical protein nfa36720 [Nocardia farcinica IFM 10152]
 gi|54017150|dbj|BAD58520.1| hypothetical protein [Nocardia farcinica IFM 10152]
          Length = 717

 Score = 44.8 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 25/112 (22%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R        +   P+  +E          S           +S+   +  R  +      
Sbjct: 14  RRADPDERAQWARPYDEDEMGPPRRRDDGSRPRRPAGDAARVSDRAREAPRRPRPDHAPG 73

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
                ++      RR  A          +     + + +      P+ P   
Sbjct: 74  ERPAPERGRATGERRTEAPRTRSGGRPAAERTGRTPRPDGARGGRPARPKAD 125



 Score = 44.8 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 9/115 (7%), Positives = 24/115 (20%), Gaps = 6/115 (5%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK--- 297
           +RE+      +E                R R +            + +   +    +   
Sbjct: 9   VRERGRRADPDERAQWARPYDEDEMGPPRRRDDGSRPRRPAGDAARVSDRAREAPRRPRP 68

Query: 298 -QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP--SFPSKRSLRR 349
                  P   R  A+     +   +                P  +   + +  +
Sbjct: 69  DHAPGERPAPERGRATGERRTEAPRTRSGGRPAAERTGRTPRPDGARGGRPARPK 123



 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 9/110 (8%), Positives = 29/110 (26%), Gaps = 9/110 (8%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            +++GP    +       P   +  +             D    ++ + ++   + +++ 
Sbjct: 30  EDEMGPPRRRDDGSRPRRPAGDAARVSDRAREAPRRPRPDHAPGERPAPERGRATGERRT 89

Query: 302 ATPVHRRNLAS------NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
             P  R                 G          + + +H    +  + R
Sbjct: 90  EAPRTRSGGRPAAERTGRTPRPDGARGGR---PARPKADHTADRAMGAPR 136



 Score = 36.3 bits (82), Expect = 7.3,   Method: Composition-based stats.
 Identities = 8/94 (8%), Positives = 16/94 (17%)

Query: 259 APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAK 318
                       R +            +             +   P       S+     
Sbjct: 3   REHEPPVRERGRRADPDERAQWARPYDEDEMGPPRRRDDGSRPRRPAGDAARVSDRAREA 62

Query: 319 GIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                     G+R    R   +   +    RT +
Sbjct: 63  PRRPRPDHAPGERPAPERGRATGERRTEAPRTRS 96


>gi|26554211|ref|NP_758145.1| 30S ribosomal protein S4 [Mycoplasma penetrans HF-2]
 gi|41017842|sp|Q8EV12|RS4_MYCPE RecName: Full=30S ribosomal protein S4
 gi|26454220|dbj|BAC44549.1| ribosomal protein S4 [Mycoplasma penetrans HF-2]
          Length = 202

 Score = 44.8 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 11/74 (14%), Positives = 25/74 (33%), Gaps = 1/74 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  ++ R G A +RR   +++    + ++G  +   +  V     IEV           
Sbjct: 95  RLDNLVYRMGFAPTRRAARQLVNHGHILLDGKKVTIPSCMVKLEQTIEVAPKSKDLPIVA 154

Query: 74  RLWLYHKPIGLVTT 87
                     + + 
Sbjct: 155 AGASNTPCKFVDSD 168


>gi|308461538|ref|XP_003093060.1| hypothetical protein CRE_13111 [Caenorhabditis remanei]
 gi|308251683|gb|EFO95635.1| hypothetical protein CRE_13111 [Caenorhabditis remanei]
          Length = 609

 Score = 44.8 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 24/112 (21%), Gaps = 1/112 (0%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +  G     + +    A   +  +                 R +   S        K+ +
Sbjct: 490 DVRGRPRTVQTRGTKGARGRNQGSATGATRGANRGSATGAARGRNQGSATGATRGAKRGS 549

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                R         +G        +        R  +    R   R +A +
Sbjct: 550 ATGAARGGN-RGSATRGARGRNQGSATGAARGGNRGSATRGARGGNRGTATR 600


>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 = 44.8 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 27/244 (11%), Positives = 57/244 (23%), Gaps = 39/244 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIE--- 61
           V +     R+   IAR    SR     +I    V V+G    + +  V +     +    
Sbjct: 9   VPDGLEGDRLDSAIARMFGLSRTRAAEIIGDGGVLVDGSEAAK-SDRVSAGAWLEVTLPP 67

Query: 62  -----------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                      V G+ +   +   + +      +        G S +   L S      S
Sbjct: 68  PPTAPVPRPEAVPGMRIVHEDTDIIVVDKPVGVVAHPTVGWTGPSVLEGLLASGVQVATS 127

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
                      L     G +       +   L+              L        ++G 
Sbjct: 128 GAAERQGIVHRLDANTTGLMVVAKSETAYSVLKRAFKERTVDKHYHTLVQ-GHPDPLRGT 186

Query: 171 CYGDM--------QVTLDTQKGSN-------------AWVTVGLREGKNREIKKVFEFFN 209
               +        +  +      +             + + + L  G+  +I+       
Sbjct: 187 VDAPIDRHPAGDGRWAVVAGGRPSVTHYDTQEAFRAASLLEIKLETGRTHQIRVHMSALR 246

Query: 210 WKVN 213
               
Sbjct: 247 HPCV 250


>gi|241206829|ref|YP_002977925.1| RNA-binding S4 domain protein [Rhizobium leguminosarum bv.
          trifolii WSM1325]
 gi|240860719|gb|ACS58386.1| RNA-binding S4 domain protein [Rhizobium leguminosarum bv.
          trifolii WSM1325]
          Length = 134

 Score = 44.8 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          QR+ K +  A +A SR   +  I    V++NG    + +  V   D IE+
Sbjct: 13 QRIDKWLFFARMAKSRSVAQSHIQSGHVRINGERCSQPSQMVKPGDRIEL 62


>gi|188585944|ref|YP_001917489.1| RNA-binding S4 domain protein [Natranaerobius thermophilus
           JW/NM-WN-LF]
 gi|179350631|gb|ACB84901.1| RNA-binding S4 domain protein [Natranaerobius thermophilus
           JW/NM-WN-LF]
          Length = 265

 Score = 44.8 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 14/60 (23%), Positives = 27/60 (45%), Gaps = 2/60 (3%)

Query: 7   VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           ++   +  R+  V A  G   SR ++ ++I  +R+K+N    +     V   D I + G 
Sbjct: 182 IKGTVSSLRLDAV-ASIGFGASRSKMSQLIKAERIKLNWQPTKDPKATVSEGDVISLRGK 240


>gi|47230110|emb|CAG10524.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 516

 Score = 44.8 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 44/339 (12%), Positives = 105/339 (30%), Gaps = 30/339 (8%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLR-KAERTRLWLYHKP 81
           ++   + R+++N   ++  ++ + + DH++         V G PL    +   + +  KP
Sbjct: 134 QKAAKEGRIRLNEQAVDDLSLVLRNNDHMKNTVHRHEPPVVGKPLEVLVDDGEVLVVDKP 193

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLT----NDGGLARVLE 135
             +          +TV   L          +V RLD  T G+LL          L +++ 
Sbjct: 194 ASIPVHPCGRFRHNTVIFILGKELGISELHTVHRLDRLTSGVLLFARTLETSKKLDQLVR 253

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--------KGSNA 187
               +   V RV      ++         +  +           + +         G  +
Sbjct: 254 DRKLEKEYVCRVEGEFPEEEVICEQPILVVSFKVGLCRVDPKGKECRTVFQRLSFNGKTS 313

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNR---LIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            V      G+  +I+   ++  + +         ++GP +      G   +  +++L+  
Sbjct: 314 VVRCLPVTGRTHQIRVHLQYLGFPILNDPIYGSSAWGPHRGKG---GLLDKSDEELLKAL 370

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           +  H  +E    LD P    E         ++    D    ++        +      T 
Sbjct: 371 VEEHRSQENLHLLDLPDDVCEQEPEQHTASVTAGKSDGAEGQQPHIDPAPPAGFSSTWTT 430

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
           V   +  +     +    +  S +   +     +P    
Sbjct: 431 VTESSGVNADVSERPPAETNRSPAEAADRGQTSAPGSRD 469


>gi|325287073|ref|YP_004262863.1| 30S ribosomal protein S4 [Cellulophaga lytica DSM 7489]
 gi|324322527|gb|ADY29992.1| ribosomal protein S4 [Cellulophaga lytica DSM 7489]
          Length = 201

 Score = 44.8 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GI+ SRR   ++++ + + VNG L+   + ++   D + V
Sbjct: 94  RLDNVVYRMGISNSRRGARQLVSHRHITVNGELVNIPSYSLKPGDVVGV 142


>gi|322701515|gb|EFY93264.1| hypothetical protein MAC_00502 [Metarhizium acridum CQMa 102]
          Length = 192

 Score = 44.8 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 9/103 (8%), Positives = 23/103 (22%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                E   +  A   +          +         R +  S +       +    P  
Sbjct: 1   MARTREEATSASADAPARRASRASADGVSKPEAGGRARGRPRSDKPPKEPTGRPRGRPRL 60

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
            +         +G         G+++   + + +    R   R
Sbjct: 61  NKPPKEPSGRPRGRPKGSGKKPGEKKTPTKTTAAGAGSRGRPR 103


>gi|227502698|ref|ZP_03932747.1| ribosomal protein S4 [Corynebacterium accolens ATCC 49725]
 gi|227076428|gb|EEI14391.1| ribosomal protein S4 [Corynebacterium accolens ATCC 49725]
          Length = 178

 Score = 44.8 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR+  ++++     VNG  +   +  +   D I+V
Sbjct: 69  RLDNVVYRAGLARTRRQARQLVSHGHFTVNGKNINIPSYRITQYDIIDV 117


>gi|156841474|ref|XP_001644110.1| hypothetical protein Kpol_505p29 [Vanderwaltozyma polyspora DSM
           70294]
 gi|156114745|gb|EDO16252.1| hypothetical protein Kpol_505p29 [Vanderwaltozyma polyspora DSM
           70294]
          Length = 482

 Score = 44.8 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 12/54 (22%), Positives = 21/54 (38%), Gaps = 1/54 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+   + R+  AS  R+  + I    V VNG  ++     +   D   V    +
Sbjct: 104 RLDFALFRSMFASSIRQARQFIIHGNVYVNGTKVKHPGYTLKPGDMFNVKPEMV 157


>gi|189424436|ref|YP_001951613.1| 30S ribosomal protein S4 [Geobacter lovleyi SZ]
 gi|226699069|sp|B3E856|RS4_GEOLS RecName: Full=30S ribosomal protein S4
 gi|189420695|gb|ACD95093.1| ribosomal protein S4 [Geobacter lovleyi SZ]
          Length = 208

 Score = 44.8 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G AS R E  +++      +NG      ++ V + D I +
Sbjct: 99  RLDNVVYRLGFASSRSEARQLVRHGHFVLNGRKATIPSIQVKAGDTIVL 147


>gi|86739322|ref|YP_479722.1| 30S ribosomal protein S4 [Frankia sp. CcI3]
 gi|123751487|sp|Q2JFE9|RS4_FRASC RecName: Full=30S ribosomal protein S4
 gi|86566184|gb|ABD09993.1| SSU ribosomal protein S4P [Frankia sp. CcI3]
          Length = 209

 Score = 44.8 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           R+  V+ R G A SR    + +    V+VNG  ++  +  +   D +E+    
Sbjct: 99  RLDNVVYRGGFAPSRDAARQAVRHGHVQVNGRKVDIPSYRISENDIVEIAPKA 151


>gi|332673797|gb|AEE70614.1| RNA pseudouridine synthase [Helicobacter pylori 83]
          Length = 242

 Score = 44.8 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 28/211 (13%), Positives = 62/211 (29%), Gaps = 28/211 (13%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWL 77
           K+++     S ++ + +I    V V G               + V    L K     +  
Sbjct: 6   KILSVQENISHKKAKALIDLGLVSVGGK-------------KLMVARKELPKNTHFSVQK 52

Query: 78  YHKPIGLVTTHSDPDGRSTVF---DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             KP  +    +        F    +L S F   + + RLD  T G++LL  +     + 
Sbjct: 53  VEKPGVIFEDENILALFKPPFIESYDLVSFFKGWVLLHRLDKETSGVILLVRENSEFHLK 112

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--------- 185
              + +   V +          +        ++               + +         
Sbjct: 113 AKKAFKDRAVKKEYLALAQGIIEEEQEINAPILTFKTTKAFSKISKKGQEAVTMITPLKI 172

Query: 186 ---NAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 + VG++ G+  +I+   +  N  + 
Sbjct: 173 INKKTLLKVGIKTGRTHQIRVHLKHINHPII 203


>gi|301628935|ref|XP_002943604.1| PREDICTED: 30S ribosomal protein S4-like, partial [Xenopus
           (Silurana) tropicalis]
          Length = 212

 Score = 44.8 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G  S R E  ++++ + + VNG  +   +  V   D + V
Sbjct: 103 RLDNMVYRMGFGSTRAEARQLVSHKAILVNGQAVNIPSFLVKVGDVVSV 151


>gi|163791292|ref|ZP_02185706.1| 30S ribosomal protein S4 [Carnobacterium sp. AT7]
 gi|159873433|gb|EDP67523.1| 30S ribosomal protein S4 [Carnobacterium sp. AT7]
          Length = 201

 Score = 44.8 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G+A+ RR+  +++    + V+G  ++  + +V     I V
Sbjct: 93  QRLDNVVYRLGLATTRRQSRQLVNHGHILVDGKRVDIPSYSVSVGQVISV 142


>gi|307248854|ref|ZP_07530867.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar 2
           str. S1536]
 gi|307262278|ref|ZP_07543927.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar
           12 str. 1096]
 gi|306854781|gb|EFM86971.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar 2
           str. S1536]
 gi|306868041|gb|EFM99868.1| 30S ribosomal protein S4 [Actinobacillus pleuropneumoniae serovar
           12 str. 1096]
          Length = 204

 Score = 44.8 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R E  ++++ + + VNG ++   +  V   D + V
Sbjct: 95  RLDNVVYRMGFAATRAEARQLVSHKSIVVNGRVVNIPSYQVSVDDVVAV 143


>gi|291286338|ref|YP_003503154.1| 30S ribosomal protein S4 [Denitrovibrio acetiphilus DSM 12809]
 gi|290883498|gb|ADD67198.1| ribosomal protein S4 [Denitrovibrio acetiphilus DSM 12809]
          Length = 208

 Score = 44.8 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ RAG   SR+E  +M+      ++G  ++  +  V     IEV
Sbjct: 99  RLDNIVYRAGFAGSRKEARQMVKHSHFLIDGKKVDIPSFLVKPGMVIEV 147


>gi|116493045|ref|YP_804780.1| 30S ribosomal protein S4 [Pediococcus pentosaceus ATCC 25745]
 gi|122265491|sp|Q03EN4|RS4_PEDPA RecName: Full=30S ribosomal protein S4
 gi|116103195|gb|ABJ68338.1| SSU ribosomal protein S4P [Pediococcus pentosaceus ATCC 25745]
          Length = 202

 Score = 44.8 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A+ RR+  +++    + V+G  ++  +  V     I V
Sbjct: 94  RLDNMVYRLGLATTRRQARQLVNHGHITVDGKRVDIPSYEVEIGQVIGV 142


>gi|83590545|ref|YP_430554.1| tyrosyl-tRNA synthetase [Moorella thermoacetica ATCC 39073]
 gi|115305809|sp|Q2RHS8|SYY_MOOTA RecName: Full=Tyrosyl-tRNA synthetase; AltName: Full=Tyrosine--tRNA
           ligase; Short=TyrRS
 gi|83573459|gb|ABC20011.1| tyrosyl-tRNA synthetase [Moorella thermoacetica ATCC 39073]
          Length = 413

 Score = 44.8 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 1/38 (2%)

Query: 18  KVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNV 54
           +++ +AG+A S  E  R+I Q  VK++G  +      V
Sbjct: 355 RLMVQAGLAPSTSEARRLIRQGAVKIDGERVTDPDTEV 392


>gi|119387071|ref|YP_918126.1| DEAD/DEAH box helicase domain-containing protein [Paracoccus
           denitrificans PD1222]
 gi|119377666|gb|ABL72430.1| DEAD/DEAH box helicase domain protein [Paracoccus denitrificans
           PD1222]
          Length = 687

 Score = 44.8 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 9/110 (8%), Positives = 25/110 (22%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +    ++ +  P    +     +A    +      +    +            S      
Sbjct: 578 LDPDEVKPRPAPEAAADRVPEPEAAPRKARWSAEKKLAQKAAPKAGPRAAGFKSHGAAPR 637

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
             +         R   +  + +      +   +G +       P  P KR
Sbjct: 638 DDRPARGEGAEARPKRAAGFKSHKPAGGWQGKAGDKPFRSGAKPGKPGKR 687


>gi|254881348|ref|ZP_05254058.1| 30S ribosomal protein S4 [Bacteroides sp. 4_3_47FAA]
 gi|319640349|ref|ZP_07995074.1| hypothetical protein HMPREF9011_00671 [Bacteroides sp. 3_1_40A]
 gi|254834141|gb|EET14450.1| 30S ribosomal protein S4 [Bacteroides sp. 4_3_47FAA]
 gi|317388124|gb|EFV68978.1| hypothetical protein HMPREF9011_00671 [Bacteroides sp. 3_1_40A]
          Length = 201

 Score = 44.8 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA +R    ++++ + + V+G ++   + +V     + V
Sbjct: 93  RLDNVVFRLGIAPTRAAARQLVSHKHITVDGKVVNIPSFSVKPGQIVGV 141


>gi|148270449|ref|YP_001244909.1| 30S ribosomal protein S4 [Thermotoga petrophila RKU-1]
 gi|170289156|ref|YP_001739394.1| RNA-binding S4 domain-containing protein [Thermotoga sp. RQ2]
 gi|281412756|ref|YP_003346835.1| ribosomal protein S4 [Thermotoga naphthophila RKU-10]
 gi|172047881|sp|A5IMB0|RS4_THEP1 RecName: Full=30S ribosomal protein S4
 gi|226695093|sp|B1LBL3|RS4_THESQ RecName: Full=30S ribosomal protein S4
 gi|147735993|gb|ABQ47333.1| SSU ribosomal protein S4P [Thermotoga petrophila RKU-1]
 gi|170176659|gb|ACB09711.1| RNA-binding S4 domain protein [Thermotoga sp. RQ2]
 gi|281373859|gb|ADA67421.1| ribosomal protein S4 [Thermotoga naphthophila RKU-10]
          Length = 209

 Score = 44.8 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+  +++      VNG  +   +  +   D +E+
Sbjct: 99  RLDNVVYRMGFAINRRQARQLVNHGHFLVNGKKVNIPSYLLKPNDVVEL 147


>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 = 44.8 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 31/253 (12%), Positives = 61/253 (24%), Gaps = 41/253 (16%)

Query: 1   MKDKNIV--QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M D   +   E    +RV   I+R    SR     + A   V VNG  + + +  V   D
Sbjct: 4   MSDSRTMLVPEGLQGERVDAAISRLFGLSRTRAADLAADGGVAVNGASVGK-SHRVHGGD 62

Query: 59  HIE------------------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
            +E                  V G+ +   +   + +               G + +   
Sbjct: 63  LLELTLPSNDASPTLEVIAEPVPGMSIIHDDDDIVVVDKPVGVAAHPSVGWTGPTVLGGL 122

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD---- 156
             + +    S           L +   G +           L+        +        
Sbjct: 123 AAAGYRISTSGASERQGIVSRLDVGTSGLMVVCKSERGYSVLKRAFKERTVEKTYHTLVQ 182

Query: 157 ----------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
                                 K  V++   +      L       + + + L  G+  +
Sbjct: 183 GLPDPLVGTIDAPIARHPGHDYKFAVMESGKHAVTHYELIEAFRYASLLDIRLETGRTHQ 242

Query: 201 IKKVFEFFNWKVN 213
           I+  F        
Sbjct: 243 IRVHFSALRHPCV 255


>gi|291334081|gb|ADD93754.1| ribosomal protein S4 [uncultured marine bacterium
           MedDCM-OCT-S05-C114]
          Length = 202

 Score = 44.8 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R+   + +    + VNG  ++  +  V   D I V
Sbjct: 93  RLDNVVYRLGFAKTRKAARQYVNHGHILVNGKKVDIPSFAVSVGDEIGV 141


>gi|259506742|ref|ZP_05749642.1| 30S ribosomal protein S4 [Corynebacterium efficiens YS-314]
 gi|259165683|gb|EEW50237.1| 30S ribosomal protein S4 [Corynebacterium efficiens YS-314]
          Length = 178

 Score = 44.8 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR+  ++++     VNG  ++  +  V   D I+V
Sbjct: 69  RLDNVVYRAGLARTRRQARQLVSHGHFVVNGKAVDVPSFRVSQYDIIDV 117


>gi|255524046|ref|ZP_05391008.1| RNA-binding S4 domain protein [Clostridium carboxidivorans P7]
 gi|296186902|ref|ZP_06855303.1| S4 domain protein [Clostridium carboxidivorans P7]
 gi|255512333|gb|EET88611.1| RNA-binding S4 domain protein [Clostridium carboxidivorans P7]
 gi|296048616|gb|EFG88049.1| S4 domain protein [Clostridium carboxidivorans P7]
          Length = 86

 Score = 44.8 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   +      RV +N  + +  +  V   D IE+
Sbjct: 1  MRLDKYLKVSRIIKRRTVAKEACEGGRVSINDKIAK-PSTEVKEGDIIEI 49


>gi|227549867|ref|ZP_03979916.1| 30S ribosomal protein S4 [Corynebacterium lipophiloflavum DSM
           44291]
 gi|227078122|gb|EEI16085.1| 30S ribosomal protein S4 [Corynebacterium lipophiloflavum DSM
           44291]
          Length = 178

 Score = 44.8 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR+  ++++     VNG      +  V   D I+V
Sbjct: 69  RLDNVVYRAGLARTRRQARQLVSHGHFTVNGKRTNVPSYRVSRYDIIDV 117


>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 = 44.8 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 29/211 (13%), Positives = 63/211 (29%), Gaps = 28/211 (13%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWL 77
           K+++     S ++ + +I    V V G               + V    L K  R  +  
Sbjct: 6   KLLSVQENISHKKAKALIDLGLVSVGGK-------------KLMVARKELPKNTRFSVQK 52

Query: 78  YHKPIGLVTTHSDPDGRSTVF---DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             KP  +    +        F    +L S F   + + RLD  T G++LL  +     + 
Sbjct: 53  VEKPGVIFEDENILALFKPPFIESYDLLSFFKGWVLLHRLDKETSGVILLVKENSEFHLK 112

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--------- 185
              + +   V +          +        ++               + +         
Sbjct: 113 AKKAFKNRAVKKEYLALAQGIIEEEREINAPILTFKTTKAFSKISKKGQEAVTIITPLKI 172

Query: 186 ---NAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 + VG++ G+  +I+   +  N  + 
Sbjct: 173 INKKTLLKVGIKTGRTHQIRVHLKHINHPII 203


>gi|227878368|ref|ZP_03996323.1| S4 RNA-binding domain protein [Lactobacillus crispatus JV-V01]
 gi|256844411|ref|ZP_05549897.1| conserved hypothetical protein [Lactobacillus crispatus
          125-2-CHN]
 gi|256849201|ref|ZP_05554634.1| conserved hypothetical protein [Lactobacillus crispatus MV-1A-US]
 gi|262047217|ref|ZP_06020175.1| ribosome-associated heat shock protein [Lactobacillus crispatus
          MV-3A-US]
 gi|293380358|ref|ZP_06626429.1| S4 domain protein [Lactobacillus crispatus 214-1]
 gi|227862047|gb|EEJ69611.1| S4 RNA-binding domain protein [Lactobacillus crispatus JV-V01]
 gi|256613489|gb|EEU18692.1| conserved hypothetical protein [Lactobacillus crispatus
          125-2-CHN]
 gi|256713977|gb|EEU28965.1| conserved hypothetical protein [Lactobacillus crispatus MV-1A-US]
 gi|260572462|gb|EEX29024.1| ribosome-associated heat shock protein [Lactobacillus crispatus
          MV-3A-US]
 gi|290923041|gb|EFD99972.1| S4 domain protein [Lactobacillus crispatus 214-1]
          Length = 80

 Score = 44.8 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR   + M  Q R+KVNG +++  + +V   D IEV
Sbjct: 1  MRIDKFLKVSRLVKRRTVAKEMADQGRIKVNGRVVKS-SYDVKIDDIIEV 49


>gi|262202727|ref|YP_003273935.1| hemolysin A [Gordonia bronchialis DSM 43247]
 gi|262086074|gb|ACY22042.1| hemolysin A [Gordonia bronchialis DSM 43247]
          Length = 275

 Score = 44.8 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+   + R G+A SR     ++    VKVNG++  + A NV     + V
Sbjct: 6  RLDAELVRRGLARSREHARHLVDSGVVKVNGVVATKPATNVTRDTPVLV 54


>gi|150003363|ref|YP_001298107.1| 30S ribosomal protein S4 [Bacteroides vulgatus ATCC 8482]
 gi|212695280|ref|ZP_03303408.1| hypothetical protein BACDOR_04820 [Bacteroides dorei DSM 17855]
 gi|237711700|ref|ZP_04542181.1| 30S ribosomal protein S4 [Bacteroides sp. 9_1_42FAA]
 gi|237725859|ref|ZP_04556340.1| 30S ribosomal protein S4 [Bacteroides sp. D4]
 gi|265753119|ref|ZP_06088688.1| 30S ribosomal protein S4 [Bacteroides sp. 3_1_33FAA]
 gi|294777845|ref|ZP_06743289.1| ribosomal protein S4 [Bacteroides vulgatus PC510]
 gi|172048640|sp|A6KYH1|RS4_BACV8 RecName: Full=30S ribosomal protein S4
 gi|149931787|gb|ABR38485.1| 30S ribosomal protein S4 [Bacteroides vulgatus ATCC 8482]
 gi|212662190|gb|EEB22764.1| hypothetical protein BACDOR_04820 [Bacteroides dorei DSM 17855]
 gi|229435667|gb|EEO45744.1| 30S ribosomal protein S4 [Bacteroides dorei 5_1_36/D4]
 gi|229454395|gb|EEO60116.1| 30S ribosomal protein S4 [Bacteroides sp. 9_1_42FAA]
 gi|263236305|gb|EEZ21800.1| 30S ribosomal protein S4 [Bacteroides sp. 3_1_33FAA]
 gi|294448299|gb|EFG16855.1| ribosomal protein S4 [Bacteroides vulgatus PC510]
          Length = 201

 Score = 44.8 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA +R    ++++ + + V+G ++   + +V     + V
Sbjct: 93  RLDNVVFRLGIAPTRAAARQLVSHKHITVDGKVVNIPSFSVKPGQIVGV 141


>gi|153952811|ref|YP_001393576.1| hypothetical protein CKL_0158 [Clostridium kluyveri DSM 555]
 gi|219853476|ref|YP_002470598.1| hypothetical protein CKR_0133 [Clostridium kluyveri NBRC 12016]
 gi|146345692|gb|EDK32228.1| Conserved hypothetical protein [Clostridium kluyveri DSM 555]
 gi|219567200|dbj|BAH05184.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 81

 Score = 44.8 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   +      RV +NG + +  +  V   D IE+
Sbjct: 1  MRLDKYLKVSRIIKRRTIAKEACEGGRVTINGKMAK-PSTEVKEGDIIEI 49


>gi|269837093|ref|YP_003319321.1| 30S ribosomal protein S4 [Sphaerobacter thermophilus DSM 20745]
 gi|269786356|gb|ACZ38499.1| ribosomal protein S4 [Sphaerobacter thermophilus DSM 20745]
          Length = 214

 Score = 44.8 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            R+  V+ R G A SR +  +++      VNG      +  V   D + V
Sbjct: 103 MRLDNVVYRLGFADSRNQARQLVRHGHFTVNGRKTNIPSFIVKPGDVVAV 152


>gi|262383201|ref|ZP_06076338.1| ATP-dependent RNA helicase [Bacteroides sp. 2_1_33B]
 gi|298373901|ref|ZP_06983859.1| ATP-dependent RNA helicase, DEAD/DEAH box family [Bacteroides sp.
           3_1_19]
 gi|262296079|gb|EEY84010.1| ATP-dependent RNA helicase [Bacteroides sp. 2_1_33B]
 gi|298268269|gb|EFI09924.1| ATP-dependent RNA helicase, DEAD/DEAH box family [Bacteroides sp.
           3_1_19]
          Length = 609

 Score = 44.8 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 16/125 (12%), Positives = 30/125 (24%), Gaps = 6/125 (4%)

Query: 230 AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
            G  R + +  LR+      +EE + N      +   +   R ++              S
Sbjct: 490 PGKVR-IGRIDLRDNFSFFEVEEGEANRVMDSMNGFEVDGRRISVEPAQAKGEGGKGGRS 548

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
            +                R    +        S      G+R       P         R
Sbjct: 549 PRGGSRGGNGFRDRRDSGRGGRDSRRE-----SDRGDRGGRRSSRSDDKPKRKFYEDTPR 603

Query: 350 TSAKK 354
           +  K+
Sbjct: 604 SRKKR 608


>gi|220903959|ref|YP_002479271.1| 30S ribosomal protein S4 [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
 gi|254764584|sp|B8IYL6|RS4_DESDA RecName: Full=30S ribosomal protein S4
 gi|219868258|gb|ACL48593.1| ribosomal protein S4 [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
          Length = 208

 Score = 44.8 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SR +  +++      +NG  +   ++ V   D IEV
Sbjct: 99  RLDNVVYRLGFANSRNQARQLVRHGVFTLNGRKVNIPSLQVRLGDTIEV 147


>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 = 44.8 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 27/211 (12%), Positives = 62/211 (29%), Gaps = 28/211 (13%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWL 77
           K+++     S ++ + +I    V + G               + V    L K     +  
Sbjct: 6   KILSVQENISHKKAKALIDLGLVSIGGK-------------KLMVARKELPKNTHFSVQK 52

Query: 78  YHKPIGLVTTHSDPDGRSTVF---DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             KP  +    +        F    +L S F   + + RLD  T G++LL  +     + 
Sbjct: 53  VEKPGVIFEDENILALFKPPFIESYDLLSFFKGWVLLHRLDKETSGVILLVKENSEFHLK 112

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--------- 185
              + +   V +          +        ++               + +         
Sbjct: 113 AKKAFKNRAVKKEYLALTQGIIEEEREINAPILTIKTTKAFSKISKKGQEAVTIITPLKI 172

Query: 186 ---NAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 + VG++ G+  +I+   +  N  + 
Sbjct: 173 INKKTLLKVGIKTGRTHQIRVHLKHINHPII 203


>gi|167764347|ref|ZP_02436472.1| hypothetical protein BACSTE_02731 [Bacteroides stercoris ATCC
           43183]
 gi|167697752|gb|EDS14331.1| hypothetical protein BACSTE_02731 [Bacteroides stercoris ATCC
           43183]
          Length = 201

 Score = 44.8 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA +R    ++++ + + V+G ++   +  V     I V
Sbjct: 93  RLDNVVFRLGIAPTRAAARQLVSHKHITVDGEVVNIPSYAVKPGQVIGV 141


>gi|56418214|gb|AAV91028.1| unknown protein [Grouper iridovirus]
          Length = 1008

 Score = 44.8 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 16/135 (11%), Positives = 34/135 (25%), Gaps = 6/135 (4%)

Query: 226 GTLLAGSTREVSKKILREQLGPHL-----LEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
             L       + K  L + +  H       +++       +  S +  R R         
Sbjct: 12  KALGIRGYSSMRKAELEDAIKQHQAGVSKQKKSPDKRPDSLRKSASPERSRDKSPRSPRS 71

Query: 281 DFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
                      ++      +       R+        +    S      +R  + RR   
Sbjct: 72  PRRPRDSPERSRDKRPASPRRPRDSPERSRDKRPASPRRPRDSPERSRDKRPASPRRPRD 131

Query: 341 FPSK-RSLRRTSAKK 354
            P + R  R  S ++
Sbjct: 132 SPERSRDKRPASPRR 146



 Score = 41.7 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 11/101 (10%), Positives = 25/101 (24%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           + L      E   +       S    RD P    +      R  ++S +++   +     
Sbjct: 50  DSLRKSASPERSRDKSPRSPRSPRRPRDSPERSRDKRPASPRRPRDSPERSRDKRPASPR 109

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
            P      + +   A         +  + +          S
Sbjct: 110 RPRDSPERSRDKRPASPRRPRDSPERSRDKRPASPRRPRGS 150



 Score = 39.8 bits (91), Expect = 0.70,   Method: Composition-based stats.
 Identities = 7/107 (6%), Positives = 21/107 (19%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +             + +     S    R              +   +  +     ++ + 
Sbjct: 43  KSPDKRPDSLRKSASPERSRDKSPRSPRSPRRPRDSPERSRDKRPASPRRPRDSPERSRD 102

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
             P   R    +   ++    +         E  R       +R   
Sbjct: 103 KRPASPRRPRDSPERSRDKRPASPRRPRDSPERSRDKRPASPRRPRG 149


>gi|262066971|ref|ZP_06026583.1| ribosomal protein S4 [Fusobacterium periodonticum ATCC 33693]
 gi|291379319|gb|EFE86837.1| ribosomal protein S4 [Fusobacterium periodonticum ATCC 33693]
          Length = 195

 Score = 44.8 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+  ++++   + VNG  +  A+  V   D + V
Sbjct: 89  RLENVVYRLGFAKTRRQARQIVSHGHIAVNGRRVNIASFRVKVGDVVSV 137


>gi|218131301|ref|ZP_03460105.1| hypothetical protein BACEGG_02912 [Bacteroides eggerthii DSM 20697]
 gi|317476331|ref|ZP_07935580.1| ribosomal protein S4 [Bacteroides eggerthii 1_2_48FAA]
 gi|217986518|gb|EEC52854.1| hypothetical protein BACEGG_02912 [Bacteroides eggerthii DSM 20697]
 gi|316907357|gb|EFV29062.1| ribosomal protein S4 [Bacteroides eggerthii 1_2_48FAA]
          Length = 201

 Score = 44.8 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA +R    ++++ + + V+G ++   +  V     I V
Sbjct: 93  RLDNVVFRLGIAPTRAAARQLVSHKHITVDGEVVNIPSYAVKPGQVIGV 141


>gi|86742161|ref|YP_482561.1| RNA-binding S4 [Frankia sp. CcI3]
 gi|86569023|gb|ABD12832.1| RNA-binding S4 [Frankia sp. CcI3]
          Length = 74

 Score = 44.8 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 16/62 (25%), Positives = 26/62 (41%), Gaps = 9/62 (14%)

Query: 12 TPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
             R+ + +       AG     EV+ ++A   V+VNG +  R    +   D + V G  
Sbjct: 15 DGIRLGQFLKLADVVEAG----SEVKELLAGGMVRVNGEVETRRGRQLAPGDEVAVAGEA 70

Query: 67 LR 68
          LR
Sbjct: 71 LR 72


>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 = 44.8 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 27/211 (12%), Positives = 61/211 (28%), Gaps = 28/211 (13%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWL 77
           K+++     S ++ + +I    V + G               + V    L K     +  
Sbjct: 6   KILSVQENISHKKAKALIDSGLVSIGGK-------------KLMVARKELPKNTHFSVQK 52

Query: 78  YHKPIGLVTTHSDPDGRSTVF---DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             KP  +    +        F    +L S F     + RLD  T G++LL  +     + 
Sbjct: 53  VEKPSVIFEDENILALFKPPFIESYDLASFFKGWALLHRLDKETSGVVLLVKENSEFHLK 112

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--------- 185
              + +   V +          +        ++               + +         
Sbjct: 113 AKKAFKDRAVKKEYLALTQGIIEEEREINAPILTFKTTKAFSKISKKGQEAVTIITPLKI 172

Query: 186 ---NAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 + VG++ G+  +I+   +  N  + 
Sbjct: 173 INKKTLLKVGIKTGRTHQIRVHLKHINHPII 203


>gi|146277599|ref|YP_001167758.1| RNA-binding S4 domain-containing protein [Rhodobacter sphaeroides
          ATCC 17025]
 gi|145555840|gb|ABP70453.1| RNA-binding S4 domain protein [Rhodobacter sphaeroides ATCC
          17025]
          Length = 100

 Score = 44.8 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 11/51 (21%), Positives = 22/51 (43%), Gaps = 1/51 (1%)

Query: 13 PQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            R+ K + +A    +R     ++   RV++NG  + + A  V   D +  
Sbjct: 8  TIRLDKWLVQARFFKTRALASALVEAGRVRLNGQHVAKPAQPVGEGDMLTF 58


>gi|330684381|gb|EGG96107.1| ribosomal protein S4 [Staphylococcus epidermidis VCU121]
          Length = 200

 Score = 44.8 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+   G+A +RR+  +++    ++V+G  ++  + ++     I V
Sbjct: 93  RLDAVVYSLGLARTRRQARQLVNHGHIEVDGRRVDIPSYSLKPGQEIAV 141


>gi|299535430|ref|ZP_07048752.1| 30S ribosomal protein S4 [Lysinibacillus fusiformis ZC1]
 gi|298729191|gb|EFI69744.1| 30S ribosomal protein S4 [Lysinibacillus fusiformis ZC1]
          Length = 200

 Score = 44.8 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR   +++    + V+G  ++  + +V     I +
Sbjct: 93  RLDNLVYRLGLARTRRGARQLVNHGHILVDGKRVDIPSYSVKPGQTISL 141


>gi|256847990|ref|ZP_05553434.1| ribosomal protein S4 [Lactobacillus coleohominis 101-4-CHN]
 gi|256715050|gb|EEU30027.1| ribosomal protein S4 [Lactobacillus coleohominis 101-4-CHN]
          Length = 202

 Score = 44.8 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A+ RR+  +++    + V+G  ++  +  V     I V
Sbjct: 94  RLDNMVYRLGLATTRRQARQLVNHGHITVDGKRVDIPSYEVSVDQVIGV 142


>gi|195729249|gb|ACG50755.1| VtaA5 [Haemophilus parasuis]
          Length = 1099

 Score = 44.8 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 6/99 (6%), Positives = 16/99 (16%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           +      A           + +                 +     +Q             
Sbjct: 687 DKGEPGQAGPAGPRGPAGPKGDTGQRGETGSAGPAGPKGEPGPKGEQGIPGQAGPAGPRG 746

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                          + G+      R P+ P   +  + 
Sbjct: 747 PQGTAGAQGPKGDKGEPGEAGPAGPRGPAGPKGDAGPKG 785



 Score = 37.5 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 12/112 (10%), Positives = 19/112 (16%), Gaps = 7/112 (6%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           GP                        P  +        +  K    + G +  +  A P 
Sbjct: 647 GPVGPMGPAGAAGLVGPMGPQGPAGPPGPVGPAGAAGPKGDKGEPGQAGPAGPRGPAGPK 706

Query: 306 HRRNLASNVWMAKGIHSSFLSDS-------GQREENHRRSPSFPSKRSLRRT 350
                      A                  GQ      R P   +     + 
Sbjct: 707 GDTGQRGETGSAGPAGPKGEPGPKGEQGIPGQAGPAGPRGPQGTAGAQGPKG 758


>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 = 44.8 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 24/194 (12%), Positives = 61/194 (31%), Gaps = 3/194 (1%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV-PLR-KAERTRL 75
           K++A     S R  + +I +  V   G  +  A   +  +   +++ + P++   E   +
Sbjct: 6   KLLALQEGISNRAAKELIDRGVVYAAGKKVSVARGELSPSTKFKIEKIAPIKVLFEDEYI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
               KP  + +       +  +   L    S V+ + + D   +  +       + +   
Sbjct: 66  MAVDKPAFITSEEVAEIKKLPLLHRLDRETSGVLLLTKDDEFRQKAVNAFKKREVHKEYI 125

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
                 +          +   K N     I   G       +     +G  + + V +  
Sbjct: 126 AIVEGKVVEATEVNAPILTIKKGNTAYSKISPDGKEA-ISYIEPLMIEGKRSKIKVTIET 184

Query: 196 GKNREIKKVFEFFN 209
           G+  +I+   +   
Sbjct: 185 GRTHQIRVHLKSIG 198


>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 = 44.8 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 25/214 (11%), Positives = 56/214 (26%), Gaps = 32/214 (14%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--------------PLRKAERTR 74
           R V + +   R+ VNG  + +    +   D IE+                  +   +   
Sbjct: 31  RFVRKAVRDGRIFVNGEKVIK-KHKLSQDDLIEIYMQEDEHQNIEPEDINIEIVYEDSDI 89

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-----GRLDINTEGLLLLTNDGG 129
           + +  KP  +V         +     L     +          RLD +T GL+++  +  
Sbjct: 90  IVINKKPGIVVHPTKSHSTGTLSNGILYHFKKKGEKSIVRLVNRLDRDTSGLVIVAKNQF 149

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
               L    ++                +        + +       ++  +  + S    
Sbjct: 150 SHMRLASDMSKDSFRKIYIAVVHGSMKEKEGRINLPIYKEENESIKRIVDERGQESITTY 209

Query: 190 TV------------GLREGKNREIKKVFEFFNWK 211
            V             L  G+  +I+         
Sbjct: 210 EVLEELSKGSVVKLELETGRTHQIRVHMSHLGHH 243


>gi|167759834|ref|ZP_02431961.1| hypothetical protein CLOSCI_02197 [Clostridium scindens ATCC 35704]
 gi|167662453|gb|EDS06583.1| hypothetical protein CLOSCI_02197 [Clostridium scindens ATCC 35704]
          Length = 181

 Score = 44.8 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +RRE  +++  + + VNG  +   +  + + D IE+
Sbjct: 72  RLDNVVFRLGLARTRREARQIVDHKHILVNGKQINIPSYLIKAGDVIEI 120


>gi|121730284|ref|ZP_01682658.1| topoisomerase IV subunit A [Vibrio cholerae V52]
 gi|121627964|gb|EAX60527.1| topoisomerase IV subunit A [Vibrio cholerae V52]
          Length = 102

 Score = 44.8 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 11/65 (16%), Positives = 27/65 (41%), Gaps = 1/65 (1%)

Query: 23 AGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKP 81
           G   +R E  ++++ + + VNG ++   + NV + D + V     +++         + 
Sbjct: 1  MGFGATRAEARQLVSHKAILVNGKVVNVPSFNVAANDVVAVREKAKKQSRIKAALEVAEQ 60

Query: 82 IGLVT 86
              T
Sbjct: 61 REKPT 65


>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 = 44.8 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 6/64 (9%)

Query: 4  KNIVQENFTPQRVSKV----IARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
          +  V +     R+ K+    + RAG A SR  V+R IA  RV V+G     A+V V ++ 
Sbjct: 11 RFRVDDGDPRDRLDKLVVHLLERAGHAASRAAVQRWIAAGRVLVDGEPAR-ASVAVRASA 69

Query: 59 HIEV 62
           +EV
Sbjct: 70 LVEV 73


>gi|153871948|ref|ZP_02000981.1| 30S ribosomal protein S4 [Beggiatoa sp. PS]
 gi|152071584|gb|EDN69017.1| 30S ribosomal protein S4 [Beggiatoa sp. PS]
          Length = 206

 Score = 44.8 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V+ R G A +R E  ++++ + + VN   +   +  V + D I + G 
Sbjct: 97  RLDNVVYRMGFAVTRAEARQLVSHKAILVNEKSVNIPSYQVKAGDVIAIRGK 148


>gi|327444033|gb|EGE90687.1| ribosomal protein S4 [Propionibacterium acnes HL043PA1]
 gi|327449433|gb|EGE96087.1| ribosomal protein S4 [Propionibacterium acnes HL043PA2]
          Length = 201

 Score = 44.8 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+  AG+A +RR+  +M++     VNG  +   +  V + D I+V
Sbjct: 92  RLDNVVYLAGLAATRRQARQMVSHGHFLVNGKKVNIPSYRVSTHDIIDV 140


>gi|323141381|ref|ZP_08076272.1| ribosomal protein S4 [Phascolarctobacterium sp. YIT 12067]
 gi|322414130|gb|EFY04958.1| ribosomal protein S4 [Phascolarctobacterium sp. YIT 12067]
          Length = 197

 Score = 44.8 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +RR+  +++    + VNG  L+  +  V   D + V
Sbjct: 88  RIDNVVFRLGLANTRRQARQIVRHGHIAVNGKRLDIPSALVRVGDVVTV 136


>gi|313892885|ref|ZP_07826462.1| ribosomal protein S4 [Veillonella sp. oral taxon 158 str. F0412]
 gi|313442238|gb|EFR60653.1| ribosomal protein S4 [Veillonella sp. oral taxon 158 str. F0412]
          Length = 195

 Score = 44.8 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  ++ R G   S R+  +M+    + VNG  ++  + +    D IE+
Sbjct: 86  QRLDNLVYRIGFGNSIRQARQMVNHGHILVNGRRVDIPSYSCKPGDVIEL 135


>gi|303229707|ref|ZP_07316494.1| ribosomal protein S4 [Veillonella atypica ACS-134-V-Col7a]
 gi|303231269|ref|ZP_07318007.1| ribosomal protein S4 [Veillonella atypica ACS-049-V-Sch6]
 gi|302514176|gb|EFL56180.1| ribosomal protein S4 [Veillonella atypica ACS-049-V-Sch6]
 gi|302515629|gb|EFL57584.1| ribosomal protein S4 [Veillonella atypica ACS-134-V-Col7a]
          Length = 195

 Score = 44.8 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  ++ R G   S R+  +M+    + VNG  ++  + +    D IE+
Sbjct: 86  QRLDNLVYRIGFGNSIRQARQMVNHGHILVNGRRVDIPSYSCKPGDVIEL 135


>gi|289770162|ref|ZP_06529540.1| LOW QUALITY PROTEIN: transcriptional regulatory protein [Streptomyces
            lividans TK24]
 gi|289700361|gb|EFD67790.1| LOW QUALITY PROTEIN: transcriptional regulatory protein [Streptomyces
            lividans TK24]
          Length = 1202

 Score = 44.8 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 8/97 (8%), Positives = 20/97 (20%)

Query: 257  LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
                      +                        ++   +  + A   HR   A     
Sbjct: 988  RHPVADRRRRMPAGAGRRPRGAGPGDGGTAAGPGVEHAAHRGPRPARAGHRHRRAPRPGT 1047

Query: 317  AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             +G  +     + +         + P   +  R  A+
Sbjct: 1048 GRGGRTDPAGRARRHRHGADPRAARPGPPAPGRGRAR 1084



 Score = 43.2 bits (100), Expect = 0.065,   Method: Composition-based stats.
 Identities = 8/98 (8%), Positives = 20/98 (20%)

Query: 252  EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
            E   +       +    R  P   +          +    ++G   +     P       
Sbjct: 1023 EHAAHRGPRPARAGHRHRRAPRPGTGRGGRTDPAGRARRHRHGADPRAARPGPPAPGRGR 1082

Query: 312  SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
            +               +  R        + P++    R
Sbjct: 1083 ARTRPGPAARGGGTGRTQGRPALAHPGRAGPARGRRPR 1120



 Score = 41.7 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 8/101 (7%), Positives = 19/101 (18%)

Query: 248  HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            H + + +  + A                +  P       +         + ++   P   
Sbjct: 989  HPVADRRRRMPAGAGRRPRGAGPGDGGTAAGPGVEHAAHRGPRPARAGHRHRRAPRPGTG 1048

Query: 308  RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
            R   ++       H         R             R   
Sbjct: 1049 RGGRTDPAGRARRHRHGADPRAARPGPPAPGRGRARTRPGP 1089



 Score = 36.7 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 11/125 (8%), Positives = 19/125 (15%), Gaps = 13/125 (10%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK- 300
            R +  P          D    +        P      P    R +  +            
Sbjct: 1038 RHRRAPRPGTGRGGRTDPAGRARRHRHGADPRAARPGPPAPGRGRARTRPGPAARGGGTG 1097

Query: 301  ----------LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP--SFPSKRSLR 348
                             R                           RR P      + +  
Sbjct: 1098 RTQGRPALAHPGRAGPARGRRPRPGGVPHRRRRPDRQRAPDRRTGRRRPHQHRDRRPAAP 1157

Query: 349  RTSAK 353
            R + +
Sbjct: 1158 RPAHR 1162


>gi|289550525|ref|YP_003471429.1| SSU ribosomal protein S4p (S9e) [Staphylococcus lugdunensis
           HKU09-01]
 gi|315658019|ref|ZP_07910892.1| 30S ribosomal protein S4 [Staphylococcus lugdunensis M23590]
 gi|289180057|gb|ADC87302.1| SSU ribosomal protein S4p (S9e) [Staphylococcus lugdunensis
           HKU09-01]
 gi|315496909|gb|EFU85231.1| 30S ribosomal protein S4 [Staphylococcus lugdunensis M23590]
          Length = 200

 Score = 44.8 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+   G+A +RR+  +++    ++V+G  ++  + ++     I V
Sbjct: 93  RLDAVVYALGLARTRRQARQLVGHGHIEVDGRRVDIPSYSLKPGQVITV 141


>gi|77548468|gb|ABA91265.1| retrotransposon protein, putative, unclassified [Oryza sativa
           Japonica Group]
          Length = 1068

 Score = 44.8 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 6/100 (6%), Positives = 20/100 (20%), Gaps = 1/100 (1%)

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW 315
            +   + +SE       +             +              + P + R       
Sbjct: 297 TIMMAVGASEERAPKGHDGAGGSRRGEQSTPRGGHASGSRDSGPGSSRPANARGKRKQGG 356

Query: 316 MAKGIHSSF-LSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                      +           +P+   +   ++   +K
Sbjct: 357 TPPPSPPRGDGAARASSRRPEGAAPASQPEGERKKKRPRK 396


>gi|239637962|ref|ZP_04678923.1| ribosomal protein S4 [Staphylococcus warneri L37603]
 gi|239596525|gb|EEQ79061.1| ribosomal protein S4 [Staphylococcus warneri L37603]
          Length = 200

 Score = 44.8 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 9/49 (18%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+   G+A +RR+  +++    ++V+G  ++  + ++     + V
Sbjct: 93  RLDAVVYSLGLARTRRQARQLVNHGHIEVDGRRVDIPSYSLKPGQEVAV 141


>gi|115665433|ref|XP_001183266.1| PREDICTED: similar to apolipoprotein D; apoD [Strongylocentrotus
           purpuratus]
 gi|115939290|ref|XP_001181564.1| PREDICTED: similar to apolipoprotein D; apoD [Strongylocentrotus
           purpuratus]
          Length = 333

 Score = 44.8 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 15/123 (12%), Positives = 33/123 (26%), Gaps = 5/123 (4%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           ++ + L+     +   E     + P+                  ++    +   S++ G 
Sbjct: 172 INVQKLKRTNQRNCEGEPPRPTEWPVTHRPRPSERPGTDRPRPSEEPETERPRPSEEPGT 231

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSS-----FLSDSGQREENHRRSPSFPSKRSLRRT 350
            + +    P   R   S     +    S           +  E  R  PS   +    R 
Sbjct: 232 DRPRPSEGPGTDRPRPSEEPETERPRPSEEPGTDRPRPSEEPETERPRPSEEPETERPRP 291

Query: 351 SAK 353
           S +
Sbjct: 292 SEE 294



 Score = 42.9 bits (99), Expect = 0.087,   Method: Composition-based stats.
 Identities = 12/117 (10%), Positives = 30/117 (25%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           S++++ + L     +   V                      V       ++  + +   S
Sbjct: 156 SEEVIEDALRKLGEQGINVQKLKRTNQRNCEGEPPRPTEWPVTHRPRPSERPGTDRPRPS 215

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           ++ +   P       ++         +      +  E  R  PS        R S +
Sbjct: 216 EEPETERPRPSEEPGTDRPRPSEGPGTDRPRPSEEPETERPRPSEEPGTDRPRPSEE 272



 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 14/117 (11%), Positives = 22/117 (18%), Gaps = 2/117 (1%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
                 E   P   EE   +   P     T                +        +    
Sbjct: 213 RPSEEPETERPRPSEEPGTDRPRPSEGPGTDRPRPSEEPETERPRPSEEPGTDRPRPSEE 272

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            + +   P                 S+      +  E  R  PS        R S +
Sbjct: 273 PETERPRPSEEPETERP--RPSEEPSTDRPRPSEEPETERPRPSEEPGTDRPRPSEE 327



 Score = 41.3 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 17/154 (11%), Positives = 27/154 (17%), Gaps = 17/154 (11%)

Query: 209 NWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLV 268
              V +L R                             P   E    +   P    ET  
Sbjct: 171 GINVQKLKRT--------NQRNCEGEPPRPTEWPVTHRPRPSERPGTDRPRPSEEPETER 222

Query: 269 RDRPNIISEVPDDFTRMKKNSSQKNGLS----KQKKLATPVHRRNLASNVWMAKGIHSSF 324
                         +        +        + +    P   R   S     +    S 
Sbjct: 223 PRPSEEPGTDRPRPSEGPGTDRPRPSEEPETERPRPSEEPGTDRPRPSEEPETERPRPSE 282

Query: 325 -----LSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                     +     R  PS   +    R S +
Sbjct: 283 EPETERPRPSEEPSTDRPRPSEEPETERPRPSEE 316


>gi|111220573|ref|YP_711367.1| 30S ribosomal protein S4 [Frankia alni ACN14a]
 gi|123339013|sp|Q0RRP4|RS4_FRAAA RecName: Full=30S ribosomal protein S4
 gi|111148105|emb|CAJ59773.1| 30S ribosomal subunit protein S4 [Frankia alni ACN14a]
          Length = 209

 Score = 44.8 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           R+  V+ R G A SR    + +    V+VNG  ++  +  +   D +E+    
Sbjct: 99  RLDNVVYRGGFAPSRDAARQAVRHGHVQVNGRKVDIPSYRISENDIVEIAPKA 151


>gi|269792997|ref|YP_003317901.1| radical SAM enzyme, Cfr family [Thermanaerovibrio acidaminovorans
           DSM 6589]
 gi|269100632|gb|ACZ19619.1| radical SAM enzyme, Cfr family [Thermanaerovibrio acidaminovorans
           DSM 6589]
          Length = 462

 Score = 44.8 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 18/111 (16%), Positives = 25/111 (22%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
             G     E       P   S+           +         K S   +G S++     
Sbjct: 348 PQGGQRGGEQAPKAPGPAGDSKPDRGPNKGGRRQASASKGEGGKASGGDSGGSRRGGHKK 407

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           P      A      +G        SG       R P     R  R   A +
Sbjct: 408 PAAGGRSAPEGNRPRGEGPGKRDRSGPGPAGRPRGPRGNGPRGKRPGGAGR 458



 Score = 40.5 bits (93), Expect = 0.40,   Method: Composition-based stats.
 Identities = 15/115 (13%), Positives = 30/115 (26%), Gaps = 1/115 (0%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           LR Q+ P + E +          +        +   +   +    ++ S+ K    K   
Sbjct: 335 LRRQVSPGIQEASPQGGQRGGEQAPKAPGPAGDSKPDRGPNKGGRRQASASKGEGGKASG 394

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS-PSFPSKRSLRRTSAKK 354
             +   RR                    G+      RS P    +    R +  +
Sbjct: 395 GDSGGSRRGGHKKPAAGGRSAPEGNRPRGEGPGKRDRSGPGPAGRPRGPRGNGPR 449



 Score = 39.0 bits (89), Expect = 1.00,   Method: Composition-based stats.
 Identities = 9/86 (10%), Positives = 18/86 (20%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G      A           ++    R           +  + N  +  G  K+ +     
Sbjct: 377 GGRRQASASKGEGGKASGGDSGGSRRGGHKKPAAGGRSAPEGNRPRGEGPGKRDRSGPGP 436

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQR 331
             R         +G        +  R
Sbjct: 437 AGRPRGPRGNGPRGKRPGGAGRNKGR 462



 Score = 35.9 bits (81), Expect = 9.2,   Method: Composition-based stats.
 Identities = 14/115 (12%), Positives = 25/115 (21%), Gaps = 4/115 (3%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +  G       QV+      S +   R                      K G  +     
Sbjct: 327 DVGGACGQLRRQVSPGIQEASPQGGQRGGEQAPKAPGPAGDSKPDRGPNKGGRRQASASK 386

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL----RRTSAK 353
               + +   +    +G H    +      E +R     P KR           +
Sbjct: 387 GEGGKASGGDSGGSRRGGHKKPAAGGRSAPEGNRPRGEGPGKRDRSGPGPAGRPR 441


>gi|150392132|ref|YP_001322181.1| ribosomal protein S4 [Alkaliphilus metalliredigens QYMF]
 gi|171460826|sp|A6TWF4|RS4A_ALKMQ RecName: Full=30S ribosomal protein S4 A
 gi|149951994|gb|ABR50522.1| ribosomal protein S4 [Alkaliphilus metalliredigens QYMF]
          Length = 207

 Score = 44.8 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 15/67 (22%), Positives = 28/67 (41%), Gaps = 1/67 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  ++ R G+AS R E  +++      VNG  ++  +  V + D + V        +  
Sbjct: 99  RLDNLVYRLGLASSRAEARQLVVHGHFTVNGGKVDIPSYLVKAGDAVAVSEKSTNSPKFK 158

Query: 74  RLWLYHK 80
            L    K
Sbjct: 159 ELKENFK 165


>gi|332637745|ref|ZP_08416608.1| 30S ribosomal protein S4 [Weissella cibaria KACC 11862]
          Length = 203

 Score = 44.8 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+AS R++  +++    + V+G  ++  +  V     I V
Sbjct: 94  RLDNIVYRLGLASTRQQARQLVNHGHILVDGKRVDIPSYEVTVGQEISV 142


>gi|281342698|gb|EFB18282.1| hypothetical protein PANDA_016315 [Ailuropoda melanoleuca]
          Length = 2138

 Score = 44.8 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 10/120 (8%), Positives = 26/120 (21%), Gaps = 1/120 (0%)

Query: 235  EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
             +  +           +    +  +   S                   +   ++ + + G
Sbjct: 1834 RLKGREEDAYPQREDPQARPQDGPSGEDSPSERQAPPSQGPRSTKRRASWTSRDVAGQGG 1893

Query: 295  LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS-KRSLRRTSAK 353
             S  +    P  +R    +V +A                +   +P     K    R    
Sbjct: 1894 ESDSESTQKPPAKRPTLQDVRLAPSPRPRGEEGPEAPTPSLPAAPGDTGVKEPPPRAPEA 1953


>gi|226311930|ref|YP_002771824.1| hemolysin A [Brevibacillus brevis NBRC 100599]
 gi|226094878|dbj|BAH43320.1| putative hemolysin A [Brevibacillus brevis NBRC 100599]
          Length = 272

 Score = 44.8 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 15/177 (8%), Positives = 41/177 (23%), Gaps = 2/177 (1%)

Query: 10  NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +   +R+  ++   G   +R + +  +    V+V G   ++          I V G  + 
Sbjct: 2   SVRKERIDVLLVERGHYETREKAKAAVMAGLVQVAGDRCDKPGTKFAEDVAITVKGE-VH 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                      K + +            +  +        +  G   +    +       
Sbjct: 61  PYVSRGGLKLEKALRVFEIDMKDRVMMDIGASTGGFTDCALQNGARLVYAIDVGYGQLAW 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            L +   +   +      +       +           I       +     T  G 
Sbjct: 121 SLRQDERVVVMERTNFRHMDPDAFEHERPNAASIDVSFISLRLILPVLYRFLTDGGD 177


>gi|167768372|ref|ZP_02440425.1| hypothetical protein CLOSS21_02929 [Clostridium sp. SS2/1]
 gi|317497689|ref|ZP_07956004.1| S4 domain-containing protein [Lachnospiraceae bacterium
          5_1_63FAA]
 gi|167709896|gb|EDS20475.1| hypothetical protein CLOSS21_02929 [Clostridium sp. SS2/1]
 gi|291560345|emb|CBL39145.1| Ribosome-associated heat shock protein implicated in the
          recycling of the 50S subunit (S4 paralog)
          [butyrate-producing bacterium SSC/2]
 gi|316895023|gb|EFV17190.1| S4 domain-containing protein [Lachnospiraceae bacterium
          5_1_63FAA]
          Length = 79

 Score = 44.8 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 14/48 (29%), Positives = 20/48 (41%), Gaps = 2/48 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+ K +  + +  RR       +  RV VNG   + A  NV   D I
Sbjct: 1  MRLDKFLKVSRLIKRRTVANEACSAGRVLVNGKAAK-AGTNVKPGDRI 47


>gi|121603259|ref|YP_980588.1| 30S ribosomal protein S4 [Polaromonas naphthalenivorans CJ2]
 gi|152112243|sp|A1VJ39|RS4_POLNA RecName: Full=30S ribosomal protein S4
 gi|120592228|gb|ABM35667.1| SSU ribosomal protein S4P [Polaromonas naphthalenivorans CJ2]
          Length = 207

 Score = 44.8 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V + D I V   
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAMTVNGQSVNIPSYMVKAGDVIAVRDK 149


>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 = 44.8 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 17/161 (10%), Positives = 53/161 (32%), Gaps = 3/161 (1%)

Query: 56  STDHIEVD---GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
             D I ++   G+P+  +           +       +        + L    S +  V 
Sbjct: 37  DEDIIVINKAAGMPIHPSLNNYRNSLANALMWYYEQQNKPFIFRCTNRLDRDTSGLTVVA 96

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           +  +++  L  +T    + R         +  +    +  + +   +L+++ I  +   +
Sbjct: 97  KHMVSSNILSSMTARHQIEREYLAIVRGHVTPFEGTINAPIGRTGSSLIERKIDFENGEH 156

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                    +K   + V++ L  G+  +I+   +   + + 
Sbjct: 157 AITHYHTVFEKNGLSLVSLILETGRTHQIRVHMKHLGFPLI 197


>gi|294792833|ref|ZP_06757980.1| ribosomal protein S4 [Veillonella sp. 6_1_27]
 gi|294794587|ref|ZP_06759723.1| ribosomal protein S4 [Veillonella sp. 3_1_44]
 gi|294454917|gb|EFG23290.1| ribosomal protein S4 [Veillonella sp. 3_1_44]
 gi|294456732|gb|EFG25095.1| ribosomal protein S4 [Veillonella sp. 6_1_27]
          Length = 195

 Score = 44.8 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  ++ R G   S R+  +M+    + VNG  ++  + +    D IE+
Sbjct: 86  QRLDNLVYRIGFGNSIRQARQMVNHGHILVNGRRVDIPSFSCKPGDVIEL 135


>gi|302510661|ref|XP_003017282.1| hypothetical protein ARB_04161 [Arthroderma benhamiae CBS 112371]
 gi|291180853|gb|EFE36637.1| hypothetical protein ARB_04161 [Arthroderma benhamiae CBS 112371]
          Length = 526

 Score = 44.8 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 1/56 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+   I RA  AS  R+  + +    V VNG  ++     +   D  +VD   +  
Sbjct: 135 RLDVAIFRAMFASSTRQARQFVIHGGVTVNGKKMQYPGYLLNPGDMFQVDPERVMY 190


>gi|188584474|ref|YP_001927919.1| OmpA/MotB domain protein [Methylobacterium populi BJ001]
 gi|179347972|gb|ACB83384.1| OmpA/MotB domain protein [Methylobacterium populi BJ001]
          Length = 718

 Score = 44.8 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 13/107 (12%), Positives = 25/107 (23%), Gaps = 2/107 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R         + + +        E   R       E P+   R ++    +         
Sbjct: 106 RPARPERPAPQERPDRQERPERQERPDRQERPDRQERPERQERPERQERPERPERAPAPA 165

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
             P   R+       A    +       +RE   R +P+        
Sbjct: 166 QRPD--RSEERPTPPAARERTPDREAPARRETPEREAPARREAPDRP 210



 Score = 39.8 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 7/102 (6%), Positives = 18/102 (17%), Gaps = 2/102 (1%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
                             R    +    D         +     +  +   P  +     
Sbjct: 74  PPARERPDRPERPERPEPRQAPAARERPDPAERPARPERPAPQERPDRQERPERQERPDR 133

Query: 313 NVWMAKGIHSSF--LSDSGQREENHRRSPSFPSKRSLRRTSA 352
                +          +  +R E   R+P+   +        
Sbjct: 134 QERPDRQERPERQERPERQERPERPERAPAPAQRPDRSEERP 175



 Score = 36.7 bits (83), Expect = 5.9,   Method: Composition-based stats.
 Identities = 11/116 (9%), Positives = 22/116 (18%), Gaps = 5/116 (4%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R +  P      +   D    +             E PD   R  +    +      ++ 
Sbjct: 170 RSEERPTPPAARERTPDREAPARRETPEREAPARREAPDRPDRDGQTRPARPADRDGERP 229

Query: 302 ATPVHRRNLASNVWMAKGIHSSFL-----SDSGQREENHRRSPSFPSKRSLRRTSA 352
                +R                       +  Q      + P  P +        
Sbjct: 230 DAAPAQRRAPEAPTPPAAERPERPTPPSVPNPAQPGTPPNQRPGVPGRPVAPNPPQ 285


>gi|134302562|ref|YP_001122532.1| 30S ribosomal protein S4 [Francisella tularensis subsp. tularensis
           WY96-3418]
 gi|152060949|sp|A4IZR0|RS4_FRATW RecName: Full=30S ribosomal protein S4
 gi|134050339|gb|ABO47410.1| ribosomal protein S4 [Francisella tularensis subsp. tularensis
           WY96-3418]
          Length = 206

 Score = 44.8 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 29/73 (39%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G A +R E  +++  + + VNG      +  V + D + V     ++    
Sbjct: 97  RLDNVVYRMGFAATRAEARQLVVHKGIMVNGHTCNVPSAQVKAGDVVTVREKAKKQLRIQ 156

Query: 74  RLWLYHKPIGLVT 86
                 K    ++
Sbjct: 157 NAVELAKHRKELS 169


>gi|20302774|gb|AAM18895.1|AF391295_4 unknown [Branchiostoma floridae]
          Length = 651

 Score = 44.8 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 25/161 (15%), Positives = 36/161 (22%), Gaps = 13/161 (8%)

Query: 207 FFNWKVNRLI--R--ISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIY 262
                V  L   R  I Y    L   L    + V    L  +                  
Sbjct: 471 QLAVDVLALHALRQMIRYADNYLDDHLDRHIQMVRADTLSPRQESEEDGSLPRTPATERE 530

Query: 263 SSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT----PVHRRNLASNVWMAK 318
            S    R R    S                +G  + +        P    +         
Sbjct: 531 DSPHQDRPRKEKASYANKRHVPHPSWEKPGSGSRRSQPPTRTSVTPRTHSSQRPETKEDD 590

Query: 319 GIHSSFLSDSGQR-----EENHRRSPSFPSKRSLRRTSAKK 354
              S       +      EE+ RR PS  SK+S  +    +
Sbjct: 591 PPRSRSSPPKSRAESTKEEEDQRRPPSTASKKSTPKERRPE 631


>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 = 44.8 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 31/243 (12%), Positives = 71/243 (29%), Gaps = 39/243 (16%)

Query: 8   QENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
                P RV K +  R   A+R ++++      ++ N  ++++    V   D I V    
Sbjct: 24  DTGQKPLRVDKFLMTRIRNATRNKIQQAARDGNIRANEQVIKQ-NYRVKPGDTIRVLFEH 82

Query: 67  ---------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                          +   +   L +      +V         + V   +  +    ++ 
Sbjct: 83  PPYENLLLPEDIPLDIVYEDEVLLVVNKPAGMVVHPGHGNYTGTLVNALVHHLDQLPLNS 142

Query: 112 -------GRLDINTEGLLLLTNDGGLARVLELP-------------STQWLRVYRVRFHG 151
                   R+D  T GLL++         L                    +        G
Sbjct: 143 DNRPGLVHRIDKETSGLLVIAKTEAAMANLARQFFDKTTRREYLALVWGNVADDSGTVEG 202

Query: 152 QVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            + ++  N L+  +   G    +      ++ + G    V+  L  G+  +I+   +   
Sbjct: 203 PIGRNPKNRLQMQVFPDGSQGKEAVTHYRVEERLGYVTLVSCRLETGRTHQIRVHMQHIG 262

Query: 210 WKV 212
             +
Sbjct: 263 HTI 265


>gi|301782447|ref|XP_002926638.1| PREDICTED: general transcription factor 3C polypeptide 1-like
            [Ailuropoda melanoleuca]
          Length = 2124

 Score = 44.8 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 10/120 (8%), Positives = 26/120 (21%), Gaps = 1/120 (0%)

Query: 235  EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
             +  +           +    +  +   S                   +   ++ + + G
Sbjct: 1820 RLKGREEDAYPQREDPQARPQDGPSGEDSPSERQAPPSQGPRSTKRRASWTSRDVAGQGG 1879

Query: 295  LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS-KRSLRRTSAK 353
             S  +    P  +R    +V +A                +   +P     K    R    
Sbjct: 1880 ESDSESTQKPPAKRPTLQDVRLAPSPRPRGEEGPEAPTPSLPAAPGDTGVKEPPPRAPEA 1939


>gi|171462904|ref|YP_001797017.1| ribosomal protein S4 [Polynucleobacter necessarius subsp.
           necessarius STIR1]
 gi|226699102|sp|B1XSS6|RS4_POLNS RecName: Full=30S ribosomal protein S4
 gi|171192442|gb|ACB43403.1| ribosomal protein S4 [Polynucleobacter necessarius subsp.
           necessarius STIR1]
          Length = 207

 Score = 44.8 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++   + +NG  +   ++ V   D + +
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHCAILLNGNPVNIPSIQVKPGDVVAI 146


>gi|152978165|ref|YP_001343794.1| 30S ribosomal protein S4 [Actinobacillus succinogenes 130Z]
 gi|171704198|sp|A6VLL2|RS4_ACTSZ RecName: Full=30S ribosomal protein S4
 gi|150839888|gb|ABR73859.1| ribosomal protein S4 [Actinobacillus succinogenes 130Z]
          Length = 206

 Score = 44.8 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R E  ++++ + + VNG ++   +  V   D + +
Sbjct: 97  RLDNVVYRMGFAATRAEARQLVSHKAIVVNGRVVNIPSFQVSVDDVVAI 145


>gi|307107657|gb|EFN55899.1| hypothetical protein CHLNCDRAFT_57787 [Chlorella variabilis]
          Length = 2226

 Score = 44.8 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 10/119 (8%), Positives = 27/119 (22%), Gaps = 15/119 (12%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           ++          S+    R R     +  +        S  ++G   +   ++    R  
Sbjct: 187 KQGSGKEQRRPRSASPPRRQRSGSHEQARERRGSGGSASRSRHGSPSRAPRSSGSSPRPR 246

Query: 311 ASNVWMAKGI---------------HSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             +                               +       +P+ P +RS +     +
Sbjct: 247 DKDRGRPARAEGGGEGQRRRRSASLPREEFQPPTRSPPGSAEAPAGPGRRSKQPQPQAR 305



 Score = 44.0 bits (102), Expect = 0.031,   Method: Composition-based stats.
 Identities = 11/96 (11%), Positives = 32/96 (33%), Gaps = 2/96 (2%)

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           +  H+      +   P      L +         P   +  ++  S  +  +++++ +  
Sbjct: 163 VRGHMGPPPAADFRPPPGFDTLLSKQGSGKEQRRPRSASPPRRQRSGSHEQARERRGSGG 222

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
              R+   +   A    SS  S   + ++  R + +
Sbjct: 223 SASRSRHGSPSRAP--RSSGSSPRPRDKDRGRPARA 256


>gi|288553742|ref|YP_003425677.1| 30S ribosomal protein S4 [Bacillus pseudofirmus OF4]
 gi|288544902|gb|ADC48785.1| 30S ribosomal protein S4 [Bacillus pseudofirmus OF4]
          Length = 200

 Score = 44.8 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR   +++    + V+G  ++  +  V     I +
Sbjct: 93  RLDNLVYRMGLARTRRAARQLVNHGHIMVDGGRVDIPSYRVKPGQTIAL 141


>gi|270291002|ref|ZP_06197225.1| 30S ribosomal protein S4 [Pediococcus acidilactici 7_4]
 gi|304385274|ref|ZP_07367619.1| 30S ribosomal protein S4 [Pediococcus acidilactici DSM 20284]
 gi|270280398|gb|EFA26233.1| 30S ribosomal protein S4 [Pediococcus acidilactici 7_4]
 gi|304328481|gb|EFL95702.1| 30S ribosomal protein S4 [Pediococcus acidilactici DSM 20284]
          Length = 202

 Score = 44.8 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A+ RR+  +++    + V+G  ++  +  V     I V
Sbjct: 94  RLDNMVYRLGLATTRRQARQLVNHGHITVDGKRVDIPSYEVEIGQVIGV 142


>gi|237749539|ref|ZP_04580019.1| small subunit ribosomal protein S4 [Oxalobacter formigenes OXCC13]
 gi|229380901|gb|EEO30992.1| small subunit ribosomal protein S4 [Oxalobacter formigenes OXCC13]
          Length = 207

 Score = 44.8 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ Q + VNG ++   +  V   D I +
Sbjct: 98  RLDNVVYRMGFGSTRAESRQLVSHQALMVNGKVVNIPSYLVKPEDVITI 146


>gi|197122707|ref|YP_002134658.1| Fis family transcriptional regulator [Anaeromyxobacter sp. K]
 gi|196172556|gb|ACG73529.1| transcriptional regulator, Fis family [Anaeromyxobacter sp. K]
          Length = 555

 Score = 44.8 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 8/94 (8%), Positives = 18/94 (19%), Gaps = 2/94 (2%)

Query: 261 IYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGI 320
                +         +         +    ++    +      P  R             
Sbjct: 336 PAGDASAPEWPGRRFARPERADRAPRGAGGERPPRRRTPGAGRPPERGGRPPRTGDRPPR 395

Query: 321 HSSFLSDSGQ--REENHRRSPSFPSKRSLRRTSA 352
             +    S Q  R     R  + P +   R  + 
Sbjct: 396 TGAGRPASPQPWRPRTPDRHGAGPGRGPARPGAG 429



 Score = 44.0 bits (102), Expect = 0.030,   Method: Composition-based stats.
 Identities = 12/114 (10%), Positives = 23/114 (20%), Gaps = 1/114 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R  L      +A          +     DR    +       R    + +      +   
Sbjct: 329 RLGLELGPAGDASAPEWPGRRFARPERADRAPRGAGGERPPRRRTPGAGRPPERGGRPPR 388

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS-KRSLRRTSAKK 354
                 R  A      +          G         P     +RS    ++ +
Sbjct: 389 TGDRPPRTGAGRPASPQPWRPRTPDRHGAGPGRGPARPGAGGVERSPAAGASPR 442


>gi|46580462|ref|YP_011270.1| hypothetical protein DVU2057 [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|46449881|gb|AAS96530.1| conserved hypothetical protein [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|311234205|gb|ADP87059.1| PSP1 domain protein [Desulfovibrio vulgaris RCH1]
          Length = 487

 Score = 44.8 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 13/114 (11%), Positives = 29/114 (25%)

Query: 229 LAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
             G  + +   + R  L        ++ +    +      R         P    R +  
Sbjct: 229 NRGPVKVLRANMFRNSLMAFTDTGEEIEISLDEWQQLDPRRPDQQPQQARPPRRDRPEGG 288

Query: 289 SSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
           S++     +    ++               G  +   SD G R +   R+    
Sbjct: 289 SARDGNGDRAPAPSSDRAAGATGGEAARHGGGRAGERSDRGGRPDRAERADRRG 342



 Score = 37.9 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 10/109 (9%), Positives = 20/109 (18%), Gaps = 2/109 (1%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             +++  +   +Q                           P+             ++   
Sbjct: 261 EWQQLDPRRPDQQPQQARPPRRDRPEGGSARDGNGDRAPAPSSDRAAGATGGEAARHGGG 320

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
           + G            R   A    M  G             E    +PS
Sbjct: 321 RAGERSD--RGGRPDRAERADRRGMPHGDVPGSGETPPAGGEAEADAPS 367


>gi|238018666|ref|ZP_04599092.1| hypothetical protein VEIDISOL_00510 [Veillonella dispar ATCC 17748]
 gi|269798510|ref|YP_003312410.1| ribosomal protein S4 [Veillonella parvula DSM 2008]
 gi|282849905|ref|ZP_06259288.1| ribosomal protein S4 [Veillonella parvula ATCC 17745]
 gi|237865137|gb|EEP66427.1| hypothetical protein VEIDISOL_00510 [Veillonella dispar ATCC 17748]
 gi|269095139|gb|ACZ25130.1| ribosomal protein S4 [Veillonella parvula DSM 2008]
 gi|282580342|gb|EFB85742.1| ribosomal protein S4 [Veillonella parvula ATCC 17745]
          Length = 195

 Score = 44.8 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  ++ R G   S R+  +M+    + VNG  ++  + +    D IE+
Sbjct: 86  QRLDNLVYRIGFGNSIRQARQMVNHGHILVNGRRVDIPSFSCKPGDVIEL 135


>gi|223042027|ref|ZP_03612208.1| 30S ribosomal protein S4 [Actinobacillus minor 202]
 gi|240948151|ref|ZP_04752554.1| 30S ribosomal protein S4 [Actinobacillus minor NM305]
 gi|198246529|gb|ACH82221.1| 30S ribosomal protein S4 [Actinobacillus minor 202]
 gi|240297504|gb|EER48011.1| 30S ribosomal protein S4 [Actinobacillus minor NM305]
          Length = 208

 Score = 44.8 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R E  ++++ + + VNG ++   +  V   D + V
Sbjct: 99  RLDNVVYRMGFAATRAEARQLVSHKSIVVNGRVVNIPSFQVSVDDVVAV 147


>gi|160914699|ref|ZP_02076913.1| hypothetical protein EUBDOL_00706 [Eubacterium dolichum DSM 3991]
 gi|158433239|gb|EDP11528.1| hypothetical protein EUBDOL_00706 [Eubacterium dolichum DSM 3991]
          Length = 94

 Score = 44.8 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRREV-ERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  A I  RR V + +   +RV VNG + +  A +V   D ++V
Sbjct: 1  MRLDKYLKTARILKRRSVSKELADNERVYVNGRVAK-PATDVKIGDIVKV 49


>gi|16272743|ref|NP_438961.1| 30S ribosomal protein S4 [Haemophilus influenzae Rd KW20]
 gi|260579893|ref|ZP_05847723.1| ribosomal protein S4 [Haemophilus influenzae RdAW]
 gi|1173260|sp|P44373|RS4_HAEIN RecName: Full=30S ribosomal protein S4
 gi|1573812|gb|AAC22460.1| ribosomal protein S4 (rpS4) [Haemophilus influenzae Rd KW20]
 gi|260093177|gb|EEW77110.1| ribosomal protein S4 [Haemophilus influenzae RdAW]
 gi|301169520|emb|CBW29121.1| 30S ribosomal subunit protein S4 [Haemophilus influenzae 10810]
          Length = 206

 Score = 44.8 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A+ R E  ++++ + + VNG ++   +  V   D + +
Sbjct: 97  RLDNVVYRMGFATTRAEARQLVSHKAIVVNGRVVNIPSFQVSVNDVVAI 145


>gi|68249397|ref|YP_248509.1| 30S ribosomal protein S4 [Haemophilus influenzae 86-028NP]
 gi|145628304|ref|ZP_01784105.1| 30S ribosomal protein S4 [Haemophilus influenzae 22.1-21]
 gi|145630548|ref|ZP_01786328.1| 30S ribosomal protein S4 [Haemophilus influenzae R3021]
 gi|145632160|ref|ZP_01787895.1| 30S ribosomal protein S4 [Haemophilus influenzae 3655]
 gi|145634787|ref|ZP_01790495.1| 30S ribosomal protein S4 [Haemophilus influenzae PittAA]
 gi|145636640|ref|ZP_01792307.1| 30S ribosomal protein S4 [Haemophilus influenzae PittHH]
 gi|145638397|ref|ZP_01794007.1| 30S ribosomal protein S4 [Haemophilus influenzae PittII]
 gi|145640900|ref|ZP_01796482.1| 30S ribosomal protein S4 [Haemophilus influenzae R3021]
 gi|148826554|ref|YP_001291307.1| 30S ribosomal protein S4 [Haemophilus influenzae PittEE]
 gi|148827990|ref|YP_001292743.1| 30S ribosomal protein S4 [Haemophilus influenzae PittGG]
 gi|229844669|ref|ZP_04464808.1| 30S ribosomal protein S4 [Haemophilus influenzae 6P18H1]
 gi|229845852|ref|ZP_04465964.1| 30S ribosomal protein S4 [Haemophilus influenzae 7P49H1]
 gi|260581618|ref|ZP_05849415.1| ribosomal protein S4 [Haemophilus influenzae NT127]
 gi|319775264|ref|YP_004137752.1| 30S ribosomal subunit protein S4 [Haemophilus influenzae F3047]
 gi|319897704|ref|YP_004135901.1| 30S ribosomal subunit protein s4 [Haemophilus influenzae F3031]
 gi|329122807|ref|ZP_08251379.1| 30S ribosomal protein S4 [Haemophilus aegyptius ATCC 11116]
 gi|81336176|sp|Q4QM98|RS4_HAEI8 RecName: Full=30S ribosomal protein S4
 gi|172048051|sp|A5UDS3|RS4_HAEIE RecName: Full=30S ribosomal protein S4
 gi|172048057|sp|A5UHV4|RS4_HAEIG RecName: Full=30S ribosomal protein S4
 gi|68057596|gb|AAX87849.1| 30S ribosomal protein S4 [Haemophilus influenzae 86-028NP]
 gi|144980079|gb|EDJ89738.1| 30S ribosomal protein S4 [Haemophilus influenzae 22.1-21]
 gi|144983938|gb|EDJ91380.1| 30S ribosomal protein S4 [Haemophilus influenzae R3021]
 gi|144987067|gb|EDJ93597.1| 30S ribosomal protein S4 [Haemophilus influenzae 3655]
 gi|145267953|gb|EDK07949.1| 30S ribosomal protein S4 [Haemophilus influenzae PittAA]
 gi|145270166|gb|EDK10102.1| 30S ribosomal protein S4 [Haemophilus influenzae PittHH]
 gi|145272726|gb|EDK12633.1| 30S ribosomal protein S4 [Haemophilus influenzae PittII]
 gi|145274414|gb|EDK14278.1| 30S ribosomal protein S4 [Haemophilus influenzae 22.4-21]
 gi|148716714|gb|ABQ98924.1| 30S ribosomal protein S4 [Haemophilus influenzae PittEE]
 gi|148719232|gb|ABR00360.1| 30S ribosomal protein S4 [Haemophilus influenzae PittGG]
 gi|229810856|gb|EEP46573.1| 30S ribosomal protein S4 [Haemophilus influenzae 7P49H1]
 gi|229812383|gb|EEP48073.1| 30S ribosomal protein S4 [Haemophilus influenzae 6P18H1]
 gi|260095211|gb|EEW79102.1| ribosomal protein S4 [Haemophilus influenzae NT127]
 gi|309751537|gb|ADO81521.1| 30S ribosomal protein S4 [Haemophilus influenzae R2866]
 gi|309973707|gb|ADO96908.1| 30S ribosomal protein S4 [Haemophilus influenzae R2846]
 gi|317433210|emb|CBY81585.1| 30S ribosomal subunit protein S4 [Haemophilus influenzae F3031]
 gi|317449855|emb|CBY86066.1| 30S ribosomal subunit protein S4 [Haemophilus influenzae F3047]
 gi|327472071|gb|EGF17509.1| 30S ribosomal protein S4 [Haemophilus aegyptius ATCC 11116]
          Length = 206

 Score = 44.8 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R E  ++++ + + VNG ++   +  V   D + +
Sbjct: 97  RLDNVVYRMGFAATRAEARQLVSHKAIVVNGRVVNIPSFQVSVNDVVAI 145


>gi|327188063|gb|EGE55290.1| hemolysin A [Rhizobium etli CNPAF512]
          Length = 261

 Score = 44.8 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 9/48 (18%), Positives = 22/48 (45%), Gaps = 1/48 (2%)

Query: 9  ENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVM 55
           +   QR+ +++   G  ASR      + +  V++ G ++ +A   + 
Sbjct: 15 SDQNSQRLDQLLVSRGLFASRSRARDAVQRGTVRIGGQVVTKAGALIS 62


>gi|283769109|ref|ZP_06342014.1| ribosomal protein S4 [Bulleidia extructa W1219]
 gi|283104295|gb|EFC05673.1| ribosomal protein S4 [Bulleidia extructa W1219]
          Length = 200

 Score = 44.8 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 9/56 (16%), Positives = 23/56 (41%), Gaps = 1/56 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+  ++ R G A +R+   +++    + V+G  +   +  +     I +    L  
Sbjct: 93  RLDNIVYRMGFARTRKAARQLVNHGHILVDGKKVNIPSALIKPGQEISLKEKSLNL 148


>gi|255948696|ref|XP_002565115.1| Pc22g11690 [Penicillium chrysogenum Wisconsin 54-1255]
 gi|211592132|emb|CAP98457.1| Pc22g11690 [Penicillium chrysogenum Wisconsin 54-1255]
          Length = 457

 Score = 44.8 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 1/65 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+   I RA  AS  R+  + +    V VNG  ++  +  +   D  +VD   +  A   
Sbjct: 124 RLDVAIFRALFASSARQARQFVIHGAVTVNGQKMKHPSYLLNPGDLFQVDPDRVLYATGH 183

Query: 74  RLWLY 78
               Y
Sbjct: 184 TKTPY 188


>gi|194227934|ref|XP_001917939.1| PREDICTED: hypothetical protein [Equus caballus]
          Length = 665

 Score = 44.8 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 16/112 (14%), Positives = 22/112 (19%), Gaps = 7/112 (6%)

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
               A         +S      R            R + +S       ++     P  RR
Sbjct: 358 RPAPAPGPAVRRRRASSPGPAVRRRPAPAPGPAVRRRRASSPGPAVRRRRAPAPGPAVRR 417

Query: 309 NLASNVWM-------AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              S           A G                RR    P     RR +  
Sbjct: 418 RAPSPGPAVRRRPAPAPGPAVRRRPAPAPGPAVRRRRAPSPGPAVRRRRAPS 469



 Score = 44.4 bits (103), Expect = 0.024,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 23/108 (21%), Gaps = 4/108 (3%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                     +       +           +  P    R +  S       +      P 
Sbjct: 307 ALRSPASEPRDAVLRRRPAPAPGPAVRRRRAPSPGPAVRRRAPSPGPAVRCRPAPAPGPA 366

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            RR  AS+   A     +            RR  S P     RR +  
Sbjct: 367 VRRRRASSPGPAVRRRPA----PAPGPAVRRRRASSPGPAVRRRRAPA 410



 Score = 43.2 bits (100), Expect = 0.057,   Method: Composition-based stats.
 Identities = 16/111 (14%), Positives = 25/111 (22%), Gaps = 6/111 (5%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                +         +       R    S       R    +       ++     P  R
Sbjct: 345 RRRAPSPGPAVRCRPAPAPGPAVRRRRASSPGPAVRRRPAPAPGPAVRRRRASSPGPAVR 404

Query: 308 RNLASNVWMAKGIH-SSFLSDSGQREENH-----RRSPSFPSKRSLRRTSA 352
           R  A     A      S      +R         RR P+     ++RR  A
Sbjct: 405 RRRAPAPGPAVRRRAPSPGPAVRRRPAPAPGPAVRRRPAPAPGPAVRRRRA 455



 Score = 43.2 bits (100), Expect = 0.063,   Method: Composition-based stats.
 Identities = 13/106 (12%), Positives = 21/106 (19%), Gaps = 5/106 (4%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                          +       R            R + +S       +      P  R
Sbjct: 333 RRRRAPSPGPAVRRRAPSPGPAVRCRPAPAPGPAVRRRRASSPGPAVRRRPAPAPGPAVR 392

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           R  AS+   A     +       R       P+       RR +  
Sbjct: 393 RRRASSPGPAVRRRRAPAPGPAVRRRAPSPGPAV-----RRRPAPA 433



 Score = 40.5 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 12/97 (12%), Positives = 17/97 (17%), Gaps = 4/97 (4%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                           + +         +  P    R +  S       +      P  R
Sbjct: 380 RRRPAPAPGPAVRRRRASSPGPAVRRRRAPAPGPAVRRRAPSPGPAVRRRPAPAPGPAVR 439

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           R  A     A G                RR    P  
Sbjct: 440 RRPAP----APGPAVRRRRAPSPGPAVRRRRAPSPGP 472



 Score = 40.2 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 9/109 (8%), Positives = 17/109 (15%), Gaps = 2/109 (1%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                    +     SS      R    +  P    R   +        +       V R
Sbjct: 358 RPAPAPGPAVRRRRASSPGPAVRRRPAPAPGPAVRRRRASSPGPAVRRRRAPAPGPAVRR 417

Query: 308 R--NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           R  +    V                            +         ++
Sbjct: 418 RAPSPGPAVRRRPAPAPGPAVRRRPAPAPGPAVRRRRAPSPGPAVRRRR 466



 Score = 39.8 bits (91), Expect = 0.58,   Method: Composition-based stats.
 Identities = 8/107 (7%), Positives = 16/107 (14%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           +R +         +         +    R      +              ++        
Sbjct: 367 VRRRRASSPGPAVRRRPAPAPGPAVRRRRASSPGPAVRRRRAPAPGPAVRRRAPSPGPAV 426

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
              P      A     A     +             R    PS    
Sbjct: 427 RRRPAPAPGPAVRRRPAPAPGPAVRRRRAPSPGPAVRRRRAPSPGPA 473



 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 16/111 (14%), Positives = 31/111 (27%), Gaps = 7/111 (6%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
             +A     A +           +  SE  D   R +   +    + +++  +     R 
Sbjct: 287 RSQANATGPALLSRRTPPGPALRSPASEPRDAVLRRRPAPAPGPAVRRRRAPSPGPAVRR 346

Query: 310 LASNVWMAKGIHSSFLSDSGQREENH-------RRSPSFPSKRSLRRTSAK 353
            A +   A     +       R           RR P+     ++RR  A 
Sbjct: 347 RAPSPGPAVRCRPAPAPGPAVRRRRASSPGPAVRRRPAPAPGPAVRRRRAS 397


>gi|229916421|ref|YP_002885067.1| ribosomal protein S4 [Exiguobacterium sp. AT1b]
 gi|259495280|sp|C4L4A0|RS4_EXISA RecName: Full=30S ribosomal protein S4
 gi|229467850|gb|ACQ69622.1| ribosomal protein S4 [Exiguobacterium sp. AT1b]
          Length = 199

 Score = 44.8 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR   +++    + V+G  ++ A+  V     I V
Sbjct: 92  RLDNLVYRFGLARTRRGARQLVNHGHITVDGSRVDIASYRVKPGQVIAV 140


>gi|126651345|ref|ZP_01723552.1| 30S ribosomal protein S4 [Bacillus sp. B14905]
 gi|169829591|ref|YP_001699749.1| 30S ribosomal protein S4 [Lysinibacillus sphaericus C3-41]
 gi|226699085|sp|B1HX43|RS4_LYSSC RecName: Full=30S ribosomal protein S4
 gi|126591874|gb|EAZ85957.1| 30S ribosomal protein S4 [Bacillus sp. B14905]
 gi|168994079|gb|ACA41619.1| 30S ribosomal protein S4 [Lysinibacillus sphaericus C3-41]
          Length = 200

 Score = 44.8 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR   +++    + V+G  ++  + +V     I +
Sbjct: 93  RLDNLVYRLGLARTRRGARQLVNHGHILVDGKRVDIPSFSVKPGQTISL 141


>gi|157693366|ref|YP_001487828.1| 30S ribosomal protein S4 [Bacillus pumilus SAFR-032]
 gi|172046056|sp|A8FGA1|RS4_BACP2 RecName: Full=30S ribosomal protein S4
 gi|157682124|gb|ABV63268.1| ribosomal protein S4 [Bacillus pumilus SAFR-032]
          Length = 200

 Score = 44.8 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR+  +++    + V+G  ++  + +V     I +
Sbjct: 93  RLDNLVYRLGLARTRRQARQLVNHGHILVDGSRVDIPSFSVKPGQTIAL 141


>gi|118602237|ref|YP_903452.1| SSU ribosomal protein S4P [Candidatus Ruthia magnifica str. Cm
           (Calyptogena magnifica)]
 gi|152112257|sp|A1AVM4|RS4_RUTMC RecName: Full=30S ribosomal protein S4
 gi|118567176|gb|ABL01981.1| SSU ribosomal protein S4P [Candidatus Ruthia magnifica str. Cm
           (Calyptogena magnifica)]
          Length = 208

 Score = 44.8 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 12/60 (20%), Positives = 29/60 (48%), Gaps = 1/60 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G  S R E  ++++ + + +NG+++   +  V   D I +     +++   
Sbjct: 99  RLDNVVYRMGFGSTRAEARQLVSHKSILMNGLVVNIPSYQVSVNDEISIREKAKKQSRIQ 158


>gi|221310909|ref|ZP_03592756.1| 30S ribosomal protein S4 [Bacillus subtilis subsp. subtilis str.
           168]
          Length = 200

 Score = 44.8 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ + G+A +RR+  +++    + V+G  ++  +  V     I V
Sbjct: 93  RLDNVVYKLGLARTRRQARQLVNHGHILVDGSRVDIPSYLVKPGQTIGV 141


>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 = 44.8 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 32/245 (13%), Positives = 57/245 (23%), Gaps = 21/245 (8%)

Query: 41  KVNGILLERAAVNVMSTDHI----EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRST 96
           +VNG L    +  V   D I    ++   P    E     +Y KP    T          
Sbjct: 40  RVNGRLERFESYKVQPGDCIALTLQIRSEPKILWEDQHCCIYDKPTHTTTEDLAKTTGLH 99

Query: 97  VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
           +   L    +  I   +   +   L  L     + +          +             
Sbjct: 100 IVHRLDRDTTGCILFAKNTNSAHALSELFKKRKIHKQYTALVFGHPKKSSGTLISYTAPK 159

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                           G + +T  +   S    T+ L +   G+  +I+         + 
Sbjct: 160 SRRCGAVIFGNTDKHSGKLTITHWSVLHSYKHYTLMLCQPFTGRTHQIRLHMHMLGNPIV 219

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPN 273
                       G L  G  R+   K +   L           L              P 
Sbjct: 220 ------------GDLDYG--RKEQPKNIFRPLLHAHSLTFTSPLSQEKVDVVASSSGDPR 265

Query: 274 IISEV 278
            ++  
Sbjct: 266 KVAPH 270


>gi|325295044|ref|YP_004281558.1| pseudouridine synthase [Desulfurobacterium thermolithotrophum DSM
           11699]
 gi|325065492|gb|ADY73499.1| pseudouridine synthase [Desulfurobacterium thermolithotrophum DSM
           11699]
          Length = 280

 Score = 44.4 bits (103), Expect = 0.023,   Method: Composition-based stats.
 Identities = 31/192 (16%), Positives = 62/192 (32%), Gaps = 6/192 (3%)

Query: 26  ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPL---RKAERTRLWLYHKP 81
            S++  +++I +    VNGI       N+     +E      L    K E      Y   
Sbjct: 24  GSKKRAKKVIDEGLCAVNGIKERFYRKNLKPNTIVEFSIPKLLFTKTKIEILYEDEYFLV 83

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
           +      +       V   L   F  +    RLD  T G L++     +  + +L   + 
Sbjct: 84  VNKPPFINSNKNFPDVESLLRKRFKSIYVAHRLDKQTSGALIIAKSKEVFELFKLKFKKK 143

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
               +       +  K +   K  +         +  +  + G   ++ V +  G+  +I
Sbjct: 144 EVKKKYLALVAGNLKKNSGKIKFSI--DGKEAISRYQVVERVGKTDFLEVEILTGRKHQI 201

Query: 202 KKVFEFFNWKVN 213
           +K F   N  + 
Sbjct: 202 RKHFVSVNHPII 213


>gi|313204943|ref|YP_004043600.1| SSU ribosomal protein s4p [Paludibacter propionicigenes WB4]
 gi|312444259|gb|ADQ80615.1| SSU ribosomal protein S4P [Paludibacter propionicigenes WB4]
          Length = 201

 Score = 44.4 bits (103), Expect = 0.023,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G A +R    ++++ + + V+G ++  A+ +V +   I V
Sbjct: 93  RLDNIVYRLGFAPTRSGARQLVSHKHITVDGKVVNIASYHVRAGQVIAV 141


>gi|304315775|ref|YP_003850920.1| RNA-binding S4 domain protein [Thermoanaerobacterium
          thermosaccharolyticum DSM 571]
 gi|302777277|gb|ADL67836.1| RNA-binding S4 domain protein [Thermoanaerobacterium
          thermosaccharolyticum DSM 571]
          Length = 79

 Score = 44.4 bits (103), Expect = 0.023,   Method: Composition-based stats.
 Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 3/67 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRKAE 71
           R+ K +  + +  RR   +    +  V VNG + + A   +   D IE+D G  + KAE
Sbjct: 1  MRLDKFLKLSRLIKRRTVAKEACDKGMVSVNGKVAK-AGDILKVGDIIEIDFGTRVIKAE 59

Query: 72 RTRLWLY 78
             L  +
Sbjct: 60 VLDLKEH 66


>gi|300787880|ref|YP_003768171.1| hemolysin-like protein [Amycolatopsis mediterranei U32]
 gi|299797394|gb|ADJ47769.1| putative hemolysin-like protein [Amycolatopsis mediterranei U32]
          Length = 275

 Score = 44.4 bits (103), Expect = 0.024,   Method: Composition-based stats.
 Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          R+   + R G+A SR +   +I   +V V G++  + A  V S   I V   
Sbjct: 6  RLDAELVRRGLARSREQASALITDGKVTVRGMVATKPATGVESGAPIVVKDE 57


>gi|256394567|ref|YP_003116131.1| hemolysin A [Catenulispora acidiphila DSM 44928]
 gi|256360793|gb|ACU74290.1| hemolysin A [Catenulispora acidiphila DSM 44928]
          Length = 296

 Score = 44.4 bits (103), Expect = 0.024,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+   + R  +A SR +   +I   RV V G    + A  V +   I V
Sbjct: 6  RLDAELVRRNLARSREQARELIEAGRVSVGGQKAGKPATQVETAAAIVV 54


>gi|194017389|ref|ZP_03056001.1| ribosomal protein S4 [Bacillus pumilus ATCC 7061]
 gi|194011257|gb|EDW20827.1| ribosomal protein S4 [Bacillus pumilus ATCC 7061]
          Length = 200

 Score = 44.4 bits (103), Expect = 0.024,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A +RR+  +++    + V+G  ++  + +V     I +
Sbjct: 93  RLDNLVYRLGLARTRRQARQLVNHGHILVDGSRVDIPSFSVKPGQTIAL 141


>gi|150388013|ref|YP_001318062.1| RNA-binding S4 domain-containing protein [Alkaliphilus
          metalliredigens QYMF]
 gi|149947875|gb|ABR46403.1| RNA-binding S4 domain protein [Alkaliphilus metalliredigens QYMF]
          Length = 82

 Score = 44.4 bits (103), Expect = 0.024,   Method: Composition-based stats.
 Identities = 20/70 (28%), Positives = 30/70 (42%), Gaps = 3/70 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRKAE 71
           R+ K +  + I  RR   +      RV +NG   +     V   D IE+  G  + +AE
Sbjct: 1  MRLDKYLKISRIIKRRTVAKEACEGGRVSINGKTAK-PGTEVAVGDEIEIRFGDKVLRAE 59

Query: 72 RTRLWLYHKP 81
           TRL  + K 
Sbjct: 60 VTRLAEHVKK 69


>gi|78221325|ref|YP_383072.1| RNA-binding S4 [Geobacter metallireducens GS-15]
 gi|78192580|gb|ABB30347.1| RNA-binding S4 [Geobacter metallireducens GS-15]
          Length = 65

 Score = 44.4 bits (103), Expect = 0.024,   Method: Composition-based stats.
 Identities = 15/62 (24%), Positives = 27/62 (43%), Gaps = 1/62 (1%)

Query: 7  VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          ++      ++   + A   +AS  E + +IA   V+VNG +  R    +   D +E  G 
Sbjct: 1  MKIETEYIKLDSFLKAENIVASGGEAKIIIADGEVRVNGEVETRRGRKLRVGDRVEAGGE 60

Query: 66 PL 67
           L
Sbjct: 61 TL 62


>gi|26399543|sp|Q9S0Q9|RS4_SHEVI RecName: Full=30S ribosomal protein S4
 gi|5913931|dbj|BAA84524.1| ribosomal protein S4 [Shewanella violacea]
          Length = 206

 Score = 44.4 bits (103), Expect = 0.024,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG ++   +  V ++D I +
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKSILVNGSVVNIPSFKVSASDVISI 145


>gi|227485499|ref|ZP_03915815.1| ribosomal protein S4 [Anaerococcus lactolyticus ATCC 51172]
 gi|227236498|gb|EEI86513.1| ribosomal protein S4 [Anaerococcus lactolyticus ATCC 51172]
          Length = 197

 Score = 44.4 bits (103), Expect = 0.024,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V  R+G+A +RRE  +++    + VNG  ++  +  +   D IEV
Sbjct: 88  RLDNVAFRSGLARTRREARQIVTHGHLLVNGKQVDIPSYLIEEGDVIEV 136


>gi|328914578|gb|AEB55411.1| ribosomal large subunit pseudouridine synthase C [Chlamydophila
           psittaci 6BC]
          Length = 279

 Score = 44.4 bits (103), Expect = 0.024,   Method: Composition-based stats.
 Identities = 19/180 (10%), Positives = 39/180 (21%), Gaps = 7/180 (3%)

Query: 41  KVNGILLERAAVNVMSTDHIEV----DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRST 96
           +VNG L    +  V   D + +       P    E     +Y+KP    T          
Sbjct: 44  RVNGRLERFESYRVQPGDRVTLTVQTRLEPQILWEDEHYCIYNKPSHTSTEDLAKITGLN 103

Query: 97  VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
           +   L    +  I   +       L  L     + +          +             
Sbjct: 104 IVHRLDRDTTGCILFAKHASAAHALSELFKKRKIHKQYTALVFGHPKKSSGTLISYTAPK 163

Query: 157 KLNL---LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +              Q ++         +      G+  +I+         + 
Sbjct: 164 SRRCGAVIFGNTQKNHGKLTITQWSILCAYKQYTLMRCEPITGRTHQIRLHMHTLGHPIV 223


>gi|303328069|ref|ZP_07358508.1| ribosomal protein S4 [Desulfovibrio sp. 3_1_syn3]
 gi|302861895|gb|EFL84830.1| ribosomal protein S4 [Desulfovibrio sp. 3_1_syn3]
          Length = 208

 Score = 44.4 bits (103), Expect = 0.024,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SR +  +++      +NG  +   ++ V   D +EV
Sbjct: 99  RLDNVVYRLGFANSRNQARQLVRHGIFTLNGHKVTIPSLQVKVGDSVEV 147


>gi|225570597|ref|ZP_03779622.1| hypothetical protein CLOHYLEM_06699 [Clostridium hylemonae DSM
           15053]
 gi|225160610|gb|EEG73229.1| hypothetical protein CLOHYLEM_06699 [Clostridium hylemonae DSM
           15053]
          Length = 945

 Score = 44.4 bits (103), Expect = 0.024,   Method: Composition-based stats.
 Identities = 13/112 (11%), Positives = 24/112 (21%), Gaps = 6/112 (5%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL--ATPV 305
              +  Q    A         R   +          + +           Q +     P 
Sbjct: 163 QSQDRPQNTRPAYHQDRPQGARQAQSQDRPQGSRPAQSQDRPQGARPSYNQDRPQNGRPA 222

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRS----PSFPSKRSLRRTSAK 353
              +   N    +G         G R +N R S        S+    +   +
Sbjct: 223 QGADRNGNRGERQGNRPQNGRPQGTRPQNGRPSYNQDRPQGSRTGRPQGGDR 274



 Score = 38.2 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 8/105 (7%), Positives = 19/105 (18%), Gaps = 3/105 (2%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
             Q    A         R              + +           Q +       ++  
Sbjct: 131 RPQNARPAQSQDRPQNARPVQGQDRPQGSRPAQSQDRPQNTRPAYHQDRPQGARQAQSQD 190

Query: 312 SNVWMAKGI---HSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                              S  ++      P+  + R+  R   +
Sbjct: 191 RPQGSRPAQSQDRPQGARPSYNQDRPQNGRPAQGADRNGNRGERQ 235


>gi|212704608|ref|ZP_03312736.1| hypothetical protein DESPIG_02670 [Desulfovibrio piger ATCC 29098]
 gi|212672007|gb|EEB32490.1| hypothetical protein DESPIG_02670 [Desulfovibrio piger ATCC 29098]
          Length = 208

 Score = 44.4 bits (103), Expect = 0.024,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SR +  +++      +NG  +   ++ V   D IEV
Sbjct: 99  RLDNVVYRLGFANSRNQARQLVRHGIFTLNGHKVTIPSLQVRVGDTIEV 147


>gi|17557218|ref|NP_505646.1| COLlagen family member (col-149) [Caenorhabditis elegans]
 gi|3873667|emb|CAA94874.1| C. elegans protein B0024.1, confirmed by transcript evidence
           [Caenorhabditis elegans]
          Length = 297

 Score = 44.4 bits (103), Expect = 0.024,   Method: Composition-based stats.
 Identities = 15/112 (13%), Positives = 23/112 (20%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           ++   GP         +  P          R            +       ++G   Q  
Sbjct: 148 IKCPAGPPGPSGTCGQVGRPGPDGRPGQPGRRGNDGRPGQPGPQGNAGQPGRDGNPGQPG 207

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                 RR   S     +          G       R PS P   + R    
Sbjct: 208 HPGKDGRRGHGSPGAPGRAGQPGRQGAPGNPGRPGERGPSGPCGPAGRSGQP 259



 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 9/115 (7%), Positives = 19/115 (16%), Gaps = 3/115 (2%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R     +    A           +          +              Q        + 
Sbjct: 126 RNGQDNYNTIRAPACPPRNQDCIKCPAGPPGPSGTCGQVGRPGPDGRPGQPGRRGNDGRP 185

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF---PSKRSLRRTSAK 353
             P  + N                   G+R      +P     P ++       +
Sbjct: 186 GQPGPQGNAGQPGRDGNPGQPGHPGKDGRRGHGSPGAPGRAGQPGRQGAPGNPGR 240


>gi|54022803|ref|YP_117045.1| 30S ribosomal protein S4 [Nocardia farcinica IFM 10152]
 gi|61215422|sp|Q5Z1L0|RS4_NOCFA RecName: Full=30S ribosomal protein S4
 gi|54014311|dbj|BAD55681.1| putative ribosomal protein S4 [Nocardia farcinica IFM 10152]
          Length = 201

 Score = 44.4 bits (103), Expect = 0.024,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 1/61 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ RAG+A +RR+  ++++     VNG+ ++  +  V   D I+V    L      
Sbjct: 92  RLDNVVYRAGLARTRRQARQLVSHGHFLVNGVKVDVPSYRVSQYDIIDVKEKSLSTLPFQ 151

Query: 74  R 74
            
Sbjct: 152 V 152


>gi|238798926|ref|ZP_04642391.1| ATP-dependent RNA helicase rhlE [Yersinia mollaretii ATCC 43969]
 gi|238717236|gb|EEQ09087.1| ATP-dependent RNA helicase rhlE [Yersinia mollaretii ATCC 43969]
          Length = 451

 Score = 44.4 bits (103), Expect = 0.024,   Method: Composition-based stats.
 Identities = 13/101 (12%), Positives = 29/101 (28%), Gaps = 2/101 (1%)

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL--SKQKKLATPVHRRNLAS 312
           V+    +   E L++     I+    +     K    +NG      ++            
Sbjct: 351 VDEHKLLRDIERLLKREIPRIALEGYEPDPSIKADPIQNGRQGRGAQRPGMGRGSSAGRP 410

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                        +   + + + +R P+ PS R   R   +
Sbjct: 411 QNGGGAAGRGDSRNSRPRSQADGQRRPAGPSSRGRSRNPGE 451


>gi|296111608|ref|YP_003621990.1| hypothetical protein LKI_07410 [Leuconostoc kimchii IMSNU 11154]
 gi|295833140|gb|ADG41021.1| hypothetical protein LKI_07410 [Leuconostoc kimchii IMSNU 11154]
          Length = 96

 Score = 44.4 bits (103), Expect = 0.024,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 28/50 (56%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRREVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR V + IA Q R+ +NG + + ++  V + D +EV
Sbjct: 1  MRLDKYLKVSRLIKRRTVAKEIADQGRISINGKVAKSSSD-VSTNDELEV 49


>gi|167756759|ref|ZP_02428886.1| hypothetical protein CLORAM_02306 [Clostridium ramosum DSM 1402]
 gi|167702934|gb|EDS17513.1| hypothetical protein CLORAM_02306 [Clostridium ramosum DSM 1402]
          Length = 216

 Score = 44.4 bits (103), Expect = 0.024,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V+ R G A +RR   +++      VNGI  +  +  V   D IEV   
Sbjct: 107 RLDNVVYRLGFAPTRRAARQLVNHGHFLVNGIKTDIPSFRVKVGDVIEVKEK 158


>gi|167521497|ref|XP_001745087.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163776701|gb|EDQ90320.1| predicted protein [Monosiga brevicollis MX1]
          Length = 401

 Score = 44.4 bits (103), Expect = 0.024,   Method: Composition-based stats.
 Identities = 31/203 (15%), Positives = 55/203 (27%), Gaps = 25/203 (12%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRKA-ERTRLWLYHKPIGL 84
           I +  + VN   +      + +   I          V   PL    E   L    KP  +
Sbjct: 72  ITEGLITVNSERVP-LDFIIDNNHIILNKVHRHEPPVTNDPLSIVGETPDLLAIDKPASI 130

Query: 85  VTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL 142
                     +TV   L     R       RLD  T GLL+   +  +A+  E   TQ  
Sbjct: 131 PVHPCGRYRHNTVQAILGHEHDRWRVYPCHRLDRLTSGLLIFCKNPAMAKQFEQWITQHQ 190

Query: 143 RVYRVRFHGQVDQD------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +     Q   +                L    V         +  +  +      + 
Sbjct: 191 VEKQYICRVQGRVEQSVLFCDAPLKICDQRLGLCCVHPEGKASLTRFRVIRRDKDTTVLH 250

Query: 191 VGLREGKNREIKKVFEFFNWKVN 213
              + G+  +I+   ++    + 
Sbjct: 251 CFPKTGRMHQIRVHVQYLGHPIV 273


>gi|86132569|ref|ZP_01051162.1| 30S ribosomal protein S4 [Dokdonia donghaensis MED134]
 gi|85816811|gb|EAQ37996.1| 30S ribosomal protein S4 [Dokdonia donghaensis MED134]
          Length = 201

 Score = 44.4 bits (103), Expect = 0.024,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G++ SR    +++  + + VNG ++   +  V + D I V
Sbjct: 94  RLDNVVYRMGMSPSRSGARQLVGHRHITVNGNIVNIPSYQVKAGDVIAV 142


>gi|254302865|ref|ZP_04970223.1| ribosomal protein S4 [Fusobacterium nucleatum subsp. polymorphum
           ATCC 10953]
 gi|148323057|gb|EDK88307.1| ribosomal protein S4 [Fusobacterium nucleatum subsp. polymorphum
           ATCC 10953]
          Length = 195

 Score = 44.4 bits (103), Expect = 0.025,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+  ++++   + VNG  +  A+  V   D + V
Sbjct: 89  RLENVVYRLGFAKTRRQARQIVSHGHIAVNGRRVNIASFRVKVGDVVSV 137


>gi|16080018|ref|NP_390844.1| 30S ribosomal protein S4 [Bacillus subtilis subsp. subtilis str.
           168]
 gi|221315235|ref|ZP_03597040.1| 30S ribosomal protein S4 [Bacillus subtilis subsp. subtilis str.
           NCIB 3610]
 gi|221320153|ref|ZP_03601447.1| 30S ribosomal protein S4 [Bacillus subtilis subsp. subtilis str.
           JH642]
 gi|221324434|ref|ZP_03605728.1| 30S ribosomal protein S4 [Bacillus subtilis subsp. subtilis str.
           SMY]
 gi|321312503|ref|YP_004204790.1| 30S ribosomal protein S4 [Bacillus subtilis BSn5]
 gi|133949|sp|P21466|RS4_BACSU RecName: Full=30S ribosomal protein S4; Short=BS4
 gi|143467|gb|AAA22717.1| ribosomal protein S4 [Bacillus subtilis]
 gi|2293319|gb|AAC00397.1| ribosomal protein S4 [Bacillus subtilis]
 gi|2635450|emb|CAB14944.1| ribosomal protein S4 (BS4) [Bacillus subtilis subsp. subtilis str.
           168]
 gi|291485397|dbj|BAI86472.1| 30S ribosomal protein S4 [Bacillus subtilis subsp. natto BEST195]
 gi|320018777|gb|ADV93763.1| 30S ribosomal protein S4 [Bacillus subtilis BSn5]
          Length = 200

 Score = 44.4 bits (103), Expect = 0.025,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ + G+A +RR+  +++    + V+G  ++  +  V     I V
Sbjct: 93  RLDNVVYKLGLARTRRQARQLVNHGHILVDGSRVDIPSYLVKPGQTIGV 141


>gi|328955886|ref|YP_004373219.1| SSU ribosomal protein S4P [Coriobacterium glomerans PW2]
 gi|328456210|gb|AEB07404.1| SSU ribosomal protein S4P [Coriobacterium glomerans PW2]
          Length = 198

 Score = 44.4 bits (103), Expect = 0.025,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R+E  + +      VNG  ++  +  V   D I V
Sbjct: 89  RLDNVVFRLGFARTRKEARQTVRHGHFTVNGHRVDIPSYLVKEGDVIAV 137


>gi|300114712|ref|YP_003761287.1| 30S ribosomal protein S4 [Nitrosococcus watsonii C-113]
 gi|299540649|gb|ADJ28966.1| ribosomal protein S4 [Nitrosococcus watsonii C-113]
          Length = 208

 Score = 44.4 bits (103), Expect = 0.025,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++I  + + VNG  +   +  V + D + V
Sbjct: 99  RLDNVVYRMGFGSTRAEARQLINHKGILVNGQGINIPSYQVRAEDVVAV 147


>gi|257470859|ref|ZP_05634949.1| 30S ribosomal protein S4 [Fusobacterium ulcerans ATCC 49185]
 gi|317065062|ref|ZP_07929547.1| SSU ribosomal protein S4P [Fusobacterium ulcerans ATCC 49185]
 gi|313690738|gb|EFS27573.1| SSU ribosomal protein S4P [Fusobacterium ulcerans ATCC 49185]
          Length = 195

 Score = 44.4 bits (103), Expect = 0.025,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+  ++++   V VNG  +  A+  V   D + V
Sbjct: 89  RLENVVYRLGFAKTRRQARQVVSHGHVAVNGRRVNIASYRVKVGDVVSV 137


>gi|237739946|ref|ZP_04570427.1| SSU ribosomal protein S4P [Fusobacterium sp. 2_1_31]
 gi|294782962|ref|ZP_06748288.1| ribosomal protein S4 [Fusobacterium sp. 1_1_41FAA]
 gi|229421963|gb|EEO37010.1| SSU ribosomal protein S4P [Fusobacterium sp. 2_1_31]
 gi|294481603|gb|EFG29378.1| ribosomal protein S4 [Fusobacterium sp. 1_1_41FAA]
          Length = 195

 Score = 44.4 bits (103), Expect = 0.025,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+  ++++   + VNG  +  A+  V   D + V
Sbjct: 89  RLENVVYRLGFAKTRRQARQIVSHGHIAVNGRRVNIASFRVKVGDVVSV 137


>gi|254362773|ref|ZP_04978855.1| ribosomal protein S4 [Mannheimia haemolytica PHL213]
 gi|261492716|ref|ZP_05989264.1| ribosomal protein S4 [Mannheimia haemolytica serotype A2 str.
           BOVINE]
 gi|261495669|ref|ZP_05992115.1| ribosomal protein S4 [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|153094402|gb|EDN75251.1| ribosomal protein S4 [Mannheimia haemolytica PHL213]
 gi|261308776|gb|EEY10033.1| ribosomal protein S4 [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|261311569|gb|EEY12724.1| ribosomal protein S4 [Mannheimia haemolytica serotype A2 str.
           BOVINE]
          Length = 208

 Score = 44.4 bits (103), Expect = 0.025,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R E  ++++ + + VNG ++   +  V   D + V
Sbjct: 99  RLDNVVYRMGFAATRAEARQLVSHKSIVVNGRVVNIPSFQVSVDDVVAV 147


>gi|323698575|ref|ZP_08110487.1| DEAD/DEAH box helicase domain protein [Desulfovibrio sp. ND132]
 gi|323458507|gb|EGB14372.1| DEAD/DEAH box helicase domain protein [Desulfovibrio desulfuricans
           ND132]
          Length = 645

 Score = 44.4 bits (103), Expect = 0.025,   Method: Composition-based stats.
 Identities = 8/108 (7%), Positives = 24/108 (22%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
            H    A           +     R         D    ++  ++        + +    
Sbjct: 451 LHGKPAAPDTASEAQREPQRERPARKRGGRNRRSDEPSGERRQARPAPAETADEPSQAKP 510

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           R +        +           ++    R   + P +      +A++
Sbjct: 511 RPSEGRQPREDRQPREDRQPREDRQPREEREPEARPGEAEQPSPAARE 558


>gi|256786271|ref|ZP_05524702.1| transcriptional regulatory protein [Streptomyces lividans TK24]
          Length = 1271

 Score = 44.4 bits (103), Expect = 0.025,   Method: Composition-based stats.
 Identities = 8/97 (8%), Positives = 20/97 (20%)

Query: 257  LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
                      +                        ++   +  + A   HR   A     
Sbjct: 988  RHPVADRRRRMPAGAGRRPRGAGPGDGGTAAGPGVEHAAHRGPRPARAGHRHRRAPRPGT 1047

Query: 317  AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             +G  +     + +         + P   +  R  A+
Sbjct: 1048 GRGGRTDPAGRARRHRHGADPRAARPGPPAPGRGRAR 1084



 Score = 42.9 bits (99), Expect = 0.075,   Method: Composition-based stats.
 Identities = 8/98 (8%), Positives = 20/98 (20%)

Query: 252  EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
            E   +       +    R  P   +          +    ++G   +     P       
Sbjct: 1023 EHAAHRGPRPARAGHRHRRAPRPGTGRGGRTDPAGRARRHRHGADPRAARPGPPAPGRGR 1082

Query: 312  SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
            +               +  R        + P++    R
Sbjct: 1083 ARTRPGPAARGGGTGRTQGRPALAHPGRAGPARGRRPR 1120



 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 8/101 (7%), Positives = 19/101 (18%)

Query: 248  HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            H + + +  + A                +  P       +         + ++   P   
Sbjct: 989  HPVADRRRRMPAGAGRRPRGAGPGDGGTAAGPGVEHAAHRGPRPARAGHRHRRAPRPGTG 1048

Query: 308  RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
            R   ++       H         R             R   
Sbjct: 1049 RGGRTDPAGRARRHRHGADPRAARPGPPAPGRGRARTRPGP 1089



 Score = 36.3 bits (82), Expect = 6.4,   Method: Composition-based stats.
 Identities = 11/125 (8%), Positives = 19/125 (15%), Gaps = 13/125 (10%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK- 300
            R +  P          D    +        P      P    R +  +            
Sbjct: 1038 RHRRAPRPGTGRGGRTDPAGRARRHRHGADPRAARPGPPAPGRGRARTRPGPAARGGGTG 1097

Query: 301  ----------LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP--SFPSKRSLR 348
                             R                           RR P      + +  
Sbjct: 1098 RTQGRPALAHPGRAGPARGRRPRPGGVPHRRRRPDRQRAPDRRTGRRRPHQHRDRRPAAP 1157

Query: 349  RTSAK 353
            R + +
Sbjct: 1158 RPAHR 1162


>gi|270294726|ref|ZP_06200927.1| 30S ribosomal protein S4 [Bacteroides sp. D20]
 gi|270273973|gb|EFA19834.1| 30S ribosomal protein S4 [Bacteroides sp. D20]
          Length = 201

 Score = 44.4 bits (103), Expect = 0.025,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R GIA +R    ++++ + + V+G ++   +  V     I V
Sbjct: 93  RLDNIVFRLGIAPTRAAARQLVSHKHITVDGEVVNIPSYAVKPGQVIGV 141


>gi|160888373|ref|ZP_02069376.1| hypothetical protein BACUNI_00786 [Bacteroides uniformis ATCC 8492]
 gi|317477726|ref|ZP_07936919.1| ribosomal protein S4 [Bacteroides sp. 4_1_36]
 gi|319900951|ref|YP_004160679.1| SSU ribosomal protein S4P [Bacteroides helcogenes P 36-108]
 gi|156862050|gb|EDO55481.1| hypothetical protein BACUNI_00786 [Bacteroides uniformis ATCC 8492]
 gi|316906071|gb|EFV27832.1| ribosomal protein S4 [Bacteroides sp. 4_1_36]
 gi|319415982|gb|ADV43093.1| SSU ribosomal protein S4P [Bacteroides helcogenes P 36-108]
          Length = 201

 Score = 44.4 bits (103), Expect = 0.025,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R GIA +R    ++++ + + V+G ++   +  V     I V
Sbjct: 93  RLDNIVFRLGIAPTRAAARQLVSHKHITVDGEVVNIPSYAVKPGQVIGV 141


>gi|149181086|ref|ZP_01859586.1| 30S ribosomal protein S4 [Bacillus sp. SG-1]
 gi|148851173|gb|EDL65323.1| 30S ribosomal protein S4 [Bacillus sp. SG-1]
          Length = 200

 Score = 44.4 bits (103), Expect = 0.025,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +RR+  +++    V V+G  ++  +  + +   I V
Sbjct: 93  RLDNVVYRLGLARTRRQARQLVNHGHVTVDGSRVDIPSYRLQAGQTIGV 141


>gi|34763719|ref|ZP_00144640.1| SSU ribosomal protein S4P [Fusobacterium nucleatum subsp. vincentii
           ATCC 49256]
 gi|27886498|gb|EAA23752.1| SSU ribosomal protein S4P [Fusobacterium nucleatum subsp. vincentii
           ATCC 49256]
          Length = 187

 Score = 44.4 bits (103), Expect = 0.025,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+  ++++   + VNG  +  A+  V   D + V
Sbjct: 81  RLENVVYRLGFAKTRRQARQIVSHGHIAVNGRRVNIASFRVKVGDIVSV 129


>gi|320352938|ref|YP_004194277.1| 30S ribosomal protein S4P [Desulfobulbus propionicus DSM 2032]
 gi|320121440|gb|ADW16986.1| SSU ribosomal protein S4P [Desulfobulbus propionicus DSM 2032]
          Length = 209

 Score = 44.4 bits (103), Expect = 0.026,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R+G AS R +  +M+      +NG  +   +  V + D I +
Sbjct: 100 RLDNVLYRSGFASSRDQARQMVRHNLFTLNGKKVNIPSHQVNAGDIIAL 148


>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 = 44.4 bits (103), Expect = 0.026,   Method: Composition-based stats.
 Identities = 24/218 (11%), Positives = 49/218 (22%), Gaps = 39/218 (17%)

Query: 34  MIAQQRVKV--NGILLERA-AVNVMSTDHI----------------EVDGVPLRKAERTR 74
            I    V V  NG  ++   +  + + D +                +VDG  +   +   
Sbjct: 47  WIRDGHVTVTNNGKTVKIGKSYKLSAGDEVVVDAPAPRDLADIRPEKVDGFRIVHLDDDI 106

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +               G + +   +    S   S           L +   G +    
Sbjct: 107 VVVDKPAGVAAHPSPGWHGPTVISALMGEGISVATSGAAERQGIVHRLDVGTSGLMVVAR 166

Query: 135 ELPSTQWLRVYRVRFHGQVDQD--------------------KLNLLKKGIVIQGICYGD 174
              +   L+                                       K  V++      
Sbjct: 167 SERAYTELKRAFKERTVDKVYHTLVQGLPDPLRGTIDAPIGRHPGNEWKFAVVEDGRNSI 226

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
               +    G  + V V L  G+  +I+  F       
Sbjct: 227 THYDVLEAFGPASLVEVHLETGRTHQIRVHFSALRHPC 264


>gi|67923326|ref|ZP_00516809.1| Ycf66, N-terminal [Crocosphaera watsonii WH 8501]
 gi|67854849|gb|EAM50125.1| Ycf66, N-terminal [Crocosphaera watsonii WH 8501]
          Length = 290

 Score = 44.4 bits (103), Expect = 0.026,   Method: Composition-based stats.
 Identities = 18/138 (13%), Positives = 36/138 (26%), Gaps = 10/138 (7%)

Query: 226 GTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
                  TR  ++  + ++L P+  EE     +  +        +R     E      R 
Sbjct: 101 DDRRVSKTRVYTEAEI-DRLEPYEDEEPISRNNPRLEGYADPRSNRSYSQEETRTRKPRR 159

Query: 286 KKNSSQKNGLSKQKKLATPVHRRNLASN---------VWMAKGIHSSFLSDSGQREENHR 336
           + +SS      +      P   R    N         +W  +           +      
Sbjct: 160 RPSSSNDPYGDRPSPRRKPSPTRPTNDNYDAWDSRDDMWEDRPKKRRPSRPRPENSSPET 219

Query: 337 RSPSFPSKRSLRRTSAKK 354
            S S   +R       ++
Sbjct: 220 SSGSPRKRRPRPSNPERR 237


>gi|253581361|ref|ZP_04858587.1| ribosomal protein S4 [Fusobacterium varium ATCC 27725]
 gi|251836725|gb|EES65259.1| ribosomal protein S4 [Fusobacterium varium ATCC 27725]
          Length = 195

 Score = 44.4 bits (103), Expect = 0.026,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+  ++++   V VNG  +  A+  V   D + V
Sbjct: 89  RLENVVYRLGFAKTRRQARQVVSHGHVAVNGRRVNIASYRVKVGDVVSV 137


>gi|269792766|ref|YP_003317670.1| 30S ribosomal protein S4 [Thermanaerovibrio acidaminovorans DSM
           6589]
 gi|269100401|gb|ACZ19388.1| ribosomal protein S4 [Thermanaerovibrio acidaminovorans DSM 6589]
          Length = 208

 Score = 44.4 bits (103), Expect = 0.026,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SRR+   ++      VNG  L+  +  + + D + V
Sbjct: 99  RLDNVVYRLGFAVSRRQARELVRHGHFLVNGRKLDVPSALLRAGDVVTV 147


>gi|221142354|ref|ZP_03566847.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus str.
           JKD6009]
 gi|302751546|gb|ADL65723.1| 30S ribosomal protein S4 [Staphylococcus aureus subsp. aureus str.
           JKD6008]
          Length = 200

 Score = 44.4 bits (103), Expect = 0.026,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+   G+A +RR+  +++    + V+G  ++  + +V     I V
Sbjct: 93  RLDAVVYSLGLARTRRQARQLVNHSHILVDGKRVDIPSYSVKPGQTISV 141


>gi|18044855|gb|AAH20052.1| Jmy-pending protein [Mus musculus]
          Length = 446

 Score = 44.4 bits (103), Expect = 0.026,   Method: Composition-based stats.
 Identities = 22/150 (14%), Positives = 36/150 (24%), Gaps = 16/150 (10%)

Query: 221 GPFQLGTLLAGSTREVSKKILREQLGP------HLLEEAQVNLDAPIYSSETLVRDRPNI 274
             F L   L      V   +  E+            E            +    R     
Sbjct: 1   MSFALEETLESDWVAVRPHVFDEREKHKFVFIVAWNEIEGKFAITCHNRTAQRQRSGSRE 60

Query: 275 ISEVPDDFTRMKKNSSQKNGLSKQKKL-----ATPVHRRNLASNVWMAKGIHSSFLSDSG 329
            +  P         S    G S+          +P  R++ A     +     S   D  
Sbjct: 61  QAVTPASDGSRGPGSPAARGRSEAAASATAALRSPGPRKSQAWAEGGSPRSARSLKGDPP 120

Query: 330 QREENHR-----RSPSFPSKRSLRRTSAKK 354
           +           RSP+      LRR++  +
Sbjct: 121 RGPAGRGPESPLRSPARAKASPLRRSAESR 150


>gi|295698627|ref|YP_003603282.1| ribosomal protein S4 [Candidatus Riesia pediculicola USDA]
 gi|291157482|gb|ADD79927.1| ribosomal protein S4 [Candidatus Riesia pediculicola USDA]
          Length = 206

 Score = 44.4 bits (103), Expect = 0.026,   Method: Composition-based stats.
 Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 1/48 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           R+  V+ R G+ S R E  ++++ + + VN  ++   +  V   D IE
Sbjct: 97  RLDNVVYRIGLGSTRSEARQLVSHKSILVNKKIVNIPSYQVNIDDIIE 144


>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 = 44.4 bits (103), Expect = 0.027,   Method: Composition-based stats.
 Identities = 30/242 (12%), Positives = 57/242 (23%), Gaps = 36/242 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           V + F  +RV   +AR    SR  V  + A   V+ N +     +  + + D +EVD   
Sbjct: 8   VPDGFDGERVDTALARMTGLSRSRVGDLCAHGDVRRN-VEALTKSDRLHAGDLLEVDLPD 66

Query: 64  ------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                       G+ L   +   + +              DG   +            S 
Sbjct: 67  PRPVEPVATPVKGMALLYEDEDIVVVDKPAGVAAHPSMGWDGPDVLGALKAMHVRVATSG 126

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--------------- 156
                     L +   G +       +   L+                            
Sbjct: 127 AAERQGIVSRLDVGTSGVMIVAKGERAYSVLKRAFREHMVDKVYHALVQGHLDPSHGTID 186

Query: 157 -----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                  +   K  +++G         +           V L  G+  +I+         
Sbjct: 187 APIGRHPSREWKMAIVEGGRESVTHYDVIEAMPGACLAEVHLETGRTHQIRVHMAAVGHP 246

Query: 212 VN 213
             
Sbjct: 247 CV 248


>gi|293390661|ref|ZP_06634995.1| ribosomal protein S4 [Aggregatibacter actinomycetemcomitans D7S-1]
 gi|290951195|gb|EFE01314.1| ribosomal protein S4 [Aggregatibacter actinomycetemcomitans D7S-1]
          Length = 206

 Score = 44.4 bits (103), Expect = 0.027,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R E  ++++ + + VNG ++   +  V   D + V
Sbjct: 97  RLDNVVYRMGFAATRAEARQLVSHKAIVVNGRVVNIPSFQVSVDDLVAV 145


>gi|268609565|ref|ZP_06143292.1| small subunit ribosomal protein S4 [Ruminococcus flavefaciens FD-1]
          Length = 199

 Score = 44.4 bits (103), Expect = 0.027,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +RRE  +++      VNG  +   +  V   D I +
Sbjct: 90  RLDSVVYRMGLALTRREARQLVVHSHYTVNGKKVNIPSYRVKVGDVIAL 138


>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 = 44.4 bits (103), Expect = 0.027,   Method: Composition-based stats.
 Identities = 30/235 (12%), Positives = 63/235 (26%), Gaps = 33/235 (14%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN----------------VM 55
              R+ + +A A   SR   +  I + RV+V   ++++ A                  V+
Sbjct: 7   EGLRLDQAVAEALGVSRARAQAWILEGRVRVGEKVVDKPAYRLKGEEVVVEPKEERPLVV 66

Query: 56  STDH---IEVDGV-PLRKAERTRLWLYHKPIGL----------VTTHSDPDGRSTVFDNL 101
             D    I  +    L   +   L  +  P                      R  +    
Sbjct: 67  PEDLPLPILYEDEDLLVLNKPPGLLTHPAPGVYTGTVVNALLGRYYEPKAVERPEMVRPG 126

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
                   + G L +   G  L          L +     L     +    +     + +
Sbjct: 127 IVHRLDKDTSGVLVVAKHGGALEALSQAFRDRLVMKRYLALTEGHPKEGTLIAPIGRHPV 186

Query: 162 KKGIVIQGI---CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           ++  +  G     Y +    +    G +A V      G+  +I+   +     + 
Sbjct: 187 ERHKMHVGGVAPRYAETHFQVLATAGPHALVEARPHTGRTHQIRVHLKHLRAPIL 241


>gi|304387559|ref|ZP_07369748.1| heat shock protein 15 [Neisseria meningitidis ATCC 13091]
 gi|304338446|gb|EFM04567.1| heat shock protein 15 [Neisseria meningitidis ATCC 13091]
          Length = 133

 Score = 44.4 bits (103), Expect = 0.027,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 6/61 (9%)

Query: 1  MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          MKDK+    + +  R+ K + A     +R   ++ I   RV+VNG  ++ +   +   D 
Sbjct: 1  MKDKH----DSSAMRLDKWLWAARFFKTRSLAQKHIELGRVQVNGSKVKNSKT-IDIGDI 55

Query: 60 I 60
          I
Sbjct: 56 I 56


>gi|237653971|ref|YP_002890285.1| 30S ribosomal protein S4 [Thauera sp. MZ1T]
 gi|237625218|gb|ACR01908.1| ribosomal protein S4 [Thauera sp. MZ1T]
          Length = 209

 Score = 44.4 bits (103), Expect = 0.027,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V  R G   SR E  +++    V VNG  +   +  V   D +E+
Sbjct: 100 RLDAVAYRMGFGASRAEARQVVRHNGVLVNGKRVNIPSYVVRPGDVVEL 148


>gi|167771524|ref|ZP_02443577.1| hypothetical protein ANACOL_02894 [Anaerotruncus colihominis DSM
          17241]
 gi|167666164|gb|EDS10294.1| hypothetical protein ANACOL_02894 [Anaerotruncus colihominis DSM
          17241]
          Length = 80

 Score = 44.4 bits (103), Expect = 0.027,   Method: Composition-based stats.
 Identities = 13/51 (25%), Positives = 22/51 (43%), Gaps = 2/51 (3%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+ K +    +  RR          R+ VNG +   A+ +V   D IE++
Sbjct: 1  MRLDKYLKVTRLIKRRTVANEACDAGRIVVNGKVAR-ASYDVKEGDVIEIN 50


>gi|331004148|ref|ZP_08327628.1| 30S ribosomal protein S4 [Lachnospiraceae oral taxon 107 str.
           F0167]
 gi|330411558|gb|EGG90968.1| 30S ribosomal protein S4 [Lachnospiraceae oral taxon 107 str.
           F0167]
          Length = 197

 Score = 44.4 bits (103), Expect = 0.027,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           R+  V+ R G+  +R+E  +++  + V VNG  +   +  V + D IE+    
Sbjct: 88  RLDNVVFRMGLGRTRKETRQIVDHKHVLVNGKCVNIPSYLVKAGDVIEIKEKA 140


>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 = 44.4 bits (103), Expect = 0.027,   Method: Composition-based stats.
 Identities = 19/180 (10%), Positives = 39/180 (21%), Gaps = 7/180 (3%)

Query: 41  KVNGILLERAAVNVMSTDHIEVDG----VPLRKAERTRLWLYHKPIGLVTTHSDPDGRST 96
           +VNG L    +  V   D + +       P    E     +Y+KP    T          
Sbjct: 40  RVNGRLERFESYRVQPGDRVTLTVQTRLEPQILWEDEHYCIYNKPSHTSTEDLAKITGLN 99

Query: 97  VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
           +   L    +  I   +       L  L     + +          +             
Sbjct: 100 IVHRLDRDTTGCILFAKHASAAHALSELFKKRKIHKQYTALVFGHPKKSSGTLISYTAPK 159

Query: 157 KLNL---LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +              Q ++         +      G+  +I+         + 
Sbjct: 160 SRRCGAVIFGNTQKNHGKLTITQWSILCAYKQYTLMRCEPITGRTHQIRLHMHTLGHPIV 219


>gi|308453266|ref|XP_003089369.1| hypothetical protein CRE_17740 [Caenorhabditis remanei]
 gi|308240567|gb|EFO84519.1| hypothetical protein CRE_17740 [Caenorhabditis remanei]
          Length = 626

 Score = 44.4 bits (103), Expect = 0.027,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 24/112 (21%), Gaps = 1/112 (0%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +  G     + +    A   +  +                 R +   S        K+ +
Sbjct: 507 DVRGRPRTVQTRGTKGARGRNQGSATGATRGAKRGSATGAARGRNQGSATGATRGAKRGS 566

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                R         +G        +        R  +    R   R +A +
Sbjct: 567 ATGAARGGN-RGSATRGARGRNQGSATGAARGGNRGTATRGARGGNRGTATR 617


>gi|241895757|ref|ZP_04783053.1| ribosomal protein S4 [Weissella paramesenteroides ATCC 33313]
 gi|241870800|gb|EER74551.1| ribosomal protein S4 [Weissella paramesenteroides ATCC 33313]
          Length = 203

 Score = 44.4 bits (103), Expect = 0.027,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+AS R++  +++    + V+G  ++  +  V     I V
Sbjct: 94  RLDNIVYRLGLASTRQQARQLVNHGHILVDGKRVDIPSYEVSVGQEISV 142


>gi|326390362|ref|ZP_08211921.1| S4 domain protein YaaA [Thermoanaerobacter ethanolicus JW 200]
 gi|325993639|gb|EGD52072.1| S4 domain protein YaaA [Thermoanaerobacter ethanolicus JW 200]
          Length = 68

 Score = 44.4 bits (103), Expect = 0.027,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 20/36 (55%)

Query: 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          + ++ I + +VKVNG +  +    +   D IEV+G 
Sbjct: 28 QAKQFILEGKVKVNGAIELKRGKKLRKNDIIEVEGK 63


>gi|302844558|ref|XP_002953819.1| hypothetical protein VOLCADRAFT_118458 [Volvox carteri f.
           nagariensis]
 gi|300260927|gb|EFJ45143.1| hypothetical protein VOLCADRAFT_118458 [Volvox carteri f.
           nagariensis]
          Length = 1173

 Score = 44.4 bits (103), Expect = 0.027,   Method: Composition-based stats.
 Identities = 18/123 (14%), Positives = 36/123 (29%), Gaps = 13/123 (10%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDR--PNIISEVPDDFTRMKKNSSQKNGLSKQK 299
           R     H + E          S     R     +      +  +   +  + K+   ++ 
Sbjct: 249 RASPPLHFMMEDGSPPPRRWVSKSPPPRRWVSKSPPPRRFESKSPPLRRFNSKSPPRRRW 308

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP--------SFPSKRSLRRTS 351
              +P  RR  + +            S   +R     RSP        S P +R+  R+ 
Sbjct: 309 VSRSPPLRRFESKS---PPPRRWVSRSPPPRRTGAGSRSPLQRRWVSRSPPPRRATSRSP 365

Query: 352 AKK 354
            ++
Sbjct: 366 QRR 368



 Score = 42.5 bits (98), Expect = 0.095,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 34/112 (30%), Gaps = 7/112 (6%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
             + ++         S      +  +      +  +  ++    ++   ++ +  +P  R
Sbjct: 267 RWVSKSPPPRRWVSKSPPPRRFESKSPPLRRFNSKSPPRRRWVSRSPPLRRFESKSPPPR 326

Query: 308 R-------NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           R          +       +   ++S S        RSP    +R+  + +A
Sbjct: 327 RWVSRSPPPRRTGAGSRSPLQRRWVSRSPPPRRATSRSPQRRGRRASEQGNA 378



 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 18/106 (16%), Positives = 33/106 (31%), Gaps = 4/106 (3%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           LR            V+   P+   E+        +S  P            ++ L ++  
Sbjct: 295 LRRFNSKSPPRRRWVSRSPPLRRFESKSPPPRRWVSRSPPPRRTGAG---SRSPLQRRWV 351

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
             +P  RR   S     +G  +S   ++G R  +  R  + P    
Sbjct: 352 SRSPPPRRAT-SRSPQRRGRRASEQGNAGSRSPSLSRQQATPLPPP 396


>gi|297180260|gb|ADI16479.1| hypothetical protein [uncultured bacterium HF4000_05M23]
          Length = 208

 Score = 44.4 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 13/47 (27%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  V+ R G A SR +  +++    ++VNG  +   +  V   D I
Sbjct: 97  RLDNVVYRLGFADSRPQARQIVGHGHIRVNGKKVNIPSYQVSPGDRI 143


>gi|182412027|ref|YP_001817093.1| ribosomal protein S4 [Opitutus terrae PB90-1]
 gi|226699097|sp|B1ZNC4|RS4_OPITP RecName: Full=30S ribosomal protein S4
 gi|177839241|gb|ACB73493.1| ribosomal protein S4 [Opitutus terrae PB90-1]
          Length = 203

 Score = 44.4 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+   G+A SR    + +    ++VNG  ++ A+ NV + D IEV   P  +   T
Sbjct: 93  RLDSVVYLLGLAKSRAAARQFVNHGHIRVNGHKVDIASYNVKAGDEIEVKNSPASRQLAT 152

Query: 74  RLWLYHKPIGLV 85
           R    ++   + 
Sbjct: 153 RCLEENRIRNVP 164


>gi|149019516|ref|ZP_01834835.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
          pneumoniae SP23-BS72]
 gi|147930891|gb|EDK81871.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
          pneumoniae SP23-BS72]
          Length = 64

 Score = 44.4 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 9/32 (28%), Positives = 14/32 (43%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGIL 46
          R+ K ++     SR      I   +V VNG +
Sbjct: 11 RLDKALSDLSELSRSLANEQIKSGQVLVNGQV 42


>gi|145588266|ref|YP_001154863.1| ribosomal protein S4 [Polynucleobacter necessarius subsp.
           asymbioticus QLW-P1DMWA-1]
 gi|189045391|sp|A4SUY5|RS4_POLSQ RecName: Full=30S ribosomal protein S4
 gi|145046672|gb|ABP33299.1| SSU ribosomal protein S4P [Polynucleobacter necessarius subsp.
           asymbioticus QLW-P1DMWA-1]
          Length = 207

 Score = 44.4 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++   + +NG  +   ++ V   D + +
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHCAILLNGSPVNIPSIQVKPGDVVAI 146


>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 = 44.4 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 25/230 (10%), Positives = 55/230 (23%), Gaps = 31/230 (13%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVM------------------ 55
           R+ + +A+     SR  ++  I    VKVNGI++ RA   V                   
Sbjct: 19  RLDQALAQLFPDYSRSRIKVWIENDLVKVNGIIVNRARGKVFGGEQIEIQAEIEEEIRFE 78

Query: 56  ----STDHIEVDGVPLRKAERTRLWLYHKPIG---LVTTHSDPDGRSTVFDNLPSIFSRV 108
                 + +  D   +   +   L ++         V                  I  R+
Sbjct: 79  PQNIPLNIVHEDDDIIIINKPKNLVVHPGAGNPDGTVLNALLYYYPPIAEVPRAGIIHRL 138

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKK 163
                  +     +        A      + ++  +           D            
Sbjct: 139 DKDTTGLMVVAKNIPAQTHLVTALQKRRITREYEAIASGIMTQGGKVDEPMARHPTKRTA 198

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             V            +  +  +   + + L  G+  +I+         + 
Sbjct: 199 MAVHPMGKPAITHYRIMERFRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 248


>gi|304321690|ref|YP_003855333.1| 3'-5' exoribonuclease, VacB and RNase II/Ribonuclease R
           [Parvularcula bermudensis HTCC2503]
 gi|303300592|gb|ADM10191.1| 3'-5' exoribonuclease, VacB and RNase II/Ribonuclease R
           [Parvularcula bermudensis HTCC2503]
          Length = 830

 Score = 44.4 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 19/121 (15%), Positives = 31/121 (25%), Gaps = 4/121 (3%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           S + +         E+A     A   +     +              R  K+++Q    S
Sbjct: 710 SPEAVETAPAASSAEKAAKKRGATDGARGRPGQKPRGAKRGKRGAEDRPPKSAAQDKPAS 769

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENH----RRSPSFPSKRSLRRTSA 352
             K+      R+   S    A           G   EN+    RR P     R   +   
Sbjct: 770 SAKRAPATPPRKATKSTKPAAGPPSPGKAPSPGDHAENNGPKIRRRPKKAGPRRSAKPPR 829

Query: 353 K 353
            
Sbjct: 830 S 830



 Score = 37.5 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 12/114 (10%), Positives = 28/114 (24%), Gaps = 2/114 (1%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           L +++   LLE   +          +         +   +   + +  +    G   QK 
Sbjct: 685 LGQRVEVRLLEVTPLQGGLRFEMLSSPEAVETAPAASSAEKAAKKRGATDGARGRPGQKP 744

Query: 301 LATPVHRRN--LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                 +R          A+   +S    +           + P+        A
Sbjct: 745 RGAKRGKRGAEDRPPKSAAQDKPASSAKRAPATPPRKATKSTKPAAGPPSPGKA 798


>gi|289577268|ref|YP_003475895.1| S4 domain protein YaaA [Thermoanaerobacter italicus Ab9]
 gi|297543501|ref|YP_003675803.1| S4 domain-containing protein YaaA [Thermoanaerobacter mathranii
          subsp. mathranii str. A3]
 gi|289526981|gb|ADD01333.1| S4 domain protein YaaA [Thermoanaerobacter italicus Ab9]
 gi|296841276|gb|ADH59792.1| S4 domain protein YaaA [Thermoanaerobacter mathranii subsp.
          mathranii str. A3]
          Length = 68

 Score = 44.4 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 20/36 (55%)

Query: 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          + ++ I + +VKVNG +  +    +   D IEV+G 
Sbjct: 28 QAKQFILEGKVKVNGAIELKRGKKLRKNDIIEVEGK 63


>gi|325981829|ref|YP_004294231.1| 30S ribosomal protein S4 [Nitrosomonas sp. AL212]
 gi|325531348|gb|ADZ26069.1| ribosomal protein S4 [Nitrosomonas sp. AL212]
          Length = 208

 Score = 44.4 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V    G   SR E  +++    + +NG  +   +  V + D +EV
Sbjct: 99  RLDNVAFHMGFGASRSEARQIVRHNGILINGSRVNIPSYRVKAGDTVEV 147


>gi|149371654|ref|ZP_01891070.1| 30S ribosomal protein S4 [unidentified eubacterium SCB49]
 gi|149355281|gb|EDM43841.1| 30S ribosomal protein S4 [unidentified eubacterium SCB49]
          Length = 201

 Score = 44.4 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA SR    ++++ + + VNG  +   +  + + D + V
Sbjct: 94  RLDNVVYRMGIAPSRPAARQLVSHRHITVNGEKVNIPSYQLKAGDVVAV 142


>gi|121534659|ref|ZP_01666480.1| ribosomal protein S4 [Thermosinus carboxydivorans Nor1]
 gi|121306679|gb|EAX47600.1| ribosomal protein S4 [Thermosinus carboxydivorans Nor1]
          Length = 208

 Score = 44.4 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A +R +  +++      VNG  ++  +  V   D I+V
Sbjct: 99  RLDNVVYRLGLAANRTQARQLVRHGHFTVNGRRVDIPSFQVKVGDVIQV 147


>gi|114330597|ref|YP_746819.1| 30S ribosomal protein S4 [Nitrosomonas eutropha C91]
 gi|122314409|sp|Q0AIH2|RS4_NITEC RecName: Full=30S ribosomal protein S4
 gi|114307611|gb|ABI58854.1| SSU ribosomal protein S4P [Nitrosomonas eutropha C91]
          Length = 208

 Score = 44.4 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 20/49 (40%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V    G   SR E  ++I    + +NG      +  +   D IEV
Sbjct: 99  RLDNVAYNMGFGASRAEARQIIRHDCILLNGKKANIPSQLIGPGDQIEV 147


>gi|256820007|ref|YP_003141286.1| 30S ribosomal protein S4 [Capnocytophaga ochracea DSM 7271]
 gi|256581590|gb|ACU92725.1| ribosomal protein S4 [Capnocytophaga ochracea DSM 7271]
          Length = 201

 Score = 44.4 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA +R    ++++ + + VNG ++   + ++   D + V
Sbjct: 94  RLDNVVYRMGIAPTRSAARQLVSHRHITVNGNIVNIPSYSLKPGDVVGV 142


>gi|32892110|gb|AAP88994.1| ribosomal protein S4 [Passiflora incarnata]
          Length = 183

 Score = 44.4 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 13/82 (15%), Positives = 29/82 (35%), Gaps = 1/82 (1%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+  ++ R G+AS   +  +++  + + VNG +++  +      D I V      K   
Sbjct: 71  MRLDNILFRLGMASTIPQARQLVNHRHILVNGRIVDIPSYRCKPQDLITVKDEQKSKDMI 130

Query: 73  TRLWLYHKPIGLVTTHSDPDGR 94
                      L    +    +
Sbjct: 131 QNSLHSFPQEKLPKHLTLHPFQ 152


>gi|330833751|ref|YP_004402576.1| 30S ribosomal protein S4 [Streptococcus suis ST3]
 gi|329307974|gb|AEB82390.1| 30S ribosomal protein S4 [Streptococcus suis ST3]
          Length = 203

 Score = 44.4 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 11/57 (19%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           R+  V+ R G+A+  R+  + +    + V+G  ++  +  V     I V    ++  
Sbjct: 94  RLDNVVYRLGLATTHRQARQFVNHGHILVDGKRVDIPSYRVEVGQVISVREKSIKVP 150


>gi|300690185|ref|YP_003751180.1| 30S ribosomal subunit protein S4 [Ralstonia solanacearum PSI07]
 gi|299077245|emb|CBJ49871.1| 30S ribosomal subunit protein S4 [Ralstonia solanacearum PSI07]
          Length = 207

 Score = 44.4 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  L   +  V + D + +
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAILVNGQALNVPSAQVKAGDVVAI 146


>gi|47124122|gb|AAH69906.1| Jmy protein [Mus musculus]
          Length = 621

 Score = 44.4 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 20/150 (13%), Positives = 39/150 (26%), Gaps = 16/150 (10%)

Query: 221 GPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIY----SSETLVRDRPNIIS 276
             F L   L      V   +  E+     +     N     +     + T  R R     
Sbjct: 1   MSFALEETLESDWVAVRPHVFDEREKHKFVFIVAWNEIEGKFAITCHNRTAQRQRSGSRE 60

Query: 277 EVPDDFTRMKKNSSQKNGLSKQKKL-------ATPVHRRNLASNVWMAKGIHSSFLSDSG 329
           +     +   +         + +          +P  R++ A     +     S   D  
Sbjct: 61  QAGTPASDGSRGPGSPAARGRSEAAASATAALRSPGPRKSQAWAEGGSPRSARSLKGDPP 120

Query: 330 QREENHR-----RSPSFPSKRSLRRTSAKK 354
           +           RSP+      LRR++  +
Sbjct: 121 RGPAGRGPESPLRSPARAKASPLRRSAESR 150


>gi|312879541|ref|ZP_07739341.1| 23S rRNA m(2)A-2503 methyltransferase [Aminomonas paucivorans DSM
           12260]
 gi|310782832|gb|EFQ23230.1| 23S rRNA m(2)A-2503 methyltransferase [Aminomonas paucivorans DSM
           12260]
          Length = 635

 Score = 44.4 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 8/115 (6%), Positives = 19/115 (16%), Gaps = 2/115 (1%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
              E   P  +   +        +     +         P       + +         +
Sbjct: 340 EGAEGGRPLGVLPPEPERLPRPAAPAPRDKGVSPSRKPRPQGGGNPSRENRPHRPGEPDR 399

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +      R    +      G                   P+   K      S  +
Sbjct: 400 RPYAGPPRSGRPAPQGK--GDRPGEPDRRPYAGPPRSGRPAPQGKGDRPGESEGR 452



 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 11/116 (9%), Positives = 20/116 (17%), Gaps = 5/116 (4%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK-- 300
           ++ G                       D        P       ++       S++    
Sbjct: 444 DRPGESEGRPRTPAGGERGRDFRPPREDGRPDRENRPHRPGEPDRHPYAGPSRSERPAQA 503

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLS---DSGQREENHRRSPSFPSKRSLRRTSAK 353
                  R  AS                     R  +    P     R  R  + +
Sbjct: 504 REGTHPGRTGASREGFPAEDRPRGPRGDDRRPGRSPSPTGRPDREGPRDRREGAGR 559



 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 7/98 (7%), Positives = 16/98 (16%), Gaps = 2/98 (2%)

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
                         + RP        +    +     +   +   +   P  +     + 
Sbjct: 362 AAPAPRDKGVSPSRKPRPQGGGNPSRENRPHRPGEPDRRPYAGPPRSGRPAPQ--GKGDR 419

Query: 315 WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                           R     +           RT A
Sbjct: 420 PGEPDRRPYAGPPRSGRPAPQGKGDRPGESEGRPRTPA 457



 Score = 40.2 bits (92), Expect = 0.45,   Method: Composition-based stats.
 Identities = 12/128 (9%), Positives = 22/128 (17%), Gaps = 8/128 (6%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIIS-EVPDDFTRMKKNSSQK 292
           RE       E         ++    A         R   +       D     + +  + 
Sbjct: 476 RENRPHRPGEPDRHPYAGPSRSERPAQAREGTHPGRTGASREGFPAEDRPRGPRGDDRRP 535

Query: 293 NGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS-------PSFPSKR 345
                          R+         G  S         ++  RR              +
Sbjct: 536 GRSPSPTGRPDREGPRDRREGAGRPFGPRSQGGEGPAPGQDAPRRRDDAGRGSSGSQGGK 595

Query: 346 SLRRTSAK 353
                  K
Sbjct: 596 PRPSGPGK 603



 Score = 40.2 bits (92), Expect = 0.51,   Method: Composition-based stats.
 Identities = 8/103 (7%), Positives = 19/103 (18%), Gaps = 3/103 (2%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           E++     P           P        +    +     ++  +   +   P   R   
Sbjct: 448 ESEGRPRTPAGGERGRDFRPPREDGRPDRENRPHRPGEPDRHPYAGPSRSERPAQAREGT 507

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                          D  +      R P    +         +
Sbjct: 508 HPGRTGASREGFPAEDRPRGPRGDDRRP---GRSPSPTGRPDR 547



 Score = 39.8 bits (91), Expect = 0.66,   Method: Composition-based stats.
 Identities = 18/126 (14%), Positives = 29/126 (23%), Gaps = 4/126 (3%)

Query: 229 LAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
            AG +R       RE   P     ++    A          DR    S  P      +  
Sbjct: 491 YAGPSRSERPAQAREGTHPGRTGASREGFPAEDRPRGPRGDDRRPGRSPSPTGRPDREGP 550

Query: 289 SSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
             ++ G     +   P  +                         +  +  PS P  +   
Sbjct: 551 RDRREGA---GRPFGPRSQGGEGPAPGQDAPRRRDDAGRGSSGSQGGKPRPSGPG-KGRP 606

Query: 349 RTSAKK 354
             S  K
Sbjct: 607 SGSGDK 612



 Score = 39.8 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 13/107 (12%), Positives = 22/107 (20%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G    +              T            P +  R  + +         +      
Sbjct: 435 GRPAPQGKGDRPGESEGRPRTPAGGERGRDFRPPREDGRPDRENRPHRPGEPDRHPYAGP 494

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            R    +          +  S  G   E+  R P    +R  R  S 
Sbjct: 495 SRSERPAQAREGTHPGRTGASREGFPAEDRPRGPRGDDRRPGRSPSP 541



 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 4/91 (4%), Positives = 14/91 (15%)

Query: 264 SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSS 323
            + +          V           +      K    +     +   +     +     
Sbjct: 336 RQRVEGAEGGRPLGVLPPEPERLPRPAAPAPRDKGVSPSRKPRPQGGGNPSRENRPHRPG 395

Query: 324 FLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                          P+   K        ++
Sbjct: 396 EPDRRPYAGPPRSGRPAPQGKGDRPGEPDRR 426



 Score = 37.9 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 12/111 (10%), Positives = 21/111 (18%), Gaps = 4/111 (3%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           RE       E  +     P  S     + + +   E           S +     K  + 
Sbjct: 387 RENRPHRPGEPDRRPYAGPPRSGRPAPQGKGDRPGEPDRRPYAGPPRSGRPAPQGKGDRP 446

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                 R               F         +    P  P +      + 
Sbjct: 447 -GESEGRPRTPAGGE---RGRDFRPPREDGRPDRENRPHRPGEPDRHPYAG 493



 Score = 37.5 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 6/114 (5%), Positives = 20/114 (17%), Gaps = 2/114 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+         ++ N        +      P             +     +   +   + 
Sbjct: 375 RKPRPQGGGNPSRENRPHRPGEPDRRPYAGPPRSGRPAPQGKGDRPGEPDRRPYAGPPRS 434

Query: 302 ATPVH--RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             P    + +            +        R       P   ++        +
Sbjct: 435 GRPAPQGKGDRPGESEGRPRTPAGGERGRDFRPPREDGRPDRENRPHRPGEPDR 488



 Score = 37.1 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 8/113 (7%), Positives = 20/113 (17%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R           + +         +             +   R +  +  + G   +   
Sbjct: 410 RPAPQGKGDRPGEPDRRPYAGPPRSGRPAPQGKGDRPGESEGRPRTPAGGERGRDFRPPR 469

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                 R    +       H        +R    R         + R     +
Sbjct: 470 EDGRPDRENRPHRPGEPDRHPYAGPSRSERPAQAREGTHPGRTGASREGFPAE 522


>gi|320108369|ref|YP_004183959.1| 30S ribosomal protein S4 [Terriglobus saanensis SP1PR4]
 gi|319926890|gb|ADV83965.1| ribosomal protein S4 [Terriglobus saanensis SP1PR4]
          Length = 209

 Score = 44.4 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+  +++    V VNG  +   +  V   D IE+
Sbjct: 100 RLDNVVYRLGFAIARRQSRQVVRHGHVNVNGRKVNIPSFQVKVGDVIEL 148


>gi|37519960|ref|NP_923337.1| hypothetical protein gll0391 [Gloeobacter violaceus PCC 7421]
 gi|35210952|dbj|BAC88332.1| gll0391 [Gloeobacter violaceus PCC 7421]
          Length = 262

 Score = 44.4 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 2/52 (3%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+   I  AG   SR ++   I    V +N   + + + NV + D I + G 
Sbjct: 188 RID-AIGSAGFGLSRNKMVESIEAGEVTLNWKTVTQPSKNVQTGDRITLRGR 238


>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 = 44.4 bits (103), Expect = 0.029,   Method: Composition-based stats.
 Identities = 11/41 (26%), Positives = 20/41 (48%)

Query: 7  VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILL 47
          V +    +RV   I+R    SR +   + A  +V V+G ++
Sbjct: 12 VPDGLEGERVDAAISRMFGFSRTKAAELAAAGKVTVDGSVV 52


>gi|164688743|ref|ZP_02212771.1| hypothetical protein CLOBAR_02390 [Clostridium bartlettii DSM
           16795]
 gi|164602219|gb|EDQ95684.1| hypothetical protein CLOBAR_02390 [Clostridium bartlettii DSM
           16795]
          Length = 197

 Score = 44.4 bits (103), Expect = 0.029,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A S R+  +M+    + VNG  ++  +  V   D + +
Sbjct: 89  RLDNVVYRLGFANSIRQARQMVVHGHILVNGKKVDIPSFAVQVGDEVSL 137


>gi|74613776|sp|Q7RX84|CWC22_NEUCR RecName: Full=Pre-mRNA-splicing factor cwc-22
          Length = 1010

 Score = 44.4 bits (103), Expect = 0.029,   Method: Composition-based stats.
 Identities = 16/98 (16%), Positives = 28/98 (28%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
             +              R    S  P + T    +       S  ++  +P  RR+ + +
Sbjct: 13  PHDATRSPSPRTQSPSPRDEDGSRSPGERTPSPPSRDPSPYRSPGERTPSPSPRRDRSLS 72

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                  H    S + + +   RRS   PS R      
Sbjct: 73  PRDQPHSHPRSRSPTPRSQSPSRRSVRSPSPRQGSPAR 110


>gi|331004909|ref|ZP_08328325.1| SSU ribosomal protein S4p (S9e) [gamma proteobacterium IMCC1989]
 gi|330421296|gb|EGG95546.1| SSU ribosomal protein S4p (S9e) [gamma proteobacterium IMCC1989]
          Length = 205

 Score = 44.4 bits (103), Expect = 0.029,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V + D I +
Sbjct: 97  RLDNVVYRMGFGSTRAESRQLVSHKSILVNGSTVNIPSYQVKAEDVISI 145


>gi|242242984|ref|ZP_04797429.1| 30S ribosomal protein S4 [Staphylococcus epidermidis W23144]
 gi|242233585|gb|EES35897.1| 30S ribosomal protein S4 [Staphylococcus epidermidis W23144]
 gi|319401032|gb|EFV89251.1| ribosomal protein S4 [Staphylococcus epidermidis FRI909]
          Length = 200

 Score = 44.4 bits (103), Expect = 0.029,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+   G+A +RR+  +++    ++V+G  ++  + ++     I V
Sbjct: 93  RLDAVVYSLGLARTRRQARQLVNHGHIEVDGGRVDIPSYSLKPGQVITV 141


>gi|187930339|ref|YP_001900826.1| 30S ribosomal protein S4 [Ralstonia pickettii 12J]
 gi|226699109|sp|B2UEJ4|RS4_RALPJ RecName: Full=30S ribosomal protein S4
 gi|187727229|gb|ACD28394.1| ribosomal protein S4 [Ralstonia pickettii 12J]
          Length = 207

 Score = 44.4 bits (103), Expect = 0.029,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  L   +  V S D I +
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAILVNGQALNVPSAQVKSGDVIAI 146


>gi|299065440|emb|CBJ36609.1| 30S ribosomal subunit protein S4 [Ralstonia solanacearum CMR15]
          Length = 207

 Score = 44.4 bits (103), Expect = 0.029,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  L   +  + S D + +
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAILVNGQALNVPSAQIKSGDVVTI 146


>gi|237743161|ref|ZP_04573642.1| conserved hypothetical protein [Fusobacterium sp. 7_1]
 gi|229433457|gb|EEO43669.1| conserved hypothetical protein [Fusobacterium sp. 7_1]
          Length = 71

 Score = 44.4 bits (103), Expect = 0.029,   Method: Composition-based stats.
 Identities = 11/71 (15%), Positives = 28/71 (39%), Gaps = 9/71 (12%)

Query: 1  MKDKNIVQENFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
          MK+   V+ +    ++ + +       +G     + +++I   +VKVN  +  R    + 
Sbjct: 1  MKNIEKVKISTEFIKLDQFLKWLAVVDSG----SQAKQVILDGKVKVNDEVETRRGRKIY 56

Query: 56 STDHIEVDGVP 66
              +E+    
Sbjct: 57 PEYKVEIFDRI 67


>gi|157689488|gb|ABV65300.1| ribosomal protein S4 [Hirtella bicornis]
          Length = 172

 Score = 44.4 bits (103), Expect = 0.029,   Method: Composition-based stats.
 Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 5/55 (9%)

Query: 14  QRVSKVIARAGIAS---RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
            R+  ++ R G+AS   R    +++  + + VNG +++  +      D I V   
Sbjct: 60  MRLDNILFRLGMASTIPR--ARQLVNHRHILVNGRIVDIPSYRCKPRDIITVKDE 112


>gi|260655137|ref|ZP_05860625.1| ribosomal protein S4 [Jonquetella anthropi E3_33 E1]
 gi|260630059|gb|EEX48253.1| ribosomal protein S4 [Jonquetella anthropi E3_33 E1]
          Length = 206

 Score = 44.4 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  + R +  +++      VNG  ++  +  V + D I +
Sbjct: 99  RLDNVVYRLGFCTTRPQARQLVCHGHFAVNGRKVDIPSARVSAGDVISI 147


>gi|257066610|ref|YP_003152866.1| G5 domain-containing protein [Anaerococcus prevotii DSM 20548]
 gi|256798490|gb|ACV29145.1| G5 domain protein [Anaerococcus prevotii DSM 20548]
          Length = 1859

 Score = 44.4 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 15/115 (13%), Positives = 27/115 (23%), Gaps = 3/115 (2%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            +E       +E           S+   ++ P+   E  D     +K    K G  +    
Sbjct: 1660 KEDPSKPGEKEDPSKPGEKEDPSKPGEKEDPSKPGEKEDPSKPGEKEDPSKPGEKEDPSK 1719

Query: 302  ATPVHRRNLASNVWMAKGIHSSFLSDSG---QREENHRRSPSFPSKRSLRRTSAK 353
                             G             + E+     P+ P K +      K
Sbjct: 1720 PGEKEEPGKPGETPEQPGKPGDPEIPGENTEKPEDPTDPKPNKPGKPNEPGNPEK 1774


>gi|198455645|ref|XP_001360084.2| GA12417 [Drosophila pseudoobscura pseudoobscura]
 gi|198133334|gb|EAL29237.2| GA12417 [Drosophila pseudoobscura pseudoobscura]
          Length = 579

 Score = 44.4 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 18/114 (15%), Positives = 33/114 (28%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            +K + +Q  P     +           E     R   ++       R +K+S  ++   
Sbjct: 177 RRKRVADQSPPRRRRGSPDQSPPRRKRDEDQSPPRRKRVNSDQSPPRRGRKSSPDQSPPR 236

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
           +++       RR  + N   +        S         RRS    S    RR 
Sbjct: 237 RRRDSDQSPPRRRRSHNSNQSPPRKGRRSSADQSPPRKGRRSSPDQSPPRRRRD 290



 Score = 42.9 bits (99), Expect = 0.071,   Method: Composition-based stats.
 Identities = 16/113 (14%), Positives = 35/113 (30%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+       +E        I   +       ++  +      R K++  Q     K+   
Sbjct: 124 RKATAVKTTKERSAQSPLAIKIKQEKRSTSRDLSPKRDFSAARRKRSPDQSPPRRKRVAD 183

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +P  RR  + +    +       S   ++  N  +SP    ++S    S  +
Sbjct: 184 QSPPRRRRGSPDQSPPRRKRDEDQSPPRRKRVNSDQSPPRRGRKSSPDQSPPR 236



 Score = 39.8 bits (91), Expect = 0.61,   Method: Composition-based stats.
 Identities = 17/110 (15%), Positives = 31/110 (28%), Gaps = 3/110 (2%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              +E Q        +S+     R    S       R + +        +         R
Sbjct: 201 RKRDEDQSPPRRKRVNSDQSPPRRGRKSSPDQSPPRRRRDSDQSPPRRRRSHNSNQSPPR 260

Query: 308 RNLASNVWMAK---GIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +   S+   +    G  SS      +R  +  +SP    K S +    K+
Sbjct: 261 KGRRSSADQSPPRKGRRSSPDQSPPRRRRDVDQSPDRRRKDSDQSPPRKR 310



 Score = 39.4 bits (90), Expect = 0.85,   Method: Composition-based stats.
 Identities = 13/115 (11%), Positives = 25/115 (21%), Gaps = 2/115 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +        + +                 R    S       R +          +    
Sbjct: 159 KRDFSAARRKRSPDQSPPRRKRVADQSPPRRRRGSPDQSPPRRKRDEDQSPPRRKRVNSD 218

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENH--RRSPSFPSKRSLRRTSAKK 354
            +P  R   +S                 +R  +H   +SP    +RS    S  +
Sbjct: 219 QSPPRRGRKSSPDQSPPRRRRDSDQSPPRRRRSHNSNQSPPRKGRRSSADQSPPR 273



 Score = 37.5 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 14/113 (12%), Positives = 26/113 (23%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R    P  ++  Q         S                   R K+ + Q     ++   
Sbjct: 135 RSAQSPLAIKIKQEKRSTSRDLSPKRDFSAARRKRSPDQSPPRRKRVADQSPPRRRRGSP 194

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                RR    +    +    +      +R        S P +R     S  +
Sbjct: 195 DQSPPRRKRDEDQSPPRRKRVNSDQSPPRRGRKSSPDQSPPRRRRDSDQSPPR 247



 Score = 35.9 bits (81), Expect = 8.6,   Method: Composition-based stats.
 Identities = 9/105 (8%), Positives = 20/105 (19%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                    ++      ++        +             +        S  ++     
Sbjct: 147 QEKRSTSRDLSPKRDFSAARRKRSPDQSPPRRKRVADQSPPRRRRGSPDQSPPRRKRDED 206

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                   V   +         S  +    RR  S  S    RR+
Sbjct: 207 QSPPRRKRVNSDQSPPRRGRKSSPDQSPPRRRRDSDQSPPRRRRS 251


>gi|222054352|ref|YP_002536714.1| RNA-binding S4 domain protein [Geobacter sp. FRC-32]
 gi|221563641|gb|ACM19613.1| RNA-binding S4 domain protein [Geobacter sp. FRC-32]
          Length = 65

 Score = 44.4 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 11/60 (18%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 7  VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          ++ +    ++   + A   + S  E + +I +  V+VNG +  R    +   D + + G 
Sbjct: 1  MKIDTEYIKLDSFLKAVNAVCSGGEAKIIIGEGEVEVNGEVELRRGRKLRPGDRVSLGGK 60


>gi|27468314|ref|NP_764951.1| 30S ribosomal protein S4 [Staphylococcus epidermidis ATCC 12228]
 gi|57867241|ref|YP_188856.1| 30S ribosomal protein S4 [Staphylococcus epidermidis RP62A]
 gi|251811109|ref|ZP_04825582.1| 30S ribosomal protein S4 [Staphylococcus epidermidis BCM-HMP0060]
 gi|282875859|ref|ZP_06284726.1| ribosomal protein S4 [Staphylococcus epidermidis SK135]
 gi|293366334|ref|ZP_06613014.1| 30S ribosomal protein S4 [Staphylococcus epidermidis
           M23864:W2(grey)]
 gi|38258357|sp|Q8CS54|RS4_STAES RecName: Full=30S ribosomal protein S4
 gi|81674196|sp|Q5HNI5|RS4_STAEQ RecName: Full=30S ribosomal protein S4
 gi|27315860|gb|AAO04995.1|AE016748_229 30S ribosomal protein S4 [Staphylococcus epidermidis ATCC 12228]
 gi|57637899|gb|AAW54687.1| ribosomal protein S4 [Staphylococcus epidermidis RP62A]
 gi|251805329|gb|EES57986.1| 30S ribosomal protein S4 [Staphylococcus epidermidis BCM-HMP0060]
 gi|281294884|gb|EFA87411.1| ribosomal protein S4 [Staphylococcus epidermidis SK135]
 gi|291319572|gb|EFE59938.1| 30S ribosomal protein S4 [Staphylococcus epidermidis
           M23864:W2(grey)]
 gi|329727885|gb|EGG64335.1| ribosomal protein S4 [Staphylococcus epidermidis VCU144]
 gi|329737374|gb|EGG73628.1| ribosomal protein S4 [Staphylococcus epidermidis VCU028]
 gi|329737515|gb|EGG73768.1| ribosomal protein S4 [Staphylococcus epidermidis VCU045]
          Length = 200

 Score = 44.4 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+   G+A +RR+  +++    ++V+G  ++  + ++     I V
Sbjct: 93  RLDAVVYSLGLARTRRQARQLVNHGHIEVDGGRVDIPSYSLKPGQVITV 141


>gi|258651411|ref|YP_003200567.1| 30S ribosomal protein S4 [Nakamurella multipartita DSM 44233]
 gi|258554636|gb|ACV77578.1| ribosomal protein S4 [Nakamurella multipartita DSM 44233]
          Length = 201

 Score = 44.4 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR   ++++    +VNG+ ++  +  V   D I V
Sbjct: 92  RLDNVVYRAGLARTRRHARQLVSHGHFEVNGVRVDVPSYRVEQYDLITV 140


>gi|73992763|ref|XP_543108.2| PREDICTED: similar to Hypothetical zinc finger protein KIAA1196
           [Canis familiaris]
          Length = 934

 Score = 44.4 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 20/140 (14%), Positives = 35/140 (25%), Gaps = 6/140 (4%)

Query: 202 KKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV-SKKILREQLGPHLLEEAQVNLDAP 260
               E     V+ L          G  L G    +   K    + G           +  
Sbjct: 796 NDCCEAIYSSVSGLK-AHLASCSKGDHLVGKYCCLLCPKEFSSESGVKYHILKTHAENWF 854

Query: 261 IYSSETLVRDRPN----IISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
             S++ L + R         E        KK   +    + ++       RR+       
Sbjct: 855 RTSADPLPKHRSQDSLAPKKEEKKSLAGGKKRGRKPKERTPEEPAPKMPPRRDDWPPGGR 914

Query: 317 AKGIHSSFLSDSGQREENHR 336
            KG   S    +G  +   +
Sbjct: 915 DKGARGSTGRKAGASKAPEK 934


>gi|119384564|ref|YP_915620.1| RNA-binding S4 domain-containing protein [Paracoccus
          denitrificans PD1222]
 gi|119374331|gb|ABL69924.1| heat shock protein Hsp15 [Paracoccus denitrificans PD1222]
          Length = 89

 Score = 44.4 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 1/58 (1%)

Query: 6  IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          + QE     R+ + +  A    +R      I    ++VNG    + A  V   D + V
Sbjct: 1  MSQEAAGAIRLDRWLHHARLFKTRTLAADAIGAGGIRVNGQPCSKPAQAVRGGDTVTV 58


>gi|320040475|gb|EFW22408.1| 30S ribosomal subunit S4 [Coccidioides posadasii str. Silveira]
          Length = 463

 Score = 44.4 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 23/54 (42%), Gaps = 1/54 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+   I RA  AS  R+  + +    V VNG  ++     +   D  +VD   +
Sbjct: 132 RLDVAIFRAMFASSTRQARQFVVHGAVTVNGKKMQYPGYLLNPGDLFQVDPERV 185


>gi|239833213|ref|ZP_04681542.1| translation initiation factor IF-2 [Ochrobactrum intermedium LMG
           3301]
 gi|239825480|gb|EEQ97048.1| translation initiation factor IF-2 [Ochrobactrum intermedium LMG
           3301]
          Length = 961

 Score = 44.4 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 6/111 (5%), Positives = 22/111 (19%), Gaps = 8/111 (7%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
                       ++   +        +P    R ++    +      +       + +  
Sbjct: 204 RQAEEEARLKAEADARRKAEEEAAKRMPQPEARTERRDDARPAPQGNRPREAGRPQGSRP 263

Query: 312 SNVWMAKGIHSSFLS--------DSGQREENHRRSPSFPSKRSLRRTSAKK 354
                 +                      ++  R P        RR + ++
Sbjct: 264 PQSGRPQQGGPRPAPSLVDAAPIPGKPLPQSQLRKPGQSDDDDDRRGAVRR 314



 Score = 42.1 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 13/116 (11%), Positives = 29/116 (25%), Gaps = 2/116 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R + +  +RE +        +    A   +     R+         +   + + ++ +K 
Sbjct: 164 RALEEAQVRE-VEERARAVEEAKRRAEEEARRAKEREESARRQAEEEARLKAEADARRKA 222

Query: 294 GLSKQKKLATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                K++  P  R     +   A  G                   P     R   
Sbjct: 223 EEEAAKRMPQPEARTERRDDARPAPQGNRPREAGRPQGSRPPQSGRPQQGGPRPAP 278


>gi|149197866|ref|ZP_01874915.1| 30S ribosomal protein S4 [Lentisphaera araneosa HTCC2155]
 gi|149139087|gb|EDM27491.1| 30S ribosomal protein S4 [Lentisphaera araneosa HTCC2155]
          Length = 205

 Score = 44.4 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 10/51 (19%), Positives = 23/51 (45%), Gaps = 1/51 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+  V+ R G A +R    +++    +++NG      + +V   D + +  
Sbjct: 97  RLDNVVYRLGFAPTRSAARQLVGHGHIRINGRRCNIPSYSVRPGDVVSLKD 147


>gi|119196147|ref|XP_001248677.1| hypothetical protein CIMG_02448 [Coccidioides immitis RS]
 gi|303321920|ref|XP_003070954.1| S4 domain containing protein [Coccidioides posadasii C735 delta
           SOWgp]
 gi|240110651|gb|EER28809.1| S4 domain containing protein [Coccidioides posadasii C735 delta
           SOWgp]
          Length = 463

 Score = 44.4 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 23/54 (42%), Gaps = 1/54 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+   I RA  AS  R+  + +    V VNG  ++     +   D  +VD   +
Sbjct: 132 RLDVAIFRAMFASSTRQARQFVVHGAVTVNGKKMQYPGYLLNPGDLFQVDPERV 185


>gi|213962933|ref|ZP_03391193.1| ribosomal protein S4 [Capnocytophaga sputigena Capno]
 gi|213954590|gb|EEB65912.1| ribosomal protein S4 [Capnocytophaga sputigena Capno]
          Length = 201

 Score = 44.0 bits (102), Expect = 0.030,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA +R    ++++ + + VNG ++   + ++   D + V
Sbjct: 94  RLDNVVYRMGIAPTRSAARQLVSHRHITVNGNIVNIPSYSLKPGDVVGV 142


>gi|116629861|ref|YP_815033.1| 30S ribosomal protein S4 [Lactobacillus gasseri ATCC 33323]
 gi|116095443|gb|ABJ60595.1| SSU ribosomal protein S4P [Lactobacillus gasseri ATCC 33323]
          Length = 224

 Score = 44.0 bits (102), Expect = 0.030,   Method: Composition-based stats.
 Identities = 10/52 (19%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  ++ R G+AS R +  +++    + V+G  ++  +  V     I +   
Sbjct: 115 RLDNIVYRLGLASTREQARQLVNHGHILVDGKRVDIPSYEVKVGQEISLRDK 166


>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 = 44.0 bits (102), Expect = 0.031,   Method: Composition-based stats.
 Identities = 30/256 (11%), Positives = 68/256 (26%), Gaps = 48/256 (18%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            + I+QE+   QRV K + +   A  +  + + I  +++KVN       A  ++  DH+ 
Sbjct: 2   REFIIQEDDANQRVDKFLQKTLPALPKSLMYKYIRNKKIKVNRKRC-EIAQRLLPGDHVL 60

Query: 62  V--------------------------------------------DGVPLRKAERTRLWL 77
                                                        D   ++     R   
Sbjct: 61  CFIAEEFFETGEDCSFLKVSSELDVLYEDANVILMKKPSGLLTHKDSNEIQDNLADRFLH 120

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           Y    G     +       +   L      ++   +       +     +  + +     
Sbjct: 121 YLYKKGQYDPQTRQSFTPALCHRLDRNTEGIVIGAKTAEALRRMNAYIREHKVEKHYVCI 180

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVTVGLRE 195
               +            +D  +        +      ++ +     Q    A+V V L  
Sbjct: 181 VEGVMEQKTGHVVLWHKKDAKSNKVHLYAHEQKNSQRIETSYRTLHQGKRYAYVEVQLHT 240

Query: 196 GKNREIKKVFEFFNWK 211
           GK+ +I+ V  + +  
Sbjct: 241 GKSHQIRAVMAYLHHP 256


>gi|242374009|ref|ZP_04819583.1| 30S ribosomal protein S4 [Staphylococcus epidermidis M23864:W1]
 gi|242348260|gb|EES39862.1| 30S ribosomal protein S4 [Staphylococcus epidermidis M23864:W1]
          Length = 200

 Score = 44.0 bits (102), Expect = 0.031,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+   G+A +RR+  +++    ++V+G  ++  + ++     I V
Sbjct: 93  RLDAVVYSLGLARTRRQARQLVNHGHIEVDGGRVDIPSYSLKPGQVITV 141


>gi|239905883|ref|YP_002952622.1| 30S ribosomal protein S4 [Desulfovibrio magneticus RS-1]
 gi|259495275|sp|C4XLK2|RS4_DESMR RecName: Full=30S ribosomal protein S4
 gi|239795747|dbj|BAH74736.1| 30S ribosomal protein S4 [Desulfovibrio magneticus RS-1]
          Length = 208

 Score = 44.0 bits (102), Expect = 0.031,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   I R G A SR +  +++      +NG  +   ++ V   D IEV
Sbjct: 99  RLDNTIYRLGFATSRNQARQLVRHGLFTLNGRRVNIPSLQVKVGDVIEV 147


>gi|254675189|ref|NP_001157036.1| H/ACA ribonucleoprotein complex non-core subunit NAF1 [Mus
           musculus]
          Length = 597

 Score = 44.0 bits (102), Expect = 0.031,   Method: Composition-based stats.
 Identities = 12/103 (11%), Positives = 19/103 (18%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P   E+ +      +          P          +                    P 
Sbjct: 24  APQPPEDRREAPPPGVQPPPPAPSSDPGGRPPPLPAPSSDPGGRPPPLPAPNSDPGGRPP 83

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                +S+         +  SD G R        S P  R   
Sbjct: 84  PLPAPSSDPGGRPPPLPAPNSDPGGRPPPLPAPSSDPGGRPPP 126



 Score = 40.5 bits (93), Expect = 0.36,   Method: Composition-based stats.
 Identities = 13/90 (14%), Positives = 17/90 (18%)

Query: 259 APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAK 318
           A     E      P  +   P   +                    P       S+     
Sbjct: 23  AAPQPPEDRREAPPPGVQPPPPAPSSDPGGRPPPLPAPSSDPGGRPPPLPAPNSDPGGRP 82

Query: 319 GIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
               +  SD G R        S P  R   
Sbjct: 83  PPLPAPSSDPGGRPPPLPAPNSDPGGRPPP 112



 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 12/99 (12%), Positives = 17/99 (17%), Gaps = 2/99 (2%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK--KNSSQKNGL 295
            +  RE   P +          P      L     +     P                  
Sbjct: 28  PEDRREAPPPGVQPPPPAPSSDPGGRPPPLPAPSSDPGGRPPPLPAPNSDPGGRPPPLPA 87

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREEN 334
                   P       S+         +  SD G R   
Sbjct: 88  PSSDPGGRPPPLPAPNSDPGGRPPPLPAPSSDPGGRPPP 126



 Score = 37.9 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 11/98 (11%), Positives = 14/98 (14%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
            E                           D                       P      
Sbjct: 1   MEVVEAAAQLQTLKFGGSGQGSAAPQPPEDRREAPPPGVQPPPPAPSSDPGGRPPPLPAP 60

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           +S+         +  SD G R        S P  R   
Sbjct: 61  SSDPGGRPPPLPAPNSDPGGRPPPLPAPSSDPGGRPPP 98


>gi|291548010|emb|CBL21118.1| SSU ribosomal protein S4P [Ruminococcus sp. SR1/5]
          Length = 197

 Score = 44.0 bits (102), Expect = 0.031,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G A +RRE  +++  + V VNG  +   +    + D IE+
Sbjct: 88  RLDNIVFRMGFARTRREARQIVDHKHVLVNGKCVNIPSYLCKAGDTIEI 136


>gi|257095016|ref|YP_003168657.1| 30S ribosomal protein S4 [Candidatus Accumulibacter phosphatis
           clade IIA str. UW-1]
 gi|257047540|gb|ACV36728.1| ribosomal protein S4 [Candidatus Accumulibacter phosphatis clade
           IIA str. UW-1]
          Length = 209

 Score = 44.0 bits (102), Expect = 0.031,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V  R G A SR E  +++    V VNG  +   +  V   D +EV
Sbjct: 100 RLDSVAYRMGFAASRSESRQVVRHNGVLVNGRRVNIPSYQVRPGDVVEV 148


>gi|223043626|ref|ZP_03613671.1| ribosomal protein S4 [Staphylococcus capitis SK14]
 gi|222443114|gb|EEE49214.1| ribosomal protein S4 [Staphylococcus capitis SK14]
          Length = 200

 Score = 44.0 bits (102), Expect = 0.031,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+   G+A +RR+  +++    ++V+G  ++  + ++     I V
Sbjct: 93  RLDAVVYSLGLARTRRQARQLVNHGHIEVDGGRVDIPSYSLKPGQVITV 141


>gi|315225425|ref|ZP_07867239.1| 30S ribosomal protein S4 [Capnocytophaga ochracea F0287]
 gi|314944698|gb|EFS96733.1| 30S ribosomal protein S4 [Capnocytophaga ochracea F0287]
          Length = 201

 Score = 44.0 bits (102), Expect = 0.031,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA +R    ++++ + + VNG ++   + ++   D + V
Sbjct: 94  RLDNVVYRMGIAPTRSAARQLVSHRHITVNGNIVNIPSYSLKPGDVVGV 142


>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 = 44.0 bits (102), Expect = 0.031,   Method: Composition-based stats.
 Identities = 30/232 (12%), Positives = 66/232 (28%), Gaps = 34/232 (14%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK----------AERTRLWL 77
           R  ++  +A+ +V VNGI        +     + +    +             E   + +
Sbjct: 30  RNSIKSALARGQVSVNGIPRTVHNFPLEQGQTVALSKEKVAPVVPLTGLRILHEDEAIIV 89

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV------GRLDINTEGLLLLTN----D 127
            HK  GL++  S  +   T +  L +   R           RLD +T G+++        
Sbjct: 90  IHKDAGLLSVASAQEQEVTAYRQLTAHVRREHPYNRIFVLHRLDRDTSGVMMFAKSEAIQ 149

Query: 128 GGLARVLELPSTQWLRV---------YRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
             + +  +    +   +                 + + K   +          +      
Sbjct: 150 QEMQQAWKEVVYERTYIALVEGQVKKETGTITSWLKESKTLKMYSSPYPNDGQHAVTHYK 209

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI-----SYGPFQL 225
                   + + V L  G+  +I+   E     +    +      S G   L
Sbjct: 210 RLQANRHFSLLEVRLETGRKNQIRVHMEDIGHPIVGDKKYGSKSKSIGRLGL 261


>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 = 44.0 bits (102), Expect = 0.031,   Method: Composition-based stats.
 Identities = 28/243 (11%), Positives = 63/243 (25%), Gaps = 40/243 (16%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------------- 62
           ++  G   R  V+ ++A+ +V VNG         +     + V                 
Sbjct: 61  LSSTG---RNAVKSILARGQVSVNGQATTAYNYPLKPGFTVTVSKEKIEEAPPLIGLVIL 117

Query: 63  --DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
             D   +   +   L                  + T    + +  +R+  V RLD +T G
Sbjct: 118 HEDDDIVVVQKDAGLLSISSDKENKENELTAYRQLTAHVRVHNPRNRIFVVHRLDRDTSG 177

Query: 121 LLLLTNDGGLARVLELPSTQWLRVY-------------RVRFHGQVDQDKLNLLKKGIVI 167
           +++        + L+    + ++                      + +     +      
Sbjct: 178 VMMFAKTEAAQQQLQNNWQEVVKERSYIALVDGKVRKAEGTITSWLRESSTLKMYSSFRE 237

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI----RIS-YGP 222
               +              + + V L  G+  +I+   E     +        R    G 
Sbjct: 238 GDGQHAVTHYKTLQTNQHYSLLEVHLETGRKNQIRVHMEDIGHPIAGDKKYGSRSREIGR 297

Query: 223 FQL 225
             L
Sbjct: 298 LGL 300


>gi|297622733|ref|YP_003704167.1| RNA-binding S4 domain-containing protein [Truepera radiovictrix
          DSM 17093]
 gi|297163913|gb|ADI13624.1| RNA-binding S4 domain protein [Truepera radiovictrix DSM 17093]
          Length = 83

 Score = 44.0 bits (102), Expect = 0.031,   Method: Composition-based stats.
 Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 4/46 (8%)

Query: 20 IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          +A+ G     + + MI   RV+VNG +  R    +   D + V   
Sbjct: 28 LAQTGG----QAKLMIQSGRVRVNGEVETRRKRKLREGDTVTVGDE 69


>gi|226329505|ref|ZP_03805023.1| hypothetical protein PROPEN_03414 [Proteus penneri ATCC 35198]
 gi|225202691|gb|EEG85045.1| hypothetical protein PROPEN_03414 [Proteus penneri ATCC 35198]
          Length = 102

 Score = 44.0 bits (102), Expect = 0.031,   Method: Composition-based stats.
 Identities = 11/41 (26%), Positives = 21/41 (51%), Gaps = 1/41 (2%)

Query: 23 AGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           G   +R E  +M++ + + VNG ++  A+  V   D + V
Sbjct: 1  MGFGATRAEARQMVSHKAIMVNGRVVNIASYQVSPNDVVSV 41


>gi|152980403|ref|YP_001355076.1| 30S ribosomal protein S4 [Janthinobacterium sp. Marseille]
 gi|179308084|sp|A6T3H9|RS4_JANMA RecName: Full=30S ribosomal protein S4
 gi|151280480|gb|ABR88890.1| small subunit ribosomal protein S4 [Janthinobacterium sp.
           Marseille]
          Length = 207

 Score = 44.0 bits (102), Expect = 0.031,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ +   VNGI++  A+  V   D I V
Sbjct: 98  RLDNVVYRMGFGSTRAEGRQLVSHKAFTVNGIVVNIASYQVKPGDVIAV 146


>gi|160880642|ref|YP_001559610.1| hemolysin A [Clostridium phytofermentans ISDg]
 gi|160429308|gb|ABX42871.1| hemolysin A [Clostridium phytofermentans ISDg]
          Length = 266

 Score = 44.0 bits (102), Expect = 0.031,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 14 QRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          +R+  ++ AR    SR + + +I    V V+G   ++A         IEV G  ++ 
Sbjct: 3  ERLDVLLVARNLAESREKAKAIIMSGNVYVDGQKEDKAGSMFKPEVSIEVKGTAMKY 59


>gi|45440809|ref|NP_992348.1| ATP-dependent RNA helicase RhlE [Yersinia pestis biovar Microtus
           str. 91001]
 gi|45435667|gb|AAS61225.1| Superfamily II DNA and RNA helicases [Yersinia pestis biovar
           Microtus str. 91001]
          Length = 470

 Score = 44.0 bits (102), Expect = 0.031,   Method: Composition-based stats.
 Identities = 13/101 (12%), Positives = 29/101 (28%), Gaps = 2/101 (1%)

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL--SKQKKLATPVHRRNLAS 312
           V+    +   E L++     I+    +     K    +NG      ++            
Sbjct: 370 VDEHKLLRDIERLLKREIPRIALDGYEPDPSIKADPIQNGRQGRGAQRPGMGRGSSAGRP 429

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                        +   + + + +R P+ PS R   R   +
Sbjct: 430 QNGGGAAGRGDSRNSRPRSQADGQRRPAGPSSRGRSRNPGE 470


>gi|218513418|ref|ZP_03510258.1| hemolysin A [Rhizobium etli 8C-3]
          Length = 211

 Score = 44.0 bits (102), Expect = 0.032,   Method: Composition-based stats.
 Identities = 9/48 (18%), Positives = 22/48 (45%), Gaps = 1/48 (2%)

Query: 9  ENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVM 55
           +   QR+ +++   G  ASR      + +  V++ G ++ +A   + 
Sbjct: 15 SDQNSQRLDQLLVSRGLFASRSRARDAVQRGTVRIGGQVVTKAGALIS 62


>gi|78213345|ref|YP_382124.1| RNA-binding S4 [Synechococcus sp. CC9605]
 gi|78197804|gb|ABB35569.1| RNA-binding S4 [Synechococcus sp. CC9605]
          Length = 73

 Score = 44.0 bits (102), Expect = 0.032,   Method: Composition-based stats.
 Identities = 13/62 (20%), Positives = 26/62 (41%), Gaps = 1/62 (1%)

Query: 6  IVQENFTPQRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          +V    +P ++ + +   G  S   E ++ I    V+VNG +  R    +   D + + G
Sbjct: 1  MVSSELSPMKLDQFLKWKGWVSTGGEAKQRIQMGEVEVNGSVETRRGRQLSPGDRVVLAG 60

Query: 65 VP 66
            
Sbjct: 61 EE 62


>gi|320014325|gb|ADV97896.1| putative ATP-dependent RNA helicase [Yersinia pestis biovar
           Medievalis str. Harbin 35]
          Length = 451

 Score = 44.0 bits (102), Expect = 0.032,   Method: Composition-based stats.
 Identities = 13/101 (12%), Positives = 29/101 (28%), Gaps = 2/101 (1%)

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL--SKQKKLATPVHRRNLAS 312
           V+    +   E L++     I+    +     K    +NG      ++            
Sbjct: 351 VDEHKLLRDIERLLKREIPRIALDGYEPDPSIKADPIQNGRQGRGAQRPGMGRGSSAGRP 410

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                        +   + + + +R P+ PS R   R   +
Sbjct: 411 QNGGGAAGRGDSRNSRPRSQADGQRRPAGPSSRGRSRNPGE 451


>gi|311899101|dbj|BAJ31509.1| putative hemolysin [Kitasatospora setae KM-6054]
          Length = 268

 Score = 44.0 bits (102), Expect = 0.032,   Method: Composition-based stats.
 Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 1/41 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNV 54
          R+   + R  +A SR     +IA  RV V G +  + A  V
Sbjct: 5  RLDAELVRRKLARSREHASELIAAGRVTVGGAVATKPATQV 45


>gi|224476810|ref|YP_002634416.1| 30S ribosomal protein S4 [Staphylococcus carnosus subsp. carnosus
           TM300]
 gi|254764610|sp|B9DN91|RS4_STACT RecName: Full=30S ribosomal protein S4
 gi|222421417|emb|CAL28231.1| 30S ribosomal protein S4 [Staphylococcus carnosus subsp. carnosus
           TM300]
          Length = 201

 Score = 44.0 bits (102), Expect = 0.032,   Method: Composition-based stats.
 Identities = 9/49 (18%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+   G+A +RR+  +++    ++V+G  +   +  +     + V
Sbjct: 93  RLDAVVYALGLARTRRQARQLVGHGHIEVDGKRVNIPSYTLKPGQVVSV 141


>gi|325299106|ref|YP_004259023.1| ribosomal protein S4 [Bacteroides salanitronis DSM 18170]
 gi|324318659|gb|ADY36550.1| ribosomal protein S4 [Bacteroides salanitronis DSM 18170]
          Length = 201

 Score = 44.0 bits (102), Expect = 0.032,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R GIA +R    ++++ + + V+G ++   +  V     I V
Sbjct: 93  RLDNIVFRLGIAPTRAAARQLVSHKHITVDGKVVNIPSFAVKPGQLIGV 141


>gi|124003687|ref|ZP_01688535.1| ribosomal protein S4 [Microscilla marina ATCC 23134]
 gi|123990742|gb|EAY30209.1| ribosomal protein S4 [Microscilla marina ATCC 23134]
          Length = 200

 Score = 44.0 bits (102), Expect = 0.032,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   + R GIA +RR   +++  + + VNG +    + ++   D + V
Sbjct: 93  RLDNTVYRLGIAPTRRAARQLVIHKHITVNGEVANVPSYSLKPGDIVGV 141


>gi|51595558|ref|YP_069749.1| ATP-dependent RNA helicase RhlE [Yersinia pseudotuberculosis IP
           32953]
 gi|108807091|ref|YP_651007.1| ATP-dependent RNA helicase RhlE [Yersinia pestis Antiqua]
 gi|108812974|ref|YP_648741.1| ATP-dependent RNA helicase RhlE [Yersinia pestis Nepal516]
 gi|153950333|ref|YP_001401773.1| ATP-dependent RNA helicase RhlE [Yersinia pseudotuberculosis IP
           31758]
 gi|166211637|ref|ZP_02237672.1| ATP-dependent RNA helicase, DEAD/DEAH box family [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|167400295|ref|ZP_02305808.1| ATP-dependent RNA helicase, DEAD/DEAH box family [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167423922|ref|ZP_02315675.1| ATP-dependent RNA helicase, DEAD/DEAH box family [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|170025120|ref|YP_001721625.1| ATP-dependent RNA helicase RhlE [Yersinia pseudotuberculosis YPIII]
 gi|186894614|ref|YP_001871726.1| ATP-dependent RNA helicase RhlE [Yersinia pseudotuberculosis PB1/+]
 gi|229894068|ref|ZP_04509254.1| putative ATP-dependent RNA helicase [Yersinia pestis Pestoides A]
 gi|229903411|ref|ZP_04518524.1| putative ATP-dependent RNA helicase [Yersinia pestis Nepal516]
 gi|294503186|ref|YP_003567248.1| DEAD/DEAH box helicase [Yersinia pestis Z176003]
 gi|51588840|emb|CAH20454.1| putative ATP-dependent RNA helicase rhlE [Yersinia
           pseudotuberculosis IP 32953]
 gi|108776622|gb|ABG19141.1| DEAD/DEAH box helicase [Yersinia pestis Nepal516]
 gi|108779004|gb|ABG13062.1| DEAD/DEAH box helicase [Yersinia pestis Antiqua]
 gi|152961828|gb|ABS49289.1| ATP-dependent RNA helicase, DEAD/DEAH box family [Yersinia
           pseudotuberculosis IP 31758]
 gi|166207408|gb|EDR51888.1| ATP-dependent RNA helicase, DEAD/DEAH box family [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|167050244|gb|EDR61652.1| ATP-dependent RNA helicase, DEAD/DEAH box family [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167056771|gb|EDR66534.1| ATP-dependent RNA helicase, DEAD/DEAH box family [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|169751654|gb|ACA69172.1| DEAD/DEAH box helicase domain protein [Yersinia pseudotuberculosis
           YPIII]
 gi|186697640|gb|ACC88269.1| DEAD/DEAH box helicase domain protein [Yersinia pseudotuberculosis
           PB1/+]
 gi|229679181|gb|EEO75284.1| putative ATP-dependent RNA helicase [Yersinia pestis Nepal516]
 gi|229703953|gb|EEO90966.1| putative ATP-dependent RNA helicase [Yersinia pestis Pestoides A]
 gi|262361223|gb|ACY57944.1| DEAD/DEAH box helicase [Yersinia pestis D106004]
 gi|294353645|gb|ADE63986.1| DEAD/DEAH box helicase [Yersinia pestis Z176003]
          Length = 451

 Score = 44.0 bits (102), Expect = 0.032,   Method: Composition-based stats.
 Identities = 13/101 (12%), Positives = 29/101 (28%), Gaps = 2/101 (1%)

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL--SKQKKLATPVHRRNLAS 312
           V+    +   E L++     I+    +     K    +NG      ++            
Sbjct: 351 VDEHKLLRDIERLLKREIPRIALDGYEPDPSIKADPIQNGRQGRGAQRPGMGRGSSAGRP 410

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                        +   + + + +R P+ PS R   R   +
Sbjct: 411 QNGGGAAGRGDSRNSRPRSQADGQRRPAGPSSRGRSRNPGE 451


>gi|237734477|ref|ZP_04564958.1| 30S ribosomal protein S4 [Mollicutes bacterium D7]
 gi|229382297|gb|EEO32388.1| 30S ribosomal protein S4 [Coprobacillus sp. D7]
          Length = 201

 Score = 44.0 bits (102), Expect = 0.033,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR   +++      VNGI  +  +  V   D IEV
Sbjct: 92  RLDNVVYRLGFAPTRRAARQLVNHGHFLVNGIKTDIPSFRVKVGDVIEV 140


>gi|307244571|ref|ZP_07526676.1| ribosomal protein S4 [Peptostreptococcus stomatis DSM 17678]
 gi|306492098|gb|EFM64146.1| ribosomal protein S4 [Peptostreptococcus stomatis DSM 17678]
          Length = 201

 Score = 44.0 bits (102), Expect = 0.033,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A S R+  +M++   + VNG  ++  +  V   D I +
Sbjct: 90  RLDNLVYRMGLANSIRQARQMVSHGNIHVNGRKVDIPSYIVSVGDEISL 138


>gi|7525035|ref|NP_051061.1| ribosomal protein S4 [Arabidopsis thaliana]
 gi|6685914|sp|P56799|RR4_ARATH RecName: Full=30S ribosomal protein S4, chloroplastic
 gi|5881696|dbj|BAA84387.1| ribosomal protein S4 [Arabidopsis thaliana]
          Length = 201

 Score = 44.0 bits (102), Expect = 0.033,   Method: Composition-based stats.
 Identities = 10/53 (18%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
            R+  ++ R G+A +  +  +++    + VNG +++  +      D I V   
Sbjct: 89  MRLDNILFRLGMALTIPQARQLVNHGHILVNGRIVDIPSYRCKPRDIITVKDE 141


>gi|19704619|ref|NP_604181.1| 30S ribosomal protein S4 [Fusobacterium nucleatum subsp. nucleatum
           ATCC 25586]
 gi|296329034|ref|ZP_06871540.1| 30S ribosomal protein S4 [Fusobacterium nucleatum subsp. nucleatum
           ATCC 23726]
 gi|26399398|sp|Q8RE43|RS4_FUSNN RecName: Full=30S ribosomal protein S4
 gi|19714919|gb|AAL95480.1| SSU ribosomal protein S4P [Fusobacterium nucleatum subsp. nucleatum
           ATCC 25586]
 gi|296153838|gb|EFG94650.1| 30S ribosomal protein S4 [Fusobacterium nucleatum subsp. nucleatum
           ATCC 23726]
          Length = 195

 Score = 44.0 bits (102), Expect = 0.033,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+  ++++   + VNG  +  A+  V   D + V
Sbjct: 89  RLENVVYRLGFAKTRRQARQIVSHGHIAVNGRRVNIASFRVKVGDIVSV 137


>gi|329666674|gb|AEB92622.1| S4 RNA-binding domain protein [Lactobacillus johnsonii DPC 6026]
          Length = 80

 Score = 44.0 bits (102), Expect = 0.033,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR   + M  Q RVKVN  +++  + +V   D IE+
Sbjct: 1  MRIDKFLKVSRLVKRRTVAKEMADQGRVKVNDRVVKS-SYDVKLGDVIEI 49


>gi|297537555|ref|YP_003673324.1| 30S ribosomal protein S4 [Methylotenera sp. 301]
 gi|297256902|gb|ADI28747.1| ribosomal protein S4 [Methylotenera sp. 301]
          Length = 209

 Score = 44.0 bits (102), Expect = 0.033,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V  R G+  SR E  +++    + VNG  +   +  V + D + V
Sbjct: 100 RLDNVTYRMGLGGSRTEARQIVRHNSILVNGRRVNIPSYQVKAGDVVSV 148


>gi|146313361|ref|YP_001178435.1| 30S ribosomal protein S4 [Enterobacter sp. 638]
 gi|172046002|sp|A4WFA4|RS4_ENT38 RecName: Full=30S ribosomal protein S4
 gi|145320237|gb|ABP62384.1| SSU ribosomal protein S4P [Enterobacter sp. 638]
          Length = 206

 Score = 44.0 bits (102), Expect = 0.033,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V + D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKAIMVNGRVVNIASYQVKANDVVCIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|114566433|ref|YP_753587.1| translation initiation factor IF-2 [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
 gi|122318495|sp|Q0AYI8|IF2_SYNWW RecName: Full=Translation initiation factor IF-2
 gi|114337368|gb|ABI68216.1| bacterial translation initiation factor 2 (bIF-2) [Syntrophomonas
           wolfei subsp. wolfei str. Goettingen]
          Length = 882

 Score = 44.0 bits (102), Expect = 0.033,   Method: Composition-based stats.
 Identities = 18/115 (15%), Positives = 28/115 (24%), Gaps = 2/115 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE S+   REQ        +          S      RP    E        + ++    
Sbjct: 111 REFSEN--REQSRKGEERHSANPRPGTQMKSPRNNAPRPTTRPENRSAGATGRTDNRAPG 168

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
              +    A     R        A    +     +  R +N    PS   +   R
Sbjct: 169 AAGRTDNRAPGAVGRTDNRGAGSASRPDNRVTRPAAGRPDNKGSRPSDAKRPPQR 223



 Score = 39.4 bits (90), Expect = 0.78,   Method: Composition-based stats.
 Identities = 16/111 (14%), Positives = 32/111 (28%), Gaps = 2/111 (1%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G     E +              R    + S   +      +  ++  G + +     P 
Sbjct: 109 GRREFSENREQSRKGEERHSANPRPGTQMKSPRNNAPRPTTRPENRSAGATGRTDNRAPG 168

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS--FPSKRSLRRTSAKK 354
                 +    A G   +  + S  R +N    P+   P  +  R + AK+
Sbjct: 169 AAGRTDNRAPGAVGRTDNRGAGSASRPDNRVTRPAAGRPDNKGSRPSDAKR 219


>gi|291413101|ref|XP_002722821.1| PREDICTED: splicing coactivator subunit SRm300-like, partial
           [Oryctolagus cuniculus]
          Length = 2699

 Score = 44.0 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 15/107 (14%), Positives = 33/107 (30%), Gaps = 2/107 (1%)

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
               +      P  +         +  S+        ++ S       +  +  +P  +R
Sbjct: 428 RHASSSPESPKPTPAPGARRELSSSPTSKNRSHGRAKREKSHSHTPSRRAARSRSPATKR 487

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRR--SPSFPSKRSLRRTSAK 353
             + +   AK  HS   S   +R  + +R      P +R   R+  +
Sbjct: 488 GRSRSRTPAKRGHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQR 534



 Score = 43.6 bits (101), Expect = 0.045,   Method: Composition-based stats.
 Identities = 17/102 (16%), Positives = 30/102 (29%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P      +++      +       R    S  P       ++ + K G S+ +  A   H
Sbjct: 441 PAPGARRELSSSPTSKNRSHGRAKREKSHSHTPSRRAARSRSPATKRGRSRSRTPAKRGH 500

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
            R+ +     ++       S S QR    R        RS  
Sbjct: 501 SRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPGWSRSRN 542



 Score = 41.3 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 15/134 (11%), Positives = 29/134 (21%), Gaps = 17/134 (12%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           K+       P        +       S +    +          + R +         S 
Sbjct: 464 KREKSHSHTPSRRAARSRSPATKRGRSRSRTPAKRGHSRSRSPQWRRSRSAQRWGRSRSP 523

Query: 298 QKKLATPVHRRNLASNVW-----------------MAKGIHSSFLSDSGQREENHRRSPS 340
           Q++  +   +R   S                                         RS +
Sbjct: 524 QRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRSHSRSPATRGRSRSRTPARRGRSRSRT 583

Query: 341 FPSKRSLRRTSAKK 354
              +RS  RT A++
Sbjct: 584 PARRRSRSRTPARR 597



 Score = 40.2 bits (92), Expect = 0.45,   Method: Composition-based stats.
 Identities = 14/98 (14%), Positives = 31/98 (31%), Gaps = 2/98 (2%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
             A  +      + R    S     ++R +    +    S ++  +          +   
Sbjct: 512 RSAQRWGRSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRSHSRSPATRGRSRSR 571

Query: 317 AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                    S +  R  +  R+P+   +RS  RT A++
Sbjct: 572 TPARRGRSRSRTPARRRSRSRTPAR--RRSRSRTPARR 607



 Score = 38.2 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 17/108 (15%), Positives = 29/108 (26%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P      +                  +  S  P   +R   +S +    +        + 
Sbjct: 391 PSEASPTRGRSPPKSPEKPPPSSSESSPPSPQPAKVSRHASSSPESPKPTPAPGARRELS 450

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               + N    +       S +  R     RSP+    RS  RT AK+
Sbjct: 451 SSPTSKNRSHGRAKREKSHSHTPSRRAARSRSPATKRGRSRSRTPAKR 498



 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 12/104 (11%), Positives = 28/104 (26%), Gaps = 7/104 (6%)

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
            A +    +   + P                +S+     + K+  +  H  +  +    +
Sbjct: 423 PAKVSRHASSSPESPKPTPAPGARRELSSSPTSKNRSHGRAKREKSHSHTPSRRAARSRS 482

Query: 318 KGIHSSFLSDSGQREENHRRSPSFPSKRSLR-------RTSAKK 354
                         +  H RS S   +RS         R+  ++
Sbjct: 483 PATKRGRSRSRTPAKRGHSRSRSPQWRRSRSAQRWGRSRSPQRR 526



 Score = 37.1 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 22/134 (16%), Positives = 35/134 (26%), Gaps = 9/134 (6%)

Query: 230 AGSTREVSKKIL---REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
            G+ RE+S       R        +            S +    R    S  P      +
Sbjct: 443 PGARRELSSSPTSKNRSHGRAKREKSHSHTPSRRAARSRSPATKRGRSRSRTPAKRGHSR 502

Query: 287 KNSSQKNGLSKQKK--LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
             S Q       ++   +    RR  + +        S      G+     R      S 
Sbjct: 503 SRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRSHSRSP 562

Query: 345 ----RSLRRTSAKK 354
               RS  RT A++
Sbjct: 563 ATRGRSRSRTPARR 576


>gi|268318834|ref|YP_003292490.1| ribosomal protein S4 [Lactobacillus johnsonii FI9785]
 gi|262397209|emb|CAX66223.1| ribosomal protein S4 [Lactobacillus johnsonii FI9785]
          Length = 80

 Score = 44.0 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR   + M  Q RVKVN  +++  + +V   D IE+
Sbjct: 1  MRIDKFLKVSRLVKRRTVAKEMADQGRVKVNDRVVKS-SYDVKLGDVIEI 49


>gi|256826013|ref|YP_003149973.1| DNA/RNA helicase [Kytococcus sedentarius DSM 20547]
 gi|256689406|gb|ACV07208.1| DNA/RNA helicase, superfamily II [Kytococcus sedentarius DSM 20547]
          Length = 573

 Score = 44.0 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 9/72 (12%), Positives = 21/72 (29%)

Query: 277 EVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR 336
               + +    ++ +     + ++ A    R    ++   A+G   S       R E   
Sbjct: 483 RFTSESSPRGGSAGRSGDAPRGERGAGRPPRNRGEASARPARGEGGSGRRPERSRPEGGS 542

Query: 337 RSPSFPSKRSLR 348
             P+     S  
Sbjct: 543 GRPARGEGGSRP 554



 Score = 37.5 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 7/59 (11%), Positives = 13/59 (22%)

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           S+         R   A       G       ++  R            +RS     + +
Sbjct: 486 SESSPRGGSAGRSGDAPRGERGAGRPPRNRGEASARPARGEGGSGRRPERSRPEGGSGR 544



 Score = 36.7 bits (83), Expect = 6.1,   Method: Composition-based stats.
 Identities = 3/73 (4%), Positives = 7/73 (9%)

Query: 261 IYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGI 320
                +  R       E         +  +       +        R             
Sbjct: 489 SPRGGSAGRSGDAPRGERGAGRPPRNRGEASARPARGEGGSGRRPERSRPEGGSGRPARG 548

Query: 321 HSSFLSDSGQREE 333
                        
Sbjct: 549 EGGSRPARAAGGS 561


>gi|240144366|ref|ZP_04742967.1| S4 RNA-binding domain protein [Roseburia intestinalis L1-82]
 gi|257203617|gb|EEV01902.1| S4 RNA-binding domain protein [Roseburia intestinalis L1-82]
 gi|291535594|emb|CBL08706.1| Ribosome-associated heat shock protein implicated in the
          recycling of the 50S subunit (S4 paralog) [Roseburia
          intestinalis M50/1]
 gi|291540839|emb|CBL13950.1| Ribosome-associated heat shock protein implicated in the
          recycling of the 50S subunit (S4 paralog) [Roseburia
          intestinalis XB6B4]
          Length = 80

 Score = 44.0 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR          RV VNG   + A+VNV   D IE+
Sbjct: 1  MRLDKFLKVSRLIKRRTVANEACDAGRVSVNGKPAK-ASVNVKVGDIIEI 49


>gi|195158196|ref|XP_002019980.1| GL12707 [Drosophila persimilis]
 gi|194116571|gb|EDW38614.1| GL12707 [Drosophila persimilis]
          Length = 579

 Score = 44.0 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 16/113 (14%), Positives = 35/113 (30%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+       +E        I   +       ++  +      R K++  Q     K+   
Sbjct: 124 RKATAVKTTKERSAQSPLAIKIKQEKRSTSRDLSPKRDFSAARRKRSPDQSPPRRKRVAD 183

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +P  RR  + +    +       S   ++  N  +SP    ++S    S  +
Sbjct: 184 QSPPRRRRGSPDQSPPRRKRDEDQSPPRRKRVNSDQSPPRGGRKSSPDQSPPR 236



 Score = 43.2 bits (100), Expect = 0.058,   Method: Composition-based stats.
 Identities = 17/114 (14%), Positives = 32/114 (28%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            +K + +Q  P     +           E     R   ++         +K+S  ++   
Sbjct: 177 RRKRVADQSPPRRRRGSPDQSPPRRKRDEDQSPPRRKRVNSDQSPPRGGRKSSPDQSPPR 236

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
           +++       RR  + N   +        S         RRS    S    RR 
Sbjct: 237 RRRDSDQSPPRRRRSHNSNQSPPRKGRRSSADQSPPRKGRRSSPDQSPPRRRRD 290



 Score = 40.5 bits (93), Expect = 0.39,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 32/109 (29%), Gaps = 2/109 (1%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                 Q        S +     R     + P    R+  + S   G  K     +P  R
Sbjct: 178 RKRVADQSPPRRRRGSPDQSPPRRKRDEDQSPPRRKRVNSDQSPPRGGRKSSPDQSPPRR 237

Query: 308 RNLA--SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           R  +  S     +  +S+       R  +  +SP    +RS    S  +
Sbjct: 238 RRDSDQSPPRRRRSHNSNQSPPRKGRRSSADQSPPRKGRRSSPDQSPPR 286



 Score = 38.2 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 16/110 (14%), Positives = 30/110 (27%), Gaps = 3/110 (2%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              +E Q        +S+          S       R + +        +         R
Sbjct: 201 RKRDEDQSPPRRKRVNSDQSPPRGGRKSSPDQSPPRRRRDSDQSPPRRRRSHNSNQSPPR 260

Query: 308 RNLASNVWMAK---GIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +   S+   +    G  SS      +R  +  +SP    K S +    K+
Sbjct: 261 KGRRSSADQSPPRKGRRSSPDQSPPRRRRDVDQSPDQRRKDSDQSPPRKR 310



 Score = 37.5 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 14/109 (12%), Positives = 28/109 (25%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +E+         + +  A                        R + +  Q     K+ + 
Sbjct: 147 QEKRSTSRDLSPKRDFSAARRKRSPDQSPPRRKRVADQSPPRRRRGSPDQSPPRRKRDED 206

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
            +P  R+ + S+    +G   S    S  R            +RS    
Sbjct: 207 QSPPRRKRVNSDQSPPRGGRKSSPDQSPPRRRRDSDQSPPRRRRSHNSN 255



 Score = 36.7 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 15/115 (13%), Positives = 30/115 (26%), Gaps = 2/115 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R    P  ++  Q         S                   R K+ + Q     ++   
Sbjct: 135 RSAQSPLAIKIKQEKRSTSRDLSPKRDFSAARRKRSPDQSPPRRKRVADQSPPRRRRGSP 194

Query: 302 ATPVHRRNLASNVWMAKGIH--SSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                RR    +    +     S      G R+ +  +SP    + S +    ++
Sbjct: 195 DQSPPRRKRDEDQSPPRRKRVNSDQSPPRGGRKSSPDQSPPRRRRDSDQSPPRRR 249


>gi|238784236|ref|ZP_04628248.1| ATP-dependent RNA helicase rhlE [Yersinia bercovieri ATCC 43970]
 gi|238714803|gb|EEQ06803.1| ATP-dependent RNA helicase rhlE [Yersinia bercovieri ATCC 43970]
          Length = 451

 Score = 44.0 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 13/101 (12%), Positives = 29/101 (28%), Gaps = 2/101 (1%)

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL--SKQKKLATPVHRRNLAS 312
           V+    +   E L++     I+    +     K    +NG      ++            
Sbjct: 351 VDEHKLLRDIERLLKREIPRIALDGYEPDPSIKADPIQNGRQGRGAQRPGMGRGSSAGRP 410

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                        +   + + + +R P+ PS R   R   +
Sbjct: 411 QNGGGAAGRGDSRNSRPRSQADGQRRPAGPSSRGRSRNPGE 451


>gi|296813367|ref|XP_002847021.1| RecQ family helicase MusN [Arthroderma otae CBS 113480]
 gi|238842277|gb|EEQ31939.1| RecQ family helicase MusN [Arthroderma otae CBS 113480]
          Length = 1550

 Score = 44.0 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 12/128 (9%), Positives = 33/128 (25%), Gaps = 10/128 (7%)

Query: 226  GTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
               + G     S+  L          E            +     +  +      +    
Sbjct: 1421 DDEMYGDW---SEDEL-------NCAEEAQKQSPYFPPDDVAPSFKARVSQFEFSENAES 1470

Query: 286  KKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
             +  ++    S++ +      RR+     +      S+  +   Q  ++ +R  S  + R
Sbjct: 1471 SRQENRSKSNSQRPRSRQTNTRRSRPPKSFRGSKSSSNKFNKRPQGSKSGKRKSSPAASR 1530

Query: 346  SLRRTSAK 353
                +   
Sbjct: 1531 PRSSSKPA 1538


>gi|150020872|ref|YP_001306226.1| 30S ribosomal protein S4 [Thermosipho melanesiensis BI429]
 gi|172048669|sp|A6LLP0|RS4_THEM4 RecName: Full=30S ribosomal protein S4
 gi|149793393|gb|ABR30841.1| RNA-binding S4 domain protein [Thermosipho melanesiensis BI429]
          Length = 209

 Score = 44.0 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R    ++++     VNG  +   +  V   D IEV
Sbjct: 99  RLDNVVYRLGFAVNRTTARQLVSHGHFLVNGKKVNIPSYQVRPGDVIEV 147


>gi|300172732|ref|YP_003771897.1| heat shock protein 15 [Leuconostoc gasicomitatum LMG 18811]
 gi|299887110|emb|CBL91078.1| Heat shock protein 15 [Leuconostoc gasicomitatum LMG 18811]
          Length = 94

 Score = 44.0 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 28/50 (56%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRREVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR V + IA Q R+ +NG + + ++  V + D +EV
Sbjct: 1  MRLDKYLKVSRLIKRRTVAKEIADQGRISINGKVAKSSSD-VSTNDELEV 49


>gi|169831089|ref|YP_001717071.1| translation initiation factor IF-2 [Candidatus Desulforudis
           audaxviator MP104C]
 gi|169637933|gb|ACA59439.1| translation initiation factor IF-2 [Candidatus Desulforudis
           audaxviator MP104C]
          Length = 888

 Score = 44.0 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 8/115 (6%), Positives = 23/115 (20%), Gaps = 1/115 (0%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            + ++         E  V        +    +   +  +         +   +  +    
Sbjct: 100 GEEVKAPAPAPKPPEIPVEARPAPPPAAPAPQPEQHRPTPPTRPVPDRRPQPAGPHARPP 159

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                     R   +     +    +       R     R P+ P +    R   
Sbjct: 160 YAGRPQSGGPRPPQAGGGPPRPQAPAGRYPGPPRPAQGAR-PAVPGRPPQHRGRP 213



 Score = 41.7 bits (96), Expect = 0.15,   Method: Composition-based stats.
 Identities = 10/113 (8%), Positives = 17/113 (15%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
            +  +  P     A          +                          Q  G    +
Sbjct: 114 EIPVEARPAPPPAAPAPQPEQHRPTPPTRPVPDRRPQPAGPHARPPYAGRPQSGGPRPPQ 173

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
               P   +  A                   R   HR  P   +  +      
Sbjct: 174 AGGGPPRPQAPAGRYPGPPRPAQGARPAVPGRPPQHRGRPGVAAAGAPHPGPG 226



 Score = 40.5 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 9/99 (9%), Positives = 17/99 (17%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P           A    S      +       P           +    ++      P 
Sbjct: 148 RPQPAGPHARPPYAGRPQSGGPRPPQAGGGPPRPQAPAGRYPGPPRPAQGARPAVPGRPP 207

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
             R                 +    R    +  P  P++
Sbjct: 208 QHRGRPGVAAAGAPHPGPGGARPPARGILSKAIPKPPAE 246


>gi|32892106|gb|AAP88992.1| ribosomal protein S4 [Passiflora edulis]
          Length = 183

 Score = 44.0 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 13/82 (15%), Positives = 29/82 (35%), Gaps = 1/82 (1%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+  ++ R G+AS   +  +++  + + VNG +++  +      D I V      K   
Sbjct: 71  MRLDNILFRLGMASTIPQARQLVNHRHILVNGRIVDIPSYRCKPQDLITVKDEQKSKDMI 130

Query: 73  TRLWLYHKPIGLVTTHSDPDGR 94
                      L    +    +
Sbjct: 131 QNSLHSFPQEKLPKHLTLHPFQ 152


>gi|51894364|ref|YP_077055.1| hypothetical protein STH3229 [Symbiobacterium thermophilum IAM
          14863]
 gi|51858053|dbj|BAD42211.1| conserved hypothetical protein [Symbiobacterium thermophilum IAM
          14863]
          Length = 97

 Score = 44.0 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 2/51 (3%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+ K +  + I  RR   + +    RV+V G + + A   V   D I +D
Sbjct: 1  MRIDKFLKVSRIIKRRTLAKEVCDAGRVQVGGKVAK-AGTEVKPGDTISID 50


>gi|329939001|ref|ZP_08288375.1| protein kinase [Streptomyces griseoaurantiacus M045]
 gi|329301886|gb|EGG45779.1| protein kinase [Streptomyces griseoaurantiacus M045]
          Length = 461

 Score = 44.0 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 10/91 (10%), Positives = 19/91 (20%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
            E            +      P          +      ++  G ++    A P      
Sbjct: 272 AEMYAEQRTQRRPQDPSATPPPRSGGPSRTGGSARTGGDTRPTGGARTGGEARPTGGSRP 331

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSF 341
                 A G  S        + +  R +P  
Sbjct: 332 TGGSRPAGGARSGARQQPPAQRKGARPAPGS 362



 Score = 41.3 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 12/106 (11%), Positives = 21/106 (19%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
             +       P     ++    A                   P   +R    S    G  
Sbjct: 283 RPQDPSATPPPRSGGPSRTGGSARTGGDTRPTGGARTGGEARPTGGSRPTGGSRPAGGAR 342

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
              +   P  R+         +         +  R     R P+ P
Sbjct: 343 SGARQQPPAQRKGARPAPGSGRRPGPRDGRRTPPRTTGTGRRPANP 388



 Score = 39.8 bits (91), Expect = 0.69,   Method: Composition-based stats.
 Identities = 18/119 (15%), Positives = 29/119 (24%), Gaps = 2/119 (1%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
             +     L   L  +     +A   +       R +            +  + Q+    
Sbjct: 224 DPEERPSTLQLSLRLKEIAAREAQGLTDARPPAQRGSPDLPDRPSGRLAEMYAEQRTQRR 283

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR--EENHRRSPSFPSKRSLRRTSAK 353
            Q   ATP  R    S    +           G R   E      S P+  S     A+
Sbjct: 284 PQDPSATPPPRSGGPSRTGGSARTGGDTRPTGGARTGGEARPTGGSRPTGGSRPAGGAR 342



 Score = 38.2 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 13/117 (11%), Positives = 25/117 (21%), Gaps = 2/117 (1%)

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           ++  EQ      ++                          P    R    +    G    
Sbjct: 273 EMYAEQRTQRRPQDPSATPPPRSGGPSRTGGSARTGGDTRPTGGARTGGEARPTGGSRPT 332

Query: 299 K--KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              + A               KG   +  S       + RR+P   +    R  + +
Sbjct: 333 GGSRPAGGARSGARQQPPAQRKGARPAPGSGRRPGPRDGRRTPPRTTGTGRRPANPR 389


>gi|237742279|ref|ZP_04572760.1| SSU ribosomal protein S4P [Fusobacterium sp. 4_1_13]
 gi|256845558|ref|ZP_05551016.1| ribosomal protein S4 [Fusobacterium sp. 3_1_36A2]
 gi|294785153|ref|ZP_06750441.1| ribosomal protein S4 [Fusobacterium sp. 3_1_27]
 gi|229429927|gb|EEO40139.1| SSU ribosomal protein S4P [Fusobacterium sp. 4_1_13]
 gi|256719117|gb|EEU32672.1| ribosomal protein S4 [Fusobacterium sp. 3_1_36A2]
 gi|294486867|gb|EFG34229.1| ribosomal protein S4 [Fusobacterium sp. 3_1_27]
          Length = 195

 Score = 44.0 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+  ++++   + VNG  +  A+  V   D + V
Sbjct: 89  RLENVVYRLGFAKTRRQARQIVSHGHIAVNGRRVNIASFRVKVGDIVSV 137


>gi|218134790|ref|ZP_03463594.1| hypothetical protein BACPEC_02693 [Bacteroides pectinophilus ATCC
          43243]
 gi|217990175|gb|EEC56186.1| hypothetical protein BACPEC_02693 [Bacteroides pectinophilus ATCC
          43243]
          Length = 90

 Score = 44.0 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 2/57 (3%)

Query: 7  VQENFTPQRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          +  N    R+ K +  + +  RR          RV VN  +++ A+ +V   D IE+
Sbjct: 1  MDRNGVSMRLDKYLKVSRLIKRRTVANDACDAGRVIVNDKVVK-ASYDVKEGDVIEI 56


>gi|56961872|ref|YP_173594.1| heat shock protein [Bacillus clausii KSM-K16]
 gi|56908106|dbj|BAD62633.1| heat shock protein [Bacillus clausii KSM-K16]
          Length = 98

 Score = 44.0 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 3/64 (4%)

Query: 1  MKDK-NIVQENFTPQRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTD 58
          MK K N+  +     R+ K +  + +  RR   + +  Q RV VNG + + A   V + D
Sbjct: 1  MKRKANLTNKRSDWMRLDKFLKVSRLIKRRTLAKEVSDQGRVTVNGQVAK-AGTTVKAGD 59

Query: 59 HIEV 62
           + +
Sbjct: 60 ELAI 63


>gi|300932967|ref|ZP_07148223.1| 30S ribosomal protein S4 [Corynebacterium resistens DSM 45100]
          Length = 201

 Score = 44.0 bits (102), Expect = 0.035,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR+  ++++     VNG      +  V   D I+V
Sbjct: 92  RLDNVVYRAGLARTRRQARQLVSHGHFTVNGKKTNVPSFRVTQYDIIDV 140


>gi|42518365|ref|NP_964295.1| hypothetical protein LJ0278 [Lactobacillus johnsonii NCC 533]
 gi|41582650|gb|AAS08261.1| hypothetical protein LJ_0278 [Lactobacillus johnsonii NCC 533]
          Length = 80

 Score = 44.0 bits (102), Expect = 0.035,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR   + M  Q RVKVN  +++  + +V   D IE+
Sbjct: 1  MRIDKFLKVSRLVKRRTVAKEMADQGRVKVNDRVVKS-SYDVKLDDVIEI 49


>gi|116624175|ref|YP_826331.1| 30S ribosomal protein S4P [Candidatus Solibacter usitatus
           Ellin6076]
 gi|122253109|sp|Q01WB9|RS4_SOLUE RecName: Full=30S ribosomal protein S4
 gi|116227337|gb|ABJ86046.1| SSU ribosomal protein S4P [Candidatus Solibacter usitatus
           Ellin6076]
          Length = 210

 Score = 44.0 bits (102), Expect = 0.035,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI R G   SR +  +++    + VNG      +  +   D I V
Sbjct: 100 RLDSVIYRMGFGTSRAQARQVVRHGHINVNGRKCNIPSALINVGDEITV 148


>gi|81869425|sp|Q9QXM1|JMY_MOUSE RecName: Full=Junction-mediating and -regulatory protein
 gi|6573115|gb|AAF17555.1|AF201390_1 p300 transcriptional cofactor JMY [Mus musculus]
          Length = 983

 Score = 44.0 bits (102), Expect = 0.035,   Method: Composition-based stats.
 Identities = 20/150 (13%), Positives = 39/150 (26%), Gaps = 16/150 (10%)

Query: 221 GPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIY----SSETLVRDRPNIIS 276
             F L   L      V   +  E+     +     N     +     + T  R R     
Sbjct: 1   MSFALEETLESDWVAVRPHVFDEREKHKFVFIVAWNEIEGKFAITCHNRTAQRQRSGSRE 60

Query: 277 EVPDDFTRMKKNSSQKNGLSKQKKL-------ATPVHRRNLASNVWMAKGIHSSFLSDSG 329
           +     +   +         + +          +P  R++ A     +     S   D  
Sbjct: 61  QAGTPASDGSRGPGSPAARGRSEAAASATAALRSPGPRKSQAWAEGGSPRSARSLKGDPP 120

Query: 330 QREENHR-----RSPSFPSKRSLRRTSAKK 354
           +           RSP+      LRR++  +
Sbjct: 121 RGPAGRGPESPLRSPARAKASPLRRSAESR 150


>gi|148652953|ref|YP_001280046.1| DEAD/DEAH box helicase domain-containing protein [Psychrobacter sp.
           PRwf-1]
 gi|148572037|gb|ABQ94096.1| DEAD/DEAH box helicase domain protein [Psychrobacter sp. PRwf-1]
          Length = 516

 Score = 44.0 bits (102), Expect = 0.035,   Method: Composition-based stats.
 Identities = 12/110 (10%), Positives = 21/110 (19%)

Query: 233 TREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
             E+     ++      +  A                +R                 S +K
Sbjct: 405 VEEIEGMEPKKNTKDMHVGTAAKRGRGGNRRGGPGAGNRRGGNGGGGYRGKSADNASGEK 464

Query: 293 NGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
            G    +    P  RR        + G           R    R +    
Sbjct: 465 RGAGAGRPSGKPAGRRFGGKPTGASAGKPGGQRRSGPARSGEGRPARRSS 514


>gi|323450156|gb|EGB06039.1| hypothetical protein AURANDRAFT_72086 [Aureococcus anophagefferens]
          Length = 3973

 Score = 44.0 bits (102), Expect = 0.036,   Method: Composition-based stats.
 Identities = 16/146 (10%), Positives = 43/146 (29%), Gaps = 7/146 (4%)

Query: 211  KVNRLIR--ISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLV 268
            +V +L +     G  +L          +  +   +  G   + +    L     +    +
Sbjct: 2999 RVVKLKKALKRIGQLRLED-----YATLKTEQRVKIHGEADVLDELRTLGVDADALRLKL 3053

Query: 269  RDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDS 328
            +            +++ + ++ +K      +    P  RR  A +         +  + +
Sbjct: 3054 QPGLPTPMPRSRAWSKERDDAREKQKAEDARNYRPPAKRRARAESALRMPAAVKNQNTAT 3113

Query: 329  GQREENHRRSPSFPSKRSLRRTSAKK 354
              R  +   + + P      R   KK
Sbjct: 3114 RSRRSSAGAAEAAPEAPKRSRGRPKK 3139


>gi|15894872|ref|NP_348221.1| 30S ribosomal protein S4 [Clostridium acetobutylicum ATCC 824]
 gi|26399602|sp|Q97IP6|RS4C_CLOAB RecName: Full=Putative 30S ribosomal protein S4 C
 gi|15024549|gb|AAK79561.1|AE007669_4 Ribosomal protein S4 [Clostridium acetobutylicum ATCC 824]
 gi|325509010|gb|ADZ20646.1| 30S ribosomal protein S4 [Clostridium acetobutylicum EA 2018]
          Length = 196

 Score = 44.0 bits (102), Expect = 0.036,   Method: Composition-based stats.
 Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 4/66 (6%)

Query: 1   MKDKNIVQENFTPQ---RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMS 56
           MK+K     +       R+  V+ R G A S R+  +M++   + VNG  L+  +  V  
Sbjct: 71  MKNKEASGSSLLKILECRLDNVVYRIGFANSIRQARQMVSHGLILVNGKKLDIPSYEVQV 130

Query: 57  TDHIEV 62
            D + +
Sbjct: 131 GDVVSL 136


>gi|47458904|ref|YP_015766.1| 30S ribosomal protein S4 [Mycoplasma mobile 163K]
 gi|61215559|sp|Q6KIM1|RS4_MYCMO RecName: Full=30S ribosomal protein S4
 gi|47458232|gb|AAT27555.1| 30s ribosomal protein s4 [Mycoplasma mobile 163K]
          Length = 199

 Score = 44.0 bits (102), Expect = 0.036,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G A +RR+  +++      +NG   +  +  +   D IE+
Sbjct: 95  RLDNIVYRMGFAQTRRQARQLVNHGHFLLNGKKADIPSQRINVGDTIEL 143


>gi|25027127|ref|NP_737181.1| 30S ribosomal protein S4 [Corynebacterium efficiens YS-314]
 gi|41017843|sp|Q8FS34|RS4_COREF RecName: Full=30S ribosomal protein S4
 gi|23492407|dbj|BAC17381.1| putative 30S ribosomal protein S4 [Corynebacterium efficiens
           YS-314]
          Length = 201

 Score = 44.0 bits (102), Expect = 0.036,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR+  ++++     VNG  ++  +  V   D I+V
Sbjct: 92  RLDNVVYRAGLARTRRQARQLVSHGHFVVNGKAVDVPSFRVSQYDIIDV 140


>gi|323700831|ref|ZP_08112743.1| ribosomal protein S4 [Desulfovibrio sp. ND132]
 gi|323460763|gb|EGB16628.1| ribosomal protein S4 [Desulfovibrio desulfuricans ND132]
          Length = 208

 Score = 44.0 bits (102), Expect = 0.036,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI R G A SR +  +++     K+NG  +   ++ V + D IEV
Sbjct: 99  RLDNVIYRLGFANSRDQARQLVLHGIFKLNGRRVSIPSMQVKAEDVIEV 147


>gi|300172651|ref|YP_003771816.1| 30S ribosomal protein S4 [Leuconostoc gasicomitatum LMG 18811]
 gi|299887029|emb|CBL90997.1| 30S ribosomal protein S4 [Leuconostoc gasicomitatum LMG 18811]
          Length = 203

 Score = 44.0 bits (102), Expect = 0.036,   Method: Composition-based stats.
 Identities = 10/53 (18%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           QR+  ++ R G+A+ R++  +++    + V+   ++  + +V     I V   
Sbjct: 93  QRLDSLVYRLGLATTRQQARQLVNHGHIMVDSKRVDIPSFSVTPGQVISVRDK 145


>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 = 44.0 bits (102), Expect = 0.036,   Method: Composition-based stats.
 Identities = 21/207 (10%), Positives = 45/207 (21%), Gaps = 27/207 (13%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEV-------------DGVPLRKAERTRLWLYH 79
           R+I   +V+VN    ++    V + D + +              G      E     +  
Sbjct: 42  RLIRTGQVRVNSKR-KKPYDRVYAGDTVRIPPHFPETGDDPQRAGELQIVFENPDFTVLD 100

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
           KP G+         R  +   L   ++       L    +                    
Sbjct: 101 KPAGVPVHSGTSARRDNMVLRLRKHYAGADFSPALVHRLDKETSGLLLAAKNYAWLRRIQ 160

Query: 140 QWLRVY-------------RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
                                     ++   +   +K            +V         
Sbjct: 161 AMWNKNLVEKTYLAWVHGSWPSRWVNLEHRLIKTFEKMQPSPEGRPALSRVRSIASSRDK 220

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVN 213
             V + +  G+  +I+         V 
Sbjct: 221 TLVQIRIITGRTHQIRTQLSLSGHPVI 247


>gi|34763295|ref|ZP_00144253.1| hypothetical protein [Fusobacterium nucleatum subsp. vincentii
          ATCC 49256]
 gi|27887043|gb|EAA24156.1| hypothetical protein [Fusobacterium nucleatum subsp. vincentii
          ATCC 49256]
          Length = 71

 Score = 44.0 bits (102), Expect = 0.036,   Method: Composition-based stats.
 Identities = 10/71 (14%), Positives = 27/71 (38%), Gaps = 9/71 (12%)

Query: 1  MKDKNIVQENFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
          MK+   V+ +    ++ + +       +G     + +++I    VKVN  +  R    + 
Sbjct: 1  MKNIEKVKISTEFIKLDQFLKWLAVVDSG----SQAKQVILDGEVKVNDEVETRRGRKIY 56

Query: 56 STDHIEVDGVP 66
              +++    
Sbjct: 57 PEYKVKIFDKI 67


>gi|307718230|ref|YP_003873762.1| 30S ribosomal protein S4 [Spirochaeta thermophila DSM 6192]
 gi|306531955|gb|ADN01489.1| 30S ribosomal protein S4 [Spirochaeta thermophila DSM 6192]
          Length = 211

 Score = 44.0 bits (102), Expect = 0.036,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R   AS R++  +++    V VNG  +   +  V   D +E+
Sbjct: 100 RLDNIVYRMHFASSRKQARQIVGHGHVLVNGRKVNIPSYLVREGDRVEI 148


>gi|227894502|ref|ZP_04012307.1| S4 RNA-binding domain protein [Lactobacillus ultunensis DSM
          16047]
 gi|227863661|gb|EEJ71082.1| S4 RNA-binding domain protein [Lactobacillus ultunensis DSM
          16047]
          Length = 92

 Score = 44.0 bits (102), Expect = 0.037,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR   + M  Q R+KVNG +++  + +V   D IE+
Sbjct: 13 MRIDKFLKVSRLVKRRTVAKEMADQGRIKVNGRVVKS-SYDVKIDDIIEI 61


>gi|300775038|ref|ZP_07084901.1| 30S ribosomal protein S4 [Chryseobacterium gleum ATCC 35910]
 gi|300506853|gb|EFK37988.1| 30S ribosomal protein S4 [Chryseobacterium gleum ATCC 35910]
          Length = 202

 Score = 44.0 bits (102), Expect = 0.037,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R    ++++ + + VNG +L   +  V + D I V
Sbjct: 96  RLDNVVYRFGFAKTRSAARQLVSHRHITVNGEILNIPSYLVKAGDVIAV 144


>gi|198474334|ref|XP_002132666.1| GA25955 [Drosophila pseudoobscura pseudoobscura]
 gi|198138346|gb|EDY70068.1| GA25955 [Drosophila pseudoobscura pseudoobscura]
          Length = 1342

 Score = 44.0 bits (102), Expect = 0.037,   Method: Composition-based stats.
 Identities = 12/104 (11%), Positives = 27/104 (25%), Gaps = 5/104 (4%)

Query: 252  EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
            E                +   N   +    F+  ++   ++ G    ++  +   R +  
Sbjct: 1153 EGPPMGREQERQPHYHHQLNGNGARKREPSFSAHEERHPERRGERDARRGESGGLRGDSR 1212

Query: 312  SNVWMAKGIHSSFLSDSG-----QREENHRRSPSFPSKRSLRRT 350
                 + G      S  G       +   RR  +   +   RR 
Sbjct: 1213 GFRGESGGRRGDSGSRRGESRGLHGDSGGRRPETRRGESQGRRN 1256



 Score = 41.3 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 10/103 (9%), Positives = 23/103 (22%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            R+    H L         P +S+            +     +   +  S+        + 
Sbjct: 1163 RQPHYHHQLNGNGARKREPSFSAHEERHPERRGERDARRGESGGLRGDSRGFRGESGGRR 1222

Query: 302  ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
                 RR  +  +    G           +   + R      +
Sbjct: 1223 GDSGSRRGESRGLHGDSGGRRPETRRGESQGRRNDRGEQRGGR 1265


>gi|152993918|ref|YP_001359639.1| 30S ribosomal protein S4 [Sulfurovum sp. NBC37-1]
 gi|172048747|sp|A6QCS3|RS4_SULNB RecName: Full=30S ribosomal protein S4
 gi|151425779|dbj|BAF73282.1| 30S ribosomal protein S4 [Sulfurovum sp. NBC37-1]
          Length = 208

 Score = 44.0 bits (102), Expect = 0.037,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G A+ R    + +    V V+G  ++  +  V +   IE+
Sbjct: 98  QRLDNVVYRMGFATTRASARQFVNHGHVLVDGKRVDIPSYRVKAGQKIEI 147


>gi|254785103|ref|YP_003072531.1| ribosomal protein S4 [Teredinibacter turnerae T7901]
 gi|259495299|sp|C5BQ85|RS4_TERTT RecName: Full=30S ribosomal protein S4
 gi|237687392|gb|ACR14656.1| ribosomal protein S4 [Teredinibacter turnerae T7901]
          Length = 206

 Score = 44.0 bits (102), Expect = 0.037,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + VNG  L   +  V   D I V
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKAILVNGKALNIPSYQVSEGDVIAV 145


>gi|319948696|ref|ZP_08022817.1| 30S ribosomal protein S4 [Dietzia cinnamea P4]
 gi|319437598|gb|EFV92597.1| 30S ribosomal protein S4 [Dietzia cinnamea P4]
          Length = 201

 Score = 44.0 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR+  +++A     VN   +   +  V   D I+V
Sbjct: 92  RLDNVVYRAGLARTRRQARQLVAHGHFLVNDQKVTIPSYRVSQYDIIDV 140


>gi|314933871|ref|ZP_07841236.1| ribosomal protein S4 [Staphylococcus caprae C87]
 gi|313654021|gb|EFS17778.1| ribosomal protein S4 [Staphylococcus caprae C87]
          Length = 200

 Score = 44.0 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+   G+A +RR+  +++    ++V+G  ++  + ++     I V
Sbjct: 93  RLDAVVFSLGLARTRRQARQLVNHGHIEVDGGRVDIPSYSLKPGQVITV 141


>gi|288574373|ref|ZP_06392730.1| ribosomal protein S4 [Dethiosulfovibrio peptidovorans DSM 11002]
 gi|288570114|gb|EFC91671.1| ribosomal protein S4 [Dethiosulfovibrio peptidovorans DSM 11002]
          Length = 205

 Score = 44.0 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+ S R +  +++      +N   ++  +  V   D I V
Sbjct: 98  RLDNVVYRLGLCSTRPQARQLVRHGHFTLNDRKVDIPSALVKPGDVIAV 146


>gi|87301305|ref|ZP_01084146.1| translation initiation factor IF-2 [Synechococcus sp. WH 5701]
 gi|87284273|gb|EAQ76226.1| translation initiation factor IF-2 [Synechococcus sp. WH 5701]
          Length = 1122

 Score = 44.0 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 9/109 (8%), Positives = 19/109 (17%), Gaps = 4/109 (3%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                    +     +    D     S  P   T  +           +           
Sbjct: 204 PSRPPAPPVSKPEPPQVRKPDSAAATSPSPRPATSPRPVPRGSAPAPSRPATPQRPGAPA 263

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS----LRRTSAKK 354
              N           +      +      P+ PS R         + ++
Sbjct: 264 PVRNASGGGSGRPQLVGRPQPGQPGTSNRPAPPSGRPALSQRPAGAPQR 312



 Score = 39.8 bits (91), Expect = 0.72,   Method: Composition-based stats.
 Identities = 7/108 (6%), Positives = 19/108 (17%), Gaps = 1/108 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P     ++                     +  P    R    +  +    ++     PV
Sbjct: 206 RPPAPPVSKPEPPQVRKPDSAAATSPSPRPATSPRPVPRGSAPAPSRPATPQRPGAPAPV 265

Query: 306 HRRNLASNVWMAKGIHSSFLSDS-GQREENHRRSPSFPSKRSLRRTSA 352
              +   +                  R       P+   + +      
Sbjct: 266 RNASGGGSGRPQLVGRPQPGQPGTSNRPAPPSGRPALSQRPAGAPQRP 313



 Score = 39.4 bits (90), Expect = 0.84,   Method: Composition-based stats.
 Identities = 10/113 (8%), Positives = 24/113 (21%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           + ++ R       LE     +           R    +   +P    +            
Sbjct: 314 TPQVGRPTQARSPLELVGKPIRRDAAGPGGTSRPGAPVRPGMPQGMRKPVAPGELMQLQK 373

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
              +      RR   S         ++    + +R        + P +     
Sbjct: 374 PGSRPIAAPPRRPERSEGSPDAPRPTATPPAAPRRPAFRTPQAAGPGRARRPE 426



 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 10/116 (8%), Positives = 19/116 (16%), Gaps = 2/116 (1%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
            VSK    +   P        +               P                    +G
Sbjct: 211 PVSKPEPPQVRKPDSAAATSPSPRPATSPRPVPRGSAPAPSRPATPQRPGAPAPVRNASG 270

Query: 295 LSKQKKL--ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
               +      P   +   SN         +         +        P++    
Sbjct: 271 GGSGRPQLVGRPQPGQPGTSNRPAPPSGRPALSQRPAGAPQRPTPQVGRPTQARSP 326



 Score = 36.3 bits (82), Expect = 6.9,   Method: Composition-based stats.
 Identities = 12/117 (10%), Positives = 31/117 (26%), Gaps = 8/117 (6%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD---DFTRMKKNSSQKNGLSKQKKLA 302
            P            P  + +                      ++++++   G S+     
Sbjct: 292 RPAPPSGRPALSQRPAGAPQRPTPQVGRPTQARSPLELVGKPIRRDAAGPGGTSRPGAPV 351

Query: 303 TPVHRRNLASNVWMA-----KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            P   + +   V        +   S  ++   +R E    SP  P   +    + ++
Sbjct: 352 RPGMPQGMRKPVAPGELMQLQKPGSRPIAAPPRRPERSEGSPDAPRPTATPPAAPRR 408


>gi|299768690|ref|YP_003730716.1| 30S ribosomal protein S4 [Acinetobacter sp. DR1]
 gi|298698778|gb|ADI89343.1| 30S ribosomal protein S4 [Acinetobacter sp. DR1]
          Length = 208

 Score = 44.0 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + +NG  +  A++ V + D I V
Sbjct: 99  RLDNVVYRMGFGSTRAEARQLVSHRSITLNGRRVNIASIQVKAGDVIAV 147


>gi|262280201|ref|ZP_06057985.1| 30S ribosomal protein S4 [Acinetobacter calcoaceticus RUH2202]
 gi|262257979|gb|EEY76713.1| 30S ribosomal protein S4 [Acinetobacter calcoaceticus RUH2202]
          Length = 208

 Score = 44.0 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + +NG  +  A++ V + D I V
Sbjct: 99  RLDNVVYRMGFGSTRAEARQLVSHRSITLNGRRVNIASIQVKAGDVIAV 147


>gi|255319791|ref|ZP_05360996.1| ribosomal protein S4 [Acinetobacter radioresistens SK82]
 gi|262380324|ref|ZP_06073478.1| ribosomal protein S4 [Acinetobacter radioresistens SH164]
 gi|255303110|gb|EET82322.1| ribosomal protein S4 [Acinetobacter radioresistens SK82]
 gi|262297770|gb|EEY85685.1| ribosomal protein S4 [Acinetobacter radioresistens SH164]
          Length = 207

 Score = 44.0 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + +NG  +  A++ V + D I V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHRSITLNGRRVNIASIQVKAGDVIAV 146


>gi|237744174|ref|ZP_04574655.1| SSU ribosomal protein S4P [Fusobacterium sp. 7_1]
 gi|256027711|ref|ZP_05441545.1| 30S ribosomal protein S4 [Fusobacterium sp. D11]
 gi|260494240|ref|ZP_05814371.1| ribosomal protein S4 [Fusobacterium sp. 3_1_33]
 gi|289765670|ref|ZP_06525048.1| SSU ribosomal protein S4P [Fusobacterium sp. D11]
 gi|229431403|gb|EEO41615.1| SSU ribosomal protein S4P [Fusobacterium sp. 7_1]
 gi|260198386|gb|EEW95902.1| ribosomal protein S4 [Fusobacterium sp. 3_1_33]
 gi|289717225|gb|EFD81237.1| SSU ribosomal protein S4P [Fusobacterium sp. D11]
          Length = 195

 Score = 44.0 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RR+  ++++   + VNG  +  A+  V   D + V
Sbjct: 89  RLENVVYRLGFAKTRRQARQIVSHGHIAVNGRRVNIASFRVKVGDIVSV 137


>gi|256825859|ref|YP_003149819.1| 30S ribosomal protein S4 [Kytococcus sedentarius DSM 20547]
 gi|256689252|gb|ACV07054.1| SSU ribosomal protein S4P [Kytococcus sedentarius DSM 20547]
          Length = 202

 Score = 44.0 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI RAGIA +RR   +++      +NG  ++  ++ V   D I+V
Sbjct: 92  RLDNVIYRAGIAPTRRAARQLVTHGHFLLNGQRVDVPSIQVSKFDIIDV 140


>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 = 44.0 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 11/41 (26%), Positives = 20/41 (48%)

Query: 7  VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILL 47
          V +    +RV   I+R    SR +   + A  +V V+G ++
Sbjct: 12 VPDGLEGERVDAAISRMFGFSRTKAAELAASGKVTVDGSVV 52


>gi|148668617|gb|EDL00936.1| junction-mediating and regulatory protein [Mus musculus]
          Length = 769

 Score = 44.0 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 20/150 (13%), Positives = 39/150 (26%), Gaps = 16/150 (10%)

Query: 221 GPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIY----SSETLVRDRPNIIS 276
             F L   L      V   +  E+     +     N     +     + T  R R     
Sbjct: 1   MSFALEETLESDWVAVRPHVFDEREKHKFVFIVAWNEIEGKFAITCHNRTAQRQRSGSRE 60

Query: 277 EVPDDFTRMKKNSSQKNGLSKQKKL-------ATPVHRRNLASNVWMAKGIHSSFLSDSG 329
           +     +   +         + +          +P  R++ A     +     S   D  
Sbjct: 61  QAGTPASDGSRGPGSPAARGRSEAAASATAALRSPGPRKSQAWAEGGSPRSARSLKGDPP 120

Query: 330 QREENHR-----RSPSFPSKRSLRRTSAKK 354
           +           RSP+      LRR++  +
Sbjct: 121 RGPAGRGPESPLRSPARAKASPLRRSAESR 150


>gi|89902965|ref|YP_525436.1| 30S ribosomal protein S4 [Rhodoferax ferrireducens T118]
 gi|122478015|sp|Q21QP8|RS4_RHOFD RecName: Full=30S ribosomal protein S4
 gi|89347702|gb|ABD71905.1| SSU ribosomal protein S4P [Rhodoferax ferrireducens T118]
          Length = 207

 Score = 44.0 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V + D I V   
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAMTVNGKSVNIPSYMVKAGDMIAVRDK 149


>gi|260549816|ref|ZP_05824032.1| ribosomal protein S4 [Acinetobacter sp. RUH2624]
 gi|260407066|gb|EEX00543.1| ribosomal protein S4 [Acinetobacter sp. RUH2624]
          Length = 208

 Score = 44.0 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + +NG  +  A++ V + D I V
Sbjct: 99  RLDNVVYRMGFGSTRAEARQLVSHRSITLNGRRVNIASIQVKAGDVIAV 147


>gi|260495359|ref|ZP_05815486.1| conserved hypothetical protein [Fusobacterium sp. 3_1_33]
 gi|260197137|gb|EEW94657.1| conserved hypothetical protein [Fusobacterium sp. 3_1_33]
          Length = 71

 Score = 44.0 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 12/67 (17%), Positives = 29/67 (43%), Gaps = 1/67 (1%)

Query: 1  MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          MK+   V+ +    ++ + +   A + S  + +++I   +VKVN  +  R    +     
Sbjct: 1  MKNIEKVKISTEFIKLDQFLKWLAVVDSGSQAKQVILDGKVKVNDEVETRRGRKIYPEYR 60

Query: 60 IEVDGVP 66
          +E+    
Sbjct: 61 VEIFDRI 67


>gi|226305369|ref|YP_002765327.1| 30S ribosomal protein S4 [Rhodococcus erythropolis PR4]
 gi|229489412|ref|ZP_04383275.1| ribosomal protein S4 [Rhodococcus erythropolis SK121]
 gi|259495289|sp|C0ZW53|RS4_RHOE4 RecName: Full=30S ribosomal protein S4
 gi|226184484|dbj|BAH32588.1| 30S ribosomal protein S4 [Rhodococcus erythropolis PR4]
 gi|229323509|gb|EEN89267.1| ribosomal protein S4 [Rhodococcus erythropolis SK121]
          Length = 201

 Score = 44.0 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ RAG+A +RR+  +++    + VN   ++  +  V   D I+V    L      
Sbjct: 92  RLDNVVYRAGLARTRRQARQLVTHGHLLVNNKKVDIPSYRVSQYDIIDVKEKSLSTLPFQ 151

Query: 74  R 74
            
Sbjct: 152 V 152


>gi|169350323|ref|ZP_02867261.1| hypothetical protein CLOSPI_01084 [Clostridium spiroforme DSM 1552]
 gi|169293106|gb|EDS75239.1| hypothetical protein CLOSPI_01084 [Clostridium spiroforme DSM 1552]
          Length = 201

 Score = 44.0 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G A +RR   +++      VNG+  +  +  V   D +EV
Sbjct: 91  QRLDNVVYRLGFAPTRRAARQLVNHGHFLVNGVKTDIPSYTVKVGDVVEV 140


>gi|160881758|ref|YP_001560726.1| RNA-binding S4 domain-containing protein [Clostridium
           phytofermentans ISDg]
 gi|189045375|sp|A9KJG7|RS4_CLOPH RecName: Full=30S ribosomal protein S4
 gi|160430424|gb|ABX43987.1| RNA-binding S4 domain protein [Clostridium phytofermentans ISDg]
          Length = 198

 Score = 44.0 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 12/71 (16%), Positives = 24/71 (33%), Gaps = 1/71 (1%)

Query: 17  SKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
             V+ R G   +R E  +++  + V VNG  +   +  V + D I +            +
Sbjct: 91  DNVMFRMGYGRTRTEARQIVDHKHVLVNGKCVNIPSYQVKAGDVISIKEKCKSAQRYKDI 150

Query: 76  WLYHKPIGLVT 86
                   +  
Sbjct: 151 LEVTDGRTVPA 161


>gi|139387254|ref|YP_001123375.1| ribosomal protein S4 [Capsella bursa-pastoris]
 gi|297837951|ref|XP_002886857.1| ribosomal protein S4 [Arabidopsis lyrata subsp. lyrata]
 gi|152060547|sp|A4QKJ4|RR4_CAPBU RecName: Full=30S ribosomal protein S4, chloroplastic
 gi|134286575|dbj|BAF50199.1| ribosomal protein S4 [Capsella bursa-pastoris]
 gi|297332698|gb|EFH63116.1| ribosomal protein S4 [Arabidopsis lyrata subsp. lyrata]
          Length = 201

 Score = 44.0 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 10/53 (18%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
            R+  ++ R G+A +  +  +++    + VNG +++  +      D I V   
Sbjct: 89  MRLDNILFRLGMALTIPQARQLVNHGHILVNGRIVDIPSYRCKPRDIITVKDE 141


>gi|262370554|ref|ZP_06063879.1| ribosomal protein S4 [Acinetobacter johnsonii SH046]
 gi|262314354|gb|EEY95396.1| ribosomal protein S4 [Acinetobacter johnsonii SH046]
          Length = 208

 Score = 44.0 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + +NG  +  A++ V + D I V
Sbjct: 99  RLDNVVYRMGFGSTRAEARQLVSHRSITLNGRRVNIASIQVKAGDVIAV 147


>gi|302923188|ref|XP_003053622.1| hypothetical protein NECHADRAFT_65680 [Nectria haematococca mpVI
           77-13-4]
 gi|256734563|gb|EEU47909.1| hypothetical protein NECHADRAFT_65680 [Nectria haematococca mpVI
           77-13-4]
          Length = 1285

 Score = 44.0 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 15/110 (13%), Positives = 26/110 (23%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             L P L  + Q +      S            +  P      +       G  +     
Sbjct: 609 NNLPPPLNLQKQRSRSPLAQSPYGPPSPYARGPNSRPGTSDGKRSPMPPGMGPPRSPHPQ 668

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            P  R ++  +               G+R  + RR      + S  R   
Sbjct: 669 NPNRRPDMGPDGRRPSDPRRPGPGPDGRRPSDPRRPGPDGRRPSDPRGPG 718



 Score = 41.7 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 12/110 (10%), Positives = 26/110 (23%), Gaps = 2/110 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R  L              P     T    R  +   +    +   +N +++  +    + 
Sbjct: 623 RSPLAQSPYGPPSPYARGPNSRPGTSDGKRSPMPPGMGPPRSPHPQNPNRRPDMGPDGRR 682

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
            +   R     +               G+R  + R       + S  R  
Sbjct: 683 PSDPRRPGPGPDGRRPSDPRRPG--PDGRRPSDPRGPGPDGRRPSDPRAR 730



 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 9/110 (8%), Positives = 20/110 (18%), Gaps = 4/110 (3%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                + +        S           +               ++   +       +  
Sbjct: 619 KQRSRSPLAQSPYGPPSPYARGPNSRPGTSDGKRSPMPPGMGPPRSPHPQNPNRRPDMGP 678

Query: 308 RNLASNVWMAKGIHSSFLSDS-GQREENHRRSPS---FPSKRSLRRTSAK 353
                +     G        S  +R     R PS    P     R +  +
Sbjct: 679 DGRRPSDPRRPGPGPDGRRPSDPRRPGPDGRRPSDPRGPGPDGRRPSDPR 728


>gi|169632374|ref|YP_001706110.1| 30S ribosomal protein S4 [Acinetobacter baumannii SDF]
 gi|169794618|ref|YP_001712411.1| 30S ribosomal protein S4 [Acinetobacter baumannii AYE]
 gi|213158811|ref|YP_002320809.1| ribosomal protein S4 [Acinetobacter baumannii AB0057]
 gi|215482207|ref|YP_002324389.1| ribosomal protein S4 [Acinetobacter baumannii AB307-0294]
 gi|239503210|ref|ZP_04662520.1| 30S ribosomal protein S4 [Acinetobacter baumannii AB900]
 gi|260557051|ref|ZP_05829268.1| ribosomal protein S4 [Acinetobacter baumannii ATCC 19606]
 gi|293610848|ref|ZP_06693148.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|301345034|ref|ZP_07225775.1| 30S ribosomal protein S4 [Acinetobacter baumannii AB056]
 gi|301512035|ref|ZP_07237272.1| 30S ribosomal protein S4 [Acinetobacter baumannii AB058]
 gi|301595208|ref|ZP_07240216.1| 30S ribosomal protein S4 [Acinetobacter baumannii AB059]
 gi|332853163|ref|ZP_08434600.1| ribosomal protein S4 [Acinetobacter baumannii 6013150]
 gi|332868591|ref|ZP_08438247.1| ribosomal protein S4 [Acinetobacter baumannii 6013113]
 gi|332876059|ref|ZP_08443843.1| ribosomal protein S4 [Acinetobacter baumannii 6014059]
 gi|152060924|sp|A3M960|RS4_ACIBT RecName: Full=30S ribosomal protein S4
 gi|226697785|sp|B7GW26|RS4_ACIB3 RecName: Full=30S ribosomal protein S4
 gi|226697786|sp|B7IA15|RS4_ACIB5 RecName: Full=30S ribosomal protein S4
 gi|226697788|sp|B0VQU2|RS4_ACIBS RecName: Full=30S ribosomal protein S4
 gi|226697789|sp|B0V6U6|RS4_ACIBY RecName: Full=30S ribosomal protein S4
 gi|169147545|emb|CAM85406.1| 30S ribosomal protein S4 [Acinetobacter baumannii AYE]
 gi|169151166|emb|CAO99838.1| 30S ribosomal protein S4 [Acinetobacter baumannii]
 gi|193078463|gb|ABO13454.2| 30S ribosomal protein S4 [Acinetobacter baumannii ATCC 17978]
 gi|213057971|gb|ACJ42873.1| ribosomal protein S4 [Acinetobacter baumannii AB0057]
 gi|213986640|gb|ACJ56939.1| ribosomal protein S4 [Acinetobacter baumannii AB307-0294]
 gi|260409657|gb|EEX02958.1| ribosomal protein S4 [Acinetobacter baumannii ATCC 19606]
 gi|292827192|gb|EFF85557.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|322509484|gb|ADX04938.1| 30S ribosomal protein S4 [Acinetobacter baumannii 1656-2]
 gi|323519505|gb|ADX93886.1| 30S ribosomal protein S4 [Acinetobacter baumannii TCDC-AB0715]
 gi|325123580|gb|ADY83103.1| 30S ribosomal protein S4 [Acinetobacter calcoaceticus PHEA-2]
 gi|332728832|gb|EGJ60191.1| ribosomal protein S4 [Acinetobacter baumannii 6013150]
 gi|332733268|gb|EGJ64462.1| ribosomal protein S4 [Acinetobacter baumannii 6013113]
 gi|332735677|gb|EGJ66720.1| ribosomal protein S4 [Acinetobacter baumannii 6014059]
          Length = 208

 Score = 43.6 bits (101), Expect = 0.040,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + +NG  +  A++ V + D I V
Sbjct: 99  RLDNVVYRMGFGSTRAEARQLVSHRSITLNGRRVNIASIQVKAGDVIAV 147


>gi|134096297|ref|YP_001101372.1| 30S ribosomal protein S4 [Herminiimonas arsenicoxydans]
 gi|172044175|sp|A4G9R4|RS4_HERAR RecName: Full=30S ribosomal protein S4
 gi|133740200|emb|CAL63251.1| 30S ribosomal subunit protein S4 [Herminiimonas arsenicoxydans]
          Length = 207

 Score = 43.6 bits (101), Expect = 0.040,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ +   VNGI++  A+  V   D + V
Sbjct: 98  RLDNVVYRMGFGSTRAEGRQLVSHKAFTVNGIVVNIASYQVKPGDIVAV 146


>gi|61098108|ref|NP_067285.2| junction-mediating and -regulatory protein [Mus musculus]
 gi|60552527|gb|AAH90835.1| Junction-mediating and regulatory protein [Mus musculus]
          Length = 983

 Score = 43.6 bits (101), Expect = 0.040,   Method: Composition-based stats.
 Identities = 20/150 (13%), Positives = 39/150 (26%), Gaps = 16/150 (10%)

Query: 221 GPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIY----SSETLVRDRPNIIS 276
             F L   L      V   +  E+     +     N     +     + T  R R     
Sbjct: 1   MSFALEETLESDWVAVRPHVFDEREKHKFVFIVAWNEIEGKFAITCHNRTAQRQRSGSRE 60

Query: 277 EVPDDFTRMKKNSSQKNGLSKQKKL-------ATPVHRRNLASNVWMAKGIHSSFLSDSG 329
           +     +   +         + +          +P  R++ A     +     S   D  
Sbjct: 61  QAGTPASDGSRGPGSPAARGRSEAAASATAALRSPGPRKSQAWAEGGSPRSARSLKGDPP 120

Query: 330 QREENHR-----RSPSFPSKRSLRRTSAKK 354
           +           RSP+      LRR++  +
Sbjct: 121 RGPAGRGPESPLRSPARAKASPLRRSAESR 150


>gi|317495364|ref|ZP_07953733.1| ribosomal protein S4 [Gemella moribillum M424]
 gi|316914423|gb|EFV35900.1| ribosomal protein S4 [Gemella moribillum M424]
          Length = 200

 Score = 43.6 bits (101), Expect = 0.040,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+   G+A + R+  +++    V V+G  ++ A+  V     + V
Sbjct: 93  RLDSVVYSLGLARTNRQARQLVNHGHVLVDGKKVDIASYAVKPGQVVSV 141


>gi|241889823|ref|ZP_04777121.1| ribosomal protein S4 [Gemella haemolysans ATCC 10379]
 gi|241863445|gb|EER67829.1| ribosomal protein S4 [Gemella haemolysans ATCC 10379]
          Length = 200

 Score = 43.6 bits (101), Expect = 0.040,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+   G+A + R+  +++    V V+G  ++ A+  V     + V
Sbjct: 93  RLDSVVYSLGLARTNRQARQLVNHGHVLVDGKKVDIASYAVKPGQVVSV 141


>gi|197303047|ref|ZP_03168095.1| hypothetical protein RUMLAC_01774 [Ruminococcus lactaris ATCC
           29176]
 gi|197297902|gb|EDY32454.1| hypothetical protein RUMLAC_01774 [Ruminococcus lactaris ATCC
           29176]
          Length = 908

 Score = 43.6 bits (101), Expect = 0.040,   Method: Composition-based stats.
 Identities = 16/116 (13%), Positives = 28/116 (24%), Gaps = 3/116 (2%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRP--NIISEVPDDFTRMKKNSSQKNG 294
           +++   ++    +  E               VR            D   R  ++S    G
Sbjct: 142 TRQEKTDRAERTVRTERPAQTAGRTSGEGRPVRQERNDRPQRPGSDRENRPVRDSRDARG 201

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                    P   R    N   A+G           R+  + +      K   RR 
Sbjct: 202 GRPNGDGRGPRQERGPRDN-RDARGGREQGFGGRDNRDGRNGQGSRPDRKNDNRRN 256



 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 9/110 (8%), Positives = 17/110 (15%), Gaps = 1/110 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
               +  A                 R              +   +      + + +    
Sbjct: 118 ENRPVRAAGAEGRPVRTERAAQAGTRQEKTDRAERTVRTERPAQTAGRTSGEGRPVRQER 177

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS-FPSKRSLRRTSAKK 354
           + R                    G R     R P      R  R     +
Sbjct: 178 NDRPQRPGSDRENRPVRDSRDARGGRPNGDGRGPRQERGPRDNRDARGGR 227


>gi|329766877|ref|ZP_08258405.1| 30S ribosomal protein S4 [Gemella haemolysans M341]
 gi|328837602|gb|EGF87227.1| 30S ribosomal protein S4 [Gemella haemolysans M341]
          Length = 200

 Score = 43.6 bits (101), Expect = 0.040,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+   G+A + R+  +++    V V+G  ++ A+  V     + V
Sbjct: 93  RLDSVVYSLGLARTNRQARQLVNHGHVLVDGKKVDIASYAVKPGQVVSV 141


>gi|297840979|ref|XP_002888371.1| ribosomal protein S4 [Arabidopsis lyrata subsp. lyrata]
 gi|297334212|gb|EFH64630.1| ribosomal protein S4 [Arabidopsis lyrata subsp. lyrata]
          Length = 201

 Score = 43.6 bits (101), Expect = 0.040,   Method: Composition-based stats.
 Identities = 10/53 (18%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
            R+  ++ R G+A +  +  +++    + VNG +++  +      D I V   
Sbjct: 89  MRLDNILFRLGMALTIPQARQLVNHGHILVNGRIVDIPSYRCKPRDIITVKDE 141


>gi|220931768|ref|YP_002508676.1| RNA-binding S4 domain protein [Halothermothrix orenii H 168]
 gi|219993078|gb|ACL69681.1| RNA-binding S4 domain protein [Halothermothrix orenii H 168]
          Length = 262

 Score = 43.6 bits (101), Expect = 0.040,   Method: Composition-based stats.
 Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 2/54 (3%)

Query: 13  PQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
             R+  V + AG   SR ++ R+I  ++VKVN       A  V   D I + G 
Sbjct: 185 SMRLDAV-SSAGFGDSRNKISRIIKSEKVKVNWKKENNPAQTVEIGDLISIKGR 237


>gi|53803440|ref|YP_114764.1| 30S ribosomal protein S4 [Methylococcus capsulatus str. Bath]
 gi|61215442|sp|Q605D6|RS4_METCA RecName: Full=30S ribosomal protein S4
 gi|53757201|gb|AAU91492.1| ribosomal protein S4 [Methylococcus capsulatus str. Bath]
          Length = 206

 Score = 43.6 bits (101), Expect = 0.040,   Method: Composition-based stats.
 Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           R+  V+ R G AS R E  ++++ + + +NG  L   +  V S D +E+    
Sbjct: 97  RLDNVVYRMGFASTRAEARQLVSHKAINLNGRTLNIPSYQVQSGDVVEIRDKA 149


>gi|301620407|ref|XP_002939567.1| PREDICTED: hypothetical protein LOC100493347 [Xenopus (Silurana)
           tropicalis]
          Length = 1177

 Score = 43.6 bits (101), Expect = 0.041,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 27/108 (25%), Gaps = 2/108 (1%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK--QKKLAT 303
           G    E            +    R R +   + P    R     S   G+S   ++   +
Sbjct: 112 GSAPAEVGGRGRSQAARGNPGSPRQRGSGERQDPAGGCRRDPQGSAPGGVSAVGEEPPTS 171

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
              R          +G        +   +   RRS     + +  R  
Sbjct: 172 RPGREREPEPTAQQRGARQQSAEPTRGEQPGSRRSRDRGPRATPSRGR 219



 Score = 40.9 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 11/127 (8%), Positives = 25/127 (19%), Gaps = 14/127 (11%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R +     + +      A              +         R    S ++ G  +++  
Sbjct: 86  RGRDARRSVTDPAATRPARRVRGAAAGSAPAEVGGRGRSQAARGNPGSPRQRGSGERQDP 145

Query: 302 ATPVHRRNLASNVW-------MAKGIHSSFLS-------DSGQREENHRRSPSFPSKRSL 347
           A    R    S                              G R+++   +         
Sbjct: 146 AGGCRRDPQGSAPGGVSAVGEEPPTSRPGREREPEPTAQQRGARQQSAEPTRGEQPGSRR 205

Query: 348 RRTSAKK 354
            R    +
Sbjct: 206 SRDRGPR 212



 Score = 36.3 bits (82), Expect = 6.8,   Method: Composition-based stats.
 Identities = 15/100 (15%), Positives = 23/100 (23%), Gaps = 3/100 (3%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               +            E             P    R  +  S +    +Q        R
Sbjct: 150 RRDPQGSAPGGVSAVGEEPPTSRPGREREPEPTAQQRGARQQSAEPTRGEQPGSRRSRDR 209

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
              A+         S   S +G+R    RR  S   +R  
Sbjct: 210 GPRATPSRGRCWERSPTGSRTGERARLGRRDSS---RRPA 246


>gi|254673233|emb|CBA08218.1| probable heat shock protein [Neisseria meningitidis alpha275]
          Length = 133

 Score = 43.6 bits (101), Expect = 0.041,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 6/61 (9%)

Query: 1  MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          MKDK+    + +  R+ K + A     +R   ++ I   RV+VNG  ++ +   +   D 
Sbjct: 1  MKDKH----DSSAMRLDKWLWAARFFKTRSLAQKHIELGRVQVNGSKVKNSKT-IDIGDI 55

Query: 60 I 60
          I
Sbjct: 56 I 56


>gi|332310625|gb|EGJ23720.1| hypothetical protein LMOSA_11090 [Listeria monocytogenes str.
          Scott A]
          Length = 95

 Score = 43.6 bits (101), Expect = 0.041,   Method: Composition-based stats.
 Identities = 15/85 (17%), Positives = 28/85 (32%), Gaps = 4/85 (4%)

Query: 7  VQENFTPQRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVD 63
          + +  T  R+ K +  + +  RR   + +  + R+ VNG+  +    NV S D   I   
Sbjct: 1  MNKMATTMRLDKYLKVSRLIKRRTVAKEVAEKGRIAVNGVTAK-PGTNVKSGDELVIRFG 59

Query: 64 GVPLRKAERTRLWLYHKPIGLVTTH 88
             +            K        
Sbjct: 60 PKIVTAKIERLEENAKKEQATEMYT 84


>gi|170102226|ref|XP_001882329.1| predicted protein [Laccaria bicolor S238N-H82]
 gi|164642701|gb|EDR06956.1| predicted protein [Laccaria bicolor S238N-H82]
          Length = 899

 Score = 43.6 bits (101), Expect = 0.041,   Method: Composition-based stats.
 Identities = 12/116 (10%), Positives = 30/116 (25%), Gaps = 4/116 (3%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           E++ + L                 +    +       P           +   + + +  
Sbjct: 576 ELTSQPLPLDHPHSSTPNQPAPGTSSSAPTPLRTTTAPPSSRARTRMPRQSSPHRASRKH 635

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSD----SGQREENHRRSPSFPSKRS 346
             ++ +  +P  RR  +      +    S             +N   SP+ P+  S
Sbjct: 636 GRRRSRTPSPPRRRGDSYRPTGEEDRRRSTRRPSEAVPAPPPQNPWSSPTLPAPNS 691



 Score = 39.8 bits (91), Expect = 0.63,   Method: Composition-based stats.
 Identities = 8/95 (8%), Positives = 18/95 (18%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                          +   + R      +       R +  S  +      +       R
Sbjct: 603 APTPLRTTTAPPSSRARTRMPRQSSPHRASRKHGRRRSRTPSPPRRRGDSYRPTGEEDRR 662

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
           R+                  S      +  +P+ P
Sbjct: 663 RSTRRPSEAVPAPPPQNPWSSPTLPAPNSWAPANP 697



 Score = 38.2 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 14/106 (13%), Positives = 27/106 (25%), Gaps = 2/106 (1%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
             L    + LD P  S+        +  +  P   T    +S  +  + +Q        +
Sbjct: 575 PELTSQPLPLDHPHSSTPNQPAPGTSSSAPTPLRTTTAPPSSRARTRMPRQSSPHRASRK 634

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHR--RSPSFPSKRSLRRTS 351
                +   +              E+  R  R PS        +  
Sbjct: 635 HGRRRSRTPSPPRRRGDSYRPTGEEDRRRSTRRPSEAVPAPPPQNP 680


>gi|325208128|gb|ADZ03580.1| heat shock protein 15 [Neisseria meningitidis NZ-05/33]
          Length = 133

 Score = 43.6 bits (101), Expect = 0.041,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 6/61 (9%)

Query: 1  MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          MKDK+    + +  R+ K + A     +R   ++ I   RV+VNG  ++ +   +   D 
Sbjct: 1  MKDKH----DSSAMRLDKWLWAARFFKTRSLAQKHIELGRVQVNGSKVKNSKT-IDIGDI 55

Query: 60 I 60
          I
Sbjct: 56 I 56


>gi|315925228|ref|ZP_07921442.1| 30S ribosomal protein S4 [Pseudoramibacter alactolyticus ATCC
           23263]
 gi|315621462|gb|EFV01429.1| 30S ribosomal protein S4 [Pseudoramibacter alactolyticus ATCC
           23263]
          Length = 209

 Score = 43.6 bits (101), Expect = 0.041,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+   + R G+  SR+E  +++      VNG  +  A+  + + D I V   
Sbjct: 100 RLDNAVYRMGMGQSRKEARQLVLHGHFLVNGAKVNVASYQLKAGDVISVADK 151


>gi|296314263|ref|ZP_06864204.1| heat shock protein 15 [Neisseria polysaccharea ATCC 43768]
 gi|296839060|gb|EFH22998.1| heat shock protein 15 [Neisseria polysaccharea ATCC 43768]
 gi|325130240|gb|EGC53010.1| heat shock protein 15 [Neisseria meningitidis OX99.30304]
          Length = 133

 Score = 43.6 bits (101), Expect = 0.041,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 6/61 (9%)

Query: 1  MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          MKDK+    + +  R+ K + A     +R   ++ I   RV+VNG  ++ +   +   D 
Sbjct: 1  MKDKH----DSSAMRLDKWLWAARFFKTRSLAQKHIELGRVQVNGSKVKNSKT-IDIGDI 55

Query: 60 I 60
          I
Sbjct: 56 I 56


>gi|156938197|ref|YP_001435993.1| 30S ribosomal protein S4e [Ignicoccus hospitalis KIN4/I]
 gi|189045350|sp|A8ACD4|RS4E_IGNH4 RecName: Full=30S ribosomal protein S4e
 gi|156567181|gb|ABU82586.1| SSU ribosomal protein S4E [Ignicoccus hospitalis KIN4/I]
          Length = 255

 Score = 43.6 bits (101), Expect = 0.041,   Method: Composition-based stats.
 Identities = 15/88 (17%), Positives = 30/88 (34%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTH 88
           RE  ++IA+ R+KV+G + +     V + D IE+ G             Y  P+ +    
Sbjct: 61  REARKLIAEGRIKVDGRVRKDYKFPVGAMDVIEIVGADEYYRMIPYPVKYLVPMRIDAEE 120

Query: 89  SDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           +                   +++     
Sbjct: 121 AKKKICRIENKVTVKGGHVQLNLHDGRN 148


>gi|59801233|ref|YP_207945.1| hypothetical protein NGO0822 [Neisseria gonorrhoeae FA 1090]
 gi|194098551|ref|YP_002001613.1| Ribosome-associated heat shock protein Hsp15 [Neisseria
          gonorrhoeae NCCP11945]
 gi|239998934|ref|ZP_04718858.1| Ribosome-associated heat shock protein Hsp15 [Neisseria
          gonorrhoeae 35/02]
 gi|240014157|ref|ZP_04721070.1| Ribosome-associated heat shock protein Hsp15 [Neisseria
          gonorrhoeae DGI18]
 gi|240016592|ref|ZP_04723132.1| Ribosome-associated heat shock protein Hsp15 [Neisseria
          gonorrhoeae FA6140]
 gi|240112852|ref|ZP_04727342.1| Ribosome-associated heat shock protein Hsp15 [Neisseria
          gonorrhoeae MS11]
 gi|240115608|ref|ZP_04729670.1| Ribosome-associated heat shock protein Hsp15 [Neisseria
          gonorrhoeae PID18]
 gi|240121719|ref|ZP_04734681.1| Ribosome-associated heat shock protein Hsp15 [Neisseria
          gonorrhoeae PID24-1]
 gi|240123460|ref|ZP_04736416.1| Ribosome-associated heat shock protein Hsp15 [Neisseria
          gonorrhoeae PID332]
 gi|254493720|ref|ZP_05106891.1| conserved hypothetical protein [Neisseria gonorrhoeae 1291]
 gi|260440581|ref|ZP_05794397.1| Ribosome-associated heat shock protein Hsp15 [Neisseria
          gonorrhoeae DGI2]
 gi|268594779|ref|ZP_06128946.1| conserved hypothetical protein [Neisseria gonorrhoeae 35/02]
 gi|268598932|ref|ZP_06133099.1| conserved hypothetical protein [Neisseria gonorrhoeae MS11]
 gi|268601286|ref|ZP_06135453.1| conserved hypothetical protein [Neisseria gonorrhoeae PID18]
 gi|268682087|ref|ZP_06148949.1| conserved hypothetical protein [Neisseria gonorrhoeae PID332]
 gi|291043884|ref|ZP_06569600.1| conserved hypothetical protein [Neisseria gonorrhoeae DGI2]
 gi|59718128|gb|AAW89533.1| conserved hypothetical protein [Neisseria gonorrhoeae FA 1090]
 gi|193933841|gb|ACF29665.1| Ribosome-associated heat shock protein Hsp15 [Neisseria
          gonorrhoeae NCCP11945]
 gi|226512760|gb|EEH62105.1| conserved hypothetical protein [Neisseria gonorrhoeae 1291]
 gi|268548168|gb|EEZ43586.1| conserved hypothetical protein [Neisseria gonorrhoeae 35/02]
 gi|268583063|gb|EEZ47739.1| conserved hypothetical protein [Neisseria gonorrhoeae MS11]
 gi|268585417|gb|EEZ50093.1| conserved hypothetical protein [Neisseria gonorrhoeae PID18]
 gi|268622371|gb|EEZ54771.1| conserved hypothetical protein [Neisseria gonorrhoeae PID332]
 gi|291012347|gb|EFE04336.1| conserved hypothetical protein [Neisseria gonorrhoeae DGI2]
 gi|317164224|gb|ADV07765.1| hypothetical protein NGTW08_0796 [Neisseria gonorrhoeae
          TCDC-NG08107]
          Length = 133

 Score = 43.6 bits (101), Expect = 0.041,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 6/61 (9%)

Query: 1  MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          MKDK+    + +  R+ K + A     +R   ++ I   RV+VNG  ++ +   +   D 
Sbjct: 1  MKDKH----DSSAMRLDKWLWAARFFKTRSLAQKHIELGRVQVNGSKVKNSKT-IDIGDI 55

Query: 60 I 60
          I
Sbjct: 56 I 56


>gi|50086191|ref|YP_047701.1| 30S ribosomal protein S4 [Acinetobacter sp. ADP1]
 gi|61215531|sp|Q6F7T6|RS4_ACIAD RecName: Full=30S ribosomal protein S4
 gi|49532167|emb|CAG69879.1| 30S ribosomal protein S4 [Acinetobacter sp. ADP1]
          Length = 207

 Score = 43.6 bits (101), Expect = 0.041,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + +NG  +  A++ V + D I V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHRSITLNGRRVNIASIQVKAGDVIAV 146


>gi|15677015|ref|NP_274167.1| hypothetical protein NMB1138 [Neisseria meningitidis MC58]
 gi|15677051|ref|NP_274203.1| hypothetical protein NMB1176 [Neisseria meningitidis MC58]
 gi|121634877|ref|YP_975122.1| hypothetical protein NMC1077 [Neisseria meningitidis FAM18]
 gi|161870024|ref|YP_001599193.1| ribosome-associated heat shock protein Hsp15 [Neisseria
          meningitidis 053442]
 gi|218768192|ref|YP_002342704.1| hypothetical protein NMA1348 [Neisseria meningitidis Z2491]
 gi|254804968|ref|YP_003083189.1| probable heat shock protein [Neisseria meningitidis alpha14]
 gi|7226375|gb|AAF41526.1| conserved hypothetical protein [Neisseria meningitidis MC58]
 gi|7226413|gb|AAF41561.1| conserved hypothetical protein [Neisseria meningitidis MC58]
 gi|120866583|emb|CAM10334.1| hypothetical protein NMC1077 [Neisseria meningitidis FAM18]
 gi|121052200|emb|CAM08523.1| hypothetical protein NMA1348 [Neisseria meningitidis Z2491]
 gi|161595577|gb|ABX73237.1| ribosome-associated heat shock protein Hsp15 [Neisseria
          meningitidis 053442]
 gi|254668510|emb|CBA05877.1| probable heat shock protein [Neisseria meningitidis alpha14]
 gi|308389281|gb|ADO31601.1| hypothetical protein NMBB_1265 [Neisseria meningitidis alpha710]
 gi|316985029|gb|EFV63982.1| heat shock protein 15 [Neisseria meningitidis H44/76]
 gi|319410439|emb|CBY90799.1| putative RNA-binding protein [Neisseria meningitidis WUE 2594]
 gi|325128270|gb|EGC51155.1| heat shock protein 15 [Neisseria meningitidis N1568]
 gi|325132249|gb|EGC54943.1| heat shock protein 15 [Neisseria meningitidis M6190]
 gi|325134337|gb|EGC56983.1| heat shock protein 15 [Neisseria meningitidis M13399]
 gi|325138173|gb|EGC60744.1| heat shock protein 15 [Neisseria meningitidis ES14902]
 gi|325140363|gb|EGC62885.1| heat shock protein 15 [Neisseria meningitidis CU385]
 gi|325144444|gb|EGC66744.1| heat shock protein 15 [Neisseria meningitidis M01-240013]
 gi|325198320|gb|ADY93776.1| heat shock protein 15 [Neisseria meningitidis G2136]
 gi|325200185|gb|ADY95640.1| heat shock protein 15 [Neisseria meningitidis H44/76]
 gi|325206039|gb|ADZ01492.1| heat shock protein 15 [Neisseria meningitidis M04-240196]
          Length = 133

 Score = 43.6 bits (101), Expect = 0.041,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 6/61 (9%)

Query: 1  MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          MKDK+    + +  R+ K + A     +R   ++ I   RV+VNG  ++ +   +   D 
Sbjct: 1  MKDKH----DSSAMRLDKWLWAARFFKTRSLAQKHIELGRVQVNGSKVKNSKT-IDIGDI 55

Query: 60 I 60
          I
Sbjct: 56 I 56


>gi|325972637|ref|YP_004248828.1| ribosomal protein S4 [Spirochaeta sp. Buddy]
 gi|324027875|gb|ADY14634.1| ribosomal protein S4 [Spirochaeta sp. Buddy]
          Length = 213

 Score = 43.6 bits (101), Expect = 0.042,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R   A SR +  + +    + VNG  +   +  +   D + V
Sbjct: 101 QRLDNVVFRLHFAASRNQAAQFVNHGHIFVNGKRVSIPSYRLRPGDVVSV 150


>gi|74273231|gb|ABA01315.1| ribosomal protein S4 [Ancistrothyrsus sp. LBF-2005]
          Length = 187

 Score = 43.6 bits (101), Expect = 0.042,   Method: Composition-based stats.
 Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 5/55 (9%)

Query: 14  QRVSKVIARAGIAS---RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
            R+  ++ R G+AS   R    +++  + + VNG +++  +      D I V   
Sbjct: 74  MRLDNILFRLGMASTIPR--ARQLVNHRHILVNGRIVDIPSYRCKPRDLITVKDE 126


>gi|291298741|ref|YP_003510019.1| 30S ribosomal protein S4 [Stackebrandtia nassauensis DSM 44728]
 gi|290567961|gb|ADD40926.1| ribosomal protein S4 [Stackebrandtia nassauensis DSM 44728]
          Length = 208

 Score = 43.6 bits (101), Expect = 0.042,   Method: Composition-based stats.
 Identities = 15/61 (24%), Positives = 25/61 (40%), Gaps = 1/61 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ RAG A SR    +++      VNG  +   +  V + D +EV    +      
Sbjct: 99  RLDNVVYRAGFAKSRDMARQLVLHGHFIVNGRKVNIPSYRVTAKDIVEVRPKSVEMTPFV 158

Query: 74  R 74
            
Sbjct: 159 V 159


>gi|262373497|ref|ZP_06066775.1| ribosomal protein S4 [Acinetobacter junii SH205]
 gi|262311250|gb|EEY92336.1| ribosomal protein S4 [Acinetobacter junii SH205]
          Length = 208

 Score = 43.6 bits (101), Expect = 0.042,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + +NG  +  A++ V + D I V
Sbjct: 99  RLDNVVYRMGFGSTRAEARQLVSHRSITLNGRRVNIASIQVKAGDVIAV 147


>gi|240080781|ref|ZP_04725324.1| Ribosome-associated heat shock protein Hsp15 [Neisseria
          gonorrhoeae FA19]
 gi|240117901|ref|ZP_04731963.1| Ribosome-associated heat shock protein Hsp15 [Neisseria
          gonorrhoeae PID1]
 gi|240125705|ref|ZP_04738591.1| Ribosome-associated heat shock protein Hsp15 [Neisseria
          gonorrhoeae SK-92-679]
 gi|240128161|ref|ZP_04740822.1| Ribosome-associated heat shock protein Hsp15 [Neisseria
          gonorrhoeae SK-93-1035]
 gi|268596897|ref|ZP_06131064.1| conserved hypothetical protein [Neisseria gonorrhoeae FA19]
 gi|268603611|ref|ZP_06137778.1| conserved hypothetical protein [Neisseria gonorrhoeae PID1]
 gi|268684297|ref|ZP_06151159.1| conserved hypothetical protein [Neisseria gonorrhoeae SK-92-679]
 gi|268686555|ref|ZP_06153417.1| conserved hypothetical protein [Neisseria gonorrhoeae SK-93-1035]
 gi|268550685|gb|EEZ45704.1| conserved hypothetical protein [Neisseria gonorrhoeae FA19]
 gi|268587742|gb|EEZ52418.1| conserved hypothetical protein [Neisseria gonorrhoeae PID1]
 gi|268624581|gb|EEZ56981.1| conserved hypothetical protein [Neisseria gonorrhoeae SK-92-679]
 gi|268626839|gb|EEZ59239.1| conserved hypothetical protein [Neisseria gonorrhoeae SK-93-1035]
          Length = 133

 Score = 43.6 bits (101), Expect = 0.042,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 6/61 (9%)

Query: 1  MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          MKDK+    + +  R+ K + A     +R   ++ I   RV+VNG  ++ +   +   D 
Sbjct: 1  MKDKH----DSSAMRLDKWLWAARFFKTRSLAQKHIELGRVQVNGSKVKNSKT-IDIGDI 55

Query: 60 I 60
          I
Sbjct: 56 I 56


>gi|225544126|ref|YP_002720114.1| rps4 [Jatropha curcas]
 gi|224979567|gb|ACN72694.1| rps4 [Jatropha curcas]
          Length = 201

 Score = 43.6 bits (101), Expect = 0.042,   Method: Composition-based stats.
 Identities = 15/84 (17%), Positives = 30/84 (35%), Gaps = 5/84 (5%)

Query: 14  QRVSKVIARAGIAS---RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            R+  ++ R GIAS   R    +++  + + VNG +++  +      D I V      +A
Sbjct: 89  MRLDNILFRLGIASTIPR--ARQLVNHRHILVNGRIVDIPSYRCKPRDVITVRDEQKSRA 146

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGR 94
                        L    +    +
Sbjct: 147 MIPNYLDSSPQEELPKHLTLHPIQ 170


>gi|139389803|ref|YP_001123464.1| ribosomal protein S4 [Crucihimalaya wallichii]
 gi|152060549|sp|A4QKT3|RR4_CRUWA RecName: Full=30S ribosomal protein S4, chloroplastic
 gi|134286665|dbj|BAF50288.1| ribosomal protein S4 [Crucihimalaya wallichii]
          Length = 201

 Score = 43.6 bits (101), Expect = 0.042,   Method: Composition-based stats.
 Identities = 10/53 (18%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
            R+  ++ R G+A +  +  +++    + VNG +++  +      D I V   
Sbjct: 89  MRLDNILFRLGMALTIPQARQLVNHGHILVNGRIVDIPSYRCKPRDIITVKDE 141


>gi|139388096|ref|YP_001123288.1| ribosomal protein S4 [Barbarea verna]
 gi|139388912|ref|YP_001123639.1| ribosomal protein S4 [Lepidium virginicum]
 gi|139389098|ref|YP_001123816.1| ribosomal protein S4 [Nasturtium officinale]
 gi|152060546|sp|A4QKA7|RR4_BARVE RecName: Full=30S ribosomal protein S4, chloroplastic
 gi|152060553|sp|A4QLA8|RR4_LEPVR RecName: Full=30S ribosomal protein S4, chloroplastic
 gi|152060555|sp|A4QLT5|RR4_NASOF RecName: Full=30S ribosomal protein S4, chloroplastic
 gi|134286487|dbj|BAF50112.1| ribosomal protein S4 [Barbarea verna]
 gi|134286842|dbj|BAF50463.1| ribosomal protein S4 [Lepidium virginicum]
 gi|134287021|dbj|BAF50640.1| ribosomal protein S4 [Nasturtium officinale]
          Length = 201

 Score = 43.6 bits (101), Expect = 0.042,   Method: Composition-based stats.
 Identities = 10/53 (18%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
            R+  ++ R G+A +  +  +++    + VNG +++  +      D I V   
Sbjct: 89  MRLDNILFRLGMALTIPQARQLVNHGHILVNGRIVDIPSYRCKPRDIITVKDE 141


>gi|111225026|ref|YP_715820.1| putative pseudouridylate synthase [Frankia alni ACN14a]
 gi|111152558|emb|CAJ64299.1| Conserved hypothetical protein; putative Pseudouridylate synthase
          [Frankia alni ACN14a]
          Length = 68

 Score = 43.6 bits (101), Expect = 0.042,   Method: Composition-based stats.
 Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 5/60 (8%)

Query: 12 TPQRVSKVIARA---GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
             R+ + +  A   G+ S  +V+ ++A   V+VNG +  R    ++  D + V G  LR
Sbjct: 9  DAIRLGQFLKLADVVGVGS--DVKGLLAGGMVRVNGEVESRRGRQLVPGDEVVVSGERLR 66


>gi|326799154|ref|YP_004316973.1| ribosomal protein S4 [Sphingobacterium sp. 21]
 gi|326549918|gb|ADZ78303.1| ribosomal protein S4 [Sphingobacterium sp. 21]
          Length = 202

 Score = 43.6 bits (101), Expect = 0.042,   Method: Composition-based stats.
 Identities = 17/69 (24%), Positives = 31/69 (44%), Gaps = 9/69 (13%)

Query: 3   DKNIVQENFTPQRVSKVI--------ARAGIA-SRREVERMIAQQRVKVNGILLERAAVN 53
           DK   +E  T + + K +         R GIA +R    +++  + + VNG ++   + +
Sbjct: 74  DKAASKEGITGENLLKFLEARLDNTVFRLGIAPTRAGARQLVGHKHITVNGQVVNIPSYS 133

Query: 54  VMSTDHIEV 62
           V   D I V
Sbjct: 134 VRPGDVIAV 142


>gi|296234004|ref|XP_002762257.1| PREDICTED: hypothetical protein LOC100394361 isoform 2 [Callithrix
           jacchus]
          Length = 727

 Score = 43.6 bits (101), Expect = 0.042,   Method: Composition-based stats.
 Identities = 17/126 (13%), Positives = 32/126 (25%), Gaps = 1/126 (0%)

Query: 230 AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
            G  R+ S+     +        +                              R +  S
Sbjct: 395 PGKDRDRSQSESPNKQRDCSRSRSPSEKKDHTRGRSRSPSQERARGRSRSPSQERARGRS 454

Query: 290 SQKNGLSKQKKLATPVHRRNL-ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
              +    + +  +P   R    S     +       S S +R     RSPS    R   
Sbjct: 455 RSPSQERARGRSRSPSQERARGRSRSPSQERARGRSRSPSQERARGRSRSPSQERARGRS 514

Query: 349 RTSAKK 354
           R+ +++
Sbjct: 515 RSPSQE 520



 Score = 40.9 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 28/108 (25%), Gaps = 1/108 (0%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
           H    ++                             R +  S   +    + +  +P   
Sbjct: 425 HTRGRSRSPSQERARGRSRSPSQERARGRSRSPSQERARGRSRSPSQERARGRSRSPSQE 484

Query: 308 RNL-ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           R    S     +       S S +R     RSPS    R   R+ +++
Sbjct: 485 RARGRSRSPSQERARGRSRSPSQERARGRSRSPSQERARGRSRSPSQE 532



 Score = 37.5 bits (85), Expect = 2.8,   Method: Composition-based stats.
 Identities = 20/100 (20%), Positives = 33/100 (33%)

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
              D    SS    RDR    S          ++ S+K   ++ +  +    R    S  
Sbjct: 385 KERDRRGSSSPGKDRDRSQSESPNKQRDCSRSRSPSEKKDHTRGRSRSPSQERARGRSRS 444

Query: 315 WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              +       S S +R     RSPS    R   R+ +++
Sbjct: 445 PSQERARGRSRSPSQERARGRSRSPSQERARGRSRSPSQE 484



 Score = 36.7 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 18/113 (15%), Positives = 34/113 (30%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R     +               S +  RDR    S   D      ++ +++   S+ +  
Sbjct: 360 RRGRSHNWSRTPSKERSHSPSRSSSKERDRRGSSSPGKDRDRSQSESPNKQRDCSRSRSP 419

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +         S     +       S S +R     RSPS    R   R+ +++
Sbjct: 420 SEKKDHTRGRSRSPSQERARGRSRSPSQERARGRSRSPSQERARGRSRSPSQE 472



 Score = 36.3 bits (82), Expect = 6.6,   Method: Composition-based stats.
 Identities = 17/107 (15%), Positives = 30/107 (28%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                   + D     S    RD     S          ++ S     ++ +  +    R
Sbjct: 390 RGSSSPGKDRDRSQSESPNKQRDCSRSRSPSEKKDHTRGRSRSPSQERARGRSRSPSQER 449

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               S     +       S S +R     RSPS    R   R+ +++
Sbjct: 450 ARGRSRSPSQERARGRSRSPSQERARGRSRSPSQERARGRSRSPSQE 496


>gi|119025372|ref|YP_909217.1| translation initiation factor IF-2 [Bifidobacterium adolescentis
           ATCC 15703]
 gi|166226250|sp|A1A0A2|IF2_BIFAA RecName: Full=Translation initiation factor IF-2
 gi|118764956|dbj|BAF39135.1| translation initiation factor IF-2 [Bifidobacterium adolescentis
           ATCC 15703]
          Length = 931

 Score = 43.6 bits (101), Expect = 0.042,   Method: Composition-based stats.
 Identities = 14/119 (11%), Positives = 29/119 (24%), Gaps = 1/119 (0%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           + K   E     + + A  +   P   +    R   +            +   S+++G  
Sbjct: 67  TAKKPAEPASHSMPKPAAPSAPKPAAPAAPKPRHAASKSDAPKPGHRAPRPGESRQHGNR 126

Query: 297 KQKKLATP-VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                  P    R  +       G      +        +   P  P  R      ++K
Sbjct: 127 PNGNAPRPQGGDRRQSGRPTAVPGARPQHGNAPQGGNNANGAKPHTPGPRPGNNPFSRK 185


>gi|306819785|ref|ZP_07453440.1| 30S ribosomal protein S4 [Eubacterium yurii subsp. margaretiae ATCC
           43715]
 gi|304552154|gb|EFM40090.1| 30S ribosomal protein S4 [Eubacterium yurii subsp. margaretiae ATCC
           43715]
          Length = 192

 Score = 43.6 bits (101), Expect = 0.042,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 22/50 (44%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            R+  +  R G  S  R+  +++    + VNG  ++  +  V   D I +
Sbjct: 84  MRLDNIAYRLGFGSSIRQARQIVNHGHLLVNGKKVDIPSYKVSVGDTITL 133


>gi|293399094|ref|ZP_06643259.1| hsp15-like protein [Neisseria gonorrhoeae F62]
 gi|291610508|gb|EFF39618.1| hsp15-like protein [Neisseria gonorrhoeae F62]
          Length = 133

 Score = 43.6 bits (101), Expect = 0.042,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 6/61 (9%)

Query: 1  MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          MKDK+    + +  R+ K + A     +R   ++ I   RV+VNG  ++ +   +   D 
Sbjct: 1  MKDKH----DSSAMRLDKWLWAARFFKTRSLAQKHIELGRVQVNGSKVKNSKT-IDIGDI 55

Query: 60 I 60
          I
Sbjct: 56 I 56


>gi|198282663|ref|YP_002218984.1| 30S ribosomal protein S4 [Acidithiobacillus ferrooxidans ATCC
           53993]
 gi|218667358|ref|YP_002424856.1| ribosomal protein S4 [Acidithiobacillus ferrooxidans ATCC 23270]
 gi|226697790|sp|B7J4A3|RS4_ACIF2 RecName: Full=30S ribosomal protein S4
 gi|226697791|sp|B5EM98|RS4_ACIF5 RecName: Full=30S ribosomal protein S4
 gi|198247184|gb|ACH82777.1| ribosomal protein S4 [Acidithiobacillus ferrooxidans ATCC 53993]
 gi|218519571|gb|ACK80157.1| ribosomal protein S4 [Acidithiobacillus ferrooxidans ATCC 23270]
          Length = 208

 Score = 43.6 bits (101), Expect = 0.042,   Method: Composition-based stats.
 Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 1/42 (2%)

Query: 22  RAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R G   SR E  +++    + VNG  ++  +  V + D + V
Sbjct: 106 RLGFGASRAEARQVVRHGHILVNGRRVDIPSYQVRAGDVVSV 147


>gi|184159574|ref|YP_001847913.1| 30S ribosomal protein S4 [Acinetobacter baumannii ACICU]
 gi|226697787|sp|B2HZ84|RS4_ACIBC RecName: Full=30S ribosomal protein S4
 gi|183211168|gb|ACC58566.1| 30S ribosomal protein S4 [Acinetobacter baumannii ACICU]
          Length = 208

 Score = 43.6 bits (101), Expect = 0.042,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + +NG  +  A++ V S D I V
Sbjct: 99  RLDNVVYRMGFGSTRAEARQLVSHRSITLNGRRVNIASIQVKSGDVIAV 147


>gi|157689496|gb|ABV65304.1| ribosomal protein S4 [Hypericum kalmianum]
          Length = 184

 Score = 43.6 bits (101), Expect = 0.042,   Method: Composition-based stats.
 Identities = 10/53 (18%), Positives = 23/53 (43%), Gaps = 1/53 (1%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
            R+  ++ R G+ S   +  +++  + + VNG ++   +      D I V   
Sbjct: 72  MRLDNILFRLGMGSTIPQARQLVNHRHIFVNGHIVNIPSFRCKPGDIITVRDE 124


>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 = 43.6 bits (101), Expect = 0.042,   Method: Composition-based stats.
 Identities = 21/215 (9%), Positives = 56/215 (26%), Gaps = 33/215 (15%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--------------LRKAERTR 74
           R + + +   RV VN   + +    +   D IE+                  +   +   
Sbjct: 31  RFIRKAVRDGRVFVNKEKVIK-KHKLSQDDLIEIYMQEDEHQNIEPEDMNIEIVYEDNDI 89

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------------------ISVGRLDI 116
           + +  +P  +V         +     L                         I + +   
Sbjct: 90  IVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKNQF 149

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +   L    +     ++        ++    R +  +  ++ +   K IV +        
Sbjct: 150 SHMRLASDMSKDSFRKIYIAVVHGSMKEKEGRINLPIYNEEESESIKRIVDERGQESITT 209

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +  +    + V + L  G+  +I+         
Sbjct: 210 YEVLEELSKGSVVRLELETGRTHQIRVHMSHLGHP 244


>gi|170742492|ref|YP_001771147.1| triple helix repeat-containing collagen [Methylobacterium sp. 4-46]
 gi|168196766|gb|ACA18713.1| Collagen triple helix repeat [Methylobacterium sp. 4-46]
          Length = 344

 Score = 43.6 bits (101), Expect = 0.042,   Method: Composition-based stats.
 Identities = 7/113 (6%), Positives = 15/113 (13%), Gaps = 5/113 (4%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           GP                                +   + +     + G   +       
Sbjct: 128 GPAGQPGPTGPQGVAGLPGPKGDPGPQGPAGPKGEPGPKGEPGPKGEPGPKGEPGPKGEP 187

Query: 306 HRRNLASNVWMA-----KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             +               G             +    S   P  R       +
Sbjct: 188 GPKGEPGPKGEPGPKGEPGPRGEAGPQGALGPKGEAGSRGEPGPRGEPGPKGE 240



 Score = 39.0 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 12/106 (11%), Positives = 16/106 (15%), Gaps = 2/106 (1%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
             GP   +        P    E   +  P    E         K      G    +  A 
Sbjct: 153 PQGPAGPKGEPGPKGEPGPKGEPGPKGEPGPKGEPGPKGEPGPKGEPGPKGEPGPRGEAG 212

Query: 304 PVH--RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
           P         +      G                         R  
Sbjct: 213 PQGALGPKGEAGSRGEPGPRGEPGPKGEAGLAGAPGPKGEAGPRGP 258


>gi|325116578|emb|CBZ52132.1| conserved hypothetical protein [Neospora caninum Liverpool]
          Length = 1282

 Score = 43.6 bits (101), Expect = 0.043,   Method: Composition-based stats.
 Identities = 10/121 (8%), Positives = 27/121 (22%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           + +  K +R+              +    +      D      +   D    +    Q  
Sbjct: 441 KRLETKEVRQGTEVKEAHATAGRRNVRQGTQADPKEDDKREDGDCDQDEAEREDAEDQGR 500

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              +         +         A            +  +    + S   +R  RR + +
Sbjct: 501 ASGEPVPEEQRPKQGREEVEGGEAPEELRRARRGDAEAPDGRASAASPSGRRGARRGTDQ 560

Query: 354 K 354
           +
Sbjct: 561 R 561


>gi|256821686|ref|YP_003145649.1| 30S ribosomal protein S4 [Kangiella koreensis DSM 16069]
 gi|256795225|gb|ACV25881.1| ribosomal protein S4 [Kangiella koreensis DSM 16069]
          Length = 206

 Score = 43.6 bits (101), Expect = 0.043,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R E  ++++ + + +NG  +   +  V + D + V
Sbjct: 97  RLDNVVYRMGYAATRGEARQLVSHKAILINGETVNIPSYTVKAEDVVSV 145


>gi|218189774|gb|EEC72201.1| hypothetical protein OsI_05282 [Oryza sativa Indica Group]
          Length = 1224

 Score = 43.6 bits (101), Expect = 0.043,   Method: Composition-based stats.
 Identities = 9/109 (8%), Positives = 23/109 (21%), Gaps = 2/109 (1%)

Query: 236  VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
            ++ +              + ++      + +  +D        P                
Sbjct: 976  LAPRQRASSPMKAPPPPPKRDVPHNEKGAPSAEKDVQQRREPSPRRKPASPPRKRTPPNR 1035

Query: 296  SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
              +     P        +         +  S   + +   RR P  P K
Sbjct: 1036 RIESPRRQPDPSPRRRPDS--PPIRRRADASPVRRGDTPPRRRPGSPVK 1082



 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 20/131 (15%), Positives = 40/131 (30%), Gaps = 3/131 (2%)

Query: 227  TLLAG-STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
             L  G    E  K+   E+   ++           +  +    +   + +   P    R 
Sbjct: 937  NLPRGYGYIEFKKRTDAEKALLYMDGGQIDGNVVKLRFTLAPRQRASSPMKAPPPPPKRD 996

Query: 286  KKNSSQKNGLSKQK--KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
              ++ +    +++   +   P  RR  AS        +    S   Q + + RR P  P 
Sbjct: 997  VPHNEKGAPSAEKDVQQRREPSPRRKPASPPRKRTPPNRRIESPRRQPDPSPRRRPDSPP 1056

Query: 344  KRSLRRTSAKK 354
             R     S  +
Sbjct: 1057 IRRRADASPVR 1067



 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 11/101 (10%), Positives = 23/101 (22%), Gaps = 2/101 (1%)

Query: 256  NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV-HRRNLASNV 314
             L     +S  +    P    +VP +               +      P    R      
Sbjct: 975  TLAPRQRASSPMKAPPPPPKRDVPHNEKGAPSAEKDVQQRREPSPRRKPASPPRKRTPPN 1034

Query: 315  WMAKGIHSSFLSDSGQREENHR-RSPSFPSKRSLRRTSAKK 354
               +           +R ++   R  +  S      T  ++
Sbjct: 1035 RRIESPRRQPDPSPRRRPDSPPIRRRADASPVRRGDTPPRR 1075


>gi|210623214|ref|ZP_03293653.1| hypothetical protein CLOHIR_01603 [Clostridium hiranonis DSM 13275]
 gi|210153751|gb|EEA84757.1| hypothetical protein CLOHIR_01603 [Clostridium hiranonis DSM 13275]
          Length = 207

 Score = 43.6 bits (101), Expect = 0.043,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A SR+E  +++      +NG  ++  ++ V   D I V
Sbjct: 99  RLDNVVYRMGLAASRKEARQLVTHAHFTLNGKKVDIPSLTVNVGDVIAV 147


>gi|188996212|ref|YP_001930463.1| ribosomal protein S4 [Sulfurihydrogenibium sp. YO3AOP1]
 gi|226695086|sp|B2V7I6|RS4_SULSY RecName: Full=30S ribosomal protein S4
 gi|188931279|gb|ACD65909.1| ribosomal protein S4 [Sulfurihydrogenibium sp. YO3AOP1]
          Length = 204

 Score = 43.6 bits (101), Expect = 0.043,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R +  +++      VNG  ++  +  +   D IEV
Sbjct: 95  RLDNVVYRLGFAKTRLQARQLVKHGHFLVNGKKVDIPSYELDKGDIIEV 143


>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 = 43.6 bits (101), Expect = 0.043,   Method: Composition-based stats.
 Identities = 14/51 (27%), Positives = 27/51 (52%), Gaps = 1/51 (1%)

Query: 13 PQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          P+R+ + +AR     SR  ++ +I +  V+++G  +  AAV V     + V
Sbjct: 16 PERLDRALARTWPDLSRSRLQGLIREGGVRLDGAEIRDAAVRVAGGQTVAV 66


>gi|163814657|ref|ZP_02206046.1| hypothetical protein COPEUT_00808 [Coprococcus eutactus ATCC
          27759]
 gi|158450292|gb|EDP27287.1| hypothetical protein COPEUT_00808 [Coprococcus eutactus ATCC
          27759]
          Length = 79

 Score = 43.6 bits (101), Expect = 0.043,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 20/50 (40%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR          RV VN  + + A   V   D IE+
Sbjct: 1  MRLDKYLKVSRIIKRRTVANEACDAGRVMVNDKVAK-AGTEVKVGDVIEI 49


>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 = 43.6 bits (101), Expect = 0.043,   Method: Composition-based stats.
 Identities = 28/237 (11%), Positives = 64/237 (27%), Gaps = 32/237 (13%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGI-----------------LLE 48
            V E     ++   + R    S R ++      R+++N                   L++
Sbjct: 9   TVDEKDEGLKLRYYLQRVQRLSGRLIKGAALSGRIEINNKRVKLNHIVKSGESISLNLVK 68

Query: 49  RAAVNVMS-----------TDHIEVDGVPLRKAERTRLWL---YHKPIGLVTTHSDPDGR 94
             + NV              D I V+  P      TR +        +         D  
Sbjct: 69  EESQNVEPEKMDIEVAYEDDDLIVVNKRPGIVVHPTRSYPSGTLANGLMYYFKEKGEDCI 128

Query: 95  STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD 154
             +   L    S +I VG+       L          +         ++         + 
Sbjct: 129 VRLVSRLDMDTSGLIIVGKNQFAHMALARDMKSEEFEKSYIAVIHGKMKENEGTIDLPIY 188

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           + +   +++ I  +G         +     ++  + + L  G+  +I+    +    
Sbjct: 189 RQEGEDIRRIIDERGQK-SITHYKVIKDFKNDQLLKLTLETGRTHQIRVHLSYLGHP 244


>gi|116254343|ref|YP_770181.1| heat shock protein 15 [Rhizobium leguminosarum bv. viciae 3841]
 gi|115258991|emb|CAK10100.1| putative heat shock protein 15 [Rhizobium leguminosarum bv.
          viciae 3841]
          Length = 134

 Score = 43.6 bits (101), Expect = 0.043,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          QR+ K +  A +A SR   +  I    V++NG      +  V   D IE+
Sbjct: 13 QRIDKWLFFARMAKSRSVAQSHIQSGHVRINGERCSYPSQMVKPGDRIEL 62


>gi|39931303|sp|Q9AC25|IF2_CAUCR RecName: Full=Translation initiation factor IF-2
          Length = 1009

 Score = 43.6 bits (101), Expect = 0.043,   Method: Composition-based stats.
 Identities = 7/100 (7%), Positives = 19/100 (19%), Gaps = 1/100 (1%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
                                    E   D    + +++      +  +       R  A
Sbjct: 183 APSAPRQDAPRQDTRAAAPGQTRTYEPSRDRRDDRPSTTTYRPAPQGDRPFNQRAPRPDA 242

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPS-KRSLRRT 350
           +  +  +          G R +  R        +    + 
Sbjct: 243 NANFGQRAPRPEGDRPRGPRPDGDRPQGDRGGYRGDRPQG 282



 Score = 39.4 bits (90), Expect = 0.79,   Method: Composition-based stats.
 Identities = 9/107 (8%), Positives = 20/107 (18%), Gaps = 1/107 (0%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                          ++    R          D  +      + +      ++   P   
Sbjct: 184 PSAPRQDAPRQDTRAAAPGQTRTYEPSRDRRDDRPSTTTYRPAPQGDRPFNQRAPRPDAN 243

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            N        +G         G R +   R      +    R    +
Sbjct: 244 ANFGQRAPRPEGDRPRGPRPDGDRPQG-DRGGYRGDRPQGDRPQGDR 289



 Score = 35.9 bits (81), Expect = 9.2,   Method: Composition-based stats.
 Identities = 6/84 (7%), Positives = 14/84 (16%), Gaps = 1/84 (1%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
               + +      +     +         P                  + +   P   R 
Sbjct: 209 PSRDRRDDRPSTTTYRPAPQGDRPFNQRAPRPDANANFGQRAPRPEGDRPRGPRPDGDRP 268

Query: 310 LASNVWMAKGIHSSFLSDSGQREE 333
                   +G         G R +
Sbjct: 269 QGDRGGY-RGDRPQGDRPQGDRPQ 291


>gi|15828060|ref|NP_302323.1| 30S ribosomal protein S4 [Mycobacterium leprae TN]
 gi|221230537|ref|YP_002503953.1| 30S ribosomal protein S4 [Mycobacterium leprae Br4923]
 gi|7388198|sp|Q9X799|RS4_MYCLE RecName: Full=30S ribosomal protein S4
 gi|254764601|sp|B8ZSH7|RS4_MYCLB RecName: Full=30S ribosomal protein S4
 gi|4539113|emb|CAB39834.1| putative 30S ribosomal protein S4 [Mycobacterium leprae]
 gi|13093613|emb|CAC30913.1| 30S ribosomal protein S4 [Mycobacterium leprae]
 gi|219933644|emb|CAR72055.1| 30S ribosomal protein S4 [Mycobacterium leprae Br4923]
          Length = 201

 Score = 43.6 bits (101), Expect = 0.043,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  VI RAG+A +RR   ++++     VNG+ +   +  V   D I++    L      
Sbjct: 92  RLDNVIYRAGLARTRRMARQLVSHGHFSVNGVHVNVPSYRVSQYDIIDIRDKSLDTVPFQ 151

Query: 74  R 74
            
Sbjct: 152 I 152


>gi|108758664|ref|YP_631524.1| 30S ribosomal protein S4 [Myxococcus xanthus DK 1622]
 gi|122981072|sp|Q1D749|RS4A_MYXXD RecName: Full=30S ribosomal protein S4 A
 gi|108462544|gb|ABF87729.1| ribosomal protein S4 [Myxococcus xanthus DK 1622]
          Length = 208

 Score = 43.6 bits (101), Expect = 0.044,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R E  +++     +VNG  +   +  V     +EV
Sbjct: 99  RLDNVVFRMGFADTRNEARQLVRHGHFQVNGRKVNIPSFAVKPGTAVEV 147


>gi|305665112|ref|YP_003861399.1| 30S ribosomal protein S4 [Maribacter sp. HTCC2170]
 gi|88709864|gb|EAR02096.1| 30S ribosomal protein S4 [Maribacter sp. HTCC2170]
          Length = 201

 Score = 43.6 bits (101), Expect = 0.044,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+  SRR   ++++ + + VNG L+   + ++ + D + V
Sbjct: 94  RLDNVVYRMGVSTSRRGARQLVSHRHITVNGELVNIPSYSLKAGDVVGV 142


>gi|74273177|gb|ABA01288.1| ribosomal protein S4 [Passiflora ischnoclada]
          Length = 183

 Score = 43.6 bits (101), Expect = 0.044,   Method: Composition-based stats.
 Identities = 13/82 (15%), Positives = 29/82 (35%), Gaps = 1/82 (1%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+  ++ R G+AS   +  +++  + + VNG +++  +      D I V      K   
Sbjct: 71  MRLDNILFRLGMASTIPQARQLVNHRHILVNGRIVDIPSYRCKPQDLITVKDEQKSKDMI 130

Query: 73  TRLWLYHKPIGLVTTHSDPDGR 94
                      L    +    +
Sbjct: 131 QNSLDSFPQKKLPKHLTLHPFQ 152


>gi|294674745|ref|YP_003575361.1| 30S ribosomal protein S4 [Prevotella ruminicola 23]
 gi|294473372|gb|ADE82761.1| ribosomal protein S4 [Prevotella ruminicola 23]
          Length = 202

 Score = 43.6 bits (101), Expect = 0.044,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA +R    +++  + + V+G ++   +  V     + V
Sbjct: 93  RLDNVVFRLGIAPTRAAARQLVGHKHITVDGQVVNIPSYAVKPGQVVAV 141


>gi|262377288|ref|ZP_06070512.1| ribosomal protein S4 [Acinetobacter lwoffii SH145]
 gi|262307741|gb|EEY88880.1| ribosomal protein S4 [Acinetobacter lwoffii SH145]
          Length = 208

 Score = 43.6 bits (101), Expect = 0.044,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + +NG  +  A++ V + D I V
Sbjct: 99  RLDNVVYRMGFGSTRAEARQLVSHRSITLNGRRVNIASIQVKAGDVIAV 147


>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 = 43.6 bits (101), Expect = 0.044,   Method: Composition-based stats.
 Identities = 21/215 (9%), Positives = 57/215 (26%), Gaps = 33/215 (15%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--------------LRKAERTR 74
           R + + +   RV VN   + +    +   D IE+                  +   +   
Sbjct: 31  RFIRKAVRDGRVFVNEEKVIK-KHKLSQDDLIEIYMQEDEHQNIEPEDMNIEIVYEDNDI 89

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------------------ISVGRLDI 116
           + +  +P  +V         +     L                         I + +   
Sbjct: 90  IVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKNQF 149

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +   L    +     ++        ++    R +  + +++ +   K IV +        
Sbjct: 150 SHMRLASDMSKDSFRKIYIAVVHGSMKEKEKRINLPIYKEEESESIKRIVDERGQESITT 209

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +  +    + V + L  G+  +I+         
Sbjct: 210 YKVLEELSKGSVVRLELETGRTHQIRVHMSHLGHP 244


>gi|23011993|ref|ZP_00052190.1| COG0513: Superfamily II DNA and RNA helicases [Magnetospirillum
           magnetotacticum MS-1]
          Length = 551

 Score = 43.6 bits (101), Expect = 0.044,   Method: Composition-based stats.
 Identities = 11/101 (10%), Positives = 22/101 (21%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
                   P    +    +             R       +    +  +   P  +R+  
Sbjct: 441 RPGQRQGRPGGRGQEGRGEGRGEHRAHEARGGRPGGQPGHRQDQRQDSRGPRPDGQRSDQ 500

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                A           G R  + RR  + P++       A
Sbjct: 501 RRPERAGEGRPQGARPQGGRPNDGRRGDARPARSGAEGGRA 541


>gi|256829787|ref|YP_003158515.1| DEAD/DEAH box helicase domain-containing protein [Desulfomicrobium
           baculatum DSM 4028]
 gi|256578963|gb|ACU90099.1| DEAD/DEAH box helicase domain protein [Desulfomicrobium baculatum
           DSM 4028]
          Length = 545

 Score = 43.6 bits (101), Expect = 0.044,   Method: Composition-based stats.
 Identities = 14/110 (12%), Positives = 26/110 (23%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E+      E+     D+      T   D  +     PD   R ++N         +K   
Sbjct: 436 EKSDARKAEDKDTRPDSKPRGRSTGKPDARSGKDSGPDAKGRGRRNERTDTRTGSEKNSG 495

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                R   +         +     + + +     S      R   R   
Sbjct: 496 PESKGRGRRNERSEDSRAGADKRGGNTRGKAARPDSRPAQPARGRSRGRG 545


>gi|16124298|ref|NP_418862.1| translation initiation factor IF-2 [Caulobacter crescentus CB15]
 gi|221232980|ref|YP_002515416.1| translation initiation factor IF-2 [Caulobacter crescentus NA1000]
 gi|13421134|gb|AAK22030.1| translation initiation factor IF-2 [Caulobacter crescentus CB15]
 gi|220962152|gb|ACL93508.1| bacterial protein translation initiation factor 2 IF-2 [Caulobacter
           crescentus NA1000]
          Length = 1037

 Score = 43.6 bits (101), Expect = 0.044,   Method: Composition-based stats.
 Identities = 7/100 (7%), Positives = 19/100 (19%), Gaps = 1/100 (1%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
                                    E   D    + +++      +  +       R  A
Sbjct: 211 APSAPRQDAPRQDTRAAAPGQTRTYEPSRDRRDDRPSTTTYRPAPQGDRPFNQRAPRPDA 270

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPS-KRSLRRT 350
           +  +  +          G R +  R        +    + 
Sbjct: 271 NANFGQRAPRPEGDRPRGPRPDGDRPQGDRGGYRGDRPQG 310



 Score = 39.4 bits (90), Expect = 0.82,   Method: Composition-based stats.
 Identities = 9/107 (8%), Positives = 20/107 (18%), Gaps = 1/107 (0%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                          ++    R          D  +      + +      ++   P   
Sbjct: 212 PSAPRQDAPRQDTRAAAPGQTRTYEPSRDRRDDRPSTTTYRPAPQGDRPFNQRAPRPDAN 271

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            N        +G         G R +   R      +    R    +
Sbjct: 272 ANFGQRAPRPEGDRPRGPRPDGDRPQG-DRGGYRGDRPQGDRPQGDR 317



 Score = 35.9 bits (81), Expect = 9.3,   Method: Composition-based stats.
 Identities = 7/88 (7%), Positives = 15/88 (17%), Gaps = 1/88 (1%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
               + +      +     +         P                  + +   P   R 
Sbjct: 237 PSRDRRDDRPSTTTYRPAPQGDRPFNQRAPRPDANANFGQRAPRPEGDRPRGPRPDGDRP 296

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRR 337
                   +G         G R +   R
Sbjct: 297 QGDRGGY-RGDRPQGDRPQGDRPQQTVR 323


>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 = 43.6 bits (101), Expect = 0.045,   Method: Composition-based stats.
 Identities = 10/50 (20%), Positives = 20/50 (40%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+ K++A+    SRR     +   R+ + G L +     V     +  +
Sbjct: 26 VRLDKLVAQRFGLSRRAAGDAVLNGRIDLEGQLCDEPGRLVPPESVLRFN 75


>gi|255038115|ref|YP_003088736.1| 30S ribosomal protein S4 [Dyadobacter fermentans DSM 18053]
 gi|254950871|gb|ACT95571.1| ribosomal protein S4 [Dyadobacter fermentans DSM 18053]
          Length = 201

 Score = 43.6 bits (101), Expect = 0.045,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   + R GIA +RR   ++++ + + V+G ++   + ++     + V
Sbjct: 93  RLDNTVYRLGIAPTRRAARQLVSHKHILVDGEIVNIPSYSLRPGQVVTV 141


>gi|78776527|ref|YP_392842.1| 30S ribosomal protein S4 [Sulfurimonas denitrificans DSM 1251]
 gi|90101735|sp|Q30TS4|RS4_SULDN RecName: Full=30S ribosomal protein S4
 gi|78497067|gb|ABB43607.1| SSU ribosomal protein S4P [Sulfurimonas denitrificans DSM 1251]
          Length = 208

 Score = 43.6 bits (101), Expect = 0.045,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G A+ RR   +++    + V+G  L+  +  V     IE+
Sbjct: 98  QRLDNVVYRMGFATTRRFARQLVTHGHLLVDGAKLDIPSYRVRPGQKIEI 147


>gi|256375863|ref|YP_003099523.1| RNA-binding S4 domain protein [Actinosynnema mirum DSM 43827]
 gi|255920166|gb|ACU35677.1| RNA-binding S4 domain protein [Actinosynnema mirum DSM 43827]
          Length = 91

 Score = 43.6 bits (101), Expect = 0.045,   Method: Composition-based stats.
 Identities = 14/60 (23%), Positives = 24/60 (40%), Gaps = 7/60 (11%)

Query: 11 FTPQRVSKVIARAGIASRRE----VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
              R+ + +  AG+A   E       ++ +  V VNG    R    + + D + VDG  
Sbjct: 10 DDMIRLGQFLKLAGLA---EHGAHARELVEEGEVTVNGRPESRRGAQLKNGDVVAVDGEK 66


>gi|32892082|gb|AAP88980.1| ribosomal protein S4 [Passiflora haematostigma]
 gi|74273095|gb|ABA01247.1| ribosomal protein S4 [Passiflora rhamnifolia]
          Length = 183

 Score = 43.6 bits (101), Expect = 0.045,   Method: Composition-based stats.
 Identities = 11/53 (20%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
            R+  ++ R G+AS   +  +++  + + VNG +++  +      D I V   
Sbjct: 71  MRLDNILFRLGMASTIPQARQLVNHRHILVNGRIVDIPSYRCKPGDLITVKDE 123


>gi|86742862|ref|YP_483262.1| serine/threonine protein kinase [Frankia sp. CcI3]
 gi|86569724|gb|ABD13533.1| serine/threonine protein kinase [Frankia sp. CcI3]
          Length = 719

 Score = 43.6 bits (101), Expect = 0.045,   Method: Composition-based stats.
 Identities = 11/108 (10%), Positives = 19/108 (17%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R                 P   +                        +        +   
Sbjct: 303 RGSPPARTPPARTPPARTPPARTPPARTPPARTPPARTPPARTPPARTPPARTPPARTPP 362

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           A     R        A    ++            RRS +  ++R LR 
Sbjct: 363 ARTPPARTPPDTPPSAVPPPATASPRRWSAGVIRRRSLNRTARRDLRP 410


>gi|91200693|emb|CAJ73744.1| strongly similar to 30S ribosomal protein S4 [Candidatus Kuenenia
           stuttgartiensis]
          Length = 208

 Score = 43.6 bits (101), Expect = 0.046,   Method: Composition-based stats.
 Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 1/48 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           R+  V+     A SR+   ++I    V VN   ++ A+  V   D I 
Sbjct: 99  RLDNVVHLLTFAHSRKSARQLILHGNVTVNDKKVDIASFLVKVGDVIR 146


>gi|156606|gb|AAA28264.1| SpId [Chironomus tentans]
          Length = 749

 Score = 43.6 bits (101), Expect = 0.046,   Method: Composition-based stats.
 Identities = 21/117 (17%), Positives = 36/117 (30%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            K   ++      E    +  +  + +++    RP   S+      +  K+ S+    SK
Sbjct: 252 PKQDDDEKETQPAETDDDSGSSEGHDNKSGSGSRPEKRSKSGSRPEKRSKSGSRPEKRSK 311

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                    +           G      S SG R E    S   P KRS   +  +K
Sbjct: 312 SGSRPEKRSKSGSRPEKRSKSGSRPEKRSKSGSRPEKRSESGPRPEKRSKSGSRPEK 368



 Score = 41.3 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 19/108 (17%), Positives = 32/108 (29%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P   ++ +          ++   +  +  S       +  K+ S+    SK         
Sbjct: 251 PPKQDDDEKETQPAETDDDSGSSEGHDNKSGSGSRPEKRSKSGSRPEKRSKSGSRPEKRS 310

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +           G      S SG R E   +S S P KRS      +K
Sbjct: 311 KSGSRPEKRSKSGSRPEKRSKSGSRPEKRSKSGSRPEKRSESGPRPEK 358



 Score = 39.4 bits (90), Expect = 0.79,   Method: Composition-based stats.
 Identities = 17/102 (16%), Positives = 27/102 (26%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
            +          +       +  S   +       + S+    SK         +     
Sbjct: 247 KKPTPPKQDDDEKETQPAETDDDSGSSEGHDNKSGSGSRPEKRSKSGSRPEKRSKSGSRP 306

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                 G      S SG R E   +S S P KRS   +  +K
Sbjct: 307 EKRSKSGSRPEKRSKSGSRPEKRSKSGSRPEKRSKSGSRPEK 348



 Score = 37.5 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 17/71 (23%), Positives = 24/71 (33%)

Query: 283 TRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
           +R  K+ S+    SK         +           G      S SG R E   +S S P
Sbjct: 617 SRPSKSGSRPEKRSKSGSRPEKRSKSGSRPEKRSKSGSRPEKRSKSGSRPEKRSKSGSRP 676

Query: 343 SKRSLRRTSAK 353
            KRS   +  +
Sbjct: 677 EKRSKSGSRPE 687


>gi|226940953|ref|YP_002796027.1| ribosome-associated heat shock protein HSP15 [Laribacter
          hongkongensis HLHK9]
 gi|226715880|gb|ACO75018.1| probable ribosome-associated heat shock protein HSP15 [Laribacter
          hongkongensis HLHK9]
          Length = 131

 Score = 43.6 bits (101), Expect = 0.046,   Method: Composition-based stats.
 Identities = 12/57 (21%), Positives = 23/57 (40%), Gaps = 2/57 (3%)

Query: 7  VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          + +     R+ K + A     +R   +  I    V +NG   +  +  V + D IE+
Sbjct: 1  MSDMQDRVRLDKWLWAARFYKTRGLAQDAIEAGHVSLNGERAK-PSRLVKAGDRIEL 56


>gi|89891131|ref|ZP_01202639.1| 30S ribosomal protein S4 [Flavobacteria bacterium BBFL7]
 gi|89516775|gb|EAS19434.1| 30S ribosomal protein S4 [Flavobacteria bacterium BBFL7]
          Length = 201

 Score = 43.6 bits (101), Expect = 0.046,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA +RR   ++++ + + VNG L+   +  +   D + V
Sbjct: 94  RLDNVVYRMGIAKTRRGARQLVSHRHMTVNGELVNIPSYQLKPGDVVAV 142


>gi|269140530|ref|YP_003297231.1| putative Fe-S oxidoreductase [Edwardsiella tarda EIB202]
 gi|267986191|gb|ACY86020.1| putative Fe-S oxidoreductase [Edwardsiella tarda EIB202]
 gi|304560315|gb|ADM42979.1| Fe-S oxidoreductase [Edwardsiella tarda FL6-60]
          Length = 754

 Score = 43.6 bits (101), Expect = 0.047,   Method: Composition-based stats.
 Identities = 11/102 (10%), Positives = 21/102 (20%), Gaps = 2/102 (1%)

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           + +  Q       E  V               + N+   +        + + +       
Sbjct: 655 EEMGLQHLIGNRRECLVPAPTLEEQRAARRGYQRNMTPAMTKHTGAHPQGTGRPATRGAA 714

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
           K  A P  R     N            +    R     + P 
Sbjct: 715 KGAAQPAPRSGGKGNNGRP--ARPEGRNARPARPAGQAKKPR 754



 Score = 39.4 bits (90), Expect = 0.82,   Method: Composition-based stats.
 Identities = 15/123 (12%), Positives = 28/123 (22%), Gaps = 7/123 (5%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVR------DRPNIISEVPDDFTRMKK 287
           R + K +LR     +         +  +       R                  + R   
Sbjct: 632 RRLHKALLRYHDPANWPMIRAALEEMGLQHLIGNRRECLVPAPTLEEQRAARRGYQRNMT 691

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP-SKRS 346
            +  K+  +  +    P  R         A        +    R E     P+ P  +  
Sbjct: 692 PAMTKHTGAHPQGTGRPATRGAAKGAAQPAPRSGGKGNNGRPARPEGRNARPARPAGQAK 751

Query: 347 LRR 349
             R
Sbjct: 752 KPR 754


>gi|227541761|ref|ZP_03971810.1| 30S ribosomal protein S4 [Corynebacterium glucuronolyticum ATCC
           51866]
 gi|227182467|gb|EEI63439.1| 30S ribosomal protein S4 [Corynebacterium glucuronolyticum ATCC
           51866]
          Length = 178

 Score = 43.6 bits (101), Expect = 0.047,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI RAG+A +RR+  +++      VNG+     +  V   D I+V
Sbjct: 69  RLDNVIYRAGLARTRRQARQLVTHGHFLVNGVKTNIPSFQVSQYDIIDV 117


>gi|154505534|ref|ZP_02042272.1| hypothetical protein RUMGNA_03071 [Ruminococcus gnavus ATCC
          29149]
 gi|153794192|gb|EDN76612.1| hypothetical protein RUMGNA_03071 [Ruminococcus gnavus ATCC
          29149]
          Length = 79

 Score = 43.6 bits (101), Expect = 0.047,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR          RV VNG   + A+V V   D IE+
Sbjct: 1  MRLDKFLKVSRLIKRRTVANEACDAGRVLVNGKPAK-ASVKVKVGDVIEI 49


>gi|317182255|dbj|BAJ60039.1| hypothetical protein HPF57_0965 [Helicobacter pylori F57]
          Length = 242

 Score = 43.6 bits (101), Expect = 0.047,   Method: Composition-based stats.
 Identities = 29/211 (13%), Positives = 63/211 (29%), Gaps = 28/211 (13%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWL 77
           K+++     S ++ + +I    V V G               + V    L K  R  +  
Sbjct: 6   KILSVQENISHKKAKALIDLGLVSVGGK-------------KLMVARKELPKNTRFSVQK 52

Query: 78  YHKPIGLVTTHSDPDGRSTVF---DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             KP  +    +        F    +L S F   + + RLD  T G++LL  +     + 
Sbjct: 53  VEKPSVIFEDENILALFKPPFIESYDLVSFFKGWVLLHRLDKETSGVILLVKENSEFHLK 112

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--------- 185
              + +   V +          +        ++               + +         
Sbjct: 113 AKKAFKDRAVKKEYLALTQGIIEEEQEINAPILTIKTTKAFSKISKKGQEAVTIITPLKI 172

Query: 186 ---NAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 + VG++ G+  +I+   +  N  + 
Sbjct: 173 INKKTLLKVGIKTGRTHQIRVHLKHINHPII 203


>gi|300779797|ref|ZP_07089653.1| 30S ribosomal protein S4 [Corynebacterium genitalium ATCC 33030]
 gi|300533907|gb|EFK54966.1| 30S ribosomal protein S4 [Corynebacterium genitalium ATCC 33030]
          Length = 201

 Score = 43.6 bits (101), Expect = 0.047,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR+  ++++     VNG+     +  V   D I+V
Sbjct: 92  RLDNVVYRAGLARTRRQARQLVSHGHFTVNGVKTNVPSYQVTQYDIIDV 140


>gi|226313743|ref|YP_002773637.1| 30S ribosomal protein S4 [Brevibacillus brevis NBRC 100599]
 gi|254764572|sp|C0ZHK9|RS4_BREBN RecName: Full=30S ribosomal protein S4
 gi|226096691|dbj|BAH45133.1| 30S ribosomal protein S4 [Brevibacillus brevis NBRC 100599]
          Length = 199

 Score = 43.6 bits (101), Expect = 0.047,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G A +R    +++      VNG  +   +  V   D I +
Sbjct: 92  RLDNLVYRMGFAPTRPAARQLVNHGHFLVNGKKVNIPSYRVQPGDVISI 140


>gi|293339917|ref|XP_001056343.2| PREDICTED: serine/arginine repetitive matrix 2 [Rattus norvegicus]
          Length = 2535

 Score = 43.6 bits (101), Expect = 0.048,   Method: Composition-based stats.
 Identities = 16/102 (15%), Positives = 29/102 (28%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P      +++      +       R    S  P       ++ + K G S+ +      H
Sbjct: 442 PAPGSRREISSSPTSKNRSHGRAKRDKSHSHTPSHRAGRSRSPATKRGRSRSRTPTKRGH 501

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
            R+ +     ++       S S QR    R        RS  
Sbjct: 502 SRSRSPQWRRSRSAQRWGKSRSPQRRGRSRSPQRPGWSRSRN 543



 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 14/110 (12%), Positives = 32/110 (29%), Gaps = 2/110 (1%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                  +      P  +  +      +  S+        +  S       +  +  +P 
Sbjct: 426 KLSRHASSSPESLKPTPAPGSRREISSSPTSKNRSHGRAKRDKSHSHTPSHRAGRSRSPA 485

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRR--SPSFPSKRSLRRTSAK 353
            +R  + +    K  HS   S   +R  + +R      P +R   R+  +
Sbjct: 486 TKRGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGKSRSPQRRGRSRSPQR 535



 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 14/125 (11%), Positives = 27/125 (21%), Gaps = 17/125 (13%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P        +       S +    +          + R +         S Q++  +   
Sbjct: 474 PSHRAGRSRSPATKRGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGKSRSPQRRGRSRSP 533

Query: 307 RRNLASNVW-----------------MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           +R   S                                         RS +   +RS  R
Sbjct: 534 QRPGWSRSRNTQRRGRSRSARRGRSHSRSPATRGRSRSRTPARRGRSRSRTPARRRSRSR 593

Query: 350 TSAKK 354
           T A++
Sbjct: 594 TPARR 598



 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 14/98 (14%), Positives = 31/98 (31%), Gaps = 2/98 (2%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
             A  +      + R    S     ++R +    +    S ++  +          +   
Sbjct: 513 RSAQRWGKSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRSHSRSPATRGRSRSR 572

Query: 317 AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                    S +  R  +  R+P+   +RS  RT A++
Sbjct: 573 TPARRGRSRSRTPARRRSRSRTPAR--RRSRSRTPARR 608


>gi|139389644|ref|YP_001123201.1| ribosomal protein S4 [Arabis hirsuta]
 gi|139390154|ref|YP_001123727.1| ribosomal protein S4 [Lobularia maritima]
 gi|152060545|sp|A4QK20|RR4_ARAHI RecName: Full=30S ribosomal protein S4, chloroplastic
 gi|152060554|sp|A4QLJ6|RR4_LOBMA RecName: Full=30S ribosomal protein S4, chloroplastic
 gi|134286399|dbj|BAF50025.1| ribosomal protein S4 [Arabis hirsuta]
 gi|134286931|dbj|BAF50551.1| ribosomal protein S4 [Lobularia maritima]
          Length = 201

 Score = 43.6 bits (101), Expect = 0.048,   Method: Composition-based stats.
 Identities = 10/53 (18%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
            R+  ++ R G+A +  +  +++    + VNG +++  +      D I V   
Sbjct: 89  MRLDNILFRLGMALTIPQARQLVNHGHILVNGRIVDIPSYRCKPRDIITVKDE 141


>gi|126341726|ref|XP_001380909.1| PREDICTED: similar to eukaryotic translation initiation factor 4
           gamma, 1, [Monodelphis domestica]
          Length = 1945

 Score = 43.6 bits (101), Expect = 0.048,   Method: Composition-based stats.
 Identities = 16/112 (14%), Positives = 29/112 (25%), Gaps = 7/112 (6%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P           +P   S  +           P+  +   K  S        ++ ++PV 
Sbjct: 627 PERPSSPSAKPGSPERPSSPVKGPSSPAKPGSPERPSSPVKGPSSPAKPGSPERPSSPV- 685

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRR-----SPSFPSKRSLRRTSAK 353
            +  +S          S  +  G  E          SP+ P       +  K
Sbjct: 686 -KGPSSPAKPGSPERPSSPAKPGSPERPSSPVKCPSSPAKPGSPERPSSPVK 736



 Score = 43.2 bits (100), Expect = 0.058,   Method: Composition-based stats.
 Identities = 17/108 (15%), Positives = 31/108 (28%), Gaps = 4/108 (3%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G      + V   +      +  R         P+  +   K  S        ++ ++PV
Sbjct: 776 GSPERPSSPVKCPSSPAKPGSPERPSSPAKPGSPERPSSPVKCPSSPAKPGSPERPSSPV 835

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             +  +S          S  +  G  E     SP+ P       + AK
Sbjct: 836 --KGPSSPAKPGSPERPSSPAKPGSPERPS--SPAKPGSPERPSSPAK 879



 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 14/109 (12%), Positives = 26/109 (23%), Gaps = 7/109 (6%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P           +P           P      P      ++ SS        ++ ++PV 
Sbjct: 538 PERPSSHAKCPSSPAKPGSPERPSSPAKGPSSPAKPGSPERPSSPPAKPGSPERPSSPVK 597

Query: 307 RRNLASNVWMA-----KGIHSSFLSDSGQ--REENHRRSPSFPSKRSLR 348
             +  +               S  +  G   R  +    P  P + S  
Sbjct: 598 GPSSPAKPGSPERPSSPAKLPSSPAKPGSPERPSSPSAKPGSPERPSSP 646



 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 16/113 (14%), Positives = 30/113 (26%), Gaps = 7/113 (6%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G      + V   +      +  R         P+  +   K  S        ++ ++PV
Sbjct: 676 GSPERPSSPVKGPSSPAKPGSPERPSSPAKPGSPERPSSPVKCPSSPAKPGSPERPSSPV 735

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRR-----SPSFPSKRSLRRTSAK 353
             +  +S          S  +  G  E          SP+ P       +  K
Sbjct: 736 --KGPSSPAKPGSPERPSSPAKPGSPERPSSPVKCPSSPAKPGSPERPSSPVK 786



 Score = 40.5 bits (93), Expect = 0.34,   Method: Composition-based stats.
 Identities = 14/105 (13%), Positives = 28/105 (26%), Gaps = 2/105 (1%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                   + + P   ++    +RP+   + P    +        + +      A P   
Sbjct: 788 PSSPAKPGSPERPSSPAKPGSPERPSSPVKCPSSPAKPGSPERPSSPVKGPSSPAKPGSP 847

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
              +S          S  +  G  E     SP+ P       + A
Sbjct: 848 ERPSSPAKPGSPERPSSPAKPGSPERPS--SPAKPGSPERPSSPA 890



 Score = 39.8 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 16/113 (14%), Positives = 30/113 (26%), Gaps = 7/113 (6%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G      + V   +      +  R         P+  +   K  S        ++ ++PV
Sbjct: 726 GSPERPSSPVKGPSSPAKPGSPERPSSPAKPGSPERPSSPVKCPSSPAKPGSPERPSSPV 785

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRR-----SPSFPSKRSLRRTSAK 353
             +  +S          S  +  G  E          SP+ P       +  K
Sbjct: 786 --KCPSSPAKPGSPERPSSPAKPGSPERPSSPVKCPSSPAKPGSPERPSSPVK 836



 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 15/97 (15%), Positives = 27/97 (27%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           +++              R   +     P   +   K    +   S  K  ++P    +  
Sbjct: 499 QSRAETTPTPGQQCRPPRPDNSNTPGSPVCPSSPAKPGIPERPSSHAKCPSSPAKPGSPE 558

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                AKG  S     S +R  +    P  P + S  
Sbjct: 559 RPSSPAKGPSSPAKPGSPERPSSPPAKPGSPERPSSP 595



 Score = 37.5 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 12/96 (12%), Positives = 22/96 (22%), Gaps = 3/96 (3%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL---A 302
           G      +     +P   S  +           P+  +   K  S        ++    A
Sbjct: 795 GSPERPSSPAKPGSPERPSSPVKCPSSPAKPGSPERPSSPVKGPSSPAKPGSPERPSSPA 854

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS 338
            P      +S          S  +  G  E     +
Sbjct: 855 KPGSPERPSSPAKPGSPERPSSPAKPGSPERPSSPA 890


>gi|262400804|gb|ACY66293.1| ribosomal protein S4 [Brassica napus]
          Length = 201

 Score = 43.6 bits (101), Expect = 0.048,   Method: Composition-based stats.
 Identities = 10/53 (18%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
            R+  ++ R G+A +  +  +++    + VNG +++  +      D I V   
Sbjct: 89  MRLDNILFRLGMALTIPQARQLVNHGHILVNGRIVDIPSYRCKPRDIITVKDE 141


>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 = 43.6 bits (101), Expect = 0.048,   Method: Composition-based stats.
 Identities = 21/215 (9%), Positives = 57/215 (26%), Gaps = 33/215 (15%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--------------LRKAERTR 74
           R + + +   RV VN   + +    +   D IE+                  +   +   
Sbjct: 31  RFIRKAVRDGRVFVNKEKVIK-KHKLSQDDLIEIYMQEDEHQNIEPEDMNIEIVYEDNDI 89

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------------------ISVGRLDI 116
           + +  +P  +V         +     L                         I + +   
Sbjct: 90  IVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKNQF 149

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +   L    +     ++        ++    R +  + +++ +   K IV +        
Sbjct: 150 SHMRLASDMSKDSFRKIYIAVVHGSMKEKEKRINLPIYKEEESESIKRIVDERGQESITT 209

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +  +    + V + L  G+  +I+         
Sbjct: 210 YKVLEELSKGSVVRLELETGRTHQIRVHMSHLGHP 244


>gi|308461244|ref|XP_003092916.1| hypothetical protein CRE_16373 [Caenorhabditis remanei]
 gi|308252043|gb|EFO95995.1| hypothetical protein CRE_16373 [Caenorhabditis remanei]
          Length = 660

 Score = 43.6 bits (101), Expect = 0.049,   Method: Composition-based stats.
 Identities = 12/115 (10%), Positives = 23/115 (20%), Gaps = 3/115 (2%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG---LSKQ 298
           R+   P                S   +  R    S  P    R     S+        + 
Sbjct: 519 RQNPAPSRSPPPLNRRRPATSRSPPPLNRRRPATSRSPQPQDRQNPAPSRSPPPLNRRRP 578

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               +P            +            +      R  + PS+    +   +
Sbjct: 579 ATSRSPPPLNRRRPATSRSPQPQDRQNPAPSRSPPPLNRRRAAPSRSPSPQHLRR 633



 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 22/119 (18%), Positives = 31/119 (26%), Gaps = 6/119 (5%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R        +       AP  S   L R RP      P    R    S       +Q   
Sbjct: 506 RRPATSRSPQPQDRQNPAPSRSPPPLNRRRPATSRSPPPLNRRRPATSRSPQPQDRQNPA 565

Query: 302 ATPV-----HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR-SLRRTSAKK 354
            +        RR   S             S S Q ++    +PS      + RR +  +
Sbjct: 566 PSRSPPPLNRRRPATSRSPPPLNRRRPATSRSPQPQDRQNPAPSRSPPPLNRRRAAPSR 624



 Score = 40.5 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 7/106 (6%), Positives = 20/106 (18%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              ++ Q  + +   +     R   +   +  D        S       +     +P   
Sbjct: 486 PQPQDRQNPVPSHSPTPLNRRRPATSRSPQPQDRQNPAPSRSPPPLNRRRPATSRSPPPL 545

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                    +            +      R     S+        +
Sbjct: 546 NRRRPATSRSPQPQDRQNPAPSRSPPPLNRRRPATSRSPPPLNRRR 591



 Score = 40.2 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 17/116 (14%), Positives = 28/116 (24%), Gaps = 4/116 (3%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            +  +  +  H          A   S +   R  P      P    R    S     L++
Sbjct: 488 PQDRQNPVPSHSPTPLNRRRPATSRSPQPQDRQNPAPSRSPPPLNRRRPATSRSPPPLNR 547

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                 P   R+             S    + +R    R  P    +R     S +
Sbjct: 548 ----RRPATSRSPQPQDRQNPAPSRSPPPLNRRRPATSRSPPPLNRRRPATSRSPQ 599



 Score = 38.2 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 18/118 (15%), Positives = 25/118 (21%), Gaps = 10/118 (8%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK----- 300
                +        P  S   L R RP      P    R    S       +Q       
Sbjct: 440 RQRSPQPQNRQNPVPSRSPTPLNRRRPATSRSPPPLNRRRPATSRSPQPQDRQNPVPSHS 499

Query: 301 -----LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                   P   R+             S    + +R    R  P    +R     S +
Sbjct: 500 PTPLNRRRPATSRSPQPQDRQNPAPSRSPPPLNRRRPATSRSPPPLNRRRPATSRSPQ 557



 Score = 37.9 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 18/119 (15%), Positives = 27/119 (22%), Gaps = 6/119 (5%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R                A   S +   R  P           R    S       +Q   
Sbjct: 464 RRPATSRSPPPLNRRRPATSRSPQPQDRQNPVPSHSPTPLNRRRPATSRSPQPQDRQNPA 523

Query: 302 ATPV-----HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR-SLRRTSAKK 354
            +        RR   S             S S Q ++    +PS      + RR +  +
Sbjct: 524 PSRSPPPLNRRRPATSRSPPPLNRRRPATSRSPQPQDRQNPAPSRSPPPLNRRRPATSR 582


>gi|302533023|ref|ZP_07285365.1| carbamoyltransferase [Streptomyces sp. C]
 gi|302441918|gb|EFL13734.1| carbamoyltransferase [Streptomyces sp. C]
          Length = 338

 Score = 43.6 bits (101), Expect = 0.049,   Method: Composition-based stats.
 Identities = 6/86 (6%), Positives = 17/86 (19%)

Query: 268 VRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSD 327
            + R              +    +        + A     ++  +      G        
Sbjct: 226 RQHRRGDGHHPVLAGAPGEDPPGRPQPHRAPLRPARRPVHQDHRTGPVRVPGPRRHRAGR 285

Query: 328 SGQREENHRRSPSFPSKRSLRRTSAK 353
            G   +     P+   +R       +
Sbjct: 286 PGAGRDGPGARPAAGDRRDHADDRGR 311


>gi|296191294|ref|XP_002806589.1| PREDICTED: LOW QUALITY PROTEIN: voltage-dependent N-type calcium
           channel subunit alpha-1B-like [Callithrix jacchus]
          Length = 2338

 Score = 43.6 bits (101), Expect = 0.049,   Method: Composition-based stats.
 Identities = 16/123 (13%), Positives = 27/123 (21%), Gaps = 11/123 (8%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R        + A    D     +       P    E P       K ++       ++  
Sbjct: 849 RRHHRHRDKDRAPAAGDQDRAEAPKAESGEPGAREERPRPHRSHSKEAAGPPEARSERGR 908

Query: 302 ATPV------HRRNLASNVWMAKGIHSSFLS-----DSGQREENHRRSPSFPSKRSLRRT 350
                     HRR     V   +               G   +  RR+      R+  R 
Sbjct: 909 GPGPEGGRRHHRRGSPEEVAEREPRRHRTHRHQDPGKEGAGAKGERRARHRGGPRTGPRE 968

Query: 351 SAK 353
           +  
Sbjct: 969 AES 971



 Score = 41.3 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 9/136 (6%), Positives = 26/136 (19%), Gaps = 28/136 (20%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G    +  Q   + P  +       R       P    + +  + +        +   P 
Sbjct: 828 GTVGGKARQEAAEVPEGADPPRRHHRHRDKDRAPAAGDQDRAEAPKAESGEPGAREERPR 887

Query: 306 HRRNLASNVWMAKGIH----------------------------SSFLSDSGQREENHRR 337
             R+ +                                               ++     
Sbjct: 888 PHRSHSKEAAGPPEARSERGRGPGPEGGRRHHRRGSPEEVAEREPRRHRTHRHQDPGKEG 947

Query: 338 SPSFPSKRSLRRTSAK 353
           + +   +R+  R   +
Sbjct: 948 AGAKGERRARHRGGPR 963



 Score = 38.2 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 21/152 (13%), Positives = 43/152 (28%), Gaps = 20/152 (13%)

Query: 223 FQLGTL---LAGSTREVSKKI-LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEV 278
            +L  L         E+  +  LR     HL  + + +LD P+         R  +  + 
Sbjct: 775 LRLQNLRASCEALYSEMDPEERLRFATTRHLRPDMKTHLDRPLVVELGRDGARGTVGGKA 834

Query: 279 PDDFTR-MKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
             +     +     +     + K   P       +    A+        +  +   +H +
Sbjct: 835 RQEAAEVPEGADPPRRHHRHRDKDRAPAAGDQDRAEAPKAESGEPGAREERPRPHRSHSK 894

Query: 338 -SPSFPSKRSL--------------RRTSAKK 354
            +   P  RS               RR S ++
Sbjct: 895 EAAGPPEARSERGRGPGPEGGRRHHRRGSPEE 926


>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 = 43.6 bits (101), Expect = 0.049,   Method: Composition-based stats.
 Identities = 21/215 (9%), Positives = 57/215 (26%), Gaps = 33/215 (15%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--------------LRKAERTR 74
           R + + +   RV VN   + +    +   D IE+                  +   +   
Sbjct: 31  RFIRKAVRDGRVFVNKEKVIK-KHKLSQDDLIEIYMQEDEHQNIEPEDMNIEIVYEDNDI 89

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------------------ISVGRLDI 116
           + +  +P  +V         +     L                         I + +   
Sbjct: 90  IVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKNQF 149

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +   L    +     ++        ++    R +  + +++ +   K IV +        
Sbjct: 150 SHMRLASDMSKDSFRKIYIAVVHGSMKEKEKRINLPIYKEEESESIKRIVDERGQESITT 209

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +  +    + V + L  G+  +I+         
Sbjct: 210 YKVLEELSKGSVVRLELETGRTHQIRVHMSHLGHP 244


>gi|89257421|gb|ABD64913.1| Chloroplast 30S ribosomal protein S4 [Brassica oleracea]
          Length = 201

 Score = 43.6 bits (101), Expect = 0.049,   Method: Composition-based stats.
 Identities = 10/53 (18%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
            R+  ++ R G+A +  +  +++    + VNG +++  +      D I V   
Sbjct: 89  MRLDNILFRLGMALTIPQARQLVNHGHILVNGRIVDIPSYRCKPRDIITVKDE 141


>gi|289705623|ref|ZP_06502012.1| conserved hypothetical protein [Micrococcus luteus SK58]
 gi|289557647|gb|EFD50949.1| conserved hypothetical protein [Micrococcus luteus SK58]
          Length = 447

 Score = 43.6 bits (101), Expect = 0.049,   Method: Composition-based stats.
 Identities = 15/120 (12%), Positives = 26/120 (21%), Gaps = 5/120 (4%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           E + +  RE  G                             S   D       +  ++ G
Sbjct: 3   EDTPRERREDRG-----SEGRGPRGGNDGRRRGADRDGRPRSGAGDRRRSGGPHEDRRRG 57

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +   +       R          G    F   S  R    R+    P +R       ++
Sbjct: 58  SADGPRRQDGAADRGPRREESGRDGARRRFRPTSEDRRRGPRQDGGRPERRGAPTGPRRE 117



 Score = 39.8 bits (91), Expect = 0.62,   Method: Composition-based stats.
 Identities = 12/123 (9%), Positives = 27/123 (21%), Gaps = 2/123 (1%)

Query: 230 AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNII--SEVPDDFTRMKK 287
               RE      R   G +       + D    S     R                  ++
Sbjct: 6   PRERREDRGSEGRGPRGGNDGRRRGADRDGRPRSGAGDRRRSGGPHEDRRRGSADGPRRQ 65

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
           + +   G  +++       RR   ++    +G          +      R      + + 
Sbjct: 66  DGAADRGPRREESGRDGARRRFRPTSEDRRRGPRQDGGRPERRGAPTGPRREDRAERPAH 125

Query: 348 RRT 350
              
Sbjct: 126 NPG 128


>gi|111023124|ref|YP_706096.1| 30S ribosomal protein S4 [Rhodococcus jostii RHA1]
 gi|226365623|ref|YP_002783406.1| 30S ribosomal protein S4 [Rhodococcus opacus B4]
 gi|122955187|sp|Q0S3E8|RS4_RHOSR RecName: Full=30S ribosomal protein S4
 gi|254764607|sp|C1B040|RS4_RHOOB RecName: Full=30S ribosomal protein S4
 gi|110822654|gb|ABG97938.1| 30S ribosomal protein S4 [Rhodococcus jostii RHA1]
 gi|226244113|dbj|BAH54461.1| 30S ribosomal protein S4 [Rhodococcus opacus B4]
          Length = 201

 Score = 43.6 bits (101), Expect = 0.049,   Method: Composition-based stats.
 Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ RAG+A +RR+  +++    + VN   ++  +  V   D I+V    L      
Sbjct: 92  RLDNVVYRAGLARTRRQARQLVTHGHLLVNNKKVDIPSYRVSQYDIIDVKEKSLSTLPFQ 151

Query: 74  R 74
            
Sbjct: 152 V 152


>gi|15612636|ref|NP_240939.1| hypothetical protein BH0073 [Bacillus halodurans C-125]
 gi|17433248|sp|Q9KGI8|Y073_BACHD RecName: Full=Uncharacterized protein BH0073
 gi|10172685|dbj|BAB03792.1| BH0073 [Bacillus halodurans C-125]
          Length = 88

 Score = 43.6 bits (101), Expect = 0.049,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR   + +  Q R+ VNG + + A   V   D + +
Sbjct: 1  MRLDKFLKVSRLIKRRTLAKEVCEQGRITVNGNVAK-AGTVVKEGDELVI 49


>gi|294632692|ref|ZP_06711251.1| secreted protein [Streptomyces sp. e14]
 gi|292830473|gb|EFF88823.1| secreted protein [Streptomyces sp. e14]
          Length = 755

 Score = 43.6 bits (101), Expect = 0.049,   Method: Composition-based stats.
 Identities = 8/106 (7%), Positives = 23/106 (21%), Gaps = 1/106 (0%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                  +  D     +        +   + P          S      + +        
Sbjct: 596 RRPMTRVLRGDRAPEDAGPADEAVRSGPGDTPAGTREHGAGESGPGSRGEDRDAEGTGAG 655

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               + V   +    +  +  G+R      + + P+     R   +
Sbjct: 656 PPGTTRVRTGRARRPARTNRRGRRPPPGS-ARTTPTPTDRARQPTR 700


>gi|6942292|gb|AAF32394.1|AF224466_1 putative pseudouridylate synthase [Haemophilus ducreyi]
          Length = 250

 Score = 43.6 bits (101), Expect = 0.049,   Method: Composition-based stats.
 Identities = 25/230 (10%), Positives = 55/230 (23%), Gaps = 31/230 (13%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVM------------------ 55
           R+ + +A+     SR  ++  I    VKVNGI++ RA   V                   
Sbjct: 19  RLDQALAQLFPDYSRSRIKVWIENDLVKVNGIIVNRARGKVFGGEQIEIQAEIEEEIRFE 78

Query: 56  ----STDHIEVDGVPLRKAERTRLWLYHKPIG---LVTTHSDPDGRSTVFDNLPSIFSRV 108
                 + +  D   +   +   L ++         V                  I  R+
Sbjct: 79  PQNIPLNIVHEDDDIIIINKPKNLVVHPGAGNPDGTVLNALLYYYPPIAEVPRAGIIHRL 138

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-----KLNLLKK 163
                  +     +        A      + ++  +           D            
Sbjct: 139 DKDTTGLMVVAKNIPAQTHLVTALQKRRITREYEAIASGIMTQGGKVDEPMARHPTKRTA 198

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             V            +  +  +   + + L  G+  +I+         + 
Sbjct: 199 MAVHPMGKPAITHYRIMERFRNYTRLRLRLETGRTHQIRVHMAHIAHPLL 248


>gi|85057521|ref|YP_456437.1| 30S ribosomal protein S4 [Aster yellows witches'-broom phytoplasma
           AYWB]
 gi|123518331|sp|Q2NJN5|RS4_AYWBP RecName: Full=30S ribosomal protein S4
 gi|84789626|gb|ABC65358.1| SSU ribosomal protein S4P [Aster yellows witches'-broom phytoplasma
           AYWB]
          Length = 198

 Score = 43.6 bits (101), Expect = 0.049,   Method: Composition-based stats.
 Identities = 9/49 (18%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R +  +++    + V+G  ++ A+  +     + +
Sbjct: 92  RLDNVVYRLGFAKTRAQARQLVNHGHILVDGKKVDIASYRLKPGQTVTL 140


>gi|242620095|ref|YP_003002099.1| 30S ribosomal protein S4 [Aureococcus anophagefferens]
 gi|239997340|gb|ACS36863.1| 30S ribosomal protein S4 [Aureococcus anophagefferens]
          Length = 204

 Score = 43.6 bits (101), Expect = 0.050,   Method: Composition-based stats.
 Identities = 14/79 (17%), Positives = 25/79 (31%), Gaps = 9/79 (11%)

Query: 14  QRVSKVIARAGIA-----SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
            R+  ++ R GI      SR    +++    + VNG  +   +      D IEV      
Sbjct: 93  MRLDNIVYRLGIGNTIPASR----QIVNHGHIYVNGKKVTIPSFQCSPNDVIEVRNRVTS 148

Query: 69  KAERTRLWLYHKPIGLVTT 87
           K    +         +   
Sbjct: 149 KELAKQYLEKPSYNTVPQY 167


>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 = 43.6 bits (101), Expect = 0.050,   Method: Composition-based stats.
 Identities = 27/211 (12%), Positives = 62/211 (29%), Gaps = 28/211 (13%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWL 77
           K+++     S ++ + +I    V + G               + V    L +  R  +  
Sbjct: 6   KLLSVQENISHKKAKALIDSGLVSIGGQ-------------KLMVARKELPQNTRFSVQK 52

Query: 78  YHKPIGLVTTHSDPDGRSTVF---DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             KP  +    +        F    +L S F     + RLD  T G++LL  +     + 
Sbjct: 53  VEKPSVIFEDENILALFKPPFIESYDLVSFFKGWALLHRLDKETSGVILLVKENSEFHLK 112

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--------- 185
              + +   V +          +        ++               + +         
Sbjct: 113 AKKAFKDRAVKKEYLAIVQGIIEEEREINAPILTIKTTKAFSKISKKGQEAVTIITPLKI 172

Query: 186 ---NAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 + VG++ G+  +I+   +  N  + 
Sbjct: 173 INKKTLLKVGIKTGRTHQIRVHLKHINHPII 203


>gi|74273103|gb|ABA01251.1| ribosomal protein S4 [Passiflora ceratocarpa]
          Length = 183

 Score = 43.6 bits (101), Expect = 0.050,   Method: Composition-based stats.
 Identities = 11/53 (20%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
            R+  ++ R G+AS   +  +++  + + VNG +++  +      D I V   
Sbjct: 71  MRLDNILFRLGMASTIPQARQLVNHRHILVNGRIVDIPSYRCKPGDLITVKDE 123


>gi|255690029|ref|ZP_05413704.1| ribosomal protein S4 [Bacteroides finegoldii DSM 17565]
 gi|260624636|gb|EEX47507.1| ribosomal protein S4 [Bacteroides finegoldii DSM 17565]
          Length = 201

 Score = 43.6 bits (101), Expect = 0.050,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA +R    ++++ + + V+G ++   +  V     I V
Sbjct: 93  RLDNVVFRLGIAPTRAAARQLVSHKHITVDGEVVNIPSYAVKPGQLIGV 141


>gi|328720911|ref|XP_001948965.2| PREDICTED: hypothetical protein LOC100167279 [Acyrthosiphon pisum]
          Length = 685

 Score = 43.6 bits (101), Expect = 0.051,   Method: Composition-based stats.
 Identities = 20/126 (15%), Positives = 33/126 (26%), Gaps = 5/126 (3%)

Query: 231 GSTR----EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
           G  R     V   + R+       +            S+     R        DD    +
Sbjct: 213 GPWRSARCNVDDDVARKPFSGRFDDSESGRRPFSDRRSDDSEGGRRPFGDRRGDDSEGGR 272

Query: 287 KNSSQKNGLSKQKKLATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKR 345
           +    + G   +        RR   S+      G      SDSG+R    RR      ++
Sbjct: 273 RPFGDRRGDDSESGRRPFGDRRGDDSDSGRRPFGDRRYDDSDSGRRPFGERRDDVEGGRK 332

Query: 346 SLRRTS 351
               + 
Sbjct: 333 PFGESR 338



 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 18/103 (17%), Positives = 26/103 (25%), Gaps = 2/103 (1%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           +  V         +     R        DD    ++    + G   +        RR   
Sbjct: 223 DDDVARKPFSGRFDDSESGRRPFSDRRSDDSEGGRRPFGDRRGDDSEGGRRPFGDRRGDD 282

Query: 312 SNVWMAK-GIHSSFLSDSGQREENHRR-SPSFPSKRSLRRTSA 352
           S       G      SDSG+R    RR   S   +R       
Sbjct: 283 SESGRRPFGDRRGDDSDSGRRPFGDRRYDDSDSGRRPFGERRD 325


>gi|197122723|ref|YP_002134674.1| hypothetical protein AnaeK_2318 [Anaeromyxobacter sp. K]
 gi|196172572|gb|ACG73545.1| conserved hypothetical protein [Anaeromyxobacter sp. K]
          Length = 473

 Score = 43.6 bits (101), Expect = 0.051,   Method: Composition-based stats.
 Identities = 12/113 (10%), Positives = 24/113 (21%), Gaps = 6/113 (5%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P     +     AP  +            +      TR    S+  +G + +       
Sbjct: 278 RPAPGARSDGGRVAPGSAPSRGDGRGAPGYAPPSPGETRGAPGSAPPSGGATRGAPGYAP 337

Query: 306 HRRN------LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            R          +               S        R+P    +  + R + 
Sbjct: 338 PRGGETRGTPGYAPRGGGPSAAPPARGPSAAPPARGGRAPDAGPRGEVPRAAP 390



 Score = 39.0 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 11/96 (11%), Positives = 21/96 (21%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P                +           +  P      +   +   G   +   A P 
Sbjct: 332 APGYAPPRGGETRGTPGYAPRGGGPSAAPPARGPSAAPPARGGRAPDAGPRGEVPRAAPG 391

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF 341
           + R        A G          +     RR+P++
Sbjct: 392 YARQDRGGDAGAYGGSYGSYGAPARAAPPVRRAPAY 427



 Score = 36.7 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 6/104 (5%), Positives = 19/104 (18%), Gaps = 2/104 (1%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
             ++ +       +     +        P      +           + +       R  
Sbjct: 295 APSRGDGRGAPGYAPPSPGETRGAPGSAPPSGGATRGAPGYAPPRGGETRGTPGYAPRGG 354

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSP--SFPSKRSLRRTSA 352
             +        S+     G R  +          +    R+   
Sbjct: 355 GPSAAPPARGPSAAPPARGGRAPDAGPRGEVPRAAPGYARQDRG 398


>gi|167752863|ref|ZP_02424990.1| hypothetical protein ALIPUT_01125 [Alistipes putredinis DSM
          17216]
 gi|167659932|gb|EDS04062.1| hypothetical protein ALIPUT_01125 [Alistipes putredinis DSM
          17216]
          Length = 132

 Score = 43.6 bits (101), Expect = 0.051,   Method: Composition-based stats.
 Identities = 15/85 (17%), Positives = 27/85 (31%), Gaps = 2/85 (2%)

Query: 12 TPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             R+ K + A     +R +    I Q RV VN    +  +  V   D I V  +P+   
Sbjct: 2  EAIRLDKYLWAVRIFKTRSDAAEAIRQNRVLVNDAYAK-PSREVRIGDRIAVKRMPVTYL 60

Query: 71 ERTRLWLYHKPIGLVTTHSDPDGRS 95
               ++  +           +   
Sbjct: 61 FEVVGYVSSRQPAKNVPDYCRNITP 85


>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 = 43.6 bits (101), Expect = 0.051,   Method: Composition-based stats.
 Identities = 25/235 (10%), Positives = 67/235 (28%), Gaps = 36/235 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------D---GVPLRKAERTR 74
           SR  V+ ++ + +V V+  +  +    +     + +         D   G+ +   +   
Sbjct: 38  SRNSVKSILTRGQVSVDDHIETKHNFMLNKGSTVRILKNKAAIQQDVFVGMSIMYEDDDI 97

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-----ISVGRLDINTEGLLLLTNDGG 129
           + +  +   L          + +   +  +  +        V RLD +T G+++   +  
Sbjct: 98  IVIEKESGLLSIATEKERKHTALHQLMHYVKQQHPANRVYVVHRLDKDTSGVMMFAKNER 157

Query: 130 LARVLELP-------------STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           + R L+                   +   +      + +     +    V         +
Sbjct: 158 VKRKLQNNWKDIVKERTYVALVEGQVAKEKGYIVSWLKESATRKMYSSRVKNDGQRAATR 217

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS------YGPFQL 225
             +       + + + L  G+  +I+   E     V    R         G   L
Sbjct: 218 YRVLQTNNRYSLLELQLETGRKNQIRVHMEELGHPVVGDKRYGSKGRSVIGRLGL 272


>gi|148690326|gb|EDL22273.1| serine/arginine repetitive matrix 2 [Mus musculus]
          Length = 2532

 Score = 43.6 bits (101), Expect = 0.051,   Method: Composition-based stats.
 Identities = 16/102 (15%), Positives = 29/102 (28%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P      +++      +       R    S  P       ++ + K G S+ +      H
Sbjct: 342 PAPGSRREISSSPTSKNRSHGRAKRDKSHSHTPSHRAGRSRSPATKRGRSRSRTPTKRGH 401

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
            R+ +     ++       S S QR    R        RS  
Sbjct: 402 SRSRSPQWRRSRSAQRWGKSRSPQRRGRSRSPQRPGWSRSRN 443



 Score = 41.7 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 14/113 (12%), Positives = 33/113 (29%), Gaps = 2/113 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +         +      P  +  +      +  S+        +  S       +  +  
Sbjct: 323 QPTKVSRHASSSPESLKPTPAPGSRREISSSPTSKNRSHGRAKRDKSHSHTPSHRAGRSR 382

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR--SPSFPSKRSLRRTSAK 353
           +P  +R  + +    K  HS   S   +R  + +R      P +R   R+  +
Sbjct: 383 SPATKRGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGKSRSPQRRGRSRSPQR 435



 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 14/125 (11%), Positives = 27/125 (21%), Gaps = 17/125 (13%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P        +       S +    +          + R +         S Q++  +   
Sbjct: 374 PSHRAGRSRSPATKRGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGKSRSPQRRGRSRSP 433

Query: 307 RRNLASNVW-----------------MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           +R   S                                         RS +   +RS  R
Sbjct: 434 QRPGWSRSRNTQRRGRSRSARRGRSHSRSPATRGRSRSRTPARRGRSRSRTPARRRSRSR 493

Query: 350 TSAKK 354
           T A++
Sbjct: 494 TPARR 498



 Score = 41.3 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 14/98 (14%), Positives = 31/98 (31%), Gaps = 2/98 (2%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
             A  +      + R    S     ++R +    +    S ++  +          +   
Sbjct: 413 RSAQRWGKSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRSHSRSPATRGRSRSR 472

Query: 317 AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                    S +  R  +  R+P+   +RS  RT A++
Sbjct: 473 TPARRGRSRSRTPARRRSRSRTPAR--RRSRSRTPARR 508



 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 13/114 (11%), Positives = 31/114 (27%), Gaps = 3/114 (2%)

Query: 230 AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
            G +R  S +  R +      +           S +     R           +  +  S
Sbjct: 399 RGHSRSRSPQWRRSRSAQRWGKSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRS 458

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
             ++  ++ +  +    RR  +              S +  R  +  R+P+   
Sbjct: 459 HSRSPATRGRSRSRTPARRGRS---RSRTPARRRSRSRTPARRRSRSRTPARRG 509



 Score = 36.3 bits (82), Expect = 7.7,   Method: Composition-based stats.
 Identities = 14/81 (17%), Positives = 24/81 (29%)

Query: 274 IISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREE 333
             S  P   +R   +S +    +        +     + N    +       S +     
Sbjct: 319 PPSPQPTKVSRHASSSPESLKPTPAPGSRREISSSPTSKNRSHGRAKRDKSHSHTPSHRA 378

Query: 334 NHRRSPSFPSKRSLRRTSAKK 354
              RSP+    RS  RT  K+
Sbjct: 379 GRSRSPATKRGRSRSRTPTKR 399


>gi|145345025|ref|XP_001417024.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144577250|gb|ABO95317.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 123

 Score = 43.6 bits (101), Expect = 0.051,   Method: Composition-based stats.
 Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 3/66 (4%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K+     E+   +RV K++ + G A +R +V+ MI   RV V G  +ER    V+ +  +
Sbjct: 40  KENEATFESAKRKRVDKMLIKHGYAKTRSDVDDMIKDGRVCVGGAPVER-ESRVLLSA-L 97

Query: 61  EVDGVP 66
            VDG  
Sbjct: 98  TVDGKA 103


>gi|13473300|ref|NP_104867.1| MgpS, ATP-dependent helicase [Mesorhizobium loti MAFF303099]
 gi|14024048|dbj|BAB50653.1| ATP-dependent helicase; MgpS [Mesorhizobium loti MAFF303099]
          Length = 1092

 Score = 43.6 bits (101), Expect = 0.051,   Method: Composition-based stats.
 Identities = 13/107 (12%), Positives = 25/107 (23%), Gaps = 1/107 (0%)

Query: 248  HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               +  + +            R R N  +E     T         +   +      P   
Sbjct: 948  RFEQRPRHHEGRNNRQRNGQARGRGNAPAEAGTAQTTGAPGERPAHEGRRDG-AGKPRFD 1006

Query: 308  RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            R+        +G         G+R E     P +   R   +    +
Sbjct: 1007 RSKFKPKPQGEGEQRRDGRPQGERPERREGRPDWKGGRPEGKGGPDR 1053



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 10/121 (8%), Positives = 25/121 (20%), Gaps = 9/121 (7%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            +  L        Q        ++           +   +  T     +  +    + ++ 
Sbjct: 939  KPILLWRQGRFEQRPRHHEGRNNRQRNGQARGRGNAPAEAGTAQTTGAPGERPAHEGRRD 998

Query: 302  ATPVHRRNLASNVWMAKG-------IHSSFLS--DSGQREENHRRSPSFPSKRSLRRTSA 352
                 R + +      +G                    R +     P         + SA
Sbjct: 999  GAGKPRFDRSKFKPKPQGEGEQRRDGRPQGERPERREGRPDWKGGRPEGKGGPDRGKGSA 1058

Query: 353  K 353
            K
Sbjct: 1059 K 1059


>gi|258591342|emb|CBE67641.1| 30S ribosomal subunit protein S4 [NC10 bacterium 'Dutch sediment']
          Length = 192

 Score = 43.6 bits (101), Expect = 0.051,   Method: Composition-based stats.
 Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G A SR +   +I    + VNG   + A+  V   + IEV
Sbjct: 82  QRLDSVVHRLGFAASRAQARLLITHGHILVNGRKTDIASYRVRQGETIEV 131


>gi|282857447|ref|ZP_06266680.1| S4 RNA-binding domain protein [Pyramidobacter piscolens W5455]
 gi|282584732|gb|EFB90067.1| S4 RNA-binding domain protein [Pyramidobacter piscolens W5455]
          Length = 94

 Score = 43.6 bits (101), Expect = 0.051,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRREV-ERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR   + MI    V+VNG  ++  A +V + D IEV
Sbjct: 2  IRLDKFLKLSQLVKRRAAAQEMIEVGAVRVNGRKVK-PASDVKAGDLIEV 50


>gi|255721325|ref|XP_002545597.1| conserved hypothetical protein [Candida tropicalis MYA-3404]
 gi|240136086|gb|EER35639.1| conserved hypothetical protein [Candida tropicalis MYA-3404]
          Length = 461

 Score = 43.6 bits (101), Expect = 0.051,   Method: Composition-based stats.
 Identities = 17/95 (17%), Positives = 31/95 (32%), Gaps = 1/95 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+   + R+  AS  R+  + I    VKVNG++++  +  + S D   VD   +  A   
Sbjct: 105 RLEVALFRSMFASSLRQARQFILGGFVKVNGVVMKYPSFPLQSGDVFSVDPEKVLYALGK 164

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                 K + +                        
Sbjct: 165 DKPSLEKALSVDRKQIKSWNHYVYEAKKNPEKIWN 199


>gi|170744521|ref|YP_001773176.1| DEAD/DEAH box helicase domain-containing protein [Methylobacterium
           sp. 4-46]
 gi|168198795|gb|ACA20742.1| DEAD/DEAH box helicase domain protein [Methylobacterium sp. 4-46]
          Length = 499

 Score = 43.6 bits (101), Expect = 0.051,   Method: Composition-based stats.
 Identities = 11/113 (9%), Positives = 33/113 (29%), Gaps = 1/113 (0%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E+L    + E  +       S +           +      R ++    + G   Q +  
Sbjct: 363 ERLTRQKVPEMAIPEGFVPPSRQEAAVAEAEAERDRRQPGPRGQRPGRPQGGRPPQTQGG 422

Query: 303 TPVHRRNLASNVWM-AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            P   R   +      +   ++      ++ ++ R +       + R+   ++
Sbjct: 423 RPAEARPRPARQGQDGRQARTNQDGRPARQGQDARPAHHRAEGPNHRQGQPQR 475



 Score = 40.9 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 15/125 (12%), Positives = 27/125 (21%), Gaps = 6/125 (4%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
               ++++ + E   P        +      +     RDR                   Q
Sbjct: 361 DIERLTRQKVPEMAIP--EGFVPPSRQEAAVAEAEAERDRRQPGPRGQRPGRPQGGRPPQ 418

Query: 292 KNGLSKQKKLATPVH----RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
             G    +    P       R   +N              +  R E        P +R  
Sbjct: 419 TQGGRPAEARPRPARQGQDGRQARTNQDGRPARQGQDARPAHHRAEGPNHRQGQPQRRDH 478

Query: 348 RRTSA 352
            R + 
Sbjct: 479 ARPAQ 483


>gi|37912969|gb|AAR05301.1| ribosomal protein S4 [uncultured marine gamma proteobacterium
           EB000-45B06]
 gi|40063200|gb|AAR38037.1| ribosomal protein S4 [uncultured marine bacterium 562]
          Length = 207

 Score = 43.6 bits (101), Expect = 0.051,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  +M++ +  KVNG ++   +  + + D ++V
Sbjct: 98  RMDNVVYRMGFGSTRAEARQMVSHKAFKVNGEVVNIPSYQMKAGDEVQV 146


>gi|12045167|ref|NP_072978.1| 30S ribosomal protein S4 [Mycoplasma genitalium G37]
 gi|255660353|ref|ZP_05405762.1| 30S ribosomal protein S4 [Mycoplasma genitalium G37]
 gi|1350998|sp|P47553|RS4_MYCGE RecName: Full=30S ribosomal protein S4
 gi|1046011|gb|AAC71533.1| ribosomal protein S4 [Mycoplasma genitalium G37]
 gi|166078669|gb|ABY79287.1| ribosomal protein S4 [synthetic Mycoplasma genitalium JCVI-1.0]
          Length = 205

 Score = 43.6 bits (101), Expect = 0.051,   Method: Composition-based stats.
 Identities = 9/49 (18%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G A +R+   +M+    V +N   ++  ++ +   D + +
Sbjct: 96  RLDNIVYRMGFAPTRKSARQMVNHGHVILNDQTVDTPSIIINPGDKVRL 144


>gi|330815273|ref|YP_004358978.1| 30S ribosomal protein S4 [Burkholderia gladioli BSR3]
 gi|327367666|gb|AEA59022.1| 30S ribosomal protein S4 [Burkholderia gladioli BSR3]
          Length = 207

 Score = 43.2 bits (100), Expect = 0.052,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  +++  + + VNGI+    ++ V + D I +
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVGHKAITVNGIVSNIPSLQVKAGDIIAI 146


>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 = 43.2 bits (100), Expect = 0.052,   Method: Composition-based stats.
 Identities = 28/211 (13%), Positives = 62/211 (29%), Gaps = 28/211 (13%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWL 77
           K+++     S ++ + +I    V + G               + V    L K  R  +  
Sbjct: 6   KLLSVQENISHKKAKALIDSGLVSIGGQ-------------KLMVARKELPKNTRFSVQK 52

Query: 78  YHKPIGLVTTHSDPDGRSTVF---DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             KP  +    +        F    +L S F     + RLD  T G++LL  +     + 
Sbjct: 53  VEKPSVIFEDENILALFKPPFIESYDLVSFFKDWALLHRLDKETSGVILLVKENSEFHLK 112

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--------- 185
              + +   V +          +        ++               + +         
Sbjct: 113 AKKAFKDRAVKKEYLAIVQGIIEEEREINAPILTIKTTKAFSKISKKGQEAITIITPLKI 172

Query: 186 ---NAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 + VG++ G+  +I+   +  N  + 
Sbjct: 173 INKKTLLKVGIKTGRTHQIRVHLKHINHPII 203


>gi|295094508|emb|CBK83599.1| Ribosome-associated heat shock protein implicated in the
          recycling of the 50S subunit (S4 paralog) [Coprococcus
          sp. ART55/1]
          Length = 79

 Score = 43.2 bits (100), Expect = 0.052,   Method: Composition-based stats.
 Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 2/51 (3%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+ K +  + I  RR          RV VN  + + A  +V   D IE++
Sbjct: 1  MRLDKYLKVSRIIKRRTVANEACDAGRVMVNDKVAK-AGTDVKVGDVIEIE 50


>gi|238922940|ref|YP_002936453.1| hypothetical protein EUBREC_0528 [Eubacterium rectale ATCC 33656]
 gi|238874612|gb|ACR74319.1| Hypothetical protein EUBREC_0528 [Eubacterium rectale ATCC 33656]
 gi|291523827|emb|CBK89414.1| Ribosome-associated heat shock protein implicated in the
          recycling of the 50S subunit (S4 paralog) [Eubacterium
          rectale DSM 17629]
 gi|291528705|emb|CBK94291.1| Ribosome-associated heat shock protein implicated in the
          recycling of the 50S subunit (S4 paralog) [Eubacterium
          rectale M104/1]
          Length = 79

 Score = 43.2 bits (100), Expect = 0.052,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR          RV VNG   + A+VNV   D IE+
Sbjct: 1  MRLDKFLKVSRLIKRRTVANEACDAGRVTVNGRPAK-ASVNVKVGDIIEI 49


>gi|261342766|ref|ZP_05970624.1| ribosomal protein S4 [Enterobacter cancerogenus ATCC 35316]
 gi|288314945|gb|EFC53883.1| ribosomal protein S4 [Enterobacter cancerogenus ATCC 35316]
          Length = 206

 Score = 43.2 bits (100), Expect = 0.052,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V + D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVSHKAIMVNGRVVNIASYQVKANDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|32892112|gb|AAP88995.1| ribosomal protein S4 [Passiflora mansoi]
          Length = 183

 Score = 43.2 bits (100), Expect = 0.052,   Method: Composition-based stats.
 Identities = 11/53 (20%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
            R+  ++ R G+AS   +  +++  + + VNG +++  +      D I V   
Sbjct: 71  MRLDNILFRLGMASTIPQARQLVNHRHILVNGRIVDIPSYRCKPGDLITVKDE 123


>gi|309777973|ref|ZP_07672915.1| S4 domain protein [Erysipelotrichaceae bacterium 3_1_53]
 gi|308914262|gb|EFP60060.1| S4 domain protein [Erysipelotrichaceae bacterium 3_1_53]
          Length = 88

 Score = 43.2 bits (100), Expect = 0.052,   Method: Composition-based stats.
 Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRREV-ERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  A I  RR V + +  Q+RV VNG + +  + +V   D I+V
Sbjct: 1  MRLDKYLKTARILKRRTVSKELADQERVYVNGKIAK-PSTDVKIGDTIKV 49


>gi|58336613|ref|YP_193198.1| hypothetical protein LBA0274 [Lactobacillus acidophilus NCFM]
 gi|315037512|ref|YP_004031080.1| hypothetical protein LA2_01460 [Lactobacillus amylovorus GRL
          1112]
 gi|325955976|ref|YP_004286586.1| hypothetical protein LAC30SC_01285 [Lactobacillus acidophilus
          30SC]
 gi|58253930|gb|AAV42167.1| hypothetical protein LBA0274 [Lactobacillus acidophilus NCFM]
 gi|312275645|gb|ADQ58285.1| hypothetical protein LA2_01460 [Lactobacillus amylovorus GRL
          1112]
 gi|325332541|gb|ADZ06449.1| hypothetical protein LAC30SC_01285 [Lactobacillus acidophilus
          30SC]
 gi|327182808|gb|AEA31255.1| hypothetical protein LAB52_01350 [Lactobacillus amylovorus GRL
          1118]
          Length = 80

 Score = 43.2 bits (100), Expect = 0.052,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR   + M  Q R+KVNG +++  + +V   D IE+
Sbjct: 1  MRIDKFLKVSRLVKRRTVAKEMADQGRIKVNGRVVKS-SYDVKIDDIIEI 49


>gi|296105004|ref|YP_003615150.1| 30S ribosomal protein S4 [Enterobacter cloacae subsp. cloacae ATCC
           13047]
 gi|295059463|gb|ADF64201.1| 30S ribosomal protein S4 [Enterobacter cloacae subsp. cloacae ATCC
           13047]
          Length = 202

 Score = 43.2 bits (100), Expect = 0.053,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + VNG ++  A+  V + D + +     +++   
Sbjct: 93  RLDNVVYRMGFGATRAESRQLVSHKAIMVNGRVVNIASYQVKANDVVSIREKAKKQSRVK 152

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 153 AALELAEQREKPT 165


>gi|90416840|ref|ZP_01224769.1| 30S ribosomal protein S4 [marine gamma proteobacterium HTCC2207]
 gi|90331187|gb|EAS46431.1| 30S ribosomal protein S4 [marine gamma proteobacterium HTCC2207]
          Length = 206

 Score = 43.2 bits (100), Expect = 0.053,   Method: Composition-based stats.
 Identities = 12/47 (25%), Positives = 22/47 (46%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  V+ R G   +R E  +++A   + VNG  +   +  V   D +
Sbjct: 97  RLDNVVYRMGFGATRAESRQLVAHNSIVVNGQKVNIPSFKVQEGDVV 143


>gi|29348111|ref|NP_811614.1| 30S ribosomal protein S4 [Bacteroides thetaiotaomicron VPI-5482]
 gi|253569617|ref|ZP_04847027.1| 30S ribosomal protein S4 [Bacteroides sp. 1_1_6]
 gi|298386205|ref|ZP_06995762.1| ribosomal protein S4 [Bacteroides sp. 1_1_14]
 gi|41017839|sp|Q8A4A1|RS4_BACTN RecName: Full=30S ribosomal protein S4
 gi|29340014|gb|AAO77808.1| 30S ribosomal protein S4 [Bacteroides thetaiotaomicron VPI-5482]
 gi|251841636|gb|EES69717.1| 30S ribosomal protein S4 [Bacteroides sp. 1_1_6]
 gi|298261433|gb|EFI04300.1| ribosomal protein S4 [Bacteroides sp. 1_1_14]
          Length = 201

 Score = 43.2 bits (100), Expect = 0.053,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA +R    ++++ + + V+G ++   +  V     I V
Sbjct: 93  RLDNVVFRLGIAPTRAAARQLVSHKHITVDGEVVNIPSFAVKPGQLIGV 141


>gi|325294122|ref|YP_004279986.1| ribosome-associated heat shock protein [Agrobacterium sp. H13-3]
 gi|325061975|gb|ADY65666.1| putative ribosome-associated heat shock protein [Agrobacterium
          sp. H13-3]
          Length = 138

 Score = 43.2 bits (100), Expect = 0.053,   Method: Composition-based stats.
 Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
            T QR+ K +  A +A SR   +  I   +VKVNG+ + + +  V + D 
Sbjct: 9  ESTRQRLDKWLFFARMAKSRSLAQSYIQSGKVKVNGVSIRQPSHLVKAGDR 59


>gi|324997813|ref|ZP_08118925.1| RNA-binding S4 domain protein [Pseudonocardia sp. P1]
          Length = 71

 Score = 43.2 bits (100), Expect = 0.053,   Method: Composition-based stats.
 Identities = 15/71 (21%), Positives = 22/71 (30%), Gaps = 9/71 (12%)

Query: 1  MKDKNIVQENFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
          M     V     P R+ + +     A  G         ++    V VNG    R    + 
Sbjct: 1  MTTPQDVPIREEPIRIGQFLKLANLAEDGG----HARELLEAGLVTVNGEPEYRRGAQLQ 56

Query: 56 STDHIEVDGVP 66
            D + VDG  
Sbjct: 57 RGDVVSVDGHR 67


>gi|160883039|ref|ZP_02064042.1| hypothetical protein BACOVA_01002 [Bacteroides ovatus ATCC 8483]
 gi|237717425|ref|ZP_04547906.1| 30S ribosomal protein S4 [Bacteroides sp. D1]
 gi|237718717|ref|ZP_04549198.1| 30S ribosomal protein S4 [Bacteroides sp. 2_2_4]
 gi|260175442|ref|ZP_05761854.1| 30S ribosomal protein S4 [Bacteroides sp. D2]
 gi|262406190|ref|ZP_06082740.1| ribosomal protein S4 [Bacteroides sp. 2_1_22]
 gi|293372094|ref|ZP_06618485.1| ribosomal protein S4 [Bacteroides ovatus SD CMC 3f]
 gi|294644083|ref|ZP_06721860.1| ribosomal protein S4 [Bacteroides ovatus SD CC 2a]
 gi|294806543|ref|ZP_06765382.1| ribosomal protein S4 [Bacteroides xylanisolvens SD CC 1b]
 gi|298483090|ref|ZP_07001271.1| ribosomal protein S4 [Bacteroides sp. D22]
 gi|299144598|ref|ZP_07037666.1| ribosomal protein S4 [Bacteroides sp. 3_1_23]
 gi|315923671|ref|ZP_07919911.1| 30S ribosomal protein S4 [Bacteroides sp. D2]
 gi|156111511|gb|EDO13256.1| hypothetical protein BACOVA_01002 [Bacteroides ovatus ATCC 8483]
 gi|229443408|gb|EEO49199.1| 30S ribosomal protein S4 [Bacteroides sp. D1]
 gi|229451849|gb|EEO57640.1| 30S ribosomal protein S4 [Bacteroides sp. 2_2_4]
 gi|262357065|gb|EEZ06155.1| ribosomal protein S4 [Bacteroides sp. 2_1_22]
 gi|292632886|gb|EFF51473.1| ribosomal protein S4 [Bacteroides ovatus SD CMC 3f]
 gi|292640607|gb|EFF58848.1| ribosomal protein S4 [Bacteroides ovatus SD CC 2a]
 gi|294446238|gb|EFG14866.1| ribosomal protein S4 [Bacteroides xylanisolvens SD CC 1b]
 gi|295085403|emb|CBK66926.1| SSU ribosomal protein S4P [Bacteroides xylanisolvens XB1A]
 gi|298270834|gb|EFI12414.1| ribosomal protein S4 [Bacteroides sp. D22]
 gi|298515089|gb|EFI38970.1| ribosomal protein S4 [Bacteroides sp. 3_1_23]
 gi|313697546|gb|EFS34381.1| 30S ribosomal protein S4 [Bacteroides sp. D2]
          Length = 201

 Score = 43.2 bits (100), Expect = 0.053,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA +R    ++++ + + V+G ++   +  V     I V
Sbjct: 93  RLDNVVFRLGIAPTRAAARQLVSHKHITVDGEVVNIPSFAVKPGQLIGV 141


>gi|153814895|ref|ZP_01967563.1| hypothetical protein RUMTOR_01110 [Ruminococcus torques ATCC 27756]
 gi|317500408|ref|ZP_07958632.1| RNA-binding S4 protein [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331089585|ref|ZP_08338484.1| hypothetical protein HMPREF1025_02067 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|145847926|gb|EDK24844.1| hypothetical protein RUMTOR_01110 [Ruminococcus torques ATCC 27756]
 gi|316898163|gb|EFV20210.1| RNA-binding S4 protein [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330404953|gb|EGG84491.1| hypothetical protein HMPREF1025_02067 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 266

 Score = 43.2 bits (100), Expect = 0.053,   Method: Composition-based stats.
 Identities = 11/35 (31%), Positives = 15/35 (42%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R ++  +I   RV VNG L+          D I V
Sbjct: 204 RTKLSGLIEGGRVFVNGKLITSNGYQPNEGDLISV 238


>gi|295425670|ref|ZP_06818357.1| S4 domain protein [Lactobacillus amylolyticus DSM 11664]
 gi|295064686|gb|EFG55607.1| S4 domain protein [Lactobacillus amylolyticus DSM 11664]
          Length = 80

 Score = 43.2 bits (100), Expect = 0.054,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR   + +  Q R+KVNG +++  + +V   D IEV
Sbjct: 1  MRIDKFLKVSRLVKRRTVAKELADQGRIKVNGRVVKS-SYDVKVGDSIEV 49


>gi|261392548|emb|CAX50103.1| putative RNA-binding protein [Neisseria meningitidis 8013]
 gi|325204173|gb|ADY99626.1| heat shock protein 15 [Neisseria meningitidis M01-240355]
          Length = 133

 Score = 43.2 bits (100), Expect = 0.054,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 6/61 (9%)

Query: 1  MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          MKDK+    + +  R+ K + A     +R   ++ I   RV+VNG  ++ +   +   D 
Sbjct: 1  MKDKH----HSSAMRLDKWLWAARFFKTRSLAQKHIELGRVQVNGSKVKNSKT-IDIGDI 55

Query: 60 I 60
          I
Sbjct: 56 I 56


>gi|225016258|ref|ZP_03705450.1| hypothetical protein CLOSTMETH_00161 [Clostridium methylpentosum
           DSM 5476]
 gi|224950933|gb|EEG32142.1| hypothetical protein CLOSTMETH_00161 [Clostridium methylpentosum
           DSM 5476]
          Length = 208

 Score = 43.2 bits (100), Expect = 0.054,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ RAG AS R E  +++     ++NG  +   ++ V   D IEV
Sbjct: 99  RLDNIVYRAGFASSRAEARQLVLHNHFRLNGKKVNICSLLVKPGDVIEV 147


>gi|296119325|ref|ZP_06837893.1| ribosomal protein S4 [Corynebacterium ammoniagenes DSM 20306]
 gi|295967717|gb|EFG80974.1| ribosomal protein S4 [Corynebacterium ammoniagenes DSM 20306]
          Length = 178

 Score = 43.2 bits (100), Expect = 0.054,   Method: Composition-based stats.
 Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  V+ RAG+A +RR+  ++++     VNG      +  V   D I
Sbjct: 69  RLDNVVYRAGLARTRRQARQLVSHGHFTVNGKKTNVPSYQVSQYDII 115


>gi|139390350|ref|YP_001122948.1| ribosomal protein S4 [Aethionema cordifolium]
 gi|152060542|sp|A4QJB7|RR4_AETCO RecName: Full=30S ribosomal protein S4, chloroplastic
 gi|134286143|dbj|BAF49772.1| ribosomal protein S4 [Aethionema cordifolium]
          Length = 201

 Score = 43.2 bits (100), Expect = 0.054,   Method: Composition-based stats.
 Identities = 10/53 (18%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
            R+  ++ R G+A +  +  +++    + VNG +++  +      D I V   
Sbjct: 89  MRLDNILFRLGMALTIPQARQLVNHGHILVNGRIVDIPSYRCKPRDIITVKDE 141


>gi|304382454|ref|ZP_07364952.1| heat shock protein 15 [Prevotella marshii DSM 16973]
 gi|304336407|gb|EFM02645.1| heat shock protein 15 [Prevotella marshii DSM 16973]
          Length = 137

 Score = 43.2 bits (100), Expect = 0.055,   Method: Composition-based stats.
 Identities = 13/56 (23%), Positives = 20/56 (35%), Gaps = 2/56 (3%)

Query: 15 RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          R+ K + A     +R          RV +NG   +  +  V   D I V   P+  
Sbjct: 4  RIDKWLWAARIFKTRSIAADACKNGRVSINGTTAK-PSRTVKEGDTISVKKAPVVY 58


>gi|294787673|ref|ZP_06752917.1| heat shock protein 15 [Simonsiella muelleri ATCC 29453]
 gi|294483966|gb|EFG31649.1| heat shock protein 15 [Simonsiella muelleri ATCC 29453]
          Length = 137

 Score = 43.2 bits (100), Expect = 0.055,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 25/61 (40%), Gaps = 2/61 (3%)

Query: 1  MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          M  +    E     R+ K + A     +R    R I   RV VNG+ ++ +   V+  D 
Sbjct: 1  MSKQENKDERDDTMRLDKWLWAARFFKTRSLASRQIDLGRVSVNGVKVKTSKYIVV-GDV 59

Query: 60 I 60
          I
Sbjct: 60 I 60


>gi|195728950|gb|ACG50741.1| VtaA16 [Haemophilus parasuis]
          Length = 1070

 Score = 43.2 bits (100), Expect = 0.055,   Method: Composition-based stats.
 Identities = 11/105 (10%), Positives = 21/105 (20%), Gaps = 2/105 (1%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           GP     A   +                          + +   +   G   +   A P 
Sbjct: 657 GPMGPAGAAGLVGPMGPQGPAGPPGPVGPAGAAGPKGDKGEPGQAGPAGPRGEPGQAGPA 716

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
             R                  + G+      R P+ P   +  + 
Sbjct: 717 GPRGPQGTTGAQGPK--GDKGEPGEAGPAGPRGPAGPKGDAGPKG 759


>gi|183981907|ref|YP_001850198.1| translation initiation factor IF-2 InfB [Mycobacterium marinum M]
 gi|238689248|sp|B2HKS2|IF2_MYCMM RecName: Full=Translation initiation factor IF-2
 gi|183175233|gb|ACC40343.1| translation initiation factor IF-2 InfB [Mycobacterium marinum M]
          Length = 947

 Score = 43.2 bits (100), Expect = 0.055,   Method: Composition-based stats.
 Identities = 11/93 (11%), Positives = 15/93 (16%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
             AP        +     ++         K         +     A PV R         
Sbjct: 157 RPAPTPGKPAAPQAPHPGMAPGARPGPVPKPGVRTPRVGNNPFSSAQPVDRPIPRPQAPR 216

Query: 317 AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                       G    N    P   S      
Sbjct: 217 PGAPRPGAPRPGGASPGNMPPRPGGASGGPRPP 249


>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 = 43.2 bits (100), Expect = 0.055,   Method: Composition-based stats.
 Identities = 11/54 (20%), Positives = 21/54 (38%), Gaps = 1/54 (1%)

Query: 9  ENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
                R+ +V+A      SR  ++ +IA+ RV   G  +   +  V   +   
Sbjct: 23 PQDEGLRLDRVLANHLPELSRTRLQALIAEGRVLRAGRPVAGGSAKVAPGEVFT 76


>gi|325265440|ref|ZP_08132163.1| S4 domain protein [Clostridium sp. D5]
 gi|324029298|gb|EGB90590.1| S4 domain protein [Clostridium sp. D5]
          Length = 71

 Score = 43.2 bits (100), Expect = 0.056,   Method: Composition-based stats.
 Identities = 11/42 (26%), Positives = 19/42 (45%)

Query: 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
          E + ++    VKVNG    R    +   D +E DG  ++  +
Sbjct: 30 EAKEVVQDGMVKVNGETDTRRGRKLYDGDKVEFDGQEIKIEK 71


>gi|262204299|ref|YP_003275507.1| drug exporter of the RND superfamily-like protein [Gordonia
           bronchialis DSM 43247]
 gi|262087646|gb|ACY23614.1| drug exporter of the RND superfamily-like protein [Gordonia
           bronchialis DSM 43247]
          Length = 1095

 Score = 43.2 bits (100), Expect = 0.056,   Method: Composition-based stats.
 Identities = 13/115 (11%), Positives = 26/115 (22%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
              LR++        A   +     S     R         P + T   + ++ +    +
Sbjct: 770 PDELRDRSAAAKTMSAGTLVAEAPTSVMARPRVARPASMGPPPERTAPARRAADRARTPE 829

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
              +AT    R       +      +  +  G         P      S      
Sbjct: 830 PTTVATERPTRTRPPAETVPPAARPARGARVGPSAPPSGPQPVGAGATSAPGGPP 884


>gi|254430135|ref|ZP_05043838.1| translation initiation factor IF-2, putative [Cyanobium sp. PCC
           7001]
 gi|197624588|gb|EDY37147.1| translation initiation factor IF-2, putative [Cyanobium sp. PCC
           7001]
          Length = 1078

 Score = 43.2 bits (100), Expect = 0.056,   Method: Composition-based stats.
 Identities = 11/77 (14%), Positives = 19/77 (24%)

Query: 275 ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREEN 334
               P      +K          + +L          SN     G   +        + +
Sbjct: 203 RPSRPGTPAPSRKPEPPSRPGGGRPQLVGRPISPQGGSNRPAPPGSRPATSQRPAPPQRS 262

Query: 335 HRRSPSFPSKRSLRRTS 351
              SPS P +   R  +
Sbjct: 263 GAPSPSRPGQGGGRPAA 279



 Score = 41.3 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 9/110 (8%), Positives = 22/110 (20%), Gaps = 4/110 (3%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                       P   S         +   +       +         + Q+        
Sbjct: 204 PSRPGTPAPSRKPEPPSRPGGGRPQLVGRPISPQGGSNRPAPPGSRPATSQRPAPPQRSG 263

Query: 308 RNLASNVWMAKGIHSSFL----SDSGQREENHRRSPSFPSKRSLRRTSAK 353
               S      G  ++          +R+ +    P+ P +  +     K
Sbjct: 264 APSPSRPGQGGGRPAATPLELVGKPIRRDSSGGNRPAAPGRPGMPAGMRK 313


>gi|108802859|ref|YP_642796.1| RNA-binding S4 [Rubrobacter xylanophilus DSM 9941]
 gi|108764102|gb|ABG02984.1| RNA-binding S4 [Rubrobacter xylanophilus DSM 9941]
          Length = 64

 Score = 43.2 bits (100), Expect = 0.056,   Method: Composition-based stats.
 Identities = 12/40 (30%), Positives = 19/40 (47%)

Query: 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          E + +I    V+VNG +  R    + + D +EV G  L  
Sbjct: 24 EAKLVIRAGEVRVNGEVETRRGRRLRAGDVVEVGGERLEA 63


>gi|317009613|gb|ADU80193.1| hypothetical protein HPIN_04885 [Helicobacter pylori India7]
          Length = 242

 Score = 43.2 bits (100), Expect = 0.056,   Method: Composition-based stats.
 Identities = 27/211 (12%), Positives = 63/211 (29%), Gaps = 28/211 (13%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWL 77
           K+++     S ++ + +I    V + G               + V    L +  R  +  
Sbjct: 6   KILSVQENISHKKAKALIDLGLVSIGGK-------------KLMVARKELPQNTRFSVQK 52

Query: 78  YHKPIGLVTTHSDPDGRSTVF---DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             KP  +    +        F    +L S F   + + RLD  T G++LL  +     + 
Sbjct: 53  IEKPGVIFEDENILALFKPPFIESYDLVSFFKGWVLLHRLDKETSGVVLLVKENSEFHLK 112

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--------- 185
              + +   V +          +        ++               + +         
Sbjct: 113 AKKAFKDRAVKKEYLALAQGIIEEEREINAPILTIKTTKAFSKISKKGQEAVTIITPLKI 172

Query: 186 ---NAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 + VG++ G+  +I+   +  N  + 
Sbjct: 173 INKKTLLKVGIKTGRTHQIRVHLKHINHPII 203


>gi|302877826|ref|YP_003846390.1| 30S ribosomal protein S4 [Gallionella capsiferriformans ES-2]
 gi|302580615|gb|ADL54626.1| ribosomal protein S4 [Gallionella capsiferriformans ES-2]
          Length = 209

 Score = 43.2 bits (100), Expect = 0.056,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V  R G   SR E  +++    + VNG  +   +  V   D +EV
Sbjct: 100 RLDNVSYRMGFGASRAEARQVVRHNALLVNGKRVNIPSYQVRPGDVVEV 148


>gi|114572970|ref|XP_001138810.1| PREDICTED: hypothetical protein [Pan troglodytes]
          Length = 317

 Score = 43.2 bits (100), Expect = 0.056,   Method: Composition-based stats.
 Identities = 12/100 (12%), Positives = 26/100 (26%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
             +      +     +   R       PD    +   ++   G        +   R    
Sbjct: 7   AKEARPPGQVVPKCRVPGPRHPRPVAGPDAPRSLLLRAAATRGRPAAVTPRSAGPRPGGG 66

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
           +    A G  S+     G     + R+ S  + +   R +
Sbjct: 67  APSGCAAGARSARPRAPGPAIPGYPRARSRTTSQDAPRAA 106


>gi|300362406|ref|ZP_07058582.1| S4 domain protein [Lactobacillus gasseri JV-V03]
 gi|300353397|gb|EFJ69269.1| S4 domain protein [Lactobacillus gasseri JV-V03]
          Length = 80

 Score = 43.2 bits (100), Expect = 0.056,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR   + M  Q RVKVN  +++  + +V   D IE+
Sbjct: 1  MRIDKFLKVSRLVKRRTVAKEMADQGRVKVNDRVVKS-SYDVKVGDVIEI 49


>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 = 43.2 bits (100), Expect = 0.056,   Method: Composition-based stats.
 Identities = 21/215 (9%), Positives = 57/215 (26%), Gaps = 33/215 (15%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--------------LRKAERTR 74
           R + + +   RV VN   + +    +   D IE+                  +   +   
Sbjct: 31  RFIRKAVRDGRVFVNKEKVIK-KHKLSQDDLIEIYMQEDEHQNIEPEDMNIEIVYEDNDI 89

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------------------ISVGRLDI 116
           + +  +P  +V         +     L                         I + +   
Sbjct: 90  IVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKNQF 149

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +   L    +     ++        ++    R +  + +++ +   K IV +        
Sbjct: 150 SHMRLASDMSKDSFRKIYIAVVHGSMKEKEGRINLPIYKEEESESIKRIVDERGQESITT 209

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +  +    + V + L  G+  +I+         
Sbjct: 210 YEVLEELSKGSVVRLELETGRTHQIRVHMSHLGHP 244


>gi|56707502|ref|YP_169398.1| 30S ribosomal protein S4 [Francisella tularensis subsp. tularensis
           SCHU S4]
 gi|89255694|ref|YP_513055.1| 30S ribosomal protein S4 [Francisella tularensis subsp. holarctica
           LVS]
 gi|110669973|ref|YP_666530.1| 30S ribosomal protein S4 [Francisella tularensis subsp. tularensis
           FSC198]
 gi|118496876|ref|YP_897926.1| 30S ribosomal protein S4 [Francisella tularensis subsp. novicida
           U112]
 gi|156501642|ref|YP_001427707.1| 30S ribosomal protein S4 [Francisella tularensis subsp. holarctica
           FTNF002-00]
 gi|167010989|ref|ZP_02275920.1| ribosomal protein S4 [Francisella tularensis subsp. holarctica
           FSC200]
 gi|194324098|ref|ZP_03057872.1| ribosomal protein S4 [Francisella tularensis subsp. novicida FTE]
 gi|208780324|ref|ZP_03247665.1| ribosomal protein S4 [Francisella novicida FTG]
 gi|224456565|ref|ZP_03665038.1| 30S ribosomal protein S4 [Francisella tularensis subsp. tularensis
           MA00-2987]
 gi|254367075|ref|ZP_04983110.1| 30S ribosomal protein S4 [Francisella tularensis subsp. holarctica
           257]
 gi|254368645|ref|ZP_04984660.1| 30S ribosomal protein S4 [Francisella tularensis subsp. holarctica
           FSC022]
 gi|254370809|ref|ZP_04986814.1| 30S ribosomal protein S4 [Francisella tularensis subsp. tularensis
           FSC033]
 gi|254372233|ref|ZP_04987724.1| 30S ribosomal protein S4 [Francisella tularensis subsp. novicida
           GA99-3549]
 gi|254373715|ref|ZP_04989198.1| 30S ribosomal protein S4 [Francisella novicida GA99-3548]
 gi|254874322|ref|ZP_05247032.1| 30S ribosomal protein S4 rpsD [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|290953189|ref|ZP_06557810.1| 30S ribosomal protein S4 [Francisella tularensis subsp. holarctica
           URFT1]
 gi|295313557|ref|ZP_06804146.1| 30S ribosomal protein S4 [Francisella tularensis subsp. holarctica
           URFT1]
 gi|61215374|sp|Q5NHU4|RS4_FRATT RecName: Full=30S ribosomal protein S4
 gi|122501251|sp|Q2A5E6|RS4_FRATH RecName: Full=30S ribosomal protein S4
 gi|123359595|sp|Q14J96|RS4_FRAT1 RecName: Full=30S ribosomal protein S4
 gi|152060948|sp|A0Q4K7|RS4_FRATN RecName: Full=30S ribosomal protein S4
 gi|171769925|sp|A7N9U8|RS4_FRATF RecName: Full=30S ribosomal protein S4
 gi|54113157|gb|AAV29212.1| NT02FT0049 [synthetic construct]
 gi|56603994|emb|CAG44982.1| 30S ribosomal protein S4 [Francisella tularensis subsp. tularensis
           SCHU S4]
 gi|89143525|emb|CAJ78701.1| 30S ribosomal protein S4 [Francisella tularensis subsp. holarctica
           LVS]
 gi|110320306|emb|CAL08365.1| 30S ribosomal protein S4 [Francisella tularensis subsp. tularensis
           FSC198]
 gi|118422782|gb|ABK89172.1| 30S ribosomal protein S4 [Francisella novicida U112]
 gi|134252900|gb|EBA51994.1| 30S ribosomal protein S4 [Francisella tularensis subsp. holarctica
           257]
 gi|151569052|gb|EDN34706.1| 30S ribosomal protein S4 [Francisella tularensis subsp. tularensis
           FSC033]
 gi|151569962|gb|EDN35616.1| 30S ribosomal protein S4 [Francisella novicida GA99-3549]
 gi|151571436|gb|EDN37090.1| 30S ribosomal protein S4 [Francisella novicida GA99-3548]
 gi|156252245|gb|ABU60751.1| ribosomal protein S4 [Francisella tularensis subsp. holarctica
           FTNF002-00]
 gi|157121553|gb|EDO65738.1| 30S ribosomal protein S4 [Francisella tularensis subsp. holarctica
           FSC022]
 gi|194321545|gb|EDX19029.1| ribosomal protein S4 [Francisella tularensis subsp. novicida FTE]
 gi|208743692|gb|EDZ89995.1| ribosomal protein S4 [Francisella novicida FTG]
 gi|254840321|gb|EET18757.1| 30S ribosomal protein S4 rpsD [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|282158646|gb|ADA78037.1| 30S ribosomal protein S4 [Francisella tularensis subsp. tularensis
           NE061598]
 gi|328675431|gb|AEB28106.1| SSU ribosomal protein S4p (S9e) [Francisella cf. novicida 3523]
 gi|328676345|gb|AEB27215.1| SSU ribosomal protein S4p (S9e) [Francisella cf. novicida Fx1]
          Length = 206

 Score = 43.2 bits (100), Expect = 0.056,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 29/73 (39%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G A +R E  +++  + + VNG      +  V + D + V     ++    
Sbjct: 97  RLDNVVYRMGFAATRAEARQLVVHKGIMVNGHTCNVPSAQVKAGDVVAVREKAKKQLRIQ 156

Query: 74  RLWLYHKPIGLVT 86
                 K    ++
Sbjct: 157 NAVELAKHRKELS 169


>gi|322807303|emb|CBZ04877.1| similar to ribosomal large subunit pseudouridine synthase D,
           CAC1266-type [Clostridium botulinum H04402 065]
          Length = 300

 Score = 43.2 bits (100), Expect = 0.057,   Method: Composition-based stats.
 Identities = 21/215 (9%), Positives = 57/215 (26%), Gaps = 33/215 (15%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--------------LRKAERTR 74
           R + + +   RV VN   + +    +   D IE+                  +   +   
Sbjct: 31  RFIRKAVRDGRVFVNKEKVIK-KHKLSQDDLIEIYMQEDEHQNIEPEDMNIEIVYEDNDI 89

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------------------ISVGRLDI 116
           + +  +P  +V         +     L                         I + +   
Sbjct: 90  IVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKNQF 149

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +   L    +     ++        ++    R +  + +++ +   K IV +        
Sbjct: 150 SHMRLASDMSKDSFRKIYIAVVHGSMKEKEGRINLPIYKEEESESIKRIVDERGQESITT 209

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +  +    + V + L  G+  +I+         
Sbjct: 210 YEVLEELSKGSVVRLELETGRTHQIRVHMSHLGHP 244


>gi|254670216|emb|CBA05381.1| probable heat shock protein [Neisseria meningitidis alpha153]
 gi|325136326|gb|EGC58934.1| heat shock protein 15 [Neisseria meningitidis M0579]
 gi|325202118|gb|ADY97572.1| heat shock protein 15 [Neisseria meningitidis M01-240149]
          Length = 133

 Score = 43.2 bits (100), Expect = 0.057,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 6/61 (9%)

Query: 1  MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          MKDK+    + +  R+ K + A     +R   ++ I   RV+VNG  ++ +   +   D 
Sbjct: 1  MKDKH----DSSAMRLDKWLWAARFFKTRSLAQKHIELGRVQVNGSKVKNSKT-IDIGDI 55

Query: 60 I 60
          I
Sbjct: 56 I 56


>gi|220930853|ref|YP_002507761.1| RNA-binding S4 domain protein [Halothermothrix orenii H 168]
 gi|219992163|gb|ACL68766.1| RNA-binding S4 domain protein [Halothermothrix orenii H 168]
          Length = 72

 Score = 43.2 bits (100), Expect = 0.057,   Method: Composition-based stats.
 Identities = 16/66 (24%), Positives = 31/66 (46%), Gaps = 4/66 (6%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          MKD  I   N    ++ +++  A I A+  + + +I   +V VNG    R    ++  D 
Sbjct: 1  MKDIKI---NTEKIKLDQLLKYANIVATGGQAKNLIQAGKVMVNGEEELRRGRKLVPGDE 57

Query: 60 IEVDGV 65
          +++ G 
Sbjct: 58 VQLVGE 63


>gi|315497226|ref|YP_004086030.1| translation initiation factor if-2 [Asticcacaulis excentricus CB
           48]
 gi|315415238|gb|ADU11879.1| translation initiation factor IF-2 [Asticcacaulis excentricus CB
           48]
          Length = 1072

 Score = 43.2 bits (100), Expect = 0.057,   Method: Composition-based stats.
 Identities = 12/111 (10%), Positives = 21/111 (18%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           + E L        + +             DRP           R + +  Q +     + 
Sbjct: 190 IEEALSRPAQRAPREDRRDGFRDDRAPRSDRPQGDRPQGQYGDRPRGDRPQGDRPQGDRP 249

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                  R          G         G R +          +    R  
Sbjct: 250 PFNRDGNRPQGDRPQGQYGDRPRGDRPQGDRPQGQYGDRPRGDRPQGDRPP 300



 Score = 39.4 bits (90), Expect = 0.82,   Method: Composition-based stats.
 Identities = 11/107 (10%), Positives = 20/107 (18%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               +            +    DRP       D     +  +  +    + +    P   
Sbjct: 215 APRSDRPQGDRPQGQYGDRPRGDRPQGDRPQGDRPPFNRDGNRPQGDRPQGQYGDRPRGD 274

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           R          G         G R   +R        R        +
Sbjct: 275 RPQGDRPQGQYGDRPRGDRPQGDRPPFNRDGNRPQGDRPNYGERTPR 321



 Score = 37.1 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 9/86 (10%), Positives = 22/86 (25%)

Query: 269 RDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDS 328
           +      S + +  +R  + + +++     +    P   R          G         
Sbjct: 181 QAEAPRRSPIEEALSRPAQRAPREDRRDGFRDDRAPRSDRPQGDRPQGQYGDRPRGDRPQ 240

Query: 329 GQREENHRRSPSFPSKRSLRRTSAKK 354
           G R +  R   +    R        +
Sbjct: 241 GDRPQGDRPPFNRDGNRPQGDRPQGQ 266


>gi|95930497|ref|ZP_01313233.1| RNA-binding S4 [Desulfuromonas acetoxidans DSM 684]
 gi|95133537|gb|EAT15200.1| RNA-binding S4 [Desulfuromonas acetoxidans DSM 684]
          Length = 206

 Score = 43.2 bits (100), Expect = 0.057,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+AS R E    +      VNG  ++  +  V + D IEV
Sbjct: 96  RLDNMVFRLGLASTRSEARLFVRHGHFLVNGRKVDIPSYLVRAGDVIEV 144


>gi|325119213|emb|CBZ54767.1| conserved hypothetical protein [Neospora caninum Liverpool]
          Length = 2302

 Score = 43.2 bits (100), Expect = 0.058,   Method: Composition-based stats.
 Identities = 11/90 (12%), Positives = 19/90 (21%)

Query: 260 PIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKG 319
                      +    S       + K      + +   ++   P  RR    +    + 
Sbjct: 542 MADRDGFPRGSKGQRASAASGSPKKGKGRRRAPSDVDSAEREEKPKPRRERKQDASRERK 601

Query: 320 IHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                 S         RR      K   RR
Sbjct: 602 KSRGKPSGPTGGAAGSRRRRERTVKAQARR 631


>gi|302541383|ref|ZP_07293725.1| vegetative cell wall protein gp1 (Hydroxyproline-rich glycoprotein
           1) [Streptomyces hygroscopicus ATCC 53653]
 gi|302459001|gb|EFL22094.1| vegetative cell wall protein gp1 (Hydroxyproline-rich glycoprotein
           1) [Streptomyces himastatinicus ATCC 53653]
          Length = 700

 Score = 43.2 bits (100), Expect = 0.058,   Method: Composition-based stats.
 Identities = 15/125 (12%), Positives = 22/125 (17%), Gaps = 14/125 (11%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R       L+E      A         RD P   +         +       G       
Sbjct: 533 RRAHTMPELQELLWQAIAFGRGENRPHRDHPVAGAATRTGRPGGRTPRPGALGRRPAPGP 592

Query: 302 ATPVHRRNLASNVWMAKG--------------IHSSFLSDSGQREENHRRSPSFPSKRSL 347
             P    + +      +                               RR P     R  
Sbjct: 593 GRPDPAPHRSPRPGARRHPALRPLPHPRHPLDAAHRPRHRPLAAPPAGRRRPPAGQGRRR 652

Query: 348 RRTSA 352
            R +A
Sbjct: 653 HRPAA 657



 Score = 37.5 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 20/130 (15%), Positives = 36/130 (27%), Gaps = 1/130 (0%)

Query: 219 SYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEV 278
           S G   LG L     R   +  + E L P L   A+       ++    +  R + + E+
Sbjct: 483 SVGAADLGRLDH-QLRRGQEHTVFEALRPWLEAGAERVDHELTFALARSLGRRAHTMPEL 541

Query: 279 PDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS 338
            +   +       +N   +   +A    R           G      +    R +     
Sbjct: 542 QELLWQAIAFGRGENRPHRDHPVAGAATRTGRPGGRTPRPGALGRRPAPGPGRPDPAPHR 601

Query: 339 PSFPSKRSLR 348
              P  R   
Sbjct: 602 SPRPGARRHP 611


>gi|227891600|ref|ZP_04009405.1| S4 RNA-binding domain protein [Lactobacillus salivarius ATCC
          11741]
 gi|227866747|gb|EEJ74168.1| S4 RNA-binding domain protein [Lactobacillus salivarius ATCC
          11741]
          Length = 89

 Score = 43.2 bits (100), Expect = 0.058,   Method: Composition-based stats.
 Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 2/51 (3%)

Query: 14 QRVSKVIARAGIASRREVERMIA-QQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+ K +  + I  RR V + I+ Q R+ +NG + +  + NV   D I ++
Sbjct: 1  MRLDKFLKISRIIKRRTVAKEISSQGRITINGKVAKS-SSNVNVRDEIVIN 50


>gi|312880344|ref|ZP_07740144.1| SSU ribosomal protein S4P [Aminomonas paucivorans DSM 12260]
 gi|310783635|gb|EFQ24033.1| SSU ribosomal protein S4P [Aminomonas paucivorans DSM 12260]
          Length = 208

 Score = 43.2 bits (100), Expect = 0.058,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A SRR+   ++      VNG  L+  +  + + D + V
Sbjct: 99  RLDNVVYRLGLAVSRRQARELVRHGHFLVNGRKLDIPSAVLRAGDVVSV 147


>gi|87122791|ref|ZP_01078664.1| 30S ribosomal protein S4 [Marinomonas sp. MED121]
 gi|86161956|gb|EAQ63248.1| 30S ribosomal protein S4 [Marinomonas sp. MED121]
          Length = 206

 Score = 43.2 bits (100), Expect = 0.058,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG   +R E  +++A + ++VNG  +  A+  V + D + V
Sbjct: 97  RLDNVVYRAGFGATRAESRQLVAHKGIQVNGATVNIASYQVKAGDVVSV 145


>gi|319937684|ref|ZP_08012087.1| S4 RNA-binding protein [Coprobacillus sp. 29_1]
 gi|319807119|gb|EFW03733.1| S4 RNA-binding protein [Coprobacillus sp. 29_1]
          Length = 90

 Score = 43.2 bits (100), Expect = 0.059,   Method: Composition-based stats.
 Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 3/67 (4%)

Query: 14 QRVSKVIARAGIASRREVERMI-AQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRKAE 71
           R+ K +  + I  RR V + I    RVKVNG + +  +  +   D IE++ G  +   +
Sbjct: 1  MRLDKFLKVSRIIKRRTVSKEISESSRVKVNGKMAK-PSTKLKIGDIIEIEFGRSILVVQ 59

Query: 72 RTRLWLY 78
             L  +
Sbjct: 60 VKDLKDH 66


>gi|157689494|gb|ABV65303.1| ribosomal protein S4 [Hymenanthera alpina]
          Length = 169

 Score = 43.2 bits (100), Expect = 0.059,   Method: Composition-based stats.
 Identities = 13/72 (18%), Positives = 26/72 (36%), Gaps = 5/72 (6%)

Query: 14  QRVSKVIARAGIAS---RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            R+  ++ R G+AS   R    +++  + + VNG +++         D I V      +A
Sbjct: 50  MRLDNILFRLGMASTIPR--ARQLVNHRHILVNGRIVDIPNYRCKPRDIITVKDKKKSRA 107

Query: 71  ERTRLWLYHKPI 82
                       
Sbjct: 108 MIQNYLKSLPRK 119


>gi|150390763|ref|YP_001320812.1| 30S ribosomal protein S4 [Alkaliphilus metalliredigens QYMF]
 gi|172052482|sp|A6TSI5|RS4B_ALKMQ RecName: Full=30S ribosomal protein S4 B
 gi|149950625|gb|ABR49153.1| RNA-binding S4 domain protein [Alkaliphilus metalliredigens QYMF]
          Length = 199

 Score = 43.2 bits (100), Expect = 0.059,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G  S  R+  +M+    + VNG  ++R +  V   D I +
Sbjct: 89  RLDNLVYRTGFGSSIRQARQMVVHGHILVNGKKVDRPSFAVSVGDDISL 137


>gi|297588666|ref|ZP_06947309.1| S4 RNA-binding domain protein [Finegoldia magna ATCC 53516]
 gi|297574039|gb|EFH92760.1| S4 RNA-binding domain protein [Finegoldia magna ATCC 53516]
          Length = 81

 Score = 43.2 bits (100), Expect = 0.060,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   +     QRVK+N  + +    NV   D IE+
Sbjct: 1  MRLDKFLKNSRIIKRRTVAKTACESQRVKINEKIAK-PGDNVKVGDIIEI 49


>gi|58040211|ref|YP_192175.1| 30S ribosomal protein S4 [Gluconobacter oxydans 621H]
 gi|81672625|sp|Q5FQ27|RS4_GLUOX RecName: Full=30S ribosomal protein S4
 gi|58002625|gb|AAW61519.1| SSU ribosomal protein S4P [Gluconobacter oxydans 621H]
          Length = 205

 Score = 43.2 bits (100), Expect = 0.060,   Method: Composition-based stats.
 Identities = 13/38 (34%), Positives = 17/38 (44%), Gaps = 4/38 (10%)

Query: 25  IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            ASR    + I+   V VNG  +   +  V   D IEV
Sbjct: 110 FASR----QFISHGHVTVNGKKVNIPSYLVKEGDVIEV 143


>gi|268553367|ref|XP_002634669.1| Hypothetical protein CBG19652 [Caenorhabditis briggsae]
 gi|187023966|emb|CAP36859.1| hypothetical protein CBG_19652 [Caenorhabditis briggsae AF16]
          Length = 269

 Score = 43.2 bits (100), Expect = 0.060,   Method: Composition-based stats.
 Identities = 11/93 (11%), Positives = 16/93 (17%), Gaps = 2/93 (2%)

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW-- 315
             P   S              P      +    +      +   + P   R+  S     
Sbjct: 74  RPPGSRSPESRPPGSRPPGSRPPGSRPPESRPPESRPPGSRPPESRPPESRSPESRPPES 133

Query: 316 MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
              G           R    R   S P      
Sbjct: 134 RPPGSRPRESRPPESRPPESRPPESRPPGSRSP 166



 Score = 41.3 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 11/116 (9%), Positives = 19/116 (16%), Gaps = 4/116 (3%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           ++  +    G    E        P                  P      +    +     
Sbjct: 68  TQVTVSRPPGSRSPESRPPGSRPPGSRPPGSRPPESRPPESRPPGSRPPESRPPESRSPE 127

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            +   + P   R   S             S   +      RSP             
Sbjct: 128 SRPPESRPPGSRPRESR----PPESRPPESRPPESRPPGSRSPDLGHPDPGHPDPG 179



 Score = 40.9 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 12/113 (10%), Positives = 20/113 (17%), Gaps = 4/113 (3%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R ++      E +          +                       S +      +   
Sbjct: 33  RIKVTRSGPPERRSPYPGHPDPGQPNQGHPVRATRTQVTVSRPPGSRSPESRPPGSRPPG 92

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           + P   R   S                  R     RSP      S    S  +
Sbjct: 93  SRPPGSRPPESR---PPESRPPGSRPPESRP-PESRSPESRPPESRPPGSRPR 141



 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 13/106 (12%), Positives = 21/106 (19%)

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
            L   +      I  +   V          P          +Q + +   +   T     
Sbjct: 17  WLALKRSTQVTLIQVNRIKVTRSGPPERRSPYPGHPDPGQPNQGHPVRATRTQVTVSRPP 76

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              S      G         G R    R   S P       +   +
Sbjct: 77  GSRSPESRPPGSRPPGSRPPGSRPPESRPPESRPPGSRPPESRPPE 122



 Score = 36.7 bits (83), Expect = 6.1,   Method: Composition-based stats.
 Identities = 10/110 (9%), Positives = 23/110 (20%)

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           L      +  +     I  + +   +R +     PD     + +  +             
Sbjct: 18  LALKRSTQVTLIQVNRIKVTRSGPPERRSPYPGHPDPGQPNQGHPVRATRTQVTVSRPPG 77

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                         G           R    R   S P +     + + +
Sbjct: 78  SRSPESRPPGSRPPGSRPPGSRPPESRPPESRPPGSRPPESRPPESRSPE 127


>gi|332295330|ref|YP_004437253.1| RNA-binding S4 domain protein [Thermodesulfobium narugense DSM
          14796]
 gi|332178433|gb|AEE14122.1| RNA-binding S4 domain protein [Thermodesulfobium narugense DSM
          14796]
          Length = 74

 Score = 43.2 bits (100), Expect = 0.060,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +   G+  RR   + M     V VNG +  +   +V   D IE+
Sbjct: 1  MRLDKWLKVTGLIKRRAIAKEMCESGFVLVNGRI-GKPDYSVRVGDKIEI 49


>gi|302550687|ref|ZP_07303029.1| LOW QUALITY PROTEIN: ABC transporter [Streptomyces
           viridochromogenes DSM 40736]
 gi|302468305|gb|EFL31398.1| LOW QUALITY PROTEIN: ABC transporter [Streptomyces
           viridochromogenes DSM 40736]
          Length = 655

 Score = 43.2 bits (100), Expect = 0.060,   Method: Composition-based stats.
 Identities = 8/93 (8%), Positives = 17/93 (18%), Gaps = 2/93 (2%)

Query: 264 SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSS 323
                R     +                     +  +      RR         +     
Sbjct: 28  EPARRRVPGAELPGHDRPAAVPAGVQPAARPAGRPGRRTDRPGRRGRPGCGAGGEPARGQ 87

Query: 324 FLSDS--GQREENHRRSPSFPSKRSLRRTSAKK 354
             +    G+R +    +   P      R  A +
Sbjct: 88  QRAGRADGRRSDRGPAARCRPGAGHRGRRDAAR 120


>gi|268567175|ref|XP_002647734.1| Hypothetical protein CBG17929 [Caenorhabditis briggsae]
 gi|187025458|emb|CAP35465.1| hypothetical protein CBG_17929 [Caenorhabditis briggsae AF16]
          Length = 266

 Score = 43.2 bits (100), Expect = 0.060,   Method: Composition-based stats.
 Identities = 17/114 (14%), Positives = 31/114 (27%), Gaps = 2/114 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E   P   E +         S E      P        +  +     ++K G  + +K  
Sbjct: 112 EARKPGSPEASVSPEARKPGSPEARKPGSPEARKPGSPEARKPGSPEARKPGSPEARKPG 171

Query: 303 TPVHRRNLASNVWMA--KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +P  R+  +                 ++ +      R P  P  R      A+K
Sbjct: 172 SPEARKPGSPEARKPGSPEARKPGSPEARKPGSPEARKPGSPEARKPGSPEARK 225



 Score = 42.9 bits (99), Expect = 0.080,   Method: Composition-based stats.
 Identities = 17/114 (14%), Positives = 31/114 (27%), Gaps = 2/114 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E   P   E  +        S E      P        +  +     ++K G  + +K  
Sbjct: 104 EARKPGSPEARKPGSPEASVSPEARKPGSPEARKPGSPEARKPGSPEARKPGSPEARKPG 163

Query: 303 TPVHRRNLASNVWMA--KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +P  R+  +                 ++ +      R P  P  R      A+K
Sbjct: 164 SPEARKPGSPEARKPGSPEARKPGSPEARKPGSPEARKPGSPEARKPGSPEARK 217



 Score = 38.2 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 16/111 (14%), Positives = 31/111 (27%), Gaps = 2/111 (1%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P  LE  +              R   ++ +  P      K  S + +   + +K  +P 
Sbjct: 75  KPESLEARKQKSPEAWKPVSLEARKPVSLEARKPGSPEARKPGSPEASVSPEARKPGSPE 134

Query: 306 HRRNLASNVWMA--KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            R+  +                 ++ +      R P  P  R      A+K
Sbjct: 135 ARKPGSPEARKPGSPEARKPGSPEARKPGSPEARKPGSPEARKPGSPEARK 185



 Score = 35.9 bits (81), Expect = 8.7,   Method: Composition-based stats.
 Identities = 14/103 (13%), Positives = 30/103 (29%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
             +        S E   +  P     V  +  +     ++K G  + +K  +P    +  
Sbjct: 67  SRKPGSPWKPESLEARKQKSPEAWKPVSLEARKPVSLEARKPGSPEARKPGSPEASVSPE 126

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +    +         ++ +      R P  P  R      A+K
Sbjct: 127 ARKPGSPEARKPGSPEARKPGSPEARKPGSPEARKPGSPEARK 169


>gi|26354955|dbj|BAC41104.1| unnamed protein product [Mus musculus]
          Length = 2607

 Score = 43.2 bits (100), Expect = 0.060,   Method: Composition-based stats.
 Identities = 16/102 (15%), Positives = 29/102 (28%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P      +++      +       R    S  P       ++ + K G S+ +      H
Sbjct: 347 PAPGSRREISSSPTSKNRSHGRAKRDKSHSHTPSHRAGRSRSPATKRGRSRSRTPTKRGH 406

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
            R+ +     ++       S S QR    R        RS  
Sbjct: 407 SRSRSPQWRRSRSAQRWGKSRSPQRRGRSRSPQRPGWSRSRN 448



 Score = 41.7 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 14/113 (12%), Positives = 33/113 (29%), Gaps = 2/113 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +         +      P  +  +      +  S+        +  S       +  +  
Sbjct: 328 QPTKVSRHASSSPESLKPTPAPGSRREISSSPTSKNRSHGRAKRDKSHSHTPSHRAGRSR 387

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR--SPSFPSKRSLRRTSAK 353
           +P  +R  + +    K  HS   S   +R  + +R      P +R   R+  +
Sbjct: 388 SPATKRGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGKSRSPQRRGRSRSPQR 440



 Score = 41.3 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 14/125 (11%), Positives = 27/125 (21%), Gaps = 17/125 (13%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P        +       S +    +          + R +         S Q++  +   
Sbjct: 379 PSHRAGRSRSPATKRGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGKSRSPQRRGRSRSP 438

Query: 307 RRNLASNVW-----------------MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           +R   S                                         RS +   +RS  R
Sbjct: 439 QRPGWSRSRNTQRRGRSRSARRGRSHSRSPATRGRSRSRTPARRGRSRSRTPARRRSRSR 498

Query: 350 TSAKK 354
           T A++
Sbjct: 499 TPARR 503



 Score = 41.3 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 14/98 (14%), Positives = 31/98 (31%), Gaps = 2/98 (2%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
             A  +      + R    S     ++R +    +    S ++  +          +   
Sbjct: 418 RSAQRWGKSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRSHSRSPATRGRSRSR 477

Query: 317 AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                    S +  R  +  R+P+   +RS  RT A++
Sbjct: 478 TPARRGRSRSRTPARRRSRSRTPAR--RRSRSRTPARR 513



 Score = 35.9 bits (81), Expect = 8.6,   Method: Composition-based stats.
 Identities = 14/81 (17%), Positives = 24/81 (29%)

Query: 274 IISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREE 333
             S  P   +R   +S +    +        +     + N    +       S +     
Sbjct: 324 PPSPQPTKVSRHASSSPESLKPTPAPGSRREISSSPTSKNRSHGRAKRDKSHSHTPSHRA 383

Query: 334 NHRRSPSFPSKRSLRRTSAKK 354
              RSP+    RS  RT  K+
Sbjct: 384 GRSRSPATKRGRSRSRTPTKR 404


>gi|294632674|ref|ZP_06711233.1| pyoverdine sidechain peptide synthetase III, L-Thr-L-Ser component
            [Streptomyces sp. e14]
 gi|292830455|gb|EFF88805.1| pyoverdine sidechain peptide synthetase III, L-Thr-L-Ser component
            [Streptomyces sp. e14]
          Length = 2291

 Score = 43.2 bits (100), Expect = 0.061,   Method: Composition-based stats.
 Identities = 11/109 (10%), Positives = 22/109 (20%), Gaps = 1/109 (0%)

Query: 243  EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             +LG       +      +                 P      + +  ++    +  +  
Sbjct: 1848 ARLGRGHSPRRRRLHLPGLPRPGQPADRLRQGGRRQPQRVRAGRVDLPRRPVRLRPARAD 1907

Query: 303  TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK-RSLRRT 350
             P  R      V    G      +     +   RR        R   R 
Sbjct: 1908 QPRRRAPAGRAVPADPGGDGRRPAGRRPGQLPGRRGTRPAGGVRDRPRH 1956



 Score = 36.7 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 10/108 (9%), Positives = 20/108 (18%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            R       L +        + +    +  RP  +     D  R +  + +          
Sbjct: 1868 RPGQPADRLRQGGRRQPQRVRAGRVDLPRRPVRLRPARADQPRRRAPAGRAVPADPGGDG 1927

Query: 302  ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
              P  RR                             +P+         
Sbjct: 1928 RRPAGRRPGQLPGRRGTRPAGGVRDRPRHGLPGRLPAPAVRGAGRAHP 1975


>gi|222087732|ref|YP_002546269.1| heat shock protein (ribosome-associated) [Agrobacterium
          radiobacter K84]
 gi|221725180|gb|ACM28336.1| heat shock protein (ribosome-associated) [Agrobacterium
          radiobacter K84]
          Length = 134

 Score = 43.2 bits (100), Expect = 0.061,   Method: Composition-based stats.
 Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 4/64 (6%)

Query: 1  MKDKNIVQENFTPQRVSKVI--ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
          M D+         QR+ K +  AR  + SR   +  + +  V+VNG  + + +  V + D
Sbjct: 1  MTDERQSSSGSR-QRIDKWLFFARM-LKSRSLAQVYVQKGNVRVNGERITQPSHGVKAGD 58

Query: 59 HIEV 62
           IE+
Sbjct: 59 RIEL 62


>gi|126157504|ref|NP_780438.2| serine/arginine repetitive matrix protein 2 [Mus musculus]
          Length = 2607

 Score = 43.2 bits (100), Expect = 0.061,   Method: Composition-based stats.
 Identities = 16/102 (15%), Positives = 29/102 (28%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P      +++      +       R    S  P       ++ + K G S+ +      H
Sbjct: 347 PAPGSRREISSSPTSKNRSHGRAKRDKSHSHTPSHRAGRSRSPATKRGRSRSRTPTKRGH 406

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
            R+ +     ++       S S QR    R        RS  
Sbjct: 407 SRSRSPQWRRSRSAQRWGKSRSPQRRGRSRSPQRPGWSRSRN 448



 Score = 41.3 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 14/107 (13%), Positives = 32/107 (29%), Gaps = 2/107 (1%)

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
               +      P  +  +      +  S+        +  S       +  +  +P  +R
Sbjct: 334 RHASSSPESLKPTPAPGSRREISSSPTSKNRSHGRAKRDKSHSHTPSHRAGRSRSPATKR 393

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRR--SPSFPSKRSLRRTSAK 353
             + +    K  HS   S   +R  + +R      P +R   R+  +
Sbjct: 394 GRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGKSRSPQRRGRSRSPQR 440



 Score = 41.3 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 14/125 (11%), Positives = 27/125 (21%), Gaps = 17/125 (13%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P        +       S +    +          + R +         S Q++  +   
Sbjct: 379 PSHRAGRSRSPATKRGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGKSRSPQRRGRSRSP 438

Query: 307 RRNLASNVW-----------------MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           +R   S                                         RS +   +RS  R
Sbjct: 439 QRPGWSRSRNTQRRGRSRSARRGRSHSRSPATRGRSRSRTPARRGRSRSRTPARRRSRSR 498

Query: 350 TSAKK 354
           T A++
Sbjct: 499 TPARR 503



 Score = 40.9 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 14/98 (14%), Positives = 31/98 (31%), Gaps = 2/98 (2%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
             A  +      + R    S     ++R +    +    S ++  +          +   
Sbjct: 418 RSAQRWGKSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRSHSRSPATRGRSRSR 477

Query: 317 AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                    S +  R  +  R+P+   +RS  RT A++
Sbjct: 478 TPARRGRSRSRTPARRRSRSRTPAR--RRSRSRTPARR 513



 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 13/114 (11%), Positives = 31/114 (27%), Gaps = 3/114 (2%)

Query: 230 AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
            G +R  S +  R +      +           S +     R           +  +  S
Sbjct: 404 RGHSRSRSPQWRRSRSAQRWGKSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRS 463

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
             ++  ++ +  +    RR  +              S +  R  +  R+P+   
Sbjct: 464 HSRSPATRGRSRSRTPARRGRS---RSRTPARRRSRSRTPARRRSRSRTPARRG 514



 Score = 36.3 bits (82), Expect = 7.2,   Method: Composition-based stats.
 Identities = 14/81 (17%), Positives = 24/81 (29%)

Query: 274 IISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREE 333
             S  P   +R   +S +    +        +     + N    +       S +     
Sbjct: 324 PPSPQPTKGSRHASSSPESLKPTPAPGSRREISSSPTSKNRSHGRAKRDKSHSHTPSHRA 383

Query: 334 NHRRSPSFPSKRSLRRTSAKK 354
              RSP+    RS  RT  K+
Sbjct: 384 GRSRSPATKRGRSRSRTPTKR 404


>gi|218283273|ref|ZP_03489328.1| hypothetical protein EUBIFOR_01917 [Eubacterium biforme DSM 3989]
 gi|218215963|gb|EEC89501.1| hypothetical protein EUBIFOR_01917 [Eubacterium biforme DSM 3989]
          Length = 89

 Score = 43.2 bits (100), Expect = 0.061,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRREV-ERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  A I  RRE  + +  Q R+ VN  + +  +  +   D I +
Sbjct: 1  MRLDKYLKTARILKRREAAKELALQGRIWVNDRVAK-PSTELKIGDTIRI 49


>gi|331092507|ref|ZP_08341329.1| hypothetical protein HMPREF9477_01972 [Lachnospiraceae bacterium
          2_1_46FAA]
 gi|330400728|gb|EGG80331.1| hypothetical protein HMPREF9477_01972 [Lachnospiraceae bacterium
          2_1_46FAA]
          Length = 79

 Score = 43.2 bits (100), Expect = 0.062,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR          RV VNG++ + A+  V   D IE+
Sbjct: 1  MRLDKFLKVSRLIKRRTVANEACDAGRVLVNGLVAK-ASQKVKVGDIIEI 49


>gi|260893345|ref|YP_003239442.1| ribosomal protein S4 [Ammonifex degensii KC4]
 gi|260865486|gb|ACX52592.1| ribosomal protein S4 [Ammonifex degensii KC4]
          Length = 208

 Score = 43.2 bits (100), Expect = 0.062,   Method: Composition-based stats.
 Identities = 12/51 (23%), Positives = 19/51 (37%)

Query: 26  ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW 76
           ASR E  +++    + VNG  ++  +  V   D I  D           L 
Sbjct: 111 ASRAEARQLVRHGHILVNGRRVDIPSYLVEVGDKISFDPRSKESPRIQELL 161


>gi|114152161|sp|Q8BTI8|SRRM2_MOUSE RecName: Full=Serine/arginine repetitive matrix protein 2
          Length = 2703

 Score = 43.2 bits (100), Expect = 0.062,   Method: Composition-based stats.
 Identities = 16/102 (15%), Positives = 29/102 (28%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P      +++      +       R    S  P       ++ + K G S+ +      H
Sbjct: 443 PAPGSRREISSSPTSKNRSHGRAKRDKSHSHTPSHRAGRSRSPATKRGRSRSRTPTKRGH 502

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
            R+ +     ++       S S QR    R        RS  
Sbjct: 503 SRSRSPQWRRSRSAQRWGKSRSPQRRGRSRSPQRPGWSRSRN 544



 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 14/113 (12%), Positives = 33/113 (29%), Gaps = 2/113 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +         +      P  +  +      +  S+        +  S       +  +  
Sbjct: 424 QPTKVSRHASSSPESLKPTPAPGSRREISSSPTSKNRSHGRAKRDKSHSHTPSHRAGRSR 483

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR--SPSFPSKRSLRRTSAK 353
           +P  +R  + +    K  HS   S   +R  + +R      P +R   R+  +
Sbjct: 484 SPATKRGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGKSRSPQRRGRSRSPQR 536



 Score = 41.3 bits (95), Expect = 0.26,   Method: Composition-based stats.
 Identities = 14/125 (11%), Positives = 27/125 (21%), Gaps = 17/125 (13%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P        +       S +    +          + R +         S Q++  +   
Sbjct: 475 PSHRAGRSRSPATKRGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGKSRSPQRRGRSRSP 534

Query: 307 RRNLASNVW-----------------MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           +R   S                                         RS +   +RS  R
Sbjct: 535 QRPGWSRSRNTQRRGRSRSARRGRSHSRSPATRGRSRSRTPARRGRSRSRTPARRRSRSR 594

Query: 350 TSAKK 354
           T A++
Sbjct: 595 TPARR 599



 Score = 40.9 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 14/98 (14%), Positives = 31/98 (31%), Gaps = 2/98 (2%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
             A  +      + R    S     ++R +    +    S ++  +          +   
Sbjct: 514 RSAQRWGKSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRSHSRSPATRGRSRSR 573

Query: 317 AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                    S +  R  +  R+P+   +RS  RT A++
Sbjct: 574 TPARRGRSRSRTPARRRSRSRTPAR--RRSRSRTPARR 609



 Score = 35.9 bits (81), Expect = 9.1,   Method: Composition-based stats.
 Identities = 14/81 (17%), Positives = 24/81 (29%)

Query: 274 IISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREE 333
             S  P   +R   +S +    +        +     + N    +       S +     
Sbjct: 420 PPSPQPTKVSRHASSSPESLKPTPAPGSRREISSSPTSKNRSHGRAKRDKSHSHTPSHRA 479

Query: 334 NHRRSPSFPSKRSLRRTSAKK 354
              RSP+    RS  RT  K+
Sbjct: 480 GRSRSPATKRGRSRSRTPTKR 500


>gi|297588221|ref|ZP_06946865.1| 30S ribosomal protein S4 [Finegoldia magna ATCC 53516]
 gi|297574910|gb|EFH93630.1| 30S ribosomal protein S4 [Finegoldia magna ATCC 53516]
          Length = 198

 Score = 43.2 bits (100), Expect = 0.062,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ RA  AS  R+  +M++   ++VNG  ++  +  V     IE+
Sbjct: 91  RLDNLVLRASFASSIRQARQMVSHGLIRVNGKKVDIPSYQVAEGSVIEL 139


>gi|187932119|ref|YP_001892104.1| 30S ribosomal protein S4 [Francisella tularensis subsp.
           mediasiatica FSC147]
 gi|226699067|sp|B2SDW1|RS4_FRATM RecName: Full=30S ribosomal protein S4
 gi|187713028|gb|ACD31325.1| 30S ribosomal protein S4 [Francisella tularensis subsp.
           mediasiatica FSC147]
          Length = 206

 Score = 43.2 bits (100), Expect = 0.062,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 29/73 (39%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G A +R E  +++  + + VNG      +  V + D + V     ++    
Sbjct: 97  RLDNVVYRMGFAATRAEARQLVVHKGIMVNGHTCNVPSAQVKAGDVVAVREKAKKQLRIQ 156

Query: 74  RLWLYHKPIGLVT 86
                 K    ++
Sbjct: 157 NAVELAKHRKELS 169


>gi|150398308|ref|YP_001328775.1| RNA-binding S4 domain-containing protein [Sinorhizobium medicae
          WSM419]
 gi|150029823|gb|ABR61940.1| RNA-binding S4 domain protein [Sinorhizobium medicae WSM419]
          Length = 137

 Score = 43.2 bits (100), Expect = 0.062,   Method: Composition-based stats.
 Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 3/62 (4%)

Query: 3  DKNIVQENFTPQRVSKVI--ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
          +K       T QR+ K +  AR  I SR   ++ I    V VNG    +++  + + D +
Sbjct: 2  EKQPPSAPATRQRLDKWLFFARL-IKSRSLAQKAIEAGHVVVNGKRETQSSAQIKAGDML 60

Query: 61 EV 62
          EV
Sbjct: 61 EV 62


>gi|51894183|ref|YP_076874.1| 30S ribosomal protein S4 [Symbiobacterium thermophilum IAM 14863]
 gi|81691984|sp|Q67JX0|RS4A_SYMTH RecName: Full=30S ribosomal protein S4 A
 gi|51857872|dbj|BAD42030.1| 30S ribosomal protein S4 [Symbiobacterium thermophilum IAM 14863]
          Length = 207

 Score = 43.2 bits (100), Expect = 0.062,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SR E  +++    ++VNG  +   +  V   D + V
Sbjct: 99  RLDNVVYRMGFAASRAEARQIVKHSHIEVNGRKVNIPSYLVREGDVVAV 147


>gi|238788773|ref|ZP_04632564.1| ATP-dependent RNA helicase rhlE [Yersinia frederiksenii ATCC 33641]
 gi|238723078|gb|EEQ14727.1| ATP-dependent RNA helicase rhlE [Yersinia frederiksenii ATCC 33641]
          Length = 451

 Score = 43.2 bits (100), Expect = 0.062,   Method: Composition-based stats.
 Identities = 14/101 (13%), Positives = 31/101 (30%), Gaps = 2/101 (1%)

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN--LAS 312
           V+    +   E L++     I+    +     K    +NG   +      + R +     
Sbjct: 351 VDEHKLLRDIERLLKREIPRIALDGYEPDPSIKADPIQNGRQGRGAQRPGMGRGSNAGRP 410

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                        +   + + + +R P+ PS R   R   +
Sbjct: 411 QNGGGAASRGDSRNSRPRSQADGQRRPAGPSSRGRSRNPGE 451


>gi|300702805|ref|YP_003744406.1| 30S ribosomal protein S4 [Ralstonia solanacearum CFBP2957]
 gi|299070467|emb|CBJ41762.1| 30S ribosomal subunit protein S4 [Ralstonia solanacearum CFBP2957]
          Length = 207

 Score = 43.2 bits (100), Expect = 0.063,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  L   +  + + D + +
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAILVNGQALNVPSAQIKAGDVVAI 146


>gi|207081122|gb|ACI22845.1| differential display clone 8 [Peromyscus polionotus subgriseus]
          Length = 536

 Score = 43.2 bits (100), Expect = 0.063,   Method: Composition-based stats.
 Identities = 14/125 (11%), Positives = 35/125 (28%), Gaps = 4/125 (3%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             RE   + +R+    +L             ++ T+        ++      R +    +
Sbjct: 49  EWREARLQQVRDMERLYLTHLLDEATGRAGGNNLTMNERNQRRSAKHMRSKGRNRAAFRE 108

Query: 292 KNGLSKQKKLATPVHRR----NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
           + G  ++     P  R+    +       A+G + S      +   +       P     
Sbjct: 109 EKGHREEHPRQHPKSRKKATCSERQGSSKARGQNPSEKGKGKRVPSSKSNGGYQPLGPRT 168

Query: 348 RRTSA 352
            R + 
Sbjct: 169 GRGAD 173


>gi|207081120|gb|ACI22844.1| differential display clone 8 [Peromyscus maniculatus bairdii]
          Length = 536

 Score = 43.2 bits (100), Expect = 0.063,   Method: Composition-based stats.
 Identities = 14/125 (11%), Positives = 35/125 (28%), Gaps = 4/125 (3%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             RE   + +R+    +L             ++ T+        ++      R +    +
Sbjct: 49  EWREARLQQVRDMERLYLTHLLDEATGRAGGNNLTMNERNQRRSAKHMRSKGRNRAAFRE 108

Query: 292 KNGLSKQKKLATPVHRR----NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
           + G  ++     P  R+    +       A+G + S      +   +       P     
Sbjct: 109 EKGHREEHPRQHPKSRKKATCSERQGSSKARGQNPSEKGKGKRVPSSKSNGGYQPLGPRT 168

Query: 348 RRTSA 352
            R + 
Sbjct: 169 GRGAD 173


>gi|161506856|ref|YP_001576810.1| hypothetical protein lhv_0292 [Lactobacillus helveticus DPC 4571]
 gi|260102337|ref|ZP_05752574.1| S4 domain protein [Lactobacillus helveticus DSM 20075]
 gi|160347845|gb|ABX26519.1| hypothetical protein lhv_0292 [Lactobacillus helveticus DPC 4571]
 gi|260083846|gb|EEW67966.1| S4 domain protein [Lactobacillus helveticus DSM 20075]
 gi|323465805|gb|ADX69492.1| S4 RNA-binding domain protein [Lactobacillus helveticus H10]
 gi|328463462|gb|EGF35113.1| hypothetical protein AAULH_01602 [Lactobacillus helveticus MTCC
          5463]
          Length = 80

 Score = 43.2 bits (100), Expect = 0.063,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR   + M  Q R+KVNG +++  + +V   D IE+
Sbjct: 1  MRIDKFLKVSRLVKRRTVAKEMADQGRIKVNGRVVKS-SYDVKIDDIIEL 49


>gi|86747675|ref|YP_484171.1| RNA-binding S4 [Rhodopseudomonas palustris HaA2]
 gi|86570703|gb|ABD05260.1| RNA-binding S4 [Rhodopseudomonas palustris HaA2]
          Length = 89

 Score = 43.2 bits (100), Expect = 0.063,   Method: Composition-based stats.
 Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 1/52 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            QR+ K +  A I  +R     ++    V+VNG+  +     + + D + +
Sbjct: 2  ERQRLDKWLWHARIVRARSTAAALVESGHVRVNGVREKSPGHGIKTGDVVTI 53


>gi|239943995|ref|ZP_04695932.1| hypothetical protein SrosN15_23551 [Streptomyces roseosporus NRRL
           15998]
          Length = 606

 Score = 43.2 bits (100), Expect = 0.065,   Method: Composition-based stats.
 Identities = 17/140 (12%), Positives = 28/140 (20%), Gaps = 11/140 (7%)

Query: 224 QLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
           +L  +  G  R V  +   E  G             P                       
Sbjct: 432 RLRGVEPGD-RPVLPRT-DEAAGLRHRAARGDRGRGPAAGPLPRRLRGARPGPRTGMAAA 489

Query: 284 RMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP---- 339
                + +   L +  +                ++            R    RR      
Sbjct: 490 DRLPAAERSPHLRRTPRGRRNQAEAQDRRRPGRSRVARRGGGDADRARPGPGRRHRHAHL 549

Query: 340 -----SFPSKRSLRRTSAKK 354
                + P  RS RR S  +
Sbjct: 550 PCLGGTGPDGRSARRGSPVR 569



 Score = 37.9 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 16/108 (14%), Positives = 28/108 (25%), Gaps = 1/108 (0%)

Query: 238 KKILR-EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            + LR  + GP     A   L A   S       R         D  R  ++   + G  
Sbjct: 472 PRRLRGARPGPRTGMAAADRLPAAERSPHLRRTPRGRRNQAEAQDRRRPGRSRVARRGGG 531

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
              +      RR+  +++    G      S           + +    
Sbjct: 532 DADRARPGPGRRHRHAHLPCLGGTGPDGRSARRGSPVRAAHAVAAGPP 579



 Score = 37.1 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 14/117 (11%), Positives = 24/117 (20%), Gaps = 5/117 (4%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E  G      A   L         ++                 +        L ++ + A
Sbjct: 419 EYDGESPPVHALGRLRGVEPGDRPVLPRTDEAAGLRHRAARGDRGRGPAAGPLPRRLRGA 478

Query: 303 TPVHRRN-----LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            P  R              +  +  +      Q E   RR P            A +
Sbjct: 479 RPGPRTGMAAADRLPAAERSPHLRRTPRGRRNQAEAQDRRRPGRSRVARRGGGDADR 535


>gi|194228495|ref|XP_001494502.2| PREDICTED: similar to hCG2014439 [Equus caballus]
          Length = 397

 Score = 43.2 bits (100), Expect = 0.065,   Method: Composition-based stats.
 Identities = 8/98 (8%), Positives = 21/98 (21%)

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
            +L            +                  S   +G ++ ++        +     
Sbjct: 13  PSLGQDRARPPPGRSEGRARSRSGSPASGGGASGSPPTDGETEARRTRATREEGSGGHPP 72

Query: 315 WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                + S        R     R+P   ++ +  R   
Sbjct: 73  PADPRLRSPSELRPSGRSPRGNRAPPRGAEAAGGRGRP 110


>gi|262199637|ref|YP_003270846.1| hypothetical protein Hoch_6484 [Haliangium ochraceum DSM 14365]
 gi|262082984|gb|ACY18953.1| Tetratricopeptide TPR_2 repeat protein [Haliangium ochraceum DSM
           14365]
          Length = 1257

 Score = 43.2 bits (100), Expect = 0.066,   Method: Composition-based stats.
 Identities = 10/123 (8%), Positives = 29/123 (23%), Gaps = 2/123 (1%)

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G   E+    + +   P    +               +R         P      ++ + 
Sbjct: 233 GDFAEMPPTSMIQLDAPMQGRQRSAPPVPSPRVPAQPLRAEQPTRESEPIRPRAAEQPTR 292

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
           +   +  +        R   +++      +          R      S    +  S+ R+
Sbjct: 293 ESEPIRPRASAPQAQPRSPSSASPG--PRLRPDPEPRPAPRPSAVPGSGPTAAPTSMPRS 350

Query: 351 SAK 353
            + 
Sbjct: 351 PSS 353


>gi|260655919|ref|ZP_05861388.1| S4 domain protein [Jonquetella anthropi E3_33 E1]
 gi|260629535|gb|EEX47729.1| S4 domain protein [Jonquetella anthropi E3_33 E1]
          Length = 102

 Score = 43.2 bits (100), Expect = 0.066,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +     +  R     MI    V++NG  ++  A +V   D + V
Sbjct: 1  MRLDKYLKLSCLVKRRSVAAEMIDAGAVRLNGRPVK-PASDVSDGDIVSV 49


>gi|225165765|ref|ZP_03727555.1| ABC transporter related [Opitutaceae bacterium TAV2]
 gi|224799989|gb|EEG18428.1| ABC transporter related [Opitutaceae bacterium TAV2]
          Length = 636

 Score = 43.2 bits (100), Expect = 0.066,   Method: Composition-based stats.
 Identities = 13/111 (11%), Positives = 28/111 (25%), Gaps = 2/111 (1%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           L ++             D    S        P+            K  ++     +  K+
Sbjct: 513 LHDRFHGRPPLANPAPRDRHPASGVFPPPLPPHAQPNQKTPRRSRKTGATHHRIGNPAKR 572

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                  R+  +     +G      +   +R    R       +R+ RR+ 
Sbjct: 573 THR--RARSPRNLRRPRQGAPPQPRTHRRRRSTPGRHPRMGTGRRTPRRSR 621



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 9/86 (10%), Positives = 19/86 (22%)

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
                   +      +     P   T  +  S +     +Q     P   R   S     
Sbjct: 548 PNQKTPRRSRKTGATHHRIGNPAKRTHRRARSPRNLRRPRQGAPPQPRTHRRRRSTPGRH 607

Query: 318 KGIHSSFLSDSGQREENHRRSPSFPS 343
             + +   +    R+      P+   
Sbjct: 608 PRMGTGRRTPRRSRKFPIAPPPARAK 633



 Score = 38.2 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 12/109 (11%), Positives = 21/109 (19%), Gaps = 3/109 (2%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA--- 302
            P   +    +   P         ++           T  +  +  K    + +      
Sbjct: 525 NPAPRDRHPASGVFPPPLPPHAQPNQKTPRRSRKTGATHHRIGNPAKRTHRRARSPRNLR 584

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
            P             +          G      RRS  FP      R  
Sbjct: 585 RPRQGAPPQPRTHRRRRSTPGRHPRMGTGRRTPRRSRKFPIAPPPARAK 633



 Score = 36.3 bits (82), Expect = 7.3,   Method: Composition-based stats.
 Identities = 12/126 (9%), Positives = 34/126 (26%), Gaps = 5/126 (3%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R +++ +L    G       + +       +        +     P       ++    +
Sbjct: 476 RSLAENVLHVHSGRITPYAGKYDYYLDKSKATNGRGRLHDRFHGRPPLANPAPRDRHPAS 535

Query: 294 G-----LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           G     L    +      RR+  +     +  + +  +    R   + R P   +    R
Sbjct: 536 GVFPPPLPPHAQPNQKTPRRSRKTGATHHRIGNPAKRTHRRARSPRNLRRPRQGAPPQPR 595

Query: 349 RTSAKK 354
               ++
Sbjct: 596 THRRRR 601


>gi|169823881|ref|YP_001691492.1| 30S ribosomal protein S4 [Finegoldia magna ATCC 29328]
 gi|302379778|ref|ZP_07268262.1| ribosomal protein S4 [Finegoldia magna ACS-171-V-Col3]
 gi|303234754|ref|ZP_07321380.1| ribosomal protein S4 [Finegoldia magna BVS033A4]
 gi|226699066|sp|B0RZT8|RS4_FINM2 RecName: Full=30S ribosomal protein S4
 gi|167830686|dbj|BAG07602.1| 30S ribosomal protein S4 [Finegoldia magna ATCC 29328]
 gi|302312366|gb|EFK94363.1| ribosomal protein S4 [Finegoldia magna ACS-171-V-Col3]
 gi|302494095|gb|EFL53875.1| ribosomal protein S4 [Finegoldia magna BVS033A4]
          Length = 198

 Score = 43.2 bits (100), Expect = 0.066,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ RA  AS  R+  +M++   ++VNG  ++  +  V     IE+
Sbjct: 91  RLDNLVLRASFASSIRQARQMVSHGLIRVNGKKVDIPSFQVAEGSVIEL 139


>gi|114569405|ref|YP_756085.1| hypothetical protein Mmar10_0854 [Maricaulis maris MCS10]
 gi|114339867|gb|ABI65147.1| hypothetical protein Mmar10_0854 [Maricaulis maris MCS10]
          Length = 500

 Score = 43.2 bits (100), Expect = 0.066,   Method: Composition-based stats.
 Identities = 13/116 (11%), Positives = 29/116 (25%), Gaps = 8/116 (6%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P +      +   P    +   R         PD     ++  ++  G     +   P  
Sbjct: 78  PPVTRPTSRDRPGPTSRPDRPRRPESRPGGRSPDARPGGRRPDARPGGRGPDTRPGRPAT 137

Query: 307 RRN------LASNVWMAKGIHSSFLSDSGQREENHRR--SPSFPSKRSLRRTSAKK 354
           R                 G++ +      +R    R    P  P +      + ++
Sbjct: 138 RPGGTRPDTRPGRPGRPVGVNPNDRRPDARRPGGTRPDTRPGRPGRPVGVNPNDRR 193



 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 9/108 (8%), Positives = 20/108 (18%), Gaps = 8/108 (7%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN- 309
            + +    A                  V  +    + ++ +  G     +   P      
Sbjct: 128 PDTRPGRPATRPGGTRPDTRPGRPGRPVGVNPNDRRPDARRPGGTRPDTRPGRPGRPVGV 187

Query: 310 ----LASNVWMAKGIHSSFLSDSGQREE---NHRRSPSFPSKRSLRRT 350
                  +     G           R +      R P    +   R  
Sbjct: 188 NPNDRRPDARRPGGTRPDTRPGRPGRPDTRGPGDRRPDTRGRDGRRPD 235



 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 13/121 (10%), Positives = 27/121 (22%), Gaps = 2/121 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R    +    + G    +                   RP   +  P       +      
Sbjct: 94  RPDRPRRPESRPGGRSPDARPGGRRPDARPGGRGPDTRPGRPATRPGGTRPDTRPGRPGR 153

Query: 294 GLSKQKKLATPVHRRNL--ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
            +        P  RR      +    +      ++ + +R +  R   + P  R  R   
Sbjct: 154 PVGVNPNDRRPDARRPGGTRPDTRPGRPGRPVGVNPNDRRPDARRPGGTRPDTRPGRPGR 213

Query: 352 A 352
            
Sbjct: 214 P 214



 Score = 42.1 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 12/107 (11%), Positives = 19/107 (17%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P      +     P   +      RP+     P     +  N  + +            
Sbjct: 118 RPDARPGGRGPDTRPGRPATRPGGTRPDTRPGRPGRPVGVNPNDRRPDARRPGGTRPDTR 177

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             R                    G R +     P  P  R       
Sbjct: 178 PGRPGRPVGVNPNDRRPDARRPGGTRPDTRPGRPGRPDTRGPGDRRP 224



 Score = 42.1 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 16/121 (13%), Positives = 27/121 (22%), Gaps = 2/121 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R      +R   G      A+   +     + T    R           TR         
Sbjct: 32  RRGGGDEVRRSDGNDSGRGARRGGNPQRGEARTERTRRDAATRRDAPPVTRPTSRDR-PG 90

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             S+  +   P  R    S      G         G+  +     P+     +   T   
Sbjct: 91  PTSRPDRPRRPESRPGGRSPDARPGGRRPD-ARPGGRGPDTRPGRPATRPGGTRPDTRPG 149

Query: 354 K 354
           +
Sbjct: 150 R 150



 Score = 41.7 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 12/113 (10%), Positives = 24/113 (21%), Gaps = 1/113 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R    P   E           +             + P   +R  +    ++    +   
Sbjct: 52  RRGGNPQRGEARTERTRRDAATRRDAPPVTRPTSRDRPGPTSRPDRPRRPESRPGGRSPD 111

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           A P  RR  A              +            P  P +      + ++
Sbjct: 112 ARPGGRRPDARPGGRGPDTRPGRPATRPGGTRP-DTRPGRPGRPVGVNPNDRR 163



 Score = 40.9 bits (94), Expect = 0.26,   Method: Composition-based stats.
 Identities = 12/109 (11%), Positives = 24/109 (22%), Gaps = 2/109 (1%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P  +       DA                  V  +    + ++ +  G     +   P 
Sbjct: 153 RPVGVNPNDRRPDARRPGGTRPDTRPGRPGRPVGVNPNDRRPDARRPGGTRPDTRPGRPG 212

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            R +                     R +  RR  + P  R    +   +
Sbjct: 213 -RPDTRGPGDRRPDTRGRDGRRPDTRPDRPRRPDTRPGGR-RPDSRPGR 259



 Score = 40.5 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 9/114 (7%), Positives = 20/114 (17%), Gaps = 1/114 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R    P                       RP+                 +  G++   + 
Sbjct: 134 RPATRPGGTRPDTRPGRPGRPVGVNPNDRRPDARRPGGTRPDTRPGRPGRPVGVNPNDRR 193

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS-KRSLRRTSAKK 354
                      +    +           +R +   R    P  +    R    +
Sbjct: 194 PDARRPGGTRPDTRPGRPGRPDTRGPGDRRPDTRGRDGRRPDTRPDRPRRPDTR 247



 Score = 40.2 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 13/112 (11%), Positives = 27/112 (24%), Gaps = 5/112 (4%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +G +  +             +T        +   P+D     +        ++  +   
Sbjct: 154 PVGVNPNDRRPDARRPGGTRPDTRPGRPGRPVGVNPNDRRPDARRPGGTRPDTRPGRPGR 213

Query: 304 PVHRRN--LASNVWMAKGIHSSFLSDSGQREE---NHRRSPSFPSKRSLRRT 350
           P  R       +     G       D  +R +     RR  S P +      
Sbjct: 214 PDTRGPGDRRPDTRGRDGRRPDTRPDRPRRPDTRPGGRRPDSRPGRGHRDTG 265



 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 10/94 (10%), Positives = 22/94 (23%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +G +  +             +T         +  P D     +    +   ++  +   
Sbjct: 184 PVGVNPNDRRPDARRPGGTRPDTRPGRPGRPDTRGPGDRRPDTRGRDGRRPDTRPDRPRR 243

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
           P  R             H     D  +R  +  R
Sbjct: 244 PDTRPGGRRPDSRPGRGHRDTGWDRDRRRPDAHR 277


>gi|73980916|ref|XP_540196.2| PREDICTED: similar to B-cell linker [Canis familiaris]
          Length = 459

 Score = 43.2 bits (100), Expect = 0.066,   Method: Composition-based stats.
 Identities = 15/114 (13%), Positives = 26/114 (22%), Gaps = 5/114 (4%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G        +   A    S           +       R   + +    LS   + + P 
Sbjct: 16  GLRHDTSVLLRQWAYCKKSNRKPGRSCESGASPSRRGPRGGASGATVRDLSATPRSSGPS 75

Query: 306 HRRNLASNVWM-----AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             R+            A G      + + +       SPS        RT   +
Sbjct: 76  GMRSRGPGRHSGSRLSAPGTRRHTRAQAVRAPPPGTTSPSKQWAEGRSRTPDAQ 129


>gi|158828236|gb|ABW81113.1| proline-rich protein [Boechera divaricarpa]
          Length = 883

 Score = 43.2 bits (100), Expect = 0.066,   Method: Composition-based stats.
 Identities = 13/81 (16%), Positives = 23/81 (28%)

Query: 274 IISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREE 333
                       ++ S       ++        RR+ +      +   S     S     
Sbjct: 309 ARRRRSPSPLARRRRSPSPPARRRRSPSPPARSRRSPSPPARRRRSPLSFRRRRSPSPPA 368

Query: 334 NHRRSPSFPSKRSLRRTSAKK 354
             RRSPS   +R+  R+   K
Sbjct: 369 RRRRSPSPLYRRNRSRSPLAK 389



 Score = 42.9 bits (99), Expect = 0.073,   Method: Composition-based stats.
 Identities = 15/105 (14%), Positives = 32/105 (30%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                 +   L     S     R R +         +       +++ LS +++ +    
Sbjct: 308 LARRRRSPSPLARRRRSPSPPARRRRSPSPPARSRRSPSPPARRRRSPLSFRRRRSPSPP 367

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
            R   S   + +   S       +R ++  RSPS  + R     +
Sbjct: 368 ARRRRSPSPLYRRNRSRSPLAKRERSDSQGRSPSPVANRRAPTGA 412



 Score = 42.1 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 12/110 (10%), Positives = 23/110 (20%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R +                        R                ++ S       ++   
Sbjct: 267 RSRSPIRHHRRPSPEGRRQSPPPSRRRRSPSPFRRRRSPSPLARRRRSPSPLARRRRSPS 326

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                RR+ +      +                 RRSPS P++R    + 
Sbjct: 327 PPARRRRSPSPPARSRRSPSPPARRRRSPLSFRRRRSPSPPARRRRSPSP 376



 Score = 37.5 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 11/113 (9%), Positives = 26/113 (23%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R ++       ++  +      S    R  P             ++ S       ++   
Sbjct: 257 RRRIHSPYGSRSRSPIRHHRRPSPEGRRQSPPPSRRRRSPSPFRRRRSPSPLARRRRSPS 316

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                RR+ +      +       S         RR      +R    +   +
Sbjct: 317 PLARRRRSPSPPARRRRSPSPPARSRRSPSPPARRRRSPLSFRRRRSPSPPAR 369


>gi|332881080|ref|ZP_08448748.1| ribosomal protein S4 [Capnocytophaga sp. oral taxon 329 str. F0087]
 gi|332680992|gb|EGJ53921.1| ribosomal protein S4 [Capnocytophaga sp. oral taxon 329 str. F0087]
          Length = 201

 Score = 43.2 bits (100), Expect = 0.067,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA +R    ++++ + + +NG ++   +  +   D + V
Sbjct: 94  RLDNVVYRMGIAPTRSAARQLVSHRHITLNGEIVNIPSYLLKPGDVVGV 142


>gi|229552047|ref|ZP_04440772.1| ribosomal protein S4 [Lactobacillus rhamnosus LMS2-1]
 gi|229314624|gb|EEN80597.1| ribosomal protein S4 [Lactobacillus rhamnosus LMS2-1]
          Length = 239

 Score = 43.2 bits (100), Expect = 0.067,   Method: Composition-based stats.
 Identities = 11/47 (23%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  ++ R G+AS R +  +++    + V+G  L+  +  V     I
Sbjct: 130 RLDNLVFRLGLASSRPQARQLVNHGHITVDGKRLDIPSYEVQPGQVI 176


>gi|260837406|ref|XP_002613695.1| hypothetical protein BRAFLDRAFT_131621 [Branchiostoma floridae]
 gi|229299083|gb|EEN69704.1| hypothetical protein BRAFLDRAFT_131621 [Branchiostoma floridae]
          Length = 1027

 Score = 43.2 bits (100), Expect = 0.067,   Method: Composition-based stats.
 Identities = 15/110 (13%), Positives = 25/110 (22%), Gaps = 2/110 (1%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G                  E   R +   I        +  + +  +    K ++     
Sbjct: 804 GRVRGGRKNQAGRQGRRPGEVSARRQRIKIPRTRQPKRKKPERTFGRRQRKKPERGRRQR 863

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREEN--HRRSPSFPSKRSLRRTSAK 353
            R          K    +F      R E    RR    P +   RR   +
Sbjct: 864 TRPEGTIGRRQRKKPERTFGRRQRTRPEGTIGRRQRKKPERTFGRRQRTR 913



 Score = 42.9 bits (99), Expect = 0.081,   Method: Composition-based stats.
 Identities = 12/101 (11%), Positives = 20/101 (19%), Gaps = 3/101 (2%)

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
               A                        R     S +    K  +   P  ++   +  
Sbjct: 790 KPTGAFGTRQPPETGRVRGGRKNQAGRQGRRPGEVSARRQRIKIPRTRQPKRKKPERT-F 848

Query: 315 WMAKGIHSSFLSDSGQREEN--HRRSPSFPSKRSLRRTSAK 353
              +            R E    RR    P +   RR   +
Sbjct: 849 GRRQRKKPERGRRQRTRPEGTIGRRQRKKPERTFGRRQRTR 889


>gi|207081118|gb|ACI22843.1| differential display clone 8 [Peromyscus leucopus]
          Length = 536

 Score = 43.2 bits (100), Expect = 0.067,   Method: Composition-based stats.
 Identities = 14/125 (11%), Positives = 35/125 (28%), Gaps = 4/125 (3%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             RE   + +R+    +L             ++ T+        ++      R +    +
Sbjct: 49  EWREARLQQVRDMERLYLTHLLDEATGRARGNNLTMNERNQRRSAKHMRSKGRNRAAFRE 108

Query: 292 KNGLSKQKKLATPVHRR----NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
           + G  ++     P  R+    +       A+G + S      +   +       P     
Sbjct: 109 EKGHREEHPRQHPKSRKKATCSERQGSSKARGQNPSEKGKGKRVPSSKSNGGYQPLGPRT 168

Query: 348 RRTSA 352
            R + 
Sbjct: 169 GRGAD 173


>gi|89072968|ref|ZP_01159515.1| putative Fe-S oxidoreductase family 2 [Photobacterium sp. SKA34]
 gi|89051186|gb|EAR56642.1| putative Fe-S oxidoreductase family 2 [Photobacterium sp. SKA34]
          Length = 788

 Score = 43.2 bits (100), Expect = 0.067,   Method: Composition-based stats.
 Identities = 14/118 (11%), Positives = 32/118 (27%), Gaps = 2/118 (1%)

Query: 229 LAGSTREVSKKILR--EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
             G+  E++    R   + G         N        +     R    +         +
Sbjct: 671 PPGTEAELTPAERRGSGRHGAKRFATKHPNQPDIRKDGKRSSTARNGKPTVKGKPSANGR 730

Query: 287 KNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
             ++ K   +  +       R N  SN     G  +   + +G+    ++ + S    
Sbjct: 731 PTANSKPAGTGNRSETNGNKRPNNGSNAGARNGKPAGNTNRNGKAGRPNKPTRSRAGA 788


>gi|194289240|ref|YP_002005147.1| ribosome-associated heat shock protein 15 [Cupriavidus
          taiwanensis LMG 19424]
 gi|193223075|emb|CAQ69080.1| ribosome-associated heat shock protein 15 [Cupriavidus
          taiwanensis LMG 19424]
          Length = 131

 Score = 43.2 bits (100), Expect = 0.067,   Method: Composition-based stats.
 Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 2/60 (3%)

Query: 5  NIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          N+  E    QR+ K +       +R      + + RV VNG L +  +  V   D + ++
Sbjct: 2  NVDFEADARQRIDKWLWCARFFKTRSLAAEAVERGRVTVNGQLCKN-SREVKPGDKVVLE 60


>gi|225570638|ref|ZP_03779661.1| hypothetical protein CLOHYLEM_06738 [Clostridium hylemonae DSM
           15053]
 gi|225160556|gb|EEG73175.1| hypothetical protein CLOHYLEM_06738 [Clostridium hylemonae DSM
           15053]
          Length = 269

 Score = 42.9 bits (99), Expect = 0.068,   Method: Composition-based stats.
 Identities = 27/221 (12%), Positives = 61/221 (27%), Gaps = 20/221 (9%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  ++ +  +A SR + + +I    V V G   ++A         IEV G  L    R
Sbjct: 3   ERLDILLVKRNLAASREKAKAVIMSGNVFVEGQREDKAGTTFPEEAKIEVRGSTLPYVSR 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L         +                    ++  G + +    +     D  L +
Sbjct: 63  GGLKLEKALKSFDVSVDGKVCTDVGSST-GGFTDCMLQNGAVKVFAIDVGRGQLDWKLRQ 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV--- 189
              +   +   +  V      +  + + +    +        ++  L       A +   
Sbjct: 122 DDRVVCMEKTNIRYVTPEDIGEPVEFSSIDVSFISLTKVLEPIRNYLADHGQIVALIKPQ 181

Query: 190 ----------TVGLREGKNRE-----IKKVFEFFNWKVNRL 215
                        +RE +        + +      + V  L
Sbjct: 182 FEAGREKVGKKGVVREPRTHVEVISKVIRYAMSIGFAVLNL 222


>gi|126661881|ref|ZP_01732880.1| heat shock protein 15 [Flavobacteria bacterium BAL38]
 gi|126625260|gb|EAZ95949.1| heat shock protein 15 [Flavobacteria bacterium BAL38]
          Length = 132

 Score = 42.9 bits (99), Expect = 0.068,   Method: Composition-based stats.
 Identities = 12/83 (14%), Positives = 27/83 (32%), Gaps = 2/83 (2%)

Query: 14 QRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ K++       +R      + +  + VNG + + A+  V  TD I +    +     
Sbjct: 1  MRIDKLLWCLRYYKTRSIATEAVKKGHITVNGQVAK-ASREVYPTDKITLRKDQINYKLT 59

Query: 73 TRLWLYHKPIGLVTTHSDPDGRS 95
                ++    +      D   
Sbjct: 60 ILDMPQNRLGAKLVDMYRKDETP 82


>gi|126722672|ref|NP_001075660.1| voltage-dependent N-type calcium channel subunit alpha-1B
           [Oryctolagus cuniculus]
 gi|5921693|sp|Q05152|CAC1B_RABIT RecName: Full=Voltage-dependent N-type calcium channel subunit
           alpha-1B; AltName: Full=Brain calcium channel III;
           Short=BIII; AltName: Full=Calcium channel, L type,
           alpha-1 polypeptide isoform 5; AltName:
           Full=Voltage-gated calcium channel subunit alpha Cav2.2
 gi|217716|dbj|BAA03202.1| calcium channel BIII [Oryctolagus cuniculus]
          Length = 2339

 Score = 42.9 bits (99), Expect = 0.068,   Method: Composition-based stats.
 Identities = 8/107 (7%), Positives = 20/107 (18%), Gaps = 1/107 (0%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                     +          R   +  +    +    +       G  +  +  +P   
Sbjct: 873 RAEALRAEGGELGPREERGRPRRSRSKEAPGAPEVRSDRGRGPCPEGGRRHHRRGSPEEA 932

Query: 308 RNLASNVWMAKGIHSSFLSDSGQ-REENHRRSPSFPSKRSLRRTSAK 353
                    A         +         RR+      R+  R +  
Sbjct: 933 AEREPRRHRAHRHGPDPGKEGPASGTRGERRARHRTGPRACPREAES 979



 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 26/169 (15%), Positives = 41/169 (24%), Gaps = 37/169 (21%)

Query: 223 FQLGTL---LAGSTREVSKKI-LREQLGPHLLEEAQVNLDAP-IYSSETLVRDRPNIISE 277
            +L  L         E+  +  LR     HL  + + +LD P +          P     
Sbjct: 776 LRLQNLRASCEALYSEMDPEERLRYATARHLRPDVKTHLDRPLVVEPGRDAPRGPPGGKS 835

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW---------------------- 315
            PD     +     +     + K   P    +                            
Sbjct: 836 RPDGSEAPEGADPPRRHHRHRDKDKAPATVPSAGEQDRAEALRAEGGELGPREERGRPRR 895

Query: 316 ----MAKGI------HSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                A G               G R  + R SP   ++R  RR  A +
Sbjct: 896 SRSKEAPGAPEVRSDRGRGPCPEGGRRHHRRGSPEEAAEREPRRHRAHR 944


>gi|291546821|emb|CBL19929.1| bacterial translation initiation factor 2 (bIF-2) [Ruminococcus sp.
           SR1/5]
          Length = 897

 Score = 42.9 bits (99), Expect = 0.068,   Method: Composition-based stats.
 Identities = 11/104 (10%), Positives = 26/104 (25%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G     +            +   +      +   +   +    S Q      + +   P 
Sbjct: 57  GGKGRRKPAAGERKGPARPQNGGQRSAGANTRNGESGEQRNGQSGQNRTQGGRPQGNRPE 116

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
            RR+   +    +G         G R +N    P+   + +   
Sbjct: 117 GRRDGNRDGRTFEGRRDGGNRFGGNRSQNGEGRPARQGEGNRGP 160



 Score = 42.9 bits (99), Expect = 0.080,   Method: Composition-based stats.
 Identities = 11/125 (8%), Positives = 27/125 (21%), Gaps = 7/125 (5%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYS-------SETLVRDRPNIISEVPDDFTR 284
             R++      E+      E  +        +              +        +    
Sbjct: 13  QYRQLDTPKTEEKTTTVNTEGNKSEAPKKKKNIIRVFHAQNASDGGKGRRKPAAGERKGP 72

Query: 285 MKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
            +  +  +       +      +RN  S     +G         G+R+ N         +
Sbjct: 73  ARPQNGGQRSAGANTRNGESGEQRNGQSGQNRTQGGRPQGNRPEGRRDGNRDGRTFEGRR 132

Query: 345 RSLRR 349
               R
Sbjct: 133 DGGNR 137


>gi|116617524|ref|YP_817895.1| ribosome-associated heat shock protein implicated in the
          recycling of the 50S subunit S4-like protein
          [Leuconostoc mesenteroides subsp. mesenteroides ATCC
          8293]
 gi|227432632|ref|ZP_03914608.1| S4 RNA-binding domain protein [Leuconostoc mesenteroides subsp.
          cremoris ATCC 19254]
 gi|116096371|gb|ABJ61522.1| Ribosome-associated heat shock protein implicated in the
          recycling of the 50S subunit (S4 paralog) [Leuconostoc
          mesenteroides subsp. mesenteroides ATCC 8293]
 gi|227351602|gb|EEJ41852.1| S4 RNA-binding domain protein [Leuconostoc mesenteroides subsp.
          cremoris ATCC 19254]
          Length = 93

 Score = 42.9 bits (99), Expect = 0.068,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 28/50 (56%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRREVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR V + IA Q R+ +NG + + ++  V + D +EV
Sbjct: 1  MRLDKYLKISRLIKRRTVAKEIADQGRISINGKVAKSSSD-VSTNDELEV 49


>gi|108806879|ref|YP_650795.1| helicase [Yersinia pestis Antiqua]
 gi|108812966|ref|YP_648733.1| helicase [Yersinia pestis Nepal516]
 gi|170025113|ref|YP_001721618.1| helicase domain-containing protein [Yersinia pseudotuberculosis
           YPIII]
 gi|229894166|ref|ZP_04509352.1| putative ATP-dependent RNA helicase [Yersinia pestis Pestoides A]
 gi|229903400|ref|ZP_04518513.1| putative ATP-dependent RNA helicase [Yersinia pestis Nepal516]
 gi|108776614|gb|ABG19133.1| Helicase [Yersinia pestis Nepal516]
 gi|108778792|gb|ABG12850.1| helicase [Yersinia pestis Antiqua]
 gi|169751647|gb|ACA69165.1| helicase domain protein [Yersinia pseudotuberculosis YPIII]
 gi|229679170|gb|EEO75273.1| putative ATP-dependent RNA helicase [Yersinia pestis Nepal516]
 gi|229704051|gb|EEO91064.1| putative ATP-dependent RNA helicase [Yersinia pestis Pestoides A]
 gi|320015993|gb|ADV99564.1| putative ATP-dependent RNA helicase [Yersinia pestis biovar
           Medievalis str. Harbin 35]
          Length = 334

 Score = 42.9 bits (99), Expect = 0.070,   Method: Composition-based stats.
 Identities = 13/101 (12%), Positives = 29/101 (28%), Gaps = 2/101 (1%)

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL--SKQKKLATPVHRRNLAS 312
           V+    +   E L++     I+    +     K    +NG      ++            
Sbjct: 234 VDEHKLLRDIERLLKREIPRIALDGYEPDPSIKADPIQNGRQGRGAQRPGMGRGSSAGRP 293

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                        +   + + + +R P+ PS R   R   +
Sbjct: 294 QNGGGAAGRGDSRNSRPRSQADGQRRPAGPSSRGRSRNPGE 334


>gi|227514818|ref|ZP_03944867.1| ribosomal protein S4e [Lactobacillus fermentum ATCC 14931]
 gi|227086808|gb|EEI22120.1| ribosomal protein S4e [Lactobacillus fermentum ATCC 14931]
          Length = 262

 Score = 42.9 bits (99), Expect = 0.070,   Method: Composition-based stats.
 Identities = 16/65 (24%), Positives = 31/65 (47%), Gaps = 1/65 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKAERT 73
           R+  V+A +   SR   +++I + +V+VN   ++R    + S D I V  G  ++  E  
Sbjct: 186 RLDAVVAASFNYSRNRAKQLIERGQVRVNWEEIDRPDYELASRDLISVRHGGRIKVQEEL 245

Query: 74  RLWLY 78
               +
Sbjct: 246 GQNRH 250


>gi|184155056|ref|YP_001843396.1| hypothetical protein LAF_0580 [Lactobacillus fermentum IFO 3956]
 gi|183226400|dbj|BAG26916.1| conserved hypothetical protein [Lactobacillus fermentum IFO 3956]
          Length = 262

 Score = 42.9 bits (99), Expect = 0.070,   Method: Composition-based stats.
 Identities = 16/65 (24%), Positives = 31/65 (47%), Gaps = 1/65 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKAERT 73
           R+  V+A +   SR   +++I + +V+VN   ++R    + S D I V  G  ++  E  
Sbjct: 186 RLDAVVAASFNYSRNRAKQLIERGQVRVNWEEIDRPDYELASRDLISVRHGGRIKVQEEL 245

Query: 74  RLWLY 78
               +
Sbjct: 246 GQNRH 250


>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 = 42.9 bits (99), Expect = 0.070,   Method: Composition-based stats.
 Identities = 21/215 (9%), Positives = 57/215 (26%), Gaps = 33/215 (15%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--------------LRKAERTR 74
           R + + +   RV VN   + +    +   D IE+                  +   +   
Sbjct: 31  RFIRKAVRDGRVFVNKEKVIK-KHKLSQDDLIEIYMQEDEHQNIEPEDMNIEIVYEDNDI 89

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------------------ISVGRLDI 116
           + +  +P  +V         +     L                         I + +   
Sbjct: 90  IVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKNQF 149

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +   L    +     ++        ++    R +  + +++ +   K IV +        
Sbjct: 150 SHMRLASDMSKDRFRKIYIAVVHGSMKEKEGRINLPIYKEEESESIKRIVDERGQESITT 209

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +  +    + V + L  G+  +I+         
Sbjct: 210 YEVLEELSKGSVVRLELETGRTHQIRVHMSHLGHP 244


>gi|116749359|ref|YP_846046.1| pseudouridine synthase [Syntrophobacter fumaroxidans MPOB]
 gi|116698423|gb|ABK17611.1| pseudouridine synthase [Syntrophobacter fumaroxidans MPOB]
          Length = 304

 Score = 42.9 bits (99), Expect = 0.070,   Method: Composition-based stats.
 Identities = 32/232 (13%), Positives = 64/232 (27%), Gaps = 37/232 (15%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-------------EV 62
           ++++IAR  + S    E +I    V ++G +    A  +   + I             E+
Sbjct: 25  LARLIARYLLISEDRAEDLIDFGSVYIDGRVERNPARTLRGGEEIVVNWPRHGTQRHYEI 84

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           D   +   +   L  Y K  G+ +  +  D  + ++  L    +         +     L
Sbjct: 85  DPARILYRDAH-LLAYDKEAGVPSQQTPADAYNNLYAALIRFLAGEARASAPYVALHHRL 143

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL---------NLLKKGIVIQGICYG 173
                G +   L+    + L           D                 + I  +   Y 
Sbjct: 144 DRETSGVMVFALDRAVNRRLGESFQEKRVVKDYLAWVDGVPVLDRWTAVEDICRKDGRYR 203

Query: 174 DMQVTLDTQKGSNAWVTVGLR------------EGKNREIKKVFEFFNWKVN 213
                    K +   + V LR             G+  +I+         V 
Sbjct: 204 TCPQ--GRGKAARTLLRVLLRAGDRALIAARPVTGRTHQIRLHLAACGHPVI 253


>gi|81074820|gb|ABB55376.1| putative arginine/serine-rich protein-like [Solanum tuberosum]
          Length = 392

 Score = 42.9 bits (99), Expect = 0.070,   Method: Composition-based stats.
 Identities = 16/119 (13%), Positives = 33/119 (27%), Gaps = 1/119 (0%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +  K++  +      ++A     A   SS        N   +V  D    ++        
Sbjct: 176 IDGKVVHARFTLPERKKAASPPRAVATSSRRDAPRTDNAPVDVEKD-GPKRQQDLSPRRK 234

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                  +P+ RR        +     +            RR P+ P +R       ++
Sbjct: 235 PASPPRRSPIGRRGSPRRGPDSPVRRRANSPFRRGSPPPQRRRPASPMRRRSPSPPLRR 293



 Score = 40.9 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 11/118 (9%), Positives = 23/118 (19%), Gaps = 4/118 (3%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           L E+        A                                ++  +     S   +
Sbjct: 187 LPERKKAASPPRAVATSSRRDAPRTDNAPVDVEKDGPKRQQDLSPRRKPASPPRRSPIGR 246

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK----RSLRRTSAKK 354
             +P    +                    +R  +  R  S        R+  R S ++
Sbjct: 247 RGSPRRGPDSPVRRRANSPFRRGSPPPQRRRPASPMRRRSPSPPLRRHRTPPRGSPRR 304


>gi|309782859|ref|ZP_07677579.1| ribosomal protein S4 [Ralstonia sp. 5_7_47FAA]
 gi|308918283|gb|EFP63960.1| ribosomal protein S4 [Ralstonia sp. 5_7_47FAA]
          Length = 207

 Score = 42.9 bits (99), Expect = 0.071,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  L   +  + + D I +
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAILVNGQALNVPSAQIKTGDVIAI 146


>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 = 42.9 bits (99), Expect = 0.071,   Method: Composition-based stats.
 Identities = 37/245 (15%), Positives = 73/245 (29%), Gaps = 46/245 (18%)

Query: 12  TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             QR+   +AR      R  + R++    V+VNG     A   + S+D + +  V + + 
Sbjct: 19  EGQRLDNFLARHLKGVPRSHIHRIVRSGEVRVNGGRA-SADQKLQSSDQVRIPPVRVAQP 77

Query: 71  ERTR---------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV--GR 113
           +  R               L   +KP G+            +     +  +        R
Sbjct: 78  DAPRAAPALQFPVVFEDDFLLAINKPEGVAVHGGSGVSFGVIEALRAARPTAKFLELVHR 137

Query: 114 LDINTEGLLLLTNDGG-----LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           LD +T GLLL+           A + E  + +           +        L K ++  
Sbjct: 138 LDRDTSGLLLIAKKRSALTTLHAALRERHADKRYLALVAGLWTRGAVMIEAPLHKYLLAN 197

Query: 169 GICYGDMQVTLDTQKGSNAWVT---------------VGLRE-----GKNREIKKVFEFF 208
           G     ++V +   + S                    + L +     G+  +I+      
Sbjct: 198 GE--RRVRVDVQQGQESRTQFRSQEQFALPGLGPWGGLSLMQARLLTGRTHQIRVHLAHC 255

Query: 209 NWKVN 213
              + 
Sbjct: 256 GHPIV 260


>gi|302660531|ref|XP_003021944.1| hypothetical protein TRV_03930 [Trichophyton verrucosum HKI 0517]
 gi|291185865|gb|EFE41326.1| hypothetical protein TRV_03930 [Trichophyton verrucosum HKI 0517]
          Length = 509

 Score = 42.9 bits (99), Expect = 0.071,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 1/56 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+   I RA  AS  R+  + +    V VNG  ++     +   D  +VD   +  
Sbjct: 138 RLDVAIFRAMFASSTRQARQFVIHGGVTVNGKKMQYPGYLLNPGDMFQVDPERVMY 193


>gi|241664507|ref|YP_002982867.1| 30S ribosomal protein S4 [Ralstonia pickettii 12D]
 gi|240866534|gb|ACS64195.1| ribosomal protein S4 [Ralstonia pickettii 12D]
          Length = 207

 Score = 42.9 bits (99), Expect = 0.071,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  L   +  + + D I +
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAILVNGQALNVPSAQIKTGDVIAI 146


>gi|41410330|ref|NP_963166.1| 30S ribosomal protein S4 [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|118464319|ref|YP_883534.1| 30S ribosomal protein S4 [Mycobacterium avium 104]
 gi|254776831|ref|ZP_05218347.1| 30S ribosomal protein S4 [Mycobacterium avium subsp. avium ATCC
           25291]
 gi|61215639|sp|Q73S44|RS4_MYCPA RecName: Full=30S ribosomal protein S4
 gi|152112231|sp|A0QKU6|RS4_MYCA1 RecName: Full=30S ribosomal protein S4
 gi|41399164|gb|AAS06782.1| RpsD [Mycobacterium avium subsp. paratuberculosis K-10]
 gi|118165606|gb|ABK66503.1| ribosomal protein S4 [Mycobacterium avium 104]
          Length = 201

 Score = 42.9 bits (99), Expect = 0.071,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ RAG+A +RR   +++      VNG+ ++  +  V   D I+V    L      
Sbjct: 92  RLDNVVYRAGLARTRRMARQLVTHGHFTVNGVRVDVPSYRVSQYDIIDVREQSLNSVPFQ 151

Query: 74  R 74
            
Sbjct: 152 I 152


>gi|322418690|ref|YP_004197913.1| translation initiation factor IF-2 [Geobacter sp. M18]
 gi|320125077|gb|ADW12637.1| translation initiation factor IF-2 [Geobacter sp. M18]
          Length = 970

 Score = 42.9 bits (99), Expect = 0.071,   Method: Composition-based stats.
 Identities = 13/89 (14%), Positives = 20/89 (22%), Gaps = 1/89 (1%)

Query: 261 IYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGI 320
                T  R R     E+P    R  +    +     ++    P   R +          
Sbjct: 211 EPEKPTATRARILGRVEIPIPAQRPAERREYQRPAQGERPAPRPGMPRGVERPGTERPAP 270

Query: 321 HSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                   G+R    R        R  R 
Sbjct: 271 RP-GAGRPGERPAPGRPGERPTGPRPDRP 298



 Score = 40.9 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 9/115 (7%), Positives = 21/115 (18%), Gaps = 7/115 (6%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
              +L   ++ + A   +     +         P                + +     P 
Sbjct: 219 RARILGRVEIPIPAQRPAERREYQRPAQGERPAPRPGMPRGVERPGTERPAPRPGAGRPG 278

Query: 306 HRRNLASNVWMAKGIHSSF-------LSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            R           G                   +    R P+        + + K
Sbjct: 279 ERPAPGRPGERPTGPRPDRPAPLTPIEPPPLLDDRRKGRKPAPAGGADFGKNAKK 333


>gi|301616980|ref|XP_002937928.1| PREDICTED: hypothetical protein LOC100497221 [Xenopus (Silurana)
           tropicalis]
          Length = 1037

 Score = 42.9 bits (99), Expect = 0.072,   Method: Composition-based stats.
 Identities = 10/97 (10%), Positives = 22/97 (22%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
                 +S        +     P    R  +  + ++   ++ + A     R        
Sbjct: 68  ATPRASTSGPPPEAGTSGARRSPRVAERAAQTPTHRDPDDQEGRGAQTRSGRRRGDTAGA 127

Query: 317 AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +        S +G      R            R  A+
Sbjct: 128 SGWNGGRRGSATGPGAARGRSVRRRIDPEVRPREMAR 164



 Score = 37.5 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 11/102 (10%), Positives = 17/102 (16%), Gaps = 2/102 (1%)

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
               A                S    +           +    +        RR   +  
Sbjct: 68  ATPRASTSGPPPEAGTSGARRSPRVAERAAQTPTHRDPDDQEGRGAQTRSGRRRGDTAGA 127

Query: 315 WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL--RRTSAKK 354
               G      +  G       R    P  R     R S  +
Sbjct: 128 SGWNGGRRGSATGPGAARGRSVRRRIDPEVRPREMARDSPTR 169



 Score = 37.5 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 16/107 (14%), Positives = 27/107 (25%), Gaps = 4/107 (3%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV-- 305
                               V +R        D   +  + +  ++G  +          
Sbjct: 72  ASTSGPPPEAGTSGARRSPRVAERAAQTPTHRDPDDQEGRGAQTRSGRRRGDTAGASGWN 131

Query: 306 -HRRNLASNVWMAKGIHSSFLSDSGQREENHRR-SPSFPSKRSLRRT 350
             RR  A+    A+G       D   R     R SP+ P +     T
Sbjct: 132 GGRRGSATGPGAARGRSVRRRIDPEVRPREMARDSPTRPGQGIRNST 178


>gi|299783031|gb|ADJ41029.1| Ribosomal protein S4e [Lactobacillus fermentum CECT 5716]
          Length = 261

 Score = 42.9 bits (99), Expect = 0.072,   Method: Composition-based stats.
 Identities = 16/65 (24%), Positives = 31/65 (47%), Gaps = 1/65 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKAERT 73
           R+  V+A +   SR   +++I + +V+VN   ++R    + S D I V  G  ++  E  
Sbjct: 185 RLDAVVAASFNYSRNRAKQLIERGQVRVNWEEIDRPDYELASRDLISVRHGGRIKVQEEL 244

Query: 74  RLWLY 78
               +
Sbjct: 245 GQNRH 249


>gi|260663600|ref|ZP_05864489.1| RNA-binding S4 domain-containing protein [Lactobacillus fermentum
           28-3-CHN]
 gi|260551826|gb|EEX24941.1| RNA-binding S4 domain-containing protein [Lactobacillus fermentum
           28-3-CHN]
          Length = 261

 Score = 42.9 bits (99), Expect = 0.072,   Method: Composition-based stats.
 Identities = 16/65 (24%), Positives = 31/65 (47%), Gaps = 1/65 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKAERT 73
           R+  V+A +   SR   +++I + +V+VN   ++R    + S D I V  G  ++  E  
Sbjct: 185 RLDAVVAASFNYSRNRAKQLIERGQVRVNWEEIDRPDYELASRDLISVRHGGRIKVQEEL 244

Query: 74  RLWLY 78
               +
Sbjct: 245 GQNRH 249


>gi|229829399|ref|ZP_04455468.1| hypothetical protein GCWU000342_01489 [Shuttleworthia satelles DSM
           14600]
 gi|229791830|gb|EEP27944.1| hypothetical protein GCWU000342_01489 [Shuttleworthia satelles DSM
           14600]
          Length = 197

 Score = 42.9 bits (99), Expect = 0.072,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +RRE  +++  + V VNG  +   +  V + D +E+
Sbjct: 88  RLDNVVFRLGWARTRREARQIVDHKFVAVNGRKVNIPSYLVKAGDLVEI 136


>gi|254510000|ref|ZP_05122067.1| ribosomal protein S4 [Rhodobacteraceae bacterium KLH11]
 gi|221533711|gb|EEE36699.1| ribosomal protein S4 [Rhodobacteraceae bacterium KLH11]
          Length = 206

 Score = 42.9 bits (99), Expect = 0.072,   Method: Composition-based stats.
 Identities = 10/35 (28%), Positives = 14/35 (40%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
             + +    VKVNG  +   +  V   D IEV   
Sbjct: 112 ARQFVNHGHVKVNGKRVNIPSYRVKEGDVIEVRDK 146


>gi|109638462|ref|YP_656668.1| ORF13 [Ranid herpesvirus 1]
 gi|109138230|gb|ABG25707.1| ORF13 [Ranid herpesvirus 1]
          Length = 3149

 Score = 42.9 bits (99), Expect = 0.072,   Method: Composition-based stats.
 Identities = 15/105 (14%), Positives = 31/105 (29%), Gaps = 12/105 (11%)

Query: 262 YSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIH 321
                  R+ P        +  + ++ +S   G +K ++  +P   R  A          
Sbjct: 95  KVRSKTQRNSPTNNKAPAKERGKARRPASPPEGRNKARRSTSPTKERGRAKRSASPIKER 154

Query: 322 SSFLSDSG----QREENHRRSPSFPSKRSLR--------RTSAKK 354
                       + +     SP+    RS R        R+ A++
Sbjct: 155 GRTRRSPTPDNERSKPGGAVSPAKEGARSRRVDPLPTKDRSKARR 199



 Score = 40.5 bits (93), Expect = 0.40,   Method: Composition-based stats.
 Identities = 10/108 (9%), Positives = 29/108 (26%), Gaps = 3/108 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK---NGLSKQK 299
           ++  P   +            +           S  P       K S+      G +++ 
Sbjct: 101 QRNSPTNNKAPAKERGKARRPASPPEGRNKARRSTSPTKERGRAKRSASPIKERGRTRRS 160

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
                   +   +     +G  S  +     ++ +  R  + P+++  
Sbjct: 161 PTPDNERSKPGGAVSPAKEGARSRRVDPLPTKDRSKARRSASPTRKKA 208



 Score = 39.8 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 14/101 (13%), Positives = 35/101 (34%), Gaps = 5/101 (4%)

Query: 259 APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP-----VHRRNLASN 313
                +    R +    +  P+   + ++++S      + K+ A+P       RR+   +
Sbjct: 105 PTNNKAPAKERGKARRPASPPEGRNKARRSTSPTKERGRAKRSASPIKERGRTRRSPTPD 164

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              +K   +   +  G R       P+    ++ R  S  +
Sbjct: 165 NERSKPGGAVSPAKEGARSRRVDPLPTKDRSKARRSASPTR 205



 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 9/113 (7%), Positives = 23/113 (20%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R          + ++ +              +   + P +  R       +   S  +  
Sbjct: 34  RATSQECEARGSSIDSNPSHERRRGRHERERSRSRDRPRERARSPAKDKTRPRRSSSRSP 93

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                +    S             +         R      +  +  R  AK+
Sbjct: 94  LKVRSKTQRNSPTNNKAPAKERGKARRPASPPEGRNKARRSTSPTKERGRAKR 146


>gi|332261676|ref|XP_003279891.1| PREDICTED: voltage-dependent N-type calcium channel subunit
           alpha-1B, partial [Nomascus leucogenys]
          Length = 2179

 Score = 42.9 bits (99), Expect = 0.073,   Method: Composition-based stats.
 Identities = 17/112 (15%), Positives = 30/112 (26%), Gaps = 3/112 (2%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           GP   +      +AP          R     + P    + +  + +        +   P 
Sbjct: 762 GPVAGKARPEAAEAPEGVDPPRRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPR 821

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREEN---HRRSPSFPSKRSLRRTSAKK 354
             R+ +          S      G         R SP   ++R  RR  A +
Sbjct: 822 PHRSHSKEAAGPPEARSERGRGPGPEGGRRHHRRGSPEEAAEREPRRHRAHR 873



 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 13/125 (10%), Positives = 24/125 (19%), Gaps = 15/125 (12%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK---- 297
           R        ++     D     +       P    E P       K ++           
Sbjct: 783 RRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPRPHRSHSKEAAGPPEARSERGR 842

Query: 298 ---------QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                      +  +P            A        S      +  RR+      R+  
Sbjct: 843 GPGPEGGRRHHRRGSPEEAAEREPRRHRAH--RHQDPSKECAGTKGERRARHRGGPRAGP 900

Query: 349 RTSAK 353
           R +  
Sbjct: 901 REAES 905



 Score = 39.4 bits (90), Expect = 0.84,   Method: Composition-based stats.
 Identities = 15/132 (11%), Positives = 32/132 (24%), Gaps = 24/132 (18%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL---- 301
           G    E A+              RD+    +    D     K  S + G  +++      
Sbjct: 766 GKARPEAAEAPEGVDPPRRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPRPHRS 825

Query: 302 -----ATPVHRRN---------------LASNVWMAKGIHSSFLSDSGQREENHRRSPSF 341
                A P   R+                  +   A             ++ +   + + 
Sbjct: 826 HSKEAAGPPEARSERGRGPGPEGGRRHHRRGSPEEAAEREPRRHRAHRHQDPSKECAGTK 885

Query: 342 PSKRSLRRTSAK 353
             +R+  R   +
Sbjct: 886 GERRARHRGGPR 897



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 23/152 (15%), Positives = 43/152 (28%), Gaps = 20/152 (13%)

Query: 223 FQLGTL---LAGSTREVSKKI-LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPN-IISE 277
            +L  L         E+  +  LR     HL  + + +LD P+         R       
Sbjct: 709 LRLQNLRASCEALYSEMDPEERLRFATTRHLRPDMKTHLDRPLVVELGRDGARGPVAGKA 768

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
            P+     +     +     + K  TP       +    A+        +  +   +H +
Sbjct: 769 RPEAAEAPEGVDPPRRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPRPHRSHSK 828

Query: 338 -SPSFPSKRSL--------------RRTSAKK 354
            +   P  RS               RR S ++
Sbjct: 829 EAAGPPEARSERGRGPGPEGGRRHHRRGSPEE 860


>gi|256371242|ref|YP_003109066.1| ribosomal protein S4 [Acidimicrobium ferrooxidans DSM 10331]
 gi|256007826|gb|ACU53393.1| ribosomal protein S4 [Acidimicrobium ferrooxidans DSM 10331]
          Length = 208

 Score = 42.9 bits (99), Expect = 0.073,   Method: Composition-based stats.
 Identities = 5/40 (12%), Positives = 17/40 (42%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           SR +  +++    V V+G  ++  +  +     + ++   
Sbjct: 113 SRAQARQLVRHGHVLVDGQRVDIPSYRLRPGQVVTLNPKA 152


>gi|108798084|ref|YP_638281.1| 30S ribosomal protein S4 [Mycobacterium sp. MCS]
 gi|119867180|ref|YP_937132.1| 30S ribosomal protein S4 [Mycobacterium sp. KMS]
 gi|126433744|ref|YP_001069435.1| 30S ribosomal protein S4 [Mycobacterium sp. JLS]
 gi|123070558|sp|Q1BD09|RS4_MYCSS RecName: Full=30S ribosomal protein S4
 gi|152112233|sp|A3PVL7|RS4_MYCSJ RecName: Full=30S ribosomal protein S4
 gi|152112234|sp|A1UBY4|RS4_MYCSK RecName: Full=30S ribosomal protein S4
 gi|108768503|gb|ABG07225.1| SSU ribosomal protein S4P [Mycobacterium sp. MCS]
 gi|119693269|gb|ABL90342.1| SSU ribosomal protein S4P [Mycobacterium sp. KMS]
 gi|126233544|gb|ABN96944.1| SSU ribosomal protein S4P [Mycobacterium sp. JLS]
          Length = 201

 Score = 42.9 bits (99), Expect = 0.073,   Method: Composition-based stats.
 Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+  V+ RAG+A +RR   ++++     VNG+ ++  +  V   D I+V    L     
Sbjct: 92  RLDNVVYRAGLARTRRMARQLVSHGHFTVNGVKVDIPSYRVSQYDIIDVREKSLNTDPF 150


>gi|83748174|ref|ZP_00945201.1| SSU ribosomal protein S4P [Ralstonia solanacearum UW551]
 gi|207744551|ref|YP_002260943.1| 30s ribosomal protein s4 [Ralstonia solanacearum IPO1609]
 gi|83725142|gb|EAP72293.1| SSU ribosomal protein S4P [Ralstonia solanacearum UW551]
 gi|206595957|emb|CAQ62884.1| 30s ribosomal protein s4 [Ralstonia solanacearum IPO1609]
          Length = 207

 Score = 42.9 bits (99), Expect = 0.073,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  L   +  + S D + +
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAILVNGQALNVPSAQIKSGDVVAI 146


>gi|297260713|ref|XP_002798338.1| PREDICTED: hypothetical protein LOC100426833 [Macaca mulatta]
          Length = 368

 Score = 42.9 bits (99), Expect = 0.074,   Method: Composition-based stats.
 Identities = 16/127 (12%), Positives = 28/127 (22%), Gaps = 1/127 (0%)

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           L  G  + VSK  +    G      +              +                   
Sbjct: 15  LRVGLLKVVSKLGISNVPGRPPRARSPQKAAREGDQRGRRLPSPGRAHRPHEWKGAPGSS 74

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR-RSPSFPSKRS 346
                 G            +R+  +     +      L        + R  +P+ P   S
Sbjct: 75  RPPTCQGRRSPPLARARPGQRDGVAPGAEPRRQDPGILGPEPADPASPRFPAPAAPELGS 134

Query: 347 LRRTSAK 353
            RRT  +
Sbjct: 135 RRRTWPR 141



 Score = 36.3 bits (82), Expect = 7.7,   Method: Composition-based stats.
 Identities = 10/75 (13%), Positives = 19/75 (25%), Gaps = 1/75 (1%)

Query: 281 DFTRMKKNSSQKNGLSKQKKLAT-PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
                +  S QK      ++    P   R    + W      S   +  G+R     R+ 
Sbjct: 32  PGRPPRARSPQKAAREGDQRGRRLPSPGRAHRPHEWKGAPGSSRPPTCQGRRSPPLARAR 91

Query: 340 SFPSKRSLRRTSAKK 354
                        ++
Sbjct: 92  PGQRDGVAPGAEPRR 106


>gi|291320521|ref|YP_003515785.1| 30S ribosomal protein S4 [Mycoplasma agalactiae]
 gi|290752856|emb|CBH40831.1| 30S ribosomal protein S4 [Mycoplasma agalactiae]
          Length = 198

 Score = 42.9 bits (99), Expect = 0.074,   Method: Composition-based stats.
 Identities = 14/77 (18%), Positives = 31/77 (40%), Gaps = 1/77 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R   V+ RAG A+ RR+  +++A    ++NG   +  ++++   D I +        +  
Sbjct: 94  RFDNVVYRAGFATTRRQARQLVAHGHFQLNGKNADIPSMHISVGDVITLKAKTQNNNQVK 153

Query: 74  RLWLYHKPIGLVTTHSD 90
                      +T  + 
Sbjct: 154 AALESKPAAAWLTVKNF 170


>gi|148377824|ref|YP_001256700.1| 30S ribosomal protein S4 [Mycoplasma agalactiae PG2]
 gi|148291870|emb|CAL59261.1| 30S ribosomal protein S4 [Mycoplasma agalactiae PG2]
          Length = 198

 Score = 42.9 bits (99), Expect = 0.074,   Method: Composition-based stats.
 Identities = 14/77 (18%), Positives = 31/77 (40%), Gaps = 1/77 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R   V+ RAG A+ RR+  +++A    ++NG   +  ++++   D I +        +  
Sbjct: 94  RFDNVVYRAGFATTRRQARQLVAHGHFQLNGKNADIPSMHISVGDVITLKAKTQNNNQVK 153

Query: 74  RLWLYHKPIGLVTTHSD 90
                      +T  + 
Sbjct: 154 AALESKPAAAWLTVKNF 170


>gi|163859246|ref|YP_001633544.1| 30S ribosomal protein S4 [Bordetella petrii DSM 12804]
 gi|226697810|sp|A9IHR7|RS4_BORPD RecName: Full=30S ribosomal protein S4
 gi|163262974|emb|CAP45277.1| 30S ribosomal protein S4 [Bordetella petrii]
          Length = 207

 Score = 42.9 bits (99), Expect = 0.075,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + ++VNG   + A++ V + D I V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHRAIEVNGHTADIASLIVKAGDVITV 146


>gi|327295753|ref|XP_003232571.1| 30S ribosomal subunit S4 [Trichophyton rubrum CBS 118892]
 gi|326464882|gb|EGD90335.1| 30S ribosomal subunit S4 [Trichophyton rubrum CBS 118892]
          Length = 500

 Score = 42.9 bits (99), Expect = 0.076,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 1/56 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+   I RA  AS  R+  + +    V VNG  ++     +   D  +VD   +  
Sbjct: 125 RLDVAIFRAMFASSTRQARQFVIHGGVTVNGKKMQYPGYLLNPGDMFQVDPERVMY 180


>gi|307945603|ref|ZP_07660939.1| ribosomal protein S4 [Roseibium sp. TrichSKD4]
 gi|307771476|gb|EFO30701.1| ribosomal protein S4 [Roseibium sp. TrichSKD4]
          Length = 205

 Score = 42.9 bits (99), Expect = 0.076,   Method: Composition-based stats.
 Identities = 10/32 (31%), Positives = 14/32 (43%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             + I    +KVNG  +   +  V   D IEV
Sbjct: 112 ARQFINHGHIKVNGKRVNIPSYRVRPGDVIEV 143


>gi|55962840|emb|CAI17143.1| calcium channel, voltage-dependent, N type, alpha 1B subunit [Homo
           sapiens]
 gi|57209532|emb|CAI40686.1| calcium channel, voltage-dependent, N type, alpha 1B subunit [Homo
           sapiens]
          Length = 2338

 Score = 42.9 bits (99), Expect = 0.076,   Method: Composition-based stats.
 Identities = 17/112 (15%), Positives = 30/112 (26%), Gaps = 3/112 (2%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           GP   +      +AP          R     + P    + +  + +        +   P 
Sbjct: 829 GPVGGKARPEAAEAPEGVDPPRRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPR 888

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREEN---HRRSPSFPSKRSLRRTSAKK 354
             R+ +          S      G         R SP   ++R  RR  A +
Sbjct: 889 PHRSHSKEAAGPPEARSERGRGPGPEGGRRHHRRGSPEEAAEREPRRHRAHR 940



 Score = 42.5 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 13/125 (10%), Positives = 24/125 (19%), Gaps = 15/125 (12%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK---- 297
           R        ++     D     +       P    E P       K ++           
Sbjct: 850 RRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPRPHRSHSKEAAGPPEARSERGR 909

Query: 298 ---------QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                      +  +P            A        S      +  RR+      R+  
Sbjct: 910 GPGPEGGRRHHRRGSPEEAAEREPRRHRAH--RHQDPSKECAGAKGERRARHRGGPRAGP 967

Query: 349 RTSAK 353
           R +  
Sbjct: 968 REAES 972



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 23/152 (15%), Positives = 43/152 (28%), Gaps = 20/152 (13%)

Query: 223 FQLGTL---LAGSTREVSKKI-LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPN-IISE 277
            +L  L         E+  +  LR     HL  + + +LD P+         R       
Sbjct: 776 LRLQNLRASCEALYSEMDPEERLRFATTRHLRPDMKTHLDRPLVVELGRDGARGPVGGKA 835

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
            P+     +     +     + K  TP       +    A+        +  +   +H +
Sbjct: 836 RPEAAEAPEGVDPPRRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPRPHRSHSK 895

Query: 338 -SPSFPSKRSL--------------RRTSAKK 354
            +   P  RS               RR S ++
Sbjct: 896 EAAGPPEARSERGRGPGPEGGRRHHRRGSPEE 927


>gi|55962839|emb|CAI17142.1| calcium channel, voltage-dependent, N type, alpha 1B subunit [Homo
           sapiens]
 gi|57209534|emb|CAI40688.1| calcium channel, voltage-dependent, N type, alpha 1B subunit [Homo
           sapiens]
          Length = 2337

 Score = 42.9 bits (99), Expect = 0.076,   Method: Composition-based stats.
 Identities = 17/112 (15%), Positives = 30/112 (26%), Gaps = 3/112 (2%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           GP   +      +AP          R     + P    + +  + +        +   P 
Sbjct: 828 GPVGGKARPEAAEAPEGVDPPRRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPR 887

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREEN---HRRSPSFPSKRSLRRTSAKK 354
             R+ +          S      G         R SP   ++R  RR  A +
Sbjct: 888 PHRSHSKEAAGPPEARSERGRGPGPEGGRRHHRRGSPEEAAEREPRRHRAHR 939



 Score = 42.5 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 13/125 (10%), Positives = 24/125 (19%), Gaps = 15/125 (12%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK---- 297
           R        ++     D     +       P    E P       K ++           
Sbjct: 849 RRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPRPHRSHSKEAAGPPEARSERGR 908

Query: 298 ---------QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                      +  +P            A        S      +  RR+      R+  
Sbjct: 909 GPGPEGGRRHHRRGSPEEAAEREPRRHRAH--RHQDPSKECAGAKGERRARHRGGPRAGP 966

Query: 349 RTSAK 353
           R +  
Sbjct: 967 REAES 971



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 23/152 (15%), Positives = 43/152 (28%), Gaps = 20/152 (13%)

Query: 223 FQLGTL---LAGSTREVSKKI-LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPN-IISE 277
            +L  L         E+  +  LR     HL  + + +LD P+         R       
Sbjct: 775 LRLQNLRASCEALYSEMDPEERLRFATTRHLRPDMKTHLDRPLVVELGRDGARGPVGGKA 834

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
            P+     +     +     + K  TP       +    A+        +  +   +H +
Sbjct: 835 RPEAAEAPEGVDPPRRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPRPHRSHSK 894

Query: 338 -SPSFPSKRSL--------------RRTSAKK 354
            +   P  RS               RR S ++
Sbjct: 895 EAAGPPEARSERGRGPGPEGGRRHHRRGSPEE 926


>gi|4502523|ref|NP_000709.1| voltage-dependent N-type calcium channel subunit alpha-1B [Homo
           sapiens]
 gi|1705854|sp|Q00975|CAC1B_HUMAN RecName: Full=Voltage-dependent N-type calcium channel subunit
           alpha-1B; AltName: Full=Brain calcium channel III;
           Short=BIII; AltName: Full=Calcium channel, L type,
           alpha-1 polypeptide isoform 5; AltName:
           Full=Voltage-gated calcium channel subunit alpha Cav2.2
 gi|179758|gb|AAA51897.1| N-type calcium channel alpha-1 subunit [Homo sapiens]
 gi|55962841|emb|CAI17144.1| calcium channel, voltage-dependent, N type, alpha 1B subunit [Homo
           sapiens]
 gi|57209533|emb|CAI40687.1| calcium channel, voltage-dependent, N type, alpha 1B subunit [Homo
           sapiens]
          Length = 2339

 Score = 42.9 bits (99), Expect = 0.076,   Method: Composition-based stats.
 Identities = 17/112 (15%), Positives = 30/112 (26%), Gaps = 3/112 (2%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           GP   +      +AP          R     + P    + +  + +        +   P 
Sbjct: 828 GPVGGKARPEAAEAPEGVDPPRRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPR 887

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREEN---HRRSPSFPSKRSLRRTSAKK 354
             R+ +          S      G         R SP   ++R  RR  A +
Sbjct: 888 PHRSHSKEAAGPPEARSERGRGPGPEGGRRHHRRGSPEEAAEREPRRHRAHR 939



 Score = 42.5 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 13/125 (10%), Positives = 24/125 (19%), Gaps = 15/125 (12%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK---- 297
           R        ++     D     +       P    E P       K ++           
Sbjct: 849 RRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPRPHRSHSKEAAGPPEARSERGR 908

Query: 298 ---------QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                      +  +P            A        S      +  RR+      R+  
Sbjct: 909 GPGPEGGRRHHRRGSPEEAAEREPRRHRAH--RHQDPSKECAGAKGERRARHRGGPRAGP 966

Query: 349 RTSAK 353
           R +  
Sbjct: 967 REAES 971



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 23/152 (15%), Positives = 43/152 (28%), Gaps = 20/152 (13%)

Query: 223 FQLGTL---LAGSTREVSKKI-LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPN-IISE 277
            +L  L         E+  +  LR     HL  + + +LD P+         R       
Sbjct: 775 LRLQNLRASCEALYSEMDPEERLRFATTRHLRPDMKTHLDRPLVVELGRDGARGPVGGKA 834

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
            P+     +     +     + K  TP       +    A+        +  +   +H +
Sbjct: 835 RPEAAEAPEGVDPPRRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPRPHRSHSK 894

Query: 338 -SPSFPSKRSL--------------RRTSAKK 354
            +   P  RS               RR S ++
Sbjct: 895 EAAGPPEARSERGRGPGPEGGRRHHRRGSPEE 926


>gi|89096443|ref|ZP_01169336.1| ATP-dependent RNA helicase [Bacillus sp. NRRL B-14911]
 gi|89089297|gb|EAR68405.1| ATP-dependent RNA helicase [Bacillus sp. NRRL B-14911]
          Length = 543

 Score = 42.9 bits (99), Expect = 0.076,   Method: Composition-based stats.
 Identities = 23/154 (14%), Positives = 39/154 (25%), Gaps = 17/154 (11%)

Query: 216 IRI-SYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVN--------LDAPIYSSET 266
            RI   G      L      E  +  L+       +   +           D    SS  
Sbjct: 347 HRIGRTGRAGKDGLAVTFYAEKDEAALKAIEQELNIRLPKEESTATANTTADGEKSSSGD 406

Query: 267 LVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGI------ 320
             ++R +         +R +     +   S++ +      RRN +S    A G       
Sbjct: 407 KPKNRSDRDRRAGGAESRRRTGGRTEGRGSREVRSTRSGERRNRSSEGRRADGEIRSYTH 466

Query: 321 --HSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                    SG R        S   + + R    
Sbjct: 467 DERRENGRRSGDRRSLSDGRRSSGGRSAERNPRP 500


>gi|332833474|ref|XP_520396.3| PREDICTED: voltage-dependent N-type calcium channel subunit
           alpha-1B [Pan troglodytes]
          Length = 2322

 Score = 42.9 bits (99), Expect = 0.077,   Method: Composition-based stats.
 Identities = 17/112 (15%), Positives = 30/112 (26%), Gaps = 3/112 (2%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           GP   +      +AP          R     + P    + +  + +        +   P 
Sbjct: 817 GPVGGKARPEAAEAPEGVDPPRRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPR 876

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREEN---HRRSPSFPSKRSLRRTSAKK 354
             R+ +          S      G         R SP   ++R  RR  A +
Sbjct: 877 PHRSHSKEAAGPPEARSERGRGPGPEGGRRHHRRGSPEEAAEREPRRHRAHR 928



 Score = 42.5 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 13/125 (10%), Positives = 24/125 (19%), Gaps = 15/125 (12%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK---- 297
           R        ++     D     +       P    E P       K ++           
Sbjct: 838 RRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPRPHRSHSKEAAGPPEARSERGR 897

Query: 298 ---------QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                      +  +P            A        S      +  RR+      R+  
Sbjct: 898 GPGPEGGRRHHRRGSPEEAAEREPRRHRAH--RHQDPSKECAGAKGERRARHRGGPRAGP 955

Query: 349 RTSAK 353
           R +  
Sbjct: 956 REAES 960



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 23/152 (15%), Positives = 43/152 (28%), Gaps = 20/152 (13%)

Query: 223 FQLGTL---LAGSTREVSKKI-LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPN-IISE 277
            +L  L         E+  +  LR     HL  + + +LD P+         R       
Sbjct: 764 LRLQNLRASCEALYSEMDPEERLRFATTRHLRPDMKTHLDRPLVVELGRDGARGPVGGKA 823

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
            P+     +     +     + K  TP       +    A+        +  +   +H +
Sbjct: 824 RPEAAEAPEGVDPPRRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPRPHRSHSK 883

Query: 338 -SPSFPSKRSL--------------RRTSAKK 354
            +   P  RS               RR S ++
Sbjct: 884 EAAGPPEARSERGRGPGPEGGRRHHRRGSPEE 915


>gi|326472324|gb|EGD96333.1| 30S ribosomal subunit S4 [Trichophyton tonsurans CBS 112818]
          Length = 483

 Score = 42.9 bits (99), Expect = 0.077,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 1/56 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+   I RA  AS  R+  + +    V VNG  ++     +   D  +VD   +  
Sbjct: 125 RLDVAIFRAMFASSTRQARQFVIHGGVTVNGKKMQYPGYLLNPGDMFQVDPERVMY 180


>gi|304310039|ref|YP_003809637.1| 30S ribosomal protein S4 [gamma proteobacterium HdN1]
 gi|301795772|emb|CBL43971.1| 30S ribosomal protein S4 [gamma proteobacterium HdN1]
          Length = 206

 Score = 42.9 bits (99), Expect = 0.077,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R E  ++++ + + +NG  +   +  + + D + V
Sbjct: 97  RLDNVVFRMGFGATRAEARQLVSHKAILINGKTVNIPSYQLAAGDVVSV 145


>gi|326792579|ref|YP_004310400.1| ribosomal protein S4 [Clostridium lentocellum DSM 5427]
 gi|326543343|gb|ADZ85202.1| ribosomal protein S4 [Clostridium lentocellum DSM 5427]
          Length = 208

 Score = 42.9 bits (99), Expect = 0.077,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 17/36 (47%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           SR E  +++    + VNG  +   +  V   D IEV
Sbjct: 112 SRTEARQVVRHNLITVNGKRVNIPSYQVKVGDVIEV 147


>gi|157689416|gb|ABV65264.1| ribosomal protein S4 [Atuna racemosa]
          Length = 193

 Score = 42.9 bits (99), Expect = 0.077,   Method: Composition-based stats.
 Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 5/55 (9%)

Query: 14  QRVSKVIARAGIAS---RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
            R+  ++ R G+AS   R    +++  + + VNG +++  +      D I V   
Sbjct: 81  MRLDNILFRLGMASTIPR--ARQLVNHRHILVNGRIVDIPSYRCKPRDIITVKDE 133


>gi|154293126|ref|XP_001547113.1| hypothetical protein BC1G_14515 [Botryotinia fuckeliana B05.10]
 gi|150845660|gb|EDN20853.1| hypothetical protein BC1G_14515 [Botryotinia fuckeliana B05.10]
          Length = 423

 Score = 42.9 bits (99), Expect = 0.077,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 1/54 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+   I RA  AS  R+  + +   +VKVNG  +      +   D  +VD   +
Sbjct: 125 RLDTAIFRALFASSARQARQFVVHGKVKVNGKKMSYPGYLLNPGDMFQVDVERV 178


>gi|152988184|ref|YP_001345923.1| putative ATP-dependent RNA helicase [Pseudomonas aeruginosa PA7]
 gi|150963342|gb|ABR85367.1| probable ATP-dependent RNA helicase [Pseudomonas aeruginosa PA7]
          Length = 635

 Score = 42.9 bits (99), Expect = 0.078,   Method: Composition-based stats.
 Identities = 14/105 (13%), Positives = 24/105 (22%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +   P  +       +      +   RD+     E      +    ++   G    +K A
Sbjct: 378 QGFDPEAVLPEVAQPEPREAPQKQPRRDKERRSRERKPKEAQAPAENAAVAGQDGAEKPA 437

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
               RR   +      G           R     R P     R  
Sbjct: 438 GKRRRRGGKNKENREAGQAQQPRQSREARPAKPNRPPEIDGNRDP 482


>gi|31414574|dbj|BAC58076.2| large tegument protein [Cercopithecine herpesvirus 1]
          Length = 3326

 Score = 42.9 bits (99), Expect = 0.079,   Method: Composition-based stats.
 Identities = 10/112 (8%), Positives = 15/112 (13%), Gaps = 1/112 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            EQ  P            P           P      P                      
Sbjct: 399 DEQTRPAAGPRPPTPASRPPTPGAPPTPGAPPTPGAPPTPGAPPTPAGPTTASSEPPTPA 458

Query: 302 ATPVHRRNLAS-NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             P                      + +G+      R P+   +        
Sbjct: 459 GRPPTPAGRPPTPAGRPPTPAGRPPTPAGRPPTPAGRPPTPAGRPPTPAGRP 510



 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 4/79 (5%), Positives = 9/79 (11%), Gaps = 1/79 (1%)

Query: 276 SEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS-NVWMAKGIHSSFLSDSGQREEN 334
              P                        P                      + +G+    
Sbjct: 454 PPTPAGRPPTPAGRPPTPAGRPPTPAGRPPTPAGRPPTPAGRPPTPAGRPPTPAGRPPTP 513

Query: 335 HRRSPSFPSKRSLRRTSAK 353
              + S          +  
Sbjct: 514 ANPTASSEPPTPNPEGAPA 532



 Score = 37.9 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 6/89 (6%), Positives = 12/89 (13%), Gaps = 1/89 (1%)

Query: 261 IYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK-KLATPVHRRNLASNVWMAKG 319
                   R                           +       P               
Sbjct: 452 SEPPTPAGRPPTPAGRPPTPAGRPPTPAGRPPTPAGRPPTPAGRPPTPAGRPPTPAGRPP 511

Query: 320 IHSSFLSDSGQREENHRRSPSFPSKRSLR 348
             ++  + S     N   +P+  S     
Sbjct: 512 TPANPTASSEPPTPNPEGAPAPSSNEQPP 540


>gi|17547713|ref|NP_521115.1| 30S ribosomal protein S4 [Ralstonia solanacearum GMI1000]
 gi|26399428|sp|Q8XV37|RS4_RALSO RecName: Full=30S ribosomal protein S4
 gi|17430018|emb|CAD16703.1| probable 30s ribosomal protein s4 [Ralstonia solanacearum GMI1000]
          Length = 207

 Score = 42.9 bits (99), Expect = 0.079,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + + VNG  L   +  + S D + +
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAILVNGQALNVPSAQIKSGDVVAI 146


>gi|332161012|ref|YP_004297589.1| ATP-dependent RNA helicase RhlE [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|318604884|emb|CBY26382.1| ATP-dependent RNA helicase RhlE [Yersinia enterocolitica subsp.
           palearctica Y11]
 gi|325665242|gb|ADZ41886.1| ATP-dependent RNA helicase RhlE [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
          Length = 451

 Score = 42.9 bits (99), Expect = 0.079,   Method: Composition-based stats.
 Identities = 14/101 (13%), Positives = 30/101 (29%), Gaps = 2/101 (1%)

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL--SKQKKLATPVHRRNLAS 312
           V+    +   E L++     I+    +     K    +NG      ++            
Sbjct: 351 VDEHKLLRDIERLLKREIPRIALDGYEPDPSIKADPIQNGRQGRGAQRPGMGRGSSAGRP 410

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               A        +   + + + +R P+ PS R   R   +
Sbjct: 411 QNGGAAAGRGDSRTSRPRSQADGQRRPAGPSSRGRSRKPGE 451


>gi|302542821|ref|ZP_07295163.1| translation initiation factor IF-2 [Streptomyces hygroscopicus ATCC
           53653]
 gi|302460439|gb|EFL23532.1| translation initiation factor IF-2 [Streptomyces himastatinicus
           ATCC 53653]
          Length = 287

 Score = 42.9 bits (99), Expect = 0.079,   Method: Composition-based stats.
 Identities = 19/112 (16%), Positives = 32/112 (28%), Gaps = 3/112 (2%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                  A+V       ++       P           R K+ +       +      P 
Sbjct: 122 RRRPHSPAEVRPAGARQATALARPAPPQSHRAPGARDARPKRTAHPARPGRRPAAHHAPR 181

Query: 306 HRRNLASNVWMAKG-IHSSFLSDSGQREENHR--RSPSFPSKRSLRRTSAKK 354
           HRR+ A     A         + S  R   H+  R P  P+   +++  A K
Sbjct: 182 HRRSAAHRPGQAPHHARPHKPASSPARPGPHKPPRKPVDPAPDPVKKPPAAK 233



 Score = 40.2 bits (92), Expect = 0.51,   Method: Composition-based stats.
 Identities = 9/124 (7%), Positives = 20/124 (16%), Gaps = 1/124 (0%)

Query: 230 AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
               R    +       P   +  +           T    RP             +  +
Sbjct: 128 PAEVRPAGARQATALARPAPPQSHRAPGARDARPKRTAHPARPGRRPAAHHAPRHRRSAA 187

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
            +        +   P             +           +        P+ P      +
Sbjct: 188 HRPGQAPHHARPHKPASSPARPGPHKPPRKPVDPAPDPVKKPPAAKPGKPAEPGP-DRPQ 246

Query: 350 TSAK 353
              K
Sbjct: 247 NPGK 250



 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 8/107 (7%), Positives = 18/107 (16%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +        +A+    A                          +     +          
Sbjct: 149 QSHRAPGARDARPKRTAHPARPGRRPAAHHAPRHRRSAAHRPGQAPHHARPHKPASSPAR 208

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
              H+            +     +  G+  E     P  P K   + 
Sbjct: 209 PGPHKPPRKPVDPAPDPVKKPPAAKPGKPAEPGPDRPQNPGKGQAKP 255



 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 15/112 (13%), Positives = 24/112 (21%), Gaps = 3/112 (2%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP- 304
             H  E      D P         +     +       R     S +   ++  +     
Sbjct: 106 EDHDDEYDPYAQDGPDRRRPHSPAEVRPAGARQATALARPAPPQSHRAPGARDARPKRTA 165

Query: 305 -VHRRNLASNVWMAKGIHSSFLSDSGQREENHRR-SPSFPSKRSLRRTSAKK 354
              R         A     S     GQ   + R   P+    R       +K
Sbjct: 166 HPARPGRRPAAHHAPRHRRSAAHRPGQAPHHARPHKPASSPARPGPHKPPRK 217


>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 = 42.9 bits (99), Expect = 0.079,   Method: Composition-based stats.
 Identities = 28/230 (12%), Positives = 62/230 (26%), Gaps = 38/230 (16%)

Query: 22  RAGIASRREV-------ERM---IA-QQRVKVNGILLERAAVNVMSTDHIEVDGVP---- 66
            AG   R+         E++   I     + VNG  +   +  + + D +          
Sbjct: 11  HAGCCVRQAARGPMHLSEKLWRKIKWNGTITVNGSPVSSPSHRLEAGDRLVFRWEEKAAV 70

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTV-----FDNLPSIFSRVISVGR 113
                   L   +   L +      L+         + V     +         +  + R
Sbjct: 71  IPVHLPLSLLYEDEDLLVVDKPAGMLIHPTWSGARDTLVQAVGGYFRRTGQHCGIHPLYR 130

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV---DQDKLNLLKKGIVIQGI 170
           LD +T G+L++         L    +Q  R Y     G+         + + +       
Sbjct: 131 LDRDTTGVLMVAKSAFAKHALTRDHSQIYREYLAVCEGRWGIPQGRIEHPIGRVAEGVDR 190

Query: 171 CY-----GDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                       +  +  +      + + L  G+  +I+  F      + 
Sbjct: 191 WTVRPDGRPAVTEYRILEENQEWTVLKIHLLTGRTHQIRVHFAHEGHPLV 240


>gi|260436174|ref|ZP_05790144.1| translation initiation factor IF-2 [Synechococcus sp. WH 8109]
 gi|260414048|gb|EEX07344.1| translation initiation factor IF-2 [Synechococcus sp. WH 8109]
          Length = 1117

 Score = 42.9 bits (99), Expect = 0.079,   Method: Composition-based stats.
 Identities = 12/118 (10%), Positives = 25/118 (21%), Gaps = 5/118 (4%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRD-----RPNIISEVPDDFTRMKKNSSQ 291
             +I+R           +        +            +P           + +   S+
Sbjct: 233 KPQIIRAGAPSRPGAPTRAGAPTKPGAPSRPTPRPELVGKPVPRRPAGTGVPQRQGGPSR 292

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
               ++Q +   P    N    V        S              +P  P   +  R
Sbjct: 293 PGSPTRQGRPGMPPRSGNTLELVGKPIRRDGSSTGSGRPGAPTRPGAPGRPGMPAGMR 350



 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 8/113 (7%), Positives = 20/113 (17%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           + +L       A+     P  +            S       + +         +  +  
Sbjct: 187 KPELVSKPKSAAKPTAPTPRPTPARPAPRPAGAGSPARPAPGQGQPKPQIIRAGAPSRPG 246

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           A                      +     R       P      S   +  ++
Sbjct: 247 APTRAGAPTKPGAPSRPTPRPELVGKPVPRRPAGTGVPQRQGGPSRPGSPTRQ 299



 Score = 37.9 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 15/106 (14%), Positives = 23/106 (21%), Gaps = 7/106 (6%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL---ATPVHRRNL 310
                      +   +         P   TR    +          +      PV RR  
Sbjct: 220 GSPARPAPGQGQPKPQIIRAGAPSRPGAPTRAGAPTKPGAPSRPTPRPELVGKPVPRRPA 279

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFP----SKRSLRRTSA 352
            + V   +G  S   S + Q                 K   R  S+
Sbjct: 280 GTGVPQRQGGPSRPGSPTRQGRPGMPPRSGNTLELVGKPIRRDGSS 325


>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 = 42.9 bits (99), Expect = 0.079,   Method: Composition-based stats.
 Identities = 22/216 (10%), Positives = 53/216 (24%), Gaps = 31/216 (14%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------------DGVPLRKAERTRL 75
           ++V   +  Q V VNG ++ +    +   D + +             D + +   +   L
Sbjct: 27  KQVRTWLKHQAVVVNGRVVTQFNHPLKPGDIVAIRSDRFAVPGTVVGDDIRICFEDAALL 86

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE---------------- 119
            +   P  L         ++  F     +    +                          
Sbjct: 87  VIDKPPDLLTIASEAEQEKTVYFQLTEYLRGNDVHSRERVWIVHRLDRETSGIMVFAKTP 146

Query: 120 --GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
               LL T      +  +      L   +  F   +D+     +          +     
Sbjct: 147 QAKGLLQTGWDKAEKRYQAVIEGSLPNDKGTFRSYLDETDPFRVISVPRTPTTRHAVTHY 206

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +  +      V + L  G+  +I+         + 
Sbjct: 207 RVLKRGKGRTLVELTLETGRRHQIRVHLADAGCPIV 242


>gi|34541515|ref|NP_905994.1| 30S ribosomal protein S4 [Porphyromonas gingivalis W83]
 gi|188995706|ref|YP_001929958.1| 30S ribosomal protein S4 [Porphyromonas gingivalis ATCC 33277]
 gi|41017819|sp|Q7MTN9|RS4_PORGI RecName: Full=30S ribosomal protein S4
 gi|226699103|sp|B2RLW6|RS4_PORG3 RecName: Full=30S ribosomal protein S4
 gi|34397832|gb|AAQ66893.1| ribosomal protein S4 [Porphyromonas gingivalis W83]
 gi|188595386|dbj|BAG34361.1| 30S ribosomal protein S4 [Porphyromonas gingivalis ATCC 33277]
          Length = 201

 Score = 42.9 bits (99), Expect = 0.079,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA +R    ++++ + + V+G ++   + +V     I V
Sbjct: 93  RLDNVVFRLGIAPTRSAARQLVSHRHITVDGSVVNIPSYSVKPGQVIGV 141


>gi|78213597|ref|YP_382376.1| translation initiation factor IF-2 [Synechococcus sp. CC9605]
 gi|123729668|sp|Q3AHW1|IF2_SYNSC RecName: Full=Translation initiation factor IF-2
 gi|78198056|gb|ABB35821.1| translation initiation factor IF-2 [Synechococcus sp. CC9605]
          Length = 1104

 Score = 42.9 bits (99), Expect = 0.081,   Method: Composition-based stats.
 Identities = 13/118 (11%), Positives = 26/118 (22%), Gaps = 5/118 (4%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRD-----RPNIISEVPDDFTRMKKNSSQ 291
             +I+R           +    A   +            +P           + +   S+
Sbjct: 220 KPQIIRSGAPSRPGAPTRAGAPAKPGAPSRPTPRPELVGKPVPRRPAGTGVPQRQGGPSR 279

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
               ++Q +   P    N    V        S              +P  P   +  R
Sbjct: 280 PGAPTRQGRPGMPPRSGNTLELVGKPIRRDGSTTGSGRPGAPTRPGAPGRPGMPAGMR 337



 Score = 37.5 bits (85), Expect = 2.8,   Method: Composition-based stats.
 Identities = 14/105 (13%), Positives = 23/105 (21%), Gaps = 7/105 (6%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL---ATPVHRRNL 310
                      +   +   +     P   TR    +          +      PV RR  
Sbjct: 207 GSPARPTPGQGQPKPQIIRSGAPSRPGAPTRAGAPAKPGAPSRPTPRPELVGKPVPRRPA 266

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFP----SKRSLRRTS 351
            + V   +G  S   + + Q                 K   R  S
Sbjct: 267 GTGVPQRQGGPSRPGAPTRQGRPGMPPRSGNTLELVGKPIRRDGS 311



 Score = 36.3 bits (82), Expect = 7.4,   Method: Composition-based stats.
 Identities = 10/111 (9%), Positives = 18/111 (16%), Gaps = 2/111 (1%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                 +A     AP               +  P   T  +     +   S         
Sbjct: 176 KLVSKPKATAKPTAPTPRPTPARPTPRPAGAGSPARPTPGQGQPKPQIIRSGAPSRPGAP 235

Query: 306 HRRNLASNVWMA--KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            R    +              +     R       P      S      ++
Sbjct: 236 TRAGAPAKPGAPSRPTPRPELVGKPVPRRPAGTGVPQRQGGPSRPGAPTRQ 286


>gi|90101684|sp|Q3S664|RS4_CORAM RecName: Full=30S ribosomal protein S4
 gi|73913590|gb|AAZ91711.1| 30S Ribosomal protein S4 [Corynebacterium stationis]
          Length = 201

 Score = 42.9 bits (99), Expect = 0.081,   Method: Composition-based stats.
 Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  V+ RAG+A +RR+  ++++     VNG      +  V   D I
Sbjct: 92  RLDNVVYRAGLARTRRQARQLVSHGHFTVNGKKTNVPSYRVSQYDII 138


>gi|315274591|ref|ZP_07869465.1| S4 domain-containing protein [Listeria marthii FSL S4-120]
 gi|313615780|gb|EFR89034.1| S4 domain-containing protein [Listeria marthii FSL S4-120]
          Length = 77

 Score = 42.9 bits (99), Expect = 0.081,   Method: Composition-based stats.
 Identities = 15/78 (19%), Positives = 28/78 (35%), Gaps = 4/78 (5%)

Query: 7  VQENFTPQRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVD 63
          + +  T  R+ K +  + +  RR   + +  + R+ VNG+  +    NV S D   I   
Sbjct: 1  MDKMATTMRLDKYLKVSRLIKRRTVAKEVAEKGRIAVNGVTAK-PGTNVKSGDELVIRFG 59

Query: 64 GVPLRKAERTRLWLYHKP 81
             +            K 
Sbjct: 60 PKIVTAKIERLEENAKKE 77


>gi|312622072|ref|YP_004023685.1| 30S ribosomal protein S4 [Caldicellulosiruptor kronotskyensis 2002]
 gi|312202539|gb|ADQ45866.1| ribosomal protein S4 [Caldicellulosiruptor kronotskyensis 2002]
          Length = 208

 Score = 42.9 bits (99), Expect = 0.081,   Method: Composition-based stats.
 Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+  V+ R G AS R E   +++    KVNG  +   +  V   D IEVD
Sbjct: 99  RLDNVVYRLGFASSRGEARLLVSHAHFKVNGRTVNIPSYLVKVGDVIEVD 148


>gi|300361435|ref|ZP_07057612.1| 30S ribosomal protein S4 [Lactobacillus gasseri JV-V03]
 gi|300354054|gb|EFJ69925.1| 30S ribosomal protein S4 [Lactobacillus gasseri JV-V03]
          Length = 208

 Score = 42.9 bits (99), Expect = 0.081,   Method: Composition-based stats.
 Identities = 10/52 (19%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  ++ R G+AS R +  +++    + V+G  ++  +  V     I +   
Sbjct: 99  RLDNIVYRLGLASTREQARQLVNHGHILVDGKRVDIPSYEVKVGQEISLRDK 150


>gi|242309344|ref|ZP_04808499.1| 30S ribosomal protein S4 [Helicobacter pullorum MIT 98-5489]
 gi|239523915|gb|EEQ63781.1| 30S ribosomal protein S4 [Helicobacter pullorum MIT 98-5489]
          Length = 208

 Score = 42.9 bits (99), Expect = 0.081,   Method: Composition-based stats.
 Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 1/68 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G A+ RR   +++    + V+G  L   +  V +   IE+     +  +  
Sbjct: 99  RLDNVVYRMGFATTRRFARQLVVHGHILVDGKRLNIPSAFVNAGQKIEICEKTKKNPQIQ 158

Query: 74  RLWLYHKP 81
           R     K 
Sbjct: 159 RAIELTKQ 166


>gi|82400144|gb|ABB72811.1| putative arginine/serine-rich protein [Solanum tuberosum]
          Length = 392

 Score = 42.9 bits (99), Expect = 0.081,   Method: Composition-based stats.
 Identities = 16/119 (13%), Positives = 33/119 (27%), Gaps = 1/119 (0%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +  K++  +      ++A     A   SS        N   +V  D    ++        
Sbjct: 176 IDGKVVHARFTLPERKKAASPPRAVATSSRRDAPRTDNAPVDVEKD-GPKRQQDLSPRRK 234

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                  +P+ RR        +     +            RR P+ P +R       ++
Sbjct: 235 PASPPRRSPIGRRGSPRRGPDSPVRRRANSPFRRGSPPPQRRRPASPMRRRSPSPPLRR 293



 Score = 40.5 bits (93), Expect = 0.35,   Method: Composition-based stats.
 Identities = 11/118 (9%), Positives = 23/118 (19%), Gaps = 4/118 (3%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           L E+        A                                ++  +     S   +
Sbjct: 187 LPERKKAASPPRAVATSSRRDAPRTDNAPVDVEKDGPKRQQDLSPRRKPASPPRRSPIGR 246

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK----RSLRRTSAKK 354
             +P    +                    +R  +  R  S        R+  R S ++
Sbjct: 247 RGSPRRGPDSPVRRRANSPFRRGSPPPQRRRPASPMRRRSPSPPLRRHRTPPRGSPRR 304



 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 13/101 (12%), Positives = 24/101 (23%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R    P  +E+        +                      R   +  ++   S  ++ 
Sbjct: 210 RTDNAPVDVEKDGPKRQQDLSPRRKPASPPRRSPIGRRGSPRRGPDSPVRRRANSPFRRG 269

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
           + P  RR  AS +             +  R    R   S  
Sbjct: 270 SPPPQRRRPASPMRRRSPSPPLRRHRTPPRGSPRRIRGSPG 310


>gi|115495587|ref|NP_001069025.1| serine/threonine-protein kinase PRP4 homolog [Bos taurus]
 gi|122132413|sp|Q08DZ2|PRP4B_BOVIN RecName: Full=Serine/threonine-protein kinase PRP4 homolog;
           AltName: Full=PRP4 pre-mRNA-processing factor 4 homolog
 gi|115305048|gb|AAI23500.1| PRP4 pre-mRNA processing factor 4 homolog B (yeast) [Bos taurus]
 gi|296473980|gb|DAA16095.1| serine/threonine-protein kinase PRP4 homolog [Bos taurus]
          Length = 1008

 Score = 42.9 bits (99), Expect = 0.081,   Method: Composition-based stats.
 Identities = 14/107 (13%), Positives = 30/107 (28%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
              + ++++                     S  P D     K+   ++   K K+     
Sbjct: 262 KAKVEDKSKAKDRKKSPVINESRSRDRGKKSRSPVDLRGKSKDRRSRSKERKSKRPEADK 321

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            ++ + S    A     +            RRS S   +   RR+ +
Sbjct: 322 EKKPVKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKQRDKSRRSRS 368



 Score = 39.4 bits (90), Expect = 0.87,   Method: Composition-based stats.
 Identities = 13/113 (11%), Positives = 36/113 (31%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +++    ++ E++         S   +R +         +    +  + ++    K    
Sbjct: 272 KDRKKSPVINESRSRDRGKKSRSPVDLRGKSKDRRSRSKERKSKRPEADKEKKPVKSPSK 331

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                + N + +    +      LS   + +    RSP    +RS +  S  +
Sbjct: 332 DASSGKENRSPSRRPGRSPKRRSLSPKQRDKSRRSRSPLVNDRRSKQSKSPSR 384



 Score = 37.1 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 12/117 (10%), Positives = 34/117 (29%), Gaps = 4/117 (3%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +E++G                 ++   +      S   D   + +     +     ++  
Sbjct: 249 QEKVGKARSPVDDKAKVEDKSKAKDRKKSPVINESRSRDRGKKSRSPVDLRGKSKDRRSR 308

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR----SLRRTSAKK 354
           +     +   ++         S  + SG+   +  R P    KR      +R  +++
Sbjct: 309 SKERKSKRPEADKEKKPVKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKQRDKSRR 365


>gi|269118644|ref|YP_003306821.1| RNA-binding S4 domain protein [Sebaldella termitidis ATCC 33386]
 gi|268612522|gb|ACZ06890.1| RNA-binding S4 domain protein [Sebaldella termitidis ATCC 33386]
          Length = 70

 Score = 42.9 bits (99), Expect = 0.082,   Method: Composition-based stats.
 Identities = 12/40 (30%), Positives = 19/40 (47%)

Query: 30 EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
          E    I +  V+VNG   +R    +   D IE+DG  ++ 
Sbjct: 28 EARYHILEGNVRVNGETEKRRGKKIYENDIIELDGEKIKI 67


>gi|227903170|ref|ZP_04020975.1| S4 RNA-binding domain protein [Lactobacillus acidophilus ATCC
          4796]
 gi|227868975|gb|EEJ76396.1| S4 RNA-binding domain protein [Lactobacillus acidophilus ATCC
          4796]
          Length = 92

 Score = 42.9 bits (99), Expect = 0.082,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR   + M  Q R+KVNG +++  + +V   D IE+
Sbjct: 13 MRIDKFLKVSRLVKRRTVAKEMADQGRIKVNGRVVKS-SYDVKIDDIIEI 61


>gi|301620539|ref|XP_002939631.1| PREDICTED: hypothetical protein LOC100485640 [Xenopus (Silurana)
           tropicalis]
          Length = 1037

 Score = 42.9 bits (99), Expect = 0.083,   Method: Composition-based stats.
 Identities = 10/97 (10%), Positives = 22/97 (22%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
                 +S        +     P    R  +  + ++   ++ + A     R        
Sbjct: 68  ATPRASTSGPPPEAGTSGARRSPRVAERAAQTPTHRDPDDQEGRGAQTRSGRRRGDTAGA 127

Query: 317 AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +        S +G      R            R  A+
Sbjct: 128 SGWNGGRRGSATGPGAARGRSVRRRIDPEVRPREMAR 164



 Score = 37.5 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 11/102 (10%), Positives = 17/102 (16%), Gaps = 2/102 (1%)

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
               A                S    +           +    +        RR   +  
Sbjct: 68  ATPRASTSGPPPEAGTSGARRSPRVAERAAQTPTHRDPDDQEGRGAQTRSGRRRGDTAGA 127

Query: 315 WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL--RRTSAKK 354
               G      +  G       R    P  R     R S  +
Sbjct: 128 SGWNGGRRGSATGPGAARGRSVRRRIDPEVRPREMARDSPTR 169



 Score = 37.1 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 16/107 (14%), Positives = 27/107 (25%), Gaps = 4/107 (3%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV-- 305
                               V +R        D   +  + +  ++G  +          
Sbjct: 72  ASTSGPPPEAGTSGARRSPRVAERAAQTPTHRDPDDQEGRGAQTRSGRRRGDTAGASGWN 131

Query: 306 -HRRNLASNVWMAKGIHSSFLSDSGQREENHRR-SPSFPSKRSLRRT 350
             RR  A+    A+G       D   R     R SP+ P +     T
Sbjct: 132 GGRRGSATGPGAARGRSVRRRIDPEVRPREMARDSPTRPGQGIRNST 178


>gi|227487075|ref|ZP_03917391.1| ribosomal protein S4 [Corynebacterium glucuronolyticum ATCC 51867]
 gi|227093149|gb|EEI28461.1| ribosomal protein S4 [Corynebacterium glucuronolyticum ATCC 51867]
          Length = 201

 Score = 42.9 bits (99), Expect = 0.084,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI RAG+A +RR+  +++      VNG+     +  V   D I+V
Sbjct: 92  RLDNVIYRAGLARTRRQARQLVTHGHFLVNGVKTNIPSFQVSQYDIIDV 140


>gi|317503955|ref|ZP_07961963.1| 30S ribosomal protein S4 [Prevotella salivae DSM 15606]
 gi|315664981|gb|EFV04640.1| 30S ribosomal protein S4 [Prevotella salivae DSM 15606]
          Length = 201

 Score = 42.9 bits (99), Expect = 0.085,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA +R    +++  + + V+G ++   +  V     + V
Sbjct: 93  RLDNVVYRLGIAPTRAAARQLVGHKHITVDGKVVNIPSFAVKPGMVVAV 141


>gi|302526975|ref|ZP_07279317.1| predicted protein [Streptomyces sp. AA4]
 gi|302435870|gb|EFL07686.1| predicted protein [Streptomyces sp. AA4]
          Length = 958

 Score = 42.9 bits (99), Expect = 0.085,   Method: Composition-based stats.
 Identities = 13/95 (13%), Positives = 18/95 (18%)

Query: 259 APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAK 318
                               P            + G   Q +       R         +
Sbjct: 174 QRDRGDRAPGTREHRRTRRGPGRIRPHPDRRVGRRGPEAQPRGGAVPGPRRRNGAARTGR 233

Query: 319 GIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                 L   G R    RR P+  S R     S +
Sbjct: 234 AAPRDGLPGRGSRGVAARRRPAGRSARGGGGGSDR 268



 Score = 40.9 bits (94), Expect = 0.26,   Method: Composition-based stats.
 Identities = 11/104 (10%), Positives = 18/104 (17%), Gaps = 1/104 (0%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                        +                   TR  + + +  G  +         R  
Sbjct: 151 RPRTAGRGRPRRRARPGRPGAEGQRDRGDRAPGTREHRRTRRGPGRIRPHPDRRVGRRGP 210

Query: 310 LASNVWMA-KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            A     A  G      +    R       P   S+    R   
Sbjct: 211 EAQPRGGAVPGPRRRNGAARTGRAAPRDGLPGRGSRGVAARRRP 254


>gi|55962838|emb|CAI17141.1| calcium channel, voltage-dependent, N type, alpha 1B subunit [Homo
           sapiens]
 gi|57209531|emb|CAI40685.1| calcium channel, voltage-dependent, N type, alpha 1B subunit [Homo
           sapiens]
          Length = 2237

 Score = 42.9 bits (99), Expect = 0.085,   Method: Composition-based stats.
 Identities = 17/112 (15%), Positives = 30/112 (26%), Gaps = 3/112 (2%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           GP   +      +AP          R     + P    + +  + +        +   P 
Sbjct: 828 GPVGGKARPEAAEAPEGVDPPRRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPR 887

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREEN---HRRSPSFPSKRSLRRTSAKK 354
             R+ +          S      G         R SP   ++R  RR  A +
Sbjct: 888 PHRSHSKEAAGPPEARSERGRGPGPEGGRRHHRRGSPEEAAEREPRRHRAHR 939



 Score = 42.5 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 13/125 (10%), Positives = 24/125 (19%), Gaps = 15/125 (12%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK---- 297
           R        ++     D     +       P    E P       K ++           
Sbjct: 849 RRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPRPHRSHSKEAAGPPEARSERGR 908

Query: 298 ---------QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                      +  +P            A        S      +  RR+      R+  
Sbjct: 909 GPGPEGGRRHHRRGSPEEAAEREPRRHRAH--RHQDPSKECAGAKGERRARHRGGPRAGP 966

Query: 349 RTSAK 353
           R +  
Sbjct: 967 REAES 971



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 23/152 (15%), Positives = 43/152 (28%), Gaps = 20/152 (13%)

Query: 223 FQLGTL---LAGSTREVSKKI-LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPN-IISE 277
            +L  L         E+  +  LR     HL  + + +LD P+         R       
Sbjct: 775 LRLQNLRASCEALYSEMDPEERLRFATTRHLRPDMKTHLDRPLVVELGRDGARGPVGGKA 834

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
            P+     +     +     + K  TP       +    A+        +  +   +H +
Sbjct: 835 RPEAAEAPEGVDPPRRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPRPHRSHSK 894

Query: 338 -SPSFPSKRSL--------------RRTSAKK 354
            +   P  RS               RR S ++
Sbjct: 895 EAAGPPEARSERGRGPGPEGGRRHHRRGSPEE 926


>gi|111019055|ref|YP_702027.1| hypothetical protein RHA1_ro02062 [Rhodococcus jostii RHA1]
 gi|110818585|gb|ABG93869.1| conserved hypothetical protein [Rhodococcus jostii RHA1]
          Length = 497

 Score = 42.9 bits (99), Expect = 0.085,   Method: Composition-based stats.
 Identities = 16/106 (15%), Positives = 26/106 (24%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                  +          +   R R    +   D   R         G  +  +    + 
Sbjct: 39  ERHPGPVRREARRATRPRQGAGRGRTPDSAHPGDPPARRPSRRLAVRGARRGHRATPALP 98

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           RR       +  G  S   + +G R    R  P+    R  RR   
Sbjct: 99  RRRRRRRGRVPAGTRSPRQARAGVRPAVRRGRPARTCARGARRGRH 144


>gi|179760|gb|AAA51898.1| N-type calcium channel alpha-1 subunit [Homo sapiens]
          Length = 2237

 Score = 42.9 bits (99), Expect = 0.085,   Method: Composition-based stats.
 Identities = 17/112 (15%), Positives = 30/112 (26%), Gaps = 3/112 (2%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           GP   +      +AP          R     + P    + +  + +        +   P 
Sbjct: 828 GPVGGKARPEAAEAPEGVDPPRRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPR 887

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREEN---HRRSPSFPSKRSLRRTSAKK 354
             R+ +          S      G         R SP   ++R  RR  A +
Sbjct: 888 PHRSHSKEAAGPPEARSERGRGPGPEGGRRHHRRGSPEEAAEREPRRHRAHR 939



 Score = 42.5 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 13/125 (10%), Positives = 24/125 (19%), Gaps = 15/125 (12%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK---- 297
           R        ++     D     +       P    E P       K ++           
Sbjct: 849 RRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPRPHRSHSKEAAGPPEARSERGR 908

Query: 298 ---------QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                      +  +P            A        S      +  RR+      R+  
Sbjct: 909 GPGPEGGRRHHRRGSPEEAAEREPRRHRAH--RHQDPSKECAGAKGERRARHRGGPRAGP 966

Query: 349 RTSAK 353
           R +  
Sbjct: 967 REAES 971



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 23/152 (15%), Positives = 43/152 (28%), Gaps = 20/152 (13%)

Query: 223 FQLGTL---LAGSTREVSKKI-LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPN-IISE 277
            +L  L         E+  +  LR     HL  + + +LD P+         R       
Sbjct: 775 LRLQNLRASCEALYSEMDPEERLRFATTRHLRPDMKTHLDRPLVVELGRDGARGPVGGKA 834

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
            P+     +     +     + K  TP       +    A+        +  +   +H +
Sbjct: 835 RPEAAEAPEGVDPPRRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPRPHRSHSK 894

Query: 338 -SPSFPSKRSL--------------RRTSAKK 354
            +   P  RS               RR S ++
Sbjct: 895 EAAGPPEARSERGRGPGPEGGRRHHRRGSPEE 926


>gi|313611251|gb|EFR86030.1| S4 domain-containing protein [Listeria monocytogenes FSL F2-208]
          Length = 95

 Score = 42.9 bits (99), Expect = 0.086,   Method: Composition-based stats.
 Identities = 15/85 (17%), Positives = 28/85 (32%), Gaps = 4/85 (4%)

Query: 7  VQENFTPQRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVD 63
          + +  T  R+ K +  + +  RR   + +  + R+ VNG+  +    NV S D   I   
Sbjct: 1  MDKMATTMRLDKYLKVSRLIKRRTVAKEVAEKGRIAVNGVTAK-PGTNVKSGDELVIRFG 59

Query: 64 GVPLRKAERTRLWLYHKPIGLVTTH 88
             +            K        
Sbjct: 60 PKIVTAKIERLEENAKKEQATEMYT 84


>gi|312140890|ref|YP_004008226.1| 30S ribosomal protein s4 rpsd [Rhodococcus equi 103S]
 gi|325675472|ref|ZP_08155156.1| 30S ribosomal protein S4 [Rhodococcus equi ATCC 33707]
 gi|311890229|emb|CBH49547.1| 30S ribosomal protein S4 RpsD [Rhodococcus equi 103S]
 gi|325553443|gb|EGD23121.1| 30S ribosomal protein S4 [Rhodococcus equi ATCC 33707]
          Length = 201

 Score = 42.9 bits (99), Expect = 0.086,   Method: Composition-based stats.
 Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ RAG+A +RR+  +++    + VN   ++  +  V   D I+V    L      
Sbjct: 92  RLDNVVYRAGLARTRRQARQLVTHGHLLVNNKKVDIPSYRVSQYDIIDVREKSLATLPFQ 151

Query: 74  R 74
            
Sbjct: 152 V 152


>gi|315045031|ref|XP_003171891.1| 37S ribosomal protein NAM9 [Arthroderma gypseum CBS 118893]
 gi|311344234|gb|EFR03437.1| 37S ribosomal protein NAM9 [Arthroderma gypseum CBS 118893]
          Length = 475

 Score = 42.9 bits (99), Expect = 0.086,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 1/56 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+   I RA  AS  R+  + +    V VNG  ++     +   D  +VD   +  
Sbjct: 123 RLDVAIFRAMFASSTRQARQFVIHGGVTVNGKKMQYPGYLLNPGDMFQVDPERVMY 178


>gi|33601491|ref|NP_889051.1| putative heat shock protein [Bordetella bronchiseptica RB50]
 gi|33575927|emb|CAE33006.1| putative heat shock protein [Bordetella bronchiseptica RB50]
          Length = 126

 Score = 42.9 bits (99), Expect = 0.086,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 2/52 (3%)

Query: 12 TPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             R+ K + A     +R    + I + RV+VNG   +  A  V   D + +
Sbjct: 2  DKIRLDKWLWAARFYKTRSLAVQEIGKGRVQVNGQPAK-PAREVAPGDVVCI 52


>gi|291447461|ref|ZP_06586851.1| predicted protein [Streptomyces roseosporus NRRL 15998]
 gi|291350408|gb|EFE77312.1| predicted protein [Streptomyces roseosporus NRRL 15998]
          Length = 615

 Score = 42.9 bits (99), Expect = 0.087,   Method: Composition-based stats.
 Identities = 17/140 (12%), Positives = 28/140 (20%), Gaps = 11/140 (7%)

Query: 224 QLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
           +L  +  G  R V  +   E  G             P                       
Sbjct: 441 RLRGVEPGD-RPVLPRT-DEAAGLRHRAARGDRGRGPAAGPLPRRLRGARPGPRTGMAAA 498

Query: 284 RMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP---- 339
                + +   L +  +                ++            R    RR      
Sbjct: 499 DRLPAAERSPHLRRTPRGRRNQAEAQDRRRPGRSRVARRGGGDADRARPGPGRRHRHAHL 558

Query: 340 -----SFPSKRSLRRTSAKK 354
                + P  RS RR S  +
Sbjct: 559 PCLGGTGPDGRSARRGSPVR 578



 Score = 37.9 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 16/108 (14%), Positives = 28/108 (25%), Gaps = 1/108 (0%)

Query: 238 KKILR-EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            + LR  + GP     A   L A   S       R         D  R  ++   + G  
Sbjct: 481 PRRLRGARPGPRTGMAAADRLPAAERSPHLRRTPRGRRNQAEAQDRRRPGRSRVARRGGG 540

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
              +      RR+  +++    G      S           + +    
Sbjct: 541 DADRARPGPGRRHRHAHLPCLGGTGPDGRSARRGSPVRAAHAVAAGPP 588



 Score = 36.7 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 14/117 (11%), Positives = 24/117 (20%), Gaps = 5/117 (4%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E  G      A   L         ++                 +        L ++ + A
Sbjct: 428 EYDGESPPVHALGRLRGVEPGDRPVLPRTDEAAGLRHRAARGDRGRGPAAGPLPRRLRGA 487

Query: 303 TPVHRRN-----LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            P  R              +  +  +      Q E   RR P            A +
Sbjct: 488 RPGPRTGMAAADRLPAAERSPHLRRTPRGRRNQAEAQDRRRPGRSRVARRGGGDADR 544


>gi|222529703|ref|YP_002573585.1| 30S ribosomal protein S4 [Caldicellulosiruptor bescii DSM 6725]
 gi|254764564|sp|B9MKF4|RS4_ANATD RecName: Full=30S ribosomal protein S4
 gi|222456550|gb|ACM60812.1| ribosomal protein S4 [Caldicellulosiruptor bescii DSM 6725]
          Length = 208

 Score = 42.9 bits (99), Expect = 0.087,   Method: Composition-based stats.
 Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+  V+ R G AS R E   +++    KVNG  +   +  V   D IEVD
Sbjct: 99  RLDNVVYRLGFASSRGEARLLVSHAHFKVNGRTVNIPSYLVKVGDVIEVD 148


>gi|189501628|ref|YP_001957345.1| RNA-binding S4 domain-containing protein [Candidatus Amoebophilus
           asiaticus 5a2]
 gi|226697797|sp|B3EUJ7|RS4_AMOA5 RecName: Full=30S ribosomal protein S4
 gi|189497069|gb|ACE05616.1| RNA-binding S4 domain protein [Candidatus Amoebophilus asiaticus
           5a2]
          Length = 200

 Score = 42.9 bits (99), Expect = 0.087,   Method: Composition-based stats.
 Identities = 12/47 (25%), Positives = 25/47 (53%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  V+ R GI  +RR   ++++ + + VNG ++   +  +   D I
Sbjct: 92  RLDNVVYRLGITPTRRSARQLVSHKHITVNGKIVNIPSYALKVGDII 138


>gi|146297258|ref|YP_001181029.1| ribosomal protein S4 [Caldicellulosiruptor saccharolyticus DSM
           8903]
 gi|172046028|sp|A4XLQ3|RS4_CALS8 RecName: Full=30S ribosomal protein S4
 gi|145410834|gb|ABP67838.1| SSU ribosomal protein S4P [Caldicellulosiruptor saccharolyticus DSM
           8903]
          Length = 208

 Score = 42.9 bits (99), Expect = 0.087,   Method: Composition-based stats.
 Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G AS R E   +++    KVNG  +   +  V   D IEV
Sbjct: 99  RLDNVVYRLGFASSRGEARVLVSHAHFKVNGKTVNIPSYLVDVGDVIEV 147


>gi|115373138|ref|ZP_01460440.1| ATP-dependent RNA helicase RhlE [Stigmatella aurantiaca DW4/3-1]
 gi|115369894|gb|EAU68827.1| ATP-dependent RNA helicase RhlE [Stigmatella aurantiaca DW4/3-1]
          Length = 606

 Score = 42.9 bits (99), Expect = 0.087,   Method: Composition-based stats.
 Identities = 9/114 (7%), Positives = 23/114 (20%), Gaps = 1/114 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R    P      +    +     +                 +  +  + ++      ++ 
Sbjct: 476 RTHSRPTSGGRGKARGASHPGEGQERRGKGARRKGAPGRGGSSARGTAPRRENEEAPRRE 535

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL-RRTSAKK 354
                RR               F      + +   R P  P  +    R    +
Sbjct: 536 RPVSPRRGEGGREREPARGEKRFGGQRTGKGKGFARGPKRPGGKGAGPRGKPPR 589



 Score = 37.1 bits (84), Expect = 3.7,   Method: Composition-based stats.
 Identities = 9/110 (8%), Positives = 22/110 (20%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
            L +  G                     V   P+       +    K  + + N   +  
Sbjct: 416 ELTKPRGLPRPTGVSAKGGRRGGGRARAVDAFPSDEVLPGWEEPGDKGPTRRGNSGREAD 475

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           +  +             +           G R +         ++ +  R
Sbjct: 476 RTHSRPTSGGRGKARGASHPGEGQERRGKGARRKGAPGRGGSSARGTAPR 525


>gi|240948380|ref|ZP_04752766.1| heat shock-like protein 15 [Actinobacillus minor NM305]
 gi|240297419|gb|EER47960.1| heat shock-like protein 15 [Actinobacillus minor NM305]
          Length = 58

 Score = 42.5 bits (98), Expect = 0.089,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 20/50 (40%), Gaps = 1/50 (2%)

Query: 1  MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLER 49
          MK    + +N    R+ K + A     +R   + MI   +V  NG   + 
Sbjct: 1  MKKGEKMADNINEVRLDKWLWAACFYKTRSIAKAMIEGGKVHYNGQRAKT 50


>gi|224417910|ref|ZP_03655916.1| 30S ribosomal protein S4 [Helicobacter canadensis MIT 98-5491]
 gi|253827249|ref|ZP_04870134.1| 30S ribosomal protein S4 [Helicobacter canadensis MIT 98-5491]
 gi|313141451|ref|ZP_07803644.1| 30S ribosomal protein S4 [Helicobacter canadensis MIT 98-5491]
 gi|253510655|gb|EES89314.1| 30S ribosomal protein S4 [Helicobacter canadensis MIT 98-5491]
 gi|313130482|gb|EFR48099.1| 30S ribosomal protein S4 [Helicobacter canadensis MIT 98-5491]
          Length = 208

 Score = 42.5 bits (98), Expect = 0.089,   Method: Composition-based stats.
 Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 1/68 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G A+ RR   +++    + V+G  L   +  V +   IE+     +  +  
Sbjct: 99  RLDNVVYRMGFATTRRFARQLVVHGHILVDGKRLNIPSAFVSAGQKIEICEKTKKNPQIQ 158

Query: 74  RLWLYHKP 81
           R     K 
Sbjct: 159 RAIELTKQ 166


>gi|322701051|gb|EFY92802.1| Noc1p protein, putative [Metarhizium acridum CQMa 102]
          Length = 895

 Score = 42.5 bits (98), Expect = 0.089,   Method: Composition-based stats.
 Identities = 15/102 (14%), Positives = 30/102 (29%), Gaps = 1/102 (0%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P  L +   ++     +     + +P      PD   R  + +              P  
Sbjct: 207 PPGLPKFSASVGPGARAPSPGPKRQPRTSLPRPDSPVRRTQMTPGPRPSIGTPAPRPPAR 266

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
             +  +N   A+ +  +   D  ++     R PS    RS  
Sbjct: 267 YGSPTNNSRFAQSVRGT-AGDPNKKPSRLDRKPSIGGPRSAS 307


>gi|312793912|ref|YP_004026835.1| 30S ribosomal protein S4 [Caldicellulosiruptor kristjanssonii
           177R1B]
 gi|312181052|gb|ADQ41222.1| ribosomal protein S4 [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 208

 Score = 42.5 bits (98), Expect = 0.089,   Method: Composition-based stats.
 Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+  V+ R G AS R E   +++    KVNG  +   +  V   D IEVD
Sbjct: 99  RLDNVVYRLGFASSRGEARVLVSHAHFKVNGRTVNIPSYLVKVGDVIEVD 148


>gi|260432821|ref|ZP_05786792.1| ribosomal protein S4 [Silicibacter lacuscaerulensis ITI-1157]
 gi|260416649|gb|EEX09908.1| ribosomal protein S4 [Silicibacter lacuscaerulensis ITI-1157]
          Length = 206

 Score = 42.5 bits (98), Expect = 0.089,   Method: Composition-based stats.
 Identities = 10/35 (28%), Positives = 14/35 (40%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
             + +    VKVNG  +   +  V   D IEV   
Sbjct: 112 ARQFVNHGHVKVNGKRVNIPSYRVKEGDVIEVRDK 146


>gi|238855039|ref|ZP_04645367.1| ribosome-associated heat shock protein implicated in the
          recycling of the 50S subunit [Lactobacillus jensenii
          269-3]
 gi|260664823|ref|ZP_05865674.1| S4 domain-containing protein [Lactobacillus jensenii SJ-7A-US]
 gi|282934825|ref|ZP_06340059.1| S4 RNA-binding domain protein [Lactobacillus jensenii 208-1]
 gi|313472622|ref|ZP_07813111.1| S4 domain protein [Lactobacillus jensenii 1153]
 gi|238832283|gb|EEQ24592.1| ribosome-associated heat shock protein implicated in the
          recycling of the 50S subunit [Lactobacillus jensenii
          269-3]
 gi|239529426|gb|EEQ68427.1| S4 domain protein [Lactobacillus jensenii 1153]
 gi|260561306|gb|EEX27279.1| S4 domain-containing protein [Lactobacillus jensenii SJ-7A-US]
 gi|281301097|gb|EFA93407.1| S4 RNA-binding domain protein [Lactobacillus jensenii 208-1]
          Length = 80

 Score = 42.5 bits (98), Expect = 0.090,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR   + M  Q R++VNG +++  + +V   D I +
Sbjct: 1  MRLDKYLKVSRLVKRRTVAKEMADQGRIEVNGRVVKS-SYDVKLDDVISI 49


>gi|71905986|ref|YP_283573.1| 30S ribosomal protein S4 [Dechloromonas aromatica RCB]
 gi|90101686|sp|Q47J78|RS4_DECAR RecName: Full=30S ribosomal protein S4
 gi|71845607|gb|AAZ45103.1| SSU ribosomal protein S4P [Dechloromonas aromatica RCB]
          Length = 209

 Score = 42.5 bits (98), Expect = 0.090,   Method: Composition-based stats.
 Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 1/53 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           R+  V  R G   SR E  +++    + VNG  +   +  V   D +++    
Sbjct: 100 RLDSVAYRMGFGASRSESRQVVRHNGILVNGKRVNIPSFIVKPGDVVQLTDRA 152


>gi|310824350|ref|YP_003956708.1| ATP-dependent RNA helicase [Stigmatella aurantiaca DW4/3-1]
 gi|309397422|gb|ADO74881.1| ATP-dependent RNA helicase [Stigmatella aurantiaca DW4/3-1]
          Length = 579

 Score = 42.5 bits (98), Expect = 0.091,   Method: Composition-based stats.
 Identities = 9/114 (7%), Positives = 23/114 (20%), Gaps = 1/114 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R    P      +    +     +                 +  +  + ++      ++ 
Sbjct: 449 RTHSRPTSGGRGKARGASHPGEGQERRGKGARRKGAPGRGGSSARGTAPRRENEEAPRRE 508

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL-RRTSAKK 354
                RR               F      + +   R P  P  +    R    +
Sbjct: 509 RPVSPRRGEGGREREPARGEKRFGGQRTGKGKGFARGPKRPGGKGAGPRGKPPR 562



 Score = 37.5 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 9/110 (8%), Positives = 22/110 (20%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
            L +  G                     V   P+       +    K  + + N   +  
Sbjct: 389 ELTKPRGLPRPTGVSAKGGRRGGGRARAVDAFPSDEVLPGWEEPGDKGPTRRGNSGREAD 448

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           +  +             +           G R +         ++ +  R
Sbjct: 449 RTHSRPTSGGRGKARGASHPGEGQERRGKGARRKGAPGRGGSSARGTAPR 498


>gi|297199270|ref|ZP_06916667.1| multi-sensor histidine kinase [Streptomyces sviceus ATCC 29083]
 gi|297147346|gb|EDY60486.2| multi-sensor histidine kinase [Streptomyces sviceus ATCC 29083]
          Length = 576

 Score = 42.5 bits (98), Expect = 0.091,   Method: Composition-based stats.
 Identities = 15/112 (13%), Positives = 25/112 (22%), Gaps = 4/112 (3%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P        +      +     R         P   T   ++          +    P  
Sbjct: 157 PAARTGPDRDPQPAGRAGLPGRRGPAAGRHPRPGPDTADHRSDPAARLRRPDQHPPHPCG 216

Query: 307 RRNLASNV----WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            R  A                       R++ HR  PS P+  + RR    +
Sbjct: 217 TRPGAVAPAVHRRHPPSCPRGPGHRRHPRDQRHRPGPSRPAPGARRRAGPAR 268


>gi|238489961|ref|XP_002376218.1| 30S ribosomal subunit  S4, putative [Aspergillus flavus NRRL3357]
 gi|220698606|gb|EED54946.1| 30S ribosomal subunit S4, putative [Aspergillus flavus NRRL3357]
          Length = 455

 Score = 42.5 bits (98), Expect = 0.092,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 22/56 (39%), Gaps = 1/56 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+   I RA  AS  R+  + +    V VNG  +      +   D  +VD   +  
Sbjct: 121 RLDVAIFRAMFASSARQARQFVVHGAVTVNGKQMRYPGYLLNPGDLFQVDPERVMY 176


>gi|169830463|ref|YP_001716445.1| RNA-binding S4 domain-containing protein [Candidatus Desulforudis
           audaxviator MP104C]
 gi|226732175|sp|B1I1B2|RS4_DESAP RecName: Full=30S ribosomal protein S4
 gi|169637307|gb|ACA58813.1| RNA-binding S4 domain protein [Candidatus Desulforudis audaxviator
           MP104C]
          Length = 208

 Score = 42.5 bits (98), Expect = 0.092,   Method: Composition-based stats.
 Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 1/47 (2%)

Query: 17  SKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             VI R G+  SR E  +++     KVNG  ++  +  V   D I V
Sbjct: 101 DNVIYRLGLGASRAEARQLVRHGHFKVNGRKVDIPSYQVRVGDVIAV 147


>gi|268558174|ref|XP_002637077.1| C. briggsae CBR-COL-149 protein [Caenorhabditis briggsae]
 gi|187031733|emb|CAP29032.1| CBR-COL-149 protein [Caenorhabditis briggsae AF16]
          Length = 297

 Score = 42.5 bits (98), Expect = 0.092,   Method: Composition-based stats.
 Identities = 11/121 (9%), Positives = 23/121 (19%), Gaps = 4/121 (3%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
             + ++   GP         +  P          R            +       ++G  
Sbjct: 144 DPECVKCPAGPPGPSGTCGPVGRPGPDGRPGQPGRRGNDGRPGQPGPQGNAGQPGRDGRP 203

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP----SFPSKRSLRRTSA 352
            Q        RR   +     +          G   +   R P        +   +    
Sbjct: 204 GQPGHPGKDGRRGHGAPGAPGRAGQPGRAGAPGHPGKPGERGPHGYCGPAGRPGQQGNRG 263

Query: 353 K 353
            
Sbjct: 264 S 264



 Score = 41.3 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 9/106 (8%), Positives = 17/106 (16%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R     H                +          +  P           Q        + 
Sbjct: 126 RRGQDNHNTISPPACPARDPECVKCPAGPPGPSGTCGPVGRPGPDGRPGQPGRRGNDGRP 185

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
             P  + N        +          G+R      +P    +   
Sbjct: 186 GQPGPQGNAGQPGRDGRPGQPGHPGKDGRRGHGAPGAPGRAGQPGR 231



 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 11/105 (10%), Positives = 17/105 (16%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              E  +     P  S       RP           R       + G            R
Sbjct: 143 RDPECVKCPAGPPGPSGTCGPVGRPGPDGRPGQPGRRGNDGRPGQPGPQGNAGQPGRDGR 202

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                +               G+  +  R        +   R   
Sbjct: 203 PGQPGHPGKDGRRGHGAPGAPGRAGQPGRAGAPGHPGKPGERGPH 247


>gi|312795516|ref|YP_004028438.1| ribonuclease E [Burkholderia rhizoxinica HKI 454]
 gi|312167291|emb|CBW74294.1| Ribonuclease E (EC 3.1.4.-) [Burkholderia rhizoxinica HKI 454]
          Length = 1100

 Score = 42.5 bits (98), Expect = 0.092,   Method: Composition-based stats.
 Identities = 25/154 (16%), Positives = 43/154 (27%), Gaps = 14/154 (9%)

Query: 214 RLIRISYGPFQLGTLLAGSTR--EVSKKILR-EQLGPHLLEEAQVNLDAPIYSSETLVRD 270
           +L R+ +   +L      S R  E + + L  E        +A+   +A +      +  
Sbjct: 482 KLERLRHDDVRLDE-PRASWRMAEEAARELESETGYSKRDSDAKPKQEAAVKGITPDMPA 540

Query: 271 RPNIISEVPDDFTRMKKNSSQKNGLS----------KQKKLATPVHRRNLASNVWMAKGI 320
                  VP         +                   +  A P      A+      G 
Sbjct: 541 PSATPRPVPPQARPSAPVTPAATASGGFIGWLKRIFSGEPPAQPAQATVKATPARPTGGR 600

Query: 321 HSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             S      +R   HRR P   S+ +  R  A +
Sbjct: 601 AGSEARQGTERNRPHRRGPQSGSRDAAPRDVAAQ 634


>gi|312135469|ref|YP_004002807.1| 30S ribosomal protein S4 [Caldicellulosiruptor owensensis OL]
 gi|311775520|gb|ADQ05007.1| ribosomal protein S4 [Caldicellulosiruptor owensensis OL]
          Length = 208

 Score = 42.5 bits (98), Expect = 0.092,   Method: Composition-based stats.
 Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+  V+ R G AS R E   +++    KVNG  +   +  V   D IEVD
Sbjct: 99  RLDNVVYRLGFASSRGEARVLVSHAHFKVNGRTVNIPSYLVKVGDVIEVD 148


>gi|323341678|ref|ZP_08081911.1| 30S ribosomal protein S4 [Erysipelothrix rhusiopathiae ATCC 19414]
 gi|322464103|gb|EFY09296.1| 30S ribosomal protein S4 [Erysipelothrix rhusiopathiae ATCC 19414]
          Length = 200

 Score = 42.5 bits (98), Expect = 0.092,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R  ++ +RR   +++    + V+G  ++  +  V     IEV
Sbjct: 93  RLDNVVYRMNLSRTRRGARQLVNHGHILVDGKKVDIPSYIVKPGQTIEV 141


>gi|302871525|ref|YP_003840161.1| ribosomal protein S4 [Caldicellulosiruptor obsidiansis OB47]
 gi|312127253|ref|YP_003992127.1| 30S ribosomal protein S4 [Caldicellulosiruptor hydrothermalis 108]
 gi|302574384|gb|ADL42175.1| ribosomal protein S4 [Caldicellulosiruptor obsidiansis OB47]
 gi|311777272|gb|ADQ06758.1| ribosomal protein S4 [Caldicellulosiruptor hydrothermalis 108]
          Length = 208

 Score = 42.5 bits (98), Expect = 0.093,   Method: Composition-based stats.
 Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+  V+ R G AS R E   +++    KVNG  +   +  V   D IEVD
Sbjct: 99  RLDNVVYRLGFASSRGEARVLVSHAHFKVNGRTVNIPSYLVKVGDVIEVD 148


>gi|326790216|ref|YP_004308037.1| RNA-binding S4 domain protein [Clostridium lentocellum DSM 5427]
 gi|326540980|gb|ADZ82839.1| RNA-binding S4 domain protein [Clostridium lentocellum DSM 5427]
          Length = 79

 Score = 42.5 bits (98), Expect = 0.093,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 21/50 (42%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   +      RV VN  L +    +V   D IE+
Sbjct: 1  MRIDKYLKISRIIKRRTIAQEACDSGRVMVNDKLAK-PGTDVKIGDVIEI 49


>gi|194673041|ref|XP_881008.3| PREDICTED: RNA binding motif protein 12-like isoform 4 [Bos taurus]
 gi|297482529|ref|XP_002692866.1| PREDICTED: RNA binding motif protein 12-like [Bos taurus]
 gi|296480442|gb|DAA22557.1| RNA binding motif protein 12-like [Bos taurus]
          Length = 984

 Score = 42.5 bits (98), Expect = 0.093,   Method: Composition-based stats.
 Identities = 16/132 (12%), Positives = 27/132 (20%), Gaps = 9/132 (6%)

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNII-----SEVPDDF 282
           L  G  R   ++  R           + +   P         +             P + 
Sbjct: 655 LPPGEWRRQPEEDFRRPPEEDFRRPPEEDFWRPHQEDFRRSPEEDFRGSPEDFRRPPPEH 714

Query: 283 TRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKG----IHSSFLSDSGQREENHRRS 338
            R       +       +   P H R      +           S        +E  RR 
Sbjct: 715 FRRPPPEHFRRPPPDHFRRLPPEHFRRPPQEHFRRPPQEHFRRPSQEHFRRPPQELFRRP 774

Query: 339 PSFPSKRSLRRT 350
           P    +R     
Sbjct: 775 PQEHFRRPREED 786


>gi|86157973|ref|YP_464758.1| hypothetical protein Adeh_1548 [Anaeromyxobacter dehalogenans
           2CP-C]
 gi|85774484|gb|ABC81321.1| hypothetical protein Adeh_1548 [Anaeromyxobacter dehalogenans
           2CP-C]
          Length = 487

 Score = 42.5 bits (98), Expect = 0.093,   Method: Composition-based stats.
 Identities = 7/118 (5%), Positives = 21/118 (17%), Gaps = 5/118 (4%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
            +              +    +       R        +        + +      S   
Sbjct: 268 EVSIYRPDARPAPGARSDGGRVAPGSAPTRGDGRGAPGLAPPSRGETRGAPGYAPPSGGG 327

Query: 300 KLATPVHRRNLASNV-----WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             + P +  +  +                    S        R+P    +  + R + 
Sbjct: 328 TRSAPGNAPSRGAPGYAPPRGGGPSAAPPARGPSAAPPARGGRAPDAGPRGEVPRAAP 385


>gi|325479433|gb|EGC82529.1| S4 domain protein [Anaerococcus prevotii ACS-065-V-Col13]
          Length = 81

 Score = 42.5 bits (98), Expect = 0.094,   Method: Composition-based stats.
 Identities = 9/36 (25%), Positives = 16/36 (44%), Gaps = 1/36 (2%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLE 48
           R+ K +  + I  RR+  +      RV +N  L +
Sbjct: 1  MRIDKFLKNSRIIKRRQVAKEACENGRVTINDKLAK 36


>gi|328877055|gb|EGG25418.1| midasin [Dictyostelium fasciculatum]
          Length = 1101

 Score = 42.5 bits (98), Expect = 0.095,   Method: Composition-based stats.
 Identities = 11/102 (10%), Positives = 24/102 (23%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           VS K   ++         + +   P+  +    + RP      P    +   +S+     
Sbjct: 701 VSDKEPAKKAATKPTAATKPSSKPPVKETPVAEKKRPTKPDTKPSATAKRPPSSAPAKRP 760

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
                   P            A        + + +      R
Sbjct: 761 PSSAPAKRPPSSAPAKRPPSSAPAKRPPSSAPAKRPPLRPSR 802



 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 19/134 (14%), Positives = 38/134 (28%), Gaps = 7/134 (5%)

Query: 222 PFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD 281
              L  ++      ++K  + ++    + ++      A +   E   +      +     
Sbjct: 668 DLDLDGIVP-----LTKG-IAKKAANLISDKKPAKKAASVSDKEPAKKAATKPTAATKPS 721

Query: 282 FTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF 341
                K +         K    P        +   AK   SS  +         +R PS 
Sbjct: 722 SKPPVKETPVAEKKRPTKPDTKPSATAKRPPSSAPAKRPPSSAPAKRPPSSAPAKRPPSS 781

Query: 342 -PSKRSLRRTSAKK 354
            P+KR      AK+
Sbjct: 782 APAKRPPSSAPAKR 795



 Score = 42.1 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 8/110 (7%), Positives = 18/110 (16%), Gaps = 4/110 (3%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P     +  + +    ++                +    +K    K           P 
Sbjct: 693 KPAKKAASVSDKEPAKKAATKPTAATKPSSKPPVKETPVAEKKRPTKPDTKPSATAKRPP 752

Query: 306 HRRNLASNVWMAKGIHSSF----LSDSGQREENHRRSPSFPSKRSLRRTS 351
                      A                        S +   +  LR + 
Sbjct: 753 SSAPAKRPPSSAPAKRPPSSAPAKRPPSSAPAKRPPSSAPAKRPPLRPSR 802


>gi|311275192|ref|XP_003134634.1| PREDICTED: hypothetical protein LOC100523650 [Sus scrofa]
          Length = 1339

 Score = 42.5 bits (98), Expect = 0.095,   Method: Composition-based stats.
 Identities = 8/115 (6%), Positives = 16/115 (13%), Gaps = 4/115 (3%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           +    R                     +        +       D     +     +G  
Sbjct: 61  TAHECRRAPVAPPEPSEGRAAGFGSAPAGGRTPPTGDGPRPQGTDPAHRGRTPPTGDGPR 120

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                 T    R              +  +  G+        P         R  
Sbjct: 121 ---PQGTDPAHRGRTPPTGDGPRPQGTDPAHRGRTPPTGD-GPRPQGTDPAHRGR 171



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 7/99 (7%), Positives = 15/99 (15%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                 +   P  +        P          T               +   T    R 
Sbjct: 91  RTPPTGDGPRPQGTDPAHRGRTPPTGDGPRPQGTDPAHRGRTPPTGDGPRPQGTDPAHRG 150

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                        +  +  G+         + P   +  
Sbjct: 151 RTPPTGDGPRPQGTDPAHRGRTPPTGGGLRTPPVPGTPP 189


>gi|168058654|ref|XP_001781322.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162667215|gb|EDQ53850.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 883

 Score = 42.5 bits (98), Expect = 0.095,   Method: Composition-based stats.
 Identities = 12/107 (11%), Positives = 27/107 (25%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
              + +         +  + +  R R    +  P       K  S   G     +  +P 
Sbjct: 222 RRAVSKAPSPTRRRSVSKAPSPTRRRATSKAPSPTRRRSTSKAPSPTRGRRGVSRNPSPT 281

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            R    +     + +         +R    R       +R + R  +
Sbjct: 282 RRAVSKAPSPTRRAVSRVVSPVKARRRSPSRNPSPTRGRRGVSRGPS 328



 Score = 40.5 bits (93), Expect = 0.34,   Method: Composition-based stats.
 Identities = 16/117 (13%), Positives = 38/117 (32%), Gaps = 1/117 (0%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           +++ +   + P     ++        +S+     R    S+ P    R   + +      
Sbjct: 163 TRRSVSRNISPTRRSTSRNPSPTRRSTSKAPSPTRRRSTSKDPSSTRRRSVSKAPSPTRR 222

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF-PSKRSLRRTSA 352
           +    A    RR   S         ++  + S  R  +  ++PS    +R + R  +
Sbjct: 223 RAVSKAPSPTRRRSVSKAPSPTRRRATSKAPSPTRRRSTSKAPSPTRGRRGVSRNPS 279



 Score = 40.2 bits (92), Expect = 0.54,   Method: Composition-based stats.
 Identities = 11/118 (9%), Positives = 22/118 (18%), Gaps = 10/118 (8%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           ++         ++        +                   TR +  S   +   ++   
Sbjct: 203 KDPSSTRRRSVSKAPSPTRRRAVSKAPSPTRRRSVSKAPSPTRRRATSKAPSPTRRRSTS 262

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREEN----------HRRSPSFPSKRSLRR 349
             P   R              +                      RRSPS     +  R
Sbjct: 263 KAPSPTRGRRGVSRNPSPTRRAVSKAPSPTRRAVSRVVSPVKARRRSPSRNPSPTRGR 320



 Score = 36.7 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 14/118 (11%), Positives = 36/118 (30%), Gaps = 1/118 (0%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +    +      +     +        +  +  R+            +  ++ S+ K+  
Sbjct: 147 IRGVEIEPYSSLNTSPTRRSVSRNISPTRRSTSRNPSPTRRSTSKAPSPTRRRSTSKDPS 206

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           S +++  +          V  A    +   S S       RR+ S     + RR+++K
Sbjct: 207 STRRRSVSKAPSPTRRRAVSKAPSP-TRRRSVSKAPSPTRRRATSKAPSPTRRRSTSK 263


>gi|319760353|ref|YP_004124291.1| 30S ribosomal protein S4 [Candidatus Blochmannia vafer str. BVAF]
 gi|318039067|gb|ADV33617.1| 30S ribosomal protein S4 [Candidatus Blochmannia vafer str. BVAF]
          Length = 207

 Score = 42.5 bits (98), Expect = 0.095,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + V VNG ++   +  VMS   I++
Sbjct: 97  RLDNVVYRMGFGSTRAESRQLVSHKSVVVNGRVVNIPSYQVMSDTVIQI 145


>gi|297618356|ref|YP_003703515.1| ribosomal protein S4 [Syntrophothermus lipocalidus DSM 12680]
 gi|297146193|gb|ADI02950.1| ribosomal protein S4 [Syntrophothermus lipocalidus DSM 12680]
          Length = 209

 Score = 42.5 bits (98), Expect = 0.096,   Method: Composition-based stats.
 Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 1/62 (1%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   SR E  ++I      +NG  +   ++ V   D I+V    +  A+  
Sbjct: 100 RLDNVVYRLGFAGSRPEARQLITHGHFLLNGRKVNIPSILVKVGDVIQVKEKSMESAKFK 159

Query: 74  RL 75
            L
Sbjct: 160 EL 161


>gi|168335346|ref|ZP_02693442.1| RNA-binding S4 [Epulopiscium sp. 'N.t. morphotype B']
          Length = 80

 Score = 42.5 bits (98), Expect = 0.096,   Method: Composition-based stats.
 Identities = 12/51 (23%), Positives = 23/51 (45%), Gaps = 2/51 (3%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+ K +  + I  RR   +    + RV +NG + +     V   D +E++
Sbjct: 1  MRIDKFLKVSRIIKRRTIAQEACEKGRVLINGKVAK-PGSVVKIGDMLELN 50


>gi|331696871|ref|YP_004333110.1| hypothetical protein Psed_3058 [Pseudonocardia dioxanivorans
           CB1190]
 gi|326951560|gb|AEA25257.1| hypothetical protein Psed_3058 [Pseudonocardia dioxanivorans
           CB1190]
          Length = 1061

 Score = 42.5 bits (98), Expect = 0.097,   Method: Composition-based stats.
 Identities = 7/116 (6%), Positives = 17/116 (14%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            ++                            +  R      VP D  R            
Sbjct: 294 RQQEQVAAAEKTAAAGGSPAPTPAPDPVTAAIPVRSAPYRPVPYDVDRPDGRRPAGPRPP 353

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                      R              +  + +   +   R       +  +   + 
Sbjct: 354 HAAPPGRGPAGRPEGPRPGDPVRGRPAARNGAPGPDAQPRPVAPRGGRGPVNGGAP 409



 Score = 38.2 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 11/97 (11%), Positives = 20/97 (20%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              E  +                  +            ++ + +  G       A     
Sbjct: 747 RPGEPMRPGPAGRADRPFEAGWTGGSGPRHGGPAGAAPEQPAHRAPGRETVDPFAGRPLD 806

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
               S    A G   +F   +G R    RR+      
Sbjct: 807 GPPRSGRRAADGGREAFRPPAGARPGGRRRADDPGRP 843



 Score = 37.5 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 6/105 (5%), Positives = 20/105 (19%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              +     +         +  D        P            +    + +        
Sbjct: 316 PAPDPVTAAIPVRSAPYRPVPYDVDRPDGRRPAGPRPPHAAPPGRGPAGRPEGPRPGDPV 375

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           R   +    A G  +     + +         +  + R+    + 
Sbjct: 376 RGRPAARNGAPGPDAQPRPVAPRGGRGPVNGGAPVNGRAPVDGAP 420



 Score = 37.5 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 13/112 (11%), Positives = 22/112 (19%), Gaps = 6/112 (5%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               +          +                         S  ++G         P HR
Sbjct: 731 RPAADGGAFGRPGDPARPGEPMRPGPAGRADRPFEAGWTGGSGPRHGGPAGAAPEQPAHR 790

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRR------SPSFPSKRSLRRTSAK 353
                 V    G        SG+R  +  R      + + P  R       +
Sbjct: 791 APGRETVDPFAGRPLDGPPRSGRRAADGGREAFRPPAGARPGGRRRADDPGR 842



 Score = 36.7 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 9/116 (7%), Positives = 24/116 (20%), Gaps = 5/116 (4%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R           + +       +              P+     +    +       + L
Sbjct: 747 RPGEPMRPGPAGRADRPFEAGWTGGSGPRHGGPAGAAPEQPA-HRAPGRETVDPFAGRPL 805

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR----SLRRTSAK 353
             P      A++         +     G+R  +    P +   R         + +
Sbjct: 806 DGPPRSGRRAADGGREAFRPPAGARPGGRRRADDPGRPQYVDPRGTLAGPPPGAGR 861


>gi|238759754|ref|ZP_04620912.1| ATP-dependent RNA helicase rhlE [Yersinia aldovae ATCC 35236]
 gi|238701986|gb|EEP94545.1| ATP-dependent RNA helicase rhlE [Yersinia aldovae ATCC 35236]
          Length = 452

 Score = 42.5 bits (98), Expect = 0.097,   Method: Composition-based stats.
 Identities = 11/76 (14%), Positives = 24/76 (31%)

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
            PD   +     + + G   Q+      +      +   A        +   + + + +R
Sbjct: 377 EPDPSIKADPIQNGRQGRGAQRPGMGRGNGAGRPQSSAGAAAGRGDSRTSRPRSQADGQR 436

Query: 338 SPSFPSKRSLRRTSAK 353
            P+ PS R   R   +
Sbjct: 437 RPAAPSARGRSRKPGE 452


>gi|190890624|ref|YP_001977166.1| hemolysin protein [Rhizobium etli CIAT 652]
 gi|190695903|gb|ACE89988.1| hemolysin protein [Rhizobium etli CIAT 652]
          Length = 248

 Score = 42.5 bits (98), Expect = 0.097,   Method: Composition-based stats.
 Identities = 10/48 (20%), Positives = 22/48 (45%), Gaps = 1/48 (2%)

Query: 9  ENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVM 55
           +   QR+ +++   G  ASR      + +  V++ G L+ +A   + 
Sbjct: 2  SDQNSQRLDQLLVSRGLFASRSRARDAVQRGTVRIGGQLVTKAGALIS 49


>gi|73971174|ref|XP_538625.2| PREDICTED: similar to follistatin-like 4 [Canis familiaris]
          Length = 1169

 Score = 42.5 bits (98), Expect = 0.098,   Method: Composition-based stats.
 Identities = 15/139 (10%), Positives = 33/139 (23%), Gaps = 4/139 (2%)

Query: 217 RISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIIS 276
           R  +G      L   + R      LR                   +              
Sbjct: 213 REQFGGRSGRELGPKAARA--AGDLRPPAPACAPLRPPAPAQEACFKFGGHPGGADRARR 270

Query: 277 EVPDDFT-RMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENH 335
                     ++ +S +  L + ++    + RR    ++             +       
Sbjct: 271 SGSGRREWAPERGASFRGPLERTERRPGVLARRLPPEDLGSRPSGKGRRPPQAATPAGAE 330

Query: 336 RRSPSFPS-KRSLRRTSAK 353
           R  P     +R+  RT+ +
Sbjct: 331 RAGPRGAGPRRAAPRTAGR 349


>gi|169763980|ref|XP_001727890.1| S4 domain containing protein [Aspergillus oryzae RIB40]
 gi|83770918|dbj|BAE61051.1| unnamed protein product [Aspergillus oryzae]
          Length = 455

 Score = 42.5 bits (98), Expect = 0.098,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 22/56 (39%), Gaps = 1/56 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+   I RA  AS  R+  + +    V VNG  +      +   D  +VD   +  
Sbjct: 121 RLDVAIFRAMFASSARQARQFVVHGAVTVNGKQMRYPGYLLNPGDLFQVDPERVMY 176


>gi|305664658|ref|YP_003860945.1| heat shock protein 15 [Maribacter sp. HTCC2170]
 gi|88707359|gb|EAQ99605.1| heat shock protein 15 [Maribacter sp. HTCC2170]
          Length = 124

 Score = 42.5 bits (98), Expect = 0.100,   Method: Composition-based stats.
 Identities = 13/83 (15%), Positives = 26/83 (31%), Gaps = 2/83 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ K +       +R        + +VK+NG + +  A  +  TD I V    +     
Sbjct: 1  MRIDKYLWHTRYFKTRNIASTACKKGQVKINGQVAK-PAREIYPTDQIVVRKNQINYQFT 59

Query: 73 TRLWLYHKPIGLVTTHSDPDGRS 95
                ++    +      D   
Sbjct: 60 VLDIPKNRVGAKLVDIYRKDTTP 82


>gi|302543334|ref|ZP_07295676.1| ribosomal protein S4 [Streptomyces hygroscopicus ATCC 53653]
 gi|302460952|gb|EFL24045.1| ribosomal protein S4 [Streptomyces himastatinicus ATCC 53653]
          Length = 208

 Score = 42.5 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG A SR    +++      VNG+  +  +  V   D IEV
Sbjct: 99  RLDNVVYRAGFAKSRDHARQLVRHGHFTVNGVKTDIPSARVAVNDIIEV 147


>gi|299141173|ref|ZP_07034310.1| ribosomal protein S4 [Prevotella oris C735]
 gi|298577133|gb|EFI49002.1| ribosomal protein S4 [Prevotella oris C735]
          Length = 201

 Score = 42.5 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA +R    +++  + + V+G ++   +  V     I V
Sbjct: 93  RLDNVVFRLGIAPTRAAARQLVGHKHITVDGKVVNIPSFAVKPGMVIAV 141


>gi|281423813|ref|ZP_06254726.1| ribosomal protein S4 [Prevotella oris F0302]
 gi|281402040|gb|EFB32871.1| ribosomal protein S4 [Prevotella oris F0302]
          Length = 201

 Score = 42.5 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIA +R    +++  + + V+G ++   +  V     I V
Sbjct: 93  RLDNVVFRLGIAPTRAAARQLVGHKHITVDGKVVNIPSFAVKPGMVIAV 141


>gi|168058710|ref|XP_001781350.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162667243|gb|EDQ53878.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 762

 Score = 42.5 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 11/102 (10%), Positives = 21/102 (20%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
               + +A         S           +S  P    R+   ++    + ++     P 
Sbjct: 59  RRRSVSKAPSPTRRRSMSKAPSPTRGRRGVSRNPSPTRRLASRAASPAKIRRRSPSRNPS 118

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
             R                    G      RR  S     + 
Sbjct: 119 PTRGRRGMSRGLSPTRGRRGMSRGPSPTRGRRGVSRGPSPTR 160



 Score = 40.2 bits (92), Expect = 0.45,   Method: Composition-based stats.
 Identities = 13/110 (11%), Positives = 25/110 (22%), Gaps = 5/110 (4%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                   +       S+     R   +S+ P      +  S   +   +    A    +
Sbjct: 48  RRSMSKAPSPTRRRSVSKAPSPTRRRSMSKAPSPTRGRRGVSRNPSPTRRLASRAASPAK 107

Query: 308 RNLASNVWMAKGIHSSFLSDSG----QREENHRRSPSF-PSKRSLRRTSA 352
               S                G    +      R PS    +R + R  +
Sbjct: 108 IRRRSPSRNPSPTRGRRGMSRGLSPTRGRRGMSRGPSPTRGRRGVSRGPS 157



 Score = 38.2 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 16/100 (16%), Positives = 30/100 (30%), Gaps = 3/100 (3%)

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR---RNLASNV 314
              +  + +  R R    +  P     M K  S   G     +  +P  R   R  +   
Sbjct: 48  RRSMSKAPSPTRRRSVSKAPSPTRRRSMSKAPSPTRGRRGVSRNPSPTRRLASRAASPAK 107

Query: 315 WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              +    +     G+R  +   SP+   +   R  S  +
Sbjct: 108 IRRRSPSRNPSPTRGRRGMSRGLSPTRGRRGMSRGPSPTR 147



 Score = 37.9 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 11/115 (9%), Positives = 23/115 (20%), Gaps = 7/115 (6%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ-KNGLSKQKKLATP 304
           G   +             + +  + R    S  P      +  S        ++     P
Sbjct: 84  GRRGVSRNPSPTRRLASRAASPAKIRRRSPSRNPSPTRGRRGMSRGLSPTRGRRGMSRGP 143

Query: 305 VHRRNLASNVWMAKGIH-----SSFLSDSGQREENHRRSPSFP-SKRSLRRTSAK 353
              R                   +  +    R  +  R        RS   +  +
Sbjct: 144 SPTRGRRGVSRGPSPTRVTRLTPATPARVHSRPASPTRRRDTSVGPRSRATSPQR 198



 Score = 37.1 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 19/112 (16%), Positives = 31/112 (27%), Gaps = 1/112 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R               D     S      R   +S  P    R    +          K 
Sbjct: 7   RSTTRKQYDIRGVEIEDPLGGRSINRSPSRRRSMSRQPSFTRRSMSKAPSPTRRRSVSKA 66

Query: 302 ATPVHRRNLASNVWMAKGIHS-SFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            +P  RR+++      +G    S      +R  +   SP+   +RS  R  +
Sbjct: 67  PSPTRRRSMSKAPSPTRGRRGVSRNPSPTRRLASRAASPAKIRRRSPSRNPS 118


>gi|241766538|ref|ZP_04764400.1| RNA-binding S4 domain protein [Acidovorax delafieldii 2AN]
 gi|241363233|gb|EER58802.1| RNA-binding S4 domain protein [Acidovorax delafieldii 2AN]
          Length = 56

 Score = 42.5 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 2/53 (3%)

Query: 11 FTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
              R+ K +       +R      IA+ RV VNG   + AA ++ S D + +
Sbjct: 4  PETMRLDKWLWCARFYKTRSLATEEIAKGRVTVNGQPAK-AARDLRSGDTVAL 55


>gi|194382890|dbj|BAG59001.1| unnamed protein product [Homo sapiens]
          Length = 1061

 Score = 42.5 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 27/108 (25%), Gaps = 3/108 (2%)

Query: 247  PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
            P   +EA+               + P              +   ++     +     P  
Sbjct: 940  PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 999

Query: 307  RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS--FPSKRSLRRTSA 352
            RR              +   +     E  RR      PS++  RR +A
Sbjct: 1000 RRVGDVEPSRKPKRRRAADVEPSS-PEPKRRRVGDVEPSRKPKRRRAA 1046



 Score = 40.5 bits (93), Expect = 0.40,   Method: Composition-based stats.
 Identities = 9/117 (7%), Positives = 25/117 (21%), Gaps = 2/117 (1%)

Query: 238  KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            +    +   P     A++              +                    ++  +  
Sbjct: 945  EAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGD 1004

Query: 298  QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             +    P  RR         +            R+   +R  +   + SL     ++
Sbjct: 1005 VEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKP--KRRRAADVEPSLPEPKRRR 1059



 Score = 36.7 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 13/120 (10%), Positives = 29/120 (24%), Gaps = 6/120 (5%)

Query: 235  EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
             ++ +    +       +    ++ P       V D              ++ +S +   
Sbjct: 940  PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 999

Query: 295  LS-KQKKLATPVHRRNLASNVWMAKGIHSSF-----LSDSGQREENHRRSPSFPSKRSLR 348
                  + +    RR  A     +             S   +R       PS P  +  R
Sbjct: 1000 RRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKPKRRRAADVEPSLPEPKRRR 1059



 Score = 36.3 bits (82), Expect = 6.3,   Method: Composition-based stats.
 Identities = 13/108 (12%), Positives = 22/108 (20%), Gaps = 5/108 (4%)

Query: 246  GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                L     + +       T   +              M+     K       + +   
Sbjct: 923  RLRGLLPPSADDNLKTPPLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKP 982

Query: 306  HRRNLASNVWMAKGIHSSF-----LSDSGQREENHRRSPSFPSKRSLR 348
             RR  A     +             S   +R       PS P  +  R
Sbjct: 983  KRRRAADVEPSSPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKRRR 1030


>gi|87125352|ref|ZP_01081198.1| translation initiation factor [Synechococcus sp. RS9917]
 gi|86167121|gb|EAQ68382.1| translation initiation factor [Synechococcus sp. RS9917]
          Length = 1103

 Score = 42.5 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 11/99 (11%), Positives = 24/99 (24%), Gaps = 4/99 (4%)

Query: 259 APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAK 318
               +            +  P    + +     ++        A P  +R   S   +A 
Sbjct: 174 KGGGAGRPSAPAPVKRTAPAPQRPAKPELVGRPQSNKPAAGAPARPQGQRPGVSPRPVAP 233

Query: 319 GI---HSSFLSDSGQREENHRR-SPSFPSKRSLRRTSAK 353
                  +     G  +       P  P + +  R  A+
Sbjct: 234 SAQNQRPAMPQRPGAPQRPGAPQRPGAPQRPTSPRGGAR 272



 Score = 40.9 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 9/100 (9%), Positives = 22/100 (22%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
           +   + P   +    + +   +S  P   +   +  +        ++   P         
Sbjct: 205 RPQSNKPAAGAPARPQGQRPGVSPRPVAPSAQNQRPAMPQRPGAPQRPGAPQRPGAPQRP 264

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                G   +       R          P +R     S  
Sbjct: 265 TSPRGGARPNAGRPGQPRSGGGLELVGKPIRRDGPGGSGA 304


>gi|291518020|emb|CBK73241.1| SSU ribosomal protein S4P [Butyrivibrio fibrisolvens 16/4]
          Length = 197

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R+E  +++  +   VNG  +   +  V + D IEV
Sbjct: 88  RLDNVVFRMGFARTRKEARQVVDHKMFLVNGKAVNIPSYLVKAGDVIEV 136


>gi|317506767|ref|ZP_07964546.1| cysteine-rich domain-containing protein [Segniliparus rugosus ATCC
           BAA-974]
 gi|316254932|gb|EFV14223.1| cysteine-rich domain-containing protein [Segniliparus rugosus ATCC
           BAA-974]
          Length = 1081

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 11/84 (13%), Positives = 23/84 (27%), Gaps = 3/84 (3%)

Query: 259 APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAK 318
           A     +   +     IS         K   S++   S + +  +P H+R+   +     
Sbjct: 892 ADEPEQKDAEQKDAEPISAADPSPPTSKGRPSKRLPPSSRSRPQSPRHKRSRFPS---PP 948

Query: 319 GIHSSFLSDSGQREENHRRSPSFP 342
             +         R       P+  
Sbjct: 949 TRNPRPTRARRSRPSASASRPARN 972



 Score = 37.5 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 11/82 (13%), Positives = 20/82 (24%)

Query: 267 LVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLS 326
              D P        D   +            +     P   R+   +    +    S  +
Sbjct: 890 TSADEPEQKDAEQKDAEPISAADPSPPTSKGRPSKRLPPSSRSRPQSPRHKRSRFPSPPT 949

Query: 327 DSGQREENHRRSPSFPSKRSLR 348
            + +     R  PS  + R  R
Sbjct: 950 RNPRPTRARRSRPSASASRPAR 971


>gi|148240415|ref|YP_001225802.1| translation initiation factor IF-2 [Synechococcus sp. WH 7803]
 gi|166198941|sp|A5GNJ0|IF2_SYNPW RecName: Full=Translation initiation factor IF-2
 gi|147848954|emb|CAK24505.1| Translation initiation factor IF-2 [Synechococcus sp. WH 7803]
          Length = 1123

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 11/111 (9%), Positives = 24/111 (21%), Gaps = 5/111 (4%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R                    +        P   +  P+   R +    +     +    
Sbjct: 197 RAAPNDAPRPANAPPSRPQPKTPVNRTAPPPQRPAAKPELVGRPQPRRPEGPPTRQGAGP 256

Query: 302 ATPVHRRNLASNVW-----MAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            +P    +   +       M +    +    +  R       PS P   +L
Sbjct: 257 GSPRPAVSPRPSAPGSQRNMPQRPAGAQRPGAPTRPGTGAGRPSRPGGNTL 307



 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 14/107 (13%), Positives = 30/107 (28%), Gaps = 6/107 (5%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
                 DAP  ++    R +P           +      +  G  + ++   P  R+   
Sbjct: 196 RRAAPNDAPRPANAPPSRPQPKTPVNRTAPPPQRPAAKPELVGRPQPRRPEGPPTRQGAG 255

Query: 312 SNVWM----AKGIHSSFLSDSGQREENHRR--SPSFPSKRSLRRTSA 352
                     +        +  QR    +R  +P+ P   + R +  
Sbjct: 256 PGSPRPAVSPRPSAPGSQRNMPQRPAGAQRPGAPTRPGTGAGRPSRP 302



 Score = 42.1 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 11/105 (10%), Positives = 23/105 (21%), Gaps = 2/105 (1%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
            + +        +     R      S         +     +   +K + +  P  RR  
Sbjct: 187 AKPRGTAPIRRAAPNDAPRPANAPPSRPQPKTPVNRTAPPPQRPAAKPELVGRPQPRRPE 246

Query: 311 ASNV--WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                     G     +S       + R  P  P+         +
Sbjct: 247 GPPTRQGAGPGSPRPAVSPRPSAPGSQRNMPQRPAGAQRPGAPTR 291



 Score = 40.9 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 10/109 (9%), Positives = 18/109 (16%), Gaps = 1/109 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P    E  V+      +     +  P           R    +      +       P 
Sbjct: 158 KPKTAPERTVSRPPSPPARPVPQQPSPPSAKPRGTAPIRRAAPNDAPRPANAPPSRPQPK 217

Query: 306 HRRNLASNVWMAKGIHSS-FLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              N  +                  +R E                 S +
Sbjct: 218 TPVNRTAPPPQRPAAKPELVGRPQPRRPEGPPTRQGAGPGSPRPAVSPR 266


>gi|324999251|ref|ZP_08120363.1| 30S ribosomal protein S4 [Pseudonocardia sp. P1]
          Length = 201

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR   +++      VNG  ++  +  V   D I+V
Sbjct: 92  RLDNVVYRAGLARTRRMARQLVNHGHFLVNGKKVDIPSFKVSKYDIIDV 140


>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 = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 24/218 (11%), Positives = 49/218 (22%), Gaps = 39/218 (17%)

Query: 34  MIAQQRVKV--NGILLERA-AVNVMSTDHI----------------EVDGVPLRKAERTR 74
            I    V V  NG  ++   +  + + D +                +VDG  +   +   
Sbjct: 47  WILDGHVTVTNNGKAVKIGKSYKLSAGDEVVVDASAPRDLADIRPEKVDGFRIVHLDEDI 106

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +               G + +   +    S   S           L +   G +    
Sbjct: 107 VVVDKPAGVAAHPSPGWHGPTVISALMGEGISVATSGAAERQGIVHRLDVGTSGLMVVAR 166

Query: 135 ELPSTQWLRVYRVRFHGQVDQD--------------------KLNLLKKGIVIQGICYGD 174
              +   L+                                       K  V++      
Sbjct: 167 SERAYTELKRAFKERTVDKVYHTLVQGLPDPLRGTIDAPIGRHPGNEWKFAVVEDGRNSI 226

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
               +    G  + V V L  G+  +I+  F       
Sbjct: 227 THYDVLEAFGPASLVEVHLETGRTHQIRVHFSALRHPC 264


>gi|259046817|ref|ZP_05737218.1| 30S ribosomal protein S4 [Granulicatella adiacens ATCC 49175]
 gi|259036440|gb|EEW37695.1| 30S ribosomal protein S4 [Granulicatella adiacens ATCC 49175]
          Length = 203

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 11/40 (27%), Positives = 23/40 (57%), Gaps = 1/40 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAV 52
           QR+  V+ R G+A+ RR+  +++    + VNG  ++  + 
Sbjct: 93  QRLDNVVYRLGLATTRRQARQLVNHGHITVNGKRVDIPSF 132


>gi|301780650|ref|XP_002925743.1| PREDICTED: zinc finger protein 512B-like [Ailuropoda melanoleuca]
 gi|281343240|gb|EFB18824.1| hypothetical protein PANDA_015280 [Ailuropoda melanoleuca]
          Length = 904

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 20/140 (14%), Positives = 34/140 (24%), Gaps = 6/140 (4%)

Query: 202 KKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV-SKKILREQLGPHLLEEAQVNLDAP 260
               E     V+ L          G  L G    +   K    + G           +  
Sbjct: 766 NDCCEAIYSSVSGLK-AHLASCSKGEHLVGKYCCLLCPKEFSSESGVKYHILKTHAENWF 824

Query: 261 IYSSETLVRDRPN----IISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
             S++ L + R         E        KK   +    + ++       RR+       
Sbjct: 825 RTSADPLPKHRSQDSLAPKKEEKKSLAGGKKRGRKPKERTPEEPAPKMPPRRDDWPPGGR 884

Query: 317 AKGIHSSFLSDSGQREENHR 336
            KG   S     G  +   +
Sbjct: 885 DKGARGSTGRKGGASKAPEK 904


>gi|134299804|ref|YP_001113300.1| translation initiation factor IF-2 [Desulfotomaculum reducens MI-1]
 gi|172044304|sp|A4J5X2|IF2_DESRM RecName: Full=Translation initiation factor IF-2
 gi|134052504|gb|ABO50475.1| bacterial translation initiation factor 2 (bIF-2) [Desulfotomaculum
           reducens MI-1]
          Length = 985

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 11/111 (9%), Positives = 20/111 (18%), Gaps = 3/111 (2%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
             G                  +           +      R +    +  G   Q   + 
Sbjct: 223 PYGDRPQGGQGRPYGDRPQGGQGRPYGDRPQGGQSRPYGDRPQGGQGRPYGDRPQGGQSR 282

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDS--GQREENHRRSPSFPSKRSLRRTSA 352
           P   R          G           G R +  +  P    +    R + 
Sbjct: 283 PYGDRPQGGQ-GRPYGDRPQGGQGRHYGDRPQGGQGRPQGAGRPGANRGAG 332


>gi|258508250|ref|YP_003171001.1| 30S ribosomal protein S4P [Lactobacillus rhamnosus GG]
 gi|258539461|ref|YP_003173960.1| 30S ribosomal protein S4P [Lactobacillus rhamnosus Lc 705]
 gi|257148177|emb|CAR87150.1| SSU/30S ribosomal protein S4P [Lactobacillus rhamnosus GG]
 gi|257151137|emb|CAR90109.1| SSU/30S ribosomal protein S4P [Lactobacillus rhamnosus Lc 705]
 gi|259649567|dbj|BAI41729.1| 30S ribosomal protein S4 [Lactobacillus rhamnosus GG]
          Length = 203

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 11/47 (23%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  ++ R G+AS R +  +++    + V+G  L+  +  V     I
Sbjct: 94  RLDNLVFRLGLASSRPQARQLVNHGHITVDGKRLDIPSYEVQPGQVI 140


>gi|199597503|ref|ZP_03210932.1| Ribosomal protein S4 [Lactobacillus rhamnosus HN001]
 gi|199591526|gb|EDY99603.1| Ribosomal protein S4 [Lactobacillus rhamnosus HN001]
          Length = 203

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 11/47 (23%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  ++ R G+AS R +  +++    + V+G  L+  +  V     I
Sbjct: 94  RLDNLVFRLGLASSRPQARQLVNHGHITVDGKRLDIPSYEVQPGQVI 140


>gi|42518876|ref|NP_964806.1| 30S ribosomal protein S4 [Lactobacillus johnsonii NCC 533]
 gi|227889735|ref|ZP_04007540.1| 30S ribosomal protein S4 [Lactobacillus johnsonii ATCC 33200]
 gi|238853696|ref|ZP_04644064.1| ribosomal protein S4 [Lactobacillus gasseri 202-4]
 gi|268319727|ref|YP_003293383.1| ribosomal protein S4 [Lactobacillus johnsonii FI9785]
 gi|282851624|ref|ZP_06260989.1| ribosomal protein S4 [Lactobacillus gasseri 224-1]
 gi|311110502|ref|ZP_07711899.1| ribosomal protein S4 [Lactobacillus gasseri MV-22]
 gi|61215653|sp|Q74K05|RS4_LACJO RecName: Full=30S ribosomal protein S4
 gi|152060955|sp|Q042M7|RS4_LACGA RecName: Full=30S ribosomal protein S4
 gi|41583162|gb|AAS08772.1| 30S ribosomal protein S4 [Lactobacillus johnsonii NCC 533]
 gi|227849599|gb|EEJ59685.1| 30S ribosomal protein S4 [Lactobacillus johnsonii ATCC 33200]
 gi|238833734|gb|EEQ26003.1| ribosomal protein S4 [Lactobacillus gasseri 202-4]
 gi|262398102|emb|CAX67116.1| ribosomal protein S4 [Lactobacillus johnsonii FI9785]
 gi|282557592|gb|EFB63189.1| ribosomal protein S4 [Lactobacillus gasseri 224-1]
 gi|311065656|gb|EFQ45996.1| ribosomal protein S4 [Lactobacillus gasseri MV-22]
          Length = 203

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 10/52 (19%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  ++ R G+AS R +  +++    + V+G  ++  +  V     I +   
Sbjct: 94  RLDNIVYRLGLASTREQARQLVNHGHILVDGKRVDIPSYEVKVGQEISLRDK 145


>gi|21224799|ref|NP_630578.1| dehydrogenase [Streptomyces coelicolor A3(2)]
 gi|3861428|emb|CAA22033.1| putative dehydrogenase [Streptomyces coelicolor A3(2)]
          Length = 629

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 10/127 (7%), Positives = 31/127 (24%), Gaps = 6/127 (4%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           +       ++Q G    +                 +++P              KN     
Sbjct: 454 KHADGDEGKKQPGGEPAKGQPGGEPGKNQPGGEPGKNQPGGEPGKNQPGGEPAKNQPGGE 513

Query: 294 GLSKQK------KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
              +        +      +R+ + +   +     +  +   +        P   S+ S 
Sbjct: 514 PAERGPDASAGSRSHGERAKRSQSGSPRASGKPRRAVEAAGPRSARGGSGKPGKSSRASG 573

Query: 348 RRTSAKK 354
             ++ K+
Sbjct: 574 TGSAGKR 580



 Score = 36.7 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 10/113 (8%), Positives = 25/113 (22%), Gaps = 2/113 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E        E   N             +                 ++  ++   + K+  
Sbjct: 477 EPGKNQPGGEPGKNQPGGEPGKNQPGGEPAKNQPGGEPAERGPDASAGSRSHGERAKRSQ 536

Query: 303 TPVHRRNLASNVW-MAKGIHS-SFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +   R +        A G  S    S    +      + S   + +     ++
Sbjct: 537 SGSPRASGKPRRAVEAAGPRSARGGSGKPGKSSRASGTGSAGKRPTAPSGPSR 589


>gi|329667577|gb|AEB93525.1| 30S ribosomal protein S4 [Lactobacillus johnsonii DPC 6026]
          Length = 203

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 10/52 (19%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  ++ R G+AS R +  +++    + V+G  ++  +  V     I +   
Sbjct: 94  RLDNIVYRLGLASTREQARQLVNHGHILVDGKRVDIPSYEVKVGQEISLRDK 145


>gi|289767920|ref|ZP_06527298.1| dehydrogenase [Streptomyces lividans TK24]
 gi|289698119|gb|EFD65548.1| dehydrogenase [Streptomyces lividans TK24]
          Length = 626

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 10/127 (7%), Positives = 31/127 (24%), Gaps = 6/127 (4%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           +       ++Q G    +                 +++P              KN     
Sbjct: 451 KHADGDEGKKQPGGEPAKGQPGGEPGKNQPGGEPGKNQPGGEPGKNQPGGEPAKNQPGGE 510

Query: 294 GLSKQK------KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
              +        +      +R+ + +   +     +  +   +        P   S+ S 
Sbjct: 511 PAERGPDASAGSRSHGERAKRSQSGSPRASGKPRRAVEAAGPRSARGGSGKPGKSSRASG 570

Query: 348 RRTSAKK 354
             ++ K+
Sbjct: 571 TGSAGKR 577



 Score = 36.7 bits (83), Expect = 6.1,   Method: Composition-based stats.
 Identities = 10/113 (8%), Positives = 25/113 (22%), Gaps = 2/113 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E        E   N             +                 ++  ++   + K+  
Sbjct: 474 EPGKNQPGGEPGKNQPGGEPGKNQPGGEPAKNQPGGEPAERGPDASAGSRSHGERAKRSQ 533

Query: 303 TPVHRRNLASNVW-MAKGIHS-SFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +   R +        A G  S    S    +      + S   + +     ++
Sbjct: 534 SGSPRASGKPRRAVEAAGPRSARGGSGKPGKSSRASGTGSAGKRPTAPSGPSR 586


>gi|317153933|ref|YP_004121981.1| 30S ribosomal protein S4 [Desulfovibrio aespoeensis Aspo-2]
 gi|316944184|gb|ADU63235.1| ribosomal protein S4 [Desulfovibrio aespoeensis Aspo-2]
          Length = 208

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI R G A SR +  +++     ++NG  +   ++ V + D I+V
Sbjct: 99  RLDNVIFRLGFANSRDQARQLVRHGIFQLNGRRVNVPSMQVKAEDVIQV 147


>gi|122692493|ref|NP_001073703.1| zinc finger CCHC domain-containing protein 3 [Bos taurus]
 gi|119224044|gb|AAI26596.1| Zinc finger, CCHC domain containing 3 [Bos taurus]
 gi|296481063|gb|DAA23178.1| zinc finger, CCHC domain containing 3 [Bos taurus]
          Length = 404

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 17/113 (15%), Positives = 30/113 (26%), Gaps = 1/113 (0%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL-SKQ 298
             RE   P   EE+       + +   L                + ++         S++
Sbjct: 53  EFRESRPPRREEESGSGAGGGLGAPAGLATPSLGDFPPAGRGDPKGRRRDPAGEAADSRK 112

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
           KK A    RR  A    M          D+  R     ++ +  S     +  
Sbjct: 113 KKGAAEAGRRKKAEAAAMTTPARPDAAEDAADRPPQDEQATAAGSAAGPGKGR 165



 Score = 35.9 bits (81), Expect = 9.9,   Method: Composition-based stats.
 Identities = 11/113 (9%), Positives = 31/113 (27%), Gaps = 2/113 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           RE++G   + +           S    R+  +               +          + 
Sbjct: 35  REKMGWAQVVKNLAEKKGEFRESRPPRREEESGSGAGGGLGAPAGLATPSLGDFPPAGRG 94

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                 R        A        +++G+R++    + + P++      +A +
Sbjct: 95  D--PKGRRRDPAGEAADSRKKKGAAEAGRRKKAEAAAMTTPARPDAAEDAADR 145


>gi|295676677|ref|YP_003605201.1| Fertility inhibition FinO-like protein [Burkholderia sp. CCGE1002]
 gi|295436520|gb|ADG15690.1| Fertility inhibition FinO-like protein [Burkholderia sp. CCGE1002]
          Length = 299

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 10/73 (13%), Positives = 17/73 (23%)

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
              D     + +S+  G       A P       +N     G        +        +
Sbjct: 24  GKPDRKSAARPASKSAGKPASNPGAHPGSNAERGANPGAKPGGRPGGKPAAKAGGRPDGK 83

Query: 338 SPSFPSKRSLRRT 350
             S P +    R 
Sbjct: 84  PGSRPGRPQPARH 96


>gi|261377820|ref|ZP_05982393.1| heat shock protein 15 [Neisseria cinerea ATCC 14685]
 gi|269146122|gb|EEZ72540.1| heat shock protein 15 [Neisseria cinerea ATCC 14685]
          Length = 133

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 6/63 (9%)

Query: 1  MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          MKD N    + +  R+ K + A     +R   ++ I   RV+VNG  ++  + +V   D 
Sbjct: 1  MKDNN----DSSAIRLDKWLWAARFFKTRSLAQKHIELGRVQVNGSKVKN-SKSVGIGDI 55

Query: 60 IEV 62
          IE+
Sbjct: 56 IEL 58


>gi|220928235|ref|YP_002505144.1| ribosomal protein S4 [Clostridium cellulolyticum H10]
 gi|254764580|sp|B8I807|RS4_CLOCE RecName: Full=30S ribosomal protein S4
 gi|219998563|gb|ACL75164.1| ribosomal protein S4 [Clostridium cellulolyticum H10]
          Length = 208

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+  SR E  +++      VNG  +   +  +   D I V
Sbjct: 99  RLDNVVYRLGLGTSRPESRQLVTHGHFTVNGKRVNIPSYLIKVGDVIAV 147


>gi|308189877|ref|YP_003922808.1| 30S ribosomal protein S4 [Mycoplasma fermentans JER]
 gi|307624619|gb|ADN68924.1| 30S ribosomal protein S4 [Mycoplasma fermentans JER]
          Length = 198

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ RAG AS RR+  ++++     +NG   +  ++NV     I++
Sbjct: 94  RLDNLVYRAGFASTRRQARQLVSHGHFTLNGHKADIPSMNVEVGSKIQL 142


>gi|256158666|ref|ZP_05456549.1| translation initiation factor IF-2 [Brucella ceti M490/95/1]
 gi|256254070|ref|ZP_05459606.1| translation initiation factor IF-2 [Brucella ceti B1/94]
 gi|261221211|ref|ZP_05935492.1| translation initiation factor IF-2 [Brucella ceti B1/94]
 gi|265997172|ref|ZP_06109729.1| translation initiation factor IF-2 [Brucella ceti M490/95/1]
 gi|260919795|gb|EEX86448.1| translation initiation factor IF-2 [Brucella ceti B1/94]
 gi|262551640|gb|EEZ07630.1| translation initiation factor IF-2 [Brucella ceti M490/95/1]
          Length = 951

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 8/117 (6%), Positives = 32/117 (27%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +S+  +  +       + +   +      E   R   +       + +  ++   +    
Sbjct: 151 LSRSEMDARRRALEEAQIREVEERARAVEEAKRRAEEDARRAKEREESARRQAEEEARRK 210

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           ++++           +     A+            R +  R  P+   ++   R + 
Sbjct: 211 AEEEAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAP 267



 Score = 41.3 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 12/110 (10%), Positives = 24/110 (21%), Gaps = 4/110 (3%)

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           + + E+       + +   DA           R               K   Q    S++
Sbjct: 169 REVEERARAVEEAKRRAEEDARRAKEREESARRQAEEEARRKAEEEAAKRMPQPEARSER 228

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           +  A P             +G           R +     P+     +  
Sbjct: 229 RDDARPAPYGARPQQAGRPQGGRP----QPAGRPQQGSPRPAPIIADAAP 274


>gi|238809857|dbj|BAH69647.1| hypothetical protein [Mycoplasma fermentans PG18]
          Length = 216

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ RAG AS RR+  ++++     +NG   +  ++NV     I++
Sbjct: 112 RLDNLVYRAGFASTRRQARQLVSHGHFTLNGHKADIPSMNVEVGSKIQL 160


>gi|153004799|ref|YP_001379124.1| 30S ribosomal protein S4 [Anaeromyxobacter sp. Fw109-5]
 gi|171769305|sp|A7HBP4|RS4_ANADF RecName: Full=30S ribosomal protein S4
 gi|152028372|gb|ABS26140.1| RNA-binding S4 domain protein [Anaeromyxobacter sp. Fw109-5]
          Length = 208

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  V+ R G A +R E  +++     KVNG  +   +    + D +E+   
Sbjct: 99  RLDNVVFRLGFADTRNEARQLVRHGHFKVNGRKVNIPSYLCRAGDKVELRDR 150


>gi|114763012|ref|ZP_01442442.1| ATP-dependent RNA helicase, DEAD/DEAH box family protein
           [Pelagibaca bermudensis HTCC2601]
 gi|114544336|gb|EAU47344.1| ATP-dependent RNA helicase, DEAD/DEAH box family protein
           [Roseovarius sp. HTCC2601]
          Length = 727

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 19/139 (13%), Positives = 36/139 (25%), Gaps = 9/139 (6%)

Query: 225 LGTLLAGSTRE--VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDF 282
           LG L  GST E  V+ + +            +    +    ++   +D P       D  
Sbjct: 505 LGGLGDGSTLEDGVTVRAVEGTPEFASRPPRRDGPRSDGPRNDRPRKDGPRKPRPEGDAP 564

Query: 283 TRMKKNSSQKNGLSKQKKLATP-------VHRRNLASNVWMAKGIHSSFLSDSGQREENH 335
            R + +           K   P          +         +G         G R ++ 
Sbjct: 565 ARKRPDGEAWGAKGGSAKGDKPKGSFKRDDRPKGDKPKYDKPRGDKPWGDKPRGDRPKSD 624

Query: 336 RRSPSFPSKRSLRRTSAKK 354
           +     P     +    K+
Sbjct: 625 KPWGDKPRGEGGKDWKPKR 643



 Score = 40.5 bits (93), Expect = 0.44,   Method: Composition-based stats.
 Identities = 13/112 (11%), Positives = 29/112 (25%), Gaps = 9/112 (8%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           + + +            +       +   +  +  K      G  K  K   P   R+  
Sbjct: 605 KPRGDKPWGDKPRGDRPKSDKPWGDKPRGEGGKDWKPKRDGEGGGKPFKSKRPGEGRDGP 664

Query: 312 S----NVWMAKGIHSSFLSDSGQREENH-----RRSPSFPSKRSLRRTSAKK 354
           S         +    +   D  +R  N      R  P+  + +  R    ++
Sbjct: 665 SKGFGGKPGGRPARPAAQGDKPKRPANAADTSQRFDPTGRASKGARPGKPRQ 716



 Score = 37.1 bits (84), Expect = 3.7,   Method: Composition-based stats.
 Identities = 9/111 (8%), Positives = 25/111 (22%), Gaps = 3/111 (2%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G    ++ + +            +       +   D  R  +  S K    K +      
Sbjct: 579 GSAKGDKPKGSFKRDDRPKGDKPKYDKPRGDKPWGDKPRGDRPKSDKPWGDKPRGEGGKD 638

Query: 306 HRRNLASNVWMAK--GIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +                     D   +    +     P++ + +    K+
Sbjct: 639 WKPKRDGEGGGKPFKSKRPGEGRDGPSKGFGGKPG-GRPARPAAQGDKPKR 688


>gi|227888872|ref|ZP_04006677.1| RNA-binding heat shock protein [Lactobacillus johnsonii ATCC
          33200]
 gi|227850565|gb|EEJ60651.1| RNA-binding heat shock protein [Lactobacillus johnsonii ATCC
          33200]
          Length = 90

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR   + M  Q RVKVN  +++  + +V   D IE+
Sbjct: 11 MRIDKFLKVSRLVKRRTVAKEMADQGRVKVNDRVVKS-SYDVKLGDVIEI 59


>gi|227823780|ref|YP_002827753.1| RNA-binding S4 domain protein [Sinorhizobium fredii NGR234]
 gi|227342782|gb|ACP27000.1| RNA-binding S4 domain protein [Sinorhizobium fredii NGR234]
          Length = 136

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 3/62 (4%)

Query: 3  DKNIVQENFTPQRVSKVI--ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
          +K         QR+ K +  AR  I SR   ++ I    V VNG    +++  V + D +
Sbjct: 2  EKQPPSPPAARQRLDKWLFFARL-IKSRSLAQKAIEAGHVAVNGARATQSSATVKAGDTL 60

Query: 61 EV 62
          E+
Sbjct: 61 EL 62


>gi|213619079|ref|ZP_03372905.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
          enterica serovar Typhi str. E98-2068]
          Length = 27

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 12/26 (46%), Positives = 18/26 (69%)

Query: 13 PQRVSKVIARAGIASRREVERMIAQQ 38
           +++ KV+ARAG  SRRE+E +I   
Sbjct: 2  SEKLQKVLARAGHGSRREIESIIEAG 27


>gi|207081116|gb|ACI22842.1| differential display clone 8 [Peromyscus aztecus hylocetes]
          Length = 507

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 15/125 (12%), Positives = 36/125 (28%), Gaps = 4/125 (3%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             RE   + +R+    +L             ++ TL        ++      R +    +
Sbjct: 26  EWREARLQQVRDMERLYLAHLLDEATGRAGGNNLTLNERNQRRSAKHMRAKGRNRAAFRE 85

Query: 292 KNGLSKQKKLATPVHRR----NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
           + G  ++     P  R+    +       A+G + S      +   +       P    +
Sbjct: 86  EKGHREEHPRQHPKSRKKATCSERQGSSKARGQNPSEKGKGKRVPSSKSSGGYQPLGPRM 145

Query: 348 RRTSA 352
            R + 
Sbjct: 146 GRGAD 150


>gi|148263164|ref|YP_001229870.1| 30S ribosomal protein S4 [Geobacter uraniireducens Rf4]
 gi|189045382|sp|A5GAU5|RS4_GEOUR RecName: Full=30S ribosomal protein S4
 gi|146396664|gb|ABQ25297.1| SSU ribosomal protein S4P [Geobacter uraniireducens Rf4]
          Length = 208

 Score = 42.5 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +  R G AS R E  +++      +NG  +   ++ V + D +E+
Sbjct: 99  RLDNIAYRLGFASSRIEARQLVRHGHFTLNGRKVTIPSIQVKAGDVLEL 147


>gi|291165887|gb|EFE27934.1| S4 domain protein YaaA [Filifactor alocis ATCC 35896]
          Length = 70

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 15/71 (21%), Positives = 33/71 (46%), Gaps = 8/71 (11%)

Query: 1  MKDKNIVQENFTPQRVSKVI--AR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
          MK++ I  +     ++ +++  +   +      E +  I  + VKVNG +  R    + S
Sbjct: 1  MKEQRIKIDT-EFIKLDQLLKLSNQVSTGG---EAKVCILSEEVKVNGEIETRRGKKIRS 56

Query: 57 TDHIEVDGVPL 67
           D +E++G  +
Sbjct: 57 GDKVEINGELI 67


>gi|312114758|ref|YP_004012354.1| RNA-binding S4 domain protein [Rhodomicrobium vannielii ATCC
          17100]
 gi|311219887|gb|ADP71255.1| RNA-binding S4 domain protein [Rhodomicrobium vannielii ATCC
          17100]
          Length = 105

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 11 FTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
             QR+ K +  A  + SR    ++I +  ++VN   + +AA  +   D + 
Sbjct: 4  SDEQRLDKWLWHARFVKSRSLAAKLIEEGCIRVNRQRVVKAATCIKCGDVLT 55


>gi|29833341|ref|NP_827975.1| serine/threonine protein kinase [Streptomyces avermitilis MA-4680]
 gi|29610464|dbj|BAC74510.1| putative serine/threonine protein kinase [Streptomyces avermitilis
           MA-4680]
          Length = 433

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 14/101 (13%), Positives = 20/101 (19%), Gaps = 4/101 (3%)

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
             + A        VR                ++ + Q+     Q    TP  R       
Sbjct: 278 KEIAAREAQGIADVRPPAQRGEPDRPSGRLAEQYAEQRTQRRPQGAPGTPPPRTGGGPRS 337

Query: 315 WMAKGIHSSFLSDSGQREEN----HRRSPSFPSKRSLRRTS 351
                      + SG R        R SP            
Sbjct: 338 GSRPTPAPRNSTRSGSRPAPRSGAGRSSPRTTGTGRRPANP 378


>gi|319943531|ref|ZP_08017813.1| translation initiation factor IF-2 [Lautropia mirabilis ATCC 51599]
 gi|319743346|gb|EFV95751.1| translation initiation factor IF-2 [Lautropia mirabilis ATCC 51599]
          Length = 500

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 10/135 (7%), Positives = 24/135 (17%), Gaps = 18/135 (13%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS- 296
            +  R++  P               +     +      S  P       +          
Sbjct: 321 PEEFRQKQAPAQPARKPGQPGQRHGAPGGKPQGNRRHGSGRPGGKPGEGRQGKAAAAQGP 380

Query: 297 -----------------KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
                            +Q +                 +   +      G+   N    P
Sbjct: 381 AGNTPEAAAQDANAPANRQGRPHGKGRHGQPRRAEGGNRPSRNPADGKQGENTANAGNRP 440

Query: 340 SFPSKRSLRRTSAKK 354
           S   +R       ++
Sbjct: 441 SQGPRRPRTEQEGRR 455


>gi|319777073|ref|YP_004136724.1| 30S ribosomal protein s4 [Mycoplasma fermentans M64]
 gi|318038148|gb|ADV34347.1| 30S ribosomal protein S4 [Mycoplasma fermentans M64]
          Length = 198

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ RAG AS RR+  ++++     +NG   +  ++NV     I++
Sbjct: 94  RLDNLVYRAGFASTRRQARQLVSHGHFTLNGHKADIPSMNVEVGSKIQL 142


>gi|309390250|gb|ADO78130.1| SSU ribosomal protein S4P [Halanaerobium praevalens DSM 2228]
          Length = 198

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  ++ RAG A S R+  +M+    + VNG  ++  +  +   D I +   
Sbjct: 89  RLDNLVYRAGFARSIRQARQMVVHGHILVNGKKIDIPSYAIKIGDQISLRNK 140


>gi|327279406|ref|XP_003224447.1| PREDICTED: serine/threonine-protein kinase PRP4 homolog [Anolis
           carolinensis]
          Length = 1005

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 12/127 (9%), Positives = 29/127 (22%), Gaps = 6/127 (4%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R+      R +    +    +      + S       +     E        +  S ++ 
Sbjct: 254 RKSRSPEDRSKAEEKIKSRERKKSPVVVESKSRDRGKKSKSPVEQRSKSKDRRSRSKERK 313

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL------ 347
               + +      +          +    S       +  +    P    +RS       
Sbjct: 314 SRRSETEREKKPIKSPSKDASSGKENRSPSRRPGRSPKGRSLTPKPRDKLRRSRSPLLND 373

Query: 348 RRTSAKK 354
           RR+   K
Sbjct: 374 RRSKQSK 380



 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 15/119 (12%), Positives = 33/119 (27%), Gaps = 2/119 (1%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           ++ ++ +         +         S++ V  R            R  + S  +     
Sbjct: 266 EEKIKSRERKKSPVVVESKSRDRGKKSKSPVEQRSKSKDRRSRSKERKSRRSETEREKKP 325

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF--PSKRSLRRTSAKK 354
            K  +          +     G      S + +  +  RRS S     +RS +  S  +
Sbjct: 326 IKSPSKDASSGKENRSPSRRPGRSPKGRSLTPKPRDKLRRSRSPLLNDRRSKQSKSPSR 384



 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 16/102 (15%), Positives = 23/102 (22%), Gaps = 6/102 (5%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
            +        S     R R         +  R KK     +  +   K      RR   S
Sbjct: 290 KKSKSPVEQRSKSKDRRSRSKERKSRRSETEREKKPIKSPSKDASSGKENRSPSRRPGRS 349

Query: 313 NVWMAKGIHSSFLSDSGQ------REENHRRSPSFPSKRSLR 348
               +            +      R     +SPS     S R
Sbjct: 350 PKGRSLTPKPRDKLRRSRSPLLNDRRSKQSKSPSRNRSPSRR 391



 Score = 37.5 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 13/119 (10%), Positives = 33/119 (27%), Gaps = 6/119 (5%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R     +    +  +        ++  R +  ++ E        K  S  +     + + 
Sbjct: 247 RRSQEKNRKSRSPEDRSKAEEKIKSRERKKSPVVVESKSRDRGKKSKSPVEQRSKSKDRR 306

Query: 302 ATPVHRRNLASNVW------MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +    R++  S          +    +S   ++        RSP   S     R   ++
Sbjct: 307 SRSKERKSRRSETEREKKPIKSPSKDASSGKENRSPSRRPGRSPKGRSLTPKPRDKLRR 365


>gi|297159624|gb|ADI09336.1| 30S ribosomal protein S4 [Streptomyces bingchenggensis BCW-1]
          Length = 208

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG A SR    +++    + VNG   +  +  V   D IEV
Sbjct: 99  RLDNVVYRAGFAKSRDHARQLVRHGHINVNGRKTDIPSARVAVNDIIEV 147


>gi|282864223|ref|ZP_06273279.1| serine/threonine protein kinase [Streptomyces sp. ACTE]
 gi|282560710|gb|EFB66256.1| serine/threonine protein kinase [Streptomyces sp. ACTE]
          Length = 451

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 14/111 (12%), Positives = 23/111 (20%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R        +E                  R +  +  P    R    S            
Sbjct: 279 RRPPAQRRGQELDRPTGRLEGPYTEQQTRRSSGPASAPRPSARRPAPSRSGAAPRTGGSG 338

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             P   R  A          ++  + +  R        +  + RS  R  A
Sbjct: 339 PRPQVSRGGARPGKRPHTTGAAGGAGTKGRPGTRPGPRTTGTGRSGPRRPA 389



 Score = 41.7 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 13/114 (11%), Positives = 31/114 (27%), Gaps = 1/114 (0%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           + + L P +      + +    + +  +R +     E      R      +   L +   
Sbjct: 236 VHDALAPLVRACLAKDPEERPSTLQLSMRLKEIAAREAQGLHERRPPAQRRGQELDRPTG 295

Query: 301 L-ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               P   +    +   A     S    +  R     R+     +  + R  A+
Sbjct: 296 RLEGPYTEQQTRRSSGPASAPRPSARRPAPSRSGAAPRTGGSGPRPQVSRGGAR 349



 Score = 40.5 bits (93), Expect = 0.43,   Method: Composition-based stats.
 Identities = 18/129 (13%), Positives = 25/129 (19%), Gaps = 13/129 (10%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
             +     L   +  +     +A           R     + P           Q    S
Sbjct: 251 DPEERPSTLQLSMRLKEIAAREAQGLHERRPPAQRRGQELDRPTGRLEGPYTEQQTRRSS 310

Query: 297 KQKKLATPVHRRNLASNVWMAK---GIHSSFLSDSGQREENHRR----------SPSFPS 343
                  P  RR   S    A    G         G      R           +   P 
Sbjct: 311 GPASAPRPSARRPAPSRSGAAPRTGGSGPRPQVSRGGARPGKRPHTTGAAGGAGTKGRPG 370

Query: 344 KRSLRRTSA 352
            R   RT+ 
Sbjct: 371 TRPGPRTTG 379



 Score = 36.3 bits (82), Expect = 6.5,   Method: Composition-based stats.
 Identities = 12/91 (13%), Positives = 17/91 (18%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           +++  R   GP           AP  S             +V     R  K         
Sbjct: 302 TEQQTRRSSGPASAPRPSARRPAPSRSGAAPRTGGSGPRPQVSRGGARPGKRPHTTGAAG 361

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSD 327
                  P  R    +      G        
Sbjct: 362 GAGTKGRPGTRPGPRTTGTGRSGPRRPANPR 392


>gi|218780078|ref|YP_002431396.1| hypothetical protein Dalk_2235 [Desulfatibacillum alkenivorans
           AK-01]
 gi|218761462|gb|ACL03928.1| hypothetical protein Dalk_2235 [Desulfatibacillum alkenivorans
           AK-01]
          Length = 407

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 9/82 (10%), Positives = 19/82 (23%)

Query: 272 PNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR 331
            N     P    R  ++S         K+      ++    +     G        + + 
Sbjct: 325 ENSGRGKPYRQGRQSRHSGSDQWEQPDKRRGGGGFQKPGKKDGPERPGPRKGPGKPAAKG 384

Query: 332 EENHRRSPSFPSKRSLRRTSAK 353
               R       K +  R   +
Sbjct: 385 SGPGRPKAKPGRKPNAPRKKNR 406



 Score = 40.2 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 12/94 (12%), Positives = 28/94 (29%), Gaps = 2/94 (2%)

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
            + D P +S  +          +     +   +   ++ G    +K              
Sbjct: 316 KDEDQPDFSENSGRGKPYRQGRQSRHSGSDQWEQPDKRRGGGGFQKPGKKD--GPERPGP 373

Query: 315 WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
               G  ++  S  G+ +    R P+ P K++  
Sbjct: 374 RKGPGKPAAKGSGPGRPKAKPGRKPNAPRKKNRP 407


>gi|260799037|ref|XP_002594506.1| hypothetical protein BRAFLDRAFT_87699 [Branchiostoma floridae]
 gi|229279740|gb|EEN50517.1| hypothetical protein BRAFLDRAFT_87699 [Branchiostoma floridae]
          Length = 219

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 7/117 (5%), Positives = 15/117 (12%), Gaps = 2/117 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT--RMKKNSSQ 291
           R    + + E +   L     +    P                         R       
Sbjct: 64  RLFEGREMPEGIERLLERLLGLRPKRPGPDGRPERPGPDGRPERPGPGGRPERPGPGGRP 123

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           +      +        R                         +    P    +    
Sbjct: 124 ERPGPDGRPERPGPGDRPERPGPGDRPERPGPGDRPERPGPGDRPERPGPGGRPERP 180


>gi|21674972|ref|NP_663037.1| 30S ribosomal protein S4 [Chlorobium tepidum TLS]
 gi|26399358|sp|P59129|RS4_CHLTE RecName: Full=30S ribosomal protein S4
 gi|21648204|gb|AAM73379.1| ribosomal protein S4 [Chlorobium tepidum TLS]
          Length = 203

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G + SR    +++    + VNG  +   +  V   D IE 
Sbjct: 94  RLDNVVYRCGFSPSRAGARQLVTHGHMLVNGKKVNIPSFLVSPGDQIEF 142


>gi|71657429|ref|XP_817230.1| hypothetical protein [Trypanosoma cruzi strain CL Brener]
 gi|70882408|gb|EAN95379.1| hypothetical protein, conserved [Trypanosoma cruzi]
          Length = 937

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 12/119 (10%), Positives = 34/119 (28%), Gaps = 1/119 (0%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           + +    E+      +E      A          ++        +     ++ + Q+   
Sbjct: 140 MRRAEQEEEARRRAEQEEMARRRAEQEEEARRRAEQEEEARRRAEQEEEARRRAEQEEEA 199

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            ++ +      RR         +           ++EE  RR  +   + + RR   ++
Sbjct: 200 RRRAEQEGMARRRAEQEEEARRRAEQEGMARRRAEQEEEARRR-AEQEEEARRRAEQEE 257



 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 11/110 (10%), Positives = 25/110 (22%), Gaps = 1/110 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                 E +          E   R                +     +     +++     
Sbjct: 138 EAMRRAEQEEEARRRAEQEEMARRRAEQEEEARRRAEQEEEARRRAEQEEEARRRAEQEE 197

Query: 306 HRRNLASNVWMAKGIHSS-FLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             R  A    MA+        +     +E   R  +   + + RR   ++
Sbjct: 198 EARRRAEQEGMARRRAEQEEEARRRAEQEGMARRRAEQEEEARRRAEQEE 247



 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 10/115 (8%), Positives = 31/115 (26%), Gaps = 1/115 (0%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
              E+      +E +    A          ++        +     ++ + Q+    ++ 
Sbjct: 164 EQEEEARRRAEQEEEARRRAEQEEEARRRAEQEEEARRRAEQEGMARRRAEQEEEARRRA 223

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +      RR         +           ++EE   R  +   + +  R   ++
Sbjct: 224 EQEGMARRRAEQEEEARRRAEQEEEARRRAEQEE-EARRRAEQEEMARSRAEQEE 277


>gi|312877392|ref|ZP_07737357.1| ribosomal protein S4 [Caldicellulosiruptor lactoaceticus 6A]
 gi|311795866|gb|EFR12230.1| ribosomal protein S4 [Caldicellulosiruptor lactoaceticus 6A]
          Length = 208

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+  V+ R G AS R E   ++     KVNG  +   +  V   D IEVD
Sbjct: 99  RLDNVVYRLGFASSRGEARVLVTHAHFKVNGRTVNIPSYLVKVGDEIEVD 148


>gi|157737265|ref|YP_001489948.1| 30S ribosomal protein S4 [Arcobacter butzleri RM4018]
 gi|315636982|ref|ZP_07892206.1| 30S ribosomal protein S4 [Arcobacter butzleri JV22]
 gi|172045648|sp|A8ETK5|RS4_ARCB4 RecName: Full=30S ribosomal protein S4
 gi|157699119|gb|ABV67279.1| 30S ribosomal protein S4 [Arcobacter butzleri RM4018]
 gi|315478812|gb|EFU69521.1| 30S ribosomal protein S4 [Arcobacter butzleri JV22]
          Length = 208

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G A+ R    +      V V+G  ++  +  V     IE+
Sbjct: 98  QRLDNVVFRMGFATTRANARQFTTHGHVLVDGKKVDIPSYLVKPGQKIEI 147


>gi|166211472|ref|ZP_02237507.1| putative ATP-dependent RNA helicase RhlE [Yersinia pestis biovar
           Antiqua str. B42003004]
 gi|167400283|ref|ZP_02305796.1| putative ATP-dependent RNA helicase RhlE [Yersinia pestis biovar
           Antiqua str. UG05-0454]
 gi|167424187|ref|ZP_02315940.1| putative ATP-dependent RNA helicase RhlE [Yersinia pestis biovar
           Mediaevalis str. K1973002]
 gi|294503190|ref|YP_003567252.1| putative ATP-dependent RNA helicase rhlE [Yersinia pestis Z176003]
 gi|166207243|gb|EDR51723.1| putative ATP-dependent RNA helicase RhlE [Yersinia pestis biovar
           Antiqua str. B42003004]
 gi|167050232|gb|EDR61640.1| putative ATP-dependent RNA helicase RhlE [Yersinia pestis biovar
           Antiqua str. UG05-0454]
 gi|167057036|gb|EDR66799.1| putative ATP-dependent RNA helicase RhlE [Yersinia pestis biovar
           Mediaevalis str. K1973002]
 gi|262361229|gb|ACY57950.1| putative ATP-dependent RNA helicase rhlE [Yersinia pestis D106004]
 gi|294353649|gb|ADE63990.1| putative ATP-dependent RNA helicase rhlE [Yersinia pestis Z176003]
          Length = 305

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 13/101 (12%), Positives = 29/101 (28%), Gaps = 2/101 (1%)

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL--SKQKKLATPVHRRNLAS 312
           V+    +   E L++     I+    +     K    +NG      ++            
Sbjct: 205 VDEHKLLRDIERLLKREIPRIALDGYEPDPSIKADPIQNGRQGRGAQRPGMGRGSSAGRP 264

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                        +   + + + +R P+ PS R   R   +
Sbjct: 265 QNGGGAAGRGDSRNSRPRSQADGQRRPAGPSSRGRSRNPGE 305


>gi|148243069|ref|YP_001228226.1| translation initiation factor IF-2 [Synechococcus sp. RCC307]
 gi|166198942|sp|A5GVG4|IF2_SYNR3 RecName: Full=Translation initiation factor IF-2
 gi|147851379|emb|CAK28873.1| Translation initiation factor IF-2 [Synechococcus sp. RCC307]
          Length = 1106

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 9/126 (7%), Positives = 24/126 (19%), Gaps = 6/126 (4%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           E+  K +R +       +                     ++            +  ++  
Sbjct: 306 ELVGKPIRREPNAPQGRQGGAPSRPGGPGGMRKPVSPGELMQLQKPGSRPTPGDGPRRPP 365

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK------RSLR 348
                +            N   A      +   +        R P +         RS  
Sbjct: 366 ARPGSEAPRRPGEAPNRPNAPTAPPRRPGYRPAAAPGMAGRPRRPDWDDSARLDALRSRS 425

Query: 349 RTSAKK 354
               ++
Sbjct: 426 PQKQRQ 431



 Score = 35.9 bits (81), Expect = 8.6,   Method: Composition-based stats.
 Identities = 11/102 (10%), Positives = 19/102 (18%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G        V+    +   +   R  P      P      +         ++      P 
Sbjct: 331 GGPGGMRKPVSPGELMQLQKPGSRPTPGDGPRRPPARPGSEAPRRPGEAPNRPNAPTAPP 390

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            R                          +  RS S   +R  
Sbjct: 391 RRPGYRPAAAPGMAGRPRRPDWDDSARLDALRSRSPQKQRQK 432


>gi|295838449|ref|ZP_06825382.1| YjeF family protein [Streptomyces sp. SPB74]
 gi|295827000|gb|EFG65175.1| YjeF family protein [Streptomyces sp. SPB74]
          Length = 706

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 14/107 (13%), Positives = 22/107 (20%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G      A  +  +P  S     R             +R  +           +      
Sbjct: 426 GSRPRARATSSPVSPAPSWPPASRRATPPRPPPTSTGSRPAERPVAAGAAPPSRPTTWRR 485

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             R        A+G      +    R+      P    K    R  A
Sbjct: 486 RSRERGGTYGRAEGARKGGATRPRARKGRGAARPPRAEKDVTPRPRA 532


>gi|283780493|ref|YP_003371248.1| hypothetical protein Psta_2720 [Pirellula staleyi DSM 6068]
 gi|283438946|gb|ADB17388.1| hypothetical protein Psta_2720 [Pirellula staleyi DSM 6068]
          Length = 768

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 9/108 (8%), Positives = 17/108 (15%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G       Q        + E   +       E P      +    +      +     P 
Sbjct: 232 GQQADTREQAEAILKDIAKEAGDQVPGEGSGEAPSGSKPGEGKPGEGKPGEGKPGEGKPG 291

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             +         K              +     P        +    K
Sbjct: 292 EGKPGEGKPGEGKPGEGKPGEGKPGEGKPGEGKPGEGKPGEGKPGEGK 339



 Score = 41.7 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 10/103 (9%), Positives = 18/103 (17%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           REQ    L + A+   D                    P +    +    +      +   
Sbjct: 238 REQAEAILKDIAKEAGDQVPGEGSGEAPSGSKPGEGKPGEGKPGEGKPGEGKPGEGKPGE 297

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
             P   +         K              +     P     
Sbjct: 298 GKPGEGKPGEGKPGEGKPGEGKPGEGKPGEGKPGEGKPGEGKP 340



 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 10/117 (8%), Positives = 24/117 (20%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            +K + E       E  Q         ++T  +    +     +   ++    S +    
Sbjct: 208 KQKAILEATESVRAEGIQKLGPIAGQQADTREQAEAILKDIAKEAGDQVPGEGSGEAPSG 267

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            +     P   +         K              +     P        +    K
Sbjct: 268 SKPGEGKPGEGKPGEGKPGEGKPGEGKPGEGKPGEGKPGEGKPGEGKPGEGKPGEGK 324



 Score = 37.9 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 6/99 (6%), Positives = 13/99 (13%)

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
               A        +       +          +  S       +     P   +      
Sbjct: 231 AGQQADTREQAEAILKDIAKEAGDQVPGEGSGEAPSGSKPGEGKPGEGKPGEGKPGEGKP 290

Query: 315 WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              K              +     P        +    K
Sbjct: 291 GEGKPGEGKPGEGKPGEGKPGEGKPGEGKPGEGKPGEGK 329


>gi|254383925|ref|ZP_04999272.1| hypothetical protein SSAG_03672 [Streptomyces sp. Mg1]
 gi|194342817|gb|EDX23783.1| hypothetical protein SSAG_03672 [Streptomyces sp. Mg1]
          Length = 810

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 11/131 (8%), Positives = 26/131 (19%), Gaps = 2/131 (1%)

Query: 226 GTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
             L     RE+      ++ G H   +                R          +     
Sbjct: 620 KGLRPPEWREIRTPAYADRPGRHARLDGAGRPVRRPARRGDRARRAHQGRVRRGEPVHGP 679

Query: 286 KKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS--FPS 343
            ++  +      +         R     +   +    +      Q     R         
Sbjct: 680 GRHGPRGPPAGLRPARGLQAVHRPGRQRLRAERRRPRAPDRPGDQHPRAGRHQRPVVRGQ 739

Query: 344 KRSLRRTSAKK 354
           +R+ R     +
Sbjct: 740 RRAARPVRQGR 750


>gi|114327047|ref|YP_744204.1| 23S rRNA Gm2251 methyltransferase [Granulibacter bethesdensis
           CGDNIH1]
 gi|114315221|gb|ABI61281.1| 23S rRNA Gm2251 methyltransferase [Granulibacter bethesdensis
           CGDNIH1]
          Length = 441

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 10/125 (8%), Positives = 26/125 (20%)

Query: 230 AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
            G+ R       R +      E  +   +            +            R    +
Sbjct: 48  EGTARSEQGGEYRSRSDKQHFEGNRPTREQRFAERGERPSYQGGERPAGGKPSFRSHDGA 107

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
            +    S ++    P          +  +    +     G+R    R             
Sbjct: 108 PRSGHHSSERTERRPRFEAPREEQSFGERTERPTRHRQGGERPSGGRSFRPRDGANRSDE 167

Query: 350 TSAKK 354
            + ++
Sbjct: 168 HAERR 172


>gi|260438332|ref|ZP_05792148.1| translation initiation factor IF-2 [Butyrivibrio crossotus DSM
           2876]
 gi|292808919|gb|EFF68124.1| translation initiation factor IF-2 [Butyrivibrio crossotus DSM
           2876]
          Length = 938

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 15/106 (14%), Positives = 23/106 (21%), Gaps = 1/106 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R Q      +   V  D           DRP       D   R             +   
Sbjct: 153 RPQGAIRPSDRVNVKPDKQQGDRPARSGDRPYGDRNQGDRPQRNNNRPYGDRNQGDRPAR 212

Query: 302 ATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRS 346
                  +       A+ G       + G R + +   P+    R 
Sbjct: 213 NGDRPYGDRNQGDRPARNGDRPYGDRNQGDRPQRNNDRPARNGGRF 258



 Score = 37.5 bits (85), Expect = 2.8,   Method: Composition-based stats.
 Identities = 17/105 (16%), Positives = 25/105 (23%), Gaps = 1/105 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R Q         +   D           DRP       D   R             + + 
Sbjct: 187 RNQGDRPQRNNNRPYGDRNQGDRPARNGDRPYGDRNQGDRPARNGDRPYGDRNQGDRPQR 246

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLS-DSGQREENHRRSPSFPSKR 345
                 RN        +G    F   D+G R + +   P+    R
Sbjct: 247 NNDRPARNGGRFNDKFQGGKPEFNKEDNGSRPQRNNDRPARRDDR 291


>gi|258406160|ref|YP_003198902.1| 30S ribosomal protein S4 [Desulfohalobium retbaense DSM 5692]
 gi|257798387|gb|ACV69324.1| ribosomal protein S4 [Desulfohalobium retbaense DSM 5692]
          Length = 208

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SR +  +++     ++NG  +   ++ V   D IEV
Sbjct: 99  RLDNVVYRLGFANSREQARQLVRHGHFELNGRRVNIPSLQVREGDAIEV 147


>gi|290962169|ref|YP_003493351.1| protein serine/threonine kinase [Streptomyces scabiei 87.22]
 gi|260651695|emb|CBG74820.1| putative protein serine/threonine kinase [Streptomyces scabiei
           87.22]
          Length = 655

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 6/112 (5%), Positives = 18/112 (16%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           ++  + ++        + +  L A +                                  
Sbjct: 262 LTAMLAKDPAHRITAADTEAALSAIVTPETRPRTGPVPGPRPRWAHAPAPAGPGGPALPR 321

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
                            + W      SS  ++           P    +   
Sbjct: 322 PAPGPPWHAPSDGPGGQDGWSPPERRSSGGTEPAPPPRTAGDRPGAGGRVRR 373


>gi|296810354|ref|XP_002845515.1| 37S ribosomal protein NAM9 [Arthroderma otae CBS 113480]
 gi|238842903|gb|EEQ32565.1| 37S ribosomal protein NAM9 [Arthroderma otae CBS 113480]
          Length = 477

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 1/56 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+   I RA  AS  R+  + +    V VNG  ++     +   D  +VD   +  
Sbjct: 131 RLDVAIFRALFASSTRQARQFVIHGGVTVNGKKMQYPGYLLNPGDMFQVDPERVMY 186


>gi|255505517|ref|ZP_05346586.3| putative ribosome-associated heat shock protein Hsp15 [Bryantella
          formatexigens DSM 14469]
 gi|255267350|gb|EET60555.1| putative ribosome-associated heat shock protein Hsp15 [Bryantella
          formatexigens DSM 14469]
          Length = 106

 Score = 42.1 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 25/61 (40%), Gaps = 2/61 (3%)

Query: 3  DKNIVQENFTPQRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +       T  R+ K +  + +  RR          RV VNG   + A+VN+   D IE
Sbjct: 17 SRRDKDVRETEMRLDKFLKVSRLIKRRTVANEACDAGRVLVNGRTAK-ASVNIKEGDIIE 75

Query: 62 V 62
          +
Sbjct: 76 I 76


>gi|293363785|ref|ZP_06610526.1| ribosomal protein S4 [Mycoplasma alligatoris A21JP2]
 gi|292552651|gb|EFF41420.1| ribosomal protein S4 [Mycoplasma alligatoris A21JP2]
          Length = 199

 Score = 42.1 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 11/91 (12%), Positives = 32/91 (35%), Gaps = 1/91 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  ++ RAG A +RR+  +++      V+G   +  ++++     + +     +  + T
Sbjct: 95  RLDNLVYRAGFAQTRRQARQLVNHNHFLVDGKKADIPSMSIKLGSVVTLKEKTQKNVQVT 154

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
                      +T          + +     
Sbjct: 155 DALANKPAAAWLTRKDFTVKFDRLPERNEMH 185


>gi|289523408|ref|ZP_06440262.1| S4 RNA-binding domain protein [Anaerobaculum hydrogeniformans
          ATCC BAA-1850]
 gi|289503100|gb|EFD24264.1| S4 RNA-binding domain protein [Anaerobaculum hydrogeniformans
          ATCC BAA-1850]
          Length = 89

 Score = 42.1 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   + MIA   V++NG  ++ A+  V   D +EV
Sbjct: 1  MRIDKYLKISHIVKRRSVAQEMIAAGVVRLNGRPVK-ASSMVKVGDIVEV 49


>gi|256784039|ref|ZP_05522470.1| dehydrogenase [Streptomyces lividans TK24]
          Length = 632

 Score = 42.1 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 10/127 (7%), Positives = 31/127 (24%), Gaps = 6/127 (4%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           +       ++Q G    +                 +++P              KN     
Sbjct: 457 KHADGDEGKKQPGGEPAKGQPGGEPGKNQPGGEPGKNQPGGEPGKNQPGGEPAKNQPGGE 516

Query: 294 GLSKQK------KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
              +        +      +R+ + +   +     +  +   +        P   S+ S 
Sbjct: 517 PAERGPDASAGSRSHGERAKRSQSGSPRASGKPRRAVEAAGPRSARGGSGKPGKSSRASG 576

Query: 348 RRTSAKK 354
             ++ K+
Sbjct: 577 TGSAGKR 583



 Score = 36.3 bits (82), Expect = 7.1,   Method: Composition-based stats.
 Identities = 10/113 (8%), Positives = 25/113 (22%), Gaps = 2/113 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E        E   N             +                 ++  ++   + K+  
Sbjct: 480 EPGKNQPGGEPGKNQPGGEPGKNQPGGEPAKNQPGGEPAERGPDASAGSRSHGERAKRSQ 539

Query: 303 TPVHRRNLASNVW-MAKGIHS-SFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +   R +        A G  S    S    +      + S   + +     ++
Sbjct: 540 SGSPRASGKPRRAVEAAGPRSARGGSGKPGKSSRASGTGSAGKRPTAPSGPSR 592


>gi|212704405|ref|ZP_03312533.1| hypothetical protein DESPIG_02460 [Desulfovibrio piger ATCC 29098]
 gi|212672126|gb|EEB32609.1| hypothetical protein DESPIG_02460 [Desulfovibrio piger ATCC 29098]
          Length = 675

 Score = 42.1 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 13/120 (10%), Positives = 27/120 (22%), Gaps = 1/120 (0%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R  S +  R  +     E+   +        E   +D          D    + +  +  
Sbjct: 554 RSASPEEPRRNVRDRQ-EDRYGDRPFGRRPGERDGQDGSFRDRRNGSDRPPRRDDRREAP 612

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               + +   P    +   +                 R    RRS       +  R   +
Sbjct: 613 ERPARHQDRRPGRYEDGRPDRRDDPRAFPRNDRRPDGRRPGDRRSGDRRQGDASGRGRGR 672


>gi|111224987|ref|YP_715781.1| hypothetical protein FRAAL5624 [Frankia alni ACN14a]
 gi|111152519|emb|CAJ64257.2| hypothetical protein FRAAL5624 [Frankia alni ACN14a]
          Length = 174

 Score = 42.1 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 10/114 (8%), Positives = 22/114 (19%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R +    L       L  ++            T+ R +            R ++ +    
Sbjct: 39  RTLPVGSLSRPEAITLSSDSGQIEARSCRGFGTVFRPKTVPNPRHDSVHGRSQRGTKWVA 98

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
                +        R+                     R    R  P    + + 
Sbjct: 99  RPVAAEGGEPTPRPRSGRPGSGRPGSGRPRSGRSGPGRSGPGRSGPGRSDRAAR 152



 Score = 37.1 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 9/78 (11%), Positives = 14/78 (17%)

Query: 274 IISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREE 333
               VP+         SQ+      + +A                            R  
Sbjct: 74  RPKTVPNPRHDSVHGRSQRGTKWVARPVAAEGGEPTPRPRSGRPGSGRPGSGRPRSGRSG 133

Query: 334 NHRRSPSFPSKRSLRRTS 351
             R  P         R +
Sbjct: 134 PGRSGPGRSGPGRSDRAA 151


>gi|33596095|ref|NP_883738.1| putative heat shock protein [Bordetella parapertussis 12822]
 gi|33573098|emb|CAE36740.1| putative heat shock protein [Bordetella parapertussis]
          Length = 126

 Score = 42.1 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 2/52 (3%)

Query: 12 TPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             R+ K + A     +R    + I + RV+VNG   +  A  V   D + +
Sbjct: 2  DKIRLDKWLWAARFYKTRSLAVQEIGKGRVQVNGQPAK-PAREVAPGDVVCI 52


>gi|162451363|ref|YP_001613730.1| 30S ribosomal protein S4 [Sorangium cellulosum 'So ce 56']
 gi|161161945|emb|CAN93250.1| 30S ribosomal protein S4 [Sorangium cellulosum 'So ce 56']
          Length = 203

 Score = 42.1 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 3/50 (6%)

Query: 15  RVSKVIARAGIASRR--EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI RAG A R      +++A   V +NG  ++  +  V   + + V
Sbjct: 93  RLDNVIFRAGFA-RTIPAARQLVAHGHVLINGKRVDIPSYRVTIGETVSV 141


>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 = 42.1 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 8/97 (8%), Positives = 26/97 (26%), Gaps = 2/97 (2%)

Query: 259 APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA- 317
               + + L +  P             +  ++       + +   P+  R          
Sbjct: 1   MSRRTKKPLAKRGPGGDRPKAGRPAAKRGPAASGPVRGNRGEDGRPISARPQREPRGERA 60

Query: 318 -KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            +       ++  +R  + R   + P +   R  ++ 
Sbjct: 61  ERPATKRPAAERPERPASDRPQSARPGRPPARFGASS 97



 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 6/107 (5%), Positives = 18/107 (16%), Gaps = 1/107 (0%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                +  +    P        R                +    +      Q++      
Sbjct: 1   MSRRTKKPLAKRGPGGDRPKAGRPAAKRGPAASGPVRGNRGEDGRPISARPQREPRGERA 60

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            R         +    +       R      +    S  +    + +
Sbjct: 61  ERPATKRPAAERPERPASDRPQSARP-GRPPARFGASSATRPPRAQR 106


>gi|115314194|ref|YP_762917.1| 30S ribosomal protein S4 [Francisella tularensis subsp. holarctica
           OSU18]
 gi|122325768|sp|Q0BNQ4|RS4_FRATO RecName: Full=30S ribosomal protein S4
 gi|115129093|gb|ABI82280.1| ribosomal protein S4 [Francisella tularensis subsp. holarctica
           OSU18]
          Length = 206

 Score = 42.1 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 28/73 (38%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G A +R E  +++  + + VNG      +  V   D + V     ++    
Sbjct: 97  RLDNVVYRMGFAATRAEARQLVVHKGIMVNGHTCNVPSAQVKVGDVVAVREKAKKQLRIQ 156

Query: 74  RLWLYHKPIGLVT 86
                 K    ++
Sbjct: 157 NAVELAKHRKELS 169


>gi|111022834|ref|YP_705806.1| hypothetical protein RHA1_ro05871 [Rhodococcus jostii RHA1]
 gi|110822364|gb|ABG97648.1| conserved hypothetical protein [Rhodococcus jostii RHA1]
          Length = 280

 Score = 42.1 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 15/99 (15%), Positives = 25/99 (25%)

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
                             +       R    SE      R +   + +      ++ ATP
Sbjct: 143 QQRKTGPARTSERRRAQRAPRAARPRRAPEESEQSPPPRRARDKDAAREHPRSARRAATP 202

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
             RR+ +S    A        +    R    R S +  S
Sbjct: 203 PPRRSSSSGGRTAPPPPMVDRAAQAPRSAPPRTSQAPRS 241


>gi|32492136|emb|CAE03024.1| OSJNBa0091D06.20 [Oryza sativa Japonica Group]
          Length = 884

 Score = 42.1 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 14/109 (12%), Positives = 26/109 (23%), Gaps = 2/109 (1%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
             L  + +      I        +R     +      R ++++    G +   +   P  
Sbjct: 221 LPLSCDPERANILTIMQEVGASGERAPRGHDGAGGSRRGEQSTPGG-GRASGPRDGGPGG 279

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQRE-ENHRRSPSFPSKRSLRRTSAKK 354
            R   +     +    S     G        R P      S      KK
Sbjct: 280 SRPTDARGKRKQEDTPSPSPPRGGGAVRASSRRPEGAVPTSRPEGKRKK 328



 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 13/115 (11%), Positives = 25/115 (21%), Gaps = 1/115 (0%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +S+ +L     P       +  +                 S   +  T     +S     
Sbjct: 216 ISQGVLPLSCDPERANILTIMQEVGASGERAPRGHDGAGGSRRGEQSTPGGGRASGPRDG 275

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFL-SDSGQREENHRRSPSFPSKRSLRR 349
                  T    +    +               S +R E    +     KR  +R
Sbjct: 276 GPGGSRPTDARGKRKQEDTPSPSPPRGGGAVRASSRRPEGAVPTSRPEGKRKKKR 330


>gi|119608821|gb|EAW88415.1| calcium channel, voltage-dependent, L type, alpha 1B subunit,
           isoform CRA_a [Homo sapiens]
 gi|119608822|gb|EAW88416.1| calcium channel, voltage-dependent, L type, alpha 1B subunit,
           isoform CRA_a [Homo sapiens]
 gi|119608823|gb|EAW88417.1| calcium channel, voltage-dependent, L type, alpha 1B subunit,
           isoform CRA_a [Homo sapiens]
 gi|119608824|gb|EAW88418.1| calcium channel, voltage-dependent, L type, alpha 1B subunit,
           isoform CRA_a [Homo sapiens]
          Length = 1005

 Score = 42.1 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 17/112 (15%), Positives = 30/112 (26%), Gaps = 3/112 (2%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           GP   +      +AP          R     + P    + +  + +        +   P 
Sbjct: 828 GPVGGKARPEAAEAPEGVDPPRRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPR 887

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREEN---HRRSPSFPSKRSLRRTSAKK 354
             R+ +          S      G         R SP   ++R  RR  A +
Sbjct: 888 PHRSHSKEAAGPPEARSERGRGPGPEGGRRHHRRGSPEEAAEREPRRHRAHR 939



 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 23/152 (15%), Positives = 43/152 (28%), Gaps = 20/152 (13%)

Query: 223 FQLGTL---LAGSTREVSKKI-LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPN-IISE 277
            +L  L         E+  +  LR     HL  + + +LD P+         R       
Sbjct: 775 LRLQNLRASCEALYSEMDPEERLRFATTRHLRPDMKTHLDRPLVVELGRDGARGPVGGKA 834

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
            P+     +     +     + K  TP       +    A+        +  +   +H +
Sbjct: 835 RPEAAEAPEGVDPPRRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPRPHRSHSK 894

Query: 338 -SPSFPSKRSL--------------RRTSAKK 354
            +   P  RS               RR S ++
Sbjct: 895 EAAGPPEARSERGRGPGPEGGRRHHRRGSPEE 926


>gi|260807247|ref|XP_002598420.1| hypothetical protein BRAFLDRAFT_83204 [Branchiostoma floridae]
 gi|229283693|gb|EEN54432.1| hypothetical protein BRAFLDRAFT_83204 [Branchiostoma floridae]
          Length = 1080

 Score = 42.1 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 13/109 (11%), Positives = 36/109 (33%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G  +     V+        + + +         P +    ++ S  ++   +Q+  +   
Sbjct: 43  GTRIRSSVVVHKQRRSDDDDDVGKAGDGDAQRSPSESPPRRQRSPSESPQRRQRSPSGSP 102

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +R    +   ++       S+S QR ++  RSP    +        ++
Sbjct: 103 PKRTRDRSPKDSRHRQKRATSESPQRRDDSSRSPVKRQRSPSESPPRRQ 151



 Score = 35.9 bits (81), Expect = 8.9,   Method: Composition-based stats.
 Identities = 12/125 (9%), Positives = 26/125 (20%), Gaps = 13/125 (10%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +   G      ++         SE+  R + +     P          S+        + 
Sbjct: 66  KAGDGDAQRSPSESPPRRQRSPSESPQRRQRSPSGSPPKRTRDRSPKDSRHRQKRATSES 125

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR-------------SPSFPSKRSLR 348
                  + +          S          E   R             SP+   +  + 
Sbjct: 126 PQRRDDSSRSPVKRQRSPSESPPRRQRSSSPEARDRRTSRSRSPARRERSPARRDRSPVA 185

Query: 349 RTSAK 353
           R   +
Sbjct: 186 RGRGR 190


>gi|218779737|ref|YP_002431055.1| ribosomal protein S4 [Desulfatibacillum alkenivorans AK-01]
 gi|226697835|sp|B8FER0|RS4_DESAA RecName: Full=30S ribosomal protein S4
 gi|218761121|gb|ACL03587.1| ribosomal protein S4 [Desulfatibacillum alkenivorans AK-01]
          Length = 208

 Score = 42.1 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI R G A  R +  +M+      VNG  +   +  V   D IEV
Sbjct: 99  RLDNVIYRLGFADCRTQARQMVRHNHFTVNGHKVNIPSAQVSIGDTIEV 147


>gi|15610594|ref|NP_217975.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis H37Rv]
 gi|15843053|ref|NP_338090.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis CDC1551]
 gi|31794634|ref|NP_857127.1| 30S ribosomal protein S4 [Mycobacterium bovis AF2122/97]
 gi|121639378|ref|YP_979602.1| 30S ribosomal protein S4 [Mycobacterium bovis BCG str. Pasteur
           1173P2]
 gi|148663323|ref|YP_001284846.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis H37Ra]
 gi|148824668|ref|YP_001289422.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis F11]
 gi|167966775|ref|ZP_02549052.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis H37Ra]
 gi|215405497|ref|ZP_03417678.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis 02_1987]
 gi|215413372|ref|ZP_03422056.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis 94_M4241A]
 gi|215428965|ref|ZP_03426884.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis T92]
 gi|215432429|ref|ZP_03430348.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis EAS054]
 gi|215447795|ref|ZP_03434547.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis T85]
 gi|218755236|ref|ZP_03534032.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis GM 1503]
 gi|219559526|ref|ZP_03538602.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis T17]
 gi|224991874|ref|YP_002646563.1| 30S ribosomal protein S4 [Mycobacterium bovis BCG str. Tokyo 172]
 gi|253800503|ref|YP_003033504.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis KZN 1435]
 gi|254366059|ref|ZP_04982104.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis str.
           Haarlem]
 gi|254552561|ref|ZP_05143008.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis '98-R604
           INH-RIF-EM']
 gi|260188513|ref|ZP_05765987.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis CPHL_A]
 gi|260202641|ref|ZP_05770132.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis T46]
 gi|260206829|ref|ZP_05774320.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis K85]
 gi|289445058|ref|ZP_06434802.1| SSU ribosomal protein S4 [Mycobacterium tuberculosis T46]
 gi|289449162|ref|ZP_06438906.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis CPHL_A]
 gi|289555729|ref|ZP_06444939.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis KZN 605]
 gi|289571692|ref|ZP_06451919.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis T17]
 gi|289576194|ref|ZP_06456421.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis K85]
 gi|289747291|ref|ZP_06506669.1| ribosomal protein S4 [Mycobacterium tuberculosis 02_1987]
 gi|289752182|ref|ZP_06511560.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis T92]
 gi|289755591|ref|ZP_06514969.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis EAS054]
 gi|289759621|ref|ZP_06518999.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis T85]
 gi|289763640|ref|ZP_06523018.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis GM 1503]
 gi|297636117|ref|ZP_06953897.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis KZN 4207]
 gi|297733117|ref|ZP_06962235.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis KZN R506]
 gi|298526942|ref|ZP_07014351.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis 94_M4241A]
 gi|306777805|ref|ZP_07416142.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis SUMu001]
 gi|306782524|ref|ZP_07420861.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis SUMu002]
 gi|306786343|ref|ZP_07424665.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis SUMu003]
 gi|306790712|ref|ZP_07429034.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis SUMu004]
 gi|306795240|ref|ZP_07433542.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis SUMu005]
 gi|306799430|ref|ZP_07437732.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis SUMu006]
 gi|306805276|ref|ZP_07441944.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis SUMu008]
 gi|306809462|ref|ZP_07446130.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis SUMu007]
 gi|306969570|ref|ZP_07482231.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis SUMu009]
 gi|306973924|ref|ZP_07486585.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis SUMu010]
 gi|307081633|ref|ZP_07490803.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis SUMu011]
 gi|307086239|ref|ZP_07495352.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis SUMu012]
 gi|313660448|ref|ZP_07817328.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis KZN V2475]
 gi|6094181|sp|O06325|RS4_MYCTU RecName: Full=30S ribosomal protein S4
 gi|32700063|sp|P45811|RS4_MYCBO RecName: Full=30S ribosomal protein S4
 gi|152112232|sp|A1KPE4|RS4_MYCBP RecName: Full=30S ribosomal protein S4
 gi|172047916|sp|A5U8D4|RS4_MYCTA RecName: Full=30S ribosomal protein S4
 gi|254764600|sp|C1AHR6|RS4_MYCBT RecName: Full=30S ribosomal protein S4
 gi|2104381|emb|CAB08724.1| PROBABLE 30S RIBOSOMAL PROTEIN S4 RPSD [Mycobacterium tuberculosis
           H37Rv]
 gi|13883397|gb|AAK47904.1| ribosomal protein S4 [Mycobacterium tuberculosis CDC1551]
 gi|31620231|emb|CAD95674.1| PROBABLE 30S RIBOSOMAL PROTEIN S4 RPSD [Mycobacterium bovis
           AF2122/97]
 gi|121495026|emb|CAL73512.1| Probable 30S ribosomal protein S4 rpsD [Mycobacterium bovis BCG
           str. Pasteur 1173P2]
 gi|134151572|gb|EBA43617.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis str.
           Haarlem]
 gi|148507475|gb|ABQ75284.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis H37Ra]
 gi|148723195|gb|ABR07820.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis F11]
 gi|224774989|dbj|BAH27795.1| 30S ribosomal protein S4 [Mycobacterium bovis BCG str. Tokyo 172]
 gi|253322006|gb|ACT26609.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis KZN 1435]
 gi|289417977|gb|EFD15217.1| SSU ribosomal protein S4 [Mycobacterium tuberculosis T46]
 gi|289422120|gb|EFD19321.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis CPHL_A]
 gi|289440361|gb|EFD22854.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis KZN 605]
 gi|289540625|gb|EFD45203.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis K85]
 gi|289545446|gb|EFD49094.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis T17]
 gi|289687819|gb|EFD55307.1| ribosomal protein S4 [Mycobacterium tuberculosis 02_1987]
 gi|289692769|gb|EFD60198.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis T92]
 gi|289696178|gb|EFD63607.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis EAS054]
 gi|289711146|gb|EFD75162.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis GM 1503]
 gi|289715185|gb|EFD79197.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis T85]
 gi|298496736|gb|EFI32030.1| 30S ribosomal protein S4 [Mycobacterium tuberculosis 94_M4241A]
 gi|308213890|gb|EFO73289.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis SUMu001]
 gi|308324841|gb|EFP13692.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis SUMu002]
 gi|308329095|gb|EFP17946.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis SUMu003]
 gi|308332903|gb|EFP21754.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis SUMu004]
 gi|308336563|gb|EFP25414.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis SUMu005]
 gi|308340438|gb|EFP29289.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis SUMu006]
 gi|308344302|gb|EFP33153.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis SUMu007]
 gi|308348193|gb|EFP37044.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis SUMu008]
 gi|308352917|gb|EFP41768.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis SUMu009]
 gi|308356760|gb|EFP45611.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis SUMu010]
 gi|308360705|gb|EFP49556.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis SUMu011]
 gi|308364320|gb|EFP53171.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis SUMu012]
 gi|323717942|gb|EGB27131.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis CDC1551A]
 gi|326905304|gb|EGE52237.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis W-148]
 gi|328460234|gb|AEB05657.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis KZN 4207]
          Length = 201

 Score = 42.1 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  VI RAG+A +RR   ++++     VNG+ +   +  V   D ++V    L      
Sbjct: 92  RLDNVIYRAGLARTRRMARQLVSHGHFNVNGVHVNVPSYRVSQYDIVDVRDKSLNTVPFQ 151

Query: 74  R 74
            
Sbjct: 152 I 152


>gi|268316434|ref|YP_003290153.1| 30S ribosomal protein S4 [Rhodothermus marinus DSM 4252]
 gi|262333968|gb|ACY47765.1| ribosomal protein S4 [Rhodothermus marinus DSM 4252]
          Length = 200

 Score = 42.1 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   + R G A +RR+  +++  + + VNG ++   +  +   D + V
Sbjct: 93  RLDNTVYRMGFARTRRQARQLVVHRHIMVNGQVVNVPSYQLRPGDVVAV 141


>gi|254451859|ref|ZP_05065296.1| ribosomal protein S4 [Octadecabacter antarcticus 238]
 gi|198266265|gb|EDY90535.1| ribosomal protein S4 [Octadecabacter antarcticus 238]
          Length = 206

 Score = 42.1 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 9/32 (28%), Positives = 13/32 (40%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             + +    V VNG  +   +  V   D IEV
Sbjct: 112 ARQFVNHGHVTVNGKKVNIPSYRVKEGDIIEV 143


>gi|116054159|ref|YP_788602.1| ATP-dependent RNA helicase [Pseudomonas aeruginosa UCBPP-PA14]
 gi|313111948|ref|ZP_07797737.1| putative ATP-dependent RNA helicase, DEAD box family [Pseudomonas
           aeruginosa 39016]
 gi|115589380|gb|ABJ15395.1| putative ATP-dependent RNA helicase, DEAD box family [Pseudomonas
           aeruginosa UCBPP-PA14]
 gi|310884239|gb|EFQ42833.1| putative ATP-dependent RNA helicase, DEAD box family [Pseudomonas
           aeruginosa 39016]
          Length = 639

 Score = 42.1 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 17/102 (16%), Positives = 24/102 (23%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
              L E AQ              ++R +     P D      +S+        +K A   
Sbjct: 383 EAVLPEVAQPEPREAPQKQPRRDKERRSSRERKPKDAQASNPDSNVAAAQDGTEKPAGKR 442

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            RR   +      G           R     R P     R  
Sbjct: 443 RRRGGKNKENREAGQAQQPRQSREARPAKPNRPPEVDGNRDP 484


>gi|325511407|sp|A6NJU9|YP038_HUMAN RecName: Full=Putative NPIP-like protein LOC613037
          Length = 1138

 Score = 42.1 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 27/108 (25%), Gaps = 3/108 (2%)

Query: 247  PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
            P   +EA+               + P              +   ++     +     P  
Sbjct: 1017 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPKPKR 1076

Query: 307  RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS--FPSKRSLRRTSA 352
            RR              +   +     E  RR      PS++  RR +A
Sbjct: 1077 RRVGDVEPSRKPKRRRAADVEPSS-PEPKRRRVGDVEPSRKPKRRRAA 1123



 Score = 39.8 bits (91), Expect = 0.66,   Method: Composition-based stats.
 Identities = 12/115 (10%), Positives = 25/115 (21%), Gaps = 4/115 (3%)

Query: 238  KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            +    +   P     A++              +                    ++  +  
Sbjct: 1022 EAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPKPKRRRVGD 1081

Query: 298  QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS----PSFPSKRSLR 348
             +    P  RR         +            R+   RR+    PS P  +  R
Sbjct: 1082 VEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKRRR 1136



 Score = 37.1 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 28/112 (25%), Gaps = 3/112 (2%)

Query: 243  EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            E+L   L   A  NL  P  +++    ++P                  ++     +    
Sbjct: 999  ERLRGPLPPSADDNLKTPPLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRK 1058

Query: 303  TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                R                   +  ++    +R  +   + S      ++
Sbjct: 1059 PKRRRAADVEPSSPKPKRRRVGDVEPSRKP---KRRRAADVEPSSPEPKRRR 1107


>gi|157689492|gb|ABV65302.1| ribosomal protein S4 [Humiria balsamifera]
          Length = 189

 Score = 42.1 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 14/84 (16%), Positives = 30/84 (35%), Gaps = 5/84 (5%)

Query: 14  QRVSKVIARAGIAS---RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            R+  ++ R G+AS   R    +++  + + VNG +++  +      D I   G    +A
Sbjct: 77  MRLDNILFRLGMASTIPR--ARQLVNHRHILVNGRIVDIPSYRCKPRDIITARGEQKSRA 134

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGR 94
                        L    +    +
Sbjct: 135 MIQNYLDSSPQEELPKHLTLHPFQ 158


>gi|329851321|ref|ZP_08266078.1| ribosomal protein S4 [Asticcacaulis biprosthecum C19]
 gi|328840167|gb|EGF89739.1| ribosomal protein S4 [Asticcacaulis biprosthecum C19]
          Length = 205

 Score = 42.1 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 8/32 (25%), Positives = 13/32 (40%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             + +    V VNG  +   +  V   D +EV
Sbjct: 112 ARQFVNHGHVTVNGQRVNIPSYRVKPDDVVEV 143


>gi|296386927|ref|ZP_06876426.1| ATP-dependent RNA helicase [Pseudomonas aeruginosa PAb1]
          Length = 639

 Score = 42.1 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 17/102 (16%), Positives = 24/102 (23%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
              L E AQ              ++R +     P D      +S+        +K A   
Sbjct: 383 EAVLPEVAQPEPREAPQKQPRRDKERRSSRERKPKDAQASNPDSNVAAAQDGTEKPAGKR 442

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            RR   +      G           R     R P     R  
Sbjct: 443 RRRGGKNKENREAGQAQQPRQSREARPAKPNRPPEVDGNRDP 484


>gi|217979370|ref|YP_002363517.1| helicase domain protein [Methylocella silvestris BL2]
 gi|217504746|gb|ACK52155.1| helicase domain protein [Methylocella silvestris BL2]
          Length = 1139

 Score = 42.1 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 11/138 (7%), Positives = 31/138 (22%), Gaps = 18/138 (13%)

Query: 235  EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS----- 289
            E++  +   +  P   E   + +  P        R                +  +     
Sbjct: 960  ELAPDLAGTEAEPAEAEPVLIEVWRPHRQHFHARRPEARAAKRPERRRAAPQGETPELAA 1019

Query: 290  ----------SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ---REENHR 336
                         +   +  +      +           G H+       +   R  +  
Sbjct: 1020 AAPEAGAAEPRANHSRPRNGRGGANPEQGGRERQGGGPSGAHAGGPGKPSRGQGRPNDRD 1079

Query: 337  RSPSFPSKRSLRRTSAKK 354
            R  S  +  S  + + ++
Sbjct: 1080 RRESQGAASSRPQDNDRR 1097


>gi|153005960|ref|YP_001380285.1| hypothetical protein Anae109_3105 [Anaeromyxobacter sp. Fw109-5]
 gi|152029533|gb|ABS27301.1| protein of unknown function RIO1 [Anaeromyxobacter sp. Fw109-5]
          Length = 450

 Score = 42.1 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 12/122 (9%), Positives = 27/122 (22%), Gaps = 1/122 (0%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE++   +     P          +          R                 +   +  
Sbjct: 235 RELTPDFVPSGRAPEAPRGGGERHERHGGGQGERHRPAHPGNRRNDARGRGRPERPERPE 294

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGI-HSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                    +       +S     +G       S    + +   R PS P +R   +   
Sbjct: 295 RGGGAGGGHSSREAHPPSSERSQPQGGNRRRNGSPERGQPQGGDRRPSRPPERGQPQGGD 354

Query: 353 KK 354
           ++
Sbjct: 355 RR 356



 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 10/100 (10%), Positives = 25/100 (25%), Gaps = 5/100 (5%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
               E    + +          R+      +      R  +   +       ++ + P  
Sbjct: 303 HSSREAHPPSSERSQPQGGNRRRNGSPERGQPQGGDRRPSRPPERGQPQGGDRRSSRPPE 362

Query: 307 RR-----NLASNVWMAKGIHSSFLSDSGQREENHRRSPSF 341
           R      +   N     G      +    R ++ R +P+ 
Sbjct: 363 RGQPQGSDRRPNAARPPGPGQGSGNRPPGRGQDRRSAPAP 402



 Score = 40.2 bits (92), Expect = 0.44,   Method: Composition-based stats.
 Identities = 10/100 (10%), Positives = 26/100 (26%), Gaps = 1/100 (1%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
             + +A   SSE       N       +  + +    + +   ++ +      R +    
Sbjct: 303 HSSREAHPPSSERSQPQGGNRRRNGSPERGQPQGGDRRPSRPPERGQPQGGDRRSSRPPE 362

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               +G      +               P +   RR++  
Sbjct: 363 RGQPQGSDRRPNAARPPGP-GQGSGNRPPGRGQDRRSAPA 401


>gi|218889170|ref|YP_002438034.1| putative ATP-dependent RNA helicase [Pseudomonas aeruginosa LESB58]
 gi|218769393|emb|CAW25153.1| probable ATP-dependent RNA helicase [Pseudomonas aeruginosa LESB58]
          Length = 639

 Score = 42.1 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 17/102 (16%), Positives = 24/102 (23%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
              L E AQ              ++R +     P D      +S+        +K A   
Sbjct: 383 EAVLPEVAQPEPREAPQKQPRRDKERRSSRERKPKDAQASNPDSNVAAAQDGTEKPAGKR 442

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            RR   +      G           R     R P     R  
Sbjct: 443 RRRGGKNKENREAGQAQQPRQSREARPAKPNRPPEVDGNRDP 484


>gi|15595625|ref|NP_249119.1| ATP-dependent RNA helicase [Pseudomonas aeruginosa PAO1]
 gi|9946285|gb|AAG03817.1|AE004480_1 probable ATP-dependent RNA helicase [Pseudomonas aeruginosa PAO1]
          Length = 639

 Score = 42.1 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 17/102 (16%), Positives = 24/102 (23%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
              L E AQ              ++R +     P D      +S+        +K A   
Sbjct: 383 EAVLPEVAQPEPREAPQKQPRRDKERRSSRERKPKDAQASNPDSNVAAAQDGTEKPAGKR 442

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            RR   +      G           R     R P     R  
Sbjct: 443 RRRGGKNKENREAGQAQQPRQSREARPAKPNRPPEVDGNRDP 484


>gi|312114757|ref|YP_004012353.1| helicase [Rhodomicrobium vannielii ATCC 17100]
 gi|311219886|gb|ADP71254.1| helicase domain protein [Rhodomicrobium vannielii ATCC 17100]
          Length = 1147

 Score = 42.1 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 7/114 (6%), Positives = 21/114 (18%), Gaps = 2/114 (1%)

Query: 243  EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            +        +            +   R         P     +  ++             
Sbjct: 961  QHRRHGAAGQGAAGQGERGGQRQPGERGPRPRSDNAPQPAIAVGTDAPAGQPEGAAASGD 1020

Query: 303  TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP--SFPSKRSLRRTSAKK 354
                R                   +   R + +R  P  + P +      + ++
Sbjct: 1021 HAPRRDFSRDRSGPRDQNRERGDRNRQPRSDGNRDRPQGARPGEAPRADNAERR 1074



 Score = 40.9 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 11/119 (9%), Positives = 30/119 (25%), Gaps = 7/119 (5%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            R +          V  DAP    E       +             ++ +++ G   ++  
Sbjct: 990  RPRSDNAPQPAIAVGTDAPAGQPEGAAASGDHAPRRDFSRDRSGPRDQNRERGDRNRQPR 1049

Query: 302  ATPVHRRNLASNVWMAKGI----HSSFLSDSGQREENHRRSPSFPSKRS---LRRTSAK 353
            +     R   +    A         +      + +      P+  ++ S     +   +
Sbjct: 1050 SDGNRDRPQGARPGEAPRADNAERRTGGGQPNRPQHQRSDRPNDRNRDSLPPRPQGRQQ 1108



 Score = 38.2 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 9/92 (9%), Positives = 20/92 (21%)

Query: 261  IYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGI 320
             +       +R     +      R         G  ++     P  R     +    +  
Sbjct: 941  RFRRPKPKFERGEGQGDRRSQHRRHGAAGQGAAGQGERGGQRQPGERGPRPRSDNAPQPA 1000

Query: 321  HSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             +        + E    S     +R   R  +
Sbjct: 1001 IAVGTDAPAGQPEGAAASGDHAPRRDFSRDRS 1032



 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 8/126 (6%), Positives = 22/126 (17%), Gaps = 14/126 (11%)

Query: 240  ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
               E       +      +          R                ++   ++    +  
Sbjct: 935  EFEEVWRFRRPKPKFERGEGQGDRRSQHRRHGAAGQGAAGQGERGGQRQPGERGPRPRSD 994

Query: 300  KLATPVHRRNLASNVWMAKGIHSSFLSDSGQ--------------REENHRRSPSFPSKR 345
                P       +     +G  +S      +                 +  R P     R
Sbjct: 995  NAPQPAIAVGTDAPAGQPEGAAASGDHAPRRDFSRDRSGPRDQNRERGDRNRQPRSDGNR 1054

Query: 346  SLRRTS 351
               + +
Sbjct: 1055 DRPQGA 1060


>gi|182420026|ref|ZP_02951260.1| S4 domain protein [Clostridium butyricum 5521]
 gi|237669519|ref|ZP_04529499.1| RNA-binding S4 domain protein [Clostridium butyricum E4 str. BoNT
          E BL5262]
 gi|182376063|gb|EDT73650.1| S4 domain protein [Clostridium butyricum 5521]
 gi|237654963|gb|EEP52523.1| RNA-binding S4 domain protein [Clostridium butyricum E4 str. BoNT
          E BL5262]
          Length = 86

 Score = 42.1 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 10/50 (20%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   + +    R+ +N  + +  +  +   D IE+
Sbjct: 1  MRLDKYLKVSRIIKRRTVAKEVCESGRININDKVAK-PSTKIKEGDIIEI 49


>gi|114771201|ref|ZP_01448621.1| 30S ribosomal protein S4 [alpha proteobacterium HTCC2255]
 gi|114548126|gb|EAU51013.1| 30S ribosomal protein S4 [alpha proteobacterium HTCC2255]
          Length = 206

 Score = 42.1 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 9/32 (28%), Positives = 13/32 (40%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             + +    V VNG  +   +  V   D IEV
Sbjct: 112 ARQFVNHGHVTVNGKKVNIPSYRVKEGDVIEV 143


>gi|321309627|ref|YP_004191956.1| 30S ribosomal protein S4 [Mycoplasma haemofelis str. Langford 1]
 gi|319801471|emb|CBY92117.1| ribosomal protein S4 [Mycoplasma haemofelis str. Langford 1]
          Length = 204

 Score = 42.1 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 9/36 (25%), Positives = 19/36 (52%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +RR   ++++   V VNG  ++  ++ V   D I +
Sbjct: 110 TRRAARQLVSHGHVLVNGKQVDIPSLWVNINDEIAI 145


>gi|319944771|ref|ZP_08019035.1| 30S ribosomal protein S4 [Lautropia mirabilis ATCC 51599]
 gi|319742020|gb|EFV94443.1| 30S ribosomal protein S4 [Lautropia mirabilis ATCC 51599]
          Length = 207

 Score = 42.1 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+AS R E  ++++ + + VNG +L   +  +   D I V
Sbjct: 98  RLDNVVYRMGLASTRAEARQLVSHRAILVNGAILNVPSAAIKPNDVISV 146


>gi|317181016|dbj|BAJ58802.1| 30S ribosomal protein S4 [Helicobacter pylori F32]
          Length = 208

 Score = 42.1 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 1/65 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G A+ R    +++    V V+G  L+  +  V S   IE+        +  
Sbjct: 99  RLDNVVYRMGFATTRSSARQLVTHGHVLVDGKRLDVPSYFVRSGQKIEIKEKTKNNPQVV 158

Query: 74  RLWLY 78
           R    
Sbjct: 159 RAMEL 163


>gi|297191461|ref|ZP_06908859.1| conserved hypothetical protein [Streptomyces pristinaespiralis ATCC
           25486]
 gi|297150935|gb|EFH30880.1| conserved hypothetical protein [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 526

 Score = 42.1 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 11/116 (9%), Positives = 28/116 (24%), Gaps = 6/116 (5%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           + + +R++                   +  +   R    +         +  + +     
Sbjct: 393 TPRRVRDRPRLPGRPAGARGRQQHRPRTALVRVRRRRRRTGRAGVDVDARAAAGRSRPAP 452

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR---RSPSFPSKRSLRR 349
              +   P    + A+      G H+          +  R   R P    + S  R
Sbjct: 453 AAARPGRP---HDPAAGHGGPPGTHAVPTGPRRPGADGWRCGLRRPRAGGRHSRPR 505



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 8/76 (10%), Positives = 14/76 (18%)

Query: 268 VRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSD 327
            R         P      + +             A P   R   ++ W            
Sbjct: 441 ARAAAGRSRPAPAAARPGRPHDPAAGHGGPPGTHAVPTGPRRPGADGWRCGLRRPRAGGR 500

Query: 328 SGQREENHRRSPSFPS 343
             +        P+ P 
Sbjct: 501 HSRPRRLPSDRPARPG 516


>gi|126733337|ref|ZP_01749084.1| 30S ribosomal protein S4 [Roseobacter sp. CCS2]
 gi|126716203|gb|EBA13067.1| 30S ribosomal protein S4 [Roseobacter sp. CCS2]
          Length = 206

 Score = 42.1 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 9/32 (28%), Positives = 13/32 (40%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             + +    V VNG  +   +  V   D IEV
Sbjct: 112 ARQFVNHGHVTVNGKKVNIPSYRVKEGDVIEV 143


>gi|114567813|ref|YP_754967.1| 30S ribosomal protein S4 [Syntrophomonas wolfei subsp. wolfei str.
           Goettingen]
 gi|122317309|sp|Q0AUK8|RS4_SYNWW RecName: Full=30S ribosomal protein S4
 gi|114338748|gb|ABI69596.1| SSU ribosomal protein S4P [Syntrophomonas wolfei subsp. wolfei str.
           Goettingen]
          Length = 209

 Score = 42.1 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G AS R+E  +++      +NG      ++ V   D IEV
Sbjct: 100 RLDNVVYRLGFASSRKEARQLVNHGHFFINGHKANIPSMLVRVGDIIEV 148


>gi|314982287|gb|EFT26380.1| ribosomal protein S4 [Propionibacterium acnes HL110PA3]
          Length = 201

 Score = 42.1 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG+A +RR+  + ++     VNG  +   +  V + D I+V
Sbjct: 92  RLDNVVYRAGLAATRRQARQKVSHGHFLVNGKKVNIPSYRVSTHDIIDV 140


>gi|119496387|ref|XP_001264967.1| 30S ribosomal subunit S4, putative [Neosartorya fischeri NRRL 181]
 gi|119413129|gb|EAW23070.1| 30S ribosomal subunit S4, putative [Neosartorya fischeri NRRL 181]
          Length = 469

 Score = 42.1 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 13/56 (23%), Positives = 22/56 (39%), Gaps = 1/56 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+   I RA  AS  R+  + +    V VNG  +      +   D  +V+   +  
Sbjct: 130 RLDVAIFRAMFASSTRQARQFVVHGAVTVNGKKMRYPGYLLNPGDLFQVEPERVMY 185


>gi|70991196|ref|XP_750447.1| 30S ribosomal subunit  S4 [Aspergillus fumigatus Af293]
 gi|66848079|gb|EAL88409.1| 30S ribosomal subunit  S4, putative [Aspergillus fumigatus Af293]
 gi|159130921|gb|EDP56034.1| 30S ribosomal subunit S4, putative [Aspergillus fumigatus A1163]
          Length = 469

 Score = 42.1 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 13/56 (23%), Positives = 22/56 (39%), Gaps = 1/56 (1%)

Query: 15  RVSKVIARAGIASR-REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+   I RA  AS  R+  + +    V VNG  +      +   D  +V+   +  
Sbjct: 130 RLDVAIFRAMFASSTRQARQFVVHGAVTVNGKKMRYPGYLLNPGDLFQVEPERVMY 185


>gi|220930447|ref|YP_002507356.1| RNA-binding S4 domain protein [Clostridium cellulolyticum H10]
 gi|220000775|gb|ACL77376.1| RNA-binding S4 domain protein [Clostridium cellulolyticum H10]
          Length = 79

 Score = 42.1 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 3/67 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRKAE 71
           R+ K +  + +  RR     +  Q RVK+N  + +     V   D +E+  G  + K E
Sbjct: 1  MRIDKYLKVSRLIKRRTVANEVCEQGRVKINDRIAK-PGSEVKVGDIVEIQFGNNITKIE 59

Query: 72 RTRLWLY 78
           TR+  +
Sbjct: 60 ITRITEH 66


>gi|307197722|gb|EFN78871.1| hypothetical protein EAI_02279 [Harpegnathos saltator]
          Length = 3886

 Score = 41.7 bits (96), Expect = 0.15,   Method: Composition-based stats.
 Identities = 17/117 (14%), Positives = 30/117 (25%), Gaps = 3/117 (2%)

Query: 241  LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
            LRE   P  +  A     +P    E   +                +K     +   K + 
Sbjct: 1309 LREDDRPKPIPAAGKPSRSPPRERERSPQRPAEHGRPSEARPKSPEKLRDYTSPSRKPQP 1368

Query: 301  LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP---SKRSLRRTSAKK 354
             A    R               +  +   + E      PS P   S++  R    ++
Sbjct: 1369 AAGKPSRPEERPLAARRPDEQPAGPTRPTEPERPAAGRPSRPADKSRKPERAEKPRR 1425


>gi|86359602|ref|YP_471494.1| putative heat shock protein (ribosome-associated) [Rhizobium etli
          CFN 42]
 gi|86283704|gb|ABC92767.1| putative heat shock protein (ribosome-associated) [Rhizobium etli
          CFN 42]
          Length = 134

 Score = 41.7 bits (96), Expect = 0.15,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          QR+ K +     + SR   +  +    V++NG    + +  V   D IE+
Sbjct: 13 QRIDKWLFFTRMVKSRSLAQSHVQSGHVRINGERCSQPSQMVKPGDRIEL 62


>gi|294101656|ref|YP_003553514.1| ribosomal protein S4 [Aminobacterium colombiense DSM 12261]
 gi|293616636|gb|ADE56790.1| ribosomal protein S4 [Aminobacterium colombiense DSM 12261]
          Length = 209

 Score = 41.7 bits (96), Expect = 0.15,   Method: Composition-based stats.
 Identities = 9/49 (18%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G+A SR +  +++      V+G  ++  +  + +   + V
Sbjct: 100 RLDNIVYRMGLATSRSQARQLVLHGHFTVDGRKVDVPSYLIRAGAVVAV 148


>gi|194383244|dbj|BAG64593.1| unnamed protein product [Homo sapiens]
          Length = 833

 Score = 41.7 bits (96), Expect = 0.15,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 27/108 (25%), Gaps = 3/108 (2%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P   +EA+               + P              +   ++     +     P  
Sbjct: 712 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 771

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS--FPSKRSLRRTSA 352
           RR              +   +     E  RR      PS++  RR +A
Sbjct: 772 RRVGDVEPSRKPKRRRAADVEPSS-PEPKRRRVGDVEPSRKPKRRRAA 818



 Score = 40.2 bits (92), Expect = 0.56,   Method: Composition-based stats.
 Identities = 9/117 (7%), Positives = 25/117 (21%), Gaps = 2/117 (1%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +    +   P     A++              +                    ++  +  
Sbjct: 717 EAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGD 776

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +    P  RR         +            R+   +R  +   + SL     ++
Sbjct: 777 VEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKP--KRRRAADVEPSLPEPKRRR 831



 Score = 37.9 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 28/112 (25%), Gaps = 3/112 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E+L   L   A  NL  P  +++    ++P                  ++     +    
Sbjct: 694 ERLRGPLPPSADDNLKTPPLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRK 753

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               R                   +  ++    +R  +   + S      ++
Sbjct: 754 PKRRRAADVEPSSPEPKRRRVGDVEPSRKP---KRRRAADVEPSSPEPKRRR 802



 Score = 36.3 bits (82), Expect = 8.0,   Method: Composition-based stats.
 Identities = 13/120 (10%), Positives = 29/120 (24%), Gaps = 6/120 (5%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
            ++ +    +       +    ++ P       V D              ++ +S +   
Sbjct: 712 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 771

Query: 295 LS-KQKKLATPVHRRNLASNVWMAKGIHSSF-----LSDSGQREENHRRSPSFPSKRSLR 348
                 + +    RR  A     +             S   +R       PS P  +  R
Sbjct: 772 RRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKPKRRRAADVEPSLPEPKRRR 831


>gi|323466846|gb|ADX70533.1| 30S ribosomal protein S4 [Lactobacillus helveticus H10]
          Length = 203

 Score = 41.7 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 9/47 (19%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  ++ R G+A+ R +  ++++   + V+G  ++  +  V     I
Sbjct: 94  RLDSIVYRLGLATTREQARQLVSHGHITVDGKRVDIPSYEVSVGQTI 140


>gi|222619908|gb|EEE56040.1| hypothetical protein OsJ_04833 [Oryza sativa Japonica Group]
          Length = 1120

 Score = 41.7 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 7/105 (6%), Positives = 21/105 (20%), Gaps = 2/105 (1%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           ++ +              + ++      + +  +D        P                
Sbjct: 873 LAPRQRASSPMKAPPPPPKRDVPHNEKGAPSAEKDVQQRREPSPRRKPASPPRKRTPPNR 932

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
             +     P        +         +  S   + +   RR P 
Sbjct: 933 RIESPRRQPDPSPRRRPDS--PPIRRRADASPVRRGDTPPRRRPG 975



 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 20/131 (15%), Positives = 40/131 (30%), Gaps = 3/131 (2%)

Query: 227 TLLAG-STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
            L  G    E  K+   E+   ++           +  +    +   + +   P    R 
Sbjct: 834 NLPRGYGYIEFKKRTDAEKALLYMDGGQIDGNVVKLRFTLAPRQRASSPMKAPPPPPKRD 893

Query: 286 KKNSSQKNGLSKQK--KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
             ++ +    +++   +   P  RR  AS        +    S   Q + + RR P  P 
Sbjct: 894 VPHNEKGAPSAEKDVQQRREPSPRRKPASPPRKRTPPNRRIESPRRQPDPSPRRRPDSPP 953

Query: 344 KRSLRRTSAKK 354
            R     S  +
Sbjct: 954 IRRRADASPVR 964


>gi|223044406|ref|ZP_03614439.1| S4 domain protein [Staphylococcus capitis SK14]
 gi|314932728|ref|ZP_07840098.1| S4 domain protein [Staphylococcus caprae C87]
 gi|222442195|gb|EEE48307.1| S4 domain protein [Staphylococcus capitis SK14]
 gi|313654558|gb|EFS18310.1| S4 domain protein [Staphylococcus caprae C87]
          Length = 87

 Score = 41.7 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 3/67 (4%)

Query: 14 QRVSKVIARAGIASRREVERMI-AQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRKAE 71
           R+ K +  + +  RR + + I  Q RV VNG + + A  +V   D + +  G  L   +
Sbjct: 1  MRLDKYLKVSRLVKRRTLAKEISDQGRVTVNGNVAK-AGTDVKENDELVIRFGQKLVTVK 59

Query: 72 RTRLWLY 78
           T L  +
Sbjct: 60 VTGLNEH 66


>gi|163760000|ref|ZP_02167084.1| RNA-binding S4 [Hoeflea phototrophica DFL-43]
 gi|162282958|gb|EDQ33245.1| RNA-binding S4 [Hoeflea phototrophica DFL-43]
          Length = 130

 Score = 41.7 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          QR+ K +  A +  SR    + +A  +V+VNG  +++ +  V   D + +
Sbjct: 7  QRIDKWLFFARVIKSRTLAAKFVAGGKVRVNGDKIDQPSFAVKPDDVLTI 56


>gi|170781471|ref|YP_001709803.1| Ftsk/SpoIIIE family protein [Clavibacter michiganensis subsp.
            sepedonicus]
 gi|169156039|emb|CAQ01176.1| Ftsk/SpoIIIE family protein [Clavibacter michiganensis subsp.
            sepedonicus]
          Length = 1385

 Score = 41.7 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 16/121 (13%), Positives = 30/121 (24%), Gaps = 7/121 (5%)

Query: 241  LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK- 299
            LR+     ++  +    +  I       R  P      P   T             ++  
Sbjct: 1248 LRDNGATAVVVMSGERSEGQIVPGIHAERMVPGRAPRAPRRPTAADPGGHAGRPRPRRGG 1307

Query: 300  -----KLATPVHRRNLASNVWMAKGIHSSFLSDSGQRE-ENHRRSPSFPSKRSLRRTSAK 353
                 +   P      A     +        +    R   + R S + P +R    T A 
Sbjct: 1308 SRACLRPGRPSSVPESAPRCASSSPARPGASAPPRPRPWCSRRCSAAPPGRRRSPTTRAA 1367

Query: 354  K 354
            +
Sbjct: 1368 R 1368


>gi|126324047|ref|XP_001367172.1| PREDICTED: similar to CG9434-PA [Monodelphis domestica]
          Length = 412

 Score = 41.7 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 10/108 (9%), Positives = 19/108 (17%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                         P  ++    R          +       N     G    +      
Sbjct: 169 EAERPSPGGAEWPRPRGTNRPSPRGAEQPRPRGAERPRPRGTNRPSPRGAGWPRPRGAGR 228

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                A+          S       R     R     ++R   R + +
Sbjct: 229 SSPRGANWPSPRGAERPSPGGAEWPRPRGTNRPSPRGAERPRPRGTNR 276



 Score = 41.7 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 9/103 (8%), Positives = 18/103 (17%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
              + N  +P  +     R                    S     ++         R   
Sbjct: 294 SPREANRPSPGGAERPRPRGTNRPSPRGAGRPRPRGARRSSPREANRPSPGGAERPRPRG 353

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                               R     R     ++R   R + +
Sbjct: 354 TERPRPRGAGRPRPRGTERPRPRGAGRPRPRGTERPRPRGAGR 396



 Score = 39.8 bits (91), Expect = 0.63,   Method: Composition-based stats.
 Identities = 10/110 (9%), Positives = 21/110 (19%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
               +           P  ++    R             +  + N     G  + +   T
Sbjct: 295 PREANRPSPGGAERPRPRGTNRPSPRGAGRPRPRGARRSSPREANRPSPGGAERPRPRGT 354

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              R   A                   R     R     + R +   + +
Sbjct: 355 ERPRPRGAGRPRPRGTERPRPRGAGRPRPRGTERPRPRGAGRPIPGGADR 404



 Score = 39.8 bits (91), Expect = 0.70,   Method: Composition-based stats.
 Identities = 10/103 (9%), Positives = 21/103 (20%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
              + +  AP        R          +       N     G    +           
Sbjct: 102 APEEQSGQAPEGQIGLAPRGAEQPRPRGAERPRPRGTNRPSPRGAGWPRPRGAGRSSPRG 161

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           A+     +    S       R     R     +++   R + +
Sbjct: 162 ANWPSPGEAERPSPGGAEWPRPRGTNRPSPRGAEQPRPRGAER 204



 Score = 39.4 bits (90), Expect = 0.81,   Method: Composition-based stats.
 Identities = 12/107 (11%), Positives = 16/107 (14%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G   L         P  +     R                    S   G +         
Sbjct: 113 GQIGLAPRGAEQPRPRGAERPRPRGTNRPSPRGAGWPRPRGAGRSSPRGANWPSPGEAER 172

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                A           S       R     R     + R   R + 
Sbjct: 173 PSPGGAEWPRPRGTNRPSPRGAEQPRPRGAERPRPRGTNRPSPRGAG 219



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 11/117 (9%), Positives = 22/117 (18%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
                    G +           P  +  +  R          +  +       +  G +
Sbjct: 128 RGAERPRPRGTNRPSPRGAGWPRPRGAGRSSPRGANWPSPGEAERPSPGGAEWPRPRGTN 187

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +         R   A           S       R     RS    +     R + +
Sbjct: 188 RPSPRGAEQPRPRGAERPRPRGTNRPSPRGAGWPRPRGAGRSSPRGANWPSPRGAER 244



 Score = 37.5 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 8/117 (6%), Positives = 17/117 (14%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           S +                  + P        R R    S   +        + +     
Sbjct: 294 SPREANRPSPGGAERPRPRGTNRPSPRGAGRPRPRGARRSSPREANRPSPGGAERPRPRG 353

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            ++       R                      +R          P       +   
Sbjct: 354 TERPRPRGAGRPRPRGTERPRPRGAGRPRPRGTERPRPRGAGRPIPGGADRPSSGGA 410



 Score = 37.5 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 11/111 (9%), Positives = 18/111 (16%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E+      E                  +RP                  +  G S  +   
Sbjct: 104 EEQSGQAPEGQIGLAPRGAEQPRPRGAERPRPRGTNRPSPRGAGWPRPRGAGRSSPRGAN 163

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            P        +   A+       +    R     R       R        
Sbjct: 164 WPSPGEAERPSPGGAEWPRPRGTNRPSPRGAEQPRPRGAERPRPRGTNRPS 214



 Score = 36.3 bits (82), Expect = 6.6,   Method: Composition-based stats.
 Identities = 8/111 (7%), Positives = 16/111 (14%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
              G             P  ++    R             +    N        +     
Sbjct: 118 APRGAEQPRPRGAERPRPRGTNRPSPRGAGWPRPRGAGRSSPRGANWPSPGEAERPSPGG 177

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               R    +                  R     R     +     R + +
Sbjct: 178 AEWPRPRGTNRPSPRGAEQPRPRGAERPRPRGTNRPSPRGAGWPRPRGAGR 228



 Score = 36.3 bits (82), Expect = 7.3,   Method: Composition-based stats.
 Identities = 10/101 (9%), Positives = 20/101 (19%), Gaps = 2/101 (1%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT-- 303
           G         N  +P  + +   R          +  +       +  G  +        
Sbjct: 177 GAEWPRPRGTNRPSPRGAEQPRPRGAERPRPRGTNRPSPRGAGWPRPRGAGRSSPRGANW 236

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           P  R     +   A+       +    R     R       
Sbjct: 237 PSPRGAERPSPGGAEWPRPRGTNRPSPRGAERPRPRGTNRP 277


>gi|182439779|ref|YP_001827498.1| putative serine/threonine protein kinase [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|178468295|dbj|BAG22815.1| putative serine/threonine protein kinase [Streptomyces griseus
           subsp. griseus NBRC 13350]
          Length = 439

 Score = 41.7 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 17/123 (13%), Positives = 32/123 (26%), Gaps = 6/123 (4%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDF------TRMKKNSS 290
             +     L   +  +     +A           R    ++ P          +  + S 
Sbjct: 251 DPEERPSTLQLSMRLKEIAAREAQGLHESRPPVQRSAQDADRPTGRMADPYADQHTRRSE 310

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
             +G   Q        R              S   + SG+R+     +   P  RS  RT
Sbjct: 311 GPSGSRPQPGRRGASGRSGPPRTGGSRPQQASRDTTRSGRRQGPPPGTNGRPGTRSGGRT 370

Query: 351 SAK 353
           ++ 
Sbjct: 371 TSA 373



 Score = 40.9 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 14/115 (12%), Positives = 32/115 (27%), Gaps = 6/115 (5%)

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           +E++ +    L E   P        +      +     +                ++ +S
Sbjct: 266 KEIAAREAQGLHESRPPVQRSAQDADRPTGRMADPYADQHTRRSEGPSGSRPQPGRRGAS 325

Query: 291 QKNGLSKQKKLATPVHRRNL---ASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
            ++G  +          R+            G +    + SG R  +  R P+ P
Sbjct: 326 GRSGPPRTGGSRPQQASRDTTRSGRRQGPPPGTNGRPGTRSGGRTTSAGRRPANP 380


>gi|126335335|ref|XP_001371550.1| PREDICTED: similar to splicing coactivator subunit SRm300
           [Monodelphis domestica]
          Length = 2785

 Score = 41.7 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 28/111 (25%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R +                  S     R R    +      +R +  + +++      + 
Sbjct: 552 RSRNAQRRGRSRSAARRGRSRSRSPATRGRSRSRTPARRGRSRSRTPARRRSRSRTPARR 611

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            +                      + S  R  +  RSP+    RS  RT A
Sbjct: 612 RSRSRTPARRGRSRSRTPARRRSRTRSPVRRRSRTRSPARRGGRSRSRTPA 662



 Score = 40.9 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 17/125 (13%), Positives = 36/125 (28%), Gaps = 3/125 (2%)

Query: 230 AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
            G +R  + +  R +                  S +     R           +  ++  
Sbjct: 511 RGRSRSRTPQWRRSRSPQRWGRSRSPQRRGRSRSPQRPGWSRSRNAQRRGRSRSAARRGR 570

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           S+    + + +  +    R   S             S +  R  +  R+P+    RS  R
Sbjct: 571 SRSRSPATRGRSRSRTPARRGRSRSRTP--ARRRSRSRTPARRRSRSRTPARRG-RSRSR 627

Query: 350 TSAKK 354
           T A++
Sbjct: 628 TPARR 632



 Score = 40.2 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 16/131 (12%), Positives = 31/131 (23%), Gaps = 18/131 (13%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R       +  ++         S +   +R          + R +         S Q++ 
Sbjct: 481 RSHTPTRRVGRSRSPATTRRGRSRSRTPNRRGRSRSRTPQWRRSRSPQRWGRSRSPQRRG 540

Query: 302 ATPVHRRNLASNVWMA------------------KGIHSSFLSDSGQREENHRRSPSFPS 343
            +   +R   S    A                                     RS +   
Sbjct: 541 RSRSPQRPGWSRSRNAQRRGRSRSAARRGRSRSRSPATRGRSRSRTPARRGRSRSRTPAR 600

Query: 344 KRSLRRTSAKK 354
           +RS  RT A++
Sbjct: 601 RRSRSRTPARR 611



 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 18/111 (16%), Positives = 32/111 (28%), Gaps = 1/111 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R +           + +A           R    S  P    R +  +  + G S+ +  
Sbjct: 539 RGRSRSPQRPGWSRSRNAQRRGRSRSAARRGRSRSRSPATRGRSRSRTPARRGRSRSRTP 598

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           A     R+       ++    +    S  R    RRS +    R   RT +
Sbjct: 599 AR-RRSRSRTPARRRSRSRTPARRGRSRSRTPARRRSRTRSPVRRRSRTRS 648



 Score = 38.2 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 13/113 (11%), Positives = 25/113 (22%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R  +       +         S     R   +          R +  +  + G S+ +  
Sbjct: 637 RSPVRRRSRTRSPARRGGRSRSRTPARRGGRSRSRTPARRGGRSRSRTPARRGRSRSRTP 696

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           A     R+            S             RR  S  S     ++   +
Sbjct: 697 ARRGRTRSRTPARRGRSRTRSPVRRGRSHSRTPQRRGRSGSSSERKNKSRTSQ 749



 Score = 35.9 bits (81), Expect = 9.0,   Method: Composition-based stats.
 Identities = 8/107 (7%), Positives = 24/107 (22%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                   +           V      +S  P   +   +  ++++              
Sbjct: 433 PAKAPRHGSSSPESPPKPAPVPAPRRELSPSPTTKSSRSRGRAKRDKSRSHTPTRRVGRS 492

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           R+ A+         +       +      R    P +    R+  ++
Sbjct: 493 RSPATTRRGRSRSRTPNRRGRSRSRTPQWRRSRSPQRWGRSRSPQRR 539



 Score = 35.9 bits (81), Expect = 9.0,   Method: Composition-based stats.
 Identities = 17/127 (13%), Positives = 32/127 (25%), Gaps = 4/127 (3%)

Query: 230 AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
            G +R  + +             ++    A    S +    R            R +  +
Sbjct: 548 PGWSRSRNAQRRGRSRSAARRGRSRSRSPATRGRSRSRTPARRGRSRSRTPARRRSRSRT 607

Query: 290 SQKNGLSKQKKLATPVHRRN----LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
             +     +        R        S         S   S + +   +  R+P+    R
Sbjct: 608 PARRRSRSRTPARRGRSRSRTPARRRSRTRSPVRRRSRTRSPARRGGRSRSRTPARRGGR 667

Query: 346 SLRRTSA 352
           S  RT A
Sbjct: 668 SRSRTPA 674


>gi|149202433|ref|ZP_01879406.1| 30S ribosomal protein S4 [Roseovarius sp. TM1035]
 gi|149144531|gb|EDM32562.1| 30S ribosomal protein S4 [Roseovarius sp. TM1035]
          Length = 206

 Score = 41.7 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 9/35 (25%), Positives = 13/35 (37%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
             + +    V VNG  +   +  V   D IEV   
Sbjct: 112 ARQFVNHGHVTVNGQRVNIPSYRVKEGDVIEVRDR 146


>gi|291449364|ref|ZP_06588754.1| LOW QUALITY PROTEIN: conserved hypothetical protein [Streptomyces
           roseosporus NRRL 15998]
 gi|291352311|gb|EFE79215.1| LOW QUALITY PROTEIN: conserved hypothetical protein [Streptomyces
           roseosporus NRRL 15998]
          Length = 787

 Score = 41.7 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 12/93 (12%), Positives = 16/93 (17%)

Query: 260 PIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKG 319
           P        R R            R      +      ++  A    RR        A  
Sbjct: 137 PRRHPGPGGRGRTAAAPRGRARGGRSDGRPGRPRPRGGRRVRAARPGRRTADRTRGRAPR 196

Query: 320 IHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                 +    R     R          RR   
Sbjct: 197 ERHPSRTSRRARPAGPHRRRPPAGPDRARRPRH 229



 Score = 40.5 bits (93), Expect = 0.39,   Method: Composition-based stats.
 Identities = 11/92 (11%), Positives = 25/92 (27%), Gaps = 1/92 (1%)

Query: 263 SSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHS 322
             +     R       P    R +  ++   G ++  +      R        +      
Sbjct: 125 PGDGRDAHRGRCPRRHPGPGGRGR-TAAAPRGRARGGRSDGRPGRPRPRGGRRVRAARPG 183

Query: 323 SFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              +D  +      R PS  S+R+      ++
Sbjct: 184 RRTADRTRGRAPRERHPSRTSRRARPAGPHRR 215



 Score = 35.9 bits (81), Expect = 9.1,   Method: Composition-based stats.
 Identities = 11/97 (11%), Positives = 20/97 (20%), Gaps = 1/97 (1%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                                              D    +          +  +   P 
Sbjct: 196 RERHPSRTSRRARPAGPHRRRPPAGPDRARRPRHPDRRLRRPVRRPCGPGHRPYREGRPH 255

Query: 306 HRRNLASNV-WMAKGIHSSFLSDSGQREENHRRSPSF 341
             R  A++    A G     L ++G+R    R  P+ 
Sbjct: 256 RARGGAADRCRGAPGRGPDRLREAGRRPRTARTGPAG 292


>gi|328953131|ref|YP_004370465.1| ribosomal protein S4 [Desulfobacca acetoxidans DSM 11109]
 gi|328453455|gb|AEB09284.1| ribosomal protein S4 [Desulfobacca acetoxidans DSM 11109]
          Length = 208

 Score = 41.7 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SR +  +++      VNG  +   +  V   D IE+
Sbjct: 99  RLDNVVYRLGFANSRAQARQLVRHNHFLVNGKKINIPSYLVNVGDTIEL 147


>gi|242371664|ref|ZP_04817238.1| RNA-binding S4 domain heat shock protein [Staphylococcus
          epidermidis M23864:W1]
 gi|242350613|gb|EES42214.1| RNA-binding S4 domain heat shock protein [Staphylococcus
          epidermidis M23864:W1]
          Length = 87

 Score = 41.7 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 3/67 (4%)

Query: 14 QRVSKVIARAGIASRREVERMI-AQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRKAE 71
           R+ K +  + +  RR + + I  Q RV VNG + + A  +V   D + +  G  L   +
Sbjct: 1  MRLDKYLKVSRLVKRRTLAKEISDQGRVTVNGNVAK-AGTDVKENDELVIRFGQKLVTVK 59

Query: 72 RTRLWLY 78
           T L  +
Sbjct: 60 VTGLNEH 66


>gi|209529739|ref|NP_001129337.1| nuclear pore complex interacting protein family member [Homo sapiens]
 gi|325511394|sp|A8MRT5|K220L_HUMAN RecName: Full=Putative NPIP-like protein LOC100132247
          Length = 1133

 Score = 41.7 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 27/108 (25%), Gaps = 3/108 (2%)

Query: 247  PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
            P   +EA+               + P              +   ++     +     P  
Sbjct: 1012 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 1071

Query: 307  RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS--FPSKRSLRRTSA 352
            RR              +   +     E  RR      PS++  RR +A
Sbjct: 1072 RRVGDVEPSRKPKRRRAADVEPSS-PEPKRRRVGDVEPSRKPKRRRAA 1118



 Score = 39.8 bits (91), Expect = 0.59,   Method: Composition-based stats.
 Identities = 9/117 (7%), Positives = 25/117 (21%), Gaps = 2/117 (1%)

Query: 238  KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            +    +   P     A++              +                    ++  +  
Sbjct: 1017 EAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGD 1076

Query: 298  QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             +    P  RR         +            R+   +R  +   + SL     ++
Sbjct: 1077 VEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKP--KRRRAADVEPSLPEPKRRR 1131



 Score = 37.5 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 28/112 (25%), Gaps = 3/112 (2%)

Query: 243  EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            E+L   L   A  NL  P  +++    ++P                  ++     +    
Sbjct: 994  ERLRGPLPPSADDNLKTPPLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRK 1053

Query: 303  TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                R                   +  ++    +R  +   + S      ++
Sbjct: 1054 PKRRRAADVEPSSPEPKRRRVGDVEPSRKP---KRRRAADVEPSSPEPKRRR 1102



 Score = 35.9 bits (81), Expect = 8.4,   Method: Composition-based stats.
 Identities = 13/120 (10%), Positives = 29/120 (24%), Gaps = 6/120 (5%)

Query: 235  EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
             ++ +    +       +    ++ P       V D              ++ +S +   
Sbjct: 1012 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 1071

Query: 295  LS-KQKKLATPVHRRNLASNVWMAKGIHSSF-----LSDSGQREENHRRSPSFPSKRSLR 348
                  + +    RR  A     +             S   +R       PS P  +  R
Sbjct: 1072 RRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKPKRRRAADVEPSLPEPKRRR 1131


>gi|194382938|dbj|BAG59025.1| unnamed protein product [Homo sapiens]
          Length = 1133

 Score = 41.7 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 27/108 (25%), Gaps = 3/108 (2%)

Query: 247  PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
            P   +EA+               + P              +   ++     +     P  
Sbjct: 1012 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 1071

Query: 307  RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS--FPSKRSLRRTSA 352
            RR              +   +     E  RR      PS++  RR +A
Sbjct: 1072 RRVGDVEPSRKPKRRRAADVEPSS-PEPKRRRVGDVEPSRKPKRRRAA 1118



 Score = 39.8 bits (91), Expect = 0.59,   Method: Composition-based stats.
 Identities = 9/117 (7%), Positives = 25/117 (21%), Gaps = 2/117 (1%)

Query: 238  KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            +    +   P     A++              +                    ++  +  
Sbjct: 1017 EAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGD 1076

Query: 298  QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             +    P  RR         +            R+   +R  +   + SL     ++
Sbjct: 1077 VEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKP--KRRRAADVEPSLPEPKRRR 1131



 Score = 37.5 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 28/112 (25%), Gaps = 3/112 (2%)

Query: 243  EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            E+L   L   A  NL  P  +++    ++P                  ++     +    
Sbjct: 994  ERLRGPLPPSADDNLKTPPLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRK 1053

Query: 303  TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                R                   +  ++    +R  +   + S      ++
Sbjct: 1054 PKRRRAADVEPSSPEPKRRRVGDVEPSRKP---KRRRAADVEPSSPEPKRRR 1102



 Score = 35.9 bits (81), Expect = 8.4,   Method: Composition-based stats.
 Identities = 13/120 (10%), Positives = 29/120 (24%), Gaps = 6/120 (5%)

Query: 235  EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
             ++ +    +       +    ++ P       V D              ++ +S +   
Sbjct: 1012 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 1071

Query: 295  LS-KQKKLATPVHRRNLASNVWMAKGIHSSF-----LSDSGQREENHRRSPSFPSKRSLR 348
                  + +    RR  A     +             S   +R       PS P  +  R
Sbjct: 1072 RRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKPKRRRAADVEPSLPEPKRRR 1131


>gi|254243526|ref|ZP_04936848.1| hypothetical protein PA2G_04344 [Pseudomonas aeruginosa 2192]
 gi|126196904|gb|EAZ60967.1| hypothetical protein PA2G_04344 [Pseudomonas aeruginosa 2192]
          Length = 639

 Score = 41.7 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 17/102 (16%), Positives = 24/102 (23%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
              L E AQ              ++R +     P D      +S+        +K A   
Sbjct: 383 EAVLPEVAQPEPREAPQKQPRRDKERRSSRERKPKDAQASNPDSNVAAAQDGTEKPAGKR 442

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            RR   +      G           R     R P     R  
Sbjct: 443 RRRGGKNKENREAGQAQQPRQSREARPAKPNRPPEVDGNRDP 484


>gi|315587183|gb|ADU41564.1| 30S ribosomal protein S4 [Helicobacter pylori 35A]
          Length = 208

 Score = 41.7 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 1/65 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G A+ R    +++    V V+G  L+  +  V S   IE+        +  
Sbjct: 99  RLDNVVYRMGFATTRSSARQLVTHGHVLVDGKRLDIPSYFVRSGQKIEIKEKTKNNPQVV 158

Query: 74  RLWLY 78
           R    
Sbjct: 159 RAMEL 163


>gi|291447041|ref|ZP_06586431.1| conserved hypothetical protein [Streptomyces roseosporus NRRL
           15998]
 gi|291349988|gb|EFE76892.1| conserved hypothetical protein [Streptomyces roseosporus NRRL
           15998]
          Length = 600

 Score = 41.7 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 12/106 (11%), Positives = 23/106 (21%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              L  A+     P          R +            +   ++  G  +  +    + 
Sbjct: 463 LPRLAGARQPRHGPRPRPPHRNPGRRHRAGRPRPPLRTERGEGAEHPGARRGHRPLERLA 522

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                 +   A             R     R+P  P +   RR   
Sbjct: 523 GHGRRRDPGRADRGRGHGGPRPRVRGRAPCRAPLDPGRPGHRRHRP 568


>gi|262280249|ref|ZP_06058033.1| cold-shock DEAD box protein A (ATP-dependent RNA helicase deaD)
           [Acinetobacter calcoaceticus RUH2202]
 gi|262258027|gb|EEY76761.1| cold-shock DEAD box protein A (ATP-dependent RNA helicase deaD)
           [Acinetobacter calcoaceticus RUH2202]
          Length = 640

 Score = 41.7 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 15/131 (11%), Positives = 31/131 (23%), Gaps = 15/131 (11%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE +    R + G +     + N D      +   R            F    +     +
Sbjct: 486 REFTSDRPRREGGFNDKPRFESNDDNRGNRVDYKPRREAGFGDRPKRSFGGEDRPRRSFD 545

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSF---------------LSDSGQREENHRRS 338
              + ++ A     R   S     +G   +F                      ++     
Sbjct: 546 DKPRGERPAFGGEDRPRRSFDDKPRGERPAFGGGDDRPKRSFGGEDRPRRSFDDKPRGER 605

Query: 339 PSFPSKRSLRR 349
           P+F       +
Sbjct: 606 PAFGGGDDRPK 616



 Score = 39.4 bits (90), Expect = 0.97,   Method: Composition-based stats.
 Identities = 6/105 (5%), Positives = 18/105 (17%)

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
                  E   +            R   N  +       + ++ +   +   +       
Sbjct: 480 FEDRPRREFTSDRPRREGGFNDKPRFESNDDNRGNRVDYKPRREAGFGDRPKRSFGGEDR 539

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
             R                        ++     P+F       +
Sbjct: 540 PRRSFDDKPRGERPAFGGEDRPRRSFDDKPRGERPAFGGGDDRPK 584



 Score = 37.5 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 10/128 (7%), Positives = 26/128 (20%), Gaps = 15/128 (11%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            ++      ++ +    A             +          R ++  +      +    
Sbjct: 441 DDRPRRSFDDKPRGERPAFGGEDRPRREFNSDRPRREGGFEDRPRREFTSDRPRREGGFN 500

Query: 302 ATPV---------------HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
             P                 RR         +             ++     P+F  +  
Sbjct: 501 DKPRFESNDDNRGNRVDYKPRREAGFGDRPKRSFGGEDRPRRSFDDKPRGERPAFGGEDR 560

Query: 347 LRRTSAKK 354
            RR+   K
Sbjct: 561 PRRSFDDK 568



 Score = 37.1 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 13/120 (10%), Positives = 25/120 (20%), Gaps = 8/120 (6%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +               +                 E P      +   S  +    ++   
Sbjct: 517 DYKPRREAGFGDRPKRSFGGEDRPRRSFDDKPRGERPAFGGEDRPRRSFDDKPRGERPAF 576

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREE----NHRRSPSFPSKRSLRR----TSAKK 354
                R   S     +   S      G+R      + R   SF  +   RR       ++
Sbjct: 577 GGGDDRPKRSFGGEDRPRRSFDDKPRGERPAFGGGDDRPKRSFGGEDRPRRSFDDKPPRR 636


>gi|261838613|gb|ACX98379.1| ribosomal protein S4 [Helicobacter pylori 51]
          Length = 208

 Score = 41.7 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 1/65 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G A+ R    +++    V V+G  L+  +  V S   IE+        +  
Sbjct: 99  RLDNVVYRMGFATTRSSARQLVTHGHVLVDGKRLDIPSYFVRSGQKIEIKEKTKNNPQVV 158

Query: 74  RLWLY 78
           R    
Sbjct: 159 RAMEL 163


>gi|239932411|ref|ZP_04689364.1| 30S ribosomal protein S4 [Streptomyces ghanaensis ATCC 14672]
 gi|291440777|ref|ZP_06580167.1| 30S ribosomal protein S4 [Streptomyces ghanaensis ATCC 14672]
 gi|291343672|gb|EFE70628.1| 30S ribosomal protein S4 [Streptomyces ghanaensis ATCC 14672]
          Length = 204

 Score = 41.7 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 28/53 (52%), Gaps = 3/53 (5%)

Query: 15  RVSKVIARAGIASRR--EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  ++ R+GIA R   +  +M+    ++VNG  +++ +  V   D ++V   
Sbjct: 93  RLDALVLRSGIA-RTIYQARQMVTHGHIQVNGKKVDKPSFRVRPDDVVQVRDR 144


>gi|194381954|dbj|BAG64346.1| unnamed protein product [Homo sapiens]
          Length = 660

 Score = 41.7 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 27/108 (25%), Gaps = 3/108 (2%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P   +EA+               + P              +   ++     +     P  
Sbjct: 539 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 598

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS--FPSKRSLRRTSA 352
           RR              +   +     E  RR      PS++  RR +A
Sbjct: 599 RRVGDVEPSRKPKRRRAADVEPSS-PEPKRRRVGDVEPSRKPKRRRAA 645



 Score = 39.8 bits (91), Expect = 0.60,   Method: Composition-based stats.
 Identities = 9/117 (7%), Positives = 25/117 (21%), Gaps = 2/117 (1%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +    +   P     A++              +                    ++  +  
Sbjct: 544 EAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGD 603

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +    P  RR         +            R+   +R  +   + SL     ++
Sbjct: 604 VEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKP--KRRRAADVEPSLPEPKRRR 658



 Score = 37.5 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 28/112 (25%), Gaps = 3/112 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E+L   L   A  NL  P  +++    ++P                  ++     +    
Sbjct: 521 ERLRGPLPPSADDNLKTPPLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRK 580

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               R                   +  ++    +R  +   + S      ++
Sbjct: 581 PKRRRAADVEPSSPEPKRRRVGDVEPSRKP---KRRRAADVEPSSPEPKRRR 629



 Score = 35.9 bits (81), Expect = 8.5,   Method: Composition-based stats.
 Identities = 13/120 (10%), Positives = 29/120 (24%), Gaps = 6/120 (5%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
            ++ +    +       +    ++ P       V D              ++ +S +   
Sbjct: 539 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 598

Query: 295 LS-KQKKLATPVHRRNLASNVWMAKGIHSSF-----LSDSGQREENHRRSPSFPSKRSLR 348
                 + +    RR  A     +             S   +R       PS P  +  R
Sbjct: 599 RRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKPKRRRAADVEPSLPEPKRRR 658


>gi|47224529|emb|CAG08779.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 945

 Score = 41.7 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 18/158 (11%), Positives = 36/158 (22%), Gaps = 7/158 (4%)

Query: 200 EIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDA 259
           +I K        V  +   S G   L      +   + K+ +++Q        A      
Sbjct: 133 QIVKFLIEHGAHVGAVN--SEGELPLDVATEDAMERLLKEEIKKQGEKPAASTAAGTSGH 190

Query: 260 PIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN-----GLSKQKKLATPVHRRNLASNV 314
                 +  R                   + ++         +  + A  + +R   S  
Sbjct: 191 LSRLLSSRNRCGQGQEGGGAGHAAGSHGRAGRRRHALASPQHQGDRPARGLGKRLHRSPE 250

Query: 315 WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             A           G+ +   RR P             
Sbjct: 251 GAAALRRGREQQGRGRLDAPARRRPLGAGGGVRPARRQ 288


>gi|168186545|ref|ZP_02621180.1| ribosomal protein S4 [Clostridium botulinum C str. Eklund]
 gi|169295481|gb|EDS77614.1| ribosomal protein S4 [Clostridium botulinum C str. Eklund]
          Length = 196

 Score = 41.7 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 16/66 (24%), Positives = 31/66 (46%), Gaps = 4/66 (6%)

Query: 1   MKDKNIVQE---NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMS 56
           MK K++  +        R+  ++ R G A S R+  +M+    + VNG  ++  +  V  
Sbjct: 71  MKSKDVTGDILLKLLECRLDNLVYRIGFANSIRQARQMVNHGHILVNGSKVDIPSYEVKV 130

Query: 57  TDHIEV 62
            D +E+
Sbjct: 131 GDKVEL 136


>gi|134096724|ref|YP_001102385.1| hypothetical protein SACE_0106 [Saccharopolyspora erythraea NRRL
           2338]
 gi|133909347|emb|CAL99459.1| hypothetical protein SACE_0106 [Saccharopolyspora erythraea NRRL
           2338]
          Length = 649

 Score = 41.7 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 29/111 (26%), Gaps = 2/111 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            E+ G    +                        +    + T +             +  
Sbjct: 370 EERNGADRRDRPAPPDRLDDREPRRAAFPESGRAAFPETEVTSLPAAEDATRRRMPPRDP 429

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           + P HRR  A++         S  +   +R  +   +PS P +R     S 
Sbjct: 430 SAPAHRR--AADPGEPSHGSPSPWTPPTRRAPDPAAAPSRPHQRPRPPASP 478



 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 10/104 (9%), Positives = 19/104 (18%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
            E    +        + L    P   +          +        ++         R  
Sbjct: 370 EERNGADRRDRPAPPDRLDDREPRRAAFPESGRAAFPETEVTSLPAAEDATRRRMPPRDP 429

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            A     A                  RR+P   +  S      +
Sbjct: 430 SAPAHRRAADPGEPSHGSPSPWTPPTRRAPDPAAAPSRPHQRPR 473


>gi|118468301|ref|YP_885905.1| 30S ribosomal protein S4 [Mycobacterium smegmatis str. MC2 155]
 gi|171472975|sp|A0QSL7|RS4_MYCS2 RecName: Full=30S ribosomal protein S4
 gi|118169588|gb|ABK70484.1| ribosomal protein S4 [Mycobacterium smegmatis str. MC2 155]
          Length = 201

 Score = 41.7 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 1/61 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ RAG+A +RR   ++++     VNG+ ++  +  V   D I+V    L      
Sbjct: 92  RLDNVVYRAGLARTRRMARQLVSHGHFLVNGVKVDIPSYRVSQYDIIDVKEKSLNTLPFQ 151

Query: 74  R 74
            
Sbjct: 152 I 152


>gi|219128175|ref|XP_002184294.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217404095|gb|EEC44043.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 707

 Score = 41.7 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 16/113 (14%), Positives = 35/113 (30%), Gaps = 3/113 (2%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLV--RDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
           +E +    + +   +++        +   R +  +    P   T  ++ +   +     +
Sbjct: 223 KESVRLRKIPDIPQDVEHSPPEVHAVAIYRGKARVSKRGPSSVTGHRRRTDSNDSARSHE 282

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           K      RR          G      +   +R  +H  SP  P  +S RR   
Sbjct: 283 KPRRSRTRREHTHAYAEKTGAGKGESASPRRRHRSHTHSPVRP-PKSPRRHRQ 334


>gi|332665947|ref|YP_004448735.1| transcription termination factor Rho [Haliscomenobacter hydrossis
           DSM 1100]
 gi|332334761|gb|AEE51862.1| transcription termination factor Rho [Haliscomenobacter hydrossis
           DSM 1100]
          Length = 695

 Score = 41.7 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 13/100 (13%), Positives = 26/100 (26%), Gaps = 2/100 (2%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R++       E     D      E     R    S         + +S  +    +++  
Sbjct: 145 RDRNERTEKPERDPERDERGGRVEPQRPTREERPSRDERPIRDERPSSRDERPSREERPS 204

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF 341
                 R+   +                +R E + R+P F
Sbjct: 205 RDERPTRDDRPSRDERPT--RDDRPSRDERPERNERTPRF 242


>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 = 41.7 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 21/215 (9%), Positives = 57/215 (26%), Gaps = 33/215 (15%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--------------LRKAERTR 74
           R + + +   RV VN   + +    +   D IE+                  +   +   
Sbjct: 31  RFIRKAVRDGRVFVNKEKVIK-KNKLSQDDLIEIYMQEDEHQNIEPEDMNIEIVYEDNDI 89

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------------------ISVGRLDI 116
           + +  +P  +V         +     L                         I + +   
Sbjct: 90  IVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKNQF 149

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +   L    +     ++        ++    R +  + +++ +   K IV +        
Sbjct: 150 SHMRLASDMSKDSFRKIYIAVVHGSMKEKEGRINLPIYKEEESESIKRIVDERGQESITT 209

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +  +    + V + L  G+  +I+         
Sbjct: 210 YEVLEELSKGSVVRLELETGRTHQIRVHMSHLGHP 244


>gi|301627633|ref|XP_002942975.1| PREDICTED: voltage-dependent N-type calcium channel subunit
           alpha-1B-like [Xenopus (Silurana) tropicalis]
          Length = 1548

 Score = 41.7 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 15/121 (12%), Positives = 31/121 (25%), Gaps = 4/121 (3%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           + +  R++      +E   + +                      +    +++   +    
Sbjct: 138 NDREERQRQHRSRSKEEDGSKETGRGERNRSQERGKRHHRRASPEDGTEREHRRHRTHRH 197

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQRE-ENHRRSPSFPS---KRSLRRTSA 352
              +     + +  +      K  H    S SG RE E   R          RS  R   
Sbjct: 198 SADRQGKEGNGQPPSGGKGERKSRHRGGGSRSGNREGEGTNRGTGENGEEPPRSRHRNRH 257

Query: 353 K 353
           K
Sbjct: 258 K 258


>gi|115762736|ref|XP_785240.2| PREDICTED: similar to WD repeat domain 60, partial
           [Strongylocentrotus purpuratus]
          Length = 1073

 Score = 41.7 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 10/109 (9%), Positives = 28/109 (25%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
             H  ++   +            +DR     +  D   R  +         ++++     
Sbjct: 44  ERHRDKDRDKDSHRDKEHERKRDKDRDRQKEKDKDRERRKDREGESSKEKDRERRKDREK 103

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                       +        +S + ++   +  S   ++   R   KK
Sbjct: 104 DSSKDKDRREKDRDGRKEREKESSKEKDRGEKDRSKHREKEKDRDREKK 152


>gi|34496917|ref|NP_901132.1| translation initiation factor IF-2 [Chromobacterium violaceum ATCC
           12472]
 gi|39931211|sp|Q7NY13|IF2_CHRVO RecName: Full=Translation initiation factor IF-2
 gi|34102773|gb|AAQ59137.1| translation initiation factor IF-2 [Chromobacterium violaceum ATCC
           12472]
          Length = 964

 Score = 41.7 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 10/97 (10%), Positives = 20/97 (20%), Gaps = 1/97 (1%)

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
               L         AP+   +   R      +   D+      ++          +   P
Sbjct: 206 QAAKLAASQPAPEPAPVVEPQREERRDDRRGAPSGDNRGPRGNDNRGPRPAGAGDRGPRP 265

Query: 305 VHR-RNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
               R         +G      +   +      R P 
Sbjct: 266 GGDNRGPRPAGAGDRGPRPGGDNRGPRPAGAGDRGPR 302



 Score = 40.2 bits (92), Expect = 0.45,   Method: Composition-based stats.
 Identities = 10/112 (8%), Positives = 22/112 (19%), Gaps = 3/112 (2%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R +    + E+ +                        P    R        +G ++  + 
Sbjct: 188 RARQEALMREKIEREERRQAAKLAASQPAPEPAPVVEPQREERRDDRRGAPSGDNRGPRG 247

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                 R         +G      +   +      R P         R +  
Sbjct: 248 ND---NRGPRPAGAGDRGPRPGGDNRGPRPAGAGDRGPRPGGDNRGPRPAGA 296



 Score = 37.9 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 13/112 (11%), Positives = 23/112 (20%), Gaps = 3/112 (2%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P       V         +       +      +D    +   +   G         P 
Sbjct: 214 QPAPEPAPVVEPQREERRDDRRGAPSGDNRGPRGNDNRGPRPAGAGDRGPRPGGDNRGPR 273

Query: 306 HRR---NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                          +G   +   D G R      +PS P   +   +   K
Sbjct: 274 PAGAGDRGPRPGGDNRGPRPAGAGDRGPRPAPAAAAPSQPPAPAPGGSRPGK 325



 Score = 37.1 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 10/114 (8%), Positives = 23/114 (20%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +S + +  +      + A       +   +    +R                   +    
Sbjct: 169 LSPEEIAAREAEEKRQAAFRARQEALMREKIEREERRQAAKLAASQPAPEPAPVVEPQRE 228

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
            ++          N        +G   +   D G R     R P          
Sbjct: 229 ERRDDRRGAPSGDNRGPRGNDNRGPRPAGAGDRGPRPGGDNRGPRPAGAGDRGP 282



 Score = 36.3 bits (82), Expect = 8.2,   Method: Composition-based stats.
 Identities = 10/111 (9%), Positives = 21/111 (18%), Gaps = 3/111 (2%)

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           + P   E       AP   +     +               +     +           P
Sbjct: 223 VEPQREERRDDRRGAPSGDNRGPRGNDNRGPRPAGAGDRGPRPGGDNRGPRPAGAGDRGP 282

Query: 305 VHR---RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                 R         +G   +  + +  +        S P K       +
Sbjct: 283 RPGGDNRGPRPAGAGDRGPRPAPAAAAPSQPPAPAPGGSRPGKGKKGGERS 333


>gi|238062179|ref|ZP_04606888.1| RNA helicase [Micromonospora sp. ATCC 39149]
 gi|237883990|gb|EEP72818.1| RNA helicase [Micromonospora sp. ATCC 39149]
          Length = 707

 Score = 41.7 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 16/115 (13%), Positives = 27/115 (23%), Gaps = 2/115 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVR--DRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
           R+  G     +                R  DRP       D  +  ++   +  G  +  
Sbjct: 563 RDGRGERGFGDRPAGERRYGDRPAGERRYDDRPAGERRYDDRPSGGRRFDERAGGERRYG 622

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              T   R +                   G R    RR      +    RT  ++
Sbjct: 623 DRPTGEQRYDDRPTAPRRYEDRPVGERRYGDRPAGERRFAERGERGGDPRTGDRR 677



 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 25/154 (16%), Positives = 40/154 (25%), Gaps = 18/154 (11%)

Query: 217 RISYGPFQLGTLLAGSTREVSKKILREQ-LGPHLLEEAQVNLDAPIYSSETLVRDRPNII 275
           R+  G   L  L     RE S   +R++   P    +            E    DRP   
Sbjct: 469 RVRAGDPALAELT--GAREPSGVPVRDEAPAPRRHGDRPSAPRRFEDRGERRYGDRPTGE 526

Query: 276 SEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR--NLASNVWMAKGIHSSFLSDSGQREE 333
               D   R ++    +    ++        RR  +         G   +     G R  
Sbjct: 527 RRYGDRDGRGERGFGDRPAGERRYGDRPTGERRYDDRDGRGERGFGDRPAGERRYGDRPA 586

Query: 334 NHRR-------------SPSFPSKRSLRRTSAKK 354
             RR              PS   +   R    ++
Sbjct: 587 GERRYDDRPAGERRYDDRPSGGRRFDERAGGERR 620



 Score = 39.8 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 17/140 (12%), Positives = 35/140 (25%), Gaps = 2/140 (1%)

Query: 216 IRISYGPFQLGTLLAGSTREVSKK-ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNI 274
            R +    +   +    TR  +    L E  G        V  +AP           P  
Sbjct: 451 RRTTLAMLEKAGVEPAETRVRAGDPALAELTGAREPSGVPVRDEAPAPRRHGDRPSAPRR 510

Query: 275 ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREEN 334
             +  +     +    ++ G    +       R                +    G+ E  
Sbjct: 511 FEDRGERRYGDRPTGERRYGDRDGRGERGFGDRPAGERRYGDRPTGERRYDDRDGRGERG 570

Query: 335 HRRSPSFPSKRSLRRTSAKK 354
               P+   +R   R + ++
Sbjct: 571 FGDRPA-GERRYGDRPAGER 589


>gi|15645907|ref|NP_208086.1| 30S ribosomal protein S4 [Helicobacter pylori 26695]
 gi|217032048|ref|ZP_03437548.1| hypothetical protein HPB128_16g8 [Helicobacter pylori B128]
 gi|298735681|ref|YP_003728206.1| 30S ribosomal protein S4 [Helicobacter pylori B8]
 gi|2500400|sp|P56011|RS4_HELPY RecName: Full=30S ribosomal protein S4
 gi|2314460|gb|AAD08337.1| ribosomal protein S4 (rps4) [Helicobacter pylori 26695]
 gi|216946196|gb|EEC24804.1| hypothetical protein HPB128_16g8 [Helicobacter pylori B128]
 gi|298354870|emb|CBI65742.1| small subunit ribosomal protein S4 [Helicobacter pylori B8]
 gi|307637965|gb|ADN80415.1| SSU ribosomal protein S4p:S9e [Helicobacter pylori 908]
 gi|325996570|gb|ADZ51975.1| 30S ribosomal protein S4 [Helicobacter pylori 2018]
 gi|325998160|gb|ADZ50368.1| 30S ribosomal protein S4 [Helicobacter pylori 2017]
          Length = 208

 Score = 41.7 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A+ R    +++    V V+G  L+  +  V S   IE+
Sbjct: 99  RLDNVVYRMGFATTRSSARQLVTHGHVLVDGKRLDIPSYFVRSGQKIEI 147


>gi|332978670|gb|EGK15368.1| ATP-dependent RNA helicase RhlE [Psychrobacter sp. 1501(2011)]
          Length = 519

 Score = 41.7 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 18/130 (13%), Positives = 31/130 (23%), Gaps = 11/130 (8%)

Query: 224 QLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
           QL  +     R +S + +         ++  V   A                    +   
Sbjct: 391 QLDAINRYLKRTMSVEEIEGMEPKKNTKDMHVGAAAKRGRGGNRRGGPGAGNRRGGNGGG 450

Query: 284 RMKKNS-------SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR 336
             +  S        +  G    +    P  RR        A     S      +R    R
Sbjct: 451 GYRGKSNDNASGEKRGAGAGAGRPSGKPAGRRFGGKPAGSAGAGKPSG----QRRAAPSR 506

Query: 337 RSPSFPSKRS 346
                P++RS
Sbjct: 507 SGEGRPARRS 516


>gi|120603476|ref|YP_967876.1| translation initiation factor IF-2 [Desulfovibrio vulgaris DP4]
 gi|166232543|sp|A1VG83|IF2_DESVV RecName: Full=Translation initiation factor IF-2
 gi|120563705|gb|ABM29449.1| bacterial translation initiation factor 2 (bIF-2) [Desulfovibrio
           vulgaris DP4]
          Length = 1079

 Score = 41.7 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 12/91 (13%), Positives = 18/91 (19%)

Query: 260 PIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKG 319
                      RP    E        ++   +  G  + +    P   R        A  
Sbjct: 298 RPGGQRPEGGYRPEGQREGGYRPEGQREGGYRPGGAPRPEGGYRPGGPRPEGGYRPGAPR 357

Query: 320 IHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
               +    G R E  R     P        
Sbjct: 358 PEGGYRPAGGPRPEGQREGGYRPGAPRPEGG 388



 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 9/109 (8%), Positives = 21/109 (19%), Gaps = 1/109 (0%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           +R    P     AQ  +       +                +    +         +++ 
Sbjct: 267 VRVISRPDPAAVAQQQMQQQAAQQQREAGGYRPGGQRPEGGYRPEGQREGGYRPEGQREG 326

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
              P          +   G         G         P+   +   +R
Sbjct: 327 GYRPGGA-PRPEGGYRPGGPRPEGGYRPGAPRPEGGYRPAGGPRPEGQR 374



 Score = 35.9 bits (81), Expect = 9.7,   Method: Composition-based stats.
 Identities = 6/106 (5%), Positives = 18/106 (16%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
             ++ + +V       +       +     +      R      +     + ++      
Sbjct: 261 EAVVPQVRVISRPDPAAVAQQQMQQQAAQQQREAGGYRPGGQRPEGGYRPEGQREGGYRP 320

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                                 G         P  P      R + 
Sbjct: 321 EGQREGGYRPGGAPRPEGGYRPGGPRPEGGYRPGAPRPEGGYRPAG 366


>gi|46578923|ref|YP_009731.1| translation initiation factor IF-2 [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|81830507|sp|Q72ER1|IF2_DESVH RecName: Full=Translation initiation factor IF-2
 gi|46448335|gb|AAS94990.1| translation initiation factor IF-2 [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|311232781|gb|ADP85635.1| translation initiation factor IF-2 [Desulfovibrio vulgaris RCH1]
          Length = 1079

 Score = 41.7 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 12/91 (13%), Positives = 18/91 (19%)

Query: 260 PIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKG 319
                      RP    E        ++   +  G  + +    P   R        A  
Sbjct: 298 RPGGQRPEGGYRPEGQREGGYRPEGQREGGYRPGGAPRPEGGYRPGGPRPEGGYRPGAPR 357

Query: 320 IHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
               +    G R E  R     P        
Sbjct: 358 PEGGYRPAGGPRPEGQREGGYRPGAPRPEGG 388



 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 9/109 (8%), Positives = 21/109 (19%), Gaps = 1/109 (0%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           +R    P     AQ  +       +                +    +         +++ 
Sbjct: 267 VRVISRPDPAAVAQQQMQQQAAQQQREAGGYRPGGQRPEGGYRPEGQREGGYRPEGQREG 326

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
              P          +   G         G         P+   +   +R
Sbjct: 327 GYRPGGA-PRPEGGYRPGGPRPEGGYRPGAPRPEGGYRPAGGPRPEGQR 374



 Score = 35.9 bits (81), Expect = 9.7,   Method: Composition-based stats.
 Identities = 6/106 (5%), Positives = 18/106 (16%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
             ++ + +V       +       +     +      R      +     + ++      
Sbjct: 261 EAVVPQVRVISRPDPAAVAQQQMQQQAAQQQREAGGYRPGGQRPEGGYRPEGQREGGYRP 320

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                                 G         P  P      R + 
Sbjct: 321 EGQREGGYRPGGAPRPEGGYRPGGPRPEGGYRPGAPRPEGGYRPAG 366


>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 = 41.7 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 31/232 (13%), Positives = 68/232 (29%), Gaps = 34/232 (14%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK----------AERTRLWL 77
           R  ++  +A+ +V VNGI        +     + +    +             E   + +
Sbjct: 74  RNSIKSALARGQVSVNGIPRTVHNFPLEQGQTVALSKEKVTPVVPLTGLRILHEDEAIIV 133

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV------GRLDINTEGLLLLTNDGGLA 131
            HK  GL++  S  +   T +  L +   R           RLD +T G+++      + 
Sbjct: 134 IHKDAGLLSVASAQEQEVTAYRQLTAHVRREHPYNRIFVLHRLDRDTSGVMMFAKSEAIQ 193

Query: 132 RVLELPSTQWLRVYR-------------VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           + ++    + +                       + + K   +          +      
Sbjct: 194 QEMQKAWKEVVYERTYIALVEGQVKKAEGTITSWLKESKTLKMYSSPYPNDGQHAVTHYK 253

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI-----SYGPFQL 225
           L       + + V L  G+  +I+   E     +    +      S G   L
Sbjct: 254 LLQANRHFSLLEVRLETGRKNQIRVHMEDIGHPIVGDKKYGSKSKSIGRLGL 305


>gi|109946782|ref|YP_664010.1| 30S ribosomal protein S4 [Helicobacter acinonychis str. Sheeba]
 gi|188528082|ref|YP_001910769.1| 30S ribosomal protein S4 [Helicobacter pylori Shi470]
 gi|207092545|ref|ZP_03240332.1| 30S ribosomal protein S4 [Helicobacter pylori HPKX_438_AG0C1]
 gi|208435192|ref|YP_002266858.1| ribosomal protein S4 [Helicobacter pylori G27]
 gi|210135453|ref|YP_002301892.1| 30S ribosomal protein S4 [Helicobacter pylori P12]
 gi|217033613|ref|ZP_03439041.1| hypothetical protein HP9810_899g49 [Helicobacter pylori 98-10]
 gi|254779836|ref|YP_003057942.1| 30S ribosomal protein S4 [Helicobacter pylori B38]
 gi|308183404|ref|YP_003927531.1| 30S ribosomal protein S4 [Helicobacter pylori PeCan4]
 gi|308185046|ref|YP_003929179.1| 30S ribosomal protein S4 [Helicobacter pylori SJM180]
 gi|123362789|sp|Q17ZB5|RS4_HELAH RecName: Full=30S ribosomal protein S4
 gi|226699072|sp|B6JND4|RS4_HELP2 RecName: Full=30S ribosomal protein S4
 gi|226699073|sp|B5Z8U3|RS4_HELPG RecName: Full=30S ribosomal protein S4
 gi|226699074|sp|B2UV57|RS4_HELPS RecName: Full=30S ribosomal protein S4
 gi|109714003|emb|CAJ99011.1| 30S ribosomal protein S4 [Helicobacter acinonychis str. Sheeba]
 gi|188144322|gb|ACD48739.1| 30S ribosomal protein S4 [Helicobacter pylori Shi470]
 gi|208433121|gb|ACI27992.1| ribosomal protein S4 [Helicobacter pylori G27]
 gi|210133421|gb|ACJ08412.1| 30S ribosomal protein S4 [Helicobacter pylori P12]
 gi|216943959|gb|EEC23393.1| hypothetical protein HP9810_899g49 [Helicobacter pylori 98-10]
 gi|254001748|emb|CAX29979.1| 30S ribosomal subunit protein S4 [Helicobacter pylori B38]
 gi|308060966|gb|ADO02862.1| 30S ribosomal protein S4 [Helicobacter pylori SJM180]
 gi|308062579|gb|ADO04467.1| 30S ribosomal protein S4 [Helicobacter pylori Cuz20]
 gi|308064071|gb|ADO05958.1| 30S ribosomal protein S4 [Helicobacter pylori Sat464]
 gi|308065589|gb|ADO07481.1| 30S ribosomal protein S4 [Helicobacter pylori PeCan4]
 gi|317009977|gb|ADU80557.1| 30S ribosomal protein S4 [Helicobacter pylori India7]
 gi|317011494|gb|ADU85241.1| 30S ribosomal protein S4 [Helicobacter pylori SouthAfrica7]
 gi|317013081|gb|ADU83689.1| 30S ribosomal protein S4 [Helicobacter pylori Lithuania75]
 gi|317014685|gb|ADU82121.1| 30S ribosomal protein S4 [Helicobacter pylori Gambia94/24]
 gi|317178033|dbj|BAJ55822.1| 30S ribosomal protein S4 [Helicobacter pylori F16]
 gi|317178415|dbj|BAJ56203.1| 30S ribosomal protein S4 [Helicobacter pylori F30]
 gi|317182540|dbj|BAJ60324.1| 30S ribosomal protein S4 [Helicobacter pylori F57]
          Length = 208

 Score = 41.7 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 1/65 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G A+ R    +++    V V+G  L+  +  V S   IE+        +  
Sbjct: 99  RLDNVVYRMGFATTRSSARQLVTHGHVLVDGKRLDIPSYFVRSGQKIEIKEKTKSNPQVV 158

Query: 74  RLWLY 78
           R    
Sbjct: 159 RAMEL 163


>gi|15612279|ref|NP_223932.1| 30S ribosomal protein S4 [Helicobacter pylori J99]
 gi|7388210|sp|Q9ZJT4|RS4_HELPJ RecName: Full=30S ribosomal protein S4
 gi|4155842|gb|AAD06816.1| 30S RIBOSOMAL PROTEIN S4 [Helicobacter pylori J99]
 gi|261840009|gb|ACX99774.1| 30S ribosomal protein S4 [Helicobacter pylori 52]
 gi|297380476|gb|ADI35363.1| ribosomal protein S4 [Helicobacter pylori v225d]
 gi|332674094|gb|AEE70911.1| 30S ribosomal protein S4 [Helicobacter pylori 83]
          Length = 208

 Score = 41.7 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 1/65 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G A+ R    +++    V V+G  L+  +  V S   IE+        +  
Sbjct: 99  RLDNVVYRMGFATTRSSARQLVTHGHVLVDGKRLDIPSYFVRSGQKIEIKEKTKSNPQVV 158

Query: 74  RLWLY 78
           R    
Sbjct: 159 RAMEL 163


>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 = 41.7 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 21/215 (9%), Positives = 57/215 (26%), Gaps = 33/215 (15%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--------------LRKAERTR 74
           R + + +   RV VN   + +    +   D IE+                  +   +   
Sbjct: 31  RFIRKAVRDGRVFVNKEKVIK-KNKLSQDDLIEIYMQEDEHQNIEPEDMNIEIVYEDNDI 89

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------------------ISVGRLDI 116
           + +  +P  +V         +     L                         I + +   
Sbjct: 90  IVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKNQF 149

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +   L    +     ++        ++    R +  + +++ +   K IV +        
Sbjct: 150 SHMRLASDMSKDSFRKIYIAVVHGSMKEKEGRINLPIYKEEESESIKRIVDERGQESITT 209

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +  +    + V + L  G+  +I+         
Sbjct: 210 YEVLEELSKGSVVRLELETGRTHQIRVHMSHLGHP 244


>gi|325285318|ref|YP_004261108.1| RNA-binding S4 domain-containing protein [Cellulophaga lytica DSM
           7489]
 gi|324320772|gb|ADY28237.1| RNA-binding S4 domain protein [Cellulophaga lytica DSM 7489]
          Length = 149

 Score = 41.7 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 11/83 (13%), Positives = 25/83 (30%), Gaps = 2/83 (2%)

Query: 14  QRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+ K +       +R        +  +KVN  +++  + +V   D I V    +     
Sbjct: 23  MRIDKYLWCTRYFKTRNIATEACKKGHIKVNDKVVK-PSRDVFPMDKITVRKNQINYQFT 81

Query: 73  TRLWLYHKPIGLVTTHSDPDGRS 95
                 ++    +      D   
Sbjct: 82  ILDVPPNRVGAKLVDMYRKDTTP 104


>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 = 41.7 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 32/269 (11%), Positives = 80/269 (29%), Gaps = 41/269 (15%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V EN   QR+   +  R     +R + R+I   +++V+   +   +  V   D I++  
Sbjct: 18  FVDENSLFQRIDNFLIKRLKRVPKRLIYRLIRIGKIRVDDSKV-NPSYRVQKEDLIKIPI 76

Query: 63  -----DGVPLRKAERTRLWLYHKPIG---------------LVTTHSDPDGRSTVFDNLP 102
                    +    +   W+  + +                + +      G   +   + 
Sbjct: 77  SLSYSQDKSISIQRKNFYWIKKRILYEDSEILVLNKPSGIAVHSGSKFSFGIIEILREVY 136

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
                +  + R+D  T G+LL+     + ++++          +                
Sbjct: 137 FQSKYLELIHRIDKETSGILLIAKSRNILQLIQKQFCSQKIFKKYIVLVHGVWPSKIKRI 196

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIKKVFEFF 208
              + + I     +     + G  +     ++E              G+  +I+   +  
Sbjct: 197 SCFLEKKISQKKEKKIEIKKNGRMSETLFQIKERFASFTLMLATPITGRKHQIRLHTKKI 256

Query: 209 NWKVNRLIRISYGPFQLG-TLLAGSTREV 236
           N  +    R  YG  +L   L     + +
Sbjct: 257 NHPIVLDKR--YGNRKLDRNLKESGLKRL 283


>gi|115964466|ref|XP_001191416.1| PREDICTED: similar to WD repeat domain 60 [Strongylocentrotus
           purpuratus]
          Length = 1077

 Score = 41.7 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 10/109 (9%), Positives = 28/109 (25%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
             H  ++   +            +DR     +  D   R  +         ++++     
Sbjct: 48  ERHRDKDRDKDSHRDKEHERKRDKDRDRQKEKDKDRERRKDREGESSKEKDRERRKDREK 107

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                       +        +S + ++   +  S   ++   R   KK
Sbjct: 108 DSSKDKDRREKDRDGRKEREKESSKEKDRGEKDRSKHREKEKDRDREKK 156


>gi|315504490|ref|YP_004083377.1| hypothetical protein ML5_3715 [Micromonospora sp. L5]
 gi|315411109|gb|ADU09226.1| hypothetical protein ML5_3715 [Micromonospora sp. L5]
          Length = 407

 Score = 41.7 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 11/83 (13%), Positives = 21/83 (25%), Gaps = 3/83 (3%)

Query: 274 IISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREE 333
             +  P   +  +  +  +     +   +  + R       W       S         +
Sbjct: 66  AAASRPGARSSHRPPAGSRRSAGGRGPGSRQLSRPGSRRPSWPEPARPGSRRPSWPGSLQ 125

Query: 334 NHRRSPSFPS---KRSLRRTSAK 353
              R PS P      S R  S +
Sbjct: 126 PGSRRPSRPGSARPGSRRPGSPR 148



 Score = 37.9 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 15/124 (12%), Positives = 27/124 (21%), Gaps = 6/124 (4%)

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G+ R VS      + G                      R      S  P      +  S 
Sbjct: 57  GARRWVSGYAAASRPGARSSHRPPAGSRRSAGGRGPGSRQLSRPGSRRPSWPEPARPGSR 116

Query: 291 QKNGLSK----QKKLATPVHRRNLASNVWMAKGI--HSSFLSDSGQREENHRRSPSFPSK 344
           + +         ++ + P   R  +      +     S   +   +      R P   S 
Sbjct: 117 RPSWPGSLQPGSRRPSRPGSARPGSRRPGSPRPAVLRSDGGTAWSRPSTPGPRRPRAGSS 176

Query: 345 RSLR 348
               
Sbjct: 177 GDGS 180


>gi|326203868|ref|ZP_08193730.1| ribosomal protein S4 [Clostridium papyrosolvens DSM 2782]
 gi|325985966|gb|EGD46800.1| ribosomal protein S4 [Clostridium papyrosolvens DSM 2782]
          Length = 208

 Score = 41.7 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+  SR E  +++      +NG  +   +  +   D I V
Sbjct: 99  RLDNVVYRLGLGTSRPESRQLVTHGHFTINGKRVNIPSYLIKVGDVIAV 147


>gi|108563664|ref|YP_627980.1| 30S ribosomal protein S4 [Helicobacter pylori HPAG1]
 gi|122980453|sp|Q1CRW6|RS4_HELPH RecName: Full=30S ribosomal protein S4
 gi|107837437|gb|ABF85306.1| ribosomal protein S4 [Helicobacter pylori HPAG1]
          Length = 208

 Score = 41.7 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A+ R    +++    V V+G  L+  +  V S   IE+
Sbjct: 99  RLDNVVYRMGFATTRSSARQLVTHGHVLVDGKRLDIPSYFVRSGQKIEI 147


>gi|15890001|ref|NP_355682.1| hypothetical protein Atu2752 [Agrobacterium tumefaciens str. C58]
 gi|15157972|gb|AAK88467.1| conserved hypothetical protein [Agrobacterium tumefaciens str.
          C58]
          Length = 138

 Score = 41.7 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 1/51 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
            T QR+ K +  A +A SR   +  I    VKVNG  + + +  + + D 
Sbjct: 9  ESTRQRLDKWLFFARMAKSRSLAQSYIQSGHVKVNGATIRQPSHMLKAGDR 59


>gi|318040504|ref|ZP_07972460.1| hypothetical protein SCB01_02311 [Synechococcus sp. CB0101]
          Length = 300

 Score = 41.7 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 13/121 (10%), Positives = 28/121 (23%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R    + LR ++        + + D          R      +   D++    +      
Sbjct: 121 RFDEPQPLRRRIRSREDGYGERDEDDLYRPRRAPARAAIPERAASRDEWDGRSERREAPP 180

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             S+ +  + P                 S   +      E   RS   P        +  
Sbjct: 181 TASRFRAGSGPSEGPGREFGSRRQDRDESRRGTRPATSSEPMPRSSRRPGPSDRPEGTPY 240

Query: 354 K 354
           +
Sbjct: 241 R 241



 Score = 37.1 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 16/101 (15%), Positives = 28/101 (27%), Gaps = 3/101 (2%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ--- 298
           R++   +    A      P  ++     D  +   E P   +R +  S    G  ++   
Sbjct: 142 RDEDDLYRPRRAPARAAIPERAASRDEWDGRSERREAPPTASRFRAGSGPSEGPGREFGS 201

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
           ++      RR             SS       R E     P
Sbjct: 202 RRQDRDESRRGTRPATSSEPMPRSSRRPGPSDRPEGTPYRP 242


>gi|294651664|ref|ZP_06728967.1| ATP-dependent RNA helicase [Acinetobacter haemolyticus ATCC 19194]
 gi|292822443|gb|EFF81343.1| ATP-dependent RNA helicase [Acinetobacter haemolyticus ATCC 19194]
          Length = 647

 Score = 41.7 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 10/112 (8%), Positives = 24/112 (21%), Gaps = 4/112 (3%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            ++      ++ +    +             +          R ++  +      +    
Sbjct: 440 DDRPRRSFDDKPRGERPSFGGEDRPRREFNSDRPRREGGFEDRPRREFNSDRPRREGGFE 499

Query: 302 ATPVHR----RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
             P       R      +  +   S    D  +RE N  R           R
Sbjct: 500 DRPRREFNSDRPRREGGFDDRPKRSFGGEDRPRREFNSDRPRREGGFNDKPR 551



 Score = 36.3 bits (82), Expect = 8.2,   Method: Composition-based stats.
 Identities = 10/107 (9%), Positives = 24/107 (22%), Gaps = 9/107 (8%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR----RNLAS 312
            +           D+P           R ++  +      +      P       R    
Sbjct: 436 REGGDDRPRRSFDDKPRGERPSFGGEDRPRREFNSDRPRREGGFEDRPRREFNSDRPRRE 495

Query: 313 NVWMAKGIHS-SFLSDSGQREENHRRSPSFPSKRSLRR----TSAKK 354
             +  +     +      +   + R   SF  +   RR       ++
Sbjct: 496 GGFEDRPRREFNSDRPRREGGFDDRPKRSFGGEDRPRREFNSDRPRR 542


>gi|85858172|ref|YP_460374.1| 30S ribosomal protein S4P [Syntrophus aciditrophicus SB]
 gi|123515693|sp|Q2LQD0|RS4_SYNAS RecName: Full=30S ribosomal protein S4
 gi|85721263|gb|ABC76206.1| SSU ribosomal protein S4P [Syntrophus aciditrophicus SB]
          Length = 209

 Score = 41.7 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 26/72 (36%), Gaps = 7/72 (9%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------DGVPL 67
           R+  ++ R G A SR E  +++      VNG  +   +  V   D IEV      +   +
Sbjct: 100 RLDNMVYRLGFANSRNEARQLVRHNHFLVNGRKVNIPSFLVNIGDFIEVTEEGRKNNKII 159

Query: 68  RKAERTRLWLYH 79
              E        
Sbjct: 160 EAMETIVRRGIP 171


>gi|33601856|ref|NP_889416.1| hypothetical protein BB2880 [Bordetella bronchiseptica RB50]
 gi|33576293|emb|CAE33372.1| putative membrane protein [Bordetella bronchiseptica RB50]
          Length = 409

 Score = 41.7 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 19/113 (16%), Positives = 31/113 (27%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+Q  P            P                  P    R   +S  +   ++Q+  
Sbjct: 254 RDQAAPAPGARGPAGQGRPGQDRAAGQGGPRADDVSAPRRDARPSPDSVPRQAGARQENT 313

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                RRN ++    +     +       R    RR    P +RS R   A +
Sbjct: 314 RQENVRRNQSTPRQESAPRQHNAPRPERARPAEPRRDAGSPPERSSRPAPAPR 366


>gi|332529321|ref|ZP_08405283.1| RNA-binding s4 domain protein [Hylemonella gracilis ATCC 19624]
 gi|332041238|gb|EGI77602.1| RNA-binding s4 domain protein [Hylemonella gracilis ATCC 19624]
          Length = 162

 Score = 41.7 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 24/52 (46%), Gaps = 2/52 (3%)

Query: 12 TPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             R+ K + A     +R      I++ R +VNG + +  A ++   D +E+
Sbjct: 21 DTMRLDKWLWAARFYKTRALAAEEISKGRARVNGQVAK-PARDLKPGDTVEL 71


>gi|291393965|ref|XP_002713340.1| PREDICTED: membrane associated guanylate kinase, WW and PDZ domain
            containing 1 isoform 2 [Oryctolagus cuniculus]
          Length = 1452

 Score = 41.7 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 19/99 (19%), Positives = 28/99 (28%), Gaps = 1/99 (1%)

Query: 251  EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
               +    A         R   N     P +  R    S+      ++K+      RR  
Sbjct: 1292 CRPKDRAAADGRRDAQPERSAANGPKRRPPEKRREGTRSADNTLERREKRRDGSPERRRE 1351

Query: 311  ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
             S     +    S    S +R  + RRSP      S  R
Sbjct: 1352 RSP-GRGRDSSPSHRRRSLERLLDQRRSPERRRAGSPER 1389



 Score = 40.5 bits (93), Expect = 0.35,   Method: Composition-based stats.
 Identities = 14/115 (12%), Positives = 28/115 (24%), Gaps = 4/115 (3%)

Query: 244  QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
              G                S +       N  S  PD      K+ +  +G    +   +
Sbjct: 1252 PHGERRAHARDAKGIREYGSRQPSEHHTWNGTSRKPDGGACRPKDRAAADGRRDAQPERS 1311

Query: 304  PVHRRNLASNVWMAKGIHSSF----LSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              +           +G  S+       +  +     RR    P +      S ++
Sbjct: 1312 AANGPKRRPPEKRREGTRSADNTLERREKRRDGSPERRRERSPGRGRDSSPSHRR 1366



 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 13/122 (10%), Positives = 27/122 (22%), Gaps = 5/122 (4%)

Query: 237  SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
              K +RE  G     E                R +    ++   D    +  ++      
Sbjct: 1262 DAKGIREY-GSRQPSEHHTWNGTSRKPDGGACRPKDRAAADGRRDAQPERSAANGPKRRP 1320

Query: 297  KQKKLATPVHR----RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             +K+                    +           G+      R  S       RR+  
Sbjct: 1321 PEKRREGTRSADNTLERREKRRDGSPERRRERSPGRGRDSSPSHRRRSLERLLDQRRSPE 1380

Query: 353  KK 354
            ++
Sbjct: 1381 RR 1382



 Score = 37.9 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 9/102 (8%), Positives = 20/102 (19%), Gaps = 8/102 (7%)

Query: 248  HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               + A  +         +          E   + TR   N+ ++    +         R
Sbjct: 1293 RPKDRAAADGRRDAQPERSAANGPKRRPPEKRREGTRSADNTLERREKRRDGSPERRRER 1352

Query: 308  RNLASNVWMAKGIHS--------SFLSDSGQREENHRRSPSF 341
                                       +  +     RR+ S 
Sbjct: 1353 SPGRGRDSSPSHRRRSLERLLDQRRSPERRRAGSPERRAKST 1394



 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 14/117 (11%), Positives = 32/117 (27%), Gaps = 5/117 (4%)

Query: 243  EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            +  G      +       + ++    R  P++ S  P D  +   +  ++      K + 
Sbjct: 1208 DPGGDRNGAPSGAQGVPQVRAAPPDRRPHPSLESSYPPDLHKSSPHGERRAHARDAKGIR 1267

Query: 303  TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS-----LRRTSAKK 354
                R+    + W          +   +             +RS      RR   K+
Sbjct: 1268 EYGSRQPSEHHTWNGTSRKPDGGACRPKDRAAADGRRDAQPERSAANGPKRRPPEKR 1324


>gi|302661836|ref|XP_003022580.1| SH3 domain protein [Trichophyton verrucosum HKI 0517]
 gi|291186534|gb|EFE41962.1| SH3 domain protein [Trichophyton verrucosum HKI 0517]
          Length = 1004

 Score = 41.7 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 19/123 (15%), Positives = 33/123 (26%), Gaps = 2/123 (1%)

Query: 222 PFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD 281
              L +L      E++++I +     H +             S    R       +    
Sbjct: 253 GIDLHSLTPTQEDELTERIAQAFRRRHRVPSPTHISRRRESPSPAQPRPVSQDRQQQQPH 312

Query: 282 FTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGI--HSSFLSDSGQREENHRRSP 339
                 ++S     +++     P   R        A     H    SD G      R SP
Sbjct: 313 QQERSPSASASTPRAREPTRRAPPTSRPRLLEPLTAHHAANHRRSASDQGTGTRRRRTSP 372

Query: 340 SFP 342
           + P
Sbjct: 373 TPP 375


>gi|291393963|ref|XP_002713339.1| PREDICTED: membrane associated guanylate kinase, WW and PDZ domain
            containing 1 isoform 1 [Oryctolagus cuniculus]
          Length = 1481

 Score = 41.7 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 19/99 (19%), Positives = 28/99 (28%), Gaps = 1/99 (1%)

Query: 251  EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
               +    A         R   N     P +  R    S+      ++K+      RR  
Sbjct: 1321 CRPKDRAAADGRRDAQPERSAANGPKRRPPEKRREGTRSADNTLERREKRRDGSPERRRE 1380

Query: 311  ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
             S     +    S    S +R  + RRSP      S  R
Sbjct: 1381 RSP-GRGRDSSPSHRRRSLERLLDQRRSPERRRAGSPER 1418



 Score = 40.5 bits (93), Expect = 0.35,   Method: Composition-based stats.
 Identities = 14/115 (12%), Positives = 28/115 (24%), Gaps = 4/115 (3%)

Query: 244  QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
              G                S +       N  S  PD      K+ +  +G    +   +
Sbjct: 1281 PHGERRAHARDAKGIREYGSRQPSEHHTWNGTSRKPDGGACRPKDRAAADGRRDAQPERS 1340

Query: 304  PVHRRNLASNVWMAKGIHSSF----LSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              +           +G  S+       +  +     RR    P +      S ++
Sbjct: 1341 AANGPKRRPPEKRREGTRSADNTLERREKRRDGSPERRRERSPGRGRDSSPSHRR 1395



 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 13/122 (10%), Positives = 27/122 (22%), Gaps = 5/122 (4%)

Query: 237  SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
              K +RE  G     E                R +    ++   D    +  ++      
Sbjct: 1291 DAKGIREY-GSRQPSEHHTWNGTSRKPDGGACRPKDRAAADGRRDAQPERSAANGPKRRP 1349

Query: 297  KQKKLATPVHR----RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             +K+                    +           G+      R  S       RR+  
Sbjct: 1350 PEKRREGTRSADNTLERREKRRDGSPERRRERSPGRGRDSSPSHRRRSLERLLDQRRSPE 1409

Query: 353  KK 354
            ++
Sbjct: 1410 RR 1411



 Score = 37.9 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 9/102 (8%), Positives = 20/102 (19%), Gaps = 8/102 (7%)

Query: 248  HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               + A  +         +          E   + TR   N+ ++    +         R
Sbjct: 1322 RPKDRAAADGRRDAQPERSAANGPKRRPPEKRREGTRSADNTLERREKRRDGSPERRRER 1381

Query: 308  RNLASNVWMAKGIHS--------SFLSDSGQREENHRRSPSF 341
                                       +  +     RR+ S 
Sbjct: 1382 SPGRGRDSSPSHRRRSLERLLDQRRSPERRRAGSPERRAKST 1423



 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 14/117 (11%), Positives = 32/117 (27%), Gaps = 5/117 (4%)

Query: 243  EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            +  G      +       + ++    R  P++ S  P D  +   +  ++      K + 
Sbjct: 1237 DPGGDRNGAPSGAQGVPQVRAAPPDRRPHPSLESSYPPDLHKSSPHGERRAHARDAKGIR 1296

Query: 303  TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS-----LRRTSAKK 354
                R+    + W          +   +             +RS      RR   K+
Sbjct: 1297 EYGSRQPSEHHTWNGTSRKPDGGACRPKDRAAADGRRDAQPERSAANGPKRRPPEKR 1353


>gi|238491480|ref|XP_002376977.1| AT DNA binding protein (Thy28), putative [Aspergillus flavus
           NRRL3357]
 gi|220697390|gb|EED53731.1| AT DNA binding protein (Thy28), putative [Aspergillus flavus
           NRRL3357]
          Length = 307

 Score = 41.7 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 10/91 (10%), Positives = 24/91 (26%)

Query: 264 SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSS 323
             T+   +    S    +     K ++  +  + +K+      +    S    + G    
Sbjct: 1   MTTMPVKKRKSESVPAAEENNSPKRAAVPDPATGEKRKRGRPRKYPEGSGPKPSPGPKRG 60

Query: 324 FLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                     +    PS P +        +K
Sbjct: 61  RGRPRKDPSASTPSKPSTPKEGKRPVGRPRK 91


>gi|223936404|ref|ZP_03628316.1| ribosomal protein S4 [bacterium Ellin514]
 gi|223894922|gb|EEF61371.1| ribosomal protein S4 [bacterium Ellin514]
          Length = 202

 Score = 41.7 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 12/48 (25%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           R+  V+   G A +R    ++++   V+VNG  +   +  +   D IE
Sbjct: 93  RLDNVVFHLGFANTRAAARQLVSHGHVRVNGRKVNIPSFALKVNDVIE 140


>gi|126739832|ref|ZP_01755523.1| 30S ribosomal protein S4 [Roseobacter sp. SK209-2-6]
 gi|126719064|gb|EBA15775.1| 30S ribosomal protein S4 [Roseobacter sp. SK209-2-6]
          Length = 206

 Score = 41.7 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 8/35 (22%), Positives = 12/35 (34%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
             + +    V VNG  +   +  V   D I V   
Sbjct: 112 ARQFVNHGHVTVNGKRVNIPSYRVKEGDVIAVRDK 146


>gi|118617682|ref|YP_906014.1| translation initiation factor IF-2 [Mycobacterium ulcerans Agy99]
 gi|166232562|sp|A0PQC4|IF2_MYCUA RecName: Full=Translation initiation factor IF-2
 gi|118569792|gb|ABL04543.1| translation initiation factor IF-2 InfB [Mycobacterium ulcerans
           Agy99]
          Length = 945

 Score = 41.7 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 11/93 (11%), Positives = 16/93 (17%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
             AP        +     ++         K+        +     A PV R         
Sbjct: 155 RPAPTPGKPAAPQAPHPGMAPGARPGPVPKQGVRTPRVGNNPFSSAQPVDRPIPRPQAPR 214

Query: 317 AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                       G    N    P   S      
Sbjct: 215 PGAPRPGAPRPGGASSGNMPPRPGGASGGPRPP 247


>gi|187476573|ref|YP_784597.1| 30S ribosomal protein S4 [Bordetella avium 197N]
 gi|123515214|sp|Q2L242|RS4_BORA1 RecName: Full=30S ribosomal protein S4
 gi|115421159|emb|CAJ47643.1| 30S ribosomal protein S4 [Bordetella avium 197N]
          Length = 207

 Score = 41.7 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G  S R E  ++++ + +++NG   + A++ V + D I V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHRAIELNGHTADIASMLVKAGDVITV 146


>gi|268559888|ref|XP_002646089.1| C. briggsae CBR-RSR-1 protein [Caenorhabditis briggsae]
          Length = 572

 Score = 41.7 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 12/107 (11%), Positives = 24/107 (22%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                +                  P+     P   +   +  +      K ++  +   +
Sbjct: 299 RRQSGSPPRGARKGSPEAKKPGRSPSGSPRGPRKLSGSPRRRAASPEARKPRRSPSGSPK 358

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           R  A          S     S        RSP    +R    + A +
Sbjct: 359 RRQAFPAARRPPSGSPPRRRSPPAASKFGRSPPESPRRRRSGSPAAR 405



 Score = 40.5 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 12/108 (11%), Positives = 26/108 (24%), Gaps = 1/108 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                     +   P   S +  R   +  +  P           Q    +++    +P 
Sbjct: 316 AKKPGRSPSGSPRGPRKLSGSPRRRAASPEARKPRRSPSGSPKRRQAFPAARRPPSGSPP 375

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS-KRSLRRTSA 352
            RR+  +     +    S            +   S     R  R+  +
Sbjct: 376 RRRSPPAASKFGRSPPESPRRRRSGSPAARKPGRSPSGSPRGARKGRS 423



 Score = 40.2 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 15/105 (14%), Positives = 23/105 (21%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+  G      A      P  S     + R    +          +  S        +  
Sbjct: 331 RKLSGSPRRRAASPEARKPRRSPSGSPKRRQAFPAARRPPSGSPPRRRSPPAASKFGRSP 390

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
                RR   S      G   S      ++  +   SP    K  
Sbjct: 391 PESPRRRRSGSPAARKPGRSPSGSPRGARKGRSPSGSPGRRQKSP 435



 Score = 39.8 bits (91), Expect = 0.60,   Method: Composition-based stats.
 Identities = 14/108 (12%), Positives = 28/108 (25%), Gaps = 4/108 (3%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P     +          S +  R +    +  P   +  ++ S        +    +P  
Sbjct: 337 PRRRAASPEARKPRRSPSGSPKRRQAFPAARRPPSGSPPRRRSPPAASKFGRSPPESPRR 396

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           RR+ +              S S +     R     P +R       +K
Sbjct: 397 RRSGSPAARKP----GRSPSGSPRGARKGRSPSGSPGRRQKSPEVVRK 440



 Score = 39.4 bits (90), Expect = 0.94,   Method: Composition-based stats.
 Identities = 12/106 (11%), Positives = 25/106 (23%), Gaps = 2/106 (1%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ--KKLATPVHRR 308
            EA+    +P  S     +   +          R  + S   +   +Q       P    
Sbjct: 314 PEAKKPGRSPSGSPRGPRKLSGSPRRRAASPEARKPRRSPSGSPKRRQAFPAARRPPSGS 373

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                   A         +S +R  +   +   P +         +
Sbjct: 374 PPRRRSPPAASKFGRSPPESPRRRRSGSPAARKPGRSPSGSPRGAR 419



 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 12/120 (10%), Positives = 24/120 (20%), Gaps = 2/120 (1%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           E+ +K +                           R R +            +     ++ 
Sbjct: 265 ELRRKAI-ASQARRSKSPRGSPRRRSPRGRSPEARRRQSGSPPRGARKGSPEAKKPGRSP 323

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREE-NHRRSPSFPSKRSLRRTSAK 353
               +            +    A+    S      +R+     R P   S    R   A 
Sbjct: 324 SGSPRGPRKLSGSPRRRAASPEARKPRRSPSGSPKRRQAFPAARRPPSGSPPRRRSPPAA 383



 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 31/109 (28%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                E  +  + +    S++                 R +++ S   G  K    A   
Sbjct: 260 RHEEAELRRKAIASQARRSKSPRGSPRRRSPRGRSPEARRRQSGSPPRGARKGSPEAKKP 319

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            R    S     K   S     +       RRSPS   KR     +A++
Sbjct: 320 GRSPSGSPRGPRKLSGSPRRRAASPEARKPRRSPSGSPKRRQAFPAARR 368



 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 14/107 (13%), Positives = 29/107 (27%), Gaps = 1/107 (0%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT-PV 305
           P    +       P  S     R    +           +    +++     K+    P 
Sbjct: 306 PRGARKGSPEAKKPGRSPSGSPRGPRKLSGSPRRRAASPEARKPRRSPSGSPKRRQAFPA 365

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            RR  + +    +   ++        E   RR    P+ R   R+ +
Sbjct: 366 ARRPPSGSPPRRRSPPAASKFGRSPPESPRRRRSGSPAARKPGRSPS 412


>gi|229825290|ref|ZP_04451359.1| hypothetical protein GCWU000182_00644 [Abiotrophia defectiva ATCC
           49176]
 gi|229790662|gb|EEP26776.1| hypothetical protein GCWU000182_00644 [Abiotrophia defectiva ATCC
           49176]
          Length = 198

 Score = 41.7 bits (96), Expect = 0.20,   Method: Composition-based stats.
 Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 1/45 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           R+  VI R G+A +R+E  +M+  + V VNG  +   +  V   D
Sbjct: 89  RLDNVIFRLGLARTRKEARQMVGHKMVLVNGKQVNIPSYTVAVGD 133


>gi|332255860|ref|XP_003277045.1| PREDICTED: RNA exonuclease 1 homolog [Nomascus leucogenys]
          Length = 1216

 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 8/85 (9%), Positives = 19/85 (22%), Gaps = 1/85 (1%)

Query: 264 SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSS 323
            +   R              + + +       S + K   P   R+ A+ V  +      
Sbjct: 390 KDGAQRKDKTKDKGRGRPAEKPRADKKGPQASSPRHKAERPEGPRSSATPVASSGKGRPD 449

Query: 324 FLSDSGQREENHRRSPSFPSKRSLR 348
             +       +    P+        
Sbjct: 450 QPARRPS-PTSGDSRPAAGRGPPRP 473


>gi|291575122|ref|NP_569731.2| putative NPIP-like protein KIAA0220-like [Homo sapiens]
          Length = 1133

 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 27/108 (25%), Gaps = 3/108 (2%)

Query: 247  PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
            P   +EA+               + P              +   ++     +     P  
Sbjct: 1012 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 1071

Query: 307  RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS--FPSKRSLRRTSA 352
            RR              +   +     E  RR      PS++  RR +A
Sbjct: 1072 RRVGDVEPSRKPKRRRAADVEPSS-PEPKRRRVGDVEPSRKPKRRRAA 1118



 Score = 39.8 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 9/117 (7%), Positives = 25/117 (21%), Gaps = 2/117 (1%)

Query: 238  KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            +    +   P     A++              +                    ++  +  
Sbjct: 1017 EAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGD 1076

Query: 298  QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             +    P  RR         +            R+   +R  +   + SL     ++
Sbjct: 1077 VEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKP--KRRRAADVEPSLPEPKRRR 1131



 Score = 37.5 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 28/112 (25%), Gaps = 3/112 (2%)

Query: 243  EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            E+L   L   A  NL  P  +++    ++P                  ++     +    
Sbjct: 994  ERLRGPLPPSADDNLKTPPLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRK 1053

Query: 303  TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                R                   +  ++    +R  +   + S      ++
Sbjct: 1054 PKRRRAADVEPSSPEPKRRRVGDVEPSRKP---KRRRAADVEPSSPEPKRRR 1102



 Score = 35.9 bits (81), Expect = 9.3,   Method: Composition-based stats.
 Identities = 13/120 (10%), Positives = 29/120 (24%), Gaps = 6/120 (5%)

Query: 235  EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
             ++ +    +       +    ++ P       V D              ++ +S +   
Sbjct: 1012 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 1071

Query: 295  LS-KQKKLATPVHRRNLASNVWMAKGIHSSF-----LSDSGQREENHRRSPSFPSKRSLR 348
                  + +    RR  A     +             S   +R       PS P  +  R
Sbjct: 1072 RRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKPKRRRAADVEPSLPEPKRRR 1131


>gi|237752998|ref|ZP_04583478.1| 30s ribosomal protein s4 [Helicobacter winghamensis ATCC BAA-430]
 gi|229375265|gb|EEO25356.1| 30s ribosomal protein s4 [Helicobacter winghamensis ATCC BAA-430]
          Length = 208

 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 14/68 (20%), Positives = 28/68 (41%), Gaps = 1/68 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G A+ RR   +++    + V+G  L+  +  V     +E+     +  +  
Sbjct: 99  RLDNVVYRMGFATTRRFARQLVVHGHILVDGKKLDIPSALVGVGQKVEICEKTKKNPQVQ 158

Query: 74  RLWLYHKP 81
           R     K 
Sbjct: 159 RAIELTKQ 166


>gi|254471009|ref|ZP_05084412.1| translation initiation factor IF-2 [Pseudovibrio sp. JE062]
 gi|211960151|gb|EEA95348.1| translation initiation factor IF-2 [Pseudovibrio sp. JE062]
          Length = 1010

 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 14/141 (9%), Positives = 30/141 (21%), Gaps = 14/141 (9%)

Query: 224 QLGTLLAGSTREV-----------SKKIL---REQLGPHLLEEAQVNLDAPIYSSETLVR 269
           +L  L     REV            ++ L   R         E +         +    +
Sbjct: 143 RLAALKMAKVREVEDQKRRVEEAKRQEELARQRAIEAEKQRVEDEARAKREAEEAAVRAK 202

Query: 270 DRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSG 329
                 ++   +       + +     ++        R     +     G       D G
Sbjct: 203 AEAEAKAKAEAEAKAKAAEAPKPAQREERPARGDRPQRSGDRGDRPQRSGDRPHRGGDRG 262

Query: 330 QREENHRRSPSFPSKRSLRRT 350
            R +  R       +      
Sbjct: 263 PRPQGERGPRPGGDRGPRPAG 283



 Score = 37.1 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 8/104 (7%), Positives = 20/104 (19%), Gaps = 2/104 (1%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +   R +                   +E   + +     +      R  +    +    +
Sbjct: 185 EDEARAKREAEEAAVRAKAEAEAKAKAEAEAKAKAAEAPKPAQREERPARGDRPQRSGDR 244

Query: 298 QKKLATPVHRRNLASNVWMAKGI--HSSFLSDSGQREENHRRSP 339
             +      R +   +               D G R    R   
Sbjct: 245 GDRPQRSGDRPHRGGDRGPRPQGERGPRPGGDRGPRPAGDRGPR 288



 Score = 35.9 bits (81), Expect = 8.5,   Method: Composition-based stats.
 Identities = 8/98 (8%), Positives = 23/98 (23%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           RE     +  +A+    A   +            ++  +   R  +     +   + ++ 
Sbjct: 192 REAEEAAVRAKAEAEAKAKAEAEAKAKAAEAPKPAQREERPARGDRPQRSGDRGDRPQRS 251

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
               HR          +           +   +    P
Sbjct: 252 GDRPHRGGDRGPRPQGERGPRPGGDRGPRPAGDRGPRP 289


>gi|194381794|dbj|BAG64266.1| unnamed protein product [Homo sapiens]
          Length = 849

 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 27/108 (25%), Gaps = 3/108 (2%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P   +EA+               + P              +   ++     +     P  
Sbjct: 728 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 787

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS--FPSKRSLRRTSA 352
           RR              +   +     E  RR      PS++  RR +A
Sbjct: 788 RRVGDVEPSRKPKRRRAADVEPSS-PEPKRRRVGDVEPSRKPKRRRAA 834



 Score = 39.8 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 9/117 (7%), Positives = 25/117 (21%), Gaps = 2/117 (1%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +    +   P     A++              +                    ++  +  
Sbjct: 733 EAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGD 792

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +    P  RR         +            R+   +R  +   + SL     ++
Sbjct: 793 VEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKP--KRRRAADVEPSLPEPKRRR 847



 Score = 37.5 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 28/112 (25%), Gaps = 3/112 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E+L   L   A  NL  P  +++    ++P                  ++     +    
Sbjct: 710 ERLRGPLPPSADDNLKTPPLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRK 769

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               R                   +  ++    +R  +   + S      ++
Sbjct: 770 PKRRRAADVEPSSPEPKRRRVGDVEPSRKP---KRRRAADVEPSSPEPKRRR 818



 Score = 35.9 bits (81), Expect = 9.5,   Method: Composition-based stats.
 Identities = 13/120 (10%), Positives = 29/120 (24%), Gaps = 6/120 (5%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
            ++ +    +       +    ++ P       V D              ++ +S +   
Sbjct: 728 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 787

Query: 295 LS-KQKKLATPVHRRNLASNVWMAKGIHSSF-----LSDSGQREENHRRSPSFPSKRSLR 348
                 + +    RR  A     +             S   +R       PS P  +  R
Sbjct: 788 RRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKPKRRRAADVEPSLPEPKRRR 847


>gi|167957551|ref|ZP_02544625.1| ribosomal protein S4 [candidate division TM7 single-cell isolate
           TM7c]
          Length = 205

 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 15/77 (19%), Positives = 30/77 (38%), Gaps = 1/77 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+   + RAG AS RR   ++++     +NG  ++  ++ + + D I V     +    T
Sbjct: 94  RLDNAVYRAGFASSRRAARQLVSHGHFILNGRRVDIPSIRLKAGDEISVRPKSTKSGYFT 153

Query: 74  RLWLYHKPIGLVTTHSD 90
            +    K          
Sbjct: 154 HIDDIVKNSNQTALSWM 170


>gi|149634646|ref|XP_001514639.1| PREDICTED: similar to p167 [Ornithorhynchus anatinus]
          Length = 1362

 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 15/137 (10%), Positives = 32/137 (23%), Gaps = 7/137 (5%)

Query: 216  IRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNII 275
             R S G ++         R       R             + + P+   E   R   +  
Sbjct: 914  DRDSEGTWRKSAEPEAEWR-------RGPPEKEWRRGEGRDEERPLRRDEDRPRRAGDDE 966

Query: 276  SEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENH 335
             + P       +   +     +  +      R    S         ++      +R  + 
Sbjct: 967  EKEPPARADEDRVPRRGLDEDRGPRRGVDEDRFPRRSADEDRGSWRNADDDRPPRRAVDE 1026

Query: 336  RRSPSFPSKRSLRRTSA 352
             R P  P++        
Sbjct: 1027 DRGPWRPAEDDRPPRRG 1043


>gi|119605885|gb|EAW85479.1| serine/arginine repetitive matrix 2, isoform CRA_c [Homo sapiens]
          Length = 2662

 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 9/108 (8%), Positives = 21/108 (19%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                            S   +     +              + +    + + +  AT  
Sbjct: 335 RHASSSPESPKPAPAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAK 394

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R+ +          S        R          P +R   R+  +
Sbjct: 395 RGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQR 442



 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 13/107 (12%), Positives = 25/107 (23%), Gaps = 1/107 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P      +++      +       R    S  P       ++ +       + +  T  
Sbjct: 347 APAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKR 406

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                 S  W        +      +     RSP  P   S  R + 
Sbjct: 407 GHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPG-WSRSRNTQ 452



 Score = 39.4 bits (90), Expect = 0.96,   Method: Composition-based stats.
 Identities = 22/135 (16%), Positives = 34/135 (25%), Gaps = 10/135 (7%)

Query: 230 AGSTREV----SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
            GS RE+    + K             +         S       R    S  P      
Sbjct: 350 PGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKRGHS 409

Query: 286 KKNSSQKNGLSKQKK--LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
           +  S Q       ++   +    RR  + +        S      G+     R      S
Sbjct: 410 RSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRSHSRS 469

Query: 344 K----RSLRRTSAKK 354
                RS  RT A++
Sbjct: 470 PATRGRSRSRTPARR 484


>gi|242278683|ref|YP_002990812.1| ribosomal protein S4 [Desulfovibrio salexigens DSM 2638]
 gi|259495273|sp|C6C1B0|RS4_DESAD RecName: Full=30S ribosomal protein S4
 gi|242121577|gb|ACS79273.1| ribosomal protein S4 [Desulfovibrio salexigens DSM 2638]
          Length = 208

 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   + R G A SR +  +++       NG  +   +++V   D IEV
Sbjct: 99  RLDNTVYRLGFANSRAQARQLVKHGIFTKNGRRVNVPSMHVKPGDVIEV 147


>gi|207108317|ref|ZP_03242479.1| 30S ribosomal protein S4 [Helicobacter pylori HPKX_438_CA4C1]
          Length = 178

 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 1/65 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G A+ R    +++    V V+G  L+  +  V S   IE+        +  
Sbjct: 99  RLDNVVYRMGFATTRSSARQLVTHGHVLVDGKRLDIPSYFVRSGQKIEIKEKTKSNPQVV 158

Query: 74  RLWLY 78
           R    
Sbjct: 159 RAMEL 163


>gi|194390556|dbj|BAG62037.1| unnamed protein product [Homo sapiens]
          Length = 1043

 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 27/108 (25%), Gaps = 3/108 (2%)

Query: 247  PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
            P   +EA+               + P              +   ++     +     P  
Sbjct: 922  PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 981

Query: 307  RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS--FPSKRSLRRTSA 352
            RR              +   +     E  RR      PS++  RR +A
Sbjct: 982  RRVGDVEPSRKPKRRRAADVEPSS-PEPKRRRVGDVEPSRKPKRRRAA 1028



 Score = 39.8 bits (91), Expect = 0.69,   Method: Composition-based stats.
 Identities = 9/117 (7%), Positives = 25/117 (21%), Gaps = 2/117 (1%)

Query: 238  KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            +    +   P     A++              +                    ++  +  
Sbjct: 927  EAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGD 986

Query: 298  QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             +    P  RR         +            R+   +R  +   + SL     ++
Sbjct: 987  VEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKP--KRRRAADVEPSLPEPKRRR 1041



 Score = 37.5 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 28/112 (25%), Gaps = 3/112 (2%)

Query: 243  EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            E+L   L   A  NL  P  +++    ++P                  ++     +    
Sbjct: 904  ERLRGPLPPSADDNLKTPPLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRK 963

Query: 303  TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                R                   +  ++    +R  +   + S      ++
Sbjct: 964  PKRRRAADVEPSSPEPKRRRVGDVEPSRKP---KRRRAADVEPSSPEPKRRR 1012



 Score = 35.9 bits (81), Expect = 9.6,   Method: Composition-based stats.
 Identities = 13/120 (10%), Positives = 29/120 (24%), Gaps = 6/120 (5%)

Query: 235  EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
             ++ +    +       +    ++ P       V D              ++ +S +   
Sbjct: 922  PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 981

Query: 295  LS-KQKKLATPVHRRNLASNVWMAKGIHSSF-----LSDSGQREENHRRSPSFPSKRSLR 348
                  + +    RR  A     +             S   +R       PS P  +  R
Sbjct: 982  RRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKPKRRRAADVEPSLPEPKRRR 1041


>gi|73540741|ref|YP_295261.1| RNA-binding S4 [Ralstonia eutropha JMP134]
 gi|72118154|gb|AAZ60417.1| RNA-binding S4 [Ralstonia eutropha JMP134]
          Length = 131

 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 12/61 (19%), Positives = 24/61 (39%), Gaps = 5/61 (8%)

Query: 7  VQENFTPQ---RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          +  +F P    R+ K +       +R      + + +V VNG   +  +  V   D I +
Sbjct: 1  MNVSFEPDARLRIDKWLWCARFFKTRSLAAEAVERGKVTVNGQPCKN-SREVKPGDTIVL 59

Query: 63 D 63
          +
Sbjct: 60 E 60


>gi|38346193|emb|CAD39524.2| OSJNBa0027O01.9 [Oryza sativa Japonica Group]
          Length = 953

 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 15/124 (12%), Positives = 30/124 (24%)

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G  R   +  L E   P         L A        +    ++   +         N +
Sbjct: 346 GPVRWGRQNHLGETSFPLQSGRLTDPLAARSRRVPPAIPSPASLRPRIRRPQRPSGGNLT 405

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
            +       K   P         +       +      G+R +  R       ++   R 
Sbjct: 406 GERPRIAYGKPRRPPGLARPRKPLGRRPPGPARPGKPLGRRPDFARTRRWRLPRQLATRP 465

Query: 351 SAKK 354
            A++
Sbjct: 466 RARR 469


>gi|84514475|ref|ZP_01001839.1| 30S ribosomal protein S4 [Loktanella vestfoldensis SKA53]
 gi|84511526|gb|EAQ07979.1| 30S ribosomal protein S4 [Loktanella vestfoldensis SKA53]
          Length = 206

 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 9/32 (28%), Positives = 13/32 (40%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             + +    V VNG  +   +  V   D IEV
Sbjct: 112 ARQFVNHGHVTVNGQRVNIPSYRVKEGDVIEV 143


>gi|326780443|ref|ZP_08239708.1| serine/threonine protein kinase [Streptomyces cf. griseus
           XylebKG-1]
 gi|326660776|gb|EGE45622.1| serine/threonine protein kinase [Streptomyces cf. griseus
           XylebKG-1]
          Length = 439

 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 12/104 (11%), Positives = 23/104 (22%)

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
              R  +     +  +         ++   R      +  P    R     S        
Sbjct: 277 HESRPPVQRSAQDADRPTGRMADPYADQHTRRSEGPSASRPQPGRRGAPGRSGPPRTGGS 336

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
           +                   G +    + SG R  +  R P+ P
Sbjct: 337 RPQQASRDTTRSGRRQGPPPGTNGRPGTRSGGRTTSAGRRPANP 380



 Score = 41.3 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 16/123 (13%), Positives = 31/123 (25%), Gaps = 6/123 (4%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDF------TRMKKNSS 290
             +     L   +  +     +A           R    ++ P          +  + S 
Sbjct: 251 DPEERPSTLQLSMRLKEIAAREAQGLHESRPPVQRSAQDADRPTGRMADPYADQHTRRSE 310

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
             +    Q        R              S   + SG+R+     +   P  RS  RT
Sbjct: 311 GPSASRPQPGRRGAPGRSGPPRTGGSRPQQASRDTTRSGRRQGPPPGTNGRPGTRSGGRT 370

Query: 351 SAK 353
           ++ 
Sbjct: 371 TSA 373


>gi|269961856|ref|ZP_06176213.1| ATP-dependent RNA helicase [Vibrio harveyi 1DA3]
 gi|269833434|gb|EEZ87536.1| ATP-dependent RNA helicase [Vibrio harveyi 1DA3]
          Length = 526

 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 13/98 (13%), Positives = 27/98 (27%), Gaps = 2/98 (2%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              +    +        +     +     +   +     ++ + K G++K      P   
Sbjct: 431 KNGKGENKSGKGGAGKPKGNRDGQARPNGKPSGNKPNNNQSGANKPGVNKNGNGGKPSGN 490

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
           R    N     G   S    SG +    RR P   + +
Sbjct: 491 R--KPNSGKPAGAKPSNGKPSGNKPSGQRRKPRPQTAK 526



 Score = 40.9 bits (94), Expect = 0.28,   Method: Composition-based stats.
 Identities = 14/116 (12%), Positives = 30/116 (25%), Gaps = 6/116 (5%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
             +   G +  +    + +          +          D   R     S     + Q 
Sbjct: 412 EKKNSGGNNKPKRRFNSDNKNGKGENKSGKGGAGKPKGNRDGQARPNGKPSGNKPNNNQS 471

Query: 300 KLATPVHRRNLASNVWMAKG-IHSSFLSDSGQREENHRR---SPSFPSKRSLRRTS 351
               P   +N   N     G    +    +G +  N +     PS   ++   +T+
Sbjct: 472 GANKPGVNKNG--NGGKPSGNRKPNSGKPAGAKPSNGKPSGNKPSGQRRKPRPQTA 525


>gi|226953843|ref|ZP_03824307.1| ATP-dependent RNA helicase [Acinetobacter sp. ATCC 27244]
 gi|226835434|gb|EEH67817.1| ATP-dependent RNA helicase [Acinetobacter sp. ATCC 27244]
          Length = 647

 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 10/112 (8%), Positives = 24/112 (21%), Gaps = 4/112 (3%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            ++      ++ +    +             +          R ++  +      +    
Sbjct: 440 DDRPRRSFDDKPRGERPSFGGEDRPRREFNSDRPRREGGFEDRPRREFNSDRPRREGGFE 499

Query: 302 ATPVHR----RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
             P       R      +  +   S    D  +RE N  R           R
Sbjct: 500 DRPRREFNSDRPRREGGFDDRPKRSFGGEDRPRREFNSDRPRREGGFNDKPR 551



 Score = 35.9 bits (81), Expect = 8.7,   Method: Composition-based stats.
 Identities = 10/107 (9%), Positives = 24/107 (22%), Gaps = 9/107 (8%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR----RNLAS 312
            +           D+P           R ++  +      +      P       R    
Sbjct: 436 REGGDDRPRRSFDDKPRGERPSFGGEDRPRREFNSDRPRREGGFEDRPRREFNSDRPRRE 495

Query: 313 NVWMAKGIHS-SFLSDSGQREENHRRSPSFPSKRSLRR----TSAKK 354
             +  +     +      +   + R   SF  +   RR       ++
Sbjct: 496 GGFEDRPRREFNSDRPRREGGFDDRPKRSFGGEDRPRREFNSDRPRR 542


>gi|46485873|gb|AAS98498.1| unknown protein [Oryza sativa Japonica Group]
 gi|50300523|gb|AAT73665.1| hypothetical protein [Oryza sativa Japonica Group]
          Length = 1068

 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 16/113 (14%), Positives = 22/113 (19%), Gaps = 7/113 (6%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +G    EE           S           +  P D        +   G  KQ     
Sbjct: 299 MMGVGASEEVAPKGHDGAGGSRQEESTPGGGRASGPRDGGSGSNRPADARGKRKQGGTPP 358

Query: 304 PVHRRN-------LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           P   R               A            +  +     PS  +  S  R
Sbjct: 359 PSPPRGDGAVRASRRRPEGAAPTSQPETERKKKRLRKTGETEPSRGNLISPPR 411



 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 12/102 (11%), Positives = 24/102 (23%), Gaps = 1/102 (0%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
             +  + +     +                  ++ S+   G +   +       R   + 
Sbjct: 289 DPDRASILTIMMGVGASEEVAPKGHDGAGGSRQEESTPGGGRASGPRDGGSGSNRPADAR 348

Query: 314 VWMAKGIHSSFLSDSGQRE-ENHRRSPSFPSKRSLRRTSAKK 354
               +G         G       RR P   +  S   T  KK
Sbjct: 349 GKRKQGGTPPPSPPRGDGAVRASRRRPEGAAPTSQPETERKK 390


>gi|291393967|ref|XP_002713341.1| PREDICTED: membrane associated guanylate kinase, WW and PDZ domain
            containing 1 isoform 3 [Oryctolagus cuniculus]
          Length = 1469

 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 19/99 (19%), Positives = 28/99 (28%), Gaps = 1/99 (1%)

Query: 251  EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
               +    A         R   N     P +  R    S+      ++K+      RR  
Sbjct: 1309 CRPKDRAAADGRRDAQPERSAANGPKRRPPEKRREGTRSADNTLERREKRRDGSPERRRE 1368

Query: 311  ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
             S     +    S    S +R  + RRSP      S  R
Sbjct: 1369 RSP-GRGRDSSPSHRRRSLERLLDQRRSPERRRAGSPER 1406



 Score = 40.5 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 14/115 (12%), Positives = 28/115 (24%), Gaps = 4/115 (3%)

Query: 244  QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
              G                S +       N  S  PD      K+ +  +G    +   +
Sbjct: 1269 PHGERRAHARDAKGIREYGSRQPSEHHTWNGTSRKPDGGACRPKDRAAADGRRDAQPERS 1328

Query: 304  PVHRRNLASNVWMAKGIHSSF----LSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              +           +G  S+       +  +     RR    P +      S ++
Sbjct: 1329 AANGPKRRPPEKRREGTRSADNTLERREKRRDGSPERRRERSPGRGRDSSPSHRR 1383



 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 13/122 (10%), Positives = 27/122 (22%), Gaps = 5/122 (4%)

Query: 237  SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
              K +RE  G     E                R +    ++   D    +  ++      
Sbjct: 1279 DAKGIREY-GSRQPSEHHTWNGTSRKPDGGACRPKDRAAADGRRDAQPERSAANGPKRRP 1337

Query: 297  KQKKLATPVHR----RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             +K+                    +           G+      R  S       RR+  
Sbjct: 1338 PEKRREGTRSADNTLERREKRRDGSPERRRERSPGRGRDSSPSHRRRSLERLLDQRRSPE 1397

Query: 353  KK 354
            ++
Sbjct: 1398 RR 1399



 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 9/102 (8%), Positives = 20/102 (19%), Gaps = 8/102 (7%)

Query: 248  HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               + A  +         +          E   + TR   N+ ++    +         R
Sbjct: 1310 RPKDRAAADGRRDAQPERSAANGPKRRPPEKRREGTRSADNTLERREKRRDGSPERRRER 1369

Query: 308  RNLASNVWMAKGIHS--------SFLSDSGQREENHRRSPSF 341
                                       +  +     RR+ S 
Sbjct: 1370 SPGRGRDSSPSHRRRSLERLLDQRRSPERRRAGSPERRAKST 1411



 Score = 37.5 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 14/117 (11%), Positives = 32/117 (27%), Gaps = 5/117 (4%)

Query: 243  EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            +  G      +       + ++    R  P++ S  P D  +   +  ++      K + 
Sbjct: 1225 DPGGDRNGAPSGAQGVPQVRAAPPDRRPHPSLESSYPPDLHKSSPHGERRAHARDAKGIR 1284

Query: 303  TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS-----LRRTSAKK 354
                R+    + W          +   +             +RS      RR   K+
Sbjct: 1285 EYGSRQPSEHHTWNGTSRKPDGGACRPKDRAAADGRRDAQPERSAANGPKRRPPEKR 1341


>gi|255261708|ref|ZP_05341050.1| ribosomal protein S4 [Thalassiobium sp. R2A62]
 gi|255104043|gb|EET46717.1| ribosomal protein S4 [Thalassiobium sp. R2A62]
          Length = 206

 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 10/35 (28%), Positives = 14/35 (40%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
             + +    VKVNG  +   +  V   D IEV   
Sbjct: 112 ARQFVNHGHVKVNGKKVNIPSYRVKEGDVIEVRDR 146


>gi|15967012|ref|NP_387365.1| HEAT shock-like protein [Sinorhizobium meliloti 1021]
 gi|307302480|ref|ZP_07582237.1| RNA-binding S4 domain protein [Sinorhizobium meliloti BL225C]
 gi|307316190|ref|ZP_07595634.1| RNA-binding S4 domain protein [Sinorhizobium meliloti AK83]
 gi|15076285|emb|CAC47838.1| Heat shock protein 15 (HSP15) [Sinorhizobium meliloti 1021]
 gi|306898030|gb|EFN28772.1| RNA-binding S4 domain protein [Sinorhizobium meliloti AK83]
 gi|306903150|gb|EFN33740.1| RNA-binding S4 domain protein [Sinorhizobium meliloti BL225C]
          Length = 143

 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 3/51 (5%)

Query: 14 QRVSKVI--ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          QR+ K +  AR  I SR   ++ I    V VNG    +++  + + D +EV
Sbjct: 13 QRLDKWLFFARL-IKSRSLAQKAIEAGHVAVNGKRETQSSAQIKAGDMLEV 62


>gi|254234050|ref|ZP_04927375.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis C]
 gi|124599579|gb|EAY58683.1| 30S ribosomal protein S4 rpsD [Mycobacterium tuberculosis C]
          Length = 201

 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  VI RAG+A +RR   ++++     VNG  +   +  V   D ++V    L      
Sbjct: 92  RLDNVIYRAGLARTRRMARQLVSHGHFNVNGAHVNVPSYRVSQYDIVDVRDKSLNTVPFQ 151

Query: 74  R 74
            
Sbjct: 152 I 152


>gi|319901020|ref|YP_004160748.1| PSP1 domain protein [Bacteroides helcogenes P 36-108]
 gi|319416051|gb|ADV43162.1| PSP1 domain protein [Bacteroides helcogenes P 36-108]
          Length = 460

 Score = 41.3 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 17/153 (11%), Positives = 42/153 (27%), Gaps = 11/153 (7%)

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTR--EVSKKILREQLGPHLLEEAQVNLDAPIYSSETL 267
           +++  L R    P     L+  + R        L EQ      +  + + +    + E  
Sbjct: 310 FEIIGLNRRGIKP---DNLMEETHRSEPKKPVDLLEQESLTRFDRGRKSRNNGESNGENG 366

Query: 268 VRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSD 327
             +R     +  ++  +    + Q     + ++      +R+  S               
Sbjct: 367 NGNRNRKRKKSNNNRIQGNGPTPQPQDQKQGEQATQEEAKRSQQSRQGEQPRPKDQQKQG 426

Query: 328 SGQREE------NHRRSPSFPSKRSLRRTSAKK 354
            G R +           P    ++S       +
Sbjct: 427 GGDRPQRTSNRKPRNSKPRPQGEKSSNNDKPSQ 459


>gi|220917490|ref|YP_002492794.1| transcriptional regulator, Fis family [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|219955344|gb|ACL65728.1| transcriptional regulator, Fis family [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 613

 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 11/77 (14%), Positives = 20/77 (25%)

Query: 272 PNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR 331
           P   +  P+   R      + +   +      P  RR   +     +G       D   R
Sbjct: 336 PAGDASAPEWPGRRFARPERADRAPRGASGERPPRRRTPGTGRPPERGGRPPRTGDRPAR 395

Query: 332 EENHRRSPSFPSKRSLR 348
               R +   P +    
Sbjct: 396 TGAGRPAGPQPWRPRTP 412



 Score = 36.3 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 12/124 (9%), Positives = 20/124 (16%), Gaps = 22/124 (17%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R  L      +A          +     DR    +       R    + +      +   
Sbjct: 329 RLGLELGPAGDASAPEWPGRRFARPERADRAPRGASGERPPRRRTPGTGRPPERGGRPPR 388

Query: 302 ATPVHRRNLASNVWMAKGIHSS----------------------FLSDSGQREENHRRSP 339
                 R  A      +                               +G      R  P
Sbjct: 389 TGDRPARTGAGRPAGPQPWRPRTPDRRGAGPGPGPARPGAGGGEGSPAAGASPRPARSGP 448

Query: 340 SFPS 343
             P 
Sbjct: 449 GRPG 452


>gi|332864595|ref|XP_518946.3| PREDICTED: protein sidekick-1 [Pan troglodytes]
          Length = 2213

 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 11/69 (15%), Positives = 17/69 (24%), Gaps = 3/69 (4%)

Query: 283 TRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
            R  + S+   G    +        R   S+   A     S     G      R +P  P
Sbjct: 2   ARGARPSAAGGGGGGAEPPERAGPGRPRGSSPGRA---RPSPAPRPGPEPSRPRAAPETP 58

Query: 343 SKRSLRRTS 351
              +     
Sbjct: 59  GGDTAGAGR 67



 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 7/83 (8%), Positives = 15/83 (18%), Gaps = 1/83 (1%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
           +        A          +R            R +  S       +  +         
Sbjct: 1   MARGARPSAAGGGGGGAEPPERAGPGRPRGSSPGRARP-SPAPRPGPEPSRPRAAPETPG 59

Query: 310 LASNVWMAKGIHSSFLSDSGQRE 332
             +      G   +     G+R 
Sbjct: 60  GDTAGAGRCGGRRAAKLGPGRRG 82


>gi|327191765|gb|EGE58767.1| putative heat shock protein (ribosome-associated) [Rhizobium etli
          CNPAF512]
          Length = 134

 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          QR+ K +     + SR   +  +    V++NG    + +  V   D IE+
Sbjct: 13 QRIDKWLFFTRMVKSRSLAQSHVQSGHVRINGERCSQPSQMVKPGDRIEL 62


>gi|190893875|ref|YP_001980417.1| heat shock protein (ribosome-associated) [Rhizobium etli CIAT
          652]
 gi|218507914|ref|ZP_03505792.1| putative heat shock protein (ribosome-associated) [Rhizobium etli
          Brasil 5]
 gi|190699154|gb|ACE93239.1| putative heat shock protein (ribosome-associated) [Rhizobium etli
          CIAT 652]
          Length = 134

 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          QR+ K +     + SR   +  +    V++NG    + +  V   D IE+
Sbjct: 13 QRIDKWLFFTRMVKSRSLAQSHVQSGHVRINGERCSQPSQMVKPGDRIEL 62


>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 = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 10/96 (10%), Positives = 22/96 (22%), Gaps = 3/96 (3%)

Query: 260 PIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL-ATPVHRRNLASNVWMAK 318
               ++  +  R               K    +   S+  +  +    R           
Sbjct: 1   MSRRTKKPLAKRGPGGDRPKAGSRPAAKAGPVRGNRSEDGRPISARPQREPRGERAERPA 60

Query: 319 GIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               +    +  R  + R  P  P  RS   +   +
Sbjct: 61  AKRPAAERSAADRPASAR--PGRPPARSASSSRPPR 94



 Score = 39.8 bits (91), Expect = 0.72,   Method: Composition-based stats.
 Identities = 16/106 (15%), Positives = 30/106 (28%), Gaps = 2/106 (1%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL-ATPVH 306
             L +     D P   S    +  P   +   D      +   +  G   ++     P  
Sbjct: 7   KPLAKRGPGGDRPKAGSRPAAKAGPVRGNRSEDGRPISARPQREPRGERAERPAAKRPAA 66

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENH-RRSPSFPSKRSLRRTS 351
            R+ A     A+       S S  R     R  P+   ++ +   +
Sbjct: 67  ERSAADRPASARPGRPPARSASSSRPPRAQRPEPAPEPEKIVPEPA 112


>gi|289760773|ref|ZP_06520151.1| glycosyl hydrolase family protein [Mycobacterium tuberculosis GM
            1503]
 gi|289708279|gb|EFD72295.1| glycosyl hydrolase family protein [Mycobacterium tuberculosis GM
            1503]
          Length = 1137

 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 10/126 (7%), Positives = 20/126 (15%), Gaps = 1/126 (0%)

Query: 229  LAGSTRE-VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
              G+ R  +                      A                            
Sbjct: 1010 HPGAQRAVLPPAACGGAATATGRAAGGRLAAARRAGRLGAAGRAQGGRQPAGSRQRAAGP 1069

Query: 288  NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
                   +    +   P H R  A           +  +    +       P+  S R  
Sbjct: 1070 TRRGGAAIGANDRSRHPGHHRLRAGQGRRPPAGRPAGNAARNGKGAQVVHRPARLSGRHR 1129

Query: 348  RRTSAK 353
               + +
Sbjct: 1130 AGPARR 1135


>gi|323703521|ref|ZP_08115167.1| ribosomal protein S4 [Desulfotomaculum nigrificans DSM 574]
 gi|323531512|gb|EGB21405.1| ribosomal protein S4 [Desulfotomaculum nigrificans DSM 574]
          Length = 208

 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 1/47 (2%)

Query: 17  SKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             VI R G+  SR E  +++      VNG  +   +  V   D I V
Sbjct: 101 DNVIYRLGLGASRVEARQLVRHGHFTVNGRKVNIPSYQVRVGDEIAV 147


>gi|323357599|ref|YP_004223995.1| superfamily II DNA and RNA helicase [Microbacterium testaceum
           StLB037]
 gi|323273970|dbj|BAJ74115.1| superfamily II DNA and RNA helicase [Microbacterium testaceum
           StLB037]
          Length = 746

 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 12/111 (10%), Positives = 26/111 (23%), Gaps = 5/111 (4%)

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH-- 306
               +  +     +          N       D     +  +         +   P    
Sbjct: 102 RPARSFDDRPRRDFGDRPARSFDRNDRPARSFDRDERPRRDAGDRPARSFDRSDRPARSF 161

Query: 307 ---RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               R   S     +   S    +  +R+   R + SF      RR + ++
Sbjct: 162 DRSDRPARSFDRNDRPARSFDRDERPRRDAGDRPARSFDRDERPRRDAGER 212



 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 7/107 (6%), Positives = 19/107 (17%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                 + + DA     +       +            +             +   P   
Sbjct: 83  RDDRFGRSDRDATAGRRDERPARSFDDRPRRDFGDRPARSFDRNDRPARSFDRDERPRRD 142

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                     +    +   D   R          P++   R    ++
Sbjct: 143 AGDRPARSFDRSDRPARSFDRSDRPARSFDRNDRPARSFDRDERPRR 189


>gi|227486465|ref|ZP_03916781.1| S4 RNA-binding domain protein [Anaerococcus lactolyticus ATCC
          51172]
 gi|227235646|gb|EEI85661.1| S4 RNA-binding domain protein [Anaerococcus lactolyticus ATCC
          51172]
          Length = 81

 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           RV K +  + I  RR+  +     +RVK+N  + + A   V   D IE+
Sbjct: 1  MRVDKFLKNSRIIKRRQVAKEACENERVKINDKIAK-AGSEVCKGDIIEI 49


>gi|56698644|ref|YP_169021.1| DEAD-box ATP dependent DNA helicase [Ruegeria pomeroyi DSS-3]
 gi|56680381|gb|AAV97047.1| ATP-dependent RNA helicase, DEAD/DEAH box family [Ruegeria pomeroyi
           DSS-3]
          Length = 709

 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 17/114 (14%), Positives = 23/114 (20%), Gaps = 4/114 (3%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE +         P    E   +  A    +                      K SS+  
Sbjct: 599 REATP----APAKPRRAREDGADRPAKPARATLHAGKSEKPYKPRKPASGPGVKPSSKPG 654

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
           G    K    P  +      V           +    R    R     P KR  
Sbjct: 655 GKPSDKPGGKPWAKPGAKPGVKPGGKKPGGKPTAGASRPAAGRPGGEAPPKRKR 708



 Score = 40.9 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 11/118 (9%), Positives = 25/118 (21%), Gaps = 4/118 (3%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
            +  +L   + E  +     P   S+                       +++     +++
Sbjct: 541 EITARLLDGVPEMTRGPQGKPRPRSDRPAAKPFKPAKPRHKADRDSAAPAAEPRPFRERE 600

Query: 300 KLATPV-HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP---SKRSLRRTSAK 353
               P   RR              + L      +    R P+        S       
Sbjct: 601 ATPAPAKPRRAREDGADRPAKPARATLHAGKSEKPYKPRKPASGPGVKPSSKPGGKPS 658



 Score = 39.4 bits (90), Expect = 0.78,   Method: Composition-based stats.
 Identities = 17/128 (13%), Positives = 36/128 (28%), Gaps = 2/128 (1%)

Query: 226 GTLLAGSTREVSKKILREQLGPHLLE-EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
           G L      +++ +     +       +  ++   P    E  +  R            +
Sbjct: 499 GNLEKSQIGKITMQAQETHVELAEAAVQGFLDQIGPSGVVEGEITARLLDGVPEMTRGPQ 558

Query: 285 MKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
            K         +K  K A P H+ +  S    A+        ++       RR+    + 
Sbjct: 559 GKPRPRSDRPAAKPFKPAKPRHKADRDSAAPAAE-PRPFREREATPAPAKPRRAREDGAD 617

Query: 345 RSLRRTSA 352
           R  +   A
Sbjct: 618 RPAKPARA 625


>gi|83854847|ref|ZP_00948377.1| 30S ribosomal protein S4 [Sulfitobacter sp. NAS-14.1]
 gi|83941370|ref|ZP_00953832.1| 30S ribosomal protein S4 [Sulfitobacter sp. EE-36]
 gi|83842690|gb|EAP81857.1| 30S ribosomal protein S4 [Sulfitobacter sp. NAS-14.1]
 gi|83847190|gb|EAP85065.1| 30S ribosomal protein S4 [Sulfitobacter sp. EE-36]
          Length = 206

 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 10/35 (28%), Positives = 14/35 (40%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
             + +    VKVNG  +   +  V   D IEV   
Sbjct: 112 ARQFVNHGHVKVNGKKVNIPSYRVKEGDVIEVRDR 146


>gi|168704700|ref|ZP_02736977.1| 30S ribosomal protein S4 [Gemmata obscuriglobus UQM 2246]
          Length = 196

 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A +R    +M++   + VNG+  + A++ V   D I+V
Sbjct: 83  RLDNVVHRLGFAVNRTSARQMVSHGHILVNGVKCDIASMLVKPGDVIKV 131


>gi|117924179|ref|YP_864796.1| 30S ribosomal protein S4P [Magnetococcus sp. MC-1]
 gi|152060958|sp|A0L5Z7|RS4_MAGSM RecName: Full=30S ribosomal protein S4
 gi|117607935|gb|ABK43390.1| SSU ribosomal protein S4P [Magnetococcus sp. MC-1]
          Length = 208

 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A SR E  ++I+ + + VNG ++   +      D + V
Sbjct: 99  RLDNVVYRLGLAASRTEARQIISHKTLLVNGKMVNVPSYLCKPGDVVAV 147


>gi|325684425|gb|EGD26593.1| 30S ribosomal protein S4 [Lactobacillus delbrueckii subsp. lactis
           DSM 20072]
          Length = 203

 Score = 41.3 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G+A+ R +  +++    + V+G  ++  +  V     I +
Sbjct: 94  RLDNVVYRLGLATTREQARQLVNHGHITVDGKRVDIPSYEVKVGQTISL 142


>gi|291437113|ref|ZP_06576503.1| oligopeptide/dipeptide ABC transporter [Streptomyces ghanaensis
           ATCC 14672]
 gi|291340008|gb|EFE66964.1| oligopeptide/dipeptide ABC transporter [Streptomyces ghanaensis
           ATCC 14672]
          Length = 857

 Score = 41.3 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 15/101 (14%), Positives = 25/101 (24%), Gaps = 3/101 (2%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
              +  A           R      V D+  R  + + Q+NG             R    
Sbjct: 105 PGPDGPAAPQGPHHRRPCRVRRHGPVHDEPVRPPRPARQRNGDDLPGPAVLAQPGRADRR 164

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                 G         G+      R P+ P +      +A+
Sbjct: 165 AGHRDPGAPPRDE---GRGRPQGGRPPAGPGRHPRPDPAAQ 202


>gi|215274263|sp|Q92617|NPPL3_HUMAN RecName: Full=Nuclear pore complex-interacting protein-like 3;
            AltName: Full=Protein pps22-1
          Length = 1050

 Score = 41.3 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 27/108 (25%), Gaps = 3/108 (2%)

Query: 247  PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
            P   +EA+               + P              +   ++     +     P  
Sbjct: 929  PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 988

Query: 307  RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS--FPSKRSLRRTSA 352
            RR              +   +     E  RR      PS++  RR +A
Sbjct: 989  RRVGDVEPSRKPKRRRAADVEPSS-PEPKRRRVGDVEPSRKPKRRRAA 1035



 Score = 39.4 bits (90), Expect = 0.78,   Method: Composition-based stats.
 Identities = 9/117 (7%), Positives = 25/117 (21%), Gaps = 2/117 (1%)

Query: 238  KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            +    +   P     A++              +                    ++  +  
Sbjct: 934  EAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGD 993

Query: 298  QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             +    P  RR         +            R+   +R  +   + SL     ++
Sbjct: 994  VEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKP--KRRRAADVEPSLPEPKRRR 1048



 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 28/112 (25%), Gaps = 3/112 (2%)

Query: 243  EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            E+L   L   A  NL  P  +++    ++P                  ++     +    
Sbjct: 911  ERLRGPLPPSADDNLKTPPLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRK 970

Query: 303  TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                R                   +  ++    +R  +   + S      ++
Sbjct: 971  PKRRRAADVEPSSPEPKRRRVGDVEPSRKP---KRRRAADVEPSSPEPKRRR 1019


>gi|76782235|gb|ABA54892.1| collagen-like surface protein 1 [Streptococcus pyogenes]
          Length = 428

 Score = 41.3 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 15/135 (11%), Positives = 29/135 (21%), Gaps = 4/135 (2%)

Query: 220 YGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVP 279
           YG +          +  + + L+E L        + +        E   +          
Sbjct: 74  YGTYFKEENFQEELKNFTGERLKEILDLIEKGATKGDKGDAGPRGERGPKGDTGKAGAKG 133

Query: 280 DDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
           D   +  K      G         P   +         +G      +   Q  +      
Sbjct: 134 DTGPKGDKGDPGAPGKDGAVGAQGPKGDKGDTGE----RGEKGDTGATGAQGPQGEAGKD 189

Query: 340 SFPSKRSLRRTSAKK 354
             P K        +K
Sbjct: 190 GAPGKDGAPGEKGEK 204


>gi|254235140|ref|ZP_04928463.1| hypothetical protein PACG_01025 [Pseudomonas aeruginosa C3719]
 gi|126167071|gb|EAZ52582.1| hypothetical protein PACG_01025 [Pseudomonas aeruginosa C3719]
          Length = 413

 Score = 41.3 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 14/103 (13%), Positives = 26/103 (25%), Gaps = 2/103 (1%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
            + L     S +     +P   S        +++  +             P  R      
Sbjct: 197 MLRLRRRRLSPDPGADRQPAPGSAQGHLPADVRRPGTHPRPRRTAFAQERPALRPGQRGR 256

Query: 314 VWMAKGIHSSFLS--DSGQREENHRRSPSFPSKRSLRRTSAKK 354
                G          +  R    RR P+   +RSL     ++
Sbjct: 257 RLPRTGQPRLRRPLQPAPGRPRGGRRLPADQWRRSLSLHRRQR 299



 Score = 37.9 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 14/97 (14%), Positives = 22/97 (22%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P    + Q    +        VR            F + +          +  +   P  
Sbjct: 207 PDPGADRQPAPGSAQGHLPADVRRPGTHPRPRRTAFAQERPALRPGQRGRRLPRTGQPRL 266

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
           RR L       +G          +    HRR    P 
Sbjct: 267 RRPLQPAPGRPRGGRRLPADQWRRSLSLHRRQRPVPG 303


>gi|62088844|dbj|BAD92869.1| PI-3-kinase-related kinase SMG-1 isoform 1homolog [Homo sapiens]
          Length = 854

 Score = 41.3 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 27/108 (25%), Gaps = 3/108 (2%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P   +EA+               + P              +   ++     +     P  
Sbjct: 733 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 792

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS--FPSKRSLRRTSA 352
           RR              +   +     E  RR      PS++  RR +A
Sbjct: 793 RRVGDVEPSRKPKRRRAADVEPSS-PEPKRRRVGDVEPSRKPKRRRAA 839



 Score = 39.4 bits (90), Expect = 0.78,   Method: Composition-based stats.
 Identities = 9/117 (7%), Positives = 25/117 (21%), Gaps = 2/117 (1%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +    +   P     A++              +                    ++  +  
Sbjct: 738 EAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGD 797

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +    P  RR         +            R+   +R  +   + SL     ++
Sbjct: 798 VEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKP--KRRRAADVEPSLPEPKRRR 852



 Score = 37.5 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 28/112 (25%), Gaps = 3/112 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E+L   L   A  NL  P  +++    ++P                  ++     +    
Sbjct: 715 ERLRGPLPPSADDNLKTPPLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRK 774

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               R                   +  ++    +R  +   + S      ++
Sbjct: 775 PKRRRAADVEPSSPEPKRRRVGDVEPSRKP---KRRRAADVEPSSPEPKRRR 823


>gi|18311460|ref|NP_563394.1| S4 domain protein [Clostridium perfringens str. 13]
 gi|110801090|ref|YP_697166.1| S4 domain-containing protein [Clostridium perfringens ATCC 13124]
 gi|168213402|ref|ZP_02639027.1| S4 domain protein [Clostridium perfringens CPE str. F4969]
 gi|168217595|ref|ZP_02643220.1| S4 domain protein [Clostridium perfringens NCTC 8239]
 gi|169343246|ref|ZP_02864257.1| S4 domain protein [Clostridium perfringens C str. JGS1495]
 gi|18146144|dbj|BAB82184.1| conserved hypothetical protein [Clostridium perfringens str. 13]
 gi|110675737|gb|ABG84724.1| S4 domain protein [Clostridium perfringens ATCC 13124]
 gi|169298544|gb|EDS80625.1| S4 domain protein [Clostridium perfringens C str. JGS1495]
 gi|170714997|gb|EDT27179.1| S4 domain protein [Clostridium perfringens CPE str. F4969]
 gi|182380289|gb|EDT77768.1| S4 domain protein [Clostridium perfringens NCTC 8239]
          Length = 86

 Score = 41.3 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   +      RV +NG + +  + ++   D IE+
Sbjct: 1  MRLDKYLKVSRIIKRRTVAKEACESGRVIINGKVAK-PSNDIKEGDIIEI 49


>gi|90420129|ref|ZP_01228037.1| hemolysin A [Aurantimonas manganoxydans SI85-9A1]
 gi|90335463|gb|EAS49213.1| hemolysin A [Aurantimonas manganoxydans SI85-9A1]
          Length = 254

 Score = 41.3 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 9/30 (30%), Positives = 16/30 (53%)

Query: 35 IAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          I +  VKV+G  + + ++NV     I +D 
Sbjct: 34 IMRGHVKVDGQTVTKPSLNVPPESEITLDD 63


>gi|72161417|ref|YP_289074.1| 30S ribosomal protein S4 [Thermobifida fusca YX]
 gi|90101732|sp|Q47R66|RS4_THEFY RecName: Full=30S ribosomal protein S4
 gi|71915149|gb|AAZ55051.1| SSU ribosomal protein S4P [Thermobifida fusca YX]
          Length = 203

 Score = 41.3 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R++ V+ RAG A S     + I    + V+G  ++  +  V     + V
Sbjct: 93  RLATVLLRAGFAASIYAARQFINHGHITVDGKKVDIPSYQVKPGQIVSV 141


>gi|302917019|ref|XP_003052320.1| hypothetical protein NECHADRAFT_11630 [Nectria haematococca mpVI
           77-13-4]
 gi|256733259|gb|EEU46607.1| hypothetical protein NECHADRAFT_11630 [Nectria haematococca mpVI
           77-13-4]
          Length = 781

 Score = 41.3 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 8/105 (7%), Positives = 27/105 (25%), Gaps = 2/105 (1%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           +A+   D+      +      +  ++          +S        +++  +P   RN  
Sbjct: 675 QARGRRDSYASEGRSPSPPPRDRRNKPRQYSRSPSYDSRSPPPRRAKQENRSPPPVRNGG 734

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFP--SKRSLRRTSAKK 354
            +  +          +        +R       S+        ++
Sbjct: 735 RDSQLRSPSPPRRGGNRPASPVPAKRRRYSDSVSRSPPPVKRGRR 779


>gi|99080415|ref|YP_612569.1| RNA-binding S4 [Ruegeria sp. TM1040]
 gi|99036695|gb|ABF63307.1| RNA-binding S4 [Ruegeria sp. TM1040]
          Length = 124

 Score = 41.3 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 12/57 (21%), Positives = 23/57 (40%), Gaps = 1/57 (1%)

Query: 7  VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          + ++    RV K +  A    +R    + +    V+VNG    + + NV   D +  
Sbjct: 1  MSDHADKMRVDKWLWHARFFKTRSLAAKQVGAGHVRVNGSKAAKPSQNVSIGDVLTF 57


>gi|302344330|ref|YP_003808859.1| ribosomal protein S4 [Desulfarculus baarsii DSM 2075]
 gi|301640943|gb|ADK86265.1| ribosomal protein S4 [Desulfarculus baarsii DSM 2075]
          Length = 209

 Score = 41.3 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SR +  + +      VNG  +   +  V + D + V
Sbjct: 100 RLDNVVFRLGFANSRTQARQWVRHSHFTVNGHKVNIPSALVKAGDVVAV 148


>gi|302522316|ref|ZP_07274658.1| conserved hypothetical protein [Streptomyces sp. SPB78]
 gi|302431211|gb|EFL03027.1| conserved hypothetical protein [Streptomyces sp. SPB78]
          Length = 930

 Score = 41.3 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 16/128 (12%), Positives = 30/128 (23%), Gaps = 9/128 (7%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN-SSQKNG 294
           V    +R+QL       A     A   ++    R      +   +   R  ++      G
Sbjct: 572 VEPDEIRQQLRGRAGRPAARRSAAGPAAACDSARAAGTGSATEGEPEARASQSVEGTPEG 631

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG--------IHSSFLSDSGQREENHRRSPSFPSKRS 346
               +            +     KG           +      +R     +  S      
Sbjct: 632 GRGGETTERRAVGGRRRTGSGARKGSAARTDSAARPATRRRDARRPGGAAQGGSEGKAVK 691

Query: 347 LRRTSAKK 354
            R   AK+
Sbjct: 692 RREGGAKE 699


>gi|255561268|ref|XP_002521645.1| arsenite-resistance protein, putative [Ricinus communis]
 gi|223539157|gb|EEF40752.1| arsenite-resistance protein, putative [Ricinus communis]
          Length = 823

 Score = 41.3 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 13/108 (12%), Positives = 22/108 (20%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R           +     P        R        +P    R    + +     + ++ 
Sbjct: 138 RRDFYERNHNHHRSPPLPPREREREYKRRNSLSPPPIPYRDRRHSPPARRSPPYKRSRRD 197

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                 R  +       G         G  E      P +P  R   R
Sbjct: 198 DGGYDGRRGSPRGGFGPGDRRFGYDYGGGYEREMGGRPGYPDDRPRGR 245


>gi|254486907|ref|ZP_05100112.1| ribosomal protein S4 [Roseobacter sp. GAI101]
 gi|214043776|gb|EEB84414.1| ribosomal protein S4 [Roseobacter sp. GAI101]
          Length = 206

 Score = 41.3 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 10/35 (28%), Positives = 14/35 (40%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
             + +    VKVNG  +   +  V   D IEV   
Sbjct: 112 ARQFVNHGHVKVNGKKVNIPSYRVKEGDVIEVRDR 146


>gi|332246247|ref|XP_003272265.1| PREDICTED: serine/threonine-protein kinase PRP4 homolog [Nomascus
           leucogenys]
          Length = 1006

 Score = 41.3 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 17/103 (16%), Positives = 31/103 (30%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
           +E+   + D                 S  P D     K+   ++   K K+  T   ++ 
Sbjct: 265 IEDKSKSKDRKKSPIINERSRDRGKKSRSPVDLRGKSKDRRSRSKERKSKRSETDKEKKP 324

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           + S    A     +            RRS S   +   RR+ +
Sbjct: 325 IKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKPRDKSRRSRS 367


>gi|297269755|ref|XP_002799951.1| PREDICTED: voltage-dependent N-type calcium channel subunit
           alpha-1B-like [Macaca mulatta]
          Length = 1790

 Score = 41.3 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 15/112 (13%), Positives = 27/112 (24%), Gaps = 3/112 (2%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           GP   +      +AP          R     + P    + +  + +        +   P 
Sbjct: 455 GPVGGKARPEAAEAPEGVDPPRRHHRHRDKDKTPAAGDQDRAEAPKAESGEPVAREERPR 514

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP---SKRSLRRTSAKK 354
             R+ +          S      G            P    +R  RR  A +
Sbjct: 515 PHRSHSKEAAGPPEARSERGRGPGPEGGRRHHRRGSPEEAPEREPRRHRAHR 566



 Score = 40.2 bits (92), Expect = 0.49,   Method: Composition-based stats.
 Identities = 13/151 (8%), Positives = 35/151 (23%), Gaps = 25/151 (16%)

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           L      E+ ++  R  +G     EA    +              +      D       
Sbjct: 440 LDRPLVVELGREGARGPVGGKARPEAAEAPEGVDPPRRHHRHRDKDKTPAAGDQDRAEAP 499

Query: 288 NSSQKNGLSKQKKLA----------TPVHRRN---------------LASNVWMAKGIHS 322
            +     ++++++             P   R+                  +   A     
Sbjct: 500 KAESGEPVAREERPRPHRSHSKEAAGPPEARSERGRGPGPEGGRRHHRRGSPEEAPEREP 559

Query: 323 SFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                   ++ N   + +   +R+  R   +
Sbjct: 560 RRHRAHRHQDPNKECAGAKGERRARHRGGPR 590



 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 12/121 (9%), Positives = 23/121 (19%), Gaps = 15/121 (12%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK---- 297
           R        ++     D     +       P    E P       K ++           
Sbjct: 476 RRHHRHRDKDKTPAAGDQDRAEAPKAESGEPVAREERPRPHRSHSKEAAGPPEARSERGR 535

Query: 298 ---------QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                      +  +P            A        +      +  RR+      R+  
Sbjct: 536 GPGPEGGRRHHRRGSPEEAPEREPRRHRAH--RHQDPNKECAGAKGERRARHRGGPRAGP 593

Query: 349 R 349
           R
Sbjct: 594 R 594



 Score = 36.7 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 18/152 (11%), Positives = 35/152 (23%), Gaps = 20/152 (13%)

Query: 223 FQLGTL---LAGSTREVSKKILREQLGPHLLEEAQVN--LDAPIYSSETLVRDRPNIISE 277
            +L  L         E+  +  R       L            +          P     
Sbjct: 402 LRLQNLRASCEALYSEMDPEERRRFATTRHLRPDMKTHLDRPLVVELGREGARGPVGGKA 461

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
            P+     +     +     + K  TP       +    A+        +  +   +H +
Sbjct: 462 RPEAAEAPEGVDPPRRHHRHRDKDKTPAAGDQDRAEAPKAESGEPVAREERPRPHRSHSK 521

Query: 338 -SPSFPSKRSL--------------RRTSAKK 354
            +   P  RS               RR S ++
Sbjct: 522 EAAGPPEARSERGRGPGPEGGRRHHRRGSPEE 553


>gi|260434066|ref|ZP_05788037.1| RNA-binding S4 [Silicibacter lacuscaerulensis ITI-1157]
 gi|260417894|gb|EEX11153.1| RNA-binding S4 [Silicibacter lacuscaerulensis ITI-1157]
          Length = 123

 Score = 41.3 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 24/57 (42%), Gaps = 1/57 (1%)

Query: 7  VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          + E     R+ K + +A    +R    R ++   V+VNG   ++ A  V   D +  
Sbjct: 1  MAEALAKLRIDKWLWQARFFKTRSLAARQVSAGHVRVNGDRAQKPAQTVGPGDVLTF 57


>gi|301780470|ref|XP_002925655.1| PREDICTED: zinc finger and BTB domain-containing protein 17-like
           [Ailuropoda melanoleuca]
          Length = 673

 Score = 41.3 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 6/73 (8%), Positives = 18/73 (24%), Gaps = 5/73 (6%)

Query: 281 DFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
                ++  + + G   +    + +  R+  +                G+R       P+
Sbjct: 302 GEAGSRQGPAGRRGSRAEPPPHSRMATRSRENARRRGPPEAEEARPRGGKRP-----KPA 356

Query: 341 FPSKRSLRRTSAK 353
                +  R    
Sbjct: 357 PGGASAASRGPQA 369


>gi|283779700|ref|YP_003370455.1| peptidase M56 BlaR1 [Pirellula staleyi DSM 6068]
 gi|283438153|gb|ADB16595.1| peptidase M56 BlaR1 [Pirellula staleyi DSM 6068]
          Length = 607

 Score = 41.3 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 8/114 (7%), Positives = 21/114 (18%), Gaps = 1/114 (0%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            +            E  ++     +                     +RM+ +  +     
Sbjct: 464 RRDEQERAREVPERENPEMRELIMLLRKLNAEVSSLRAEVNQLKANSRMQPDRPRPEADR 523

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK-RSLRR 349
            + +   P    +                     R    +  P  P +     R
Sbjct: 524 PRPEGDRPRGEGDRPREGARPDQPRPDQPRREADRPRPDQPRPDQPKREGDRPR 577



 Score = 41.3 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 11/106 (10%), Positives = 25/106 (23%), Gaps = 1/106 (0%)

Query: 234 REVSKKILREQLGPHLL-EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
           REV ++   E     +L  +    + +       L  +          +  R +    + 
Sbjct: 472 REVPERENPEMRELIMLLRKLNAEVSSLRAEVNQLKANSRMQPDRPRPEADRPRPEGDRP 531

Query: 293 NGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS 338
            G   + +      +         A             + E  R  
Sbjct: 532 RGEGDRPREGARPDQPRPDQPRREADRPRPDQPRPDQPKREGDRPR 577



 Score = 37.5 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 13/151 (8%), Positives = 30/151 (19%), Gaps = 28/151 (18%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             RE   + ++ +  P    E       P    E           E      R ++  ++
Sbjct: 413 EVREDENREVKREGAPAREREVGERERDPNREVERDREGDREGRREDRPAPRRDEQERAR 472

Query: 292 KNGLSKQK----------------------------KLATPVHRRNLASNVWMAKGIHSS 323
           +    +                                     R    ++    +G    
Sbjct: 473 EVPERENPEMRELIMLLRKLNAEVSSLRAEVNQLKANSRMQPDRPRPEADRPRPEGDRPR 532

Query: 324 FLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              D  +      +      +R   R    +
Sbjct: 533 GEGDRPREGARPDQPRPDQPRREADRPRPDQ 563



 Score = 36.7 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 12/113 (10%), Positives = 27/113 (23%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            ++  P   E+ +        + E                  R + N  + N   +  + 
Sbjct: 458 EDRPAPRRDEQERAREVPERENPEMRELIMLLRKLNAEVSSLRAEVNQLKANSRMQPDRP 517

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                R     +    +G      +   Q   +  R  +   +    R    K
Sbjct: 518 RPEADRPRPEGDRPRGEGDRPREGARPDQPRPDQPRREADRPRPDQPRPDQPK 570


>gi|269836359|ref|YP_003318587.1| 30S ribosomal protein S4 [Sphaerobacter thermophilus DSM 20745]
 gi|269785622|gb|ACZ37765.1| ribosomal protein S4 [Sphaerobacter thermophilus DSM 20745]
          Length = 203

 Score = 41.3 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G   +R    +++    V VNG  ++  +  V   D I +
Sbjct: 95  RLDNVVYRLGFTPTRPMARQLVNHGHVLVNGRRVDIPSYRVSPGDTIAL 143


>gi|34015242|gb|AAQ56434.1| hypothetical protein OSJNBa0074N12.2 [Oryza sativa Japonica Group]
 gi|34015286|gb|AAQ56477.1| putative retrotransposon protein [Oryza sativa Japonica Group]
          Length = 1049

 Score = 41.3 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 16/113 (14%), Positives = 22/113 (19%), Gaps = 7/113 (6%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +G    EE           S           +  P D        +   G  KQ     
Sbjct: 299 MMGVGASEEVAPKGHDGAGGSRQEESTPGGGRASGPRDGGSGSNRPADARGKRKQGGTPP 358

Query: 304 PVHRRN-------LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           P   R               A            +  +     PS  +  S  R
Sbjct: 359 PSPPRGDGAVRASRRRPEGAAPTSQPETERKKKRLRKTGETEPSRGNLISPPR 411



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 12/102 (11%), Positives = 24/102 (23%), Gaps = 1/102 (0%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
             +  + +     +                  ++ S+   G +   +       R   + 
Sbjct: 289 DPDRASILTIMMGVGASEEVAPKGHDGAGGSRQEESTPGGGRASGPRDGGSGSNRPADAR 348

Query: 314 VWMAKGIHSSFLSDSGQRE-ENHRRSPSFPSKRSLRRTSAKK 354
               +G         G       RR P   +  S   T  KK
Sbjct: 349 GKRKQGGTPPPSPPRGDGAVRASRRRPEGAAPTSQPETERKK 390


>gi|73973019|ref|XP_852010.1| PREDICTED: similar to Calpain-11 (Calcium-activated neutral
           proteinase 11) (CANP 11) [Canis familiaris]
          Length = 870

 Score = 41.3 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 12/102 (11%), Positives = 20/102 (19%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R + G      + V L    +         P                         + + 
Sbjct: 671 RSEGGWSAGSPSPVPLWGHGHLFSRRSPASPAAGLPKRSSPRNGAGRDRAGRARGGRPRS 730

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
            +    R     V    G            E    R+P+ P 
Sbjct: 731 RSQPLSRPRPRPVRPGAGCELGPRPQPRGEEAARNRTPASPG 772


>gi|221046306|dbj|BAH14830.1| unnamed protein product [Homo sapiens]
          Length = 992

 Score = 41.3 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 27/108 (25%), Gaps = 3/108 (2%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P   +EA+               + P              +   ++     +     P  
Sbjct: 871 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 930

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS--FPSKRSLRRTSA 352
           RR              +   +     E  RR      PS++  RR +A
Sbjct: 931 RRVGDVEPSRKPKRRRAADVEPSS-PEPKRRRVGDVEPSRKPKRRRAA 977



 Score = 39.4 bits (90), Expect = 0.82,   Method: Composition-based stats.
 Identities = 9/117 (7%), Positives = 25/117 (21%), Gaps = 2/117 (1%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +    +   P     A++              +                    ++  +  
Sbjct: 876 EAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGD 935

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +    P  RR         +            R+   +R  +   + SL     ++
Sbjct: 936 VEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKP--KRRRAADVEPSLPEPKRRR 990



 Score = 37.1 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 28/112 (25%), Gaps = 3/112 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E+L   L   A  NL  P  +++    ++P                  ++     +    
Sbjct: 853 ERLRGPLPPSADDNLKTPPLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRK 912

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               R                   +  ++    +R  +   + S      ++
Sbjct: 913 PKRRRAADVEPSSPEPKRRRVGDVEPSRKP---KRRRAADVEPSSPEPKRRR 961


>gi|194382726|dbj|BAG64533.1| unnamed protein product [Homo sapiens]
          Length = 992

 Score = 41.3 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 27/108 (25%), Gaps = 3/108 (2%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P   +EA+               + P              +   ++     +     P  
Sbjct: 871 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 930

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS--FPSKRSLRRTSA 352
           RR              +   +     E  RR      PS++  RR +A
Sbjct: 931 RRVGDVEPSRKPKRRRAADVEPSS-PEPKRRRVGDVEPSRKPKRRRAA 977



 Score = 39.4 bits (90), Expect = 0.81,   Method: Composition-based stats.
 Identities = 9/117 (7%), Positives = 25/117 (21%), Gaps = 2/117 (1%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +    +   P     A++              +                    ++  +  
Sbjct: 876 EAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGD 935

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +    P  RR         +            R+   +R  +   + SL     ++
Sbjct: 936 VEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKP--KRRRAADVEPSLPEPKRRR 990



 Score = 37.1 bits (84), Expect = 3.7,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 28/112 (25%), Gaps = 3/112 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E+L   L   A  NL  P  +++    ++P                  ++     +    
Sbjct: 853 ERLRGPLPPSADDNLKTPPLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRK 912

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               R                   +  ++    +R  +   + S      ++
Sbjct: 913 PKRRRAADVEPSSPEPKRRRVGDVEPSRKP---KRRRAADVEPSSPEPKRRR 961


>gi|194377228|dbj|BAG63175.1| unnamed protein product [Homo sapiens]
          Length = 1076

 Score = 41.3 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 27/108 (25%), Gaps = 3/108 (2%)

Query: 247  PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
            P   +EA+               + P              +   ++     +     P  
Sbjct: 955  PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 1014

Query: 307  RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS--FPSKRSLRRTSA 352
            RR              +   +     E  RR      PS++  RR +A
Sbjct: 1015 RRVGDVEPSRKPKRRRAADVEPSS-PEPKRRRVGDVEPSRKPKRRRAA 1061



 Score = 39.4 bits (90), Expect = 0.81,   Method: Composition-based stats.
 Identities = 9/117 (7%), Positives = 25/117 (21%), Gaps = 2/117 (1%)

Query: 238  KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            +    +   P     A++              +                    ++  +  
Sbjct: 960  EAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGD 1019

Query: 298  QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             +    P  RR         +            R+   +R  +   + SL     ++
Sbjct: 1020 VEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKP--KRRRAADVEPSLPEPKRRR 1074



 Score = 37.1 bits (84), Expect = 3.7,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 28/112 (25%), Gaps = 3/112 (2%)

Query: 243  EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            E+L   L   A  NL  P  +++    ++P                  ++     +    
Sbjct: 937  ERLRGPLPPSADDNLKTPPLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRK 996

Query: 303  TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                R                   +  ++    +R  +   + S      ++
Sbjct: 997  PKRRRAADVEPSSPEPKRRRVGDVEPSRKP---KRRRAADVEPSSPEPKRRR 1045


>gi|40788916|dbj|BAA13210.2| KIAA0220 [Homo sapiens]
          Length = 884

 Score = 41.3 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 27/108 (25%), Gaps = 3/108 (2%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P   +EA+               + P              +   ++     +     P  
Sbjct: 763 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 822

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS--FPSKRSLRRTSA 352
           RR              +   +     E  RR      PS++  RR +A
Sbjct: 823 RRVGDVEPSRKPKRRRAADVEPSS-PEPKRRRVGDVEPSRKPKRRRAA 869



 Score = 39.4 bits (90), Expect = 0.81,   Method: Composition-based stats.
 Identities = 9/117 (7%), Positives = 25/117 (21%), Gaps = 2/117 (1%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +    +   P     A++              +                    ++  +  
Sbjct: 768 EAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGD 827

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +    P  RR         +            R+   +R  +   + SL     ++
Sbjct: 828 VEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKP--KRRRAADVEPSLPEPKRRR 882



 Score = 37.1 bits (84), Expect = 3.7,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 28/112 (25%), Gaps = 3/112 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E+L   L   A  NL  P  +++    ++P                  ++     +    
Sbjct: 745 ERLRGPLPPSADDNLKTPPLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRK 804

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               R                   +  ++    +R  +   + S      ++
Sbjct: 805 PKRRRAADVEPSSPEPKRRRVGDVEPSRKP---KRRRAADVEPSSPEPKRRR 853


>gi|262377334|ref|ZP_06070558.1| II DNA/RNA helicase [Acinetobacter lwoffii SH145]
 gi|262307787|gb|EEY88926.1| II DNA/RNA helicase [Acinetobacter lwoffii SH145]
          Length = 624

 Score = 41.3 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 10/104 (9%), Positives = 25/104 (24%), Gaps = 2/104 (1%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           E      +           D+P        +    +    +     +      P  +R+ 
Sbjct: 426 ESNFKRREGGDDRPRRSFDDKPRGERPAFGEDRPRRDFGDRPAPRREGGFGDRP--QRSF 483

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                   G   +   + G  +   R     P +    R + ++
Sbjct: 484 DDRPKRDFGDRPAPRREGGFGDRPQRSFDDRPKRDFGDRPAPRR 527



 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 6/107 (5%), Positives = 19/107 (17%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +        +         +              +  D     ++        S      
Sbjct: 484 DDRPKRDFGDRPAPRREGGFGDRPQRSFDDRPKRDFGDRPAPRREGGFGDRPRSNDDNRG 543

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
             V  +      +  +         + +RE      P+        +
Sbjct: 544 NRVDYKPAREGGYGDRPKRDFGDRPAPRREGGFGDRPARSFGDDRPK 590



 Score = 37.5 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 14/114 (12%), Positives = 20/114 (17%), Gaps = 1/114 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR-MKKNSSQKNGLSKQKK 300
           RE                   +       R       P        +     +   K+  
Sbjct: 432 REGGDDRPRRSFDDKPRGERPAFGEDRPRRDFGDRPAPRREGGFGDRPQRSFDDRPKRDF 491

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              P  RR         +        D G R    R        RS       +
Sbjct: 492 GDRPAPRREGGFGDRPQRSFDDRPKRDFGDRPAPRREGGFGDRPRSNDDNRGNR 545


>gi|169630850|ref|YP_001704499.1| 30S ribosomal protein S4 [Mycobacterium abscessus ATCC 19977]
 gi|226699092|sp|B1MGA0|RS4_MYCA9 RecName: Full=30S ribosomal protein S4
 gi|169242817|emb|CAM63845.1| 30S ribosomal protein S4 [Mycobacterium abscessus]
          Length = 201

 Score = 41.3 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 14/61 (22%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ RAG+A +RR   ++++     VN + ++  +  V   D I++    L      
Sbjct: 92  RLDNVVYRAGLARTRRMARQLVSHGHFTVNNVKVDVPSYRVSQYDIIDIKPKSLNTLPFE 151

Query: 74  R 74
            
Sbjct: 152 V 152


>gi|74003856|ref|XP_856902.1| PREDICTED: similar to serine/threonine-protein kinase PRP4K isoform
           15 [Canis familiaris]
          Length = 1031

 Score = 41.3 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 15/105 (14%), Positives = 31/105 (29%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            + ++++                     S  P D     K+   ++   K K+  T   +
Sbjct: 298 KIEDKSRSKDRKKSPIINESRSRDRGKKSRSPVDLRGKSKDRRSRSKERKSKRSDTDKEK 357

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           + + S    A     +            RRS S   +   RR+ +
Sbjct: 358 KPIKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKQRDKSRRSRS 402



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 13/113 (11%), Positives = 37/113 (32%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +++    ++ E++         S   +R +         +    + ++ ++    K    
Sbjct: 306 KDRKKSPIINESRSRDRGKKSRSPVDLRGKSKDRRSRSKERKSKRSDTDKEKKPIKSPSK 365

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                + N + +    +      LS   + +    RSP    +RS +  S  +
Sbjct: 366 DASSGKENRSPSRRPGRSPKRRSLSPKQRDKSRRSRSPLVNDRRSKQSKSPSR 418



 Score = 37.9 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 20/131 (15%), Positives = 39/131 (29%), Gaps = 8/131 (6%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             R+     LR +    + +      D      ++  +DR               K S  
Sbjct: 269 QARKSKSPTLRRRSQEKIGKARSPPDDKVKIEDKSRSKDRKKSPIINESRSRDRGKKSRS 328

Query: 292 K---NGLSKQKKLATPVHRRNLASNVWMAKG-IHSSFLSDSGQREENHRRSPSFPSKR-- 345
                G SK ++  +   +   +      K     S  + SG+   +  R P    KR  
Sbjct: 329 PVDLRGKSKDRRSRSKERKSKRSDTDKEKKPIKSPSKDASSGKENRSPSRRPGRSPKRRS 388

Query: 346 --SLRRTSAKK 354
               +R  +++
Sbjct: 389 LSPKQRDKSRR 399


>gi|53791302|dbj|BAD52567.1| hypothetical protein [Oryza sativa Japonica Group]
 gi|53791452|dbj|BAD52504.1| hypothetical protein [Oryza sativa Japonica Group]
          Length = 1027

 Score = 41.3 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 16/113 (14%), Positives = 22/113 (19%), Gaps = 7/113 (6%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +G    EE           S           +  P D        +   G  KQ     
Sbjct: 299 MMGVGASEEVAPKGHDGAGGSRQEESTPGGGRASGPRDGGSGSNRPADARGKRKQGGTPP 358

Query: 304 PVHRRN-------LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           P   R               A            +  +     PS  +  S  R
Sbjct: 359 PSPPRGDGAVRASRRRPEGAAPTSQPETERKKKRLRKTGETEPSRGNLISPPR 411



 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 12/102 (11%), Positives = 24/102 (23%), Gaps = 1/102 (0%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
             +  + +     +                  ++ S+   G +   +       R   + 
Sbjct: 289 DPDRASILTIMMGVGASEEVAPKGHDGAGGSRQEESTPGGGRASGPRDGGSGSNRPADAR 348

Query: 314 VWMAKGIHSSFLSDSGQRE-ENHRRSPSFPSKRSLRRTSAKK 354
               +G         G       RR P   +  S   T  KK
Sbjct: 349 GKRKQGGTPPPSPPRGDGAVRASRRRPEGAAPTSQPETERKK 390


>gi|83949926|ref|ZP_00958659.1| 30S ribosomal protein S4 [Roseovarius nubinhibens ISM]
 gi|83837825|gb|EAP77121.1| 30S ribosomal protein S4 [Roseovarius nubinhibens ISM]
          Length = 206

 Score = 41.3 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 10/35 (28%), Positives = 14/35 (40%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
             + +    VKVNG  +   +  V   D IEV   
Sbjct: 112 ARQFVNHGHVKVNGQRVNIPSYRVKEGDVIEVRDR 146


>gi|256830946|ref|YP_003159674.1| PSP1 domain-containing protein [Desulfomicrobium baculatum DSM
           4028]
 gi|256580122|gb|ACU91258.1| PSP1 domain protein [Desulfomicrobium baculatum DSM 4028]
          Length = 423

 Score = 41.3 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 11/140 (7%), Positives = 29/140 (20%), Gaps = 15/140 (10%)

Query: 230 AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
                 +    +R +             +                 ++  +   R  +  
Sbjct: 284 PAELAALMDPEVRNKSSQSDRRTKPPRREQRSRPGGERPPGPRPDRADRSERPERSDRPD 343

Query: 290 SQKNGLSKQKKLATPVHRRNLASN-----------VWMAKGIHSSFLSDSGQR----EEN 334
             +      +    P   +N  ++           V               +R      +
Sbjct: 344 RPERSDRSDRPERGPSRHKNDDASAAPAAPAASAAVGDRPESRPESSGPPRERKEYRPRD 403

Query: 335 HRRSPSFPSKRSLRRTSAKK 354
            RR P    K    + S ++
Sbjct: 404 KRRKPGSGRKDHSSKPSGQQ 423


>gi|162457295|ref|YP_001619662.1| hypothetical protein sce9010 [Sorangium cellulosum 'So ce 56']
 gi|161167877|emb|CAN99182.1| hypothetical protein sce9010 [Sorangium cellulosum 'So ce 56']
          Length = 243

 Score = 41.3 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 20/126 (15%), Positives = 32/126 (25%), Gaps = 1/126 (0%)

Query: 224 QLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
           +LG +     RE   K     LG    E      +AP     +            P    
Sbjct: 118 ELGKVADTELREAIAKAAARNLGWQEAEAGARPRNAPPPLQPSAAPAPRVSPPPAPHGAA 177

Query: 284 RMKKNSSQ-KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
           R  + + +         + A P      A      +G      + S     +    PS  
Sbjct: 178 RPAQPAPRVSRVSRASPEAAAPATPGGDAEATSPRRGARDPRSAASRTARSDRTTEPSGA 237

Query: 343 SKRSLR 348
            +R   
Sbjct: 238 GRRGRS 243


>gi|85079797|ref|XP_956421.1| hypothetical protein NCU05047 [Neurospora crassa OR74A]
 gi|28917485|gb|EAA27185.1| predicted protein [Neurospora crassa OR74A]
          Length = 2992

 Score = 41.3 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 13/128 (10%), Positives = 32/128 (25%), Gaps = 13/128 (10%)

Query: 234  REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
            R++S     ++ G         +        +     +P    E      + ++      
Sbjct: 1856 RQLSPDEPEQEQG-----GNNEDAGDGQKDRQRPATSQPQGRREAGRGQGQSQRQPPSGR 1910

Query: 294  GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDS--------GQREENHRRSPSFPSKR 345
              +       P    +  S          S                +++ R  P  P+ R
Sbjct: 1911 AQAAAPGGDPPSQPSSQGSEGRRPGRRVGSSPHRPISISSRESTSSDDDGRSPPRQPAGR 1970

Query: 346  SLRRTSAK 353
            + +R  + 
Sbjct: 1971 NPKRGPSA 1978


>gi|325263921|ref|ZP_08130654.1| putative S4 domain protein [Clostridium sp. D5]
 gi|324030959|gb|EGB92241.1| putative S4 domain protein [Clostridium sp. D5]
          Length = 258

 Score = 41.3 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 11/31 (35%), Positives = 15/31 (48%)

Query: 34  MIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +I   +V VNG L+   +  V   D I V G
Sbjct: 202 LIEGGKVFVNGKLMTTNSCQVKEEDIISVRG 232


>gi|224117596|ref|XP_002317618.1| predicted protein [Populus trichocarpa]
 gi|222860683|gb|EEE98230.1| predicted protein [Populus trichocarpa]
          Length = 418

 Score = 41.3 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 15/127 (11%), Positives = 39/127 (30%), Gaps = 8/127 (6%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +   ++R +      ++          + +       N  ++   D  + ++  S     
Sbjct: 172 IDGNVVRAKFTLPPRQKLSPPPKPIAAAPKRDAPKTDNASADAEKDGPKRQREPSPHRKP 231

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR--------EENHRRSPSFPSKRSL 347
               +  +PV RR  +    +         S   +R        E   RR P+ P++   
Sbjct: 232 LASPRRRSPVARRGGSPRRQLDSPPRRRADSPGRRRVESPYRRGETPPRRRPASPARGRS 291

Query: 348 RRTSAKK 354
             +  ++
Sbjct: 292 PSSPPRR 298



 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 13/102 (12%), Positives = 36/102 (35%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           +A    +A   + +   + +           +  +++   + G S +++L +P  RR  +
Sbjct: 203 DAPKTDNASADAEKDGPKRQREPSPHRKPLASPRRRSPVARRGGSPRRQLDSPPRRRADS 262

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                 +  +    +   +R  +  R  S  S     R+  +
Sbjct: 263 PGRRRVESPYRRGETPPRRRPASPARGRSPSSPPRRYRSPLR 304


>gi|291243503|ref|XP_002741641.1| PREDICTED: serine/threonine-protein kinase PRP4h-like [Saccoglossus
           kowalevskii]
          Length = 908

 Score = 41.3 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 17/112 (15%), Positives = 36/112 (32%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E+      +  +    +   S+    + R    S      +  +  S +    S +K+  
Sbjct: 209 ERRRSKRSQSPRDKKHSRHRSASPRHKIRKRSKSPRKRSKSPKRNRSPRMRSRSPRKRSK 268

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +P  R          +   S   S   +R  +  R P   +++S  R S  +
Sbjct: 269 SPKRRSKSPKRENRRRKSRSRSKSPIKKRPRSPLRQPMQTTRQSPPRISPAR 320



 Score = 40.9 bits (94), Expect = 0.28,   Method: Composition-based stats.
 Identities = 16/112 (14%), Positives = 27/112 (24%), Gaps = 3/112 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +     L    +  ++          +   N  S  P    R  K S         +  +
Sbjct: 170 DNEIKQLSPPRKGRVNDYSPVIAAKHKRSRNRHSRSPSVERRRSKRSQSPRDKKHSRHRS 229

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                +              S      +      RSP   SK   RR+ + K
Sbjct: 230 ASPRHKIRK---RSKSPRKRSKSPKRNRSPRMRSRSPRKRSKSPKRRSKSPK 278



 Score = 36.3 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 9/106 (8%), Positives = 19/106 (17%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
             H    +          S++  +   +                  K+   + K      
Sbjct: 222 KKHSRHRSASPRHKIRKRSKSPRKRSKSPKRNRSPRMRSRSPRKRSKSPKRRSKSPKREN 281

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
            RR   S                  +          P++R      
Sbjct: 282 RRRKSRSRSKSPIKKRPRSPLRQPMQTTRQSPPRISPARRMSESPR 327


>gi|224048571|ref|XP_002191711.1| PREDICTED: collagen, type XIX, alpha 1 [Taeniopygia guttata]
          Length = 1413

 Score = 41.3 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 14/113 (12%), Positives = 25/113 (22%), Gaps = 3/113 (2%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           ++++ LRE                  +         P  ++E      R           
Sbjct: 86  LAQQELRE---LGCPSGTGAAPARRRHPDRAATDLAPLGVAEGAAAGARPLPALGAHRAP 142

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
               +   P   R          G  S   S +     + R +P      S  
Sbjct: 143 GAAGRGREPGRARRREPGRGAEPGPESGSGSGAEALPASSRAAPGAARLPSRP 195


>gi|118616624|ref|YP_904956.1| 30S ribosomal protein S4 [Mycobacterium ulcerans Agy99]
 gi|152112235|sp|A0PMB6|RS4_MYCUA RecName: Full=30S ribosomal protein S4
 gi|118568734|gb|ABL03485.1| 30S ribosomal protein S4, RpsD [Mycobacterium ulcerans Agy99]
          Length = 201

 Score = 41.3 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ RAG+A +RR   ++++     VNG+ +   +  V   D I+V    L      
Sbjct: 92  RLDNVVYRAGLARTRRMARQLVSHGHFSVNGVHVNVPSYRVSQYDIIDVRDNSLNTVPFQ 151

Query: 74  R 74
            
Sbjct: 152 I 152


>gi|307325497|ref|ZP_07604699.1| serine/threonine protein kinase [Streptomyces violaceusniger Tu
           4113]
 gi|306888966|gb|EFN19950.1| serine/threonine protein kinase [Streptomyces violaceusniger Tu
           4113]
          Length = 463

 Score = 41.3 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 10/120 (8%), Positives = 19/120 (15%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           E     L+  L    +   + +            R          D  T  +  S+    
Sbjct: 253 EDRPSTLQLSLRLKEIAAREAHGHDAGGYGGGPGRPPARHPEAYADQHTERRPGSTPAPR 312

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                                       +     G R          P          ++
Sbjct: 313 NGSPSSRPGASTGGASGRPTGRNTPARPAQAQRRGPRPPARTDRSGRPVNTVRTSPGGRR 372


>gi|296268580|ref|YP_003651212.1| 30S ribosomal protein S4 [Thermobispora bispora DSM 43833]
 gi|296091367|gb|ADG87319.1| ribosomal protein S4 [Thermobispora bispora DSM 43833]
          Length = 208

 Score = 41.3 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ RAG A SR    + +      VNG  +   +  V   D IEV
Sbjct: 99  RLDNVVYRAGFAESRDAARQQVRHGHFLVNGRKVNIPSYRVREHDVIEV 147


>gi|295835249|ref|ZP_06822182.1| mixed type I polyketide synthase- peptide synthetase [Streptomyces
           sp. SPB74]
 gi|295825386|gb|EDY45091.2| mixed type I polyketide synthase- peptide synthetase [Streptomyces
           sp. SPB74]
          Length = 928

 Score = 41.3 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 7/92 (7%), Positives = 13/92 (14%)

Query: 263 SSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHS 322
              +              +      + +           A P   R  A           
Sbjct: 835 PPASEDGAPRAAPRPRSHEHAPAAGHDTGPAPGHGPTTAAAPGPGRGPARRHAPPGPAEP 894

Query: 323 SFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                 G+     R            R    +
Sbjct: 895 PRHDAPGRTRRARRPGEGPGGIPRAGRGRPPR 926


>gi|239939997|ref|ZP_04691934.1| putative serine/threonine protein kinase [Streptomyces roseosporus
           NRRL 15998]
 gi|239986480|ref|ZP_04707144.1| putative serine/threonine protein kinase [Streptomyces roseosporus
           NRRL 11379]
          Length = 467

 Score = 41.3 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 21/120 (17%), Positives = 37/120 (30%), Gaps = 7/120 (5%)

Query: 236 VSKKIL--REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           +  K +  RE  G H   E++  +      +E       +  ++           S  + 
Sbjct: 263 MRLKEIAAREAQGLH---ESRPPVQRSAQDAERPTGRMADPYADQHTRRAEGPSGSRPQP 319

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           G       + P   R   S    A    +     SG+R      +   P  RS  RT++ 
Sbjct: 320 GRRGAPVRSGPP--RTGGSRPQQASRNTTRSGGKSGKRPGAPAGTNGRPGTRSGGRTTSA 377



 Score = 40.2 bits (92), Expect = 0.50,   Method: Composition-based stats.
 Identities = 11/121 (9%), Positives = 30/121 (24%), Gaps = 6/121 (4%)

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           +E++ +    L E   P               +     +                ++ + 
Sbjct: 266 KEIAAREAQGLHESRPPVQRSAQDAERPTGRMADPYADQHTRRAEGPSGSRPQPGRRGAP 325

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQRE--ENHRRSPSFPSKRSLR 348
            ++G  +      P       +      G      + +  R    +  R+ S   + +  
Sbjct: 326 VRSGPPRTGGS-RPQQASRNTTRSGGKSGKRPGAPAGTNGRPGTRSGGRTTSAGRRPANP 384

Query: 349 R 349
           R
Sbjct: 385 R 385



 Score = 37.9 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 11/116 (9%), Positives = 20/116 (17%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
             +     L   +  +     +A           R    +E P                 
Sbjct: 251 DPEERPSTLQLSMRLKEIAAREAQGLHESRPPVQRSAQDAERPTGRMADPYADQHTRRAE 310

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                     RR         +   S     S     +  +S   P   +      
Sbjct: 311 GPSGSRPQPGRRGAPVRSGPPRTGGSRPQQASRNTTRSGGKSGKRPGAPAGTNGRP 366


>gi|9631280|ref|NP_048059.1| RNA-dependent RNA polymerase [Nudaurelia capensis beta virus]
 gi|81982129|sp|Q9YRB3|RDRP_NCBVS RecName: Full=Methyltransferase/helicase/RNA-directed RNA polymerase
 gi|4028587|gb|AAC97509.1| RNA-dependent RNA polymerase [Nudaurelia capensis beta virus]
          Length = 1925

 Score = 41.3 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 14/143 (9%), Positives = 34/143 (23%), Gaps = 7/143 (4%)

Query: 219  SYGPFQLGTLL--AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIIS 276
            ++G  ++  L    G    V+   + E++        + +              +    +
Sbjct: 1283 AFGHTKMSDLHLDPGFVMRVTPMKVDERVYSGQDGCQRADKTREKQPEPGQPGPQQQQQA 1342

Query: 277  EVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR 336
               +  ++    S          +   P        +        S      G       
Sbjct: 1343 STQEAGSKTSPRSRTDYQPRPDGRTREPREHPGQPRSDTREGVKASDDGESHGSDIRGMD 1402

Query: 337  RSPSFPSKR-----SLRRTSAKK 354
               S P +R       R  S ++
Sbjct: 1403 SRLSRPGRRIQDEPGRRENSRRR 1425


>gi|283777916|ref|YP_003368671.1| PSP1 domain-containing protein [Pirellula staleyi DSM 6068]
 gi|283436369|gb|ADB14811.1| PSP1 domain protein [Pirellula staleyi DSM 6068]
          Length = 453

 Score = 41.3 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 12/133 (9%), Positives = 36/133 (27%), Gaps = 9/133 (6%)

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G  R + ++IL +QL   + +  ++ +      +                        + 
Sbjct: 232 GRARVLGQEILSQQLLVQMEDGRRIMIPLTDVVTVLKAGTGKRTREPFGPPQPEGDAPAE 291

Query: 291 QKNGLSKQKKLATPVHRRNLA---------SNVWMAKGIHSSFLSDSGQREENHRRSPSF 341
            +    +  +       +                 A    S+    +G++    R     
Sbjct: 292 GRRDQRRDSRPPRGDRNQADRHSAPTGESEPAASDAPPAESTGERPAGEQPRPQRDQQRS 351

Query: 342 PSKRSLRRTSAKK 354
             +R  +R + ++
Sbjct: 352 GDRRPPQRGAYQQ 364


>gi|84500893|ref|ZP_00999128.1| S4 domain protein [Oceanicola batsensis HTCC2597]
 gi|84390960|gb|EAQ03378.1| S4 domain protein [Oceanicola batsensis HTCC2597]
          Length = 130

 Score = 41.3 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 7  VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          + E  T  R+ K I +A  + SR     ++    V+VNG+   + +  V   D +  
Sbjct: 1  MAEQPTKFRLDKWIWQARFVKSRSLAAGLVTGGHVRVNGMRAAKPSHGVQPGDVLTF 57


>gi|251809812|ref|ZP_04824285.1| RNA-binding S4 domain heat shock protein [Staphylococcus
          epidermidis BCM-HMP0060]
 gi|282875436|ref|ZP_06284308.1| S4 domain protein [Staphylococcus epidermidis SK135]
 gi|251806680|gb|EES59337.1| RNA-binding S4 domain heat shock protein [Staphylococcus
          epidermidis BCM-HMP0060]
 gi|281295793|gb|EFA88315.1| S4 domain protein [Staphylococcus epidermidis SK135]
 gi|329733026|gb|EGG69365.1| S4 domain protein [Staphylococcus epidermidis VCU028]
          Length = 87

 Score = 41.3 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRREVERMI-AQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + +  RR + + I  Q RV VNG + + A  ++   D + +
Sbjct: 1  MRLDKYLKVSRLVKRRTLAKEISEQGRVTVNGNVAK-AGTDIKENDELII 49


>gi|126338914|ref|XP_001379631.1| PREDICTED: hypothetical protein [Monodelphis domestica]
          Length = 1255

 Score = 41.3 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 12/115 (10%), Positives = 27/115 (23%), Gaps = 5/115 (4%)

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
            G      +         S            +    D   + +  ++    S  +    P
Sbjct: 200 FGERRGPRSAAAGQLLSPSETDEPAPARRGGARYGADGRALAEQPNELRARSGCRGREAP 259

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHR-RSPSF----PSKRSLRRTSAKK 354
                  + V +         + SG   ++ + R P          +  R +  K
Sbjct: 260 EGPPPPRTRVRVPSPRAPPGGARSGADPQDPQLRRPPPHSYPGGPDTRSRNAHTK 314



 Score = 37.9 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 15/122 (12%), Positives = 25/122 (20%), Gaps = 5/122 (4%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDF----TRMKKNSSQKN 293
              LR + G    E  +              R  P       D       R   +S    
Sbjct: 244 PNELRARSGCRGREAPEGPPPPRTRVRVPSPRAPPGGARSGADPQDPQLRRPPPHSYPGG 303

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF-PSKRSLRRTSA 352
             ++ +   T    R           +          R  + R         R+      
Sbjct: 304 PDTRSRNAHTKPEARLWTPESPAPSQVTPRPRRPRLPRRLSTRGKAGRLQGPRTPPGGQR 363

Query: 353 KK 354
           +K
Sbjct: 364 RK 365


>gi|34536310|dbj|BAC87606.1| unnamed protein product [Homo sapiens]
          Length = 834

 Score = 41.3 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 27/108 (25%), Gaps = 3/108 (2%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P   +EA+               + P              +   ++     +     P  
Sbjct: 713 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 772

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS--FPSKRSLRRTSA 352
           RR              +   +     E  RR      PS++  RR +A
Sbjct: 773 RRVGDVEPSRKPKRRRAADVEPSS-PEPKRRRVGDVEPSRKPKRRRAA 819



 Score = 39.4 bits (90), Expect = 0.84,   Method: Composition-based stats.
 Identities = 9/117 (7%), Positives = 25/117 (21%), Gaps = 2/117 (1%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +    +   P     A++              +                    ++  +  
Sbjct: 718 EAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGD 777

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +    P  RR         +            R+   +R  +   + SL     ++
Sbjct: 778 VEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKP--KRRRAADVEPSLPEPKRRR 832



 Score = 37.1 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 28/112 (25%), Gaps = 3/112 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E+L   L   A  NL  P  +++    ++P                  ++     +    
Sbjct: 695 ERLRGPLPPSADDNLKTPPLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRK 754

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               R                   +  ++    +R  +   + S      ++
Sbjct: 755 PKRRRAADVEPSSPEPKRRRVGDVEPSRKP---KRRRAADVEPSSPEPKRRR 803


>gi|83745736|ref|ZP_00942793.1| Endonuclease III [Ralstonia solanacearum UW551]
 gi|83727426|gb|EAP74547.1| Endonuclease III [Ralstonia solanacearum UW551]
          Length = 531

 Score = 41.3 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 22/129 (17%), Positives = 35/129 (27%), Gaps = 10/129 (7%)

Query: 224 QLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
           +LG L  G+ R           GP  L   Q    A      +    +    +       
Sbjct: 182 RLGRLEPGAGR----------CGPRPLRLPQRPPGARAGRERSAPGCQGRSQAGRRQRRA 231

Query: 284 RMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
             ++  +++ G            R   A     A+   S      G+     RRS S P 
Sbjct: 232 ARRRCGTRRPGPQAGDHPGRHRARAPEAGRDGRARARSSQRHRRPGRGAGPDRRSRSAPQ 291

Query: 344 KRSLRRTSA 352
                  +A
Sbjct: 292 AHRRPGPAA 300



 Score = 38.2 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 16/113 (14%), Positives = 28/113 (24%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R      L   A      P+   +     R       P    R +    Q+    ++   
Sbjct: 179 RTHRLGRLEPGAGRCGPRPLRLPQRPPGARAGRERSAPGCQGRSQAGRRQRRAARRRCGT 238

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             P  +         A+   +     +  R     R P   +    R  SA +
Sbjct: 239 RRPGPQAGDHPGRHRARAPEAGRDGRARARSSQRHRRPGRGAGPDRRSRSAPQ 291


>gi|241730143|ref|XP_002412270.1| hypothetical protein IscW_ISCW011299 [Ixodes scapularis]
 gi|215505509|gb|EEC15003.1| hypothetical protein IscW_ISCW011299 [Ixodes scapularis]
          Length = 600

 Score = 41.3 bits (95), Expect = 0.26,   Method: Composition-based stats.
 Identities = 19/99 (19%), Positives = 33/99 (33%), Gaps = 1/99 (1%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
             + +  +P   S      RP   ++ P       K S ++     +K  A    R + +
Sbjct: 106 RPKGSSKSPGRKSSPGKVGRPKKSAKSPGRKPSPAKKSPKRKPSPVKKSPARSGARAS-S 164

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
           S+    K       +          +SPS PS    RR+
Sbjct: 165 SDRGPVKSAAPKSPAKRADTPRAQSKSPSRPSMAGGRRS 203



 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 13/119 (10%), Positives = 30/119 (25%), Gaps = 1/119 (0%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
            ++  ++R++        +          +          +           + SS    
Sbjct: 64  RLASTVVRDKSSSPSRGRSPKPSPPGKRQASRSRSRSQGRVGRPKGSSKSPGRKSSPGKV 123

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIH-SSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
              +K   +P  + + A      K        + SG R  +  R P   +        A
Sbjct: 124 GRPKKSAKSPGRKPSPAKKSPKRKPSPVKKSPARSGARASSSDRGPVKSAAPKSPAKRA 182


>gi|119595590|gb|EAW75184.1| hCG2018436 [Homo sapiens]
          Length = 1031

 Score = 41.3 bits (95), Expect = 0.26,   Method: Composition-based stats.
 Identities = 21/142 (14%), Positives = 37/142 (26%), Gaps = 6/142 (4%)

Query: 202 KKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV-SKKILREQLGPHLLEEAQVNLDAP 260
            +  E     V+ L          G  LAG  R +   K    + G           +  
Sbjct: 736 SRCCEAIYSSVSGLK-AHLASCSKGAHLAGKYRCLLCPKEFSSESGVKYHILKTHAENWF 794

Query: 261 IYSSETLVRDRPN----IISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
             S++   + R         E   +    KK   +    + ++ +A    RR+       
Sbjct: 795 RTSADPPPKHRSQDSLVPKKEKKKNLAGGKKRGRKPKERTPEEPVAKLPPRRDDWPPGCR 854

Query: 317 AKGIHSSFLSDSGQREENHRRS 338
            KG   S    +          
Sbjct: 855 DKGARGSTGRKALPGPFPGYPK 876


>gi|149608379|ref|XP_001511689.1| PREDICTED: similar to Uncharacterized protein KIAA1383
           [Ornithorhynchus anatinus]
          Length = 773

 Score = 40.9 bits (94), Expect = 0.26,   Method: Composition-based stats.
 Identities = 16/128 (12%), Positives = 31/128 (24%), Gaps = 5/128 (3%)

Query: 226 GTLLAGSTRE--VSKKILR---EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
             L     R   +    LR    +  P L E  +          +   R    +     +
Sbjct: 235 DGLRPDGLRPDGLRPDGLRPDGLRRLPLLRELLRELALLDGQLGDGSPRPAWVVQDAATE 294

Query: 281 DFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
                 + + +     +++    P  R      V  A  + +      G R E  R +  
Sbjct: 295 APEFPARPAGRPVRRGRERPPGLPPERDGGPGQVPTASPLRAGEGPKDGTRPEKARGARG 354

Query: 341 FPSKRSLR 348
                   
Sbjct: 355 DGPPGKKP 362


>gi|145613640|ref|XP_363542.2| hypothetical protein MGG_01468 [Magnaporthe oryzae 70-15]
 gi|145020693|gb|EDK04822.1| hypothetical protein MGG_01468 [Magnaporthe oryzae 70-15]
          Length = 2523

 Score = 40.9 bits (94), Expect = 0.26,   Method: Composition-based stats.
 Identities = 16/107 (14%), Positives = 33/107 (30%), Gaps = 1/107 (0%)

Query: 248  HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                + + N +          R+  +         TR  +N+         +  A    R
Sbjct: 1688 RESRDGRGNREPRDARETREPRESRDTRDARDSRETRDARNTDSTRSERSARDFAGSERR 1747

Query: 308  RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR-RTSAK 353
             +  +N    +    S      + +++ RR  S   + S   R SA+
Sbjct: 1748 GSDNNNTGSREAGRPSDKDRGSRNDQSSRRIESVSERDSRPSRDSAR 1794



 Score = 37.5 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 18/134 (13%), Positives = 31/134 (23%), Gaps = 14/134 (10%)

Query: 232  STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD-------DFTR 284
             TRE   +  R+        E +   +     SE   RD         D       +  R
Sbjct: 1704 ETRE--PRESRDTRDARDSRETRDARNTDSTRSERSARDFAGSERRGSDNNNTGSREAGR 1761

Query: 285  MKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP----- 339
                          +++ +   R +  S              +      +    P     
Sbjct: 1762 PSDKDRGSRNDQSSRRIESVSERDSRPSRDSARDSARDLPRDNLKDLPRDRNTGPRSHDG 1821

Query: 340  SFPSKRSLRRTSAK 353
              P  R   R S+ 
Sbjct: 1822 GRPGPRDAPRDSSS 1835


>gi|309362577|emb|CAP27875.2| CBR-RSR-1 protein [Caenorhabditis briggsae AF16]
          Length = 581

 Score = 40.9 bits (94), Expect = 0.26,   Method: Composition-based stats.
 Identities = 12/107 (11%), Positives = 24/107 (22%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                +                  P+     P   +   +  +      K ++  +   +
Sbjct: 299 RRQSGSPPRGARKGSPEAKKPGRSPSGSPRGPRKLSGSPRRRAASPEARKPRRSPSGSPK 358

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           R  A          S     S        RSP    +R    + A +
Sbjct: 359 RRQAFPAARRPPSGSPPRRRSPPAASKFGRSPPESPRRRRSGSPAAR 405



 Score = 40.2 bits (92), Expect = 0.57,   Method: Composition-based stats.
 Identities = 12/108 (11%), Positives = 26/108 (24%), Gaps = 1/108 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                     +   P   S +  R   +  +  P           Q    +++    +P 
Sbjct: 316 AKKPGRSPSGSPRGPRKLSGSPRRRAASPEARKPRRSPSGSPKRRQAFPAARRPPSGSPP 375

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS-KRSLRRTSA 352
            RR+  +     +    S            +   S     R  R+  +
Sbjct: 376 RRRSPPAASKFGRSPPESPRRRRSGSPAARKPGRSPSGSPRGARKGRS 423



 Score = 39.8 bits (91), Expect = 0.73,   Method: Composition-based stats.
 Identities = 15/105 (14%), Positives = 23/105 (21%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+  G      A      P  S     + R    +          +  S        +  
Sbjct: 331 RKLSGSPRRRAASPEARKPRRSPSGSPKRRQAFPAARRPPSGSPPRRRSPPAASKFGRSP 390

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
                RR   S      G   S      ++  +   SP    K  
Sbjct: 391 PESPRRRRSGSPAARKPGRSPSGSPRGARKGRSPSGSPGRRQKSP 435



 Score = 39.4 bits (90), Expect = 0.84,   Method: Composition-based stats.
 Identities = 14/108 (12%), Positives = 28/108 (25%), Gaps = 4/108 (3%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P     +          S +  R +    +  P   +  ++ S        +    +P  
Sbjct: 337 PRRRAASPEARKPRRSPSGSPKRRQAFPAARRPPSGSPPRRRSPPAASKFGRSPPESPRR 396

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           RR+ +              S S +     R     P +R       +K
Sbjct: 397 RRSGSPAARKP----GRSPSGSPRGARKGRSPSGSPGRRQKSPEVVRK 440



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 12/106 (11%), Positives = 25/106 (23%), Gaps = 2/106 (1%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ--KKLATPVHRR 308
            EA+    +P  S     +   +          R  + S   +   +Q       P    
Sbjct: 314 PEAKKPGRSPSGSPRGPRKLSGSPRRRAASPEARKPRRSPSGSPKRRQAFPAARRPPSGS 373

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                   A         +S +R  +   +   P +         +
Sbjct: 374 PPRRRSPPAASKFGRSPPESPRRRRSGSPAARKPGRSPSGSPRGAR 419



 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 12/120 (10%), Positives = 24/120 (20%), Gaps = 2/120 (1%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           E+ +K +                           R R +            +     ++ 
Sbjct: 265 ELRRKAI-ASQARRSKSPRGSPRRRSPRGRSPEARRRQSGSPPRGARKGSPEAKKPGRSP 323

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREE-NHRRSPSFPSKRSLRRTSAK 353
               +            +    A+    S      +R+     R P   S    R   A 
Sbjct: 324 SGSPRGPRKLSGSPRRRAASPEARKPRRSPSGSPKRRQAFPAARRPPSGSPPRRRSPPAA 383



 Score = 37.5 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 31/109 (28%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                E  +  + +    S++                 R +++ S   G  K    A   
Sbjct: 260 RHEEAELRRKAIASQARRSKSPRGSPRRRSPRGRSPEARRRQSGSPPRGARKGSPEAKKP 319

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            R    S     K   S     +       RRSPS   KR     +A++
Sbjct: 320 GRSPSGSPRGPRKLSGSPRRRAASPEARKPRRSPSGSPKRRQAFPAARR 368



 Score = 37.5 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 14/103 (13%), Positives = 31/103 (30%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
            + +          S +    R    S      +   +   +    S +++ A P  RR 
Sbjct: 310 RKGSPEAKKPGRSPSGSPRGPRKLSGSPRRRAASPEARKPRRSPSGSPKRRQAFPAARRP 369

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            + +    +   ++        E   RR    P+ R   R+ +
Sbjct: 370 PSGSPPRRRSPPAASKFGRSPPESPRRRRSGSPAARKPGRSPS 412


>gi|114587477|ref|XP_001156166.1| PREDICTED: hypothetical protein [Pan troglodytes]
          Length = 347

 Score = 40.9 bits (94), Expect = 0.26,   Method: Composition-based stats.
 Identities = 13/117 (11%), Positives = 30/117 (25%), Gaps = 2/117 (1%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           ++   ++         +      +     L    P      P +  R ++        + 
Sbjct: 50  ERERGDKRARARRRRRRRRQRGRLSPRPELRLQLPGAGGAFPAEPRRHERGRPLTAARAG 109

Query: 298 QKKLATPVH--RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            ++   P    +R+ +  V   +    S       R       P  P+  S  R   
Sbjct: 110 SQRARRPEELSQRSRSRAVKTTRPQPRSPAPKPQSRPLGSAPKPRNPAPTSRLRPQP 166


>gi|183981109|ref|YP_001849400.1| 30S ribosomal protein S4, RpsD [Mycobacterium marinum M]
 gi|226699093|sp|B2HCX3|RS4_MYCMM RecName: Full=30S ribosomal protein S4
 gi|183174435|gb|ACC39545.1| 30S ribosomal protein S4, RpsD [Mycobacterium marinum M]
          Length = 201

 Score = 40.9 bits (94), Expect = 0.26,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ RAG+A +RR   ++++     VNG+ +   +  V   D I+V    L      
Sbjct: 92  RLDNVVYRAGLARTRRMARQLVSHGHFSVNGVHVNVPSYRVSQYDIIDVRDNSLNTVPFQ 151

Query: 74  R 74
            
Sbjct: 152 I 152


>gi|194224220|ref|XP_001497267.2| PREDICTED: similar to transmembrane channel-like 2 [Equus caballus]
          Length = 906

 Score = 40.9 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 13/72 (18%), Positives = 18/72 (25%), Gaps = 1/72 (1%)

Query: 276 SEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENH 335
           S              +    S          RR        A+G      +  G++E   
Sbjct: 2   SRQLQGLGEEAGGGVRGRARSGSPGTGDRSGRRPSRKQAPKAQGAPGKRGAPPGRKERAG 61

Query: 336 RRSPSFPSKRSL 347
             SP   S RS 
Sbjct: 62  G-SPRPGSPRSK 72



 Score = 39.4 bits (90), Expect = 0.84,   Method: Composition-based stats.
 Identities = 16/114 (14%), Positives = 26/114 (22%), Gaps = 1/114 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS-KQKK 300
           R+  G        V   A   S  T  R       +                G   +   
Sbjct: 3   RQLQGLGEEAGGGVRGRARSGSPGTGDRSGRRPSRKQAPKAQGAPGKRGAPPGRKERAGG 62

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              P   R+  +     +         + +R    RR     +    +R   KK
Sbjct: 63  SPRPGSPRSKQAERRRPREELRKPERSTAERTSKGRRKSDGRTSFKEQRAPPKK 116


>gi|163788648|ref|ZP_02183093.1| heat shock protein 15 [Flavobacteriales bacterium ALC-1]
 gi|159875885|gb|EDP69944.1| heat shock protein 15 [Flavobacteriales bacterium ALC-1]
          Length = 122

 Score = 40.9 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 2/58 (3%)

Query: 14 QRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           RV K +       +R    +   + +VKVNG +++  +  V  TD IE+    +   
Sbjct: 1  MRVDKYLWCVRYYKTRSIATKACKKGQVKVNGSVIK-PSREVYPTDKIELRKNQISYK 57


>gi|291449777|ref|ZP_06589167.1| histidine kinase [Streptomyces albus J1074]
 gi|291352726|gb|EFE79628.1| histidine kinase [Streptomyces albus J1074]
          Length = 834

 Score = 40.9 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 14/132 (10%), Positives = 30/132 (22%), Gaps = 17/132 (12%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
            LR+  GP  + E  +     +              +    +    +   ++++      
Sbjct: 670 ELRDSSGPGTIAEITLPPGVLVTMERNTAASPWETGTPPGAELAGGRPRPARRSAPRPSG 729

Query: 300 KLATPVHRR----------------NLASNVWMAKGIHSSFLSDSGQ-REENHRRSPSFP 342
             A     R                   S   +     ++        + EN  R P   
Sbjct: 730 STAVAERERVPAPPPPPAGEPADRIAGVSASGLPVRKRNAPQQWPSANKRENTERRPGTT 789

Query: 343 SKRSLRRTSAKK 354
             R   R    +
Sbjct: 790 GPRKPPRRRDSR 801


>gi|218533090|ref|YP_002423906.1| OmpA/MotB domain protein [Methylobacterium chloromethanicum CM4]
 gi|218525393|gb|ACK85978.1| OmpA/MotB domain protein [Methylobacterium chloromethanicum CM4]
          Length = 723

 Score = 40.9 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 11/107 (10%), Positives = 22/107 (20%), Gaps = 5/107 (4%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P      +          +          +E P    R      Q+    +++       
Sbjct: 76  PARERPERSERPERPEPRQAPAARERPEPAERPARPERPAAQERQERPERQERPDRQERQ 135

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            R                 +   QR +     P+ P+ R        
Sbjct: 136 ERPDRQERPDRP-----ERAAPPQRPDRSEERPAAPASRERTPDRDA 177



 Score = 36.7 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 15/122 (12%), Positives = 30/122 (24%), Gaps = 16/122 (13%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E+  P    +      A   S E           E P+     ++ S  +     Q +  
Sbjct: 148 ERAAPPQRPDRSEERPAAPASRERTPDRDAPARREAPEREAPARRESPDRLDRDGQDRPG 207

Query: 303 TPVHRRNLAS----NVWMAKGIHSSFLSDSGQREE------------NHRRSPSFPSKRS 346
            P  R         N   A    +   ++  ++                 + P  P + +
Sbjct: 208 RPAGREADRPDSAPNQRRAPNAPTPPNAERPEQPTTPSAPNPAQPNTPPNQRPGVPGRPA 267

Query: 347 LR 348
             
Sbjct: 268 TP 269


>gi|6649242|gb|AAF21439.1|AF201422_1 splicing coactivator subunit SRm300 [Homo sapiens]
          Length = 2296

 Score = 40.9 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 9/108 (8%), Positives = 21/108 (19%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                            S   +     +              + +    + + +  AT  
Sbjct: 432 RHASSSPESPKPAPAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAK 491

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R+ +          S        R          P +R   R+  +
Sbjct: 492 RGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQR 539



 Score = 40.9 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 13/107 (12%), Positives = 25/107 (23%), Gaps = 1/107 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P      +++      +       R    S  P       ++ +       + +  T  
Sbjct: 444 APAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKR 503

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                 S  W        +      +     RSP  P   S  R + 
Sbjct: 504 GHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPG-WSRSRNTQ 549



 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 22/135 (16%), Positives = 34/135 (25%), Gaps = 10/135 (7%)

Query: 230 AGSTREV----SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
            GS RE+    + K             +         S       R    S  P      
Sbjct: 447 PGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKRGHS 506

Query: 286 KKNSSQKNGLSKQKK--LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
           +  S Q       ++   +    RR  + +        S      G+     R      S
Sbjct: 507 RSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRSHSRS 566

Query: 344 K----RSLRRTSAKK 354
                RS  RT A++
Sbjct: 567 PATRGRSRSRTPARR 581


>gi|46580818|ref|YP_011626.1| radical SAM domain-containing protein [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|46450238|gb|AAS96886.1| radical SAM domain protein [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|311234522|gb|ADP87376.1| Radical SAM domain protein [Desulfovibrio vulgaris RCH1]
          Length = 680

 Score = 40.9 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 12/115 (10%), Positives = 25/115 (21%), Gaps = 2/115 (1%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
             + LR+            + DA         +           D    + +    N   
Sbjct: 565 DAERLRQHGILMPDTGRPPSRDADNRRRGDARQSETGRGKAGTRDGRPHRSDRDTGNANR 624

Query: 297 --KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
               +       R     +     G      ++ G+ +   RR       +   R
Sbjct: 625 HDGGRSDRRGGRRDEDRPDRGRRNGARPDGGANRGRADAEERREGRKGGSKRPPR 679


>gi|239977852|ref|ZP_04700376.1| putative sensor-like histidine kinase [Streptomyces albus J1074]
          Length = 769

 Score = 40.9 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 14/132 (10%), Positives = 30/132 (22%), Gaps = 17/132 (12%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
            LR+  GP  + E  +     +              +    +    +   ++++      
Sbjct: 605 ELRDSSGPGTIAEITLPPGVLVTMERNTAASPWETGTPPGAELAGGRPRPARRSAPRPSG 664

Query: 300 KLATPVHRR----------------NLASNVWMAKGIHSSFLSDSGQ-REENHRRSPSFP 342
             A     R                   S   +     ++        + EN  R P   
Sbjct: 665 STAVAERERVPAPPPPPAGEPADRIAGVSASGLPVRKRNAPQQWPSANKRENTERRPGTT 724

Query: 343 SKRSLRRTSAKK 354
             R   R    +
Sbjct: 725 GPRKPPRRRDSR 736


>gi|242019442|ref|XP_002430170.1| conserved hypothetical protein [Pediculus humanus corporis]
 gi|212515261|gb|EEB17432.1| conserved hypothetical protein [Pediculus humanus corporis]
          Length = 818

 Score = 40.9 bits (94), Expect = 0.28,   Method: Composition-based stats.
 Identities = 19/110 (17%), Positives = 37/110 (33%), Gaps = 3/110 (2%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                +  +  +   S  +      +  S      +   K S   +  SK+ +  +   +
Sbjct: 223 RSRSGSAASRRSRSGSVVSKHSRNGSPASRRSRSGSAASKRSRSGSAASKRSRSGSAASK 282

Query: 308 RNLASNV---WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           R+ + +        G  +S  S SG       RS S  S+RS   ++  K
Sbjct: 283 RSRSGSAASRRSRSGSAASRRSRSGSAASRRSRSGSAASRRSRSGSAGSK 332



 Score = 40.5 bits (93), Expect = 0.36,   Method: Composition-based stats.
 Identities = 18/110 (16%), Positives = 43/110 (39%), Gaps = 3/110 (2%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                +  +  +   S+ +      +++S+   + +   + S   +  SK+ +  +   +
Sbjct: 213 RSRSGSAASRRSRSGSAASRRSRSGSVVSKHSRNGSPASRRSRSGSAASKRSRSGSAASK 272

Query: 308 RNLASNV---WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           R+ + +        G  +S  S SG       RS S  S+RS   ++A +
Sbjct: 273 RSRSGSAASKRSRSGSAASRRSRSGSAASRRSRSGSAASRRSRSGSAASR 322



 Score = 39.4 bits (90), Expect = 0.78,   Method: Composition-based stats.
 Identities = 20/110 (18%), Positives = 40/110 (36%), Gaps = 3/110 (2%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                +  +  +   S+ +      +  S+     +   K S   +  SK+ +  +   +
Sbjct: 303 RSRSGSAASRRSRSGSAASRRSRSGSAGSKRSRSGSAASKRSRSGSAASKRSRSGSAASK 362

Query: 308 RNLASNV---WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           R+ + +        G  +S  S SG       RS S  S+RS   ++A K
Sbjct: 363 RSRSGSATSKRSRSGSAASKRSRSGSAASKRSRSGSAVSRRSRSGSAASK 412



 Score = 39.4 bits (90), Expect = 0.84,   Method: Composition-based stats.
 Identities = 19/110 (17%), Positives = 42/110 (38%), Gaps = 3/110 (2%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
           H    +  +  +   S+ +      +  S      + + K+S   +  S++ +  +   +
Sbjct: 203 HSRNGSPASRRSRSGSAASRRSRSGSAASRRSRSGSVVSKHSRNGSPASRRSRSGSAASK 262

Query: 308 RNLASNV---WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           R+ + +        G  +S  S SG       RS S  S+RS   ++A +
Sbjct: 263 RSRSGSAASKRSRSGSAASKRSRSGSAASRRSRSGSAASRRSRSGSAASR 312



 Score = 39.4 bits (90), Expect = 0.87,   Method: Composition-based stats.
 Identities = 20/113 (17%), Positives = 33/113 (29%), Gaps = 6/113 (5%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                   ++ +    + +    R    S            S +    S   K +     
Sbjct: 230 ASRRSRSGSVVSKHSRNGSPASRRSRSGSAASKRSRSGSAASKRSRSGSAASKRSRSGSA 289

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENH----RRSPSF--PSKRSLRRTSAKK 354
            +  S    A    S   S + +R  +     RRS S    SKRS   ++A K
Sbjct: 290 ASRRSRSGSAASRRSRSGSAASRRSRSGSAASRRSRSGSAGSKRSRSGSAASK 342



 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 38/108 (35%), Gaps = 1/108 (0%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                +  +  +   S+ +      +  S+     +   K S   +  SK+ +  +   +
Sbjct: 333 RSRSGSAASKRSRSGSAASKRSRSGSAASKRSRSGSATSKRSRSGSAASKRSRSGSAASK 392

Query: 308 RNLASNVWMAKGIHSSFLSDSGQ-REENHRRSPSFPSKRSLRRTSAKK 354
           R+ + +    +    S  S   +      RRS S     +  R+++K+
Sbjct: 393 RSRSGSAVSRRSRSGSAASKRSRSGSAASRRSRSGSKGSNRSRSNSKE 440



 Score = 37.5 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 14/107 (13%), Positives = 34/107 (31%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                +  +  +   S+ +      +  S+     +   K S   +  SK+ +  +   +
Sbjct: 323 RSRSGSAGSKRSRSGSAASKRSRSGSAASKRSRSGSAASKRSRSGSATSKRSRSGSAASK 382

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           R+ + +    +    S +S   +      +     S  S R  S  K
Sbjct: 383 RSRSGSAASKRSRSGSAVSRRSRSGSAASKRSRSGSAASRRSRSGSK 429


>gi|164659147|ref|XP_001730698.1| hypothetical protein MGL_2152 [Malassezia globosa CBS 7966]
 gi|159104595|gb|EDP43484.1| hypothetical protein MGL_2152 [Malassezia globosa CBS 7966]
          Length = 1251

 Score = 40.9 bits (94), Expect = 0.28,   Method: Composition-based stats.
 Identities = 10/91 (10%), Positives = 18/91 (19%), Gaps = 1/91 (1%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR-RNLA 311
              ++      S       P  ++  P    R            +     +P    R + 
Sbjct: 48  RPSHVPMAGRRSPMPPSRSPVPLARSPAPGARPSMAPRSPAPGPRPSPARSPAPGMRPMM 107

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
                   +  S       R       P  P
Sbjct: 108 PPRSPVPSMRPSPARSPLPRRTGVSPRPGMP 138



 Score = 40.5 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 12/100 (12%), Positives = 22/100 (22%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
                      S            +        +   S   G   Q + +        + 
Sbjct: 1   MDPRPQMMRGPSPRPPASASGPTMQQVGRPRPPQPQRSPAPGSRAQVRPSHVPMAGRRSP 60

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                  +  +     G R     RSP+   + S  R+ A
Sbjct: 61  MPPSRSPVPLARSPAPGARPSMAPRSPAPGPRPSPARSPA 100



 Score = 36.3 bits (82), Expect = 6.5,   Method: Composition-based stats.
 Identities = 14/109 (12%), Positives = 26/109 (23%), Gaps = 2/109 (1%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P ++        A           RP             +      +     ++   P 
Sbjct: 4   RPQMMRGPSPRPPASASGPTMQQVGRPRPPQPQRSPAPGSRAQVRPSHVPMAGRRSPMPP 63

Query: 306 HRRNLASNVWMAKGIHSS--FLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            R  +      A G   S    S +     +  RSP+   +  +   S 
Sbjct: 64  SRSPVPLARSPAPGARPSMAPRSPAPGPRPSPARSPAPGMRPMMPPRSP 112


>gi|301057497|ref|ZP_07198593.1| ribosomal protein S4 [delta proteobacterium NaphS2]
 gi|300448425|gb|EFK12094.1| ribosomal protein S4 [delta proteobacterium NaphS2]
          Length = 209

 Score = 40.9 bits (94), Expect = 0.28,   Method: Composition-based stats.
 Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 1/48 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           R+  V+ + G A SR +  ++I      VN   +   +  V   D +E
Sbjct: 100 RLDNVVYKMGFAASRTQARQLIRHNHFLVNQKKVNIPSYQVKVGDVVE 147


>gi|296393970|ref|YP_003658854.1| hypothetical protein Srot_1561 [Segniliparus rotundus DSM 44985]
 gi|296181117|gb|ADG98023.1| conserved hypothetical protein [Segniliparus rotundus DSM 44985]
          Length = 319

 Score = 40.9 bits (94), Expect = 0.28,   Method: Composition-based stats.
 Identities = 11/87 (12%), Positives = 20/87 (22%), Gaps = 2/87 (2%)

Query: 263 SSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHS 322
             +    DR         D  + +    ++ G     +   P  RR      W  +G   
Sbjct: 5   RPQHDSGDRRPRGPRREGDGGQWQPRGPRREGDGGPWRPRGP--RREGDGGPWRPRGPRR 62

Query: 323 SFLSDSGQREENHRRSPSFPSKRSLRR 349
                  +     R       +    R
Sbjct: 63  EGDGGPWRPRGPRREGDGGQWRPRGPR 89



 Score = 37.1 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 11/79 (13%), Positives = 17/79 (21%), Gaps = 2/79 (2%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
                   E               D    +    ++ G     +   P  RR      W 
Sbjct: 27  WQPRGPRREGDGGPWRPRGPRREGDGGPWRPRGPRREGDGGPWRPRGP--RREGDGGQWR 84

Query: 317 AKGIHSSFLSDSGQREENH 335
            +G      SD+    E  
Sbjct: 85  PRGPRRDQDSDANHSTEPE 103


>gi|118486874|gb|ABK95271.1| unknown [Populus trichocarpa]
          Length = 418

 Score = 40.9 bits (94), Expect = 0.28,   Method: Composition-based stats.
 Identities = 15/127 (11%), Positives = 39/127 (30%), Gaps = 8/127 (6%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +   ++R +      ++          + +       N  ++   D  + ++  S     
Sbjct: 172 IDGNVVRAKFTLPPRQKLSPPPKPIAAAPKRDAPKTDNASADAEKDGPKRQREPSPHRKP 231

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR--------EENHRRSPSFPSKRSL 347
               +  +PV RR  +    +         S   +R        E   RR P+ P++   
Sbjct: 232 LASPRRRSPVARRGGSPRRQLDSPPRRRADSPGRRRVESPYRRGETPPRRRPASPARGRS 291

Query: 348 RRTSAKK 354
             +  ++
Sbjct: 292 PSSPPRR 298



 Score = 38.2 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 13/102 (12%), Positives = 36/102 (35%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           +A    +A   + +   + +           +  +++   + G S +++L +P  RR  +
Sbjct: 203 DAPKTDNASADAEKDGPKRQREPSPHRKPLASPRRRSPVARRGGSPRRQLDSPPRRRADS 262

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                 +  +    +   +R  +  R  S  S     R+  +
Sbjct: 263 PGRRRVESPYRRGETPPRRRPASPARGRSPSSPPRRYRSPLR 304


>gi|32423695|gb|AAP81238.1| ribosomal protein S4 [Candidatus Portiera aleyrodidarum]
          Length = 203

 Score = 40.9 bits (94), Expect = 0.28,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R G + +R E  +++  + +KVNG ++  ++  V   D I +
Sbjct: 97  RLDNIVYRMGFSVTRAEARQLVNHKTIKVNGRIVNISSYKVTVGDCISI 145


>gi|83769076|dbj|BAE59213.1| unnamed protein product [Aspergillus oryzae]
          Length = 304

 Score = 40.9 bits (94), Expect = 0.28,   Method: Composition-based stats.
 Identities = 9/87 (10%), Positives = 22/87 (25%)

Query: 268 VRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSD 327
              +    S    +     K ++  +  + +K+      +    S    + G        
Sbjct: 2   PVKKRKSESVPAAEENNSPKRAAVPDPATGEKRKRGRPRKYPEGSGPKPSPGPKRGRGRP 61

Query: 328 SGQREENHRRSPSFPSKRSLRRTSAKK 354
                 +    PS P +        +K
Sbjct: 62  RKDPSASTPSKPSTPKEGKRPVGRPRK 88


>gi|149481063|ref|XP_001521407.1| PREDICTED: hypothetical protein [Ornithorhynchus anatinus]
          Length = 763

 Score = 40.9 bits (94), Expect = 0.28,   Method: Composition-based stats.
 Identities = 16/139 (11%), Positives = 33/139 (23%), Gaps = 6/139 (4%)

Query: 222 PFQLGTLLAGSTR-EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
           P  L  + AG TR  +      ++           +      +  T  +  P        
Sbjct: 12  PISLRKVPAGWTRARLDSDDEDDRANRRSPSTDGGSQATNGSAPPTANQRSPATNGAPRP 71

Query: 281 DFTRMKKNSSQKNGLSKQK-----KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENH 335
                ++         +           P       +N    +         + +     
Sbjct: 72  PMGAPRQQPMGAPRPPRGAPRPPMGAPRPPMGSPRPTNQRSGRRSPPRLNEPAERGPARA 131

Query: 336 RRSPSFPSKRSLRRTSAKK 354
           R SP+ P+K   R     +
Sbjct: 132 RPSPAQPAKDRPRGQRGHR 150



 Score = 38.2 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 13/127 (10%), Positives = 28/127 (22%), Gaps = 15/127 (11%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ------KNGL 295
           R  +G    +               +   RP + S  P +    +++  +      +   
Sbjct: 70  RPPMGAPRQQPMGAPRPPRGAPRPPMGAPRPPMGSPRPTNQRSGRRSPPRLNEPAERGPA 129

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREE---------NHRRSPSFPSKRS 346
             +   A P   R              +                   +    P+ PS   
Sbjct: 130 RARPSPAQPAKDRPRGQRGHRGHRAAGAPGGAHPAGPRLAFPLAFRTSLPGCPADPSDLP 189

Query: 347 LRRTSAK 353
             R  + 
Sbjct: 190 RPRGPSS 196


>gi|163745685|ref|ZP_02153045.1| 30S ribosomal protein S4 [Oceanibulbus indolifex HEL-45]
 gi|161382503|gb|EDQ06912.1| 30S ribosomal protein S4 [Oceanibulbus indolifex HEL-45]
          Length = 206

 Score = 40.9 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 9/35 (25%), Positives = 14/35 (40%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
             + +    V+VNG  +   +  V   D IEV   
Sbjct: 112 ARQFVNHGHVRVNGKKVNIPSYRVKEGDVIEVRDR 146


>gi|126347778|emb|CAJ89496.1| putative IS117 transposase [Streptomyces ambofaciens ATCC 23877]
          Length = 277

 Score = 40.9 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 15/99 (15%), Positives = 22/99 (22%), Gaps = 1/99 (1%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
              P  SS              PD        S  +N    +        R    +    
Sbjct: 43  RPRPANSSRPPRHSPGRATDPHPDPGRPQASRSPARNRSRGRTSPRGLPRRVGPPAATGR 102

Query: 317 AKGIHSSFLSDSGQREENHRRSPS-FPSKRSLRRTSAKK 354
                +            HRR P+     RSL +    +
Sbjct: 103 GLARQADARPPHPAGRGLHRRRPARRSDGRSLPQHPDAE 141


>gi|322705413|gb|EFY96999.1| hypothetical protein MAA_07545 [Metarhizium anisopliae ARSEF 23]
          Length = 366

 Score = 40.9 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 14/138 (10%), Positives = 28/138 (20%), Gaps = 16/138 (11%)

Query: 230 AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
               + + K    ++L P          +          R   +     P+  ++     
Sbjct: 231 PFEYKSLIKD---KKLKPAPTRPGLPPPNPLPKPPRPNTRPGGSNGGPPPNPLSKPPTKP 287

Query: 290 SQKNGLSKQKKL--------ATPVHRRNLASNVW-----MAKGIHSSFLSDSGQREENHR 336
           + K G S               P      +S           G             +   
Sbjct: 288 NTKPGGSNGGPPFNPLSPPGGKPNTNPGGSSGGPPFNPLSPPGGKPGTNPGGSTDNQGGD 347

Query: 337 RSPSFPSKRSLRRTSAKK 354
             P+ P          K+
Sbjct: 348 GKPAKPKPTRRPNGRPKR 365


>gi|15675773|ref|NP_269947.1| collagen-like surface protei [Streptococcus pyogenes M1 GAS]
 gi|8917583|gb|AAF81278.1|AF252861_1 collagen-like protein Scl [Streptococcus pyogenes]
 gi|13622997|gb|AAK34668.1| collagen-like surface protei [Streptococcus pyogenes M1 GAS]
          Length = 348

 Score = 40.9 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 13/134 (9%), Positives = 30/134 (22%)

Query: 220 YGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVP 279
           YG +          ++ ++K L+E L        + +      +     + +        
Sbjct: 77  YGTYFKEEDFQKELKDFTEKRLKEILDLIGKSGIKGDRGETGPAGPAGPQGKTGERGAQG 136

Query: 280 DDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
               R ++    K G   ++                 A        +             
Sbjct: 137 PKGDRGEQGIQGKAGEKGERGEKGDKGETGERGEKGEAGIQGPQGEAGKDGAPGKDGAPG 196

Query: 340 SFPSKRSLRRTSAK 353
               K     T A+
Sbjct: 197 EKGEKGDRGETGAQ 210


>gi|195153275|ref|XP_002017554.1| GL17248 [Drosophila persimilis]
 gi|194113350|gb|EDW35393.1| GL17248 [Drosophila persimilis]
          Length = 323

 Score = 40.9 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 15/118 (12%), Positives = 34/118 (28%), Gaps = 1/118 (0%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNI-ISEVPDDFTRMKKNSSQKNGLS 296
              +R++ G  L E+            +       +  I    D   R ++ S Q+   S
Sbjct: 58  PDTIRKEFGWFLPEKTSAPKPPTTLGIQAAKCRWEDDVIPREGDQAPRREETSPQREKTS 117

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            Q++   P    +       A        ++ G        +P+     +    +  +
Sbjct: 118 PQREGDQPPEGGDTPPEGEDAPAEGGDAPAEGGDAPAEGGDAPAEGEAPAEGGDAPAE 175


>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 = 40.9 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 27/240 (11%), Positives = 60/240 (25%), Gaps = 42/240 (17%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKV--------------NGILLERAA 51
           V++ F   R+   +++     SR  ++ +I Q  V V              + I +    
Sbjct: 8   VEKEFDNVRLDLYLSKIFEDKSRSYLQGIIDQGSVLVNNKKKKRNYKLKVGDNIEVNIPE 67

Query: 52  ---VNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
              + +   D I++D   +   ++  + +      +V         + V   L       
Sbjct: 68  PKLLQIEPED-IKLD---IIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNALLHHCKDLS 123

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD------------ 156
              G         +     G L       S   L                          
Sbjct: 124 GINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGIIKDEQG 183

Query: 157 --------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                         K  V++   +      +  +  ++  V   L  G+  +I+      
Sbjct: 184 TIEAPIGRHPVDRIKMAVVKDGRHAVTHYKVIERFKNHTLVECRLETGRTHQIRVHMSHI 243


>gi|167629352|ref|YP_001679851.1| heat shock s4 domain protein [Heliobacterium modesticaldum Ice1]
 gi|167592092|gb|ABZ83840.1| heat shock s4 domain protein [Heliobacterium modesticaldum Ice1]
          Length = 87

 Score = 40.9 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   + +    RV VNG   + A   V   D + +
Sbjct: 1  MRLDKFLKVSRIIKRRTLAKEVCDGGRVTVNGRPAK-AGTEVQPGDRLTL 49


>gi|90422069|ref|YP_530439.1| helicase-like [Rhodopseudomonas palustris BisB18]
 gi|90104083|gb|ABD86120.1| helicase-like [Rhodopseudomonas palustris BisB18]
          Length = 1169

 Score = 40.9 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 11/114 (9%), Positives = 24/114 (21%), Gaps = 3/114 (2%)

Query: 240  ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
             L E   P    +                  +    +   +     +    +    ++ +
Sbjct: 999  ELVEVWRPGGRADDHRPRHDRNRYRNPDRAAQAGQPASAGEAGEAEQGKGDRP---NRGR 1055

Query: 300  KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            +   P  RR        A     +       R     R P    +   +    K
Sbjct: 1056 RDRKPEFRRPRTDAPVAAAADAPAAEGTPDARPAQAPRPPRDRERFQGKGGRGK 1109


>gi|206589575|emb|CAQ36536.1| putative magnesium-chelatase subunit chli homolog (partial
           sequence) protein [Ralstonia solanacearum MolK2]
          Length = 1456

 Score = 40.9 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 13/113 (11%), Positives = 26/113 (23%), Gaps = 2/113 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R Q  P     A+         S        +          R++++  +       +  
Sbjct: 399 RRQAQPRHRHAARPRHRRGAERSTVPAGGGRHAAPRAAAQPGRLQRDPRRPARAGPCRPP 458

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR-RSPSFPSKRSLRRTSAK 353
             P         +      H +       R    R  +P       L R + +
Sbjct: 459 GQPDPAGGGRLRLDGRAPPHGAGQGRR-ARPAAGRLPAPRPGGADLLPRRAGR 510



 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 6/105 (5%), Positives = 14/105 (13%)

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
                                   + +          +  +         ++ A     R
Sbjct: 397 RHRRQAQPRHRHAARPRHRRGAERSTVPAGGGRHAAPRAAAQPGRLQRDPRRPARAGPCR 456

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                     G                RR+     +    R    
Sbjct: 457 PPGQPDPAGGGRLRLDGRAPPHGAGQGRRARPAAGRLPAPRPGGA 501


>gi|312144221|ref|YP_003995667.1| ribosomal protein S4 [Halanaerobium sp. 'sapolanicus']
 gi|311904872|gb|ADQ15313.1| ribosomal protein S4 [Halanaerobium sp. 'sapolanicus']
          Length = 208

 Score = 40.9 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 1/40 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVN 53
           R+  V+ R G AS R E  + +    +KVNG  ++  +  
Sbjct: 99  RLDNVVYRMGFASSRNEARQFVLHGHIKVNGRKVDIPSYQ 138


>gi|149280100|ref|ZP_01886224.1| hypothetical protein PBAL39_10945 [Pedobacter sp. BAL39]
 gi|149229114|gb|EDM34509.1| hypothetical protein PBAL39_10945 [Pedobacter sp. BAL39]
          Length = 479

 Score = 40.9 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 16/148 (10%), Positives = 38/148 (25%), Gaps = 7/148 (4%)

Query: 213 NRLIRIS-YGPFQLGTLLAGSTRE-----VSKKILREQLGPHLLEEAQVNLDAPIYSSET 266
            ++ R+          L   + +E     V   ++ +      +                
Sbjct: 271 LKVDRVKEIMAMNKKGLKPSNLKEEAVELVHAAVVEKVHDYENVVGQDSLTRLDDKPKNK 330

Query: 267 LVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLS 326
             R+  N  ++  +   R ++N   +      +      +  N        +G       
Sbjct: 331 GNRNNRNKGADRGERGERSERNDRAEQRNGGNRNPEQKANSGNRNDR-GQKQGGQGKSRP 389

Query: 327 DSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +   R E   RS     + +  R    K
Sbjct: 390 EGAARPEQQNRSEGSRPENNRNREQQAK 417


>gi|110802506|ref|YP_699734.1| S4 domain-containing protein [Clostridium perfringens SM101]
 gi|110683007|gb|ABG86377.1| S4 domain protein [Clostridium perfringens SM101]
          Length = 86

 Score = 40.9 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR   +      RV +NG + +  + ++   D IE+
Sbjct: 1  MRLDKYLKVSRIIKRRTVAKEACESGRVIINGKVAK-PSNDIKEEDIIEI 49


>gi|11096139|gb|AAG30209.1|AF296329_1 collagen-like surface protein [Streptococcus pyogenes]
          Length = 309

 Score = 40.9 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 13/134 (9%), Positives = 30/134 (22%)

Query: 220 YGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVP 279
           YG +          ++ ++K L+E L        + +      +     + +        
Sbjct: 77  YGTYFKEEDFQKELKDFTEKRLKEILDLIGKSGIKGDRGETGPAGPAGPQGKTGERGAQG 136

Query: 280 DDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
               R ++    K G   ++                 A        +             
Sbjct: 137 PKGDRGEQGIQGKAGEKGERGEKGDKGETGERGEKGEAGIQGPQGEAGKDGAPGKDGAPG 196

Query: 340 SFPSKRSLRRTSAK 353
               K     T A+
Sbjct: 197 EKGEKGDRGETGAQ 210


>gi|39997623|ref|NP_953574.1| hypothetical protein GSU2528 [Geobacter sulfurreducens PCA]
 gi|39984515|gb|AAR35901.1| conserved domain protein [Geobacter sulfurreducens PCA]
          Length = 704

 Score = 40.9 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 9/118 (7%), Positives = 23/118 (19%), Gaps = 3/118 (2%)

Query: 229 LAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
                R++  + +R        +   V           + R       E     +  ++ 
Sbjct: 497 PPERIRKLKPEEVRRDRRTVPGDAGSVFSPGRQADEMRVKRRETPHRQEAAPAPSGSRQG 556

Query: 289 SSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
                G             +   +                  R ++  R P    +  
Sbjct: 557 G---KGAGLPSGRERTPEGKGRNAPPPPVPRAVPGKAPSPPPRPDDAVRQPRVQQRSP 611


>gi|21220050|ref|NP_625829.1| protein kinase [Streptomyces coelicolor A3(2)]
 gi|7106668|emb|CAB76070.1| putative eukaryotic-type protein kinase [Streptomyces coelicolor
           A3(2)]
          Length = 493

 Score = 40.9 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 12/119 (10%), Positives = 17/119 (14%), Gaps = 11/119 (9%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P   E             E   R              R    S                
Sbjct: 295 APRSGEADVPTGRLADTYPERAQRRPQGRPGPQGTPAPRGTSASRGSAPRGSVPSRGGAP 354

Query: 306 HRRNLASNVWMAKG-----------IHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            R    S                    S       +       S +   + + R  S +
Sbjct: 355 SRGGTPSRGGTPSRGGTSSRGGGTGARSGSRPTPTRDTTGRNSSRNDGGRPAPRGGSGR 413


>gi|85707561|ref|ZP_01038631.1| S4 domain protein [Roseovarius sp. 217]
 gi|85667918|gb|EAQ22809.1| S4 domain protein [Roseovarius sp. 217]
          Length = 126

 Score = 40.9 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 11/57 (19%), Positives = 23/57 (40%), Gaps = 1/57 (1%)

Query: 7  VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          +       R+ K + +A    +R    + ++   V+VNG  + + A  V   D +  
Sbjct: 1  MDGPGVKIRLDKWLWQARFFKTRTLAAKEVSAGHVRVNGARVSKPAQAVGPQDVLTF 57


>gi|74003832|ref|XP_848551.1| PREDICTED: similar to serine/threonine-protein kinase PRP4K isoform
           3 [Canis familiaris]
 gi|74003834|ref|XP_545321.2| PREDICTED: similar to serine/threonine-protein kinase PRP4K isoform
           1 [Canis familiaris]
 gi|74003836|ref|XP_856489.1| PREDICTED: similar to serine/threonine-protein kinase PRP4K isoform
           5 [Canis familiaris]
 gi|74003838|ref|XP_856532.1| PREDICTED: similar to serine/threonine-protein kinase PRP4K isoform
           6 [Canis familiaris]
 gi|74003840|ref|XP_856573.1| PREDICTED: similar to serine/threonine-protein kinase PRP4K isoform
           7 [Canis familiaris]
 gi|74003842|ref|XP_856614.1| PREDICTED: similar to serine/threonine-protein kinase PRP4K isoform
           8 [Canis familiaris]
 gi|74003844|ref|XP_856655.1| PREDICTED: similar to serine/threonine-protein kinase PRP4K isoform
           9 [Canis familiaris]
 gi|74003846|ref|XP_856692.1| PREDICTED: similar to serine/threonine-protein kinase PRP4K isoform
           10 [Canis familiaris]
 gi|74003848|ref|XP_856733.1| PREDICTED: similar to serine/threonine-protein kinase PRP4K isoform
           11 [Canis familiaris]
 gi|74003850|ref|XP_856777.1| PREDICTED: similar to serine/threonine-protein kinase PRP4K isoform
           12 [Canis familiaris]
 gi|74003852|ref|XP_856817.1| PREDICTED: similar to serine/threonine-protein kinase PRP4K isoform
           13 [Canis familiaris]
 gi|74003854|ref|XP_856855.1| PREDICTED: similar to serine/threonine-protein kinase PRP4K isoform
           14 [Canis familiaris]
          Length = 1042

 Score = 40.9 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 15/105 (14%), Positives = 31/105 (29%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            + ++++                     S  P D     K+   ++   K K+  T   +
Sbjct: 298 KIEDKSRSKDRKKSPIINESRSRDRGKKSRSPVDLRGKSKDRRSRSKERKSKRSDTDKEK 357

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           + + S    A     +            RRS S   +   RR+ +
Sbjct: 358 KPIKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKQRDKSRRSRS 402



 Score = 38.2 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 13/113 (11%), Positives = 37/113 (32%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +++    ++ E++         S   +R +         +    + ++ ++    K    
Sbjct: 306 KDRKKSPIINESRSRDRGKKSRSPVDLRGKSKDRRSRSKERKSKRSDTDKEKKPIKSPSK 365

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                + N + +    +      LS   + +    RSP    +RS +  S  +
Sbjct: 366 DASSGKENRSPSRRPGRSPKRRSLSPKQRDKSRRSRSPLVNDRRSKQSKSPSR 418



 Score = 37.5 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 20/131 (15%), Positives = 39/131 (29%), Gaps = 8/131 (6%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             R+     LR +    + +      D      ++  +DR               K S  
Sbjct: 269 QARKSKSPTLRRRSQEKIGKARSPPDDKVKIEDKSRSKDRKKSPIINESRSRDRGKKSRS 328

Query: 292 K---NGLSKQKKLATPVHRRNLASNVWMAKG-IHSSFLSDSGQREENHRRSPSFPSKR-- 345
                G SK ++  +   +   +      K     S  + SG+   +  R P    KR  
Sbjct: 329 PVDLRGKSKDRRSRSKERKSKRSDTDKEKKPIKSPSKDASSGKENRSPSRRPGRSPKRRS 388

Query: 346 --SLRRTSAKK 354
               +R  +++
Sbjct: 389 LSPKQRDKSRR 399


>gi|188584864|ref|YP_001916409.1| SSU ribosomal protein S4P [Natranaerobius thermophilus JW/NM-WN-LF]
 gi|226699094|sp|B2A4P9|RS4_NATTJ RecName: Full=30S ribosomal protein S4
 gi|179349551|gb|ACB83821.1| SSU ribosomal protein S4P [Natranaerobius thermophilus JW/NM-WN-LF]
          Length = 209

 Score = 40.9 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 1/42 (2%)

Query: 22  RAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R G A SR E  + +    + VNG  +  A+  V   D + V
Sbjct: 107 RMGFAASRAEARQFVNHGHIMVNGKRVNVASYEVKPGDEVVV 148


>gi|16264922|ref|NP_437714.1| putative ATP-dependent RNA helicase protein [Sinorhizobium meliloti
           1021]
 gi|15141061|emb|CAC49574.1| putative ATP-dependent RNA helicase protein [Sinorhizobium meliloti
           1021]
          Length = 503

 Score = 40.9 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 13/131 (9%), Positives = 30/131 (22%), Gaps = 15/131 (11%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
              +R       L   Q+ + +    ++     +              +   +       
Sbjct: 352 PDEIRLLRDIEKLMGIQIAVASGEAPADQARPSKGRGGRGNGQPRGNGQPRGNGAGQRQG 411

Query: 298 QKKLATPVHR---------------RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
             +   P  +               R+       A G   +     G R    ++    P
Sbjct: 412 GPRRDRPQRQAAAGGFAGDELLRDERSHERRDQRAAGHGPADGRPEGHRNHKAQKHHGRP 471

Query: 343 SKRSLRRTSAK 353
             +  RR S +
Sbjct: 472 GPQQARRGSEQ 482


>gi|293351338|ref|XP_220207.5| PREDICTED: serine/arginine repetitive matrix 2 [Rattus norvegicus]
          Length = 2050

 Score = 40.9 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 14/98 (14%), Positives = 31/98 (31%), Gaps = 2/98 (2%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
             A  +      + R    S     ++R +    +    S ++  +          +   
Sbjct: 379 RSAQRWGKSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRSHSRSPATRGRSRSR 438

Query: 317 AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                    S +  R  +  R+P+   +RS  RT A++
Sbjct: 439 TPARRGRSRSRTPARRRSRSRTPAR--RRSRSRTPARR 474



 Score = 39.8 bits (91), Expect = 0.60,   Method: Composition-based stats.
 Identities = 9/96 (9%), Positives = 17/96 (17%)

Query: 259 APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAK 318
                     R                 ++  +      +        R           
Sbjct: 369 RSRSPQWRRSRSAQRWGKSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRSHSRS 428

Query: 319 GIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                             RS +   +RS  RT A++
Sbjct: 429 PATRGRSRSRTPARRGRSRSRTPARRRSRSRTPARR 464



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 12/105 (11%), Positives = 22/105 (20%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              L         P+ +       R            +    S       + +    P  
Sbjct: 345 LRSLLSNMATPHDPLQTPTKRGHSRSRSPQWRRSRSAQRWGKSRSPQRRGRSRSPQRPGW 404

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
            R+  +             S S       R     P++R   R+ 
Sbjct: 405 SRSRNTQRRGRSRSARRGRSHSRSPATRGRSRSRTPARRGRSRSR 449


>gi|21222630|ref|NP_628409.1| cysteinyl-tRNA synthetase [Streptomyces coelicolor A3(2)]
 gi|30316185|sp|Q9L0Q6|SYC_STRCO RecName: Full=Cysteinyl-tRNA synthetase; AltName:
           Full=Cysteine--tRNA ligase; Short=CysRS
 gi|7242756|emb|CAB77329.1| putative cysteinyl-tRNA synthetase [Streptomyces coelicolor A3(2)]
          Length = 613

 Score = 40.9 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 27/111 (24%), Gaps = 7/111 (6%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK---LA 302
           G       + +   P   S    R  P       D     +     +    +  +    A
Sbjct: 6   GTPRRPAVRGSAPHPARGSAPGPRPMPTHHPTRGDKKRARRPGVPTRGDKKRAPRLGVPA 65

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS----PSFPSKRSLRR 349
               +R     V   +    +       R +  R      P+   K+  RR
Sbjct: 66  RGDKKRARRPGVPAREDKKRAPRPGVPTRGDKKRAPRLGVPARGDKKRARR 116



 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 9/97 (9%), Positives = 20/97 (20%)

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
            +    +      R +            +   +       +K+   P             
Sbjct: 1   MSAGAGTPRRPAVRGSAPHPARGSAPGPRPMPTHHPTRGDKKRARRPGVPTRGDKKRAPR 60

Query: 318 KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            G+ +       +R     R     + R    T   K
Sbjct: 61  LGVPARGDKKRARRPGVPAREDKKRAPRPGVPTRGDK 97



 Score = 37.1 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 11/94 (11%), Positives = 21/94 (22%), Gaps = 2/94 (2%)

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
                      R        +       KK + +    +++ K   P        +   A
Sbjct: 41  KKRARRPGVPTRGDKKRAPRLGVPARGDKKRARRPGVPAREDKKRAPRPGVPTRGDKKRA 100

Query: 318 K--GIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
              G+ +       +R     R     S     R
Sbjct: 101 PRLGVPARGDKKRARRPGVPTRGGVARSGNDGPR 134


>gi|134298120|ref|YP_001111616.1| 30S ribosomal protein S4 [Desulfotomaculum reducens MI-1]
 gi|172044238|sp|A4J138|RS4_DESRM RecName: Full=30S ribosomal protein S4
 gi|134050820|gb|ABO48791.1| SSU ribosomal protein S4P [Desulfotomaculum reducens MI-1]
          Length = 208

 Score = 40.9 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 1/42 (2%)

Query: 22  RAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R G+  SR E  +++      VNG  +   +  V   D I V
Sbjct: 106 RLGLGASRVEARQLVRHGHFTVNGKKVNIPSFQVRVGDEIAV 147


>gi|311263994|ref|XP_003129944.1| PREDICTED: hypothetical protein LOC100511339 [Sus scrofa]
          Length = 504

 Score = 40.9 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 10/120 (8%), Positives = 29/120 (24%), Gaps = 3/120 (2%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R+ +++ L              +        E     + N                    
Sbjct: 260 RKSTEQQLAAGARRGWPA---PSPTLSCCFPEPARPLKKNPSRTREPRQRARSGGRRAAR 316

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              +  +   P    +  + V  A+            ++   + +P+ P +   ++  A 
Sbjct: 317 RRGEGPRANAPRRPADGDTAVARAQLGRDPAHQSPPLQDAPLQPAPALPGRGGRKKGKAS 376


>gi|302561720|ref|ZP_07314062.1| 30S ribosomal protein S4 [Streptomyces griseoflavus Tu4000]
 gi|302479338|gb|EFL42431.1| 30S ribosomal protein S4 [Streptomyces griseoflavus Tu4000]
          Length = 204

 Score = 40.9 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 28/50 (56%), Gaps = 3/50 (6%)

Query: 15  RVSKVIARAGIASRR--EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R+GIA R   +  +M+    ++VNG  +++ +  V   D ++V
Sbjct: 93  RLDALVLRSGIA-RTIYQARQMVVHGHIQVNGKKVDKPSFRVRPDDVVQV 141


>gi|26399364|sp|P59132|RS4_SHIFL RecName: Full=30S ribosomal protein S4
          Length = 206

 Score = 40.9 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 12/73 (16%), Positives = 30/73 (41%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + V G ++  A+  V   D + +     +++   
Sbjct: 97  RLDNVVYRMGFGATRAEARQLVSHKAIMVPGRVVNIASYQVSPNDVVSIREKAKKQSRVK 156

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 157 AALELAEQREKPT 169


>gi|332845061|ref|XP_003314977.1| PREDICTED: hypothetical protein LOC453842 [Pan troglodytes]
          Length = 2752

 Score = 40.9 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 9/108 (8%), Positives = 21/108 (19%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                            S   +     +              + +    + + +  AT  
Sbjct: 432 RHASSSPESPKPAPAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAK 491

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R+ +          S        R          P +R   R+  +
Sbjct: 492 RGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQR 539



 Score = 40.5 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 13/107 (12%), Positives = 25/107 (23%), Gaps = 1/107 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P      +++      +       R    S  P       ++ +       + +  T  
Sbjct: 444 APAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKR 503

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                 S  W        +      +     RSP  P   S  R + 
Sbjct: 504 GHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPGW-SRSRNTQ 549



 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 22/135 (16%), Positives = 34/135 (25%), Gaps = 10/135 (7%)

Query: 230 AGSTREV----SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
            GS RE+    + K             +         S       R    S  P      
Sbjct: 447 PGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKRGHS 506

Query: 286 KKNSSQKNGLSKQKK--LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
           +  S Q       ++   +    RR  + +        S      G+     R      S
Sbjct: 507 RSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRSHSRS 566

Query: 344 K----RSLRRTSAKK 354
                RS  RT A++
Sbjct: 567 PATRGRSRSRTPARR 581


>gi|168272954|dbj|BAG10316.1| serine/arginine repetitive matrix protein 2 [synthetic construct]
          Length = 2752

 Score = 40.9 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 9/108 (8%), Positives = 21/108 (19%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                            S   +     +              + +    + + +  AT  
Sbjct: 432 RHASSSPESPKPAPAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAK 491

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R+ +          S        R          P +R   R+  +
Sbjct: 492 RGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQR 539



 Score = 40.5 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 11/98 (11%), Positives = 22/98 (22%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P      +++      +       R    S  P       ++ +       + +  T  
Sbjct: 444 APAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKR 503

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
                 S  W        +      +     RSP  P 
Sbjct: 504 GHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPG 541



 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 22/135 (16%), Positives = 34/135 (25%), Gaps = 10/135 (7%)

Query: 230 AGSTREV----SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
            GS RE+    + K             +         S       R    S  P      
Sbjct: 447 PGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKRGHS 506

Query: 286 KKNSSQKNGLSKQKK--LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
           +  S Q       ++   +    RR  + +        S      G+     R      S
Sbjct: 507 RSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRSHSRS 566

Query: 344 K----RSLRRTSAKK 354
                RS  RT A++
Sbjct: 567 PATRGRSRSRTPARR 581


>gi|118572613|ref|NP_057417.3| serine/arginine repetitive matrix protein 2 [Homo sapiens]
 gi|143928063|sp|Q9UQ35|SRRM2_HUMAN RecName: Full=Serine/arginine repetitive matrix protein 2; AltName:
           Full=300 kDa nuclear matrix antigen; AltName:
           Full=Serine/arginine-rich splicing factor-related
           nuclear matrix protein of 300 kDa; Short=SR-related
           nuclear matrix protein of 300 kDa; Short=Ser/Arg-related
           nuclear matrix protein of 300 kDa; AltName:
           Full=Splicing coactivator subunit SRm300; AltName:
           Full=Tax-responsive enhancer element-binding protein
           803; Short=TaxREB803
 gi|119605883|gb|EAW85477.1| serine/arginine repetitive matrix 2, isoform CRA_a [Homo sapiens]
 gi|119605886|gb|EAW85480.1| serine/arginine repetitive matrix 2, isoform CRA_a [Homo sapiens]
          Length = 2752

 Score = 40.9 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 9/108 (8%), Positives = 21/108 (19%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                            S   +     +              + +    + + +  AT  
Sbjct: 432 RHASSSPESPKPAPAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAK 491

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R+ +          S        R          P +R   R+  +
Sbjct: 492 RGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQR 539



 Score = 40.5 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 11/98 (11%), Positives = 22/98 (22%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P      +++      +       R    S  P       ++ +       + +  T  
Sbjct: 444 APAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKR 503

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
                 S  W        +      +     RSP  P 
Sbjct: 504 GHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPG 541



 Score = 38.2 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 22/135 (16%), Positives = 34/135 (25%), Gaps = 10/135 (7%)

Query: 230 AGSTREV----SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
            GS RE+    + K             +         S       R    S  P      
Sbjct: 447 PGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKRGHS 506

Query: 286 KKNSSQKNGLSKQKK--LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
           +  S Q       ++   +    RR  + +        S      G+     R      S
Sbjct: 507 RSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRSHSRS 566

Query: 344 K----RSLRRTSAKK 354
                RS  RT A++
Sbjct: 567 PATRGRSRSRTPARR 581


>gi|16799325|ref|NP_469593.1| hypothetical protein lin0248 [Listeria innocua Clip11262]
 gi|116871598|ref|YP_848379.1| S4 RNA-binding domain-containing protein [Listeria welshimeri
          serovar 6b str. SLCC5334]
 gi|16412677|emb|CAC95481.1| lin0248 [Listeria innocua Clip11262]
 gi|116740476|emb|CAK19596.1| S4 RNA-binding domain protein [Listeria welshimeri serovar 6b
          str. SLCC5334]
 gi|313625443|gb|EFR95198.1| S4 RNA-binding domain-containing protein [Listeria innocua FSL
          J1-023]
          Length = 92

 Score = 40.9 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 15/80 (18%), Positives = 26/80 (32%), Gaps = 4/80 (5%)

Query: 12 TPQRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLR 68
          T  R+ K +  + +  RR   + +  + R+ VNG+  +    NV S D   I      + 
Sbjct: 3  TTMRLDKYLKVSRLIKRRTVAKEVAEKGRIAVNGVTAK-PGTNVKSGDELVIRFGPKIVT 61

Query: 69 KAERTRLWLYHKPIGLVTTH 88
                     K        
Sbjct: 62 AKIERLEENAKKEQATEMYT 81


>gi|5821153|dbj|BAA83718.1| RNA binding protein [Homo sapiens]
          Length = 2752

 Score = 40.9 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 9/108 (8%), Positives = 21/108 (19%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                            S   +     +              + +    + + +  AT  
Sbjct: 432 RHASSSPESPKPAPAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAK 491

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R+ +          S        R          P +R   R+  +
Sbjct: 492 RGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQR 539



 Score = 40.5 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 11/98 (11%), Positives = 22/98 (22%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P      +++      +       R    S  P       ++ +       + +  T  
Sbjct: 444 APAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKR 503

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
                 S  W        +      +     RSP  P 
Sbjct: 504 GHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPG 541



 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 22/135 (16%), Positives = 34/135 (25%), Gaps = 10/135 (7%)

Query: 230 AGSTREV----SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
            GS RE+    + K             +         S       R    S  P      
Sbjct: 447 PGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKRGHS 506

Query: 286 KKNSSQKNGLSKQKK--LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
           +  S Q       ++   +    RR  + +        S      G+     R      S
Sbjct: 507 RSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRSHSRS 566

Query: 344 K----RSLRRTSAKK 354
                RS  RT A++
Sbjct: 567 PATRGRSRSRTPARR 581


>gi|301791476|ref|XP_002930707.1| PREDICTED: hypothetical protein LOC100480895 [Ailuropoda
           melanoleuca]
          Length = 630

 Score = 40.9 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 8/85 (9%), Positives = 15/85 (17%)

Query: 266 TLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFL 325
           +      +  S    D    +K+   +      ++      RR  A              
Sbjct: 489 SRGAQVHSKRSSRISDSGTNRKDPLCREDPGGGRRAEPKGLRRKSAQGRRRGAAGRPGRA 548

Query: 326 SDSGQREENHRRSPSFPSKRSLRRT 350
              G                   R 
Sbjct: 549 RPPGPGRIPGAERRPRVESPDRPRG 573



 Score = 37.5 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 17/107 (15%), Positives = 31/107 (28%), Gaps = 2/107 (1%)

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           +G      AQV+       S++    +  +  E P    R +    ++     +++ A  
Sbjct: 484 VGMAGSRGAQVHSKRSSRISDSGTNRKDPLCREDPGGGRRAEPKGLRRKSAQGRRRGAAG 543

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREEN--HRRSPSFPSKRSLRR 349
              R          G       +S  R      RR P      +  R
Sbjct: 544 RPGRARPPGPGRIPGAERRPRVESPDRPRGEWGRRRPRRADDPTAGR 590


>gi|317505828|ref|ZP_07963673.1| ribosomal protein S4 [Segniliparus rugosus ATCC BAA-974]
 gi|316255910|gb|EFV15135.1| ribosomal protein S4 [Segniliparus rugosus ATCC BAA-974]
          Length = 201

 Score = 40.5 bits (93), Expect = 0.34,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI RAG+A +RR   +++      VN   ++  +  V   D I+V
Sbjct: 92  RLDNVIYRAGLARTRRHARQLVTHGHFLVNQKRVDVPSYRVSQYDIIDV 140


>gi|56480311|ref|NP_709084.2| 30S ribosomal protein S4 [Shigella flexneri 2a str. 301]
 gi|56383862|gb|AAN44791.2| 30S ribosomal subunit protein S4 [Shigella flexneri 2a str. 301]
          Length = 202

 Score = 40.5 bits (93), Expect = 0.34,   Method: Composition-based stats.
 Identities = 12/73 (16%), Positives = 30/73 (41%), Gaps = 1/73 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V+ R G   +R E  ++++ + + V G ++  A+  V   D + +     +++   
Sbjct: 93  RLDNVVYRMGFGATRAEARQLVSHKAIMVPGRVVNIASYQVSPNDVVSIREKAKKQSRVK 152

Query: 74  RLWLYHKPIGLVT 86
                 +     T
Sbjct: 153 AALELAEQREKPT 165


>gi|3043596|dbj|BAA25462.1| KIAA0536 protein [Homo sapiens]
          Length = 1028

 Score = 40.5 bits (93), Expect = 0.34,   Method: Composition-based stats.
 Identities = 15/105 (14%), Positives = 31/105 (29%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            + ++++                     S  P D     K+   ++   K K+  T   +
Sbjct: 285 KIEDKSKSKDRKKSPIINESRSRDRGKKSRSPVDLRGKSKDRRSRSKERKSKRSETDKEK 344

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           + + S    A     +            RRS S   +   RR+ +
Sbjct: 345 KPIKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKPRDKSRRSRS 389



 Score = 37.1 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 13/107 (12%), Positives = 33/107 (30%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            ++ E++         S   +R +         +    +  + ++    K         +
Sbjct: 299 PIINESRSRDRGKKSRSPVDLRGKSKDRRSRSKERKSKRSETDKEKKPIKSPSKDASSGK 358

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            N + +    +      LS   + +    RSP    +RS +  S  +
Sbjct: 359 ENRSPSRRPGRSPKRRSLSPKPRDKSRRSRSPLLNDRRSKQSKSPSR 405


>gi|328883901|emb|CCA57140.1| putative ATP-dependent RNA helicase [Streptomyces venezuelae ATCC
           10712]
          Length = 772

 Score = 40.5 bits (93), Expect = 0.34,   Method: Composition-based stats.
 Identities = 14/121 (11%), Positives = 29/121 (23%), Gaps = 10/121 (8%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM---------KKNSSQK 292
           R+  G    E    +  +  +  +       N        F R          +++    
Sbjct: 630 RDDRGGRSFERRDNDRPSGGFRRDDRPSGGFNRDDRGGRSFERRDNDRPSGGFRRDDRPS 689

Query: 293 NGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            G ++  +      RR+   +                 R     R P    +   RR   
Sbjct: 690 GGFNRDDRGGRSFDRRDDRPSGGHRGSDRPFNRDRRDDRPSGGFR-PGGGDRPYGRRDDH 748

Query: 353 K 353
           +
Sbjct: 749 R 749



 Score = 39.8 bits (91), Expect = 0.71,   Method: Composition-based stats.
 Identities = 10/109 (9%), Positives = 19/109 (17%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+  G    E    +  +  +  +       N        F R   +          +  
Sbjct: 598 RDDRGGRSFERRDNDRPSGGFRRDDRPSGGFNRDDRGGRSFERRDNDRPSGGFRRDDRPS 657

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                      +         S       R            +   RR 
Sbjct: 658 GGFNRDDRGGRSFERRDNDRPSGGFRRDDRPSGGFNRDDRGGRSFDRRD 706



 Score = 37.5 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 11/91 (12%), Positives = 18/91 (19%), Gaps = 4/91 (4%)

Query: 267 LVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM----AKGIHS 322
              DRP+      D   R  +           ++   P    N                 
Sbjct: 587 RRDDRPSGGFNRDDRGGRSFERRDNDRPSGGFRRDDRPSGGFNRDDRGGRSFERRDNDRP 646

Query: 323 SFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           S       R            +   RR + +
Sbjct: 647 SGGFRRDDRPSGGFNRDDRGGRSFERRDNDR 677



 Score = 35.9 bits (81), Expect = 9.2,   Method: Composition-based stats.
 Identities = 14/109 (12%), Positives = 25/109 (22%), Gaps = 4/109 (3%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+  G    E    +  +  +  +       N        F R     S  +  S +   
Sbjct: 662 RDDRGGRSFERRDNDRPSGGFRRDDRPSGGFNRDDRGGRSFDRRDDRPSGGHRGSDRPFN 721

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDS-GQREENHRRSPSFPSKRSLRR 349
                RR+   +     G            R      +  F  +    R
Sbjct: 722 RD---RRDDRPSGGFRPGGGDRPYGRRDDHRGTGTGSAGGFARRDDKPR 767


>gi|319638355|ref|ZP_07993117.1| hsp15-like protein [Neisseria mucosa C102]
 gi|317400104|gb|EFV80763.1| hsp15-like protein [Neisseria mucosa C102]
          Length = 133

 Score = 40.5 bits (93), Expect = 0.34,   Method: Composition-based stats.
 Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 6/61 (9%)

Query: 1  MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          MK+      + +  R+ K + A     +R   ++ I   RV VNG  ++  + N+ + D 
Sbjct: 1  MKN----NHDNSSMRLDKWLWAARFFKTRALAQKHIELGRVLVNGSKVKN-SKNISAGDT 55

Query: 60 I 60
          I
Sbjct: 56 I 56


>gi|23271009|gb|AAH34969.1| PRP4 pre-mRNA processing factor 4 homolog B (yeast) [Homo sapiens]
          Length = 1007

 Score = 40.5 bits (93), Expect = 0.34,   Method: Composition-based stats.
 Identities = 15/105 (14%), Positives = 31/105 (29%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            + ++++                     S  P D     K+   ++   K K+  T   +
Sbjct: 264 KIEDKSKSKDRKKSPIINESRSRDRGKKSRSPVDLRGKSKDRRSRSKERKSKRSETDKEK 323

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           + + S    A     +            RRS S   +   RR+ +
Sbjct: 324 KPIKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKPRDKSRRSRS 368



 Score = 37.1 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 13/107 (12%), Positives = 33/107 (30%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            ++ E++         S   +R +         +    +  + ++    K         +
Sbjct: 278 PIINESRSRDRGKKSRSPVDLRGKSKDRRSRSKERKSKRSETDKEKKPIKSPSKDASSGK 337

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            N + +    +      LS   + +    RSP    +RS +  S  +
Sbjct: 338 ENRSPSRRPGRSPKRRSLSPKPRDKSRRSRSPLLNDRRSKQSKSPSR 384


>gi|29833389|ref|NP_828023.1| 30S ribosomal protein S4 [Streptomyces avermitilis MA-4680]
 gi|41017832|sp|Q827S7|RS4_STRAW RecName: Full=30S ribosomal protein S4
 gi|29610512|dbj|BAC74558.1| putative ribosomal protein S4 [Streptomyces avermitilis MA-4680]
          Length = 204

 Score = 40.5 bits (93), Expect = 0.34,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 3/50 (6%)

Query: 15  RVSKVIARAGIASRR--EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R+GIA R   +  +M+    ++VNG  +++ +  V   D + V
Sbjct: 93  RLDALVLRSGIA-RTIYQARQMVVHGHIEVNGQKVDKPSFRVKPDDVVMV 141


>gi|296197494|ref|XP_002746301.1| PREDICTED: serine/threonine-protein kinase PRP4 homolog [Callithrix
           jacchus]
          Length = 1007

 Score = 40.5 bits (93), Expect = 0.35,   Method: Composition-based stats.
 Identities = 15/105 (14%), Positives = 31/105 (29%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            + ++++                     S  P D     K+   ++   K K+  T   +
Sbjct: 264 KIEDKSKSKDRKKSPIINESRSRDRGKRSRSPVDLRGKSKDRRSRSKERKSKRSETDKEK 323

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           + + S    A     +            RRS S   +   RR+ +
Sbjct: 324 KPIKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKPRDKSRRSRS 368



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 12/124 (9%), Positives = 29/124 (23%), Gaps = 6/124 (4%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           S    + ++      + +        S       R     ++       +  S ++    
Sbjct: 257 SPTDDKVKIEDKSKSKDRKKSPIINESRSRDRGKRSRSPVDLRGKSKDRRSRSKERKSKR 316

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL------RRT 350
            +        +          +    S       +  +    P   S+RS       RR+
Sbjct: 317 SETDKEKKPIKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKPRDKSRRSRSPLLNDRRS 376

Query: 351 SAKK 354
              K
Sbjct: 377 KQSK 380



 Score = 37.1 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 13/107 (12%), Positives = 33/107 (30%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            ++ E++         S   +R +         +    +  + ++    K         +
Sbjct: 278 PIINESRSRDRGKRSRSPVDLRGKSKDRRSRSKERKSKRSETDKEKKPIKSPSKDASSGK 337

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            N + +    +      LS   + +    RSP    +RS +  S  +
Sbjct: 338 ENRSPSRRPGRSPKRRSLSPKPRDKSRRSRSPLLNDRRSKQSKSPSR 384



 Score = 36.7 bits (83), Expect = 4.9,   Method: Composition-based stats.
 Identities = 19/119 (15%), Positives = 37/119 (31%), Gaps = 11/119 (9%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           + E       + ++  +D    S +   R +         D  +    S  K+  S ++ 
Sbjct: 280 INESRSRDRGKRSRSPVDLRGKSKDRRSRSKERKSKRSETDKEKKPIKSPSKDASSGKEN 339

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQ------REENHRRSPSF---PSKRSLRRT 350
            +    RR   S    +        S   +      R     +SPS    P +R+  R+
Sbjct: 340 RS--PSRRPGRSPKRRSLSPKPRDKSRRSRSPLLNDRRSKQSKSPSRTLSPGRRAKSRS 396


>gi|153807757|ref|ZP_01960425.1| hypothetical protein BACCAC_02040 [Bacteroides caccae ATCC 43185]
 gi|149129366|gb|EDM20580.1| hypothetical protein BACCAC_02040 [Bacteroides caccae ATCC 43185]
          Length = 140

 Score = 40.5 bits (93), Expect = 0.35,   Method: Composition-based stats.
 Identities = 17/91 (18%), Positives = 34/91 (37%), Gaps = 2/91 (2%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ K + A     +R        + RV +NG L++ AA  V   D I+V   P+  + + 
Sbjct: 5   RIDKWMWAVRIFKTRTIAAEACKKGRVTINGALVK-AARMVKPGDVIQVKKPPITYSFKV 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
              +  +    +      +  +     L  +
Sbjct: 64  LQAIEKRIGAKLVPEMMENVTTPDQYELLEM 94


>gi|197100068|ref|NP_001126223.1| serine/threonine-protein kinase PRP4 homolog [Pongo abelii]
 gi|75041493|sp|Q5R814|PRP4B_PONAB RecName: Full=Serine/threonine-protein kinase PRP4 homolog;
           AltName: Full=PRP4 pre-mRNA-processing factor 4 homolog
 gi|55730751|emb|CAH92096.1| hypothetical protein [Pongo abelii]
          Length = 1007

 Score = 40.5 bits (93), Expect = 0.35,   Method: Composition-based stats.
 Identities = 15/105 (14%), Positives = 31/105 (29%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            + ++++                     S  P D     K+   ++   K K+  T   +
Sbjct: 264 KIEDKSKSKDRKKSPIINESRSRDRGKKSRSPVDLRGKSKDRRSRSKERKSKRSETDKEK 323

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           + + S    A     +            RRS S   +   RR+ +
Sbjct: 324 KPIKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKPRDKSRRSRS 368



 Score = 37.1 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 13/107 (12%), Positives = 33/107 (30%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            ++ E++         S   +R +         +    +  + ++    K         +
Sbjct: 278 PIINESRSRDRGKKSRSPVDLRGKSKDRRSRSKERKSKRSETDKEKKPIKSPSKDASSGK 337

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            N + +    +      LS   + +    RSP    +RS +  S  +
Sbjct: 338 ENRSPSRRPGRSPKRRSLSPKPRDKSRRSRSPLLNDRRSKQSKSPSR 384


>gi|296272961|ref|YP_003655592.1| 30S ribosomal protein S4 [Arcobacter nitrofigilis DSM 7299]
 gi|296097135|gb|ADG93085.1| ribosomal protein S4 [Arcobacter nitrofigilis DSM 7299]
          Length = 208

 Score = 40.5 bits (93), Expect = 0.35,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 1/50 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           QR+  V+ R G A+ R    +      + V+G  ++  +  V     IE+
Sbjct: 98  QRLDNVVYRMGFATTRANARQFTTHGHILVDGQKVDIPSFVVKPGQKIEI 147


>gi|89276756|ref|NP_003904.3| serine/threonine-protein kinase PRP4 homolog [Homo sapiens]
 gi|317373526|sp|Q13523|PRP4B_HUMAN RecName: Full=Serine/threonine-protein kinase PRP4 homolog;
           AltName: Full=PRP4 kinase; AltName: Full=PRP4
           pre-mRNA-processing factor 4 homolog
 gi|56204543|emb|CAI20480.1| PRP4 pre-mRNA processing factor 4 homolog B (yeast) [Homo sapiens]
 gi|57208333|emb|CAI42121.1| PRP4 pre-mRNA processing factor 4 homolog B (yeast) [Homo sapiens]
 gi|119575550|gb|EAW55146.1| PRP4 pre-mRNA processing factor 4 homolog B (yeast), isoform CRA_a
           [Homo sapiens]
 gi|119575551|gb|EAW55147.1| PRP4 pre-mRNA processing factor 4 homolog B (yeast), isoform CRA_a
           [Homo sapiens]
 gi|119575552|gb|EAW55148.1| PRP4 pre-mRNA processing factor 4 homolog B (yeast), isoform CRA_a
           [Homo sapiens]
 gi|119575553|gb|EAW55149.1| PRP4 pre-mRNA processing factor 4 homolog B (yeast), isoform CRA_a
           [Homo sapiens]
 gi|119575554|gb|EAW55150.1| PRP4 pre-mRNA processing factor 4 homolog B (yeast), isoform CRA_a
           [Homo sapiens]
 gi|119575555|gb|EAW55151.1| PRP4 pre-mRNA processing factor 4 homolog B (yeast), isoform CRA_a
           [Homo sapiens]
          Length = 1007

 Score = 40.5 bits (93), Expect = 0.35,   Method: Composition-based stats.
 Identities = 15/105 (14%), Positives = 31/105 (29%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            + ++++                     S  P D     K+   ++   K K+  T   +
Sbjct: 264 KIEDKSKSKDRKKSPIINESRSRDRGKKSRSPVDLRGKSKDRRSRSKERKSKRSETDKEK 323

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           + + S    A     +            RRS S   +   RR+ +
Sbjct: 324 KPIKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKPRDKSRRSRS 368



 Score = 37.1 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 13/107 (12%), Positives = 33/107 (30%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            ++ E++         S   +R +         +    +  + ++    K         +
Sbjct: 278 PIINESRSRDRGKKSRSPVDLRGKSKDRRSRSKERKSKRSETDKEKKPIKSPSKDASSGK 337

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            N + +    +      LS   + +    RSP    +RS +  S  +
Sbjct: 338 ENRSPSRRPGRSPKRRSLSPKPRDKSRRSRSPLLNDRRSKQSKSPSR 384


>gi|332823214|ref|XP_518214.3| PREDICTED: serine/threonine-protein kinase PRP4 homolog [Pan
           troglodytes]
 gi|20330554|gb|AAM19101.1|AF283465_1 PRP4 kinase [Homo sapiens]
 gi|14571506|gb|AAK38155.1| serine/threonine-protein kinase [Homo sapiens]
 gi|168278643|dbj|BAG11201.1| serine/threonine-protein kinase PRP4 homolog [synthetic construct]
          Length = 1007

 Score = 40.5 bits (93), Expect = 0.35,   Method: Composition-based stats.
 Identities = 15/105 (14%), Positives = 31/105 (29%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            + ++++                     S  P D     K+   ++   K K+  T   +
Sbjct: 264 KIEDKSKSKDRKKSPIINESRSRDRGKKSRSPVDLRGKSKDRRSRSKERKSKRSETDKEK 323

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           + + S    A     +            RRS S   +   RR+ +
Sbjct: 324 KPIKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKPRDKSRRSRS 368



 Score = 37.1 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 13/107 (12%), Positives = 33/107 (30%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            ++ E++         S   +R +         +    +  + ++    K         +
Sbjct: 278 PIINESRSRDRGKKSRSPVDLRGKSKDRRSRSKERKSKRSETDKEKKPIKSPSKDASSGK 337

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            N + +    +      LS   + +    RSP    +RS +  S  +
Sbjct: 338 ENRSPSRRPGRSPKRRSLSPKPRDKSRRSRSPLLNDRRSKQSKSPSR 384


>gi|298506562|gb|ADI85285.1| FecR domain protein [Geobacter sulfurreducens KN400]
          Length = 626

 Score = 40.5 bits (93), Expect = 0.35,   Method: Composition-based stats.
 Identities = 9/118 (7%), Positives = 23/118 (19%), Gaps = 3/118 (2%)

Query: 229 LAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
                R++  + +R        +   V           + R       E     +  ++ 
Sbjct: 419 PPERIRKLKPEEVRRDRRTVPGDAGSVFSPGRQADEMRVKRRETPHRQEAAPAPSGSRQG 478

Query: 289 SSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
                G             +   +                  R ++  R P    +  
Sbjct: 479 G---KGAGLPSGRERTPEGKGRNAPPPPVPRAVPGKAPSPPPRPDDAVRQPRVQQRSP 533


>gi|296268175|ref|YP_003650807.1| ECF subfamily RNA polymerase sigma-24 [Thermobispora bispora DSM
           43833]
 gi|296090962|gb|ADG86914.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermobispora
           bispora DSM 43833]
          Length = 825

 Score = 40.5 bits (93), Expect = 0.35,   Method: Composition-based stats.
 Identities = 18/180 (10%), Positives = 36/180 (20%), Gaps = 40/180 (22%)

Query: 213 NRLIRISY----GPFQ-----LGTLLAGSTREVSKK------------------------ 239
           + L R+      GP +     L  LL G  R +                           
Sbjct: 245 SDLRRVRQEARRGPVRGVLLPLARLLPGLWRRLPPAQRAAAAGAALLLSAVTVILSAEPV 304

Query: 240 -ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN------SSQK 292
              R   G  L      +      + +   R      +   D               + +
Sbjct: 305 GERRAVGGLALPTLPSPDSAVTGQAGDGPGRPERGERARPRDGHRAGGPGGAPDGLPAGE 364

Query: 293 NGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            G   ++    P   R   ++     G     +       +      +          + 
Sbjct: 365 AGSGPRRGTGAPAGSRASDASARPQPGAGGLPVRRPLAARDPGPAPSAAGVPDPAPAGAD 424


>gi|11096141|gb|AAG30210.1|AF296330_1 collagen-like surface protein [Streptococcus pyogenes]
          Length = 312

 Score = 40.5 bits (93), Expect = 0.35,   Method: Composition-based stats.
 Identities = 13/134 (9%), Positives = 30/134 (22%)

Query: 220 YGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVP 279
           YG +          ++ ++K L+E L        + +      +     + +        
Sbjct: 77  YGTYFKEEDFQKELKDFTEKRLKEILDLIGKSGIKGDRGETGPAGPAGPQGKTGERGAQG 136

Query: 280 DDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
               R ++    K G   ++                 A        +             
Sbjct: 137 PKGDRGEQGIQGKAGEKGERGEKGDKGETGERGEKGEAGIQGPQGEAGKDGAPGKDGAPG 196

Query: 340 SFPSKRSLRRTSAK 353
               K     T A+
Sbjct: 197 EKGEKGDRGETGAQ 210


>gi|83816564|ref|YP_445191.1| 30S ribosomal protein S4 [Salinibacter ruber DSM 13855]
 gi|294507075|ref|YP_003571133.1| 30S ribosomal protein S4 [Salinibacter ruber M8]
 gi|123529117|sp|Q2S3P0|RS4_SALRD RecName: Full=30S ribosomal protein S4
 gi|83757958|gb|ABC46071.1| ribosomal protein S4 [Salinibacter ruber DSM 13855]
 gi|294343403|emb|CBH24181.1| 30S ribosomal protein S4 [Salinibacter ruber M8]
          Length = 200

 Score = 40.5 bits (93), Expect = 0.35,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   + R GIA +RR+  + +A + + VN  +++  +  +   D + V
Sbjct: 93  RLDNTVFRMGIARTRRQARQFVAHRHIMVNDEVVDIPSYEMSPDDVVSV 141


>gi|158421854|ref|YP_001523146.1| helicase [Azorhizobium caulinodans ORS 571]
 gi|158328743|dbj|BAF86228.1| helicase [Azorhizobium caulinodans ORS 571]
          Length = 1218

 Score = 40.5 bits (93), Expect = 0.36,   Method: Composition-based stats.
 Identities = 8/102 (7%), Positives = 15/102 (14%)

Query: 246  GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            G                      R                +     +     +++   P 
Sbjct: 1099 GQKREGRGDNRGGERRDGRPGGQRRNGPPGDRPGQGHRPPRPEGEGEAAAQGERQGNRPP 1158

Query: 306  HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
                       A           G  ++  RR        S 
Sbjct: 1159 RSERFRVPQGDAPRGPRPERHGGGAPQQQDRRREKQADPDSP 1200



 Score = 39.4 bits (90), Expect = 0.86,   Method: Composition-based stats.
 Identities = 5/64 (7%), Positives = 12/64 (18%), Gaps = 2/64 (3%)

Query: 290  SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                     ++   P  +R    +     G          +R       P    +     
Sbjct: 1084 RPGRPPGAPRREGAPGQKREGRGDNR--GGERRDGRPGGQRRNGPPGDRPGQGHRPPRPE 1141

Query: 350  TSAK 353
               +
Sbjct: 1142 GEGE 1145


>gi|158255924|dbj|BAF83933.1| unnamed protein product [Homo sapiens]
          Length = 1007

 Score = 40.5 bits (93), Expect = 0.36,   Method: Composition-based stats.
 Identities = 15/105 (14%), Positives = 31/105 (29%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            + ++++                     S  P D     K+   ++   K K+  T   +
Sbjct: 264 KIEDKSKSKDRKKSPIINESRSRDRGKKSRSPVDLRGKSKDRRSRSKERKSKRSETDKEK 323

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           + + S    A     +            RRS S   +   RR+ +
Sbjct: 324 KPIKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKPRDKSRRSRS 368



 Score = 37.1 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 13/107 (12%), Positives = 33/107 (30%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            ++ E++         S   +R +         +    +  + ++    K         +
Sbjct: 278 PIINESRSRDRGKKSRSPVDLRGKSKDRRSRSKERKSKRSETDKEKKPIKSPSKDASSGK 337

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            N + +    +      LS   + +    RSP    +RS +  S  +
Sbjct: 338 ENRSPSRRPGRSPKRRSLSPKPRDKSRRSRSPLLNDRRSKQSKSPSR 384


>gi|83592722|ref|YP_426474.1| DEAD/DEAH box helicase [Rhodospirillum rubrum ATCC 11170]
 gi|83575636|gb|ABC22187.1| DEAD/DEAH box helicase [Rhodospirillum rubrum ATCC 11170]
          Length = 677

 Score = 40.5 bits (93), Expect = 0.36,   Method: Composition-based stats.
 Identities = 9/120 (7%), Positives = 27/120 (22%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           + V    +            + +      +SE  V       +    +    +   S   
Sbjct: 558 KPVDALEVATAGDEAAAAAPRASAPRAPRASEPRVTKPYEPRAPRSTEPRAPRAARSADR 617

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               +            +      +   +   ++     +   ++   P   S  +T  K
Sbjct: 618 PTEARAPRTAEPRPPRASDRASEPRAAKAPRRTEKPAVGKAMVKTWGKPKPGSRPKTKQK 677


>gi|194381198|dbj|BAG64167.1| unnamed protein product [Homo sapiens]
          Length = 993

 Score = 40.5 bits (93), Expect = 0.36,   Method: Composition-based stats.
 Identities = 15/105 (14%), Positives = 31/105 (29%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            + ++++                     S  P D     K+   ++   K K+  T   +
Sbjct: 250 KIEDKSKSKDRKKSPIINESRSRDRGKKSRSPVDLRGKSKDRRSRSKERKSKRSETDKEK 309

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           + + S    A     +            RRS S   +   RR+ +
Sbjct: 310 KPIKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKPRDKSRRSRS 354



 Score = 37.1 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 13/107 (12%), Positives = 33/107 (30%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            ++ E++         S   +R +         +    +  + ++    K         +
Sbjct: 264 PIINESRSRDRGKKSRSPVDLRGKSKDRRSRSKERKSKRSETDKEKKPIKSPSKDASSGK 323

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            N + +    +      LS   + +    RSP    +RS +  S  +
Sbjct: 324 ENRSPSRRPGRSPKRRSLSPKPRDKSRRSRSPLLNDRRSKQSKSPSR 370


>gi|171473924|gb|AAX24501.3| SJCHGC09636 protein [Schistosoma japonicum]
          Length = 139

 Score = 40.5 bits (93), Expect = 0.36,   Method: Composition-based stats.
 Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 1/48 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           R+  V+ RAG+A +RR   +M+     +VNG  ++  +  V   D I 
Sbjct: 92  RLDSVVYRAGLARTRRGARQMVTHGHFEVNGKRVDVPSYRVEQYDIIT 139


>gi|196968459|gb|ACG80803.1| hypothetical protein [Chlamydophila pecorum]
          Length = 131

 Score = 40.5 bits (93), Expect = 0.36,   Method: Composition-based stats.
 Identities = 23/130 (17%), Positives = 40/130 (30%), Gaps = 6/130 (4%)

Query: 224 QLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
           +L  L   S++E+S K       P   E +   L     SS+ L    P+     P + +
Sbjct: 2   ELKDLETSSSKELSPKE------PSPKEPSSKELSPKEPSSKELSPKEPSPKEPSPKELS 55

Query: 284 RMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
             + +  + +      K  +P        +         S    S +       SP  PS
Sbjct: 56  PKEPSPKELSPKEPSPKEPSPKEPSPKEPSPKEPSPKELSPKEPSPKEPSPKEPSPKEPS 115

Query: 344 KRSLRRTSAK 353
            + L      
Sbjct: 116 PKELSPKEPS 125


>gi|254431173|ref|ZP_05044876.1| Ycf66 protein N-terminal domain protein [Cyanobium sp. PCC 7001]
 gi|197625626|gb|EDY38185.1| Ycf66 protein N-terminal domain protein [Cyanobium sp. PCC 7001]
          Length = 309

 Score = 40.5 bits (93), Expect = 0.36,   Method: Composition-based stats.
 Identities = 13/119 (10%), Positives = 27/119 (22%), Gaps = 6/119 (5%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R +  +   E L            +      +          +  P  +T      +   
Sbjct: 134 RRIPSREPEEDLYRMRRASRAAIPERAASRRDETPGWDSGSAAPEPSRYTAGGGRGASDF 193

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           G  ++++   P  RR             SS      +R       P      +    + 
Sbjct: 194 GARRRERDNQPEPRRGSRPTAAAEAPPRSS------RRPAAAGGRPGSAPGSATPERAG 246



 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 7/106 (6%), Positives = 17/106 (16%), Gaps = 3/106 (2%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL---A 302
                   +        ++    R          D   R ++  +Q       +      
Sbjct: 158 ERAASRRDETPGWDSGSAAPEPSRYTAGGGRGASDFGARRRERDNQPEPRRGSRPTAAAE 217

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
            P       +      G      +             S  +     
Sbjct: 218 APPRSSRRPAAAGGRPGSAPGSATPERAGIPQGTPIRSTAAGGPRP 263



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 11/109 (10%), Positives = 18/109 (16%)

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
            G    E                    P           R                  TP
Sbjct: 193 FGARRRERDNQPEPRRGSRPTAAAEAPPRSSRRPAAAGGRPGSAPGSATPERAGIPQGTP 252

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +           A    + F   S +        P+    +   R+  +
Sbjct: 253 IRSTAAGGPRPSAPISDADFSPISSRPAPTPTGRPAAGPAQEAPRSRPR 301


>gi|194377482|dbj|BAG57689.1| unnamed protein product [Homo sapiens]
          Length = 1011

 Score = 40.5 bits (93), Expect = 0.36,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 27/108 (25%), Gaps = 3/108 (2%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P   +EA+               + P              +   ++     +     P  
Sbjct: 890 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 949

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS--FPSKRSLRRTSA 352
           RR              +   +     E  RR      PS++  RR +A
Sbjct: 950 RRVGDVEPSRKPKRRRAADVEPSS-PEPKRRRVGDVEPSRKPKRRRAA 996



 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 9/117 (7%), Positives = 25/117 (21%), Gaps = 2/117 (1%)

Query: 238  KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            +    +   P     A++              +                    ++  +  
Sbjct: 895  EAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGD 954

Query: 298  QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             +    P  RR         +            R+   +R  +   + SL     ++
Sbjct: 955  VEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKP--KRRRAADVEPSLPEPKRRR 1009



 Score = 36.7 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 28/112 (25%), Gaps = 3/112 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E+L   L   A  NL  P  +++    ++P                  ++     +    
Sbjct: 872 ERLRGPLPPSADDNLKTPPLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRK 931

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               R                   +  ++    +R  +   + S      ++
Sbjct: 932 PKRRRAADVEPSSPEPKRRRVGDVEPSRKP---KRRRAADVEPSSPEPKRRR 980


>gi|153814918|ref|ZP_01967586.1| hypothetical protein RUMTOR_01133 [Ruminococcus torques ATCC 27756]
 gi|317500430|ref|ZP_07958654.1| translation initiation factor IF-2 [Lachnospiraceae bacterium
           8_1_57FAA]
 gi|331089563|ref|ZP_08338462.1| hypothetical protein HMPREF1025_02045 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|145847949|gb|EDK24867.1| hypothetical protein RUMTOR_01133 [Ruminococcus torques ATCC 27756]
 gi|316898185|gb|EFV20232.1| translation initiation factor IF-2 [Lachnospiraceae bacterium
           8_1_57FAA]
 gi|330404931|gb|EGG84469.1| hypothetical protein HMPREF1025_02045 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 930

 Score = 40.5 bits (93), Expect = 0.36,   Method: Composition-based stats.
 Identities = 11/115 (9%), Positives = 26/115 (22%), Gaps = 4/115 (3%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
             G    ++     + P+       +   N      +   R   +   +     +     
Sbjct: 164 PQGVRQEKQQPARAEKPVQVQSEKEKRTENDRPARENREARQSNDRPVRENRDGKPVRDG 223

Query: 304 PVHRR----NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               R    +  SN    +            R+         P  ++ R    K+
Sbjct: 224 KPSDRQGRFDRGSNDRSRQERPQGNRQFGDGRQSRGGDRDRRPGGQNGRSDREKR 278


>gi|325117073|emb|CBZ52625.1| putative ATP-dependent RNA helicase [Neospora caninum Liverpool]
          Length = 1056

 Score = 40.5 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 13/118 (11%), Positives = 27/118 (22%), Gaps = 3/118 (2%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
                ++  G       +           +      +      ++  R +K+  Q     
Sbjct: 107 RPSETQDTDGHEKDRRGKRKEAKREGQDASARPVTEDGEDVHMEEDKRKEKDDDQGRKAK 166

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           K+ +       R  A           S     G+  E  R   S       R+    +
Sbjct: 167 KEIRREG---DRRRAKEKDDKHSSSRSEKRKRGRSPERSREKKSSGGGDRRRKEKDGR 221



 Score = 35.9 bits (81), Expect = 8.6,   Method: Composition-based stats.
 Identities = 11/121 (9%), Positives = 26/121 (21%), Gaps = 4/121 (3%)

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G    + +   +E+      +  +               D+ +          R  + S 
Sbjct: 144 GEDVHMEEDKRKEKDDDQGRKAKKEIRREGDRRRAKEKDDKHSSSRSEKRKRGRSPERSR 203

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGI----HSSFLSDSGQREENHRRSPSFPSKRS 346
           +K       +       R  +++             S     G          + P  R 
Sbjct: 204 EKKSSGGGDRRRKEKDGRKGSASASRPSLSPSLTRPSSAPSRGSSLATEAPEAARPGARR 263

Query: 347 L 347
            
Sbjct: 264 P 264


>gi|255692810|ref|ZP_05416485.1| heat shock protein 15 [Bacteroides finegoldii DSM 17565]
 gi|260621439|gb|EEX44310.1| heat shock protein 15 [Bacteroides finegoldii DSM 17565]
          Length = 138

 Score = 40.5 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 17/91 (18%), Positives = 34/91 (37%), Gaps = 2/91 (2%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ K + A     +R        + RV +NG L++ AA  V   D I+V   P+  + + 
Sbjct: 5   RIDKWMWAVRIFKTRTIAAEACKKGRVTINGALVK-AARMVKPGDVIQVKKPPITYSFKV 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
              +  +    +      +  +     L  +
Sbjct: 64  LQAIEKRIGAKLVPEMMENVTTPDQYELLEM 94


>gi|172039993|ref|YP_001799707.1| hypothetical protein cur_0313 [Corynebacterium urealyticum DSM
           7109]
 gi|171851297|emb|CAQ04273.1| hypothetical protein cu0313 [Corynebacterium urealyticum DSM 7109]
          Length = 491

 Score = 40.5 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 14/109 (12%), Positives = 23/109 (21%), Gaps = 4/109 (3%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK----KLA 302
           P   EEA                         P    R +     +    + +    +  
Sbjct: 97  PLSQEEAGTPRSRQGQPQRRPRPQASEGGRPTPPSQRRPRPQGEPQRPRLQGEPQRLRPQ 156

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
             + RR          G            +  +RR          RRT+
Sbjct: 157 GELQRRRPQVPADGQPGARRPRHPRPAGEQPRYRRDDQPVGSAPRRRTA 205



 Score = 39.8 bits (91), Expect = 0.72,   Method: Composition-based stats.
 Identities = 10/112 (8%), Positives = 21/112 (18%), Gaps = 8/112 (7%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                   +                     S       + + +     G  + +    P 
Sbjct: 34  RRANTPAPERKAGQRSTRDPRSADHGTAHGSRPRPRAQQPRGSRPIPEGEQRPRSQGGPQ 93

Query: 306 HR--------RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
            R            S     +       S+ G+     +R P    +    R
Sbjct: 94  RRCPLSQEEAGTPRSRQGQPQRRPRPQASEGGRPTPPSQRRPRPQGEPQRPR 145



 Score = 37.5 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 15/124 (12%), Positives = 29/124 (23%), Gaps = 11/124 (8%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           L         E           ++    R      +  P        + S+    ++Q +
Sbjct: 15  LPAPRSAPSDEGGPQPPTYRRANTPAPERKAGQRSTRDPRSADHGTAHGSRPRPRAQQPR 74

Query: 301 LATPVHRRNLASNVWMAKGIH------SSFLSDSGQREENHRRSP-----SFPSKRSLRR 349
            + P+                       +    S Q +   R  P       P+  S RR
Sbjct: 75  GSRPIPEGEQRPRSQGGPQRRCPLSQEEAGTPRSRQGQPQRRPRPQASEGGRPTPPSQRR 134

Query: 350 TSAK 353
              +
Sbjct: 135 PRPQ 138



 Score = 36.3 bits (82), Expect = 7.7,   Method: Composition-based stats.
 Identities = 8/115 (6%), Positives = 22/115 (19%), Gaps = 2/115 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS-QKNGLSKQKK 300
           R        E+   +   P         +     S       R +  +S         ++
Sbjct: 74  RGSRPIPEGEQRPRSQGGPQRRCPLSQEEAGTPRSRQGQPQRRPRPQASEGGRPTPPSQR 133

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP-SFPSKRSLRRTSAKK 354
              P             + +         + +      P +   +         +
Sbjct: 134 RPRPQGEPQRPRLQGEPQRLRPQGELQRRRPQVPADGQPGARRPRHPRPAGEQPR 188


>gi|296131863|ref|YP_003639110.1| ribosomal protein S4 [Thermincola sp. JR]
 gi|296030441|gb|ADG81209.1| ribosomal protein S4 [Thermincola potens JR]
          Length = 208

 Score = 40.5 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 12/56 (21%), Positives = 21/56 (37%), Gaps = 1/56 (1%)

Query: 22  RAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW 76
           R G AS R E  +++      VN   +   + ++   D I++    L       L 
Sbjct: 106 RLGFASSRTEARQLVRHGHFTVNDKKVNIPSYSLKVGDVIKIKEKSLELPRIKELL 161


>gi|294628350|ref|ZP_06706910.1| 30S ribosomal protein S4 [Streptomyces sp. e14]
 gi|292831683|gb|EFF90032.1| 30S ribosomal protein S4 [Streptomyces sp. e14]
          Length = 204

 Score = 40.5 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 28/53 (52%), Gaps = 3/53 (5%)

Query: 15  RVSKVIARAGIASRR--EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  ++ R+GIA R   +  +M+    ++VNG  +++ +  V   D ++V   
Sbjct: 93  RLDALVLRSGIA-RTIYQARQMVVHGHIQVNGQKVDKPSFRVRPDDVVQVRDR 144


>gi|222150212|ref|YP_002551169.1| hypothetical protein Avi_4348 [Agrobacterium vitis S4]
 gi|221737194|gb|ACM38157.1| conserved hypothetical protein [Agrobacterium vitis S4]
          Length = 133

 Score = 40.5 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 3/49 (6%)

Query: 13 PQRVSKVI--ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           QR+ K +  AR    SR   ++ I   RV+VNG   ++ ++ V   D 
Sbjct: 11 SQRIDKWLFFARI-FKSRTLAQQQIVSGRVRVNGKPGKQPSIIVRPGDV 58


>gi|238064220|ref|ZP_04608929.1| polyketide synthase [Micromonospora sp. ATCC 39149]
 gi|237886031|gb|EEP74859.1| polyketide synthase [Micromonospora sp. ATCC 39149]
          Length = 1117

 Score = 40.5 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 13/97 (13%), Positives = 21/97 (21%), Gaps = 3/97 (3%)

Query: 260  PIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT---PVHRRNLASNVWM 316
                     R R    +      TR  +  S +    +         P HR   A++   
Sbjct: 926  RRGHPRRPARCRAGDGAASGGLPTRHHRAGSGRPAARRSGAGRHRVHPGHRTGDAAHPAG 985

Query: 317  AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              G      S         R  P    +        +
Sbjct: 986  DGGRRPRGASRPAGHVHRDRHRPGRTDRNRRHPPGRR 1022


>gi|71891780|dbj|BAA20782.3| KIAA0324 protein [Homo sapiens]
          Length = 2800

 Score = 40.5 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 9/108 (8%), Positives = 21/108 (19%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                            S   +     +              + +    + + +  AT  
Sbjct: 480 RHASSSPESPKPAPAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAK 539

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R+ +          S        R          P +R   R+  +
Sbjct: 540 RGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQR 587



 Score = 40.5 bits (93), Expect = 0.43,   Method: Composition-based stats.
 Identities = 11/98 (11%), Positives = 22/98 (22%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P      +++      +       R    S  P       ++ +       + +  T  
Sbjct: 492 APAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKR 551

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
                 S  W        +      +     RSP  P 
Sbjct: 552 GHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPG 589



 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 22/135 (16%), Positives = 34/135 (25%), Gaps = 10/135 (7%)

Query: 230 AGSTREV----SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
            GS RE+    + K             +         S       R    S  P      
Sbjct: 495 PGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKRGHS 554

Query: 286 KKNSSQKNGLSKQKK--LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
           +  S Q       ++   +    RR  + +        S      G+     R      S
Sbjct: 555 RSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRSHSRS 614

Query: 344 K----RSLRRTSAKK 354
                RS  RT A++
Sbjct: 615 PATRGRSRSRTPARR 629


>gi|311256485|ref|XP_003126672.1| PREDICTED: SRSF2-interacting protein-like [Sus scrofa]
          Length = 1455

 Score = 40.5 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 12/112 (10%), Positives = 31/112 (27%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +       ++E   ++  P  S    +       +      +     S  K+   ++K+ 
Sbjct: 747 KNMSSSDPVKEKVESVSQPSESPIDTIEKAKKPRTRRSRFHSPSTTWSPNKDTAREKKRS 806

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            +P  RR        ++       S  G++    +       +      S  
Sbjct: 807 QSPSPRRETGKESRKSQSPSPKKESARGRKSSRSQSPKKDSGRERRPSQSRS 858



 Score = 40.2 bits (92), Expect = 0.45,   Method: Composition-based stats.
 Identities = 12/113 (10%), Positives = 28/113 (24%), Gaps = 5/113 (4%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P+     +              ++     S  P   +   + SS+     K         
Sbjct: 795 PNKDTAREKKRSQSPSPRRETGKESRKSQSPSPKKESARGRKSSRSQSPKKDSGRERRPS 854

Query: 307 RRNLASNVWMAKGIH-----SSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +          +G           +    R    R   S P ++S  ++  ++
Sbjct: 855 QSRSPKRDGAKEGKRSESLSPKRDTSRENRRSQPRVKGSSPREKSRSQSGERE 907



 Score = 37.1 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 11/108 (10%), Positives = 29/108 (26%), Gaps = 7/108 (6%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEV-------PDDFTRMKKNS 289
           + +  +    P    E           S      R    S           +    +  S
Sbjct: 799 TAREKKRSQSPSPRRETGKESRKSQSPSPKKESARGRKSSRSQSPKKDSGRERRPSQSRS 858

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
            +++G  + K+  +   +R+ +     ++            R ++  R
Sbjct: 859 PKRDGAKEGKRSESLSPKRDTSRENRRSQPRVKGSSPREKSRSQSGER 906


>gi|209964288|ref|YP_002297203.1| hypothetical protein RC1_0966 [Rhodospirillum centenum SW]
 gi|209957754|gb|ACI98390.1| hypothetical protein RC1_0966 [Rhodospirillum centenum SW]
          Length = 201

 Score = 40.5 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 15/141 (10%), Positives = 31/141 (21%), Gaps = 7/141 (4%)

Query: 209 NWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLV 268
              + RL R S G            R+   + +R  L     + A  +         T  
Sbjct: 61  GNVLARLRRESAGD---RGHFFSEIRKAR-EEVRSALAARPFDPAAADAAFTSVRQATAA 116

Query: 269 RDRP---NIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFL 325
             +     ++  + ++  R            +      P   R         +       
Sbjct: 117 MQQRLQEAVVRTMAEEQARGTLPPPPPPKERRSSGRERPDRDRGGPERHGPDRPGPDRPG 176

Query: 326 SDSGQREENHRRSPSFPSKRS 346
            D    +      P+      
Sbjct: 177 PDRPGPDGPGPARPAPGGPEP 197


>gi|73948111|ref|XP_855013.1| PREDICTED: hypothetical protein XP_849920 [Canis familiaris]
          Length = 384

 Score = 40.5 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 21/116 (18%), Positives = 30/116 (25%), Gaps = 1/116 (0%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R V    LRE      L E+      P        R    +           +K      
Sbjct: 242 RRVDAVALREATRDGSLRESSAPWPRPAALRSRGERAPRGLPRAGRTAAAPRQKKGRAGA 301

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           G    +        R   S    A+G  S   +  G+   + RR     S  +  R
Sbjct: 302 GAHGSESARGRKAGRGGGSPPGAARGARSRADA-PGRCPPSLRRGGLPASPPASPR 356


>gi|320103641|ref|YP_004179232.1| 30S ribosomal protein S4P [Isosphaera pallida ATCC 43644]
 gi|319750923|gb|ADV62683.1| SSU ribosomal protein S4P [Isosphaera pallida ATCC 43644]
          Length = 209

 Score = 40.5 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           R+  V+ R G A SR +  ++I+   + VNG  L+  +  V + + I +    
Sbjct: 99  RLDNVVTRLGFAISRPQARQLISHGHILVNGRKLDIPSYLVRAGESITLKDRE 151


>gi|302534176|ref|ZP_07286518.1| predicted protein [Streptomyces sp. C]
 gi|302443071|gb|EFL14887.1| predicted protein [Streptomyces sp. C]
          Length = 534

 Score = 40.5 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 18/146 (12%), Positives = 28/146 (19%), Gaps = 7/146 (4%)

Query: 205 FEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYS 263
                  V      +YG   LG  +  G   E+ ++     +  H      V   A    
Sbjct: 172 LGAVGVNVTA----NYGGVYLGDPVYDGIFAELDER--SAVVDTHPHNLPAVPAVAGGPG 225

Query: 264 SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSS 323
                          P    R  + +                    L +          +
Sbjct: 226 GPGGAGAAGPPGPGTPGAGRRPGEPAEPGRPPGAGLPTEAGRPGAGLPTEARRPGTGLPT 285

Query: 324 FLSDSGQREENHRRSPSFPSKRSLRR 349
                G       R P        RR
Sbjct: 286 EARRPGTGLPTEARRPGTGLPTEARR 311


>gi|295836128|ref|ZP_06823061.1| conserved hypothetical protein [Streptomyces sp. SPB74]
 gi|197695223|gb|EDY42156.1| conserved hypothetical protein [Streptomyces sp. SPB74]
          Length = 743

 Score = 40.5 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 16/122 (13%), Positives = 31/122 (25%), Gaps = 3/122 (2%)

Query: 236 VSKKILREQL---GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
           V  + +R++L                A   +            SE     +R    +S+ 
Sbjct: 391 VEPEEIRQRLCGSPRRPTAHRSSARPASARTGSAADGAGRGATSEQEAGVSRSAAGASEG 450

Query: 293 NGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
               +  +  T   RR + S         S+               PS   + + R    
Sbjct: 451 APEGEVAEPGTGDGRRRVRSASRTGSASRSAASRSGVSARTGPTARPSTRRRDTRRPGGP 510

Query: 353 KK 354
            +
Sbjct: 511 AQ 512


>gi|120601867|ref|YP_966267.1| radical SAM domain-containing protein [Desulfovibrio vulgaris DP4]
 gi|120562096|gb|ABM27840.1| Radical SAM N-terminal domain protein [Desulfovibrio vulgaris DP4]
          Length = 680

 Score = 40.5 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 12/115 (10%), Positives = 24/115 (20%), Gaps = 2/115 (1%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
             + LR+            + DA         +           D    + +    N   
Sbjct: 565 DAERLRQHGILMPDTGRPPSRDADNRRRGDARQSETGRGKAGTRDGRPHRSDRDTGNANR 624

Query: 297 --KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
               +       R     +     G      ++ G  +   RR       +   R
Sbjct: 625 HDGGRSDRRGGRRDEDRPDRGRRNGARPDGGANRGGADAEERREGRKGGSKRPPR 679


>gi|86741852|ref|YP_482252.1| tetratricopeptide TPR_2 [Frankia sp. CcI3]
 gi|86568714|gb|ABD12523.1| Tetratricopeptide TPR_2 [Frankia sp. CcI3]
          Length = 654

 Score = 40.5 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 10/117 (8%), Positives = 25/117 (21%), Gaps = 3/117 (2%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           +  +             +       +   D      +        +  +       +   
Sbjct: 201 VAAEAAWRERRGRPGAEETGRSGRPSSRPDHGRPGRDSSVSHRPGQARAGSDGPRPRHDG 260

Query: 301 LATPVHRRNLASNVWMAKGIH---SSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              P H R   S+     G          D G+     R +     +R     + ++
Sbjct: 261 PERPTHGRVWRSDGDRPAGTRSAGPRPGGDRGRESRGPRDTSGGGDRRDGAARAERR 317



 Score = 37.5 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 12/120 (10%), Positives = 23/120 (19%), Gaps = 9/120 (7%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
             G       +    A   +                 + T      S +    +  + ++
Sbjct: 180 PRGDRGASGDRGASGASARNRVAAEAAWRERRGRPGAEETGRSGRPSSRPDHGRPGRDSS 239

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDS---------GQREENHRRSPSFPSKRSLRRTSAKK 354
             HR   A                          G R    R +   P     R +   +
Sbjct: 240 VSHRPGQARAGSDGPRPRHDGPERPTHGRVWRSDGDRPAGTRSAGPRPGGDRGRESRGPR 299


>gi|296394891|ref|YP_003659775.1| 30S ribosomal protein S4 [Segniliparus rotundus DSM 44985]
 gi|296182038|gb|ADG98944.1| ribosomal protein S4 [Segniliparus rotundus DSM 44985]
          Length = 201

 Score = 40.5 bits (93), Expect = 0.39,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  VI RAG+A +RR   +++      VN   ++  +  V   D I+V
Sbjct: 92  RLDNVIYRAGLARTRRHARQLVTHGHFLVNQKRVDVPSYRVSQYDIIDV 140


>gi|324513570|gb|ADY45572.1| Cuticle collagen 10 [Ascaris suum]
          Length = 305

 Score = 40.5 bits (93), Expect = 0.39,   Method: Composition-based stats.
 Identities = 11/100 (11%), Positives = 19/100 (19%), Gaps = 1/100 (1%)

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
              +     + P   +    +  P              + +    G            R 
Sbjct: 186 HGNDGPPGPEGPAGEAGRKGQPGPPGAPGPDGKDGERGRGAPGPKGPDGAPGPNGKPGRP 245

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
               N      +  +  S    R E  R  P       L 
Sbjct: 246 GAKGNKGAPGPVGPAGESGKAGR-EGERGKPGGAGSPGLP 284


>gi|299768643|ref|YP_003730669.1| putative ATP-dependent RNA helicase [Acinetobacter sp. DR1]
 gi|298698731|gb|ADI89296.1| putative ATP-dependent RNA helicase [Acinetobacter sp. DR1]
          Length = 644

 Score = 40.5 bits (93), Expect = 0.39,   Method: Composition-based stats.
 Identities = 19/117 (16%), Positives = 30/117 (25%), Gaps = 1/117 (0%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE      R + G +       N D      +   R            F    +     +
Sbjct: 484 REFGSDRPRREGGFNDKPRFDSNDDNRGNRVDYKPRRESGFGDRPKRSFGGEDRPRRSFD 543

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLS-DSGQREENHRRSPSFPSKRSLRR 349
              + ++ A     R   S     +G   +F   D  +RE N  R           R
Sbjct: 544 DKPRGERPAFGGEDRPRRSFDDKPRGERPAFGGEDRPRREFNSDRPRREGGFSDKPR 600



 Score = 38.2 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 13/109 (11%), Positives = 24/109 (22%), Gaps = 2/109 (1%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                   +     +  +           + P      K    +     + +        
Sbjct: 528 PKRSFGGEDRPRRSFDDKPRGERPAFGGEDRPRRSFDDKPRGERPAFGGEDRPRREFNSD 587

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENH--RRSPSFPSKRSLRRTSAKK 354
           R      +  K   S      G+R      R   SF  +   RR+   K
Sbjct: 588 RPRREGGFSDKPRRSFDDKPRGERPAFGEDRPKRSFGGEDRPRRSFDDK 636



 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 9/114 (7%), Positives = 22/114 (19%), Gaps = 4/114 (3%)

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
                  E   +            R   N  +       + ++ S   +   +       
Sbjct: 478 FEDRPRREFGSDRPRREGGFNDKPRFDSNDDNRGNRVDYKPRRESGFGDRPKRSFGGEDR 537

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR----TSAKK 354
             R                        ++     P+F  +   RR       ++
Sbjct: 538 PRRSFDDKPRGERPAFGGEDRPRRSFDDKPRGERPAFGGEDRPRREFNSDRPRR 591



 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 13/115 (11%), Positives = 26/115 (22%), Gaps = 9/115 (7%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
             R +         +               D+P           R ++  +      +  
Sbjct: 535 EDRPRRSFDDKPRGERPAFGGEDRPRRSFDDKPRGERPAFGGEDRPRREFNSDRPRREGG 594

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               P       S     +G   +F  D  +R       P    +RS      ++
Sbjct: 595 FSDKP-----RRSFDDKPRGERPAFGEDRPKRSFGGEDRP----RRSFDDKPPRR 640



 Score = 36.7 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 10/128 (7%), Positives = 25/128 (19%), Gaps = 15/128 (11%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            ++      ++ +    A             +          R ++         +    
Sbjct: 439 DDRPRRSFDDKPRGERPAFGGEDRPRREFNSDRPRREGGFEDRPRREFGSDRPRREGGFN 498

Query: 302 ATPV---------------HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
             P                 RR         +             ++     P+F  +  
Sbjct: 499 DKPRFDSNDDNRGNRVDYKPRRESGFGDRPKRSFGGEDRPRRSFDDKPRGERPAFGGEDR 558

Query: 347 LRRTSAKK 354
            RR+   K
Sbjct: 559 PRRSFDDK 566


>gi|302550146|ref|ZP_07302488.1| ribosomal protein S4 [Streptomyces viridochromogenes DSM 40736]
 gi|302467764|gb|EFL30857.1| ribosomal protein S4 [Streptomyces viridochromogenes DSM 40736]
          Length = 204

 Score = 40.5 bits (93), Expect = 0.39,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 27/53 (50%), Gaps = 3/53 (5%)

Query: 15  RVSKVIARAGIASRR--EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           R+  ++ R+GIA R   +  +M+    + VNG  +++ +  V   D ++V   
Sbjct: 93  RLDALVLRSGIA-RTIYQARQMVVHGHIAVNGKKVDKPSFRVRPDDVVQVRDR 144


>gi|254564113|ref|YP_003071208.1| hypothetical protein METDI5803 [Methylobacterium extorquens DM4]
 gi|254271391|emb|CAX27404.1| Conserved hypothetical protein; putative OmpA family member
           [Methylobacterium extorquens DM4]
          Length = 717

 Score = 40.5 bits (93), Expect = 0.39,   Method: Composition-based stats.
 Identities = 10/97 (10%), Positives = 16/97 (16%), Gaps = 1/97 (1%)

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
                  E   R       + P    R +             +       R         
Sbjct: 75  PPARERPERSERPERPEPRQAPAARERPEPAERPARPERPAAQERQERPERPDRQERQER 134

Query: 318 KGIHSSFLSD-SGQREENHRRSPSFPSKRSLRRTSAK 353
                        QR +     P+ P+ R        
Sbjct: 135 PDRQERPERAAPPQRPDRTEERPAAPASRERTPDRDA 171



 Score = 39.4 bits (90), Expect = 0.77,   Method: Composition-based stats.
 Identities = 9/109 (8%), Positives = 24/109 (22%), Gaps = 1/109 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G                        R    +    +         +     +Q++   P 
Sbjct: 68  GGVERGGPPARERPERSERPERPEPRQAPAARERPEPAERPARPERPAAQERQERPERPD 127

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +          +   ++       R E    +P+   +   R   A++
Sbjct: 128 RQERQERPDRQERPERAAP-PQRPDRTEERPAAPASRERTPDRDAPARR 175



 Score = 37.9 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 17/128 (13%), Positives = 32/128 (25%), Gaps = 16/128 (12%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            ++   E+  P    +      A   S E           E PD     ++ S ++    
Sbjct: 136 DRQERPERAAPPQRPDRTEERPAAPASRERTPDRDAPARREAPDREAPARRESPERPDRD 195

Query: 297 KQKKLATPVHRRNLAS----------------NVWMAKGIHSSFLSDSGQREENHRRSPS 340
            Q +   P  R                     NV   +       ++  Q      + P 
Sbjct: 196 GQDRPGRPAGREADRPDSAPNQRRVPNAPTPPNVERPEQPTPPTATNPAQPNTPPNQRPG 255

Query: 341 FPSKRSLR 348
            P + +  
Sbjct: 256 VPGRPATP 263


>gi|307110511|gb|EFN58747.1| hypothetical protein CHLNCDRAFT_140448 [Chlorella variabilis]
          Length = 610

 Score = 40.5 bits (93), Expect = 0.40,   Method: Composition-based stats.
 Identities = 12/97 (12%), Positives = 18/97 (18%), Gaps = 3/97 (3%)

Query: 260 PIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKG 319
               + +          E P                +       P  R            
Sbjct: 513 RAKYARSAAARDEEHARERPPRVREPSPGGEGWRRGAGDGANGGPAPRGFRDDRPARPPS 572

Query: 320 IHSSFLSDSGQR---EENHRRSPSFPSKRSLRRTSAK 353
             +       +R   EE  RR    P  R   R   +
Sbjct: 573 GAAGHDDRPPRRGGFEERGRRDSFPPRDRDSSRDKPR 609


>gi|291239696|ref|XP_002739749.1| PREDICTED: hypothetical protein [Saccoglossus kowalevskii]
          Length = 1434

 Score = 40.5 bits (93), Expect = 0.40,   Method: Composition-based stats.
 Identities = 9/99 (9%), Positives = 30/99 (30%), Gaps = 4/99 (4%)

Query: 237  SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
                ++        +   +  ++P+                 P D  R + +S  + G  
Sbjct: 1337 DADEIKSTEEDKKPKAEMIE-ESPVKIQYAGRGRGRRGGRRSPTDMGRGRGDSPARRGRG 1395

Query: 297  KQKKLATPVHRRNLASNVWM---AKGIHSSFLSDSGQRE 332
            ++++ ++P  +R   S+                 + ++ 
Sbjct: 1396 QRERDSSPPRKRTTRSSGGADICDPLPPPQKRRRAKEKP 1434


>gi|242280538|ref|YP_002992667.1| DEAD/DEAH box helicase domain protein [Desulfovibrio salexigens DSM
           2638]
 gi|242123432|gb|ACS81128.1| DEAD/DEAH box helicase domain protein [Desulfovibrio salexigens DSM
           2638]
          Length = 493

 Score = 40.5 bits (93), Expect = 0.40,   Method: Composition-based stats.
 Identities = 14/115 (12%), Positives = 27/115 (23%), Gaps = 3/115 (2%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            +      +E+A           +          +       R      +  G  +  + 
Sbjct: 348 DDLRLMREIEKAVGYSIEHRTLEDFDYDKPNTHPAPAKRGGGRKPAADRKPAGERRPGRG 407

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS--KRSLRRTSAKK 354
             P   R+         G   S               P+  S  +R  R +S +K
Sbjct: 408 RKPAEARDGDE-SRKPAGERKSGGRRKPGGGRKPSGGPAKSSDERRDSRPSSKRK 461



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 11/116 (9%), Positives = 29/116 (25%)

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           + + + +G  +      + D    ++      R        D     ++   +    ++ 
Sbjct: 354 REIEKAVGYSIEHRTLEDFDYDKPNTHPAPAKRGGGRKPAADRKPAGERRPGRGRKPAEA 413

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +             +    K       S    +  + RR     SKR        +
Sbjct: 414 RDGDESRKPAGERKSGGRRKPGGGRKPSGGPAKSSDERRDSRPSSKRKSGGPKGNQ 469


>gi|146278925|ref|YP_001169084.1| DEAD/DEAH box helicase domain-containing protein [Rhodobacter
           sphaeroides ATCC 17025]
 gi|145557166|gb|ABP71779.1| DEAD/DEAH box helicase domain protein [Rhodobacter sphaeroides ATCC
           17025]
          Length = 764

 Score = 40.5 bits (93), Expect = 0.40,   Method: Composition-based stats.
 Identities = 7/109 (6%), Positives = 17/109 (15%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P           A         +             +          G  + +      
Sbjct: 626 RPARPAYKGAATRAEGTGRSAGYKSHGGTAGRSTGYKSHGAAGDDAPRGKPRGEGAPRAA 685

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             ++         G           R   ++ +      +       KK
Sbjct: 686 GFKSHDKPARDETGPRERGPDARPARPSGYKGARDDRPAKPRAEGGVKK 734



 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 10/102 (9%), Positives = 29/102 (28%), Gaps = 3/102 (2%)

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           L        +   +    + +   R         P  F   +++ + ++G +   + A P
Sbjct: 530 LERPERAPRKPFAERTPRTRDEAPRREKAPYQPKPSRFVEEERDEAPRSGWTPDDRPARP 589

Query: 305 VHRRNL---ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
               +       +    G       +  +  +     P+ P+
Sbjct: 590 RREDSGHVAKREMQEGTGARREGSDEGRKPRQPQGERPARPA 631


>gi|50954032|ref|YP_061320.1| hypothetical protein Lxx01410 [Leifsonia xyli subsp. xyli str.
           CTCB07]
 gi|50950514|gb|AAT88215.1| conserved hypothetical protein [Leifsonia xyli subsp. xyli str.
           CTCB07]
          Length = 558

 Score = 40.5 bits (93), Expect = 0.40,   Method: Composition-based stats.
 Identities = 14/112 (12%), Positives = 27/112 (24%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R   G       +       Y  +   R  P       +   + +K + +     + K  
Sbjct: 117 RSGQGKPSFRGERSGGGKTSYRDDRAGRPSPRGERSRGEKPEKPEKPAYRGERAGEGKPP 176

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                     S    A    +     S  R + + + P    +RS       
Sbjct: 177 YRCGRAGAGDSAGERAGRFGNGNDRGSDGRPDRNGQRPKRNDRRSGYGDRDA 228



 Score = 37.9 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 10/98 (10%), Positives = 20/98 (20%)

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW 315
               P  +  +    +P+               S  +    ++         R   S   
Sbjct: 62  EGKPPFRAKRSADGRQPSRGERPYAVSPYRGDRSGDRKPYRREPSEGGAPPYRGERSGQG 121

Query: 316 MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                            ++    PS   +RS      K
Sbjct: 122 KPSFRGERSGGGKTSYRDDRAGRPSPRGERSRGEKPEK 159


>gi|16802262|ref|NP_463747.1| hypothetical protein lmo0216 [Listeria monocytogenes EGD-e]
 gi|46906448|ref|YP_012837.1| S4 domain-containing protein [Listeria monocytogenes serotype 4b
          str. F2365]
 gi|47093158|ref|ZP_00230933.1| S4 domain protein [Listeria monocytogenes str. 4b H7858]
 gi|47096209|ref|ZP_00233808.1| S4 domain protein [Listeria monocytogenes str. 1/2a F6854]
 gi|217965698|ref|YP_002351376.1| S4 RNA-binding domain protein [Listeria monocytogenes HCC23]
 gi|224500333|ref|ZP_03668682.1| S4 RNA-binding domain protein [Listeria monocytogenes Finland
          1988]
 gi|224503464|ref|ZP_03671771.1| S4 RNA-binding domain protein [Listeria monocytogenes FSL R2-561]
 gi|226222845|ref|YP_002756952.1| YabO protein [Listeria monocytogenes Clip81459]
 gi|254825870|ref|ZP_05230871.1| S4 domain-containing protein [Listeria monocytogenes FSL J1-194]
 gi|254829307|ref|ZP_05233994.1| S4 domain-containing protein [Listeria monocytogenes FSL N3-165]
 gi|254832463|ref|ZP_05237118.1| YabO protein [Listeria monocytogenes 10403S]
 gi|254854446|ref|ZP_05243794.1| S4 domain-containing protein [Listeria monocytogenes FSL R2-503]
 gi|254900999|ref|ZP_05260923.1| YabO protein [Listeria monocytogenes J0161]
 gi|254913933|ref|ZP_05263945.1| S4 domain-containing protein [Listeria monocytogenes J2818]
 gi|254933056|ref|ZP_05266415.1| S4 domain-containing protein [Listeria monocytogenes HPB2262]
 gi|254938277|ref|ZP_05269974.1| S4 domain-containing protein [Listeria monocytogenes F6900]
 gi|254992852|ref|ZP_05275042.1| YabO protein [Listeria monocytogenes FSL J2-064]
 gi|255016645|ref|ZP_05288771.1| YabO protein [Listeria monocytogenes FSL F2-515]
 gi|255025716|ref|ZP_05297702.1| YabO protein [Listeria monocytogenes FSL J2-003]
 gi|255521746|ref|ZP_05388983.1| YabO protein [Listeria monocytogenes FSL J1-175]
 gi|284803045|ref|YP_003414910.1| hypothetical protein LM5578_2802 [Listeria monocytogenes 08-5578]
 gi|284996186|ref|YP_003417954.1| hypothetical protein LM5923_2751 [Listeria monocytogenes 08-5923]
 gi|289433571|ref|YP_003463443.1| S4 domain protein [Listeria seeligeri serovar 1/2b str. SLCC3954]
 gi|290894276|ref|ZP_06557243.1| S4 domain-containing protein [Listeria monocytogenes FSL J2-071]
 gi|300766349|ref|ZP_07076308.1| hypothetical protein LMHG_11018 [Listeria monocytogenes FSL
          N1-017]
 gi|4090865|gb|AAC98902.1| unknown protein [Listeria monocytogenes]
 gi|16409581|emb|CAD00743.1| lmo0216 [Listeria monocytogenes EGD-e]
 gi|46879712|gb|AAT03014.1| S4 domain protein [Listeria monocytogenes serotype 4b str. F2365]
 gi|47015457|gb|EAL06391.1| S4 domain protein [Listeria monocytogenes str. 1/2a F6854]
 gi|47018465|gb|EAL09223.1| S4 domain protein [Listeria monocytogenes str. 4b H7858]
 gi|217334968|gb|ACK40762.1| S4 RNA-binding domain protein [Listeria monocytogenes HCC23]
 gi|225875307|emb|CAS04004.1| Putative YabO protein [Listeria monocytogenes serotype 4b str.
          CLIP 80459]
 gi|258601720|gb|EEW15045.1| S4 domain-containing protein [Listeria monocytogenes FSL N3-165]
 gi|258607846|gb|EEW20454.1| S4 domain-containing protein [Listeria monocytogenes FSL R2-503]
 gi|258610887|gb|EEW23495.1| S4 domain-containing protein [Listeria monocytogenes F6900]
 gi|284058607|gb|ADB69548.1| hypothetical protein LM5578_2802 [Listeria monocytogenes 08-5578]
 gi|284061653|gb|ADB72592.1| hypothetical protein LM5923_2751 [Listeria monocytogenes 08-5923]
 gi|289169815|emb|CBH26353.1| S4 domain protein [Listeria seeligeri serovar 1/2b str. SLCC3954]
 gi|290556160|gb|EFD89707.1| S4 domain-containing protein [Listeria monocytogenes FSL J2-071]
 gi|293584614|gb|EFF96646.1| S4 domain-containing protein [Listeria monocytogenes HPB2262]
 gi|293591951|gb|EFG00286.1| S4 domain-containing protein [Listeria monocytogenes J2818]
 gi|293595109|gb|EFG02870.1| S4 domain-containing protein [Listeria monocytogenes FSL J1-194]
 gi|300512948|gb|EFK40036.1| hypothetical protein LMHG_11018 [Listeria monocytogenes FSL
          N1-017]
 gi|307569755|emb|CAR82934.1| S4 domain protein [Listeria monocytogenes L99]
 gi|313639800|gb|EFS04535.1| S4 domain-containing protein [Listeria seeligeri FSL S4-171]
 gi|328469742|gb|EGF40664.1| S4 domain protein [Listeria monocytogenes 220]
          Length = 92

 Score = 40.5 bits (93), Expect = 0.40,   Method: Composition-based stats.
 Identities = 15/80 (18%), Positives = 26/80 (32%), Gaps = 4/80 (5%)

Query: 12 TPQRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLR 68
          T  R+ K +  + +  RR   + +  + R+ VNG+  +    NV S D   I      + 
Sbjct: 3  TTMRLDKYLKVSRLIKRRTVAKEVAEKGRIAVNGVTAK-PGTNVKSGDELVIRFGPKIVT 61

Query: 69 KAERTRLWLYHKPIGLVTTH 88
                     K        
Sbjct: 62 AKIERLEENAKKEQATEMYT 81


>gi|194909535|ref|XP_001981966.1| GG12335 [Drosophila erecta]
 gi|190656604|gb|EDV53836.1| GG12335 [Drosophila erecta]
          Length = 647

 Score = 40.5 bits (93), Expect = 0.41,   Method: Composition-based stats.
 Identities = 8/113 (7%), Positives = 29/113 (25%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R++         +        + +    D+              ++  S ++   +++  
Sbjct: 201 RKRRDSDQSPPRKARNGNQSPARKRRDSDQSPPRKRTGKPSPTRRRRESDQSPPRRRRSN 260

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +     R                     +R +    SP    ++   ++  +K
Sbjct: 261 SDQSPPRRRRDQDSTPPRRRKDADQSPPRRRKADDPSPVRRGRKDSDQSPPRK 313



 Score = 40.2 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 12/107 (11%), Positives = 34/107 (31%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           RE++G       +          +    ++         D +  +K + + +   ++++ 
Sbjct: 190 RERVGDQSPPRRKRRDSDQSPPRKARNGNQSPARKRRDSDQSPPRKRTGKPSPTRRRRES 249

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                RR  +++            S   +R ++  +SP    K    
Sbjct: 250 DQSPPRRRRSNSDQSPPRRRRDQDSTPPRRRKDADQSPPRRRKADDP 296



 Score = 37.1 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 12/113 (10%), Positives = 30/113 (26%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R++ G       +   D           D+         D T  ++         +++K 
Sbjct: 234 RKRTGKPSPTRRRRESDQSPPRRRRSNSDQSPPRRRRDQDSTPPRRRKDADQSPPRRRKA 293

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             P   R    +   +          S  R+           +R  +++  ++
Sbjct: 294 DDPSPVRRGRKDSDQSPPRKRRGNDQSPVRKRRDSDQSPPRRRRDDKQSPPRR 346



 Score = 36.3 bits (82), Expect = 6.8,   Method: Composition-based stats.
 Identities = 16/134 (11%), Positives = 33/134 (24%), Gaps = 6/134 (4%)

Query: 227 TLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
            L    +R+  K+    Q      E +  +        +     R    S+         
Sbjct: 157 DLSPARSRKPPKREDSPQGRRRRAESSDQSPPRRERVGDQSPPRRKRRDSDQSPPRKARN 216

Query: 287 KNSSQKNGLS------KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
            N S             +K+   P   R    +         S    S  R    + S  
Sbjct: 217 GNQSPARKRRDSDQSPPRKRTGKPSPTRRRRESDQSPPRRRRSNSDQSPPRRRRDQDSTP 276

Query: 341 FPSKRSLRRTSAKK 354
              ++   ++  ++
Sbjct: 277 PRRRKDADQSPPRR 290



 Score = 35.9 bits (81), Expect = 9.2,   Method: Composition-based stats.
 Identities = 12/112 (10%), Positives = 30/112 (26%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R +         +   D           D+        +D + ++K         ++++ 
Sbjct: 279 RRKDADQSPPRRRKADDPSPVRRGRKDSDQSPPRKRRGNDQSPVRKRRDSDQSPPRRRRD 338

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                 R   ++                +R+ +  +SP     +S RR    
Sbjct: 339 DKQSPPRRRRNSDQSPPRRPKDEDQSPPRRKRDFDQSPLRKRDKSPRRRRDS 390


>gi|153005292|ref|YP_001379617.1| molybdopterin-guanine dinucleotide biosynthesis protein B
           [Anaeromyxobacter sp. Fw109-5]
 gi|152028865|gb|ABS26633.1| molybdopterin-guanine dinucleotide biosynthesis protein B
           [Anaeromyxobacter sp. Fw109-5]
          Length = 293

 Score = 40.5 bits (93), Expect = 0.41,   Method: Composition-based stats.
 Identities = 12/91 (13%), Positives = 29/91 (31%)

Query: 264 SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSS 323
               +  +              +++ + ++   ++   AT   R     +    KG   S
Sbjct: 195 RRERMPKKTTNRKSATARTRGGRRSGASRSDAGRKGGNATLRARGPEFYSEIGRKGGKKS 254

Query: 324 FLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               S  +     R  +   + + RR +AK+
Sbjct: 255 RGGRSSAKSSTGTRRGATTKRGTARRGAAKR 285


>gi|149517458|ref|XP_001516925.1| PREDICTED: similar to AIDA1C transcript, partial [Ornithorhynchus
           anatinus]
          Length = 609

 Score = 40.5 bits (93), Expect = 0.41,   Method: Composition-based stats.
 Identities = 12/105 (11%), Positives = 20/105 (19%), Gaps = 2/105 (1%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           LRE+    +    +         S           +                 G    + 
Sbjct: 175 LREEAPAPVTRPGREARPRESPRSADRFGRGSRGPTVAGAAPASRPARRGLDRGAGGDRL 234

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSD--SGQREENHRRSPSFPS 343
            A     R+  +             S   +  R    R  P  P 
Sbjct: 235 PAGAASPRSRRAPAGARGWTRPRSGSPVVAVGRPSALRARPGRPG 279



 Score = 35.9 bits (81), Expect = 9.6,   Method: Composition-based stats.
 Identities = 9/84 (10%), Positives = 23/84 (27%), Gaps = 1/84 (1%)

Query: 267 LVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLS 326
                  +     +   R    S+ + G   +          +  +   + +G       
Sbjct: 176 REEAPAPVTRPGREARPRESPRSADRFGRGSRGPTVAGAAPASRPARRGLDRGAGGD-RL 234

Query: 327 DSGQREENHRRSPSFPSKRSLRRT 350
            +G      RR+P+     +  R+
Sbjct: 235 PAGAASPRSRRAPAGARGWTRPRS 258


>gi|297198341|ref|ZP_06915738.1| ribosomal protein S4 [Streptomyces sviceus ATCC 29083]
 gi|197714395|gb|EDY58429.1| ribosomal protein S4 [Streptomyces sviceus ATCC 29083]
          Length = 204

 Score = 40.5 bits (93), Expect = 0.41,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 3/50 (6%)

Query: 15  RVSKVIARAGIASRR--EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R+GIA R   +  +M+    ++VNG  +++ +  V   D + V
Sbjct: 93  RLDALVLRSGIA-RTIYQARQMVVHGHIEVNGQKVDKPSFRVRPDDVVMV 141


>gi|29830837|ref|NP_825471.1| penicillin-binding protein [Streptomyces avermitilis MA-4680]
 gi|29607950|dbj|BAC72006.1| putative penicillin-binding protein [Streptomyces avermitilis
           MA-4680]
          Length = 929

 Score = 40.5 bits (93), Expect = 0.41,   Method: Composition-based stats.
 Identities = 12/97 (12%), Positives = 26/97 (26%), Gaps = 1/97 (1%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
              P           P   ++        +  S  +  L + ++      RR  ++    
Sbjct: 2   RKRPHPYLGGTGNQPPFPGAQRCACPRSNRSMSEHRRKLPQPQEGGRAAARRGQSAPSGR 61

Query: 317 AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                ++  S S          P +  +   RR S +
Sbjct: 62  RAAPRAATGSPSDSYGAGDEERP-YGGRAEARRASQR 97


>gi|21220006|ref|NP_625785.1| 30S ribosomal protein S4 [Streptomyces coelicolor A3(2)]
 gi|256788896|ref|ZP_05527327.1| 30S ribosomal protein S4 [Streptomyces lividans TK24]
 gi|289772782|ref|ZP_06532160.1| 30S ribosomal protein S4 [Streptomyces lividans TK24]
 gi|26399515|sp|Q9KXP5|RS4_STRCO RecName: Full=30S ribosomal protein S4
 gi|8249964|emb|CAB93385.1| 30S ribosomal protein S4 [Streptomyces coelicolor A3(2)]
 gi|289702981|gb|EFD70410.1| 30S ribosomal protein S4 [Streptomyces lividans TK24]
          Length = 204

 Score = 40.5 bits (93), Expect = 0.41,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 28/50 (56%), Gaps = 3/50 (6%)

Query: 15  RVSKVIARAGIASRR--EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R+GIA R   +  +M+    ++VNG  +++ +  V   D ++V
Sbjct: 93  RLDALVLRSGIA-RTIYQARQMVVHGHIQVNGQKVDKPSFRVRPDDVVQV 141


>gi|322436380|ref|YP_004218592.1| hypothetical protein AciX9_2789 [Acidobacterium sp. MP5ACTX9]
 gi|321164107|gb|ADW69812.1| hypothetical protein AciX9_2789 [Acidobacterium sp. MP5ACTX9]
          Length = 759

 Score = 40.5 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 13/112 (11%), Positives = 24/112 (21%), Gaps = 6/112 (5%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                   +   P +S      DR +          +   + S +     +     P   
Sbjct: 480 RPPRRDFGDSPRPSFSDRPSFSDRGDRGERPAAGGFKRPGSYSPRPSFGGKPSFGGPRED 539

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK------RSLRRTSAK 353
           R    +             + G    +    PSF  +       S  R    
Sbjct: 540 RGERPSGGGFAPRKPFTPREGGGGSFDRPSRPSFGDRPSYDRKPSFPRNEQS 591



 Score = 39.4 bits (90), Expect = 0.79,   Method: Composition-based stats.
 Identities = 14/116 (12%), Positives = 27/116 (23%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE    + R+          +   +     +        +  ++ P  FT          
Sbjct: 368 RERRPFVKRDDDRGARPTFNKPWDEDRSARTPRPDSGSADQGTDAPRTFTPRPSRPFGDR 427

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
             +   +      R          +   S   +   +RE      PSF       R
Sbjct: 428 PSAGAGRPGGFQKRSFGGDREGGPRKTFSKPGTFGRKREGGFDSKPSFGGDSRPPR 483



 Score = 38.2 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 9/115 (7%), Positives = 21/115 (18%), Gaps = 3/115 (2%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            ++       ++               R              R      +  G  ++   
Sbjct: 392 EDRSARTPRPDSGSADQGTDAPRTFTPRPSRPFGDRPSAGAGRPGGFQKRSFGGDREGGP 451

Query: 302 ATPVHRRN---LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                +                     S   +R+      PSF  + S      +
Sbjct: 452 RKTFSKPGTFGRKREGGFDSKPSFGGDSRPPRRDFGDSPRPSFSDRPSFSDRGDR 506



 Score = 36.7 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 11/114 (9%), Positives = 20/114 (17%), Gaps = 5/114 (4%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P              +  +     R            R     S+ +     +      
Sbjct: 427 RPSAGAGRPGGFQKRSFGGDREGGPRKTFSKPGTFGRKREGGFDSKPSFGGDSRPPRRDF 486

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQ-----REENHRRSPSFPSKRSLRRTSAKK 354
                 S              +        R  ++   PSF  K S       +
Sbjct: 487 GDSPRPSFSDRPSFSDRGDRGERPAAGGFKRPGSYSPRPSFGGKPSFGGPREDR 540


>gi|325981553|ref|YP_004293955.1| RNA-binding S4 domain-containing protein [Nitrosomonas sp. AL212]
 gi|325531072|gb|ADZ25793.1| RNA-binding S4 domain protein [Nitrosomonas sp. AL212]
          Length = 134

 Score = 40.5 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 2/56 (3%)

Query: 8  QENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           EN    R+ K + A     +R      I + RV +N   ++  A  V   D +E+
Sbjct: 4  NENNEKYRIDKWLFAARFFKTRALAAEAIDRGRVAINDQKIK-PAKTVAVGDKVEI 58


>gi|149203654|ref|ZP_01880623.1| ATP-dependent RNA helicase, DEAD/DEAH box family protein
           [Roseovarius sp. TM1035]
 gi|149142771|gb|EDM30813.1| ATP-dependent RNA helicase, DEAD/DEAH box family protein
           [Roseovarius sp. TM1035]
          Length = 759

 Score = 40.5 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 9/96 (9%), Positives = 19/96 (19%), Gaps = 1/96 (1%)

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
              +         +P   +       +   +  +  G    K    P   R    +    
Sbjct: 586 TRAVEDGTVTPYRKPRAEAGDAPRPAKKPWSGDKPAGKPANKPFGKPAGDRKPGKSFGKP 645

Query: 318 KGIH-SSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           +G       S  G +      +          R   
Sbjct: 646 EGRPYDKSDSKPGAKPYGKPGAKPSDKPFDKPRARP 681


>gi|255023220|ref|ZP_05295206.1| S4 RNA-binding domain-containing protein [Listeria monocytogenes
          FSL J1-208]
          Length = 66

 Score = 40.5 bits (93), Expect = 0.43,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 25/52 (48%), Gaps = 2/52 (3%)

Query: 12 TPQRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          T  R+ K +  + +  RR   + +  + R+ VNG+  +    NV S D + +
Sbjct: 3  TTMRLDKYLKVSRLIKRRTVAKEVAEKGRIAVNGVTAK-PGTNVKSGDELVI 53


>gi|226306119|ref|YP_002766079.1| translation initiation factor IF-2 [Rhodococcus erythropolis PR4]
 gi|259491499|sp|C0ZYA5|IF2_RHOE4 RecName: Full=Translation initiation factor IF-2
 gi|226185236|dbj|BAH33340.1| translation initiation factor IF-2 [Rhodococcus erythropolis PR4]
          Length = 981

 Score = 40.5 bits (93), Expect = 0.43,   Method: Composition-based stats.
 Identities = 6/103 (5%), Positives = 12/103 (11%), Gaps = 1/103 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                            +  +            P            +    +      P 
Sbjct: 165 AKPGGPRPGPKAPRVGNNPYSSAPAERPAPRPAPGAPRPGAGQGGSRPAPGQGGPRPAPG 224

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                 +                    +   R PS  S     
Sbjct: 225 QGGPRPAPGQGGPRPAPGQGGPRPPAGQGGPR-PSPGSMPPRP 266



 Score = 37.9 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 9/96 (9%), Positives = 18/96 (18%), Gaps = 1/96 (1%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
                           N             + +         +  + P   +        
Sbjct: 165 AKPGGPRPGPKAPRVGNNPYSSAPAERPAPRPAPGAPRPGAGQGGSRPAPGQGGPRPAPG 224

Query: 317 AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             G   +     G R    +  P  P+ +   R S 
Sbjct: 225 QGGPRPAPG-QGGPRPAPGQGGPRPPAGQGGPRPSP 259


>gi|330836918|ref|YP_004411559.1| rRNA (guanine-N(2)-)-methyltransferase [Spirochaeta coccoides DSM
           17374]
 gi|329748821|gb|AEC02177.1| rRNA (guanine-N(2)-)-methyltransferase [Spirochaeta coccoides DSM
           17374]
          Length = 865

 Score = 40.5 bits (93), Expect = 0.43,   Method: Composition-based stats.
 Identities = 11/114 (9%), Positives = 24/114 (21%), Gaps = 1/114 (0%)

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           +  R++              +  +          +   +    +   +   +        
Sbjct: 567 EERRDERKNGDRPRYNDERGSRSFDRPRGGDRPFDRSRDDRPRYNSDRPRFNDDRPRGGD 626

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           +        R   S     +G    F      R   +   PSF   R  R    
Sbjct: 627 RPFDRSRDDRPRFSRDRDDRGGRP-FDRSRDDRPRYNSDRPSFSRDRDDRGGRP 679



 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 15/116 (12%), Positives = 28/116 (24%), Gaps = 4/116 (3%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+  G    +  +        S +   R   +  S   D   R  +   +      +   
Sbjct: 730 RDDRGGRPFDRPRGGDRPFDRSRDDRPRYNSDRPSFSRDRDDRGGRPFDRSRDDRPRFNS 789

Query: 302 ATPVHRRNLASNVWMA----KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             P   R+            +G    F      R   +   P F   R    +  +
Sbjct: 790 DRPSFSRDRDDRGGRPFDRPRGGDRPFDRSRDDRPRFNSDRPRFNEDRPRTESKKR 845



 Score = 38.2 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 14/125 (11%), Positives = 28/125 (22%), Gaps = 4/125 (3%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R   ++  R    P   +              +      +      D      ++   + 
Sbjct: 580 RYNDERGSRSFDRPRGGDRPFDRSRDDRPRYNSDRPRFNDDRPRGGDRPFDRSRDDRPRF 639

Query: 294 GLSKQKKLATPVHR-RNLASNVWMAKGIHSSFLSDSGQRE---ENHRRSPSFPSKRSLRR 349
              +  +   P  R R+        +   S    D G R        R      + S  R
Sbjct: 640 SRDRDDRGGRPFDRSRDDRPRYNSDRPSFSRDRDDRGGRPFDRSRDDRPRYNSDRPSFSR 699

Query: 350 TSAKK 354
               +
Sbjct: 700 DRDDR 704



 Score = 37.9 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 17/120 (14%), Positives = 35/120 (29%), Gaps = 7/120 (5%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG---LSKQ 298
           R+  G    + ++ +         +  RDR +      D     +   +         + 
Sbjct: 643 RDDRGGRPFDRSRDDRPRYNSDRPSFSRDRDDRGGRPFDRSRDDRPRYNSDRPSFSRDRD 702

Query: 299 KKLATPVHR-RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP---SKRSLRRTSAKK 354
            +   P  R R+        +   S    D G R  +  R    P   S+    R ++ +
Sbjct: 703 DRGGRPFDRSRDDRPRFNSDRPSFSRDRDDRGGRPFDRPRGGDRPFDRSRDDRPRYNSDR 762



 Score = 36.7 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 15/107 (14%), Positives = 24/107 (22%), Gaps = 4/107 (3%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
            +           S +   R   +  S   D   R  +   +      +     P   R+
Sbjct: 670 RDRDDRGGRPFDRSRDDRPRYNSDRPSFSRDRDDRGGRPFDRSRDDRPRFNSDRPSFSRD 729

Query: 310 LASNVWMA----KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                       +G    F      R   +   PSF   R  R    
Sbjct: 730 RDDRGGRPFDRPRGGDRPFDRSRDDRPRYNSDRPSFSRDRDDRGGRP 776



 Score = 36.7 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 13/116 (11%), Positives = 24/116 (20%), Gaps = 6/116 (5%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+       E    +         +   DRP       D     +   +         + 
Sbjct: 563 RKAFEERRDERKNGDRPRYNDERGSRSFDRPRGGDRPFDRSRDDRPRYNSDRPRFNDDRP 622

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQRE---ENHRRSPSFPSKRSLRRTSAKK 354
                  + +      +   S    D G R        R      + S  R    +
Sbjct: 623 RGGDRPFDRS---RDDRPRFSRDRDDRGGRPFDRSRDDRPRYNSDRPSFSRDRDDR 675



 Score = 36.7 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 14/130 (10%), Positives = 30/130 (23%), Gaps = 17/130 (13%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+  G    + ++ +         +  RDR +      D      +   +      +   
Sbjct: 701 RDDRGGRPFDRSRDDRPRFNSDRPSFSRDRDDRGGRPFDRPRGGDRPFDRSRDDRPRYNS 760

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSD--------------SGQREENHRRSPSFP---SK 344
             P   R+                                 G R  +  R    P   S+
Sbjct: 761 DRPSFSRDRDDRGGRPFDRSRDDRPRFNSDRPSFSRDRDDRGGRPFDRPRGGDRPFDRSR 820

Query: 345 RSLRRTSAKK 354
               R ++ +
Sbjct: 821 DDRPRFNSDR 830



 Score = 36.3 bits (82), Expect = 6.5,   Method: Composition-based stats.
 Identities = 11/114 (9%), Positives = 22/114 (19%), Gaps = 2/114 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+       +           S +   R   +  S   D   R  +   +      +   
Sbjct: 633 RDDRPRFSRDRDDRGGRPFDRSRDDRPRYNSDRPSFSRDRDDRGGRPFDRSRDDRPRYNS 692

Query: 302 ATPVHRRNLASNVWMA-KGIHSSFLSDSGQREENHRRSPSFPSKR-SLRRTSAK 353
             P   R+                   +  R    R       +     R   +
Sbjct: 693 DRPSFSRDRDDRGGRPFDRSRDDRPRFNSDRPSFSRDRDDRGGRPFDRPRGGDR 746



 Score = 36.3 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 14/99 (14%), Positives = 23/99 (23%), Gaps = 1/99 (1%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
           +   +  +  +    R      S+   D  R +K   ++    K          R   S 
Sbjct: 531 EWGEEPALSPASKAERGFSKDDSDNGRDNARGRKAFEERRDERKNGDRPRYNDERGSRSF 590

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                G    F      R   +   P F   R       
Sbjct: 591 DRPRGGDRP-FDRSRDDRPRYNSDRPRFNDDRPRGGDRP 628


>gi|297707606|ref|XP_002830593.1| PREDICTED: LOW QUALITY PROTEIN: zinc finger protein 512B-like [Pongo
            abelii]
          Length = 1083

 Score = 40.5 bits (93), Expect = 0.43,   Method: Composition-based stats.
 Identities = 22/140 (15%), Positives = 38/140 (27%), Gaps = 6/140 (4%)

Query: 202  KKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV-SKKILREQLGPHLLEEAQVNLDAP 260
                E     V+ L          G  LAG  R +   K    + G           +  
Sbjct: 945  NDCCEAIYSSVSGLK-AHLASCSKGAHLAGKYRCLLCPKEFSSESGVKYHILKTHAENWF 1003

Query: 261  IYSSETLVRDRPN----IISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
              S++   + R         E   +    KK   +    + ++ +A    RR+       
Sbjct: 1004 RTSADPPPKHRSQDSLVPKKEKKKNLAGGKKRGRKPKERTPEEPVAKLPPRRDDWPPGCR 1063

Query: 317  AKGIHSSFLSDSGQREENHR 336
             KG   S     G  +   +
Sbjct: 1064 DKGARGSTGRKVGASKAPEK 1083


>gi|195147888|ref|XP_002014906.1| GL19425 [Drosophila persimilis]
 gi|194106859|gb|EDW28902.1| GL19425 [Drosophila persimilis]
          Length = 1337

 Score = 40.5 bits (93), Expect = 0.43,   Method: Composition-based stats.
 Identities = 13/105 (12%), Positives = 29/105 (27%), Gaps = 9/105 (8%)

Query: 246  GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            GP +  E +         +    R R    S   +     +     + G S+  +  +  
Sbjct: 1156 GPPMGREQERQPHYHHQLNGNGARKREPSFSAHEERHPERRGERDARRGESRGLRGDSGG 1215

Query: 306  HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
             R +  S    ++G+         +         +   +   RR 
Sbjct: 1216 RRGDSGSRRGESRGLRGDSGGRRPE---------TRRGESQGRRN 1251



 Score = 40.2 bits (92), Expect = 0.49,   Method: Composition-based stats.
 Identities = 12/102 (11%), Positives = 26/102 (25%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
             ++  PH   +   N       S +   +R        D      +     +G  +    
Sbjct: 1162 EQERQPHYHHQLNGNGARKREPSFSAHEERHPERRGERDARRGESRGLRGDSGGRRGDSG 1221

Query: 302  ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
            +     R L  +    +       S   + +   +R     S
Sbjct: 1222 SRRGESRGLRGDSGGRRPETRRGESQGRRNDRGEQRGGRLGS 1263



 Score = 39.4 bits (90), Expect = 0.81,   Method: Composition-based stats.
 Identities = 10/107 (9%), Positives = 26/107 (24%)

Query: 248  HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               +E     +            +P+   ++  +  R ++ S   +     ++      R
Sbjct: 1143 KTRKEDSDGFNLEGPPMGREQERQPHYHHQLNGNGARKREPSFSAHEERHPERRGERDAR 1202

Query: 308  RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            R  +  +    G                R         + R  S  +
Sbjct: 1203 RGESRGLRGDSGGRRGDSGSRRGESRGLRGDSGGRRPETRRGESQGR 1249



 Score = 36.7 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 11/103 (10%), Positives = 23/103 (22%), Gaps = 7/103 (6%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            R+    H L         P +S+            +     +R  +  S         + 
Sbjct: 1165 RQPHYHHQLNGNGARKREPSFSAHEERHPERRGERDARRGESRGLRGDS-------GGRR 1217

Query: 302  ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
                 RR  +  +    G           +   + R      +
Sbjct: 1218 GDSGSRRGESRGLRGDSGGRRPETRRGESQGRRNDRGEQRGGR 1260


>gi|5821143|dbj|BAA83713.1| RNA binding protein [Homo sapiens]
          Length = 1262

 Score = 40.5 bits (93), Expect = 0.44,   Method: Composition-based stats.
 Identities = 9/108 (8%), Positives = 21/108 (19%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                            S   +     +              + +    + + +  AT  
Sbjct: 222 RHASSSPESPKPAPAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAK 281

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R+ +          S        R          P +R   R+  +
Sbjct: 282 RGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQR 329



 Score = 40.2 bits (92), Expect = 0.51,   Method: Composition-based stats.
 Identities = 11/98 (11%), Positives = 22/98 (22%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P      +++      +       R    S  P       ++ +       + +  T  
Sbjct: 234 APAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKR 293

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
                 S  W        +      +     RSP  P 
Sbjct: 294 GHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPG 331



 Score = 37.5 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 22/135 (16%), Positives = 34/135 (25%), Gaps = 10/135 (7%)

Query: 230 AGSTREV----SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
            GS RE+    + K             +         S       R    S  P      
Sbjct: 237 PGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKRGHS 296

Query: 286 KKNSSQKNGLSKQKK--LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
           +  S Q       ++   +    RR  + +        S      G+     R      S
Sbjct: 297 RSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRSHSRS 356

Query: 344 K----RSLRRTSAKK 354
                RS  RT A++
Sbjct: 357 PATRGRSRSRTPARR 371


>gi|149045217|gb|EDL98303.1| rCG43985 [Rattus norvegicus]
          Length = 1007

 Score = 40.2 bits (92), Expect = 0.44,   Method: Composition-based stats.
 Identities = 17/102 (16%), Positives = 30/102 (29%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           EE     D              +  S+ P D     K+   ++   K K+      ++ +
Sbjct: 267 EEKGKIKDRKKSPIVNERSRDRSKKSKSPVDLRDKSKDRRSRSKERKSKRSEIDKEKKPI 326

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            S    A     +            RRS S   +   RR+ +
Sbjct: 327 KSPSKDASSGKENRSPSRRPGRSPKRRSLSPKQRDKSRRSRS 368


>gi|6690017|gb|AAF23950.1| NTR [Papiine herpesvirus 1]
          Length = 608

 Score = 40.2 bits (92), Expect = 0.44,   Method: Composition-based stats.
 Identities = 16/121 (13%), Positives = 24/121 (19%), Gaps = 4/121 (3%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            +      GP                S    R R +     P      + +       + 
Sbjct: 24  GREAGRTWGPCPAPSPPPAFQVHGPRSPRTERRRGSAQRGHPPPGAGQRPSGPTGGHPAA 83

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS----LRRTSAK 353
                    R                           H  +P  P  RS     RR SA+
Sbjct: 84  PGAPGPRSPRTERRRGSAQRGHPPPGAGQRPSGPTGGHPAAPGAPGPRSPRTERRRGSAQ 143

Query: 354 K 354
           +
Sbjct: 144 R 144



 Score = 39.8 bits (91), Expect = 0.57,   Method: Composition-based stats.
 Identities = 16/105 (15%), Positives = 23/105 (21%), Gaps = 4/105 (3%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
                AP   S    R R +     P      + +       +          R      
Sbjct: 81  PAAPGAPGPRSPRTERRRGSAQRGHPPPGAGQRPSGPTGGHPAAPGAPGPRSPRTERRRG 140

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS----LRRTSAKK 354
                                H  +P  P  RS     RR SA++
Sbjct: 141 SAQRGHPPPGAGQRPSGPTGGHPAAPGAPGPRSPRTERRRGSAQR 185



 Score = 39.8 bits (91), Expect = 0.57,   Method: Composition-based stats.
 Identities = 16/105 (15%), Positives = 23/105 (21%), Gaps = 4/105 (3%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
                AP   S    R R +     P      + +       +          R      
Sbjct: 122 PAAPGAPGPRSPRTERRRGSAQRGHPPPGAGQRPSGPTGGHPAAPGAPGPRSPRTERRRG 181

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS----LRRTSAKK 354
                                H  +P  P  RS     RR SA++
Sbjct: 182 SAQRGHPPPGAGQRPSGPTGGHPAAPGAPGPRSPRTERRRGSAQR 226



 Score = 39.8 bits (91), Expect = 0.57,   Method: Composition-based stats.
 Identities = 16/105 (15%), Positives = 23/105 (21%), Gaps = 4/105 (3%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
                AP   S    R R +     P      + +       +          R      
Sbjct: 163 PAAPGAPGPRSPRTERRRGSAQRGHPPPGAGQRPSGPTGGHPAAPGAPGPRSPRTERRRG 222

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS----LRRTSAKK 354
                                H  +P  P  RS     RR SA++
Sbjct: 223 SAQRGHPPPGAGQRPSGPTGGHPAAPGAPGPRSPRTERRRGSAQR 267



 Score = 39.8 bits (91), Expect = 0.57,   Method: Composition-based stats.
 Identities = 16/105 (15%), Positives = 23/105 (21%), Gaps = 4/105 (3%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
                AP   S    R R +     P      + +       +          R      
Sbjct: 204 PAAPGAPGPRSPRTERRRGSAQRGHPPPGAGQRPSGPTGGHPAAPGAPGPRSPRTERRRG 263

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS----LRRTSAKK 354
                                H  +P  P  RS     RR SA++
Sbjct: 264 SAQRGHPPPGAGQRPSGPTGGHPAAPGAPGPRSPRTERRRGSAQR 308



 Score = 39.8 bits (91), Expect = 0.57,   Method: Composition-based stats.
 Identities = 16/105 (15%), Positives = 23/105 (21%), Gaps = 4/105 (3%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
                AP   S    R R +     P      + +       +          R      
Sbjct: 245 PAAPGAPGPRSPRTERRRGSAQRGHPPPGAGQRPSGPTGGHPAAPGAPGPRSPRTERRRG 304

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS----LRRTSAKK 354
                                H  +P  P  RS     RR SA++
Sbjct: 305 SAQRGHPPPGAGQRPSGPTGGHPAAPGAPGPRSPRTERRRGSAQR 349



 Score = 39.8 bits (91), Expect = 0.57,   Method: Composition-based stats.
 Identities = 16/105 (15%), Positives = 23/105 (21%), Gaps = 4/105 (3%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
                AP   S    R R +     P      + +       +          R      
Sbjct: 286 PAAPGAPGPRSPRTERRRGSAQRGHPPPGAGQRPSGPTGGHPAAPGAPGPRSPRTERRRG 345

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS----LRRTSAKK 354
                                H  +P  P  RS     RR SA++
Sbjct: 346 SAQRGHPPPGAGQRPSGPTGGHPAAPGAPGPRSPRTERRRGSAQR 390



 Score = 39.8 bits (91), Expect = 0.57,   Method: Composition-based stats.
 Identities = 16/105 (15%), Positives = 23/105 (21%), Gaps = 4/105 (3%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
                AP   S    R R +     P      + +       +          R      
Sbjct: 327 PAAPGAPGPRSPRTERRRGSAQRGHPPPGAGQRPSGPTGGHPAAPGAPGPRSPRTERRRG 386

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS----LRRTSAKK 354
                                H  +P  P  RS     RR SA++
Sbjct: 387 SAQRGHPPPGAGQRPSGPTGGHPAAPGAPGPRSPRTERRRGSAQR 431



 Score = 39.8 bits (91), Expect = 0.57,   Method: Composition-based stats.
 Identities = 16/105 (15%), Positives = 23/105 (21%), Gaps = 4/105 (3%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
                AP   S    R R +     P      + +       +          R      
Sbjct: 368 PAAPGAPGPRSPRTERRRGSAQRGHPPPGAGQRPSGPTGGHPAAPGAPGPRSPRTERRRG 427

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS----LRRTSAKK 354
                                H  +P  P  RS     RR SA++
Sbjct: 428 SAQRGHPPPGAGQRPSGPTGGHPAAPGAPGPRSPRTERRRGSAQR 472



 Score = 39.8 bits (91), Expect = 0.57,   Method: Composition-based stats.
 Identities = 16/105 (15%), Positives = 23/105 (21%), Gaps = 4/105 (3%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
                AP   S    R R +     P      + +       +          R      
Sbjct: 409 PAAPGAPGPRSPRTERRRGSAQRGHPPPGAGQRPSGPTGGHPAAPGAPGPRSPRTERRRG 468

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS----LRRTSAKK 354
                                H  +P  P  RS     RR SA++
Sbjct: 469 SAQRGHPPPGAGQRPSGPTGGHPAAPGAPGPRSPRTERRRGSAQR 513



 Score = 39.8 bits (91), Expect = 0.57,   Method: Composition-based stats.
 Identities = 16/105 (15%), Positives = 23/105 (21%), Gaps = 4/105 (3%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
                AP   S    R R +     P      + +       +          R      
Sbjct: 450 PAAPGAPGPRSPRTERRRGSAQRGHPPPGAGQRPSGPTGGHPAAPGAPGPRSPRTERRRG 509

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS----LRRTSAKK 354
                                H  +P  P  RS     RR SA++
Sbjct: 510 SAQRGHPPPGAGQRPSGPTGGHPAAPGAPGPRSPRTERRRGSAQR 554


>gi|58865416|ref|NP_001011923.1| serine/threonine-protein kinase PRP4 homolog [Rattus norvegicus]
 gi|81883388|sp|Q5RKH1|PRP4B_RAT RecName: Full=Serine/threonine-protein kinase PRP4 homolog;
           AltName: Full=PRP4 pre-mRNA-processing factor 4 homolog
 gi|55715685|gb|AAH85927.1| PRP4 pre-mRNA processing factor 4 homolog B (yeast) [Rattus
           norvegicus]
          Length = 1007

 Score = 40.2 bits (92), Expect = 0.44,   Method: Composition-based stats.
 Identities = 17/102 (16%), Positives = 30/102 (29%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           EE     D              +  S+ P D     K+   ++   K K+      ++ +
Sbjct: 267 EEKGKIKDRKKSPIVNERSRDRSKKSKSPVDLRDKSKDRRSRSKERKSKRSEIDKEKKPI 326

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            S    A     +            RRS S   +   RR+ +
Sbjct: 327 KSPSKDASSGKENRSPSRRPGRSPKRRSLSPKQRDKSRRSRS 368


>gi|297162095|gb|ADI11807.1| magnesium or manganese-dependent protein phosphatase [Streptomyces
           bingchenggensis BCW-1]
          Length = 591

 Score = 40.2 bits (92), Expect = 0.45,   Method: Composition-based stats.
 Identities = 14/109 (12%), Positives = 21/109 (19%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R  +                       R         P              G  +  + 
Sbjct: 403 RHTVPRRPESARHRPCPHGRPRRRPAPRRHDPAPRPCPRALRGAHHELGVPRGPGRGHRR 462

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
            T             A   H +    +G +    RR P  P+     RT
Sbjct: 463 PTGHRPPAGRLGTGRAGLHHRTGRQRAGHQRHPLRRRPGRPAAHPQERT 511


>gi|150391088|ref|YP_001321137.1| DEAD/DEAH box helicase domain-containing protein [Alkaliphilus
           metalliredigens QYMF]
 gi|149950950|gb|ABR49478.1| DEAD/DEAH box helicase domain protein [Alkaliphilus metalliredigens
           QYMF]
          Length = 549

 Score = 40.2 bits (92), Expect = 0.45,   Method: Composition-based stats.
 Identities = 14/101 (13%), Positives = 26/101 (25%), Gaps = 3/101 (2%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
               + +            RDRP+     P D      ++  + G +K +         +
Sbjct: 416 RPGDKRDRPTDKKGRPGDKRDRPSDNKGRPGDKRDRPSDNKGRPGDNKGRPGDNKGRPGD 475

Query: 310 LASNVWMAKGIHSSFLSDSG---QREENHRRSPSFPSKRSL 347
                   KG         G    R  +++  P     R  
Sbjct: 476 NKGRPGDNKGRPGDNKGRPGDNKGRPGDNKGRPGDNKGRPG 516



 Score = 39.8 bits (91), Expect = 0.71,   Method: Composition-based stats.
 Identities = 12/103 (11%), Positives = 25/103 (24%), Gaps = 3/103 (2%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                 +           +  + RP    + P D      ++  + G +K +        
Sbjct: 421 RDRPTDKKGRPGDKRDRPSDNKGRPGDKRDRPSDNKGRPGDNKGRPGDNKGRPGDNKGRP 480

Query: 308 RNLASNVWMAKGIHSSFLSDSG---QREENHRRSPSFPSKRSL 347
            +        KG         G    R  +++  P     R  
Sbjct: 481 GDNKGRPGDNKGRPGDNKGRPGDNKGRPGDNKGRPGDNKGRPG 523



 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 13/108 (12%), Positives = 29/108 (26%), Gaps = 3/108 (2%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
               + +  +         RDRP+     P D      ++  + G +K +         +
Sbjct: 430 RPGDKRDRPSDNKGRPGDKRDRPSDNKGRPGDNKGRPGDNKGRPGDNKGRPGDNKGRPGD 489

Query: 310 LASNVWMAKGIHSSFLSDSG---QREENHRRSPSFPSKRSLRRTSAKK 354
                   KG         G    R  +++  P    +   +     +
Sbjct: 490 NKGRPGDNKGRPGDNKGRPGDNKGRPGDNKGRPGDNKESGYKGNKNTR 537



 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 17/98 (17%), Positives = 26/98 (26%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
            EE Q    +P        +D               KK            K   P  +R+
Sbjct: 377 DEEEQDTKKSPKGRGNDKSKDFKKGKYGDKKGKPGDKKGRPGDKRDRPTDKKGRPGDKRD 436

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
             S+     G      SD+  R  +++  P     R  
Sbjct: 437 RPSDNKGRPGDKRDRPSDNKGRPGDNKGRPGDNKGRPG 474



 Score = 36.7 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 9/120 (7%), Positives = 24/120 (20%), Gaps = 1/120 (0%)

Query: 230 AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
            G  R+      + + G      +                      ++      + +   
Sbjct: 431 PGDKRD-RPSDNKGRPGDKRDRPSDNKGRPGDNKGRPGDNKGRPGDNKGRPGDNKGRPGD 489

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           ++      + +      R                   +SG +   + R     S     R
Sbjct: 490 NKGRPGDNKGRPGDNKGRPGDNKGRPGDNKGRPGDNKESGYKGNKNTRGNQSSSNNKRSR 549


>gi|301620046|ref|XP_002939395.1| PREDICTED: membrane-associated guanylate kinase, WW and PDZ
            domain-containing protein 1 isoform 1 [Xenopus (Silurana)
            tropicalis]
          Length = 1452

 Score = 40.2 bits (92), Expect = 0.45,   Method: Composition-based stats.
 Identities = 16/103 (15%), Positives = 30/103 (29%), Gaps = 2/103 (1%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            R+   P      Q +              R        +   R +KN  +K    ++ + 
Sbjct: 1286 RKDRSPEGRRPRQADRTMTNGQKRQSPEKRNEGTRSAENTLERREKNERRKEVSPQKPRE 1345

Query: 302  ATPVHRRNLASNVWMAKGIH--SSFLSDSGQREENHRRSPSFP 342
             +PV RR+ +                S   +RE +  R  +  
Sbjct: 1346 RSPVRRRDGSPTRRRKSLDRFMDQRRSPDRRRESSPDRRRAKS 1388



 Score = 36.7 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 19/134 (14%), Positives = 29/134 (21%), Gaps = 5/134 (3%)

Query: 226  GTLLAGSTREV--SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
             +L  G  R      K  RE   PH                       P        D T
Sbjct: 1243 KSLQHGDKRAYVKDPKGNREYGRPHNEHHTWNGSSKNYSVQNNRKDRSPEGRRPRQADRT 1302

Query: 284  RMKKNSSQKNGLSKQKKLATPV--HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF 341
                   Q      +   +      RR                 S   +R+ +  R    
Sbjct: 1303 MTNGQKRQSPEKRNEGTRSAENTLERREKNERRKEVSPQKPRERSPVRRRDGSPTRRRKS 1362

Query: 342  PSKR-SLRRTSAKK 354
              +    RR+  ++
Sbjct: 1363 LDRFMDQRRSPDRR 1376


>gi|283853178|ref|ZP_06370431.1| ribosomal protein S4 [Desulfovibrio sp. FW1012B]
 gi|283571436|gb|EFC19443.1| ribosomal protein S4 [Desulfovibrio sp. FW1012B]
          Length = 208

 Score = 40.2 bits (92), Expect = 0.45,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R G A SR +  +++      +NG  +   ++ V   D IEV
Sbjct: 99  RMDNVVYRLGFANSRNQARQLVRHGLFVLNGHRVTIPSLQVKVGDVIEV 147


>gi|258513667|ref|YP_003189889.1| 30S ribosomal protein S4 [Desulfotomaculum acetoxidans DSM 771]
 gi|257777372|gb|ACV61266.1| ribosomal protein S4 [Desulfotomaculum acetoxidans DSM 771]
          Length = 208

 Score = 40.2 bits (92), Expect = 0.45,   Method: Composition-based stats.
 Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 1/47 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           R+  VI R G+  SR E  +++      VNG  ++  +  V   D I
Sbjct: 99  RMDNVIFRMGLGASRVEARQLVTHGHFTVNGRKVDIPSFLVKVGDVI 145


>gi|163854145|ref|YP_001642188.1| OmpA/MotB domain-containing protein [Methylobacterium extorquens
           PA1]
 gi|163665750|gb|ABY33117.1| OmpA/MotB domain protein [Methylobacterium extorquens PA1]
          Length = 717

 Score = 40.2 bits (92), Expect = 0.45,   Method: Composition-based stats.
 Identities = 9/109 (8%), Positives = 24/109 (22%), Gaps = 1/109 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G                        R    +    +         +     +Q++   P 
Sbjct: 68  GGVERGGPPARERPERSERPERPEPRQAPAARERPEPAERPARPERPAAQERQERPERPD 127

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +          +   ++       R E    +P+   +   R   A++
Sbjct: 128 RQERQERPDRQERPERATP-PQRPDRSEEQPAAPASRERAPDRDAPARR 175



 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 12/128 (9%), Positives = 30/128 (23%), Gaps = 16/128 (12%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            ++   E+  P    +      A   S E           E P+     ++ + ++    
Sbjct: 136 DRQERPERATPPQRPDRSEEQPAAPASRERAPDRDAPARREAPEREAPARRETPERPDRD 195

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREE----------------NHRRSPS 340
            Q +   P  R     +    +    +  +                          + P 
Sbjct: 196 GQDRPGRPAGREADRPDGAPNQRRAPNAPTPPNAERPEQATPPTATNPAQPNTPPNQRPG 255

Query: 341 FPSKRSLR 348
            P + +  
Sbjct: 256 VPGRPATP 263


>gi|332975433|gb|EGK12325.1| heat shock protein 15 [Kingella kingae ATCC 23330]
          Length = 137

 Score = 40.2 bits (92), Expect = 0.46,   Method: Composition-based stats.
 Identities = 15/61 (24%), Positives = 23/61 (37%), Gaps = 2/61 (3%)

Query: 1  MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          M       E     R+ K + A     +R    + I   RV VNGI  + +   V+  D 
Sbjct: 1  MSKHQHEDERDDTMRLDKWLWAARFFKTRSLASKHIELGRVSVNGIKTKTSKYIVV-GDV 59

Query: 60 I 60
          +
Sbjct: 60 V 60


>gi|86157987|ref|YP_464772.1| Fis family transcriptional regulator [Anaeromyxobacter dehalogenans
           2CP-C]
 gi|85774498|gb|ABC81335.1| DNA-binding protein Fis / transcriptional regulator, Fis family
           [Anaeromyxobacter dehalogenans 2CP-C]
          Length = 526

 Score = 40.2 bits (92), Expect = 0.46,   Method: Composition-based stats.
 Identities = 10/105 (9%), Positives = 20/105 (19%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                   + P  +      +R              ++      G   +     P     
Sbjct: 335 PAAGSSPAEWPGPARRPARPERAGRPPRPAGGERTPRRRMPGAGGPPDRGGRRPPRTGDR 394

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            A          + +   +  R     RSP         R    +
Sbjct: 395 PARAGAAGPAGAAPWRPRTSDRARGGERSPGAGGSPRPPRAGPGR 439


>gi|45433533|ref|NP_956114.2| eukaryotic translation initiation factor 3 subunit A [Danio rerio]
 gi|44890368|gb|AAH66670.1| Eukaryotic translation initiation factor 3, subunit 10 (theta) [Danio
            rerio]
          Length = 1267

 Score = 40.2 bits (92), Expect = 0.46,   Method: Composition-based stats.
 Identities = 14/129 (10%), Positives = 25/129 (19%), Gaps = 5/129 (3%)

Query: 229  LAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
                 RE  ++  RE          +                  +       D  R  + 
Sbjct: 914  WRQEGREGREEPDREDRDLPFRRGGESARRGASDEKGLRRGCDDDRGPRRGGDDERPPRR 973

Query: 289  SSQKNGLSKQKKLATPVHRRNLASNVWMA-----KGIHSSFLSDSGQREENHRRSPSFPS 343
                +  +++        RR              +G       D G R  +  R P    
Sbjct: 974  GFDDDRGTRRGFDDDRGQRRGDDDRGPRRGMDDDRGPRRPIDDDRGPRRSDDDRGPRRGF 1033

Query: 344  KRSLRRTSA 352
                     
Sbjct: 1034 DDDRGPRRG 1042



 Score = 36.3 bits (82), Expect = 7.5,   Method: Composition-based stats.
 Identities = 15/119 (12%), Positives = 28/119 (23%), Gaps = 2/119 (1%)

Query: 234  REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
            R V  +  R++      E  + + D P        R       E             ++ 
Sbjct: 907  RPVPDRDWRQEGREGREEPDREDRDLPFRRGGESARR--GASDEKGLRRGCDDDRGPRRG 964

Query: 294  GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            G  ++         R         +G          +R  +  R P  P         +
Sbjct: 965  GDDERPPRRGFDDDRGTRRGFDDDRGQRRGDDDRGPRRGMDDDRGPRRPIDDDRGPRRS 1023


>gi|114621761|ref|XP_001134783.1| PREDICTED: hypothetical protein [Pan troglodytes]
          Length = 374

 Score = 40.2 bits (92), Expect = 0.47,   Method: Composition-based stats.
 Identities = 10/113 (8%), Positives = 23/113 (20%), Gaps = 1/113 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+         +     +         R+ P               +  + +  +  +  
Sbjct: 77  RQCRDGAPSAGSGPPSTSSRALPRRGTRNPPGRAPSPAPLQGPPLPSWRRGDPPATGRPR 136

Query: 302 ATPVHRRNLASNVWMAKGIHSSF-LSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             P                  +    + G R      S    S+  L R   +
Sbjct: 137 PAPRVPHTPQPRAGALPAEKHTPLREEPGARPAPRAPSRRPSSRERLGRGRPR 189



 Score = 37.1 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 14/103 (13%), Positives = 27/103 (26%), Gaps = 1/103 (0%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
              +    AP+         R +  +           ++ Q    +   +  TP+     
Sbjct: 106 PPGRAPSPAPLQGPPLPSWRRGDPPATGRPRPAPRVPHTPQPRAGALPAEKHTPLREEPG 165

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS-KRSLRRTSA 352
           A     A     S     G+       +P  P+ +    R S 
Sbjct: 166 ARPAPRAPSRRPSSRERLGRGRPRLWATPPGPAERARAPRNSP 208


>gi|326917060|ref|XP_003204822.1| PREDICTED: serine/threonine-protein kinase PRP4 homolog [Meleagris
           gallopavo]
          Length = 1046

 Score = 40.2 bits (92), Expect = 0.47,   Method: Composition-based stats.
 Identities = 21/130 (16%), Positives = 40/130 (30%), Gaps = 7/130 (5%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNII---SEVPDDFTRMKKN 288
            TR+    +L+ +      +      D      ++  RDR            D  R  K+
Sbjct: 275 QTRKSRSPMLKRRSQEKNRKSKSPPEDRNKADDKSKSRDRRKSPVVNESKSRDRGRKSKS 334

Query: 289 SSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR----EENHRRSPSFPSK 344
            ++    SK ++  +   +   +      K I S     S  +         RSP   S 
Sbjct: 335 PAELRSKSKDRRSRSKDRKSRRSETDKDKKPIKSPSKDASSGKENRSPRRPGRSPKGRSL 394

Query: 345 RSLRRTSAKK 354
               R  +++
Sbjct: 395 SPKPREKSRR 404



 Score = 39.4 bits (90), Expect = 0.79,   Method: Composition-based stats.
 Identities = 13/102 (12%), Positives = 29/102 (28%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
              + D    S         +          + +++ + K+    +         +   S
Sbjct: 322 ESKSRDRGRKSKSPAELRSKSKDRRSRSKDRKSRRSETDKDKKPIKSPSKDASSGKENRS 381

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                +      LS   + +    RSP F  +RS +  S  +
Sbjct: 382 PRRPGRSPKGRSLSPKPREKSRRSRSPLFNDRRSKQSKSPSR 423



 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 13/109 (11%), Positives = 31/109 (28%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E       +    +       +E+  RDR        +  ++ K   S+      ++   
Sbjct: 300 EDRNKADDKSKSRDRRKSPVVNESKSRDRGRKSKSPAELRSKSKDRRSRSKDRKSRRSET 359

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
               +   + +   + G  +      G+  +    SP    K    R+ 
Sbjct: 360 DKDKKPIKSPSKDASSGKENRSPRRPGRSPKGRSLSPKPREKSRRSRSP 408



 Score = 36.3 bits (82), Expect = 7.7,   Method: Composition-based stats.
 Identities = 12/111 (10%), Positives = 31/111 (27%), Gaps = 1/111 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R++           +      S     + R +   +         K++S        ++ 
Sbjct: 326 RDRGRKSKSPAELRSKSKDRRSRSKDRKSRRSETDKDKKPIKSPSKDASSGKENRSPRRP 385

Query: 302 ATPVHRRNLASNVWMAKGIHSSF-LSDSGQREENHRRSPSFPSKRSLRRTS 351
                 R+L+           S   +D   ++         P++R   R++
Sbjct: 386 GRSPKGRSLSPKPREKSRRSRSPLFNDRRSKQSKSPSRTRSPARRLRSRSA 436


>gi|82237696|sp|Q6PCR7|EIF3A_DANRE RecName: Full=Eukaryotic translation initiation factor 3 subunit A;
            Short=eIF3a; AltName: Full=Eukaryotic translation
            initiation factor 3 subunit 10; AltName: Full=eIF-3-theta
 gi|37589184|gb|AAH59196.1| Eukaryotic translation initiation factor 3, subunit 10 (theta) [Danio
            rerio]
          Length = 1267

 Score = 40.2 bits (92), Expect = 0.47,   Method: Composition-based stats.
 Identities = 14/129 (10%), Positives = 25/129 (19%), Gaps = 5/129 (3%)

Query: 229  LAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
                 RE  ++  RE          +                  +       D  R  + 
Sbjct: 914  WRQEGREGREEPDREDRDLPFRRGGESARRGASDEKGLRRGCDDDRGPRRGGDDERPPRR 973

Query: 289  SSQKNGLSKQKKLATPVHRRNLASNVWMA-----KGIHSSFLSDSGQREENHRRSPSFPS 343
                +  +++        RR              +G       D G R  +  R P    
Sbjct: 974  GFDDDRGTRRGFDDDRGQRRGDDDRGPRRGMDDDRGPRRPIDDDRGPRRSDDDRGPRRGF 1033

Query: 344  KRSLRRTSA 352
                     
Sbjct: 1034 DDDRGPRRG 1042



 Score = 36.3 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 15/119 (12%), Positives = 28/119 (23%), Gaps = 2/119 (1%)

Query: 234  REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
            R V  +  R++      E  + + D P        R       E             ++ 
Sbjct: 907  RPVPDRDWRQEGREGREEPDREDRDLPFRRGGESARR--GASDEKGLRRGCDDDRGPRRG 964

Query: 294  GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            G  ++         R         +G          +R  +  R P  P         +
Sbjct: 965  GDDERPPRRGFDDDRGTRRGFDDDRGQRRGDDDRGPRRGMDDDRGPRRPIDDDRGPRRS 1023


>gi|225024022|ref|ZP_03713214.1| hypothetical protein EIKCOROL_00889 [Eikenella corrodens ATCC
          23834]
 gi|224943047|gb|EEG24256.1| hypothetical protein EIKCOROL_00889 [Eikenella corrodens ATCC
          23834]
          Length = 136

 Score = 40.2 bits (92), Expect = 0.48,   Method: Composition-based stats.
 Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 4/61 (6%)

Query: 1  MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          M  KN   E+    R+ K + A     +R   ++ I   RV VNG  ++  + N+   D 
Sbjct: 1  MAGKNSHDEHH--MRLDKWLWAARFFKTRGMAQKHIELGRVLVNGAKVKN-SKNIEPGDT 57

Query: 60 I 60
          I
Sbjct: 58 I 58


>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 = 40.2 bits (92), Expect = 0.48,   Method: Composition-based stats.
 Identities = 21/261 (8%), Positives = 57/261 (21%), Gaps = 54/261 (20%)

Query: 3   DKNIVQENFTPQRVSKVIA----RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           ++ IV       R+ +         G      +++++   +V+++G   + A   + +  
Sbjct: 5   EQKIVDTGEAGMRLDRWFKVHYPGLGFG---HLQKLLRSGQVRIDGSRAK-ADTRIQAGQ 60

Query: 59  HIEV----------------------DG----VPLRKAERTRLWLYHKPIGLVTTHSDPD 92
            + +                      DG      L   +             V   S   
Sbjct: 61  TVRIPPLGVDEKAVGPVTARTIRSQQDGDVLSQMLLYEDPKVYVFNKPAGLAVQGGSGVS 120

Query: 93  GRSTVFDNLPSIFS-------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY 145
                                  I      +                  E  + +     
Sbjct: 121 RHVDGMLEAWRNKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTTAFRERDTKKTYWAL 180

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV------------TLDTQKGSN-AWVTVG 192
                 + +      L +     G      Q              +  + G+N  W+ + 
Sbjct: 181 VKGVPRKREDKISTWLVREQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNLTWLEME 240

Query: 193 LREGKNREIKKVFEFFNWKVN 213
              G+  +++    +    + 
Sbjct: 241 PYTGRTHQLRVHAAYIGHPII 261


>gi|327399594|ref|YP_004340463.1| hemolysin A [Hippea maritima DSM 10411]
 gi|327182223|gb|AEA34404.1| hemolysin A [Hippea maritima DSM 10411]
          Length = 236

 Score = 40.2 bits (92), Expect = 0.49,   Method: Composition-based stats.
 Identities = 6/41 (14%), Positives = 20/41 (48%), Gaps = 1/41 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVN 53
           R+   +   G   +R   +++I +  V+++  ++ + + N
Sbjct: 1  MRLDLFLVENGFVETRSRAKQIIEEGGVRISEKVITKPSFN 41


>gi|291453328|ref|ZP_06592718.1| predicted protein [Streptomyces albus J1074]
 gi|291356277|gb|EFE83179.1| predicted protein [Streptomyces albus J1074]
          Length = 663

 Score = 40.2 bits (92), Expect = 0.49,   Method: Composition-based stats.
 Identities = 12/121 (9%), Positives = 20/121 (16%), Gaps = 5/121 (4%)

Query: 233 TREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
            R       R   G      A+              R     +           +    +
Sbjct: 31  VRPGDPTEARHAEGRRGRGTARGAEGRGRRGGVEETRREAAGVRPRGPHPRAPPRTVPGR 90

Query: 293 NGLSKQKKLATPVH-----RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            G                    +   V        +     G R    R     P +R+ 
Sbjct: 91  PGEEGHPARRHRRRQGRHLAGPVRRRVHRQAPGPPAHPERHGHRPARRRHPLGGPGRRAG 150

Query: 348 R 348
            
Sbjct: 151 P 151


>gi|197301723|ref|ZP_03166793.1| hypothetical protein RUMLAC_00449 [Ruminococcus lactaris ATCC
           29176]
 gi|197299163|gb|EDY33693.1| hypothetical protein RUMLAC_00449 [Ruminococcus lactaris ATCC
           29176]
          Length = 270

 Score = 40.2 bits (92), Expect = 0.49,   Method: Composition-based stats.
 Identities = 11/30 (36%), Positives = 13/30 (43%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           I   +V VNG L+      V   D I V G
Sbjct: 215 IEGAKVFVNGKLITSNGYQVKENDLISVRG 244


>gi|225868146|ref|YP_002744094.1| collagen-binding collagen-like cell surface-anchored protein FneC
           [Streptococcus equi subsp. zooepidemicus]
 gi|225701422|emb|CAW98522.1| putative collagen-binding collagen-like cell surface-anchored
           protein FneC [Streptococcus equi subsp. zooepidemicus]
          Length = 677

 Score = 40.2 bits (92), Expect = 0.49,   Method: Composition-based stats.
 Identities = 13/110 (11%), Positives = 21/110 (19%), Gaps = 1/110 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R   GP   +        P    +T  R              +       + G    +  
Sbjct: 366 RGPAGPQGPKGENGKDGQPGPKGDTGARGPAGPQGPQGFPGKQGPAGEKGEPGKQGDRGP 425

Query: 302 ATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
             P   R             +       G+R          P+     R 
Sbjct: 426 VGPQGPRGDKGETGEKGLQGNPGKDGKPGERGPKGDTGDRGPAGPQGPRG 475



 Score = 39.4 bits (90), Expect = 0.93,   Method: Composition-based stats.
 Identities = 12/115 (10%), Positives = 22/115 (19%), Gaps = 4/115 (3%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL----SK 297
           R   G                  E   R              +  + +  +NG      K
Sbjct: 294 RGPQGEPGKSGRDGLPGPTGPKGEPGARGPAGPQGPQGLPGKQGPQGTPGRNGQDGKPGK 353

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             +   P  +              +      G + +   R P+ P          
Sbjct: 354 DGQDGKPGDKGERGPAGPQGPKGENGKDGQPGPKGDTGARGPAGPQGPQGFPGKQ 408


>gi|291443426|ref|ZP_06582816.1| serine/threonine protein kinase [Streptomyces roseosporus NRRL
           15998]
 gi|291346373|gb|EFE73277.1| serine/threonine protein kinase [Streptomyces roseosporus NRRL
           15998]
          Length = 554

 Score = 40.2 bits (92), Expect = 0.50,   Method: Composition-based stats.
 Identities = 21/120 (17%), Positives = 37/120 (30%), Gaps = 7/120 (5%)

Query: 236 VSKKIL--REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           +  K +  RE  G H   E++  +      +E       +  ++           S  + 
Sbjct: 350 MRLKEIAAREAQGLH---ESRPPVQRSAQDAERPTGRMADPYADQHTRRAEGPSGSRPQP 406

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           G       + P   R   S    A    +     SG+R      +   P  RS  RT++ 
Sbjct: 407 GRRGAPVRSGPP--RTGGSRPQQASRNTTRSGGKSGKRPGAPAGTNGRPGTRSGGRTTSA 464



 Score = 39.4 bits (90), Expect = 0.93,   Method: Composition-based stats.
 Identities = 16/97 (16%), Positives = 30/97 (30%), Gaps = 2/97 (2%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              E     +  P     T   + P+     P       ++   + G S+ ++ +    R
Sbjct: 375 QDAERPTGRMADPYADQHTRRAEGPSGSRPQPGRRGAPVRSGPPRTGGSRPQQASRNTTR 434

Query: 308 RNLAS--NVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
               S        G +    + SG R  +  R P+ P
Sbjct: 435 SGGKSGKRPGAPAGTNGRPGTRSGGRTTSAGRRPANP 471



 Score = 39.0 bits (89), Expect = 0.99,   Method: Composition-based stats.
 Identities = 11/121 (9%), Positives = 30/121 (24%), Gaps = 6/121 (4%)

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           +E++ +    L E   P               +     +                ++ + 
Sbjct: 353 KEIAAREAQGLHESRPPVQRSAQDAERPTGRMADPYADQHTRRAEGPSGSRPQPGRRGAP 412

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQRE--ENHRRSPSFPSKRSLR 348
            ++G  +      P       +      G      + +  R    +  R+ S   + +  
Sbjct: 413 VRSGPPRTGGS-RPQQASRNTTRSGGKSGKRPGAPAGTNGRPGTRSGGRTTSAGRRPANP 471

Query: 349 R 349
           R
Sbjct: 472 R 472



 Score = 37.1 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 11/116 (9%), Positives = 20/116 (17%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
             +     L   +  +     +A           R    +E P                 
Sbjct: 338 DPEERPSTLQLSMRLKEIAAREAQGLHESRPPVQRSAQDAERPTGRMADPYADQHTRRAE 397

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                     RR         +   S     S     +  +S   P   +      
Sbjct: 398 GPSGSRPQPGRRGAPVRSGPPRTGGSRPQQASRNTTRSGGKSGKRPGAPAGTNGRP 453


>gi|194222979|ref|XP_001489270.2| PREDICTED: similar to Serine/threonine-protein kinase PRP4 homolog
           (PRP4 pre-mRNA-processing factor 4 homolog) (PRP4
           kinase) [Equus caballus]
          Length = 1009

 Score = 40.2 bits (92), Expect = 0.50,   Method: Composition-based stats.
 Identities = 15/105 (14%), Positives = 31/105 (29%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            + ++++                     S  P D     K+   ++   K K+  T   +
Sbjct: 265 KIEDKSKSKDRKKSPIVNESRSRDRGKKSRSPVDLRGKSKDRRSRSKERKSKRSETDKEK 324

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           + + S    A     +            RRS S   +   RR+ +
Sbjct: 325 KPIKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKQRDKSRRSRS 369



 Score = 35.9 bits (81), Expect = 8.9,   Method: Composition-based stats.
 Identities = 13/103 (12%), Positives = 31/103 (30%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           E++         S   +R +         +    +  + ++    K         + N +
Sbjct: 283 ESRSRDRGKKSRSPVDLRGKSKDRRSRSKERKSKRSETDKEKKPIKSPSKDASSGKENRS 342

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +    +      LS   + +    RSP    +RS +  S  +
Sbjct: 343 PSRRPGRSPKRRSLSPKQRDKSRRSRSPLLNDRRSKQSKSPSR 385


>gi|308805530|ref|XP_003080077.1| aberrant pollen transmission 1 (ISS) [Ostreococcus tauri]
 gi|116058536|emb|CAL53725.1| aberrant pollen transmission 1 (ISS) [Ostreococcus tauri]
          Length = 2412

 Score = 40.2 bits (92), Expect = 0.50,   Method: Composition-based stats.
 Identities = 16/135 (11%), Positives = 35/135 (25%), Gaps = 14/135 (10%)

Query: 229  LAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
              G  R+++   L+  L   +L+         +              +     ++R   +
Sbjct: 2269 YRGRWRDLTA-ELKNHLVWSVLKSLVGIRGKYVEHKIDAKAT--PDANRRRRPWSRRHAD 2325

Query: 289  SSQKNGLSKQKKLATPVHRR---------NLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
            S   +      +      RR             ++  +     +    +  R    R  P
Sbjct: 2326 SRCPHPARSSARSGRKTRRRYIHLTRLTHRRRISLADSPPSALARTRQAEARPRTGRHPP 2385

Query: 340  S--FPSKRSLRRTSA 352
                P+ RS  R   
Sbjct: 2386 RVTAPAPRSRVRGPP 2400


>gi|301606717|ref|XP_002932960.1| PREDICTED: BUD13 homolog [Xenopus (Silurana) tropicalis]
          Length = 804

 Score = 40.2 bits (92), Expect = 0.51,   Method: Composition-based stats.
 Identities = 10/119 (8%), Positives = 19/119 (15%), Gaps = 6/119 (5%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R                          R R +     P    R            +    
Sbjct: 205 RRGRHASPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSP 264

Query: 302 ATPVHRRNLASNVWMAKGIHSS------FLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                RR    +   +                 G+ +      P      S   +  ++
Sbjct: 265 DPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRR 323



 Score = 39.8 bits (91), Expect = 0.60,   Method: Composition-based stats.
 Identities = 10/119 (8%), Positives = 19/119 (15%), Gaps = 6/119 (5%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R                          R R +     P    R            +    
Sbjct: 192 RRGRHASPGPSPPRRGRHASPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSP 251

Query: 302 ATPVHRRNLASNVWMAKGIHSS------FLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                RR    +   +                 G+ +      P      S   +  ++
Sbjct: 252 DPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRR 310



 Score = 39.8 bits (91), Expect = 0.60,   Method: Composition-based stats.
 Identities = 10/119 (8%), Positives = 19/119 (15%), Gaps = 6/119 (5%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R                          R R +     P    R            +    
Sbjct: 218 RRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSP 277

Query: 302 ATPVHRRNLASNVWMAKGIHSS------FLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                RR    +   +                 G+ +      P      S   +  ++
Sbjct: 278 DPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRR 336



 Score = 39.8 bits (91), Expect = 0.60,   Method: Composition-based stats.
 Identities = 10/119 (8%), Positives = 19/119 (15%), Gaps = 6/119 (5%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R                          R R +     P    R            +    
Sbjct: 231 RRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSP 290

Query: 302 ATPVHRRNLASNVWMAKGIHSS------FLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                RR    +   +                 G+ +      P      S   +  ++
Sbjct: 291 DPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRR 349



 Score = 39.8 bits (91), Expect = 0.60,   Method: Composition-based stats.
 Identities = 10/119 (8%), Positives = 19/119 (15%), Gaps = 6/119 (5%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R                          R R +     P    R            +    
Sbjct: 244 RRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSP 303

Query: 302 ATPVHRRNLASNVWMAKGIHSS------FLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                RR    +   +                 G+ +      P      S   +  ++
Sbjct: 304 DPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRR 362



 Score = 39.4 bits (90), Expect = 0.97,   Method: Composition-based stats.
 Identities = 10/119 (8%), Positives = 18/119 (15%), Gaps = 6/119 (5%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R                          R R       P    R            +    
Sbjct: 179 RRGRHNSTDPSPPRRGRHASPGPSPPRRGRHASPDPSPPRRGRHDSPDPSPPRRGRHDSP 238

Query: 302 ATPVHRRNLASNVWMAKGIHSS------FLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                RR    +   +                 G+ +      P      S   +  ++
Sbjct: 239 DPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRR 297



 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 9/111 (8%), Positives = 18/111 (16%), Gaps = 6/111 (5%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
            +                 R R       P    R            +         RR 
Sbjct: 174 DKSLPRRGRHNSTDPSPPRRGRHASPGPSPPRRGRHASPDPSPPRRGRHDSPDPSPPRRG 233

Query: 310 LASNVWMAKGIHSS------FLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              +   +                 G+ +      P      S   +  ++
Sbjct: 234 RHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRR 284



 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 10/111 (9%), Positives = 18/111 (16%), Gaps = 6/111 (5%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                              R R N     P    R            +         RR 
Sbjct: 161 DPSPPPRKRQDSSDKSLPRRGRHNSTDPSPPRRGRHASPGPSPPRRGRHASPDPSPPRRG 220

Query: 310 LASNVWMAKGIHSS------FLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              +   +                 G+ +      P      S   +  ++
Sbjct: 221 RHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRR 271



 Score = 35.9 bits (81), Expect = 9.9,   Method: Composition-based stats.
 Identities = 9/103 (8%), Positives = 21/103 (20%), Gaps = 6/103 (5%)

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
                 +    R R +     P    R   +        +         RR   ++   +
Sbjct: 143 KDDSSDASPPCRKRHDSSDPSPPPRKRQDSSDKSLPRRGRHNSTDPSPPRRGRHASPGPS 202

Query: 318 KGIHSS------FLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                            G+ +      P      S   +  ++
Sbjct: 203 PPRRGRHASPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRR 245


>gi|305680721|ref|ZP_07403528.1| translation initiation factor IF-2 [Corynebacterium matruchotii
           ATCC 14266]
 gi|305658926|gb|EFM48426.1| translation initiation factor IF-2 [Corynebacterium matruchotii
           ATCC 14266]
          Length = 1009

 Score = 40.2 bits (92), Expect = 0.51,   Method: Composition-based stats.
 Identities = 7/109 (6%), Positives = 14/109 (12%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                                         +  P    +               K   P 
Sbjct: 59  NHEAPAAKSTQSTPAAKPGAPKPGAGGAKSAVKPGPAAKPGAPKPGATAKPGAVKPGAPK 118

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                A +               G   +     P      + +  +  K
Sbjct: 119 PGAGGAKSAVKPGPAAKPGAPKPGATAKPGMPKPGAVKPGAPKPGATAK 167



 Score = 39.4 bits (90), Expect = 0.97,   Method: Composition-based stats.
 Identities = 9/111 (8%), Positives = 19/111 (17%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           ++  H              +  T         +  P                    K   
Sbjct: 46  KMKEHYASLGITTNHEAPAAKSTQSTPAAKPGAPKPGAGGAKSAVKPGPAAKPGAPKPGA 105

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                 +           +      G   +     P   +K  + +  A K
Sbjct: 106 TAKPGAVKPGAPKPGAGGAKSAVKPGPAAKPGAPKPGATAKPGMPKPGAVK 156



 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 9/101 (8%), Positives = 19/101 (18%), Gaps = 2/101 (1%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
                       +     +  P      P    R +     K G    +    P      
Sbjct: 197 PAKAATPTFTEPTKSGTPKPTPKPGMPTPGTMPRPQAKPGPKPGARAPRVANNPFSTGGD 256

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                   G  ++  +    +        +  S     R +
Sbjct: 257 RQAPR--PGGRNAGGNRRPGQGGGANDRANQRSNNRGGRGA 295



 Score = 37.9 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 10/112 (8%), Positives = 23/112 (20%), Gaps = 2/112 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +  + P    +                       +  P    +                 
Sbjct: 125 KSAVKPGPAAKPGAPKPGATAKPGMPKPGAVKPGAPKPGATAKPGAVKPGAPKPGAGTAA 184

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              + +    +    AK    +F   +          P  P+  ++ R  AK
Sbjct: 185 KPGMPKPGGTATP--AKAATPTFTEPTKSGTPKPTPKPGMPTPGTMPRPQAK 234



 Score = 37.5 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 9/113 (7%), Positives = 18/113 (15%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
             + ++           +   +       T   + P   S       +         G  
Sbjct: 28  KGEFVKTASSTIEPPVVKKMKEHYASLGITTNHEAPAAKSTQSTPAAKPGAPKPGAGGAK 87

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
              K                  G         G         P   +K    +
Sbjct: 88  SAVKPGPAAKPGAPKPGATAKPGAVKPGAPKPGAGGAKSAVKPGPAAKPGAPK 140



 Score = 37.5 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 7/107 (6%), Positives = 17/107 (15%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P   +       + +          P   +       +         G     K     
Sbjct: 75  KPGAPKPGAGGAKSAVKPGPAAKPGAPKPGATAKPGAVKPGAPKPGAGGAKSAVKPGPAA 134

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                        G+        G  +      P      + +  + 
Sbjct: 135 KPGAPKPGATAKPGMPKPGAVKPGAPKPGATAKPGAVKPGAPKPGAG 181



 Score = 37.1 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 12/107 (11%), Positives = 20/107 (18%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G      A                 R    +  P         ++Q++     +      
Sbjct: 240 GARAPRVANNPFSTGGDRQAPRPGGRNAGGNRRPGQGGGANDRANQRSNNRGGRGANQSD 299

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            R          +G   S      Q       S S        R  +
Sbjct: 300 QRTPRPGGQGTGQGRRPSPAMMPSQPSPGQMPSRSASGGAGGPRGRS 346



 Score = 36.7 bits (83), Expect = 4.9,   Method: Composition-based stats.
 Identities = 7/105 (6%), Positives = 15/105 (14%), Gaps = 1/105 (0%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               ++ V                    +  P         +          K   P   
Sbjct: 83  AGGAKSAVKPGPAAKPGAPKPGATAKPGAVKPGAPKPGAGGAKSAVKPGPAAKPGAPKPG 142

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                 +     +        G   +     P  P   +      
Sbjct: 143 ATAKPGMPKPGAVKP-GAPKPGATAKPGAVKPGAPKPGAGTAAKP 186



 Score = 35.9 bits (81), Expect = 8.3,   Method: Composition-based stats.
 Identities = 13/125 (10%), Positives = 34/125 (27%), Gaps = 4/125 (3%)

Query: 229 LAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
           + G  R      L +QLG    E      +   +         P ++ ++ + +  +   
Sbjct: 1   MPGKLRV---HELAKQLGVTSKELLATLKEKGEFVKTASSTIEPPVVKKMKEHYASLGIT 57

Query: 289 SSQKNGLSKQKKLATPVHRRNLASNVWMAKGI-HSSFLSDSGQREENHRRSPSFPSKRSL 347
           ++ +   +K  +                AK        +  G  +      P      + 
Sbjct: 58  TNHEAPAAKSTQSTPAAKPGAPKPGAGGAKSAVKPGPAAKPGAPKPGATAKPGAVKPGAP 117

Query: 348 RRTSA 352
           +  + 
Sbjct: 118 KPGAG 122



 Score = 35.9 bits (81), Expect = 9.6,   Method: Composition-based stats.
 Identities = 12/105 (11%), Positives = 22/105 (20%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G            A   +     +      +  P   T       Q     K    A  V
Sbjct: 187 GMPKPGGTATPAKAATPTFTEPTKSGTPKPTPKPGMPTPGTMPRPQAKPGPKPGARAPRV 246

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                ++             +   +R      +    ++RS  R 
Sbjct: 247 ANNPFSTGGDRQAPRPGGRNAGGNRRPGQGGGANDRANQRSNNRG 291


>gi|254391328|ref|ZP_05006532.1| 30S ribosomal protein S4 [Streptomyces clavuligerus ATCC 27064]
 gi|294811568|ref|ZP_06770211.1| 30S ribosomal protein S4 [Streptomyces clavuligerus ATCC 27064]
 gi|326440047|ref|ZP_08214781.1| 30S ribosomal protein S4 [Streptomyces clavuligerus ATCC 27064]
 gi|197705019|gb|EDY50831.1| 30S ribosomal protein S4 [Streptomyces clavuligerus ATCC 27064]
 gi|294324167|gb|EFG05810.1| 30S ribosomal protein S4 [Streptomyces clavuligerus ATCC 27064]
          Length = 205

 Score = 40.2 bits (92), Expect = 0.51,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 3/50 (6%)

Query: 15  RVSKVIARAGIASRR--EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R+GIA R   +  +M+    ++VNG  +++ +  V   D + V
Sbjct: 93  RLDALLLRSGIA-RTIYQARQMVVHGHIEVNGGKVDKPSFRVRPDDVVMV 141


>gi|299820649|ref|ZP_07052538.1| S4 domain protein [Listeria grayi DSM 20601]
 gi|299817670|gb|EFI84905.1| S4 domain protein [Listeria grayi DSM 20601]
          Length = 91

 Score = 40.2 bits (92), Expect = 0.51,   Method: Composition-based stats.
 Identities = 10/52 (19%), Positives = 24/52 (46%), Gaps = 2/52 (3%)

Query: 12 TPQRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             R+ K +  + +  RR   + +  + R++VNG + +    N+   D + +
Sbjct: 3  ETMRLDKFLKVSRLIKRRTVAKEVAEKGRIEVNGNVAK-PGTNIKVNDELVI 53


>gi|198426361|ref|XP_002130630.1| PREDICTED: similar to eukaryotic translation initiation factor 3,
            subunit 10 (theta) [Ciona intestinalis]
          Length = 1082

 Score = 40.2 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 15/120 (12%), Positives = 28/120 (23%), Gaps = 5/120 (4%)

Query: 233  TREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS-- 290
             R  + K   ++       +A               R         P       ++    
Sbjct: 889  WRRDTPKTDADRGAWRRGGDAPRERGEWGRGDTRNERSEEPWRRGPPTRDVGRNRSPPSQ 948

Query: 291  ---QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
               +   + ++    +P        N W  +       S  G+R     R  S P   S 
Sbjct: 949  GAWRPRTVQREADRPSPRGAPTREENSWRRRSPSPRRTSPQGRRSSPPGRRVSPPGNASP 1008


>gi|188583653|ref|YP_001927098.1| DEAD/DEAH box helicase domain protein [Methylobacterium populi
           BJ001]
 gi|179347151|gb|ACB82563.1| DEAD/DEAH box helicase domain protein [Methylobacterium populi
           BJ001]
          Length = 501

 Score = 40.2 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 8/95 (8%), Positives = 23/95 (24%), Gaps = 1/95 (1%)

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW 315
           + +          R              +  + ++++   S+ +    P   R+      
Sbjct: 381 DTEGDEPRRRRGTRRARGSEKGSERGAEKAAERTAERPSESRSRGGRRPASGRSRGEESG 440

Query: 316 MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
               I  +      +         +   +R  RR 
Sbjct: 441 REP-IREAEPVSPAREPARSAPDRARSERRPPRRD 474


>gi|111224609|ref|YP_715403.1| hypothetical protein FRAAL5236 [Frankia alni ACN14a]
 gi|111152141|emb|CAJ63869.1| hypothetical protein; putative signal peptide [Frankia alni ACN14a]
          Length = 447

 Score = 40.2 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 9/112 (8%), Positives = 19/112 (16%), Gaps = 1/112 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R +       +++              R       +      R              +++
Sbjct: 297 RRRDPDSRASDSRAPDPRASGPRALDSRRPDPRYQDADLPDPRRGGPRPADLDRGDPRRV 356

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR-RSPSFPSKRSLRRTSA 352
             P   R         +G         G        R P+            
Sbjct: 357 PGPADTRPPDPRHSDPRGPDPRGPDPRGPDPRRADPRRPASRQPDPRPSDPH 408



 Score = 39.8 bits (91), Expect = 0.71,   Method: Composition-based stats.
 Identities = 19/121 (15%), Positives = 29/121 (23%), Gaps = 4/121 (3%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           +   LR         E  V  D P Y       D     S  PD      +    +    
Sbjct: 269 TGPRLRRGERGAARGERPVAADGPDYPHRRRDPDSRASDSRAPDPRASGPRALDSRRPDP 328

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR----RSPSFPSKRSLRRTSA 352
           + +    P  RR       + +G        +  R  + R    R P             
Sbjct: 329 RYQDADLPDPRRGGPRPADLDRGDPRRVPGPADTRPPDPRHSDPRGPDPRGPDPRGPDPR 388

Query: 353 K 353
           +
Sbjct: 389 R 389



 Score = 37.5 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 12/112 (10%), Positives = 26/112 (23%), Gaps = 2/112 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +            +  +   + +        + S  PD   +       + G  +   L 
Sbjct: 290 DGPDYPHRRRDPDSRASDSRAPDPRASGPRALDSRRPDPRYQDADLPDPRRGGPRPADLD 349

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               RR              S     G            P +   RR ++++
Sbjct: 350 RGDPRRVPGPADTRPPDPRHSD--PRGPDPRGPDPRGPDPRRADPRRPASRQ 399


>gi|258653199|ref|YP_003202355.1| LuxR family two component transcriptional regulator [Nakamurella
           multipartita DSM 44233]
 gi|258556424|gb|ACV79366.1| two component transcriptional regulator, LuxR family [Nakamurella
           multipartita DSM 44233]
          Length = 815

 Score = 40.2 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 11/101 (10%), Positives = 20/101 (19%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           +++ LR       +             +      R       P D  R       + G  
Sbjct: 397 TERALRLSRRRIAVAGDPGTAPHRPRPARRGAAARDQPRPARPADPARAGPGRDGRLGRG 456

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
              +   P  R         A     +     G      + 
Sbjct: 457 PAHRGDHPAGRGAQPDRGHHAGPAGRAGHRLRGAGPGRPQH 497


>gi|126345418|ref|XP_001373146.1| PREDICTED: hypothetical protein [Monodelphis domestica]
          Length = 845

 Score = 40.2 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 7/100 (7%), Positives = 20/100 (20%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
            +   +              R          F       + +     +   A     +  
Sbjct: 441 PKTPRDTPHRTPGGSRRRPQRARGKKRDTTRFGSGGARRNDRFPGRPRGGSAGTAPAKPR 500

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
            ++   + G   S    +G+ +           +R     
Sbjct: 501 PASRPNSTGARGSPGRQAGRADAGDGTHRQTQRRRPRGGG 540



 Score = 39.4 bits (90), Expect = 0.78,   Method: Composition-based stats.
 Identities = 16/121 (13%), Positives = 37/121 (30%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE                +  V  D+   +        P      P      K+++++  
Sbjct: 414 REGGPPDDERAGEGGGAGKRPVVRDSVPKTPRDTPHRTPGGSRRRPQRARGKKRDTTRFG 473

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               ++    P   R  ++    AK   +S  + +G R    R++    +     R + +
Sbjct: 474 SGGARRNDRFPGRPRGGSAGTAPAKPRPASRPNSTGARGSPGRQAGRADAGDGTHRQTQR 533

Query: 354 K 354
           +
Sbjct: 534 R 534



 Score = 36.3 bits (82), Expect = 6.3,   Method: Composition-based stats.
 Identities = 10/108 (9%), Positives = 24/108 (22%), Gaps = 2/108 (1%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                   +  A             + + + P D        S++     + K       
Sbjct: 413 RREGGPPDDERAGEGGGAGKRPVVRDSVPKTPRDTPHRTPGGSRRRPQRARGKKRDTTRF 472

Query: 308 RNLASNVWMAKGIHSSFLSDS--GQREENHRRSPSFPSKRSLRRTSAK 353
            +  +             S      +     R  S  ++ S  R + +
Sbjct: 473 GSGGARRNDRFPGRPRGGSAGTAPAKPRPASRPNSTGARGSPGRQAGR 520


>gi|317420085|emb|CBN82121.1| Serine/threonine-protein kinase PRP4 homolog [Dicentrarchus labrax]
          Length = 1018

 Score = 40.2 bits (92), Expect = 0.53,   Method: Composition-based stats.
 Identities = 9/108 (8%), Positives = 22/108 (20%), Gaps = 6/108 (5%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
               +      +  +  R R +          +  +   +       +       RR+ +
Sbjct: 267 SRSKDRKRSDSADRSKERTRKSNSPSSWRGEQKGSRTDKRSTPPRDDRPNQERASRRSRS 326

Query: 312 SNVWMAKGIHSSFLSDSGQREENH------RRSPSFPSKRSLRRTSAK 353
                     +       +            RSP      S  R  + 
Sbjct: 327 PGRERPSRSDADRDKRPAKSPSKDASSGKENRSPHRRGPHSPMRKRSA 374


>gi|212379273|gb|ACJ24889.1| putative methyltransferase [Streptomyces pactum]
          Length = 430

 Score = 40.2 bits (92), Expect = 0.53,   Method: Composition-based stats.
 Identities = 17/110 (15%), Positives = 27/110 (24%), Gaps = 3/110 (2%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G    +   V   A                +  P   T      S+   +          
Sbjct: 23  GRSRKDTVGVRSGAGCTERGPGSPRVTPEGTRPPAGRTVRTDTRSRTGAVRPAHSRGDLP 82

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR---RTSA 352
           HRR  A+  W + G      +   +       SP  P ++  R   R   
Sbjct: 83  HRRRQAAEEWPSPGRAHPHDTRHRRGPAGRHASPRRPGRKGARHRERGRP 132


>gi|63100354|gb|AAH94882.1| LOC23117 protein [Homo sapiens]
          Length = 739

 Score = 40.2 bits (92), Expect = 0.53,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 27/108 (25%), Gaps = 3/108 (2%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P   +EA+               + P              +   ++     +     P  
Sbjct: 618 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 677

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS--FPSKRSLRRTSA 352
           RR              +   +     E  RR      PS++  RR +A
Sbjct: 678 RRVGDVEPSRKPKRRRAADVEPSS-PEPKRRRVGDVEPSRKPKRRRAA 724



 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 9/117 (7%), Positives = 25/117 (21%), Gaps = 2/117 (1%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +    +   P     A++              +                    ++  +  
Sbjct: 623 EAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGD 682

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +    P  RR         +            R+   +R  +   + SL     ++
Sbjct: 683 VEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKP--KRRRAADVEPSLPEPKRRR 737



 Score = 36.3 bits (82), Expect = 7.1,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 28/112 (25%), Gaps = 3/112 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E+L   L   A  NL  P  +++    ++P                  ++     +    
Sbjct: 600 ERLRGPLPPSADDNLKTPPLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRK 659

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               R                   +  ++    +R  +   + S      ++
Sbjct: 660 PKRRRAADVEPSSPEPKRRRVGDVEPSRKP---KRRRAADVEPSSPEPKRRR 708


>gi|323451412|gb|EGB07289.1| hypothetical protein AURANDRAFT_64979 [Aureococcus anophagefferens]
          Length = 908

 Score = 40.2 bits (92), Expect = 0.53,   Method: Composition-based stats.
 Identities = 13/123 (10%), Positives = 31/123 (25%), Gaps = 7/123 (5%)

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           + LR+++     E A    +A           R              +  + +       
Sbjct: 455 QTLRDEIDTLRREAADARHEARRARRGDRASPRDGARRNGERRAASPRDEARRAASPRDG 514

Query: 299 KKLATPVH---RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL----RRTS 351
           ++ AT      RR  +      +       +       +  R  + P   +      R  
Sbjct: 515 ERRATSPRDETRRAASPRDEERRATSPRDETRRAASPRDEERRAASPRDEARRATSPRNG 574

Query: 352 AKK 354
            ++
Sbjct: 575 ERR 577



 Score = 40.2 bits (92), Expect = 0.54,   Method: Composition-based stats.
 Identities = 9/98 (9%), Positives = 18/98 (18%), Gaps = 2/98 (2%)

Query: 259 APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAK 318
           A           R              +  S +                 +       A 
Sbjct: 490 ARRNGERRAASPRDEARRAASPRDGERRATSPRDETRRAASPRDEERRATSPRDETRRAA 549

Query: 319 GIHSSFLSDSGQREENHRRSPSFPSKRSL--RRTSAKK 354
                    +  R+E  R +     +R     R   ++
Sbjct: 550 SPRDEERRAASPRDEARRATSPRNGERRATSPRDEERR 587



 Score = 40.2 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 12/117 (10%), Positives = 30/117 (25%), Gaps = 4/117 (3%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R++      E   +  +A     E     R +  S         ++ ++     +++   
Sbjct: 451 RDEAQTLRDEIDTLRREAADARHEARRARRGDRASPRDGARRNGERRAASPRDEARRAAS 510

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL----RRTSAKK 354
                RR  +      +               +  R  + P          R  A++
Sbjct: 511 PRDGERRATSPRDETRRAASPRDEERRATSPRDETRRAASPRDEERRAASPRDEARR 567


>gi|315301116|ref|ZP_07872405.1| S4 domain-containing protein [Listeria ivanovii FSL F6-596]
 gi|313630515|gb|EFR98359.1| S4 domain-containing protein [Listeria ivanovii FSL F6-596]
          Length = 92

 Score = 40.2 bits (92), Expect = 0.54,   Method: Composition-based stats.
 Identities = 16/80 (20%), Positives = 26/80 (32%), Gaps = 4/80 (5%)

Query: 12 TPQRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLR 68
          T  R+ K +  + +  RR   + +  + R+ VNGI  +    NV S D   I      + 
Sbjct: 3  TTMRLDKFLKVSRLIKRRTVAKEVAEKGRIAVNGITAK-PGTNVKSGDELVIRFGPKIVT 61

Query: 69 KAERTRLWLYHKPIGLVTTH 88
                     K        
Sbjct: 62 AKIERLEENAKKEQATEMYT 81


>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 = 40.2 bits (92), Expect = 0.54,   Method: Composition-based stats.
 Identities = 23/261 (8%), Positives = 58/261 (22%), Gaps = 54/261 (20%)

Query: 3   DKNIVQENFTPQRVSKVIA----RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           ++ IV       R+ +         G      +++++   +++++G   + A   V +  
Sbjct: 5   EQKIVDTGEAGMRLDRWFKVHYPGLGFG---HLQKLLRSGQIRIDGSRAK-ADTRVQAGQ 60

Query: 59  HIEV----------------------DG----VPLRKAERTRLWLYHKPIGLVTTHSDPD 92
            + +                      DG      L   +             V   S   
Sbjct: 61  TVRIPPLGVDEKATGPVTARTIRSQQDGDVLSQMLLYEDPKVYVFNKPAGLAVQGGSGVT 120

Query: 93  GRSTVFDNLPSIFS-------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY 145
                                  I      +              A   E  + +     
Sbjct: 121 RHIDGMLEAWRNKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTAAFRERDTKKTYWAL 180

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV------------TLDTQKGSN-AWVTVG 192
                 + +      L K     G      Q              +  + G+N  W+ + 
Sbjct: 181 VKGVPRKREDKISTWLVKDQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNLTWLEME 240

Query: 193 LREGKNREIKKVFEFFNWKVN 213
              G+  +++    +    + 
Sbjct: 241 PYTGRTHQLRVHAAYIGHPII 261


>gi|257440057|ref|ZP_05615812.1| putative ATP-dependent RNA helicase RhlE [Faecalibacterium
           prausnitzii A2-165]
 gi|257197409|gb|EEU95693.1| putative ATP-dependent RNA helicase RhlE [Faecalibacterium
           prausnitzii A2-165]
          Length = 641

 Score = 40.2 bits (92), Expect = 0.54,   Method: Composition-based stats.
 Identities = 10/97 (10%), Positives = 25/97 (25%), Gaps = 3/97 (3%)

Query: 259 APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAK 318
                   + +      +       +  +          +++      R    +    A+
Sbjct: 498 PEATPLRPVKKAPAAQPAAKQTAPAQNGQRQRGGQPARAEQRTDRNDPRTEQRAE-RNAR 556

Query: 319 GIHSSFLSDS--GQREENHRRSPSFPSKRSLRRTSAK 353
               +  S S  G R       P+ P+K    R  ++
Sbjct: 557 NARPAQNSQSQQGSRNAAQSSRPARPAKSEAPRGRSR 593


>gi|195038159|ref|XP_001990528.1| GH19401 [Drosophila grimshawi]
 gi|193894724|gb|EDV93590.1| GH19401 [Drosophila grimshawi]
          Length = 596

 Score = 40.2 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 13/121 (10%), Positives = 35/121 (28%), Gaps = 1/121 (0%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE +    ++        ++ V+      +S+     R    S      +   K      
Sbjct: 148 REPTPWEQQQSPRRRKRRDSDVSPMRKRRNSDQSPPRRQRDQSLPRRHKSPSIKRRDSDQ 207

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              ++   A     R    +         +      +R  +  +SP+   +R   ++  +
Sbjct: 208 SPPRRHPNADQSPPRRRKHSDQSPPRRRPAANQTPPRRRADSDQSPARR-RRDSDQSPPR 266

Query: 354 K 354
           +
Sbjct: 267 R 267



 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 13/110 (11%), Positives = 28/110 (25%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +      +          S     +       +      R   N+ Q     ++    +
Sbjct: 171 PMRKRRNSDQSPPRRQRDQSLPRRHKSPSIKRRDSDQSPPRRHPNADQSPPRRRKHSDQS 230

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           P  RR  A+     +   S       +R+ +        +    RR S +
Sbjct: 231 PPRRRPAANQTPPRRRADSDQSPARRRRDSDQSPPRRPQTSPRNRRNSDQ 280


>gi|83814360|ref|YP_444420.1| collagen a1 [Salinibacter ruber DSM 13855]
 gi|83755754|gb|ABC43867.1| collagen a1 [Salinibacter ruber DSM 13855]
          Length = 425

 Score = 40.2 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 19/168 (11%), Positives = 42/168 (25%), Gaps = 7/168 (4%)

Query: 194 REGKNREIKKVFEFFNWKV-NRLIRISYGPFQLGTLLAGSTREVSKKIL----REQLGPH 248
            E  +  +          V N L R       L  +  G  R + +++L    RE++   
Sbjct: 254 TEVDHHVVAGHLGRLEHPVHNALRRGDVRDVLLDGVRVGDDRRLGQRLLLQDRRERVHGL 313

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
                  N            R           +  R K  S +++   +  +      +R
Sbjct: 314 TGSPQGQNGPEHEEGRGERNRYGTQTRHCRGSENDRQKSASEKRDWGHRADRPDIAFPKR 373

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRR--SPSFPSKRSLRRTSAKK 354
              ++         +            R     + P   +      ++
Sbjct: 374 GGRTDRSRPSDARRAGQDGQPMGRVAVRAPLPGARPKTGARPPAPGER 421


>gi|290986009|ref|XP_002675717.1| predicted protein [Naegleria gruberi]
 gi|284089315|gb|EFC42973.1| predicted protein [Naegleria gruberi]
          Length = 442

 Score = 40.2 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 12/103 (11%), Positives = 23/103 (22%), Gaps = 5/103 (4%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
              P  S     R   +     P      ++   +     ++        RR        
Sbjct: 210 PPRPFPSGGRPPRPDHSGRRPHPRPEHSGERPHPRPAHSGERPPRPDHSGRRPRPGPQPD 269

Query: 317 AKGIHSSF-----LSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             G              G R +    + S   +R  R   + +
Sbjct: 270 QSGRPPRPYPEHSGERPGPRPQPQESTSSLIGERPPRPDRSGR 312



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 7/108 (6%), Positives = 16/108 (14%), Gaps = 4/108 (3%)

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           L P                     R   +     P      ++     +   + +    P
Sbjct: 209 LPPRPFPSGGRPPRPDHSGRRPHPRPEHSGERPHPRPAHSGERPPRPDHSGRRPRPGPQP 268

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREEN----HRRSPSFPSKRSLR 348
                         G          +   +        P    +    
Sbjct: 269 DQSGRPPRPYPEHSGERPGPRPQPQESTSSLIGERPPRPDRSGRPPRP 316


>gi|226226159|ref|YP_002760265.1| hypothetical protein GAU_0753 [Gemmatimonas aurantiaca T-27]
 gi|226089350|dbj|BAH37795.1| hypothetical protein [Gemmatimonas aurantiaca T-27]
          Length = 698

 Score = 40.2 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 16/127 (12%), Positives = 34/127 (26%), Gaps = 7/127 (5%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           E+S + LRE++              P    E          +E   +    ++ + +   
Sbjct: 283 ELSVERLREKVREREGTRGLDGAPPPESRRERQRSRDREREAESRANERAPERGAERGAE 342

Query: 295 LSKQKKLATPVHRRNLASNV-------WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
              ++        R+   +          A                + R  PS P +   
Sbjct: 343 RGAERSAERAAGERSSRRDRSSEQTTERTADRAPERSGRPERGESSSPRERPSRPERPDR 402

Query: 348 RRTSAKK 354
            R  A++
Sbjct: 403 ARVRAEQ 409


>gi|301620035|ref|XP_002939394.1| PREDICTED: hypothetical protein LOC100036715 [Xenopus (Silurana)
            tropicalis]
          Length = 2705

 Score = 40.2 bits (92), Expect = 0.56,   Method: Composition-based stats.
 Identities = 15/86 (17%), Positives = 27/86 (31%)

Query: 267  LVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLS 326
              +              R + + S+KN  SK        H ++L+ +   +        S
Sbjct: 2199 SSKSPTRKKRSHSRSDARKRHSRSRKNSRSKSPIWRNRSHSKSLSRSPSKSLSRRHHSKS 2258

Query: 327  DSGQREENHRRSPSFPSKRSLRRTSA 352
               +R        + P K S RR  +
Sbjct: 2259 RLPKRYSRSGSRSASPGKHSRRRNRS 2284


>gi|23270703|gb|AAH36263.1| LOC23117 protein [Homo sapiens]
          Length = 678

 Score = 40.2 bits (92), Expect = 0.56,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 27/108 (25%), Gaps = 3/108 (2%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P   +EA+               + P              +   ++     +     P  
Sbjct: 557 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 616

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS--FPSKRSLRRTSA 352
           RR              +   +     E  RR      PS++  RR +A
Sbjct: 617 RRVGDVEPSRKPKRRRAADVEPSS-PEPKRRRVGDVEPSRKPKRRRAA 663



 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 9/117 (7%), Positives = 25/117 (21%), Gaps = 2/117 (1%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +    +   P     A++              +                    ++  +  
Sbjct: 562 EAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGD 621

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +    P  RR         +            R+   +R  +   + SL     ++
Sbjct: 622 VEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKP--KRRRAADVEPSLPEPKRRR 676



 Score = 36.3 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 28/112 (25%), Gaps = 3/112 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E+L   L   A  NL  P  +++    ++P                  ++     +    
Sbjct: 539 ERLRGPLPPSADDNLKTPPLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRK 598

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               R                   +  ++    +R  +   + S      ++
Sbjct: 599 PKRRRAADVEPSSPEPKRRRVGDVEPSRKP---KRRRAADVEPSSPEPKRRR 647


>gi|78213775|ref|YP_382554.1| hypothetical protein Syncc9605_2262 [Synechococcus sp. CC9605]
 gi|78198234|gb|ABB35999.1| conserved hypothetical protein [Synechococcus sp. CC9605]
          Length = 310

 Score = 40.2 bits (92), Expect = 0.56,   Method: Composition-based stats.
 Identities = 15/107 (14%), Positives = 23/107 (21%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
             R++  P          +    S      +RP                S          
Sbjct: 197 EARDERRPDFGSRRTDREEQRRGSRPIGRPERPAGERAPSGAEDAAFAPSRSSAPSGSAP 256

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
               P    N AS+   +     +    S  R+      PS    R 
Sbjct: 257 NRGRPSGNPNTASDSRRSGEPPVASNRPSSNRQPPRSSRPSSGRPRD 303



 Score = 37.1 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 14/108 (12%), Positives = 25/108 (23%), Gaps = 6/108 (5%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               ++  + +          R         PD  +R      Q+ G     +   P   
Sbjct: 173 RDQGDSGWDQNDERSRRMARFRAGEARDERRPDFGSRRTDREEQRRGSRPIGRPERPAGE 232

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK---RSLRRTSA 352
           R   +         +   S +      +R  PS        S R    
Sbjct: 233 R---APSGAEDAAFAPSRSSAPSGSAPNRGRPSGNPNTASDSRRSGEP 277


>gi|317154268|ref|YP_004122316.1| single-stranded nucleic acid-binding R3H domain-containing protein
           [Desulfovibrio aespoeensis Aspo-2]
 gi|316944519|gb|ADU63570.1| single-stranded nucleic acid binding R3H domain-containing protein
           [Desulfovibrio aespoeensis Aspo-2]
          Length = 434

 Score = 40.2 bits (92), Expect = 0.56,   Method: Composition-based stats.
 Identities = 13/110 (11%), Positives = 26/110 (23%), Gaps = 1/110 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA-TP 304
            P       V+  A         + RP    E   +  R  +   Q+ G  + ++    P
Sbjct: 133 EPEDDINGNVDQTAKPPRKPRERKPRPEGQREGRPEGQREGQREGQREGQREGQREGQRP 192

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             +R        A+            R    +                ++
Sbjct: 193 DGQRGNGQRSEKARSDRPRSEKPRQDRTRPEKPRQDRVRNGDRPDRGPRE 242


>gi|163801279|ref|ZP_02195178.1| ATP-dependent RNA helicase RhlE [Vibrio sp. AND4]
 gi|159174768|gb|EDP59568.1| ATP-dependent RNA helicase RhlE [Vibrio sp. AND4]
          Length = 472

 Score = 40.2 bits (92), Expect = 0.56,   Method: Composition-based stats.
 Identities = 12/114 (10%), Positives = 31/114 (27%), Gaps = 1/114 (0%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           ++++++ L    L         P    +T                      ++++N  +K
Sbjct: 359 ERLIQQLLPRKELAGFAPTNVVPESKLDTRPIKPKKPKKPKSPSAGGGSAQANERNAANK 418

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
            K+     ++      V    G   S               PS   ++   + +
Sbjct: 419 PKRRFNSDNKSGRGEAVKSGNGGKPSGNRKPNSGNSGG-AKPSGQRRKPRPQAA 471


>gi|152965411|ref|YP_001361195.1| translation initiation factor IF-2 [Kineococcus radiotolerans
           SRS30216]
 gi|189028327|sp|A6W7Z2|IF2_KINRD RecName: Full=Translation initiation factor IF-2
 gi|151359928|gb|ABS02931.1| translation initiation factor IF-2 [Kineococcus radiotolerans
           SRS30216]
          Length = 1044

 Score = 40.2 bits (92), Expect = 0.57,   Method: Composition-based stats.
 Identities = 8/88 (9%), Positives = 14/88 (15%), Gaps = 5/88 (5%)

Query: 270 DRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSG 329
           DRP                        ++++   P   R              +     G
Sbjct: 207 DRPERSERPDRGDRPQGDRPRSDRPQGERQQGDRPQGDRPGRPGAPGGAPRPGAGAPRPG 266

Query: 330 QREENH-----RRSPSFPSKRSLRRTSA 352
                      R     P        + 
Sbjct: 267 NNPFAPSQGMPRSQGDRPGGAPRPGNNP 294



 Score = 39.4 bits (90), Expect = 0.75,   Method: Composition-based stats.
 Identities = 6/50 (12%), Positives = 13/50 (26%)

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              R          +G         G+R++  R     P +      + +
Sbjct: 208 RPERSERPDRGDRPQGDRPRSDRPQGERQQGDRPQGDRPGRPGAPGGAPR 257



 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 7/84 (8%), Positives = 18/84 (21%)

Query: 263 SSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHS 322
             E   R       +     +   +   Q+    +  +   P            A    +
Sbjct: 208 RPERSERPDRGDRPQGDRPRSDRPQGERQQGDRPQGDRPGRPGAPGGAPRPGAGAPRPGN 267

Query: 323 SFLSDSGQREENHRRSPSFPSKRS 346
           +  + S     +    P    +  
Sbjct: 268 NPFAPSQGMPRSQGDRPGGAPRPG 291



 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 7/106 (6%), Positives = 16/106 (15%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P +                                  R      +     +  +   P  
Sbjct: 164 PPVSGGPGQGPRPGARPGGPGAPGARPGAPGAGGPGARRPGPGDRPERSERPDRGDRPQG 223

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            R  +      +        D   R      +P   +       + 
Sbjct: 224 DRPRSDRPQGERQQGDRPQGDRPGRPGAPGGAPRPGAGAPRPGNNP 269



 Score = 37.5 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 7/58 (12%), Positives = 12/58 (20%), Gaps = 1/58 (1%)

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR-SPSFPSKRSLRRTSAKK 354
            +   +    R         +          G R +  R   P  P         A +
Sbjct: 207 DRPERSERPDRGDRPQGDRPRSDRPQGERQQGDRPQGDRPGRPGAPGGAPRPGAGAPR 264


>gi|311266609|ref|XP_003131165.1| PREDICTED: poly [ADP-ribose] polymerase 4-like [Sus scrofa]
          Length = 266

 Score = 39.8 bits (91), Expect = 0.57,   Method: Composition-based stats.
 Identities = 9/67 (13%), Positives = 17/67 (25%), Gaps = 1/67 (1%)

Query: 289 SSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFL-SDSGQREENHRRSPSFPSKRSL 347
              +  + + +       R              +    +  G+R E     P  P KR  
Sbjct: 33  PPARRSVGRPEPRGRSRKRSPRXPATRAGSSERAVRGWARPGRRPEPGNPEPGAPGKRKH 92

Query: 348 RRTSAKK 354
           R     +
Sbjct: 93  RGGQRPR 99


>gi|288922023|ref|ZP_06416231.1| FHA domain containing protein [Frankia sp. EUN1f]
 gi|288346639|gb|EFC80960.1| FHA domain containing protein [Frankia sp. EUN1f]
          Length = 497

 Score = 39.8 bits (91), Expect = 0.58,   Method: Composition-based stats.
 Identities = 10/117 (8%), Positives = 18/117 (15%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
               RE       +++                            F         +     
Sbjct: 313 GDDYREGPSARFRDDSGPRPARRDGGPRPDGYGADEYREGPSARFRDDSGPRPARRDGGP 372

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +         R   S  +   G         G       R P +       R    +
Sbjct: 373 RPDGYGADEYREGPSARFRDDGPPPRGGDRGGWPGAGPDRGPGYGRDPQRERGRGYR 429



 Score = 36.3 bits (82), Expect = 7.5,   Method: Composition-based stats.
 Identities = 14/117 (11%), Positives = 26/117 (22%), Gaps = 1/117 (0%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             RE      R+  GP               + E           + P      +     
Sbjct: 348 EYREGPSARFRDDSGPRPARRDGGPRPDGYGADEYREGPSARFRDDGPPPRGGDRGGWPG 407

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMA-KGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
                       P   R        +  G   +   +  + + + R+ P+  S   L
Sbjct: 408 AGPDRGPGYGRDPQRERGRGYRAESSVGGARDAGGDEMYRSQPDPRQRPAARSDDGL 464


>gi|239980799|ref|ZP_04703323.1| hypothetical protein SalbJ_15242 [Streptomyces albus J1074]
 gi|291452658|ref|ZP_06592048.1| conserved hypothetical protein [Streptomyces albus J1074]
 gi|291355607|gb|EFE82509.1| conserved hypothetical protein [Streptomyces albus J1074]
          Length = 346

 Score = 39.8 bits (91), Expect = 0.58,   Method: Composition-based stats.
 Identities = 16/124 (12%), Positives = 33/124 (26%), Gaps = 6/124 (4%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           S   +R  LG            A    +          +     + TR +      + +S
Sbjct: 48  SLDEIRGLLGTLPGPSRMPADVAGRIDAALAAEALLGTMEPGTGEATRPEPVEHPHDDVS 107

Query: 297 KQKKLAT------PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
           ++    T      P            + G      +    R E   R  + P +++  R 
Sbjct: 108 RETSRETVAAGAEPQEADADGPTPPSSAGASGQGGAARSGRPEGRGRGSTGPGRKTGNRA 167

Query: 351 SAKK 354
             ++
Sbjct: 168 RRRR 171


>gi|255074263|ref|XP_002500806.1| predicted protein [Micromonas sp. RCC299]
 gi|226516069|gb|ACO62064.1| predicted protein [Micromonas sp. RCC299]
          Length = 733

 Score = 39.8 bits (91), Expect = 0.58,   Method: Composition-based stats.
 Identities = 13/107 (12%), Positives = 24/107 (22%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G   L+ + +  +                              + QK   +         
Sbjct: 389 GWADLDPSYMRFNPQRKPRPPPRPQSARPARASTGAPRNPDTETGQKQRAAATPATQKTA 448

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            +       W A             R  +  R+PS   + + RR S 
Sbjct: 449 QKTAGRRPGWNASPRVRPASGGPLGRPASAPRTPSSGDRAAARRASG 495


>gi|170284751|gb|AAI61419.1| LOC100145651 protein [Xenopus (Silurana) tropicalis]
          Length = 715

 Score = 39.8 bits (91), Expect = 0.58,   Method: Composition-based stats.
 Identities = 10/119 (8%), Positives = 19/119 (15%), Gaps = 6/119 (5%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R                          R R +     P    R            +    
Sbjct: 246 RRGRHDSPDPSPPRKGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSP 305

Query: 302 ATPVHRRNLASNVWMAKGIHSS------FLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                RR    +   +                 G+ +      P      S   +  ++
Sbjct: 306 DPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRR 364



 Score = 39.8 bits (91), Expect = 0.70,   Method: Composition-based stats.
 Identities = 10/119 (8%), Positives = 19/119 (15%), Gaps = 6/119 (5%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R                          R R +     P    R            +    
Sbjct: 220 RRGRHASPGPSPPQRGRHDSPDPSPPRRGRHDSPDPSPPRKGRHDSPDPSPPRRGRHDSP 279

Query: 302 ATPVHRRNLASNVWMAKGIHSS------FLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                RR    +   +                 G+ +      P      S   +  ++
Sbjct: 280 DPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRR 338



 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 10/111 (9%), Positives = 20/111 (18%), Gaps = 6/111 (5%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                              R R N     P    R    +       +         RR 
Sbjct: 163 DPSPPPRKRQDSSDKSLPRRGRHNSTDPSPPRRGRHASPNPSPPRRGRHASPGPSPPRRG 222

Query: 310 LASNVWMAKGIHSS------FLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             ++   +                 G+ +      P      S   +  ++
Sbjct: 223 RHASPGPSPPQRGRHDSPDPSPPRRGRHDSPDPSPPRKGRHDSPDPSPPRR 273



 Score = 38.2 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 8/112 (7%), Positives = 18/112 (16%), Gaps = 6/112 (5%)

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
                               + R +     P    R            +         RR
Sbjct: 240 PDPSPPRRGRHDSPDPSPPRKGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRR 299

Query: 309 NLASNVWMAKGIHSS------FLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               +   +                 G+ +      P      S   +  ++
Sbjct: 300 GRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRR 351



 Score = 38.2 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 10/119 (8%), Positives = 19/119 (15%), Gaps = 6/119 (5%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R                          R R +     P    R            +    
Sbjct: 207 RRGRHASPGPSPPRRGRHASPGPSPPQRGRHDSPDPSPPRRGRHDSPDPSPPRKGRHDSP 266

Query: 302 ATPVHRRNLASNVWMAKGIHSS------FLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                RR    +   +                 G+ +      P      S   +  ++
Sbjct: 267 DPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRR 325



 Score = 37.9 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 10/119 (8%), Positives = 19/119 (15%), Gaps = 6/119 (5%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R                    +     R R       P    R            +    
Sbjct: 181 RRGRHNSTDPSPPRRGRHASPNPSPPRRGRHASPGPSPPRRGRHASPGPSPPQRGRHDSP 240

Query: 302 ATPVHRRNLASNVWMAKGIHSS------FLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                RR    +   +                 G+ +      P      S   +  ++
Sbjct: 241 DPSPPRRGRHDSPDPSPPRKGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRR 299



 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 9/119 (7%), Positives = 18/119 (15%), Gaps = 6/119 (5%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R                          R R       P    R            +    
Sbjct: 194 RRGRHASPNPSPPRRGRHASPGPSPPRRGRHASPGPSPPQRGRHDSPDPSPPRRGRHDSP 253

Query: 302 ATPVHRRNLASNVWMAKGIHSS------FLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                R+    +   +                 G+ +      P      S   +  ++
Sbjct: 254 DPSPPRKGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRRGRHDSPDPSPPRR 312


>gi|333028302|ref|ZP_08456366.1| putative serine/threonine protein kinase [Streptomyces sp. Tu6071]
 gi|332748154|gb|EGJ78595.1| putative serine/threonine protein kinase [Streptomyces sp. Tu6071]
          Length = 446

 Score = 39.8 bits (91), Expect = 0.58,   Method: Composition-based stats.
 Identities = 13/142 (9%), Positives = 29/142 (20%), Gaps = 19/142 (13%)

Query: 229 LAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
             GSTR   ++ + E+    L E+           +      R    +       R ++ 
Sbjct: 277 HPGSTRGPGQREVIERPTGRLAEQYAEQATQQRPVTPAPRGRRRPETAAPAQAQPRGERP 336

Query: 289 SSQKNGLSKQKKLA-------------------TPVHRRNLASNVWMAKGIHSSFLSDSG 329
           +  + G  +                         P      +                + 
Sbjct: 337 APAREGRPQPGGTGAGRGARRPGPGTQGGGPETRPSQGAERSPVAGRPPRATGGQRRPAA 396

Query: 330 QREENHRRSPSFPSKRSLRRTS 351
            R     R+ +           
Sbjct: 397 SRTGGTARTGARTGTGRRPANP 418



 Score = 36.7 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 10/129 (7%), Positives = 23/129 (17%), Gaps = 10/129 (7%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRD---RPNIISEVPDDFTRMKKNSSQK 292
           +  K +  +   H            I      + +                R ++     
Sbjct: 265 LRLKEIAARETQHPGSTRGPGQREVIERPTGRLAEQYAEQATQQRPVTPAPRGRRRPETA 324

Query: 293 NGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP-------SKR 345
                Q +   P   R              +     G +       PS          + 
Sbjct: 325 APAQAQPRGERPAPAREGRPQPGGTGAGRGARRPGPGTQGGGPETRPSQGAERSPVAGRP 384

Query: 346 SLRRTSAKK 354
                  ++
Sbjct: 385 PRATGGQRR 393


>gi|325294636|ref|YP_004281150.1| RNA-binding S4 domain protein [Desulfurobacterium
          thermolithotrophum DSM 11699]
 gi|325065084|gb|ADY73091.1| RNA-binding S4 domain protein [Desulfurobacterium
          thermolithotrophum DSM 11699]
          Length = 95

 Score = 39.8 bits (91), Expect = 0.58,   Method: Composition-based stats.
 Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 2/51 (3%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+ + +  + I  RR + + +   + VKVNG + +  +  V   D IE+D
Sbjct: 1  MRLDQFLKLSRIVKRRSQAKELCDLKVVKVNGQVAK-PSREVKVGDTIEID 50


>gi|145199237|ref|NP_065746.3| RNA exonuclease 1 homolog [Homo sapiens]
 gi|296452990|sp|Q8N1G1|REXO1_HUMAN RecName: Full=RNA exonuclease 1 homolog; AltName:
           Full=Elongin-A-binding protein 1; Short=EloA-BP1;
           AltName: Full=Transcription elongation factor B
           polypeptide 3-binding protein 1
          Length = 1221

 Score = 39.8 bits (91), Expect = 0.58,   Method: Composition-based stats.
 Identities = 6/84 (7%), Positives = 20/84 (23%), Gaps = 1/84 (1%)

Query: 265 ETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSF 324
           +   + +        +     KK     +   K ++      + + A+ V  +       
Sbjct: 394 QGKDKTKDKGRGRPVEKPRADKKGPQASSPRRKAERPEGTKKKPSSATPVATSGKGRPDR 453

Query: 325 LSDSGQREENHRRSPSFPSKRSLR 348
            +       +    P+        
Sbjct: 454 PARRPS-PTSGDSRPAAGRGPPRP 476



 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 9/90 (10%), Positives = 21/90 (23%), Gaps = 3/90 (3%)

Query: 267 LVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLS 326
               +     +         +   +     K  + ++P  +              +   +
Sbjct: 386 APSCKDGAQGKDKTKDKGRGRPVEKPRADKKGPQASSPRRKAERPEGTKKKPSSATPVAT 445

Query: 327 DSGQREENHRRSPSFPSKRSLR---RTSAK 353
               R +   R PS  S  S     R   +
Sbjct: 446 SGKGRPDRPARRPSPTSGDSRPAAGRGPPR 475


>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 = 39.8 bits (91), Expect = 0.59,   Method: Composition-based stats.
 Identities = 38/432 (8%), Positives = 90/432 (20%), Gaps = 87/432 (20%)

Query: 3   DKNIVQENFTPQRVSKV----IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
            + +V  +    R+ +     + + G A+   V R     +++V+G         ++   
Sbjct: 11  RQFVVGRDDDGVRLDRWFKRHLPQVGFAT---VSRWARTGQIRVDGKRA-DVDTRLVPGQ 66

Query: 59  HIEVDG-------------------------VPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
            + V                             +   +     + +KP GL T       
Sbjct: 67  TLRVPPGGTQAPGSRGPRTRKPLTEEEMALAERIVLTQDRAAIVLNKPPGLATQGGSGTH 126

Query: 94  RSTV--------FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY 145
                        ++        +      +        +            + +     
Sbjct: 127 SHVDGLLDAYAGDNDPRPRLVHRLDKDTSGVLLIARTPGSAAYFSRHFSGRSAKKIYWAL 186

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGIC----------YGDMQVTLDTQKGSNA-WVTVGLR 194
            +      D      L K     G                +  +  + G+ A WV +   
Sbjct: 187 VMGIPEINDGYIDLPLAKQPGTGGEKMMVDESGEGQTARTRYRVIDRAGNRAAWVELQPL 246

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQ--LGT-----LLAGSTREVSKK------IL 241
            G+  +++         +       YG     L       L   + R +          +
Sbjct: 247 TGRTHQLRVHMAAIGHPIVGDG--KYGGQAAFLSGSISRKLHLHARRLLIPHPEGDTIDV 304

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS------------ 289
              L  H                  L + +     +      R                 
Sbjct: 305 VAPLPEHFAASLAQLGFTESEGDLPLEKPQVIDPRDAQKRAARAHSKDLRKERRGERRKR 364

Query: 290 --------SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF 341
                    ++       K       +  A+ V  + G        +G R          
Sbjct: 365 GDSGKEWSGKERSGKPTGKPGGKPTGKPGAAPVGKSGGKFGKAPGKTGGRPAGKPAGKPM 424

Query: 342 PSKRSLRRTSAK 353
               +     ++
Sbjct: 425 AKGPARPPRPSR 436


>gi|302502070|ref|XP_003013026.1| SH3 domain protein [Arthroderma benhamiae CBS 112371]
 gi|291176588|gb|EFE32386.1| SH3 domain protein [Arthroderma benhamiae CBS 112371]
          Length = 1064

 Score = 39.8 bits (91), Expect = 0.59,   Method: Composition-based stats.
 Identities = 19/123 (15%), Positives = 33/123 (26%), Gaps = 2/123 (1%)

Query: 222 PFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD 281
              L +L      E++++I +     H +             S    R       +    
Sbjct: 253 GIDLHSLTPTQEDELTERIAQAFKRRHRVPSPTHISRRRESESPAQPRPVSQDRQQQQPR 312

Query: 282 FTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGI--HSSFLSDSGQREENHRRSP 339
                 ++S     +++     P   R        A     H    SD G      R SP
Sbjct: 313 QQERSPSASASTPRAREPTRRAPPTSRPRLLEPLTAHHAANHRRSASDQGMGTRRRRTSP 372

Query: 340 SFP 342
           + P
Sbjct: 373 TPP 375


>gi|21595518|gb|AAH32244.1| REX1, RNA exonuclease 1 homolog (S. cerevisiae) [Homo sapiens]
          Length = 1221

 Score = 39.8 bits (91), Expect = 0.59,   Method: Composition-based stats.
 Identities = 6/84 (7%), Positives = 20/84 (23%), Gaps = 1/84 (1%)

Query: 265 ETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSF 324
           +   + +        +     KK     +   K ++      + + A+ V  +       
Sbjct: 394 QGKDKTKDKGRGRPVEKPRADKKGPQASSPRRKAERPEGTKKKPSSATPVATSGKGRPDR 453

Query: 325 LSDSGQREENHRRSPSFPSKRSLR 348
            +       +    P+        
Sbjct: 454 PARRPS-PTSGDSRPAAGRGPPRP 476



 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 9/90 (10%), Positives = 21/90 (23%), Gaps = 3/90 (3%)

Query: 267 LVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLS 326
               +     +         +   +     K  + ++P  +              +   +
Sbjct: 386 APSCKDGAQGKDKTKDKGRGRPVEKPRADKKGPQASSPRRKAERPEGTKKKPSSATPVAT 445

Query: 327 DSGQREENHRRSPSFPSKRSLR---RTSAK 353
               R +   R PS  S  S     R   +
Sbjct: 446 SGKGRPDRPARRPSPTSGDSRPAAGRGPPR 475


>gi|168269702|dbj|BAG09978.1| RNA exonuclease 1 homolog [synthetic construct]
          Length = 1221

 Score = 39.8 bits (91), Expect = 0.59,   Method: Composition-based stats.
 Identities = 6/84 (7%), Positives = 20/84 (23%), Gaps = 1/84 (1%)

Query: 265 ETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSF 324
           +   + +        +     KK     +   K ++      + + A+ V  +       
Sbjct: 394 QGKDKTKDKGRGRPVEKPRADKKGPQASSPRRKAERPEGTKKKPSSATPVATSGKGRPDR 453

Query: 325 LSDSGQREENHRRSPSFPSKRSLR 348
            +       +    P+        
Sbjct: 454 PARRPS-PTSGDSRPAAGRGPPRP 476



 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 9/90 (10%), Positives = 21/90 (23%), Gaps = 3/90 (3%)

Query: 267 LVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLS 326
               +     +         +   +     K  + ++P  +              +   +
Sbjct: 386 APSCKDGAQGKDKTKDKGRGRPVEKPRADKKGPQASSPRRKAERPEGTKKKPSSATPVAT 445

Query: 327 DSGQREENHRRSPSFPSKRSLR---RTSAK 353
               R +   R PS  S  S     R   +
Sbjct: 446 SGKGRPDRPARRPSPTSGDSRPAAGRGPPR 475


>gi|168041934|ref|XP_001773445.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162675321|gb|EDQ61818.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 696

 Score = 39.8 bits (91), Expect = 0.60,   Method: Composition-based stats.
 Identities = 14/107 (13%), Positives = 29/107 (27%), Gaps = 3/107 (2%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM--KKNSSQKNGLSKQKKLATPV 305
                        +  + +  R R    +  P    R   +  S  +  +SK        
Sbjct: 49  RATSRQPPPTRRSMSKAPSPTRRRSMSKAPSPTRGRRGVSRNPSPSRRAMSKAPSPTRQS 108

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             R  +           +     G+R  +   SP+   +R + R  +
Sbjct: 109 TARAASPVRTRRLSPSRNPSPTRGRRGVSRNPSPTR-GRRGVSRGPS 154



 Score = 36.3 bits (82), Expect = 7.7,   Method: Composition-based stats.
 Identities = 12/112 (10%), Positives = 23/112 (20%), Gaps = 4/112 (3%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
              + +           S       R    +  P   +  +  S  +       +  +P 
Sbjct: 71  RRSMSKAPSPTRGRRGVSRNPSPSRRAMSKAPSPTRQSTARAASPVRTRRLSPSRNPSPT 130

Query: 306 HRRNL----ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R       S     +G+        G R      +       S  R    
Sbjct: 131 RGRRGVSRNPSPTRGRRGVSRGPSPTRGARLTPASPARIQTRPTSPTRGREA 182


>gi|225075257|ref|ZP_03718456.1| hypothetical protein NEIFLAOT_00260 [Neisseria flavescens
          NRL30031/H210]
 gi|241758831|ref|ZP_04756944.1| RNA-binding S4 domain protein [Neisseria flavescens SK114]
 gi|261380145|ref|ZP_05984718.1| heat shock protein 15 [Neisseria subflava NJ9703]
 gi|224953432|gb|EEG34641.1| hypothetical protein NEIFLAOT_00260 [Neisseria flavescens
          NRL30031/H210]
 gi|241321039|gb|EER57252.1| RNA-binding S4 domain protein [Neisseria flavescens SK114]
 gi|284796982|gb|EFC52329.1| heat shock protein 15 [Neisseria subflava NJ9703]
          Length = 133

 Score = 39.8 bits (91), Expect = 0.60,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 25/52 (48%), Gaps = 2/52 (3%)

Query: 10 NFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
          + +  R+ K + A     +R   ++ I   RV VNG  ++  + N+ + D I
Sbjct: 6  DNSSMRLDKWLWAARFFKTRALAQKHIELGRVLVNGSKVKN-SKNISAGDTI 56


>gi|196968461|gb|ACG80804.1| hypothetical protein [Chlamydophila pecorum]
          Length = 131

 Score = 39.8 bits (91), Expect = 0.61,   Method: Composition-based stats.
 Identities = 20/131 (15%), Positives = 38/131 (29%), Gaps = 1/131 (0%)

Query: 224 QLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
           +L  L   S++E+S K       P   E +         S +       +     P + +
Sbjct: 2   ELKDLETSSSKELSPKE-PSPKEPSPKEPSPKEPSPKELSPKEPSSKELSPKELSPKEPS 60

Query: 284 RMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
             + +S + +      K  +P    +   +         S    S +       SP  PS
Sbjct: 61  PKEPSSKELSPKEPSPKEPSPKEPSSKELSPKEPSPKEPSSKELSPKEPSPKEPSPKEPS 120

Query: 344 KRSLRRTSAKK 354
            +        K
Sbjct: 121 SKEPSSKEPSK 131


>gi|239990404|ref|ZP_04711068.1| putative NRPS [Streptomyces roseosporus NRRL 11379]
          Length = 1337

 Score = 39.8 bits (91), Expect = 0.61,   Method: Composition-based stats.
 Identities = 11/87 (12%), Positives = 23/87 (26%)

Query: 261  IYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGI 320
                  L   R   +        R +     ++   +  +      RR     V      
Sbjct: 999  RGEPPRLRPGRGAAVHSPAAPTGRQRPRPGPRDAPHRHGRALGRADRRGPPGAVHGGPRR 1058

Query: 321  HSSFLSDSGQREENHRRSPSFPSKRSL 347
              S L  + + +    R+ + P +  L
Sbjct: 1059 TPSGLRPARRDDRRGPRAAARPGRPGL 1085



 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 8/82 (9%), Positives = 22/82 (26%), Gaps = 1/82 (1%)

Query: 272  PNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR 331
                  +         + +   G  + +        R+  +     +      +    +R
Sbjct: 999  RGEPPRLRPGRGAAVHSPAAPTGRQRPRPGPRDAPHRHGRALGRADRRGPPGAVHGGPRR 1058

Query: 332  EENHRRSPSFPSKRSLRRTSAK 353
              +  R P+    R   R +A+
Sbjct: 1059 TPSGLR-PARRDDRRGPRAAAR 1079


>gi|120537346|gb|AAI29001.1| LOC100036715 protein [Xenopus (Silurana) tropicalis]
          Length = 2667

 Score = 39.8 bits (91), Expect = 0.61,   Method: Composition-based stats.
 Identities = 15/86 (17%), Positives = 27/86 (31%)

Query: 267  LVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLS 326
              +              R + + S+KN  SK        H ++L+ +   +        S
Sbjct: 2216 SSKSPTRKKRSHSRSDARKRHSRSRKNSRSKSPIWRNRSHSKSLSRSPSKSLSRRHHSKS 2275

Query: 327  DSGQREENHRRSPSFPSKRSLRRTSA 352
               +R        + P K S RR  +
Sbjct: 2276 RLPKRYSRSGSRSASPGKHSRRRNRS 2301


>gi|159474390|ref|XP_001695308.1| protein required for templated centriole assembly [Chlamydomonas
           reinhardtii]
 gi|37624751|gb|AAQ95705.1| variable flagellar number protein [Chlamydomonas reinhardtii]
 gi|37624753|gb|AAQ95706.1| variable flagellar number protein [Chlamydomonas reinhardtii]
 gi|158275791|gb|EDP01566.1| protein required for templated centriole assembly [Chlamydomonas
           reinhardtii]
          Length = 603

 Score = 39.8 bits (91), Expect = 0.61,   Method: Composition-based stats.
 Identities = 17/128 (13%), Positives = 32/128 (25%), Gaps = 6/128 (4%)

Query: 232 STREVSKK--ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN- 288
             RE+  +   L E L          +    +Y+  +       +    P    R   + 
Sbjct: 268 QIRELKMRIRQLTEDLEARDRRMNSTDRIRSVYARGSNDGSTSGVAPRRPSSGGRGPSSN 327

Query: 289 ---SSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
               ++        +            N     G    F      R+   R S +   +R
Sbjct: 328 YMAPTRGADSRSNSRGRGTSSAERSRPNSAPIGGPRPRFDPTEYVRQRKERESAAVGGRR 387

Query: 346 SLRRTSAK 353
           S   T  +
Sbjct: 388 SNAPTPPR 395



 Score = 37.5 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 9/112 (8%), Positives = 24/112 (21%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +        + + +       S      R    S           ++ +   +       
Sbjct: 367 DPTEYVRQRKERESAAVGGRRSNAPTPPRSAGTSRASSVVGSRPASAERLPPIRTASPTN 426

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +                  +S     G  +    R P   + RS   + + +
Sbjct: 427 SRPSSTERYRPGSGGPPGRTSAGGSRGAADRAGARGPDPYAPRSRGASPSGR 478


>gi|331701920|ref|YP_004398879.1| RNA-binding S4 domain-containing protein [Lactobacillus buchneri
          NRRL B-30929]
 gi|329129263|gb|AEB73816.1| RNA-binding S4 domain protein [Lactobacillus buchneri NRRL
          B-30929]
          Length = 90

 Score = 39.8 bits (91), Expect = 0.62,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 14 QRVSKVIARAGIASRREVERMIAQ-QRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  + I  RR V + IA   R+ +NG   +  +  V   D + +
Sbjct: 1  MRIDKFLKVSRIIKRRSVAKEIADKGRIFINGRAAKS-STEVKPNDEVVI 49


>gi|269967184|ref|ZP_06181249.1| ATP-dependent RNA helicase [Vibrio alginolyticus 40B]
 gi|269828174|gb|EEZ82443.1| ATP-dependent RNA helicase [Vibrio alginolyticus 40B]
          Length = 522

 Score = 39.8 bits (91), Expect = 0.62,   Method: Composition-based stats.
 Identities = 10/109 (9%), Positives = 27/109 (24%), Gaps = 2/109 (1%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              E A          +    R      +   +   +      + N   + +  + P  R
Sbjct: 406 AAGENAPATEKKAGNGANKPKRRFNGGNNGNKNSTNQGGAGKPKGNREGQGRANSKPDDR 465

Query: 308 R--NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +      N     G   +        + +  R P+       + +  ++
Sbjct: 466 KPNGNKPNSNKPSGNKPNGNKSGNAGKPSGNRKPNNAKPAGNKPSGQRR 514



 Score = 39.4 bits (90), Expect = 0.84,   Method: Composition-based stats.
 Identities = 7/107 (6%), Positives = 21/107 (19%), Gaps = 1/107 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                  A          +           +  P      +  ++ K    K        
Sbjct: 415 EKKAGNGANKPKRRFNGGNNGNKNSTNQGGAGKPKGNREGQGRANSKPDDRKPNGNKPNS 474

Query: 306 HRRNLASNVWMAKG-IHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
           ++ +         G       +      +     PS   ++   + +
Sbjct: 475 NKPSGNKPNGNKSGNAGKPSGNRKPNNAKPAGNKPSGQRRKPRPQAA 521


>gi|224824793|ref|ZP_03697900.1| putative RNA methylase [Lutiella nitroferrum 2002]
 gi|224603286|gb|EEG09462.1| putative RNA methylase [Lutiella nitroferrum 2002]
          Length = 844

 Score = 39.8 bits (91), Expect = 0.62,   Method: Composition-based stats.
 Identities = 11/120 (9%), Positives = 25/120 (20%), Gaps = 7/120 (5%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+Q       +A         + +   ++        PD     +    ++ G    ++ 
Sbjct: 14  RDQTHRDRQAQAAPTTGNDAPAGKPPRQEERRHFDRKPDSRPHGQGKPPRREGEGFGQQE 73

Query: 302 ATPVHRRNLASNVW-------MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                 +                 G          Q        P F   R       ++
Sbjct: 74  RRQFGDKPRFGQPRQQGEGQERRPGPRREGEGFGQQERRQFGDKPRFGQPRQQGEGQERR 133



 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 12/126 (9%), Positives = 24/126 (19%), Gaps = 5/126 (3%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R    +   E          +          +   + R     +  +   R      +  
Sbjct: 82  RFGQPRQQGEGQERRPGPRREGEGFGQQERRQFGDKPRFGQPRQQGEGQERRPGPRREGE 141

Query: 294 GLSKQKKL-----ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           G  +Q++            R          G          Q        P F   R   
Sbjct: 142 GFGQQERRQFGDKPRFGQARQQGEGQERRPGPRREGEGFGQQERRPIGDKPRFGQARQQG 201

Query: 349 RTSAKK 354
               ++
Sbjct: 202 EGQERR 207



 Score = 36.7 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 13/128 (10%), Positives = 25/128 (19%), Gaps = 5/128 (3%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             R   +K      G       +          +   + R     +  +   R      +
Sbjct: 43  ERRHFDRKPDSRPHGQGKPPRREGEGFGQQERRQFGDKPRFGQPRQQGEGQERRPGPRRE 102

Query: 292 KNGLSKQKKL-----ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
             G  +Q++            R          G          Q        P F   R 
Sbjct: 103 GEGFGQQERRQFGDKPRFGQPRQQGEGQERRPGPRREGEGFGQQERRQFGDKPRFGQARQ 162

Query: 347 LRRTSAKK 354
                 ++
Sbjct: 163 QGEGQERR 170


>gi|195331685|ref|XP_002032530.1| GM23476 [Drosophila sechellia]
 gi|194121473|gb|EDW43516.1| GM23476 [Drosophila sechellia]
          Length = 642

 Score = 39.8 bits (91), Expect = 0.62,   Method: Composition-based stats.
 Identities = 10/113 (8%), Positives = 32/113 (28%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R++         +   D P  + +    D+              ++  S ++   +++  
Sbjct: 201 RKRRDSDQSPPRKARNDKPSPAGKRRDSDQSPPRKRTGKASPTRRRRDSDQSPPRRRRSN 260

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +     R                     +R +   +SP    ++   ++  +K
Sbjct: 261 SDQSPPRRRRDQDSTPPRRRRDSDQSPPRRRKADDQSPVRRERKDSDQSPPRK 313



 Score = 36.7 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 11/105 (10%), Positives = 28/105 (26%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R + G       +          +               D +  +K + + +   +++  
Sbjct: 190 RGRDGDQSPSRRKRRDSDQSPPRKARNDKPSPAGKRRDSDQSPPRKRTGKASPTRRRRDS 249

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
                RR  +++            S   +R  +  +SP    K  
Sbjct: 250 DQSPPRRRRSNSDQSPPRRRRDQDSTPPRRRRDSDQSPPRRRKAD 294



 Score = 36.3 bits (82), Expect = 6.6,   Method: Composition-based stats.
 Identities = 12/113 (10%), Positives = 29/113 (25%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R             + D      +    D+        D  +   K         +++  
Sbjct: 179 RAASSDQSPPRRGRDGDQSPSRRKRRDSDQSPPRKARNDKPSPAGKRRDSDQSPPRKRTG 238

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                RR   S+    +   S+      +R  +   +P    + S +    ++
Sbjct: 239 KASPTRRRRDSDQSPPRRRRSNSDQSPPRRRRDQDSTPPRRRRDSDQSPPRRR 291



 Score = 36.3 bits (82), Expect = 6.6,   Method: Composition-based stats.
 Identities = 15/112 (13%), Positives = 31/112 (27%), Gaps = 2/112 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+            +        +   +  P           R +++S Q     ++   
Sbjct: 281 RDSDQSPPRRRKADDQSPVRRERKDSDQSPPRKRRGNDQYPVRRRRDSDQSPPRRRRDDK 340

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            TP  RR  +                  +R+ +  +SP+    +S RR    
Sbjct: 341 QTPPRRRRNSDQS--PPRRPKDEDQSPPRRKRDFDQSPNRKRDKSPRRRRDS 390



 Score = 36.3 bits (82), Expect = 7.3,   Method: Composition-based stats.
 Identities = 10/103 (9%), Positives = 31/103 (30%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P  +++ + +    +  + +    +     +           S  + G    +  +    
Sbjct: 144 PVRIKQEKRSSSRDLSPARSRKPAKREESPQRGRRRAASSDQSPPRRGRDGDQSPSRRKR 203

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           R +  S    A+    S        +++  R  +  +  + RR
Sbjct: 204 RDSDQSPPRKARNDKPSPAGKRRDSDQSPPRKRTGKASPTRRR 246



 Score = 36.3 bits (82), Expect = 8.0,   Method: Composition-based stats.
 Identities = 10/104 (9%), Positives = 27/104 (25%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           ++                +   +            K+  S + G  +         RR  
Sbjct: 133 KDEFSPSRRRSPVRIKQEKRSSSRDLSPARSRKPAKREESPQRGRRRAASSDQSPPRRGR 192

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             +   ++           ++  N + SP+   + S +    K+
Sbjct: 193 DGDQSPSRRKRRDSDQSPPRKARNDKPSPAGKRRDSDQSPPRKR 236


>gi|313205991|ref|YP_004045168.1| heat shock protein hsp15 [Riemerella anatipestifer DSM 15868]
 gi|312445307|gb|ADQ81662.1| heat shock protein Hsp15 [Riemerella anatipestifer DSM 15868]
 gi|315022304|gb|EFT35332.1| Ribosome-associated heat shock protein [Riemerella anatipestifer
          RA-YM]
 gi|325336568|gb|ADZ12842.1| Ribosome-associated heat shock protein implicated in the
          recycling of the 50S subunit (S4 paralog) [Riemerella
          anatipestifer RA-GD]
          Length = 144

 Score = 39.8 bits (91), Expect = 0.63,   Method: Composition-based stats.
 Identities = 12/58 (20%), Positives = 23/58 (39%), Gaps = 2/58 (3%)

Query: 14 QRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           R+ K + +     +R      I + RV V G  + + +  VM  D I++    +   
Sbjct: 1  MRIDKFLWSVRFFKTRSIAAEEIKKNRVSV-GEQVAKPSREVMEGDIIKIRKNQIDYK 57


>gi|225621051|ref|YP_002722309.1| 30S ribosomal protein S4 [Brachyspira hyodysenteriae WA1]
 gi|225215871|gb|ACN84605.1| 30S ribosomal protein S4 [Brachyspira hyodysenteriae WA1]
          Length = 189

 Score = 39.8 bits (91), Expect = 0.63,   Method: Composition-based stats.
 Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 1/42 (2%)

Query: 22  RAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R G+A SR +  + +A   + VNG  +   +  V   D +  
Sbjct: 87  RLGLAKSRNQARQFVAHGFISVNGKRMTIPSYCVKVGDKVSF 128


>gi|260905190|ref|ZP_05913512.1| translation initiation factor IF-2 [Brevibacterium linens BL2]
          Length = 1004

 Score = 39.8 bits (91), Expect = 0.63,   Method: Composition-based stats.
 Identities = 11/86 (12%), Positives = 20/86 (23%)

Query: 268 VRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSD 327
                +  +  P       + +      +  K  A P              G        
Sbjct: 148 ETKADDTAAAAPAAAEASAEQAKPAPRANAPKPGAAPKPGAAPKPGSAPKPGSAPKPGGR 207

Query: 328 SGQREENHRRSPSFPSKRSLRRTSAK 353
           S  R  N+  +P+    +   R   K
Sbjct: 208 SPARPGNNPFAPAQGMPKPAGRGGPK 233


>gi|255726284|ref|XP_002548068.1| predicted protein [Candida tropicalis MYA-3404]
 gi|240133992|gb|EER33547.1| predicted protein [Candida tropicalis MYA-3404]
          Length = 318

 Score = 39.8 bits (91), Expect = 0.63,   Method: Composition-based stats.
 Identities = 13/98 (13%), Positives = 27/98 (27%)

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW 315
                 ++S      +    ++  D   R +K +       +      P      +++  
Sbjct: 41  KTSKNPFASAMESSPQRKNSTQQSDSTPRRQKQAPPPRPPKEFNAPPPPYTPSENSNSYP 100

Query: 316 MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             K   S+    S +R  +  R    P      R   K
Sbjct: 101 KEKESRSTSEQRSRERPRDEHRHRDRPRDEHRSRDRPK 138


>gi|6329915|dbj|BAA86452.1| KIAA1138 protein [Homo sapiens]
          Length = 1239

 Score = 39.8 bits (91), Expect = 0.63,   Method: Composition-based stats.
 Identities = 6/84 (7%), Positives = 20/84 (23%), Gaps = 1/84 (1%)

Query: 265 ETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSF 324
           +   + +        +     KK     +   K ++      + + A+ V  +       
Sbjct: 412 QGKDKTKDKGRGRPVEKPRADKKGPQASSPRRKAERPEGTKKKPSSATPVATSGKGRPDR 471

Query: 325 LSDSGQREENHRRSPSFPSKRSLR 348
            +       +    P+        
Sbjct: 472 PARRPS-PTSGDSRPAAGRGPPRP 494



 Score = 39.0 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 9/90 (10%), Positives = 21/90 (23%), Gaps = 3/90 (3%)

Query: 267 LVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLS 326
               +     +         +   +     K  + ++P  +              +   +
Sbjct: 404 APSCKDGAQGKDKTKDKGRGRPVEKPRADKKGPQASSPRRKAERPEGTKKKPSSATPVAT 463

Query: 327 DSGQREENHRRSPSFPSKRSLR---RTSAK 353
               R +   R PS  S  S     R   +
Sbjct: 464 SGKGRPDRPARRPSPTSGDSRPAAGRGPPR 493


>gi|117594|sp|P06914|CSP_PLAYO RecName: Full=Circumsporozoite protein; Short=CS; Flags: Precursor
 gi|72382|pir||OZZQMY circumsporozoite protein precursor - Plasmodium yoelii
 gi|160223|gb|AAA29558.1| circumsporozoite protein [Plasmodium yoelii]
 gi|225519|prf||1305264A circumsporozoite protein
          Length = 367

 Score = 39.8 bits (91), Expect = 0.63,   Method: Composition-based stats.
 Identities = 9/95 (9%), Positives = 16/95 (16%), Gaps = 1/95 (1%)

Query: 259 APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP-VHRRNLASNVWMA 317
           A    ++ +V D                +      G    +    P              
Sbjct: 123 AQNKLNQPVVADENVDQGPGAPQGPGAPQGPGAPQGPGAPQGPGAPQGPGAPQGPGAPQG 182

Query: 318 KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            G      +  G        +P  P          
Sbjct: 183 PGAPQGPGAPQGPGAPQGPGAPQGPGAPQGPGAPQ 217


>gi|323454689|gb|EGB10559.1| hypothetical protein AURANDRAFT_62446 [Aureococcus anophagefferens]
          Length = 547

 Score = 39.8 bits (91), Expect = 0.64,   Method: Composition-based stats.
 Identities = 12/98 (12%), Positives = 23/98 (23%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           E   V  DA             N         +R +   +   G +   +      R+  
Sbjct: 274 ELPAVAWDAQANGQAPGGAPPGNQARPQSAPVSRDRDGGAAPFGSAPPGRAGAQPSRKPR 333

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                      +      G R +  R+  + P  +   
Sbjct: 334 PGTPAAQARGGAPATQSRGPRPQGPRQQRAAPPPQDRP 371



 Score = 37.1 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 8/93 (8%), Positives = 19/93 (20%)

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           +        Q    AP  +         +   +                  S++ +  TP
Sbjct: 278 VAWDAQANGQAPGGAPPGNQARPQSAPVSRDRDGGAAPFGSAPPGRAGAQPSRKPRPGTP 337

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
             +    +    ++G                 R
Sbjct: 338 AAQARGGAPATQSRGPRPQGPRQQRAAPPPQDR 370


>gi|291409415|ref|XP_002720996.1| PREDICTED: serine/threonine-protein kinase PRP4K [Oryctolagus
           cuniculus]
          Length = 994

 Score = 39.8 bits (91), Expect = 0.64,   Method: Composition-based stats.
 Identities = 13/105 (12%), Positives = 29/105 (27%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            + ++ +                     S  P D     K+   ++   K ++      +
Sbjct: 251 KIEDKNKSKDRKKSPIINESRSRDRGKKSRSPIDLRGKSKDRRSRSKERKSRRSEIDKEK 310

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           + + S    A     +            RRS S   +   RR+ +
Sbjct: 311 KPIKSPSKDASSGKENRSPSRRPGRSPKRRSLSPRPRDKSRRSRS 355



 Score = 39.8 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 19/131 (14%), Positives = 37/131 (28%), Gaps = 8/131 (6%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             R+     LR +    + +      D      +   +DR               K S  
Sbjct: 222 QARKSKSPTLRRRSQEKVGKARSPTDDKVKIEDKNKSKDRKKSPIINESRSRDRGKKSRS 281

Query: 292 K---NGLSKQKKLATPVHRRNLAS-NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR-- 345
                G SK ++  +   +   +  +         S  + SG+   +  R P    KR  
Sbjct: 282 PIDLRGKSKDRRSRSKERKSRRSEIDKEKKPIKSPSKDASSGKENRSPSRRPGRSPKRRS 341

Query: 346 --SLRRTSAKK 354
                R  +++
Sbjct: 342 LSPRPRDKSRR 352



 Score = 39.4 bits (90), Expect = 0.82,   Method: Composition-based stats.
 Identities = 13/113 (11%), Positives = 35/113 (30%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +++    ++ E++         S   +R +         +    +    ++    K    
Sbjct: 259 KDRKKSPIINESRSRDRGKKSRSPIDLRGKSKDRRSRSKERKSRRSEIDKEKKPIKSPSK 318

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                + N + +    +      LS   + +    RSP    +RS +  S  +
Sbjct: 319 DASSGKENRSPSRRPGRSPKRRSLSPRPRDKSRRSRSPLINDRRSKQSKSPSR 371



 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 11/102 (10%), Positives = 23/102 (22%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
            +      +       R R         +  + KK     +  +   K      RR   S
Sbjct: 277 KKSRSPIDLRGKSKDRRSRSKERKSRRSEIDKEKKPIKSPSKDASSGKENRSPSRRPGRS 336

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               +        S   +    + R        S   +  ++
Sbjct: 337 PKRRSLSPRPRDKSRRSRSPLINDRRSKQSKSPSRTLSPGRR 378



 Score = 37.9 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 11/124 (8%), Positives = 29/124 (23%), Gaps = 6/124 (4%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           S    + ++      + +        S       +     ++       +  S ++    
Sbjct: 244 SPTDDKVKIEDKNKSKDRKKSPIINESRSRDRGKKSRSPIDLRGKSKDRRSRSKERKSRR 303

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL------RRT 350
            +        +          +    S       +  +    P   S+RS       RR+
Sbjct: 304 SEIDKEKKPIKSPSKDASSGKENRSPSRRPGRSPKRRSLSPRPRDKSRRSRSPLINDRRS 363

Query: 351 SAKK 354
              K
Sbjct: 364 KQSK 367


>gi|194374391|dbj|BAG57091.1| unnamed protein product [Homo sapiens]
 gi|221046052|dbj|BAH14703.1| unnamed protein product [Homo sapiens]
          Length = 552

 Score = 39.8 bits (91), Expect = 0.64,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 27/108 (25%), Gaps = 3/108 (2%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P   +EA+               + P              +   ++     +     P  
Sbjct: 431 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 490

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS--FPSKRSLRRTSA 352
           RR              +   +     E  RR      PS++  RR +A
Sbjct: 491 RRVGDVEPSRKPKRRRAADVEPSS-PEPKRRRVGDVEPSRKPKRRRAA 537



 Score = 38.2 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 10/120 (8%), Positives = 32/120 (26%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
            ++ +    +       +    ++ P       V D              ++ +S +   
Sbjct: 431 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 490

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                   +   +R  A++V  +            +     +R  +   + SL     ++
Sbjct: 491 RRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKPKRRRAADVEPSLPEPKRRR 550



 Score = 35.9 bits (81), Expect = 8.4,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 28/112 (25%), Gaps = 3/112 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E+L   L   A  NL  P  +++    ++P                  ++     +    
Sbjct: 413 ERLRGPLPPSADDNLKTPPLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRK 472

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               R                   +  ++    +R  +   + S      ++
Sbjct: 473 PKRRRAADVEPSSPEPKRRRVGDVEPSRKP---KRRRAADVEPSSPEPKRRR 521


>gi|256380796|ref|YP_003104456.1| cell envelope-related transcriptional attenuator [Actinosynnema
           mirum DSM 43827]
 gi|255925099|gb|ACU40610.1| cell envelope-related transcriptional attenuator [Actinosynnema
           mirum DSM 43827]
          Length = 1336

 Score = 39.8 bits (91), Expect = 0.65,   Method: Composition-based stats.
 Identities = 11/124 (8%), Positives = 29/124 (23%)

Query: 221 GPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
           G   +  LL   +R    + +         +       +   ++      R         
Sbjct: 5   GGLSVSDLLEQHSRTNIPRPIPPGQSDSGPQRGAAPEPSGRRAAPEPPAHRSEPQGPESG 64

Query: 281 DFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
                 ++   +     +++ A          +     G        +G+R      +  
Sbjct: 65  RQQGDHEHRPAQEPQQGRRRAARGPEDDVQGPSHPAGPGQPGETGPRTGRRARPEPSASP 124

Query: 341 FPSK 344
            PS 
Sbjct: 125 EPSA 128



 Score = 37.5 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 14/111 (12%), Positives = 33/111 (29%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            E+         + +  A          + P+     P++    ++ + + +  +   + 
Sbjct: 130 EEETRYAAPVRVEPDPAAEAGGRRARHDEAPSGRRAAPEEPRTGRRAAPEADRDAAAPEG 189

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            +   RR        +    +         EE  RR    P +   RR+ A
Sbjct: 190 VSRASRRARHDEPAPSGRRSAPEDGVPAHEEEPGRRGRQAPDEGVGRRSRA 240



 Score = 37.5 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 9/107 (8%), Positives = 26/107 (24%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E+ G H     +                R   +          ++++S+ + L+  +   
Sbjct: 249 EEGGRHEPAARRGRSFTDEAPWPQAADRRRPDVRGDEGLEDAGEESASRMSRLAPGEPNG 308

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                          +       +    R +   + P    +R+   
Sbjct: 309 RRSLPPRGPEVDGRGQRGPGPEATGRRARPDAGPQGPDATGRRARPE 355


>gi|300796618|ref|NP_001179237.1| RNA exonuclease 1 homolog [Bos taurus]
          Length = 1211

 Score = 39.8 bits (91), Expect = 0.65,   Method: Composition-based stats.
 Identities = 16/130 (12%), Positives = 38/130 (29%), Gaps = 11/130 (8%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           E+ +  LRE     +  + +     P       +    +     P+  +  +    +K+G
Sbjct: 328 ELEEGSLRETKEMAVQCDVEDLGPPPRSPGRPPLAKPSSPARAAPERSSPKEGRPKKKSG 387

Query: 295 L----------SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +           K  K       R         +G  +       +R +  ++ PS  + 
Sbjct: 388 VSPTASHKDSVRKTDKGKDGARGRPAEKPAADRRGPQAGSPRHKAERPQGTKKKPSSATP 447

Query: 345 -RSLRRTSAK 353
             S  +   +
Sbjct: 448 VASSGKGRPE 457


>gi|116623271|ref|YP_825427.1| ribonuclease [Candidatus Solibacter usitatus Ellin6076]
 gi|116226433|gb|ABJ85142.1| ribonuclease, Rne/Rng family [Candidatus Solibacter usitatus
           Ellin6076]
          Length = 913

 Score = 39.8 bits (91), Expect = 0.65,   Method: Composition-based stats.
 Identities = 13/118 (11%), Positives = 25/118 (21%), Gaps = 1/118 (0%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           E+      E        E     +A   +        P  I        R ++ S   + 
Sbjct: 390 ELEGDAEGELEADAEGGEPHAEGEAGAETVVEDEGPEPARIPTSLTATLR-EQGSRYPHR 448

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           +S++ +      R      +   +            R E            S      
Sbjct: 449 VSRRTRRKGRGERGPDRGPLPEGQRPPQGEPRPQEGRPEQRTSPRPEGRPESRPEARP 506



 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 12/106 (11%), Positives = 24/106 (22%), Gaps = 2/106 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E     ++E+          S    +R++ +         TR K    +        +  
Sbjct: 413 EAGAETVVEDEGPEPARIPTSLTATLREQGSRYPHRVSRRTRRKGRGERGPDRGPLPEGQ 472

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
            P             +            R E   R  +   +  L 
Sbjct: 473 RPPQGEPRPQEGRPEQRTSPRPEGRPESRPEA--RPDARSDRPPLP 516


>gi|297477210|ref|XP_002689195.1| PREDICTED: REX1, RNA exonuclease 1 homolog (S. cerevisiae) [Bos
           taurus]
 gi|296485401|gb|DAA27516.1| REX1, RNA exonuclease 1 homolog [Bos taurus]
          Length = 1211

 Score = 39.8 bits (91), Expect = 0.65,   Method: Composition-based stats.
 Identities = 16/130 (12%), Positives = 38/130 (29%), Gaps = 11/130 (8%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           E+ +  LRE     +  + +     P       +    +     P+  +  +    +K+G
Sbjct: 328 ELEEGSLRETKEMAVQCDVEDLGPPPRSPGRPPLAKPSSPARAAPERSSPKEGRPKKKSG 387

Query: 295 L----------SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           +           K  K       R         +G  +       +R +  ++ PS  + 
Sbjct: 388 VSPTASHKDSVRKTDKGKDGARGRPAEKPAADRRGPQAGSPRHKAERPQGTKKKPSSATP 447

Query: 345 -RSLRRTSAK 353
             S  +   +
Sbjct: 448 VASSGKGRPE 457


>gi|86156689|ref|YP_463474.1| hypothetical protein Adeh_0261 [Anaeromyxobacter dehalogenans
           2CP-C]
 gi|85773200|gb|ABC80037.1| protein of unknown function UPF0044 [Anaeromyxobacter dehalogenans
           2CP-C]
          Length = 187

 Score = 39.8 bits (91), Expect = 0.65,   Method: Composition-based stats.
 Identities = 16/117 (13%), Positives = 32/117 (27%), Gaps = 4/117 (3%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
            + ++L    ++ AQV     +       R R              +    +  G  ++ 
Sbjct: 72  EIADRLLAEDVQVAQVLGRTVLAYRRHPERPRFEPAPAGAAAERAERPEPRRAPGKGRRA 131

Query: 300 KLATPVH--RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               P    R   A                +G+R   + + P+   +R   R    K
Sbjct: 132 PTRGPRAAAREQRAPAKGKRPLAKGKRAPANGRRPPANGKRPAT--RRPAPRAKRTK 186


>gi|297463503|ref|XP_001249390.3| PREDICTED: hypothetical protein [Bos taurus]
          Length = 903

 Score = 39.8 bits (91), Expect = 0.66,   Method: Composition-based stats.
 Identities = 13/108 (12%), Positives = 23/108 (21%), Gaps = 1/108 (0%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P    E + +    +          P      P    R  + ++  +   +      PV 
Sbjct: 650 PPPGAEGRGHARGRVRQQRQARATGPPAPRVPPGKGGRRGRPATPPDPRPRHASPPPPVP 709

Query: 307 RRNLASNVWMAKGIH-SSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            R         +             R        S P     RR   +
Sbjct: 710 ARGRGPAAGKRRRARRPEAGRRRQGRPPPSPSRASAPPHGGRRRPLDR 757



 Score = 37.5 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 10/111 (9%), Positives = 20/111 (18%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+      +  +               R R    +                         
Sbjct: 636 RKGHADARVPSSFPPPPGAEGRGHARGRVRQQRQARATGPPAPRVPPGKGGRRGRPATPP 695

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                  +    V       ++      +R E  RR    P     R ++ 
Sbjct: 696 DPRPRHASPPPPVPARGRGPAAGKRRRARRPEAGRRRQGRPPPSPSRASAP 746



 Score = 36.7 bits (83), Expect = 5.0,   Method: Composition-based stats.
 Identities = 7/108 (6%), Positives = 14/108 (12%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                         P                +   D               +        
Sbjct: 606 RLVDRAGPPSGGQVPAGRLVDPSLRGRKGARKGHADARVPSSFPPPPGAEGRGHARGRVR 665

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            +R   +    A  +        G+        P   S         +
Sbjct: 666 QQRQARATGPPAPRVPPGKGGRRGRPATPPDPRPRHASPPPPVPARGR 713


>gi|326202458|ref|ZP_08192327.1| RNA-binding S4 domain protein [Clostridium papyrosolvens DSM
          2782]
 gi|325987576|gb|EGD48403.1| RNA-binding S4 domain protein [Clostridium papyrosolvens DSM
          2782]
          Length = 79

 Score = 39.8 bits (91), Expect = 0.66,   Method: Composition-based stats.
 Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 3/67 (4%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRKAE 71
           R+ K +  + +  RR     +  Q RVK+N    +     V   D +E+  G  + K E
Sbjct: 1  MRIDKYLKVSRLIKRRTVANEVCEQGRVKINDRAAK-PGSEVKVGDIVEIQFGNNITKIE 59

Query: 72 RTRLWLY 78
           TR+  +
Sbjct: 60 ITRITEH 66


>gi|224613414|gb|ACN60286.1| KH domain-containing, RNA-binding, signal transduction-associated
           protein 1 [Salmo salar]
          Length = 315

 Score = 39.8 bits (91), Expect = 0.66,   Method: Composition-based stats.
 Identities = 7/113 (6%), Positives = 18/113 (15%)

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             +++ L P  ++    +    I         +       P         +S        
Sbjct: 89  DEVKKFLIPDTMDGICQDQFMEIGYLNGGQDSQSRGRGGPPGRGRGAPPPNSVGARGRGM 148

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                                        +         +P+        R  
Sbjct: 149 PPRGGAPRGGTQRGGASRGGPPRGGSARGAPAGRGGPPSTPARGGTTPRSRPP 201


>gi|194674644|ref|XP_616882.4| PREDICTED: hypothetical protein [Bos taurus]
          Length = 1684

 Score = 39.8 bits (91), Expect = 0.66,   Method: Composition-based stats.
 Identities = 14/131 (10%), Positives = 27/131 (20%), Gaps = 12/131 (9%)

Query: 231  GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
            G  R +    +  +      E     + A         ++   I +       R    S 
Sbjct: 1282 GRKRGMPSYQVNREPRLSQPEHLPSRIGAFNSEKSGAPQETCIIAAAATHSGPRRGGRSG 1341

Query: 291  QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSS------------FLSDSGQREENHRRS 338
                    ++   P                                +  +G  +E    S
Sbjct: 1342 SPGKKKAPRRAGQPARSPRGTPRHLRPPSKCPCAPPPASPPTPLPRVPGAGGSQEPLVTS 1401

Query: 339  PSFPSKRSLRR 349
            P    +  L R
Sbjct: 1402 PGSGGRGRLPR 1412


>gi|333026367|ref|ZP_08454431.1| hypothetical protein STTU_3871 [Streptomyces sp. Tu6071]
 gi|332746219|gb|EGJ76660.1| hypothetical protein STTU_3871 [Streptomyces sp. Tu6071]
          Length = 477

 Score = 39.8 bits (91), Expect = 0.66,   Method: Composition-based stats.
 Identities = 11/114 (9%), Positives = 22/114 (19%), Gaps = 5/114 (4%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
            +  +  R          A+               +     +E      R      +   
Sbjct: 223 YLRGQERRRFAYTMDRRRAEDAAARLRDHGRGERTEDHAPAAERHHAAERHPAAERRPGP 282

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
             +      P   R  A     A    S+             R P+   + +  
Sbjct: 283 DRRPAPDRRPAPDRRQAPERRPAHEGRSAPERRP-----APERRPAADDRPTEP 331


>gi|255066806|ref|ZP_05318661.1| heat shock protein 15 [Neisseria sicca ATCC 29256]
 gi|255048881|gb|EET44345.1| heat shock protein 15 [Neisseria sicca ATCC 29256]
          Length = 133

 Score = 39.8 bits (91), Expect = 0.66,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 31/61 (50%), Gaps = 6/61 (9%)

Query: 1  MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          MK+++    + T  R+ K + A     +R   ++ I   RV+VNG  ++  + N+ + D 
Sbjct: 1  MKNEH----DNTAMRLDKWLWAARFFKTRALAQKHIELGRVQVNGAKVKN-SKNISAGDI 55

Query: 60 I 60
          I
Sbjct: 56 I 56


>gi|237837393|ref|XP_002367994.1| hypothetical protein TGME49_030930 [Toxoplasma gondii ME49]
 gi|211965658|gb|EEB00854.1| hypothetical protein TGME49_030930 [Toxoplasma gondii ME49]
 gi|221509244|gb|EEE34813.1| conserved hypothetical protein [Toxoplasma gondii VEG]
          Length = 314

 Score = 39.8 bits (91), Expect = 0.66,   Method: Composition-based stats.
 Identities = 18/119 (15%), Positives = 31/119 (26%), Gaps = 5/119 (4%)

Query: 224 QLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
           +      GS   V  K  + QL      E        +   E   R           +  
Sbjct: 137 EKKGHEQGSWEVVLTKQQKHQLHRAAQAETLP-----LSGREGRTRRPDRERDNRHANAD 191

Query: 284 RMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
           R + N     G    ++ A    +R    +   A G   +   ++  +    RR     
Sbjct: 192 RQRGNEHPSAGRRADRQTAAGPVQRRRRDSRGEAGGFRRAGGQNATGKAATGRRRGRQG 250


>gi|119605884|gb|EAW85478.1| serine/arginine repetitive matrix 2, isoform CRA_b [Homo sapiens]
          Length = 2334

 Score = 39.8 bits (91), Expect = 0.66,   Method: Composition-based stats.
 Identities = 9/108 (8%), Positives = 21/108 (19%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                            S   +     +              + +    + + +  AT  
Sbjct: 432 RHASSSPESPKPAPAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAK 491

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R+ +          S        R          P +R   R+  +
Sbjct: 492 RGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQR 539



 Score = 39.4 bits (90), Expect = 0.78,   Method: Composition-based stats.
 Identities = 11/98 (11%), Positives = 22/98 (22%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P      +++      +       R    S  P       ++ +       + +  T  
Sbjct: 444 APAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKR 503

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
                 S  W        +      +     RSP  P 
Sbjct: 504 GHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPG 541



 Score = 36.7 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 22/135 (16%), Positives = 34/135 (25%), Gaps = 10/135 (7%)

Query: 230 AGSTREV----SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
            GS RE+    + K             +         S       R    S  P      
Sbjct: 447 PGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKRGHS 506

Query: 286 KKNSSQKNGLSKQKK--LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
           +  S Q       ++   +    RR  + +        S      G+     R      S
Sbjct: 507 RSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRSHSRS 566

Query: 344 K----RSLRRTSAKK 354
                RS  RT A++
Sbjct: 567 PATRGRSRSRTPARR 581


>gi|158317713|ref|YP_001510221.1| hypothetical protein Franean1_5971 [Frankia sp. EAN1pec]
 gi|158113118|gb|ABW15315.1| hypothetical protein Franean1_5971 [Frankia sp. EAN1pec]
          Length = 326

 Score = 39.8 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 10/120 (8%), Positives = 23/120 (19%), Gaps = 1/120 (0%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           E+      E        E   N       +           +  P+     +     +  
Sbjct: 36  EIQAGEPSEPDSGRWRSEEAANP-GSERDTGQWPPPAWPPQAWRPEPAVPRRGRPDHERP 94

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             ++     P H           +        +   RE      P+            ++
Sbjct: 95  DHERPDHGWPDHGWPERGRPDHGRPGRGRQAGERPGREGPGWGRPADGGADRGSDRRQRR 154


>gi|301777704|ref|XP_002924271.1| PREDICTED: serine/threonine-protein kinase PRP4 homolog [Ailuropoda
           melanoleuca]
          Length = 1009

 Score = 39.8 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 14/105 (13%), Positives = 30/105 (28%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            + ++++                     S  P D     K+   ++   K K+      +
Sbjct: 265 KIEDKSRSKDRKKSPIINESRSRDRGKKSRSPIDLRGKSKDRRSRSKERKSKRSDMDKEK 324

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           + + S    A     +            RRS S   +   RR+ +
Sbjct: 325 KPIKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKQRDKSRRSRS 369



 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 14/120 (11%), Positives = 41/120 (34%), Gaps = 6/120 (5%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           + ++      +++ +  ++         R   ++  +  D  +R K+  S+++ + K+KK
Sbjct: 266 IEDKSRSKDRKKSPIINESRSRDRGKKSRSPIDLRGKSKDRRSRSKERKSKRSDMDKEKK 325

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSG------QREENHRRSPSFPSKRSLRRTSAKK 354
                 +   +     +                  + +    RSP    +RS +  S  +
Sbjct: 326 PIKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKQRDKSRRSRSPLVNDRRSKQSKSPSR 385



 Score = 36.7 bits (83), Expect = 5.0,   Method: Composition-based stats.
 Identities = 19/131 (14%), Positives = 39/131 (29%), Gaps = 8/131 (6%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             R+     LR +    + +      D      ++  +DR               K S  
Sbjct: 236 QARKSKSPTLRRRSQEKIGKARSPPDDKVKIEDKSRSKDRKKSPIINESRSRDRGKKSRS 295

Query: 292 K---NGLSKQKKLATPVHRRNLAS-NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR-- 345
                G SK ++  +   +   +  +         S  + SG+   +  R P    KR  
Sbjct: 296 PIDLRGKSKDRRSRSKERKSKRSDMDKEKKPIKSPSKDASSGKENRSPSRRPGRSPKRRS 355

Query: 346 --SLRRTSAKK 354
               +R  +++
Sbjct: 356 LSPKQRDKSRR 366


>gi|318077128|ref|ZP_07984460.1| hypothetical protein SSA3_10493 [Streptomyces sp. SA3_actF]
          Length = 416

 Score = 39.8 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 5/66 (7%), Positives = 12/66 (18%)

Query: 281 DFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
              + K +         + +      RR   S     +           +   +      
Sbjct: 279 PGAKPKPDRGTPRTPPSRSRRPGCPRRRARRSTGSAPRAPRGPGRRVPPRGPSSSWPRTR 338

Query: 341 FPSKRS 346
               R 
Sbjct: 339 PAPTRP 344



 Score = 37.5 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 2/74 (2%), Positives = 10/74 (13%)

Query: 266 TLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFL 325
              + +P+  +         +    ++                                 
Sbjct: 279 PGAKPKPDRGTPRTPPSRSRRPGCPRRRARRSTGSAPRAPRGPGRRVPPRGPSSSWPRTR 338

Query: 326 SDSGQREENHRRSP 339
               +        P
Sbjct: 339 PAPTRPTSWAATCP 352


>gi|259417109|ref|ZP_05741028.1| RNA-binding S4 [Silicibacter sp. TrichCH4B]
 gi|259346015|gb|EEW57829.1| RNA-binding S4 [Silicibacter sp. TrichCH4B]
          Length = 124

 Score = 39.8 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 12/57 (21%), Positives = 23/57 (40%), Gaps = 1/57 (1%)

Query: 7  VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          + ++    RV K +  A    +R    + +    V+VNG    + + NV   D +  
Sbjct: 1  MSDHADKMRVDKWLWHARFFKTRSLAAKQVGAGHVRVNGSKASKPSQNVAVGDVLTF 57


>gi|118094258|ref|XP_422303.2| PREDICTED: similar to alpha-1 (type XI) collagen isoform 3 [Gallus
           gallus]
          Length = 1805

 Score = 39.8 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 9/111 (8%), Positives = 15/111 (13%), Gaps = 1/111 (0%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           L+   G       +                 P       +             G    K 
Sbjct: 793 LKGDRGEVGQPGPRGEDGPEGPKGRAGPSGDPGAAGPAGEKGKLGVPGLPGYPGRQGPKG 852

Query: 301 LATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                                        G       R P  P+ +   + 
Sbjct: 853 STGFPGFPGANGEKGARGLHGKPGPRGQRGPTGPRGSRGPRGPTGKPGPKG 903


>gi|109069479|ref|XP_001094163.1| PREDICTED: serine/threonine-protein kinase PRP4 homolog [Macaca
           mulatta]
          Length = 1007

 Score = 39.8 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 15/105 (14%), Positives = 31/105 (29%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            + ++++                     S  P D     K+   ++   K K+  T   +
Sbjct: 264 KIEDKSKSKDRKKSPIVNESRSRDRCKKSRSPIDLRGKSKDGRSRSKERKSKRSETDKEK 323

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           + + S    A     +            RRS S   +   RR+ +
Sbjct: 324 KPIKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKPRDKSRRSRS 368



 Score = 35.9 bits (81), Expect = 8.4,   Method: Composition-based stats.
 Identities = 13/103 (12%), Positives = 31/103 (30%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           E++         S   +R +         +    +  + ++    K         + N +
Sbjct: 282 ESRSRDRCKKSRSPIDLRGKSKDGRSRSKERKSKRSETDKEKKPIKSPSKDASSGKENRS 341

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +    +      LS   + +    RSP    +RS +  S  +
Sbjct: 342 PSRRPGRSPKRRSLSPKPRDKSRRSRSPLLNDRRSKQSKSPSR 384


>gi|21105301|gb|AAM34600.1|AF448525_1 precollagen-P [Mytilus galloprovincialis]
          Length = 894

 Score = 39.8 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 12/114 (10%), Positives = 18/114 (15%), Gaps = 7/114 (6%)

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
            GP                     +                 +  S + G         P
Sbjct: 526 QGPAGPAGPSGEQGPGGERGAQGPQGAEGPSGPAGPRGPAGHQGPSGERGAPGSPGKKGP 585

Query: 305 VHRRNLASNVWMAK--GIHSSFLSD-----SGQREENHRRSPSFPSKRSLRRTS 351
              R    +       G      S       G+      R    P      R +
Sbjct: 586 NGDRGNQGSPGAPGKNGARGDRGSRGSNGSPGRSGSPGSRGKPGPQGPHGPRGA 639



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 9/108 (8%), Positives = 19/108 (17%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E+           +  A                +           +   +       K  
Sbjct: 543 ERGAQGPQGAEGPSGPAGPRGPAGHQGPSGERGAPGSPGKKGPNGDRGNQGSPGAPGKNG 602

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
               R +  SN    +          G +  +  R       +   R 
Sbjct: 603 ARGDRGSRGSNGSPGRSGSPGSRGKPGPQGPHGPRGARGSPGQKGPRG 650



 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 9/109 (8%), Positives = 17/109 (15%), Gaps = 2/109 (1%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           ++GP               +                       +      G +  +  A 
Sbjct: 471 EVGPQGPSGPAGPQGPQGKNGVKGPAGDQGARGPEGKAGPGGPQGEQGPKGPTGAQGPAG 530

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           P                                R P+     S  R + 
Sbjct: 531 PAGPSGEQGPGGERGAQGPQGAEGPSG--PAGPRGPAGHQGPSGERGAP 577


>gi|326494512|dbj|BAJ90525.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 247

 Score = 39.8 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 14/112 (12%), Positives = 26/112 (23%), Gaps = 2/112 (1%)

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           L     +    + D       +  R      S  P    R + +     G  +       
Sbjct: 135 LRDDDEKRNGYSPDRRGGRDRSPDRRDNRGRSASPYGRGRERGSPDYGRGRERGSPDYGK 194

Query: 305 VHRRNLAS--NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              R+           G      +      E    SP++  +RS       +
Sbjct: 195 GGARDSPDYVRGGSPYGSKGDDRASPKYDRERREASPAYDRRRSRSPAREDR 246


>gi|281340704|gb|EFB16288.1| hypothetical protein PANDA_013578 [Ailuropoda melanoleuca]
          Length = 995

 Score = 39.8 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 14/105 (13%), Positives = 30/105 (28%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            + ++++                     S  P D     K+   ++   K K+      +
Sbjct: 251 KIEDKSRSKDRKKSPIINESRSRDRGKKSRSPIDLRGKSKDRRSRSKERKSKRSDMDKEK 310

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           + + S    A     +            RRS S   +   RR+ +
Sbjct: 311 KPIKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKQRDKSRRSRS 355



 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 14/120 (11%), Positives = 41/120 (34%), Gaps = 6/120 (5%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           + ++      +++ +  ++         R   ++  +  D  +R K+  S+++ + K+KK
Sbjct: 252 IEDKSRSKDRKKSPIINESRSRDRGKKSRSPIDLRGKSKDRRSRSKERKSKRSDMDKEKK 311

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSG------QREENHRRSPSFPSKRSLRRTSAKK 354
                 +   +     +                  + +    RSP    +RS +  S  +
Sbjct: 312 PIKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKQRDKSRRSRSPLVNDRRSKQSKSPSR 371



 Score = 36.7 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 19/131 (14%), Positives = 39/131 (29%), Gaps = 8/131 (6%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             R+     LR +    + +      D      ++  +DR               K S  
Sbjct: 222 QARKSKSPTLRRRSQEKIGKARSPPDDKVKIEDKSRSKDRKKSPIINESRSRDRGKKSRS 281

Query: 292 K---NGLSKQKKLATPVHRRNLAS-NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR-- 345
                G SK ++  +   +   +  +         S  + SG+   +  R P    KR  
Sbjct: 282 PIDLRGKSKDRRSRSKERKSKRSDMDKEKKPIKSPSKDASSGKENRSPSRRPGRSPKRRS 341

Query: 346 --SLRRTSAKK 354
               +R  +++
Sbjct: 342 LSPKQRDKSRR 352


>gi|29833013|ref|NP_827647.1| hypothetical protein SAV_6471 [Streptomyces avermitilis MA-4680]
 gi|29610134|dbj|BAC74182.1| putative membrane protein [Streptomyces avermitilis MA-4680]
          Length = 671

 Score = 39.8 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 10/124 (8%), Positives = 22/124 (17%), Gaps = 12/124 (9%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R  +             AP         D    +    +      + + +     + ++ 
Sbjct: 514 RTDVPQRTESPKHAGPYAPSRPYRPANPDTNPYLRVPEELRAAEGRRAPEDGRAPEARRP 573

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR------------RSPSFPSKRSLRR 349
           A      +                + S                      P  P +RS   
Sbjct: 574 AGGAAPGDRDVRPGDRDVRRPEGAAPSQGVRPPDDVYGAPTVIGPITPPPRSPGRRSRPA 633

Query: 350 TSAK 353
               
Sbjct: 634 APGA 637


>gi|88807311|ref|ZP_01122823.1| translation initiation factor IF-2 [Synechococcus sp. WH 7805]
 gi|88788525|gb|EAR19680.1| translation initiation factor IF-2 [Synechococcus sp. WH 7805]
          Length = 1139

 Score = 39.8 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 14/108 (12%), Positives = 21/108 (19%), Gaps = 2/108 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R    P    + +  ++      +        +    P                S     
Sbjct: 216 RPANAPPSRPQPKTPVNRNAPPPQRPAAKPELVGRPQPKRPAGPPSAGPPTRQNSGAGSP 275

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSG--QREENHRRSPSFPSKRSL 347
              V  R  A           +     G   R       PS P   SL
Sbjct: 276 RPAVSPRPSAPGSQRNMPQRPAGAQRPGSPARPGTGSGRPSRPGGNSL 323



 Score = 39.4 bits (90), Expect = 0.84,   Method: Composition-based stats.
 Identities = 10/111 (9%), Positives = 18/111 (16%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R                    +        P   +  P+   R +         +     
Sbjct: 208 RSSPNDAPRPANAPPSRPQPKTPVNRNAPPPQRPAAKPELVGRPQPKRPAGPPSAGPPTR 267

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                     +         S               SP+ P   S R +  
Sbjct: 268 QNSGAGSPRPAVSPRPSAPGSQRNMPQRPAGAQRPGSPARPGTGSGRPSRP 318



 Score = 36.3 bits (82), Expect = 7.1,   Method: Composition-based stats.
 Identities = 12/113 (10%), Positives = 26/113 (23%), Gaps = 7/113 (6%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               + +        S     R      S         +     +   +K + +  P  +
Sbjct: 195 ASSPKPRGAAPMRRSSPNDAPRPANAPPSRPQPKTPVNRNAPPPQRPAAKPELVGRPQPK 254

Query: 308 R-------NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           R          +      G     +S       + R  P  P+      + A+
Sbjct: 255 RPAGPPSAGPPTRQNSGAGSPRPAVSPRPSAPGSQRNMPQRPAGAQRPGSPAR 307


>gi|329938951|ref|ZP_08288325.1| 30S ribosomal protein S4 [Streptomyces griseoaurantiacus M045]
 gi|329301836|gb|EGG45729.1| 30S ribosomal protein S4 [Streptomyces griseoaurantiacus M045]
          Length = 204

 Score = 39.8 bits (91), Expect = 0.69,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 3/50 (6%)

Query: 15  RVSKVIARAGIASRR--EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R+GIA R   +  +M+    ++VNG  +++ +  V   D + V
Sbjct: 93  RLDALVLRSGIA-RTIYQARQMVVHGHIEVNGHKVDKPSFRVKPDDVVMV 141


>gi|119605889|gb|EAW85483.1| serine/arginine repetitive matrix 2, isoform CRA_f [Homo sapiens]
          Length = 2237

 Score = 39.8 bits (91), Expect = 0.69,   Method: Composition-based stats.
 Identities = 9/108 (8%), Positives = 21/108 (19%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                            S   +     +              + +    + + +  AT  
Sbjct: 336 RHASSSPESPKPAPAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAK 395

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R+ +          S        R          P +R   R+  +
Sbjct: 396 RGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQR 443



 Score = 39.4 bits (90), Expect = 0.80,   Method: Composition-based stats.
 Identities = 11/98 (11%), Positives = 22/98 (22%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P      +++      +       R    S  P       ++ +       + +  T  
Sbjct: 348 APAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKR 407

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
                 S  W        +      +     RSP  P 
Sbjct: 408 GHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPG 445



 Score = 36.7 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 22/135 (16%), Positives = 34/135 (25%), Gaps = 10/135 (7%)

Query: 230 AGSTREV----SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
            GS RE+    + K             +         S       R    S  P      
Sbjct: 351 PGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKRGHS 410

Query: 286 KKNSSQKNGLSKQKK--LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
           +  S Q       ++   +    RR  + +        S      G+     R      S
Sbjct: 411 RSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRSHSRS 470

Query: 344 K----RSLRRTSAKK 354
                RS  RT A++
Sbjct: 471 PATRGRSRSRTPARR 485


>gi|290961835|ref|YP_003493017.1| 30S ribosomal protein S4 [Streptomyces scabiei 87.22]
 gi|260651361|emb|CBG74483.1| 30S ribosomal protein S4 [Streptomyces scabiei 87.22]
          Length = 204

 Score = 39.8 bits (91), Expect = 0.70,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 3/50 (6%)

Query: 15  RVSKVIARAGIASRR--EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R+GIA R   +  +M+    ++VNG  +++ +  V   D + V
Sbjct: 93  RLDALVLRSGIA-RTIYQARQMVVHGHIEVNGHKVDKPSFRVKPDDVVMV 141


>gi|196232202|ref|ZP_03131057.1| hypothetical protein CfE428DRAFT_4223 [Chthoniobacter flavus
           Ellin428]
 gi|196223924|gb|EDY18439.1| hypothetical protein CfE428DRAFT_4223 [Chthoniobacter flavus
           Ellin428]
          Length = 896

 Score = 39.8 bits (91), Expect = 0.70,   Method: Composition-based stats.
 Identities = 12/146 (8%), Positives = 31/146 (21%), Gaps = 21/146 (14%)

Query: 230 AGSTREVSKKIL--REQLGPHLLEEAQVNLDAPIYSSET--LVRDRPNIISEVPDDFTRM 285
            G T E   + +       P+        +      +            + +  +   + 
Sbjct: 629 PGETIEKPGQTIPGEAPGKPNQPPRKPGEVIEKPGQTIPGEAPGKPNQPLRKPGEVIAKP 688

Query: 286 KKNSSQKNGLSKQKKLATPVH--RRNLASNVWMAKGIHSSFLSDSG-------------- 329
            +    +      +    P     +   +    A G  +      G              
Sbjct: 689 GQTIPGEAPGKPNQPPRKPGETIEKPGQTIPGEAPGKPNQPPRKPGETIEKPGQTIPGEA 748

Query: 330 -QREENHRRSPSFPSKRSLRRTSAKK 354
             +     R P+   K +      +K
Sbjct: 749 PGKPNQPPRKPAEAEKPAPPEKKPEK 774



 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 7/100 (7%), Positives = 21/100 (21%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
             + +      +  +                      + P +    +  +        ++
Sbjct: 773 EKKSERPAQPQQPIEKPEKPAKPQKPERPPKEEIKRPQAPVEPMTKRPPAEAPKEKRPEQ 832

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
            +  P   R             S   +    + EN  + P
Sbjct: 833 PVPKPPEERPREGKHKEPAPQVSRPETKEAPKPENKSKEP 872



 Score = 36.3 bits (82), Expect = 6.5,   Method: Composition-based stats.
 Identities = 17/125 (13%), Positives = 28/125 (22%), Gaps = 8/125 (6%)

Query: 230 AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
            G T E   + +    G    +  Q                +P   SE P    +  +  
Sbjct: 733 PGETIEKPGQTI---PGEAPGKPNQPPRKPAEAEKPAPPEKKPEKKSERPAQPQQPIEKP 789

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
             +     QK    P                     +   +R E     P    +   R 
Sbjct: 790 --EKPAKPQKPERPPKEEIKRPQAPVEPMTKRPPAEAPKEKRPEQPVPKP---PEERPRE 844

Query: 350 TSAKK 354
              K+
Sbjct: 845 GKHKE 849


>gi|119605887|gb|EAW85481.1| serine/arginine repetitive matrix 2, isoform CRA_d [Homo sapiens]
          Length = 2341

 Score = 39.8 bits (91), Expect = 0.70,   Method: Composition-based stats.
 Identities = 9/108 (8%), Positives = 21/108 (19%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                            S   +     +              + +    + + +  AT  
Sbjct: 432 RHASSSPESPKPAPAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAK 491

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R+ +          S        R          P +R   R+  +
Sbjct: 492 RGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQR 539



 Score = 39.4 bits (90), Expect = 0.80,   Method: Composition-based stats.
 Identities = 11/98 (11%), Positives = 22/98 (22%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P      +++      +       R    S  P       ++ +       + +  T  
Sbjct: 444 APAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKR 503

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
                 S  W        +      +     RSP  P 
Sbjct: 504 GHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPG 541



 Score = 36.7 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 22/135 (16%), Positives = 34/135 (25%), Gaps = 10/135 (7%)

Query: 230 AGSTREV----SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
            GS RE+    + K             +         S       R    S  P      
Sbjct: 447 PGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKRGHS 506

Query: 286 KKNSSQKNGLSKQKK--LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
           +  S Q       ++   +    RR  + +        S      G+     R      S
Sbjct: 507 RSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRSHSRS 566

Query: 344 K----RSLRRTSAKK 354
                RS  RT A++
Sbjct: 567 PATRGRSRSRTPARR 581


>gi|73998667|ref|XP_544044.2| PREDICTED: similar to eukaryotic translation initiation factor 3,
            subunit 10 (theta) isoform 1 [Canis familiaris]
          Length = 1291

 Score = 39.8 bits (91), Expect = 0.70,   Method: Composition-based stats.
 Identities = 23/141 (16%), Positives = 44/141 (31%), Gaps = 9/141 (6%)

Query: 216  IRISYGPFQLGTLLAGSTREVSKK------ILREQLGPHLLEEAQVNLDAPIYSSETLVR 269
             R S G ++ G  +    R    +        R++  PH  EE +          E+ +R
Sbjct: 892  DRDSEGTWRKGPEVDSEWRRGPPEKEWRRGEGRDEERPHRREEDRPRRLGDEEERESSLR 951

Query: 270  DRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSG 329
               + I     D  R  +    ++  S++        RR L  +        ++      
Sbjct: 952  PDDDRIPRRGMDDDRGPRRGLDEDRFSRRGADDDRPPRRGLDEDRG---SWRTADEDRGP 1008

Query: 330  QREENHRRSPSFPSKRSLRRT 350
            +R  +  R P        R +
Sbjct: 1009 RRGMDEDRGPRRGGADDERSS 1029


>gi|118089933|ref|XP_420424.2| PREDICTED: similar to hedgehog-interacting protein [Gallus gallus]
          Length = 1391

 Score = 39.8 bits (91), Expect = 0.71,   Method: Composition-based stats.
 Identities = 5/117 (4%), Positives = 19/117 (16%), Gaps = 6/117 (5%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS-KQKK 300
           RE +         +        +                     ++    +     +  +
Sbjct: 523 REAVARRRGRTPALPSGRLPVEAAAPTYGARLPPGNRGAPPLPDERGPRARGTAGCRGPE 582

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLS-----DSGQREENHRRSPSFPSKRSLRRTSA 352
             +    R+         G             +         +P      +    + 
Sbjct: 583 GESGAATRSRRPPPGDRYGARRRRAPLSLSSRAPAARAERGPAPLARGPGARPGAAP 639


>gi|119605888|gb|EAW85482.1| serine/arginine repetitive matrix 2, isoform CRA_e [Homo sapiens]
          Length = 2340

 Score = 39.8 bits (91), Expect = 0.73,   Method: Composition-based stats.
 Identities = 9/108 (8%), Positives = 21/108 (19%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                            S   +     +              + +    + + +  AT  
Sbjct: 432 RHASSSPESPKPAPAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAK 491

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R+ +          S        R          P +R   R+  +
Sbjct: 492 RGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQR 539



 Score = 39.4 bits (90), Expect = 0.81,   Method: Composition-based stats.
 Identities = 11/98 (11%), Positives = 22/98 (22%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P      +++      +       R    S  P       ++ +       + +  T  
Sbjct: 444 APAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKR 503

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
                 S  W        +      +     RSP  P 
Sbjct: 504 GHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPG 541



 Score = 36.7 bits (83), Expect = 5.9,   Method: Composition-based stats.
 Identities = 22/135 (16%), Positives = 34/135 (25%), Gaps = 10/135 (7%)

Query: 230 AGSTREV----SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
            GS RE+    + K             +         S       R    S  P      
Sbjct: 447 PGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKRGHS 506

Query: 286 KKNSSQKNGLSKQKK--LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
           +  S Q       ++   +    RR  + +        S      G+     R      S
Sbjct: 507 RSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRSHSRS 566

Query: 344 K----RSLRRTSAKK 354
                RS  RT A++
Sbjct: 567 PATRGRSRSRTPARR 581


>gi|297626626|ref|YP_003688389.1| Translation initiation factor IF-2 [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
 gi|296922391|emb|CBL56963.1| Translation initiation factor IF-2 [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
          Length = 973

 Score = 39.8 bits (91), Expect = 0.74,   Method: Composition-based stats.
 Identities = 10/122 (8%), Positives = 24/122 (19%)

Query: 233 TREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
            R V++KI  E+ G       +         +    +                 +     
Sbjct: 43  VRRVTEKITSERGGADTSSAPKAGAKGATPKTSGAPKSARPAAKPGAGTTPVTPQAPKAA 102

Query: 293 NGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
              S +         +        A        S           + + P   +      
Sbjct: 103 KASSVKPAPRPAAKVKPTPGPQVHATPKAPVPHSGPVSSPTPRPGASARPGSPAHTPHPP 162

Query: 353 KK 354
           ++
Sbjct: 163 RR 164


>gi|220916674|ref|YP_002491978.1| response regulator receiver protein [Anaeromyxobacter dehalogenans
           2CP-1]
 gi|219954528|gb|ACL64912.1| response regulator receiver protein [Anaeromyxobacter dehalogenans
           2CP-1]
          Length = 476

 Score = 39.4 bits (90), Expect = 0.76,   Method: Composition-based stats.
 Identities = 10/118 (8%), Positives = 24/118 (20%), Gaps = 5/118 (4%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
            LR   G      +        +           +         R      +       +
Sbjct: 211 ELR--PGMPPGARSPAPGAPAGFRPGAAPPPGARLPGPGTPPGARPAAPGMRPGMAPGAR 268

Query: 300 KLATPVHRRNLASNVWMAKGIH---SSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                +          M  G      S      +       + + PS   + + +A++
Sbjct: 269 PPGPGLPPPGARPAAGMPPGARPAMPSGAPAGFRPGPGMPPTGARPSPTPIPQPAARR 326


>gi|325928307|ref|ZP_08189507.1| hypothetical protein XPE_3559 [Xanthomonas perforans 91-118]
 gi|325541318|gb|EGD12860.1| hypothetical protein XPE_3559 [Xanthomonas perforans 91-118]
          Length = 244

 Score = 39.4 bits (90), Expect = 0.76,   Method: Composition-based stats.
 Identities = 8/87 (9%), Positives = 14/87 (16%), Gaps = 2/87 (2%)

Query: 264 SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSS 323
                 +R               K +   N   + +    P    +   N          
Sbjct: 15  KSAPKPERKPDARPAARAHGNGGKPAPGGNRPGQGRGPQRPHAAASTDGNGERKPAGRPE 74

Query: 324 FL--SDSGQREENHRRSPSFPSKRSLR 348
                  G        +      R  R
Sbjct: 75  RRHDGKPGAAPRPQHAAADRRGPRPAR 101



 Score = 37.1 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 8/101 (7%), Positives = 16/101 (15%), Gaps = 1/101 (0%)

Query: 239 KILREQL-GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
             LR+QL G       +         +     +                         + 
Sbjct: 3   DTLRDQLLGLGFKSAPKPERKPDARPAARAHGNGGKPAPGGNRPGQGRGPQRPHAAASTD 62

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS 338
                 P  R     +            +   +     R  
Sbjct: 63  GNGERKPAGRPERRHDGKPGAAPRPQHAAADRRGPRPARTR 103


>gi|315656403|ref|ZP_07909292.1| translation initiation factor IF2 [Mobiluncus curtisii subsp.
           holmesii ATCC 35242]
 gi|315492962|gb|EFU82564.1| translation initiation factor IF2 [Mobiluncus curtisii subsp.
           holmesii ATCC 35242]
          Length = 922

 Score = 39.4 bits (90), Expect = 0.77,   Method: Composition-based stats.
 Identities = 16/116 (13%), Positives = 24/116 (20%), Gaps = 7/116 (6%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ-----KNG 294
                  P   +       A + +  +   D P   + +P    R   N           
Sbjct: 123 ETPAAPQPTPEKTDSSPSPAKLQAKPSAHPDIPKPGAGIPKPGARPGNNPFASAQGMPRP 182

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                  A P  RR    N   A     S       +       P    +    R 
Sbjct: 183 GGTSGIKAKPGPRRGRLGNNPFASAQGMSQGIPRPGQ--GGGPRPKPGDRMGSPRG 236


>gi|298345262|ref|YP_003717949.1| translation initiation factor IF-2 [Mobiluncus curtisii ATCC 43063]
 gi|298235323|gb|ADI66455.1| translation initiation factor IF-2 [Mobiluncus curtisii ATCC 43063]
          Length = 922

 Score = 39.4 bits (90), Expect = 0.77,   Method: Composition-based stats.
 Identities = 16/116 (13%), Positives = 24/116 (20%), Gaps = 7/116 (6%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ-----KNG 294
                  P   +       A + +  +   D P   + +P    R   N           
Sbjct: 123 ETPAAPQPTPEKTDSSPSPAKLQAKPSAHPDIPKPGAGIPKPGARPGNNPFASAQGMPRP 182

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                  A P  RR    N   A     S       +       P    +    R 
Sbjct: 183 GGTSGIKAKPGPRRGRLGNNPFASAQGMSQGIPRPGQ--GGGPRPKPGDRMGSPRG 236


>gi|118094262|ref|XP_001231651.1| PREDICTED: similar to alpha-1 (type XI) collagen isoform 2 [Gallus
           gallus]
          Length = 1766

 Score = 39.4 bits (90), Expect = 0.77,   Method: Composition-based stats.
 Identities = 9/111 (8%), Positives = 15/111 (13%), Gaps = 1/111 (0%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           L+   G       +                 P       +             G    K 
Sbjct: 754 LKGDRGEVGQPGPRGEDGPEGPKGRAGPSGDPGAAGPAGEKGKLGVPGLPGYPGRQGPKG 813

Query: 301 LATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                                        G       R P  P+ +   + 
Sbjct: 814 STGFPGFPGANGEKGARGLHGKPGPRGQRGPTGPRGSRGPRGPTGKPGPKG 864


>gi|297155790|gb|ADI05502.1| 30S ribosomal protein S4 [Streptomyces bingchenggensis BCW-1]
          Length = 204

 Score = 39.4 bits (90), Expect = 0.78,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 3/50 (6%)

Query: 15  RVSKVIARAGIASRR--EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R+GIA R   +  +M+    ++VNG  +++ +  V   D + V
Sbjct: 93  RLDALVLRSGIA-RTIYQARQMVVHGHIEVNGRKVDKPSFRVRPDDVVMV 141


>gi|221488751|gb|EEE26965.1| conserved hypothetical protein [Toxoplasma gondii GT1]
          Length = 314

 Score = 39.4 bits (90), Expect = 0.78,   Method: Composition-based stats.
 Identities = 18/119 (15%), Positives = 31/119 (26%), Gaps = 5/119 (4%)

Query: 224 QLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
           +      GS   V  K  + QL      E        +   E   R           +  
Sbjct: 137 EKKGHEQGSWEVVLTKQQKHQLHRAAQAETLP-----LSGREGRTRRPDRERDNRHANAD 191

Query: 284 RMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
           R + N     G    ++ A    +R    +   A G   +   ++  +    RR     
Sbjct: 192 RQRGNEHPSAGRRADRQTAAGPVQRRRRDSRGEAGGFRRAGGQNATGKAATGRRRGRQG 250


>gi|325267950|ref|ZP_08134599.1| heat shock protein 15 [Kingella denitrificans ATCC 33394]
 gi|324980636|gb|EGC16299.1| heat shock protein 15 [Kingella denitrificans ATCC 33394]
          Length = 138

 Score = 39.4 bits (90), Expect = 0.78,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 2/60 (3%)

Query: 2  KDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
          K ++  +E     R+ K + A     +R    + I   RV VNG   + +   +   D +
Sbjct: 3  KQQHDNEERDDEMRLDKWLWAARFFKTRSLASKQIELGRVSVNGAKAKTSKY-ISVGDVV 61


>gi|196968467|gb|ACG80807.1| hypothetical protein [Chlamydophila pecorum]
          Length = 216

 Score = 39.4 bits (90), Expect = 0.78,   Method: Composition-based stats.
 Identities = 19/130 (14%), Positives = 38/130 (29%), Gaps = 1/130 (0%)

Query: 224 QLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
           +L  L   S++E+S K       P   E +     +   S +      P+     P + +
Sbjct: 2   ELKDLETSSSKELSPKE-PLPKEPSPKEPSSKEPSSKELSPKESSPKEPSPKEPSPKEPS 60

Query: 284 RMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
             + +  + +      K  +P    +   +         S    S +       SP  PS
Sbjct: 61  SKEPSPKEPSSKEPSPKEPSPKEPSSKEPSPKELSPKEPSPKEPSPKELSPKEPSPKEPS 120

Query: 344 KRSLRRTSAK 353
            +        
Sbjct: 121 SKEPSSKEPS 130



 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 16/120 (13%), Positives = 33/120 (27%), Gaps = 1/120 (0%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           +E+S K       P   E +     +   S +      P+     P + +  + +  + +
Sbjct: 37  KELSPKE-SSPKEPSPKEPSPKEPSSKEPSPKEPSSKEPSPKEPSPKEPSSKEPSPKELS 95

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                 K  +P        +         S    S +   +   SP  PS +        
Sbjct: 96  PKEPSPKEPSPKELSPKEPSPKEPSSKEPSSKEPSPKEPSSKEPSPKEPSPKEPSPKEPS 155


>gi|118094260|ref|XP_001231624.1| PREDICTED: similar to alpha-1 (type XI) collagen isoform 1 [Gallus
           gallus]
          Length = 1817

 Score = 39.4 bits (90), Expect = 0.78,   Method: Composition-based stats.
 Identities = 9/111 (8%), Positives = 15/111 (13%), Gaps = 1/111 (0%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           L+   G       +                 P       +             G    K 
Sbjct: 805 LKGDRGEVGQPGPRGEDGPEGPKGRAGPSGDPGAAGPAGEKGKLGVPGLPGYPGRQGPKG 864

Query: 301 LATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                                        G       R P  P+ +   + 
Sbjct: 865 STGFPGFPGANGEKGARGLHGKPGPRGQRGPTGPRGSRGPRGPTGKPGPKG 915


>gi|114664951|ref|XP_001168849.1| PREDICTED: nuclear pore complex-interacting protein-like 3-like
           [Pan troglodytes]
          Length = 325

 Score = 39.4 bits (90), Expect = 0.78,   Method: Composition-based stats.
 Identities = 14/113 (12%), Positives = 25/113 (22%), Gaps = 5/113 (4%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           L+         EA+         +  +    P        D     +   ++        
Sbjct: 196 LKTPPLATQEAEAEKPPKPKRPRAADVETSSPEPKRRRVGDVEPSSRKPKRQRAGDVDPS 255

Query: 301 LATPVHRRNLASNVWMAKGIHSS-----FLSDSGQREENHRRSPSFPSKRSLR 348
              P  RR    +   +K            S   +R       PS    +  R
Sbjct: 256 SRKPKRRRADDVDPSSSKPKRRRADDVDPSSRKPKRRRADDVDPSSSKPKRRR 308



 Score = 35.9 bits (81), Expect = 8.3,   Method: Composition-based stats.
 Identities = 9/108 (8%), Positives = 22/108 (20%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P   +    + +        +         +   D     +   ++         + P 
Sbjct: 216 RPRAADVETSSPEPKRRRVGDVEPSSRKPKRQRAGDVDPSSRKPKRRRADDVDPSSSKPK 275

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            RR    +    K              +  RR        S +    +
Sbjct: 276 RRRADDVDPSSRKPKRRRADDVDPSSSKPKRRRADDVEPSSRKPKRRR 323


>gi|315655683|ref|ZP_07908581.1| translation initiation factor IF2 [Mobiluncus curtisii ATCC 51333]
 gi|315489747|gb|EFU79374.1| translation initiation factor IF2 [Mobiluncus curtisii ATCC 51333]
          Length = 922

 Score = 39.4 bits (90), Expect = 0.79,   Method: Composition-based stats.
 Identities = 16/116 (13%), Positives = 24/116 (20%), Gaps = 7/116 (6%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ-----KNG 294
                  P   +       A + +  +   D P   + +P    R   N           
Sbjct: 123 ETPAAPQPTPEKTDSSPSPAKLQAKPSAHPDIPKPGAGIPKPGARPGNNPFASAQGMPRP 182

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                  A P  RR    N   A     S       +       P    +    R 
Sbjct: 183 GGTSGIKAKPGPRRGRLGNNPFASAQGMSQGIPRPGQ--GGGPRPKPGDRMGSPRG 236


>gi|254384581|ref|ZP_04999921.1| hypothetical protein SSAG_04306 [Streptomyces sp. Mg1]
 gi|194343466|gb|EDX24432.1| hypothetical protein SSAG_04306 [Streptomyces sp. Mg1]
          Length = 452

 Score = 39.4 bits (90), Expect = 0.79,   Method: Composition-based stats.
 Identities = 20/139 (14%), Positives = 35/139 (25%), Gaps = 8/139 (5%)

Query: 216 IRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNII 275
           +R+  G   L     G        +L   +              P+       R  P   
Sbjct: 320 VRVPLGNVHLAGHRQG------GGLLHRPVHGQRPARQLGQPLRPVVRPGQGTRRGPPAP 373

Query: 276 SEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENH 335
               D   R+    +++ G +       P HR          +           +R  + 
Sbjct: 374 RRAGD--RRVGPGPARRPGGAPAHAADRPGHRGQGRGPARAVRPCRERPQGSRLERLHHG 431

Query: 336 RRSPSFPSKRSLRRTSAKK 354
           RR         LRR   ++
Sbjct: 432 RRLWRRAGAGVLRRGPGRR 450


>gi|170782512|ref|YP_001710845.1| putative ATP-dependent helicase [Clavibacter michiganensis subsp.
           sepedonicus]
 gi|169157081|emb|CAQ02256.1| putative ATP-dependent helicase [Clavibacter michiganensis subsp.
           sepedonicus]
          Length = 761

 Score = 39.4 bits (90), Expect = 0.79,   Method: Composition-based stats.
 Identities = 7/108 (6%), Positives = 24/108 (22%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P     A+        + E                    +     + G ++ ++   P 
Sbjct: 51  RPQRGGAARPARGGDRPNWEPRAERPAGRGERPAYGDRPNRAGQRPERGDARPQRGERPS 110

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +           +  + +      +R       P+   +      + +
Sbjct: 111 YGGGNDRGQRSERPSYGAERGQRSERPSYGNARPARDERSERPSYNDR 158



 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 11/109 (10%), Positives = 21/109 (19%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R           + N +                           + ++  + G       
Sbjct: 54  RGGAARPARGGDRPNWEPRAERPAGRGERPAYGDRPNRAGQRPERGDARPQRGERPSYGG 113

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                +R+   +    +G  S   S    R     RS          R 
Sbjct: 114 GNDRGQRSERPSYGAERGQRSERPSYGNARPARDERSERPSYNDRAPRN 162



 Score = 38.2 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 8/99 (8%), Positives = 24/99 (24%), Gaps = 4/99 (4%)

Query: 259 APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAK 318
            P  +       R    S  P+        + +K   +  ++        +       A+
Sbjct: 1   MPYNNDSPRGAKRAPAGSRSPNHRGYNSDPAPKKQRWNADERAQRSGQD-DRPQRGGAAR 59

Query: 319 GIHSSFLS---DSGQREENHRRSPSFPSKRSLRRTSAKK 354
                         +R       P++  + +      ++
Sbjct: 60  PARGGDRPNWEPRAERPAGRGERPAYGDRPNRAGQRPER 98



 Score = 37.1 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 13/110 (11%), Positives = 26/110 (23%), Gaps = 6/110 (5%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL-ATP 304
            P     A                 RP      P    R         G   ++      
Sbjct: 70  EPRAERPAGRGERPAYGDRPNRAGQRPERGDARPQRGERPSYGGGNDRGQRSERPSYGAE 129

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             +R+   +   A+        +  +R   + R+P    + S      ++
Sbjct: 130 RGQRSERPSYGNARPAR----DERSERPSYNDRAP-RNDRPSYGNDRPQR 174


>gi|145601287|ref|XP_363177.2| hypothetical protein MGG_08761 [Magnaporthe oryzae 70-15]
 gi|145009304|gb|EDJ94015.1| hypothetical protein MGG_08761 [Magnaporthe oryzae 70-15]
          Length = 932

 Score = 39.4 bits (90), Expect = 0.79,   Method: Composition-based stats.
 Identities = 17/126 (13%), Positives = 27/126 (21%)

Query: 229 LAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
                RE+    L  + G             P+              S       R  + 
Sbjct: 25  PPQYLREMKNPRLEGRPGSEFAPVNGDGRGGPLGPPVDAKFSTTEAQSADYPTDARPDQG 84

Query: 289 SSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
            S  +G       ATP             K             +   + +P  P+ +   
Sbjct: 85  QSAPSGPVPNAPAATPPAPPPSTPGQPAPKPAPEQPAPKPAPEQPAPKPAPEQPAPKPAP 144

Query: 349 RTSAKK 354
              A K
Sbjct: 145 EQPAPK 150


>gi|76818401|ref|YP_335445.1| polyphosphate kinase 2 family protein [Burkholderia pseudomallei
           1710b]
 gi|76582874|gb|ABA52348.1| Polyphosphate kinase 2 family [Burkholderia pseudomallei 1710b]
          Length = 513

 Score = 39.4 bits (90), Expect = 0.79,   Method: Composition-based stats.
 Identities = 10/105 (9%), Positives = 23/105 (21%), Gaps = 1/105 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA-TP 304
                  A +  +A           RP    +  +   R  ++ ++      +      P
Sbjct: 53  QAPNRAPAGLPTEARPSPDRAPTETRPRPDRDPTETRPRPDRDPTETRPRPDRGPTETRP 112

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
              R+            +       +     R  P      +  R
Sbjct: 113 RPDRDPTETRPRPDRDPTEPRPRPDRDPTEARPRPDRGPTETRPR 157



 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 11/111 (9%), Positives = 21/111 (18%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
              P  L            +      DR    +    D    +       G ++ +    
Sbjct: 56  NRAPAGLPTEARPSPDRAPTETRPRPDRDPTETRPRPDRDPTETRPRPDRGPTETRPRPD 115

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                                  D  +      R P+    R  R  +  +
Sbjct: 116 RDPTETRPRPDRDPTEPRPRPDRDPTEARPRPDRGPTETRPRPNRGPTEAQ 166



 Score = 38.2 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 11/114 (9%), Positives = 21/114 (18%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
               R        E        P  +     RD            T  +    +    ++
Sbjct: 63  PTEARPSPDRAPTETRPRPDRDPTETRPRPDRDPTETRPRPDRGPTETRPRPDRDPTETR 122

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
            +    P   R                     +   N   + + P   +   T 
Sbjct: 123 PRPDRDPTEPRPRPDRDPTEARPRPDRGPTETRPRPNRGPTEAQPGSPTKLPTK 176



 Score = 36.7 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 9/115 (7%), Positives = 20/115 (17%), Gaps = 3/115 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +Q         +        SS T                T  + +  +    ++ +   
Sbjct: 24  DQRAARARSTERSPRARRGGSSSTRPSVDQAPNRAPAGLPTEARPSPDRAPTETRPRPDR 83

Query: 303 TPVHRRNLASNVWMAKGIHSSFLS---DSGQREENHRRSPSFPSKRSLRRTSAKK 354
            P   R                           +     P      +  R    +
Sbjct: 84  DPTETRPRPDRDPTETRPRPDRGPTETRPRPDRDPTETRPRPDRDPTEPRPRPDR 138


>gi|260812920|ref|XP_002601168.1| hypothetical protein BRAFLDRAFT_75617 [Branchiostoma floridae]
 gi|229286459|gb|EEN57180.1| hypothetical protein BRAFLDRAFT_75617 [Branchiostoma floridae]
          Length = 979

 Score = 39.4 bits (90), Expect = 0.80,   Method: Composition-based stats.
 Identities = 8/114 (7%), Positives = 15/114 (13%)

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           +  R                           D       + D       +   +      
Sbjct: 472 QEERGPPDRRGPPGEIPGEFQGRPDQSGPPEDFRGQGRPMQDPRGPPPGDRDSRGPPRWS 531

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           +    P                  +       R E  +R P             
Sbjct: 532 EGRRGPPGDHRPPRGEGERGPPRGNMEQRGPPRGEREQRGPPRGDMEQGGPPRG 585


>gi|331698284|ref|YP_004334523.1| xenobiotic-transporting ATPase [Pseudonocardia dioxanivorans CB1190]
 gi|326952973|gb|AEA26670.1| Xenobiotic-transporting ATPase [Pseudonocardia dioxanivorans CB1190]
          Length = 1596

 Score = 39.4 bits (90), Expect = 0.81,   Method: Composition-based stats.
 Identities = 14/110 (12%), Positives = 25/110 (22%), Gaps = 1/110 (0%)

Query: 244  QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            Q+G         +      + +  V D             R  +  +  +    +    T
Sbjct: 987  QVGHRGGSRRPGDTRHDGAAHDGPVPDGRPASRPGAPAPDRSARRVNG-HDHGVRSDNGT 1045

Query: 304  PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               RR+                   G R +N         +R  R   A 
Sbjct: 1046 APDRRDGRDPAHDDSAARRINGHPRGFRSDNGTGPDRPSPRRDGRPDRAA 1095



 Score = 37.9 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 14/101 (13%), Positives = 22/101 (21%)

Query: 248  HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                    +       + T    R        D   R      +            P  R
Sbjct: 1027 RSARRVNGHDHGVRSDNGTAPDRRDGRDPAHDDSAARRINGHPRGFRSDNGTGPDRPSPR 1086

Query: 308  RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
            R+   +        +   +    R    RR+    S RS R
Sbjct: 1087 RDGRPDRAAHVDDRTPGEARRYDRTGADRRAGDQRSGRSRR 1127


>gi|256374879|ref|YP_003098539.1| hypothetical protein Amir_0730 [Actinosynnema mirum DSM 43827]
 gi|255919182|gb|ACU34693.1| hypothetical protein Amir_0730 [Actinosynnema mirum DSM 43827]
          Length = 247

 Score = 39.4 bits (90), Expect = 0.81,   Method: Composition-based stats.
 Identities = 12/80 (15%), Positives = 22/80 (27%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
            V++  L  +  P   ++    ++A           RP   +   D     +   S  +G
Sbjct: 156 RVTQDELDAEEAPRPPKKRPRPVEAEDAVEADERPKRPRKPAPAEDGERPRRPRPSGASG 215

Query: 295 LSKQKKLATPVHRRNLASNV 314
             K      P   R      
Sbjct: 216 EKKPTGEKKPSGERPRKPAG 235


>gi|283850801|ref|ZP_06368087.1| translation initiation factor IF-2 [Desulfovibrio sp. FW1012B]
 gi|283573724|gb|EFC21698.1| translation initiation factor IF-2 [Desulfovibrio sp. FW1012B]
          Length = 902

 Score = 39.4 bits (90), Expect = 0.83,   Method: Composition-based stats.
 Identities = 9/63 (14%), Positives = 11/63 (17%)

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
            +   +      P  R         A G    F                 P         
Sbjct: 182 PDPKKEPTPAPRPAGREAPRPGARPAPGGAPRFTPGGAPGGAPRPAGRPVPGAPPAPTDD 241

Query: 352 AKK 354
           AKK
Sbjct: 242 AKK 244


>gi|330859406|emb|CBX69751.1| hypothetical protein YEW_GJ27370 [Yersinia enterocolitica W22703]
          Length = 213

 Score = 39.4 bits (90), Expect = 0.84,   Method: Composition-based stats.
 Identities = 14/101 (13%), Positives = 30/101 (29%), Gaps = 2/101 (1%)

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL--SKQKKLATPVHRRNLAS 312
           V+    +   E L++     I+    +     K    +NG      ++            
Sbjct: 113 VDEHKLLRDIERLLKREIPRIALDGYEPDPSIKADPIQNGRQGRGAQRPGMGRGSSAGRP 172

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               A        +   + + + +R P+ PS R   R   +
Sbjct: 173 QNGGAAAGRGDSRTSRPRSQADGQRRPAGPSSRGRSRKPGE 213


>gi|195111454|ref|XP_002000293.1| GI22604 [Drosophila mojavensis]
 gi|193916887|gb|EDW15754.1| GI22604 [Drosophila mojavensis]
          Length = 639

 Score = 39.4 bits (90), Expect = 0.84,   Method: Composition-based stats.
 Identities = 10/113 (8%), Positives = 31/113 (27%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            +Q  P    + Q          +     R            + + N  +     ++   
Sbjct: 196 DDQSPPRRRRDDQSPPRRIKGDDDDQSPPRNRRDDNQSPPRRKKRDNHDKSPPSRRRDDD 255

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +P  R+    +         +      +R ++  +SP    + + +    ++
Sbjct: 256 HSPPRRKKRDDDDQSPPRRRFNADQSPPRRRKDADKSPPRRVRNTDQSPPRRR 308



 Score = 37.5 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 13/113 (11%), Positives = 34/113 (30%), Gaps = 2/113 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            +   P   ++   +  +P        +  P    +      R  +N+ Q     ++   
Sbjct: 253 DDDHSPPRRKKRDDDDQSPPRRRFNADQSPPRRRKDADKSPPRRVRNTDQSPPRRRRDSD 312

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +P  RR  +           S       +  +  +SP    +  L++   ++
Sbjct: 313 QSPPRRRKDSDQS--PPRKRRSSDQSPPIKRRDSDQSPPRRRQADLKQHKNRR 363



 Score = 36.7 bits (83), Expect = 6.3,   Method: Composition-based stats.
 Identities = 13/112 (11%), Positives = 31/112 (27%), Gaps = 1/112 (0%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +Q  P   +    +        ++  R       +      R   N S      +     
Sbjct: 186 DQSPPRRRKNDDQSPPRRRRDDQSPPRRIKGDDDDQSPPRNRRDDNQSPPRRKKRDNHDK 245

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +P  RR    +    +           +R  N  +SP    ++   ++  ++
Sbjct: 246 SPPSRRRDDDHSPPRRKKRDDDDQSPPRRRFNADQSPPRR-RKDADKSPPRR 296



 Score = 36.3 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 12/113 (10%), Positives = 27/113 (23%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R         E  V+   P                +          +  Q    +++   
Sbjct: 172 RSDEEKPNKRERNVDQSPPRRRKNDDQSPPRRRRDDQSPPRRIKGDDDDQSPPRNRRDDN 231

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +P  R+   ++                +R++      S P +R     S  +
Sbjct: 232 QSPPRRKKRDNHDKSPPSRRRDDDHSPPRRKKRDDDDQSPPRRRFNADQSPPR 284


>gi|321476845|gb|EFX87805.1| hypothetical protein DAPPUDRAFT_306491 [Daphnia pulex]
          Length = 1014

 Score = 39.4 bits (90), Expect = 0.84,   Method: Composition-based stats.
 Identities = 15/127 (11%), Positives = 28/127 (22%), Gaps = 6/127 (4%)

Query: 216 IRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNII 275
            R+  G      +       V  K  R++  P      Q               +  N  
Sbjct: 159 RRVGSGRLTGRDVEPA---PVPAKEPRDRREPLRAPAPQRERTFDREPQRNERGNERNDR 215

Query: 276 SEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL---ASNVWMAKGIHSSFLSDSGQRE 332
            +  +   R ++N           +   P  +       S                  R 
Sbjct: 216 HDRNERNERSERNGRTFQPSRADPRDKDPAEKDRRNFDRSGYDRDYSGRGDRGDRYNSRR 275

Query: 333 ENHRRSP 339
           +N   +P
Sbjct: 276 KNEDDTP 282


>gi|254456438|ref|ZP_05069867.1| ribosomal protein S4 [Candidatus Pelagibacter sp. HTCC7211]
 gi|207083440|gb|EDZ60866.1| ribosomal protein S4 [Candidatus Pelagibacter sp. HTCC7211]
          Length = 205

 Score = 39.4 bits (90), Expect = 0.85,   Method: Composition-based stats.
 Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 15/75 (20%)

Query: 3   DKNIVQENFTPQ--------RVSKVIARAGIA----SRREVERMIAQQRVKVNGILLERA 50
            K ++ +  T +        R+  VI RA  A    S     ++I    V+VNG  +   
Sbjct: 75  KKAVMLKGDTGENLIGLLERRLDAVIYRAKFATTIFS---ARQLINHNHVRVNGKKVNIG 131

Query: 51  AVNVMSTDHIEVDGV 65
           +  V   D IE+   
Sbjct: 132 SYLVKEEDSIEIRDK 146


>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 = 39.4 bits (90), Expect = 0.85,   Method: Composition-based stats.
 Identities = 26/240 (10%), Positives = 59/240 (24%), Gaps = 42/240 (17%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKV--------------NGILLERAA 51
           V++ F   R+   +++     SR  ++ +I +  V V              + I +    
Sbjct: 8   VEKEFDNVRLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNKKKKRNYKLKVGDNIEVNIPE 67

Query: 52  VN---VMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                +   D I++D   +   ++  + +      +V         + V   L       
Sbjct: 68  PKLLEIEPED-IKLD---IIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNALLNHCKDLS 123

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD------------ 156
              G         +     G L       S   L                          
Sbjct: 124 GINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGIIKDEQG 183

Query: 157 --------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                         K  V++   +      +  +  ++  V   L  G+  +I+      
Sbjct: 184 TIEAPIGRHPVDRIKMAVVKDGRHAVTHYKVIERFKNHTLVECRLETGRTHQIRVHMSHI 243


>gi|84494425|ref|ZP_00993544.1| ATP-dependent RNA helicase [Janibacter sp. HTCC2649]
 gi|84383918|gb|EAP99798.1| ATP-dependent RNA helicase [Janibacter sp. HTCC2649]
          Length = 774

 Score = 39.4 bits (90), Expect = 0.85,   Method: Composition-based stats.
 Identities = 14/110 (12%), Positives = 29/110 (26%), Gaps = 9/110 (8%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           +                 +      S   D   R  +         +  + ++   R + 
Sbjct: 23  QSKGPKKTHRGQPEGPRTKAPRAERSPRWDREDRGARPERSDRPERRDDRASSGPRRDDR 82

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRR---------SPSFPSKRSLRRTS 351
           + +    +G  S   S  G +  + R           P+F  +R  R  S
Sbjct: 83  SDSRGGYQGRDSRSDSRGGYQGRDTRPDSRGDSRGERPAFGQRRDDRSDS 132



 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 12/113 (10%), Positives = 27/113 (23%), Gaps = 7/113 (6%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                   + +         +    R +          R  ++ S+     +  +  +  
Sbjct: 54  EDRGARPERSDRPERRDDRASSGPRRDDRSDSRGGYQGRDSRSDSRGGYQGRDTRPDSRG 113

Query: 306 HRRNLASNVWMAKGIHSSFL-------SDSGQREENHRRSPSFPSKRSLRRTS 351
             R         +   S          S    R ++    P+F  +R  R  S
Sbjct: 114 DSRGERPAFGQRRDDRSDSRGGYQGRDSRPDSRGDSRGERPAFGQRRDDRSDS 166


>gi|302541221|ref|ZP_07293563.1| argininosuccinate lyase [Streptomyces hygroscopicus ATCC 53653]
 gi|302458839|gb|EFL21932.1| argininosuccinate lyase [Streptomyces himastatinicus ATCC 53653]
          Length = 421

 Score = 39.4 bits (90), Expect = 0.86,   Method: Composition-based stats.
 Identities = 14/113 (12%), Positives = 27/113 (23%), Gaps = 2/113 (1%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            + L  +L  H  EE   +  A         R              R++       G   
Sbjct: 284 PRRLLHRLLDHAAEEEPGHRRAGPRQVRPPHRQPHRAAGHAEGPAARVQPRPPGGQGAGL 343

Query: 298 Q--KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           +  +    P  R +        +               +  R  + P  R++ 
Sbjct: 344 RLLRPAGGPAPRLHRHDGDADRQPGAHGGAGPRRVLAGHRHRRVARPGGRAVP 396


>gi|291454478|ref|ZP_06593868.1| translation initiation factor IF-2 [Streptomyces albus J1074]
 gi|291357427|gb|EFE84329.1| translation initiation factor IF-2 [Streptomyces albus J1074]
          Length = 802

 Score = 39.4 bits (90), Expect = 0.86,   Method: Composition-based stats.
 Identities = 6/69 (8%), Positives = 12/69 (17%)

Query: 267 LVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLS 326
             +      +  P            + G +   +           S   M +        
Sbjct: 8   RPQAPRPGGAPRPGGSQGGPGAPRPQGGPAGAPRPQGGQGGAGRPSPGNMPRPQAPRPGG 67

Query: 327 DSGQREENH 335
             G R    
Sbjct: 68  AGGNRPNPG 76



 Score = 37.1 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 6/57 (10%), Positives = 14/57 (24%)

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           + +   P        +                 R +  +     PS  ++ R  A +
Sbjct: 8   RPQAPRPGGAPRPGGSQGGPGAPRPQGGPAGAPRPQGGQGGAGRPSPGNMPRPQAPR 64


>gi|291414655|ref|XP_002723579.1| PREDICTED: TRIO and F-actin binding protein [Oryctolagus cuniculus]
          Length = 2060

 Score = 39.4 bits (90), Expect = 0.87,   Method: Composition-based stats.
 Identities = 13/128 (10%), Positives = 35/128 (27%), Gaps = 6/128 (4%)

Query: 230  AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
             G TR   ++     L            +    +  +      +      +   R ++  
Sbjct: 984  PGETRHNLEREEYTVLADLPPPRRLAQREPGPQAQGSNGGRTHSPGRAEVERLFRQERRK 1043

Query: 290  SQKNGL---SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
            S+  G      + +   P   ++       +            ++ +   RS + P   S
Sbjct: 1044 SEAPGALQARDEGRSQRPSQGQSQLLRRQSSPAPSRQAAKLPVKQADPAGRSRTQP---S 1100

Query: 347  LRRTSAKK 354
              R+  ++
Sbjct: 1101 RPRSPERR 1108


>gi|149463902|ref|XP_001506662.1| PREDICTED: similar to splicing coactivator subunit SRm300, partial
           [Ornithorhynchus anatinus]
          Length = 2677

 Score = 39.4 bits (90), Expect = 0.87,   Method: Composition-based stats.
 Identities = 18/116 (15%), Positives = 30/116 (25%), Gaps = 7/116 (6%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK--LAT 303
                  ++        S       R    S  P    R +  + Q       ++   + 
Sbjct: 348 AKRDKSRSRSPSRRVGRSRSPATTRRGRSRSRTPARKGRSRSRTPQWRRSRSPQRWGRSR 407

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS-----KRSLRRTSAKK 354
              RR  + +        S      G+     RR  S         RS  RT A++
Sbjct: 408 SPQRRGRSRSPQRPGWSRSRNAQRRGRSRSTARRGRSRSKTPATRGRSRSRTPARR 463



 Score = 35.9 bits (81), Expect = 9.7,   Method: Composition-based stats.
 Identities = 6/84 (7%), Positives = 18/84 (21%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
                 S     + R +   +        ++    ++        +    RR  + +   
Sbjct: 381 PARKGRSRSRTPQWRRSRSPQRWGRSRSPQRRGRSRSPQRPGWSRSRNAQRRGRSRSTAR 440

Query: 317 AKGIHSSFLSDSGQREENHRRSPS 340
                S   +  G+          
Sbjct: 441 RGRSRSKTPATRGRSRSRTPARRG 464


>gi|302894465|ref|XP_003046113.1| hypothetical protein NECHADRAFT_76622 [Nectria haematococca mpVI
           77-13-4]
 gi|256727040|gb|EEU40400.1| hypothetical protein NECHADRAFT_76622 [Nectria haematococca mpVI
           77-13-4]
          Length = 796

 Score = 39.4 bits (90), Expect = 0.88,   Method: Composition-based stats.
 Identities = 22/145 (15%), Positives = 35/145 (24%), Gaps = 10/145 (6%)

Query: 212 VNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDR 271
             RL R   G      L    TR V  +  +    P    +   +   P  +     R  
Sbjct: 617 CIRLDRSRQGVVPRTCLS---TRPVKPRPAQAGPRPGPPVKPVGSPRGPGPNHPQGQRPM 673

Query: 272 PNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR 331
            +  +  P             NG ++ +    P    +      M+ G  S         
Sbjct: 674 TSQGNFGPGRPASPAGRPMTPNG-NRPQSPMGPPMGPHGRPAGPMSPGPRSQSPGPRQGP 732

Query: 332 ------EENHRRSPSFPSKRSLRRT 350
                      +SP     RS    
Sbjct: 733 PNRAMSPSPRSQSPGPAGGRSQSPN 757



 Score = 38.2 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 14/100 (14%), Positives = 24/100 (24%), Gaps = 2/100 (2%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR--RNLA 311
           +    A    +    R +  +   +          S      S   +   P      +  
Sbjct: 683 RPASPAGRPMTPNGNRPQSPMGPPMGPHGRPAGPMSPGPRSQSPGPRQGPPNRAMSPSPR 742

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
           S      G  S   +   +R      SP  PS+      S
Sbjct: 743 SQSPGPAGGRSQSPNGMNRRNSPPGPSPMNPSQAPRPGPS 782


>gi|194693980|gb|ACF81074.1| unknown [Zea mays]
          Length = 229

 Score = 39.4 bits (90), Expect = 0.88,   Method: Composition-based stats.
 Identities = 20/165 (12%), Positives = 44/165 (26%), Gaps = 5/165 (3%)

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            V + EG    +  V   F   +  + R + G  +LG L        +   + +      
Sbjct: 70  KVDILEGM--HVTSVGCGFGLSLIVVDRANVGD-RLGQLEI--YDGDTGAEVEKVEVQVT 124

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
            + +           +T          +  DD      + +     SK ++   P +R  
Sbjct: 125 KKASASTNSRANKRKKTKDVSESESEEDDDDDEDESGDDENGGVEESKGRRGRKPANRGR 184

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                        S       ++       +  +    +R   +K
Sbjct: 185 GRGGKKATPEAKPSGRGRGRPKKTESSAQKAGGTSGRGKRGRPRK 229


>gi|299065800|emb|CBJ36977.1| ribosome-associated heat shock protein 15 [Ralstonia solanacearum
          CMR15]
          Length = 131

 Score = 39.4 bits (90), Expect = 0.89,   Method: Composition-based stats.
 Identities = 11/59 (18%), Positives = 24/59 (40%), Gaps = 2/59 (3%)

Query: 5  NIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +  +     R+ K + A     +R +    + + RV++N   +   A +V   D + V
Sbjct: 2  KVSTDAADRVRIDKWLWAARFFKTRSQATDAVERGRVQINDQPVR-PAKDVKIGDRVRV 59


>gi|224057274|ref|XP_002186777.1| PREDICTED: similar to collagen, type XI, alpha 1 isoform 1
           [Taeniopygia guttata]
          Length = 1805

 Score = 39.4 bits (90), Expect = 0.89,   Method: Composition-based stats.
 Identities = 9/111 (8%), Positives = 16/111 (14%), Gaps = 1/111 (0%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           L+   G       +           +     P       +             G    K 
Sbjct: 793 LKGDRGEIGQPGPRGEDGPEGPKGRSGPSGDPGAAGPAGEKGKLGVPGLPGYPGRQGPKG 852

Query: 301 LATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                                        G       R P  P+ +   + 
Sbjct: 853 STGFPGFPGANGEKGARGLHGKPGPRGQRGPTGPRGSRGPRGPTGKPGPKG 903


>gi|38181902|gb|AAH61522.1| LOC23117 protein [Homo sapiens]
          Length = 420

 Score = 39.4 bits (90), Expect = 0.89,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 27/108 (25%), Gaps = 3/108 (2%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P   +EA+               + P              +   ++     +     P  
Sbjct: 299 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 358

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS--FPSKRSLRRTSA 352
           RR              +   +     E  RR      PS++  RR +A
Sbjct: 359 RRVGDVEPSRKPKRRRAADVEPSS-PEPKRRRVGDVEPSRKPKRRRAA 405



 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 10/120 (8%), Positives = 32/120 (26%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
            ++ +    +       +    ++ P       V D              ++ +S +   
Sbjct: 299 PLATQEAEAEKPRKPKRQRAAEMEPPPEPKRRRVGDVEPSRKPKRRRAADVEPSSPEPKR 358

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                   +   +R  A++V  +            +     +R  +   + SL     ++
Sbjct: 359 RRVGDVEPSRKPKRRRAADVEPSSPEPKRRRVGDVEPSRKPKRRRAADVEPSLPEPKRRR 418


>gi|323519553|gb|ADX93934.1| superfamily II DNA/RNA helicase [Acinetobacter baumannii
           TCDC-AB0715]
          Length = 606

 Score = 39.4 bits (90), Expect = 0.89,   Method: Composition-based stats.
 Identities = 10/108 (9%), Positives = 24/108 (22%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           RE         +  +       +           +          ++  +++   + +  
Sbjct: 420 REGGRDDRPRRSFDDKPRGERPAFGGEDRPRREFNSDRPRREGGFEDRPRRSFGGEDRPR 479

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                 R      +  +   S    D  +RE N  R           R
Sbjct: 480 REFNSDRPRREGGFEDRPKRSFGGEDRPRREFNSDRPRREGGFNDKPR 527



 Score = 37.1 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 10/81 (12%), Positives = 19/81 (23%)

Query: 269 RDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDS 328
           + R     + P      K    +     + +        R      +  +   S    D 
Sbjct: 418 KRREGGRDDRPRRSFDDKPRGERPAFGGEDRPRREFNSDRPRREGGFEDRPRRSFGGEDR 477

Query: 329 GQREENHRRSPSFPSKRSLRR 349
            +RE N  R           +
Sbjct: 478 PRREFNSDRPRREGGFEDRPK 498



 Score = 36.7 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 9/102 (8%), Positives = 22/102 (21%), Gaps = 5/102 (4%)

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
                        R        +      ++  ++   S + +       R   S     
Sbjct: 417 FKRREGGRDDRPRRSFDDKPRGERPAFGGEDRPRREFNSDRPRREGGFEDRPRRSFGGED 476

Query: 318 KGIHS-SFLSDSGQREENHRRSPSFPSKRSLRR----TSAKK 354
           +     +      +     R   SF  +   RR       ++
Sbjct: 477 RPRREFNSDRPRREGGFEDRPKRSFGGEDRPRREFNSDRPRR 518


>gi|195573522|ref|XP_002104741.1| GD18284 [Drosophila simulans]
 gi|194200668|gb|EDX14244.1| GD18284 [Drosophila simulans]
          Length = 647

 Score = 39.4 bits (90), Expect = 0.90,   Method: Composition-based stats.
 Identities = 8/113 (7%), Positives = 31/113 (27%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R++         +   D    + +    D+              ++  + ++   +++  
Sbjct: 201 RKRRDSDQSPPRKARNDKHSPARKRRDSDQSPPRKRTGKASPTRRRRDADQSPPRRRRSN 260

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +     R                     +R +   +SP    ++   ++  +K
Sbjct: 261 SDQSPPRRRRDKDSTPPRRRRDSDQSPPRRRKADDQSPVRRERKDSDQSPPRK 313



 Score = 37.5 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 13/112 (11%), Positives = 29/112 (25%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+            +        +   +  P           R +++S Q     ++   
Sbjct: 281 RDSDQSPPRRRKADDQSPVRRERKDSDQSPPRKRRGSDQSPVRRRRDSDQSPPRRRRDDK 340

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            TP  RR  +      +           +R+ +   +         RR S +
Sbjct: 341 QTPPRRRRNSDQSPPRRPKDEDQSPPRRKRDFDQSPNKKRDKSPRRRRDSDQ 392



 Score = 36.3 bits (82), Expect = 6.6,   Method: Composition-based stats.
 Identities = 12/113 (10%), Positives = 26/113 (23%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            ++   ++         Q          ++  R +     + P    R  K+S  +    
Sbjct: 168 KREECPQRGRRRAASSDQSPPRRGRDGDQSPPRRKRRDSDQSPPRKARNDKHSPARKRRD 227

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
             +        +   +               S   +   RR     S    RR
Sbjct: 228 SDQSPPRKRTGKASPTRRRRDADQSPPRRRRSNSDQSPPRRRRDKDSTPPRRR 280



 Score = 36.3 bits (82), Expect = 6.8,   Method: Composition-based stats.
 Identities = 11/105 (10%), Positives = 28/105 (26%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R + G       +          +               D +  +K + + +   +++  
Sbjct: 190 RGRDGDQSPPRRKRRDSDQSPPRKARNDKHSPARKRRDSDQSPPRKRTGKASPTRRRRDA 249

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
                RR  +++            S   +R  +  +SP    K  
Sbjct: 250 DQSPPRRRRSNSDQSPPRRRRDKDSTPPRRRRDSDQSPPRRRKAD 294



 Score = 36.3 bits (82), Expect = 8.1,   Method: Composition-based stats.
 Identities = 14/120 (11%), Positives = 33/120 (27%), Gaps = 4/120 (3%)

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ----KNG 294
              +E  G         +  +P      +   +    S       R +K + +    + G
Sbjct: 117 DEEQEMWGRKATVVKVKDEFSPSRRKSPVRIKQEKRSSSRDLSPARSRKPAKREECPQRG 176

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             +         RR    +    +           ++  N + SP+   + S +    K+
Sbjct: 177 RRRAASSDQSPPRRGRDGDQSPPRRKRRDSDQSPPRKARNDKHSPARKRRDSDQSPPRKR 236



 Score = 35.9 bits (81), Expect = 9.6,   Method: Composition-based stats.
 Identities = 10/113 (8%), Positives = 30/113 (26%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R +         + + D             P        D +  +K         ++++ 
Sbjct: 268 RRRDKDSTPPRRRRDSDQSPPRRRKADDQSPVRRERKDSDQSPPRKRRGSDQSPVRRRRD 327

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +     R    +         +      +R ++  +SP    +   +  + K+
Sbjct: 328 SDQSPPRRRRDDKQTPPRRRRNSDQSPPRRPKDEDQSPPRRKRDFDQSPNKKR 380


>gi|238062560|ref|ZP_04607269.1| monooxygenase, FAD-binding [Micromonospora sp. ATCC 39149]
 gi|237884371|gb|EEP73199.1| monooxygenase, FAD-binding [Micromonospora sp. ATCC 39149]
          Length = 712

 Score = 39.4 bits (90), Expect = 0.91,   Method: Composition-based stats.
 Identities = 12/111 (10%), Positives = 28/111 (25%), Gaps = 1/111 (0%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +   P               +            +++     R          L++  + A
Sbjct: 113 DAAEPRPGRGDGDRGRGGAGAQPGRGHRPARCAAQLRGGPARPDPADDPPGALAEPDRAA 172

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               RR+  + V       ++       R +  RR    P+    R  + +
Sbjct: 173 RQPRRRSGPARVPEV-AARAARRPPQPGRPDLPRRRAGGPAVNGGRGAAHR 222


>gi|149583840|ref|XP_001517926.1| PREDICTED: hypothetical protein [Ornithorhynchus anatinus]
          Length = 644

 Score = 39.4 bits (90), Expect = 0.91,   Method: Composition-based stats.
 Identities = 11/87 (12%), Positives = 26/87 (29%)

Query: 267 LVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLS 326
           + +      +          +  +++    K+ +   P  +      V    G   S   
Sbjct: 225 VKKTEERPRTAEELREREFLERRNKRGDRGKEGRKKGPSQKEAPPPKVGRGPGERPSRSL 284

Query: 327 DSGQREENHRRSPSFPSKRSLRRTSAK 353
                    +  P+ PS++  R  +AK
Sbjct: 285 PHPAAGPERKSRPAAPSEKHTRPATAK 311



 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 11/109 (10%), Positives = 21/109 (19%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +   G            +     +     +P+     P      K +S + +G  +    
Sbjct: 345 QAPPGLTKTSAGGAQRPSGEQGLKRPTSSQPSHSRPGPSPHNGAKLSSGKSSGPGRTGNS 404

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
             P              G           R       P+  S       
Sbjct: 405 PGPGRPAGGLGPGRPNAGPGRPAGGLGPGRPNAGPGKPASGSGPGRPAG 453



 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 9/99 (9%), Positives = 16/99 (16%), Gaps = 1/99 (1%)

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW 315
               P  +  +    RP              + +              P           
Sbjct: 394 KSSGPGRTGNSPGPGRPAGGLGPGRPNAGPGRPAGGLGPGRPNAGPGKPASGSGPGRPAG 453

Query: 316 MAKGIHSSFLSDSG-QREENHRRSPSFPSKRSLRRTSAK 353
                  S             R +   P   S+  T  +
Sbjct: 454 GLGPGRPSSGPSRPAGGPGPERTNAGRPPPGSVPPTRPR 492


>gi|224052940|ref|XP_002187874.1| PREDICTED: similar to EIF6 protein [Taeniopygia guttata]
          Length = 1480

 Score = 39.4 bits (90), Expect = 0.92,   Method: Composition-based stats.
 Identities = 8/121 (6%), Positives = 23/121 (19%)

Query: 232  STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
              R    +              + +       ++   R   +     P       +   +
Sbjct: 1023 DWRRGDPRDDERPFRRGDDLPRRGDDLPRRGPADEKERPPESAEDRPPRREGDEDRPPRR 1082

Query: 292  KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
            +    +  +      R              ++      +R  +  R P            
Sbjct: 1083 EGDEDRPPRRGLDEDRPPRRGLDDDRGSWRAADDDRGPRRVLDDDRPPRRALDDDRPPRR 1142

Query: 352  A 352
            A
Sbjct: 1143 A 1143



 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 18/112 (16%), Gaps = 1/112 (0%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            +E        E+         S         +     P D  R  +              
Sbjct: 992  KESRWGDRESESSWRRGGEPESEWRRAPVERDWRRGDPRDDERPFRRGDDLPRRGDDLPR 1051

Query: 302  ATPVHRRNLASNVWM-AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
              P   +                      +RE +  R P             
Sbjct: 1052 RGPADEKERPPESAEDRPPRREGDEDRPPRREGDEDRPPRRGLDEDRPPRRG 1103


>gi|195389440|ref|XP_002053385.1| GJ23850 [Drosophila virilis]
 gi|194151471|gb|EDW66905.1| GJ23850 [Drosophila virilis]
          Length = 639

 Score = 39.4 bits (90), Expect = 0.92,   Method: Composition-based stats.
 Identities = 15/113 (13%), Positives = 28/113 (24%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           REQ   H L+    +   P    +                  R +          +    
Sbjct: 155 REQSPAHNLKRRTSDQSPPRRRLDANQSPHRQRRDSDHSPVRRRRGADQSPPRRGRDVDQ 214

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           + P  RR+   +    +          G+  +         + +S  R  A K
Sbjct: 215 SPPRRRRDADQSPPRRRKDADQSPPRRGRDADQSPPRRKRDADQSPPRRRANK 267



 Score = 37.1 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 13/123 (10%), Positives = 31/123 (25%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             R+     +R + G       +               D+         D +  ++    
Sbjct: 186 QRRDSDHSPVRRRRGADQSPPRRGRDVDQSPPRRRRDADQSPPRRRKDADQSPPRRGRDA 245

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                ++K+ A     R  A+                 +R      SP    + + + + 
Sbjct: 246 DQSPPRRKRDADQSPPRRRANKDQSPTRRRRDSDQSPPRRGRVVDESPPRRGRDADQSSD 305

Query: 352 AKK 354
            K+
Sbjct: 306 GKR 308



 Score = 35.9 bits (81), Expect = 8.9,   Method: Composition-based stats.
 Identities = 15/114 (13%), Positives = 28/114 (24%), Gaps = 4/114 (3%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R +L  +     Q               D+         D +  ++         +++K 
Sbjct: 174 RRRLDANQSPHRQRRDSDHSPVRRRRGADQSPPRRGRDVDQSPPRRRRDADQSPPRRRKD 233

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS----LRRTS 351
           A     R                     +R  N  +SP+   + S     RR  
Sbjct: 234 ADQSPPRRGRDADQSPPRRKRDADQSPPRRRANKDQSPTRRRRDSDQSPPRRGR 287


>gi|302694413|ref|XP_003036885.1| hypothetical protein SCHCODRAFT_103232 [Schizophyllum commune H4-8]
 gi|300110582|gb|EFJ01983.1| hypothetical protein SCHCODRAFT_103232 [Schizophyllum commune H4-8]
          Length = 2063

 Score = 39.4 bits (90), Expect = 0.93,   Method: Composition-based stats.
 Identities = 10/106 (9%), Positives = 25/106 (23%), Gaps = 2/106 (1%)

Query: 248  HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                 +     AP   S+       + + + P      +  S++++   + +       R
Sbjct: 1908 RTESTSGPPPSAPAAPSQPAGGTLLSRLDKAPSLGGGRRDESARRDDGPRGEAARGDGPR 1967

Query: 308  RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            R+         G                 R  +F  +         
Sbjct: 1968 RDEGGR--RDDGPRRDEGPRGEGARREEDRKRTFAERDDGPDNGPA 2011



 Score = 37.5 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 3/86 (3%), Positives = 10/86 (11%)

Query: 268  VRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSD 327
                                      G   ++                  +G        
Sbjct: 1937 KAPSLGGGRRDESARRDDGPRGEAARGDGPRRDEGGRRDDGPRRDEGPRGEGARREEDRK 1996

Query: 328  SGQREENHRRSPSFPSKRSLRRTSAK 353
                E +        +    +    +
Sbjct: 1997 RTFAERDDGPDNGPAANGDGQNKRQR 2022



 Score = 36.7 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 10/99 (10%), Positives = 31/99 (31%)

Query: 255  VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
             +            RDR    S       + ++++++++  +  ++      R++   + 
Sbjct: 1715 KDEHRKDDKDRDRDRDRKERESSRAAGARQDERSTTRQDDRASARQDDRASARQDARPDA 1774

Query: 315  WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              A     +     G+R        +   KR      ++
Sbjct: 1775 PAAGPGRPAAEEGLGKRRRGDDDVSAPDPKRPRSAERSQ 1813


>gi|261364545|ref|ZP_05977428.1| heat shock protein 15 [Neisseria mucosa ATCC 25996]
 gi|288567111|gb|EFC88671.1| heat shock protein 15 [Neisseria mucosa ATCC 25996]
          Length = 133

 Score = 39.4 bits (90), Expect = 0.93,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 2/52 (3%)

Query: 10 NFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
          + T  R+ K + A     +R   ++ I   RV+VNG  ++  + N+ + D I
Sbjct: 6  DNTAMRLDKWLWAARFFKTRALAQKHIELGRVQVNGAKVKN-SKNISAGDTI 56


>gi|194440691|ref|NP_001101456.2| serine/arginine repetitive matrix protein 1 [Rattus norvegicus]
 gi|187469661|gb|AAI66715.1| Srrm1 protein [Rattus norvegicus]
          Length = 908

 Score = 39.4 bits (90), Expect = 0.93,   Method: Composition-based stats.
 Identities = 12/101 (11%), Positives = 28/101 (27%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
           +         +S      R    S  P           Q++    +++  +   +    S
Sbjct: 609 SPSPPPKRRTASPPPPPKRRASPSPPPKRRVSHSPPPKQRSPPVTKRRSPSLSSKHRKGS 668

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +   +     S   +         R+P   S   +RR ++ 
Sbjct: 669 SPGRSTREARSPQPNKRHSPSPRPRAPQTSSPPPVRRGASA 709


>gi|167758068|ref|ZP_02430195.1| hypothetical protein CLOSCI_00406 [Clostridium scindens ATCC 35704]
 gi|167663965|gb|EDS08095.1| hypothetical protein CLOSCI_00406 [Clostridium scindens ATCC 35704]
          Length = 900

 Score = 39.4 bits (90), Expect = 0.93,   Method: Composition-based stats.
 Identities = 9/111 (8%), Positives = 25/111 (22%), Gaps = 1/111 (0%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
               +                      +    R       +        ++ +  +   +
Sbjct: 107 RPMQVNNGRPAKQQARPAAPAQETTQQARPQERPADKSFEQAKRPAAASQERAQTQERQA 166

Query: 297 KQKKLATP-VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           ++         RR   S+        +S     G R + +R+     S+  
Sbjct: 167 ERPASDRSQAPRRQERSDDRRQDTRGNSGNRPQGGRPQGNRQDRPQGSRPQ 217


>gi|158854005|ref|NP_038858.2| serine/threonine-protein kinase PRP4 homolog [Mus musculus]
 gi|26350865|dbj|BAC39069.1| unnamed protein product [Mus musculus]
 gi|148708949|gb|EDL40895.1| PRP4 pre-mRNA processing factor 4 homolog B (yeast), isoform CRA_b
           [Mus musculus]
 gi|187954769|gb|AAI41274.1| PRP4 pre-mRNA processing factor 4 homolog B (yeast) [Mus musculus]
 gi|187954931|gb|AAI41273.1| PRP4 pre-mRNA processing factor 4 homolog B (yeast) [Mus musculus]
          Length = 1007

 Score = 39.4 bits (90), Expect = 0.93,   Method: Composition-based stats.
 Identities = 17/107 (15%), Positives = 30/107 (28%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                EE     D              +  S+ P D     K+   ++   K K+     
Sbjct: 262 EKMKSEEKGKIKDRKKSPIVNERSRDRSKKSKSPVDLRDKSKDRRSRSKERKSKRSEIDK 321

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            ++ + S    A     +            RRS S   +   RR+ +
Sbjct: 322 EKKPIKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKLRDKSRRSRS 368


>gi|23831386|sp|Q61136|PRP4B_MOUSE RecName: Full=Serine/threonine-protein kinase PRP4 homolog;
           AltName: Full=PRP4 pre-mRNA-processing factor 4 homolog;
           AltName: Full=Pre-mRNA protein kinase
 gi|20330556|gb|AAM19102.1|AF283466_1 PRP4 kinase [Mus musculus]
          Length = 1007

 Score = 39.4 bits (90), Expect = 0.93,   Method: Composition-based stats.
 Identities = 17/107 (15%), Positives = 30/107 (28%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                EE     D              +  S+ P D     K+   ++   K K+     
Sbjct: 262 EKMKSEEKGKIKDRKKSPIVNERSRDRSKKSKSPVDLRDKSKDRRSRSKERKSKRSEIDK 321

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            ++ + S    A     +            RRS S   +   RR+ +
Sbjct: 322 EKKPIKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKLRDKSRRSRS 368


>gi|184159623|ref|YP_001847962.1| superfamily II DNA/RNA helicase [Acinetobacter baumannii ACICU]
 gi|332876108|ref|ZP_08443892.1| DEAD/DEAH box helicase [Acinetobacter baumannii 6014059]
 gi|183211217|gb|ACC58615.1| Superfamily II DNA and RNA helicase [Acinetobacter baumannii ACICU]
 gi|332735726|gb|EGJ66769.1| DEAD/DEAH box helicase [Acinetobacter baumannii 6014059]
          Length = 615

 Score = 39.4 bits (90), Expect = 0.94,   Method: Composition-based stats.
 Identities = 10/108 (9%), Positives = 24/108 (22%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           RE         +  +       +           +          ++  +++   + +  
Sbjct: 429 REGGRDDRPRRSFDDKPRGERPAFGGEDRPRREFNSDRPRREGGFEDRPRRSFGGEDRPR 488

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                 R      +  +   S    D  +RE N  R           R
Sbjct: 489 REFNSDRPRREGGFEDRPKRSFGGEDRPRREFNSDRPRREGGFNDKPR 536



 Score = 36.7 bits (83), Expect = 5.0,   Method: Composition-based stats.
 Identities = 10/81 (12%), Positives = 19/81 (23%)

Query: 269 RDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDS 328
           + R     + P      K    +     + +        R      +  +   S    D 
Sbjct: 427 KRREGGRDDRPRRSFDDKPRGERPAFGGEDRPRREFNSDRPRREGGFEDRPRRSFGGEDR 486

Query: 329 GQREENHRRSPSFPSKRSLRR 349
            +RE N  R           +
Sbjct: 487 PRREFNSDRPRREGGFEDRPK 507



 Score = 36.3 bits (82), Expect = 6.6,   Method: Composition-based stats.
 Identities = 9/102 (8%), Positives = 22/102 (21%), Gaps = 5/102 (4%)

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
                        R        +      ++  ++   S + +       R   S     
Sbjct: 426 FKRREGGRDDRPRRSFDDKPRGERPAFGGEDRPRREFNSDRPRREGGFEDRPRRSFGGED 485

Query: 318 KGIHS-SFLSDSGQREENHRRSPSFPSKRSLRR----TSAKK 354
           +     +      +     R   SF  +   RR       ++
Sbjct: 486 RPRREFNSDRPRREGGFEDRPKRSFGGEDRPRREFNSDRPRR 527


>gi|115522157|ref|YP_779068.1| helicase domain-containing protein [Rhodopseudomonas palustris
            BisA53]
 gi|115516104|gb|ABJ04088.1| helicase domain protein [Rhodopseudomonas palustris BisA53]
          Length = 1116

 Score = 39.4 bits (90), Expect = 0.94,   Method: Composition-based stats.
 Identities = 12/103 (11%), Positives = 26/103 (25%)

Query: 252  EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
                  D          R      +  P   +      ++     + ++   P  RR   
Sbjct: 961  RPGGRSDDRPKHDRNRPRHGHRPSAAAPAAASGEAGEPAKGERPDRGRRDRKPDFRRPRP 1020

Query: 312  SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            ++  +  G  ++       RE    +      K    + S  K
Sbjct: 1021 ADAPVEAGATAAPSEGRPPRERERFQGKGRSDKGPRDKGSKDK 1063



 Score = 37.9 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 17/117 (14%), Positives = 27/117 (23%), Gaps = 7/117 (5%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            R + G      A               R         PD       ++  + G +     
Sbjct: 976  RPRHGHRPSAAAPAAASGEAGEPAKGERPDRGRRDRKPDFRRPRPADAPVEAGATAAPSE 1035

Query: 302  ATPVHRRNLASNVWMA-KGIHSSFLSDSGQREENH------RRSPSFPSKRSLRRTS 351
              P   R        + KG       D G +           R+P   S ++  R  
Sbjct: 1036 GRPPRERERFQGKGRSDKGPRDKGSKDKGFKGGREGREGGGDRAPRVFSSQAAPRER 1092



 Score = 36.7 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 10/106 (9%), Positives = 21/106 (19%), Gaps = 1/106 (0%)

Query: 250  LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                       ++       DRP      P    R    +         +        R 
Sbjct: 948  DTAVAEPEMVEVWRPGGRSDDRPKHDRNRPRHGHRPSAAAPAAASGEAGEPAKGERPDRG 1007

Query: 310  LASNVWMAKGIHSSFLS-DSGQREENHRRSPSFPSKRSLRRTSAKK 354
                    +    +    ++G         P    +R   +  + K
Sbjct: 1008 RRDRKPDFRRPRPADAPVEAGATAAPSEGRPPRERERFQGKGRSDK 1053


>gi|301782355|ref|XP_002926593.1| PREDICTED: serine/arginine repetitive matrix protein 2-like
           [Ailuropoda melanoleuca]
          Length = 2728

 Score = 39.4 bits (90), Expect = 0.95,   Method: Composition-based stats.
 Identities = 9/108 (8%), Positives = 20/108 (18%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                            S   +     +              + S    + + +   T  
Sbjct: 430 RHASSSPESPKPAPAPGSRREISSSPASKSRSHGRAKRDKSHSHSPSRRVGRSRSPTTTK 489

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R+ +          S        R          P +R   R+  +
Sbjct: 490 RGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQR 537



 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 12/98 (12%), Positives = 22/98 (22%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P      +++      S       R    S  P       ++ +       + +  T  
Sbjct: 442 APAPGSRREISSSPASKSRSHGRAKRDKSHSHSPSRRVGRSRSPTTTKRGRSRSRTPTKR 501

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
                 S  W        +      +     RSP  P 
Sbjct: 502 GHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPG 539


>gi|169632326|ref|YP_001706062.1| putative ATP-dependent RNA helicase [Acinetobacter baumannii SDF]
 gi|169151118|emb|CAO99784.1| putative ATP-dependent RNA helicase [Acinetobacter baumannii]
          Length = 619

 Score = 39.4 bits (90), Expect = 0.95,   Method: Composition-based stats.
 Identities = 10/108 (9%), Positives = 24/108 (22%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           RE         +  +       +           +          ++  +++   + +  
Sbjct: 433 REGGRDDRPRRSFDDKPRGERPAFGGEDRPRREFNSDRPRREGGFEDRPKRSFGGEDRPR 492

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                 R      +  +   S    D  +RE N  R           R
Sbjct: 493 REFNSDRPRREGGFEDRPKRSFGGEDRPRREFNSDRPRREGGFNDKPR 540



 Score = 36.7 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 10/92 (10%), Positives = 21/92 (22%), Gaps = 6/92 (6%)

Query: 269 RDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDS 328
           + R     + P      K    +     + +        R      +  +   S    D 
Sbjct: 431 KRREGGRDDRPRRSFDDKPRGERPAFGGEDRPRREFNSDRPRREGGFEDRPKRSFGGEDR 490

Query: 329 GQREENHRRSPSFPSKRSLRR------TSAKK 354
            +RE N  R           +         ++
Sbjct: 491 PRREFNSDRPRREGGFEDRPKRSFGGEDRPRR 522


>gi|169794570|ref|YP_001712363.1| putative ATP-dependent RNA helicase [Acinetobacter baumannii AYE]
 gi|260557002|ref|ZP_05829219.1| DEAD/DEAH box helicase [Acinetobacter baumannii ATCC 19606]
 gi|169147497|emb|CAM85358.1| putative ATP-dependent RNA helicase [Acinetobacter baumannii AYE]
 gi|260409608|gb|EEX02909.1| DEAD/DEAH box helicase [Acinetobacter baumannii ATCC 19606]
          Length = 619

 Score = 39.4 bits (90), Expect = 0.95,   Method: Composition-based stats.
 Identities = 10/108 (9%), Positives = 24/108 (22%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           RE         +  +       +           +          ++  +++   + +  
Sbjct: 433 REGGRDDRPRRSFDDKPRGERPAFGGEDRPRREFNSDRPRREGGFEDRPKRSFGGEDRPR 492

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                 R      +  +   S    D  +RE N  R           R
Sbjct: 493 REFNSDRPRREGGFEDRPKRSFGGEDRPRREFNSDRPRREGGFNDKPR 540



 Score = 37.1 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 10/81 (12%), Positives = 19/81 (23%)

Query: 269 RDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDS 328
           + R     + P      K    +     + +        R      +  +   S    D 
Sbjct: 431 KRREGGRDDRPRRSFDDKPRGERPAFGGEDRPRREFNSDRPRREGGFEDRPKRSFGGEDR 490

Query: 329 GQREENHRRSPSFPSKRSLRR 349
            +RE N  R           +
Sbjct: 491 PRREFNSDRPRREGGFEDRPK 511


>gi|27674605|ref|XP_228426.1| PREDICTED: mortality factor 4 like 2-like [Rattus norvegicus]
 gi|109511486|ref|XP_001058275.1| PREDICTED: mortality factor 4 like 2-like [Rattus norvegicus]
          Length = 2298

 Score = 39.4 bits (90), Expect = 0.95,   Method: Composition-based stats.
 Identities = 13/107 (12%), Positives = 25/107 (23%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              +      D  + +     R              +        +    +     P   
Sbjct: 507 RPNKRVPAEEDRSLKNISASRRPSGGKDRPARSRSNKSGPTKEGWSVEGSRSTSGRPSEG 566

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           ++ +                S     +  R PS    RS RR+S+ K
Sbjct: 567 KDRSGGRGRPNKSGPEKEGPSVNDSRSTSRGPSAGKDRSARRSSSNK 613



 Score = 38.2 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 17/109 (15%), Positives = 28/109 (25%), Gaps = 3/109 (2%)

Query: 249  LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL---ATPV 305
               +     + P           P+   + P       K+S +K G S +        P 
Sbjct: 994  YPNKNSPKKEGPSVKGSRSTSRGPSAGKDRPGGRGYPNKSSPKKEGPSVKGSRSTSRGPS 1053

Query: 306  HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              ++                  S +   +  R PS    R  RR    K
Sbjct: 1054 AGKDRPGRRGYPNKSSPKKEGPSVKGSRSTSRGPSAGKDRPGRRGYPNK 1102



 Score = 37.9 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 17/109 (15%), Positives = 30/109 (27%), Gaps = 3/109 (2%)

Query: 249  LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL---ATPV 305
               ++    + P           P+   + P   +   K+S +K G S +        P 
Sbjct: 1309 YPNKSSPKKEGPSVKGSRSTSRGPSAGKDHPGRRSYPNKSSPKKEGPSVKGSRSTSRGPS 1368

Query: 306  HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              ++                  S +   +  R PS    R  RR    K
Sbjct: 1369 AGKDRPGRRGYPNKSSPKKEGPSVKGSRSTSRGPSAGKDRPGRRGYPNK 1417



 Score = 37.5 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 18/109 (16%), Positives = 29/109 (26%), Gaps = 3/109 (2%)

Query: 249  LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL---ATPV 305
               ++    + P           P+   + P       KNS +K G S +        P 
Sbjct: 959  YPNKSSPKKEGPSVKGSRSTSRGPSTGKDRPGRRGYPNKNSPKKEGPSVKGSRSTSRGPS 1018

Query: 306  HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              ++                  S +   +  R PS    R  RR    K
Sbjct: 1019 AGKDRPGGRGYPNKSSPKKEGPSVKGSRSTSRGPSAGKDRPGRRGYPNK 1067



 Score = 36.7 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 18/112 (16%), Positives = 28/112 (25%), Gaps = 3/112 (2%)

Query: 246  GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL---A 302
            G   L E       P           P+   + P    R  K+S  +   S +       
Sbjct: 1236 GRSHLNECGPEKKCPSVKDSRSTSRGPSAGKDRPGRRGRSNKSSPTEESRSVEGSRSTSR 1295

Query: 303  TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             P   ++                  S +   +  R PS       RR+   K
Sbjct: 1296 GPSAGKDRPGRRGYPNKSSPKKEGPSVKGSRSTSRGPSAGKDHPGRRSYPNK 1347


>gi|261494821|ref|ZP_05991299.1| Hsp15 family heat shock protein [Mannheimia haemolytica serotype
          A2 str. OVINE]
 gi|261309532|gb|EEY10757.1| Hsp15 family heat shock protein [Mannheimia haemolytica serotype
          A2 str. OVINE]
          Length = 138

 Score = 39.4 bits (90), Expect = 0.95,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 1  MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLE 48
          MK+K+  ++N    R+ K + A     +R   + MI   +V  NG   +
Sbjct: 1  MKNKHEKEQNDAEVRLDKWLWAARFYKTRSIAKAMIEGGKVHYNGQRAK 49


>gi|32401852|gb|AAP80914.1| small ribosomal protein 4 [Microstrobos fitzgeraldii]
          Length = 204

 Score = 39.4 bits (90), Expect = 0.95,   Method: Composition-based stats.
 Identities = 11/115 (9%), Positives = 28/115 (24%), Gaps = 9/115 (7%)

Query: 14  QRVSKVIARAGI-----ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
            R+  ++ R G+            ++I  + + VNG +++  +      D I +      
Sbjct: 64  MRLDNILFRLGMTFTIPG----ARQLINHRHILVNGRIVDIPSYRCNPKDVITIKDQQRS 119

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           +    +     K              S            +       +       
Sbjct: 120 RNIINKNIDLSKKHQAKKHQERLRPISKNILFFKFKKREMKHEVPFHLILYSSQY 174


>gi|281342144|gb|EFB17728.1| hypothetical protein PANDA_016259 [Ailuropoda melanoleuca]
          Length = 2726

 Score = 39.4 bits (90), Expect = 0.96,   Method: Composition-based stats.
 Identities = 9/108 (8%), Positives = 20/108 (18%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                            S   +     +              + S    + + +   T  
Sbjct: 430 RHASSSPESPKPAPAPGSRREISSSPASKSRSHGRAKRDKSHSHSPSRRVGRSRSPTTTK 489

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R+ +          S        R          P +R   R+  +
Sbjct: 490 RGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQR 537



 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 12/98 (12%), Positives = 22/98 (22%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P      +++      S       R    S  P       ++ +       + +  T  
Sbjct: 442 APAPGSRREISSSPASKSRSHGRAKRDKSHSHSPSRRVGRSRSPTTTKRGRSRSRTPTKR 501

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
                 S  W        +      +     RSP  P 
Sbjct: 502 GHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPG 539


>gi|256997200|dbj|BAI22793.1| mKIAA0536 protein [Mus musculus]
          Length = 1011

 Score = 39.4 bits (90), Expect = 0.96,   Method: Composition-based stats.
 Identities = 17/107 (15%), Positives = 30/107 (28%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                EE     D              +  S+ P D     K+   ++   K K+     
Sbjct: 266 EKMKSEEKGKIKDRKKSPIVNERSRDRSKKSKSPVDLRDKSKDRRSRSKERKSKRSEIDK 325

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            ++ + S    A     +            RRS S   +   RR+ +
Sbjct: 326 EKKPIKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKLRDKSRRSRS 372


>gi|218532734|ref|YP_002423550.1| helicase [Methylobacterium chloromethanicum CM4]
 gi|218525037|gb|ACK85622.1| helicase domain protein [Methylobacterium chloromethanicum CM4]
          Length = 1136

 Score = 39.4 bits (90), Expect = 0.96,   Method: Composition-based stats.
 Identities = 11/109 (10%), Positives = 23/109 (21%), Gaps = 1/109 (0%)

Query: 247  PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
             HL    +     P          +        D     ++    +     + +   P  
Sbjct: 1004 WHLHRPQRHTGPRPGRGQGRPEGRQDGRQEGRQDGRQDGRRGDGPRRPREDRPEGGRPAR 1063

Query: 307  RRNLASNVWMAKGIHSSFLSDSGQREENHRRS-PSFPSKRSLRRTSAKK 354
                  +    +G         G R    RR     P+         ++
Sbjct: 1064 ADGRGESRREGQGEGGPRREHQGGRNRPDRRDENRRPNPEQRPPRRERQ 1112



 Score = 37.9 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 15/103 (14%), Positives = 22/103 (21%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            R   G    E  Q              R          D     +   +   G S+++  
Sbjct: 1016 RPGRGQGRPEGRQDGRQEGRQDGRQDGRRGDGPRRPREDRPEGGRPARADGRGESRREGQ 1075

Query: 302  ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
                 RR              +   +  QR     R P   S 
Sbjct: 1076 GEGGPRREHQGGRNRPDRRDENRRPNPEQRPPRRERQPDPDSP 1118


>gi|254362274|ref|ZP_04978387.1| Hsp15 family heat shock protein [Mannheimia haemolytica PHL213]
 gi|153093851|gb|EDN74783.1| Hsp15 family heat shock protein [Mannheimia haemolytica PHL213]
          Length = 138

 Score = 39.4 bits (90), Expect = 0.97,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 1  MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLE 48
          MK+K+  ++N    R+ K + A     +R   + MI   +V  NG   +
Sbjct: 1  MKNKHEKEQNDAEVRLDKWLWAARFYKTRSIAKAMIEGGKVHYNGQRAK 49


>gi|240006673|gb|ACS37556.1| matrix extracellular phosphoglycoprotein [Echinops telfairi]
          Length = 540

 Score = 39.0 bits (89), Expect = 0.98,   Method: Composition-based stats.
 Identities = 19/116 (16%), Positives = 36/116 (31%), Gaps = 2/116 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           REV++     ++  +     +        +  T   ++            R  +  S K+
Sbjct: 408 REVTQSTKDNEIPKNGKSGTRKGAGHSHRNQVTSTEEQKPPGKRKSPGPARGNEIGSYKS 467

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
             S++ ++A     R L +  W         +S      E   R P     R  RR
Sbjct: 468 PASEENRVAHNDGGRRLYAPPWRNNAARGKGVSRGNGSREP--RRPHSNRSRDRRR 521


>gi|238059632|ref|ZP_04604341.1| serine/threonine protein kinase [Micromonospora sp. ATCC 39149]
 gi|237881443|gb|EEP70271.1| serine/threonine protein kinase [Micromonospora sp. ATCC 39149]
          Length = 1212

 Score = 39.0 bits (89), Expect = 0.98,   Method: Composition-based stats.
 Identities = 12/65 (18%), Positives = 17/65 (26%)

Query: 289 SSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           +   +        A P  RR   +      G       DS       RR P     R+  
Sbjct: 268 AHPAHAQPAGPGPAQPGVRRTGPAPAHARAGRSGRARPDSPPATAGGRRRPGVGPGRAAL 327

Query: 349 RTSAK 353
           R +  
Sbjct: 328 RRAGA 332



 Score = 38.2 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 9/110 (8%), Positives = 21/110 (19%), Gaps = 1/110 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           GP      +         +    R RP+          R      +            P 
Sbjct: 279 GPAQPGVRRTGPAPAHARAGRSGRARPDSPPATAGGRRRPGVGPGRAALRRAGAGPGRPH 338

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF-PSKRSLRRTSAKK 354
                     +  G   +  +     +       +      + R    ++
Sbjct: 339 QPGARPGARTLPPGGGPADHAGGQGAQRGVDAGGTGVSDTPTRREGPGRQ 388



 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 12/111 (10%), Positives = 23/111 (20%), Gaps = 12/111 (10%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R  LG  +L             +              P         +  + G S + + 
Sbjct: 246 RPVLGRVVLAARAQRRRRRGVPAHPAHAQPAGPGPAQPGVRRTGPAPAHARAGRSGRARP 305

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            +P           +  G                RR+ + P +        
Sbjct: 306 DSPPATAGGRRRPGVGPG------------RAALRRAGAGPGRPHQPGARP 344


>gi|126643119|ref|YP_001086103.1| putative ATP-dependent RNA helicase [Acinetobacter baumannii ATCC
           17978]
 gi|213158859|ref|YP_002320857.1| DEAD/DEAH box helicase [Acinetobacter baumannii AB0057]
 gi|126389003|gb|ABO13501.1| putative ATP-dependent RNA helicase [Acinetobacter baumannii ATCC
           17978]
 gi|213058019|gb|ACJ42921.1| DEAD/DEAH box helicase [Acinetobacter baumannii AB0057]
          Length = 615

 Score = 39.0 bits (89), Expect = 0.98,   Method: Composition-based stats.
 Identities = 10/108 (9%), Positives = 24/108 (22%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           RE         +  +       +           +          ++  +++   + +  
Sbjct: 429 REGGRDDRPRRSFDDKPRGERPAFGGEDRPRREFNSDRPRREGGFEDRPKRSFGGEDRPR 488

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                 R      +  +   S    D  +RE N  R           R
Sbjct: 489 REFNSDRPRREGGFEDRPKRSFGGEDRPRREFNSDRPRREGGFNDKPR 536



 Score = 37.1 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 10/81 (12%), Positives = 19/81 (23%)

Query: 269 RDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDS 328
           + R     + P      K    +     + +        R      +  +   S    D 
Sbjct: 427 KRREGGRDDRPRRSFDDKPRGERPAFGGEDRPRREFNSDRPRREGGFEDRPKRSFGGEDR 486

Query: 329 GQREENHRRSPSFPSKRSLRR 349
            +RE N  R           +
Sbjct: 487 PRREFNSDRPRREGGFEDRPK 507


>gi|318056613|ref|ZP_07975336.1| gcn5-related n-acetyltransferase [Streptomyces sp. SA3_actG]
          Length = 337

 Score = 39.0 bits (89), Expect = 0.99,   Method: Composition-based stats.
 Identities = 15/113 (13%), Positives = 32/113 (28%), Gaps = 1/113 (0%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK-NGLSKQKKL 301
           +   P   + +      P  S+       P   S       R  + +         ++  
Sbjct: 216 QNPAPATPDASPTPTPPPTPSTPPASNSSPAPTSPGSGAARRSPRGAGAACTARRSRRAP 275

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           A+P H  +  S    A     S  + +  R +  R +         R + + +
Sbjct: 276 ASPPHAASGTSRSTRAPTARPSCAASASWRSQPRRPTSGRRPPGDFRDSVSSR 328


>gi|298712516|emb|CBJ26784.1| Unknown (protein for IMAGE:7297131) [Ectocarpus siliculosus]
          Length = 560

 Score = 39.0 bits (89), Expect = 1.00,   Method: Composition-based stats.
 Identities = 13/103 (12%), Positives = 25/103 (24%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           +      A    S           S +     R   ++++  G S   +      R    
Sbjct: 242 QDGQEGGARKGGSRRGDSQEAERDSMMAKRAERFGASANEPRGSSNNDRKGRGQFRAGGP 301

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            N    K        D  +R        +     S  R  +++
Sbjct: 302 GNKNNDKRAGGRDGRDGERRPSEMNVKDALAGGLSAPRGGSRR 344


>gi|296271061|ref|YP_003653693.1| family 51 glycosyl transferase [Thermobispora bispora DSM 43833]
 gi|296093848|gb|ADG89800.1| glycosyl transferase family 51 [Thermobispora bispora DSM 43833]
          Length = 719

 Score = 39.0 bits (89), Expect = 1.00,   Method: Composition-based stats.
 Identities = 17/122 (13%), Positives = 25/122 (20%), Gaps = 8/122 (6%)

Query: 220 YGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVP 279
           YG    GTL A   R      L    G  + E          + S      R    +E P
Sbjct: 570 YGELYGGTLPAQIWRHFMSAALE---GEPVKEFPPPVTWNGHWGSYATTGPREPEATEEP 626

Query: 280 DDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA-----SNVWMAKGIHSSFLSDSGQREEN 334
            D         +       +         + A                        R ++
Sbjct: 627 TDAAPTPGAEDRARDAGADRSEPRGETGGDGAGDEGDRPGGEQPAERPGDGRPGEGRPDD 686

Query: 335 HR 336
             
Sbjct: 687 GS 688


>gi|115488040|ref|NP_001066507.1| Os12g0256300 [Oryza sativa Japonica Group]
 gi|77554176|gb|ABA96972.1| Pre-mRNA splicing factor cwc22, putative, expressed [Oryza sativa
           Japonica Group]
 gi|113649014|dbj|BAF29526.1| Os12g0256300 [Oryza sativa Japonica Group]
 gi|156622336|emb|CAO82941.1| putative pre-mRNA-splicing factor cwc-22 [Oryza sativa Japonica
           Group]
 gi|215707245|dbj|BAG93705.1| unnamed protein product [Oryza sativa Japonica Group]
          Length = 787

 Score = 39.0 bits (89), Expect = 1.00,   Method: Composition-based stats.
 Identities = 16/119 (13%), Positives = 25/119 (21%), Gaps = 10/119 (8%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R     H     +        S       +           +   +++ +  G S+    
Sbjct: 13  RRHRHRHDDSPPRRRRRHDDDSPRHRDDRKRRASPSPSPSPSPSDRDADRHRGKSRASPP 72

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREE----------NHRRSPSFPSKRSLRRT 350
             P       SN   A         D   R            + RR PS  S       
Sbjct: 73  RRPRDSDPAESNGGGAPKPGGDNGGDRSPRRARVPDAEEEGGDRRRRPSRVSDDDKEGG 131


>gi|301613955|ref|XP_002936474.1| PREDICTED: serine/threonine-protein kinase PRP4 homolog [Xenopus
           (Silurana) tropicalis]
          Length = 995

 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 16/114 (14%), Positives = 28/114 (24%), Gaps = 1/114 (0%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           LR Q     ++      +                 S      ++   +   K+   + K 
Sbjct: 239 LRRQSPEKNIKTKSPQEERMKSRDRKKSPVASESKSRERTKKSKSPVSRRSKSKERRSKS 298

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                 RR+ +          S   S   +     RR    P  RSL      +
Sbjct: 299 KEKKP-RRSDSDRDRKPLKSPSKDASSGKENRSPGRRPARSPKARSLSPKQRDR 351


>gi|224057280|ref|XP_002186803.1| PREDICTED: similar to collagen, type XI, alpha 1 isoform 2
           [Taeniopygia guttata]
          Length = 1766

 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 9/111 (8%), Positives = 16/111 (14%), Gaps = 1/111 (0%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           L+   G       +           +     P       +             G    K 
Sbjct: 754 LKGDRGEIGQPGPRGEDGPEGPKGRSGPSGDPGAAGPAGEKGKLGVPGLPGYPGRQGPKG 813

Query: 301 LATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                                        G       R P  P+ +   + 
Sbjct: 814 STGFPGFPGANGEKGARGLHGKPGPRGQRGPTGPRGSRGPRGPTGKPGPKG 864


>gi|156934713|ref|YP_001438629.1| ATP-dependent RNA helicase RhlE [Cronobacter sakazakii ATCC
           BAA-894]
 gi|156532967|gb|ABU77793.1| hypothetical protein ESA_02548 [Cronobacter sakazakii ATCC BAA-894]
          Length = 474

 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 11/116 (9%), Positives = 32/116 (27%), Gaps = 5/116 (4%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +++L+ ++    +   + +   P        + R     +      + +       G   
Sbjct: 361 ERLLKREIPRMAIPGYEPDPSIPAEPIVNGRQSRGGRGGQGGGGRGQGQPRRQNGEGNRS 420

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             + + P   R    +     G  +    +  +R       P+    R+ R     
Sbjct: 421 SGERSRPAGERGRRQD-----GEGNRPSGERSRRPAGEGNRPAGNKPRTRRAPRKA 471


>gi|3236351|gb|AAC32042.1| PRP4 protein kinase homolog [Mus musculus]
          Length = 823

 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 17/107 (15%), Positives = 30/107 (28%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                EE     D              +  S+ P D     K+   ++   K K+     
Sbjct: 78  EKMKSEEKGKIKDRKKSPIVNERSRDRSKKSKSPVDLRDKSKDRRSRSKERKSKRSEIDK 137

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            ++ + S    A     +            RRS S   +   RR+ +
Sbjct: 138 EKKPIKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKLRDKSRRSRS 184


>gi|268574914|ref|XP_002642436.1| Hypothetical protein CBG06840 [Caenorhabditis briggsae]
 gi|187033791|emb|CAP27079.1| hypothetical protein CBG_06840 [Caenorhabditis briggsae AF16]
          Length = 465

 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 13/118 (11%), Positives = 24/118 (20%), Gaps = 2/118 (1%)

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM--KKNSSQKNGLS 296
           K ++E+        A+                R +     P          NS  +    
Sbjct: 90  KEVKEEPLSPGASPARKPRQRHDSDESPRRPRRRHDSDNSPVRQRTRHDSDNSPPRPSRR 149

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +          R              +            RR     S  S  R  +++
Sbjct: 150 RHNSDEDNSPPRRPRQRHDSDDSPPRANRKRRDSDNSPPRRRQRQDSDNSPPRGRSRR 207



 Score = 36.3 bits (82), Expect = 7.1,   Method: Composition-based stats.
 Identities = 12/112 (10%), Positives = 26/112 (23%), Gaps = 1/112 (0%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            ++ P    + +        + +   R   +     P        +  ++          
Sbjct: 84  AEVEPLKEVKEEPLSPGASPARKPRQRHDSDESPRRPRRRHDSDNSPVRQRTRHDSDNSP 143

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               RR   S+   +         DS        R     S  S  R   ++
Sbjct: 144 PRPSRRRHNSDEDNSPPRRPRQRHDSDDSPPRANRKR-RDSDNSPPRRRQRQ 194


>gi|297197616|ref|ZP_06915013.1| magnesium or manganese-dependent protein phosphatase [Streptomyces
           sviceus ATCC 29083]
 gi|297146799|gb|EFH28350.1| magnesium or manganese-dependent protein phosphatase [Streptomyces
           sviceus ATCC 29083]
          Length = 684

 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 11/117 (9%), Positives = 21/117 (17%), Gaps = 10/117 (8%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R      L    +              R   +       D  R ++         + +  
Sbjct: 479 RPGGRLPLPARGRHRRGRRRLVRRHPARRGQDRAGRGRCDGQRHQRRRDHGPAAHRDQHP 538

Query: 302 ATPVHRRNLASNVWMAKGIHSSF----------LSDSGQREENHRRSPSFPSKRSLR 348
             P      A                        S      +  RR+P+  +     
Sbjct: 539 GLPRPGPGQAPRTPRPDHRGPGPLHRHLRVRRARSGPRAVPDRQRRAPASGAAAPRP 595



 Score = 36.7 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 10/105 (9%), Positives = 17/105 (16%), Gaps = 1/105 (0%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P    + +              RD                             +   P+H
Sbjct: 504 PARRGQDRAGRGRCDGQRHQRRRDHGPAAHRDQHPGLPRPGPGQAPRTPRPDHRGPGPLH 563

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
           R                    +          PS P+  +  R  
Sbjct: 564 RHLRVRRARSGPRAVPDRQRRAPASGAAA-PRPSPPNCSNCPRGR 607


>gi|118086455|ref|XP_001232309.1| PREDICTED: serine/threonine-protein kinase PRP4K [Gallus gallus]
          Length = 1005

 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 21/130 (16%), Positives = 40/130 (30%), Gaps = 7/130 (5%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNII---SEVPDDFTRMKKN 288
            TR+    +L+ +      +      D      ++  RDR            D  R  K+
Sbjct: 234 QTRKSRSPMLKRRSQEKNRKSKSPPDDRNKADDKSKSRDRRKSPVVNESKSRDRGRKSKS 293

Query: 289 SSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR----EENHRRSPSFPSK 344
            ++    SK ++  +   +   +      K I S     S  +         RSP   S 
Sbjct: 294 PAELRSKSKDRRSRSKDRKSRRSETDKDKKPIKSPSKDASSGKENRSPRRPGRSPKGRSL 353

Query: 345 RSLRRTSAKK 354
               R  +++
Sbjct: 354 SPKPREKSRR 363



 Score = 39.0 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 13/102 (12%), Positives = 29/102 (28%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
              + D    S         +          + +++ + K+    +         +   S
Sbjct: 281 ESKSRDRGRKSKSPAELRSKSKDRRSRSKDRKSRRSETDKDKKPIKSPSKDASSGKENRS 340

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                +      LS   + +    RSP F  +RS +  S  +
Sbjct: 341 PRRPGRSPKGRSLSPKPREKSRRSRSPLFNDRRSKQSKSPSR 382



 Score = 37.1 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 12/109 (11%), Positives = 31/109 (28%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +       +    +       +E+  RDR        +  ++ K   S+      ++   
Sbjct: 259 DDRNKADDKSKSRDRRKSPVVNESKSRDRGRKSKSPAELRSKSKDRRSRSKDRKSRRSET 318

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
               +   + +   + G  +      G+  +    SP    K    R+ 
Sbjct: 319 DKDKKPIKSPSKDASSGKENRSPRRPGRSPKGRSLSPKPREKSRRSRSP 367


>gi|86742010|ref|YP_482410.1| hypothetical protein Francci3_3324 [Frankia sp. CcI3]
 gi|86568872|gb|ABD12681.1| hypothetical protein Francci3_3324 [Frankia sp. CcI3]
          Length = 511

 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 14/93 (15%), Positives = 18/93 (19%), Gaps = 4/93 (4%)

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW 315
              +                   P    R +       G         PV  R       
Sbjct: 339 EPRSLPDPGRRRRGQSQPGPHRQPRSQPRPRPAGDTSVGGEGDPGGREPVGDRRGGPGT- 397

Query: 316 MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
            A G     +S    R      SP    +R  R
Sbjct: 398 AASGGRPGQVS---LRRRPSSASPGGSVERERR 427



 Score = 36.7 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 12/80 (15%), Positives = 21/80 (26%), Gaps = 5/80 (6%)

Query: 276 SEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM---AKGIHSSFLSDSGQRE 332
                D  R ++  SQ     +    + P  R    ++V       G         G   
Sbjct: 340 PRSLPDPGRRRRGQSQPGPHRQ--PRSQPRPRPAGDTSVGGEGDPGGREPVGDRRGGPGT 397

Query: 333 ENHRRSPSFPSKRSLRRTSA 352
                 P   S R    +++
Sbjct: 398 AASGGRPGQVSLRRRPSSAS 417


>gi|54025577|ref|YP_119819.1| putative RNA-binding Sun protein [Nocardia farcinica IFM 10152]
 gi|54017085|dbj|BAD58455.1| putative RNA-binding Sun protein [Nocardia farcinica IFM 10152]
          Length = 627

 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 10/84 (11%), Positives = 19/84 (22%), Gaps = 1/84 (1%)

Query: 264 SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSS 323
                R R     ++   + R      +     ++     P   R+ A      +G    
Sbjct: 1   MSAAERPRKADDRDIDGGWARRAAREQEARRSGRKPGDGEPPESRHRAGGD-RGRGAPGR 59

Query: 324 FLSDSGQREENHRRSPSFPSKRSL 347
                G+  E           R  
Sbjct: 60  SEGRGGRAGEPRAPRADRAGGRGA 83



 Score = 37.5 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 11/90 (12%), Positives = 23/90 (25%), Gaps = 1/90 (1%)

Query: 265 ETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSF 324
           +              +  +R    S    G S  +         +   +         S 
Sbjct: 96  DERSPRGERGGIPRRERESRGDARSDAARGSSTARSGRATPGPGSGNQHGGRRGPDGGSG 155

Query: 325 LSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                +  +  RRS   P  R+  + +A +
Sbjct: 156 AGGRSRAADADRRSAGRPG-RTGPKNAAGR 184


>gi|307107076|gb|EFN55320.1| hypothetical protein CHLNCDRAFT_23425 [Chlorella variabilis]
          Length = 70

 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 10/48 (20%), Positives = 21/48 (43%), Gaps = 1/48 (2%)

Query: 200 EIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           +++ + E    +V  L R+  G +++   L  G   E+    +R  L 
Sbjct: 16  QVRNLVEHAGLEVRTLRRVRIGGYRMPRDLAFGQFVELRPHEVRRVLN 63


>gi|227504826|ref|ZP_03934875.1| possible translation initiation factor IF-2 [Corynebacterium
           striatum ATCC 6940]
 gi|227198676|gb|EEI78724.1| possible translation initiation factor IF-2 [Corynebacterium
           striatum ATCC 6940]
          Length = 300

 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 10/106 (9%), Positives = 24/106 (22%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                     +A    + +  +  P   +  P      K  ++ +   + +     P   
Sbjct: 111 PKEAAPTAKAEASQKPAASAAKPGPKPGASKPAPKAPQKSQANAEAKSAPKPGGERPTPG 170

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            ++   +    G      +          R    P      R   K
Sbjct: 171 NSMPRPMPKPGGSRRVANNPFSTGGAGGDRPGPRPGGSKGPRPGGK 216


>gi|224057276|ref|XP_002186827.1| PREDICTED: similar to collagen, type XI, alpha 1 isoform 3
           [Taeniopygia guttata]
          Length = 1817

 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 9/111 (8%), Positives = 16/111 (14%), Gaps = 1/111 (0%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           L+   G       +           +     P       +             G    K 
Sbjct: 805 LKGDRGEIGQPGPRGEDGPEGPKGRSGPSGDPGAAGPAGEKGKLGVPGLPGYPGRQGPKG 864

Query: 301 LATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                                        G       R P  P+ +   + 
Sbjct: 865 STGFPGFPGANGEKGARGLHGKPGPRGQRGPTGPRGSRGPRGPTGKPGPKG 915


>gi|63168791|gb|AAY34563.1| circumsporozoite protein [Plasmodium yoelii]
          Length = 427

 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 9/95 (9%), Positives = 16/95 (16%), Gaps = 1/95 (1%)

Query: 259 APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP-VHRRNLASNVWMA 317
           A    ++ +V D                +      G    +    P              
Sbjct: 123 AQNKLNQPVVADENVDQGPGAPQGPGAPQGPGAPQGPGAPQGPGAPQGPGAPQGPGAPQG 182

Query: 318 KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            G      +  G        +P  P          
Sbjct: 183 PGAPQGPGAPQGPGAPQGPGAPQGPGAPQGPGAPQ 217


>gi|83953300|ref|ZP_00962022.1| dead-box protein, ATP-independent RNA helicase [Sulfitobacter sp.
           NAS-14.1]
 gi|83842268|gb|EAP81436.1| dead-box protein, ATP-independent RNA helicase [Sulfitobacter sp.
           NAS-14.1]
          Length = 731

 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 20/198 (10%), Positives = 44/198 (22%), Gaps = 34/198 (17%)

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKN-----REIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                     G + W ++ +  G+N     R I  +                G      +
Sbjct: 434 PADERPRGDFGPSVWFSISI--GRNDDAEPRTILPMIC------------RMGDLTKDDV 479

Query: 229 LAGSTREVSKK---ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
             G+ R         +        +     ++     +  T +   P++           
Sbjct: 480 --GAIRVQPSHTFVEILATSADKFINALGPDMKVEDGAVVTKLDKAPDLSRGPKPGGRGP 537

Query: 286 KKNSSQKNGLSKQKKLATPVHRRNL-ASNVWMAKGIHSSFL---------SDSGQREENH 335
           K N       +  +    P   R     +   A     +              G R +  
Sbjct: 538 KPNRGGPRSDNGPRPDRGPRPDRAPYDPDAPRAPRKPRAASTEEPSVTYDKPRGPRPDKG 597

Query: 336 RRSPSFPSKRSLRRTSAK 353
              P     +  +  + K
Sbjct: 598 FDKPRGDKPKFDKPKAPK 615



 Score = 35.9 bits (81), Expect = 8.8,   Method: Composition-based stats.
 Identities = 9/115 (7%), Positives = 22/115 (19%), Gaps = 3/115 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E+      +      D                 +   +   +  K            K  
Sbjct: 580 EEPSVTYDKPRGPRPDKGFDKPRGDKPKFDKPKAPKGERPPKSHKTERSPMKPGATPKPK 639

Query: 303 TPVHRRNLASNVWMAKGI---HSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +     +        K          +D G         P+    ++     +K+
Sbjct: 640 SAGKPDSFDKPGGKPKAKAVWKKEKPADRGADRPRGDGKPADKPFKARAADPSKR 694


>gi|333024012|ref|ZP_08452076.1| hypothetical protein STTU_1516 [Streptomyces sp. Tu6071]
 gi|332743864|gb|EGJ74305.1| hypothetical protein STTU_1516 [Streptomyces sp. Tu6071]
          Length = 848

 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 16/128 (12%), Positives = 28/128 (21%), Gaps = 9/128 (7%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN-SSQKNG 294
           V    +R+QL       A     A   ++    R      +   +   R  ++      G
Sbjct: 488 VEPDEIRQQLRGRAGRPAARRSAAGPAAACDSARATGTESATAGEREARASQSVEGTPEG 547

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG--------IHSSFLSDSGQREENHRRSPSFPSKRS 346
               +            +     KG           +       R        S      
Sbjct: 548 GRGGETTERRAVGGRRRTGSGARKGSAARTDSAARPATRRRDAGRPGGVAPGGSGGKAMK 607

Query: 347 LRRTSAKK 354
            R   AK+
Sbjct: 608 RREGGAKE 615


>gi|298293649|ref|YP_003695588.1| helicase [Starkeya novella DSM 506]
 gi|296930160|gb|ADH90969.1| helicase domain protein [Starkeya novella DSM 506]
          Length = 1161

 Score = 39.0 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 10/105 (9%), Positives = 23/105 (21%), Gaps = 4/105 (3%)

Query: 254  QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
            +       +      +   +  ++   D  +  +            +   P  RR+   N
Sbjct: 997  RPGRPPGQHRPAHQRKGAHSGGNQGNRDGAQQNRGPRTDAAPGAPAEGGRPDFRRDRPEN 1056

Query: 314  VWMAKGIHSSFLSDS----GQREENHRRSPSFPSKRSLRRTSAKK 354
                               G +    RR       R  R+    +
Sbjct: 1057 GGRRPPRDDQRRERRPEGEGAQARGDRRDDQRQGNRPPRQDRGDR 1101



 Score = 37.1 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 15/116 (12%), Positives = 27/116 (23%), Gaps = 5/116 (4%)

Query: 244  QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
              G     +                  RP+   + P++  R      Q+     + + A 
Sbjct: 1019 NQGNRDGAQQNRGPRTDAAPGAPAEGGRPDFRRDRPENGGRRPPRDDQRRERRPEGEGAQ 1078

Query: 304  PVHRRNLASNVWMAKGIHSSF-LSDSGQREENHRRSPSFP----SKRSLRRTSAKK 354
                R                   D G R +N +            R   R  A++
Sbjct: 1079 ARGDRRDDQRQGNRPPRQDRGDRPDRGNRPDNRQDRGDNRHDRFGSRPDNRNDARR 1134


>gi|302541108|ref|ZP_07293450.1| ribosomal protein S4 [Streptomyces hygroscopicus ATCC 53653]
 gi|302458726|gb|EFL21819.1| ribosomal protein S4 [Streptomyces himastatinicus ATCC 53653]
          Length = 203

 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 3/50 (6%)

Query: 15  RVSKVIARAGIASRR--EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R+GIA R   +  +M+    ++VNG  +++ +  V   D + V
Sbjct: 92  RLDALVLRSGIA-RTIYQARQMVVHGHIEVNGRKVDKPSFRVRPDDVVMV 140


>gi|149520722|ref|XP_001515308.1| PREDICTED: similar to RBM15B protein [Ornithorhynchus anatinus]
          Length = 595

 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 15/121 (12%), Positives = 28/121 (23%), Gaps = 3/121 (2%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           + + L    G      ++             VR R            R +   S     +
Sbjct: 267 TPERLNAPEGHGRSTRSRSGDRWGGAGDRGPVRAREERRKRRSPSGDRGRAPRSPHEERA 326

Query: 297 KQKKLATPVHRRNLASNV-WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL--RRTSAK 353
             K    P  R          A G   +     G   ++   +     + S    R   +
Sbjct: 327 GPKAGGPPSERSPERPRREHRAPGRAGADEEQGGSLPDDRHAAERRAGRESPEPPRGKKR 386

Query: 354 K 354
           +
Sbjct: 387 E 387



 Score = 37.1 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 16/114 (14%), Positives = 28/114 (24%), Gaps = 2/114 (1%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK- 299
           +R++  PHLL   +         +            E     TR +          +   
Sbjct: 239 VRDRTPPHLLYSDRERGFGEGDRAVPARTPERLNAPEGHGRSTRSRSGDRWGGAGDRGPV 298

Query: 300 -KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                   RR+ + +   A        +          RSP  P +       A
Sbjct: 299 RAREERRKRRSPSGDRGRAPRSPHEERAGPKAGGPPSERSPERPRREHRAPGRA 352


>gi|332559951|ref|ZP_08414273.1| DEAD/DEAH box helicase domain-containing protein [Rhodobacter
           sphaeroides WS8N]
 gi|332277663|gb|EGJ22978.1| DEAD/DEAH box helicase domain-containing protein [Rhodobacter
           sphaeroides WS8N]
          Length = 777

 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 9/125 (7%), Positives = 22/125 (17%), Gaps = 2/125 (1%)

Query: 230 AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
                E      R    P    E          +                       +  
Sbjct: 564 PSRFVEEDPGEARGGWTPDDRPERAPRPRREDGAPFAKRDMNDAPRPRRESAAEDEGRKP 623

Query: 290 SQKNGLSKQKKL--ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            + +     +          ++       + G  S   +    + ++    P  P     
Sbjct: 624 RRTSDERPARPAAAGRSAGFKSHGGTASRSAGYKSHGDAAPRGKRDDEGPRPYKPRGEDA 683

Query: 348 RRTSA 352
            R + 
Sbjct: 684 PRAAG 688



 Score = 36.7 bits (83), Expect = 5.8,   Method: Composition-based stats.
 Identities = 16/112 (14%), Positives = 27/112 (24%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
              G    E  +        +                 D  R +   S  +  +K     
Sbjct: 663 APRGKRDDEGPRPYKPRGEDAPRAAGFKSHGKPVRAEGDVPRARPARSADDRPAKAGGFK 722

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               R         A+    S       +++  R+  +  S  S R T  KK
Sbjct: 723 AREDRPAKPRAEGAAERPARSGFKKDFGKKDAPRKPRAEASDTSRRFTPPKK 774


>gi|329895164|ref|ZP_08270848.1| Ribosome-associated heat shock protein implicated in the
          recycling of the 50S subunit [gamma proteobacterium
          IMCC3088]
 gi|328922478|gb|EGG29819.1| Ribosome-associated heat shock protein implicated in the
          recycling of the 50S subunit [gamma proteobacterium
          IMCC3088]
          Length = 130

 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 2/49 (4%)

Query: 15 RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+ K + A     +R   ++ I   +V VNG  ++ +   V+  D I V
Sbjct: 5  RLDKWLWAARFYKTRSLCKQAIEGGKVHVNGQRVKVSKD-VIVGDEIRV 52


>gi|289705452|ref|ZP_06501846.1| putative ATP-dependent DNA helicase PcrA [Micrococcus luteus SK58]
 gi|289557837|gb|EFD51134.1| putative ATP-dependent DNA helicase PcrA [Micrococcus luteus SK58]
          Length = 963

 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 18/121 (14%), Positives = 31/121 (25%), Gaps = 4/121 (3%)

Query: 237 SKKILRE--QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
            +K L E  + G    +    +           V   P   ++          +     G
Sbjct: 666 DEKELAEERRRGLRGPDARPPSPVPDARRGTLAVGPAPVQPAQPVPRGDPGGAHRLGAGG 725

Query: 295 LSKQKKLATPVHRR--NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                +L  P  RR   L   V       +            H R  +     +LRR + 
Sbjct: 726 HHALGRLVEPDRRRHLALRGAVRGRAAGLAVPGRRRRAAPAPHPRGRAGGPHGALRRGAG 785

Query: 353 K 353
           +
Sbjct: 786 E 786


>gi|332824170|ref|XP_518490.3| PREDICTED: zinc finger protein 318 [Pan troglodytes]
          Length = 2321

 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 9/62 (14%), Positives = 18/62 (29%)

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
               ++    + + A+P   R    +    +    S     G+R      +    S R  
Sbjct: 54  ARRPRSPSGHRGRRASPSPPRGRRVSPSPPRARRGSPSPPRGRRLFPPGPAGFRGSSRGE 113

Query: 348 RR 349
            R
Sbjct: 114 SR 115


>gi|302561381|ref|ZP_07313723.1| LOW QUALITY PROTEIN: RNA polymerase ECF-subfamily sigma factor
           [Streptomyces griseoflavus Tu4000]
 gi|302478999|gb|EFL42092.1| LOW QUALITY PROTEIN: RNA polymerase ECF-subfamily sigma factor
           [Streptomyces griseoflavus Tu4000]
          Length = 311

 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 9/123 (7%), Positives = 25/123 (20%)

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           L+      + +  +   +G          L     +                  + R   
Sbjct: 147 LVLRHWLGLKESEIAAAMGISRGSVKTQGLARDRRAHPGDGGAAMTHRFCYSVAWHRPGP 206

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
           +  +    +   +           + +          L    +R    R   +    R+ 
Sbjct: 207 HGPRAGPAASAGRRPHRTGTPGRPAGLGRRGAARPGRLPHGPRRVAAPRTQAAAGPHRAR 266

Query: 348 RRT 350
           R  
Sbjct: 267 RGG 269


>gi|294631843|ref|ZP_06710403.1| conserved hypothetical protein [Streptomyces sp. e14]
 gi|292835176|gb|EFF93525.1| conserved hypothetical protein [Streptomyces sp. e14]
          Length = 546

 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 11/110 (10%), Positives = 23/110 (20%), Gaps = 4/110 (3%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK----KNSSQKNGLSKQKKLA 302
           PH    A  + D+ + ++                   R +     + +  +   +  +  
Sbjct: 437 PHDAPLAGDDADSGVRNTTAHRGRGVTRAVPDATPARRRRPRPDGSGTAAHPAPEGTRPT 496

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            P   R                            R P    +R      A
Sbjct: 497 APGGGRTRPGPSPAPSRTRPHAAGKGAAPRRRDARQPGAGLRRHTPEGRA 546


>gi|332845493|ref|XP_003315056.1| PREDICTED: putative NPIP-like protein LOC613037-like [Pan
           troglodytes]
          Length = 308

 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 14/113 (12%), Positives = 25/113 (22%), Gaps = 5/113 (4%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           L+         EA+         +  +    P        D     +   ++        
Sbjct: 179 LKTPPLATQEAEAEKPPKPKRPRAADVETSSPEPKRRRVGDVEPSSRKPKRQRAGDVDPS 238

Query: 301 LATPVHRRNLASNVWMAKGIHSS-----FLSDSGQREENHRRSPSFPSKRSLR 348
              P  RR    +   +K            S   +R       PS    +  R
Sbjct: 239 SRKPKRRRADDVDPSSSKPKRRRADDVEPSSRKPKRRRADDVDPSSSKPKRRR 291


>gi|324998761|ref|ZP_08119873.1| sodium/hydrogen exchanger [Pseudonocardia sp. P1]
          Length = 488

 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 10/100 (10%), Positives = 21/100 (21%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R        +     + +      T   D   + + V     R +  +    G  +    
Sbjct: 389 RSYPATTAGDPGPSPVASRRGRPGTGGPDHLAVAAPVTRPGLRRRGAAPTPGGGRRAGAR 448

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF 341
                 R+            +      G+     R  P  
Sbjct: 449 PGRGSPRDRRPGPGRRGPSSARRGGRPGRAPRRSRPWPGR 488



 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 13/93 (13%), Positives = 21/93 (22%), Gaps = 12/93 (12%)

Query: 268 VRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN---VWMAKGIHSSF 324
                      P    R +  +   + L+    +  P  RR  A+         G     
Sbjct: 392 PATTAGDPGPSPVASRRGRPGTGGPDHLAVAAPVTRPGLRRRGAAPTPGGGRRAGARPGR 451

Query: 325 LSDSGQR---------EENHRRSPSFPSKRSLR 348
            S   +R                P    +RS  
Sbjct: 452 GSPRDRRPGPGRRGPSSARRGGRPGRAPRRSRP 484


>gi|148708948|gb|EDL40894.1| PRP4 pre-mRNA processing factor 4 homolog B (yeast), isoform CRA_a
           [Mus musculus]
          Length = 1021

 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 17/107 (15%), Positives = 30/107 (28%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                EE     D              +  S+ P D     K+   ++   K K+     
Sbjct: 276 EKMKSEEKGKIKDRKKSPIVNERSRDRSKKSKSPVDLRDKSKDRRSRSKERKSKRSEIDK 335

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            ++ + S    A     +            RRS S   +   RR+ +
Sbjct: 336 EKKPIKSPSKDASSGKENRSPSRRPGRSPKRRSLSPKLRDKSRRSRS 382


>gi|195427177|ref|XP_002061655.1| GK17071 [Drosophila willistoni]
 gi|194157740|gb|EDW72641.1| GK17071 [Drosophila willistoni]
          Length = 1358

 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 21/127 (16%), Positives = 37/127 (29%), Gaps = 6/127 (4%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE SK+  R + G     +          S E            V    ++ ++ S Q+ 
Sbjct: 768 REKSKERQRSRDGKQRSVDRTARSKERQRSREKQRSKDRQGRQSVERQRSKDRQRSKQRQ 827

Query: 294 GLSKQKKLATPVHRRN------LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
                        RR+             +        S+S  R+ N  R  +  +  S 
Sbjct: 828 PSRSAGSKERNQQRRDRSKDRHRRDRRSNSNSRRQRSPSNSSSRKRNDDRKSTRATTPSP 887

Query: 348 RRTSAKK 354
            R+  +K
Sbjct: 888 TRSRKQK 894



 Score = 35.9 bits (81), Expect = 9.5,   Method: Composition-based stats.
 Identities = 14/103 (13%), Positives = 30/103 (29%), Gaps = 2/103 (1%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
                     + ++  R R +      D     +++ S+    SK+++ +    R    S
Sbjct: 700 PPRRESQKKDTQKSRERPRSSERQRSKDRQRSRERHISKDRHRSKERQRSKERQRSVEKS 759

Query: 313 NVWMAKGIHSSFLSDSGQREENHRR--SPSFPSKRSLRRTSAK 353
           NV                R+   R     +   +R   R   +
Sbjct: 760 NVRSVNKEREKSKERQRSRDGKQRSVDRTARSKERQRSREKQR 802


>gi|37676819|ref|NP_937215.1| DNA and RNA helicase [Vibrio vulnificus YJ016]
 gi|37201363|dbj|BAC97185.1| DNA and RNA helicase [Vibrio vulnificus YJ016]
          Length = 509

 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 12/126 (9%), Positives = 34/126 (26%), Gaps = 8/126 (6%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
            TR +  K  ++   P          DA    ++              +   + + ++ +
Sbjct: 386 DTRPIKPKKPKKPKKPKAPNAEAAGSDASSKGNQKAKAADKPQGQNRGNGKAKRQFSAPK 445

Query: 292 KNGLSKQKKLATPVHRRNLASNV------WMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
           +       K   P  + +  +N               +       +  N    PS   ++
Sbjct: 446 EGNNDSANKGKRPNTKGSKPANNANGKTHGKPSHAKPNSAKTGNSKPANG--KPSAQRRK 503

Query: 346 SLRRTS 351
              +++
Sbjct: 504 PRPQSA 509


>gi|320158915|ref|YP_004191293.1| ATP-dependent RNA helicase RhlE [Vibrio vulnificus MO6-24/O]
 gi|319934227|gb|ADV89090.1| ATP-dependent RNA helicase RhlE [Vibrio vulnificus MO6-24/O]
          Length = 509

 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 6/109 (5%), Positives = 22/109 (20%), Gaps = 2/109 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
                    +A    +    +++                    + N+   N   +     
Sbjct: 403 APNAEAAGSDASSKGNQKAKTADKPQGQNRGNGKAKRQFSAPKEGNNDSANKGKRPNTKG 462

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
           +                   +       +  N    PS   ++   +++
Sbjct: 463 SKPANNANGKTNGKPSHAKPNSAKTGNSKPANG--KPSAQRRKPRPQSA 509


>gi|242074680|ref|XP_002447276.1| hypothetical protein SORBIDRAFT_06g031820 [Sorghum bicolor]
 gi|241938459|gb|EES11604.1| hypothetical protein SORBIDRAFT_06g031820 [Sorghum bicolor]
          Length = 552

 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 19/163 (11%), Positives = 52/163 (31%), Gaps = 15/163 (9%)

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            V + EG    +  V   F   +  + R + G              + +  + +      
Sbjct: 390 KVDILEGM--HVTSVGCGFGLSLIVVDRANVGD------------RLDQLEIYDGDTSPE 435

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
           +E+ +V +     +S     ++     +V +  +    +   ++G  +   +  P  RR 
Sbjct: 436 VEKVEVQVTKKASASTNSRANKRKKTKDVSESESEEDDDDDDESGDDENGDIEEPKGRRG 495

Query: 310 LASNVWMAKGIHS-SFLSDSGQREENHRRSPSFPSKRSLRRTS 351
              +    +G    +  +    R     +    P++++    S
Sbjct: 496 RKPSRGRGRGAKKATPEAKPSGRGRGRPKKTESPAQKAGTSGS 538


>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 = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 29/213 (13%), Positives = 68/213 (31%), Gaps = 33/213 (15%)

Query: 33  RMIAQQRVKVNGI--------LLERAAVNVMSTDH--------IE-VDGVPLRKAERTRL 75
           ++I   ++KVN          + +   + V   D         +E  +       E   L
Sbjct: 30  KLIMNGQIKVNEKLTFKNSLIVAKDDVIKVEIHDETTSDFITSVEPYNLKLEVLFEDKDL 89

Query: 76  WLYHKPIGLVTTHSDPDGRST--VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +KP GL+T  +  + +++        +  + V  V RLD +T G +++  +      
Sbjct: 90  MVINKPSGLLTHPTTFNEKASLLAACIFHNNKNPVYLVHRLDRDTSGAIVVCKNQASLLN 149

Query: 134 LELPSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDMQ-----VTL 179
           L+                    +            +    ++ +       +       +
Sbjct: 150 LQNQLQNRTLKRYYVALVHFPFNALTGSINAPLARVNNNKVMFKIAQTAKAKQAITKFKV 209

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             Q    A +++ L  G+  +I+   +F    V
Sbjct: 210 INQNEKAALISLELLTGRTHQIRVHLKFIQHPV 242


>gi|261492813|ref|ZP_05989360.1| Hsp15 family heat shock protein [Mannheimia haemolytica serotype
          A2 str. BOVINE]
 gi|261311495|gb|EEY12651.1| Hsp15 family heat shock protein [Mannheimia haemolytica serotype
          A2 str. BOVINE]
          Length = 144

 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 1  MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLE 48
          MK+K+  ++N    R+ K + A     +R   + MI   +V  NG   +
Sbjct: 7  MKNKHEKEQNDAEVRLDKWLWAARFYKTRSIAKAMIEGGKVHYNGQRAK 55


>gi|269795516|ref|YP_003314971.1| hypothetical protein Sked_22180 [Sanguibacter keddieii DSM 10542]
 gi|269097701|gb|ACZ22137.1| hypothetical protein Sked_22180 [Sanguibacter keddieii DSM 10542]
          Length = 750

 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 11/108 (10%), Positives = 22/108 (20%), Gaps = 2/108 (1%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              ++                 DRP        D  R              +        
Sbjct: 44  PRRDDRPQGDRPSYGDRGPRRDDRPQGERPAYGDRPRRDDRPQGDRPSYGDRGPRRDDRA 103

Query: 308 RNLASNVWMAK--GIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +    +       G   S+     + +      PS+  +   R   A+
Sbjct: 104 QGGRPSYGDRPTSGDRPSYGDRPRRDDRPQGDRPSYGDRGPRRDDRAQ 151



 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 11/109 (10%), Positives = 21/109 (19%), Gaps = 1/109 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R   G       +          +           +      R         G    ++ 
Sbjct: 340 RPSYGDRPATGDRAPRRDDRPQGDRPSYGDRGPRRDDRPQGGRPSYGDRPATGDRAPRRD 399

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR-RSPSFPSKRSLRR 349
             P   R   S+    +   +        R    R  + S   +    R
Sbjct: 400 DRPQGDRPSYSDRGPRRDDRAQGDRPRQDRPRQDRAPARSEAPRDRAPR 448



 Score = 37.1 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 13/111 (11%), Positives = 22/111 (19%), Gaps = 1/111 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R   G       +          +           +      R         G    ++ 
Sbjct: 298 RPASGDRPSYGDRGPRRDDRPQGDRPSYGDRGPRRDDRAQGGRPSYGDRPATGDRAPRRD 357

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDS-GQREENHRRSPSFPSKRSLRRTS 351
             P   R    +    +         S G R     R+P    +    R S
Sbjct: 358 DRPQGDRPSYGDRGPRRDDRPQGGRPSYGDRPATGDRAPRRDDRPQGDRPS 408



 Score = 35.9 bits (81), Expect = 9.2,   Method: Composition-based stats.
 Identities = 12/103 (11%), Positives = 20/103 (19%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           +     D           DRP      P    R + +         ++       R +  
Sbjct: 327 DRGPRRDDRAQGGRPSYGDRPATGDRAPRRDDRPQGDRPSYGDRGPRRDDRPQGGRPSYG 386

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                            G R     R P    +    R    +
Sbjct: 387 DRPATGDRAPRRDDRPQGDRPSYSDRGPRRDDRAQGDRPRQDR 429



 Score = 35.9 bits (81), Expect = 9.8,   Method: Composition-based stats.
 Identities = 16/117 (13%), Positives = 24/117 (20%), Gaps = 5/117 (4%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R   G       + +        +    DRP+     P    R +               
Sbjct: 107 RPSYGDRPTSGDRPSYGDRPRRDDRPQGDRPSYGDRGPRRDDRAQGGRPSYGDRPASGDR 166

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR-----SPSFPSKRSLRRTSAK 353
           A     R                    G R     R      PS+  +   R   A+
Sbjct: 167 APRRDDRPQGDRPSYGDRGPRRDDRAQGGRPSYGDRPTSGDRPSYGDRGPRRDDRAQ 223


>gi|226365342|ref|YP_002783125.1| hypothetical protein ROP_59330 [Rhodococcus opacus B4]
 gi|226243832|dbj|BAH54180.1| hypothetical membrane protein [Rhodococcus opacus B4]
          Length = 289

 Score = 39.0 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 21/143 (14%), Positives = 38/143 (26%), Gaps = 10/143 (6%)

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAP 260
           + +        V  L+    G  +L  L    T                  +       P
Sbjct: 118 VNRFPVMLAATVVTLL---IGGLRLFLLQQRKTGPARTSE-------RRRAQRAPRTARP 167

Query: 261 IYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGI 320
             ++E   +  P        D  R     + +      ++ ATP  RR+ +S    A   
Sbjct: 168 RLAAEESEQAPPPRRRARDRDGVRDTARDAAREHPRSARRAATPPPRRSSSSGGRTAPPP 227

Query: 321 HSSFLSDSGQREENHRRSPSFPS 343
                +    R    R + +  S
Sbjct: 228 PMVDRAAQAPRSAPPRTTQAPRS 250


>gi|311107469|ref|YP_003980322.1| heat shock protein 15 [Achromobacter xylosoxidans A8]
 gi|310762158|gb|ADP17607.1| heat shock protein 15 [Achromobacter xylosoxidans A8]
          Length = 126

 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 20/52 (38%), Gaps = 2/52 (3%)

Query: 12 TPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             R+ K + A     +R    + I + RV VN    +  A  V   D + V
Sbjct: 2  DKIRLDKWLWAARFYKTRSLAVQEIGKGRVLVNDQPAK-PAREVAPGDLVTV 52


>gi|332240104|ref|XP_003269230.1| PREDICTED: serine/arginine repetitive matrix protein 2 [Nomascus
           leucogenys]
          Length = 2079

 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 9/108 (8%), Positives = 20/108 (18%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                            S   +     +              + +    + +    AT  
Sbjct: 431 RHASSSPESPKPAPAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRVGRSHSPATTK 490

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R+ +          S        R          P +R   R+  +
Sbjct: 491 RGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQR 538



 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 11/98 (11%), Positives = 21/98 (21%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P      +++      +       R    S  P        + +       + +  T  
Sbjct: 443 APAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRVGRSHSPATTKRGRSRSRTPTKR 502

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
                 S  W        +      +     RSP  P 
Sbjct: 503 GHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPG 540



 Score = 37.5 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 20/113 (17%), Positives = 31/113 (27%), Gaps = 10/113 (8%)

Query: 230 AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
            GS RE+S         P     +          S T  R      S       R +  +
Sbjct: 446 PGSHREISS-------SPTSKNRSHGRAKRDKSHSHTPSRRVGRSHSPATTKRGRSRSRT 498

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
             K G S   +  +P  RR+ ++  W               +     RS +  
Sbjct: 499 PTKRGHS---RSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPGWSRSRNTQ 548


>gi|149636482|ref|XP_001508424.1| PREDICTED: similar to PRP4 pre-mRNA processing factor 4 homolog B
           (yeast) [Ornithorhynchus anatinus]
          Length = 1011

 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 16/108 (14%), Positives = 30/108 (27%), Gaps = 2/108 (1%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                ++A+                     S+ P +     K+   ++   K K+  T  
Sbjct: 265 KLKTEDKAKSKDRKKSPVVNESKTRDRGKKSKSPTELRSKSKDRRSRSKDRKSKRSETEK 324

Query: 306 HRRNLASNVWMAKGIH--SSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
            ++ L S    A       S     G+  +    SP    K    R+ 
Sbjct: 325 EKKPLKSPSKDASSGKENRSPSRRPGRSPKGRSSSPKQRDKLRRSRSP 372



 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 14/113 (12%), Positives = 36/113 (31%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +++    ++ E++         S T +R +         D    +  + ++    K    
Sbjct: 275 KDRKKSPVVNESKTRDRGKKSKSPTELRSKSKDRRSRSKDRKSKRSETEKEKKPLKSPSK 334

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                + N + +    +       S   + +    RSP    +RS +  S  +
Sbjct: 335 DASSGKENRSPSRRPGRSPKGRSSSPKQRDKLRRSRSPLLNDRRSKQSKSPSR 387



 Score = 37.1 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 16/107 (14%), Positives = 27/107 (25%), Gaps = 9/107 (8%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
            +      + S     R R         +  + KK     +  +   K      RR   S
Sbjct: 293 KKSKSPTELRSKSKDRRSRSKDRKSKRSETEKEKKPLKSPSKDASSGKENRSPSRRPGRS 352

Query: 313 NVWMAKGIHSSFLSDSGQ------REENHRRSPSF---PSKRSLRRT 350
               +            +      R     +SPS    P +R   R+
Sbjct: 353 PKGRSSSPKQRDKLRRSRSPLLNDRRSKQSKSPSRTQSPGRRVRSRS 399



 Score = 37.1 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 13/105 (12%), Positives = 30/105 (28%), Gaps = 1/105 (0%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
               +  L     +     +  P +      D  +  K+ ++    SK ++  +   +  
Sbjct: 259 KSPMEEKLKTEDKAKSKDRKKSPVVNESKTRDRGKKSKSPTELRSKSKDRRSRSKDRKSK 318

Query: 310 LASNVWMAKG-IHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            +      K     S  + SG+   +  R P    K        +
Sbjct: 319 RSETEKEKKPLKSPSKDASSGKENRSPSRRPGRSPKGRSSSPKQR 363


>gi|74316527|ref|YP_314267.1| RNA-binding S4 protein [Thiobacillus denitrificans ATCC 25259]
 gi|74056022|gb|AAZ96462.1| RNA-binding S4 protein [Thiobacillus denitrificans ATCC 25259]
          Length = 134

 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 14/65 (21%), Positives = 27/65 (41%), Gaps = 2/65 (3%)

Query: 11 FTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
              R+ K + A     +R    + IA  RV+++G  ++  A  V   D +++    L  
Sbjct: 9  SERMRLDKWLWAARFFKTRSLAVQAIAHGRVRLDGERVK-PAREVKCGDRLDIQIEVLEW 67

Query: 70 AERTR 74
          +   R
Sbjct: 68 SVTVR 72


>gi|319441436|ref|ZP_07990592.1| translation initiation factor IF-2 [Corynebacterium variabile DSM
           44702]
          Length = 134

 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 13/118 (11%), Positives = 30/118 (25%), Gaps = 7/118 (5%)

Query: 229 LAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
           + G  R      L +QLG    E      +   +         P +  ++ + +     +
Sbjct: 1   MPGKLRV---HELAKQLGVTSKELLATLKEQGEFVKSASSTVEPPVAKKMRNHYGAGSAS 57

Query: 289 SSQKNGLSKQKKLATPVH--RRNLASNVWMAK--GIHSSFLSDSGQREENHRRSPSFP 342
                G +       P    + +           G   +  +  G   +     P+  
Sbjct: 58  KDATPGAASATPGPVPGSSAKPSAKPTPGAKPTPGAKPTPGAKPGAAGQKPGPKPATG 115


>gi|146337227|ref|YP_001202275.1| translation initiation factor IF-2 [Bradyrhizobium sp. ORS278]
 gi|166226252|sp|A4YJE9|IF2_BRASO RecName: Full=Translation initiation factor IF-2
 gi|146190033|emb|CAL74025.1| Translation initiation factor IF-2 [Bradyrhizobium sp. ORS278]
          Length = 921

 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 11/106 (10%), Positives = 18/106 (16%), Gaps = 1/106 (0%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               E +         +       P      P    +         G   Q+        
Sbjct: 167 KRKAELEAKKRFGEGEAPRPAAAAPQPTVSAPARPAQAPGRPQGAPGSRPQQIGGPSSRP 226

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP-SKRSLRRTSA 352
                      G   +     G+        P      R +RR   
Sbjct: 227 GGSQPGGARPAGPRPAGGGPLGRAPAAVAAGPDEDEGPRQIRRGPG 272



 Score = 38.2 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 15/128 (11%), Positives = 25/128 (19%), Gaps = 13/128 (10%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK--KNSSQKNG 294
            K  L  +      E  +    AP  +     R             +R +     S + G
Sbjct: 168 RKAELEAKKRFGEGEAPRPAAAAPQPTVSAPARPAQAPGRPQGAPGSRPQQIGGPSSRPG 227

Query: 295 LSKQKKLATPVHRRNLASNVWMAK-----------GIHSSFLSDSGQREENHRRSPSFPS 343
            S+         R      +  A            G         G          +   
Sbjct: 228 GSQPGGARPAGPRPAGGGPLGRAPAAVAAGPDEDEGPRQIRRGPGGAARPAPPPKTTHKP 287

Query: 344 KRSLRRTS 351
               +R  
Sbjct: 288 GPQKQRGR 295


>gi|302406486|ref|XP_003001079.1| pre-mRNA-splicing factor cwc22 [Verticillium albo-atrum VaMs.102]
 gi|261360337|gb|EEY22765.1| pre-mRNA-splicing factor cwc22 [Verticillium albo-atrum VaMs.102]
          Length = 845

 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 9/119 (7%), Positives = 28/119 (23%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R +++     +   +    ++    AP  ++        +  S          ++   + 
Sbjct: 586 RSLTRSPPPARRRRNSSSVSRSRSPAPKRAAAREPARSLSPYSRRAAGLAARPRSPPARE 645

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
              ++     P    +  S         +     +        R     +  S  R   
Sbjct: 646 PARREPPRREPSRSLSPYSRRAAGLVGRARSPPPARVPAPPPGRRRESSAGGSAPRKKP 704



 Score = 35.9 bits (81), Expect = 8.3,   Method: Composition-based stats.
 Identities = 14/92 (15%), Positives = 22/92 (23%), Gaps = 4/92 (4%)

Query: 259 APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAK 318
                            S +P   +R  +  S  +              R  + +     
Sbjct: 742 RSPSPVPPRRVAASRSPSPLPAKDSRGGRQGSYDSRSPSPAPRRDGGSARGRSRS----P 797

Query: 319 GIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
           G      S      E+  RS S P  +  RR 
Sbjct: 798 GAPGGGASKRRLHSESVSRSRSPPPPKRGRRN 829


>gi|47087429|ref|NP_998614.1| serine/threonine-protein kinase PRP4 homolog [Danio rerio]
 gi|29124615|gb|AAH48879.1| PRP4 pre-mRNA processing factor 4 homolog B [Danio rerio]
          Length = 1010

 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 10/106 (9%), Positives = 19/106 (17%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               + + +         +   D          D    K  S          +      +
Sbjct: 279 RHSADRKPDQKGRPDRRSSPHMDEKREQVRQRSDSQGGKSQSQGSKDGQNVGRSENDREK 338

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           R   S          +             R  S P  R  +    +
Sbjct: 339 RPGKSPSKDPSSGKENRSPQQRPALSPQHRRSSSPRHRDRQSNQPR 384


>gi|332976359|gb|EGK13213.1| ribosomal large subunit pseudouridine synthase D [Desmospora sp.
           8437]
          Length = 270

 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 23/213 (10%), Positives = 55/213 (25%), Gaps = 34/213 (15%)

Query: 35  IAQQRVKVNGILLER-----AAVNVM-----------------------STDHIEVD--- 63
           I + RV+V+G +++          V                          D I V+   
Sbjct: 1   IREHRVRVDGRIVKSNHRLQGGEQVEVAVPPPEEAEVKPEALPLEVVFEDGDVIMVNKPR 60

Query: 64  GVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           G+ +     +    L           +      R  +   +    S +I V + D     
Sbjct: 61  GMVVHPAPGSPSGTLVNALLAHCDDLSGIGGVLRPGIVHRIDKDTSGLIMVAKNDFAHRS 120

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L     +  + R         +   R      + +D  +  +  +  +          + 
Sbjct: 121 LAAQLKNHTVDREYTALVQGNIPHDRGTVDAPIGRDPHHRKRMAVEHRHGKPAVTHFEVI 180

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +      +   L  G+  +I+   +     + 
Sbjct: 181 ERFSRATLIRCRLETGRTHQIRVHMKSIGHPLV 213


>gi|119621262|gb|EAX00857.1| retinol dehydrogenase 14 (all-trans and 9-cis), isoform CRA_c [Homo
           sapiens]
          Length = 419

 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 9/89 (10%), Positives = 23/89 (25%)

Query: 266 TLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFL 325
            +    P   ++ P    R       +   +  +    P  R    +    + G H    
Sbjct: 90  AVAGGPPVRGAQGPAAAQRRGPRPHAREDCADHRGEQRPGPRHGRRATAPGSAGDHGLPG 149

Query: 326 SDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             + +         + P +    R   ++
Sbjct: 150 PRARRGGGGSAPPRAPPGRGVRPRAWRQR 178


>gi|325962892|ref|YP_004240798.1| hypothetical protein Asphe3_14940 [Arthrobacter phenanthrenivorans
           Sphe3]
 gi|323468979|gb|ADX72664.1| hypothetical protein Asphe3_14940 [Arthrobacter phenanthrenivorans
           Sphe3]
          Length = 618

 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 11/114 (9%), Positives = 26/114 (22%), Gaps = 2/114 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           ++      E  + + +          R         P      +    +     +  +  
Sbjct: 64  DRDKKPFGERPRRDGEGDRRGFGGGERKPFGDRDRKPYGDRENRSFGERPRRDGEGDRRG 123

Query: 303 -TPVHRRNLASNVWMAKGIHSSFL-SDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                R+          G   +    D  +R+    R      +R   R   +K
Sbjct: 124 FGGGERKPFGDRDRKPYGDRENRTFGDRPRRDGEGDRRGFGGGERKPFRDRDRK 177



 Score = 36.3 bits (82), Expect = 6.9,   Method: Composition-based stats.
 Identities = 12/109 (11%), Positives = 18/109 (16%), Gaps = 1/109 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P    E                RDR          +   +  S         +      
Sbjct: 151 RPRRDGEGDRRGFGGGERKPFRDRDRKPFGDRDRKPYGDRENRSFGDRPRRDGEGDRRGF 210

Query: 306 HRRNLASNVWMAKGIHSSF-LSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                           +     D   R  +   S      RS  R   +
Sbjct: 211 GGGENRKPFGDRSERPARGDRQDRAPRSFDRGASRGDAGPRSFGRDRQE 259


>gi|301120670|ref|XP_002908062.1| conserved hypothetical protein [Phytophthora infestans T30-4]
 gi|262103093|gb|EEY61145.1| conserved hypothetical protein [Phytophthora infestans T30-4]
          Length = 530

 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 14/110 (12%), Positives = 26/110 (23%), Gaps = 3/110 (2%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           +     P  +E    +      S     R       +      R + +   ++ +    +
Sbjct: 233 IDTTAKPVTMESVPPSSGRSSASGRFSARGHSGRARQHSSPSPRGRNHHRSRDWIRSPTR 292

Query: 301 LATPVHRRNLASNVWMAKGIHS---SFLSDSGQREENHRRSPSFPSKRSL 347
             T  HR    S                S S +       S S   +R  
Sbjct: 293 RHTSDHRGRSRSRDHFQPDRRPLGEPGGSQSSRGPSPRNHSRSPHRERDR 342


>gi|58399156|gb|AAH89300.1| LOC733159 protein [Xenopus laevis]
          Length = 821

 Score = 39.0 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 12/113 (10%), Positives = 22/113 (19%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R +         +        +S        +  +  P        + S    +      
Sbjct: 187 RGRHDSPDTSPPRRGRHDSPDTSPPRRGRHDSPDTSPPRRGRHESPDPSPPRRVRYDSPD 246

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +P  R    S                         SP+    R  R  S  +
Sbjct: 247 QSPPRRGRHDSPAQSPPRRGRHDSPAQSPPRRGRHDSPAQSPPRRGRHDSPAQ 299



 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 17/124 (13%), Positives = 29/124 (23%), Gaps = 3/124 (2%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R  S      + G H   +          S +     R    S       R + +S  ++
Sbjct: 202 RHDSPDTSPPRRGRHDSPDTSPPRRGRHESPDPSPPRRVRYDSPDQSPPRRGRHDSPAQS 261

Query: 294 GLSKQK---KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
              + +      +P  R    S                         SP+    R  R  
Sbjct: 262 PPRRGRHDSPAQSPPRRGRHDSPAQSPPRRGRHDSPAQSPPRRGRHDSPAQSPPRRGRHD 321

Query: 351 SAKK 354
           S  +
Sbjct: 322 SPAQ 325



 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 19/124 (15%), Positives = 32/124 (25%), Gaps = 3/124 (2%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R  S      + G H   +          S +T    R    S  P    R++ +S  ++
Sbjct: 189 RHDSPDTSPPRRGRHDSPDTSPPRRGRHDSPDTSPPRRGRHESPDPSPPRRVRYDSPDQS 248

Query: 294 GLSKQK---KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
              + +      +P  R    S                         SP+    R  R  
Sbjct: 249 PPRRGRHDSPAQSPPRRGRHDSPAQSPPRRGRHDSPAQSPPRRGRHDSPAQSPPRRGRHD 308

Query: 351 SAKK 354
           S  +
Sbjct: 309 SPAQ 312



 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 13/104 (12%), Positives = 23/104 (22%), Gaps = 1/104 (0%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
                       +    R R +     P    R     +      + +       RR   
Sbjct: 183 SPPRRGRHDSPDTSPPRRGRHDSPDTSPPRRGRHDSPDTSPPRRGRHESPDPSPPRRVRY 242

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRR-SPSFPSKRSLRRTSAKK 354
            +   +        S +       R  SP+    R  R  S  +
Sbjct: 243 DSPDQSPPRRGRHDSPAQSPPRRGRHDSPAQSPPRRGRHDSPAQ 286



 Score = 37.1 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 11/119 (9%), Positives = 23/119 (19%), Gaps = 6/119 (5%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R                          R R +     P    R     +      +    
Sbjct: 160 RRSRHDSSDTSPPPRKTQDSSDGSPPRRGRHDSPDTSPPRRGRHDSPDTSPPRRGRHDSP 219

Query: 302 ATPVHRRNLASNVWMAKGIH------SSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            T   RR    +   +                 G+ +   +  P      S  ++  ++
Sbjct: 220 DTSPPRRGRHESPDPSPPRRVRYDSPDQSPPRRGRHDSPAQSPPRRGRHDSPAQSPPRR 278


>gi|27367036|ref|NP_762563.1| ATP-dependent RNA helicase RhlE [Vibrio vulnificus CMCP6]
 gi|27358604|gb|AAO07553.1| ATP-dependent RNA helicase RhlE [Vibrio vulnificus CMCP6]
          Length = 509

 Score = 39.0 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 12/106 (11%), Positives = 31/106 (29%), Gaps = 3/106 (2%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                + +         + +   ++R N  ++      +   N S   G     K + P 
Sbjct: 407 EAAGSDASSKGNQKAKAADKPQGQNRGNGKAKRQFSAPKEGNNDSTNKGKRPNTKGSKPA 466

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
           +  N  +N         +       +  N    PS   ++   +++
Sbjct: 467 NNANGKTN-GKPSHAKPNSAKTGNSKPANG--KPSAQRRKPRPQSA 509


>gi|293610799|ref|ZP_06693099.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292827143|gb|EFF85508.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 639

 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 14/108 (12%), Positives = 27/108 (25%), Gaps = 6/108 (5%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
            +V+      +       R     + P      K    + +   + +        R    
Sbjct: 528 NRVDYKPRRENGFGDRPKRSFGGEDRPRRSFDDKPRGERPSFGGEDRPRREFNSDRPRRE 587

Query: 313 NVWMAKGIHSSFLSDSGQREE---NHRRSPSFPSKRSLRR---TSAKK 354
             +  K   S      G+R       R   SF  +   RR      ++
Sbjct: 588 GGFNDKPRRSFDDKPRGERPAFGGEDRPKRSFGGEDRPRRSFDDKPRR 635



 Score = 37.9 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 12/132 (9%), Positives = 29/132 (21%), Gaps = 19/132 (14%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+       ++                    +          R ++  +      +    
Sbjct: 455 RDDRPRRSFDDKPRGERPFGGEDRPRREFNSDRPRREGGFEDRPRREFNSDRPRREGGFN 514

Query: 302 ATPVHR------------RNLASNVWMAKGIHSSFLSDSGQR---EENHRRSPSFPSKRS 346
             P               +    N +  +   S    D  +R   ++     PSF  +  
Sbjct: 515 DKPRFDSNDDNRGNRVDYKPRRENGFGDRPKRSFGGEDRPRRSFDDKPRGERPSFGGEDR 574

Query: 347 LRR----TSAKK 354
            RR       ++
Sbjct: 575 PRREFNSDRPRR 586



 Score = 37.5 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 20/109 (18%), Positives = 34/109 (31%), Gaps = 1/109 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R +      +  +   ++     E    D+P   S   +   R+     ++NG   + K 
Sbjct: 487 RPRREGGFEDRPRREFNSDRPRREGGFNDKPRFDSNDDNRGNRVDYKPRRENGFGDRPKR 546

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLS-DSGQREENHRRSPSFPSKRSLRR 349
           +     R   S     +G   SF   D  +RE N  R           R
Sbjct: 547 SFGGEDRPRRSFDDKPRGERPSFGGEDRPRREFNSDRPRREGGFNDKPR 595



 Score = 37.1 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 19/120 (15%), Positives = 28/120 (23%), Gaps = 6/120 (5%)

Query: 230 AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
            G  R + +  L  +L    +E  +              RD                   
Sbjct: 386 RGKIRAL-EDYLDARLSVSEIEGLEP-----SPPPARSGRDGGGRGRGGNGRRGGGFGGG 439

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
            +  G S  K+       R   S     +G       D  +RE N  R           R
Sbjct: 440 RRFEGESNFKRREGGRDDRPRRSFDDKPRGERPFGGEDRPRREFNSDRPRREGGFEDRPR 499


>gi|256370560|ref|YP_003108071.1| translation initiation factor IF-2 [Brucella microti CCM 4915]
 gi|256000723|gb|ACU49122.1| translation initiation factor IF-2 [Brucella microti CCM 4915]
          Length = 973

 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 12/98 (12%), Positives = 27/98 (27%), Gaps = 2/98 (2%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R + +  +RE +        +    A   +     R+         +   + +  + +K 
Sbjct: 192 RALEEAQIRE-VEERARAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARRKA 250

Query: 294 GLSKQKKLATPVHRRNLASNVWMAK-GIHSSFLSDSGQ 330
                K++  P  R     +   A  G      S    
Sbjct: 251 EEEAAKRMPQPEARSERRDDARPAPYGARPQQGSPRPA 288


>gi|269792831|ref|YP_003317735.1| RNA-binding S4 domain-containing protein [Thermanaerovibrio
          acidaminovorans DSM 6589]
 gi|269100466|gb|ACZ19453.1| RNA-binding S4 domain protein [Thermanaerovibrio acidaminovorans
          DSM 6589]
          Length = 89

 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 2/51 (3%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           RV K +  A I  RR   + M     V+V+G + +  +  V + D +EVD
Sbjct: 1  MRVDKFLKLARIVKRRTVAQEMAEAGAVRVSGRVAK-PSTEVRAGDQLEVD 50


>gi|188584090|ref|YP_001927535.1| helicase domain protein [Methylobacterium populi BJ001]
 gi|179347588|gb|ACB83000.1| helicase domain protein [Methylobacterium populi BJ001]
          Length = 1138

 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 6/118 (5%), Positives = 22/118 (18%), Gaps = 1/118 (0%)

Query: 237  SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            + ++           + Q          +   ++             R      +     
Sbjct: 998  TVEVWHLHRPQRHAGQRQGRGQGRPDGRQDGRQEGRQDGRPDGRHGERRGDGPRRPREDR 1057

Query: 297  KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             +         R         +G           R +    +    ++    R   ++
Sbjct: 1058 PEGGRPARAEGRGEGRRDGQGEGGPRRDHQGPRNRPDRRDENRRPNAEARPPR-RERQ 1114



 Score = 37.1 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 9/128 (7%), Positives = 19/128 (14%), Gaps = 1/128 (0%)

Query: 228  LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDF-TRMK 286
            L    T E                E        ++      R               R  
Sbjct: 968  LPTEETNEAPAAETAASDAGSEPAEPAAPETVEVWHLHRPQRHAGQRQGRGQGRPDGRQD 1027

Query: 287  KNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
                 +       +                 +G   +     G+   + +          
Sbjct: 1028 GRQEGRQDGRPDGRHGERRGDGPRRPREDRPEGGRPARAEGRGEGRRDGQGEGGPRRDHQ 1087

Query: 347  LRRTSAKK 354
              R    +
Sbjct: 1088 GPRNRPDR 1095



 Score = 36.3 bits (82), Expect = 7.3,   Method: Composition-based stats.
 Identities = 10/92 (10%), Positives = 19/92 (20%)

Query: 253  AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
             Q              R          D     +   ++  G  ++        RR+   
Sbjct: 1029 RQEGRQDGRPDGRHGERRGDGPRRPREDRPEGGRPARAEGRGEGRRDGQGEGGPRRDHQG 1088

Query: 313  NVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
                      +   ++  R     R P   S 
Sbjct: 1089 PRNRPDRRDENRRPNAEARPPRRERQPDPDSP 1120


>gi|119595588|gb|EAW75182.1| hCG2040175, isoform CRA_a [Homo sapiens]
          Length = 898

 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 22/140 (15%), Positives = 39/140 (27%), Gaps = 6/140 (4%)

Query: 202 KKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV-SKKILREQLGPHLLEEAQVNLDAP 260
            +  E     V+ L          G  LAG  R +   K    + G           +  
Sbjct: 760 SRCCEAIYSSVSGLK-AHLASCSKGAHLAGKYRCLLCPKEFSSESGVKYHILKTHAENWF 818

Query: 261 IYSSETLVRDRPN----IISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
             S++   + R         E   +    KK   +    + ++ +A    RR+       
Sbjct: 819 RTSADPPPKHRSQDSLVPKKEKKKNLAGGKKRGRKPKERTPEEPVAKLPPRRDDWPPGCR 878

Query: 317 AKGIHSSFLSDSGQREENHR 336
            KG   S     G  +   +
Sbjct: 879 DKGARGSTGRKVGVSKAPEK 898


>gi|148232738|ref|NP_001088314.1| PRP4 pre-mRNA processing factor 4 homolog B [Xenopus laevis]
 gi|54038078|gb|AAH84355.1| LOC495151 protein [Xenopus laevis]
          Length = 991

 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 21/125 (16%), Positives = 32/125 (25%), Gaps = 4/125 (3%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R  S+  LR           +              R+R               KN+    
Sbjct: 224 RSKSEDQLRRSPALRHQSPEKNIKTKSPQEERVKSRERRKSPVASEIKSRERTKNTKSPV 283

Query: 294 GLSKQKKLATPV----HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
             SK K+  +       RR+ +          S   S   +     RR+   P  RSL  
Sbjct: 284 SRSKSKERRSKSKERKPRRSDSDRDKKPLKSPSKDASSGKENRSPGRRTAWSPKARSLSP 343

Query: 350 TSAKK 354
               +
Sbjct: 344 KQRDR 348


>gi|20140663|sp|Q92F59|Y248_LISIN RecName: Full=Uncharacterized protein Lin0248
 gi|313621007|gb|EFR92134.1| S4 RNA-binding domain-containing protein [Listeria innocua FSL
          S4-378]
          Length = 88

 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 14/78 (17%), Positives = 25/78 (32%), Gaps = 4/78 (5%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
           R+ K +  + +  RR   + +  + R+ VNG+  +    NV S D   I      +   
Sbjct: 1  MRLDKYLKVSRLIKRRTVAKEVAEKGRIAVNGVTAK-PGTNVKSGDELVIRFGPKIVTAK 59

Query: 71 ERTRLWLYHKPIGLVTTH 88
                   K        
Sbjct: 60 IERLEENAKKEQATEMYT 77


>gi|222616895|gb|EEE53027.1| hypothetical protein OsJ_35744 [Oryza sativa Japonica Group]
          Length = 1003

 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 16/119 (13%), Positives = 25/119 (21%), Gaps = 10/119 (8%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R     H     +        S       +           +   +++ +  G S+    
Sbjct: 13  RRHRHRHDDSPPRRRRRHDDDSPRHRDDRKRRASPSPSPSPSPSDRDADRHRGKSRASPP 72

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREE----------NHRRSPSFPSKRSLRRT 350
             P       SN   A         D   R            + RR PS  S       
Sbjct: 73  RRPRDSDPAESNGGGAPKPGGDNGGDRSPRRARVPDAEEEGGDRRRRPSRVSDDDKEGG 131


>gi|126305413|ref|XP_001380458.1| PREDICTED: similar to centromere autoantigen B (CENP-B)
           [Monodelphis domestica]
          Length = 822

 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 5/111 (4%), Positives = 16/111 (14%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +               A   S                      ++ ++  +   + +   
Sbjct: 107 DPPPLGRPLPLPAPARAGSPSLPAAASRGERAERSAAGSGGGQRRRAAASSDRRRAQGQP 166

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               R   ++     +                          R   R    
Sbjct: 167 ATSLRAPRSARPGRGQAGRLPGRLCPPPGPGPLCLGRRSGGPRGSPRPRDA 217



 Score = 37.1 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 10/99 (10%), Positives = 23/99 (23%)

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
               +P   +     +R    +       R +  +S     ++ +   +    R+     
Sbjct: 121 ARAGSPSLPAAASRGERAERSAAGSGGGQRRRAAASSDRRRAQGQPATSLRAPRSARPGR 180

Query: 315 WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             A  +        G       R    P      R +  
Sbjct: 181 GQAGRLPGRLCPPPGPGPLCLGRRSGGPRGSPRPRDAPS 219


>gi|156977695|ref|YP_001448601.1| hypothetical protein VIBHAR_06483 [Vibrio harveyi ATCC BAA-1116]
 gi|156529289|gb|ABU74374.1| hypothetical protein VIBHAR_06483 [Vibrio harveyi ATCC BAA-1116]
          Length = 527

 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 12/128 (9%), Positives = 34/128 (26%), Gaps = 5/128 (3%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
            TR +  K  ++   P    E     +          R R N  ++      +  K  + 
Sbjct: 386 DTRPIKPKKPKKPKKPKAEGENGQTAEKKNSDGNNKPRRRFNSDNKNDKGENKSGKAGAG 445

Query: 292 KNGLSKQKKLATPVHRRNLASN-----VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           K   ++  +  +   +     N             +          + +   P+     +
Sbjct: 446 KPKGNRDGQARSNGKQSGNKPNNNQSGASKPGASKNGNGGKPSGNRKPNSGKPAGAKPSN 505

Query: 347 LRRTSAKK 354
            + +  ++
Sbjct: 506 GKPSGQRR 513


>gi|134287217|ref|YP_001110913.1| hypothetical protein HVAV3e_gp060 [Heliothis virescens ascovirus
           3e]
 gi|133722125|gb|ABO37247.1| hypothetical protein [Heliothis virescens ascovirus 3e]
          Length = 597

 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 15/100 (15%), Positives = 34/100 (34%), Gaps = 2/100 (2%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN--LASNV 314
                   +++ R R    S V        K+ +++  +++ +       RR     S  
Sbjct: 306 RTKSPARRQSVARSRSRSKSPVRKTTRSRTKSPARRQSVARSRSRTKSPARRQSVARSRS 365

Query: 315 WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                     ++ S  R ++  R  S    RS  ++ A++
Sbjct: 366 RSKSPARRQSVARSRSRSKSPARRQSVAKSRSRSKSPARR 405



 Score = 37.5 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 11/104 (10%), Positives = 27/104 (25%), Gaps = 1/104 (0%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               ++     +   S                    R +  +  ++      +  +    
Sbjct: 304 KSRTKSPARRQSVARSRSRSKSPVRKTTRSRTKSPARRQSVARSRSRTKSPARRQSVARS 363

Query: 308 RNL-ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
           R+   S         S   S S  R ++  +S S     + R++
Sbjct: 364 RSRSKSPARRQSVARSRSRSKSPARRQSVAKSRSRSKSPARRQS 407



 Score = 35.9 bits (81), Expect = 10.0,   Method: Composition-based stats.
 Identities = 13/115 (11%), Positives = 30/115 (26%), Gaps = 2/115 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+         ++    +           +    S          ++ S+       +  
Sbjct: 275 RKYRRIKTPARSRSRSRSNSVGRRRTTAVKSRTKSPARRQSVARSRSRSKSPVRKTTRSR 334

Query: 302 ATPVHRRN--LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                RR     S            ++ S  R ++  R  S    RS  ++ A++
Sbjct: 335 TKSPARRQSVARSRSRTKSPARRQSVARSRSRSKSPARRQSVARSRSRSKSPARR 389


>gi|254387915|ref|ZP_05003152.1| bifunctional glyoxylate cycle protein [Streptomyces clavuligerus
           ATCC 27064]
 gi|197701639|gb|EDY47451.1| bifunctional glyoxylate cycle protein [Streptomyces clavuligerus
           ATCC 27064]
          Length = 824

 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 19/133 (14%), Positives = 34/133 (25%), Gaps = 10/133 (7%)

Query: 226 GTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD---- 281
           G L  G+ R  +    R +L P        + +A       + R  P  +          
Sbjct: 66  GGLPPGAERHGAGDRARTRLRPVRRSAVDGDRNAGPRPGPGVRRGDPRPVPGAAAGLQLL 125

Query: 282 -----FTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR 336
                  R  +   ++                     +   + + S      G R +   
Sbjct: 126 PVLQLEGRPGRRPDRQVPARAGGDGVPVPVHHPRRVPLPQPRHVRSRPRL-RGARHDRLC 184

Query: 337 RSPSFPSKRSLRR 349
           R P    +R  RR
Sbjct: 185 RPPGAGVRRPGRR 197


>gi|83951704|ref|ZP_00960436.1| ATP-dependent RNA helicase, DEAD/DEAH box family protein
           [Roseovarius nubinhibens ISM]
 gi|83836710|gb|EAP76007.1| ATP-dependent RNA helicase, DEAD/DEAH box family protein
           [Roseovarius nubinhibens ISM]
          Length = 786

 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 12/110 (10%), Positives = 23/110 (20%), Gaps = 1/110 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G    + +      P          +P+             K   +  G    K    P 
Sbjct: 675 GKPAGKPSGKPGGKPSGKFGDKPGGKPSGKPGGKPAGKSFGKAEGKPAGKPAGKPAGKPA 734

Query: 306 HRRNLASNVWMAKGIHSSFLSD-SGQREENHRRSPSFPSKRSLRRTSAKK 354
            +         A+    +          +   R P  P  R       ++
Sbjct: 735 GKPGAKPAAKPARDGRDTSKRFTPPGGLKPGARQPRKPGSRPGGGEPPRR 784


>gi|119888778|ref|XP_001252332.1| PREDICTED: serine/arginine repetitive matrix 1 isoform 1 [Bos
           taurus]
 gi|297472235|ref|XP_002685753.1| PREDICTED: serine/arginine repetitive matrix 1 [Bos taurus]
 gi|296490065|gb|DAA32178.1| serine/arginine repetitive matrix 1 [Bos taurus]
          Length = 915

 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 14/105 (13%), Positives = 28/105 (26%), Gaps = 2/105 (1%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
           ++        P   + +         S  P    R+  +   K   S   K  +P     
Sbjct: 612 IQRRYSPSPPPKRRTASPPPPPKRRASPSPPPKRRVSHSPPPKQRSSPVTKRRSPSLSSK 671

Query: 310 LASNVWMAKGIHSSFLSDSGQR--EENHRRSPSFPSKRSLRRTSA 352
                  ++    +      +R       R+P   S    RR ++
Sbjct: 672 HRKGSSPSRSAREARSPQPNKRHSPSPRPRAPQTSSPPPARRGAS 716



 Score = 37.5 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 12/113 (10%), Positives = 29/113 (25%), Gaps = 4/113 (3%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R        +    +   P     +        +S  P    R    + +++     K  
Sbjct: 614 RRYSPSPPPKRRTASPPPPPKRRASPSPPPKRRVSHSPPPKQRSSPVTKRRSPSLSSKHR 673

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                 R+       A+    +       R    + S   P++R    +  ++
Sbjct: 674 KGSSPSRS----AREARSPQPNKRHSPSPRPRAPQTSSPPPARRGASLSPQRR 722


>gi|318061483|ref|ZP_07980204.1| hypothetical protein SSA3_26313 [Streptomyces sp. SA3_actG]
          Length = 683

 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 13/119 (10%), Positives = 28/119 (23%), Gaps = 2/119 (1%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             R +    L +  G  L +  +      I  +    R              ++ K++ +
Sbjct: 326 EARTLLGDALAKTAGKRLRKRRKSLAPPIISKTGKKRRKEKPAPPPPRGVLDKVVKDTPK 385

Query: 292 KNG--LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                             R    +            + +     +   +P  P  RS R
Sbjct: 386 PPPTMPRAGAAKKKSAGGRRRKWSFRKVFRKRPKKNTGATTGPGSAGTAPGSPGSRSRR 444


>gi|301788240|ref|XP_002929538.1| PREDICTED: PHD and RING finger domain-containing protein 1-like
            [Ailuropoda melanoleuca]
          Length = 1645

 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 13/77 (16%), Positives = 20/77 (25%), Gaps = 8/77 (10%)

Query: 286  KKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIH--------SSFLSDSGQREENHRR 337
               SS + G   +         ++     W                  S S +R     +
Sbjct: 1129 SPPSSLERGRRHRHPREKSPREKSPRERSWEQPRARWGSHERRKRRSRSPSTERRSREHQ 1188

Query: 338  SPSFPSKRSLRRTSAKK 354
             P    KR   R+  KK
Sbjct: 1189 RPRSHEKRPRPRSPEKK 1205


>gi|153812992|ref|ZP_01965660.1| hypothetical protein RUMOBE_03399 [Ruminococcus obeum ATCC 29174]
 gi|149830939|gb|EDM86029.1| hypothetical protein RUMOBE_03399 [Ruminococcus obeum ATCC 29174]
          Length = 893

 Score = 38.6 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 7/109 (6%), Positives = 20/109 (18%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
              E   P  + +A    +              N   +   +    + +     G   + 
Sbjct: 83  ETPETKKPTEIRQAAPVQNNSARPQRQEQSGYNNNRGQNRQNNRDGRDSGRDNRGGDNRG 142

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                   +  +           +   +   R +   R           
Sbjct: 143 NRDFRGGEKRFSDRNGNNGQGRPNRDGNRPARPQGEGRPARQGDGNGRP 191


>gi|115970763|ref|XP_001187475.1| PREDICTED: similar to PARD3 protein [Strongylocentrotus purpuratus]
          Length = 1510

 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 16/125 (12%), Positives = 33/125 (26%), Gaps = 6/125 (4%)

Query: 236  VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
            + K+  RE                    S+     +     E   D  R  +    +   
Sbjct: 1236 LDKQEKREGDEKERERRPNERRAEYASRSDRSTERKNPKRDEQRQDARRDDRYKDSRYDG 1295

Query: 296  SKQKKLATPVHRRNLASNVWMAK------GIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
             K ++       R+   +           G      S   ++     R   +P +R   R
Sbjct: 1296 RKDERHPEREGERDDRFDARRDDRYYDQDGGRRQEDSRRDRQPPREERHDKYPDQRDRYR 1355

Query: 350  TSAKK 354
            T+ ++
Sbjct: 1356 TAPQE 1360


>gi|296120279|ref|YP_003628057.1| nucleic acid binding OB-fold tRNA/helicase-type [Planctomyces
           limnophilus DSM 3776]
 gi|296012619|gb|ADG65858.1| nucleic acid binding OB-fold tRNA/helicase-type [Planctomyces
           limnophilus DSM 3776]
          Length = 377

 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 8/85 (9%), Positives = 13/85 (15%), Gaps = 3/85 (3%)

Query: 271 RPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW--MAKGIHSSFLSDS 328
                 + P                 +      P   R           +G         
Sbjct: 27  WAQPPGDDPRPAGDRPAGDRPGRPRPEGDNPDRPRPERGGPERGGPERPRGERPEGRGPE 86

Query: 329 GQREENHRRSPSFP-SKRSLRRTSA 352
           G+  E        P  +    R   
Sbjct: 87  GRGPEGRGPEGRGPEGRGPEGRGPE 111



 Score = 37.5 bits (85), Expect = 2.8,   Method: Composition-based stats.
 Identities = 11/102 (10%), Positives = 22/102 (21%), Gaps = 3/102 (2%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK-NGLSKQKKL--ATPVHRRNL 310
            +   + +++       RP       D   R +           ++       P   R  
Sbjct: 19  PLTGVSNVWAQPPGDDPRPAGDRPAGDRPGRPRPEGDNPDRPRPERGGPERGGPERPRGE 78

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                  +G         G+  E        P      +  A
Sbjct: 79  RPEGRGPEGRGPEGRGPEGRGPEGRGPEGRGPEGPHRPQGEA 120


>gi|289615697|emb|CBI57618.1| unnamed protein product [Sordaria macrospora]
          Length = 1139

 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 17/128 (13%), Positives = 37/128 (28%), Gaps = 11/128 (8%)

Query: 223  FQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDF 282
             +L  +  G   E   K LR++      E  +   +    ++           S      
Sbjct: 971  IELKDID-GEWHEFESKALRKENERKEREARRAVKEGAPATTAAPSGVSGGSSST----- 1024

Query: 283  TRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
               ++          + + A P  R +   ++  A        + S   ++  +R P   
Sbjct: 1025 ---REKDRDPRKRPAEGREAPPSERDSKRPHLDPAAATKPPTTTSSSAPQQ--QRGPERS 1079

Query: 343  SKRSLRRT 350
            S  +  R 
Sbjct: 1080 SVPTRPRG 1087


>gi|226323228|ref|ZP_03798746.1| hypothetical protein COPCOM_01000 [Coprococcus comes ATCC 27758]
 gi|225208418|gb|EEG90772.1| hypothetical protein COPCOM_01000 [Coprococcus comes ATCC 27758]
          Length = 876

 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 12/123 (9%), Positives = 24/123 (19%), Gaps = 5/123 (4%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            KK + +   P   +      +       +    RP                  +    +
Sbjct: 57  KKKNIVQVFRPQNSQGGGRGRNGQGRQQGSRNGQRPQGNGNGQGRPQGNGNRQERPQNGN 116

Query: 297 KQKKLATPVHRRNLASNVWMAK-----GIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
            Q +       R    N          G       +   R +   R        +  R  
Sbjct: 117 SQGRPQGNGQGRPQNGNRQERPQGNGNGQGRPQNGNRQDRPQGENRDNRQRRNPNGPRNG 176

Query: 352 AKK 354
             +
Sbjct: 177 QDQ 179



 Score = 37.9 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 8/97 (8%), Positives = 18/97 (18%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G    +      + P   +                +     + +    G  +        
Sbjct: 98  GQGRPQGNGNRQERPQNGNSQGRPQGNGQGRPQNGNRQERPQGNGNGQGRPQNGNRQDRP 157

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
              N  +          +       R  + RR   F 
Sbjct: 158 QGENRDNRQRRNPNGPRNGQDQRQGRPGDGRRDGGFQ 194


>gi|295839931|ref|ZP_06826864.1| ribosomal protein S4 [Streptomyces sp. SPB74]
 gi|302517976|ref|ZP_07270318.1| ribosomal protein S4 [Streptomyces sp. SPB78]
 gi|318057087|ref|ZP_07975810.1| 30S ribosomal protein S4 [Streptomyces sp. SA3_actG]
 gi|318077859|ref|ZP_07985191.1| 30S ribosomal protein S4 [Streptomyces sp. SA3_actF]
 gi|333028346|ref|ZP_08456410.1| putative 30S ribosomal protein S4 [Streptomyces sp. Tu6071]
 gi|197696761|gb|EDY43694.1| ribosomal protein S4 [Streptomyces sp. SPB74]
 gi|302426871|gb|EFK98686.1| ribosomal protein S4 [Streptomyces sp. SPB78]
 gi|332748198|gb|EGJ78639.1| putative 30S ribosomal protein S4 [Streptomyces sp. Tu6071]
          Length = 204

 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 3/50 (6%)

Query: 15  RVSKVIARAGIASRR--EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R+GIA R   +  +M+    ++VNG  +++ +  V   D + V
Sbjct: 93  RLDALVLRSGIA-RTIYQARQMVVHGHIEVNGTKVDKPSFRVRPDDVVMV 141


>gi|302518014|ref|ZP_07270356.1| serine/threonine protein kinase [Streptomyces sp. SPB78]
 gi|302426909|gb|EFK98724.1| serine/threonine protein kinase [Streptomyces sp. SPB78]
          Length = 446

 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 14/142 (9%), Positives = 29/142 (20%), Gaps = 19/142 (13%)

Query: 229 LAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
             GSTR   ++ + E+    L E+           +      R    +       R ++ 
Sbjct: 277 HPGSTRGPGQREVIERPTGRLAEQYAEQATQQRPVTPAPRGRRRPETAAPAQAQPRGERP 336

Query: 289 SSQKNGLS-------------------KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSG 329
           +S + G                            P      +                + 
Sbjct: 337 ASAREGRPLPGGSGAGRGARRPGPGTQGGGPETRPSQGAERSPVAGRPPRATGGQRRPAA 396

Query: 330 QREENHRRSPSFPSKRSLRRTS 351
            R     R+ +           
Sbjct: 397 SRTGGTARTGARTGTGRRPANP 418


>gi|239944067|ref|ZP_04696004.1| membrane translocator [Streptomyces roseosporus NRRL 15998]
          Length = 609

 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 15/130 (11%), Positives = 31/130 (23%), Gaps = 9/130 (6%)

Query: 234 REVSK----KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPN-IISEVPDDFTRMKKN 288
           R +      + +               L A + S +   R  P                 
Sbjct: 422 RYLRPDARDREIAAMADAVGTRSTWNTLLARLGSLDAESRTGPALPGRTAARRPRPRLSR 481

Query: 289 SSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLS----DSGQREENHRRSPSFPSK 344
            +      +  + A P  R    + V    G              +R +     P+ P +
Sbjct: 482 RTAAADPRRGHQPARPGRRDPRRAGVRRPAGRAGRRRPPDRLGPPRRPDPGDGRPAHPVR 541

Query: 345 RSLRRTSAKK 354
              R  + ++
Sbjct: 542 HPRRTPAYQR 551


>gi|74221393|dbj|BAE42172.1| unnamed protein product [Mus musculus]
          Length = 745

 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 16/102 (15%), Positives = 29/102 (28%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P      +++      +       R    S  P       ++ + K G S+ +      H
Sbjct: 443 PAPGSRREISSSPTSKNRSHGRAKRDKSHSHTPSHRAGRSRSPATKRGRSRSRTPTKRGH 502

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
            R+ +     ++       S S QR    R        RS  
Sbjct: 503 SRSRSPQWRRSRSAQRWGKSRSPQRRGRSRSPQRPGWSRSRN 544



 Score = 36.7 bits (83), Expect = 5.9,   Method: Composition-based stats.
 Identities = 14/113 (12%), Positives = 33/113 (29%), Gaps = 2/113 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +         +      P  +  +      +  S+        +  S       +  +  
Sbjct: 424 QPTKVSRHASSSPESLKPTPAPGSRREISSSPTSKNRSHGRAKRDKSHSHTPSHRAGRSR 483

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR--SPSFPSKRSLRRTSAK 353
           +P  +R  + +    K  HS   S   +R  + +R      P +R   R+  +
Sbjct: 484 SPATKRGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGKSRSPQRRGRSRSPQR 536



 Score = 36.3 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 14/98 (14%), Positives = 31/98 (31%), Gaps = 2/98 (2%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
             A  +      + R    S     ++R +    +    S ++  +          +   
Sbjct: 514 RSAQRWGKSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGRSHSRSPATRGRSRSR 573

Query: 317 AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                    S +  R  +  R+P+   +RS  RT A++
Sbjct: 574 TPARRGRSRSRTPARRRSRSRTPAR--RRSRSRTPARR 609



 Score = 36.3 bits (82), Expect = 8.2,   Method: Composition-based stats.
 Identities = 9/107 (8%), Positives = 18/107 (16%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                 +              R                 ++  +      +        R
Sbjct: 493 RSRTPTKRGHSRSRSPQWRRSRSAQRWGKSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSR 552

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                                        RS +   +RS  RT A++
Sbjct: 553 SARRGRSHSRSPATRGRSRSRTPARRGRSRSRTPARRRSRSRTPARR 599


>gi|330470647|ref|YP_004408390.1| hypothetical protein VAB18032_03530 [Verrucosispora maris
           AB-18-032]
 gi|328813618|gb|AEB47790.1| hypothetical protein VAB18032_03530 [Verrucosispora maris
           AB-18-032]
          Length = 576

 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 14/106 (13%), Positives = 22/106 (20%), Gaps = 2/106 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R         +       P     +L   R       P     +    +   G       
Sbjct: 425 RLPGSTAPSGQRGAASGRPAAPPPSLGGQRGATPGTPPKAGGPLGSRPATPPGGRASGPG 484

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
           A     R   S          +  +  G      R +P+ P  R  
Sbjct: 485 AKGSAGRPDLS--GRTGAARPAPATGPGPSLSGRRGAPAAPGARKG 528


>gi|115893502|ref|XP_785679.2| PREDICTED: similar to PARD3 protein, partial [Strongylocentrotus
            purpuratus]
          Length = 1508

 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 16/125 (12%), Positives = 33/125 (26%), Gaps = 6/125 (4%)

Query: 236  VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
            + K+  RE                    S+     +     E   D  R  +    +   
Sbjct: 1234 LDKQEKREGDEKERERRPNERRAEYASRSDRSTERKNPKRDEQRQDARRDDRYKDSRYDG 1293

Query: 296  SKQKKLATPVHRRNLASNVWMAK------GIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
             K ++       R+   +           G      S   ++     R   +P +R   R
Sbjct: 1294 RKDERHPEREGERDDRFDARRDDRYYDQDGGRRQEDSRRDRQPPREERHDKYPDQRDRYR 1353

Query: 350  TSAKK 354
            T+ ++
Sbjct: 1354 TAPQE 1358


>gi|229462763|sp|Q04118|PRB3_HUMAN RecName: Full=Basic salivary proline-rich protein 3; AltName:
           Full=Parotid salivary glycoprotein G1; AltName:
           Full=Proline-rich protein G1; Flags: Precursor
 gi|64653170|gb|AAH96210.1| PRB3 protein [Homo sapiens]
 gi|64654760|gb|AAH96209.1| PRB3 protein [Homo sapiens]
          Length = 309

 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 9/112 (8%), Positives = 22/112 (19%), Gaps = 2/112 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           + L   + +E   ++ +                +  P      +             +  
Sbjct: 17  QSLNEDVSQEESPSVISGKPEGRRPQGGNQPQRTPPPPGKPEGRPPQGGNQSQGPPPRPG 76

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            P        N               GQ  +   +S   P +         +
Sbjct: 77  KPEGPPPQGGNQSQGPPPRP--GKPEGQPPQGGNQSQGPPPRPGKPEGPPPQ 126



 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 11/124 (8%), Positives = 22/124 (17%), Gaps = 6/124 (4%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           E S  ++  +      +        P    +   R                K       G
Sbjct: 26  EESPSVISGKPEGRRPQGGNQPQRTPPPPGKPEGRPPQGGNQSQGPPPRPGKPEGPPPQG 85

Query: 295 ----LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                    +   P  +     N               G   +   +S   P +      
Sbjct: 86  GNQSQGPPPRPGKPEGQPPQGGNQSQGPPPRP--GKPEGPPPQGGNQSQGPPPRPGKPEG 143

Query: 351 SAKK 354
              +
Sbjct: 144 PPPQ 147



 Score = 36.7 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 6/104 (5%), Positives = 13/104 (12%), Gaps = 2/104 (1%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           +                     +                          +   P      
Sbjct: 130 QSQGPPPRPGKPEGPPPQGGNQSQGPPPHPGKPEGPPPQGGNQSQGPPPRPGKPEGPPPQ 189

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             N               G   +   +S   P +      S  +
Sbjct: 190 GGNQSQGPPPRP--GKPEGPPPQGGNQSQGPPPRPGKPEGSPSQ 231


>gi|309358637|emb|CAP33963.2| hypothetical protein CBG_15796 [Caenorhabditis briggsae AF16]
          Length = 881

 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 11/126 (8%), Positives = 34/126 (26%), Gaps = 13/126 (10%)

Query: 221 GPFQLGTLLAGSTREV-------------SKKILREQLGPHLLEEAQVNLDAPIYSSETL 267
           G  +L  L     +++               K  + +     +E+ +      +   + +
Sbjct: 279 GTIRLKALKPEKYQKLVDLAKSRGKLKSEDVKAEKSEKPEKPVEKIEKIDKPVVEKLKPV 338

Query: 268 VRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSD 327
            +       +     ++ +K    +     +KK   P   ++   +              
Sbjct: 339 EKSSEKSTDKRDRPSSKSEKPEKPERSERSEKKSERPPSGKSDRRSSERPSERPEKKPEK 398

Query: 328 SGQREE 333
             +R E
Sbjct: 399 PSKRPE 404


>gi|117306167|ref|NP_006240.4| basic salivary proline-rich protein 3 precursor [Homo sapiens]
          Length = 309

 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 9/112 (8%), Positives = 22/112 (19%), Gaps = 2/112 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           + L   + +E   ++ +                +  P      +             +  
Sbjct: 17  QSLNEDVSQEESPSVISGKPEGRRPQGGNQPQRTPPPPGKPEGRPPQGGNQSQGPPPRPG 76

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            P        N               GQ  +   +S   P +         +
Sbjct: 77  KPEGPPPQGGNQSQGPPPRP--GKPEGQPPQGGNQSQGPPPRPGKPEGPPPQ 126



 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 11/124 (8%), Positives = 22/124 (17%), Gaps = 6/124 (4%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           E S  ++  +      +        P    +   R                K       G
Sbjct: 26  EESPSVISGKPEGRRPQGGNQPQRTPPPPGKPEGRPPQGGNQSQGPPPRPGKPEGPPPQG 85

Query: 295 ----LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                    +   P  +     N               G   +   +S   P +      
Sbjct: 86  GNQSQGPPPRPGKPEGQPPQGGNQSQGPPPRP--GKPEGPPPQGGNQSQGPPPRPGKPEG 143

Query: 351 SAKK 354
              +
Sbjct: 144 PPPQ 147



 Score = 36.7 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 5/104 (4%), Positives = 13/104 (12%), Gaps = 2/104 (1%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           +                     +            +             +   P      
Sbjct: 67  QSQGPPPRPGKPEGPPPQGGNQSQGPPPRPGKPEGQPPQGGNQSQGPPPRPGKPEGPPPQ 126

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             N               G   +   +S   P +         +
Sbjct: 127 GGNQSQGPPPRP--GKPEGPPPQGGNQSQGPPPRPGKPEGPPPQ 168


>gi|261335063|emb|CBH18057.1| hypothetical protein, conserved [Trypanosoma brucei gambiense
           DAL972]
          Length = 672

 Score = 38.6 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 7/74 (9%), Positives = 18/74 (24%)

Query: 275 ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREEN 334
             ++        + +  +       K      +    S    A     S  S S +R  +
Sbjct: 456 GRKLRRADEGSPEAAGAQRRGRSTTKTKGGKQKTRQKSRGSSATPRRPSRKSSSKRRNRS 515

Query: 335 HRRSPSFPSKRSLR 348
             +  +    +   
Sbjct: 516 GSKRRNRSGSKRRN 529


>gi|303289291|ref|XP_003063933.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226454249|gb|EEH51555.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 126

 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 34/125 (27%), Positives = 55/125 (44%), Gaps = 16/125 (12%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
             VGRLD +++GL+LLT+DG +   L  P+ +  + Y V       +++L  L+ G+VI+
Sbjct: 2   FPVGRLDRDSDGLVLLTDDGRVPDALLDPTRKATKTYHVDVRPAPSEEELRRLRGGVVIE 61

Query: 169 -----GICYGDMQVTLDTQKG-----------SNAWVTVGLREGKNREIKKVFEFFNWKV 212
                G            +              N    +   EG+NR+I+K+ E     V
Sbjct: 62  TTQQRGGVSTTAPTVRARRGDSLSNPTRQRGLPNHIARIRDAEGRNRQIRKMCEAIGVDV 121

Query: 213 NRLIR 217
            RL R
Sbjct: 122 LRLRR 126


>gi|183232752|ref|XP_652896.2| hypothetical protein [Entamoeba histolytica HM-1:IMSS]
 gi|169801900|gb|EAL47510.2| hypothetical protein EHI_059870 [Entamoeba histolytica HM-1:IMSS]
          Length = 867

 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 9/107 (8%), Positives = 15/107 (14%), Gaps = 7/107 (6%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ-------KKLATPV 305
                        T    R            R       +    ++              
Sbjct: 354 MAAIAARANRGGSTPHPTRGAPAPRGMPSRGRGGMMPPTQAPEPEEQETPVMHTAPQGMP 413

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            R + A       G   +             R     + R   R   
Sbjct: 414 PRGSPAPRGMPRGGPRGAPRGAPRGAPRGAPRGAPRGAPRGAPRGRG 460


>gi|122889864|emb|CAM14855.1| serine/arginine repetitive matrix 1 [Mus musculus]
 gi|123252129|emb|CAM21198.1| serine/arginine repetitive matrix 1 [Mus musculus]
          Length = 909

 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 12/101 (11%), Positives = 28/101 (27%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
           +         +S      R    S  P           Q++    +++  +   +    S
Sbjct: 610 SPSPPPKRRTASPPPPPKRRASPSPPPKRRVSHSPPPKQRSPTVTKRRSPSLSSKHRKGS 669

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +   +     S   +         R+P   S   +RR ++ 
Sbjct: 670 SPGRSTREARSPQPNKRHSPSPRPRAPQTSSPPPVRRGASA 710


>gi|148698040|gb|EDL29987.1| serine/arginine repetitive matrix 1, isoform CRA_c [Mus musculus]
          Length = 904

 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 12/101 (11%), Positives = 28/101 (27%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
           +         +S      R    S  P           Q++    +++  +   +    S
Sbjct: 631 SPSPPPKRRTASPPPPPKRRASPSPPPKRRVSHSPPPKQRSPTVTKRRSPSLSSKHRKGS 690

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +   +     S   +         R+P   S   +RR ++ 
Sbjct: 691 SPGRSTREARSPQPNKRHSPSPRPRAPQTSSPPPVRRGASA 731


>gi|221506559|gb|EEE32176.1| hypothetical protein TGVEG_073220 [Toxoplasma gondii VEG]
          Length = 2218

 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 16/113 (14%), Positives = 30/113 (26%)

Query: 241  LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
            LRE       +       +    +E+   +R   +       +  ++ SSQ+        
Sbjct: 1559 LREADRASRSQSRGPERPSGGGLAESRKGERRRHLLSPLRPESPERRPSSQRRLRESDDG 1618

Query: 301  LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                  R         +         DS  R    RR  +   +   RR   +
Sbjct: 1619 EDAREGRSAFPRGRSRSFSGSRGEEKDSASRPGTLRRERAESGEERGRRGKQR 1671


>gi|254383598|ref|ZP_04998948.1| 30S ribosomal protein S4 [Streptomyces sp. Mg1]
 gi|194342493|gb|EDX23459.1| 30S ribosomal protein S4 [Streptomyces sp. Mg1]
          Length = 203

 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 3/50 (6%)

Query: 15  RVSKVIARAGIASRR--EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R+GIA R   +  +M+    ++VNG  +++ +  V   D I V
Sbjct: 92  RLDALVLRSGIA-RTIYQARQMVVHGHIEVNGDKVDKPSFRVRPDDVITV 140


>gi|91224087|ref|ZP_01259350.1| ATP-dependent RNA helicase RhlE [Vibrio alginolyticus 12G01]
 gi|91190998|gb|EAS77264.1| ATP-dependent RNA helicase RhlE [Vibrio alginolyticus 12G01]
          Length = 517

 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 5/107 (4%), Positives = 25/107 (23%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                 +        +     + +         +     +  + K   +++ +       
Sbjct: 403 APNAAGENAPATEKKAGNGANKPKRRFNGGNNGNKNSTNQGGAGKPKGNREGQGRANSKP 462

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +   N     G   +        + +  R P+       + +  ++
Sbjct: 463 DDRKPNGNKPNGNKPNGNKSGNAGKPSGNRKPNNAKPAGNKPSGQRR 509


>gi|24584968|ref|NP_609877.2| nucampholin [Drosophila melanogaster]
 gi|74869383|sp|Q9VJ87|CWC22_DROME RecName: Full=Pre-mRNA-splicing factor CWC22 homolog; AltName:
            Full=Nucampholin
 gi|22946749|gb|AAF53667.3| nucampholin [Drosophila melanogaster]
 gi|261260015|gb|ACX54942.1| LD29051p [Drosophila melanogaster]
          Length = 1330

 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 10/102 (9%), Positives = 22/102 (21%)

Query: 241  LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
            +RE   P          +      +   R+  +   E  D   R  +      G    + 
Sbjct: 1211 IRENSAPREKRMESSRSEKDSRRGDRSSRNERSDRGERSDRGERSDRGERSDRGERSDRG 1270

Query: 301  LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
              +    R+                    + +   +R     
Sbjct: 1271 ERSDRGERSDREKERSRAKERERDRDRDLKGQRERKRERDDG 1312


>gi|321468839|gb|EFX79822.1| hypothetical protein DAPPUDRAFT_224986 [Daphnia pulex]
          Length = 724

 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 12/113 (10%), Positives = 28/113 (24%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +E+       +++ +  +                 +   + +R    S ++     +  +
Sbjct: 232 KEESKKPTKTDSKADNVSAKSHLGARPHADDRRTRKTETNESRRSHPSPKRRKSRSRSPI 291

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                 R   S             S S  R   + R  S       R  +  K
Sbjct: 292 GRRPLSRRSRSRSPPRNRARIRPRSRSPARSPPYHRKRSRSPAIQKRPATPPK 344



 Score = 36.3 bits (82), Expect = 6.4,   Method: Composition-based stats.
 Identities = 14/111 (12%), Positives = 31/111 (27%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           + +  P   EE++        +     +          D  TR  + +  +      K+ 
Sbjct: 224 KTESKPRAKEESKKPTKTDSKADNVSAKSHLGARPHADDRRTRKTETNESRRSHPSPKRR 283

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            +          +       S   + +  R  +   + S P  R   R+ A
Sbjct: 284 KSRSRSPIGRRPLSRRSRSRSPPRNRARIRPRSRSPARSPPYHRKRSRSPA 334


>gi|195490501|ref|XP_002093167.1| GE20934 [Drosophila yakuba]
 gi|194179268|gb|EDW92879.1| GE20934 [Drosophila yakuba]
          Length = 1080

 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 19/121 (15%), Positives = 41/121 (33%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R++SK     +    L E  + N        +     + +   +   D  R K+    K 
Sbjct: 564 RQLSKDRQLSKDRQGLKERQRSNERKRSKERQHSKDRQRSRERQPSKDRQRSKERQRSKE 623

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               + +  +   +R+        +   S     S  R++  +RSP+  S++    T   
Sbjct: 624 PQQSKDRQRSKERQRSRERPAKEPRPTRSPRERSSKTRDDRRQRSPTNASRKRQDDTKLS 683

Query: 354 K 354
           +
Sbjct: 684 R 684


>gi|94309947|ref|YP_583157.1| RNA-binding S4 [Cupriavidus metallidurans CH34]
 gi|93353799|gb|ABF07888.1| ribosome-associated heat shock protein [Cupriavidus metallidurans
          CH34]
          Length = 131

 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 5/61 (8%)

Query: 7  VQENFTPQ---RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          +Q +F P    R+ K +       +R      + + RV VNG   +  +  V   D + +
Sbjct: 1  MQVDFEPDARLRIDKWLWCARFFKTRSLAAEAVERGRVSVNGQPCKN-SREVKPGDTVIL 59

Query: 63 D 63
          +
Sbjct: 60 E 60


>gi|298243962|ref|ZP_06967769.1| ribosomal protein S3 [Ktedonobacter racemifer DSM 44963]
 gi|297557016|gb|EFH90880.1| ribosomal protein S3 [Ktedonobacter racemifer DSM 44963]
          Length = 339

 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 11/82 (13%), Positives = 19/82 (23%)

Query: 272 PNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR 331
           P    E  +     ++      G   Q        R          +G            
Sbjct: 234 PTAPRESGERRPDRRRGEGGPRGQRPQGDRPRGGERPQRGPRPQGERGPRPQGDRPPRGP 293

Query: 332 EENHRRSPSFPSKRSLRRTSAK 353
                R+P    +R+ R  S +
Sbjct: 294 RPQGERAPRPQGERAPRPQSER 315


>gi|289768286|ref|ZP_06527664.1| conserved hypothetical protein [Streptomyces lividans TK24]
 gi|289698485|gb|EFD65914.1| conserved hypothetical protein [Streptomyces lividans TK24]
          Length = 215

 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 7/94 (7%), Positives = 16/94 (17%)

Query: 261 IYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGI 320
                  V    + +     +       S +    + Q     P  R    +      G 
Sbjct: 11  AMRVTVPVGPHASPVPGRGAERAPGSGRSGRARPRAGQSGGTRPPRRTVDRAEHDPIPGG 70

Query: 321 HSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                     +            +        K+
Sbjct: 71  RPRRNPAPDGQARRDPAPDGQAGRDPNPDGQPKR 104


>gi|187736374|ref|YP_001878486.1| hypothetical protein Amuc_1891 [Akkermansia muciniphila ATCC
           BAA-835]
 gi|187426426|gb|ACD05705.1| hypothetical protein Amuc_1891 [Akkermansia muciniphila ATCC
           BAA-835]
          Length = 295

 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 15/102 (14%), Positives = 25/102 (24%), Gaps = 7/102 (6%)

Query: 259 APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAK 318
            P+         RP+      +         +Q+    K   L  P       +      
Sbjct: 127 RPMAKPPMKPHFRPDHFRPGNNRPAPQPGRPNQRPDFGKPGNLQRPPAHHPGINQPGRPS 186

Query: 319 GIHSSFLSDSGQ-------REENHRRSPSFPSKRSLRRTSAK 353
              ++  S  G        R E +R S     + S   T   
Sbjct: 187 RPSANNPSRPGGTNRPVINRPEGNRPSRPDFGRPSRPSTLPS 228


>gi|3153821|gb|AAC17422.1| plenty-of-prolines-101 [Mus musculus]
          Length = 897

 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 12/101 (11%), Positives = 28/101 (27%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
           +         +S      R    S  P           Q++    +++  +   +    S
Sbjct: 624 SPSPPPKRRTASPPPPPKRRASPSPPPKRRVSHSPPPKQRSPTVTKRRSPSLSSKHRKGS 683

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +   +     S   +         R+P   S   +RR ++ 
Sbjct: 684 SPGRSTREARSPQPNKRHSPSPRPRAPQTSSPPPVRRGASA 724


>gi|296813299|ref|XP_002846987.1| conserved hypothetical protein [Arthroderma otae CBS 113480]
 gi|238842243|gb|EEQ31905.1| conserved hypothetical protein [Arthroderma otae CBS 113480]
          Length = 343

 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 10/69 (14%), Positives = 17/69 (24%), Gaps = 4/69 (5%)

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHS----SFLSDSGQREENHRRSPSFPSKR 345
           S   G SK         +   +     A G                   +R SP    + 
Sbjct: 27  SGAPGSSKPGSSKPGSSKPGSSKPGSGAPGGRPDESNGPGQPGSDAPAENRPSPGTSDEN 86

Query: 346 SLRRTSAKK 354
                S+++
Sbjct: 87  PRPGDSSRQ 95


>gi|118093099|ref|XP_421787.2| PREDICTED: similar to p167 [Gallus gallus]
          Length = 1505

 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 12/114 (10%), Positives = 24/114 (21%), Gaps = 1/114 (0%)

Query: 240  ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
              R+   P    +        +      +  R     +        +    ++ G   + 
Sbjct: 1054 EARDDERPFRRGDDLPRRSDDLPRRGDDLPRRGPAEEKERPSVESSEDRPPRREGDEDRP 1113

Query: 300  KLATPVHRRNLASNVWMAKGIHSSFLSDSGQ-REENHRRSPSFPSKRSLRRTSA 352
                    R L   +   +        D G  R  +  R P            A
Sbjct: 1114 PRREGDEDRPLRRGLDEDRPPRRGLDDDRGSWRAADDDRGPRRGMDDDRPPRRA 1167



 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 10/112 (8%), Positives = 23/112 (20%), Gaps = 6/112 (5%)

Query: 247  PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
            P   ++      A      ++            D+    ++   +   L +      P  
Sbjct: 1076 PRRGDDLPRRGPAEEKERPSVESSEDRPPRREGDEDRPPRREGDEDRPLRRGLDEDRPPR 1135

Query: 307  RR------NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            R       +  +                 +R  +  R P            A
Sbjct: 1136 RGLDDDRGSWRAADDDRGPRRGMDDDRPPRRALDDDRPPRRALDDDRPPRRA 1187



 Score = 36.3 bits (82), Expect = 7.3,   Method: Composition-based stats.
 Identities = 9/115 (7%), Positives = 22/115 (19%), Gaps = 4/115 (3%)

Query: 238  KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
                +E+      E+     +           D    +    D+    ++      G  +
Sbjct: 1087 PAEEKERPSVESSEDRPPRREGDEDRPPRREGDEDRPLRRGLDEDRPPRRGLDDDRGSWR 1146

Query: 298  QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                     R              +       +R  +  R P            +
Sbjct: 1147 AADDDRGPRRGMDDDR----PPRRALDDDRPPRRALDDDRPPRRALDDDRPPRRS 1197


>gi|291437153|ref|ZP_06576543.1| LOW QUALITY PROTEIN: glycogen branching enzyme [Streptomyces
           ghanaensis ATCC 14672]
 gi|291340048|gb|EFE67004.1| LOW QUALITY PROTEIN: glycogen branching enzyme [Streptomyces
           ghanaensis ATCC 14672]
          Length = 796

 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 13/119 (10%), Positives = 26/119 (21%), Gaps = 12/119 (10%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN---------GLSKQ 298
              E                 R R   +  V     R  +   ++          G +  
Sbjct: 80  AAAERHASRPALRARRPSGARRGRLPGVQAVRPGGDRGLRGPHRRAARRRRRVLLGPAAA 139

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP---SKRSLRRTSAKK 354
            +       R++  +    +G           R    RR P+       R     +  +
Sbjct: 140 ARGTGVPPARDVRGDGAGDRGRLPFPAHARRVRPAPDRRGPARGAVDGARRAPDDAPGR 198


>gi|194440682|ref|NP_058079.2| serine/arginine repetitive matrix protein 1 isoform 1 [Mus
           musculus]
          Length = 923

 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 12/101 (11%), Positives = 28/101 (27%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
           +         +S      R    S  P           Q++    +++  +   +    S
Sbjct: 624 SPSPPPKRRTASPPPPPKRRASPSPPPKRRVSHSPPPKQRSPTVTKRRSPSLSSKHRKGS 683

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +   +     S   +         R+P   S   +RR ++ 
Sbjct: 684 SPGRSTREARSPQPNKRHSPSPRPRAPQTSSPPPVRRGASA 724


>gi|194440687|ref|NP_001123949.1| serine/arginine repetitive matrix protein 1 isoform 2 [Mus
           musculus]
 gi|122889865|emb|CAM14856.1| serine/arginine repetitive matrix 1 [Mus musculus]
 gi|123252128|emb|CAM21197.1| serine/arginine repetitive matrix 1 [Mus musculus]
          Length = 918

 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 12/101 (11%), Positives = 28/101 (27%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
           +         +S      R    S  P           Q++    +++  +   +    S
Sbjct: 619 SPSPPPKRRTASPPPPPKRRASPSPPPKRRVSHSPPPKQRSPTVTKRRSPSLSSKHRKGS 678

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +   +     S   +         R+P   S   +RR ++ 
Sbjct: 679 SPGRSTREARSPQPNKRHSPSPRPRAPQTSSPPPVRRGASA 719


>gi|7388544|sp|Q9ZIM1|Y216_LISMO RecName: Full=Uncharacterized protein Lmo0216
 gi|328467972|gb|EGF38999.1| S4 domain protein [Listeria monocytogenes 1816]
          Length = 88

 Score = 38.6 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 14/78 (17%), Positives = 25/78 (32%), Gaps = 4/78 (5%)

Query: 14 QRVSKVIARAGIASRR-EVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
           R+ K +  + +  RR   + +  + R+ VNG+  +    NV S D   I      +   
Sbjct: 1  MRLDKYLKVSRLIKRRTVAKEVAEKGRIAVNGVTAK-PGTNVKSGDELVIRFGPKIVTAK 59

Query: 71 ERTRLWLYHKPIGLVTTH 88
                   K        
Sbjct: 60 IERLEENAKKEQATEMYT 77


>gi|256392312|ref|YP_003113876.1| hypothetical protein Caci_3126 [Catenulispora acidiphila DSM 44928]
 gi|256358538|gb|ACU72035.1| protein of unknown function DUF881 [Catenulispora acidiphila DSM
           44928]
          Length = 571

 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 15/119 (12%), Positives = 31/119 (26%), Gaps = 9/119 (7%)

Query: 241 LREQLGPHLLEEAQV------NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           LR+ L      E +                +   +                 ++SS+++ 
Sbjct: 162 LRDLLPESETPEDKAADSGESEPSREQEQEQEQEQSESAAGDPPSRSTPDESESSSEQDR 221

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               +  A     R          G H   +       E  RR P+   + + R  + +
Sbjct: 222 SEDSEPTAGEPPLRRRTPP---EPGEHDPAVRRRTGEGEPPRRRPAPGGQPARRPGAGQ 277


>gi|148698041|gb|EDL29988.1| serine/arginine repetitive matrix 1, isoform CRA_d [Mus musculus]
          Length = 927

 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 12/101 (11%), Positives = 28/101 (27%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
           +         +S      R    S  P           Q++    +++  +   +    S
Sbjct: 628 SPSPPPKRRTASPPPPPKRRASPSPPPKRRVSHSPPPKQRSPTVTKRRSPSLSSKHRKGS 687

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +   +     S   +         R+P   S   +RR ++ 
Sbjct: 688 SPGRSTREARSPQPNKRHSPSPRPRAPQTSSPPPVRRGASA 728


>gi|78358202|ref|YP_389651.1| translation initiation factor IF-2 [Desulfovibrio desulfuricans
           subsp. desulfuricans str. G20]
 gi|90101359|sp|Q30WJ0|IF2_DESDG RecName: Full=Translation initiation factor IF-2
 gi|78220607|gb|ABB39956.1| bacterial translation initiation factor 2 (bIF-2) [Desulfovibrio
           desulfuricans subsp. desulfuricans str. G20]
          Length = 984

 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 13/116 (11%), Positives = 28/116 (24%), Gaps = 3/116 (2%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIIS--EVPDDFTRMKKNSSQK 292
           EVS +  ++ +      +   +        +         +     PD      + ++  
Sbjct: 210 EVSMEPEKDSVQADTEADGDADGGRKKKKKKKREETAGPQVRVISRPDPAAVQAQAAAAA 269

Query: 293 NGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSG-QREENHRRSPSFPSKRSL 347
               ++ +      R   A       G      S  G  R      +P     R  
Sbjct: 270 QAREERAERPDRGPRPAGARPAGPRPGGPRQGDSRPGDGRPAPRSGAPRPGGARPA 325



 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 10/109 (9%), Positives = 24/109 (22%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E     +  + + + DA     +   + R           +R    + Q    +  +   
Sbjct: 214 EPEKDSVQADTEADGDADGGRKKKKKKKREETAGPQVRVISRPDPAAVQAQAAAAAQARE 273

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
               R +       A+                    P+  S       +
Sbjct: 274 ERAERPDRGPRPAGARPAGPRPGGPRQGDSRPGDGRPAPRSGAPRPGGA 322


>gi|262373548|ref|ZP_06066826.1| DEAD/DEAH box helicase [Acinetobacter junii SH205]
 gi|262311301|gb|EEY92387.1| DEAD/DEAH box helicase [Acinetobacter junii SH205]
          Length = 642

 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 13/104 (12%), Positives = 24/104 (23%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P     +    D P     +    R     + P      K    + +   + +      
Sbjct: 445 KPRGERPSFGGEDRPRREFNSDRPRREGGFEDRPRRNFDDKPRGERPSFGGEDRPRREFN 504

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
             R      +  +   +    D  +RE N  R           R
Sbjct: 505 SDRPRREGGFDDRPKRTFGGEDRPRREFNSDRPRREGGYNDKPR 548



 Score = 37.5 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 11/93 (11%), Positives = 24/93 (25%), Gaps = 1/93 (1%)

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
           +            R        +  +   ++  ++   S + +       R   +     
Sbjct: 427 NFKRRKGGDDRPRRSFDDKPRGERPSFGGEDRPRREFNSDRPRREGGFEDRPRRNFDDKP 486

Query: 318 KGIHSSFLS-DSGQREENHRRSPSFPSKRSLRR 349
           +G   SF   D  +RE N  R           +
Sbjct: 487 RGERPSFGGEDRPRREFNSDRPRREGGFDDRPK 519


>gi|294663004|ref|YP_003579825.1| ribosomal protein S4 [Dictyostelium citrinum]
 gi|162416159|sp|P0C5Y3|RT04_DICCI RecName: Full=Ribosomal protein S4, mitochondrial
 gi|187479911|gb|ACD12712.1| ribosomal protein S4 [Dictyostelium citrinum]
          Length = 325

 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 14/63 (22%), Positives = 29/63 (46%), Gaps = 5/63 (7%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRR--EVERMIAQQRVKVNGILLERAAVNVMSTDH 59
            +K I+Q+     R+  ++ R+G   R   E  ++I  + + VNG +    +  +   D 
Sbjct: 136 NEKIIIQQLEK--RIDMILLRSGFV-RSIYEARQLINHKHILVNGNIARIPSYTLNVGDI 192

Query: 60  IEV 62
           I +
Sbjct: 193 ISI 195


>gi|148698038|gb|EDL29985.1| serine/arginine repetitive matrix 1, isoform CRA_a [Mus musculus]
          Length = 897

 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 12/101 (11%), Positives = 28/101 (27%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
           +         +S      R    S  P           Q++    +++  +   +    S
Sbjct: 624 SPSPPPKRRTASPPPPPKRRASPSPPPKRRVSHSPPPKQRSPTVTKRRSPSLSSKHRKGS 683

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +   +     S   +         R+P   S   +RR ++ 
Sbjct: 684 SPGRSTREARSPQPNKRHSPSPRPRAPQTSSPPPVRRGASA 724


>gi|74710940|sp|Q6ZQP7|YV021_HUMAN RecName: Full=Uncharacterized protein LOC284861
          Length = 286

 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 12/104 (11%), Positives = 19/104 (18%), Gaps = 3/104 (2%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
                                P   S          + +      ++    A+P      
Sbjct: 100 ARTPPTESPARTPPTASPARTPPRASPTRTPPRASPRRTPSTASPTRTPPRASPRRTPPR 159

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           AS                       R  P     R+  R S K+
Sbjct: 160 ASPTRTPPRASPKRTPPRA---SPRRTPPRASPTRAPPRASPKR 200



 Score = 36.7 bits (83), Expect = 5.9,   Method: Composition-based stats.
 Identities = 14/114 (12%), Positives = 23/114 (20%), Gaps = 3/114 (2%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           L                              P   S      T     +  +   ++   
Sbjct: 72  LTRPPTRAPPTRMPPTAPPTRTPPTASPARTPPTESPARTPPTASPARTPPRASPTRTPP 131

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            A+P    + AS                       R  P    KR+  R S ++
Sbjct: 132 RASPRRTPSTASPTRTPPRASPRRTPPRA---SPTRTPPRASPKRTPPRASPRR 182



 Score = 36.3 bits (82), Expect = 6.7,   Method: Composition-based stats.
 Identities = 15/119 (12%), Positives = 23/119 (19%), Gaps = 6/119 (5%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R                          R  P   S          K +      ++    
Sbjct: 154 RRTPPRASPTRTPPRASPKRTPPRASPRRTPPRASPTRAPPRASPKRTPPTASPTRTPPR 213

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLS------DSGQREENHRRSPSFPSKRSLRRTSAKK 354
           A+P       S          +          +  R    R  P     R+  R S K+
Sbjct: 214 ASPTRTPPTESPARTPPRASPTRTPPTESPARTPSRASTRRTPPRASPTRTPPRASPKR 272


>gi|38344349|emb|CAD40171.2| OSJNBa0061A09.10 [Oryza sativa Japonica Group]
          Length = 1030

 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 6/97 (6%), Positives = 20/97 (20%)

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
            A   S E   +           + +  +   +  +             R          
Sbjct: 237 MAVGASEERAPKGHDGAGGSRRGEQSTPRGGRASGSRGRGPGSSRPADARGKRKQGGTPP 296

Query: 318 KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                   +     +     +P+   +   ++   +K
Sbjct: 297 PSPPRGGGAARASSKRPEGAAPASQPEGERKKKRPRK 333


>gi|256389503|ref|YP_003111067.1| hypothetical protein Caci_0273 [Catenulispora acidiphila DSM 44928]
 gi|256355729|gb|ACU69226.1| hypothetical protein Caci_0273 [Catenulispora acidiphila DSM 44928]
          Length = 492

 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 10/102 (9%), Positives = 27/102 (26%), Gaps = 1/102 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G     +       P        R  P     +  D ++  +   +     + + +    
Sbjct: 303 GWLRRGKPARGEQVPRTGGVAEPRKAPRRGEPLDADPSQRSRGPREPKAPRRGEPIDVDP 362

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            +R+       +     S  +   +R +   R+P    +   
Sbjct: 363 SQRSRRPPEAKSPRRDESGEAQRPRR-DPEPRAPRRGDRPDA 403



 Score = 37.5 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 7/117 (5%), Positives = 21/117 (17%), Gaps = 1/117 (0%)

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS-SQKNGLSK 297
           +  ++            +               P             +            
Sbjct: 284 RENKDARQAADSGPIAGSGGWLRRGKPARGEQVPRTGGVAEPRKAPRRGEPLDADPSQRS 343

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +        RR    +V  ++       + S +R+E+                   +
Sbjct: 344 RGPREPKAPRRGEPIDVDPSQRSRRPPEAKSPRRDESGEAQRPRRDPEPRAPRRGDR 400


>gi|221486863|gb|EEE25109.1| hypothetical protein TGGT1_008740 [Toxoplasma gondii GT1]
          Length = 2230

 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 16/113 (14%), Positives = 30/113 (26%)

Query: 241  LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
            LRE       +       +    +E+   +R   +       +  ++ SSQ+        
Sbjct: 1571 LREADRASRSQSRGPERPSGGGLAESRKGERRRHLLSPLRPESPERRPSSQRRLRESDDG 1630

Query: 301  LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                  R         +         DS  R    RR  +   +   RR   +
Sbjct: 1631 EDAREGRSAFPRGRSRSFSGSRGEEKDSASRPGTLRRERAESGEERGRRGKQR 1683


>gi|254443370|ref|ZP_05056846.1| DEAD/DEAH box helicase domain protein [Verrucomicrobiae bacterium
           DG1235]
 gi|198257678|gb|EDY81986.1| DEAD/DEAH box helicase domain protein [Verrucomicrobiae bacterium
           DG1235]
          Length = 469

 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 13/100 (13%), Positives = 22/100 (22%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
             E +  L       +  V               +   N  +    +  +         +
Sbjct: 347 CSEEEAYLVDIEKVLKREVPLFELSPRGKIGHQVQRIANPKKPKKTAVSRPPRQHPRPDS 406

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
             S          S  S   Q  ++  R    P  RS  R
Sbjct: 407 RHSGGSGKPSSRPSGKSSPRQAGKSSPRPAGRPGPRSADR 446



 Score = 36.7 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 7/96 (7%), Positives = 23/96 (23%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E++    +   +++    I      + +             R       ++     K  +
Sbjct: 358 EKVLKREVPLFELSPRGKIGHQVQRIANPKKPKKTAVSRPPRQHPRPDSRHSGGSGKPSS 417

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS 338
            P  + +       +          S  R +    +
Sbjct: 418 RPSGKSSPRQAGKSSPRPAGRPGPRSADRADGSASA 453


>gi|170742912|ref|YP_001771567.1| RNA-binding S4 domain-containing protein [Methylobacterium sp.
          4-46]
 gi|168197186|gb|ACA19133.1| RNA-binding S4 domain protein [Methylobacterium sp. 4-46]
          Length = 93

 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
             QR+ K +  A  A +R    R+IA   V+VNG   E A+  V   D
Sbjct: 3  DDRQRLDKWLWFARFAKTRSLAARLIADGYVRVNGQRAEAASKAVAVGD 51


>gi|281344859|gb|EFB20443.1| hypothetical protein PANDA_019725 [Ailuropoda melanoleuca]
          Length = 1578

 Score = 38.6 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 13/77 (16%), Positives = 20/77 (25%), Gaps = 8/77 (10%)

Query: 286  KKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIH--------SSFLSDSGQREENHRR 337
               SS + G   +         ++     W                  S S +R     +
Sbjct: 1063 SPPSSLERGRRHRHPREKSPREKSPRERSWEQPRARWGSHERRKRRSRSPSTERRSREHQ 1122

Query: 338  SPSFPSKRSLRRTSAKK 354
             P    KR   R+  KK
Sbjct: 1123 RPRSHEKRPRPRSPEKK 1139


>gi|296126890|ref|YP_003634142.1| ribosomal protein S4 [Brachyspira murdochii DSM 12563]
 gi|296018706|gb|ADG71943.1| ribosomal protein S4 [Brachyspira murdochii DSM 12563]
          Length = 208

 Score = 38.6 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 3/49 (6%)

Query: 22  RAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPL 67
           R G A SR +  + +A   + VNG  +   + ++   D I    +G  +
Sbjct: 106 RLGFAKSRNQARQFVAHGFISVNGKKMSIPSYSIKVGDKISFTENGNAI 154


>gi|119616636|gb|EAW96230.1| proline-rich protein BstNI subfamily 3 [Homo sapiens]
          Length = 309

 Score = 38.6 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 9/112 (8%), Positives = 22/112 (19%), Gaps = 2/112 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           + L   + +E   ++ +                +  P      +             +  
Sbjct: 17  QSLNEDVSQEESPSVISGKPEGRRPQGGNQPQRTPPPPGKPEGRPPQGGNQSQGPPPRPG 76

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            P        N               GQ  +   +S   P +         +
Sbjct: 77  KPEGPPPQGGNQSQGPPPRP--GKPEGQPPQGGNQSQGPPPRPGKPEGPPPQ 126



 Score = 37.5 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 11/124 (8%), Positives = 22/124 (17%), Gaps = 6/124 (4%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           E S  ++  +      +        P    +   R                K       G
Sbjct: 26  EESPSVISGKPEGRRPQGGNQPQRTPPPPGKPEGRPPQGGNQSQGPPPRPGKPEGPPPQG 85

Query: 295 ----LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                    +   P  +     N               G   +   +S   P +      
Sbjct: 86  GNQSQGPPPRPGKPEGQPPQGGNQSQGPPPRP--GKPEGPPPQGGNQSQGPPPRPGKPEG 143

Query: 351 SAKK 354
              +
Sbjct: 144 PPPQ 147



 Score = 37.1 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 6/104 (5%), Positives = 13/104 (12%), Gaps = 2/104 (1%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           +                     +                          +   P      
Sbjct: 130 QSQGPPPRPGKPEGPPPQGGNQSQGPPPRPGKPEGPPPQGGNQSQGPPPRPGKPEGPPPQ 189

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             N               G   +   +S   P +      S  +
Sbjct: 190 GGNQSQGPPPRP--GKPEGPPPQGGNQSQGPPPRPGKPEGSPSQ 231



 Score = 36.3 bits (82), Expect = 6.6,   Method: Composition-based stats.
 Identities = 5/104 (4%), Positives = 13/104 (12%), Gaps = 2/104 (1%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           +                     +            +             +   P      
Sbjct: 67  QSQGPPPRPGKPEGPPPQGGNQSQGPPPRPGKPEGQPPQGGNQSQGPPPRPGKPEGPPPQ 126

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             N               G   +   +S   P +         +
Sbjct: 127 GGNQSQGPPPRP--GKPEGPPPQGGNQSQGPPPRPGKPEGPPPQ 168



 Score = 36.3 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 5/104 (4%), Positives = 12/104 (11%), Gaps = 2/104 (1%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           +                     +                          +   P      
Sbjct: 109 QSQGPPPRPGKPEGPPPQGGNQSQGPPPRPGKPEGPPPQGGNQSQGPPPRPGKPEGPPPQ 168

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             N               G   +   +S   P +         +
Sbjct: 169 GGNQSQGPPPRP--GKPEGPPPQGGNQSQGPPPRPGKPEGPPPQ 210



 Score = 36.3 bits (82), Expect = 8.0,   Method: Composition-based stats.
 Identities = 5/104 (4%), Positives = 13/104 (12%), Gaps = 2/104 (1%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           +             +       +                          +   P      
Sbjct: 88  QSQGPPPRPGKPEGQPPQGGNQSQGPPPRPGKPEGPPPQGGNQSQGPPPRPGKPEGPPPQ 147

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             N               G   +   +S   P +         +
Sbjct: 148 GGNQSQGPPPRP--GKPEGPPPQGGNQSQGPPPRPGKPEGPPPQ 189


>gi|21355513|ref|NP_651272.1| CG13625 [Drosophila melanogaster]
 gi|7301183|gb|AAF56315.1| CG13625 [Drosophila melanogaster]
 gi|15010486|gb|AAK77291.1| GH07383p [Drosophila melanogaster]
 gi|220945000|gb|ACL85043.1| CG13625-PA [synthetic construct]
 gi|220954826|gb|ACL89956.1| CG13625-PA [synthetic construct]
          Length = 647

 Score = 38.6 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 7/106 (6%), Positives = 26/106 (24%)

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
                +          +    D+              ++  S ++   +++  +     R
Sbjct: 208 QSPPRKARNGNQSPVRKRRDSDQSPPRKRTGKASPTRRRRDSDQSPPRRRRSNSDQSPPR 267

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                                +R +   +SP    ++   ++  +K
Sbjct: 268 RRRDKDSTPPRRRKDSDQSPPRRRKADDQSPVRRERKDSDQSPPRK 313



 Score = 36.3 bits (82), Expect = 6.8,   Method: Composition-based stats.
 Identities = 11/105 (10%), Positives = 32/105 (30%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R + G       +          +    ++  +      D +  +K + + +   +++  
Sbjct: 190 RGRDGDQSPPRQKHRDSDQSPPRKARNGNQSPVRKRRDSDQSPPRKRTGKASPTRRRRDS 249

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
                RR  +++            S   +R ++  +SP    K  
Sbjct: 250 DQSPPRRRRSNSDQSPPRRRRDKDSTPPRRRKDSDQSPPRRRKAD 294



 Score = 35.9 bits (81), Expect = 9.2,   Method: Composition-based stats.
 Identities = 14/108 (12%), Positives = 32/108 (29%), Gaps = 2/108 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           ++            +        +   +  P    +      R +++S Q     ++   
Sbjct: 281 KDSDQSPPRRRKADDQSPVRRERKDSDQSPPRKRRDNDQSPVRRRRDSDQSPPRRRRDDK 340

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
            TP  RR  +                  +R+ +  +SP+    +S RR
Sbjct: 341 QTPPRRRRNSDQS--PPRRPKDVDQSPPRRKRDFDQSPTRKRDKSPRR 386


>gi|127511538|ref|YP_001092735.1| DEAD/DEAH box helicase domain-containing protein [Shewanella
           loihica PV-4]
 gi|126636833|gb|ABO22476.1| DEAD/DEAH box helicase domain protein [Shewanella loihica PV-4]
          Length = 491

 Score = 38.6 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 12/116 (10%), Positives = 28/116 (24%), Gaps = 3/116 (2%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           + +  +      H L E  +                 +      +  +  +++       
Sbjct: 366 LPRAEVEGFEPTHTLPETNLTPKRHGQHKGPRNPKPKSNSQRSSNRSSNGQRSDKAGQPR 425

Query: 296 S---KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                Q        RR  AS              + G++E     +P+   +R   
Sbjct: 426 RGDQAQGNKEGQGRRRTGASTGTSKPASEGQQAQNQGKQEHRDGNAPARRRRRRRP 481


>gi|269838860|gb|ACZ48692.1| circumsporozoite protein [Plasmodium yoelii yoelii]
          Length = 408

 Score = 38.2 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 9/95 (9%), Positives = 16/95 (16%), Gaps = 1/95 (1%)

Query: 259 APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP-VHRRNLASNVWMA 317
           A    ++ +V D                +      G    +    P              
Sbjct: 114 AQNKLNQPVVADENVDQGPGAPQGPGAPQGPGAPQGPGAPQGPGAPQGPGAPQGPGAPQG 173

Query: 318 KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            G      +  G        +P  P          
Sbjct: 174 PGAPQGPGAPQGPGAPQGPGAPQGPGAPQGPGAPQ 208


>gi|118462925|ref|YP_882261.1| hemolysin A [Mycobacterium avium 104]
 gi|118164212|gb|ABK65109.1| hemolysin A [Mycobacterium avium 104]
          Length = 269

 Score = 38.2 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 11/38 (28%), Positives = 20/38 (52%), Gaps = 1/38 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAA 51
          RV   + R G+A SR++   +I   RV ++G+   +  
Sbjct: 6  RVDAELVRRGLARSRQQAAELIGAGRVSIDGMPARKPG 43


>gi|64654299|gb|AAH96211.1| PRB3 protein [Homo sapiens]
          Length = 309

 Score = 38.2 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 9/112 (8%), Positives = 22/112 (19%), Gaps = 2/112 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           + L   + +E   ++ +                +  P      +             +  
Sbjct: 17  QSLNEDVSQEESPSVISGKPEGRRPQGGNQPQRTPPPPGKPEGRPPQGGNQSQGPPPRPG 76

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            P        N               GQ  +   +S   P +         +
Sbjct: 77  KPEGPPPQGGNQSQGPPPRP--GKPEGQPPQGGNQSQGPPPRPGKPEGPPPQ 126



 Score = 37.5 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 11/124 (8%), Positives = 22/124 (17%), Gaps = 6/124 (4%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           E S  ++  +      +        P    +   R                K       G
Sbjct: 26  EESPSVISGKPEGRRPQGGNQPQRTPPPPGKPEGRPPQGGNQSQGPPPRPGKPEGPPPQG 85

Query: 295 ----LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                    +   P  +     N               G   +   +S   P +      
Sbjct: 86  GNQSQGPPPRPGKPEGQPPQGGNQSQGPPPRP--GKPEGPPPQGGNQSQGPPPRPGKPEG 143

Query: 351 SAKK 354
              +
Sbjct: 144 PPPQ 147



 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 6/104 (5%), Positives = 14/104 (13%), Gaps = 2/104 (1%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           +                     +                          +   P  +   
Sbjct: 130 QSQGPPPRPGKPEGPPPQGGNQSQGPPPRPGKPEGPPPQGGNQSQGPPPRPGKPEGQPPQ 189

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             N               G   +   +S   P +      S  +
Sbjct: 190 GGNQSQGPPPRP--GKPEGPPPQGGNQSQGPPPRPGKPEGSPSQ 231



 Score = 36.3 bits (82), Expect = 6.6,   Method: Composition-based stats.
 Identities = 5/104 (4%), Positives = 13/104 (12%), Gaps = 2/104 (1%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           +                     +            +             +   P      
Sbjct: 67  QSQGPPPRPGKPEGPPPQGGNQSQGPPPRPGKPEGQPPQGGNQSQGPPPRPGKPEGPPPQ 126

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             N               G   +   +S   P +         +
Sbjct: 127 GGNQSQGPPPRP--GKPEGPPPQGGNQSQGPPPRPGKPEGPPPQ 168


>gi|256112487|ref|ZP_05453408.1| translation initiation factor IF-2 [Brucella melitensis bv. 3 str.
           Ether]
 gi|265993923|ref|ZP_06106480.1| translation initiation factor IF-2 [Brucella melitensis bv. 3 str.
           Ether]
 gi|262764904|gb|EEZ10825.1| translation initiation factor IF-2 [Brucella melitensis bv. 3 str.
           Ether]
          Length = 428

 Score = 38.2 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 11/121 (9%), Positives = 28/121 (23%), Gaps = 1/121 (0%)

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           L     REV ++  R         E           S     +    +    +   + ++
Sbjct: 163 LEEAQIREVEERA-RAVEEAKRRAEEDARRAKEHEESARRQAEEEARLKAEAEARRKAEE 221

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            ++++    + +       R           G           R +     P+     + 
Sbjct: 222 EAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAPIIADAA 281

Query: 348 R 348
            
Sbjct: 282 P 282



 Score = 38.2 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 13/116 (11%), Positives = 28/116 (24%), Gaps = 2/116 (1%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R + +  +RE +        +    A   +      +         +   + +  + +K 
Sbjct: 161 RALEEAQIRE-VEERARAVEEAKRRAEEDARRAKEHEESARRQAEEEARLKAEAEARRKA 219

Query: 294 GLSKQKKLATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                K++  P  R     +   A  G                   P   S R   
Sbjct: 220 EEEAAKRMPQPEARSERRDDARPAPYGARPQQAGRPQGGRPQPAGRPQQGSPRPAP 275


>gi|326476380|gb|EGE00390.1| hypothetical protein TESG_07700 [Trichophyton tonsurans CBS 112818]
          Length = 983

 Score = 38.2 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 13/128 (10%), Positives = 30/128 (23%), Gaps = 2/128 (1%)

Query: 222 PFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD 281
              L +L      E++++I +     H +             S    R       + P  
Sbjct: 253 GIDLHSLTPTQEDELTERIAQAFRRRHRVPSPTRTSRRRESQSPAQPRPVSQDRQQQPQQ 312

Query: 282 FTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW--MAKGIHSSFLSDSGQREENHRRSP 339
             + ++     +  +   +   P  R    S          H +        ++      
Sbjct: 313 QQQQQQQERSPSASASTPRSREPTRRAPPTSRPRLLEPTTAHHAANHRRSASDQGTGTRR 372

Query: 340 SFPSKRSL 347
              S    
Sbjct: 373 RRTSPTPP 380


>gi|297200725|ref|ZP_06918122.1| ATP-dependent RNA helicase [Streptomyces sviceus ATCC 29083]
 gi|197712294|gb|EDY56328.1| ATP-dependent RNA helicase [Streptomyces sviceus ATCC 29083]
          Length = 721

 Score = 38.2 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 8/99 (8%), Positives = 17/99 (17%)

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW 315
           N D                           + +    N   +  + +     R+      
Sbjct: 580 NRDRRDDRPSGGFNRDRRDERPSGGFRRDDRPSGGGFNRDRRDDRPSGGGFNRDRRDERP 639

Query: 316 MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                     S  G   +     PS            ++
Sbjct: 640 SGGFRRDDRPSGGGFNRDRRDERPSTHRGSDRPFNRDRQ 678



 Score = 37.1 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 9/112 (8%), Positives = 19/112 (16%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E+ G    +             +       N             ++   +      ++  
Sbjct: 550 ERGGFRRDDRRDDRGGRSFERRDDRSSGGFNRDRRDDRPSGGFNRDRRDERPSGGFRRDD 609

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            P                         +R     R    PS     R    +
Sbjct: 610 RPSGGGFNRDRRDDRPSGGGFNRDRRDERPSGGFRRDDRPSGGGFNRDRRDE 661


>gi|118090326|ref|XP_001234888.1| PREDICTED: hypothetical protein [Gallus gallus]
          Length = 423

 Score = 38.2 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 9/107 (8%), Positives = 18/107 (16%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                                        +   +         +          A    R
Sbjct: 309 APRRGGAAAPTCRHRDRPRPAAASAQGEEKGGGEGKERPGMGGELRTSGGGTGPAAVGTR 368

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              A+             +    R +    +  + S   L R S K+
Sbjct: 369 SPRAAPGPCGTAWRPRREAGREARGQPASGARPYGSHGKLPRGSQKQ 415


>gi|239978418|ref|ZP_04700942.1| 30S ribosomal protein S4 [Streptomyces albus J1074]
 gi|291450314|ref|ZP_06589704.1| 30S ribosomal protein S4 [Streptomyces albus J1074]
 gi|291353263|gb|EFE80165.1| 30S ribosomal protein S4 [Streptomyces albus J1074]
          Length = 204

 Score = 38.2 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 3/50 (6%)

Query: 15  RVSKVIARAGIASRR--EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R+GIA R   +  +M+    ++VNG  +++ +  V   D + V
Sbjct: 93  RLDALVLRSGIA-RTIYQARQMVVHGHIEVNGHKVDKPSYRVRPDDVVMV 141


>gi|116073745|ref|ZP_01471007.1| translation initiation factor IF-2 [Synechococcus sp. RS9916]
 gi|116069050|gb|EAU74802.1| translation initiation factor IF-2 [Synechococcus sp. RS9916]
          Length = 906

 Score = 38.2 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 15/129 (11%), Positives = 31/129 (24%), Gaps = 7/129 (5%)

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK---- 286
           G  R  + +   E +G  +  + Q        +       RP + + +       +    
Sbjct: 82  GVNRPGAPRAAVELVGKPIRRDGQGAGGGRDANGRPAPPTRPGMPAGMRKPVAPGQLMQL 141

Query: 287 -KNSSQKNGLSKQKKLATPVHRRNLASNVWM--AKGIHSSFLSDSGQREENHRRSPSFPS 343
            K S +      ++   TPV  R                +               P+  +
Sbjct: 142 QKPSGRPGAPPPRRPDGTPVSPRAGEGTTGKAVPPVARPATPPSPATAPRRPGYRPAPGA 201

Query: 344 KRSLRRTSA 352
               R    
Sbjct: 202 GGQRRPGRP 210



 Score = 36.7 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 7/76 (9%), Positives = 20/76 (26%)

Query: 277 EVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR 336
           +      +      +  G  + K+ A P  R        ++     +   +         
Sbjct: 2   KRTVPSPQRPAPKPELVGRPQPKRPAGPPTRPGSGQRPGVSPRPTQAGNQNQRPGSPQRP 61

Query: 337 RSPSFPSKRSLRRTSA 352
            +P  P   +    ++
Sbjct: 62  GAPQRPGAPTRPGAAS 77


>gi|325123630|gb|ADY83153.1| ATP-dependent RNA helicase [Acinetobacter calcoaceticus PHEA-2]
          Length = 620

 Score = 38.2 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 15/105 (14%), Positives = 27/105 (25%), Gaps = 3/105 (2%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
            +V+      +       R     + P      K    + +   + +        R    
Sbjct: 509 NRVDYKPRRENGFGDRPKRSFGGEDRPRRSFDDKPRGERPSFGGEDRPRREFSSDRPRRE 568

Query: 313 NVWMAKGIHSSFLSDSGQREE---NHRRSPSFPSKRSLRRTSAKK 354
             +  K   S      G+R       R   SF  +   RR+   K
Sbjct: 569 GGFNDKPRRSFDDKPRGERPAFGGEDRPKRSFGGEDRPRRSFDDK 613



 Score = 37.5 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 12/132 (9%), Positives = 29/132 (21%), Gaps = 19/132 (14%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+       ++                    +          R ++  +      +    
Sbjct: 436 RDDRPRRSFDDKPRGERPFGGEDRPRREFNSDRPRREGGFEDRPRREFNSDRPRREGGFN 495

Query: 302 ATPVHR------------RNLASNVWMAKGIHSSFLSDSGQR---EENHRRSPSFPSKRS 346
             P               +    N +  +   S    D  +R   ++     PSF  +  
Sbjct: 496 DKPRFDSNDDNRGNRVDYKPRRENGFGDRPKRSFGGEDRPRRSFDDKPRGERPSFGGEDR 555

Query: 347 LRR----TSAKK 354
            RR       ++
Sbjct: 556 PRREFSSDRPRR 567



 Score = 37.5 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 17/120 (14%), Positives = 24/120 (20%), Gaps = 2/120 (1%)

Query: 230 AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
            G  R +  +   +        E       P  S                          
Sbjct: 363 RGKIRAL--EDYLDARLSVSEIEGLEPSPPPARSGRDGGGRGRGGNGGRDGRRGGGFGGG 420

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
            +  G S  K+       R   S     +G       D  +RE N  R           R
Sbjct: 421 RRFEGESNFKRREGGRDDRPRRSFDDKPRGERPFGGEDRPRREFNSDRPRREGGFEDRPR 480



 Score = 36.7 bits (83), Expect = 4.9,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 34/109 (31%), Gaps = 1/109 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R +      +  +   ++     E    D+P   S   +   R+     ++NG   + K 
Sbjct: 468 RPRREGGFEDRPRREFNSDRPRREGGFNDKPRFDSNDDNRGNRVDYKPRRENGFGDRPKR 527

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLS-DSGQREENHRRSPSFPSKRSLRR 349
           +     R   S     +G   SF   D  +RE +  R           R
Sbjct: 528 SFGGEDRPRRSFDDKPRGERPSFGGEDRPRREFSSDRPRREGGFNDKPR 576


>gi|311107260|ref|YP_003980113.1| NOL1/NOP2/sun family protein [Achromobacter xylosoxidans A8]
 gi|310761949|gb|ADP17398.1| NOL1/NOP2/sun family protein [Achromobacter xylosoxidans A8]
          Length = 809

 Score = 38.2 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 10/109 (9%), Positives = 23/109 (21%), Gaps = 6/109 (5%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
             +        +S    R           D  R +    ++     +++   P  R +  
Sbjct: 159 APRGEGRGGERASYGSERREGRPGPRPSYDAPRGEGRGGERASYGSERREGRPGPRPSYD 218

Query: 312 SNVWMAKGIHS------SFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +     +G               G R                   S ++
Sbjct: 219 APRGEGRGGERASYGSERREGRPGPRPSYDAPRGEGRGGERASYGSERR 267



 Score = 38.2 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 9/109 (8%), Positives = 22/109 (20%), Gaps = 6/109 (5%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
             +        +     R           D  R +    ++     +++   P  R +  
Sbjct: 129 APRGENRGGERAPYGSERREGRPGPRPSYDAPRGEGRGGERASYGSERREGRPGPRPSYD 188

Query: 312 SNVWMAKGIHS------SFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +     +G               G R                   S ++
Sbjct: 189 APRGEGRGGERASYGSERREGRPGPRPSYDAPRGEGRGGERASYGSERR 237



 Score = 38.2 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 10/109 (9%), Positives = 23/109 (21%), Gaps = 6/109 (5%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
             +        +S    R           D  R +    ++     +++   P  R +  
Sbjct: 99  APRGENRGGERASYGSERREGRPAPRPSYDAPRGENRGGERAPYGSERREGRPGPRPSYD 158

Query: 312 SNVWMAKGIHS------SFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +     +G               G R                   S ++
Sbjct: 159 APRGEGRGGERASYGSERREGRPGPRPSYDAPRGEGRGGERASYGSERR 207



 Score = 37.1 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 11/114 (9%), Positives = 24/114 (21%), Gaps = 2/114 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +   P   + A+ +            R  P    + P    R  +  S  +   + +   
Sbjct: 34  DARTPVARDSARDDRSGGSRDERASGRPAPRPSYDAPRGENRGGERGSYGSERREGRPGP 93

Query: 303 TPVHRRNLASNVWMAKG--IHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            P +      N    +              R                   S ++
Sbjct: 94  RPSYDAPRGENRGGERASYGSERREGRPAPRPSYDAPRGENRGGERAPYGSERR 147



 Score = 37.1 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 13/123 (10%), Positives = 27/123 (21%), Gaps = 9/123 (7%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
             R         E +     P  S +    +             R  +   + +  + + 
Sbjct: 133 ENRGGERAPYGSERREGRPGPRPSYDAPRGEGRGGERASYGSERREGRPGPRPSYDAPRG 192

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR------RSPSFPSKR---SLRRT 350
           +          +       G   S+ +  G+     R      R    P  R      R 
Sbjct: 193 EGRGGERASYGSERREGRPGPRPSYDAPRGEGRGGERASYGSERREGRPGPRPSYDAPRG 252

Query: 351 SAK 353
             +
Sbjct: 253 EGR 255



 Score = 36.7 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 13/123 (10%), Positives = 28/123 (22%), Gaps = 9/123 (7%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
             R         E +     P  S +    +             R  + + + +  + + 
Sbjct: 73  ENRGGERGSYGSERREGRPGPRPSYDAPRGENRGGERASYGSERREGRPAPRPSYDAPRG 132

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR------RSPSFPSKR---SLRRT 350
           +          +       G   S+ +  G+     R      R    P  R      R 
Sbjct: 133 ENRGGERAPYGSERREGRPGPRPSYDAPRGEGRGGERASYGSERREGRPGPRPSYDAPRG 192

Query: 351 SAK 353
             +
Sbjct: 193 EGR 195



 Score = 36.7 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 10/109 (9%), Positives = 22/109 (20%), Gaps = 6/109 (5%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
             +         S    R           D  R +    ++     +++   P  R +  
Sbjct: 69  APRGENRGGERGSYGSERREGRPGPRPSYDAPRGENRGGERASYGSERREGRPAPRPSYD 128

Query: 312 SNVWMAKGIHS------SFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +     +G               G R                   S ++
Sbjct: 129 APRGENRGGERAPYGSERREGRPGPRPSYDAPRGEGRGGERASYGSERR 177



 Score = 36.7 bits (83), Expect = 6.3,   Method: Composition-based stats.
 Identities = 12/106 (11%), Positives = 23/106 (21%), Gaps = 2/106 (1%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR-- 307
               + + DAP   +    R              R   ++ +  G   ++       R  
Sbjct: 120 RPAPRPSYDAPRGENRGGERAPYGSERREGRPGPRPSYDAPRGEGRGGERASYGSERREG 179

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           R      + A          +    E     P         R   +
Sbjct: 180 RPGPRPSYDAPRGEGRGGERASYGSERREGRPGPRPSYDAPRGEGR 225


>gi|254254329|ref|ZP_04947646.1| ABC-type sugar transport system ATPase component [Burkholderia
           dolosa AUO158]
 gi|124898974|gb|EAY70817.1| ABC-type sugar transport system ATPase component [Burkholderia
           dolosa AUO158]
          Length = 695

 Score = 38.2 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 16/130 (12%), Positives = 32/130 (24%), Gaps = 10/130 (7%)

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G  RE+ ++  R           +                         D   R  +   
Sbjct: 34  GRPREIPEREARRYAERQAGARGRAVGHREHDFRAPEPEGDLQRERRRLDGRARGDRELR 93

Query: 291 QKNGLSKQKK--------LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
           Q +   ++++            +  R     V    G H +   D    +     +   P
Sbjct: 94  QGHQADERRRRAGGRRRDPEAELEVRRDDRAVPGRPGAHRARHRDR--AQVGRDGAEGDP 151

Query: 343 SKRSLRRTSA 352
            +R  RR+  
Sbjct: 152 GRREGRRSQQ 161


>gi|315051062|ref|XP_003174905.1| RING finger domain-containing protein [Arthroderma gypseum CBS
           118893]
 gi|311340220|gb|EFQ99422.1| RING finger domain-containing protein [Arthroderma gypseum CBS
           118893]
          Length = 999

 Score = 38.2 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 19/124 (15%), Positives = 37/124 (29%), Gaps = 3/124 (2%)

Query: 222 PFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD 281
              L +L      E++++I +     H +     ++      S    R       + P  
Sbjct: 249 GIDLHSLTPTQEDELTERIAQAFRRRHRVPSPPRSIRQRESESPAQQRPVSQDRQQQPQQ 308

Query: 282 FTRMKK-NSSQKNGLSKQKKLATPVHRRNL--ASNVWMAKGIHSSFLSDSGQREENHRRS 338
             + +  ++S     +++     P   R              H    SD G      R S
Sbjct: 309 QQQERSLSASGSTPRAREPTRRAPPTSRPRLLEPATANRGANHRRSASDQGTGTRRRRTS 368

Query: 339 PSFP 342
           P+ P
Sbjct: 369 PTPP 372


>gi|197102648|ref|NP_001126712.1| serine/arginine repetitive matrix protein 1 [Pongo abelii]
 gi|75041142|sp|Q5R5Q2|SRRM1_PONAB RecName: Full=Serine/arginine repetitive matrix protein 1
 gi|55732426|emb|CAH92914.1| hypothetical protein [Pongo abelii]
          Length = 917

 Score = 38.2 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 12/113 (10%), Positives = 28/113 (24%), Gaps = 4/113 (3%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R        +    +   P     +        +S  P    R    + +++     K  
Sbjct: 616 RRYSPSPPPKRRTASPPPPPKRRASPSPPPKRRVSHSPPPKQRSSPVTKRRSPSLSSKHR 675

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                 R+       A+    +       R    + S   P +R    +  ++
Sbjct: 676 KGSSPSRSTR----EARSPQPNKRHSPSPRPRAPQTSSPPPVRRGASSSPQRR 724



 Score = 37.1 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 14/106 (13%), Positives = 29/106 (27%), Gaps = 2/106 (1%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
           ++        P   + +         S  P    R+  +   K   S   K  +P     
Sbjct: 614 IQRRYSPSPPPKRRTASPPPPPKRRASPSPPPKRRVSHSPPPKQRSSPVTKRRSPSLSSK 673

Query: 310 LASNVWMAKGIHSSFLSDSGQR--EENHRRSPSFPSKRSLRRTSAK 353
                  ++    +      +R       R+P   S   +RR ++ 
Sbjct: 674 HRKGSSPSRSTREARSPQPNKRHSPSPRPRAPQTSSPPPVRRGASS 719


>gi|186477250|ref|YP_001858720.1| RNA-binding S4 domain-containing protein [Burkholderia phymatum
          STM815]
 gi|184193709|gb|ACC71674.1| RNA-binding S4 domain protein [Burkholderia phymatum STM815]
          Length = 149

 Score = 38.2 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 14/69 (20%), Positives = 27/69 (39%), Gaps = 2/69 (2%)

Query: 3  DKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
          +  I  E     R+ K + A     +R      + + RV++ G  ++  A  V   D +E
Sbjct: 16 NYRISTEPGARLRIDKWLWAARFFKTRSLAADAVEKGRVRIGGATVK-PAKEVRVGDLVE 74

Query: 62 VDGVPLRKA 70
          +D   +   
Sbjct: 75 IDIERIVWQ 83


>gi|238063080|ref|ZP_04607789.1| hypothetical protein MCAG_04046 [Micromonospora sp. ATCC 39149]
 gi|237884891|gb|EEP73719.1| hypothetical protein MCAG_04046 [Micromonospora sp. ATCC 39149]
          Length = 400

 Score = 38.2 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 9/97 (9%), Positives = 20/97 (20%), Gaps = 1/97 (1%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT-PV 305
           P     AQ           +    R        +        +     + +  +      
Sbjct: 292 PEHFTGAQRQEWRAYGPPRSAPGVRRESNRPRREAGADAHGGTDAPRPVRRPGRSRRLAD 351

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
             R+       A G   +    +   ++    SP   
Sbjct: 352 AGRDRLRRRGAAAGPQRAARRGAEGAKKRMPTSPPPG 388


>gi|77552761|gb|ABA95558.1| retrotransposon protein, putative, unclassified [Oryza sativa
           Japonica Group]
          Length = 1068

 Score = 38.2 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 6/97 (6%), Positives = 20/97 (20%)

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
            A   S E   +           + +  +   +  +             R          
Sbjct: 300 MAVGASEERAPKGHDGAGGSRRGEQSTPRGGRASGSRGRGPGSSRPTDARGKRKQGGTPP 359

Query: 318 KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                   +     +     +P+   +   ++   +K
Sbjct: 360 PSPPRGGGAARASSKRPEGAAPASQPEGERKKKRPRK 396


>gi|149572127|ref|XP_001512982.1| PREDICTED: similar to Numa1 protein, partial [Ornithorhynchus
           anatinus]
          Length = 488

 Score = 38.2 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 12/114 (10%), Positives = 28/114 (24%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R ++ +  +E   P L  +++ +  A      +  +              R  +    ++
Sbjct: 375 RPLTPRTRQEGRRPGLGADSEESATAGKRPPASGPQRVTRRAGPGSSPEARTGRREGSRS 434

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
                ++         L        G     L   G        +     KR  
Sbjct: 435 PGRSARRAGAGPASAGLPPRADGDGGDGEGGLPPGGDAPHPAAWAGRADGKRPG 488



 Score = 37.9 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 14/114 (12%), Positives = 25/114 (21%), Gaps = 6/114 (5%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R++ K++  E        E++ +            R          D         S   
Sbjct: 347 RQLRKRVSGESHQGPGTPESKKSAGCFSRPLTPRTRQEGRRPGLGADSEE------SATA 400

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
           G          V RR    +   A+          G+        P+       
Sbjct: 401 GKRPPASGPQRVTRRAGPGSSPEARTGRREGSRSPGRSARRAGAGPASAGLPPR 454


>gi|126345806|ref|XP_001369148.1| PREDICTED: hypothetical protein [Monodelphis domestica]
          Length = 958

 Score = 38.2 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 9/105 (8%), Positives = 23/105 (21%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           GP    + +     P  +                  F       + +     +   A   
Sbjct: 429 GPCDDPQPRPTPPRPRKTPTANPPPSSKRKKRDTTRFGSGGARRNDRFPGRPRGGSAGTA 488

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
             +   ++   + G   S    +G+ +           +R     
Sbjct: 489 PAKPRPASRPNSTGARGSPGRQAGRADAGDGTHRQTQRRRPRGGG 533


>gi|81882280|sp|Q52KI8|SRRM1_MOUSE RecName: Full=Serine/arginine repetitive matrix protein 1; AltName:
           Full=Plenty-of-prolines 101
 gi|62948087|gb|AAH94322.1| Srrm1 protein [Mus musculus]
          Length = 946

 Score = 38.2 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 12/101 (11%), Positives = 28/101 (27%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
           +         +S      R    S  P           Q++    +++  +   +    S
Sbjct: 624 SPSPPPKRRTASPPPPPKRRASPSPPPKRRVSHSPPPKQRSPTVTKRRSPSLSSKHRKGS 683

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +   +     S   +         R+P   S   +RR ++ 
Sbjct: 684 SPGRSTREARSPQPNKRHSPSPRPRAPQTSSPPPVRRGASA 724


>gi|326487704|dbj|BAK05524.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 343

 Score = 38.2 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 16/117 (13%), Positives = 29/117 (24%), Gaps = 5/117 (4%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           +RE L  +   +    L       E   R+R        DD+    +   +     + + 
Sbjct: 225 VREFLTEYKAAKEADKLAKEKEVEERQNRERGYHNRGHRDDYRERSREHDRDRYYERSRD 284

Query: 301 LATPVHRRNLASNVWMAK--GIHSSFLSDSGQREENHRRSPSFPSK---RSLRRTSA 352
              P  +    S+           S  +    R          P +   RS      
Sbjct: 285 RERPYEQGGRGSDYRGGSYNSRRDSERARPRDRNGGDFSRRGDPGRMRSRSRSPGRH 341


>gi|307544638|ref|YP_003897117.1| hemolysin A [Halomonas elongata DSM 2581]
 gi|307216662|emb|CBV41932.1| K06442 putative hemolysin [Halomonas elongata DSM 2581]
          Length = 251

 Score = 38.2 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 2/42 (4%)

Query: 27 SRREVERMIAQQRVKV--NGILLERAAVNVMSTDHIEVDGVP 66
          SR   +R+I   RV+   +G +L R    +  T  + VD  P
Sbjct: 16 SRTRAQRLIRHGRVRRADDGKVLTRPGEKLAETVELIVDDDP 57


>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 = 38.2 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 7/56 (12%), Positives = 19/56 (33%), Gaps = 2/56 (3%)

Query: 161 LKKGIVIQGICYGDMQVTLDTQKG--SNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
           L K  V+        +  +  ++    N    + L  G+  +I+    +  + +  
Sbjct: 194 LIKRKVLFSEKAKRSKTEIFVEERIRDNTLCKIKLHTGRTHQIRVHCSYLGYPLVS 249


>gi|119962017|ref|YP_947412.1| hypothetical protein AAur_1649 [Arthrobacter aurescens TC1]
 gi|119948876|gb|ABM07787.1| conserved hypothetical protein [Arthrobacter aurescens TC1]
          Length = 698

 Score = 38.2 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 16/127 (12%), Positives = 32/127 (25%), Gaps = 3/127 (2%)

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G  R       R+  G      A+     P  +  +  +   +     P +F   +++  
Sbjct: 72  GERRSFGGDRDRKPFGDRNDRPARDGERRPFNNDRSDRKPFGDRPERGPRNFDGPRRDGD 131

Query: 291 QKN--GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
            +   G  + +K       R                    G R        SF  +    
Sbjct: 132 DRRAFGGDRDRKPFGDRGDRPARDGERRPFNNDRGDRKPFGDRPARDGERRSFGDRGDRP 191

Query: 349 -RTSAKK 354
            R   ++
Sbjct: 192 ARDGERR 198


>gi|329936586|ref|ZP_08286322.1| antigen penicillin-binding protein [Streptomyces griseoaurantiacus
           M045]
 gi|329304101|gb|EGG47983.1| antigen penicillin-binding protein [Streptomyces griseoaurantiacus
           M045]
          Length = 1215

 Score = 38.2 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 12/99 (12%), Positives = 22/99 (22%)

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
           + +E+Q    A            P   S+ PD       +  +  G        +     
Sbjct: 1   MSDESQRQQSAQGGPPGKPEPPAPGPASQRPDRGAAPSADRPKAAGKPAGAGTGSGEAAP 60

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
                        +      G R       P+   + S 
Sbjct: 61  GAGEAPASGSAGGADRTKTPGARPATGTPKPTGRGRTSG 99


>gi|318062087|ref|ZP_07980808.1| hypothetical protein SSA3_29395 [Streptomyces sp. SA3_actG]
          Length = 462

 Score = 38.2 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 8/82 (9%), Positives = 17/82 (20%), Gaps = 1/82 (1%)

Query: 267 LVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLS 326
               R     +   +  R            +      P   R  A +   A     +   
Sbjct: 228 RDHGRGERAEDHAPEAERHPAADRHPAAERRPGPDRRPATDRRPAPDRRQAPDRRPAPER 287

Query: 327 DSGQREENHR-RSPSFPSKRSL 347
                  +   R P+   + + 
Sbjct: 288 RPAHEGRSAPERRPAPERRPAA 309


>gi|291443969|ref|ZP_06583359.1| membrane-associated oxidoreductase [Streptomyces roseosporus NRRL
           15998]
 gi|291346916|gb|EFE73820.1| membrane-associated oxidoreductase [Streptomyces roseosporus NRRL
           15998]
          Length = 492

 Score = 38.2 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 9/95 (9%), Positives = 23/95 (24%)

Query: 259 APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAK 318
           A           RP+          R    +   +   +    A P  R +  +      
Sbjct: 151 ALPGRPGHPADRRPDRHGSADQPAQRGPGPARAGHRRGRYDGRAGPPGRDDRDAGRAEPA 210

Query: 319 GIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                  ++  ++    R  P+   + +    +  
Sbjct: 211 RDEGGRFAEPARQPAARRGGPARAERPAADGGAHA 245



 Score = 35.9 bits (81), Expect = 8.7,   Method: Composition-based stats.
 Identities = 10/102 (9%), Positives = 19/102 (18%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
                     +                    R  ++ S      +    A   HRR    
Sbjct: 132 RAAPAGGGTAADRGRSASAALPGRPGHPADRRPDRHGSADQPAQRGPGPARAGHRRGRYD 191

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                 G        +    +   R      + + RR    +
Sbjct: 192 GRAGPPGRDDRDAGRAEPARDEGGRFAEPARQPAARRGGPAR 233


>gi|291447533|ref|ZP_06586923.1| membrane translocator [Streptomyces roseosporus NRRL 15998]
 gi|291350480|gb|EFE77384.1| membrane translocator [Streptomyces roseosporus NRRL 15998]
          Length = 561

 Score = 38.2 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 15/130 (11%), Positives = 31/130 (23%), Gaps = 9/130 (6%)

Query: 234 REVSK----KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPN-IISEVPDDFTRMKKN 288
           R +      + +               L A + S +   R  P                 
Sbjct: 374 RYLRPDARDREIAAMADAVGTRSTWNTLLARLGSLDAESRTGPALPGRTAARRPRPRLSR 433

Query: 289 SSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLS----DSGQREENHRRSPSFPSK 344
            +      +  + A P  R    + V    G              +R +     P+ P +
Sbjct: 434 RTAAADPRRGHQPARPGRRDPRRAGVRRPAGRAGRRRPPDRLGPPRRPDPGDGRPAHPVR 493

Query: 345 RSLRRTSAKK 354
              R  + ++
Sbjct: 494 HPRRTPAYQR 503


>gi|157823383|ref|NP_001101279.1| zinc finger protein 512B [Rattus norvegicus]
 gi|149033915|gb|EDL88698.1| uridine kinase-like 1 (predicted) [Rattus norvegicus]
          Length = 875

 Score = 38.2 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 17/139 (12%), Positives = 40/139 (28%), Gaps = 3/139 (2%)

Query: 202 KKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV-SKKILREQLGPHLLEEAQVNLDAP 260
               E     V+ L    +     G  L G  R +   K    + G           +  
Sbjct: 737 NDCCEAIYSSVSGLK-AHFASCSKGDHLVGKYRCLLCPKEFSSESGVKYHILKTHGENWF 795

Query: 261 IYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGI 320
             S++   + +    S +P    +   +  +K G   +++ +     +   +      G 
Sbjct: 796 RTSADPPSKHKSQD-SLMPRKEKKKSLSGGKKRGRKPKERSSEEPASKLPPNRDDWPPGG 854

Query: 321 HSSFLSDSGQREENHRRSP 339
                  S  ++    ++P
Sbjct: 855 RDRGARSSTGKKAGAGKAP 873


>gi|294629410|ref|ZP_06707970.1| DNA polymerase III, epsilon subunit [Streptomyces sp. e14]
 gi|292832743|gb|EFF91092.1| DNA polymerase III, epsilon subunit [Streptomyces sp. e14]
          Length = 653

 Score = 38.2 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 11/106 (10%), Positives = 21/106 (19%), Gaps = 4/106 (3%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             R  +      Q    + E    +   P  ++   V   P      P+     +    +
Sbjct: 299 EVRPGTPHE--HQPSKKIPEATPPDAPTPSPAATAAVATVPEPRRPEPEQSAPRRPEPER 356

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
                   +   P                  +       R    RR
Sbjct: 357 PEPGQSAPRRPAPERPAPEGPEPRQPDPERPATR--RPARPFGRRR 400



 Score = 36.7 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 5/107 (4%), Positives = 17/107 (15%), Gaps = 3/107 (2%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              +     +   P               S              +        +   P  
Sbjct: 297 LSEVRPGTPHEHQPSKKIPEATPPDAPTPSPAATAAVATVPEPRRPEPEQSAPRRPEPER 356

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                S          +      ++ +     P+   + +      +
Sbjct: 357 PEPGQSAPRRPAPERPAPEGPEPRQPDPE--RPATR-RPARPFGRRR 400


>gi|194769472|ref|XP_001966828.1| GF19228 [Drosophila ananassae]
 gi|190618349|gb|EDV33873.1| GF19228 [Drosophila ananassae]
          Length = 1429

 Score = 38.2 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 21/144 (14%), Positives = 39/144 (27%), Gaps = 7/144 (4%)

Query: 215 LIRISYGPFQLGTLLAGSTREVSKKI----LREQLGPHLLEEAQVNLDAPIYSSETLVRD 270
           L R+ +G     +  +G T  +S  +    LR+               A     E    +
Sbjct: 813 LERVQWGG--DKSSASGETESMSPHVRSRSLRKLQKERKPRVKTKVHQAGESRGEEGRTE 870

Query: 271 RPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ 330
                     D    +  + +  G   +         +     V   +G       D G 
Sbjct: 871 EGRAGEGRAGDGRAGESRAKEDRGREDRAGERRGEEEKVRDDRVREDRGREDRGREDRG- 929

Query: 331 REENHRRSPSFPSKRSLRRTSAKK 354
           RE+  R   +  S+    R    +
Sbjct: 930 REDRGREVRAGESRAREDRAREDR 953


>gi|17547361|ref|NP_520763.1| heat shock protein 15 [Ralstonia solanacearum GMI1000]
 gi|17429664|emb|CAD16349.1| putative heat shock protein 15 [Ralstonia solanacearum GMI1000]
          Length = 131

 Score = 38.2 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 14 QRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K + A     +R +    + + RV++N   +   A +V   D + V
Sbjct: 11 VRIDKWLWAARFFKTRSQATDAVERGRVQINDQPVR-PAKDVKIGDRVRV 59


>gi|114320586|ref|YP_742269.1| ribonuclease E [Alkalilimnicola ehrlichii MLHE-1]
 gi|114226980|gb|ABI56779.1| RNAse E [Alkalilimnicola ehrlichii MLHE-1]
          Length = 1073

 Score = 38.2 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 12/114 (10%), Positives = 29/114 (25%), Gaps = 1/114 (0%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           ++++ ++    P L +       A   +S           +          +  +  +  
Sbjct: 762 ITEEEIQGSATPQLKDWPPRGQVATEAASPESAPADDESGTAAGSPKATQAQRPATADTE 821

Query: 296 SKQKKLATPVHRRNLAS-NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           +   K   P       +     A        + +   E+     P    KRS  
Sbjct: 822 ASDTKADAPASSGETPADQPTGAPPAAGGDGAKAPTAEKAAGEKPGARRKRSKP 875


>gi|73987471|ref|XP_542182.2| PREDICTED: similar to amino-terminal enhancer of split isoform a
           [Canis familiaris]
          Length = 447

 Score = 38.2 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 17/110 (15%), Positives = 27/110 (24%), Gaps = 3/110 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
               P +     + L  P           P      P +         ++ G  +    A
Sbjct: 146 AHGAPRIQAVGALGLHLPPALPRGGRGRAPPPAEGGPANAPPQPGGGGERGGPGRTHPFA 205

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            P  RR   +    A G  ++     G      R S + P      R   
Sbjct: 206 FPRERRGQEARAGAAPGAVNTG---PGSGARGGRCSCACPGGHPAPRGPD 252


>gi|296234002|ref|XP_002762256.1| PREDICTED: hypothetical protein LOC100394361 isoform 1 [Callithrix
           jacchus]
          Length = 714

 Score = 38.2 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 18/118 (15%), Positives = 38/118 (32%), Gaps = 1/118 (0%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           S    ++        + + +  + I S E  +    +   E   +  R +  S  +    
Sbjct: 403 SPSEKKDHSQSGSPNKERDHSQSRIPSKEKDLSRSGSPSKERDQERARGRSRSPSQERAR 462

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            + +  +    R   S     +       S S +R     RSPS    R   R+ +++
Sbjct: 463 GRSRSPSQERARGR-SRSPSQERARGRSRSPSQERARGRSRSPSQERARGRSRSPSQE 519


>gi|170037615|ref|XP_001846652.1| conserved hypothetical protein [Culex quinquefasciatus]
 gi|167880863|gb|EDS44246.1| conserved hypothetical protein [Culex quinquefasciatus]
          Length = 538

 Score = 38.2 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 15/118 (12%), Positives = 28/118 (23%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            +K   ++       E            E   RD      +   D +  ++ S       
Sbjct: 146 RRKERADRSPVRKRYEDSDASPPRRKDKERDKRDARKERRKYSSDESPPRRKSKSPARKR 205

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                 +P  +R+   +              S  R+    R     +    RR    K
Sbjct: 206 YSDSDPSPPRKRDKHWDEPSKGSRRGHDSDQSPPRKSRSNRRRDSDASPPRRRHDQVK 263


>gi|237831969|ref|XP_002365282.1| hypothetical protein TGME49_061490 [Toxoplasma gondii ME49]
 gi|211962946|gb|EEA98141.1| hypothetical protein TGME49_061490 [Toxoplasma gondii ME49]
          Length = 2128

 Score = 38.2 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 16/113 (14%), Positives = 30/113 (26%)

Query: 241  LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
            LRE       +       +    +E+   +R   +       +  ++ SSQ+        
Sbjct: 1469 LREADRASRSQSRGPERPSGGGLAESRKGERRRHLLSPLRPESPERRPSSQRRLRESDDG 1528

Query: 301  LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                  R         +         DS  R    RR  +   +   RR   +
Sbjct: 1529 EDAREGRSAFPRGRSRSFSGSRGEEKDSASRPGTLRRERAESGEERGRRGKQR 1581


>gi|170029346|ref|XP_001842554.1| conserved hypothetical protein [Culex quinquefasciatus]
 gi|167881657|gb|EDS45040.1| conserved hypothetical protein [Culex quinquefasciatus]
          Length = 1452

 Score = 38.2 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 28/215 (13%), Positives = 57/215 (26%), Gaps = 13/215 (6%)

Query: 142  LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
             +V R +   +V  D    L   +  +       +V  +     +    + ++E ++R +
Sbjct: 954  CQVSRDQADSRVHVDFEVPLGNQVNRENQVTMVHRVYRECPDLRDLQDQLVIKELRDRLV 1013

Query: 202  KKVFEFF-NWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAP 260
              V     +  V    R+  GP     L+    R +    + +     L++  + +    
Sbjct: 1014 NLVRRALLDVSVT---RVRLGP-----LVHRVFRVLPDFPVLQGHKVKLVKPVKGDYAGI 1065

Query: 261  IYSSETLVRDRPNI-ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKG 319
                    +  P        D     +K      GL   + L  P        +V    G
Sbjct: 1066 DGPPGPRGKPGPPGLDGPKGDAGEHGQKGVKGHRGLIGLQGLPGPAGNPGDKGDVG-PAG 1124

Query: 320  IHSSFLSDSGQREENHRRSPSFPSKRS--LRRTSA 352
                      +       SP           R   
Sbjct: 1125 QPGKPGEAGPRGPPGRDGSPGPQGMLGMAGPRGPP 1159


>gi|115380443|ref|ZP_01467430.1| hypothetical protein STIAU_8296 [Stigmatella aurantiaca DW4/3-1]
 gi|115362552|gb|EAU61800.1| hypothetical protein STIAU_8296 [Stigmatella aurantiaca DW4/3-1]
          Length = 720

 Score = 38.2 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 8/66 (12%), Positives = 16/66 (24%), Gaps = 1/66 (1%)

Query: 287 KNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           + + +   L        P  R+       +         +  G        +P+  S R 
Sbjct: 41  QQARRGRHLPCPPAPRGPGSRQQPRLTRALRLKASPRRPAAPGG-PPGRGAAPARASPRP 99

Query: 347 LRRTSA 352
             R   
Sbjct: 100 RPRARG 105


>gi|301613640|ref|XP_002936322.1| PREDICTED: hypothetical protein LOC100488725 [Xenopus (Silurana)
           tropicalis]
          Length = 1382

 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 10/99 (10%), Positives = 20/99 (20%)

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
              D   +  +    DRP       D     +    +      ++        +      
Sbjct: 724 SKEDRDRFRDDRSKEDRPRDERSKEDRPRDERSKEDRPRDERSKEDRPRDERSKEDRPRD 783

Query: 315 WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              K            R  + R     P    L+    +
Sbjct: 784 ERLKEDRPRDERLKEDRPRDERLKEDRPRDERLKEDRPR 822



 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 10/108 (9%), Positives = 18/108 (16%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                              E    DRP       D     +    +      ++      
Sbjct: 725 KEDRDRFRDDRSKEDRPRDERSKEDRPRDERSKEDRPRDERSKEDRPRDERSKEDRPRDE 784

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             +         K            R  + R     P    L+    +
Sbjct: 785 RLKEDRPRDERLKEDRPRDERLKEDRPRDERLKEDRPRDERLKEDRPR 832



 Score = 36.7 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 9/121 (7%), Positives = 24/121 (19%), Gaps = 1/121 (0%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISE-VPDDFTRMKKNSSQK 292
           R+   K  R +      +  +          +   ++          D     +    + 
Sbjct: 742 RDERSKEDRPRDERSKEDRPRDERSKEDRPRDERSKEDRPRDERLKEDRPRDERLKEDRP 801

Query: 293 NGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                ++        +         K            R  + R     P    L+    
Sbjct: 802 RDERLKEDRPRDERLKEDRPRDERLKEDRPRDERLKEDRPRDERLKEDRPRDERLKEDRP 861

Query: 353 K 353
           +
Sbjct: 862 R 862



 Score = 36.3 bits (82), Expect = 8.2,   Method: Composition-based stats.
 Identities = 10/106 (9%), Positives = 18/106 (16%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                            E    DRP       D     +    +      ++        
Sbjct: 737 KEDRPRDERSKEDRPRDERSKEDRPRDERSKEDRPRDERSKEDRPRDERLKEDRPRDERL 796

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +         K            R  + R     P    L+    +
Sbjct: 797 KEDRPRDERLKEDRPRDERLKEDRPRDERLKEDRPRDERLKEDRPR 842


>gi|238064403|ref|ZP_04609112.1| beta-ketoacyl synthase [Micromonospora sp. ATCC 39149]
 gi|237886214|gb|EEP75042.1| beta-ketoacyl synthase [Micromonospora sp. ATCC 39149]
          Length = 1961

 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 11/76 (14%), Positives = 13/76 (17%), Gaps = 1/76 (1%)

Query: 266  TLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFL 325
                 R   +   P   +R         G           HRR            H    
Sbjct: 1770 HPPGRRCGGVPPQPHRRSRRPGGDHHPVGGRHSGSRRPGHHRRPGRGERTGRVQPHGGGR 1829

Query: 326  S-DSGQREENHRRSPS 340
            S D           P 
Sbjct: 1830 SLDRAAHRAGGHHRPG 1845


>gi|258650897|ref|YP_003200053.1| DNA polymerase III subunits gamma and tau [Nakamurella multipartita
           DSM 44233]
 gi|258554122|gb|ACV77064.1| DNA polymerase III, subunits gamma and tau [Nakamurella
           multipartita DSM 44233]
          Length = 743

 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 10/106 (9%), Positives = 17/106 (16%), Gaps = 2/106 (1%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                         P     T       + +      T              +   A P 
Sbjct: 447 QQRPAASRPAAPARPQRPEATPAGPDLGLPAPPTLRSTARAARPDASRPEQPRPDQARPD 506

Query: 306 HRRNLASNVWMAKG--IHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
             R    +           +  +    R      SP+        R
Sbjct: 507 QARTTPPDSRRTPPDQARPAARAPEPDRNRPAAGSPAGGQPPGSDR 552



 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 14/108 (12%), Positives = 25/108 (23%), Gaps = 1/108 (0%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK-NGLS 296
              LR        + ++     P  +     R  P      P D  R    + +      
Sbjct: 478 PPTLRSTARAARPDASRPEQPRPDQARPDQARTTPPDSRRTPPDQARPAARAPEPDRNRP 537

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
                A      +            S+    +      H  SP+  S+
Sbjct: 538 AAGSPAGGQPPGSDRVARPAPAAASSAPTRSAESAPAAHESSPTPASE 585



 Score = 37.1 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 14/114 (12%), Positives = 28/114 (24%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           L E  GP    E +        ++E     RP             +  +  +    +   
Sbjct: 409 LAEPAGPEPAAEPEQRTGTAERAAERTAAGRPAQGPNAQQRPAASRPAAPARPQRPEATP 468

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               +      +    A+            R +  R   +  +    RRT   +
Sbjct: 469 AGPDLGLPAPPTLRSTARAARPDASRPEQPRPDQARPDQARTTPPDSRRTPPDQ 522


>gi|83747195|ref|ZP_00944238.1| Transcriptional regulator, TetR family [Ralstonia solanacearum
           UW551]
 gi|83726170|gb|EAP73305.1| Transcriptional regulator, TetR family [Ralstonia solanacearum
           UW551]
          Length = 455

 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 11/106 (10%), Positives = 19/106 (17%)

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
                 V             +                 +    +       + A PV R 
Sbjct: 97  RPALRAVPERDQSRQDHAAAQPHHVGRDRRARRRRAEPRLHPHRRRQRSGPRHAGPVARG 156

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             A+                G+R  +    P  P      R    +
Sbjct: 157 GGAARHPHHLPRRRHPQHPRGRRPAHAPLPPVRPRTGDPHRPRRLR 202



 Score = 36.3 bits (82), Expect = 7.1,   Method: Composition-based stats.
 Identities = 12/110 (10%), Positives = 21/110 (19%), Gaps = 2/110 (1%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           LR         +            +   R R       P    +                
Sbjct: 100 LRAVPERDQSRQDHAAAQPHHVGRDRRARRRRAEPRLHPHRRRQRSGPRHAGPVARGGGA 159

Query: 301 LATPV--HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
              P    RR    +    +  H+       +  + HR     P   +  
Sbjct: 160 ARHPHHLPRRRHPQHPRGRRPAHAPLPPVRPRTGDPHRPRRLRPGHGARP 209


>gi|67523541|ref|XP_659830.1| hypothetical protein AN2226.2 [Aspergillus nidulans FGSC A4]
 gi|40744755|gb|EAA63911.1| hypothetical protein AN2226.2 [Aspergillus nidulans FGSC A4]
 gi|259487612|tpe|CBF86420.1| TPA: THO complex component (Rlr1), putative (AFU_orthologue;
            AFUA_5G07180) [Aspergillus nidulans FGSC A4]
          Length = 2429

 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 14/134 (10%), Positives = 29/134 (21%), Gaps = 17/134 (12%)

Query: 238  KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            ++  R  L    L   +++L        + +R   +     P      +   S +   + 
Sbjct: 1901 EREDRRSLPTRPLTPPKLDLPNRPERFPSDIRKPASNTQPPPRGEEMPRGPRSDRPPRTP 1960

Query: 298  QKKLATPVHRRNLASNVWM----------AKGIHSSFLSDSGQREENHRRSPSFPSK--- 344
             +              V              G  S      G R        + P     
Sbjct: 1961 MEGPDPRDSVPGSDLPVGRSRQADLMSDIPSGPRSRTAPGRGGRNPPAPHPSAGPPGSGP 2020

Query: 345  ----RSLRRTSAKK 354
                R       ++
Sbjct: 2021 AVNDRPPPTGPGRQ 2034


>gi|310659475|ref|YP_003937196.1| 30S ribosomal protein S4 [Clostridium sticklandii DSM 519]
 gi|308826253|emb|CBH22291.1| 30S ribosomal subunit protein S4 [Clostridium sticklandii]
          Length = 207

 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 1/42 (2%)

Query: 22  RAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R G+A SR+E  +++      +NG      ++ +   D I V
Sbjct: 106 RMGLAASRKEARQLVRHGHFNLNGHKANIPSMTISVGDVITV 147


>gi|239992386|ref|ZP_04713050.1| SARP family transcriptional regulator [Streptomyces roseosporus
           NRRL 11379]
          Length = 410

 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 18/138 (13%), Positives = 35/138 (25%), Gaps = 12/138 (8%)

Query: 216 IRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNII 275
           +R   G F L  LL    RE+            +  +        +  S      R    
Sbjct: 285 VRERAGRFGLDVLLRSYAREL------------IGADEAHTARRRLVLSRAPGPVRHGTG 332

Query: 276 SEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENH 335
            +           S  ++G  ++ + + P+    +      A    +        R    
Sbjct: 333 RDNCSGSYASSAGSRAQSGGDRKDRRSAPLPSAGVGHPEASAPSGPAGGSRTGPSRTVGR 392

Query: 336 RRSPSFPSKRSLRRTSAK 353
             +PS    R       +
Sbjct: 393 TAAPSRAEPREPGVHRHE 410


>gi|268535202|ref|XP_002632734.1| Hypothetical protein CBG18769 [Caenorhabditis briggsae]
          Length = 204

 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 8/106 (7%), Positives = 18/106 (16%), Gaps = 2/106 (1%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                   +              +                K    +  G   + +   P 
Sbjct: 19  QRPKGPRPKAQGPKARRPEGPKAQGPTPKGQRPRPKAQGSKAQRPKAKGPRPKVQGPRPK 78

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
            +R    N    K      ++   +        P     R   +  
Sbjct: 79  AQRAKGPNAQRPKAQRP--MAQKPKGPRPKGPRPKAQGPRPKAQGP 122



 Score = 37.5 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 11/127 (8%), Positives = 23/127 (18%), Gaps = 2/127 (1%)

Query: 230 AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
             + R    +   +       E  +     P                          +  
Sbjct: 16  PKAQRPKGPRPKAQGPKARRPEGPKAQGPTPKGQRPRPKAQGSKAQRPKAKGPRPKVQGP 75

Query: 290 SQKNGLSKQKKLATPVHRRN--LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
             K   +K      P  +R           KG          + +    + P    K   
Sbjct: 76  RPKAQRAKGPNAQRPKAQRPMAQKPKGPRPKGPRPKAQGPRPKAQGPWPKGPCPWPKAQR 135

Query: 348 RRTSAKK 354
            +    +
Sbjct: 136 PKGPKAQ 142



 Score = 37.1 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 11/109 (10%), Positives = 21/109 (19%), Gaps = 1/109 (0%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS-KQKKLATPV 305
               ++       P   ++     RP             K       G   + K   +  
Sbjct: 1   MPNAQKPNAQAQGPSPKAQRPKGPRPKAQGPKARRPEGPKAQGPTPKGQRPRPKAQGSKA 60

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            R          +G         G   +  +       K    R    +
Sbjct: 61  QRPKAKGPRPKVQGPRPKAQRAKGPNAQRPKAQRPMAQKPKGPRPKGPR 109


>gi|332703354|ref|ZP_08423442.1| ribosomal protein S4 [Desulfovibrio africanus str. Walvis Bay]
 gi|332553503|gb|EGJ50547.1| ribosomal protein S4 [Desulfovibrio africanus str. Walvis Bay]
          Length = 208

 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 1/47 (2%)

Query: 17  SKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             VI R G   SR +  +++      +NG  +   ++ +   D I V
Sbjct: 101 DNVIYRMGFTNSRNQARQLVRHGVFVLNGHKVTVPSLQLKPGDTITV 147


>gi|321268723|gb|ADW79172.1| ribosomal protein S4 [Cyanophora paradoxa]
          Length = 447

 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 9/128 (7%), Positives = 32/128 (25%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTH 88
           +   ++I  + V V+  L+      + +   I +  + +   +       ++ +      
Sbjct: 120 KAARQLIMHKNVFVDNRLITNPGYLLSNGQIIHIKKINIVYLKIKINNKNNEFVYKKFKT 179

Query: 89  SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
                          + +  I    L    + +++   +      L          Y  +
Sbjct: 180 ILKKRILFKNYYKNFLLNTTIYNACLPSYLKYIVIQNKNYNYHTFLFNTPRLIEIPYPNK 239

Query: 149 FHGQVDQD 156
                   
Sbjct: 240 MWIHSICK 247


>gi|320545415|ref|NP_001097475.2| CG7971, isoform F [Drosophila melanogaster]
 gi|318069094|gb|ABW08438.2| CG7971, isoform F [Drosophila melanogaster]
          Length = 1655

 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 18/121 (14%), Positives = 40/121 (33%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE SK   R +      E         +   +     + +   +   +  R ++    + 
Sbjct: 775 RERSKDRQRSRERRRSKEGQLSKDRQGLKERQRSNERKRSKERQPSKEKQRSRERQRSRE 834

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            L  + +  +   +R+       A+   S     S  R++   RSP+  S++    T   
Sbjct: 835 PLQSKDRQRSKERQRSRERPAKEARPTRSPRERSSKSRDDRRHRSPTNASRKQKDDTKLS 894

Query: 354 K 354
           +
Sbjct: 895 R 895


>gi|195504747|ref|XP_002099211.1| GE10789 [Drosophila yakuba]
 gi|194185312|gb|EDW98923.1| GE10789 [Drosophila yakuba]
          Length = 642

 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 11/116 (9%), Positives = 31/116 (26%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            +  ++            +        +   +  P           R +++S Q     +
Sbjct: 272 PRRKKDSDQSPPRRRKAEDQSPARRVRKDSDQSPPRKRRGNDQSPVRKRRDSDQSPPRRR 331

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           ++   +P  RR  +      +           +R+ +   +         RR S +
Sbjct: 332 REDKQSPPRRRRNSDQSPPRRPKDEDQSPPRRKRDFDQSPTRKRDKSPRRRRDSDQ 387



 Score = 36.3 bits (82), Expect = 6.7,   Method: Composition-based stats.
 Identities = 11/109 (10%), Positives = 33/109 (30%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G    +  Q          ++  R R +     P   T  ++  + ++   +++  +   
Sbjct: 200 GRKRRDSDQSPPRKAKNGDQSPARKRRDSDQSPPRKRTERRRRDTDQSPPRRRRSNSDQS 259

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             R                     +R +   +SP+   ++   ++  +K
Sbjct: 260 PPRRRRDKDSTPPRRKKDSDQSPPRRRKAEDQSPARRVRKDSDQSPPRK 308


>gi|301100326|ref|XP_002899253.1| conserved hypothetical protein [Phytophthora infestans T30-4]
 gi|262104170|gb|EEY62222.1| conserved hypothetical protein [Phytophthora infestans T30-4]
          Length = 584

 Score = 38.2 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 14/108 (12%), Positives = 31/108 (28%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R    +    + G  +++    + D          +  P +    PD  T  + ++  K+
Sbjct: 109 RFKKMQEEAARNGTPMVKSRLQDTDWDKVPIPKKKKQAPQVDKSTPDATTSKRSSNDSKH 168

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF 341
                 K           ++     G   S  + S + +   RR    
Sbjct: 169 AGKAHNKRRKKNSGSAKKTSGSSYYGPQGSQSAKSDKYDSPSRRRRGR 216


>gi|139438943|ref|ZP_01772403.1| Hypothetical protein COLAER_01409 [Collinsella aerofaciens ATCC
           25986]
 gi|133775654|gb|EBA39474.1| Hypothetical protein COLAER_01409 [Collinsella aerofaciens ATCC
           25986]
          Length = 749

 Score = 38.2 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 12/82 (14%), Positives = 18/82 (21%)

Query: 269 RDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDS 328
           R R     E      R    S  + G    +           +      +G  S+     
Sbjct: 605 RRRSGRDDERGGRDERRGGESRGERGARGGESRGGKRFEERGSRGGERREGARSNGGRGG 664

Query: 329 GQREENHRRSPSFPSKRSLRRT 350
             R    R      + R  R  
Sbjct: 665 AGRSNESRDRRDPRASRDRRDD 686


>gi|239931572|ref|ZP_04688525.1| glycosyl transferase [Streptomyces ghanaensis ATCC 14672]
          Length = 731

 Score = 37.9 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 22/129 (17%), Positives = 32/129 (24%), Gaps = 12/129 (9%)

Query: 226 GTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
           G L AG TR +    LR +LG    E    +      +  T+ R R  +      D    
Sbjct: 364 GALAAGLTRLLGDADLRARLGAAGRERVLRHFTWARAAEGTVARYREAMDRAGGRDTADA 423

Query: 286 KKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
           +        L    +     H                        R     R P    + 
Sbjct: 424 RTAGHGPARLRAAARRPLRDH------------AARPPRGPRGQGRRARLPRGPGRRVRD 471

Query: 346 SLRRTSAKK 354
             R    +K
Sbjct: 472 HSRNLRPRK 480


>gi|269126403|ref|YP_003299773.1| hemolysin A [Thermomonospora curvata DSM 43183]
 gi|268311361|gb|ACY97735.1| hemolysin A [Thermomonospora curvata DSM 43183]
          Length = 268

 Score = 37.9 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 1/36 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLER 49
          R+   + R  +A SR +   +I Q RV+V G    +
Sbjct: 7  RLDAELVRRNLARSREQARELIEQGRVRVGGRPATK 42


>gi|238026297|ref|YP_002910528.1| putative heat shock protein [Burkholderia glumae BGR1]
 gi|237875491|gb|ACR27824.1| Putative heat shock protein [Burkholderia glumae BGR1]
          Length = 135

 Score = 37.9 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 13/61 (21%), Positives = 27/61 (44%), Gaps = 2/61 (3%)

Query: 3  DKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
          +  I  E     R+ K + A     +R      + + RV++ G+ ++  + +V   D +E
Sbjct: 2  NHRISTEPGAKLRIDKWLWAARFFKTRSLAAEAVEKGRVRIGGVPVK-PSKDVRVGDRVE 60

Query: 62 V 62
          V
Sbjct: 61 V 61


>gi|271967346|ref|YP_003341542.1| hypothetical protein Sros_6067 [Streptosporangium roseum DSM 43021]
 gi|270510521|gb|ACZ88799.1| hypothetical protein Sros_6067 [Streptosporangium roseum DSM 43021]
          Length = 936

 Score = 37.9 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 14/114 (12%), Positives = 28/114 (24%), Gaps = 1/114 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+  G     E + +     Y  +    DR            R  ++        +  + 
Sbjct: 7   RDGAGRRDEGENRGSGGQGGYRGDRAGSDRGRPGDGPRYGERREGRSGGSYGSRDRGDRP 66

Query: 302 ATPVHR-RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           A      R+        +               +  + PS P     RR+   +
Sbjct: 67  AGGYRDSRSGGDRPPFNRDDRPGGGGQRSYGSRDGGQRPSGPRDSGERRSYGDR 120


>gi|255544704|ref|XP_002513413.1| ribonucleic acid binding protein S1, putative [Ricinus communis]
 gi|223547321|gb|EEF48816.1| ribonucleic acid binding protein S1, putative [Ricinus communis]
          Length = 423

 Score = 37.9 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 16/128 (12%), Positives = 38/128 (29%), Gaps = 10/128 (7%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +   ++R +      ++          + +       N  ++V  D  + +K S      
Sbjct: 176 IDGNVVRARFTLPPRQKVSPPPKPIAAAPKRDAPKTDNAGADVEKDGPKRQKESPPHRKP 235

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQRE---------ENHRRSPSFPSKRS 346
               +  +P+ RR  +              S   +R             RR P+ P+ R 
Sbjct: 236 LASPRRRSPIARRGGSPRRLPDSPPRRRADSPPARRRMDSPYRRGDTPPRRRPASPA-RG 294

Query: 347 LRRTSAKK 354
              +  ++
Sbjct: 295 RSPSPPRR 302



 Score = 37.9 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 12/103 (11%), Positives = 21/103 (20%), Gaps = 1/103 (0%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK-LATPVHRRNL 310
                 D      E     R              ++ S         ++   +P  RR  
Sbjct: 206 RDAPKTDNAGADVEKDGPKRQKESPPHRKPLASPRRRSPIARRGGSPRRLPDSPPRRRAD 265

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +                  +R          PS     R+ A+
Sbjct: 266 SPPARRRMDSPYRRGDTPPRRRPASPARGRSPSPPRRYRSPAR 308


>gi|297155854|gb|ADI05566.1| putative serine/threonine protein kinase [Streptomyces
           bingchenggensis BCW-1]
          Length = 502

 Score = 37.9 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 10/105 (9%), Positives = 25/105 (23%), Gaps = 3/105 (2%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
            + ++               +R    +  P    +  + S+ + G     + A       
Sbjct: 344 RQPSERPSGRRADEYTRQRTERRPGGTPPPAPRAQAPRASAPRPGPGTGGRSAGSAGAPG 403

Query: 310 LASNVWMAKGIHSSFLSDSGQ---REENHRRSPSFPSKRSLRRTS 351
              +     G   +    SG+   R            +R +    
Sbjct: 404 STGSTGRNSGARPTPARPSGRNGARPPVRTLRTPRNGRRPVGPDR 448



 Score = 37.1 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 11/95 (11%), Positives = 23/95 (24%)

Query: 260 PIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKG 319
              S     R       +  +         + +    +             ++    A G
Sbjct: 344 RQPSERPSGRRADEYTRQRTERRPGGTPPPAPRAQAPRASAPRPGPGTGGRSAGSAGAPG 403

Query: 320 IHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              S   +SG R    R S    ++  +R     +
Sbjct: 404 STGSTGRNSGARPTPARPSGRNGARPPVRTLRTPR 438


>gi|237833651|ref|XP_002366123.1| protein kinase, putative [Toxoplasma gondii ME49]
 gi|211963787|gb|EEA98982.1| protein kinase, putative [Toxoplasma gondii ME49]
          Length = 1678

 Score = 37.9 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 13/101 (12%), Positives = 22/101 (21%), Gaps = 3/101 (2%)

Query: 257  LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
                 + S    R                  N +        K+           S  + 
Sbjct: 942  AAESRFESPHSTRRGLPSAQRDGHPAREGSANGAASLVYRHHKRRDGREESEGNRSRTFN 1001

Query: 317  AKGIHSSFLSDSGQREENHR---RSPSFPSKRSLRRTSAKK 354
                 SS L  +    ++ R   +S      R   R   +K
Sbjct: 1002 RSKRRSSELQKAPGGRDSRRSLNKSRRPSDARDRSRGRDEK 1042


>gi|194770864|ref|XP_001967507.1| GF20705 [Drosophila ananassae]
 gi|190618517|gb|EDV34041.1| GF20705 [Drosophila ananassae]
          Length = 580

 Score = 37.9 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 10/109 (9%), Positives = 27/109 (24%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
               +++ + +    +    +  +      S       R +    +K   S Q       
Sbjct: 136 QKRQIKQEKRSRSRDLSPERSKKKKNHPDQSPPRRKADRDQSPRGRKRKDSDQSPPRRAR 195

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                            S      +R  +  +SP    +    ++  +K
Sbjct: 196 DSPPRRRQDASPVRKRRSSDQSPPRRRRDDDQSPPRRRRNDSDQSPPRK 244



 Score = 37.5 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 13/119 (10%), Positives = 33/119 (27%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R++S +  +++         +   D          +D          D    ++  +   
Sbjct: 149 RDLSPERSKKKKNHPDQSPPRRKADRDQSPRGRKRKDSDQSPPRRARDSPPRRRQDASPV 208

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
              +    + P  RR+   +    +   S       +RE +  R      +   R+   
Sbjct: 209 RKRRSSDQSPPRRRRDDDQSPPRRRRNDSDQSPPRKRREPSPVRRRRDSDQSPPRKRRD 267


>gi|332157866|ref|YP_004423145.1| 30S ribosomal protein S4 [Pyrococcus sp. NA2]
 gi|331033329|gb|AEC51141.1| 30S ribosomal protein S4 [Pyrococcus sp. NA2]
          Length = 180

 Score = 37.9 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 25/52 (48%), Gaps = 5/52 (9%)

Query: 15  RVSKVIARAGIASR--REVERMIAQQRVKVNGILLERAAVNV--MSTDHIEV 62
           R+  ++ R G+A R  R+  ++I    ++VNG ++   +  V     D I  
Sbjct: 104 RLQTIVYRKGLA-RTMRQARQLIVHGHIEVNGQIIRSPSYLVLKEEEDKITY 154


>gi|212530576|ref|XP_002145445.1| THO complex component (Rlr1), putative [Penicillium marneffei ATCC
            18224]
 gi|210074843|gb|EEA28930.1| THO complex component (Rlr1), putative [Penicillium marneffei ATCC
            18224]
          Length = 2348

 Score = 37.9 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 15/144 (10%), Positives = 32/144 (22%), Gaps = 26/144 (18%)

Query: 237  SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT------------- 283
                 R         E + +       +     +R N+I   PD                
Sbjct: 1805 DDDQFRASRDSRHHREPEADRAGSSRPATQPHPERANVIQGHPDRLALIEGDNQRRDASR 1864

Query: 284  ----------RMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREE 333
                             ++ G    +  A P   R   S++   + +        G+  +
Sbjct: 1865 HDRDDRRHRLSSPARGDERRGPRHDEFPAGPRSDRVARSDLPEGRELRPGGDVSHGRGPQ 1924

Query: 334  NHRRSPSFPSKRS---LRRTSAKK 354
            + R +             R    +
Sbjct: 1925 DSRTARQPEPANEIPLGPRGRQSR 1948


>gi|325293279|ref|YP_004279143.1| outer membrane protein, OmpA family protein [Agrobacterium sp.
           H13-3]
 gi|325061132|gb|ADY64823.1| putative outer membrane protein, OmpA family protein [Agrobacterium
           sp. H13-3]
          Length = 771

 Score = 37.9 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 13/122 (10%), Positives = 29/122 (23%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
              E + + L  +      E        P    +     R    +E      R +     
Sbjct: 85  QAEEQNPEELLRKQRQQAEEAQPKPEPEPKKQEQAPEPQREQPKAEAAPAEPRPEPKREA 144

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
           +    ++ +       +   +    A            Q E     +P+    +   R  
Sbjct: 145 QPEPQREPQPEPKRQPQQREAQPEPAPAEQPPARKQRPQPEPEAAPAPAEQQPQERPRKP 204

Query: 352 AK 353
           A+
Sbjct: 205 AR 206


>gi|325116375|emb|CBZ51928.1| putative KH domain-containing protein [Neospora caninum Liverpool]
          Length = 1073

 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 13/110 (11%), Positives = 26/110 (23%)

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           +  +E+   +   E     D    + +   R R                +   +      
Sbjct: 36  EEAKEREKDNREREGGDGKDRRRDTDKERERGRGRGSDRGDRGNAGRDGSRDGEKDRRDD 95

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           K+      RR+ +          S     S  R    +R      +R   
Sbjct: 96  KEKERKKSRRDESEESDRESTGRSRSKDRSSPRHRRDKRKREETKEREAS 145


>gi|317507622|ref|ZP_07965335.1| D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase
           [Segniliparus rugosus ATCC BAA-974]
 gi|316254099|gb|EFV13456.1| D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase
           [Segniliparus rugosus ATCC BAA-974]
          Length = 871

 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 12/103 (11%), Positives = 19/103 (18%), Gaps = 4/103 (3%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P          D  +       R     +   PD     +          +  + A    
Sbjct: 270 PAPERLQDREPDGALADPPQRARSPAARLRPRPDPRGGERSGLDAPADGRRSGRGAAQDP 329

Query: 307 RRNLASNVWMAKGIHSSFLS---DSGQREENHRRSPSFPSKRS 346
              +   V  A            D     E   R P    +  
Sbjct: 330 DHPVPRAVRQAAHARRRPPRLADDRAAHPEGLDR-PRRSGRPP 371


>gi|325288604|ref|YP_004264785.1| SSU ribosomal protein S4P [Syntrophobotulus glycolicus DSM 8271]
 gi|324964005|gb|ADY54784.1| SSU ribosomal protein S4P [Syntrophobotulus glycolicus DSM 8271]
          Length = 209

 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 9/39 (23%), Positives = 18/39 (46%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           SR E  + +    + VNG  ++ A+  +   + I V+  
Sbjct: 113 SRAEARQFVTHGHITVNGKRVDIASYLIKVGEVIAVNEK 151


>gi|295657795|ref|XP_002789463.1| conserved hypothetical protein [Paracoccidioides brasiliensis Pb01]
 gi|226283797|gb|EEH39363.1| conserved hypothetical protein [Paracoccidioides brasiliensis Pb01]
          Length = 932

 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 16/119 (13%), Positives = 34/119 (28%), Gaps = 1/119 (0%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
            + +K L++       EE               V+ R ++IS               ++ 
Sbjct: 456 HLDRKKLKDSTPSQTGEEPIKRRRLIAGRPPDRVKRRESLISSDSHSGRDETAKLPAEHT 515

Query: 295 LSKQKKLATPVH-RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            S  K        +R+ +S              D   R+   +R      +  L  +++
Sbjct: 516 NSDAKPTKKAGSLKRSRSSVSPEPPQARGRQRKDEDSRDTLKKRRRVRSEENDLSSSNS 574


>gi|221508115|gb|EEE33702.1| protein kinase, putative [Toxoplasma gondii VEG]
          Length = 1678

 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 13/101 (12%), Positives = 22/101 (21%), Gaps = 3/101 (2%)

Query: 257  LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
                 + S    R                  N +        K+           S  + 
Sbjct: 942  AAESRFESPHSTRRGLPSAQRDGHPAREGSANGAASLVYRHHKRRDGREESEGNRSRTFN 1001

Query: 317  AKGIHSSFLSDSGQREENHR---RSPSFPSKRSLRRTSAKK 354
                 SS L  +    ++ R   +S      R   R   +K
Sbjct: 1002 RSKRRSSELQKAPGGRDSRRSLNKSRRPSDARDRSRGRDEK 1042


>gi|195377218|ref|XP_002047389.1| GJ13409 [Drosophila virilis]
 gi|194154547|gb|EDW69731.1| GJ13409 [Drosophila virilis]
          Length = 1893

 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 18/129 (13%), Positives = 44/129 (34%), Gaps = 11/129 (8%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRP-------NIISEVPDDFTRMKKNS 289
             K +RE       E ++   + P   +    + R           S+      + ++ S
Sbjct: 426 RSKDIRECSNNRQSERSKDRKEFPNDKNIERPKQRRESSYDKQRERSKDKRIGDKPRERS 485

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSF----LSDSGQREENHRRSPSFPSKR 345
            +K   S +K+      ++  +          S+      S  G+R+ ++         R
Sbjct: 486 KEKLDRSIEKQRERSKEKKRDSDQSKEKSTSRSTEKLSLESKKGRRDRSNDGRSKKSRHR 545

Query: 346 SLRRTSAKK 354
           +  R++++K
Sbjct: 546 TRSRSNSRK 554


>gi|148271239|ref|YP_001220800.1| putative cell filamentation protein [Clavibacter michiganensis
           subsp. michiganensis NCPPB 382]
 gi|147829169|emb|CAN00076.1| putative cell filamentation protein [Clavibacter michiganensis
           subsp. michiganensis NCPPB 382]
          Length = 318

 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 8/97 (8%), Positives = 19/97 (19%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             + +    LR      +    +   D            R    +          +    
Sbjct: 162 DWKRIDVDELRHHRLQAIAGTDRPLADYLRAHLIDTAPTRGPEAAAPLSAARSAGREQGG 221

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDS 328
                +   L  P  RR   +     +   +   +  
Sbjct: 222 VARRRRGTGLQPPRARRARDAPHGGDRPGRAQCAAPR 258


>gi|126343128|ref|XP_001370338.1| PREDICTED: similar to En/Spm-like transposon protein [Monodelphis
           domestica]
          Length = 285

 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 14/118 (11%), Positives = 26/118 (22%), Gaps = 8/118 (6%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                 L         P  +          + +         K   +   G    ++L  
Sbjct: 24  PRQQRTLRSRPTRKSRPRAALRPKEPSYKEVPTPSSSRPKGPKPQGAFLQGSPDSEQLRA 83

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF--------PSKRSLRRTSAK 353
           P       S    A G           ++   R +P          P ++S  R +  
Sbjct: 84  PRSHPTRKSQPRAAPGRRPEAPRSRPTKKSRPRAAPGRRPKAPRSCPKRKSRPRAAPS 141



 Score = 35.9 bits (81), Expect = 8.5,   Method: Composition-based stats.
 Identities = 12/105 (11%), Positives = 28/105 (26%), Gaps = 1/105 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT-RMKKNSSQKNGLSKQKK 300
           R +      E +   +  P  S     + +   +   PD    R  ++   +    +   
Sbjct: 39  RPRAALRPKEPSYKEVPTPSSSRPKGPKPQGAFLQGSPDSEQLRAPRSHPTRKSQPRAAP 98

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
              P   R+  +     +              +   R  + PS +
Sbjct: 99  GRRPEAPRSRPTKKSRPRAAPGRRPKAPRSCPKRKSRPRAAPSPK 143


>gi|302540001|ref|ZP_07292343.1| methylmalonyl-CoA mutase, beta subunit [Streptomyces hygroscopicus
           ATCC 53653]
 gi|302457619|gb|EFL20712.1| methylmalonyl-CoA mutase, beta subunit [Streptomyces himastatinicus
           ATCC 53653]
          Length = 525

 Score = 37.9 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 11/105 (10%), Positives = 18/105 (17%), Gaps = 21/105 (20%)

Query: 266 TLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGI----- 320
              R                         L++ ++     HRR        A G      
Sbjct: 414 PGDRAGRGTGRRPRLRAGARPAGRHLGAPLARPRQPQGADHRRERVPQPGRAAGPARGRA 473

Query: 321 ----------------HSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                             +            R +P  P +    R
Sbjct: 474 RAVRRRAAAGAPRRGVRGAPRPLRRAAGRPGRPAPGVPGRAGTPR 518


>gi|126326295|ref|XP_001367657.1| PREDICTED: hypothetical protein [Monodelphis domestica]
          Length = 749

 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 10/111 (9%), Positives = 32/111 (28%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R +         + + +      +               + ++  ++ + ++  S+ K  
Sbjct: 476 RHEEKRMRSRSKERDHEKVKEKEKHSDSRIKEREKSRSKERSKRAESKNNEHDHSRSKDK 535

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                 ++    V   K   +    +  +  +  RR+ S    R   R+  
Sbjct: 536 DKRAKSKSREREVTKGKHSSNGRTRERSRSRDKGRRARSRSKDRDRSRSKE 586


>gi|111224975|ref|YP_715769.1| hypothetical protein FRAAL5611 [Frankia alni ACN14a]
 gi|111152507|emb|CAJ64244.1| hypothetical protein FRAAL5611 [Frankia alni ACN14a]
          Length = 448

 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 15/140 (10%), Positives = 35/140 (25%), Gaps = 9/140 (6%)

Query: 224 QLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRP---NIISEVPD 280
            L  L     RE+   +  +  G   +       + P+       R         + +P 
Sbjct: 297 SLRDLDPTKFREIDVSVGDKYTGTAWVTLPGHPANPPLGDDPVAARSPDVPVGAGASLPG 356

Query: 281 DFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
             T    +         + +   P        +      + +  +  +         +P 
Sbjct: 357 AVTLPASDPRGDLPRPAEPRADMPRPAEPRGISEGETSPVAAEGVGTTAAAASPAAGAPG 416

Query: 341 FPSKRSLR------RTSAKK 354
            P + + R      R   K+
Sbjct: 417 LPGEDTARGRIGVLRGRRKR 436


>gi|239503259|ref|ZP_04662569.1| Cold-shock DEAD box protein A(ATP-dependent RNA helicasedeaD)
           [Acinetobacter baumannii AB900]
          Length = 586

 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 11/81 (13%), Positives = 19/81 (23%)

Query: 269 RDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDS 328
           + R     + P      K    +     + +        R      +  +   S    D 
Sbjct: 427 KRREGGRDDRPRRSFDDKPRGERPAFGGEDRPRREFNSDRPRREGGFEDRPKRSFGGEDR 486

Query: 329 GQREENHRRSPSFPSKRSLRR 349
            +RE N  R           R
Sbjct: 487 PRREFNSDRPRREGGFNDKPR 507


>gi|220915404|ref|YP_002490708.1| protein of unknown function UPF0044 [Anaeromyxobacter dehalogenans
           2CP-1]
 gi|219953258|gb|ACL63642.1| protein of unknown function UPF0044 [Anaeromyxobacter dehalogenans
           2CP-1]
          Length = 177

 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 10/109 (9%), Positives = 19/109 (17%), Gaps = 2/109 (1%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
              + +                V            +       + +        K     
Sbjct: 70  RLEIADRLLAEDVQVAQVLGRTVLAYRRHPERPRYEPAPAGARAERPEAKRAAAKGRRAP 129

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +   A                 GQR     + P+   +R   R    K
Sbjct: 130 AKEKRAPARGQRAPARERRAPARGQRAPAKGQRPA--GRRPAPRAKRTK 176


>gi|312378649|gb|EFR25165.1| hypothetical protein AND_09747 [Anopheles darlingi]
          Length = 1138

 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 13/109 (11%), Positives = 30/109 (27%), Gaps = 1/109 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G     + + +  +   +      D        P      +         +   +   P 
Sbjct: 892 GAAGDAKQESDWRSRPAAPAAGGGDDQQPGGAAPPKKDVWQPRRDGGPRAAGAGRDDGPR 951

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              +  S+ W  +G      + +G   +  RR P    +R   R   ++
Sbjct: 952 GGESAPSDKWR-RGPEDDKDNQAGAGRDGPRRGPGGEMRRGDDRGPIRR 999


>gi|289644990|ref|ZP_06477028.1| serine/threonine protein kinase [Frankia symbiont of Datisca
            glomerata]
 gi|289505205|gb|EFD26266.1| serine/threonine protein kinase [Frankia symbiont of Datisca
            glomerata]
          Length = 1625

 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 14/112 (12%), Positives = 30/112 (26%)

Query: 243  EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
              LG    ++          S                  +      S + +G     +  
Sbjct: 1512 NHLGARRHQQRHSGHRHHPSSQVAARGRLRPPRGSHRGGWRERSARSRRSSGRELAGRAG 1571

Query: 303  TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            T   RR       +         +D G+ + +   S   P + ++RR +  +
Sbjct: 1572 TAAQRRGDGGRARLPDARLLRRDADPGRPDCHRPGSDRLPERAAVRRGATPR 1623


>gi|284047202|ref|YP_003397542.1| ribosomal protein S4 [Conexibacter woesei DSM 14684]
 gi|283951423|gb|ADB54167.1| ribosomal protein S4 [Conexibacter woesei DSM 14684]
          Length = 210

 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 1/42 (2%)

Query: 22  RAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R G+AS R +  + +    V VNG   + A+  V   D + V
Sbjct: 109 RLGLASTRPQARQFVGHGHVLVNGQRCDIASRQVKPGDVVMV 150


>gi|312115898|ref|YP_004013494.1| translation initiation factor IF-2 [Rhodomicrobium vannielii ATCC
           17100]
 gi|311221027|gb|ADP72395.1| translation initiation factor IF-2 [Rhodomicrobium vannielii ATCC
           17100]
          Length = 972

 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 16/126 (12%), Positives = 27/126 (21%), Gaps = 8/126 (6%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +  K   E       E A+        +     R         PD    + +    +   
Sbjct: 163 LRAKEAAEPKPEAPKEPARQEAAPAAPAPRPTSRSAEPPRRVGPDTVRVIARPQDDRRPP 222

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS--------FPSKRSL 347
                 A     R   +      G   +     G R +    + +        F   R  
Sbjct: 223 RAPAPDARTADARPTDARGPARDGTRPAGARPDGARPQGGAGARAGAPGARPGFNGPRGA 282

Query: 348 RRTSAK 353
             T A 
Sbjct: 283 AATPAS 288


>gi|116669977|ref|YP_830910.1| translation initiation factor IF-2 [Arthrobacter sp. FB24]
 gi|189028280|sp|A0JUU0|IF2_ARTS2 RecName: Full=Translation initiation factor IF-2
 gi|116610086|gb|ABK02810.1| bacterial translation initiation factor 2 (bIF-2) [Arthrobacter sp.
           FB24]
          Length = 968

 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 7/102 (6%), Positives = 20/102 (19%), Gaps = 2/102 (1%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           +          +     R      +  P          +   G+ + +        R   
Sbjct: 134 KPGARPAPKAEAPAAPARSGGQGSAPRPGGPRPGNNPFATSQGMPRGRGGDNERPPRPGN 193

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            N +              + E      P+  +       + +
Sbjct: 194 -NPFAPSQGMPRPGGSRTEGERPGGPRPAAGAGGPRP-GAPR 233


>gi|114053273|ref|NP_001039496.1| junctional sarcoplasmic reticulum protein 1 [Bos taurus]
 gi|122138177|sp|Q2YDF7|JSPR1_BOVIN RecName: Full=Junctional sarcoplasmic reticulum protein 1
 gi|82571705|gb|AAI10245.1| Junctional sarcoplasmic reticulum protein 1 [Bos taurus]
          Length = 337

 Score = 37.9 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 16/122 (13%), Positives = 29/122 (23%), Gaps = 4/122 (3%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
             +   E+      E A                 +     E P      K+   +K    
Sbjct: 209 RSEEAAEKDEWESEEAADGEHVPLAGRGPKEKLKKEKPRKERPGKEKPQKEERPRKEKPR 268

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR----SPSFPSKRSLRRTSA 352
           K++K       +      W A+              E+ +R    S   P +        
Sbjct: 269 KEEKPRGAREPQGALPRRWEAREGGHRPWGRDSGAPEDRKRQAWVSLRRPDEEDRPLGRQ 328

Query: 353 KK 354
           K+
Sbjct: 329 KR 330


>gi|326924051|ref|XP_003208246.1| PREDICTED: LOW QUALITY PROTEIN: eukaryotic translation initiation
            factor 3 subunit A-like [Meleagris gallopavo]
          Length = 1359

 Score = 37.9 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 9/112 (8%), Positives = 24/112 (21%), Gaps = 6/112 (5%)

Query: 247  PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
            P   ++      A      ++  +         D+    ++   +   L +      P  
Sbjct: 930  PRRGDDLPRRGPAEEKERPSVESNEDRPPRREGDEDRPPRREGDEDRPLRRGLDEDRPPR 989

Query: 307  RR------NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            R       +  +         +       +R  +  R P             
Sbjct: 990  RGLDDDRGSWRAADDDRPPRRALDDDRPPRRALDDDRPPRRTLDDDRPPRRG 1041



 Score = 35.9 bits (81), Expect = 9.4,   Method: Composition-based stats.
 Identities = 7/116 (6%), Positives = 22/116 (18%), Gaps = 2/116 (1%)

Query: 237  SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            ++   R           +   D   +     +  R + +        + + +        
Sbjct: 898  TESEWRRAPVERDWRRGEARDDERPFRRSDDLPRRGDDLPRRGPAEEKERPSVESNED-- 955

Query: 297  KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            +  +      R                      +R  +  R     +        A
Sbjct: 956  RPPRREGDEDRPPRREGDEDRPLRRGLDEDRPPRRGLDDDRGSWRAADDDRPPRRA 1011


>gi|321459981|gb|EFX71028.1| hypothetical protein DAPPUDRAFT_112184 [Daphnia pulex]
          Length = 675

 Score = 37.9 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 13/156 (8%), Positives = 38/156 (24%), Gaps = 6/156 (3%)

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRI--SYGPFQLGTLLAGSTRE---VSKKILREQ 244
            +G+RE +N   ++     +  V  L  +    G  +  TL+  +  +   +  +    +
Sbjct: 232 EIGIRELRNEVQERQTRDRDMHVVSLQVLANRVGELERNTLIMEARMDAANLFPRETGAR 291

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
                             ++                      ++ +   G  +    +  
Sbjct: 292 PRAQRQSSRSPERRRQGAAAPNRGEPPEYGSPPPSYSSATRPQDDNWGRGRGRATAPSPQ 351

Query: 305 VHRRNLASNV-WMAKGIHSSFLSDSGQREENHRRSP 339
                 A N     +       +   +       +P
Sbjct: 352 RREGPRARNATPQREAPRPRTATPPREAPRPRTATP 387


>gi|290961784|ref|YP_003492966.1| protein kinase [Streptomyces scabiei 87.22]
 gi|260651310|emb|CBG74432.1| putative protein kinase [Streptomyces scabiei 87.22]
          Length = 438

 Score = 37.9 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 15/110 (13%), Positives = 29/110 (26%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           QL   L E A               R  P+  S    +    ++   Q     + +  + 
Sbjct: 262 QLSLRLKEIAAREAQGLSDLRPPAPRTDPDRASGRLAEQYVEQRTLRQPPDTRRSQPGSP 321

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                  +       G  +   S  G R    R +     + + R  + +
Sbjct: 322 SPRTGGGSRTGGGVGGARTGSGSRPGPRPAPSRGTTGSGRRPAPRSGAGR 371


>gi|215482158|ref|YP_002324340.1| Cold-shock DEAD box protein A(ATP-dependent RNA helicasedeaD)
           [Acinetobacter baumannii AB307-0294]
 gi|332868649|ref|ZP_08438296.1| DEAD/DEAH box helicase [Acinetobacter baumannii 6013113]
 gi|213986281|gb|ACJ56580.1| Cold-shock DEAD box protein A(ATP-dependent RNA helicasedeaD)
           [Acinetobacter baumannii AB307-0294]
 gi|332733221|gb|EGJ64416.1| DEAD/DEAH box helicase [Acinetobacter baumannii 6013113]
          Length = 586

 Score = 37.9 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 11/81 (13%), Positives = 19/81 (23%)

Query: 269 RDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDS 328
           + R     + P      K    +     + +        R      +  +   S    D 
Sbjct: 427 KRREGGRDDRPRRSFDDKPRGERPAFGGEDRPRREFNSDRPRREGGFEDRPKRSFGGEDR 486

Query: 329 GQREENHRRSPSFPSKRSLRR 349
            +RE N  R           R
Sbjct: 487 PRREFNSDRPRREGGFNDKPR 507


>gi|183985422|ref|YP_001853713.1| hypothetical protein MMAR_5451 [Mycobacterium marinum M]
 gi|183178748|gb|ACC43858.1| conserved hypothetical alanine and proline rich membrane protein
           [Mycobacterium marinum M]
          Length = 879

 Score = 37.9 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 13/131 (9%), Positives = 32/131 (24%), Gaps = 4/131 (3%)

Query: 226 GTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
             L A + R +  +    + GP   E +  +      S  TL R    + +         
Sbjct: 458 DDLEATAVRPLPTREPMRRNGPAADESSTASFAWLQQSQPTLDRPSGPMPAAPGAPVESA 517

Query: 286 KKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP----SF 341
              +  +    + +   +     +            +                P      
Sbjct: 518 PGRADGRRARRRAESRTSAASTPSPLVPTRAQPPGPTRAQPPRTAAPAQPATEPLPDAGA 577

Query: 342 PSKRSLRRTSA 352
           P+++S +    
Sbjct: 578 PAEQSKKPNKP 588


>gi|88855477|ref|ZP_01130141.1| hemolysin [marine actinobacterium PHSC20C1]
 gi|88815384|gb|EAR25242.1| hemolysin [marine actinobacterium PHSC20C1]
          Length = 264

 Score = 37.9 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 12/36 (33%), Positives = 19/36 (52%)

Query: 27 SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          SR    ++IA   V V+G+ + +A+  V     IEV
Sbjct: 18 SRTHAAKLIADNLVTVSGVAVPKASTPVSDEHEIEV 53


>gi|195574499|ref|XP_002105226.1| GD21371 [Drosophila simulans]
 gi|194201153|gb|EDX14729.1| GD21371 [Drosophila simulans]
          Length = 1003

 Score = 37.9 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 12/113 (10%), Positives = 39/113 (34%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            +     + +  +    A     ++  +   +   +  D   + +++  +K   S  +K 
Sbjct: 698 EDSQDKKIQDSKRQEYSAGKKREDSPSKKLKDSDRKRQDSPVKRQESPGRKRQDSPGRKR 757

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +P  R   +++      +     S   +R ++  R       R  + + A++
Sbjct: 758 DSPDKRAAESADKKQQDSLAKRQDSPGRRRRDSPERKRRDSPDRRRKDSPARR 810



 Score = 37.1 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 14/109 (12%), Positives = 36/109 (33%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                   +   D+     +   R   +   +  D  ++  K+S +K   S  K+  +P 
Sbjct: 687 RKRKDSANRKREDSQDKKIQDSKRQEYSAGKKREDSPSKKLKDSDRKRQDSPVKRQESPG 746

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +R  +           +  S   +++++  +    P +R       K+
Sbjct: 747 RKRQDSPGRKRDSPDKRAAESADKKQQDSLAKRQDSPGRRRRDSPERKR 795



 Score = 36.7 bits (83), Expect = 5.0,   Method: Composition-based stats.
 Identities = 16/109 (14%), Positives = 33/109 (30%), Gaps = 3/109 (2%)

Query: 231 GSTREVSK-KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
           G  RE S  K L++          +          ++  R R +      +   + +++S
Sbjct: 716 GKKREDSPSKKLKDSDRKRQDSPVKRQESPGRKRQDSPGRKRDSPDKRAAESADKKQQDS 775

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAK--GIHSSFLSDSGQREENHR 336
             K   S  ++      R+   S     K         S   +R++   
Sbjct: 776 LAKRQDSPGRRRRDSPERKRRDSPDRRRKDSPARRRQESSGRRRQDPDG 824



 Score = 36.3 bits (82), Expect = 7.8,   Method: Composition-based stats.
 Identities = 12/114 (10%), Positives = 38/114 (33%), Gaps = 1/114 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS-QKNGLSKQKK 300
           ++       +     +        +  + R +  S+   D  R +++S  ++     +K+
Sbjct: 690 KDSANRKREDSQDKKIQDSKRQEYSAGKKREDSPSKKLKDSDRKRQDSPVKRQESPGRKR 749

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             +P  +R+                S + +++   RR    P ++       ++
Sbjct: 750 QDSPGRKRDSPDKRAAESADKKQQDSLAKRQDSPGRRRRDSPERKRRDSPDRRR 803


>gi|167916838|ref|ZP_02503929.1| rhamnosyltransferase [Burkholderia pseudomallei 112]
          Length = 364

 Score = 37.9 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 19/143 (13%), Positives = 35/143 (24%), Gaps = 18/143 (12%)

Query: 216 IRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNII 275
            R   GPF+L  +  G         LR   G            A    +     D     
Sbjct: 226 RRHKVGPFELTAMHHGW--------LRRYYGARNAMHGAAVRVAVSGGAGAESADDLAGG 277

Query: 276 SEVPDDFTRMKKNSSQK----------NGLSKQKKLATPVHRRNLASNVWMAKGIHSSFL 325
                     ++ +  +           G+ +      P   R   +    A     +  
Sbjct: 278 PGGAVRAGEGREAARDRAGRARRGVRAPGVVRGGARGPPHGTRGGDARSAAAVVRRGART 337

Query: 326 SDSGQREENHRRSPSFPSKRSLR 348
             S +R+E    + + P    + 
Sbjct: 338 PASARRDERGEGTTARPGAHGIP 360


>gi|109037680|ref|XP_001091622.1| PREDICTED: membrane-associated guanylate kinase, WW and PDZ
            domain-containing protein 1 isoform 4 [Macaca mulatta]
          Length = 1470

 Score = 37.9 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 8/112 (7%), Positives = 28/112 (25%), Gaps = 1/112 (0%)

Query: 243  EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            ++ GP    +    + A     +    +               +K +  ++    ++   
Sbjct: 1224 DRHGPPTGPQGVPEVRAGPDRRQHPSLESSYPPDLHKSSP-HGEKRAHARDPKGSREYSR 1282

Query: 303  TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             P                       + +   + +   +  +    RR+  K+
Sbjct: 1283 QPNEHHTWNGTSRKPDSGACRPKDRAPEGRRDAQAERTAAANGPKRRSPEKR 1334


>gi|333025552|ref|ZP_08453616.1| hypothetical protein STTU_3058 [Streptomyces sp. Tu6071]
 gi|332745404|gb|EGJ75845.1| hypothetical protein STTU_3058 [Streptomyces sp. Tu6071]
          Length = 272

 Score = 37.9 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 8/76 (10%), Positives = 21/76 (27%)

Query: 273 NIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQRE 332
             + +      R +   ++    +     +     ++LA+      G   S  + S    
Sbjct: 85  RAVPQGGGTPGRARPGGARPEPSASPSPRSGRPTAKDLATPDGDRPGPRPSKPTASRPDR 144

Query: 333 ENHRRSPSFPSKRSLR 348
                 P+   + S  
Sbjct: 145 SAPPTRPAPTGRPSTP 160


>gi|2388676|gb|AAB80719.1| precollagen P [Mytilus edulis]
          Length = 902

 Score = 37.9 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 8/99 (8%), Positives = 17/99 (17%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
               +  A                            +   +       K     +R +  
Sbjct: 559 AEGPSGPAGPRGPAGSQGPSGERGEPGAPGKKGPNGDRGNQGSPGAPGKNGARGNRGSRG 618

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
           SN    +          G +  +  R       +   R 
Sbjct: 619 SNGSPGRSGSPGSRGKPGPQGPHGPRGLRGSPGQKGPRG 657


>gi|296485625|gb|DAA27740.1| junctional sarcoplasmic reticulum protein 1 [Bos taurus]
          Length = 337

 Score = 37.9 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 16/122 (13%), Positives = 29/122 (23%), Gaps = 4/122 (3%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
             +   E+      E A                 +     E P      K+   +K    
Sbjct: 209 RSEEAAEKDEWESEEAADGEHVPLAGRGPKEKLKKEKPRKERPGKEKPQKEERPRKEKPR 268

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR----SPSFPSKRSLRRTSA 352
           K++K       +      W A+              E+ +R    S   P +        
Sbjct: 269 KEEKPRGAREPQGALPRRWEAREGGHRPWGRDSGAPEDRKRQAWVSLRRPDEEDRPLGRQ 328

Query: 353 KK 354
           K+
Sbjct: 329 KR 330


>gi|302901454|ref|XP_003048441.1| hypothetical protein NECHADRAFT_105186 [Nectria haematococca mpVI
           77-13-4]
 gi|256729374|gb|EEU42728.1| hypothetical protein NECHADRAFT_105186 [Nectria haematococca mpVI
           77-13-4]
          Length = 787

 Score = 37.9 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 10/79 (12%), Positives = 21/79 (26%)

Query: 276 SEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENH 335
              P   + M +   +++  +   K   P  R             H         R    
Sbjct: 205 RPAPHLASEMLRGRPRRHPPAGPAKPQAPPERPAKTQAAPERSAKHQGSHERPPVRPPAE 264

Query: 336 RRSPSFPSKRSLRRTSAKK 354
           + S   P K + +    ++
Sbjct: 265 KPSEKTPEKPAEKPAPDQQ 283


>gi|238062349|ref|ZP_04607058.1| LOW QUALITY PROTEIN: CDP-glycerol:poly(glycerophosphate)
           glycerophosphotransferase [Micromonospora sp. ATCC
           39149]
 gi|237884160|gb|EEP72988.1| LOW QUALITY PROTEIN: CDP-glycerol:poly(glycerophosphate)
           glycerophosphotransferase [Micromonospora sp. ATCC
           39149]
          Length = 735

 Score = 37.9 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 9/111 (8%), Positives = 22/111 (19%), Gaps = 2/111 (1%)

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
             P    +          +     R    + ++ P    R+         + + +     
Sbjct: 527 QRPAGHRDLHRGTRGARPARPGPRRPGRAVRADAPRAPARVPAAVRPGAAVRRARPHRPA 586

Query: 305 VHRRN--LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              ++         +           G      R  P        RR   +
Sbjct: 587 AGAQSLLRRPRSAASPRPRPRAGLRPGAGARRQRPRPGGGPLPRRRRAGHR 637



 Score = 37.1 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 9/99 (9%), Positives = 16/99 (16%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R   G              + +       R            R + +       S  ++ 
Sbjct: 537 RGTRGARPARPGPRRPGRAVRADAPRAPARVPAAVRPGAAVRRARPHRPAAGAQSLLRRP 596

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
            +    R                    G      RR   
Sbjct: 597 RSAASPRPRPRAGLRPGAGARRQRPRPGGGPLPRRRRAG 635



 Score = 36.3 bits (82), Expect = 8.2,   Method: Composition-based stats.
 Identities = 14/101 (13%), Positives = 27/101 (26%), Gaps = 2/101 (1%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                A   + A +     + R RP+  +       R  ++++      +         R
Sbjct: 558 ADAPRAPARVPAAVRPGAAVRRARPHRPAAGAQSLLRRPRSAASPRPRPRAGLRPGAGAR 617

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           R                       +   RR  + P+ R LR
Sbjct: 618 RQRPRPGGGPLPRRRRAGHRLLVGDVRLRR--AGPADRGLR 656


>gi|241664054|ref|YP_002982414.1| RNA-binding S4 domain-containing protein [Ralstonia pickettii
          12D]
 gi|240866081|gb|ACS63742.1| RNA-binding S4 domain protein [Ralstonia pickettii 12D]
          Length = 132

 Score = 37.9 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 2/59 (3%)

Query: 5  NIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +  +     R+ K + A     +R +    + + RV++N   +   A +V   DH+ V
Sbjct: 2  KVSTDAADRVRIDKWLWAARFFKTRSQATDAVERGRVQINDQAVR-PAKDVKIGDHVRV 59


>gi|268555766|ref|XP_002635872.1| Hypothetical protein CBG01089 [Caenorhabditis briggsae]
          Length = 696

 Score = 37.9 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 16/114 (14%), Positives = 35/114 (30%), Gaps = 2/114 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           ++ G        +       S E      P    +   +  +      +K G  + ++  
Sbjct: 172 QKPGSPDPRIPGIPEVQEPGSPEARKPRSPEAQIQGIPEDRKPGSPDPRKPGFREFRRSR 231

Query: 303 TPVHRRNLASNVW--MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +P  R+  +       + G   S   ++ +      R P  P   +  R  A+K
Sbjct: 232 SPEARKPRSPEARILGSPGFRRSRSPEARKPGSPEARKPGSPDPGNSGRPEARK 285



 Score = 36.3 bits (82), Expect = 8.0,   Method: Composition-based stats.
 Identities = 12/118 (10%), Positives = 25/118 (21%), Gaps = 3/118 (2%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
             R+   P            P                +      R       +     + 
Sbjct: 434 EARKPGSPGFRRSRSPEARKPGSPEARKPGSPDPGARKPGGPEARKPGFPEARISGIPEA 493

Query: 300 KLATPVH---RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +          R+  +    +     S   ++ +      R P  P   +  R  A+K
Sbjct: 494 RNPGSPEFWKSRSPEARKPGSPDPRDSGGPEARKPGSPEARKPGSPDPGNSGRPEARK 551


>gi|310791660|gb|EFQ27187.1| MIF4G domain-containing protein [Glomerella graminicola M1.001]
          Length = 910

 Score = 37.9 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 17/103 (16%), Positives = 35/103 (33%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                 +      +S ++               +R    +S  +  S+      P   R+
Sbjct: 772 RSSKPDSRRTARRNSSSVSSVPRKRARYDSRSPSRSPSRASSYDSRSRSPVRRGPRDSRS 831

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             +       I     +   +R+++  RSPS   +RSL+R+S 
Sbjct: 832 PPARPRDIASISPPPRARVARRDDSASRSPSPAPRRSLKRSSP 874


>gi|281333903|gb|ADA61156.1| granule bound starch synthase [Panicum miliaceum]
 gi|281333905|gb|ADA61157.1| granule bound starch synthase [Panicum miliaceum]
 gi|281333911|gb|ADA61160.1| granule bound starch synthase [Panicum miliaceum]
 gi|281333913|gb|ADA61161.1| granule bound starch synthase [Panicum miliaceum]
          Length = 450

 Score = 37.9 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 11/116 (9%), Positives = 23/116 (19%), Gaps = 1/116 (0%)

Query: 226 GTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
           G +     R V    LR+                P   +  + R                
Sbjct: 286 GQVHRHQVRRVDGH-LRQGAQQGGAAGRGRPPRGPEDPAGGVRRQARGAEGPRRHGRRHP 344

Query: 286 KKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF 341
             +   +       +        +        +G     +        + RR P+ 
Sbjct: 345 AAHGGGRPDRPSGHREEEVRAHADERGGEVPRQGARRGEVQRGAGAPHHGRRRPAR 400


>gi|295836315|ref|ZP_06823248.1| LOW QUALITY PROTEIN: hsp90-like protein [Streptomyces sp. SPB74]
 gi|295825957|gb|EFG64572.1| LOW QUALITY PROTEIN: hsp90-like protein [Streptomyces sp. SPB74]
          Length = 611

 Score = 37.9 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 8/91 (8%), Positives = 19/91 (20%)

Query: 263 SSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHS 322
                   RP +   + +      + + ++ G         P   R              
Sbjct: 15  PGRPARPGRPPLPPSLRESTRLSARAAPERGGRRHGAPRDGPRRARAHPPAHRWRAAERH 74

Query: 323 SFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                 G+              ++ RR   +
Sbjct: 75  RHGHRPGRARHARAARDDRAQFQARRRNRGR 105


>gi|254294585|ref|YP_003060608.1| DEAD/DEAH box helicase [Hirschia baltica ATCC 49814]
 gi|254043116|gb|ACT59911.1| DEAD/DEAH box helicase domain protein [Hirschia baltica ATCC 49814]
          Length = 769

 Score = 37.9 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 7/97 (7%), Positives = 23/97 (23%)

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
           +           DR     +      R      + +    +            +      
Sbjct: 602 ENRGGYQGRDGGDRRPPNRDERMAGERPPSRGYEGSNPRPRTNYDKTRAADGRSWGNDRK 661

Query: 318 KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +G  S      G     +++  +   ++   R  +++
Sbjct: 662 EGGRSEGGRSEGGERTWNKKKSADGERKQTPRGRSER 698


>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 = 37.9 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 28/254 (11%), Positives = 65/254 (25%), Gaps = 66/254 (25%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRV--------------KVNGILLERAAVNVMS 56
               R+ K I+        E+E       +              KVN   ++  +  +  
Sbjct: 6   DEIIRIDKFISD-------ELEE------IPREKIKDFIKDKKIKVNNSFVK-PSFKLSE 51

Query: 57  TDHIEVDGVPLRKAERTRLWL---------------------YHKPIGLVTTHSDP---- 91
            D IE+D       E     +                      H    ++T         
Sbjct: 52  GDEIEIDDSLFHVPELKAEDMELKIVYENDDYAIIDKDSNVIVHPAGKIITGTLVNGLLG 111

Query: 92  ------------DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
                       D R  +   L    + +I++ + +   +    +     + +       
Sbjct: 112 RYGYDGLSHIGGDDRPGIVHRLDKDTTGLIAITKTNEAYKYFKKMFETRKVDKYYYAIVF 171

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
                 +      +D+D  N  K  +   G         + ++    + V + +  G+  
Sbjct: 172 GNFDKKKGTIDNFMDRDVHNRRKMAVRNTGRRA-VSHYEVISEVEGFSLVRIKIETGRTH 230

Query: 200 EIKKVFEFFNWKVN 213
           +I+      N  + 
Sbjct: 231 QIRVHMTHINHPIL 244


>gi|115709908|ref|XP_783664.2| PREDICTED: similar to MGC84161 protein [Strongylocentrotus
           purpuratus]
 gi|115954672|ref|XP_001192738.1| PREDICTED: similar to MGC84161 protein [Strongylocentrotus
           purpuratus]
          Length = 805

 Score = 37.9 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 18/108 (16%), Positives = 35/108 (32%), Gaps = 15/108 (13%)

Query: 259 APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAK 318
               ++       P+  S      T   K S+ K      KK A    +R+ +++   + 
Sbjct: 578 KSGKNAPPRPDKPPSKKSGGSQPKTSTPKKSAPKQSPKADKKNAKSSPKRSGSASPSKSG 637

Query: 319 GIHSSFLSDSGQREEN---------------HRRSPSFPSKRSLRRTS 351
           G+  +       +  +                +RSPS   KRS  ++ 
Sbjct: 638 GVKKTSAKTKSAKPASTTKSPKSKTSPKSKSAKRSPSKSPKRSPTKSP 685


>gi|71051451|gb|AAH34980.1| LOC100170229 protein [Homo sapiens]
          Length = 603

 Score = 37.9 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 14/107 (13%), Positives = 26/107 (24%), Gaps = 1/107 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                  +         S       + +       +  R +  S        + +  +P 
Sbjct: 381 KERDHRGSSSPRKESGRSQSGSPNKQRDHSRSRSPNKARDRSRSRSPYKARDRSRSRSPN 440

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             R   S             S S  +  +H RS S    R   R+ +
Sbjct: 441 KAR-DCSRSRSPYKARDRSRSRSPNKARDHSRSRSPNKARDRSRSRS 486



 Score = 36.3 bits (82), Expect = 7.5,   Method: Composition-based stats.
 Identities = 19/112 (16%), Positives = 33/112 (29%), Gaps = 1/112 (0%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                   ++        +S         +          R +  S   N      +  +
Sbjct: 391 PRKESGRSQSGSPNKQRDHSRSRSPNKARDRSRSRSPYKARDRSRSRSPNKARDCSRSRS 450

Query: 304 PVHRRNL-ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           P   R+   S        HS   S +  R+ +  RSP+  S  S  R S+K+
Sbjct: 451 PYKARDRSRSRSPNKARDHSRSRSPNKARDRSRSRSPNKQSGYSRPRASSKE 502


>gi|332524912|ref|ZP_08401098.1| hypothetical protein RBXJA2T_03848 [Rubrivivax benzoatilyticus JA2]
 gi|332108207|gb|EGJ09431.1| hypothetical protein RBXJA2T_03848 [Rubrivivax benzoatilyticus JA2]
          Length = 261

 Score = 37.9 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 5/62 (8%), Positives = 13/62 (20%)

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
           +    ++ +      R          +G         G R +  R       +       
Sbjct: 196 EQARRERAERPPMPPREARPGGPRPDRGPRRDGERGPGPRRDGARPQGPRGERGPRPEGQ 255

Query: 352 AK 353
            +
Sbjct: 256 GR 257


>gi|298709398|emb|CBJ31331.1| conserved unknown protein [Ectocarpus siliculosus]
          Length = 629

 Score = 37.9 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 14/93 (15%), Positives = 23/93 (24%)

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
           D           D      +        +       G            RR+ +S+   A
Sbjct: 116 DMSPPRRRRRRHDSSEDGGDASPPRRNPRNGGRSDPGDDGDASPPRRRRRRHDSSDGEDA 175

Query: 318 KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                +     G R +      + PS+R  RR 
Sbjct: 176 SPARRNPRDGRGGRTDPGDDGDASPSRRQRRRH 208


>gi|53981930|gb|AAV25048.1| putative polyprotein [Oryza sativa Japonica Group]
          Length = 1093

 Score = 37.9 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 6/97 (6%), Positives = 21/97 (21%)

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
            A   S E   +           + +  +   +  + +           R          
Sbjct: 300 MAVGASEERAPKGHDGAGGSRRGEQSTPRGGRASGSRVRGPGSNRPADARGKRKQGGTPP 359

Query: 318 KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                   +     +     +P+   +   ++   +K
Sbjct: 360 PSPPRGGGAARASSKRPEGAAPASQPEGERKKKRPRK 396


>gi|284991446|ref|YP_003410000.1| hypothetical protein Gobs_3019 [Geodermatophilus obscurus DSM
           43160]
 gi|284064691|gb|ADB75629.1| conserved hypothetical protein [Geodermatophilus obscurus DSM
           43160]
          Length = 658

 Score = 37.9 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 11/112 (9%), Positives = 25/112 (22%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R        +    +   P      + R          D     +     +    ++   
Sbjct: 137 RPSADRGRDDRPGRDDRRPQGDRPAVGRSDWRDRRPSADRGRDDRAGQDDRRPQGERPAR 196

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            +   RR+        +    S+       E      P+  S +  R    +
Sbjct: 197 GSWQDRRSAGERPQGERPARGSWQDRRSAGERPQGERPARGSWQDRRSAGER 248



 Score = 37.5 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 10/81 (12%), Positives = 19/81 (23%)

Query: 270 DRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSG 329
            R        +   R      +  G   Q +       ++  S     +G   +  +   
Sbjct: 202 RRSAGERPQGERPARGSWQDRRSAGERPQGERPARGSWQDRRSAGERPQGERPARSTWQD 261

Query: 330 QREENHRRSPSFPSKRSLRRT 350
           +R    R        R   R 
Sbjct: 262 RRSAGERPQGEQTGWRDRPRG 282


>gi|157125581|ref|XP_001654397.1| hypothetical protein AaeL_AAEL010246 [Aedes aegypti]
 gi|108873576|gb|EAT37801.1| conserved hypothetical protein [Aedes aegypti]
          Length = 569

 Score = 37.9 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 15/102 (14%), Positives = 27/102 (26%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
                      + E+  R           D +  +++  Q +      +      R+   
Sbjct: 205 SDHSPPRKRGNNDESPPRRSHKERKRRNSDESPPRRSRRQSDSDQSPPRKRQDDSRKARR 264

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                +        S          RSPS  S+ SLRR   +
Sbjct: 265 RKDSDSDVSPPRRSSKPDHNRVKQERSPSRASEFSLRRVKQE 306


>gi|24658459|ref|NP_647974.1| CG5146 [Drosophila melanogaster]
 gi|23094104|gb|AAF50767.2| CG5146 [Drosophila melanogaster]
          Length = 1929

 Score = 37.9 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 13/113 (11%), Positives = 31/113 (27%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            E  G     +            + L R +   +S+  D+     +N++      + +  
Sbjct: 338 DEGRGKGRERDLFRRKSRERSQDKNLNRAKSMNLSKEKDEVGGEPRNTASGKSQERDQSR 397

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                R              S     +  +  +   + +   KRS  R   ++
Sbjct: 398 GKTKDRSRERDRTRNKTREKSQARDQTRSKANDAEHTRAKSRKRSSSRDKRRE 450


>gi|237833839|ref|XP_002366217.1| hypothetical protein TGME49_025440 [Toxoplasma gondii ME49]
 gi|211963881|gb|EEA99076.1| hypothetical protein TGME49_025440 [Toxoplasma gondii ME49]
          Length = 1590

 Score = 37.5 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 11/108 (10%), Positives = 32/108 (29%)

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G   E+ ++  R+  G   +                 +  + +  +    +  R +    
Sbjct: 370 GRFTELFQRFSRDLEGARHVTSQTAEQLVAFSQVLLRLAHQSSRDAPKGSEAARERAGRD 429

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS 338
           + +   K+ +   P  RR+               + ++G+ +   R  
Sbjct: 430 RASTDEKEARGRPPKRRRDAGERNRGDSVEREETIGEAGKGDGRKRGK 477


>gi|187734944|ref|YP_001877056.1| ribosomal protein S4 [Akkermansia muciniphila ATCC BAA-835]
 gi|226697794|sp|B2UNG3|RS4_AKKM8 RecName: Full=30S ribosomal protein S4
 gi|187424996|gb|ACD04275.1| ribosomal protein S4 [Akkermansia muciniphila ATCC BAA-835]
          Length = 203

 Score = 37.5 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 11/52 (21%), Positives = 20/52 (38%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLY 78
           +R    ++++   + VNG     A+ +    D I V G    +   TR    
Sbjct: 107 TRAGARQLVSHGHITVNGKKTNIASYSCRPGDVIAVGGKASSQQLVTRFLDL 158


>gi|196968455|gb|ACG80801.1| hypothetical protein [Chlamydophila pecorum]
          Length = 121

 Score = 37.5 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 21/121 (17%), Positives = 38/121 (31%), Gaps = 1/121 (0%)

Query: 224 QLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
           +L  L   S++E+S K       P   E +   L     SS+ L     +     P + +
Sbjct: 2   ELKDLETSSSKELSPKE-PSPKEPSPKEPSPKELSPKEPSSKELSPKELSPKEPSPKEPS 60

Query: 284 RMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
             + +  + +      K  +P        +         S    S +   +   S   PS
Sbjct: 61  SKELSPKEPSPKEPSSKELSPKEPSPKEPSSKELSPKEPSPKEPSPKEPSSKEPSSKEPS 120

Query: 344 K 344
           K
Sbjct: 121 K 121


>gi|194747085|ref|XP_001955983.1| GF24975 [Drosophila ananassae]
 gi|190623265|gb|EDV38789.1| GF24975 [Drosophila ananassae]
          Length = 1051

 Score = 37.5 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 13/113 (11%), Positives = 30/113 (26%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +E+     +E+ +              R                 +  S +    +++  
Sbjct: 500 KERDRKGSVEKERRERKKSPERERDRKRSVEKERGRKRSPEKERDRKRSPEKERDRKRSA 559

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                R+  A        +  +       +E   RRS    S    RR+  ++
Sbjct: 560 EKERDRKRSAEKEREKPKVRPASKERHRSKEIKRRRSKDRQSSNDRRRSKDRQ 612


>gi|326487698|dbj|BAK05521.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 1238

 Score = 37.5 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 14/138 (10%), Positives = 34/138 (24%), Gaps = 24/138 (17%)

Query: 241  LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG------ 294
            +++  G    E  +  + A    +              P    R +    +  G      
Sbjct: 885  IKKGRGRPRKERPEAAVSAESGDTALAATRPRKEKRGRPRKEKRGRPRKERPEGAISAES 944

Query: 295  --------LSKQKKLATPVHRRNL---ASNVWMAKGIHSSFLSDSGQRE-------ENHR 336
                      +++K   P   R     ++    A+           +         E+  
Sbjct: 945  GDAAFLAARPRKEKRGRPRKERPEWAISAESGEAERPRKEKRGRPRKERPQAAISGESGD 1004

Query: 337  RSPSFPSKRSLRRTSAKK 354
             + +    R  +R   +K
Sbjct: 1005 GALTEARPRKEKRGRPRK 1022



 Score = 37.1 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 6/123 (4%), Positives = 18/123 (14%), Gaps = 11/123 (8%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
              L +       E           +                    + +    ++   + 
Sbjct: 841 DDHLGDLEMEKPTEAIFAETVDARSAETGAAMPGEKAGDSASAGIKKGRGRPRKERPEAA 900

Query: 298 -----------QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
                        +       R         +         +   +     +     KR 
Sbjct: 901 VSAESGDTALAATRPRKEKRGRPRKEKRGRPRKERPEGAISAESGDAAFLAARPRKEKRG 960

Query: 347 LRR 349
             R
Sbjct: 961 RPR 963


>gi|153003160|ref|YP_001377485.1| hypothetical protein Anae109_0283 [Anaeromyxobacter sp. Fw109-5]
 gi|152026733|gb|ABS24501.1| protein of unknown function UPF0044 [Anaeromyxobacter sp. Fw109-5]
          Length = 168

 Score = 37.5 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 11/72 (15%), Positives = 21/72 (29%), Gaps = 1/72 (1%)

Query: 279 PDDFTRMKKNSSQKNGLSKQKKLATPVHR-RNLASNVWMAKGIHSSFLSDSGQREENHRR 337
                + +  +       K+ +   P  R +   S    AKG         G +      
Sbjct: 97  RRHPEKPRYEAPTARPALKELESPAPRTRGKARRSPARGAKGPARGAKPGRGAKGAARGA 156

Query: 338 SPSFPSKRSLRR 349
            P+  + R+  R
Sbjct: 157 KPARGAARTRSR 168


>gi|39936655|ref|NP_948931.1| triple helix repeat-containing collagen [Rhodopseudomonas palustris
           CGA009]
 gi|39650511|emb|CAE29034.1| Collagen triple helix repeat:Antifreeze protein, type I
           [Rhodopseudomonas palustris CGA009]
          Length = 212

 Score = 37.5 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 8/99 (8%), Positives = 14/99 (14%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
               ++           R                    +    KQ  +  P  +      
Sbjct: 1   MAEAESTRRGRPGPQGPRGRPGEPGRPGPQGHPGRPGPEGPRGKQGPVGKPGPQGKAGPQ 60

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                          G      +  P  P      R   
Sbjct: 61  GKPGIAGKPGPDGKPGPIGPQGKPGPQGPRGEQGLRGEQ 99


>gi|301123055|ref|XP_002909254.1| conserved hypothetical protein [Phytophthora infestans T30-4]
 gi|262100016|gb|EEY58068.1| conserved hypothetical protein [Phytophthora infestans T30-4]
          Length = 713

 Score = 37.5 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 11/110 (10%), Positives = 22/110 (20%), Gaps = 6/110 (5%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT-- 303
           GP+       +       +       P        +         +    S  +      
Sbjct: 464 GPNGPPNMFPSRGRSRSPNRPPPNMFPPRGRSRSPNRPPPNMFPPRGRSRSPNRPPPNMF 523

Query: 304 PVHRRNLASNVWMAKG--IHSSFLSDSGQREENHRRSP--SFPSKRSLRR 349
           P   R+ + N               + G    +  R P      +    R
Sbjct: 524 PPRGRSRSPNRPPPGDMMRKRDRSWERGGPPPDMMRRPFNGPGGRPDSPR 573



 Score = 36.7 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 12/104 (11%), Positives = 19/104 (18%), Gaps = 4/104 (3%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS----QKNGLSKQKKLAT 303
                 +   +       +   +RP      P   +R             G S+      
Sbjct: 477 RSRSPNRPPPNMFPPRGRSRSPNRPPPNMFPPRGRSRSPNRPPPNMFPPRGRSRSPNRPP 536

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
           P          W   G     +            SP     R  
Sbjct: 537 PGDMMRKRDRSWERGGPPPDMMRRPFNGPGGRPDSPRMMEPRPF 580


>gi|218530745|ref|YP_002421561.1| DEAD/DEAH box helicase [Methylobacterium chloromethanicum CM4]
 gi|218523048|gb|ACK83633.1| DEAD/DEAH box helicase domain protein [Methylobacterium
           chloromethanicum CM4]
          Length = 510

 Score = 37.5 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 11/109 (10%), Positives = 18/109 (16%), Gaps = 2/109 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            E   P    + +                         +                +    
Sbjct: 391 EEARRPPRQPQGRPGQRQGRPGGGRGQGGEGRGEPRAHEARGGRPGGQPGHRQDQRAAGA 450

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR--SPSFPSKRSLR 348
             P  +R        A           G R  + RR   P+       R
Sbjct: 451 PRPDGQRQDQRRPERAGEARPQGARPQGARPSDGRRDGRPARSGGEGGR 499


>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 = 37.5 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 30/250 (12%), Positives = 66/250 (26%), Gaps = 48/250 (19%)

Query: 7   VQENFTPQRVSKVIARAG-----IASRREVERMIAQQRVKVNGILLE----RAAVNVMST 57
           V      +R+ + +           SR +V+R I+   V+           +A+  V + 
Sbjct: 11  VSAEDAGERLDRWLTDRLQEDEIEVSRTQVQRWISDGCVR----RARPGRLKASDPVEAG 66

Query: 58  DHIEVD-------------GVP--LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
           D  EVD             GVP  +   +   + +      +V   +     + V   L 
Sbjct: 67  DLYEVDVPEEEPMELAPDAGVPFAVAYEDDDVVVVDKPRGVVVHPGAGHMRGTLVNGLLA 126

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ------- 155
                    G +       +     G +       + +WL         + +        
Sbjct: 127 RGTQLCTLAGAMRPGVVHRIDKDTSGLVVFAKSDRAYRWLVEAFRAHDVEREYVAIAHGR 186

Query: 156 -------------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                              ++  V QG         +       +++ + L  G+  +I+
Sbjct: 187 MSHREGTIDMPIARDPADRQRMAVRQGGKRAVTHFEVLESFAKYSYLRLRLETGRTHQIR 246

Query: 203 KVFEFFNWKV 212
                    +
Sbjct: 247 VHLAAIGHPI 256


>gi|167644006|ref|YP_001681669.1| translation initiation factor IF-2 [Caulobacter sp. K31]
 gi|189028306|sp|B0T167|IF2_CAUSK RecName: Full=Translation initiation factor IF-2
 gi|167346436|gb|ABZ69171.1| translation initiation factor IF-2 [Caulobacter sp. K31]
          Length = 1045

 Score = 37.5 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 9/102 (8%), Positives = 18/102 (17%), Gaps = 1/102 (0%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
           + + D     S T             D     +    +       +       R      
Sbjct: 227 EPSRDRRDDRSSTTTYRPGPGAPPQGDRPQGDRPQGDRPFNQRAPRPDGPYNQRTPRPDA 286

Query: 314 VWMAKGIHSSF-LSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               +G            R +  R     P     +     +
Sbjct: 287 GGPPRGPRPEGAGGFRNDRPQGDRPQGDRPQGDRPQGDRPTQ 328



 Score = 37.5 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 12/107 (11%), Positives = 17/107 (15%), Gaps = 1/107 (0%)

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G TR       R                 P        R + +              N  
Sbjct: 221 GQTRTYEPSRDRRDDRSSTTTYRPGPGAPPQGDRPQGDRPQGDRPFNQRAPRPDGPYNQR 280

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
                +       P             +G         G R +  R 
Sbjct: 281 TPRPDAG-GPPRGPRPEGAGGFRNDRPQGDRPQGDRPQGDRPQGDRP 326


>gi|163851993|ref|YP_001640036.1| DEAD/DEAH box helicase domain-containing protein [Methylobacterium
           extorquens PA1]
 gi|240139120|ref|YP_002963595.1| RNA helicase [Methylobacterium extorquens AM1]
 gi|163663598|gb|ABY30965.1| DEAD/DEAH box helicase domain protein [Methylobacterium extorquens
           PA1]
 gi|240009092|gb|ACS40318.1| RNA helicase [Methylobacterium extorquens AM1]
          Length = 510

 Score = 37.5 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 11/109 (10%), Positives = 18/109 (16%), Gaps = 2/109 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            E   P    + +                         +                +    
Sbjct: 391 EEARRPPRQPQGRPGQRQGRPGGGRGQGGEGRGEPRAHEARGGRPGGQPGHRQDQRAAGA 450

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR--SPSFPSKRSLR 348
             P  +R        A           G R  + RR   P+       R
Sbjct: 451 PRPDGQRQDQRRPERAGEARPQGARPQGARPSDGRRDGRPARSGGEGGR 499


>gi|307326779|ref|ZP_07605971.1| ribosomal protein S4 [Streptomyces violaceusniger Tu 4113]
 gi|306887542|gb|EFN18536.1| ribosomal protein S4 [Streptomyces violaceusniger Tu 4113]
          Length = 203

 Score = 37.5 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 3/50 (6%)

Query: 15  RVSKVIARAGIASRR--EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  ++ R+GIA R   +  +M+    ++VNG  +++ +  V   D + V
Sbjct: 92  RLDALVLRSGIA-RTIYQSRQMVTHGHIEVNGRKVDKPSFRVRPDDVVMV 140


>gi|291244371|ref|XP_002742070.1| PREDICTED: hypothetical protein [Saccoglossus kowalevskii]
          Length = 803

 Score = 37.5 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 21/108 (19%), Positives = 36/108 (33%), Gaps = 1/108 (0%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P    + +  L+ PI         R +            +K S+     ++Q K  +P  
Sbjct: 574 PPRRTQRESPLEEPIEKKSESPPRRTHREKSASPHRRSHRKKSTSPPRKTEQNKSYSPHR 633

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           R    S     K    S +    +R ++H    S   +RS    S K+
Sbjct: 634 REKRRSQTPSPKRSRGSRMKKE-RRRKSHSPRTSEKRRRSSISPSGKR 680


>gi|254561714|ref|YP_003068809.1| RNA helicase [Methylobacterium extorquens DM4]
 gi|254268992|emb|CAX24953.1| RNA helicase [Methylobacterium extorquens DM4]
          Length = 510

 Score = 37.5 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 11/109 (10%), Positives = 18/109 (16%), Gaps = 2/109 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            E   P    + +                         +                +    
Sbjct: 391 EEARRPPRQPQGRPGQRQGRPGGGRGQGGEGRGEPRAHEARGGRPGGQPGHRQDQRAAGA 450

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR--SPSFPSKRSLR 348
             P  +R        A           G R  + RR   P+       R
Sbjct: 451 PRPDGQRQDQRRPERAGEARPQGARPQGARPSDGRRDGRPARSGGEGGR 499


>gi|268535680|ref|XP_002632975.1| C. briggsae CBR-COL-119 protein [Caenorhabditis briggsae]
 gi|187022386|emb|CAP38437.1| CBR-COL-119 protein [Caenorhabditis briggsae AF16]
          Length = 289

 Score = 37.5 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 6/72 (8%), Positives = 14/72 (19%), Gaps = 1/72 (1%)

Query: 281 DFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
                +  +  + G   Q     P  +              ++       R +     P 
Sbjct: 199 RNGEPQPGAPGEPGRPGQPGPRGPAGQPGKDGAQGGPGEKGANGEPGQPGR-DGQPGRPG 257

Query: 341 FPSKRSLRRTSA 352
            P +        
Sbjct: 258 QPGRDGHPGEKG 269


>gi|323451283|gb|EGB07161.1| hypothetical protein AURANDRAFT_71859 [Aureococcus anophagefferens]
          Length = 446

 Score = 37.5 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 12/113 (10%), Positives = 28/113 (24%), Gaps = 2/113 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R Q          +             R  P +         + +++  + +G   +K  
Sbjct: 224 RAQGPLRPRALPPLPPRRHKIRDGLRGRHDPPLGRRAAGRGLKSRRSHPKSSGCFAKKNA 283

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                 R          G  S  L        + R +    ++     +S+ +
Sbjct: 284 ERLP--RGGPRTASAPPGARSRGLRGRRAAPGSRRAARRETNQDDRPGSSSAR 334


>gi|294886057|ref|XP_002771535.1| conserved hypothetical protein [Perkinsus marinus ATCC 50983]
 gi|239875241|gb|EER03351.1| conserved hypothetical protein [Perkinsus marinus ATCC 50983]
          Length = 285

 Score = 37.5 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 16/116 (13%), Positives = 37/116 (31%), Gaps = 3/116 (2%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +    +RE       +    + +  +   +  V+ R   +      F R K    ++ G 
Sbjct: 134 LDDAEVREADLTAKAQAVVPDEERAVKHRKGAVKRRKGAVKRRKGAFKRRKGAFKRRKGA 193

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
            K +K A    +  +       KG   +     G++    RR  +   ++   +  
Sbjct: 194 VKGRKGAVKGRKGAVKRRKGAVKGRKGAVK---GRKGAVKRRKGAVKGRKGAVKGR 246


>gi|309781354|ref|ZP_07676090.1| heat shock protein 15 [Ralstonia sp. 5_7_47FAA]
 gi|308919767|gb|EFP65428.1| heat shock protein 15 [Ralstonia sp. 5_7_47FAA]
          Length = 132

 Score = 37.5 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 2/59 (3%)

Query: 5  NIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +  +     R+ K + A     +R +    + + RV+VN   +   A  V   DH+ V
Sbjct: 2  KVSTDAADRVRIDKWLWAARFFKTRSQATDAVERGRVQVNDQGVR-PAKEVKIGDHVRV 59


>gi|256783012|ref|ZP_05521443.1| non-ribosomal peptide synthase [Streptomyces lividans TK24]
          Length = 687

 Score = 37.5 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 15/118 (12%), Positives = 24/118 (20%), Gaps = 1/118 (0%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           +++ LR    P       V            V          P   T        + G  
Sbjct: 564 TERALRRPGTPTSPHRRVVPRLPDPPPGRPRVDRAGPRPLAGPPAGTATAARPPLRPGPG 623

Query: 297 KQKKLA-TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             ++    P         +   +        D   R     R      +R  RR    
Sbjct: 624 DARRPRLHPAPAEPAGRGLAGRQAGRRPARPDPVHRPARPVRGGPGGLERGRRRDRHA 681


>gi|52352850|gb|AAU43855.1| HMGA2e' [Homo sapiens]
 gi|52352852|gb|AAU43856.1| HMGA2e [Homo sapiens]
          Length = 147

 Score = 37.5 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 5/81 (6%), Positives = 17/81 (20%), Gaps = 2/81 (2%)

Query: 276 SEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ--REE 333
           S   +   +   ++  +      +K      R+                     +     
Sbjct: 2   SARGEGAGQPSTSAQGQPAAPAPQKRGRGRPRKQQQEPTGEPSPKRPRGRPKGSKNKSPS 61

Query: 334 NHRRSPSFPSKRSLRRTSAKK 354
              +  +  +     R   +K
Sbjct: 62  KAAQKKAEATGEKRPRGRPRK 82


>gi|308176801|ref|YP_003916207.1| translation initiation factor IF-2 [Arthrobacter arilaitensis
           Re117]
 gi|307744264|emb|CBT75236.1| translation initiation factor IF-2 [Arthrobacter arilaitensis
           Re117]
          Length = 980

 Score = 37.5 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 11/100 (11%), Positives = 18/100 (18%), Gaps = 2/100 (2%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           Q G    E  +                 P      P +     +   +  G     +   
Sbjct: 166 QQGMRGAESGERRGGGNREGGRAPRPGAPRPGGPRPGNNPFSSQQGMRGEGGQGGPRPPR 225

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREEN-HRRSPSFP 342
              R    +      G         G R        P+  
Sbjct: 226 DGQRSPRPARDGQG-GPRPPRDGQRGPRPAGAGGPRPAGQ 264


>gi|163854395|ref|YP_001628693.1| putative ATP-dependent RNA helicase [Bordetella petrii DSM 12804]
 gi|163258123|emb|CAP40422.1| putative ATP-dependent RNA helicase [Bordetella petrii]
          Length = 162

 Score = 37.5 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 7/91 (7%), Positives = 16/91 (17%)

Query: 263 SSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHS 322
                            D+    ++ +    G    +    P       +      G   
Sbjct: 54  PPAGSSAAAYERQERDEDNRQPRRQGARGNGGDRAGRPGQAPRQGNGGRAAAQGRPGGQR 113

Query: 323 SFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              +  G R           +     R +  
Sbjct: 114 QAPAPRGDRPSGGGHRADNRTAPQAPRQAES 144


>gi|254705163|ref|ZP_05166991.1| translation initiation factor IF-2 [Brucella suis bv. 3 str. 686]
 gi|261755868|ref|ZP_05999577.1| translation initiation factor IF-2 [Brucella suis bv. 3 str. 686]
 gi|261745621|gb|EEY33547.1| translation initiation factor IF-2 [Brucella suis bv. 3 str. 686]
          Length = 437

 Score = 37.5 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 16/125 (12%), Positives = 34/125 (27%), Gaps = 4/125 (3%)

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           L     REV ++  R         E           S     +    +    +   + + 
Sbjct: 163 LEEAQIREVEERA-RAVEEAKRRAEEDARRAKEREESARRQAEEEARLKAEAEARLKAEA 221

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            + +K      K++  P  R     +   A+            R +  R  P+   ++  
Sbjct: 222 EARRKAEEEAAKRMPQPEARSERRDD---ARPAPYGARPQQAGRPQGGRPQPAGRPQQGS 278

Query: 348 RRTSA 352
            R + 
Sbjct: 279 PRPAP 283


>gi|221125712|ref|XP_002153929.1| PREDICTED: similar to Arginine/serine-rich coiled-coil 2 [Hydra
           magnipapillata]
          Length = 406

 Score = 37.5 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 15/118 (12%), Positives = 28/118 (23%), Gaps = 3/118 (2%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRP---NIISEVPDDFTRMKKNSS 290
           + +S    R+   P    +          SS +  R                 R   + S
Sbjct: 76  KNLSPSPRRKNSSPSPRRKNLSPSPRFKNSSSSPRRKNSSLSPRRKNSSPSPRRKNLSPS 135

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
            +   S                          S      +++++  RSP    +RS  
Sbjct: 136 PRRKNSSPSPRRRNSSLSPRRKRSRTPPRKRHSRSRSFERKKKSRSRSPDRKRRRSRS 193


>gi|4585621|emb|CAB40849.1| HMGI/Y protein [Zea mays]
          Length = 190

 Score = 37.5 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 15/99 (15%), Positives = 25/99 (25%), Gaps = 2/99 (2%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
             A    +    R R         +       S    G  +  K  +P+  R  A +  M
Sbjct: 77  FRADAPPNAPPKRGRGRPPKARDPNAPAPAPKSPSSRGAGRPPKAKSPLEARREAGHRGM 136

Query: 317 AKGIHSSFLSDSGQREENHRRSPSFPSKRSLR--RTSAK 353
            K           +   +   SP+     S    R   +
Sbjct: 137 PKPRGRPPKKAKTEGAASPSPSPAPAGDGSTPGKRGRGR 175


>gi|311899483|dbj|BAJ31891.1| putative heat shock protein 15 [Kitasatospora setae KM-6054]
          Length = 130

 Score = 37.5 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 21/57 (36%), Gaps = 2/57 (3%)

Query: 7  VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          +  +    R+   I A   I +R           VKVNG   +  A +V   D + V
Sbjct: 1  MSADEASVRIDSWIWAIRLIKTRSAAGAACRAGHVKVNGATAK-PAQHVKPGDDVRV 56


>gi|330925703|ref|XP_003301157.1| hypothetical protein PTT_12592 [Pyrenophora teres f. teres 0-1]
 gi|311324336|gb|EFQ90747.1| hypothetical protein PTT_12592 [Pyrenophora teres f. teres 0-1]
          Length = 550

 Score = 37.5 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 11/101 (10%), Positives = 17/101 (16%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R    P    E                      +S          K      G +     
Sbjct: 261 RNMFPPTPPPETDRRGGDRGSGGRAADPPSNAPMSRAQSVRGGGPKPQPLNLGRAAFDPP 320

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
                RR         +   S   S   + + + R      
Sbjct: 321 RDEPPRRQPTQRSASERPPPSRSESQRDRGDRSDRSQRGSQ 361


>gi|194207888|ref|XP_001917928.1| PREDICTED: similar to serine/arginine repetitive matrix 1 [Equus
           caballus]
          Length = 830

 Score = 37.5 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 13/113 (11%), Positives = 28/113 (24%), Gaps = 4/113 (3%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R        +    +   P     +        +S  P    R    S +++     K  
Sbjct: 531 RRYSPSPPPKRRTASPPPPPKRRASPSPPPKRRVSHSPPPKQRSPPASKRRSPSLSSKHR 590

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                 R+       A+    +       R    + S   P +R    +  ++
Sbjct: 591 KGASPSRSTR----EARSPQPNKRHSPSPRPRAPQTSSPPPVRRGASSSPQRR 639


>gi|242080077|ref|XP_002444807.1| hypothetical protein SORBIDRAFT_07g028330 [Sorghum bicolor]
 gi|241941157|gb|EES14302.1| hypothetical protein SORBIDRAFT_07g028330 [Sorghum bicolor]
          Length = 508

 Score = 37.5 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 8/114 (7%), Positives = 32/114 (28%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +    + +                   +     +      S+  +D  + +K  + ++  
Sbjct: 201 LDSDEVSDGKDERRKRAHSSLGHKKEENRSRHKKQHREDSSDSDNDEPQRRKQDASEDDE 260

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
            ++++      RR    +    +    +      +++++  R          RR
Sbjct: 261 PRRRQQDDNEPRRRQRDDNEPRRRRQDNGEPRRRRQDDDEPRRRRQDDDEPRRR 314


>gi|311898201|dbj|BAJ30609.1| hypothetical protein KSE_48310 [Kitasatospora setae KM-6054]
          Length = 770

 Score = 37.5 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 10/125 (8%), Positives = 26/125 (20%), Gaps = 5/125 (4%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSE-----TLVRDRPNIISEVPDDFTRMKKN 288
           R +   +++ ++      E                            +  P+        
Sbjct: 75  RPIPPVVVQSKVKDEKPAEPSGPRHRGSAGDPVLGVMDAGARTGTPPTLPPEWQEPAAPK 134

Query: 289 SSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           + +               ++        A    +    D    E +    P+  + R   
Sbjct: 135 APKGGPDGGDTGEWFKPRQKGRPEPAPAAAPAPAPAGPDRSAAERSAAERPAPGADRPAP 194

Query: 349 RTSAK 353
           R S  
Sbjct: 195 RPSGA 199


>gi|296232458|ref|XP_002761600.1| PREDICTED: junctional sarcoplasmic reticulum protein 1-like
           [Callithrix jacchus]
          Length = 326

 Score = 37.5 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 15/117 (12%), Positives = 31/117 (26%), Gaps = 2/117 (1%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
             +   E+      E               L           P      K+   +K    
Sbjct: 204 RSREASEKDEGEPGEATGEAAGEDRAPLADLGPKERPRREGKPRKEKPRKEERPKKERPR 263

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           K+ +    + RR  +           S  +++ +R+     SP  P +    R+  +
Sbjct: 264 KEGRPREALPRRWESREGSHRPWARDSRDAEAKKRQV--WVSPRRPDEEERPRSRQR 318


>gi|167892636|ref|ZP_02480038.1| hypothetical protein Bpse7_02654 [Burkholderia pseudomallei 7894]
          Length = 702

 Score = 37.5 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 9/113 (7%), Positives = 28/113 (24%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+ L P    +    +            + P   +          +   +    +++   
Sbjct: 406 RDPLEPVGAADVPHAVARDPARVGVRPGEDPGADARARAGDRPDARPHQRGEAATRRGGA 465

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                R     +    +G  ++ +  + +   +    P     R   R    +
Sbjct: 466 RIRSERAGRRDDRDSGRGDRAAAVPQARRFPVDRHERPDPVHARDRPRGQRGR 518


>gi|167844131|ref|ZP_02469639.1| hypothetical protein BpseB_02497 [Burkholderia pseudomallei B7210]
          Length = 708

 Score = 37.5 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 9/113 (7%), Positives = 28/113 (24%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+ L P    +    +            + P   +          +   +    +++   
Sbjct: 406 RDPLEPVGAADVPHAVARDPARVGVRPGEDPGADARARAGDRPDARPHQRGEAATRRGGA 465

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                R     +    +G  ++ +  + +   +    P     R   R    +
Sbjct: 466 RIRSERAGRRDDRDSGRGDRAAAVPQARRFPVDRHERPDPVHARDRPRGQRGR 518


>gi|187929944|ref|YP_001900431.1| RNA-binding S4 domain-containing protein [Ralstonia pickettii
          12J]
 gi|187726834|gb|ACD27999.1| RNA-binding S4 domain protein [Ralstonia pickettii 12J]
          Length = 132

 Score = 37.5 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 11/59 (18%), Positives = 24/59 (40%), Gaps = 2/59 (3%)

Query: 5  NIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +  +     R+ K + A     +R +    + + RV++N   +   A +V   D + V
Sbjct: 2  KVSTDAADRVRIDKWLWAARFFKTRSQATDAVERGRVQINDQAVR-PAKDVKIGDRVRV 59


>gi|291224856|ref|XP_002732409.1| PREDICTED: hypothetical protein [Saccoglossus kowalevskii]
          Length = 295

 Score = 37.5 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 8/94 (8%), Positives = 18/94 (19%), Gaps = 3/94 (3%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
            +        ++    + R            + + +           + +    R +   
Sbjct: 179 PEEPFVGDAVNNNDDTQRRGQGRRPHGSRPCKPRPSGMPPRPSGHPPRPSGHPPRPSGHP 238

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
                     S       R   H   PS    R 
Sbjct: 239 PRPSGHPPRPSGHPP---RPSGHPPRPSGYPPRP 269



 Score = 36.3 bits (82), Expect = 7.0,   Method: Composition-based stats.
 Identities = 12/116 (10%), Positives = 23/116 (19%)

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G  R           G    +      +      +         + +  ++    ++   
Sbjct: 140 GEDRPGRPDDSDIPEGAVKPKPPLRPEEEDCDDVDDDEIPEEPFVGDAVNNNDDTQRRGQ 199

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
            +     +     P       S        H    S    R   H   PS    R 
Sbjct: 200 GRRPHGSRPCKPRPSGMPPRPSGHPPRPSGHPPRPSGHPPRPSGHPPRPSGHPPRP 255


>gi|116199185|ref|XP_001225404.1| hypothetical protein CHGG_07748 [Chaetomium globosum CBS 148.51]
 gi|88179027|gb|EAQ86495.1| hypothetical protein CHGG_07748 [Chaetomium globosum CBS 148.51]
          Length = 1225

 Score = 37.5 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 11/113 (9%), Positives = 22/113 (19%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R++   H               S    +                + + S +      +  
Sbjct: 168 RDRARKHHPSGPIPLPQRSRGRSVEPPQQDTQRRRRDQARSPNRRSDHSFEPSHRSPRGR 227

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                          +           G R+E   R      +R+ R     K
Sbjct: 228 RGRSPEPTRRREPRASPDRRPPDHRSPGPRKEVQGRPDDRIRRRASRSPVPSK 280


>gi|269793375|ref|YP_003312830.1| serine/threonine protein kinase [Sanguibacter keddieii DSM 10542]
 gi|269095560|gb|ACZ19996.1| serine/threonine protein kinase [Sanguibacter keddieii DSM 10542]
          Length = 663

 Score = 37.5 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 11/105 (10%), Positives = 25/105 (23%), Gaps = 1/105 (0%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ-KNGLSKQKKLATPVHRR 308
            E  +        S+      +    + V D     +++     +G             R
Sbjct: 443 DEPTRTLPQRQPRSAPEQRSAQWEPQTPVWDAVDSPRRSPDAAGHGQQPPAPSEQTGAVR 502

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               +        +S    S        R+P+   +     + A 
Sbjct: 503 RRVPHTGATDRARTSDQPRSAGPRSGLPRTPAAGGRTGASASPAA 547


>gi|332863597|ref|XP_001170783.2| PREDICTED: putative NPIP-like protein LOC100132247-like, partial
           [Pan troglodytes]
          Length = 414

 Score = 37.5 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 8/106 (7%), Positives = 20/106 (18%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              E    +       +  +    P        +         ++     +     P  R
Sbjct: 248 RAAEVKPSSPKPKRRRAAEVKPSSPKPKRRRAAEVKPSSPKPKRRRAAEVKPSSPKPKRR 307

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           R         +              +  RR  +     S +    +
Sbjct: 308 RVADVESSSPEPKRQRAAEVKPSSPKPKRRRAAEVEPSSPKPKRQR 353



 Score = 36.7 bits (83), Expect = 5.0,   Method: Composition-based stats.
 Identities = 9/108 (8%), Positives = 20/108 (18%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                E    +          +    P    +   +         ++     +     P 
Sbjct: 291 RRRAAEVKPSSPKPKRRRVADVESSSPEPKRQRAAEVKPSSPKPKRRRAAEVEPSSPKPK 350

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            +R         K              E  RR  +     S +    +
Sbjct: 351 RQRAAVMEPSSPKPKRRRAADVKPSSPEPKRRRAAEVKPSSPKPKRQR 398



 Score = 35.9 bits (81), Expect = 8.4,   Method: Composition-based stats.
 Identities = 11/111 (9%), Positives = 22/111 (19%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E L   L      +       +  +    P        +         ++     +    
Sbjct: 198 ECLITPLPPSPPPSPPPSRRRAAEVKPSSPKPKRRRAAEVKLSSPKPKKRRAAEVKPSSP 257

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            P  RR         K              +  RR  +     S +    +
Sbjct: 258 KPKRRRAAEVKPSSPKPKRRRAAEVKPSSPKPKRRRAAEVKPSSPKPKRRR 308



 Score = 35.9 bits (81), Expect = 8.4,   Method: Composition-based stats.
 Identities = 9/109 (8%), Positives = 28/109 (25%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                 E + +   P       V+              +      ++   ++ K  +   
Sbjct: 245 KKRRAAEVKPSSPKPKRRRAAEVKPSSPKPKRRRAAEVKPSSPKPKRRRAAEVKPSSPKP 304

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            RR +A     +        ++        +R  +   + S  +   ++
Sbjct: 305 KRRRVADVESSSPEPKRQRAAEVKPSSPKPKRRRAAEVEPSSPKPKRQR 353



 Score = 35.9 bits (81), Expect = 8.9,   Method: Composition-based stats.
 Identities = 13/108 (12%), Positives = 21/108 (19%), Gaps = 5/108 (4%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                E    +       +  +    P        D         ++     +     P 
Sbjct: 276 RRRAAEVKPSSPKPKRRRAAEVKPSSPKPKRRRVADVESSSPEPKRQRAAEVKPSSPKPK 335

Query: 306 HRRNLASNVWMAKGIHSS-----FLSDSGQREENHRRSPSFPSKRSLR 348
            RR         K            S   +R       PS P  +  R
Sbjct: 336 RRRAAEVEPSSPKPKRQRAAVMEPSSPKPKRRRAADVKPSSPEPKRRR 383


>gi|115372875|ref|ZP_01460180.1| RIO1//family protein [Stigmatella aurantiaca DW4/3-1]
 gi|310818555|ref|YP_003950913.1| rio kinase family protein [Stigmatella aurantiaca DW4/3-1]
 gi|115370142|gb|EAU69072.1| RIO1 family protein [Stigmatella aurantiaca DW4/3-1]
 gi|309391627|gb|ADO69086.1| RIO kinase family protein [Stigmatella aurantiaca DW4/3-1]
          Length = 511

 Score = 37.5 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 7/91 (7%), Positives = 17/91 (18%)

Query: 262 YSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIH 321
            S E                 +   +   +    ++                     G  
Sbjct: 400 RSGEGRGPRGDRRSPSHGSGRSSSPQAGGRPPPPAQGGGRPAHAGSHGGRPAHVGPHGGR 459

Query: 322 SSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            +      + E +    P        RR ++
Sbjct: 460 PAHAGQEPRGERSQGAFPPSRQAGQGRRGAS 490



 Score = 37.1 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 9/83 (10%), Positives = 23/83 (27%), Gaps = 1/83 (1%)

Query: 272 PNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR 331
            +     P    R   + S ++   +      P  +         + G   + +   G R
Sbjct: 400 RSGEGRGPRGDRRSPSHGSGRSSSPQAGGRPPPPAQGGGRPAHAGSHGGRPAHVGPHGGR 459

Query: 332 EENHRRSPSF-PSKRSLRRTSAK 353
             +  + P    S+ +   +   
Sbjct: 460 PAHAGQEPRGERSQGAFPPSRQA 482


>gi|239945915|ref|ZP_04697852.1| SARP family transcriptional regulator [Streptomyces roseosporus
           NRRL 15998]
 gi|291449371|ref|ZP_06588761.1| hypothetical protein SSGG_06589 [Streptomyces roseosporus NRRL
           15998]
 gi|291352318|gb|EFE79222.1| hypothetical protein SSGG_06589 [Streptomyces roseosporus NRRL
           15998]
          Length = 829

 Score = 37.5 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 18/138 (13%), Positives = 35/138 (25%), Gaps = 12/138 (8%)

Query: 216 IRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNII 275
           +R   G F L  LL    RE+            +  +        +  S      R    
Sbjct: 704 VRERAGRFGLDVLLRSYAREL------------IGADEAHTARRRLVLSRAPGPVRHGTG 751

Query: 276 SEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENH 335
            +           S  ++G  ++ + + P+    +      A    +        R    
Sbjct: 752 RDNCSGSYASSAGSRAQSGGDRKDRRSAPLPSAGVGHPEASAPSGPAGGSRTGPSRTVGR 811

Query: 336 RRSPSFPSKRSLRRTSAK 353
             +PS    R       +
Sbjct: 812 TAAPSRAEPREPGVHRHE 829


>gi|196968457|gb|ACG80802.1| hypothetical protein [Chlamydophila pecorum]
          Length = 121

 Score = 37.5 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 19/121 (15%), Positives = 36/121 (29%), Gaps = 1/121 (0%)

Query: 224 QLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
           +L  L   S++E+S K       P   E +         S + L     +     P + +
Sbjct: 2   ELKDLETSSSKELSPKE-PSPKEPSPKEPSPKEPSPKEPSPKELSPKELSPKEPSPKEPS 60

Query: 284 RMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
             + +  + +      K  +P        +         S    S +   +   S   PS
Sbjct: 61  SKELSPKEPSPKEPSSKELSPKEPSPKEPSSKELSPKEPSPKEPSPKEPSSKEPSSKEPS 120

Query: 344 K 344
           K
Sbjct: 121 K 121


>gi|149728424|ref|XP_001490321.1| PREDICTED: similar to oocyte-specific H1 histone [Equus caballus]
          Length = 353

 Score = 37.5 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 17/120 (14%), Positives = 29/120 (24%), Gaps = 6/120 (5%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           L++ L   +     V          T                      + ++ G +K K 
Sbjct: 91  LKQALATGMHRGLLVRPTNSKARGATGSFKLVPKHKRKIQSKKTSTTTAPRRPGEAKGKG 150

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLS------DSGQREENHRRSPSFPSKRSLRRTSAKK 354
              P   +    N    K                G  E+   +  S    +  RR  A+K
Sbjct: 151 PKKPSEAKKDPPNAGEMKKGPRRPGEVMTASLKPGAAEKKAPKKGSRTKDQESRRGEARK 210


>gi|194375646|dbj|BAG56768.1| unnamed protein product [Homo sapiens]
          Length = 380

 Score = 37.5 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 9/122 (7%), Positives = 31/122 (25%), Gaps = 7/122 (5%)

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
           +++++     +             S +     P       +    + ++  +K   +  +
Sbjct: 12  VVKQERLSPEVAPPAHRRPDHSGGSPSPPTSEPARSGHRGNRARGVSRSPPKKKNKASGR 71

Query: 300 KLATPVHRRNLAS-------NVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           +  +P  +RN +                         +         +  S R   R  +
Sbjct: 72  RSKSPRSKRNRSPHHSTVKVKQEREDHPRRGREDRQHREPSEQEHRRARNSDRDRHRGRS 131

Query: 353 KK 354
            +
Sbjct: 132 HQ 133


>gi|219666517|ref|YP_002456952.1| 30S ribosomal protein S4 [Desulfitobacterium hafniense DCB-2]
 gi|254764585|sp|B8G1Z3|RS4_DESHD RecName: Full=30S ribosomal protein S4
 gi|219536777|gb|ACL18516.1| ribosomal protein S4 [Desulfitobacterium hafniense DCB-2]
          Length = 208

 Score = 37.5 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 10/42 (23%), Positives = 19/42 (45%), Gaps = 1/42 (2%)

Query: 22  RAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           + G A SR E  +++      +NG  ++  +  V   D + V
Sbjct: 107 QLGFATSRPEARQLVRHGHFTINGRRVDIPSFLVRVGDVVGV 148


>gi|158138501|ref|NP_037050.2| voltage-dependent P/Q-type calcium channel subunit alpha-1A [Rattus
            norvegicus]
          Length = 2368

 Score = 37.5 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 8/103 (7%), Positives = 29/103 (28%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            +++       + + +     +         P+      +     +  + ++       + 
Sbjct: 2145 KDRDQDRGRPKDRKHRPHHHHHHHHHHPPAPDRERYAQERPDTGRARAREQRWSRSPSEG 2204

Query: 302  ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
                  R  +S+V  +    +S  S   +      ++P  P  
Sbjct: 2205 REHATHRQGSSSVSGSPAPSTSGTSTPRRGRRQLPQTPCTPRP 2247


>gi|331245896|ref|XP_003335583.1| hypothetical protein PGTG_16909 [Puccinia graminis f. sp. tritici
           CRL 75-36-700-3]
 gi|309314573|gb|EFP91164.1| hypothetical protein PGTG_16909 [Puccinia graminis f. sp. tritici
           CRL 75-36-700-3]
          Length = 551

 Score = 37.5 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 20/156 (12%), Positives = 38/156 (24%), Gaps = 18/156 (11%)

Query: 217 RISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDA---------------PI 261
           R++ G            R  S+   RE+  P    + +                    P 
Sbjct: 391 RVALGDRAKSNDDRHKKRRGSEDESREKEYPSKRRDGERERSGGGGRRSDDRDRRHYSPP 450

Query: 262 YSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGI- 320
              E   R + +       +          ++G  +          R+         G  
Sbjct: 451 RRDEERDRSKDDNRRLHDRERRDYSPKRPGRDGDRRDYSPKRSGRERDRRDYSPKQPGRE 510

Query: 321 --HSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                +      RE + R +    S+R   R+   K
Sbjct: 511 RDRRDYSPKRAGRERDRREASPKQSERDRDRSRDGK 546


>gi|167539468|ref|XP_001751125.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163770303|gb|EDQ84062.1| predicted protein [Monosiga brevicollis MX1]
          Length = 1232

 Score = 37.5 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 10/84 (11%), Positives = 19/84 (22%), Gaps = 5/84 (5%)

Query: 275 ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL-----ASNVWMAKGIHSSFLSDSG 329
            + +P                      A P   R+                  S      
Sbjct: 299 PAHMPPRGPPHDARRFSPARGGFGPPSAGPPRSRSRERFDDRPAYGRPGAPAFSRGPAPP 358

Query: 330 QREENHRRSPSFPSKRSLRRTSAK 353
           + +E    +  +PS  +  R  A+
Sbjct: 359 RMDERPWPAQRYPSHDTPPRGEAR 382


>gi|308457290|ref|XP_003091031.1| CRE-LST-3 protein [Caenorhabditis remanei]
 gi|308258569|gb|EFP02522.1| CRE-LST-3 protein [Caenorhabditis remanei]
          Length = 1191

 Score = 37.5 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 18/112 (16%), Positives = 36/112 (32%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +E       +    N       S           S      +  +++S +++    ++  
Sbjct: 191 QESQRWGSNDRGDRNGGGRGNESPLHRSAPQRRHSPPARRASPPRRSSPKRDTRPSREPR 250

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                RR+      ++    SS  +   + +    RSPS     S+RR SA 
Sbjct: 251 EAREPRRSPPPRRAVSPRRASSPATAPVKNDRKRERSPSGSVAPSIRRDSAS 302


>gi|227833354|ref|YP_002835061.1| translation initiation factor IF-2 [Corynebacterium aurimucosum
           ATCC 700975]
 gi|262184340|ref|ZP_06043761.1| translation initiation factor IF-2 [Corynebacterium aurimucosum
           ATCC 700975]
 gi|254803452|sp|C3PH19|IF2_CORA7 RecName: Full=Translation initiation factor IF-2
 gi|227454370|gb|ACP33123.1| translation initiation factor IF-2 [Corynebacterium aurimucosum
           ATCC 700975]
          Length = 905

 Score = 37.5 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 8/102 (7%), Positives = 19/102 (18%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           +          +               P      K   + K G + +   A     +   
Sbjct: 75  KKPTEKKPATAAKPGPKPSAAPKPGAAPKPGGAPKPGGAPKPGATPKPGGAPKPGAQRKN 134

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           +     + +    +   G          S  S         +
Sbjct: 135 TEKGSERAVTPRSMPKPGGTRRVANNPFSTGSSSDRPSPGPR 176


>gi|17539418|ref|NP_501561.1| COLlagen family member (col-119) [Caenorhabditis elegans]
 gi|3875169|emb|CAA92453.1| C. elegans protein C53B4.5, confirmed by transcript evidence
           [Caenorhabditis elegans]
          Length = 289

 Score = 37.5 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 7/75 (9%), Positives = 14/75 (18%), Gaps = 1/75 (1%)

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
                   +  S  + G   Q     P  +              ++       R +    
Sbjct: 196 ENGRNGEPQPGSPGEPGRPGQPGSRGPAGQPGKDGAQGGPGEKGANGEPGQPGR-DGQPG 254

Query: 338 SPSFPSKRSLRRTSA 352
            P  P +        
Sbjct: 255 RPGQPGRDGHPGEKG 269


>gi|89893244|ref|YP_516731.1| 30S ribosomal protein S4 [Desulfitobacterium hafniense Y51]
 gi|122483915|sp|Q250K5|RS4_DESHY RecName: Full=30S ribosomal protein S4
 gi|89332692|dbj|BAE82287.1| 30S ribosomal protein S4 [Desulfitobacterium hafniense Y51]
          Length = 208

 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 10/42 (23%), Positives = 19/42 (45%), Gaps = 1/42 (2%)

Query: 22  RAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           + G A SR E  +++      +NG  ++  +  V   D + V
Sbjct: 107 QLGFATSRPEARQLVRHGHFTINGRRVDIPSFLVRVGDVVGV 148


>gi|294812753|ref|ZP_06771396.1| TT_ORF1 domain-containing protein [Streptomyces clavuligerus ATCC
           27064]
 gi|294325352|gb|EFG06995.1| TT_ORF1 domain-containing protein [Streptomyces clavuligerus ATCC
           27064]
          Length = 498

 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 14/109 (12%), Positives = 28/109 (25%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G     +        +  +    +    +    P          + +  L++  +   P 
Sbjct: 258 GGAGGRQTARGRPQTLRRTAAHRQAEQPLHPRPPSRSRARPGRHAGRRRLARHPRPDHPR 317

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             R L      A            +R    RRS + P     R   A++
Sbjct: 318 DLRRLLRVSRPAHRPGPDARPRPHRRPAGPRRSRTRPGADRHRAHPARR 366


>gi|258653317|ref|YP_003202473.1| bifunctional glutamine-synthetase
           adenylyltransferase/deadenyltransferase [Nakamurella
           multipartita DSM 44233]
 gi|258556542|gb|ACV79484.1| (Glutamate--ammonia-ligase) adenylyltransferase [Nakamurella
           multipartita DSM 44233]
          Length = 1157

 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 15/97 (15%), Positives = 27/97 (27%)

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
           D   Y     VR                   + ++     Q +   P   R        A
Sbjct: 845 DEFRYPRRRAVRPGRGRDPPDQGAGGHRTDAAHRRPDHPHQARPGRPGRHRVDHPAAAAA 904

Query: 318 KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             +  +  + S     + RR P    +R  RR + ++
Sbjct: 905 ARLRGARPAHSAHPAGHRRRRPGRVDQRRGRRVADQR 941



 Score = 36.3 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 13/111 (11%), Positives = 19/111 (17%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           LR +      E       A         R         P D       +   +       
Sbjct: 825 LRARPIAGDRELGAAFAAAADEFRYPRRRAVRPGRGRDPPDQGAGGHRTDAAHRRPDHPH 884

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
            A P        +   A        +               P +   RR  
Sbjct: 885 QARPGRPGRHRVDHPAAAAAARLRGARPAHSAHPAGHRRRRPGRVDQRRGR 935


>gi|209964678|ref|YP_002297593.1| DeaD [Rhodospirillum centenum SW]
 gi|209958144|gb|ACI98780.1| DeaD [Rhodospirillum centenum SW]
          Length = 528

 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 7/69 (10%), Positives = 21/69 (30%), Gaps = 2/69 (2%)

Query: 288 NSSQKNGLSKQKKLATPVHRR-NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
              ++ G   + + A P   R    +    +          + + E + R   + P +  
Sbjct: 395 EGRKEEGRKSEPRSARPPRSRAADRTEAGDSAAATPVPEERAARPERSERSVRARPERTD 454

Query: 347 LR-RTSAKK 354
              +   ++
Sbjct: 455 RPVQDRPER 463


>gi|156549296|ref|XP_001600207.1| PREDICTED: similar to eukaryotic initiation factor 4B protein
           [Nasonia vitripennis]
          Length = 555

 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 17/126 (13%), Positives = 27/126 (21%), Gaps = 5/126 (3%)

Query: 230 AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
            G+ R+  +  L E+  P   +                 RD                +  
Sbjct: 225 PGNWRDAPRSELAERPRPSYRDSRGPGGPGDDRGES---RDWNRFADRTRGPPRDGSRER 281

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP--SFPSKRSL 347
             +   S          R   +       G  +    +      N  R P    P     
Sbjct: 282 DGERAGSSFGNRDRDGERGGSSFGPRRTYGEDTDRDRERWGSLRNQPREPISDGPPASDA 341

Query: 348 RRTSAK 353
            RT  K
Sbjct: 342 PRTRPK 347


>gi|319441535|ref|ZP_07990691.1| translation initiation factor IF-2 [Corynebacterium variabile DSM
           44702]
          Length = 811

 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 11/102 (10%), Positives = 18/102 (17%), Gaps = 3/102 (2%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
           H           P  + +             P      +      N  S   +   P  R
Sbjct: 5   HKPAAKPAPGAKPGAAGQKPGPRPGGPAGHKPGPKPGGRAPRVANNPFSSGTERPAPRPR 64

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
               +   M              R     R     + +   R
Sbjct: 65  PGQGAKSDMP---RPGGNRSGAPRPGAAPRPGGTGAAKPGGR 103



 Score = 36.3 bits (82), Expect = 7.4,   Method: Composition-based stats.
 Identities = 10/92 (10%), Positives = 20/92 (21%), Gaps = 3/92 (3%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR---RNL 310
                 P   +  +  +  +  +E P    R  + +          +   P      R  
Sbjct: 34  HKPGPKPGGRAPRVANNPFSSGTERPAPRPRPGQGAKSDMPRPGGNRSGAPRPGAAPRPG 93

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
            +      G   S  S           + S  
Sbjct: 94  GTGAAKPGGRRPSPASMPSHPSPGQMPAKSSN 125



 Score = 35.9 bits (81), Expect = 9.5,   Method: Composition-based stats.
 Identities = 8/92 (8%), Positives = 16/92 (17%), Gaps = 1/92 (1%)

Query: 263 SSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHS 322
                        +       R    +  K G     +     +    +     A     
Sbjct: 6   KPAAKPAPGAKPGAAGQKPGPRPGGPAGHKPGPKPGGRAPRVANNPFSSGTERPAPRPRP 65

Query: 323 SFLSDSGQREENHRRSPS-FPSKRSLRRTSAK 353
              + S        RS +  P        +  
Sbjct: 66  GQGAKSDMPRPGGNRSGAPRPGAAPRPGGTGA 97


>gi|301781863|ref|XP_002926347.1| PREDICTED: membrane-associated guanylate kinase, WW and PDZ
            domain-containing protein 1-like isoform 1 [Ailuropoda
            melanoleuca]
          Length = 1459

 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 14/119 (11%), Positives = 27/119 (22%), Gaps = 4/119 (3%)

Query: 240  ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
                    H    A      P   +    R +   +               +K    K  
Sbjct: 1205 EYDPSSDRHGPAAAAGAQGFPEVRAAPPDRRQHPSLESSYPPDLHKSSQHGEKRAHGKDP 1264

Query: 300  KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK----RSLRRTSAKK 354
            K +    R+    + W          +   +      R  + P +       RR+  K+
Sbjct: 1265 KGSREYSRQPNEHHTWNGTSRKPDSGACRPKDRAPEGRREAPPERMVTNGPKRRSPEKR 1323


>gi|167909351|ref|ZP_02496442.1| hypothetical protein Bpse112_02582 [Burkholderia pseudomallei 112]
          Length = 702

 Score = 37.5 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 9/113 (7%), Positives = 28/113 (24%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+ L P    +    +            + P   +          +   +    +++   
Sbjct: 406 RDPLEPVGAADVPHAVARDPARVGVRPGEDPGADARARAGDRPDARPHQRGEAATRRGGA 465

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                R     +    +G  ++ +  + +   +    P     R   R    +
Sbjct: 466 RIRSERAGRRDDRDSGRGDRAAAVPQARRFPVDRHERPDPVHARDRPRGQRGR 518


>gi|167901131|ref|ZP_02488336.1| hypothetical protein BpseN_02554 [Burkholderia pseudomallei NCTC
           13177]
          Length = 704

 Score = 37.5 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 9/113 (7%), Positives = 28/113 (24%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+ L P    +    +            + P   +          +   +    +++   
Sbjct: 406 RDPLEPVGAADVPHAVARDPARVGVRPGEDPGADARARAGDRPDARPHQRGEAATRRGGA 465

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                R     +    +G  ++ +  + +   +    P     R   R    +
Sbjct: 466 RIRSERAGRRDDRDSGRGDRAAAVPQARRFPVDRHERPDPVHARDRPRGQRGR 518


>gi|76810730|ref|YP_332072.1| hypothetical protein BURPS1710b_0659 [Burkholderia pseudomallei
           1710b]
 gi|76580183|gb|ABA49658.1| hypothetical protein BURPS1710b_0659 [Burkholderia pseudomallei
           1710b]
          Length = 708

 Score = 37.5 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 9/113 (7%), Positives = 28/113 (24%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+ L P    +    +            + P   +          +   +    +++   
Sbjct: 406 RDPLEPVGAADVPHAVARDPARVGVRPGEDPGADARARAGDRPDARPHQRGEAATRRGGA 465

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                R     +    +G  ++ +  + +   +    P     R   R    +
Sbjct: 466 RIRSERAGRRDDRDSGRGDRAAAVPQARRFPVDRHERPDPVHARDRPRGQRGR 518


>gi|281345202|gb|EFB20786.1| hypothetical protein PANDA_015982 [Ailuropoda melanoleuca]
          Length = 1320

 Score = 37.5 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 14/119 (11%), Positives = 27/119 (22%), Gaps = 4/119 (3%)

Query: 240  ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
                    H    A      P   +    R +   +               +K    K  
Sbjct: 1066 EYDPSSDRHGPAAAAGAQGFPEVRAAPPDRRQHPSLESSYPPDLHKSSQHGEKRAHGKDP 1125

Query: 300  KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK----RSLRRTSAKK 354
            K +    R+    + W          +   +      R  + P +       RR+  K+
Sbjct: 1126 KGSREYSRQPNEHHTWNGTSRKPDSGACRPKDRAPEGRREAPPERMVTNGPKRRSPEKR 1184


>gi|220926974|ref|YP_002502276.1| DEAD/DEAH box helicase domain-containing protein [Methylobacterium
           nodulans ORS 2060]
 gi|219951581|gb|ACL61973.1| DEAD/DEAH box helicase domain protein [Methylobacterium nodulans
           ORS 2060]
          Length = 506

 Score = 37.5 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 8/110 (7%), Positives = 18/110 (16%)

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           +  R  L        Q   +  I         +    +    +  R +     +      
Sbjct: 353 EEERAYLRDIERLTRQKVPEMAIPVGFVPPSRQEAAEAVAEAERDRRQPGPRGQRPGRSH 412

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                              +G                   P  P++    
Sbjct: 413 GARPQGGPGGRPQGGRQHGQGGRPGEGRPRDGGRPAQEARPGRPAQDGRP 462


>gi|307548922|ref|NP_001182597.1| collagen alpha-2(I) chain [Oryctolagus cuniculus]
          Length = 1364

 Score = 37.5 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 13/110 (11%), Positives = 21/110 (19%), Gaps = 4/110 (3%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           GP   +    N   P  +             +            +   GL          
Sbjct: 347 GPAGTKGESGNKGEPGSAGPQGPPGPSGEEGKRGSPGEPGSAGPAGPPGLRGSPGSRGLP 406

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP---SKRSLRRTSA 352
              +  + V    G   S      +        P  P     R L  +  
Sbjct: 407 GA-DGRAGVMGPPGSRGSTGPAGVRGPNGDSGRPGEPGLMGPRGLPGSPG 455


>gi|47221182|emb|CAG05503.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 1037

 Score = 37.5 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 13/112 (11%), Positives = 26/112 (23%), Gaps = 3/112 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E+         +     P    +      P+  +    +     + +       +     
Sbjct: 274 ERPSRQSRSPRRERPSRPEADRDKRPGKSPSKDASSGKENRSPHRRAPHSPARKRSASPR 333

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               RR+ AS          S             RSP        RR + ++
Sbjct: 334 HKDARRHSASASERTAKRSHSPSRARTPPRRGRSRSPDVS---IRRREAERQ 382


>gi|317401916|gb|EFV82522.1| ribonuclease E [Achromobacter xylosoxidans C54]
          Length = 794

 Score = 37.5 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 9/95 (9%), Positives = 25/95 (26%)

Query: 260 PIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKG 319
           P  ++    ++             + +     +    ++       +RR  +       G
Sbjct: 572 PAKTASAAAQEETGAKRAASPARGKGRGAHDGQERRGERHGSDRNRNRRGESRTEGAEGG 631

Query: 320 IHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                     +R E  R       +R+ R    ++
Sbjct: 632 EGGRHHIRGNRRPEGERGERQERGERNNRNERGER 666


>gi|302784746|ref|XP_002974145.1| hypothetical protein SELMODRAFT_442338 [Selaginella moellendorffii]
 gi|300158477|gb|EFJ25100.1| hypothetical protein SELMODRAFT_442338 [Selaginella moellendorffii]
          Length = 700

 Score = 37.5 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 15/107 (14%), Positives = 33/107 (30%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                 + + +           D          D +  +          ++++  +P  R
Sbjct: 316 PPRRRQRTDTEDLSPPRRRSGSDLSPRRKAGGGDLSPPRHRPRTDTSPPRRREDLSPPRR 375

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           RN +      +    S LS   +R+       S P ++S R  S ++
Sbjct: 376 RNGSDLSPRRRKAGGSDLSPPRRRQRTDTEDLSPPRRKSGRDLSPRR 422


>gi|312193986|ref|YP_004014047.1| hypothetical protein FraEuI1c_0089 [Frankia sp. EuI1c]
 gi|311225322|gb|ADP78177.1| Protein of unknown function DUF2662 [Frankia sp. EuI1c]
          Length = 610

 Score = 37.5 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 16/108 (14%), Positives = 29/108 (26%), Gaps = 3/108 (2%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R++L P    E +                         +       + S   G   + + 
Sbjct: 291 RDRLEPRDRLEPRDRPGPRGDQYRDRPDGPVRPDRPAGNRPDEPFNDRSGARGEPYRDRP 350

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
             P  R +    +         F   SG R E +R   + P++    R
Sbjct: 351 PGPA-RADRPDRLGARPDEP--FNDRSGARGEPYRDRQAGPARADRPR 395


>gi|291444643|ref|ZP_06584033.1| conserved hypothetical protein [Streptomyces roseosporus NRRL 15998]
 gi|291347590|gb|EFE74494.1| conserved hypothetical protein [Streptomyces roseosporus NRRL 15998]
          Length = 1109

 Score = 37.5 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 9/63 (14%), Positives = 15/63 (23%), Gaps = 2/63 (3%)

Query: 282  FTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSD--SGQREENHRRSP 339
              R    + +  G  +    A P  RR             +        G+R  +     
Sbjct: 996  PARTVGGARRVAGARRPAPPAGPDDRRRTGRADRSRPADRAGHRHRADPGRRPAHRAHRA 1055

Query: 340  SFP 342
              P
Sbjct: 1056 GGP 1058


>gi|148678999|gb|EDL10946.1| calcium channel, voltage-dependent, P/Q type, alpha 1A subunit,
            isoform CRA_d [Mus musculus]
          Length = 2328

 Score = 37.1 bits (84), Expect = 3.7,   Method: Composition-based stats.
 Identities = 12/88 (13%), Positives = 18/88 (20%)

Query: 258  DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
            + P          R +       + T  ++ SS  +G        T   RR         
Sbjct: 2184 ERPDTGRARAREQRWSRSPSEGREHTTHRQGSSSVSGSPAPSTSGTSTPRRGRRQLPQTP 2243

Query: 318  KGIHSSFLSDSGQREENHRRSPSFPSKR 345
                         R    R  P      
Sbjct: 2244 CTPRPLVSYSPAPRRPGARTIPRRGRPG 2271


>gi|321455858|gb|EFX66980.1| hypothetical protein DAPPUDRAFT_115843 [Daphnia pulex]
          Length = 879

 Score = 37.1 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 11/115 (9%), Positives = 31/115 (26%), Gaps = 4/115 (3%)

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           + ++E+L   LL   ++  +    +        P      P    +  ++  ++   +  
Sbjct: 247 REVKEELQQTLLGVDRLERN----TLIDAADRYPRETGARPRAQRQASRSPERQRSRAAA 302

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            +   P    +   +   A             R     R        +  R + +
Sbjct: 303 PERGEPHEYGSPPPSYTSATRPQDDSWGRGRGRPPAQEREVPRARNATPPREAPR 357


>gi|257790639|ref|YP_003181245.1| Flp pilus assembly protein CpaB [Eggerthella lenta DSM 2243]
 gi|257474536|gb|ACV54856.1| Flp pilus assembly protein CpaB [Eggerthella lenta DSM 2243]
          Length = 432

 Score = 37.1 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 12/115 (10%), Positives = 27/115 (23%), Gaps = 7/115 (6%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P              +      R      +         ++++      S       P  
Sbjct: 52  PAASASVPSAPQGAPFPQRRDERPAQGRPAYEDQHGPAPRQSAPAPQPASPSAPQGAPAP 111

Query: 307 RRNLASNVWMAKGI-------HSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           RR       M   +             +S  R E  R + +   + +    +A++
Sbjct: 112 RREARDARRMEADVHQQENTYRHEPAQESAYRPEPSRPAYAGDDRGAKTEAAAEE 166


>gi|47224904|emb|CAG06474.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 1369

 Score = 37.1 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 14/109 (12%), Positives = 22/109 (20%), Gaps = 1/109 (0%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           GP    +      +                S V          + ++     +   A   
Sbjct: 447 GPAWGLQPLQAGSSARQDLPAPAGPHRPRASGVAPAAQAPCAAAPREPPRGPEDPGAERP 506

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             R                   S      HR  P  P  R LR    ++
Sbjct: 507 RGRRREGAAAAEPRPGPQRRPGSPGGAPRHRPHPEDPG-RPLRSGQERQ 554


>gi|326524195|dbj|BAJ97108.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 560

 Score = 37.1 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 9/117 (7%), Positives = 25/117 (21%), Gaps = 1/117 (0%)

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNII-SEVPDDFTRMKKNSSQKNGLSK 297
           + LR  L   +    + +     +  +       + +                 +     
Sbjct: 116 RALRRHLQQQVGSAPRHHHHHDDHDDDHHHHQHLHPLLRRRGQPAAGQPGQPHSRRARGG 175

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           + + A P  RR    +                          +   +R      A++
Sbjct: 176 RGEHAEPRRRRPTRDSDPPLAAPRPRRGHARAPDHGARAGGAAPLVRRQGAPPGARR 232


>gi|56418220|gb|AAV91034.1| neurofilament triplet H1 protein [Grouper iridovirus]
          Length = 178

 Score = 37.1 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 11/108 (10%), Positives = 19/108 (17%)

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
                              S        +          +               +  +P
Sbjct: 14  HAMVAQPAQPACPLTAKKPSRCPSGCVKSPAKRKSPTSRKSPARRKSPTSRKSPARRKSP 73

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             R++ A           +       R+   RR      K   RR S 
Sbjct: 74  TSRKSPARRKSPTSRKSPARRKSPTSRKSPARRKSPTSRKSPARRKSP 121


>gi|323454617|gb|EGB10487.1| hypothetical protein AURANDRAFT_71135 [Aureococcus anophagefferens]
          Length = 1808

 Score = 37.1 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 11/108 (10%), Positives = 24/108 (22%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G    +E + +        ET      N  +            +        +     P 
Sbjct: 409 GAEPKKEPEASKWGDDEEEETAPLKSENGSAGAMKKTGSWAAIAKTGAPEEDEAAPPPPP 468

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R  +      +          G+ ++        P  +   R  A+
Sbjct: 469 VERTPSDKTKSPRDKGGKGERGPGRGKDAKGDGRGTPRAKGEGRGRAR 516


>gi|317124438|ref|YP_004098550.1| DEAD/DEAH box helicase [Intrasporangium calvum DSM 43043]
 gi|315588526|gb|ADU47823.1| DEAD/DEAH box helicase domain protein [Intrasporangium calvum DSM
           43043]
          Length = 807

 Score = 37.1 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 10/131 (7%), Positives = 29/131 (22%), Gaps = 2/131 (1%)

Query: 226 GTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
                   R+      R           +   +     +                     
Sbjct: 109 DDRRPFERRDDRTSERRPFERRDDRTSERRPFERRDDRTSERRPFERRDDRTSERRPFER 168

Query: 286 KKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP--SFPS 343
           + + + +    +++    P  RR+  ++                + +    R P      
Sbjct: 169 RDDRTSERRPFERRDDRRPFERRDDRTSERRPFERRDDRRPFERRDDRTSERRPFERRDD 228

Query: 344 KRSLRRTSAKK 354
           + S RR   ++
Sbjct: 229 RTSERRPFERR 239



 Score = 36.3 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 15/118 (12%), Positives = 34/118 (28%), Gaps = 5/118 (4%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG---LSKQ 298
            ++       E + +        +    +R +  +     F R    +S++        +
Sbjct: 87  DDRTSERRPFERRDDRRPFERRDDRRPFERRDDRTSERRPFERRDDRTSERRPFERRDDR 146

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP--SFPSKRSLRRTSAKK 354
                P  RR+  ++            S+    E    R P      + S RR   ++
Sbjct: 147 TSERRPFERRDDRTSERRPFERRDDRTSERRPFERRDDRRPFERRDDRTSERRPFERR 204



 Score = 36.3 bits (82), Expect = 7.7,   Method: Composition-based stats.
 Identities = 18/128 (14%), Positives = 36/128 (28%), Gaps = 5/128 (3%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             R    +   ++       E + +  +     E     RP    +    F R    +S+
Sbjct: 64  DWRGPRDERRDDRTSERRPSERRDDRTSERRPFERRDDRRPFERRDDRRPFERRDDRTSE 123

Query: 292 KNG---LSKQKKLATPVHRRNLASNVWMAKGIHSSFLS-DSGQREENHRRSPSFP-SKRS 346
           +        +     P  RR+  ++            S        + R S   P  +R 
Sbjct: 124 RRPFERRDDRTSERRPFERRDDRTSERRPFERRDDRTSERRPFERRDDRTSERRPFERRD 183

Query: 347 LRRTSAKK 354
            RR   ++
Sbjct: 184 DRRPFERR 191



 Score = 35.9 bits (81), Expect = 8.6,   Method: Composition-based stats.
 Identities = 13/113 (11%), Positives = 27/113 (23%), Gaps = 3/113 (2%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG---LSKQ 298
            ++       E + +        +     RP    +    F R    +S++        +
Sbjct: 170 DDRTSERRPFERRDDRRPFERRDDRTSERRPFERRDDRRPFERRDDRTSERRPFERRDDR 229

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                P  RR+  ++            S+    E    R P            
Sbjct: 230 TSERRPFERRDDRTSERRPFERRDDRTSERRPFERRDDRRPFERRDDRGPSDR 282


>gi|256824993|ref|YP_003148953.1| translation initiation factor 2 [Kytococcus sedentarius DSM 20547]
 gi|256688386|gb|ACV06188.1| bacterial translation initiation factor 2 (bIF-2) [Kytococcus
           sedentarius DSM 20547]
          Length = 969

 Score = 37.1 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 14/98 (14%), Positives = 24/98 (24%), Gaps = 1/98 (1%)

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS-NV 314
           N   P   +       P   +  P + +   + +SQ      QK   TP    +  S   
Sbjct: 133 NAPTPGAPAAPGRSSGPTSATPAPSEGSAAARQASQDAPARSQKPAPTPGPAPSPKSARP 192

Query: 315 WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                  S  +   G      +     P       +  
Sbjct: 193 GNNPFAPSQGMPKPGSARGAGKPGAPRPGNNPFAPSQG 230


>gi|134099735|ref|YP_001105396.1| 3-isopropylmalate dehydrogenase [Saccharopolyspora erythraea NRRL
           2338]
 gi|291005674|ref|ZP_06563647.1| 3-isopropylmalate dehydrogenase [Saccharopolyspora erythraea NRRL
           2338]
 gi|133912358|emb|CAM02471.1| 3-isopropylmalate dehydrogenase [Saccharopolyspora erythraea NRRL
           2338]
          Length = 407

 Score = 37.1 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 16/110 (14%), Positives = 27/110 (24%), Gaps = 1/110 (0%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
             IL ++     +   Q      +  ++     R     +   D    +   +       
Sbjct: 248 GDILSDRRRSGHVPVGQHRRGRGVLRADPRQCARHRGPGQGEPDLADPRGRDAAGAPRPP 307

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
               A P HRR                 +    R+  HRR  S    R  
Sbjct: 308 PSGPARP-HRRGGGVPHRGDPAGRRITGARHRGRDPRHRRGGSRRLTRPR 356


>gi|126738450|ref|ZP_01754155.1| translation initiation factor IF-2 [Roseobacter sp. SK209-2-6]
 gi|126720249|gb|EBA16955.1| translation initiation factor IF-2 [Roseobacter sp. SK209-2-6]
          Length = 830

 Score = 37.1 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 12/106 (11%), Positives = 23/106 (21%), Gaps = 2/106 (1%)

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
             E +         +              P   +  + ++S+       +K       R 
Sbjct: 128 KAEDEERKKREAEEAAKRAAAEAEKKKAEPATSSAPRNSASRPAPQQTPRKSDREREERG 187

Query: 310 LASNVWMAKGIHSSFL--SDSGQREENHRRSPSFPSKRSLRRTSAK 353
                    G   S           + +R+      KR   R   K
Sbjct: 188 RGKGRGDNSGGRRSGKLTLGQATGGDGNRQRSMASMKRKQERARQK 233


>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 = 37.1 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 31/244 (12%), Positives = 72/244 (29%), Gaps = 49/244 (20%)

Query: 8   QENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVM----- 55
           +EN   +++ +V       +A   +       + + ++ +KVNG+ ++     V      
Sbjct: 7   EENHEGKKIDRVVRDFFPNLASGMLY------KALRKKDIKVNGVRIKE-DYIVSFGDKI 59

Query: 56  -----------STDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
                        D    DG  +   +   L +  +    V    +    + +       
Sbjct: 60  DIYIIDDYLIGRDD----DGFSVVYDDDNLLIVNKETGIPVHPDKNQKEATLIDKLQSIY 115

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL---- 160
              +    RLD NT GL+++  +     V+                     +K N     
Sbjct: 116 GPNLALCHRLDRNTSGLVIIAKNPATLEVMLEKIKNREIQKYYTCIVSGKMEKKNAELVD 175

Query: 161 -LKKGIVIQGICYGDMQ----------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            L+K   +  +     +            +     S   + V L  G+  +I+    ++ 
Sbjct: 176 YLEKNEKLSRVFINPEKTRNSVQIITRYRILASMNSLNLLEVELVTGRTHQIRAHLAYYG 235

Query: 210 WKVN 213
             + 
Sbjct: 236 HPII 239


>gi|297462152|ref|XP_001787716.2| PREDICTED: zinc finger protein 701-like [Bos taurus]
          Length = 369

 Score = 37.1 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 9/106 (8%), Positives = 15/106 (14%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               E            +      P           R +  +                 R
Sbjct: 115 PGQREGGHARGRVRQRRQARATGPPAPRVPPGKGARRGRPATPPDPRPRLASPPPPVPAR 174

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               +     +            R        S P     RR   +
Sbjct: 175 GRGPAAGKRRRARRPEAGRRRQGRPPPSPSRASAPPHGGRRRPLDR 220



 Score = 35.9 bits (81), Expect = 8.9,   Method: Composition-based stats.
 Identities = 7/87 (8%), Positives = 15/87 (17%)

Query: 261 IYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGI 320
             +                    R +  S      ++ +  A    RR         +  
Sbjct: 138 PPAPRVPPGKGARRGRPATPPDPRPRLASPPPPVPARGRGPAAGKRRRARRPEAGRRRQG 197

Query: 321 HSSFLSDSGQREENHRRSPSFPSKRSL 347
                        +  R       R+ 
Sbjct: 198 RPPPSPSRASAPPHGGRRRPLDRPRTG 224


>gi|326323999|gb|ADZ54063.1| virulence-associated trimeric autotransporter [Haemophilus parasuis
           SH0165]
          Length = 1479

 Score = 37.1 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 11/111 (9%), Positives = 20/111 (18%), Gaps = 16/111 (14%)

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW 315
           +   P  +     R  P             +   +   G         P   +       
Sbjct: 695 DKGEPGQAGPAGPRGEPGQAGPAGPRGEPGQAGPAGPRGPQGTAGAQGPKGDKGDPGQAG 754

Query: 316 MAKGIH----------------SSFLSDSGQREENHRRSPSFPSKRSLRRT 350
            A                         + GQ      R P+ P   +  + 
Sbjct: 755 PAGPRGPAGPPGPVGPAGAAGPKGDKGEPGQAGPAGPRGPAGPKGDAGPKG 805


>gi|325120389|emb|CBZ55943.1| conserved hypothetical protein [Neospora caninum Liverpool]
          Length = 258

 Score = 37.1 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 18/105 (17%), Positives = 34/105 (32%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            +  E Q + +     +  L R R       P      +  S   +  S  ++       
Sbjct: 16  KMKSELQRDGEEDSEDAMPLKRRRTIAKKPRPAKKLEEESPSEDDSDDSDHEEKPAKKKS 75

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           R+  +     K   +     S  R +  R++P  PS  +  R+ A
Sbjct: 76  RSKPAKPPATKKAAAGKGPSSAARPKAKRKAPKSPSAETKSRSRA 120



 Score = 36.7 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 10/122 (8%), Positives = 35/122 (28%), Gaps = 2/122 (1%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
            + K+ ++ +L     E+++  +      +          + E          +  ++  
Sbjct: 11  PLKKRKMKSELQRDGEEDSEDAMPLKRRRTIAKKPRPAKKLEEESPSEDDSDDSDHEEKP 70

Query: 295 LSKQKK--LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             K+ +   A P   +  A+    +          + +      +S S       + +  
Sbjct: 71  AKKKSRSKPAKPPATKKAAAGKGPSSAARPKAKRKAPKSPSAETKSRSRAGAAGAKASRT 130

Query: 353 KK 354
            +
Sbjct: 131 GR 132


>gi|289769380|ref|ZP_06528758.1| magnesium or manganese-dependent protein phosphatase [Streptomyces
           lividans TK24]
 gi|289699579|gb|EFD67008.1| magnesium or manganese-dependent protein phosphatase [Streptomyces
           lividans TK24]
          Length = 707

 Score = 37.1 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 10/86 (11%), Positives = 23/86 (26%)

Query: 269 RDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDS 328
           R  P      P      ++    +         +    RR   +      G  +   S +
Sbjct: 5   RRAPPGPRYRPRGAPGRRRPPRARPPRGSSSTPSRAPSRRRSPTRTARGPGPRAFPYSRT 64

Query: 329 GQREENHRRSPSFPSKRSLRRTSAKK 354
             +      +   P++R + R    +
Sbjct: 65  AGKRAAGSPAVCRPARRHVSRPRTAR 90


>gi|149434073|ref|XP_001513232.1| PREDICTED: similar to seven transmembrane helix receptor, partial
           [Ornithorhynchus anatinus]
          Length = 337

 Score = 37.1 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 15/110 (13%), Positives = 23/110 (20%)

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           LG              +                 P    R + +S         ++   P
Sbjct: 27  LGGEGRAGDPGRFRDLLRLGAAGCSPVRREHPSNPSPTRRRRHDSDSPPSRRGSRRPPDP 86

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                       +    S       +R      S S PS      + AKK
Sbjct: 87  DLSPPRIGRGRASGPRGSDSDLSPPRRRRRAGSSDSDPSPPRRGPSGAKK 136


>gi|320093766|ref|ZP_08025614.1| ATP-dependent RNA helicase [Actinomyces sp. oral taxon 178 str.
           F0338]
 gi|319979303|gb|EFW10798.1| ATP-dependent RNA helicase [Actinomyces sp. oral taxon 178 str.
           F0338]
          Length = 800

 Score = 37.1 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 16/115 (13%), Positives = 28/115 (24%), Gaps = 1/115 (0%)

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
            VS + LR ++        +         S    R   +  SE  D   R ++      G
Sbjct: 610 YVSGRQLRIRVDEGPGRRDRFERGGFERPSRGERRSDRDDRSEREDRGGRDERFDRPSRG 669

Query: 295 LSKQKKLATPVH-RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
             +  +       RR                     +R +   R P    +    
Sbjct: 670 DRRSDRDDRLGEDRRGGFERSGRGDRFDRGDRGGRDERFDREDRRPGRGDRFDRS 724


>gi|269956137|ref|YP_003325926.1| hypothetical protein Xcel_1337 [Xylanimonas cellulosilytica DSM
           15894]
 gi|269304818|gb|ACZ30368.1| hypothetical protein Xcel_1337 [Xylanimonas cellulosilytica DSM
           15894]
          Length = 788

 Score = 37.1 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 5/95 (5%), Positives = 14/95 (14%)

Query: 260 PIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKG 319
                +                    ++    + G  ++                    G
Sbjct: 337 DDRGGDRPTGGFRRDDRGEGAPRGGDRREGGFRGGDRREGGHRRDDRSSEFRGGDRRDGG 396

Query: 320 IHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                   S         +     + S  R    +
Sbjct: 397 ARRDDRGRSDGGRREGPGAGDRGGRPSFERDRPAR 431


>gi|268535022|ref|XP_002632644.1| Hypothetical protein CBG21565 [Caenorhabditis briggsae]
 gi|187022510|emb|CAP38325.1| hypothetical protein CBG_21565 [Caenorhabditis briggsae AF16]
          Length = 145

 Score = 37.1 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 12/118 (10%), Positives = 26/118 (22%), Gaps = 3/118 (2%)

Query: 233 TREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
            R++      +  GP   +      D    + +   R +                    +
Sbjct: 21  WRDLDPGPRTQDPGPRTQDPGPRTQDPGPRTQDPGPRTQDPGPRTQDPGPRTQDPGPRTQ 80

Query: 293 NGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
           +      +   P  R           G  +       Q      + P   ++    RT
Sbjct: 81  DP---GPRTQDPGPRTQDPGPRTQDPGPRTQDPGPRTQDPGPMTQDPGPRTQDPGPRT 135


>gi|66823955|ref|XP_645332.1| proteasome component region PCI  domain-containing protein
           [Dictyostelium discoideum AX4]
 gi|74860574|sp|Q86B20|EIF3A_DICDI RecName: Full=Eukaryotic translation initiation factor 3 subunit A;
           Short=eIF3a; AltName: Full=Eukaryotic translation
           initiation factor 3 subunit 10
 gi|60473455|gb|EAL71400.1| proteasome component region PCI  domain-containing protein
           [Dictyostelium discoideum AX4]
          Length = 1030

 Score = 37.1 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 13/115 (11%), Positives = 25/115 (21%), Gaps = 8/115 (6%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           S++  R+                      +   +             R  +      G  
Sbjct: 779 SRRTFRDDDDEREESGRWGGRRGGDDFGRSKADEGDRWGRREDAPPPRRDEG-----GDR 833

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
             ++   P  RR+   + W   G                RR  + P +R      
Sbjct: 834 WGRREDAPPPRRDEGGDRW---GKREDAPPPRRDEGGWGRRDDAPPPRRDEGGDR 885


>gi|291440266|ref|ZP_06579656.1| LOW QUALITY PROTEIN: ATP-binding RNA helicase [Streptomyces
           ghanaensis ATCC 14672]
 gi|291343161|gb|EFE70117.1| LOW QUALITY PROTEIN: ATP-binding RNA helicase [Streptomyces
           ghanaensis ATCC 14672]
          Length = 861

 Score = 37.1 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 6/76 (7%), Positives = 14/76 (18%), Gaps = 2/76 (2%)

Query: 274 IISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW--MAKGIHSSFLSDSGQR 331
            +           +   +   +    +L  P              A G        +   
Sbjct: 743 GLRPGRAPRRTGARADHRAQRVRDPDRLLRPGAAGARREAPGDVRAPGDAPGGRRAAAGA 802

Query: 332 EENHRRSPSFPSKRSL 347
                R+     +R  
Sbjct: 803 PVVPGRTAGRGDRRPR 818


>gi|290957979|ref|YP_003489161.1| hypothetical protein SCAB_35191 [Streptomyces scabiei 87.22]
 gi|260647505|emb|CBG70610.1| putative membrane protein [Streptomyces scabiei 87.22]
          Length = 296

 Score = 37.1 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 12/107 (11%), Positives = 25/107 (23%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                          +++   RDR    S   D            +         +    
Sbjct: 188 RPRSTDNAPARPGPATADHPDRDRGPTASRQRDGVDPSHTGGKGNDKGKGNGNGTSEGDA 247

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           R  +S    A    +    D  ++     R P+   ++      A +
Sbjct: 248 RRPSSRPGAAGVPDAPGPPDGVRKPPGAERGPAGTGRKPRGEVRAPE 294


>gi|194216481|ref|XP_001917486.1| PREDICTED: similar to NHS-like 1 [Equus caballus]
          Length = 1389

 Score = 37.1 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 12/112 (10%), Positives = 21/112 (18%), Gaps = 5/112 (4%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            +   P                     R      +             +      + K  
Sbjct: 888 EDARSPFRDSGRAEPPREACRRLPDPERQAAPADNPGGSADGAAAPELTPAAPQDRGKPS 947

Query: 302 ATPVHRRN-----LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           A+P  R +       S    A G   +     G    +     + P     R
Sbjct: 948 ASPKSRNSTREMQRDSPPACAPGARPTPAGSPGGGRGDAGDPGAGPGTSPSR 999


>gi|47200812|emb|CAF87659.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 222

 Score = 37.1 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 13/104 (12%), Positives = 23/104 (22%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P   E +  +L  P     +    R     E      R  ++        ++ +     
Sbjct: 26  RPRDPERSGPHLRRPRDPERSRPHLRRPRDPERSGPRLRRPRDPEWSGPRLRRPRDPERS 85

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
             R          G       D  +     RR        +  R
Sbjct: 86  GPRLRRPRDPERSGPRLRRPRDPERSGPRLRRPRDLERNETRPR 129



 Score = 37.1 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 16/97 (16%), Positives = 24/97 (24%)

Query: 257 LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM 316
              P  S   L R R    S       R  + S  +    +  + + P  RR        
Sbjct: 27  PRDPERSGPHLRRPRDPERSRPHLRRPRDPERSGPRLRRPRDPEWSGPRLRRPRDPERSG 86

Query: 317 AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            +         SG R    R       +    R   +
Sbjct: 87  PRLRRPRDPERSGPRLRRPRDPERSGPRLRRPRDLER 123



 Score = 36.7 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 15/91 (16%), Positives = 22/91 (24%)

Query: 263 SSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHS 322
           S   L R R    S       R  + S       +  + + P  RR         +    
Sbjct: 20  SGPRLRRPRDPERSGPHLRRPRDPERSRPHLRRPRDPERSGPRLRRPRDPEWSGPRLRRP 79

Query: 323 SFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                SG R    R       +    R   +
Sbjct: 80  RDPERSGPRLRRPRDPERSGPRLRRPRDPER 110


>gi|195161402|ref|XP_002021557.1| GL26577 [Drosophila persimilis]
 gi|194103357|gb|EDW25400.1| GL26577 [Drosophila persimilis]
          Length = 765

 Score = 37.1 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 24/150 (16%), Positives = 44/150 (29%), Gaps = 10/150 (6%)

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLD 258
           R++ K+      +            +L  LL    R +SK++          +  + + D
Sbjct: 487 RQVSKLKGDAGNE----------DLKLDKLLDAKYRTISKQLDIASKRKKSKKSRRKSSD 536

Query: 259 APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAK 318
           +   SS      R        DD     +    + G S ++  A      + +S      
Sbjct: 537 SSNESSTDERARRRESEHRRRDDRNGSSRLRENRRGNSPEEPRANRGGSSSHSSRRQHQT 596

Query: 319 GIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
               S      +RE + R      S  S  
Sbjct: 597 ERRRSPERGPPRRERDQRDRSRGRSDHSRN 626


>gi|297154831|gb|ADI04543.1| tyramine oxidase [Streptomyces bingchenggensis BCW-1]
          Length = 1185

 Score = 37.1 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 11/90 (12%), Positives = 23/90 (25%), Gaps = 1/90 (1%)

Query: 266 TLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFL 325
            ++    +                 + +G         P  R   A+             
Sbjct: 390 PVLGRSAHAGRPGRLPGRPGPAADPRPDGAGSDGPGRRPGRRAGPATLGGRRPRHRPRNA 449

Query: 326 SDSGQREENHRRSPSFPSKRSLR-RTSAKK 354
             +G+     RR    P +R+ R R+   +
Sbjct: 450 DPAGRARVRPRRHARLPVERTGRCRSRPHR 479


>gi|289584242|gb|ADD10954.1| hypothetical protein [Chlamydophila pecorum]
          Length = 241

 Score = 37.1 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 19/122 (15%), Positives = 40/122 (32%), Gaps = 1/122 (0%)

Query: 224 QLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
           +L  L   S++E+S K       P   E +     +   S +     +P+     P + +
Sbjct: 2   ELKDLETSSSKELSPKE-PLPKEPSPKEPSSKEPSSKELSPKESSPKKPSPKEPSPKEPS 60

Query: 284 RMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
             + +  + +      K  +P    +   +         S    S +     + SP  PS
Sbjct: 61  SKEPSPKEPSSKEPSPKEPSPKEPSSKEPSPKELSPKELSPKESSPKELSPKKPSPKEPS 120

Query: 344 KR 345
            +
Sbjct: 121 SK 122


>gi|289706442|ref|ZP_06502800.1| pyridine nucleotide-disulfide oxidoreductase, dimerization domain
           protein [Micrococcus luteus SK58]
 gi|289556937|gb|EFD50270.1| pyridine nucleotide-disulfide oxidoreductase, dimerization domain
           protein [Micrococcus luteus SK58]
          Length = 439

 Score = 37.1 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 14/99 (14%), Positives = 24/99 (24%), Gaps = 11/99 (11%)

Query: 267 LVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIH----- 321
            +R R +       D  R  +   +  G         P HR          +        
Sbjct: 211 RLRRRGDRPGAGRADPARRVRRGPRLPGRGPAGPRRAPGHRGLRHGLRRGRRRPARGPRG 270

Query: 322 ----SSFLSDSGQREENHRRSPSFPSKRSL--RRTSAKK 354
                     +G      RR P+   +R    R    ++
Sbjct: 271 GRADRRGHRGAGHGPRVDRRGPAPGGRRHRAGREGLHRR 309


>gi|308451497|ref|XP_003088692.1| hypothetical protein CRE_04450 [Caenorhabditis remanei]
 gi|308246066|gb|EFO90018.1| hypothetical protein CRE_04450 [Caenorhabditis remanei]
          Length = 593

 Score = 37.1 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 20/113 (17%), Positives = 31/113 (27%), Gaps = 2/113 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R   G    EEA    +    S+  +V  R   +  VP    R  +       + + ++ 
Sbjct: 3   RSPHGLARAEEAVPAGEGAHRSAARVVPRRRERLPPVPHLLRRRHRRGHAGADVRRPRRP 62

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLS-DSGQREENHRRSPSFPSKR-SLRRTSA 352
                RR          G          G R     R  + PS+    R    
Sbjct: 63  LGARGRRRHPRPRHRGAGPRRVRRDLRPGVRRHPVDRQGAGPSREVDRRSGRE 115


>gi|192292479|ref|YP_001993084.1| Collagen triple helix repeat [Rhodopseudomonas palustris TIE-1]
 gi|192286228|gb|ACF02609.1| Collagen triple helix repeat [Rhodopseudomonas palustris TIE-1]
          Length = 212

 Score = 37.1 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 8/99 (8%), Positives = 14/99 (14%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
               ++           R                    +    KQ  +  P  +      
Sbjct: 1   MAEAESTRRGRPGPQGPRGRPGEPGRPGPQGHPGRPGPEGPRGKQGPVGKPGPQGKAGPQ 60

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                          G      +  P  P      R   
Sbjct: 61  GKPGIAGKPGPDGKPGPIGPQGKAGPQGPRGEQGLRGEQ 99


>gi|57790554|gb|AAW56205.1| CACNA1A [Mus musculus]
          Length = 2369

 Score = 37.1 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 15/115 (13%), Positives = 27/115 (23%), Gaps = 20/115 (17%)

Query: 258  DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
            + P          R +       + T  ++ SS  +G        T   RR         
Sbjct: 2184 ERPDTGRARAREQRWSRSPSEGREHTTHRQGSSSVSGSPAPSTSGTSTPRRGRRQLPQTP 2243

Query: 318  KGIHS-----------------SFLSDSGQREENHRRSPSFPS---KRSLRRTSA 352
                                     +  G      RR+P +P+   +    R + 
Sbjct: 2244 CTPRPLVSYSPAPRRPAARRMAGPAAPPGGSPRGCRRAPRWPAHAPEGPRPRGAD 2298



 Score = 37.1 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 8/91 (8%), Positives = 16/91 (17%), Gaps = 14/91 (15%)

Query: 277  EVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL---ASNVWMAKGIHSSFLSDSGQREE 333
              P           ++           P  R        +     G        S +   
Sbjct: 2265 AGPAAPPGGSPRGCRRAPRWPAHAPEGPRPRGADYTEPDSPREPPGGAHDPAPRSPRTPR 2324

Query: 334  NHRRSPSFPSKR-----------SLRRTSAK 353
                +     +R              RT+ +
Sbjct: 2325 AAGCASPRHGRRLPNGYYAGHGAPRPRTARR 2355


>gi|74181109|dbj|BAE27823.1| unnamed protein product [Mus musculus]
          Length = 2368

 Score = 37.1 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 15/115 (13%), Positives = 27/115 (23%), Gaps = 20/115 (17%)

Query: 258  DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
            + P          R +       + T  ++ SS  +G        T   RR         
Sbjct: 2183 ERPDTGRARAREQRWSRSPSEGREHTTHRQGSSSVSGSPAPSTSGTSTPRRGRRQLPQTP 2242

Query: 318  KGIHS-----------------SFLSDSGQREENHRRSPSFPS---KRSLRRTSA 352
                                     +  G      RR+P +P+   +    R + 
Sbjct: 2243 CTPRPLVSYSPAPRRPAARRMAGPAAPPGGSPRGCRRAPRWPAHAPEGPRPRGAD 2297



 Score = 37.1 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 8/91 (8%), Positives = 16/91 (17%), Gaps = 14/91 (15%)

Query: 277  EVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL---ASNVWMAKGIHSSFLSDSGQREE 333
              P           ++           P  R        +     G        S +   
Sbjct: 2264 AGPAAPPGGSPRGCRRAPRWPAHAPEGPRPRGADYTEPDSPREPPGGAHDPAPRSPRTPR 2323

Query: 334  NHRRSPSFPSKR-----------SLRRTSAK 353
                +     +R              RT+ +
Sbjct: 2324 AAGCASPRHGRRLPNGYYAGHGAPRPRTARR 2354



 Score = 36.3 bits (82), Expect = 7.2,   Method: Composition-based stats.
 Identities = 8/103 (7%), Positives = 29/103 (28%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            +++       + + +     +         P+      +     +  + ++       + 
Sbjct: 2145 KDRDQDRGRPKDRKHRPHHHHHHHHHHPPAPDRDRYAQERPDTGRARAREQRWSRSPSEG 2204

Query: 302  ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
                  R  +S+V  +    +S  S   +      ++P  P  
Sbjct: 2205 REHTTHRQGSSSVSGSPAPSTSGTSTPRRGRRQLPQTPCTPRP 2247


>gi|297563760|ref|YP_003682734.1| glycosyl transferase family 51 [Nocardiopsis dassonvillei subsp.
           dassonvillei DSM 43111]
 gi|296848208|gb|ADH70228.1| glycosyl transferase family 51 [Nocardiopsis dassonvillei subsp.
           dassonvillei DSM 43111]
          Length = 978

 Score = 37.1 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 11/100 (11%), Positives = 19/100 (19%), Gaps = 20/100 (20%)

Query: 264 SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW-------- 315
             T  R   +      D      +    +       +      RR   +           
Sbjct: 1   MSTERRRNADGGRRRADGPADGSRGGGGRRRADGPPRDEPSGGRRRPDAGDGFWGDDTGP 60

Query: 316 ------------MAKGIHSSFLSDSGQREENHRRSPSFPS 343
                                  D  +R E  RR+P+   
Sbjct: 61  ERPRRRRPPEQDARSEGRRRSEGDRPRRPEGQRRAPADGD 100


>gi|116174795|ref|NP_031604.3| voltage-dependent P/Q-type calcium channel subunit alpha-1A [Mus
            musculus]
 gi|125987800|sp|P97445|CAC1A_MOUSE RecName: Full=Voltage-dependent P/Q-type calcium channel subunit
            alpha-1A; AltName: Full=Brain calcium channel I;
            Short=BI; AltName: Full=Calcium channel, L type, alpha-1
            polypeptide isoform 4; AltName: Full=Voltage-gated
            calcium channel subunit alpha Cav2.1
          Length = 2368

 Score = 37.1 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 15/115 (13%), Positives = 27/115 (23%), Gaps = 20/115 (17%)

Query: 258  DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
            + P          R +       + T  ++ SS  +G        T   RR         
Sbjct: 2183 ERPDTGRARAREQRWSRSPSEGREHTTHRQGSSSVSGSPAPSTSGTSTPRRGRRQLPQTP 2242

Query: 318  KGIHS-----------------SFLSDSGQREENHRRSPSFPS---KRSLRRTSA 352
                                     +  G      RR+P +P+   +    R + 
Sbjct: 2243 CTPRPLVSYSPAPRRPAARRMAGPAAPPGGSPRGCRRAPRWPAHAPEGPRPRGAD 2297



 Score = 37.1 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 8/91 (8%), Positives = 16/91 (17%), Gaps = 14/91 (15%)

Query: 277  EVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL---ASNVWMAKGIHSSFLSDSGQREE 333
              P           ++           P  R        +     G        S +   
Sbjct: 2264 AGPAAPPGGSPRGCRRAPRWPAHAPEGPRPRGADYTEPDSPREPPGGAHDPAPRSPRTPR 2323

Query: 334  NHRRSPSFPSKR-----------SLRRTSAK 353
                +     +R              RT+ +
Sbjct: 2324 AAGCASPRHGRRLPNGYYAGHGAPRPRTARR 2354



 Score = 36.3 bits (82), Expect = 7.3,   Method: Composition-based stats.
 Identities = 8/103 (7%), Positives = 29/103 (28%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            +++       + + +     +         P+      +     +  + ++       + 
Sbjct: 2145 KDRDQDRGRPKDRKHRPHHHHHHHHHHPPAPDRDRYAQERPDTGRARAREQRWSRSPSEG 2204

Query: 302  ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
                  R  +S+V  +    +S  S   +      ++P  P  
Sbjct: 2205 REHTTHRQGSSSVSGSPAPSTSGTSTPRRGRRQLPQTPCTPRP 2247


>gi|194745953|ref|XP_001955449.1| GF18772 [Drosophila ananassae]
 gi|190628486|gb|EDV44010.1| GF18772 [Drosophila ananassae]
          Length = 621

 Score = 37.1 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 14/124 (11%), Positives = 29/124 (23%), Gaps = 5/124 (4%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             R+ S +  R +            L     +++       +     P    R ++   Q
Sbjct: 422 ERRQNSDREQRSRRRSSSRSRNDRKLSWSKNNTDKGRSRSKDRTERRPGSKGRTEQRPYQ 481

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS-LRRT 350
                   +       R    N       +     +   +   H        K S   R+
Sbjct: 482 AR----DHRPDRFPQDRRRQENEGRQVTRNRDKSPEPRHQARRHESRDRENGKNSNRNRS 537

Query: 351 SAKK 354
             +K
Sbjct: 538 PERK 541


>gi|126322417|ref|XP_001378453.1| PREDICTED: similar to serine/threonine-protein kinase [Monodelphis
           domestica]
          Length = 1338

 Score = 37.1 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 17/107 (15%), Positives = 29/107 (27%), Gaps = 9/107 (8%)

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
            +      + S     R R         +  + KK     +  +   K      RR   S
Sbjct: 620 KKSKSPIELRSKSKDRRSRSKDRKSKRSEIDKEKKPIKSPSKDASSGKENRSPSRRPGRS 679

Query: 313 NVWMAKGIHSSFLSDSGQ------REENHRRSPSF---PSKRSLRRT 350
               +        S   +      R     +SPS    P +R+  R+
Sbjct: 680 PKGKSLSPKQRDKSRRSRSPLLNDRRSKQSKSPSRTLSPGRRAKSRS 726



 Score = 36.3 bits (82), Expect = 7.7,   Method: Composition-based stats.
 Identities = 14/107 (13%), Positives = 32/107 (29%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            ++ E++         S   +R +         D    +    ++    K         +
Sbjct: 608 PIINESKSRDRGKKSKSPIELRSKSKDRRSRSKDRKSKRSEIDKEKKPIKSPSKDASSGK 667

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            N + +    +      LS   + +    RSP    +RS +  S  +
Sbjct: 668 ENRSPSRRPGRSPKGKSLSPKQRDKSRRSRSPLLNDRRSKQSKSPSR 714


>gi|332839100|ref|XP_001162933.2| PREDICTED: hypothetical protein LOC744431 [Pan troglodytes]
          Length = 311

 Score = 37.1 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 5/78 (6%), Positives = 16/78 (20%)

Query: 277 EVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR 336
                              S ++    P+ ++   +     K           +      
Sbjct: 207 PRNPPARARPAGVPSPITSSPERGRGRPMKQQQEPTGEPSPKRPRGRPKGSKNKSPSKAA 266

Query: 337 RSPSFPSKRSLRRTSAKK 354
           +  +  +     R   +K
Sbjct: 267 QKKAEATGEKRPRGRPRK 284


>gi|302538386|ref|ZP_07290728.1| secreted protein [Streptomyces sp. C]
 gi|302447281|gb|EFL19097.1| secreted protein [Streptomyces sp. C]
          Length = 371

 Score = 37.1 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 9/110 (8%), Positives = 24/110 (21%), Gaps = 2/110 (1%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP- 304
           GP    +                   P  +          ++        +++     P 
Sbjct: 242 GPRQTLQPPRRRGDDHRLPPARPPGHPAHLHRPHPAAAAHRQGDRPPPPRARRTAAGDPL 301

Query: 305 -VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              R    +     +G     ++    R +         S  +  R+  +
Sbjct: 302 VPRRPRAQAVRGTHRGPRRRTVAARPARPQAVGERHRPHSLGARPRSRPR 351


>gi|296809373|ref|XP_002845025.1| tho2 protein [Arthroderma otae CBS 113480]
 gi|238844508|gb|EEQ34170.1| tho2 protein [Arthroderma otae CBS 113480]
          Length = 2423

 Score = 37.1 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 15/109 (13%), Positives = 25/109 (22%), Gaps = 1/109 (0%)

Query: 241  LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
            + E  G   L E  +                 + I     ++                ++
Sbjct: 1691 VMESRGFGRLSEKDMARRPYPEDHIGRPTHMRDPIGPRDQEWRERHSRGRLNPPDHLNQR 1750

Query: 301  LATPVHRRNLASNVWM-AKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
               P   R+  SN    A   H         R +   R P   S+    
Sbjct: 1751 PDQPRSLRDEESNASRHANMQHPHEYPHRPARPQREDRRPPHGSRPPTP 1799


>gi|257068215|ref|YP_003154470.1| translation initiation factor 2 [Brachybacterium faecium DSM 4810]
 gi|256559033|gb|ACU84880.1| bacterial translation initiation factor 2 (bIF-2) [Brachybacterium
           faecium DSM 4810]
          Length = 957

 Score = 37.1 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 5/102 (4%), Positives = 14/102 (13%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           +       P               +   ++     +   +      Q        R    
Sbjct: 154 KPGAEKPIPTPKPGGERPAPRPGGARPGNNPFASSQGMPRPGRKPGQGGPRPGGPRPGNN 213

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                                E     P+          + +
Sbjct: 214 PFASSQGMPRPGQRPSRPGGTEQAAGRPAREGGAPRPGGAPR 255


>gi|74181089|dbj|BAE27814.1| unnamed protein product [Mus musculus]
 gi|74184694|dbj|BAE27952.1| unnamed protein product [Mus musculus]
 gi|74188682|dbj|BAE28080.1| unnamed protein product [Mus musculus]
          Length = 2321

 Score = 37.1 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 15/115 (13%), Positives = 27/115 (23%), Gaps = 20/115 (17%)

Query: 258  DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
            + P          R +       + T  ++ SS  +G        T   RR         
Sbjct: 2136 ERPDTGRARAREQRWSRSPSEGREHTTHRQGSSSVSGSPAPSTSGTSTPRRGRRQLPQTP 2195

Query: 318  KGIHS-----------------SFLSDSGQREENHRRSPSFPS---KRSLRRTSA 352
                                     +  G      RR+P +P+   +    R + 
Sbjct: 2196 CTPRPLVSYSPAPRRPAARRMAGPAAPPGGSPRGCRRAPRWPAHAPEGPRPRGAD 2250



 Score = 36.7 bits (83), Expect = 4.9,   Method: Composition-based stats.
 Identities = 8/91 (8%), Positives = 16/91 (17%), Gaps = 14/91 (15%)

Query: 277  EVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL---ASNVWMAKGIHSSFLSDSGQREE 333
              P           ++           P  R        +     G        S +   
Sbjct: 2217 AGPAAPPGGSPRGCRRAPRWPAHAPEGPRPRGADYTEPDSPREPPGGAHDPAPRSPRTPR 2276

Query: 334  NHRRSPSFPSKR-----------SLRRTSAK 353
                +     +R              RT+ +
Sbjct: 2277 AAGCASPRHGRRLPNGYYAGHGAPRPRTARR 2307



 Score = 36.3 bits (82), Expect = 7.4,   Method: Composition-based stats.
 Identities = 8/103 (7%), Positives = 29/103 (28%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            +++       + + +     +         P+      +     +  + ++       + 
Sbjct: 2098 KDRDQDRGRPKDRKHRPHHHHHHHHHHPPAPDRDRYAQERPDTGRARAREQRWSRSPSEG 2157

Query: 302  ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
                  R  +S+V  +    +S  S   +      ++P  P  
Sbjct: 2158 REHTTHRQGSSSVSGSPAPSTSGTSTPRRGRRQLPQTPCTPRP 2200


>gi|325114486|emb|CBZ50042.1| hypothetical protein NCLIV_005180 [Neospora caninum Liverpool]
          Length = 1855

 Score = 36.7 bits (83), Expect = 4.9,   Method: Composition-based stats.
 Identities = 9/83 (10%), Positives = 22/83 (26%)

Query: 272 PNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR 331
               S      +R  +  +  +         +  +  +  +      G   S     G+ 
Sbjct: 22  HRASSRSYCGTSRSTRRDALDDRGRSSASHYSSRYSSSSRATAPRDSGQRPSSRRARGRE 81

Query: 332 EENHRRSPSFPSKRSLRRTSAKK 354
           EE+    P    +    R +  +
Sbjct: 82  EEDRDSRPCRSGREDRGRGARPE 104


>gi|289773546|ref|ZP_06532924.1| tetracycline resistance protein [Streptomyces lividans TK24]
 gi|289703745|gb|EFD71174.1| tetracycline resistance protein [Streptomyces lividans TK24]
          Length = 638

 Score = 36.7 bits (83), Expect = 4.9,   Method: Composition-based stats.
 Identities = 17/128 (13%), Positives = 33/128 (25%), Gaps = 5/128 (3%)

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G  R  + + LR++ G H                               D   R   ++ 
Sbjct: 405 GGARGDTGRGLRDRGGVHAGPRPVPGASGGHRRGRGGDAVARPHPVLRDDRAARRTGSAR 464

Query: 291 QKNGLS-----KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
            + GL      ++     P  RR         +          G  +    +  +   +R
Sbjct: 465 LRRGLRVRDGARRAPPGLPPGRRGDRPRHAADRAHRCGGHRLPGHADPLRLQLAAQHGRR 524

Query: 346 SLRRTSAK 353
             R  +A+
Sbjct: 525 LPRADTAR 532


>gi|116311009|emb|CAH67942.1| H0303A11-B0406H05.2 [Oryza sativa Indica Group]
          Length = 1053

 Score = 36.7 bits (83), Expect = 4.9,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 25/108 (23%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
             L  +        I ++     +R     +      R  +++      S  +       
Sbjct: 284 LPLCSDPDRASILTIMTAVRASEERAPKGHDGAGGSRRGDQSTPGGGRASGSRDGGPGSS 343

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           RR  A       G         G       R P   +  S      KK
Sbjct: 344 RRADARGKRKQGGTPPPSPPRGGGAVRASSRRPKGAAPTSQPEGERKK 391


>gi|302520008|ref|ZP_07272350.1| conserved hypothetical protein [Streptomyces sp. SPB78]
 gi|302428903|gb|EFL00719.1| conserved hypothetical protein [Streptomyces sp. SPB78]
          Length = 695

 Score = 36.7 bits (83), Expect = 5.0,   Method: Composition-based stats.
 Identities = 8/80 (10%), Positives = 15/80 (18%)

Query: 274 IISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREE 333
                       +  +  +   S     + P  R N       A             R +
Sbjct: 573 RGRLRHRLRPHRRGTAPTRCTASPASPNSPPRRRANRHRPPGRAGAADGGRRHPHRHRPD 632

Query: 334 NHRRSPSFPSKRSLRRTSAK 353
                     +R     S +
Sbjct: 633 RGAEPVPTGERRPRGSPSPR 652


>gi|91974763|ref|YP_567422.1| helicase-like [Rhodopseudomonas palustris BisB5]
 gi|91681219|gb|ABE37521.1| helicase-like [Rhodopseudomonas palustris BisB5]
          Length = 1119

 Score = 36.7 bits (83), Expect = 5.0,   Method: Composition-based stats.
 Identities = 11/113 (9%), Positives = 23/113 (20%), Gaps = 6/113 (5%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            R +      +  Q                              ++++  +  G    +  
Sbjct: 984  RNRQRHRPPQAGQAAAPEGEAGEAKRGDRPDRGGRRGDRKGADVRRDRREGEGQGAPRSE 1043

Query: 302  ATPVHRRNLASNVWMA------KGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
            A    R +              KG       + G        S + P +R   
Sbjct: 1044 AAGEGRPSRERFKGRDKSQDKFKGGPKGGRDNQGGGSHRQVHSSAPPRERDRP 1096


>gi|299748031|ref|XP_002911244.1| tho2 protein [Coprinopsis cinerea okayama7#130]
 gi|298407787|gb|EFI27750.1| tho2 protein [Coprinopsis cinerea okayama7#130]
          Length = 2474

 Score = 36.7 bits (83), Expect = 5.0,   Method: Composition-based stats.
 Identities = 11/81 (13%), Positives = 23/81 (28%), Gaps = 1/81 (1%)

Query: 274  IISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL-ASNVWMAKGIHSSFLSDSGQRE 332
                 P       +N+ +  G  ++        R++    +    +        D G+ E
Sbjct: 2176 PSRPEPSRHRPSAQNADESLGKRRRPNDDDRSSRKDGHRDSDRGRRPGQEKDAHDRGRGE 2235

Query: 333  ENHRRSPSFPSKRSLRRTSAK 353
             + RR    P     R +   
Sbjct: 2236 SDRRRKEREPENSEARESRGS 2256


>gi|239979286|ref|ZP_04701810.1| hypothetical protein SalbJ_07609 [Streptomyces albus J1074]
 gi|291451165|ref|ZP_06590555.1| predicted protein [Streptomyces albus J1074]
 gi|291354114|gb|EFE81016.1| predicted protein [Streptomyces albus J1074]
          Length = 385

 Score = 36.7 bits (83), Expect = 5.0,   Method: Composition-based stats.
 Identities = 11/121 (9%), Positives = 27/121 (22%), Gaps = 5/121 (4%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
              + E               A   +            +         +     K   ++
Sbjct: 219 GDTVSEAGDTASEAAGSAGRTARRTAEVGSSGRTARRGARHEGGSRAERVARKAKPAAAR 278

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF----PSKRSLRRTSAK 353
           + +   P  +        +  G   +       R    R +P+     P +  +  T A 
Sbjct: 279 RHRRE-PALKLRPGHRDGLPGGGRLAAARHPPARPRGARPTPAPGHGCPRRAPVPPTGAA 337

Query: 354 K 354
           +
Sbjct: 338 R 338


>gi|153832249|ref|ZP_01984916.1| putative ATP-dependent RNA helicase RhlE [Vibrio harveyi HY01]
 gi|148871560|gb|EDL70415.1| putative ATP-dependent RNA helicase RhlE [Vibrio harveyi HY01]
          Length = 499

 Score = 36.7 bits (83), Expect = 5.0,   Method: Composition-based stats.
 Identities = 11/130 (8%), Positives = 30/130 (23%), Gaps = 17/130 (13%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           + +K L      ++L E++++            +              +    +++    
Sbjct: 366 LPRKELEGYAPTNVLPESKLDTRPIKPKKPKKPKKPKAEGENGHTAEKKNSGGNNKPKRR 425

Query: 296 SKQKKLATPVH--------------RRNLASNVWMAKGIHSSFLSDSGQREENHRR---S 338
                                    R   A +     G        +G +  N +     
Sbjct: 426 FNSDNKNGKGENKSGKGGAGKPKGNRDGQARSNGKPSGNRKPNNKPAGAKPSNGKPSGNK 485

Query: 339 PSFPSKRSLR 348
           PS   ++   
Sbjct: 486 PSGQRRKPRP 495


>gi|117928722|ref|YP_873273.1| translation initiation factor IF-2 [Acidothermus cellulolyticus
           11B]
 gi|166226241|sp|A0LV27|IF2_ACIC1 RecName: Full=Translation initiation factor IF-2
 gi|117649185|gb|ABK53287.1| bacterial translation initiation factor 2 (bIF-2) [Acidothermus
           cellulolyticus 11B]
          Length = 879

 Score = 36.7 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 10/106 (9%), Positives = 20/106 (18%), Gaps = 5/106 (4%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK----QKKLATPVHR 307
           E       P+   +                       +S           Q+   TP   
Sbjct: 114 EKIATPPRPVKLPQPPRPAPAVPKPPSGPPRMGNNPFTSPMPRPMPPRPVQRPTGTPGTP 173

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                 +        +  +    R    R +P   +   L     +
Sbjct: 174 GIPRPPLRPGAPGRPTPGAMPP-RPAAGRAAPGRGAPIRLPGGLGR 218


>gi|323450962|gb|EGB06841.1| hypothetical protein AURANDRAFT_71929 [Aureococcus anophagefferens]
          Length = 1511

 Score = 36.7 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 14/108 (12%), Positives = 25/108 (23%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            R  +               +       R    I    P    R  +     +G  ++   
Sbjct: 1188 RAHVPVRAAGRGGAPGLQGLLEGRGGPRRSARIRGAAPGRLARRARGPGDLHGHVRRGPR 1247

Query: 302  ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
            A      + A       G  +  L    +R    R  P+  +     R
Sbjct: 1248 AALGRDHDRAPGAAGGPGRRARPLLQRDRRPAPDRDRPAHGADVREPR 1295


>gi|113955476|ref|YP_731570.1| translation initiation factor IF-2 [Synechococcus sp. CC9311]
 gi|123327604|sp|Q0I7K2|IF2_SYNS3 RecName: Full=Translation initiation factor IF-2
 gi|113882827|gb|ABI47785.1| translation initiation factor IF-2 [Synechococcus sp. CC9311]
          Length = 1129

 Score = 36.7 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 12/119 (10%), Positives = 25/119 (21%), Gaps = 6/119 (5%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R          A+    +P+    +                       +      K + +
Sbjct: 180 RPTSARPTPAPARPTGTSPVKRPGSEASSPRPTAPPTRPQPKAPVNRGAPARPAPKPELV 239

Query: 302 ATPVHRRNLASNVWMAKGIHSS---FLSDSGQREENHRRSPS---FPSKRSLRRTSAKK 354
             P  +R          G         S    +  N  + P+    P   +    +  K
Sbjct: 240 GRPQPKRAAPGAPVRQIGQRPGVSPRPSGPPGQRANMPQRPAGSQRPGAPTRPGNAPSK 298


>gi|47124032|gb|AAH70050.1| SRRM2 protein [Homo sapiens]
          Length = 1022

 Score = 36.7 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 9/108 (8%), Positives = 21/108 (19%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                            S   +     +              + +    + + +  AT  
Sbjct: 432 RHASSSPESPKPAPAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAK 491

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R+ +          S        R          P +R   R+  +
Sbjct: 492 RGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQR 539



 Score = 36.7 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 11/98 (11%), Positives = 22/98 (22%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P      +++      +       R    S  P       ++ +       + +  T  
Sbjct: 444 APAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKR 503

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
                 S  W        +      +     RSP  P 
Sbjct: 504 GHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPG 541


>gi|302753422|ref|XP_002960135.1| hypothetical protein SELMODRAFT_402166 [Selaginella moellendorffii]
 gi|300171074|gb|EFJ37674.1| hypothetical protein SELMODRAFT_402166 [Selaginella moellendorffii]
          Length = 502

 Score = 36.7 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 13/107 (12%), Positives = 16/107 (14%)

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           P     +     A                     D               K     +P H
Sbjct: 279 PRRASPSNAPPRAVAPHPPPSHSREHGAPPPPARDHPAAPPPPPPGRHREKGPPPQSPPH 338

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           RR              S       R    R  P      +   T   
Sbjct: 339 RRPATHGTAPPHRGSPSGGRTPSARSPPFRSKPPPTPLSAGSETPPA 385


>gi|330469862|ref|YP_004407605.1| transcription termination factor Rho [Verrucosispora maris
           AB-18-032]
 gi|328812833|gb|AEB47005.1| transcription termination factor Rho [Verrucosispora maris
           AB-18-032]
          Length = 680

 Score = 36.7 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 15/96 (15%), Positives = 28/96 (29%), Gaps = 1/96 (1%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E+ G    E A+   D     +E   R           D     +   +     + ++ A
Sbjct: 159 ERGGERAAERAERTADRSGERAERGERAAERGDRAERGDRAERAERGDRAERGERAERGA 218

Query: 303 TPVHRRNLASNV-WMAKGIHSSFLSDSGQREENHRR 337
               R           +G  ++   + G R E  +R
Sbjct: 219 ERGERAERGERTERGDRGERAAERGERGDRGERGQR 254


>gi|162456422|ref|YP_001618789.1| hypothetical protein sce8139 [Sorangium cellulosum 'So ce 56']
 gi|161167004|emb|CAN98309.1| hypothetical protein sce8139 [Sorangium cellulosum 'So ce 56']
          Length = 254

 Score = 36.7 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 12/104 (11%), Positives = 24/104 (23%), Gaps = 1/104 (0%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E L    + ++          +      +            +       +     QK   
Sbjct: 147 EALLARNVAKSMPAATGRRARTAKPSARKAAAKRPPAKRAPKRASTQRAEPARGAQKGRR 206

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           T    R  A+    AK   ++       R     R+     + S
Sbjct: 207 TTTTGRKKAAATAPAKTGRAAPARKPS-RPAKTSRTGRKGGRAS 249


>gi|326323998|gb|ADZ54062.1| virulence-associated trimeric autotransporter [Haemophilus parasuis
           SH0165]
          Length = 1202

 Score = 36.7 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 11/111 (9%), Positives = 20/111 (18%), Gaps = 16/111 (14%)

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW 315
           +   P  +     R  P             +   +   G         P   +       
Sbjct: 673 DKGEPGQAGPAGPRGEPGQAGPAGPRGEPGQAGPAGPRGPQGTAGAQGPKGDKGDPGQAG 732

Query: 316 MAKGIH----------------SSFLSDSGQREENHRRSPSFPSKRSLRRT 350
            A                         + GQ      R P+ P   +  + 
Sbjct: 733 PAGPRGPAGPPGPVGPAGAAGPKGDKGEPGQAGPAGPRGPAGPKGDAGPKG 783


>gi|318060453|ref|ZP_07979176.1| ATP-dependent DNA helicase [Streptomyces sp. SA3_actG]
          Length = 1839

 Score = 36.7 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 12/112 (10%), Positives = 27/112 (24%), Gaps = 3/112 (2%)

Query: 244  QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +L       +  N       +        +I +  P    R  ++         + +   
Sbjct: 1113 ELEERGPGRSPGNPPRRRPPAPVSPAPYASIRAHPPRPAQRSARHPLHPRATRVRHRAPR 1172

Query: 304  PVHRRNL---ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            P   R       +    +    +     G+   + R       +R   RT  
Sbjct: 1173 PARHRGRCGLGQDDGDGRPRRLAGRYGHGRPRASPRSHLHQQGRRRAGRTRP 1224


>gi|240140800|ref|YP_002965280.1| RNA helicase [Methylobacterium extorquens AM1]
 gi|240010777|gb|ACS42003.1| RNA helicase [Methylobacterium extorquens AM1]
          Length = 519

 Score = 36.7 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 5/113 (4%), Positives = 22/113 (19%), Gaps = 1/113 (0%)

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             +            +         +++  R      +   +      ++   +   +++
Sbjct: 380 DEVEGDEPRRRRGSRRAKETKGGEETKSGGRSTERSAAPASESPRSENRSRGGRRPAAER 439

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDS-GQREENHRRSPSFPSKRSLRRT 350
            +   P                          +         +   +R  RR 
Sbjct: 440 SRADAPRRDPVREPEPVAVAPSAPPAPPRELAREPVRSAPERARGERRPPRRD 492


>gi|163853383|ref|YP_001641426.1| DEAD/DEAH box helicase domain-containing protein [Methylobacterium
           extorquens PA1]
 gi|163664988|gb|ABY32355.1| DEAD/DEAH box helicase domain protein [Methylobacterium extorquens
           PA1]
          Length = 519

 Score = 36.7 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 5/113 (4%), Positives = 22/113 (19%), Gaps = 1/113 (0%)

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             +            +         +++  R      +   +      ++   +   +++
Sbjct: 380 DEVEGDEPRRRRGSRRAKETKGGEETKSGGRSTERSAAPASESPRSENRSRGGRRPAAER 439

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDS-GQREENHRRSPSFPSKRSLRRT 350
            +   P                          +         +   +R  RR 
Sbjct: 440 SRADAPRRDPVREPEPVAVVPSAPPAPPRELAREPVRSAPERARGERRPPRRD 492


>gi|74190142|dbj|BAE37196.1| unnamed protein product [Mus musculus]
          Length = 493

 Score = 36.7 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 14/113 (12%), Positives = 35/113 (30%), Gaps = 2/113 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +         + + +  A  +      + R    S     ++R +    +    S ++  
Sbjct: 193 KRGHSRSPSPQWRRSRSAQRWGKSRSPQRRGRSRSPQRPGWSRSRNTQRRGRSRSARRGR 252

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +          +            S +  R  +  R+P+   +RS  RT A++
Sbjct: 253 SHSRSPATRGRSRSRTPARRGRSRSRTPARRRSRSRTPAR--RRSRSRTPARR 303


>gi|284990255|ref|YP_003408809.1| NAD-glutamate dehydrogenase [Geodermatophilus obscurus DSM 43160]
 gi|284063500|gb|ADB74438.1| NAD-glutamate dehydrogenase [Geodermatophilus obscurus DSM 43160]
          Length = 985

 Score = 36.7 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 12/112 (10%), Positives = 30/112 (26%), Gaps = 3/112 (2%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E          ++   A   +     R R   +         ++         + +   A
Sbjct: 872 ELAAAGRRRRGRLRRPARERAGPLHRRPRAGHVRPRRRPGPGVRGGGGAAPAGADRGLTA 931

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               +R  +     +  + ++     G R      +     +RS  R S ++
Sbjct: 932 AGAPQRARSGPGRGSPPVRTAGRPGRGSRPAA---AVGPGPRRSAARGSGRR 980


>gi|282162783|ref|YP_003355168.1| hypothetical protein MCP_0113 [Methanocella paludicola SANAE]
 gi|282155097|dbj|BAI60185.1| conserved hypothetical protein [Methanocella paludicola SANAE]
          Length = 477

 Score = 36.7 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 15/107 (14%), Positives = 34/107 (31%), Gaps = 3/107 (2%)

Query: 233 TREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
             ++++K + + L   +  E  V +     + +   +   N   E   +     +   + 
Sbjct: 247 VEDLTQKEIIKALRSKVPVEQVVEVPPRRRNKQQQQQREENGKPEGRPEGRPEGRPEGRP 306

Query: 293 NGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
            G  + +    P  R          +G       + G+R E  RR  
Sbjct: 307 EGRPEGRPEGRPEGREYPREQ---REGYQRPERQERGERGETPRRKS 350


>gi|197120692|ref|YP_002132643.1| hypothetical protein AnaeK_0272 [Anaeromyxobacter sp. K]
 gi|196170541|gb|ACG71514.1| protein of unknown function UPF0044 [Anaeromyxobacter sp. K]
          Length = 170

 Score = 36.7 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 10/119 (8%), Positives = 34/119 (28%), Gaps = 2/119 (1%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           ++ ++++ ++G    E+     D  +     + +     +        R +   +     
Sbjct: 53  LAHELVKLKVGTESPEDRLEIADRLLAEDVQVAQVLGRTVLAYRRHPERPRYEPAPAGAR 112

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +++ +      +   A                  +R     + P+   +R   R    K
Sbjct: 113 AERPEPKRAAAKGRRAPVKEKRAPARGQRAPARERRAPAKGQRPA--GRRPAPRAKRTK 169


>gi|46048885|ref|NP_990121.1| collagen alpha-1(V) chain [Gallus gallus]
 gi|6759903|gb|AAF28099.1| alpha 1 (V) collagen [Gallus gallus]
          Length = 1835

 Score = 36.7 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 7/113 (6%), Positives = 18/113 (15%), Gaps = 1/113 (0%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           ++   G       +           +     P  +    +             G    K 
Sbjct: 820 IKGDRGEIGPPGPRGEDGPEGPKGRSGPNGDPGPLGPAGEKGKLGVPGLPGYPGRQGPKG 879

Query: 301 LATPVHRRNLASNVW-MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                                        G       R P   + +   + ++
Sbjct: 880 SIGFPGFPGANGEKGTRGTPGKPGPRGQRGPTGPRGERGPRGSTGKPGPKGNS 932


>gi|326924976|ref|XP_003208698.1| PREDICTED: collagen alpha-1(XI) chain-like [Meleagris gallopavo]
          Length = 1736

 Score = 36.7 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 9/111 (8%), Positives = 16/111 (14%), Gaps = 1/111 (0%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           L+   G       +                 P       +             G    K 
Sbjct: 724 LKGDRGEVGQPGPRGEDGPEGPKGRAGPSGDPGAAGPAGEKGKLGVPGLPGYPGRQGPKG 783

Query: 301 LATPVHRRNLASNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                                       +G       R P  P+ +   + 
Sbjct: 784 STGFPGFPGANGEKGARGLHGKPGPQRTAGPTGPRGSRGPRGPTGKPGPKG 834


>gi|307110176|gb|EFN58412.1| hypothetical protein CHLNCDRAFT_50177 [Chlorella variabilis]
          Length = 780

 Score = 36.7 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 8/98 (8%), Positives = 18/98 (18%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           E          +     RD+        D         +      K++ +     +    
Sbjct: 483 ERGAKDAKDRGAKVAADRDKERAGKVAADRDKERAGKVAADRDKDKERAVKGKADKDKER 542

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                 +       S      E         S+    +
Sbjct: 543 ERGGKGRDKEKDKASKPAGPSEGREERSHRSSRPEREK 580


>gi|254418805|ref|ZP_05032529.1| hypothetical protein BBAL3_1115 [Brevundimonas sp. BAL3]
 gi|196184982|gb|EDX79958.1| hypothetical protein BBAL3_1115 [Brevundimonas sp. BAL3]
          Length = 323

 Score = 36.7 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 12/116 (10%), Positives = 32/116 (27%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           K++L        L          +     + R++ +         TR ++ +  +   S+
Sbjct: 2   KRLLMAFTAVAALGAPLAAPIQALAQDRQVDREQRDADRPQRPQITRGERPTPNRTLQSR 61

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
            +  + P   R         +            R +      + P +  +R    +
Sbjct: 62  PEAPSRPERPRPERPGFGETRPARPDRPQTGEDRPDRPNYGGARPDRPDVRPGRPE 117


>gi|118092373|ref|XP_001235893.1| PREDICTED: hypothetical protein [Gallus gallus]
          Length = 252

 Score = 36.7 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 13/123 (10%), Positives = 28/123 (22%), Gaps = 10/123 (8%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           RE         A      P  +       R    +       R+   +  + G  ++   
Sbjct: 13  REGGVLGAGGPALRCAHPPRRALPPGPGPRQRRRALQHGGGRRLPCAAPPRRGGPREPGA 72

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP----------SFPSKRSLRRTS 351
             P  R         A+       +  G    +    P          +  ++    R +
Sbjct: 73  PRPAARTAEPQPPDRAQTCRGPGTAPPGGAAPSGSPDPLPPAHDAGRAAGGTRDPRPRRA 132

Query: 352 AKK 354
             +
Sbjct: 133 EVR 135


>gi|291519301|emb|CBK74522.1| bacterial translation initiation factor 2 (bIF-2) [Butyrivibrio
           fibrisolvens 16/4]
          Length = 898

 Score = 36.7 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 14/111 (12%), Positives = 25/111 (22%), Gaps = 4/111 (3%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E +     EEA         +      +R            R ++           +   
Sbjct: 158 EFVSKRNNEEAAERPVKKERTERPERNERTERNERPERREGRQERTERGDRPARGDRPAG 217

Query: 303 TPVHRRNLAS-NVWMAKGIHSSFLSDSGQRE---ENHRRSPSFPSKRSLRR 349
               R +    N    +        D   R         +PS  + +  RR
Sbjct: 218 KRPERNDRPERNDRGDRPARPDNRGDRNSRPSQNAAPDMAPSNNNGKGGRR 268


>gi|325120549|emb|CBZ56103.1| conserved hypothetical protein [Neospora caninum Liverpool]
          Length = 2388

 Score = 36.7 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 17/126 (13%), Positives = 35/126 (27%)

Query: 229 LAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
             G    +       +      E  +     P  +S+     R       P    R   +
Sbjct: 739 FPGGVEVLPTDFSHSRGDRRDEELEEDERRGPPRASDLRGSGRGLSPRGRPSGGGRDISD 798

Query: 289 SSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           S       + + LA    R   + ++  +       L   G++     RS S   +++  
Sbjct: 799 SRSPKRRRRDENLARDSRRGRPSRSLSRSPTKGEDALKGPGRKGREAGRSASREGRKARA 858

Query: 349 RTSAKK 354
             S  +
Sbjct: 859 SLSPAR 864


>gi|291443474|ref|ZP_06582864.1| LOW QUALITY PROTEIN: transcriptional regulator [Streptomyces
           roseosporus NRRL 15998]
 gi|291346421|gb|EFE73325.1| LOW QUALITY PROTEIN: transcriptional regulator [Streptomyces
           roseosporus NRRL 15998]
          Length = 479

 Score = 36.7 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 11/113 (9%), Positives = 25/113 (22%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R            +             R  P             ++  ++ +    ++  
Sbjct: 3   RRTGHFPAGRAQPLLSWWKAAVQPGARRTVPGQPRHRLPRHRPARRRGARHHPPRLRRVP 62

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                R        +A G+        G+     R   +   +RS  R    +
Sbjct: 63  GGAPRRTARPGRHVLAGGVAERRRRTRGRAAYGRRLRGAGHPRRSTARGHRAQ 115


>gi|213964714|ref|ZP_03392914.1| putative translation initiation factor IF-2 [Corynebacterium
           amycolatum SK46]
 gi|213952907|gb|EEB64289.1| putative translation initiation factor IF-2 [Corynebacterium
           amycolatum SK46]
          Length = 947

 Score = 36.7 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 8/85 (9%), Positives = 15/85 (17%)

Query: 263 SSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHS 322
           S             +        K  +      +               SN+   +G + 
Sbjct: 151 SRSPKPGQEMPRPPKPAGPKPGPKPGARAPRVANNPFSTGGSSRPAPRPSNMPRPQGGNG 210

Query: 323 SFLSDSGQREENHRRSPSFPSKRSL 347
                 G R+   R           
Sbjct: 211 RPGPKPGGRQGGPRPQGGNGRPGPK 235


>gi|289642932|ref|ZP_06475066.1| 6-deoxyerythronolide-B synthase [Frankia symbiont of Datisca
            glomerata]
 gi|289507237|gb|EFD28202.1| 6-deoxyerythronolide-B synthase [Frankia symbiont of Datisca
            glomerata]
          Length = 2670

 Score = 36.7 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 9/103 (8%), Positives = 21/103 (20%)

Query: 252  EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
                        +   +R   +          R +     +      +  A    RR   
Sbjct: 2425 RTAAPGRRRAGGTRPELRRPAHRWRARDHRQGRPRACPGHRLRDRADRPDAAAGRRRGSG 2484

Query: 312  SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              +   +   +           +  R P  P  R       ++
Sbjct: 2485 DGLRGGRASAAPRPDRRRPAPAHRGRGPCHPPARRAGGAGHRR 2527



 Score = 35.9 bits (81), Expect = 9.1,   Method: Composition-based stats.
 Identities = 13/100 (13%), Positives = 22/100 (22%)

Query: 242  REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            R   G         +        +   R  P        D         + +G   +   
Sbjct: 2432 RRAGGTRPELRRPAHRWRARDHRQGRPRACPGHRLRDRADRPDAAAGRRRGSGDGLRGGR 2491

Query: 302  ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF 341
            A+   R +        +G               HRR P+ 
Sbjct: 2492 ASAAPRPDRRRPAPAHRGRGPCHPPARRAGGAGHRRGPAR 2531


>gi|108709264|gb|ABF97059.1| retrotransposon protein, putative, Ty3-gypsy subclass [Oryza sativa
           Japonica Group]
          Length = 506

 Score = 36.7 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 11/113 (9%), Positives = 28/113 (24%), Gaps = 3/113 (2%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             RE+  + +         +     ++  +  +  L R       E          +   
Sbjct: 34  EKREIRGREINHGDRHSWPK---AAVEVELTGARGLGRRTSGCDREGGRLTAGGSGDDGG 90

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
            +G ++Q+       R     N              +  RE     + +   +
Sbjct: 91  GDGGARQRGSGDTAARERRRGNGGAGTAARRHRNDSAAARERRRGGTRATARR 143


>gi|301610223|ref|XP_002934650.1| PREDICTED: hypothetical protein LOC100495464 [Xenopus (Silurana)
           tropicalis]
          Length = 559

 Score = 36.7 bits (83), Expect = 5.8,   Method: Composition-based stats.
 Identities = 10/87 (11%), Positives = 19/87 (21%)

Query: 267 LVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLS 326
                 N          +  +   +       +       R                  +
Sbjct: 391 SKDKERNKEKRSRSKDRQRDRGQDRDRSREGYRGQDRARSREGERDRSREGNRGQDRDRN 450

Query: 327 DSGQREENHRRSPSFPSKRSLRRTSAK 353
             G R ++  RSP    +RS  R   +
Sbjct: 451 REGYRGQDRDRSPEGDRERSRERNRDR 477



 Score = 36.3 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 12/113 (10%), Positives = 26/113 (23%), Gaps = 1/113 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK- 300
           R + G                + E       +   E   + +R +     + G   Q + 
Sbjct: 429 RSREGERDRSREGNRGQDRDRNREGYRGQDRDRSPEGDRERSRERNRDRSREGNRGQDRD 488

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                +R              S   +    ++ +  R       R   R   +
Sbjct: 489 RNQEGYRGQDRDRSREGDRERSKEKNRGRGQDRDRNREGYRGQDRDRDRNRGQ 541


>gi|291239418|ref|XP_002739620.1| PREDICTED: U2 small nuclear RNA auxiliary factor 1-like 2-like,
           partial [Saccoglossus kowalevskii]
          Length = 641

 Score = 36.7 bits (83), Expect = 5.8,   Method: Composition-based stats.
 Identities = 13/115 (11%), Positives = 21/115 (18%)

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            K  R   G       +++              R               +  S   G  +
Sbjct: 327 GKDRRHSRGRERGHRDRIDKGRSNSRGRDRSCSRDRSDRGRGHSRDGSDRGRSHSRGRDR 386

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           +                       S           +  RSPS     S  R  +
Sbjct: 387 RHSRGRDRSHSKGGDRNHSKGRGRSHSKGRGRSHSRDKDRSPSRDRSHSRGRDRS 441


>gi|301119549|ref|XP_002907502.1| conserved hypothetical protein [Phytophthora infestans T30-4]
 gi|262106014|gb|EEY64066.1| conserved hypothetical protein [Phytophthora infestans T30-4]
          Length = 1700

 Score = 36.7 bits (83), Expect = 5.8,   Method: Composition-based stats.
 Identities = 13/112 (11%), Positives = 28/112 (25%)

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            K   +  + P     A          +      +P    +         ++++  +G S
Sbjct: 63  KKAEPKPAVAPKQAAPAPAAKKPEPKPAAKQPDAKPAAAPKSAGRPPTSDQSTAPSSGNS 122

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                  P          +   G   +  S +G R      + S P+     
Sbjct: 123 AAGGRPAPSSGNGGRPAPFNGNGGRPTPSSGNGGRPAPMPTAASAPAPERRS 174


>gi|158313582|ref|YP_001506090.1| hypothetical protein Franean1_1746 [Frankia sp. EAN1pec]
 gi|158108987|gb|ABW11184.1| conserved hypothetical protein [Frankia sp. EAN1pec]
          Length = 1079

 Score = 36.7 bits (83), Expect = 5.8,   Method: Composition-based stats.
 Identities = 7/101 (6%), Positives = 21/101 (20%)

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           ++    DA   +     R   +  +  PD   R  + +    G    +   +       +
Sbjct: 427 QSGATGDARTSNGSGYDRGHRSDRASGPDRGYRPDRGAGSDRGYRSDRGAGSDRGDSRRS 486

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
                             ++  +         +        
Sbjct: 487 GPPSGGSSARPYTRPTHREQPASGTDRVDRAERTDRPDAPG 527



 Score = 35.9 bits (81), Expect = 8.4,   Method: Composition-based stats.
 Identities = 12/103 (11%), Positives = 22/103 (21%), Gaps = 1/103 (0%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR-N 309
                      +      + R            R  + +S + G  ++     P   R +
Sbjct: 116 PGQGAGRPKAAWRPAGTGQGRGGAGGSGGPGGERWGRPASSREGGPREASGGRPAGDRWS 175

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             +    A G         G R           +  S  R   
Sbjct: 176 GGAGRPGAHGRPEGQGRSEGGRPARRWEGSGRSAPASDSRGRQ 218


>gi|329939931|ref|ZP_08289213.1| sensory histidine kinase [Streptomyces griseoaurantiacus M045]
 gi|329300757|gb|EGG44653.1| sensory histidine kinase [Streptomyces griseoaurantiacus M045]
          Length = 1171

 Score = 36.7 bits (83), Expect = 5.9,   Method: Composition-based stats.
 Identities = 15/95 (15%), Positives = 27/95 (28%), Gaps = 1/95 (1%)

Query: 246  GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            GP  + E       P  +       R +     P+D     +     +GL +Q     P 
Sbjct: 1014 GPDRVGERDGREPDPAGARHRPRGHRGDPGRPQPEDRRGRLRRDPGTSGLHQQD-DRQPA 1072

Query: 306  HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
               +      +A+G   + L           R  +
Sbjct: 1073 RHHDRQQGAGLAQGQPGAHLRPHAGPPRPGGRRLA 1107


>gi|327300447|ref|XP_003234916.1| hypothetical protein TERG_03967 [Trichophyton rubrum CBS 118892]
 gi|326462268|gb|EGD87721.1| hypothetical protein TERG_03967 [Trichophyton rubrum CBS 118892]
          Length = 2550

 Score = 36.7 bits (83), Expect = 5.9,   Method: Composition-based stats.
 Identities = 16/111 (14%), Positives = 29/111 (26%), Gaps = 3/111 (2%)

Query: 244  QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
             + P           A     E  +   P++           ++  S+            
Sbjct: 1830 MVEPRGFGRLSEKEMAHRPYPEDHLGRPPHMREHTGPRDQEWRERHSRGRLNPPDNLSQR 1889

Query: 304  PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            P H R+L  ++ M    H         R     R P      S   T +++
Sbjct: 1890 PDHPRSLRDDMNMQ---HPHEYPHRPGRPSREDRRPPPHGHGSRPPTPSQQ 1937


>gi|148678997|gb|EDL10944.1| calcium channel, voltage-dependent, P/Q type, alpha 1A subunit,
            isoform CRA_b [Mus musculus]
          Length = 1789

 Score = 36.7 bits (83), Expect = 5.9,   Method: Composition-based stats.
 Identities = 12/88 (13%), Positives = 18/88 (20%)

Query: 258  DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA 317
            + P          R +       + T  ++ SS  +G        T   RR         
Sbjct: 1645 ERPDTGRARAREQRWSRSPSEGREHTTHRQGSSSVSGSPAPSTSGTSTPRRGRRQLPQTP 1704

Query: 318  KGIHSSFLSDSGQREENHRRSPSFPSKR 345
                         R    R  P      
Sbjct: 1705 CTPRPLVSYSPAPRRPGARTIPRRGRPG 1732


>gi|73973945|ref|XP_868674.1| PREDICTED: hypothetical protein XP_863581 [Canis familiaris]
          Length = 432

 Score = 36.7 bits (83), Expect = 5.9,   Method: Composition-based stats.
 Identities = 10/111 (9%), Positives = 22/111 (19%), Gaps = 2/111 (1%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G      A         ++    +      ++      R           +       P 
Sbjct: 66  GHQSRVAAVSEKRERESATAAPRKQWAPRPAQGKGAAARSASGPLAPAARATAAPAPGPT 125

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS--KRSLRRTSAKK 354
              +     +  +G           R  + R S        R   R   ++
Sbjct: 126 SEASGRGRCFGTRGARRGQRPGRSARPPDRRESGERGPHITREAPRGPQRR 176


>gi|283852393|ref|ZP_06369663.1| Ribosomal small subunit Rsm22 [Desulfovibrio sp. FW1012B]
 gi|283572241|gb|EFC20231.1| Ribosomal small subunit Rsm22 [Desulfovibrio sp. FW1012B]
          Length = 544

 Score = 36.7 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 7/91 (7%), Positives = 17/91 (18%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           ++             AP                      ++   +          ++   
Sbjct: 367 EVAVPPDAPQDAKSGAPRVRLAGDPAAPAPGRPAAGRPDSKPAPSDRSGKSGRPDREGRP 426

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREEN 334
               R+        +G  SS      +R   
Sbjct: 427 DKESRSDRDASGGGRGPRSSRQPSRPRRPNG 457


>gi|5821145|dbj|BAA83714.1| RNA binding protein [Homo sapiens]
          Length = 956

 Score = 36.7 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 9/108 (8%), Positives = 21/108 (19%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                            S   +     +              + +    + + +  AT  
Sbjct: 397 RHASSSPESPKPAPAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAK 456

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R+ +          S        R          P +R   R+  +
Sbjct: 457 RGRSRSRTPTKRGHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQR 504



 Score = 36.3 bits (82), Expect = 6.3,   Method: Composition-based stats.
 Identities = 11/98 (11%), Positives = 22/98 (22%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            P      +++      +       R    S  P       ++ +       + +  T  
Sbjct: 409 APAPGSHREISSSPTSKNRSHGRAKRDKSHSHTPSRRMGRSRSPATAKRGRSRSRTPTKR 468

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
                 S  W        +      +     RSP  P 
Sbjct: 469 GHSRSRSPQWRRSRSAQRWGRSRSPQRRGRSRSPQRPG 506


>gi|323525911|ref|YP_004228064.1| Fertility inhibition FinO-like protein [Burkholderia sp. CCGE1001]
 gi|323382913|gb|ADX55004.1| Fertility inhibition FinO-like protein [Burkholderia sp. CCGE1001]
          Length = 274

 Score = 36.7 bits (83), Expect = 6.1,   Method: Composition-based stats.
 Identities = 6/72 (8%), Positives = 12/72 (16%)

Query: 261 IYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGI 320
                                  R +  S  +  +    K A    +           G 
Sbjct: 10  KKQLAAARAQAAPAAKGDGKSGARPEGRSEARRDVRSDGKPAANAAKPGTGKASGARAGA 69

Query: 321 HSSFLSDSGQRE 332
             +      +R 
Sbjct: 70  RPAGKPAQPRRG 81


>gi|239931897|ref|ZP_04688850.1| ATP-binding RNA helicase [Streptomyces ghanaensis ATCC 14672]
          Length = 814

 Score = 36.7 bits (83), Expect = 6.1,   Method: Composition-based stats.
 Identities = 6/76 (7%), Positives = 14/76 (18%), Gaps = 2/76 (2%)

Query: 274 IISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVW--MAKGIHSSFLSDSGQR 331
            +           +   +   +    +L  P              A G        +   
Sbjct: 668 GLRPGRAPRRTGARADHRAQRVRDPDRLLRPGAAGARREAPGDVRAPGDAPGGRRAAAGA 727

Query: 332 EENHRRSPSFPSKRSL 347
                R+     +R  
Sbjct: 728 PVVPGRTAGRGDRRPR 743


>gi|119719556|ref|YP_920051.1| hypothetical protein Tpen_0646 [Thermofilum pendens Hrk 5]
 gi|119524676|gb|ABL78048.1| hypothetical protein Tpen_0646 [Thermofilum pendens Hrk 5]
          Length = 708

 Score = 36.7 bits (83), Expect = 6.1,   Method: Composition-based stats.
 Identities = 12/106 (11%), Positives = 23/106 (21%), Gaps = 1/106 (0%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            +      +L A                +       R +       G S++  +  P   
Sbjct: 43  RVSNPTLPSLGALPDREGFNEPRARGGPARGEGGVARGEPRGYASPGPSERPGVGRPSRA 102

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           R                    G+R      +P +     L R   +
Sbjct: 103 RGERLAAGRPGPGALDTRGRRGRRGSGA-PAPGWGVSPRLGRDRPR 147



 Score = 36.3 bits (82), Expect = 7.4,   Method: Composition-based stats.
 Identities = 9/123 (7%), Positives = 26/123 (21%), Gaps = 4/123 (3%)

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +  +    +              A                        R ++ ++ + G 
Sbjct: 55  LPDREGFNEPRARGGPARGEGGVARGEPRGYASPGPSERPGVGRPSRARGERLAAGRPGP 114

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ--REENHRRS--PSFPSKRSLRRTS 351
                      R + A                 G+  + +   R    +   +R   R +
Sbjct: 115 GALDTRGRRGRRGSGAPAPGWGVSPRLGRDRPRGRFVKPDTMSRKVTVAPSKRRRPSRGA 174

Query: 352 AKK 354
            ++
Sbjct: 175 GQR 177


>gi|118086156|ref|XP_001235974.1| PREDICTED: hypothetical protein [Gallus gallus]
          Length = 232

 Score = 36.7 bits (83), Expect = 6.1,   Method: Composition-based stats.
 Identities = 14/100 (14%), Positives = 25/100 (25%), Gaps = 4/100 (4%)

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
                  +  +P  ++   +  R +     P         + +        + A P  R 
Sbjct: 32  RHTAPLPSRGSPAANNRGALSRRLSPAPRRPGGRAPPSPAARRGGPQRGAGRGAAPEVRT 91

Query: 309 NLASNVWMAKGIHSSFL----SDSGQREENHRRSPSFPSK 344
                   A G   S         G+RE    RS     +
Sbjct: 92  RRGQAPRRAPGPRHSPRLGCAEREGRREAAAPRSGHSGGR 131


>gi|37595358|gb|AAQ94565.1| RNA binding motif protein [Danio rerio]
          Length = 277

 Score = 36.7 bits (83), Expect = 6.1,   Method: Composition-based stats.
 Identities = 13/113 (11%), Positives = 22/113 (19%)

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE++ K L  +              +            P+             +    + 
Sbjct: 67  REMNGKPLDGKPIKVEQATKPQFETSGRRGPPPPRSRGPSRGLRGSRGGPSGMRGPPSRE 126

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
              K      P   +              S  S    R    R     P +R 
Sbjct: 127 PFFKGMSSRGPPPMKRGPPERNGGPPPKRSAPSGPMGRPSRDRDPYGPPPRRD 179



 Score = 36.3 bits (82), Expect = 8.2,   Method: Composition-based stats.
 Identities = 11/104 (10%), Positives = 19/104 (18%)

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E  G       +    +                      F  M             ++  
Sbjct: 90  ETSGRRGPPPPRSRGPSRGLRGSRGGPSGMRGPPSREPFFKGMSSRGPPPMKRGPPERNG 149

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
            P  +R+  S                 +R+    R    P  R 
Sbjct: 150 GPPPKRSAPSGPMGRPSRDRDPYGPPPRRDSLMSRRDDGPPHRD 193


>gi|194673942|ref|XP_612405.4| PREDICTED: jumonji, AT rich interactive domain 1B [Bos taurus]
          Length = 1723

 Score = 36.7 bits (83), Expect = 6.1,   Method: Composition-based stats.
 Identities = 15/115 (13%), Positives = 24/115 (20%), Gaps = 12/115 (10%)

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              E              +  R  P+          R +  +      +   + A P  R
Sbjct: 72  PGEEGLLETWHPDGARLRSGCRRYPSPAPARKAMPARPRLAALGPESRTTGSERAQPPGR 131

Query: 308 RNLASNVWMAKG-----------IHSSFLSDSGQREENHRRSPSF-PSKRSLRRT 350
           R  A                         +   +R  N R  P     +   RR 
Sbjct: 132 RAAAEQTMQRAPRPRALRRPANQRPRRPANQRPRRPANQRPRPGSLKKEGPARRG 186


>gi|270009729|gb|EFA06177.1| hypothetical protein TcasGA2_TC009024 [Tribolium castaneum]
          Length = 1060

 Score = 36.7 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 15/115 (13%), Positives = 28/115 (24%)

Query: 221 GPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
               L  +  G      KK    Q      E+ + +     ++            +    
Sbjct: 85  MNMLLENMGQGEWETRVKKKKNRQASASKQEKTEESAGGDDWNDVPSAGGGGGAGNGNEK 144

Query: 281 DFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENH 335
           D  R K    + +G     +      ++    N+    G    F  D   R    
Sbjct: 145 DKPRNKSGPPRLHGRHNDSRGWRGREKQENERNLEEGGGGGRDFHRDRRGRPGGS 199


>gi|189239298|ref|XP_971413.2| PREDICTED: similar to lingerer [Tribolium castaneum]
          Length = 1064

 Score = 36.7 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 15/115 (13%), Positives = 28/115 (24%)

Query: 221 GPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
               L  +  G      KK    Q      E+ + +     ++            +    
Sbjct: 85  MNMLLENMGQGEWETRVKKKKNRQASASKQEKTEESAGGDDWNDVPSAGGGGGAGNGNEK 144

Query: 281 DFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENH 335
           D  R K    + +G     +      ++    N+    G    F  D   R    
Sbjct: 145 DKPRNKSGPPRLHGRHNDSRGWRGREKQENERNLEEGGGGGRDFHRDRRGRPGGS 199


>gi|328885883|emb|CCA59122.1| hypothetical protein SVEN_5836 [Streptomyces venezuelae ATCC 10712]
          Length = 579

 Score = 36.7 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 13/106 (12%), Positives = 26/106 (24%), Gaps = 2/106 (1%)

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
             A+    A   S+                   R    + Q +   +          R  
Sbjct: 127 SPARETPAARETSAAGETPAARQTSPARETPAARQTPAAPQTSPAQQTPPAPRTPPARQT 186

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK--RSLRRTSAKK 354
            S         +S    +    +N   SP+ P +   +  + S  +
Sbjct: 187 PSAPQNPPTPQASPARQTPSAPQNPPTSPASPGRETPAAPQASPAR 232


>gi|156335447|ref|XP_001619585.1| hypothetical protein NEMVEDRAFT_v1g224042 [Nematostella vectensis]
 gi|156203087|gb|EDO27485.1| predicted protein [Nematostella vectensis]
          Length = 277

 Score = 36.7 bits (83), Expect = 6.3,   Method: Composition-based stats.
 Identities = 14/117 (11%), Positives = 26/117 (22%), Gaps = 4/117 (3%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ----KNGLSK 297
           R Q GP   +E                R          +   R ++   +         +
Sbjct: 36  RHQEGPRRHKEGPRWHREGPRRHREGPRRHREGPRRHREGPRRHREGPRRHREGPRRHQE 95

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             +      RR+        +G           +E   R        R   R   ++
Sbjct: 96  GPRRHQEGPRRHQEGPRRHQEGPRRHQEGPRRHQEGPRRHQEGPRRHRKGPRRHRRQ 152


>gi|301767378|ref|XP_002919104.1| PREDICTED: LOW QUALITY PROTEIN: collagen alpha-2(VI) chain-like
           [Ailuropoda melanoleuca]
          Length = 1011

 Score = 36.3 bits (82), Expect = 6.4,   Method: Composition-based stats.
 Identities = 11/83 (13%), Positives = 15/83 (18%), Gaps = 5/83 (6%)

Query: 277 EVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMA-----KGIHSSFLSDSGQR 331
              D   +    S+   G         P        N          G      +     
Sbjct: 423 RRGDPGAKGSPGSNGPKGEKGDPGPEGPRGLAGEVGNKGAKGDRGLPGPRGPQGALGEPG 482

Query: 332 EENHRRSPSFPSKRSLRRTSAKK 354
           +E  R  P     R        K
Sbjct: 483 KEGSRGDPGDAGPRGESGQPGPK 505


>gi|170649594|gb|ACB21183.1| BUD13 homolog (predicted) [Callicebus moloch]
          Length = 660

 Score = 36.3 bits (82), Expect = 6.4,   Method: Composition-based stats.
 Identities = 13/109 (11%), Positives = 25/109 (22%), Gaps = 1/109 (0%)

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                           P ++S  +   R    S  P    R + +S   +   +  +  +
Sbjct: 177 PRRARHDSPDPPPPRKPQHNSSGVSPRRVRHDSPDPSPPRRARHDSPDPSPPRRA-RHDS 235

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           P       +                       RR+    S  S  R + 
Sbjct: 236 PDPSPPRRARHDSPDPSPPRRARHDSPDPSPPRRARHDSSGISPPRRAH 284



 Score = 35.9 bits (81), Expect = 9.6,   Method: Composition-based stats.
 Identities = 7/101 (6%), Positives = 18/101 (17%)

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
             + +  +                           R  ++ S      ++ +  +P    
Sbjct: 168 HHDASDTSPPRRARHDSPDPPPPRKPQHNSSGVSPRRVRHDSPDPSPPRRARHDSPDPSP 227

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
              +                       RR+       S  R
Sbjct: 228 PRRARHDSPDPSPPRRARHDSPDPSPPRRARHDSPDPSPPR 268


>gi|323457078|gb|EGB12944.1| expressed protein [Aureococcus anophagefferens]
          Length = 1113

 Score = 36.3 bits (82), Expect = 6.5,   Method: Composition-based stats.
 Identities = 12/106 (11%), Positives = 22/106 (20%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G  +                                  R + +     G     +     
Sbjct: 788 GLPVPAPGPRRGRRAQRPGRPRPVGARARAPGAEQVRRRRRGDEDPLQGRHLHGRPRARA 847

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
           H R   +            ++  G R    RR P+  + R+  R  
Sbjct: 848 HVRGGVAGRARRPPPVRRVVAALGARTRAGRRVPARDAPRARGRGP 893


>gi|301630801|ref|XP_002944505.1| PREDICTED: hypothetical protein LOC100494531 [Xenopus (Silurana)
           tropicalis]
          Length = 1075

 Score = 36.3 bits (82), Expect = 6.5,   Method: Composition-based stats.
 Identities = 12/114 (10%), Positives = 25/114 (21%), Gaps = 1/114 (0%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R          A+    A                 +      R +   + +   +     
Sbjct: 43  RAPNRLSPSPPARRRRAATRSPGPARTGTGTTGTPQQATPGGRGRTRKTPQQTGTAPTAA 102

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR-SLRRTSAKK 354
                RR   +          +  +    R E   R P    +  + +R  A +
Sbjct: 103 PERDSRRGRGAGEQRRNSPGPTTRAGVSGRSEVGTRGPGMERRGLARQRGEASR 156


>gi|194380132|dbj|BAG63833.1| unnamed protein product [Homo sapiens]
          Length = 1348

 Score = 36.3 bits (82), Expect = 6.5,   Method: Composition-based stats.
 Identities = 11/126 (8%), Positives = 25/126 (19%), Gaps = 3/126 (2%)

Query: 230 AGSTR---EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
            G+ R   E   +  R             + D      E   R   +     P       
Sbjct: 862 EGTWRKGPEADSEWRRGPPEKEWRRGEGRDEDRSHRRDEERPRRLGDDEDREPSLRPDDD 921

Query: 287 KNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +   +     +  +      R +            ++      +R  +  R     +   
Sbjct: 922 RVPRRGMDDDRGPRRGPEEDRFSRRGAGDDRPSWRNTDDDRPPRRIADEDRGNWRHADDD 981

Query: 347 LRRTSA 352
                 
Sbjct: 982 RPPRRG 987


>gi|126305639|ref|XP_001366667.1| PREDICTED: similar to CDK2-associated protein 1, [Monodelphis
           domestica]
          Length = 279

 Score = 36.3 bits (82), Expect = 6.5,   Method: Composition-based stats.
 Identities = 15/161 (9%), Positives = 30/161 (18%), Gaps = 24/161 (14%)

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
            EG+ R      +     V  L R                R      LR           
Sbjct: 1   MEGRGR-----SQAVGLPVRSLRR-------------AMWRRFRGGELRAGQASSAGSGF 42

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV------HR 307
           ++   A    ++                     +  S+ +   +++    P        R
Sbjct: 43  ELRGGASARIAQATRGPPLPPFQSRGPARPPSSQTPSRGSRSGQRQAWRRPGAACVLAQR 102

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                             S    +      +   P +    
Sbjct: 103 TPPGPWDSRTGEQARRRGSKEHGQSRPKPEASRLPGRSPRP 143


>gi|311252256|ref|XP_003125018.1| PREDICTED: hypothetical protein LOC100524080 [Sus scrofa]
          Length = 800

 Score = 36.3 bits (82), Expect = 6.6,   Method: Composition-based stats.
 Identities = 9/96 (9%), Positives = 18/96 (18%), Gaps = 5/96 (5%)

Query: 264 SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK-----KLATPVHRRNLASNVWMAK 318
            E      P  +          ++      G                   +      +  
Sbjct: 295 PEAGRPGWPEGLHCHGAGEGEGRRRGPLPAGARPSGLIPDAAARPAGPGASGPRRGLVLP 354

Query: 319 GIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                         +  RR  S P  R  R  + ++
Sbjct: 355 PSRKGSARPPSGAADGGRRQRSRPGTRRARPVAGRQ 390


>gi|17554518|ref|NP_498982.1| hypothetical protein R08D7.1 [Caenorhabditis elegans]
 gi|267547|sp|P30640|BUD13_CAEEL RecName: Full=BUD13 homolog
 gi|3878934|emb|CAA78047.1| C. elegans protein R08D7.1, confirmed by transcript evidence
           [Caenorhabditis elegans]
          Length = 458

 Score = 36.3 bits (82), Expect = 6.6,   Method: Composition-based stats.
 Identities = 18/103 (17%), Positives = 28/103 (27%), Gaps = 3/103 (2%)

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
           +V+    I        + P        D        S+K           P   R+ +  
Sbjct: 86  EVDAPKVIKPEPLSPDNSPPRGKRQRHDSDNSPPRPSRKRN-DSDNSPPRPSRNRHDSDK 144

Query: 314 VWMAKGIHSSFLSDSGQREENHRR--SPSFPSKRSLRRTSAKK 354
                        +S  R     R  SPS  ++RS  RT   +
Sbjct: 145 DNSPPRRRRHDSDNSPPRPSRKIREESPSARNRRSPPRTRRDR 187


>gi|268555196|ref|XP_002635586.1| Hypothetical protein CBG20574 [Caenorhabditis briggsae]
 gi|187023296|emb|CAP37559.1| hypothetical protein CBG_20574 [Caenorhabditis briggsae AF16]
          Length = 169

 Score = 36.3 bits (82), Expect = 6.7,   Method: Composition-based stats.
 Identities = 17/118 (14%), Positives = 27/118 (22%), Gaps = 5/118 (4%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R +       EA+                +P             +K  S +       + 
Sbjct: 5   RTRTRKPGNPEARKPGSPEARKPGNPEARKPGSPEARKPGSPEARKPGSPEARKPGSPEA 64

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREE-----NHRRSPSFPSKRSLRRTSAKK 354
             P +          A+   S      G+ E         R P  P  R      A+K
Sbjct: 65  RKPGNPEARKPGSPEAQKPGSPEARKPGRPEARNPGSPETRKPGSPEARKPGSPEARK 122


>gi|126345781|ref|XP_001368549.1| PREDICTED: hypothetical protein [Monodelphis domestica]
          Length = 832

 Score = 36.3 bits (82), Expect = 6.8,   Method: Composition-based stats.
 Identities = 12/93 (12%), Positives = 25/93 (26%)

Query: 262 YSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIH 321
              +       +   + P         S ++ G     + A     R  A     A G  
Sbjct: 286 PPQQPRGSTVFSDHRQPPRGRAPTGAPSGRREGGPPDDERAGEGGERESARWSGTAGGAR 345

Query: 322 SSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +       R  +   +P+ P   S   ++  +
Sbjct: 346 RNDRFPGRPRGGSAGTAPAKPRPASRPNSTGAR 378


>gi|284045721|ref|YP_003396061.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Conexibacter
           woesei DSM 14684]
 gi|283949942|gb|ADB52686.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Conexibacter
           woesei DSM 14684]
          Length = 666

 Score = 36.3 bits (82), Expect = 6.8,   Method: Composition-based stats.
 Identities = 16/126 (12%), Positives = 24/126 (19%), Gaps = 3/126 (2%)

Query: 230 AGSTREVSKKILR--EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
            G TR+     +R                       SE +   RP      P    R   
Sbjct: 481 PGHTRQEPPGDIRGNAPDNTRQEPPGHRGESRRRGGSERIPDGRPKDPPATPPGARRRGP 540

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
            +      +     A P                            +   R P  P   + 
Sbjct: 541 AAPTDRVRATPDGSAAPRPGPPPDRGAGRPP-ADPGGRGPGRPPADTGGRGPGRPPADTG 599

Query: 348 RRTSAK 353
            R   +
Sbjct: 600 GRGPGR 605


>gi|225448767|ref|XP_002281756.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 301

 Score = 36.3 bits (82), Expect = 6.8,   Method: Composition-based stats.
 Identities = 16/88 (18%), Positives = 27/88 (30%)

Query: 264 SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSS 323
                 +R    S  P D    K+  +       +K+  TP  R     +        ++
Sbjct: 183 KRERSAERLERRSRSPHDSRSPKRRKASPPPSKGRKRSPTPDERSPKERSPSPRDRKQTT 242

Query: 324 FLSDSGQREENHRRSPSFPSKRSLRRTS 351
             SD         RSP+  ++R   R  
Sbjct: 243 NGSDYSDSPRVKSRSPALDAERDSPRDR 270


>gi|164565411|ref|NP_056549.2| collagen alpha-1(V) chain precursor [Mus musculus]
 gi|125987810|sp|O88207|CO5A1_MOUSE RecName: Full=Collagen alpha-1(V) chain; Flags: Precursor
 gi|126541052|emb|CAM46247.1| procollagen type V alpha 1 [Mus musculus]
 gi|151357808|emb|CAO78165.1| procollagen type V alpha 1 [Mus musculus]
 gi|223461040|gb|AAI38448.1| Collagen, type V, alpha 1 [Mus musculus]
 gi|223461042|gb|AAI38450.1| Collagen, type V, alpha 1 [Mus musculus]
          Length = 1838

 Score = 36.3 bits (82), Expect = 6.8,   Method: Composition-based stats.
 Identities = 8/113 (7%), Positives = 18/113 (15%), Gaps = 1/113 (0%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           ++   G       +                 P  +    +             G    K 
Sbjct: 824 IKGDRGEIGPPGPRGEDGPEGPKGRGGPNGDPGPLGPTGEKGKLGVPGLPGYPGRQGPKG 883

Query: 301 LAT-PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
               P                        G       R P   + +   + ++
Sbjct: 884 SIGFPGFPGANGEKGGRGTPGKPGPRGQRGPTGPRGERGPRGITGKPGPKGNS 936


>gi|3219172|dbj|BAA28786.1| collagen a1(V) [Mus musculus]
          Length = 1838

 Score = 36.3 bits (82), Expect = 6.8,   Method: Composition-based stats.
 Identities = 8/113 (7%), Positives = 18/113 (15%), Gaps = 1/113 (0%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           ++   G       +                 P  +    +             G    K 
Sbjct: 824 IKGDRGEIGPPGPRGEDGPEGPKGRGGPNGDPGPLGPTGEKGKLGVPGLPGYPGRQGPKG 883

Query: 301 LAT-PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
               P                        G       R P   + +   + ++
Sbjct: 884 SIGFPGFPGANGEKGGRGTPGKPGPRGQRGPTGPRGERGPRGITGKPGPKGNS 936


>gi|304391684|ref|ZP_07373626.1| probable ATP-dependent RNA helicase Exp9 [Ahrensia sp. R2A130]
 gi|303295913|gb|EFL90271.1| probable ATP-dependent RNA helicase Exp9 [Ahrensia sp. R2A130]
          Length = 532

 Score = 36.3 bits (82), Expect = 6.9,   Method: Composition-based stats.
 Identities = 11/131 (8%), Positives = 35/131 (26%), Gaps = 3/131 (2%)

Query: 226 GTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
                 +   ++   +       + +    +              + +   E P    R 
Sbjct: 353 DDRYIKAVMALTGDEIEYLGRAPIAKADDADEADDKPKRGRRAAPKSDDSGEAPKRARRS 412

Query: 286 KKNSSQKNGLSKQKKLAT--PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
           K+ +  ++  + + +        +R   ++    +       +     +E   R    P 
Sbjct: 413 KRAAPAEDEAAPEAETDGEERSTKRPRRTSRRAPEQETKVEEAAPVAAKEPAERQE-RPK 471

Query: 344 KRSLRRTSAKK 354
           +   R   A+K
Sbjct: 472 REPRRDDRAEK 482


>gi|326779089|ref|ZP_08238354.1| Peptidoglycan glycosyltransferase [Streptomyces cf. griseus
           XylebKG-1]
 gi|326659422|gb|EGE44268.1| Peptidoglycan glycosyltransferase [Streptomyces cf. griseus
           XylebKG-1]
          Length = 968

 Score = 36.3 bits (82), Expect = 6.9,   Method: Composition-based stats.
 Identities = 7/87 (8%), Positives = 14/87 (16%)

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
                         R         P       ++       + +     P   R      
Sbjct: 768 ATGGDGGSGRNGDSRGDDRTGRGQPGRRQASFRSGRSGPTDTTRSNPPNPRTGRRPPRAD 827

Query: 315 WMAKGIHSSFLSDSGQREENHRRSPSF 341
                  +   +   Q     R +P  
Sbjct: 828 RAPASGRTPRPAPRPQHGPRGRTAPGR 854


>gi|294628559|ref|ZP_06707119.1| ATPase [Streptomyces sp. e14]
 gi|292831892|gb|EFF90241.1| ATPase [Streptomyces sp. e14]
          Length = 390

 Score = 36.3 bits (82), Expect = 6.9,   Method: Composition-based stats.
 Identities = 13/117 (11%), Positives = 25/117 (21%), Gaps = 2/117 (1%)

Query: 221 GPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
           GPF L  L+ G  R      ++ +       + +         +                
Sbjct: 199 GPF-LAGLVPGGLRPGPGAAVQRRRLSDGHRDRRGGRGGQGPLAAAAPGGLRRADPRRGQ 257

Query: 281 DFTRMKKNSSQKNGLSKQKKLATPVHRRN-LASNVWMAKGIHSSFLSDSGQREENHR 336
              R     + +      +       RR+        A G   +       R     
Sbjct: 258 AHGRAGAVPAAQPHRRPARPGPQRAGRRHHQRGPGAAAPGRGPAGPLSGPDRGGEAD 314


>gi|118081943|ref|XP_425512.2| PREDICTED: similar to Phf7 protein [Gallus gallus]
          Length = 548

 Score = 36.3 bits (82), Expect = 6.9,   Method: Composition-based stats.
 Identities = 11/65 (16%), Positives = 21/65 (32%), Gaps = 1/65 (1%)

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           S     ++     +P+  R         +G  +   S    R   +  S S P + S  R
Sbjct: 481 SGTRRSTRSATSRSPMASRVPRRRGPSRQGGRALSQSPPPGRRRANN-SRSSPQRGSRSR 539

Query: 350 TSAKK 354
              ++
Sbjct: 540 AQQRR 544


>gi|14251117|ref|NP_116479.1| t123 [Tupaiid herpesvirus 1]
 gi|14210811|gb|AAK57174.1| t123 [Tupaiid herpesvirus 1]
          Length = 367

 Score = 36.3 bits (82), Expect = 6.9,   Method: Composition-based stats.
 Identities = 17/150 (11%), Positives = 43/150 (28%), Gaps = 26/150 (17%)

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVT---VGLRE--------GKN------REIKKVF 205
               I+      +         ++A +    + + E        G+N      REI ++ 
Sbjct: 192 MKQKIEAEMTLAVGGVHLLMDRADAVLRHMAILIMEEVTAAMLAGRNQPRVILREIMEMC 251

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSE 265
           ++ +  V +  R + G         G+ R +  + +RE            +      +S 
Sbjct: 252 KYISRAVRQTHRYALG--------LGAYRVLCPQEMREMHRRRPHVSTLDDPYYHHDTSM 303

Query: 266 TLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
             +  +       P      ++   +    
Sbjct: 304 GAMSTQDEEN-PGPAGEEDSREEGPEDPPR 332


>gi|76819623|ref|YP_336508.1| hypothetical protein BURPS1710b_A1351 [Burkholderia pseudomallei
           1710b]
 gi|76584096|gb|ABA53570.1| putative exported protein [Burkholderia pseudomallei 1710b]
          Length = 864

 Score = 36.3 bits (82), Expect = 6.9,   Method: Composition-based stats.
 Identities = 10/110 (9%), Positives = 24/110 (21%), Gaps = 2/110 (1%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
               +   +          +       +     P      +  +    G  + ++ A   
Sbjct: 175 ALRSVSRQRRARRRHALPPQPAADAPRSPNRTRPRMRGDGRGATEPTRGQHRARRAAPLG 234

Query: 306 HRRNLASNVWMAKGIHSSFLS--DSGQREENHRRSPSFPSKRSLRRTSAK 353
              +  +      G          S     +HR +P   +   L R    
Sbjct: 235 ESDDDPNRARRQAGNRRDAGPLFRSPLDPFSHRGAPGRRAAHRLSRGRPS 284


>gi|19745166|ref|NP_604447.1| collagen alpha-1(V) chain precursor [Rattus norvegicus]
 gi|81917473|sp|Q9JI03|CO5A1_RAT RecName: Full=Collagen alpha-1(V) chain; Flags: Precursor
 gi|8568096|gb|AAF76433.1|AF272662_1 alpha 1 type V collagen [Rattus norvegicus]
          Length = 1840

 Score = 36.3 bits (82), Expect = 6.9,   Method: Composition-based stats.
 Identities = 8/113 (7%), Positives = 18/113 (15%), Gaps = 1/113 (0%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           ++   G       +                 P  +    +             G    K 
Sbjct: 826 IKGDRGEIGPPGPRGEDGPEGPKGRGGPNGDPGPLGPTGEKGKLGVPGLPGYPGRQGPKG 885

Query: 301 LAT-PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
               P                        G       R P   + +   + ++
Sbjct: 886 SIGFPGFPGANGEKGGRGTPGKPGPRGQRGPTGPRGERGPRGITGKPGPKGNS 938


>gi|81910407|sp|Q60467|CO5A1_CRILO RecName: Full=Collagen alpha-1(V) chain; Flags: Precursor
 gi|191151|gb|AAA37002.1| pro-alpha-1 type V collagen [Cricetulus longicaudatus]
          Length = 1840

 Score = 36.3 bits (82), Expect = 6.9,   Method: Composition-based stats.
 Identities = 8/113 (7%), Positives = 18/113 (15%), Gaps = 1/113 (0%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           ++   G       +                 P  +    +             G    K 
Sbjct: 826 IKGDRGEIGPPGPRGEDGPEGPKGRGGPNGDPGPLGPTGEKGKLGVPGLPGYPGRQGPKG 885

Query: 301 LAT-PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
               P                        G       R P   + +   + ++
Sbjct: 886 SIGFPGFPGANGEKGGRGTPGKPGPRGQRGPTGPRGERGPRGITGKPGPKGNS 938


>gi|315049213|ref|XP_003173981.1| hypothetical protein MGYG_04155 [Arthroderma gypseum CBS 118893]
 gi|311341948|gb|EFR01151.1| hypothetical protein MGYG_04155 [Arthroderma gypseum CBS 118893]
          Length = 576

 Score = 36.3 bits (82), Expect = 7.0,   Method: Composition-based stats.
 Identities = 9/106 (8%), Positives = 21/106 (19%)

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
               ++    +    +       P             +  S  +     + +      R 
Sbjct: 73  WAPPSRPRPRSRSPGNFRPRSRSPLFRGRERGPNFGNRPRSPFRRPSPSRDRPPRFNRRS 132

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                    +        D      N  R+P      S  R   ++
Sbjct: 133 RSPPPFDRNRSPSLRRGRDPSPSAINAPRAPKRERNNSPPRNRFER 178


>gi|7441219|pir||S18803 collagen alpha 1(V) chain - hamster
          Length = 1843

 Score = 36.3 bits (82), Expect = 7.0,   Method: Composition-based stats.
 Identities = 8/113 (7%), Positives = 18/113 (15%), Gaps = 1/113 (0%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           ++   G       +                 P  +    +             G    K 
Sbjct: 829 IKGDRGEIGPPGPRGEDGPEGPKGRGGPNGDPGPLGPTGEKGKLGVPGLPGYPGRQGPKG 888

Query: 301 LAT-PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
               P                        G       R P   + +   + ++
Sbjct: 889 SIGFPGFPGANGEKGGRGTPGKPGPRGQRGPTGPRGERGPRGITGKPGPKGNS 941


>gi|261341381|ref|ZP_05969239.1| ATP-dependent RNA helicase RhlE [Enterobacter cancerogenus ATCC
           35316]
 gi|288316692|gb|EFC55630.1| ATP-dependent RNA helicase RhlE [Enterobacter cancerogenus ATCC
           35316]
          Length = 457

 Score = 36.3 bits (82), Expect = 7.0,   Method: Composition-based stats.
 Identities = 7/96 (7%), Positives = 21/96 (21%)

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           + +   L   +        D         +++             +  + S      +  
Sbjct: 358 RDIERLLKKEIPRITTEGYDVDPSIQAEPIQNGRQQRGGGGGRGQQQPRRSEGGAPKASG 417

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREEN 334
           K        ++   N W +     +      +R   
Sbjct: 418 KPPRRNGEAKSGGENPWRSGEARPAGEGQRRRRPRK 453


>gi|62122588|dbj|BAD93256.1| COL11A2 [Oryzias latipes]
          Length = 1827

 Score = 36.3 bits (82), Expect = 7.0,   Method: Composition-based stats.
 Identities = 11/104 (10%), Positives = 15/104 (14%), Gaps = 2/104 (1%)

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           G                        +         D  R         G      L    
Sbjct: 588 GLKGEGGDPGPQGPRGPQGVMGPPGKSGRRGRAGADGARGMPGEPGTKGDRGFDGLPGLP 647

Query: 306 HRRNLASNVW--MAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
             +    +       G            +   R  P  P  R L
Sbjct: 648 GDKGHRGDSGPLGPPGSQGEDGERGDDGDVGPRGLPGEPGPRGL 691


>gi|297159298|gb|ADI09010.1| hypothetical protein SBI_05890 [Streptomyces bingchenggensis BCW-1]
          Length = 275

 Score = 36.3 bits (82), Expect = 7.1,   Method: Composition-based stats.
 Identities = 14/104 (13%), Positives = 24/104 (23%), Gaps = 5/104 (4%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ-- 298
           LR+   P     ++        ++             VP      +  +   +G      
Sbjct: 157 LRDLTPPLWGPRSRWRPALRAAAAPRQAPGPGPRPEPVPAPAPGHRPGTGPGSGPGAGPG 216

Query: 299 ---KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
              +    P      A       G   S  S    R     R+P
Sbjct: 217 SGSEADPGPGSGPGAAPRPGSRPGPRRSRGSRGSPRGRAAVRAP 260


>gi|149039207|gb|EDL93427.1| procollagen, type V, alpha 1 [Rattus norvegicus]
          Length = 1840

 Score = 36.3 bits (82), Expect = 7.1,   Method: Composition-based stats.
 Identities = 8/113 (7%), Positives = 18/113 (15%), Gaps = 1/113 (0%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           ++   G       +                 P  +    +             G    K 
Sbjct: 826 IKGDRGEIGPPGPRGEDGPEGPKGRGGPNGDPGPLGPTGEKGKLGVPGLPGYPGRQGPKG 885

Query: 301 LAT-PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
               P                        G       R P   + +   + ++
Sbjct: 886 SIGFPGFPGANGEKGGRGTPGKPGPRGQRGPTGPRGERGPRGITGKPGPKGNS 938


>gi|302420169|ref|XP_003007915.1| conserved hypothetical protein [Verticillium albo-atrum VaMs.102]
 gi|261353566|gb|EEY15994.1| conserved hypothetical protein [Verticillium albo-atrum VaMs.102]
          Length = 293

 Score = 36.3 bits (82), Expect = 7.1,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 25/108 (23%), Gaps = 2/108 (1%)

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +                A                    D     + +        +Q + 
Sbjct: 10  KAAAETENQYAVPPQAGADHGRHVRHRPGAHGAPPGEQDIRRSHRPHDGASRSAPRQTRP 69

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQR--EENHRRSPSFPSKRSL 347
             P HR        +A  +     SD   R      R SP+ P+ R+ 
Sbjct: 70  RPPGHRAPRRDRPRLAARLDGPHHSDLPGRDGPVPERGSPARPAPRAP 117


>gi|148676427|gb|EDL08374.1| procollagen, type V, alpha 1 [Mus musculus]
          Length = 1838

 Score = 36.3 bits (82), Expect = 7.1,   Method: Composition-based stats.
 Identities = 8/113 (7%), Positives = 18/113 (15%), Gaps = 1/113 (0%)

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           ++   G       +                 P  +    +             G    K 
Sbjct: 824 IKGDRGEIGPPGPRGEDGPEGPKGRGGPNGDPGPLGPTGEKGKLGVPGLPGYPGRQGPKG 883

Query: 301 LAT-PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
               P                        G       R P   + +   + ++
Sbjct: 884 SIGFPGFPGANGEKGGRGTPGKPGPRGQRGPTGPRGERGPRGITGKPGPKGNS 936


>gi|153006078|ref|YP_001380403.1| hypothetical protein Anae109_3224 [Anaeromyxobacter sp. Fw109-5]
 gi|152029651|gb|ABS27419.1| conserved hypothetical protein [Anaeromyxobacter sp. Fw109-5]
          Length = 227

 Score = 36.3 bits (82), Expect = 7.1,   Method: Composition-based stats.
 Identities = 13/82 (15%), Positives = 27/82 (32%), Gaps = 1/82 (1%)

Query: 274 IISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREE 333
             +         K +     G S+ +  A P   R  A+    A     +  + + +  +
Sbjct: 91  RETAAARSRGESKASRKSARGGSRGRAGARPAGSRAGAARDRKAGAGAGTRKAGAARSRK 150

Query: 334 NHRRSPSFPSKRSL-RRTSAKK 354
              R+P    + +   R  AK+
Sbjct: 151 AGGRTPKVGGRSAASSRGGAKR 172


>gi|24796773|gb|AAN64450.1| putative gypsy-type retrotransposon RIRE2 protein [Oryza sativa
           Japonica Group]
          Length = 463

 Score = 36.3 bits (82), Expect = 7.1,   Method: Composition-based stats.
 Identities = 11/113 (9%), Positives = 28/113 (24%), Gaps = 3/113 (2%)

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             RE+  + +         +     ++  +  +  L R       E          +   
Sbjct: 34  EKREIRGREINHGDRHSWPK---AAVEVELTGARGLGRRTSGCDREGGRLTAGGSGDDGG 90

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
            +G ++Q+       R     N              +  RE     + +   +
Sbjct: 91  GDGGARQRGSGDTAARERRRGNGGAGTAARRHRNDSAAARERRRGGTRATARR 143


>gi|88855474|ref|ZP_01130138.1| hypothetical protein A20C1_01586 [marine actinobacterium PHSC20C1]
 gi|88815381|gb|EAR25239.1| hypothetical protein A20C1_01586 [marine actinobacterium PHSC20C1]
          Length = 384

 Score = 36.3 bits (82), Expect = 7.1,   Method: Composition-based stats.
 Identities = 8/89 (8%), Positives = 19/89 (21%), Gaps = 5/89 (5%)

Query: 271 RPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ 330
                   P         S  +    +  +      +    +          +  SD   
Sbjct: 7   NDGRRESRPHGNRSGAPRSGGRPTGGRPGEGRPSDGKPRRDNAAGGPARGKPASGSDRPA 66

Query: 331 REENHRRSPSF-----PSKRSLRRTSAKK 354
           R + +  S        P + +      +K
Sbjct: 67  RPQRNDGSGRPERGGHPDRGARSDGPPEK 95


>gi|40788877|dbj|BAA09488.2| KIAA0139 [Homo sapiens]
          Length = 1388

 Score = 36.3 bits (82), Expect = 7.2,   Method: Composition-based stats.
 Identities = 11/126 (8%), Positives = 25/126 (19%), Gaps = 3/126 (2%)

Query: 230  AGSTR---EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
             G+ R   E   +  R             + D      E   R   +     P       
Sbjct: 902  EGTWRKGPEADSEWRRGPPEKEWRRGEGRDEDRSHRRDEERPRRLGDDEDREPSLRPDDD 961

Query: 287  KNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
            +   +     +  +      R +            ++      +R  +  R     +   
Sbjct: 962  RVPRRGMDDDRGPRRGPEEDRFSRRGADDDRPSWRNTDDDRPPRRIADEDRGNWRHADDD 1021

Query: 347  LRRTSA 352
                  
Sbjct: 1022 RPPRRG 1027


>gi|4503509|ref|NP_003741.1| eukaryotic translation initiation factor 3 subunit A [Homo sapiens]
 gi|6685537|sp|Q14152|EIF3A_HUMAN RecName: Full=Eukaryotic translation initiation factor 3 subunit A;
            Short=eIF3a; AltName: Full=Eukaryotic translation
            initiation factor 3 subunit 10; AltName:
            Full=eIF-3-theta; AltName: Full=eIF3 p167; AltName:
            Full=eIF3 p180; AltName: Full=eIF3 p185
 gi|1808985|gb|AAB41584.1| p167 [Homo sapiens]
 gi|2501783|gb|AAB80695.1| translation initiation factor 3 large subunit [Homo sapiens]
 gi|55958708|emb|CAI14127.1| eukaryotic translation initiation factor 3, subunit 10 theta,
            150/170kDa [Homo sapiens]
 gi|119569793|gb|EAW49408.1| eukaryotic translation initiation factor 3, subunit 10 theta,
            150/170kDa [Homo sapiens]
 gi|168274396|dbj|BAG09618.1| eukaryotic translation initiation factor 3 subunit 10 [synthetic
            construct]
          Length = 1382

 Score = 36.3 bits (82), Expect = 7.2,   Method: Composition-based stats.
 Identities = 11/126 (8%), Positives = 25/126 (19%), Gaps = 3/126 (2%)

Query: 230  AGSTR---EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
             G+ R   E   +  R             + D      E   R   +     P       
Sbjct: 896  EGTWRKGPEADSEWRRGPPEKEWRRGEGRDEDRSHRRDEERPRRLGDDEDREPSLRPDDD 955

Query: 287  KNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
            +   +     +  +      R +            ++      +R  +  R     +   
Sbjct: 956  RVPRRGMDDDRGPRRGPEEDRFSRRGADDDRPSWRNTDDDRPPRRIADEDRGNWRHADDD 1015

Query: 347  LRRTSA 352
                  
Sbjct: 1016 RPPRRG 1021


  Database: nr
    Posted date:  May 22, 2011 12:22 AM
  Number of letters in database: 999,999,966
  Number of sequences in database:  2,987,313
  
  Database: /data/usr2/db/fasta/nr.01
    Posted date:  May 22, 2011 12:30 AM
  Number of letters in database: 999,999,796
  Number of sequences in database:  2,903,041
  
  Database: /data/usr2/db/fasta/nr.02
    Posted date:  May 22, 2011 12:36 AM
  Number of letters in database: 999,999,281
  Number of sequences in database:  2,904,016
  
  Database: /data/usr2/db/fasta/nr.03
    Posted date:  May 22, 2011 12:41 AM
  Number of letters in database: 999,999,960
  Number of sequences in database:  2,935,328
  
  Database: /data/usr2/db/fasta/nr.04
    Posted date:  May 22, 2011 12:46 AM
  Number of letters in database: 842,794,627
  Number of sequences in database:  2,394,679
  
Lambda     K      H
   0.308    0.124    0.322 

Lambda     K      H
   0.267   0.0383    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,418,255,165
Number of Sequences: 14124377
Number of extensions: 138025624
Number of successful extensions: 1144034
Number of sequences better than 10.0: 10000
Number of HSP's better than 10.0 without gapping: 40807
Number of HSP's successfully gapped in prelim test: 17292
Number of HSP's that attempted gapping in prelim test: 782242
Number of HSP's gapped (non-prelim): 263596
length of query: 354
length of database: 4,842,793,630
effective HSP length: 140
effective length of query: 214
effective length of database: 2,865,380,850
effective search space: 613191501900
effective search space used: 613191501900
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.2 bits)
S2: 81 (35.9 bits)